# BugSigDB 2026-02-07_16:04_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org
BSDB ID,Study,Study design,PMID,DOI,URL,Authors list,Title,Journal,Year,Keywords,Experiment,Location of subjects,Host species,Body site,UBERON ID,Condition,EFO ID,Group 0 name,Group 1 name,Group 1 definition,Group 0 sample size,Group 1 sample size,Antibiotics exclusion,Sequencing type,16S variable region,Sequencing platform,Data transformation,Statistical test,Significance threshold,MHT correction,LDA Score above,Matched on,Confounders controlled for,Pielou,Shannon,Chao1,Simpson,Inverse Simpson,Richness,Signature page name,Source,Curated date,Curator,Revision editor,Description,Abundance in Group 1,MetaPhlAn taxon names,NCBI Taxonomy IDs,State,Reviewer
bsdb:11/1/1,Study 11,time series / longitudinal observational,NA,NA,NA,NA,NA,NA,NA,NA,Experiment 1,Brazil,Homo sapiens,Uterus,UBERON:0000995,Cervical glandular intraepithelial neoplasia,EFO:1000165,HIV pateints with normal tissue at 6 months,HIV patients with lesion at 12 months,Cases were identified by HIV rapid or ELISA test and subsequent Western blot following recommendations for HIV diagnosis by the Brazilian Ministry of Health.,5,5,NA,16S,3456,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Gardnerella vaginalis abundance longitudinal analysis at six and twelve months postpartum in paired samples,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,1783272|201174|1760|85004|31953|2701|2702,Complete,NA
bsdb:39/1/1,Study 39,time series / longitudinal observational,NA,NA,NA,NA,NA,NA,NA,NA,Experiment 1,Philippines,Homo sapiens,Skin of body,UBERON:0002097,Body odor measurement,EFO:0008386,youth underarm before,youth underarm after exercise,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,30,30,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1& S3,10 January 2021,Shaimaa Elsafoury,WikiWorks,List of microbes at the genus level that show significant correlation with odor intensity in at least one age group,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,1783272|1239|91061|1385|90964|1279|1282,Complete,NA
bsdb:39/1/2,Study 39,time series / longitudinal observational,NA,NA,NA,NA,NA,NA,NA,NA,Experiment 1,Philippines,Homo sapiens,Skin of body,UBERON:0002097,Body odor measurement,EFO:0008386,youth underarm before,youth underarm after exercise,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,30,30,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1& S3,10 January 2021,Shaimaa Elsafoury,WikiWorks,List of microbes at the genus level that show significant correlation with odor intensity in at least one age group,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,3379134|1224|28211|204455|31989|265,Complete,NA
bsdb:39/2/1,Study 39,time series / longitudinal observational,NA,NA,NA,NA,NA,NA,NA,NA,Experiment 2,Philippines,Homo sapiens,Skin of body,UBERON:0002097,Body odor measurement,EFO:0008386,after excercise,youth Neck before,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,30,30,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1& S3,10 January 2021,Shaimaa Elsafoury,WikiWorks,List of microbes at the genus level that show significant correlation with odor intensity in at least one age group,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium granulosum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter schindleri",3379134|1224|1236|2887326|468|469;1783272|201174|1760|85009|31957|1912216|33011;3379134|1224|1236|2887326|468|469|108981,Complete,NA
bsdb:39/3/1,Study 39,time series / longitudinal observational,NA,NA,NA,NA,NA,NA,NA,NA,Experiment 3,Philippines,Homo sapiens,Skin of body,UBERON:0002097,Body odor measurement,EFO:0008386,after excercise,Children underarm before,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1& S3,10 January 2021,Shaimaa Elsafoury,WikiWorks,List of microbes at the genus level that show significant correlation with odor intensity in at least one age group,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,3379134|1224|28211|204455|31989|265,Complete,NA
bsdb:83/1/1,Study 83,time series / longitudinal observational,NA,NA,NA,NA,NA,NA,NA,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,after surgery,before surgery,Roux-en-Y gastric-bypass operation were recruited according to the S3 guidelines of the German Society for Obesity,6,6,3 weeks,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2 &Table 3,10 January 2021,Marianthi Thomatos,"Fatima,WikiWorks",gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter johnsonii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira hyodysenteriae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Fibrobacterota|c__Fibrobacteria|o__Fibrobacterales|f__Fibrobacteraceae|g__Fibrobacter|s__Fibrobacter succinogenes,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Leptospirales|f__Leptospiraceae|g__Leptospira|s__Leptospira interrogans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium kansasii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Nakamurellales|f__Nakamurellaceae|g__Nakamurella|s__Nakamurella multipartita,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Ectopseudomonas|s__Ectopseudomonas mendocina,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Pseudomonadati|p__Thermomicrobiota|c__Thermomicrobia|o__Thermomicrobiales|f__Thermomicrobiaceae|g__Thermomicrobium|s__Thermomicrobium roseum,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema pallidum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,p__Evosea|c__Eumycetozoa|o__Dictyosteliales|f__Dictyosteliaceae|g__Dictyostelium,p__Ciliophora|c__Litostomatea|o__Entodiniomorphida|f__Ophryoscolecidae|g__Epidinium",3379134|1224|1236|2887326|468|469|40214;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|207244|105841;3379134|203691|203692|1643686|143786|29521|159;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;3379134|65842|204430|218872|204431|832|833;3384189|32066|203490|203491|203492|848|860;3379134|29547|3031852|213849|72293|209;1783272|1239|91061|186826|33958|1578|1579;3379134|203691|203692|1643688|170|171|173;1783272|1239|91061|186826|33958|2742598|1598;1783272|201174|1760|85007|1762|1763|1768;1783272|201174|1760|1643684|85031|53460|53461;3379134|1224|1236|72274|135621|3236654|300;1783272|1239|91061|1385|90964|1279|1282;3379134|3027942|189775|189776|189777|499|500;3379134|203691|203692|136|2845253|157|160;1783272|1239|526524|526525|2810280|3025755|29348;2605435|142796|2058949|2058185|5782;5878|5988|40634|47890|40637,Complete,Fatima
bsdb:83/1/2,Study 83,time series / longitudinal observational,NA,NA,NA,NA,NA,NA,NA,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,after surgery,before surgery,Roux-en-Y gastric-bypass operation were recruited according to the S3 guidelines of the German Society for Obesity,6,6,3 weeks,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2 &Table 3,10 January 2021,Marianthi Thomatos,"Fatima,WikiWorks",gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cancerogenus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella boydii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Sordariaceae|g__Neurospora",3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|547|69218;3379134|1224|1236|91347|543|590;3379134|1224|1236|91347|543|590|28901;3379134|1224|1236|91347|543|620|621;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|909932|1843489|31977|29465|29466;4751|4890|147550|5139|5148|5140,Complete,Fatima
bsdb:84/1/1,Study 84,case-control,NA,NA,NA,NA,NA,NA,NA,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean controls,after surgery,Roux-en-Y gastric-bypass operation were recruited according to the S3 guidelines of the German Society for Obesity,6,NA,3 weeks,WMS,NA,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cancerogenus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella boydii",3379134|1224|1236|91347|543|547|69218;1783272|1239|909932|1843489|31977|29465|29466;3379134|1224|1236|91347|543|620|621,Complete,NA
bsdb:84/1/2,Study 84,case-control,NA,NA,NA,NA,NA,NA,NA,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean controls,after surgery,Roux-en-Y gastric-bypass operation were recruited according to the S3 guidelines of the German Society for Obesity,6,NA,3 weeks,WMS,NA,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira hyodysenteriae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Pseudomonadati|p__Thermomicrobiota|c__Thermomicrobia|o__Thermomicrobiales|f__Thermomicrobiaceae|g__Thermomicrobium|s__Thermomicrobium roseum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Pseudomonadati|p__Fibrobacterota|c__Fibrobacteria|o__Fibrobacterales|f__Fibrobacteraceae|g__Fibrobacter|s__Fibrobacter succinogenes",1783272|1239|526524|526525|2810280|3025755|29348;3379134|203691|203692|1643686|143786|29521|159;1783272|1239|91061|186826|33958|2742598|1598;1783272|1239|186801|3085636|186803|207244|105841;3384189|32066|203490|203491|203492|848|860;3379134|3027942|189775|189776|189777|499|500;1783272|1239|91061|1385|90964|1279|1282;3379134|65842|204430|218872|204431|832|833,Complete,NA
bsdb:501/1/1,Study 501,"cross-sectional observational, not case-control",NA,https://doi.org/10.21767/2476-1974.100036,https://reproductive-immunology.imedpub.com/reproductive-microbiomes-using-the-microbiome-as-a-novel-diagnostic-tool-for-endometriosis.php?aid=20437,NA,NA,NA,NA,NA,Experiment 1,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,Endometriosis,EFO:0001065,Women scheduled for laparoscopic surgery for benign uterine/ ovarian conditions as well as women with Stage I or Stage II endometriosis,One (1) Stage III Endometriosis patient,One (1) Stage III Endometriosis patient was diagnosed via laparoscopic surgery and categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).,17,1,NA,16S,345,Illumina,NA,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Table 2,8 August 2021,Samara.Khan,Samara.Khan,"In this experiment, 9 patients had stage I, II or III endometriosis. The nine patients in the control group were undergoing laparoscopic surgery for other gynecological reasons, for a total of 18 patients.

The researchers found no difference when comparing the microbiome composition of control patients to experimental patients. However, when they compared the one (1) stage III endometriosis patient to the rest of the 17 patient cohort, they found 56 OTUs were significantly different, with 22 OTUs only present in the cervix of the stage III patient. 

The results of this signature are therefore not statistically reliable. However, the OTUs present in the stage III endometriosis patients can be used as a reference when looking at other studies who involved stage III endometriosis patients. 

It should also be noted that multiple unidentified species of Barnesiella were reported to be significantly different, but researchers did not specify which species so these were excluded from curation. There were also multiple unidentified species of Ruminococcus and Clostridium.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinilabiliaceae|g__Alkalitalea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",1783272|1239|186801|3120394|3120654|35829;3379134|1224|28216|80840|506|222;3379134|976|200643|1970189|558415|1193324;1783272|1239|526524|526525|128827|174708;1783272|1239|186801|186802|216572|244127;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|3085642|580596;1783272|1239|526524|526525|2810280|100883;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|946234;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|2005525|375288;1783272|201174|1760|85009|31957|1743;3384189|32066|203490|203491|1129771|168808;1783272|1239|91061|1385|90964|1279;1783272|1239|526524|526525|2810281|191303,Complete,NA
bsdb:513/1/1,Study 513,"cross-sectional observational, not case-control",NA,https://doi.org/10.3390/applmicrobiol1020014,https://www.mdpi.com/2673-8007/1/2/14,"Feehan, A.K., Rose, R., Nolan, D.J., Spitz, A.M., Graubics, K., Colwell, R.R., Garcia-Diaz, J. and Lamers, S.L.",Nasopharyngeal Microbiome Community Composition and Structure Is Associated with Severity of COVID-19 Disease and Breathing Treatment,Applied Microbiology,2021,"SARS-CoV-2, Serratia, hospital, metagenomic sequencing",Experiment 1,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls,COVID-19 positive patients,Patients who were confirmed PCR positive for SARS-CoV-2,20,79,NA,WMS,NA,Illumina,relative abundances,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Table S5,6 August 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients and non-COVID-19 patients,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|1224|1236|91347|1903411|613;1783272|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:513/3/1,Study 513,"cross-sectional observational, not case-control",NA,https://doi.org/10.3390/applmicrobiol1020014,https://www.mdpi.com/2673-8007/1/2/14,"Feehan, A.K., Rose, R., Nolan, D.J., Spitz, A.M., Graubics, K., Colwell, R.R., Garcia-Diaz, J. and Lamers, S.L.",Nasopharyngeal Microbiome Community Composition and Structure Is Associated with Severity of COVID-19 Disease and Breathing Treatment,Applied Microbiology,2021,"SARS-CoV-2, Serratia, hospital, metagenomic sequencing",Experiment 3,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 positive patients without antibiotic use,COVID-19 positive patients with antibiotic use,COVID-19 positive patients with antibiotic use,81,27,NA,WMS,NA,Illumina,relative abundances,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Table S5,27 July 2023,Atrayees,Atrayees,Differential microbial abundance between COVID-19 patients who used antibiotics and who didn't,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia",1783272|1239|1737404|1737405|1570339|150022;3379134|1224|1236|91347|1903411|613,Complete,Atrayees
bsdb:562/1/1,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 1,"Italy,Luxembourg,United States of America",Homo sapiens,Vagina,UBERON:0000996,Health study participation,EFO:0010130,NA,healthy adult vagina 50% up,NA,NA,96,NA,WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,Haoyanzh,healthy adult vagina genus >=50%,NA,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Lwaldron
bsdb:562/1/3,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 1,"Italy,Luxembourg,United States of America",Homo sapiens,Vagina,UBERON:0000996,Health study participation,EFO:0010130,NA,healthy adult vagina 50% up,NA,NA,96,NA,WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 3,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,"Haoyanzh,Lwaldron",healthy adult vagina species >=50%,NA,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,1783272|1239|91061|186826|33958|1578|47770,Complete,Lwaldron
bsdb:562/2/1,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 2,"China,India,Italy,Malaysia,Singapore,United States of America",Homo sapiens,Skin of body,UBERON:0002097,Health study participation,EFO:0010130,none,healthy adult skin 50% up,NA,NA,362,NA,WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,Haoyanzh,healthy adult skin genus >=50%,NA,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,p__Ciliophora|c__Litostomatea|o__Haptorida|f__Trachelophyllidae|g__Enchelyodon|s__Enchelyodon sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",1783272|1239|91061|1385|90964|1279;1783272|201174|1760|85009|31957|1912216;5878|5988|5989|197900|55195|55196;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|186826|1300|1301;1783272|201174|1760|85006|1268|1269;1783272|1239|1737404|1737405|1570339|150022;3379134|1224|1236|2887326|468|475;1783272|201174|1760|85006|1268|32207,Complete,Lwaldron
bsdb:562/2/2,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 2,"China,India,Italy,Malaysia,Singapore,United States of America",Homo sapiens,Skin of body,UBERON:0002097,Health study participation,EFO:0010130,none,healthy adult skin 50% up,NA,NA,362,NA,WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,Haoyanzh,healthy adult skin species in >=50% samples,NA,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium pseudogenitalium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium granulosum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium namnetense,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia globosa,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus luteus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Faucicola|s__Faucicola osloensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus capitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis",1783272|201174|1760|85007|1653|1716|38303;1783272|201174|1760|85009|31957|1912216|1747;1783272|201174|1760|85009|31957|1912216|33011;1783272|201174|1760|85009|31957|1912216|1574624;1783272|1239|1737404|1737405|1570339|150022|1260;4751|5204|1538075|162474|742845|55193|76773;4751|5204|1538075|162474|742845|55193|76775;1783272|201174|1760|85006|1268|1269|1270;3379134|1224|1236|2887326|468|1604696|34062;1783272|1239|91061|1385|90964|1279|29388;1783272|1239|91061|1385|90964|1279|1282;1783272|1239|91061|1385|90964|1279|1290;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|91061|186826|1300|1301|1303,Complete,Lwaldron
bsdb:562/3/1,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 3,"Australia,Canada,China,Denmark,Finland,France,Germany,India,Ireland,Israel,Italy,Japan,Luxembourg,Netherlands,South Korea,Spain,Switzerland,United Kingdom,United Republic of Tanzania,United States of America",Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,none - 50% prevalence threshold,feces from healthy adult,non-disease adult participants from curatedMetagenomicData,0,9623,"no (n=5572), yes (n=276)",WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,Haoyanzh,healthy adult stool genus in >= 50% samples,NA,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Lawsonibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|84998|1643822|1643826|447020;1783272|1239|186801|186802|3085642|2048137;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|2569097;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005519|397864;1783272|201174|1760|85004|31953|1678;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|189330;3379134|1224|1236|91347|543|561;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|204475;1783272|201174|84998|1643822|1643826|644652;1783272|1239|186801|3082720|186804|1505657;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|186802|216572|2172004;1783272|1239|186801|3085636|186803|2316020;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|577310;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|815|909656;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1905344;1783272|1239|91061|186826|1300|1301,Complete,Lwaldron
bsdb:562/3/2,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 3,"Australia,Canada,China,Denmark,Finland,France,Germany,India,Ireland,Israel,Italy,Japan,Luxembourg,Netherlands,South Korea,Spain,Switzerland,United Kingdom,United Republic of Tanzania,United States of America",Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,none - 50% prevalence threshold,feces from healthy adult,non-disease adult participants from curatedMetagenomicData,0,9623,"no (n=5572), yes (n=276)",WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,Haoyanzh,healthy adult stool species in >=50% samples,NA,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum butyriciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:83,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 57_20,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. CAG:241,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Wegman et al. 2014),k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,p__Ciliophora|c__Spirotrichea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:38,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:471,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:110,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Zingiberales|f__Cannaceae|g__Canna|s__Canna indica",1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|1407607|1150298;3379134|976|200643|171549|815|816|820;1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|186801|186802|3085642|2048137|1628085;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|189330|39486;1783272|201174|84998|84999|84107|102106|74426;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|841|360807;3379134|976|200643|171549|2005525|375288|823;1783272|1239|186801|186802|204475|745368;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803|841|301302;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|171550|239759|28117;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|1262992;1783272|1239|91061|186826|1300|1301|1304;1783272|201174|1760|85004|31953|1678|216816;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|171550|239759|214856;1783272|1239|186801|186802|186806|1730|39490;1783272|1239|186801|186802|216572|459786|1897011;3379134|976|200643|171549|171550|239759|328814;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|186802|216572|1263|40518;3379134|976|200643|171549|2005525|375288|46503;1783272|201174|84998|1643822|1643826|447020|446660;1783272|1239|186801|186802|216572|459786|1262911;3379134|976|200643|171549|815|816|47678;1783272|1239|186801|186802|216572|1263|1160721;3379134|976|200643|171549|2005519|397864|487174;1783272|201174|84998|1643822|1643826|644652|471189;1783272|201174|1760|85004|31953|1678|1680;3379134|976|200643|171549|815|816|371601;5878|33829;3379134|976|200643|171549|815|909656|357276;1783272|1239|186801|186802|186806|1730|1262889;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|216572|39492;1783272|1239|91061|186826|1300|1301|1318;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|3085636|186803|28050|28052;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|216572|1535;3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|3085636|186803|841|1262948;3379134|1224|28216|80840|995019|577310|487175;3379134|976|200643|171549|1853231|574697|544645;1783272|201174|84998|84999|84107|102106|147207;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|1263000;1783272|1239|186801|3082720|186804|1505657|261299;33090|35493|3398|4618|4626|4627|4628,Complete,Lwaldron
bsdb:562/4/1,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 4,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Health study participation,EFO:0010130,none - 50% prevalence threshold,nasal cavity from healthy adult,non-disease adult participants from curatedMetagenomicData,0,92,NA,WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,Haoyanzh,healthy adult nasal cavity genus in >=50% samples,NA,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia",1783272|201174|1760|85009|31957|1912216;1783272|1239|91061|1385|90964|1279;1783272|201174|1760|85007|1653|1716;4751|5204|1538075|162474|742845|55193,Complete,Lwaldron
bsdb:562/4/2,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 4,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Health study participation,EFO:0010130,none - 50% prevalence threshold,nasal cavity from healthy adult,non-disease adult participants from curatedMetagenomicData,0,92,NA,WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,Haoyanzh,healthy adult nasal cavity species in >=50% samples,NA,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium accolens,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium granulosum",1783272|201174|1760|85009|31957|1912216|1747;1783272|1239|91061|1385|90964|1279|1282;1783272|201174|1760|85007|1653|1716|38284;4751|5204|1538075|162474|742845|55193|76775;1783272|201174|1760|85009|31957|1912216|33011,Complete,Lwaldron
bsdb:562/5/1,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 5,"Italy,Philippines,United States of America",Homo sapiens,Nasal cavity,UBERON:0001707,Health study participation,EFO:0010130,none - 50% prevalence threshold,oral cavity from healthy adult,non-disease adult participants from curatedMetagenomicData,0,659,No (n=16),WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,Haoyanzh,healthy adult oral cavity genus in >=50% samples,NA,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Ornithinimicrobiaceae|g__Serinicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus",1783272|1239|91061|186826|1300|1301;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|2037|2049|1654;1783272|1239|909932|1843489|31977|29465;3379134|976|200643|171549|171552|838;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378;3379134|1224|28216|206351|481|482;3379134|1224|1236|135625|712|724;3379134|976|200643|171549|171551|836;3379134|29547|3031852|213849|72294|194;1783272|201174|1760|2037|2049|2529408;3379134|976|117743|200644|49546|1016;3384189|32066|203490|203491|1129771|32067;1783272|201174|1760|85007|1653|1716;3379134|1224|28216|80840|119060|47670;3379134|1224|1236|135625|712|416916;3379134|976|200643|171549|2005525|195950;3379134|976|200643|171549|171552|1283313;1783272|1239|91061|186826|186828|117563;1783272|201174|1760|85006|2805590|265976;1783272|1239|186801|3085636|186803|1164882;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|909932|909929|1843491|970;3379134|203691|203692|136|2845253|157;1783272|1239|91061|186826|186827|46123;3379134|1224|28216|206351|481|32257;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|3085636|186803|1213720;1783272|1239|526524|526525|128827|123375;3379134|1224|1236|135615|868|2717;1783272|1239|909932|1843489|31977|906;3379134|1224|28216|206351|481|538;1783272|1239|186801|3082720|186804|1257,Complete,Lwaldron
bsdb:562/5/2,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 5,"Italy,Philippines,United States of America",Homo sapiens,Nasal cavity,UBERON:0001707,Health study participation,EFO:0010130,none - 50% prevalence threshold,oral cavity from healthy adult,non-disease adult participants from curatedMetagenomicData,0,659,No (n=16),WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,Haoyanzh,healthy adult oral cavity species in >=50% samples,NA,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sicca,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia wadei,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus haemolyticus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella infantium,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Asparagales|f__Orchidaceae|s__Epidendroideae|g__Lockhartia|s__Lockhartia amoena,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella serpentiformis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 215,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter sp. oral taxon 458,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. HMSC035G02,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum saburreum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. ICM47,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 212,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella rimae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudopneumoniae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp. T11011-6,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum longum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC034E03,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp. oral taxon 473,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia sp. HMSC24B09,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria mucosa,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oulorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] brachy,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium diversum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sputorum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. A12,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 225,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC067H01,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella jejuni,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 306,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus quentini,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 879,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] sulci,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola",1783272|1239|91061|186826|1300|1301|1303;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|91061|186826|1300|1301|28037;3379134|1224|1236|135625|712|724|729;1783272|201174|1760|85006|1268|32207|2047;1783272|1239|91061|1385|539738|1378|1379;1783272|1239|91061|186826|1300|1301|1305;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|1385|539738|1378|84135;1783272|1239|91061|1385|539738|1378|29391;3384189|32066|203490|203491|203492|848|851;1783272|201174|1760|2037|2049|1654|544580;1783272|1239|91061|186826|1300|1301|68892;3379134|976|200643|171549|171552|838|28132;1783272|201174|1760|2037|2049|2529408|1660;3379134|1224|28216|206351|481|482|484;3379134|1224|28216|206351|481|482|490;3379134|29547|3031852|213849|72294|194|199;3379134|976|200643|171549|171551|836|322095;3384189|32066|203490|203491|203492|848|860;3379134|1224|28216|80840|119060|47670|47671;1783272|1239|91061|186826|1300|1301|1318;3379134|976|117743|200644|49546|1016|327575;3384189|32066|203490|203491|1129771|32067|157687;1783272|201174|1760|85006|1268|32207|172042;1783272|1239|909932|1843489|31977|29465|39778;3379134|976|117743|200644|49546|1016|1019;3379134|976|117743|200644|49546|1016|1017;3379134|1224|1236|135625|712|724|726;1783272|201174|1760|85007|1653|1716|43768;1783272|1239|91061|186826|186828|117563|46124;1783272|1239|909932|1843489|31977|29465|1911679;33090|35493|3398|73496|4747|158332|125137|154688;1783272|1239|91061|186826|1300|1301|1302;3379134|29547|3031852|213849|72294|194|204;3379134|976|200643|171549|2005525|195950|712710;3384189|32066|203490|203491|1129771|32067|712359;1783272|1239|909932|1843489|31977|29465|39777;3379134|976|200643|171549|171552|838|28133;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|1300|1301|45634;3379134|1224|1236|135625|712|416916|712148;1783272|201174|1760|2037|2049|1654|1739406;1783272|1239|186801|3085636|186803|1164882|467210;3379134|1224|1236|135625|712|416916|739;3379134|976|200643|171549|171552|2974251|28135;3379134|1224|28216|206351|481|482|495;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|201174|84998|84999|1643824|2767353|1382;1783272|201174|1760|2037|2049|1654|936548;3379134|1224|28216|206351|481|482|28449;3379134|976|200643|171549|171552|838|60133;3384189|32066|203490|203491|1129771|32067|712357;1783272|1239|91061|186826|1300|1301|113107;1783272|1239|186801|3085636|186803|265975|237576;1783272|201174|84998|84999|1643824|2767353|1383;1783272|201174|1760|85007|1653|1716|61592;1783272|1239|91061|186826|1300|1301|257758;3379134|976|117743|200644|49546|1016|1018;1783272|1239|909932|1843489|31977|29465|2027459;1783272|201174|1760|2037|2049|1654|1655;1783272|201174|1760|2037|2049|1654|55565;3379134|976|200643|171549|171552|2974251|228604;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|171552|1283313|76122;1783272|1239|186801|3085636|186803|1213720|796942;1783272|1239|91061|186826|1300|1301|1739309;1783272|1239|526524|526525|128827|123375|102148;3379134|976|200643|171549|171552|1283313|712469;1783272|1239|91061|186826|186827|46123|1581061;3379134|976|200643|171549|171552|838|470565;3379134|1224|28216|206351|481|482|488;3379134|976|117743|200644|49546|1016|45242;3379134|976|200643|171549|171552|2974251|28136;1783272|1239|186801|3082720|543314|35517;1783272|1239|186801|3082720|543314|86331|114527;3379134|1224|1236|135625|712|724|1078480;1783272|1239|91061|186826|1300|1301|1759399;3384189|32066|203490|203491|1129771|32067|671213;3379134|1224|1236|135615|868|2717|2718;1783272|1239|91061|186826|186827|46123|46125;1783272|1239|909932|1843489|31977|906|187326;1783272|1239|91061|186826|1300|1301|1739491;3379134|976|200643|171549|171552|838|1177574;3379134|1224|28216|206351|481|538|539;3379134|976|200643|171549|171552|838|712461;3379134|1224|1236|135625|712|724|123834;3384189|32066|203490|203491|1129771|32067|1227267;1783272|1239|186801|3082720|543314|143393;1783272|1239|186801|3082720|186804|1257|341694;3384189|32066|203490|203491|1129771|32067|40542;3379134|976|200643|171549|171552|838|28129,Complete,Lwaldron
bsdb:562/6/1,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 6,Italy,Homo sapiens,Milk,UBERON:0001913,Health study participation,EFO:0010130,none - 50% prevalence threshold,milk from healthy adult,non-disease adult participants from curatedMetagenomicData,0,8,NA,WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,Haoyanzh,healthy adult milk genus in >=50% samples,NA,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,Lwaldron
bsdb:562/7/1,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 7,"Italy,Luxembourg,United States of America",Homo sapiens,Vagina,UBERON:0000996,Health study participation,EFO:0010130,NA,healthy adult vagina 70% up,NA,NA,96,NA,WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,27 January 2022,Haoyanzh,Haoyanzh,healthy adult vagina genus in >=70% samples,NA,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Lwaldron
bsdb:562/8/1,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 8,"China,India,Italy,Malaysia,Singapore,United States of America",Homo sapiens,Skin of body,UBERON:0002097,Health study participation,EFO:0010130,none,healthy adult skin 70% up,NA,NA,362,NA,WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,27 January 2022,Haoyanzh,"Haoyanzh,Lwaldron",healthy adult skin genus in >=70% samples,NA,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85009|31957|1912216;4751|5204|1538075|162474|742845|55193;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301,Complete,Lwaldron
bsdb:562/8/2,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 8,"China,India,Italy,Malaysia,Singapore,United States of America",Homo sapiens,Skin of body,UBERON:0002097,Health study participation,EFO:0010130,none,healthy adult skin 70% up,NA,NA,362,NA,WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,10.5281/zenodo.5565690,27 January 2022,Haoyanzh,Haoyanzh,healthy adult skin species in >=70% samples,NA,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus capitis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium granulosum",1783272|201174|1760|85009|31957|1912216|1747;1783272|1239|91061|1385|90964|1279|1282;4751|5204|1538075|162474|742845|55193|76775;1783272|1239|91061|1385|90964|1279|29388;1783272|201174|1760|85009|31957|1912216|33011,Complete,Lwaldron
bsdb:562/9/1,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 9,"Australia,Canada,China,Denmark,Finland,France,Germany,India,Ireland,Israel,Italy,Japan,Luxembourg,Netherlands,South Korea,Spain,Switzerland,United Kingdom,United Republic of Tanzania,United States of America",Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,none - 70% prevalence threshold,feces from healthy adult,non-disease adult participants from curatedMetagenomicData,0,9623,"no (n=5572), yes (n=276)",WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,27 January 2022,Haoyanzh,Haoyanzh,healthy adult stool genus in >= 70% samples,NA,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium",1783272|201174|84998|1643822|1643826|447020;1783272|1239|186801|186802|3085642|2048137;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|2569097;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|204475;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|2316020;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|815|909656;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|1905344,Complete,Lwaldron
bsdb:562/9/2,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 9,"Australia,Canada,China,Denmark,Finland,France,Germany,India,Ireland,Israel,Italy,Japan,Luxembourg,Netherlands,South Korea,Spain,Switzerland,United Kingdom,United Republic of Tanzania,United States of America",Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,none - 70% prevalence threshold,feces from healthy adult,non-disease adult participants from curatedMetagenomicData,0,9623,"no (n=5572), yes (n=276)",WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,10.5281/zenodo.5565690,27 January 2022,Haoyanzh,Haoyanzh,healthy adult stool species in >= 70% samples,NA,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum butyriciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:83,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 57_20,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii",1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|1407607|1150298;3379134|976|200643|171549|815|816|820;1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|186801|186802|3085642|2048137|1628085;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|189330|39486;1783272|201174|84998|84999|84107|102106|74426;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|841|360807;3379134|976|200643|171549|2005525|375288|823;1783272|1239|186801|186802|204475|745368;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803|841|301302;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|171550|239759|28117;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|1262992;1783272|1239|91061|186826|1300|1301|1304;1783272|201174|1760|85004|31953|1678|216816;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|171550|239759|214856;1783272|1239|186801|186802|186806|1730|39490;1783272|1239|186801|186802|216572|459786|1897011;3379134|976|200643|171549|171550|239759|328814;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|186802|216572|946234|292800,Complete,Lwaldron
bsdb:562/10/1,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 10,"Australia,Canada,China,Denmark,Finland,France,Germany,India,Ireland,Israel,Italy,Japan,Luxembourg,Netherlands,South Korea,Spain,Switzerland,United Kingdom,United Republic of Tanzania,United States of America",Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,none - 0% prevalence threshold,feces from healthy adult,non-disease adult participants from curatedMetagenomicData,0,9623,"no (n=5572), yes (n=276)",WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,7 February 2022,Haoyanzh,Haoyanzh,healthy stool genus in any adult sample,NA,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Acholeplasma,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Acidipropionibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinotignum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Aeriscardovia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Agitococcus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Aliarcobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Alkalihalobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Ectothiorhodospiraceae|g__Alkalilimnicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Alkanindiges,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomicrobiaceae|g__Allosphingosinicella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Amnimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Anaerobiospirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Aneurinibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Aquamicrobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Oscillatoriales|f__Microcoleaceae|g__Arthrospira,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Atlantibacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Bavariicoccus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Bordetella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Boseaceae|g__Bosea,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Brevibacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Brochothrix,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Caldibacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Calidifontibacter,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida,k__Methanobacteriati|p__Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomethylophilaceae|g__Methanomethylophilus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Cellulosilyticaceae|g__Cellulosilyticum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae|g__Cellulosimicrobium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Chelatococcaceae|g__Chelatococcus,k__Pseudomonadati|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Clavibacter,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Companilactobacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Metazoa|p__Arthropoda|c__Insecta|o__Blattodea|f__Rhinotermitidae|s__Coptotermitinae|g__Coptotermes|s__Coptotermes heimi,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Corticimicrobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Criibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Cryobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Cytobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Dellaglioa,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Denitrobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Dermabacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Desemzia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfomicrobiaceae|g__Desulfomicrobium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Devosia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Duganella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Edwardsiella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Elizabethkingia,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae|g__Elusimicrobium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Empedobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Ensifer,p__Evosea|o__Mastigamoebida|f__Entamoebidae|g__Entamoeba,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Epilithonimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Eremococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Ewingella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|g__Exiguobacterium,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalicoccus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Gemmatales|f__Gemmataceae|g__Fimbriiglobus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Franconibacter,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Orbales|f__Orbaceae|g__Frischella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Fructilactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Gemmatales|f__Gemmataceae|g__Gemmata,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Geobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Geodermatophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Allobogoriellales|f__Allobogoriellaceae|g__Georgenia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Orbales|f__Orbaceae|g__Gilliamella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Globicatella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Gluconacetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Gluconobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Glutamicibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Haematobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Helcococcus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Hephaestia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Hornefia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Nevskiales|f__Nevskiaceae|g__Hydrocarboniphaga,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillales Family X. Incertae Sedis|g__Hydrogenibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Hydrogenophilus,k__Metazoa|p__Arthropoda|c__Collembola|o__Poduromorpha|f__Hypogastruridae|g__Hypogastrura|s__Hypogastrura sp. BOLD:AAI2333,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Ignavigranum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Ileibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Immundisolibacterales|f__Immundisolibacteraceae|g__Immundisolibacter,k__Orthornavirae|p__Negarnaviricota|c__Insthoviricetes|o__Articulavirales|f__Orthomyxoviridae|g__Alphainfluenzavirus|s__Alphainfluenzavirus influenzae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Jeotgalibacillus,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Jonquetella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Kaistella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Kerstersia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kluyvera,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Knoellia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kosakonia,k__Bacillati|p__Chloroflexota|c__Chloroflexia|o__Chloroflexales|f__Roseiflexaceae|g__Kouleothrix,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Kurthia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Kytococcaceae|g__Kytococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Lactonifactor,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lapidilactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Latilactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Lawsonia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Lawsonibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Leclercia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leifsonia,p__Euglenozoa|c__Kinetoplastea|o__Trypanosomatida|f__Trypanosomatidae|s__Leishmaniinae|g__Leishmania,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lentilactobacillus,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Leptospirales|f__Leptospiraceae|g__Leptospira,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 223,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leucobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Levilactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Limnochordia|o__Limnochordales|f__Limnochordaceae|g__Limnochorda,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Liquorilactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Listeria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Loigolactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Luteipulveratus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Macrococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Mageeibacillus,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Mammaliicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Heyndrickxia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Marmoricola,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Mediterranea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Meiothermus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Melaminivora,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Melissococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Phytobacter,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Methanobacteriati|p__Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanosphaera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Methylibium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae|g__Methyloceanibacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylorubrum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Oscillatoriales|f__Microcoleaceae|g__Microcoleus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Microlunatus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Micropruina,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Aquaspirillaceae|g__Microvirgula,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Mixta,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Modestobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Moellerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Morococcus,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Murimonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycolicibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycolicibacterium,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mycoplasmopsis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Nakamurellales|f__Nakamurellaceae|g__Nakamurella,k__Pseudomonadati|p__Myxococcota|o__Nannocystales|f__Nannocystaceae|g__Nannocystis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Nesterenkonia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Nocardia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Streptosporangiales|f__Nocardiopsidaceae|g__Nocardiopsis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Oenococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Oligella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Ornithinimicrobiaceae|g__Ornithinimicrobium,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Oscillatoriales|f__Oscillatoriaceae|g__Oscillatoria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ottowia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Paeniclostridium,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Isosphaerales|f__Isosphaeraceae|g__Paludisphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Paraclostridium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Parascardovia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella,k__Bacillati|p__Actinomycetota|c__Thermoleophilia|o__Solirubrobacterales|f__Patulibacteraceae|g__Patulibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Paucilactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Pauljensenia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Pectobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Pelistega,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptacetobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Peribacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Phytobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Thermoactinomycetaceae|g__Planifilum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Planomicrobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Plantibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Plesiomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pluralibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Prauserella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Priestia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Prolinoborus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionimicrobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Pseudarthrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pseudescherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae|g__Pseudoalteromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pseudocitrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Pseudoglutamicibacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Pseudoleptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Pseudonocardia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Pseudoxanthomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Psychrobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Pulveribacter,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Methanobacteriati|p__Methanobacteriota|c__Thermococci|o__Thermococcales|f__Thermococcaceae|g__Pyrococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rahnella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae|g__Rheinheimera,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Rhodanobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Rickettsiaceae|g__Rickettsia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Rodentibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Roseomonadaceae|g__Roseicella,k__Bacillati|p__Chloroflexota|c__Chloroflexia|o__Chloroflexales|f__Roseiflexaceae|g__Roseiflexus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Roseomonadaceae|g__Roseomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Rossellomorea,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Metazoa|p__Nematoda|c__Chromadorea|o__Rhabditida|f__Hoplolaimidae|s__Rotylenchulinae|g__Rotylenchus|s__Rotylenchus urmiaensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rouxiella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Rubellimicrobium,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Saccharopolyspora,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Salinicoccus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Salinicola,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Salipiger,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Sanguibacteraceae|g__Sanguibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Schizophyllaceae|g__Schizophyllum|s__Schizophyllum 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037|2049|1069494;1783272|201174|1760|85007|85028|2060;1783272|1239|526524|526525|2810281|191303;3379134|1224|28216|80840|995019|1918598;1783272|1239|186801|3085636|186803|1506577;1783272|544448|2790996|2790998|2129;1783272|1239|91061|186826|81852|2737;1783272|201174|1760|2037|2049|184869;3379134|1224|28216|80840|80864|34072;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|135623|641|662;3379134|256845|1313211|278082|255528|172900;3379134|976|117743|200644|2762318|1013;1783272|1239|91061|1385|186817|2817139;1783272|201174|1760|85007|85025|85043;1783272|201174|1760|2037|2049|2692118;3379134|1224|1236|135614|32033|338;3379134|1224|1236|91347|1903411|629;3379134|1224|1236|91347|543|158876;3379134|1224|28211|204457|2844881|541,Complete,Lwaldron
bsdb:562/11/1,Study 562,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for adults,NA,NA,NA,Experiment 11,"Australia,Canada,China,Denmark,Finland,France,Germany,India,Ireland,Israel,Italy,Japan,Luxembourg,Netherlands,South Korea,Spain,Switzerland,United Kingdom,United Republic of Tanzania,United States of America",Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,none - 30% prevalence threshold,feces from healthy adult,non-disease adult participants from curatedMetagenomicData,0,9623,NA,WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,24 March 2022,Haoyanzh,Haoyanzh,healthy stool genus prevalence >=30%,NA,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Lawsonibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Tractidigestivibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|2316020;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|186806|1730;3379134|976|200643|171549|815|909656;1783272|1239|186801|3085636|186803|1407607;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|33042;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|186802|3085642|2048137;1783272|1239|186801|3085636|186803|2569097;1783272|1239|186801|186802|216572|1263;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|28050;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|204475;1783272|1239|186801|186802|216572|1905344;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|31979|1485;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|946234;1783272|201174|84998|1643822|1643826|447020;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|2005519|397864;1783272|201174|84998|1643822|1643826|644652;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|186802|216572|2172004;3379134|1224|1236|91347|543|561;3379134|200940|3031449|213115|194924|35832;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|1853231|574697;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|3082720|186804|1505657;1783272|1239|91061|186826|33958|1578;1783272|1239|526524|526525|2810280|1505663;1783272|201174|84998|1643822|1643826|84108;1783272|1239|186801|3085636|186803|2719313;3379134|976|200643|171549|2005519|1348911;1783272|201174|84998|1643822|1643826|84111;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|29465;1783272|201174|84998|84999|84107|1472762;1783272|1239|186801|186802|1392389;3379134|1224|1236|135625|712|724;1783272|1239|186801|186802|3082771|1924093;1783272|1239|526524|526525|128827|1573535;3366610|28890|183925|2158|2159|2172;1783272|1239|526524|526525|128827|61170;3379134|976|200643|171549|171552|577309;1783272|201174|84998|84999|1643824|2847313;1783272|1239|526524|526525|2810281|191303;3379134|1224|28216|80840|995019|1918598;1783272|201174|1760|2037|2049|1654,Complete,Lwaldron
bsdb:608/1/1,Study 608,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for children,NA,NA,NA,Experiment 1,"Italy,United States of America",Homo sapiens,Oral cavity,UBERON:0000167,Health study participation,EFO:0010130,none,healthy child oral 50% up,NA,NA,81,NA,16S,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,26 January 2022,Haoyanzh,Haoyanzh,healthy child oral genus in >=50% study samples,NA,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",1783272|1239|91061|186826|1300|1301;1783272|201174|1760|85006|1268|32207;1783272|1239|909932|1843489|31977|29465;3379134|976|200643|171549|171552|838;1783272|1239|91061|1385|539738|1378;3379134|1224|28216|206351|481|482;3379134|1224|1236|135625|712|724,Complete,Lwaldron
bsdb:608/1/2,Study 608,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for children,NA,NA,NA,Experiment 1,"Italy,United States of America",Homo sapiens,Oral cavity,UBERON:0000167,Health study participation,EFO:0010130,none,healthy child oral 50% up,NA,NA,81,NA,16S,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,10.5281/zenodo.5565690,26 January 2022,Haoyanzh,Haoyanzh,healthy child oral species in >= 50% samples,NA,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",1783272|1239|91061|186826|1300|1301|28037;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1303;3379134|976|200643|171549|171552|838|28132;1783272|1239|91061|1385|539738|1378|1379;1783272|1239|91061|186826|1300|1301|68892;1783272|1239|91061|1385|539738|1378|84135;3379134|1224|28216|206351|481|482|484;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|909932|1843489|31977|29465|39778,Complete,Lwaldron
bsdb:608/2/1,Study 608,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for children,NA,NA,NA,Experiment 2,"Bangladesh,China,Estonia,Finland,Germany,India,Ireland,Italy,Luxembourg,Netherlands,Russian Federation,Spain,Sweden,United Kingdom,United Republic of Tanzania,United States of America",Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,none,healthy child stool 50% up,NA,NA,3375,NA,16S,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,26 January 2022,Haoyanzh,Haoyanzh,healthy child stool genus in >= 50% samples,NA,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Lycoperdaceae|g__Calvatia|s__Calvatia complutensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter",1783272|1239|91061|186826|1300|1301;1783272|201174|1760|85004|31953|1678;3379134|1224|1236|91347|543|561;1783272|1239|909932|1843489|31977|29465;3379134|976|200643|171549|815|816;4751|5204|155619|5338|5426|68761|90956;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|2316020,Complete,NA
bsdb:608/2/2,Study 608,meta-analysis,NA,10.5281/zenodo.7544549,https://doi.org/10.5281/zenodo.7544549,NA,Body site-typical microbiome signatures for children,NA,NA,NA,Experiment 2,"Bangladesh,China,Estonia,Finland,Germany,India,Ireland,Italy,Luxembourg,Netherlands,Russian Federation,Spain,Sweden,United Kingdom,United Republic of Tanzania,United States of America",Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,none,healthy child stool 50% up,NA,NA,3375,NA,16S,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,10.5281/zenodo.5565690,26 January 2022,Haoyanzh,Haoyanzh,healthy child stool species in >= 50% samples,NA,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis",1783272|201174|1760|85004|31953|1678|216816;1783272|1239|91061|186826|1300|1301|1304;3379134|1224|1236|91347|543|561|562;1783272|1239|91061|186826|1300|1301|1318,Complete,NA
bsdb:817/1/1,Study 817,case-control,NA,NA,https://www.sciencedirect.com/science/article/abs/pii/S0044848623000224,"Christina Pavloudi, Efthimia Antonopoulou, Maria Ioanna Tsertou","Investigation of systemic granulomatosis in cultured meagre, Argyrosomus  regius, using clinical metagenomics",Aquaculture,2023,"16S, rRNA, amplicon, sequencing, Metagenomics,  Granuloma,  Meagre,  Microbiome,  Lesion",Experiment 1,Greece,Argyrosomus regius,Kidney,UBERON:0002113,Granulomatosis with Polyangiitis,EFO:0005297,Healthy/Healthy with no visible granuloma,Kidneys with calcification,Meagre fishes with tissue calcification in their kidneys,7,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 6, Table 2",9 March 2024,Barrakat,Barrakat,The differential abundance of microbial taxa as identified by LefSe in two health groups (healthy and kidney with calcification),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Candidatus Actinomarinales|f__Candidatus Actinomarinaceae|g__Candidatus Actinomarina|s__Candidatus Actinomarina sp.,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae",1783272|201174|1760|1389450|1389452|1389453|2578121;3379134|976|117743|200644|49546,Complete,Svetlana up
bsdb:817/1/2,Study 817,case-control,NA,NA,https://www.sciencedirect.com/science/article/abs/pii/S0044848623000224,"Christina Pavloudi, Efthimia Antonopoulou, Maria Ioanna Tsertou","Investigation of systemic granulomatosis in cultured meagre, Argyrosomus  regius, using clinical metagenomics",Aquaculture,2023,"16S, rRNA, amplicon, sequencing, Metagenomics,  Granuloma,  Meagre,  Microbiome,  Lesion",Experiment 1,Greece,Argyrosomus regius,Kidney,UBERON:0002113,Granulomatosis with Polyangiitis,EFO:0005297,Healthy/Healthy with no visible granuloma,Kidneys with calcification,Meagre fishes with tissue calcification in their kidneys,7,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Table 2, Figure 6",10 March 2024,Barrakat,"Barrakat,Svetlana up",The differential abundance of microbial taxa as identified by LefSe in two health groups (healthy and kidney with calcification),decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Anoxybacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus",1783272|1239|91061|1385|3120669|150247;1783272|201174|1760|85006|145357|57495;1783272|201174|1760|85006|1268|1269;3379134|1224|28211|204455|31989|265,Complete,Svetlana up
bsdb:817/2/1,Study 817,case-control,NA,NA,https://www.sciencedirect.com/science/article/abs/pii/S0044848623000224,"Christina Pavloudi, Efthimia Antonopoulou, Maria Ioanna Tsertou","Investigation of systemic granulomatosis in cultured meagre, Argyrosomus  regius, using clinical metagenomics",Aquaculture,2023,"16S, rRNA, amplicon, sequencing, Metagenomics,  Granuloma,  Meagre,  Microbiome,  Lesion",Experiment 2,Greece,Argyrosomus regius,Kidney,UBERON:0002113,Granulomatosis with Polyangiitis,EFO:0005297,Systemic Granulomatosis (SG)-affected,Sick with Kidney calcification,Meagre fishes with tissue calcifications in their kidneys,10,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 6, Table 2",9 March 2024,Barrakat,Barrakat,"The differential abundance of microbial taxa as identified by LefSe in two health groups:
Systemic granulomatosis (SG)-affected and kidney with calcification.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Candidatus Actinomarinales|f__Candidatus Actinomarinaceae|g__Candidatus Actinomarina|s__Candidatus Actinomarina sp.,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae",1783272|201174|1760|1389450|1389452|1389453|2578121;3379134|976|117743|200644|49546,Complete,Svetlana up
bsdb:817/2/2,Study 817,case-control,NA,NA,https://www.sciencedirect.com/science/article/abs/pii/S0044848623000224,"Christina Pavloudi, Efthimia Antonopoulou, Maria Ioanna Tsertou","Investigation of systemic granulomatosis in cultured meagre, Argyrosomus  regius, using clinical metagenomics",Aquaculture,2023,"16S, rRNA, amplicon, sequencing, Metagenomics,  Granuloma,  Meagre,  Microbiome,  Lesion",Experiment 2,Greece,Argyrosomus regius,Kidney,UBERON:0002113,Granulomatosis with Polyangiitis,EFO:0005297,Systemic Granulomatosis (SG)-affected,Sick with Kidney calcification,Meagre fishes with tissue calcifications in their kidneys,10,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2 Fig 6,10 March 2024,Barrakat,Barrakat,"The differential abundance of microbial taxa as identified by LefSe in two health groups:
Systemic granulomatosis (SG)-affected and kidney with calcification.",decreased,",k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Pseudomonadati|p__Acidobacteriota|c__Blastocatellia|o__Blastocatellales|f__Pyrinomonadaceae|g__Pyrinomonas,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Beijerinckiaceae",;3379134|1224|28216|80840|119060;3379134|1224|28211|204455|31989|265;3379134|57723|1562566|1748771|2048906|1562565;3379134|976|117747|200666;3379134|1224|28211|356|45404,Complete,Svetlana up
bsdb:817/3/1,Study 817,case-control,NA,NA,https://www.sciencedirect.com/science/article/abs/pii/S0044848623000224,"Christina Pavloudi, Efthimia Antonopoulou, Maria Ioanna Tsertou","Investigation of systemic granulomatosis in cultured meagre, Argyrosomus  regius, using clinical metagenomics",Aquaculture,2023,"16S, rRNA, amplicon, sequencing, Metagenomics,  Granuloma,  Meagre,  Microbiome,  Lesion",Experiment 3,Greece,Argyrosomus regius,Kidney,UBERON:0002113,Granulomatosis with Polyangiitis,EFO:0005297,Healthy/Healthy with no visible granuloma,Sick,Meagre fishes with SG-affected kidneys and tissue calcification in their kidneys,7,20,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 2, Supplementary Figure 2, Supplementary Figure 3",9 March 2024,Barrakat,"Barrakat,Svetlana up","The differential abundance of microbial taxa as identified by LefSe in two health groups
(healthy and sick)",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Gallionellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales",3379134|1224|28216|80840|119060;3379134|1224|28216|32003|90627;3379134|1224|28211|204455,Complete,Svetlana up
bsdb:817/3/2,Study 817,case-control,NA,NA,https://www.sciencedirect.com/science/article/abs/pii/S0044848623000224,"Christina Pavloudi, Efthimia Antonopoulou, Maria Ioanna Tsertou","Investigation of systemic granulomatosis in cultured meagre, Argyrosomus  regius, using clinical metagenomics",Aquaculture,2023,"16S, rRNA, amplicon, sequencing, Metagenomics,  Granuloma,  Meagre,  Microbiome,  Lesion",Experiment 3,Greece,Argyrosomus regius,Kidney,UBERON:0002113,Granulomatosis with Polyangiitis,EFO:0005297,Healthy/Healthy with no visible granuloma,Sick,Meagre fishes with SG-affected kidneys and tissue calcification in their kidneys,7,20,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Table 2, Supplementary Figure 2, Supplementary Figure 3",10 March 2024,Barrakat,"Barrakat,Svetlana up","The differential abundance of microbial taxa as identified by LefSe in two health groups
(healthy and sick)",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Coraliomargaritaceae|g__Coraliomargarita,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Meiothermus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061|1385;1783272|1239|91061|1385|186817|1386;3379134|74201|414999|415001|3056371|442430;3384194|1297|188787|68933|188786|65551;3379134|1224|28211|204455|31989|265;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:879/1/1,Study 879,prospective cohort,NA,10.22541/au.169511765.50376146/v1,https://www.authorea.com/users/666162/articles/667143-oral-lesion-and-microbiome-diversity-in-covid-19-hospitalized-patients,"Alessandra Lunis, Bernal Stewart, Cesar Augusto Migliorati, Ester Cerdeira Sabino, Joyce Vanessa Da Silva Fonseca, Nazareno Scaccia, Pablo Andres Munoz Torres, Paulo Henrique Braz Da Silva, Roberta Pilleggii, Rodrigo Melim Zerbinati, Silvia Figueiredo Costa, Sumatra Melo Da Costa Pereira Jales",Oral lesion and microbiome diversity in COVID-19 hospitalized patients,Authorea Inc.,2023,"Brazil, Oral lesion, covid-19, hospitalized patients, sars coronavirus",Experiment 1,Brazil,Homo sapiens,Oral cavity,UBERON:0000167,Oral ulcer,HP:0000155,Covid-19 patients without oral lesions,Covid-19 with oral lesions,COVID-19 patients with the presence of oral lesions,115,14,NA,16S,4,Ion Torrent,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,decreased,NA,NA,NA,NA,Signature 1,Fourth paragraph in section 3.3,6 March 2024,Nekembe,"Nekembe,Aleru Divine",Significant difference found in Covid-10 patients who had oral lesions.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,Peace Sandy
bsdb:879/2/1,Study 879,prospective cohort,NA,10.22541/au.169511765.50376146/v1,https://www.authorea.com/users/666162/articles/667143-oral-lesion-and-microbiome-diversity-in-covid-19-hospitalized-patients,"Alessandra Lunis, Bernal Stewart, Cesar Augusto Migliorati, Ester Cerdeira Sabino, Joyce Vanessa Da Silva Fonseca, Nazareno Scaccia, Pablo Andres Munoz Torres, Paulo Henrique Braz Da Silva, Roberta Pilleggii, Rodrigo Melim Zerbinati, Silvia Figueiredo Costa, Sumatra Melo Da Costa Pereira Jales",Oral lesion and microbiome diversity in COVID-19 hospitalized patients,Authorea Inc.,2023,"Brazil, Oral lesion, covid-19, hospitalized patients, sars coronavirus",Experiment 2,Brazil,Homo sapiens,Oral cavity,UBERON:0000167,Illness severity status,EFO:0007863,Non severe COVID patients,Severe COVID patients,COVID-19 patients with severe symptoms,NA,NA,NA,16S,4,Ion Torrent,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,decreased,NA,NA,NA,NA,Signature 1,Fourth paragraph in section 3.3,7 March 2024,Nekembe,"Nekembe,Aleru Divine",Significant differences found in Covid-10 patients who had severe symptoms.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,Peace Sandy
bsdb:879/3/1,Study 879,prospective cohort,NA,10.22541/au.169511765.50376146/v1,https://www.authorea.com/users/666162/articles/667143-oral-lesion-and-microbiome-diversity-in-covid-19-hospitalized-patients,"Alessandra Lunis, Bernal Stewart, Cesar Augusto Migliorati, Ester Cerdeira Sabino, Joyce Vanessa Da Silva Fonseca, Nazareno Scaccia, Pablo Andres Munoz Torres, Paulo Henrique Braz Da Silva, Roberta Pilleggii, Rodrigo Melim Zerbinati, Silvia Figueiredo Costa, Sumatra Melo Da Costa Pereira Jales",Oral lesion and microbiome diversity in COVID-19 hospitalized patients,Authorea Inc.,2023,"Brazil, Oral lesion, covid-19, hospitalized patients, sars coronavirus",Experiment 3,Brazil,Homo sapiens,Oral cavity,UBERON:0000167,Antimicrobial agent,CHEBI:33281,No antibiotics use,Antibiotics use,COVID-19 patients who had antibiotic therapy in the previous 3 months.,NA,NA,NA,16S,4,Ion Torrent,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,decreased,NA,NA,NA,NA,Signature 1,Paragraph 4 in section 3.3 and Paragraph 5 in the discussion section,7 March 2024,Nekembe,"Nekembe,Aleru Divine,Peace Sandy",Significant differences found in Covid-10 patients who were on antibiotic therapy in the previous 3 months.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",1783272|1239|91061|186826|33958|1578;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|838;1783272|1239|91061|1385|90964|1279;1783272|1239|909932|1843489|31977|29465;3384189|32066|203490|203491|203492|848,Complete,Peace Sandy
bsdb:879/4/1,Study 879,prospective cohort,NA,10.22541/au.169511765.50376146/v1,https://www.authorea.com/users/666162/articles/667143-oral-lesion-and-microbiome-diversity-in-covid-19-hospitalized-patients,"Alessandra Lunis, Bernal Stewart, Cesar Augusto Migliorati, Ester Cerdeira Sabino, Joyce Vanessa Da Silva Fonseca, Nazareno Scaccia, Pablo Andres Munoz Torres, Paulo Henrique Braz Da Silva, Roberta Pilleggii, Rodrigo Melim Zerbinati, Silvia Figueiredo Costa, Sumatra Melo Da Costa Pereira Jales",Oral lesion and microbiome diversity in COVID-19 hospitalized patients,Authorea Inc.,2023,"Brazil, Oral lesion, covid-19, hospitalized patients, sars coronavirus",Experiment 4,Brazil,Homo sapiens,Oral cavity,UBERON:0000167,Oxygen,CHEBI:15379,No oxygen therapy,Oxygen therapy,COVID-19 patients who had oxygen therapy.,NA,NA,NA,16S,4,Ion Torrent,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,decreased,Signature 1,Paragraph 4 in section 3.3 and Paragraph 5 in the discussion section,7 March 2024,Nekembe,"Nekembe,Aleru Divine,Peace Sandy",Significant differences found in Covid-10 patients who were on oxygen therapy.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|1385|90964|1279,Complete,Peace Sandy
bsdb:879/5/1,Study 879,prospective cohort,NA,10.22541/au.169511765.50376146/v1,https://www.authorea.com/users/666162/articles/667143-oral-lesion-and-microbiome-diversity-in-covid-19-hospitalized-patients,"Alessandra Lunis, Bernal Stewart, Cesar Augusto Migliorati, Ester Cerdeira Sabino, Joyce Vanessa Da Silva Fonseca, Nazareno Scaccia, Pablo Andres Munoz Torres, Paulo Henrique Braz Da Silva, Roberta Pilleggii, Rodrigo Melim Zerbinati, Silvia Figueiredo Costa, Sumatra Melo Da Costa Pereira Jales",Oral lesion and microbiome diversity in COVID-19 hospitalized patients,Authorea Inc.,2023,"Brazil, Oral lesion, covid-19, hospitalized patients, sars coronavirus",Experiment 5,Brazil,Homo sapiens,Oral cavity,UBERON:0000167,Illness severity status,EFO:0007863,Non ICU patients,ICU patients,COVID-19 patients who were in intensive care units.,NA,NA,NA,16S,4,Ion Torrent,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Paragraph 4 in section 3.3 and Paragraph 6 in the discussion section,29 March 2024,Aleru Divine,Aleru Divine,Significant differences found in Covid-10 patients who were in the Intensive Care Unit (ICU).,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|29465,Complete,Peace Sandy
bsdb:879/5/2,Study 879,prospective cohort,NA,10.22541/au.169511765.50376146/v1,https://www.authorea.com/users/666162/articles/667143-oral-lesion-and-microbiome-diversity-in-covid-19-hospitalized-patients,"Alessandra Lunis, Bernal Stewart, Cesar Augusto Migliorati, Ester Cerdeira Sabino, Joyce Vanessa Da Silva Fonseca, Nazareno Scaccia, Pablo Andres Munoz Torres, Paulo Henrique Braz Da Silva, Roberta Pilleggii, Rodrigo Melim Zerbinati, Silvia Figueiredo Costa, Sumatra Melo Da Costa Pereira Jales",Oral lesion and microbiome diversity in COVID-19 hospitalized patients,Authorea Inc.,2023,"Brazil, Oral lesion, covid-19, hospitalized patients, sars coronavirus",Experiment 5,Brazil,Homo sapiens,Oral cavity,UBERON:0000167,Illness severity status,EFO:0007863,Non ICU patients,ICU patients,COVID-19 patients who were in intensive care units.,NA,NA,NA,16S,4,Ion Torrent,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Paragraph 4 in section 3.3 and Paragraph 6 in the discussion section,29 March 2024,Aleru Divine,Aleru Divine,Significant differences found in Covid-10 patients who were in the Intensive Care Unit (ICU).,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,3379134|1224|1236|135625|712|724,Complete,Peace Sandy
bsdb:1078/1/1,Study 1078,laboratory experiment,NA,10.1016/j.jff.2024.106106,https://www.sciencedirect.com/science/article/pii/S1756464624001087#s0125,"Haoyu Wang, Kaiwei Chen, Liang Xiao, Ningning He, Shangyong Li, Shengnan Yu, Xiaoqian Lin, Yuanqiang Zou, Zhinan Wu",Stachyose ameliorates obesity-related metabolic syndrome via improving intestinal barrier function and remodeling gut microbiota,Journal of Functional Foods,2024,"Butyrate-producing strains, Stachyose, gut microbiota, intestinal barrier, metabolic syndrome",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,High fat diet,EFO:0002757,High-Fat Diet fed Mice (HFD),Stachyose-treated High-Fat Diet fed Mice (STA),"Male C57BL/6J mice (18–20g, 6 weeks old) which were fed a High-Fat Diet (D12492-HFD diet, #XTHF60-1) with 60% of energy from fat, for 12 weeks and treatment with stachyose in the last 8 weeks (200 mg/ kg/day).",7,7,NA,WMS,NA,DNBSEQ-T7,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 5A,2 May 2024,Joan Chuks,Joan Chuks,Bacterial taxa identified by Linear discriminant analysis effect size (LEfSe) as differentially abundant in mice fed with Stachyose-treated High-Fat Diet compared to mice fed with High-Fat Diet.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella stercoris,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum|s__Allobaculum mucilyticum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Thermophilibacter|s__Thermophilibacter immobilis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella|s__Parolsenella catena,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parafannyhessea|s__Parafannyhessea umbonata",1783272|201174|84998|84999|84107|102106|147206;1783272|1239|526524|526525|128827|174708|2834459;1783272|201174|84998|84999|1643824|2847307|2779519;1783272|201174|84998|84999|1643824|2082587|2003188;1783272|201174|84998|84999|1643824|2847312|604330,Complete,Svetlana up
bsdb:1078/1/2,Study 1078,laboratory experiment,NA,10.1016/j.jff.2024.106106,https://www.sciencedirect.com/science/article/pii/S1756464624001087#s0125,"Haoyu Wang, Kaiwei Chen, Liang Xiao, Ningning He, Shangyong Li, Shengnan Yu, Xiaoqian Lin, Yuanqiang Zou, Zhinan Wu",Stachyose ameliorates obesity-related metabolic syndrome via improving intestinal barrier function and remodeling gut microbiota,Journal of Functional Foods,2024,"Butyrate-producing strains, Stachyose, gut microbiota, intestinal barrier, metabolic syndrome",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,High fat diet,EFO:0002757,High-Fat Diet fed Mice (HFD),Stachyose-treated High-Fat Diet fed Mice (STA),"Male C57BL/6J mice (18–20g, 6 weeks old) which were fed a High-Fat Diet (D12492-HFD diet, #XTHF60-1) with 60% of energy from fat, for 12 weeks and treatment with stachyose in the last 8 weeks (200 mg/ kg/day).",7,7,NA,WMS,NA,DNBSEQ-T7,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 5A,2 May 2024,Joan Chuks,Joan Chuks,Bacterial taxa identified by Linear discriminant analysis effect size (LEfSe) as differentially abundant in mice fed with Stachyose-treated High-Fat Diet compared to mice fed with High-Fat Diet.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia marmotae,3379134|1224|1236|91347|543|561|1499973,Complete,Svetlana up
bsdb:1129/1/1,Study 1129,case-control,NA,https://doi.org/10.1038/s41467-024-51464-w,NA,"Dennis S. Nielsin, Getnet tesfaw, Nina langeland, abigail c. mapes, alemseged abdissa, ashley kates, dawd s. siraj, nasia safdar, zeleke mekonnen",Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia,Nature communications,2024,"acute diarrhea, diarrhea, gut microbiota, Prolonged or persistent Diarrhea (ProPD)",Experiment 1,Ethiopia,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Non-diarrheal controls.,Diarrhea,The aim of our study was to decipher what differentiates the GM of children with diarrhea (AD and ProPD) from healthy controls,663,650,NA,16S,4,Illumina,relative abundances,DESeq2,0.05,TRUE,NA,NA,breast feeding,NA,increased,NA,NA,NA,increased,Signature 1,Figure 4a,23 January 2025,Miss Lulu,Miss Lulu,Diarrhea cases compared with non-diarrheal controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp.,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae",3379134|1224|1236|91347|543|561|1884818;3379134|29547|3031852|213849|72294|194|205;1783272|1239|91061|186826|1300|1301|1306;3379134|1224|1236|135625|712|724|729,Complete,NA
bsdb:1129/1/2,Study 1129,case-control,NA,https://doi.org/10.1038/s41467-024-51464-w,NA,"Dennis S. Nielsin, Getnet tesfaw, Nina langeland, abigail c. mapes, alemseged abdissa, ashley kates, dawd s. siraj, nasia safdar, zeleke mekonnen",Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia,Nature communications,2024,"acute diarrhea, diarrhea, gut microbiota, Prolonged or persistent Diarrhea (ProPD)",Experiment 1,Ethiopia,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Non-diarrheal controls.,Diarrhea,The aim of our study was to decipher what differentiates the GM of children with diarrhea (AD and ProPD) from healthy controls,663,650,NA,16S,4,Illumina,relative abundances,DESeq2,0.05,TRUE,NA,NA,breast feeding,NA,increased,NA,NA,NA,increased,Signature 2,Figure 4a,23 January 2025,Miss Lulu,Miss Lulu,Diarrhea cases compared with non-diarrheal controls,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella corporis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus",3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|171552|838|28128;1783272|1239|186801|186802|216572|216851|853;1783272|1239|909932|1843489|31977|39948|487173,Complete,NA
bsdb:1129/2/1,Study 1129,case-control,NA,https://doi.org/10.1038/s41467-024-51464-w,NA,"Dennis S. Nielsin, Getnet tesfaw, Nina langeland, abigail c. mapes, alemseged abdissa, ashley kates, dawd s. siraj, nasia safdar, zeleke mekonnen",Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia,Nature communications,2024,"acute diarrhea, diarrhea, gut microbiota, Prolonged or persistent Diarrhea (ProPD)",Experiment 2,Ethiopia,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Non-diarrheal controls.,Acute Diarrhea,The aim of our study was to decipher what differentiates the GM of children with diarrhea (AD and ProPD) from healthy controls,663,554,NA,16S,1234,Illumina,relative abundances,DESeq2,0.05,TRUE,NA,NA,"age,breast feeding,sex",NA,increased,NA,NA,NA,increased,Signature 1,Figure 4b and Figure 7,23 January 2025,Miss Lulu,Miss Lulu,AD cases compared with non-diarrheal controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp.,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.",3379134|1224|1236|91347|543|561|1884818;3379134|29547|3031852|213849|72294|194|205;1783272|1239|91061|186826|1300|1301|1306,Complete,NA
bsdb:1129/2/2,Study 1129,case-control,NA,https://doi.org/10.1038/s41467-024-51464-w,NA,"Dennis S. Nielsin, Getnet tesfaw, Nina langeland, abigail c. mapes, alemseged abdissa, ashley kates, dawd s. siraj, nasia safdar, zeleke mekonnen",Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia,Nature communications,2024,"acute diarrhea, diarrhea, gut microbiota, Prolonged or persistent Diarrhea (ProPD)",Experiment 2,Ethiopia,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Non-diarrheal controls.,Acute Diarrhea,The aim of our study was to decipher what differentiates the GM of children with diarrhea (AD and ProPD) from healthy controls,663,554,NA,16S,1234,Illumina,relative abundances,DESeq2,0.05,TRUE,NA,NA,"age,breast feeding,sex",NA,increased,NA,NA,NA,increased,Signature 2,Figure 4b and Figure 7,23 January 2025,Miss Lulu,Miss Lulu,AD cases compared with non-diarrheal controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella corporis",1783272|1239|186801|186802|216572|216851|853;3379134|976|200643|171549|171552|838|28128,Complete,NA
bsdb:1129/3/1,Study 1129,case-control,NA,https://doi.org/10.1038/s41467-024-51464-w,NA,"Dennis S. Nielsin, Getnet tesfaw, Nina langeland, abigail c. mapes, alemseged abdissa, ashley kates, dawd s. siraj, nasia safdar, zeleke mekonnen",Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia,Nature communications,2024,"acute diarrhea, diarrhea, gut microbiota, Prolonged or persistent Diarrhea (ProPD)",Experiment 3,Ethiopia,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Non-diarrheal controls.,Prolonged or persistent Diarrhea (ProPD),The aim of our study was to decipher what differentiates the GM of children with diarrhea (AD and ProPD) from healthy controls,663,95,NA,16S,1234,Illumina,relative abundances,DESeq2,0.05,TRUE,NA,NA,"age,breast feeding,sex",NA,increased,NA,NA,NA,increased,Signature 1,Figure 4c and Figure 8,23 January 2025,Miss Lulu,Miss Lulu,ProPD cases compared with non-diarrheal controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp.,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.",3379134|1224|1236|91347|543|561|1884818;3379134|29547|3031852|213849|72294|194|205;1783272|1239|91061|186826|1300|1301|1306,Complete,NA
bsdb:1129/4/1,Study 1129,case-control,NA,https://doi.org/10.1038/s41467-024-51464-w,NA,"Dennis S. Nielsin, Getnet tesfaw, Nina langeland, abigail c. mapes, alemseged abdissa, ashley kates, dawd s. siraj, nasia safdar, zeleke mekonnen",Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia,Nature communications,2024,"acute diarrhea, diarrhea, gut microbiota, Prolonged or persistent Diarrhea (ProPD)",Experiment 4,Ethiopia,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Acute Diarrhea,Prolonged or persistent Diarrhea (ProPD),The aim of our study was to decipher what differentiates the GM of children with Prolonged or persistent diarrhea (ProPD) as compared with Acute Diarrhea,554,95,NA,16S,1234,Illumina,NA,DESeq2,0.05,TRUE,NA,NA,"age,breast feeding,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4d and Figure 9,23 January 2025,Miss Lulu,Miss Lulu,ProPD cases compared with AD cases,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|2742598|97478,Complete,NA
bsdb:1129/4/2,Study 1129,case-control,NA,https://doi.org/10.1038/s41467-024-51464-w,NA,"Dennis S. Nielsin, Getnet tesfaw, Nina langeland, abigail c. mapes, alemseged abdissa, ashley kates, dawd s. siraj, nasia safdar, zeleke mekonnen",Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia,Nature communications,2024,"acute diarrhea, diarrhea, gut microbiota, Prolonged or persistent Diarrhea (ProPD)",Experiment 4,Ethiopia,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Acute Diarrhea,Prolonged or persistent Diarrhea (ProPD),The aim of our study was to decipher what differentiates the GM of children with Prolonged or persistent diarrhea (ProPD) as compared with Acute Diarrhea,554,95,NA,16S,1234,Illumina,NA,DESeq2,0.05,TRUE,NA,NA,"age,breast feeding,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4d and Figure 9,23 January 2025,Miss Lulu,Miss Lulu,ProPD cases compared with AD cases,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|186801|186802|216572|216851|853;3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|3085636|186803|207244|649756;1783272|201174|84998|84999|84107;3379134|976|200643|171549|815|816,Complete,NA
bsdb:1238/1/1,Study 1238,prospective cohort,NA,https://doi.org/10.3390/nu16223942,NA,"Axel Künstner, Caroline Roduit, Felicitas Bellutti Enders, Hauke Busch, Karin Hartmann, Michael Olbrich, Michèle S. Roth, Misa Hirose, Muriel d’Aujourd’hui, Saleh Ibrahim",Characterization of the Gut and Skin Microbiome over Time in Young Children with IgE-Mediated Food Allergy,Nutrients,2024,"atopic dermatitis, fecal microbiome, immediate hypersensitivity, infant, longitudinal, microbiota, paediatric, peanut allergy, pediatric, tree nut allergy",Experiment 1,"Germany,Switzerland",Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,Control Group,Patients at enrollment (t0),Children with Immunoglobulin-E (IgE)-mediated food allergy (FA) at enrollment (denoted by t0).,8,22,NA,16S,12,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure S2D,24 November 2024,Aleru Divine,Aleru Divine,"Violin plot showing differences in genus abundances in fecal samples among controls, patients at enrollment (t0), and patients at follow-up (t1).",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella sp. CAG:1427",1783272|1239|91061|1385|186817|1386;1783272|201174|84998|1643822|1643826|84111|1262874,Complete,Svetlana up
bsdb:1238/2/1,Study 1238,prospective cohort,NA,https://doi.org/10.3390/nu16223942,NA,"Axel Künstner, Caroline Roduit, Felicitas Bellutti Enders, Hauke Busch, Karin Hartmann, Michael Olbrich, Michèle S. Roth, Misa Hirose, Muriel d’Aujourd’hui, Saleh Ibrahim",Characterization of the Gut and Skin Microbiome over Time in Young Children with IgE-Mediated Food Allergy,Nutrients,2024,"atopic dermatitis, fecal microbiome, immediate hypersensitivity, infant, longitudinal, microbiota, paediatric, peanut allergy, pediatric, tree nut allergy",Experiment 2,"Germany,Switzerland",Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,Control Group,Patients at follow-up (t1),Children with Immunoglobulin-E (IgE)-mediated food allergy (FA) at follow-up (denoted by t1).,8,20,NA,16S,12,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure S2D,24 November 2024,Aleru Divine,Aleru Divine,"Violin plot showing differences in genus abundances in fecal samples among controls, patients at enrollment (t0), and patients at follow-up (t1).",increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,1783272|1239|91061|1385|186817|1386,Complete,Svetlana up
bsdb:1238/2/2,Study 1238,prospective cohort,NA,https://doi.org/10.3390/nu16223942,NA,"Axel Künstner, Caroline Roduit, Felicitas Bellutti Enders, Hauke Busch, Karin Hartmann, Michael Olbrich, Michèle S. Roth, Misa Hirose, Muriel d’Aujourd’hui, Saleh Ibrahim",Characterization of the Gut and Skin Microbiome over Time in Young Children with IgE-Mediated Food Allergy,Nutrients,2024,"atopic dermatitis, fecal microbiome, immediate hypersensitivity, infant, longitudinal, microbiota, paediatric, peanut allergy, pediatric, tree nut allergy",Experiment 2,"Germany,Switzerland",Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,Control Group,Patients at follow-up (t1),Children with Immunoglobulin-E (IgE)-mediated food allergy (FA) at follow-up (denoted by t1).,8,20,NA,16S,12,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure S2D,24 November 2024,Aleru Divine,Aleru Divine,"Violin plot showing differences in genus abundances in fecal samples among controls, patients at enrollment (t0), and patients at follow-up (t1).",decreased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella sp. CAG:1427,1783272|201174|84998|1643822|1643826|84111|1262874,Complete,Svetlana up
bsdb:1238/3/1,Study 1238,prospective cohort,NA,https://doi.org/10.3390/nu16223942,NA,"Axel Künstner, Caroline Roduit, Felicitas Bellutti Enders, Hauke Busch, Karin Hartmann, Michael Olbrich, Michèle S. Roth, Misa Hirose, Muriel d’Aujourd’hui, Saleh Ibrahim",Characterization of the Gut and Skin Microbiome over Time in Young Children with IgE-Mediated Food Allergy,Nutrients,2024,"atopic dermatitis, fecal microbiome, immediate hypersensitivity, infant, longitudinal, microbiota, paediatric, peanut allergy, pediatric, tree nut allergy",Experiment 3,"Germany,Switzerland",Homo sapiens,Skin of forearm,UBERON:0003403,Food allergy,EFO:1001890,Control Group,Patients at enrollment (t0),Children with Immunoglobulin-E (IgE)-mediated food allergy (FA) at enrollment (denoted by t0).,8,23,NA,16S,12,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 1D and Figure S5,24 November 2024,Aleru Divine,Aleru Divine,"Violin plot showing differences in genus and species abundances in forearm samples among controls, patients at enrollment (t0), and patients at follow-up (t1).",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp. oral taxon 780",3379134|976|200643|171549|171552|1283313;1783272|201174|1760|85009|31957|2801844;3379134|976|117743|200644|49546|1016;3384189|32066|203490|203491|203492|848;3379134|1224|1236|135625|712|724;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3379134|1224|1236|72274|135621|286;1783272|1239|909932|1843489|31977|29465|671229,Complete,Svetlana up
bsdb:1238/3/2,Study 1238,prospective cohort,NA,https://doi.org/10.3390/nu16223942,NA,"Axel Künstner, Caroline Roduit, Felicitas Bellutti Enders, Hauke Busch, Karin Hartmann, Michael Olbrich, Michèle S. Roth, Misa Hirose, Muriel d’Aujourd’hui, Saleh Ibrahim",Characterization of the Gut and Skin Microbiome over Time in Young Children with IgE-Mediated Food Allergy,Nutrients,2024,"atopic dermatitis, fecal microbiome, immediate hypersensitivity, infant, longitudinal, microbiota, paediatric, peanut allergy, pediatric, tree nut allergy",Experiment 3,"Germany,Switzerland",Homo sapiens,Skin of forearm,UBERON:0003403,Food allergy,EFO:1001890,Control Group,Patients at enrollment (t0),Children with Immunoglobulin-E (IgE)-mediated food allergy (FA) at enrollment (denoted by t0).,8,23,NA,16S,12,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 1D and Figure S5,24 November 2024,Aleru Divine,Aleru Divine,"Violin plot showing differences in genus and species abundances in forearm samples among controls, patients at enrollment (t0), and patients at follow-up (t1).",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus equorum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus lugdunensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus pasteuri,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus pettenkoferi,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus pragensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus simulans,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus warneri,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus pseudolugdunensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus auricularis",1783272|1239|91061|1385|539738|1378;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|1385|90964|1279|1282;1783272|1239|91061|1385|90964|1279|246432;1783272|1239|91061|1385|90964|1279|28035;1783272|1239|91061|1385|90964|1279|45972;1783272|1239|91061|1385|90964|1279|170573;1783272|1239|91061|1385|90964|1279|1611836;1783272|1239|91061|1385|90964|1279|1286;1783272|1239|91061|1385|90964|1279|1292;1783272|1239|91061|1385|90964|1279|425474;1783272|1239|91061|1385|90964|1279|29379,Complete,Svetlana up
bsdb:1238/4/1,Study 1238,prospective cohort,NA,https://doi.org/10.3390/nu16223942,NA,"Axel Künstner, Caroline Roduit, Felicitas Bellutti Enders, Hauke Busch, Karin Hartmann, Michael Olbrich, Michèle S. Roth, Misa Hirose, Muriel d’Aujourd’hui, Saleh Ibrahim",Characterization of the Gut and Skin Microbiome over Time in Young Children with IgE-Mediated Food Allergy,Nutrients,2024,"atopic dermatitis, fecal microbiome, immediate hypersensitivity, infant, longitudinal, microbiota, paediatric, peanut allergy, pediatric, tree nut allergy",Experiment 4,"Germany,Switzerland",Homo sapiens,Skin of forearm,UBERON:0003403,Food allergy,EFO:1001890,Control Group,Patients at follow-up (t1),Children with Immunoglobulin-E (IgE)-mediated food allergy (FA) at follow-up (denoted by t1).,8,21,NA,16S,12,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 1D and Figure S5,24 November 2024,Aleru Divine,Aleru Divine,"Violin plot showing differences in genus and species abundances in forearm samples among controls, patients at enrollment (t0), and patients at follow-up (t1).",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp. oral taxon 780,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",3379134|976|200643|171549|171552|1283313;1783272|201174|1760|85009|31957|2801844;3379134|976|117743|200644|49546|1016;1783272|1239|909932|1843489|31977|29465|671229;3384189|32066|203490|203491|203492|848;3379134|1224|1236|135625|712|724;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3379134|1224|1236|72274|135621|286,Complete,Svetlana up
bsdb:1238/4/2,Study 1238,prospective cohort,NA,https://doi.org/10.3390/nu16223942,NA,"Axel Künstner, Caroline Roduit, Felicitas Bellutti Enders, Hauke Busch, Karin Hartmann, Michael Olbrich, Michèle S. Roth, Misa Hirose, Muriel d’Aujourd’hui, Saleh Ibrahim",Characterization of the Gut and Skin Microbiome over Time in Young Children with IgE-Mediated Food Allergy,Nutrients,2024,"atopic dermatitis, fecal microbiome, immediate hypersensitivity, infant, longitudinal, microbiota, paediatric, peanut allergy, pediatric, tree nut allergy",Experiment 4,"Germany,Switzerland",Homo sapiens,Skin of forearm,UBERON:0003403,Food allergy,EFO:1001890,Control Group,Patients at follow-up (t1),Children with Immunoglobulin-E (IgE)-mediated food allergy (FA) at follow-up (denoted by t1).,8,21,NA,16S,12,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 1D and Figure S5,24 November 2024,Aleru Divine,Aleru Divine,"Violin plot showing differences in genus and species abundances in forearm samples among controls, patients at enrollment (t0), and patients at follow-up (t1).",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus auricularis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus equorum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus lugdunensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus pasteuri,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus pettenkoferi,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus pragensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus pseudolugdunensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus simulans,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus warneri",1783272|1239|91061|1385|539738|1378;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|1385|90964|1279|29379;1783272|1239|91061|1385|90964|1279|1282;1783272|1239|91061|1385|90964|1279|246432;1783272|1239|91061|1385|90964|1279|28035;1783272|1239|91061|1385|90964|1279|45972;1783272|1239|91061|1385|90964|1279|170573;1783272|1239|91061|1385|90964|1279|1611836;1783272|1239|91061|1385|90964|1279|425474;1783272|1239|91061|1385|90964|1279|1286;1783272|1239|91061|1385|90964|1279|1292,Complete,Svetlana up
bsdb:1238/5/1,Study 1238,prospective cohort,NA,https://doi.org/10.3390/nu16223942,NA,"Axel Künstner, Caroline Roduit, Felicitas Bellutti Enders, Hauke Busch, Karin Hartmann, Michael Olbrich, Michèle S. Roth, Misa Hirose, Muriel d’Aujourd’hui, Saleh Ibrahim",Characterization of the Gut and Skin Microbiome over Time in Young Children with IgE-Mediated Food Allergy,Nutrients,2024,"atopic dermatitis, fecal microbiome, immediate hypersensitivity, infant, longitudinal, microbiota, paediatric, peanut allergy, pediatric, tree nut allergy",Experiment 5,Switzerland,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,Patients at enrollment (t0),Patients at follow-up (t1),Children with Immunoglobulin-E (IgE)-mediated food allergy (FA) at follow-up (denoted by t1).,22,20,NA,16S,12,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 2C,24 November 2024,Aleru Divine,Aleru Divine,"Violin plot showing differences in genus abundances in fecal samples at different sampling time points (at enrollment (t0), and follow-up (t1)).",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas",1783272|1239|91061|1385|186817|1386;1783272|1239|186801|186802|216572|216851;3379134|1224|1236|72274|135621|286;1783272|1239|186801|3085636|186803|1769710,Complete,Svetlana up
bsdb:1238/5/2,Study 1238,prospective cohort,NA,https://doi.org/10.3390/nu16223942,NA,"Axel Künstner, Caroline Roduit, Felicitas Bellutti Enders, Hauke Busch, Karin Hartmann, Michael Olbrich, Michèle S. Roth, Misa Hirose, Muriel d’Aujourd’hui, Saleh Ibrahim",Characterization of the Gut and Skin Microbiome over Time in Young Children with IgE-Mediated Food Allergy,Nutrients,2024,"atopic dermatitis, fecal microbiome, immediate hypersensitivity, infant, longitudinal, microbiota, paediatric, peanut allergy, pediatric, tree nut allergy",Experiment 5,Switzerland,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,Patients at enrollment (t0),Patients at follow-up (t1),Children with Immunoglobulin-E (IgE)-mediated food allergy (FA) at follow-up (denoted by t1).,22,20,NA,16S,12,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 2C,24 November 2024,Aleru Divine,Aleru Divine,"Violin plot showing differences in genus abundances in fecal samples at different sampling time points (at enrollment (t0), and follow-up (t1)).",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Pseudoclavibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|85006|85023|255204;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:1238/6/1,Study 1238,prospective cohort,NA,https://doi.org/10.3390/nu16223942,NA,"Axel Künstner, Caroline Roduit, Felicitas Bellutti Enders, Hauke Busch, Karin Hartmann, Michael Olbrich, Michèle S. Roth, Misa Hirose, Muriel d’Aujourd’hui, Saleh Ibrahim",Characterization of the Gut and Skin Microbiome over Time in Young Children with IgE-Mediated Food Allergy,Nutrients,2024,"atopic dermatitis, fecal microbiome, immediate hypersensitivity, infant, longitudinal, microbiota, paediatric, peanut allergy, pediatric, tree nut allergy",Experiment 6,Switzerland,Homo sapiens,Skin of forearm,UBERON:0003403,Food allergy,EFO:1001890,Patients at enrollment (t0),Patients at follow-up (t1),Children with Immunoglobulin-E (IgE)-mediated food allergy (FA) at follow-up (denoted by t1).,23,21,NA,16S,12,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 2D,24 November 2024,Aleru Divine,Aleru Divine,"Violin plot showing differences in genus abundances in forearm samples at different sampling time points (at enrollment (t0), and follow-up (t1)).",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Knoellia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",1783272|1239|91061|186826|186827|46123;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85009|31957|2801844;3379134|1224|28216|206351|481|32257;1783272|201174|1760|85006|85021|136099;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|206351|481|482,Complete,Svetlana up
bsdb:1238/6/2,Study 1238,prospective cohort,NA,https://doi.org/10.3390/nu16223942,NA,"Axel Künstner, Caroline Roduit, Felicitas Bellutti Enders, Hauke Busch, Karin Hartmann, Michael Olbrich, Michèle S. Roth, Misa Hirose, Muriel d’Aujourd’hui, Saleh Ibrahim",Characterization of the Gut and Skin Microbiome over Time in Young Children with IgE-Mediated Food Allergy,Nutrients,2024,"atopic dermatitis, fecal microbiome, immediate hypersensitivity, infant, longitudinal, microbiota, paediatric, peanut allergy, pediatric, tree nut allergy",Experiment 6,Switzerland,Homo sapiens,Skin of forearm,UBERON:0003403,Food allergy,EFO:1001890,Patients at enrollment (t0),Patients at follow-up (t1),Children with Immunoglobulin-E (IgE)-mediated food allergy (FA) at follow-up (denoted by t1).,23,21,NA,16S,12,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 2D,24 November 2024,Aleru Divine,Aleru Divine,"Violin plot showing differences in genus abundances in forearm samples at different sampling time points (at enrollment (t0), and follow-up (t1)).",decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Pseudoxanthomonas,3379134|1224|1236|135614|32033|83618,Complete,Svetlana up
bsdb:1238/7/1,Study 1238,prospective cohort,NA,https://doi.org/10.3390/nu16223942,NA,"Axel Künstner, Caroline Roduit, Felicitas Bellutti Enders, Hauke Busch, Karin Hartmann, Michael Olbrich, Michèle S. Roth, Misa Hirose, Muriel d’Aujourd’hui, Saleh Ibrahim",Characterization of the Gut and Skin Microbiome over Time in Young Children with IgE-Mediated Food Allergy,Nutrients,2024,"atopic dermatitis, fecal microbiome, immediate hypersensitivity, infant, longitudinal, microbiota, paediatric, peanut allergy, pediatric, tree nut allergy",Experiment 7,Switzerland,Homo sapiens,Skin of elbow,UBERON:0001517,Food allergy,EFO:1001890,Patients at enrollment (t0),Patients at follow-up (t1),Children with Immunoglobulin-E (IgE)-mediated food allergy (FA) at follow-up (denoted by t1).,23,21,NA,16S,12,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 2E,24 November 2024,Aleru Divine,Aleru Divine,"Violin plot showing differences in genus abundances in elbow samples at different sampling time points (at enrollment (t0), and follow-up (t1)).",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus",1783272|1239|91061|186826|186827|46123;1783272|1239|91061|186826|1300|1357,Complete,Svetlana up
bsdb:1238/8/1,Study 1238,prospective cohort,NA,https://doi.org/10.3390/nu16223942,NA,"Axel Künstner, Caroline Roduit, Felicitas Bellutti Enders, Hauke Busch, Karin Hartmann, Michael Olbrich, Michèle S. Roth, Misa Hirose, Muriel d’Aujourd’hui, Saleh Ibrahim",Characterization of the Gut and Skin Microbiome over Time in Young Children with IgE-Mediated Food Allergy,Nutrients,2024,"atopic dermatitis, fecal microbiome, immediate hypersensitivity, infant, longitudinal, microbiota, paediatric, peanut allergy, pediatric, tree nut allergy",Experiment 8,Switzerland,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,No nut group,Nut group,Patients with Immunoglobulin-E (IgE)-mediated tree nut and/or peanut allergy at enrollment.,8,15,NA,16S,12,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3C,24 November 2024,Aleru Divine,Aleru Divine,"Violin plot showing differences in genus abundances in fecal samples at enrollment (t0), between patients with an IgE-mediated FA other than tree nut and/or peanut, (no nut) and patients with a tree nut and/or peanut allergy (nut).",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|2719313;1783272|201174|1760|85007|2805586|1847725;3379134|976|200643|171549|815|909656,Complete,Svetlana up
bsdb:1238/8/2,Study 1238,prospective cohort,NA,https://doi.org/10.3390/nu16223942,NA,"Axel Künstner, Caroline Roduit, Felicitas Bellutti Enders, Hauke Busch, Karin Hartmann, Michael Olbrich, Michèle S. Roth, Misa Hirose, Muriel d’Aujourd’hui, Saleh Ibrahim",Characterization of the Gut and Skin Microbiome over Time in Young Children with IgE-Mediated Food Allergy,Nutrients,2024,"atopic dermatitis, fecal microbiome, immediate hypersensitivity, infant, longitudinal, microbiota, paediatric, peanut allergy, pediatric, tree nut allergy",Experiment 8,Switzerland,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,No nut group,Nut group,Patients with Immunoglobulin-E (IgE)-mediated tree nut and/or peanut allergy at enrollment.,8,15,NA,16S,12,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3C,24 November 2024,Aleru Divine,Aleru Divine,"Violin plot showing differences in genus abundances in fecal samples at enrollment (t0), between patients with an IgE-mediated FA other than tree nut and/or peanut, (no nut) and patients with a tree nut and/or peanut allergy (nut).",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|91061|186826|81852|1350;3379134|1224|28216|206351|481|482;3379134|1224|1236|72274|135621|286;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:1238/9/1,Study 1238,prospective cohort,NA,https://doi.org/10.3390/nu16223942,NA,"Axel Künstner, Caroline Roduit, Felicitas Bellutti Enders, Hauke Busch, Karin Hartmann, Michael Olbrich, Michèle S. Roth, Misa Hirose, Muriel d’Aujourd’hui, Saleh Ibrahim",Characterization of the Gut and Skin Microbiome over Time in Young Children with IgE-Mediated Food Allergy,Nutrients,2024,"atopic dermatitis, fecal microbiome, immediate hypersensitivity, infant, longitudinal, microbiota, paediatric, peanut allergy, pediatric, tree nut allergy",Experiment 9,Switzerland,Homo sapiens,Skin of forearm,UBERON:0003403,Food allergy,EFO:1001890,No nut group,Nut group,Patients with Immunoglobulin-E (IgE)-mediated tree nut and/or peanut allergy at enrollment.,8,15,NA,16S,12,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3D,24 November 2024,Aleru Divine,Aleru Divine,"Violin plot showing differences in genus abundances in forearm samples at enrollment (t0), between patients with an IgE-mediated FA other than tree nut and/or peanut, (no nut) and patients with a tree nut and/or peanut allergy (nut).",increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,1783272|201174|1760|85009|31957|1912216,Complete,Svetlana up
bsdb:1238/9/2,Study 1238,prospective cohort,NA,https://doi.org/10.3390/nu16223942,NA,"Axel Künstner, Caroline Roduit, Felicitas Bellutti Enders, Hauke Busch, Karin Hartmann, Michael Olbrich, Michèle S. Roth, Misa Hirose, Muriel d’Aujourd’hui, Saleh Ibrahim",Characterization of the Gut and Skin Microbiome over Time in Young Children with IgE-Mediated Food Allergy,Nutrients,2024,"atopic dermatitis, fecal microbiome, immediate hypersensitivity, infant, longitudinal, microbiota, paediatric, peanut allergy, pediatric, tree nut allergy",Experiment 9,Switzerland,Homo sapiens,Skin of forearm,UBERON:0003403,Food allergy,EFO:1001890,No nut group,Nut group,Patients with Immunoglobulin-E (IgE)-mediated tree nut and/or peanut allergy at enrollment.,8,15,NA,16S,12,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3D,24 November 2024,Aleru Divine,Aleru Divine,"Violin plot showing differences in genus abundances in forearm samples at enrollment (t0), between patients with an IgE-mediated FA other than tree nut and/or peanut, (no nut) and patients with a tree nut and/or peanut allergy (nut).",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella,p__Candidatus Saccharimonadota|c__Candidatus Nanosyncoccalia|o__Candidatus Nanogingivales|f__Candidatus Nanogingivalaceae|g__Candidatus Nanogingivalis,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Nanosynbacterales|f__Candidatus Nanosynbacteraceae|g__Candidatus Nanosynbacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Pauljensenia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;1783272|201174|84998|84999|1643824|2767353;95818|2171982|2171984|2171990|2171991;95818|2093818|2093819|2093822|2093823;1783272|201174|1760|2037|2049|2740557;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:1238/10/1,Study 1238,prospective cohort,NA,https://doi.org/10.3390/nu16223942,NA,"Axel Künstner, Caroline Roduit, Felicitas Bellutti Enders, Hauke Busch, Karin Hartmann, Michael Olbrich, Michèle S. Roth, Misa Hirose, Muriel d’Aujourd’hui, Saleh Ibrahim",Characterization of the Gut and Skin Microbiome over Time in Young Children with IgE-Mediated Food Allergy,Nutrients,2024,"atopic dermatitis, fecal microbiome, immediate hypersensitivity, infant, longitudinal, microbiota, paediatric, peanut allergy, pediatric, tree nut allergy",Experiment 10,Switzerland,Homo sapiens,Skin of elbow,UBERON:0001517,Food allergy,EFO:1001890,No nut group,Nut group,Patients with Immunoglobulin-E (IgE)-mediated tree nut and/or peanut allergy at enrollment.,8,15,NA,16S,12,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3E,24 November 2024,Aleru Divine,Aleru Divine,"Violin plot showing differences in genus abundances in elbow samples at enrollment (t0), between patients with an IgE-mediated FA other than tree nut and/or peanut, (no nut) and patients with a tree nut and/or peanut allergy (nut).",increased,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,3379134|1224|28211|204457|41297|13687,Complete,Svetlana up
bsdb:1238/11/1,Study 1238,prospective cohort,NA,https://doi.org/10.3390/nu16223942,NA,"Axel Künstner, Caroline Roduit, Felicitas Bellutti Enders, Hauke Busch, Karin Hartmann, Michael Olbrich, Michèle S. Roth, Misa Hirose, Muriel d’Aujourd’hui, Saleh Ibrahim",Characterization of the Gut and Skin Microbiome over Time in Young Children with IgE-Mediated Food Allergy,Nutrients,2024,"atopic dermatitis, fecal microbiome, immediate hypersensitivity, infant, longitudinal, microbiota, paediatric, peanut allergy, pediatric, tree nut allergy",Experiment 11,Switzerland,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,No nut group,Nut group,Patients with Immunoglobulin-E (IgE)-mediated tree nut and/or peanut allergy.,8,15,NA,16S,12,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Figure S6,27 December 2024,Aleru Divine,Aleru Divine,Correlation of gut and skin microbiome of patients with tree nut and/or peanut allergy and total IgE.,increased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,1783272|201174|84998|84999|84107|102106,Complete,Svetlana up
bsdb:1238/12/1,Study 1238,prospective cohort,NA,https://doi.org/10.3390/nu16223942,NA,"Axel Künstner, Caroline Roduit, Felicitas Bellutti Enders, Hauke Busch, Karin Hartmann, Michael Olbrich, Michèle S. Roth, Misa Hirose, Muriel d’Aujourd’hui, Saleh Ibrahim",Characterization of the Gut and Skin Microbiome over Time in Young Children with IgE-Mediated Food Allergy,Nutrients,2024,"atopic dermatitis, fecal microbiome, immediate hypersensitivity, infant, longitudinal, microbiota, paediatric, peanut allergy, pediatric, tree nut allergy",Experiment 12,Switzerland,Homo sapiens,Skin of elbow,UBERON:0001517,Food allergy,EFO:1001890,No nut group,Nut group,Patients with Immunoglobulin-E (IgE)-mediated tree nut and/or peanut allergy.,8,15,NA,16S,12,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Figure S6,27 December 2024,Aleru Divine,Aleru Divine,Correlation of gut and skin microbiome of patients with tree nut and/or peanut allergy and total IgE.,increased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,1783272|201174|84998|84999|84107|102106,Complete,Svetlana up
bsdb:1238/13/1,Study 1238,prospective cohort,NA,https://doi.org/10.3390/nu16223942,NA,"Axel Künstner, Caroline Roduit, Felicitas Bellutti Enders, Hauke Busch, Karin Hartmann, Michael Olbrich, Michèle S. Roth, Misa Hirose, Muriel d’Aujourd’hui, Saleh Ibrahim",Characterization of the Gut and Skin Microbiome over Time in Young Children with IgE-Mediated Food Allergy,Nutrients,2024,"atopic dermatitis, fecal microbiome, immediate hypersensitivity, infant, longitudinal, microbiota, paediatric, peanut allergy, pediatric, tree nut allergy",Experiment 13,Switzerland,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,Low group,High group,Patients with allergies/sensitization greater than or equal to 3.,12,11,NA,16S,12,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,27 December 2024,Aleru Divine,Aleru Divine,Correlation of gut and skin microbiome of patients with number of allergies/sensitizations.,increased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,1783272|201174|84998|84999|84107|102106,Complete,Svetlana up
bsdb:1238/14/1,Study 1238,prospective cohort,NA,https://doi.org/10.3390/nu16223942,NA,"Axel Künstner, Caroline Roduit, Felicitas Bellutti Enders, Hauke Busch, Karin Hartmann, Michael Olbrich, Michèle S. Roth, Misa Hirose, Muriel d’Aujourd’hui, Saleh Ibrahim",Characterization of the Gut and Skin Microbiome over Time in Young Children with IgE-Mediated Food Allergy,Nutrients,2024,"atopic dermatitis, fecal microbiome, immediate hypersensitivity, infant, longitudinal, microbiota, paediatric, peanut allergy, pediatric, tree nut allergy",Experiment 14,Switzerland,Homo sapiens,Skin of forearm,UBERON:0003403,Food allergy,EFO:1001890,Low group,High group,Patients with allergies/sensitization greater than or equal to 3.,12,11,NA,16S,12,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,27 December 2024,Aleru Divine,Aleru Divine,Correlation of gut and skin microbiome of patients with number of allergies/sensitizations.,increased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,1783272|201174|84998|84999|84107|102106,Complete,Svetlana up
bsdb:1272/1/1,Study 1272,case-control,NA,https://doi.org/10.1186/s41983-021-00407-z,NA,"Ahmed Alaa, Anwar M. Ali, Ayman Gamea, Eman M. Khedr, Enas Deaf, Hebatallah M. Hassan",Gut microbiota in Parkinson’s disease patients: hospital-based study,The Egyptian Journal of Neurology,2021,"GIT domain non-motor symptoms, gut microbiota, parkinson's disease",Experiment 1,Egypt,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy relatives,Parkinson's disease patients,patients with parkinson's disease,31,46,3 months,16S,NA,NA,NA,Kruskall-Wallis,0.05,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,22 February 2025,Karima,Karima,Increased copy number of gut microbiota among Total Parkinson’s disease patients and control group,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",3379134|74201|203494|48461|1647988|239934;1783272|201174|1760|85004|31953|1678,Complete,Svetlana up
bsdb:1272/1/2,Study 1272,case-control,NA,https://doi.org/10.1186/s41983-021-00407-z,NA,"Ahmed Alaa, Anwar M. Ali, Ayman Gamea, Eman M. Khedr, Enas Deaf, Hebatallah M. Hassan",Gut microbiota in Parkinson’s disease patients: hospital-based study,The Egyptian Journal of Neurology,2021,"GIT domain non-motor symptoms, gut microbiota, parkinson's disease",Experiment 1,Egypt,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy relatives,Parkinson's disease patients,patients with parkinson's disease,31,46,3 months,16S,NA,NA,NA,Kruskall-Wallis,0.05,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,22 February 2025,Karima,Karima,Decreased copy number of gut microbiota among Total Parkinson’s disease patients and control group,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Svetlana up
bsdb:1272/2/1,Study 1272,case-control,NA,https://doi.org/10.1186/s41983-021-00407-z,NA,"Ahmed Alaa, Anwar M. Ali, Ayman Gamea, Eman M. Khedr, Enas Deaf, Hebatallah M. Hassan",Gut microbiota in Parkinson’s disease patients: hospital-based study,The Egyptian Journal of Neurology,2021,"GIT domain non-motor symptoms, gut microbiota, parkinson's disease",Experiment 2,Egypt,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy relatives,Treated PD patients,patients with parkinson's disease under treatments,31,39,3 months,16S,NA,NA,NA,Kruskall-Wallis,0.05,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,22 February 2025,Karima,Karima,Increased copy number of gut microbiota among treated PD patients versus control,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",3379134|74201|203494|48461|1647988|239934;1783272|201174|1760|85004|31953|1678,Complete,Svetlana up
bsdb:1272/2/2,Study 1272,case-control,NA,https://doi.org/10.1186/s41983-021-00407-z,NA,"Ahmed Alaa, Anwar M. Ali, Ayman Gamea, Eman M. Khedr, Enas Deaf, Hebatallah M. Hassan",Gut microbiota in Parkinson’s disease patients: hospital-based study,The Egyptian Journal of Neurology,2021,"GIT domain non-motor symptoms, gut microbiota, parkinson's disease",Experiment 2,Egypt,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy relatives,Treated PD patients,patients with parkinson's disease under treatments,31,39,3 months,16S,NA,NA,NA,Kruskall-Wallis,0.05,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,22 February 2025,Karima,Karima,Decreased copy number of gut microbiota among treated PD patients versus control,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Svetlana up
bsdb:1272/3/1,Study 1272,case-control,NA,https://doi.org/10.1186/s41983-021-00407-z,NA,"Ahmed Alaa, Anwar M. Ali, Ayman Gamea, Eman M. Khedr, Enas Deaf, Hebatallah M. Hassan",Gut microbiota in Parkinson’s disease patients: hospital-based study,The Egyptian Journal of Neurology,2021,"GIT domain non-motor symptoms, gut microbiota, parkinson's disease",Experiment 3,Egypt,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy relatives,Newly PD patients,Newly diagnosed patients with parkinson's disease ( non-treated patients),31,7,3 months,16S,NA,NA,NA,Kruskall-Wallis,0.05,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,22 February 2025,Karima,Karima,Increased copy number of gut microbiota among Newly diagnosed PD patients and control group,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Svetlana up
bsdb:1272/4/1,Study 1272,case-control,NA,https://doi.org/10.1186/s41983-021-00407-z,NA,"Ahmed Alaa, Anwar M. Ali, Ayman Gamea, Eman M. Khedr, Enas Deaf, Hebatallah M. Hassan",Gut microbiota in Parkinson’s disease patients: hospital-based study,The Egyptian Journal of Neurology,2021,"GIT domain non-motor symptoms, gut microbiota, parkinson's disease",Experiment 4,Egypt,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Newly PD patients,Treated PD patients,Parkinson's disease patients under treatments,7,39,3 months,16S,NA,NA,NA,Kruskall-Wallis,0.05,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,22 February 2025,Karima,Karima,Increased copy number of gut microbiota among treated PD patients and non-treated patients,increased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,3379134|74201|203494|48461|1647988|239934,Complete,Svetlana up
bsdb:1272/6/1,Study 1272,case-control,NA,https://doi.org/10.1186/s41983-021-00407-z,NA,"Ahmed Alaa, Anwar M. Ali, Ayman Gamea, Eman M. Khedr, Enas Deaf, Hebatallah M. Hassan",Gut microbiota in Parkinson’s disease patients: hospital-based study,The Egyptian Journal of Neurology,2021,"GIT domain non-motor symptoms, gut microbiota, parkinson's disease",Experiment 6,Egypt,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,PD patients non exposed to pesticide,PD patients exposed to pesticide,Parkinson's disease patients exposed to pesticide,35,11,3 months,16S,NA,NA,NA,"Mann-Whitney (Wilcoxon),Spearman Correlation",0.05,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,22 February 2025,Karima,Karima,Correlation between gut microbiota and pesticide exposure in PD,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Svetlana up
bsdb:1272/7/1,Study 1272,case-control,NA,https://doi.org/10.1186/s41983-021-00407-z,NA,"Ahmed Alaa, Anwar M. Ali, Ayman Gamea, Eman M. Khedr, Enas Deaf, Hebatallah M. Hassan",Gut microbiota in Parkinson’s disease patients: hospital-based study,The Egyptian Journal of Neurology,2021,"GIT domain non-motor symptoms, gut microbiota, parkinson's disease",Experiment 7,Egypt,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,PD patients without constipation,PD patients with constipation,Parkinson's disease Patients with constipation,24,22,3 months,16S,NA,NA,NA,"Mann-Whitney (Wilcoxon),Spearman Correlation",0.05,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,22 February 2025,Karima,Karima,Correlation between gut microbiota and constipation in Parkinson’s disease,increased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,3379134|74201|203494|48461|1647988|239934,Complete,Svetlana up
bsdb:1284/1/1,Study 1284,"cross-sectional observational, not case-control",NA,https://doi.org/10.1038/s41598-023-37720-x,NA,"Aarti Darra, Anish Bhattacharya, Anupam Kumar Singh, Anuraag Jena, Anurag Agrawal, Pankaj Gupta, Priyanka Popli, Ritambhra Nada, Sanjay Kumar Bhadada, Usha Dutta, Vandana Singh, Vishal Sharma",Hyperglycemia is associated with duodenal dysbiosis and altered duodenal microenvironment,Scientific reports,2023,NA,Experiment 1,India,Homo sapiens,Duodenum,UBERON:0002114,Hyperglycemia,HP:0003074,Normoglycemic group,Hyperglycemic group,The hyperglycemic group consists of subjects with fasting plasma glucose(FPG) > 100 mg/dl and hemoglobin A1C (HbA1c) ≥ 5.7%.,21,33,2 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,age,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3C,6 February 2025,Aleru Divine,Aleru Divine,"Histograms showing the differential abundant features in duodenal microbiota obtained using DESeq2 in hyperglycemic and normoglycemic subjects at order, family, and genus-species level.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter haemolyticus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum pigrum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella tobetsuensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus",3379134|1224|1236|91347|543|1940338;3379134|1224|1236|2887326|468|469|29430;1783272|1239|526524|526525|2810281|191303|154288;1783272|1239|91061|186826|186828|29393|29394;3379134|1224|28216|206351|481|482|28449;1783272|1239|909932|1843489|31977|29465|1110546;1783272|1239|91061|186826|1300|1301|45634,Complete,Svetlana up
bsdb:1284/1/2,Study 1284,"cross-sectional observational, not case-control",NA,https://doi.org/10.1038/s41598-023-37720-x,NA,"Aarti Darra, Anish Bhattacharya, Anupam Kumar Singh, Anuraag Jena, Anurag Agrawal, Pankaj Gupta, Priyanka Popli, Ritambhra Nada, Sanjay Kumar Bhadada, Usha Dutta, Vandana Singh, Vishal Sharma",Hyperglycemia is associated with duodenal dysbiosis and altered duodenal microenvironment,Scientific reports,2023,NA,Experiment 1,India,Homo sapiens,Duodenum,UBERON:0002114,Hyperglycemia,HP:0003074,Normoglycemic group,Hyperglycemic group,The hyperglycemic group consists of subjects with fasting plasma glucose(FPG) > 100 mg/dl and hemoglobin A1C (HbA1c) ≥ 5.7%.,21,33,2 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,age,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3C,6 February 2025,Aleru Divine,Aleru Divine,"Histograms showing the differential abundant features in duodenal microbiota obtained using DESeq2 in hyperglycemic and normoglycemic subjects at order, family, and genus-species level.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter junii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium|s__Brachybacterium muris,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Epilithonimonas|s__Epilithonimonas hominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parafannyhessea|s__Parafannyhessea umbonata,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",1783272|1239|91061|186826|1300|1357;3379134|1224|1236|2887326|468|469|40215;1783272|1239|186801|3085636|186803|1164882;3379134|29547|3031852|213849|72294|194|199;1783272|201174|1760|85006|85020|43668|219301;3379134|976|117743|200644|2762318|2782229|420404;3379134|976|200643|171549|171552|838|470565;1783272|201174|1760|85007|85026|2053;3379134|74201|203494|48461|1647988|239934|239935;1783272|201174|84998|84999|1643824|2847312|604330;1783272|201174|84998|84999|84107|102106|74426;3379134|976|200643|171549|815|816;1783272|201174|84998|84999|1643824|2767353|1382;3379134|1224|1236|72274;1783272|201174|1760|85010;3379134|1224|28211|204458;1783272|201174|1760|85010|2070;3379134|976|200643|171549|2005525;3379134|1224|28211|204458|76892;1783272|201174|1760|85007|85025;3379134|74201|203494|48461|1647988;1783272|201174|84998|84999|84107,Complete,Svetlana up
bsdb:1284/2/1,Study 1284,"cross-sectional observational, not case-control",NA,https://doi.org/10.1038/s41598-023-37720-x,NA,"Aarti Darra, Anish Bhattacharya, Anupam Kumar Singh, Anuraag Jena, Anurag Agrawal, Pankaj Gupta, Priyanka Popli, Ritambhra Nada, Sanjay Kumar Bhadada, Usha Dutta, Vandana Singh, Vishal Sharma",Hyperglycemia is associated with duodenal dysbiosis and altered duodenal microenvironment,Scientific reports,2023,NA,Experiment 2,India,Homo sapiens,"Feces,Duodenum","UBERON:0001988,UBERON:0002114",Sampling site,EFO:0000688,Stool samples,Biopsy samples,Duodenal biopsy samples from 54 participants.,54,54,2 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 1,6 February 2025,Aleru Divine,Aleru Divine,"Table depicting differentially abundant species in biopsy compared to stool, analyzed using DESeq2 package.",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium|s__Carnobacterium maltaromaticum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter johnsonii,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes|s__Alcaligenes faecalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Epilithonimonas|s__Epilithonimonas hominis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter bouvetii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Pseudonocardia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|g__Exiguobacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Pseudonocardia|s__Pseudonocardia alni|s__Pseudonocardia alni subsp. carboxydivorans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Flectobacillaceae|g__Flectobacillus|s__Flectobacillus roseus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Nesterenkonia|s__Nesterenkonia xinjiangensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum pigrum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus|s__Paracoccus sphaerophysae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter haemolyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum longum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia wadei,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter pylori,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Curtobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella shahii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter junii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella tobetsuensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria mucosa,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sputorum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] brachy,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] sulci,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus lylae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium mucifaciens,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella parahaemolysans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium|s__Sphingobacterium alimentarium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Solilutibacter|s__Solilutibacter tolerans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium|s__Methylobacterium jeotgali,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium|s__Brachybacterium muris,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica",1783272|1239|91061|186826|186828|2747|2751;3379134|1224|1236|91347|1903411|613;1783272|1239|91061|186826|186828|117563|137732;3379134|1224|1236|135614|32033|40323;3379134|1224|1236|2887326|468|469;3379134|976|200643|171549|171552|2974257|425941;3379134|1224|28211|204457|41297|13687;3379134|1224|1236|2887326|468|469|40214;1783272|1239|186801|3082720|186804|1257|341694;3379134|976|200643|171549|171551|836|1583331;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|1385|186817|1386;3379134|976|200643|171549|171552|2974251|228604;3379134|976|200643|171549|171552|838|28132;1783272|1239|91061|186826|33958|1578|147802;3379134|1224|28216|80840|506|507|511;1783272|201174|1760|85007|1653|1716;3379134|976|200643|171549|171552|838|470565;3379134|976|117743|200644|2762318|2782229|420404;1783272|1239|909932|1843488|909930|33024|33025;3379134|1224|28216|80840|119060|32008;3379134|1224|1236|2887326|468|469|202951;3379134|976|200643|171549|171552|838|28133;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|838;1783272|1239|91061|1385|539738|1378|29391;1783272|201174|1760|85010|2070|1847;1783272|1239|186801|3085636|186803|1164882;3379134|976|200643|171549|171552|838|60133;1783272|1239|91061|186826|1300|1301;3384189|32066|203490|203491|203492|848|860;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|33986;3379134|976|117743|200644|49546|1016|327575;3379134|1224|28211|356|118882|528;3379134|1224|1236|91347|1903414|583;3384189|32066|203490|203491|203492|848|851;1783272|201174|1760|85010|2070|1847|33907|415010;3379134|1224|1236|91347|1903414|586;3379134|976|768503|768507|3141701|101|502259;3379134|1224|28216|80840|2975441|93681;1783272|201174|1760|85006|1268|57494|225327;1783272|1239|909932|1843489|31977|39948|39950;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|1239|91061|186826|186828|29393|29394;3379134|1224|28211|204455|31989|265|690417;1783272|1239|91061|186826|1300|1301|45634;1783272|1239|186801|3085636|186803|265975|1501329;3379134|1224|1236|2887326|468|469|29430;1783272|1239|186801|3085636|186803|1213720|796942;3384189|32066|203490|203491|1129771|32067|157687;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|43675;3379134|29547|3031852|213849|72293|209|210;1783272|201174|1760|85006|85023|2034;1783272|1239|186801|3085636|186803|265975|237576;3379134|976|200643|171549|171552|2974257|228603;3379134|1224|1236|2887326|468|469|40215;3379134|976|200643|171549|171551|836|28124;1783272|201174|1760|85006|1268|32207|2047;1783272|1239|91061|1385|539738|1378|84135;3379134|1224|1236|135625|712|416916|739;3379134|1224|1236|135625|712|724;3379134|29547|3031852|213849|72294|194;1783272|1239|91061|186826|1300|1357;3379134|29547|3031852|213849|72294|194|199;3379134|1224|28216|206351|481|482|28449;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|909932|1843489|31977|29465|423477;1783272|1239|909932|1843489|31977|906|187326;1783272|1239|909932|1843489|31977|29465|1110546;3379134|1224|28216|206351|481|482|488;3379134|1224|1236|135624|84642|642;3379134|1224|1236|135625|712|724|729;3379134|1224|1236|135625|712|724|1078480;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|186801|3082720|543314|35517;1783272|1239|186801|3082720|543314|143393;1783272|1239|186801|3082720|3118655|44259|143361;1783272|1239|909932|1843489|31977|29465|29466;1783272|201174|1760|85006|1268|1269|1273;1783272|201174|1760|85007|1653|1716|57171;1783272|1239|91061|1385|539738|1378|1179782;3379134|1224|28216|80840|119060|47670|47671;3379134|1224|1236|91347|543|570|573;3379134|976|117747|200666|84566|28453|797292;3379134|1224|1236|135614|32033|3382695|1604334;1783272|201174|1760|85007|85026|2053;3379134|1224|28211|356|119045|407|381630;1783272|201174|1760|85006|85023|33882;1783272|201174|1760|85006|85020|43668|219301;1783272|201174|1760|2037|2049|2529408|1660,Complete,Svetlana up
bsdb:1284/2/2,Study 1284,"cross-sectional observational, not case-control",NA,https://doi.org/10.1038/s41598-023-37720-x,NA,"Aarti Darra, Anish Bhattacharya, Anupam Kumar Singh, Anuraag Jena, Anurag Agrawal, Pankaj Gupta, Priyanka Popli, Ritambhra Nada, Sanjay Kumar Bhadada, Usha Dutta, Vandana Singh, Vishal Sharma",Hyperglycemia is associated with duodenal dysbiosis and altered duodenal microenvironment,Scientific reports,2023,NA,Experiment 2,India,Homo sapiens,"Feces,Duodenum","UBERON:0001988,UBERON:0002114",Sampling site,EFO:0000688,Stool samples,Biopsy samples,Duodenal biopsy samples from 54 participants.,54,54,2 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 2,6 February 2025,Aleru Divine,Aleru Divine,Table depicting differentially abundant species in stool compared to biopsy analysed using DESeq2 package.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus delbrueckii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia massiliensis (ex Liu et al. 2021),k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella jalaludinii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Liu et al. 2021),k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister histaminiformans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium angulatum",1783272|1239|909932|1843489|31977|906;3379134|976|200643|171549|815|816|820;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|1263|40518;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|3085636|186803|189330|88431;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|171550|239759|28117;1783272|1239|186801|186802|216572|216851;1783272|1239|91061|186826|33958|1578|1584;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|186801|3085636|186803|572511|3062492;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|3342669|45851;1783272|1239|186801|3085636|186803|3570277|116085;3379134|1224|28216|80840|995019|40544|40545;1783272|1239|186801|3085636|186803|2569097|39488;3379134|976|200643|171549|815|816;1783272|1239|909932|909929|1843491|52225|52226;1783272|1239|186801|3085636|186803|1407607|1150298;3379134|976|200643|171549|815|816|46506;1783272|1239|186801|3085636|186803|841|360807;3379134|976|200643|171549|1853231|283168|28118;1783272|1239|909932|909929|1843491|52225|187979;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|572511|871665;1783272|201174|84998|1643822|1643826|84108|572010;1783272|1239|186801|3085636|186803|33042|33043;1783272|1239|186801|3085636|186803|841|301301;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|3085636|186803|841|166486;3379134|976|200643|171549|171550|239759|1288121;3379134|976|200643|171549|171550|239759|2585118;1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|526524|526525|128827|1573535|1735;1783272|1239|91061|186826|33958|2767887|1623;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|216572|1263|3062497;1783272|1239|186801|3085636|186803|1898203;1783272|1239|909932|1843489|31977|39948|209880;3379134|1224|28216|80840|995019|577310|487175;1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549|2005525|375288|823;1783272|1239|186801|3082720|186804|1505657|261299;3379134|1224|1236|91347|543|1940338;3379134|976|200643|171549|171550|239759|328814;3379134|1224|1236|91347|543|570;1783272|201174|1760|85004|31953|1678|1683,Complete,Svetlana up
bsdb:1284/3/1,Study 1284,"cross-sectional observational, not case-control",NA,https://doi.org/10.1038/s41598-023-37720-x,NA,"Aarti Darra, Anish Bhattacharya, Anupam Kumar Singh, Anuraag Jena, Anurag Agrawal, Pankaj Gupta, Priyanka Popli, Ritambhra Nada, Sanjay Kumar Bhadada, Usha Dutta, Vandana Singh, Vishal Sharma",Hyperglycemia is associated with duodenal dysbiosis and altered duodenal microenvironment,Scientific reports,2023,NA,Experiment 3,India,Homo sapiens,"Feces,Duodenum","UBERON:0001988,UBERON:0002114",Sampling site,EFO:0000688,Stool samples,Biopsy samples,Duodenal biopsy samples from participants with hyperglycemia.,33,33,2 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 1,7 February 2025,Aleru Divine,Aleru Divine,"Boxplot showing the comparison of top taxa between hyperglycemic and normoglycemic groups in stool and duodenum samples at Phylum, Class, Order and Family levels.",increased,"k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Actinomycetota,k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae",3379134|1224;1783272|201174;3384189|32066;1783272|201174|84992;3379134|1224|28211;1783272|1239|91061;3379134|29547|3031852;3384189|32066|203490;3379134|1224|1236;1783272|1239|909932;3379134|1224|1236|135625;1783272|1239|909932|909929;3379134|1224|1236|72274;1783272|1239|91061|186826;3379134|1224|1236|91347;1783272|201174|1760|85006;3379134|1224|28216|80840|119060;3379134|1224|1236|135625|712;1783272|1239|909932|1843489|31977;3379134|1224|1236|72274|135621;1783272|1239|91061|186826|186828;3379134|1224|28216|206351|481,Complete,Svetlana up
bsdb:1284/3/2,Study 1284,"cross-sectional observational, not case-control",NA,https://doi.org/10.1038/s41598-023-37720-x,NA,"Aarti Darra, Anish Bhattacharya, Anupam Kumar Singh, Anuraag Jena, Anurag Agrawal, Pankaj Gupta, Priyanka Popli, Ritambhra Nada, Sanjay Kumar Bhadada, Usha Dutta, Vandana Singh, Vishal Sharma",Hyperglycemia is associated with duodenal dysbiosis and altered duodenal microenvironment,Scientific reports,2023,NA,Experiment 3,India,Homo sapiens,"Feces,Duodenum","UBERON:0001988,UBERON:0002114",Sampling site,EFO:0000688,Stool samples,Biopsy samples,Duodenal biopsy samples from participants with hyperglycemia.,33,33,2 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 1,7 February 2025,Aleru Divine,Aleru Divine,"Boxplot showing the comparison of top taxa between hyperglycemic and normoglycemic groups in stool and duodenum samples at Phylum, Class, Order and Family levels.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae",3379134|1224|1236|135624;1783272|1239;3379134|976|200643|171549;3379134|976|200643;3379134|976;1783272|1239|186801;1783272|1239|526524;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171552;3379134|1224|1236|135624|83763,Complete,Svetlana up
bsdb:1284/4/1,Study 1284,"cross-sectional observational, not case-control",NA,https://doi.org/10.1038/s41598-023-37720-x,NA,"Aarti Darra, Anish Bhattacharya, Anupam Kumar Singh, Anuraag Jena, Anurag Agrawal, Pankaj Gupta, Priyanka Popli, Ritambhra Nada, Sanjay Kumar Bhadada, Usha Dutta, Vandana Singh, Vishal Sharma",Hyperglycemia is associated with duodenal dysbiosis and altered duodenal microenvironment,Scientific reports,2023,NA,Experiment 4,India,Homo sapiens,"Feces,Duodenum","UBERON:0001988,UBERON:0002114",Sampling site,EFO:0000688,Stool samples,Biopsy samples,Duodenal biopsy samples from normoglycemic participants.,21,21,2 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 1,7 February 2025,Aleru Divine,Aleru Divine,"Boxplot showing the comparison of top taxa between hyperglycemic and normoglycemic groups in stool and duodenum samples at Phylum, Class, Order and Family levels.",increased,"k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Actinomycetota,k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae",3379134|1224;1783272|201174;3384189|32066;1783272|201174|84992;3379134|1224|28211;1783272|1239|91061;3379134|29547|3031852;3384189|32066|203490;3379134|1224|1236;1783272|1239|909932;3379134|1224|1236|135625;1783272|1239|909932|909929;3379134|1224|1236|72274;1783272|1239|91061|186826;3379134|1224|1236|91347;1783272|201174|1760|85006;3379134|1224|28216|80840|119060;3379134|1224|1236|135625|712;1783272|1239|909932|1843489|31977;3379134|1224|1236|72274|135621;1783272|1239|91061|186826|186828;3379134|1224|28216|206351|481,Complete,Svetlana up
bsdb:1284/4/2,Study 1284,"cross-sectional observational, not case-control",NA,https://doi.org/10.1038/s41598-023-37720-x,NA,"Aarti Darra, Anish Bhattacharya, Anupam Kumar Singh, Anuraag Jena, Anurag Agrawal, Pankaj Gupta, Priyanka Popli, Ritambhra Nada, Sanjay Kumar Bhadada, Usha Dutta, Vandana Singh, Vishal Sharma",Hyperglycemia is associated with duodenal dysbiosis and altered duodenal microenvironment,Scientific reports,2023,NA,Experiment 4,India,Homo sapiens,"Feces,Duodenum","UBERON:0001988,UBERON:0002114",Sampling site,EFO:0000688,Stool samples,Biopsy samples,Duodenal biopsy samples from normoglycemic participants.,21,21,2 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 1,7 February 2025,Aleru Divine,Aleru Divine,"Boxplot showing the comparison of top taxa between hyperglycemic and normoglycemic groups in stool and duodenum samples at Phylum, Class, Order and Family levels.",decreased,"k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|976;1783272|1239;3379134|976|200643;1783272|1239|186801;1783272|1239|526524;3379134|976|200643|171549;3379134|1224|1236|135624;1783272|1239|186801|186802;3379134|976|200643|171549|171552;3379134|1224|1236|135624|83763;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:10202341/1/1,10202341,prospective cohort,10202341,10.1046/j.1365-2222.1999.00560.x,NA,"Björkstén B., Naaber P., Sepp E. , Mikelsaar M.",The intestinal microflora in allergic Estonian and Swedish 2-year-old children,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,1999,NA,Experiment 1,"Estonia,Sweden",Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,Nonallergic  Estonian children.,Allergic Estonian children.,2-year-old children with confirmed diagnosis of allergy,16,13,NA,NA,NA,NA,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 1,10 January 2021,Lucy Mellor,"WikiWorks,Peace Sandy","Intestinal microflora of 13 allergic (grey) and 16 nonallergic
(white) Estonian children. The results are presented as colonization
rate (%, columns) and counts (log CFU/g, range and median, lines
and filled symbols).",increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,1783272|1239|91061|1385|90964|1279|1280,Complete,Peace Sandy
bsdb:10202341/1/2,10202341,prospective cohort,10202341,10.1046/j.1365-2222.1999.00560.x,NA,"Björkstén B., Naaber P., Sepp E. , Mikelsaar M.",The intestinal microflora in allergic Estonian and Swedish 2-year-old children,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,1999,NA,Experiment 1,"Estonia,Sweden",Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,Nonallergic  Estonian children.,Allergic Estonian children.,2-year-old children with confirmed diagnosis of allergy,16,13,NA,NA,NA,NA,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 1.,10 January 2021,Lucy Mellor,"WikiWorks,Peace Sandy","Intestinal microflora of 13 allergic (grey) and 16 nonallergic (white) Estonian children. The results are presented as colonization rate (%, columns) and counts (log CFU/g, range and median, lines and filled symbols).",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|1578,Complete,Peace Sandy
bsdb:10202341/2/1,10202341,prospective cohort,10202341,10.1046/j.1365-2222.1999.00560.x,NA,"Björkstén B., Naaber P., Sepp E. , Mikelsaar M.",The intestinal microflora in allergic Estonian and Swedish 2-year-old children,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,1999,NA,Experiment 2,"Estonia,Sweden",Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,Non-allergic Swedish children.,Allergic Swedish children,2-year-old children with confirmed diagnosis of allergy,19,14,NA,NA,NA,NA,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 2,29 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","Intestinal microflora of 14 allergic (grey) and 19 nonallergic
(white) Swedish children. The results are presented as colonization
rate (%, columns) and counts (log CFU/g, range and median, lines
and filled symbols).",increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,1783272|1239|91061|1385|90964|1279|1280,Complete,Peace Sandy
bsdb:10202341/2/2,10202341,prospective cohort,10202341,10.1046/j.1365-2222.1999.00560.x,NA,"Björkstén B., Naaber P., Sepp E. , Mikelsaar M.",The intestinal microflora in allergic Estonian and Swedish 2-year-old children,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,1999,NA,Experiment 2,"Estonia,Sweden",Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,Non-allergic Swedish children.,Allergic Swedish children,2-year-old children with confirmed diagnosis of allergy,19,14,NA,NA,NA,NA,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 2.,29 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","Intestinal microflora of 14 allergic (grey) and 19 nonallergic(white) Swedish children. The results are presented as colonization rate (%, columns) and counts (log CFU/g, range and median, lines and filled symbols).",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85004|31953|1678,Complete,Peace Sandy
bsdb:12345678/1/1,12345678,NA,12345678,10.1234/2013/999990,NA,Ministerial Meeting on Population of the Non-Aligned Movement (1993: Bali),Denpasar Declaration on Population and Development,"Integration (Tokyo, Japan)",1994,"Developing Countries, Development Policy, Economic Development, Economic Factors, International Cooperation, Policy, Population Policy, Social Policy",Experiment 1,NA,Homo sapiens,feces,UBERON:0001988,healthy,NA,control,case,Test case group,50,50,NA,16S,NA,NA,NA,NA,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2A,2 January 2026,Alexvpickering,Alexvpickering,Test signature - increased in case group,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Levilactobacillus|s__Levilactobacillus brevis",1783272|1239|91061|186826|33958|1578|1579;1783272|1239|91061|186826|33958|2767886|1580,Complete,NA
bsdb:15987522/1/1,15987522,case-control,15987522,10.1186/1479-5876-3-27,NA,"Mager D.L., Haffajee A.D., Devlin P.M., Norris C.M., Posner M.R. , Goodson J.M.","The salivary microbiota as a diagnostic indicator of oral cancer: a descriptive, non-randomized study of cancer-free and oral squamous cell carcinoma subjects",Journal of translational medicine,2005,NA,Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Oral squamous cell carcinoma,EFO:0000199,Controls,oral squamous cell carcinoma (OSCC),"disgnosed oral squamous cell carcinoma via biopsy, age 18 years or older and immunocompetent",229,45,3 months,NA,NA,DNA-DNA Hybridization,relative abundances,Mann-Whitney (Wilcoxon),0.001,TRUE,NA,"age,sex,smoking behavior",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1 , Text",10 January 2021,Utsav Patel,WikiWorks,Relative abundance of oral microbiome in oral squamous cell carcinoma patients and controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea",3379134|976|200643|171549|171552|838|28132;3379134|976|117743|200644|49546|1016|1017;1783272|1239|91061|186826|1300|1301|28037;3379134|976|117743|200644|49546|1016|1018,Complete,Rimsha Azhar
bsdb:15987522/1/2,15987522,case-control,15987522,10.1186/1479-5876-3-27,NA,"Mager D.L., Haffajee A.D., Devlin P.M., Norris C.M., Posner M.R. , Goodson J.M.","The salivary microbiota as a diagnostic indicator of oral cancer: a descriptive, non-randomized study of cancer-free and oral squamous cell carcinoma subjects",Journal of translational medicine,2005,NA,Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Oral squamous cell carcinoma,EFO:0000199,Controls,oral squamous cell carcinoma (OSCC),"disgnosed oral squamous cell carcinoma via biopsy, age 18 years or older and immunocompetent",229,45,3 months,NA,NA,DNA-DNA Hybridization,relative abundances,Mann-Whitney (Wilcoxon),0.001,TRUE,NA,"age,sex,smoking behavior",NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 1 , Text",10 January 2021,Utsav Patel,WikiWorks,Relative abundance of oral microbiome in oral squamous cell carcinoma patients and controls,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum saburreum",3384189|32066|203490|203491|1129771|32067|40542;1783272|1239|186801|3085636|186803|1164882|467210,Complete,Rimsha Azhar
bsdb:17631127/1/1,17631127,case-control,17631127,10.1053/j.gastro.2007.04.005,https://pubmed.ncbi.nlm.nih.gov/17631127/,"Kassinen A., Krogius-Kurikka L., Mäkivuokko H., Rinttilä T., Paulin L., Corander J., Malinen E., Apajalahti J. , Palva A.",The fecal microbiota of irritable bowel syndrome patients differs significantly from that of healthy subjects,Gastroenterology,2007,NA,Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS patients,"24 IBS patients (IBS-D, IBS-C, IBS-M) fulfilling Rome II criteria; age- and sex-matched to controls.",23,24,Ongoing antibiotic treatment was an exclusion criterion for controls; IBS patients had no ongoing antibiotics.,16S,123456789,Sanger,raw counts,Mann-Whitney (Wilcoxon),0.05,FALSE,0,"age,sex","age,sex",NA,NA,NA,NA,NA,NA,Signature 1,"qPCR (Figure 3, Collinsella aerofaciens)",29 November 2025,Aqc576444,Aqc576444,"Collinsella aerofaciens significantly reduced in fecal samples from IBS patients compared with age- and sex-matched healthy controls, based on phylotype-specific qPCR (Mann–Whitney P = 0.01).",decreased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,1783272|201174|84998|84999|84107|102106|74426,Complete,NA
bsdb:17631127/1/3,17631127,case-control,17631127,10.1053/j.gastro.2007.04.005,https://pubmed.ncbi.nlm.nih.gov/17631127/,"Kassinen A., Krogius-Kurikka L., Mäkivuokko H., Rinttilä T., Paulin L., Corander J., Malinen E., Apajalahti J. , Palva A.",The fecal microbiota of irritable bowel syndrome patients differs significantly from that of healthy subjects,Gastroenterology,2007,NA,Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS patients,"24 IBS patients (IBS-D, IBS-C, IBS-M) fulfilling Rome II criteria; age- and sex-matched to controls.",23,24,Ongoing antibiotic treatment was an exclusion criterion for controls; IBS patients had no ongoing antibiotics.,16S,123456789,Sanger,raw counts,Mann-Whitney (Wilcoxon),0.05,FALSE,0,"age,sex","age,sex",NA,NA,NA,NA,NA,NA,Signature 3,qPCR (Figure 3 – Total bacteria),29 November 2025,Aqc576444,Aqc576444,IBS patients showed significantly lower total fecal bacterial 16S rRNA gene copy numbers compared with healthy controls (qPCR; Mann–Whitney P < 0.05). This indicates reduced total bacterial load in IBS.,decreased,NA,NA,Complete,NA
bsdb:19533811/1/2,19533811,case-control,19533811,10.3748/wjg.15.2887,NA,"Kerckhoffs A.P., Samsom M., van der Rest M.E., de Vogel J., Knol J., Ben-Amor K. , Akkermans L.M.",Lower Bifidobacteria counts in both duodenal mucosa-associated and fecal microbiota in irritable bowel syndrome patients,World journal of gastroenterology,2009,NA,Experiment 1,Netherlands,Homo sapiens,"Feces,Mucosa of small intestine","UBERON:0001204,UBERON:0001988",Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS,"Twelve male and 29 female IBS patients included in this study fulfilled the Rome II criteria for IBS and were categorized as diarrhea predominant (IBS-D), constipation predominant (IBS-C) or alternating IBS subgroup (IBS-A)",26,41,NA,NA,NA,RT-qPCR,raw counts,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Tables 2 and 3,19 July 2021,Kwekuamoo,"Chloe,Kwekuamoo,WikiWorks","Real time PCR analysis of fecal bifidobacteria in HS, IBS patients and IBS subgroups",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia lituseburensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|201174|1760|85004|31953|1678|1686;1783272|1239|186801|3082720|186804|1501226|1537;1783272|201174|1760|85004|31953|1678,Complete,Chloe
bsdb:19533811/2/NA,19533811,case-control,19533811,10.3748/wjg.15.2887,NA,"Kerckhoffs A.P., Samsom M., van der Rest M.E., de Vogel J., Knol J., Ben-Amor K. , Akkermans L.M.",Lower Bifidobacteria counts in both duodenal mucosa-associated and fecal microbiota in irritable bowel syndrome patients,World journal of gastroenterology,2009,NA,Experiment 2,Netherlands,Homo sapiens,"Feces,Mucosa of small intestine","UBERON:0001204,UBERON:0001988",Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-D,IBS patients included in this study fulfilled the Rome II criteria for IBS and were categorized as diarrhea predominant (IBS-D),26,14,NA,NA,NA,RT-qPCR,raw counts,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:19533811/3/NA,19533811,case-control,19533811,10.3748/wjg.15.2887,NA,"Kerckhoffs A.P., Samsom M., van der Rest M.E., de Vogel J., Knol J., Ben-Amor K. , Akkermans L.M.",Lower Bifidobacteria counts in both duodenal mucosa-associated and fecal microbiota in irritable bowel syndrome patients,World journal of gastroenterology,2009,NA,Experiment 3,Netherlands,Homo sapiens,"Feces,Mucosa of small intestine","UBERON:0001204,UBERON:0001988",Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-A,IBS patients included in this study fulfilled the Rome II criteria for IBS and were categorized as  alternating IBS subgroup (IBS-A),26,16,NA,NA,NA,RT-qPCR,raw counts,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:19533811/4/NA,19533811,case-control,19533811,10.3748/wjg.15.2887,NA,"Kerckhoffs A.P., Samsom M., van der Rest M.E., de Vogel J., Knol J., Ben-Amor K. , Akkermans L.M.",Lower Bifidobacteria counts in both duodenal mucosa-associated and fecal microbiota in irritable bowel syndrome patients,World journal of gastroenterology,2009,NA,Experiment 4,Netherlands,Homo sapiens,"Feces,Mucosa of small intestine","UBERON:0001204,UBERON:0001988",Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-C,IBS patients included in this study fulfilled the Rome II criteria for IBS and were categorized as  constipation predominant (IBS-C),26,11,NA,NA,NA,RT-qPCR,raw counts,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:19849869/1/1,19849869,case-control,19849869,10.1017/S0007114509992182,NA,"Balamurugan R., George G., Kabeerdoss J., Hepsiba J., Chandragunasekaran A.M. , Ramakrishna B.S.",Quantitative differences in intestinal Faecalibacterium prausnitzii in obese Indian children,The British journal of nutrition,2010,NA,Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,non-obese,obese,(Private) School Children,13,15,1 month,16S,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,class/grade level,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,10 January 2021,Mst Afroza Parvin,WikiWorks,Quantitative PCR of different bacterial groups from the faeces of obese (OB) and non-obese (NOB) participants,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,1783272|1239|186801|186802|216572|216851|853,Complete,NA
bsdb:19903265/1/1,19903265,case-control,19903265,10.1111/j.1365-2982.2009.01427.x,NA,"Tana C., Umesaki Y., Imaoka A., Handa T., Kanazawa M. , Fukudo S.",Altered profiles of intestinal microbiota and organic acids may be the origin of symptoms in irritable bowel syndrome,Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society,2010,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS,"All patients were diagnosed with IBS after conducting a medical interview based on Rome II criteria and positive judgment by a Rome II modular questionnaire retrospectively and positively fulfilling Rome III criteria. According to Rome II criteria related to bowel habits, 11 subjects had constipation-predominant IBS (IBS-C), eight had diarrhoea-predominant IBS (IBS-D) and seven had mixed IBS (IBS-M).",26,26,NA,WMS,NA,RT-qPCR,NA,Spearman Correlation,0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,4 July 2021,Kwekuamoo,"Kwekuamoo,Atrayees,WikiWorks","Comparison of GI microbiota between IBS patients and the
controls",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|33958|1578,Complete,Atrayees
bsdb:19903265/1/2,19903265,case-control,19903265,10.1111/j.1365-2982.2009.01427.x,NA,"Tana C., Umesaki Y., Imaoka A., Handa T., Kanazawa M. , Fukudo S.",Altered profiles of intestinal microbiota and organic acids may be the origin of symptoms in irritable bowel syndrome,Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society,2010,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS,"All patients were diagnosed with IBS after conducting a medical interview based on Rome II criteria and positive judgment by a Rome II modular questionnaire retrospectively and positively fulfilling Rome III criteria. According to Rome II criteria related to bowel habits, 11 subjects had constipation-predominant IBS (IBS-C), eight had diarrhoea-predominant IBS (IBS-D) and seven had mixed IBS (IBS-M).",26,26,NA,WMS,NA,RT-qPCR,NA,Spearman Correlation,0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,text,19 July 2023,Atrayees,"Atrayees,WikiWorks","Comparison of GI microbiota between IBS patients and the controls

Abundance in",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,1783272|1239|186801|186802|31979|1485,Complete,Atrayees
bsdb:20140211/1/1,20140211,case-control,20140211,10.1371/journal.pone.0009085,NA,"Larsen N., Vogensen F.K., van den Berg F.W., Nielsen D.S., Andreasen A.S., Pedersen B.K., Al-Soud W.A., Sørensen S.J., Hansen L.H. , Jakobsen M.",Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults,PloS one,2010,NA,Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Control,Diabetes Type 2,The diabetic group had elevated concentration of plasma glucose as determined by a fasting oral glucose tolerance test (OGTT),10,10,NA,16S,4,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 2 + Text,10 January 2021,Phyu Han,WikiWorks,Relative abundances (%) of bacteria were determined in feces from human adults with type 2 diabetes and non-diabetic adult (all are males),increased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,3379134|1224|28216,Complete,Shaimaa Elsafoury
bsdb:20140211/1/2,20140211,case-control,20140211,10.1371/journal.pone.0009085,NA,"Larsen N., Vogensen F.K., van den Berg F.W., Nielsen D.S., Andreasen A.S., Pedersen B.K., Al-Soud W.A., Sørensen S.J., Hansen L.H. , Jakobsen M.",Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults,PloS one,2010,NA,Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Control,Diabetes Type 2,The diabetic group had elevated concentration of plasma glucose as determined by a fasting oral glucose tolerance test (OGTT),10,10,NA,16S,4,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 2 + Text,10 January 2021,Phyu Han,WikiWorks,Relative abundances (%) of bacteria were determined in feces from human adults with type 2 diabetes and non-diabetic adult (all are males),decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia",1783272|1239;1783272|1239|186801,Complete,Shaimaa Elsafoury
bsdb:20566857/1/NA,20566857,"cross-sectional observational, not case-control",20566857,10.1073/pnas.1002601107,NA,"Dominguez-Bello M.G., Costello E.K., Contreras M., Magris M., Hidalgo G., Fierer N. , Knight R.",Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns,Proceedings of the National Academy of Sciences of the United States of America,2010,NA,Experiment 1,Venezuela,Homo sapiens,"Mucosa of oral region,Vagina,Skin of forehead,Skin of forearm","UBERON:0003343,UBERON:0016475,UBERON:0000996,UBERON:0003403",Cesarean section,EFO:0009636,vaginal delivery (Va),C-section (Cesarean section),NA,4,5,NA,16S,2,Roche454,NA,ANOSIM,0.001,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:20603222/1/1,20603222,case-control,20603222,10.1016/j.anaerobe.2010.06.008,NA,"Finegold S.M., Dowd S.E., Gontcharova V., Liu C., Henley K.E., Wolcott R.D., Youn E., Summanen P.H., Granpeesheh D., Dixon D., Liu M., Molitoris D.R. , Green J.A.",Pyrosequencing study of fecal microflora of autistic and control children,Anaerobe,2010,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Autism,EFO:0003758,non-sibling control,severely autistic,"Cases were diagnosed with autistic spectrum disorder. Moreover, they were evaluated for autism and their diagnoses were validated based on impairment in social skills, impairment in language skills and verbal communication, sensory disturbances, repetitive stereotypical behaviors, and gastrointestinal disturbances.",8,11,1 month,16S,NA,Roche454,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,increased,NA,NA,increased,Signature 1,Table 2 + Table 3 +  Table 5 + Table 6 + Table 8,10 January 2021,Marianthi Thomatos,WikiWorks,Significant fecal microflora of autistic and control children,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinilabiliaceae|g__Alkaliflexus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio desulfuricans,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota",1783272|1239|526524|526525|2810281|191303;3379134|976|200643|171549|815|816;3379134|976|200643|1970189|558415|286729;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|216572|258514;3379134|976|200643|171549|2005525|375288;3379134|200940|3031449|213115|194924|872|901;3379134|200940|3031449|213115|194924|872|876;3379134|200940|3031449|213115|194924|872|58621;3379134|976|200643|171549|815|909656|821;3379134|976;3379134|1224,Complete,Shaimaa Elsafoury
bsdb:20603222/1/2,20603222,case-control,20603222,10.1016/j.anaerobe.2010.06.008,NA,"Finegold S.M., Dowd S.E., Gontcharova V., Liu C., Henley K.E., Wolcott R.D., Youn E., Summanen P.H., Granpeesheh D., Dixon D., Liu M., Molitoris D.R. , Green J.A.",Pyrosequencing study of fecal microflora of autistic and control children,Anaerobe,2010,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Autism,EFO:0003758,non-sibling control,severely autistic,"Cases were diagnosed with autistic spectrum disorder. Moreover, they were evaluated for autism and their diagnoses were validated based on impairment in social skills, impairment in language skills and verbal communication, sensory disturbances, repetitive stereotypical behaviors, and gastrointestinal disturbances.",8,11,1 month,16S,NA,Roche454,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,increased,NA,NA,increased,Signature 2,Table 2 + Table 3 +  Table 5 + Table 6 + Table 8,10 January 2021,Marianthi Thomatos,"Lwaldron,WikiWorks",Significant fecal microflora of autistic and control children,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium angulatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Helcococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum",1783272|201174;1783272|1239|186801|3082720|3118656|114627;1783272|1239|186801|186802|216572|52784;1783272|1239|186801|3082720|543314|109326;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|1683;1783272|201174|1760|85004|31953|1678|216816|1679;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|186801|186802|216572|253238;1783272|1239;1783272|1239|1737404|1737405|1570339|31983;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1243;1783272|1239|186801|186802|186806|113286;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|33958|46255;1783272|1239|186801|186802|216572|1535,Complete,Fatima
bsdb:20613793/1/1,20613793,time series / longitudinal observational,20613793,10.1038/ismej.2010.92,NA,"Giongo A., Gano K.A., Crabb D.B., Mukherjee N., Novelo L.L., Casella G., Drew J.C., Ilonen J., Knip M., Hyöty H., Veijola R., Simell T., Simell O., Neu J., Wasserfall C.H., Schatz D., Atkinson M.A. , Triplett E.W.",Toward defining the autoimmune microbiome for type 1 diabetes,The ISME journal,2011,NA,Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Autoimmune disease,EFO:0005140,Control 1,Case 1,"Samples from children diagnosed with autoimmunity, determined by the appearance of at least two autoantibodies at four months after birth.",3,3,NA,16S,3,Roche454,raw counts,Chi-Square,0.01,TRUE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Table 3, 4, S2, S3, S4, S5",3 March 2025,Aleru Divine,Aleru Divine,Mean percent of total reads for six taxonomic levels identified in the case and control samples.,increased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella para-adiacens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus rhamnosus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239;3379134|1224;3379134|1224|1236|91347|543|561|562;1783272|1239|91061|186826|186828|117563|321195;1783272|1239|91061|186826|33958|2759736|47715;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|91061;1783272|1239|186801;3379134|1224|1236;1783272|1239|186801|186802;3379134|1224|1236|91347;1783272|1239|91061|186826;1783272|1239|91061|186826|186828;3379134|1224|1236|91347|543;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|1300;1783272|1239|909932|1843489|31977;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|561;1783272|1239|91061|186826|186828|117563;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:20613793/1/2,20613793,time series / longitudinal observational,20613793,10.1038/ismej.2010.92,NA,"Giongo A., Gano K.A., Crabb D.B., Mukherjee N., Novelo L.L., Casella G., Drew J.C., Ilonen J., Knip M., Hyöty H., Veijola R., Simell T., Simell O., Neu J., Wasserfall C.H., Schatz D., Atkinson M.A. , Triplett E.W.",Toward defining the autoimmune microbiome for type 1 diabetes,The ISME journal,2011,NA,Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Autoimmune disease,EFO:0005140,Control 1,Case 1,"Samples from children diagnosed with autoimmunity, determined by the appearance of at least two autoantibodies at four months after birth.",3,3,NA,16S,3,Roche454,raw counts,Chi-Square,0.01,TRUE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Table 3, 4, S2, S3, S4, S5",3 March 2025,Aleru Divine,Aleru Divine,Mean percent of total reads for six taxonomic levels identified in the case and control samples.,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium DJF_VR07,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp. DJF_B086,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|976;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|818;1783272|1239|186801|186802|31979|537373;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|2005525|375288|537292;1783272|1239|186801|3085636|186803|2316020|33038;3379134|976|200643;3379134|976|200643|171549;3379134|976|200643|171549|815;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|186806;3379134|976|200643|171549|171551;1783272|1239|186801|186802|216572;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979|1485;3379134|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:20613793/2/1,20613793,time series / longitudinal observational,20613793,10.1038/ismej.2010.92,NA,"Giongo A., Gano K.A., Crabb D.B., Mukherjee N., Novelo L.L., Casella G., Drew J.C., Ilonen J., Knip M., Hyöty H., Veijola R., Simell T., Simell O., Neu J., Wasserfall C.H., Schatz D., Atkinson M.A. , Triplett E.W.",Toward defining the autoimmune microbiome for type 1 diabetes,The ISME journal,2011,NA,Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Autoimmune disease,EFO:0005140,Control 2,Case 2,"Samples from children diagnosed with autoimmunity, determined by the appearance of at least two autoantibodies at 1 year after birth.",3,3,NA,16S,3,Roche454,raw counts,Chi-Square,0.01,TRUE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Table 3, 4, S2, S3, S4, S5",3 March 2025,Aleru Divine,Aleru Divine,Mean percent of total reads for six taxonomic levels identified in the case and control samples.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CJ78,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister sp. E2_20,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp. ADV 3107.03,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,s__bacterium mpn-isolate group 18,s__swine fecal bacterium RF3E-Xyl1,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|1224|28216|80840|506;1783272|1239;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|188902;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|820;3379134|976|200643;3379134|976;3379134|1224|28216;3379134|1224|28216|80840;1783272|1239|186801;1783272|1239|909932|1843489|31977|39948|189712;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;3384189|32066|203490|203491|203492|848;3379134|1224|1236;1783272|1239|186801|3085636|186803|1649459|154046;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|823;3379134|1224|28216|80840|995019|577310|487175;3379134|976|200643|171549|171551;3379134|1224;3379134|976|200643|171549|171550;1783272|1239|909932|1843489|31977|29465|269267;1783272|1239|909932|1843489|31977;157949;621345;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:20613793/2/2,20613793,time series / longitudinal observational,20613793,10.1038/ismej.2010.92,NA,"Giongo A., Gano K.A., Crabb D.B., Mukherjee N., Novelo L.L., Casella G., Drew J.C., Ilonen J., Knip M., Hyöty H., Veijola R., Simell T., Simell O., Neu J., Wasserfall C.H., Schatz D., Atkinson M.A. , Triplett E.W.",Toward defining the autoimmune microbiome for type 1 diabetes,The ISME journal,2011,NA,Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Autoimmune disease,EFO:0005140,Control 2,Case 2,"Samples from children diagnosed with autoimmunity, determined by the appearance of at least two autoantibodies at 1 year after birth.",3,3,NA,16S,3,Roche454,raw counts,Chi-Square,0.01,TRUE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Table 3, 4, S2, S3, S4, S5",3 March 2025,Aleru Divine,Aleru Divine,Mean percent of total reads for six taxonomic levels identified in the case and control samples.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides galacturonicus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. DJF_VR20,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,s__human intestinal firmicute CO19,s__human intestinal firmicute CO35,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|384639;1783272|1239|186801|186802|216572|216851|537281;3379134|1224|1236|135625|712|724|729;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|2316020|33038;3379134|976|200643|171549|815|909656|357276;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|909932|1843489|31977|29465|39778;165137;165261;1783272|1239|526524|526525;1783272|1239|91061|186826;3379134|1224|1236|135625;1783272|1239|186801|186802|186806;1783272|1239|186801|3085636|186803;3379134|1224|1236|135625|712;3379134|976|200643|171549|171552;1783272|1239|91061|186826|1300;1783272|1239|186801|186802|186806|1730;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:20613793/3/1,20613793,time series / longitudinal observational,20613793,10.1038/ismej.2010.92,NA,"Giongo A., Gano K.A., Crabb D.B., Mukherjee N., Novelo L.L., Casella G., Drew J.C., Ilonen J., Knip M., Hyöty H., Veijola R., Simell T., Simell O., Neu J., Wasserfall C.H., Schatz D., Atkinson M.A. , Triplett E.W.",Toward defining the autoimmune microbiome for type 1 diabetes,The ISME journal,2011,NA,Experiment 3,Finland,Homo sapiens,Feces,UBERON:0001988,Autoimmune disease,EFO:0005140,Control 3,Case 3,"Samples from children diagnosed with autoimmunity, determined by the appearance of at least two autoantibodies at 2 years after birth.",3,3,NA,16S,3,Roche454,raw counts,Chi-Square,0.01,TRUE,NA,age,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Table 3, 4, S2, S3, S4, S5",3 March 2025,Aleru Divine,Aleru Divine,Mean percent of total reads for six taxonomic levels identified in the case and control samples.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. B2,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CJ78,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium 80/3,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium 80/4,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CJ67,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. NII-26,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium DJF_RP14,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CB3,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CO27,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. ID8,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,s__bacterium mpn-isolate group 18,s__swine fecal bacterium RF3E-Xyl1,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|536478;3379134|976|200643|171549|815|816|188902;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|820;3379134|976;1783272|1239|186801|186802|500389;1783272|1239|186801|186802|620858;1783272|1239|186801|186802|31979|1485|1506;1783272|1239|186801|186802|31979|1485|188893;3379134|1224|1236|91347|543|547|634877;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|537393;1783272|1239|186801|3085636|186803|2316020|33038;3379134|976|200643|171549|815|909656|357276;3379134|1224;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|1263|165151;1783272|1239|186801|186802|216572|1263|165152;1783272|1239|186801|186802|216572|1263|320872;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|186801|186802|31979|1485|1522;157949;621345;1783272|1239|91061;3379134|976|200643;1783272|1239|526524;3379134|1224|1236;3379134|976|200643|171549;1783272|1239|526524|526525;1783272|1239|91061|186826;3379134|976|200643|171549|815;1783272|1239|186801|186802|31979;3379134|976|200643|171549|171550;1783272|1239|91061|186826|1300;1783272|1239|909932|1843489|31977;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:20613793/3/2,20613793,time series / longitudinal observational,20613793,10.1038/ismej.2010.92,NA,"Giongo A., Gano K.A., Crabb D.B., Mukherjee N., Novelo L.L., Casella G., Drew J.C., Ilonen J., Knip M., Hyöty H., Veijola R., Simell T., Simell O., Neu J., Wasserfall C.H., Schatz D., Atkinson M.A. , Triplett E.W.",Toward defining the autoimmune microbiome for type 1 diabetes,The ISME journal,2011,NA,Experiment 3,Finland,Homo sapiens,Feces,UBERON:0001988,Autoimmune disease,EFO:0005140,Control 3,Case 3,"Samples from children diagnosed with autoimmunity, determined by the appearance of at least two autoantibodies at 2 years after birth.",3,3,NA,16S,3,Roche454,raw counts,Chi-Square,0.01,TRUE,NA,age,NA,NA,decreased,NA,NA,NA,NA,Signature 2,"Table 3, 4, S2, S3, S4, S5",3 March 2025,Aleru Divine,Aleru Divine,Mean percent of total reads for six taxonomic levels identified in the case and control samples.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp. CK3,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. DJF_VR20,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. M10,s__human intestinal firmicute CB47,s__human intestinal firmicute CO19,s__human intestinal firmicute CO35,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239;3379134|976|200643|171549|815|816|817;3379134|1224|1236|91347|543|544|543888;1783272|1239|186801;1783272|1239|186801|3085636|186803|2719313|358742;1783272|1239|186801|186802|186806;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|216851|537281;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;3379134|1224|1236|135625|712|724|729;1783272|1239|186801|3085636|186803|1649459|154046;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|171551;1783272|1239|186801|186802|216572|1263|390634;165138;165137;165261;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:20679230/1/1,20679230,"cross-sectional observational, not case-control",20679230,10.1073/pnas.1005963107,https://pubmed.ncbi.nlm.nih.gov/20679230/,"De Filippo C., Cavalieri D., Di Paola M., Ramazzotti M., Poullet J.B., Massart S., Collini S., Pieraccini G. , Lionetti P.",Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa,Proceedings of the National Academy of Sciences of the United States of America,2010,NA,Experiment 1,"Italy,Burkina Faso",Homo sapiens,Feces,UBERON:0001988,"Place of residence measurement,Ethnic group","EFO:0009583,EFO:0001799",European Children in Italy,Rural African Children in Burkina Faso,"14 healthy children (nine male and six female) living in the rural village of Boulpon district of Nanoro, Boulkiemde province, Burkina Faso.",15,14,6 months,16S,56,Roche454,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Supporting Info. Table S5 + Fig. S2,17 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Atrayees,ChiomaBlessing,WikiWorks",Report of the species assignment for BF and EU populations relative to the most abundant bacterial genera found by the RDP classifier,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Anaplasmataceae|g__Aegyptianella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales str. KB11,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales str. KB13,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Prevotella heparinolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. TP-5,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis|s__Bifidobacterium animalis subsp. lactis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pullorum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium ruminantium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium simiae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium thermophilum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Budviciaceae|g__Budvicia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Coriobacterium,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae|g__Cytophaga,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella aff. ruminicola Tc2-24,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella aurantiaca,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Ruminobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella paludivivens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Uruburuella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter brevis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter oryzae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter ruminicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__butyrate-producing bacterium M21/2,s__butyrate-producing bacterium PH07AY5,s__butyrate-producing bacterium PH07BY04",3379134|1224|28211|766|942|203861;1783272|1239|186801|186802|216572|52784;3379134|976|200643|171549|185297;3379134|976|200643|171549|185299;3379134|976|200643|171549|815|816|28113;3379134|976|200643|171549|815|816|643958;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|28025;1783272|201174|1760|85004|31953|1678|28025|302911;1783272|201174|1760|85004|31953|1678|1681;1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|28026;1783272|201174|1760|85004|31953|1678|78448;1783272|201174|1760|85004|31953|1678|78346;1783272|201174|1760|85004|31953|1678|180216;1783272|201174|1760|85004|31953|1678|33905;3379134|1224|1236|91347|1903416|82978;1783272|1239|186801|3085636|186803|830;3379134|29547|3031852|213849|72294|194;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|33870;3379134|976|768503|768507|89373|978;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|216572|216851|853;3379134|976|200643|171549|171552|52228;1783272|1239|186801|3085636|186803|140625;1783272|1239|91061|186826|33958|1243;3379134|976|200643|171549|171552|2974265|363265;1783272|1239|909932|909929|1843491|52225;3379134|1224|1236|91347|1903414|581;3379134|976|200643|171549|2005523|346096;3379134|976|200643|171549|171552|838|81582;3379134|976|200643|171549|171552|838|596085;3379134|976|200643|171549|171552|838|28129;3379134|976|200643|171549|171552|838|59823;3379134|1224|1236|135624|83763|866;1783272|1239|186801|186802|31979|1266;3379134|976|200643|171549|171552|2974251|165179;3379134|976|200643|171549|171552|2974251|185294;1783272|201174|84998|1643822|1643826|84108;3379134|1224|1236|135624|83763|83768;3379134|1224|1236|135624|83763|83770;3379134|203691|203692|136|2845253|157;3379134|203691|203692|136|2845253|157|166;3379134|1224|28216|206351|481|299568;1783272|1239|91061|186826|33958|46255;3379134|976|200643|171549|171552|558436|83231;3379134|976|200643|171549|171552|558436|185293;3379134|976|200643|171549|171552|558436|839;1783272|1239|186801|186802|245005;340481;340484,Complete,ChiomaBlessing
bsdb:20679230/1/2,20679230,"cross-sectional observational, not case-control",20679230,10.1073/pnas.1005963107,https://pubmed.ncbi.nlm.nih.gov/20679230/,"De Filippo C., Cavalieri D., Di Paola M., Ramazzotti M., Poullet J.B., Massart S., Collini S., Pieraccini G. , Lionetti P.",Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa,Proceedings of the National Academy of Sciences of the United States of America,2010,NA,Experiment 1,"Italy,Burkina Faso",Homo sapiens,Feces,UBERON:0001988,"Place of residence measurement,Ethnic group","EFO:0009583,EFO:0001799",European Children in Italy,Rural African Children in Burkina Faso,"14 healthy children (nine male and six female) living in the rural village of Boulpon district of Nanoro, Boulkiemde province, Burkina Faso.",15,14,6 months,16S,56,Roche454,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Supporting Info. Table S5 + Fig. S2,17 July 2022,Kaluifeanyi101,"Kaluifeanyi101,ChiomaBlessing,WikiWorks",Report of the species assignment for BF and EU populations relative to the most abundant bacterial genera found by the RDP classifier,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. AR20,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. XO77B42,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium ruminantium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp. PL1,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp. h12,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp. DJF_VR33k2,s__bacterium ic1395,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__butyrate-producing bacterium M21/2,s__butyrate-producing bacterium PH07AY5,s__butyrate-producing bacterium PH07BY04,s__swine fecal bacterium RF3E-Xyl1,s__swine fecal bacterium RF3G-Cel1,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Gracilibacteraceae|g__Gracilibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XII. Incertae Sedis|g__Guggenheimella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Oxobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Propionispira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Thermoactinomycetaceae|g__Seinonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Thermobacillus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chitinibacteraceae|g__Chitinibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kluyvera,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Lawsonia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Rickettsiaceae|g__Orientia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Phocoenobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Telluria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Thalassobacter",3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|171550|239759|626932;3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|28111;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|329854;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|93974;3379134|976|200643|171549|815|816|371598;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|820;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|1681;1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|28026;1783272|201174|1760|85004|31953|1678|78346;1783272|201174|1760|85004|31953|1678|138809;1783272|201174|1760|85004|31953|1678|308029;1783272|1239|186801|186802|216572|216851|853;3379134|976|200643|171549|815|909656|310298;3379134|976|200643|171549|815|909656|204516;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|186802|216572|292632|537421;330061;1783272|1239|186801|186802|245005;340481;340484;621345;621352;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|186802|541019|342658;1783272|1239|186801|186802|543313|228923;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|186802|31979|44261;1783272|1239|909932|909929|1843491|84034;1783272|1239|186801|186802|186806|113286;1783272|1239|91061|1385|186824|292637;1783272|1239|91061|1385|186822|76632;3384189|32066|203490|203491|203492|848;1783272|201174|84998|1643822|1643826|84111;3379134|200940|3031449|213115|194924|35832;3379134|1224|1236|91347|543|158483;3379134|1224|28216|206351|2897177|230666;3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|579;3379134|200940|3031449|213115|194924|41707;3379134|1224|28216|80840|75682|149698;3379134|1224|28211|766|775|69474;3379134|1224|1236|135625|712|146805;3379134|1224|1236|91347|543|590;3379134|1224|1236|91347|543|620;3379134|1224|28216|80840|995019|40544;3379134|1224|28216|80840|75682|34069;3379134|1224|28211|204455|2854170|266808,Complete,ChiomaBlessing
bsdb:20679230/2/1,20679230,"cross-sectional observational, not case-control",20679230,10.1073/pnas.1005963107,https://pubmed.ncbi.nlm.nih.gov/20679230/,"De Filippo C., Cavalieri D., Di Paola M., Ramazzotti M., Poullet J.B., Massart S., Collini S., Pieraccini G. , Lionetti P.",Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa,Proceedings of the National Academy of Sciences of the United States of America,2010,NA,Experiment 2,"Burkina Faso,Italy",Homo sapiens,Feces,UBERON:0001988,"Ethnic group,Place of residence measurement","EFO:0001799,EFO:0009583",European Children in Italy,Rural African Children in Burkina Faso,"14 healthy children (nine male and six female) living in the rural village of Boulpon district of Nanoro, Boulkiemde province, Burkina Faso.",15,14,6 months,16S,56,Roche454,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure 3B,11 July 2023,Atrayees,"Atrayees,ChiomaBlessing,WikiWorks","Number of sequences relative to principal Enterobacteriaceae genera, in BF and EU children microbiota.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella",3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|620,Complete,ChiomaBlessing
bsdb:20844065/1/1,20844065,time series / longitudinal observational,20844065,10.3945/ajcn.2010.29877,NA,"Collado M.C., Isolauri E., Laitinen K. , Salminen S.","Effect of mother's weight on infant's microbiota acquisition, composition, and activity during early infancy: a prospective follow-up study initiated in early pregnancy",The American journal of clinical nutrition,2010,NA,Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,infants of normal weight mother at age 1 month,infants of overweight mothers,mothers whose prepregnancy body mass index (BMI; in kg/m2) was >25,26,16,NA,16S,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2 & Tale 4,10 January 2021,Rimsha Azhar,WikiWorks,Mirobial groups in feacal samples at 1 and 6 months of age according to maternal weight gain during pregnancy and BMI,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|976|200643|171549|815|816;3379134|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
bsdb:20844065/2/1,20844065,time series / longitudinal observational,20844065,10.3945/ajcn.2010.29877,NA,"Collado M.C., Isolauri E., Laitinen K. , Salminen S.","Effect of mother's weight on infant's microbiota acquisition, composition, and activity during early infancy: a prospective follow-up study initiated in early pregnancy",The American journal of clinical nutrition,2010,NA,Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,infants of normal weight mother at age 6 month,infants of overweight mothers,mothers whose prepregnancy body mass index (BMI; in kg/m2) was >25,26,16,NA,16S,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2 & Tale 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Mirobial groups in feacal samples at 1 and 6 months of age according to maternal weight gain during pregnancy and BMI,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Hathewaya|s__Hathewaya histolytica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum",1783272|1239|186801|186802|31979|1769729|1498;1783272|201174|1760|85004|31953|1678|1686,Complete,Shaimaa Elsafoury
bsdb:20844065/3/1,20844065,time series / longitudinal observational,20844065,10.3945/ajcn.2010.29877,NA,"Collado M.C., Isolauri E., Laitinen K. , Salminen S.","Effect of mother's weight on infant's microbiota acquisition, composition, and activity during early infancy: a prospective follow-up study initiated in early pregnancy",The American journal of clinical nutrition,2010,NA,Experiment 3,Finland,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,infants of normal maternal weight gain mothers at age 1 month,infants of excessive maternal weight gain mothers,Weight gain >16.0 kg in women with BMI (in kg/m2) <25 and >11.5 kg in women with BMI >25 was considered excessive,20,22,NA,16S,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Bacterial counts in infant fecal samples at 1 and 6 months of age according to maternal weight gain during pregnancy,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|976|200643|171549|815|816;3379134|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
bsdb:20844065/4/1,20844065,time series / longitudinal observational,20844065,10.3945/ajcn.2010.29877,NA,"Collado M.C., Isolauri E., Laitinen K. , Salminen S.","Effect of mother's weight on infant's microbiota acquisition, composition, and activity during early infancy: a prospective follow-up study initiated in early pregnancy",The American journal of clinical nutrition,2010,NA,Experiment 4,Finland,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,infants of normal maternal weight gain mothers at age 6 months,infants of excessive maternal weight gain mothers,Weight gain >16.0 kg in women with BMI (in kg/m2) <25 and >11.5 kg in women with BMI >25 was considered excessive,20,22,NA,16S,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Bacterial counts in infant fecal samples at 1 and 6 months of age according to maternal weight gain during pregnancy,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Hathewaya|s__Hathewaya histolytica,1783272|1239|186801|186802|31979|1769729|1498,Complete,Shaimaa Elsafoury
bsdb:21188149/1/1,21188149,case-control,21188149,10.1371/journal.pone.0015216,NA,"Charlson E.S., Chen J., Custers-Allen R., Bittinger K., Li H., Sinha R., Hwang J., Bushman F.D. , Collman R.G.",Disordered microbial communities in the upper respiratory tract of cigarette smokers,PloS one,2010,NA,Experiment 1,United States of America,Homo sapiens,Oropharynx,UBERON:0001729,Smoking behavior,EFO:0004318,right oropharynx of nonsmokers,right oropharynx of smokers,"Smokers were defined as current smoking of .2 cigarettes daily for more than 6 months, and nonsmokers were defined as less than 100 cigarettes lifetime.",33,29,3 months,16S,12,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table3 + Table S3,10 January 2021,Rimsha Azhar,WikiWorks,Bacterial taxa that distinguish airway microbial communities of smokers from nonsmokers,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",3379134|976|117743|200644|49546|1016;1783272|1239|186801|3082720|186804|1257;3384189|32066|203490|203491|203492|848;3379134|1224|28216|80840|80864|12916;3379134|1224|1236|135625|712|724;3379134|1224|28216|206351|481|482,Complete,Shaimaa Elsafoury
bsdb:21188149/1/2,21188149,case-control,21188149,10.1371/journal.pone.0015216,NA,"Charlson E.S., Chen J., Custers-Allen R., Bittinger K., Li H., Sinha R., Hwang J., Bushman F.D. , Collman R.G.",Disordered microbial communities in the upper respiratory tract of cigarette smokers,PloS one,2010,NA,Experiment 1,United States of America,Homo sapiens,Oropharynx,UBERON:0001729,Smoking behavior,EFO:0004318,right oropharynx of nonsmokers,right oropharynx of smokers,"Smokers were defined as current smoking of .2 cigarettes daily for more than 6 months, and nonsmokers were defined as less than 100 cigarettes lifetime.",33,29,3 months,16S,12,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table3 + Table S4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Bacterial taxa that distinguish airway microbial communities of smokers from nonsmokers,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843489|31977|29465;3379134|976|200643|171549|171552|52228;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|541000,Complete,Shaimaa Elsafoury
bsdb:21188149/2/1,21188149,case-control,21188149,10.1371/journal.pone.0015216,NA,"Charlson E.S., Chen J., Custers-Allen R., Bittinger K., Li H., Sinha R., Hwang J., Bushman F.D. , Collman R.G.",Disordered microbial communities in the upper respiratory tract of cigarette smokers,PloS one,2010,NA,Experiment 2,United States of America,Homo sapiens,Oropharynx,UBERON:0001729,Smoking behavior,EFO:0004318,left oropharynx of nonsmokers,left oropharynx of smokers,"Smokers were defined as current smoking of .2 cigarettes daily for more than 6 months, and nonsmokers were defined as less than 100 cigarettes lifetime.",33,29,3 months,16S,12,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table3 + Table S5,10 January 2021,Rimsha Azhar,WikiWorks,Bacterial taxa that distinguish airway microbial communities of smokers from nonsmokers,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter",3379134|976|117743|200644|49546|1016;3384189|32066|203490|203491|203492|848;3379134|1224|28216|206351|481|482;3379134|1224|1236|135625|712|416916,Complete,Shaimaa Elsafoury
bsdb:21188149/2/2,21188149,case-control,21188149,10.1371/journal.pone.0015216,NA,"Charlson E.S., Chen J., Custers-Allen R., Bittinger K., Li H., Sinha R., Hwang J., Bushman F.D. , Collman R.G.",Disordered microbial communities in the upper respiratory tract of cigarette smokers,PloS one,2010,NA,Experiment 2,United States of America,Homo sapiens,Oropharynx,UBERON:0001729,Smoking behavior,EFO:0004318,left oropharynx of nonsmokers,left oropharynx of smokers,"Smokers were defined as current smoking of .2 cigarettes daily for more than 6 months, and nonsmokers were defined as less than 100 cigarettes lifetime.",33,29,3 months,16S,12,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table3 + Table S6,10 January 2021,Shaimaa Elsafoury,WikiWorks,Bacterial taxa that distinguish airway microbial communities of smokers from nonsmokers,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus",1783272|201174|1760|2037|2049|1654;1783272|201174|84998|1643822|1643826|84111;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843489|31977|29465;3384189|32066|203490|203491|1129771|34104,Complete,Shaimaa Elsafoury
bsdb:21188149/3/1,21188149,case-control,21188149,10.1371/journal.pone.0015216,NA,"Charlson E.S., Chen J., Custers-Allen R., Bittinger K., Li H., Sinha R., Hwang J., Bushman F.D. , Collman R.G.",Disordered microbial communities in the upper respiratory tract of cigarette smokers,PloS one,2010,NA,Experiment 3,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,Smoking behavior,EFO:0004318,right nasopharynx of nonsmokers,right nasopharynx of smokers,"Smokers were defined as current smoking of .2 cigarettes daily for more than 6 months, and nonsmokers were defined as less than 100 cigarettes lifetime.",33,29,3 months,16S,12,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table3 + Table S7,10 January 2021,Rimsha Azhar,WikiWorks,Bacterial taxa that distinguish airway microbial communities of smokers from nonsmokers,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Aquitalea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Zoogloea",1783272|201174|1760|2037|2049|1654;1783272|1239|91061|186826|33958|1243;3379134|1224|1236|2887326|468|469;3379134|1224|28216|206351|1499392|407217;3379134|1224|1236|91347|543|620;3379134|1224|28216|206389|2008794|349,Complete,Shaimaa Elsafoury
bsdb:21188149/3/2,21188149,case-control,21188149,10.1371/journal.pone.0015216,NA,"Charlson E.S., Chen J., Custers-Allen R., Bittinger K., Li H., Sinha R., Hwang J., Bushman F.D. , Collman R.G.",Disordered microbial communities in the upper respiratory tract of cigarette smokers,PloS one,2010,NA,Experiment 3,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,Smoking behavior,EFO:0004318,right nasopharynx of nonsmokers,right nasopharynx of smokers,"Smokers were defined as current smoking of .2 cigarettes daily for more than 6 months, and nonsmokers were defined as less than 100 cigarettes lifetime.",33,29,3 months,16S,12,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table3 + Table S8,10 January 2021,Rimsha Azhar,WikiWorks,Bacterial taxa that distinguish airway microbial communities of smokers from nonsmokers,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum",1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|186806|1730;1783272|1239|91061|186826|186827|46123;1783272|1239|526524|526525|128827|174708;1783272|1239|186801|3082720|543314|109326;1783272|1239|186801|3085636|186803|33042;1783272|1239|526524|526525|128827;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|91061|1385|539738|1378;1783272|1239|186801|3085636|186803;1783272|1239|186801|3082720|186804;1783272|1239|186801|186802|541000;1783272|1239|186801|3085636|186803|84036;1783272|1239|186801|186802|216572|52784,Complete,Shaimaa Elsafoury
bsdb:21188149/4/1,21188149,case-control,21188149,10.1371/journal.pone.0015216,NA,"Charlson E.S., Chen J., Custers-Allen R., Bittinger K., Li H., Sinha R., Hwang J., Bushman F.D. , Collman R.G.",Disordered microbial communities in the upper respiratory tract of cigarette smokers,PloS one,2010,NA,Experiment 4,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,Smoking behavior,EFO:0004318,left nasopharynx of nonsmokers,left nasopharynx of smokers,"Smokers were defined as current smoking of .2 cigarettes daily for more than 6 months, and nonsmokers were defined as less than 100 cigarettes lifetime.",33,29,3 months,16S,12,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table3 + Table S9,10 January 2021,Shaimaa Elsafoury,WikiWorks,Bacterial taxa that distinguish airway microbial communities of smokers from nonsmokers,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|976|117743|200644|49546|237;1783272|1239|526524|526525|128827|1647;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|91347|543|620;3379134|1224|28216|80840|995019|40544,Complete,Shaimaa Elsafoury
bsdb:21188149/4/2,21188149,case-control,21188149,10.1371/journal.pone.0015216,NA,"Charlson E.S., Chen J., Custers-Allen R., Bittinger K., Li H., Sinha R., Hwang J., Bushman F.D. , Collman R.G.",Disordered microbial communities in the upper respiratory tract of cigarette smokers,PloS one,2010,NA,Experiment 4,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,Smoking behavior,EFO:0004318,left nasopharynx of nonsmokers,left nasopharynx of smokers,"Smokers were defined as current smoking of .2 cigarettes daily for more than 6 months, and nonsmokers were defined as less than 100 cigarettes lifetime.",33,29,3 months,16S,12,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table3 + Table S10,10 January 2021,Shaimaa Elsafoury,WikiWorks,Bacterial taxa that distinguish airway microbial communities of smokers from nonsmokers,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",1783272|201174|84998|1643822|1643826|84111;3379134|976|200643|171549|171551|836;1783272|1239|91061|186826|186827|46123;1783272|1239|186801|186802|216572|52784;1783272|1239|186801|3082720|543314|109326;1783272|1239|186801|3085636|186803|189330;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|541000;1783272|1239|186801|3085636|186803|84036;3379134|29547|3031852|213849|72294|194;3379134|1224|1236|135625|712|724;3379134|1224|1236|135614|32033|40323,Complete,Shaimaa Elsafoury
bsdb:21737778/1/1,21737778,case-control,21737778,https://doi.org/10.1152%2Fajpgi.00154.2011,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3220325/,"Carroll I.M., Ringel-Kulka T., Keku T.O., Chang Y.H., Packey C.D., Sartor R.B. , Ringel Y.",Molecular analysis of the luminal- and mucosal-associated intestinal microbiota in diarrhea-predominant irritable bowel syndrome,American journal of physiology. Gastrointestinal and liver physiology,2011,NA,Experiment 1,United States of America,Homo sapiens,"Feces,Colonic mucosa","UBERON:0001988,UBERON:0000317",Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-D,Individual who have been diagnosed with diarrhea-predominant Irritable bowel syndrome(IBS-D),21,16,2 months,PCR,NA,Non-quantitative PCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Table 2, Table 3.",28 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","Percent contribution of predominant T-RFs in fecal and mucosal samples from healthy controls and D-IBS patients. 

Values are means ± SE of normalized terminal-restriction fragment (T-RF) peak abundance from top 90% of contributors (predominant contributors) within each group. Predicted bacterial group refers to bacterial phylum, class, order, or family assigned to a T-RF based on the resolution of the Microbial Community Analysis (MiCA) database (41). NBG, numerous bacterial groups (i.e., MiCA database provided a large number of bacterial groups for this T-RF that are too numerous to list); NC, no contribution (i.e., T-RF does not contribute to the top 90% of T-RFs in a sample). Underlined bacterial groups are those consistently identified by T-RFs generated from 3 restriction enzymes (Hha I, Hae III, and Msp I) that contributed 90% of microbiota in healthy controls but not D-IBS patients. Significantly different from % contribution in healthy controls:

Table 3.
Hae III- and Msp I-generated T-RFs that contribute to 90% of the fecal microbiota in healthy controls but not D-IBS patients",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Planctomycetales|f__Planctomycetaceae",1783272|1239|186801|186802|1898207;3379134|203682|203683|112|126,Complete,Peace Sandy
bsdb:21741921/1/1,21741921,case-control,21741921,10.1053/j.gastro.2011.06.072,NA,"Saulnier D.M., Riehle K., Mistretta T.A., Diaz M.A., Mandal D., Raza S., Weidler E.M., Qin X., Coarfa C., Milosavljevic A., Petrosino J.F., Highlander S., Gibbs R., Lynch S.V., Shulman R.J. , Versalovic J.",Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome,Gastroenterology,2011,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS,Children ages 7-12 who met the Pediatric Rome III criteria for IBS (Table 1). Subtyping of IBS was based on previous recommendations for IBS in adults because no Pediatric Rome subtype criteria exist for children.,27,28,6 months,16S,123,PhyloChip,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 2; Supplementary Table 1A,8 July 2021,Kwekuamoo,"Kwekuamoo,Claregrieve1,WikiWorks",Differential microbial abundance between IBS patients and controls,increased,"k__Pseudomonadati|p__Acidobacteriota|c__Terriglobia|o__Terriglobales|f__Acidobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Cellulomonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales|f__Desulfobacteraceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Nitrospirota|c__Nitrospiria|o__Nitrospirales|f__Nitrospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Myxococcota|o__Polyangiales|f__Polyangiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Syntrophobacteria|o__Syntrophobacterales|f__Syntrophobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Thiotrichaceae",3379134|57723|204432|204433|204434;3379134|1224|1236|135624|84642;3379134|1224|1236|135622|72275;1783272|1239|91061|1385|186817;1783272|201174|1760|85006|85016;1783272|1239|186801|186802|31979;3379134|1224|1236|118969|118968;3379134|200940|3024418|213118|213119;3379134|200940|3031449|213115|194924;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|186806;1783272|1239|186801|3085636|186803;3379134|40117|203693|189778|189779;3379134|1224|1236|135625|712;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3082720|186804;3379134|2818505|3031712|49;3379134|976|200643|171549|171552;1783272|201174|1760|85006|85017;1783272|1239|91061|186826|1300;3379134|200940|3024408|213462|213465;3379134|1224|1236|72273|135617,Complete,Claregrieve1
bsdb:21741921/1/2,21741921,case-control,21741921,10.1053/j.gastro.2011.06.072,NA,"Saulnier D.M., Riehle K., Mistretta T.A., Diaz M.A., Mandal D., Raza S., Weidler E.M., Qin X., Coarfa C., Milosavljevic A., Petrosino J.F., Highlander S., Gibbs R., Lynch S.V., Shulman R.J. , Versalovic J.",Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome,Gastroenterology,2011,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS,Children ages 7-12 who met the Pediatric Rome III criteria for IBS (Table 1). Subtyping of IBS was based on previous recommendations for IBS in adults because no Pediatric Rome subtype criteria exist for children.,27,28,6 months,16S,123,PhyloChip,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Figure 2; Supplementary Table 1B,8 July 2021,Kwekuamoo,"Kwekuamoo,Claregrieve1,WikiWorks",Differential microbial abundance between IBS patients and controls,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Cellulomonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus",3379134|976|200643|171549|815;1783272|201174|1760|85006|85016;1783272|1239|186801|3085636|186803;1783272|1239|91061|1385|186822;3379134|976|200643|171549|171551;1783272|1239|91061|186826|1300;3379134|976;3379134|976|200643|171549|815|909656|821,Complete,Claregrieve1
bsdb:21820992/1/1,21820992,"case-control,prospective cohort",21820992,10.1053/j.gastro.2011.07.043,NA,"Rajilić-Stojanović M., Biagi E., Heilig H.G., Kajander K., Kekkonen R.A., Tims S. , de Vos W.M.",Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome,Gastroenterology,2011,NA,Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-A,IBS patients fulfilled the Rome II criteria. Alternating IBS (IBS-A),46,19,NA,16S,NA,Human Intestinal Tract Chip,NA,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1.,15 July 2021,Kwekuamoo,"Kwekuamoo,WikiWorks","Differences Between Intestinal Microbiota in Healthy and IBS.
NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171552|1283313|76122;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|329854;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|816|820;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|2005525|195950,Complete,Lwaldron
bsdb:21820992/1/2,21820992,"case-control,prospective cohort",21820992,10.1053/j.gastro.2011.07.043,NA,"Rajilić-Stojanović M., Biagi E., Heilig H.G., Kajander K., Kekkonen R.A., Tims S. , de Vos W.M.",Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome,Gastroenterology,2011,NA,Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-A,IBS patients fulfilled the Rome II criteria. Alternating IBS (IBS-A),46,19,NA,16S,NA,Human Intestinal Tract Chip,NA,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1.,15 July 2021,Kwekuamoo,"Kwekuamoo,WikiWorks","Differences Between Intestinal Microbiota in Healthy and IBS.
NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora sphenoides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus intermedius,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas nexilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacillati|p__Bacillota|c__Clostridia|s__uncultured Clostridia bacterium",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|186801|3085636|186803|33042|33043;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|2719231|29370;1783272|1239|186801|3085636|186803|248744;1783272|1239|186801|186802|216572|100175;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|91061|186826|1300|1301|1338;1783272|1239|186801|3085636|186803|2005355|29361;1783272|1239|186801|3085636|186803|2941495|1512;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|186803|2316020|46228;1783272|1239|186801|244328,Complete,Lwaldron
bsdb:21820992/2/1,21820992,"case-control,prospective cohort",21820992,10.1053/j.gastro.2011.07.043,NA,"Rajilić-Stojanović M., Biagi E., Heilig H.G., Kajander K., Kekkonen R.A., Tims S. , de Vos W.M.",Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome,Gastroenterology,2011,NA,Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-C,IBS patients fulfilled the Rome II criteria. Constipation-predominant IBS (IBS-C),46,18,NA,16S,NA,Human Intestinal Tract Chip,NA,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1.,15 July 2021,Kwekuamoo,"Kwekuamoo,WikiWorks",Differences Between Intestinal Microbiota in Healthy and IBS. NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella oralis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter ruminicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Bacteroidota|s__uncultured Bacteroidota bacterium",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171552|1283313|76122;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|329854;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|171552|2974257|28134;3379134|976|200643|171549|171552|558436|839;3379134|976|200643|171549|2005525|195950;3379134|976|152509,Complete,Lwaldron
bsdb:21820992/2/2,21820992,"case-control,prospective cohort",21820992,10.1053/j.gastro.2011.07.043,NA,"Rajilić-Stojanović M., Biagi E., Heilig H.G., Kajander K., Kekkonen R.A., Tims S. , de Vos W.M.",Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome,Gastroenterology,2011,NA,Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-C,IBS patients fulfilled the Rome II criteria. Constipation-predominant IBS (IBS-C),46,18,NA,16S,NA,Human Intestinal Tract Chip,NA,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1.,15 July 2021,Kwekuamoo,"Kwekuamoo,WikiWorks",Differences Between Intestinal Microbiota in Healthy and IBS. NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Aneurinibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas nexilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] cellulosi,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",1783272|1239|186801|186802|216572|244127;1783272|1239|186801|3082720|543314|109326;1783272|1239|91061|1385|186822|55079;1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|186801|3085636|186803|33042|33043;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|248744;1783272|1239|186801|186802|216572|100175;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|3085636|186803|2005355|29361;1783272|1239|186801|186802|216572|29343;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|3085636|186803|2941495|1512;1783272|1239|186801|3085636|186803|2316020|33038,Complete,Lwaldron
bsdb:21820992/3/1,21820992,"case-control,prospective cohort",21820992,10.1053/j.gastro.2011.07.043,NA,"Rajilić-Stojanović M., Biagi E., Heilig H.G., Kajander K., Kekkonen R.A., Tims S. , de Vos W.M.",Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome,Gastroenterology,2011,NA,Experiment 3,Finland,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-D,IBS patients fulfilled the Rome II criteria. Diarrhea-predominant IBS (IBS-D),46,25,NA,16S,NA,Human Intestinal Tract Chip,NA,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1.,15 July 2021,Kwekuamoo,"Kwekuamoo,WikiWorks",Differences Between Intestinal Microbiota in Healthy and IBS. NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella oralis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",3379134|976|200643|171549|171552|1283313|76122;3379134|976|200643|171549|815|816|329854;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|171552|2974257|28134;3379134|976|200643|171549|2005525|195950,Complete,Lwaldron
bsdb:21820992/3/2,21820992,"case-control,prospective cohort",21820992,10.1053/j.gastro.2011.07.043,NA,"Rajilić-Stojanović M., Biagi E., Heilig H.G., Kajander K., Kekkonen R.A., Tims S. , de Vos W.M.",Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome,Gastroenterology,2011,NA,Experiment 3,Finland,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-D,IBS patients fulfilled the Rome II criteria. Diarrhea-predominant IBS (IBS-D),46,25,NA,16S,NA,Human Intestinal Tract Chip,NA,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1.,15 July 2021,Kwekuamoo,"Kwekuamoo,WikiWorks",Differences Between Intestinal Microbiota in Healthy and IBS. NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas nexilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris",1783272|1239|186801|3085636|186803|830;1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|2005355|29361;1783272|1239|186801|3085636|186803|2941495|1512;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|186803|2316020|46228,Complete,Lwaldron
bsdb:21820992/4/1,21820992,"case-control,prospective cohort",21820992,10.1053/j.gastro.2011.07.043,NA,"Rajilić-Stojanović M., Biagi E., Heilig H.G., Kajander K., Kekkonen R.A., Tims S. , de Vos W.M.",Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome,Gastroenterology,2011,NA,Experiment 4,Finland,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS (All patients),IBS patients fulfilled the Rome II criteria. All IBS patients.,46,62,NA,16S,NA,Human Intestinal Tract Chip,NA,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1.,15 July 2021,Kwekuamoo,"Kwekuamoo,WikiWorks",Differences Between Intestinal Microbiota in Healthy and IBS. NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella oralis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter ruminicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Bacteroidota|s__uncultured Bacteroidota bacterium,k__Bacillati|p__Bacillota|c__Clostridia|s__uncultured Clostridia bacterium",1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|329854;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|46506;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|2974257|28134;3379134|976|200643|171549|171552|558436|839;3379134|976|200643|171549|171552|1283313|76122;3379134|976|200643|171549|2005525|195950;3379134|976|152509;1783272|1239|186801|244328,Complete,Lwaldron
bsdb:21820992/4/2,21820992,"case-control,prospective cohort",21820992,10.1053/j.gastro.2011.07.043,NA,"Rajilić-Stojanović M., Biagi E., Heilig H.G., Kajander K., Kekkonen R.A., Tims S. , de Vos W.M.",Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome,Gastroenterology,2011,NA,Experiment 4,Finland,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS (All patients),IBS patients fulfilled the Rome II criteria. All IBS patients.,46,62,NA,16S,NA,Human Intestinal Tract Chip,NA,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1.,15 July 2021,Kwekuamoo,"Kwekuamoo,WikiWorks",Differences Between Intestinal Microbiota in Healthy and IBS. NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Aneurinibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus intermedius,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas nexilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris",1783272|1239|91061|1385|186822|55079;1783272|1239|91061|186826|1300|1301|1338;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|186802|216572|100175;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3082720|543314|109326;1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|248744;1783272|1239|186801|3085636|186803|2005355|29361;1783272|1239|186801|3085636|186803|2941495|1512;1783272|1239|186801|3085636|186803|33042|33043;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|186803|2316020|46228,Complete,Lwaldron
bsdb:21829158/1/1,21829158,case-control,21829158,10.1038/ijo.2011.153,NA,"Million M., Maraninchi M., Henry M., Armougom F., Richet H., Carrieri P., Valero R., Raccah D., Vialettes B. , Raoult D.",Obesity-associated gut microbiota is enriched in Lactobacillus reuteri and depleted in Bifidobacterium animalis and Methanobrevibacter smithii,International journal of obesity (2005),2012,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean controls,obese,"Obese patients, as defined by a BMI>=30 kg/m2",47,68,1 month,16S,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,"Text & Tables 2, 3, 4 & 5",10 January 2021,Marianthi Thomatos,WikiWorks,Gut alterations of Lactobacillus or bifidobacterium species between obese and controls,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Shaimaa Elsafoury
bsdb:21829158/1/2,21829158,case-control,21829158,10.1038/ijo.2011.153,NA,"Million M., Maraninchi M., Henry M., Armougom F., Richet H., Carrieri P., Valero R., Raccah D., Vialettes B. , Raoult D.",Obesity-associated gut microbiota is enriched in Lactobacillus reuteri and depleted in Bifidobacterium animalis and Methanobrevibacter smithii,International journal of obesity (2005),2012,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean controls,obese,"Obese patients, as defined by a BMI>=30 kg/m2",47,68,1 month,16S,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 2,"Text & Tables 2, 3, 4 & 5",10 January 2021,Marianthi Thomatos,WikiWorks,Gut alterations of Lactobacillus or bifidobacterium species between obese and controls,decreased,"k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus paracasei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus|s__Lactiplantibacillus plantarum",3366610|28890|183925|2158|2159|2172|2173;1783272|201174|1760|85004|31953|1678|28025;1783272|1239|91061|186826|33958|2759736|1597;1783272|1239|91061|186826|33958|2767842|1590,Complete,Shaimaa Elsafoury
bsdb:21850056/1/1,21850056,case-control,21850056,10.1038/ismej.2011.109,NA,"Wang T., Cai G., Qiu Y., Fei N., Zhang M., Pang X., Jia W., Cai S. , Zhao L.",Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers,The ISME journal,2012,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy controls,Colrectal cancer patients,All patients were categorized according to histopathological features by TNM classification of malignant tumors after surgery,56,46,3 months,16S,3,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,List of genera that were significantly different between Healthy controls and Colorectal cancer patients,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus",3379134|976|200643|171549|171551|836;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|620;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3082720|186804|1257,Complete,Shaimaa Elsafoury
bsdb:21850056/1/2,21850056,case-control,21850056,10.1038/ismej.2011.109,NA,"Wang T., Cai G., Qiu Y., Fei N., Zhang M., Pang X., Jia W., Cai S. , Zhao L.",Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers,The ISME journal,2012,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy controls,Colrectal cancer patients,All patients were categorized according to histopathological features by TNM classification of malignant tumors after surgery,56,46,3 months,16S,3,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,List of genera that were significantly different between Healthy controls and Colorectal cancer patients,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|841;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|186806|1730;3379134|1224|28216|80840|995019|577310,Complete,Shaimaa Elsafoury
bsdb:21885731/1/1,21885731,"cross-sectional observational, not case-control",21885731,10.1126/science.1208344,NA,"Wu G.D., Chen J., Hoffmann C., Bittinger K., Chen Y.Y., Keilbaugh S.A., Bewtra M., Knights D., Walters W.A., Knight R., Sinha R., Gilroy E., Gupta K., Baldassano R., Nessel L., Li H., Bushman F.D. , Lewis J.D.",Linking long-term dietary patterns with gut microbial enterotypes,"Science (New York, N.Y.)",2011,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,low animal protein,High animal protein,high protein / low fiber,98,98,6 months,16S,12,Roche454,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2C and text,10 January 2021,Lora Kasselman,WikiWorks,"The association of dietary components with each enterotype. The strength and direction of each association, as measured by the means of the standardized nutrient measurements, is shown by the color key at the lower right. Enterotype is shown at the right. Red indicates greater amounts, blue lesser amounts of each nutrient in each enterotype (complete lists of nutrients are in table S2). Columns were clustered by Euclidean distance.",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,NA
bsdb:21885731/1/2,21885731,"cross-sectional observational, not case-control",21885731,10.1126/science.1208344,NA,"Wu G.D., Chen J., Hoffmann C., Bittinger K., Chen Y.Y., Keilbaugh S.A., Bewtra M., Knights D., Walters W.A., Knight R., Sinha R., Gilroy E., Gupta K., Baldassano R., Nessel L., Li H., Bushman F.D. , Lewis J.D.",Linking long-term dietary patterns with gut microbial enterotypes,"Science (New York, N.Y.)",2011,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,low animal protein,High animal protein,high protein / low fiber,98,98,6 months,16S,12,Roche454,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2C and text,10 January 2021,Lora Kasselman,WikiWorks,"The association of dietary components with each enterotype. The strength and direction of each association, as measured by the means of the standardized nutrient measurements, is shown by the color key at the lower right. Enterotype is shown at the right. Red indicates greater amounts, blue lesser amounts of each nutrient in each enterotype (complete lists of nutrients are in table S2). Columns were clustered by Euclidean distance.",decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,3379134|976|200643|171549|171552,Complete,NA
bsdb:21885731/2/1,21885731,"cross-sectional observational, not case-control",21885731,10.1126/science.1208344,NA,"Wu G.D., Chen J., Hoffmann C., Bittinger K., Chen Y.Y., Keilbaugh S.A., Bewtra M., Knights D., Walters W.A., Knight R., Sinha R., Gilroy E., Gupta K., Baldassano R., Nessel L., Li H., Bushman F.D. , Lewis J.D.",Linking long-term dietary patterns with gut microbial enterotypes,"Science (New York, N.Y.)",2011,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,high fiber,Low fiber,high protein / low fiber,98,98,6 months,16S,12,Roche454,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2C and text,10 January 2021,Lora Kasselman,WikiWorks,"The association of dietary components with each enterotype. The strength and direction of each association, as measured by the means of the standardized nutrient measurements, is shown by the color key at the lower right. Enterotype is shown at the right. Red indicates greater amounts, blue lesser amounts of each nutrient in each enterotype (complete lists of nutrients are in table S2). Columns were clustered by Euclidean distance.",increased,"k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota",3379134|976;1783272|201174,Complete,NA
bsdb:21885731/2/2,21885731,"cross-sectional observational, not case-control",21885731,10.1126/science.1208344,NA,"Wu G.D., Chen J., Hoffmann C., Bittinger K., Chen Y.Y., Keilbaugh S.A., Bewtra M., Knights D., Walters W.A., Knight R., Sinha R., Gilroy E., Gupta K., Baldassano R., Nessel L., Li H., Bushman F.D. , Lewis J.D.",Linking long-term dietary patterns with gut microbial enterotypes,"Science (New York, N.Y.)",2011,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,high fiber,Low fiber,high protein / low fiber,98,98,6 months,16S,12,Roche454,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2C and text,10 January 2021,Lora Kasselman,WikiWorks,"The association of dietary components with each enterotype. The strength and direction of each association, as measured by the means of the standardized nutrient measurements, is shown by the color key at the lower right. Enterotype is shown at the right. Red indicates greater amounts, blue lesser amounts of each nutrient in each enterotype (complete lists of nutrients are in table S2). Columns were clustered by Euclidean distance.",decreased,k__Bacillati|p__Actinomycetota,1783272|201174,Complete,NA
bsdb:21957459/1/1,21957459,time series / longitudinal observational,21957459,10.1371/journal.pone.0024767,NA,"Wang Y., Gilbreath T.M., Kukutla P., Yan G. , Xu J.",Dynamic gut microbiome across life history of the malaria mosquito Anopheles gambiae in Kenya,PloS one,2011,NA,Experiment 1,Kenya,Anopheles gambiae,"Instar larval stage,Pupa","UBERON:0004730,UBERON:0003143",Sampling site,EFO:0000688,Pupal (Triplicates),Newly emerged adult guts,"1-day-old adult, no feeding (triplicates)",9,6,NA,16S,123,Roche454,raw counts,Metastats,0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,Table S5,20 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","Differentially abundant families between pupal and newly emerged adult guts

The differential abundant taxa between collections were detected with Metastats",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae",3379134|1224|1236|91347|543;1783272|201174|1760|85009|31957,Complete,Peace Sandy
bsdb:21957459/1/2,21957459,time series / longitudinal observational,21957459,10.1371/journal.pone.0024767,NA,"Wang Y., Gilbreath T.M., Kukutla P., Yan G. , Xu J.",Dynamic gut microbiome across life history of the malaria mosquito Anopheles gambiae in Kenya,PloS one,2011,NA,Experiment 1,Kenya,Anopheles gambiae,"Instar larval stage,Pupa","UBERON:0004730,UBERON:0003143",Sampling site,EFO:0000688,Pupal (Triplicates),Newly emerged adult guts,"1-day-old adult, no feeding (triplicates)",9,6,NA,16S,123,Roche454,raw counts,Metastats,0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,Table S5,20 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","Differentially abundant families between pupal and newly emerged adult guts 

The differential abundant taxa between collections were detected with Metastats",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae",3379134|1224|28216|80840|80864;3379134|1224|28211|204457|335929;3379134|1224|28211|204455|31989;3379134|1224|1236|135624|84642;3379134|1224|1236|135614|1775411,Complete,Peace Sandy
bsdb:21957459/2/1,21957459,time series / longitudinal observational,21957459,10.1371/journal.pone.0024767,NA,"Wang Y., Gilbreath T.M., Kukutla P., Yan G. , Xu J.",Dynamic gut microbiome across life history of the malaria mosquito Anopheles gambiae in Kenya,PloS one,2011,NA,Experiment 2,Kenya,Anopheles gambiae,"Instar larval stage,Pupa","UBERON:0004730,UBERON:0003143",Response to diet,EFO:0010757,"Sugar fed mosquito - 3-day-old,sugar (triplicates)",Blood fed mosquito - 2 days post blood meal (triplicates),Blood-fed mosquito at different time points,6,6,NA,16S,123,Roche454,raw counts,Metastats,0.05,FALSE,NA,NA,NA,NA,NA,increased,NA,NA,increased,Signature 1,Table S7 and Table S6,20 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","Differentially abundant genera before and after a blood meal

Differentially abundant families before and after a blood meal",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Elizabethkingia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae",3379134|1224|1236|91347|543|547;3379134|976|117743|200644|2762318|308865;3379134|1224|1236|91347|543;3379134|1224|1236|135624|84642;3379134|1224|1236|72274|135621,Complete,Peace Sandy
bsdb:21957459/2/2,21957459,time series / longitudinal observational,21957459,10.1371/journal.pone.0024767,NA,"Wang Y., Gilbreath T.M., Kukutla P., Yan G. , Xu J.",Dynamic gut microbiome across life history of the malaria mosquito Anopheles gambiae in Kenya,PloS one,2011,NA,Experiment 2,Kenya,Anopheles gambiae,"Instar larval stage,Pupa","UBERON:0004730,UBERON:0003143",Response to diet,EFO:0010757,"Sugar fed mosquito - 3-day-old,sugar (triplicates)",Blood fed mosquito - 2 days post blood meal (triplicates),Blood-fed mosquito at different time points,6,6,NA,16S,123,Roche454,raw counts,Metastats,0.05,FALSE,NA,NA,NA,NA,NA,increased,NA,NA,increased,Signature 2,Table S7 and Table S6,20 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","Differentially abundant genera before and after a blood meal

Differentially abundant families before and after a blood meal",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae",3379134|1224|28216|80840|80864;3379134|976|117743|200644|49546;3379134|1224|1236|2887326|468;1783272|201174|1760|85009|31957;3379134|1224|1236|91347|543|160674;3379134|1224|28211|204457|41297;3379134|1224|1236|135614|32033,Complete,Peace Sandy
bsdb:22009990/1/1,22009990,"cross-sectional observational, not case-control",22009990,10.1101/gr.126573.111,NA,"Kostic A.D., Gevers D., Pedamallu C.S., Michaud M., Duke F., Earl A.M., Ojesina A.I., Jung J., Bass A.J., Tabernero J., Baselga J., Liu C., Shivdasani R.A., Ogino S., Birren B.W., Huttenhower C., Garrett W.S. , Meyerson M.",Genomic analysis identifies association of Fusobacterium with colorectal carcinoma,Genome research,2012,NA,Experiment 1,Spain,Homo sapiens,Colon,UBERON:0001155,Colorectal carcinoma,EFO:1001951,Adjacent normal colonic tissue,Colon Tumor,Tumor tissues with colorectal carcinoma,9,9,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,1.8,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 1C,8 April 2024,MyleeeA,"MyleeeA,WikiWorks","Linear discriminant analysis (LDA) coupled with effect size measurements identifies Fusobacterium as the most differentially abundant taxon in colon tumor versus normal specimens by whole-genome sequencing in nine individuals. Tumor-enriched taxa are indicated with a positive LDA score (black), and taxa enriched in normal tissue have a negative score (gray).",increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter aphrophilus",3384189|32066|203490|203491|203492;3384189|32066|203490|203491|203492|848|851;1783272|1239|91061|186826|1300;3379134|1224|1236|135625|712|416916;3379134|1224|1236|135625|712|416916|732,Complete,Svetlana up
bsdb:22009990/1/2,22009990,"cross-sectional observational, not case-control",22009990,10.1101/gr.126573.111,NA,"Kostic A.D., Gevers D., Pedamallu C.S., Michaud M., Duke F., Earl A.M., Ojesina A.I., Jung J., Bass A.J., Tabernero J., Baselga J., Liu C., Shivdasani R.A., Ogino S., Birren B.W., Huttenhower C., Garrett W.S. , Meyerson M.",Genomic analysis identifies association of Fusobacterium with colorectal carcinoma,Genome research,2012,NA,Experiment 1,Spain,Homo sapiens,Colon,UBERON:0001155,Colorectal carcinoma,EFO:1001951,Adjacent normal colonic tissue,Colon Tumor,Tumor tissues with colorectal carcinoma,9,9,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,1.8,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 1C,8 April 2024,MyleeeA,"MyleeeA,WikiWorks","Linear discriminant analysis (LDA) coupled with effect size measurements identifies Fusobacterium as the most differentially abundant taxon in colon tumor versus normal specimens by whole-genome sequencing in nine individuals. Tumor-enriched taxa are indicated with a positive LDA score (black), and taxa enriched in normal tissue have a negative score (gray).",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter sp.",3379134|1224|1236|91347|543|547|550;3379134|1224|1236|91347|543|547;3379134|1224|1236|2887326|468|469|470;3379134|1224|1236|2887326|468|469;3379134|1224|1236|2887326|468|469|472,Complete,Svetlana up
bsdb:22009990/2/1,22009990,"cross-sectional observational, not case-control",22009990,10.1101/gr.126573.111,NA,"Kostic A.D., Gevers D., Pedamallu C.S., Michaud M., Duke F., Earl A.M., Ojesina A.I., Jung J., Bass A.J., Tabernero J., Baselga J., Liu C., Shivdasani R.A., Ogino S., Birren B.W., Huttenhower C., Garrett W.S. , Meyerson M.",Genomic analysis identifies association of Fusobacterium with colorectal carcinoma,Genome research,2012,NA,Experiment 2,Spain,Homo sapiens,Colon,UBERON:0001155,Colorectal carcinoma,EFO:1001951,Adjacent normal colonic tissue,Colon Tumor,Tumor tissues with colorectal carcinoma,95,95,NA,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,4.2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 2C,8 April 2024,MyleeeA,"MyleeeA,WikiWorks","Linear discriminant analysis (LDA) coupled with effect size measurements identifies Fusobacterium as the most differentially abundant taxon in colon tumor versus normal specimens by 16S rDNA sequencing in 95 individuals. Tumor-enriched taxa are indicated with a positive LDA score (black), and taxa enriched in normal tissue have a negative score (gray).",increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia",3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490|203491|203492|848;3384189|32066|203490,Complete,Svetlana up
bsdb:22009990/2/2,22009990,"cross-sectional observational, not case-control",22009990,10.1101/gr.126573.111,NA,"Kostic A.D., Gevers D., Pedamallu C.S., Michaud M., Duke F., Earl A.M., Ojesina A.I., Jung J., Bass A.J., Tabernero J., Baselga J., Liu C., Shivdasani R.A., Ogino S., Birren B.W., Huttenhower C., Garrett W.S. , Meyerson M.",Genomic analysis identifies association of Fusobacterium with colorectal carcinoma,Genome research,2012,NA,Experiment 2,Spain,Homo sapiens,Colon,UBERON:0001155,Colorectal carcinoma,EFO:1001951,Adjacent normal colonic tissue,Colon Tumor,Tumor tissues with colorectal carcinoma,95,95,NA,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,4.2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 2C,8 April 2024,MyleeeA,"MyleeeA,WikiWorks","Linear discriminant analysis (LDA) coupled with effect size measurements identifies Fusobacterium as the most differentially abundant taxon in colon tumor versus normal specimens by 16S rDNA sequencing in 95 individuals. Tumor-enriched taxa are indicated with a positive LDA score (black), and taxa enriched in normal tissue have a negative score (gray).",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota",1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815;1783272|1239|186801|186802|216572;3379134|976|200643;3379134|976|200643|171549;1783272|1239|186801|186802;1783272|1239|186801;1783272|1239,Complete,Svetlana up
bsdb:22153774/1/1,22153774,prospective cohort,22153774,10.1016/j.jaci.2011.10.025,NA,"Abrahamsson T.R., Jakobsson H.E., Andersson A.F., Björkstén B., Engstrand L. , Jenmalm M.C.",Low diversity of the gut microbiota in infants with atopic eczema,The Journal of allergy and clinical immunology,2012,NA,Experiment 1,Sweden,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy infant,infant with atopic eczema,infant with atopic eczema- at 12 months,20,20,NA,16S,34,Roche454,relative abundances,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,Lucy Mellor,"WikiWorks,ChiomaBlessing",Relative abundance of dominant taxa in stool samples obtained at 12 months from infants with atopic eczema compared to infants without atopic eczema during the first 2 years of life,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",1783272|1239|91061|186826|81852|1350;1783272|1239|186801|3082720|186804,Complete,ChiomaBlessing
bsdb:22153774/1/2,22153774,prospective cohort,22153774,10.1016/j.jaci.2011.10.025,NA,"Abrahamsson T.R., Jakobsson H.E., Andersson A.F., Björkstén B., Engstrand L. , Jenmalm M.C.",Low diversity of the gut microbiota in infants with atopic eczema,The Journal of allergy and clinical immunology,2012,NA,Experiment 1,Sweden,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy infant,infant with atopic eczema,infant with atopic eczema- at 12 months,20,20,NA,16S,34,Roche454,relative abundances,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 3,10 January 2021,Lucy Mellor,"WikiWorks,ChiomaBlessing",Relative abundance of dominant taxa in stool samples obtained at 12 months from infants with atopic eczema compared to infants without atopic eczema during the first 2 years of life,decreased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,ChiomaBlessing
bsdb:22153774/2/1,22153774,prospective cohort,22153774,10.1016/j.jaci.2011.10.025,NA,"Abrahamsson T.R., Jakobsson H.E., Andersson A.F., Björkstén B., Engstrand L. , Jenmalm M.C.",Low diversity of the gut microbiota in infants with atopic eczema,The Journal of allergy and clinical immunology,2012,NA,Experiment 2,Sweden,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy infant,infant with atopic eczema,infant with atopic eczema- at 1 month,20,20,NA,16S,34,Roche454,relative abundances,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 2,26 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Relative abundance of dominant taxa in stool samples obtained at 1 month from infants with atopic eczema compared to infants without atopic eczema during the first 2 years of life,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|976;3379134|976|200643|171549|815|816,Complete,ChiomaBlessing
bsdb:22170749/1/1,22170749,case-control,22170749,10.1002/ibd.22860,NA,"Michail S., Durbin M., Turner D., Griffiths A.M., Mack D.R., Hyams J., Leleiko N., Kenche H., Stolfi A. , Wine E.",Alterations in the gut microbiome of children with severe ulcerative colitis,Inflammatory bowel diseases,2012,NA,Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,healthy controls,children with ulcerative colitis,Children hospitalized for intravenous corticosteroid therapy for acute UC,26,27,1 month,16S,NA,RT-qPCR,relative abundances,T-Test,0.05,TRUE,NA,age,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Table 2,20 October 2022,Fatima,"Fatima,WikiWorks",Phylum and Class comparisons for healthy children and children with ulcerative colitis (UC).,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia,c__Deltaproteobacteria,k__Pseudomonadati|p__Campylobacterota,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota,k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Lentisphaerales|f__Lentisphaeraceae|g__Lentisphaera,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Spirochaetota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia",1783272|201174;1783272|201174|1760;3379134|1224|28211;1783272|1239|91061;3379134|976|200643;3379134|1224|28216;1783272|1239|186801;28221;3379134|29547;1783272|1239|526524;1783272|1239;3384189|32066;3379134|1224|1236;3379134|256845|1313211|278081|566277|256846;3379134|1224;3379134|203691;3379134|74201|203494;1783272|201174|84998,Complete,Fatima
bsdb:22180058/1/1,22180058,NA,22180058,10.1136/gutjnl-2011-301501,NA,"Jeffery I.B., O'Toole P.W., Öhman L., Claesson M.J., Deane J., Quigley E.M. , Simrén M.",An irritable bowel syndrome subtype defined by species-specific alterations in faecal microbiota,Gut,2012,NA,Experiment 1,Ireland,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS,Patients diagnosed with irritable bowel syndrome according to Rome II criteria.,22,37,Yes (recent antibiotic use excluded),16S,12,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"IBS vs Healthy Controls (Results section, differential abundance analysis)",8 January 2026,Aqc576444,Aqc576444,"IBS patients showed a significant decrease in butyrate-producing genera compared to healthy controls, including Faecalibacterium and Roseburia, indicating reduced fermentative capacity in IBS.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|841,Complete,NA
bsdb:22180058/1/2,22180058,NA,22180058,10.1136/gutjnl-2011-301501,NA,"Jeffery I.B., O'Toole P.W., Öhman L., Claesson M.J., Deane J., Quigley E.M. , Simrén M.",An irritable bowel syndrome subtype defined by species-specific alterations in faecal microbiota,Gut,2012,NA,Experiment 1,Ireland,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS,Patients diagnosed with irritable bowel syndrome according to Rome II criteria.,22,37,Yes (recent antibiotic use excluded),16S,12,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,IBS-D vs Healthy Controls,8 January 2026,Aqc576444,Aqc576444,"Patients with diarrhea predominant IBS (IBS-D) exhibited a significant increase in Enterobacteriaceae compared to healthy controls, consistent with a dysbiotic, inflammation-associated profile.",increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,NA
bsdb:22180058/1/3,22180058,NA,22180058,10.1136/gutjnl-2011-301501,NA,"Jeffery I.B., O'Toole P.W., Öhman L., Claesson M.J., Deane J., Quigley E.M. , Simrén M.",An irritable bowel syndrome subtype defined by species-specific alterations in faecal microbiota,Gut,2012,NA,Experiment 1,Ireland,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS,Patients diagnosed with irritable bowel syndrome according to Rome II criteria.,22,37,Yes (recent antibiotic use excluded),16S,12,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 3,IBS-C vs Healthy Controls,8 January 2026,Aqc576444,Aqc576444,"Constipation predominant IBS (IBS-C) patients showed a significant reduction in Bifidobacterium relative to healthy controls, suggesting altered carbohydrate fermentation in IBS-C.",decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,NA
bsdb:22228076/1/1,22228076,"cross-sectional observational, not case-control",22228076,10.1097/MPG.0b013e318249039c.,https://pubmed.ncbi.nlm.nih.gov/22228076/,"Grześkowiak Ł., Collado M.C., Mangani C., Maleta K., Laitinen K., Ashorn P., Isolauri E. , Salminen S.",Distinct gut microbiota in southeastern African and northern European infants,Journal of pediatric gastroenterology and nutrition,2012,NA,Experiment 1,"Finland,Malawi",Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,High-Income country (Finland),Low-income country (Malawi),44 healthy 6-month-old rural infants from Malawi,31,44,6 months,WMS,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,13 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1,WikiWorks",Differential microbial abundance between Finnish and Malawian infants,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|201174|1760|85004|31953|1678|1681;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678,Complete,Claregrieve1
bsdb:22228076/1/2,22228076,"cross-sectional observational, not case-control",22228076,10.1097/MPG.0b013e318249039c.,https://pubmed.ncbi.nlm.nih.gov/22228076/,"Grześkowiak Ł., Collado M.C., Mangani C., Maleta K., Laitinen K., Ashorn P., Isolauri E. , Salminen S.",Distinct gut microbiota in southeastern African and northern European infants,Journal of pediatric gastroenterology and nutrition,2012,NA,Experiment 1,"Finland,Malawi",Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,High-Income country (Finland),Low-income country (Malawi),44 healthy 6-month-old rural infants from Malawi,31,44,6 months,WMS,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,13 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1,WikiWorks",Differential microbial abundance between Finnish and Malawian infants,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum",3379134|74201|203494|48461|1647988|239934|239935;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|1686;1783272|1239|186801|3085636|186803|572511|1532;1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|186801|186802|31979|1485|1502;1783272|1239|91061|1385|90964|1279|1280;1783272|1239|186801|186802|216572|1535,Complete,Claregrieve1
bsdb:22315951/1/1,22315951,case-control,22315951,10.1111/j.1365-2036.2012.05007.x,NA,"Chassard C., Dapoigny M., Scott K.P., Crouzet L., Del'homme C., Marquet P., Martin J.C., Pickering G., Ardid D., Eschalier A., Dubray C., Flint H.J. , Bernalier-Donadille A.",Functional dysbiosis within the gut microbiota of patients with constipated-irritable bowel syndrome,Alimentary pharmacology & therapeutics,2012,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,constipated-IBS,"The 14 women IBS patients (age range: 36–59, mean age: 48) included in this study fulfilled the Rome II criteria for IBS. They were classified as IBS with constipation (C-IBS) by a questionnaire following the Rome II subgrouping criteria which have been recognized as valid also in the Rome III criteria.",12,14,2 months,16S,NA,NA,relative abundances,T-Test,0.05,FALSE,NA,sex,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1a, 1b",6 April 2022,Rimsha,"Rimsha,WikiWorks",FISH analysis of main bacterial taxonomic groups in faeces of healthy and IBS patients,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803|841,Complete,Rimsha
bsdb:22315951/1/2,22315951,case-control,22315951,10.1111/j.1365-2036.2012.05007.x,NA,"Chassard C., Dapoigny M., Scott K.P., Crouzet L., Del'homme C., Marquet P., Martin J.C., Pickering G., Ardid D., Eschalier A., Dubray C., Flint H.J. , Bernalier-Donadille A.",Functional dysbiosis within the gut microbiota of patients with constipated-irritable bowel syndrome,Alimentary pharmacology & therapeutics,2012,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,constipated-IBS,"The 14 women IBS patients (age range: 36–59, mean age: 48) included in this study fulfilled the Rome II criteria for IBS. They were classified as IBS with constipation (C-IBS) by a questionnaire following the Rome II subgrouping criteria which have been recognized as valid also in the Rome III criteria.",12,14,2 months,16S,NA,NA,relative abundances,T-Test,0.05,FALSE,NA,sex,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,6 April 2022,Rimsha,"Rimsha,WikiWorks",Comparison of the population levels of microbial communities involved in carbohydrate metabolism in faecel samples from healthy and C-IBS individials,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,Rimsha
bsdb:22315951/1/3,22315951,case-control,22315951,10.1111/j.1365-2036.2012.05007.x,NA,"Chassard C., Dapoigny M., Scott K.P., Crouzet L., Del'homme C., Marquet P., Martin J.C., Pickering G., Ardid D., Eschalier A., Dubray C., Flint H.J. , Bernalier-Donadille A.",Functional dysbiosis within the gut microbiota of patients with constipated-irritable bowel syndrome,Alimentary pharmacology & therapeutics,2012,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,constipated-IBS,"The 14 women IBS patients (age range: 36–59, mean age: 48) included in this study fulfilled the Rome II criteria for IBS. They were classified as IBS with constipation (C-IBS) by a questionnaire following the Rome II subgrouping criteria which have been recognized as valid also in the Rome III criteria.",12,14,2 months,16S,NA,NA,relative abundances,T-Test,0.05,FALSE,NA,sex,NA,NA,NA,NA,NA,NA,NA,Signature 3,Table 1,6 April 2022,Rimsha,"Rimsha,Lwaldron,WikiWorks",Comparison of the population levels of microbial communities involved in carbohydrate metabolism in faecel samples from healthy and C-IBS individials,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85004|31953|1678,Complete,Rimsha
bsdb:22339879/1/1,22339879,case-control,22339879,10.1111/j.1365-2982.2012.01891.x,NA,"Carroll I.M., Ringel-Kulka T., Siddle J.P. , Ringel Y.",Alterations in composition and diversity of the intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome,Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society,2012,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,healthy controls,diarrhea-predominant irritable bowel syndrome,Diarrhea-Predominant irritable bowel syndrome,23,23,2 months,16S,123,Roche454,raw counts,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Table 2,10 January 2021,Rimsha Azhar,WikiWorks,Bacterial taxa that differ between D-IBS patients and healthy controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",3379134|1224|1236|91347;3379134|1224|1236|91347|543,Complete,Atrayees
bsdb:22339879/1/2,22339879,case-control,22339879,10.1111/j.1365-2982.2012.01891.x,NA,"Carroll I.M., Ringel-Kulka T., Siddle J.P. , Ringel Y.",Alterations in composition and diversity of the intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome,Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society,2012,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,healthy controls,diarrhea-predominant irritable bowel syndrome,Diarrhea-Predominant irritable bowel syndrome,23,23,2 months,16S,123,Roche454,raw counts,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,Table 2,10 January 2021,Rimsha Azhar,WikiWorks,Bacterial taxa that differ between D-IBS patients and healthy controls,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,1783272|1239|186801|186802|216572|216851,Complete,Atrayees
bsdb:22339879/2/1,22339879,case-control,22339879,10.1111/j.1365-2982.2012.01891.x,NA,"Carroll I.M., Ringel-Kulka T., Siddle J.P. , Ringel Y.",Alterations in composition and diversity of the intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome,Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society,2012,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,healthy controls,diarrhea-predominant irritable bowel syndrome,Diarrhea-Predominant irritable bowel syndrome,23,23,2 months,16S,6,Roche454,NA,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Table 2,10 January 2021,Rimsha Azhar,WikiWorks,Bacterial taxa that differ between D-IBS patients and healthy controls,increased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens",3379134|1224;3379134|1224|1236;3379134|1224|1236|91347|543;1783272|1239|186801|186802|216572|253238,Complete,Atrayees
bsdb:22356587/1/1,22356587,case-control,22356587,10.1111/j.1365-2982.2012.01893.x,NA,"Duboc H., Rainteau D., Rajca S., Humbert L., Farabos D., Maubert M., Grondin V., Jouet P., Bouhassira D., Seksik P., Sokol H., Coffin B. , Sabaté J.M.",Increase in fecal primary bile acids and dysbiosis in patients with diarrhea-predominant irritable bowel syndrome,Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society,2012,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-D,The diagnosis of IBS-D was defined by the Rome 3 criteria,18,14,3 months,16S,NA,RT-qPCR,relative abundances,"Mann-Whitney (Wilcoxon),T-Test",0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,19 July 2021,Kwekuamoo,"Kwekuamoo,WikiWorks","Comparison of fecal counts (A) in all bacteria, Faecalibacterium prausnitzii, lactobacillus and bifidobacterium and (B) of the main fecal bacterial groups that transform bile acid (coccoides, bacteroides, Escherichia coli, and leptum) in feces of healthy subjects (white bar) and diarrhea predominant IBS patients (gray bar) by quantitative polymerase chain reaction. All results are expressed in log10 bacteria per gram of stool.",increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,3379134|1224|1236|91347|543|561|562,Complete,Atrayees
bsdb:22356587/1/2,22356587,case-control,22356587,10.1111/j.1365-2982.2012.01893.x,NA,"Duboc H., Rainteau D., Rajca S., Humbert L., Farabos D., Maubert M., Grondin V., Jouet P., Bouhassira D., Seksik P., Sokol H., Coffin B. , Sabaté J.M.",Increase in fecal primary bile acids and dysbiosis in patients with diarrhea-predominant irritable bowel syndrome,Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society,2012,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-D,The diagnosis of IBS-D was defined by the Rome 3 criteria,18,14,3 months,16S,NA,RT-qPCR,relative abundances,"Mann-Whitney (Wilcoxon),T-Test",0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,19 July 2021,Kwekuamoo,"Kwekuamoo,Aiyshaaaa,WikiWorks","Comparison of fecal counts (A) in all bacteria, Faecalibacterium prausnitzii, lactobacillus and bifidobacterium and (B) of the main fecal bacterial groups that transform bile acid (coccoides, bacteroides, Escherichia coli, and leptum) in feces of healthy subjects (white bar) and diarrhea predominant IBS patients (gray bar) by quantitative polymerase chain reaction. All results are expressed in log10 bacteria per gram of stool.",decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Atrayees
bsdb:22546742/1/1,22546742,case-control,22546742,10.1038/oby.2012.110,NA,"Karlsson C.L., Onnerfält J., Xu J., Molin G., Ahrné S. , Thorngren-Jerneck K.",The microbiota of the gut in preschool children with normal and excessive body weight,"Obesity (Silver Spring, Md.)",2012,NA,Experiment 1,Sweden,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control (BMI at normal range),overweight/obese,Overweight/ obese children with BMI ranging 17.6-25.8 kg/m2,20,20,NA,16S,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Table 3,10 January 2021,Mst Afroza Parvin,"WikiWorks,ChiomaBlessing",Concentrations of specific bacterial groups in feces of overweight/ obese children compared to normal weight children,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,ChiomaBlessing
bsdb:22546742/1/2,22546742,case-control,22546742,10.1038/oby.2012.110,NA,"Karlsson C.L., Onnerfält J., Xu J., Molin G., Ahrné S. , Thorngren-Jerneck K.",The microbiota of the gut in preschool children with normal and excessive body weight,"Obesity (Silver Spring, Md.)",2012,NA,Experiment 1,Sweden,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control (BMI at normal range),overweight/obese,Overweight/ obese children with BMI ranging 17.6-25.8 kg/m2,20,20,NA,16S,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Table 3,10 January 2021,Mst Afroza Parvin,"WikiWorks,ChiomaBlessing",Concentrations of specific bacterial groups in feces of overweight/ obese children compared to normal weight children,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",3379134|74201|203494|48461|1647988|239934|239935;3379134|200940|3031449|213115|194924|872,Complete,ChiomaBlessing
bsdb:22576262/1/1,22576262,case-control,22576262,10.1002/art.34539,NA,"Scher J.U., Ubeda C., Equinda M., Khanin R., Buischi Y., Viale A., Lipuma L., Attur M., Pillinger M.H., Weissmann G., Littman D.R., Pamer E.G., Bretz W.A. , Abramson S.B.",Periodontal disease and the oral microbiota in new-onset rheumatoid arthritis,Arthritis and rheumatism,2012,NA,Experiment 1,United States of America,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,Healthy controls,NORA - [New-Onset Rheumatoid Arthritis] Patient,Patients with NORA - [New-Onset Rheumatoid Arthritis],18,31,3 months,16S,12,Roche454,relative abundances,T-Test,0.05,TRUE,NA,"age,ethnic group,sex",NA,NA,unchanged,increased,increased,NA,NA,Signature 1,Table 2,2 November 2022,Tislam,"Tislam,Peace Sandy,WikiWorks","Oral microbiota differ significantly among patients with new-onset rheumatoid arthritis (NORA), patients with chronic rheumatoid arthritis (CRA), and healthy control participants, and between individuals with healthy gingiva versus periodontal diseases (PD), at the level of both genus and species/operational taxonomic unit (OTU).",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",1783272|1239|909932|1843489|31977|156454;3379134|976|200643|171549|171552;3379134|976|200643|171549|815|909656;3384189|32066|203490|203491|1129771|32067;3379134|976|200643|171549|171552|838;1783272|1239|909932|909929|1843491|970;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171551|836,Complete,Peace Sandy
bsdb:22576262/1/2,22576262,case-control,22576262,10.1002/art.34539,NA,"Scher J.U., Ubeda C., Equinda M., Khanin R., Buischi Y., Viale A., Lipuma L., Attur M., Pillinger M.H., Weissmann G., Littman D.R., Pamer E.G., Bretz W.A. , Abramson S.B.",Periodontal disease and the oral microbiota in new-onset rheumatoid arthritis,Arthritis and rheumatism,2012,NA,Experiment 1,United States of America,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,Healthy controls,NORA - [New-Onset Rheumatoid Arthritis] Patient,Patients with NORA - [New-Onset Rheumatoid Arthritis],18,31,3 months,16S,12,Roche454,relative abundances,T-Test,0.05,TRUE,NA,"age,ethnic group,sex",NA,NA,unchanged,increased,increased,NA,NA,Signature 2,Table 2,2 November 2022,Tislam,"Tislam,Peace Sandy,WikiWorks","Oral microbiota differ significantly among patients with new-onset rheumatoid arthritis (NORA), patients with chronic rheumatoid arthritis (CRA), and healthy control participants, and between individuals with healthy gingiva versus periodontal diseases (PD), at the level of both genus and species/operational taxonomic unit (OTU).",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",1783272|201174|1760|85007|1653|1716;1783272|1239|909932|909929|1843491|52225;1783272|1239|91061|186826|1300|1301;3384189|32066|203490|203491|1129771|32067,Complete,Peace Sandy
bsdb:22576262/2/1,22576262,case-control,22576262,10.1002/art.34539,NA,"Scher J.U., Ubeda C., Equinda M., Khanin R., Buischi Y., Viale A., Lipuma L., Attur M., Pillinger M.H., Weissmann G., Littman D.R., Pamer E.G., Bretz W.A. , Abramson S.B.",Periodontal disease and the oral microbiota in new-onset rheumatoid arthritis,Arthritis and rheumatism,2012,NA,Experiment 2,United States of America,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,CRA - [Chronic Established  Rheumatoid Arthritis],NORA - [New-Onset Rheumatoid Arthritis] Patient,Patients with NORA - [New-Onset Rheumatoid Arthritis],34,31,3 months,16S,12,Roche454,relative abundances,T-Test,0.05,TRUE,NA,"age,ethnic group,sex",NA,NA,unchanged,increased,increased,NA,NA,Signature 1,Table 2,1 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","Oral microbiota differ significantly among patients with new-onset rheumatoid arthritis (NORA), patients with chronic rheumatoid arthritis (CRA), and healthy control participants, and between individuals with healthy gingiva versus periodontal diseases (PD), at the level of both genus and species/operational taxonomic unit
(OTU).",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",3379134|976|200643|171549|171551|836;1783272|1239|909932|909929|1843491|970;3379134|976|200643|171549|171552|838;3379134|203691|203692|136|2845253|157;3379134|976|200643|171549|2005525|195950,Complete,Peace Sandy
bsdb:22576262/2/2,22576262,case-control,22576262,10.1002/art.34539,NA,"Scher J.U., Ubeda C., Equinda M., Khanin R., Buischi Y., Viale A., Lipuma L., Attur M., Pillinger M.H., Weissmann G., Littman D.R., Pamer E.G., Bretz W.A. , Abramson S.B.",Periodontal disease and the oral microbiota in new-onset rheumatoid arthritis,Arthritis and rheumatism,2012,NA,Experiment 2,United States of America,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,CRA - [Chronic Established  Rheumatoid Arthritis],NORA - [New-Onset Rheumatoid Arthritis] Patient,Patients with NORA - [New-Onset Rheumatoid Arthritis],34,31,3 months,16S,12,Roche454,relative abundances,T-Test,0.05,TRUE,NA,"age,ethnic group,sex",NA,NA,unchanged,increased,increased,NA,NA,Signature 2,Table 2,1 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","Oral microbiota differ significantly among patients with new-onset rheumatoid arthritis (NORA), patients with chronic rheumatoid arthritis (CRA), and healthy control participants, and between individuals with healthy gingiva versus periodontal diseases (PD), at the level of both genus and species/operational taxonomic unit
(OTU).",decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|909932|1843489|31977;1783272|1239|909932|909929|1843491|52225;3379134|976|200643|171549|171552|838,Complete,Peace Sandy
bsdb:22576262/3/1,22576262,case-control,22576262,10.1002/art.34539,NA,"Scher J.U., Ubeda C., Equinda M., Khanin R., Buischi Y., Viale A., Lipuma L., Attur M., Pillinger M.H., Weissmann G., Littman D.R., Pamer E.G., Bretz W.A. , Abramson S.B.",Periodontal disease and the oral microbiota in new-onset rheumatoid arthritis,Arthritis and rheumatism,2012,NA,Experiment 3,United States of America,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,Healthy Controls,All [RA] - Rheumatoid Arthritis Patients,"All [RA] - Rheumatoid Arthritis Patients, which includes NORA [new-onset RA] and CRA [Chronic-established RA]",18,65,3 months,16S,12,Roche454,relative abundances,T-Test,0.05,TRUE,NA,"age,ethnic group,sex",NA,NA,unchanged,increased,increased,NA,NA,Signature 1,Table 2,1 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","Oral microbiota differ significantly among patients with new-onset rheumatoid arthritis (NORA), patients with chronic rheumatoid arthritis (CRA), and healthy control participants, and between individuals with healthy gingiva versus periodontal diseases (PD), at the level of both genus and species/operational taxonomic unit
(OTU).",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",1783272|1239|909932|1843489|31977|156454;3379134|976|200643|171549|171552|838;1783272|1239|909932|909929|1843491|970,Complete,Peace Sandy
bsdb:22576262/3/2,22576262,case-control,22576262,10.1002/art.34539,NA,"Scher J.U., Ubeda C., Equinda M., Khanin R., Buischi Y., Viale A., Lipuma L., Attur M., Pillinger M.H., Weissmann G., Littman D.R., Pamer E.G., Bretz W.A. , Abramson S.B.",Periodontal disease and the oral microbiota in new-onset rheumatoid arthritis,Arthritis and rheumatism,2012,NA,Experiment 3,United States of America,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,Healthy Controls,All [RA] - Rheumatoid Arthritis Patients,"All [RA] - Rheumatoid Arthritis Patients, which includes NORA [new-onset RA] and CRA [Chronic-established RA]",18,65,3 months,16S,12,Roche454,relative abundances,T-Test,0.05,TRUE,NA,"age,ethnic group,sex",NA,NA,unchanged,increased,increased,NA,NA,Signature 2,Table 2,1 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","Oral microbiota differ significantly among patients with new-onset rheumatoid arthritis (NORA), patients with chronic rheumatoid arthritis (CRA), and healthy control participants, and between individuals with healthy gingiva versus periodontal diseases (PD), at the level of both genus and species/operational taxonomic unit
(OTU).",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga",1783272|201174|1760|85007|1653|1716;3384189|32066|203490|203491|1129771|32067;3379134|976|117743|200644|49546|1016,Complete,Peace Sandy
bsdb:22622349/1/1,22622349,case-control,22622349,10.1038/ismej.2012.43,https://pubmed.ncbi.nlm.nih.gov/22622349/,"Sanapareddy N., Legge R.M., Jovov B., McCoy A., Burcal L., Araujo-Perez F., Randall T.A., Galanko J., Benson A., Sandler R.S., Rawls J.F., Abdo Z., Fodor A.A. , Keku T.O.",Increased rectal microbial richness is associated with the presence of colorectal adenomas in humans,The ISME journal,2012,NA,Experiment 1,United States of America,Homo sapiens,Colorectal mucosa,UBERON:0013067,Colorectal adenoma,EFO:0005406,Adenoma-free (controls),Adenoma patients (cases),Patients who have colorectal adenoma,38,33,3 months,16S,12,NA,centered log-ratio,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Supplementary Table 1 and 2,1 May 2024,Rahila,"Rahila,Scholastica,WikiWorks",Wilcoxon-tests on log-normalized abundances of of all phyla and genera in cases (33 subjects) versus controls (38 subjects).,increased,"k__Pseudomonadati|p__Acidobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Aquabacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Azonexaceae|g__Azonexus,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Azonexaceae|g__Dechloromonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",3379134|57723;3379134|1224|28216|80840|80864|12916;3379134|1224|1236|2887326|468|469;3379134|976|117743|200644|2762318|501783;3379134|1224|28211|356|82115|357;3379134|74201|203494|48461|1647988|239934;3379134|1224|28216|80840|92793;3379134|1224|28216|206389|2008795|146936;1783272|1117;3379134|1224|28216|206389|2008795|73029;3379134|1224|28216|80840|80864|80865;3379134|29547|3031852|213849|72293|209;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|33958|1243;1783272|1239|186801|3085636|186803|248744;3379134|1224|28211|204457|3423717|165695;3379134|1224|1236|135614|32033|40323;3379134|1224|1236|135624|83763|83770;1783272|1239|526524|526525|2810281|191303;3379134|74201;1783272|1239|91061|186826|33958|46255,Complete,ChiomaBlessing
bsdb:22713265/1/1,22713265,randomized controlled trial,22713265,https://doi.org/10.4161/gmic.21009,https://www.tandfonline.com/doi/full/10.4161/gmic.21009,"Maccaferri S., Candela M., Turroni S., Centanni M., Severgnini M., Consolandi C., Cavina P. , Brigidi P.",IBS-associated phylogenetic unbalances of the intestinal microbiota are not reverted by probiotic supplementation,Gut microbes,2012,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS,Fulfilled the Rome III criteria for the diagnosis of IBS.,24,19,2 months,16S,23,HTF-Microbi.Array,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 1.,18 July 2021,Kwekuamoo,"Kwekuamoo,WikiWorks","Bacterial groups significantly altered in IBS subjects (IBS; Constipation IBS, C-IBS; Diarrhea IBS, D-IBS; Mixed IBS, M-IBS), with respect to healthy subjects (HS)",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Shouchella|s__Shouchella clausii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus cereus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lentilactobacillus|s__Lentilactobacillus buchneri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",1783272|1239|91061|1385|186817|2893057|79880;1783272|1239|91061|1385|186817|1386|1396;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|1678|216816;3379134|29547|3031852|213849|72294|194;1783272|1239|186801|3082720|186804|1870884|1496;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852|1350|1352;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|2767893|1581;1783272|1239|91061|186826|33958|2767887|1624;1783272|1239|186801|3082720|186804;1783272|1239|186801|3085636|186803|1766253|39491,Complete,Atrayees
bsdb:22713265/1/2,22713265,randomized controlled trial,22713265,https://doi.org/10.4161/gmic.21009,https://www.tandfonline.com/doi/full/10.4161/gmic.21009,"Maccaferri S., Candela M., Turroni S., Centanni M., Severgnini M., Consolandi C., Cavina P. , Brigidi P.",IBS-associated phylogenetic unbalances of the intestinal microbiota are not reverted by probiotic supplementation,Gut microbes,2012,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS,Fulfilled the Rome III criteria for the diagnosis of IBS.,24,19,2 months,16S,23,HTF-Microbi.Array,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 1.,18 July 2021,Kwekuamoo,"Kwekuamoo,Atrayees,WikiWorks","Bacterial groups significantly altered in IBS subjects (IBS; Constipation IBS, C-IBS; Diarrhea IBS, D-IBS; Mixed IBS, M-IBS), with respect to healthy subjects (HS)",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|976|200643|171549|815|816;1783272|1239|909932|1843489|31977|29465;3379134|976|200643|171549|171552|838,Complete,Atrayees
bsdb:22713265/2/1,22713265,randomized controlled trial,22713265,https://doi.org/10.4161/gmic.21009,https://www.tandfonline.com/doi/full/10.4161/gmic.21009,"Maccaferri S., Candela M., Turroni S., Centanni M., Severgnini M., Consolandi C., Cavina P. , Brigidi P.",IBS-associated phylogenetic unbalances of the intestinal microbiota are not reverted by probiotic supplementation,Gut microbes,2012,NA,Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-C,Fulfilled the Rome III criteria for the diagnosis of IBS. Constipation IBS (IBS-C),24,4,2 months,16S,23,HTF-Microbi.Array,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 1.,18 July 2021,Kwekuamoo,"Kwekuamoo,WikiWorks","Bacterial groups significantly altered in IBS subjects (IBS; Constipation IBS, C-IBS; Diarrhea IBS, D-IBS; Mixed IBS, M-IBS), with respect to healthy subjects (HS)",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Shouchella|s__Shouchella clausii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae",1783272|1239|91061|1385|186817|2893057|79880;1783272|201174|1760|85004|31953,Complete,Atrayees
bsdb:22713265/2/2,22713265,randomized controlled trial,22713265,https://doi.org/10.4161/gmic.21009,https://www.tandfonline.com/doi/full/10.4161/gmic.21009,"Maccaferri S., Candela M., Turroni S., Centanni M., Severgnini M., Consolandi C., Cavina P. , Brigidi P.",IBS-associated phylogenetic unbalances of the intestinal microbiota are not reverted by probiotic supplementation,Gut microbes,2012,NA,Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-C,Fulfilled the Rome III criteria for the diagnosis of IBS. Constipation IBS (IBS-C),24,4,2 months,16S,23,HTF-Microbi.Array,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 1.,18 July 2021,Kwekuamoo,"Kwekuamoo,Atrayees,WikiWorks","Bacterial groups significantly altered in IBS subjects (IBS; Constipation IBS, C-IBS; Diarrhea IBS, D-IBS; Mixed IBS, M-IBS), with respect to healthy subjects (HS)",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|976|200643|171549|815|816;3379134|976|200643|171549|171552|838,Complete,Atrayees
bsdb:22713265/3/1,22713265,randomized controlled trial,22713265,https://doi.org/10.4161/gmic.21009,https://www.tandfonline.com/doi/full/10.4161/gmic.21009,"Maccaferri S., Candela M., Turroni S., Centanni M., Severgnini M., Consolandi C., Cavina P. , Brigidi P.",IBS-associated phylogenetic unbalances of the intestinal microbiota are not reverted by probiotic supplementation,Gut microbes,2012,NA,Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-D,Fulfilled the Rome III criteria for the diagnosis of IBS. Diarrhea IBS (IBS-D).,24,10,2 months,16S,23,HTF-Microbi.Array,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 1.,18 July 2021,Kwekuamoo,"Kwekuamoo,WikiWorks","Bacterial groups significantly altered in IBS subjects (IBS; Constipation IBS, C-IBS; Diarrhea IBS, D-IBS; Mixed IBS, M-IBS), with respect to healthy subjects (HS)",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Shouchella|s__Shouchella clausii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus cereus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",1783272|1239|91061|1385|186817|2893057|79880;1783272|1239|91061|1385|186817|1386|1396;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|3082720|186804|1870884|1496;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852|1350|1352;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|2767887|1624;1783272|1239|186801|3082720|186804;1783272|1239|186801|3085636|186803|1766253|39491,Complete,Atrayees
bsdb:22713265/3/2,22713265,randomized controlled trial,22713265,https://doi.org/10.4161/gmic.21009,https://www.tandfonline.com/doi/full/10.4161/gmic.21009,"Maccaferri S., Candela M., Turroni S., Centanni M., Severgnini M., Consolandi C., Cavina P. , Brigidi P.",IBS-associated phylogenetic unbalances of the intestinal microbiota are not reverted by probiotic supplementation,Gut microbes,2012,NA,Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-D,Fulfilled the Rome III criteria for the diagnosis of IBS. Diarrhea IBS (IBS-D).,24,10,2 months,16S,23,HTF-Microbi.Array,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 1.,18 July 2021,Kwekuamoo,"Kwekuamoo,Atrayees,WikiWorks","Bacterial groups significantly altered in IBS subjects (IBS; Constipation IBS, C-IBS; Diarrhea IBS, D-IBS; Mixed IBS, M-IBS), with respect to healthy subjects (HS)",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|976|200643|171549|815|816;3379134|976|200643|171549|171552|838,Complete,Atrayees
bsdb:22713265/4/1,22713265,randomized controlled trial,22713265,https://doi.org/10.4161/gmic.21009,https://www.tandfonline.com/doi/full/10.4161/gmic.21009,"Maccaferri S., Candela M., Turroni S., Centanni M., Severgnini M., Consolandi C., Cavina P. , Brigidi P.",IBS-associated phylogenetic unbalances of the intestinal microbiota are not reverted by probiotic supplementation,Gut microbes,2012,NA,Experiment 4,Italy,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-M,Fulfilled the Rome III criteria for the diagnosis of IBS. Mixed IBS (IBS-M).,24,5,2 months,16S,23,HTF-Microbi.Array,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 1.,18 July 2021,Kwekuamoo,"Kwekuamoo,WikiWorks","Bacterial groups significantly altered in IBS subjects (IBS; Constipation IBS, C-IBS; Diarrhea IBS, D-IBS; Mixed IBS, M-IBS), with respect to healthy subjects (HS)",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Shouchella|s__Shouchella clausii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lentilactobacillus|s__Lentilactobacillus buchneri",1783272|1239|91061|1385|186817|2893057|79880;1783272|201174|1760|85004|31953;3379134|29547|3031852|213849|72294|194;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852|1350|1352;1783272|1239|91061|186826|33958|2767893|1581,Complete,Atrayees
bsdb:22728514/1/1,22728514,randomized controlled trial,22728514,10.1053/j.gastro.2012.06.031,NA,"Vrieze A., Van Nood E., Holleman F., Salojärvi J., Kootte R.S., Bartelsman J.F., Dallinga-Thie G.M., Ackermans M.T., Serlie M.J., Oozeer R., Derrien M., Druesne A., Van Hylckama Vlieg J.E., Bloks V.W., Groen A.K., Heilig H.G., Zoetendal E.G., Stroes E.S., de Vos W.M., Hoekstra J.B. , Nieuwdorp M.",Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome,Gastroenterology,2012,NA,Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Allogenic (Baseline samples),Allogenic (6 weeks samples),Fecal samples collected from the participants 6 weeks after allogenic lean donor gut microbiota treatment.,9,9,3 months,16S,34,Human Intestinal Tract Chip,relative abundances,Mixed-Effects Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 3,4 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Significant changes in 16 fecal gut microbiota within the allogenic lean donor gut microbiota treatment group after 6 weeks,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora sphenoides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Aneurinibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas nexilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter|s__Sporobacter termitidis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter|s__Oxalobacter formigenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus intestinalis",1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|186803|2719231|29370;1783272|1239|186801|3085636|186803|2941495|1512;1783272|1239|526524|526525|2810280|100883|100884;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|91061|1385|186822|55079;1783272|1239|186801|3085636|186803|2316020|46228;1783272|1239|186801|3085636|186803|2005355|29361;1783272|1239|186801|186802|216572|244127|169435;1783272|1239|186801|186802|216572|39492;1783272|1239|186801|186802|216572|44748|44749;3379134|1224|28216|80840|75682|846|847;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|1263|2763066,Complete,Svetlana up
bsdb:22728514/3/1,22728514,randomized controlled trial,22728514,10.1053/j.gastro.2012.06.031,NA,"Vrieze A., Van Nood E., Holleman F., Salojärvi J., Kootte R.S., Bartelsman J.F., Dallinga-Thie G.M., Ackermans M.T., Serlie M.J., Oozeer R., Derrien M., Druesne A., Van Hylckama Vlieg J.E., Bloks V.W., Groen A.K., Heilig H.G., Zoetendal E.G., Stroes E.S., de Vos W.M., Hoekstra J.B. , Nieuwdorp M.",Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome,Gastroenterology,2012,NA,Experiment 3,Netherlands,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Autologous (6 weeks samples),Allogenic (6 weeks samples),Fecal samples collected from the participants 6 weeks after allogenic lean donor gut microbiota treatment.,9,9,3 months,16S,34,Human Intestinal Tract Chip,relative abundances,Mixed-Effects Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 3,4 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Differences in gut microbiota identified between allogenic and autologous treatment groups.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora sphenoides,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas nexilis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter|s__Oxalobacter formigenes",1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|2719231|29370;1783272|1239|526524|526525|2810280|100883|100884;1783272|1239|186801|3085636|186803|2316020|46228;1783272|1239|186801|3085636|186803|2005355|29361;3379134|1224|28216|80840|75682|846|847,Complete,Svetlana up
bsdb:22728514/4/1,22728514,randomized controlled trial,22728514,10.1053/j.gastro.2012.06.031,NA,"Vrieze A., Van Nood E., Holleman F., Salojärvi J., Kootte R.S., Bartelsman J.F., Dallinga-Thie G.M., Ackermans M.T., Serlie M.J., Oozeer R., Derrien M., Druesne A., Van Hylckama Vlieg J.E., Bloks V.W., Groen A.K., Heilig H.G., Zoetendal E.G., Stroes E.S., de Vos W.M., Hoekstra J.B. , Nieuwdorp M.",Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome,Gastroenterology,2012,NA,Experiment 4,Netherlands,Homo sapiens,Small intestine,UBERON:0002108,Response to transplant,EFO:0007043,Autologous (6 weeks samples),Allogenic (6 weeks samples),Small intestinal biopsy samples collected from the participants 6 weeks after allogenic lean donor gut microbiota treatment.,9,9,3 months,16S,34,Human Intestinal Tract Chip,relative abundances,Mixed-Effects Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 4,4 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Differences in gut microbiota identified between allogenic and autologous treatment groups.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes|s__Alcaligenes faecalis",3379134|1224|1236|91347|543|561|562;1783272|201174|1760|85007|1653|1716|1720;3379134|1224|28216|80840|506|507|511,Complete,Svetlana up
bsdb:22730468/1/1,22730468,case-control,22730468,10.1136/gutjnl-2012-302167,NA,"Simrén M., Barbara G., Flint H.J., Spiegel B.M., Spiller R.C., Vanner S., Verdu E.F., Whorwell P.J. , Zoetendal E.G.",Intestinal microbiota in functional bowel disorders: a Rome foundation report,Gut,2013,NA,Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS,Individuals diagnosed with irritable bowel syndrome according to Rome criteria,21,37,Yes (recent antibiotic use excluded; exact duration not consistently specified → do not invent months),16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Main Results section; Figure 1 (fecal microbiota composition),13 January 2026,Aqc576444,Aqc576444,Increased relative abundance of fecal Proteobacteria in individuals with IBS compared with healthy controls at baseline.,increased,NA,NA,Complete,NA
bsdb:22730468/1/2,22730468,case-control,22730468,10.1136/gutjnl-2012-302167,NA,"Simrén M., Barbara G., Flint H.J., Spiegel B.M., Spiller R.C., Vanner S., Verdu E.F., Whorwell P.J. , Zoetendal E.G.",Intestinal microbiota in functional bowel disorders: a Rome foundation report,Gut,2013,NA,Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS,Individuals diagnosed with irritable bowel syndrome according to Rome criteria,21,37,Yes (recent antibiotic use excluded; exact duration not consistently specified → do not invent months),16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Main Results section; Figure 1,13 January 2026,Aqc576444,Aqc576444,Decreased relative abundance of fecal Firmicutes and Bacteroidetes in individuals with IBS compared with healthy controls at baseline.,decreased,NA,NA,Complete,NA
bsdb:22761885/1/1,22761885,"cross-sectional observational, not case-control",22761885,10.1371/journal.pone.0039743,NA,"Chen W., Liu F., Ling Z., Tong X. , Xiang C.",Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer,PloS one,2012,NA,Experiment 1,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,Healthy volunteers (swc),CRC patients (swp),"37-88 years of age, diagnosed with colorectal cancer (swp = gut swab)",34,32,1 month,16S,123,Sanger,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 4A,4 July 2022,Jeshudy,"Jeshudy,WikiWorks",Relative abundance of significantly different genera between CRC patients and healthy controls. (A) Genera different between swp and swc.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira",1783272|1239|186801|3085636|186803|207244;1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|572511;1783272|201174|1760|85004|31953|2701;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|28050,Complete,Atrayees
bsdb:22761885/1/2,22761885,"cross-sectional observational, not case-control",22761885,10.1371/journal.pone.0039743,NA,"Chen W., Liu F., Ling Z., Tong X. , Xiang C.",Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer,PloS one,2012,NA,Experiment 1,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,Healthy volunteers (swc),CRC patients (swp),"37-88 years of age, diagnosed with colorectal cancer (swp = gut swab)",34,32,1 month,16S,123,Sanger,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 4A,4 July 2022,Jeshudy,"Jeshudy,WikiWorks",Relative abundance of significantly different genera between CRC patients and healthy controls. (A) Genera different between swp and swc.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor",1783272|1239|186801|3085636|186803|43996;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|91347|543|570;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836;1783272|1239|909932|909929|1843491|970;1783272|1239|186801|3082720|3118655|44259,Complete,Atrayees
bsdb:22761885/3/1,22761885,"cross-sectional observational, not case-control",22761885,10.1371/journal.pone.0039743,NA,"Chen W., Liu F., Ling Z., Tong X. , Xiang C.",Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer,PloS one,2012,NA,Experiment 3,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,paracancerous tissue (pa2t),cancerous tissue (cat),"37-88 years of age, cancerous tissue.

Note: Group 0 = paracancerous tissue 2-5 cm from cancerous tissue",27,27,1 month,16S,123,Sanger,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table 3,3 July 2022,Jeshudy,"Jeshudy,WikiWorks",Phylotypes significantly different between cat and pa2t,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria",3379134|1224|28211|356|118882|528;3379134|1224|28211,Complete,Atrayees
bsdb:22761885/4/1,22761885,"cross-sectional observational, not case-control",22761885,10.1371/journal.pone.0039743,NA,"Chen W., Liu F., Ling Z., Tong X. , Xiang C.",Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer,PloS one,2012,NA,Experiment 4,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,Healthy volunteers (stc),CRC patients (stp),"37-88 years of age, diagnosed with colorectal cancer (stp = stool sample)",22,21,1 month,16S,123,Sanger,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 4B,4 July 2022,Jeshudy,"Jeshudy,WikiWorks",Figure 4. Relative abundance of significantly different genera between CRC patients and healthy controls. Genera differing between stp and stc.,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus",1783272|1239|1737404|1737405|1570339|165779;1783272|1239|186801|186802|216572|244127;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3082720|543314|86331;1783272|201174|84998|1643822|1643826|84108;3379134|976|200643|171549|171552|577309;3379134|200940|3031449|213115|194924|872;3379134|976|200643|171549|171551|836;1783272|1239|186801|3082720|186804|1257,Complete,Atrayees
bsdb:22762355/1/1,22762355,case-control,22762355,10.1111/j.1600-0765.2012.01498.x,NA,"Casarin R.C., Barbagallo A., Meulman T., Santos V.R., Sallum E.A., Nociti F.H., Duarte P.M., Casati M.Z. , Gonçalves R.B.",Subgingival biodiversity in subjects with uncontrolled type-2 diabetes and chronic periodontitis,Journal of periodontal research,2013,NA,Experiment 1,Brazil,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Type II diabetes mellitus,MONDO:0005148,Non-diabetic,Diabetic,"chronic periodontitis, according to the criteria of the 1999 International Classification; the presence of at least 15 teeth; >= 30% of the sites and at least nine teeth pre-senting a probing pocket depth of >= 5 mm with bleeding on probing (with two or more of these teeth having a probing pocket depth of >= 7 mm); uncontrolled type-2 DM, determined by a glycated hemoglobin (HbA1c) concentration of > 8%",11,12,3 months,16S,NA,Illumina,raw counts,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2 & Table 3 & text,10 January 2021,Yaseen Javaid,WikiWorks,Subgingival biodiversity in subjects with uncontrolled type-2 diabetes and chronic periodontitis.,increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Deferribacterota,k__Bacillati|p__Bacillota,k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",1783272|201174;3379134|200930;1783272|1239;3384189|32066;3379134|1224;1783272|1239|91061|186826|1300|1301|28037;3384189|32066|203490|203491|203492|848|851;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|909932|1843489|31977|29465|39778;3379134|1224|28216|206351|481|538|539;3379134|1224|1236|135625|712|416916;3379134|1224|28216|206351|481|482;1783272|1239|91061|1385|539738|1378;3379134|1224|28216|206351|481|538;1783272|201174|1760|2037|2049|1654;3379134|976|117743|200644|49546|1016;3384189|32066|203490|203491|203492|848;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|909929|1843491|970,Complete,Shaimaa Elsafoury
bsdb:22762355/1/2,22762355,case-control,22762355,10.1111/j.1600-0765.2012.01498.x,NA,"Casarin R.C., Barbagallo A., Meulman T., Santos V.R., Sallum E.A., Nociti F.H., Duarte P.M., Casati M.Z. , Gonçalves R.B.",Subgingival biodiversity in subjects with uncontrolled type-2 diabetes and chronic periodontitis,Journal of periodontal research,2013,NA,Experiment 1,Brazil,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Type II diabetes mellitus,MONDO:0005148,Non-diabetic,Diabetic,"chronic periodontitis, according to the criteria of the 1999 International Classification; the presence of at least 15 teeth; >= 30% of the sites and at least nine teeth pre-senting a probing pocket depth of >= 5 mm with bleeding on probing (with two or more of these teeth having a probing pocket depth of >= 7 mm); uncontrolled type-2 DM, determined by a glycated hemoglobin (HbA1c) concentration of > 8%",11,12,3 months,16S,NA,Illumina,raw counts,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2 & Table 3 & text,10 January 2021,Yaseen Javaid,WikiWorks,Subgingival biodiversity in subjects with uncontrolled type-2 diabetes and chronic periodontitis.,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Spirochaetota,k__Thermotogati|p__Synergistota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",3379134|976;3379134|203691;3384194|508458;1783272|1239|186801|3082720|3118655|44259|143361;3379134|976|200643|171549|171551|836|837;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3082720|3118655|44259;3379134|976|200643|171549|171551|836;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|2005525|195950|28112;3379134|976|200643|171549|2005525|195950;3379134|203691|203692|136|2845253|157,Complete,Shaimaa Elsafoury
bsdb:22948872/1/1,22948872,prospective cohort,22948872,10.1128/AAC.00789-12,NA,"Fouhy F., Guinane C.M., Hussey S., Wall R., Ryan C.A., Dempsey E.M., Murphy B., Ross R.P., Fitzgerald G.F., Stanton C. , Cotter P.D.","High-throughput sequencing reveals the incomplete, short-term recovery of infant gut microbiota following parenteral antibiotic treatment with ampicillin and gentamicin",Antimicrobial agents and chemotherapy,2012,NA,Experiment 1,Ireland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Untreated controls (week 4),Antibiotic treated (week 4),Had received parenteral antibiotic treatment with a combination of ampicillin and gentamicin within 48 hours of birth,9,9,NA,16S,4,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Figure 1, Figure 2, Figure 3",7 October 2021,Mmarin,"Mmarin,WikiWorks","Figure 1: Microbial distributions at the phylum level in the samples from treated and control infants at week 4 and week 8. Statistically significant differences between treated infants and controls at week 4 are indicated by asterisks (P < 0.05). Percentages are based on proportions of assignable tags.

Figure 2: Microbial distributions at the family level in the samples from treated and control infants at week 4 and week 8. Statistically significant differences between treated infants and controls at week 4 are indicated by asterisks (P < 0.05). Percentages are based on proportions of assignable reads.

Figure 3: Microbial distributions at the genus level in the samples from treated and control infants at week 4 and week 8. Statistically significant differences between treated infants and controls at week 4 are indicated by asterisks (P < 0.05).  Percentages are based on proportions of assignable reads.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",3379134|1224|1236|91347|543;1783272|1239|91061|186826|81850;1783272|1239|186801|3082720|186804;3379134|1224;3379134|1224|1236|91347|543,Complete,Chloe
bsdb:22948872/1/2,22948872,prospective cohort,22948872,10.1128/AAC.00789-12,NA,"Fouhy F., Guinane C.M., Hussey S., Wall R., Ryan C.A., Dempsey E.M., Murphy B., Ross R.P., Fitzgerald G.F., Stanton C. , Cotter P.D.","High-throughput sequencing reveals the incomplete, short-term recovery of infant gut microbiota following parenteral antibiotic treatment with ampicillin and gentamicin",Antimicrobial agents and chemotherapy,2012,NA,Experiment 1,Ireland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Untreated controls (week 4),Antibiotic treated (week 4),Had received parenteral antibiotic treatment with a combination of ampicillin and gentamicin within 48 hours of birth,9,9,NA,16S,4,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"Figure 1, Figure 2, Figure 3",7 October 2021,Mmarin,"Mmarin,WikiWorks","Figure 1: Microbial distributions at the phylum level in the samples from treated and control infants at week 4 and week 8. Statistically significant differences between treated infants and controls at week 4 are indicated by asterisks (P < 0.05). Percentages are based on proportions of assignable tags.

Figure 2: Microbial distributions at the family level in the samples from treated and control infants at week 4 and week 8. Statistically significant differences between treated infants and controls at week 4 are indicated by asterisks (P < 0.05). Percentages are based on proportions of assignable reads.

Figure 3: Microbial distributions at the genus level in the samples from treated and control infants at week 4 and week 8. Statistically significant differences between treated infants and controls at week 4 are indicated by asterisks (P < 0.05). Percentages are based on proportions of assignable reads.",decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|201174;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|1578,Complete,Chloe
bsdb:22948872/2/1,22948872,prospective cohort,22948872,10.1128/AAC.00789-12,NA,"Fouhy F., Guinane C.M., Hussey S., Wall R., Ryan C.A., Dempsey E.M., Murphy B., Ross R.P., Fitzgerald G.F., Stanton C. , Cotter P.D.","High-throughput sequencing reveals the incomplete, short-term recovery of infant gut microbiota following parenteral antibiotic treatment with ampicillin and gentamicin",Antimicrobial agents and chemotherapy,2012,NA,Experiment 2,Ireland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Untreated controls (week 8),Antibiotic treated (week 8),Received parenteral antibiotic treatment with a combination of ampicillin and gentamicin within 48 hours of birth,9,9,NA,16S,4,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Figure 1, Figure 2, Figure 3",7 October 2021,Mmarin,"Mmarin,WikiWorks","Figure 1: Microbial distributions at the phylum level in the samples from treated and control infants at week 4 and week 8. 
Figure 2: Microbial distributions at the family level in the samples from treated and control infants at week 4 and week 8. 
Figure 3: Microbial distributions at the genus level in the samples from treated and control infants at week 4 and week 8. 

Statistically significant differences between treated infants and controls at week 8 are indicated by asterisks. Percentages are based on proportions of assignable tags.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",3379134|1224|1236|91347|543;3379134|1224;3379134|1224|1236|91347|543,Complete,Chloe
bsdb:22948872/3/1,22948872,prospective cohort,22948872,10.1128/AAC.00789-12,NA,"Fouhy F., Guinane C.M., Hussey S., Wall R., Ryan C.A., Dempsey E.M., Murphy B., Ross R.P., Fitzgerald G.F., Stanton C. , Cotter P.D.","High-throughput sequencing reveals the incomplete, short-term recovery of infant gut microbiota following parenteral antibiotic treatment with ampicillin and gentamicin",Antimicrobial agents and chemotherapy,2012,NA,Experiment 3,Ireland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Week 4 (treated),Week 8 (treated),Had received parenteral antibiotic treatment with a combination of ampicillin and gentamicin within 48 hours of birth,9,9,NA,16S,4,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,"Figure 1, Figure 2, Figure 3",7 October 2021,Mmarin,"Mmarin,WikiWorks","Figure 1: Microbial distributions at the phylum level in the samples from treated and control infants at week 4 and week 8. 
Figure 2: Microbial distributions at the family level in the samples from treated and control infants at week 4 and week 8. 
Figure 3: Microbial distributions at the genus level in the samples from treated and control infants at week 4 and week 8.

A statistically significant difference between treated infants at week 4 and week 8 (i.e., the recovery of the treated infants) is indicated by a diamond. Percentages are based on proportions of assignable tags.",increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|201174;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678,Complete,Chloe
bsdb:22948872/3/2,22948872,prospective cohort,22948872,10.1128/AAC.00789-12,NA,"Fouhy F., Guinane C.M., Hussey S., Wall R., Ryan C.A., Dempsey E.M., Murphy B., Ross R.P., Fitzgerald G.F., Stanton C. , Cotter P.D.","High-throughput sequencing reveals the incomplete, short-term recovery of infant gut microbiota following parenteral antibiotic treatment with ampicillin and gentamicin",Antimicrobial agents and chemotherapy,2012,NA,Experiment 3,Ireland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Week 4 (treated),Week 8 (treated),Had received parenteral antibiotic treatment with a combination of ampicillin and gentamicin within 48 hours of birth,9,9,NA,16S,4,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,"Figure 1, Figure 2, Figure 3",7 October 2021,Mmarin,"Mmarin,WikiWorks","Figure 1: Microbial distributions at the phylum level in the samples from treated and control infants at week 4 and week 8. 
Figure 2: Microbial distributions at the family level in the samples from treated and control infants at week 4 and week 8. 
Figure 3: Microbial distributions at the genus level in the samples from treated and control infants at week 4 and week 8.

A statistically significant difference between treated infants at week 4 and week 8 (i.e., the recovery of the treated infants) is indicated by a diamond. Percentages are based on proportions of assignable tags.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",3379134|1224|1236|91347|543;1783272|1239|186801|3082720|186804;3379134|1224;3379134|1224|1236|91347|543,Complete,Chloe
bsdb:22949626/1/1,22949626,"cross-sectional observational, not case-control",22949626,10.1093/jac/dks348,NA,"O'Sullivan O., Coakley M., Lakshminarayanan B., Conde S., Claesson M.J., Cusack S., Fitzgerald A.P., O'Toole P.W., Stanton C. , Ross R.P.",Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy,The Journal of antimicrobial chemotherapy,2013,NA,Experiment 1,Ireland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Antibiotic untreated,Antibiotic treated,subjects receiving antibiotics within 1 month prior to visiting an ELDERMET Clinic,143,42,NA,16S,4,Roche454,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,age,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure S2, Table S4",10 September 2021,Mmarin,"Mmarin,Claregrieve1,WikiWorks",Differential microbial abundance between antibiotic-treated and -untreated elderly subjects,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira",1783272|201174|1760|85004|31953|1678|41200;1783272|1239|909932|1843488|909930|904;1783272|1239|186801|3085636|186803|830;1783272|1239|186801|3085636|186803|28050,Complete,Claregrieve1
bsdb:22949626/1/2,22949626,"cross-sectional observational, not case-control",22949626,10.1093/jac/dks348,NA,"O'Sullivan O., Coakley M., Lakshminarayanan B., Conde S., Claesson M.J., Cusack S., Fitzgerald A.P., O'Toole P.W., Stanton C. , Ross R.P.",Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy,The Journal of antimicrobial chemotherapy,2013,NA,Experiment 1,Ireland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Antibiotic untreated,Antibiotic treated,subjects receiving antibiotics within 1 month prior to visiting an ELDERMET Clinic,143,42,NA,16S,4,Roche454,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,age,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table S4,16 September 2021,Mmarin,"Mmarin,Claregrieve1,WikiWorks",Differential microbial abundance between antibiotic-treated and -untreated elderly subjects,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Lactonifactor,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Penicillium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus",1783272|1239|1737404|1737405|1570339|165779;1783272|1239|186801|186802|31979|420345;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|906;4751|4890|147545|5042|1131492|5073;3379134|1224|1236|91347|1903414|583,Complete,Claregrieve1
bsdb:22949626/2/1,22949626,"cross-sectional observational, not case-control",22949626,10.1093/jac/dks348,NA,"O'Sullivan O., Coakley M., Lakshminarayanan B., Conde S., Claesson M.J., Cusack S., Fitzgerald A.P., O'Toole P.W., Stanton C. , Ross R.P.",Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy,The Journal of antimicrobial chemotherapy,2013,NA,Experiment 2,Ireland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Antibiotic untreated subjects in day hospital,Antibiotic treated subjects in day hospital,subjects who were antibiotic-treated in a day hospital,33,7,NA,16S,4,Roche454,relative abundances,"Chi-Square,Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,16 September 2021,Mmarin,"Mmarin,Claregrieve1,WikiWorks",comparison of microbiota between antibiotic-treated and untreated groups in day hospital facility,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|3085636|186803|437755;1783272|1239|1737404|1737405|1570339|162289;3379134|256845|1313211|278082|255528|172900;1783272|1239|91061|186826|33958|46255,Complete,Claregrieve1
bsdb:22949626/2/2,22949626,"cross-sectional observational, not case-control",22949626,10.1093/jac/dks348,NA,"O'Sullivan O., Coakley M., Lakshminarayanan B., Conde S., Claesson M.J., Cusack S., Fitzgerald A.P., O'Toole P.W., Stanton C. , Ross R.P.",Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy,The Journal of antimicrobial chemotherapy,2013,NA,Experiment 2,Ireland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Antibiotic untreated subjects in day hospital,Antibiotic treated subjects in day hospital,subjects who were antibiotic-treated in a day hospital,33,7,NA,16S,4,Roche454,relative abundances,"Chi-Square,Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,16 September 2021,Mmarin,"Mmarin,Claregrieve1,WikiWorks",comparison of microbiota between antibiotic-treated and untreated groups in day hospital facility,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|216851,Complete,Claregrieve1
bsdb:22949626/3/1,22949626,"cross-sectional observational, not case-control",22949626,10.1093/jac/dks348,NA,"O'Sullivan O., Coakley M., Lakshminarayanan B., Conde S., Claesson M.J., Cusack S., Fitzgerald A.P., O'Toole P.W., Stanton C. , Ross R.P.",Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy,The Journal of antimicrobial chemotherapy,2013,NA,Experiment 3,Ireland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Antibiotic untreated community dwelling subjects,Antibiotic treated community dwelling subjects,community-dwelling subjects treated with antibiotics within 1 month of study,64,9,NA,16S,4,Roche454,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon),Chi-Square",0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,16 September 2021,Mmarin,"Mmarin,Claregrieve1,WikiWorks",comparison of microbiota between antibiotic-treated and untreated community-dwelling subjects,decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota",1783272|1239;3379134|1224,Complete,Claregrieve1
bsdb:22949626/3/2,22949626,"cross-sectional observational, not case-control",22949626,10.1093/jac/dks348,NA,"O'Sullivan O., Coakley M., Lakshminarayanan B., Conde S., Claesson M.J., Cusack S., Fitzgerald A.P., O'Toole P.W., Stanton C. , Ross R.P.",Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy,The Journal of antimicrobial chemotherapy,2013,NA,Experiment 3,Ireland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Antibiotic untreated community dwelling subjects,Antibiotic treated community dwelling subjects,community-dwelling subjects treated with antibiotics within 1 month of study,64,9,NA,16S,4,Roche454,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon),Chi-Square",0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,16 September 2021,Mmarin,"Mmarin,Claregrieve1,WikiWorks",comparison of microbiota between antibiotic-treated and untreated community-dwelling subjects,decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota",1783272|1239;3379134|1224,Complete,Claregrieve1
bsdb:23032991/1/1,23032991,case-control,23032991,10.1038/tpj.2012.43,NA,"Graessler J., Qin Y., Zhong H., Zhang J., Licinio J., Wong M.L., Xu A., Chavakis T., Bornstein A.B., Ehrhart-Bornstein M., Lamounier-Zepter V., Lohmann T., Wolf T. , Bornstein S.R.",Metagenomic sequencing of the human gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes: correlation with inflammatory and metabolic parameters,The pharmacogenomics journal,2013,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean controls,before surgery,Roux-en-Y gastric-bypass operation were recruited according to the S3 guidelines of the German Society for Obesity,6,NA,3 weeks,WMS,NA,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Marianthi Thomatos,WikiWorks,gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,1783272|1239|186801|186802|216572|216851|853,Complete,Shaimaa Elsafoury
bsdb:23032991/1/2,23032991,case-control,23032991,10.1038/tpj.2012.43,NA,"Graessler J., Qin Y., Zhong H., Zhang J., Licinio J., Wong M.L., Xu A., Chavakis T., Bornstein A.B., Ehrhart-Bornstein M., Lamounier-Zepter V., Lohmann T., Wolf T. , Bornstein S.R.",Metagenomic sequencing of the human gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes: correlation with inflammatory and metabolic parameters,The pharmacogenomics journal,2013,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean controls,before surgery,Roux-en-Y gastric-bypass operation were recruited according to the S3 guidelines of the German Society for Obesity,6,NA,3 weeks,WMS,NA,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,10 January 2021,Marianthi Thomatos,WikiWorks,gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira hyodysenteriae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum",1783272|1239|526524|526525|2810280|3025755|29348;3379134|203691|203692|1643686|143786|29521|159;3384189|32066|203490|203491|203492|848|860,Complete,Shaimaa Elsafoury
bsdb:23038174/1/1,23038174,randomized controlled trial,23038174,10.1038/ismej.2012.104,NA,"Martínez I., Lattimer J.M., Hubach K.L., Case J.A., Yang J., Weber C.G., Louk J.A., Rose D.J., Kyureghian G., Peterson D.A., Haub M.D. , Walter J.",Gut microbiome composition is linked to whole grain-induced immunological improvements,The ISME journal,2013,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,baseline,barley (WGB),subjects who took a daily 60g dose of barley,28,28,3 months,16S,123,Roche454,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 1,"Table 2, text",10 January 2021,Lora Kasselman,"Fatima,Claregrieve1,WikiWorks",Differential microbial abundance between baseline and end of study for barley study group,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|1766253|39491,Complete,Claregrieve1
bsdb:23038174/1/2,23038174,randomized controlled trial,23038174,10.1038/ismej.2012.104,NA,"Martínez I., Lattimer J.M., Hubach K.L., Case J.A., Yang J., Weber C.G., Louk J.A., Rose D.J., Kyureghian G., Peterson D.A., Haub M.D. , Walter J.",Gut microbiome composition is linked to whole grain-induced immunological improvements,The ISME journal,2013,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,baseline,barley (WGB),subjects who took a daily 60g dose of barley,28,28,3 months,16S,123,Roche454,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 2,"Table 2, text",10 January 2021,Lora Kasselman,"Claregrieve1,WikiWorks",Differential microbial abundance between baseline and end of study for barley study group,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",3379134|976;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|171551;3379134|976;3379134|976|200643|171549|815;1783272|1239|186801|3085636|186803|841;1783272|1239|909932|1843489|31977|39948,Complete,Claregrieve1
bsdb:23038174/2/1,23038174,randomized controlled trial,23038174,10.1038/ismej.2012.104,NA,"Martínez I., Lattimer J.M., Hubach K.L., Case J.A., Yang J., Weber C.G., Louk J.A., Rose D.J., Kyureghian G., Peterson D.A., Haub M.D. , Walter J.",Gut microbiome composition is linked to whole grain-induced immunological improvements,The ISME journal,2013,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,baseline,brown rice (BR),subjects who took a daily 60g dose of brown rice fiber,28,28,3 months,16S,123,Roche454,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 1,"Table 2, text",10 January 2021,Lora Kasselman,"Claregrieve1,WikiWorks",Differential microbial abundance between baseline and end of study for brown rice study group,increased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Claregrieve1
bsdb:23038174/2/2,23038174,randomized controlled trial,23038174,10.1038/ismej.2012.104,NA,"Martínez I., Lattimer J.M., Hubach K.L., Case J.A., Yang J., Weber C.G., Louk J.A., Rose D.J., Kyureghian G., Peterson D.A., Haub M.D. , Walter J.",Gut microbiome composition is linked to whole grain-induced immunological improvements,The ISME journal,2013,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,baseline,brown rice (BR),subjects who took a daily 60g dose of brown rice fiber,28,28,3 months,16S,123,Roche454,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 2,"Table 2, text",10 January 2021,Lora Kasselman,"Claregrieve1,WikiWorks",Differential microbial abundance between baseline and end of study for brown rice study group,decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Claregrieve1
bsdb:23038174/3/1,23038174,randomized controlled trial,23038174,10.1038/ismej.2012.104,NA,"Martínez I., Lattimer J.M., Hubach K.L., Case J.A., Yang J., Weber C.G., Louk J.A., Rose D.J., Kyureghian G., Peterson D.A., Haub M.D. , Walter J.",Gut microbiome composition is linked to whole grain-induced immunological improvements,The ISME journal,2013,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,baseline,brown rice + barley (BR + WGB),subjects who took a daily dose of 30g barley + 30g brown rice,28,28,3 months,16S,123,Roche454,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 1,"Table 2, text",10 January 2021,Lora Kasselman,"Claregrieve1,WikiWorks",Differential microbial abundance between baseline and end of study for barley+brown rice study group,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota",1783272|1239|186801|3085636|186803|572511;1783272|1239,Complete,Claregrieve1
bsdb:23038174/3/2,23038174,randomized controlled trial,23038174,10.1038/ismej.2012.104,NA,"Martínez I., Lattimer J.M., Hubach K.L., Case J.A., Yang J., Weber C.G., Louk J.A., Rose D.J., Kyureghian G., Peterson D.A., Haub M.D. , Walter J.",Gut microbiome composition is linked to whole grain-induced immunological improvements,The ISME journal,2013,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,baseline,brown rice + barley (BR + WGB),subjects who took a daily dose of 30g barley + 30g brown rice,28,28,3 months,16S,123,Roche454,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 2,"Table 2, text",10 January 2021,Lora Kasselman,"Claregrieve1,WikiWorks",Differential microbial abundance between baseline and end of study for barley+brown rice study group,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976,Complete,Claregrieve1
bsdb:23056268/1/1,23056268,laboratory experiment,23056268,10.1371/journal.pone.0046231,NA,"Bangsgaard Bendtsen K.M., Krych L., Sørensen D.B., Pang W., Nielsen D.S., Josefsen K., Hansen L.H., Sørensen S.J. , Hansen A.K.",Gut microbiota composition is correlated to grid floor induced stress and behavior in the BALB/c mouse,PloS one,2012,NA,Experiment 1,Denmark,Mus musculus,Caecum,UBERON:0001153,Stimulus or stress design,EFO:0001762,control,grid floor induced stress,cases were exposed to a stress factor which is a grid floor exposure for two weeks. this implies that the use of grid floor is a sufficient stressor for inducing a depression-like behavioral state in the TST.,14,14,NA,16S,4,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Fatima Zohra,WikiWorks,Significantly different taxa between control mice and grid floor housed mice,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|171550|239759,Complete,Shaimaa Elsafoury
bsdb:23071781/1/1,23071781,case-control,23071781,10.1371/journal.pone.0047305,NA,"Pragman A.A., Kim H.B., Reilly C.S., Wendt C. , Isaacson R.E.",The lung microbiome in moderate and severe chronic obstructive pulmonary disease,PloS one,2012,NA,Experiment 1,United States of America,Homo sapiens,Lung,UBERON:0002048,Chronic obstructive pulmonary disease,EFO:0000341,controls,Chronic obstructive pulmonary disease,Patients who have Chronic obstructive pulmonary disease,10,22,2 months,16S,3,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,age,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Table 2,10 January 2021,Fatima Zohra,"Lwaldron,Fatima,WikiWorks",Metastats Analysis of Differential Abundance of moderate and severe COPD Lung microbiome compared to controls,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Cryptobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales|f__Desulfobacteraceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Pseudomonadati|p__Campylobacterota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Microvirga,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales",1783272|1239|91061|186826|186827|46123;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|1239|91061|186826|186827;3379134|1224|1236|135624|84642;3379134|1224|1236|135624;3379134|1224|1236|135624|84642|642;1783272|1239|186801|3085636|186803|653683;1783272|201174|84998|84999|1643824|1380;1783272|201174|1760|85004|31953|1678;1783272|1239|526524|526525|128827|118747;1783272|1239|186801|3085636|186803|830;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294;3379134|29547|3031852|213849;3379134|976|117743|200644|49546|1016;1783272|1239|186801|3085636|186803|43996;1783272|1239|909932|909929|1843491|82202;1783272|201174|84998|84999|84107;1783272|201174|84998|1643822|1643826|84162;3379134|200940|3024418|213118|213119;3379134|200940|3024418|213118;3379134|200940|3031451|3024411|213121|893;1783272|1239|909932|1843489|31977|39948;3379134|976|200643|171549|2005520|156973;3379134|29547;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|186806|1730;3384189|32066;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|171552|52228;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826;3384189|32066|203490|203491|1129771|32067;3384189|32066|203490|203491|1129771;1783272|201174|1760|85006|1268;3379134|1224|28211|356|119045|186650;3379134|1224|28216|206351|481;3379134|1224|28216|206351;1783272|201174|1760|85009|85015|1839;1783272|201174|84998|84999|1643824|133925;1783272|1239|186801|3085636|186803|265975;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171552|838;3379134|1224|28211|204441;1783272|201174|1760|85006|1268|32207;1783272|1239|909932|909929|1843491|970;3379134|1224|1236|91347|1903411|613;1783272|1239|526524|526525|128827|123375;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|2005525|195950;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977;1783272|201174|84998|84999,Complete,Fatima
bsdb:23071781/1/2,23071781,case-control,23071781,10.1371/journal.pone.0047305,NA,"Pragman A.A., Kim H.B., Reilly C.S., Wendt C. , Isaacson R.E.",The lung microbiome in moderate and severe chronic obstructive pulmonary disease,PloS one,2012,NA,Experiment 1,United States of America,Homo sapiens,Lung,UBERON:0002048,Chronic obstructive pulmonary disease,EFO:0000341,controls,Chronic obstructive pulmonary disease,Patients who have Chronic obstructive pulmonary disease,10,22,2 months,16S,3,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,age,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Table 2,10 January 2021,Fatima Zohra,WikiWorks,Metastats Analysis of Differential Abundance of moderate and severe COPD Lung microbiome compared to controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Blastococcus|s__Candidatus Blastococcus massiliensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Modestobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Nakamurellales|f__Nakamurellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Thermoactinomycetaceae|g__Thermoactinomyces,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Thermoactinomycetaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter",1783272|1239|186801|186802|31979|1485;1783272|201174|1760|1643682|85030|38501|1470358;1783272|201174|1760|1643682|85030|88138;1783272|201174|1760|1643684|85031;1783272|1239|91061|1385|186824|2023;1783272|1239|91061|1385|186824;3379134|1224|1236|91347|543|544;1783272|201174|1760|85006|1268|1663,Complete,Shaimaa Elsafoury
bsdb:23071781/2/1,23071781,case-control,23071781,10.1371/journal.pone.0047305,NA,"Pragman A.A., Kim H.B., Reilly C.S., Wendt C. , Isaacson R.E.",The lung microbiome in moderate and severe chronic obstructive pulmonary disease,PloS one,2012,NA,Experiment 2,United States of America,Homo sapiens,Lung,UBERON:0002048,Chronic obstructive pulmonary disease,EFO:0000341,moderate Chronic obstructive pulmonary disease,Severe,Patients who have severe Chronic obstructive pulmonary disease,8,14,2 months,16S,3,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,age,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Metastats Analysis of Differential Abundance of moderate and severe COPD Lung microbiome compared to controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Pontibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Microvirga,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas",3379134|1224|1236|135624;3379134|200940|3024418|213118;3379134|1224|1236|135624|84642;3379134|200940|3031451|3024411|213121;1783272|201174|1760|85009|85015|1839;1783272|1239|91061|1385|186817|289201;1783272|1239|186801|186802|31979|1485;3379134|1224|28211|356|119045|186650;3379134|1224|1236|135624|84642|642,Complete,Shaimaa Elsafoury
bsdb:23153041/1/1,23153041,prospective cohort,23153041,10.1186/gb-2012-13-11-r101,NA,"Zeeuwen P.L., Boekhorst J., van den Bogaard E.H., de Koning H.D., van de Kerkhof P.M., Saulnier D.M., van Swam I.I., van Hijum S.A., Kleerebezem M., Schalkwijk J. , Timmerman H.M.",Microbiome dynamics of human epidermis following skin barrier disruption,Genome biology,2012,NA,Experiment 1,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Psoriasis,EFO:0000676,Female,Psoriasis Male,"tape stripping method involves the repeated application of adhesive tape to the skin surface, thereby removing stratum corneum layers, it creates a superficial wound showing slight skin irritation (erythema) and loss of barrier function (transepidermal water loss)",6,6,NA,16S,34,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.1,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 4,10 January 2021,WikiWorks,WikiWorks,Difference in microbial community composition of upper buttok skin between males and females,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Tepidibacteraceae|g__Sporacetigenium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Dermabacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Eremococcus",1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|186827;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|186802|31979;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|186801|3082720|186804;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|909932|1843489|31977;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|3082720|3120162|360541;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|2037;1783272|201174|1760|85006|85020;1783272|201174|1760|85006|85020|43668;1783272|201174|1760|85006|1268|32207;1783272|201174;1783272|201174|1760;1783272|201174|1760|85006|85023;1783272|201174|1760|85006|85023|33882;1783272|201174|1760|85006|145357|57495;3379134|976|117743;3379134|976|117743|200644;3379134|976|117743|200644|49546;3379134|976|117743|200644|49546|1016;3379134|1224|1236|2887326|468|469;1783272|201174|1760|85006|85020|36739;1783272|1239|91061|186826|186827|171412,Complete,Shaimaa Elsafoury
bsdb:23153041/1/2,23153041,prospective cohort,23153041,10.1186/gb-2012-13-11-r101,NA,"Zeeuwen P.L., Boekhorst J., van den Bogaard E.H., de Koning H.D., van de Kerkhof P.M., Saulnier D.M., van Swam I.I., van Hijum S.A., Kleerebezem M., Schalkwijk J. , Timmerman H.M.",Microbiome dynamics of human epidermis following skin barrier disruption,Genome biology,2012,NA,Experiment 1,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Psoriasis,EFO:0000676,Female,Psoriasis Male,"tape stripping method involves the repeated application of adhesive tape to the skin surface, thereby removing stratum corneum layers, it creates a superficial wound showing slight skin irritation (erythema) and loss of barrier function (transepidermal water loss)",6,6,NA,16S,34,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.1,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 4,10 January 2021,WikiWorks,WikiWorks,Difference in microbial community composition of upper buttok skin between males and females,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium",1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85009|31957;1783272|201174|1760|85009|31957|1743;1783272|201174|1760|85004;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|2701;3379134|1224;3379134|1224|1236;3379134|1224|1236|72274;3379134|1224|1236|2887326|468;3379134|1224|28211|356|212791;1783272|201174|1760|85006|85019;1783272|201174|1760|85006|85019|1696,Complete,Shaimaa Elsafoury
bsdb:23167452/1/1,23167452,case-control,23167452,https://doi.org/10.1111/1469-0691.12054,NA,"Leung R.K., Zhou J.W., Guan W., Li S.K., Yang Z.F. , Tsui S.K.",Modulation of potential respiratory pathogens by pH1N1 viral infection,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"Cell motility, chemotaxis, microbiota, pH1N1, pneumonia",Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,Influenza A (H1N1),EFO:1001488,Pneumonia patients without any influenza A infection,Pneumonia patients with pH1N1 infection,"Positive lab test (real-time PCR or cell culture) and criteria for pneumonia simultaneously met, with pH1N1 infection",11,11,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1a-c,9 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Relative microbial abundance of pH1N1-infected and uninfected pneumonia patients,increased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus",1783272|1239;3379134|1224;1783272|1239|91061|1385|186817;3379134|1224|1236|2887326|468;3379134|1224|1236|72274|135621;3379134|1224|1236|2887326|468|469;3379134|1224|1236|72274|135621|286;1783272|1239|91061|1385|186817|1386,Complete,Fatima
bsdb:23167452/1/2,23167452,case-control,23167452,https://doi.org/10.1111/1469-0691.12054,NA,"Leung R.K., Zhou J.W., Guan W., Li S.K., Yang Z.F. , Tsui S.K.",Modulation of potential respiratory pathogens by pH1N1 viral infection,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"Cell motility, chemotaxis, microbiota, pH1N1, pneumonia",Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,Influenza A (H1N1),EFO:1001488,Pneumonia patients without any influenza A infection,Pneumonia patients with pH1N1 infection,"Positive lab test (real-time PCR or cell culture) and criteria for pneumonia simultaneously met, with pH1N1 infection",11,11,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1a-c,9 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Relative microbial abundance of pH1N1-infected and uninfected pneumonia patients,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976;3379134|976|200643|171549|171552;1783272|1239|909932|1843489|31977;3379134|1224|28216|206351|481;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|838;1783272|1239|909932|1843489|31977|29465,Complete,Fatima
bsdb:23167452/1/3,23167452,case-control,23167452,https://doi.org/10.1111/1469-0691.12054,NA,"Leung R.K., Zhou J.W., Guan W., Li S.K., Yang Z.F. , Tsui S.K.",Modulation of potential respiratory pathogens by pH1N1 viral infection,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"Cell motility, chemotaxis, microbiota, pH1N1, pneumonia",Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,Influenza A (H1N1),EFO:1001488,Pneumonia patients without any influenza A infection,Pneumonia patients with pH1N1 infection,"Positive lab test (real-time PCR or cell culture) and criteria for pneumonia simultaneously met, with pH1N1 infection",11,11,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 3,Figure 1b,9 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Relative microbial abundance of pH1N1-infected and uninfected pneumonia patients at the family level,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae",1783272|1239|91061|1385|186817;3379134|1224|1236|2887326|468;3379134|1224|1236|72274|135621,Complete,Fatima
bsdb:23167452/1/4,23167452,case-control,23167452,https://doi.org/10.1111/1469-0691.12054,NA,"Leung R.K., Zhou J.W., Guan W., Li S.K., Yang Z.F. , Tsui S.K.",Modulation of potential respiratory pathogens by pH1N1 viral infection,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"Cell motility, chemotaxis, microbiota, pH1N1, pneumonia",Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,Influenza A (H1N1),EFO:1001488,Pneumonia patients without any influenza A infection,Pneumonia patients with pH1N1 infection,"Positive lab test (real-time PCR or cell culture) and criteria for pneumonia simultaneously met, with pH1N1 infection",11,11,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 4,Figure 1b,9 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Relative microbial abundance of pH1N1-infected and uninfected pneumonia patients at the family level,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|1224|28216|206351|481;3379134|976|200643|171549|171552;1783272|1239|909932|1843489|31977,Complete,Fatima
bsdb:23167452/1/5,23167452,case-control,23167452,https://doi.org/10.1111/1469-0691.12054,NA,"Leung R.K., Zhou J.W., Guan W., Li S.K., Yang Z.F. , Tsui S.K.",Modulation of potential respiratory pathogens by pH1N1 viral infection,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"Cell motility, chemotaxis, microbiota, pH1N1, pneumonia",Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,Influenza A (H1N1),EFO:1001488,Pneumonia patients without any influenza A infection,Pneumonia patients with pH1N1 infection,"Positive lab test (real-time PCR or cell culture) and criteria for pneumonia simultaneously met, with pH1N1 infection",11,11,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 5,Figure 1c,9 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Relative microbial abundance of pH1N1-infected and uninfected pneumonia patients at the genus level,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",3379134|1224|1236|2887326|468|469;1783272|1239|91061|1385|186817|1386;3379134|1224|1236|72274|135621|286,Complete,Fatima
bsdb:23167452/1/6,23167452,case-control,23167452,https://doi.org/10.1111/1469-0691.12054,NA,"Leung R.K., Zhou J.W., Guan W., Li S.K., Yang Z.F. , Tsui S.K.",Modulation of potential respiratory pathogens by pH1N1 viral infection,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"Cell motility, chemotaxis, microbiota, pH1N1, pneumonia",Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,Influenza A (H1N1),EFO:1001488,Pneumonia patients without any influenza A infection,Pneumonia patients with pH1N1 infection,"Positive lab test (real-time PCR or cell culture) and criteria for pneumonia simultaneously met, with pH1N1 infection",11,11,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 6,Figure 1c,9 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Relative microbial abundance of pH1N1-infected and uninfected pneumonia patients at the genus level,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|838;1783272|1239|909932|1843489|31977|29465,Complete,Fatima
bsdb:23274889/1/1,23274889,case-control,23274889,10.2337/db12-0526,NA,"de Goffau M.C., Luopajärvi K., Knip M., Ilonen J., Ruohtula T., Härkönen T., Orivuori L., Hakala S., Welling G.W., Harmsen H.J. , Vaarala O.",Fecal microbiota composition differs between children with β-cell autoimmunity and those without,Diabetes,2013,NA,Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Autoimmune disease,EFO:0005140,Controls,Cases,"Children who had the development of signs of progressive β-cell autoimmunity, i.e., tested positive for at least two diabetes-associated autoantibodies.",18,18,3 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,feeding practices,sex",NA,NA,NA,decreased,NA,NA,decreased,Signature 1,Table 2,3 March 2025,Aleru Divine,Aleru Divine,Association between bacterial species and signs of β-cell autoimmunity,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis",1783272|201174|1760|85004|31953|1678|28025;1783272|1239|91061|186826|33958|1578|1579;1783272|1239|186801|186802|31979|1485|1502;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|817,Complete,Svetlana up
bsdb:23274889/1/2,23274889,case-control,23274889,10.2337/db12-0526,NA,"de Goffau M.C., Luopajärvi K., Knip M., Ilonen J., Ruohtula T., Härkönen T., Orivuori L., Hakala S., Welling G.W., Harmsen H.J. , Vaarala O.",Fecal microbiota composition differs between children with β-cell autoimmunity and those without,Diabetes,2013,NA,Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Autoimmune disease,EFO:0005140,Controls,Cases,"Children who had the development of signs of progressive β-cell autoimmunity, i.e., tested positive for at least two diabetes-associated autoantibodies.",18,18,3 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,feeding practices,sex",NA,NA,NA,decreased,NA,NA,decreased,Signature 2,Table 2,3 March 2025,Aleru Divine,Aleru Divine,Association between bacterial species and signs of β-cell autoimmunity,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerocolumna|s__Anaerocolumna xylanovorans,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus gorbachii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium|s__Acetanaerobacterium elongatum",1783272|1239|186801|3085636|186803|841|301302;3379134|976|200643|171549|815|816|818;1783272|1239|186801|3085636|186803|1843210|100134;1783272|1239|1737404|1737405|1570339|162289|411567;1783272|1239|186801|186802|216572|258514|258515,Complete,Svetlana up
bsdb:23339708/1/1,23339708,prospective cohort,23339708,10.1186/1471-2180-13-12,NA,"Nylund L., Satokari R., Nikkilä J., Rajilić-Stojanović M., Kalliomäki M., Isolauri E., Salminen S. , de Vos W.M.",Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease,BMC microbiology,2013,NA,Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,child with eczema,19,15,NA,16S,NA,Human Intestinal Tract Chip,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,increased,NA,Signature 1,Table 2,10 January 2021,Lucy Mellor,"Fatima,WikiWorks",Differences in microbiota of healthy and eczematous children at 18 months of age,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas nexilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] cellulosi",1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|3085636|186803|2005355|29361;1783272|1239|186801|3085636|186803|2316020|46228;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|186802|216572|29343,Complete,Folakunmi
bsdb:23339708/1/2,23339708,prospective cohort,23339708,10.1186/1471-2180-13-12,NA,"Nylund L., Satokari R., Nikkilä J., Rajilić-Stojanović M., Kalliomäki M., Isolauri E., Salminen S. , de Vos W.M.",Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease,BMC microbiology,2013,NA,Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,child with eczema,19,15,NA,16S,NA,Human Intestinal Tract Chip,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,increased,NA,Signature 2,Table 2,10 January 2021,Lucy Mellor,WikiWorks,Differences in microbiota of healthy and eczematous children at 18 months of age,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Pseudomonadati|p__Bacteroidota",3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|816|46506;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|171552|1283313|76122;3379134|976,Complete,Folakunmi
bsdb:23339708/2/1,23339708,prospective cohort,23339708,10.1186/1471-2180-13-12,NA,"Nylund L., Satokari R., Nikkilä J., Rajilić-Stojanović M., Kalliomäki M., Isolauri E., Salminen S. , de Vos W.M.",Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease,BMC microbiology,2013,NA,Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,infant at 6 months,infant at 18 months,infant 18 months of age,34,34,NA,16S,NA,Human Intestinal Tract Chip,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,increased,NA,Signature 1,Figure 1,10 January 2021,Lucy Mellor,"WikiWorks,Merit,Folakunmi,Aleru Divine",Relative contribution of phylum-like bacterial groups to the total HITChip signals of infants at 6 and 18 months of age,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,1783272|1239|186801|3085636|186803|572511|1532,Complete,Folakunmi
bsdb:23339708/2/2,23339708,prospective cohort,23339708,10.1186/1471-2180-13-12,NA,"Nylund L., Satokari R., Nikkilä J., Rajilić-Stojanović M., Kalliomäki M., Isolauri E., Salminen S. , de Vos W.M.",Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease,BMC microbiology,2013,NA,Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,infant at 6 months,infant at 18 months,infant 18 months of age,34,34,NA,16S,NA,Human Intestinal Tract Chip,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,increased,NA,Signature 2,Figure 1,10 January 2021,Lucy Mellor,WikiWorks,Relative contribution of phylum-like bacterial groups to the total HITChip signals of infants at 6 and 18 months of age,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli",1783272|201174;1783272|1239|91061,Complete,Folakunmi
bsdb:23339708/3/1,23339708,prospective cohort,23339708,10.1186/1471-2180-13-12,NA,"Nylund L., Satokari R., Nikkilä J., Rajilić-Stojanović M., Kalliomäki M., Isolauri E., Salminen S. , de Vos W.M.",Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease,BMC microbiology,2013,NA,Experiment 3,Finland,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,infant at 6 months,infant at 18 months,infant 18 months of age,34,34,NA,16S,NA,Human Intestinal Tract Chip,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,increased,NA,Signature 1,Table 1,10 January 2021,Lucy Mellor,"WikiWorks,Folakunmi","Genus-like phylogenetic groups changing statistically significantly from 6 to 18 months of age as assessed by
HITChip analysis",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium|s__Lachnobacterium bovis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|s__uncultured Mollicutes bacterium",1783272|1239|186801|3085636|186803|3342669|45851;1783272|1239|526524|526525|2810280|100883|100884;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|140625|140626;1783272|1239|909932|1843488|909930|33024|33025;3379134|1224|1236|91347|1903414|583;1783272|1239|186801|186802|216572|1263|40518;3379134|1224|28216|80840|995019|40544|40545;1783272|1239|186801|3085636|186803|2941495|1512;1783272|544448|31969|220137,Complete,Folakunmi
bsdb:23339708/3/2,23339708,prospective cohort,23339708,10.1186/1471-2180-13-12,NA,"Nylund L., Satokari R., Nikkilä J., Rajilić-Stojanović M., Kalliomäki M., Isolauri E., Salminen S. , de Vos W.M.",Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease,BMC microbiology,2013,NA,Experiment 3,Finland,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,infant at 6 months,infant at 18 months,infant 18 months of age,34,34,NA,16S,NA,Human Intestinal Tract Chip,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,increased,NA,Signature 2,Table 1,10 January 2021,Lucy Mellor,WikiWorks,"Genus-like phylogenetic groups changing statistically significantly from 6 to 18 months of age as assessed by
HITChip analysis",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus|s__Lactiplantibacillus plantarum",1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|2767842|1590,Complete,Folakunmi
bsdb:23339708/4/1,23339708,prospective cohort,23339708,10.1186/1471-2180-13-12,NA,"Nylund L., Satokari R., Nikkilä J., Rajilić-Stojanović M., Kalliomäki M., Isolauri E., Salminen S. , de Vos W.M.",Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease,BMC microbiology,2013,NA,Experiment 4,Finland,Homo sapiens,Feces,UBERON:0001988,Lactobacillus rhamnosus GG,NCBITAXON:568703,placebo group at 18 months,children supplemented with LGG at 18 months,children who have been supplemented with L. rhamnosus GG at the age of 18 months i.e. a year after the cessation of the probiotic supplementation,15,19,NA,16S,NA,Human Intestinal Tract Chip,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Additional file 9,25 February 2024,Folakunmi,"Folakunmi,WikiWorks","The microbiota differences between the intervention groups (LGG or
placebo) at the age of 18 months as assessed by HITChip analysis.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum",1783272|1239|186801|3085636|186803|207244|105841;1783272|1239|186801|186802|186806|1730|39496,Complete,Folakunmi
bsdb:23339708/4/2,23339708,prospective cohort,23339708,10.1186/1471-2180-13-12,NA,"Nylund L., Satokari R., Nikkilä J., Rajilić-Stojanović M., Kalliomäki M., Isolauri E., Salminen S. , de Vos W.M.",Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease,BMC microbiology,2013,NA,Experiment 4,Finland,Homo sapiens,Feces,UBERON:0001988,Lactobacillus rhamnosus GG,NCBITAXON:568703,placebo group at 18 months,children supplemented with LGG at 18 months,children who have been supplemented with L. rhamnosus GG at the age of 18 months i.e. a year after the cessation of the probiotic supplementation,15,19,NA,16S,NA,Human Intestinal Tract Chip,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Additional file 9,25 February 2024,Folakunmi,"Folakunmi,WikiWorks","The microbiota differences between the intervention groups (LGG or
placebo) at the age of 18 months as assessed by HITChip analysis.",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,1783272|1239|186801|3082720|186804|1870884|1496,Complete,Folakunmi
bsdb:23349750/1/1,23349750,"cross-sectional observational, not case-control",23349750,10.1371/journal.pone.0053838,https://pubmed.ncbi.nlm.nih.gov/23349750/,"Lin A., Bik E.M., Costello E.K., Dethlefsen L., Haque R., Relman D.A. , Singh U.",Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States,PloS one,2013,NA,Experiment 1,"United States of America,Bangladesh",Homo sapiens,Feces,UBERON:0001988,"Ethnic group,Socioeconomic status","EFO:0001799,EXO:0000114",US children,Bangladesh Children (Household income < $61),"Fecal specimens from 6 Bangladeshi children (ages 8–13), in low socioeconomic conditions with an average monthly income per family of,5,000 takas (the U.S. $61).",4,6,3 months,16S,123,Roche454,NA,ANOSIM,0.1,TRUE,NA,NA,"age,sex",NA,increased,increased,NA,NA,NA,Signature 1,Table 3,19 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1,WikiWorks",Differential microbial abundance between Bangladeshi children and US children,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239|186801|3085636|186803|830;1783272|1239|186801|186802,Complete,Claregrieve1
bsdb:23349750/1/2,23349750,"cross-sectional observational, not case-control",23349750,10.1371/journal.pone.0053838,https://pubmed.ncbi.nlm.nih.gov/23349750/,"Lin A., Bik E.M., Costello E.K., Dethlefsen L., Haque R., Relman D.A. , Singh U.",Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States,PloS one,2013,NA,Experiment 1,"United States of America,Bangladesh",Homo sapiens,Feces,UBERON:0001988,"Ethnic group,Socioeconomic status","EFO:0001799,EXO:0000114",US children,Bangladesh Children (Household income < $61),"Fecal specimens from 6 Bangladeshi children (ages 8–13), in low socioeconomic conditions with an average monthly income per family of,5,000 takas (the U.S. $61).",4,6,3 months,16S,123,Roche454,NA,ANOSIM,0.1,TRUE,NA,NA,"age,sex",NA,increased,increased,NA,NA,NA,Signature 2,Table 3,20 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1,WikiWorks",Differential microbial abundance between Bangladeshi children and US children,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",3379134|976|200643|171549|815|816|818;1783272|1239|186801|186802|216572|216851|853,Complete,Claregrieve1
bsdb:23433344/1/1,23433344,case-control,23433344,10.1186/1741-7015-11-46,NA,"Murri M., Leiva I., Gomez-Zumaquero J.M., Tinahones F.J., Cardona F., Soriguer F. , Queipo-Ortuño M.I.",Gut microbiota in children with type 1 diabetes differs from that in healthy children: a case-control study,BMC medicine,2013,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Type I diabetes mellitus,MONDO:0005147,healthy controls,children with type 1 diabetes,"Type 1 diabetes was diagnosed following the criteria of the American Diabetes Association and the appearance of at least two persistent, confirmed anti-islet autoantibodies (insulin autoantibodies, glutamic acid decarboxylase autoantibodies or tyrosine phosphatase autoantibodies)",16,16,3 months,16S,23,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,breastfeeding duration,delivery procedure,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 5 &6,10 January 2021,Yaseen Javaid,WikiWorks,Gut microbiota in children with type 1 diabetes differs from that in healthy children: a case-control study.,increased,"k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976;1783272|1239|186801|186802|31979|1485;3379134|976|200643|171549|815|816;1783272|1239|909932|1843489|31977|29465,Complete,Shaimaa Elsafoury
bsdb:23433344/1/2,23433344,case-control,23433344,10.1186/1741-7015-11-46,NA,"Murri M., Leiva I., Gomez-Zumaquero J.M., Tinahones F.J., Cardona F., Soriguer F. , Queipo-Ortuño M.I.",Gut microbiota in children with type 1 diabetes differs from that in healthy children: a case-control study,BMC medicine,2013,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Type I diabetes mellitus,MONDO:0005147,healthy controls,children with type 1 diabetes,"Type 1 diabetes was diagnosed following the criteria of the American Diabetes Association and the appearance of at least two persistent, confirmed anti-islet autoantibodies (insulin autoantibodies, glutamic acid decarboxylase autoantibodies or tyrosine phosphatase autoantibodies)",16,16,3 months,16S,23,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,breastfeeding duration,delivery procedure,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 5 &6,10 January 2021,Yaseen Javaid,WikiWorks,Gut microbiota in children with type 1 diabetes differs from that in healthy children: a case-control study.,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|201174;1783272|1239;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|572511|1532;1783272|1239|186801|3085636|186803|1766253|39491;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|1578,Complete,Shaimaa Elsafoury
bsdb:23454028/1/1,23454028,case-control,23454028,10.1016/j.cgh.2013.02.015,NA,"Raman M., Ahmed I., Gillevet P.M., Probert C.S., Ratcliffe N.M., Smith S., Greenwood R., Sikaroodi M., Lam V., Crotty P., Bailey J., Myers R.P. , Rioux K.P.",Fecal microbiome and volatile organic compound metabolome in obese humans with nonalcoholic fatty liver disease,Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association,2013,NA,Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,healthy controls,nonalcoholic fatty liver disease,Obese patients with a body mass index (BMI) greater than 30 kg/m2 and clinically suspected non-alcoholic fatty liver disease,30,30,3 months,16S,NA,Roche454,relative abundances,Metastats,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Rimsha Azhar,WikiWorks,Significant taxa distinguishing in control and NAFLD,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Kiloniellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea",3379134|1224|28211|204441|597359;3379134|1224|1236|135625|712;1783272|1239|91061|186826|33958;1783272|1239|909932|1843489|31977;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|588605;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|189330,Complete,Claregrieve1
bsdb:23454028/1/2,23454028,case-control,23454028,10.1016/j.cgh.2013.02.015,NA,"Raman M., Ahmed I., Gillevet P.M., Probert C.S., Ratcliffe N.M., Smith S., Greenwood R., Sikaroodi M., Lam V., Crotty P., Bailey J., Myers R.P. , Rioux K.P.",Fecal microbiome and volatile organic compound metabolome in obese humans with nonalcoholic fatty liver disease,Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association,2013,NA,Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,healthy controls,nonalcoholic fatty liver disease,Obese patients with a body mass index (BMI) greater than 30 kg/m2 and clinically suspected non-alcoholic fatty liver disease,30,30,3 months,16S,NA,Roche454,relative abundances,Metastats,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 4,10 January 2021,Rimsha Azhar,WikiWorks,Significant taxa distinguishing in control and NAFLD,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",1783272|1239|186801|186802|541000;3379134|976|200643|171549|171551;1783272|1239|186801|186802|216572|459786,Complete,Claregrieve1
bsdb:23459324/1/1,23459324,"cross-sectional observational, not case-control",23459324,10.1038/ijo.2013.20,NA,"Million M., Angelakis E., Maraninchi M., Henry M., Giorgi R., Valero R., Vialettes B. , Raoult D.","Correlation between body mass index and gut concentrations of Lactobacillus reuteri, Bifidobacterium animalis, Methanobrevibacter smithii and Escherichia coli",International journal of obesity (2005),2013,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,"anorexic, lean, and overweight subjects",obese subjects,patients who were obese by BMI (BMI>30 kg m−2),128,134,6 months,WMS,NA,RT-qPCR,NA,Chi-Square,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 1,10 January 2021,Mst Afroza Parvin,"Claregrieve1,WikiWorks,Folakunmi",Differential microbial abundance between the obese group and all the other groups,decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Claregrieve1
bsdb:23459324/2/1,23459324,"cross-sectional observational, not case-control",23459324,10.1038/ijo.2013.20,NA,"Million M., Angelakis E., Maraninchi M., Henry M., Giorgi R., Valero R., Vialettes B. , Raoult D.","Correlation between body mass index and gut concentrations of Lactobacillus reuteri, Bifidobacterium animalis, Methanobrevibacter smithii and Escherichia coli",International journal of obesity (2005),2013,NA,Experiment 2,France,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean and anorexic subjects,obese and overweight subjects,patients who were overweight or obese by BMI,91,171,6 months,WMS,NA,RT-qPCR,NA,Chi-Square,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 1,10 January 2021,Mst Afroza Parvin,"Claregrieve1,WikiWorks,Folakunmi",Differential microbial abundance between the obese and overweight group and the lean and anorexic group,decreased,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,3366610|28890|183925|2158|2159|2172|2173,Complete,Claregrieve1
bsdb:23459324/3/1,23459324,"cross-sectional observational, not case-control",23459324,10.1038/ijo.2013.20,NA,"Million M., Angelakis E., Maraninchi M., Henry M., Giorgi R., Valero R., Vialettes B. , Raoult D.","Correlation between body mass index and gut concentrations of Lactobacillus reuteri, Bifidobacterium animalis, Methanobrevibacter smithii and Escherichia coli",International journal of obesity (2005),2013,NA,Experiment 3,France,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean subjects,obese subjects,obese patients defined by BMI  (BMI>30 kg m−2),64,108,6 months,WMS,NA,RT-qPCR,NA,Chi-Square,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 1,10 January 2021,Mst Afroza Parvin,"Claregrieve1,WikiWorks,Folakunmi",Differential microbial abundance between obese and lean subjects (species level),decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,1783272|201174|1760|85004|31953|1678|28025,Complete,Claregrieve1
bsdb:23459324/3/2,23459324,"cross-sectional observational, not case-control",23459324,10.1038/ijo.2013.20,NA,"Million M., Angelakis E., Maraninchi M., Henry M., Giorgi R., Valero R., Vialettes B. , Raoult D.","Correlation between body mass index and gut concentrations of Lactobacillus reuteri, Bifidobacterium animalis, Methanobrevibacter smithii and Escherichia coli",International journal of obesity (2005),2013,NA,Experiment 3,France,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean subjects,obese subjects,obese patients defined by BMI  (BMI>30 kg m−2),64,108,6 months,WMS,NA,RT-qPCR,NA,Chi-Square,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 1,9 August 2022,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between obese and lean subjects,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,1783272|1239|91061|186826|33958|2742598|1598,Complete,Folakunmi
bsdb:23459324/4/1,23459324,"cross-sectional observational, not case-control",23459324,10.1038/ijo.2013.20,NA,"Million M., Angelakis E., Maraninchi M., Henry M., Giorgi R., Valero R., Vialettes B. , Raoult D.","Correlation between body mass index and gut concentrations of Lactobacillus reuteri, Bifidobacterium animalis, Methanobrevibacter smithii and Escherichia coli",International journal of obesity (2005),2013,NA,Experiment 4,France,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean subjects,overweight subjects,patients who were overweight by BMI  (BMI>25 and <30 kg m−2),64,32,6 months,WMS,NA,RT-qPCR,NA,Chi-Square,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 1,10 January 2021,Mst Afroza Parvin,"Claregrieve1,WikiWorks",Differential microbial abundance between overweight and lean subjects,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,1783272|1239|91061|186826|33958|2742598|1598,Complete,Folakunmi
bsdb:23459324/5/1,23459324,"cross-sectional observational, not case-control",23459324,10.1038/ijo.2013.20,NA,"Million M., Angelakis E., Maraninchi M., Henry M., Giorgi R., Valero R., Vialettes B. , Raoult D.","Correlation between body mass index and gut concentrations of Lactobacillus reuteri, Bifidobacterium animalis, Methanobrevibacter smithii and Escherichia coli",International journal of obesity (2005),2013,NA,Experiment 5,France,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,"anorexic, lean, and overweight subjects (species level)",obese subjects (species level),patients who were obese by BMI (BMI>30 kg m−2),111,108,6 months,WMS,NA,RT-qPCR,NA,Chi-Square,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 1,9 August 2022,Claregrieve1,"Claregrieve1,Folakunmi,WikiWorks",Differential microbial abundance between the obese group and all the other groups at the species level,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,1783272|201174|1760|85004|31953|1678|28025,Complete,Folakunmi
bsdb:23459324/6/1,23459324,"cross-sectional observational, not case-control",23459324,10.1038/ijo.2013.20,NA,"Million M., Angelakis E., Maraninchi M., Henry M., Giorgi R., Valero R., Vialettes B. , Raoult D.","Correlation between body mass index and gut concentrations of Lactobacillus reuteri, Bifidobacterium animalis, Methanobrevibacter smithii and Escherichia coli",International journal of obesity (2005),2013,NA,Experiment 6,France,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean and anorexic subjects,obese and overweight subjects,patients who were overweight or obese by BMI,79,140,6 months,WMS,NA,RT-qPCR,NA,Chi-Square,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 1,29 January 2024,Folakunmi,"Folakunmi,WikiWorks",Differential microbial abundance between the obese and overweight group and the lean and anorexic group at species level,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,1783272|1239|91061|186826|33958|2742598|1598,Complete,Folakunmi
bsdb:23491408/1/1,23491408,prospective cohort,23491408,https://doi.org/10.1164/rccm.201210-1913oc,https://pubmed.ncbi.nlm.nih.gov/23491408/,"Morris A., Beck J.M., Schloss P.D., Campbell T.B., Crothers K., Curtis J.L., Flores S.C., Fontenot A.P., Ghedin E., Huang L., Jablonski K., Kleerup E., Lynch S.V., Sodergren E., Twigg H., Young V.B., Bassis C.M., Venkataraman A., Schmidt T.M. , Weinstock G.M.",Comparison of the respiratory microbiome in healthy nonsmokers and smokers,American journal of respiratory and critical care medicine,2013,NA,Experiment 1,United States of America,Homo sapiens,Mouth,UBERON:0000165,Smoking behavior,EFO:0004318,Healthy non-smokers,Healthy current smokers,Subjects who currently smoke.,45,19,3 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),NA,NA,NA,NA,"body mass index,sex,smoking status",NA,increased,NA,NA,increased,increased,Signature 1,"Figure 3A, 4A",5 June 2023,Atrayees,"Atrayees,ChiomaBlessing,WikiWorks",Relative abundance of bacterial taxa in the oral wash samples from nonsmokers and smokers at V1-V3 regions,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301;3384189|32066|203490|203491|203492|848,Complete,Atrayees
bsdb:23491408/1/2,23491408,prospective cohort,23491408,https://doi.org/10.1164/rccm.201210-1913oc,https://pubmed.ncbi.nlm.nih.gov/23491408/,"Morris A., Beck J.M., Schloss P.D., Campbell T.B., Crothers K., Curtis J.L., Flores S.C., Fontenot A.P., Ghedin E., Huang L., Jablonski K., Kleerup E., Lynch S.V., Sodergren E., Twigg H., Young V.B., Bassis C.M., Venkataraman A., Schmidt T.M. , Weinstock G.M.",Comparison of the respiratory microbiome in healthy nonsmokers and smokers,American journal of respiratory and critical care medicine,2013,NA,Experiment 1,United States of America,Homo sapiens,Mouth,UBERON:0000165,Smoking behavior,EFO:0004318,Healthy non-smokers,Healthy current smokers,Subjects who currently smoke.,45,19,3 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),NA,NA,NA,NA,"body mass index,sex,smoking status",NA,increased,NA,NA,increased,increased,Signature 2,"Figure 3A, 4A",5 June 2023,Atrayees,"Atrayees,ChiomaBlessing,WikiWorks",Relative abundance of bacterial taxa in the oral wash samples from nonsmokers and smokers at V1-V3 regions,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|201174|1760|2037|2049|1654;3384189|32066|203490|203491|203492|848;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;3379134|976|200643|171549|171552|838,Complete,Atrayees
bsdb:23491408/2/1,23491408,prospective cohort,23491408,https://doi.org/10.1164/rccm.201210-1913oc,https://pubmed.ncbi.nlm.nih.gov/23491408/,"Morris A., Beck J.M., Schloss P.D., Campbell T.B., Crothers K., Curtis J.L., Flores S.C., Fontenot A.P., Ghedin E., Huang L., Jablonski K., Kleerup E., Lynch S.V., Sodergren E., Twigg H., Young V.B., Bassis C.M., Venkataraman A., Schmidt T.M. , Weinstock G.M.",Comparison of the respiratory microbiome in healthy nonsmokers and smokers,American journal of respiratory and critical care medicine,2013,NA,Experiment 2,United States of America,Homo sapiens,Middle lobe of lung,UBERON:0008955,Smoking behavior,EFO:0004318,Healthy non-smokers,Healthy current smokers,Subjects who currently smoke.,45,19,3 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),NA,NA,NA,NA,"body mass index,sex,smoking status",NA,decreased,NA,NA,increased,increased,Signature 1,Figure 3A,5 June 2023,Atrayees,"Atrayees,ChiomaBlessing,WikiWorks",Relative abundance of bacterial taxa in the bronchoscopic alveolar lavages from nonsmokers and smokers at VI-V3 regions.,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301,Complete,ChiomaBlessing
bsdb:23491408/2/2,23491408,prospective cohort,23491408,https://doi.org/10.1164/rccm.201210-1913oc,https://pubmed.ncbi.nlm.nih.gov/23491408/,"Morris A., Beck J.M., Schloss P.D., Campbell T.B., Crothers K., Curtis J.L., Flores S.C., Fontenot A.P., Ghedin E., Huang L., Jablonski K., Kleerup E., Lynch S.V., Sodergren E., Twigg H., Young V.B., Bassis C.M., Venkataraman A., Schmidt T.M. , Weinstock G.M.",Comparison of the respiratory microbiome in healthy nonsmokers and smokers,American journal of respiratory and critical care medicine,2013,NA,Experiment 2,United States of America,Homo sapiens,Middle lobe of lung,UBERON:0008955,Smoking behavior,EFO:0004318,Healthy non-smokers,Healthy current smokers,Subjects who currently smoke.,45,19,3 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),NA,NA,NA,NA,"body mass index,sex,smoking status",NA,decreased,NA,NA,increased,increased,Signature 2,Figure 3A,5 June 2023,Atrayees,"Atrayees,ChiomaBlessing,WikiWorks",Relative abundance of bacterial taxa in the bronchoscopic alveolar lavages from nonsmokers and smokers at VI-V3 regions.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,c__Raphidophyceae|o__Chattonellales|f__Chattonellaceae|g__Heterosigma|s__Heterosigma akashiwo,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|2037|2049|1654;38410|658125|658124|2828|28465;1783272|1239|909932|1843489|31977|29465,Complete,ChiomaBlessing
bsdb:23491408/3/1,23491408,prospective cohort,23491408,https://doi.org/10.1164/rccm.201210-1913oc,https://pubmed.ncbi.nlm.nih.gov/23491408/,"Morris A., Beck J.M., Schloss P.D., Campbell T.B., Crothers K., Curtis J.L., Flores S.C., Fontenot A.P., Ghedin E., Huang L., Jablonski K., Kleerup E., Lynch S.V., Sodergren E., Twigg H., Young V.B., Bassis C.M., Venkataraman A., Schmidt T.M. , Weinstock G.M.",Comparison of the respiratory microbiome in healthy nonsmokers and smokers,American journal of respiratory and critical care medicine,2013,NA,Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Healthy non-smokers,Healthy current smokers,Subjects who currently smoke.,45,19,3 months,16S,345,Roche454,relative abundances,Mann-Whitney (Wilcoxon),NA,NA,NA,NA,"body mass index,sex,smoking status",NA,increased,NA,NA,increased,increased,Signature 1,Figure 3B and Figure 4B,5 June 2023,Atrayees,"Atrayees,ChiomaBlessing,WikiWorks",Relative abundance of bacterial taxa in the oral wash samples from nonsmokers and smokers at V3-V5 region.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium",3379134|976|200643|171549;1783272|1239|91061|186826;3379134|1224|28216|206351|481|482;1783272|1239|186801|3085636|186803|265975;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;33090|35493|3398|72025|3803|3814|508215;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378;3379134|976|200643|171549|2030927,Complete,ChiomaBlessing
bsdb:23491408/3/2,23491408,prospective cohort,23491408,https://doi.org/10.1164/rccm.201210-1913oc,https://pubmed.ncbi.nlm.nih.gov/23491408/,"Morris A., Beck J.M., Schloss P.D., Campbell T.B., Crothers K., Curtis J.L., Flores S.C., Fontenot A.P., Ghedin E., Huang L., Jablonski K., Kleerup E., Lynch S.V., Sodergren E., Twigg H., Young V.B., Bassis C.M., Venkataraman A., Schmidt T.M. , Weinstock G.M.",Comparison of the respiratory microbiome in healthy nonsmokers and smokers,American journal of respiratory and critical care medicine,2013,NA,Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Healthy non-smokers,Healthy current smokers,Subjects who currently smoke.,45,19,3 months,16S,345,Roche454,relative abundances,Mann-Whitney (Wilcoxon),NA,NA,NA,NA,"body mass index,sex,smoking status",NA,increased,NA,NA,increased,increased,Signature 2,Figure 3B and Figure 4B,5 June 2023,Atrayees,"Atrayees,ChiomaBlessing,WikiWorks",Relative abundance of bacterial taxa in the oral wash samples from nonsmokers and smokers at V3-V5 region.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Tropherymataceae|g__Tropheryma,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|1760|2037|2049|1654;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|265975;3379134|1224|1236|135625|712;3379134|976|200643|171549|171552|838;1783272|201174|1760|85006|2805591|2038;1783272|1239|91061|186826|1300|1301,Complete,ChiomaBlessing
bsdb:23491408/4/1,23491408,prospective cohort,23491408,https://doi.org/10.1164/rccm.201210-1913oc,https://pubmed.ncbi.nlm.nih.gov/23491408/,"Morris A., Beck J.M., Schloss P.D., Campbell T.B., Crothers K., Curtis J.L., Flores S.C., Fontenot A.P., Ghedin E., Huang L., Jablonski K., Kleerup E., Lynch S.V., Sodergren E., Twigg H., Young V.B., Bassis C.M., Venkataraman A., Schmidt T.M. , Weinstock G.M.",Comparison of the respiratory microbiome in healthy nonsmokers and smokers,American journal of respiratory and critical care medicine,2013,NA,Experiment 4,United States of America,Homo sapiens,Middle lobe of lung,UBERON:0008955,Smoking behavior,EFO:0004318,Healthy non-smokers,Healthy current smokers,Subjects who currently smoke.,45,19,3 months,16S,345,Roche454,relative abundances,Mann-Whitney (Wilcoxon),NA,NA,NA,NA,"body mass index,sex,smoking status",NA,decreased,NA,NA,decreased,decreased,Signature 1,Figure 3B,5 June 2023,Atrayees,"Atrayees,ChiomaBlessing,WikiWorks",Relative abundance of bacterial taxa in the bronchoscopic alveolar lavages from nonsmokers and smokers at V3-V5 regions.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,ChiomaBlessing
bsdb:23491408/4/2,23491408,prospective cohort,23491408,https://doi.org/10.1164/rccm.201210-1913oc,https://pubmed.ncbi.nlm.nih.gov/23491408/,"Morris A., Beck J.M., Schloss P.D., Campbell T.B., Crothers K., Curtis J.L., Flores S.C., Fontenot A.P., Ghedin E., Huang L., Jablonski K., Kleerup E., Lynch S.V., Sodergren E., Twigg H., Young V.B., Bassis C.M., Venkataraman A., Schmidt T.M. , Weinstock G.M.",Comparison of the respiratory microbiome in healthy nonsmokers and smokers,American journal of respiratory and critical care medicine,2013,NA,Experiment 4,United States of America,Homo sapiens,Middle lobe of lung,UBERON:0008955,Smoking behavior,EFO:0004318,Healthy non-smokers,Healthy current smokers,Subjects who currently smoke.,45,19,3 months,16S,345,Roche454,relative abundances,Mann-Whitney (Wilcoxon),NA,NA,NA,NA,"body mass index,sex,smoking status",NA,decreased,NA,NA,decreased,decreased,Signature 2,Figure 3B,5 June 2023,Atrayees,"Atrayees,ChiomaBlessing,WikiWorks",Relative abundance of bacterial taxa in the bronchoscopic alveolar lavages from nonsmokers and smokers at V3-V5 regions.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Tropherymataceae|g__Tropheryma,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|186801|3085636|186803|265975;3379134|1224|1236|135625|712;1783272|201174|1760|85006|2805591|2038;1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|171552|838,Complete,ChiomaBlessing
bsdb:23526699/1/1,23526699,case-control,23526699,10.1002/oby.20466,NA,"Verdam F.J., Fuentes S., de Jonge C., Zoetendal E.G., Erbil R., Greve J.W., Buurman W.A., de Vos W.M. , Rensen S.S.",Human intestinal microbiota composition is associated with local and systemic inflammation in obesity,"Obesity (Silver Spring, Md.)",2013,NA,Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,non-obese,obese,obesity: BMI 30.5-60.3 kg/m2,13,15,6 months,16S,NA,Human Intestinal Tract Chip,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Marianthi Thomatos,"WikiWorks,ChiomaBlessing",Differential microbial abundance between obese and non-obese individuals,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter|s__Papillibacter cinnamivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum",1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|186802|216572|100175|100176;1783272|1239|186801|3085636|186803|2941495|1512,Complete,Shaimaa Elsafoury
bsdb:23526699/1/2,23526699,case-control,23526699,10.1002/oby.20466,NA,"Verdam F.J., Fuentes S., de Jonge C., Zoetendal E.G., Erbil R., Greve J.W., Buurman W.A., de Vos W.M. , Rensen S.S.",Human intestinal microbiota composition is associated with local and systemic inflammation in obesity,"Obesity (Silver Spring, Md.)",2013,NA,Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,non-obese,obese,obesity: BMI 30.5-60.3 kg/m2,13,15,6 months,16S,NA,Human Intestinal Tract Chip,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,10 January 2021,Marianthi Thomatos,"WikiWorks,ChiomaBlessing",Differential microbial abundance between obese and non-obese individuals,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella oralis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter ruminicola",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171552|1283313|76122;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|329854;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|46506;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|171552|2974257|28134;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|2005525|195950;3379134|976|200643|171549|171552|558436|839,Complete,Shaimaa Elsafoury
bsdb:23526699/2/1,23526699,case-control,23526699,10.1002/oby.20466,NA,"Verdam F.J., Fuentes S., de Jonge C., Zoetendal E.G., Erbil R., Greve J.W., Buurman W.A., de Vos W.M. , Rensen S.S.",Human intestinal microbiota composition is associated with local and systemic inflammation in obesity,"Obesity (Silver Spring, Md.)",2013,NA,Experiment 2,Netherlands,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Nonobese microbiota cluster,obese,obesity: BMI 30.5-60.3 kg/m3,13,15,6 months,16S,NA,Human Intestinal Tract Chip,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 1,Table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Association of intestinal microbiota with local and systemic inflammation in obesity,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] colinum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii",1783272|1239|186801|3085636|186803|2941495|1512;1783272|1239|186801|3085636|186803|1506577|36835;1783272|1239|186801|3085636|186803|2569097|39488,Complete,Shaimaa Elsafoury
bsdb:23526699/2/2,23526699,case-control,23526699,10.1002/oby.20466,NA,"Verdam F.J., Fuentes S., de Jonge C., Zoetendal E.G., Erbil R., Greve J.W., Buurman W.A., de Vos W.M. , Rensen S.S.",Human intestinal microbiota composition is associated with local and systemic inflammation in obesity,"Obesity (Silver Spring, Md.)",2013,NA,Experiment 2,Netherlands,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Nonobese microbiota cluster,obese,obesity: BMI 30.5-60.3 kg/m3,13,15,6 months,16S,NA,Human Intestinal Tract Chip,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 2,Table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Association of intestinal microbiota with local and systemic inflammation in obesity,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira|s__Oscillospira guilliermondii",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|329854;3379134|976|200643|171549|1853231|283168|28118;1783272|1239|186801|186802|216572|119852|119853,Complete,Shaimaa Elsafoury
bsdb:23526699/3/1,23526699,case-control,23526699,10.1002/oby.20466,NA,"Verdam F.J., Fuentes S., de Jonge C., Zoetendal E.G., Erbil R., Greve J.W., Buurman W.A., de Vos W.M. , Rensen S.S.",Human intestinal microbiota composition is associated with local and systemic inflammation in obesity,"Obesity (Silver Spring, Md.)",2013,NA,Experiment 3,Netherlands,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,low BMI,high BMI,obesity: BMI 30.5-60.3 kg/m4,13,15,6 months,16S,NA,Human Intestinal Tract Chip,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,Marianthi Thomatos,"WikiWorks,ChiomaBlessing",Differential microbial abundance between high-BMI and low-BMI individuals,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Aneurinibacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium limosum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter|s__Papillibacter cinnamivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] colinum",1783272|1239|91061|1385|186822|55079;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|186802|186806|1730|1736;3379134|1224|1236|91347|543|570|548;3379134|1224|1236|91347|543|570|573;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|186802|216572|100175|100176;1783272|1239|186801|3085636|186803|841|166486;3379134|1224|1236|135623|641|662;3379134|1224|1236|91347|1903411|629;1783272|1239|186801|3085636|186803|1506577|36835,Complete,Shaimaa Elsafoury
bsdb:23526699/3/2,23526699,case-control,23526699,10.1002/oby.20466,NA,"Verdam F.J., Fuentes S., de Jonge C., Zoetendal E.G., Erbil R., Greve J.W., Buurman W.A., de Vos W.M. , Rensen S.S.",Human intestinal microbiota composition is associated with local and systemic inflammation in obesity,"Obesity (Silver Spring, Md.)",2013,NA,Experiment 3,Netherlands,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,low BMI,high BMI,obesity: BMI 30.5-60.3 kg/m4,13,15,6 months,16S,NA,Human Intestinal Tract Chip,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,10 January 2021,Marianthi Thomatos,"WikiWorks,ChiomaBlessing",Differential microbial abundance between high-BMI and low-BMI individuals,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes|s__Alcaligenes faecalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella oralis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter ruminicola",3379134|1224|28216|80840|506|507|511;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|329854;3379134|976|200643|171549|815|816|820;1783272|1239|526524|526525|2810280|100883|100884;1783272|1239|186801|186802|216572|216851|853;3379134|976|200643|171549|171552|2974257|28134;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|2005525|195950;3379134|976|200643|171549|171552|558436|839,Complete,Shaimaa Elsafoury
bsdb:23526699/4/1,23526699,case-control,23526699,10.1002/oby.20466,NA,"Verdam F.J., Fuentes S., de Jonge C., Zoetendal E.G., Erbil R., Greve J.W., Buurman W.A., de Vos W.M. , Rensen S.S.",Human intestinal microbiota composition is associated with local and systemic inflammation in obesity,"Obesity (Silver Spring, Md.)",2013,NA,Experiment 4,Netherlands,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,low C-Reactive Protein,high C-Reactive Protein,obesity: BMI 30.5-60.3 kg/m5,13,15,6 months,16S,NA,Human Intestinal Tract Chip,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Differential microbial abundance between high C-reactive protein group and low C-reactive protein group,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Aneurinibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora sphenoides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter|s__Papillibacter cinnamivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum variabile",1783272|1239|91061|1385|186822|55079;1783272|1239|186801|3085636|186803|2719231|29370;1783272|1239|186801|186802|216572|100175|100176;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|186802|216572|292632|214851,Complete,Shaimaa Elsafoury
bsdb:23526699/4/2,23526699,case-control,23526699,10.1002/oby.20466,NA,"Verdam F.J., Fuentes S., de Jonge C., Zoetendal E.G., Erbil R., Greve J.W., Buurman W.A., de Vos W.M. , Rensen S.S.",Human intestinal microbiota composition is associated with local and systemic inflammation in obesity,"Obesity (Silver Spring, Md.)",2013,NA,Experiment 4,Netherlands,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,low C-Reactive Protein,high C-Reactive Protein,obesity: BMI 30.5-60.3 kg/m5,13,15,6 months,16S,NA,Human Intestinal Tract Chip,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Differential microbial abundance between high C-reactive protein group and low C-reactive protein group,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816|329854;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|2005525|195950,Complete,Shaimaa Elsafoury
bsdb:23553152/1/1,23553152,case-control,23553152,10.3945/ajcn.112.046607,https://www.sciencedirect.com/science/article/pii/S0002916523055120?via=ihub,"Chen HM, Fang DC, Fang JY, Kong X, Lin YW, Liu F, Liu ZJ, Wang JL, Wu JX, Yang CQ, Yang L, Yu YN, Yuan YZ, Zhong L, Zou W",Decreased dietary fiber intake and structural alteration of gut microbiota in patients with advanced colorectal adenoma,The American journal of clinical nutrition,2013,"colorectal adenoma, colorectal cancer, dietary fiber, short-chain fatty acids",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,Healthy control group (HC),Advanced colorectal adenoma group (A-CRA),Patients with a diagnosis of A-CRA by pathological examination were enrolled in the A-CRA group.,47,47,6 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 4,31 May 2022,Jeshudy,"WikiWorks,Jeshudy",Significant differences in some genera identified between the HC (n = 47) and A-CRA (n = 47) groups,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",3379134|976|200643|171549|815|816;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|81852|1350,Complete,Rimsha
bsdb:23553152/1/2,23553152,case-control,23553152,10.3945/ajcn.112.046607,https://www.sciencedirect.com/science/article/pii/S0002916523055120?via=ihub,"Chen HM, Fang DC, Fang JY, Kong X, Lin YW, Liu F, Liu ZJ, Wang JL, Wu JX, Yang CQ, Yang L, Yu YN, Yuan YZ, Zhong L, Zou W",Decreased dietary fiber intake and structural alteration of gut microbiota in patients with advanced colorectal adenoma,The American journal of clinical nutrition,2013,"colorectal adenoma, colorectal cancer, dietary fiber, short-chain fatty acids",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,Healthy control group (HC),Advanced colorectal adenoma group (A-CRA),Patients with a diagnosis of A-CRA by pathological examination were enrolled in the A-CRA group.,47,47,6 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 4,24 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",Significant differences in some genera identified between the HC (n = 47) and A-CRA (n = 47) groups,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|31979|1485,Complete,Rimsha
bsdb:23565884/1/1,23565884,prospective cohort,23565884,10.1111/1469-0691.12213,NA,"Lazarevic V., Manzano S., Gaïa N., Girard M., Whiteson K., Hibbs J., François P., Gervaix A. , Schrenzel J.",Effects of amoxicillin treatment on the salivary microbiota in children with acute otitis media,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"Antibiotics, metagenomics, microbiota, otitis media, saliva",Experiment 1,Switzerland,Homo sapiens,Saliva,UBERON:0001836,Chronic otitis media,MONDO:0021204,Control(Unexposed to Amoxicillin),Amoxicillin-exposed,This is the group of children who were exposed to amoxicillin treatment for acute otitis media (AOM). They received amoxicillin as part of their treatment.,15,18,6 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,"age,sex",NA,increased,NA,NA,NA,increased,Signature 1,Supplementary file: Table 2.,15 October 2023,Chinelsy,"Chinelsy,WikiWorks",Changes in taxa abundance at different visits (A2 vs. A1),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|28216|80840;3384189|32066|203490|203491|203492;3384189|32066|203490|203491|203492|848;3379134|1224,Complete,Chinelsy
bsdb:23565884/2/1,23565884,prospective cohort,23565884,10.1111/1469-0691.12213,NA,"Lazarevic V., Manzano S., Gaïa N., Girard M., Whiteson K., Hibbs J., François P., Gervaix A. , Schrenzel J.",Effects of amoxicillin treatment on the salivary microbiota in children with acute otitis media,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"Antibiotics, metagenomics, microbiota, otitis media, saliva",Experiment 2,Switzerland,Homo sapiens,Saliva,UBERON:0001836,Chronic otitis media,MONDO:0021204,Control(Unexposed to Amoxicillin),Amoxicillin-exposed,This is the group of children who were exposed to amoxicillin treatment for acute otitis media (AOM). They received amoxicillin as part of their treatment.,15,18,6 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,"age,sex",NA,increased,NA,NA,NA,increased,Signature 1,Supplementary file: Table 2.,20 July 2021,Chloe,"Chloe,Lwaldron,Chinelsy,WikiWorks",Changes in taxa abundance at different visits (A3 vs. A1),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|28216|80840;3384189|32066|203490|203491|203492;3384189|32066|203490|203491|203492|848;3379134|1224,Complete,Chinelsy
bsdb:23613868/1/1,23613868,case-control,23613868,10.1371/journal.pone.0061516,NA,"Zhou M., Rong R., Munro D., Zhu C., Gao X., Zhang Q. , Dong Q.",Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing,PloS one,2013,NA,Experiment 1,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Periodontitis,EFO:0000649,No Periodontitis within negative diabetic background only,periodontitis,"Periodontitis was defined by the following criteria: at least 30% of sites with probing depth and attachment loss, and more than four with probing depth >=4 mm and clinical attachment loss >=2 mm. Subjects with type 2 diabetes had been diagnosed for at least one year with HbA1c >= 6.5%, fasting plasma glucose test >=7.0 mmol/L, or OGTT 2 hour glucose test >=11.1 mmol/L",5,6,3 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,10 January 2021,Yaseen Javaid,"WikiWorks,ChiomaBlessing",Significant differential abundant bacteria in periodontitis group VS healthy group within the diabetes-negative group,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii",3379134|976|200643|171549|171552;1783272|1239|909932|909929|1843491|970|69823;1783272|1239|91061|186826|1300|1301|1302,Complete,Shaimaa Elsafoury
bsdb:23613868/1/2,23613868,case-control,23613868,10.1371/journal.pone.0061516,NA,"Zhou M., Rong R., Munro D., Zhu C., Gao X., Zhang Q. , Dong Q.",Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing,PloS one,2013,NA,Experiment 1,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Periodontitis,EFO:0000649,No Periodontitis within negative diabetic background only,periodontitis,"Periodontitis was defined by the following criteria: at least 30% of sites with probing depth and attachment loss, and more than four with probing depth >=4 mm and clinical attachment loss >=2 mm. Subjects with type 2 diabetes had been diagnosed for at least one year with HbA1c >= 6.5%, fasting plasma glucose test >=7.0 mmol/L, or OGTT 2 hour glucose test >=11.1 mmol/L",5,6,3 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,10 January 2021,Yaseen Javaid,"Fatima,WikiWorks,ChiomaBlessing",Significant differential abundant bacteria in periodontitis group VS healthy group within the diabetes-negative group,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium valvarum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella loescheii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas noxia",3379134|1224|1236|135625|712|416916;3379134|976|117743|200644|49546|1016|1019;3379134|1224|1236|135615|868|2717|2718;3379134|1224|1236|135615|868|2717|194702;1783272|201174|1760|85007|1653|1716|43768;3379134|976|200643|171549|171552|2974257|840;3384189|32066|203490|203491|1129771|32067;3384189|32066|203490|203491|1129771;3379134|1224|28216|206351|481|482|484;3379134|976|200643|171549|171551|836|1924944;1783272|201174|1760|85009|31957;1783272|1239|909932|909929|1843491|970|135083,Complete,Fatima
bsdb:23613868/2/1,23613868,case-control,23613868,10.1371/journal.pone.0061516,NA,"Zhou M., Rong R., Munro D., Zhu C., Gao X., Zhang Q. , Dong Q.",Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing,PloS one,2013,NA,Experiment 2,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Type II diabetes mellitus,MONDO:0005148,Non-diabetic within negative periodontitis,Diabetic,"Periodontitis was defined by the following criteria: at least 30% of sites with probing depth and attachment loss, and more than four with probing depth >=4 mm and clinical attachment loss >=2 mm. Subjects with type 2 diabetes had been diagnosed for at least one year with HbA1c >= 6.5%, fasting plasma glucose test >=7.0 mmol/L, or OGTT 2 hour glucose test >=11.1 mmol/L",5,8,3 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Yaseen Javaid,"WikiWorks,ChiomaBlessing",Significant differential abundant bacteria in diabetic VS non-diabetic group within periodontitis-negative samples,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia",1783272|201174|1760|2037;3379134|1224|28216|80840;3379134|1224|28216|206351;3379134|976|200643|171549|2005525|195950|28112,Complete,Shaimaa Elsafoury
bsdb:23613868/2/2,23613868,case-control,23613868,10.1371/journal.pone.0061516,NA,"Zhou M., Rong R., Munro D., Zhu C., Gao X., Zhang Q. , Dong Q.",Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing,PloS one,2013,NA,Experiment 2,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Type II diabetes mellitus,MONDO:0005148,Non-diabetic within negative periodontitis,Diabetic,"Periodontitis was defined by the following criteria: at least 30% of sites with probing depth and attachment loss, and more than four with probing depth >=4 mm and clinical attachment loss >=2 mm. Subjects with type 2 diabetes had been diagnosed for at least one year with HbA1c >= 6.5%, fasting plasma glucose test >=7.0 mmol/L, or OGTT 2 hour glucose test >=11.1 mmol/L",5,8,3 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,10 January 2021,Yaseen Javaid,"WikiWorks,ChiomaBlessing",Significant differential abundant bacteria in diabetic VS non-diabetic group within periodontitis-negative samples,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium valvarum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella loescheii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens",3379134|976|117743|200644|49546|1016|1018;3379134|1224|1236|135615|868|2717|194702;1783272|201174|1760|85007|1653|1716|43768;3379134|976|200643|171549|171552|2974257|840;3379134|1224|28216|206351|481|482|484,Complete,Shaimaa Elsafoury
bsdb:23613868/3/1,23613868,case-control,23613868,10.1371/journal.pone.0061516,NA,"Zhou M., Rong R., Munro D., Zhu C., Gao X., Zhang Q. , Dong Q.",Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing,PloS one,2013,NA,Experiment 3,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Type II diabetes mellitus,MONDO:0005148,Non-diabetic within positive periodontitis,Diabetic,"Periodontitis was defined by the following criteria: at least 30% of sites with probing depth and attachment loss, and more than four with probing depth >=4 mm and clinical attachment loss >=2 mm. Subjects with type 2 diabetes had been diagnosed for at least one year with HbA1c >= 6.5%, fasting plasma glucose test >=7.0 mmol/L, or OGTT 2 hour glucose test >=11.1 mmol/L",6,12,3 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Significant differential abundant bacteria in diabetic VS non-diabetic group within periodontitis-positive samples,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae",3379134|976|117743|200644|49546|1016|1019;1783272|201174|1760|85009|31957,Complete,Shaimaa Elsafoury
bsdb:23613868/4/1,23613868,case-control,23613868,10.1371/journal.pone.0061516,NA,"Zhou M., Rong R., Munro D., Zhu C., Gao X., Zhang Q. , Dong Q.",Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing,PloS one,2013,NA,Experiment 4,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Periodontitis,EFO:0000649,No Periodontitis within positive diabetic background only,periodontitis,"Periodontitis was defined by the following criteria: at least 30% of sites with probing depth and attachment loss, and more than four with probing depth >=4 mm and clinical attachment loss >=2 mm. Subjects with type 2 diabetes had been diagnosed for at least one year with HbA1c >= 6.5%, fasting plasma glucose test >=7.0 mmol/L, or OGTT 2 hour glucose test >=11.1 mmol/L",8,12,3 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Significant differential abundant bacteria in periodontitis group VS healthy group within the diabetes-positive background,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema medium",3379134|976|200643|171549;1783272|1239|186801|3082720|3118655|44259|143361;3384189|32066|203490|203491|1129771|32067;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|171551|836|837;3384194|508458|649775|649776|649777;3379134|976|200643|171549|2005525|195950|28112;3379134|203691|203692|136|2845253|157|58231,Complete,Shaimaa Elsafoury
bsdb:23613868/4/2,23613868,case-control,23613868,10.1371/journal.pone.0061516,NA,"Zhou M., Rong R., Munro D., Zhu C., Gao X., Zhang Q. , Dong Q.",Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing,PloS one,2013,NA,Experiment 4,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Periodontitis,EFO:0000649,No Periodontitis within positive diabetic background only,periodontitis,"Periodontitis was defined by the following criteria: at least 30% of sites with probing depth and attachment loss, and more than four with probing depth >=4 mm and clinical attachment loss >=2 mm. Subjects with type 2 diabetes had been diagnosed for at least one year with HbA1c >= 6.5%, fasting plasma glucose test >=7.0 mmol/L, or OGTT 2 hour glucose test >=11.1 mmol/L",8,12,3 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Significant differential abundant bacteria in periodontitis group VS healthy group within the diabetes-positive background,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|1224|1236|135625|712|724|729;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481|482|495;1783272|201174|1760|85006|1268|32207|2047;1783272|1239|909932|1843489|31977|29465,Complete,Shaimaa Elsafoury
bsdb:23613868/5/1,23613868,case-control,23613868,10.1371/journal.pone.0061516,NA,"Zhou M., Rong R., Munro D., Zhu C., Gao X., Zhang Q. , Dong Q.",Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing,PloS one,2013,NA,Experiment 5,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Periodontitis,EFO:0000649,No Periodontitis within both positive and negative diabetic background,periodontitis,"Periodontitis was defined by the following criteria: at least 30% of sites with probing depth and attachment loss, and more than four with probing depth >=4 mm and clinical attachment loss >=2 mm. Subjects with type 2 diabetes had been diagnosed for at least one year with HbA1c >= 6.5%, fasting plasma glucose test >=7.0 mmol/L, or OGTT 2 hour glucose test >=11.1 mmol/L",13,18,3 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Significant differential abundant bacteria in periodontitis group VS healthy group within both the diabetes-positive and diabetes-negative background,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola",3379134|976|200643|171549|171552|838|28131;3379134|976|200643|171549|171552;3379134|203691|203692|136|2845253|157|158,Complete,Shaimaa Elsafoury
bsdb:23613868/5/2,23613868,case-control,23613868,10.1371/journal.pone.0061516,NA,"Zhou M., Rong R., Munro D., Zhu C., Gao X., Zhang Q. , Dong Q.",Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing,PloS one,2013,NA,Experiment 5,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Periodontitis,EFO:0000649,No Periodontitis within both positive and negative diabetic background,periodontitis,"Periodontitis was defined by the following criteria: at least 30% of sites with probing depth and attachment loss, and more than four with probing depth >=4 mm and clinical attachment loss >=2 mm. Subjects with type 2 diabetes had been diagnosed for at least one year with HbA1c >= 6.5%, fasting plasma glucose test >=7.0 mmol/L, or OGTT 2 hour glucose test >=11.1 mmol/L",13,18,3 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Significant differential abundant bacteria in periodontitis group VS healthy group within both the diabetes-positive and diabetes-negative background,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis",1783272|201174|1760|2037|2049|1654|1655;1783272|1239|91061|186826|1300|1301|1302;1783272|1239|91061|186826|1300|1301|68892,Complete,Shaimaa Elsafoury
bsdb:23631345/1/1,23631345,"cross-sectional observational, not case-control",23631345,10.1186/1757-4749-5-10,NA,"Bervoets L., Van Hoorenbeeck K., Kortleven I., Van Noten C., Hens N., Vael C., Goossens H., Desager K.N. , Vankerckhoven V.",Differences in gut microbiota composition between obese and lean children: a cross-sectional study,Gut pathogens,2013,NA,Experiment 1,Belgium,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control (lean/normal weight),obese (obese/overweight/morbidly obese),Children who are obese by BMI (classified based on the international BMI cut-off values of the Extended International Obesity Task Force (IOTF) for children aged 2 to 18),27,26,1 month,16S,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,10 January 2021,Mst Afroza Parvin,WikiWorks,Differences in bacterial genera between O/O and C group.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,1783272|1239|91061|186826|33958|1578|1591,Complete,Claregrieve1
bsdb:23631345/1/2,23631345,"cross-sectional observational, not case-control",23631345,10.1186/1757-4749-5-10,NA,"Bervoets L., Van Hoorenbeeck K., Kortleven I., Van Noten C., Hens N., Vael C., Goossens H., Desager K.N. , Vankerckhoven V.",Differences in gut microbiota composition between obese and lean children: a cross-sectional study,Gut pathogens,2013,NA,Experiment 1,Belgium,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control (lean/normal weight),obese (obese/overweight/morbidly obese),Children who are obese by BMI (classified based on the international BMI cut-off values of the Extended International Obesity Task Force (IOTF) for children aged 2 to 18),27,26,1 month,16S,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1,10 January 2021,Mst Afroza Parvin,WikiWorks,Differences in bacterial genera between O/O and C group.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,3379134|976|200643|171549|815|909656|821,Complete,Claregrieve1
bsdb:23638009/1/1,23638009,laboratory experiment,23638009,10.1371/journal.pone.0062220,NA,"Kish L., Hotte N., Kaplan G.G., Vincent R., Tso R., Gänzle M., Rioux K.P., Thiesen A., Barkema H.W., Wine E. , Madsen K.L.",Environmental particulate matter induces murine intestinal inflammatory responses and alters the gut microbiome,PloS one,2013,NA,Experiment 1,Canada,Mus musculus,Feces,UBERON:0001988,Air pollution,ENVO:02500037,healthy mice,Chronic treatment group,6-week old female wild-type 129/SvEv mice in chronic treatment group were fed mouse chow ± PM10 (0.09 gm/kg) for 35 days,7,8,NA,16S,NA,Non-quantitative PCR,relative abundances,PLS-DA (Partial least square discriminant analysis),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,10 January 2021,Zyaijah Bailey,"WikiWorks,Claregrieve1",Microbiota composition in stool samples from WT and IL-10−/− mice after 35 days of treatment with PM10.,increased,k__Pseudomonadati|p__Verrucomicrobiota,3379134|74201,Complete,Claregrieve1
bsdb:23638009/2/1,23638009,laboratory experiment,23638009,10.1371/journal.pone.0062220,NA,"Kish L., Hotte N., Kaplan G.G., Vincent R., Tso R., Gänzle M., Rioux K.P., Thiesen A., Barkema H.W., Wine E. , Madsen K.L.",Environmental particulate matter induces murine intestinal inflammatory responses and alters the gut microbiome,PloS one,2013,NA,Experiment 2,Canada,Mus musculus,Feces,UBERON:0001988,Air pollution,ENVO:02500037,healthy mice,IL-10−/−  mice fed mouse chow with PM10,IL-10−/−  mice in chronic treatment group were  fed mouse chow ± PM10 (0.09 gm/kg) for 35 days,9,7,NA,16S,NA,Non-quantitative PCR,relative abundances,PLS-DA (Partial least square discriminant analysis),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,10 January 2021,Zyaijah Bailey,"WikiWorks,Claregrieve1",Microbiota composition in stool samples from WT and IL-10−/− mice after 35 days of treatment with PM10.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. (in: firmicutes),1783272|1239|91061|1385|186817|1386|1409,Complete,Claregrieve1
bsdb:23638009/2/2,23638009,laboratory experiment,23638009,10.1371/journal.pone.0062220,NA,"Kish L., Hotte N., Kaplan G.G., Vincent R., Tso R., Gänzle M., Rioux K.P., Thiesen A., Barkema H.W., Wine E. , Madsen K.L.",Environmental particulate matter induces murine intestinal inflammatory responses and alters the gut microbiome,PloS one,2013,NA,Experiment 2,Canada,Mus musculus,Feces,UBERON:0001988,Air pollution,ENVO:02500037,healthy mice,IL-10−/−  mice fed mouse chow with PM10,IL-10−/−  mice in chronic treatment group were  fed mouse chow ± PM10 (0.09 gm/kg) for 35 days,9,7,NA,16S,NA,Non-quantitative PCR,relative abundances,PLS-DA (Partial least square discriminant analysis),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5,10 January 2021,Zyaijah Bailey,"WikiWorks,Claregrieve1",Microbiota composition in stool samples from WT and IL-10−/− mice after 35 days of treatment with PM10.,decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Claregrieve1
bsdb:23717441/1/1,23717441,"cross-sectional observational, not case-control",23717441,10.1371/journal.pone.0063514,NA,"Lee J.E., Lee S., Lee H., Song Y.M., Lee K., Han M.J., Sung J. , Ko G.",Association of the vaginal microbiota with human papillomavirus infection in a Korean twin cohort,PloS one,2013,NA,Experiment 1,South Korea,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV infection through PCR confirmation,9,9,6 months,16S,23,Roche454,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,figure 3,10 January 2021,Cynthia Anderson,"WikiWorks,Atrayees,Merit",A comparison of the vaginal microbiota among nine HPV infection-discordant twin pairs,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sp.,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",1783272|1239|909932|1843489|31977|39948;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066;1783272|1239|909932|1843489|31977|906;3384189|32066|203490|203491|1129771|168808;3384189|32066|203490|203491|1129771|168808|2776143;3384189|32066|203490|203491|203492|848,Complete,Fatima Zohra
bsdb:23717441/1/2,23717441,"cross-sectional observational, not case-control",23717441,10.1371/journal.pone.0063514,NA,"Lee J.E., Lee S., Lee H., Song Y.M., Lee K., Han M.J., Sung J. , Ko G.",Association of the vaginal microbiota with human papillomavirus infection in a Korean twin cohort,PloS one,2013,NA,Experiment 1,South Korea,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV infection through PCR confirmation,9,9,6 months,16S,23,Roche454,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,figure 3,10 January 2021,Cynthia Anderson,"WikiWorks,Merit",A comparison of the vaginal microbiota among nine HPV infection-discordant twin pairs,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826;1783272|1239|91061|186826|33958,Complete,Fatima Zohra
bsdb:23717441/2/1,23717441,"cross-sectional observational, not case-control",23717441,10.1371/journal.pone.0063514,NA,"Lee J.E., Lee S., Lee H., Song Y.M., Lee K., Han M.J., Sung J. , Ko G.",Association of the vaginal microbiota with human papillomavirus infection in a Korean twin cohort,PloS one,2013,NA,Experiment 2,South Korea,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ through PCR confirmation,26,19,6 months,16S,23,Roche454,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,figure 1b,10 January 2021,Cynthia Anderson,WikiWorks,Comparison of the vaginal microbiotas of the HIV+ and HIV- women without CIN,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales",3384189|32066|203490|203491|1129771|168808;3384189|32066|203490|203491|203492;3384189|32066|203490|203491,Complete,Fatima Zohra
bsdb:23717441/3/1,23717441,"cross-sectional observational, not case-control",23717441,10.1371/journal.pone.0063514,NA,"Lee J.E., Lee S., Lee H., Song Y.M., Lee K., Han M.J., Sung J. , Ko G.",Association of the vaginal microbiota with human papillomavirus infection in a Korean twin cohort,PloS one,2013,NA,Experiment 3,South Korea,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV-,HR-HPV+,"HR-HPV+ through PCR confirmation, HPV genotype 16, 18, 33, 35, 39, 45, 51, 52, 56, 58, 59, and 66",26,13,6 months,16S,23,Roche454,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,figure 1c,10 January 2021,Cynthia Anderson,WikiWorks,Comparison of the vaginal microbiotas of HIV- and women infected with high risk high risk HPV types,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales",3384189|32066|203490|203491|1129771|168808;3384189|32066|203490|203491|203492;3384189|32066|203490|203491,Complete,Fatima Zohra
bsdb:23717441/3/2,23717441,"cross-sectional observational, not case-control",23717441,10.1371/journal.pone.0063514,NA,"Lee J.E., Lee S., Lee H., Song Y.M., Lee K., Han M.J., Sung J. , Ko G.",Association of the vaginal microbiota with human papillomavirus infection in a Korean twin cohort,PloS one,2013,NA,Experiment 3,South Korea,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV-,HR-HPV+,"HR-HPV+ through PCR confirmation, HPV genotype 16, 18, 33, 35, 39, 45, 51, 52, 56, 58, 59, and 66",26,13,6 months,16S,23,Roche454,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,figure 1c,10 January 2021,Cynthia Anderson,WikiWorks,Comparison of the vaginal microbiotas of HIV- and women infected with high risk high risk HPV types,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,1783272|1239|91061|186826,Complete,Fatima Zohra
bsdb:23724144/1/1,23724144,laboratory experiment,23724144,10.1371/journal.pone.0065465,NA,"Queipo-Ortuño M.I., Seoane L.M., Murri M., Pardo M., Gomez-Zumaquero J.M., Cardona F., Casanueva F. , Tinahones F.J.",Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels,PloS one,2013,NA,Experiment 1,Spain,Rattus norvegicus,Feces,UBERON:0001988,Physical activity,EFO:0003940,exercise group,Activity Based Anorexia group,"(a) Activity based anorexia (ABA) group: rats starved by restricting food access to 23 hours per day and confined to running wheels except during a 60 min meal per day, (b) Control ABA group: rats submitted to the same food restriction schedule as ABA with no wheel access exercise, (c) Exercise group: rats feed ad libitum with free access to the activity wheel and (d) Ad libitum group: rats feed ad libitum but without access to the activity wheel.",10,10,NA,16S,23,RT-qPCR,NA,Kruskall-Wallis,0.05,TRUE,NA,body weight,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3 and Text,10 January 2021,Yaseen Javaid,WikiWorks,Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels,increased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Methanobacteriati|p__Methanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|1224;3379134|976|200643|171549|171552|838;3366610|28890;1783272|1239|186801|186802|31979|1485;1783272|1239|91061|186826|81852|1350;3379134|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
bsdb:23724144/1/2,23724144,laboratory experiment,23724144,10.1371/journal.pone.0065465,NA,"Queipo-Ortuño M.I., Seoane L.M., Murri M., Pardo M., Gomez-Zumaquero J.M., Cardona F., Casanueva F. , Tinahones F.J.",Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels,PloS one,2013,NA,Experiment 1,Spain,Rattus norvegicus,Feces,UBERON:0001988,Physical activity,EFO:0003940,exercise group,Activity Based Anorexia group,"(a) Activity based anorexia (ABA) group: rats starved by restricting food access to 23 hours per day and confined to running wheels except during a 60 min meal per day, (b) Control ABA group: rats submitted to the same food restriction schedule as ABA with no wheel access exercise, (c) Exercise group: rats feed ad libitum with free access to the activity wheel and (d) Ad libitum group: rats feed ad libitum but without access to the activity wheel.",10,10,NA,16S,23,RT-qPCR,NA,Kruskall-Wallis,0.05,TRUE,NA,body weight,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3 and Text,10 January 2021,Yaseen Javaid,"Fatima,WikiWorks",Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels,decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",1783272|201174;3379134|976|200643|171549|815|816;3379134|976;1783272|201174|1760|85004|31953|1678;1783272|1239;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|1766253|39491,Complete,Fatima
bsdb:23724144/2/1,23724144,laboratory experiment,23724144,10.1371/journal.pone.0065465,NA,"Queipo-Ortuño M.I., Seoane L.M., Murri M., Pardo M., Gomez-Zumaquero J.M., Cardona F., Casanueva F. , Tinahones F.J.",Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels,PloS one,2013,NA,Experiment 2,Spain,Rattus norvegicus,Feces,UBERON:0001988,Physical activity,EFO:0003940,exercise group,Ad libitum group,"(a) Activity based anorexia (ABA) group: rats starved by restricting food access to 23 hours per day and confined to running wheels except during a 60 min meal per day, (b) Control ABA group: rats submitted to the same food restriction schedule as ABA with no wheel access exercise, (c) Exercise group: rats feed ad libitum with free access to the activity wheel and (d) Ad libitum group: rats feed ad libitum but without access to the activity wheel.",10,10,NA,16S,23,RT-qPCR,NA,Kruskall-Wallis,0.05,TRUE,NA,body weight,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3 and Text,10 January 2021,Yaseen Javaid,WikiWorks,Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",3379134|976|200643|171549|815|816;3379134|976|200643|171549|171552|838;1783272|1239;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|31979|1485,Complete,Shaimaa Elsafoury
bsdb:23724144/2/2,23724144,laboratory experiment,23724144,10.1371/journal.pone.0065465,NA,"Queipo-Ortuño M.I., Seoane L.M., Murri M., Pardo M., Gomez-Zumaquero J.M., Cardona F., Casanueva F. , Tinahones F.J.",Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels,PloS one,2013,NA,Experiment 2,Spain,Rattus norvegicus,Feces,UBERON:0001988,Physical activity,EFO:0003940,exercise group,Ad libitum group,"(a) Activity based anorexia (ABA) group: rats starved by restricting food access to 23 hours per day and confined to running wheels except during a 60 min meal per day, (b) Control ABA group: rats submitted to the same food restriction schedule as ABA with no wheel access exercise, (c) Exercise group: rats feed ad libitum with free access to the activity wheel and (d) Ad libitum group: rats feed ad libitum but without access to the activity wheel.",10,10,NA,16S,23,RT-qPCR,NA,Kruskall-Wallis,0.05,TRUE,NA,body weight,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3 and Text,10 January 2021,Yaseen Javaid,"Fatima,WikiWorks",Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",1783272|201174;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|1766253|39491,Complete,Fatima
bsdb:23733170/1/1,23733170,case-control,23733170,10.1007/s00248-013-0245-9,NA,"Wu N., Yang X., Zhang R., Li J., Xiao X., Hu Y., Chen Y., Yang F., Lu N., Wang Z., Luan C., Liu Y., Wang B., Xiang C., Wang Y., Zhao F., Gao G.F., Wang S., Li L., Zhang H. , Zhu B.",Dysbiosis signature of fecal microbiota in colorectal cancer patients,Microbial ecology,2013,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls,CRC patients,NA,20,19,3 months,16S,3,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Shaimaa Elsafoury,"Fatima,WikiWorks",Cladogram of Colorectal cancer and healthy microbiota,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Tissierellia",1783272|1239|1737404|1737405|1570339|165779;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|236752;3384189|32066|203490|203491|203492;3384189|32066|203490;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378;1783272|1239|526524|526525|128827|61170;3379134|1224|28216|206351|481|32257;3384189|32066|203490|203491|1129771|32067;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836;1783272|1239|526524|526525|128827|123375;1783272|1239|91061|1385|90964;1783272|1239|1737404,Complete,Fatima
bsdb:23733170/1/2,23733170,case-control,23733170,10.1007/s00248-013-0245-9,NA,"Wu N., Yang X., Zhang R., Li J., Xiao X., Hu Y., Chen Y., Yang F., Lu N., Wang Z., Luan C., Liu Y., Wang B., Xiang C., Wang Y., Zhao F., Gao G.F., Wang S., Li L., Zhang H. , Zhu B.",Dysbiosis signature of fecal microbiota in colorectal cancer patients,Microbial ecology,2013,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls,CRC patients,NA,20,19,3 months,16S,3,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Cladogram of Colorectal cancer and healthy microbiota,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061|186826|33958|1243;1783272|1239|91061|186826|1300|1301,Complete,Shaimaa Elsafoury
bsdb:23758857/1/1,23758857,case-control,23758857,10.1186/1471-2334-13-271,NA,"Gao W., Weng J., Gao Y. , Chen X.",Comparison of the vaginal microbiota diversity of women with and without human papillomavirus infection: a cross-sectional study,BMC infectious diseases,2013,NA,Experiment 1,China,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,HPV negative women,HPV positive women,women positive for HPV infection,38,32,1 month,16S,23,NA,NA,Chi-Square,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between HPV positive and HPV negative women,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri",1783272|201174|1760|85004|31953|2701|2702;1783272|1239|91061|186826|33958|1578|1596,Complete,Claregrieve1
bsdb:23791918/1/1,23791918,case-control,23791918,10.1016/j.anaerobe.2013.06.002,NA,"Frémont M., Coomans D., Massart S. , De Meirleir K.",High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients,Anaerobe,2013,"Chronic fatigue syndrome, High-throughput sequencing, Intestinal microbiota, Myalgic encephalomyelitis",Experiment 1,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic fatigue syndrome,EFO:0004540,Belgian controls,Norweigan controls,Patients were diagnosed for CFS according to the clinical criteria of Fukuda et al,19,17,1 month,16S,56,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,table 1,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differentiately abundant mictobiota between Norwegian controls and Belgian controls.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania",1783272|1239|186801|3085636|186803|841;1783272|1239|526524|526525|128827|61170,Complete,Shaimaa Elsafoury
bsdb:23791918/1/2,23791918,case-control,23791918,10.1016/j.anaerobe.2013.06.002,NA,"Frémont M., Coomans D., Massart S. , De Meirleir K.",High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients,Anaerobe,2013,"Chronic fatigue syndrome, High-throughput sequencing, Intestinal microbiota, Myalgic encephalomyelitis",Experiment 1,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic fatigue syndrome,EFO:0004540,Belgian controls,Norweigan controls,Patients were diagnosed for CFS according to the clinical criteria of Fukuda et al,19,17,1 month,16S,56,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,table 1,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differentiately abundant mictobiota between Norwegian controls and Belgian controls,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|976|200643|171549|815|816;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|2005525|375288,Complete,Shaimaa Elsafoury
bsdb:23791918/2/1,23791918,case-control,23791918,10.1016/j.anaerobe.2013.06.002,NA,"Frémont M., Coomans D., Massart S. , De Meirleir K.",High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients,Anaerobe,2013,"Chronic fatigue syndrome, High-throughput sequencing, Intestinal microbiota, Myalgic encephalomyelitis",Experiment 2,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic fatigue syndrome,EFO:0004540,Norweigan controls,Norweigan CFS/ME patients,Patients were diagnosed for CFS according to the clinical criteria of Fukuda et al,17,25,1 month,16S,56,Roche454,NA,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differentiately abundant mictobiota between Norwegian CFS patients and Norwegian controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Lactonifactor",3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|31979|420345,Complete,Shaimaa Elsafoury
bsdb:23791918/2/2,23791918,case-control,23791918,10.1016/j.anaerobe.2013.06.002,NA,"Frémont M., Coomans D., Massart S. , De Meirleir K.",High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients,Anaerobe,2013,"Chronic fatigue syndrome, High-throughput sequencing, Intestinal microbiota, Myalgic encephalomyelitis",Experiment 2,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic fatigue syndrome,EFO:0004540,Norweigan controls,Norweigan CFS/ME patients,Patients were diagnosed for CFS according to the clinical criteria of Fukuda et al,17,25,1 month,16S,56,Roche454,NA,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differentiately abundant mictobiota between Norwegian CFS patients and Norwegian controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus",1783272|1239|186801|3085636|186803|841;1783272|1239|526524|526525|128827|61170;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|84036,Complete,Shaimaa Elsafoury
bsdb:23791918/3/1,23791918,case-control,23791918,10.1016/j.anaerobe.2013.06.002,NA,"Frémont M., Coomans D., Massart S. , De Meirleir K.",High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients,Anaerobe,2013,"Chronic fatigue syndrome, High-throughput sequencing, Intestinal microbiota, Myalgic encephalomyelitis",Experiment 3,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic fatigue syndrome,EFO:0004540,Belgian controls,Belgian CFS/ME patients,Patients were diagnosed for CFS according to the clinical criteria of Fukuda et al,19,18,1 month,16S,56,Roche454,NA,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differentiately abundant mictobiota between Belgian CFS patients and Belgian controls,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Lactonifactor,1783272|1239|186801|186802|31979|420345,Complete,Shaimaa Elsafoury
bsdb:23791918/3/2,23791918,case-control,23791918,10.1016/j.anaerobe.2013.06.002,NA,"Frémont M., Coomans D., Massart S. , De Meirleir K.",High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients,Anaerobe,2013,"Chronic fatigue syndrome, High-throughput sequencing, Intestinal microbiota, Myalgic encephalomyelitis",Experiment 3,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic fatigue syndrome,EFO:0004540,Belgian controls,Belgian CFS/ME patients,Patients were diagnosed for CFS according to the clinical criteria of Fukuda et al,19,18,1 month,16S,56,Roche454,NA,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differentiately abundant mictobiota between Belgian CFS patients and Belgian controls,decreased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Asaccharobacter,1783272|201174|84998|1643822|1643826|553372,Complete,Shaimaa Elsafoury
bsdb:23829394/1/1,23829394,time series / longitudinal observational,23829394,10.1111/1469-0691.12287,NA,"Ye Y., Carlsson G., Agholme M.B., Wilson J.A., Roos A., Henriques-Normark B., Engstrand L., Modéer T. , Pütsep K.",Oral bacterial community dynamics in paediatric patients with malignancies in relation to chemotherapy-related oral mucositis: a prospective study,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"16S rRNA gene, 454 pyrosequencing, cancer, oral microflora, stomatitis",Experiment 1,Sweden,Homo sapiens,"Lower lip,Buccal mucosa","UBERON:0001835,UBERON:0006956",Oral mucositis,EFO:1001904,reference,patients with newly diagnosed malignancies,patients that are newly diagnosed with malignancies (before chemotherapy treatment) that are between ages 4 and 18 years old that are treated with cytostatic drug and has a national population registration number (Sweden),38,37,NA,16S,NA,Roche454,relative abundances,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Figure 1a, Supplemental Table S2",10 January 2021,William Lam,WikiWorks,Comparison of the oral bacterial community between reference individuals and patients at the time of malignancy diagnosis (before chemotherapy),increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Derxia",1783272|1239|91061|186826|186827|46123;1783272|1239|91061|186826|1300|1357;3379134|1224|28216|80840|506|203697,Complete,Rimsha
bsdb:23829394/1/2,23829394,time series / longitudinal observational,23829394,10.1111/1469-0691.12287,NA,"Ye Y., Carlsson G., Agholme M.B., Wilson J.A., Roos A., Henriques-Normark B., Engstrand L., Modéer T. , Pütsep K.",Oral bacterial community dynamics in paediatric patients with malignancies in relation to chemotherapy-related oral mucositis: a prospective study,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"16S rRNA gene, 454 pyrosequencing, cancer, oral microflora, stomatitis",Experiment 1,Sweden,Homo sapiens,"Lower lip,Buccal mucosa","UBERON:0001835,UBERON:0006956",Oral mucositis,EFO:1001904,reference,patients with newly diagnosed malignancies,patients that are newly diagnosed with malignancies (before chemotherapy treatment) that are between ages 4 and 18 years old that are treated with cytostatic drug and has a national population registration number (Sweden),38,37,NA,16S,NA,Roche454,relative abundances,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 2,"Figure 1a, Supplemental Table S2",10 January 2021,William Lam,WikiWorks,Comparison of the oral bacterial community between reference individuals and patients at the time of malignancy diagnosis (before chemotherapy),decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus",1783272|201174|1760|85004|31953;1783272|201174|1760|85007|1653|1716;1783272|201174|84998|84999|84107;3379134|976|200643|171549|2005523|346096;3379134|976|117747;1783272|1239|91061|1385|539738|1378;1783272|1239|186801|3085636|186803;3384189|32066|203490|203491|203492|848;3379134|1224|1236|135622|267890|22;3379134|1224|1236|135619|28256|2745;3379134|1224|1236|135625|712|713,Complete,Claregrieve1
bsdb:23829394/2/1,23829394,time series / longitudinal observational,23829394,10.1111/1469-0691.12287,NA,"Ye Y., Carlsson G., Agholme M.B., Wilson J.A., Roos A., Henriques-Normark B., Engstrand L., Modéer T. , Pütsep K.",Oral bacterial community dynamics in paediatric patients with malignancies in relation to chemotherapy-related oral mucositis: a prospective study,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"16S rRNA gene, 454 pyrosequencing, cancer, oral microflora, stomatitis",Experiment 2,Sweden,Homo sapiens,"Lower lip,Buccal mucosa","UBERON:0001835,UBERON:0006956",Oral mucositis,EFO:1001904,no oral mucositis,oral mucositis,patients that are newly diagnosed with malignancies (before chemotherapy treatment) that are between ages 4 and 18 years old that are treated with cytostatic drug and has a national population registration number (Sweden) that has later developed oral mucositis (graded by the World Health Organization),12,25,NA,16S,NA,Roche454,NA,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Comparison of the oral bacterial community at the time of malignancy diagnosis (before chemotherapy) in patients who later developed oral mucositis and those who did not develop oral mucositis,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",3379134|976|117743|200644|49546|1016;3384189|32066;1783272|1239|91061|186826|1300|1357;3379134|203691|203692|136|137|146;1783272|1239|186801|3082720|186804,Complete,Claregrieve1
bsdb:23829394/3/1,23829394,time series / longitudinal observational,23829394,10.1111/1469-0691.12287,NA,"Ye Y., Carlsson G., Agholme M.B., Wilson J.A., Roos A., Henriques-Normark B., Engstrand L., Modéer T. , Pütsep K.",Oral bacterial community dynamics in paediatric patients with malignancies in relation to chemotherapy-related oral mucositis: a prospective study,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"16S rRNA gene, 454 pyrosequencing, cancer, oral microflora, stomatitis",Experiment 3,Sweden,Homo sapiens,"Lower lip,Buccal mucosa","UBERON:0001835,UBERON:0006956",Oral mucositis,EFO:1001904,at malignancy diagnosis,during chemotherapy,patients that are newly diagnosed with malignancies that are between ages 4 and 18 years old that are treated with cytostatic drug and has a national population registration number (Sweden) that has later developed oral mucositis (graded by the World Health Organization) during chemotherapy treatment,12,12,NA,16S,NA,Roche454,NA,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential microbial abundance between the malignancy diagnosis (pre-chemotherapy) timepoint and during chemotherapy timepoint in those who have oral mucositis,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:23829394/3/2,23829394,time series / longitudinal observational,23829394,10.1111/1469-0691.12287,NA,"Ye Y., Carlsson G., Agholme M.B., Wilson J.A., Roos A., Henriques-Normark B., Engstrand L., Modéer T. , Pütsep K.",Oral bacterial community dynamics in paediatric patients with malignancies in relation to chemotherapy-related oral mucositis: a prospective study,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"16S rRNA gene, 454 pyrosequencing, cancer, oral microflora, stomatitis",Experiment 3,Sweden,Homo sapiens,"Lower lip,Buccal mucosa","UBERON:0001835,UBERON:0006956",Oral mucositis,EFO:1001904,at malignancy diagnosis,during chemotherapy,patients that are newly diagnosed with malignancies that are between ages 4 and 18 years old that are treated with cytostatic drug and has a national population registration number (Sweden) that has later developed oral mucositis (graded by the World Health Organization) during chemotherapy treatment,12,12,NA,16S,NA,Roche454,NA,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential microbial abundance between the malignancy diagnosis (pre-chemotherapy) timepoint and during chemotherapy timepoint in those who have oral mucositis,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Derxia,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|28216|80840|506|203697;3379134|1224,Complete,Claregrieve1
bsdb:23829394/4/1,23829394,time series / longitudinal observational,23829394,10.1111/1469-0691.12287,NA,"Ye Y., Carlsson G., Agholme M.B., Wilson J.A., Roos A., Henriques-Normark B., Engstrand L., Modéer T. , Pütsep K.",Oral bacterial community dynamics in paediatric patients with malignancies in relation to chemotherapy-related oral mucositis: a prospective study,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"16S rRNA gene, 454 pyrosequencing, cancer, oral microflora, stomatitis",Experiment 4,Sweden,Homo sapiens,"Lower lip,Buccal mucosa","UBERON:0001835,UBERON:0006956",Oral mucositis,EFO:1001904,at malignancy diagnosis,during chemotherapy,patients that are newly diagnosed with malignancies that are between ages 4 and 18 years old that are treated with cytostatic drug and has a national population registration number (Sweden) that did not develop oral mucositis (graded by the World Health Organization) during chemotherapy treatment,10,10,NA,16S,NA,Roche454,NA,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential microbial abundance between the malignancy diagnosis (pre-chemotherapy) timepoint and during chemotherapy timepoint in those who do not have oral mucositis,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas,3379134|1224|1236|135614|32033|338,Complete,Claregrieve1
bsdb:23829394/5/1,23829394,time series / longitudinal observational,23829394,10.1111/1469-0691.12287,NA,"Ye Y., Carlsson G., Agholme M.B., Wilson J.A., Roos A., Henriques-Normark B., Engstrand L., Modéer T. , Pütsep K.",Oral bacterial community dynamics in paediatric patients with malignancies in relation to chemotherapy-related oral mucositis: a prospective study,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"16S rRNA gene, 454 pyrosequencing, cancer, oral microflora, stomatitis",Experiment 5,Sweden,Homo sapiens,"Lower lip,Buccal mucosa","UBERON:0001835,UBERON:0006956",Oral mucositis,EFO:1001904,all samples,mucositis lesions,samples from mucositis lesions,97,27,NA,16S,NA,Roche454,NA,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Supplemental Table S4, Figure S1, S2",10 January 2021,William Lam,"Claregrieve1,WikiWorks",Relative abundance (%) of taxa with different levels between all mucosal samples from lip and bucca and samples from mucositis lesions,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,p__candidate phylum NAG2,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma",1783272|1239|91061|186826|186827|46123;1783272|201174|1760|2037|2049|1654;1783272|1239|91061|1385|186817|1386;1783272|1239|526524|526525|128827;1783272|1239|91061|186826|1300|1357;3379134|976|200643|171549|171550;1783272|201174|1760|85004|31953|196081;1783272|1239|91061|1385|90964|1279;1448937;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3082720|186804|1257;3379134|1224|1236|135614|32033|40323;1783272|544448;1783272|544448|31969|2085|2092|2093,Complete,Claregrieve1
bsdb:23829394/5/2,23829394,time series / longitudinal observational,23829394,10.1111/1469-0691.12287,NA,"Ye Y., Carlsson G., Agholme M.B., Wilson J.A., Roos A., Henriques-Normark B., Engstrand L., Modéer T. , Pütsep K.",Oral bacterial community dynamics in paediatric patients with malignancies in relation to chemotherapy-related oral mucositis: a prospective study,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,"16S rRNA gene, 454 pyrosequencing, cancer, oral microflora, stomatitis",Experiment 5,Sweden,Homo sapiens,"Lower lip,Buccal mucosa","UBERON:0001835,UBERON:0006956",Oral mucositis,EFO:1001904,all samples,mucositis lesions,samples from mucositis lesions,97,27,NA,16S,NA,Roche454,NA,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,"Supplemental Table S4, Figure S1, S2",10 January 2021,William Lam,"Claregrieve1,WikiWorks",Relative abundance (%) of taxa with different levels between all mucosal samples from lip and bucca and samples from mucositis lesions,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",3379134|1224|1236|135625|712|713;3379134|1224|1236|135625|712|416916;3379134|1224|1236|135625|712|724,Complete,Claregrieve1
bsdb:23844187/1/1,23844187,case-control,23844187,10.1371/journal.pone.0068322,NA,"Kang D.W., Park J.G., Ilhan Z.E., Wallstrom G., Labaer J., Adams J.B. , Krajmalnik-Brown R.",Reduced incidence of Prevotella and other fermenters in intestinal microflora of autistic children,PloS one,2013,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Neurotypical children,Children with Autism Spectrum Disorder (ASD),"Children with ASD were assessed with the Autism Diagnostics Interview – Revised (ADI- Revised), Autism Diagnostics Observation Schedule (ADOS), Autism Treatment Evaluation Checklist (ATEC), and Pervasive Developmental Disorder Behavior Inventory (PDD-BI) to ensure that they had a diagnosis of autism.",20,20,1 month,16S,23,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,Table S7,14 December 2024,AlishaM,"AlishaM,WikiWorks",Genera presenting significant difference between neurotypical and autistic children by two-tailed Student’s t-test results,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella",1783272|201174|84998|84999|84107;1783272|201174|84998|1643822|1643826|84111,Complete,NA
bsdb:23844187/1/2,23844187,case-control,23844187,10.1371/journal.pone.0068322,NA,"Kang D.W., Park J.G., Ilhan Z.E., Wallstrom G., Labaer J., Adams J.B. , Krajmalnik-Brown R.",Reduced incidence of Prevotella and other fermenters in intestinal microflora of autistic children,PloS one,2013,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Neurotypical children,Children with Autism Spectrum Disorder (ASD),"Children with ASD were assessed with the Autism Diagnostics Interview – Revised (ADI- Revised), Autism Diagnostics Observation Schedule (ADOS), Autism Treatment Evaluation Checklist (ATEC), and Pervasive Developmental Disorder Behavior Inventory (PDD-BI) to ensure that they had a diagnosis of autism.",20,20,1 month,16S,23,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,Figure S7,14 December 2024,AlishaM,"AlishaM,WikiWorks",Genera presenting significant difference between neurotypical and autistic children by two-tailed Student’s t-test results,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Fusibacteraceae|g__Fusibacter,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|3679999|76008;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115|194924|872;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279,Complete,NA
bsdb:23844187/2/1,23844187,case-control,23844187,10.1371/journal.pone.0068322,NA,"Kang D.W., Park J.G., Ilhan Z.E., Wallstrom G., Labaer J., Adams J.B. , Krajmalnik-Brown R.",Reduced incidence of Prevotella and other fermenters in intestinal microflora of autistic children,PloS one,2013,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Neurotypical children,Children with Autism Spectrum Disorder (ASD),"Children with ASD were assessed with the Autism Diagnostics Interview – Revised (ADI- Revised), Autism Diagnostics Observation Schedule (ADOS), Autism Treatment Evaluation Checklist (ATEC), and Pervasive Developmental Disorder Behavior Inventory (PDD-BI) to ensure that they had a diagnosis of autism.",20,20,1 month,16S,23,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,"Table 4, Table S8",14 December 2024,AlishaM,"AlishaM,WikiWorks",Genera presenting significant difference between neurotypical and autistic children by nonparametric ranksum test (two-tailed Mann-Whitney test),increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella",1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|186806|1730;1783272|201174|84998|84999|84107;1783272|201174|84998|1643822|1643826|84111,Complete,NA
bsdb:23844187/2/2,23844187,case-control,23844187,10.1371/journal.pone.0068322,NA,"Kang D.W., Park J.G., Ilhan Z.E., Wallstrom G., Labaer J., Adams J.B. , Krajmalnik-Brown R.",Reduced incidence of Prevotella and other fermenters in intestinal microflora of autistic children,PloS one,2013,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Neurotypical children,Children with Autism Spectrum Disorder (ASD),"Children with ASD were assessed with the Autism Diagnostics Interview – Revised (ADI- Revised), Autism Diagnostics Observation Schedule (ADOS), Autism Treatment Evaluation Checklist (ATEC), and Pervasive Developmental Disorder Behavior Inventory (PDD-BI) to ensure that they had a diagnosis of autism.",20,20,1 month,16S,23,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,"Table 4, Table S8",14 December 2024,AlishaM,"AlishaM,WikiWorks",Genera presenting significant difference between neurotypical and autistic children by nonparametric ranksum test (two-tailed Mann-Whitney test),decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Fusibacteraceae|g__Fusibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Succinispira,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea",1783272|1239|909932|1843489|31977;3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|33042;3379134|1224|28216|80840|506;3379134|1224|28216|80840|995019|40544;3379134|976|200643|171549|171551;3379134|976|200643|171549|1853231|574697;3379134|976|200643|171549|171552|577309;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|3679999|76008;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;1783272|1239|909932|1843488|909930|78119;1783272|1239|1737404|1737405|1570339|543311;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|3085636|186803|189330,Complete,NA
bsdb:23844187/3/1,23844187,case-control,23844187,10.1371/journal.pone.0068322,NA,"Kang D.W., Park J.G., Ilhan Z.E., Wallstrom G., Labaer J., Adams J.B. , Krajmalnik-Brown R.",Reduced incidence of Prevotella and other fermenters in intestinal microflora of autistic children,PloS one,2013,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Neurotypical children,Children with Autism Spectrum Disorder (ASD),"Children with ASD were assessed with the Autism Diagnostics Interview – Revised (ADI- Revised), Autism Diagnostics Observation Schedule (ADOS), Autism Treatment Evaluation Checklist (ATEC), and Pervasive Developmental Disorder Behavior Inventory (PDD-BI) to ensure that they had a diagnosis of autism.",20,20,1 month,16S,23,Illumina,relative abundances,"Linear Regression,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,Table 5,15 December 2024,AlishaM,"AlishaM,WikiWorks",Permutation-based test on univariate regression model with the autistic status and top 10 genera generating the highest AUC.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium",1783272|1239|186801|186802|186806;1783272|1239|186801|186802|186806|1730,Complete,NA
bsdb:23844187/3/2,23844187,case-control,23844187,10.1371/journal.pone.0068322,NA,"Kang D.W., Park J.G., Ilhan Z.E., Wallstrom G., Labaer J., Adams J.B. , Krajmalnik-Brown R.",Reduced incidence of Prevotella and other fermenters in intestinal microflora of autistic children,PloS one,2013,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Neurotypical children,Children with Autism Spectrum Disorder (ASD),"Children with ASD were assessed with the Autism Diagnostics Interview – Revised (ADI- Revised), Autism Diagnostics Observation Schedule (ADOS), Autism Treatment Evaluation Checklist (ATEC), and Pervasive Developmental Disorder Behavior Inventory (PDD-BI) to ensure that they had a diagnosis of autism.",20,20,1 month,16S,23,Illumina,relative abundances,"Linear Regression,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,Table 5,15 December 2024,AlishaM,"AlishaM,WikiWorks",Permutation-based test on univariate regression model with the autistic status and top 10 genera generating the highest AUC.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",1783272|1239|909932|1843489|31977;3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|33042;3379134|1224|28216|80840|506;3379134|1224|28216|80840|995019|40544;3379134|976|200643|171549|171552|577309,Complete,NA
bsdb:23844187/4/1,23844187,case-control,23844187,10.1371/journal.pone.0068322,NA,"Kang D.W., Park J.G., Ilhan Z.E., Wallstrom G., Labaer J., Adams J.B. , Krajmalnik-Brown R.",Reduced incidence of Prevotella and other fermenters in intestinal microflora of autistic children,PloS one,2013,NA,Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Neurotypical children,Children with Autism Spectrum Disorder (ASD),"Children with ASD were assessed with the Autism Diagnostics Interview – Revised (ADI- Revised), Autism Diagnostics Observation Schedule (ADOS), Autism Treatment Evaluation Checklist (ATEC), and Pervasive Developmental Disorder Behavior Inventory (PDD-BI) to ensure that they had a diagnosis of autism.",20,20,1 month,16S,23,Illumina,relative abundances,"Linear Regression,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,NA,age,NA,NA,decreased,NA,NA,decreased,Signature 1,Table 5,15 December 2024,AlishaM,"AlishaM,WikiWorks",Permutation-based test on multivariate regression model with the autistic status and top 10 genera generating the highest AUC.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",1783272|1239|909932|1843489|31977;3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|33042;3379134|976|200643|171549|171552|577309,Complete,NA
bsdb:23940645/1/1,23940645,case-control,23940645,10.1371/journal.pone.0070803,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3735522/,"Weir T.L., Manter D.K., Sheflin A.M., Barnett B.A., Heuberger A.L. , Ryan E.P.",Stool microbiome and metabolome differences between colorectal cancer patients and healthy adults,PloS one,2013,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls,Colorectal Cancer patients (CRC),Patients recently diagnosed with Colorectal cancer prior to surgery for colonic resection.,11,10,2 months,16S,4,NA,raw counts,T-Test,0.01,FALSE,NA,NA,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 1,Table 3,6 January 2022,Itslanapark,"Itslanapark,Aiyshaaaa,Atrayees,WikiWorks",Bacterial species significantly over-represented in CRC stool samples.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter farmeri,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Acidaminobacteraceae|g__Acidaminobacter",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|909932|1843488|909930|33024;3379134|1224|1236|91347|543|544|67824;1783272|1239|186801|3082720|3118653|65402,Complete,Atrayees
bsdb:23940645/1/2,23940645,case-control,23940645,10.1371/journal.pone.0070803,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3735522/,"Weir T.L., Manter D.K., Sheflin A.M., Barnett B.A., Heuberger A.L. , Ryan E.P.",Stool microbiome and metabolome differences between colorectal cancer patients and healthy adults,PloS one,2013,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls,Colorectal Cancer patients (CRC),Patients recently diagnosed with Colorectal cancer prior to surgery for colonic resection.,11,10,2 months,16S,4,NA,raw counts,T-Test,0.01,FALSE,NA,NA,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 2,Table 2,6 January 2022,Itslanapark,"Itslanapark,Aiyshaaaa,WikiWorks",Bacterial species that were significantly more abundant in the stool of healthy individuals compared to CRC patients,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium|s__Lachnobacterium bovis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio|s__Pseudobutyrivibrio ruminis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus albus",3379134|976|200643|171549|815|816|338188;3379134|976|200643|171549|815|816|329854;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|909932|1843489|31977|39948|39950;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|140625|140626;1783272|1239|186801|3085636|186803|28050|28052;1783272|1239|909932|909929|1843491|158846|158847;3379134|976|200643|171549|171552|2974251|165179;3379134|976|200643|171549|171552|2974251|28135;1783272|1239|186801|3085636|186803|46205|46206;1783272|1239|186801|186802|216572|1017280|106588;1783272|1239|186801|186802|216572|1263|1264,Complete,Atrayees
bsdb:24013136/1/1,24013136,"cross-sectional observational, not case-control",24013136,10.1371/journal.pone.0071108,NA,"Zhang X., Shen D., Fang Z., Jie Z., Qiu X., Zhang C., Chen Y. , Ji L.",Human gut microbiota changes reveal the progression of glucose intolerance,PloS one,2013,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Diabetes mellitus,EFO:0000400,Normal Glucose Tolerance (NGT),Type 2 diabetes mellitus (T2DM),Subjects with newly diagnosed Type 2 diabetes mellitus (T2DM).,44,13,1 month,16S,345,Roche454,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Table 2, Table S3 and Table S4",7 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",The relative abundance of OTUs enriched in the NGT and T2DM groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803;1783272|1239|186801|3082720|186804|1257;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|186802|216572|292632;1783272|1239|91061|186826|186827|46123;3379134|1224|28216,Complete,Svetlana up
bsdb:24013136/1/2,24013136,"cross-sectional observational, not case-control",24013136,10.1371/journal.pone.0071108,NA,"Zhang X., Shen D., Fang Z., Jie Z., Qiu X., Zhang C., Chen Y. , Ji L.",Human gut microbiota changes reveal the progression of glucose intolerance,PloS one,2013,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Diabetes mellitus,EFO:0000400,Normal Glucose Tolerance (NGT),Type 2 diabetes mellitus (T2DM),Subjects with newly diagnosed Type 2 diabetes mellitus (T2DM).,44,13,1 month,16S,345,Roche454,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Table 2, Table S3 and Table S4",7 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",The relative abundance of OTUs enriched in the NGT and T2DM groups.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|3085636|186803|841;3379134|74201|203494;3379134|74201,Complete,Svetlana up
bsdb:24013136/2/1,24013136,"cross-sectional observational, not case-control",24013136,10.1371/journal.pone.0071108,NA,"Zhang X., Shen D., Fang Z., Jie Z., Qiu X., Zhang C., Chen Y. , Ji L.",Human gut microbiota changes reveal the progression of glucose intolerance,PloS one,2013,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Prediabetes syndrome,EFO:1001121,Normal Glucose Tolerance (NGT),Prediabetes (Pre-DM),Prediabetes subjects including those with impaired fasting glucose and impaired glucose tolerance.,44,64,1 month,16S,345,Roche454,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table S3 and Table S4,7 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",The relative abundance of OTUs enriched in the NGT and PreDM groups.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,3379134|1224|28216,Complete,Svetlana up
bsdb:24013136/2/2,24013136,"cross-sectional observational, not case-control",24013136,10.1371/journal.pone.0071108,NA,"Zhang X., Shen D., Fang Z., Jie Z., Qiu X., Zhang C., Chen Y. , Ji L.",Human gut microbiota changes reveal the progression of glucose intolerance,PloS one,2013,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Prediabetes syndrome,EFO:1001121,Normal Glucose Tolerance (NGT),Prediabetes (Pre-DM),Prediabetes subjects including those with impaired fasting glucose and impaired glucose tolerance.,44,64,1 month,16S,345,Roche454,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table S3 and Table S4,7 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",The relative abundance of OTUs enriched in the NGT and PreDM groups.,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota",3379134|74201|203494;3379134|74201,Complete,Svetlana up
bsdb:24013136/3/1,24013136,"cross-sectional observational, not case-control",24013136,10.1371/journal.pone.0071108,NA,"Zhang X., Shen D., Fang Z., Jie Z., Qiu X., Zhang C., Chen Y. , Ji L.",Human gut microbiota changes reveal the progression of glucose intolerance,PloS one,2013,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Diabetes mellitus,EFO:0000400,Prediabetes (Pre-DM),Type 2 diabetes mellitus (T2DM),Subjects with newly diagnosed Type 2 diabetes mellitus (T2DM).,64,13,1 month,16S,345,Roche454,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table S3 and Table S4,7 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",The relative abundance of OTUs enriched in the T2DM and PreDM groups.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota",3379134|74201|203494;3379134|74201,Complete,Svetlana up
bsdb:24013136/3/2,24013136,"cross-sectional observational, not case-control",24013136,10.1371/journal.pone.0071108,NA,"Zhang X., Shen D., Fang Z., Jie Z., Qiu X., Zhang C., Chen Y. , Ji L.",Human gut microbiota changes reveal the progression of glucose intolerance,PloS one,2013,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Diabetes mellitus,EFO:0000400,Prediabetes (Pre-DM),Type 2 diabetes mellitus (T2DM),Subjects with newly diagnosed Type 2 diabetes mellitus (T2DM).,64,13,1 month,16S,345,Roche454,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table S3 and Table S4,7 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",The relative abundance of OTUs enriched in the T2DM and PreDM groups.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,3379134|1224|28216,Complete,Svetlana up
bsdb:24013136/4/1,24013136,"cross-sectional observational, not case-control",24013136,10.1371/journal.pone.0071108,NA,"Zhang X., Shen D., Fang Z., Jie Z., Qiu X., Zhang C., Chen Y. , Ji L.",Human gut microbiota changes reveal the progression of glucose intolerance,PloS one,2013,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Diabetes mellitus,EFO:0000400,Normal Glucose Tolerance (NGT),Type 2 diabetes mellitus (T2DM),Subjects with newly diagnosed Type 2 diabetes mellitus (T2DM).,44,13,1 month,16S,345,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure S4,7 February 2025,Aleru Divine,"Aleru Divine,WikiWorks","Changes in abundance for operational taxonomic units (OTUs,) that exhibited a significant difference in the Wilcoxon rank sum test between the NGT, Pre-DM, and T2DM groups.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3082720|186804|1257;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|186827|46123,Complete,Svetlana up
bsdb:24013136/4/2,24013136,"cross-sectional observational, not case-control",24013136,10.1371/journal.pone.0071108,NA,"Zhang X., Shen D., Fang Z., Jie Z., Qiu X., Zhang C., Chen Y. , Ji L.",Human gut microbiota changes reveal the progression of glucose intolerance,PloS one,2013,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Diabetes mellitus,EFO:0000400,Normal Glucose Tolerance (NGT),Type 2 diabetes mellitus (T2DM),Subjects with newly diagnosed Type 2 diabetes mellitus (T2DM).,44,13,1 month,16S,345,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure S4,7 February 2025,Aleru Divine,"Aleru Divine,WikiWorks","Changes in abundance for operational taxonomic units (OTUs,) that exhibited a significant difference in the Wilcoxon rank sum test between the NGT, Pre-DM, and T2DM groups.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511,Complete,Svetlana up
bsdb:24013136/5/1,24013136,"cross-sectional observational, not case-control",24013136,10.1371/journal.pone.0071108,NA,"Zhang X., Shen D., Fang Z., Jie Z., Qiu X., Zhang C., Chen Y. , Ji L.",Human gut microbiota changes reveal the progression of glucose intolerance,PloS one,2013,NA,Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Prediabetes syndrome,EFO:1001121,Normal Glucose Tolerance (NGT),Prediabetes (Pre-DM),Prediabetes subjects including those with impaired fasting glucose and impaired glucose tolerance.,44,64,1 month,16S,345,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure S4,7 February 2025,Aleru Divine,"Aleru Divine,WikiWorks","Changes in abundance for operational taxonomic units (OTUs,) that exhibited a significant difference in the Wilcoxon rank sum test between the NGT, Pre-DM, and T2DM groups.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|186827|46123,Complete,Svetlana up
bsdb:24013136/5/2,24013136,"cross-sectional observational, not case-control",24013136,10.1371/journal.pone.0071108,NA,"Zhang X., Shen D., Fang Z., Jie Z., Qiu X., Zhang C., Chen Y. , Ji L.",Human gut microbiota changes reveal the progression of glucose intolerance,PloS one,2013,NA,Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Prediabetes syndrome,EFO:1001121,Normal Glucose Tolerance (NGT),Prediabetes (Pre-DM),Prediabetes subjects including those with impaired fasting glucose and impaired glucose tolerance.,44,64,1 month,16S,345,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure S4,7 February 2025,Aleru Divine,"Aleru Divine,WikiWorks","Changes in abundance for operational taxonomic units (OTUs,) that exhibited a significant difference in the Wilcoxon rank sum test between the NGT, Pre-DM, and T2DM groups.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511,Complete,Svetlana up
bsdb:24013136/6/1,24013136,"cross-sectional observational, not case-control",24013136,10.1371/journal.pone.0071108,NA,"Zhang X., Shen D., Fang Z., Jie Z., Qiu X., Zhang C., Chen Y. , Ji L.",Human gut microbiota changes reveal the progression of glucose intolerance,PloS one,2013,NA,Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Diabetes mellitus,EFO:0000400,Prediabetes (Pre-DM),Type 2 diabetes mellitus (T2DM),Subjects with newly diagnosed Type 2 diabetes mellitus (T2DM).,64,13,1 month,16S,345,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure S4,7 February 2025,Aleru Divine,"Aleru Divine,WikiWorks","Changes in abundance for operational taxonomic units (OTUs,) that exhibited a significant difference in the Wilcoxon rank sum test between the NGT, Pre-DM, and T2DM groups.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia",1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803;1783272|1239|186801|3082720|186804|1257;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|186827|46123,Complete,Svetlana up
bsdb:24013136/6/2,24013136,"cross-sectional observational, not case-control",24013136,10.1371/journal.pone.0071108,NA,"Zhang X., Shen D., Fang Z., Jie Z., Qiu X., Zhang C., Chen Y. , Ji L.",Human gut microbiota changes reveal the progression of glucose intolerance,PloS one,2013,NA,Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Diabetes mellitus,EFO:0000400,Prediabetes (Pre-DM),Type 2 diabetes mellitus (T2DM),Subjects with newly diagnosed Type 2 diabetes mellitus (T2DM).,64,13,1 month,16S,345,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure S4,7 February 2025,Aleru Divine,"Aleru Divine,WikiWorks","Changes in abundance for operational taxonomic units (OTUs,) that exhibited a significant difference in the Wilcoxon rank sum test between the NGT, Pre-DM, and T2DM groups.",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,1783272|1239|186801|3085636|186803|572511,Complete,Svetlana up
bsdb:24192039/1/1,24192039,case-control,24192039,https://doi.org/10.7554/eLife.01202.003,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3816614/,"Scher J.U., Sczesnak A., Longman R.S., Segata N., Ubeda C., Bielski C., Rostron T., Cerundolo V., Pamer E.G., Abramson S.B., Huttenhower C. , Littman D.R.",Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis,eLife,2013,"arthritis, autoimmunity, inflammation, metagenomics, microbiome, rheumatoid",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Arthritis,EFO:0005856,Healthy controls,New-onset rheumatoid arthritis - NORA,Patients with new-onset rheumatoid arthritis - NORA,28,44,3 months,16S,12,Roche454,relative abundances,LEfSe,0.05,TRUE,2,"age,ethnic group,sex",NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 1,30 November 2021,Tislam,"Tislam,Lwaldron,Aiyshaaaa,Peace Sandy,Chloe,Chikamso,Folakunmi,WikiWorks","(A) LEfSe (Segata et al., 2011) was used to compare the abundances of all detected clades among all groups, producing an effect size for each comparison (‘Materials and methods’). All results shown are highly significant (q<0.01) by Kruskal-Wallis test adjusted with the Benjamini-Hochberg procedure for multiple testing, except that indicated with an asterisk, which is significant at q<0.05. Negative values (left) correspond to effect sizes representative of NORA groups, while positive values (right) correspond to effect sizes in HLT subjects. Prevotella was found to be over-represented in NORA patients, while Bacteroides was over-represented in all other groups.",increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp.",1783272|1239|526524|526525|2810280|135858;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|1926307,Complete,Peace Sandy
bsdb:24192039/1/2,24192039,case-control,24192039,https://doi.org/10.7554/eLife.01202.003,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3816614/,"Scher J.U., Sczesnak A., Longman R.S., Segata N., Ubeda C., Bielski C., Rostron T., Cerundolo V., Pamer E.G., Abramson S.B., Huttenhower C. , Littman D.R.",Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis,eLife,2013,"arthritis, autoimmunity, inflammation, metagenomics, microbiome, rheumatoid",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Arthritis,EFO:0005856,Healthy controls,New-onset rheumatoid arthritis - NORA,Patients with new-onset rheumatoid arthritis - NORA,28,44,3 months,16S,12,Roche454,relative abundances,LEfSe,0.05,TRUE,2,"age,ethnic group,sex",NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 1,30 November 2021,Tislam,"Tislam,Peace Sandy,WikiWorks","(A) LEfSe (Segata et al., 2011) was used to compare the abundances of all detected clades among all groups, producing an effect size for each comparison (‘Materials and methods’). All results shown are highly significant (q<0.01) by Kruskal-Wallis test adjusted with the Benjamini-Hochberg procedure for multiple testing, except that indicated with an asterisk, which is significant at q<0.05. Negative values (left) correspond to effect sizes representative of NORA groups, while positive values (right) correspond to effect sizes in HLT subjects. Prevotella was found to be over-represented in NORA patients, while Bacteroides was over-represented in all other groups.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801;1783272|1239|186801|3085636|186803;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3085636|186803,Complete,Peace Sandy
bsdb:24223144/1/1,24223144,"cross-sectional observational, not case-control",24223144,10.1371/journal.pone.0078257,NA,"Hu J., Nomura Y., Bashir A., Fernandez-Hernandez H., Itzkowitz S., Pei Z., Stone J., Loudon H. , Peter I.",Diversified microbiota of meconium is affected by maternal diabetes status,PloS one,2013,NA,Experiment 1,United States of America,Homo sapiens,Meconium,UBERON:0007109,Type II diabetes mellitus,MONDO:0005148,adult stool,Healthy baby meconium,NA,9,13,9 months,16S,34,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text + Figure 2,10 January 2021,Rimsha Azhar,WikiWorks,Bacterial Composition of the Meconium and Comparison to the healthy Adult and healthy Infant Microbiome,increased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella",3379134|1224;3379134|1224|28216|80840|80864;3379134|1224|1236|91347|543;3379134|1224|28216|80840|80864|283;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|1903414|583;3379134|1224|1236|91347|543|620,Complete,Shaimaa Elsafoury
bsdb:24223144/1/2,24223144,"cross-sectional observational, not case-control",24223144,10.1371/journal.pone.0078257,NA,"Hu J., Nomura Y., Bashir A., Fernandez-Hernandez H., Itzkowitz S., Pei Z., Stone J., Loudon H. , Peter I.",Diversified microbiota of meconium is affected by maternal diabetes status,PloS one,2013,NA,Experiment 1,United States of America,Homo sapiens,Meconium,UBERON:0007109,Type II diabetes mellitus,MONDO:0005148,adult stool,Healthy baby meconium,NA,9,13,9 months,16S,34,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Text + Figure 2,10 January 2021,Rimsha Azhar,WikiWorks,Bacterial Composition of the Meconium and Comparison to the healthy Adult and healthy Infant Microbiome,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|976;1783272|1239;3379134|74201;3379134|976|200643|171549|815;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|541000;1783272|1239|909932|1843489|31977,Complete,Shaimaa Elsafoury
bsdb:24223144/2/1,24223144,"cross-sectional observational, not case-control",24223144,10.1371/journal.pone.0078257,NA,"Hu J., Nomura Y., Bashir A., Fernandez-Hernandez H., Itzkowitz S., Pei Z., Stone J., Loudon H. , Peter I.",Diversified microbiota of meconium is affected by maternal diabetes status,PloS one,2013,NA,Experiment 2,United States of America,Homo sapiens,Meconium,UBERON:0007109,Gestational diabetes,EFO:0004593,Healthy baby meconium,Baby meconium with GDM mothers,NA,13,5,9 months,16S,34,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text + Figure 4,10 January 2021,Rimsha Azhar,WikiWorks,Significant difference between neonates from mothers with different diabetes states,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",3379134|1224|28216;3379134|1224|28211|356|118882;3379134|1224|28216|80840|506;3379134|1224|28216|80840|80864;3379134|1224|28211|356|335928;3379134|1224|28216|80840|506|507;3379134|1224|28216|80840|119060|106589;3379134|1224|28216|80840|80864|283;3379134|1224|28216|80840|80864|80865;3379134|1224|1236|135614|32033|40323,Complete,Shaimaa Elsafoury
bsdb:24223144/3/1,24223144,"cross-sectional observational, not case-control",24223144,10.1371/journal.pone.0078257,NA,"Hu J., Nomura Y., Bashir A., Fernandez-Hernandez H., Itzkowitz S., Pei Z., Stone J., Loudon H. , Peter I.",Diversified microbiota of meconium is affected by maternal diabetes status,PloS one,2013,NA,Experiment 3,United States of America,Homo sapiens,Meconium,UBERON:0007109,Type II diabetes mellitus,MONDO:0005148,Healthy baby meconium,Baby meconium with DM mothers,NA,13,5,9 months,16S,34,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text + Figure 4,10 January 2021,Rimsha Azhar,"Lwaldron,WikiWorks",Significant difference between neonates from mothers with different diabetes states,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Arsenicicoccus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Modestobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Planomicrobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Roseomonadaceae|g__Roseomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|1224|28211|3120395|433;1783272|1239|909932|1843488|909930|904;1783272|201174|1760|85006|85021|267408;1783272|201174|84998|84999|1643824|1380;3379134|976|200643|171549|815;3379134|976;3379134|976|200643;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549|1853231|574697;1783272|1239|526524|526525|2810280|135858;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|33042;1783272|201174|84998|84999|84107;1783272|201174|1760|85006|85020;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|189330;3379134|976|200643|171549|2005520|156973;1783272|1239|526524|526525|128827;1783272|1239|526524;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|186806|1730;1783272|1239|91061|1385|539738|1378;1783272|201174|1760|85007|85026|2053;1783272|1239|526524|526525|128827|61170;1783272|201174|1760|85006|1268|57493;1783272|1239|186801|3085636|186803;1783272|201174|1760|85006|85023|33882;1783272|201174|1760|1643682|85030|88138;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;3379134|1224|28211|356|69277;1783272|1239|91061|1385|186818|162291;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|841;3379134|1224|28211|3120395|3385906|125216;1783272|1239|186801|186802|216572|1263;1783272|1239|526524|526525|2810281|191303;1783272|1239|909932|1843489|31977,Complete,Fatima
bsdb:24265786/1/1,24265786,case-control,24265786,10.1371/journal.pone.0079812,NA,"Liu M.B., Xu S.R., He Y., Deng G.H., Sheng H.F., Huang X.M., Ouyang C.Y. , Zhou H.W.",Diverse vaginal microbiomes in reproductive-age women with vulvovaginal candidiasis,PloS one,2013,NA,Experiment 1,China,Homo sapiens,Vagina,UBERON:0000996,Vulvovaginitis,EFO:1001240,Normal controls,Women with BV,BV assessment with a gram-stain score => 7,30,10,1 month,16S,6,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplemental Figure 1,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between normal controls and women with BV,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Pseudomonadota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae",1783272|201174;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;1783272|201174|84998|84999|1643824|1380;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|1239|526524|526525|128827|118747;1783272|1239|186801;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|1239|909932|1843489|31977|39948;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|186801|186802;3384189|32066;3384189|32066|203490|203491;1783272|201174|1760|85004|31953|2701;1783272|201174|1760|2037|2049|2050;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836;3379134|1224;3384189|32066|203490|203491|1129771|168808;1783272|1239|909932|1843489|31977;3384189|32066|203490|203491|1129771,Complete,Claregrieve1
bsdb:24265786/1/2,24265786,case-control,24265786,10.1371/journal.pone.0079812,NA,"Liu M.B., Xu S.R., He Y., Deng G.H., Sheng H.F., Huang X.M., Ouyang C.Y. , Zhou H.W.",Diverse vaginal microbiomes in reproductive-age women with vulvovaginal candidiasis,PloS one,2013,NA,Experiment 1,China,Homo sapiens,Vagina,UBERON:0000996,Vulvovaginitis,EFO:1001240,Normal controls,Women with BV,BV assessment with a gram-stain score => 7,30,10,1 month,16S,6,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Supplemental Figure 1,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between normal controls and women with BV,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578,Complete,Claregrieve1
bsdb:24265786/2/1,24265786,case-control,24265786,10.1371/journal.pone.0079812,NA,"Liu M.B., Xu S.R., He Y., Deng G.H., Sheng H.F., Huang X.M., Ouyang C.Y. , Zhou H.W.",Diverse vaginal microbiomes in reproductive-age women with vulvovaginal candidiasis,PloS one,2013,NA,Experiment 2,China,Homo sapiens,Vagina,UBERON:0000996,Vulvovaginitis,EFO:1001240,Normal controls,Women with BV and VVC,Women infected with both BV and VVC,30,16,1 month,16S,6,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplemental Figure 1,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between normal controls and women with candida vulvovaginitis and BV,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|976|200643|171549;3379134|976;3379134|976|200643;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552,Complete,Claregrieve1
bsdb:24273047/1/1,24273047,"cross-sectional observational, not case-control",24273047,10.1093/rheumatology/ket362,NA,"Wolff B., Berger T., Frese C., Max R., Blank N., Lorenz H.M. , Wolff D.","Oral status in patients with early rheumatoid arthritis: a prospective, case-control study","Rheumatology (Oxford, England)",2014,"case–control studies, oral hygiene, periodontal attachment loss, periodontal index, plaque index, rheumatoid arthritis",Experiment 1,Germany,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,Healthy Controls,Early Rheumatoid Arthritis,Patients with Early Rheumatoid Arthritis,22,22,6 months,PCR,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 3, Table 4,  Text",2 November 2022,Tislam,"Tislam,Atrayees,Peace Sandy,WikiWorks","Microbiological data and quantitative real-time PCR measurements of abundance of subgingival microbiota in ERA patients and controls. 

Microbiological data and quantitative real-time PCR measurements of abundance of supragingival microbiota in ERA patients and controls",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus",3379134|976|200643|171549|2005525|195950|28112;1783272|1239|91061|186826|1300|1301|1328,Complete,Peace Sandy
bsdb:24273047/1/2,24273047,"cross-sectional observational, not case-control",24273047,10.1093/rheumatology/ket362,NA,"Wolff B., Berger T., Frese C., Max R., Blank N., Lorenz H.M. , Wolff D.","Oral status in patients with early rheumatoid arthritis: a prospective, case-control study","Rheumatology (Oxford, England)",2014,"case–control studies, oral hygiene, periodontal attachment loss, periodontal index, plaque index, rheumatoid arthritis",Experiment 1,Germany,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,Healthy Controls,Early Rheumatoid Arthritis,Patients with Early Rheumatoid Arthritis,22,22,6 months,PCR,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Table 3, Table 4,  Text",2 November 2022,Tislam,"Tislam,Peace Sandy,WikiWorks","Microbiological data and quantitative real-time PCR measurements of abundance of subgingival microbiota in ERA patients and controls

Microbiological data and quantitative real-time PCR measurements of abundance of supragingival microbiota in ERA patients and controls",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|201174|1760|2037|2049|1654|29317;1783272|201174|1760|85007|1653|1716|61592;3384189|32066;1783272|1239|91061|186826|33958|1578|1596;3384189|32066|203490|203491|1129771|32067|104608;1783272|201174|1760|85006|1268|32207|2047;1783272|1239|91061|186826|1300|1301|1302;1783272|1239|91061|186826|33958|1578,Complete,Peace Sandy
bsdb:24296500/1/1,24296500,randomized controlled trial,24296500,10.1128/AEM.03549-13,NA,"Roager H.M., Licht T.R., Poulsen S.K., Larsen T.M. , Bahl M.I.","Microbial enterotypes, inferred by the prevotella-to-bacteroides ratio, remained stable during a 6-month randomized controlled diet intervention with the new nordic diet",Applied and environmental microbiology,2014,NA,Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,before Average Danish Diet,6 months after Average Danish Diet,"the dietary intervention study of the NND compared to the ADD was performed as a 6-month, nonblinded, parallel, randomized, controlled, ad libitum dietary intervention trial and was carried out between October 2010 and July 2011.",26,26,NA,16S,NA,RT-qPCR,raw counts,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S3,10 January 2021,Lora Kasselman,WikiWorks,"Changes in bacterial groups following the diet intervention within A) Firmicutes, B) Bacteroidetes, C) Actinobacteria, and D) γ-proteobacteria and other bacterial groups for the two diet groups ADD (n = 26, white bars) and NND (n = 36, black bars). Columns show means of log2 transformed data and error bars represent standard errors of the means. Asterisks indicate a significant difference (q < 0.05) compared to baseline. BCoAT: Butyryl-CoA:acetate CoAtransferase, NND: New Nordic Diet, ADD: Average Danish",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",1783272|1239|186801|3085636|186803|2569097|39488;1783272|201174;3379134|200940|3031449|213115|194924|872,Complete,Shaimaa Elsafoury
bsdb:24296500/2/1,24296500,randomized controlled trial,24296500,10.1128/AEM.03549-13,NA,"Roager H.M., Licht T.R., Poulsen S.K., Larsen T.M. , Bahl M.I.","Microbial enterotypes, inferred by the prevotella-to-bacteroides ratio, remained stable during a 6-month randomized controlled diet intervention with the new nordic diet",Applied and environmental microbiology,2014,NA,Experiment 2,Denmark,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,before  New Nordic Diet,6 months after  New Nordic Diet,"the dietary intervention study of the NND compared to the ADD was performed as a 6-month, nonblinded, parallel, randomized, controlled, ad libitum dietary intervention trial and was carried out between October 2010 and July 2011.",36,36,NA,16S,NA,RT-qPCR,raw counts,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S3,10 January 2021,Shaimaa Elsafoury,WikiWorks,"Changes in bacterial groups following the diet intervention within A) Firmicutes, B) Bacteroidetes, C) Actinobacteria, and D) γ-proteobacteria and other bacterial groups for the two diet groups ADD (n = 26, white bars) and NND (n = 36, black bars). Columns show means of log2 transformed data and error bars represent standard errors of the means. Asterisks indicate a significant difference (q < 0.05) compared to baseline. BCoAT: Butyryl-CoA:acetate CoAtransferase, NND: New Nordic Diet, ADD: Average Danish",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|91061|186826|33958|1578|1579;1783272|201174;3379134|1224|1236|91347|543|561|562;3379134|200940|3031449|213115|194924|872,Complete,Shaimaa Elsafoury
bsdb:24296500/2/2,24296500,randomized controlled trial,24296500,10.1128/AEM.03549-13,NA,"Roager H.M., Licht T.R., Poulsen S.K., Larsen T.M. , Bahl M.I.","Microbial enterotypes, inferred by the prevotella-to-bacteroides ratio, remained stable during a 6-month randomized controlled diet intervention with the new nordic diet",Applied and environmental microbiology,2014,NA,Experiment 2,Denmark,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,before  New Nordic Diet,6 months after  New Nordic Diet,"the dietary intervention study of the NND compared to the ADD was performed as a 6-month, nonblinded, parallel, randomized, controlled, ad libitum dietary intervention trial and was carried out between October 2010 and July 2011.",36,36,NA,16S,NA,RT-qPCR,raw counts,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S3,10 January 2021,Shaimaa Elsafoury,WikiWorks,"Changes in bacterial groups following the diet intervention within A) Firmicutes, B) Bacteroidetes, C) Actinobacteria, and D) γ-proteobacteria and other bacterial groups for the two diet groups ADD (n = 26, white bars) and NND (n = 36, black bars). Columns show means of log2 transformed data and error bars represent standard errors of the means. Asterisks indicate a significant difference (q < 0.05) compared to baseline. BCoAT: Butyryl-CoA:acetate CoAtransferase, NND: New Nordic Diet, ADD: Average Danish",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii",3379134|976|200643|171549|171550|239759;3366610|28890|183925|2158|2159|2172|2173,Complete,Shaimaa Elsafoury
bsdb:24316595/1/1,24316595,case-control,24316595,10.1093/jnci/djt300,https://pubmed.ncbi.nlm.nih.gov/24316595/,"Ahn J., Sinha R., Pei Z., Dominianni C., Wu J., Shi J., Goedert J.J., Hayes R.B. , Yang L.",Human gut microbiome and risk for colorectal cancer,Journal of the National Cancer Institute,2013,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,controls with no cancer,patients with adenocarcinoma,"patients with newly diagnosed, histologically confirmed adenocarcinoma of the colon or rectum",94,47,1 year,16S,34,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"body mass index,sex","age,body mass index,race,sex,smoking behavior",unchanged,decreased,NA,NA,NA,NA,Signature 1,Table 1,10 December 2021,Itslanapark,"Itslanapark,Claregrieve1,ChiomaBlessing,WikiWorks",Differential microbial abundance between patients with colorectal cancer and control subjects,decreased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803,Complete,ChiomaBlessing
bsdb:24370189/1/1,24370189,"case-control,time series / longitudinal observational",24370189,https://doi.org/10.1016/j.archoralbio.2013.10.011,https://www.sciencedirect.com/science/article/abs/pii/S0003996913003282?via=ihub,"Xu Y., Teng F., Huang S., Lin Z., Yuan X., Zeng X. , Yang F.",Changes of saliva microbiota in nasopharyngeal carcinoma patients under chemoradiation therapy,Archives of oral biology,2014,"Nasopharyngeal carcinoma, Oral microbiota, Pyrosequencing, Radiation therapy, Saliva",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Nasopharyngeal squamous cell carcinoma,NA,Healthy controls at Baseline,Nasopharyngeal carcinoma patients at baseline,Patients who have not received treatment yet,3,3,1 month,16S,123,Roche454,NA,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table 3,30 August 2023,Andre,"Andre,WikiWorks",Genus level comparison of the organismal composition of the saliva microbiota between Cancer patients and control groups at baseline via Metastas analysis.,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",3384189|32066|203490|203491|1129771|32067;3379134|1224|28216|206351|481|482;3379134|1224;3379134|1224|1236|72274|135621|286,Complete,Folakunmi
bsdb:24370189/1/2,24370189,"case-control,time series / longitudinal observational",24370189,https://doi.org/10.1016/j.archoralbio.2013.10.011,https://www.sciencedirect.com/science/article/abs/pii/S0003996913003282?via=ihub,"Xu Y., Teng F., Huang S., Lin Z., Yuan X., Zeng X. , Yang F.",Changes of saliva microbiota in nasopharyngeal carcinoma patients under chemoradiation therapy,Archives of oral biology,2014,"Nasopharyngeal carcinoma, Oral microbiota, Pyrosequencing, Radiation therapy, Saliva",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Nasopharyngeal squamous cell carcinoma,NA,Healthy controls at Baseline,Nasopharyngeal carcinoma patients at baseline,Patients who have not received treatment yet,3,3,1 month,16S,123,Roche454,NA,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Table 3,30 August 2023,Andre,"Andre,WikiWorks",Genus level comparison of the organismal composition of the saliva microbiota between Cancer patients and control groups at baseline via Metastas analysis.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota",1783272|1239|91061|186826|1300|1301;1783272|1239,Complete,Folakunmi
bsdb:24370189/2/1,24370189,"case-control,time series / longitudinal observational",24370189,https://doi.org/10.1016/j.archoralbio.2013.10.011,https://www.sciencedirect.com/science/article/abs/pii/S0003996913003282?via=ihub,"Xu Y., Teng F., Huang S., Lin Z., Yuan X., Zeng X. , Yang F.",Changes of saliva microbiota in nasopharyngeal carcinoma patients under chemoradiation therapy,Archives of oral biology,2014,"Nasopharyngeal carcinoma, Oral microbiota, Pyrosequencing, Radiation therapy, Saliva",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Nasopharyngeal squamous cell carcinoma,NA,Nasopharyngeal carcinoma patients at baseline,Nasopharyngeal carcinoma patients after treatment,Patients who have received treatment after 7 or 12 months,3,3,1 month,16S,123,Roche454,NA,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure 3 and within results text (under taxonomy-based characterisation of saliva microbiota, paragraph 4)",30 August 2023,Andre,"Andre,Folakunmi,WikiWorks",Alteration of saliva microbiota between pretreatment (CB) and post-treatment (CA1 or CA2) in each patient.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:24370189/2/2,24370189,"case-control,time series / longitudinal observational",24370189,https://doi.org/10.1016/j.archoralbio.2013.10.011,https://www.sciencedirect.com/science/article/abs/pii/S0003996913003282?via=ihub,"Xu Y., Teng F., Huang S., Lin Z., Yuan X., Zeng X. , Yang F.",Changes of saliva microbiota in nasopharyngeal carcinoma patients under chemoradiation therapy,Archives of oral biology,2014,"Nasopharyngeal carcinoma, Oral microbiota, Pyrosequencing, Radiation therapy, Saliva",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Nasopharyngeal squamous cell carcinoma,NA,Nasopharyngeal carcinoma patients at baseline,Nasopharyngeal carcinoma patients after treatment,Patients who have received treatment after 7 or 12 months,3,3,1 month,16S,123,Roche454,NA,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 3 and  within results text (under taxonomy-based characterisation of saliva microbiota, paragraph 4)",30 August 2023,Andre,"Andre,Folakunmi,WikiWorks",Alteration of saliva microbiota between pretreatment (CB) and post-treatment (CA1 or CA2) in each patient.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|838,Complete,Folakunmi
bsdb:24399150/1/1,24399150,"cross-sectional observational, not case-control",24399150,10.1038/mi.2013.116,NA,"Dillon S.M., Lee E.J., Kotter C.V., Austin G.L., Dong Z., Hecht D.K., Gianella S., Siewe B., Smith D.M., Landay A.L., Robertson C.E., Frank D.N. , Wilson C.C.",An altered intestinal mucosal microbiome in HIV-1 infection is associated with mucosal and systemic immune activation and endotoxemia,Mucosal immunology,2014,NA,Experiment 1,United States of America,Homo sapiens,Colonic mucosa,UBERON:0000317,HIV infection,EFO:0000764,uninfected controls,HIV-infected subjects,Subjects with untreated chronic HIV-1 infection,14,18,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,"Figure 1, Supplemental table S1",10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks","Differential microbial abundance in the colonic mucosa comparing healthy controls to subjects with chronic, untreated HIV-1 infections",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae",3379134|1224|1236|2887326|468|469;3379134|1224|28211|356|118882;3379134|1224|1236|2887326|468;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|1224;3379134|1224|1236|135614|32033,Complete,Claregrieve1
bsdb:24399150/1/2,24399150,"cross-sectional observational, not case-control",24399150,10.1038/mi.2013.116,NA,"Dillon S.M., Lee E.J., Kotter C.V., Austin G.L., Dong Z., Hecht D.K., Gianella S., Siewe B., Smith D.M., Landay A.L., Robertson C.E., Frank D.N. , Wilson C.C.",An altered intestinal mucosal microbiome in HIV-1 infection is associated with mucosal and systemic immune activation and endotoxemia,Mucosal immunology,2014,NA,Experiment 1,United States of America,Homo sapiens,Colonic mucosa,UBERON:0000317,HIV infection,EFO:0000764,uninfected controls,HIV-infected subjects,Subjects with untreated chronic HIV-1 infection,14,18,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,"Figure 1, Supplemental table S1",10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks","Differential microbial abundance in the colonic mucosa comparing healthy controls to subjects with chronic, untreated HIV-1 infections",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|33042;1783272|1239;3379134|976|200643|171549|171551;3379134|976|200643|171549|171550,Complete,Claregrieve1
bsdb:24402367/1/1,24402367,prospective cohort,24402367,10.1007/s00248-013-0355-4,NA,"Montassier E., Batard E., Massart S., Gastinne T., Carton T., Caillon J., Le Fresne S., Caroff N., Hardouin J.B., Moreau P., Potel G., Le Vacon F. , de La Cochetière M.F.",16S rRNA gene pyrosequencing reveals shift in patient faecal microbiota during high-dose chemotherapy as conditioning regimen for bone marrow transplantation,Microbial ecology,2014,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Non-Hodgkins lymphoma,EFO:0005952,pre-chemotherapy,post-chemotherapy,"patients ages 40 to 60 years old diagnosis with non-Hodgkin's lymphoma undergoing post-chemotherapy high-dose carmustine, etoposide, aracytin and melphalan",8,8,NA,16S,56,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Figure 4, 5, text",10 January 2021,William Lam,"WikiWorks,Aiyshaaaa,Atrayees","Cumulative percentage of family and genera sequences detected in the prechemotherapy and postchemotherapy fecl, compared using multiple Wilcoxon rank tests for paired data",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota",3379134|976|200643|171549|815|816;3379134|976;3379134|1224|1236|91347|543|561;3379134|1224,Complete,Atrayees
bsdb:24402367/1/2,24402367,prospective cohort,24402367,10.1007/s00248-013-0355-4,NA,"Montassier E., Batard E., Massart S., Gastinne T., Carton T., Caillon J., Le Fresne S., Caroff N., Hardouin J.B., Moreau P., Potel G., Le Vacon F. , de La Cochetière M.F.",16S rRNA gene pyrosequencing reveals shift in patient faecal microbiota during high-dose chemotherapy as conditioning regimen for bone marrow transplantation,Microbial ecology,2014,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Non-Hodgkins lymphoma,EFO:0005952,pre-chemotherapy,post-chemotherapy,"patients ages 40 to 60 years old diagnosis with non-Hodgkin's lymphoma undergoing post-chemotherapy high-dose carmustine, etoposide, aracytin and melphalan",8,8,NA,16S,56,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"Figure 4, 5, text",10 January 2021,William Lam,"WikiWorks,Atrayees","Cumulative percentage of family and genera sequences detected in the prechemotherapy and postchemotherapy fecl, compared using multiple Wilcoxon rank tests for paired data",decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|1239;1783272|201174;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|841;1783272|201174|1760|85004|31953|1678,Complete,Atrayees
bsdb:24421902/1/1,24421902,case-control,24421902,10.1371/journal.pone.0083744,NA,"Xuan C., Shamonki J.M., Chung A., Dinome M.L., Chung M., Sieling P.A. , Lee D.J.",Microbial dysbiosis is associated with human breast cancer,PloS one,2014,NA,Experiment 1,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast carcinoma,EFO:0000305,normal tissue,tumor tissue,NA,20,20,NA,16S,4,Illumina,raw counts,T-Test,0.05,FALSE,NA,NA,age,NA,NA,NA,NA,NA,unchanged,Signature 1,Table S2 and Figure 1d,10 January 2021,Rimsha Azhar,"WikiWorks,Atrayees",OTUs enriched in paired normal or tumor tissue,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium|s__Methylobacterium radiotolerans,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae",3379134|1224|28211|356|119045|407|31998;3379134|976|117743|200644|49546|237;3379134|1224|28211|356|119045|407;3379134|1224|28211|356|119045,Complete,Atrayees
bsdb:24421902/1/2,24421902,case-control,24421902,10.1371/journal.pone.0083744,NA,"Xuan C., Shamonki J.M., Chung A., Dinome M.L., Chung M., Sieling P.A. , Lee D.J.",Microbial dysbiosis is associated with human breast cancer,PloS one,2014,NA,Experiment 1,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast carcinoma,EFO:0000305,normal tissue,tumor tissue,NA,20,20,NA,16S,4,Illumina,raw counts,T-Test,0.05,FALSE,NA,NA,age,NA,NA,NA,NA,NA,unchanged,Signature 2,Table S2 and Figure 1d,10 January 2021,Rimsha Azhar,"WikiWorks,Atrayees",OTUs enriched in paired normal or tumor tissue,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium|s__Sphingobium yanoikuyae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Nitrosomonadaceae|g__Nitrosomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium|s__Novosphingobium aromaticivorans,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudopneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae",3379134|1224|28211|204457|3423717|165695|13690;3379134|1224|28211|204457|41297|13687;3379134|1224|28216|32003|206379|914;3379134|1224|28211|204457|41297|165696|48935;3379134|1224|28211|356|41294|374;1783272|1239|91061|186826|1300|1301|257758;3379134|1224|28211|204457|41297,Complete,Atrayees
bsdb:24448554/1/1,24448554,"cross-sectional observational, not case-control",24448554,10.1038/srep03814,NA,"Mejía-León M.E., Petrosino J.F., Ajami N.J., Domínguez-Bello M.G. , de la Barca A.M.",Fecal microbiota imbalance in Mexican children with type 1 diabetes,Scientific reports,2014,NA,Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Type I diabetes mellitus,MONDO:0005147,controls,Type I diabetic children at onset,"T1D diagnose as established according to the American Diabetes Association criteria1, a positive anti-GAD and/or anti-IA-2 auto- antibodies result, HbA1C levels , 8%",8,8,3 months,16S,4,Roche454,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,text,10 January 2021,Yaseen Javaid,WikiWorks,Fecal microbiota imbalance in Mexican children with type 1 diabetes,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
bsdb:24448554/1/2,24448554,"cross-sectional observational, not case-control",24448554,10.1038/srep03814,NA,"Mejía-León M.E., Petrosino J.F., Ajami N.J., Domínguez-Bello M.G. , de la Barca A.M.",Fecal microbiota imbalance in Mexican children with type 1 diabetes,Scientific reports,2014,NA,Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Type I diabetes mellitus,MONDO:0005147,controls,Type I diabetic children at onset,"T1D diagnose as established according to the American Diabetes Association criteria1, a positive anti-GAD and/or anti-IA-2 auto- antibodies result, HbA1C levels , 8%",8,8,3 months,16S,4,Roche454,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,text,10 January 2021,Yaseen Javaid,WikiWorks,Fecal microbiota imbalance in Mexican children with type 1 diabetes,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",3379134|976|200643|171549|171552|838;1783272|1239|909932|1843488|909930|904;1783272|1239|909932|909929|1843491|158846,Complete,Shaimaa Elsafoury
bsdb:24451087/1/1,24451087,"cross-sectional observational, not case-control",24451087,10.1186/2049-2618-1-26,NA,"McHardy I.H., Li X., Tong M., Ruegger P., Jacobs J., Borneman J., Anton P. , Braun J.",HIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota,Microbiome,2013,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Healthy controls,HIV infected cART negative,HIV infected patients not on combined anti-retroviral therapy,20,20,NA,16S,4,Illumina,NA,Kruskall-Wallis,0.15,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Phylogenetic differences between HIV subjects not on combination anti-retroviral therapy and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",1783272|1239|1737404|1737405|1570339|165779;3384189|32066;3384189|32066|203490|203491|203492;3384189|32066|203490;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836,Complete,Claregrieve1
bsdb:24451087/1/2,24451087,"cross-sectional observational, not case-control",24451087,10.1186/2049-2618-1-26,NA,"McHardy I.H., Li X., Tong M., Ruegger P., Jacobs J., Borneman J., Anton P. , Braun J.",HIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota,Microbiome,2013,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Healthy controls,HIV infected cART negative,HIV infected patients not on combined anti-retroviral therapy,20,20,NA,16S,4,Illumina,NA,Kruskall-Wallis,0.15,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Figure 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Phylogenetic differences between HIV subjects not on combination anti-retroviral therapy and healthy controls,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",3379134|976|200643|171549|171550|239759;1783272|1239|186801;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730;1783272|1239;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|541000;3379134|976|200643|171549|171550;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263,Complete,Claregrieve1
bsdb:24532064/1/1,24532064,case-control,24532064,10.1128/AEM.00003-14,NA,"Ling Z., Li Z., Liu X., Cheng Y., Luo Y., Tong X., Yuan L., Wang Y., Sun J., Li L. , Xiang C.",Altered fecal microbiota composition associated with food allergy in infants,Applied and environmental microbiology,2014,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,healthy controls,infants with food allergies,infant with food allergy,45,34,1 month,16S,123,Roche454,relative abundances,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 1a, Text",10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Differentially abundant taxons between infants with food allergy and health controls,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Bacillati|p__Bacillota,k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|1239|186801|186802|31979;3379134|976|768503|768507|89373;1783272|201174|1760|85007|85025;1783272|1239;3384189|32066;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|31979|1485;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|946234;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|171552|838;1783272|1239|91061|1385|90964|1279,Complete,Atrayees
bsdb:24532064/1/2,24532064,case-control,24532064,10.1128/AEM.00003-14,NA,"Ling Z., Li Z., Liu X., Cheng Y., Luo Y., Tong X., Yuan L., Wang Y., Sun J., Li L. , Xiang C.",Altered fecal microbiota composition associated with food allergy in infants,Applied and environmental microbiology,2014,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,healthy controls,infants with food allergies,infant with food allergy,45,34,1 month,16S,123,Roche454,relative abundances,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 1a, Text",10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Differentially abundant taxons between infants with food allergy and health controls,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|1224|28216|80840|506;1783272|1239|186801|3082720|543314;3379134|1224|28211|356|69277;3379134|1224|1236|135614|32033;3379134|976|117743|200644|49546;3379134|1224|1236|2887326|468;3379134|976;3379134|1224;1783272|201174;3379134|74201;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3082720|186804;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:24532064/2/1,24532064,case-control,24532064,10.1128/AEM.00003-14,NA,"Ling Z., Li Z., Liu X., Cheng Y., Luo Y., Tong X., Yuan L., Wang Y., Sun J., Li L. , Xiang C.",Altered fecal microbiota composition associated with food allergy in infants,Applied and environmental microbiology,2014,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,healthy controls,infants with food allergies,infant with food allergy,45,34,1 month,16S,123,Roche454,relative abundances,LEfSe,2,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 1d, Text",10 January 2021,Lucy Mellor,"Merit,WikiWorks",Differentially abundant taxons between infants with food allergy and health controls,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae",1783272|201174|1760|2037;;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;3379134|976|768503|768507|89373;1783272|201174|1760|85007|85025,Complete,Atrayees
bsdb:24532064/2/2,24532064,case-control,24532064,10.1128/AEM.00003-14,NA,"Ling Z., Li Z., Liu X., Cheng Y., Luo Y., Tong X., Yuan L., Wang Y., Sun J., Li L. , Xiang C.",Altered fecal microbiota composition associated with food allergy in infants,Applied and environmental microbiology,2014,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,healthy controls,infants with food allergies,infant with food allergy,45,34,1 month,16S,123,Roche454,relative abundances,LEfSe,2,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 1d, Text",10 January 2021,Lucy Mellor,WikiWorks,Differentially abundant taxons between infants with food allergy and health controls,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas",1783272|1239|909932|1843489|31977|906;1783272|1239|186801|186802|541000;3379134|976|117743|200644|49546;3379134|1224|28211|356|69277;3379134|1224|28211|356|69277|68287;3379134|1224|28216|80840|506|222;3379134|1224|28216|80840|506;3379134|976|117743|200644;1783272|201174|84998|1643822|1643826|84111;3379134|976|117743|200644|49546|237;3379134|1224|1236|135614|32033;3379134|1224|1236|135614|32033|40323;1783272|1239|186801|3082720|543314|86331;3379134|976|117743|200644|2762318|59732;1783272|1239|186801|3082720|543314;3379134|1224|1236|135614;3379134|1224|28211|204458|76892;3379134|1224|28216|80840|80864|283,Complete,Atrayees
bsdb:24532064/3/1,24532064,case-control,24532064,10.1128/AEM.00003-14,NA,"Ling Z., Li Z., Liu X., Cheng Y., Luo Y., Tong X., Yuan L., Wang Y., Sun J., Li L. , Xiang C.",Altered fecal microbiota composition associated with food allergy in infants,Applied and environmental microbiology,2014,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,infants non-IgE mediated,infants IgE mediated,infant IgE mediated,17,17,1 month,16S,123,Roche454,relative abundances,LEfSe,2,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2a, Text",10 January 2021,Lucy Mellor,WikiWorks,Differentially abundant taxons between IgE-mediated food allergy infants and non-IgE-mediated food allergy infants,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia",1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802;1783272|1239|186801,Complete,Atrayees
bsdb:24532064/3/2,24532064,case-control,24532064,10.1128/AEM.00003-14,NA,"Ling Z., Li Z., Liu X., Cheng Y., Luo Y., Tong X., Yuan L., Wang Y., Sun J., Li L. , Xiang C.",Altered fecal microbiota composition associated with food allergy in infants,Applied and environmental microbiology,2014,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,infants non-IgE mediated,infants IgE mediated,infant IgE mediated,17,17,1 month,16S,123,Roche454,relative abundances,LEfSe,2,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2a, Text",10 January 2021,Lucy Mellor,"Merit,WikiWorks",Differentially abundant taxons between IgE-mediated food allergy infants and non-IgE-mediated food allergy infants,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|186801|3085636|186803;1783272|201174|1760|85007|85025,Complete,Atrayees
bsdb:24532064/4/1,24532064,case-control,24532064,10.1128/AEM.00003-14,NA,"Ling Z., Li Z., Liu X., Cheng Y., Luo Y., Tong X., Yuan L., Wang Y., Sun J., Li L. , Xiang C.",Altered fecal microbiota composition associated with food allergy in infants,Applied and environmental microbiology,2014,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,infants non-IgE mediated,infants IgE mediated,infant IgE mediated,17,17,1 month,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2c, Text",10 January 2021,Lucy Mellor,WikiWorks,Differentially abundant taxons between IgE-mediated food allergy infants and non-IgE-mediated food allergy infants,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,1783272|1239|186801|186802|31979|1485,Complete,Atrayees
bsdb:24532064/4/2,24532064,case-control,24532064,10.1128/AEM.00003-14,NA,"Ling Z., Li Z., Liu X., Cheng Y., Luo Y., Tong X., Yuan L., Wang Y., Sun J., Li L. , Xiang C.",Altered fecal microbiota composition associated with food allergy in infants,Applied and environmental microbiology,2014,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,infants non-IgE mediated,infants IgE mediated,infant IgE mediated,17,17,1 month,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2c, Text",10 January 2021,Lucy Mellor,"Merit,WikiWorks",Differentially abundant taxons between IgE-mediated food allergy infants and non-IgE-mediated food allergy infants,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",3379134|976|200643|171549|815|816;3379134|976|200643|171549,Complete,Atrayees
bsdb:24614698/1/1,24614698,"cross-sectional observational, not case-control",24614698,10.1371/journal.pone.0090784,NA,"Ardissone A.N., de la Cruz D.M., Davis-Richardson A.G., Rechcigl K.T., Li N., Drew J.C., Murgas-Torrazza R., Sharma R., Hudak M.L., Triplett E.W. , Neu J.",Meconium microbiome analysis identifies bacteria correlated with premature birth,PloS one,2014,NA,Experiment 1,United States of America,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,vaginal delivery,C-section,the study groups are devided into two groups acc to the gestational age. 1) gestational age < 33 weeks. 2) gestational age >/= 33 weeks,19,33,NA,16S,4,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"birth weight,chorioamnionitis,feeding practices,sex",NA,increased,increased,NA,NA,NA,Signature 1,Table S6 in File S1,10 January 2021,Rimsha Azhar,WikiWorks,Meconium microbiome related to mode of delivery in premature infants,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio",1783272|1239|91061|186826|33958|1243;1783272|1239|909932|1843489|31977|909928;1783272|1239|91061|186826|81852|2737;1783272|1239|186801|3085636|186803|830,Complete,Shaimaa Elsafoury
bsdb:24614698/2/1,24614698,"cross-sectional observational, not case-control",24614698,10.1371/journal.pone.0090784,NA,"Ardissone A.N., de la Cruz D.M., Davis-Richardson A.G., Rechcigl K.T., Li N., Drew J.C., Murgas-Torrazza R., Sharma R., Hudak M.L., Triplett E.W. , Neu J.",Meconium microbiome analysis identifies bacteria correlated with premature birth,PloS one,2014,NA,Experiment 2,United States of America,Homo sapiens,Meconium,UBERON:0007109,Premature birth,EFO:0003917,>/=33 weeks,infants <33 weeks gestational age,the study groups are devided into two groups acc to the gestational age. 1) gestational age < 33 weeks. 2) gestational age >/= 33 weeks,17,35,NA,16S,4,Ion Torrent,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,"birth weight,chorioamnionitis,feeding practices,sex",NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table 1,10 January 2021,Rimsha Azhar,WikiWorks,"Phyla, family, and genera taxonomy significantly correlated with gestational age",increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Photorhabdus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacillati|p__Actinomycetota",1783272|1239;1783272|1239|91061|1385|186817;1783272|1239|91061|1385|90964;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|81850;1783272|1239|186801|186802|31979;1783272|1239|186801|3082720|186804;1783272|1239|909932|1843489|31977;1783272|1239|526524|526525|128827;1783272|201174|1760|85004|31953;3379134|1224|1236|91347|543;1783272|1239|91061|1385|186817|1386;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|81852|2737;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1243;1783272|1239|186801|186802|31979|1485;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|909928;1783272|201174|1760|85004|31953|1678;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|1903409|551;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|543|160674;3379134|1224|1236|91347|1903409|53335;3379134|1224|1236|91347|1903414|29487;3379134|976|200643|171549|2005525|195950;1783272|201174,Complete,Shaimaa Elsafoury
bsdb:24614698/2/2,24614698,"cross-sectional observational, not case-control",24614698,10.1371/journal.pone.0090784,NA,"Ardissone A.N., de la Cruz D.M., Davis-Richardson A.G., Rechcigl K.T., Li N., Drew J.C., Murgas-Torrazza R., Sharma R., Hudak M.L., Triplett E.W. , Neu J.",Meconium microbiome analysis identifies bacteria correlated with premature birth,PloS one,2014,NA,Experiment 2,United States of America,Homo sapiens,Meconium,UBERON:0007109,Premature birth,EFO:0003917,>/=33 weeks,infants <33 weeks gestational age,the study groups are devided into two groups acc to the gestational age. 1) gestational age < 33 weeks. 2) gestational age >/= 33 weeks,17,35,NA,16S,4,Ion Torrent,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,"birth weight,chorioamnionitis,feeding practices,sex",NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Table 1,10 January 2021,Rimsha Azhar,WikiWorks,"Phyla, family, and genera taxonomy significantly correlated with gestational age",decreased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalicibacterium,3379134|1224|28216|80840|75682|223927,Complete,Shaimaa Elsafoury
bsdb:24629344/1/1,24629344,case-control,24629344,https:/doi.org/10.1016/j.chom.2014.02.005,https://pubmed.ncbi.nlm.nih.gov/24629344/,"Gevers D., Kugathasan S., Denson L.A., Vázquez-Baeza Y., Van Treuren W., Ren B., Schwager E., Knights D., Song S.J., Yassour M., Morgan X.C., Kostic A.D., Luo C., González A., McDonald D., Haberman Y., Walters T., Baker S., Rosh J., Stephens M., Heyman M., Markowitz J., Baldassano R., Griffiths A., Sylvester F., Mack D., Kim S., Crandall W., Hyams J., Huttenhower C., Knight R. , Xavier R.J.",The treatment-naive microbiome in new-onset Crohn's disease,Cell host & microbe,2014,NA,Experiment 1,China,Homo sapiens,"Ileum,Rectum","UBERON:0002116,UBERON:0001052",Crohn's disease,EFO:0000384,Healthy control,Crohn's disease,Treatment-naive pediatric patients (ages 3-17) with new-onset Crohn's disease,221,447,NA,16S,4,Illumina,raw counts,Linear Regression,NA,NA,NA,NA,"age,antibiotic exposure,race,sex",NA,NA,NA,NA,NA,decreased,Signature 1,Table S2A,13 March 2023,Khadeeejah,"Khadeeejah,Atrayees,Chloe,Aiyshaaaa,WikiWorks","Alteration in the abundance of several taxa in the ileal and rectal samples, in the diagnosis variable.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",1783272|201174|1760|85006|1268;3379134|29547|3031852|213849;3379134|1224|28216|206351|481|482;1783272|1239|909932|1843489|31977|29465|29466;3379134|1224|1236|135625|712|713;3379134|1224|1236|135625|712|416916;3379134|1224|1236|135625|712|416916|739;3379134|1224|28216|206351|481;1783272|1239|909932|1843489|31977|29465|39778;3384189|32066|203490|203491;3384189|32066|203490|203491|203492;3379134|1224|28216|80840|119060;1783272|1239|909932|1843489|31977;3379134|1224|28216;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712|724|729;3379134|1224|1236|135625|712;3379134|1224|1236|91347|543,Complete,Atrayees
bsdb:24629344/1/2,24629344,case-control,24629344,https:/doi.org/10.1016/j.chom.2014.02.005,https://pubmed.ncbi.nlm.nih.gov/24629344/,"Gevers D., Kugathasan S., Denson L.A., Vázquez-Baeza Y., Van Treuren W., Ren B., Schwager E., Knights D., Song S.J., Yassour M., Morgan X.C., Kostic A.D., Luo C., González A., McDonald D., Haberman Y., Walters T., Baker S., Rosh J., Stephens M., Heyman M., Markowitz J., Baldassano R., Griffiths A., Sylvester F., Mack D., Kim S., Crandall W., Hyams J., Huttenhower C., Knight R. , Xavier R.J.",The treatment-naive microbiome in new-onset Crohn's disease,Cell host & microbe,2014,NA,Experiment 1,China,Homo sapiens,"Ileum,Rectum","UBERON:0002116,UBERON:0001052",Crohn's disease,EFO:0000384,Healthy control,Crohn's disease,Treatment-naive pediatric patients (ages 3-17) with new-onset Crohn's disease,221,447,NA,16S,4,Illumina,raw counts,Linear Regression,NA,NA,NA,NA,"age,antibiotic exposure,race,sex",NA,NA,NA,NA,NA,decreased,Signature 2,Table S2A,13 March 2023,Khadeeejah,"Khadeeejah,Aiyshaaaa,Chloe,Atrayees,WikiWorks","Alteration in the abundance of several taxa in the ileal and rectal samples, in the diagnosis variable.",decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila",1783272|1239;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|526524|526525|128827;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|815|816|820;1783272|1239|186801|186802|186806|1730;1783272|201174|1760|85004|31953|1678;1783272|1239|526524|526525|128827|2749846|31971;1783272|201174|1760|85004|31953;1783272|201174;1783272|1239|526524|526525|128827|1573535|1735;1783272|1239|186801|186802|31979|1485;1783272|201174|1760|85004|31953|1678|1680;1783272|1239|186801|3085636|186803|3570277|116085;3379134|74201|203494|48461|203557;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|216572|1263|40518;3379134|74201|203494|48461|1647988|239934|239935,Complete,Atrayees
bsdb:24629344/2/1,24629344,case-control,24629344,https:/doi.org/10.1016/j.chom.2014.02.005,https://pubmed.ncbi.nlm.nih.gov/24629344/,"Gevers D., Kugathasan S., Denson L.A., Vázquez-Baeza Y., Van Treuren W., Ren B., Schwager E., Knights D., Song S.J., Yassour M., Morgan X.C., Kostic A.D., Luo C., González A., McDonald D., Haberman Y., Walters T., Baker S., Rosh J., Stephens M., Heyman M., Markowitz J., Baldassano R., Griffiths A., Sylvester F., Mack D., Kim S., Crandall W., Hyams J., Huttenhower C., Knight R. , Xavier R.J.",The treatment-naive microbiome in new-onset Crohn's disease,Cell host & microbe,2014,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Healthy control,Crohn's disease,Treatment-naive pediatric patients (ages 3-17) with new-onset Crohn's disease,221,447,NA,16S,4,Illumina,raw counts,Linear Regression,NA,NA,NA,NA,"age,antibiotic exposure,race,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table S2B,4 April 2023,Khadeeejah,"Khadeeejah,Aiyshaaaa,Atrayees,WikiWorks",Taxa in stool samples significantly associated with disease.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|572511|33035;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Atrayees
bsdb:24629344/3/1,24629344,case-control,24629344,https:/doi.org/10.1016/j.chom.2014.02.005,https://pubmed.ncbi.nlm.nih.gov/24629344/,"Gevers D., Kugathasan S., Denson L.A., Vázquez-Baeza Y., Van Treuren W., Ren B., Schwager E., Knights D., Song S.J., Yassour M., Morgan X.C., Kostic A.D., Luo C., González A., McDonald D., Haberman Y., Walters T., Baker S., Rosh J., Stephens M., Heyman M., Markowitz J., Baldassano R., Griffiths A., Sylvester F., Mack D., Kim S., Crandall W., Hyams J., Huttenhower C., Knight R. , Xavier R.J.",The treatment-naive microbiome in new-onset Crohn's disease,Cell host & microbe,2014,NA,Experiment 3,China,Homo sapiens,"Ileum,Feces,Rectum","UBERON:0001988,UBERON:0002116,UBERON:0001052",Crohn's disease,EFO:0000384,Healthy control,Crohn's disease,Treatment-naive pediatric patients (ages 3-17) with new-onset Crohn's disease,221,447,NA,16S,4,Illumina,raw counts,Linear Regression,NA,NA,NA,NA,"age,antibiotic exposure,race,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table S2C,4 April 2023,Khadeeejah,"Khadeeejah,Aiyshaaaa,Atrayees,WikiWorks",precise differences between the mucosal tissue and stool samples within patients with new-onset CD,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239|91061|186826|33958;1783272|1239|186801|186802|186806;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|572511|33035;1783272|1239|526524|526525|128827|2749846|31971;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|186802|31979|1485;1783272|1239|91061;1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|31979;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572;1783272|1239|91061|186826;1783272|1239|91061|186826|1300;1783272|201174|84998|84999|84107;1783272|201174;1783272|1239|526524|526525|128827;1783272|1239|186801|3085636|186803|33042;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803;1783272|1239;1783272|1239|186801|186802,Complete,Atrayees
bsdb:24629344/3/2,24629344,case-control,24629344,https:/doi.org/10.1016/j.chom.2014.02.005,https://pubmed.ncbi.nlm.nih.gov/24629344/,"Gevers D., Kugathasan S., Denson L.A., Vázquez-Baeza Y., Van Treuren W., Ren B., Schwager E., Knights D., Song S.J., Yassour M., Morgan X.C., Kostic A.D., Luo C., González A., McDonald D., Haberman Y., Walters T., Baker S., Rosh J., Stephens M., Heyman M., Markowitz J., Baldassano R., Griffiths A., Sylvester F., Mack D., Kim S., Crandall W., Hyams J., Huttenhower C., Knight R. , Xavier R.J.",The treatment-naive microbiome in new-onset Crohn's disease,Cell host & microbe,2014,NA,Experiment 3,China,Homo sapiens,"Ileum,Feces,Rectum","UBERON:0001988,UBERON:0002116,UBERON:0001052",Crohn's disease,EFO:0000384,Healthy control,Crohn's disease,Treatment-naive pediatric patients (ages 3-17) with new-onset Crohn's disease,221,447,NA,16S,4,Illumina,raw counts,Linear Regression,NA,NA,NA,NA,"age,antibiotic exposure,race,sex",NA,NA,NA,NA,NA,NA,Signature 2,Tabls S2C,4 April 2023,Khadeeejah,"Khadeeejah,Aiyshaaaa,Atrayees,WikiWorks",precise differences between the mucosal tissue and stool samples within patients with new-onset CD,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Rhodocyclaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",3379134|976|200643|171549|815|816;3379134|1224;3379134|976|200643|171549;3379134|976|200643;3379134|1224|1236;3379134|1224|28216;3379134|976|200643|171549|815|816|817;3379134|1224|28216|80840;3379134|200940|3031449|213115|194924;3379134|1224|28216|206389|75787;3379134|1224|28211|204457;3379134|1224|1236|135625|712|416916;3379134|1224|1236|72274;3379134|1224|1236|2887326|468;3379134|1224|1236|2887326|468|469;3384189|32066|203490|203491;3384189|32066|203490|203491|203492;1783272|1239|91061|1385|90964|1279;3379134|1224|28216|206351|481;1783272|1239|91061|1385;1783272|1239|1737404|1737405|1737406;3379134|1224|28216|206351|481|482;3379134|976|117743|200644|2762318;1783272|201174|1760|85006|1268;33090|35493|3398|72025|3803|3814|508215;3379134|29547|3031852|213849;1783272|201174|1760|85006|1268|32207|43675;1783272|201174|1760|85007|1653|1716;3379134|976|200643|171549|171551|836,Complete,Atrayees
bsdb:24748167/1/1,24748167,time series / longitudinal observational,24748167,10.1371/journal.pone.0095476,NA,"Panda S., El khader I., Casellas F., López Vivancos J., García Cors M., Santiago A., Cuenca S., Guarner F. , Manichanh C.",Short-term effect of antibiotics on human gut microbiota,PloS one,2014,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,before antibiotic exposure,patients that took amoxiclav,took amoxiclav for 7 days,7,7,2 months,16S,4,"RT-qPCR,Roche454",relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,"Results within text- Page 3, 2nd paragraph under sub-heading ""Effect of B-lactams""",10 January 2021,Gina Celentano,"WikiWorks,ChiomaBlessing","Microbial taxa affected by amoxiclav, before and after exposure",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota",3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976,Complete,ChiomaBlessing
bsdb:24748167/1/2,24748167,time series / longitudinal observational,24748167,10.1371/journal.pone.0095476,NA,"Panda S., El khader I., Casellas F., López Vivancos J., García Cors M., Santiago A., Cuenca S., Guarner F. , Manichanh C.",Short-term effect of antibiotics on human gut microbiota,PloS one,2014,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,before antibiotic exposure,patients that took amoxiclav,took amoxiclav for 7 days,7,7,2 months,16S,4,"RT-qPCR,Roche454",relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,"Results within text- Page 3, 2nd paragraph under sub-heading ""Effect of B-lactams""",10 January 2021,Gina Celentano,"WikiWorks,ChiomaBlessing","Microbial taxa affected by amoxiclav, before and after exposure",decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,ChiomaBlessing
bsdb:24748167/2/1,24748167,time series / longitudinal observational,24748167,10.1371/journal.pone.0095476,NA,"Panda S., El khader I., Casellas F., López Vivancos J., García Cors M., Santiago A., Cuenca S., Guarner F. , Manichanh C.",Short-term effect of antibiotics on human gut microbiota,PloS one,2014,NA,Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,before antibiotic exposure,patients that took levofloxacin,took levofloxacin for 7 days,8,8,2 months,16S,4,"RT-qPCR,Roche454",relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,Supporting Info file: Table S2,10 January 2021,Gina Celentano,"WikiWorks,ChiomaBlessing","Microbial taxa affected by levofloxacin, before and after exposure",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572,Complete,ChiomaBlessing
bsdb:24748167/2/2,24748167,time series / longitudinal observational,24748167,10.1371/journal.pone.0095476,NA,"Panda S., El khader I., Casellas F., López Vivancos J., García Cors M., Santiago A., Cuenca S., Guarner F. , Manichanh C.",Short-term effect of antibiotics on human gut microbiota,PloS one,2014,NA,Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,before antibiotic exposure,patients that took levofloxacin,took levofloxacin for 7 days,8,8,2 months,16S,4,"RT-qPCR,Roche454",relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,Supporting Info file: Table S2,10 January 2021,Gina Celentano,"WikiWorks,ChiomaBlessing","Microbial taxa affected by levofloxacin, before and after exposure",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,1783272|1239|186801|3085636|186803|572511,Complete,ChiomaBlessing
bsdb:24819377/1/1,24819377,time series / longitudinal observational,24819377,10.1038/pr.2014.69,NA,"Dardas M., Gill S.R., Grier A., Pryhuber G.S., Gill A.L., Lee Y.H. , Guillet R.",The impact of postnatal antibiotics on the preterm intestinal microbiome,Pediatric research,2014,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,10 d old 2 day treatment infants,10 d old 7-10 day treatment infants,Infants who received antibiotics for 7-10 days,15,12,NA,16S,123,Roche454,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,delivery procedure,NA,decreased,NA,NA,NA,unchanged,Signature 1,"Results within text- Page 4, 3rd paragraph, under subheading ""Discussion""",10 January 2021,Mst Afroza Parvin,"WikiWorks,ChiomaBlessing",Genus level differential abundance of breast milk–fed infants at age 10 d with 7days of antibiotic treatment,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus",3379134|976|200643|171549|815|816;1783272|1239|91061|186826|1300|1357,Complete,ChiomaBlessing
bsdb:24819377/2/NA,24819377,time series / longitudinal observational,24819377,10.1038/pr.2014.69,NA,"Dardas M., Gill S.R., Grier A., Pryhuber G.S., Gill A.L., Lee Y.H. , Guillet R.",The impact of postnatal antibiotics on the preterm intestinal microbiome,Pediatric research,2014,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,30 d old minimal antibiotics exposure (2 day treatment infants),30 d old prolonged antibiotics exposure (>=7 day treatment infants),prolonged antibiotics exposure (greater than or equal to 7 day treatment infants),8,11,NA,16S,123,Roche454,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,delivery procedure,NA,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:24828543/1/1,24828543,laboratory experiment,24828543,10.1038/srep04985,http://www.nature.com/scientificreports,"Liang X., Li H., Tian G. , Li S.",Dynamic microbe and molecule networks in a mouse model of colitis-associated colorectal cancer,Scientific reports,2014,NA,Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Control group,AOS/DSS (Azoxymethane/Dextran Sodium Sulphate)-treated group,Mice treated with AOM/DSS to induce chronic colitis and colorectal cancer,10,11,NA,16S,3,Illumina,log transformation,edgeR,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table S2, Fig. 4B",16 November 2024,Wendy640,"Wendy640,KateRasheed,WikiWorks","Differential OTUs between control mice and AOM/DSS-treated mice, showing significant microbial shifts associated with colorectal cancer progression.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus hamsteri,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus lutetiensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Crocinitomicaceae|g__Wandonia,s__bacterium AF12,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella|s__Moryella indoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Candidatus Phytoplasma|s__Candidatus Phytoplasma solani,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis",3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|820;1783272|1239|91061|186826|33958|1578|96565;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|3085636|186803|2941495|1512;1783272|1239|91061|186826|1300|1301|150055;3379134|976|200643|171549|2005473;1783272|1239|526524|526525|128827;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|140625;3379134|976|117743|200644|1853230|1115103;1729795;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|216851|853;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|437755|371674;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|33042;3379134|976|200643|171549|1853231|283168;1783272|544448|31969|186329|2146|33926|69896;1783272|1239|186801|3085636|186803|841|301302,Complete,Svetlana up
bsdb:24828543/1/2,24828543,laboratory experiment,24828543,10.1038/srep04985,http://www.nature.com/scientificreports,"Liang X., Li H., Tian G. , Li S.",Dynamic microbe and molecule networks in a mouse model of colitis-associated colorectal cancer,Scientific reports,2014,NA,Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Control group,AOS/DSS (Azoxymethane/Dextran Sodium Sulphate)-treated group,Mice treated with AOM/DSS to induce chronic colitis and colorectal cancer,10,11,NA,16S,3,Illumina,log transformation,edgeR,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Table S2, Fig. 4B",19 November 2024,Wendy640,"Wendy640,KateRasheed,WikiWorks","Differential OTUs between control mice and AOM/DSS-treated mice, showing significant microbial shifts associated with colorectal cancer progression.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella|s__Moryella indoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Candidatus Phytoplasma|s__Candidatus Phytoplasma citri,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Candidatus Phytoplasma|s__Candidatus Phytoplasma solani,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|186803|437755|371674;1783272|1239|186801|3085636|186803|265975;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|171550|28138;3379134|976|200643|171549;1783272|1239|186801|3085636|186803;1783272|544448|31969;3379134|976|200643|171549|2005473;3379134|976|200643|171549|171550;1783272|544448|31969|186329|2146|33926|180978;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3082720|543314|86331;1783272|544448|31969|186329|2146|33926|69896;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:24828543/2/1,24828543,laboratory experiment,24828543,10.1038/srep04985,http://www.nature.com/scientificreports,"Liang X., Li H., Tian G. , Li S.",Dynamic microbe and molecule networks in a mouse model of colitis-associated colorectal cancer,Scientific reports,2014,NA,Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Mice with inflammation,Mice with dysplasia/cancer,Mice that developed dysplasia and cancer and were treated with 3-4 AOM/DSS cycles,NA,NA,NA,16S,3,Illumina,log transformation,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 1,Table S3,19 November 2024,Wendy640,"Wendy640,KateRasheed,WikiWorks","OTUs distinguishing inflammation from colorectal cancer, highlighting taxa involved in cancer-related microbiome changes.",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,3379134|976|200643|171549|2005473,Complete,Svetlana up
bsdb:24828543/2/2,24828543,laboratory experiment,24828543,10.1038/srep04985,http://www.nature.com/scientificreports,"Liang X., Li H., Tian G. , Li S.",Dynamic microbe and molecule networks in a mouse model of colitis-associated colorectal cancer,Scientific reports,2014,NA,Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Mice with inflammation,Mice with dysplasia/cancer,Mice that developed dysplasia and cancer and were treated with 3-4 AOM/DSS cycles,NA,NA,NA,16S,3,Illumina,log transformation,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 2,Table S3,18 November 2024,Wendy640,"Wendy640,KateRasheed,WikiWorks",Differential OTUs between mice with Inflammation and cancer,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium succinicans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,s__rumen bacterium YS2,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|216851|853;3379134|976|117743|200644|49546|237|29536;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171550;209265;1783272|1239|186801|3082768|990719;1783272|1239|526524|526525|128827;3379134|976|200643|171549|2005473,Complete,Svetlana up
bsdb:24828543/3/1,24828543,laboratory experiment,24828543,10.1038/srep04985,http://www.nature.com/scientificreports,"Liang X., Li H., Tian G. , Li S.",Dynamic microbe and molecule networks in a mouse model of colitis-associated colorectal cancer,Scientific reports,2014,NA,Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Control mice,AOM/DSS Cycle 1 group,Mice treated with AOM/DSS cycle 1,10,NA,NA,16S,3,Illumina,log transformation,edgeR,0.05,TRUE,NA,NA,NA,NA,decreased,unchanged,decreased,decreased,unchanged,Signature 1,Table S4,18 November 2024,Wendy640,"Wendy640,KateRasheed,WikiWorks",Differential OTUs after treatment of different AOM/DSS cycles,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,s__bacterium AF12,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Crocinitomicaceae|g__Wandonia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Candidatus Phytoplasma|s__Candidatus Phytoplasma solani,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio",3379134|976|200643|171549|2005473;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171550;1783272|1239|526524|526525|128827|174708;1729795;1783272|1239|186801|186802|216572|216851|853;3379134|976|117743|200644|1853230|1115103;1783272|1239|526524|526525|128827;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|119852;1783272|544448|31969|186329|2146|33926|69896;1783272|1239|186801|3085636|186803|830,Complete,Svetlana up
bsdb:24828543/3/3,24828543,laboratory experiment,24828543,10.1038/srep04985,http://www.nature.com/scientificreports,"Liang X., Li H., Tian G. , Li S.",Dynamic microbe and molecule networks in a mouse model of colitis-associated colorectal cancer,Scientific reports,2014,NA,Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Control mice,AOM/DSS Cycle 1 group,Mice treated with AOM/DSS cycle 1,10,NA,NA,16S,3,Illumina,log transformation,edgeR,0.05,TRUE,NA,NA,NA,NA,decreased,unchanged,decreased,decreased,unchanged,Signature 3,Table S4,18 November 2024,Wendy640,"Wendy640,KateRasheed,WikiWorks",Differential OTUs after treatment of different AOM/DSS cycles,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",1783272|1239|186801|3085636|186803|841;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|2316020|33038,Complete,Svetlana up
bsdb:24828543/4/1,24828543,laboratory experiment,24828543,10.1038/srep04985,http://www.nature.com/scientificreports,"Liang X., Li H., Tian G. , Li S.",Dynamic microbe and molecule networks in a mouse model of colitis-associated colorectal cancer,Scientific reports,2014,NA,Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Control group,AOM/DSS Cycle 2 group,Mice treated with AOM/DSS cycle 2,10,NA,NA,16S,3,Illumina,log transformation,edgeR,0.05,TRUE,NA,NA,NA,NA,decreased,unchanged,decreased,decreased,unchanged,Signature 1,Table S4,19 November 2024,Wendy640,"Wendy640,KateRasheed,WikiWorks","Differential OTUs after 2 cycles of AOM/DSS treatment, showing intermediate changes in the gut microbiota.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae|g__Salinispora|s__Salinispora tropica,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Crocinitomicaceae|g__Wandonia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium succinicans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|s__Acholeplasmatales bacterium canine oral taxon 172,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella|s__Moryella indoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio",3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|816|820;1783272|1239|526524|526525|128827;3379134|976|200643|171549|2005473;1783272|201174|1760|85008|28056|168694|168695;3379134|976|117743|200644|1853230|1115103;3379134|976|117743|200644|49546|237|29536;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|1263|40519;1783272|544448|31969|186329|1151604;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|28050;3379134|976|200643|171549|815|816|28116;1783272|1239|186801|3085636|186803|437755|371674;1783272|1239|186801|3085636|186803|830,Complete,Svetlana up
bsdb:24828543/4/2,24828543,laboratory experiment,24828543,10.1038/srep04985,http://www.nature.com/scientificreports,"Liang X., Li H., Tian G. , Li S.",Dynamic microbe and molecule networks in a mouse model of colitis-associated colorectal cancer,Scientific reports,2014,NA,Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Control group,AOM/DSS Cycle 2 group,Mice treated with AOM/DSS cycle 2,10,NA,NA,16S,3,Illumina,log transformation,edgeR,0.05,TRUE,NA,NA,NA,NA,decreased,unchanged,decreased,decreased,unchanged,Signature 2,Table S4,19 November 2024,Wendy640,"Wendy640,KateRasheed,WikiWorks","Differential OTUs after 2 cycles of AOM/DSS treatment, showing intermediate changes in the gut microbiota.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|s__Enterococcaceae bacterium RF39",1783272|1239|186801|186802|216572;3379134|976|200643|171549|171550|28138;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|186803|177971;3379134|976|200643|171549|171550;1783272|1239|186801|3085636|186803|841;1783272|1239|91061|186826|81852|423410,Complete,Svetlana up
bsdb:24828543/5/1,24828543,laboratory experiment,24828543,10.1038/srep04985,http://www.nature.com/scientificreports,"Liang X., Li H., Tian G. , Li S.",Dynamic microbe and molecule networks in a mouse model of colitis-associated colorectal cancer,Scientific reports,2014,NA,Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Control Group,AOM/DSS Cycle 3 group,Mice treated with AOM/DSS cycle 3,10,NA,NA,16S,3,Illumina,log transformation,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 1,Table S4,19 November 2024,Wendy640,"Wendy640,KateRasheed,WikiWorks","Differential OTUs after 3 cycles of AOM/DSS treatment, indicating microbial changes at advanced disease stages.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus garvieae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Crocinitomicaceae|g__Wandonia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,s__bacterium AF12,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|s__Enterococcaceae bacterium RF39,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Rickettsiaceae|g__Rickettsia|s__Rickettsia endosymbiont of Deronectes platynotus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",1783272|1239|186801|3085636|186803|140625;3379134|1224|28216|80840|995019|40544;3379134|976|200643|171549|2005473;1783272|1239|91061|186826|1300|1357|1363;1783272|1239|186801|186802|216572;3379134|976|117743|200644|1853230|1115103;3379134|1224|1236|91347|1903414|583;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|207244;1729795;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|81852|423410;1783272|1239|186801|186802|216572|1263|40519;3379134|976|200643|171549|815|816|820;1783272|1239|526524|526525|128827;3379134|976|200643|171549|171550;3379134|1224|28211|766|775|780|544465;1783272|1239|186801|3085636|186803|2316020|33038,Complete,Svetlana up
bsdb:24828543/5/2,24828543,laboratory experiment,24828543,10.1038/srep04985,http://www.nature.com/scientificreports,"Liang X., Li H., Tian G. , Li S.",Dynamic microbe and molecule networks in a mouse model of colitis-associated colorectal cancer,Scientific reports,2014,NA,Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Control Group,AOM/DSS Cycle 3 group,Mice treated with AOM/DSS cycle 3,10,NA,NA,16S,3,Illumina,log transformation,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 2,Table S4,19 November 2024,Wendy640,"Wendy640,KateRasheed,WikiWorks","Differential OTUs after 3 cycles of AOM/DSS treatment, indicating microbial changes at advanced disease stages.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella|s__Moryella indoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|3085636|186803|177971;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171550;1783272|1239|186801|3085636|186803|3570277|116085;3379134|976|200643|171549|171552|838;1783272|1239|186801|3082768|990719;1783272|1239|186801|3085636|186803|437755|371674;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:24828543/6/1,24828543,laboratory experiment,24828543,10.1038/srep04985,http://www.nature.com/scientificreports,"Liang X., Li H., Tian G. , Li S.",Dynamic microbe and molecule networks in a mouse model of colitis-associated colorectal cancer,Scientific reports,2014,NA,Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Control Group,AOM/DSS Cycle 4 group,Mice treated with AOM/DSS cycle 4,10,NA,NA,16S,3,Illumina,log transformation,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 1,Table S4,19 November 2024,Wendy640,"Wendy640,KateRasheed,WikiWorks","Differential OTUs after 4 cycles of AOM/DSS treatment, representing microbiota alterations during late-stage colorectal cancer.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella|s__Moryella indoligenes,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Crocinitomicaceae|g__Wandonia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus garvieae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis",1783272|1239|186801|3085636|186803|140625;3379134|976|200643|171549|2005473;1783272|1239|186801|3085636|186803|437755|371674;3379134|976|117743|200644|1853230|1115103;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|91061|186826|1300|1357|1363;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|33042;3379134|976|200643|171549|171550;3379134|976|200643|171549|815|816|820,Complete,Svetlana up
bsdb:24828543/6/2,24828543,laboratory experiment,24828543,10.1038/srep04985,http://www.nature.com/scientificreports,"Liang X., Li H., Tian G. , Li S.",Dynamic microbe and molecule networks in a mouse model of colitis-associated colorectal cancer,Scientific reports,2014,NA,Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Control Group,AOM/DSS Cycle 4 group,Mice treated with AOM/DSS cycle 4,10,NA,NA,16S,3,Illumina,log transformation,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 2,Table S4,19 November 2024,Wendy640,"Wendy640,KateRasheed,WikiWorks","Differential OTUs after 4 cycles of AOM/DSS treatment, representing microbiota alterations during late-stage colorectal cancer.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella|s__Moryella indoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|s__Enterococcaceae bacterium RF39,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Candidatus Phytoplasma|s__Candidatus Phytoplasma solani,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Candidatus Phytoplasma|s__Candidatus Phytoplasma citri",1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|437755|371674;1783272|1239|186801|3085636|186803|177971;3379134|976|200643|171549|2005473;3379134|976|200643|171549|171550;1783272|1239|186801|3085636|186803|189330;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|216572|253238;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|91061|186826|81852|423410;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|3082768|990719;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|3570277|116085;3379134|976|200643|171549;1783272|1239|186801|3085636|186803|841|301302;3379134|976|200643|171549|171550|28138;3379134|976|200643|171549|1853231|283168;1783272|544448|31969|186329|2146|33926|69896;1783272|544448|31969|186329|2146|33926|180978,Complete,Svetlana up
bsdb:25012901/1/1,25012901,"cross-sectional observational, not case-control",25012901,https://doi.org/10.1038/ismej.2014.114,https://pubmed.ncbi.nlm.nih.gov/25012901/,"Mason M.R., Preshaw P.M., Nagaraja H.N., Dabdoub S.M., Rahman A. , Kumar P.S.",The subgingival microbiome of clinically healthy current and never smokers,The ISME journal,2015,NA,Experiment 1,United States of America,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Smoking behavior,EFO:0004318,Never smokers,Healthy Current Smokers,people who are current smokers,100,100,3 months,16S,123456789,Roche454,relative abundances,T-Test,0.05,FALSE,NA,"age,education level,race,sex,socioeconomic status",NA,NA,increased,NA,NA,NA,NA,Signature 1,Text,14 March 2023,Kelvin Joseph,"Kelvin Joseph,Claregrieve1,WikiWorks",The relative abundance of selected species in current smokers and nonsmokers.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter guillouiae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter haemolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter johnsonii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter schindleri,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera geminata,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus|s__Desulfobulbus sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium naviforme,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sueciensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Ectopseudomonas|s__Ectopseudomonas oleovorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter|s__Pseudoramibacter alactolyticus",3379134|1224|1236|2887326|468|469|470;3379134|1224|1236|2887326|468|469|106649;3379134|1224|1236|2887326|468|469|29430;3379134|1224|1236|2887326|468|469|40214;3379134|1224|1236|2887326|468|469|108981;1783272|1239|909932|1843489|31977|906|156456;3379134|200940|3031451|3024411|213121|893|895;1783272|1239|909932|1843489|31977|39948|309120;1783272|1239|186801|3082720|3118655|44259|143361;3384189|32066|203490|203491|203492|848|77917;3384189|32066|203490|203491|203492|848|851;1783272|1239|909932|1843489|31977|906|907;1783272|1239|909932|1843489|31977|906|187326;1783272|1239|909932|1843489|31977|906|349094;3379134|1224|1236|72274|135621|3236654|330;1783272|1239|186801|186802|186806|113286|113287,Complete,Claregrieve1
bsdb:25012901/1/2,25012901,"cross-sectional observational, not case-control",25012901,https://doi.org/10.1038/ismej.2014.114,https://pubmed.ncbi.nlm.nih.gov/25012901/,"Mason M.R., Preshaw P.M., Nagaraja H.N., Dabdoub S.M., Rahman A. , Kumar P.S.",The subgingival microbiome of clinically healthy current and never smokers,The ISME journal,2015,NA,Experiment 1,United States of America,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Smoking behavior,EFO:0004318,Never smokers,Healthy Current Smokers,people who are current smokers,100,100,3 months,16S,123456789,Roche454,relative abundances,T-Test,0.05,FALSE,NA,"age,education level,race,sex,socioeconomic status",NA,NA,increased,NA,NA,NA,NA,Signature 2,Text,14 March 2023,Kelvin Joseph,"Kelvin Joseph,Claregrieve1,WikiWorks",The relative abundance of selected species in current smokers and nonsmokers.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces israelii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces viscosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces dentalis",1783272|201174|1760|2037|2049|1654|1659;1783272|201174|1760|2037|2049|1654|1656;1783272|1239|91061|186826|186828|117563|46124;1783272|1239|91061|186826|186828|117563|137732;3379134|1224|1236|135625|712|724|729;3379134|1224|28216|206351|481|482|28449;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1305;1783272|201174|1760|2037|2049|1654|272548,Complete,Claregrieve1
bsdb:25023578/1/1,25023578,case-control,25023578,https://doi.org/10.1097/MPG.0000000000000495,NA,"Walia R., Garg S., Song Y., Girotra M., Cuffari C., Fricke W.F. , Dutta S.K.",Efficacy of fecal microbiota transplantation in 2 children with recurrent Clostridium difficile infection and its impact on their growth and gut microbiome,Journal of pediatric gastroenterology and nutrition,2014,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Clostridium difficile infection,EFO:0009130,NA,Children with recurrent Clostridium difficile Infection,Efficacy of Fecal Microbiota Transplantation on Children with Recurrent Clostridium difficile Infection.,NA,2,NA,16S,NA,Illumina,relative abundances,NA,NA,NA,NA,NA,"age,antibiotic exposure,cesarean section,premature birth",NA,increased,NA,NA,NA,NA,Signature 1,Figure 2b,5 March 2024,Victoria,"Victoria,WikiWorks",Histograms showing relative abundances of microbiota members at the taxonomic phylum level.,increased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,NA
bsdb:25023578/1/2,25023578,case-control,25023578,https://doi.org/10.1097/MPG.0000000000000495,NA,"Walia R., Garg S., Song Y., Girotra M., Cuffari C., Fricke W.F. , Dutta S.K.",Efficacy of fecal microbiota transplantation in 2 children with recurrent Clostridium difficile infection and its impact on their growth and gut microbiome,Journal of pediatric gastroenterology and nutrition,2014,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Clostridium difficile infection,EFO:0009130,NA,Children with recurrent Clostridium difficile Infection,Efficacy of Fecal Microbiota Transplantation on Children with Recurrent Clostridium difficile Infection.,NA,2,NA,16S,NA,Illumina,relative abundances,NA,NA,NA,NA,NA,"age,antibiotic exposure,cesarean section,premature birth",NA,increased,NA,NA,NA,NA,Signature 2,Figure 2b,5 March 2024,Victoria,"Victoria,WikiWorks",Histograms showing relative abundances of microbiota members at the taxonomic phylum level.,decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Actinomycetota",1783272|1239;3379134|1224;3379134|74201;1783272|201174,Complete,NA
bsdb:25038099/1/1,25038099,laboratory experiment,25038099,10.1128/AEM.01357-14,NA,"Lee H. , Ko G.",Effect of metformin on metabolic improvement and gut microbiota,Applied and environmental microbiology,2014,NA,Experiment 1,South Korea,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,High-Fat-Diet to Normal Diet group (HFD-ND) and High-Fat-Diet + Metformin group (HFD-Met),High-Fat-Diet group (HFD),Group of mice receiving HFD without metformin treatment (HFD group).,NA,NA,NA,16S,123,Roche454,relative abundances,LEfSe,0.05,FALSE,4,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4E,13 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Microbial difference in the bacterial community between groups categorized according to diet and metformin treatment.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira|s__Oscillospira guilliermondii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|186807|51514;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572|119852|119853;1783272|1239|186801|186802|186807;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:25038099/2/1,25038099,laboratory experiment,25038099,10.1128/AEM.01357-14,NA,"Lee H. , Ko G.",Effect of metformin on metabolic improvement and gut microbiota,Applied and environmental microbiology,2014,NA,Experiment 2,South Korea,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,High-Fat-Diet group (HFD) and High-Fat-Diet + Metformin group (HFD-Met),High-Fat-Diet to Normal Diet group (HFD-ND),Group of mice that received a dietary change from a High-Fat-Diet to Normal Diet group (HFD-ND).,NA,NA,NA,16S,123,Roche454,relative abundances,LEfSe,0.05,FALSE,4,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4E,13 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Microbial difference in the bacterial community between groups categorized according to diet and metformin treatment.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia cocleata,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|815;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3082720|543314;1783272|1239|526524|526525|2810280|3025755|69824;3379134|74201|203494|48461|203557;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:25038099/3/1,25038099,laboratory experiment,25038099,10.1128/AEM.01357-14,NA,"Lee H. , Ko G.",Effect of metformin on metabolic improvement and gut microbiota,Applied and environmental microbiology,2014,NA,Experiment 3,South Korea,Mus musculus,Feces,UBERON:0001988,Response to metformin,GO:1901558,High-Fat-Diet to Normal Diet group (HFD-ND) and High-Fat-Diet group (HFD),High-Fat-Diet + Metformin group (HFD-Met),"Group of mice that had Metformin (300 mg/kg of body weight 1,1-dimethylbiguanide hydrochloride; Sigma-Aldrich) administered every day during the HFD for 10 weeks (HFD-Met group).",NA,NA,NA,16S,123,Roche454,relative abundances,LEfSe,0.05,FALSE,4,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4E,13 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Microbial difference in the bacterial community between groups categorized according to diet and metformin treatment.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550,Complete,Svetlana up
bsdb:25038099/4/1,25038099,laboratory experiment,25038099,10.1128/AEM.01357-14,NA,"Lee H. , Ko G.",Effect of metformin on metabolic improvement and gut microbiota,Applied and environmental microbiology,2014,NA,Experiment 4,South Korea,Mus musculus,Feces,UBERON:0001988,Response to metformin,GO:1901558,Normal Diet group (ND),Normal Diet + Met group(ND-Met),Group of mice receiving Normal Diet (ND) with metformin treatment (ND-Met).,NA,NA,NA,16S,123,Roche454,relative abundances,LEfSe,0.05,FALSE,4,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4F,13 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Microbial difference in the bacterial community between groups categorized according to diet and metformin treatment.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|216572;3379134|74201|203494|48461|203557;3379134|74201|203494|48461|1647988|239934|239935;3379134|74201|203494|48461|1647988|239934,Complete,Svetlana up
bsdb:25038099/4/2,25038099,laboratory experiment,25038099,10.1128/AEM.01357-14,NA,"Lee H. , Ko G.",Effect of metformin on metabolic improvement and gut microbiota,Applied and environmental microbiology,2014,NA,Experiment 4,South Korea,Mus musculus,Feces,UBERON:0001988,Response to metformin,GO:1901558,Normal Diet group (ND),Normal Diet + Met group(ND-Met),Group of mice receiving Normal Diet (ND) with metformin treatment (ND-Met).,NA,NA,NA,16S,123,Roche454,relative abundances,LEfSe,0.05,FALSE,4,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4F,13 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Microbial difference in the bacterial community between groups categorized according to diet and metformin treatment.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",1783272|1239|91061|186826|33958|1578|147802;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958,Complete,Svetlana up
bsdb:25038099/5/1,25038099,laboratory experiment,25038099,10.1128/AEM.01357-14,NA,"Lee H. , Ko G.",Effect of metformin on metabolic improvement and gut microbiota,Applied and environmental microbiology,2014,NA,Experiment 5,South Korea,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Male mice,Female mice,Group of female mice on High-Fat-Diet (HFD).,NA,NA,NA,16S,123,Roche454,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,13 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Differences in the gut microbiota between male and female mice in the HFD group.,increased,",k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae",;3379134|976|200643|171549|815|816;3379134|976;3379134|976|200643|171549|815,Complete,Svetlana up
bsdb:25038099/5/2,25038099,laboratory experiment,25038099,10.1128/AEM.01357-14,NA,"Lee H. , Ko G.",Effect of metformin on metabolic improvement and gut microbiota,Applied and environmental microbiology,2014,NA,Experiment 5,South Korea,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Male mice,Female mice,Group of female mice on High-Fat-Diet (HFD).,NA,NA,NA,16S,123,Roche454,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5A,13 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Differences in the gut microbiota between male and female mice in the HFD group.,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,s__unidentified",1783272|1239|526524|526525|128827|174708;1783272|1239|91061;1783272|1239;1783272|1239|186801|186802|186807|51514;1783272|1239|526524|526525|128827;1783272|1239|526524;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|147802;1783272|544448;1783272|1239|186801|186802|216572|119852;1783272|1239|186801;1783272|1239|526524|526525|128827;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958|1578;32644,Complete,Svetlana up
bsdb:25038099/6/1,25038099,laboratory experiment,25038099,10.1128/AEM.01357-14,NA,"Lee H. , Ko G.",Effect of metformin on metabolic improvement and gut microbiota,Applied and environmental microbiology,2014,NA,Experiment 6,South Korea,Mus musculus,Feces,UBERON:0001988,Response to metformin,GO:1901558,Male mice,Female mice,"Group of female mice that were administered Metformin (300 mg/kg of body weight 1,1-dimethylbiguanide hydrochloride; Sigma-Aldrich) every day during the HFD for 10 weeks (HFD-Met group).",NA,NA,NA,16S,123,Roche454,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5B,13 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Differences in the gut microbiota between male and female mice in the HFD-Met group.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii",3379134|976|200643;1783272|1239|91061|186826|33958;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|216572|946234|292800,Complete,Svetlana up
bsdb:25038099/6/2,25038099,laboratory experiment,25038099,10.1128/AEM.01357-14,NA,"Lee H. , Ko G.",Effect of metformin on metabolic improvement and gut microbiota,Applied and environmental microbiology,2014,NA,Experiment 6,South Korea,Mus musculus,Feces,UBERON:0001988,Response to metformin,GO:1901558,Male mice,Female mice,"Group of female mice that were administered Metformin (300 mg/kg of body weight 1,1-dimethylbiguanide hydrochloride; Sigma-Aldrich) every day during the HFD for 10 weeks (HFD-Met group).",NA,NA,NA,16S,123,Roche454,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5B,13 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Differences in the gut microbiota between male and female mice in the HFD-Met group.,decreased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,1783272|1239|526524|526525|2810280|100883,Complete,Svetlana up
bsdb:25038099/7/1,25038099,laboratory experiment,25038099,10.1128/AEM.01357-14,NA,"Lee H. , Ko G.",Effect of metformin on metabolic improvement and gut microbiota,Applied and environmental microbiology,2014,NA,Experiment 7,South Korea,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Male mice,Female mice,Group of female mice that received a dietary change from a High-Fat-Diet to Normal Diet group (HFD-ND).,NA,NA,NA,16S,123,Roche454,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5C,13 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Differences in the gut microbiota between male and female mice in the HFD-ND group.,decreased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Mycoplasmatota",1783272|544448|31969;1783272|544448,Complete,Svetlana up
bsdb:25038099/8/1,25038099,laboratory experiment,25038099,10.1128/AEM.01357-14,NA,"Lee H. , Ko G.",Effect of metformin on metabolic improvement and gut microbiota,Applied and environmental microbiology,2014,NA,Experiment 8,South Korea,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Male mice,Female mice,Group of female mice receiving Normal Diet (ND).,NA,NA,NA,16S,123,Roche454,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5D,13 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Differences in the gut microbiota between male and female mice in the ND group.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",1783272|1239|526524|526525|128827;3379134|976|200643|171549|171551;3379134|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:25052961/1/1,25052961,prospective cohort,25052961,10.1111/hel.12145,NA,"Eun C.S., Kim B.K., Han D.S., Kim S.Y., Kim K.M., Choi B.Y., Song K.S., Kim Y.S. , Kim J.F.","Differences in gastric mucosal microbiota profiling in patients with chronic gastritis, intestinal metaplasia, and gastric cancer using pyrosequencing methods",Helicobacter,2014,"16S ribosomal RNA, H. pylori, carcinogenesis, gastric cancer",Experiment 1,South Korea,Homo sapiens,Mucosa of stomach,UBERON:0001199,Gastric cancer,MONDO:0001056,chronic gastritis and intestinal metaplasia,gastric cancer,noncardia gastric cancer patients whose diagnosis were confirmed by histopathology,20,11,6 months,16S,5,Roche454,NA,NA,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Supplemental Fig S1, S2",10 January 2021,Fatima Zohra,WikiWorks,"Relative bacterial abundance of gastric mucosa at the class and family level in Helicobacter-dominant patients with chronic gastritis, intestinal metplasia and gastric cancer",increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",1783272|1239|91061;1783272|1239|91061|186826|1300,Complete,Folakunmi
bsdb:25052961/1/2,25052961,prospective cohort,25052961,10.1111/hel.12145,NA,"Eun C.S., Kim B.K., Han D.S., Kim S.Y., Kim K.M., Choi B.Y., Song K.S., Kim Y.S. , Kim J.F.","Differences in gastric mucosal microbiota profiling in patients with chronic gastritis, intestinal metaplasia, and gastric cancer using pyrosequencing methods",Helicobacter,2014,"16S ribosomal RNA, H. pylori, carcinogenesis, gastric cancer",Experiment 1,South Korea,Homo sapiens,Mucosa of stomach,UBERON:0001199,Gastric cancer,MONDO:0001056,chronic gastritis and intestinal metaplasia,gastric cancer,noncardia gastric cancer patients whose diagnosis were confirmed by histopathology,20,11,6 months,16S,5,Roche454,NA,NA,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Supplemental Fig S1, S2",10 January 2021,Fatima Zohra,"WikiWorks,Folakunmi","Relative bacterial abundance of gastric mucosa at the class and family level in Helicobacter-dominant patients with chronic gastritis, intestinal metplasia and gastric cancer",decreased,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,3379134|29547|3031852|213849|72293,Complete,Folakunmi
bsdb:25052961/2/1,25052961,prospective cohort,25052961,10.1111/hel.12145,NA,"Eun C.S., Kim B.K., Han D.S., Kim S.Y., Kim K.M., Choi B.Y., Song K.S., Kim Y.S. , Kim J.F.","Differences in gastric mucosal microbiota profiling in patients with chronic gastritis, intestinal metaplasia, and gastric cancer using pyrosequencing methods",Helicobacter,2014,"16S ribosomal RNA, H. pylori, carcinogenesis, gastric cancer",Experiment 2,South Korea,Homo sapiens,Mucosa of stomach,UBERON:0001199,Gastric cancer,MONDO:0001056,H. pylori negative chronic gastritis,H. pylori positive chronic gastritis,H. pylori positive chronic gastritis patients who were diagnosed by conventional laboratory method including rapid urease test and histopathology,0,7,6 months,16S,5,Roche454,NA,NA,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplemental Fig S3,10 January 2021,Fatima Zohra,WikiWorks,Comparison of the gastric microbial profiles between H. pylori positive and H. pylori negative chronic gastritis patients,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae",3379134|1224|28211|356|41294;3379134|1224|28211|204458|76892;1783272|1239|91061|186826|33958;3379134|1224|28216|80840|119060,Complete,Folakunmi
bsdb:25057045/1/1,25057045,case-control,25057045,10.1093/infdis/jiu409,NA,"Dinh D.M., Volpe G.E., Duffalo C., Bhalchandra S., Tai A.K., Kane A.V., Wanke C.A. , Ward H.D.","Intestinal microbiota, microbial translocation, and systemic inflammation in chronic HIV infection",The Journal of infectious diseases,2015,"HIV, dysbiosis, inflammation, microbial translocation, microbiota",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,HIV-uninfected controls,Chronic HIV-infected cases,Patients with HIV infection receiving suppressive ART and had an undetectable plasma HIV RNA levels,16,21,1 month,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3A-B,14 October 2024,Agatha,"Agatha,KateRasheed,WikiWorks",Differential abundance of microbiota between cases and controls using LEfSe.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota",3379134|976|200643|171549|2005519|397864;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;3379134|1224|1236;3379134|1224,Complete,Svetlana up
bsdb:25057045/1/4,25057045,case-control,25057045,10.1093/infdis/jiu409,NA,"Dinh D.M., Volpe G.E., Duffalo C., Bhalchandra S., Tai A.K., Kane A.V., Wanke C.A. , Ward H.D.","Intestinal microbiota, microbial translocation, and systemic inflammation in chronic HIV infection",The Journal of infectious diseases,2015,"HIV, dysbiosis, inflammation, microbial translocation, microbiota",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,HIV-uninfected controls,Chronic HIV-infected cases,Patients with HIV infection receiving suppressive ART and had an undetectable plasma HIV RNA levels,16,21,1 month,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 4,Figure 3A-B,22 October 2024,Agatha,"Agatha,KateRasheed,WikiWorks",Differential abundance of microbiota between cases and controls using LEfSe.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550,Complete,Svetlana up
bsdb:25057045/2/1,25057045,case-control,25057045,10.1093/infdis/jiu409,NA,"Dinh D.M., Volpe G.E., Duffalo C., Bhalchandra S., Tai A.K., Kane A.V., Wanke C.A. , Ward H.D.","Intestinal microbiota, microbial translocation, and systemic inflammation in chronic HIV infection",The Journal of infectious diseases,2015,"HIV, dysbiosis, inflammation, microbial translocation, microbiota",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,HIV-uninfected controls,Chronic HIV-infected cases,Patients with HIV infection receiving suppressive ART and had an undetectable plasma HIV RNA levels,16,21,1 month,16S,345,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3C,25 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of microbiota between cases and controls using Mann-Whitney.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550,Complete,Svetlana up
bsdb:25057045/2/2,25057045,case-control,25057045,10.1093/infdis/jiu409,NA,"Dinh D.M., Volpe G.E., Duffalo C., Bhalchandra S., Tai A.K., Kane A.V., Wanke C.A. , Ward H.D.","Intestinal microbiota, microbial translocation, and systemic inflammation in chronic HIV infection",The Journal of infectious diseases,2015,"HIV, dysbiosis, inflammation, microbial translocation, microbiota",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,HIV-uninfected controls,Chronic HIV-infected cases,Patients with HIV infection receiving suppressive ART and had an undetectable plasma HIV RNA levels,16,21,1 month,16S,345,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3C,26 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of microbiota between cases and controls using Mann-Whitney.,increased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella",3379134|1224;3379134|1224|1236;3379134|1224|1236|91347|543;1783272|1239|526524;1783272|1239|526524|526525;3379134|1224|1236|91347;1783272|1239|526524|526525|128827;3379134|976|200643|171549|2005519|397864,Complete,Svetlana up
bsdb:25058515/1/1,25058515,time series / longitudinal observational,25058515,10.1371/journal.ppat.1004262,https://pubmed.ncbi.nlm.nih.gov/25058515/,"Liu C.M., Osborne B.J., Hungate B.A., Shahabi K., Huibner S., Lester R., Dwan M.G., Kovacs C., Contente-Cuomo T.L., Benko E., Aziz M., Price L.B. , Kaul R.",The semen microbiome and its relationship with local immunology and viral load in HIV infection,PLoS pathogens,2014,NA,Experiment 1,Canada,Homo sapiens,Semen,UBERON:0001968,HIV infection,EFO:0000764,HIV-uninfected men,HIV-infected men,MSM with HIV infection,22,27,6 months,16S,3456,Roche454,relative abundances,ANOVA,0.05,FALSE,NA,age,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Table S2,11 January 2022,Joyessa,"Joyessa,Claregrieve1,WikiWorks",Differential microbial abundance between HIV- and HIV+ men,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Pseudonocardia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leifsonia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Friedmanniella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Nakamurellales|f__Nakamurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Nostocoides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Rhodoferax",1783272|201174|1760|85004|31953|1678;3379134|1224|28211|356|212791;1783272|201174|1760|85010|2070|1847;1783272|201174|1760|1643682|85030;1783272|201174|1760|85008|28056;3379134|1224|28216|80840|75682|149698;3379134|1224|1236|91347|1903409|551;1783272|201174|1760|85006|85023|110932;3379134|1224|28216|80840|80864|12916;1783272|201174|1760|85009|85015|53387;1783272|201174|1760|1643684|85031;3379134|1224|1236|2887326|468|469;1783272|1239|91061|1385|186817|1386;1783272|201174|1760|2037;3379134|976;3379134|1224|28216|80840;3379134|1224|28216|80840|80864|34072;3379134|1224|28211|204455;1783272|201174|1760|85006|85021|99479;1783272|1239|186801|186802|541000;3379134|976|768503|768507|1853232|89966;3379134|1224|28216|80840|80864|28065,Complete,Claregrieve1
bsdb:25058515/1/2,25058515,time series / longitudinal observational,25058515,10.1371/journal.ppat.1004262,https://pubmed.ncbi.nlm.nih.gov/25058515/,"Liu C.M., Osborne B.J., Hungate B.A., Shahabi K., Huibner S., Lester R., Dwan M.G., Kovacs C., Contente-Cuomo T.L., Benko E., Aziz M., Price L.B. , Kaul R.",The semen microbiome and its relationship with local immunology and viral load in HIV infection,PLoS pathogens,2014,NA,Experiment 1,Canada,Homo sapiens,Semen,UBERON:0001968,HIV infection,EFO:0000764,HIV-uninfected men,HIV-infected men,MSM with HIV infection,22,27,6 months,16S,3456,Roche454,relative abundances,ANOVA,0.05,FALSE,NA,age,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Table S2,11 January 2022,Joyessa,"Joyessa,Claregrieve1,WikiWorks",Differential microbial abundance between HIV- and HIV+ men,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Actinomycetospora",1783272|1239|909932|1843489|31977|29465;1783272|201174|1760|85010|2070|402649,Complete,Claregrieve1
bsdb:25073603/1/1,25073603,case-control,25073603,doi:10.1152/physiolgenomics.00082.2014,NA,"Zhu L., Liu W., Alkhouri R., Baker R.D., Bard J.E., Quigley E.M. , Baker S.S.",Structural changes in the gut microbiome of constipated patients,Physiological genomics,2014,"Prevotella, butyrate, constipation, microbiota",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,Control,Constipation,Patients diagnosed with constipation based on clinical guidelines,14,8,3 months,16S,45,Roche454,relative abundances,"Mann-Whitney (Wilcoxon),T-Test",0.05,FALSE,NA,NA,NA,NA,NA,increased,NA,NA,NA,Signature 1,"Table 2, Table 3, Figure 3, Figure 4, Figure 5",19 March 2025,Anne-mariesharp,Anne-mariesharp,"Abundant taxa in the gut microbiome of the
constipated patients and controls",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|186802|216572|244127;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:25073603/1/2,25073603,case-control,25073603,doi:10.1152/physiolgenomics.00082.2014,NA,"Zhu L., Liu W., Alkhouri R., Baker R.D., Bard J.E., Quigley E.M. , Baker S.S.",Structural changes in the gut microbiome of constipated patients,Physiological genomics,2014,"Prevotella, butyrate, constipation, microbiota",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,Control,Constipation,Patients diagnosed with constipation based on clinical guidelines,14,8,3 months,16S,45,Roche454,relative abundances,"Mann-Whitney (Wilcoxon),T-Test",0.05,FALSE,NA,NA,NA,NA,NA,increased,NA,NA,NA,Signature 2,"Table 2, Table 3, Figure 3, Figure 4, Figure 5",19 March 2025,Anne-mariesharp,Anne-mariesharp,"Abundant taxa in the gut microbiome of the
constipated patients and controls",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota",3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|976,Complete,Svetlana up
bsdb:25104642/1/1,25104642,case-control,25104642,10.1158/1940-6207.CAPR-14-0129,NA,"Zackular J.P., Rogers M.A., Ruffin M.T. , Schloss P.D.",The human gut microbiome as a screening tool for colorectal cancer,"Cancer prevention research (Philadelphia, Pa.)",2014,NA,Experiment 1,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Controls,carcinoma,Patients with colonic adenocarcinoma,30,30,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Figure 2 and text,10 January 2021,Lora Kasselman,"WikiWorks,Peace Sandy",LeFSe analysis for healthy vs. carcinoma clinical groups. LDA values are represented for OTUs enriched in healthy and carcinoma clinical groups.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",3379134|1224|1236|91347|543;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171551|836;1783272|1239|186801|186802|31979|1485;3379134|976|200643|171549|171551,Complete,Peace Sandy
bsdb:25104642/1/2,25104642,case-control,25104642,10.1158/1940-6207.CAPR-14-0129,NA,"Zackular J.P., Rogers M.A., Ruffin M.T. , Schloss P.D.",The human gut microbiome as a screening tool for colorectal cancer,"Cancer prevention research (Philadelphia, Pa.)",2014,NA,Experiment 1,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Controls,carcinoma,Patients with colonic adenocarcinoma,30,30,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Figure 2 and text,10 January 2021,Lora Kasselman,"WikiWorks,Peace Sandy",LeFSe analysis for healthy vs. carcinoma clinical groups. LDA values are represented for OTUs enriched in healthy and carcinoma clinical groups.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",3379134|976|200643|171549|815|816;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|91061|1385|90964|1279;1783272|1239|186801|186802|31979|1485,Complete,Peace Sandy
bsdb:25104642/2/1,25104642,case-control,25104642,10.1158/1940-6207.CAPR-14-0129,NA,"Zackular J.P., Rogers M.A., Ruffin M.T. , Schloss P.D.",The human gut microbiome as a screening tool for colorectal cancer,"Cancer prevention research (Philadelphia, Pa.)",2014,NA,Experiment 2,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Controls,Adenoma,Patients with colonic adenoma,30,30,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Figure 1,19 January 2024,Peace Sandy,"Peace Sandy,WikiWorks",LeFSe analysis for healthy vs. adenoma clinical groups. LDA values are represented for OTUs enriched in healthy and adenoma clinical groups.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",1783272|1239|186801|186802|31979|1485;3379134|976|200643|171549|171551;3379134|1224|1236|72274|135621|286,Complete,Peace Sandy
bsdb:25104642/2/2,25104642,case-control,25104642,10.1158/1940-6207.CAPR-14-0129,NA,"Zackular J.P., Rogers M.A., Ruffin M.T. , Schloss P.D.",The human gut microbiome as a screening tool for colorectal cancer,"Cancer prevention research (Philadelphia, Pa.)",2014,NA,Experiment 2,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Controls,Adenoma,Patients with colonic adenoma,30,30,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Figure 1,19 January 2024,Peace Sandy,"Peace Sandy,WikiWorks",LeFSe analysis for healthy vs. adenoma clinical groups. LDA values are represented for OTUs enriched in healthy and adenoma clinical groups.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|1853231|283168,Complete,Peace Sandy
bsdb:25104642/3/1,25104642,case-control,25104642,10.1158/1940-6207.CAPR-14-0129,NA,"Zackular J.P., Rogers M.A., Ruffin M.T. , Schloss P.D.",The human gut microbiome as a screening tool for colorectal cancer,"Cancer prevention research (Philadelphia, Pa.)",2014,NA,Experiment 3,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Controls,Colonic lesions,Combination of the clinical and microbiome data from adenoma and carcinoma subjects to create a combined colonic lesion group.,30,60,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Figure 3,19 January 2024,Peace Sandy,"Peace Sandy,WikiWorks",LeFSe analysis for healthy vs. colonic lesion clinical groups.  Adenoma and carcinoma clinical groups were combined into one clinical group (colonic lesion clinical group).  LDA values are represented for OTUs enriched in healthy and combined colonic lesions clinical groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",3379134|976|200643|171549|171551;3379134|1224|1236|72274|135621|286,Complete,Peace Sandy
bsdb:25104642/3/2,25104642,case-control,25104642,10.1158/1940-6207.CAPR-14-0129,NA,"Zackular J.P., Rogers M.A., Ruffin M.T. , Schloss P.D.",The human gut microbiome as a screening tool for colorectal cancer,"Cancer prevention research (Philadelphia, Pa.)",2014,NA,Experiment 3,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Controls,Colonic lesions,Combination of the clinical and microbiome data from adenoma and carcinoma subjects to create a combined colonic lesion group.,30,60,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Figure 3.,19 January 2024,Peace Sandy,"Peace Sandy,WikiWorks",LeFSe analysis for healthy vs. colonic lesion clinical groups. Adenoma and carcinoma clinical groups were combined into one clinical group (colonic lesion clinical group). LDA values are represented for OTUs enriched in healthy and combined colonic lesions clinical groups.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|31979|1485,Complete,Peace Sandy
bsdb:25104642/4/1,25104642,case-control,25104642,10.1158/1940-6207.CAPR-14-0129,NA,"Zackular J.P., Rogers M.A., Ruffin M.T. , Schloss P.D.",The human gut microbiome as a screening tool for colorectal cancer,"Cancer prevention research (Philadelphia, Pa.)",2014,NA,Experiment 4,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Adenoma,Carcinoma,Patients with colonic adenocarcinoma,30,30,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Figure 4.,19 January 2024,Peace Sandy,"Peace Sandy,WikiWorks",LeFSe analysis for adenoma vs. carcinoma clinical groups. LDA values are represented for OTUs enriched in adenoma and carcinoma clinical groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979|1485;3384189|32066|203490|203491|203492|848;3379134|1224|28216|80840|995019|577310;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171551|836,Complete,Peace Sandy
bsdb:25104642/4/2,25104642,case-control,25104642,10.1158/1940-6207.CAPR-14-0129,NA,"Zackular J.P., Rogers M.A., Ruffin M.T. , Schloss P.D.",The human gut microbiome as a screening tool for colorectal cancer,"Cancer prevention research (Philadelphia, Pa.)",2014,NA,Experiment 4,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Adenoma,Carcinoma,Patients with colonic adenocarcinoma,30,30,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Figure 4,19 January 2024,Peace Sandy,"Peace Sandy,WikiWorks",LeFSe analysis for adenoma vs. carcinoma clinical groups. LDA values are represented for OTUs enriched in adenoma and carcinoma clinical groups.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|31979|1485,Complete,Peace Sandy
bsdb:25202708/1/1,25202708,case-control,25202708,10.1155/2014/906168,https://pmc.ncbi.nlm.nih.gov/articles/PMC4150407/,"Chiu C.M., Huang W.C., Weng S.L., Tseng H.C., Liang C., Wang W.C., Yang T., Yang T.L., Weng C.T., Chang T.H. , Huang H.D.",Systematic analysis of the association between gut flora and obesity through high-throughput sequencing and bioinformatics approaches,BioMed research international,2014,NA,Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Normal (N-like group),Case (OB-like group),Participants with a Body Mass Index ≥ 27,45,36,NA,16S,4,Illumina,relative abundances,"ANOVA,Kolmogorov-Smirnov Test",0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Table 2,8 May 2025,Shulamite,"Shulamite,Anne-mariesharp",Genera with significantly different proportions between normal and case samples.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella",3379134|1224|1236|2887326|468|469;3379134|1224|1236|135619|28256|2745;1783272|1239|186801|3085636|186803|28050;1783272|1239|909932|909929|1843491|158846;3379134|1224|1236|135622|267890|22,Complete,KateRasheed
bsdb:25202708/1/2,25202708,case-control,25202708,10.1155/2014/906168,https://pmc.ncbi.nlm.nih.gov/articles/PMC4150407/,"Chiu C.M., Huang W.C., Weng S.L., Tseng H.C., Liang C., Wang W.C., Yang T., Yang T.L., Weng C.T., Chang T.H. , Huang H.D.",Systematic analysis of the association between gut flora and obesity through high-throughput sequencing and bioinformatics approaches,BioMed research international,2014,NA,Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Normal (N-like group),Case (OB-like group),Participants with a Body Mass Index ≥ 27,45,36,NA,16S,4,Illumina,relative abundances,"ANOVA,Kolmogorov-Smirnov Test",0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Table 2,8 May 2025,Shulamite,"Shulamite,Anne-mariesharp",Genera with significantly different proportions between normal and case samples.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Tatumella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Leclercia",3379134|1224|1236|91347|1903409|551;3379134|1224|1236|91347|1903414|581;3379134|1224|1236|91347|1903411|613;3379134|1224|1236|91347|1903409|82986;1783272|201174|84998|84999|84107|102106;3379134|976|200643|171549|2005519|397864;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|459786;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543|413496;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|83654,Complete,KateRasheed
bsdb:25202708/2/1,25202708,case-control,25202708,10.1155/2014/906168,https://pmc.ncbi.nlm.nih.gov/articles/PMC4150407/,"Chiu C.M., Huang W.C., Weng S.L., Tseng H.C., Liang C., Wang W.C., Yang T., Yang T.L., Weng C.T., Chang T.H. , Huang H.D.",Systematic analysis of the association between gut flora and obesity through high-throughput sequencing and bioinformatics approaches,BioMed research international,2014,NA,Experiment 2,Taiwan,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Normal (N-like group),Case (OB-like group),Participants with a Body Mass Index ≥ 27,45,36,NA,16S,4,Illumina,relative abundances,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Table 3 and S2,8 May 2025,Shulamite,"Shulamite,Anne-mariesharp",Genera & species with a significantly different presence between normal and case samples,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Aliivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Aliivibrio|s__Aliivibrio fischeri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Apilactobacillus|s__Apilactobacillus kunkeei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae|g__Marinomonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae|g__Pseudoalteromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella|s__Shewanella algae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae|g__Marinomonas|s__Marinomonas posidonica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae|g__Pseudoalteromonas|s__Pseudoalteromonas piscicida",3379134|1224|1236|2887326|468|469;3379134|1224|1236|135623|641|511678;3379134|1224|1236|135623|641|511678|668;1783272|1239|91061|186826|33958|2767877|148814;3379134|1224|1236|135619|135620|28253;3379134|976|200643|171549|2005525|375288|823;3379134|1224|1236|135622|267888|53246;3379134|1224|1236|135622|267890|22;3379134|1224|1236|135622|267890|22|38313;3379134|1224|1236|135619|135620|28253|936476;3379134|1224|1236|135622|267888|53246|43662,Complete,KateRasheed
bsdb:25202708/2/2,25202708,case-control,25202708,10.1155/2014/906168,https://pmc.ncbi.nlm.nih.gov/articles/PMC4150407/,"Chiu C.M., Huang W.C., Weng S.L., Tseng H.C., Liang C., Wang W.C., Yang T., Yang T.L., Weng C.T., Chang T.H. , Huang H.D.",Systematic analysis of the association between gut flora and obesity through high-throughput sequencing and bioinformatics approaches,BioMed research international,2014,NA,Experiment 2,Taiwan,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Normal (N-like group),Case (OB-like group),Participants with a Body Mass Index ≥ 27,45,36,NA,16S,4,Illumina,relative abundances,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Table 3 and S2,8 May 2025,Shulamite,"Shulamite,Anne-mariesharp",Genera & species with a significantly different presence between normal and case samples,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum desmolans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter amalonaticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. Clone-17,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter|s__Cronobacter sakazakii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium|s__Lachnobacterium bovis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Leclercia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Leclercia|s__Leclercia adecarboxylata,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Pectinatus|s__Pectinatus cerevisiiphilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rahnella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rahnella|s__Rahnella sp. EMA-83,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus albus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. ID1,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia proteamaculans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia sp. DAP4,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia sp. M1,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Tatumella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Tatumella|s__Tatumella sp. L3-179,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__uncultured Lachnospira sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__uncultured Serratia sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__uncultured Shigella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Pectinatus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus|s__Syntrophococcus sucromutans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas testosteroni,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio sp. enrichment culture clone Jdgsrb011,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp. I91-10,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia|s__Erwinia rhapontici",1783272|1239|186801|186802|3085642|2048137|39484;3379134|976|200643|171549|171550|239759|328814;1783272|1239|186801|3085636|186803|572511|33035;3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543|544|35703;1783272|1239|186801|186802|31979|1485|1003366;3379134|1224|1236|91347|543|413496;3379134|1224|1236|91347|543|413496|28141;3379134|1224|1236|91347|543|547|550;3379134|1224|1236|91347|543|547|158836;1783272|1239|186801|3085636|186803|2719313|358742;1783272|1239|186801|3085636|186803|140625|140626;3379134|1224|1236|91347|543|83654;3379134|1224|1236|91347|543|83654|83655;3379134|976|200643|171549|2005525|375288|46503;1783272|1239|909932|909929|1843491|864|86956;3379134|1224|1236|91347|1903411|34037;3379134|1224|1236|91347|1903411|34037|1054200;1783272|1239|186801|186802|216572|1263|1264;1783272|1239|186801|186802|216572|1263|320877;3379134|1224|1236|91347|1903411|613|28151;3379134|1224|1236|91347|1903411|613|490233;3379134|1224|1236|91347|1903411|613|648695;3379134|1224|1236|91347|543|620;3379134|1224|28216|80840|995019|40544|40545;3379134|1224|1236|91347|1903409|82986;3379134|1224|1236|91347|1903409|82986|1166366;1783272|1239|186801|3085636|186803|28050|446043;3379134|1224|1236|91347|1903411|613|239175;3379134|1224|1236|91347|543|620|286134;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|3085636|186803|830;1783272|1239|186801|3085636|186803|140625;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|84036;1783272|1239|909932|909929|1843491|864;3379134|1224|28216|80840|80864|283;3379134|976|200643|171549|1853231|574697|544645;1783272|1239|186801|3085636|186803|84036|84037;3379134|1224|28216|80840|80864|283|285;3379134|200940|3031449|213115|194924|872|675926;3379134|1224|1236|91347|543|544|349544;3379134|1224|1236|91347|1903409|551|55212,Complete,KateRasheed
bsdb:25239901/1/1,25239901,case-control,25239901,10.1128/AEM.02329-14,NA,"Gong H., Shi Y., Zhou X., Wu C., Cao P., Xu C., Hou D., Wang Y. , Zhou L.",Microbiota in the Throat and Risk Factors for Laryngeal Carcinoma,Applied and environmental microbiology,2014,NA,Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,Squamous cell carcinoma,EFO:0000707,controls,laryngeal squamous cell carcinoma (LSCC),histopathological confirmation of Laryngeal squamous cell carcinoma and underwent total laryngectomy,28,27,3 months,16S,12,Roche454,raw counts,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 2, Text, Supplementary Table S2",10 January 2021,Utsav Patel,WikiWorks,Differences in bacterial communities in the throats of LSCC patients and control subjects,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|171552|838;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|43996;1783272|1239|909932|909929|1843491|970;3379134|203691|203692|136|2845253|157;3379134|1224|28216|80840|119060|32008;1783272|1239|186801|3082720|186804,Complete,Rimsha Azhar
bsdb:25239901/1/2,25239901,case-control,25239901,10.1128/AEM.02329-14,NA,"Gong H., Shi Y., Zhou X., Wu C., Cao P., Xu C., Hou D., Wang Y. , Zhou L.",Microbiota in the Throat and Risk Factors for Laryngeal Carcinoma,Applied and environmental microbiology,2014,NA,Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,Squamous cell carcinoma,EFO:0000707,controls,laryngeal squamous cell carcinoma (LSCC),histopathological confirmation of Laryngeal squamous cell carcinoma and underwent total laryngectomy,28,27,3 months,16S,12,Roche454,raw counts,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Table 2, Text, Supplementary Table S2",10 January 2021,Utsav Patel,WikiWorks,Differences in bacterial communities in the throats of LSCC patients and control subjects,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",1783272|1239|91061|186826|1300|1301;1783272|201174|1760|85006|1268|32207,Complete,Rimsha Azhar
bsdb:25239901/2/1,25239901,case-control,25239901,10.1128/AEM.02329-14,NA,"Gong H., Shi Y., Zhou X., Wu C., Cao P., Xu C., Hou D., Wang Y. , Zhou L.",Microbiota in the Throat and Risk Factors for Laryngeal Carcinoma,Applied and environmental microbiology,2014,NA,Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Squamous cell carcinoma,EFO:0000707,Site 2 (site below the epiglottis in the throat),Site 1 (upper portion of throat near the epiglottis),histopathological confirmation of Laryngeal squamous cell carcinoma and underwent total laryngectomy,28,27,3 months,16S,12,Roche454,NA,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 2, Text, Supplementary Table S2",10 January 2021,Utsav Patel,WikiWorks,Differences in bacterial communities in the throats of LSCC patients and control subjects,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,p__Candidatus Saccharimonadota",1783272|1239|909932|1843489|31977|29465;3384189|32066|203490|203491|1129771|32067;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|186826|186828|117563;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3085636|186803|265975;1783272|201174|84998|84999|1643824|1380;1783272|1239|186801|3085636|186803|437755;95818,Complete,Rimsha Azhar
bsdb:25239901/2/2,25239901,case-control,25239901,10.1128/AEM.02329-14,NA,"Gong H., Shi Y., Zhou X., Wu C., Cao P., Xu C., Hou D., Wang Y. , Zhou L.",Microbiota in the Throat and Risk Factors for Laryngeal Carcinoma,Applied and environmental microbiology,2014,NA,Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Squamous cell carcinoma,EFO:0000707,Site 2 (site below the epiglottis in the throat),Site 1 (upper portion of throat near the epiglottis),histopathological confirmation of Laryngeal squamous cell carcinoma and underwent total laryngectomy,28,27,3 months,16S,12,Roche454,NA,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Table 2, Text, Supplementary Table S2",10 January 2021,Utsav Patel,WikiWorks,Differences in bacterial communities in the throats of LSCC patients and control subjects,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|171552|838;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836;1783272|1239|909932|1843489|31977|39948;1783272|544448|31969|2085|2092|2093;1783272|1239|186801|3082720|3118655|44259;1783272|1239|186801|3085636|186803|43996;3379134|1224|28216|206351|481|538;3379134|203691|203692|136|2845253|157;3379134|1224|1236|135625|712|416916;1783272|1239|186801|3082720|186804,Complete,Rimsha Azhar
bsdb:25278091/1/1,25278091,case-control,25278091,https://doi.org/10.1186/s12866-014-0250-2,https://pubmed.ncbi.nlm.nih.gov/25278091/,"Thomas A.M., Gleber-Netto F.O., Fernandes G.R., Amorim M., Barbosa L.F., Francisco A.L., de Andrade A.G., Setubal J.C., Kowalski L.P., Nunes D.N. , Dias-Neto E.",Alcohol and tobacco consumption affects bacterial richness in oral cavity mucosa biofilms,BMC microbiology,2014,NA,Experiment 1,Brazil,Homo sapiens,Mouth mucosa,UBERON:0003729,Smoking behavior,EFO:0004318,Controls (C),Smokers (S),All individuals in this group reported the use of at least 20 cigarettes/day with a regular smoking history of at least 10 years.,9,6,3 months,16S,1,Ion Torrent,relative abundances,Kruskall-Wallis,NA,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,"Supplementary Table 1, Supplementary Table 2, Figure 5",7 June 2023,Atrayees,"Atrayees,Folakunmi,WikiWorks",Relatively abundant phyla and genera found in the groups.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Pseudomonadati|p__Acidobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Armatimonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Atopostipes,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Brachymonas,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae|g__Oceanobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Psychromonadaceae|g__Psychromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Rhodanobacter,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Sulfurovaceae|g__Sulfurovum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Piscirickettsiaceae|g__Thiomicrospira,p__Candidatus Altimarinota,p__Candidatus Saccharimonadota",1783272|1239|91061|186826|186827|46123;3379134|57723;3379134|1224|1236|135625|712|416916;1783272|67819;1783272|1239|91061|186826|186828|292480;1783272|1239;1783272|1239|91061|1385|186817|1386;3379134|976|117743|200644|2762318|59735;3379134|1224|28216|80840|80864|28219;1783272|1117;1783272|1239|186801|186802;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563;3379134|1224|28216|206351|481|32257;1783272|1239|186801|3085636|186803;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|3085636|186803|437755;1783272|544448;3379134|1224|28216|206351|481|482;3379134|1224|1236|135619|135620|196079;1783272|1239|186801|3085636|186803|265975;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|3082720|186804|1257;3379134|1224;3379134|1224|1236|135622|267894|67572;3379134|1224|1236|135614|1775411|75309;1783272|201174|84995|84996|84997|42255;3379134|203691|203692;1783272|1239|91061|1385|90964|1279;3379134|29547|3031852|213849|2771472|265570;3379134|1224|1236|72273|135616|933;363464;95818,Complete,Folakunmi
bsdb:25278091/1/2,25278091,case-control,25278091,https://doi.org/10.1186/s12866-014-0250-2,https://pubmed.ncbi.nlm.nih.gov/25278091/,"Thomas A.M., Gleber-Netto F.O., Fernandes G.R., Amorim M., Barbosa L.F., Francisco A.L., de Andrade A.G., Setubal J.C., Kowalski L.P., Nunes D.N. , Dias-Neto E.",Alcohol and tobacco consumption affects bacterial richness in oral cavity mucosa biofilms,BMC microbiology,2014,NA,Experiment 1,Brazil,Homo sapiens,Mouth mucosa,UBERON:0003729,Smoking behavior,EFO:0004318,Controls (C),Smokers (S),All individuals in this group reported the use of at least 20 cigarettes/day with a regular smoking history of at least 10 years.,9,6,3 months,16S,1,Ion Torrent,relative abundances,Kruskall-Wallis,NA,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,"Supplementary Table 1, Supplementary Table 2, Figure 5",7 June 2023,Atrayees,"Atrayees,Folakunmi,WikiWorks",Relatively abundant phyla and genera found in the groups.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Agreia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Elizabethkingia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Halanaerobiales|f__Halothermotrichaceae|g__Halothermothrix,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leifsonia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Halanaerobiales|f__Halanaerobiaceae|g__Halocella",3379134|1224|28216|80840|506|222;1783272|201174;1783272|201174|1760|85006|85023|110934;3379134|1224|28216|80840|506|507;1783272|201174|1760|2037|2049|28263;1783272|201174|1760|85006|1268|1663;3379134|976|117743|200644|49546|1016;3379134|976|117743|200644|2762318|308865;3384189|32066|203490;3384189|32066|203490|203491|203492|848;1783272|1239|186801|53433|3046412|32636;1783272|201174|1760|85006|85023|110932;1783272|201174|1760|85006|85023|33882;3379134|976|200643|171549|171552|838;3379134|1224|28216|80840|119060|48736;3379134|976|200643|171549|171550;3379134|1224|28211|204457|41297|13687;3379134|1224|1236|135614|32033|40323;3379134|976|200643|171549|2005525|195950;3379134|1224|28216|80840|80864|34072;3379134|976|117747|200666|84566|84567;1783272|1239|186801|53433|972|46466,Complete,Folakunmi
bsdb:25278091/2/1,25278091,case-control,25278091,https://doi.org/10.1186/s12866-014-0250-2,https://pubmed.ncbi.nlm.nih.gov/25278091/,"Thomas A.M., Gleber-Netto F.O., Fernandes G.R., Amorim M., Barbosa L.F., Francisco A.L., de Andrade A.G., Setubal J.C., Kowalski L.P., Nunes D.N. , Dias-Neto E.",Alcohol and tobacco consumption affects bacterial richness in oral cavity mucosa biofilms,BMC microbiology,2014,NA,Experiment 2,Brazil,Homo sapiens,Mouth mucosa,UBERON:0003729,"Alcohol drinking,Smoking behavior","EFO:0004329,EFO:0004318",Controls (C),Smokers/Drinkers (SD),"All individuals in this group reported the use of at least 20 cigarettes/day with a regular smoking history of at least 10 years. These individuals also reported daily drinking habits (>1×/day, >3 drinks/occasion) and a regular drinking history of at least 10 years.",9,7,3 months,16S,1,Ion Torrent,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,"Supplementary Table 1, Supplementary Table 2, Figure 5",7 June 2023,Atrayees,"Atrayees,Folakunmi,WikiWorks",Relatively abundant phyla and genera found in the groups.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium,k__Bacillati|p__Armatimonadota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Brachymonas,k__Bacillati|p__Chloroflexota|c__Chloroflexia,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Halanaerobiales|f__Halanaerobiaceae|g__Halocella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leifsonia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae|g__Oceanobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Psychromonadaceae|g__Psychromonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Rhodanobacter,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Sulfurovaceae|g__Sulfurovum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Piscirickettsiaceae|g__Thiomicrospira,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax,p__Candidatus Altimarinota,p__Candidatus Saccharimonadota",1783272|1239|91061|186826|186827|46123;3379134|1224|1236|135625|712|416916;1783272|201174|1760|2037|2049|28263;1783272|67819;1783272|201174|1760|85006|1268|1663;1783272|1239;1783272|1239|91061|1385|186817|1386;3379134|976|200643;3379134|976|117743|200644|2762318|59735;3379134|1224|28216|80840|80864|28219;1783272|200795|32061;1783272|1117;1783272|1239|186801|186802;3379134|976|117743|200644|49546|237;3384189|32066|203490;3384189|32066|203490|203491|203492|848;1783272|1239|186801|53433|972|46466;3379134|1224|28216|206351|481|32257;1783272|1239|186801|3085636|186803;1783272|201174|1760|85006|85023|110932;1783272|201174|1760|85006|85023|33882;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|3085636|186803|437755;3379134|1224|28216|206351|481|482;3379134|1224|1236|135619|135620|196079;1783272|1239|186801|3085636|186803|265975;3379134|976|117747|200666|84566|84567;1783272|1239|186801|3082720|186804|1257;3379134|1224;3379134|1224|1236|135622|267894|67572;3379134|1224|28216|80840|119060|48736;3379134|1224|1236|135614|1775411|75309;1783272|201174|84995|84996|84997|42255;3379134|1224|28211|204457|41297|13687;1783272|1239|91061|1385|90964|1279;3379134|29547|3031852|213849|2771472|265570;3379134|976|200643|171549|2005525|195950;3379134|1224|1236|72273|135616|933;3379134|1224|28216|80840|80864|34072;363464;95818,Complete,Folakunmi
bsdb:25278091/2/2,25278091,case-control,25278091,https://doi.org/10.1186/s12866-014-0250-2,https://pubmed.ncbi.nlm.nih.gov/25278091/,"Thomas A.M., Gleber-Netto F.O., Fernandes G.R., Amorim M., Barbosa L.F., Francisco A.L., de Andrade A.G., Setubal J.C., Kowalski L.P., Nunes D.N. , Dias-Neto E.",Alcohol and tobacco consumption affects bacterial richness in oral cavity mucosa biofilms,BMC microbiology,2014,NA,Experiment 2,Brazil,Homo sapiens,Mouth mucosa,UBERON:0003729,"Alcohol drinking,Smoking behavior","EFO:0004329,EFO:0004318",Controls (C),Smokers/Drinkers (SD),"All individuals in this group reported the use of at least 20 cigarettes/day with a regular smoking history of at least 10 years. These individuals also reported daily drinking habits (>1×/day, >3 drinks/occasion) and a regular drinking history of at least 10 years.",9,7,3 months,16S,1,Ion Torrent,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,"Supplementary Table 1, Supplementary Table 2, Figure 5",7 June 2023,Atrayees,"Atrayees,Folakunmi,WikiWorks",Relatively abundant phyla and genera found in the groups.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Pseudomonadati|p__Acidobacteriota,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Agreia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Halanaerobiales|f__Halothermotrichaceae|g__Halothermothrix,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae|g__Oceanobacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",3379134|1224|28216|80840|506|222;3379134|57723;1783272|201174;1783272|201174|1760|85006|85023|110934;3379134|1224|28216|80840|506|507;3379134|976|117743|200644|49546|1016;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563;1783272|1239|186801|53433|3046412|32636;1783272|544448;3379134|1224|1236|135619|135620|196079;1783272|1239|1737404|1737405|1570339|162289;3379134|976|200643|171549|171552|838;3379134|1224|1236|135614|32033|40323,Complete,Folakunmi
bsdb:25283067/1/1,25283067,case-control,25283067,https://doi.org/10.1111/omi.12086,https://pubmed.ncbi.nlm.nih.gov/25283067/,"Moon J.H., Lee J.H. , Lee J.Y.",Subgingival microbiome in smokers and non-smokers in Korean chronic periodontitis patients,Molecular oral microbiology,2015,"Korean, periodontitis, pyrosequencing, smoking, subgingival microflora",Experiment 1,Republic of Korea,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Smoking behavior,EFO:0004318,Non-smokers,Smokers,A patient was defined as a smoker if he was currently smoking and had been smoking five or more cigarettes a day for at least 10 years.,36,57,3 months,16S,123,Roche454,relative abundances,NA,NA,NA,NA,"age,sex",NA,NA,increased,NA,unchanged,NA,unchanged,Signature 1,"text, Figure 1, Figure 2, Figure 3",13 March 2023,Atrayees,"Atrayees,Lwaldron,Claregrieve1,WikiWorks","Genera, phylum and species showing differences in relative abundance.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella oralis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum orale,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum saburreum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sicca,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella baroniae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella buccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella maculosa,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Thermotogati|p__Synergistota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|976|200643|171549|815|816;3379134|29547|3031852|213849|72294|194|199;3379134|29547|3031852|213849|72294|194|204;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85007|1653|1716|43768;3379134|200940|3031451|3024411|213121|893;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3082720|3118655|44259;1783272|1239|186801|3082720|3118655|44259|143361;3384194|508458|649775|649776|3029087|1434006;3384189|32066|203490;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492|848|851;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563;3379134|976|200643|171549|171552|2974257|28134;1783272|1239|186801|3085636|186803|1164882|979627;1783272|1239|186801|3085636|186803|1164882|467210;3379134|1224|28216|80840|119060|47670;3384189|32066|203490|203491|1129771;1783272|1239|186801|3082720|543314|86331;3379134|1224|28216|206351|481|482|1107316;3379134|1224|28216|206351|481|482|490;1783272|1239|1737404|1737405|1570339|543311;3379134|976|200643|171549|171552|2974251|305719;3379134|976|200643|171549|171552|2974251|28126;3379134|976|200643|171549|171552|2974251|439703;3379134|976|200643|171549|171552|2974251|228604;1783272|201174|1760|85006|1268|32207;3379134|203691|203692;1783272|1239|91061|186826|1300|1301;3384194|508458;3379134|976|200643|171549|2005525|195950;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|186801|3085636|186803|43996;3384189|32066|203490|203491|1129771|32067;3379134|976|200643|171549|171551;3379134|203691|203692|136|2845253|157;1783272|1239|909932|1843489|31977,Complete,Claregrieve1
bsdb:25283067/1/2,25283067,case-control,25283067,https://doi.org/10.1111/omi.12086,https://pubmed.ncbi.nlm.nih.gov/25283067/,"Moon J.H., Lee J.H. , Lee J.Y.",Subgingival microbiome in smokers and non-smokers in Korean chronic periodontitis patients,Molecular oral microbiology,2015,"Korean, periodontitis, pyrosequencing, smoking, subgingival microflora",Experiment 1,Republic of Korea,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Smoking behavior,EFO:0004318,Non-smokers,Smokers,A patient was defined as a smoker if he was currently smoking and had been smoking five or more cigarettes a day for at least 10 years.,36,57,3 months,16S,123,Roche454,relative abundances,NA,NA,NA,NA,"age,sex",NA,NA,increased,NA,unchanged,NA,unchanged,Signature 2,"text, Figure 1, Figure 2, Figure 3",13 March 2023,Atrayees,"Atrayees,Aiyshaaaa,Claregrieve1,WikiWorks","Genera, phylum and species showing differences in relative abundance",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces johnsonii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces viscosus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium canifelinum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella seregens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia trevisanii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium timidum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria bacilliformis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria mucosa,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria perflava,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oulorum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas noxia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudopneumoniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema lecithinolyticum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rodentium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] brachy,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] saphenum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter|s__[Eubacterium] yurii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",1783272|201174|1760|2037|2049|1654|544581;1783272|201174|1760|2037|2049|1654|1656;3379134|1224|1236|135625|712|416916;3379134|1224|1236|135625|712|416916|739;3379134|976|200643;3379134|29547|3031852|213849|72294|194;3379134|976|117743|200644|49546|1016|1018;3379134|976|117743|200644|49546|1016|1019;3379134|1224|1236|135615|868|2717;3384189|32066|203490|203491|203492|848|285729;1783272|1239|91061|186826|186828|117563|46124;3379134|1224|1236|135625|712|724;3379134|976|200643|171549|171552|52228|52229;3379134|1224|28216|80840|119060|47670|47671;3384189|32066|203490|203491|1129771|32067|40542;3384189|32066|203490|203491|1129771|32067|109328;1783272|1239|909932|1843489|31977|906|187326;1783272|1239|186801|3082720|543314|86331|35519;3379134|1224|28216|206351|481|482|267212;3379134|1224|28216|206351|481|482|495;3379134|1224|28216|206351|481|482|484;3379134|1224|28216|206351|481|482|488;3379134|1224|28216|206351|481|482|33053;3379134|976|200643|171549|171551;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|28129;3379134|976|200643|171549|171552|838|28131;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552|838|28133;3379134|976|200643|171549|171552|2974251|28136;3379134|976|200643|171549|171552|838|60133;3379134|976|200643|171549|171552;3379134|1224;1783272|201174|1760|85006|1268|32207|172042;1783272|201174|1760|85006|1268|32207|2047;1783272|201174|1760|2037|2049|2529408|1660;1783272|1239|909932|909929|1843491|970|135083;1783272|1239|91061|186826|1300|1301|45634;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|91061|186826|1300|1301|257758;1783272|1239|91061|186826|1300|1301|1305;3379134|203691|203692|136|2845253|157|59892;3379134|203691|203692|136|2845253|157|53418;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|909932|1843489|31977|29465|248315;1783272|1239|186801|3082720|543314|35517;1783272|1239|186801|3082720|543314|35518;1783272|1239|186801|3082720|543314|51123;1783272|1239|186801|3082720|3118655|1913599|39498;3379134|1224|1236|135625|712|416916;3384194|508458|649775|649776|3029087|1434006;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|1239|909932|909929|1843491|970;3379134|203691|203692|136|2845253|157,Complete,Claregrieve1
bsdb:25319745/1/1,25319745,"cross-sectional observational, not case-control",25319745,10.1002/art.38892,NA,"Scher J.U., Ubeda C., Artacho A., Attur M., Isaac S., Reddy S.M., Marmon S., Neimann A., Brusca S., Patel T., Manasson J., Pamer E.G., Littman D.R. , Abramson S.B.","Decreased bacterial diversity characterizes the altered gut microbiota in patients with psoriatic arthritis, resembling dysbiosis in inflammatory bowel disease","Arthritis & rheumatology (Hoboken, N.J.)",2015,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Psoriatic arthritis,EFO:0003778,healthy controls,psoriatic arthiritis,patients fulfilling the criteria of the Classification of Psoriatic arthritis (CASPAR),17,16,3 months,16S,12,Roche454,relative abundances,LEfSe,0.2,TRUE,2,"age,ethnic group,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Figure 1a, Figure 2a",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differences in bacterial taxa between patients with psoriatic arthritis  (PsA) compared to healthy controls (HLT),decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|46205;1783272|1239|186801|186802|216572|1263;3379134|74201;3379134|74201|203494;3379134|74201|203494|48461,Complete,Claregrieve1
bsdb:25319745/2/1,25319745,"cross-sectional observational, not case-control",25319745,10.1002/art.38892,NA,"Scher J.U., Ubeda C., Artacho A., Attur M., Isaac S., Reddy S.M., Marmon S., Neimann A., Brusca S., Patel T., Manasson J., Pamer E.G., Littman D.R. , Abramson S.B.","Decreased bacterial diversity characterizes the altered gut microbiota in patients with psoriatic arthritis, resembling dysbiosis in inflammatory bowel disease","Arthritis & rheumatology (Hoboken, N.J.)",2015,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Psoriatic arthritis,EFO:0003778,healthy controls,skin psoriasis,patients fulfilling the skin psoriasis criteria of the Classification of Psoriatic arthritis (CASPAR),17,15,3 months,16S,12,Roche454,relative abundances,LEfSe,0.2,TRUE,2,"age,ethnic group,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Figure 1b, Figure 2b",10 January 2021,Rimsha Azhar,WikiWorks,Differences in bacterial taxa between patients with skin psoriasis (PS) compared to healthy controls (HLT),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota",3379134|976|200643|171549|171551;3379134|976|200643|171549|2005525|375288;1783272|1239|186801;1783272|1239|526524|526525|128827;1783272|1239|526524;1783272|201174|1760;1783272|201174;1783272|1239|526524|526525|2810280|100883;1783272|1239|526524|526525;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|541000;3379134|976,Complete,Claregrieve1
bsdb:25319745/3/1,25319745,"cross-sectional observational, not case-control",25319745,10.1002/art.38892,NA,"Scher J.U., Ubeda C., Artacho A., Attur M., Isaac S., Reddy S.M., Marmon S., Neimann A., Brusca S., Patel T., Manasson J., Pamer E.G., Littman D.R. , Abramson S.B.","Decreased bacterial diversity characterizes the altered gut microbiota in patients with psoriatic arthritis, resembling dysbiosis in inflammatory bowel disease","Arthritis & rheumatology (Hoboken, N.J.)",2015,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Psoriatic arthritis,EFO:0003778,skin psoriasis,psoriatic arthiritis,patients fulfilling the psoriatic arthritis criteria of the Classification of Psoriatic arthritis (CASPAR),15,16,3 months,16S,12,Roche454,relative abundances,LEfSe,0.2,TRUE,2,"age,ethnic group,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1c, Figure 2c",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Difference in bacterial taxa between psoriatic arthiritis compared to psoriasis samples,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Pseudomonadati|p__Bacteroidota",1783272|1239|526524|526525|2810280|100883;3379134|976,Complete,Claregrieve1
bsdb:25319745/3/2,25319745,"cross-sectional observational, not case-control",25319745,10.1002/art.38892,NA,"Scher J.U., Ubeda C., Artacho A., Attur M., Isaac S., Reddy S.M., Marmon S., Neimann A., Brusca S., Patel T., Manasson J., Pamer E.G., Littman D.R. , Abramson S.B.","Decreased bacterial diversity characterizes the altered gut microbiota in patients with psoriatic arthritis, resembling dysbiosis in inflammatory bowel disease","Arthritis & rheumatology (Hoboken, N.J.)",2015,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Psoriatic arthritis,EFO:0003778,skin psoriasis,psoriatic arthiritis,patients fulfilling the psoriatic arthritis criteria of the Classification of Psoriatic arthritis (CASPAR),15,16,3 months,16S,12,Roche454,relative abundances,LEfSe,0.2,TRUE,2,"age,ethnic group,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 1c, Figure 2c",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Difference in bacterial taxa between psoriatic arthiritis compared to psoriasis samples,decreased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",1783272|1239|186801;1783272|1239|186801|186802;1783272|1239;3379134|74201;3379134|74201|203494|48461|203557,Complete,NA
bsdb:25432777/1/1,25432777,"cross-sectional observational, not case-control",25432777,10.15252/msb.20145645,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299606/,"Zeller G., Tap J., Voigt A.Y., Sunagawa S., Kultima J.R., Costea P.I., Amiot A., Böhm J., Brunetti F., Habermann N., Hercog R., Koch M., Luciani A., Mende D.R., Schneider M.A., Schrotz-King P., Tournigand C., Tran Van Nhieu J., Yamada T., Zimmermann J., Benes V., Kloor M., Ulrich C.M., von Knebel Doeberitz M., Sobhani I. , Bork P.",Potential of fecal microbiota for early-stage detection of colorectal cancer,Molecular systems biology,2014,"cancer screening, colorectal cancer, fecal biomarkers, human gut microbiome, metagenomics",Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Colorectal carcinoma,EFO:1001951,Neoplasia-free,CRC patients,patients referred for colonoscopy that had cancerous tumors,61,53,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary Figure S2,19 January 2022,Itslanapark,"Itslanapark,Fatima,WikiWorks",significant differences in the abundance of specific taxa,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium animalis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum|s__Fusobacterium nucleatum subsp. nucleatum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium polymorphum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium vincentii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter rectus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] hylemonae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum",3379134|976|200643|171549|815|816;3379134|200940|3031449|213115|194924|35832;3379134|200940|3031449|213115|194924|872;3384189|32066;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492|848|76859;3384189|32066|203490|203491|203492|848|851|76856;3384189|32066|203490|203491|203492|848|76857;3384189|32066|203490|203491|203492|848|155615;3384189|32066|203490|203491|1129771|32067;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171551|836|28123;3379134|976|200643|171549|171552|838|28133;1783272|1239|186801|186802|216572|1017280;1783272|1239|186801|186802|216572|1017280|106588;3379134|1224;1783272|1239|909932|909929|1843491|970;1783272|1239|186801|186802|216572|707003;1783272|1239|186801|3082720|186804|1257|341694;3384189|32066|203490|203491|1129771|32067|157688;1783272|1239|1737404|1737405|1570339|543311;3384189|32066|203490|203491|203492|848|860;1783272|1239|1737404|1737405|1570339|543311|33033;3379134|976|200643|171549|815|816|817;3379134|200940|3031449|213115|194924|35832|35833;3379134|1224|28216|206351|481|482;3379134|29547|3031852|213849|72294|194|203;1783272|1239|909932|909929|1843491|970|69823;3384189|32066|203490|203491|1129771|32067|40542;1783272|1239|186801|3085636|186803|1506553|89153;1783272|1239|186801|3085636|186803|2941495|1512,Complete,Fatima
bsdb:25432777/1/2,25432777,"cross-sectional observational, not case-control",25432777,10.15252/msb.20145645,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299606/,"Zeller G., Tap J., Voigt A.Y., Sunagawa S., Kultima J.R., Costea P.I., Amiot A., Böhm J., Brunetti F., Habermann N., Hercog R., Koch M., Luciani A., Mende D.R., Schneider M.A., Schrotz-King P., Tournigand C., Tran Van Nhieu J., Yamada T., Zimmermann J., Benes V., Kloor M., Ulrich C.M., von Knebel Doeberitz M., Sobhani I. , Bork P.",Potential of fecal microbiota for early-stage detection of colorectal cancer,Molecular systems biology,2014,"cancer screening, colorectal cancer, fecal biomarkers, human gut microbiome, metagenomics",Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Colorectal carcinoma,EFO:1001951,Neoplasia-free,CRC patients,patients referred for colonoscopy that had cancerous tumors,61,53,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplementary Figure S2,19 January 2022,Itslanapark,"Itslanapark,Fatima,WikiWorks",significant differences in the abundance of specific taxa,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",3379134|1224|1236|2887326|468|469;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239;3379134|29547|3031852|213849|72294|194;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|1766253|39491,Complete,Fatima
bsdb:25432777/2/1,25432777,"cross-sectional observational, not case-control",25432777,10.15252/msb.20145645,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299606/,"Zeller G., Tap J., Voigt A.Y., Sunagawa S., Kultima J.R., Costea P.I., Amiot A., Böhm J., Brunetti F., Habermann N., Hercog R., Koch M., Luciani A., Mende D.R., Schneider M.A., Schrotz-King P., Tournigand C., Tran Van Nhieu J., Yamada T., Zimmermann J., Benes V., Kloor M., Ulrich C.M., von Knebel Doeberitz M., Sobhani I. , Bork P.",Potential of fecal microbiota for early-stage detection of colorectal cancer,Molecular systems biology,2014,"cancer screening, colorectal cancer, fecal biomarkers, human gut microbiome, metagenomics",Experiment 2,France,Homo sapiens,Feces,UBERON:0001988,Colorectal carcinoma,EFO:1001951,Adenoma patients,CRC patients,patients referred for colonoscopy that had cancerous tumors,42,53,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary Figure S2,7 March 2023,Fatima,"Fatima,WikiWorks",significant differences in the abundance of specific taxa between CRC and Adenoma patients,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium animalis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum|s__Fusobacterium nucleatum subsp. nucleatum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium polymorphum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium vincentii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella uli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus",3384189|32066|203490;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492|848|76859;3384189|32066|203490|203491|203492|848|851|76856;3384189|32066|203490|203491|203492|848|76857;3384189|32066|203490|203491|203492|848|155615;1783272|201174|84998|84999|1643824|133925;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171551|836|28123;3379134|1224;3379134|976|200643|171549|171552|838|28133;1783272|1239|186801|3082720|186804|1257|341694;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|201174|84998|84999|1643824|133925|133926;1783272|1239|91061|186826|1300|1301|1328,Complete,Fatima
bsdb:25432777/2/2,25432777,"cross-sectional observational, not case-control",25432777,10.15252/msb.20145645,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299606/,"Zeller G., Tap J., Voigt A.Y., Sunagawa S., Kultima J.R., Costea P.I., Amiot A., Böhm J., Brunetti F., Habermann N., Hercog R., Koch M., Luciani A., Mende D.R., Schneider M.A., Schrotz-King P., Tournigand C., Tran Van Nhieu J., Yamada T., Zimmermann J., Benes V., Kloor M., Ulrich C.M., von Knebel Doeberitz M., Sobhani I. , Bork P.",Potential of fecal microbiota for early-stage detection of colorectal cancer,Molecular systems biology,2014,"cancer screening, colorectal cancer, fecal biomarkers, human gut microbiome, metagenomics",Experiment 2,France,Homo sapiens,Feces,UBERON:0001988,Colorectal carcinoma,EFO:1001951,Adenoma patients,CRC patients,patients referred for colonoscopy that had cancerous tumors,42,53,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplementary Figure S2,7 March 2023,Fatima,"Fatima,WikiWorks",significant differences in the abundance of specific taxa between CRC and Adenoma patients,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|186802|186806|1730,Complete,Fatima
bsdb:25432777/3/1,25432777,"cross-sectional observational, not case-control",25432777,10.15252/msb.20145645,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299606/,"Zeller G., Tap J., Voigt A.Y., Sunagawa S., Kultima J.R., Costea P.I., Amiot A., Böhm J., Brunetti F., Habermann N., Hercog R., Koch M., Luciani A., Mende D.R., Schneider M.A., Schrotz-King P., Tournigand C., Tran Van Nhieu J., Yamada T., Zimmermann J., Benes V., Kloor M., Ulrich C.M., von Knebel Doeberitz M., Sobhani I. , Bork P.",Potential of fecal microbiota for early-stage detection of colorectal cancer,Molecular systems biology,2014,"cancer screening, colorectal cancer, fecal biomarkers, human gut microbiome, metagenomics",Experiment 3,France,Homo sapiens,Feces,UBERON:0001988,Colorectal carcinoma,EFO:1001951,Neoplasia free,Adenoma patients,patients referred for colonoscopy that had cancerous tumors,61,42,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary Figure S2,7 March 2023,Fatima,"Fatima,WikiWorks",significant differences in the abundance of specific taxa between Adenoma patients and neoplasia free,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,1783272|1239|186801|186802|216572|1263,Complete,Fatima
bsdb:25432777/4/1,25432777,"cross-sectional observational, not case-control",25432777,10.15252/msb.20145645,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299606/,"Zeller G., Tap J., Voigt A.Y., Sunagawa S., Kultima J.R., Costea P.I., Amiot A., Böhm J., Brunetti F., Habermann N., Hercog R., Koch M., Luciani A., Mende D.R., Schneider M.A., Schrotz-King P., Tournigand C., Tran Van Nhieu J., Yamada T., Zimmermann J., Benes V., Kloor M., Ulrich C.M., von Knebel Doeberitz M., Sobhani I. , Bork P.",Potential of fecal microbiota for early-stage detection of colorectal cancer,Molecular systems biology,2014,"cancer screening, colorectal cancer, fecal biomarkers, human gut microbiome, metagenomics",Experiment 4,France,Homo sapiens,Feces,UBERON:0001988,Colorectal carcinoma,EFO:1001951,Neoplasia free control,CRC,patients referred for colonoscopy that had cancerous tumors,88,53,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S3,7 March 2023,Fatima,"Fatima,WikiWorks",Microbial taxa significantly different between CRC patients to the control group (consisting of neoplasia-free and ones with small adenomas),increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium animalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium vincentii,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium gonidiaformans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica",3384189|32066|203490;3379134|1224;3379134|200940|3031449|213115|194924|872;3384189|32066|203490|203491|203492|848;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;1783272|1239|186801|186802|216572|1017280;3379134|976|200643|171549|171551|836;3379134|29547|3031852|213849|72294|194;3384189|32066|203490|203491|203492|848|76859;1783272|1239|186801|3082720|186804|1257|341694;3379134|976|200643|171549|815|816|817;1783272|1239|186801|3085636|186803|2941495|1512;1783272|1239|1737404|1737405|1570339|543311|33033;3384189|32066|203490|203491|203492|848|155615;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|186802|216572|1017280|106588;1783272|1239|186801|3085636|186803|1649459|154046;1783272|1239|1737404|1737405|1570339|543311;3384189|32066|203490|203491|203492|848|860;3384189|32066|203490|203491|203492|848|849;3379134|976|200643|171549|171552|2974251|28135;3379134|976|200643|171549|171552|838|28133;3379134|976|200643|171549|171551|836|28123,Complete,Fatima
bsdb:25432777/4/2,25432777,"cross-sectional observational, not case-control",25432777,10.15252/msb.20145645,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299606/,"Zeller G., Tap J., Voigt A.Y., Sunagawa S., Kultima J.R., Costea P.I., Amiot A., Böhm J., Brunetti F., Habermann N., Hercog R., Koch M., Luciani A., Mende D.R., Schneider M.A., Schrotz-King P., Tournigand C., Tran Van Nhieu J., Yamada T., Zimmermann J., Benes V., Kloor M., Ulrich C.M., von Knebel Doeberitz M., Sobhani I. , Bork P.",Potential of fecal microbiota for early-stage detection of colorectal cancer,Molecular systems biology,2014,"cancer screening, colorectal cancer, fecal biomarkers, human gut microbiome, metagenomics",Experiment 4,France,Homo sapiens,Feces,UBERON:0001988,Colorectal carcinoma,EFO:1001951,Neoplasia free control,CRC,patients referred for colonoscopy that had cancerous tumors,88,53,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure S3,7 March 2023,Fatima,"Fatima,WikiWorks",Microbial taxa significantly different between CRC patients to the control group (consisting of neoplasia-free and ones with small adenomas),decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanosphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanosphaera|s__Methanosphaera stadtmanae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum",1783272|1239;3379134|200940|3031449|213115|194924|35832;3366610|28890|183925|2158|2159|2316;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|186806|1730;3366610|28890|183925|2158|2159|2316|2317;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|186802|186806|1730|39496,Complete,Fatima
bsdb:25444008/1/1,25444008,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S., Sánchez B., Milani C., Duranti S., Solís G., Fernández N., de los Reyes-Gavilán C.G., Ventura M., Margolles A. , Gueimonde M.",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Premature birth,EFO:0003917,2-day old Full-term infants(born after uncomplicated pregnancy),2-day old Pre-term infants,infants born at gestational ages between 24 and 32 weeks,13,27,NA,16S,34,Ion Torrent,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Results within text under the subheading ""Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants"" Line 7 to 15",10 January 2021,Mst Afroza Parvin,"WikiWorks,ChiomaBlessing",Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales",1783272|201174|1760|85004|31953;3379134|1224|28216|80840|80864;1783272|201174|1760|85009|31957;1783272|1239|91061|186826|1300;1783272|201174;1783272|1239|91061;1783272|1239|91061|186826,Complete,ChiomaBlessing
bsdb:25444008/1/2,25444008,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S., Sánchez B., Milani C., Duranti S., Solís G., Fernández N., de los Reyes-Gavilán C.G., Ventura M., Margolles A. , Gueimonde M.",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Premature birth,EFO:0003917,2-day old Full-term infants(born after uncomplicated pregnancy),2-day old Pre-term infants,infants born at gestational ages between 24 and 32 weeks,13,27,NA,16S,34,Ion Torrent,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Results within text under the subheading ""Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants"" (Line 7 to 15)",10 January 2021,Mst Afroza Parvin,"WikiWorks,ChiomaBlessing",Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",3379134|976|200643|171549|815;1783272|1239|186801|186802|31979;1783272|201174|1760|85006|1268;3379134|1224|1236|135625|712;3379134|976|200643|171549|171551,Complete,ChiomaBlessing
bsdb:25444008/2/1,25444008,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S., Sánchez B., Milani C., Duranti S., Solís G., Fernández N., de los Reyes-Gavilán C.G., Ventura M., Margolles A. , Gueimonde M.",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Premature birth,EFO:0003917,10-day old Full-term infants(born after uncomplicated pregnancy),10-day old Pre-term,born at gestational ages between 24 and 32 weeks,13,27,NA,16S,34,Ion Torrent,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Results within text under the subheading ""Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants"" (line 15 to 22)",10 January 2021,Mst Afroza Parvin,"WikiWorks,ChiomaBlessing",Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae",3379134|1224|1236|91347|543;3379134|1224|1236;1783272|201174|1760|85006|1268,Complete,ChiomaBlessing
bsdb:25444008/2/2,25444008,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S., Sánchez B., Milani C., Duranti S., Solís G., Fernández N., de los Reyes-Gavilán C.G., Ventura M., Margolles A. , Gueimonde M.",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Premature birth,EFO:0003917,10-day old Full-term infants(born after uncomplicated pregnancy),10-day old Pre-term,born at gestational ages between 24 and 32 weeks,13,27,NA,16S,34,Ion Torrent,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Results within text under the subheading ""Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants"" (line 15 to 22)",10 January 2021,Mst Afroza Parvin,"WikiWorks,Atrayees,ChiomaBlessing",Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Actinomycetota",1783272|1239|909932|1843489|31977;3379134|976|200643|171549|815;1783272|201174|1760|85004|31953;1783272|1239|186801|186802|31979;1783272|201174|84998|84999|84107;1783272|1239|91061|186826|81850;3379134|1224|1236|135625|712;3379134|976|200643|171549|171551;1783272|201174,Complete,ChiomaBlessing
bsdb:25444008/3/1,25444008,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S., Sánchez B., Milani C., Duranti S., Solís G., Fernández N., de los Reyes-Gavilán C.G., Ventura M., Margolles A. , Gueimonde M.",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Premature birth,EFO:0003917,30 and 90-day old Full-term infants,30 and 90-day old Pre-term infants,infants born at gestational ages between 24 and 32 weeks,13,27,NA,16S,34,Ion Torrent,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Results within text under the subheading ""Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants"" (line 23 to 26)",10 January 2021,Mst Afroza Parvin,"WikiWorks,Folakunmi",Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,Lwaldron
bsdb:25444008/3/2,25444008,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S., Sánchez B., Milani C., Duranti S., Solís G., Fernández N., de los Reyes-Gavilán C.G., Ventura M., Margolles A. , Gueimonde M.",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Premature birth,EFO:0003917,30 and 90-day old Full-term infants,30 and 90-day old Pre-term infants,infants born at gestational ages between 24 and 32 weeks,13,27,NA,16S,34,Ion Torrent,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Results within text under the subheading ""Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants"" (line 23 to 26)",10 January 2021,Mst Afroza Parvin,"WikiWorks,Folakunmi",Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,3379134|976|200643|171549|815,Complete,Lwaldron
bsdb:25444008/4/1,25444008,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S., Sánchez B., Milani C., Duranti S., Solís G., Fernández N., de los Reyes-Gavilán C.G., Ventura M., Margolles A. , Gueimonde M.",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 4,Spain,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,10-day old cesarean-delivered pre-term neontes,10-day old vaginally-delivered pre-term neonates,10-day old pre-term infants who were delivered vaginally.,20,7,NA,PCR,NA,Ion Torrent,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Results within text under the sub-heading ""Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota"" (Line 6-8)",20 November 2023,Folakunmi,"Folakunmi,WikiWorks","Impact of Delivery method on the Intestinal Microbiota between 10-day old vaginally-delivered pre-term neonates and cesarean-delivered pre-term neonates, as observed by qPCR.",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,ChiomaBlessing
bsdb:25444008/5/1,25444008,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S., Sánchez B., Milani C., Duranti S., Solís G., Fernández N., de los Reyes-Gavilán C.G., Ventura M., Margolles A. , Gueimonde M.",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 5,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,2-day old full-term neonates not exposed to antibiotics (IAP/postnatal),2-day old pre-tem neonates exposed to antibiotics (IAP),antenatal/postnatal antibiotic exposure,14,10,NA,16S,34,Ion Torrent,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Results within text under the subheading ""Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota"" (2nd paragraph, from line 11)",10 January 2021,Mst Afroza Parvin,"WikiWorks,Folakunmi,ChiomaBlessing",Impact of Antibiotics Use on the Intestinal Microbiota between 2-day old full-term neonates not exposed to antibiotics (IAP/postnatal) and 2-day old pre-term neonates exposed to antibiotics (IAP),decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,1783272|1239|91061|186826|33958,Complete,Atrayees
bsdb:25444008/6/1,25444008,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S., Sánchez B., Milani C., Duranti S., Solís G., Fernández N., de los Reyes-Gavilán C.G., Ventura M., Margolles A. , Gueimonde M.",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 6,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,10-day old full-term neonates not exposed to antibiotics (IAP/postnatal),10-day old pre-tem neonates exposed to antibiotics (IAP),antenatal/postnatal antibiotic exposure,14,10,NA,16S,34,Ion Torrent,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Results within text under the subheading ""Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota"" (2nd paragraph, from line 11)",10 January 2021,Mst Afroza Parvin,"WikiWorks,ChiomaBlessing",Impact of Antibiotics Use on the Intestinal Microbiota between 10-day old full-term neonates not exposed to antibiotics (IAP/postnatal) and 10-day old pre-tem neonates exposed to antibiotics (IAP),decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae",1783272|201174|1760|85006|1268;1783272|201174|1760|85009|31957,Complete,Atrayees
bsdb:25444008/7/1,25444008,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S., Sánchez B., Milani C., Duranti S., Solís G., Fernández N., de los Reyes-Gavilán C.G., Ventura M., Margolles A. , Gueimonde M.",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 7,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,30-day old full-term neonates not exposed to antibiotics (IAP/postnatal),30-day old pre-tem neonates exposed to antibiotics (IAP),antenatal/postnatal antibiotic exposure,14,10,NA,16S,34,Ion Torrent,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Results within text under the subheading ""Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota"" (2nd paragraph, from line 18)",10 January 2021,Mst Afroza Parvin,"WikiWorks,Atrayees,ChiomaBlessing",Impact of Antibiotics Use on the Intestinal Microbiota between 30-day old full-term neonates not exposed to antibiotics (IAP/postnatal) and 30-day old pre-term neonates exposed to antibiotics (IAP),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli",3379134|1224|28216|80840|80864;1783272|1239|91061|1385|90964;1783272|1239|91061,Complete,Atrayees
bsdb:25444008/8/1,25444008,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S., Sánchez B., Milani C., Duranti S., Solís G., Fernández N., de los Reyes-Gavilán C.G., Ventura M., Margolles A. , Gueimonde M.",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 8,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,90-day old full-term neonates not exposed to antibiotics (IAP/postnatal),90-day old pre-term neonates with mothers exposed to antibiotics (IAP),90-day old pre-term neonates whose mothers received antibiotics (IAP) independently on whether or not the infant received antibiotics.,14,10,NA,16S,34,Ion Torrent,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Results within text under the subheading ""Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota"" (2nd paragraph, from line 31)",10 January 2021,Mst Afroza Parvin,"WikiWorks,ChiomaBlessing",Impact of Antibiotics Use on the Intestinal Microbiota between 90-day old full-term neonates not exposed to antibiotics (IAP/postnatal) and 90-day old pre-term neonates with mothers exposed to antibiotics (IAP),decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,1783272|1239|186801|186802|541000,Complete,Atrayees
bsdb:25444008/9/1,25444008,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S., Sánchez B., Milani C., Duranti S., Solís G., Fernández N., de los Reyes-Gavilán C.G., Ventura M., Margolles A. , Gueimonde M.",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 9,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,30-day old full-term neonates not exposed to antibiotics (IAP/postnatal),30-day old pre-tem neonates with mothers exposed to antibiotics (IAP),30-day old pre-term neonates whose mothers received antibiotics (IAP) independently on whether or not the infant received antibiotics.,5,14,NA,16S,34,Ion Torrent,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Results within text under the subheading ""Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota"" (2nd paragraph, from line 24)",10 January 2021,Mst Afroza Parvin,"WikiWorks,ChiomaBlessing",Impact of Antibiotics Use on the Intestinal Microbiota between 30-day old full-term neonates not exposed to antibiotics (IAP/postnatal) and 30-day old pre-term neonates with mothers exposed to antibiotics (IAP),increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,ChiomaBlessing
bsdb:25444008/9/2,25444008,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S., Sánchez B., Milani C., Duranti S., Solís G., Fernández N., de los Reyes-Gavilán C.G., Ventura M., Margolles A. , Gueimonde M.",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 9,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,30-day old full-term neonates not exposed to antibiotics (IAP/postnatal),30-day old pre-tem neonates with mothers exposed to antibiotics (IAP),30-day old pre-term neonates whose mothers received antibiotics (IAP) independently on whether or not the infant received antibiotics.,5,14,NA,16S,34,Ion Torrent,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Results within text under the subheading ""Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota"" (2nd paragraph, from line 20)",10 January 2021,Mst Afroza Parvin,"WikiWorks,ChiomaBlessing",Impact of Antibiotics Use on the Intestinal Microbiota between 30-day old full-term neonates not exposed to antibiotics (IAP/postnatal) and 30-day old pre-term neonates with mothers exposed to antibiotics (IAP),decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Actinomycetota",1783272|201174|1760|85004|31953;1783272|1239|91061|186826|1300;1783272|1239|91061|186826;1783272|201174,Complete,ChiomaBlessing
bsdb:25444008/10/1,25444008,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S., Sánchez B., Milani C., Duranti S., Solís G., Fernández N., de los Reyes-Gavilán C.G., Ventura M., Margolles A. , Gueimonde M.",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 10,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,30-day old pre-term neonates not exposed to antibiotics (IAP/postnatal),30-day old pre-tem neonates exposed to antibiotics (IAP/postnatal),pre-term infants and mothers exposed to antibiotics,5,9,NA,PCR,NA,Ion Torrent,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Results for qtPCR within text under the subheading ""Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota"", 5th paragraph)",10 January 2021,Mst Afroza Parvin,"WikiWorks,Atrayees,ChiomaBlessing",Impact of Antibiotics Use on the Intestinal Microbiota between 30-day old pre-term neonates not exposed to antibiotics (IAP/postnatal) and 30-day old pre-term neonates exposed to antibiotics (IAP/postnatal),decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,1783272|1239|91061|1385|90964,Complete,ChiomaBlessing
bsdb:25444008/10/2,25444008,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S., Sánchez B., Milani C., Duranti S., Solís G., Fernández N., de los Reyes-Gavilán C.G., Ventura M., Margolles A. , Gueimonde M.",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 10,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,30-day old pre-term neonates not exposed to antibiotics (IAP/postnatal),30-day old pre-tem neonates exposed to antibiotics (IAP/postnatal),pre-term infants and mothers exposed to antibiotics,5,9,NA,PCR,NA,Ion Torrent,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Results for qtPCR within text under the subheading ""Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota"", 5th paragraph)",20 November 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Impact of Antibiotics Use on the Intestinal Microbiota between 30-day old pre-term neonates not exposed to antibiotics (IAP/postnatal) and 30-day old pre-term neonates exposed to antibiotics (IAP/postnatal),increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,ChiomaBlessing
bsdb:25444008/11/1,25444008,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S., Sánchez B., Milani C., Duranti S., Solís G., Fernández N., de los Reyes-Gavilán C.G., Ventura M., Margolles A. , Gueimonde M.",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,NA,Experiment 11,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,90-day old pre-term neonates not exposed to antibiotics (IAP/postnatal),90-day old pre-tem neonates exposed to antibiotics (IAP/postnatal),pre-term infants and mothers exposed to antibiotics,5,9,NA,PCR,NA,Ion Torrent,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Results for qtPCR within text under the subheading ""Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota"" (5th paragraph)",10 January 2021,Mst Afroza Parvin,"WikiWorks,ChiomaBlessing",Impact of Antibiotics Use on the Intestinal Microbiota between 90-day old pre-term neonates not exposed to antibiotics (IAP/postnatal) and 90-day old pre-term neonates exposed to antibiotics (IAP/postnatal),decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,ChiomaBlessing
bsdb:25476529/1/1,25476529,case-control,25476529,https://doi.org/10.1002/mds.26069,NA,"Scheperjans F., Aho V., Pereira P.A., Koskinen K., Paulin L., Pekkonen E., Haapaniemi E., Kaakkola S., Eerola-Rautio J., Pohja M., Kinnunen E., Murros K. , Auvinen P.",Gut microbiota are related to Parkinson's disease and clinical phenotype,Movement disorders : official journal of the Movement Disorder Society,2015,"biomarker, gastrointestinal dysfunction, gut-brain-axis, microbiome, non-motor symptoms",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls,Parkinson's disease,Patients diagnosed with Parkinson's disease,72,72,1 month,16S,123,Roche454,relative abundances,Metastats,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 1,eTable 4,9 March 2024,Junie,"Junie,Svetlana up,WikiWorks",Difference between the gut microbiome of patients with Parkinson's disease and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",1783272|1239|91061|186826|33958;3379134|1224|28211|356|41294;1783272|1239|186801|186802|216572;3379134|74201|203494|48461|203557,Complete,Svetlana up
bsdb:25476529/1/2,25476529,case-control,25476529,https://doi.org/10.1002/mds.26069,NA,"Scheperjans F., Aho V., Pereira P.A., Koskinen K., Paulin L., Pekkonen E., Haapaniemi E., Kaakkola S., Eerola-Rautio J., Pohja M., Kinnunen E., Murros K. , Auvinen P.",Gut microbiota are related to Parkinson's disease and clinical phenotype,Movement disorders : official journal of the Movement Disorder Society,2015,"biomarker, gastrointestinal dysfunction, gut-brain-axis, microbiome, non-motor symptoms",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls,Parkinson's disease,Patients diagnosed with Parkinson's disease,72,72,1 month,16S,123,Roche454,relative abundances,Metastats,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 2,eTable 4,9 March 2024,Junie,"Junie,WikiWorks",Difference in the abundance of the gut microbiome in patients with Parkinson's disease.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,3379134|976|200643|171549|171552,Complete,Svetlana up
bsdb:25484919/1/1,25484919,case-control,25484919,10.1186/s13073-014-0099-x,https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-014-0099-x,"Zhou Y., Holland M.J., Makalo P., Joof H., Roberts C.H., Mabey D.C., Bailey R.L., Burton M.J., Weinstock G.M. , Burr S.E.",The conjunctival microbiome in health and trachomatous disease: a case control study,Genome medicine,2014,NA,Experiment 1,Gambia,Homo sapiens,Conjunctiva,UBERON:0001811,Chlamydia trachomatis,NCBITAXON:813,Controls aged < = 0 years,Controls aged > 10 years,Control individuals with normal conjunctiva (F0P0C0 - 1981 WHO trachoma grading system) and age > 10 years old.,50,170,NA,16S,123,Roche454,NA,Metastats,0.05,TRUE,NA,"age,ethnic group,geographic area,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Table 2,28 June 2023,Andre,"Andre,Folakunmi,WikiWorks",Changes in taxa abundance between control individuals aged <= 10 years and > 10 years,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae|g__Myceligenerans,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium",1783272|201174|1760|2037;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85006|85017|253183;3379134|1224|28211|204455|31989|265;1783272|201174|1760|85006|85017;1783272|201174|1760|85009|31957|1743,Complete,Peace Sandy
bsdb:25484919/1/2,25484919,case-control,25484919,10.1186/s13073-014-0099-x,https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-014-0099-x,"Zhou Y., Holland M.J., Makalo P., Joof H., Roberts C.H., Mabey D.C., Bailey R.L., Burton M.J., Weinstock G.M. , Burr S.E.",The conjunctival microbiome in health and trachomatous disease: a case control study,Genome medicine,2014,NA,Experiment 1,Gambia,Homo sapiens,Conjunctiva,UBERON:0001811,Chlamydia trachomatis,NCBITAXON:813,Controls aged < = 0 years,Controls aged > 10 years,Control individuals with normal conjunctiva (F0P0C0 - 1981 WHO trachoma grading system) and age > 10 years old.,50,170,NA,16S,123,Roche454,NA,Metastats,0.05,TRUE,NA,"age,ethnic group,geographic area,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Table 2,28 June 2023,Andre,"Andre,Folakunmi,WikiWorks",Changes in taxa abundance between control individuals aged <= 10 years and > 10 years,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|1760|85006|85020|43668;1783272|201174|1760|85006|1268|57493;1783272|201174|1760|85006|1268|1269;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301,Complete,Peace Sandy
bsdb:25484919/2/1,25484919,case-control,25484919,10.1186/s13073-014-0099-x,https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-014-0099-x,"Zhou Y., Holland M.J., Makalo P., Joof H., Roberts C.H., Mabey D.C., Bailey R.L., Burton M.J., Weinstock G.M. , Burr S.E.",The conjunctival microbiome in health and trachomatous disease: a case control study,Genome medicine,2014,NA,Experiment 2,Gambia,Homo sapiens,Conjunctiva,UBERON:0001811,Chlamydia trachomatis,NCBITAXON:813,Controls aged > 10 years with samples collected in the dry season,Controls aged > 10 years with samples collected in the wet season,"Control individuals with normal conjunctiva (F0P0C0 - 1981 WHO trachoma grading system) and age > 10 years old with samples collected during the dry season. Of note, all samples from participants <= 10 years old were collected during the wet season, therefore, were not included in the analysis of the seasonal effect on the conjunctival microbiome.",126,94,NA,16S,123,Roche454,NA,Metastats,0.05,TRUE,NA,"age,ethnic group,geographic area,sex",NA,NA,increased,NA,NA,NA,increased,Signature 1,Table 2,28 June 2023,Andre,"Andre,Folakunmi,Peace Sandy,WikiWorks",Difference in taxa abundance between normal conjunctiva in wet season and normal conjunctiva in dry season,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae|g__Tumebacillus",1783272|1239|91061|1385|186817|1386;1783272|1239|91061|1385|186823|432330,Complete,Peace Sandy
bsdb:25484919/3/1,25484919,case-control,25484919,10.1186/s13073-014-0099-x,https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-014-0099-x,"Zhou Y., Holland M.J., Makalo P., Joof H., Roberts C.H., Mabey D.C., Bailey R.L., Burton M.J., Weinstock G.M. , Burr S.E.",The conjunctival microbiome in health and trachomatous disease: a case control study,Genome medicine,2014,NA,Experiment 3,Gambia,Homo sapiens,Conjunctiva,UBERON:0001811,Chlamydia trachomatis,NCBITAXON:813,"Cases with conjunctival scarring (C > 0) alone, with samples collected in the dry season","Cases with conjunctival scarring (C = 0) alone, with samples collected in the dry season",Participants aged = 10 years with clinical signs of conjunctival scarring (Cicatricae = 0)  sampled in the dry season. Bacterial community structure was different between the two groups during the dry season but not during the wet season.,63,63,NA,16S,123,Roche454,NA,Metastats,0.05,TRUE,NA,"age,ethnic group,geographic area,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 2,16 February 2024,Peace Sandy,"Peace Sandy,WikiWorks",Changes in taxa abundance between groups,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Globicatella,1783272|1239|91061|186826|186827|13075,Complete,Peace Sandy
bsdb:25484919/3/2,25484919,case-control,25484919,10.1186/s13073-014-0099-x,https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-014-0099-x,"Zhou Y., Holland M.J., Makalo P., Joof H., Roberts C.H., Mabey D.C., Bailey R.L., Burton M.J., Weinstock G.M. , Burr S.E.",The conjunctival microbiome in health and trachomatous disease: a case control study,Genome medicine,2014,NA,Experiment 3,Gambia,Homo sapiens,Conjunctiva,UBERON:0001811,Chlamydia trachomatis,NCBITAXON:813,"Cases with conjunctival scarring (C > 0) alone, with samples collected in the dry season","Cases with conjunctival scarring (C = 0) alone, with samples collected in the dry season",Participants aged = 10 years with clinical signs of conjunctival scarring (Cicatricae = 0)  sampled in the dry season. Bacterial community structure was different between the two groups during the dry season but not during the wet season.,63,63,NA,16S,123,Roche454,NA,Metastats,0.05,TRUE,NA,"age,ethnic group,geographic area,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 2,16 February 2024,Peace Sandy,"Peace Sandy,WikiWorks",Changes in taxa abundance between groups,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|1760|85007|1653|1716;1783272|1239|91061|186826|1300|1301,Complete,Peace Sandy
bsdb:25484919/4/1,25484919,case-control,25484919,10.1186/s13073-014-0099-x,https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-014-0099-x,"Zhou Y., Holland M.J., Makalo P., Joof H., Roberts C.H., Mabey D.C., Bailey R.L., Burton M.J., Weinstock G.M. , Burr S.E.",The conjunctival microbiome in health and trachomatous disease: a case control study,Genome medicine,2014,NA,Experiment 4,Gambia,Homo sapiens,Conjunctiva,UBERON:0001811,Chlamydia trachomatis,NCBITAXON:813,Cases aged > 10 years with clinical signs of conjunctival scarring sampled during the dry season,Cases aged = 10 years with clinical signs of conjunctival scarring sampled during the dry season,Participants aged 10 years with clinical signs of conjunctival scarring in dry season,63,63,NA,16S,123,Roche454,NA,Metastats,0.05,TRUE,NA,"age,ethnic group,geographic area,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 2,20 July 2023,Andre,"Andre,Folakunmi,Peace Sandy,WikiWorks",Changes in taxa abundance between groups,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Globicatella,1783272|1239|91061|186826|186827|13075,Complete,Peace Sandy
bsdb:25484919/4/2,25484919,case-control,25484919,10.1186/s13073-014-0099-x,https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-014-0099-x,"Zhou Y., Holland M.J., Makalo P., Joof H., Roberts C.H., Mabey D.C., Bailey R.L., Burton M.J., Weinstock G.M. , Burr S.E.",The conjunctival microbiome in health and trachomatous disease: a case control study,Genome medicine,2014,NA,Experiment 4,Gambia,Homo sapiens,Conjunctiva,UBERON:0001811,Chlamydia trachomatis,NCBITAXON:813,Cases aged > 10 years with clinical signs of conjunctival scarring sampled during the dry season,Cases aged = 10 years with clinical signs of conjunctival scarring sampled during the dry season,Participants aged 10 years with clinical signs of conjunctival scarring in dry season,63,63,NA,16S,123,Roche454,NA,Metastats,0.05,TRUE,NA,"age,ethnic group,geographic area,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 2,20 July 2023,Andre,"Andre,Folakunmi,Peace Sandy,WikiWorks",Changes in taxa abundance between groups,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|1760|85007|1653|1716;1783272|1239|91061|186826|1300|1301,Complete,Peace Sandy
bsdb:25484919/6/1,25484919,case-control,25484919,10.1186/s13073-014-0099-x,https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-014-0099-x,"Zhou Y., Holland M.J., Makalo P., Joof H., Roberts C.H., Mabey D.C., Bailey R.L., Burton M.J., Weinstock G.M. , Burr S.E.",The conjunctival microbiome in health and trachomatous disease: a case control study,Genome medicine,2014,NA,Experiment 6,Gambia,Homo sapiens,Conjunctiva,UBERON:0001811,Chlamydia trachomatis,NCBITAXON:813,"Cases with conjunctival scarring (C>0) alone, with samples collected in the dry season","Cases with conjunctival scarring (C>0) and trachomatous trichiasis (TT),with samples collected in the dry season",Participants aged >10 years with clinical signs of conjunctival scarring (Cicatricae > 0) and with  trachomatous trichiasis (TT)) sampled in the dry season. Bacterial community structure was different between the two groups during the dry season but not during the wet season.,63,63,NA,16S,123,Roche454,NA,Metastats,0.05,TRUE,NA,"age,ethnic group,geographic area,sex",NA,NA,decreased,NA,NA,NA,unchanged,Signature 1,Table 2,20 July 2023,Andre,"Andre,Folakunmi,WikiWorks",Changes in taxa abundance between groups,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria",1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85006|1268|57493,Complete,Peace Sandy
bsdb:25484919/6/2,25484919,case-control,25484919,10.1186/s13073-014-0099-x,https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-014-0099-x,"Zhou Y., Holland M.J., Makalo P., Joof H., Roberts C.H., Mabey D.C., Bailey R.L., Burton M.J., Weinstock G.M. , Burr S.E.",The conjunctival microbiome in health and trachomatous disease: a case control study,Genome medicine,2014,NA,Experiment 6,Gambia,Homo sapiens,Conjunctiva,UBERON:0001811,Chlamydia trachomatis,NCBITAXON:813,"Cases with conjunctival scarring (C>0) alone, with samples collected in the dry season","Cases with conjunctival scarring (C>0) and trachomatous trichiasis (TT),with samples collected in the dry season",Participants aged >10 years with clinical signs of conjunctival scarring (Cicatricae > 0) and with  trachomatous trichiasis (TT)) sampled in the dry season. Bacterial community structure was different between the two groups during the dry season but not during the wet season.,63,63,NA,16S,123,Roche454,NA,Metastats,0.05,TRUE,NA,"age,ethnic group,geographic area,sex",NA,NA,decreased,NA,NA,NA,unchanged,Signature 2,Table 2,20 July 2023,Andre,"Andre,Folakunmi,WikiWorks",Changes in taxa abundance between groups,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae|g__Myceligenerans,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae",1783272|201174|1760|2037;1783272|201174|1760|85006|85017|253183;3379134|1224|28211|204455|31989|265;1783272|201174|1760|85006|85017,Complete,Peace Sandy
bsdb:25487798/1/1,25487798,randomized controlled trial,25487798,10.1128/AAC.04506-14,NA,"Arat S., Spivak A., Van Horn S., Thomas E., Traini C., Sathe G., Livi G.P., Ingraham K., Jones L., Aubart K., Holmes D.J., Naderer O. , Brown J.R.","Microbiome changes in healthy volunteers treated with GSK1322322, a novel antibiotic targeting bacterial peptide deformylase",Antimicrobial agents and chemotherapy,2015,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,received oral-i.v.-administered GSK1322322 (prestudy),received oral-i.v.-administered GSK1322322 (end-of-study),received oral-i.v.-administered GSK1322322,38,38,NA,16S,4,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Table 2,18 November 2021,Mmarin,"Mmarin,WikiWorks",Significantly changed gut bacterial operational taxonomic units in subjects receiving oral-i.v.-administered GSK1322322 in prestudy versus end-of-study comparisons,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|1694;3379134|1224|1236|91347|543;1783272|1239|186801|3085636|186803;3379134|1224|28216|80840|995019|40544,Complete,Atrayees
bsdb:25487798/1/2,25487798,randomized controlled trial,25487798,10.1128/AAC.04506-14,NA,"Arat S., Spivak A., Van Horn S., Thomas E., Traini C., Sathe G., Livi G.P., Ingraham K., Jones L., Aubart K., Holmes D.J., Naderer O. , Brown J.R.","Microbiome changes in healthy volunteers treated with GSK1322322, a novel antibiotic targeting bacterial peptide deformylase",Antimicrobial agents and chemotherapy,2015,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,received oral-i.v.-administered GSK1322322 (prestudy),received oral-i.v.-administered GSK1322322 (end-of-study),received oral-i.v.-administered GSK1322322,38,38,NA,16S,4,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Table 2,18 November 2021,Mmarin,"Mmarin,Atrayees,WikiWorks",Significantly changed gut bacterial operational taxonomic units in subjects receiving oral-i.v.-administered GSK1322322 in prestudy versus end-of-study comparisons,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae",1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549;3379134|976|200643|171549|815|816|820;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|40520;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|2005519,Complete,Atrayees
bsdb:25487798/1/3,25487798,randomized controlled trial,25487798,10.1128/AAC.04506-14,NA,"Arat S., Spivak A., Van Horn S., Thomas E., Traini C., Sathe G., Livi G.P., Ingraham K., Jones L., Aubart K., Holmes D.J., Naderer O. , Brown J.R.","Microbiome changes in healthy volunteers treated with GSK1322322, a novel antibiotic targeting bacterial peptide deformylase",Antimicrobial agents and chemotherapy,2015,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,received oral-i.v.-administered GSK1322322 (prestudy),received oral-i.v.-administered GSK1322322 (end-of-study),received oral-i.v.-administered GSK1322322,38,38,NA,16S,4,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 3,Figure 5,19 November 2021,Mmarin,"Mmarin,Atrayees,WikiWorks","Phylogenetic tree of peptide deformylase amino acid sequences for species of gastrointestinal (GI) microbiota detected in this study and bacterial pathogens with available MIC data for GSK1322322. Bacterial pathogens were classified as low susceptible (red) or high susceptible (green) according to an MIC cutoff of ≥ 8.0 μg/ml (see Materials and Methods). GI bacteria were classified by changes in oral-i.v. end-of-study compared to prestudy samples as having a statistically significant increase (blue) or decrease (orange) in the relative abundances, or as no change (black). The phylogenetic tree was reconstructed using the neighbor-joining method with the JTT option in the software MEGA6. Support for nodes in 1,000 bootstrap replicates is indicated by increased sizes as well as weighting to the red color spectrum of the circles at the nodes.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Enterobacteriaceae bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella parvirubra,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|1689;1783272|201174|1760|85004|31953|1678|41200;3379134|1224|1236|91347|543|1849603;3379134|1224|28216|80840|995019|40544|437898;3379134|1224|28216|80840|995019|40544|40545;3379134|976|200643|171549|815|816|818;3379134|1224|1236|135614|32033|40323,Complete,NA
bsdb:25487798/2/1,25487798,randomized controlled trial,25487798,10.1128/AAC.04506-14,NA,"Arat S., Spivak A., Van Horn S., Thomas E., Traini C., Sathe G., Livi G.P., Ingraham K., Jones L., Aubart K., Holmes D.J., Naderer O. , Brown J.R.","Microbiome changes in healthy volunteers treated with GSK1322322, a novel antibiotic targeting bacterial peptide deformylase",Antimicrobial agents and chemotherapy,2015,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,received oral-i.v.-administered GSK1322322 (prestudy),received oral-i.v.-administered GSK1322322 (end-of-study),received oral-i.v.-administered GSK1322322,38,38,NA,16S,4,Illumina,relative abundances,NA,0.05,NA,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Figure 5,13 January 2022,Mmarin,"Mmarin,WikiWorks","Phylogenetic tree of peptide deformylase amino acid sequences for species of gastrointestinal (GI) microbiota detected in this study and bacterial pathogens with available MIC data for GSK1322322. Bacterial pathogens were classified as low susceptible (red) or high susceptible (green) according to an MIC cutoff of ≥ 8.0 μg/ml (see Materials and Methods). GI bacteria were classified by changes in oral-i.v. end-of-study compared to prestudy samples as having a statistically significant increase (blue) or decrease (orange) in the relative abundances, or as no change (black). The phylogenetic tree was reconstructed using the neighbor-joining method with the JTT option in the software MEGA6. Support for nodes in 1,000 bootstrap replicates is indicated by increased sizes as well as weighting to the red color spectrum of the circles at the nodes.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Enterobacteriaceae bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella parvirubra,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis",1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|1689;1783272|201174|1760|85004|31953|1678|41200;3379134|1224|1236|91347|543|1849603;3379134|1224|28216|80840|995019|40544|437898;3379134|1224|28216|80840|995019|40544|40545,Complete,NA
bsdb:25487798/2/2,25487798,randomized controlled trial,25487798,10.1128/AAC.04506-14,NA,"Arat S., Spivak A., Van Horn S., Thomas E., Traini C., Sathe G., Livi G.P., Ingraham K., Jones L., Aubart K., Holmes D.J., Naderer O. , Brown J.R.","Microbiome changes in healthy volunteers treated with GSK1322322, a novel antibiotic targeting bacterial peptide deformylase",Antimicrobial agents and chemotherapy,2015,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,received oral-i.v.-administered GSK1322322 (prestudy),received oral-i.v.-administered GSK1322322 (end-of-study),received oral-i.v.-administered GSK1322322,38,38,NA,16S,4,Illumina,relative abundances,NA,0.05,NA,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Figure 5,13 January 2022,Mmarin,"Mmarin,WikiWorks","Phylogenetic tree of peptide deformylase amino acid sequences for species of gastrointestinal (GI) microbiota detected in this study and bacterial pathogens with available MIC data for GSK1322322. Bacterial pathogens were classified as low susceptible (red) or high susceptible (green) according to an MIC cutoff of ≥ 8.0 μg/ml (see Materials and Methods). GI bacteria were classified by changes in oral-i.v. end-of-study compared to prestudy samples as having a statistically significant increase (blue) or decrease (orange) in the relative abundances, or as no change (black). The phylogenetic tree was reconstructed using the neighbor-joining method with the JTT option in the software MEGA6. Support for nodes in 1,000 bootstrap replicates is indicated by increased sizes as well as weighting to the red color spectrum of the circles at the nodes.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter laneus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hydrogenotrophica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus champanellensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|171552|2974251|165179;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|1853231|283168|626933;1783272|1239|186801|186802|216572|2485925;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|2316020|46228;1783272|1239|186801|3085636|186803|572511|1322;1783272|1239|186801|186802|216572|1263|41978;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|572511|53443;1783272|1239|186801|3085636|186803|207244|1872530;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|1263|1161942;1783272|1239|186801|3085636|186803|2316020|33038,Complete,NA
bsdb:25495462/1/1,25495462,"cross-sectional observational, not case-control",25495462,10.1186/s12866-014-0311-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4275940/,"Escobar J.S., Klotz B., Valdes B.E. , Agudelo G.M.","The gut microbiota of Colombians differs from that of Americans, Europeans and Asians",BMC microbiology,2014,NA,Experiment 1,"United States of America,Colombia,South Korea,Japan,Spain,France,Denmark",Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,USA data,Colombia data,"30 healthy Colombia adults of both genders from the general population living in Medellin, Colombia South America.",13,30,4 months,16S,123,Roche454,relative abundances,PERMANOVA,0.05,TRUE,NA,NA,"age,sex,waist circumference",NA,NA,NA,NA,NA,NA,Signature 1,Table 2,20 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Peace Sandy,WikiWorks","Taxonomic composition of the gut microbiota in the different datasets.

Data presented as average ± standard deviation; P-values from ANOVA testing differences among lean, overweight, and obese subjects. WC = waist circumference;
NA = not available.",increased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Peace Sandy
bsdb:25495462/1/2,25495462,"cross-sectional observational, not case-control",25495462,10.1186/s12866-014-0311-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4275940/,"Escobar J.S., Klotz B., Valdes B.E. , Agudelo G.M.","The gut microbiota of Colombians differs from that of Americans, Europeans and Asians",BMC microbiology,2014,NA,Experiment 1,"United States of America,Colombia,South Korea,Japan,Spain,France,Denmark",Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,USA data,Colombia data,"30 healthy Colombia adults of both genders from the general population living in Medellin, Colombia South America.",13,30,4 months,16S,123,Roche454,relative abundances,PERMANOVA,0.05,TRUE,NA,NA,"age,sex,waist circumference",NA,NA,NA,NA,NA,NA,Signature 2,Table 2,20 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Peace Sandy,WikiWorks","Taxonomic composition of the gut microbiota in the different datasets.

Data presented as average ± standard deviation; P-values from ANOVA testing differences among lean, overweight, and obese subjects. WC = waist circumference; NA = not available.",decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,Peace Sandy
bsdb:25495462/2/2,25495462,"cross-sectional observational, not case-control",25495462,10.1186/s12866-014-0311-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4275940/,"Escobar J.S., Klotz B., Valdes B.E. , Agudelo G.M.","The gut microbiota of Colombians differs from that of Americans, Europeans and Asians",BMC microbiology,2014,NA,Experiment 2,"Colombia,Denmark,France,Spain,United States of America,South Korea,Japan",Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,USA data,Europe data,"The European dataset consisted of the subset of 13 healthy volunteers (three women and 10 men) among Spanish, French, and Danish inhabitants whose microbiomes were published by the MetaHIT Consortium",13,13,4 months,16S,123,Roche454,relative abundances,PERMANOVA,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 2,21 July 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks","Taxonomic composition of the gut microbiota in the different datasets.

Data presented as average ± standard deviation; P-values from ANOVA testing differences among lean, overweight, and obese subjects. WC = waist circumference; NA = not available.",decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Peace Sandy
bsdb:25495462/3/2,25495462,"cross-sectional observational, not case-control",25495462,10.1186/s12866-014-0311-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4275940/,"Escobar J.S., Klotz B., Valdes B.E. , Agudelo G.M.","The gut microbiota of Colombians differs from that of Americans, Europeans and Asians",BMC microbiology,2014,NA,Experiment 3,"Colombia,Denmark,France,Spain,United States of America,South Korea,Japan",Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,USA data,South Korea data,The Korean dataset consisted of 14 lean and four overweight individuals (six women and 12 men),54,14,4 months,16S,123,Roche454,relative abundances,PERMANOVA,0.05,TRUE,NA,NA,"age,sex,waist circumference",NA,NA,NA,NA,NA,NA,Signature 2,Table 2,21 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Peace Sandy,WikiWorks","Taxonomic composition of the gut microbiota in the different datasets

Data presented as average ± standard deviation; P-values from ANOVA testing differences among lean, overweight, and obese subjects. WC = waist circumference;
NA = not available.",decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Peace Sandy
bsdb:25495462/4/1,25495462,"cross-sectional observational, not case-control",25495462,10.1186/s12866-014-0311-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4275940/,"Escobar J.S., Klotz B., Valdes B.E. , Agudelo G.M.","The gut microbiota of Colombians differs from that of Americans, Europeans and Asians",BMC microbiology,2014,NA,Experiment 4,"Colombia,Denmark,France,South Korea,Spain,United States of America,Japan",Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,USA data,Japan data,The Japanese dataset consisted of 454-generated V1 and V2 16S rDNA sequences of 10 lean and one overweight adult (six females and five males) that participated in an intervention with probiotics,54,11,4 months,16S,12,Roche454,relative abundances,PERMANOVA,0.05,TRUE,NA,NA,"age,sex,waist circumference",NA,NA,NA,NA,NA,NA,Signature 1,Table 2,21 July 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks","Taxonomic composition of the gut microbiota in the different datasets.

Data presented as average ± standard deviation; P-values from ANOVA testing differences among lean, overweight, and obese subjects. WC = waist circumference;
NA = not available.",increased,k__Bacillati|p__Actinomycetota,1783272|201174,Complete,Peace Sandy
bsdb:25495462/4/2,25495462,"cross-sectional observational, not case-control",25495462,10.1186/s12866-014-0311-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4275940/,"Escobar J.S., Klotz B., Valdes B.E. , Agudelo G.M.","The gut microbiota of Colombians differs from that of Americans, Europeans and Asians",BMC microbiology,2014,NA,Experiment 4,"Colombia,Denmark,France,South Korea,Spain,United States of America,Japan",Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,USA data,Japan data,The Japanese dataset consisted of 454-generated V1 and V2 16S rDNA sequences of 10 lean and one overweight adult (six females and five males) that participated in an intervention with probiotics,54,11,4 months,16S,12,Roche454,relative abundances,PERMANOVA,0.05,TRUE,NA,NA,"age,sex,waist circumference",NA,NA,NA,NA,NA,NA,Signature 2,Table 2,21 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Peace Sandy,WikiWorks","Taxonomic composition of the gut microbiota in the different datasets

Data presented as average ± standard deviation; P-values from ANOVA testing differences among lean, overweight, and obese subjects. WC = waist circumference;
NA = not available.",decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Peace Sandy
bsdb:25540641/1/1,25540641,case-control,25540641,10.3389/fmicb.2014.00678,NA,"Davis-Richardson A.G., Ardissone A.N., Dias R., Simell V., Leonard M.T., Kemppainen K.M., Drew J.C., Schatz D., Atkinson M.A., Kolaczkowski B., Ilonen J., Knip M., Toppari J., Nurminen N., Hyöty H., Veijola R., Simell T., Mykkänen J., Simell O. , Triplett E.W.",Bacteroides dorei dominates gut microbiome prior to autoimmunity in Finnish children at high risk for type 1 diabetes,Frontiers in microbiology,2014,"Bacteroides dorei, Bacteroides vulgatus, autoimmunity, microbiome, type-1 diabetes",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Autoimmune type 1 diabetes,EFO:0009756,Healthy controls,Cases,"This cases included 29 children who developed type 1 diabetes (T1D)-related autoimmunity, with 22 later progressing to T1D.",47,29,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.001,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Tables S6–S8,24 February 2025,Aleru Divine,Aleru Divine,"The relative abundances of taxa at ranks Phylum, Genus, and Species were compared between all samples from all cases and controls using the non-parametric Mann–Whitney U-test.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Prosthecobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola barnesiae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecichinchillae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides reticulotermitis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercorirosoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium|s__Sphingobacterium multivorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus flavefaciens",3379134|976|200643|171549|171552|838;1783272|201174|84998|1643822|1643826|447020;3379134|976|200643|171549|815|816;3379134|976|200643|171549|1853231|574697;1783272|1239|526524|526525|2810280|100883;1783272|1239|186801|3085636|186803|140625;3379134|976|200643|171549|2005523|346096;3379134|976|200643|171549|2005525|375288;3379134|74201|203494|48461|203557|48463;1783272|1239|186801|186802|216572|1263;3379134|976|117747|200666|84566|28453;3379134|976;3379134|976|200643|171549|815|816|85831;3379134|976|200643|171549|815|909656|376804;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|246787;3379134|976|200643|171549|815|816|626929;3379134|976|200643|171549|815|816|28111;3379134|976|200643|171549|815|816|871325;3379134|976|200643|171549|815|816|338188;3379134|976|200643|171549|815|816|329854;3379134|976|200643|171549|815|909656|204516;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|1133319;3379134|976|200643|171549|815|816|871324;3379134|976|200643|171549|815|816|46506;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|815|816|371601;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|186801|3085636|186803|841|301302;3379134|976|117747|200666|84566|28453|28454;1783272|1239|186801|186802|216572|1263|1265,Complete,Svetlana up
bsdb:25540641/1/2,25540641,case-control,25540641,10.3389/fmicb.2014.00678,NA,"Davis-Richardson A.G., Ardissone A.N., Dias R., Simell V., Leonard M.T., Kemppainen K.M., Drew J.C., Schatz D., Atkinson M.A., Kolaczkowski B., Ilonen J., Knip M., Toppari J., Nurminen N., Hyöty H., Veijola R., Simell T., Mykkänen J., Simell O. , Triplett E.W.",Bacteroides dorei dominates gut microbiome prior to autoimmunity in Finnish children at high risk for type 1 diabetes,Frontiers in microbiology,2014,"Bacteroides dorei, Bacteroides vulgatus, autoimmunity, microbiome, type-1 diabetes",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Autoimmune type 1 diabetes,EFO:0009756,Healthy controls,Cases,"This cases included 29 children who developed type 1 diabetes (T1D)-related autoimmunity, with 22 later progressing to T1D.",47,29,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.001,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Tables S6–S8,24 February 2025,Aleru Divine,Aleru Divine,"The relative abundances of taxa at ranks Phylum, Genus, and Species were compared between all samples from all cases and controls using the non-parametric Mann–Whitney U-test.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Azonexaceae|g__Dechloromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Dickeya,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Methylibium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Photorhabdus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Plesiomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae|g__Salinispora,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Salinivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Bruguierivoracaceae|g__Sodalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Syntrophobacteria|o__Syntrophobacterales|f__Syntrophobacteraceae|g__Syntrophobacter,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium neonatale,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Pantoea dispersa,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia|s__Erwinia oleae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia|s__Erwinia soli,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium|s__Janthinobacterium lividum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Methylibium|s__Methylibium petroleiphilum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella|s__Morganella morganii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Plesiomonas|s__Plesiomonas shigelloides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae|g__Salinispora|s__Salinispora tropica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Salinivibrio|s__Salinivibrio costicola,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia marcescens,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus equorum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae",1783272|1239|186801|186802|186806|1730;3379134|1224|1236|2887326|468|469;1783272|1239|91061|186826|186827|1375;1783272|1239|186801|186802|186806|264995;3379134|1224|1236|135615|868|2717;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|186802|31979|1485;3379134|1224|28216|206389|2008795|73029;3379134|1224|1236|91347|1903410|204037;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|1903409|551;1783272|1239|91061|186826|186827|66831;1783272|1239|91061|186826|186828|117563;3379134|1224|28216|80840|75682|29580;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|80840|2975441|316612;3379134|1224|1236|91347|1903414|581;3379134|1224|1236|91347|1903414|29487;3379134|1224|1236|91347|543|702;3379134|1224|1236|91347|1903414|583;3379134|1224|1236|91347|1903414|586;1783272|201174|1760|85008|28056|168694;3379134|1224|1236|135623|641|51366;3379134|1224|1236|91347|543|590;3379134|1224|1236|91347|1903411|613;3379134|1224|1236|135622|267890|22;3379134|1224|1236|91347|2812006|84565;1783272|1239|91061|1385|90964|1279;3379134|200940|3024408|213462|213465|29526;3379134|1224;1783272|544448;1783272|1239|526524|526525|128827|2749846|31971;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|186802|31979|1485|137838;1783272|1239|186801|186802|31979|1485|1502;3379134|1224|1236|91347|1903409|53335|59814;3379134|1224|1236|91347|1903409|551|796334;3379134|1224|1236|91347|1903409|551|441667;3379134|1224|28216|80840|75682|29580|29581;3379134|1224|28216|80840|2975441|316612|105560;3379134|1224|1236|91347|1903414|581|582;3379134|1224|1236|91347|543|702|703;1783272|201174|1760|85008|28056|168694|168695;3379134|1224|1236|135623|641|51366|51367;3379134|1224|1236|91347|543|590|28901;3379134|1224|1236|91347|1903411|613|615;1783272|1239|91061|1385|90964|1279|246432;1783272|1239|91061|186826|1300|1301|1311,Complete,Svetlana up
bsdb:25599982/1/1,25599982,case-control,25599982,10.1111/cea.12487,NA,"Azad M.B., Konya T., Guttman D.S., Field C.J., Sears M.R., HayGlass K.T., Mandhane P.J., Turvey S.E., Subbarao P., Becker A.B., Scott J.A. , Kozyrskyj A.L.",Infant gut microbiota and food sensitization: associations in the first year of life,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,2015,NA,Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,non-sensitized group,sensitized group,3 months infants with food sensitization at 1 year,154,12,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Table 3,10 January 2021,Lucy Mellor,"WikiWorks,ChiomaBlessing",Relative abundance of dominant phyla in fecal microbiota of sensitized infants VS non-sensitized infants at 3 months according to food sensitization at 1 year,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|1236|91347|543;3379134|1224,Complete,ChiomaBlessing
bsdb:25599982/2/1,25599982,case-control,25599982,10.1111/cea.12487,NA,"Azad M.B., Konya T., Guttman D.S., Field C.J., Sears M.R., HayGlass K.T., Mandhane P.J., Turvey S.E., Subbarao P., Becker A.B., Scott J.A. , Kozyrskyj A.L.",Infant gut microbiota and food sensitization: associations in the first year of life,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,2015,NA,Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,non-sensitized group,sensitized group,1 year infants with food sensitization at 1 year,154,12,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 3,10 January 2021,Lucy Mellor,"WikiWorks,ChiomaBlessing",Relative abundance of dominant phyla in fecal microbiota of sensitized infants VS non-sensitized infants at 1 year according to food sensitization at 1 year,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,ChiomaBlessing
bsdb:25599982/2/2,25599982,case-control,25599982,10.1111/cea.12487,NA,"Azad M.B., Konya T., Guttman D.S., Field C.J., Sears M.R., HayGlass K.T., Mandhane P.J., Turvey S.E., Subbarao P., Becker A.B., Scott J.A. , Kozyrskyj A.L.",Infant gut microbiota and food sensitization: associations in the first year of life,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,2015,NA,Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,non-sensitized group,sensitized group,1 year infants with food sensitization at 1 year,154,12,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 3,10 January 2021,Lucy Mellor,"WikiWorks,ChiomaBlessing",Relative abundance of dominant phyla in fecal microbiota of sensitized infants VS non-sensitized infants at 1 year according to food sensitization at 1 year,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae",3379134|976;3379134|976|200643|171549|815,Complete,ChiomaBlessing
bsdb:25658522/1/1,25658522,prospective cohort,25658522,10.1016/j.cmi.2014.11.016,NA,"Stewardson A.J., Gaïa N., François P., Malhotra-Kumar S., Delémont C., Martinez de Tejada B., Schrenzel J., Harbarth S. , Lazarevic V.",Collateral damage from oral ciprofloxacin versus nitrofurantoin in outpatients with urinary tract infections: a culture-free analysis of gut microbiota,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2015,"Antibiotics, ecologic damage, microbiomics, microbiota, urinary tract infection",Experiment 1,Switzerland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,baseline of the ciprofloxacin treated,ciprofloxacin treated,UTI patients treated with ciprofloxacin 500mg twice daily,10,10,2 months,16S,34,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3,23 September 2021,Mmarin,"Mmarin,Claregrieve1,WikiWorks",Differential microbial abundance between baseline (timepoint 1) and timepoint 2 in ciprofloxacin treated patients,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|201174|1760|85004|31953;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|1263,Complete,Claregrieve1
bsdb:25658522/1/2,25658522,prospective cohort,25658522,10.1016/j.cmi.2014.11.016,NA,"Stewardson A.J., Gaïa N., François P., Malhotra-Kumar S., Delémont C., Martinez de Tejada B., Schrenzel J., Harbarth S. , Lazarevic V.",Collateral damage from oral ciprofloxacin versus nitrofurantoin in outpatients with urinary tract infections: a culture-free analysis of gut microbiota,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2015,"Antibiotics, ecologic damage, microbiomics, microbiota, urinary tract infection",Experiment 1,Switzerland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,baseline of the ciprofloxacin treated,ciprofloxacin treated,UTI patients treated with ciprofloxacin 500mg twice daily,10,10,2 months,16S,34,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 3,23 September 2021,Mmarin,"Mmarin,Claregrieve1,WikiWorks",Differential microbial abundance between baseline (timepoint 1) and timepoint 2 in ciprofloxacin treated patients,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",3379134|976|200643|171549|815;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|841,Complete,Claregrieve1
bsdb:25658522/2/1,25658522,prospective cohort,25658522,10.1016/j.cmi.2014.11.016,NA,"Stewardson A.J., Gaïa N., François P., Malhotra-Kumar S., Delémont C., Martinez de Tejada B., Schrenzel J., Harbarth S. , Lazarevic V.",Collateral damage from oral ciprofloxacin versus nitrofurantoin in outpatients with urinary tract infections: a culture-free analysis of gut microbiota,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2015,"Antibiotics, ecologic damage, microbiomics, microbiota, urinary tract infection",Experiment 2,Switzerland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Baseline of the Nitrofurantoin treated,Nitrofurantoin treated,UTI patients treated with nitrofurantoin macrocrystals 100mg twice daily,10,10,2 months,16S,34,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3,23 September 2021,Mmarin,"Mmarin,Claregrieve1,WikiWorks",Differential microbial abundance between baseline and post-treatment timepoints in nitrofurantoin treated group,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,1783272|1239|186801|186802|31979,Complete,Claregrieve1
bsdb:25658522/2/2,25658522,prospective cohort,25658522,10.1016/j.cmi.2014.11.016,NA,"Stewardson A.J., Gaïa N., François P., Malhotra-Kumar S., Delémont C., Martinez de Tejada B., Schrenzel J., Harbarth S. , Lazarevic V.",Collateral damage from oral ciprofloxacin versus nitrofurantoin in outpatients with urinary tract infections: a culture-free analysis of gut microbiota,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2015,"Antibiotics, ecologic damage, microbiomics, microbiota, urinary tract infection",Experiment 2,Switzerland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Baseline of the Nitrofurantoin treated,Nitrofurantoin treated,UTI patients treated with nitrofurantoin macrocrystals 100mg twice daily,10,10,2 months,16S,34,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 3,23 September 2021,Mmarin,"Mmarin,Claregrieve1,WikiWorks",Differential microbial abundance between baseline and post-treatment timepoints in nitrofurantoin treated group,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,1783272|1239|186801|186802|216572|216851,Complete,Claregrieve1
bsdb:25658522/6/1,25658522,prospective cohort,25658522,10.1016/j.cmi.2014.11.016,NA,"Stewardson A.J., Gaïa N., François P., Malhotra-Kumar S., Delémont C., Martinez de Tejada B., Schrenzel J., Harbarth S. , Lazarevic V.",Collateral damage from oral ciprofloxacin versus nitrofurantoin in outpatients with urinary tract infections: a culture-free analysis of gut microbiota,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2015,"Antibiotics, ecologic damage, microbiomics, microbiota, urinary tract infection",Experiment 6,Switzerland,Homo sapiens,Feces,UBERON:0001988,"Antimicrobial agent,Urinary tract infection","CHEBI:33281,EFO:0003103",control group (timepoint 2),Ciprofloxacin treated group (timepoint 2),ciprofloxacin group at end of antibiotic treatment,10,10,2 months,16S,34,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table S2,15 October 2021,Mmarin,"Mmarin,Claregrieve1,WikiWorks",Differential microbial abundance between the control group and ciprofloxacin-treated group at timepoint 2,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;3379134|976|200643|171549|171550;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|909932|1843489|31977,Complete,Claregrieve1
bsdb:25658522/7/1,25658522,prospective cohort,25658522,10.1016/j.cmi.2014.11.016,NA,"Stewardson A.J., Gaïa N., François P., Malhotra-Kumar S., Delémont C., Martinez de Tejada B., Schrenzel J., Harbarth S. , Lazarevic V.",Collateral damage from oral ciprofloxacin versus nitrofurantoin in outpatients with urinary tract infections: a culture-free analysis of gut microbiota,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2015,"Antibiotics, ecologic damage, microbiomics, microbiota, urinary tract infection",Experiment 7,Switzerland,Homo sapiens,Feces,UBERON:0001988,"Antimicrobial agent,Urinary tract infection","CHEBI:33281,EFO:0003103",controls (timepoint 2),nitrofurantoin treated group (timepoint 2),nitrofurantoin-treated group at end of treatment,10,10,2 months,16S,34,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table S2,15 October 2021,Mmarin,"Mmarin,Claregrieve1,WikiWorks",Differential microbial abundance between the control group and nitrofurantoin-treated group at timepoint 2,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549;3379134|976|200643;3379134|976;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|171550,Complete,Claregrieve1
bsdb:25658868/1/1,25658868,"cross-sectional observational, not case-control",25658868,10.1371/journal.pone.0117427,https://pubmed.ncbi.nlm.nih.gov/25658868/,"Greenhill A.R., Tsuji H., Ogata K., Natsuhara K., Morita A., Soli K., Larkins J.A., Tadokoro K., Odani S., Baba J., Naito Y., Tomitsuka E., Nomoto K., Siba P.M., Horwood P.F. , Umezaki M.",Characterization of the gut microbiota of Papua New Guineans using reverse transcription quantitative PCR,PloS one,2015,NA,Experiment 1,Papua New Guinea,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,High SES (low land region),Low SES (high land region),Participants living a subsistence lifestyle in the high-land rural areas of Papua New Guinea,29,86,NA,16S,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 4,15 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1,WikiWorks",Comparison of population numbers of selected microbial groups in the highland and lowland study participants.,increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|201174;3379134|976;3379134|1224|1236|91347|543;1783272|1239;1783272|1239|91061|186826|33958|1578,Complete,Fatima
bsdb:25699023/1/1,25699023,case-control,25699023,10.3389/fmicb.2015.00020,https://www.frontiersin.org/articles/10.3389/fmicb.2015.00020/full,"Gao Z., Guo B., Gao R., Zhu Q. , Qin H.",Microbiota disbiosis is associated with colorectal cancer,Frontiers in microbiology,2015,"colorectal cancer, distal colon, gut dysbiosis, mucosa-associated microbiota, proximal colon",Experiment 1,China,Homo sapiens,Colorectal mucosa,UBERON:0013067,Colorectal cancer,EFO:0005842,Healthy controls,Colorectal Cancer Patients,"Individuals that have been diagnosed with cancer that originates in the colon, part of the digestive system.",30,31,2 months,16S,3,Roche454,relative abundances,"Fisher's Exact Test,Chi-Square,T-Test,LEfSe",0.05,FALSE,3,"age,body mass index,sex",NA,NA,decreased,unchanged,increased,NA,unchanged,Signature 1,"Figure 2B, Figure 3",25 July 2023,Andre,"Andre,Deacme,ChiomaBlessing,WikiWorks",Different structures of gut microbiota between healthy individuals and CRC patients,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",3379134|1224|1236|91347|543|1940338;3384189|32066|203490|203491|203492|848;1783272|1239|91061|186826|1300|1357;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171552|838;3384189|32066|203490|203491|203492;3379134|976|200643;3379134|976|200643|171549|171552;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|1385|539738;3379134|976|200643|171549|171551;3379134|1224|1236|135622|267890|22;3379134|1224|1236|135622|267890;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|909932|1843489|31977|39948,Complete,Lwaldron
bsdb:25699023/1/2,25699023,case-control,25699023,10.3389/fmicb.2015.00020,https://www.frontiersin.org/articles/10.3389/fmicb.2015.00020/full,"Gao Z., Guo B., Gao R., Zhu Q. , Qin H.",Microbiota disbiosis is associated with colorectal cancer,Frontiers in microbiology,2015,"colorectal cancer, distal colon, gut dysbiosis, mucosa-associated microbiota, proximal colon",Experiment 1,China,Homo sapiens,Colorectal mucosa,UBERON:0013067,Colorectal cancer,EFO:0005842,Healthy controls,Colorectal Cancer Patients,"Individuals that have been diagnosed with cancer that originates in the colon, part of the digestive system.",30,31,2 months,16S,3,Roche454,relative abundances,"Fisher's Exact Test,Chi-Square,T-Test,LEfSe",0.05,FALSE,3,"age,body mass index,sex",NA,NA,decreased,unchanged,increased,NA,unchanged,Signature 2,"Figure 2, Figure 3",25 July 2023,Andre,"Andre,Deacme,ChiomaBlessing,WikiWorks",Different structures of gut microbiota between healthy individuals and CRC patients,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Buttiauxella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Epilithonimonas,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rahnella,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Brochothrix,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales",3379134|1224|28216|80840|80864|12916;3379134|1224|1236|2887326|468|469;3379134|1224|28211;3379134|1224|28211|204458|76892|41275;3379134|1224|1236|91347|543|82976;3379134|1224|28211|204458|76892|75;3379134|976|117743|200644|2762318|2782229;3379134|976|117743|200644|49546|237;3379134|1224|28216|80840|75682|29580;3379134|976|117747|200666|84566|84567;1783272|201174|1760|85009|31957|1743;3379134|1224|1236|72274|135621|286;3379134|1224|1236|2887326|468|497;3379134|1224|1236|91347|1903411|34037;3379134|976|117747|200666|84566|28453;3379134|1224|28211|204457|41297|13687;3379134|1224|1236|135614|32033|40323;1783272|1239|91061|1385|186820|2755;3379134|1224|1236|2887326|468;3379134|976|117743|200644|49546;3379134|976|117743|200644;3379134|1224|1236|72274|135621;3379134|1224;3379134|1224|1236;3379134|1224|1236|72274,Complete,Lwaldron
bsdb:25699023/2/1,25699023,case-control,25699023,10.3389/fmicb.2015.00020,https://www.frontiersin.org/articles/10.3389/fmicb.2015.00020/full,"Gao Z., Guo B., Gao R., Zhu Q. , Qin H.",Microbiota disbiosis is associated with colorectal cancer,Frontiers in microbiology,2015,"colorectal cancer, distal colon, gut dysbiosis, mucosa-associated microbiota, proximal colon",Experiment 2,China,Homo sapiens,Colorectal mucosa,UBERON:0013067,Colorectal cancer,EFO:0005842,adjacent non-cancerous tissues,cancerous tissues,"Individuals that have been diagnosed with cancer that originates in the colon, part of the digestive system.",20,31,2 months,16S,3,Roche454,relative abundances,"Fisher's Exact Test,Chi-Square,T-Test",0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,increased,NA,unchanged,Signature 1,Figure 2D,26 July 2023,Andre,"Andre,Tolulopeo,WikiWorks",The dominant genera of group cancerous compared to non-cancerous mucosa,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|976|200643|171549|815|816;1783272|1239|91061|186826|1300|1357;3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301,Complete,Lwaldron
bsdb:25699023/2/2,25699023,case-control,25699023,10.3389/fmicb.2015.00020,https://www.frontiersin.org/articles/10.3389/fmicb.2015.00020/full,"Gao Z., Guo B., Gao R., Zhu Q. , Qin H.",Microbiota disbiosis is associated with colorectal cancer,Frontiers in microbiology,2015,"colorectal cancer, distal colon, gut dysbiosis, mucosa-associated microbiota, proximal colon",Experiment 2,China,Homo sapiens,Colorectal mucosa,UBERON:0013067,Colorectal cancer,EFO:0005842,adjacent non-cancerous tissues,cancerous tissues,"Individuals that have been diagnosed with cancer that originates in the colon, part of the digestive system.",20,31,2 months,16S,3,Roche454,relative abundances,"Fisher's Exact Test,Chi-Square,T-Test",0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,increased,NA,unchanged,Signature 2,Figure 2D,26 July 2023,Andre,"Andre,Tolulopeo,WikiWorks",The dominant genera of group cancerous compared to non-cancerous mucosa.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,3379134|1224|1236|72274|135621|286,Complete,Lwaldron
bsdb:25699023/3/1,25699023,case-control,25699023,10.3389/fmicb.2015.00020,https://www.frontiersin.org/articles/10.3389/fmicb.2015.00020/full,"Gao Z., Guo B., Gao R., Zhu Q. , Qin H.",Microbiota disbiosis is associated with colorectal cancer,Frontiers in microbiology,2015,"colorectal cancer, distal colon, gut dysbiosis, mucosa-associated microbiota, proximal colon",Experiment 3,China,Homo sapiens,Colorectal mucosa,UBERON:0013067,Sigmoid neoplasm,EFO:1001181,Proximal Colon Cancer,Distal Colorectal Cancer,"Distal colon cancer tissue samples obtained from patients diagnosed with colorectal cancer (CRC), located in the sigmoid colon (25–35 cm from anus)",15,16,2 months,16S,3,Roche454,relative abundances,"T-Test,Chi-Square,Fisher's Exact Test",0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,increased,NA,increased,Signature 1,FIGURE 4,26 July 2023,Andre,"Andre,ChiomaBlessing,WikiWorks",Comparison of Gut Microbiota Between Proximal Colon Cancer and Distal Colorectal Cancer based on Principal component analysis (PCA) scores (97% similarity level),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",3379134|1224|1236|91347|543|1940338;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|1129771|32067,Complete,Lwaldron
bsdb:25699023/3/2,25699023,case-control,25699023,10.3389/fmicb.2015.00020,https://www.frontiersin.org/articles/10.3389/fmicb.2015.00020/full,"Gao Z., Guo B., Gao R., Zhu Q. , Qin H.",Microbiota disbiosis is associated with colorectal cancer,Frontiers in microbiology,2015,"colorectal cancer, distal colon, gut dysbiosis, mucosa-associated microbiota, proximal colon",Experiment 3,China,Homo sapiens,Colorectal mucosa,UBERON:0013067,Sigmoid neoplasm,EFO:1001181,Proximal Colon Cancer,Distal Colorectal Cancer,"Distal colon cancer tissue samples obtained from patients diagnosed with colorectal cancer (CRC), located in the sigmoid colon (25–35 cm from anus)",15,16,2 months,16S,3,Roche454,relative abundances,"T-Test,Chi-Square,Fisher's Exact Test",0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,increased,NA,increased,Signature 2,FIGURE 4,26 July 2023,Andre,"Andre,ChiomaBlessing,WikiWorks",Comparison of Gut Microbiota Between Proximal Colon Cancer and Distal Colorectal Cancer based on Principal component analysis (PCA) scores (97% similarity level),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171552|838;3384194|508458|649775|649776|3029088|638847|1943581;1783272|1239|909932|909929|1843491|970,Complete,Lwaldron
bsdb:25710027/1/1,25710027,time series / longitudinal observational,25710027,10.1155/2015/806248,NA,"Damms-Machado A., Mitra S., Schollenberger A.E., Kramer K.M., Meile T., Königsrainer A., Huson D.H. , Bischoff S.C.",Effects of surgical and dietary weight loss therapy for obesity on gut microbiota composition and nutrient absorption,BioMed research international,2015,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Laparoscopic sleeve gastrectomy after 3 months and 6 months combined,Laparoscopic sleeve gastrectomy baseline,NA,3,3,3 months,WMS,NA,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S1A,10 January 2021,Marianthi Thomatos,WikiWorks,Effects of laparoscopic sleeve gastrectomy (LSG) and very low calorie diet (VLCD) for obesity on gut microbiota composition,increased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 3_1_40A,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. L2-50,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena",1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|186802|541000;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|815|816|469593;1783272|1239|186801|186802|31979|1485|411489;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|189330|88431,Complete,Shaimaa Elsafoury
bsdb:25710027/2/1,25710027,time series / longitudinal observational,25710027,10.1155/2015/806248,NA,"Damms-Machado A., Mitra S., Schollenberger A.E., Kramer K.M., Meile T., Königsrainer A., Huson D.H. , Bischoff S.C.",Effects of surgical and dietary weight loss therapy for obesity on gut microbiota composition and nutrient absorption,BioMed research international,2015,NA,Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,very low calorie diet after 3 months and 6 months,Very low calorie diet baseline,NA,3,3,3 months,WMS,NA,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S1B,10 January 2021,Marianthi Thomatos,"Fatima,WikiWorks",Effects of laparoscopic sleeve gastrectomy (LSG) and very low calorie diet (VLCD) for obesity on gut microbiota composition,decreased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hydrogenotrophica,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. D5,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. M62/1,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium limosum,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora saccharolytica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis",1783272|1239|91061;1783272|1239|186801|3085636|186803|572511|53443;1783272|1239|186801|186802|31979|1485|556261;1783272|1239|186801|186802|31979|1485|411486;1783272|1239|526524|526525|2810280|100883;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|81852|1350|1352;1783272|1239|186801|186802|186806|1730|1736;3384189|32066;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|3085636|186803|2719231|84030;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|186802|541000;1783272|1239|186801|3082720|186804;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|2941495|1512;1783272|1239|526524|526525|2810280|100883|100884,Complete,Fatima
bsdb:25758642/1/1,25758642,"cross-sectional observational, not case-control",25758642,10.1038/ncomms7528,NA,"Feng Q., Liang S., Jia H., Stadlmayr A., Tang L., Lan Z., Zhang D., Xia H., Xu X., Jie Z., Su L., Li X., Li X., Li J., Xiao L., Huber-Schönauer U., Niederseer D., Xu X., Al-Aama J.Y., Yang H., Wang J., Kristiansen K., Arumugam M., Tilg H., Datz C. , Wang J.",Gut microbiome development along the colorectal adenoma-carcinoma sequence,Nature communications,2015,NA,Experiment 1,Austria,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,Healthy Controls,Advanced Colorectal Adenoma,"colorectal adenoma patients

The study was conducted both in participants of a health screening programme according to national screening recommendations for CRC49 as well as in patients with suspected CRC undergoing colonoscopy as part of the clinical workup at the Department of Internal Medicine,
Oberndorf Hospital.",55,42,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4a,14 June 2022,Jeshudy,"Jeshudy,WikiWorks",Control versus advanced adenoma (n = 55 and 42).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis",3379134|976|200643|171549|171552|577309|454154;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|204516,Complete,Fatima
bsdb:25758642/1/2,25758642,"cross-sectional observational, not case-control",25758642,10.1038/ncomms7528,NA,"Feng Q., Liang S., Jia H., Stadlmayr A., Tang L., Lan Z., Zhang D., Xia H., Xu X., Jie Z., Su L., Li X., Li X., Li J., Xiao L., Huber-Schönauer U., Niederseer D., Xu X., Al-Aama J.Y., Yang H., Wang J., Kristiansen K., Arumugam M., Tilg H., Datz C. , Wang J.",Gut microbiome development along the colorectal adenoma-carcinoma sequence,Nature communications,2015,NA,Experiment 1,Austria,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,Healthy Controls,Advanced Colorectal Adenoma,"colorectal adenoma patients

The study was conducted both in participants of a health screening programme according to national screening recommendations for CRC49 as well as in patients with suspected CRC undergoing colonoscopy as part of the clinical workup at the Department of Internal Medicine,
Oberndorf Hospital.",55,42,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4a,14 June 2022,Jeshudy,"Jeshudy,WikiWorks",Control versus advanced adenoma (n = 55 and 42).,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans",1783272|201174|1760|85004|31953|1678|28025;1783272|1239|91061|186826|1300|1301|1309,Complete,Fatima
bsdb:25758642/2/1,25758642,"cross-sectional observational, not case-control",25758642,10.1038/ncomms7528,NA,"Feng Q., Liang S., Jia H., Stadlmayr A., Tang L., Lan Z., Zhang D., Xia H., Xu X., Jie Z., Su L., Li X., Li X., Li J., Xiao L., Huber-Schönauer U., Niederseer D., Xu X., Al-Aama J.Y., Yang H., Wang J., Kristiansen K., Arumugam M., Tilg H., Datz C. , Wang J.",Gut microbiome development along the colorectal adenoma-carcinoma sequence,Nature communications,2015,NA,Experiment 2,Austria,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Controls,Colorectal Cancer,"colorectal cancer patients

The study was conducted both in participants of a health screening programme according to national screening recommendations for CRC49 as well as in patients with suspected CRC undergoing colonoscopy as part of the clinical workup at the Department of Internal Medicine,
Oberndorf Hospital.",55,41,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure 4c,14 June 2022,Jeshudy,"Jeshudy,WikiWorks","Control versus carcinoma (n = 55 and 41). For all MLGs containing >100 genes, the direction of enrichment was determined by Wilcoxon rank-sum test (P < 0.05, Supplementary Data 3). Size of the nodes scales with the number of genes (102~3613) in the MLG.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces viscosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis",1783272|201174|1760|2037|2049|1654|1656;1783272|1239|186801|186802|31979|1485|1506;1783272|1239|91061|186826|1300|1301|1309;1783272|1239|91061|186826|1300|1301|1308;1783272|201174|1760|85004|31953|1678|28025,Complete,Fatima
bsdb:25758642/2/2,25758642,"cross-sectional observational, not case-control",25758642,10.1038/ncomms7528,NA,"Feng Q., Liang S., Jia H., Stadlmayr A., Tang L., Lan Z., Zhang D., Xia H., Xu X., Jie Z., Su L., Li X., Li X., Li J., Xiao L., Huber-Schönauer U., Niederseer D., Xu X., Al-Aama J.Y., Yang H., Wang J., Kristiansen K., Arumugam M., Tilg H., Datz C. , Wang J.",Gut microbiome development along the colorectal adenoma-carcinoma sequence,Nature communications,2015,NA,Experiment 2,Austria,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Controls,Colorectal Cancer,"colorectal cancer patients

The study was conducted both in participants of a health screening programme according to national screening recommendations for CRC49 as well as in patients with suspected CRC undergoing colonoscopy as part of the clinical workup at the Department of Internal Medicine,
Oberndorf Hospital.",55,41,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Figure 4c,14 June 2022,Jeshudy,"Jeshudy,WikiWorks","Control versus carcinoma (n = 55 and 41). For all MLGs containing >100 genes, the direction of enrichment was determined by Wilcoxon rank-sum test (P < 0.05, Supplementary Data 3). Size of the nodes scales with the number of genes (102~3613) in the MLG.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica",3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|816|29523;3379134|976|200643|171549|815|816|28111;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|815|909656|204516;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|816|371601;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|1853231|283168|28118;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|3085636|186803|1898203;1783272|1239|186801|3085636|186803|2941495|1512;3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|171552|577309|454154;3379134|1224|28216|80840|1891238;3379134|1224|28216|80840|995019|40544|40545;3379134|1224|1236|91347|543|561|562;1783272|1239|909932|1843488|909930|904|187327;1783272|1239|909932|1843489|31977|29465|39777,Complete,Fatima
bsdb:25758642/3/1,25758642,"cross-sectional observational, not case-control",25758642,10.1038/ncomms7528,NA,"Feng Q., Liang S., Jia H., Stadlmayr A., Tang L., Lan Z., Zhang D., Xia H., Xu X., Jie Z., Su L., Li X., Li X., Li J., Xiao L., Huber-Schönauer U., Niederseer D., Xu X., Al-Aama J.Y., Yang H., Wang J., Kristiansen K., Arumugam M., Tilg H., Datz C. , Wang J.",Gut microbiome development along the colorectal adenoma-carcinoma sequence,Nature communications,2015,NA,Experiment 3,Austria,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Advanced Colorectal Adenoma,Colorectal Cancer,"colorectal adenoma patients

The study was conducted both in participants of a health screening programme according to national screening recommendations for CRC49 as well as in patients with suspected CRC undergoing colonoscopy as part of the clinical workup at the Department of Internal Medicine,
Oberndorf Hospital.",42,41,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure 4b,14 June 2022,Jeshudy,"Jeshudy,WikiWorks","Advanced adenoma vs carcinoma (n = 42, 41).",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces viscosus",1783272|1239|186801|186802|31979|1485|1506;1783272|1239|91061|186826|1300|1301|1308;1783272|201174|1760|85004|31953|1678|28025;1783272|201174|1760|2037|2049|1654|1656,Complete,Fatima
bsdb:25758642/3/2,25758642,"cross-sectional observational, not case-control",25758642,10.1038/ncomms7528,NA,"Feng Q., Liang S., Jia H., Stadlmayr A., Tang L., Lan Z., Zhang D., Xia H., Xu X., Jie Z., Su L., Li X., Li X., Li J., Xiao L., Huber-Schönauer U., Niederseer D., Xu X., Al-Aama J.Y., Yang H., Wang J., Kristiansen K., Arumugam M., Tilg H., Datz C. , Wang J.",Gut microbiome development along the colorectal adenoma-carcinoma sequence,Nature communications,2015,NA,Experiment 3,Austria,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Advanced Colorectal Adenoma,Colorectal Cancer,"colorectal adenoma patients

The study was conducted both in participants of a health screening programme according to national screening recommendations for CRC49 as well as in patients with suspected CRC undergoing colonoscopy as part of the clinical workup at the Department of Internal Medicine,
Oberndorf Hospital.",42,41,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Figure 4b,14 June 2022,Jeshudy,"Jeshudy,WikiWorks","Advanced adenoma vs carcinoma (n = 42, 41).",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica",3379134|976|200643|171549|815|816|371601;3379134|976|200643|171549|815|909656|204516;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|29523;3379134|976|200643|171549|1853231|283168|28118;3379134|200940|3031449|213115|194924|35832|35833;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|171550|239759|28117;3379134|1224|28216|80840|1891238;1783272|1239|186801|3085636|186803|1898203;1783272|1239|186801|3085636|186803|2941495|1512;1783272|1239|909932|1843488|909930|904|187327;3379134|1224|1236|91347|543|561|562;3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|28111;3379134|1224|28216|80840|995019|40544|40545;1783272|1239|909932|1843489|31977|29465|39777,Complete,Fatima
bsdb:25761741/1/1,25761741,"cross-sectional observational, not case-control",25761741,10.1007/s10096-015-2355-4,NA,"Murugesan S., Ulloa-Martínez M., Martínez-Rojano H., Galván-Rodríguez F.M., Miranda-Brito C., Romano M.C., Piña-Escobedo A., Pizano-Zárate M.L., Hoyo-Vadillo C. , García-Mena J.",Study of the diversity and short-chain fatty acids production by the bacterial community in overweight and obese Mexican children,European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology,2015,NA,Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight,obese,"Unrelated children, 9–11 years old",81,80,3 months,16S,3,Ion Torrent,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Mst Afroza Parvin,WikiWorks,"Relative abundance of particular bacteria in normal, overweight, and obese Mexican children.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp.",1783272|1239|186801|186802|216572|216851|1971605;1783272|1239|186801|3085636|186803|572511|1955243;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|33042|2049024;3379134|1224|1236|91347|543;1783272|1239|186801|3085636|186803|841|2049040,Complete,NA
bsdb:25761741/1/2,25761741,"cross-sectional observational, not case-control",25761741,10.1007/s10096-015-2355-4,NA,"Murugesan S., Ulloa-Martínez M., Martínez-Rojano H., Galván-Rodríguez F.M., Miranda-Brito C., Romano M.C., Piña-Escobedo A., Pizano-Zárate M.L., Hoyo-Vadillo C. , García-Mena J.",Study of the diversity and short-chain fatty acids production by the bacterial community in overweight and obese Mexican children,European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology,2015,NA,Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight,obese,"Unrelated children, 9–11 years old",81,80,3 months,16S,3,Ion Torrent,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,10 January 2021,Mst Afroza Parvin,WikiWorks,"Relative abundance of particular bacteria in normal, overweight, and obese Mexican children.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio|s__Succinivibrio sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia|s__Erwinia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",3379134|1224|1236|135624|83763|83770|2053619;3379134|1224|1236|91347|1903409|551|558;1783272|1239|186801|186802|216572|119852,Complete,NA
bsdb:25763184/1/1,25763184,"cross-sectional observational, not case-control",25763184,10.1186/s40168-015-0072-y,NA,"Ross M.C., Muzny D.M., McCormick J.B., Gibbs R.A., Fisher-Hoch S.P. , Petrosino J.F.",16S gut community of the Cameron County Hispanic Cohort,Microbiome,2015,NA,Experiment 1,United States-Mexico Border,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Human Microbiome Project samples,Cameron County Hispanic Cohort samples,NA,213,63,NA,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.02,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,10 January 2021,Marianthi Thomatos,WikiWorks,Relative abundance comparision between Cameron County Hispanic Cohort (CCHC) and Human microbiome project (HMP) subject stool samples,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",1783272|1239;1783272|201174;1783272|1239|186801|3085636|186803;1783272|1239|909932|1843489|31977;1783272|201174|84998|84999|84107;1783272|1239|186801|186802|541000;3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|838;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|841;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|39948,Complete,Shaimaa Elsafoury
bsdb:25763184/1/2,25763184,"cross-sectional observational, not case-control",25763184,10.1186/s40168-015-0072-y,NA,"Ross M.C., Muzny D.M., McCormick J.B., Gibbs R.A., Fisher-Hoch S.P. , Petrosino J.F.",16S gut community of the Cameron County Hispanic Cohort,Microbiome,2015,NA,Experiment 1,United States-Mexico Border,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Human Microbiome Project samples,Cameron County Hispanic Cohort samples,NA,213,63,NA,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.02,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,10 January 2021,Marianthi Thomatos,WikiWorks,Relative abundance comparision between Cameron County Hispanic Cohort (CCHC) and Human microbiome project (HMP) subject stool samples,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",3379134|976;3379134|976|200643|171549|815;3379134|976|200643|171549|171550;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171550|239759,Complete,Shaimaa Elsafoury
bsdb:25764541/1/1,25764541,case-control,25764541,10.1093/femsec/fiu002,NA,"Michail S., Lin M., Frey M.R., Fanter R., Paliy O., Hilbush B. , Reo N.V.",Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease,FEMS microbiology ecology,2015,"NASH, carbohydrate, energy metabolism, gut microbiome, obesity",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,healthy controls,obese without non-alcoholic fatty liver disease,clinical diagnosis of NAFLD based on ultrasound findings and elevated transaminases.  BMI for obese children with and without clinical NAFLD were greater than the 95% for age,26,11,6 months,16S,NA,Ion Torrent,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Marianthi Thomatos,WikiWorks,Altered gut microbial energy and metabolism in children withi non-alcoholic fatty liver disease,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Actinomycetota",3379134|1224|1236;1783272|201174,Complete,Shaimaa Elsafoury
bsdb:25764541/1/2,25764541,case-control,25764541,10.1093/femsec/fiu002,NA,"Michail S., Lin M., Frey M.R., Fanter R., Paliy O., Hilbush B. , Reo N.V.",Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease,FEMS microbiology ecology,2015,"NASH, carbohydrate, energy metabolism, gut microbiome, obesity",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,healthy controls,obese without non-alcoholic fatty liver disease,clinical diagnosis of NAFLD based on ultrasound findings and elevated transaminases.  BMI for obese children with and without clinical NAFLD were greater than the 95% for age,26,11,6 months,16S,NA,Ion Torrent,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,10 January 2021,Marianthi Thomatos,WikiWorks,Altered gut microbial energy and metabolism in children withi non-alcoholic fatty liver disease,decreased,k__Bacillati|p__Bacillota|c__Clostridia,1783272|1239|186801,Complete,Shaimaa Elsafoury
bsdb:25764541/2/1,25764541,case-control,25764541,10.1093/femsec/fiu002,NA,"Michail S., Lin M., Frey M.R., Fanter R., Paliy O., Hilbush B. , Reo N.V.",Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease,FEMS microbiology ecology,2015,"NASH, carbohydrate, energy metabolism, gut microbiome, obesity",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,healthy controls,non-alcoholic fatty liver disease patients,clinical diagnosis of NAFLD based on ultrasound findings and elevated transaminases.  BMI for obese children with and without clinical NAFLD were greater than the 95% for age,26,13,6 months,16S,NA,Ion Torrent,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Marianthi Thomatos,WikiWorks,Altered gut microbial energy and metabolism in children withi non-alcoholic fatty liver disease (NAFLD),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Pseudomonadati|p__Campylobacterota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria",1783272|201174|1760;3379134|976|200643|171549|171552|838;3384189|32066|203490;3379134|29547;3379134|1224|1236,Complete,Shaimaa Elsafoury
bsdb:25764541/2/2,25764541,case-control,25764541,10.1093/femsec/fiu002,NA,"Michail S., Lin M., Frey M.R., Fanter R., Paliy O., Hilbush B. , Reo N.V.",Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease,FEMS microbiology ecology,2015,"NASH, carbohydrate, energy metabolism, gut microbiome, obesity",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,healthy controls,non-alcoholic fatty liver disease patients,clinical diagnosis of NAFLD based on ultrasound findings and elevated transaminases.  BMI for obese children with and without clinical NAFLD were greater than the 95% for age,26,13,6 months,16S,NA,Ion Torrent,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,10 January 2021,Marianthi Thomatos,WikiWorks,Altered gut microbial energy and metabolism in children withi non-alcoholic fatty liver disease (NAFLD),decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria",1783272|1239|526524;3379134|1224|28211,Complete,Shaimaa Elsafoury
bsdb:25764541/3/1,25764541,case-control,25764541,10.1093/femsec/fiu002,NA,"Michail S., Lin M., Frey M.R., Fanter R., Paliy O., Hilbush B. , Reo N.V.",Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease,FEMS microbiology ecology,2015,"NASH, carbohydrate, energy metabolism, gut microbiome, obesity",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,obese without non-alcoholic fatty liver disease,non-alcoholic fatty liver disease patients,clinical diagnosis of NAFLD based on ultrasound findings and elevated transaminases.  BMI for obese children with and without clinical NAFLD were greater than the 95% for age,11,13,6 months,16S,NA,Ion Torrent,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Altered gut microbial energy and metabolism in children withi non-alcoholic fatty liver disease (NAFLD),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Pseudomonadati|p__Campylobacterota",1783272|201174|1760;3379134|976|200643|171549|171552|838;3384189|32066|203490;3379134|29547,Complete,Shaimaa Elsafoury
bsdb:25764541/3/2,25764541,case-control,25764541,10.1093/femsec/fiu002,NA,"Michail S., Lin M., Frey M.R., Fanter R., Paliy O., Hilbush B. , Reo N.V.",Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease,FEMS microbiology ecology,2015,"NASH, carbohydrate, energy metabolism, gut microbiome, obesity",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,obese without non-alcoholic fatty liver disease,non-alcoholic fatty liver disease patients,clinical diagnosis of NAFLD based on ultrasound findings and elevated transaminases.  BMI for obese children with and without clinical NAFLD were greater than the 95% for age,11,13,6 months,16S,NA,Ion Torrent,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Altered gut microbial energy and metabolism in children withi non-alcoholic fatty liver disease (NAFLD),decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria",1783272|1239|526524;3379134|1224|28211;3379134|1224|1236,Complete,Shaimaa Elsafoury
bsdb:25766736/1/1,25766736,prospective cohort,25766736,10.1093/jac/dkv062,NA,"Vervoort J., Xavier B.B., Stewardson A., Coenen S., Godycki-Cwirko M., Adriaenssens N., Kowalczyk A., Lammens C., Harbarth S., Goossens H. , Malhotra-Kumar S.",Metagenomic analysis of the impact of nitrofurantoin treatment on the human faecal microbiota,The Journal of antimicrobial chemotherapy,2015,"16S rDNA, 16S rRNA, antibiotic resistance, compositional changes, culture independent, faecal flora, gastrointestinal flora, stool, urinary tract infections",Experiment 1,"Belgium,Poland",Homo sapiens,Feces,UBERON:0001988,Urinary tract infection,EFO:0003103,Control group,Antibiotic treated - T2,Receiving nitrofurantoin treatment (100 mg three times daily for 3–15 days),5,8,2 months,16S,345,Roche454,raw counts,Linear Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,11 December 2021,Mmarin,"Mmarin,WikiWorks","changes in mean proportions of 16S rDNA reads assigned to different phyla from baseline and between study groups. T1, day 1; T2, days 5–15; T3, days 31–43.
Bold type indicates a statistically significant difference (P<0.05); generalized linear mixed model.",decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Peace Sandy
bsdb:25766736/2/1,25766736,prospective cohort,25766736,10.1093/jac/dkv062,NA,"Vervoort J., Xavier B.B., Stewardson A., Coenen S., Godycki-Cwirko M., Adriaenssens N., Kowalczyk A., Lammens C., Harbarth S., Goossens H. , Malhotra-Kumar S.",Metagenomic analysis of the impact of nitrofurantoin treatment on the human faecal microbiota,The Journal of antimicrobial chemotherapy,2015,"16S rDNA, 16S rRNA, antibiotic resistance, compositional changes, culture independent, faecal flora, gastrointestinal flora, stool, urinary tract infections",Experiment 2,"Belgium,Poland",Homo sapiens,Feces,UBERON:0001988,Urinary tract infection,EFO:0003103,Antibiotic treated (day 1),Antibiotic treated (day 5-15),Receiving nitrofurantoin treatment (100 mg three times daily for 3–15 days),8,8,2 months,16S,345,Roche454,raw counts,Linear Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,14 January 2022,Mmarin,"Mmarin,Peace Sandy,WikiWorks","changes in mean proportions of 16S rDNA reads assigned to different phyla from baseline and between study groups. T1, day 1; T2, days 5–15; T3, days 31–43. Bold type indicates a statistically significant difference (P<0.05); generalized linear mixed model.",increased,k__Bacillati|p__Actinomycetota,1783272|201174,Complete,Peace Sandy
bsdb:25766736/3/1,25766736,prospective cohort,25766736,10.1093/jac/dkv062,NA,"Vervoort J., Xavier B.B., Stewardson A., Coenen S., Godycki-Cwirko M., Adriaenssens N., Kowalczyk A., Lammens C., Harbarth S., Goossens H. , Malhotra-Kumar S.",Metagenomic analysis of the impact of nitrofurantoin treatment on the human faecal microbiota,The Journal of antimicrobial chemotherapy,2015,"16S rDNA, 16S rRNA, antibiotic resistance, compositional changes, culture independent, faecal flora, gastrointestinal flora, stool, urinary tract infections",Experiment 3,"Belgium,Poland",Homo sapiens,Feces,UBERON:0001988,Urinary tract infection,EFO:0003103,Control (day 1),Control (day 5-15),Did not receive nitrofurantoin treatment,5,5,2 months,16S,345,Roche454,raw counts,Linear Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,14 January 2022,Mmarin,"Mmarin,Peace Sandy,WikiWorks","changes in mean proportions of 16S rDNA reads assigned to different phyla from baseline and between study groups. T1, day 1; T2, days 5–15; T3, days 31–43. Bold type indicates a statistically significant difference (P<0.05); generalized linear mixed model.",increased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Peace Sandy
bsdb:25784074/1/1,25784074,case-control,25784074,10.1007/s10620-015-3607-y,NA,"Shukla R., Ghoshal U., Dhole T.N. , Ghoshal U.C.",Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis,Digestive diseases and sciences,2015,"Dysbiosis, Functional gastrointestinal disorder, Gastrointestinal microbiota, Quantitative real-time polymerase chain reaction",Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS,"Patients with IBS diagnosed using Rome III. Patients were classified into three sub-types
using Rome III criteria: constipation predominant IBS (IBS-C), diarrhea predominant (IBS-D), and un-subtyped (IBS-U). All participants.",30,47,1 month,16S,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3.,28 June 2021,Kwekuamoo,"Kwekuamoo,MyleeeA,WikiWorks",Relative difference in 16S rRNA copy number of fecal bacteria between patients with IBS and healthy controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511|1532;1783272|1239|186801|3085636|186803|572511|33035;3379134|1224|1236|72274|135621|286|287;1783272|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:25784074/1/2,25784074,case-control,25784074,10.1007/s10620-015-3607-y,NA,"Shukla R., Ghoshal U., Dhole T.N. , Ghoshal U.C.",Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis,Digestive diseases and sciences,2015,"Dysbiosis, Functional gastrointestinal disorder, Gastrointestinal microbiota, Quantitative real-time polymerase chain reaction",Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS,"Patients with IBS diagnosed using Rome III. Patients were classified into three sub-types
using Rome III criteria: constipation predominant IBS (IBS-C), diarrhea predominant (IBS-D), and un-subtyped (IBS-U). All participants.",30,47,1 month,16S,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3.,18 July 2021,Kwekuamoo,"Kwekuamoo,WikiWorks",Relative difference in 16S rRNA copy number of fecal bacteria between patients with IBS and healthy controls,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Folakunmi
bsdb:25784074/2/1,25784074,case-control,25784074,10.1007/s10620-015-3607-y,NA,"Shukla R., Ghoshal U., Dhole T.N. , Ghoshal U.C.",Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis,Digestive diseases and sciences,2015,"Dysbiosis, Functional gastrointestinal disorder, Gastrointestinal microbiota, Quantitative real-time polymerase chain reaction",Experiment 2,India,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Health Control,IBS-C,"Patients with IBS diagnosed using Rome III. Patients were classified into three sub-types
using Rome III criteria: constipation predominant IBS (IBS-C).",30,20,1 month,16S,NA,RT-qPCR,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4.,18 July 2021,Kwekuamoo,"Kwekuamoo,MyleeeA,WikiWorks",Relative difference in 16S rRNA copy number of fecal bacteria in subgroups of patients with IBS-C and healthy controls.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511|1532;1783272|1239|186801|3085636|186803|572511|33035;1783272|1239|91061|186826|33958|1578;3379134|1224|1236|72274|135621|286|287;1783272|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:25784074/2/2,25784074,case-control,25784074,10.1007/s10620-015-3607-y,NA,"Shukla R., Ghoshal U., Dhole T.N. , Ghoshal U.C.",Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis,Digestive diseases and sciences,2015,"Dysbiosis, Functional gastrointestinal disorder, Gastrointestinal microbiota, Quantitative real-time polymerase chain reaction",Experiment 2,India,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Health Control,IBS-C,"Patients with IBS diagnosed using Rome III. Patients were classified into three sub-types
using Rome III criteria: constipation predominant IBS (IBS-C).",30,20,1 month,16S,NA,RT-qPCR,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 4.,18 July 2021,Kwekuamoo,"Kwekuamoo,MyleeeA,WikiWorks",Relative difference in 16S rRNA copy number of fecal bacteria in subgroups of patients with IBS-C and healthy controls.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,1783272|201174|1760|85004|31953|1678|1686,Complete,Folakunmi
bsdb:25784074/3/1,25784074,case-control,25784074,10.1007/s10620-015-3607-y,NA,"Shukla R., Ghoshal U., Dhole T.N. , Ghoshal U.C.",Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis,Digestive diseases and sciences,2015,"Dysbiosis, Functional gastrointestinal disorder, Gastrointestinal microbiota, Quantitative real-time polymerase chain reaction",Experiment 3,India,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Health Control,IBS-D,"Patients with IBS diagnosed using Rome III. Patients were classified into three sub-types
using Rome III criteria: diarrhea predominant IBS (IBS-D).",30,20,1 month,16S,NA,RT-qPCR,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4.,18 July 2021,Kwekuamoo,"Kwekuamoo,MyleeeA,WikiWorks",Relative difference in 16S rRNA copy number of fecal bacteria in subgroups of patients with IBS-D and healthy controls.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus|s__Candidatus Arthromitus sp. SFB-mouse,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979|49082|49118;3379134|1224|1236|72274|135621|286|287,Complete,Folakunmi
bsdb:25784074/3/2,25784074,case-control,25784074,10.1007/s10620-015-3607-y,NA,"Shukla R., Ghoshal U., Dhole T.N. , Ghoshal U.C.",Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis,Digestive diseases and sciences,2015,"Dysbiosis, Functional gastrointestinal disorder, Gastrointestinal microbiota, Quantitative real-time polymerase chain reaction",Experiment 3,India,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Health Control,IBS-D,"Patients with IBS diagnosed using Rome III. Patients were classified into three sub-types
using Rome III criteria: diarrhea predominant IBS (IBS-D).",30,20,1 month,16S,NA,RT-qPCR,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 4.,18 July 2021,Kwekuamoo,"Kwekuamoo,MyleeeA,WikiWorks",Relative difference in 16S rRNA copy number of fecal bacteria in subgroups of patients with IBS-D and healthy controls.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|201174|1760|85004|31953|1678|1686;1783272|1239|91061|186826|33958|1578,Complete,Folakunmi
bsdb:25784074/4/NA,25784074,case-control,25784074,10.1007/s10620-015-3607-y,NA,"Shukla R., Ghoshal U., Dhole T.N. , Ghoshal U.C.",Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis,Digestive diseases and sciences,2015,"Dysbiosis, Functional gastrointestinal disorder, Gastrointestinal microbiota, Quantitative real-time polymerase chain reaction",Experiment 4,India,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Health Control,IBS-U,Patients with IBS diagnosed using Rome III. Patients were classified into sub-types: un-subtyped (IBS-U).,30,7,1 month,16S,NA,RT-qPCR,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:25784074/5/1,25784074,case-control,25784074,10.1007/s10620-015-3607-y,NA,"Shukla R., Ghoshal U., Dhole T.N. , Ghoshal U.C.",Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis,Digestive diseases and sciences,2015,"Dysbiosis, Functional gastrointestinal disorder, Gastrointestinal microbiota, Quantitative real-time polymerase chain reaction",Experiment 5,India,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,"Irritable Bowel Syndrome, diarrhea predominant (IBS-D)","Irritable Bowel Syndrome, constipation predominant (IBS-C)",Patients were classified into three sub-types using Rome III criteria: diarrhea predominant IBS (IBS-D).,20,20,1 month,16S,NA,RT-qPCR,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,16 November 2023,MyleeeA,"MyleeeA,Folakunmi,WikiWorks",Relative difference in 16S rRNA copy number of fecal bacteria in subgroups of patients with IBS-C and IBS-D,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Folakunmi
bsdb:25784074/5/2,25784074,case-control,25784074,10.1007/s10620-015-3607-y,NA,"Shukla R., Ghoshal U., Dhole T.N. , Ghoshal U.C.",Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis,Digestive diseases and sciences,2015,"Dysbiosis, Functional gastrointestinal disorder, Gastrointestinal microbiota, Quantitative real-time polymerase chain reaction",Experiment 5,India,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,"Irritable Bowel Syndrome, diarrhea predominant (IBS-D)","Irritable Bowel Syndrome, constipation predominant (IBS-C)",Patients were classified into three sub-types using Rome III criteria: diarrhea predominant IBS (IBS-D).,20,20,1 month,16S,NA,RT-qPCR,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 4,9 February 2024,Folakunmi,"Folakunmi,WikiWorks",Relative difference in 16S rRNA copy number of fecal bacteria in subgroups of patients with IBS-C and IBS-D,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus|s__Candidatus Arthromitus sp. SFB-mouse",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979|49082|49118,Complete,Folakunmi
bsdb:25784074/6/1,25784074,case-control,25784074,10.1007/s10620-015-3607-y,NA,"Shukla R., Ghoshal U., Dhole T.N. , Ghoshal U.C.",Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis,Digestive diseases and sciences,2015,"Dysbiosis, Functional gastrointestinal disorder, Gastrointestinal microbiota, Quantitative real-time polymerase chain reaction",Experiment 6,India,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,No Visible abdominal distension,Visible abdominal distension,Patients with IBS showing Visible abdominal distension as symptoms,13,34,1 month,16S,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 5,16 November 2023,MyleeeA,"MyleeeA,WikiWorks",Association of IBS symptoms in relation to bacterial load,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus|s__Candidatus Arthromitus sp. SFB-mouse,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron",1783272|1239|186801|3085636|186803|572511|1532;1783272|1239|186801|186802|31979|49082|49118;3379134|1224|1236|72274|135621|286|287;3379134|976|200643|171549|815|816|818,Complete,Folakunmi
bsdb:25784074/7/1,25784074,case-control,25784074,10.1007/s10620-015-3607-y,NA,"Shukla R., Ghoshal U., Dhole T.N. , Ghoshal U.C.",Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis,Digestive diseases and sciences,2015,"Dysbiosis, Functional gastrointestinal disorder, Gastrointestinal microbiota, Quantitative real-time polymerase chain reaction",Experiment 7,India,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,No Abdominal Bloating,Abdominal Bloating,Patients with IBS showing Abdominal Bloating/Abdominal discomfort as symptoms,25,22,1 month,16S,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 5,16 November 2023,MyleeeA,"MyleeeA,WikiWorks",Association of IBS symptoms in relation to bacterial load,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,1783272|1239|186801|3085636|186803|572511|1532,Complete,Folakunmi
bsdb:25882912/1/1,25882912,case-control,25882912,10.1016/j.bbi.2015.03.016,NA,"Jiang H., Ling Z., Zhang Y., Mao H., Ma Z., Yin Y., Wang W., Tang W., Tan Z., Shi J., Li L. , Ruan B.",Altered fecal microbiota composition in patients with major depressive disorder,"Brain, behavior, and immunity",2015,"Antidepressant, Depression, Gut bacteria, Gut–brain, Inflammation",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,Healthy Controls,Active Major Depressive Disorder,The A-MDD group was defined as having an HAMDS score P20. The patients in the R-MDD group were defined as those with a baseline HAMDS scores P20 upon admission to the hospi- tal.,30,29,1 month,16S,123,Roche454,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,unchanged,NA,unchanged,Signature 1,Figure 2,10 January 2021,Fatima Zohra,WikiWorks,Taxonomic differences of fecal microbiota between Healthy Controls and Active Major Depressive Disorder groups,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",1783272|1239|186801|186802|216572|946234;3379134|976|200643|171549|1853231|574697;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550,Complete,Shaimaa Elsafoury
bsdb:25882912/1/2,25882912,case-control,25882912,10.1016/j.bbi.2015.03.016,NA,"Jiang H., Ling Z., Zhang Y., Mao H., Ma Z., Yin Y., Wang W., Tang W., Tan Z., Shi J., Li L. , Ruan B.",Altered fecal microbiota composition in patients with major depressive disorder,"Brain, behavior, and immunity",2015,"Antidepressant, Depression, Gut bacteria, Gut–brain, Inflammation",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,Healthy Controls,Active Major Depressive Disorder,The A-MDD group was defined as having an HAMDS score P20. The patients in the R-MDD group were defined as those with a baseline HAMDS scores P20 upon admission to the hospi- tal.,30,29,1 month,16S,123,Roche454,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,unchanged,NA,unchanged,Signature 2,Figure 2,10 January 2021,Fatima Zohra,WikiWorks,Taxonomic differences of fecal microbiota between Healthy Controls and Active Major Depressive Disorder groups,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella",1783272|1239|186801|186802|541000;1783272|1239|186801|186802|216572|216851;1783272|1239|909932|1843489|31977|39948;3379134|1224|1236|135625|712;3379134|1224|1236|135625;1783272|1239|186801|186802|216572|1263;3379134|1224|1236|135625|712|724;1783272|1239|186801|3082720|186804;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|620,Complete,Shaimaa Elsafoury
bsdb:25882912/2/1,25882912,case-control,25882912,10.1016/j.bbi.2015.03.016,NA,"Jiang H., Ling Z., Zhang Y., Mao H., Ma Z., Yin Y., Wang W., Tang W., Tan Z., Shi J., Li L. , Ruan B.",Altered fecal microbiota composition in patients with major depressive disorder,"Brain, behavior, and immunity",2015,"Antidepressant, Depression, Gut bacteria, Gut–brain, Inflammation",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,Healthy Controls,Responded Major Depressive Disorder,The A-MDD group was defined as having an HAMDS score P20. The patients in the R-MDD group were defined as those with a baseline HAMDS scores P20 upon admission to the hospi- tal.,30,17,1 month,16S,123,Roche454,NA,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 3,10 January 2021,Fatima Zohra,WikiWorks,Taxonomic differences of fecal microbiota between Healthy Controls and Responded Major Depressive Disorder groups,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",3379134|976|200643|171549|1853231|574697;3379134|976|200643|171549|171551,Complete,Shaimaa Elsafoury
bsdb:25882912/2/2,25882912,case-control,25882912,10.1016/j.bbi.2015.03.016,NA,"Jiang H., Ling Z., Zhang Y., Mao H., Ma Z., Yin Y., Wang W., Tang W., Tan Z., Shi J., Li L. , Ruan B.",Altered fecal microbiota composition in patients with major depressive disorder,"Brain, behavior, and immunity",2015,"Antidepressant, Depression, Gut bacteria, Gut–brain, Inflammation",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,Healthy Controls,Responded Major Depressive Disorder,The A-MDD group was defined as having an HAMDS score P20. The patients in the R-MDD group were defined as those with a baseline HAMDS scores P20 upon admission to the hospi- tal.,30,17,1 month,16S,123,Roche454,NA,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 3,10 January 2021,Fatima Zohra,WikiWorks,Taxonomic differences of fecal microbiota between Healthy Controls and Responded Major Depressive Disorder groups,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",1783272|1239|186801|186802|216572|1263;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|1224|1236|135625|712|724;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|31979,Complete,Shaimaa Elsafoury
bsdb:25893458/1/1,25893458,time series / longitudinal observational,25893458,10.1038/bmt.2015.16,NA,"Biagi E., Zama D., Nastasi C., Consolandi C., Fiori J., Rampelli S., Turroni S., Centanni M., Severgnini M., Peano C., de Bellis G., Basaglia G., Gotti R., Masetti R., Pession A., Brigidi P. , Candela M.",Gut microbiota trajectory in pediatric patients undergoing hematopoietic SCT,Bone marrow transplantation,2015,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Graft versus host disease,MONDO:0013730,non-GvHD (Graft-versus-host disease),aGvHD (acute Graft-versus-host disease),pre-HSCT (hematopoietic stem cell transplant) samples of subjects who underwent HSCT who developed acute graft-versus-host disease,5,5,NA,16S,4,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Results (Text): Page 4, 3rd paragraph under sub-heading ""aGvHD-associated gut microbiota signatures.""",10 January 2021,William Lam,"WikiWorks,Chloe,ChiomaBlessing",Gut microbiota signatures in pre-HSCT samples of subjects who developed aGvHD compared to subjects who did not develop aGvHD (non-aGvHD),decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,3379134|976|200643,Complete,ChiomaBlessing
bsdb:25893458/1/2,25893458,time series / longitudinal observational,25893458,10.1038/bmt.2015.16,NA,"Biagi E., Zama D., Nastasi C., Consolandi C., Fiori J., Rampelli S., Turroni S., Centanni M., Severgnini M., Peano C., de Bellis G., Basaglia G., Gotti R., Masetti R., Pession A., Brigidi P. , Candela M.",Gut microbiota trajectory in pediatric patients undergoing hematopoietic SCT,Bone marrow transplantation,2015,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Graft versus host disease,MONDO:0013730,non-GvHD (Graft-versus-host disease),aGvHD (acute Graft-versus-host disease),pre-HSCT (hematopoietic stem cell transplant) samples of subjects who underwent HSCT who developed acute graft-versus-host disease,5,5,NA,16S,4,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Results (Text): Page 4, 3rd paragraph under sub-heading ""aGvHD-associated gut microbiota signatures.""",1 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Gut microbiota signatures in pre-HSCT samples of subjects who developed aGvHD compared to subjects who did not develop aGvHD (non-aGvHD),increased,k__Bacillati|p__Bacillota,1783272|1239,Complete,ChiomaBlessing
bsdb:25922405/1/1,25922405,randomized controlled trial,25922405,10.1093/cid/civ137,NA,"Rashid M.U., Zaura E., Buijs M.J., Keijser B.J., Crielaard W., Nord C.E. , Weintraub A.",Determining the Long-term Effect of Antibiotic Administration on the Human Normal Intestinal Microbiota Using Culture and Pyrosequencing Methods,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2015,"antibiotics, culture, intestinal microbiota, pyrosequencing",Experiment 1,Sweden,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,before ciprofloxacin exposure,after ciprofloxacin exposure,"""healthy"" adults between the ages of 18-45 years old with normal medical histories and physical examinations who were given ciprofloxacin",9,9,3 months,16S,567,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Text (results),10 January 2021,Gina Celentano,"Claregrieve1,WikiWorks",Human normal intestinal microbiota before versus after antibiotic administration,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,Claregrieve1
bsdb:25922405/1/2,25922405,randomized controlled trial,25922405,10.1093/cid/civ137,NA,"Rashid M.U., Zaura E., Buijs M.J., Keijser B.J., Crielaard W., Nord C.E. , Weintraub A.",Determining the Long-term Effect of Antibiotic Administration on the Human Normal Intestinal Microbiota Using Culture and Pyrosequencing Methods,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2015,"antibiotics, culture, intestinal microbiota, pyrosequencing",Experiment 1,Sweden,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,before ciprofloxacin exposure,after ciprofloxacin exposure,"""healthy"" adults between the ages of 18-45 years old with normal medical histories and physical examinations who were given ciprofloxacin",9,9,3 months,16S,567,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,Text (results),10 January 2021,Gina Celentano,"Claregrieve1,WikiWorks",Human normal intestinal microbiota before versus after antibiotic administration,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572,Complete,Claregrieve1
bsdb:25922405/2/1,25922405,randomized controlled trial,25922405,10.1093/cid/civ137,NA,"Rashid M.U., Zaura E., Buijs M.J., Keijser B.J., Crielaard W., Nord C.E. , Weintraub A.",Determining the Long-term Effect of Antibiotic Administration on the Human Normal Intestinal Microbiota Using Culture and Pyrosequencing Methods,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2015,"antibiotics, culture, intestinal microbiota, pyrosequencing",Experiment 2,Sweden,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Before clindamycin exposure,after clindamycin exposure,"""healthy"" adults between the ages of 18-45 years old with normal medical histories and physical examinations who were exporsed to clindamycin",9,9,3 months,16S,567,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Text (results),10 January 2021,Gina Celentano,"Claregrieve1,WikiWorks",Human normal intestinal microbiota before versus after antibiotic administration,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263,Complete,Claregrieve1
bsdb:25944283/1/1,25944283,case-control,25944283,10.1111/cea.12566,NA,"West C.E., Rydén P., Lundin D., Engstrand L., Tulic M.K. , Prescott S.L.",Gut microbiome and innate immune response patterns in IgE-associated eczema,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,2015,"16SrRNA, TLR-ligands, diversity, eczema, hygiene hypothesis, innate immunity, intestinal colonization, microbiota, molecular microbiology",Experiment 1,Australia,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy control,IgE associated eczema,1 week old Infants with typical skin lesions responsive to topical steroids diagnosed with eczema and with severity determined using the SCORAD index,8,6,NA,16S,34,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"delivery procedure,medical procedure",NA,unchanged,unchanged,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Lucy Mellor,WikiWorks,"Relative abundance >1% of dominant phyla, classes, families and genera in stool samples at 1 week of age infants that remained non-allergic (controls) and in infants developing IgE-associated eczema",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,1783272|1239|186801|186802|541000,Complete,Folakunmi
bsdb:25944283/2/1,25944283,case-control,25944283,10.1111/cea.12566,NA,"West C.E., Rydén P., Lundin D., Engstrand L., Tulic M.K. , Prescott S.L.",Gut microbiome and innate immune response patterns in IgE-associated eczema,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,2015,"16SrRNA, TLR-ligands, diversity, eczema, hygiene hypothesis, innate immunity, intestinal colonization, microbiota, molecular microbiology",Experiment 2,Australia,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,mothers whose infants remained non-allergic,Mothers whose infants developed IgE associated eczema,Mothers whose infants developed typical skin lesions responsive to topical steroids diagnosed with eczema and with severity determined using the SCORAD index,10,9,NA,16S,34,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"delivery procedure,medical procedure",NA,unchanged,unchanged,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Lucy Mellor,WikiWorks,"Relative abundance >1% of dominant phyla, classes, families and genera in stool samples of mothers who's infants that remained non-allergic (controls) or infants developed IgE-associated eczema",increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:25944283/3/1,25944283,case-control,25944283,10.1111/cea.12566,NA,"West C.E., Rydén P., Lundin D., Engstrand L., Tulic M.K. , Prescott S.L.",Gut microbiome and innate immune response patterns in IgE-associated eczema,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,2015,"16SrRNA, TLR-ligands, diversity, eczema, hygiene hypothesis, innate immunity, intestinal colonization, microbiota, molecular microbiology",Experiment 3,Australia,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,vaginally delivered infant,caesarean delivered infant,infant born by caesarean section,7,7,NA,16S,34,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 1,"Figure 1a, Text (Effects of delivery mode on gut microbiome establishment )",10 January 2021,Lucy Mellor,"WikiWorks,Folakunmi",Median relative abundances (%) of the most abundant phyla in vaginally delivered infants and caesarean delivered infants at 1 week,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,Folakunmi
bsdb:25944283/3/2,25944283,case-control,25944283,10.1111/cea.12566,NA,"West C.E., Rydén P., Lundin D., Engstrand L., Tulic M.K. , Prescott S.L.",Gut microbiome and innate immune response patterns in IgE-associated eczema,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,2015,"16SrRNA, TLR-ligands, diversity, eczema, hygiene hypothesis, innate immunity, intestinal colonization, microbiota, molecular microbiology",Experiment 3,Australia,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,vaginally delivered infant,caesarean delivered infant,infant born by caesarean section,7,7,NA,16S,34,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 2,"Figure 1a, Text (Effects of delivery mode on gut microbiome establishment )",10 January 2021,Lucy Mellor,"WikiWorks,Folakunmi",Median relative abundances (%) of the most abundant phyla in vaginally delivered infants and caesarean delivered infants at 1 week,decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Folakunmi
bsdb:25970503/1/1,25970503,laboratory experiment,25970503,10.1371/journal.pone.0125448,NA,"Candon S., Perez-Arroyo A., Marquet C., Valette F., Foray A.P., Pelletier B., Milani C., Ventura M., Bach J.F. , Chatenoud L.",Antibiotics in early life alter the gut microbiome and increase disease incidence in a spontaneous mouse model of autoimmune insulin-dependent diabetes,PloS one,2015,NA,Experiment 1,France,Mus musculus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Control group,Vancomycin treated group,Feces samples were collected from 8-week-old mice treated with vancomycin.,13,6,NA,16S,3,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 4a,13 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Variation of bacterial taxa at genus level when mice are treated with vancomycin.,increased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum",1783272|544448|31969|186332|186333|2086;3379134|1224|1236|91347|543|561;1783272|1239|91061|186826|33958|1578;3379134|1224|28216|80840|995019|40544;;3379134|1224|1236|91347|543;3379134|976|200643|171549|2005473;3379134|200930|68337|191393|2945020|248038,Complete,Svetlana up
bsdb:25970503/1/2,25970503,laboratory experiment,25970503,10.1371/journal.pone.0125448,NA,"Candon S., Perez-Arroyo A., Marquet C., Valette F., Foray A.P., Pelletier B., Milani C., Ventura M., Bach J.F. , Chatenoud L.",Antibiotics in early life alter the gut microbiome and increase disease incidence in a spontaneous mouse model of autoimmune insulin-dependent diabetes,PloS one,2015,NA,Experiment 1,France,Mus musculus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Control group,Vancomycin treated group,Feces samples were collected from 8-week-old mice treated with vancomycin.,13,6,NA,16S,3,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 4a,13 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Variation of bacterial taxa at genus level when mice are treated with vancomycin.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|171552|838;3379134|976|200643|171549;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550,Complete,Svetlana up
bsdb:25970503/2/1,25970503,laboratory experiment,25970503,10.1371/journal.pone.0125448,NA,"Candon S., Perez-Arroyo A., Marquet C., Valette F., Foray A.P., Pelletier B., Milani C., Ventura M., Bach J.F. , Chatenoud L.",Antibiotics in early life alter the gut microbiome and increase disease incidence in a spontaneous mouse model of autoimmune insulin-dependent diabetes,PloS one,2015,NA,Experiment 2,France,Mus musculus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Control group,Strep-Col-Amp treated group,"Feces samples were collected from 8-week-old mice treated with streptomycin, colistin and ampicillin.",13,7,NA,16S,3,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 4b,13 February 2025,Aleru Divine,"Aleru Divine,WikiWorks","Variation of bacterial taxa at genus level when mice are treated with streptomycin, colistin and ampicillin.",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;3379134|1224|28216|80840|119060|32008;1783272|1239|909932|1843489|31977|39948;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|1903409|551;3379134|1224|1236|91347|543|561;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|28050;1783272|1239|91061|186826|33958|1578;3379134|1224|28211|356|119045|407;1783272|1239|186801|186802|216572|119852;3379134|1224|28216|80840|2975441|93681;3379134|976|200643|171549|171552|838;1783272|201174|1760|85009|31957|1743;3379134|1224|1236|72274|135621|286;3379134|1224|28216|80840|119060|48736;3379134|1224|28216|80840|995019|40544;;3379134|1224|1236|91347|543;1783272|201174|1760|85006|85023;3379134|1224|28216|80840|75682;3379134|1224|28211|204457|41297,Complete,Svetlana up
bsdb:25970503/2/2,25970503,laboratory experiment,25970503,10.1371/journal.pone.0125448,NA,"Candon S., Perez-Arroyo A., Marquet C., Valette F., Foray A.P., Pelletier B., Milani C., Ventura M., Bach J.F. , Chatenoud L.",Antibiotics in early life alter the gut microbiome and increase disease incidence in a spontaneous mouse model of autoimmune insulin-dependent diabetes,PloS one,2015,NA,Experiment 2,France,Mus musculus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Control group,Strep-Col-Amp treated group,"Feces samples were collected from 8-week-old mice treated with streptomycin, colistin and ampicillin.",13,7,NA,16S,3,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 4b,13 February 2025,Aleru Divine,"Aleru Divine,WikiWorks","Variation of bacterial taxa at genus level when mice are treated with streptomycin, colistin and ampicillin.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",3379134|976|200643|171549|171552|838;3379134|976|200643|171549;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550;3379134|976|200643|171549|2005473,Complete,Svetlana up
bsdb:26062721/1/1,26062721,"cross-sectional observational, not case-control",26062721,10.1017/S0950268815000965,NA,"Dareng E.O., Ma B., Famooto A.O., Adebamowo S.N., Offiong R.A., Olaniyan O., Dakum P.S., Wheeler C.M., Fadrosh D., Yang H., Gajer P., Brotman R.M., Ravel J. , Adebamowo C.A.",Prevalent high-risk HPV infection and vaginal microbiota in Nigerian women,Epidemiology and infection,2016,"HIV/AIDS, human papilloma virus (HPV), public health",Experiment 1,Nigeria,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,HPV-/HIV-,HPV+/HIV-,HR-HPV+ confirmed by medical records and HPV genotyping test,99,12,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 4b,10 January 2021,Cynthia Anderson,"WikiWorks,Atrayees",Identified phylotype biomarkers ranked by effect size in HIV–women,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium|s__Arcanobacterium sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus asaccharolyticus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sp.",1783272|1239|1737404|1737405|1570339|165779|1872515;1783272|201174|1760|2037|2049|28263;1783272|201174|1760|2037|2049|28263|72409;3379134|976|200643|171549;3379134|976|200643;3379134|976;1783272|1239|186801|186802|31979;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|39948|309120;3384189|32066|203490|203491;3384189|32066;3384189|32066|203490|203491|1129771;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843489|31977|906|2023260;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|1737404|1737405|1570339|162289|1258;1783272|1239|1737404|1737405|1570339|162289|1971214;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1257;1783272|1239|186801|3082720|186804|1257|1261;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|59823;3379134|976|200643|171549|171552;3384189|32066|203490|203491|1129771|168808;3384189|32066|203490|203491|1129771|168808|2776143,Complete,Fatima Zohra
bsdb:26062721/1/2,26062721,"cross-sectional observational, not case-control",26062721,10.1017/S0950268815000965,NA,"Dareng E.O., Ma B., Famooto A.O., Adebamowo S.N., Offiong R.A., Olaniyan O., Dakum P.S., Wheeler C.M., Fadrosh D., Yang H., Gajer P., Brotman R.M., Ravel J. , Adebamowo C.A.",Prevalent high-risk HPV infection and vaginal microbiota in Nigerian women,Epidemiology and infection,2016,"HIV/AIDS, human papilloma virus (HPV), public health",Experiment 1,Nigeria,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,HPV-/HIV-,HPV+/HIV-,HR-HPV+ confirmed by medical records and HPV genotyping test,99,12,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 4b,10 January 2021,Cynthia Anderson,"WikiWorks,Atrayees,Merit",Identified phylotype biomarkers ranked by effect size in HIV–women,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Methanobacteriati|p__Methanobacteriota|c__Halobacteria|o__Halobacteriales|f__Haloferacaceae|g__Halorubrum,k__Methanobacteriati|p__Methanobacteriota|c__Halobacteria|o__Halobacteriales|f__Haloferacaceae|g__Halorubrum|s__Halorubrum sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales",3379134|1224|28211;3366610|28890|183963|2235|1644056|56688;3366610|28890|183963|2235|1644056|56688|1879286;3379134|1224|28211|356;1783272|1239|91061|186826|33958|1578|147802;3379134|1224|1236|135614;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826,Complete,Fatima Zohra
bsdb:26068542/1/1,26068542,"cross-sectional observational, not case-control",26068542,10.2337/db14-1847,NA,"Alkanani A.K., Hara N., Gottlieb P.A., Ir D., Robertson C.E., Wagner B.D., Frank D.N. , Zipris D.",Alterations in Intestinal Microbiota Correlate With Susceptibility to Type 1 Diabetes,Diabetes,2015,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Type I diabetes mellitus,MONDO:0005147,Seropositive (Ab+) and Seronegative (Ab−),New onset type 1 diabetes (NO),Participants with newly diagnosed type 1 diabetes (up to 6 months from disease diagnosis).,38,34,1 month,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,"Table 2, Figure 2 and Supplementary Table 1",24 February 2025,Aleru Divine,Aleru Divine,Results from Wilcoxon rank-based tests after adjustment for covariates indicating the pairwise comparisons for the genera with a statistically significant difference across the groups.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Succiniclasticum",3379134|976|200643|171549|171550|239759;1783272|1239|526524|526525|2810280|135858;3379134|976|200643|171549|171552;1783272|1239|909932|1843488|909930|40840,Complete,Svetlana up
bsdb:26068542/2/1,26068542,"cross-sectional observational, not case-control",26068542,10.2337/db14-1847,NA,"Alkanani A.K., Hara N., Gottlieb P.A., Ir D., Robertson C.E., Wagner B.D., Frank D.N. , Zipris D.",Alterations in Intestinal Microbiota Correlate With Susceptibility to Type 1 Diabetes,Diabetes,2015,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Autoantibody measurement,EFO:0004866,Unrelated control (CO),Seropositive (Ab+) and Seronegative (Ab−),Participants with and without autoantibodies.,16,38,1 month,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,"Table 2, Figure 2 and Supplementary Table 1",24 February 2025,Aleru Divine,Aleru Divine,Results from Wilcoxon rank-based tests after adjustment for covariates indicating the pairwise comparisons for the genera with a statistically significant difference across the groups.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Thalassospiraceae|g__Thalassospira,k__Pseudomonadati|p__Bacteroidota",1783272|1239|526524|526525|2810280|135858;3379134|976|200643|171549|171552;3379134|1224|28211|204441|2844866|168934;3379134|976,Complete,Svetlana up
bsdb:26068542/2/2,26068542,"cross-sectional observational, not case-control",26068542,10.2337/db14-1847,NA,"Alkanani A.K., Hara N., Gottlieb P.A., Ir D., Robertson C.E., Wagner B.D., Frank D.N. , Zipris D.",Alterations in Intestinal Microbiota Correlate With Susceptibility to Type 1 Diabetes,Diabetes,2015,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Autoantibody measurement,EFO:0004866,Unrelated control (CO),Seropositive (Ab+) and Seronegative (Ab−),Participants with and without autoantibodies.,16,38,1 month,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,"Table 2, Figure 2 and Supplementary Table 1",16 March 2025,Aleru Divine,Aleru Divine,Results from Wilcoxon rank-based tests after adjustment for covariates indicating the pairwise comparisons for the genera with a statistically significant difference across the groups.,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",3379134|976;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:26068542/3/1,26068542,"cross-sectional observational, not case-control",26068542,10.2337/db14-1847,NA,"Alkanani A.K., Hara N., Gottlieb P.A., Ir D., Robertson C.E., Wagner B.D., Frank D.N. , Zipris D.",Alterations in Intestinal Microbiota Correlate With Susceptibility to Type 1 Diabetes,Diabetes,2015,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Autoantibody measurement,EFO:0004866,Unrelated control (CO),Seropositive (Ab+),Participants with one to four autoantibodies.,16,17,1 month,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,"Table 2, Figure 2 and Supplementary Table 1",24 February 2025,Aleru Divine,Aleru Divine,Results from Wilcoxon rank-based tests after adjustment for covariates indicating the pairwise comparisons for the genera with a statistically significant difference across the groups.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,3379134|976|200643|171549|171552,Complete,Svetlana up
bsdb:26068542/3/2,26068542,"cross-sectional observational, not case-control",26068542,10.2337/db14-1847,NA,"Alkanani A.K., Hara N., Gottlieb P.A., Ir D., Robertson C.E., Wagner B.D., Frank D.N. , Zipris D.",Alterations in Intestinal Microbiota Correlate With Susceptibility to Type 1 Diabetes,Diabetes,2015,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Autoantibody measurement,EFO:0004866,Unrelated control (CO),Seropositive (Ab+),Participants with one to four autoantibodies.,16,17,1 month,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,"Table 2, Figure 2 and Supplementary Table 1",16 March 2025,Aleru Divine,Aleru Divine,Results from Wilcoxon rank-based tests after adjustment for covariates indicating the pairwise comparisons for the genera with a statistically significant difference across the groups.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Bacteroidota",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|1385|90964|1279;3379134|976,Complete,Svetlana up
bsdb:26068542/4/1,26068542,"cross-sectional observational, not case-control",26068542,10.2337/db14-1847,NA,"Alkanani A.K., Hara N., Gottlieb P.A., Ir D., Robertson C.E., Wagner B.D., Frank D.N. , Zipris D.",Alterations in Intestinal Microbiota Correlate With Susceptibility to Type 1 Diabetes,Diabetes,2015,NA,Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Autoantibody measurement,EFO:0004866,Unrelated control (CO),Seronegative (Ab-),The seronegative group consists of first degree relatives (FDRs) of subjects with islet autoimmunity.,16,21,1 month,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,"Table 2, Figure 2 and Supplementary Table 1",24 February 2025,Aleru Divine,Aleru Divine,Results from Wilcoxon rank-based tests after adjustment for covariates indicating the pairwise comparisons for the genera with a statistically significant difference across the groups.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:26068542/4/2,26068542,"cross-sectional observational, not case-control",26068542,10.2337/db14-1847,NA,"Alkanani A.K., Hara N., Gottlieb P.A., Ir D., Robertson C.E., Wagner B.D., Frank D.N. , Zipris D.",Alterations in Intestinal Microbiota Correlate With Susceptibility to Type 1 Diabetes,Diabetes,2015,NA,Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Autoantibody measurement,EFO:0004866,Unrelated control (CO),Seronegative (Ab-),The seronegative group consists of first degree relatives (FDRs) of subjects with islet autoimmunity.,16,21,1 month,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,"Table 2, Figure 2 and Supplementary Table 1",8 March 2025,Aleru Divine,Aleru Divine,Results from Wilcoxon rank-based tests after adjustment for covariates indicating the pairwise comparisons for the genera with a statistically significant difference across the groups.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Thalassospiraceae|g__Thalassospira,3379134|1224|28211|204441|2844866|168934,Complete,Svetlana up
bsdb:26068542/5/1,26068542,"cross-sectional observational, not case-control",26068542,10.2337/db14-1847,NA,"Alkanani A.K., Hara N., Gottlieb P.A., Ir D., Robertson C.E., Wagner B.D., Frank D.N. , Zipris D.",Alterations in Intestinal Microbiota Correlate With Susceptibility to Type 1 Diabetes,Diabetes,2015,NA,Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Type I diabetes mellitus,MONDO:0005147,Seronegative (Ab−),New onset type 1 diabetes (NO),Participants with newly diagnosed type 1 diabetes (up to 6 months from disease diagnosis).,21,34,1 month,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,"Table 2, Figure 2 and Supplementary Table 1",24 February 2025,Aleru Divine,Aleru Divine,Results from Wilcoxon rank-based tests after adjustment for covariates indicating the pairwise comparisons for the genera with a statistically significant difference across the groups.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Succiniclasticum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843488|909930|40840;3379134|976|200643|171549|171552,Complete,Svetlana up
bsdb:26068542/5/2,26068542,"cross-sectional observational, not case-control",26068542,10.2337/db14-1847,NA,"Alkanani A.K., Hara N., Gottlieb P.A., Ir D., Robertson C.E., Wagner B.D., Frank D.N. , Zipris D.",Alterations in Intestinal Microbiota Correlate With Susceptibility to Type 1 Diabetes,Diabetes,2015,NA,Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Type I diabetes mellitus,MONDO:0005147,Seronegative (Ab−),New onset type 1 diabetes (NO),Participants with newly diagnosed type 1 diabetes (up to 6 months from disease diagnosis).,21,34,1 month,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,"Table 2, Figure 2 and Supplementary Table 1",8 March 2025,Aleru Divine,Aleru Divine,Results from Wilcoxon rank-based tests after adjustment for covariates indicating the pairwise comparisons for the genera with a statistically significant difference across the groups.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,3379134|976|200643|171549|171550|239759,Complete,Svetlana up
bsdb:26068542/6/1,26068542,"cross-sectional observational, not case-control",26068542,10.2337/db14-1847,NA,"Alkanani A.K., Hara N., Gottlieb P.A., Ir D., Robertson C.E., Wagner B.D., Frank D.N. , Zipris D.",Alterations in Intestinal Microbiota Correlate With Susceptibility to Type 1 Diabetes,Diabetes,2015,NA,Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Type I diabetes mellitus,MONDO:0005147,Seropositive (Ab+),New onset type 1 diabetes (NO),Participants with newly diagnosed type 1 diabetes (up to 6 months from disease diagnosis).,17,34,1 month,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,"Table 2, Figure 2 and Supplementary Table 1",24 February 2025,Aleru Divine,Aleru Divine,Results from Wilcoxon rank-based tests after adjustment for covariates indicating the pairwise comparisons for the genera with a statistically significant difference across the groups.,increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Succiniclasticum,1783272|1239|909932|1843488|909930|40840,Complete,Svetlana up
bsdb:26068542/6/2,26068542,"cross-sectional observational, not case-control",26068542,10.2337/db14-1847,NA,"Alkanani A.K., Hara N., Gottlieb P.A., Ir D., Robertson C.E., Wagner B.D., Frank D.N. , Zipris D.",Alterations in Intestinal Microbiota Correlate With Susceptibility to Type 1 Diabetes,Diabetes,2015,NA,Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Type I diabetes mellitus,MONDO:0005147,Seropositive (Ab+),New onset type 1 diabetes (NO),Participants with newly diagnosed type 1 diabetes (up to 6 months from disease diagnosis).,17,34,1 month,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,"Table 2, Figure 2 and Supplementary Table 1",8 March 2025,Aleru Divine,Aleru Divine,Results from Wilcoxon rank-based tests after adjustment for covariates indicating the pairwise comparisons for the genera with a statistically significant difference across the groups.,decreased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,1783272|1239|526524|526525|2810280|135858,Complete,Svetlana up
bsdb:26068542/7/1,26068542,"cross-sectional observational, not case-control",26068542,10.2337/db14-1847,NA,"Alkanani A.K., Hara N., Gottlieb P.A., Ir D., Robertson C.E., Wagner B.D., Frank D.N. , Zipris D.",Alterations in Intestinal Microbiota Correlate With Susceptibility to Type 1 Diabetes,Diabetes,2015,NA,Experiment 7,United States of America,Homo sapiens,Feces,UBERON:0001988,Autoantibody measurement,EFO:0004866,Seronegative (Ab−),Seropositive (Ab+),Participants with one to four autoantibodies.,21,17,1 month,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,"Table 2, Figure 2 and Supplementary Table 1",24 February 2025,Aleru Divine,Aleru Divine,Results from Wilcoxon rank-based tests after adjustment for covariates indicating the pairwise comparisons for the genera with a statistically significant difference across the groups.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",1783272|1239|526524|526525|2810280|135858;3379134|976|200643|171549|171552,Complete,Svetlana up
bsdb:26068542/7/2,26068542,"cross-sectional observational, not case-control",26068542,10.2337/db14-1847,NA,"Alkanani A.K., Hara N., Gottlieb P.A., Ir D., Robertson C.E., Wagner B.D., Frank D.N. , Zipris D.",Alterations in Intestinal Microbiota Correlate With Susceptibility to Type 1 Diabetes,Diabetes,2015,NA,Experiment 7,United States of America,Homo sapiens,Feces,UBERON:0001988,Autoantibody measurement,EFO:0004866,Seronegative (Ab−),Seropositive (Ab+),Participants with one to four autoantibodies.,21,17,1 month,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,"Table 2, Figure 2 and Supplementary Table 1",16 March 2025,Aleru Divine,Aleru Divine,Results from Wilcoxon rank-based tests after adjustment for covariates indicating the pairwise comparisons for the genera with a statistically significant difference across the groups.,decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Svetlana up
bsdb:26068542/8/1,26068542,"cross-sectional observational, not case-control",26068542,10.2337/db14-1847,NA,"Alkanani A.K., Hara N., Gottlieb P.A., Ir D., Robertson C.E., Wagner B.D., Frank D.N. , Zipris D.",Alterations in Intestinal Microbiota Correlate With Susceptibility to Type 1 Diabetes,Diabetes,2015,NA,Experiment 8,United States of America,Homo sapiens,Feces,UBERON:0001988,Type I diabetes mellitus,MONDO:0005147,Unrelated control (CO),New onset type 1 diabetes (NO),Participants with newly diagnosed type 1 diabetes (up to 6 months from disease diagnosis).,16,34,1 month,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,"Table 2, Figure 2 and Supplementary Table 1",24 February 2025,Aleru Divine,Aleru Divine,Results from Wilcoxon rank-based tests after adjustment for covariates indicating the pairwise comparisons for the genera with a statistically significant difference across the groups.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Thalassospiraceae|g__Thalassospira,3379134|1224|28211|204441|2844866|168934,Complete,Svetlana up
bsdb:26068542/8/2,26068542,"cross-sectional observational, not case-control",26068542,10.2337/db14-1847,NA,"Alkanani A.K., Hara N., Gottlieb P.A., Ir D., Robertson C.E., Wagner B.D., Frank D.N. , Zipris D.",Alterations in Intestinal Microbiota Correlate With Susceptibility to Type 1 Diabetes,Diabetes,2015,NA,Experiment 8,United States of America,Homo sapiens,Feces,UBERON:0001988,Type I diabetes mellitus,MONDO:0005147,Unrelated control (CO),New onset type 1 diabetes (NO),Participants with newly diagnosed type 1 diabetes (up to 6 months from disease diagnosis).,16,34,1 month,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,"Table 2, Figure 2 and Supplementary Table 1",8 March 2025,Aleru Divine,Aleru Divine,Results from Wilcoxon rank-based tests after adjustment for covariates indicating the pairwise comparisons for the genera with a statistically significant difference across the groups.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Succiniclasticum,k__Pseudomonadati|p__Bacteroidota",3379134|976|200643|171549|171550|239759;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|1385|90964|1279;1783272|1239|909932|1843488|909930|40840;3379134|976,Complete,Svetlana up
bsdb:26068542/9/1,26068542,"cross-sectional observational, not case-control",26068542,10.2337/db14-1847,NA,"Alkanani A.K., Hara N., Gottlieb P.A., Ir D., Robertson C.E., Wagner B.D., Frank D.N. , Zipris D.",Alterations in Intestinal Microbiota Correlate With Susceptibility to Type 1 Diabetes,Diabetes,2015,NA,Experiment 9,United States of America,Homo sapiens,Feces,UBERON:0001988,Autoantibody measurement,EFO:0004866,One autoantibody,Two to four autoantibodies,Participants with two to four autoantibodies.,5,16,1 month,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 3,24 February 2025,Aleru Divine,Aleru Divine,Median percent abundances of bacterial taxa in subjects with one versus multiple autoantibodies.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",3379134|976|200643|171549|815|816;3379134|74201|203494|48461|1647988|239934,Complete,Svetlana up
bsdb:26068542/9/2,26068542,"cross-sectional observational, not case-control",26068542,10.2337/db14-1847,NA,"Alkanani A.K., Hara N., Gottlieb P.A., Ir D., Robertson C.E., Wagner B.D., Frank D.N. , Zipris D.",Alterations in Intestinal Microbiota Correlate With Susceptibility to Type 1 Diabetes,Diabetes,2015,NA,Experiment 9,United States of America,Homo sapiens,Feces,UBERON:0001988,Autoantibody measurement,EFO:0004866,One autoantibody,Two to four autoantibodies,Participants with two to four autoantibodies.,5,16,1 month,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 3,24 February 2025,Aleru Divine,Aleru Divine,Median percent abundances of bacterial taxa in subjects with one versus multiple autoantibodies.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio",3379134|976|200643|171549|171552|838;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|830,Complete,Svetlana up
bsdb:26069274/1/2,26069274,"cross-sectional observational, not case-control",26069274,10.1136/gutjnl-2015-309618,NA,"Vandeputte D., Falony G., Vieira-Silva S., Tito R.Y., Joossens M. , Raes J.","Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates",Gut,2016,"INTESTINAL BACTERIA, INTESTINAL MICROBIOLOGY",Experiment 1,Belgium,Homo sapiens,Feces,UBERON:0001988,Abnormal stool composition,HP:0031685,Decreasing stool consistency in Total Dataset,Increasing stool consistency in Total Dataset,This group represents individuals with altered gut microbiota composition linked to fast intestinal transit in the Total Dataset.,NA,NA,3 months,16S,4,Illumina,relative abundances,Spearman Correlation,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,21 March 2025,Francisca,Francisca,Correlation between stool consistency (Bristol Stool Scale) and differentially abundant gut microbiota genera.,decreased,"k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanosphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas",3366610|28890|183925|2158|2159|2316;3379134|976|200643|171549|1853231|283168;3379134|1224|28216|80840|75682|846;3366610|28890|183925|2158|2159|2172;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|1853231|574697,Complete,Svetlana up
bsdb:26069274/2/1,26069274,"cross-sectional observational, not case-control",26069274,10.1136/gutjnl-2015-309618,NA,"Vandeputte D., Falony G., Vieira-Silva S., Tito R.Y., Joossens M. , Raes J.","Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates",Gut,2016,"INTESTINAL BACTERIA, INTESTINAL MICROBIOLOGY",Experiment 2,Belgium,Homo sapiens,Feces,UBERON:0001988,Abnormal stool composition,HP:0031685,Decreasing stool consistency in Ruminococcaceae-Bacteroides enterotype,Increasing stool consistency in Ruminococcaceae-Bacteroides enterotype,This group represents individuals with altered gut microbiota composition linked to fast intestinal transit in the RB enterotype.,NA,NA,3 months,16S,4,Illumina,relative abundances,Spearman Correlation,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,22 March 2025,Francisca,Francisca,"RB enterotype, indicating significant microbiome shifts associated with intestinal transit time.",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:26069274/2/2,26069274,"cross-sectional observational, not case-control",26069274,10.1136/gutjnl-2015-309618,NA,"Vandeputte D., Falony G., Vieira-Silva S., Tito R.Y., Joossens M. , Raes J.","Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates",Gut,2016,"INTESTINAL BACTERIA, INTESTINAL MICROBIOLOGY",Experiment 2,Belgium,Homo sapiens,Feces,UBERON:0001988,Abnormal stool composition,HP:0031685,Decreasing stool consistency in Ruminococcaceae-Bacteroides enterotype,Increasing stool consistency in Ruminococcaceae-Bacteroides enterotype,This group represents individuals with altered gut microbiota composition linked to fast intestinal transit in the RB enterotype.,NA,NA,3 months,16S,4,Illumina,relative abundances,Spearman Correlation,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,22 March 2025,Francisca,Francisca,"RB enterotype, indicating significant microbiome shifts associated with intestinal transit time.",decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|1853231|574697;3366610|28890|183925|2158|2159|2172;3379134|1224|28216|80840|75682|846,Complete,Svetlana up
bsdb:26147207/1/1,26147207,prospective cohort,26147207,10.1111/apt.13302,NA,"Montassier E., Gastinne T., Vangay P., Al-Ghalith G.A., Bruley des Varannes S., Massart S., Moreau P., Potel G., de La Cochetière M.F., Batard E. , Knights D.",Chemotherapy-driven dysbiosis in the intestinal microbiome,Alimentary pharmacology & therapeutics,2015,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Non-Hodgkins lymphoma,EFO:0005952,pre-chemotherapy,post-chemotherapy,"non-Hodgkin's lymphoma patients post myeloablative conditiong regimen (chemotherapy) fecal sampling for 5 consecutive days of high-dose Carmustine, Etoposide, Aracytine and Melphalan and with no antibiotics treatment after starting regimen",28,15,1 month,16S,56,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,"Supplemental Table S1a-c, text",10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential microbial taxa abundance for non-Hodgkins Lymphoma patients from the fecal samples collected before and after chemotherapy,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella",1783272|1239|91061|186826|186827;1783272|1239|91061|186826|186828;3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;3379134|1224;1783272|201174|84998|84999|1643824|1380;3379134|1224|1236|91347|543|570,Complete,Claregrieve1
bsdb:26147207/1/2,26147207,prospective cohort,26147207,10.1111/apt.13302,NA,"Montassier E., Gastinne T., Vangay P., Al-Ghalith G.A., Bruley des Varannes S., Massart S., Moreau P., Potel G., de La Cochetière M.F., Batard E. , Knights D.",Chemotherapy-driven dysbiosis in the intestinal microbiome,Alimentary pharmacology & therapeutics,2015,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Non-Hodgkins lymphoma,EFO:0005952,pre-chemotherapy,post-chemotherapy,"non-Hodgkin's lymphoma patients post myeloablative conditiong regimen (chemotherapy) fecal sampling for 5 consecutive days of high-dose Carmustine, Etoposide, Aracytine and Melphalan and with no antibiotics treatment after starting regimen",28,15,1 month,16S,56,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,"Supplemental Table S1a-c, text",10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential microbial taxa abundance for non-Hodgkins Lymphoma patients from the fecal samples collected before and after chemotherapy,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium",1783272|201174;1783272|201174|84998|1643822|1643826|447020;1783272|1239|1737404|1737405|1570339|165779;1783272|201174|84998|84999|1643824|1380;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|33042;1783272|201174|84998|84999|84107;1783272|1239|186801|3085636|186803|189330;3379134|1224|1236|91347|543;1783272|1239;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|541000;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|1898207,Complete,Claregrieve1
bsdb:26151645/1/1,26151645,case-control,26151645,10.1038/ismej.2015.99,NA,"de Steenhuijsen Piters W.A., Huijskens E.G., Wyllie A.L., Biesbroek G., van den Bergh M.R., Veenhoven R.H., Wang X., Trzciński K., Bonten M.J., Rossen J.W., Sanders E.A. , Bogaert D.",Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients,The ISME journal,2016,NA,Experiment 1,Netherlands,Homo sapiens,Mucosa of oropharynx,UBERON:0005023,Pneumonia,EFO:0003106,elderly controls,elderly pneumonia patients,patients >= 60 years of age with pneumonia,91,100,3 months,16S,567,Roche454,raw counts,T-Test,0.05,TRUE,NA,NA,"age,comorbidity,smoking behavior",NA,increased,NA,NA,NA,decreased,Signature 1,Figure 2,10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differential microbial abundance between elderly controls and elderly pneumonia patients,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudopneumoniae",1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|186826|1300|1301|257758,Complete,Claregrieve1
bsdb:26151645/1/2,26151645,case-control,26151645,10.1038/ismej.2015.99,NA,"de Steenhuijsen Piters W.A., Huijskens E.G., Wyllie A.L., Biesbroek G., van den Bergh M.R., Veenhoven R.H., Wang X., Trzciński K., Bonten M.J., Rossen J.W., Sanders E.A. , Bogaert D.",Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients,The ISME journal,2016,NA,Experiment 1,Netherlands,Homo sapiens,Mucosa of oropharynx,UBERON:0005023,Pneumonia,EFO:0003106,elderly controls,elderly pneumonia patients,patients >= 60 years of age with pneumonia,91,100,3 months,16S,567,Roche454,raw counts,T-Test,0.05,TRUE,NA,NA,"age,comorbidity,smoking behavior",NA,increased,NA,NA,NA,decreased,Signature 2,Figure 2,10 January 2021,Rimsha Azhar,"Claregrieve1,Merit,WikiWorks",Differential microbial abundance between elderly controls and elderly pneumonia patients,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Parascardovia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",3384189|32066|203490|203491|1129771|32067;1783272|201174|1760|85004|31953|196082;3379134|976|200643|171549|171552|838|28132;1783272|1239|909932|1843489|31977|29465|39778,Complete,Claregrieve1
bsdb:26151645/2/1,26151645,case-control,26151645,10.1038/ismej.2015.99,NA,"de Steenhuijsen Piters W.A., Huijskens E.G., Wyllie A.L., Biesbroek G., van den Bergh M.R., Veenhoven R.H., Wang X., Trzciński K., Bonten M.J., Rossen J.W., Sanders E.A. , Bogaert D.",Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients,The ISME journal,2016,NA,Experiment 2,Netherlands,Homo sapiens,Mucosa of oropharynx,UBERON:0005023,Pneumonia,EFO:0003106,adult controls,adult pneumonia patients,patients <60 years of age with pneumonia,187,27,3 months,16S,567,Roche454,raw counts,T-Test,0.05,TRUE,NA,NA,"age,comorbidity,smoking behavior",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2,10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differential microbial abundance between healthy adult controls and pneumonia patients,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudopneumoniae",1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|186826|1300|1301|257758,Complete,Claregrieve1
bsdb:26151645/2/2,26151645,case-control,26151645,10.1038/ismej.2015.99,NA,"de Steenhuijsen Piters W.A., Huijskens E.G., Wyllie A.L., Biesbroek G., van den Bergh M.R., Veenhoven R.H., Wang X., Trzciński K., Bonten M.J., Rossen J.W., Sanders E.A. , Bogaert D.",Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients,The ISME journal,2016,NA,Experiment 2,Netherlands,Homo sapiens,Mucosa of oropharynx,UBERON:0005023,Pneumonia,EFO:0003106,adult controls,adult pneumonia patients,patients <60 years of age with pneumonia,187,27,3 months,16S,567,Roche454,raw counts,T-Test,0.05,TRUE,NA,NA,"age,comorbidity,smoking behavior",NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2,10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differential microbial abundance between healthy adult controls and pneumonia patients,decreased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",1783272|1239|91061;3379134|1224|1236|135625|712|724;3384189|32066|203490|203491|1129771|32067;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|838|28132;1783272|1239|909932|1843489|31977|29465|39778,Complete,Claregrieve1
bsdb:26170900/1/1,26170900,"laboratory experiment,meta-analysis",26170900,10.1186/s13073-015-0177-8,NA,"Burns M.B., Lynch J., Starr T.K., Knights D. , Blekhman R.",Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment,Genome medicine,2015,NA,Experiment 1,United States of America,Homo sapiens,Colon,UBERON:0001155,Colorectal cancer,EFO:0005842,Patient-Matched Normal Colon Tissue Samples,Colorectal Tumor Samples,This group consists of primary tumor tissue samples obtained from patients diagnosed with colorectal cancer. They were collected from the site of tumor microenvironment.,44,44,NA,16S,56,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,decreased,NA,Signature 1,Figure 2 and 3A,17 March 2024,Aananditaa,"Aananditaa,Peace Sandy,WikiWorks",Differentially abundant taxa between matched normal and colorectal cancer microbiomes.,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia",3384189|32066|203490|203491|203492|848;3379134|1224|1236|91347|1903414|586,Complete,Peace Sandy
bsdb:26170900/1/2,26170900,"laboratory experiment,meta-analysis",26170900,10.1186/s13073-015-0177-8,NA,"Burns M.B., Lynch J., Starr T.K., Knights D. , Blekhman R.",Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment,Genome medicine,2015,NA,Experiment 1,United States of America,Homo sapiens,Colon,UBERON:0001155,Colorectal cancer,EFO:0005842,Patient-Matched Normal Colon Tissue Samples,Colorectal Tumor Samples,This group consists of primary tumor tissue samples obtained from patients diagnosed with colorectal cancer. They were collected from the site of tumor microenvironment.,44,44,NA,16S,56,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,decreased,NA,Signature 2,Figure 2 and 3A,18 March 2024,Aananditaa,"Aananditaa,WikiWorks",Differentially abundant taxa between matched normal and colorectal cancer microbiomes.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D16",3379134|976|200643|171549|815|816|820;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|552398,Complete,Peace Sandy
bsdb:26179554/1/1,26179554,case-control,26179554,10.1002/mds.26307,NA,"Keshavarzian A., Green S.J., Engen P.A., Voigt R.M., Naqib A., Forsyth C.B., Mutlu E. , Shannon K.M.",Colonic bacterial composition in Parkinson's disease,Movement disorders : official journal of the Movement Disorder Society,2015,"a-synuclein, colonic mucosa and feces, dysbiosis, microbiota, putative butyrate producing short-chain fatty acids",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control volunteers,Parkinson's Disease subjects,Parkinson's disease was diagnosed according to the UK Brain Bank Criteria.,34,38,3 months,16S,4,NA,relative abundances,Kruskall-Wallis,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,TABLE 1. Relative increased abundance of sequences derived from individual taxa,24 May 2023,Fcuevas3,"Fcuevas3,WikiWorks",Feces: Parkinson's disease vs. Healthy controls.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976|200643;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|216572|119852;3379134|1224;3379134|74201|203494|48461|203557;3379134|74201,Complete,Atrayees
bsdb:26179554/1/2,26179554,case-control,26179554,10.1002/mds.26307,NA,"Keshavarzian A., Green S.J., Engen P.A., Voigt R.M., Naqib A., Forsyth C.B., Mutlu E. , Shannon K.M.",Colonic bacterial composition in Parkinson's disease,Movement disorders : official journal of the Movement Disorder Society,2015,"a-synuclein, colonic mucosa and feces, dysbiosis, microbiota, putative butyrate producing short-chain fatty acids",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control volunteers,Parkinson's Disease subjects,Parkinson's disease was diagnosed according to the UK Brain Bank Criteria.,34,38,3 months,16S,4,NA,relative abundances,Kruskall-Wallis,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,TABLE 1. Relative decreased abundance of sequences derived from individual taxa,24 May 2023,Fcuevas3,"Fcuevas3,WikiWorks",Feces: Parkinson's Disease vs. Healthy Controls,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239;1783272|1239|186801|3085636|186803|572511;1783272|1239|526524|526525|2810280;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|841,Complete,Atrayees
bsdb:26179554/2/1,26179554,case-control,26179554,10.1002/mds.26307,NA,"Keshavarzian A., Green S.J., Engen P.A., Voigt R.M., Naqib A., Forsyth C.B., Mutlu E. , Shannon K.M.",Colonic bacterial composition in Parkinson's disease,Movement disorders : official journal of the Movement Disorder Society,2015,"a-synuclein, colonic mucosa and feces, dysbiosis, microbiota, putative butyrate producing short-chain fatty acids",Experiment 2,United States of America,Homo sapiens,Colonic mucosa,UBERON:0000317,Parkinson's disease,MONDO:0005180,Healthy control volunteers,Parkinson's Disease subjects,Parkinson's disease was diagnosed according to the UK Brain Bank Criteria.,34,38,3 months,16S,4,NA,relative abundances,Kruskall-Wallis,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,TABLE 1. Relative increased abundance of sequences derived from individual taxa,24 May 2023,Fcuevas3,"Fcuevas3,WikiWorks",Sigmoid Mucosa: Parkinson's Disease vs. Healthy Controls.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia",3379134|1224|28216|80840|75682;3379134|1224|28216|80840|119060|48736,Complete,Atrayees
bsdb:26179554/2/2,26179554,case-control,26179554,10.1002/mds.26307,NA,"Keshavarzian A., Green S.J., Engen P.A., Voigt R.M., Naqib A., Forsyth C.B., Mutlu E. , Shannon K.M.",Colonic bacterial composition in Parkinson's disease,Movement disorders : official journal of the Movement Disorder Society,2015,"a-synuclein, colonic mucosa and feces, dysbiosis, microbiota, putative butyrate producing short-chain fatty acids",Experiment 2,United States of America,Homo sapiens,Colonic mucosa,UBERON:0000317,Parkinson's disease,MONDO:0005180,Healthy control volunteers,Parkinson's Disease subjects,Parkinson's disease was diagnosed according to the UK Brain Bank Criteria.,34,38,3 months,16S,4,NA,relative abundances,Kruskall-Wallis,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 2,TABLE 1. Relative decreased abundance of sequences derived from individual taxa,24 May 2023,Fcuevas3,"Fcuevas3,WikiWorks",Sigmoid Mucosa: Parkinson's Disease vs. Healthy Controls,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|1239|526524|526525|2810280;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|216851,Complete,Atrayees
bsdb:26181352/1/1,26181352,"cross-sectional observational, not case-control",26181352,10.1001/jamaoncol.2015.1377,NA,"Mima K., Sukawa Y., Nishihara R., Qian Z.R., Yamauchi M., Inamura K., Kim S.A., Masuda A., Nowak J.A., Nosho K., Kostic A.D., Giannakis M., Watanabe H., Bullman S., Milner D.A., Harris C.C., Giovannucci E., Garraway L.A., Freeman G.J., Dranoff G., Chan A.T., Garrett W.S., Huttenhower C., Fuchs C.S. , Ogino S.",Fusobacterium nucleatum and T Cells in Colorectal Carcinoma,JAMA oncology,2015,NA,Experiment 1,United States of America,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,Tumor Tissue of Colorectal Cancer Cases,Adjacent Non-Tumor Tissue of Colorectal Cancer Cases,Both colon and rectal carcinomas were included on the basis of the colorectal continuum model. Patients were followed up until death or the end of follow-up.,558,558,NA,16S,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,family history of cancer,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 1B,12 June 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential abundance of Fusobacterium nucleatum in 558 pairs of colorectal carcinoma and adjacent non-tumor tissues,increased,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,3384189|32066|203490|203491|203492|848|851,Complete,Claregrieve1
bsdb:26230509/1/1,26230509,case-control,26230509,10.1371/journal.pone.0134333,NA,"Hu H.J., Park S.G., Jang H.B., Choi M.K., Choi M.G., Park K.H., Kang J.H., Park S.I., Lee H.J. , Cho S.H.",Obesity Alters the Microbial Community Profile in Korean Adolescents,PloS one,2015,NA,Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control adolescent,obese adolescent,"body mass index BMI >= 30 kg/m2, or >= 99th BMI percentile",67,67,1 month,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 2 and Table 3,10 January 2021,Marianthi Thomatos,WikiWorks,Relative microbial abundance in obese Korean adolescents (13-16 year old),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|976|200643|171549|171552;3379134|1224|28216|80840|995019;1783272|1239|909932|1843489|31977;3379134|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
bsdb:26230509/1/2,26230509,case-control,26230509,10.1371/journal.pone.0134333,NA,"Hu H.J., Park S.G., Jang H.B., Choi M.K., Choi M.G., Park K.H., Kang J.H., Park S.I., Lee H.J. , Cho S.H.",Obesity Alters the Microbial Community Profile in Korean Adolescents,PloS one,2015,NA,Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control adolescent,obese adolescent,"body mass index BMI >= 30 kg/m2, or >= 99th BMI percentile",67,67,1 month,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 2 and Table 3,10 January 2021,Marianthi Thomatos,WikiWorks,Relative microbial abundance in obese Korean adolescents (13-16 year old),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",3379134|976|200643|171549|815;3379134|976|200643|171549|171550;1783272|1239|186801|186802|541000;3379134|976|200643|171549|815|816;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|459786,Complete,Shaimaa Elsafoury
bsdb:26230509/2/1,26230509,case-control,26230509,10.1371/journal.pone.0134333,NA,"Hu H.J., Park S.G., Jang H.B., Choi M.K., Choi M.G., Park K.H., Kang J.H., Park S.I., Lee H.J. , Cho S.H.",Obesity Alters the Microbial Community Profile in Korean Adolescents,PloS one,2015,NA,Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,low BMI zscores,high BMI zscore,"body mass index BMI >= 30 kg/m2, or >= 99th BMI percentile",67,67,1 month,16S,123,Roche454,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Marianthi Thomatos,WikiWorks,Relative microbial abundance in obese Korean adolescents (13-16 year old),increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
bsdb:26230509/2/2,26230509,case-control,26230509,10.1371/journal.pone.0134333,NA,"Hu H.J., Park S.G., Jang H.B., Choi M.K., Choi M.G., Park K.H., Kang J.H., Park S.I., Lee H.J. , Cho S.H.",Obesity Alters the Microbial Community Profile in Korean Adolescents,PloS one,2015,NA,Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,low BMI zscores,high BMI zscore,"body mass index BMI >= 30 kg/m2, or >= 99th BMI percentile",67,67,1 month,16S,123,Roche454,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 4,10 January 2021,Marianthi Thomatos,WikiWorks,Relative microbial abundance in obese Korean adolescents (13-16 year old),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",3379134|976|200643|171549|815|816;3379134|976|200643|171549|171550|239759,Complete,Shaimaa Elsafoury
bsdb:26230509/3/1,26230509,case-control,26230509,10.1371/journal.pone.0134333,NA,"Hu H.J., Park S.G., Jang H.B., Choi M.K., Choi M.G., Park K.H., Kang J.H., Park S.I., Lee H.J. , Cho S.H.",Obesity Alters the Microbial Community Profile in Korean Adolescents,PloS one,2015,NA,Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,low triglycerides,high triglycerides,"body mass index BMI >= 30 kg/m2, or >= 99th BMI percentile",67,67,1 month,16S,123,Roche454,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Relative microbial abundance in obese Korean adolescents (13-16 year old),increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
bsdb:26230509/3/2,26230509,case-control,26230509,10.1371/journal.pone.0134333,NA,"Hu H.J., Park S.G., Jang H.B., Choi M.K., Choi M.G., Park K.H., Kang J.H., Park S.I., Lee H.J. , Cho S.H.",Obesity Alters the Microbial Community Profile in Korean Adolescents,PloS one,2015,NA,Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,low triglycerides,high triglycerides,"body mass index BMI >= 30 kg/m2, or >= 99th BMI percentile",67,67,1 month,16S,123,Roche454,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Relative microbial abundance in obese Korean adolescents (13-16 year old),decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
bsdb:26230509/5/1,26230509,case-control,26230509,10.1371/journal.pone.0134333,NA,"Hu H.J., Park S.G., Jang H.B., Choi M.K., Choi M.G., Park K.H., Kang J.H., Park S.I., Lee H.J. , Cho S.H.",Obesity Alters the Microbial Community Profile in Korean Adolescents,PloS one,2015,NA,Experiment 5,South Korea,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,low HDL-C,high HDL-C,"body mass index BMI >= 30 kg/m2, or >= 99th BMI percentile",67,67,1 month,16S,123,Roche454,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Relative microbial abundance in obese Korean adolescents (13-16 year old),increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
bsdb:26230509/6/1,26230509,case-control,26230509,10.1371/journal.pone.0134333,NA,"Hu H.J., Park S.G., Jang H.B., Choi M.K., Choi M.G., Park K.H., Kang J.H., Park S.I., Lee H.J. , Cho S.H.",Obesity Alters the Microbial Community Profile in Korean Adolescents,PloS one,2015,NA,Experiment 6,South Korea,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,low sensetive C reactive protein,high senstive C reactive protein,"body mass index BMI >= 30 kg/m2, or >= 99th BMI percentile",67,67,1 month,16S,123,Roche454,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Relative microbial abundance in obese Korean adolescents (13-16 year old),increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
bsdb:26230509/6/2,26230509,case-control,26230509,10.1371/journal.pone.0134333,NA,"Hu H.J., Park S.G., Jang H.B., Choi M.K., Choi M.G., Park K.H., Kang J.H., Park S.I., Lee H.J. , Cho S.H.",Obesity Alters the Microbial Community Profile in Korean Adolescents,PloS one,2015,NA,Experiment 6,South Korea,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,low sensetive C reactive protein,high senstive C reactive protein,"body mass index BMI >= 30 kg/m2, or >= 99th BMI percentile",67,67,1 month,16S,123,Roche454,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Relative microbial abundance in obese Korean adolescents (13-16 year old),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|459786,Complete,Shaimaa Elsafoury
bsdb:26237371/1/1,26237371,case-control,26237371,10.1097/MPG.0000000000000928,https://journals.lww.com/jpgn/Fulltext/2016/02000/Influence_of_Intrapartum_Antibiotic_Prophylaxis.20.aspx,"Corvaglia L., Tonti G., Martini S., Aceti A., Mazzola G., Aloisio I., Di Gioia D. , Faldella G.",Influence of Intrapartum Antibiotic Prophylaxis for Group B Streptococcus on Gut Microbiota in the First Month of Life,Journal of pediatric gastroenterology and nutrition,2016,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Control group (@7 days),IAP group (@7 days),"infants born to GBS-positive mothers who had received IAP. According to the institutional treatment protocol for GBS prophylaxis (derived from the Centers for Disease Control and Prevention guidelines (13)), intravenous ampicillin was given every 4 hours until delivery (first dose 2 g, following doses 1 g each).",49,35,NA,PCR,NA,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,"delivery procedure,feeding practices,gestational age",NA,NA,NA,NA,NA,NA,NA,Signature 1,text,19 November 2021,Mmarin,"Mmarin,Atrayees,WikiWorks",Significant change in taxa between the two groups,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,1783272|201174|1760|85004|31953|1678|41200,Complete,Atrayees
bsdb:26238090/1/1,26238090,randomized controlled trial,26238090,10.3892/mmr.2015.4124,NA,"Gao Z., Guo B., Gao R., Zhu Q., Wu W. , Qin H.",Probiotics modify human intestinal mucosa-associated microbiota in patients with colorectal cancer,Molecular medicine reports,2015,NA,Experiment 1,China,Homo sapiens,Intestinal mucosa,UBERON:0001242,Nutraceutical,CHEBI:50733,CGT group - colorectal cancer patients perioperative placebo,PGT group - colorectal cancer patients perioperative probiotics,"Patients in the PGT group received an encapsulated probiotics preparation (Shanghai Xinyi Pharmaceutical Co., Ltd., Shanghai, China) containing live combined Bifidobacterium longum, Lactobacillus acidophilus and Enterococcus faecalis (1:1:1) with no less than 1.0x107 CFU/g viable cells, three times/day, with a total daily dose of 6.0x107 CFU for five days",11,11,3 months,16S,3,Roche454,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,Fig 4,29 September 2022,Mary Bearkland,"Mary Bearkland,Peace Sandy,WikiWorks","Figure 4. Different structures of the gut microbiota in the CGT, PGT and HGT groups. Histogram of the linear discriminant analysis scores for differentially abundant genera. The cladogram was calculated by LDA and displayed according to effect size. CGT, perioperative placebo group; PGT, probiotics group; linear discriminant analysis; HGT, healthy volunteer group; LDA, linear discriminant analysis.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|1224|1236|91347|543|1940338;3379134|1224|28211|356|82115;3379134|1224|28211|356;3379134|1224|28211|356|82115|379;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;3379134|1224|28211;3379134|976|200643|171549|171552,Complete,Peace Sandy
bsdb:26238090/1/2,26238090,randomized controlled trial,26238090,10.3892/mmr.2015.4124,NA,"Gao Z., Guo B., Gao R., Zhu Q., Wu W. , Qin H.",Probiotics modify human intestinal mucosa-associated microbiota in patients with colorectal cancer,Molecular medicine reports,2015,NA,Experiment 1,China,Homo sapiens,Intestinal mucosa,UBERON:0001242,Nutraceutical,CHEBI:50733,CGT group - colorectal cancer patients perioperative placebo,PGT group - colorectal cancer patients perioperative probiotics,"Patients in the PGT group received an encapsulated probiotics preparation (Shanghai Xinyi Pharmaceutical Co., Ltd., Shanghai, China) containing live combined Bifidobacterium longum, Lactobacillus acidophilus and Enterococcus faecalis (1:1:1) with no less than 1.0x107 CFU/g viable cells, three times/day, with a total daily dose of 6.0x107 CFU for five days",11,11,3 months,16S,3,Roche454,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 2,Fig 4,30 September 2022,Mary Bearkland,"Mary Bearkland,Peace Sandy,WikiWorks","Figure 4. Different structures of the gut microbiota in the CGT, PGT and HGT groups. Histogram of the linear discriminant analysis scores for differentially abundant genera. The cladogram was calculated by LDA and displayed according to effect size. CGT, perioperative placebo group; PGT, probiotics group; linear discriminant analysis; HGT, healthy volunteer group; LDA, linear discriminant analysis.",decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillales Family X. Incertae Sedis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter",3384189|32066|203490|203491|203492;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|1385|539003;1783272|1239|186801|3082720|186804|1257;1783272|1239|186801|3085636|186803|653683,Complete,Peace Sandy
bsdb:26238090/2/1,26238090,randomized controlled trial,26238090,10.3892/mmr.2015.4124,NA,"Gao Z., Guo B., Gao R., Zhu Q., Wu W. , Qin H.",Probiotics modify human intestinal mucosa-associated microbiota in patients with colorectal cancer,Molecular medicine reports,2015,NA,Experiment 2,China,Homo sapiens,Intestinal mucosa,UBERON:0001242,Nutraceutical,CHEBI:50733,HGT Group - Healthy controls,PGT group - colorectal cancer patients perioperative probiotics,PGT group - colorectal cancer patients that received perioperative probiotics,11,11,3 months,16S,3,Roche454,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,decreased,NA,increased,Signature 1,Fig 4,30 September 2022,Mary Bearkland,"Mary Bearkland,Peace Sandy,WikiWorks","Figure 4. Different structures of the gut microbiota in the CGT, PGT and HGT groups. Histogram of the linear discriminant analysis scores for differentially abundant genera. The cladogram was calculated by LDA and displayed according to effect size. CGT, perioperative placebo group; PGT, probiotics group; linear discriminant analysis; HGT, healthy volunteer group; LDA, linear discriminant analysis.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,s__Rhizobium sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|1224|1236|91347|543|1940338;3379134|1224|28211|356|82115|379;3379134|1224|28211|356|82115;3379134|1224|28211|356;391;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;3379134|1224|28211;3379134|976|200643|171549|171552,Complete,Peace Sandy
bsdb:26238090/2/2,26238090,randomized controlled trial,26238090,10.3892/mmr.2015.4124,NA,"Gao Z., Guo B., Gao R., Zhu Q., Wu W. , Qin H.",Probiotics modify human intestinal mucosa-associated microbiota in patients with colorectal cancer,Molecular medicine reports,2015,NA,Experiment 2,China,Homo sapiens,Intestinal mucosa,UBERON:0001242,Nutraceutical,CHEBI:50733,HGT Group - Healthy controls,PGT group - colorectal cancer patients perioperative probiotics,PGT group - colorectal cancer patients that received perioperative probiotics,11,11,3 months,16S,3,Roche454,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,decreased,NA,increased,Signature 2,Fig 4,30 September 2022,Mary Bearkland,"Mary Bearkland,Peace Sandy,WikiWorks","Figure 4. Different structures of the gut microbiota in the CGT, PGT and HGT groups. Histogram of the linear discriminant analysis scores for differentially abundant genera. The cladogram was calculated by LDA and displayed according to effect size. CGT, perioperative placebo group; PGT, probiotics group; linear discriminant analysis; HGT, healthy volunteer group; LDA, linear discriminant analysis.",decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillales Family X. Incertae Sedis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter",3384189|32066|203490|203491|203492;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|1385|539003;1783272|1239|186801|3082720|186804|1257;1783272|1239|186801|3085636|186803|653683,Complete,Peace Sandy
bsdb:26238090/3/1,26238090,randomized controlled trial,26238090,10.3892/mmr.2015.4124,NA,"Gao Z., Guo B., Gao R., Zhu Q., Wu W. , Qin H.",Probiotics modify human intestinal mucosa-associated microbiota in patients with colorectal cancer,Molecular medicine reports,2015,NA,Experiment 3,China,Homo sapiens,Intestinal mucosa,UBERON:0001242,Nutraceutical,CHEBI:50733,HGT- Healthy controls,CGT- colorectal cancer patients that received perioperative placebo,Patients that received perioperative placebos,11,11,3 months,16S,3,Roche454,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,Fig 4,30 September 2022,Mary Bearkland,"Mary Bearkland,Peace Sandy,WikiWorks","Figure 4. Different structures of the gut microbiota in the CGT, PGT and HGT groups. Histogram of the linear discriminant analysis scores for differentially abundant genera. The cladogram was calculated by LDA and displayed according to effect size. CGT, perioperative placebo group; PGT, probiotics group; linear discriminant analysis; HGT, healthy volunteer group; LDA, linear discriminant analysis.",increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillales Family X. Incertae Sedis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter",3384189|32066|203490|203491|203492;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|1385|539003;1783272|1239|186801|3082720|186804|1257;1783272|1239|186801|3085636|186803|653683,Complete,Peace Sandy
bsdb:26238090/3/2,26238090,randomized controlled trial,26238090,10.3892/mmr.2015.4124,NA,"Gao Z., Guo B., Gao R., Zhu Q., Wu W. , Qin H.",Probiotics modify human intestinal mucosa-associated microbiota in patients with colorectal cancer,Molecular medicine reports,2015,NA,Experiment 3,China,Homo sapiens,Intestinal mucosa,UBERON:0001242,Nutraceutical,CHEBI:50733,HGT- Healthy controls,CGT- colorectal cancer patients that received perioperative placebo,Patients that received perioperative placebos,11,11,3 months,16S,3,Roche454,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 2,Fig 4,30 September 2022,Mary Bearkland,"Mary Bearkland,Aiyshaaaa,Peace Sandy,WikiWorks","Figure 4. Different structures of the gut microbiota in the CGT, PGT, and HGT groups. Histogram of the linear discriminant analysis scores for differentially abundant genera. The cladogram was calculated by LDA and displayed according to effect size. CGT, perioperative placebo group; PGT, probiotics group; linear discriminant analysis; HGT, healthy volunteer group; LDA, linear discriminant analysis.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae",3379134|1224|1236|72274;3379134|1224;3379134|1224|1236;3379134|1224|1236|72274|135621|286;3379134|1224|1236|72274|135621;3379134|976|117743|200644;3379134|976|117743|200644|49546;3379134|1224|1236|2887326|468,Complete,Peace Sandy
bsdb:26239401/1/1,26239401,case-control,26239401,10.1038/srep12693,NA,"Pozuelo M., Panda S., Santiago A., Mendez S., Accarino A., Santos J., Guarner F., Azpiroz F. , Manichanh C.",Reduction of butyrate- and methane-producing microorganisms in patients with Irritable Bowel Syndrome,Scientific reports,2015,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS,Patients diagnosed with irritable bowel syndrome based on Rome III criteria.,66,113,"Yes, excluded recent antibiotic use (within 3 months).",16S,4,Illumina,relative abundances,"Kruskall-Wallis,Spearman Correlation",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,IBS vs Controls,29 November 2025,Aqc576444,Aqc576444,"IBS patients showed decreased abundance of several taxa compared to healthy controls, including Tenericutes (phylum), Erysipelotrichaceae (family), Ruminococcaceae (family), and a Lachnobacterium OTU (genus level). No taxa were significantly increased in IBS at the overall group level.",decreased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,1783272|1239|526524|526525|128827,Complete,NA
bsdb:26239401/1/2,26239401,case-control,26239401,10.1038/srep12693,NA,"Pozuelo M., Panda S., Santiago A., Mendez S., Accarino A., Santos J., Guarner F., Azpiroz F. , Manichanh C.",Reduction of butyrate- and methane-producing microorganisms in patients with Irritable Bowel Syndrome,Scientific reports,2015,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS,Patients diagnosed with irritable bowel syndrome based on Rome III criteria.,66,113,"Yes, excluded recent antibiotic use (within 3 months).",16S,4,Illumina,relative abundances,"Kruskall-Wallis,Spearman Correlation",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,IBS-D vs Controls,29 November 2025,Aqc576444,Aqc576444,"Patients with diarrhea-predominant IBS (IBS-D) exhibited significant reductions in several taxa compared to healthy controls, including Ruminococcaceae, Erysipelotrichaceae, Methanobacteriaceae, and unknown Clostridiales groups. These decreases align with lower microbial diversity observed in IBS-D.",decreased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,1783272|1239|526524|526525|128827,Complete,NA
bsdb:26239401/1/3,26239401,case-control,26239401,10.1038/srep12693,NA,"Pozuelo M., Panda S., Santiago A., Mendez S., Accarino A., Santos J., Guarner F., Azpiroz F. , Manichanh C.",Reduction of butyrate- and methane-producing microorganisms in patients with Irritable Bowel Syndrome,Scientific reports,2015,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS,Patients diagnosed with irritable bowel syndrome based on Rome III criteria.,66,113,"Yes, excluded recent antibiotic use (within 3 months).",16S,4,Illumina,relative abundances,"Kruskall-Wallis,Spearman Correlation",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 3,IBS-M vs Controls,29 November 2025,Aqc576444,Aqc576444,"Mixed-type IBS (IBS-M) patients showed a pronounced reduction in Erysipelotrichaceae abundance compared to healthy controls, consistent with patterns observed in IBS-D and reflecting shared microbial signatures across non-constipation subtypes.",decreased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,1783272|1239|526524|526525|128827,Complete,NA
bsdb:26239401/1/4,26239401,case-control,26239401,10.1038/srep12693,NA,"Pozuelo M., Panda S., Santiago A., Mendez S., Accarino A., Santos J., Guarner F., Azpiroz F. , Manichanh C.",Reduction of butyrate- and methane-producing microorganisms in patients with Irritable Bowel Syndrome,Scientific reports,2015,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS,Patients diagnosed with irritable bowel syndrome based on Rome III criteria.,66,113,"Yes, excluded recent antibiotic use (within 3 months).",16S,4,Illumina,relative abundances,"Kruskall-Wallis,Spearman Correlation",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 4,Controls vs IBS-D/IBS-M,29 November 2025,Aqc576444,Aqc576444,"Several taxa, including Akkermansia, Methanobrevibacter, and unclassified members of the Ruminococcaceae and Christensenellaceae families, were significantly more abundant in healthy controls compared to IBS-D and IBS-M patients. This suggests these taxa may be protective or associated with non-diarrheal phenotypes.",decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter",3379134|74201|203494|48461|1647988|239934;3366610|28890|183925|2158|2159|2172,Complete,NA
bsdb:26258571/1/1,26258571,randomized controlled trial,26258571,10.1097/QAI.0000000000000784,NA,"Stiksrud B., Nowak P., Nwosu F.C., Kvale D., Thalme A., Sonnerborg A., Ueland P.M., Holm K., Birkeland S.E., Dahm A.E., Sandset P.M., Rudi K., Hov J.R., Dyrhol-Riise A.M. , Trøseid M.",Reduced Levels of D-dimer and Changes in Gut Microbiota Composition After Probiotic Intervention in HIV-Infected Individuals on Stable ART,Journal of acquired immune deficiency syndromes (1999),2015,NA,Experiment 1,"Norway,Sweden",Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,baseline probiotic group,Probiotic group after 8 weeks of intervention,HIV-infected on antiretroviral therapy allocated to probiotic group after 8 weeks of intervention,11,11,2 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3 & Supplementary figure S4A,10 January 2021,Michael Lutete,"WikiWorks,ChiomaBlessing",Gut microbiota composition after probiotic intervention at 8 weeks compared to baseline group (in HIV-infected individuals on stable antiretroviral therapy (ART)),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|201174|1760;1783272|1239;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|541000,Complete,ChiomaBlessing
bsdb:26258571/1/2,26258571,randomized controlled trial,26258571,10.1097/QAI.0000000000000784,NA,"Stiksrud B., Nowak P., Nwosu F.C., Kvale D., Thalme A., Sonnerborg A., Ueland P.M., Holm K., Birkeland S.E., Dahm A.E., Sandset P.M., Rudi K., Hov J.R., Dyrhol-Riise A.M. , Trøseid M.",Reduced Levels of D-dimer and Changes in Gut Microbiota Composition After Probiotic Intervention in HIV-Infected Individuals on Stable ART,Journal of acquired immune deficiency syndromes (1999),2015,NA,Experiment 1,"Norway,Sweden",Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,baseline probiotic group,Probiotic group after 8 weeks of intervention,HIV-infected on antiretroviral therapy allocated to probiotic group after 8 weeks of intervention,11,11,2 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3 & Supplementary figure S4A,10 January 2021,Michael Lutete,"WikiWorks,ChiomaBlessing",Gut microbiota composition after probiotic intervention at 8 weeks compared to baseline group (in HIV-infected individuals on stable antiretroviral therapy (ART)),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota",3379134|976|200643|171549|815|816;3379134|976,Complete,ChiomaBlessing
bsdb:26258571/2/1,26258571,randomized controlled trial,26258571,10.1097/QAI.0000000000000784,NA,"Stiksrud B., Nowak P., Nwosu F.C., Kvale D., Thalme A., Sonnerborg A., Ueland P.M., Holm K., Birkeland S.E., Dahm A.E., Sandset P.M., Rudi K., Hov J.R., Dyrhol-Riise A.M. , Trøseid M.",Reduced Levels of D-dimer and Changes in Gut Microbiota Composition After Probiotic Intervention in HIV-Infected Individuals on Stable ART,Journal of acquired immune deficiency syndromes (1999),2015,NA,Experiment 2,"Norway,Sweden",Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Non-probiotic intervention group (after 8 weeks),Probiotic intervention group (after 8 weeks),Probiotic intervention group (after 8 weeks),13,11,2 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3,10 January 2021,Michael Lutete,"WikiWorks,ChiomaBlessing",Gut microbiota composition after probiotic intervention at 8 weeks compared to non-probiotic group (in HIV-infected individuals on stable antiretroviral therapy (ART)),increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,ChiomaBlessing
bsdb:26261039/1/1,26261039,"cross-sectional observational, not case-control",26261039,10.1186/s12876-015-0330-2,NA,"Kasai C., Sugimoto K., Moritani I., Tanaka J., Oya Y., Inoue H., Tameda M., Shiraki K., Ito M., Takei Y. , Takase K.","Comparison of the gut microbiota composition between obese and non-obese individuals in a Japanese population, as analyzed by terminal restriction fragment length polymorphism and next-generation sequencing",BMC gastroenterology,2015,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,controls,obese,BMI ≥25 kg/m2,4,6,currently on antibiotics,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Table 2, Table 4 & Table 5",10 January 2021,Marianthi Thomatos,"Fatima,WikiWorks","Comparison of the gut microbiota composition between obese and non-obese individuals in a Japanese population, using  Next generation sequencing",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hydrogenotrophica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum",1783272|1239|186801|3085636|186803|572511|53443;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|3085636|186803|572511|40520,Complete,Fatima
bsdb:26261039/1/2,26261039,"cross-sectional observational, not case-control",26261039,10.1186/s12876-015-0330-2,NA,"Kasai C., Sugimoto K., Moritani I., Tanaka J., Oya Y., Inoue H., Tameda M., Shiraki K., Ito M., Takei Y. , Takase K.","Comparison of the gut microbiota composition between obese and non-obese individuals in a Japanese population, as analyzed by terminal restriction fragment length polymorphism and next-generation sequencing",BMC gastroenterology,2015,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,controls,obese,BMI ≥25 kg/m2,4,6,currently on antibiotics,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Table 2, Table 4 & Table 5",10 January 2021,Marianthi Thomatos,WikiWorks,"Comparison of the gut microbiota composition between obese and non-obese individuals in a Japanese population, using  Next generation sequencing",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecichinchillae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Pseudomonadati|p__Bacteroidota",1783272|1239|186801|186802|216572|946234|292800;3379134|976|200643|171549|815|816|871325;3379134|976|200643|171549|815|816|818;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|3085636|186803|2719313|208479;3379134|976,Complete,Shaimaa Elsafoury
bsdb:26277095/1/1,26277095,case-control,26277095,10.1186/s12920-015-0121-1,NA,"Castro-Nallar E., Shen Y., Freishtat R.J., Pérez-Losada M., Manimaran S., Liu G., Johnson W.E. , Crandall K.A.",Integrating microbial and host transcriptomics to characterize asthma-associated microbial communities,BMC medical genomics,2015,NA,Experiment 1,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,Healthy controls,Asthma Samples,"Participants ranged between the ages of 6 and 20 years, with physician-diagnosed asthma for at least one year prior to the time of recruitment.",6,8,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,increased,decreased,NA,increased,Signature 1,"Figure 3b, and within result text (Microbial identification and relative abundance in asthma and control communities, paragraphs 2 and 3)",7 November 2023,MyleeeA,"MyleeeA,Folakunmi,WikiWorks",Differential relative abundance between asthma and control communities,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella catarrhalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter|s__Psychrobacter sp. PRwf-1",3379134|1224|1236|91347|543|561|562;3379134|1224|1236|2887326|468|475|480;3379134|1224|1236|2887326|468|497|349106,Complete,Folakunmi
bsdb:26277095/1/2,26277095,case-control,26277095,10.1186/s12920-015-0121-1,NA,"Castro-Nallar E., Shen Y., Freishtat R.J., Pérez-Losada M., Manimaran S., Liu G., Johnson W.E. , Crandall K.A.",Integrating microbial and host transcriptomics to characterize asthma-associated microbial communities,BMC medical genomics,2015,NA,Experiment 1,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,Healthy controls,Asthma Samples,"Participants ranged between the ages of 6 and 20 years, with physician-diagnosed asthma for at least one year prior to the time of recruitment.",6,8,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,increased,decreased,NA,increased,Signature 2,"Figure 3b, and within result text (Microbial identification and relative abundance in asthma and control communities, paragraphs 2 and 3)",7 November 2023,MyleeeA,"MyleeeA,Folakunmi,WikiWorks",Differential relative abundance between asthma and control communities,decreased,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus prevotii,1783272|1239|1737404|1737405|1570339|165779|33034,Complete,Folakunmi
bsdb:26279179/1/1,26279179,"cross-sectional observational, not case-control",26279179,10.1038/srep13212,NA,"Fugmann M., Breier M., Rottenkolber M., Banning F., Ferrari U., Sacco V., Grallert H., Parhofer K.G., Seissler J., Clavel T. , Lechner A.","The stool microbiota of insulin resistant women with recent gestational diabetes, a high risk group for type 2 diabetes",Scientific reports,2015,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,normoglycemic controls,Women with gestational DM,Gestational Diabetes Mellitus  was diagnosed by a standardized oral glucose tolerance test (OGTT) after the 23rd week of the preceding pregnecy,35,42,2 weeks,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Text and Figure 2,10 January 2021,Yaseen Javaid,WikiWorks,Comparison of relative sequence abundances at the different bacterial taxonomic ranks between pGDM and controls.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239|909932|1843489|31977;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|1263,Complete,Shaimaa Elsafoury
bsdb:26279179/1/2,26279179,"cross-sectional observational, not case-control",26279179,10.1038/srep13212,NA,"Fugmann M., Breier M., Rottenkolber M., Banning F., Ferrari U., Sacco V., Grallert H., Parhofer K.G., Seissler J., Clavel T. , Lechner A.","The stool microbiota of insulin resistant women with recent gestational diabetes, a high risk group for type 2 diabetes",Scientific reports,2015,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,normoglycemic controls,Women with gestational DM,Gestational Diabetes Mellitus  was diagnosed by a standardized oral glucose tolerance test (OGTT) after the 23rd week of the preceding pregnecy,35,42,2 weeks,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Text and Figure 2,10 January 2021,Yaseen Javaid,WikiWorks,Comparison of relative sequence abundances at the different bacterial taxonomic ranks between pGDM and controls.,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",1783272|1239;1783272|1239|186801;1783272|1239|186801|186802;3379134|976|200643|171549|171550;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|171550|239759,Complete,Shaimaa Elsafoury
bsdb:26288821/1/1,26288821,"cross-sectional observational, not case-control",26288821,10.1016/j.ebiom.2015.04.010,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4535156/,"Goedert J.J., Gong Y., Hua X., Zhong H., He Y., Peng P., Yu G., Wang W., Ravel J., Shi J. , Zheng Y.",Fecal Microbiota Characteristics of Patients with Colorectal Adenoma Detected by Screening: A Population-based Study,EBioMedicine,2015,"Cancer screening, China, Colorectal adenoma, Colorectal cancer, Feces, Microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,Normal Participants,Colorectal Adenoma Patients,patients with precancerous colorectal adenoma,24,20,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Supplementary Table 5,2 January 2022,Itslanapark,"Itslanapark,WikiWorks",differential relative abundance at the taxa and genera level between CRA patients and controls,increased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Legionellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Trabulsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",3379134|1224;3379134|1224|1236|72274|135621;3379134|1224|1236|118969|444;3379134|1224|1236|135619|28256;3379134|1224|1236|91347|543;3379134|1224|1236|91347|1903411|613;3379134|1224|1236|91347|543|620;3379134|1224|1236|91347|543|590;3379134|1224|1236|91347|1903409|53335;3379134|1224|1236|91347|1903414|581;3379134|1224|1236|91347|543|158851;3379134|1224|1236|91347|543|561,Complete,Claregrieve1
bsdb:26290472/1/NA,26290472,"cross-sectional observational, not case-control",26290472,10.1038/srep13338,https://pubmed.ncbi.nlm.nih.gov/26290472/,"Chong C.W., Ahmad A.F., Lim Y.A., Teh C.S., Yap I.K., Lee S.C., Chin Y.T., Loke P. , Chua K.H.",Effect of ethnicity and socioeconomic variation to the gut microbiota composition among pre-adolescent in Malaysia,Scientific reports,2015,NA,Experiment 1,Malaysia,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,"Chinese Children (High SES, household income>RM500)",Malays Children (Moderate SES. house income=<RM500),"Gut microbiota from fecal samples of 24 Malays children whose household income =<RM500.

Note: Poverty line = RM 764($254).",17,24,NA,16S,345,NA,relative abundances,PERMANOVA,0.05,TRUE,NA,NA,NA,unchanged,increased,NA,NA,unchanged,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:26290472/2/1,26290472,"cross-sectional observational, not case-control",26290472,10.1038/srep13338,https://pubmed.ncbi.nlm.nih.gov/26290472/,"Chong C.W., Ahmad A.F., Lim Y.A., Teh C.S., Yap I.K., Lee S.C., Chin Y.T., Loke P. , Chua K.H.",Effect of ethnicity and socioeconomic variation to the gut microbiota composition among pre-adolescent in Malaysia,Scientific reports,2015,NA,Experiment 2,Malaysia,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,"Chinese Children (High SES, household income >RM500)","Orang Asli Children (low SES, household income<RM500)",Gut microbiota from fecal samples of 20 Orang Asli children whose household income <RM500.,17,20,NA,16S,345,NA,relative abundances,PERMANOVA,0.05,TRUE,NA,NA,NA,increased,increased,NA,NA,increased,increased,Signature 1,Table 3,24 June 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1,WikiWorks",Differential microbial abundance between Chinese and Orang Asli children.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Bacteroidota,c__Deltaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|1224|1236|135624;3379134|976;28221;1783272|1239|186801|186802;1783272|1239|186801|186802|216572,Complete,Claregrieve1
bsdb:26290472/2/2,26290472,"cross-sectional observational, not case-control",26290472,10.1038/srep13338,https://pubmed.ncbi.nlm.nih.gov/26290472/,"Chong C.W., Ahmad A.F., Lim Y.A., Teh C.S., Yap I.K., Lee S.C., Chin Y.T., Loke P. , Chua K.H.",Effect of ethnicity and socioeconomic variation to the gut microbiota composition among pre-adolescent in Malaysia,Scientific reports,2015,NA,Experiment 2,Malaysia,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,"Chinese Children (High SES, household income >RM500)","Orang Asli Children (low SES, household income<RM500)",Gut microbiota from fecal samples of 20 Orang Asli children whose household income <RM500.,17,20,NA,16S,345,NA,relative abundances,PERMANOVA,0.05,TRUE,NA,NA,NA,increased,increased,NA,NA,increased,increased,Signature 2,Table 3,24 June 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1,WikiWorks",Differential microbial abundance between Chinese and Orang Asli children.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,3379134|976|200643|171549|171550|239759,Complete,Claregrieve1
bsdb:26290472/3/1,26290472,"cross-sectional observational, not case-control",26290472,10.1038/srep13338,https://pubmed.ncbi.nlm.nih.gov/26290472/,"Chong C.W., Ahmad A.F., Lim Y.A., Teh C.S., Yap I.K., Lee S.C., Chin Y.T., Loke P. , Chua K.H.",Effect of ethnicity and socioeconomic variation to the gut microbiota composition among pre-adolescent in Malaysia,Scientific reports,2015,NA,Experiment 3,Malaysia,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,"Malays children (Moderate SES, household income =>RM500)","Orang Asli children (low SES, household income <RM500)","Gut microbiota from fecal samples of 20 Orang Asli children whose household income<RM500.

45% of the households earn < RM500

Note: Poverty line = RM 764($254).",24,20,NA,16S,345,NA,relative abundances,PERMANOVA,0.05,TRUE,NA,NA,NA,increased,increased,NA,increased,increased,NA,Signature 1,Table 3,24 June 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1,WikiWorks",Differential microbial abundance between Malay and Orang Asli children.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Spirochaetota,,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia,c__Deltaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|1224|1236|135624;3379134|203691;;3379134|976;1783272|1239|186801;28221;1783272|1239|186801|186802|216572,Complete,Claregrieve1
bsdb:26290472/3/2,26290472,"cross-sectional observational, not case-control",26290472,10.1038/srep13338,https://pubmed.ncbi.nlm.nih.gov/26290472/,"Chong C.W., Ahmad A.F., Lim Y.A., Teh C.S., Yap I.K., Lee S.C., Chin Y.T., Loke P. , Chua K.H.",Effect of ethnicity and socioeconomic variation to the gut microbiota composition among pre-adolescent in Malaysia,Scientific reports,2015,NA,Experiment 3,Malaysia,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,"Malays children (Moderate SES, household income =>RM500)","Orang Asli children (low SES, household income <RM500)","Gut microbiota from fecal samples of 20 Orang Asli children whose household income<RM500.

45% of the households earn < RM500

Note: Poverty line = RM 764($254).",24,20,NA,16S,345,NA,relative abundances,PERMANOVA,0.05,TRUE,NA,NA,NA,increased,increased,NA,increased,increased,NA,Signature 2,Table 3,24 June 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1,WikiWorks",Differential microbial abundance between Malay and Orang Asli children.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales",3379134|976|200643|171549;1783272|1239|909932|909929,Complete,Claregrieve1
bsdb:26367776/1/1,26367776,"cross-sectional observational, not case-control",26367776,10.1371/journal.pone.0137429,NA,"Miyake S., Kim S., Suda W., Oshima K., Nakamura M., Matsuoka T., Chihara N., Tomita A., Sato W., Kim S.W., Morita H., Hattori M. , Yamamura T.","Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters",PloS one,2015,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Healthy subjects (controls),"Multiple sclerosis (MS),",Japanese patients with relapsing-remitting (RR) MS,40,20,NA,16S,12,Roche454,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,"Fig. S2, Table 1.",7 October 2024,Rahila,"Rahila,WikiWorks",Fold-change in the relative abundance of 21 species showing significant differences between HC40 and MS20 samples.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus",1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|1300|1301|1308,Complete,Svetlana up
bsdb:26367776/1/2,26367776,"cross-sectional observational, not case-control",26367776,10.1371/journal.pone.0137429,NA,"Miyake S., Kim S., Suda W., Oshima K., Nakamura M., Matsuoka T., Chihara N., Tomita A., Sato W., Kim S.W., Morita H., Hattori M. , Yamamura T.","Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters",PloS one,2015,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Healthy subjects (controls),"Multiple sclerosis (MS),",Japanese patients with relapsing-remitting (RR) MS,40,20,NA,16S,12,Roche454,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,"Fig. S2, Table 1, Fig. 4",7 October 2024,Rahila,"Rahila,KateRasheed,WikiWorks",Fold-change in the relative abundance of 21 species showing significant differences between HC40 and MS20 samples.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium SH032,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. ID5,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. RT8,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfotomaculaceae|g__Desulfotomaculum|s__Desulfotomaculum sp. CYP1,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__butyrate-producing bacterium A2-175,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__butyrate-producing bacterium SL7/1",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|207244|649756;3379134|976|200643|171549|815|816|46506;1783272|1239|186801|186802|31979|498621;1783272|1239|186801|186802|31979|1485|1506;1783272|1239|186801|186802|31979|1485|320882;1783272|1239|186801|186802|31979|1485|354438;1783272|1239|186801|186802|2937910|1562|381849;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|28050|28052;1783272|1239|909932|909929|1843491|158846|437897;3379134|976|200643|171549|815|909656|310298;3379134|976|200643|171549|815|909656|387090;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|2974251|165179;3379134|1224|28216|80840|995019|40544|40545;1783272|1239|186801|186802|105839;1783272|1239|186801|186802|245010,Complete,Svetlana up
bsdb:26367776/2/1,26367776,"cross-sectional observational, not case-control",26367776,10.1371/journal.pone.0137429,NA,"Miyake S., Kim S., Suda W., Oshima K., Nakamura M., Matsuoka T., Chihara N., Tomita A., Sato W., Kim S.W., Morita H., Hattori M. , Yamamura T.","Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters",PloS one,2015,NA,Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Healthy subjects (controls),"Multiple sclerosis (MS),",Japanese patients with relapsing-remitting (RR) MS,18,20,NA,16S,12,Roche454,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,unchanged,Signature 1,Fig 6,7 October 2024,Rahila,"Rahila,WikiWorks",Fold-change in the abundance of 21 species using longitudinal HC18 samples.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus",1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|1300|1301|1308;3379134|976|200643|171549|815|909656|310298;1783272|1239|909932|909929|1843491|158846|437897;3379134|976|200643|171549|815|909656|387090,Complete,Svetlana up
bsdb:26367776/2/2,26367776,"cross-sectional observational, not case-control",26367776,10.1371/journal.pone.0137429,NA,"Miyake S., Kim S., Suda W., Oshima K., Nakamura M., Matsuoka T., Chihara N., Tomita A., Sato W., Kim S.W., Morita H., Hattori M. , Yamamura T.","Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters",PloS one,2015,NA,Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Healthy subjects (controls),"Multiple sclerosis (MS),",Japanese patients with relapsing-remitting (RR) MS,18,20,NA,16S,12,Roche454,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,unchanged,Signature 2,Fig 6,7 October 2024,Rahila,"Rahila,WikiWorks",Fold-change in the abundance of 21 species using longitudinal HC18 samples.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium SH032,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. ID5,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. RT8,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfotomaculaceae|g__Desulfotomaculum|s__Desulfotomaculum sp. CYP1,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__butyrate-producing bacterium A2-175,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__butyrate-producing bacterium SL7/1,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|3085636|186803|207244|649756;3379134|976|200643|171549|815|816|46506;1783272|1239|186801|186802|31979|498621;1783272|1239|186801|186802|31979|1485|1506;1783272|1239|186801|186802|31979|1485|320882;1783272|1239|186801|186802|31979|1485|354438;1783272|1239|186801|186802|2937910|1562|381849;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|28050|28052;1783272|1239|909932|909929|1843491|158846|437897;3379134|976|200643|171549|815|909656|310298;3379134|976|200643|171549|815|909656|387090;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|1300|1301|1308;3379134|1224|28216|80840|995019|40544|40545;1783272|1239|186801|186802|105839;1783272|1239|186801|186802|245010;3379134|976|200643|171549|171552|2974251|165179,Complete,Svetlana up
bsdb:26394008/1/1,26394008,randomized controlled trial,26394008,10.1038/ismej.2015.151,NA,"Berni Canani R., Sangwan N., Stefka A.T., Nocerino R., Paparo L., Aitoro R., Calignano A., Khan A.A., Gilbert J.A. , Nagler C.R.",Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants,The ISME journal,2016,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,healthy controls,IgE mediated cow's milk allergy,diagnosis of IgE mediated cow's milk allergy based on clinical history and level of IgE serum-specific anti-cow's milk proteins,20,19,1 month,16S,4,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,"age,body weight,sex",NA,increased,increased,NA,NA,NA,NA,Signature 1,"Figure 1d, Text (""The gut microbiota of cow's milk allergic infants exhibits significantly increased diversity and altered composition""), Supplemental Table 2",10 January 2021,Lucy Mellor,"WikiWorks,Folakunmi",Differentially abundant taxa between healthy and cow's milk allergy pre-treatment groups,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|541000;1783272|1239|186801|186802|216572|1263,Complete,Folakunmi
bsdb:26394008/1/2,26394008,randomized controlled trial,26394008,10.1038/ismej.2015.151,NA,"Berni Canani R., Sangwan N., Stefka A.T., Nocerino R., Paparo L., Aitoro R., Calignano A., Khan A.A., Gilbert J.A. , Nagler C.R.",Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants,The ISME journal,2016,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,healthy controls,IgE mediated cow's milk allergy,diagnosis of IgE mediated cow's milk allergy based on clinical history and level of IgE serum-specific anti-cow's milk proteins,20,19,1 month,16S,4,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,"age,body weight,sex",NA,increased,increased,NA,NA,NA,NA,Signature 2,"Figure 1d, Text(""The gut microbiota of cow's milk allergic infants exhibits significantly increased diversity and altered composition""), Supplemental Table 2",10 January 2021,Lucy Mellor,"WikiWorks,Folakunmi",Differentially abundant taxa between healthy and cow's milk allergy pre-treatment groups,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;3379134|1224|1236|91347|543|561;1783272|1239|91061|186826|1300,Complete,Folakunmi
bsdb:26394008/2/1,26394008,randomized controlled trial,26394008,10.1038/ismej.2015.151,NA,"Berni Canani R., Sangwan N., Stefka A.T., Nocerino R., Paparo L., Aitoro R., Calignano A., Khan A.A., Gilbert J.A. , Nagler C.R.",Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants,The ISME journal,2016,NA,Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,pre EHCF with LGG,post EHCF with LGG,cow milk allergic infants post treatment with EHCF with LGG,12,12,1 month,16S,4,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,"age,body weight,sex",NA,increased,increased,NA,NA,NA,NA,Signature 1,"text (""Treatment with LGG-supplemented EHCF increases the relative abundance of butyrate-producing bacteria and fecal butyrate levels""), Supplemental Table 2",24 January 2024,Folakunmi,"Folakunmi,WikiWorks",Differentially abundant taxa between pre EHCF with LGG and post EHCF with LGG groups,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|33042,Complete,Folakunmi
bsdb:26394008/3/1,26394008,randomized controlled trial,26394008,10.1038/ismej.2015.151,NA,"Berni Canani R., Sangwan N., Stefka A.T., Nocerino R., Paparo L., Aitoro R., Calignano A., Khan A.A., Gilbert J.A. , Nagler C.R.",Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants,The ISME journal,2016,NA,Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Lactobacillus rhamnosus GG,NCBITAXON:568703,Post EHCF treatment,Post EHCF with LGG,cow milk allergic infants post treatment with EHCF with LGG,7,12,1 month,16S,4,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,"age,body weight,sex",NA,increased,increased,NA,NA,NA,NA,Signature 1,"Within text result (""Treatment with LGG-supplemented EHCF increases the relative abundance of butyrate-producing bacteria and fecal butyrate levels"", lines 10-12), supplemental table 2",24 January 2024,Folakunmi,"Folakunmi,WikiWorks",Differentially abundant taxa between Post EHCF and Post EHCF with LGG groups,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis",1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|186806|264995,Complete,Folakunmi
bsdb:26397137/1/1,26397137,"cross-sectional observational, not case-control",26397137,10.18632/oncotarget.5166,NA,"Yu Y.N., Yu T.C., Zhao H.J., Sun T.T., Chen H.M., Chen H.Y., An H.F., Weng Y.R., Yu J., Li M., Qin W.X., Ma X., Shen N., Hong J. , Fang J.Y.",Berberine may rescue Fusobacterium nucleatum-induced colorectal tumorigenesis by modulating the tumor microenvironment,Oncotarget,2015,"Fusobacterium nucleatum, berberine, colorectal tumorigenesis, intestinal microbiota, tumor-immune cytokine",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Negative control group,CRA and CRC groups,Patients with CRA (colorectal adenoma) or CRC (colorectal carcinoma) confirmed by colonoscopy and pathological examination,52,89,6 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table 1,2 June 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between the control group and the CRA+CRC patients,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|186806|1730;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|841,Complete,Claregrieve1
bsdb:26397137/1/2,26397137,"cross-sectional observational, not case-control",26397137,10.18632/oncotarget.5166,NA,"Yu Y.N., Yu T.C., Zhao H.J., Sun T.T., Chen H.M., Chen H.Y., An H.F., Weng Y.R., Yu J., Li M., Qin W.X., Ma X., Shen N., Hong J. , Fang J.Y.",Berberine may rescue Fusobacterium nucleatum-induced colorectal tumorigenesis by modulating the tumor microenvironment,Oncotarget,2015,"Fusobacterium nucleatum, berberine, colorectal tumorigenesis, intestinal microbiota, tumor-immune cytokine",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Negative control group,CRA and CRC groups,Patients with CRA (colorectal adenoma) or CRC (colorectal carcinoma) confirmed by colonoscopy and pathological examination,52,89,6 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Table 1,2 June 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between the control group and the CRA+CRC patients,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|186801|3085636|186803|33042;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|1940338;3384189|32066|203490|203491|203492|848;1783272|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:26397137/2/1,26397137,"cross-sectional observational, not case-control",26397137,10.18632/oncotarget.5166,NA,"Yu Y.N., Yu T.C., Zhao H.J., Sun T.T., Chen H.M., Chen H.Y., An H.F., Weng Y.R., Yu J., Li M., Qin W.X., Ma X., Shen N., Hong J. , Fang J.Y.",Berberine may rescue Fusobacterium nucleatum-induced colorectal tumorigenesis by modulating the tumor microenvironment,Oncotarget,2015,"Fusobacterium nucleatum, berberine, colorectal tumorigenesis, intestinal microbiota, tumor-immune cytokine",Experiment 2,China,Mus musculus,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,Control (male C57BL/6-APCMin/+ and male wild-type C57BL/6),Fn Mice,Mice administered with F. nucleatum (Fn),10,10,NA,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,4 June 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between control mice and Fn-treated mice,increased,"k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Verrucomicrobiota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia",1783272|544448;3379134|74201;3384189|32066|203490,Complete,Claregrieve1
bsdb:26397137/3/1,26397137,"cross-sectional observational, not case-control",26397137,10.18632/oncotarget.5166,NA,"Yu Y.N., Yu T.C., Zhao H.J., Sun T.T., Chen H.M., Chen H.Y., An H.F., Weng Y.R., Yu J., Li M., Qin W.X., Ma X., Shen N., Hong J. , Fang J.Y.",Berberine may rescue Fusobacterium nucleatum-induced colorectal tumorigenesis by modulating the tumor microenvironment,Oncotarget,2015,"Fusobacterium nucleatum, berberine, colorectal tumorigenesis, intestinal microbiota, tumor-immune cytokine",Experiment 3,China,Mus musculus,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,DMH Treated Mice,Fn+DMH Treated Mice,Mice treated with Fn and DMH,10,10,NA,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,4 June 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between DMH-treated mice and Fn+DMH treated mice,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Mycoplasmatota",3384189|32066|203490;3379134|74201;1783272|544448,Complete,Claregrieve1
bsdb:26397137/4/1,26397137,"cross-sectional observational, not case-control",26397137,10.18632/oncotarget.5166,NA,"Yu Y.N., Yu T.C., Zhao H.J., Sun T.T., Chen H.M., Chen H.Y., An H.F., Weng Y.R., Yu J., Li M., Qin W.X., Ma X., Shen N., Hong J. , Fang J.Y.",Berberine may rescue Fusobacterium nucleatum-induced colorectal tumorigenesis by modulating the tumor microenvironment,Oncotarget,2015,"Fusobacterium nucleatum, berberine, colorectal tumorigenesis, intestinal microbiota, tumor-immune cytokine",Experiment 4,China,Mus musculus,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,Fn+DMH Treated Mice,BBR+Fn+DMH Treated Mice,"Mice treated with BBR, Fn and DMH",10,10,NA,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,22 May 2023,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between Fn+DMH-treated mice and BBR+Fn+DMH treated mice,decreased,"k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Verrucomicrobiota",1783272|544448;3379134|74201,Complete,Claregrieve1
bsdb:26408641/1/1,26408641,"cross-sectional observational, not case-control",26408641,https://doi.org/10.1136/gutjnl-2015-309800,https://gut.bmj.com/content/66/1/70,"Yu J., Feng Q., Wong S.H., Zhang D., Liang Q.Y., Qin Y., Tang L., Zhao H., Stenvang J., Li Y., Wang X., Xu X., Chen N., Wu W.K., Al-Aama J., Nielsen H.J., Kiilerich P., Jensen B.A., Yau T.O., Lan Z., Jia H., Li J., Xiao L., Lam T.Y., Ng S.C., Cheng A.S., Wong V.W., Chan F.K., Xu X., Yang H., Madsen L., Datz C., Tilg H., Wang J., Brünner N., Kristiansen K., Arumugam M., Sung J.J. , Wang J.",Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer,Gut,2017,"BACTERIAL INTERACTIONS, COLONIC MICROFLORA, COLORECTAL CANCER",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,control,Colorectal cancer patients,Patients with colorectal cancer.,54,74,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,Supplementary Table 8,12 March 2023,Sophy,"Sophy,Atrayees,WikiWorks","Differential abundance of IMG, mOTU and MLG species associated with CRC patients and controls.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Thiotrichaceae|g__Beggiatoa|s__Beggiatoa sp. PS,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia mallei,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus|s__Cloacibacillus evryensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium 1_7_47FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. HGF2,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus sp. 3_3_56FAA,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Methylococcales|f__Crenotrichaceae|g__Crenothrix|s__Crenothrix polyspora,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio sp. 6_1_46AFAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium necrophorum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp. oral taxon 370,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium varium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 3_1_46FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 3_1_57FAA_CT1,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 5_1_57FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 8_1_57FAA,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia globosa,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus|s__Paracoccus denitrificans,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp. oral taxon 110,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp. oral taxon 393,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus indolicus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus|s__Streptobacillus moniliformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus dysgalactiae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus equi,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus equinus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudoporcinus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp. 4_3_54A2FAA,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Sulfurovaceae|g__Sulfurovum|s__Sulfurovum sp. SCGC AAA036-O23,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes|s__Synergistes sp. 3_1_syn1,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum",3379134|976|200643|171549|171550|239759|626932;3379134|976|200643|171549|815|816|817;3379134|1224|1236|72273|135617|1021|422289;3379134|1224|28216|80840|119060|32008|13373;3384194|508458|649775|649776|649777|508459|508460;1783272|1239|186801|186802|457421;1783272|1239|186801|186802|31979|1485|908340;1783272|1239|526524|526525|2810280|100883|665941;3379134|1224|1236|135618|89377|200670|360316;3379134|200940|3031449|213115|194924|872|665942;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3082720|3118655|44259|143361;3384189|32066|203490|203491|203492|848|859;3384189|32066|203490|203491|203492|848|851;3384189|32066|203490|203491|203492|848|712288;3384189|32066|203490|203491|203492|848|856;1783272|1239|91061|1385|539738|1378|29391;1783272|1239|186801|3085636|186803|1649459|154046;1783272|1239|186801|3085636|186803|665950;1783272|1239|186801|3085636|186803|658086;1783272|1239|186801|3085636|186803|658085;1783272|1239|186801|3085636|186803|665951;3384189|32066|203490|203491|1129771|32067|40542;4751|5204|1538075|162474|742845|55193|76773;3379134|1224|28211|204455|31989|265|266;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|1239|1737404|1737405|1570339|543311|671230;1783272|1239|1737404|1737405|1570339|543311|713008;1783272|1239|1737404|1737405|1570339|162289|33030;1783272|1239|186801|3082720|186804|1257|1261;1783272|1239|186801|3082720|186804|1257|341694;3379134|976|200643|171549|171552|838|28131;1783272|1239|526524|526525|128827|123375|102148;3384189|32066|203490|203491|1129771|34104|34105;1783272|1239|91061|186826|1300|1301|76860;1783272|1239|91061|186826|1300|1301|1334;1783272|1239|91061|186826|1300|1301|1336;1783272|1239|91061|186826|1300|1301|1335;1783272|1239|91061|186826|1300|1301|361101;1783272|1239|186801|186802|216572|292632|665956;3379134|29547|3031852|213849|2771472|265570|1001764;3384194|508458|649775|649776|649777|2753|457415;1783272|1239|186801|3085636|186803|2941495|1512,Complete,Atrayees
bsdb:26408641/1/2,26408641,"cross-sectional observational, not case-control",26408641,https://doi.org/10.1136/gutjnl-2015-309800,https://gut.bmj.com/content/66/1/70,"Yu J., Feng Q., Wong S.H., Zhang D., Liang Q.Y., Qin Y., Tang L., Zhao H., Stenvang J., Li Y., Wang X., Xu X., Chen N., Wu W.K., Al-Aama J., Nielsen H.J., Kiilerich P., Jensen B.A., Yau T.O., Lan Z., Jia H., Li J., Xiao L., Lam T.Y., Ng S.C., Cheng A.S., Wong V.W., Chan F.K., Xu X., Yang H., Madsen L., Datz C., Tilg H., Wang J., Brünner N., Kristiansen K., Arumugam M., Sung J.J. , Wang J.",Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer,Gut,2017,"BACTERIAL INTERACTIONS, COLONIC MICROFLORA, COLORECTAL CANCER",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,control,Colorectal cancer patients,Patients with colorectal cancer.,54,74,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Supplementary Table 8,12 March 2023,Sophy,"Sophy,Atrayees,WikiWorks","Differential abundance of IMG, mOTU and MLG species associated with CRC patients and controls.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium 1_1_47,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Adhaeribacter|s__Adhaeribacter aquaticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp. ART55/1,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__butyrate-producing bacterium SS3/4,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. L2-50,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",3379134|1224|28216|80840|469610;1783272|1239|186801|186802|186806|1730|39496;3379134|976|768503|768507|1853232|299566|299567;1783272|1239|186801|3085636|186803|33042|751585;1783272|1239|186801|186802|245014;3379134|1224|1236|135625|712|724|729;1783272|1239|526524|526525|128827|1573535|1735;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|2316020|33039;3379134|1224|1236|91347|543|570|573;1783272|1239|186801|3085636|186803|28050|39485;3379134|976|200643|171549|815|816|626929;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|186802|31979|1485|411489;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|1766253|39491,Complete,Atrayees
bsdb:26416813/1/1,26416813,prospective cohort,26416813,10.1136/gutjnl-2015-309957,NA,"De Filippis F., Pellegrini N., Vannini L., Jeffery I.B., La Storia A., Laghi L., Serrazanetti D.I., Di Cagno R., Ferrocino I., Lazzi C., Turroni S., Cocolin L., Brigidi P., Neviani E., Gobbetti M., O'Toole P.W. , Ercolini D.",High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome,Gut,2016,"DIET, DIETARY FIBRE, ENTERIC BACTERIAL MICROFLORA, INTESTINAL BACTERIA, SHORT CHAIN FATTY ACIDS",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,vegetarians,omnivores,"individuals who eat animal products in addition to other foods (plants, grains, etc)",51,51,3 months,16S,123,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Table S2,11 February 2021,Lorakasselman,"Lorakasselman,Claregrieve1,WikiWorks",Differential microbial abundance between omnivores and vegetarians,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,1783272|1239|186801|3085636|186803|28050,Complete,Claregrieve1
bsdb:26416813/1/2,26416813,prospective cohort,26416813,10.1136/gutjnl-2015-309957,NA,"De Filippis F., Pellegrini N., Vannini L., Jeffery I.B., La Storia A., Laghi L., Serrazanetti D.I., Di Cagno R., Ferrocino I., Lazzi C., Turroni S., Cocolin L., Brigidi P., Neviani E., Gobbetti M., O'Toole P.W. , Ercolini D.",High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome,Gut,2016,"DIET, DIETARY FIBRE, ENTERIC BACTERIAL MICROFLORA, INTESTINAL BACTERIA, SHORT CHAIN FATTY ACIDS",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,vegetarians,omnivores,"individuals who eat animal products in addition to other foods (plants, grains, etc)",51,51,3 months,16S,123,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Table S2,1 January 2023,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between omnivores and vegetarians,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|186801|186802|216572|1263;1783272|1239|909932|1843489|31977,Complete,NA
bsdb:26416813/2/1,26416813,prospective cohort,26416813,10.1136/gutjnl-2015-309957,NA,"De Filippis F., Pellegrini N., Vannini L., Jeffery I.B., La Storia A., Laghi L., Serrazanetti D.I., Di Cagno R., Ferrocino I., Lazzi C., Turroni S., Cocolin L., Brigidi P., Neviani E., Gobbetti M., O'Toole P.W. , Ercolini D.",High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome,Gut,2016,"DIET, DIETARY FIBRE, ENTERIC BACTERIAL MICROFLORA, INTESTINAL BACTERIA, SHORT CHAIN FATTY ACIDS",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,vegans,omnivores,"individuals who eat animal products in addition to other foods (plants, grains, etc)",51,51,3 months,16S,123,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table S2,11 February 2021,Lorakasselman,"Lorakasselman,Claregrieve1,WikiWorks",Differential microbial abundance between omnivores and vegans,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|28050;3379134|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:26416813/2/2,26416813,prospective cohort,26416813,10.1136/gutjnl-2015-309957,NA,"De Filippis F., Pellegrini N., Vannini L., Jeffery I.B., La Storia A., Laghi L., Serrazanetti D.I., Di Cagno R., Ferrocino I., Lazzi C., Turroni S., Cocolin L., Brigidi P., Neviani E., Gobbetti M., O'Toole P.W. , Ercolini D.",High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome,Gut,2016,"DIET, DIETARY FIBRE, ENTERIC BACTERIAL MICROFLORA, INTESTINAL BACTERIA, SHORT CHAIN FATTY ACIDS",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,vegans,omnivores,"individuals who eat animal products in addition to other foods (plants, grains, etc)",51,51,3 months,16S,123,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table S2,1 January 2023,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between omnivores and vegans,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|119852,Complete,Claregrieve1
bsdb:26416813/3/1,26416813,prospective cohort,26416813,10.1136/gutjnl-2015-309957,NA,"De Filippis F., Pellegrini N., Vannini L., Jeffery I.B., La Storia A., Laghi L., Serrazanetti D.I., Di Cagno R., Ferrocino I., Lazzi C., Turroni S., Cocolin L., Brigidi P., Neviani E., Gobbetti M., O'Toole P.W. , Ercolini D.",High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome,Gut,2016,"DIET, DIETARY FIBRE, ENTERIC BACTERIAL MICROFLORA, INTESTINAL BACTERIA, SHORT CHAIN FATTY ACIDS",Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,vegans,vegetarians,individuals who do not eat meat but do eat other animal products,51,51,3 months,16S,123,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table S2,1 January 2023,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between vegetarians and vegans,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,1783272|1239|186801|186802|216572|119852,Complete,Claregrieve1
bsdb:26428446/1/1,26428446,case-control,26428446,10.1097/PSY.0000000000000247,NA,"Kleiman S.C., Watson H.J., Bulik-Sullivan E.C., Huh E.Y., Tarantino L.M., Bulik C.M. , Carroll I.M.","The Intestinal Microbiota in Acute Anorexia Nervosa and During Renourishment: Relationship to Depression, Anxiety, and Eating Disorder Psychopathology",Psychosomatic medicine,2015,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Anorexia nervosa,EFO:0004215,Healthy comparison group (HCG),Anorexia patients at T1,Patients with anorexia at hospital admission (T1),12,16,2 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,NA,decreased,NA,NA,decreased,Signature 1,Table 2,10 January 2021,Fatima Zohra,"WikiWorks,ChiomaBlessing",Differences in microbial taxa among anorexia patients at hospital admission (T1) VS healthy comparison group (HCG),increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales",1783272|1239|91061;1783272|201174|84998|84999,Complete,ChiomaBlessing
bsdb:26428446/1/2,26428446,case-control,26428446,10.1097/PSY.0000000000000247,NA,"Kleiman S.C., Watson H.J., Bulik-Sullivan E.C., Huh E.Y., Tarantino L.M., Bulik C.M. , Carroll I.M.","The Intestinal Microbiota in Acute Anorexia Nervosa and During Renourishment: Relationship to Depression, Anxiety, and Eating Disorder Psychopathology",Psychosomatic medicine,2015,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Anorexia nervosa,EFO:0004215,Healthy comparison group (HCG),Anorexia patients at T1,Patients with anorexia at hospital admission (T1),12,16,2 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,NA,decreased,NA,NA,decreased,Signature 2,Table 2,10 January 2021,Fatima Zohra,"WikiWorks,ChiomaBlessing",Differences in microbial taxa among anorexia patients at hospital admission (T1) VS healthy comparison group (HCG),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|1239|186801|3085636|186803|207244;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851,Complete,ChiomaBlessing
bsdb:26428446/2/1,26428446,case-control,26428446,10.1097/PSY.0000000000000247,NA,"Kleiman S.C., Watson H.J., Bulik-Sullivan E.C., Huh E.Y., Tarantino L.M., Bulik C.M. , Carroll I.M.","The Intestinal Microbiota in Acute Anorexia Nervosa and During Renourishment: Relationship to Depression, Anxiety, and Eating Disorder Psychopathology",Psychosomatic medicine,2015,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Anorexia nervosa,EFO:0004215,Healthy comparison group (HCG),Anorexia patients at T2,Patients with anorexia at hospital discharge (T2),12,10,2 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,NA,decreased,NA,NA,decreased,Signature 1,Table 3,10 January 2021,Fatima Zohra,"WikiWorks,ChiomaBlessing",Differences in microbial taxa among anorexia patients at hospital discharge (T2) VS healthy comparison group (HCG),increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",1783272|201174|84998|84999;3379134|976|200643|171549|2005525|375288,Complete,ChiomaBlessing
bsdb:26428446/2/2,26428446,case-control,26428446,10.1097/PSY.0000000000000247,NA,"Kleiman S.C., Watson H.J., Bulik-Sullivan E.C., Huh E.Y., Tarantino L.M., Bulik C.M. , Carroll I.M.","The Intestinal Microbiota in Acute Anorexia Nervosa and During Renourishment: Relationship to Depression, Anxiety, and Eating Disorder Psychopathology",Psychosomatic medicine,2015,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Anorexia nervosa,EFO:0004215,Healthy comparison group (HCG),Anorexia patients at T2,Patients with anorexia at hospital discharge (T2),12,10,2 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,NA,decreased,NA,NA,decreased,Signature 2,Table 3,10 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differences in microbial taxa among anorexia patients at hospital discharge (T2) VS healthy comparison group (HCG),decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,1783272|1239|186801|186802|541000,Complete,ChiomaBlessing
bsdb:26431583/1/1,26431583,"cross-sectional observational, not case-control",26431583,10.1016/j.jaci.2015.08.021,NA,"Song H., Yoo Y., Hwang J., Na Y.C. , Kim H.S.",Faecalibacterium prausnitzii subspecies-level dysbiosis in the human gut microbiome underlying atopic dermatitis,The Journal of allergy and clinical immunology,2016,"Atopic dermatitis, Faecalibacterium prausnitzii, dysbiosis, gut microbiota, microbiome",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy control,patient with atopic dermatitis,infants (<1 year old) diagnosed with atopic dermatitis based on the SCORAD scoring system,5,15,6 months,16S,12,Roche454,NA,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 1, Supplemental Figure E1",10 January 2021,Lucy Mellor,WikiWorks,Bacterial genera that are distinctive between the AD and the non-AD children age <1 year old,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|3085636|186803|140625;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|171550|239759,Complete,Claregrieve1
bsdb:26431583/1/2,26431583,"cross-sectional observational, not case-control",26431583,10.1016/j.jaci.2015.08.021,NA,"Song H., Yoo Y., Hwang J., Na Y.C. , Kim H.S.",Faecalibacterium prausnitzii subspecies-level dysbiosis in the human gut microbiome underlying atopic dermatitis,The Journal of allergy and clinical immunology,2016,"Atopic dermatitis, Faecalibacterium prausnitzii, dysbiosis, gut microbiota, microbiome",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy control,patient with atopic dermatitis,infants (<1 year old) diagnosed with atopic dermatitis based on the SCORAD scoring system,5,15,6 months,16S,12,Roche454,NA,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 1, Supplemental Figure E1",10 January 2021,Lucy Mellor,WikiWorks,Bacterial genera that are distinctive between the AD and the non-AD children age <1 year old,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|620;3379134|1224|1236|91347|543,Complete,Claregrieve1
bsdb:26431583/2/1,26431583,"cross-sectional observational, not case-control",26431583,10.1016/j.jaci.2015.08.021,NA,"Song H., Yoo Y., Hwang J., Na Y.C. , Kim H.S.",Faecalibacterium prausnitzii subspecies-level dysbiosis in the human gut microbiome underlying atopic dermatitis,The Journal of allergy and clinical immunology,2016,"Atopic dermatitis, Faecalibacterium prausnitzii, dysbiosis, gut microbiota, microbiome",Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy control,patient with atopic dermatitis,patient age 1-6 years diagnosed with atopic dermatitis based on the SCORAD scoring system,15,58,6 months,16S,12,Roche454,NA,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 1, Supplemental Figure E1",10 January 2021,Lucy Mellor,WikiWorks,Bacterial genera that are distinctive between the AD and the non-AD children age 1-6 years old,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,1783272|1239|186801|186802|216572|1263,Complete,Claregrieve1
bsdb:26431583/2/2,26431583,"cross-sectional observational, not case-control",26431583,10.1016/j.jaci.2015.08.021,NA,"Song H., Yoo Y., Hwang J., Na Y.C. , Kim H.S.",Faecalibacterium prausnitzii subspecies-level dysbiosis in the human gut microbiome underlying atopic dermatitis,The Journal of allergy and clinical immunology,2016,"Atopic dermatitis, Faecalibacterium prausnitzii, dysbiosis, gut microbiota, microbiome",Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy control,patient with atopic dermatitis,patient age 1-6 years diagnosed with atopic dermatitis based on the SCORAD scoring system,15,58,6 months,16S,12,Roche454,NA,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 1, Supplemental Figure E1",10 January 2021,Lucy Mellor,WikiWorks,Bacterial genera that are distinctive between the AD and the non-AD children age 1-6 years old,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus",1783272|1239|526524|526525|2810281|191303;1783272|1239|526524|526525|2810280|100883,Complete,Claregrieve1
bsdb:26431583/3/1,26431583,"cross-sectional observational, not case-control",26431583,10.1016/j.jaci.2015.08.021,NA,"Song H., Yoo Y., Hwang J., Na Y.C. , Kim H.S.",Faecalibacterium prausnitzii subspecies-level dysbiosis in the human gut microbiome underlying atopic dermatitis,The Journal of allergy and clinical immunology,2016,"Atopic dermatitis, Faecalibacterium prausnitzii, dysbiosis, gut microbiota, microbiome",Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy control,patient with atopic dermatitis,patient age >6 years diagnosed with atopic dermatitis based on the SCORAD scoring system,22,17,6 months,16S,12,Roche454,NA,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 1, Supplemental Figure E1",10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Bacterial genera that are distinctive between the AD and the non-AD patients age >6 years old,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella",1783272|1239|186801|3082720|186804;1783272|1239|186801|3085636|186803|588605,Complete,Claregrieve1
bsdb:26431583/3/2,26431583,"cross-sectional observational, not case-control",26431583,10.1016/j.jaci.2015.08.021,NA,"Song H., Yoo Y., Hwang J., Na Y.C. , Kim H.S.",Faecalibacterium prausnitzii subspecies-level dysbiosis in the human gut microbiome underlying atopic dermatitis,The Journal of allergy and clinical immunology,2016,"Atopic dermatitis, Faecalibacterium prausnitzii, dysbiosis, gut microbiota, microbiome",Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy control,patient with atopic dermatitis,patient age >6 years diagnosed with atopic dermatitis based on the SCORAD scoring system,22,17,6 months,16S,12,Roche454,NA,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 1, Supplemental Figure E1",10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Bacterial genera that are distinctive between the AD and the non-AD patients age >6 years old,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",1783272|1239|186801|186802|216572|244127;3379134|976|200643|171549|1853231|574697;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|186802|541000;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|171551,Complete,Claregrieve1
bsdb:26457297/1/1,26457297,case-control,26457297,10.1155/2015/173729,NA,"Hu J., Han S., Chen Y. , Ji Z.",Variations of Tongue Coating Microbiota in Patients with Gastric Cancer,BioMed research international,2015,NA,Experiment 1,China,Homo sapiens,Tongue,UBERON:0001723,Gastric cancer,MONDO:0001056,controls,gastric cancer,gastric cancer,16,34,2 months,16S,234,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Table 4, text",10 January 2021,Rimsha Azhar,WikiWorks,Relative abundances of selected tongue coating microbial taxa in 34 gastric cancer subjects and 16 control subjects.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Actinomycetota",3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;1783272|201174|1760|2037|2049|1654;3384189|32066|203490|203491|1129771|32067;1783272|201174,Complete,Atrayees
bsdb:26457297/1/2,26457297,case-control,26457297,10.1155/2015/173729,NA,"Hu J., Han S., Chen Y. , Ji Z.",Variations of Tongue Coating Microbiota in Patients with Gastric Cancer,BioMed research international,2015,NA,Experiment 1,China,Homo sapiens,Tongue,UBERON:0001723,Gastric cancer,MONDO:0001056,controls,gastric cancer,gastric cancer,16,34,2 months,16S,234,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"Table 4, text",10 January 2021,Rimsha Azhar,"WikiWorks,Atrayees",Relative abundances of selected tongue coating microbial taxa in 34 gastric cancer subjects and 16 control subjects.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|1224|28216|206351|481|482;3384189|32066|203490|203491|203492|848;3379134|1224|1236|135625|712|724;3379134|976|200643|171549|171551|836;3379134|1224;1783272|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:26515465/1/1,26515465,"cross-sectional observational, not case-control",26515465,10.1038/ncomms9727,NA,"Nakatsu G., Li X., Zhou H., Sheng J., Wong S.H., Wu W.K., Ng S.C., Tsoi H., Dong Y., Zhang N., He Y., Kang Q., Cao L., Wang K., Zhang J., Liang Q., Yu J. , Sung J.J.",Gut mucosal microbiome across stages of colorectal carcinogenesis,Nature communications,2015,NA,Experiment 1,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal adenoma,EFO:0005406,healthy controls,colorectal adenoma,histology-proven adenoma,61,47,NA,16S,1234,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,Signature 1,Supplementary Figure 9,24 June 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between patients with colorectal adenoma and controls,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter|s__Enhydrobacter sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia",1783272|1239|91061|1385;3379134|976|200643|171549|815|816|820;1783272|1239|186801|3085636|186803|572511|1955243;3379134|1224|28211|356|212791|1894999;3379134|1224|1236|91347|543|561|562;1783272|1239|91061|1385|539738|1378|1966354;1783272|1239|1737404|1737405|1570339|543311|1944660;1783272|1239|186801|3082720|186804|1257|1262;3379134|976|200643|171549|171552|838|28131,Complete,Claregrieve1
bsdb:26515465/1/2,26515465,"cross-sectional observational, not case-control",26515465,10.1038/ncomms9727,NA,"Nakatsu G., Li X., Zhou H., Sheng J., Wong S.H., Wu W.K., Ng S.C., Tsoi H., Dong Y., Zhang N., He Y., Kang Q., Cao L., Wang K., Zhang J., Liang Q., Yu J. , Sung J.J.",Gut mucosal microbiome across stages of colorectal carcinogenesis,Nature communications,2015,NA,Experiment 1,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal adenoma,EFO:0005406,healthy controls,colorectal adenoma,histology-proven adenoma,61,47,NA,16S,1234,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,Signature 2,Supplementary Figure 9,25 June 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between patients with colorectal adenoma and controls,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.",1783272|1239|91061|1385;3379134|976|200643|171549|815|816|29523;3379134|976|200643|171549|815|816|820;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|572511|1955243;1783272|1239|186801|3085636|186803|33042|2049024;1783272|1239|186801|186802|216572|216851|853;3379134|976|200643|171549|171552|838|59823,Complete,Claregrieve1
bsdb:26515465/2/1,26515465,"cross-sectional observational, not case-control",26515465,10.1038/ncomms9727,NA,"Nakatsu G., Li X., Zhou H., Sheng J., Wong S.H., Wu W.K., Ng S.C., Tsoi H., Dong Y., Zhang N., He Y., Kang Q., Cao L., Wang K., Zhang J., Liang Q., Yu J. , Sung J.J.",Gut mucosal microbiome across stages of colorectal carcinogenesis,Nature communications,2015,NA,Experiment 2,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,healthy controls,colorectal cancer (adenocarcinoma),subjects with invasive adenocarcinoma,61,52,NA,16S,1234,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,Signature 1,Supplemental Figure 9,25 June 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between patients with colorectal adenocarcinoma and controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter sp.,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas veronii",3379134|1224|1236|135625|712|416916|739;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|28116;3379134|29547|3031852|213849|72294|194|205;3384189|32066|203490|203491|203492|848|68766;1783272|1239|91061|1385|539738|1378|1966354;1783272|1239|91061|186826|186828|117563|2049028;1783272|1239|186801|186802|216572|119852;1783272|1239|1737404|1737405|1570339|543311|1944660;1783272|1239|186801|3082720|186804|1257|1262;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|171552|838|28131;3379134|976|200643|171549|171552|838|59823;3379134|1224|1236|72274|135621|286|76761,Complete,Claregrieve1
bsdb:26515465/2/2,26515465,"cross-sectional observational, not case-control",26515465,10.1038/ncomms9727,NA,"Nakatsu G., Li X., Zhou H., Sheng J., Wong S.H., Wu W.K., Ng S.C., Tsoi H., Dong Y., Zhang N., He Y., Kang Q., Cao L., Wang K., Zhang J., Liang Q., Yu J. , Sung J.J.",Gut mucosal microbiome across stages of colorectal carcinogenesis,Nature communications,2015,NA,Experiment 2,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,healthy controls,colorectal cancer (adenocarcinoma),subjects with invasive adenocarcinoma,61,52,NA,16S,1234,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,Signature 2,Supplemental Figure 9,25 June 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between patients with colorectal adenocarcinoma and controls,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas veronii",3379134|976|200643|171549|815|816|29523;1783272|1239|186801|3085636|186803|572511|1955243;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|216572|216851|853;3379134|1224|1236|72274|135621|286|76761,Complete,Claregrieve1
bsdb:26515465/3/1,26515465,"cross-sectional observational, not case-control",26515465,10.1038/ncomms9727,NA,"Nakatsu G., Li X., Zhou H., Sheng J., Wong S.H., Wu W.K., Ng S.C., Tsoi H., Dong Y., Zhang N., He Y., Kang Q., Cao L., Wang K., Zhang J., Liang Q., Yu J. , Sung J.J.",Gut mucosal microbiome across stages of colorectal carcinogenesis,Nature communications,2015,NA,Experiment 3,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,colorectal adenoma,colorectal cancer,subjects with invasive adenocarcinoma,47,52,NA,16S,1234,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,Signature 1,Supplementary Figure 9,25 June 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between patients with colorectal adenocarcinoma and colorectal adenoma,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp.,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter|s__Pedobacter cryoconitis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.",3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|29523;1783272|1239|186801|3085636|186803|572511|1955243;1783272|1239|186801|186802|1898207;3384189|32066|203490|203491|203492|848|68766;1783272|1239|91061|1385|539738|1378|1966354;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|2005525|375288|1869337;1783272|1239|1737404|1737405|1570339|543311|1944660;3379134|976|117747|200666|84566|84567|188932;1783272|1239|186801|3082720|186804|1257|1262;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|171552|838|28131;3379134|976|200643|171549|171552|838|59823;3379134|976|200643|171549|171552|2974265|363265;1783272|1239|186801|186802|216572|1263|41978,Complete,Claregrieve1
bsdb:26515465/3/2,26515465,"cross-sectional observational, not case-control",26515465,10.1038/ncomms9727,NA,"Nakatsu G., Li X., Zhou H., Sheng J., Wong S.H., Wu W.K., Ng S.C., Tsoi H., Dong Y., Zhang N., He Y., Kang Q., Cao L., Wang K., Zhang J., Liang Q., Yu J. , Sung J.J.",Gut mucosal microbiome across stages of colorectal carcinogenesis,Nature communications,2015,NA,Experiment 3,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,colorectal adenoma,colorectal cancer,subjects with invasive adenocarcinoma,47,52,NA,16S,1234,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,Signature 2,Supplemental Figure 9,25 June 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between patients with colorectal adenocarcinoma and colorectal adenoma,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter|s__Enhydrobacter sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter|s__Pedobacter cryoconitis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas veronii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia terrae",3379134|1224|28211|356|212791|1894999;3379134|1224|1236|91347|543|561|562;3379134|976|117747|200666|84566|84567|188932;3379134|1224|1236|72274|135621|286|76761;1783272|201174|1760|85006|1268|32207|396015,Complete,Claregrieve1
bsdb:26515465/4/1,26515465,"cross-sectional observational, not case-control",26515465,10.1038/ncomms9727,NA,"Nakatsu G., Li X., Zhou H., Sheng J., Wong S.H., Wu W.K., Ng S.C., Tsoi H., Dong Y., Zhang N., He Y., Kang Q., Cao L., Wang K., Zhang J., Liang Q., Yu J. , Sung J.J.",Gut mucosal microbiome across stages of colorectal carcinogenesis,Nature communications,2015,NA,Experiment 4,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,carcinoma-adjacent mucosae,carcinoma mucosae,specimens collected from adenocarcinoma tissue,52,52,NA,16S,1234,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 9,25 June 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between carcinoma-adjacent mucosae and carcinoma mucosae,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas veronii",1783272|1239|186801|3085636|186803|572511|1955243;3379134|1224|1236|72274|135621|286|76761,Complete,Claregrieve1
bsdb:26515465/4/2,26515465,"cross-sectional observational, not case-control",26515465,10.1038/ncomms9727,NA,"Nakatsu G., Li X., Zhou H., Sheng J., Wong S.H., Wu W.K., Ng S.C., Tsoi H., Dong Y., Zhang N., He Y., Kang Q., Cao L., Wang K., Zhang J., Liang Q., Yu J. , Sung J.J.",Gut mucosal microbiome across stages of colorectal carcinogenesis,Nature communications,2015,NA,Experiment 4,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,carcinoma-adjacent mucosae,carcinoma mucosae,specimens collected from adenocarcinoma tissue,52,52,NA,16S,1234,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Figure 9,25 June 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between carcinoma-adjacent mucosae and carcinoma mucosae,increased,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,3384189|32066|203490|203491|203492|848|68766,Complete,Claregrieve1
bsdb:26515465/5/1,26515465,"cross-sectional observational, not case-control",26515465,10.1038/ncomms9727,NA,"Nakatsu G., Li X., Zhou H., Sheng J., Wong S.H., Wu W.K., Ng S.C., Tsoi H., Dong Y., Zhang N., He Y., Kang Q., Cao L., Wang K., Zhang J., Liang Q., Yu J. , Sung J.J.",Gut mucosal microbiome across stages of colorectal carcinogenesis,Nature communications,2015,NA,Experiment 5,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,adenoma-adjacent,adenocarcinoma mucosae,specimens collected from adenocarcinoma tissue,47,52,NA,16S,1234,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 9,5 July 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between adenoma-adjacent samples and adenocarcinoma samples,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. (in: firmicutes),k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter|s__Enhydrobacter sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter|s__Pedobacter cryoconitis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas veronii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia terrae",1783272|1239|91061|1385|186817|1386|1409;3379134|1224|28211|356|212791|1894999;3379134|1224|1236|91347|543|561|562;3379134|976|117747|200666|84566|84567|188932;3379134|1224|1236|72274|135621|286|76761;1783272|201174|1760|85006|1268|32207|396015,Complete,Claregrieve1
bsdb:26515465/5/2,26515465,"cross-sectional observational, not case-control",26515465,10.1038/ncomms9727,NA,"Nakatsu G., Li X., Zhou H., Sheng J., Wong S.H., Wu W.K., Ng S.C., Tsoi H., Dong Y., Zhang N., He Y., Kang Q., Cao L., Wang K., Zhang J., Liang Q., Yu J. , Sung J.J.",Gut mucosal microbiome across stages of colorectal carcinogenesis,Nature communications,2015,NA,Experiment 5,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,adenoma-adjacent,adenocarcinoma mucosae,specimens collected from adenocarcinoma tissue,47,52,NA,16S,1234,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 9,5 July 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between adenoma-adjacent samples and adenocarcinoma samples,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea",3379134|976|200643|171549|815|816|817;1783272|1239|186801|3085636|186803|572511|1955243;3379134|29547|3031852|213849|72294|194|205;1783272|1239|186801|186802|1898207;3384189|32066|203490|203491|203492|848|68766;1783272|1239|91061|1385|539738|1378|1966354;1783272|1239|91061|186826|186828|117563|2049028;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|2005525|375288|1869337;1783272|1239|1737404|1737405|1570339|543311|1944660;1783272|1239|186801|3082720|186804|1257|1262;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|171552|838|28131;3379134|976|200643|171549|171552|838|59823;3379134|976|200643|171549|171552|2974265|363265,Complete,Claregrieve1
bsdb:26515465/7/1,26515465,"cross-sectional observational, not case-control",26515465,10.1038/ncomms9727,NA,"Nakatsu G., Li X., Zhou H., Sheng J., Wong S.H., Wu W.K., Ng S.C., Tsoi H., Dong Y., Zhang N., He Y., Kang Q., Cao L., Wang K., Zhang J., Liang Q., Yu J. , Sung J.J.",Gut mucosal microbiome across stages of colorectal carcinogenesis,Nature communications,2015,NA,Experiment 7,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal adenoma,EFO:0005406,healthy controls,adenoma-adjacent,specimen collected adjacent to histology-proven adenoma,61,47,NA,16S,1234,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 9,5 July 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between healthy control tissue and adenoma-adjacent tissue,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",1783272|1239|186801|3085636|186803|572511|1955243;1783272|1239|186801|3085636|186803|33042|2049024;1783272|1239|186801|3085636|186803|2719313|1531;1783272|1239|186801|186802|216572|216851|853,Complete,Claregrieve1
bsdb:26515465/7/2,26515465,"cross-sectional observational, not case-control",26515465,10.1038/ncomms9727,NA,"Nakatsu G., Li X., Zhou H., Sheng J., Wong S.H., Wu W.K., Ng S.C., Tsoi H., Dong Y., Zhang N., He Y., Kang Q., Cao L., Wang K., Zhang J., Liang Q., Yu J. , Sung J.J.",Gut mucosal microbiome across stages of colorectal carcinogenesis,Nature communications,2015,NA,Experiment 7,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal adenoma,EFO:0005406,healthy controls,adenoma-adjacent,specimen collected adjacent to histology-proven adenoma,61,47,NA,16S,1234,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Figure 9,5 July 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between healthy control tissue and adenoma-adjacent tissue,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter|s__Enhydrobacter sp.,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter|s__Pedobacter cryoconitis",3379134|1224|28211|356|212791|1894999;3384189|32066|203490|203491|203492|848|68766;3379134|976|117747|200666|84566|84567|188932,Complete,Claregrieve1
bsdb:26515465/8/1,26515465,"cross-sectional observational, not case-control",26515465,10.1038/ncomms9727,NA,"Nakatsu G., Li X., Zhou H., Sheng J., Wong S.H., Wu W.K., Ng S.C., Tsoi H., Dong Y., Zhang N., He Y., Kang Q., Cao L., Wang K., Zhang J., Liang Q., Yu J. , Sung J.J.",Gut mucosal microbiome across stages of colorectal carcinogenesis,Nature communications,2015,NA,Experiment 8,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,healthy controls,carcinoma-adjacent,specimen collected from tissue adjacent to adenocarcinoma site,61,52,NA,16S,1234,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Figure 9,5 July 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between healthy control tissue and adenocarcinoma-adjacent tissue,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.",3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|28116;3384189|32066|203490|203491|203492|848|68766;1783272|1239|91061|1385|539738|1378|1966354;1783272|1239|91061|186826|186828|117563|2049028;1783272|1239|186801|3082720|186804|1257|1262;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|171552|838|59823,Complete,Claregrieve1
bsdb:26515465/9/1,26515465,"cross-sectional observational, not case-control",26515465,10.1038/ncomms9727,NA,"Nakatsu G., Li X., Zhou H., Sheng J., Wong S.H., Wu W.K., Ng S.C., Tsoi H., Dong Y., Zhang N., He Y., Kang Q., Cao L., Wang K., Zhang J., Liang Q., Yu J. , Sung J.J.",Gut mucosal microbiome across stages of colorectal carcinogenesis,Nature communications,2015,NA,Experiment 9,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,colorectal adenoma tissue,carcinoma-adjacent tissue,specimens collected from tissue adjacent to adenocarcinoma,47,52,Not specified,16S,1234,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 9,5 July 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between adenoma samples and adenocarcinoma-adjacent samples,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.",3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|29523;3379134|976|200643|171549|815|816|820;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|572511|1955243;1783272|1239|186801|186802|1898207;1783272|1239|186801|3085636|186803|33042|2049024;1783272|1239|186801|186802|216572|216851|853;3384189|32066|203490|203491|203492|848|68766;1783272|1239|91061|1385|539738|1378|1966354;1783272|1239|186801|186802|216572|119852;1783272|1239|1737404|1737405|1570339|543311|1944660;1783272|1239|186801|3082720|186804|1257|1262;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|171552|838|28131;3379134|976|200643|171549|171552|838|59823;3379134|976|200643|171549|171552|2974265|363265;1783272|1239|186801|186802|216572|1263|41978,Complete,Claregrieve1
bsdb:26515465/9/2,26515465,"cross-sectional observational, not case-control",26515465,10.1038/ncomms9727,NA,"Nakatsu G., Li X., Zhou H., Sheng J., Wong S.H., Wu W.K., Ng S.C., Tsoi H., Dong Y., Zhang N., He Y., Kang Q., Cao L., Wang K., Zhang J., Liang Q., Yu J. , Sung J.J.",Gut mucosal microbiome across stages of colorectal carcinogenesis,Nature communications,2015,NA,Experiment 9,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,colorectal adenoma tissue,carcinoma-adjacent tissue,specimens collected from tissue adjacent to adenocarcinoma,47,52,Not specified,16S,1234,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 9,5 July 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between adenoma samples and adenocarcinoma-adjacent samples,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter|s__Enhydrobacter sp.,3379134|1224|28211|356|212791|1894999,Complete,Claregrieve1
bsdb:26551842/1/1,26551842,"cross-sectional observational, not case-control",26551842,10.1016/j.cmi.2015.10.031,NA,"Ignacio A., Fernandes M.R., Rodrigues V.A., Groppo F.C., Cardoso A.L., Avila-Campos M.J. , Nakano V.",Correlation between body mass index and faecal microbiota from children,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2016,"Anaerobic bacteria, Escherichia coli, body mass index, childhood obesity, faecal microbiota, quantitative PCR",Experiment 1,Brazil,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean children,obese children,Healthy children with obesity based on z-score of >+2,30,30,3 months,16S,NA,RT-qPCR,NA,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Mst Afroza Parvin,WikiWorks,"Bacterial prevalence and quantification verified in faeces of obese, overweight and lean children by quantitative PCR",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.",3379134|976|200643|171549|815|816|817;1783272|1239|91061|186826|33958|1578|1591,Complete,Claregrieve1
bsdb:26551842/1/2,26551842,"cross-sectional observational, not case-control",26551842,10.1016/j.cmi.2015.10.031,NA,"Ignacio A., Fernandes M.R., Rodrigues V.A., Groppo F.C., Cardoso A.L., Avila-Campos M.J. , Nakano V.",Correlation between body mass index and faecal microbiota from children,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2016,"Anaerobic bacteria, Escherichia coli, body mass index, childhood obesity, faecal microbiota, quantitative PCR",Experiment 1,Brazil,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean children,obese children,Healthy children with obesity based on z-score of >+2,30,30,3 months,16S,NA,RT-qPCR,NA,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 4,10 January 2021,Mst Afroza Parvin,WikiWorks,"Bacterial prevalence and quantification verified in faeces of obese, overweight and lean children by quantitative PCR",decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,1783272|201174|1760|85004|31953|1678|41200,Complete,Claregrieve1
bsdb:26551842/2/1,26551842,"cross-sectional observational, not case-control",26551842,10.1016/j.cmi.2015.10.031,NA,"Ignacio A., Fernandes M.R., Rodrigues V.A., Groppo F.C., Cardoso A.L., Avila-Campos M.J. , Nakano V.",Correlation between body mass index and faecal microbiota from children,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2016,"Anaerobic bacteria, Escherichia coli, body mass index, childhood obesity, faecal microbiota, quantitative PCR",Experiment 2,Brazil,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean children,overweight children,Healthy children who are considered overweight based on z-score of ≥ +1 and < +2,30,24,3 months,16S,NA,RT-qPCR,NA,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Mst Afroza Parvin,WikiWorks,"Bacterial prevalence and quantification verified in faeces of obese, overweight and lean children by quantitative PCR",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.",3379134|976|200643|171549|815|816|817;1783272|1239|91061|186826|33958|1578|1591,Complete,Claregrieve1
bsdb:26551842/3/1,26551842,"cross-sectional observational, not case-control",26551842,10.1016/j.cmi.2015.10.031,NA,"Ignacio A., Fernandes M.R., Rodrigues V.A., Groppo F.C., Cardoso A.L., Avila-Campos M.J. , Nakano V.",Correlation between body mass index and faecal microbiota from children,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2016,"Anaerobic bacteria, Escherichia coli, body mass index, childhood obesity, faecal microbiota, quantitative PCR",Experiment 3,Brazil,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean children,obese children,Healthy children with obesity based on z-score of >+2,30,30,3 months,16S,NA,RT-qPCR,NA,Logistic Regression,0.05,FALSE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Table 6,10 January 2021,Mst Afroza Parvin,WikiWorks,Factors associated with body mass index based on multiple logistic regression (logistic regression analysis using quantitative PCR results,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,3379134|976|200643|171549|815|816|817,Complete,Claregrieve1
bsdb:26551842/3/2,26551842,"cross-sectional observational, not case-control",26551842,10.1016/j.cmi.2015.10.031,NA,"Ignacio A., Fernandes M.R., Rodrigues V.A., Groppo F.C., Cardoso A.L., Avila-Campos M.J. , Nakano V.",Correlation between body mass index and faecal microbiota from children,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2016,"Anaerobic bacteria, Escherichia coli, body mass index, childhood obesity, faecal microbiota, quantitative PCR",Experiment 3,Brazil,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean children,obese children,Healthy children with obesity based on z-score of >+2,30,30,3 months,16S,NA,RT-qPCR,NA,Logistic Regression,0.05,FALSE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 2,Table 6,10 January 2021,Mst Afroza Parvin,WikiWorks,Factors associated with body mass index based on multiple logistic regression (logistic regression analysis using quantitative PCR results,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,1783272|201174|1760|85004|31953|1678|41200,Complete,Claregrieve1
bsdb:26551842/4/1,26551842,"cross-sectional observational, not case-control",26551842,10.1016/j.cmi.2015.10.031,NA,"Ignacio A., Fernandes M.R., Rodrigues V.A., Groppo F.C., Cardoso A.L., Avila-Campos M.J. , Nakano V.",Correlation between body mass index and faecal microbiota from children,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2016,"Anaerobic bacteria, Escherichia coli, body mass index, childhood obesity, faecal microbiota, quantitative PCR",Experiment 4,Brazil,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,lean children,overweight children,Healthy children who are considered overweight based on z-score of ≥ +1 and < +2,30,24,3 months,16S,NA,RT-qPCR,NA,Logistic Regression,0.05,FALSE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Table 6,10 January 2021,Mst Afroza Parvin,"Claregrieve1,WikiWorks",Factors associated with body mass index based on multiple logistic regression (logistic regression analysis using quantitative PCR results,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,1783272|1239|91061|186826|33958|1578|1591,Complete,Claregrieve1
bsdb:26574055/1/1,26574055,"cross-sectional observational, not case-control",26574055,10.1038/srep16865,NA,"Mitra A., MacIntyre D.A., Lee Y.S., Smith A., Marchesi J.R., Lehne B., Bhatia R., Lyons D., Paraskevaidis E., Li J.V., Holmes E., Nicholson J.K., Bennett P.R. , Kyrgiou M.",Cervical intraepithelial neoplasia disease progression is associated with increased vaginal microbiome diversity,Scientific reports,2015,NA,Experiment 1,United Kingdom,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Cervical glandular intraepithelial neoplasia,EFO:1000165,low grade squamus intraepithelial lesion,high grade squamus intraepithelial lesion,high grade squamus intraepithelial lesion confirmed by histology or cytology,52,92,2 weeks,16S,12,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,figure 5,10 January 2021,Cynthia Anderson,WikiWorks,Identification of vaginal microbiota biomarkers of LSIL vs. HSIL by LEfSe analysis,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus tetradius,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae",1783272|1239|186801|3082720|186804|1257|1261;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|1737404|1737405|1570339|165779|33036;3384189|32066|203490|203491|1129771|168808;3384189|32066|203490|203491;3384189|32066|203490|203491|1129771|168808|40543;3384189|32066;3384189|32066|203490|203491|1129771,Complete,Fatima Zohra
bsdb:26574055/1/2,26574055,"cross-sectional observational, not case-control",26574055,10.1038/srep16865,NA,"Mitra A., MacIntyre D.A., Lee Y.S., Smith A., Marchesi J.R., Lehne B., Bhatia R., Lyons D., Paraskevaidis E., Li J.V., Holmes E., Nicholson J.K., Bennett P.R. , Kyrgiou M.",Cervical intraepithelial neoplasia disease progression is associated with increased vaginal microbiome diversity,Scientific reports,2015,NA,Experiment 1,United Kingdom,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Cervical glandular intraepithelial neoplasia,EFO:1000165,low grade squamus intraepithelial lesion,high grade squamus intraepithelial lesion,high grade squamus intraepithelial lesion confirmed by histology or cytology,52,92,2 weeks,16S,12,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,figure 5,10 January 2021,Cynthia Anderson,WikiWorks,Identification of vaginal microbiota biomarkers of LSIL vs. HSIL by LEfSe analysis,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus jensenii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus coleohominis",1783272|1239|91061|186826|33958|1578|109790;1783272|1239|91061|186826|33958|2742598|181675,Complete,Fatima Zohra
bsdb:26600078/1/1,26600078,case-control,26600078,10.1002/hep.28356,NA,"Boursier J., Mueller O., Barret M., Machado M., Fizanne L., Araujo-Perez F., Guy C.D., Seed P.C., Rawls J.F., David L.A., Hunault G., Oberti F., Calès P. , Diehl A.M.",The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota,"Hepatology (Baltimore, Md.)",2016,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,Non-NASH,NASH,"NAFLD was defined as liver steatosis on liver biopsy after exclusion of concomitant steatosis-inducing drugs, excessive alcohol consumption (>210 g/week in men or >140 g/week in women), chronic hepatitis B or C infection, and histological evidence of other concomitant chronic liver disease. NASH was defined as the presence of each of the three following conditions: steatosis grade 1; lobular inflammation grade 1; and ballooning grade 1. “Significant fibrosis” was defined as fibrosis stage F2.",22,35,2 months,16S,4,Illumina,relative abundances,Logistic Regression,0.1,FALSE,NA,NA,"HDL cholesterol change measurement,blood pressure,body mass index,diabetes mellitus,hypertriglyceridemia,metabolic syndrome",NA,NA,NA,NA,NA,NA,Signature 1,Table 2 + text,10 January 2021,Shaimaa Elsafoury,WikiWorks,Relative significant Abundance of Gut Microbiome Taxa in Patients With NASH and Without NASH,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
bsdb:26600078/1/2,26600078,case-control,26600078,10.1002/hep.28356,NA,"Boursier J., Mueller O., Barret M., Machado M., Fizanne L., Araujo-Perez F., Guy C.D., Seed P.C., Rawls J.F., David L.A., Hunault G., Oberti F., Calès P. , Diehl A.M.",The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota,"Hepatology (Baltimore, Md.)",2016,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,Non-NASH,NASH,"NAFLD was defined as liver steatosis on liver biopsy after exclusion of concomitant steatosis-inducing drugs, excessive alcohol consumption (>210 g/week in men or >140 g/week in women), chronic hepatitis B or C infection, and histological evidence of other concomitant chronic liver disease. NASH was defined as the presence of each of the three following conditions: steatosis grade 1; lobular inflammation grade 1; and ballooning grade 1. “Significant fibrosis” was defined as fibrosis stage F2.",22,35,2 months,16S,4,Illumina,relative abundances,Logistic Regression,0.1,FALSE,NA,NA,"HDL cholesterol change measurement,blood pressure,body mass index,diabetes mellitus,hypertriglyceridemia,metabolic syndrome",NA,NA,NA,NA,NA,NA,Signature 2,Table 2 + text,10 January 2021,Shaimaa Elsafoury,WikiWorks,Relative significant Abundance of Gut Microbiome Taxa in Patients With NASH and Without NASH,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552,Complete,Shaimaa Elsafoury
bsdb:26600078/2/1,26600078,case-control,26600078,10.1002/hep.28356,NA,"Boursier J., Mueller O., Barret M., Machado M., Fizanne L., Araujo-Perez F., Guy C.D., Seed P.C., Rawls J.F., David L.A., Hunault G., Oberti F., Calès P. , Diehl A.M.",The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota,"Hepatology (Baltimore, Md.)",2016,NA,Experiment 2,France,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,mild fibrosis (F 0-1),significant fibrosis (F>2),"NAFLD was defined as liver steatosis on liver biopsy after exclusion of concomitant steatosis-inducing drugs, excessive alcohol consumption (>210 g/week in men or >140 g/week in women), chronic hepatitis B or C infection, and histological evidence of other concomitant chronic liver disease. NASH was defined as the presence of each of the three following conditions: steatosis grade 1; lobular nflammation grade 1; and ballooning grade 1. “Significant fibrosis” was defined as fibrosis stage F2.",30,27,2 months,16S,4,Illumina,NA,Logistic Regression,0.05,FALSE,NA,NA,"HDL cholesterol change measurement,blood pressure,body mass index,diabetes mellitus,hypertriglyceridemia,metabolic syndrome",NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Relative significant Abundance of Gut Microbiome Taxa in Patients With Significant F 2 Fibrosis and No/Mild Fibrosis (F0/F1 Stage),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
bsdb:26600078/2/2,26600078,case-control,26600078,10.1002/hep.28356,NA,"Boursier J., Mueller O., Barret M., Machado M., Fizanne L., Araujo-Perez F., Guy C.D., Seed P.C., Rawls J.F., David L.A., Hunault G., Oberti F., Calès P. , Diehl A.M.",The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota,"Hepatology (Baltimore, Md.)",2016,NA,Experiment 2,France,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,mild fibrosis (F 0-1),significant fibrosis (F>2),"NAFLD was defined as liver steatosis on liver biopsy after exclusion of concomitant steatosis-inducing drugs, excessive alcohol consumption (>210 g/week in men or >140 g/week in women), chronic hepatitis B or C infection, and histological evidence of other concomitant chronic liver disease. NASH was defined as the presence of each of the three following conditions: steatosis grade 1; lobular nflammation grade 1; and ballooning grade 1. “Significant fibrosis” was defined as fibrosis stage F2.",30,27,2 months,16S,4,Illumina,NA,Logistic Regression,0.05,FALSE,NA,NA,"HDL cholesterol change measurement,blood pressure,body mass index,diabetes mellitus,hypertriglyceridemia,metabolic syndrome",NA,NA,NA,NA,NA,NA,Signature 2,Table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Relative significant  Abundance of Gut Microbiome Taxa in Patients With Significant F 2 Fibrosis and No/Mild Fibrosis (F0/F1 Stage),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|838;1783272|1239|526524|526525|128827,Complete,Shaimaa Elsafoury
bsdb:26606973/1/1,26606973,case-control,26606973,10.1038/srep17098,NA,"Ling Z., Liu X., Cheng Y., Jiang X., Jiang H., Wang Y. , Li L.",Decreased Diversity of the Oral Microbiota of Patients with Hepatitis B Virus-Induced Chronic Liver Disease: A Pilot Project,Scientific reports,2015,NA,Experiment 1,China,Homo sapiens,Dental plaque,UBERON:0016482,Chronic hepatitis B virus infection,EFO:0004239,healthy controls,chronic hepatitis B,chronic hepatitis B,10,10,1 month,16S,123,Roche454,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,increased,NA,decreased,Signature 1,"Figure 3, Text",10 January 2021,Rimsha Azhar,WikiWorks,LEfSe was used to identify the most differentially abundant taxa in healthy control and CHB patient samples,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia",3379134|1224|1236|91347|543;3379134|1224|1236|91347;3379134|1224|1236|91347|1903411|629;3379134|1224|1236|135614;1783272|1239|186801|3082720|3118655|44259;3379134|1224|1236|135614|32033;1783272|1239|186801|3082720|186804;1783272|1239|186801|186802;1783272|1239|186801,Complete,Claregrieve1
bsdb:26606973/1/2,26606973,case-control,26606973,10.1038/srep17098,NA,"Ling Z., Liu X., Cheng Y., Jiang X., Jiang H., Wang Y. , Li L.",Decreased Diversity of the Oral Microbiota of Patients with Hepatitis B Virus-Induced Chronic Liver Disease: A Pilot Project,Scientific reports,2015,NA,Experiment 1,China,Homo sapiens,Dental plaque,UBERON:0016482,Chronic hepatitis B virus infection,EFO:0004239,healthy controls,chronic hepatitis B,chronic hepatitis B,10,10,1 month,16S,123,Roche454,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,increased,NA,decreased,Signature 2,"Figure 3, Text",10 January 2021,Rimsha Azhar,WikiWorks,LEfSe was used to identify the most differentially abundant taxa in healthy control and CHB patient samples,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga",3384189|32066|203490|203491|1129771;3384189|32066|203490|203491|1129771|32067;3379134|976|117743|200644;3379134|976|117743|200644|49546;3379134|976|117743;3379134|976|117743|200644|49546|1016,Complete,Claregrieve1
bsdb:26606973/2/1,26606973,case-control,26606973,10.1038/srep17098,NA,"Ling Z., Liu X., Cheng Y., Jiang X., Jiang H., Wang Y. , Li L.",Decreased Diversity of the Oral Microbiota of Patients with Hepatitis B Virus-Induced Chronic Liver Disease: A Pilot Project,Scientific reports,2015,NA,Experiment 2,China,Homo sapiens,Dental plaque,UBERON:0016482,Chronic hepatitis B virus infection,EFO:0004239,liver cirrhosis,chronic hepatitis B,chronic hepatitis B,10,10,1 month,16S,123,Roche454,NA,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,"Figure 4, Text",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Taxonomic differences in oral microbiota of the CHB and LC groups,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Spirochaetota,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",1783272|1239|186801|3082720|3118655|44259;3379134|203691|203692|136|137;3379134|203691|203692|136;3379134|203691;3379134|203691|203692;3379134|203691|203692|136|2845253|157,Complete,Claregrieve1
bsdb:26606973/2/2,26606973,case-control,26606973,10.1038/srep17098,NA,"Ling Z., Liu X., Cheng Y., Jiang X., Jiang H., Wang Y. , Li L.",Decreased Diversity of the Oral Microbiota of Patients with Hepatitis B Virus-Induced Chronic Liver Disease: A Pilot Project,Scientific reports,2015,NA,Experiment 2,China,Homo sapiens,Dental plaque,UBERON:0016482,Chronic hepatitis B virus infection,EFO:0004239,liver cirrhosis,chronic hepatitis B,chronic hepatitis B,10,10,1 month,16S,123,Roche454,NA,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,"Figure 4, Text",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Taxonomic differences in oral microbiota of the CHB and LC groups,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales",3379134|1224|28216;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481;3379134|1224|28216|206351,Complete,Claregrieve1
bsdb:26641451/1/1,26641451,case-control,26641451,10.1371/journal.pone.0143603,NA,"Chen X., Winckler B., Lu M., Cheng H., Yuan Z., Yang Y., Jin L. , Ye W.",Oral Microbiota and Risk for Esophageal Squamous Cell Carcinoma in a High-Risk Area of China,PloS one,2015,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Esophageal cancer,MONDO:0007576,Dysplasia,Esophageal Squamous cell carcinoma (ESCC),Subjects who were suspected to have esophageal cancer under endoscopy,63,87,1 month,16S,34,Roche454,relative abundances,Metastats,0.05,TRUE,NA,"age,sex","age,alcohol drinking,diet,education level,family history of cancer,number of teeth measurement,oral hygiene,sex,smoking status",NA,decreased,unchanged,NA,NA,NA,Signature 1,Table 3,10 January 2021,Utsav Patel,"WikiWorks,ChiomaBlessing",Relative abundance of significant microbiota in the ESCC group compared to the Dysplasia group,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia",1783272|1239|186801|3082720|3118655|44259;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|186827|46123,Complete,ChiomaBlessing
bsdb:26641451/1/2,26641451,case-control,26641451,10.1371/journal.pone.0143603,NA,"Chen X., Winckler B., Lu M., Cheng H., Yuan Z., Yang Y., Jin L. , Ye W.",Oral Microbiota and Risk for Esophageal Squamous Cell Carcinoma in a High-Risk Area of China,PloS one,2015,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Esophageal cancer,MONDO:0007576,Dysplasia,Esophageal Squamous cell carcinoma (ESCC),Subjects who were suspected to have esophageal cancer under endoscopy,63,87,1 month,16S,34,Roche454,relative abundances,Metastats,0.05,TRUE,NA,"age,sex","age,alcohol drinking,diet,education level,family history of cancer,number of teeth measurement,oral hygiene,sex,smoking status",NA,decreased,unchanged,NA,NA,NA,Signature 2,Table 3,10 January 2021,Utsav Patel,"WikiWorks,ChiomaBlessing",Relative abundance of significant microbiota in the ESCC group compared to the Dysplasia group,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium",3379134|1224|1236|135625|712|416916;1783272|201174|84998|84999|1643824|1380;1783272|1239|526524|526525|128827|118747;3379134|29547|3031852|213849|72294|194;1783272|1239|186801|3085636|186803|43996;1783272|201174|1760|85007|1653|1716;1783272|1239|186801|3082720|3118655|44259;3384189|32066|203490|203491|203492|848;3379134|1224|1236|135625|712|724;3379134|1224|28216|80840|75682|963;3379134|1224|28216|80840|119060|47670;3384189|32066|203490|203491|1129771|32067;3379134|1224|28216|206351|481|482;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|186802|186807|2740;1783272|201174|1760|85006|1268|32207;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|135615|868|2717,Complete,ChiomaBlessing
bsdb:26641451/2/1,26641451,case-control,26641451,10.1371/journal.pone.0143603,NA,"Chen X., Winckler B., Lu M., Cheng H., Yuan Z., Yang Y., Jin L. , Ye W.",Oral Microbiota and Risk for Esophageal Squamous Cell Carcinoma in a High-Risk Area of China,PloS one,2015,NA,Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Esophageal cancer,MONDO:0007576,Healthy controls,Esophageal Squamous cell carcinoma (ESCC),Subjects who were suspected to have esophageal cancer under endoscopy,85,87,1 month,16S,34,Roche454,relative abundances,Metastats,0.05,TRUE,NA,"age,sex","age,alcohol drinking,diet,education level,family history of cancer,oral hygiene,sex,smoking status",NA,decreased,decreased,NA,NA,NA,Signature 1,Table 3,10 January 2021,Utsav Patel,"WikiWorks,ChiomaBlessing",Relative abundance of significant microbiota in the ESCC group compared to the Healthy control group,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Elizabethkingia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio",3379134|976|200643|171549|815|816;3379134|976|117743|200644|49546|1016;3379134|976|117743|200644|2762318|308865;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|830,Complete,ChiomaBlessing
bsdb:26641451/2/2,26641451,case-control,26641451,10.1371/journal.pone.0143603,NA,"Chen X., Winckler B., Lu M., Cheng H., Yuan Z., Yang Y., Jin L. , Ye W.",Oral Microbiota and Risk for Esophageal Squamous Cell Carcinoma in a High-Risk Area of China,PloS one,2015,NA,Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Esophageal cancer,MONDO:0007576,Healthy controls,Esophageal Squamous cell carcinoma (ESCC),Subjects who were suspected to have esophageal cancer under endoscopy,85,87,1 month,16S,34,Roche454,relative abundances,Metastats,0.05,TRUE,NA,"age,sex","age,alcohol drinking,diet,education level,family history of cancer,oral hygiene,sex,smoking status",NA,decreased,decreased,NA,NA,NA,Signature 2,Table 3,10 January 2021,Utsav Patel,"WikiWorks,ChiomaBlessing,KateRasheed",Relative abundance of significant microbiota in the ESCC group compared to the Healthy control group,decreased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Acholeplasma,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae",1783272|544448|31969|186329|2146|2147;1783272|201174|1760|2037|2049|1654;3379134|1224|1236|135625|712|416916;1783272|201174|84998|84999|1643824|1380;1783272|1239|526524|526525|128827|118747;1783272|1239|186801|3085636|186803|830;3379134|29547|3031852|213849|72294|194;3379134|1224|1236|135615|868|2717;1783272|1239|186801|3085636|186803|43996;1783272|201174|1760|85007|1653|1716;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3082720|3118655|44259;3379134|1224|1236|135625|712|724;3379134|1224|28216|80840|119060|47670;3384189|32066|203490|203491|1129771|32067;1783272|1239|909932|1843489|31977|906;3379134|1224|28216|206351|481|482;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3082720|186804|1257;1783272|201174|1760|85006|1268|32207;1783272|1239|909932|909929|1843491|970;3379134|203691|203692|136|2845253|157;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|1385|186817,Complete,ChiomaBlessing
bsdb:26663491/1/1,26663491,case-control,26663491,10.1111/pai.12522,NA,"Chen C.C., Chen K.J., Kong M.S., Chang H.J. , Huang J.L.",Alterations in the gut microbiotas of children with food sensitization in early life,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2016,"454 pyrosequencing, food sensitization, linear discriminant analysis, microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,healthy controls,children with food sensitization,child with food sensitization,22,23,1 week,16S,345,Roche454,raw counts,T-Test,0.01,FALSE,NA,age,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,"Table 2, Text (Alterations at the family and genus levels)",10 January 2021,Lucy Mellor,"Fatima,WikiWorks,Folakunmi",Differentially abundant taxons between food sensitization children and healthy control,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.",3379134|74201|203494|48461|1647988|239934;1783272|201174|1760|85004|31953|1678;1783272|201174|84998|84999|84107|102106;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|216572|216851;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;3379134|1224|28211|204457|41297|13687;1783272|1239|186801|186802|216572|292632;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|31979|1485|59620,Complete,Folakunmi
bsdb:26663491/1/2,26663491,case-control,26663491,10.1111/pai.12522,NA,"Chen C.C., Chen K.J., Kong M.S., Chang H.J. , Huang J.L.",Alterations in the gut microbiotas of children with food sensitization in early life,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2016,"454 pyrosequencing, food sensitization, linear discriminant analysis, microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,healthy controls,children with food sensitization,child with food sensitization,22,23,1 week,16S,345,Roche454,raw counts,T-Test,0.01,FALSE,NA,age,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,"Table 2, Text (Alterations at the family and genus levels)",10 January 2021,Lucy Mellor,"WikiWorks,Folakunmi",Differentially abundant taxons between food sensitization children and healthy control,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:26663491/2/1,26663491,case-control,26663491,10.1111/pai.12522,NA,"Chen C.C., Chen K.J., Kong M.S., Chang H.J. , Huang J.L.",Alterations in the gut microbiotas of children with food sensitization in early life,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2016,"454 pyrosequencing, food sensitization, linear discriminant analysis, microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,healthy controls,children with food sensitization,child with food sensitization,22,23,1 week,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,"Figure 3, Text (Comparison of relative abundance through LDA score and cladogram analysis)",10 January 2021,Lucy Mellor,"Fatima,WikiWorks,Folakunmi",Differentially abundant taxons between food sensitization children and healthy control,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|1224|28211;1783272|1239;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|216572,Complete,Folakunmi
bsdb:26663491/2/2,26663491,case-control,26663491,10.1111/pai.12522,NA,"Chen C.C., Chen K.J., Kong M.S., Chang H.J. , Huang J.L.",Alterations in the gut microbiotas of children with food sensitization in early life,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2016,"454 pyrosequencing, food sensitization, linear discriminant analysis, microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,healthy controls,children with food sensitization,child with food sensitization,22,23,1 week,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,"Figure 3, Text (Comparison of relative abundance through LDA score and cladogram analysis)",10 January 2021,Lucy Mellor,"WikiWorks,Folakunmi",Differentially abundant taxons between food sensitization children and healthy control,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976;1783272|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:26682545/1/1,26682545,case-control,26682545,10.1371/journal.pone.0145274,NA,"Morita C., Tsuji H., Hata T., Gondo M., Takakura S., Kawai K., Yoshihara K., Ogata K., Nomoto K., Miyazaki K. , Sudo N.",Gut Dysbiosis in Patients with Anorexia Nervosa,PloS one,2015,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Anorexia nervosa,EFO:0004215,healthy controls,anorexia nervosa patients,female patients with anorexia nervosa,21,25,3 months,16S,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.002,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,"table 3, table 5",10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",gut microbiome dysbiosis in patients with anorexia nervosa versus healthy controls,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus|s__Lactiplantibacillus plantarum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum",3379134|976|200643|171549|815|816|817;1783272|1239|91061|186826|33958|2767842|1590;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|572511|1532;1783272|1239|186801|186802|216572|1535,Complete,Claregrieve1
bsdb:26683192/1/1,26683192,case-control,26683192,10.1371/journal.pone.0145453,NA,"Shukla S.K., Cook D., Meyer J., Vernon S.D., Le T., Clevidence D., Robertson C.E., Schrodi S.J., Yale S. , Frank D.N.",Changes in Gut and Plasma Microbiome following Exercise Challenge in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS),PloS one,2015,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Chronic fatigue syndrome,EFO:0004540,healthy controls,chronic fatigue syndrome patients,patients met the ME/CFS case definition criteria established by Fukuda et al in 1994,10,10,currently on antibiotics,16S,NA,Roche454,relative abundances,Kolmogorov-Smirnov Test,0.05,FALSE,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Relative Abundance of Bacterial Phyla in Blood and Stool Samples from ME/CFS Patients and Health Controls.,decreased,k__Pseudomonadati|p__Acidobacteriota,3379134|57723,Complete,Shaimaa Elsafoury
bsdb:26729566/1/1,26729566,"cross-sectional observational, not case-control",26729566,10.1038/srep18594,NA,"Yang I., Woltemate S., Piazuelo M.B., Bravo L.E., Yepez M.C., Romero-Gallo J., Delgado A.G., Wilson K.T., Peek R.M., Correa P., Josenhans C., Fox J.G. , Suerbaum S.",Different gastric microbiota compositions in two human populations with high and low gastric cancer risk in Colombia,Scientific reports,2016,NA,Experiment 1,Colombia,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,low gastric cancer risk patients (Tumaco residents),high gastric cancer risk patients (Tuquerres residents),individuals from Tuquerres with high gastric cancer risk,20,20,1 month,16S,NA,Illumina,NA,Metastats,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,Valentina Pineda,"Claregrieve1,WikiWorks",Differential microbial abundance between Tuquerres and Tumaco residents,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia wadei,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp.",3384189|32066|203490|203491|1129771|32067|157687;1783272|1239|909932|1843489|31977|29465|1926307,Complete,Claregrieve1
bsdb:26729566/1/2,26729566,"cross-sectional observational, not case-control",26729566,10.1038/srep18594,NA,"Yang I., Woltemate S., Piazuelo M.B., Bravo L.E., Yepez M.C., Romero-Gallo J., Delgado A.G., Wilson K.T., Peek R.M., Correa P., Josenhans C., Fox J.G. , Suerbaum S.",Different gastric microbiota compositions in two human populations with high and low gastric cancer risk in Colombia,Scientific reports,2016,NA,Experiment 1,Colombia,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,low gastric cancer risk patients (Tumaco residents),high gastric cancer risk patients (Tuquerres residents),individuals from Tuquerres with high gastric cancer risk,20,20,1 month,16S,NA,Illumina,NA,Metastats,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,10 January 2021,Valentina Pineda,"Lwaldron,Claregrieve1,WikiWorks,Merit",Differential microbial abundance between Tuquerres and Tumaco residents,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. (in: high G+C Gram-positive bacteria),k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Haematobacter|s__uncultured Haematobacter sp.",1783272|201174|1760|2037|2049|1654|29317;3379134|976|117743|200644|49546|1016|1017;3379134|976|117743|200644|49546;3379134|976|117743|200644|49546|237|239;3379134|1224|28216|206351|481|482|484;3379134|1224|28216|206351|481|482|192066;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836|1924944;3379134|976|200643|171549|171552|2974251|28135;1783272|201174|1760|85006|1268|32207|1885016;3379134|1224|28211|204457|41297;1783272|1239|91061|1385|90964|1279|29387;1783272|1239|91061|186826|1300|1301|1303;3379134|1224|28211|204455|31989|366614|1310087,Complete,Claregrieve1
bsdb:26731268/1/1,26731268,"laboratory experiment,time series / longitudinal observational",26731268,https://doi.org/10.1371/journal.pone.0146509,https://pubmed.ncbi.nlm.nih.gov/26731268/,"Kelley S.T., Skarra D.V., Rivera A.J. , Thackray V.G.",The Gut Microbiome Is Altered in a Letrozole-Induced Mouse Model of Polycystic Ovary Syndrome,PloS one,2016,NA,Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Placebo-treated,Letrozole-treated,"At 4 weeks of age, the mice were implanted subcutaneously with a 3 mg letrozole pellet (Innovative Research of America, Sarasota, FL) that provided a constant, slow release of letrozole (50 μg/day) (n = 10/group).",10,10,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,S2 Fig,5 December 2022,Testuser,"Testuser,Tolulopeo,Peace Sandy,WikiWorks",Letrozole treatment results in significant changes in 48 bacterial OTUs as assessed by Kruskal-Wallis test.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|526524|526525|128827|174708;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|841,Complete,NA
bsdb:26731268/1/2,26731268,"laboratory experiment,time series / longitudinal observational",26731268,https://doi.org/10.1371/journal.pone.0146509,https://pubmed.ncbi.nlm.nih.gov/26731268/,"Kelley S.T., Skarra D.V., Rivera A.J. , Thackray V.G.",The Gut Microbiome Is Altered in a Letrozole-Induced Mouse Model of Polycystic Ovary Syndrome,PloS one,2016,NA,Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Placebo-treated,Letrozole-treated,"At 4 weeks of age, the mice were implanted subcutaneously with a 3 mg letrozole pellet (Innovative Research of America, Sarasota, FL) that provided a constant, slow release of letrozole (50 μg/day) (n = 10/group).",10,10,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,S2 Fig,5 December 2022,Testuser,"Testuser,Peace Sandy,WikiWorks",Letrozole treatment results in significant changes in 48 bacterial OTUs as assessed by Kruskal-Wallis test.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis",3379134|976|200643|171549|2005473;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|186807|51514;3379134|976|200643|171549|2005525|375288|823,Complete,NA
bsdb:26745497/1/1,26745497,"cross-sectional observational, not case-control",26745497,10.1159/000442479,NA,"Radilla-Vázquez R.B., Parra-Rojas I., Martínez-Hernández N.E., Márquez-Sandoval Y.F., Illades-Aguiar B. , Castro-Alarcón N.",Gut Microbiota and Metabolic Endotoxemia in Young Obese Mexican Subjects,Obesity facts,2016,NA,Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight,obese,obese individuals (BMI >=30) both sexes aged between 18 to 25 years,32,32,1 month,WMS,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,Mst Afroza Parvin,"Claregrieve1,WikiWorks",Differential microbial abundance in obese and normal-weight young subjects,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239|186801|186802|216572|1535;1783272|1239|91061|186826|33958|1578,Complete,Claregrieve1
bsdb:26745497/1/2,26745497,"cross-sectional observational, not case-control",26745497,10.1159/000442479,NA,"Radilla-Vázquez R.B., Parra-Rojas I., Martínez-Hernández N.E., Márquez-Sandoval Y.F., Illades-Aguiar B. , Castro-Alarcón N.",Gut Microbiota and Metabolic Endotoxemia in Young Obese Mexican Subjects,Obesity facts,2016,NA,Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight,obese,obese individuals (BMI >=30) both sexes aged between 18 to 25 years,32,32,1 month,WMS,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,10 January 2021,Mst Afroza Parvin,"Claregrieve1,WikiWorks",Differential microbial abundance in obese and normal-weight young subjects,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|1224|1236|91347|543|561|562;3379134|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:26789999/1/1,26789999,case-control,26789999,https://doi.org/10.1159/000441768,https://pubmed.ncbi.nlm.nih.gov/26789999/,"Takahashi K., Nishida A., Fujimoto T., Fujii M., Shioya M., Imaeda H., Inatomi O., Bamba S., Sugimoto M. , Andoh A.",Reduced Abundance of Butyrate-Producing Bacteria Species in the Fecal Microbial Community in Crohn's Disease,Digestion,2016,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Healthy controls,CD patients,Patients with Crohn's disease,46,68,NA,16S,34,Illumina,raw counts,T-Test,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 2, Figure 2",9 June 2023,Atrayees,"Atrayees,WikiWorks",Relative abundance of bacteria between control and CD,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85004|31953|1678,Complete,Shaimaa Elsafoury
bsdb:26789999/1/2,26789999,case-control,26789999,https://doi.org/10.1159/000441768,https://pubmed.ncbi.nlm.nih.gov/26789999/,"Takahashi K., Nishida A., Fujimoto T., Fujii M., Shioya M., Imaeda H., Inatomi O., Bamba S., Sugimoto M. , Andoh A.",Reduced Abundance of Butyrate-Producing Bacteria Species in the Fecal Microbial Community in Crohn's Disease,Digestion,2016,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Healthy controls,CD patients,Patients with Crohn's disease,46,68,NA,16S,34,Illumina,raw counts,T-Test,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2, Table 2",9 June 2023,Atrayees,"Atrayees,WikiWorks",Relative abundance of bacteria between control and CD,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Cellulosilyticaceae|g__Cellulosilyticum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster lavalensis",1783272|1239|186801|3085636|3018741|698776;1783272|1239|186801|186802|186806|1730;1783272|1239|526524|526525|128827|61170;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1017280;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|3085636|186803|572511|871665;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803|2719313|460384,Complete,NA
bsdb:26859894/1/1,26859894,"cross-sectional observational, not case-control",26859894,10.1371/journal.pone.0148952,https://pubmed.ncbi.nlm.nih.gov/26859894/,"Miller G.E., Engen P.A., Gillevet P.M., Shaikh M., Sikaroodi M., Forsyth C.B., Mutlu E. , Keshavarzian A.",Lower Neighborhood Socioeconomic Status Associated with Reduced Diversity of the Colonic Microbiota in Healthy Adults,PloS one,2016,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,High SES,Low SES,"44 healthy participants from low-income neighborhoods with a median annual income of $20,100 and a 35% unemployment rate and neighborhoods at the high end, with a median income of $129,570 and an unemployment rate under 5%).
(Income level as a continuous variable.)",44,NA,3 months,16S,NA,Roche454,raw counts,"Linear Regression,Spearman Correlation",0.05,NA,NA,NA,"age,alcohol drinking,body mass index,race,sex,smoking status",NA,decreased,NA,NA,NA,NA,Signature 1,FIGURE 3,11 June 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks","Scatter-plot of neighborhood SES and bacterial genera. Figs depict associations between neighborhood SES and Prevotella to Bacteroides ratio (upper panel), as well as the relative abundance of Prevotella (middle panel) and Bacteroides (lower panel). Specimens are biopsies excised from sigmoid
mucosa.",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,NA
bsdb:26859894/1/2,26859894,"cross-sectional observational, not case-control",26859894,10.1371/journal.pone.0148952,https://pubmed.ncbi.nlm.nih.gov/26859894/,"Miller G.E., Engen P.A., Gillevet P.M., Shaikh M., Sikaroodi M., Forsyth C.B., Mutlu E. , Keshavarzian A.",Lower Neighborhood Socioeconomic Status Associated with Reduced Diversity of the Colonic Microbiota in Healthy Adults,PloS one,2016,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,High SES,Low SES,"44 healthy participants from low-income neighborhoods with a median annual income of $20,100 and a 35% unemployment rate and neighborhoods at the high end, with a median income of $129,570 and an unemployment rate under 5%).
(Income level as a continuous variable.)",44,NA,3 months,16S,NA,Roche454,raw counts,"Linear Regression,Spearman Correlation",0.05,NA,NA,NA,"age,alcohol drinking,body mass index,race,sex,smoking status",NA,decreased,NA,NA,NA,NA,Signature 2,FIGURE 3,11 June 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks","Scatter-plot of neighborhood SES and bacterial genera. Figs depict associations between neighborhood SES and Prevotella to Bacteroides ratio (upper panel), as well as the relative abundance of Prevotella (middle panel) and Bacteroides (lower panel). Specimens are biopsies excised from sigmoid
mucosa.",decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,NA
bsdb:26901400/1/1,26901400,case-control,26901400,10.1016/j.ejogrb.2016.01.040,NA,"Khan K.N., Fujishita A., Masumoto H., Muto H., Kitajima M., Masuzaki H. , Kitawaki J.",Molecular detection of intrauterine microbial colonization in women with endometriosis,"European journal of obstetrics, gynecology, and reproductive biology",2016,"16S rDNA metagenome assay, Cystic fluid, Endometriosis, Infection",Experiment 1,Japan,Homo sapiens,Endometrium,UBERON:0001295,Endometriosis,EFO:0001065,Untreated control women,Endometriosis patients,Patients were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM). 16 of the control patients and 16 of the endometriosis patients received GnRHa (gonadotropin releasing hormone agonist) treatment for 4-6 months.,32,32,NA,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,8 August 2021,Samara.Khan,"Samara.Khan,WikiWorks","Regardless of GnRHa treatment, patients with endometriosis had higher levels of streptococcaceae and moraxellaceae than those without endometriosis.",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae",1783272|1239|91061|186826|1300;3379134|1224|1236|2887326|468,Complete,Atrayees
bsdb:26901400/2/1,26901400,case-control,26901400,10.1016/j.ejogrb.2016.01.040,NA,"Khan K.N., Fujishita A., Masumoto H., Muto H., Kitajima M., Masuzaki H. , Kitawaki J.",Molecular detection of intrauterine microbial colonization in women with endometriosis,"European journal of obstetrics, gynecology, and reproductive biology",2016,"16S rDNA metagenome assay, Cystic fluid, Endometriosis, Infection",Experiment 2,Japan,Homo sapiens,Endometrium,UBERON:0001295,Endometriosis,EFO:0001065,Endometriosis patients not treated with GnRHa,Endometriosis patients treated with GnRHa,Patients were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM). 16 of the 32 endometriosis patients received GnRHa (gonadotropin releasing hormone agonist) treatment for 4-6 months.,16,16,NA,16S,NA,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,8 August 2021,Samara.Khan,"Samara.Khan,WikiWorks","Streptococcaceae, Staphylococaceae, Enterobacteriaceae were significantly increased (p<0.05 for each) in GnRHa-treated women with endometriosis than in GnRHa-untreated women.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae",3379134|1224|1236|91347|543;1783272|1239|91061|186826|1300;1783272|1239|91061|1385|90964,Complete,Atrayees
bsdb:26901400/2/2,26901400,case-control,26901400,10.1016/j.ejogrb.2016.01.040,NA,"Khan K.N., Fujishita A., Masumoto H., Muto H., Kitajima M., Masuzaki H. , Kitawaki J.",Molecular detection of intrauterine microbial colonization in women with endometriosis,"European journal of obstetrics, gynecology, and reproductive biology",2016,"16S rDNA metagenome assay, Cystic fluid, Endometriosis, Infection",Experiment 2,Japan,Homo sapiens,Endometrium,UBERON:0001295,Endometriosis,EFO:0001065,Endometriosis patients not treated with GnRHa,Endometriosis patients treated with GnRHa,Patients were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM). 16 of the 32 endometriosis patients received GnRHa (gonadotropin releasing hormone agonist) treatment for 4-6 months.,16,16,NA,16S,NA,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,8 August 2021,Samara.Khan,"Samara.Khan,WikiWorks",Lactobacillaceae was significantly decreased (p<0.01) in GnRHa-treated women with endometriosis compared to GnRHa-untreated women with endometriosis,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,1783272|1239|91061|186826|33958,Complete,Atrayees
bsdb:26901400/3/1,26901400,case-control,26901400,10.1016/j.ejogrb.2016.01.040,NA,"Khan K.N., Fujishita A., Masumoto H., Muto H., Kitajima M., Masuzaki H. , Kitawaki J.",Molecular detection of intrauterine microbial colonization in women with endometriosis,"European journal of obstetrics, gynecology, and reproductive biology",2016,"16S rDNA metagenome assay, Cystic fluid, Endometriosis, Infection",Experiment 3,Japan,Homo sapiens,Ovary,UBERON:0000992,Endometriosis,EFO:0001065,Patients with non-endometrioma cysts,Patients with ovarian endometrioma cysts,Patients with ovarian endometrioma had endometrial cysts in their ovaries. Researchers took samples of the fluid inside these cysts. Ovarian endometrioma is one of the many ways endometriosis manifests in the female reproductive system.,8,8,NA,16S,NA,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,8 August 2021,Samara.Khan,"Samara.Khan,WikiWorks",There was a significantly higher percentage of Streptococcaceae (p<0.01) and Staphylococaceae (p<0.05) in the cystic fluid derived from women with ovarian endometrioma comparing to that in cystic fluid collected from non-endometrioma cysts.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae",1783272|1239|91061|186826|1300;1783272|1239|91061|1385|90964,Complete,Atrayees
bsdb:26901400/3/2,26901400,case-control,26901400,10.1016/j.ejogrb.2016.01.040,NA,"Khan K.N., Fujishita A., Masumoto H., Muto H., Kitajima M., Masuzaki H. , Kitawaki J.",Molecular detection of intrauterine microbial colonization in women with endometriosis,"European journal of obstetrics, gynecology, and reproductive biology",2016,"16S rDNA metagenome assay, Cystic fluid, Endometriosis, Infection",Experiment 3,Japan,Homo sapiens,Ovary,UBERON:0000992,Endometriosis,EFO:0001065,Patients with non-endometrioma cysts,Patients with ovarian endometrioma cysts,Patients with ovarian endometrioma had endometrial cysts in their ovaries. Researchers took samples of the fluid inside these cysts. Ovarian endometrioma is one of the many ways endometriosis manifests in the female reproductive system.,8,8,NA,16S,NA,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5,7 August 2023,Atrayees,"Atrayees,WikiWorks",There was a significantly higher percentage of Streptococcaceae (p<0.01) and Staphylococaceae (p<0.05) in the cystic fluid derived from women with ovarian endometrioma comparing to that in cystic fluid collected from non-endometrioma cysts.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,1783272|1239|91061|186826|33958,Complete,Atrayees
bsdb:26919743/1/1,26919743,time series / longitudinal observational,26919743,10.1371/journal.pone.0149564,NA,"Louis S., Tappu R.M., Damms-Machado A., Huson D.H. , Bischoff S.C.",Characterization of the Gut Microbial Community of Obese Patients Following a Weight-Loss Intervention Using Whole Metagenome Shotgun Sequencing,PloS one,2016,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,baseline participants,3 months,A threshold of 10% weight loss and maintenance of it over one year has been proposed as definition for successful weight loss maintenance,16,16,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Marianthi Thomatos,"Fatima,WikiWorks",Gut microbial community of obese patients following weight-loss intervention,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Anaerobiospirillum|s__Anaerobiospirillum succiniciproducens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum variabile,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium 1_1_47",3379134|1224|1236|135624|83763|13334|13335;1783272|201174|84998|84999|84107|102106|74426;3379134|1224|28216|80840|995019|577310|487175;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|186802|216572|292632|214851;3379134|1224|28216|80840|469610,Complete,Fatima
bsdb:26919743/1/2,26919743,time series / longitudinal observational,26919743,10.1371/journal.pone.0149564,NA,"Louis S., Tappu R.M., Damms-Machado A., Huson D.H. , Bischoff S.C.",Characterization of the Gut Microbial Community of Obese Patients Following a Weight-Loss Intervention Using Whole Metagenome Shotgun Sequencing,PloS one,2016,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,baseline participants,3 months,A threshold of 10% weight loss and maintenance of it over one year has been proposed as definition for successful weight loss maintenance,16,16,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbial community of obese patients following weight-loss intervention,decreased,"k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema brennaborense,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter|s__Pedobacter heparinus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas|s__Dysgonomonas gade,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfitobacteriaceae|g__Desulfitobacterium|s__Desulfitobacterium hafniense,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Desulforamulus|s__Desulforamulus ruminis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens|s__Ethanoligenens harbinense,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania filiformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Heyndrickxia|s__Heyndrickxia coagulans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus mucilaginosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia|s__Marvinbryantia formatexigens,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Geobacterales|f__Geobacteraceae|g__Geobacter|s__Geobacter sp. M18,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Stutzerimonas|s__Stutzerimonas stutzeri,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces coelicolor,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia heliotrinireducens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Thermanaerovibrio|s__Thermanaerovibrio acidaminovorans,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum",3379134|203691|203692|136|2845253|157|81028;3379134|976|117747|200666|84566|84567|984;3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|2005520|156973|156974;1783272|1239|186801|186802|2937909|36853|49338;1783272|1239|186801|186802|186807|2916693|1564;1783272|1239|909932|909929|1843491|970|69823;1783272|1239|186801|186802|216572|244127|169435;1783272|1239|186801|186802|216572|253238|253239;1783272|1239|186801|186802|216572|459786|351091;1783272|1239|186801|186802|216572|1017280|106588;1783272|1239|526524|526525|128827|61170|61171;1783272|1239|91061|1385|186817|2837504|1398;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|91061|186826|81852|1350|1352;1783272|1239|91061|1385|186822|44249|61624;1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|186801|3085636|186803|2719313|333367;1783272|1239|186801|3085636|186803|248744|168384;3379134|200940|3031651|3031668|213422|28231|443143;3379134|1224|1236|91347|543|561|562;3379134|1224|1236|72274|135621|2901164|316;1783272|201174|1760|85011|2062|1883|1902;1783272|201174|84998|1643822|1643826|84108|84110;1783272|201174|84998|1643822|1643826|84111|84112;3379134|74201|203494|48461|1647988|239934|239935;3384194|508458|649775|649776|649777|81461|81462;3384194|508458|649775|649776|3029087|1434006|651822,Complete,Shaimaa Elsafoury
bsdb:26919743/2/1,26919743,time series / longitudinal observational,26919743,10.1371/journal.pone.0149564,NA,"Louis S., Tappu R.M., Damms-Machado A., Huson D.H. , Bischoff S.C.",Characterization of the Gut Microbial Community of Obese Patients Following a Weight-Loss Intervention Using Whole Metagenome Shotgun Sequencing,PloS one,2016,NA,Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,3 months participants,6 months,A threshold of 10% weight loss and maintenance of it over one year has been proposed as definition for successful weight loss maintenance,16,16,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbial community of obese patients following weight-loss intervention,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas|s__Dysgonomonas gade,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora saccharolytica,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio desulfuricans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Thermanaerovibrio|s__Thermanaerovibrio acidaminovorans",3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|2005520|156973|156974;1783272|1239|186801|3085636|186803|2719313|333367;1783272|1239|186801|3085636|186803|2719231|84030;3379134|200940|3031449|213115|194924|872|876;3379134|1224|1236|91347|543|561|562;1783272|201174|84998|1643822|1643826|84111|84112;1783272|201174|84998|1643822|1643826|644652|471189;3384194|508458|649775|649776|649777|81461|81462,Complete,Shaimaa Elsafoury
bsdb:26919743/2/2,26919743,time series / longitudinal observational,26919743,10.1371/journal.pone.0149564,NA,"Louis S., Tappu R.M., Damms-Machado A., Huson D.H. , Bischoff S.C.",Characterization of the Gut Microbial Community of Obese Patients Following a Weight-Loss Intervention Using Whole Metagenome Shotgun Sequencing,PloS one,2016,NA,Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,3 months participants,6 months,A threshold of 10% weight loss and maintenance of it over one year has been proposed as definition for successful weight loss maintenance,16,16,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3,10 January 2021,Marianthi Thomatos,"Fatima,WikiWorks",Gut microbial community of obese patients following weight-loss intervention,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Anaerobiospirillum|s__Anaerobiospirillum succiniciproducens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Pseudomonadati|p__Bdellovibrionota|c__Bdellovibrionia|o__Bdellovibrionales|f__Pseudobdellovibrionaceae|g__Micavibrio|s__Micavibrio aeruginosavorus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium 1_1_47",3379134|1224|1236|135624|83763|13334|13335;1783272|1239|91061|186826|1300|1357|1358;3379134|3018035|3031418|213481|213483|213485|349221;3379134|1224|28216|80840|995019|577310|487175;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|909932|1843489|31977|29465|29466;3379134|1224|28216|80840|469610,Complete,Fatima
bsdb:26919743/3/1,26919743,time series / longitudinal observational,26919743,10.1371/journal.pone.0149564,NA,"Louis S., Tappu R.M., Damms-Machado A., Huson D.H. , Bischoff S.C.",Characterization of the Gut Microbial Community of Obese Patients Following a Weight-Loss Intervention Using Whole Metagenome Shotgun Sequencing,PloS one,2016,NA,Experiment 3,Germany,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,6 months participants,24 months,A threshold of 10% weight loss and maintenance of it over one year has been proposed as definition for successful weight loss maintenance,16,16,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbial community of obese patients following weight-loss intervention,increased,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter|s__Pedobacter heparinus,3379134|976|117747|200666|84566|84567|984,Complete,Shaimaa Elsafoury
bsdb:26919743/3/2,26919743,time series / longitudinal observational,26919743,10.1371/journal.pone.0149564,NA,"Louis S., Tappu R.M., Damms-Machado A., Huson D.H. , Bischoff S.C.",Characterization of the Gut Microbial Community of Obese Patients Following a Weight-Loss Intervention Using Whole Metagenome Shotgun Sequencing,PloS one,2016,NA,Experiment 3,Germany,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,6 months participants,24 months,A threshold of 10% weight loss and maintenance of it over one year has been proposed as definition for successful weight loss maintenance,16,16,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbial community of obese patients following weight-loss intervention,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens",3379134|74201|203494|48461|1647988|239934|239935;3379134|1224|1236|91347|543|561|562;1783272|201174|84998|84999|84107|102106|74426,Complete,Shaimaa Elsafoury
bsdb:26935422/1/1,26935422,"cross-sectional observational, not case-control",26935422,10.1158/1940-6207.CAPR-15-0350,NA,"Piyathilake C.J., Ollberding N.J., Kumar R., Macaluso M., Alvarez R.D. , Morrow C.D.",Cervical Microbiota Associated with Higher Grade Cervical Intraepithelial Neoplasia in Women Infected with High-Risk Human Papillomaviruses,"Cancer prevention research (Philadelphia, Pa.)",2016,NA,Experiment 1,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical glandular intraepithelial neoplasia,EFO:1000165,CIN1,CIN2+,patients with CIN2+ confirmed by colposcopy,90,340,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Figure 2, supplemental table 1",10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Differentially abundant taxa in CIN2+ group VS CIN1 group,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Heliobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Legionellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Ectopseudomonas|s__Ectopseudomonas oleovorans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Rickettsiella",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|28111;3379134|976|200643|171549|1853231|574697;3379134|1224|1236|118969|118968;1783272|1239|186801|186802|31984;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;3379134|1224|1236|118969|444;1783272|1239|91061|186826|33958|2742598|1598;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;3379134|1224|1236|72274|135621|3236654|330;3379134|1224|1236|118969|118968|59195,Complete,Fatima Zohra
bsdb:26935422/1/2,26935422,"cross-sectional observational, not case-control",26935422,10.1158/1940-6207.CAPR-15-0350,NA,"Piyathilake C.J., Ollberding N.J., Kumar R., Macaluso M., Alvarez R.D. , Morrow C.D.",Cervical Microbiota Associated with Higher Grade Cervical Intraepithelial Neoplasia in Women Infected with High-Risk Human Papillomaviruses,"Cancer prevention research (Philadelphia, Pa.)",2016,NA,Experiment 1,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical glandular intraepithelial neoplasia,EFO:1000165,CIN1,CIN2+,patients with CIN2+ confirmed by colposcopy,90,340,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Figure 2, supplemental table 1",10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Differentially abundant taxa in CIN2+ group VS CIN1 group,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|186802;1783272|1239|186801|186802|541000,Complete,Fatima Zohra
bsdb:26935422/2/1,26935422,"cross-sectional observational, not case-control",26935422,10.1158/1940-6207.CAPR-15-0350,NA,"Piyathilake C.J., Ollberding N.J., Kumar R., Macaluso M., Alvarez R.D. , Morrow C.D.",Cervical Microbiota Associated with Higher Grade Cervical Intraepithelial Neoplasia in Women Infected with High-Risk Human Papillomaviruses,"Cancer prevention research (Philadelphia, Pa.)",2016,NA,Experiment 2,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical glandular intraepithelial neoplasia,EFO:1000165,<=38.8% 8-OHdG-positive cervical cells,>38.8% 8-OHdG-positive cervical cells,patients with >38.8% of 8-OHdG-positive cervical cells,NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Supplemental Figure 2,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Differentially abundant taxa in >38.8% 8-OHdG-positive cervical cells group VS  <=38.8% 8-OHdG-positive cervical cells group,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Limnohabitans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Phenylobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae",3379134|1224|28211|356|82115|357;3379134|1224|1236|72274|135621|351;3379134|1224|28216;3379134|1224|28216|80840;3379134|1224|28216|80840|80864;3379134|1224|28211|356;3379134|1224|28216|80840|80864|665874;3379134|1224|28216|80840|75682;3379134|1224|28211|204458|76892|20;3379134|1224|1236|72274|135621|286;3379134|1224|28211|356|82115,Complete,Fatima Zohra
bsdb:26935422/2/2,26935422,"cross-sectional observational, not case-control",26935422,10.1158/1940-6207.CAPR-15-0350,NA,"Piyathilake C.J., Ollberding N.J., Kumar R., Macaluso M., Alvarez R.D. , Morrow C.D.",Cervical Microbiota Associated with Higher Grade Cervical Intraepithelial Neoplasia in Women Infected with High-Risk Human Papillomaviruses,"Cancer prevention research (Philadelphia, Pa.)",2016,NA,Experiment 2,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical glandular intraepithelial neoplasia,EFO:1000165,<=38.8% 8-OHdG-positive cervical cells,>38.8% 8-OHdG-positive cervical cells,patients with >38.8% of 8-OHdG-positive cervical cells,NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Supplemental Figure 2,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Differentially abundant taxa in >38.8% 8-OHdG-positive cervical cells group VS <=38.8% 8-OHdG-positive cervical cells group,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,1783272|1239|186801|186802|31979,Complete,Fatima Zohra
bsdb:26935422/3/1,26935422,"cross-sectional observational, not case-control",26935422,10.1158/1940-6207.CAPR-15-0350,NA,"Piyathilake C.J., Ollberding N.J., Kumar R., Macaluso M., Alvarez R.D. , Morrow C.D.",Cervical Microbiota Associated with Higher Grade Cervical Intraepithelial Neoplasia in Women Infected with High-Risk Human Papillomaviruses,"Cancer prevention research (Philadelphia, Pa.)",2016,NA,Experiment 3,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical glandular intraepithelial neoplasia,EFO:1000165,CIN1,CIN2+,patients with CIN2+ confirmed by colposcopy,90,340,NA,16S,4,Illumina,raw counts,Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Supplemental Table 2,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Differentially abundant taxa in CIN2+ group VS CIN1 group,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|91061|186826|33958|2742598|1598,Complete,Fatima Zohra
bsdb:26935422/3/2,26935422,"cross-sectional observational, not case-control",26935422,10.1158/1940-6207.CAPR-15-0350,NA,"Piyathilake C.J., Ollberding N.J., Kumar R., Macaluso M., Alvarez R.D. , Morrow C.D.",Cervical Microbiota Associated with Higher Grade Cervical Intraepithelial Neoplasia in Women Infected with High-Risk Human Papillomaviruses,"Cancer prevention research (Philadelphia, Pa.)",2016,NA,Experiment 3,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical glandular intraepithelial neoplasia,EFO:1000165,CIN1,CIN2+,patients with CIN2+ confirmed by colposcopy,90,340,NA,16S,4,Illumina,raw counts,Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Supplemental Table 2,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Differentially abundant taxa in CIN2+ group VS CIN1 group,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|3085636|186803|572511|33035;1783272|1239|186801|186802|31979|1485|1502;1783272|201174|84998|84999|84107|102106|74426;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|91061|186826|1300|1301|1311,Complete,Fatima Zohra
bsdb:26937623/1/1,26937623,"cross-sectional observational, not case-control",26937623,10.1097/MIB.0000000000000684,NA,"Forbes J.D., Van Domselaar G. , Bernstein C.N.",Microbiome Survey of the Inflamed and Noninflamed Gut at Different Compartments Within the Gastrointestinal Tract of Inflammatory Bowel Disease Patients,Inflammatory bowel diseases,2016,NA,Experiment 1,Canada,Homo sapiens,"Cecum mucosa,Colonic mucosa,Mucosa of rectum,Ileal mucosa","UBERON:0000331,UBERON:0000314,UBERON:0000317,UBERON:0003346",Crohn's disease,EFO:0000384,non-inflammatory bowel disease who were undergoing colonoscopy either for screening or for other gastrointestinal complaints unrelated to IBD,non-inflamed crohn's disease,biopsies collected from patients with crohn's disease at colonoscopy that were deemed as non-inflamed as per the clinical pathologist.,7,15,NA,16S,6,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 1,Table 2,9 November 2023,Yjung24,"Yjung24,WikiWorks","Microbial Distribution of Taxa (Phylum and Genus) Found to Be Differentially Abundant According to Disease and Inflammatory State of Biopsy. ^aP = <0.05, ^bP = <0.01, ^cP = <0.001. Up and down arrows are comparisons to non-IBD.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|459786,Complete,Peace Sandy
bsdb:26937623/2/1,26937623,"cross-sectional observational, not case-control",26937623,10.1097/MIB.0000000000000684,NA,"Forbes J.D., Van Domselaar G. , Bernstein C.N.",Microbiome Survey of the Inflamed and Noninflamed Gut at Different Compartments Within the Gastrointestinal Tract of Inflammatory Bowel Disease Patients,Inflammatory bowel diseases,2016,NA,Experiment 2,Canada,Homo sapiens,"Cecum mucosa,Colonic mucosa,Mucosa of rectum,Ileal mucosa","UBERON:0000314,UBERON:0000317,UBERON:0000331,UBERON:0003346",Ulcerative colitis,EFO:0000729,non-inflammatory bowel disease patients who were undergoing colonoscopy either for screening or for other gastrointestinal complaints unrelated to IBD,non-inflamed ulcerative colitis,biopsies collected from patients with ulcerative colitis at colonoscopy that were deemed as non-inflamed as per the clinical pathologist.,7,21,NA,16S,6,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 1,Table 2,9 November 2023,Yjung24,"Yjung24,WikiWorks","Microbial Distribution of Taxa (Phylum and Genus) Found to Be Differentially Abundant According to Disease and Inflammatory State of Biopsy. ^aP = <0.05, ^bP = <0.01, ^cP = <0.001. Up and down arrows are comparisons to non-IBD.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Marinobacteraceae|g__Marinobacter,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",1783272|201174|1760|2037|2049|1654;1783272|1239;3379134|1224|1236|72274|2887365|2742;3379134|1224;3379134|1224|1236|72274|135621|286,Complete,Peace Sandy
bsdb:26937623/2/2,26937623,"cross-sectional observational, not case-control",26937623,10.1097/MIB.0000000000000684,NA,"Forbes J.D., Van Domselaar G. , Bernstein C.N.",Microbiome Survey of the Inflamed and Noninflamed Gut at Different Compartments Within the Gastrointestinal Tract of Inflammatory Bowel Disease Patients,Inflammatory bowel diseases,2016,NA,Experiment 2,Canada,Homo sapiens,"Cecum mucosa,Colonic mucosa,Mucosa of rectum,Ileal mucosa","UBERON:0000314,UBERON:0000317,UBERON:0000331,UBERON:0003346",Ulcerative colitis,EFO:0000729,non-inflammatory bowel disease patients who were undergoing colonoscopy either for screening or for other gastrointestinal complaints unrelated to IBD,non-inflamed ulcerative colitis,biopsies collected from patients with ulcerative colitis at colonoscopy that were deemed as non-inflamed as per the clinical pathologist.,7,21,NA,16S,6,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 2,Table 2,9 November 2023,Yjung24,"Yjung24,WikiWorks","Microbial Distribution of Taxa (Phylum and Genus) Found to Be Differentially Abundant According to Disease and Inflammatory State of Biopsy. ^aP = <0.05, ^bP = <0.01, ^cP = <0.001. Up and down arrows are comparisons to non-IBD.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;3379134|976;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171552|838,Complete,Peace Sandy
bsdb:26937623/3/1,26937623,"cross-sectional observational, not case-control",26937623,10.1097/MIB.0000000000000684,NA,"Forbes J.D., Van Domselaar G. , Bernstein C.N.",Microbiome Survey of the Inflamed and Noninflamed Gut at Different Compartments Within the Gastrointestinal Tract of Inflammatory Bowel Disease Patients,Inflammatory bowel diseases,2016,NA,Experiment 3,Canada,Homo sapiens,"Cecum mucosa,Colonic mucosa,Mucosa of rectum,Ileal mucosa","UBERON:0000314,UBERON:0000317,UBERON:0000331,UBERON:0003346",Ulcerative colitis,EFO:0000729,non-inflammatory bowel disease patients who were undergoing colonoscopy either for screening or for other gastrointestinal complaints unrelated to IBD,inflamed ulcerative colitis,biopsies collected from patients with ulcerative colitis at colonoscopy that were deemed as inflamed as per the clinical pathologist.,27,26,NA,16S,6,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,increased,increased,decreased,Signature 1,Table 2,9 November 2023,Yjung24,"Yjung24,WikiWorks","Microbial Distribution of Taxa (Phylum and Genus) Found to Be Differentially Abundant According to Disease and Inflammatory State of Biopsy. ^aP = <0.05, ^bP = <0.01, ^cP = <0.001. Up and down arrows are comparisons to non-IBD.",increased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",3379134|1224;3379134|1224|1236|72274|135621|286,Complete,Peace Sandy
bsdb:26937623/3/2,26937623,"cross-sectional observational, not case-control",26937623,10.1097/MIB.0000000000000684,NA,"Forbes J.D., Van Domselaar G. , Bernstein C.N.",Microbiome Survey of the Inflamed and Noninflamed Gut at Different Compartments Within the Gastrointestinal Tract of Inflammatory Bowel Disease Patients,Inflammatory bowel diseases,2016,NA,Experiment 3,Canada,Homo sapiens,"Cecum mucosa,Colonic mucosa,Mucosa of rectum,Ileal mucosa","UBERON:0000314,UBERON:0000317,UBERON:0000331,UBERON:0003346",Ulcerative colitis,EFO:0000729,non-inflammatory bowel disease patients who were undergoing colonoscopy either for screening or for other gastrointestinal complaints unrelated to IBD,inflamed ulcerative colitis,biopsies collected from patients with ulcerative colitis at colonoscopy that were deemed as inflamed as per the clinical pathologist.,27,26,NA,16S,6,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,increased,increased,decreased,Signature 2,Table 2,9 November 2023,Yjung24,"Yjung24,WikiWorks","Microbial Distribution of Taxa (Phylum and Genus) Found to Be Differentially Abundant According to Disease and Inflammatory State of Biopsy. ^aP = <0.05, ^bP = <0.01, ^cP = <0.001. Up and down arrows are comparisons to non-IBD.",decreased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|976;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|2005525|375288,Complete,Peace Sandy
bsdb:26962942/1/1,26962942,"cross-sectional observational, not case-control",26962942,10.1016/j.chom.2016.02.011,NA,"Monaco C.L., Gootenberg D.B., Zhao G., Handley S.A., Ghebremichael M.S., Lim E.S., Lankowski A., Baldridge M.T., Wilen C.B., Flagg M., Norman J.M., Keller B.C., Luévano J.M., Wang D., Boum Y., Martin J.N., Hunt P.W., Bangsberg D.R., Siedner M.J., Kwon D.S. , Virgin H.W.",Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome,Cell host & microbe,2016,"AIDS, AIDS enteropathy, HIV, adenovirus, microbiome, systemic inflammation, virome",Experiment 1,Uganda,Homo sapiens,Feces,UBERON:0001988,Human immunodeficiency virus,NCBITAXON:12721,HIV - uninfected,CD4 T cell counts < 200 (CD4 < 200),CD4 T cell counts < 200 (CD4 < 200)  refers to HIV infected patients who had significantly higher levels of circulating sCD14 than both HIV-negative subjects and HIV-infected subjects with CD4 > 200.,37,25,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,"Table S5, Tab 1",6 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant bacterial taxa in subjects with CD4 < 200 compared to HIV-negative subjects.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,s__rumen bacterium YS2,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus flavefaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Ruminobacter",1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|1263;3379134|1224|1236|135624|83763|83770;1783272|1239|186801|186802|31979;1783272|1239|186801|186802;1783272|544448|31969;1783272|1239|186801|186802|216572|1263|40518;209265;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|140625;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|186801|186802|216572|1263|1265;3379134|976|200643|171549|1853231|574697;1783272|1239|909932|909929|1843491|82373;3379134|1224|28216|80840|75682;3379134|976|200643|171549;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|815|816;3379134|976|200643|171549|171552|838;3379134|976|200643|171549;3366610|28890|183925|2158|2159|2172;1783272|1239|186801|3082768|990719;3379134|74152|641853|641854|641876;3379134|200940|3031449|213115|194924|872;1783272|544448|31969|186332|186333|2086;1783272|201174|84998|84999|84107;3379134|29547|3031852|213849|72294|194;3379134|976|200643|171549|2005473;3379134|203691|203692|136|2845253|157;3379134|1224|1236|135624|83763|866,Complete,Svetlana up
bsdb:26962942/1/2,26962942,"cross-sectional observational, not case-control",26962942,10.1016/j.chom.2016.02.011,NA,"Monaco C.L., Gootenberg D.B., Zhao G., Handley S.A., Ghebremichael M.S., Lim E.S., Lankowski A., Baldridge M.T., Wilen C.B., Flagg M., Norman J.M., Keller B.C., Luévano J.M., Wang D., Boum Y., Martin J.N., Hunt P.W., Bangsberg D.R., Siedner M.J., Kwon D.S. , Virgin H.W.",Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome,Cell host & microbe,2016,"AIDS, AIDS enteropathy, HIV, adenovirus, microbiome, systemic inflammation, virome",Experiment 1,Uganda,Homo sapiens,Feces,UBERON:0001988,Human immunodeficiency virus,NCBITAXON:12721,HIV - uninfected,CD4 T cell counts < 200 (CD4 < 200),CD4 T cell counts < 200 (CD4 < 200)  refers to HIV infected patients who had significantly higher levels of circulating sCD14 than both HIV-negative subjects and HIV-infected subjects with CD4 > 200.,37,25,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,"Table S5, Tab 1",7 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant bacterial taxa in subjects with CD4 < 200 compared to HIV-negative subjects.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Trabulsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Pantoea ananatis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia marcescens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus garvieae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter|s__Cronobacter dublinensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus",1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|815|816|820;1783272|1239|186801|3085636|186803|437755;3379134|1224|1236|135625|712|724;1783272|1239|909932|1843489|31977|29465;3379134|976|200643|171549|815|816;3384189|32066|203490|203491|1129771|32067;1783272|1239|909932|1843489|31977|29465|39778;3379134|1224|1236|91347|543|547|550;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|29465|29466;3379134|1224|1236|135625|712|724|729;3379134|1224|1236|135625|712|713;1783272|1239|186801|3085636|186803|265975;1783272|201174|84998|84999|1643824|1380;1783272|1239|91061|186826|33958|46255;3379134|1224|1236|91347|1903409|551;3379134|1224|1236|135625|712|416916;3379134|1224|1236|91347|543|544;3379134|29547|3031852|213849|72294|194;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|33958;1783272|1239|186801|186802;3379134|976|200643|171549|815|816|817;3379134|1224|1236|91347|543;1783272|1239|91061|186826|33958|2742598|97478;1783272|201174|1760|2037|2049|1654;3379134|1224|1236|91347|543|158851;3379134|1224|1236|91347|1903409|53335|553;3379134|1224|1236|135625|712|724|735;3384189|32066|203490|203491|203492|848;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|1903411|613|615;1783272|1239|909932|909929|1843491|52225;3379134|1224|28216|80840|80864;3379134|1224|1236|135625|712;1783272|1239|91061|186826|1300|1357|1363;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|91061|1385|539738;1783272|1239|91061|186826|1300|1301|1328;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|909932|1843489|31977|906;3379134|1224|1236|91347|543|413496|413497;1783272|1239|186801|3085636|186803|28050;3379134|976|200643|171549|815|816|28111;1783272|1239|186801|186802|216572|216851|853;3379134|1224|1236|91347|543|561|562;1783272|1239|91061|186826|186828|117563;3379134|1224|28216|80840;1783272|1239|91061|186826|81852|2737;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|33958|2767887|1623;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|171552|2974251|165179;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|3085636|186803|33042,Complete,Svetlana up
bsdb:26962942/3/1,26962942,"cross-sectional observational, not case-control",26962942,10.1016/j.chom.2016.02.011,NA,"Monaco C.L., Gootenberg D.B., Zhao G., Handley S.A., Ghebremichael M.S., Lim E.S., Lankowski A., Baldridge M.T., Wilen C.B., Flagg M., Norman J.M., Keller B.C., Luévano J.M., Wang D., Boum Y., Martin J.N., Hunt P.W., Bangsberg D.R., Siedner M.J., Kwon D.S. , Virgin H.W.",Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome,Cell host & microbe,2016,"AIDS, AIDS enteropathy, HIV, adenovirus, microbiome, systemic inflammation, virome",Experiment 3,Uganda,Homo sapiens,Feces,UBERON:0001988,Human immunodeficiency virus,NCBITAXON:12721,CD4 T cell counts >200 (CD4 > 200),CD4 T cell counts < 200 (CD4 < 200),HIV infected patients with less than 200 CD4 T cells/mL circulating in the blood.,57,25,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,"Table S5, Tab 2",8 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant bacterial taxa in subjects with CD4 < 200 compared to subjects with CD4 > 200.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira|s__Oscillospira guilliermondii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus flavefaciens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,s__rumen bacterium YS2,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,s__unidentified rumen bacterium RF32",3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|2005519;1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802;1783272|1239|526524|526525|128827|1573535|1735;1783272|1239|186801|3085636|186803|140625;1783272|1239|186801|3085636|186803;1783272|1239|909932|909929|1843491|158846;3366610|28890|183925|2158|2159|2172;3379134|976|200643|171549|2005473;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572|119852|119853;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|577309;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|1265;3379134|1224|1236|135624|83763|83770;3379134|203691|203692|136|2845253|157;1783272|1239|909932|1843489|31977;3379134|256845|1313211|278082|255528;209265;1783272|544448|31969;60675,Complete,Svetlana up
bsdb:26962942/3/2,26962942,"cross-sectional observational, not case-control",26962942,10.1016/j.chom.2016.02.011,NA,"Monaco C.L., Gootenberg D.B., Zhao G., Handley S.A., Ghebremichael M.S., Lim E.S., Lankowski A., Baldridge M.T., Wilen C.B., Flagg M., Norman J.M., Keller B.C., Luévano J.M., Wang D., Boum Y., Martin J.N., Hunt P.W., Bangsberg D.R., Siedner M.J., Kwon D.S. , Virgin H.W.",Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome,Cell host & microbe,2016,"AIDS, AIDS enteropathy, HIV, adenovirus, microbiome, systemic inflammation, virome",Experiment 3,Uganda,Homo sapiens,Feces,UBERON:0001988,Human immunodeficiency virus,NCBITAXON:12721,CD4 T cell counts >200 (CD4 > 200),CD4 T cell counts < 200 (CD4 < 200),HIV infected patients with less than 200 CD4 T cells/mL circulating in the blood.,57,25,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,"Table S5, Tab 2",8 November 2024,InimfonD,"InimfonD,KateRasheed,WikiWorks",Differentially abundant bacterial taxa in subjects with CD4 < 200 compared to subjects with CD4 > 200.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter|s__Cronobacter dublinensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus haemoperoxidus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus garvieae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia marcescens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Anaerobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Pantoea ananatis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Trabulsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|841;1783272|201174|84998|84999|84107|102106|74426;3379134|976|200643|171549|171552|2974251|165179;3379134|976|200643|171549|815|816;1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549|171552|2974265|363265;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|189330;3379134|1224|1236|91347|543;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|81852|2737;3379134|1224|1236|135625|712|724;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|2767887|1623;1783272|1239|909932|1843489|31977|29465|39778;3379134|976|200643|171549|815|816|817;3379134|1224|1236|91347|1903409|551;1783272|1239|186801|3085636|186803|207244;1783272|1239|91061|186826|186828|117563;1783272|201174|1760|85004|31953;1783272|1239|91061|1385|186818;1783272|1239|186801|3082720|543314|86331;3379134|1224|1236|91347|543|413496|413497;3379134|1224|1236|135625|712;3379134|1224|28216|206351|481;3379134|1224|1236|135625|712|724|729;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|186802|31979;3379134|1224|1236|135625|712|713;3379134|976|200643|171549|815|816|820;3379134|1224|28216|80840|80864;3379134|1224|1236|135625|712|416916;1783272|1239|1737404|1737405|1570339|162289;3379134|1224|28216|80840;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|91061|186826|81852|1350|155618;1783272|1239|91061|186826|1300|1357|1363;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|1300|1301|1328;1783272|201174|84998|84999|1643824|1380;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|91061|186826|33958;3379134|1224|1236|91347|1903411|613|615;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|33958|46255;1783272|1239|91061|1385|186817|704093;3379134|1224|1236|91347|543|544;3379134|1224|1236|135625|712|724|735;1783272|1239|186801|3085636|186803|437755;3384189|32066|203490|203491|1129771|32067;3379134|1224|1236|91347|1903409|53335|553;3379134|1224|1236|91347|543|547|550;3384189|32066|203490|203491|1129771|168808;3379134|29547|3031852|213849|72294|194;3379134|1224|1236|91347|543|158851;1783272|1239|91061|1385|539738;1783272|1239|909932|1843488|909930|904;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802,Complete,Svetlana up
bsdb:26963804/1/1,26963804,case-control,26963804,10.1080/19490976.2016.1162363,NA,"Fourie N.H., Wang D., Abey S.K., Sherwin L.B., Joseph P.V., Rahim-Williams B., Ferguson E.G. , Henderson W.A.",The microbiome of the oral mucosa in irritable bowel syndrome,Gut microbes,2016,"irritable bowel syndrome, microbiome, mucosa, oral, overweight, visceral pain",Experiment 1,United States of America,Homo sapiens,Buccal mucosa,UBERON:0006956,Irritable bowel syndrome,EFO:0000555,control,irritable bowel syndrome,IBS are who suffered from chronic visceral pain and altered bowel habits for more than 6 months for which no organic cause had been identified,20,9,NA,16S,NA,PhyloChip,raw counts,Welch's T-Test,0.05,FALSE,NA,"age,body weight,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,10 January 2021,Rimsha Azhar,WikiWorks,OTUs showed significant differential abundance between healthy controls and IBS participants,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfitobacteriaceae|g__Desulfosporosinus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|2937909|79206;1783272|1239|186801|3082720|186804|1257;3379134|1224|28216|80840|506|507;3379134|1224|28216|80840|119060|32008;3379134|1224|28216|206351|481|482,Complete,Shaimaa Elsafoury
bsdb:26963804/1/2,26963804,case-control,26963804,10.1080/19490976.2016.1162363,NA,"Fourie N.H., Wang D., Abey S.K., Sherwin L.B., Joseph P.V., Rahim-Williams B., Ferguson E.G. , Henderson W.A.",The microbiome of the oral mucosa in irritable bowel syndrome,Gut microbes,2016,"irritable bowel syndrome, microbiome, mucosa, oral, overweight, visceral pain",Experiment 1,United States of America,Homo sapiens,Buccal mucosa,UBERON:0006956,Irritable bowel syndrome,EFO:0000555,control,irritable bowel syndrome,IBS are who suffered from chronic visceral pain and altered bowel habits for more than 6 months for which no organic cause had been identified,20,9,NA,16S,NA,PhyloChip,raw counts,Welch's T-Test,0.05,FALSE,NA,"age,body weight,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6,10 January 2021,Rimsha Azhar,WikiWorks,OTUs showed significant differential abundance between healthy controls and IBS participants,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85009|31957|1743;1783272|1239|91061|186826|1300|1301;3379134|1224|28211|204457|41297|13687;3379134|1224|1236|72274|135621|286,Complete,Shaimaa Elsafoury
bsdb:26963804/2/1,26963804,case-control,26963804,10.1080/19490976.2016.1162363,NA,"Fourie N.H., Wang D., Abey S.K., Sherwin L.B., Joseph P.V., Rahim-Williams B., Ferguson E.G. , Henderson W.A.",The microbiome of the oral mucosa in irritable bowel syndrome,Gut microbes,2016,"irritable bowel syndrome, microbiome, mucosa, oral, overweight, visceral pain",Experiment 2,United States of America,Homo sapiens,Buccal mucosa,UBERON:0006956,Irritable bowel syndrome,EFO:0000555,control,overweight irritable bowel syndrome,IBS are who suffered from chronic visceral pain and altered bowel habits for more than 6 months for which no organic cause had been identified,20,11,NA,16S,NA,PhyloChip,raw counts,Welch's T-Test,0.05,FALSE,NA,"age,body weight,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,10 January 2021,Rimsha Azhar,WikiWorks,OTUs showed significant differential abundance between healthy controls and IBS participants,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Planomicrobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Aquabacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85004|31953|1678;1783272|201174|84998|84999|1643824|1380;1783272|201174|84998|84999|1643824|133925;1783272|1239|91061|1385|186817|1386;1783272|1239|91061|1385|186818|162291;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|186806|113286;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|3085636|186803|177971;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|909929|1843491|970;3379134|1224|28216|80840|92793;3379134|1224|28216|80840|80864|80865;3379134|29547|3031852|213849|72294|194;3379134|1224|1236|72274|135621|286;3379134|203691|203692|136|2845253|157;3379134|976|200643|171549|171552|838;1783272|1239|91061|1385|90964|1279,Complete,Shaimaa Elsafoury
bsdb:26963804/2/2,26963804,case-control,26963804,10.1080/19490976.2016.1162363,NA,"Fourie N.H., Wang D., Abey S.K., Sherwin L.B., Joseph P.V., Rahim-Williams B., Ferguson E.G. , Henderson W.A.",The microbiome of the oral mucosa in irritable bowel syndrome,Gut microbes,2016,"irritable bowel syndrome, microbiome, mucosa, oral, overweight, visceral pain",Experiment 2,United States of America,Homo sapiens,Buccal mucosa,UBERON:0006956,Irritable bowel syndrome,EFO:0000555,control,overweight irritable bowel syndrome,IBS are who suffered from chronic visceral pain and altered bowel habits for more than 6 months for which no organic cause had been identified,20,11,NA,16S,NA,PhyloChip,raw counts,Welch's T-Test,0.05,FALSE,NA,"age,body weight,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6,10 January 2021,Rimsha Azhar,WikiWorks,OTUs showed significant differential abundance between healthy controls and IBS participants,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Aestuariimicrobium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Haloanella,k__Bacillati|p__Chloroflexota|c__Dehalococcoidia|o__Dehalococcoidales|f__Dehalococcoidaceae|g__Dehalogenimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|201174|1760|85009|31957|396388;3379134|976|117743|200644|2762318|59732;3379134|976|117743|200644|49546|109244;1783272|200795|301297|1202465|1202464|670486;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|1300|1301;3379134|1224|28216|206351|481|482;3379134|1224|1236|135625|712|724;3379134|976|200643|171549|171552|838;1783272|1239|91061|1385|90964|1279,Complete,Shaimaa Elsafoury
bsdb:26971496/1/1,26971496,prospective cohort,26971496,10.1007/s00253-016-7410-2,NA,"Aloisio I., Quagliariello A., De Fanti S., Luiselli D., De Filippo C., Albanese D., Corvaglia L.T., Faldella G. , Di Gioia D.",Evaluation of the effects of intrapartum antibiotic prophylaxis on newborn intestinal microbiota using a sequencing approach targeted to multi hypervariable 16S rDNA regions,Applied microbiology and biotechnology,2016,"16S rDNA hypervariable regions, Gut microbiota, Intrapartum antibiotic prophylaxis, Newborns, Next generation sequencing technology",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants born by mothers negative to GBS,Infants born by mothers positive to GBS and received IAP,Infants of Mothers positive to Streptococcus (GBS) and received intrapartum antibiotic prophylaxis (IAP),10,10,perinatal antibiotics,16S,23456789,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,"Table S3, Text",10 January 2021,Mst Afroza Parvin,WikiWorks,Evaluation of microbial genus composition between Control and IAP groups,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae",1783272|201174|1760|85004|31953;3379134|976|200643|171549|815,Complete,Atrayees
bsdb:26971496/2/1,26971496,prospective cohort,26971496,10.1007/s00253-016-7410-2,NA,"Aloisio I., Quagliariello A., De Fanti S., Luiselli D., De Filippo C., Albanese D., Corvaglia L.T., Faldella G. , Di Gioia D.",Evaluation of the effects of intrapartum antibiotic prophylaxis on newborn intestinal microbiota using a sequencing approach targeted to multi hypervariable 16S rDNA regions,Applied microbiology and biotechnology,2016,"16S rDNA hypervariable regions, Gut microbiota, Intrapartum antibiotic prophylaxis, Newborns, Next generation sequencing technology",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants born by mothers negative to GBS,Infants born by mothers positive to GBS and received IAP,Infants of Mothers positive to Streptococcus (GBS) and received intrapartum antibiotic prophylaxis (IAP),10,10,perinatal antibiotics,16S,23456789,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,"Table S3, Text",10 January 2021,Mst Afroza Parvin,WikiWorks,Evaluation of microbial genus composition between Control and IAP groups,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Atrayees
bsdb:26982745/1/1,26982745,"cross-sectional observational, not case-control",26982745,10.1097/MPG.0000000000001186,https://pubmed.ncbi.nlm.nih.gov/26982745/,"Mello C.S., Carmo-Rodrigues M.S., Filho H.B., Melli L.C., Tahan S., Pignatari A.C. , de Morais M.B.",Gut Microbiota Differences in Children From Distinct Socioeconomic Levels Living in the Same Urban Area in Brazil,Journal of pediatric gastroenterology and nutrition,2016,NA,Experiment 1,Brazil,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,Private school children (High SES),Children living in slum (Low SES),"Children between 5 and 11 years old living in slums in Sao Paulo State, Brazil.",30,100,1 month,16S,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,11 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1,WikiWorks",Differential microbial abundance between the slum children and children from the private school,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Pseudomonadati|p__Bacteroidota",3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|186806|1730;1783272|1239;1783272|1239|91061|186826|33958|1578|1591;3366610|28890|183925|2158|2159|2172|2173;3379134|976,Complete,Claregrieve1
bsdb:26982745/1/2,26982745,"cross-sectional observational, not case-control",26982745,10.1097/MPG.0000000000001186,https://pubmed.ncbi.nlm.nih.gov/26982745/,"Mello C.S., Carmo-Rodrigues M.S., Filho H.B., Melli L.C., Tahan S., Pignatari A.C. , de Morais M.B.",Gut Microbiota Differences in Children From Distinct Socioeconomic Levels Living in the Same Urban Area in Brazil,Journal of pediatric gastroenterology and nutrition,2016,NA,Experiment 1,Brazil,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,Private school children (High SES),Children living in slum (Low SES),"Children between 5 and 11 years old living in slums in Sao Paulo State, Brazil.",30,100,1 month,16S,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,11 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1,WikiWorks",Differential microbial abundance between the slum children and children from the private school,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.",1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|186801|186802|31979|1485|1502;3379134|1224|1236|91347|543|590|599,Complete,Claregrieve1
bsdb:26992426/1/1,26992426,"cross-sectional observational, not case-control",26992426,10.1136/gutjnl-2015-309595,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5529966/,"Flemer B., Lynch D.B., Brown J.M., Jeffery I.B., Ryan F.J., Claesson M.J., O'Riordain M., Shanahan F. , O'Toole P.W.",Tumour-associated and non-tumour-associated microbiota in colorectal cancer,Gut,2017,"COLORECTAL CANCER, GENE EXPRESSION, INTESTINAL MICROBIOLOGY",Experiment 1,Ireland,Homo sapiens,Intestinal mucosa,UBERON:0001242,Colorectal cancer,EFO:0005842,healthy controls,colorectal cancer (CRC),The patients undergoing surgery for CRC have confirmed CRC.,56,59,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary File: Table S3 and Table S4,19 October 2023,Chinelsy,"Chinelsy,ChiomaBlessing,WikiWorks",Differential mucosal microbiota composition of patients with CRC compared to healthy controls,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549|171550|239759;1783272|1239|909932|1843489|31977|209879;3379134|976|200643|171549|815|816;3379134|976;1783272|201174|1760|85004|31953|1678;1783272|1239|909932|1843489|31977|39948;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|1940338;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563;1783272|1239|186801|3085636|186803;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|186802|216572|459786;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;1783272|1239|909932|1843488|909930|33024;3379134|1224|1236|72274|135621|286;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;3379134|256845|1313211|278082|255528|172900;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|75682;1783272|1239|186801|186802|216572|258514;3379134|29547|3031852|213849|72294|194;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|404402;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171551,Complete,Chinelsy
bsdb:26992426/1/2,26992426,"cross-sectional observational, not case-control",26992426,10.1136/gutjnl-2015-309595,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5529966/,"Flemer B., Lynch D.B., Brown J.M., Jeffery I.B., Ryan F.J., Claesson M.J., O'Riordain M., Shanahan F. , O'Toole P.W.",Tumour-associated and non-tumour-associated microbiota in colorectal cancer,Gut,2017,"COLORECTAL CANCER, GENE EXPRESSION, INTESTINAL MICROBIOLOGY",Experiment 1,Ireland,Homo sapiens,Intestinal mucosa,UBERON:0001242,Colorectal cancer,EFO:0005842,healthy controls,colorectal cancer (CRC),The patients undergoing surgery for CRC have confirmed CRC.,56,59,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary File: Table S3,2 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential mucosal microbiota composition of patients with CRC compared to healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Anaerorhabdus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|526524|526525|128827|118966;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|33042;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|189330;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|204475;1783272|1239|526524|526525|128827|61170;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|841;1783272|1239;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572,Complete,ChiomaBlessing
bsdb:26992426/3/1,26992426,"cross-sectional observational, not case-control",26992426,10.1136/gutjnl-2015-309595,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5529966/,"Flemer B., Lynch D.B., Brown J.M., Jeffery I.B., Ryan F.J., Claesson M.J., O'Riordain M., Shanahan F. , O'Toole P.W.",Tumour-associated and non-tumour-associated microbiota in colorectal cancer,Gut,2017,"COLORECTAL CANCER, GENE EXPRESSION, INTESTINAL MICROBIOLOGY",Experiment 3,Ireland,Homo sapiens,Intestinal mucosa,UBERON:0001242,Colorectal cancer,EFO:0005842,Distal (and rectal) cancer,Proximal cancer,Patients with proximal cancer,39,20,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary File: Table S8,2 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential mucosal microbiota composition of proximal cancer compared to distal cancer,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|216851;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803,Complete,ChiomaBlessing
bsdb:26992426/3/2,26992426,"cross-sectional observational, not case-control",26992426,10.1136/gutjnl-2015-309595,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5529966/,"Flemer B., Lynch D.B., Brown J.M., Jeffery I.B., Ryan F.J., Claesson M.J., O'Riordain M., Shanahan F. , O'Toole P.W.",Tumour-associated and non-tumour-associated microbiota in colorectal cancer,Gut,2017,"COLORECTAL CANCER, GENE EXPRESSION, INTESTINAL MICROBIOLOGY",Experiment 3,Ireland,Homo sapiens,Intestinal mucosa,UBERON:0001242,Colorectal cancer,EFO:0005842,Distal (and rectal) cancer,Proximal cancer,Patients with proximal cancer,39,20,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary File: Table S8,2 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential mucosal microbiota composition of proximal cancer compared to distal cancer,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella",3379134|1224|1236|135619|28256|2745;3379134|1224|1236|135622|267890|22,Complete,ChiomaBlessing
bsdb:27001291/1/1,27001291,time series / longitudinal observational,27001291,10.1038/srep23129,NA,"Collado M.C., Rautava S., Aakko J., Isolauri E. , Salminen S.",Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid,Scientific reports,2016,NA,Experiment 1,Finland,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,placenta,meconium,meconium samples,15,15,NA,16S,123,Roche454,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,increased,decreased,NA,NA,unchanged,Signature 1,Figure 4B,10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Differentially abundant bacteria in meconium sample compared to placenta sample from LEfSe analysis,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",1783272|1239|91061|1385|186817;1783272|1239|91061|186826|1300,Complete,Shaimaa Elsafoury
bsdb:27001291/1/2,27001291,time series / longitudinal observational,27001291,10.1038/srep23129,NA,"Collado M.C., Rautava S., Aakko J., Isolauri E. , Salminen S.",Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid,Scientific reports,2016,NA,Experiment 1,Finland,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,placenta,meconium,meconium samples,15,15,NA,16S,123,Roche454,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,increased,decreased,NA,NA,unchanged,Signature 2,Figure 4B,10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Differentially abundant bacteria in meconium sample compared to placenta sample from LEfSe analysis,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,Shaimaa Elsafoury
bsdb:27001291/2/1,27001291,time series / longitudinal observational,27001291,10.1038/srep23129,NA,"Collado M.C., Rautava S., Aakko J., Isolauri E. , Salminen S.",Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid,Scientific reports,2016,NA,Experiment 2,Finland,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,placenta,colostrum,maternal colostrum samples,15,15,NA,16S,123,Roche454,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,increased,unchanged,NA,NA,unchanged,Signature 1,Figure 4D,10 January 2021,Rimsha Azhar,"Merit,WikiWorks,ChiomaBlessing",Differentially abundant bacteria in colostrum samples compared to placenta samples from LEfSe analysis,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",1783272|1239|91061|1385|186817;1783272|1239|91061|186826|1300,Complete,Shaimaa Elsafoury
bsdb:27001291/2/2,27001291,time series / longitudinal observational,27001291,10.1038/srep23129,NA,"Collado M.C., Rautava S., Aakko J., Isolauri E. , Salminen S.",Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid,Scientific reports,2016,NA,Experiment 2,Finland,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,placenta,colostrum,maternal colostrum samples,15,15,NA,16S,123,Roche454,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,increased,unchanged,NA,NA,unchanged,Signature 2,Figure 4D,10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Differentially abundant bacteria in colostrum samples compared to placenta samples from LEfSe analysis,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,Shaimaa Elsafoury
bsdb:27007700/1/1,27007700,case-control,27007700,10.1089/chi.2015.0194,NA,"Borgo F., Verduci E., Riva A., Lassandro C., Riva E., Morace G. , Borghi E.",Relative Abundance in Bacterial and Fungal Gut Microbes in Obese Children: A Case Control Study,Childhood obesity (Print),2017,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,controls,pediatric obese,NA,33,28,previous month,16S,23,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text, figure 2",10 January 2021,Marianthi Thomatos,"Fatima,WikiWorks",Relative abundance of bacterial and fungal gut microbes in obese children vs. controls,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces sp.,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|s__[Candida] sp.",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|216851|853;3379134|976|200643|171549|171552|838;4751|4890|4891|4892|4893|4930|4935;4751|4890|4891|4892|1853550,Complete,Fatima
bsdb:27007700/1/2,27007700,case-control,27007700,10.1089/chi.2015.0194,NA,"Borgo F., Verduci E., Riva A., Lassandro C., Riva E., Morace G. , Borghi E.",Relative Abundance in Bacterial and Fungal Gut Microbes in Obese Children: A Case Control Study,Childhood obesity (Print),2017,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,controls,pediatric obese,NA,33,28,previous month,16S,23,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,"Text, Figure 2",17 October 2023,Uchechukwu,"Uchechukwu,Davvve,MyleeeA,WikiWorks",Difference in relative proportions of gut microbial communities in obese versus normal-weight children,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces sp.,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas|s__uncultured Candidatus Saccharimonas sp.,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|s__[Candida] sp.",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|186802|216572|216851|853;3379134|976|200643|171549|171552|838;4751|4890|4891|4892|4893|4930|4935;95818|2093818|2093825|2171986|1331051|1983405;4751|4890|4891|4892|1853550,Complete,NA
bsdb:27007700/2/1,27007700,case-control,27007700,10.1089/chi.2015.0194,NA,"Borgo F., Verduci E., Riva A., Lassandro C., Riva E., Morace G. , Borghi E.",Relative Abundance in Bacterial and Fungal Gut Microbes in Obese Children: A Case Control Study,Childhood obesity (Print),2017,NA,Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,controls,pediatric obese,Obese children,33,28,previous month,16S,23,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 1,"Text, Figure 2",17 October 2023,Uchechukwu,"Uchechukwu,Davvve,WikiWorks",Differences in relative proportions of gut microbial communities in obese versus normal-weight,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae",1783272|1239|186801|3085636|186803|1766253|39491;4751|4890|3239874|2916678|766764|5475|5476;4751|4890|4891|4892|4893|4930|4932,Complete,NA
bsdb:27015003/1/1,27015003,case-control,27015003,10.1038/ismej.2016.37,NA,"Wu J., Peters B.A., Dominianni C., Zhang Y., Pei Z., Yang L., Ma Y., Purdue M.P., Jacobs E.J., Gapstur S.M., Li H., Alekseyenko A.V., Hayes R.B. , Ahn J.",Cigarette smoking and the oral microbiome in a large study of American adults,The ISME journal,2016,NA,Experiment 1,United States of America,Homo sapiens,Mouth,UBERON:0000165,Smoking behavior,EFO:0004318,former smoker,current smoker,participants who developed head and neck or pancreatic cancer at any point after collection of the oral wash samples,521,112,NA,16S,34,Roche454,NA,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between current and former smokers,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia",1783272|201174;1783272|201174|84998,Complete,Claregrieve1
bsdb:27015003/1/2,27015003,case-control,27015003,10.1038/ismej.2016.37,NA,"Wu J., Peters B.A., Dominianni C., Zhang Y., Pei Z., Yang L., Ma Y., Purdue M.P., Jacobs E.J., Gapstur S.M., Li H., Alekseyenko A.V., Hayes R.B. , Ahn J.",Cigarette smoking and the oral microbiome in a large study of American adults,The ISME journal,2016,NA,Experiment 1,United States of America,Homo sapiens,Mouth,UBERON:0000165,Smoking behavior,EFO:0004318,former smoker,current smoker,participants who developed head and neck or pancreatic cancer at any point after collection of the oral wash samples,521,112,NA,16S,34,Roche454,NA,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 2,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between current and former smokers,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|28216;3379134|976|117743;3379134|1224|1236;3379134|1224,Complete,Claregrieve1
bsdb:27015276/1/1,27015276,case-control,27015276,10.1371/journal.pone.0152126,NA,"Sinha R., Ahn J., Sampson J.N., Shi J., Yu G., Xiong X., Hayes R.B. , Goedert J.J.","Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations",PloS one,2016,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,controls,adenocarcinoma of colon and rectum patients,Not stated,89,42,NA,16S,34,Roche454,relative abundances,Logistic Regression,0.05,FALSE,NA,"body mass index,sex","age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Fecal microbes independently associated with colorectal cancer,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|171551|836,Complete,Shaimaa Elsafoury
bsdb:27015276/1/2,27015276,case-control,27015276,10.1371/journal.pone.0152126,NA,"Sinha R., Ahn J., Sampson J.N., Shi J., Yu G., Xiong X., Hayes R.B. , Goedert J.J.","Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations",PloS one,2016,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,controls,adenocarcinoma of colon and rectum patients,Not stated,89,42,NA,16S,34,Roche454,relative abundances,Logistic Regression,0.05,FALSE,NA,"body mass index,sex","age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 2,10 January 2021,Nidhi Saini,WikiWorks,Fecal microbes independently associated with colorectal cancer,decreased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801;1783272|1239|186801|3085636|186803,Complete,Shaimaa Elsafoury
bsdb:27026576/1/1,27026576,case-control,27026576,10.1016/j.oraloncology.2016.03.007,NA,"Xiaosheng Hu, Feng Chen, Qian Zhang, Hong",Changes in the salivary microbiota of oral leukoplakia and oral cancer,Oral oncology,2016,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Oral leukoplakia,HP:0002745,healthy controls,Oral leukoplakia,Oral leukoplakia patients,19,10,NA,16S,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,NA,Signature 1,Fig 1 & 2,10 January 2021,Utsav Patel,WikiWorks,Changes in oral microbiota in oral leukoplakia vs. healthy control: a case-control study,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus",3379134|1224|1236|135625|712|724;1783272|1239|91061|1385|186817|1386,Complete,Shaimaa Elsafoury
bsdb:27026576/1/2,27026576,case-control,27026576,10.1016/j.oraloncology.2016.03.007,NA,"Xiaosheng Hu, Feng Chen, Qian Zhang, Hong",Changes in the salivary microbiota of oral leukoplakia and oral cancer,Oral oncology,2016,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Oral leukoplakia,HP:0002745,healthy controls,Oral leukoplakia,Oral leukoplakia patients,19,10,NA,16S,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,NA,Signature 2,Fig 1 & 2,10 January 2021,Utsav Patel,WikiWorks,Changes in oral microbiota in oral leukoplakia vs. healthy control: a case-control study,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia",1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|186827|46123,Complete,Shaimaa Elsafoury
bsdb:27026576/2/1,27026576,case-control,27026576,10.1016/j.oraloncology.2016.03.007,NA,"Xiaosheng Hu, Feng Chen, Qian Zhang, Hong",Changes in the salivary microbiota of oral leukoplakia and oral cancer,Oral oncology,2016,NA,Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Oral squamous cell carcinoma,EFO:0000199,healthy controls,Oral Squamous Cell Cancer patients,Oral Squamous Cell Cancer patients,19,16,NA,16S,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 1,Fig 1 & 2,10 January 2021,Utsav Patel,WikiWorks,Changes in oral microbiota in OSCC vs. healthy control: a case-control study,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus",3379134|1224|1236|135625|712|724;1783272|1239|91061|1385|186817|1386,Complete,Shaimaa Elsafoury
bsdb:27026576/2/2,27026576,case-control,27026576,10.1016/j.oraloncology.2016.03.007,NA,"Xiaosheng Hu, Feng Chen, Qian Zhang, Hong",Changes in the salivary microbiota of oral leukoplakia and oral cancer,Oral oncology,2016,NA,Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Oral squamous cell carcinoma,EFO:0000199,healthy controls,Oral Squamous Cell Cancer patients,Oral Squamous Cell Cancer patients,19,16,NA,16S,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 2,Fig 1 & 2,10 January 2021,Utsav Patel,WikiWorks,Changes in oral microbiota in OSCC vs. healthy control: a case-control study,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia",1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|186827|46123,Complete,Shaimaa Elsafoury
bsdb:27026576/3/1,27026576,case-control,27026576,10.1016/j.oraloncology.2016.03.007,NA,"Xiaosheng Hu, Feng Chen, Qian Zhang, Hong",Changes in the salivary microbiota of oral leukoplakia and oral cancer,Oral oncology,2016,NA,Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Oral leukoplakia,HP:0002745,Oral Squamous Cell Cancer patients,Oral leukoplakia,Oral leukoplakia patients,16,10,NA,16S,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,increased,NA,NA,Signature 1,Fig 1 & 2,10 January 2021,Utsav Patel,WikiWorks,Changes in oral microbiota in oral leukoplakia vs. OSCC: a case-control study,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|1300|1301,Complete,Shaimaa Elsafoury
bsdb:27026576/3/2,27026576,case-control,27026576,10.1016/j.oraloncology.2016.03.007,NA,"Xiaosheng Hu, Feng Chen, Qian Zhang, Hong",Changes in the salivary microbiota of oral leukoplakia and oral cancer,Oral oncology,2016,NA,Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Oral leukoplakia,HP:0002745,Oral Squamous Cell Cancer patients,Oral leukoplakia,Oral leukoplakia patients,16,10,NA,16S,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,increased,NA,NA,Signature 2,Fig 1 & 2,10 January 2021,Utsav Patel,WikiWorks,Changes in oral microbiota in oral leukoplakia vs. OSCC: a case-control study,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,1783272|1239|91061|1385|186817|1386,Complete,Shaimaa Elsafoury
bsdb:27027301/1/1,27027301,time series / longitudinal observational,27027301,10.1159/000443361,NA,"Ponziani F.R., Scaldaferri F., Petito V., Paroni Sterbini F., Pecere S., Lopetuso L.R., Palladini A., Gerardi V., Masucci L., Pompili M., Cammarota G., Sanguinetti M. , Gasbarrini A.",The Role of Antibiotics in Gut Microbiota Modulation: The Eubiotic Effects of Rifaximin,"Digestive diseases (Basel, Switzerland)",2016,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Patients before Rifaximin treatment,Patients after Rifaximin treatment,"Patients affected by ulcerative colitis, Chron's disease, Irritable Bowel Syndrome, diverticular disease, and liver cirrhosis with hepatic encephalopathy consecutively treated with 1,200 mg of Rifaximin daily for 10 days.",20,20,1 month,16S,123,Roche454,NA,metagenomeSeq,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,21 July 2021,Gina,"Gina,WikiWorks",Differential abundance analysis of bacterial genera compared by Rifaximin treatment at time a versus time b.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|841;1783272|1239|909932|1843489|31977|29465,Complete,Chloe
bsdb:27027301/1/2,27027301,time series / longitudinal observational,27027301,10.1159/000443361,NA,"Ponziani F.R., Scaldaferri F., Petito V., Paroni Sterbini F., Pecere S., Lopetuso L.R., Palladini A., Gerardi V., Masucci L., Pompili M., Cammarota G., Sanguinetti M. , Gasbarrini A.",The Role of Antibiotics in Gut Microbiota Modulation: The Eubiotic Effects of Rifaximin,"Digestive diseases (Basel, Switzerland)",2016,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Patients before Rifaximin treatment,Patients after Rifaximin treatment,"Patients affected by ulcerative colitis, Chron's disease, Irritable Bowel Syndrome, diverticular disease, and liver cirrhosis with hepatic encephalopathy consecutively treated with 1,200 mg of Rifaximin daily for 10 days.",20,20,1 month,16S,123,Roche454,NA,metagenomeSeq,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,21 July 2021,Gina,"Gina,WikiWorks",Differential abundance analysis of bacterial genera compared by Rifaximin treatment at time a versus time b.,increased,NA,NA,Complete,Chloe
bsdb:27027301/2/1,27027301,time series / longitudinal observational,27027301,10.1159/000443361,NA,"Ponziani F.R., Scaldaferri F., Petito V., Paroni Sterbini F., Pecere S., Lopetuso L.R., Palladini A., Gerardi V., Masucci L., Pompili M., Cammarota G., Sanguinetti M. , Gasbarrini A.",The Role of Antibiotics in Gut Microbiota Modulation: The Eubiotic Effects of Rifaximin,"Digestive diseases (Basel, Switzerland)",2016,NA,Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Patients before Rifaximin treatment,Patients 1 month after Rifaximin treatment,"Patients 1 month after Rifaximin treatment affected by ulcerative colitis, Chron's disease, Irritable Bowel Syndrome, diverticular disease, and liver cirrhosis with hepatic encephalopathy consecutively.",20,20,1 month,16S,123,Roche454,NA,metagenomeSeq,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,21 July 2021,Gina,"Gina,WikiWorks",Differential abundance analysis of bacterial genera compared by Rifaximin treatment time a versus time c.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Chloe
bsdb:27027301/2/2,27027301,time series / longitudinal observational,27027301,10.1159/000443361,NA,"Ponziani F.R., Scaldaferri F., Petito V., Paroni Sterbini F., Pecere S., Lopetuso L.R., Palladini A., Gerardi V., Masucci L., Pompili M., Cammarota G., Sanguinetti M. , Gasbarrini A.",The Role of Antibiotics in Gut Microbiota Modulation: The Eubiotic Effects of Rifaximin,"Digestive diseases (Basel, Switzerland)",2016,NA,Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Patients before Rifaximin treatment,Patients 1 month after Rifaximin treatment,"Patients 1 month after Rifaximin treatment affected by ulcerative colitis, Chron's disease, Irritable Bowel Syndrome, diverticular disease, and liver cirrhosis with hepatic encephalopathy consecutively.",20,20,1 month,16S,123,Roche454,NA,metagenomeSeq,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,21 July 2021,Gina,"Gina,WikiWorks",Differential abundance analysis of bacterial genera compared by rifaximin treatment at time a versus time c,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,1783272|1239|186801|3085636|186803|841,Complete,Chloe
bsdb:27102666/1/1,27102666,case-control,27102666,10.1186/s13073-016-0299-7,NA,"Chen J., Wright K., Davis J.M., Jeraldo P., Marietta E.V., Murray J., Nelson H., Matteson E.L. , Taneja V.",An expansion of rare lineage intestinal microbes characterizes rheumatoid arthritis,Genome medicine,2016,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Rheumatoid arthritis,EFO:0000685,healthy controls,rheumatoid arthritis patients,rheumatoid arthritis patients,32,40,NA,16S,345,Illumina,relative abundances,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"Figure 3, text",16 August 2021,Tislam,"Tislam,Rimsha,Claregrieve1,Merit,WikiWorks",Differential microbial abundance between healthy controls and RA patients,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Bacillati|p__Actinomycetota",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;1783272|201174;1783272|1239|91061;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;1783272|201174|84998|1643822|1643826|84111;3379134|1224|1236|91347|1903409|551;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|186806|1730;1783272|1239|91061|186826;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810281|191303;1783272|1239|526524|526525|2810281;1783272|201174,Complete,Claregrieve1
bsdb:27102666/1/2,27102666,case-control,27102666,10.1186/s13073-016-0299-7,NA,"Chen J., Wright K., Davis J.M., Jeraldo P., Marietta E.V., Murray J., Nelson H., Matteson E.L. , Taneja V.",An expansion of rare lineage intestinal microbes characterizes rheumatoid arthritis,Genome medicine,2016,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Rheumatoid arthritis,EFO:0000685,healthy controls,rheumatoid arthritis patients,rheumatoid arthritis patients,32,40,NA,16S,345,Illumina,relative abundances,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 2,"Figure 3, text",16 August 2021,Tislam,"Tislam,Rimsha,Claregrieve1,Merit,WikiWorks",Differential microbial abundance between healthy controls and RA patients,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Borreliaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.",3379134|976|200643|171549|2005519;3379134|203691|203692|136|1643685;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|1971605,Complete,Claregrieve1
bsdb:27115405/1/1,27115405,"cross-sectional observational, not case-control",27115405,10.1007/s00240-016-0882-9,NA,"Stern J.M., Moazami S., Qiu Y., Kurland I., Chen Z., Agalliu I., Burk R. , Davies K.P.",Evidence for a distinct gut microbiome in kidney stone formers compared to non-stone formers,Urolithiasis,2016,"Gut microbiome, Kidney stones, Nephrolithiasis, Urolithiasis",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,"Urolithiasis,Nephrolithiasis","MONDO:0024647,EFO:0004253",healthy control,kidney stone patient,patients with kidney stones,6,23,2 weeks,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2b,10 January 2021,Rimsha Azhar,"WikiWorks,Claregrieve1",Differential abundance of the microbiota between kidney stone formers and non-stone forming controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005525|375288,Complete,Claregrieve1
bsdb:27115405/1/2,27115405,"cross-sectional observational, not case-control",27115405,10.1007/s00240-016-0882-9,NA,"Stern J.M., Moazami S., Qiu Y., Kurland I., Chen Z., Agalliu I., Burk R. , Davies K.P.",Evidence for a distinct gut microbiome in kidney stone formers compared to non-stone formers,Urolithiasis,2016,"Gut microbiome, Kidney stones, Nephrolithiasis, Urolithiasis",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,"Urolithiasis,Nephrolithiasis","MONDO:0024647,EFO:0004253",healthy control,kidney stone patient,patients with kidney stones,6,23,2 weeks,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2b,10 January 2021,Rimsha Azhar,"WikiWorks,Claregrieve1",The composition of the microbiota between kidney stone formers and non-stone forming controls,decreased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum",1783272|1239|1737404|1737405|1570339|150022;1783272|1239|1737404|1737405|1570339|162289;3379134|976|200643|171549|171552|838;1783272|201174|1760|2037|2049|184869,Complete,Claregrieve1
bsdb:27121964/1/1,27121964,prospective cohort,27121964,10.1186/s13073-016-0301-4,NA,"Montassier E., Al-Ghalith G.A., Ward T., Corvec S., Gastinne T., Potel G., Moreau P., de la Cochetiere M.F., Batard E. , Knights D.",Pretreatment gut microbiome predicts chemotherapy-related bloodstream infection,Genome medicine,2016,"Bloodstream infection, Chemotherapy, Intestinal microbiome, Prediction",Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Non-Hodgkins lymphoma,EFO:0005952,non-bloodstream infection,bloodstream infection,"participants had blood stream infection, diagnosis with non-Hodgkins lymphoma (NHL), undergone hematopoeitic stem cell transplant and chemotherapy that did not had a history of inflammatory bowel disease, no exposure to probiotics, prebiotics or broad-soectrium antibiotics, no administered nasal-tube feeding or parenteral nutrition in a month prior to initiation of the study",17,11,NA,16S,56,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Figure 2, 3, aditional file 5a and b, 7",10 January 2021,William Lam,"WikiWorks,Aiyshaaaa",Relative abundance of the differentiated taxa in samples collected prior to treatment in patients who developed subsequent Blood Stream Infections and patients who did not develop Blood Stream Infections,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",1783272|1239|909932|1843489|31977|29465;1783272|1239|526524|526525|128827,Complete,NA
bsdb:27121964/1/2,27121964,prospective cohort,27121964,10.1186/s13073-016-0301-4,NA,"Montassier E., Al-Ghalith G.A., Ward T., Corvec S., Gastinne T., Potel G., Moreau P., de la Cochetiere M.F., Batard E. , Knights D.",Pretreatment gut microbiome predicts chemotherapy-related bloodstream infection,Genome medicine,2016,"Bloodstream infection, Chemotherapy, Intestinal microbiome, Prediction",Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Non-Hodgkins lymphoma,EFO:0005952,non-bloodstream infection,bloodstream infection,"participants had blood stream infection, diagnosis with non-Hodgkins lymphoma (NHL), undergone hematopoeitic stem cell transplant and chemotherapy that did not had a history of inflammatory bowel disease, no exposure to probiotics, prebiotics or broad-soectrium antibiotics, no administered nasal-tube feeding or parenteral nutrition in a month prior to initiation of the study",17,11,NA,16S,56,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"Figure 2, 3, aditional file 5a and b, 7",10 January 2021,William Lam,"WikiWorks,Merit",Relative abundance of the differentiated taxa in samples collected prior to treatment in patients who developed subsequent Blood Stream Infections and patients who did not develop Blood Stream Infections,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacillati|p__Chloroflexota|c__Dehalococcoidia|o__Dehalococcoidales|f__Dehalococcoidaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|1224|28216|80840|506;3379134|976|200643|171549|2005519;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802|186807|51514;1783272|200795|301297|1202465|1202464;3379134|200940|3031449|213115|194924;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|1853231;1783272|1239|186801|186802|216572|119852;3379134|1224|28216|80840|75682;3379134|1224|28216|80840|995019|40544,Complete,NA
bsdb:27142586/1/1,27142586,case-control,27142586,10.1007/s10096-016-2654-4,NA,"Krishna P., Jain A. , Bisen P.S.",Microbiome diversity in the sputum of patients with pulmonary tuberculosis,European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology,2016,NA,Experiment 1,India,Homo sapiens,Sputum,UBERON:0007311,Pulmonary tuberculosis,EFO:1000049,"Healthy controls (asymptomatic, TB negative)",Tuberculosis patients (PTB),"Confirmed active pulmonary TB by sputum smear, culture, and RT‑PCR; no antibiotic use prior to sampling; HIV‑negative.",16,23,NA,16S,67,Ion Torrent,relative abundances,"T-Test,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,"age,sex","HIV infection,antibiotic exposure,ethnic group,geographic area",unchanged,decreased,decreased,decreased,decreased,decreased,Signature 1,Fig. 2; Fig. 3; Table 2,7 June 2025,Nuerteye,Nuerteye,"Phyla-level relative abundance of microbial composition in TB and normal patients groups.
Genera-level relative abundance of microbial composition in TB and normal patients groups.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|1224|1236|2887326|468|469;1783272|201174|84998|84999|1643824|1380;1783272|1239|91061|1385|186817|1386;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|33958|1578;3379134|1224|28216|80840|119060|47670;1783272|1239|91061|186826|33958|1243;1783272|1239|909932|1843489|31977|906;3379134|1224|1236|2887326|468|475;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,NA
bsdb:27142586/1/2,27142586,case-control,27142586,10.1007/s10096-016-2654-4,NA,"Krishna P., Jain A. , Bisen P.S.",Microbiome diversity in the sputum of patients with pulmonary tuberculosis,European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology,2016,NA,Experiment 1,India,Homo sapiens,Sputum,UBERON:0007311,Pulmonary tuberculosis,EFO:1000049,"Healthy controls (asymptomatic, TB negative)",Tuberculosis patients (PTB),"Confirmed active pulmonary TB by sputum smear, culture, and RT‑PCR; no antibiotic use prior to sampling; HIV‑negative.",16,23,NA,16S,67,Ion Torrent,relative abundances,"T-Test,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,"age,sex","HIV infection,antibiotic exposure,ethnic group,geographic area",unchanged,decreased,decreased,decreased,decreased,decreased,Signature 2,Fig. 2; Fig. 3; Table 2,7 June 2025,Nuerteye,Nuerteye,"Phyla-level relative abundance of microbial composition in TB and normal patients groups.
Genera-level relative abundance of microbial composition in TB and normal patients groups.",decreased,NA,NA,Complete,NA
bsdb:27142586/2/NA,27142586,case-control,27142586,10.1007/s10096-016-2654-4,NA,"Krishna P., Jain A. , Bisen P.S.",Microbiome diversity in the sputum of patients with pulmonary tuberculosis,European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology,2016,NA,Experiment 2,India,Homo sapiens,Sputum,UBERON:0007311,Pulmonary tuberculosis,EFO:1000049,"Healthy controls (asymptomatic, TB negative)",Tuberculosis patients (PTB)," Confirmed active pulmonary TB by sputum smear, culture, and RT‑PCR; no antibiotic use prior to sampling; HIV‑negative.",16,23,NA,16S,67,Ion Torrent,relative abundances,"Mann-Whitney (Wilcoxon),PERMANOVA,T-Test",0.05,TRUE,NA,"age,sex","HIV infection,antibiotic exposure,ethnic group,geographic area",NA,decreased,decreased,decreased,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:27171425/1/1,27171425,"case-control,meta-analysis",27171425,10.1371/journal.pone.0155362,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4865240/,"Vogtmann E., Hua X., Zeller G., Sunagawa S., Voigt A.Y., Hercog R., Goedert J.J., Shi J., Bork P. , Sinha R.",Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing,PloS one,2016,NA,Experiment 1,"United States of America,France",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,control subjects,CRC cases,pre treatment colorectal cancer cases,94,47,NA,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"body mass index,sex","age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 3,3 February 2022,Itslanapark,"Itslanapark,Claregrieve1,WikiWorks",Differential microbial abundance between CRC cases and controls using 16S sequencing,decreased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803,Complete,Claregrieve1
bsdb:27176462/1/1,27176462,case-control,27176462,10.1111/ene.13026,NA,"Tremlett H., Fadrosh D.W., Faruqi A.A., Zhu F., Hart J., Roalstad S., Graves J., Lynch S. , Waubant E.",Gut microbiota in early pediatric multiple sclerosis: a case-control study,European journal of neurology,2016,"16S rRNA, case−control study, gut microbiome, gut microbiota, immunomodulatory drugs, pediatric multiple sclerosis, risk factors",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,healthy controls,pediatric multiple sclerosis,early pediatric multiple sclerosis,17,18,2 months,16S,4,Illumina,raw counts,Negative Binomial Regression,0.05,TRUE,NA,"age,sex","age,breast feeding,ethnic group,sex",NA,NA,NA,NA,NA,unchanged,Signature 1,"Figure 3a, 3b",10 January 2021,Rimsha Azhar,WikiWorks,Difference between multiple sclerosis and controls in the gut microbial communities,increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",3379134|200940|3031449|213115|194924|35832;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802;3379134|200940|3031449|213115|194924|872;1783272|201174|84998|84999|84107;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|541000;1783272|1239|909932|1843488|909930|33024,Complete,Atrayees
bsdb:27176462/1/2,27176462,case-control,27176462,10.1111/ene.13026,NA,"Tremlett H., Fadrosh D.W., Faruqi A.A., Zhu F., Hart J., Roalstad S., Graves J., Lynch S. , Waubant E.",Gut microbiota in early pediatric multiple sclerosis: a case-control study,European journal of neurology,2016,"16S rRNA, case−control study, gut microbiome, gut microbiota, immunomodulatory drugs, pediatric multiple sclerosis, risk factors",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,healthy controls,pediatric multiple sclerosis,early pediatric multiple sclerosis,17,18,2 months,16S,4,Illumina,raw counts,Negative Binomial Regression,0.05,TRUE,NA,"age,sex","age,breast feeding,ethnic group,sex",NA,NA,NA,NA,NA,unchanged,Signature 2,"Figure 3a, 3b",10 January 2021,Rimsha Azhar,WikiWorks,Difference between multiple sclerosis and controls in the gut microbial communities,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius",1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|186802|541000;3379134|976|200643|171549|171552|577309;1783272|1239|186801|186802;3379134|976|200643|171549|171552|2974251|165179;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|3082720|186804|1257|1261,Complete,Atrayees
bsdb:27176462/2/1,27176462,case-control,27176462,10.1111/ene.13026,NA,"Tremlett H., Fadrosh D.W., Faruqi A.A., Zhu F., Hart J., Roalstad S., Graves J., Lynch S. , Waubant E.",Gut microbiota in early pediatric multiple sclerosis: a case-control study,European journal of neurology,2016,"16S rRNA, case−control study, gut microbiome, gut microbiota, immunomodulatory drugs, pediatric multiple sclerosis, risk factors",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,IMD naive cases,IMD exposure multiple sclerosis cases,Sclerosis cases influenced by the immunomodulatory drug [IMD] exposure status.,9,9,2 months,16S,4,Illumina,relative abundances,Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 2b,10 January 2021,Rimsha Azhar,WikiWorks,Difference between multiple sclerosis and controls influenced by the immunomodulatory drug IMD exposure status of cases,increased,k__Bacillati|p__Actinomycetota,1783272|201174,Complete,Atrayees
bsdb:27176462/2/2,27176462,case-control,27176462,10.1111/ene.13026,NA,"Tremlett H., Fadrosh D.W., Faruqi A.A., Zhu F., Hart J., Roalstad S., Graves J., Lynch S. , Waubant E.",Gut microbiota in early pediatric multiple sclerosis: a case-control study,European journal of neurology,2016,"16S rRNA, case−control study, gut microbiome, gut microbiota, immunomodulatory drugs, pediatric multiple sclerosis, risk factors",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,IMD naive cases,IMD exposure multiple sclerosis cases,Sclerosis cases influenced by the immunomodulatory drug [IMD] exposure status.,9,9,2 months,16S,4,Illumina,relative abundances,Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Figure 2b,10 January 2021,Rimsha Azhar,WikiWorks,Difference between multiple sclerosis and controls influenced by the immunomodulatory drug IMD exposure status of cases,decreased,"k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Cyanobacteriota",1783272|544448;1783272|1117,Complete,Atrayees
bsdb:27176462/3/1,27176462,case-control,27176462,10.1111/ene.13026,NA,"Tremlett H., Fadrosh D.W., Faruqi A.A., Zhu F., Hart J., Roalstad S., Graves J., Lynch S. , Waubant E.",Gut microbiota in early pediatric multiple sclerosis: a case-control study,European journal of neurology,2016,"16S rRNA, case−control study, gut microbiome, gut microbiota, immunomodulatory drugs, pediatric multiple sclerosis, risk factors",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,healthy controls,IMD naive cases multiple sclerosis,NA,16,9,2 months,16S,4,Illumina,relative abundances,Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,"Supplementary Table 7a, Supp Table 7b",10 January 2021,Rimsha Azhar,"Lwaldron,WikiWorks",Taxa enriched and depleted in the IMD naive cases vs. controls,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",1783272|1239|909932|1843488|909930|904;3379134|74201|203494|48461|1647988|239934|239935;1783272|201174|84998|84999|1643824|1380;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|28116;1783272|201174|1760|85004|31953|1678;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|572511|33035;1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|3082768|990719;3379134|1224|28216|80840|80864;1783272|1239|186801|3085636|186803|33042;1783272|201174|84998|84999|84107;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|216851|853;3379134|1224|1236|135625|712|724|729;1783272|1239|186801|3085636|186803;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843489|31977|906;3366610|28890|183925|2158|2159|2172;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|541000;3379134|976|200643|171549|2005525|375288|823;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|171552|2974251|165179;3379134|976|200643|171549|171552|2974265|363265;1783272|1239|186801|186802|186806|113286;1783272|1239|186801|186802|216572|1263;3379134|1224|28216|80840|995019|40544;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|186801|3085636|186803|2316020|33038,Complete,Atrayees
bsdb:27176462/3/2,27176462,case-control,27176462,10.1111/ene.13026,NA,"Tremlett H., Fadrosh D.W., Faruqi A.A., Zhu F., Hart J., Roalstad S., Graves J., Lynch S. , Waubant E.",Gut microbiota in early pediatric multiple sclerosis: a case-control study,European journal of neurology,2016,"16S rRNA, case−control study, gut microbiome, gut microbiota, immunomodulatory drugs, pediatric multiple sclerosis, risk factors",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,healthy controls,IMD naive cases multiple sclerosis,NA,16,9,2 months,16S,4,Illumina,relative abundances,Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,"Supplementary Table 7a, Supp Table 7b",10 January 2021,Rimsha Azhar,WikiWorks,Taxa enriched and depleted in the IMD naive cases vs. controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea",1783272|1239|186801|186802|541000;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|91061|186826|33958|2767887|1623;3379134|976|200643|171549|171552|577309;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171550;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|1853231|574697;1783272|1239|909932|909929|1843491|52225|52226;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3082720|186804|1257|1261;1783272|1239|186801|3085636|186803|207244;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|815|816|28111;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|186802|216572|216851|853;3379134|976|200643|171549|815|816|817;1783272|1239|526524|526525|2810280|135858;1783272|1239|909932|1843489|31977|39948;3379134|976|200643|171549|815|909656|387090;3379134|976|200643|171549|815|816|28116;1783272|1239|186801|3085636|186803|189330,Complete,Atrayees
bsdb:27228093/1/1,27228093,"cross-sectional observational, not case-control",27228093,10.1371/journal.pone.0154090,NA,"Haro C., Rangel-Zúñiga O.A., Alcalá-Díaz J.F., Gómez-Delgado F., Pérez-Martínez P., Delgado-Lista J., Quintana-Navarro G.M., Landa B.B., Navas-Cortés J.A., Tena-Sempere M., Clemente J.C., López-Miranda J., Pérez-Jiménez F. , Camargo A.",Intestinal Microbiota Is Influenced by Gender and Body Mass Index,PloS one,2016,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Sex design,EFO:0001752,male,female,three groups according to the BMI: BMI < 30; BMI between 30- 33; and BMI > 33.,39,36,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text + Table 2,10 January 2021,Marianthi Thomatos,WikiWorks,Intestinal Microbiota Is Influenced by Gender and Body Mass Index,increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae",3379134|200940|3031449|213115|194924|35832;3379134|976|200643|171549|815|816|47678,Complete,Shaimaa Elsafoury
bsdb:27228093/1/2,27228093,"cross-sectional observational, not case-control",27228093,10.1371/journal.pone.0154090,NA,"Haro C., Rangel-Zúñiga O.A., Alcalá-Díaz J.F., Gómez-Delgado F., Pérez-Martínez P., Delgado-Lista J., Quintana-Navarro G.M., Landa B.B., Navas-Cortés J.A., Tena-Sempere M., Clemente J.C., López-Miranda J., Pérez-Jiménez F. , Camargo A.",Intestinal Microbiota Is Influenced by Gender and Body Mass Index,PloS one,2016,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Sex design,EFO:0001752,male,female,three groups according to the BMI: BMI < 30; BMI between 30- 33; and BMI > 33.,39,36,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Text + Table 2,10 January 2021,Marianthi Thomatos,WikiWorks,Intestinal Microbiota Is Influenced by Gender and Body Mass Index,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,3379134|976|200643|171549|815|909656|310297,Complete,Shaimaa Elsafoury
bsdb:27228093/2/1,27228093,"cross-sectional observational, not case-control",27228093,10.1371/journal.pone.0154090,NA,"Haro C., Rangel-Zúñiga O.A., Alcalá-Díaz J.F., Gómez-Delgado F., Pérez-Martínez P., Delgado-Lista J., Quintana-Navarro G.M., Landa B.B., Navas-Cortés J.A., Tena-Sempere M., Clemente J.C., López-Miranda J., Pérez-Jiménez F. , Camargo A.",Intestinal Microbiota Is Influenced by Gender and Body Mass Index,PloS one,2016,NA,Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,male,BMI >33 female,three groups according to the BMI: BMI < 30; BMI between 30- 33; and BMI > 33.,13,13,NA,16S,4,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text + Figure 2 +Table 2,10 January 2021,Marianthi Thomatos,WikiWorks,Intestinal Microbiota Is Influenced by Gender and Body Mass Index,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
bsdb:27228093/2/2,27228093,"cross-sectional observational, not case-control",27228093,10.1371/journal.pone.0154090,NA,"Haro C., Rangel-Zúñiga O.A., Alcalá-Díaz J.F., Gómez-Delgado F., Pérez-Martínez P., Delgado-Lista J., Quintana-Navarro G.M., Landa B.B., Navas-Cortés J.A., Tena-Sempere M., Clemente J.C., López-Miranda J., Pérez-Jiménez F. , Camargo A.",Intestinal Microbiota Is Influenced by Gender and Body Mass Index,PloS one,2016,NA,Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,male,BMI >33 female,three groups according to the BMI: BMI < 30; BMI between 30- 33; and BMI > 33.,13,13,NA,16S,4,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Text + Figure2 + Table 2,10 January 2021,Marianthi Thomatos,WikiWorks,Intestinal Microbiota Is Influenced by Gender and Body Mass Index,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,3379134|976|200643|171549|815|909656|310297,Complete,Shaimaa Elsafoury
bsdb:27229737/1/1,27229737,case-control,27229737,10.1038/srep26752,NA,"Mack I., Cuntz U., Grämer C., Niedermaier S., Pohl C., Schwiertz A., Zimmermann K., Zipfel S., Enck P. , Penders J.","Weight gain in anorexia nervosa does not ameliorate the faecal microbiota, branched chain fatty acid profiles, and gastrointestinal complaints",Scientific reports,2016,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Anorexia nervosa,EFO:0004215,normal weight participants,anorexia patients before weight gain,NA,55,55,2 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,Signature 1,figure 3,10 January 2021,Fatima Zohra,"Lwaldron,WikiWorks",gut microbiota of anorexia patients before and after weight gain compared to healthy controls,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|201174;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|216572|244127;1783272|201174|1760|85004|31953|1678;3379134|74201;1783272|1239|186801|186802|31979|1485,Complete,Lwaldron
bsdb:27229737/1/2,27229737,case-control,27229737,10.1038/srep26752,NA,"Mack I., Cuntz U., Grämer C., Niedermaier S., Pohl C., Schwiertz A., Zimmermann K., Zipfel S., Enck P. , Penders J.","Weight gain in anorexia nervosa does not ameliorate the faecal microbiota, branched chain fatty acid profiles, and gastrointestinal complaints",Scientific reports,2016,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Anorexia nervosa,EFO:0004215,normal weight participants,anorexia patients before weight gain,NA,55,55,2 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,Signature 2,figure 3,10 January 2021,Fatima Zohra,WikiWorks,gut microbiota of anorexia patients before and after weight gain compared to healthy controls,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",3379134|976;1783272|1239|186801|186802|204475;1783272|1239|186801|3085636|186803|841,Complete,Lwaldron
bsdb:27229737/2/1,27229737,case-control,27229737,10.1038/srep26752,NA,"Mack I., Cuntz U., Grämer C., Niedermaier S., Pohl C., Schwiertz A., Zimmermann K., Zipfel S., Enck P. , Penders J.","Weight gain in anorexia nervosa does not ameliorate the faecal microbiota, branched chain fatty acid profiles, and gastrointestinal complaints",Scientific reports,2016,NA,Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Anorexia nervosa,EFO:0004215,HC,anorexia patients after weight gain,NA,55,44,2 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,NA,"age,sex",NA,increased,unchanged,NA,NA,NA,Signature 1,figure 3,10 January 2021,Fatima Zohra,"Lwaldron,WikiWorks",gut microbiota of anorexia patients before and after weight gain compared to healthy controls,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|201174;1783272|1239|186801|3085636|186803|207244;1783272|201174|1760|85004|31953|1678;1783272|1239;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1357;1783272|1239|186801|186802|216572|1017280;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|186802|31979|1485,Complete,Lwaldron
bsdb:27229737/2/2,27229737,case-control,27229737,10.1038/srep26752,NA,"Mack I., Cuntz U., Grämer C., Niedermaier S., Pohl C., Schwiertz A., Zimmermann K., Zipfel S., Enck P. , Penders J.","Weight gain in anorexia nervosa does not ameliorate the faecal microbiota, branched chain fatty acid profiles, and gastrointestinal complaints",Scientific reports,2016,NA,Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Anorexia nervosa,EFO:0004215,HC,anorexia patients after weight gain,NA,55,44,2 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,NA,"age,sex",NA,increased,unchanged,NA,NA,NA,Signature 2,figure 3,10 January 2021,Fatima Zohra,"Lwaldron,WikiWorks",gut microbiota of anorexia patients before and after weight gain compared to healthy controls,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",3379134|976|200643|171549|815|816;3379134|976;1783272|1239|186801|186802|31979|1485,Complete,Lwaldron
bsdb:27231166/1/1,27231166,case-control,27231166,10.4103/0366-6999.182841,NA,"Qi C.J., Zhang Q., Yu M., Xu J.P., Zheng J., Wang T. , Xiao X.H.",Imbalance of Fecal Microbiota at Newly Diagnosed Type 1 Diabetes in Chinese Children,Chinese medical journal,2016,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Type I diabetes mellitus,MONDO:0005147,controls,type I diabetes mellitus children,type 1 diabetes mellitus,15,15,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,breastfeeding duration,delivery procedure,race,sex",NA,NA,unchanged,decreased,NA,NA,decreased,Signature 1,Table 3 +  Figure 3,10 January 2021,Yaseen Javaid,WikiWorks,Imbalance of Fecal Microbiota at Newly Diagnosed Type 1 Diabetes in Chinese Children,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus",1783272|1239|186801|3085636|186803|572511;1783272|1239|909932|1843488|909930|904,Complete,Rimsha Azhar
bsdb:27231166/1/2,27231166,case-control,27231166,10.4103/0366-6999.182841,NA,"Qi C.J., Zhang Q., Yu M., Xu J.P., Zheng J., Wang T. , Xiao X.H.",Imbalance of Fecal Microbiota at Newly Diagnosed Type 1 Diabetes in Chinese Children,Chinese medical journal,2016,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Type I diabetes mellitus,MONDO:0005147,controls,type I diabetes mellitus children,type 1 diabetes mellitus,15,15,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,breastfeeding duration,delivery procedure,race,sex",NA,NA,unchanged,decreased,NA,NA,decreased,Signature 2,Table 3 +  Figure 3,10 January 2021,Yaseen Javaid,WikiWorks,Imbalance of Fecal Microbiota at Newly Diagnosed Type 1 Diabetes in Chinese Children,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas",1783272|1239|909932|1843489|31977|39948;3379134|1224|1236|135625;3379134|1224|1236|135625|712;1783272|1239|186801|3085636|186803;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|1185407;1783272|1239|186801|3082720|543314;1783272|201174|1760|85006;3379134|1224|28211|204458;1783272|1239|186801|186802|1392389,Complete,Rimsha Azhar
bsdb:27259999/1/1,27259999,case-control,27259999,10.18632/oncotarget.9710,NA,"Guerrero-Preston R., Godoy-Vitorino F., Jedlicka A., Rodríguez-Hilario A., González H., Bondy J., Lawson F., Folawiyo O., Michailidi C., Dziedzic A., Thangavel R., Hadar T., Noordhuis M.G., Westra W., Koch W. , Sidransky D.","16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, human papilloma virus infection and surgical treatment",Oncotarget,2016,"16s rRNA, human papilloma virus (HPV), microbiome, oral cancer, oropharyngeal cancer",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Oral squamous cell carcinoma,EFO:0000199,Controls,HNSCC,histopathologically confirmed HNSCC (Head & Neck Squamous Cell Cancer) patients with at least one post-treatment salivary sample,25,17,NA,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,"Figure 6, Sup Fig1",10 January 2021,Utsav Patel,"WikiWorks,Aiyshaaaa",Relative abundance of oral microbiome in HNSCC patients and controls,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|91061|186826|33958|1578;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|2005525|195950;1783272|1239|909932|1843489|31977|29465,Complete,Rimsha Azhar
bsdb:27259999/1/2,27259999,case-control,27259999,10.18632/oncotarget.9710,NA,"Guerrero-Preston R., Godoy-Vitorino F., Jedlicka A., Rodríguez-Hilario A., González H., Bondy J., Lawson F., Folawiyo O., Michailidi C., Dziedzic A., Thangavel R., Hadar T., Noordhuis M.G., Westra W., Koch W. , Sidransky D.","16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, human papilloma virus infection and surgical treatment",Oncotarget,2016,"16s rRNA, human papilloma virus (HPV), microbiome, oral cancer, oropharyngeal cancer",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Oral squamous cell carcinoma,EFO:0000199,Controls,HNSCC,histopathologically confirmed HNSCC (Head & Neck Squamous Cell Cancer) patients with at least one post-treatment salivary sample,25,17,NA,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,"Figure 6, Sup Fig1",10 January 2021,Utsav Patel,WikiWorks,Relative abundance of oral microbiome in HNSCC patients and controls,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",3379134|1224|1236|135625|712|416916;3379134|1224|28216|80840|119060|47670;3379134|1224|1236|135625|712|724;3379134|1224|28216|206351|481|482;3384189|32066|203490|203491|1129771|32067,Complete,Rimsha Azhar
bsdb:27259999/2/1,27259999,case-control,27259999,10.18632/oncotarget.9710,NA,"Guerrero-Preston R., Godoy-Vitorino F., Jedlicka A., Rodríguez-Hilario A., González H., Bondy J., Lawson F., Folawiyo O., Michailidi C., Dziedzic A., Thangavel R., Hadar T., Noordhuis M.G., Westra W., Koch W. , Sidransky D.","16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, human papilloma virus infection and surgical treatment",Oncotarget,2016,"16s rRNA, human papilloma virus (HPV), microbiome, oral cancer, oropharyngeal cancer",Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,Oral squamous cell carcinoma,EFO:0000199,HPV -,HPV +,histopathologically confirmed HNSCC (Head & Neck Squamous Cell Cancer) patients with at least one post-treatment salivary sample who are HPV+,4,7,NA,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,"Figure 6, Text",10 January 2021,Utsav Patel,WikiWorks,Relative abundance of oral microbiome in HNSCC HPV + and HPV -,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Weeksella",1783272|1239|91061|186826|33958|1578;3379134|976|117743|200644|2762318|1013,Complete,Rimsha Azhar
bsdb:27259999/2/2,27259999,case-control,27259999,10.18632/oncotarget.9710,NA,"Guerrero-Preston R., Godoy-Vitorino F., Jedlicka A., Rodríguez-Hilario A., González H., Bondy J., Lawson F., Folawiyo O., Michailidi C., Dziedzic A., Thangavel R., Hadar T., Noordhuis M.G., Westra W., Koch W. , Sidransky D.","16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, human papilloma virus infection and surgical treatment",Oncotarget,2016,"16s rRNA, human papilloma virus (HPV), microbiome, oral cancer, oropharyngeal cancer",Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,Oral squamous cell carcinoma,EFO:0000199,HPV -,HPV +,histopathologically confirmed HNSCC (Head & Neck Squamous Cell Cancer) patients with at least one post-treatment salivary sample who are HPV+,4,7,NA,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,"Figure 6, Text",10 January 2021,Utsav Patel,WikiWorks,Relative abundance of oral microbiome in HNSCC HPV + and HPV -,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",3379134|1224|28216|206351|481|538;3379134|1224|28216|206351|481|482;3384189|32066|203490|203491|1129771|32067,Complete,Rimsha Azhar
bsdb:27259999/3/1,27259999,case-control,27259999,10.18632/oncotarget.9710,NA,"Guerrero-Preston R., Godoy-Vitorino F., Jedlicka A., Rodríguez-Hilario A., González H., Bondy J., Lawson F., Folawiyo O., Michailidi C., Dziedzic A., Thangavel R., Hadar T., Noordhuis M.G., Westra W., Koch W. , Sidransky D.","16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, human papilloma virus infection and surgical treatment",Oncotarget,2016,"16s rRNA, human papilloma virus (HPV), microbiome, oral cancer, oropharyngeal cancer",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Oral squamous cell carcinoma,EFO:0000199,surgery,chemotherapy-radiation and surgery,histopathologically confirmed HNSCC (Head & Neck Squamous Cell Cancer) patients with at least one post-treatment salivary sample who received chemo/radiation and surgery,5,13,NA,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 6, Text",10 January 2021,Utsav Patel,WikiWorks,Relative abundance of oral microbiome in chemo-radiation therapy/radiation and surgery,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578,Complete,Rimsha Azhar
bsdb:27259999/3/2,27259999,case-control,27259999,10.18632/oncotarget.9710,NA,"Guerrero-Preston R., Godoy-Vitorino F., Jedlicka A., Rodríguez-Hilario A., González H., Bondy J., Lawson F., Folawiyo O., Michailidi C., Dziedzic A., Thangavel R., Hadar T., Noordhuis M.G., Westra W., Koch W. , Sidransky D.","16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, human papilloma virus infection and surgical treatment",Oncotarget,2016,"16s rRNA, human papilloma virus (HPV), microbiome, oral cancer, oropharyngeal cancer",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Oral squamous cell carcinoma,EFO:0000199,surgery,chemotherapy-radiation and surgery,histopathologically confirmed HNSCC (Head & Neck Squamous Cell Cancer) patients with at least one post-treatment salivary sample who received chemo/radiation and surgery,5,13,NA,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 6, text",19 December 2022,Claregrieve1,"Claregrieve1,WikiWorks",Relative abundance of oral microbiome in chemo-radiation therapy/radiation and surgery,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712|416916;3384189|32066|203490|203491|1129771|32067,Complete,Claregrieve1
bsdb:27283393/1/1,27283393,case-control,27283393,10.1016/j.clim.2016.06.002,NA,"Coit P., Mumcu G., Ture-Ozdemir F., Unal A.U., Alpar U., Bostanci N., Ergun T., Direskeneli H. , Sawalha A.H.",Sequencing of 16S rRNA reveals a distinct salivary microbiome signature in Behçet's disease,"Clinical immunology (Orlando, Fla.)",2016,"16s rRNA, Behçet's disease, Genetics, Microbiome, Oral microbial diversity, Sequencing",Experiment 1,Turkey,Homo sapiens,Saliva,UBERON:0001836,Behcet's syndrome,EFO:0003780,controls,behcet's disease,Patients with Behcet's disease,15,31,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 1,Table 4,10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Differential abundant taxa in patients with Behcet's disease VS controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae",3379134|976|200643|171549|171552|1283313;3379134|1224|1236|135625|712|724|729,Complete,Shaimaa Elsafoury
bsdb:27283393/1/2,27283393,case-control,27283393,10.1016/j.clim.2016.06.002,NA,"Coit P., Mumcu G., Ture-Ozdemir F., Unal A.U., Alpar U., Bostanci N., Ergun T., Direskeneli H. , Sawalha A.H.",Sequencing of 16S rRNA reveals a distinct salivary microbiome signature in Behçet's disease,"Clinical immunology (Orlando, Fla.)",2016,"16s rRNA, Behçet's disease, Genetics, Microbiome, Oral microbial diversity, Sequencing",Experiment 1,Turkey,Homo sapiens,Saliva,UBERON:0001836,Behcet's syndrome,EFO:0003780,controls,behcet's disease,Patients with Behcet's disease,15,31,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 2,Table 4,10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Differential abundant taxa in patients with Behcet's disease VS controls,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella enoeca,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum orale,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp.,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp.",1783272|201174|1760|2037|2049|1654|55565;3379134|976|200643|171549|171552|1283313|671218;3379134|976;3379134|29547|3031852|213849|72294|194|199;1783272|1239|186801|186802;3379134|976|200643|171549|171552|2974257|76123;1783272|1239|186801|3085636|186803|1164882|979627;1783272|1239|186801|3085636|186803;1783272|201174|84998|84999|1643824|2767353|1382;3384189|32066|203490|203491|1129771|32067|104608;3379134|976|200643|171549|171552|838|60133;1783272|1239|909932|909929|1843491|970|2053611;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|909932|1843489|31977|29465|1926307,Complete,Shaimaa Elsafoury
bsdb:27283393/2/1,27283393,case-control,27283393,10.1016/j.clim.2016.06.002,NA,"Coit P., Mumcu G., Ture-Ozdemir F., Unal A.U., Alpar U., Bostanci N., Ergun T., Direskeneli H. , Sawalha A.H.",Sequencing of 16S rRNA reveals a distinct salivary microbiome signature in Behçet's disease,"Clinical immunology (Orlando, Fla.)",2016,"16s rRNA, Behçet's disease, Genetics, Microbiome, Oral microbial diversity, Sequencing",Experiment 2,Turkey,Homo sapiens,Saliva,UBERON:0001836,Behcet's syndrome,EFO:0003780,non-immunosuppressent users among behcet's patients,immunosuppressant users,NA,19,12,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text,10 January 2021,Shaimaa Elsafoury,WikiWorks,the association between the use of immunosuppressants in BD patients with gut microbiota,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas catoniae",3379134|976|117743|200644|2762318|59735;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171551|836|41976,Complete,Shaimaa Elsafoury
bsdb:27283393/2/2,27283393,case-control,27283393,10.1016/j.clim.2016.06.002,NA,"Coit P., Mumcu G., Ture-Ozdemir F., Unal A.U., Alpar U., Bostanci N., Ergun T., Direskeneli H. , Sawalha A.H.",Sequencing of 16S rRNA reveals a distinct salivary microbiome signature in Behçet's disease,"Clinical immunology (Orlando, Fla.)",2016,"16s rRNA, Behçet's disease, Genetics, Microbiome, Oral microbial diversity, Sequencing",Experiment 2,Turkey,Homo sapiens,Saliva,UBERON:0001836,Behcet's syndrome,EFO:0003780,non-immunosuppressent users among behcet's patients,immunosuppressant users,NA,19,12,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,text,10 January 2021,Shaimaa Elsafoury,WikiWorks,the association between the use of immunosuppressants in BD patients with gut microbiota,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella baroniae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp.",3379134|976|200643|171549|171552|2974251|305719;1783272|1239|186801|3085636|186803|265975|1969407,Complete,Shaimaa Elsafoury
bsdb:27288567/1/1,27288567,"cross-sectional observational, not case-control",27288567,10.1016/j.jad.2016.05.038,NA,"Aizawa E., Tsuji H., Asahara T., Takahashi T., Teraishi T., Yoshida S., Ota M., Koga N., Hattori K. , Kunugi H.",Possible association of Bifidobacterium and Lactobacillus in the gut microbiota of patients with major depressive disorder,Journal of affective disorders,2016,"Bifidobacterium, Distress, Gut microbiota, Irritable bowel syndrome, Lactobacillus, Major depressive disorder",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,controls,MDD,NA,57,43,NA,16S,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,10 January 2021,Fatima Zohra,WikiWorks,Differential abundance of gut microbiota of patients with major depressive disorder,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Amylolactobacillus|s__Amylolactobacillus amylophilus",1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|2767876|1603,Complete,NA
bsdb:27292825/1/1,27292825,time series / longitudinal observational,27292825,10.1016/j.jaci.2016.03.041,NA,"Bunyavanich S., Shen N., Grishin A., Wood R., Burks W., Dawson P., Jones S.M., Leung D.Y.M., Sampson H., Sicherer S. , Clemente J.C.",Early-life gut microbiome composition and milk allergy resolution,The Journal of allergy and clinical immunology,2016,"16s rRNA sequencing, Bacteroidetes, Clostridia, Cow's milk allergy, Firmicutes, fatty acid, food allergy, metagenome, microbiome, microbiota",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,milk allergy resolution,children with milk allergy persistence,child with persistent milk allergy at age 8,128,98,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1a,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differentially abundant taxa in children with milk allergy persistence versus milk allergy resolution at age 8,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Trabulsiella",3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|590;3379134|1224|1236|91347|543|158851,Complete,Claregrieve1
bsdb:27292825/1/2,27292825,time series / longitudinal observational,27292825,10.1016/j.jaci.2016.03.041,NA,"Bunyavanich S., Shen N., Grishin A., Wood R., Burks W., Dawson P., Jones S.M., Leung D.Y.M., Sampson H., Sicherer S. , Clemente J.C.",Early-life gut microbiome composition and milk allergy resolution,The Journal of allergy and clinical immunology,2016,"16s rRNA sequencing, Bacteroidetes, Clostridia, Cow's milk allergy, Firmicutes, fatty acid, food allergy, metagenome, microbiome, microbiota",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,milk allergy resolution,children with milk allergy persistence,child with persistent milk allergy at age 8,128,98,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1a,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differentially abundant taxa in children with milk allergy persistence versus milk allergy resolution at age 8,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|186806|1730;1783272|1239;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171552;1783272|1239|186801|186802|216572|1263,Complete,Claregrieve1
bsdb:27306058/1/1,27306058,time series / longitudinal observational,27306058,10.1186/s13073-016-0312-1,NA,"Palleja A., Kashani A., Allin K.H., Nielsen T., Zhang C., Li Y., Brach T., Liang S., Feng Q., Jørgensen N.B., Bojsen-Møller K.N., Dirksen C., Burgdorf K.S., Holst J.J., Madsbad S., Wang J., Pedersen O., Hansen T. , Arumugam M.",Roux-en-Y gastric bypass surgery of morbidly obese patients induces swift and persistent changes of the individual gut microbiota,Genome medicine,2016,NA,Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,baseline,3 Months after Roux-en-Y gastric bypass surgery,NA,13,12,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure 3 & Table S3,10 January 2021,Marianthi Thomatos,WikiWorks,Roux-en-Y gastric bypass surgery and changes of gut microbiota in morbidly obese,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|543|570|573;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|91061|186826|1300|1301|1343;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|91061|186826|1300|1301|1313;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|91061|186826|1300|1301|113107;3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|186802|31979|1485|1502;1783272|1239|91061|186826|1300|1301|68892;1783272|1239|91061|186826|1300|1301|1302;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|186801|3085636|186803|2316020|46228;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|1853231|283168|28118;1783272|201174|1760|85004|31953|1678|1689;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|909932|1843489|31977|906|187326;1783272|1239|186801|186802|216572|244127|169435;3384189|32066;3379134|1224,Complete,Shaimaa Elsafoury
bsdb:27306058/1/2,27306058,time series / longitudinal observational,27306058,10.1186/s13073-016-0312-1,NA,"Palleja A., Kashani A., Allin K.H., Nielsen T., Zhang C., Li Y., Brach T., Liang S., Feng Q., Jørgensen N.B., Bojsen-Møller K.N., Dirksen C., Burgdorf K.S., Holst J.J., Madsbad S., Wang J., Pedersen O., Hansen T. , Arumugam M.",Roux-en-Y gastric bypass surgery of morbidly obese patients induces swift and persistent changes of the individual gut microbiota,Genome medicine,2016,NA,Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,baseline,3 Months after Roux-en-Y gastric bypass surgery,NA,13,12,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Figure 3 & Table S3,10 January 2021,Marianthi Thomatos,WikiWorks,Roux-en-Y gastric bypass surgery and changes of gut microbiota in morbidly obese,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,1783272|1239|186801|186802|216572|216851|853,Complete,Shaimaa Elsafoury
bsdb:27306058/2/1,27306058,time series / longitudinal observational,27306058,10.1186/s13073-016-0312-1,NA,"Palleja A., Kashani A., Allin K.H., Nielsen T., Zhang C., Li Y., Brach T., Liang S., Feng Q., Jørgensen N.B., Bojsen-Møller K.N., Dirksen C., Burgdorf K.S., Holst J.J., Madsbad S., Wang J., Pedersen O., Hansen T. , Arumugam M.",Roux-en-Y gastric bypass surgery of morbidly obese patients induces swift and persistent changes of the individual gut microbiota,Genome medicine,2016,NA,Experiment 2,Denmark,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,baseline,one year after Roux-en-Y gastric bypass surgery,NA,13,8,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure 3 & Table S3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Roux-en-Y gastric bypass surgery and changes of gut microbiota in morbidly obese,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Pseudomonadati|p__Pseudomonadota,k__Fusobacteriati|p__Fusobacteriota",3379134|1224|1236|91347|543|570|573;3379134|1224|1236|91347|543|561|562;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|91061|186826|1300|1301|1343;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|91061|186826|1300|1301|113107;1783272|1239|91061|186826|1300|1301|68892;3379134|976|200643|171549|171550|239759|328814;1783272|1239|91061|186826|186828|117563|46124;1783272|201174|1760|2037|2049|2529408|1660;3379134|1224;3384189|32066,Complete,Shaimaa Elsafoury
bsdb:27338587/1/1,27338587,case-control,27338587,10.1186/s40168-016-0171-4,NA,"Giloteaux L., Goodrich J.K., Walters W.A., Levine S.M., Ley R.E. , Hanson M.R.",Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome,Microbiome,2016,"Beta-diversity, Chronic fatigue syndrome, Inflammation, Lipopolysaccharides, Microbial translocation, Microbiome, Myalgic encephalomyelitis",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Chronic fatigue syndrome,EFO:0004540,Healthy controls,CFS cases,"Subjects with ME/CFS were established patients of a ME/ CFS specialist, Susan Levine, M.D. and fit the Fukuda diag- nostic criteria",39,48,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,figure 5,10 January 2021,Shaimaa Elsafoury,WikiWorks,taxonomy of differentially abundant microbiota between  ME/CFS and healthy individuals,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus",1783272|1239|186801|186802|216572|119852;1783272|201174|84998|1643822|1643826|84111;1783272|1239|91061|186826|1300|1357;1783272|1239|186801|186802|216572|244127;1783272|1239|526524|526525|2810280|100883,Complete,Shaimaa Elsafoury
bsdb:27338587/1/2,27338587,case-control,27338587,10.1186/s40168-016-0171-4,NA,"Giloteaux L., Goodrich J.K., Walters W.A., Levine S.M., Ley R.E. , Hanson M.R.",Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome,Microbiome,2016,"Beta-diversity, Chronic fatigue syndrome, Inflammation, Lipopolysaccharides, Microbial translocation, Microbiome, Myalgic encephalomyelitis",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Chronic fatigue syndrome,EFO:0004540,Healthy controls,CFS cases,"Subjects with ME/CFS were established patients of a ME/ CFS specialist, Susan Levine, M.D. and fit the Fukuda diag- nostic criteria",39,48,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,figure 5,10 January 2021,Shaimaa Elsafoury,WikiWorks,taxonomy of differentially abundant microbiota between  ME/CFS and healthy individuals,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",1783272|1239|186801|186802|186807|2740;3379134|1224|1236|135625|712|724;1783272|201174|84998|84999|1643824|1380;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|1263;3379134|1224|1236|135625|712|416916;1783272|201174|1760|85004|31953|1678;1783272|201174|84998|84999|84107|102106;3379134|1224|28216|80840|995019|40544,Complete,Shaimaa Elsafoury
bsdb:27342554/1/1,27342554,case-control,27342554,10.1128/AEM.01235-16,NA,"Urbaniak C., Gloor G.B., Brackstone M., Scott L., Tangney M. , Reid G.",The Microbiota of Breast Tissue and Its Association with Breast Cancer,Applied and environmental microbiology,2016,NA,Experiment 1,Canada,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,healthy patients,BC patients,"Normal adjacent tissue, collected outside the marginal zone (approximately 5 cm away from the tumor), from patients with breast cancer (BC) undergoing lumpectomies or mastectomies.",12,20,3 months,16S,6,Illumina,centered log-ratio,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,8 July 2025,Ecsharp,Ecsharp,"Differences in relative abundances of taxa exist between healthy and cancer patients. Significance was based on the Benjamini-Hochberg corrected P value of the Wilcoxon rank test (significance threshold, P < 0.1).",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae",1783272|1239|91061|1385|186817|1386;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|91347|543;3379134|1224|28216|80840|80864,Complete,NA
bsdb:27342554/1/2,27342554,case-control,27342554,10.1128/AEM.01235-16,NA,"Urbaniak C., Gloor G.B., Brackstone M., Scott L., Tangney M. , Reid G.",The Microbiota of Breast Tissue and Its Association with Breast Cancer,Applied and environmental microbiology,2016,NA,Experiment 1,Canada,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,healthy patients,BC patients,"Normal adjacent tissue, collected outside the marginal zone (approximately 5 cm away from the tumor), from patients with breast cancer (BC) undergoing lumpectomies or mastectomies.",12,20,3 months,16S,6,Illumina,centered log-ratio,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,8 July 2025,Ecsharp,Ecsharp,"Differences in relative abundances of taxa exist between healthy and cancer patients. Significance was based on the Benjamini-Hochberg corrected P value of the Wilcoxon rank test (significance threshold, P < 0.1).",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus",3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1357;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|186826|1300|1301;1783272|201174|1760|85006|1268|1269,Complete,NA
bsdb:27342554/2/1,27342554,case-control,27342554,10.1128/AEM.01235-16,NA,"Urbaniak C., Gloor G.B., Brackstone M., Scott L., Tangney M. , Reid G.",The Microbiota of Breast Tissue and Its Association with Breast Cancer,Applied and environmental microbiology,2016,NA,Experiment 2,Canada,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,healthy patients,patients with benign tumors,"Normal adjacent tissue, collected outside the marginal zone (approximately 5 cm away from the tumor), from patients with benign tumors.",12,11,3 months,16S,6,Illumina,centered log-ratio,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table S4,9 July 2025,Ecsharp,Ecsharp,"ALDEx2 summary comparing relative abundances in breast tissue from healthy women, those with benign tumours and those with cancerous tumours. Bacterial profiles in normal adjacent breast tissue from women with benign tumours are more similar to normal adjacent tissue from women with cancerous tumours rather than healthy controls.",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|1239|91061|1385|186817|1386;1783272|1239|91061|1385|90964|1279,Complete,NA
bsdb:27342554/2/2,27342554,case-control,27342554,10.1128/AEM.01235-16,NA,"Urbaniak C., Gloor G.B., Brackstone M., Scott L., Tangney M. , Reid G.",The Microbiota of Breast Tissue and Its Association with Breast Cancer,Applied and environmental microbiology,2016,NA,Experiment 2,Canada,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,healthy patients,patients with benign tumors,"Normal adjacent tissue, collected outside the marginal zone (approximately 5 cm away from the tumor), from patients with benign tumors.",12,11,3 months,16S,6,Illumina,centered log-ratio,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table S4,9 July 2025,Ecsharp,Ecsharp,"ALDEx2 summary comparing relative abundances in breast tissue from healthy women, those with benign tumours and those with cancerous tumours. Bacterial profiles in normal adjacent breast tissue from women with benign tumours are more similar to normal adjacent tissue from women with cancerous tumours rather than healthy controls.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus",3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1357,Complete,NA
bsdb:27346372/1/1,27346372,case-control,27346372,10.1038/srep28484,NA,"Chen J., Chia N., Kalari K.R., Yao J.Z., Novotna M., Paz Soldan M.M., Luckey D.H., Marietta E.V., Jeraldo P.R., Chen X., Weinshenker B.G., Rodriguez M., Kantarci O.H., Nelson H., Murray J.A. , Mangalam A.K.",Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls,Scientific reports,2016,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Healthy controls,Multiple sclerosis,Relapsing remitting MS (RRMS),36,31,NA,16S,345,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 3, Table 2",10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy","Microbial signatures of the gut microbiota of MS patients.
(A) Barplots comparing the abundances of differentially abundant taxa between MS and control. These “signature” taxa are selected by Wilcoxon rank-sum tests and a false discovery rate of 5%. Error bars represent standard errors. Phylum, family and genus-level taxa are plotted.

Differentially abundant taxa between MS and control samples at phylum, family and genus-level.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Mycoplana,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|1236|72274|135621|351;1783272|1239|186801|3085636|186803|572511;3379134|1224|28211|204458|76892;1783272|1239|186801|3085636|186803|189330;3379134|976|117743|200644|49546;3379134|976|117743|200644|49546|237;1783272|1239|186801|3085636|186803;3379134|1224|28211|356|82115|13159;3379134|976|117747|200666|84566|84567;3379134|1224|1236|72274|135621|286;3379134|976|117747|200666|84566;3379134|1224|1236|72274|135621;3379134|1224,Complete,Peace Sandy
bsdb:27346372/1/2,27346372,case-control,27346372,10.1038/srep28484,NA,"Chen J., Chia N., Kalari K.R., Yao J.Z., Novotna M., Paz Soldan M.M., Luckey D.H., Marietta E.V., Jeraldo P.R., Chen X., Weinshenker B.G., Rodriguez M., Kantarci O.H., Nelson H., Murray J.A. , Mangalam A.K.",Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls,Scientific reports,2016,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Healthy controls,Multiple sclerosis,Relapsing remitting MS (RRMS),36,31,NA,16S,345,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 3, Table 2",10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy","Microbial signatures of the gut microbiota of MS patients. (A) Barplots comparing the abundances of differentially abundant taxa between MS and control. These “signature” taxa are selected by Wilcoxon rank-sum tests and a false discovery rate of 5%. Error bars represent standard errors. Phylum, family and genus-level taxa are plotted.

Differentially abundant taxa between MS and control samples at phylum, family and genus-level.",decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|201174;1783272|201174|84998|1643822|1643826|447020;1783272|1239|186801|3085636|186803|572511;1783272|201174|84998|84999|84107|102106;1783272|1239|526524|526525|2810280|100883;1783272|201174|84998|84999|84107;3379134|1224|1236|91347|543;1783272|1239|526524|526525|128827;3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|544448|31969|2085|2092|2093;3379134|976|200643|171549|2005525|375288;3379134|1224|1236|135625|712;3379134|976|200643|171549|171551;3379134|1224;1783272|1239|909932|1843489|31977,Complete,Peace Sandy
bsdb:27352007/1/1,27352007,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S., Gandhi R., Cox L.M., Li N., von Glehn F., Yan R., Patel B., Mazzola M.A., Liu S., Glanz B.L., Cook S., Tankou S., Stuart F., Melo K., Nejad P., Smith K., Topçuolu B.D., Holden J., Kivisäkk P., Chitnis T., De Jager P.L., Quintana F.J., Gerber G.K., Bry L. , Weiner H.L.",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,healthy controls,multiple sclerosis,multiple sclerosis patients,43,60,6 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2a, 2c, Table 2",10 January 2021,Rimsha Azhar,WikiWorks,Compositional differences in fecal microbiota between patients of MS compared to healthy controls using Illumina MiSeq,increased,"k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae|g__Micromonospora,k__Methanobacteriati|p__Methanobacteriota",3366610|28890|183925|2158|2159|2172;3379134|74201|203494|48461|1647988|239934;1783272|201174|1760|85008|28056|84593;3366610|28890,Complete,Claregrieve1
bsdb:27352007/1/2,27352007,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S., Gandhi R., Cox L.M., Li N., von Glehn F., Yan R., Patel B., Mazzola M.A., Liu S., Glanz B.L., Cook S., Tankou S., Stuart F., Melo K., Nejad P., Smith K., Topçuolu B.D., Holden J., Kivisäkk P., Chitnis T., De Jager P.L., Quintana F.J., Gerber G.K., Bry L. , Weiner H.L.",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,healthy controls,multiple sclerosis,multiple sclerosis patients,43,60,6 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2a, 2c, Table 2",10 January 2021,Rimsha Azhar,WikiWorks,Compositional differences in fecal microbiota between patients of MS compared to healthy controls using Illumina MiSeq,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,3379134|976|200643|171549|1853231|574697,Complete,Claregrieve1
bsdb:27352007/2/1,27352007,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S., Gandhi R., Cox L.M., Li N., von Glehn F., Yan R., Patel B., Mazzola M.A., Liu S., Glanz B.L., Cook S., Tankou S., Stuart F., Melo K., Nejad P., Smith K., Topçuolu B.D., Holden J., Kivisäkk P., Chitnis T., De Jager P.L., Quintana F.J., Gerber G.K., Bry L. , Weiner H.L.",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,controls,multiple sclerosis patients,patients with multiple sclerosis,43,60,6 months,16S,345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2a, 2c, Table 2",10 January 2021,Rimsha Azhar,WikiWorks,Compositional differences in fecal microbiota between patients of MS compared to healthy controls using Roche 454,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae|g__Micromonospora,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Methanobacteriati|p__Methanobacteriota",1783272|201174|1760|85008|28056|84593;3366610|28890|183925|2158|2159|2172;3379134|74201|203494|48461|1647988|239934;3366610|28890,Complete,Claregrieve1
bsdb:27352007/2/2,27352007,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S., Gandhi R., Cox L.M., Li N., von Glehn F., Yan R., Patel B., Mazzola M.A., Liu S., Glanz B.L., Cook S., Tankou S., Stuart F., Melo K., Nejad P., Smith K., Topçuolu B.D., Holden J., Kivisäkk P., Chitnis T., De Jager P.L., Quintana F.J., Gerber G.K., Bry L. , Weiner H.L.",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,controls,multiple sclerosis patients,patients with multiple sclerosis,43,60,6 months,16S,345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2a, 2c, Table 2",10 January 2021,Rimsha Azhar,WikiWorks,Compositional differences in fecal microbiota between patients of MS compared to healthy controls using Roche 454,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,3379134|976|200643|171549|1853231|574697,Complete,Claregrieve1
bsdb:27352007/3/1,27352007,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S., Gandhi R., Cox L.M., Li N., von Glehn F., Yan R., Patel B., Mazzola M.A., Liu S., Glanz B.L., Cook S., Tankou S., Stuart F., Melo K., Nejad P., Smith K., Topçuolu B.D., Holden J., Kivisäkk P., Chitnis T., De Jager P.L., Quintana F.J., Gerber G.K., Bry L. , Weiner H.L.",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,controls,untreated multiple sclerosis,untreated multiple sclerosis,43,28,6 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2a, 2c, Table 2",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Compositional differences in fecal microbiota between untreated patients of MS compared to healthy controls using Illumina MiSeq,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Verrucomicrobium",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|203557|2735,Complete,Claregrieve1
bsdb:27352007/3/2,27352007,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S., Gandhi R., Cox L.M., Li N., von Glehn F., Yan R., Patel B., Mazzola M.A., Liu S., Glanz B.L., Cook S., Tankou S., Stuart F., Melo K., Nejad P., Smith K., Topçuolu B.D., Holden J., Kivisäkk P., Chitnis T., De Jager P.L., Quintana F.J., Gerber G.K., Bry L. , Weiner H.L.",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,controls,untreated multiple sclerosis,untreated multiple sclerosis,43,28,6 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2a, 2c, Table 2",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Compositional differences in fecal microbiota between untreated patients of MS compared to healthy controls using Illumina MiSeq,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|976|200643|171549|1853231|574697;3379134|976|200643|171549|171552|838;3379134|1224|28216|80840|995019|40544,Complete,Claregrieve1
bsdb:27352007/4/1,27352007,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S., Gandhi R., Cox L.M., Li N., von Glehn F., Yan R., Patel B., Mazzola M.A., Liu S., Glanz B.L., Cook S., Tankou S., Stuart F., Melo K., Nejad P., Smith K., Topçuolu B.D., Holden J., Kivisäkk P., Chitnis T., De Jager P.L., Quintana F.J., Gerber G.K., Bry L. , Weiner H.L.",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,NA,Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,controls,untreated multiple sclerosis,untreated multiple sclerosis,43,28,6 months,16S,345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2a, 2c, Table 2",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",compositional differences in fecal microbiota between untreated patients of MS compared to healthy controls using Roche 454,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Methanobacteriati|p__Methanobacteriota,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Verrucomicrobium",3379134|74201|203494|48461|1647988|239934;3366610|28890;3366610|28890|183925|2158|2159|2172;3379134|74201|203494|48461|203557|2735,Complete,Claregrieve1
bsdb:27352007/4/2,27352007,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S., Gandhi R., Cox L.M., Li N., von Glehn F., Yan R., Patel B., Mazzola M.A., Liu S., Glanz B.L., Cook S., Tankou S., Stuart F., Melo K., Nejad P., Smith K., Topçuolu B.D., Holden J., Kivisäkk P., Chitnis T., De Jager P.L., Quintana F.J., Gerber G.K., Bry L. , Weiner H.L.",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,NA,Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,controls,untreated multiple sclerosis,untreated multiple sclerosis,43,28,6 months,16S,345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2a, 2c, Table 2",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",compositional differences in fecal microbiota between untreated patients of MS compared to healthy controls using Roche 454,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|976|200643|171549|1853231|574697;3379134|976|200643|171549|171552|838;3379134|1224|28216|80840|995019|40544,Complete,Claregrieve1
bsdb:27352007/5/1,27352007,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S., Gandhi R., Cox L.M., Li N., von Glehn F., Yan R., Patel B., Mazzola M.A., Liu S., Glanz B.L., Cook S., Tankou S., Stuart F., Melo K., Nejad P., Smith K., Topçuolu B.D., Holden J., Kivisäkk P., Chitnis T., De Jager P.L., Quintana F.J., Gerber G.K., Bry L. , Weiner H.L.",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,NA,Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,untreated multiple sclerosis,treated multiple sclerosis,treated multiple sclerosis,28,32,6 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2c, Table 2",10 January 2021,Rimsha Azhar,WikiWorks,Compositional differences in fecal microbiota between treated patients of MS compared to untreated patients using Illumina MiSeq,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|976|200643|171549|171552|838;3379134|1224|28216|80840|995019|40544,Complete,Claregrieve1
bsdb:27352007/5/2,27352007,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S., Gandhi R., Cox L.M., Li N., von Glehn F., Yan R., Patel B., Mazzola M.A., Liu S., Glanz B.L., Cook S., Tankou S., Stuart F., Melo K., Nejad P., Smith K., Topçuolu B.D., Holden J., Kivisäkk P., Chitnis T., De Jager P.L., Quintana F.J., Gerber G.K., Bry L. , Weiner H.L.",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,NA,Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,untreated multiple sclerosis,treated multiple sclerosis,treated multiple sclerosis,28,32,6 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2c, Table 2",10 January 2021,Rimsha Azhar,WikiWorks,Compositional differences in fecal microbiota between treated patients of MS compared to untreated patients using Illumina MiSeq,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,1783272|1239|186801|186802|31979|1266,Complete,Claregrieve1
bsdb:27352007/6/1,27352007,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S., Gandhi R., Cox L.M., Li N., von Glehn F., Yan R., Patel B., Mazzola M.A., Liu S., Glanz B.L., Cook S., Tankou S., Stuart F., Melo K., Nejad P., Smith K., Topçuolu B.D., Holden J., Kivisäkk P., Chitnis T., De Jager P.L., Quintana F.J., Gerber G.K., Bry L. , Weiner H.L.",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,NA,Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,untreated multiple sclerosis,treated multiple sclerosis,treated multiple sclerosis patients,28,32,6 months,16S,345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2c, Table 2",10 January 2021,Rimsha Azhar,WikiWorks,Compositional differences in fecal microbiota between treated patients of MS compared to untreated patients using Roche 454,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:27352007/6/2,27352007,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S., Gandhi R., Cox L.M., Li N., von Glehn F., Yan R., Patel B., Mazzola M.A., Liu S., Glanz B.L., Cook S., Tankou S., Stuart F., Melo K., Nejad P., Smith K., Topçuolu B.D., Holden J., Kivisäkk P., Chitnis T., De Jager P.L., Quintana F.J., Gerber G.K., Bry L. , Weiner H.L.",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,NA,Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,untreated multiple sclerosis,treated multiple sclerosis,treated multiple sclerosis patients,28,32,6 months,16S,345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2c, Table 2",10 January 2021,Rimsha Azhar,WikiWorks,Compositional differences in fecal microbiota between treated patients of MS compared to untreated patients using Roche 454,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,1783272|1239|186801|186802|31979|1266,Complete,Claregrieve1
bsdb:27362264/1/1,27362264,"cross-sectional observational, not case-control",27362264,10.1371/journal.pone.0158498,NA,"Martin R., Makino H., Cetinyurek Yavuz A., Ben-Amor K., Roelofs M., Ishikawa E., Kubota H., Swinkels S., Sakai T., Oishi K., Kushiro A. , Knol J.","Early-Life Events, Including Mode of Delivery and Type of Feeding, Siblings and Gender, Shape the Developing Gut Microbiota",PloS one,2016,NA,Experiment 1,Netherlands,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,vaginal delivery,C-section,babies that were delivered by c-section,80,28,"2 weeks prior to delivery
2 weeks after delivery",16S,NA,RT-qPCR,NA,Mixed-Effects Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,10 January 2021,Shaimaa Elsafoury,"Claregrieve1,WikiWorks",Differential microbial abundance between infants born by vaginal delivery or C-section.,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri",1783272|201174|84998|84999|1643824|1380;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|28116;1783272|201174|1760|85004|31953|1678|1686;1783272|201174|1760|85004|31953|1678|216816|1679;1783272|1239|186801|186802|31979|1485|1502;1783272|1239|91061|186826|81852|1350;3379134|976|200643|171549|815|909656|821;1783272|201174|1760|85004|31953|1678|1681;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|91061|186826|33958|2742598|1598,Complete,Claregrieve1
bsdb:27381339/1/1,27381339,case-control,27381339,10.4014/jmb.1603.03057,NA,"Ruengsomwong S., La-Ongkham O., Jiang J., Wannissorn B., Nakayama J. , Nitisinprasert S.","Microbial Community of Healthy Thai Vegetarians and Non-Vegetarians, Their Core Gut Microbiota, and Pathogen Risk",Journal of microbiology and biotechnology,2016,"Enterobacteriaceae, Fecal microbiota, Prevotella, core gut microbiota, pathogen risk, pyrosequencing",Experiment 1,Thailand,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Healthy non-vegetarian,Healthy vegetarian,"The vegetarian volunteers consisted of ovo-lacto vegetarians, lacto-vegetarians, an ovo-vegetarian, and vegans. They had all been vegetarians for at least 3 years before participating in this study.",36,36,1 month,16S,678,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Fig. 3 , Table1 and Table 3",10 January 2021,Valentina Pineda,"WikiWorks,Peace Sandy","Abundance of gut microbiota at the family, genus and species levels detected in both vegetarian and non-vegetarian groups.",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella corporis",1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|171552|838;3379134|1224|1236|91347|543|570;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|572511;3379134|1224|1236|91347|543|570|573;3379134|976|200643|171549|171552|838|28128,Complete,Peace Sandy
bsdb:27381339/1/2,27381339,case-control,27381339,10.4014/jmb.1603.03057,NA,"Ruengsomwong S., La-Ongkham O., Jiang J., Wannissorn B., Nakayama J. , Nitisinprasert S.","Microbial Community of Healthy Thai Vegetarians and Non-Vegetarians, Their Core Gut Microbiota, and Pathogen Risk",Journal of microbiology and biotechnology,2016,"Enterobacteriaceae, Fecal microbiota, Prevotella, core gut microbiota, pathogen risk, pyrosequencing",Experiment 1,Thailand,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Healthy non-vegetarian,Healthy vegetarian,"The vegetarian volunteers consisted of ovo-lacto vegetarians, lacto-vegetarians, an ovo-vegetarian, and vegans. They had all been vegetarians for at least 3 years before participating in this study.",36,36,1 month,16S,678,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Fig. 3 , Table3 and Table 1",10 January 2021,Valentina Pineda,"WikiWorks,Peace Sandy","Abundance of gut microbiota at the family, genus and species levels detected in both vegetarian and non-vegetarian groups.",decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|33042;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171550;3379134|1224|1236|91347|543|590,Complete,Peace Sandy
bsdb:27411009/1/1,27411009,randomized controlled trial,27411009,10.1016/j.cmet.2016.06.016,NA,"Reijnders D., Goossens G.H., Hermes G.D., Neis E.P., van der Beek C.M., Most J., Holst J.J., Lenaerts K., Kootte R.S., Nieuwdorp M., Groen A.K., Olde Damink S.W., Boekschoten M.V., Smidt H., Zoetendal E.G., Dejong C.H. , Blaak E.E.",Effects of Gut Microbiota Manipulation by Antibiotics on Host Metabolism in Obese Humans: A Randomized Double-Blind Placebo-Controlled Trial,Cell metabolism,2016,NA,Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,or placebo (microcrystalline cellulose),oral intake of vancomycin (directed against Gram-positive bacteria),"low-active (<3 hr organized sports activities per week), weight-stable (<2 kg body weight change 3 months prior to inclusion) overweight/obese (BMI 25–35 kg/m2) Caucasian men, between 35 and 70 years with impaired glucose metabolism (either fasting glucose >5.6 mmol/l, and/or 2 hr glucose between 7.8–11 mmol/l) and insulin resistant (homeostasis model assessment for insulin resistance; HOMA-IR > 2.2).",37,38,3 months,16S,NA,Human Intestinal Tract Chip,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 1,Table S1,10 January 2021,Mst Afroza Parvin,"Lwaldron,WikiWorks",Significantly different microbial taxa after 7 days intervention with vancomycin and placebo in feces using linear mixed models,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax|s__Anaerovorax odorimutans,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium|s__Lachnobacterium bovis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora sphenoides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus|s__Lactiplantibacillus plantarum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter|s__Papillibacter cinnamivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas nexilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] cellulosi",1783272|1239|186801|3085636|186803|207244|105841;1783272|1239|186801|3082720|543314|109326|109327;1783272|201174|84998|84999|1643824|1380;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511|40520;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|33042|33043;1783272|1239|186801|3085636|186803|189330|39486;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|140625|140626;1783272|1239|186801|3085636|186803|28050|28052;1783272|1239|186801|3085636|186803|2719231|29370;1783272|1239|91061|186826|33958|2767842|1590;1783272|1239|186801|186802|216572|100175|100176;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|3085636|186803|2005355|29361;1783272|1239|186801|186802|216572|29343,Complete,Rimsha Azhar
bsdb:27450202/1/1,27450202,case-control,27450202,10.1111/1462-2920.13463,NA,"Riva A., Borgo F., Lassandro C., Verduci E., Morace G., Borghi E. , Berry D.",Pediatric obesity is associated with an altered gut microbiota and discordant shifts in Firmicutes populations,Environmental microbiology,2017,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,controls,pediatric obese,NA,36,42,6 months,16S,NA,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 1,Table 1 & Supplementary Table 5,10 January 2021,Marianthi Thomatos,WikiWorks,Differential abundance in pediatric obesity  versus normal weight  controls,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",1783272|1239;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|186802|541000;1783272|1239|186801|186802|216572|216851|853,Complete,Shaimaa Elsafoury
bsdb:27450202/1/2,27450202,case-control,27450202,10.1111/1462-2920.13463,NA,"Riva A., Borgo F., Lassandro C., Verduci E., Morace G., Borghi E. , Berry D.",Pediatric obesity is associated with an altered gut microbiota and discordant shifts in Firmicutes populations,Environmental microbiology,2017,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,controls,pediatric obese,NA,36,42,6 months,16S,NA,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 2,Table 1 & Supplementary Table 5,10 January 2021,Marianthi Thomatos,WikiWorks,Differential abundance in pediatric obesity  versus normal weight  controls,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris",3379134|976;3379134|976|200643;3379134|976|200643|171549;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|815|816|46506,Complete,Shaimaa Elsafoury
bsdb:27474122/1/1,27474122,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B., Bangayan N.J., Curd E., Taylor P.A., Gallo R.L., Leung D.Y.M. , Li H.",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,NA,Experiment 1,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Age,EFO:0000246,2-12 years,18-62 years,adult age 18-62,13,45,1 week,16S,123,Illumina,relative abundances,T-Test,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1b, Supplemental table E2, Figure 2b text",10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Skin microorganisms differ with age in the healthy skin,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus",1783272|201174|1760|85007|1653|1716|1720;1783272|201174|1760|85009|31957|1912216|1747;1783272|1239|91061|1385|90964|1279|1282;1783272|201174|1760|85009|31957|1743;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|33958|1578;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|1737404|1737405|1570339|165779,Complete,Atrayees
bsdb:27474122/1/2,27474122,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B., Bangayan N.J., Curd E., Taylor P.A., Gallo R.L., Leung D.Y.M. , Li H.",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,NA,Experiment 1,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Age,EFO:0000246,2-12 years,18-62 years,adult age 18-62,13,45,1 week,16S,123,Illumina,relative abundances,T-Test,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 1b, Supplemental table E2, Figure 2b text",10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Skin microorganisms differ with age in the healthy skin,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",1783272|1239|91061|186826|1300|1301|1306;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|186828|117563;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135625|712|724,Complete,Atrayees
bsdb:27474122/2/1,27474122,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B., Bangayan N.J., Curd E., Taylor P.A., Gallo R.L., Leung D.Y.M. , Li H.",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,NA,Experiment 2,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,non-lesional skin,lesional skin,atopic dermatitis lesional skin,59,59,1 week,16S,123,Illumina,relative abundances,T-Test,0.05,TRUE,NA,age,NA,NA,decreased,NA,NA,NA,NA,Signature 1,text,10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Taxonomic composition of the atopic dermatitis skin microbiome at the genus level among children,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,Atrayees
bsdb:27474122/2/2,27474122,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B., Bangayan N.J., Curd E., Taylor P.A., Gallo R.L., Leung D.Y.M. , Li H.",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,NA,Experiment 2,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,non-lesional skin,lesional skin,atopic dermatitis lesional skin,59,59,1 week,16S,123,Illumina,relative abundances,T-Test,0.05,TRUE,NA,age,NA,NA,decreased,NA,NA,NA,NA,Signature 2,text,10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Taxonomic composition of the atopic dermatitis skin microbiome at the genus level among children,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium",1783272|1239|91061|186826|1300|1301;1783272|201174|1760|85009|31957|1743,Complete,Atrayees
bsdb:27474122/3/1,27474122,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B., Bangayan N.J., Curd E., Taylor P.A., Gallo R.L., Leung D.Y.M. , Li H.",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,NA,Experiment 3,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Age,EFO:0000246,2-12 years,13-62 years,teenager/adult age 13-62,59,69,1 week,16S,123,Illumina,relative abundances,T-Test,0.05,TRUE,NA,age,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplemental Table E4,10 January 2021,Lucy Mellor,WikiWorks,Taxonomic composition of the atopic dermatitis skin microbiome at the genus level among those with lesional skin,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|201174|1760|85009|31957|1743;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|186826|33958|1578,Complete,Atrayees
bsdb:27474122/3/2,27474122,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B., Bangayan N.J., Curd E., Taylor P.A., Gallo R.L., Leung D.Y.M. , Li H.",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,NA,Experiment 3,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Age,EFO:0000246,2-12 years,13-62 years,teenager/adult age 13-62,59,69,1 week,16S,123,Illumina,relative abundances,T-Test,0.05,TRUE,NA,age,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Supplemental Table E4,10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Taxonomic composition of the atopic dermatitis skin microbiome at the genus level among those with lesional skin,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|186828|117563;1783272|1239|91061|1385|539738|1378;3379134|1224|28216|206351|481|482;3379134|1224|1236|135625|712|724;1783272|201174|1760|85006|1268|32207;1783272|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:27474122/4/1,27474122,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B., Bangayan N.J., Curd E., Taylor P.A., Gallo R.L., Leung D.Y.M. , Li H.",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,NA,Experiment 4,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Age,EFO:0000246,2-12 years,18-62 years,adult age 18-62,13,45,1 week,16S,123,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplemental Table E3,10 January 2021,Lucy Mellor,WikiWorks,Taxonomic compositions of the healthy skin microbiome at the species level,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners",1783272|201174|1760|85009|31957|1912216|1747;1783272|1239|91061|1385|90964|1279|1282;1783272|1239|91061|186826|33958|1578|147802,Complete,Atrayees
bsdb:27474122/5/1,27474122,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B., Bangayan N.J., Curd E., Taylor P.A., Gallo R.L., Leung D.Y.M. , Li H.",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,NA,Experiment 5,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,non-lesional skin in young children,lesional skin in young children,atopic dermatitis lesional skin,69,69,1 week,16S,123,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplemental Table E5,10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Taxonomic composition of the atopic dermatitis skin microbiome at the species level among adults-teenagers,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium pseudogenitalium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus capitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus caprae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus",1783272|201174|1760|85009|31957|1912216|1747;1783272|201174|1760|85007|1653|1716|38303;1783272|1239|91061|1385|90964|1279|29388;1783272|1239|91061|1385|90964|1279|29380;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|91061|186826|1300|1301|1313;1783272|1239|91061|186826|1300|1301|1305;1783272|1239|91061|186826|1300|1301|45634,Complete,Atrayees
bsdb:27474122/6/1,27474122,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B., Bangayan N.J., Curd E., Taylor P.A., Gallo R.L., Leung D.Y.M. , Li H.",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,NA,Experiment 6,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,non-lesional skin,lesional skin,atopic dermatitis lesional skin,59,59,1 week,16S,123,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplemental Table E5,10 January 2021,Lucy Mellor,WikiWorks,Taxonomic composition of the atopic dermatitis skin microbiome at the species level among children,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,1783272|1239|91061|1385|90964|1279|1280,Complete,Atrayees
bsdb:27474122/7/1,27474122,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B., Bangayan N.J., Curd E., Taylor P.A., Gallo R.L., Leung D.Y.M. , Li H.",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,NA,Experiment 7,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Age,EFO:0000246,2-12 years,18-62 years,teenager/adult age 13-62,59,69,1 week,16S,123,Illumina,relative abundances,T-Test,0.05,TRUE,NA,age,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplemental Table E5,10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Taxonomic composition of the atopic dermatitis skin microbiome at the species level among those with lesional skin,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis",1783272|201174|1760|85009|31957|1912216|1747;1783272|1239|91061|186826|33958|1578|147802;1783272|1239|91061|1385|90964|1279|1282,Complete,Atrayees
bsdb:27474122/7/2,27474122,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B., Bangayan N.J., Curd E., Taylor P.A., Gallo R.L., Leung D.Y.M. , Li H.",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,NA,Experiment 7,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Age,EFO:0000246,2-12 years,18-62 years,teenager/adult age 13-62,59,69,1 week,16S,123,Illumina,relative abundances,T-Test,0.05,TRUE,NA,age,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Supplemental Table E5,10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Taxonomic composition of the atopic dermatitis skin microbiome at the species level among those with lesional skin,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa",1783272|1239|91061|186826|1300|1301|45634;1783272|201174|1760|85006|1268|32207|43675,Complete,Atrayees
bsdb:27477587/1/1,27477587,case-control,27477587,10.1038/srep30673,NA,"Ling Z., Jin C., Xie T., Cheng Y., Li L. , Wu N.",Alterations in the Fecal Microbiota of Patients with HIV-1 Infection: An Observational Study in A Chinese Population,Scientific reports,2016,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,healthy controls,HIV-1 infected patients,HIV-1 diagnosed patients,16,67,1 month,16S,123,Roche454,relative abundances,LEfSe,0.05,TRUE,2,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure 2B,2C, 2D, 2E",10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Comparison of the relative abundance in healthy controls and HIV-1 positive individuals,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",3379134|1224|28216;3379134|1224|28216|80840;1783272|1239|186801|186802|3085642|580596;1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|3085636|186803|189330;3379134|1224|1236|91347|543|547;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|186801|186802|216572|216851;1783272|1239;1783272|1239|909932|909929|1843491|158846;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|1224;3379134|1224|28216|80840|995019;1783272|1239|526524|526525|128827,Complete,Claregrieve1
bsdb:27477587/1/2,27477587,case-control,27477587,10.1038/srep30673,NA,"Ling Z., Jin C., Xie T., Cheng Y., Li L. , Wu N.",Alterations in the Fecal Microbiota of Patients with HIV-1 Infection: An Observational Study in A Chinese Population,Scientific reports,2016,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,healthy controls,HIV-1 infected patients,HIV-1 diagnosed patients,16,67,1 month,16S,123,Roche454,relative abundances,LEfSe,0.05,TRUE,2,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 2B,2C, 2D, 2E",10 January 2021,Fatima Zohra,WikiWorks,Comparison of the relative abundance in healthy controls and HIV-1 positive individuals,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|186801|3085636|186803|33042;3379134|976|200643|171549|2005519|397864;1783272|1239|909932|1843489|31977|39948;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816,Complete,Claregrieve1
bsdb:27477587/2/1,27477587,case-control,27477587,10.1038/srep30673,NA,"Ling Z., Jin C., Xie T., Cheng Y., Li L. , Wu N.",Alterations in the Fecal Microbiota of Patients with HIV-1 Infection: An Observational Study in A Chinese Population,Scientific reports,2016,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HAART-naive HIV-1 patients,HAART-treated HIV-1 patients,HIV-1 diagnosed patients,35,32,1 month,16S,123,Roche454,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3B,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Comparison of microbial abundance in HIV+ HAART-naive and HIV+ HAART-treated individuals,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;1783272|1239|186801|3085636|186803|572511;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932;3379134|1224;1783272|1239|909932|909929;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977,Complete,Claregrieve1
bsdb:27477587/2/2,27477587,case-control,27477587,10.1038/srep30673,NA,"Ling Z., Jin C., Xie T., Cheng Y., Li L. , Wu N.",Alterations in the Fecal Microbiota of Patients with HIV-1 Infection: An Observational Study in A Chinese Population,Scientific reports,2016,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HAART-naive HIV-1 patients,HAART-treated HIV-1 patients,HIV-1 diagnosed patients,35,32,1 month,16S,123,Roche454,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 3B,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Comparison of microbial abundance in HIV+ HAART-naive and HIV+ HAART-treated individuals,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales,k__Thermotogati|p__Synergistota|c__Synergistia,k__Thermotogati|p__Synergistota",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549;3379134|976;3379134|976|200643;3379134|976|200643|171549|2005519|397864;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3384194|508458|649775|649776|3029088|638847;3379134|976|200643|171549|171550;3384194|508458|649775|649776|649777;3384194|508458|649775|649776;3384194|508458|649775;3384194|508458,Complete,Claregrieve1
bsdb:27481047/1/1,27481047,laboratory experiment,27481047,10.1038/srep30594,NA,"Liu X., Zeng B., Zhang J., Li W., Mou F., Wang H., Zou Q., Zhong B., Wu L., Wei H. , Fang Y.",Role of the Gut Microbiome in Modulating Arthritis Progression in Mice,Scientific reports,2016,NA,Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Experimental arthritis,EFO:1001787,Pre–Collagen-Induced Arthritis resistant (Pre-CIAN) mice,Pre–Collagen-Induced Arthritis susceptible (Pre-CIA) mice,Collagen-Induced Arthritis (CIA)-susceptible mice prior (before) disease onset,5,5,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2A (left panel), 2B, Supplementary Table 1",17 November 2025,Tosin,Tosin,Analysis of differentially abundant taxa compared by Student’s paired t-test between collagen-induced arthritis (CIA)-resistant and collagen-induced arthritis (CIA)-susceptible mice prior to arthritis onset (left panel) included,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:27481047/1/2,27481047,laboratory experiment,27481047,10.1038/srep30594,NA,"Liu X., Zeng B., Zhang J., Li W., Mou F., Wang H., Zou Q., Zhong B., Wu L., Wei H. , Fang Y.",Role of the Gut Microbiome in Modulating Arthritis Progression in Mice,Scientific reports,2016,NA,Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Experimental arthritis,EFO:1001787,Pre–Collagen-Induced Arthritis resistant (Pre-CIAN) mice,Pre–Collagen-Induced Arthritis susceptible (Pre-CIA) mice,Collagen-Induced Arthritis (CIA)-susceptible mice prior (before) disease onset,5,5,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2A (left panel), 2B, Supplementary Table 1",18 November 2025,Tosin,Tosin,Analysis of differentially abundant taxa compared by Student’s paired t-test between collagen-induced arthritis (CIA)-resistant and collagen-induced arthritis (CIA)-susceptible mice prior to arthritis onset (left panel) included,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|244127;;1783272|1239|186801|3085636|186803|572511;95818|2093818|2093825|2171986|1331051;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;1783272|201174|84998|1643822|1643826|580024;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:27481047/2/1,27481047,laboratory experiment,27481047,10.1038/srep30594,NA,"Liu X., Zeng B., Zhang J., Li W., Mou F., Wang H., Zou Q., Zhong B., Wu L., Wei H. , Fang Y.",Role of the Gut Microbiome in Modulating Arthritis Progression in Mice,Scientific reports,2016,NA,Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Experimental arthritis,EFO:1001787,Collagen-induced arthritis resistant (AR) mice,Collagen-induced arthritis susceptible (AS) mice,Collagen-induced arthritis (CIA)-susceptible mice; mice that developed arthritis,6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,Figure 4B,18 November 2025,Allan,Allan,LEfSe (linear discriminant analysis effect size) -identified LDA bar graphs of taxa/clades with differential abundance following conventionalization with the microbiome of the collagen-induced arthritis (CIA)-susceptible (green) and the collagen-induced arthritis (CIA)-resistant (red) mice.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter",3379134|1224|28216|80840|506|222;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|1385|186818;1783272|201174|84998|84999|84107|102106;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|1853231|283168,Complete,Svetlana up
bsdb:27481047/2/2,27481047,laboratory experiment,27481047,10.1038/srep30594,NA,"Liu X., Zeng B., Zhang J., Li W., Mou F., Wang H., Zou Q., Zhong B., Wu L., Wei H. , Fang Y.",Role of the Gut Microbiome in Modulating Arthritis Progression in Mice,Scientific reports,2016,NA,Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Experimental arthritis,EFO:1001787,Collagen-induced arthritis resistant (AR) mice,Collagen-induced arthritis susceptible (AS) mice,Collagen-induced arthritis (CIA)-susceptible mice; mice that developed arthritis,6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,Figure 4B,18 November 2025,Allan,"Allan,Tosin",LEfSe (linear discriminant analysis effect size) -identified LDA bar graphs of taxa/clades with differential abundance following conventionalization with the microbiome of the collagen-induced arthritis (CIA)-susceptible (green) and the collagen-induced arthritis (CIA)-resistant (red) mice.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetitomaculum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",1783272|1239|186801|3085636|186803|31980;3379134|1224|28211|204458|76892|41275;3379134|1224|28211|204458|76892;3379134|1224|28211|204458;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;3379134|1224|1236|135614|32033;3379134|1224|1236|135614;1783272|1239|186801|186802|186807;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|135614|32033|40323;1783272|1239|526524|526525|2810281|191303,Complete,Svetlana up
bsdb:27481047/3/1,27481047,laboratory experiment,27481047,10.1038/srep30594,NA,"Liu X., Zeng B., Zhang J., Li W., Mou F., Wang H., Zou Q., Zhong B., Wu L., Wei H. , Fang Y.",Role of the Gut Microbiome in Modulating Arthritis Progression in Mice,Scientific reports,2016,NA,Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Experimental arthritis,EFO:1001787,Pre–Collagen-Induced Arthritis (Pre-CIA) mice,Collagen-Induced Arthritis (CIA) mice,Collagen-induced arthritis (CIA)-susceptible mice; mice that developed arthritis,5,5,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 2A (right panel),18 November 2025,Allan,Allan,The distribution of bacterial families with relative abundance >1% in at least onesample compared by Student’s paired t-test in collagen-induced arthritis (CIA)-susceptible mice (right panel),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",3379134|976|200643|171549|815;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|2005473,Complete,Svetlana up
bsdb:27481047/3/2,27481047,laboratory experiment,27481047,10.1038/srep30594,NA,"Liu X., Zeng B., Zhang J., Li W., Mou F., Wang H., Zou Q., Zhong B., Wu L., Wei H. , Fang Y.",Role of the Gut Microbiome in Modulating Arthritis Progression in Mice,Scientific reports,2016,NA,Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Experimental arthritis,EFO:1001787,Pre–Collagen-Induced Arthritis (Pre-CIA) mice,Collagen-Induced Arthritis (CIA) mice,Collagen-induced arthritis (CIA)-susceptible mice; mice that developed arthritis,5,5,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 2A (right panel),18 November 2025,Allan,Allan,The distribution of bacterial families with relative abundance >1% in at least one sample compared by Student’s paired t-test in collagen-induced arthritis (CIA)-susceptible mice (right panel),decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,1783272|1239|91061|186826|33958,Complete,Svetlana up
bsdb:27481047/4/1,27481047,laboratory experiment,27481047,10.1038/srep30594,NA,"Liu X., Zeng B., Zhang J., Li W., Mou F., Wang H., Zou Q., Zhong B., Wu L., Wei H. , Fang Y.",Role of the Gut Microbiome in Modulating Arthritis Progression in Mice,Scientific reports,2016,NA,Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Experimental arthritis,EFO:1001787,Collagen-induced arthritis resistant (CIAN) mice,Collagen-induced arthritis susceptible (CIA) mice,Collagen-induced arthritis (CIA)-susceptible mice; mice that developed arthritis,5,5,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,Supplementary Table 2,18 November 2025,Allan,Allan,Analysis of differentially abundant taxa between collagen-induced arthritis resistant (CIAN) mice and collagen-induced arthritis susceptible (CIA) mice,increased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,1783272|201174|84998|1643822|1643826|580024,Complete,Svetlana up
bsdb:27481047/4/2,27481047,laboratory experiment,27481047,10.1038/srep30594,NA,"Liu X., Zeng B., Zhang J., Li W., Mou F., Wang H., Zou Q., Zhong B., Wu L., Wei H. , Fang Y.",Role of the Gut Microbiome in Modulating Arthritis Progression in Mice,Scientific reports,2016,NA,Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Experimental arthritis,EFO:1001787,Collagen-induced arthritis resistant (CIAN) mice,Collagen-induced arthritis susceptible (CIA) mice,Collagen-induced arthritis (CIA)-susceptible mice; mice that developed arthritis,5,5,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,Supplementary Table 2,18 November 2025,Allan,Allan,Analysis of differentially abundant taxa between collagen-induced arthritis resistant (CIAN) mice and collagen-induced arthritis susceptible (CIA) mice,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",3379134|976|200643|171549|171550|239759;3379134|1224|1236|72274|135621|286,Complete,Svetlana up
bsdb:27481047/5/1,27481047,laboratory experiment,27481047,10.1038/srep30594,NA,"Liu X., Zeng B., Zhang J., Li W., Mou F., Wang H., Zou Q., Zhong B., Wu L., Wei H. , Fang Y.",Role of the Gut Microbiome in Modulating Arthritis Progression in Mice,Scientific reports,2016,NA,Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Experimental arthritis,EFO:1001787,Untreated control (NC) mice,Collagen-induced arthritis (CIA)-susceptible mice,Collagen-induced arthritis (CIA)-susceptible mice; mice that developed arthritis,5,5,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,"Figure 2B, Supplementary Table 2",18 November 2025,Tosin,Tosin,Analysis of differentially abundant taxa between collagen-induced arthritis (CIA) and untreated control (NC) mice after arthritis onset,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|186801|3085636|186803|1427378;;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|33042;3379134|200940|3031449|213115|194924|872;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:27481047/5/2,27481047,laboratory experiment,27481047,10.1038/srep30594,NA,"Liu X., Zeng B., Zhang J., Li W., Mou F., Wang H., Zou Q., Zhong B., Wu L., Wei H. , Fang Y.",Role of the Gut Microbiome in Modulating Arthritis Progression in Mice,Scientific reports,2016,NA,Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Experimental arthritis,EFO:1001787,Untreated control (NC) mice,Collagen-induced arthritis (CIA)-susceptible mice,Collagen-induced arthritis (CIA)-susceptible mice; mice that developed arthritis,5,5,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,"Figure 2B, Supplementary Table 2",18 November 2025,Tosin,Tosin,Analysis of differentially abundant taxa between collagen-induced arthritis (CIA) and untreated control (NC) mice after arthritis onset,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Brochothrix,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Myroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061|1385|186820|2755;1783272|201174|84998|1643822|1643826|580024;1783272|1239|91061|186826|1300|1357;3379134|976|117743|200644|49546|76831;3379134|976|200643|171549|171550|28138;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:27499582/1/1,27499582,case-control,27499582,10.3164/jcbn.15-152,NA,"Andoh A., Nishida A., Takahashi K., Inatomi O., Imaeda H., Bamba S., Kito K., Sugimoto M. , Kobayashi T.",Comparison of the gut microbial community between obese and lean peoples using 16S gene sequencing in a Japanese population,Journal of clinical biochemistry and nutrition,2016,"16S sequence, Bacteroides, Firmicutes, SCFA, datamining",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,controls,obese,NA,10,10,NA,16S,34,Illumina,raw counts,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Table 2, 3, 4",10 January 2021,Marianthi Thomatos,"Fatima,WikiWorks",Gut microbial community comparison between obese and lean Japanese population,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia meyeri,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus",1783272|1239|909932|1843488|909930|904|187327;3379134|976|200643|171549|171550|239759;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|186801|3085636|186803|33042;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378|1379;1783272|1239|91061|186826|186828|117563|46124;3379134|1224|1236|91347|543|570|573;1783272|201174|84998|84999|1643824|2767353|1382;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257|341694;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|3085636|186803|841|301302;1783272|201174|1760|85006|1268|32207|43675;1783272|201174|1760|2037|2049|2529408|52773;1783272|1239|186801|3085636|186803|207244|649756,Complete,Fatima
bsdb:27499582/1/2,27499582,case-control,27499582,10.3164/jcbn.15-152,NA,"Andoh A., Nishida A., Takahashi K., Inatomi O., Imaeda H., Bamba S., Kito K., Sugimoto M. , Kobayashi T.",Comparison of the gut microbial community between obese and lean peoples using 16S gene sequencing in a Japanese population,Journal of clinical biochemistry and nutrition,2016,"16S sequence, Bacteroides, Firmicutes, SCFA, datamining",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,controls,obese,NA,10,10,NA,16S,34,Illumina,raw counts,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,"Table 2, 3, 4",10 January 2021,Marianthi Thomatos,"Fatima,WikiWorks",Gut microbial community comparison between obese and lean Japanese population,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania filiformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum desmolans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena fissicatena",3379134|976|200643|171549|815|816;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|3085636|186803|2719313|358743;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|526524|526525|128827|61170|61171;1783272|1239|186801|3085636|186803|1164882;1783272|201174|84998|84999|1643824|133925;1783272|1239|186801|186802|216572|292632;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|186801|186802|3085642|2048137|39484;1783272|1239|186801|3085636|186803|2005359|290055,Complete,Fatima
bsdb:27503374/1/1,27503374,prospective cohort,27503374,10.1186/s13073-016-0330-z,NA,"Chu D.M., Antony K.M., Ma J., Prince A.L., Showalter L., Moller M. , Aagaard K.M.",The early infant gut microbiome varies in association with a maternal high-fat diet,Genome medicine,2016,"High-fat diet, Maternal gestational diet, Microbiome, Neonatal microbiome development",Experiment 1,United States of America,Homo sapiens,Meconium,UBERON:0007109,High fat diet,EFO:0002757,nebowrns of maternal control,newborns of maternal high-fat diet,"To determine maternal dietary intake during pregnancy, each mother was asked by trained personnel at each sample collection time point to answer the Dietary Screener Questionnaire (DSQ), which was developed and validated by the National Health and Examination Survey (NHANES) program (2009–2010)",13,13,NA,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Rimsha Azhar,WikiWorks,Neonaatal meconium identified by  LEfSe betwen maternal high-fat or maternal control diet during pregnancy,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|186828|117563;1783272|1239|91061|186826|81852|1350,Complete,Shaimaa Elsafoury
bsdb:27503374/1/2,27503374,prospective cohort,27503374,10.1186/s13073-016-0330-z,NA,"Chu D.M., Antony K.M., Ma J., Prince A.L., Showalter L., Moller M. , Aagaard K.M.",The early infant gut microbiome varies in association with a maternal high-fat diet,Genome medicine,2016,"High-fat diet, Maternal gestational diet, Microbiome, Neonatal microbiome development",Experiment 1,United States of America,Homo sapiens,Meconium,UBERON:0007109,High fat diet,EFO:0002757,nebowrns of maternal control,newborns of maternal high-fat diet,"To determine maternal dietary intake during pregnancy, each mother was asked by trained personnel at each sample collection time point to answer the Dietary Screener Questionnaire (DSQ), which was developed and validated by the National Health and Examination Survey (NHANES) program (2009–2010)",13,13,NA,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Rimsha Azhar,WikiWorks,Neonaatal meconium identified by  LEfSe betwen maternal high-fat or maternal control diet during pregnancy,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas",3379134|1224|28216|80840|995019|40544;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|815|816;3379134|1224|28216|80840|80864|283,Complete,Shaimaa Elsafoury
bsdb:27503374/2/1,27503374,prospective cohort,27503374,10.1186/s13073-016-0330-z,NA,"Chu D.M., Antony K.M., Ma J., Prince A.L., Showalter L., Moller M. , Aagaard K.M.",The early infant gut microbiome varies in association with a maternal high-fat diet,Genome medicine,2016,"High-fat diet, Maternal gestational diet, Microbiome, Neonatal microbiome development",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,High fat diet,EFO:0002757,6 months babies control,6 months babies of maternal high-fat diet,"To determine maternal dietary intake during pregnancy, each mother was asked by trained personnel at each sample collection time point to answer the Dietary Screener Questionnaire (DSQ), which was developed and validated by the National Health and Examination Survey (NHANES) program (2009–2010)",75,75,NA,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5 + Supplemental Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,The impact of maternal gestational diet persists to 6 weeks of age,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",1783272|1239|91061|186826|1300|1301;3379134|1224|1236|91347|543|561,Complete,Shaimaa Elsafoury
bsdb:27503374/2/2,27503374,prospective cohort,27503374,10.1186/s13073-016-0330-z,NA,"Chu D.M., Antony K.M., Ma J., Prince A.L., Showalter L., Moller M. , Aagaard K.M.",The early infant gut microbiome varies in association with a maternal high-fat diet,Genome medicine,2016,"High-fat diet, Maternal gestational diet, Microbiome, Neonatal microbiome development",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,High fat diet,EFO:0002757,6 months babies control,6 months babies of maternal high-fat diet,"To determine maternal dietary intake during pregnancy, each mother was asked by trained personnel at each sample collection time point to answer the Dietary Screener Questionnaire (DSQ), which was developed and validated by the National Health and Examination Survey (NHANES) program (2009–2010)",75,75,NA,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5 + Supplemental Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,The impact of maternal gestational diet persists to 6 weeks of age,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
bsdb:27527070/1/1,27527070,case-control,27527070,10.1186/s12864-016-2965-y,NA,"Rajagopala S.V., Yooseph S., Harkins D.M., Moncera K.J., Zabokrtsky K.B., Torralba M.G., Tovchigrechko A., Highlander S.K., Pieper R., Sender L. , Nelson K.E.",Gastrointestinal microbial populations can distinguish pediatric and adolescent Acute Lymphoblastic Leukemia (ALL) at the time of disease diagnosis,BMC genomics,2016,"16S rRNA gene sequencing, Gastrointestinal microbiota, Pediatric leukemia, Ribosomal RNA, rRNA",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,healthy sibling control,adolescent ALL patient,Patients with pediatric and adolescent Acute Lymphoblastic Leukemia at time of disease diagnosis,23,28,NA,16S,123,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Text,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Mean microbial taxon abundances in Acute Lymphoblastic Leukemia Patient and Control groups (prior to chemotherapy treatment-  visit 1),increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,Claregrieve1
bsdb:27527070/1/2,27527070,case-control,27527070,10.1186/s12864-016-2965-y,NA,"Rajagopala S.V., Yooseph S., Harkins D.M., Moncera K.J., Zabokrtsky K.B., Torralba M.G., Tovchigrechko A., Highlander S.K., Pieper R., Sender L. , Nelson K.E.",Gastrointestinal microbial populations can distinguish pediatric and adolescent Acute Lymphoblastic Leukemia (ALL) at the time of disease diagnosis,BMC genomics,2016,"16S rRNA gene sequencing, Gastrointestinal microbiota, Pediatric leukemia, Ribosomal RNA, rRNA",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,healthy sibling control,adolescent ALL patient,Patients with pediatric and adolescent Acute Lymphoblastic Leukemia at time of disease diagnosis,23,28,NA,16S,123,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Text,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Mean microbial taxon abundances in Acute Lymphoblastic Leukemia  Patient and Control groups (prior to chemotherapy treatment-  visit 1),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803,Complete,Claregrieve1
bsdb:27543211/1/1,27543211,randomized controlled trial,27543211,10.1016/j.jaad.2016.04.066,NA,"Gonzalez M.E., Schaffer J.V., Orlow S.J., Gao Z., Li H., Alekseyenko A.V. , Blaser M.J.",Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis,Journal of the American Academy of Dermatology,2016,"16S sequencing, Staphylococcus aureus, atopic dermatitis, bleach baths, cutaneous microbiome, quantitative polymerase chain reaction, topical corticosteroids",Experiment 1,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,healthy control,atopic dermatitis,child between the age of 3 months-5 years with moderate to severe atopic dermatitis defined as an investigator’s global assessment (IGA) score of 3 or 4 (0–4 scale),11,21,2 weeks,16S,4,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 7a, 7b",10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between baseline atopic dermatitis lesional sites versus control skin,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|1239|91061;1783272|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:27543211/1/2,27543211,randomized controlled trial,27543211,10.1016/j.jaad.2016.04.066,NA,"Gonzalez M.E., Schaffer J.V., Orlow S.J., Gao Z., Li H., Alekseyenko A.V. , Blaser M.J.",Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis,Journal of the American Academy of Dermatology,2016,"16S sequencing, Staphylococcus aureus, atopic dermatitis, bleach baths, cutaneous microbiome, quantitative polymerase chain reaction, topical corticosteroids",Experiment 1,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,healthy control,atopic dermatitis,child between the age of 3 months-5 years with moderate to severe atopic dermatitis defined as an investigator’s global assessment (IGA) score of 3 or 4 (0–4 scale),11,21,2 weeks,16S,4,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 7a, 7b",10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between baseline atopic dermatitis lesional sites versus control skin,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Actinomycetota|c__Rubrobacteria,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus",1783272|201174|1760;3379134|1224|28211;3379134|976|200643;3379134|1224|28216;1783272|1239|186801;1783272|201174|84998;1783272|1239|526524;1783272|201174|84995;3379134|74201|203494;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|80840|119060|106589,Complete,Claregrieve1
bsdb:27543211/2/1,27543211,randomized controlled trial,27543211,10.1016/j.jaad.2016.04.066,NA,"Gonzalez M.E., Schaffer J.V., Orlow S.J., Gao Z., Li H., Alekseyenko A.V. , Blaser M.J.",Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis,Journal of the American Academy of Dermatology,2016,"16S sequencing, Staphylococcus aureus, atopic dermatitis, bleach baths, cutaneous microbiome, quantitative polymerase chain reaction, topical corticosteroids",Experiment 2,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,baseline,atopic dermatitis after treatment with TCS + Bleach,child with moderate to severe atopic dermatitis after treatment with TCS + bleach,9,9,2 weeks,16S,4,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 7c,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance for children with atopic dermatitis randomized to the TCS + bleach treatment group at baseline and after treatment,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|1224|1236|2887326|468|469;1783272|201174|1760|85007|1653|1716;3379134|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:27543211/2/2,27543211,randomized controlled trial,27543211,10.1016/j.jaad.2016.04.066,NA,"Gonzalez M.E., Schaffer J.V., Orlow S.J., Gao Z., Li H., Alekseyenko A.V. , Blaser M.J.",Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis,Journal of the American Academy of Dermatology,2016,"16S sequencing, Staphylococcus aureus, atopic dermatitis, bleach baths, cutaneous microbiome, quantitative polymerase chain reaction, topical corticosteroids",Experiment 2,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,baseline,atopic dermatitis after treatment with TCS + Bleach,child with moderate to severe atopic dermatitis after treatment with TCS + bleach,9,9,2 weeks,16S,4,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 7c,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance for children with atopic dermatitis randomized to the TCS + bleach treatment group at baseline and after treatment,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:27543211/3/1,27543211,randomized controlled trial,27543211,10.1016/j.jaad.2016.04.066,NA,"Gonzalez M.E., Schaffer J.V., Orlow S.J., Gao Z., Li H., Alekseyenko A.V. , Blaser M.J.",Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis,Journal of the American Academy of Dermatology,2016,"16S sequencing, Staphylococcus aureus, atopic dermatitis, bleach baths, cutaneous microbiome, quantitative polymerase chain reaction, topical corticosteroids",Experiment 3,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,baseline,atopic dermatitis after treatment with TCS only,child with moderate to severe atopic dermatitis after treatment with TCS only,9,9,2 weeks,16S,4,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 7d,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance for children with atopic dermatitis randomized to the TCS only treatment group at baseline and after treatment,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|1224|1236|2887326|468|469;1783272|201174|1760|85007|1653|1716;3379134|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:27543211/3/2,27543211,randomized controlled trial,27543211,10.1016/j.jaad.2016.04.066,NA,"Gonzalez M.E., Schaffer J.V., Orlow S.J., Gao Z., Li H., Alekseyenko A.V. , Blaser M.J.",Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis,Journal of the American Academy of Dermatology,2016,"16S sequencing, Staphylococcus aureus, atopic dermatitis, bleach baths, cutaneous microbiome, quantitative polymerase chain reaction, topical corticosteroids",Experiment 3,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,baseline,atopic dermatitis after treatment with TCS only,child with moderate to severe atopic dermatitis after treatment with TCS only,9,9,2 weeks,16S,4,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 7d,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance for children with atopic dermatitis randomized to the TCS only treatment group at baseline and after treatment,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:27558272/1/1,27558272,prospective cohort,27558272,10.1038/srep31775,NA,"Levin A.M., Sitarik A.R., Havstad S.L., Fujimura K.E., Wegienka G., Cassidy-Bushrow A.E., Kim H., Zoratti E.M., Lukacs N.W., Boushey H.A., Ownby D.R., Lynch S.V. , Johnson C.C.","Joint effects of pregnancy, sociocultural, and environmental factors on early life gut microbiome structure and diversity",Scientific reports,2016,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Risk factor,EFO:0003919,Neonates (median age = 1.2 months),Infants (median age = 6.6 months),Infants (median age: 6.6 months) children from a Detroit-based birth cohort,130,168,NA,16S,4,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,TRUE,NA,NA,"age,breast feeding,delivery procedure,education level,household income,marital status,smoking status",increased,NA,NA,NA,NA,increased,Signature 1,"FIGURE 5 , FIGURE 6",13 June 2022,Kaluifeanyi101,"Kaluifeanyi101,Peace Sandy,WikiWorks","Top genera are significantly associated with each factor retained in multi-factor neonatal gut microbiome composition models. For plotting purposes, “top” genera for each factor were defined using two characteristics: (1) the number of taxa significantly associated with it (to avoid spurious findings) and (2) how “discriminatory” the genera was, defined by consistency in the direction of taxa-specific associations. Each 
factor displays up to the top ten genera that best discriminated each factor, given the genera had at least 5 significant taxa. Abbreviations: ETS, environmental tobacco smoke; NSV, neonatal study visit at 1-month of age.

Top genera significantly associated with each factor retained in multi-factor models of infant gut microbiome composition.
For plotting purposes, “top” genera for each factor were defined using two characteristics: (1) the number of taxa significantly associated with it (to avoid spurious findings) and (2) how “discriminatory” the genera was, defined by consistency in the direction of taxa-specific associations. Each factor displays up to the top ten genera that best discriminated each factor, given the genera had at least 5 significant taxa. Abbreviations: BMI, body mass index; ISV, infant study visit at 6-months of age.",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|74201|203494|48461|1647988|239934;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|186806|1730;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1357;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|1385|90964|1279;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|189330;1783272|1239|909932|909929|1843491|158846;3379134|976|200643|171549|171552|577309;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|3085636|186803|2383;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005520|156973;1783272|1239|909932|1843489|31977|29465,Complete,Peace Sandy
bsdb:27558272/1/2,27558272,prospective cohort,27558272,10.1038/srep31775,NA,"Levin A.M., Sitarik A.R., Havstad S.L., Fujimura K.E., Wegienka G., Cassidy-Bushrow A.E., Kim H., Zoratti E.M., Lukacs N.W., Boushey H.A., Ownby D.R., Lynch S.V. , Johnson C.C.","Joint effects of pregnancy, sociocultural, and environmental factors on early life gut microbiome structure and diversity",Scientific reports,2016,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Risk factor,EFO:0003919,Neonates (median age = 1.2 months),Infants (median age = 6.6 months),Infants (median age: 6.6 months) children from a Detroit-based birth cohort,130,168,NA,16S,4,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,TRUE,NA,NA,"age,breast feeding,delivery procedure,education level,household income,marital status,smoking status",increased,NA,NA,NA,NA,increased,Signature 2,"FIGURE 5 , FIGURE 6",13 June 2022,Kaluifeanyi101,"Kaluifeanyi101,Peace Sandy,WikiWorks","Top genera are significantly associated with each factor retained in multi-factor neonatal gut microbiome composition models. For plotting purposes, “top” genera for each factor were defined using two characteristics: (1) the number of taxa significantly associated with it (to avoid spurious findings) and (2) how “discriminatory” the genera was, defined by consistency in the direction of taxa-specific associations. Each factor displays up to the top ten genera that best discriminated each factor, given the genera had at least 5 significant taxa. Abbreviations: ETS, environmental tobacco smoke; NSV, neonatal study visit at 1-month of age.

Top genera significantly associated with each factor retained in multi-factor models of infant gut microbiome composition. For plotting purposes, “top” genera for each factor were defined using two characteristics: (1) the number of taxa significantly associated with it (to avoid spurious findings) and (2) how “discriminatory” the genera was, defined by consistency in the direction of taxa-specific associations. Each factor displays up to the top ten genera that best discriminated each factor, given the genera had at least 5 significant taxa. Abbreviations: BMI, body mass index; ISV, infant study visit at 6-months of age.",decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|74201|203494|48461|1647988|239934;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|186806|1730;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1357;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|1385|90964|1279;1783272|1239|909932|1843489|31977|906;1783272|201174|1760|2037|2049|184869;1783272|1239|186801|186802|216572|119852;1783272|1239|91061|186826|1300|1301,Complete,Peace Sandy
bsdb:27562258/1/1,27562258,case-control,27562258,10.1038/nmicrobiol.2016.106,https://www.nature.com/articles/nmicrobiol2016106,"Chng K.R., Tay A.S., Li C., Ng A.H., Wang J., Suri B.K., Matta S.A., McGovern N., Janela B., Wong X.F., Sio Y.Y., Au B.V., Wilm A., De Sessions P.F., Lim T.C., Tang M.B., Ginhoux F., Connolly J.E., Lane E.B., Chew F.T., Common J.E. , Nagarajan N.",Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare,Nature microbiology,2016,NA,Experiment 1,Singapore,Homo sapiens,Skin epithelium,UBERON:0019204,Eczema,HP:0000964,Healthy controls,Atopic dermatitis case group,Atopic dermatitis case group with volunteers reporting past atopic dermatitis episodes,15,19,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 5,30 March 2023,Ufuoma Ejite,"Ufuoma Ejite,Lwaldron,WikiWorks",Differential microbial abundance between controls and AD case group,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Lwaldron
bsdb:27562258/1/2,27562258,case-control,27562258,10.1038/nmicrobiol.2016.106,https://www.nature.com/articles/nmicrobiol2016106,"Chng K.R., Tay A.S., Li C., Ng A.H., Wang J., Suri B.K., Matta S.A., McGovern N., Janela B., Wong X.F., Sio Y.Y., Au B.V., Wilm A., De Sessions P.F., Lim T.C., Tang M.B., Ginhoux F., Connolly J.E., Lane E.B., Chew F.T., Common J.E. , Nagarajan N.",Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare,Nature microbiology,2016,NA,Experiment 1,Singapore,Homo sapiens,Skin epithelium,UBERON:0019204,Eczema,HP:0000964,Healthy controls,Atopic dermatitis case group,Atopic dermatitis case group with volunteers reporting past atopic dermatitis episodes,15,19,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 5,30 March 2023,Ufuoma Ejite,"Ufuoma Ejite,Lwaldron,WikiWorks",Differential microbial abundance between controls and AD case group,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus",1783272|201174|1760|85006|145357|57495;3379134|1224|28211|356|119045|407;3384194|1297|188787|118964|183710|1298,Complete,Lwaldron
bsdb:27562258/2/1,27562258,case-control,27562258,10.1038/nmicrobiol.2016.106,https://www.nature.com/articles/nmicrobiol2016106,"Chng K.R., Tay A.S., Li C., Ng A.H., Wang J., Suri B.K., Matta S.A., McGovern N., Janela B., Wong X.F., Sio Y.Y., Au B.V., Wilm A., De Sessions P.F., Lim T.C., Tang M.B., Ginhoux F., Connolly J.E., Lane E.B., Chew F.T., Common J.E. , Nagarajan N.",Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare,Nature microbiology,2016,NA,Experiment 2,Singapore,Homo sapiens,Skin epithelium,UBERON:0019204,Eczema,HP:0000964,Females (controls),Females (cases),Atopic dermatitis (AD) case females,7,11,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 6B,30 March 2023,Ufuoma Ejite,"Ufuoma Ejite,Lwaldron,WikiWorks",Differential microbial abundance between female controls and female AD case group,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium",1783272|201174|1760|85006|145357|57495;3379134|1224|28211|356|119045|407,Complete,Lwaldron
bsdb:27562258/3/1,27562258,case-control,27562258,10.1038/nmicrobiol.2016.106,https://www.nature.com/articles/nmicrobiol2016106,"Chng K.R., Tay A.S., Li C., Ng A.H., Wang J., Suri B.K., Matta S.A., McGovern N., Janela B., Wong X.F., Sio Y.Y., Au B.V., Wilm A., De Sessions P.F., Lim T.C., Tang M.B., Ginhoux F., Connolly J.E., Lane E.B., Chew F.T., Common J.E. , Nagarajan N.",Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare,Nature microbiology,2016,NA,Experiment 3,Singapore,Homo sapiens,Skin epithelium,UBERON:0019204,Eczema,HP:0000964,Males (control),Males (case),Atopic dermatitis (AD) case males,8,8,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 6B,30 March 2023,Ufuoma Ejite,"Ufuoma Ejite,Lwaldron,WikiWorks",Differential microbial abundance between male controls and male AD case group,decreased,"k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus",3384194|1297|188787|118964|183710|1298;1783272|201174|1760|85006|145357|57495,Complete,Lwaldron
bsdb:27562258/3/2,27562258,case-control,27562258,10.1038/nmicrobiol.2016.106,https://www.nature.com/articles/nmicrobiol2016106,"Chng K.R., Tay A.S., Li C., Ng A.H., Wang J., Suri B.K., Matta S.A., McGovern N., Janela B., Wong X.F., Sio Y.Y., Au B.V., Wilm A., De Sessions P.F., Lim T.C., Tang M.B., Ginhoux F., Connolly J.E., Lane E.B., Chew F.T., Common J.E. , Nagarajan N.",Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare,Nature microbiology,2016,NA,Experiment 3,Singapore,Homo sapiens,Skin epithelium,UBERON:0019204,Eczema,HP:0000964,Males (control),Males (case),Atopic dermatitis (AD) case males,8,8,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 6B,30 March 2023,Ufuoma Ejite,"Ufuoma Ejite,Lwaldron,WikiWorks",Differential microbial abundance between male controls and male AD case group,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",1783272|1239|91061|186826|1300|1301;1783272|1239|91061|1385|539738|1378;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|135625|712|724,Complete,Lwaldron
bsdb:27562258/4/1,27562258,case-control,27562258,10.1038/nmicrobiol.2016.106,https://www.nature.com/articles/nmicrobiol2016106,"Chng K.R., Tay A.S., Li C., Ng A.H., Wang J., Suri B.K., Matta S.A., McGovern N., Janela B., Wong X.F., Sio Y.Y., Au B.V., Wilm A., De Sessions P.F., Lim T.C., Tang M.B., Ginhoux F., Connolly J.E., Lane E.B., Chew F.T., Common J.E. , Nagarajan N.",Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare,Nature microbiology,2016,NA,Experiment 4,Singapore,Homo sapiens,Skin epithelium,UBERON:0019204,Eczema,HP:0000964,Normal control,AD cases with no reported cream usage,AD cases with no reported cream usage (no emollient creams or topical corticosteroids),15,11,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 6C,30 March 2023,Ufuoma Ejite,"Ufuoma Ejite,Lwaldron,WikiWorks",Differential microbial abundance between controls and AD case group with no cream usage,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium",1783272|201174|1760|85006|145357|57495;3379134|1224|28211|356|119045|407,Complete,Lwaldron
bsdb:27562258/4/2,27562258,case-control,27562258,10.1038/nmicrobiol.2016.106,https://www.nature.com/articles/nmicrobiol2016106,"Chng K.R., Tay A.S., Li C., Ng A.H., Wang J., Suri B.K., Matta S.A., McGovern N., Janela B., Wong X.F., Sio Y.Y., Au B.V., Wilm A., De Sessions P.F., Lim T.C., Tang M.B., Ginhoux F., Connolly J.E., Lane E.B., Chew F.T., Common J.E. , Nagarajan N.",Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare,Nature microbiology,2016,NA,Experiment 4,Singapore,Homo sapiens,Skin epithelium,UBERON:0019204,Eczema,HP:0000964,Normal control,AD cases with no reported cream usage,AD cases with no reported cream usage (no emollient creams or topical corticosteroids),15,11,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 6C,30 March 2023,Ufuoma Ejite,"Ufuoma Ejite,Lwaldron,WikiWorks",Differential microbial abundance between controls and AD case group with no cream usage,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",1783272|1239|91061|186826|1300|1301;1783272|1239|91061|1385|539738|1378;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|135625|712|724,Complete,Lwaldron
bsdb:27591074/1/1,27591074,case-control,27591074,10.1016/j.parkreldis.2016.08.019,NA,"Unger M.M., Spiegel J., Dillmann K.U., Grundmann D., Philippeit H., Bürmann J., Faßbender K., Schwiertz A. , Schäfer K.H.",Short chain fatty acids and gut microbiota differ between patients with Parkinson's disease and age-matched controls,Parkinsonism & related disorders,2016,"Butyrate, Enteric nervous system, Gut microbiota, Parkinson's disease, Short chain fatty acids",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control (control matched- CM),Parkinson's disease group,Patients with Parkinson's disease,34,34,3 months,PCR,NA,RT-qPCR,relative abundances,Kruskall-Wallis,0.01,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,10 March 2024,EniolaAde,"EniolaAde,Peace Sandy,WikiWorks",significant taxa observed in the fecal microbiota of patients with Parkinson's disease compared with healthy control matched group (CM),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",1783272|201174|1760|85004|31953|1678|41200;3379134|1224|1236|91347|543,Complete,Peace Sandy
bsdb:27591074/1/2,27591074,case-control,27591074,10.1016/j.parkreldis.2016.08.019,NA,"Unger M.M., Spiegel J., Dillmann K.U., Grundmann D., Philippeit H., Bürmann J., Faßbender K., Schwiertz A. , Schäfer K.H.",Short chain fatty acids and gut microbiota differ between patients with Parkinson's disease and age-matched controls,Parkinsonism & related disorders,2016,"Butyrate, Enteric nervous system, Gut microbiota, Parkinson's disease, Short chain fatty acids",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control (control matched- CM),Parkinson's disease group,Patients with Parkinson's disease,34,34,3 months,PCR,NA,RT-qPCR,relative abundances,Kruskall-Wallis,0.01,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1,10 March 2024,EniolaAde,"EniolaAde,Peace Sandy,ChiomaBlessing,WikiWorks",significant taxa observed in the fecal microbiota of patients with Parkinson's disease compared with healthy control matched group (CM),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus",3379134|976|200643;1783272|1239|186801|186802|216572|216851|853;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|1300|1357,Complete,Peace Sandy
bsdb:27591074/2/1,27591074,case-control,27591074,10.1016/j.parkreldis.2016.08.019,NA,"Unger M.M., Spiegel J., Dillmann K.U., Grundmann D., Philippeit H., Bürmann J., Faßbender K., Schwiertz A. , Schäfer K.H.",Short chain fatty acids and gut microbiota differ between patients with Parkinson's disease and age-matched controls,Parkinsonism & related disorders,2016,"Butyrate, Enteric nervous system, Gut microbiota, Parkinson's disease, Short chain fatty acids",Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control group (control young-CY),Parkinson's disease group,Patients with Parkinson's disease,10,34,3 months,PCR,NA,RT-qPCR,relative abundances,Kruskall-Wallis,0.01,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,10 March 2024,EniolaAde,"EniolaAde,Peace Sandy,WikiWorks",significant taxa observed in the fecal microbiota of patients with Parkinson's disease compared with healthy control young group (CY),decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,3379134|976|200643,Complete,Peace Sandy
bsdb:27609659/1/1,27609659,prospective cohort,27609659,10.1016/j.jaci.2016.07.029,NA,"Kennedy E.A., Connolly J., Hourihane J.O., Fallon P.G., McLean W.H.I., Murray D., Jo J.H., Segre J.A., Kong H.H. , Irvine A.D.",Skin microbiome before development of atopic dermatitis: Early colonization with commensal staphylococci at 2 months is associated with a lower risk of atopic dermatitis at 1 year,The Journal of allergy and clinical immunology,2017,"16S sequencing, Staphylococcus aureus, atopic dermatitis, longitudinal birth cohort, microbiome, skin",Experiment 1,Ireland,Homo sapiens,Skin of forearm,UBERON:0003403,Atopic eczema,EFO:0000274,healthy control,atopic dermatitis,child with atopic dermatis at month 12 diagnosed by experienced health care personnel using the UK Working Party Diagnostic Criteria,10,10,NA,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4b,10 January 2021,Lucy Mellor,WikiWorks,Relative abundance of major taxa in antecubital fossa at month 2 between subjects that went on to be affected with atopic dermatits at month 12 and those who went on to be unaffected,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,NA
bsdb:27625705/1/1,27625705,case-control,27625705,10.1186/s13099-016-0124-2,NA,"Aly A.M., Adel A., El-Gendy A.O., Essam T.M. , Aziz R.K.",Gut microbiome alterations in patients with stage 4 hepatitis C,Gut pathogens,2016,"Gastro-intestinal tract, High-throughput sequencing, Infectious diseases, Liver disease, Microbiome, Next-generation sequencing, Virology",Experiment 1,Egypt,Homo sapiens,Feces,UBERON:0001988,Hepatitis,NA,male healthy controls,HCV stage 4 male patients,Not stated,8,6,3 months,16S,4,Illumina,relative abundances,LEfSe,0.1,FALSE,2,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,Table 2 and Fig 5,10 January 2021,Shaimaa Elsafoury,WikiWorks,Genera that are statistically signifcantly diferent between the two groups hcv patients and healthy participants  (non-parametric t test). All participants were male.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota",3379134|1224|1236|2887326|468|469;3379134|976|200643|171549|171552|838;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843488|909930|33024;3379134|1224|1236|72274;3379134|1224|1236|2887326|468;3379134|976|200643|171549;3379134|976|200643;3379134|976,Complete,Shaimaa Elsafoury
bsdb:27625705/1/2,27625705,case-control,27625705,10.1186/s13099-016-0124-2,NA,"Aly A.M., Adel A., El-Gendy A.O., Essam T.M. , Aziz R.K.",Gut microbiome alterations in patients with stage 4 hepatitis C,Gut pathogens,2016,"Gastro-intestinal tract, High-throughput sequencing, Infectious diseases, Liver disease, Microbiome, Next-generation sequencing, Virology",Experiment 1,Egypt,Homo sapiens,Feces,UBERON:0001988,Hepatitis,NA,male healthy controls,HCV stage 4 male patients,Not stated,8,6,3 months,16S,4,Illumina,relative abundances,LEfSe,0.1,FALSE,2,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,Table 2 and Fig 5,10 January 2021,Shaimaa Elsafoury,WikiWorks,Genera that are statistically signifcantly diferent between the two groups hcv patients and healthy participants  (non-parametric t test). All participants were male.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae|g__Pseudoalteromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales,k__Pseudomonadati|p__Lentisphaerota",3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|1853231|574697;1783272|201174;1783272|201174|1760;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004;1783272|201174|1760|85004|31953;3379134|976|200643|171549|171551;1783272|544448|31969;1783272|544448;3379134|1224|1236|135622|267888|53246;3379134|1224|1236|135622|267888;3379134|1224|1236|135623;1783272|1239|909932|1843489|31977|39948;3379134|256845|1313211|278082|255528;3379134|256845|1313211|278082;3379134|256845,Complete,Shaimaa Elsafoury
bsdb:27634868/1/1,27634868,case-control,27634868,10.1042/CS20160349,NA,"Stiemsma L.T., Arrieta M.C., Dimitriu P.A., Cheng J., Thorson L., Lefebvre D.L., Azad M.B., Subbarao P., Mandhane P., Becker A., Sears M.R., Kollmann T.R., Mohn W.W., Finlay B.B. , Turvey S.E.",Shifts in Lachnospira and Clostridium sp. in the 3-month stool microbiome are associated with preschool age asthma,"Clinical science (London, England : 1979)",2016,"atopic disease, dysbiosis, gut microbiota, hygiene hypothesis, microflora hypothesis",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,healthy controls,asthma at 3 months,physician diagnosis of asthma by 4 years of age or was prescribed inhaled asthma medications (inhaled corticosteroids or bronchodilators) from 3 to 4 years of age,37,39,NA,16S,3,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"antibiotic exposure,cesarean section,feeding practices,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 1a,10 January 2021,Lucy Mellor,WikiWorks,Differentially abundant OTUs Identified by Deseq2 analysis at 3 months,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",1783272|1239;1783272|1239|186801|186802|31979,Complete,Folakunmi
bsdb:27634868/1/2,27634868,case-control,27634868,10.1042/CS20160349,NA,"Stiemsma L.T., Arrieta M.C., Dimitriu P.A., Cheng J., Thorson L., Lefebvre D.L., Azad M.B., Subbarao P., Mandhane P., Becker A., Sears M.R., Kollmann T.R., Mohn W.W., Finlay B.B. , Turvey S.E.",Shifts in Lachnospira and Clostridium sp. in the 3-month stool microbiome are associated with preschool age asthma,"Clinical science (London, England : 1979)",2016,"atopic disease, dysbiosis, gut microbiota, hygiene hypothesis, microflora hypothesis",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,healthy controls,asthma at 3 months,physician diagnosis of asthma by 4 years of age or was prescribed inhaled asthma medications (inhaled corticosteroids or bronchodilators) from 3 to 4 years of age,37,39,NA,16S,3,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"antibiotic exposure,cesarean section,feeding practices,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 1a,10 January 2021,Lucy Mellor,WikiWorks,Differentially abundant OTUs Identified by Deseq2 analysis at 3 months,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,1783272|1239|186801|186802,Complete,Folakunmi
bsdb:27634868/2/1,27634868,case-control,27634868,10.1042/CS20160349,NA,"Stiemsma L.T., Arrieta M.C., Dimitriu P.A., Cheng J., Thorson L., Lefebvre D.L., Azad M.B., Subbarao P., Mandhane P., Becker A., Sears M.R., Kollmann T.R., Mohn W.W., Finlay B.B. , Turvey S.E.",Shifts in Lachnospira and Clostridium sp. in the 3-month stool microbiome are associated with preschool age asthma,"Clinical science (London, England : 1979)",2016,"atopic disease, dysbiosis, gut microbiota, hygiene hypothesis, microflora hypothesis",Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,healthy controls,asthma at 1 year,physician diagnosis of asthma by 4 years of age or was prescribed inhaled asthma medications (inhaled corticosteroids or bronchodilators) from 3 to 4 years of age,37,39,NA,16S,3,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"antibiotic exposure,delivery procedure,feeding practices,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 1b,10 January 2021,Lucy Mellor,WikiWorks,Differentially abundant OTUs Identified by Deseq2 analysis at 1 year,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",1783272|1239|186801|3085636|186803;1783272|201174|1760|85006|1268|32207,Complete,Folakunmi
bsdb:27634868/2/2,27634868,case-control,27634868,10.1042/CS20160349,NA,"Stiemsma L.T., Arrieta M.C., Dimitriu P.A., Cheng J., Thorson L., Lefebvre D.L., Azad M.B., Subbarao P., Mandhane P., Becker A., Sears M.R., Kollmann T.R., Mohn W.W., Finlay B.B. , Turvey S.E.",Shifts in Lachnospira and Clostridium sp. in the 3-month stool microbiome are associated with preschool age asthma,"Clinical science (London, England : 1979)",2016,"atopic disease, dysbiosis, gut microbiota, hygiene hypothesis, microflora hypothesis",Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,healthy controls,asthma at 1 year,physician diagnosis of asthma by 4 years of age or was prescribed inhaled asthma medications (inhaled corticosteroids or bronchodilators) from 3 to 4 years of age,37,39,NA,16S,3,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"antibiotic exposure,delivery procedure,feeding practices,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 1b,23 January 2024,Folakunmi,"Folakunmi,WikiWorks",Differentially abundant OTUs Identified by Deseq2 analysis at 1 year,decreased,NA,NA,Complete,Folakunmi
bsdb:27640125/1/1,27640125,"cross-sectional observational, not case-control",27640125,10.1186/s40168-016-0195-9,NA,"Crespo-Salgado J., Vehaskari V.M., Stewart T., Ferris M., Zhang Q., Wang G., Blanchard E.E., Taylor C.M., Kallash M., Greenbaum L.A. , Aviles D.H.",Intestinal microbiota in pediatric patients with end stage renal disease: a Midwest Pediatric Nephrology Consortium study,Microbiome,2016,"Children, End-stage renal disease, Inflammation, Intestinal microbiota, Pyrosequencing, Uremic toxins",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,healthy controls,peritoneal dialysis,"4 groups of pediatric patients (age 2-18), hemodialysis, peritoneal dialysis, kidney transplant, healthy controls",13,8,1 month,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,age,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,Figure 2,10 January 2021,Rimsha Azhar,"WikiWorks,Atrayees,ChiomaBlessing",Relative abundance of the four dominant phyla of the intestinal microbiota in peritoneal dialysis group VS healthy control group,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota",1783272|201174;1783272|1239,Complete,Atrayees
bsdb:27640125/1/2,27640125,"cross-sectional observational, not case-control",27640125,10.1186/s40168-016-0195-9,NA,"Crespo-Salgado J., Vehaskari V.M., Stewart T., Ferris M., Zhang Q., Wang G., Blanchard E.E., Taylor C.M., Kallash M., Greenbaum L.A. , Aviles D.H.",Intestinal microbiota in pediatric patients with end stage renal disease: a Midwest Pediatric Nephrology Consortium study,Microbiome,2016,"Children, End-stage renal disease, Inflammation, Intestinal microbiota, Pyrosequencing, Uremic toxins",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,healthy controls,peritoneal dialysis,"4 groups of pediatric patients (age 2-18), hemodialysis, peritoneal dialysis, kidney transplant, healthy controls",13,8,1 month,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,age,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,Figure 2,14 July 2023,Atrayees,"Atrayees,ChiomaBlessing,WikiWorks",Relative abundance of the four dominant phyla of the intestinal microbiota in peritoneal dialysis group VS healthy control group,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,Atrayees
bsdb:27640125/2/1,27640125,"cross-sectional observational, not case-control",27640125,10.1186/s40168-016-0195-9,NA,"Crespo-Salgado J., Vehaskari V.M., Stewart T., Ferris M., Zhang Q., Wang G., Blanchard E.E., Taylor C.M., Kallash M., Greenbaum L.A. , Aviles D.H.",Intestinal microbiota in pediatric patients with end stage renal disease: a Midwest Pediatric Nephrology Consortium study,Microbiome,2016,"Children, End-stage renal disease, Inflammation, Intestinal microbiota, Pyrosequencing, Uremic toxins",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,healthy controls,hemodialysis,"4 groups of pediatric patients (age 2-18), hemodialysis, peritoneal dialysis, kidney transplant, healthy controls",13,8,1 month,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,age,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,Figure 2,10 January 2021,Rimsha Azhar,"WikiWorks,Atrayees,ChiomaBlessing",Relative abundance of the four dominant phyla of the intestinal microbiota in hemodialysis  group VS healthy control group,increased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Atrayees
bsdb:27640125/3/1,27640125,"cross-sectional observational, not case-control",27640125,10.1186/s40168-016-0195-9,NA,"Crespo-Salgado J., Vehaskari V.M., Stewart T., Ferris M., Zhang Q., Wang G., Blanchard E.E., Taylor C.M., Kallash M., Greenbaum L.A. , Aviles D.H.",Intestinal microbiota in pediatric patients with end stage renal disease: a Midwest Pediatric Nephrology Consortium study,Microbiome,2016,"Children, End-stage renal disease, Inflammation, Intestinal microbiota, Pyrosequencing, Uremic toxins",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,peritoneal dialysis,hemodialysis,"4 groups of pediatric patients (age 2-18), hemodialysis, peritoneal dialysis, kidney transplant, healthy controls",8,8,1 month,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,age,NA,NA,NA,increased,NA,NA,increased,Signature 1,Figure 2,10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Relative abundance of the four dominant phyla of the intestinal microbiota in the hemodialysis group VS peritoneal dialysis group,decreased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,Atrayees
bsdb:27640125/3/2,27640125,"cross-sectional observational, not case-control",27640125,10.1186/s40168-016-0195-9,NA,"Crespo-Salgado J., Vehaskari V.M., Stewart T., Ferris M., Zhang Q., Wang G., Blanchard E.E., Taylor C.M., Kallash M., Greenbaum L.A. , Aviles D.H.",Intestinal microbiota in pediatric patients with end stage renal disease: a Midwest Pediatric Nephrology Consortium study,Microbiome,2016,"Children, End-stage renal disease, Inflammation, Intestinal microbiota, Pyrosequencing, Uremic toxins",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,peritoneal dialysis,hemodialysis,"4 groups of pediatric patients (age 2-18), hemodialysis, peritoneal dialysis, kidney transplant, healthy controls",8,8,1 month,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,age,NA,NA,NA,increased,NA,NA,increased,Signature 2,Figure 2,14 July 2023,Atrayees,"Atrayees,ChiomaBlessing,WikiWorks",Relative abundance of the four dominant phyla of the intestinal microbiota in the hemodialysis group VS peritoneal dialysis group,increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia",1783272|201174;3379134|976|200643,Complete,Atrayees
bsdb:27672054/1/1,27672054,case-control,27672054,10.1158/1055-9965.EPI-16-0337,NA,"Hale V.L., Chen J., Johnson S., Harrington S.C., Yab T.C., Smyrk T.C., Nelson H., Boardman L.A., Druliner B.R., Levin T.R., Rex D.K., Ahnen D.J., Lance P., Ahlquist D.A. , Chia N.",Shifts in the Fecal Microbiota Associated with Adenomatous Polyps,"Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology",2017,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,Non-Adenoma,Adenoma,"Patients with colorectal adenoma as identified during a screening colonoscopy. Fecal
samples from patients in which at least one adenoma > 1 cm was identified were included in the “adenoma” group.",547,233,NA,16S,345,Illumina,raw counts,Linear Regression,0.2,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2B,1 July 2022,Jeshudy,"Jeshudy,Suwaiba,WikiWorks",−log(P value) of these taxa’s differential abundance.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,c__Deltaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|1224|28216|80840|506;3379134|976|200643|171549;3379134|976;3379134|1224|28216;3379134|200940|3031449|213115|194924|35832;3379134|1224|28216|80840;28221;1783272|1239|186801|3082720|543314|86331;3379134|1224|28216|80840|995019|40544,Complete,NA
bsdb:27672054/1/2,27672054,case-control,27672054,10.1158/1055-9965.EPI-16-0337,NA,"Hale V.L., Chen J., Johnson S., Harrington S.C., Yab T.C., Smyrk T.C., Nelson H., Boardman L.A., Druliner B.R., Levin T.R., Rex D.K., Ahnen D.J., Lance P., Ahlquist D.A. , Chia N.",Shifts in the Fecal Microbiota Associated with Adenomatous Polyps,"Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology",2017,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,Non-Adenoma,Adenoma,"Patients with colorectal adenoma as identified during a screening colonoscopy. Fecal
samples from patients in which at least one adenoma > 1 cm was identified were included in the “adenoma” group.",547,233,NA,16S,345,Illumina,raw counts,Linear Regression,0.2,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2B,1 July 2022,Jeshudy,"Jeshudy,Suwaiba,WikiWorks",−log(P value) of these taxa’s differential abundance.,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Anaerosomatales|s__unidentified Actinomycete OPB41",1783272|201174;1783272|1239|91061;1783272|1239;1783272|201174|1760|85004;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1117;3379134|1224|1236|135625|712|724;3379134|256845|1313211;1783272|544448|31969;1783272|544448;3379134|1224|1236|135625|712;3379134|1224|1236|135625;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801;1783272|201174|84998|2997383|68904,Complete,NA
bsdb:27725146/1/1,27725146,NA,27725146,10.1053/j.gastro.2016.09.049,NA,"Tap J., Derrien M., Törnblom H., Brazeilles R., Cools-Portier S., Doré J., Störsrud S., Le Nevé B., Öhman L. , Simrén M.",Identification of an Intestinal Microbiota Signature Associated With Severity of Irritable Bowel Syndrome,Gastroenterology,2017,"Bacteria, Functional Bowel Disorder, Microbiome",Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS,Patients diagnosed with irritable bowel syndrome according to Rome III criteria.,149,149,Yes,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Results section; differential abundance analysis (IBS vs healthy controls),8 January 2026,Aqc576444,Aqc576444,"IBS patients showed a significant decrease in the relative abundance of butyrate-producing genera compared to healthy controls, including Faecalibacterium and Roseburia.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|841,Complete,NA
bsdb:27725146/1/2,27725146,NA,27725146,10.1053/j.gastro.2016.09.049,NA,"Tap J., Derrien M., Törnblom H., Brazeilles R., Cools-Portier S., Doré J., Störsrud S., Le Nevé B., Öhman L. , Simrén M.",Identification of an Intestinal Microbiota Signature Associated With Severity of Irritable Bowel Syndrome,Gastroenterology,2017,"Bacteria, Functional Bowel Disorder, Microbiome",Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS,Patients diagnosed with irritable bowel syndrome according to Rome III criteria.,149,149,Yes,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Results section; differential abundance analysis (IBS vs healthy controls),8 January 2026,Aqc576444,Aqc576444,"IBS patients exhibited a significant increase in Enterobacteriaceae and Escherichia–Shigella compared to healthy controls, consistent with a dysbiotic microbial profile.",increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,NA
bsdb:27741466/1/1,27741466,case-control,27741466,10.1016/j.jad.2016.09.051,NA,"Lin P., Ding B., Feng C., Yin S., Zhang T., Qi X., Lv H., Guo X., Dong K., Zhu Y. , Li Q.",Prevotella and Klebsiella proportions in fecal microbial communities are potential characteristic parameters for patients with major depressive disorder,Journal of affective disorders,2017,"Fecal microbial communities, Klebsiella, Major depressive disorder, Prevotella",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,healthy controls,major depressive disorder (visit 1),"The patients were assessed with the major depressive disorder criteria in the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV- TR) and 17-items HAM-D scales ≥23.Three visits occurred on day 1, day 15 and day 29.",10,10,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,table 2 and table 3,10 January 2021,Fatima Zohra,WikiWorks,Major bacterial organism in subjects of MDD and control groups,increased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239;3379134|976|200643|171549|171552|838;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|1300|1301,Complete,Shaimaa Elsafoury
bsdb:27741466/1/2,27741466,case-control,27741466,10.1016/j.jad.2016.09.051,NA,"Lin P., Ding B., Feng C., Yin S., Zhang T., Qi X., Lv H., Guo X., Dong K., Zhu Y. , Li Q.",Prevotella and Klebsiella proportions in fecal microbial communities are potential characteristic parameters for patients with major depressive disorder,Journal of affective disorders,2017,"Fecal microbial communities, Klebsiella, Major depressive disorder, Prevotella",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,healthy controls,major depressive disorder (visit 1),"The patients were assessed with the major depressive disorder criteria in the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV- TR) and 17-items HAM-D scales ≥23.Three visits occurred on day 1, day 15 and day 29.",10,10,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,table 2 and table 3,10 January 2021,Fatima Zohra,WikiWorks,Major bacterial organism in subjects of MDD and control groups,decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Shaimaa Elsafoury
bsdb:27741466/2/1,27741466,case-control,27741466,10.1016/j.jad.2016.09.051,NA,"Lin P., Ding B., Feng C., Yin S., Zhang T., Qi X., Lv H., Guo X., Dong K., Zhu Y. , Li Q.",Prevotella and Klebsiella proportions in fecal microbial communities are potential characteristic parameters for patients with major depressive disorder,Journal of affective disorders,2017,"Fecal microbial communities, Klebsiella, Major depressive disorder, Prevotella",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,healthy controls,major depressive disorder (visit 2),"The patients were assessed with the major depressive disorder criteria in the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV- TR) and 17-items HAM-D scales ≥23.Three visits occurred on day 1, day 15 and day 29.",10,10,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,table 2 and table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Major bacterial organism in subjects of MDD and control groups,increased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301,Complete,Shaimaa Elsafoury
bsdb:27741466/2/2,27741466,case-control,27741466,10.1016/j.jad.2016.09.051,NA,"Lin P., Ding B., Feng C., Yin S., Zhang T., Qi X., Lv H., Guo X., Dong K., Zhu Y. , Li Q.",Prevotella and Klebsiella proportions in fecal microbial communities are potential characteristic parameters for patients with major depressive disorder,Journal of affective disorders,2017,"Fecal microbial communities, Klebsiella, Major depressive disorder, Prevotella",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,healthy controls,major depressive disorder (visit 2),"The patients were assessed with the major depressive disorder criteria in the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV- TR) and 17-items HAM-D scales ≥23.Three visits occurred on day 1, day 15 and day 29.",10,10,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,table 2 and table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Major bacterial organism in subjects of MDD and control groups,decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Shaimaa Elsafoury
bsdb:27741466/3/1,27741466,case-control,27741466,10.1016/j.jad.2016.09.051,NA,"Lin P., Ding B., Feng C., Yin S., Zhang T., Qi X., Lv H., Guo X., Dong K., Zhu Y. , Li Q.",Prevotella and Klebsiella proportions in fecal microbial communities are potential characteristic parameters for patients with major depressive disorder,Journal of affective disorders,2017,"Fecal microbial communities, Klebsiella, Major depressive disorder, Prevotella",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,healthy controls,major depressive disorder (visit 3),"The patients were assessed with the major depressive disorder criteria in the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV- TR) and 17-items HAM-D scales ≥23.Three visits occurred on day 1, day 15 and day 29.",10,10,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,table 2 and table 3,10 January 2021,Shaimaa Elsafoury,"Fatima,WikiWorks",Major bacterial organism in subjects of MDD and control groups,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",1783272|1239;1783272|1239|186801|3082720|186804,Complete,Fatima
bsdb:27741466/3/2,27741466,case-control,27741466,10.1016/j.jad.2016.09.051,NA,"Lin P., Ding B., Feng C., Yin S., Zhang T., Qi X., Lv H., Guo X., Dong K., Zhu Y. , Li Q.",Prevotella and Klebsiella proportions in fecal microbial communities are potential characteristic parameters for patients with major depressive disorder,Journal of affective disorders,2017,"Fecal microbial communities, Klebsiella, Major depressive disorder, Prevotella",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,healthy controls,major depressive disorder (visit 3),"The patients were assessed with the major depressive disorder criteria in the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV- TR) and 17-items HAM-D scales ≥23.Three visits occurred on day 1, day 15 and day 29.",10,10,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,table 2 and table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Major bacterial organism in subjects of MDD and control groups,decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Shaimaa Elsafoury
bsdb:27742762/1/1,27742762,case-control,27742762,10.1136/gutjnl-2016-312580,NA,"Fan X., Alekseyenko A.V., Wu J., Peters B.A., Jacobs E.J., Gapstur S.M., Purdue M.P., Abnet C.C., Stolzenberg-Solomon R., Miller G., Ravel J., Hayes R.B. , Ahn J.",Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study,Gut,2018,PANCREAS,Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Pancreatic carcinoma,EFO:0002618,controls,pancreatic cancer cases,subjects from the two cohorts with incident primary pancreatic adenocarcinoma,371,361,NA,16S,34,Roche454,relative abundances,Logistic Regression,0.05,FALSE,NA,"age,date,race,sex","age,alcohol drinking,body mass index,diabetes mellitus,race,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between controls and pancreatic cancer cases,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota",3379134|976|200643|171549|171552|1283313;3379134|976,Complete,Claregrieve1
bsdb:27742762/1/2,27742762,case-control,27742762,10.1136/gutjnl-2016-312580,NA,"Fan X., Alekseyenko A.V., Wu J., Peters B.A., Jacobs E.J., Gapstur S.M., Purdue M.P., Abnet C.C., Stolzenberg-Solomon R., Miller G., Ravel J., Hayes R.B. , Ahn J.",Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study,Gut,2018,PANCREAS,Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Pancreatic carcinoma,EFO:0002618,controls,pancreatic cancer cases,subjects from the two cohorts with incident primary pancreatic adenocarcinoma,371,361,NA,16S,34,Roche454,relative abundances,Logistic Regression,0.05,FALSE,NA,"age,date,race,sex","age,alcohol drinking,body mass index,diabetes mellitus,race,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 2,Table 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between controls and pancreatic cancer cases,decreased,"k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae",3384189|32066;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066|203490|203491|1129771|32067;3384189|32066|203490|203491|1129771,Complete,Claregrieve1
bsdb:27742762/2/1,27742762,case-control,27742762,10.1136/gutjnl-2016-312580,NA,"Fan X., Alekseyenko A.V., Wu J., Peters B.A., Jacobs E.J., Gapstur S.M., Purdue M.P., Abnet C.C., Stolzenberg-Solomon R., Miller G., Ravel J., Hayes R.B. , Ahn J.",Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study,Gut,2018,PANCREAS,Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,Pancreatic carcinoma,EFO:0002618,controls,pancreatic cancer cases,subjects from the CPSII cohorts with incident primary pancreatic adenocarcinoma,170,170,NA,16S,34,Roche454,relative abundances,Logistic Regression,0.05,FALSE,NA,"age,date,race,sex","age,alcohol drinking,body mass index,diabetes mellitus,race,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 3a,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Median relative abundance of selected oral microbiota in pancreatic cancer cases and controls in the Cancer Prevention Study(CPS) cohort,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae",3379134|976|200643|171549|171552|1283313;3384189|32066;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066|203490|203491|1129771|32067;3384189|32066|203490|203491|1129771,Complete,Claregrieve1
bsdb:27742762/3/1,27742762,case-control,27742762,10.1136/gutjnl-2016-312580,NA,"Fan X., Alekseyenko A.V., Wu J., Peters B.A., Jacobs E.J., Gapstur S.M., Purdue M.P., Abnet C.C., Stolzenberg-Solomon R., Miller G., Ravel J., Hayes R.B. , Ahn J.",Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study,Gut,2018,PANCREAS,Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Pancreatic carcinoma,EFO:0002618,controls,pancreatic cancer cases,subjects from the PLCO cohorts with incident primary pancreatic adenocarcinoma,201,191,NA,16S,34,Roche454,relative abundances,Logistic Regression,0.05,FALSE,NA,"age,date,race,sex","age,alcohol drinking,body mass index,diabetes mellitus,race,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 3b,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Median relative abundance of selected oral microbiota in pancreatic cancer cases and controls in the Cancer Prevention Study(CPS) cohort,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae",3384189|32066|203490|203491|1129771|32067;3384189|32066|203490|203491|1129771,Complete,ChiomaBlessing
bsdb:27776263/1/1,27776263,case-control,27776263,http://dx.doi.org/10.1016/j.neurobiolaging.2016.08.019,NA,"Cattaneo A., Cattane N., Galluzzi S., Provasi S., Lopizzo N., Festari C., Ferrari C., Guerra U.P., Paghera B., Muscio C., Bianchetti A., Volta G.D., Turla M., Cotelli M.S., Gennuso M., Prelle A., Zanetti O., Lussignoli G., Mirabile D., Bellandi D., Gentile S., Belotti G., Villani D., Harach T., Bolmont T., Padovani A., Boccardi M. , Frisoni G.B.",Association of brain amyloidosis with pro-inflammatory gut bacterial taxa and peripheral inflammation markers in cognitively impaired elderly,Neurobiology of aging,2017,"Brain amyloidosis, Cognitive impairment, Gut microbiota, Inflammation, Neurodegeneration",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healthy controls,Amyloid-positive (Amy+),Cognitively impaired patients with brain amyloidosis,10,40,NA,PCR,NA,NA,relative abundances,Kolmogorov-Smirnov Test,0.05,FALSE,NA,NA,"age,body mass index",NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,25 October 2024,AaishahM,"AaishahM,WikiWorks",Abundance of bacterial taxa in Amy+ patients,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,3379134|1224|1236|91347|543|1940338,Complete,NA
bsdb:27776263/1/2,27776263,case-control,27776263,http://dx.doi.org/10.1016/j.neurobiolaging.2016.08.019,NA,"Cattaneo A., Cattane N., Galluzzi S., Provasi S., Lopizzo N., Festari C., Ferrari C., Guerra U.P., Paghera B., Muscio C., Bianchetti A., Volta G.D., Turla M., Cotelli M.S., Gennuso M., Prelle A., Zanetti O., Lussignoli G., Mirabile D., Bellandi D., Gentile S., Belotti G., Villani D., Harach T., Bolmont T., Padovani A., Boccardi M. , Frisoni G.B.",Association of brain amyloidosis with pro-inflammatory gut bacterial taxa and peripheral inflammation markers in cognitively impaired elderly,Neurobiology of aging,2017,"Brain amyloidosis, Cognitive impairment, Gut microbiota, Inflammation, Neurodegeneration",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healthy controls,Amyloid-positive (Amy+),Cognitively impaired patients with brain amyloidosis,10,40,NA,PCR,NA,NA,relative abundances,Kolmogorov-Smirnov Test,0.05,FALSE,NA,NA,"age,body mass index",NA,NA,NA,NA,NA,NA,Signature 2,Figure 1,25 October 2024,AaishahM,"AaishahM,WikiWorks",Abundance of bacterial taxa in Amy+ patients,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",3379134|976|200643|171549|815|816|817;1783272|1239|186801|3085636|186803|1766253|39491,Complete,NA
bsdb:27776263/2/1,27776263,case-control,27776263,http://dx.doi.org/10.1016/j.neurobiolaging.2016.08.019,NA,"Cattaneo A., Cattane N., Galluzzi S., Provasi S., Lopizzo N., Festari C., Ferrari C., Guerra U.P., Paghera B., Muscio C., Bianchetti A., Volta G.D., Turla M., Cotelli M.S., Gennuso M., Prelle A., Zanetti O., Lussignoli G., Mirabile D., Bellandi D., Gentile S., Belotti G., Villani D., Harach T., Bolmont T., Padovani A., Boccardi M. , Frisoni G.B.",Association of brain amyloidosis with pro-inflammatory gut bacterial taxa and peripheral inflammation markers in cognitively impaired elderly,Neurobiology of aging,2017,"Brain amyloidosis, Cognitive impairment, Gut microbiota, Inflammation, Neurodegeneration",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healthy controls,Amyloid-negative (Amy-),Cognitively impaired patients with no brain amyloidosis,10,33,NA,PCR,NA,NA,relative abundances,Kolmogorov-Smirnov Test,0.05,FALSE,NA,NA,"age,body mass index",NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,25 October 2024,AaishahM,"AaishahM,WikiWorks",Abundance of bacterial taxa in Amy- patients,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,3379134|1224|1236|91347|543|1940338,Complete,NA
bsdb:27776263/2/2,27776263,case-control,27776263,http://dx.doi.org/10.1016/j.neurobiolaging.2016.08.019,NA,"Cattaneo A., Cattane N., Galluzzi S., Provasi S., Lopizzo N., Festari C., Ferrari C., Guerra U.P., Paghera B., Muscio C., Bianchetti A., Volta G.D., Turla M., Cotelli M.S., Gennuso M., Prelle A., Zanetti O., Lussignoli G., Mirabile D., Bellandi D., Gentile S., Belotti G., Villani D., Harach T., Bolmont T., Padovani A., Boccardi M. , Frisoni G.B.",Association of brain amyloidosis with pro-inflammatory gut bacterial taxa and peripheral inflammation markers in cognitively impaired elderly,Neurobiology of aging,2017,"Brain amyloidosis, Cognitive impairment, Gut microbiota, Inflammation, Neurodegeneration",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healthy controls,Amyloid-negative (Amy-),Cognitively impaired patients with no brain amyloidosis,10,33,NA,PCR,NA,NA,relative abundances,Kolmogorov-Smirnov Test,0.05,FALSE,NA,NA,"age,body mass index",NA,NA,NA,NA,NA,NA,Signature 2,Figure 1,25 October 2024,AaishahM,"AaishahM,WikiWorks",Abundance of bacterial taxa in Amy- patients,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,1783272|1239|186801|3085636|186803|1766253|39491,Complete,NA
bsdb:27776263/3/1,27776263,case-control,27776263,http://dx.doi.org/10.1016/j.neurobiolaging.2016.08.019,NA,"Cattaneo A., Cattane N., Galluzzi S., Provasi S., Lopizzo N., Festari C., Ferrari C., Guerra U.P., Paghera B., Muscio C., Bianchetti A., Volta G.D., Turla M., Cotelli M.S., Gennuso M., Prelle A., Zanetti O., Lussignoli G., Mirabile D., Bellandi D., Gentile S., Belotti G., Villani D., Harach T., Bolmont T., Padovani A., Boccardi M. , Frisoni G.B.",Association of brain amyloidosis with pro-inflammatory gut bacterial taxa and peripheral inflammation markers in cognitively impaired elderly,Neurobiology of aging,2017,"Brain amyloidosis, Cognitive impairment, Gut microbiota, Inflammation, Neurodegeneration",Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Amyloid-negative (Amy-),Amyloid-positive (Amy+),Cognitively impaired patients with brain amyloidosis,33,40,NA,PCR,NA,NA,relative abundances,Kolmogorov-Smirnov Test,0.05,NA,NA,NA,"age,body mass index",NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,25 October 2024,AaishahM,"AaishahM,WikiWorks",Abundance of bacterial taxa in Amy+ patients,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,3379134|1224|1236|91347|543|1940338,Complete,NA
bsdb:27776263/3/2,27776263,case-control,27776263,http://dx.doi.org/10.1016/j.neurobiolaging.2016.08.019,NA,"Cattaneo A., Cattane N., Galluzzi S., Provasi S., Lopizzo N., Festari C., Ferrari C., Guerra U.P., Paghera B., Muscio C., Bianchetti A., Volta G.D., Turla M., Cotelli M.S., Gennuso M., Prelle A., Zanetti O., Lussignoli G., Mirabile D., Bellandi D., Gentile S., Belotti G., Villani D., Harach T., Bolmont T., Padovani A., Boccardi M. , Frisoni G.B.",Association of brain amyloidosis with pro-inflammatory gut bacterial taxa and peripheral inflammation markers in cognitively impaired elderly,Neurobiology of aging,2017,"Brain amyloidosis, Cognitive impairment, Gut microbiota, Inflammation, Neurodegeneration",Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Amyloid-negative (Amy-),Amyloid-positive (Amy+),Cognitively impaired patients with brain amyloidosis,33,40,NA,PCR,NA,NA,relative abundances,Kolmogorov-Smirnov Test,0.05,NA,NA,NA,"age,body mass index",NA,NA,NA,NA,NA,NA,Signature 2,Figure 1,25 October 2024,AaishahM,"AaishahM,WikiWorks",Abundance of bacterial taxa in Amy+ patients,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,1783272|1239|186801|3085636|186803|1766253|39491,Complete,NA
bsdb:27812181/1/1,27812181,case-control,27812181,10.1371/journal.pone.0166026,NA,"Zheng H., Liang H., Wang Y., Miao M., Shi T., Yang F., Liu E., Yuan W., Ji Z.S. , Li D.K.",Altered Gut Microbiota Composition Associated with Eczema in Infants,PloS one,2016,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control infants,infants with eczema,infants with eczema,51,50,NA,16S,34,Roche454,NA,Metastats,1e-5,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Table 3, Supplemental Table S2, Supplemental Table S3",10 January 2021,Lucy Mellor,"Fatima,Claregrieve1,WikiWorks",Differentially abdundant species in the gut of infants with and without eczema,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter|s__Cronobacter sakazakii,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales|f__Desulfobacteraceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella buccae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|3085636|186803|207244;;3379134|976|200643|171549|815|816|626929;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|33042;3379134|1224|1236|91347|543|413496|28141;3379134|200940|3024418|213118|213119;3379134|200940|3031449|213115|194924|872;3379134|1224|1236|91347|543|547;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|204475;1783272|1239|186801|186802|204475|745368;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|541000;1783272|1239|91061|1385|186822;1783272|1239|91061|1385|186822|44249;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|171552|577309;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|2974251|28126;3379134|1224|28211|356|82115;3379134|1224|28211|356|82115|379;1783272|1239|186801|3085636|186803|841;1783272|1239|909932|1843489|31977|29465;3379134|74201|203494|48461|203557;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|186803;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|620;1783272|1239|186801|186802|31979|1485,Complete,Claregrieve1
bsdb:27812181/1/2,27812181,case-control,27812181,10.1371/journal.pone.0166026,NA,"Zheng H., Liang H., Wang Y., Miao M., Shi T., Yang F., Liu E., Yuan W., Ji Z.S. , Li D.K.",Altered Gut Microbiota Composition Associated with Eczema in Infants,PloS one,2016,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control infants,infants with eczema,infants with eczema,51,50,NA,16S,34,Roche454,NA,Metastats,1e-5,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Table 3, Supplemental Table S2, Supplemental Table S3",10 January 2021,Lucy Mellor,"Fatima,Claregrieve1,WikiWorks",Differentially abundant species in the gut of infants with and without eczema,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",1783272|1239|909932|1843488|909930;1783272|1239|909932|1843488|909930|904;1783272|1239|909932|1843489|31977|209879;1783272|1239|909932|1843489|31977|156454;1783272|1239|186801|186802|216572|244127;3379134|976|200643|171549|815|816|817;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|1681;1783272|201174|1760|85004|31953|1678|216816|1679;1783272|201174|1760|85006|85020|43668;1783272|201174|1760|85006|85019;1783272|201174|1760|85006|85019|1696;1783272|1239|186801|186802|3085642|580596;1783272|1239|91061|186826|186828;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85006|85020;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|189330;3379134|1224|28216|206351|481|538;1783272|1239|526524|526525|128827;1783272|1239|526524;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;1783272|1239|526524|526525|128827|1573535|1735;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|186802|216572|459786;3379134|1224|1236|135625|712;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|1385|90964;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1304;3379134|1224|28216|80840|995019|40544;1783272|1239|526524|526525|2810281|191303;1783272|1239|909932|1843489|31977;1783272|1239|526524|526525|128827,Complete,Claregrieve1
bsdb:27822556/1/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,InnuPURE,MagNAPure,"DNA isolation from human fecal samples using MagNA Pure LC DNA isolation Kit III, Roche (MagNAPure).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2D,5 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|1224|28216|80840|506;3379134|976|200643|171549|171552;1783272|1239|909932|1843489|31977,Complete,NA
bsdb:27822556/1/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,InnuPURE,MagNAPure,"DNA isolation from human fecal samples using MagNA Pure LC DNA isolation Kit III, Roche (MagNAPure).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2D,5 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",3379134|976|200643|171549|815;1783272|201174|1760|85004|31953;3379134|1224|1236|135625|712;3379134|976|200643|171549|171551;3379134|74201|203494|48461|203557,Complete,NA
bsdb:27822556/2/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 2,Denmark,Homo sapiens,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,InnuPURE,Easy-DNA,"DNA isolation from human fecal samples using Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2D,5 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",1783272|1239|909932|1843489|31977;1783272|201174|1760|85004|31953;3379134|74201|203494|48461|203557,Complete,NA
bsdb:27822556/2/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 2,Denmark,Homo sapiens,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,InnuPURE,Easy-DNA,"DNA isolation from human fecal samples using Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2D,5 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",3379134|976|200643|171549|171552;3379134|976|200643|171549|815;3379134|976|200643|171549|171551;3379134|1224|28216|80840|506;3379134|1224|1236|135625|712,Complete,NA
bsdb:27822556/3/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 3,Denmark,Homo sapiens,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,InnuPURE,FastDNA,"DNA isolation from human fecal samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2D,5 April 2024,Aleru002,"Aleru002,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",1783272|201174|1760|85004|31953;3379134|74201|203494|48461|203557,Complete,NA
bsdb:27822556/3/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 3,Denmark,Homo sapiens,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,InnuPURE,FastDNA,"DNA isolation from human fecal samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2D,5 April 2024,Aleru002,"Aleru002,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",3379134|976|200643|171549|171552;1783272|1239|909932|1843489|31977;3379134|976|200643|171549|815;3379134|976|200643|171549|171551;3379134|1224|28216|80840|506;3379134|1224|1236|135625|712,Complete,NA
bsdb:27822556/5/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 5,Denmark,Homo sapiens,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,InnuPURE,QIAStool,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2D,6 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",3379134|976|200643|171549|171552;1783272|1239|909932|1843489|31977;3379134|74201|203494|48461|203557,Complete,NA
bsdb:27822556/5/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 5,Denmark,Homo sapiens,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,InnuPURE,QIAStool,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2D,6 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",3379134|976|200643|171549|815;1783272|201174|1760|85004|31953;3379134|976|200643|171549|171551;3379134|1224|28216|80840|506;3379134|1224|1236|135625|712,Complete,NA
bsdb:27822556/6/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 6,Denmark,Homo sapiens,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,InnuPURE,QIAStool+BB,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Figure 2D,6 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,1783272|201174|1760|85004|31953,Complete,NA
bsdb:27822556/6/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 6,Denmark,Homo sapiens,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,InnuPURE,QIAStool+BB,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Figure 2D,6 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",3379134|976|200643|171549|171552;1783272|1239|909932|1843489|31977;3379134|976|200643|171549|815;3379134|74201|203494|48461|203557;3379134|976|200643|171549|171551;3379134|1224|28216|80840|506;3379134|1224|1236|135625|712,Complete,NA
bsdb:27822556/7/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 7,Denmark,Homo sapiens,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,MagNAPure,Easy-DNA,"DNA isolation from human fecal samples using Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Figure 2D,6 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae",3379134|74201|203494|48461|203557;1783272|201174|1760|85004|31953,Complete,NA
bsdb:27822556/7/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 7,Denmark,Homo sapiens,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,MagNAPure,Easy-DNA,"DNA isolation from human fecal samples using Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Figure 2D,6 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",3379134|976|200643|171549|171552;1783272|1239|909932|1843489|31977;3379134|976|200643|171549|815;3379134|976|200643|171549|171551;3379134|1224|28216|80840|506;3379134|1224|1236|135625|712,Complete,NA
bsdb:27822556/8/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 8,Denmark,Homo sapiens,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,MagNAPure,FastDNA,"DNA isolation from human fecal samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2D,6 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",1783272|201174|1760|85004|31953;3379134|74201|203494|48461|203557,Complete,NA
bsdb:27822556/8/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 8,Denmark,Homo sapiens,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,MagNAPure,FastDNA,"DNA isolation from human fecal samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2D,6 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",3379134|976|200643|171549|171552;1783272|1239|909932|1843489|31977;3379134|976|200643|171549|815;3379134|976|200643|171549|171551;3379134|1224|28216|80840|506;3379134|1224|1236|135625|712,Complete,NA
bsdb:27822556/12/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 12,Denmark,Homo sapiens,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,Easy-DNA,FastDNA,"DNA isolation from human fecal samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2D,7 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",3379134|976|200643|171549|171552;3379134|976|200643|171549|815;3379134|976|200643|171549|171551;3379134|1224|28216|80840|506;3379134|1224|1236|135625|712,Complete,NA
bsdb:27822556/12/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 12,Denmark,Homo sapiens,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,Easy-DNA,FastDNA,"DNA isolation from human fecal samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2D,7 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",1783272|1239|909932|1843489|31977;1783272|201174|1760|85004|31953;3379134|74201|203494|48461|203557,Complete,NA
bsdb:27822556/15/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 15,Denmark,Homo sapiens,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,Easy-DNA,QIAStool+BB,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2D,7 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",3379134|976|200643|171549|171552;3379134|976|200643|171549|815;3379134|976|200643|171549|171551;3379134|1224|28216|80840|506;3379134|1224|1236|135625|712,Complete,NA
bsdb:27822556/15/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 15,Denmark,Homo sapiens,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,Easy-DNA,QIAStool+BB,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2D,7 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",1783272|1239|909932|1843489|31977;1783272|201174|1760|85004|31953;3379134|74201|203494|48461|203557,Complete,NA
bsdb:27822556/16/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 16,Denmark,Homo sapiens,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,FastDNA,PowerSoil.HMP,"DNA isolation from human fecal samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,Figure 2D,7 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",3379134|976|200643|171549|171552;1783272|1239|909932|1843489|31977;3379134|976|200643|171549|815;3379134|976|200643|171549|171551;3379134|1224|28216|80840|506;3379134|1224|1236|135625|712,Complete,NA
bsdb:27822556/16/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 16,Denmark,Homo sapiens,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,FastDNA,PowerSoil.HMP,"DNA isolation from human fecal samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,Figure 2D,7 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",1783272|201174|1760|85004|31953;3379134|74201|203494|48461|203557,Complete,NA
bsdb:27822556/17/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 17,Denmark,Homo sapiens,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,FastDNA,QIAStool,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2D,7 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",3379134|976|200643|171549|171552;1783272|1239|909932|1843489|31977;3379134|976|200643|171549|815;3379134|976|200643|171549|171551;3379134|1224|28216|80840|506;3379134|1224|1236|135625|712,Complete,NA
bsdb:27822556/17/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 17,Denmark,Homo sapiens,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,FastDNA,QIAStool,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2D,7 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",1783272|201174|1760|85004|31953;3379134|74201|203494|48461|203557,Complete,NA
bsdb:27822556/19/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 19,Denmark,Homo sapiens,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,PowerSoil.HMP,QIAStool,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2D,7 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",3379134|976|200643|171549|171552;1783272|1239|909932|1843489|31977;3379134|74201|203494|48461|203557,Complete,NA
bsdb:27822556/19/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 19,Denmark,Homo sapiens,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,PowerSoil.HMP,QIAStool,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2D,7 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",3379134|976|200643|171549|815;1783272|201174|1760|85004|31953;3379134|976|200643|171549|171551;3379134|1224|28216|80840|506;3379134|1224|1236|135625|712,Complete,NA
bsdb:27822556/20/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 20,Denmark,Homo sapiens,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,PowerSoil.HMP,QIAStool+BB,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2D,7 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,1783272|201174|1760|85004|31953,Complete,NA
bsdb:27822556/20/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 20,Denmark,Homo sapiens,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,PowerSoil.HMP,QIAStool+BB,"DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2D,7 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",3379134|976|200643|171549|171552;1783272|1239|909932|1843489|31977;3379134|976|200643|171549|815;3379134|74201|203494|48461|203557;3379134|976|200643|171549|171551;3379134|1224|28216|80840|506;3379134|1224|1236|135625|712,Complete,NA
bsdb:27822556/25/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 25,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,InnuPURE,MagNAPure,"DNA isolation from pig fecal samples using MagNA Pure LC DNA isolation Kit III, Roche (MagNAPure).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2E,10 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",3379134|976|200643|171549|171552;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|186803;1783272|1239|909932|1843489|31977;1783272|1239|526524|526525|128827,Complete,NA
bsdb:27822556/25/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 25,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,InnuPURE,MagNAPure,"DNA isolation from pig fecal samples using MagNA Pure LC DNA isolation Kit III, Roche (MagNAPure).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2E,10 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,3379134|29547|3031852|213849|72294,Complete,NA
bsdb:27822556/26/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 26,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,InnuPURE,Easy-DNA,"DNA isolation from pig fecal samples using Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Figure 2E,10 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|976|200643|171549|171552;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803,Complete,NA
bsdb:27822556/26/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 26,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,InnuPURE,Easy-DNA,"DNA isolation from pig fecal samples using Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Figure 2E,10 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",1783272|1239|186801|186802|31979;3379134|29547|3031852|213849|72294;1783272|1239|909932|1843489|31977;1783272|1239|526524|526525|128827,Complete,NA
bsdb:27822556/27/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 27,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,InnuPURE,FastDNA,"DNA isolation from pig fecal samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2E,10 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|186802|216572;1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|186803,Complete,NA
bsdb:27822556/27/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 27,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,InnuPURE,FastDNA,"DNA isolation from pig fecal samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2E,10 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",3379134|976|200643|171549|171552;3379134|29547|3031852|213849|72294;1783272|1239|909932|1843489|31977;1783272|1239|526524|526525|128827,Complete,NA
bsdb:27822556/28/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 28,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,InnuPURE,PowerSoil.HMP,"DNA isolation from pig fecal samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2E,10 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803;1783272|1239|526524|526525|128827,Complete,NA
bsdb:27822556/28/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 28,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,InnuPURE,PowerSoil.HMP,"DNA isolation from pig fecal samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2E,10 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|976|200643|171549|171552;1783272|1239|186801|186802|31979;3379134|29547|3031852|213849|72294;1783272|1239|909932|1843489|31977,Complete,NA
bsdb:27822556/29/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 29,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,InnuPURE,QIAStool,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2E,10 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",3379134|976|200643|171549|171552;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|31979;1783272|1239|909932|1843489|31977;1783272|1239|526524|526525|128827,Complete,NA
bsdb:27822556/29/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 29,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,InnuPURE,QIAStool,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2E,10 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae",1783272|1239|186801|3085636|186803;3379134|29547|3031852|213849|72294,Complete,NA
bsdb:27822556/30/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 30,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,InnuPURE,QIAStool+BB,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2E,10 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",1783272|1239|186801|186802|216572;1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|186803;1783272|1239|526524|526525|128827,Complete,NA
bsdb:27822556/30/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 30,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,InnuPURE,QIAStool+BB,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2E,10 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|976|200643|171549|171552;3379134|29547|3031852|213849|72294;1783272|1239|909932|1843489|31977,Complete,NA
bsdb:27822556/32/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 32,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,MagNAPure,FastDNA,"DNA isolation from pig fecal samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2E,10 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",1783272|1239|186801|186802|216572;1783272|1239|186801|186802|31979,Complete,NA
bsdb:27822556/32/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 32,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,MagNAPure,FastDNA,"DNA isolation from pig fecal samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2E,10 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",3379134|976|200643|171549|171552;1783272|1239|186801|3085636|186803;3379134|29547|3031852|213849|72294;1783272|1239|909932|1843489|31977;1783272|1239|526524|526525|128827,Complete,NA
bsdb:27822556/33/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 33,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,MagNAPure,PowerSoil.HMP,"DNA isolation from pig fecal samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP)",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2E,10 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803;3379134|29547|3031852|213849|72294;1783272|1239|526524|526525|128827,Complete,NA
bsdb:27822556/33/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 33,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,MagNAPure,PowerSoil.HMP,"DNA isolation from pig fecal samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP)",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2E,10 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|186801|186802|31979;3379134|976|200643|171549|171552;1783272|1239|909932|1843489|31977,Complete,NA
bsdb:27822556/34/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 34,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,MagNAPure,QIAStool,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Figure 2E,10 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",3379134|976|200643|171549|171552;1783272|1239|186801|186802|31979;3379134|29547|3031852|213849|72294;1783272|1239|909932|1843489|31977;1783272|1239|526524|526525|128827,Complete,NA
bsdb:27822556/34/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 34,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,MagNAPure,QIAStool,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Figure 2E,10 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572,Complete,NA
bsdb:27822556/35/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 35,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,MagNAPure,QIAStool+BB,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2E,10 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",3379134|29547|3031852|213849|72294;1783272|1239|186801|186802|31979,Complete,NA
bsdb:27822556/35/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 35,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,MagNAPure,QIAStool+BB,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2E,10 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",3379134|976|200643|171549|171552;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803;1783272|1239|909932|1843489|31977;1783272|1239|526524|526525|128827,Complete,NA
bsdb:27822556/36/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 36,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,Easy-DNA,FastDNA,"DNA isolation from pig fecal samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2E,24 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|186801|186802|216572;1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|186803;1783272|1239|909932|1843489|31977,Complete,NA
bsdb:27822556/36/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 36,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,Easy-DNA,FastDNA,"DNA isolation from pig fecal samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2E,24 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",3379134|976|200643|171549|171552;3379134|29547|3031852|213849|72294;1783272|1239|526524|526525|128827,Complete,NA
bsdb:27822556/37/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 37,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,Easy-DNA,PowerSoil.HMP,"DNA isolation from pig fecal samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2E,24 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",1783272|1239|186801|186802|216572;1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|186803;3379134|29547|3031852|213849|72294;1783272|1239|909932|1843489|31977;1783272|1239|526524|526525|128827,Complete,NA
bsdb:27822556/37/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 37,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,Easy-DNA,PowerSoil.HMP,"DNA isolation from pig fecal samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2E,24 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,3379134|976|200643|171549|171552,Complete,NA
bsdb:27822556/38/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 38,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,Easy-DNA,QIAStool,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2E,24 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",3379134|29547|3031852|213849|72294;1783272|1239|526524|526525|128827;1783272|1239|909932|1843489|31977;1783272|1239|186801|186802|31979,Complete,NA
bsdb:27822556/38/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 38,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,Easy-DNA,QIAStool,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2E,24 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|976|200643|171549|171552;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803,Complete,NA
bsdb:27822556/39/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 39,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,Easy-DNA,QIAStool+BB,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2E,24 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",1783272|1239|186801|186802|31979;3379134|29547|3031852|213849|72294;1783272|1239|526524|526525|128827,Complete,NA
bsdb:27822556/39/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 39,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,Easy-DNA,QIAStool+BB,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2E,24 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|976|200643|171549|171552;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803;1783272|1239|909932|1843489|31977,Complete,NA
bsdb:27822556/40/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 40,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,FastDNA,PowerSoil.HMP,"DNA isolation from pig fecal samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2E,24 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803;3379134|29547|3031852|213849|72294;1783272|1239|909932|1843489|31977;1783272|1239|526524|526525|128827,Complete,NA
bsdb:27822556/40/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 40,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,FastDNA,PowerSoil.HMP,"DNA isolation from pig fecal samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2E,24 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",3379134|976|200643|171549|171552;1783272|1239|186801|186802|31979,Complete,NA
bsdb:27822556/41/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 41,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,FastDNA,QIAStool,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2E,24 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",3379134|976|200643|171549|171552;3379134|29547|3031852|213849|72294;1783272|1239|909932|1843489|31977;1783272|1239|526524|526525|128827,Complete,NA
bsdb:27822556/41/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 41,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,FastDNA,QIAStool,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2E,24 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|186802|216572;1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|186803,Complete,NA
bsdb:27822556/42/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 42,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,FastDNA,QIAStool+BB,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2E,24 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",3379134|29547|3031852|213849|72294;1783272|1239|526524|526525|128827,Complete,NA
bsdb:27822556/42/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 42,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,FastDNA,QIAStool+BB,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2E,24 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|976|200643|171549|171552;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|186803;1783272|1239|909932|1843489|31977,Complete,NA
bsdb:27822556/43/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 43,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,PowerSoil.HMP,QIAStool,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2E,24 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|976|200643|171549|171552;1783272|1239|186801|186802|31979;1783272|1239|909932|1843489|31977,Complete,NA
bsdb:27822556/43/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 43,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,PowerSoil.HMP,QIAStool,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2E,24 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803;3379134|29547|3031852|213849|72294;1783272|1239|526524|526525|128827,Complete,NA
bsdb:27822556/44/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 44,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,PowerSoil.HMP,QIAStool+BB,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2E,24 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,1783272|1239|186801|186802|31979,Complete,NA
bsdb:27822556/44/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 44,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,PowerSoil.HMP,QIAStool+BB,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2E,24 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",3379134|976|200643|171549|171552;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803;3379134|29547|3031852|213849|72294;1783272|1239|909932|1843489|31977;1783272|1239|526524|526525|128827,Complete,NA
bsdb:27822556/45/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 45,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,QIAStool,QIAStool+BB,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Figure 2E,24 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,1783272|1239|186801|3085636|186803,Complete,NA
bsdb:27822556/45/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 45,Denmark,Sus scrofa domesticus,Feces,UBERON:0001988,Extraction protocol,EFO:0000490,QIAStool,QIAStool+BB,"DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",3,3,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Figure 2E,24 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",3379134|976|200643|171549|171552;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|31979;3379134|29547|3031852|213849|72294;1783272|1239|909932|1843489|31977;1783272|1239|526524|526525|128827,Complete,NA
bsdb:27822556/49/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 49,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,InnuPURE,MagNAPure,"DNA isolation from sewage samples using MagNA Pure LC DNA isolation Kit III, Roche (MagNAPure).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",3379134|1224|1236|2887326|468;3379134|1224|28216|206351|481;3379134|74201|203494|48461|203557,Complete,NA
bsdb:27822556/49/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 49,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,InnuPURE,MagNAPure,"DNA isolation from sewage samples using MagNA Pure LC DNA isolation Kit III, Roche (MagNAPure).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",3379134|29547|3031852|213849|72294;1783272|1239|186801|186802|216572;3379134|976|200643|171549|815;1783272|1239|186801|3085636|186803;3379134|74201|414999|415000|134623,Complete,NA
bsdb:27822556/50/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 50,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,InnuPURE,Easy-DNA,"DNA isolation from sewage samples using Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",3379134|1224|1236|2887326|468;3379134|29547|3031852|213849|72294;1783272|1239|186801|186802|216572;3379134|976|200643|171549|815;3379134|1224|28216|206351|481;1783272|1239|186801|3085636|186803;3379134|74201|203494|48461|203557,Complete,NA
bsdb:27822556/50/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 50,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,InnuPURE,Easy-DNA,"DNA isolation from sewage samples using Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae,3379134|74201|414999|415000|134623,Complete,NA
bsdb:27822556/51/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 51,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,InnuPURE,FastDNA,"DNA isolation from sewage samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae",3379134|1224|1236|2887326|468;3379134|1224|28216|206351|481;3379134|74201|203494|48461|203557;3379134|74201|414999|415000|134623;3379134|976|200643|171549|815,Complete,NA
bsdb:27822556/51/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 51,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,InnuPURE,FastDNA,"DNA isolation from sewage samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|29547|3031852|213849|72294;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803,Complete,NA
bsdb:27822556/52/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 52,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,InnuPURE,PowerSoil.HMP,"DNA isolation from sewage samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",1783272|1239|186801|186802|216572;3379134|976|200643|171549|815;3379134|1224|28216|206351|481;3379134|74201|203494|48461|203557;3379134|74201|414999|415000|134623,Complete,NA
bsdb:27822556/52/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 52,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,InnuPURE,PowerSoil.HMP,"DNA isolation from sewage samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|1224|1236|2887326|468;3379134|29547|3031852|213849|72294;1783272|1239|186801|3085636|186803,Complete,NA
bsdb:27822556/53/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 53,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,InnuPURE,QIAStool,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",3379134|1224|1236|2887326|468;3379134|29547|3031852|213849|72294;1783272|1239|186801|186802|216572;3379134|976|200643|171549|815;3379134|1224|28216|206351|481;3379134|74201|203494|48461|203557;3379134|74201|414999|415000|134623,Complete,NA
bsdb:27822556/53/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 53,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,InnuPURE,QIAStool,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,1783272|1239|186801|3085636|186803,Complete,NA
bsdb:27822556/54/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 54,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,InnuPURE,QIAStool+BB,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",3379134|1224|1236|2887326|468;1783272|1239|186801|186802|216572;3379134|976|200643|171549|815;3379134|1224|28216|206351|481;3379134|74201|414999|415000|134623,Complete,NA
bsdb:27822556/54/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 54,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,InnuPURE,QIAStool+BB,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",3379134|29547|3031852|213849|72294;1783272|1239|186801|3085636|186803;3379134|74201|203494|48461|203557,Complete,NA
bsdb:27822556/55/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 55,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,MagNA Pure,Easy-DNA,"DNA isolation from sewage samples using Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|1224|1236|2887326|468;3379134|29547|3031852|213849|72294;1783272|1239|186801|186802|216572;3379134|976|200643|171549|815;1783272|1239|186801|3085636|186803,Complete,NA
bsdb:27822556/55/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 55,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,MagNA Pure,Easy-DNA,"DNA isolation from sewage samples using Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",3379134|1224|28216|206351|481;3379134|74201|203494|48461|203557;3379134|74201|414999|415000|134623,Complete,NA
bsdb:27822556/56/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 56,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,MagNA Pure,FastDNA,"DNA isolation from sewage samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",3379134|29547|3031852|213849|72294;3379134|976|200643|171549|815;1783272|1239|186801|3085636|186803;3379134|74201|414999|415000|134623,Complete,NA
bsdb:27822556/56/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 56,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,MagNA Pure,FastDNA,"DNA isolation from sewage samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",3379134|1224|1236|2887326|468;1783272|1239|186801|186802|216572;3379134|1224|28216|206351|481;3379134|74201|203494|48461|203557,Complete,NA
bsdb:27822556/57/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 57,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,MagNA Pure,PowerSoil.HMP,"DNA isolation from sewage samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",1783272|1239|186801|186802|216572;3379134|976|200643|171549|815;1783272|1239|186801|3085636|186803;3379134|74201|414999|415000|134623,Complete,NA
bsdb:27822556/57/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 57,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,MagNA Pure,PowerSoil.HMP,"DNA isolation from sewage samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",3379134|29547|3031852|213849|72294;3379134|1224|1236|2887326|468;3379134|1224|28216|206351|481;3379134|74201|203494|48461|203557,Complete,NA
bsdb:27822556/58/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 58,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,MagNA Pure,QIAStool,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|976|200643|171549|815;3379134|29547|3031852|213849|72294;3379134|74201|414999|415000|134623;1783272|1239|186801|186802|216572;3379134|74201|203494|48461|203557;1783272|1239|186801|3085636|186803,Complete,NA
bsdb:27822556/58/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 58,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,MagNA Pure,QIAStool,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae",3379134|1224|1236|2887326|468;3379134|1224|28216|206351|481,Complete,NA
bsdb:27822556/59/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 59,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,MagNA Pure,QIAStool+BB,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",3379134|29547|3031852|213849|72294;1783272|1239|186801|186802|216572;3379134|976|200643|171549|815;1783272|1239|186801|3085636|186803;3379134|74201|414999|415000|134623,Complete,NA
bsdb:27822556/59/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 59,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,MagNA Pure,QIAStool+BB,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",3379134|1224|1236|2887326|468;3379134|1224|28216|206351|481;3379134|74201|203494|48461|203557,Complete,NA
bsdb:27822556/60/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 60,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,Easy-DNA,FastDNA,"DNA isolation from sewage samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",3379134|74201|203494|48461|203557;3379134|74201|414999|415000|134623,Complete,NA
bsdb:27822556/60/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 60,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,Easy-DNA,FastDNA,"DNA isolation from sewage samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|1224|1236|2887326|468;3379134|29547|3031852|213849|72294;1783272|1239|186801|186802|216572;3379134|976|200643|171549|815;3379134|1224|28216|206351|481;1783272|1239|186801|3085636|186803,Complete,NA
bsdb:27822556/61/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 61,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,Easy-DNA,PowerSoil.HMP,"DNA isolation from sewage samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",3379134|1224|28216|206351|481;3379134|74201|203494|48461|203557;3379134|74201|414999|415000|134623,Complete,NA
bsdb:27822556/61/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 61,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,Easy-DNA,PowerSoil.HMP,"DNA isolation from sewage samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|1224|1236|2887326|468;3379134|29547|3031852|213849|72294;1783272|1239|186801|186802|216572;3379134|976|200643|171549|815;1783272|1239|186801|3085636|186803,Complete,NA
bsdb:27822556/62/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 62,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,Easy-DNA,QIAStool,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",3379134|1224|28216|206351|481;3379134|74201|203494|48461|203557;3379134|74201|414999|415000|134623,Complete,NA
bsdb:27822556/62/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 62,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,Easy-DNA,QIAStool,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|1224|1236|2887326|468;3379134|29547|3031852|213849|72294;1783272|1239|186801|186802|216572;3379134|976|200643|171549|815;1783272|1239|186801|3085636|186803,Complete,NA
bsdb:27822556/63/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 63,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,Easy-DNA,QIAStool+BB,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",3379134|1224|28216|206351|481;3379134|74201|414999|415000|134623,Complete,NA
bsdb:27822556/63/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 63,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,Easy-DNA,QIAStool+BB,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",3379134|1224|1236|2887326|468;3379134|29547|3031852|213849|72294;1783272|1239|186801|186802|216572;3379134|976|200643|171549|815;1783272|1239|186801|3085636|186803;3379134|74201|203494|48461|203557,Complete,NA
bsdb:27822556/64/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 64,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,FastDNA,PowerSoil.HMP,"DNA isolation from sewage samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",1783272|1239|186801|186802|216572;3379134|976|200643|171549|815;3379134|1224|28216|206351|481;1783272|1239|186801|3085636|186803;3379134|74201|414999|415000|134623,Complete,NA
bsdb:27822556/64/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 64,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,FastDNA,PowerSoil.HMP,"DNA isolation from sewage samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,Figure 2F,27 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",3379134|1224|1236|2887326|468;3379134|29547|3031852|213849|72294;3379134|74201|203494|48461|203557,Complete,NA
bsdb:27822556/65/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 65,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,FastDNA,QIAStool,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,Figure 2F,28 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",3379134|1224|1236|2887326|468;3379134|29547|3031852|213849|72294;1783272|1239|186801|186802|216572;3379134|976|200643|171549|815;3379134|1224|28216|206351|481;3379134|74201|203494|48461|203557;3379134|74201|414999|415000|134623,Complete,NA
bsdb:27822556/65/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 65,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,FastDNA,QIAStool,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,Figure 2F,28 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,1783272|1239|186801|3085636|186803,Complete,NA
bsdb:27822556/66/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 66,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,FastDNA,QIAStool+BB,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2F,28 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",3379134|1224|1236|2887326|468;1783272|1239|186801|186802|216572;3379134|1224|28216|206351|481;1783272|1239|186801|3085636|186803;3379134|74201|414999|415000|134623,Complete,NA
bsdb:27822556/66/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 66,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,FastDNA,QIAStool+BB,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2F,28 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",3379134|29547|3031852|213849|72294;3379134|976|200643|171549|815;3379134|74201|203494|48461|203557,Complete,NA
bsdb:27822556/67/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 67,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,PowerSoil.HMP,QIAStool,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Figure 2F,28 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",3379134|1224|1236|2887326|468;3379134|29547|3031852|213849|72294;3379134|976|200643|171549|815;3379134|74201|203494|48461|203557;3379134|74201|414999|415000|134623,Complete,NA
bsdb:27822556/67/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 67,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,PowerSoil.HMP,QIAStool,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Figure 2F,28 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|186802|216572;3379134|1224|28216|206351|481;1783272|1239|186801|3085636|186803,Complete,NA
bsdb:27822556/68/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 68,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,PowerSoil.HMP,QIAStool+BB,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 1,Figure 2F,28 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|1224|1236|2887326|468;3379134|29547|3031852|213849|72294;1783272|1239|186801|3085636|186803,Complete,NA
bsdb:27822556/68/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 68,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,PowerSoil.HMP,QIAStool+BB,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 2,Figure 2F,28 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae",1783272|1239|186801|186802|216572;3379134|976|200643|171549|815;3379134|1224|28216|206351|481;3379134|74201|203494|48461|203557;3379134|74201|414999|415000|134623,Complete,NA
bsdb:27822556/69/1,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 69,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,QIAStool,QIAStool+BB,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2F,28 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,1783272|1239|186801|3085636|186803,Complete,NA
bsdb:27822556/69/2,27822556,"cross-sectional observational, not case-control",27822556,https://doi.org/10.1128/msystems.00095-16,NA,"Knudsen B.E., Bergmark L., Munk P., Lukjancenko O., Priemé A., Aarestrup F.M. , Pamp S.J.",Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition,mSystems,2016,"16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing",Experiment 69,Denmark,Not specified,Space surrounding organism,UBERON:0013514,Extraction protocol,EFO:0000490,QIAStool,QIAStool+BB,"DNA isolation from sewage samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).",24,24,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2F,28 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae",3379134|1224|1236|2887326|468;1783272|1239|186801|186802|216572;3379134|976|200643|171549|815;3379134|29547|3031852|213849|72294;3379134|74201|203494|48461|203557;3379134|74201|414999|415000|134623;3379134|1224|28216|206351|481,Complete,NA
bsdb:27827448/4/1,27827448,"cross-sectional observational, not case-control",27827448,10.1038/srep36666,NA,"Kuang Y.S., Li S.H., Guo Y., Lu J.H., He J.R., Luo B.J., Jiang F.J., Shen H., Papasian C.J., Pang H., Xia H.M., Deng H.W. , Qiu X.",Composition of gut microbiota in infants in China and global comparison,Scientific reports,2016,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Neonates,2-month-old infants,Samples from 2-month-old infants,15,14,NA,16S,345,Roche454,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure 3,24 October 2023,OdigiriGreat,"OdigiriGreat,WikiWorks",Comparison of microbial community composition at the phylum (a) and genus (b) levels for neonates and 2-month-old infants.,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|201174;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|186802|31979|1485;1783272|1239|91061|186826|1300;1783272|1239|526524|526525|2810280;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|171552|838;1783272|201174|1760|85004|31953|1678,Complete,Folakunmi
bsdb:27827448/5/1,27827448,"cross-sectional observational, not case-control",27827448,10.1038/srep36666,NA,"Kuang Y.S., Li S.H., Guo Y., Lu J.H., He J.R., Luo B.J., Jiang F.J., Shen H., Papasian C.J., Pang H., Xia H.M., Deng H.W. , Qiu X.",Composition of gut microbiota in infants in China and global comparison,Scientific reports,2016,NA,Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,Cesarean delivered neonates,Vaginally delivered neonates,samples from neonates delivered by Vagina,9,6,NA,16S,345,Roche454,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 5,25 October 2023,OdigiriGreat,"OdigiriGreat,Folakunmi,WikiWorks",Comparison of the microbial community of vaginal and cesarean delivery subjects for neonates,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|976|200643|171549|815|816;1783272|1239|909932|909929|1843491|158846;3379134|976|200643|171549|2005525|375288,Complete,Folakunmi
bsdb:27827448/5/2,27827448,"cross-sectional observational, not case-control",27827448,10.1038/srep36666,NA,"Kuang Y.S., Li S.H., Guo Y., Lu J.H., He J.R., Luo B.J., Jiang F.J., Shen H., Papasian C.J., Pang H., Xia H.M., Deng H.W. , Qiu X.",Composition of gut microbiota in infants in China and global comparison,Scientific reports,2016,NA,Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,Cesarean delivered neonates,Vaginally delivered neonates,samples from neonates delivered by Vagina,9,6,NA,16S,345,Roche454,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 5,25 October 2023,OdigiriGreat,"OdigiriGreat,Folakunmi,WikiWorks",Comparison of the microbial community of vaginal and cesarean delivery subjects for neonates,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Trabulsiella",1783272|1239|91061|186826|1300|1301;3379134|1224|1236|91347|543|158851,Complete,Folakunmi
bsdb:27827448/6/1,27827448,"cross-sectional observational, not case-control",27827448,10.1038/srep36666,NA,"Kuang Y.S., Li S.H., Guo Y., Lu J.H., He J.R., Luo B.J., Jiang F.J., Shen H., Papasian C.J., Pang H., Xia H.M., Deng H.W. , Qiu X.",Composition of gut microbiota in infants in China and global comparison,Scientific reports,2016,NA,Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,Cesarean delivered 2-month-olds,Vaginally delivered 2-month-olds,Two months infants that were delivered vaginally,7,7,NA,16S,345,Roche454,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,"Figure 5, within text result (Effects of delivery modes on infant gut microbiota, line 12)",25 October 2023,OdigiriGreat,"OdigiriGreat,Folakunmi,WikiWorks",Comparison of the microbial community of vaginal and cesarean delivery subjects for 2-month-old infants,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|976|200643|171549|815|816;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|186802|216572,Complete,Folakunmi
bsdb:27827448/6/2,27827448,"cross-sectional observational, not case-control",27827448,10.1038/srep36666,NA,"Kuang Y.S., Li S.H., Guo Y., Lu J.H., He J.R., Luo B.J., Jiang F.J., Shen H., Papasian C.J., Pang H., Xia H.M., Deng H.W. , Qiu X.",Composition of gut microbiota in infants in China and global comparison,Scientific reports,2016,NA,Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,Cesarean delivered 2-month-olds,Vaginally delivered 2-month-olds,Two months infants that were delivered vaginally,7,7,NA,16S,345,Roche454,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Figure 5,25 October 2023,OdigiriGreat,"OdigiriGreat,Folakunmi,WikiWorks",Comparison of the microbial community of vaginal and cesarean delivery subjects for 2-month-old infants,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|186801|186802|31979|1485;3379134|976|200643|171549|171552|838,Complete,Folakunmi
bsdb:27829577/1/1,27829577,laboratory experiment,27829577,10.5056/jnm16105,NA,"Moussaoui N., Jacobs J.P., Larauche M., Biraud M., Million M., Mayer E. , Taché Y.","Chronic Early-life Stress in Rat Pups Alters Basal Corticosterone, Intestinal Permeability, and Fecal Microbiota at Weaning: Influence of Sex",Journal of neurogastroenterology and motility,2017,"Corticosterone, Microbiota, Permeability, Stress, psychological, Weaning",Experiment 1,United States of America,Rattus norvegicus,Feces,UBERON:0001988,Stimulus or stress design,EFO:0001762,controls,limited nesting stress,pups exposed to limited nesting stress,23,23,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,sex,NA,decreased,decreased,NA,NA,NA,Signature 1,Fig3C + text,10 January 2021,Fatima Zohra,WikiWorks,Genera with differentially abundance in the LNS ( limited nesting stress) group compared to control,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanosphaera",1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|186807|2740;1783272|1239|91061|186826|186827|1375;1783272|1239|91061|1385|90964|227979;1783272|1239|91061|186826|186827|66831;1783272|1239|186801|186802|31979|1485;1783272|201174|1760|85007|1653|1716;3379134|200940|3031449|213115|194924|872;1783272|1239|91061|186826|186828|117563;1783272|201174|1760|85006|1268|32207;3379134|1224|1236|91347|1903414|583;1783272|1239|186801|186802|31979;1783272|1239|526524|526525|2810280|100883;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|81852;1783272|1239|526524|526525|2810281|191303;3366610|28890|183925|2158|2159|2316,Complete,Claregrieve1
bsdb:27829577/1/2,27829577,laboratory experiment,27829577,10.5056/jnm16105,NA,"Moussaoui N., Jacobs J.P., Larauche M., Biraud M., Million M., Mayer E. , Taché Y.","Chronic Early-life Stress in Rat Pups Alters Basal Corticosterone, Intestinal Permeability, and Fecal Microbiota at Weaning: Influence of Sex",Journal of neurogastroenterology and motility,2017,"Corticosterone, Microbiota, Permeability, Stress, psychological, Weaning",Experiment 1,United States of America,Rattus norvegicus,Feces,UBERON:0001988,Stimulus or stress design,EFO:0001762,controls,limited nesting stress,pups exposed to limited nesting stress,23,23,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,sex,NA,decreased,decreased,NA,NA,NA,Signature 2,Fig3C + text,10 January 2021,Fatima Zohra,WikiWorks,Genera with differentially abundance in the LNS ( limited nesting stress) group compared to control,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum|s__Mucispirillum schaedleri,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter",1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|33042;1783272|1239|526524|526525|128827|2749846|31971;3379134|74201|203494|48461|1647988|239934|239935;3379134|200930|68337|191393|2945020|248038|248039;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|186802|541000;3379134|976|200643|171549|2005519;1783272|1239|91061|1385|90964|1279;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|186807;1783272|1239|526524|526525|128827;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|186802|216572|244127;3379134|1224|1236|135625|712|724;3379134|976|200643|171549|1853231|283168,Complete,Claregrieve1
bsdb:27833598/1/1,27833598,case-control,27833598,https://doi.org/10.3389/fmicb.2016.01703,NA,"Di Paola M., Cavalieri D., Albanese D., Sordo M., Pindo M., Donati C., Pagnini I., Giani T., Simonini G., Paladini A., Lionetti P., De Filippo C. , Cimaz R.",Alteration of Fecal Microbiota Profiles in Juvenile Idiopathic Arthritis. Associations with HLA-B27 Allele and Disease Status,Frontiers in microbiology,2016,"HLA-B27 allele, enthesitis-related arthritis, gut microbiota, juvenile idiopathic arthritis, metagenomics",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Juvenile idiopathic arthritis,EFO:0002609,HLAB27-,HLAB27+,enthesitis-related arthritis (JIA-ERA) patients with HLA-B27 allele,10,9,3 months,16S,56,Roche454,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2, text",30 November 2021,Tislam,"Tislam,Claregrieve1,WikiWorks",Comparison of relative abundance of bacterial taxa between HLA-B27+ participants and HLB27- participants,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella",3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712;1783272|201174|84998|1643822|1643826|84111,Complete,Claregrieve1
bsdb:27833598/1/2,27833598,case-control,27833598,https://doi.org/10.3389/fmicb.2016.01703,NA,"Di Paola M., Cavalieri D., Albanese D., Sordo M., Pindo M., Donati C., Pagnini I., Giani T., Simonini G., Paladini A., Lionetti P., De Filippo C. , Cimaz R.",Alteration of Fecal Microbiota Profiles in Juvenile Idiopathic Arthritis. Associations with HLA-B27 Allele and Disease Status,Frontiers in microbiology,2016,"HLA-B27 allele, enthesitis-related arthritis, gut microbiota, juvenile idiopathic arthritis, metagenomics",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Juvenile idiopathic arthritis,EFO:0002609,HLAB27-,HLAB27+,enthesitis-related arthritis (JIA-ERA) patients with HLA-B27 allele,10,9,3 months,16S,56,Roche454,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2, text",30 November 2021,Tislam,"Tislam,Fatima,Claregrieve1,WikiWorks",Comparison of relative abundance of bacterial taxa between HLA-B27+ participants and HLB27- participants,increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|31979|1485|1506;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572|596767;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572|459786;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|91061|186826|33958,Complete,Claregrieve1
bsdb:27833598/2/1,27833598,case-control,27833598,https://doi.org/10.3389/fmicb.2016.01703,NA,"Di Paola M., Cavalieri D., Albanese D., Sordo M., Pindo M., Donati C., Pagnini I., Giani T., Simonini G., Paladini A., Lionetti P., De Filippo C. , Cimaz R.",Alteration of Fecal Microbiota Profiles in Juvenile Idiopathic Arthritis. Associations with HLA-B27 Allele and Disease Status,Frontiers in microbiology,2016,"HLA-B27 allele, enthesitis-related arthritis, gut microbiota, juvenile idiopathic arthritis, metagenomics",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Juvenile idiopathic arthritis,EFO:0002609,JIA patients with active disease,JIA patients in remission,JIA patients with enthesitis-related arthritis who are in remission,8,21,3 months,16S,56,Roche454,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,30 November 2021,Tislam,"Tislam,Claregrieve1,WikiWorks",Differences in bacterial abundance between JIA patients with active disease and patients in remission,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,3379134|1224|28216|80840|995019|40544,Complete,Claregrieve1
bsdb:27833598/2/2,27833598,case-control,27833598,https://doi.org/10.3389/fmicb.2016.01703,NA,"Di Paola M., Cavalieri D., Albanese D., Sordo M., Pindo M., Donati C., Pagnini I., Giani T., Simonini G., Paladini A., Lionetti P., De Filippo C. , Cimaz R.",Alteration of Fecal Microbiota Profiles in Juvenile Idiopathic Arthritis. Associations with HLA-B27 Allele and Disease Status,Frontiers in microbiology,2016,"HLA-B27 allele, enthesitis-related arthritis, gut microbiota, juvenile idiopathic arthritis, metagenomics",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Juvenile idiopathic arthritis,EFO:0002609,JIA patients with active disease,JIA patients in remission,JIA patients with enthesitis-related arthritis who are in remission,8,21,3 months,16S,56,Roche454,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,30 November 2021,Tislam,"Tislam,Claregrieve1,WikiWorks",Differences in bacterial abundance between JIA patients with active disease and patients in remission,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter",1783272|1239|186801|186802|31979|1485|1506;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|1853231|283168,Complete,Claregrieve1
bsdb:27833598/3/1,27833598,case-control,27833598,https://doi.org/10.3389/fmicb.2016.01703,NA,"Di Paola M., Cavalieri D., Albanese D., Sordo M., Pindo M., Donati C., Pagnini I., Giani T., Simonini G., Paladini A., Lionetti P., De Filippo C. , Cimaz R.",Alteration of Fecal Microbiota Profiles in Juvenile Idiopathic Arthritis. Associations with HLA-B27 Allele and Disease Status,Frontiers in microbiology,2016,"HLA-B27 allele, enthesitis-related arthritis, gut microbiota, juvenile idiopathic arthritis, metagenomics",Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Juvenile idiopathic arthritis,EFO:0002609,Healthy subjects,JIA-ERA patients,enthesitis-related arthritis (JIA-ERA) patients,29,19,3 months,16S,56,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,2,NA,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 1,Figure 1,21 June 2022,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between JIA-ERA patients and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.",1783272|1239|186801|186802|216572;1783272|1239|186801|186802|31979|1485|1506,Complete,Claregrieve1
bsdb:27833598/3/2,27833598,case-control,27833598,https://doi.org/10.3389/fmicb.2016.01703,NA,"Di Paola M., Cavalieri D., Albanese D., Sordo M., Pindo M., Donati C., Pagnini I., Giani T., Simonini G., Paladini A., Lionetti P., De Filippo C. , Cimaz R.",Alteration of Fecal Microbiota Profiles in Juvenile Idiopathic Arthritis. Associations with HLA-B27 Allele and Disease Status,Frontiers in microbiology,2016,"HLA-B27 allele, enthesitis-related arthritis, gut microbiota, juvenile idiopathic arthritis, metagenomics",Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Juvenile idiopathic arthritis,EFO:0002609,Healthy subjects,JIA-ERA patients,enthesitis-related arthritis (JIA-ERA) patients,29,19,3 months,16S,56,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,2,NA,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 2,Figure 1,21 June 2022,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between JIA-ERA patients and healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",1783272|1239|186801|3082720|186804;1783272|1239|186801|186802|31979,Complete,Claregrieve1
bsdb:27833598/4/1,27833598,case-control,27833598,https://doi.org/10.3389/fmicb.2016.01703,NA,"Di Paola M., Cavalieri D., Albanese D., Sordo M., Pindo M., Donati C., Pagnini I., Giani T., Simonini G., Paladini A., Lionetti P., De Filippo C. , Cimaz R.",Alteration of Fecal Microbiota Profiles in Juvenile Idiopathic Arthritis. Associations with HLA-B27 Allele and Disease Status,Frontiers in microbiology,2016,"HLA-B27 allele, enthesitis-related arthritis, gut microbiota, juvenile idiopathic arthritis, metagenomics",Experiment 4,Italy,Homo sapiens,Feces,UBERON:0001988,Juvenile idiopathic arthritis,EFO:0002609,Healthy subjects,JIA-nERA patients,polyarticular arthritis (JIA-ERA) patients,29,10,3 months,16S,56,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,2,NA,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 1,Figure 1,21 June 2022,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between JIA-nERA patients and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|186801|186802|216572;1783272|1239|909932|1843489|31977,Complete,Claregrieve1
bsdb:27836847/1/1,27836847,time series / longitudinal observational,27836847,10.1128/AEM.02149-16,NA,"Stanaway I.B., Wallace J.C., Shojaie A., Griffith W.C., Hong S., Wilder C.S., Green F.H., Tsai J., Knight M., Workman T., Vigoren E.M., McLean J.S., Thompson B. , Faustman E.M.",Human Oral Buccal Microbiomes Are Associated with Farmworker Status and Azinphos-Methyl Agricultural Pesticide Exposure,Applied and environmental microbiology,2017,"16S rRNA, azinphos-methyl, bacteria, buccal mucosa, farmworkers, microbiome, oral, sequencing",Experiment 1,United States of America,Homo sapiens,Buccal mucosa,UBERON:0006956,Air pollution,ENVO:02500037,Winter individuals,Spring/Summer individuals,Individuals for whom sequencing was performed had previous spring/summer blood azinphos-methyl detection by mass spectrometry as evidence of pesticide exposure.,82,101,NA,16S,56,Ion Torrent,centered log-ratio,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,Table 1,10 January 2021,Victoria Goulbourne,"Lwaldron,Atrayees,WikiWorks,Aiyshaaaa",Wilcoxon's rank sum test of azinphos-methyl blood detection groups for compositional pertubation,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|1760|2037;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;3379134|1224|1236|135619|28256|2745;1783272|201174|1760|85006;1783272|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:27838347/1/1,27838347,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J., Lynch S.V., Nariya S., Bhakta N.R., Beigelman A., Castro M., Dyer A.M., Israel E., Kraft M., Martin R.J., Mauger D.T., Rosenberg S.R., Sharp-King T., White S.R., Woodruff P.G., Avila P.C., Denlinger L.C., Holguin F., Lazarus S.C., Lugogo N., Moore W.C., Peters S.P., Que L., Smith L.J., Sorkness C.A., Wechsler M.E., Wenzel S.E., Boushey H.A. , Huang Y.J.","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 1,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,healthy control,atopic asthma,Patients who have atopic asthma,21,42,3 months,16S,4,Illumina,raw counts,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2a, Supplemental Table S4",10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differentially abundant microbial taxa in atopic asthmatic (AA) subjects compared with healthy controls (HC),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingopyxidaceae|g__Sphingopyxis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingopyxidaceae|g__Sphingopyxis|s__Sphingopyxis alaskensis,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549|171552|1283313|76122;1783272|1239|186801|3082720|543314|109326;3379134|29547|3031852|213849|72294|194;3384189|32066|203490|203491|203492|848;3379134|1224|1236|135625|712|724;3379134|1224|28216|206351|481|32257;1783272|1239|91061|186826|33958|1578|147802;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481|482|28449;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|2974251|165179;3379134|1224|28211|204457|3423718|165697;3379134|1224|28211|204457|3423718|165697|117207;3379134|203691|203692|136|2845253|157;3379134|203691|203692|136|2845253|157|59892;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|39778,Complete,Claregrieve1
bsdb:27838347/1/2,27838347,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J., Lynch S.V., Nariya S., Bhakta N.R., Beigelman A., Castro M., Dyer A.M., Israel E., Kraft M., Martin R.J., Mauger D.T., Rosenberg S.R., Sharp-King T., White S.R., Woodruff P.G., Avila P.C., Denlinger L.C., Holguin F., Lazarus S.C., Lugogo N., Moore W.C., Peters S.P., Que L., Smith L.J., Sorkness C.A., Wechsler M.E., Wenzel S.E., Boushey H.A. , Huang Y.J.","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 1,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,healthy control,atopic asthma,Patients who have atopic asthma,21,42,3 months,16S,4,Illumina,raw counts,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2a, Supplemental Table S4",10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between atopic asthmatic (AA) subjects compared with healthy controls (HC),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria|s__Kocuria palustris,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus",3379134|1224|1236|135625|712|713;1783272|201174|1760|85006|1268|57493|71999;1783272|1239|91061|186826|33958|2759736|57037;1783272|1239|91061|186826|33958|1578;3384189|32066|203490|203491|1129771|32067;3379134|1224|28211|356|119045|407;1783272|1239|186801|3082720|186804|1257,Complete,Claregrieve1
bsdb:27838347/2/1,27838347,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J., Lynch S.V., Nariya S., Bhakta N.R., Beigelman A., Castro M., Dyer A.M., Israel E., Kraft M., Martin R.J., Mauger D.T., Rosenberg S.R., Sharp-King T., White S.R., Woodruff P.G., Avila P.C., Denlinger L.C., Holguin F., Lazarus S.C., Lugogo N., Moore W.C., Peters S.P., Que L., Smith L.J., Sorkness C.A., Wechsler M.E., Wenzel S.E., Boushey H.A. , Huang Y.J.","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 2,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,healthy control,atopic no asthma,atopic nonasthmatic subjects,21,21,3 months,16S,4,Illumina,raw counts,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2b, Supplemental Table S5",10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between atopic nonasthmatic (ANA) subjects compared with healthy controls (HC),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Flexispira,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Sharpea,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingopyxidaceae|g__Sphingopyxis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingopyxidaceae|g__Sphingopyxis|s__Sphingopyxis alaskensis,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",1783272|201174|1760|2037|2049|1654;3379134|1224|1236|135625|712|416916;3379134|1224|1236|135625|712|416916|739;1783272|201174|1760|85007|1653|1716;3379134|29547|3031852|213849|72293|2353;3384189|32066|203490|203491|203492|848;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712|724|727;3379134|1224|1236|2887326|468|475;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552|2974257|425941;1783272|1239|909932|909929|1843491|970;1783272|1239|526524|526525|2810280|519427;3379134|1224|28211|204457|3423718|165697;3379134|1224|28211|204457|3423718|165697|117207;3379134|203691|203692|136|2845253|157|59892;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|39778,Complete,Claregrieve1
bsdb:27838347/2/2,27838347,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J., Lynch S.V., Nariya S., Bhakta N.R., Beigelman A., Castro M., Dyer A.M., Israel E., Kraft M., Martin R.J., Mauger D.T., Rosenberg S.R., Sharp-King T., White S.R., Woodruff P.G., Avila P.C., Denlinger L.C., Holguin F., Lazarus S.C., Lugogo N., Moore W.C., Peters S.P., Que L., Smith L.J., Sorkness C.A., Wechsler M.E., Wenzel S.E., Boushey H.A. , Huang Y.J.","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 2,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,healthy control,atopic no asthma,atopic nonasthmatic subjects,21,21,3 months,16S,4,Illumina,raw counts,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2b, Supplemental Table S5",10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between atopic nonasthmatic (ANA) subjects compared with healthy controls (HC),decreased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|29547|3031852|213849|72293|209;1783272|1239|91061|186826|33958|2759736|57037;1783272|1239|91061|186826|33958|1578;3384189|32066|203490|203491|1129771|32067;1783272|1239|1737404|1737405|1570339|543311;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3379134|1224|1236|72274|135621|286;1783272|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:27838347/3/1,27838347,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J., Lynch S.V., Nariya S., Bhakta N.R., Beigelman A., Castro M., Dyer A.M., Israel E., Kraft M., Martin R.J., Mauger D.T., Rosenberg S.R., Sharp-King T., White S.R., Woodruff P.G., Avila P.C., Denlinger L.C., Holguin F., Lazarus S.C., Lugogo N., Moore W.C., Peters S.P., Que L., Smith L.J., Sorkness C.A., Wechsler M.E., Wenzel S.E., Boushey H.A. , Huang Y.J.","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 3,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,atopic no asthma,atopic asthma,atopic asthma subjects,21,42,3 months,16S,4,Illumina,raw counts,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2c, Supplemental Table S6",10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between atopic asthmatic (AA) subjects compared with atopic nonasthmatic (ANA) subjects,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",1783272|1239|909932|1843489|31977|39948;3384189|32066|203490|203491|203492|848;3379134|1224|1236|135625|712|724;3384189|32066|203490|203491|1129771|32067;1783272|544448|31969|2085|2092|2093;3379134|1224|28216|206351|481|482|28449;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|28131;1783272|1239|909932|909929|1843491|970,Complete,Claregrieve1
bsdb:27838347/3/2,27838347,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J., Lynch S.V., Nariya S., Bhakta N.R., Beigelman A., Castro M., Dyer A.M., Israel E., Kraft M., Martin R.J., Mauger D.T., Rosenberg S.R., Sharp-King T., White S.R., Woodruff P.G., Avila P.C., Denlinger L.C., Holguin F., Lazarus S.C., Lugogo N., Moore W.C., Peters S.P., Que L., Smith L.J., Sorkness C.A., Wechsler M.E., Wenzel S.E., Boushey H.A. , Huang Y.J.","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 3,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,atopic no asthma,atopic asthma,atopic asthma subjects,21,42,3 months,16S,4,Illumina,raw counts,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2c, Supplemental Table S6",10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between atopic asthmatic (AA) subjects compared with atopic nonasthmatic (ANA) subjects,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium columnare,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Flexispira,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Sharpea,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingopyxidaceae|g__Sphingopyxis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingopyxidaceae|g__Sphingopyxis|s__Sphingopyxis alaskensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",3379134|1224|1236|135625|712|416916;3379134|1224|1236|135625|712|416916|739;1783272|1239|526524|526525|128827|174708;3379134|976|200643|171549|815|816|817;3379134|976|117743|200644|49546|1016|1018;1783272|201174|1760|85007|1653|1716;3379134|976|117743|200644|49546|237|996;3379134|29547|3031852|213849|72293|2353;3379134|1224|1236|135625|712|724|727;3379134|1224|1236|135625|712|724|729;1783272|1239|91061|186826|33958|2759736|57037;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|2974251|165179;3379134|976|200643|171549|171552|2974257|425941;1783272|1239|526524|526525|2810280|519427;3379134|1224|28211|204457|3423718|165697;3379134|1224|28211|204457|3423718|165697|117207;1783272|1239|91061|186826|1300|1301;3379134|203691|203692|136|2845253|157|59892;1783272|1239|186801|3085636|186803|2316020|33038,Complete,Claregrieve1
bsdb:27838347/4/1,27838347,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J., Lynch S.V., Nariya S., Bhakta N.R., Beigelman A., Castro M., Dyer A.M., Israel E., Kraft M., Martin R.J., Mauger D.T., Rosenberg S.R., Sharp-King T., White S.R., Woodruff P.G., Avila P.C., Denlinger L.C., Holguin F., Lazarus S.C., Lugogo N., Moore W.C., Peters S.P., Que L., Smith L.J., Sorkness C.A., Wechsler M.E., Wenzel S.E., Boushey H.A. , Huang Y.J.","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 4,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,nonresponder,inhaled corticosteroid responder,inhaled corticosteroid (ICS) responder,10,15,3 months,16S,4,Illumina,raw counts,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6b,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks,Merit",Differential relative taxon abundance in inhaled corticosteroid (ICS) responders versus nonresponders among those with atopic asthma,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061|186826|1300;1783272|1239|526524|526525|128827;3384189|32066|203490|203491|203492;1783272|1239|186801|3085636|186803;3379134|1224|1236|2887326|468;3379134|1224|28216|206351|481;1783272|1239|186801|3082720|186804;3379134|1224|28211|204457|41297;1783272|1239|909932|1843489|31977;1783272|1239|186801|3082720|543314|86331;1783272|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:27838347/4/2,27838347,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J., Lynch S.V., Nariya S., Bhakta N.R., Beigelman A., Castro M., Dyer A.M., Israel E., Kraft M., Martin R.J., Mauger D.T., Rosenberg S.R., Sharp-King T., White S.R., Woodruff P.G., Avila P.C., Denlinger L.C., Holguin F., Lazarus S.C., Lugogo N., Moore W.C., Peters S.P., Que L., Smith L.J., Sorkness C.A., Wechsler M.E., Wenzel S.E., Boushey H.A. , Huang Y.J.","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 4,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,nonresponder,inhaled corticosteroid responder,inhaled corticosteroid (ICS) responder,10,15,3 months,16S,4,Illumina,raw counts,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6b,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential relative taxon abundance in inhaled corticosteroid (ICS) responders versus nonresponders among those with atopic asthma,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella",1783272|201174|1760|2037|2049;1783272|1239|91061|186826|186827;3379134|1224|1236|72274|135621|351;3379134|976|117743|200644|49546;1783272|1239|91061|186826|33958;1783272|201174|1760|85006|85023;1783272|544448|31969|2085|2092;3379134|1224|1236|135625|712;3379134|976|200643|171549|171551;3379134|976|200643|171549|171552;3379134|203691|203692|136|137;3379134|976|117743|200644|2762318;1783272|1239|91061|1385|539738|1378,Complete,Claregrieve1
bsdb:27838347/5/1,27838347,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J., Lynch S.V., Nariya S., Bhakta N.R., Beigelman A., Castro M., Dyer A.M., Israel E., Kraft M., Martin R.J., Mauger D.T., Rosenberg S.R., Sharp-King T., White S.R., Woodruff P.G., Avila P.C., Denlinger L.C., Holguin F., Lazarus S.C., Lugogo N., Moore W.C., Peters S.P., Que L., Smith L.J., Sorkness C.A., Wechsler M.E., Wenzel S.E., Boushey H.A. , Huang Y.J.","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 5,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,baseline (corticosteroid treatment group),post inhaled corticosteroid treatment,asthma patients after inhaled corticosteroid treatment,8,8,3 months,16S,4,Illumina,raw counts,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text, Figure 6d",10 January 2021,Lucy Mellor,WikiWorks,Taxa differentially expressed in asthmatic subjects who responded to treatment after inhaled corticosteroid (ICS) treatment,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae",1783272|201174|1760|85006|85023;3379134|1224|28216|206351|481|482;3379134|1224|1236|2887326|468|475;3379134|203691|203692|136|137;1783272|201174|1760|2037|2049;1783272|544448|31969|2085|2092,Complete,Claregrieve1
bsdb:27838347/5/2,27838347,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J., Lynch S.V., Nariya S., Bhakta N.R., Beigelman A., Castro M., Dyer A.M., Israel E., Kraft M., Martin R.J., Mauger D.T., Rosenberg S.R., Sharp-King T., White S.R., Woodruff P.G., Avila P.C., Denlinger L.C., Holguin F., Lazarus S.C., Lugogo N., Moore W.C., Peters S.P., Que L., Smith L.J., Sorkness C.A., Wechsler M.E., Wenzel S.E., Boushey H.A. , Huang Y.J.","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 5,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,baseline (corticosteroid treatment group),post inhaled corticosteroid treatment,asthma patients after inhaled corticosteroid treatment,8,8,3 months,16S,4,Illumina,raw counts,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Text, Figure 6d",10 January 2021,Lucy Mellor,WikiWorks,Taxa differentially expressed in asthmatic subjects who responded to treatment after inhaled corticosteroid (ICS) treatment,decreased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",1783272|544448|31969|186329|2146;1783272|1239|91061|186826|33958;3379134|976|200643|171549|171552;1783272|1239|186801|3085636|186803;1783272|1239|186801|3082720|186804;3384189|32066|203490|203491|203492|848;1783272|1239|909932|1843489|31977|39948,Complete,Claregrieve1
bsdb:27838347/6/1,27838347,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J., Lynch S.V., Nariya S., Bhakta N.R., Beigelman A., Castro M., Dyer A.M., Israel E., Kraft M., Martin R.J., Mauger D.T., Rosenberg S.R., Sharp-King T., White S.R., Woodruff P.G., Avila P.C., Denlinger L.C., Holguin F., Lazarus S.C., Lugogo N., Moore W.C., Peters S.P., Que L., Smith L.J., Sorkness C.A., Wechsler M.E., Wenzel S.E., Boushey H.A. , Huang Y.J.","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 6,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,baseline (placebo group),post placebo treatment,placebo treatment,8,8,3 months,16S,4,Illumina,raw counts,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text, Figure 6d",10 January 2021,Lucy Mellor,WikiWorks,Taxa differentially expressed in asthmatic subjects after placebo treatment,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae",3379134|1224|28216|206351|481|538;3379134|203691|203692|136|137;1783272|544448|31969|2085|2092,Complete,Claregrieve1
bsdb:27838347/6/2,27838347,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J., Lynch S.V., Nariya S., Bhakta N.R., Beigelman A., Castro M., Dyer A.M., Israel E., Kraft M., Martin R.J., Mauger D.T., Rosenberg S.R., Sharp-King T., White S.R., Woodruff P.G., Avila P.C., Denlinger L.C., Holguin F., Lazarus S.C., Lugogo N., Moore W.C., Peters S.P., Que L., Smith L.J., Sorkness C.A., Wechsler M.E., Wenzel S.E., Boushey H.A. , Huang Y.J.","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 6,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,baseline (placebo group),post placebo treatment,placebo treatment,8,8,3 months,16S,4,Illumina,raw counts,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Text, Figure 6d",10 January 2021,Lucy Mellor,WikiWorks,Taxa differentially expressed in asthmatic subjects after placebo treatment,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",3379134|1224|1236|2887326|468|469;1783272|201174|1760|2037|2049;3379134|976|200643|171549|171552;1783272|1239|186801|3082720|186804,Complete,Claregrieve1
bsdb:27838347/7/1,27838347,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J., Lynch S.V., Nariya S., Bhakta N.R., Beigelman A., Castro M., Dyer A.M., Israel E., Kraft M., Martin R.J., Mauger D.T., Rosenberg S.R., Sharp-King T., White S.R., Woodruff P.G., Avila P.C., Denlinger L.C., Holguin F., Lazarus S.C., Lugogo N., Moore W.C., Peters S.P., Que L., Smith L.J., Sorkness C.A., Wechsler M.E., Wenzel S.E., Boushey H.A. , Huang Y.J.","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 7,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,healthy control,atopic asthma,atopic asthma subjects,21,42,3 months,16S,4,Illumina,raw counts,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Figure E4a,10 January 2021,Lucy Mellor,WikiWorks,Bacterial phylum significantly enriched or depleted in relative abundance in atopic asthmatic (AA) subjects compared with healthy controls (HC),increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota,k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Spirochaetota",1783272|201174;3379134|976;3384189|32066;3379134|1224;3379134|203691,Complete,Claregrieve1
bsdb:27838347/7/2,27838347,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J., Lynch S.V., Nariya S., Bhakta N.R., Beigelman A., Castro M., Dyer A.M., Israel E., Kraft M., Martin R.J., Mauger D.T., Rosenberg S.R., Sharp-King T., White S.R., Woodruff P.G., Avila P.C., Denlinger L.C., Holguin F., Lazarus S.C., Lugogo N., Moore W.C., Peters S.P., Que L., Smith L.J., Sorkness C.A., Wechsler M.E., Wenzel S.E., Boushey H.A. , Huang Y.J.","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 7,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,healthy control,atopic asthma,atopic asthma subjects,21,42,3 months,16S,4,Illumina,raw counts,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Supplemental Figure E4a,10 January 2021,Lucy Mellor,WikiWorks,Bacterial phylum significantly enriched or depleted in relative abundance in atopic asthmatic (AA) subjects compared with healthy controls (HC),decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Claregrieve1
bsdb:27838347/8/1,27838347,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J., Lynch S.V., Nariya S., Bhakta N.R., Beigelman A., Castro M., Dyer A.M., Israel E., Kraft M., Martin R.J., Mauger D.T., Rosenberg S.R., Sharp-King T., White S.R., Woodruff P.G., Avila P.C., Denlinger L.C., Holguin F., Lazarus S.C., Lugogo N., Moore W.C., Peters S.P., Que L., Smith L.J., Sorkness C.A., Wechsler M.E., Wenzel S.E., Boushey H.A. , Huang Y.J.","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 8,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,healthy control,atopic no asthma,atopic no asthma,21,21,3 months,16S,4,Illumina,raw counts,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Figure E4b,10 January 2021,Lucy Mellor,WikiWorks,Bacterial phylum significantly enriched or depleted in relative abundance in atopic nonasthmatic (ANA) subjects compared with healthy controls (HC),increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota",1783272|201174;1783272|1239;3379134|1224,Complete,Claregrieve1
bsdb:27838347/8/2,27838347,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J., Lynch S.V., Nariya S., Bhakta N.R., Beigelman A., Castro M., Dyer A.M., Israel E., Kraft M., Martin R.J., Mauger D.T., Rosenberg S.R., Sharp-King T., White S.R., Woodruff P.G., Avila P.C., Denlinger L.C., Holguin F., Lazarus S.C., Lugogo N., Moore W.C., Peters S.P., Que L., Smith L.J., Sorkness C.A., Wechsler M.E., Wenzel S.E., Boushey H.A. , Huang Y.J.","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 8,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,healthy control,atopic no asthma,atopic no asthma,21,21,3 months,16S,4,Illumina,raw counts,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Supplemental Figure E4b,10 January 2021,Lucy Mellor,WikiWorks,Bacterial phylum significantly enriched or depleted in relative abundance in atopic nonasthmatic (ANA) subjects compared with healthy controls (HC),decreased,"k__Pseudomonadati|p__Bacteroidota,k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Spirochaetota",3379134|976;3384189|32066;3379134|203691,Complete,Claregrieve1
bsdb:27838347/9/1,27838347,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J., Lynch S.V., Nariya S., Bhakta N.R., Beigelman A., Castro M., Dyer A.M., Israel E., Kraft M., Martin R.J., Mauger D.T., Rosenberg S.R., Sharp-King T., White S.R., Woodruff P.G., Avila P.C., Denlinger L.C., Holguin F., Lazarus S.C., Lugogo N., Moore W.C., Peters S.P., Que L., Smith L.J., Sorkness C.A., Wechsler M.E., Wenzel S.E., Boushey H.A. , Huang Y.J.","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 9,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,atopic no asthma,atopic asthma,atopic asthma subjects,21,42,3 months,16S,4,Illumina,raw counts,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Figure E4c,10 January 2021,Lucy Mellor,WikiWorks,Bacterial phylum significantly enriched or depleted in relative abundance in atopic asthmatic (AA) subjects compared with atopic nonasthmatic (ANA),increased,"k__Pseudomonadati|p__Bacteroidota,k__Fusobacteriati|p__Fusobacteriota",3379134|976;3384189|32066,Complete,Claregrieve1
bsdb:27838347/9/2,27838347,"cross-sectional observational, not case-control",27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J., Lynch S.V., Nariya S., Bhakta N.R., Beigelman A., Castro M., Dyer A.M., Israel E., Kraft M., Martin R.J., Mauger D.T., Rosenberg S.R., Sharp-King T., White S.R., Woodruff P.G., Avila P.C., Denlinger L.C., Holguin F., Lazarus S.C., Lugogo N., Moore W.C., Peters S.P., Que L., Smith L.J., Sorkness C.A., Wechsler M.E., Wenzel S.E., Boushey H.A. , Huang Y.J.","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,"16S ribosomal RNA, Asthma, T(H)2 inflammation, atopy, bacteria, corticosteroids, metabolic pathways, microbiome, short-chain fatty acids, three-gene mean",Experiment 9,United States of America,Homo sapiens,Bronchus,UBERON:0002185,Atopic asthma,EFO:0010638,atopic no asthma,atopic asthma,atopic asthma subjects,21,42,3 months,16S,4,Illumina,raw counts,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Supplemental Figure E4c,10 January 2021,Lucy Mellor,WikiWorks,Bacterial phylum significantly enriched or depleted in relative abundance in atopic asthmatic (AA) subjects compared with atopic nonasthmatic (ANA),decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Spirochaetota",1783272|201174;1783272|1239;3379134|1224;3379134|203691,Complete,Claregrieve1
bsdb:27884202/1/1,27884202,"cross-sectional observational, not case-control",27884202,10.1186/s40168-016-0207-9,NA,"Watt E., Gemmell M.R., Berry S., Glaire M., Farquharson F., Louis P., Murray G.I., El-Omar E. , Hold G.L.",Extending colonic mucosal microbiome analysis-assessment of colonic lavage as a proxy for endoscopic colonic biopsies,Microbiome,2016,"Colonic biopsies, Colonic lavage, Microbiome analysis, Next-generation sequencing",Experiment 1,United Kingdom,Homo sapiens,Sigmoid colon,UBERON:0001159,Sampling site,EFO:0000688,Colonic Biopsy sample,Colonic Lavage Sample,Colonic lavage samples from the sigmoid colon of 23 participants undergoing colorectal cancer screening colonoscopy,23,23,3 months,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,increased,NA,unchanged,increased,Signature 1,Table S2 and Figure 6A,12 November 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",LefSe results showing differentially abundant OTUs between the two samples (Biopsy and Lavage),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|201174|1760|85004|31953|1678;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:27884202/1/2,27884202,"cross-sectional observational, not case-control",27884202,10.1186/s40168-016-0207-9,NA,"Watt E., Gemmell M.R., Berry S., Glaire M., Farquharson F., Louis P., Murray G.I., El-Omar E. , Hold G.L.",Extending colonic mucosal microbiome analysis-assessment of colonic lavage as a proxy for endoscopic colonic biopsies,Microbiome,2016,"Colonic biopsies, Colonic lavage, Microbiome analysis, Next-generation sequencing",Experiment 1,United Kingdom,Homo sapiens,Sigmoid colon,UBERON:0001159,Sampling site,EFO:0000688,Colonic Biopsy sample,Colonic Lavage Sample,Colonic lavage samples from the sigmoid colon of 23 participants undergoing colorectal cancer screening colonoscopy,23,23,3 months,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,increased,NA,unchanged,increased,Signature 2,Table S2 and Figure 6A,12 November 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",LefSe results showing differentially abundant OTUs between the two samples (Biopsy and Lavage),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Diaphorobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae",3379134|1224|1236|2887326|468|469;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|1955243;3379134|976|117743|200644|2762318|501783;3379134|1224|28216|80840|80864;3379134|1224|28216|80840|80864|238749;1783272|1239|186801|3085636|186803;1783272|1239|186801|3082720|186804;1783272|201174|1760|85009|31957|1743;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;3379134|1224|28211|356|82115,Complete,Svetlana up
bsdb:27912057/1/1,27912057,laboratory experiment,27912057,https://doi.org/10.1016%2Fj.cell.2016.11.018,NA,"Sampson T.R., Debelius J.W., Thron T., Janssen S., Shastri G.G., Ilhan Z.E., Challis C., Schretter C.E., Rocha S., Gradinaru V., Chesselet M.F., Keshavarzian A., Shannon K.M., Krajmalnik-Brown R., Wittung-Stafshede P., Knight R. , Mazmanian S.K.",Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease,Cell,2016,"Parkinson’s disease, gut-brain axis, microbiome, microglia, mouse model, short chain fatty acids, synuclein",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Wild-type (WT) mice with fecal microbes from healthy controls (HC),Wild-type (WT) mice with fecal microbes from Parkinson’s disease patients (PD),Germ-free wild-type (WT) mice colonized with fecal microbes from Parkinson’s disease patients (PD),6,6,NA,16S,4,Illumina,centered log-ratio,ANCOM,NA,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6E,20 March 2024,Toyosiolann,"Toyosiolann,Svetlana up,WikiWorks",Differentially abundant taxon in the WT mice with HC fecal transfer and the WT mice with PD fecal transfer.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter",1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|186806|113286,Complete,Svetlana up
bsdb:27912057/1/2,27912057,laboratory experiment,27912057,https://doi.org/10.1016%2Fj.cell.2016.11.018,NA,"Sampson T.R., Debelius J.W., Thron T., Janssen S., Shastri G.G., Ilhan Z.E., Challis C., Schretter C.E., Rocha S., Gradinaru V., Chesselet M.F., Keshavarzian A., Shannon K.M., Krajmalnik-Brown R., Wittung-Stafshede P., Knight R. , Mazmanian S.K.",Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease,Cell,2016,"Parkinson’s disease, gut-brain axis, microbiome, microglia, mouse model, short chain fatty acids, synuclein",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Wild-type (WT) mice with fecal microbes from healthy controls (HC),Wild-type (WT) mice with fecal microbes from Parkinson’s disease patients (PD),Germ-free wild-type (WT) mice colonized with fecal microbes from Parkinson’s disease patients (PD),6,6,NA,16S,4,Illumina,centered log-ratio,ANCOM,NA,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6E,20 March 2024,Toyosiolann,"Toyosiolann,Svetlana up,WikiWorks,Ese",Differentially abundant taxon in the WT mice with HC fecal transfer and the WT mice with PD fecal transfer.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",3379134|976|200643|171549|1853231|574697;1783272|1239|186801|3085636|186803|841;3379134|976|200643|171549|171550,Complete,Svetlana up
bsdb:27912057/2/1,27912057,laboratory experiment,27912057,https://doi.org/10.1016%2Fj.cell.2016.11.018,NA,"Sampson T.R., Debelius J.W., Thron T., Janssen S., Shastri G.G., Ilhan Z.E., Challis C., Schretter C.E., Rocha S., Gradinaru V., Chesselet M.F., Keshavarzian A., Shannon K.M., Krajmalnik-Brown R., Wittung-Stafshede P., Knight R. , Mazmanian S.K.",Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease,Cell,2016,"Parkinson’s disease, gut-brain axis, microbiome, microglia, mouse model, short chain fatty acids, synuclein",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,ASO mice with fecal microbes from healthy controls (HC),ASO mice with fecal microbes from Parkinson’s disease patients (PD),"Germ-free mice, Thy1-α-synuclein genotype (ASO) colonized with fecal microbes from Parkinson’s disease patients (PD)",6,6,NA,16S,4,Illumina,centered log-ratio,ANCOM,NA,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6E,2 April 2024,Svetlana up,"Svetlana up,WikiWorks,Ese",Differentially abundant taxon in the ASO mice with HC fecal transfer and the ASO mice with PD fecal transfer.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|976|200643|171549|815|816;3379134|200940|3031449|213115|194924|35832;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|1903414|583;1783272|1239|186801|186802|186806|113286;1783272|1239|909932|1843489|31977,Complete,Svetlana up
bsdb:27912057/2/2,27912057,laboratory experiment,27912057,https://doi.org/10.1016%2Fj.cell.2016.11.018,NA,"Sampson T.R., Debelius J.W., Thron T., Janssen S., Shastri G.G., Ilhan Z.E., Challis C., Schretter C.E., Rocha S., Gradinaru V., Chesselet M.F., Keshavarzian A., Shannon K.M., Krajmalnik-Brown R., Wittung-Stafshede P., Knight R. , Mazmanian S.K.",Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease,Cell,2016,"Parkinson’s disease, gut-brain axis, microbiome, microglia, mouse model, short chain fatty acids, synuclein",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,ASO mice with fecal microbes from healthy controls (HC),ASO mice with fecal microbes from Parkinson’s disease patients (PD),"Germ-free mice, Thy1-α-synuclein genotype (ASO) colonized with fecal microbes from Parkinson’s disease patients (PD)",6,6,NA,16S,4,Illumina,centered log-ratio,ANCOM,NA,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6E,2 April 2024,Svetlana up,"Svetlana up,WikiWorks,Ese",Differentially abundant taxon in the ASO mice with HC fecal transfer and the ASO mice with PD fecal transfer.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Hymenochaetales|f__Rickenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803;4751|5204|155619|139380|1124673;1783272|1239|186801|3082720|186804;1783272|1239|186801|186802|31979,Complete,Svetlana up
bsdb:27988330/1/1,27988330,case-control,27988330,10.1016/j.jpsychires.2016.12.007,NA,"Evans S.J., Bassis C.M., Hein R., Assari S., Flowers S.A., Kelly M.B., Young V.B., Ellingrod V.E. , McInnis M.G.",The gut microbiome composition associates with bipolar disorder and illness severity,Journal of psychiatric research,2017,"Bipolar disorder, Faecalibacterium, Generalized Anxiety Disorder scale, Microbiome, Patient Health Questionnaire, Pittsburg Sleep Quality Index",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,Healthy controls,Bipolar,Individuals with bipolar disorder,64,115,NA,16S,4,Illumina,relative abundances,Logistic Regression,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 2b,10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy","Table 2b gives the mean and (SD) values for OTU fractional representations (percent of total) for all OTUs greater than 1% total in either group. P-values derive from logistical regressions with diagnosis (1,0) as the outcome measure and OTU as the predictor, adjusting for age, gender and BMI. Values in bold remained significant following FDR correction at the p<0.05 level.t",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,1783272|1239|186801|186802|216572|216851,Complete,Peace Sandy
bsdb:28018325/1/1,28018325,time series / longitudinal observational,28018325,10.3389/fmicb.2016.01997,NA,"Nagpal R., Tsuji H., Takahashi T., Kawashima K., Nagata S., Nomoto K. , Yamashiro Y.",Sensitive Quantitative Analysis of the Meconium Bacterial Microbiota in Healthy Term Infants Born Vaginally or by Cesarean Section,Frontiers in microbiology,2016,"C-section, Lactobacillus, RT-qPCR, dysbiosis, gut bacteria, intestinal microbiota, meconium",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,vaginal delivery after 7 days of delivery,C-section delivery,NA,134,17,NA,16S,NA,RT-qPCR,raw counts,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,"Differences in the detection rate of Lactobacillus genus, subgroups and species between vaginally- and cesarean-born babies at different time-points during the first 3 years of life.",decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,1783272|1239|91061|186826|33958|1578|1596,Complete,Shaimaa Elsafoury
bsdb:28018325/2/1,28018325,time series / longitudinal observational,28018325,10.3389/fmicb.2016.01997,NA,"Nagpal R., Tsuji H., Takahashi T., Kawashima K., Nagata S., Nomoto K. , Yamashiro Y.",Sensitive Quantitative Analysis of the Meconium Bacterial Microbiota in Healthy Term Infants Born Vaginally or by Cesarean Section,Frontiers in microbiology,2016,"C-section, Lactobacillus, RT-qPCR, dysbiosis, gut bacteria, intestinal microbiota, meconium",Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,vaginal delivery after 3 months of delivery,C-section delivery,NA,134,17,NA,16S,NA,RT-qPCR,raw counts,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,"Differences in the detection rate of Lactobacillus genus, subgroups and species between vaginally- and cesarean-born babies at different time-points during the first 3 years of life.",decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Shaimaa Elsafoury
bsdb:28018325/3/1,28018325,time series / longitudinal observational,28018325,10.3389/fmicb.2016.01997,NA,"Nagpal R., Tsuji H., Takahashi T., Kawashima K., Nagata S., Nomoto K. , Yamashiro Y.",Sensitive Quantitative Analysis of the Meconium Bacterial Microbiota in Healthy Term Infants Born Vaginally or by Cesarean Section,Frontiers in microbiology,2016,"C-section, Lactobacillus, RT-qPCR, dysbiosis, gut bacteria, intestinal microbiota, meconium",Experiment 3,Japan,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,vaginal delivery after 6 months of delivery,C-section delivery,NA,134,17,NA,16S,NA,RT-qPCR,raw counts,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,"Differences in the detection rate of Lactobacillus genus, subgroups and species between vaginally- and cesarean-born babies at different time-points during the first 3 years of life.",decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,1783272|1239|91061|186826|33958|2742598|1598,Complete,Shaimaa Elsafoury
bsdb:28035686/1/1,28035686,"cross-sectional observational, not case-control",28035686,10.1002/phar.1890,NA,"Flowers S.A., Evans S.J., Ward K.M., McInnis M.G. , Ellingrod V.L.",Interaction Between Atypical Antipsychotics and the Gut Microbiome in a Bipolar Disease Cohort,Pharmacotherapy,2017,"atypical antipsychotics, metabolic disease, microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,non users,atypical antipsychotic users,Medication group was defined by the use of an Atypical Antipsychotics at the time of fecal sample collection,68,49,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,decreased,NA,Signature 1,Figure3,10 January 2021,Fatima Zohra,WikiWorks,Differentially abundant members of gut microbiota in bipolar disorder (BD) patients treated with atypical antipsychotics (AAP),increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,1783272|1239|186801|3085636|186803,Complete,Shaimaa Elsafoury
bsdb:28035686/1/2,28035686,"cross-sectional observational, not case-control",28035686,10.1002/phar.1890,NA,"Flowers S.A., Evans S.J., Ward K.M., McInnis M.G. , Ellingrod V.L.",Interaction Between Atypical Antipsychotics and the Gut Microbiome in a Bipolar Disease Cohort,Pharmacotherapy,2017,"atypical antipsychotics, metabolic disease, microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,non users,atypical antipsychotic users,Medication group was defined by the use of an Atypical Antipsychotics at the time of fecal sample collection,68,49,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,decreased,NA,Signature 2,Figure3,10 January 2021,Fatima Zohra,WikiWorks,Differentially abundant members of gut microbiota in bipolar disorder (BD) patients treated with atypical antipsychotics (AAP),decreased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,3379134|74201|203494|48461|1647988|239934,Complete,Shaimaa Elsafoury
bsdb:28038683/1/1,28038683,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters B.A., Dominianni C., Shapiro J.A., Church T.R., Wu J., Miller G., Yuen E., Freiman H., Lustbader I., Salik J., Friedlander C., Hayes R.B. , Ahn J.",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,"Adenoma, Cancer, Colorectal, Microbiome, Microbiota, Polyp, Serrated",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,controls,conventional adenoma cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,144,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,NA,NA,NA,decreased,Signature 1,Table 2 + Supplemental Table S5 + S3+ S4,10 January 2021,Levi Waldron,WikiWorks,"Differential abundance was detected by the “DESeq” function in the DESeq2 package. All classes and genera with an FDR-adjusted q < 0.10 are included in the table. Models were adjusted for sex, age, study, and categorical BMI. See Additional file 1: Table S5 for comparisons at the phylum, order, and family level",increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae",1783272|1239|91061;3379134|1224|1236;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|186826|1300|1301;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|3085636|186803|189330;1783272|1239|909932|1843488|909930|33024;3379134|1224|28216|80840|995019|40544;1783272|201174|1760|2037;1783272|201174|1760|2037|2049;3379134|1224|28216|80840|506;1783272|1239|91061|186826;1783272|1239|91061|186826|1300;1783272|1239|909932|1843489|31977;3379134|1224|1236|91347;1783272|201174|1760|85007|1653;1783272|1239|91061|186826|33958|2759736|57037;1783272|1239|91061|1385|186817|1386;1783272|1239|91061|1385|186817,Complete,Fatima
bsdb:28038683/1/2,28038683,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters B.A., Dominianni C., Shapiro J.A., Church T.R., Wu J., Miller G., Yuen E., Freiman H., Lustbader I., Salik J., Friedlander C., Hayes R.B. , Ahn J.",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,"Adenoma, Cancer, Colorectal, Microbiome, Microbiota, Polyp, Serrated",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,controls,conventional adenoma cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,144,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,NA,NA,NA,decreased,Signature 2,Table 2 + Supplemental Table S5 + S3+ S4,10 January 2021,Levi Waldron,WikiWorks,"Differential abundance was detected by the “DESeq” function in the DESeq2 package. All classes and genera with an FDR-adjusted q < 0.10 are included in the table. Models were adjusted for sex, age, study, and categorical BMI. See Additional file 1: Table S5 for comparisons at the phylum, order, and family level",decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Cyanobacteriota",1783272|1239|526524|526525|2810280|100883;1783272|1117,Complete,Shaimaa Elsafoury
bsdb:28038683/2/1,28038683,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters B.A., Dominianni C., Shapiro J.A., Church T.R., Wu J., Miller G., Yuen E., Freiman H., Lustbader I., Salik J., Friedlander C., Hayes R.B. , Ahn J.",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,"Adenoma, Cancer, Colorectal, Microbiome, Microbiota, Polyp, Serrated",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Hyperplastic Polyp,EFO:1000299,controls,hyperplastic polyp cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,40,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 2 + Supplemental Table S5 + S3+ S4,10 January 2021,Levi Waldron,WikiWorks,"Differential abundance was detected by the “DESeq” function in the DESeq2 package. All classes and genera with an FDR-adjusted q < 0.10 are included in the table. Models were adjusted for sex, age, study, and categorical BMI. See Additional file 1: Table S5 for comparisons at the phylum, order, and family level",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae",1783272|1239|186801|3085636|186803|207244;1783272|1239|91061|186826|33958|2759736|57037,Complete,Shaimaa Elsafoury
bsdb:28038683/2/2,28038683,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters B.A., Dominianni C., Shapiro J.A., Church T.R., Wu J., Miller G., Yuen E., Freiman H., Lustbader I., Salik J., Friedlander C., Hayes R.B. , Ahn J.",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,"Adenoma, Cancer, Colorectal, Microbiome, Microbiota, Polyp, Serrated",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Hyperplastic Polyp,EFO:1000299,controls,hyperplastic polyp cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,40,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 2 + Supplemental Table S5 + S3+ S4,10 January 2021,Levi Waldron,WikiWorks,"Differential abundance was detected by the “DESeq” function in the DESeq2 package. All classes and genera with an FDR-adjusted q < 0.10 are included in the table. Models were adjusted for sex, age, study, and categorical BMI. See Additional file 1: Table S5 for comparisons at the phylum, order, and family level",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales",3379134|1224|1236;1783272|1239|526524|526525|2810280|100883;3379134|1224|1236|91347,Complete,Shaimaa Elsafoury
bsdb:28038683/3/1,28038683,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters B.A., Dominianni C., Shapiro J.A., Church T.R., Wu J., Miller G., Yuen E., Freiman H., Lustbader I., Salik J., Friedlander C., Hayes R.B. , Ahn J.",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,"Adenoma, Cancer, Colorectal, Microbiome, Microbiota, Polyp, Serrated",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Colon Sessile Serrated Adenoma/Polyp,EFO:1000189,controls,Sessile serrated adenoma cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,33,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 2 + Supplemental Table S5 + S3+ S4,10 January 2021,Levi Waldron,WikiWorks,"Differential abundance was detected by the “DESeq” function in the DESeq2 package. All classes and genera with an FDR-adjusted q < 0.10 are included in the table. Models were adjusted for sex, age, study, and categorical BMI. See Additional file 1: Table S5 for comparisons at the phylum, order, and family level",decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria",1783272|1239|526524;3379134|1224|1236,Complete,Shaimaa Elsafoury
bsdb:28038683/4/1,28038683,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters B.A., Dominianni C., Shapiro J.A., Church T.R., Wu J., Miller G., Yuen E., Freiman H., Lustbader I., Salik J., Friedlander C., Hayes R.B. , Ahn J.",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,"Adenoma, Cancer, Colorectal, Microbiome, Microbiota, Polyp, Serrated",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,controls,Proximal conventional adenoma cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,87,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Table S6 + S3,10 January 2021,Marianthi Thomatos,WikiWorks,"Differentially abundant taxa (phylum‐OTU level) between controls and proximal or distal conventional adenoma cases, as detected by the DESeq function in the DESeq2 package. Models were adjusted for age, sex, categorical BMI, and study. All taxa with an FDR‐adjusted q<0.10 are included in the table.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae",1783272|201174|1760|2037;1783272|201174|1760|2037|2049;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|186826|1300;1783272|1239|186801|186802|31979|1485;3379134|976|200643|171549|171551|836;1783272|1239|91061;1783272|1239|91061|186826;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|91061|186826|1300|1301;1783272|1239|1737404|1737405|1737406;1783272|1239|1737404|1737405|1570339|165779;3379134|976|200643|171549|1853231|283168;1783272|1239|909932|1843489|31977;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|189330;3379134|1224|28216|80840|995019|40544;1783272|1239|909932|1843488|909930|33024;3379134|1224|28216|80840|506;3379134|1224|1236|91347;3379134|1224|1236;3379134|976|200643|171549|1853231,Complete,Shaimaa Elsafoury
bsdb:28038683/4/2,28038683,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters B.A., Dominianni C., Shapiro J.A., Church T.R., Wu J., Miller G., Yuen E., Freiman H., Lustbader I., Salik J., Friedlander C., Hayes R.B. , Ahn J.",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,"Adenoma, Cancer, Colorectal, Microbiome, Microbiota, Polyp, Serrated",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,controls,Proximal conventional adenoma cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,87,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplemental Table S6 + S3,10 January 2021,Marianthi Thomatos,WikiWorks,"Differentially abundant taxa (phylum‐OTU level) between controls and proximal or distal conventional adenoma cases, as detected by the DESeq function in the DESeq2 package. Models were adjusted for age, sex, categorical BMI, and study. All taxa with an FDR‐adjusted q<0.10 are included in the table.",decreased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,1783272|1239|526524|526525|2810280|100883,Complete,Shaimaa Elsafoury
bsdb:28038683/5/1,28038683,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters B.A., Dominianni C., Shapiro J.A., Church T.R., Wu J., Miller G., Yuen E., Freiman H., Lustbader I., Salik J., Friedlander C., Hayes R.B. , Ahn J.",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,"Adenoma, Cancer, Colorectal, Microbiome, Microbiota, Polyp, Serrated",Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,controls,Distal conventional adenoma cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,55,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Table S6 + S3,10 January 2021,Marianthi Thomatos,"Fatima,Merit,WikiWorks,Lwaldron,Davvve","Differentially abundant taxa (phylum‐OTU level) between controls and proximal or distal conventional adenoma cases, as detected by the DESeq function in the DESeq2 package. Models were adjusted for age, sex, categorical BMI, and study. All taxa with an FDR‐adjusted q<0.10, are included in the table.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Thermotogati|p__Synergistota,k__Thermotogati|p__Synergistota",1783272|1239|186801|3082768|990719;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|544448|31969;3384194|508458;3384194|508458,Complete,Fatima
bsdb:28038683/6/1,28038683,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters B.A., Dominianni C., Shapiro J.A., Church T.R., Wu J., Miller G., Yuen E., Freiman H., Lustbader I., Salik J., Friedlander C., Hayes R.B. , Ahn J.",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,"Adenoma, Cancer, Colorectal, Microbiome, Microbiota, Polyp, Serrated",Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,controls,Non-advanced conventional adenoma cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,121,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Table S6 + S3,10 January 2021,Marianthi Thomatos,WikiWorks,"Differentially abundant taxa (phylum‐OTU level) between controls and non‐advanced or advanced conventional adenoma cases, as detected by the DESeq function in the DESeq2 package. Models were adjusted for age, sex, categorical BMI, and study. All taxa with an FDR‐adjusted q<0.10 are included in the table.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549|1853231|283168;1783272|1239|91061;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|2759736|57037;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|189330;1783272|1239|909932|1843489|31977;3379134|1224|28216|80840|995019|40544;3379134|1224|28216|80840|506;1783272|1239|909932|1843488|909930|33024,Complete,Shaimaa Elsafoury
bsdb:28038683/7/1,28038683,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters B.A., Dominianni C., Shapiro J.A., Church T.R., Wu J., Miller G., Yuen E., Freiman H., Lustbader I., Salik J., Friedlander C., Hayes R.B. , Ahn J.",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,"Adenoma, Cancer, Colorectal, Microbiome, Microbiota, Polyp, Serrated",Experiment 7,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,controls,advanced conventional adenoma cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,22,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,NA,NA,NA,decreased,Signature 1,Supplemental Table S7 + S3,10 January 2021,Marianthi Thomatos,WikiWorks,"Differentially abundant taxa (phylum‐OTU level) between controls and non‐advanced or advanced conventional adenoma cases, as detected by the DESeq function in the DESeq2 package. Models were adjusted for age, sex, categorical BMI, and study. All taxa with an FDR‐adjusted q<0.10 are included in the table.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae",1783272|201174|1760|2037;1783272|201174|1760|2037|2049;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85007|1653|1716;3379134|976|200643|171549|171551|836;1783272|1239|1737404|1737405|1737406;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|1737404|1737405|1570339|162289;3379134|1224|1236|135625;3379134|1224|1236|135625|712;3379134|1224|1236|135625|712|724;1783272|201174|1760|85007|1653,Complete,Shaimaa Elsafoury
bsdb:28038683/7/2,28038683,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters B.A., Dominianni C., Shapiro J.A., Church T.R., Wu J., Miller G., Yuen E., Freiman H., Lustbader I., Salik J., Friedlander C., Hayes R.B. , Ahn J.",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,"Adenoma, Cancer, Colorectal, Microbiome, Microbiota, Polyp, Serrated",Experiment 7,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,controls,advanced conventional adenoma cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,22,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,NA,NA,NA,decreased,Signature 2,Supplemental Table S7 + S3,10 January 2021,Marianthi Thomatos,WikiWorks,"Differentially abundant taxa (phylum‐OTU level) between controls and non‐advanced or advanced conventional adenoma cases, as detected by the DESeq function in the DESeq2 package. Models were adjusted for age, sex, categorical BMI, and study. All taxa with an FDR‐adjusted q<0.10 are included in the table.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria",3379134|976|200643|171549|2005519;1783272|1117;1783272|1239|186801|3082768|990719;1783272|1239|186801|3085636|186803|140625;1783272|1239|186801|3085636|186803|28050;3379134|1224|28211,Complete,Shaimaa Elsafoury
bsdb:28094305/1/1,28094305,case-control,28094305,10.1038/srep40826,NA,"Zinkernagel M.S., Zysset-Burri D.C., Keller I., Berger L.E., Leichtle A.B., Largiadèr C.R., Fiedler G.M. , Wolf S.",Association of the Intestinal Microbiome with the Development of Neovascular Age-Related Macular Degeneration,Scientific reports,2017,NA,Experiment 1,Switzerland,Homo sapiens,Feces,UBERON:0001988,Age-related macular degeneration,EFO:0001365,Control,AMD (Age-related macular degeneration),Patients with clinically confirmed recent onset of neovascular Age-related macular degeneration,11,12,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3b, c",19 June 2025,Anne-mariesharp,Anne-mariesharp,LEfSe analysis identifying differentially abundant taxa in neovascular Age-related macular degeneration patients compared to controls,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",1783272|1239|186801|186802|216572|244127;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803|2316020|33039,Complete,KateRasheed
bsdb:28094305/1/2,28094305,case-control,28094305,10.1038/srep40826,NA,"Zinkernagel M.S., Zysset-Burri D.C., Keller I., Berger L.E., Leichtle A.B., Largiadèr C.R., Fiedler G.M. , Wolf S.",Association of the Intestinal Microbiome with the Development of Neovascular Age-Related Macular Degeneration,Scientific reports,2017,NA,Experiment 1,Switzerland,Homo sapiens,Feces,UBERON:0001988,Age-related macular degeneration,EFO:0001365,Control,AMD (Age-related macular degeneration),Patients with clinically confirmed recent onset of neovascular Age-related macular degeneration,11,12,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3b, c",19 June 2025,Anne-mariesharp,Anne-mariesharp,LEfSe analysis identifying differentially abundant taxa in neovascular Age-related macular degeneration patients compared to controls,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii",3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|28111,Complete,KateRasheed
bsdb:28094305/2/1,28094305,case-control,28094305,10.1038/srep40826,NA,"Zinkernagel M.S., Zysset-Burri D.C., Keller I., Berger L.E., Leichtle A.B., Largiadèr C.R., Fiedler G.M. , Wolf S.",Association of the Intestinal Microbiome with the Development of Neovascular Age-Related Macular Degeneration,Scientific reports,2017,NA,Experiment 2,Switzerland,Homo sapiens,Feces,UBERON:0001988,Age-related macular degeneration,EFO:0001365,Control,AMD (Age-related macular degeneration),Patients with clinically confirmed recent onset of neovascular Age-related macular degeneration,11,12,3 months,WMS,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3d,19 June 2025,Anne-mariesharp,Anne-mariesharp,Box plots representing the mean abundance +/−SD of bacterial genera and species associated with Age-related macular degeneration,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",1783272|1239|186801|186802|216572|244127;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|3085636|186803|2316020|33039,Complete,KateRasheed
bsdb:28094305/2/2,28094305,case-control,28094305,10.1038/srep40826,NA,"Zinkernagel M.S., Zysset-Burri D.C., Keller I., Berger L.E., Leichtle A.B., Largiadèr C.R., Fiedler G.M. , Wolf S.",Association of the Intestinal Microbiome with the Development of Neovascular Age-Related Macular Degeneration,Scientific reports,2017,NA,Experiment 2,Switzerland,Homo sapiens,Feces,UBERON:0001988,Age-related macular degeneration,EFO:0001365,Control,AMD (Age-related macular degeneration),Patients with clinically confirmed recent onset of neovascular Age-related macular degeneration,11,12,3 months,WMS,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3d,19 June 2025,Anne-mariesharp,Anne-mariesharp,Box plots representing the mean abundance +/−SD of bacterial genera and species associated with Age-related macular degeneration,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,3379134|976|200643|171549|815|816|28111,Complete,KateRasheed
bsdb:28111632/1/1,28111632,case-control,28111632,10.5430/jer.v2n2p92,NA,"Kato I., Vasquez A.A., Moyerbrailean G., Land S., Sun J., Lin H.S. , Ram J.L.",Oral microbiome and history of smoking and colorectal cancer,Journal of epidemiological research,2016,"Cigarette smoking, Colorectal cancer, Oral microbiome",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Colorectal cancer,EFO:0005842,Healthy Controls(HC),Colorectal cancer,colorectal cancer; 24% of the colorectal cancer cases were current smokers. 16% habitual alcohol drinkers,122,68,NA,16S,34,Illumina,relative abundances,"Negative Binomial Regression,Zero-Inflated Beta Regression",0.05,NA,NA,"race,region of residence,sex","age,smoking status",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 3,4 April 2023,Aiyshaaaa,"Aiyshaaaa,WikiWorks","The effects** and 95% confidence intervals (in parenthesis) of age, cancer history and current smoking on relative
bacterial count at each taxonomic level based on negative binomial models",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota",1783272|201174|1760|2037;1783272|201174;1783272|1239|91061;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85006|1268;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|43675;1783272|1239,Complete,Lwaldron
bsdb:28111632/1/2,28111632,case-control,28111632,10.5430/jer.v2n2p92,NA,"Kato I., Vasquez A.A., Moyerbrailean G., Land S., Sun J., Lin H.S. , Ram J.L.",Oral microbiome and history of smoking and colorectal cancer,Journal of epidemiological research,2016,"Cigarette smoking, Colorectal cancer, Oral microbiome",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Colorectal cancer,EFO:0005842,Healthy Controls(HC),Colorectal cancer,colorectal cancer; 24% of the colorectal cancer cases were current smokers. 16% habitual alcohol drinkers,122,68,NA,16S,34,Illumina,relative abundances,"Negative Binomial Regression,Zero-Inflated Beta Regression",0.05,NA,NA,"race,region of residence,sex","age,smoking status",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table 3,4 April 2023,Aiyshaaaa,"Aiyshaaaa,WikiWorks","The effects** and 95% confidence intervals (in parenthesis) of age, cancer history and current smoking on relative
bacterial count at each taxonomic level based on negative binomial models",decreased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia",3379134|1224;3379134|976|200643;3384189|32066|203490,Complete,Lwaldron
bsdb:28111632/3/1,28111632,case-control,28111632,10.5430/jer.v2n2p92,NA,"Kato I., Vasquez A.A., Moyerbrailean G., Land S., Sun J., Lin H.S. , Ram J.L.",Oral microbiome and history of smoking and colorectal cancer,Journal of epidemiological research,2016,"Cigarette smoking, Colorectal cancer, Oral microbiome",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Colorectal cancer,EFO:0005842,Young,Old (≥ 65 yrs),“Advanced age” was defined as 65 years or older.,103,87,NA,16S,34,Illumina,relative abundances,"Negative Binomial Regression,Zero-Inflated Beta Regression",0.05,NA,NA,"race,region of residence,sex","age,smoking status",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 3,29 July 2022,Jeshudy,"Jeshudy,Aiyshaaaa,WikiWorks","The effects** and 95% confidence intervals (in parenthesis) of age, cancer history and current smoking on relative bacterial count at each taxonomic level based on negative binomial models",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|976|200643|171549|171551|836|837;1783272|1239|91061|186826|1300|1301|1302;1783272|1239;1783272|1239|91061;1783272|1239|91061|186826;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301,Complete,Lwaldron
bsdb:28111632/3/2,28111632,case-control,28111632,10.5430/jer.v2n2p92,NA,"Kato I., Vasquez A.A., Moyerbrailean G., Land S., Sun J., Lin H.S. , Ram J.L.",Oral microbiome and history of smoking and colorectal cancer,Journal of epidemiological research,2016,"Cigarette smoking, Colorectal cancer, Oral microbiome",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Colorectal cancer,EFO:0005842,Young,Old (≥ 65 yrs),“Advanced age” was defined as 65 years or older.,103,87,NA,16S,34,Illumina,relative abundances,"Negative Binomial Regression,Zero-Inflated Beta Regression",0.05,NA,NA,"race,region of residence,sex","age,smoking status",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table 3,4 April 2023,Aiyshaaaa,"Aiyshaaaa,WikiWorks","The effects** and 95% confidence intervals (in parenthesis) of age, cancer history and current smoking on relative
bacterial count at each taxonomic level based on negative binomial models",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia",3379134|976|200643;3379134|976|200643|171549;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836;1783272|201174|1760|2037;1783272|201174|1760|85006|1268;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|43675;1783272|201174;3379134|1224;3384189|32066|203490,Complete,Lwaldron
bsdb:28111632/4/1,28111632,case-control,28111632,10.5430/jer.v2n2p92,NA,"Kato I., Vasquez A.A., Moyerbrailean G., Land S., Sun J., Lin H.S. , Ram J.L.",Oral microbiome and history of smoking and colorectal cancer,Journal of epidemiological research,2016,"Cigarette smoking, Colorectal cancer, Oral microbiome",Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,Colorectal cancer,EFO:0005842,Non Smokers,Current Smokers,"Current smokers, where defined as ever smokers who smoked at least one cigarette per day for six months or longer and were smoking within 2 year prior to interview.",138,52,NA,16S,34,Illumina,relative abundances,"Negative Binomial Regression,Zero-Inflated Beta Regression",0.05,NA,NA,"race,region of residence,sex","age,smoking status",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 3,29 July 2022,Jeshudy,"Jeshudy,Aiyshaaaa,WikiWorks","The effects** and 95% confidence intervals (in parenthesis) of age, cancer history and current smoking on relative bacterial count at each taxonomic level based on negative binomial models",increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Actinomycetota",1783272|1239;1783272|1239|186801;1783272|1239|186801|186802|1898207;1783272|1239|909932|1843489|31977;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|39777;3379134|976|200643;1783272|201174,Complete,Lwaldron
bsdb:28111632/4/2,28111632,case-control,28111632,10.5430/jer.v2n2p92,NA,"Kato I., Vasquez A.A., Moyerbrailean G., Land S., Sun J., Lin H.S. , Ram J.L.",Oral microbiome and history of smoking and colorectal cancer,Journal of epidemiological research,2016,"Cigarette smoking, Colorectal cancer, Oral microbiome",Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,Colorectal cancer,EFO:0005842,Non Smokers,Current Smokers,"Current smokers, where defined as ever smokers who smoked at least one cigarette per day for six months or longer and were smoking within 2 year prior to interview.",138,52,NA,16S,34,Illumina,relative abundances,"Negative Binomial Regression,Zero-Inflated Beta Regression",0.05,NA,NA,"race,region of residence,sex","age,smoking status",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table 3,29 July 2022,Jeshudy,"Jeshudy,Aiyshaaaa,WikiWorks","The effects** and 95% confidence intervals (in parenthesis) of age, cancer history and current smoking on relative bacterial count at each taxonomic level based on negative binomial models",decreased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria mucosa,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia",3379134|1224;3379134|1224|28216;3379134|1224|28216|206351;3379134|1224|28216|206351|481;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481|482|488;3384189|32066|203490,Complete,Lwaldron
bsdb:28112736/1/1,28112736,prospective cohort,28112736,10.1038/nm.4272,NA,"Chu D.M., Ma J., Prince A.L., Antony K.M., Seferovic M.D. , Aagaard K.M.",Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery,Nature medicine,2017,NA,Experiment 1,United States of America,Homo sapiens,"Feces,Saliva,Anterior naris,Posterior fornix of vagina,Epithelium of elbow","UBERON:0001988,UBERON:0001836,UBERON:2001427,UBERON:0016486,UBERON:0003229",Microbiome,EFO:0004982,Maternal samples taken at delivery.,Neonatal samples taken at delivery,Neonatal samples taken at delivery,82,82,NA,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. S3.,6 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","Characteristics Taxa of Neonatal and Maternal Microbiota at Delivery and 6 Weeks determined  by Linear Discriminant Analysis Effect Size (LEfSe) Representative taxa for each body site (Linear Discriminant Analysis (LDA) Score >4, p<0.05) are shown. (A) Maternal samples taken at delivery. (B) Neonatal samples taken at delivery.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85009|31957|1743;3379134|1224|28211|204457|41297|13687;1783272|201174|1760|85004|31953|2701;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|33958|1578;3379134|1224|1236|91347|543,Complete,Peace Sandy
bsdb:28112736/1/2,28112736,prospective cohort,28112736,10.1038/nm.4272,NA,"Chu D.M., Ma J., Prince A.L., Antony K.M., Seferovic M.D. , Aagaard K.M.",Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery,Nature medicine,2017,NA,Experiment 1,United States of America,Homo sapiens,"Feces,Saliva,Anterior naris,Posterior fornix of vagina,Epithelium of elbow","UBERON:0001988,UBERON:0001836,UBERON:2001427,UBERON:0016486,UBERON:0003229",Microbiome,EFO:0004982,Maternal samples taken at delivery.,Neonatal samples taken at delivery,Neonatal samples taken at delivery,82,82,NA,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. S3,6 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","Characteristics Taxa of Neonatal and Maternal Microbiota at Delivery and 6 Weeks determined by Linear Discriminant Analysis Effect Size (LEfSe) Representative taxa for each body site (Linear Discriminant Analysis (LDA) Score >4, p<0.05) are shown. (A) Maternal samples taken at delivery. (B) Neonatal samples taken at delivery.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|201174|1760|85007|1653|1716;1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|1283313;3379134|1224|28216|206351|481|482;3379134|1224|1236|135625|712|724;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|1300|1301;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|91061|1385|90964|1279;1783272|201174|1760|85009|31957|1743;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|2701;1783272|1239|91061|186826|33958|1578,Complete,Peace Sandy
bsdb:28118207/1/1,28118207,"cross-sectional observational, not case-control",28118207,10.1097/QAD.0000000000001409,NA,"Nowak R.G., Bentzen S.M., Ravel J., Crowell T.A., Dauda W., Ma B., Liu H., Blattner W.A., Baral S.D. , Charurat M.E.","Rectal microbiota among HIV-uninfected, untreated HIV, and treated HIV-infected in Nigeria","AIDS (London, England)",2017,NA,Experiment 1,Nigeria,Homo sapiens,Rectum,UBERON:0001052,HIV infection,EFO:0000764,HIV-uninfected MSM,ART-treated HIV infected MSM,Men who have sex with men (MSM) with HIV that has been treated with antiretroviral therapy (ART),55,34,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 1,10 January 2021,Michael Lutete,"WikiWorks,Folakunmi","Relative abundance of most common rectal genera within 5 phyla, stratified by HIV and ART status",increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus",1783272|1239|1737404|1737405|1570339|165779;3379134|29547|3031852|213849|72294|194;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|1737404|1737405|1570339|162289,Complete,Folakunmi
bsdb:28118207/1/2,28118207,"cross-sectional observational, not case-control",28118207,10.1097/QAD.0000000000001409,NA,"Nowak R.G., Bentzen S.M., Ravel J., Crowell T.A., Dauda W., Ma B., Liu H., Blattner W.A., Baral S.D. , Charurat M.E.","Rectal microbiota among HIV-uninfected, untreated HIV, and treated HIV-infected in Nigeria","AIDS (London, England)",2017,NA,Experiment 1,Nigeria,Homo sapiens,Rectum,UBERON:0001052,HIV infection,EFO:0000764,HIV-uninfected MSM,ART-treated HIV infected MSM,Men who have sex with men (MSM) with HIV that has been treated with antiretroviral therapy (ART),55,34,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 1,10 January 2021,Michael Lutete,"WikiWorks,Folakunmi","Relative abundance of most common rectal genera within 5 phyla, stratified by HIV and ART status",decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,Folakunmi
bsdb:28173873/1/1,28173873,case-control,28173873,10.1186/s13073-017-0405-5,NA,"Wang H., Funchain P., Bebek G., Altemus J., Zhang H., Niazi F., Peterson C., Lee W.T., Burkey B.B. , Eng C.",Microbiomic differences in tumor and paired-normal tissue in head and neck squamous cell carcinomas,Genome medicine,2017,"Bacteria, Head and neck squamous cell carcinoma (HNSCC), Microbiome",Experiment 1,United States of America,Homo sapiens,Oral cavity,UBERON:0000167,Head and neck squamous cell carcinoma,EFO:0000181,normal adjacent tissues,squamous cell carcinoma tissues,tissues with evidence of squamous cell carcinoma,121,121,NA,16S,1234,Sanger,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3 +text,10 January 2021,Nidhi Saini,WikiWorks,Significant taxa by Wilcoxon signed-rank in paired tumor and normal tissue. Box plots representing relative abundances of taxa observed to be significantly different between tumor (orange) and adjacent normal (blue) samples by paired Wilcoxon signed-rank testing after correction for FDR.,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas",1783272|1239|1737404|1737405|1737406;1783272|1239|1737404|1737405|1570339|543311,Complete,Shaimaa Elsafoury
bsdb:28173873/1/2,28173873,case-control,28173873,10.1186/s13073-017-0405-5,NA,"Wang H., Funchain P., Bebek G., Altemus J., Zhang H., Niazi F., Peterson C., Lee W.T., Burkey B.B. , Eng C.",Microbiomic differences in tumor and paired-normal tissue in head and neck squamous cell carcinomas,Genome medicine,2017,"Bacteria, Head and neck squamous cell carcinoma (HNSCC), Microbiome",Experiment 1,United States of America,Homo sapiens,Oral cavity,UBERON:0000167,Head and neck squamous cell carcinoma,EFO:0000181,normal adjacent tissues,squamous cell carcinoma tissues,tissues with evidence of squamous cell carcinoma,121,121,NA,16S,1234,Sanger,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3 +text,10 January 2021,Shaimaa Elsafoury,WikiWorks,Significant taxa by Wilcoxon signed-rank in paired tumor and normal tissue. Box plots representing relative abundances of taxa observed to be significantly different between tumor (orange) and adjacent normal (blue) samples by paired Wilcoxon signed-rank testing after correction for FDR.,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",1783272|201174;1783272|201174|1760;1783272|201174|1760|2037;1783272|201174|1760|2037|2049;1783272|201174|1760|2037|2049|1654,Complete,Shaimaa Elsafoury
bsdb:28173873/2/1,28173873,case-control,28173873,10.1186/s13073-017-0405-5,NA,"Wang H., Funchain P., Bebek G., Altemus J., Zhang H., Niazi F., Peterson C., Lee W.T., Burkey B.B. , Eng C.",Microbiomic differences in tumor and paired-normal tissue in head and neck squamous cell carcinomas,Genome medicine,2017,"Bacteria, Head and neck squamous cell carcinoma (HNSCC), Microbiome",Experiment 2,United States of America,Homo sapiens,Oral cavity,UBERON:0000167,Head and neck squamous cell carcinoma,EFO:0000181,T0-T2 low tumor stages patients,T3-T4 high tumor stages patients,Not stated,NA,NA,NA,16S,1234,Sanger,NA,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4 +text,10 January 2021,Shaimaa Elsafoury,WikiWorks,"Relative abundances of differentially represented taxa stratified by T-stage. Box plots representing relative abundances of phylum Actinobacteria (top), genus Actinomyces (middle), and genus Parvimonas (bottom) stratified by T-stage.",increased,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,1783272|1239|1737404|1737405|1570339|543311,Complete,Shaimaa Elsafoury
bsdb:28173873/2/2,28173873,case-control,28173873,10.1186/s13073-017-0405-5,NA,"Wang H., Funchain P., Bebek G., Altemus J., Zhang H., Niazi F., Peterson C., Lee W.T., Burkey B.B. , Eng C.",Microbiomic differences in tumor and paired-normal tissue in head and neck squamous cell carcinomas,Genome medicine,2017,"Bacteria, Head and neck squamous cell carcinoma (HNSCC), Microbiome",Experiment 2,United States of America,Homo sapiens,Oral cavity,UBERON:0000167,Head and neck squamous cell carcinoma,EFO:0000181,T0-T2 low tumor stages patients,T3-T4 high tumor stages patients,Not stated,NA,NA,NA,16S,1234,Sanger,NA,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4 +text,10 January 2021,Shaimaa Elsafoury,WikiWorks,"Relative abundances of differentially represented taxa stratified by T-stage. Box plots representing relative abundances of phylum Actinobacteria (top), genus Actinomyces (middle), and genus Parvimonas (bottom) stratified by T-stage.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota",1783272|201174|1760|2037|2049|1654;1783272|201174,Complete,Shaimaa Elsafoury
bsdb:28195358/1/1,28195358,case-control,28195358,10.1002/mds.26942,https://pubmed.ncbi.nlm.nih.gov/28195358/,"Hill-Burns E.M., Debelius J.W., Morton J.T., Wissemann W.T., Lewis M.R., Wallen Z.D., Peddada S.D., Factor S.A., Molho E., Zabetian C.P., Knight R. , Payami H.",Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome,Movement disorders : official journal of the Movement Disorder Society,2017,"Parkinson's disease, confounding, functional pathways, gut microbiome, medications",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Controls,Parkinson's Disease Patients,Participants diagnosed with Parkinson's disease by a movement disorder specialist according to the modified UK Brain Bank criteria.,130,197,NA,16S,NA,Illumina,relative abundances,"ANCOM,Kruskall-Wallis",0.05,TRUE,NA,NA,"age,diet,geographic area,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 1 and Table 2,17 April 2024,Aleru Divine,"Aleru Divine,Peace Sandy,WikiWorks",Taxa identified by ANCOM and Kruskal-Wallis test as having significantly different abundance in cases and controls.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|74201|203494|48461|1647988|239934;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|41200;1783272|1239|186801|3082768|990719;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|838;1783272|1239|1737404|1737405|1737406;3379134|74201|203494|48461|203557;1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|216572,Complete,Peace Sandy
bsdb:28195358/1/2,28195358,case-control,28195358,10.1002/mds.26942,https://pubmed.ncbi.nlm.nih.gov/28195358/,"Hill-Burns E.M., Debelius J.W., Morton J.T., Wissemann W.T., Lewis M.R., Wallen Z.D., Peddada S.D., Factor S.A., Molho E., Zabetian C.P., Knight R. , Payami H.",Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome,Movement disorders : official journal of the Movement Disorder Society,2017,"Parkinson's disease, confounding, functional pathways, gut microbiome, medications",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Controls,Parkinson's Disease Patients,Participants diagnosed with Parkinson's disease by a movement disorder specialist according to the modified UK Brain Bank criteria.,130,197,NA,16S,NA,Illumina,relative abundances,"ANCOM,Kruskall-Wallis",0.05,TRUE,NA,NA,"age,diet,geographic area,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 1 and Table 2,18 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Taxa identified by ANCOM and Kruskal-Wallis test as having significantly different abundance in cases and controls.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|1955243;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803;3379134|1224|1236|135625|712;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803,Complete,Peace Sandy
bsdb:28195358/2/1,28195358,case-control,28195358,10.1002/mds.26942,https://pubmed.ncbi.nlm.nih.gov/28195358/,"Hill-Burns E.M., Debelius J.W., Morton J.T., Wissemann W.T., Lewis M.R., Wallen Z.D., Peddada S.D., Factor S.A., Molho E., Zabetian C.P., Knight R. , Payami H.",Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome,Movement disorders : official journal of the Movement Disorder Society,2017,"Parkinson's disease, confounding, functional pathways, gut microbiome, medications",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Controls,Parkinson's Disease Patients,Participants diagnosed with Parkinson's disease who were not on catechol-o-methyl-transferase (COMT) inhibitors or anticholinergic drugs (AC).,130,141,NA,16S,NA,Illumina,relative abundances,"ANCOM,Kruskall-Wallis",0.05,TRUE,NA,NA,"age,diet,geographic area,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 1 and Table 2,18 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Taxa identified by ANCOM and Kruskal-Wallis test as having significantly different abundance in cases and controls.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|41200;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572;1783272|1239|186801|3082768|990719;3379134|74201|203494|48461|1647988|239934;1783272|201174|1760|85004|31953;1783272|1239|91061|186826|33958;1783272|1239|1737404|1737405|1737406;1783272|1239|186801|3082768|990719;3379134|74201|203494|48461|203557,Complete,Peace Sandy
bsdb:28195358/2/2,28195358,case-control,28195358,10.1002/mds.26942,https://pubmed.ncbi.nlm.nih.gov/28195358/,"Hill-Burns E.M., Debelius J.W., Morton J.T., Wissemann W.T., Lewis M.R., Wallen Z.D., Peddada S.D., Factor S.A., Molho E., Zabetian C.P., Knight R. , Payami H.",Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome,Movement disorders : official journal of the Movement Disorder Society,2017,"Parkinson's disease, confounding, functional pathways, gut microbiome, medications",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Controls,Parkinson's Disease Patients,Participants diagnosed with Parkinson's disease who were not on catechol-o-methyl-transferase (COMT) inhibitors or anticholinergic drugs (AC).,130,141,NA,16S,NA,Illumina,relative abundances,"ANCOM,Kruskall-Wallis",0.05,TRUE,NA,NA,"age,diet,geographic area,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 1 and Table 2,18 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Taxa identified by ANCOM and Kruskal-Wallis test as having significantly different abundance in cases and controls.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|1955243;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803;3379134|1224|1236|135625|712;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803,Complete,Peace Sandy
bsdb:28199741/1/1,28199741,"case-control,laboratory experiment",28199741,10.1111/jpi.12399,NA,"Xu P., Wang J., Hong F., Wang S., Jin X., Xue T., Jia L. , Zhai Y.",Melatonin prevents obesity through modulation of gut microbiota in mice,Journal of pineal research,2017,"gut microbiota, inflammation, insulin resistance, liver steatosis, melatonin, obesity",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,normal chow diet,high fat diet,Obesity is (BMI ≥ 30kg/m2),5,5,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 6B + Data S1,10 January 2021,Marianthi Thomatos,WikiWorks,Differential abundant taxa in gut microbiota in response to melatonin treatment,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetitomaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",1783272|1239|186801|3085636|186803|31980;3379134|976|200643|171549|171552;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|248744;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|572511,Complete,Shaimaa Elsafoury
bsdb:28199741/1/2,28199741,"case-control,laboratory experiment",28199741,10.1111/jpi.12399,NA,"Xu P., Wang J., Hong F., Wang S., Jin X., Xue T., Jia L. , Zhai Y.",Melatonin prevents obesity through modulation of gut microbiota in mice,Journal of pineal research,2017,"gut microbiota, inflammation, insulin resistance, liver steatosis, melatonin, obesity",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,normal chow diet,high fat diet,Obesity is (BMI ≥ 30kg/m2),5,5,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 6B + Data S1,10 January 2021,Marianthi Thomatos,WikiWorks,Differential abundant taxa in gut microbiota in response to melatonin treatment,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",3379134|976|200643|171549|815|816;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|3082720|543314|109326;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|3082768|990719;3379134|29547|3031852|213849|72293|209;1783272|1239|186801|3082768|990719|990721;3379134|200940|3031449|213115|194924|35832;1783272|544448;1783272|1239|186801|186802|216572|459786,Complete,Shaimaa Elsafoury
bsdb:28199741/2/1,28199741,"case-control,laboratory experiment",28199741,10.1111/jpi.12399,NA,"Xu P., Wang J., Hong F., Wang S., Jin X., Xue T., Jia L. , Zhai Y.",Melatonin prevents obesity through modulation of gut microbiota in mice,Journal of pineal research,2017,"gut microbiota, inflammation, insulin resistance, liver steatosis, melatonin, obesity",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,high fat diet,high fat diet + melatonin,Obesity is (BMI ≥ 30kg/m2),5,5,NA,16S,34,Illumina,NA,LEfSe,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,increased,NA,NA,Signature 1,Figure 6B + Data S1,10 January 2021,Marianthi Thomatos,WikiWorks,Differential abundant taxa in gut microbiota in response to melatonin treatment,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Antricoccaceae|g__Antricoccus",3379134|1224|1236|91347|1903414|583;3379134|976|200643|171549|1853231|283168;3379134|29547|3031852|213849|72293|209;1783272|1239|186801|3082720|543314|109326;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;3379134|976|200643|171549|1853231|574697;3379134|74201|203494|48461|1647988|239934;1783272|201174|1760|1643682|2805401|1920251,Complete,Shaimaa Elsafoury
bsdb:28199741/2/2,28199741,"case-control,laboratory experiment",28199741,10.1111/jpi.12399,NA,"Xu P., Wang J., Hong F., Wang S., Jin X., Xue T., Jia L. , Zhai Y.",Melatonin prevents obesity through modulation of gut microbiota in mice,Journal of pineal research,2017,"gut microbiota, inflammation, insulin resistance, liver steatosis, melatonin, obesity",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,high fat diet,high fat diet + melatonin,Obesity is (BMI ≥ 30kg/m2),5,5,NA,16S,34,Illumina,NA,LEfSe,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,increased,NA,NA,Signature 2,Figure 6B + Data S1 + Figure 7,10 January 2021,Marianthi Thomatos,WikiWorks,Differential abundant taxa in gut microbiota in response to melatonin treatment,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter marmotae",3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|244127;3379134|29547|3031852|213849|72293|209|152490,Complete,Shaimaa Elsafoury
bsdb:28211537/1/1,28211537,laboratory experiment,28211537,10.1038/srep42906,NA,"Li R., Yang J., Saffari A., Jacobs J., Baek K.I., Hough G., Larauche M.H., Ma J., Jen N., Moussaoui N., Zhou B., Kang H., Reddy S., Henning S.M., Campen M.J., Pisegna J., Li Z., Fogelman A.M., Sioutas C., Navab M. , Hsiai T.K.",Ambient Ultrafine Particle Ingestion Alters Gut Microbiota in Association with Increased Atherogenic Lipid Metabolites,Scientific reports,2017,NA,Experiment 1,United States of America,Mus musculus,Caecum,UBERON:0001153,Air pollution,ENVO:02500037,vehicle control,mice exposed to UFP,C57BL/6 mice exposed to UFP (Ultrafine particles),11,12,NA,16S,4,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2 & Supplemental Figure S1& Text,10 January 2021,Zyaijah Bailey,"Claregrieve1,WikiWorks",Differential microbial abundance between UFP-exposed mice and controls,increased,k__Pseudomonadati|p__Verrucomicrobiota,3379134|74201,Complete,Claregrieve1
bsdb:28211537/1/2,28211537,laboratory experiment,28211537,10.1038/srep42906,NA,"Li R., Yang J., Saffari A., Jacobs J., Baek K.I., Hough G., Larauche M.H., Ma J., Jen N., Moussaoui N., Zhou B., Kang H., Reddy S., Henning S.M., Campen M.J., Pisegna J., Li Z., Fogelman A.M., Sioutas C., Navab M. , Hsiai T.K.",Ambient Ultrafine Particle Ingestion Alters Gut Microbiota in Association with Increased Atherogenic Lipid Metabolites,Scientific reports,2017,NA,Experiment 1,United States of America,Mus musculus,Caecum,UBERON:0001153,Air pollution,ENVO:02500037,vehicle control,mice exposed to UFP,C57BL/6 mice exposed to UFP (Ultrafine particles),11,12,NA,16S,4,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2 & Supplemental Figure S1& Text,10 January 2021,Zyaijah Bailey,"Claregrieve1,WikiWorks",Differential microbial abundance between UFP-exposed mice and controls,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota",1783272|201174;1783272|1117;1783272|1239,Complete,Claregrieve1
bsdb:28222761/1/1,28222761,case-control,28222761,10.1186/s40168-017-0242-1,NA,"Strati F., Cavalieri D., Albanese D., De Felice C., Donati C., Hayek J., Jousson O., Leoncini S., Renzi D., Calabrò A. , De Filippo C.",New evidences on the altered gut microbiota in autism spectrum disorders,Microbiome,2017,"Autism spectrum disorders, Constipation, Gut microbiota, Metataxonomy, Mycobiota",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Autism,EFO:0003758,neurotypical,autistic,"cases were diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition.",40,40,3 months,16S,345,Roche454,raw counts,Welch's T-Test,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,10 January 2021,Fatima Zohra,WikiWorks,Mean relative abundance in autistic (AD) and neurotypical (NT) subjects,decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Shaimaa Elsafoury
bsdb:28222761/2/1,28222761,case-control,28222761,10.1186/s40168-017-0242-1,NA,"Strati F., Cavalieri D., Albanese D., De Felice C., Donati C., Hayek J., Jousson O., Leoncini S., Renzi D., Calabrò A. , De Filippo C.",New evidences on the altered gut microbiota in autism spectrum disorders,Microbiome,2017,"Autism spectrum disorders, Constipation, Gut microbiota, Metataxonomy, Mycobiota",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Autism,EFO:0003758,neurotypical,autistic,"cases were diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition.",40,40,3 months,16S,345,Roche454,relative abundances,LEfSe,0.01,FALSE,2,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Fatima Zohra,WikiWorks,Differences in the bacterial taxa between autistic (AD) and neurotypical (NT) subjects,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia",1783272|1239|91061|186826|33958|1578;1783272|201174|84998|84999|84107|102106;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85007|1653;1783272|1239|186801|3085636|186803|189330;3379134|976|200643,Complete,Shaimaa Elsafoury
bsdb:28222761/2/2,28222761,case-control,28222761,10.1186/s40168-017-0242-1,NA,"Strati F., Cavalieri D., Albanese D., De Felice C., Donati C., Hayek J., Jousson O., Leoncini S., Renzi D., Calabrò A. , De Filippo C.",New evidences on the altered gut microbiota in autism spectrum disorders,Microbiome,2017,"Autism spectrum disorders, Constipation, Gut microbiota, Metataxonomy, Mycobiota",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Autism,EFO:0003758,neurotypical,autistic,"cases were diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition.",40,40,3 months,16S,345,Roche454,relative abundances,LEfSe,0.01,FALSE,2,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,10 January 2021,Fatima Zohra,WikiWorks,Differences in the bacterial taxa between autistic (AD) and neurotypical (NT) subjects,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",3379134|976|200643|171549|171550|239759;1783272|1239|909932|1843489|31977;1783272|1239|909932|909929;1783272|1239|909932;1783272|1239|909932|1843489|31977|39948;3379134|976|200643|171549|2005525|375288;1783272|1239|909932|1843489|31977|29465;3379134|200940|3031449|213115|194924|35832;3379134|976|200643|171549,Complete,Shaimaa Elsafoury
bsdb:28222761/3/1,28222761,case-control,28222761,10.1186/s40168-017-0242-1,NA,"Strati F., Cavalieri D., Albanese D., De Felice C., Donati C., Hayek J., Jousson O., Leoncini S., Renzi D., Calabrò A. , De Filippo C.",New evidences on the altered gut microbiota in autism spectrum disorders,Microbiome,2017,"Autism spectrum disorders, Constipation, Gut microbiota, Metataxonomy, Mycobiota",Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Autism,EFO:0003758,non constipated autistic,constipated autistic,"cases were diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition.",29,5,3 months,16S,345,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differences in the bacterial taxa between constipated and non-constipated autistic (AD) patients,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|620;1783272|1239|186801|186802|31979|1485,Complete,Shaimaa Elsafoury
bsdb:28222761/4/1,28222761,case-control,28222761,10.1186/s40168-017-0242-1,NA,"Strati F., Cavalieri D., Albanese D., De Felice C., Donati C., Hayek J., Jousson O., Leoncini S., Renzi D., Calabrò A. , De Filippo C.",New evidences on the altered gut microbiota in autism spectrum disorders,Microbiome,2017,"Autism spectrum disorders, Constipation, Gut microbiota, Metataxonomy, Mycobiota",Experiment 4,Italy,Homo sapiens,Feces,UBERON:0001988,Autism,EFO:0003758,non constipated neurotypical,constipated neurotypical,"cases were diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition.",29,11,3 months,16S,345,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differences in the bacterial taxa between constipated and non-constipated neurotypical (NT) subjects,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,1783272|1239|186801|186802|204475,Complete,Shaimaa Elsafoury
bsdb:28245856/2/1,28245856,time series / longitudinal observational,28245856,10.1186/s13073-017-0409-1,NA,"Galloway-Peña J.R., Smith D.P., Sahasrabhojane P., Wadsworth W.D., Fellman B.M., Ajami N.J., Shpall E.J., Daver N., Guindani M., Petrosino J.F., Kontoyiannis D.P. , Shelburne S.A.",Characterization of oral and gut microbiome temporal variability in hospitalized cancer patients,Genome medicine,2017,"Antibiotics, Chemotherapy, Leukemia, Microbiome, Temporal variability",Experiment 2,United States of America,Homo sapiens,Buccal mucosa,UBERON:0006956,Acute myeloid leukemia,EFO:0000222,no infection,infection,acute myeloid leukemia patients that were microbiologically documented with infection during induction chemotherapy before neutrophil recovery,30,15,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 5e,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential microbial abundance between patients who experienced infection and patients who did not,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,3379134|1224|1236|135614|32033|40323,Complete,Claregrieve1
bsdb:28245856/2/2,28245856,time series / longitudinal observational,28245856,10.1186/s13073-017-0409-1,NA,"Galloway-Peña J.R., Smith D.P., Sahasrabhojane P., Wadsworth W.D., Fellman B.M., Ajami N.J., Shpall E.J., Daver N., Guindani M., Petrosino J.F., Kontoyiannis D.P. , Shelburne S.A.",Characterization of oral and gut microbiome temporal variability in hospitalized cancer patients,Genome medicine,2017,"Antibiotics, Chemotherapy, Leukemia, Microbiome, Temporal variability",Experiment 2,United States of America,Homo sapiens,Buccal mucosa,UBERON:0006956,Acute myeloid leukemia,EFO:0000222,no infection,infection,acute myeloid leukemia patients that were microbiologically documented with infection during induction chemotherapy before neutrophil recovery,30,15,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 5e,28 July 2022,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between patients who experienced infection and patients who did not,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:28245856/3/1,28245856,time series / longitudinal observational,28245856,10.1186/s13073-017-0409-1,NA,"Galloway-Peña J.R., Smith D.P., Sahasrabhojane P., Wadsworth W.D., Fellman B.M., Ajami N.J., Shpall E.J., Daver N., Guindani M., Petrosino J.F., Kontoyiannis D.P. , Shelburne S.A.",Characterization of oral and gut microbiome temporal variability in hospitalized cancer patients,Genome medicine,2017,"Antibiotics, Chemotherapy, Leukemia, Microbiome, Temporal variability",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute myeloid leukemia,EFO:0000222,no infection,infection,acute myeloid leukemia patients that were microbiologically documented with infection during induction chemotherapy before neutrophil recovery,30,15,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 5e,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential microbial abundance in stool samples between patients with infection and patients with no infection,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,3379134|1224|1236|135614|32033|40323,Complete,Claregrieve1
bsdb:28320465/1/1,28320465,case-control,28320465,10.1186/s40168-017-0250-1,NA,"Chua L.L., Rajasuriar R., Azanan M.S., Abdullah N.K., Tang M.S., Lee S.C., Woo Y.L., Lim Y.A., Ariffin H. , Loke P.",Reduced microbial diversity in adult survivors of childhood acute lymphoblastic leukemia and microbial associations with increased immune activation,Microbiome,2017,"Acute lymphoblastic leukemia, Adult survivors of childhood cancer, Alpha diversity, Immune activation, Inflammation, Microbiome, Microbiota dysbiosis",Experiment 1,Malaysia,Homo sapiens,Caecum,UBERON:0001153,Leukemia,EFO:0000565,controls,survivors of acute lymphoblastic leukemia,adult surviors of childhood leukemia,61,73,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,"Figure 2,Supplementary table S1",10 January 2021,Fatima Zohra,WikiWorks,Alterations to microbial communities in adult survivors of acute lymphoblastic leukemia,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",1783272|201174;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85007|1653;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|1737404|1737405|1570339|150022;;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;1783272|201174|1760|2037|2049|1654,Complete,NA
bsdb:28320465/1/2,28320465,case-control,28320465,10.1186/s40168-017-0250-1,NA,"Chua L.L., Rajasuriar R., Azanan M.S., Abdullah N.K., Tang M.S., Lee S.C., Woo Y.L., Lim Y.A., Ariffin H. , Loke P.",Reduced microbial diversity in adult survivors of childhood acute lymphoblastic leukemia and microbial associations with increased immune activation,Microbiome,2017,"Acute lymphoblastic leukemia, Adult survivors of childhood cancer, Alpha diversity, Immune activation, Inflammation, Microbiome, Microbiota dysbiosis",Experiment 1,Malaysia,Homo sapiens,Caecum,UBERON:0001153,Leukemia,EFO:0000565,controls,survivors of acute lymphoblastic leukemia,adult surviors of childhood leukemia,61,73,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,"Figure 2,Supplementary table S1",10 January 2021,Fatima Zohra,WikiWorks,Alterations to microbial communities in adult survivors of acute lymphoblastic leukemia,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae",3379134|976|200643|171549;3379134|976|200643;3379134|976;1783272|1239|186801|186802|541000;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|171550;1783272|1239|186801|3085636|186803|28050;3379134|200940|3031449|213115;28221;3379134|200940|3031449|213115|194924,Complete,NA
bsdb:28320468/1/1,28320468,case-control,28320468,10.1186/s40168-017-0252-z,NA,"Corrêa J.D., Calderaro D.C., Ferreira G.A., Mendonça S.M., Fernandes G.R., Xiao E., Teixeira A.L., Leys E.J., Graves D.T. , Silva T.A.",Subgingival microbiota dysbiosis in systemic lupus erythematosus: association with periodontal status,Microbiome,2017,"Cytokine, Illumina sequencing, Lupus, Oral microbiota, Periodontitis, Subgingival dental plaque",Experiment 1,Brazil,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Systemic lupus erythematosus,MONDO:0007915,Control with Non-periodontitis (C-NCP),Systemic Lupus Erythematosus with Non-periodontitis (SLE-NCP),Systemic Lupus Erythematosus (SLE) patients with Non-periodontitis (NCP),24,17,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,sex",NA,NA,NA,increased,NA,NA,increased,Signature 1,"Figures 5a, 5b",15 February 2025,Taofeecoh,"Taofeecoh,WikiWorks",OTUs with different relative abundance in control subjects and SLE patients in non-periodontitis.,increased,NA,NA,Complete,Svetlana up
bsdb:28320468/1/2,28320468,case-control,28320468,10.1186/s40168-017-0252-z,NA,"Corrêa J.D., Calderaro D.C., Ferreira G.A., Mendonça S.M., Fernandes G.R., Xiao E., Teixeira A.L., Leys E.J., Graves D.T. , Silva T.A.",Subgingival microbiota dysbiosis in systemic lupus erythematosus: association with periodontal status,Microbiome,2017,"Cytokine, Illumina sequencing, Lupus, Oral microbiota, Periodontitis, Subgingival dental plaque",Experiment 1,Brazil,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Systemic lupus erythematosus,MONDO:0007915,Control with Non-periodontitis (C-NCP),Systemic Lupus Erythematosus with Non-periodontitis (SLE-NCP),Systemic Lupus Erythematosus (SLE) patients with Non-periodontitis (NCP),24,17,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,sex",NA,NA,NA,increased,NA,NA,increased,Signature 2,"Figures 5a, 5b",15 February 2025,Taofeecoh,"Taofeecoh,WikiWorks",OTUs with different relative abundance in control subjects and SLE samples in non-periodontitis.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas",1783272|1239|186801|3082720|543314|86331;3379134|1224|28211|204457|41297|13687,Complete,Svetlana up
bsdb:28320468/2/1,28320468,case-control,28320468,10.1186/s40168-017-0252-z,NA,"Corrêa J.D., Calderaro D.C., Ferreira G.A., Mendonça S.M., Fernandes G.R., Xiao E., Teixeira A.L., Leys E.J., Graves D.T. , Silva T.A.",Subgingival microbiota dysbiosis in systemic lupus erythematosus: association with periodontal status,Microbiome,2017,"Cytokine, Illumina sequencing, Lupus, Oral microbiota, Periodontitis, Subgingival dental plaque",Experiment 2,Brazil,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Systemic lupus erythematosus,MONDO:0007915,Controls with Chronic periodontitis (C-CP),Systemic Lupus Erythematosus with Chronic periodontitis (SLE-CP),Systemic Lupus Erythematosus (SLE) patients with Chronic periodontitis (CP),28,35,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,sex",NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,"Figures 5c, 5d",15 February 2025,Taofeecoh,"Taofeecoh,WikiWorks",OTUs with different relative abundance in control subjects and SLE samples in Chronic periodontitis.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella pleuritidis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oulorum,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema maltophilum,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum",3379134|976|200643|171549|171552|2974257|407975;3379134|1224|1236|72274|135621|286;3379134|976|200643|171549|171552|2974251|28136;3379134|203691|203692|136|2845253|157|51160;3384194|508458|649775|649776|3029087|1434006|651822,Complete,Svetlana up
bsdb:28320468/2/2,28320468,case-control,28320468,10.1186/s40168-017-0252-z,NA,"Corrêa J.D., Calderaro D.C., Ferreira G.A., Mendonça S.M., Fernandes G.R., Xiao E., Teixeira A.L., Leys E.J., Graves D.T. , Silva T.A.",Subgingival microbiota dysbiosis in systemic lupus erythematosus: association with periodontal status,Microbiome,2017,"Cytokine, Illumina sequencing, Lupus, Oral microbiota, Periodontitis, Subgingival dental plaque",Experiment 2,Brazil,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Systemic lupus erythematosus,MONDO:0007915,Controls with Chronic periodontitis (C-CP),Systemic Lupus Erythematosus with Chronic periodontitis (SLE-CP),Systemic Lupus Erythematosus (SLE) patients with Chronic periodontitis (CP),28,35,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,sex",NA,NA,NA,unchanged,NA,NA,unchanged,Signature 2,"Figures 5c, 5d",15 February 2025,Taofeecoh,"Taofeecoh,WikiWorks",OTUs with different relative abundance in control subjects and SLE samples in Chronic periodontitis.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella fusca,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles|s__Roseateles puraquae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria",3379134|976|117743|200644|49546|1016|1017;3379134|1224|28216|80840|80864;1783272|1239|186801|186802;1783272|1239|91061|186826|186828|117563|46124;3379134|1224|1236|135625|712|724|729;3379134|976|200643|171549|171552|838|589436;3379134|1224|28216|80840|2975441|93681|431059;3379134|1224|28211|204457|41297|13687;1783272|1239|91061|186826|1300|1301|1305;1783272|201174|1760|85006|1268|32207|172042,Complete,Svetlana up
bsdb:28320468/3/1,28320468,case-control,28320468,10.1186/s40168-017-0252-z,NA,"Corrêa J.D., Calderaro D.C., Ferreira G.A., Mendonça S.M., Fernandes G.R., Xiao E., Teixeira A.L., Leys E.J., Graves D.T. , Silva T.A.",Subgingival microbiota dysbiosis in systemic lupus erythematosus: association with periodontal status,Microbiome,2017,"Cytokine, Illumina sequencing, Lupus, Oral microbiota, Periodontitis, Subgingival dental plaque",Experiment 3,Brazil,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Systemic lupus erythematosus,MONDO:0007915,Control with Non-periodontitis (C-NCP),Systemic Lupus Erythematosus with Non-periodontitis (SLE-NCP),Systemic Lupus Erythematosus (SLE) patients with Non-periodontitis (NCP),24,17,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,NA,increased,NA,NA,increased,Signature 1,Figure 6a,20 February 2025,Taofeecoh,Taofeecoh,OTUs with different relative abundance in control subjects and SLE patients in non-periodontitis.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Cryptobacterium|s__Cryptobacterium curtum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella multisaccharivorax,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oulorum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas noxia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri",3379134|1224|1236|135625|712|416916;1783272|201174|84998|1643822|1643826|84162|84163;3379134|976|200643|171549|171552|52228|310514;3384189|32066|203490|203491|1129771|32067;1783272|1239|186801|3085636|186803|265975|237576;3379134|976|200643|171549|171552|838|28133;3379134|976|200643|171549|171552|2974251|28135;3379134|976|200643|171549|171552|2974251|28136;1783272|1239|909932|909929|1843491|970|135083;3379134|203691|203692|136|2845253|157|59892;3379134|976|117743|200644|49546|1016|327575,Complete,Svetlana up
bsdb:28320468/3/2,28320468,case-control,28320468,10.1186/s40168-017-0252-z,NA,"Corrêa J.D., Calderaro D.C., Ferreira G.A., Mendonça S.M., Fernandes G.R., Xiao E., Teixeira A.L., Leys E.J., Graves D.T. , Silva T.A.",Subgingival microbiota dysbiosis in systemic lupus erythematosus: association with periodontal status,Microbiome,2017,"Cytokine, Illumina sequencing, Lupus, Oral microbiota, Periodontitis, Subgingival dental plaque",Experiment 3,Brazil,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Systemic lupus erythematosus,MONDO:0007915,Control with Non-periodontitis (C-NCP),Systemic Lupus Erythematosus with Non-periodontitis (SLE-NCP),Systemic Lupus Erythematosus (SLE) patients with Non-periodontitis (NCP),24,17,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,NA,increased,NA,NA,increased,Signature 2,Figure 6a,20 February 2025,Taofeecoh,Taofeecoh,OTUs with different relative abundance in control subjects and SLE samples in non-periodontitis.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter aphrophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas",3379134|1224|1236|135625|712|416916|732;3379134|1224|28216|80840|80864;1783272|1239|91061|186826|1300|1301|1328;3379134|1224|28216|80840;3379134|1224|28211|204457|41297|13687,Complete,Svetlana up
bsdb:28320468/4/1,28320468,case-control,28320468,10.1186/s40168-017-0252-z,NA,"Corrêa J.D., Calderaro D.C., Ferreira G.A., Mendonça S.M., Fernandes G.R., Xiao E., Teixeira A.L., Leys E.J., Graves D.T. , Silva T.A.",Subgingival microbiota dysbiosis in systemic lupus erythematosus: association with periodontal status,Microbiome,2017,"Cytokine, Illumina sequencing, Lupus, Oral microbiota, Periodontitis, Subgingival dental plaque",Experiment 4,Brazil,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Systemic lupus erythematosus,MONDO:0007915,Control with Chronic periodontitis (C-CP),Systemic Lupus Erythematosus Chronic periodontitis (SLE-CP),Systemic Lupus Erythematosus (SLE) patients with Chronic periodontitis (CP),28,35,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,Figure 6b,20 February 2025,Taofeecoh,Taofeecoh,OTUs with different relative abundance in control subjects and SLE samples in Chronic periodontitis.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oulorum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella multisaccharivorax,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera geminata",3379134|976|200643|171549|171552|2974251|28136;3379134|976|200643|171549|171552|52228|310514;3384194|508458|649775|649776|3029087|1434006|651822;3379134|1224|28211|204457|41297|13687;1783272|1239|909932|1843489|31977|906|156456,Complete,Svetlana up
bsdb:28320468/4/2,28320468,case-control,28320468,10.1186/s40168-017-0252-z,NA,"Corrêa J.D., Calderaro D.C., Ferreira G.A., Mendonça S.M., Fernandes G.R., Xiao E., Teixeira A.L., Leys E.J., Graves D.T. , Silva T.A.",Subgingival microbiota dysbiosis in systemic lupus erythematosus: association with periodontal status,Microbiome,2017,"Cytokine, Illumina sequencing, Lupus, Oral microbiota, Periodontitis, Subgingival dental plaque",Experiment 4,Brazil,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Systemic lupus erythematosus,MONDO:0007915,Control with Chronic periodontitis (C-CP),Systemic Lupus Erythematosus Chronic periodontitis (SLE-CP),Systemic Lupus Erythematosus (SLE) patients with Chronic periodontitis (CP),28,35,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,NA,unchanged,NA,NA,unchanged,Signature 2,Figure 6b,20 February 2025,Taofeecoh,Taofeecoh,OTUs with different relative abundance in control subjects and SLE samples in Chronic periodontitis.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria",3379134|976|200643|171549|171552|838|28131;1783272|201174|1760|85006|1268|32207|172042,Complete,Svetlana up
bsdb:28328799/1/1,28328799,"cross-sectional observational, not case-control",28328799,10.1097/MD.0000000000005821,https://pubmed.ncbi.nlm.nih.gov/28328799/,"Noguera-Julian M., Guillén Y., Peterson J., Reznik D., Harris E.V., Joseph S.J., Rivera J., Kannanganat S., Amara R., Nguyen M.L., Mutembo S., Paredes R., Read T.D. , Marconi V.C.",Oral microbiome in HIV-associated periodontitis,Medicine,2017,NA,Experiment 1,United States of America,Homo sapiens,"Dental plaque,Internal cheek pouch,Saliva","UBERON:0016482,UBERON:0001836,UBERON:0013640",Periodontitis,EFO:0000649,HIV–,HIV+,"Participants who were positive for HIV-1 infection, as verified by ELISA and confirmed by Western blot.",10,40,NA,16S,4,Illumina,NA,Wald Test,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Table 1, Figure 3",10 January 2022,Joyessa,"Joyessa,Claregrieve1,WikiWorks",Differential microbial abundance between HIV+ and HIV- participants,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia",3379134|1224|1236|135625|712|416916;3379134|1224|28216|206351|481|32257;3379134|1224|28216|206351|481|482;1783272|201174|1760|85006|1268|32207;3379134|1224|28216|206351|481;3379134|1224|1236|135625|712;1783272|1239|91061|186826|186827|46123,Complete,Claregrieve1
bsdb:28328799/1/2,28328799,"cross-sectional observational, not case-control",28328799,10.1097/MD.0000000000005821,https://pubmed.ncbi.nlm.nih.gov/28328799/,"Noguera-Julian M., Guillén Y., Peterson J., Reznik D., Harris E.V., Joseph S.J., Rivera J., Kannanganat S., Amara R., Nguyen M.L., Mutembo S., Paredes R., Read T.D. , Marconi V.C.",Oral microbiome in HIV-associated periodontitis,Medicine,2017,NA,Experiment 1,United States of America,Homo sapiens,"Dental plaque,Internal cheek pouch,Saliva","UBERON:0016482,UBERON:0001836,UBERON:0013640",Periodontitis,EFO:0000649,HIV–,HIV+,"Participants who were positive for HIV-1 infection, as verified by ELISA and confirmed by Western blot.",10,40,NA,16S,4,Illumina,NA,Wald Test,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Table 1, Figure 3",10 January 2022,Joyessa,"Joyessa,Claregrieve1,WikiWorks",Differential microbial abundance between HIV+ and HIV- participants,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|909932|909929|1843491|82202;3379134|976|200643|171549|2005525|195950;3384189|32066|203490|203491|1129771|32067;1783272|1239|909932|909929|1843491|970;3379134|203691|203692|136|2845253|157;1783272|1239|909932|1843489|31977;3379134|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:28361745/1/1,28361745,time series / longitudinal observational,28361745,10.1016/j.clnesp.2016.11.003,NA,"Tagliabue A., Ferraris C., Uggeri F., Trentani C., Bertoli S., de Giorgis V., Veggiotti P. , Elli M.",Short-term impact of a classical ketogenic diet on gut microbiota in GLUT1 Deficiency Syndrome: A 3-month prospective observational study,Clinical nutrition ESPEN,2017,"Glucose Transporter 1 Deficiency Syndrome, Ketogenic diet, Microbiota",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,pre-ketogenic diet,post-ketogenic diet,children diagnosed with GLUT-1 deficiency syndrome treated with classical ketogenic diet for 3 months,6,6,1 month,PCR,NA,RT-qPCR,log transformation,T-Test,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,9 December 2024,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of post-ketogenic diet group compared to pre-ketogenic diet group,increased,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,3379134|200940|3031449|213115|194924|872,Complete,NA
bsdb:28362071/1/2,28362071,"cross-sectional observational, not case-control",28362071,https://doi.org/10.7448/IAS.20.1.21526,NA,"Villanueva-Millán M.J., Pérez-Matute P., Recio-Fernández E., Lezana Rosales J.M. , Oteo J.A.",Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients,Journal of the International AIDS Society,2017,"HIV infection, antiretroviral therapy, bacterial diversity, gut microbiota, inflammation, microbial translocation",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Non-infected volunteers (Control),HIV-positive (naive),"This group includes untreated HIV-infected patients (HIV+(naive)) with an average viral load of 54,010 cop/mL (3,550–71,800 cop/mL))",21,5,3 months,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,NA,decreased,NA,NA,decreased,Signature 2,Table 2,19 October 2024,Joiejoie,"Joiejoie,KateRasheed,WikiWorks",The relative abundance of major phyla in the gut in HIV-positive (naive).,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,3379134|1224|28211,Complete,Svetlana up
bsdb:28362071/2/1,28362071,"cross-sectional observational, not case-control",28362071,https://doi.org/10.7448/IAS.20.1.21526,NA,"Villanueva-Millán M.J., Pérez-Matute P., Recio-Fernández E., Lezana Rosales J.M. , Oteo J.A.",Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients,Journal of the International AIDS Society,2017,"HIV infection, antiretroviral therapy, bacterial diversity, gut microbiota, inflammation, microbial translocation",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,non-infected volunteers (Control),HIV-positive (cART),This group includes HIV-infected patients on cART (HIV+(cART)) for at least one year and with viral load of <20 cop/mL.,21,45,3 months,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,9 January 2025,Joiejoie,"Joiejoie,KateRasheed,WikiWorks",Relative abundance of major phyla present in the gut in HIV-positive (cART).,increased,"c__Deltaproteobacteria,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Lentisphaerota,k__Thermotogati|p__Synergistota",28221;3379134|1224;3379134|256845;3384194|508458,Complete,Svetlana up
bsdb:28362071/2/2,28362071,"cross-sectional observational, not case-control",28362071,https://doi.org/10.7448/IAS.20.1.21526,NA,"Villanueva-Millán M.J., Pérez-Matute P., Recio-Fernández E., Lezana Rosales J.M. , Oteo J.A.",Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients,Journal of the International AIDS Society,2017,"HIV infection, antiretroviral therapy, bacterial diversity, gut microbiota, inflammation, microbial translocation",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,non-infected volunteers (Control),HIV-positive (cART),This group includes HIV-infected patients on cART (HIV+(cART)) for at least one year and with viral load of <20 cop/mL.,21,45,3 months,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,9 January 2025,Joiejoie,"Joiejoie,KateRasheed,WikiWorks",Relative abundance of major phyla present in the gut in HIV-positive (cART).,decreased,k__Methanobacteriati|p__Methanobacteriota,3366610|28890,Complete,Svetlana up
bsdb:28362071/3/2,28362071,"cross-sectional observational, not case-control",28362071,https://doi.org/10.7448/IAS.20.1.21526,NA,"Villanueva-Millán M.J., Pérez-Matute P., Recio-Fernández E., Lezana Rosales J.M. , Oteo J.A.",Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients,Journal of the International AIDS Society,2017,"HIV infection, antiretroviral therapy, bacterial diversity, gut microbiota, inflammation, microbial translocation",Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,non-infected volunteers (Control),NRTIs + PIs,This group includes patients on family treatment of nucleoside reverse transcriptase inhibitors (NRTIs) and protease inhibitors (PIs),21,15,3 months,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,NA,decreased,NA,NA,decreased,Signature 2,"In-text result of ""Gut microbiota diversity and composition""",9 January 2025,Joiejoie,"Joiejoie,KateRasheed,WikiWorks",Relative abundance of major phyla present in the gut in NRTIs + PIs.,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Svetlana up
bsdb:28362071/4/1,28362071,"cross-sectional observational, not case-control",28362071,https://doi.org/10.7448/IAS.20.1.21526,NA,"Villanueva-Millán M.J., Pérez-Matute P., Recio-Fernández E., Lezana Rosales J.M. , Oteo J.A.",Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients,Journal of the International AIDS Society,2017,"HIV infection, antiretroviral therapy, bacterial diversity, gut microbiota, inflammation, microbial translocation",Experiment 4,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,NRTIs + PIs,NRTIs + NNRTIs,This group includes patients on family treatment of nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs),15,22,3 months,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,increased,NA,NA,increased,Signature 1,Table 2,9 January 2025,Joiejoie,"Joiejoie,KateRasheed,WikiWorks",Relative abundance of major phyla present in the gut in NRTIs + INSTIs.,increased,c__Deltaproteobacteria,28221,Complete,Svetlana up
bsdb:28362071/5/1,28362071,"cross-sectional observational, not case-control",28362071,https://doi.org/10.7448/IAS.20.1.21526,NA,"Villanueva-Millán M.J., Pérez-Matute P., Recio-Fernández E., Lezana Rosales J.M. , Oteo J.A.",Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients,Journal of the International AIDS Society,2017,"HIV infection, antiretroviral therapy, bacterial diversity, gut microbiota, inflammation, microbial translocation",Experiment 5,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,NRTIs + NNRTIs,NRTIs + INSTIs,This group includes patients on family treatment of nucleoside reverse transcriptase inhibitors (NRTIs) with integrase strand transfer inhibitors (INSTIs),22,8,3 months,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,increased,NA,NA,increased,Signature 1,Table 2,9 January 2025,Joiejoie,"Joiejoie,KateRasheed,WikiWorks",Relative abundance of major phyla present in the gut in NRTIs + INSTIs.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,3379134|1224|28211,Complete,Svetlana up
bsdb:28362071/6/1,28362071,"cross-sectional observational, not case-control",28362071,https://doi.org/10.7448/IAS.20.1.21526,NA,"Villanueva-Millán M.J., Pérez-Matute P., Recio-Fernández E., Lezana Rosales J.M. , Oteo J.A.",Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients,Journal of the International AIDS Society,2017,"HIV infection, antiretroviral therapy, bacterial diversity, gut microbiota, inflammation, microbial translocation",Experiment 6,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,non-infected volunteers (Control),NRTIs+PIs,This group includes patients on family treatment of nucleoside reverse transcriptase inhibitors (NRTIs) and protease inhibitors (PIs),21,15,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex",NA,NA,NA,decreased,NA,NA,decreased,Signature 1,Table 3,9 January 2025,Joiejoie,Joiejoie,"Combined antiretroviral therapy modified the relative abundance of taxonomical groups (order, family, genus, species) in NRTIs+PIs",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|186802|1898207;1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803,Complete,NA
bsdb:28362071/6/2,28362071,"cross-sectional observational, not case-control",28362071,https://doi.org/10.7448/IAS.20.1.21526,NA,"Villanueva-Millán M.J., Pérez-Matute P., Recio-Fernández E., Lezana Rosales J.M. , Oteo J.A.",Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients,Journal of the International AIDS Society,2017,"HIV infection, antiretroviral therapy, bacterial diversity, gut microbiota, inflammation, microbial translocation",Experiment 6,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,non-infected volunteers (Control),NRTIs+PIs,This group includes patients on family treatment of nucleoside reverse transcriptase inhibitors (NRTIs) and protease inhibitors (PIs),21,15,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex",NA,NA,NA,decreased,NA,NA,decreased,Signature 2,Table 3,9 January 2025,Joiejoie,"Joiejoie,KateRasheed,WikiWorks","Relative abundance of taxonomical groups (order, family, genus, species) in NRTIs+PIs",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. (in: firmicutes),k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. 6,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. Clone-24,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus flavefaciens",1783272|201174|1760|2037;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|1224|1236|72274;1783272|1239|526524|526525|128827|123375;3379134|1224|28211|204457;3379134|1224|1236|72274|135621|286;3379134|976|200643|171549|171550|239759|1288121;1783272|1239|91061|1385|186817|1386|1409;1783272|1239|186801|186802|31979|1485|105335;1783272|1239|186801|186802|31979|1485|1003367;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|186802|216572|1263|1265,Complete,Svetlana up
bsdb:28362071/6/3,28362071,"cross-sectional observational, not case-control",28362071,https://doi.org/10.7448/IAS.20.1.21526,NA,"Villanueva-Millán M.J., Pérez-Matute P., Recio-Fernández E., Lezana Rosales J.M. , Oteo J.A.",Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients,Journal of the International AIDS Society,2017,"HIV infection, antiretroviral therapy, bacterial diversity, gut microbiota, inflammation, microbial translocation",Experiment 6,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,non-infected volunteers (Control),NRTIs+PIs,This group includes patients on family treatment of nucleoside reverse transcriptase inhibitors (NRTIs) and protease inhibitors (PIs),21,15,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex",NA,NA,NA,decreased,NA,NA,decreased,Signature 3,Table 3,17 January 2025,KateRasheed,"KateRasheed,WikiWorks","Relative abundance of taxonomical groups (order, family, genus, species) in NRTIs+PIs",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii",1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|186802|1898207;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|946234|292800,Complete,Svetlana up
bsdb:28362071/7/1,28362071,"cross-sectional observational, not case-control",28362071,https://doi.org/10.7448/IAS.20.1.21526,NA,"Villanueva-Millán M.J., Pérez-Matute P., Recio-Fernández E., Lezana Rosales J.M. , Oteo J.A.",Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients,Journal of the International AIDS Society,2017,"HIV infection, antiretroviral therapy, bacterial diversity, gut microbiota, inflammation, microbial translocation",Experiment 7,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,non-infected volunteers (Control),NRTIs + NNRTIs,This group includes patients on family treatment of nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs),21,22,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex",NA,NA,NA,decreased,NA,NA,decreased,Signature 1,Table 3,9 January 2025,Joiejoie,"Joiejoie,KateRasheed,WikiWorks","Combined antiretroviral therapy modified the relative abundance of taxonomical groups (order, family, genus, species) in NRTIs+NNRTIs",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|1239|186801|3085636|186803;3379134|1224|1236|72274|135621|286,Complete,Svetlana up
bsdb:28362071/7/2,28362071,"cross-sectional observational, not case-control",28362071,https://doi.org/10.7448/IAS.20.1.21526,NA,"Villanueva-Millán M.J., Pérez-Matute P., Recio-Fernández E., Lezana Rosales J.M. , Oteo J.A.",Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients,Journal of the International AIDS Society,2017,"HIV infection, antiretroviral therapy, bacterial diversity, gut microbiota, inflammation, microbial translocation",Experiment 7,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,non-infected volunteers (Control),NRTIs + NNRTIs,This group includes patients on family treatment of nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs),21,22,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex",NA,NA,NA,decreased,NA,NA,decreased,Signature 2,Table 3,9 January 2025,Joiejoie,"Joiejoie,KateRasheed,WikiWorks","Combined antiretroviral therapy modified the relative abundance of taxonomical groups (order, family, genus, species) in NRTIs+NNRTIs",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|s__Bacteroidaceae bacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Coriobacterium|s__Coriobacterium sp. AUH-Julong21,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter|s__Papillibacter cinnamivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus flavefaciens",1783272|1239|186801|3085636|186803|28050|39485;3379134|976|200643|171549|2030927;3379134|976|200643|171549|815|2212467;1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|171550|239759|1288121;1783272|1239|186801|3085636|186803|572511|1955243;1783272|201174|84998|84999|84107|33870|584783;1783272|1239|186801|186802|216572|100175|100176;1783272|1239|186801|186802|216572|1263|1265,Complete,Svetlana up
bsdb:28362071/8/1,28362071,"cross-sectional observational, not case-control",28362071,https://doi.org/10.7448/IAS.20.1.21526,NA,"Villanueva-Millán M.J., Pérez-Matute P., Recio-Fernández E., Lezana Rosales J.M. , Oteo J.A.",Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients,Journal of the International AIDS Society,2017,"HIV infection, antiretroviral therapy, bacterial diversity, gut microbiota, inflammation, microbial translocation",Experiment 8,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,non-infected volunteers (Control),NRTIs + INSTIs,This group includes patients on family treatment of nucleoside reverse transcriptase inhibitors (NRTIs) with integrase strand transfer inhibitors (INSTIs),21,8,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex",NA,NA,NA,decreased,NA,NA,decreased,Signature 1,Table 3,9 January 2025,Joiejoie,"Joiejoie,WikiWorks","Combined antiretroviral therapy modified the relative abundance of taxonomical groups (order, family, genus, species) in NRTIs+INSTIs",increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae",3379134|200940|3031449|213115;1783272|1239|909932|909929;1783272|1239|186801|3085636|186803;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115|194924|872;3379134|976|200643|171549|2005525|375288|46503,Complete,Svetlana up
bsdb:28362071/8/2,28362071,"cross-sectional observational, not case-control",28362071,https://doi.org/10.7448/IAS.20.1.21526,NA,"Villanueva-Millán M.J., Pérez-Matute P., Recio-Fernández E., Lezana Rosales J.M. , Oteo J.A.",Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients,Journal of the International AIDS Society,2017,"HIV infection, antiretroviral therapy, bacterial diversity, gut microbiota, inflammation, microbial translocation",Experiment 8,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,non-infected volunteers (Control),NRTIs + INSTIs,This group includes patients on family treatment of nucleoside reverse transcriptase inhibitors (NRTIs) with integrase strand transfer inhibitors (INSTIs),21,8,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex",NA,NA,NA,decreased,NA,NA,decreased,Signature 2,Table 3,9 January 2025,Joiejoie,"Joiejoie,KateRasheed,WikiWorks","Combined antiretroviral therapy modified the relative abundance of taxonomical groups (order, family, genus, species) in NRTIs+INSTIs",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. Clone-33,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. Clone-24,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus flavefaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens",1783272|1239|186801|186802;1783272|1239|186801|186802|31979|1485|1003372;1783272|1239|186801|186802|31979|1485|1003367;1783272|1239|186801|186802|216572|1263|1265;1783272|1239|186801|3085636|186803|28050|39485,Complete,Svetlana up
bsdb:28362071/9/2,28362071,"cross-sectional observational, not case-control",28362071,https://doi.org/10.7448/IAS.20.1.21526,NA,"Villanueva-Millán M.J., Pérez-Matute P., Recio-Fernández E., Lezana Rosales J.M. , Oteo J.A.",Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients,Journal of the International AIDS Society,2017,"HIV infection, antiretroviral therapy, bacterial diversity, gut microbiota, inflammation, microbial translocation",Experiment 9,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Control,HIV non coinfected patients,This group includes HIV-infected patients who are not coinfected with other infections such as hepatitis B virus (HBV) or hepatitis C virus (HCV).,21,25,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 1,8 January 2025,Joiejoie,"Joiejoie,KateRasheed,WikiWorks",Relative abundance of major phyla present in the gut in non-coinfected HIV patients,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,3379134|1224|1236,Complete,Svetlana up
bsdb:28362071/10/1,28362071,"cross-sectional observational, not case-control",28362071,https://doi.org/10.7448/IAS.20.1.21526,NA,"Villanueva-Millán M.J., Pérez-Matute P., Recio-Fernández E., Lezana Rosales J.M. , Oteo J.A.",Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients,Journal of the International AIDS Society,2017,"HIV infection, antiretroviral therapy, bacterial diversity, gut microbiota, inflammation, microbial translocation",Experiment 10,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Control,HIV coinfected patients,This group includes HIV-infected patients who are also coinfected with either hepatitis B virus (HBV) or hepatitis C virus (HCV).,21,25,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex",NA,NA,NA,decreased,NA,NA,decreased,Signature 1,Supplementary Table 1,8 January 2025,Joiejoie,"Joiejoie,KateRasheed,WikiWorks",Relative abundance of major phyla present in the gut in coinfected patients.,increased,"k__Bacillati|p__Actinomycetota,c__Deltaproteobacteria,k__Pseudomonadati|p__Pseudomonadota",1783272|201174;28221;3379134|1224,Complete,Svetlana up
bsdb:28362071/11/1,28362071,"cross-sectional observational, not case-control",28362071,https://doi.org/10.7448/IAS.20.1.21526,NA,"Villanueva-Millán M.J., Pérez-Matute P., Recio-Fernández E., Lezana Rosales J.M. , Oteo J.A.",Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients,Journal of the International AIDS Society,2017,"HIV infection, antiretroviral therapy, bacterial diversity, gut microbiota, inflammation, microbial translocation",Experiment 11,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Non-coinfected,coinfected patients,This group includes HIV-infected patients who are also coinfected with either hepatitis B virus (HBV) or hepatitis C virus (HCV).,25,25,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex",NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,"Supplementary Table 2, Supplementary Table 1",8 January 2025,Joiejoie,"Joiejoie,KateRasheed,WikiWorks","Abundance of lower taxonomic levels (genus and species) which were
significantly increased in feces from coinfected patients",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Actinomycetota",3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|46503;3379134|1224|1236;1783272|201174,Complete,Svetlana up
bsdb:28362071/11/2,28362071,"cross-sectional observational, not case-control",28362071,https://doi.org/10.7448/IAS.20.1.21526,NA,"Villanueva-Millán M.J., Pérez-Matute P., Recio-Fernández E., Lezana Rosales J.M. , Oteo J.A.",Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients,Journal of the International AIDS Society,2017,"HIV infection, antiretroviral therapy, bacterial diversity, gut microbiota, inflammation, microbial translocation",Experiment 11,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Non-coinfected,coinfected patients,This group includes HIV-infected patients who are also coinfected with either hepatitis B virus (HBV) or hepatitis C virus (HCV).,25,25,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex",NA,NA,NA,unchanged,NA,NA,unchanged,Signature 2,Supplementary Table 2,8 January 2025,Joiejoie,"Joiejoie,KateRasheed,WikiWorks","Abundance of lower taxonomic levels (genus and species) which were
significantly decreased in feces from coinfected patients",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Coriobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Sinorhizobium|s__Sinorhizobium sp.",1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|33870;3379134|1224|1236|72274|135621|286;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|186802|216572|1263;3379134|1224|28211|356|82115|28105|42445,Complete,Svetlana up
bsdb:28368458/1/1,28368458,prospective cohort,28368458,10.1093/annonc/mdx108,https://pubmed.ncbi.nlm.nih.gov/28368458/,"Chaput N., Lepage P., Coutzac C., Soularue E., Le Roux K., Monot C., Boselli L., Routier E., Cassard L., Collins M., Vaysse T., Marthey L., Eggermont A., Asvatourian V., Lanoy E., Mateus C., Robert C. , Carbonnel F.",Baseline gut microbiota predicts clinical response and colitis in metastatic melanoma patients treated with ipilimumab,Annals of oncology : official journal of the European Society for Medical Oncology,2017,"colitis, ipilimumab, melanoma, microbiota",Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,"Resistance, Non responders, No colitis","Responders, Colitis",MM patients that developed an immune-mediated colitis following ipilimumab treatment,19,7,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,3.5,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 4,24 August 2022,Fatima,"Fatima,WikiWorks",Gut microbiota composition at baseline predicts ipilimumab-induced colitis.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans",3379134|976|200643|171549|815|816|28116;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|186802|1898207;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|186802|204475|745368;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803|841|360807,Complete,Fatima
bsdb:28368458/1/2,28368458,prospective cohort,28368458,10.1093/annonc/mdx108,https://pubmed.ncbi.nlm.nih.gov/28368458/,"Chaput N., Lepage P., Coutzac C., Soularue E., Le Roux K., Monot C., Boselli L., Routier E., Cassard L., Collins M., Vaysse T., Marthey L., Eggermont A., Asvatourian V., Lanoy E., Mateus C., Robert C. , Carbonnel F.",Baseline gut microbiota predicts clinical response and colitis in metastatic melanoma patients treated with ipilimumab,Annals of oncology : official journal of the European Society for Medical Oncology,2017,"colitis, ipilimumab, melanoma, microbiota",Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,"Resistance, Non responders, No colitis","Responders, Colitis",MM patients that developed an immune-mediated colitis following ipilimumab treatment,19,7,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,3.5,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 4,24 August 2022,Fatima,"Fatima,WikiWorks",Gut microbiota composition at baseline predicts ipilimumab-induced colitis,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis",3379134|976|200643|171549|171552|838|59823;3379134|976|200643|171549|815|816|29523;3379134|976|200643|171549|815|816|820;1783272|1239|186801|186802|216572|216851|853;3379134|976|200643|171549|815|816|2778071;3379134|976|200643|171549|2005525|375288|823,Complete,Fatima
bsdb:28388647/1/1,28388647,randomized controlled trial,28388647,10.1371/journal.pone.0173802,NA,"Villar-García J., Güerri-Fernández R., Moya A., González A., Hernández J.J., Lerma E., Guelar A., Sorli L., Horcajada J.P., Artacho A., D Auria G. , Knobel H.","Impact of probiotic Saccharomyces boulardii on the gut microbiome composition in HIV-treated patients: A double-blind, randomised, placebo-controlled trial",PloS one,2017,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,baseline,immunological non-responders assigned to treatment for 12 weeks,HIV-infected immunological non-responders (INR) who received S. boulardii probiotic,22,22,2 months,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text (Saccharomyces boulardii produces changes in some gut bacterial communities, lines 3-7)",10 January 2021,Michael Lutete,"WikiWorks,Folakunmi",Changes in some gut bacterial communities produced by Saccharomyces boulardii after 12 weeks of intervention,increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",3379134|200940|3031449|213115|194924|872;1783272|1239|909932|909929|1843491|158846,Complete,Folakunmi
bsdb:28388647/1/2,28388647,randomized controlled trial,28388647,10.1371/journal.pone.0173802,NA,"Villar-García J., Güerri-Fernández R., Moya A., González A., Hernández J.J., Lerma E., Guelar A., Sorli L., Horcajada J.P., Artacho A., D Auria G. , Knobel H.","Impact of probiotic Saccharomyces boulardii on the gut microbiome composition in HIV-treated patients: A double-blind, randomised, placebo-controlled trial",PloS one,2017,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,baseline,immunological non-responders assigned to treatment for 12 weeks,HIV-infected immunological non-responders (INR) who received S. boulardii probiotic,22,22,2 months,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Text (Saccharomyces boulardii produces changes in some gut bacterial communities, lines 3-7)",10 January 2021,Michael Lutete,"WikiWorks,Folakunmi",Changes in some gut bacterial communities produced by Saccharomyces boulardii after 12 weeks of intervention,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|186802|31979,Complete,Folakunmi
bsdb:28388647/2/1,28388647,randomized controlled trial,28388647,10.1371/journal.pone.0173802,NA,"Villar-García J., Güerri-Fernández R., Moya A., González A., Hernández J.J., Lerma E., Guelar A., Sorli L., Horcajada J.P., Artacho A., D Auria G. , Knobel H.","Impact of probiotic Saccharomyces boulardii on the gut microbiome composition in HIV-treated patients: A double-blind, randomised, placebo-controlled trial",PloS one,2017,NA,Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,baseline,immunological responders assigned to treatment for 12 weeks,HIV-infected immunological responders (IR) who received S. boulardii probiotic,22,22,2 months,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text (Saccharomyces boulardii produces changes in some gut bacterial communities, lines 3-7)",10 January 2021,Michael Lutete,"WikiWorks,Folakunmi",Changes in some gut bacterial communities produced by Saccharomyces boulardii after 12 weeks of intervention,increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",3379134|200940|3031449|213115|194924|872;1783272|1239|909932|909929|1843491|158846,Complete,Folakunmi
bsdb:28388647/2/2,28388647,randomized controlled trial,28388647,10.1371/journal.pone.0173802,NA,"Villar-García J., Güerri-Fernández R., Moya A., González A., Hernández J.J., Lerma E., Guelar A., Sorli L., Horcajada J.P., Artacho A., D Auria G. , Knobel H.","Impact of probiotic Saccharomyces boulardii on the gut microbiome composition in HIV-treated patients: A double-blind, randomised, placebo-controlled trial",PloS one,2017,NA,Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,baseline,immunological responders assigned to treatment for 12 weeks,HIV-infected immunological responders (IR) who received S. boulardii probiotic,22,22,2 months,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Text (Saccharomyces boulardii produces changes in some gut bacterial communities, lines 3-7)",10 January 2021,Michael Lutete,"WikiWorks,Folakunmi",Changes in some gut bacterial communities produced by Saccharomyces boulardii after 12 weeks of intervention,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|186802|31979,Complete,Folakunmi
bsdb:28390422/1/1,28390422,laboratory experiment,28390422,10.1186/s40168-017-0258-6,NA,"Xiao L., Sonne S.B., Feng Q., Chen N., Xia Z., Li X., Fang Z., Zhang D., Fjære E., Midtbø L.K., Derrien M., Hugenholtz F., Tang L., Li J., Zhang J., Liu C., Hao Q., Vogel U.B., Mortensen A., Kleerebezem M., Licht T.R., Yang H., Wang J., Li Y., Arumugam M., Wang J., Madsen L. , Kristiansen K.",High-fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice,Microbiome,2017,"129S6/Sv mice, C57BL/6J mice, High-fat feeding, Indomethacin, Microbiome, Microbiota, Obesity",Experiment 1,Denmark,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,BL6- Low Fat,Sv129- Low Fat,"(BL6): C57BL/6JBomTac mouse strain, (Sv129):  the obesity-resistant mouse strain 129S6/SvEvTac . LF:  (LF)low-fat diet, (HF) high fat diet without indomethacin,  (HFI) high fat diet supplemented with indomethacin.",10,7,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Data S4,S7,S8,S9,S10,S11,S13,S14",10 January 2021,Shaimaa Elsafoury,"Lwaldron,WikiWorks","Relative abundance at the bacterial phylum, genus and species levesl between two strain mices fed low fat diet, fed high fat diet and high fat diet + indomethacin",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio proteoclasticus,k__Bacillati|p__Chloroflexota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Methanobacteriati|p__Methanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota,k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 7_1_58FAA,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus animalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia|s__Marvinbryantia formatexigens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Pseudomonadati|p__Planctomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Spirochaetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Thermotogati|p__Synergistota,k__Thermotogati|p__Thermotogota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] hylemonae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus|s__Candidatus Arthromitus sp. SFB-mouse",1783272|1239|186801|186802|216572|244127;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|830;1783272|1239|186801|3085636|186803|830|43305;1783272|200795;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|1649459|154046;1783272|1117;1783272|1239|186801|3085636|186803|189330;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|186801|186802|186806|1730;3366610|28890;1783272|1239|186801|186802|216572|216851;1783272|1239;3384189|32066;1783272|1239|186801|3085636|186803|658087;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|2767887|1605;1783272|1239|186801|3085636|186803|248744|168384;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|459786|351091;3379134|203682;1783272|1239|186801|186802|216572|1017280;1783272|1239|186801|186802|216572|1017280|106588;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|186802|216572|1263;3379134|203691;1783272|1239|186801|186802|216572|292632;3384194|508458;3384194|200918;1783272|1239|186801|3085636|186803|1506553|89153;1783272|1239|186801|3085636|186803|1506553|29347;1783272|1239|186801|186802|31979|49082|49118,Complete,Chloe
bsdb:28390422/1/2,28390422,laboratory experiment,28390422,10.1186/s40168-017-0258-6,NA,"Xiao L., Sonne S.B., Feng Q., Chen N., Xia Z., Li X., Fang Z., Zhang D., Fjære E., Midtbø L.K., Derrien M., Hugenholtz F., Tang L., Li J., Zhang J., Liu C., Hao Q., Vogel U.B., Mortensen A., Kleerebezem M., Licht T.R., Yang H., Wang J., Li Y., Arumugam M., Wang J., Madsen L. , Kristiansen K.",High-fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice,Microbiome,2017,"129S6/Sv mice, C57BL/6J mice, High-fat feeding, Indomethacin, Microbiome, Microbiota, Obesity",Experiment 1,Denmark,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,BL6- Low Fat,Sv129- Low Fat,"(BL6): C57BL/6JBomTac mouse strain, (Sv129):  the obesity-resistant mouse strain 129S6/SvEvTac . LF:  (LF)low-fat diet, (HF) high fat diet without indomethacin,  (HFI) high fat diet supplemented with indomethacin.",10,7,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Data S4,S7,S8,S9,S10,S11,S13,S14",10 January 2021,Shaimaa Elsafoury,"Fatima,WikiWorks","Relative abundance at the bacterial phylum, genus and species levesl between two strain mices fed low fat diet, fed high fat diet and high fat diet + indomethacin",decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Chlorobiota,k__Pseudomonadati|p__Fibrobacterota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis",1783272|201174;3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759;3379134|1090;3379134|65842;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|2005525|195950;3379134|74201;1783272|1239|526524|526525|128827|1573535|1735,Complete,Chloe
bsdb:28390422/2/1,28390422,laboratory experiment,28390422,10.1186/s40168-017-0258-6,NA,"Xiao L., Sonne S.B., Feng Q., Chen N., Xia Z., Li X., Fang Z., Zhang D., Fjære E., Midtbø L.K., Derrien M., Hugenholtz F., Tang L., Li J., Zhang J., Liu C., Hao Q., Vogel U.B., Mortensen A., Kleerebezem M., Licht T.R., Yang H., Wang J., Li Y., Arumugam M., Wang J., Madsen L. , Kristiansen K.",High-fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice,Microbiome,2017,"129S6/Sv mice, C57BL/6J mice, High-fat feeding, Indomethacin, Microbiome, Microbiota, Obesity",Experiment 2,Denmark,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,BL6-High Fat without enomithacin,Sv129-High Fat without enomithacin,"(BL6): C57BL/6JBomTac mouse strain, (Sv129):  the obesity-resistant mouse strain 129S6/SvEvTac . LF:  (LF)low-fat diet, (HF) high fat diet without indomethacin,  (HFI) high fat diet supplemented with indomethacin.",10,8,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Data S4,S7,S8,S9,S10,S11,S13,S14",10 January 2021,Shaimaa Elsafoury,"Fatima,WikiWorks","Relative abundance at the bacterial phylum, genus and species levesl between two strain mices fed low fat diet, fed high fat diet and high fat diet + indomethacin",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus animalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia|s__Marvinbryantia formatexigens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus|s__Candidatus Arthromitus sp. SFB-mouse",1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|1649459|154046;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|91061|186826|81852|1350|1352;1783272|1239|91061|186826|33958|2767887|1605;1783272|1239|186801|3085636|186803|248744|168384;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|3085636|186803|1506553|29347;1783272|1239|186801|186802|31979|49082|49118,Complete,Fatima
bsdb:28390422/2/2,28390422,laboratory experiment,28390422,10.1186/s40168-017-0258-6,NA,"Xiao L., Sonne S.B., Feng Q., Chen N., Xia Z., Li X., Fang Z., Zhang D., Fjære E., Midtbø L.K., Derrien M., Hugenholtz F., Tang L., Li J., Zhang J., Liu C., Hao Q., Vogel U.B., Mortensen A., Kleerebezem M., Licht T.R., Yang H., Wang J., Li Y., Arumugam M., Wang J., Madsen L. , Kristiansen K.",High-fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice,Microbiome,2017,"129S6/Sv mice, C57BL/6J mice, High-fat feeding, Indomethacin, Microbiome, Microbiota, Obesity",Experiment 2,Denmark,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,BL6-High Fat without enomithacin,Sv129-High Fat without enomithacin,"(BL6): C57BL/6JBomTac mouse strain, (Sv129):  the obesity-resistant mouse strain 129S6/SvEvTac . LF:  (LF)low-fat diet, (HF) high fat diet without indomethacin,  (HFI) high fat diet supplemented with indomethacin.",10,8,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Data S4,S7,S8,S9,S10,S11,S13,S14",10 January 2021,Shaimaa Elsafoury,"Fatima,WikiWorks","Relative abundance at the bacterial phylum, genus and species levesl between two strain mices fed low fat diet, fed high fat diet and high fat diet + indomethacin",decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Planctomycetota,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988|239934|239935;3379134|203682;3379134|74201;1783272|1239|526524|526525|128827|1573535|1735,Complete,Fatima
bsdb:28390422/3/1,28390422,laboratory experiment,28390422,10.1186/s40168-017-0258-6,NA,"Xiao L., Sonne S.B., Feng Q., Chen N., Xia Z., Li X., Fang Z., Zhang D., Fjære E., Midtbø L.K., Derrien M., Hugenholtz F., Tang L., Li J., Zhang J., Liu C., Hao Q., Vogel U.B., Mortensen A., Kleerebezem M., Licht T.R., Yang H., Wang J., Li Y., Arumugam M., Wang J., Madsen L. , Kristiansen K.",High-fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice,Microbiome,2017,"129S6/Sv mice, C57BL/6J mice, High-fat feeding, Indomethacin, Microbiome, Microbiota, Obesity",Experiment 3,Denmark,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,BL6-High Fat with enomithacin,Sv129-High Fat with enomithacin,"(BL6): C57BL/6JBomTac mouse strain, (Sv129):  the obesity-resistant mouse strain 129S6/SvEvTac . LF:  (LF)low-fat diet, (HF) high fat diet without indomethacin,  (HFI) high fat diet supplemented with indomethacin.",10,9,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Data S4,S7,S8,S9,S10,S11,S13,S14",10 January 2021,Shaimaa Elsafoury,WikiWorks,"Relative abundance at the bacterial phylum, genus and species levesl between two strain mices fed low fat diet, fed high fat diet and high fat diet + indomethacin",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Chlorobiota,k__Pseudomonadati|p__Fibrobacterota",3379134|976|200643|171549|815|816;3379134|976;1783272|1117;3379134|1090;3379134|65842,Complete,Shaimaa Elsafoury
bsdb:28390422/3/2,28390422,laboratory experiment,28390422,10.1186/s40168-017-0258-6,NA,"Xiao L., Sonne S.B., Feng Q., Chen N., Xia Z., Li X., Fang Z., Zhang D., Fjære E., Midtbø L.K., Derrien M., Hugenholtz F., Tang L., Li J., Zhang J., Liu C., Hao Q., Vogel U.B., Mortensen A., Kleerebezem M., Licht T.R., Yang H., Wang J., Li Y., Arumugam M., Wang J., Madsen L. , Kristiansen K.",High-fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice,Microbiome,2017,"129S6/Sv mice, C57BL/6J mice, High-fat feeding, Indomethacin, Microbiome, Microbiota, Obesity",Experiment 3,Denmark,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,BL6-High Fat with enomithacin,Sv129-High Fat with enomithacin,"(BL6): C57BL/6JBomTac mouse strain, (Sv129):  the obesity-resistant mouse strain 129S6/SvEvTac . LF:  (LF)low-fat diet, (HF) high fat diet without indomethacin,  (HFI) high fat diet supplemented with indomethacin.",10,9,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Data S4,S7,S8,S9,S10,S11,S13,S14",10 January 2021,Shaimaa Elsafoury,"Fatima,Kwekuamoo,WikiWorks","Relative abundance at the bacterial phylum, genus and species levesl between two strain mices fed low fat diet, fed high fat diet and high fat diet + indomethacin",decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Pseudomonadati|p__Planctomycetota,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptacetobacter|s__Peptacetobacter hiranonis",1783272|201174;3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|186802|216572|1535;3384189|32066;1783272|1239|526524|526525|128827|1573535|1735;3379134|203682;3379134|74201;1783272|1239|186801|3082720|186804|2743582|89152,Complete,Fatima
bsdb:28429209/1/1,28429209,case-control,28429209,10.1007/s10517-017-3700-7,https://link.springer.com/article/10.1007/s10517-017-3700-7,"Petrov V.A., Saltykova I.V., Zhukova I.A., Alifirova V.M., Zhukova N.G., Dorofeeva Y.B., Tyakht A.V., Kovarsky B.A., Alekseev D.G., Kostryukova E.S., Mironova Y.S., Izhboldina O.P., Nikitina M.A., Perevozchikova T.V., Fait E.A., Babenko V.V., Vakhitova M.T., Govorun V.M. , Sazonov A.E.",Analysis of Gut Microbiota in Patients with Parkinson's Disease,Bulletin of experimental biology and medicine,2017,"16S rRNA sequencing, Parkinson’s disease, gut microbiota",Experiment 1,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's,NA,66,89,NA,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Fatima Zohra,WikiWorks,Differences in the content of bacterial taxa in PD patients and control subjects at the genus and species level,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella minuta,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella hongkongensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter|s__Papillibacter cinnamivorans",1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|3082768|990719|270497;1783272|1239|186801|186802|216572|119852;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3082768|990719|990721|626937;1783272|1239|186801|3082768|990719|990721|270498;1783272|1239|91061|186826|33958|2742598|97478;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|100175|100176,Complete,Shaimaa Elsafoury
bsdb:28429209/1/2,28429209,case-control,28429209,10.1007/s10517-017-3700-7,https://link.springer.com/article/10.1007/s10517-017-3700-7,"Petrov V.A., Saltykova I.V., Zhukova I.A., Alifirova V.M., Zhukova N.G., Dorofeeva Y.B., Tyakht A.V., Kovarsky B.A., Alekseev D.G., Kostryukova E.S., Mironova Y.S., Izhboldina O.P., Nikitina M.A., Perevozchikova T.V., Fait E.A., Babenko V.V., Vakhitova M.T., Govorun V.M. , Sazonov A.E.",Analysis of Gut Microbiota in Patients with Parkinson's Disease,Bulletin of experimental biology and medicine,2017,"16S rRNA sequencing, Parkinson’s disease, gut microbiota",Experiment 1,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's,NA,66,89,NA,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Figure 3,10 January 2021,Fatima Zohra,WikiWorks,Differences in the content of bacterial taxa in PD patients and control subjects at the genus and species level,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia glucerasea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus|s__Candidatus Stoquefichus massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus",1783272|1239|186801|3085636|186803|189330;3379134|976|200643|171549|815|816;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|815|909656|204516;1783272|1239|186801|3085636|186803|572511|536633;1783272|1239|526524|526525|128827|1470349|1470350;3379134|976|200643|171549|815|909656|310298;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|186801|3085636|186803|189330|88431;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|171552|2974251|165179;3379134|976|200643|171549|815|909656|310297;1783272|1239|186801|3085636|186803|33042|33043,Complete,Shaimaa Elsafoury
bsdb:28441964/1/1,28441964,case-control,28441964,10.1186/s40168-017-0261-y,NA,"Nagy-Szakal D., Williams B.L., Mishra N., Che X., Lee B., Bateman L., Klimas N.G., Komaroff A.L., Levine S., Montoya J.G., Peterson D.L., Ramanan D., Jain K., Eddy M.L., Hornig M. , Lipkin W.I.",Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome,Microbiome,2017,"Chronic fatigue syndrome, Irritable bowel syndrome, Metabolic pathway, Metagenomic, Microbiota-gut-brain axis, Myalgic encephalomyelitis, Topological data analysis",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Chronic fatigue syndrome,EFO:0004540,controls,CFS/ME patients,Cases met the 1994 CDC Fukuda and the 2003 Canadian consensus criteria for ME/CFS,50,50,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.2,TRUE,2,"age,ethnic group,geographic area,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a,10 January 2021,Shaimaa Elsafoury,"Fatima,WikiWorks",Differentiately abundant mictobiota between CFS/ME and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis",1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|207244|105841;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|526524|526525|2810280|100883;1783272|1239|186801|3085636|186803|2719313|333367;1783272|1239|186801|186802|216572|1017280;1783272|1239|186801|186802|216572|1017280|106588;1783272|1239|186801|3085636|186803|1506553|29347;1783272|1239|186801|3085636|186803|2941495|1512;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|526524|526525|2810280|100883|100884,Complete,Fatima
bsdb:28441964/1/2,28441964,case-control,28441964,10.1186/s40168-017-0261-y,NA,"Nagy-Szakal D., Williams B.L., Mishra N., Che X., Lee B., Bateman L., Klimas N.G., Komaroff A.L., Levine S., Montoya J.G., Peterson D.L., Ramanan D., Jain K., Eddy M.L., Hornig M. , Lipkin W.I.",Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome,Microbiome,2017,"Chronic fatigue syndrome, Irritable bowel syndrome, Metabolic pathway, Metagenomic, Microbiota-gut-brain axis, Myalgic encephalomyelitis, Topological data analysis",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Chronic fatigue syndrome,EFO:0004540,controls,CFS/ME patients,Cases met the 1994 CDC Fukuda and the 2003 Canadian consensus criteria for ME/CFS,50,50,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.2,TRUE,2,"age,ethnic group,geographic area,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3a,10 January 2021,Shaimaa Elsafoury,"Fatima,Lwaldron,WikiWorks",Differentiately abundant mictobiota between CFS/ME and healthy controls,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.",3379134|976|200643|171549|171550|239759|28117;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712|724|729;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|2005525|375288|823;3379134|1224|1236|135625|712;3379134|1224|1236|135625;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|186802|216572|216851|1971605,Complete,Fatima
bsdb:28441964/2/1,28441964,case-control,28441964,10.1186/s40168-017-0261-y,NA,"Nagy-Szakal D., Williams B.L., Mishra N., Che X., Lee B., Bateman L., Klimas N.G., Komaroff A.L., Levine S., Montoya J.G., Peterson D.L., Ramanan D., Jain K., Eddy M.L., Hornig M. , Lipkin W.I.",Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome,Microbiome,2017,"Chronic fatigue syndrome, Irritable bowel syndrome, Metabolic pathway, Metagenomic, Microbiota-gut-brain axis, Myalgic encephalomyelitis, Topological data analysis",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Chronic fatigue syndrome,EFO:0004540,controls,CFS/ME patients with IBS,Cases met the 1994 CDC Fukuda and the 2003 Canadian consensus criteria for ME/CFS,50,21,3 months,WMS,NA,Illumina,NA,LEfSe,0.2,TRUE,2,"age,ethnic group,geographic area,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3b,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differentiately abundant mictobiota between CFS/ME with IBS and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes",1783272|1239|186801|3085636|186803|207244|105841;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|207244,Complete,Shaimaa Elsafoury
bsdb:28441964/2/2,28441964,case-control,28441964,10.1186/s40168-017-0261-y,NA,"Nagy-Szakal D., Williams B.L., Mishra N., Che X., Lee B., Bateman L., Klimas N.G., Komaroff A.L., Levine S., Montoya J.G., Peterson D.L., Ramanan D., Jain K., Eddy M.L., Hornig M. , Lipkin W.I.",Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome,Microbiome,2017,"Chronic fatigue syndrome, Irritable bowel syndrome, Metabolic pathway, Metagenomic, Microbiota-gut-brain axis, Myalgic encephalomyelitis, Topological data analysis",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Chronic fatigue syndrome,EFO:0004540,controls,CFS/ME patients with IBS,Cases met the 1994 CDC Fukuda and the 2003 Canadian consensus criteria for ME/CFS,50,21,3 months,WMS,NA,Illumina,NA,LEfSe,0.2,TRUE,2,"age,ethnic group,geographic area,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3b,10 January 2021,Shaimaa Elsafoury,"Lwaldron,WikiWorks",Differentiately abundant mictobiota between CFS/ME with IBS and healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum",1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|186802|216572|216851|1971605;1783272|1239|186801|3085636|186803|572511|40520,Complete,Shaimaa Elsafoury
bsdb:28441964/3/1,28441964,case-control,28441964,10.1186/s40168-017-0261-y,NA,"Nagy-Szakal D., Williams B.L., Mishra N., Che X., Lee B., Bateman L., Klimas N.G., Komaroff A.L., Levine S., Montoya J.G., Peterson D.L., Ramanan D., Jain K., Eddy M.L., Hornig M. , Lipkin W.I.",Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome,Microbiome,2017,"Chronic fatigue syndrome, Irritable bowel syndrome, Metabolic pathway, Metagenomic, Microbiota-gut-brain axis, Myalgic encephalomyelitis, Topological data analysis",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Chronic fatigue syndrome,EFO:0004540,controls,CFS/ME patients without IBS,Cases met the 1994 CDC Fukuda and the 2003 Canadian consensus criteria for ME/CFS,50,29,3 months,WMS,NA,Illumina,NA,LEfSe,0.2,TRUE,2,"age,ethnic group,geographic area,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3c,10 January 2021,Shaimaa Elsafoury,"Fatima,Lwaldron,WikiWorks",Differentiately abundant mictobiota between CFS/ME without IBS and healthy controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.",3379134|1224|1236|72274|135621|351;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|526524|526525|2810280|100883;1783272|1239|526524|526525|2810280|100883|100884;1783272|1239|186801|3085636|186803|189330|88431;1783272|201174|84998|1643822|1643826|84111;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|186802|216572|1017280;1783272|1239|186801|186802|216572|1017280|106588;3379134|1224|1236|72274;3379134|1224|1236|72274|135621|286;1783272|1239|186801|3085636|186803|1506553|29347;1783272|1239|186801|3085636|186803|2941495|1512;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|186802|31979|1485|1506,Complete,Fatima
bsdb:28441964/3/2,28441964,case-control,28441964,10.1186/s40168-017-0261-y,NA,"Nagy-Szakal D., Williams B.L., Mishra N., Che X., Lee B., Bateman L., Klimas N.G., Komaroff A.L., Levine S., Montoya J.G., Peterson D.L., Ramanan D., Jain K., Eddy M.L., Hornig M. , Lipkin W.I.",Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome,Microbiome,2017,"Chronic fatigue syndrome, Irritable bowel syndrome, Metabolic pathway, Metagenomic, Microbiota-gut-brain axis, Myalgic encephalomyelitis, Topological data analysis",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Chronic fatigue syndrome,EFO:0004540,controls,CFS/ME patients without IBS,Cases met the 1994 CDC Fukuda and the 2003 Canadian consensus criteria for ME/CFS,50,29,3 months,WMS,NA,Illumina,NA,LEfSe,0.2,TRUE,2,"age,ethnic group,geographic area,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3c,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differentiately abundant mictobiota between CFS/ME without IBS and healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea",1783272|1239|186801|3085636|186803|3570277|116085;3379134|976|200643|171549|2005525|375288|823;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330,Complete,Shaimaa Elsafoury
bsdb:28442250/1/1,28442250,case-control,28442250,10.1016/j.schres.2017.04.017,NA,"Schwarz E., Maukonen J., Hyytiäinen T., Kieseppä T., Orešič M., Sabunciyan S., Mantere O., Saarela M., Yolken R. , Suvisaari J.",Analysis of microbiota in first episode psychosis identifies preliminary associations with symptom severity and treatment response,Schizophrenia research,2018,"Microbiome, Psychosis, Response, Schizophrenia",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Psychosis,EFO:0005407,Controls,FIrst episode Psychosis,NA,16,28,3 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,region of residence,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,10 January 2021,Fatima Zohra,WikiWorks,Taxonomic differences of fecal microbiota between first episode psychosis patients and healthy controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Halothiobacillaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Tropherymataceae|g__Tropheryma,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Saccharophagus,k__Methanobacteriati|p__Methanobacteriota|c__Halobacteria|o__Halobacteriales|f__Haloferacaceae|g__Halorubrum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae|g__Deferribacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Halothiobacillaceae|g__Halothiobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae|g__Deferribacter|s__Deferribacter desulfuricans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia cenocepacia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfitobacteriaceae|g__Desulfosporosinus|s__Desulfosporosinus acidiphilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Halothiobacillaceae|g__Halothiobacillus|s__Halothiobacillus neapolitanus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Saccharophagus|s__Saccharophagus degradans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Francisellaceae|g__Francisella|s__Francisella hispaniensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Tropherymataceae|g__Tropheryma|s__Tropheryma whipplei,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella|s__Brucella canis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Methanobacteriati|p__Methanobacteriota|c__Halobacteria|o__Halobacteriales|f__Haloferacaceae|g__Halorubrum|s__Halorubrum lacusprofundi,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae|g__Nitrosococcus|s__Nitrosococcus halophilus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Bartonellaceae|g__Bartonella|s__Bartonella clarridgeiae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella|s__Brucella anthropi,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium",3379134|1224|28211|356|118882;1783272|1239|91061|186826|33958;3379134|1224|1236|135613|255526;1783272|201174|1760|85006|2805591|2038;3379134|1224|28211|356|118882|528;3379134|1224|1236|1706369|1706371|316625;3366610|28890|183963|2235|1644056|56688;1783272|1239|91061|186826|33958|1578;3379134|200930|68337|191393|191394|53572;3379134|1224|1236|135613|255526|109262;1783272|1239|91061|186826|33958|1578|1579;3379134|200930|68337|191393|191394|53572|197162;3379134|1224|28216|80840|119060|32008|95486;1783272|1239|186801|186802|2937909|79206|885581;3379134|1224|1236|135613|255526|109262|927;3379134|1224|1236|1706369|1706371|316625|86304;3379134|1224|1236|72273|34064|262|622488;1783272|201174|1760|85006|2805591|2038|2039;3379134|1224|28211|356|118882|234|36855;1783272|1239|91061|186826|33958|1578|33959;3366610|28890|183963|2235|1644056|56688|2247;1783272|1239|91061|186826|33958|2742598|1598;3379134|1224|1236|135613|1046|1227|133539;3379134|1224|28211|356|772|773|56426;3379134|1224|28211|356|118882|234|529;1783272|1239|91061|1385;3379134|1224|28211|356;1783272|1239|91061|186826|33958|2742598|1613;1783272|1239|91061|186826|33958|2767887|1624;1783272|1239|91061|186826|33958|1578|1596;1783272|201174|1760|85004|31953|1678|1689,Complete,Shaimaa Elsafoury
bsdb:28442250/1/2,28442250,case-control,28442250,10.1016/j.schres.2017.04.017,NA,"Schwarz E., Maukonen J., Hyytiäinen T., Kieseppä T., Orešič M., Sabunciyan S., Mantere O., Saarela M., Yolken R. , Suvisaari J.",Analysis of microbiota in first episode psychosis identifies preliminary associations with symptom severity and treatment response,Schizophrenia research,2018,"Microbiome, Psychosis, Response, Schizophrenia",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Psychosis,EFO:0005407,Controls,FIrst episode Psychosis,NA,16,28,3 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,region of residence,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2,10 January 2021,Fatima Zohra,"Lwaldron,WikiWorks",Taxonomic differences of fecal microbiota between first episode psychosis patients and healthy controls,decreased,"k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Nostocaceae|g__Anabaena,k__Pseudomonadati|p__Chlorobiota|c__Chlorobiia|o__Chlorobiales|f__Chlorobiaceae|g__Chlorobium|s__Chlorobium chlorochromatii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Gallionellaceae|g__Gallionella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Gallionellaceae|g__Gallionella|s__Gallionella capsiferriformans,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Nitrosomonadaceae|g__Nitrosomonas|s__Nitrosomonas sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Nitrosomonadaceae|g__Nitrosospira,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Nitrosomonadaceae|g__Nitrosospira|s__Nitrosospira multiformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Methanobacteriati|p__Methanobacteriota|c__Thermococci|o__Thermococcales|f__Thermococcaceae|g__Thermococcus|s__Thermococcus gammatolerans,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Nostocaceae|g__Trichormus|s__Trichormus variabilis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Xenorhabdus|s__Xenorhabdus nematophila,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc gasicomitatum",1783272|1117|3028117|1161|1162|1163;3379134|1090|191410|191411|191412|1091|337090;3379134|1224|28216|32003|90627|96;3379134|1224|28216|32003|90627|96|370405;1783272|1239|909932;3379134|1224|28216|32003|206379|914|42353;3379134|1224|28216|32003|206379|35798;3379134|1224|28216|32003|206379|35798|1231;1783272|1239|909932|909929;3366610|28890|183968|2258|2259|2263|187878;1783272|1117|3028117|1161|1162|264688|264691;1783272|1239|909932|1843489|31977;3379134|1224|1236|91347|1903414|626|628;1783272|1239|91061|186826|33958|1243|115778,Complete,Shaimaa Elsafoury
bsdb:28442250/2/1,28442250,case-control,28442250,10.1016/j.schres.2017.04.017,NA,"Schwarz E., Maukonen J., Hyytiäinen T., Kieseppä T., Orešič M., Sabunciyan S., Mantere O., Saarela M., Yolken R. , Suvisaari J.",Analysis of microbiota in first episode psychosis identifies preliminary associations with symptom severity and treatment response,Schizophrenia research,2018,"Microbiome, Psychosis, Response, Schizophrenia",Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Psychosis,EFO:0005407,Controls,FIrst episode Psychosis (physically active),NA,16,15,3 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,region of residence,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 1+results (text),10 January 2021,Fatima Zohra,WikiWorks,Taxonomic differences of fecal microbiota between physically active psychosis patients and healthy controls,increased,"k__Thermoproteati|p__Thermoproteota|c__Thermoprotei|o__Thermoproteales|f__Thermoproteaceae,k__Thermoproteati|p__Thermoproteota|c__Thermoprotei|o__Thermoproteales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",1783275|28889|183924|2266|2267;1783275|28889|183924|2266;1783272|1239|91061|186826|33958,Complete,NA
bsdb:28442250/2/2,28442250,case-control,28442250,10.1016/j.schres.2017.04.017,NA,"Schwarz E., Maukonen J., Hyytiäinen T., Kieseppä T., Orešič M., Sabunciyan S., Mantere O., Saarela M., Yolken R. , Suvisaari J.",Analysis of microbiota in first episode psychosis identifies preliminary associations with symptom severity and treatment response,Schizophrenia research,2018,"Microbiome, Psychosis, Response, Schizophrenia",Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Psychosis,EFO:0005407,Controls,FIrst episode Psychosis (physically active),NA,16,15,3 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,region of residence,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table 1+results (text),10 January 2021,Fatima Zohra,WikiWorks,Taxonomic differences of fecal microbiota between physically active psychosis patients and healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|909932;1783272|1239|909932|909929;1783272|1239|909932|1843489|31977,Complete,NA
bsdb:28449715/1/1,28449715,case-control,28449715,10.1186/s13073-017-0428-y,NA,"Bedarf J.R., Hildebrand F., Coelho L.P., Sunagawa S., Bahram M., Goeser F., Bork P. , Wüllner U.",Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients,Genome medicine,2017,"Archaea, Bacteria, Enteric nervous system, Gut-brain axis, Microbiome, Parkinson, Viruses",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy men without Parkinsons's Disease.,Men with Parkinson's Disease.,Only early stage PD men who were naïve to L-DOPA therapy as diagnosed according to the UK Brain Bank criteria.,28,31,3 months,16S,NA,Illumina,relative abundances,Kruskall-Wallis,0.1,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 1C,14 November 2021,Fcuevas3,"Fcuevas3,Claregrieve1,WikiWorks",Differential microbial abundance between PD participants and controls,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora saccharolytica,k__Bacillati|p__Bacillota,,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759|328814;1783272|1239|186801|3085636|186803|2719231|84030;1783272|1239;;1783272|1239|186801|186802|186806|1730|142586;1783272|1239|186801,Complete,Claregrieve1
bsdb:28449715/1/2,28449715,case-control,28449715,10.1186/s13073-017-0428-y,NA,"Bedarf J.R., Hildebrand F., Coelho L.P., Sunagawa S., Bahram M., Goeser F., Bork P. , Wüllner U.",Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients,Genome medicine,2017,"Archaea, Bacteria, Enteric nervous system, Gut-brain axis, Microbiome, Parkinson, Viruses",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy men without Parkinsons's Disease.,Men with Parkinson's Disease.,Only early stage PD men who were naïve to L-DOPA therapy as diagnosed according to the UK Brain Bank criteria.,28,31,3 months,16S,NA,Illumina,relative abundances,Kruskall-Wallis,0.1,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 1C,14 November 2021,Fcuevas3,"Fcuevas3,Claregrieve1,WikiWorks",Differential microbial abundance between PD participants and controls,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri",1783272|1239|526524|526525|128827|1573535|1735;3379134|976|200643|171549|171552|2974251|165179,Complete,Claregrieve1
bsdb:28457228/1/1,28457228,"cross-sectional observational, not case-control",28457228,10.1186/s40168-017-0260-z,NA,"Labus J.S., Hollister E.B., Jacobs J., Kirbach K., Oezguen N., Gupta A., Acosta J., Luna R.A., Aagaard K., Versalovic J., Savidge T., Hsiao E., Tillisch K. , Mayer E.A.",Differences in gut microbial composition correlate with regional brain volumes in irritable bowel syndrome,Microbiome,2017,"Bacteroidetes, Brain-gut-microbiome axis, Firmicutes, Irritable bowel syndrome, Metagenome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,HC (Healthy Control),IBS1 (Irritable Bowel Syndrome 1),A subgroup of irritable bowel syndrome (IBS) patients with microbial profiles distinct from healthy control (HC) subjects,23,13,3 months,16S,345,Roche454,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Results text (Figure 4C - F),25 April 2025,Anne-mariesharp,Anne-mariesharp,"The mean relative abundance for identifiable taxa demonstrating overall group differences at each taxonomic level (phylum, class, order, family, and genus)",increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales",1783272|1239|91061;1783272|1239;1783272|1239|186801;1783272|1239|526524|526525|128827|61170;1783272|1239|91061|186826,Complete,KateRasheed
bsdb:28457228/1/2,28457228,"cross-sectional observational, not case-control",28457228,10.1186/s40168-017-0260-z,NA,"Labus J.S., Hollister E.B., Jacobs J., Kirbach K., Oezguen N., Gupta A., Acosta J., Luna R.A., Aagaard K., Versalovic J., Savidge T., Hsiao E., Tillisch K. , Mayer E.A.",Differences in gut microbial composition correlate with regional brain volumes in irritable bowel syndrome,Microbiome,2017,"Bacteroidetes, Brain-gut-microbiome axis, Firmicutes, Irritable bowel syndrome, Metagenome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,HC (Healthy Control),IBS1 (Irritable Bowel Syndrome 1),A subgroup of irritable bowel syndrome (IBS) patients with microbial profiles distinct from healthy control (HC) subjects,23,13,3 months,16S,345,Roche454,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Results text (Figure 4C - F),25 April 2025,Anne-mariesharp,Anne-mariesharp,"The mean relative abundance for identifiable taxa demonstrating overall group differences at each taxonomic level (phylum, class, order, family, and genus)",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|976|200643|171549|2005525|375288,Complete,KateRasheed
bsdb:28457228/2/1,28457228,"cross-sectional observational, not case-control",28457228,10.1186/s40168-017-0260-z,NA,"Labus J.S., Hollister E.B., Jacobs J., Kirbach K., Oezguen N., Gupta A., Acosta J., Luna R.A., Aagaard K., Versalovic J., Savidge T., Hsiao E., Tillisch K. , Mayer E.A.",Differences in gut microbial composition correlate with regional brain volumes in irritable bowel syndrome,Microbiome,2017,"Bacteroidetes, Brain-gut-microbiome axis, Firmicutes, Irritable bowel syndrome, Metagenome",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,HC-like IBS(Healthy Control like Irritable Bowel Syndrome),IBS1 (Irritable Bowel Syndrome 1),A subgroup of irritable bowel syndrome (IBS) patients with microbial profiles distinct from healthy control (HC) subjects,16,13,3 months,16S,345,Roche454,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Results text (Figure 4C - F),25 April 2025,Anne-mariesharp,Anne-mariesharp,"The mean relative abundance for identifiable taxa demonstrating overall group differences at each taxonomic level (phylum, class, order, family, and genus)",increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales",1783272|1239|91061;1783272|1239|526524|526525|128827|61170;1783272|1239|91061|186826,Complete,KateRasheed
bsdb:28457228/2/2,28457228,"cross-sectional observational, not case-control",28457228,10.1186/s40168-017-0260-z,NA,"Labus J.S., Hollister E.B., Jacobs J., Kirbach K., Oezguen N., Gupta A., Acosta J., Luna R.A., Aagaard K., Versalovic J., Savidge T., Hsiao E., Tillisch K. , Mayer E.A.",Differences in gut microbial composition correlate with regional brain volumes in irritable bowel syndrome,Microbiome,2017,"Bacteroidetes, Brain-gut-microbiome axis, Firmicutes, Irritable bowel syndrome, Metagenome",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,HC-like IBS(Healthy Control like Irritable Bowel Syndrome),IBS1 (Irritable Bowel Syndrome 1),A subgroup of irritable bowel syndrome (IBS) patients with microbial profiles distinct from healthy control (HC) subjects,16,13,3 months,16S,345,Roche454,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Results text (Figure 4C - F),25 April 2025,Anne-mariesharp,Anne-mariesharp,"The mean relative abundance for identifiable taxa demonstrating overall group differences at each taxonomic level (phylum, class, order, family, and genus)",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",1783272|1239|91061|186826|186827|46123;3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|976|200643|171549|2005525|375288,Complete,KateRasheed
bsdb:28457228/3/1,28457228,"cross-sectional observational, not case-control",28457228,10.1186/s40168-017-0260-z,NA,"Labus J.S., Hollister E.B., Jacobs J., Kirbach K., Oezguen N., Gupta A., Acosta J., Luna R.A., Aagaard K., Versalovic J., Savidge T., Hsiao E., Tillisch K. , Mayer E.A.",Differences in gut microbial composition correlate with regional brain volumes in irritable bowel syndrome,Microbiome,2017,"Bacteroidetes, Brain-gut-microbiome axis, Firmicutes, Irritable bowel syndrome, Metagenome",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,HC (Healthy Control),HC-like IBS (Healthy Control like Irritable Bowel Syndrome),A subgroup of irritable bowel syndrome (IBS) patients with similar microbial composition as healthy control (HC) subjects,23,16,3 months,16S,345,Roche454,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Results text (Figure 4C - F),25 April 2025,Anne-mariesharp,Anne-mariesharp,"The mean relative abundance for identifiable taxa demonstrating overall group differences at each taxonomic level (phylum, class, order, family, and genus)",increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",1783272|1239;1783272|1239|186801;3379134|976|200643|171549|2005525|375288,Complete,KateRasheed
bsdb:28457228/3/2,28457228,"cross-sectional observational, not case-control",28457228,10.1186/s40168-017-0260-z,NA,"Labus J.S., Hollister E.B., Jacobs J., Kirbach K., Oezguen N., Gupta A., Acosta J., Luna R.A., Aagaard K., Versalovic J., Savidge T., Hsiao E., Tillisch K. , Mayer E.A.",Differences in gut microbial composition correlate with regional brain volumes in irritable bowel syndrome,Microbiome,2017,"Bacteroidetes, Brain-gut-microbiome axis, Firmicutes, Irritable bowel syndrome, Metagenome",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,HC (Healthy Control),HC-like IBS (Healthy Control like Irritable Bowel Syndrome),A subgroup of irritable bowel syndrome (IBS) patients with similar microbial composition as healthy control (HC) subjects,23,16,3 months,16S,345,Roche454,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Results text (Figure 4C - F),25 April 2025,Anne-mariesharp,Anne-mariesharp,"The mean relative abundance for identifiable taxa demonstrating overall group differences at each taxonomic level (phylum, class, order, family, and genus)",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota",3379134|976|200643|171549;3379134|976|200643;3379134|976,Complete,KateRasheed
bsdb:28457228/4/1,28457228,"cross-sectional observational, not case-control",28457228,10.1186/s40168-017-0260-z,NA,"Labus J.S., Hollister E.B., Jacobs J., Kirbach K., Oezguen N., Gupta A., Acosta J., Luna R.A., Aagaard K., Versalovic J., Savidge T., Hsiao E., Tillisch K. , Mayer E.A.",Differences in gut microbial composition correlate with regional brain volumes in irritable bowel syndrome,Microbiome,2017,"Bacteroidetes, Brain-gut-microbiome axis, Firmicutes, Irritable bowel syndrome, Metagenome",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,HC (Healthy Control),IBS1 (Irritable Bowel Syndrome 1),A subgroup of irritable bowel syndrome (IBS) patients with microbial profiles distinct from healthy control (HC) subjects,23,13,3 months,16S,345,Roche454,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Table S5,27 April 2025,UtibeIta,"UtibeIta,Anne-mariesharp",Relative abundance of operational taxonomic units and taxa showing significant group differences,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota,,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061;1783272|1239;1783272|1239|186801;1783272|1239|526524|526525|128827|61170;1783272|1239|91061|186826;1783272|1239;;1783272|1239|186801;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|3085636|186803;1783272|1239|186801|3082720|186804;1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:28457228/4/2,28457228,"cross-sectional observational, not case-control",28457228,10.1186/s40168-017-0260-z,NA,"Labus J.S., Hollister E.B., Jacobs J., Kirbach K., Oezguen N., Gupta A., Acosta J., Luna R.A., Aagaard K., Versalovic J., Savidge T., Hsiao E., Tillisch K. , Mayer E.A.",Differences in gut microbial composition correlate with regional brain volumes in irritable bowel syndrome,Microbiome,2017,"Bacteroidetes, Brain-gut-microbiome axis, Firmicutes, Irritable bowel syndrome, Metagenome",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,HC (Healthy Control),IBS1 (Irritable Bowel Syndrome 1),A subgroup of irritable bowel syndrome (IBS) patients with microbial profiles distinct from healthy control (HC) subjects,23,13,3 months,16S,345,Roche454,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Table S5,27 April 2025,UtibeIta,"UtibeIta,Anne-mariesharp",Relative abundance of operational taxonomic units and taxa showing significant group differences,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis",3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|823,Complete,KateRasheed
bsdb:28457228/5/1,28457228,"cross-sectional observational, not case-control",28457228,10.1186/s40168-017-0260-z,NA,"Labus J.S., Hollister E.B., Jacobs J., Kirbach K., Oezguen N., Gupta A., Acosta J., Luna R.A., Aagaard K., Versalovic J., Savidge T., Hsiao E., Tillisch K. , Mayer E.A.",Differences in gut microbial composition correlate with regional brain volumes in irritable bowel syndrome,Microbiome,2017,"Bacteroidetes, Brain-gut-microbiome axis, Firmicutes, Irritable bowel syndrome, Metagenome",Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,HC-like IBS(Healthy Control like Irritable Bowel Syndrome),IBS1 (Irritable Bowel Syndrome 1),A subgroup of irritable bowel syndrome (IBS) patients with microbial profiles distinct from healthy control (HC) subjects,16,13,3 months,16S,345,Roche454,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Table S5,27 April 2025,UtibeIta,"UtibeIta,Anne-mariesharp",Relative abundance of operational taxonomic units and taxa showing significant group differences,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota,,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061;1783272|1239;1783272|1239|186801;1783272|1239|526524|526525|128827|61170;1783272|1239|91061|186826;1783272|1239;;1783272|1239|186801;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|3085636|186803;1783272|1239|186801|3082720|186804;1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:28457228/5/2,28457228,"cross-sectional observational, not case-control",28457228,10.1186/s40168-017-0260-z,NA,"Labus J.S., Hollister E.B., Jacobs J., Kirbach K., Oezguen N., Gupta A., Acosta J., Luna R.A., Aagaard K., Versalovic J., Savidge T., Hsiao E., Tillisch K. , Mayer E.A.",Differences in gut microbial composition correlate with regional brain volumes in irritable bowel syndrome,Microbiome,2017,"Bacteroidetes, Brain-gut-microbiome axis, Firmicutes, Irritable bowel syndrome, Metagenome",Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,HC-like IBS(Healthy Control like Irritable Bowel Syndrome),IBS1 (Irritable Bowel Syndrome 1),A subgroup of irritable bowel syndrome (IBS) patients with microbial profiles distinct from healthy control (HC) subjects,16,13,3 months,16S,345,Roche454,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Table S5,27 April 2025,UtibeIta,"UtibeIta,Anne-mariesharp",Relative abundance of operational taxonomic units and taxa showing significant group differences,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis",3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|823,Complete,KateRasheed
bsdb:28457228/6/1,28457228,"cross-sectional observational, not case-control",28457228,10.1186/s40168-017-0260-z,NA,"Labus J.S., Hollister E.B., Jacobs J., Kirbach K., Oezguen N., Gupta A., Acosta J., Luna R.A., Aagaard K., Versalovic J., Savidge T., Hsiao E., Tillisch K. , Mayer E.A.",Differences in gut microbial composition correlate with regional brain volumes in irritable bowel syndrome,Microbiome,2017,"Bacteroidetes, Brain-gut-microbiome axis, Firmicutes, Irritable bowel syndrome, Metagenome",Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,HC (Healthy Control),HC-like IBS (Healthy Control like Irritable Bowel Syndrome),A subgroup of irritable bowel syndrome (IBS) patients with similar microbial composition as healthy control (HC) subjects,23,16,3 months,16S,345,Roche454,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table S5,27 April 2025,UtibeIta,"UtibeIta,Anne-mariesharp",Relative abundance of operational taxonomic units and taxa showing significant group differences,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Clostridia",1783272|1239;1783272|1239|186801;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|823;1783272|1239|186801,Complete,KateRasheed
bsdb:28457228/6/2,28457228,"cross-sectional observational, not case-control",28457228,10.1186/s40168-017-0260-z,NA,"Labus J.S., Hollister E.B., Jacobs J., Kirbach K., Oezguen N., Gupta A., Acosta J., Luna R.A., Aagaard K., Versalovic J., Savidge T., Hsiao E., Tillisch K. , Mayer E.A.",Differences in gut microbial composition correlate with regional brain volumes in irritable bowel syndrome,Microbiome,2017,"Bacteroidetes, Brain-gut-microbiome axis, Firmicutes, Irritable bowel syndrome, Metagenome",Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,HC (Healthy Control),HC-like IBS (Healthy Control like Irritable Bowel Syndrome),A subgroup of irritable bowel syndrome (IBS) patients with similar microbial composition as healthy control (HC) subjects,23,16,3 months,16S,345,Roche454,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Table S5,27 April 2025,UtibeIta,"UtibeIta,Anne-mariesharp",Relative abundance of operational taxonomic units and taxa showing significant group differences,decreased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",1783272|1239|91061;3379134|976|200643|171549;3379134|976|200643;3379134|976;1783272|1239|91061|186826;1783272|1239;1783272|1239|186801|3082720|186804,Complete,KateRasheed
bsdb:28467925/1/1,28467925,prospective cohort,28467925,10.1016/j.cmet.2017.04.001,NA,"Loomba R., Seguritan V., Li W., Long T., Klitgord N., Bhatt A., Dulai P.S., Caussy C., Bettencourt R., Highlander S.K., Jones M.B., Sirlin C.B., Schnabl B., Brinkac L., Schork N., Chen C.H., Brenner D.A., Biggs W., Yooseph S., Venter J.C. , Nelson K.E.",Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease,Cell metabolism,2017,"NASH, biomarker, cirrhosis, fatty liver, fibrosis, hepatic steatosis, hepatitis, liver disease, microbiome, non-invasive",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,mild/moderate fibrosis,advanced fibrosis,"Based on clinical, magnetic resonance, histology assessment; Mild/Moderate NAFLD: fibrosis 0-2. Advanced NAFLD: fibrosis 3-4",72,14,NA,WMS,NA,Illumina,relative abundances,Random Forest Analysis,0.05,TRUE,NA,NA,"age,body mass index",NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,Shaimaa Elsafoury,"Lwaldron,WikiWorks",relative abundances of top 4 phyla found in all samples and representative species from the first 3 phyla.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|1766253|39491,Complete,Fatima
bsdb:28494241/1/1,28494241,prospective cohort,28494241,10.1016/j.chom.2017.04.010,NA,"Ananthakrishnan A.N., Luo C., Yajnik V., Khalili H., Garber J.J., Stevens B.W., Cleland T. , Xavier R.J.",Gut Microbiome Function Predicts Response to Anti-integrin Biologic Therapy in Inflammatory Bowel Diseases,Cell host & microbe,2017,"Microbiome, butyrate, remission, roseburia, treatment response, vedolizumab",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Non-remitters at Baseline (Crohn's disease),Remitters at Baseline (Crohn's disease),Crohn's Disease patients whose baseline samples were collected before treatment and who later achieved clinical remission at week 14,NA,NA,NA,WMS,NA,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Fig-2a,26 April 2025,Aiyshaaaa,Aiyshaaaa,The Significantly Differentiated Taxa between Remission and Non-remission Groups in Baseline Samples,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales",1783272|1239|186801|3085636|186803|841|360807;3379134|1224|28216|80840,Complete,KateRasheed
bsdb:28494241/2/1,28494241,prospective cohort,28494241,10.1016/j.chom.2017.04.010,NA,"Ananthakrishnan A.N., Luo C., Yajnik V., Khalili H., Garber J.J., Stevens B.W., Cleland T. , Xavier R.J.",Gut Microbiome Function Predicts Response to Anti-integrin Biologic Therapy in Inflammatory Bowel Diseases,Cell host & microbe,2017,"Microbiome, butyrate, remission, roseburia, treatment response, vedolizumab",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Non Remitters Crohn's disease (CD),Remitters Crohn's disease (CD),Comparison of Crohn's Disease (CD) patients who did not achieve remission and Crohn's Disease (CD) patients who achieved remission between baseline and follow-up of week 14,24,10,NA,WMS,NA,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Fig-3c,26 April 2025,Aiyshaaaa,"Aiyshaaaa,UtibeIta",Log2FC of species that represented significant change at week 14 follow-up in comparison with baseline sample of CD divided into remission and non-remission groups,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula",1783272|201174|1760|85004|31953|1678|216816;1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|909932|1843489|31977|29465|29466,Complete,KateRasheed
bsdb:28494241/3/1,28494241,prospective cohort,28494241,10.1016/j.chom.2017.04.010,NA,"Ananthakrishnan A.N., Luo C., Yajnik V., Khalili H., Garber J.J., Stevens B.W., Cleland T. , Xavier R.J.",Gut Microbiome Function Predicts Response to Anti-integrin Biologic Therapy in Inflammatory Bowel Diseases,Cell host & microbe,2017,"Microbiome, butyrate, remission, roseburia, treatment response, vedolizumab",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Non-Remitters Ulcerative Colitis (UC),Remitters Ulcerative Colitis (UC),Comparison of Ulcerative Colitis (UC) patients who achieved remission and Ulcerative Colitis (UC) patients who did not achieve remission between baseline and follow-up of week 14,17,11,NA,WMS,NA,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Fig-3c,26 April 2025,Aiyshaaaa,"Aiyshaaaa,UtibeIta",Log2FC of species that represented significant change at week 14 follow-up in comparison with baseline sample of UC divided into remission and non-remission groups,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,1783272|1239|91061|186826|1300|1301|1304,Complete,KateRasheed
bsdb:28500319/1/1,28500319,case-control,28500319,10.1038/s41598-017-02067-7,NA,"Chiu C.Y., Chan Y.L., Tsai Y.S., Chen S.A., Wang C.J., Chen K.F. , Chung I.F.",Airway Microbial Diversity is Inversely Associated with Mite-Sensitized Rhinitis and Asthma in Early Childhood,Scientific reports,2017,NA,Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,Asthma,MONDO:0004979,healthy control,asthma,"child age 3-5 diagnosed as ever having asthma with the occurrence of recurrent wheeze in the last 12 months, or current use of asthma medication",32,32,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table 2,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differences and comparisons of bacteria in phyla and genera among children with asthma and health controls,increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,1783272|1239|909932|909929|1843491|970,Complete,Claregrieve1
bsdb:28500319/1/2,28500319,case-control,28500319,10.1038/s41598-017-02067-7,NA,"Chiu C.Y., Chan Y.L., Tsai Y.S., Chen S.A., Wang C.J., Chen K.F. , Chung I.F.",Airway Microbial Diversity is Inversely Associated with Mite-Sensitized Rhinitis and Asthma in Early Childhood,Scientific reports,2017,NA,Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,Asthma,MONDO:0004979,healthy control,asthma,"child age 3-5 diagnosed as ever having asthma with the occurrence of recurrent wheeze in the last 12 months, or current use of asthma medication",32,32,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Table 2,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differences and comparisons of bacteria in phyla and genera among children with asthma and health controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas",1783272|1239|186801|3085636|186803|830;1783272|1239|1737404|1737405|1570339|543311,Complete,Claregrieve1
bsdb:28500319/2/1,28500319,case-control,28500319,10.1038/s41598-017-02067-7,NA,"Chiu C.Y., Chan Y.L., Tsai Y.S., Chen S.A., Wang C.J., Chen K.F. , Chung I.F.",Airway Microbial Diversity is Inversely Associated with Mite-Sensitized Rhinitis and Asthma in Early Childhood,Scientific reports,2017,NA,Experiment 2,China,Homo sapiens,Throat,UBERON:0000341,Allergic rhinitis,EFO:0005854,healthy control,allergic rhinitis,"child age 3-5 diagnosed as having symptoms such as sneezing, nasal congestion, itching, and rhinorrhea in the last 12 months",32,23,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,"Table 2, Text",10 January 2021,Lucy Mellor,WikiWorks,Differences and comparisons of bacteria in phlya and genera among children with allergic rhinitis and health controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|1236|2887326|468|475;3379134|1224|28216|206351|481|482;3379134|1224|1236|135625|712|724;3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|171551|836;3379134|1224,Complete,Claregrieve1
bsdb:28500319/2/2,28500319,case-control,28500319,10.1038/s41598-017-02067-7,NA,"Chiu C.Y., Chan Y.L., Tsai Y.S., Chen S.A., Wang C.J., Chen K.F. , Chung I.F.",Airway Microbial Diversity is Inversely Associated with Mite-Sensitized Rhinitis and Asthma in Early Childhood,Scientific reports,2017,NA,Experiment 2,China,Homo sapiens,Throat,UBERON:0000341,Allergic rhinitis,EFO:0005854,healthy control,allergic rhinitis,"child age 3-5 diagnosed as having symptoms such as sneezing, nasal congestion, itching, and rhinorrhea in the last 12 months",32,23,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,"Table 2, Text",10 January 2021,Lucy Mellor,WikiWorks,Differences and comparisons of bacteria in phlya and genera among children with allergic rhinitis and health controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella",1783272|1239|186801|3085636|186803|830;3379134|1224|1236|135625|712|416916;1783272|1239|186801|3085636|186803|437755,Complete,Claregrieve1
bsdb:28506555/1/1,28506555,case-control,28506555,10.1016/j.brainres.2017.04.019,NA,"Hopfner F., Künstner A., Müller S.H., Künzel S., Zeuner K.E., Margraf N.G., Deuschl G., Baines J.F. , Kuhlenbäumer G.",Gut microbiota in Parkinson disease in a northern German cohort,Brain research,2017,"Gut microbiota, Parkinson disease, Stool",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls.,Participants with Parkinson's Disease.,Participants diagnosed with Parkinson's Disease by a movement disorder specialist in the clinic according to the UK Parkinson’s Disease Society Brain Bank Clinical Diagnostic Criteria.,29,29,3 months,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,age,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table 1.,24 April 2023,Fcuevas3,"Fcuevas3,Aiyshaaaa,Atrayees,WikiWorks",Comparison of p-values of bacteria associated with PD in this study or in previous studies.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",3379134|976|200643|171549|2005519;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|33958,Complete,Atrayees
bsdb:28512451/1/1,28512451,time series / longitudinal observational,28512451,10.3389/fmicb.2017.00738,NA,"Wampach L., Heintz-Buschart A., Hogan A., Muller E.E.L., Narayanasamy S., Laczny C.C., Hugerth L.W., Bindl L., Bottu J., Andersson A.F., de Beaufort C. , Wilmes P.","Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life",Frontiers in microbiology,2017,"amplicon sequencing, delivery mode, fungi, infant gut microbiome, microbial colonization, quantitative real-time PCR, succession",Experiment 1,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,vaginal delivery at day 3,c-section,meconium samples were collected at day 1 after delivery,6,3,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,increased,NA,NA,increased,Signature 1,Figure 7 and Fig. S4,10 January 2021,Shaimaa Elsafoury,WikiWorks,qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|33958|1578,Complete,Shaimaa Elsafoury
bsdb:28512451/2/1,28512451,time series / longitudinal observational,28512451,10.3389/fmicb.2017.00738,NA,"Wampach L., Heintz-Buschart A., Hogan A., Muller E.E.L., Narayanasamy S., Laczny C.C., Hugerth L.W., Bindl L., Bottu J., Andersson A.F., de Beaufort C. , Wilmes P.","Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life",Frontiers in microbiology,2017,"amplicon sequencing, delivery mode, fungi, infant gut microbiome, microbial colonization, quantitative real-time PCR, succession",Experiment 2,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,vaginal delivery at day 5,c-section,meconium samples were collected at day 1 after delivery,7,5,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 6S,10 January 2021,Shaimaa Elsafoury,WikiWorks,qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.,increased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Shaimaa Elsafoury
bsdb:28512451/2/2,28512451,time series / longitudinal observational,28512451,10.3389/fmicb.2017.00738,NA,"Wampach L., Heintz-Buschart A., Hogan A., Muller E.E.L., Narayanasamy S., Laczny C.C., Hugerth L.W., Bindl L., Bottu J., Andersson A.F., de Beaufort C. , Wilmes P.","Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life",Frontiers in microbiology,2017,"amplicon sequencing, delivery mode, fungi, infant gut microbiome, microbial colonization, quantitative real-time PCR, succession",Experiment 2,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,vaginal delivery at day 5,c-section,meconium samples were collected at day 1 after delivery,7,5,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 6S,10 January 2021,Shaimaa Elsafoury,WikiWorks,qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.,decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Shaimaa Elsafoury
bsdb:28512451/3/1,28512451,time series / longitudinal observational,28512451,10.3389/fmicb.2017.00738,NA,"Wampach L., Heintz-Buschart A., Hogan A., Muller E.E.L., Narayanasamy S., Laczny C.C., Hugerth L.W., Bindl L., Bottu J., Andersson A.F., de Beaufort C. , Wilmes P.","Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life",Frontiers in microbiology,2017,"amplicon sequencing, delivery mode, fungi, infant gut microbiome, microbial colonization, quantitative real-time PCR, succession",Experiment 3,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,vaginal delivery at day 28,c-section,meconium samples were collected at day 1 after delivery,7,6,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,decreased,NA,NA,unchanged,Signature 1,Figure 6S and Fig. S4,10 January 2021,Shaimaa Elsafoury,WikiWorks,qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|976;3379134|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
bsdb:28512451/4/1,28512451,time series / longitudinal observational,28512451,10.3389/fmicb.2017.00738,NA,"Wampach L., Heintz-Buschart A., Hogan A., Muller E.E.L., Narayanasamy S., Laczny C.C., Hugerth L.W., Bindl L., Bottu J., Andersson A.F., de Beaufort C. , Wilmes P.","Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life",Frontiers in microbiology,2017,"amplicon sequencing, delivery mode, fungi, infant gut microbiome, microbial colonization, quantitative real-time PCR, succession",Experiment 4,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,vaginal delivery at day 150,c-section,meconium samples were collected at day 1 after delivery,6,4,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 6S,10 January 2021,Shaimaa Elsafoury,WikiWorks,qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|976;3379134|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
bsdb:28512451/5/1,28512451,time series / longitudinal observational,28512451,10.3389/fmicb.2017.00738,NA,"Wampach L., Heintz-Buschart A., Hogan A., Muller E.E.L., Narayanasamy S., Laczny C.C., Hugerth L.W., Bindl L., Bottu J., Andersson A.F., de Beaufort C. , Wilmes P.","Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life",Frontiers in microbiology,2017,"amplicon sequencing, delivery mode, fungi, infant gut microbiome, microbial colonization, quantitative real-time PCR, succession",Experiment 5,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,vaginal delivery at day 365,c-section,meconium samples were collected at day 1 after delivery,5,5,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 6S,10 January 2021,Shaimaa Elsafoury,WikiWorks,qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.,decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Shaimaa Elsafoury
bsdb:28512451/6/1,28512451,time series / longitudinal observational,28512451,10.3389/fmicb.2017.00738,NA,"Wampach L., Heintz-Buschart A., Hogan A., Muller E.E.L., Narayanasamy S., Laczny C.C., Hugerth L.W., Bindl L., Bottu J., Andersson A.F., de Beaufort C. , Wilmes P.","Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life",Frontiers in microbiology,2017,"amplicon sequencing, delivery mode, fungi, infant gut microbiome, microbial colonization, quantitative real-time PCR, succession",Experiment 6,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Premature birth,EFO:0003917,full-term delivery >39 weeks at day 3,late preterm 34-36 weeks,meconium samples were collected at day 1 after delivery,4,5,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.01,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text pg11 and figure 7s,10 January 2021,Shaimaa Elsafoury,WikiWorks,qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.,decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Shaimaa Elsafoury
bsdb:28512451/7/1,28512451,time series / longitudinal observational,28512451,10.3389/fmicb.2017.00738,NA,"Wampach L., Heintz-Buschart A., Hogan A., Muller E.E.L., Narayanasamy S., Laczny C.C., Hugerth L.W., Bindl L., Bottu J., Andersson A.F., de Beaufort C. , Wilmes P.","Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life",Frontiers in microbiology,2017,"amplicon sequencing, delivery mode, fungi, infant gut microbiome, microbial colonization, quantitative real-time PCR, succession",Experiment 7,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,vaginal delivery,overall time point infants samples of c-section,meconium samples were collected at day 1 after delivery,8,7,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,supplemantry file 9,10 January 2021,Shaimaa Elsafoury,"Fatima,WikiWorks",qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|31979|1485;1783272|1239|909932|1843489|31977|39948;3379134|1224|1236|91347|543|547;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|216572|946234;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85009|31957|1743;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803,Complete,Fatima
bsdb:28512451/7/2,28512451,time series / longitudinal observational,28512451,10.3389/fmicb.2017.00738,NA,"Wampach L., Heintz-Buschart A., Hogan A., Muller E.E.L., Narayanasamy S., Laczny C.C., Hugerth L.W., Bindl L., Bottu J., Andersson A.F., de Beaufort C. , Wilmes P.","Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life",Frontiers in microbiology,2017,"amplicon sequencing, delivery mode, fungi, infant gut microbiome, microbial colonization, quantitative real-time PCR, succession",Experiment 7,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,vaginal delivery,overall time point infants samples of c-section,meconium samples were collected at day 1 after delivery,8,7,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,supplemantry file 9,10 January 2021,Shaimaa Elsafoury,WikiWorks,qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|815|816;3379134|976|200643|171549|171550|239759,Complete,Shaimaa Elsafoury
bsdb:28512451/8/NA,28512451,time series / longitudinal observational,28512451,10.3389/fmicb.2017.00738,NA,"Wampach L., Heintz-Buschart A., Hogan A., Muller E.E.L., Narayanasamy S., Laczny C.C., Hugerth L.W., Bindl L., Bottu J., Andersson A.F., de Beaufort C. , Wilmes P.","Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life",Frontiers in microbiology,2017,"amplicon sequencing, delivery mode, fungi, infant gut microbiome, microbial colonization, quantitative real-time PCR, succession",Experiment 8,Luxembourg,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,vaginal delivery,C-section,NA,4,6,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:28536926/1/1,28536926,case-control,28536926,10.1007/s11427-016-9001-4,NA,"Li W., Wu X., Hu X., Wang T., Liang S., Duan Y., Jin F. , Qin B.",Structural changes of gut microbiota in Parkinson's disease and its correlation with clinical features,Science China. Life sciences,2017,"16S rRNA sequencing, gastrointestinal dysfunction, gut-brain-axis, microbiome, short chain fatty acids, α-synuclein",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's disease,Patients with Parkinson's disease,14,24,3 months,16S,345,Illumina,relative abundances,Metastats,0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Supplementary Table S1,12 April 2024,MyleeeA,"MyleeeA,Scholastica,WikiWorks",Significantly abundant genera in Parkinson's disease (PD) compared to healthy control (HC) group,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|909932|1843488|909930|904;3379134|1224|1236|2887326|468|469;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|1940338;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843489|31977|906;3379134|1224|1236|91347|1903414|583;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:28536926/1/2,28536926,case-control,28536926,10.1007/s11427-016-9001-4,NA,"Li W., Wu X., Hu X., Wang T., Liang S., Duan Y., Jin F. , Qin B.",Structural changes of gut microbiota in Parkinson's disease and its correlation with clinical features,Science China. Life sciences,2017,"16S rRNA sequencing, gastrointestinal dysfunction, gut-brain-axis, microbiome, short chain fatty acids, α-synuclein",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's disease,Patients with Parkinson's disease,14,24,3 months,16S,345,Illumina,relative abundances,Metastats,0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Supplementary Table S1,13 April 2024,Shulamite,"Shulamite,Scholastica,WikiWorks",Significantly abundant genera in Parkinson's disease (PD) compared to healthy control (HC) group,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|1263,Complete,Svetlana up
bsdb:28538678/1/1,28538678,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A., Lima M., Conterno L., Gasperotti M., Bianchi M., Fava F., Vrhovsek U., Lovegrove J.A. , Tuohy K.M.",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 1,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Poorly fermentable fiber (cellulose),Renatta canada apple - at 10 hr,Healthy donors administered with Renetta Canada apple,3,3,3 months,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Table 2,10 January 2021,Lora Kasselman,"WikiWorks,ChiomaBlessing",Changes in bacterial taxa relative abundance (%) at 10 h in donors administered with Renetta Canada apple compared to those administered with poorly fermentable fiber (cellulose),decreased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium",3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802;1783272|1239|186801|3082720|543314|86331,Complete,ChiomaBlessing
bsdb:28538678/1/2,28538678,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A., Lima M., Conterno L., Gasperotti M., Bianchi M., Fava F., Vrhovsek U., Lovegrove J.A. , Tuohy K.M.",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 1,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Poorly fermentable fiber (cellulose),Renatta canada apple - at 10 hr,Healthy donors administered with Renetta Canada apple,3,3,3 months,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Table 2,20 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Changes in bacterial taxa relative abundance (%) at 10 h in donors administered with Renetta Canada apple compared to those administered with poorly fermentable fiber (cellulose),increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,ChiomaBlessing
bsdb:28538678/2/1,28538678,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A., Lima M., Conterno L., Gasperotti M., Bianchi M., Fava F., Vrhovsek U., Lovegrove J.A. , Tuohy K.M.",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 2,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Poorly fermentable fiber (cellulose),Golden delicious apple - at 10 hr,Healthy donors administered with Golden delicious apple at 10 hr,3,3,3 months,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Table 2,10 January 2021,Lora Kasselman,"WikiWorks,ChiomaBlessing",Changes in bacterial taxa relative abundance (%) at 10 h in donors administered with Golden delicious apple compared to those administered with poorly fermentable fiber (cellulose),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",1783272|1239|186801|186802;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802;3379134|976|200643|171549|2005525|375288;3379134|200940|3031449|213115|194924|35832,Complete,ChiomaBlessing
bsdb:28538678/2/2,28538678,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A., Lima M., Conterno L., Gasperotti M., Bianchi M., Fava F., Vrhovsek U., Lovegrove J.A. , Tuohy K.M.",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 2,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Poorly fermentable fiber (cellulose),Golden delicious apple - at 10 hr,Healthy donors administered with Golden delicious apple at 10 hr,3,3,3 months,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Table 2,20 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Changes in bacterial taxa relative abundance (%) at 10 h in donors administered with Golden delicious apple compared to those administered with poorly fermentable fiber (cellulose),increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,ChiomaBlessing
bsdb:28538678/3/1,28538678,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A., Lima M., Conterno L., Gasperotti M., Bianchi M., Fava F., Vrhovsek U., Lovegrove J.A. , Tuohy K.M.",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 3,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Poorly fermentable fiber (cellulose),Pink lady apple - at 10 hr,Healthy donors administered with Pink lady apple at 10 hr,3,3,3 months,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Table 2,10 January 2021,Lora Kasselman,"WikiWorks,ChiomaBlessing",Changes in bacterial taxa relative abundance (%) at 10 h in donors administered with Pink lady apple compared to those administered with poorly fermentable fiber (cellulose),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",1783272|1239|186801|186802;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802;3379134|976|200643|171549|2005525|375288;3379134|200940|3031449|213115|194924|35832,Complete,ChiomaBlessing
bsdb:28538678/4/1,28538678,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A., Lima M., Conterno L., Gasperotti M., Bianchi M., Fava F., Vrhovsek U., Lovegrove J.A. , Tuohy K.M.",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 4,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Poorly fermentable fiber (cellulose),Renetta Canada apple- at 24 hr,Healthy donors administered with Renetta Canada apple at 24 hr,3,3,3 months,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Table 2,20 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Changes in bacterial taxa relative abundance (%) at 24 h in donors administered with Renetta Canada apple compared to those administered with poorly fermentable fiber (cellulose),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802,Complete,ChiomaBlessing
bsdb:28538678/4/2,28538678,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A., Lima M., Conterno L., Gasperotti M., Bianchi M., Fava F., Vrhovsek U., Lovegrove J.A. , Tuohy K.M.",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 4,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Poorly fermentable fiber (cellulose),Renetta Canada apple- at 24 hr,Healthy donors administered with Renetta Canada apple at 24 hr,3,3,3 months,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Table 2,20 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Changes in bacterial taxa relative abundance (%) at 24 h in donors administered with Renetta Canada apple compared to those administered with poorly fermentable fiber (cellulose),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|1239|186801|186802|216572|216851;1783272|201174|1760|85004|31953|1678,Complete,ChiomaBlessing
bsdb:28538678/5/1,28538678,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A., Lima M., Conterno L., Gasperotti M., Bianchi M., Fava F., Vrhovsek U., Lovegrove J.A. , Tuohy K.M.",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 5,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Poorly fermentable fiber (cellulose),Golden delicious apple- at 24 hr,Healthy donors administered with Golden delicious apple at 24 hr,3,3,3 months,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Table 2,20 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Changes in bacterial taxa relative abundance (%) at 24 h in donors administered with Golden delicious apple compared to those administered with poorly fermentable fiber (cellulose),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802,Complete,ChiomaBlessing
bsdb:28538678/5/2,28538678,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A., Lima M., Conterno L., Gasperotti M., Bianchi M., Fava F., Vrhovsek U., Lovegrove J.A. , Tuohy K.M.",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 5,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Poorly fermentable fiber (cellulose),Golden delicious apple- at 24 hr,Healthy donors administered with Golden delicious apple at 24 hr,3,3,3 months,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Table 2,20 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Changes in bacterial taxa relative abundance (%) at 24 h in donors administered with Golden delicious apple compared to those administered with poorly fermentable fiber (cellulose),increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,ChiomaBlessing
bsdb:28538678/7/1,28538678,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A., Lima M., Conterno L., Gasperotti M., Bianchi M., Fava F., Vrhovsek U., Lovegrove J.A. , Tuohy K.M.",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 7,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Inulin,Renatta canada apple - at 10 hr,Healthy donors administered with Renatta canada apple - at 10 hr,3,3,3 months,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Table 2,26 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Changes in bacterial taxa relative abundance (%) at 10 h in donors administered with Renatta canada apple compared to those administered with inulin,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium",1783272|1239|186801|186802;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|3082720|543314|86331,Complete,ChiomaBlessing
bsdb:28538678/7/2,28538678,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A., Lima M., Conterno L., Gasperotti M., Bianchi M., Fava F., Vrhovsek U., Lovegrove J.A. , Tuohy K.M.",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 7,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Inulin,Renatta canada apple - at 10 hr,Healthy donors administered with Renatta canada apple - at 10 hr,3,3,3 months,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Table 2,26 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Changes in bacterial taxa relative abundance (%) at 10 h in donors administered with Renatta canada apple compared to those administered with inulin,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,ChiomaBlessing
bsdb:28538678/8/1,28538678,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A., Lima M., Conterno L., Gasperotti M., Bianchi M., Fava F., Vrhovsek U., Lovegrove J.A. , Tuohy K.M.",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 8,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Inulin,Golden delicious apple - at 10 hr,Healthy donors administered with Golden delicious apple - at 10 hr,3,3,3 months,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Table 2,26 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Changes in bacterial taxa relative abundance (%) at 10 h in donors administered with Golden delicious apple compared to those administered with inulin,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802,Complete,ChiomaBlessing
bsdb:28538678/8/2,28538678,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A., Lima M., Conterno L., Gasperotti M., Bianchi M., Fava F., Vrhovsek U., Lovegrove J.A. , Tuohy K.M.",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 8,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Inulin,Golden delicious apple - at 10 hr,Healthy donors administered with Golden delicious apple - at 10 hr,3,3,3 months,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Table 2,26 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Changes in bacterial taxa relative abundance (%) at 10 h in donors administered with Golden delicious apple compared to those administered with inulin,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,ChiomaBlessing
bsdb:28538678/9/1,28538678,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A., Lima M., Conterno L., Gasperotti M., Bianchi M., Fava F., Vrhovsek U., Lovegrove J.A. , Tuohy K.M.",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 9,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Inulin,Golden delicious apple - at 24 hr,Healthy donors administered with Golden delicious apple - at 24 hr,3,3,3 months,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,increased,decreased,NA,NA,decreased,Signature 1,Table 2,26 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Changes in bacterial taxa relative abundance (%) at 24 h in donors administered with Golden delicious apple compared to those administered with inulin,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,1783272|1239|186801|186802|216572|216851,Complete,ChiomaBlessing
bsdb:28538678/10/1,28538678,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A., Lima M., Conterno L., Gasperotti M., Bianchi M., Fava F., Vrhovsek U., Lovegrove J.A. , Tuohy K.M.",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 10,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Inulin,Pink Lady apple - at 10 hr,Healthy donors administered with Pink Lady apple at 10 hr,3,3,3 months,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Table 2,26 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Changes in bacterial taxa relative abundance (%) at 10 h in donors administered with Pink lady apple compared to those administered with inulin,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802,Complete,ChiomaBlessing
bsdb:28538678/11/1,28538678,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A., Lima M., Conterno L., Gasperotti M., Bianchi M., Fava F., Vrhovsek U., Lovegrove J.A. , Tuohy K.M.",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 11,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Inulin,Pink Lady apple - at 24 hr,Healthy donors administered with Pink Lady apple at 24 hr,3,3,3 months,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,increased,decreased,NA,NA,decreased,Signature 1,Table 2,26 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Changes in bacterial taxa relative abundance (%) at 24 h in donors administered with Pink lady apple compared to those administered with inulin,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,1783272|1239|186801|186802|216572|216851,Complete,ChiomaBlessing
bsdb:28538678/12/1,28538678,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A., Lima M., Conterno L., Gasperotti M., Bianchi M., Fava F., Vrhovsek U., Lovegrove J.A. , Tuohy K.M.",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 12,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Inulin,Cellulose - at 10hr,Donors administered with cellulose at 10hr,3,3,3 months,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Table 2,26 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Changes in bacterial taxa relative abundance (%) at 10 h in donors administered with cellulose compared to those administered with inulin,increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802,Complete,ChiomaBlessing
bsdb:28538678/13/1,28538678,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A., Lima M., Conterno L., Gasperotti M., Bianchi M., Fava F., Vrhovsek U., Lovegrove J.A. , Tuohy K.M.",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 13,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Inulin,Cellulose - at 24hr,Donors administered with cellulose at 24hr,3,3,3 months,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Table 2,26 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Changes in bacterial taxa relative abundance (%) at 24 h in donors administered with cellulose compared to those administered with inulin,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,1783272|1239|186801|186802|216572|216851,Complete,ChiomaBlessing
bsdb:28538678/13/2,28538678,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A., Lima M., Conterno L., Gasperotti M., Bianchi M., Fava F., Vrhovsek U., Lovegrove J.A. , Tuohy K.M.",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,"Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins",Experiment 13,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Inulin,Cellulose - at 24hr,Donors administered with cellulose at 24hr,3,3,3 months,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Table 2,26 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Changes in bacterial taxa relative abundance (%) at 24 h in donors administered with cellulose compared to those administered with inulin,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,1783272|1239|186801|186802,Complete,ChiomaBlessing
bsdb:28538949/1/1,28538949,case-control,28538949,10.1001/jamadermatol.2017.0904,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5710430/,"Ring H.C., Thorsen J., Saunte D.M., Lilje B., Bay L., Riis P.T., Larsen N., Andersen L.O., Nielsen H.V., Miller I.M., Bjarnsholt T., Fuursted K. , Jemec G.B.",The Follicular Skin Microbiome in Patients With Hidradenitis Suppurativa and Healthy Controls,JAMA dermatology,2017,NA,Experiment 1,Denmark,Homo sapiens,Axilla skin,UBERON:0015474,Hidradenitis suppurativa,EFO:1000710,Healthy controls,Hidradenitis suppurativa patients,Lesional skin of biopsy confirmed hidradenitis suppurativa,24,30,1 month,16S,34,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig4A and B,18 January 2024,Andre,"Andre,Peace Sandy,WikiWorks","A, Differential abundance at genus level between hidradenitis suppurativa (HS) lesional skin and healthy controls. Note significantly higher relative abundance of Propionibacterium in healthy controls and significantly higher relative abundance of Porphyromonas and Peptoniphilus. B, Differential abundance at species level between HS lesional skin and healthy controls. Note higher relative abundance of Propionibacterium acnes in healthy controls than in lesional samples.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus murdochii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium striatum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Aedoeadaptatus|s__Aedoeadaptatus coxii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus koenoeneniae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus",1783272|201174|1760|2037|2049|1654;1783272|1239|1737404|1737405|1570339|165779|411577;1783272|1239|1737404|1737405|1570339|165779|1287640;1783272|1239|1737404|1737405|1570339|165779|33037;1783272|201174|1760|85007|1653|1716|43770;1783272|1239|909932|1843489|31977|39948;1783272|1239|1737404|1582879;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|1737404|1737405|1570339|150022|1260;1783272|201174|1760|85007;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|1737404|1737405|1570339|2981628|755172;1783272|1239|1737404|1737405|1570339|162289|507751;1783272|1239|1737404|1737405|1570339|162289|33031;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552;3379134|1224|28211|204457|41297|13687;3379134|976|200643|171549|171551|836;1783272|1239|1737404|1737405|1570339|162289,Complete,Peace Sandy
bsdb:28538949/1/2,28538949,case-control,28538949,10.1001/jamadermatol.2017.0904,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5710430/,"Ring H.C., Thorsen J., Saunte D.M., Lilje B., Bay L., Riis P.T., Larsen N., Andersen L.O., Nielsen H.V., Miller I.M., Bjarnsholt T., Fuursted K. , Jemec G.B.",The Follicular Skin Microbiome in Patients With Hidradenitis Suppurativa and Healthy Controls,JAMA dermatology,2017,NA,Experiment 1,Denmark,Homo sapiens,Axilla skin,UBERON:0015474,Hidradenitis suppurativa,EFO:1000710,Healthy controls,Hidradenitis suppurativa patients,Lesional skin of biopsy confirmed hidradenitis suppurativa,24,30,1 month,16S,34,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig4A and B,18 January 2024,Andre,"Andre,Peace Sandy,WikiWorks","A, Differential abundance at genus level between hidradenitis suppurativa (HS) lesional skin and healthy controls. Note significantly higher relative abundance of Propionibacterium in healthy controls and significantly higher relative abundance of Porphyromonas and Peptoniphilus. B, Differential abundance at species level between HS lesional skin and healthy controls. Note higher relative abundance of Propionibacterium acnes in healthy controls than in lesional samples.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter johnsonii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus",3379134|1224|1236|2887326|468|469|40214;3379134|1224|28216|80840|80864|283;1783272|201174|1760|85009|31957|1912216|1747;1783272|201174|1760|85009|31957|1743;1783272|1239|1737404|1737405|1570339|162289,Complete,Peace Sandy
bsdb:28538949/2/1,28538949,case-control,28538949,10.1001/jamadermatol.2017.0904,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5710430/,"Ring H.C., Thorsen J., Saunte D.M., Lilje B., Bay L., Riis P.T., Larsen N., Andersen L.O., Nielsen H.V., Miller I.M., Bjarnsholt T., Fuursted K. , Jemec G.B.",The Follicular Skin Microbiome in Patients With Hidradenitis Suppurativa and Healthy Controls,JAMA dermatology,2017,NA,Experiment 2,Denmark,Homo sapiens,Axilla skin,UBERON:0015474,Hidradenitis suppurativa,EFO:1000710,Non lesional skin of Hidradenitis suppurativa patients,Lesional skin of Hidradenitis suppurativa patients,Lesional skin of biopsy confirmed hidradenitis suppurativa,29,30,1 month,16S,34,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 1,Fig4C and D,18 January 2024,Andre,"Andre,Peace Sandy,WikiWorks","C, Differential abundance at genus level between HS lesional skin and HS nonlesional skin. Note significantly higher relative abundance of Porphyromonas and Peptoniphilus in lesional skin than in nonlesional skin, Propionibacterium is more abundant in nonlesional skin. D, Differential abundance at species level between HS lesional skin and HS nonlesional skin. Note significantly reduced relative abundance of Propionibacterium acnes in HS lesional skin; higher relative abundances of Porphyromonas and Peptoniphilus are found in lesional skin. P values listed are adjusted for anatomical location. Black dots indicate the medians of each distribution.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter ureolyticus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas bennonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii",1783272|201174|1760|2037|2049|1654;1783272|1239|1737404|1737405|1570339|165779|1287640;1783272|1239|1737404|1737405|1570339|165779|33037;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294|194|827;1783272|1239|909932|1843489|31977|39948;1783272|1239|1737404|1737405|1570339|162289;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171551|836|501496;3379134|976|200643|171549|171551|836|322095;1783272|1239|1737404|1737405|1570339|162289;3379134|976|200643|171549|171551|836;3379134|1224|1236|2887326|468|469|470,Complete,NA
bsdb:28538949/2/2,28538949,case-control,28538949,10.1001/jamadermatol.2017.0904,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5710430/,"Ring H.C., Thorsen J., Saunte D.M., Lilje B., Bay L., Riis P.T., Larsen N., Andersen L.O., Nielsen H.V., Miller I.M., Bjarnsholt T., Fuursted K. , Jemec G.B.",The Follicular Skin Microbiome in Patients With Hidradenitis Suppurativa and Healthy Controls,JAMA dermatology,2017,NA,Experiment 2,Denmark,Homo sapiens,Axilla skin,UBERON:0015474,Hidradenitis suppurativa,EFO:1000710,Non lesional skin of Hidradenitis suppurativa patients,Lesional skin of Hidradenitis suppurativa patients,Lesional skin of biopsy confirmed hidradenitis suppurativa,29,30,1 month,16S,34,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 2,Fig4C and D,18 January 2024,Andre,"Andre,Peace Sandy,WikiWorks","C, Differential abundance at genus level between HS lesional skin and HS nonlesional skin. Note significantly higher relative abundance of Porphyromonas and Peptoniphilus in lesional skin than in nonlesional skin, Propionibacterium is more abundant in nonlesional skin. D, Differential abundance at species level between HS lesional skin and HS nonlesional skin.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter junii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter soli,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Alicycliphilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Aquabacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Diaphorobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Diaphorobacter|s__Diaphorobacter nitroreducens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus luteus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Rhodoluna,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella",3379134|1224|1236|2887326|468|469;3379134|1224|1236|2887326|468|469|470;3379134|1224|1236|2887326|468|469|40215;3379134|1224|1236|2887326|468|469|487316;3379134|1224|28216|80840|80864|201096;3379134|1224|28216|80840|92793;1783272|201174|1760|85009|31957|1912216|1747;3379134|1224|28216|80840|80864|238749;3379134|1224|28216|80840|80864|238749|164759;1783272|201174|1760|85006|1268|1269;1783272|201174|1760|85006|1268|1269|1270;3379134|1224|1236|2887326|468|475;3379134|1224|28211|204455|31989|265;1783272|201174|1760|85009|31957|1743;3379134|1224|1236|72274|135621|286;1783272|201174|1760|85006|85023|529883;3379134|1224|1236|2887326|468|475,Complete,Peace Sandy
bsdb:28561276/1/1,28561276,"cross-sectional observational, not case-control",28561276,10.1111/liv.13485,NA,"Heidrich B., Vital M., Plumeier I., Döscher N., Kahl S., Kirschner J., Ziegert S., Solbach P., Lenzen H., Potthoff A., Manns M.P., Wedemeyer H. , Pieper D.H.",Intestinal microbiota in patients with chronic hepatitis C with and without cirrhosis compared with healthy controls,Liver international : official journal of the International Association for the Study of the Liver,2018,"alpha diversity, cirrhosis, gut microbiome, liver elastography, microbial diversity",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Chronic hepatitis C virus infection,EFO:0004220,healthy controls,cirrhosis patients,hepatitis C patients with cirrhosis,50,38,3 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,decreased,decreased,NA,decreased,NA,NA,Signature 1,Table 3,10 January 2021,Fatima Zohra,"WikiWorks,Atrayees,Folakunmi,MyleeeA",Genera with distinct patterns and their mean abundance in predefinded groups,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171552|1283313;3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543|1940338;3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85006|1268|1269;1783272|1239|91061|186826|33958|1253;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|33958|46255;1783272|1239|186801|186802|31979|1485,Complete,Atrayees
bsdb:28561276/1/2,28561276,"cross-sectional observational, not case-control",28561276,10.1111/liv.13485,NA,"Heidrich B., Vital M., Plumeier I., Döscher N., Kahl S., Kirschner J., Ziegert S., Solbach P., Lenzen H., Potthoff A., Manns M.P., Wedemeyer H. , Pieper D.H.",Intestinal microbiota in patients with chronic hepatitis C with and without cirrhosis compared with healthy controls,Liver international : official journal of the International Association for the Study of the Liver,2018,"alpha diversity, cirrhosis, gut microbiome, liver elastography, microbial diversity",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Chronic hepatitis C virus infection,EFO:0004220,healthy controls,cirrhosis patients,hepatitis C patients with cirrhosis,50,38,3 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,decreased,decreased,NA,decreased,NA,NA,Signature 2,Table 3,10 January 2021,Fatima Zohra,"WikiWorks,Merit,Atrayees,Folakunmi",Genera with distinct patterns and their mean abundance in predefinded groups,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Candidatus Melainabacteria|c__Vampirovibriophyceae|o__Vampirovibrionales|g__Vampirovibrio,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis",1783272|1239|186801|3120394|3120654|35829;3379134|200940|3031449|213115|194924|35832;3379134|976|200643|171549|1853231|574697;1783272|1239|909932|909929|1843491|52225;1783272|1239|186801|186802|216572|1017280;1783272|1798710|3118680|2211217|213484;3379134|256845|1313211|278082|255528|172900,Complete,Atrayees
bsdb:28561276/2/1,28561276,"cross-sectional observational, not case-control",28561276,10.1111/liv.13485,NA,"Heidrich B., Vital M., Plumeier I., Döscher N., Kahl S., Kirschner J., Ziegert S., Solbach P., Lenzen H., Potthoff A., Manns M.P., Wedemeyer H. , Pieper D.H.",Intestinal microbiota in patients with chronic hepatitis C with and without cirrhosis compared with healthy controls,Liver international : official journal of the International Association for the Study of the Liver,2018,"alpha diversity, cirrhosis, gut microbiome, liver elastography, microbial diversity",Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Chronic hepatitis C virus infection,EFO:0004220,no cirrhosis,cirrhosis patients,heatitis C patients with cirrhosis,57,38,3 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,decreased,decreased,NA,decreased,NA,decreased,Signature 1,Table 3,10 January 2021,Fatima Zohra,"WikiWorks,Atrayees",Genera with distinct patterns and their mean abundance in predefinded groups,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|29465;1783272|201174|1760|85004|31953|1678;3379134|74201|203494|48461|1647988|239934;3379134|1224|1236|135625|712|724;1783272|201174|1760|85006|1268|1269;1783272|1239|91061|186826|33958|46255,Complete,Atrayees
bsdb:28561276/2/2,28561276,"cross-sectional observational, not case-control",28561276,10.1111/liv.13485,NA,"Heidrich B., Vital M., Plumeier I., Döscher N., Kahl S., Kirschner J., Ziegert S., Solbach P., Lenzen H., Potthoff A., Manns M.P., Wedemeyer H. , Pieper D.H.",Intestinal microbiota in patients with chronic hepatitis C with and without cirrhosis compared with healthy controls,Liver international : official journal of the International Association for the Study of the Liver,2018,"alpha diversity, cirrhosis, gut microbiome, liver elastography, microbial diversity",Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Chronic hepatitis C virus infection,EFO:0004220,no cirrhosis,cirrhosis patients,heatitis C patients with cirrhosis,57,38,3 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,decreased,decreased,NA,decreased,NA,decreased,Signature 2,Table 3,14 July 2023,Atrayees,"Atrayees,WikiWorks",Genera with distinct patterns and their mean abundance in predefinded groups,decreased,k__Bacillati|p__Candidatus Melainabacteria|c__Vampirovibriophyceae|o__Vampirovibrionales|g__Vampirovibrio,1783272|1798710|3118680|2211217|213484,Complete,Atrayees
bsdb:28561276/3/1,28561276,"cross-sectional observational, not case-control",28561276,10.1111/liv.13485,NA,"Heidrich B., Vital M., Plumeier I., Döscher N., Kahl S., Kirschner J., Ziegert S., Solbach P., Lenzen H., Potthoff A., Manns M.P., Wedemeyer H. , Pieper D.H.",Intestinal microbiota in patients with chronic hepatitis C with and without cirrhosis compared with healthy controls,Liver international : official journal of the International Association for the Study of the Liver,2018,"alpha diversity, cirrhosis, gut microbiome, liver elastography, microbial diversity",Experiment 3,Germany,Homo sapiens,Feces,UBERON:0001988,Chronic hepatitis C virus infection,EFO:0004220,healthy controls,No cirrhosis,Hepatitis C patients with no cirrhosis,50,57,3 months,16S,12,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,unchanged,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table 3,10 January 2021,Fatima Zohra,"WikiWorks,Folakunmi",Genera with distinct patterns and their mean abundance in predefinded groups,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio",1783272|1239|909932|909929|1843491|52225;1783272|1239|186801|186802|216572|946234;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3120394|3120654|35829,Complete,Atrayees
bsdb:28561276/3/2,28561276,"cross-sectional observational, not case-control",28561276,10.1111/liv.13485,NA,"Heidrich B., Vital M., Plumeier I., Döscher N., Kahl S., Kirschner J., Ziegert S., Solbach P., Lenzen H., Potthoff A., Manns M.P., Wedemeyer H. , Pieper D.H.",Intestinal microbiota in patients with chronic hepatitis C with and without cirrhosis compared with healthy controls,Liver international : official journal of the International Association for the Study of the Liver,2018,"alpha diversity, cirrhosis, gut microbiome, liver elastography, microbial diversity",Experiment 3,Germany,Homo sapiens,Feces,UBERON:0001988,Chronic hepatitis C virus infection,EFO:0004220,healthy controls,No cirrhosis,Hepatitis C patients with no cirrhosis,50,57,3 months,16S,12,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,unchanged,unchanged,NA,unchanged,NA,unchanged,Signature 2,Table 3,21 February 2024,Folakunmi,"Folakunmi,MyleeeA,WikiWorks",Genera with distinct patterns and their differential mean abundance between healthy control and hepatitis C patients with no cirrhosis,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",3379134|976|200643|171549|171552|1283313;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|186802|31979|1485,Complete,Folakunmi
bsdb:28620208/1/1,28620208,case-control,28620208,10.1038/s41598-017-03706-9,NA,"Xu Y., Xie Z., Wang H., Shen Z., Guo Y., Gao Y., Chen X., Wu Q., Li X. , Wang K.",Bacterial Diversity of Intestinal Microbiota in Patients with Substance Use Disorders Revealed by 16S rRNA Gene Deep Sequencing,Scientific reports,2017,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Substance-related disorder,MONDO:0002494,Healthy controls,Substance use disorder patients,NA,45,48,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,unchanged,NA,NA,increased,Signature 1,Figure 4,10 January 2021,Fatima Zohra,WikiWorks,Differential abundance in community compositions between SUD and healthy controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Rhodocyclaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Thauera",3379134|976|200643|171549|171552;3379134|1224|28211|204455|31989;3379134|1224|28216|206389|75787;3379134|1224|28211;3379134|976|200643|171549|171552|838;3379134|1224|28211|204455|31989|265;1783272|1239|186801|186802|31979|1485;3379134|1224|28216|206389|2008794|33057,Complete,Shaimaa Elsafoury
bsdb:28620208/1/2,28620208,case-control,28620208,10.1038/s41598-017-03706-9,NA,"Xu Y., Xie Z., Wang H., Shen Z., Guo Y., Gao Y., Chen X., Wu Q., Li X. , Wang K.",Bacterial Diversity of Intestinal Microbiota in Patients with Substance Use Disorders Revealed by 16S rRNA Gene Deep Sequencing,Scientific reports,2017,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Substance-related disorder,MONDO:0002494,Healthy controls,Substance use disorder patients,NA,45,48,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,unchanged,NA,NA,increased,Signature 2,Figure 4,10 January 2021,Fatima Zohra,WikiWorks,Differential abundance in community compositions between SUD and healthy controls,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Erysipelotrichia,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",3379134|976|200643|171549|815;3379134|976|200643|171549|171550;3379134|1224|1236|91347|543;1783272|1239|526524|526525|128827;3379134|200940|3031449|213115|194924;1783272|1239|91061;1783272|1239|526524;28221;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|189330;3379134|976|200643|171549|2005525|375288;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|207244;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3085636|186803|1407607;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|204475;3379134|976|200643|171549|815|816;1783272|1239|526524|526525;1783272|1239|91061|186826;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300,Complete,Shaimaa Elsafoury
bsdb:28620208/2/1,28620208,case-control,28620208,10.1038/s41598-017-03706-9,NA,"Xu Y., Xie Z., Wang H., Shen Z., Guo Y., Gao Y., Chen X., Wu Q., Li X. , Wang K.",Bacterial Diversity of Intestinal Microbiota in Patients with Substance Use Disorders Revealed by 16S rRNA Gene Deep Sequencing,Scientific reports,2017,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Substance-related disorder,MONDO:0002494,adjusted Healthy controls,Substance use disorder patients,NA,28,29,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 5B,10 January 2021,Fatima Zohra,WikiWorks,Significantly different microbial composition between SUD and age matched healthy controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Thauera,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|1224|28216|206389|2008794|33057;3379134|1224|28211|204455|31989|265;3379134|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
bsdb:28620208/2/2,28620208,case-control,28620208,10.1038/s41598-017-03706-9,NA,"Xu Y., Xie Z., Wang H., Shen Z., Guo Y., Gao Y., Chen X., Wu Q., Li X. , Wang K.",Bacterial Diversity of Intestinal Microbiota in Patients with Substance Use Disorders Revealed by 16S rRNA Gene Deep Sequencing,Scientific reports,2017,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Substance-related disorder,MONDO:0002494,adjusted Healthy controls,Substance use disorder patients,NA,28,29,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 5B,10 January 2021,Fatima Zohra,WikiWorks,Significantly different microbial composition between SUD and age matched healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter",1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|204475;3379134|200940|3031449|213115|194924|35832;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3085636|186803|1407607,Complete,Shaimaa Elsafoury
bsdb:28624933/1/1,28624933,"cross-sectional observational, not case-control",28624933,10.1007/s13105-017-0570-4,NA,"Castro-Penalonga M., Roca-Saavedra P., Miranda J.M., Porto-Arias J.J., Nebot C., Cardelle-Cobas A., Franco C.M. , Cepeda A.",Influence of food consumption patterns and Galician lifestyle on human gut microbiota,Journal of physiology and biochemistry,2018,"Actinobacteria, Atlantic Diet, Bifidobacterium, Gut microbiota, Lactobacillus, Southern European Atlantic Diet",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,low Southern European Atlantic Diet,high Southern European Atlantic Diet,"SEAD: Southern European Atlantic Diet. SEAD adherence was measured using an index of nine food components (fresh fish, cod, red meat and pork products, dairy products, legumes and vegetables, vegetable soup, po- tatoes, wholegrain bread and wine) that ranged from 0 (lowest adherence) to 9 (highest adherence).",3,7,6 months,16S,NA,RT-qPCR,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 5,10 January 2021,Lora Kasselman,WikiWorks,"Bacterial groups quantified in human fecal samples in subjects with low, intermediate, and high adherence to Southern European Atlantic Diet (SEAD)",increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Shaimaa Elsafoury
bsdb:28624933/2/1,28624933,"cross-sectional observational, not case-control",28624933,10.1007/s13105-017-0570-4,NA,"Castro-Penalonga M., Roca-Saavedra P., Miranda J.M., Porto-Arias J.J., Nebot C., Cardelle-Cobas A., Franco C.M. , Cepeda A.",Influence of food consumption patterns and Galician lifestyle on human gut microbiota,Journal of physiology and biochemistry,2018,"Actinobacteria, Atlantic Diet, Bifidobacterium, Gut microbiota, Lactobacillus, Southern European Atlantic Diet",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,low Southern European Atlantic Diet,intermediate Southern European Atlantic Diet,"SEAD: Southern European Atlantic Diet. SEAD adherence was measured using an index of nine food components (fresh fish, cod, red meat and pork products, dairy products, legumes and vegetables, vegetable soup, po- tatoes, wholegrain bread and wine) that ranged from 0 (lowest adherence) to 9 (highest adherence).",3,21,6 months,16S,NA,RT-qPCR,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 5,10 January 2021,Lora Kasselman,WikiWorks,"Bacterial groups quantified in human fecal samples in subjects with low, intermediate, and high adherence to Southern European Atlantic Diet (SEAD)",increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Shaimaa Elsafoury
bsdb:28624933/3/1,28624933,"cross-sectional observational, not case-control",28624933,10.1007/s13105-017-0570-4,NA,"Castro-Penalonga M., Roca-Saavedra P., Miranda J.M., Porto-Arias J.J., Nebot C., Cardelle-Cobas A., Franco C.M. , Cepeda A.",Influence of food consumption patterns and Galician lifestyle on human gut microbiota,Journal of physiology and biochemistry,2018,"Actinobacteria, Atlantic Diet, Bifidobacterium, Gut microbiota, Lactobacillus, Southern European Atlantic Diet",Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,<20 years participants,> 30 years participants,"SEAD: Southern European Atlantic Diet. SEAD adherence was measured using an index of nine food components (fresh fish, cod, red meat and pork products, dairy products, legumes and vegetables, vegetable soup, po- tatoes, wholegrain bread and wine) that ranged from 0 (lowest adherence) to 9 (highest adherence).",5,11,6 months,16S,NA,RT-qPCR,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Lora Kasselman,WikiWorks,Gut microbiota composition in subjects of different age,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,Shaimaa Elsafoury
bsdb:28624933/4/1,28624933,"cross-sectional observational, not case-control",28624933,10.1007/s13105-017-0570-4,NA,"Castro-Penalonga M., Roca-Saavedra P., Miranda J.M., Porto-Arias J.J., Nebot C., Cardelle-Cobas A., Franco C.M. , Cepeda A.",Influence of food consumption patterns and Galician lifestyle on human gut microbiota,Journal of physiology and biochemistry,2018,"Actinobacteria, Atlantic Diet, Bifidobacterium, Gut microbiota, Lactobacillus, Southern European Atlantic Diet",Experiment 4,Spain,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,>20 years participants,20-30 years participants,"SEAD: Southern European Atlantic Diet. SEAD adherence was measured using an index of nine food components (fresh fish, cod, red meat and pork products, dairy products, legumes and vegetables, vegetable soup, po- tatoes, wholegrain bread and wine) that ranged from 0 (lowest adherence) to 9 (highest adherence).",5,15,6 months,16S,NA,RT-qPCR,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Gut microbiota composition in subjects of different age,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,Shaimaa Elsafoury
bsdb:28624933/5/1,28624933,"cross-sectional observational, not case-control",28624933,10.1007/s13105-017-0570-4,NA,"Castro-Penalonga M., Roca-Saavedra P., Miranda J.M., Porto-Arias J.J., Nebot C., Cardelle-Cobas A., Franco C.M. , Cepeda A.",Influence of food consumption patterns and Galician lifestyle on human gut microbiota,Journal of physiology and biochemistry,2018,"Actinobacteria, Atlantic Diet, Bifidobacterium, Gut microbiota, Lactobacillus, Southern European Atlantic Diet",Experiment 5,Spain,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,20-30 years participants,> 30 years participants,"SEAD: Southern European Atlantic Diet. SEAD adherence was measured using an index of nine food components (fresh fish, cod, red meat and pork products, dairy products, legumes and vegetables, vegetable soup, po- tatoes, wholegrain bread and wine) that ranged from 0 (lowest adherence) to 9 (highest adherence).",15,11,6 months,16S,NA,RT-qPCR,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Gut microbiota composition in subjects of different age,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Shaimaa Elsafoury
bsdb:28624933/6/1,28624933,"cross-sectional observational, not case-control",28624933,10.1007/s13105-017-0570-4,NA,"Castro-Penalonga M., Roca-Saavedra P., Miranda J.M., Porto-Arias J.J., Nebot C., Cardelle-Cobas A., Franco C.M. , Cepeda A.",Influence of food consumption patterns and Galician lifestyle on human gut microbiota,Journal of physiology and biochemistry,2018,"Actinobacteria, Atlantic Diet, Bifidobacterium, Gut microbiota, Lactobacillus, Southern European Atlantic Diet",Experiment 6,Spain,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,BMI < 20,BMI >25,"SEAD: Southern European Atlantic Diet. SEAD adherence was measured using an index of nine food components (fresh fish, cod, red meat and pork products, dairy products, legumes and vegetables, vegetable soup, po- tatoes, wholegrain bread and wine) that ranged from 0 (lowest adherence) to 9 (highest adherence).",5,11,6 months,16S,NA,RT-qPCR,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Bacterial groups quantified in human fecal samples in subjects with different body mass index (BMI),increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota",1783272|201174;3379134|976,Complete,Shaimaa Elsafoury
bsdb:28624933/6/2,28624933,"cross-sectional observational, not case-control",28624933,10.1007/s13105-017-0570-4,NA,"Castro-Penalonga M., Roca-Saavedra P., Miranda J.M., Porto-Arias J.J., Nebot C., Cardelle-Cobas A., Franco C.M. , Cepeda A.",Influence of food consumption patterns and Galician lifestyle on human gut microbiota,Journal of physiology and biochemistry,2018,"Actinobacteria, Atlantic Diet, Bifidobacterium, Gut microbiota, Lactobacillus, Southern European Atlantic Diet",Experiment 6,Spain,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,BMI < 20,BMI >25,"SEAD: Southern European Atlantic Diet. SEAD adherence was measured using an index of nine food components (fresh fish, cod, red meat and pork products, dairy products, legumes and vegetables, vegetable soup, po- tatoes, wholegrain bread and wine) that ranged from 0 (lowest adherence) to 9 (highest adherence).",5,11,6 months,16S,NA,RT-qPCR,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Bacterial groups quantified in human fecal samples in subjects with different body mass index (BMI),decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Shaimaa Elsafoury
bsdb:28624933/7/1,28624933,"cross-sectional observational, not case-control",28624933,10.1007/s13105-017-0570-4,NA,"Castro-Penalonga M., Roca-Saavedra P., Miranda J.M., Porto-Arias J.J., Nebot C., Cardelle-Cobas A., Franco C.M. , Cepeda A.",Influence of food consumption patterns and Galician lifestyle on human gut microbiota,Journal of physiology and biochemistry,2018,"Actinobacteria, Atlantic Diet, Bifidobacterium, Gut microbiota, Lactobacillus, Southern European Atlantic Diet",Experiment 7,Spain,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,BMI <20,BMI 20-25,"SEAD: Southern European Atlantic Diet. SEAD adherence was measured using an index of nine food components (fresh fish, cod, red meat and pork products, dairy products, legumes and vegetables, vegetable soup, po- tatoes, wholegrain bread and wine) that ranged from 0 (lowest adherence) to 9 (highest adherence).",5,15,6 months,16S,NA,RT-qPCR,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Bacterial groups quantified in human fecal samples in subjects with different body mass index (BMI),decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Shaimaa Elsafoury
bsdb:28624933/8/1,28624933,"cross-sectional observational, not case-control",28624933,10.1007/s13105-017-0570-4,NA,"Castro-Penalonga M., Roca-Saavedra P., Miranda J.M., Porto-Arias J.J., Nebot C., Cardelle-Cobas A., Franco C.M. , Cepeda A.",Influence of food consumption patterns and Galician lifestyle on human gut microbiota,Journal of physiology and biochemistry,2018,"Actinobacteria, Atlantic Diet, Bifidobacterium, Gut microbiota, Lactobacillus, Southern European Atlantic Diet",Experiment 8,Spain,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,BMI 20-25,BMI >25,"SEAD: Southern European Atlantic Diet. SEAD adherence was measured using an index of nine food components (fresh fish, cod, red meat and pork products, dairy products, legumes and vegetables, vegetable soup, po- tatoes, wholegrain bread and wine) that ranged from 0 (lowest adherence) to 9 (highest adherence).",15,11,6 months,16S,NA,RT-qPCR,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Bacterial groups quantified in human fecal samples in subjects with different body mass index (BMI),increased,k__Bacillati|p__Actinomycetota,1783272|201174,Complete,Shaimaa Elsafoury
bsdb:28628112/1/1,28628112,case-control,28628112,10.1038/nm.4358,NA,"Liu R., Hong J., Xu X., Feng Q., Zhang D., Gu Y., Shi J., Zhao S., Liu W., Wang X., Xia H., Liu Z., Cui B., Liang P., Xi L., Jin J., Ying X., Wang X., Zhao X., Li W., Jia H., Lan Z., Li F., Wang R., Sun Y., Yang M., Shen Y., Jie Z., Li J., Chen X., Zhong H., Xie H., Zhang Y., Gu W., Deng X., Shen B., Xu X., Yang H., Xu G., Bi Y., Lai S., Wang J., Qi L., Madsen L., Wang J., Ning G., Kristiansen K. , Wang W.",Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention,Nature medicine,2017,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,controls,obese,NA,79,72,1 month,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 1,10 January 2021,Marianthi Thomatos,"Fatima,WikiWorks",Gut microbiome alterations in obesity among cohort of lean vs obese Chinese,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium ulcerans,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium varium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii",1783272|1239|186801|3085636|186803|572511|40520;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330|88431;3384189|32066|203490|203491|203492|848|861;3384189|32066|203490|203491|203492|848|856;1783272|1239|186801|3085636|186803;1783272|1239|909932|1843489|31977|906|907;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803|2569097|39488,Complete,Fatima
bsdb:28628112/1/2,28628112,case-control,28628112,10.1038/nm.4358,NA,"Liu R., Hong J., Xu X., Feng Q., Zhang D., Gu Y., Shi J., Zhao S., Liu W., Wang X., Xia H., Liu Z., Cui B., Liang P., Xi L., Jin J., Ying X., Wang X., Zhao X., Li W., Jia H., Lan Z., Li F., Wang R., Sun Y., Yang M., Shen Y., Jie Z., Li J., Chen X., Zhong H., Xie H., Zhang Y., Gu W., Deng X., Shen B., Xu X., Yang H., Xu G., Bi Y., Lai S., Wang J., Qi L., Madsen L., Wang J., Ning G., Kristiansen K. , Wang W.",Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention,Nature medicine,2017,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,controls,obese,NA,79,72,1 month,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 1,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiome alterations in obesity among cohort of lean vs obese Chinese,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|371601;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|329854;3379134|976|200643|171549|171550|239759|328814;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|815|816|28111;3379134|1224|1236|91347|543|570|573;3379134|1224|1236|91347|543|570|571;3379134|1224|1236|135625|712|724|729;1783272|1239|186801|186802|216572|216851|853;3379134|976|200643|171549|815|816;3379134|976|200643|171549|171550|239759,Complete,ChiomaBlessing
bsdb:28632934/1/1,28632934,prospective cohort,28632934,10.1111/all.13232,NA,"Savage J.H., Lee-Sarwar K.A., Sordillo J., Bunyavanich S., Zhou Y., O'Connor G., Sandel M., Bacharier L.B., Zeiger R., Sodergren E., Weinstock G.M., Gold D.R., Weiss S.T. , Litonjua A.A.",A prospective microbiome-wide association study of food sensitization and food allergy in early childhood,Allergy,2018,"Dorea, food allergy, food sensitization, microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,no food sensitization,child with food sensitization,"child with serum-specific IgE to milk, egg, peanut, soy, wheat, and walnut greater than 0.35 kU/L at age 3",131,85,1 week,16S,345,Roche454,NA,Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 2a,10 January 2021,Lucy Mellor,WikiWorks,Significant associations between food sensitization and bacterial genera. The log2 fold change is plotted for each bacterial genus significantly associated with food sensitization,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",3379134|1224|1236|135625|712|724;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|31979|1485,Complete,Atrayees
bsdb:28632934/2/1,28632934,prospective cohort,28632934,10.1111/all.13232,NA,"Savage J.H., Lee-Sarwar K.A., Sordillo J., Bunyavanich S., Zhou Y., O'Connor G., Sandel M., Bacharier L.B., Zeiger R., Sodergren E., Weinstock G.M., Gold D.R., Weiss S.T. , Litonjua A.A.",A prospective microbiome-wide association study of food sensitization and food allergy in early childhood,Allergy,2018,"Dorea, food allergy, food sensitization, microbiome",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,no food allergy,child with food allergy,"child with healthcare provider-diagnosed allergy to milk, egg, peanut, wheat, soy, or other nut allergy prior to age 3 years with evidence of IgE sensitization to that food (>0.1 kU/L) at age 3 years",202,14,1 week,16S,345,Roche454,NA,Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 2b,10 January 2021,Lucy Mellor,WikiWorks,Significant associations between food allergy and bacterial genera. The log2 fold change is plotted for each bacterial genus significantly associated with food allergy,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea",3379134|1224|1236|91347|543|544;1783272|1239|186801|186802|216572|119852;1783272|1239|91061|186826|1300|1357;1783272|1239|186801|3085636|186803|189330,Complete,Atrayees
bsdb:28636668/1/1,28636668,prospective cohort,28636668,10.1371/journal.pone.0179739,NA,"Borgo F., Riva A., Benetti A., Casiraghi M.C., Bertelli S., Garbossa S., Anselmetti S., Scarone S., Pontiroli A.E., Morace G. , Borghi E.","Microbiota in anorexia nervosa: The triangle between bacterial species, metabolites and psychological tests",PloS one,2017,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Anorexia nervosa,EFO:0004215,Controls,Aonerxia Nervosa patients,"The severity of eating disorder and psychopathology tests were assessed by means of the Symptom Checklist 90 (general psychopathology), Eating Disorder Inventory 2 (eating disorder), State Trait Anxiety Inventory (anxiety disorder) and Beck Depression Inventory (depressive symptoms). Psychologists and psychiatrists (all extensively trained in the use of the instruments) conducted clinical evaluations.",15,15,1 month,16S,NA,Illumina,relative abundances,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3 +text,10 January 2021,Fatima Zohra,WikiWorks,Significant differential abundance in anorexia nervosa vs controls,increased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii",3379134|1224;3379134|1224|1236|91347|543;3366610|28890|183925|2158|2159|2172|2173,Complete,Shaimaa Elsafoury
bsdb:28636668/1/2,28636668,prospective cohort,28636668,10.1371/journal.pone.0179739,NA,"Borgo F., Riva A., Benetti A., Casiraghi M.C., Bertelli S., Garbossa S., Anselmetti S., Scarone S., Pontiroli A.E., Morace G. , Borghi E.","Microbiota in anorexia nervosa: The triangle between bacterial species, metabolites and psychological tests",PloS one,2017,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Anorexia nervosa,EFO:0004215,Controls,Aonerxia Nervosa patients,"The severity of eating disorder and psychopathology tests were assessed by means of the Symptom Checklist 90 (general psychopathology), Eating Disorder Inventory 2 (eating disorder), State Trait Anxiety Inventory (anxiety disorder) and Beck Depression Inventory (depressive symptoms). Psychologists and psychiatrists (all extensively trained in the use of the instruments) conducted clinical evaluations.",15,15,1 month,16S,NA,Illumina,relative abundances,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3 +text,10 January 2021,Fatima Zohra,WikiWorks,Significant differential abundance in anorexia nervosa vs controls,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239;1783272|1239|186801|186802|541000;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|31979|1485,Complete,Shaimaa Elsafoury
bsdb:28683818/1/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Naive(Uninfected Untreated),Tuberculosis + isoniazid-rifampin-pyrazinamide (HRZ) (TB +HRZ group) - 2weeks(W6),"Tuberculosis + isoniazid-rifampin-pyrazinamide (HRZ) (TB +HRZ group) refers to the group of mice infected with Mycobacterium tuberculosis (H37Rv) by aerosol inhalation, that started isoniazid-rifampin-pyrazinamide (HRZ) treatment two weeks after infection.",3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Additional file 4: Figure S4,8 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant bacterial taxa between the naive and TB + HRZ groups at 2weeks post infection.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Anaerorhabdus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",1783272|1239|526524|526525|128827|118966;3379134|1224|1236|91347|1903410|71655;1783272|1239|526524|526525|2810280|1279384;3379134|976|200643|171549|2005525|195950;1783272|1239|526524|526525|2810280|3025755;3379134|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:28683818/1/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Naive(Uninfected Untreated),Tuberculosis + isoniazid-rifampin-pyrazinamide (HRZ) (TB +HRZ group) - 2weeks(W6),"Tuberculosis + isoniazid-rifampin-pyrazinamide (HRZ) (TB +HRZ group) refers to the group of mice infected with Mycobacterium tuberculosis (H37Rv) by aerosol inhalation, that started isoniazid-rifampin-pyrazinamide (HRZ) treatment two weeks after infection.",3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Additional file 4: Figure S4,8 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant bacterial taxa between the naive and TB + HRZ groups at 2weeks post infection.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Acidaminobacteraceae|g__Acidaminobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Parvibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudobacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",1783272|1239|186801|186802|216572|258514;1783272|1239|186801|3120394|3120654|35829;1783272|1239|186801|3082720|3118653|65402;1783272|1239|186801|3082720|3118656|114627;1783272|1239|186801|3082720|543314|109326;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|253238;1783272|1239|186801|186802|186806|1730;1783272|201174|84998|1643822|1643826|644652;3379134|1224|1236|135619|28256|2745;1783272|1239|186801|3085636|186803|248744;1783272|201174|84998|84999|84107|1427376;1783272|1239|91061|186826|33958|1253;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|186802|216572|1486726;1783272|1239|186801|3085636|186803|588605;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|3085636|186803|1213720;1783272|1239|186801|3085636|186803|84036;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3085636|186803|1506577,Complete,Svetlana up
bsdb:28683818/2/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Naive,TB +HRZ group - 4weeks(W8),"TB +HRZ group - 4weeks(W8) refers to the group of mice infected with Mycobacterium tuberculosis (H37Rv) by aerosol inhalation, that started isoniazid-rifampin-pyrazinamide (HRZ) treatment four weeks after infection.",3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Additional file 4: Figure S4,8 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant bacterial taxa between the naive and TB + HRZ groups at 4weeks post infection.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Anaerorhabdus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Oxobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",3379134|976|200643|171549|171550|239759;1783272|1239|526524|526525|128827|118966;1783272|1239|186801|3085636|186803|653683;3379134|976|200643|171549|2005519|397864;1783272|201174|1760|85004|31953|1678;3379134|1224|1236|91347|1903410|71655;1783272|1239|526524|526525|2810280|1279384;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|186802|31979|44261;1783272|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:28683818/2/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Naive,TB +HRZ group - 4weeks(W8),"TB +HRZ group - 4weeks(W8) refers to the group of mice infected with Mycobacterium tuberculosis (H37Rv) by aerosol inhalation, that started isoniazid-rifampin-pyrazinamide (HRZ) treatment four weeks after infection.",3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Additional file 4: Figure S4,8 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant bacterial taxa between the naive and TB + HRZ groups at 4weeks post infection.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Acidaminobacteraceae|g__Acidaminobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",1783272|1239|186801|186802|216572|258514;1783272|1239|186801|3120394|3120654|35829;1783272|1239|186801|3082720|3118653|65402;1783272|1239|186801|3082720|3118656|114627;1783272|201174|1760|85006|1268|1663;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|186802|31979|1485;3379134|976|200643|171549|2005519|1348911;1783272|1239|186801|3085636|186803|189330;3379134|976|200643|171549|2005520|156973;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|216572|253238;1783272|1239|186801|3085636|186803|248744;1783272|1239|91061|186826|33958|1253;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3085636|186803|46205;1783272|1239|186801|3085636|186803|588605;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|3085636|186803|1213720;3379134|976|200643|171549|2005525|195950;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|3085636|186803|84036;1783272|1239|526524|526525|2810281|191303,Complete,Svetlana up
bsdb:28683818/3/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 3,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Naive,TB +HRZ group - 2months into HR therapy(W12),"TB +HRZ group - 2months into HR therapy(W12) refers to the group of mice infected with Mycobacterium tuberculosis (H37Rv) by aerosol inhalation, that are two months into H-Isoniazid; R-Rifampin(HR) therapy.",3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Additional file 4: Figure S4,8 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differentially abundant bacterial taxa between the naive and TB + HRZ groups at 2months into anti-tuberculosis HR(H-Isoniazid, R-Rifampin) therapy.",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Prolixibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Anaerorhabdus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Parvibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudobacteroides,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|2005519|397864;3379134|976|200643|1970189|1471398|314318;3379134|976|200643|171549|171550|239759;3379134|200940|3031449|213115|194924|872;1783272|201174|1760|85004|31953|1678;1783272|1239|526524|526525|128827|118966;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|171552|577309;1783272|1239|186801|3085636|186803|653683;3379134|200930|68337|191393|2945020|248038;1783272|201174|84998|84999|84107|1427376;1783272|1239|186801|186802|216572|1486726;1783272|201174|84998|84999|1643824|133925;1783272|1239|526524|526525|2810280|3025755;1783272|1239|526524|526525|2810280|1279384,Complete,Svetlana up
bsdb:28683818/3/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 3,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Naive,TB +HRZ group - 2months into HR therapy(W12),"TB +HRZ group - 2months into HR therapy(W12) refers to the group of mice infected with Mycobacterium tuberculosis (H37Rv) by aerosol inhalation, that are two months into H-Isoniazid; R-Rifampin(HR) therapy.",3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Additional file 4: Figure S4,8 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differentially abundant bacterial taxa between the naive and TB + HRZ groups at 2months into anti-tuberculosis HR(H-Isoniazid, R-Rifampin) therapy.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Acidaminobacteraceae|g__Acidaminobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Asaccharobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Caloramator,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hespellia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|186802|216572|258514;1783272|1239|186801|3120394|3120654|35829;1783272|1239|186801|3082720|3118653|65402;1783272|1239|186801|3082720|3118656|114627;1783272|1239|186801|3082720|543314|109326;1783272|201174|1760|85006|1268|1663;1783272|201174|84998|1643822|1643826|553372;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|31979|44258;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|186802|31979|1485;3379134|976|200643|171549|2005519|1348911;1783272|1239|186801|3085636|186803|189330;3379134|976|200643|171549|2005520|156973;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|216572|253238;1783272|201174|84998|1643822|1643826|644652;1783272|1239|186801|3085636|186803|241189;3379134|976|200643|171549|1853231|283168;1783272|1239|91061|186826|33958|1253;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3085636|186803|46205;1783272|1239|186801|3085636|186803|588605;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|3085636|186803|1213720;1783272|1239|186801|3085636|186803|84036;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:28683818/4/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 4,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Naive,TB +HRZ group - 3months HR(W16),TB +HRZ group - 3months into HR therapy(W16) refers to the first time point of stool collection (W16) following the switch in the antibiotic regimen from triple HRZ to double HR administration.,3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Additional file 4: Figure S4,9 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differentially abundant bacterial taxa between the naive and TB + HRZ groups at 3months into anti-tuberculosis HR(H-Isoniazid, R-Rifampin) therapy.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Prolixibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Anaerorhabdus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Paraeggerthella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Parvibacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella",3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|2005525|195950;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|1853231|283168;3379134|976|200643|1970189|1471398|314318;1783272|1239|526524|526525|128827|118966;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|577309;3379134|1224|28216|80840|995019|577310;1783272|201174|84998|1643822|1643826|651554;3379134|1224|1236|91347|1903410|71655;1783272|201174|1760|85004|31953|1678;3379134|200940|3031449|213115|194924|872;1783272|201174|84998|84999|84107|1427376;1783272|201174|84998|1643822|1643826|447020;1783272|1239|186801|3085636|186803|248744;1783272|1239|526524|526525|2810280|1279384;1783272|1239|91061|186826|81852|1350;1783272|201174|84998|84999|1643824|133925,Complete,Svetlana up
bsdb:28683818/4/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 4,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Naive,TB +HRZ group - 3months HR(W16),TB +HRZ group - 3months into HR therapy(W16) refers to the first time point of stool collection (W16) following the switch in the antibiotic regimen from triple HRZ to double HR administration.,3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Additional file 4: Figure S4,9 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differentially abundant bacterial taxa between the naive and TB + HRZ groups at 3months into anti-tuberculosis HR(H-Isoniazid, R-Rifampin) therapy.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hespellia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Acidaminobacteraceae|g__Acidaminobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|3082720|3118656|114627;1783272|1239|186801|3120394|3120654|35829;1783272|1239|186801|3085636|186803|1213720;1783272|1239|186801|3082720|543314|109326;1783272|1239|186801|3085636|186803|84036;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|241189;1783272|1239|186801|3082720|3118653|65402;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|186802|216572|258514;1783272|1239|186801|3085636|186803|46205;1783272|1239|526524|526525|128827;3379134|976|200643|171549|2005520|156973;3379134|976|200643|171549|2005519|1348911;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:28683818/5/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 5,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Naive,TB +HRZ group - 4months HR(W20),"TB +HRZ group - 4months into HR therapy(W20) refers to the group of mice infected with Mycobacterium tuberculosis (H37Rv) by aerosol inhalation, that are four months into HR therapy. This is also referred to as the termination of HR therapy",3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Additional file 4: Figure S4,9 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant bacterial taxa between the naive and TB + HRZ groups at 4months into anti-tuberculosis HR therapy(end of therapy).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Anaerorhabdus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Prolixibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Paraeggerthella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Parvibacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudobacteroides",3379134|976|200643|171549|2005519|397864;1783272|1239|526524|526525|128827|118966;3379134|976|200643|171549|171551|836;3379134|976|200643|1970189|1471398|314318;3379134|976|200643|171549|2005525|195950;3379134|976|200643|171549|171552|577309;3379134|1224|28216|80840|995019|577310;3379134|74201|203494|48461|1647988|239934;1783272|1239|526524|526525|2810280|3025755;1783272|201174|84998|84999|1643824|133925;1783272|201174|1760|85004|31953|1678;3379134|200940|3031449|213115|194924|872;1783272|201174|84998|1643822|1643826|651554;1783272|1239|526524|526525|2810280|1279384;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|3082768|990719|990721;1783272|201174|84998|84999|84107|1427376;1783272|201174|84998|1643822|1643826|447020;1783272|1239|186801|186802|216572|1486726,Complete,Svetlana up
bsdb:28683818/5/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 5,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Naive,TB +HRZ group - 4months HR(W20),"TB +HRZ group - 4months into HR therapy(W20) refers to the group of mice infected with Mycobacterium tuberculosis (H37Rv) by aerosol inhalation, that are four months into HR therapy. This is also referred to as the termination of HR therapy",3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Additional file 4: Figure S4,9 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant bacterial taxa between the naive and TB + HRZ groups at 4months into anti-tuberculosis HR therapy(end of therapy).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Oxobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|31979|44261;1783272|1239|186801|186802|216572|253238;1783272|1239|186801|186802|216572|258514;1783272|1239|186801|3082720|543314|109326;1783272|1239|186801|186802|216572|1263;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|1508657;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|31979|1485;1783272|1239|526524|526525|2810281|191303;3379134|976|200643|171549|2005519|1348911;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:28683818/6/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 6,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Untreated Tuberculosis group(TB),TB +HRZ group - 2weeks(W6),"TB +HRZ group - 2weeks(W6) refers to the group of mice infected with Mycobacterium tuberculosis (H37Rv) by aerosol inhalation, that started isoniazid-rifampin-pyrazinamide (HRZ) treatment two weeks after infection.",3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Additional file 5: Figure S5,9 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between the TB and TB + HRZ groups at 2weeks post infection.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Anaerorhabdus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Prolixibacter",3379134|976|200643|171549|2005525|195950;1783272|1239|526524|526525|128827;1783272|1239|526524|526525|128827|118966;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|3085636|186803|653683;1783272|1239|526524|526525|2810280|1279384;1783272|544448|31969|186332|186333|2086;3379134|1224|1236|91347|1903410|71655;3379134|976|200643|1970189|1471398|314318,Complete,Svetlana up
bsdb:28683818/6/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 6,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Untreated Tuberculosis group(TB),TB +HRZ group - 2weeks(W6),"TB +HRZ group - 2weeks(W6) refers to the group of mice infected with Mycobacterium tuberculosis (H37Rv) by aerosol inhalation, that started isoniazid-rifampin-pyrazinamide (HRZ) treatment two weeks after infection.",3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Additional file 5: Figure S5,9 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between the TB and TB + HRZ groups at 2weeks post infection.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Parvibacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Oxobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudobacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|186801|3082768|990719|990721;1783272|1239|909932|909929|1843491|52225;1783272|201174|84998|84999|84107|1427376;1783272|201174|84998|1643822|1643826|644652;1783272|1239|186801|186802|31979|44261;1783272|1239|186801|186802|216572|1486726;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|248744;1783272|1239|186801|3085636|186803|588605;3379134|1224|1236|135619|28256|2745;1783272|1239|186801|3082720|3118656|114627;1783272|1239|186801|3120394|3120654|35829;1783272|1239|186801|3085636|186803|1213720;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|84036;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|186802|31979|1485;1783272|1239|526524|526525|2810281|191303;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:28683818/7/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 7,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Untreated Tuberculosis group(TB),TB +HRZ group - 4weeks(W8),"TB +HRZ group - 4weeks(W8) refers to the group of mice infected with Mycobacterium tuberculosis (H37Rv) by aerosol inhalation, that started isoniazid-rifampin-pyrazinamide (HRZ) treatment four weeks after infection.",3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Additional file 5: Figure S5,9 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant bacterial taxa between the TB and TB + HRZ groups at 4weeks post infection.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Anaerorhabdus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Oxobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma",3379134|976|200643|171549|2005519|397864;1783272|1239|526524|526525|128827|118966;1783272|1239|526524|526525|2810280|1279384;3379134|976|200643|171549|171550|239759;1783272|201174|1760|85004|31953|1678;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|186802|31979|44261;3379134|1224|1236|91347|1903410|71655;1783272|1239|186801|3085636|186803|653683;1783272|201174|84998|1643822|1643826|644652;1783272|544448|31969|186332|186333|2086,Complete,Svetlana up
bsdb:28683818/7/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 7,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Untreated Tuberculosis group(TB),TB +HRZ group - 4weeks(W8),"TB +HRZ group - 4weeks(W8) refers to the group of mice infected with Mycobacterium tuberculosis (H37Rv) by aerosol inhalation, that started isoniazid-rifampin-pyrazinamide (HRZ) treatment four weeks after infection.",3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Additional file 5: Figure S5,9 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant bacterial taxa between the TB and TB + HRZ groups at 4weeks post infection.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Acidaminobacteraceae|g__Acidaminobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|258514;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|3085636|186803|1213720;1783272|1239|186801|3085636|186803|248744;1783272|1239|186801|3085636|186803|46205;1783272|1239|186801|3082720|3118653|65402;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|84036;1783272|1239|186801|186802|186807|2740;3379134|976|200643|171549|2005519|1348911;3379134|976|200643|171549|2005525|375288;1783272|1239|526524|526525|2810281|191303;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005525|195950,Complete,Svetlana up
bsdb:28683818/8/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 8,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Untreated Tuberculosis group(TB),TB +HRZ group - 2months into HR therapy(W12),"TB +HRZ group - 2months into HR therapy(W12) refers to the group of mice infected with Mycobacterium tuberculosis (H37Rv) by aerosol inhalation, that are two months into H-Isoniazid; R-Rifampin(HR) therapy.",3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Additional file 5: Figure S5,9 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between the TB and TB + HRZ groups at 2months HR therapy.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Prolixibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Anaerorhabdus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Parvibacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|2005519|397864;3379134|976|200643|1970189|1471398|314318;1783272|1239|186801|3085636|186803;3379134|200940|3031449|213115|194924|872;1783272|201174|1760|85004|31953|1678;1783272|1239|526524|526525|128827|118966;1783272|1239|186801|186802|216572|946234;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|3085636|186803|653683;3379134|976|200643|171549|171552|577309;1783272|1239|186801|3085636|186803|1427378;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|186802|1392389;1783272|201174|84998|84999|84107|1427376;1783272|201174|84998|84999|1643824|133925;1783272|1239|186801|186802|216572|596767;1783272|1239|186801|3085636|186803|1432051,Complete,Svetlana up
bsdb:28683818/8/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 8,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Untreated Tuberculosis group(TB),TB +HRZ group - 2months into HR therapy(W12),"TB +HRZ group - 2months into HR therapy(W12) refers to the group of mice infected with Mycobacterium tuberculosis (H37Rv) by aerosol inhalation, that are two months into H-Isoniazid; R-Rifampin(HR) therapy.",3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Additional file 5: Figure S5,9 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between the TB and TB + HRZ groups at 2months HR therapy.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Acidaminobacteraceae|g__Acidaminobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hespellia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter",1783272|1239|186801|3120394|3120654|35829;1783272|1239|186801|3082720|3118653|65402;1783272|1239|186801|3082720|3118656|114627;1783272|1239|186801|3082720|543314|109326;1783272|201174|1760|85006|1268|1663;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|189330;3379134|976|200643|171549|2005520|156973;1783272|201174|84998|1643822|1643826|644652;1783272|1239|186801|3085636|186803|241189;1783272|1239|909932|909929|1843491|52225;1783272|1239|91061|186826|33958|1253;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3085636|186803|588605;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|3085636|186803|1213720;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3085636|186803|1506577;3379134|976|200643|171549|2005519|1348911,Complete,Svetlana up
bsdb:28683818/9/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 9,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Untreated Tuberculosis group(TB),TB +HRZ group - 3months HR(W16),TB +HRZ group - 3months into HR therapy(W16) refers to the first time point of stool collection (W16) following the switch in the antibiotic regimen from triple HRZ to double HR administration.,3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Additional file 5: Figure S5,9 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between the TB and TB + HRZ groups at 3months HR therapy.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Prolixibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Anaerorhabdus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Parvibacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum",3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|1853231|283168;3379134|976|200643|1970189|1471398|314318;1783272|1239|526524|526525|128827|118966;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171551|836;3379134|1224|1236|91347|1903410|71655;1783272|201174|1760|85004|31953|1678;3379134|1224|28216|80840|995019|577310;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|3085636|186803|248744;1783272|1239|526524|526525|2810280|1279384;1783272|1239|186801|3085636|186803|653683;1783272|1239|186801|186802|216572|946234;1783272|544448|31969|186332|186333|2086;1783272|201174|84998|84999|84107|1427376;1783272|201174|84998|84999|1643824|133925;1783272|201174|84998|1643822|1643826|447020;1783272|1239|91061|186826|81852|1350;3379134|200930|68337|191393|2945020|248038,Complete,Svetlana up
bsdb:28683818/9/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 9,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Untreated Tuberculosis group(TB),TB +HRZ group - 3months HR(W16),TB +HRZ group - 3months into HR therapy(W16) refers to the first time point of stool collection (W16) following the switch in the antibiotic regimen from triple HRZ to double HR administration.,3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Additional file 5: Figure S5,9 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between the TB and TB + HRZ groups at 3months HR therapy.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Acidaminobacteraceae|g__Acidaminobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Asaccharobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XII. Incertae Sedis|g__Guggenheimella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hespellia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Roseivirgaceae|g__Roseivirga,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas",1783272|1239|186801|186802|216572|258514;1783272|1239|186801|3120394|3120654|35829;1783272|1239|186801|3082720|3118653|65402;1783272|1239|186801|3082720|3118656|114627;1783272|1239|186801|3082720|543314|109326;1783272|201174|84998|1643822|1643826|553372;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|31979|1485;3379134|976|200643|171549|2005519|1348911;1783272|201174|84998|1643822|1643826|644652;1783272|1239|186801|186802|543313|228923;1783272|1239|186801|3085636|186803|241189;1783272|1239|91061|186826|33958|1253;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3085636|186803|46205;1783272|1239|186801|3085636|186803|588605;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;3379134|976|768503|768507|2762306|290180;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|3085636|186803|1213720;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3085636|186803|1506577;3379134|976|200643|171549|2005520|156973,Complete,Svetlana up
bsdb:28683818/10/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 10,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Untreated Tuberculosis group(TB),TB +HRZ group - 4months HR(W20),"TB +HRZ group - 4months into HR therapy(W20) refers to the group of mice infected with Mycobacterium tuberculosis (H37Rv) by aerosol inhalation, that are four months into HR therapy. This is also referred to as the termination of HR therapy.",3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Additional file 5: Figure S5,9 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between the TB and TB + HRZ groups at 4months HR therapy(termination of therapy).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Anaerorhabdus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella",3379134|976|200643|171549|171551|836;1783272|1239|526524|526525|128827|118966;3379134|976|200643|171549|2005525|195950;3379134|976|200643|171549|171552|577309;3379134|1224|28216|80840|995019|577310;1783272|1239|91061|186826|81852|1350;3379134|74201|203494|48461|1647988|239934;1783272|1239|526524|526525|2810280|3025755;1783272|201174|84998|84999|1643824|133925;1783272|1239|526524|526525|2810280|1279384;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3082768|990719|990721,Complete,Svetlana up
bsdb:28683818/10/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 10,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Untreated Tuberculosis group(TB),TB +HRZ group - 4months HR(W20),"TB +HRZ group - 4months into HR therapy(W20) refers to the group of mice infected with Mycobacterium tuberculosis (H37Rv) by aerosol inhalation, that are four months into HR therapy. This is also referred to as the termination of HR therapy.",3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Additional file 5: Figure S5,9 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between the TB and TB + HRZ groups at 4months HR therapy(termination of therapy).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Asaccharobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Roseivirgaceae|g__Roseivirga,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",1783272|1239|186801|3085636|186803|588605;1783272|1239|186801|186802|216572|253238;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|258514;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|46205;1783272|1239|186801|3082720|543314|109326;1783272|1239|186801|3085636|186803|248744;1783272|1239|186801|3085636|186803|1506577;3379134|200930|68337|191393|2945020|248038;1783272|201174|84998|1643822|1643826|553372;1783272|1239|526524|526525|128827;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|186802|186806|1730;1783272|1239|526524|526525|2810281|191303;3379134|976|768503|768507|2762306|290180;1783272|1239|186801|3085636|186803|1427378;3379134|976|200643|171549|2005520|156973;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:28683818/11/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 11,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Tuberculosis group(TB),TB +HRZ groups (all time points:M2-M5),"TB +HRZ groups (all time points:M2-M5) refers to the months (M) of stool sample collection relative to the date of infection rather than treatment. 

C57BL/6J female mice were used and treatment was terminated at month 5 of Mtb infection.",4,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.01,FALSE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Additional file 6: Figure S6,9 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between the TB and TB + HRZ groups at all timepoints (months of infection).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Salimesophilobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",1783272|1239|186801|3082768|990719|990721;1783272|201174|84998|1643822|1643826|580024;1783272|1239|186801|186802|31979|1434040;1783272|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:28683818/11/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 11,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Tuberculosis group(TB),TB +HRZ groups (all time points:M2-M5),"TB +HRZ groups (all time points:M2-M5) refers to the months (M) of stool sample collection relative to the date of infection rather than treatment. 

C57BL/6J female mice were used and treatment was terminated at month 5 of Mtb infection.",4,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.01,FALSE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Additional file 6: Figure S6,9 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between the TB and TB + HRZ groups at all timepoints (months of infection).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Caloramator,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Thermotaleaceae|g__Thermotalea,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Oxobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|186801|186802|216572|596767;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|186802|31979|44258;1783272|1239|186801|3085636|186803|1213720;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3082720|3118657|648799;3379134|200930|68337|191393|2945020|248038;1783272|201174|1760|85006|1268|1663;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|653683;1783272|1239|186801|3085636|186803|588605;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|186802|216572|258514;1783272|1239|186801|3082720|543314|109326;1783272|1239|186801|3085636|186803|46205;1783272|1239|186801|186802|31979|44261;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:28683818/12/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 12,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Untreated Tuberculosis group(TB),TB +HRZ groups (all time points:M2-M7),TB +HRZ groups (all time points:M2-M7) refers to the months (M) of stool sample collection relative to the date of infection rather than treatment. C57BL/6J-CD45a(Ly5a) female mice were used and treatment was terminated at month 7 of Mtb infection.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.01,FALSE,2,NA,NA,NA,increased,decreased,NA,NA,NA,Signature 1,Additional file 7: Figure S7,9 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between the TB and TB + HRZ groups at all timepoints (months of infection). Treatment was terminated at M7.,increased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,1783272|1239|526524|526525|2810280|1279384,Complete,Svetlana up
bsdb:28683818/12/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 12,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Untreated Tuberculosis group(TB),TB +HRZ groups (all time points:M2-M7),TB +HRZ groups (all time points:M2-M7) refers to the months (M) of stool sample collection relative to the date of infection rather than treatment. C57BL/6J-CD45a(Ly5a) female mice were used and treatment was terminated at month 7 of Mtb infection.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.01,FALSE,2,NA,NA,NA,increased,decreased,NA,NA,NA,Signature 2,Additional file 7: Figure S7,9 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between the TB and TB + HRZ groups at all timepoints (months of infection). Treatment was terminated at M7.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Acidaminobacteraceae|g__Acidaminobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XII. Incertae Sedis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Oxobacter,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Solitalea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfotomaculaceae|g__Pelotomaculum",1783272|1239|186801|186802|216572|258514;1783272|1239|186801|3082720|3118653|65402;1783272|1239|186801|3082720|543314|109326;1783272|1239|186801|186802|31979|1485;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|543313;1783272|1239|186801|186802|31979|44261;3379134|976|117747|200666|84566|929509;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|2937910|191373,Complete,Svetlana up
bsdb:28683818/13/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 13,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,TB + HRZ (W4 to W20),Post HRZ (W24 to W32),Post HRZ (W24 to W32) refers to stool samples at monthly intervals for 3 months’ post cessation of therapy.,24,12,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Additional file 8: Figure S8,9 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between the TB + HRZ and post HRZ groups.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum",1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|1213720,Complete,Svetlana up
bsdb:28683818/13/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 13,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,TB + HRZ (W4 to W20),Post HRZ (W24 to W32),Post HRZ (W24 to W32) refers to stool samples at monthly intervals for 3 months’ post cessation of therapy.,24,12,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Additional file 8: Figure S8,9 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between the TB + HRZ and post HRZ groups.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria",1783272|1239|91061|186826|33958|1578;3379134|1224|1236|91347|1903410|71655,Complete,Svetlana up
bsdb:28683818/14/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 14,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Naive,TB + HRZ groups (W4-W20 time points),"TB + HRZ groups refers to all timepoints of anti-tuberculosis treatment, that is, from day 1(W4) to the termination of therapy(W20).",NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.01,FALSE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Fig. 3C,9 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between the naïve and TB + HRZ groups from day 1(W4) to the termination of therapy(W20).,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia",1783272|1239|526524|526525|2810280|3025755;1783272|1239|526524|526525|2810280|1279384,Complete,Svetlana up
bsdb:28683818/14/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 14,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Naive,TB + HRZ groups (W4-W20 time points),"TB + HRZ groups refers to all timepoints of anti-tuberculosis treatment, that is, from day 1(W4) to the termination of therapy(W20).",NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.01,FALSE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Fig. 3C,9 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between the naïve and TB + HRZ groups from day 1(W4) to the termination of therapy(W20).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Acidaminobacteraceae|g__Acidaminobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|84036;1783272|1239|186801|3120394|3120654|35829;1783272|1239|186801|3085636|186803|46205;1783272|1239|186801|3085636|186803|588605;1783272|1239|186801|3082720|3118656|114627;1783272|1239|186801|3085636|186803|1213720;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3082720|3118653|65402;1783272|1239|186801|186802|216572|258514;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|31979|1485;3379134|976|200643|171549|2005520|156973;1783272|1239|526524|526525|2810281|191303;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:28683818/15/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 15,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Untreated Tuberculosis group(TB),TB + HRZ groups (W4-W20 time points),"TB + HRZ groups refers to all timepoints of anti-tuberculosis treatment, that is, from day 1(W4) to the termination of therapy(W20).",NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.01,FALSE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Fig. 3D,9 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between the naïve and TB + HRZ groups from day 1(W4) to the termination of therapy(W20).,increased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,1783272|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:28683818/15/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 15,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Untreated Tuberculosis group(TB),TB + HRZ groups (W4-W20 time points),"TB + HRZ groups refers to all timepoints of anti-tuberculosis treatment, that is, from day 1(W4) to the termination of therapy(W20).",NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.01,FALSE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Fig. 3D,9 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between the naïve and TB + HRZ groups from day 1(W4) to the termination of therapy(W20).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus",1783272|1239|186801|3120394|3120654|35829;1783272|1239|186801|3085636|186803|588605;1783272|1239|186801|3082720|3118656|114627;1783272|1239|186801|3085636|186803|1213720;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|216572|258514;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|186807|2740,Complete,Svetlana up
bsdb:28683818/16/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 16,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Naive,Post HRZ (W24 to W32),Post HRZ (W24 to W32) refers to stool samples at monthly intervals for 3 months’ post cessation of therapy.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Fig. 5E,9 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant genera between the naïve and post HRZ groups (W24–W32).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Prolixibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Anaerorhabdus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Paraeggerthella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Parvibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XII. Incertae Sedis",3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|171551|836;3379134|976|200643|1970189|1471398|314318;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|171552|577309;1783272|1239|526524|526525|128827|118966;3379134|1224|28216|80840|995019|577310;3379134|200940|3031449|213115|194924|872;1783272|201174|84998|1643822|1643826|447020;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3082768|990719|990721;1783272|201174|84998|1643822|1643826|651554;1783272|201174|1760|85004|31953|1678;1783272|1239|526524|526525|2810280|1279384;1783272|201174|84998|84999|1643824|133925;1783272|1239|526524|526525|2810280|3025755;1783272|201174|84998|84999|84107|1427376;1783272|1239|186801|186802|543313,Complete,Svetlana up
bsdb:28683818/16/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 16,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Naive,Post HRZ (W24 to W32),Post HRZ (W24 to W32) refers to stool samples at monthly intervals for 3 months’ post cessation of therapy.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Fig. 5E,9 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant genera between the naïve and post HRZ groups (W24–W32).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Asaccharobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Acidaminobacteraceae|g__Acidaminobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Oxobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|3120394|3120654|35829;1783272|1239|186801|3082720|543314|109326;1783272|1239|186801|3085636|186803|588605;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|186802|216572|244127;1783272|201174|84998|1643822|1643826|553372;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|3082720|3118656|114627;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|186802|216572|596767;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|253238;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|3082720|3118653|65402;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|31979|44261;1783272|1239|186801|186802|216572|258514;1783272|1239|186801|3085636|186803|46205;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3085636|186803|1427378;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|459786;1783272|1239|91061|186826|33958|1253;1783272|1239|526524|526525|128827;3379134|976|200643|171549|2005520|156973;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|2005519|1348911;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:28683818/17/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 17,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Naive,H (Isoniazid),H (Isoniazid) refers to Isoniazid treatment given to the uninfected and 4-week Mtb-infected mice.,3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Additional file 11: Figure S11,10 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant between the Naive group and Isoniazid treatment group.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium",1783272|1239|186801|186802|216572|258514;1783272|1239|186801|3085636|186803|653683;3379134|976|200643|171549|2005519|397864;1783272|1239|186801|3085636|186803|572511;1783272|1239|526524|526525|128827|1647;1783272|1239|186801|3082720|543314;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|946234;1783272|201174|84998|1643822|1643826|644652;3379134|200930|68337|191393|2945020|248038;1783272|1239|91061|186826|33958|1253;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|186802|216572|596767,Complete,Svetlana up
bsdb:28683818/17/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 17,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Naive,H (Isoniazid),H (Isoniazid) refers to Isoniazid treatment given to the uninfected and 4-week Mtb-infected mice.,3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Additional file 11: Figure S11,10 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant between the Naive group and Isoniazid treatment group.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Oxobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfotomaculaceae|g__Pelotomaculum,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",1783272|201174|1760|85006|1268|1663;1783272|1239|186801|3085636|186803|189330;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|31979|44261;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|2937910|191373;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|2005525|195950,Complete,Svetlana up
bsdb:28683818/18/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 18,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Naive,R (Rifampin),R (Rifampin) refers to Rifampin treatment given to the uninfected and 4-week Mtb-infected mice.,3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Additional file 11: Figure S11.,10 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant between the Naive group and Rifampin treatment group.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Caloramator,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus",1783272|1239|526524|526525|128827|1647;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|3085636|186803|653683;1783272|1239|186801|3085636|186803|248744;1783272|1239|186801|3085636|186803|207244;1783272|201174|84998|1643822|1643826|644652;1783272|1239|186801|186802|31979|44258;1783272|201174|84998|1643822|1643826|580024,Complete,Svetlana up
bsdb:28683818/18/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 18,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Naive,R (Rifampin),R (Rifampin) refers to Rifampin treatment given to the uninfected and 4-week Mtb-infected mice.,3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Additional file 11: Figure S11,10 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant between the Naive group and Rifampin treatment group.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Oxobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfotomaculaceae|g__Pelotomaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudobacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia",1783272|1239|186801|186802|216572|258514;1783272|1239|186801|3120394|3120654|35829;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|244127;1783272|201174|1760|85006|1268|1663;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|189330;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|31979|44261;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|2937910|191373;1783272|1239|186801|186802|216572|1486726;1783272|1239|186801|3085636|186803|46205;1783272|1239|186801|3085636|186803|588605;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|3085636|186803|1213720;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|3082720|186804|1501226,Complete,Svetlana up
bsdb:28683818/19/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 19,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Naive,Z (Pyrazinamide),Z (Pyrazinamide) refers to Pyrazinamide treatment given to uninfected and 4-week Mtb-infected mice.,3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Additional file 11: Figure S11,10 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant between the Naive group and Pyrazinamide treatment group.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix",1783272|1239|186801|3085636|186803|248744;1783272|544448|31969|186332|186333|2086;1783272|1239|526524|526525|128827|1647,Complete,Svetlana up
bsdb:28683818/19/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 19,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Naive,Z (Pyrazinamide),Z (Pyrazinamide) refers to Pyrazinamide treatment given to uninfected and 4-week Mtb-infected mice.,3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Additional file 11: Figure S11,10 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant between the Naive group and Pyrazinamide treatment group.,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|186802|216572|44748;1783272|201174|1760|85006|1268|1663;3379134|74201|203494|48461|1647988|239934,Complete,Svetlana up
bsdb:28683818/20/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 20,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Naive,"HR (H-Isoniazid, R-Rifampin)","HR (H-Isoniazid, R-Rifampin) refers to the Isoniazid and Rifampin treatment given to uninfected and 4week Mtb-infected mice.",3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Additional file 11: Figure S11,10 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differentially abundant between the Naive group and HR (H-Isoniazid, R-Rifampin) treatment group.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes",3379134|976|200643|171549|2005525|195950;3379134|976|200643|171549|2005525|375288;3379134|1224|1236|91347|1903410|71655;1783272|1239|526524|526525|128827|1647;1783272|544448|31969|186332|186333|2086;1783272|1239|186801|3085636|186803|207244,Complete,Svetlana up
bsdb:28683818/20/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 20,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Naive,"HR (H-Isoniazid, R-Rifampin)","HR (H-Isoniazid, R-Rifampin) refers to the Isoniazid and Rifampin treatment given to uninfected and 4week Mtb-infected mice.",3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Additional file 11: Figure S11,10 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differentially abundant between the Naive group and HR (H-Isoniazid, R-Rifampin) treatment group.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Oxobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XII. Incertae Sedis|g__Guggenheimella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudobacteroides,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfotomaculaceae|g__Pelotomaculum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239|186801|3085636|186803|46205;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3120394|3120654|35829;1783272|1239|186801|3085636|186803|1213720;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|588605;1783272|1239|186801|3082720|543314;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|31979|44261;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|3085636|186803|1506577;1783272|201174|1760|85006|1268|1663;1783272|1239|186801|186802|1392389;1783272|1239|186801|186802|543313|228923;1783272|1239|186801|186802|216572|1486726;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|216572|596767;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|1427378;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|2937910|191373;1783272|1239|526524|526525|128827;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:28683818/21/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 21,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Naive,"HZ (H-Isoniazid, Z-Pyrazinamide)","HZ (H-Isoniazid, Z-Pyrazinamide) refers to the Isoniazid and Pyrazinamide treatment given to uninfected and 4week Mtb-infected mice.",3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Additional file 11: Figure S11,10 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differentially abundant between the Naive group and HZ (H-Isoniazid, Z-Pyrazinamide) treatment group.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia",3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|2005520|156973;3379134|1224|1236|135622|267890|22;1783272|201174|84998|1643822|1643826|644652;1783272|1239|186801|3085636|186803|248744,Complete,Svetlana up
bsdb:28683818/21/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 21,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Naive,"HZ (H-Isoniazid, Z-Pyrazinamide)","HZ (H-Isoniazid, Z-Pyrazinamide) refers to the Isoniazid and Pyrazinamide treatment given to uninfected and 4week Mtb-infected mice.",3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Additional file 11: Figure S11,10 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differentially abundant between the Naive group and HZ (H-Isoniazid, Z-Pyrazinamide) treatment group.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XII. Incertae Sedis|g__Guggenheimella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",1783272|1239|186801|3082720|543314;1783272|1239|186801|186802|543313|228923;1783272|201174|1760|85006|1268|1663;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|216572|44748;3379134|976|200643|171549|2005519|1348911;3379134|74201|203494|48461|1647988|239934,Complete,Svetlana up
bsdb:28683818/22/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 22,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Naive,"RZ (R-Rifampin, Z-Pyrazinamide)","RZ (R-Rifampin, Z-Pyrazinamide) refers to the Rifampin and Pyrazinamide treatment given to uninfected and 4week Mtb-infected mice.",3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Additional file 11: Figure S11,10 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differentially abundant between the Naive group and RZ (R-Rifampin, Z-Pyrazinamide) treatment group.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;3379134|1224|1236|91347|1903410|71655;1783272|544448|31969|186332|186333|2086;1783272|1239|186801|3085636|186803|207244;1783272|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:28683818/22/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 22,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Naive,"RZ (R-Rifampin, Z-Pyrazinamide)","RZ (R-Rifampin, Z-Pyrazinamide) refers to the Rifampin and Pyrazinamide treatment given to uninfected and 4week Mtb-infected mice.",3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Additional file 11: Figure S11,10 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differentially abundant between the Naive group and RZ (R-Rifampin, Z-Pyrazinamide) treatment group.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XII. Incertae Sedis|g__Guggenheimella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Oxobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfotomaculaceae|g__Pelotomaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudobacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",1783272|1239|186801|186802|216572|258514;1783272|1239|186801|3085636|186803|1427378;1783272|1239|186801|3120394|3120654|35829;1783272|1239|186801|3085636|186803|653683;1783272|1239|186801|186802|216572|244127;1783272|201174|1760|85006|1268|1663;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|186802|31979|1485;3379134|976|200643|171549|2005519|1348911;1783272|1239|186801|3085636|186803|189330;3379134|976|200643|171549|2005520|156973;1783272|1239|186801|3085636|186803|1432051;1783272|201174|84998|1643822|1643826|580024;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|216572|253238;1783272|1239|186801|3082720|543314;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|543313|228923;1783272|1239|186801|186802|216572|596767;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|248744;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|31979|44261;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|2937910|191373;1783272|1239|186801|186802|216572|1486726;1783272|1239|186801|3085636|186803|46205;1783272|1239|186801|186802|216572|1017280;1783272|1239|186801|3085636|186803|588605;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|3085636|186803|1213720;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3085636|186803|1506577,Complete,Svetlana up
bsdb:28683818/23/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 23,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Naive,"HRZ(H-Isoniazid, R-Rifampin, Z-Pyrazinamide)","HRZ(H-Isoniazid, R-Rifampin, Z-Pyrazinamide) refers to the Isoniazid, Rifampin and Pyrazinamide treatment given to uninfected and 4week Mtb-infected mice.",3,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Additional file 11: Figure S11,10 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differentially abundant taxa between the Naive group and HRZ (H-Isoniazid, R-Rifampin,  Z-Pyrazinamide) treatment group.",increased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Asaccharobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",1783272|544448|31969|186332|186333|2086;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3082720|543314|109326;1783272|201174|84998|1643822|1643826|553372;3379134|976|200643|171549|2005519|397864;1783272|1239|186801|186802|3085642|580596;1783272|1239|526524|526525|128827|1647;1783272|1239|186801|3082720|543314;3379134|200930|68337|191393|2945020|248038;3379134|976|200643|171549|2005525|375288;1783272|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:28683818/23/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 23,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Naive,"HRZ(H-Isoniazid, R-Rifampin, Z-Pyrazinamide)","HRZ(H-Isoniazid, R-Rifampin, Z-Pyrazinamide) refers to the Isoniazid, Rifampin and Pyrazinamide treatment given to uninfected and 4week Mtb-infected mice.",3,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Additional file 11: Figure S11,10 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differentially abundant taxa between the Naive group and HRZ (H-Isoniazid, R-Rifampin,  Z-Pyrazinamide) treatment group.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XII. Incertae Sedis|g__Guggenheimella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Oxobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfotomaculaceae|g__Pelotomaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudobacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",1783272|1239|186801|186802|216572|258514;1783272|1239|186801|3120394|3120654|35829;1783272|201174|1760|85006|1268|1663;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485;3379134|976|200643|171549|2005519|1348911;1783272|1239|186801|3085636|186803|189330;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|543313|228923;1783272|1239|186801|186802|216572|596767;1783272|1239|186801|186802|1392389;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|31979|44261;1783272|1239|186801|186802|2937910|191373;1783272|1239|186801|186802|216572|1486726;1783272|1239|186801|3085636|186803|46205;1783272|1239|186801|3085636|186803|588605;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;3379134|1224|1236|135622|267890|22;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|3085636|186803|1213720;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3085636|186803|1506577,Complete,Svetlana up
bsdb:28683818/24/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 24,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,"VANM(uninfected mice receiving vanomycin, ampicillin, neomycin, and metronidazole)",H (Isoniazid),H (Isoniazid) refers to Isoniazid treatment given to the uninfected and 4-week Mtb-infected mice.,3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Additional file 12: Figure S12,11 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between the VANM group and Isoniazid treatment group.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Asaccharobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XII. Incertae Sedis|g__Guggenheimella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudobacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium",1783272|1239|186801|186802|216572|258514;1783272|1239|186801|3085636|186803|1427378;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|653683;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|3082720|543314|109326;1783272|201174|1760|85006|1268|1663;1783272|201174|84998|1643822|1643826|553372;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005519|397864;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3082768|990719|990721;3379134|976|200643|171549|2005519|1348911;1783272|1239|186801|3085636|186803|189330;3379134|976|200643|171549|2005520|156973;1783272|1239|186801|3085636|186803|1432051;1783272|201174|84998|1643822|1643826|580024;1783272|1239|526524|526525|128827|1647;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|216572|253238;1783272|1239|186801|186802|216572|946234;1783272|201174|84998|1643822|1643826|644652;1783272|1239|186801|186802|543313|228923;1783272|1239|186801|186802|216572|596767;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|248744;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|186802|216572|459786;1783272|1239|91061|186826|33958|1253;1783272|1239|186801|186802|216572|1486726;1783272|1239|186801|186802|216572|1017280;1783272|1239|186801|3085636|186803|588605;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|3085636|186803|1213720;3379134|976|200643|171549|2005525|195950;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|186802|186806|1730,Complete,Svetlana up
bsdb:28683818/24/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 24,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,"VANM(uninfected mice receiving vanomycin, ampicillin, neomycin, and metronidazole)",H (Isoniazid),H (Isoniazid) refers to Isoniazid treatment given to the uninfected and 4-week Mtb-infected mice.,3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Additional file 12: Figure S12,11 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between the VANM group and Isoniazid treatment group.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae",3379134|976|200643|171549|2005525|375288;3379134|1224|1236|91347|1903410|71655;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3082720|543314,Complete,Svetlana up
bsdb:28683818/25/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 25,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,"VANM(uninfected mice receiving vanomycin, ampicillin, neomycin, and metronidazole)",R (Rifampin),R (Rifampin) refers to Rifampin treatment given to the uninfected and 4-week Mtb-infected mice.,3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Additional file 12: Figure S12,11 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between the VANM group and Rifampin treatment group.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Caloramator,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XII. Incertae Sedis|g__Guggenheimella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudobacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|526524|526525|128827;1783272|1239|186801|186802|31979|44258;1783272|201174|84998|1643822|1643826|580024;1783272|1239|186801|186802|216572|253238;1783272|1239|526524|526525|2810281|191303;1783272|1239|526524|526525|2810280|3025755;1783272|201174|1760|85006|1268|1663;1783272|1239|186801|186802|543313|228923;1783272|201174|84998|1643822|1643826|644652;1783272|1239|186801|186802|216572|1486726;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|248744;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|3085636|186803|653683;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|596767;1783272|1239|186801|186802|1392389;1783272|1239|186801|186802|216572|1017280;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|1427378;3379134|976|200643|171549|2005520|156973;1783272|1239|186801|186802|216572|946234;3379134|200930|68337|191393|2945020|248038;1783272|1239|526524|526525|128827|1647;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005519|1348911;3379134|976|200643|171549|2005525|195950;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:28683818/25/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 25,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,"VANM(uninfected mice receiving vanomycin, ampicillin, neomycin, and metronidazole)",R (Rifampin),R (Rifampin) refers to Rifampin treatment given to the uninfected and 4-week Mtb-infected mice.,3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Additional file 12: Figure S12,11 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between the VANM group and Rifampin treatment group.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Salimesophilobacter",3379134|976|200643|171549|2005525|375288;3379134|1224|1236|91347|1903410|71655;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3082720|543314;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|31979|1434040,Complete,Svetlana up
bsdb:28683818/26/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 26,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,"VANM(uninfected mice receiving vanomycin, ampicillin, neomycin, and metronidazole)",Z (Pyrazinamide),Z (Pyrazinamide) refers to Pyrazinamide treatment given to uninfected and 4-week Mtb-infected mice.,3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Additional file 12: Figure S12,11 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between the VANM group and Pyrazinamide treatment group.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XII. Incertae Sedis|g__Guggenheimella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Oxobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfotomaculaceae|g__Pelotomaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudobacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium",1783272|1239|186801|186802|216572|258514;1783272|1239|186801|3085636|186803|1427378;1783272|1239|186801|3120394|3120654|35829;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;1783272|544448|31969|186332|186333|2086;1783272|1239|186801|3085636|186803|653683;1783272|1239|186801|186802|216572|244127;1783272|201174|1760|85006|1268|1663;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3082768|990719|990721;3379134|976|200643|171549|2005519|1348911;1783272|1239|186801|3085636|186803|189330;3379134|976|200643|171549|2005520|156973;1783272|1239|186801|3085636|186803|1432051;1783272|201174|84998|1643822|1643826|580024;1783272|1239|526524|526525|128827|1647;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|216572|253238;1783272|1239|186801|186802|216572|946234;1783272|201174|84998|1643822|1643826|644652;1783272|1239|186801|186802|543313|228923;1783272|1239|186801|186802|216572|596767;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|248744;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|31979|44261;1783272|1239|186801|186802|2937910|191373;1783272|1239|186801|186802|216572|1486726;1783272|1239|186801|186802|216572|1017280;1783272|1239|186801|3085636|186803|588605;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|1213720;3379134|976|200643|171549|2005525|195950;1783272|1239|526524|526525|2810280|3025755;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|186802|186806|1730,Complete,Svetlana up
bsdb:28683818/26/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 26,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,"VANM(uninfected mice receiving vanomycin, ampicillin, neomycin, and metronidazole)",Z (Pyrazinamide),Z (Pyrazinamide) refers to Pyrazinamide treatment given to uninfected and 4-week Mtb-infected mice.,3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Additional file 12: Figure S12,11 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between the VANM group and Pyrazinamide treatment group.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae",3379134|976|200643|171549|2005525|375288;3379134|1224|1236|91347|1903410|71655;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|3082720|543314,Complete,Svetlana up
bsdb:28683818/27/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 27,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,"VANM(uninfected mice receiving vanomycin, ampicillin, neomycin, and metronidazole)","HR (H-Isoniazid, R-Rifampin)","HR (H-Isoniazid, R-Rifampin) refers to the Isoniazid and Rifampin treatment given to uninfected and 4week Mtb-infected mice.",3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Additional file 12: Figure S12,11 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differentially abundant taxa between the VANM group and HR (H-Isoniazid, R-Rifampin) treatment group.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",1783272|1239|186801|3085636|186803|1427378;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;1783272|544448|31969|186332|186333|2086;1783272|1239|186801|3085636|186803|653683;1783272|1239|186801|3085636|186803|207244;1783272|201174|1760|85006|1268|1663;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|2005519|1348911;3379134|976|200643|171549|2005520|156973;1783272|201174|84998|1643822|1643826|580024;1783272|1239|526524|526525|128827|1647;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|1017280;1783272|1239|186801|3085636|186803|841;3379134|976|200643|171549|2005525|195950;1783272|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:28683818/27/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 27,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,"VANM(uninfected mice receiving vanomycin, ampicillin, neomycin, and metronidazole)","HR (H-Isoniazid, R-Rifampin)","HR (H-Isoniazid, R-Rifampin) refers to the Isoniazid and Rifampin treatment given to uninfected and 4week Mtb-infected mice.",3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Additional file 12: Figure S12,11 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differentially abundant taxa between the VANM group and HR (H-Isoniazid, R-Rifampin) treatment group.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Salimesophilobacter",3379134|976|200643|171549|2005525|375288;3379134|1224|1236|91347|1903410|71655;1783272|1239|186801|186802|216572|1508657;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3082720|543314;1783272|1239|186801|186802|31979|1434040,Complete,Svetlana up
bsdb:28683818/28/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 28,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,"VANM(uninfected mice receiving vanomycin, ampicillin, neomycin, and metronidazole)","HZ (H-Isoniazid, Z-Pyrazinamide)","HZ (H-Isoniazid, Z-Pyrazinamide) refers to the Isoniazid and Pyrazinamide treatment given to uninfected and 4week Mtb-infected mice.",3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Additional file 12: Figure S12,11 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between the VANM group and HZ,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Asaccharobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XII. Incertae Sedis|g__Guggenheimella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Oxobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudobacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens",1783272|1239|186801|186802|216572|258514;1783272|1239|186801|3085636|186803|1427378;1783272|1239|186801|3120394|3120654|35829;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|653683;1783272|1239|186801|186802|216572|244127;1783272|201174|1760|85006|1268|1663;1783272|201174|84998|1643822|1643826|553372;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005519|397864;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|3085636|186803|189330;3379134|976|200643|171549|2005520|156973;1783272|1239|186801|3085636|186803|1432051;1783272|201174|84998|1643822|1643826|580024;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|946234;1783272|201174|84998|1643822|1643826|644652;1783272|1239|186801|186802|543313|228923;1783272|1239|186801|186802|216572|596767;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|248744;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|31979|44261;1783272|1239|91061|186826|33958|1253;1783272|1239|186801|186802|216572|1486726;1783272|1239|186801|3085636|186803|46205;1783272|1239|186801|186802|216572|1017280;1783272|1239|186801|3085636|186803|588605;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|3085636|186803|1213720;3379134|976|200643|171549|2005525|195950;1783272|1239|526524|526525|2810280|3025755;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|186802|216572|253238,Complete,Svetlana up
bsdb:28683818/28/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 28,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,"VANM(uninfected mice receiving vanomycin, ampicillin, neomycin, and metronidazole)","HZ (H-Isoniazid, Z-Pyrazinamide)","HZ (H-Isoniazid, Z-Pyrazinamide) refers to the Isoniazid and Pyrazinamide treatment given to uninfected and 4week Mtb-infected mice.",3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Additional file 12: Figure S12,11 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between the VANM group and HZ treatment group.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae",3379134|976|200643|171549|2005525|375288;3379134|1224|1236|91347|1903410|71655;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3082720|543314,Complete,Svetlana up
bsdb:28683818/29/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 29,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,"VANM(uninfected mice receiving vanomycin, ampicillin, neomycin, and metronidazole)","RZ (R-Rifampin, Z-Pyrazinamide)","RZ (R-Rifampin, Z-Pyrazinamide) refers to the Rifampin and Pyrazinamide treatment given to uninfected and 4week Mtb-infected mice.",3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 1,Additional file 12: Figure S12,11 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between the VANM group and RZ treatment group.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|186801|186802|186806|1730;1783272|1239|526524|526525|128827;1783272|1239|526524|526525|2810280|3025755;1783272|544448|31969|186332|186333|2086;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|572511;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|2005525|195950;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:28683818/29/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 29,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,"VANM(uninfected mice receiving vanomycin, ampicillin, neomycin, and metronidazole)","RZ (R-Rifampin, Z-Pyrazinamide)","RZ (R-Rifampin, Z-Pyrazinamide) refers to the Rifampin and Pyrazinamide treatment given to uninfected and 4week Mtb-infected mice.",3,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 2,Additional file 12: Figure S12,11 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between the VANM group and RZ treatment group.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",3379134|976|200643|171549|2005525|375288;3379134|1224|1236|91347|1903410|71655;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3082720|543314;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:28683818/30/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 30,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,"VANM(uninfected mice receiving vanomycin, ampicillin, neomycin, and metronidazole)","HRZ(H-Isoniazid, R-Rifampin, Z-Pyrazinamide)","HRZ(H-Isoniazid, R-Rifampin, Z-Pyrazinamide) refers to the Isoniazid, Rifampin and Pyrazinamide treatment given to uninfected and 4week Mtb-infected mice.",3,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Additional file 12: Figure S12,11 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differentially abundant taxa between the VANM group and HRZ (H-Isoniazid, R-Rifampin, Z-Pyrazinamide) treatment group.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Asaccharobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudobacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus",1783272|1239|186801|3085636|186803|1427378;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;1783272|544448|31969|186332|186333|2086;1783272|1239|186801|3085636|186803|653683;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|3082720|543314|109326;1783272|201174|1760|85006|1268|1663;1783272|201174|84998|1643822|1643826|553372;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005519|397864;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3082768|990719|990721;3379134|976|200643|171549|2005520|156973;1783272|1239|186801|3085636|186803|1432051;1783272|201174|84998|1643822|1643826|580024;1783272|1239|526524|526525|128827|1647;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|216572|253238;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|1486726;1783272|1239|186801|186802|216572|1017280;1783272|1239|186801|3085636|186803|841;3379134|976|200643|171549|2005525|195950;1783272|1239|526524|526525|2810280|3025755;1783272|1239|91061|186826|33958|1253,Complete,Svetlana up
bsdb:28683818/30/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 30,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,"VANM(uninfected mice receiving vanomycin, ampicillin, neomycin, and metronidazole)","HRZ(H-Isoniazid, R-Rifampin, Z-Pyrazinamide)","HRZ(H-Isoniazid, R-Rifampin, Z-Pyrazinamide) refers to the Isoniazid, Rifampin and Pyrazinamide treatment given to uninfected and 4week Mtb-infected mice.",3,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Additional file 12: Figure S12,11 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differentially abundant taxa between the VANM group and HRZ (H-Isoniazid, R-Rifampin, Z-Pyrazinamide) treatment group.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae",3379134|976|200643|171549|2005525|375288;3379134|1224|1236|91347|1903410|71655;1783272|1239|186801|186802|216572|1508657;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3082720|543314,Complete,Svetlana up
bsdb:28683818/31/1,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 31,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Naive(Uninfected Untreated),"VANM(uninfected mice receiving vanomycin, ampicillin, neomycin, and metronidazole)","VANM refers to the uninfected mice receiving vanomycin, ampicillin, neomycin, and metronidazole.",3,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Additional file 12: Figure S12,11 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between the VANM group and Naive(untreated uninfected) group.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae",3379134|976|200643|171549|2005525|375288;3379134|1224|1236|91347|1903410|71655;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3082720|543314,Complete,Svetlana up
bsdb:28683818/31/2,28683818,laboratory experiment,28683818,10.1186/s40168-017-0286-2,NA,"Namasivayam S., Maiga M., Yuan W., Thovarai V., Costa D.L., Mittereder L.R., Wipperman M.F., Glickman M.S., Dzutsev A., Trinchieri G. , Sher A.",Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy,Microbiome,2017,"16S rRNA, Antibiotics, Dysbiosis, Microbiota, Tuberculosis",Experiment 31,United States of America,Mus musculus,Feces,UBERON:0001988,Response to anti-tuberculosis drug,EFO:0007918,Naive(Uninfected Untreated),"VANM(uninfected mice receiving vanomycin, ampicillin, neomycin, and metronidazole)","VANM refers to the uninfected mice receiving vanomycin, ampicillin, neomycin, and metronidazole.",3,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Additional file 12: Figure S12,11 November 2024,KateRasheed,"KateRasheed,WikiWorks",NA,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XII. Incertae Sedis|g__Guggenheimella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Oxobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfotomaculaceae|g__Pelotomaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudobacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor",1783272|1239|186801|186802|216572|258514;1783272|1239|186801|3120394|3120654|35829;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|653683;1783272|1239|186801|186802|216572|244127;1783272|201174|1760|85006|1268|1663;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|186802|31979|1485;3379134|976|200643|171549|2005519|1348911;1783272|1239|186801|3085636|186803|189330;3379134|976|200643|171549|2005520|156973;1783272|1239|186801|3085636|186803|1432051;1783272|201174|84998|1643822|1643826|580024;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|216572|253238;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|543313|228923;1783272|1239|186801|186802|216572|596767;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|248744;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|31979|44261;1783272|1239|186801|186802|2937910|191373;1783272|1239|186801|186802|216572|1486726;1783272|1239|186801|3085636|186803|46205;1783272|1239|186801|186802|216572|1017280;1783272|1239|186801|3085636|186803|588605;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|3085636|186803|1213720;3379134|976|200643|171549|2005525|195950;1783272|1239|526524|526525|2810280|3025755;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|3085636|186803|1427378,Complete,Svetlana up
bsdb:28708089/1/1,28708089,laboratory experiment,28708089,10.3390/nu9070756,NA,"Uebanso T., Kano S., Yoshimoto A., Naito C., Shimohata T., Mawatari K. , Takahashi A.",Effects of Consuming Xylitol on Gut Microbiota and Lipid Metabolism in Mice,Nutrients,2017,"Streptococcus mutans, capillary electrophoresis–mass spectrometry (CE–MS), caries, cholesterol, denaturing gradient gel electrophoresis (DGGE), triglyceride, xylitol",Experiment 1,Japan,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,CD-LX (Low dose xylitol group),CD-MX (Medium dose xylitol),Male mice that were given xylitol solution of 200 mg/kg body weight/day on a AIN93G 5% fiber diet.,5,5,NA,16S,23,NA,relative abundances,Post-Hoc Pairwise,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2A,4 August 2025,YokoC,YokoC,"Changes in the fecal microbiota of mice fed 40 ± 5 mg/kg body weight/day (CD-LX), and 194 ± 24 mg/kg body weight/day (CD-MX) of xylitol. An abundance of specific bacterial phylum or genus and ratio after seven weeks of xylitol supplementation.",increased,",k__Bacillati|p__Bacillota",;1783272|1239,Complete,KateRasheed
bsdb:28708089/1/2,28708089,laboratory experiment,28708089,10.3390/nu9070756,NA,"Uebanso T., Kano S., Yoshimoto A., Naito C., Shimohata T., Mawatari K. , Takahashi A.",Effects of Consuming Xylitol on Gut Microbiota and Lipid Metabolism in Mice,Nutrients,2017,"Streptococcus mutans, capillary electrophoresis–mass spectrometry (CE–MS), caries, cholesterol, denaturing gradient gel electrophoresis (DGGE), triglyceride, xylitol",Experiment 1,Japan,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,CD-LX (Low dose xylitol group),CD-MX (Medium dose xylitol),Male mice that were given xylitol solution of 200 mg/kg body weight/day on a AIN93G 5% fiber diet.,5,5,NA,16S,23,NA,relative abundances,Post-Hoc Pairwise,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2A,4 August 2025,YokoC,YokoC,"Changes in the fecal microbiota of mice fed 40 ± 5 mg/kg body weight/day (CD-LX), and 194 ± 24 mg/kg body weight/day (CD-MX) of xylitol. An abundance of specific bacterial phylum or genus and ratio after seven weeks of xylitol supplementation.",decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,KateRasheed
bsdb:28708089/2/1,28708089,laboratory experiment,28708089,10.3390/nu9070756,NA,"Uebanso T., Kano S., Yoshimoto A., Naito C., Shimohata T., Mawatari K. , Takahashi A.",Effects of Consuming Xylitol on Gut Microbiota and Lipid Metabolism in Mice,Nutrients,2017,"Streptococcus mutans, capillary electrophoresis–mass spectrometry (CE–MS), caries, cholesterol, denaturing gradient gel electrophoresis (DGGE), triglyceride, xylitol",Experiment 2,Japan,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,CD (Control diet),CD-MX (medium dose xylitol group),Male mice that were given xylitol solution of 200 mg/kg body weight/day on a AIN93G 5% fiber diet.,5,5,NA,16S,23,NA,relative abundances,Post-Hoc Pairwise,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2A,5 August 2025,YokoC,YokoC,Changes in the fecal microbiota of mice fed a control diet (CD) vs mice fed 194 ± 24 mg/kg body weight/day (CD-MX) of xylitol. An abundance of specific bacterial phylum or genus and ratio after seven weeks of xylitol supplementation.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,KateRasheed
bsdb:28708089/3/1,28708089,laboratory experiment,28708089,10.3390/nu9070756,NA,"Uebanso T., Kano S., Yoshimoto A., Naito C., Shimohata T., Mawatari K. , Takahashi A.",Effects of Consuming Xylitol on Gut Microbiota and Lipid Metabolism in Mice,Nutrients,2017,"Streptococcus mutans, capillary electrophoresis–mass spectrometry (CE–MS), caries, cholesterol, denaturing gradient gel electrophoresis (DGGE), triglyceride, xylitol",Experiment 3,Japan,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,HFD (high fat diet),HFD-MX (high fat medium dose xylitol),Male mice that were given xylitol solution of 200 mg/kg body weight/day on a high fat 2.9% fiber diet.,5,6,NA,16S,23,NA,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2B,5 August 2025,YokoC,YokoC,Changes in the fecal microbiota of mice fed a high fat diet (HDF) vs mice fed ad high fat 194 ± 24 mg/kg body weight/day (HDF-MX) of xylitol. An abundance of specific bacterial phylum or genus and ratio after seven weeks of xylitol supplementation.,increased,",k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota",;3379134|976|200643|171549|171552|838;1783272|1239,Complete,KateRasheed
bsdb:28708089/3/2,28708089,laboratory experiment,28708089,10.3390/nu9070756,NA,"Uebanso T., Kano S., Yoshimoto A., Naito C., Shimohata T., Mawatari K. , Takahashi A.",Effects of Consuming Xylitol on Gut Microbiota and Lipid Metabolism in Mice,Nutrients,2017,"Streptococcus mutans, capillary electrophoresis–mass spectrometry (CE–MS), caries, cholesterol, denaturing gradient gel electrophoresis (DGGE), triglyceride, xylitol",Experiment 3,Japan,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,HFD (high fat diet),HFD-MX (high fat medium dose xylitol),Male mice that were given xylitol solution of 200 mg/kg body weight/day on a high fat 2.9% fiber diet.,5,6,NA,16S,23,NA,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2B,5 August 2025,YokoC,YokoC,Changes in the fecal microbiota of mice fed a high fat diet (HDF) vs mice fed ad high fat 194 ± 24 mg/kg body weight/day (HDF-MX) of xylitol. An abundance of specific bacterial phylum or genus and ratio after seven weeks of xylitol supplementation.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,KateRasheed
bsdb:28714953/1/1,28714953,laboratory experiment,28714953,10.1038/nn.4606,NA,"Shen S., Lim G., You Z., Ding W., Huang P., Ran C., Doheny J., Caravan P., Tate S., Hu K., Kim H., McCabe M., Huang B., Xie Z., Kwon D., Chen L. , Mao J.",Gut microbiota is critical for the induction of chemotherapy-induced pain,Nature neuroscience,2017,NA,Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,H2O mice,Exposed abx mice,Mice fed with antibiotic water,10,10,NA,16S,NA,RT-qPCR,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 1C,22 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Phylum analysis of altered microbiota in mice after antibiotic water feeding compared to mice fed with regular water,increased,"k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota",1783272|1117;3379134|1224;1783272|1239,Complete,ChiomaBlessing
bsdb:28714953/1/2,28714953,laboratory experiment,28714953,10.1038/nn.4606,NA,"Shen S., Lim G., You Z., Ding W., Huang P., Ran C., Doheny J., Caravan P., Tate S., Hu K., Kim H., McCabe M., Huang B., Xie Z., Kwon D., Chen L. , Mao J.",Gut microbiota is critical for the induction of chemotherapy-induced pain,Nature neuroscience,2017,NA,Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,H2O mice,Exposed abx mice,Mice fed with antibiotic water,10,10,NA,16S,NA,RT-qPCR,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 1C,22 February 2024,ChiomaBlessing,"ChiomaBlessing,Scholastica,Joan Chuks,WikiWorks",Phylum analysis of altered microbiota in mice after antibiotic water feeding compared to mice fed with regular water,decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,p__Candidatus Saccharimonadota",1783272|201174;3379134|976;3384189|32066|203490;1783272|544448;3379134|74201|203494;95818,Complete,ChiomaBlessing
bsdb:28725009/1/1,28725009,case-control,28725009,10.1038/s41598-017-06361-2,NA,"Wolf A., Moissl-Eichinger C., Perras A., Koskinen K., Tomazic P.V. , Thurnher D.",The salivary microbiome as an indicator of carcinogenesis in patients with oropharyngeal squamous cell carcinoma: A pilot study,Scientific reports,2017,NA,Experiment 1,Austria,Homo sapiens,Saliva,UBERON:0001836,Squamous cell carcinoma,EFO:0000707,Healthy Controls,Oropharyngeal Squamous Cell Carcinoma,diagnosed with OSCC and SCC of the oral cavity,11,11,1 month,16S,4,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 1,"Figure 3, Text",10 January 2021,Utsav Patel,"WikiWorks,ChiomaBlessing",Significant taxa in patients with oropharyngeal squamous cell carcinoma VS controls,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Schwartzia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85004|31953|1678;3379134|200940|3031449|213115|194924|872;3384189|32066|203490|203491|1129771;1783272|1239|186801|3085636|186803|437755;1783272|1239|909932|909929|1843491|55506;1783272|1239|909932|909929|1843491|970;3379134|203691|203692|136|2845253|157,Complete,Atrayees
bsdb:28725009/1/2,28725009,case-control,28725009,10.1038/s41598-017-06361-2,NA,"Wolf A., Moissl-Eichinger C., Perras A., Koskinen K., Tomazic P.V. , Thurnher D.",The salivary microbiome as an indicator of carcinogenesis in patients with oropharyngeal squamous cell carcinoma: A pilot study,Scientific reports,2017,NA,Experiment 1,Austria,Homo sapiens,Saliva,UBERON:0001836,Squamous cell carcinoma,EFO:0000707,Healthy Controls,Oropharyngeal Squamous Cell Carcinoma,diagnosed with OSCC and SCC of the oral cavity,11,11,1 month,16S,4,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 2,"Figure 3, Text",10 January 2021,Utsav Patel,"WikiWorks,ChiomaBlessing",Significant taxa in patients with oropharyngeal squamous cell carcinoma VS controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|186801|3085636|186803|43996;3379134|1224|1236|135625|712|724;3379134|1224|28216|206351|481|482;3379134|1224|1236|135625|712;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:28725009/2/1,28725009,case-control,28725009,10.1038/s41598-017-06361-2,NA,"Wolf A., Moissl-Eichinger C., Perras A., Koskinen K., Tomazic P.V. , Thurnher D.",The salivary microbiome as an indicator of carcinogenesis in patients with oropharyngeal squamous cell carcinoma: A pilot study,Scientific reports,2017,NA,Experiment 2,Austria,Homo sapiens,Saliva,UBERON:0001836,Squamous cell carcinoma,EFO:0000707,Healthy Controls,Oropharyngeal Squamous Cell Carcinoma,diagnosed with OSCC and SCC of the oral cavity,11,11,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 1,Supplementary Figure S4,10 January 2021,Utsav Patel,"WikiWorks,ChiomaBlessing",Significant taxa in patients with oropharyngeal squamous cell carcinoma VS controls,increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,c__Deltaproteobacteria,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Spirochaetota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|201174;3379134|1224|1236|135624;3379134|1224|28211;3379134|976|200643|171549;3379134|976|200643;3379134|976;1783272|201174|1760|85004;1783272|201174|1760|85007|1653;28221;1783272|1239|526524|526525;1783272|1239|526524;3379134|976|117743|200644|49546;3379134|976|117743|200644;3379134|976|117743;1783272|1239|909932;3379134|1224|1236|135625|712;3379134|976|200643|171549|171552;3379134|1224;1783272|1239|909932|909929;3379134|976|117747|200666;3379134|976|117747;3379134|203691|203692|136|137|146;3379134|203691|203692|136|137;3379134|203691|203692|136;3379134|203691;3379134|1224|1236|135624|83763;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977,Complete,Atrayees
bsdb:28725009/2/2,28725009,case-control,28725009,10.1038/s41598-017-06361-2,NA,"Wolf A., Moissl-Eichinger C., Perras A., Koskinen K., Tomazic P.V. , Thurnher D.",The salivary microbiome as an indicator of carcinogenesis in patients with oropharyngeal squamous cell carcinoma: A pilot study,Scientific reports,2017,NA,Experiment 2,Austria,Homo sapiens,Saliva,UBERON:0001836,Squamous cell carcinoma,EFO:0000707,Healthy Controls,Oropharyngeal Squamous Cell Carcinoma,diagnosed with OSCC and SCC of the oral cavity,11,11,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 2,Supplementary Figure S4,10 January 2021,Utsav Patel,"WikiWorks,ChiomaBlessing",Significant taxa in patients with oropharyngeal squamous cell carcinoma VS controls,decreased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum",1783272|1239|91061;3379134|1224|1236;1783272|1239|186801|3082720|186804;1783272|1239|186801|3085636|186803|1213720,Complete,Atrayees
bsdb:28733895/1/1,28733895,prospective cohort,28733895,10.1007/s00277-017-3069-8,NA,"Doki N., Suyama M., Sasajima S., Ota J., Igarashi A., Mimura I., Morita H., Fujioka Y., Sugiyama D., Nishikawa H., Shimazu Y., Suda W., Takeshita K., Atarashi K., Hattori M., Sato E., Watakabe-Inamoto K., Yoshioka K., Najima Y., Kobayashi T., Kakihana K., Takahashi N., Sakamaki H., Honda K. , Ohashi K.",Clinical impact of pre-transplant gut microbial diversity on outcomes of allogeneic hematopoietic stem cell transplantation,Annals of hematology,2017,"Acute gastrointestinal graft-versus-host disease (GVHD), Allogeneic hematopoietic stem cell transplantation (allo-HSCT), Intestinal microbiota, Microbial diversity",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Graft versus host disease,MONDO:0013730,non-acute graft-versus-host disease,acute graft-versus-host disease,"participants that developed acute graft-versus-host disease after allogeneic hematopoeitic transplant and graded accordinly to pattern of organ involvement and clinical performance status using a system introduced by Glucksberg et al. (Severity Index), which includes late-onset of acute graft-versus-host disease (more than 100 days after transplantation)",NA,107,NA,16S,12,Roche454,NA,T-Test,0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,10 January 2021,William Lam,WikiWorks,pre-transplant relative abundance of phylum-level gut microbial diversity on the non-acute graft-versus-host disease compared to acute graft-versus-host disease in outcomes of allogeneic hematopoietic stem cell transplantation,increased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Atrayees
bsdb:28733895/2/1,28733895,prospective cohort,28733895,10.1007/s00277-017-3069-8,NA,"Doki N., Suyama M., Sasajima S., Ota J., Igarashi A., Mimura I., Morita H., Fujioka Y., Sugiyama D., Nishikawa H., Shimazu Y., Suda W., Takeshita K., Atarashi K., Hattori M., Sato E., Watakabe-Inamoto K., Yoshioka K., Najima Y., Kobayashi T., Kakihana K., Takahashi N., Sakamaki H., Honda K. , Ohashi K.",Clinical impact of pre-transplant gut microbial diversity on outcomes of allogeneic hematopoietic stem cell transplantation,Annals of hematology,2017,"Acute gastrointestinal graft-versus-host disease (GVHD), Allogeneic hematopoietic stem cell transplantation (allo-HSCT), Intestinal microbiota, Microbial diversity",Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Graft versus host disease,MONDO:0013730,non-acute graft-versus-host disease,acute graft-versus-host disease,"participants that developed acute graft-versus-host disease after allogeneic hematopoeitic transplant and graded accordinly to pattern of organ involvement and clinical performance status using a system introduced by Glucksberg et al. (Severity Index), which includes late-onset of acute graft-versus-host disease (more than 100 days after transplantation)",NA,107,NA,16S,12,Roche454,NA,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,10 January 2021,William Lam,WikiWorks,pre-transplant genus-level gut microbial diversity on the non-acute graft-versus-host disease compared to acute graft-versus-host disease in outcomes of allogeneic hematopoietic stem cell transplantation,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|186806|1730,Complete,Atrayees
bsdb:28743816/1/1,28743816,case-control,28743816,10.1128/mBio.00996-17,NA,"Liu C.M., Prodger J.L., Tobian A.A.R., Abraham A.G., Kigozi G., Hungate B.A., Aziz M., Nalugoda F., Sariya S., Serwadda D., Kaul R., Gray R.H. , Price L.B.",Penile Anaerobic Dysbiosis as a Risk Factor for HIV Infection,mBio,2017,"anaerobes, cytokines, foreskin inflammation, human immunodeficiency virus, penile microbiome, susceptibility",Experiment 1,Uganda,Homo sapiens,Skin of penis,UBERON:0001331,HIV infection,EFO:0000764,HIV seronegative,HIV seroconverted,HIV-infected trial participants who were randomized to the delayed circumcision arm of the trial and remained uncircumcised who seroconverted during the trial.,136,46,NA,16S,34,Illumina,relative abundances,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S1,12 January 2022,Joyessa,"Joyessa,Claregrieve1,WikiWorks,Aleru Divine",Differential microbial abundance between HIV seroconverters and HIV-negative controls,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|909932|1843489|31977|39948;1783272|201174|1760|2037|2049|2050;1783272|1239|1737404|1737405|1570339|1161127;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:28750650/1/1,28750650,case-control,28750650,10.1186/s13059-017-1271-6,https://pubmed.ncbi.nlm.nih.gov/28750650/,"Wen C., Zheng Z., Shao T., Liu L., Xie Z., Le Chatelier E., He Z., Zhong W., Fan Y., Zhang L., Li H., Wu C., Hu C., Xu Q., Zhou J., Cai S., Wang D., Huang Y., Breban M., Qin N. , Ehrlich S.D.",Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis,Genome biology,2017,"Ankylosing spondylitis, Biomarkers, Human gut microbiome, Pathogenesis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Ankylosing spondylitis,EFO:0003898,Healthy controls,Ankylosing spondylitis patients,Ankylosing spondylitis confirmed by calculating the Bath Ankylosing Spondylitis Functional Index (BASFI) and Bath Ankylosing Spondylitis Disease Activity Index (BASDAI),114,97,1 month,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.001,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,Table S4,15 March 2023,Ufuoma Ejite,"Ufuoma Ejite,Chloe,Aiyshaaaa,Atrayees,WikiWorks",Differences of phylogenetic abundance between AS patients and healthy controls,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 7_1_58FAA,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85004|31953|1678;1783272|201174|84998|84999|84107|102106;1783272|201174|1760|85007|1653|1716;1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|658087;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843489|31977|906;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|838;1783272|201174|1760|85006|1268|32207;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|3085636|186803|207244|649756,Complete,Chloe
bsdb:28750650/1/2,28750650,case-control,28750650,10.1186/s13059-017-1271-6,https://pubmed.ncbi.nlm.nih.gov/28750650/,"Wen C., Zheng Z., Shao T., Liu L., Xie Z., Le Chatelier E., He Z., Zhong W., Fan Y., Zhang L., Li H., Wu C., Hu C., Xu Q., Zhou J., Cai S., Wang D., Huang Y., Breban M., Qin N. , Ehrlich S.D.",Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis,Genome biology,2017,"Ankylosing spondylitis, Biomarkers, Human gut microbiome, Pathogenesis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Ankylosing spondylitis,EFO:0003898,Healthy controls,Ankylosing spondylitis patients,Ankylosing spondylitis confirmed by calculating the Bath Ankylosing Spondylitis Functional Index (BASFI) and Bath Ankylosing Spondylitis Disease Activity Index (BASDAI),114,97,1 month,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.001,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Table S4,15 March 2023,Ufuoma Ejite,"Ufuoma Ejite,Chloe,Aiyshaaaa,WikiWorks",Differences of phylogenetic abundance between AS patients and healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum sp. OBRC5-5,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__[Bacteroides] pectinophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__butyrate-producing bacterium SS3/4,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 6_1_63FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 9_1_43BFAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 3_1_46FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 1_1_57FAA,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 5_1_57FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 3_1_57FAA_CT1,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 2 1 46FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 2_2_44A,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 3_1_53",1783272|1239|186801|3085636|186803|830;3379134|1224|1236|91347|543|544;1783272|1239|186801|186802|31979|1485;3379134|1224|1236|91347|543|547;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|186806|1730;3384189|32066|203490|203491|203492|848;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|1164882|936595;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3082720|186804;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|384638;1783272|1239|186801|186802|245014;1783272|1239|186801|3085636|186803|658083;1783272|1239|186801|3082720|186804|1505657|261299;1783272|1239|186801|3085636|186803|658088;1783272|1239|186801|3085636|186803|665950;1783272|1239|186801|3085636|186803|658081;3379134|29547|3031852|213849|72294|194;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|3085636|186803|658085;1783272|1239|186801|3085636|186803|658086;1783272|1239|526524|526525|128827|2749846|31971;1783272|1239|186801|3085636|186803|2683689;1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|526524|526525|128827|457422;1783272|1239|526524|526525|128827|658659,Complete,Chloe
bsdb:28753429/1/1,28753429,case-control,28753429,10.1016/j.cell.2017.07.008,NA,"Yu T., Guo F., Yu Y., Sun T., Ma D., Han J., Qian Y., Kryczek I., Sun D., Nagarsheth N., Chen Y., Chen H., Hong J., Zou W. , Fang J.Y.",Fusobacterium nucleatum Promotes Chemoresistance to Colorectal Cancer by Modulating Autophagy,Cell,2017,"Colorectal cancer, F.nucleatum, Toll-like receptor, autophagy, chemoresistance, miRNA, recurrence",Experiment 1,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,Patients without CRC recurrence,Patients with CRC recurrence,Patient tissues with colorectal cancer recurrence,16,15,6 months,16S,123,Roche454,relative abundances,LEfSe,NA,NA,3.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1B,4 June 2022,Jeshudy,"Jeshudy,WikiWorks","(B) Linear discriminant analysis (LDA) coupled with the effect size measurements identifies
the significant abundance of data in A. Taxa enriched in recurrent (Red) and non-recurrent
(Blue) patients are indicated with negative (Red) or positive (Blue) LDA scores, respectively.
Only taxa greater than LDA threshold of 3.5 are shown.",increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3384189|32066|203490|203491|203492|848;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|186802|216572|1486725;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171552|838,Complete,Fatima
bsdb:28753429/1/2,28753429,case-control,28753429,10.1016/j.cell.2017.07.008,NA,"Yu T., Guo F., Yu Y., Sun T., Ma D., Han J., Qian Y., Kryczek I., Sun D., Nagarsheth N., Chen Y., Chen H., Hong J., Zou W. , Fang J.Y.",Fusobacterium nucleatum Promotes Chemoresistance to Colorectal Cancer by Modulating Autophagy,Cell,2017,"Colorectal cancer, F.nucleatum, Toll-like receptor, autophagy, chemoresistance, miRNA, recurrence",Experiment 1,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,Patients without CRC recurrence,Patients with CRC recurrence,Patient tissues with colorectal cancer recurrence,16,15,6 months,16S,123,Roche454,relative abundances,LEfSe,NA,NA,3.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1B,4 June 2022,Jeshudy,"Jeshudy,WikiWorks","Linear discriminant analysis (LDA) coupled with the effect size measurements identifies
the significant abundance of data in A. Taxa enriched in recurrent (Red) and non-recurrent
(Blue) patients are indicated with negative (Red) or positive (Blue) LDA scores, respectively.
Only taxa greater than LDA threshold of 3.5 are shown.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|1224|1236|135614|32033|40323;1783272|1239|909932|1843489|31977|29465,Complete,Fatima
bsdb:28765474/1/1,28765474,"cross-sectional observational, not case-control",28765474,10.1136/gutjnl-2017-314281,NA,"Coker O.O., Dai Z., Nie Y., Zhao G., Cao L., Nakatsu G., Wu W.K., Wong S.H., Chen Z., Sung J.J.Y. , Yu J.",Mucosal microbiome dysbiosis in gastric carcinogenesis,Gut,2018,"Gastric cancer, mucosal microbiome dysbiosis, oral bacteria",Experiment 1,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,intestinal metaplasia,gastric cancer,NA,37,17,2 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"Helicobacter pylori,age,sex",NA,NA,decreased,NA,NA,decreased,Signature 1,Supplementary Figure 1,10 January 2021,Rimsha Azhar,"Fatima,Merit,WikiWorks",The abundance of gastric cancer -enriched and -depleted operational taxonomic units across stages of gastric cancer,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales",3379134|976|200643|171549|171552|1283313;1783272|1239|186801|3085636|186803|43996;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|186806;3384189|32066|203490|203491|203492|848;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|437755;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171552|838;1783272|201174|84998|1643822|1643826|84108;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826,Complete,Atrayees
bsdb:28765474/1/2,28765474,"cross-sectional observational, not case-control",28765474,10.1136/gutjnl-2017-314281,NA,"Coker O.O., Dai Z., Nie Y., Zhao G., Cao L., Nakatsu G., Wu W.K., Wong S.H., Chen Z., Sung J.J.Y. , Yu J.",Mucosal microbiome dysbiosis in gastric carcinogenesis,Gut,2018,"Gastric cancer, mucosal microbiome dysbiosis, oral bacteria",Experiment 1,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,intestinal metaplasia,gastric cancer,NA,37,17,2 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"Helicobacter pylori,age,sex",NA,NA,decreased,NA,NA,decreased,Signature 2,Supplementary Figure 1,10 January 2021,Rimsha Azhar,WikiWorks,The abundance of gastric cancer -enriched and -depleted operational taxonomic units across stages of gastric cancer,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Vogesella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Sterolibacteriaceae|g__Methyloversatilis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Syntrophobacteria|o__Syntrophobacterales|f__Syntrophobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Candidatus Johnevansiales|f__Candidatus Johnevansiaceae|g__Candidatus Portiera",3379134|1224|1236|2887326|468|469;3379134|1224|28216|206351|1499392|57739;3379134|1224|28216|32003|2008793|378210;3379134|200940|3024408|213462|213465;3379134|1224|1236|3399795|3399796|235572,Complete,Atrayees
bsdb:28765474/2/1,28765474,"cross-sectional observational, not case-control",28765474,10.1136/gutjnl-2017-314281,NA,"Coker O.O., Dai Z., Nie Y., Zhao G., Cao L., Nakatsu G., Wu W.K., Wong S.H., Chen Z., Sung J.J.Y. , Yu J.",Mucosal microbiome dysbiosis in gastric carcinogenesis,Gut,2018,"Gastric cancer, mucosal microbiome dysbiosis, oral bacteria",Experiment 2,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,atrophic gastric,gastric cancer,NA,37,74,2 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"Helicobacter pylori,age,sex",NA,NA,unchanged,NA,NA,unchanged,Signature 1,Supplementary Figure 1,10 January 2021,Rimsha Azhar,WikiWorks,The abundance of gastric cancer -enriched and -depleted operational taxonomic units across stages of gastric cancer,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella",1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3082720|186804|1257;1783272|1239|91061|1385|539738|1378;3384189|32066|203490|203491|203492|848;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|186806|1730;3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|171552|838;1783272|1239|909932|1843489|31977|39948;1783272|201174|84998|1643822|1643826|84108;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3085636|186803|43996;1783272|1239|186801|3085636|186803|437755,Complete,Atrayees
bsdb:28765474/2/2,28765474,"cross-sectional observational, not case-control",28765474,10.1136/gutjnl-2017-314281,NA,"Coker O.O., Dai Z., Nie Y., Zhao G., Cao L., Nakatsu G., Wu W.K., Wong S.H., Chen Z., Sung J.J.Y. , Yu J.",Mucosal microbiome dysbiosis in gastric carcinogenesis,Gut,2018,"Gastric cancer, mucosal microbiome dysbiosis, oral bacteria",Experiment 2,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,atrophic gastric,gastric cancer,NA,37,74,2 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"Helicobacter pylori,age,sex",NA,NA,unchanged,NA,NA,unchanged,Signature 2,Supplementary Figure 1,10 January 2021,Rimsha Azhar,WikiWorks,The abundance of gastric cancer -enriched and -depleted operational taxonomic units across stages of gastric cancer,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Vogesella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Candidatus Johnevansiales|f__Candidatus Johnevansiaceae|g__Candidatus Portiera",3379134|1224|28216|206351|1499392|57739;3379134|1224|1236|3399795|3399796|235572,Complete,Atrayees
bsdb:28765474/3/1,28765474,"cross-sectional observational, not case-control",28765474,10.1136/gutjnl-2017-314281,NA,"Coker O.O., Dai Z., Nie Y., Zhao G., Cao L., Nakatsu G., Wu W.K., Wong S.H., Chen Z., Sung J.J.Y. , Yu J.",Mucosal microbiome dysbiosis in gastric carcinogenesis,Gut,2018,"Gastric cancer, mucosal microbiome dysbiosis, oral bacteria",Experiment 3,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,superficial gastric,gastric cancer,NA,37,77,2 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"Helicobacter pylori,age,sex",NA,NA,decreased,NA,NA,decreased,Signature 1,Supplementary Figure 1,10 January 2021,Rimsha Azhar,"Merit,WikiWorks",The abundance of gastric cancer -enriched and -depleted operational taxonomic units across stages of gastric cancer,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|976|200643|171549|171552|1283313;1783272|1239|186801|3085636|186803|43996;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|186806|1730;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|437755;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171552|838;1783272|201174|84998|1643822|1643826|84108;1783272|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:28765474/3/2,28765474,"cross-sectional observational, not case-control",28765474,10.1136/gutjnl-2017-314281,NA,"Coker O.O., Dai Z., Nie Y., Zhao G., Cao L., Nakatsu G., Wu W.K., Wong S.H., Chen Z., Sung J.J.Y. , Yu J.",Mucosal microbiome dysbiosis in gastric carcinogenesis,Gut,2018,"Gastric cancer, mucosal microbiome dysbiosis, oral bacteria",Experiment 3,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,superficial gastric,gastric cancer,NA,37,77,2 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"Helicobacter pylori,age,sex",NA,NA,decreased,NA,NA,decreased,Signature 2,Supplementary Figure 1,10 January 2021,Rimsha Azhar,WikiWorks,The abundance of gastric cancer -enriched and -depleted operational taxonomic units across stages of gastric cancer,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hydrogenophaga,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Vogesella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Sterolibacteriaceae|g__Methyloversatilis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Syntrophobacteria|o__Syntrophobacterales|f__Syntrophobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Candidatus Johnevansiales|f__Candidatus Johnevansiaceae|g__Candidatus Portiera",3379134|1224|28216|80840|80864;3379134|1224|28216|80840|80864|47420;3379134|1224|1236|2887326|468|469;3379134|1224|28216|206351|1499392|57739;3379134|1224|28216|32003|2008793|378210;3379134|200940|3024408|213462|213465;3379134|1224|1236|3399795|3399796|235572,Complete,Atrayees
bsdb:28789705/1/1,28789705,prospective cohort,28789705,10.1186/s40168-017-0313-3,NA,"Nogacka A., Salazar N., Suárez M., Milani C., Arboleya S., Solís G., Fernández N., Alaez L., Hernández-Barranco A.M., de Los Reyes-Gavilán C.G., Ventura M. , Gueimonde M.",Impact of intrapartum antimicrobial prophylaxis upon the intestinal microbiota and the prevalence of antibiotic resistance genes in vaginally delivered full-term neonates,Microbiome,2017,"Antibiotics, Intestinal microbiota, Intrapartum antimicrobial prophylaxis, Microbiome, Neonate",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Infants to mothers didn't receive IAP,Infants to mothers received IAP,Full-term (gestational ages >37 weeks) vaginally delivered infants born after an uncomplicated pregnancy,22,18,NA,16S,34,Illumina,NA,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Table S1,  Text",10 January 2021,Mst Afroza Parvin,WikiWorks,"Levels (relative frequencies; %) of the bacterial families showing differences, in at least one time point analyzed, between infants from mothers receiving IAP and those whose mothers did not receive it.",increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",3379134|29547|3031852|213849|72294;1783272|1239|186801|186802|31979;3379134|29547|3031852|213849|72293;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550,Complete,Atrayees
bsdb:28789705/1/2,28789705,prospective cohort,28789705,10.1186/s40168-017-0313-3,NA,"Nogacka A., Salazar N., Suárez M., Milani C., Arboleya S., Solís G., Fernández N., Alaez L., Hernández-Barranco A.M., de Los Reyes-Gavilán C.G., Ventura M. , Gueimonde M.",Impact of intrapartum antimicrobial prophylaxis upon the intestinal microbiota and the prevalence of antibiotic resistance genes in vaginally delivered full-term neonates,Microbiome,2017,"Antibiotics, Intestinal microbiota, Intrapartum antimicrobial prophylaxis, Microbiome, Neonate",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Infants to mothers didn't receive IAP,Infants to mothers received IAP,Full-term (gestational ages >37 weeks) vaginally delivered infants born after an uncomplicated pregnancy,22,18,NA,16S,34,Illumina,NA,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Table S1,  Text",10 January 2021,Mst Afroza Parvin,WikiWorks,"Levels (relative frequencies; %) of the bacterial families showing differences, in at least one time point analyzed, between infants from mothers receiving IAP and those whose mothers did not receive it.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota",1783272|201174|1760|85004|31953;1783272|201174,Complete,Atrayees
bsdb:28789705/2/1,28789705,prospective cohort,28789705,10.1186/s40168-017-0313-3,NA,"Nogacka A., Salazar N., Suárez M., Milani C., Arboleya S., Solís G., Fernández N., Alaez L., Hernández-Barranco A.M., de Los Reyes-Gavilán C.G., Ventura M. , Gueimonde M.",Impact of intrapartum antimicrobial prophylaxis upon the intestinal microbiota and the prevalence of antibiotic resistance genes in vaginally delivered full-term neonates,Microbiome,2017,"Antibiotics, Intestinal microbiota, Intrapartum antimicrobial prophylaxis, Microbiome, Neonate",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,breast-fed Infants to mothers didn't receive IAP,Breast-fed Infants to mothers received IAP,Full-term (gestational ages >37 weeks) vaginally delivered infants born after an uncomplicated pregnancy,18,11,NA,16S,34,Illumina,NA,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Table S2,  Text",10 January 2021,Mst Afroza Parvin,WikiWorks,Relative proportion (%; mean ± sd) of the five main bacterial phyla in the samples from breast and formula-fed infants either exposed of not to IAP,increased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Verrucomicrobiota",1783272|1239;3379134|74201,Complete,Atrayees
bsdb:28789705/2/2,28789705,prospective cohort,28789705,10.1186/s40168-017-0313-3,NA,"Nogacka A., Salazar N., Suárez M., Milani C., Arboleya S., Solís G., Fernández N., Alaez L., Hernández-Barranco A.M., de Los Reyes-Gavilán C.G., Ventura M. , Gueimonde M.",Impact of intrapartum antimicrobial prophylaxis upon the intestinal microbiota and the prevalence of antibiotic resistance genes in vaginally delivered full-term neonates,Microbiome,2017,"Antibiotics, Intestinal microbiota, Intrapartum antimicrobial prophylaxis, Microbiome, Neonate",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,breast-fed Infants to mothers didn't receive IAP,Breast-fed Infants to mothers received IAP,Full-term (gestational ages >37 weeks) vaginally delivered infants born after an uncomplicated pregnancy,18,11,NA,16S,34,Illumina,NA,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Table S2,  Text",10 January 2021,Mst Afroza Parvin,WikiWorks,Relative proportion (%; mean ± sd) of the five main bacterial phyla in the samples from breast and formula-fed infants either exposed of not to IAP,decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota",1783272|201174;3379134|976,Complete,Atrayees
bsdb:28789705/3/1,28789705,prospective cohort,28789705,10.1186/s40168-017-0313-3,NA,"Nogacka A., Salazar N., Suárez M., Milani C., Arboleya S., Solís G., Fernández N., Alaez L., Hernández-Barranco A.M., de Los Reyes-Gavilán C.G., Ventura M. , Gueimonde M.",Impact of intrapartum antimicrobial prophylaxis upon the intestinal microbiota and the prevalence of antibiotic resistance genes in vaginally delivered full-term neonates,Microbiome,2017,"Antibiotics, Intestinal microbiota, Intrapartum antimicrobial prophylaxis, Microbiome, Neonate",Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Formula-fed Infants to mothers didn't receive IAP,Formula-fed Infants to mothers received IAP,Full-term (gestational ages >37 weeks) vaginally delivered infants born after an uncomplicated pregnancy,4,7,NA,16S,34,Illumina,NA,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Table S2,  Text",10 January 2021,Mst Afroza Parvin,WikiWorks,Relative proportion (%; mean ± sd) of the five main bacterial phyla in the samples from breast and formula-fed infants either exposed of not to IAP,increased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Atrayees
bsdb:28789705/3/2,28789705,prospective cohort,28789705,10.1186/s40168-017-0313-3,NA,"Nogacka A., Salazar N., Suárez M., Milani C., Arboleya S., Solís G., Fernández N., Alaez L., Hernández-Barranco A.M., de Los Reyes-Gavilán C.G., Ventura M. , Gueimonde M.",Impact of intrapartum antimicrobial prophylaxis upon the intestinal microbiota and the prevalence of antibiotic resistance genes in vaginally delivered full-term neonates,Microbiome,2017,"Antibiotics, Intestinal microbiota, Intrapartum antimicrobial prophylaxis, Microbiome, Neonate",Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Formula-fed Infants to mothers didn't receive IAP,Formula-fed Infants to mothers received IAP,Full-term (gestational ages >37 weeks) vaginally delivered infants born after an uncomplicated pregnancy,4,7,NA,16S,34,Illumina,NA,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Table S2,  Text",10 January 2021,Mst Afroza Parvin,WikiWorks,Relative proportion (%; mean ± sd) of the five main bacterial phyla in the samples from breast and formula-fed infants either exposed of not to IAP,decreased,k__Bacillati|p__Actinomycetota,1783272|201174,Complete,Atrayees
bsdb:28793309/1/1,28793309,case-control,28793309,https://doi.org/10.1371/journal.pntd.0005826,NA,"Adebayo A.S., Suryavanshi M.V., Bhute S., Agunloye A.M., Isokpehi R.D., Anumudu C.I. , Shouche Y.S.",The microbiome in urogenital schistosomiasis and induced bladder pathologies,PLoS neglected tropical diseases,2017,NA,Experiment 1,Nigeria,Homo sapiens,Urine,UBERON:0001088,Urinary schistosomiasis,EFO:0007530,Healthy Control,Infection-Only,Urine samples infected with urogenital schistosomiasis,13,25,NA,16S,3,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 1,Figure 6B,25 April 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,Scholastica,WikiWorks",Differentially abundant microbiome between urogenital schistosomiasis (infection-only) and healthy controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae",3379134|1224|1236|2887326|468|469;1783272|1239|91061|186826|186827|1375;3379134|976|117743|200644|2762318|59732;1783272|1239|91061|186826|186827|66831;3379134|1224|1236|91347|543|570;3379134|1224|1236|72274|135621|286;3379134|1224|1236|135622|267890|22;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|186828;1783272|1239|91061|1385|186818;3379134|1224|1236|72274|135621,Complete,Svetlana up
bsdb:28793309/1/2,28793309,case-control,28793309,https://doi.org/10.1371/journal.pntd.0005826,NA,"Adebayo A.S., Suryavanshi M.V., Bhute S., Agunloye A.M., Isokpehi R.D., Anumudu C.I. , Shouche Y.S.",The microbiome in urogenital schistosomiasis and induced bladder pathologies,PLoS neglected tropical diseases,2017,NA,Experiment 1,Nigeria,Homo sapiens,Urine,UBERON:0001088,Urinary schistosomiasis,EFO:0007530,Healthy Control,Infection-Only,Urine samples infected with urogenital schistosomiasis,13,25,NA,16S,3,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 2,Figure 6B,25 April 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,Scholastica,WikiWorks",Differentially abundant microbiome between urogenital schistosomiasis (infection-only) and healthy controls,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Edwardsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Limnobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Mycoplana,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Photorhabdus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",3379134|1224|1236|2887326|468|469;3379134|1224|1236|91347|1903412|635;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|1903409|551;1783272|201174|1760|85004|31953|2701;3379134|1224|1236|91347|1903412|568;3379134|1224|28216|80840|119060|131079;3379134|1224|28211|356|82115|13159;3379134|1224|1236|91347|1903414|29487;3379134|1224|1236|2887326|468|497;1783272|1239|91061|186826|33958|46255;3379134|1224|1236|135624;1783272|201174|1760|85004|31953;3379134|1224|1236|91347|543;3379134|1224|1236|2887326|468;3379134|1224|1236|72274|135621;1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:28793309/2/1,28793309,case-control,28793309,https://doi.org/10.1371/journal.pntd.0005826,NA,"Adebayo A.S., Suryavanshi M.V., Bhute S., Agunloye A.M., Isokpehi R.D., Anumudu C.I. , Shouche Y.S.",The microbiome in urogenital schistosomiasis and induced bladder pathologies,PLoS neglected tropical diseases,2017,NA,Experiment 2,Nigeria,Homo sapiens,Urine,UBERON:0001088,Urinary schistosomiasis,EFO:0007530,Healthy Control,Advanced,Urine samples infected with urogenital schistosomiasis induced bladder pathology.,13,22,NA,16S,3,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 1,Figure 6A,29 April 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,WikiWorks",Differentially abundant microbiome between urogenital schistosomiasis induced bladder pathology (advanced) and healthy controls.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales",3379134|976|200643|171549|815|816;1783272|1239|91061|1385|90964|227979;3379134|976|200643|171549|171552|838;3384189|32066|203490|203491|203492|848;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|186827|1375;1783272|1239|91061|186826|186828|117563;1783272|1239|91061|186826|186827|66831;1783272|201174|1760|85006|85019|1696;1783272|1239|1737404|1737405|1570339|162289;3379134|1224|28211|204458|76892|75;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|2887326|468|469;3379134|1224|1236|135615,Complete,Svetlana up
bsdb:28793309/2/2,28793309,case-control,28793309,https://doi.org/10.1371/journal.pntd.0005826,NA,"Adebayo A.S., Suryavanshi M.V., Bhute S., Agunloye A.M., Isokpehi R.D., Anumudu C.I. , Shouche Y.S.",The microbiome in urogenital schistosomiasis and induced bladder pathologies,PLoS neglected tropical diseases,2017,NA,Experiment 2,Nigeria,Homo sapiens,Urine,UBERON:0001088,Urinary schistosomiasis,EFO:0007530,Healthy Control,Advanced,Urine samples infected with urogenital schistosomiasis induced bladder pathology.,13,22,NA,16S,3,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 2,Figure 6A,29 April 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,WikiWorks",Differentially abundant microbiome between urogenital schistosomiasis induced bladder pathology (advanced) and healthy controls.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Edwardsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Photorhabdus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter",1783272|1239|91061|186826|81852;1783272|201174|1760|85004|31953;3379134|1224|1236|135622|267888;3379134|1224|1236|91347|543;3379134|1224|1236|2887326|468;3379134|1224|1236|135624;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|1903412|635;1783272|1239|91061|186826|33958|46255;3379134|1224|1236|91347|1903409|551;3379134|1224|1236|91347|1903414|29487;3379134|1224|1236|91347|1903412|568;3379134|1224|1236|72274|135621|286;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|2887326|468|469,Complete,Svetlana up
bsdb:28793309/3/1,28793309,case-control,28793309,https://doi.org/10.1371/journal.pntd.0005826,NA,"Adebayo A.S., Suryavanshi M.V., Bhute S., Agunloye A.M., Isokpehi R.D., Anumudu C.I. , Shouche Y.S.",The microbiome in urogenital schistosomiasis and induced bladder pathologies,PLoS neglected tropical diseases,2017,NA,Experiment 3,Nigeria,Homo sapiens,Urine,UBERON:0001088,Urinary schistosomiasis,EFO:0007530,Non-Infected,Infected,Infected with urogenital schistosomiasis,24,46,NA,16S,3,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 1,"Figure 5A, 5B",30 April 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,WikiWorks",Differentially abundant microbiome genera in urogenital schistosomiasis (infected) and controls (non-infected).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Melissococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae",3379134|1224|1236|2887326|468|469;1783272|1239|91061|186826|186827;1783272|1239|91061|186826|186827|1375;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|201174|1760|85006|85019;1783272|201174|1760|85006|85019|1696;1783272|1239|91061|186826|186828;3379134|976|117743|200644|2762318|59732;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|186827|66831;3384189|32066|203490|203491|203492;3384189|32066|203490|203491|203492|848;1783272|1239|91061|186826|186828|117563;1783272|1239|91061|1385|90964|227979;1783272|1239|91061|186826|81850;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|81852|33969;3379134|1224|1236|2887326|468;1783272|1239|1737404|1737405|1570339|162289;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300;1783272|1239|1737404|1737405|1737406;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977;3379134|976|117743|200644|2762318;3379134|1224|1236|135615;1783272|1239|91061|186826|186828,Complete,Svetlana up
bsdb:28793309/3/2,28793309,case-control,28793309,https://doi.org/10.1371/journal.pntd.0005826,NA,"Adebayo A.S., Suryavanshi M.V., Bhute S., Agunloye A.M., Isokpehi R.D., Anumudu C.I. , Shouche Y.S.",The microbiome in urogenital schistosomiasis and induced bladder pathologies,PLoS neglected tropical diseases,2017,NA,Experiment 3,Nigeria,Homo sapiens,Urine,UBERON:0001088,Urinary schistosomiasis,EFO:0007530,Non-Infected,Infected,Infected with urogenital schistosomiasis,24,46,NA,16S,3,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 2,"Figure 5A, 5B",30 April 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,Scholastica,WikiWorks",Differentially abundant microbiome genera in urogenital schistosomiasis (infected) and controls (non-infected).,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Edwardsiella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Limnobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Mycoplana,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Photorhabdus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",3379134|1224|1236|2887326|468|469;1783272|1239|91061|1385|186817;1783272|1239|91061|1385|186817|1386;1783272|201174|1760|85004|31953;3379134|1224|28211|204458|76892;3379134|976|117743|200644|2762318|59732;3379134|1224|1236|91347|1903412|635;3379134|1224|28211|356|212791;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543;3379134|1224|1236|91347|1903409|551;1783272|201174|1760|85004|31953|2701;3379134|1224|1236|91347|1903412|568;3379134|1224|28216|80840|75682|29580;3379134|1224|28216|80840|119060|131079;3379134|1224|1236|2887326|468;3379134|1224|28211|356|82115|13159;3379134|1224|28216|80840|75682;3379134|1224|1236|91347|1903414|29487;3379134|1224|1236|135622|267888;3379134|1224|1236|2887326|468|497;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;3379134|976|117743|200644|2762318;1783272|1239|91061|186826|33958|46255;3379134|1224|1236|135624;1783272|201174|1760|85004|31953;3379134|1224|1236|135622|267888;1783272|1239|91061|186826|33958;3379134|1224|28216|80840|80864;3379134|1224|1236|2887326|468;3379134|1224|1236|91347|543,Complete,Svetlana up
bsdb:28793309/4/1,28793309,case-control,28793309,https://doi.org/10.1371/journal.pntd.0005826,NA,"Adebayo A.S., Suryavanshi M.V., Bhute S., Agunloye A.M., Isokpehi R.D., Anumudu C.I. , Shouche Y.S.",The microbiome in urogenital schistosomiasis and induced bladder pathologies,PLoS neglected tropical diseases,2017,NA,Experiment 4,Nigeria,Homo sapiens,Urine,UBERON:0001088,Urinary schistosomiasis,EFO:0007530,Pathology only,Advanced,Urogenital schistosomiasis induced bladder pathology.,10,22,NA,16S,3,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 1,Figure 5D,30 April 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,Scholastica,WikiWorks",Differentially abundant microbiome genera in non-infected bladder pathology (pathology-only) and urogenital schistosomiasis induced bladder pathology (advanced).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Wautersiella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Weeksella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hylemonella",3379134|1224|1236|2887326|468|469;1783272|1239|91061|186826|186827|1375;3379134|976|200643|171549|815|816;1783272|201174|1760|85006|85019|1696;3379134|1224|28216|80840|80864|283;1783272|1239|91061|186826|186827|66831;3384189|32066|203490|203491|203492|848;1783272|1239|91061|186826|186828|117563;1783272|1239|91061|1385|90964|227979;1783272|1239|91061|186826|33958|1578;1783272|1239|1737404|1737405|1570339|162289;3379134|976|200643|171549|171552|838;3379134|976|117747|200666|84566|28453;1783272|1239|909932|1843489|31977|29465;3379134|976|117743|200644|2762318|343873;3379134|976|117743|200644|2762318|1013;3379134|1224|1236|135615;3379134|1224|1236|72274|135621;3379134|1224|28216|80840|80864|232523,Complete,Svetlana up
bsdb:28793309/4/2,28793309,case-control,28793309,https://doi.org/10.1371/journal.pntd.0005826,NA,"Adebayo A.S., Suryavanshi M.V., Bhute S., Agunloye A.M., Isokpehi R.D., Anumudu C.I. , Shouche Y.S.",The microbiome in urogenital schistosomiasis and induced bladder pathologies,PLoS neglected tropical diseases,2017,NA,Experiment 4,Nigeria,Homo sapiens,Urine,UBERON:0001088,Urinary schistosomiasis,EFO:0007530,Pathology only,Advanced,Urogenital schistosomiasis induced bladder pathology.,10,22,NA,16S,3,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 2,Figure 5D,30 April 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,Scholastica,WikiWorks",Differentially abundant microbiome genera in non-infected bladder pathology (pathology-only) and urogenital schistosomiasis induced bladder pathology (advanced).,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Edwardsiella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Photorhabdus",3379134|1224|1236|2887326|468|469;1783272|1239|91061|1385|186817|1386;3379134|976|117743|200644|2762318|59732;3379134|1224|1236|91347|1903412|635;3379134|1224|28211|356|212791;3379134|1224|1236|91347|1903412|568;3379134|1224|28216|80840|75682|29580;3379134|1224|1236|72274|135621|286;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|135624;3379134|1224|1236|91347|543;1783272|1239|91061|1385|186818;3379134|1224|1236|135622|267888;3379134|1224|1236|91347|1903409|551;3379134|1224|1236|91347|1903414|29487,Complete,Svetlana up
bsdb:28793309/5/1,28793309,case-control,28793309,https://doi.org/10.1371/journal.pntd.0005826,NA,"Adebayo A.S., Suryavanshi M.V., Bhute S., Agunloye A.M., Isokpehi R.D., Anumudu C.I. , Shouche Y.S.",The microbiome in urogenital schistosomiasis and induced bladder pathologies,PLoS neglected tropical diseases,2017,NA,Experiment 5,Nigeria,Homo sapiens,Urine,UBERON:0001088,Urinary schistosomiasis,EFO:0007530,Infection Only,Advanced,urogenital schistosomiasis induced bladder pathology.,25,22,NA,16S,3,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 1,Figure 5C,30 April 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,WikiWorks",Differential microbiome genera between urogenital schistosomiasis (infection-only) and urogenital schistosomiasis induced bladder pathology (advanced).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Wautersiella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Limnobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Weeksella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Mycoplana,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",3379134|1224|1236|72274|135621;3379134|976|200643|171549|815|816;3379134|976|200643|171549|171552|838;1783272|1239|91061|1385|90964|227979;3379134|1224|1236|2887326|468;3379134|1224|1236|135615;3379134|1224|1236|2887326|468|497;3384189|32066|203490|203491|203492|848;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|186828|117563;1783272|1239|91061|186826|186827|66831;1783272|201174|1760|85006|85019|1696;1783272|1239|1737404|1737405|1570339|162289;1783272|201174|1760|85004|31953;3379134|1224|28211|204458|76892|75;1783272|201174|1760|85004|31953|2701;3379134|976|117747|200666|84566|28453;3379134|976|117743|200644|2762318|343873;3379134|1224|28216|80840|119060|131079;3379134|976|117743|200644|2762318|1013;1783272|1239|91061|186826|33958|1578;3379134|1224|28211|356|82115|13159;3379134|1224|1236|2887326|468|469;1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:28793309/5/2,28793309,case-control,28793309,https://doi.org/10.1371/journal.pntd.0005826,NA,"Adebayo A.S., Suryavanshi M.V., Bhute S., Agunloye A.M., Isokpehi R.D., Anumudu C.I. , Shouche Y.S.",The microbiome in urogenital schistosomiasis and induced bladder pathologies,PLoS neglected tropical diseases,2017,NA,Experiment 5,Nigeria,Homo sapiens,Urine,UBERON:0001088,Urinary schistosomiasis,EFO:0007530,Infection Only,Advanced,urogenital schistosomiasis induced bladder pathology.,25,22,NA,16S,3,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 2,Figure 5C,30 April 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,WikiWorks",Differential microbiome genera between urogenital schistosomiasis (infection-only) and urogenital schistosomiasis induced bladder pathology (advanced).,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae",1783272|1239|91061|186826|81852;1783272|1239|91061|186826|186828;3379134|976|117743|200644|2762318|59732;3379134|1224|1236|2887326|468|469;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|72274|135621|286;1783272|1239|91061|1385|186818,Complete,Svetlana up
bsdb:28793309/6/1,28793309,case-control,28793309,https://doi.org/10.1371/journal.pntd.0005826,NA,"Adebayo A.S., Suryavanshi M.V., Bhute S., Agunloye A.M., Isokpehi R.D., Anumudu C.I. , Shouche Y.S.",The microbiome in urogenital schistosomiasis and induced bladder pathologies,PLoS neglected tropical diseases,2017,NA,Experiment 6,Nigeria,Homo sapiens,Urine,UBERON:0001088,Urinary schistosomiasis,EFO:0007530,Pathology Only,Infection Only,Urogenital schistosomiasis infection,10,25,NA,16S,3,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 1,Figure S2B,30 April 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,WikiWorks",Differential abundance in the urine microbiome of persons with urogenital schistosomiasis infection without bladder pathology (infection-only) and pathology without schistosomiasis infection (pathology-only).,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter",1783272|1239|91061|186826|186827|1375;3379134|1224|1236|72274|135621;3379134|1224|28216|80840|80864|283;1783272|1239|91061|186826|81852|1350;3379134|976|117743|200644|2762318|59732;3379134|1224|1236|2887326|468|469,Complete,Svetlana up
bsdb:28793309/6/2,28793309,case-control,28793309,https://doi.org/10.1371/journal.pntd.0005826,NA,"Adebayo A.S., Suryavanshi M.V., Bhute S., Agunloye A.M., Isokpehi R.D., Anumudu C.I. , Shouche Y.S.",The microbiome in urogenital schistosomiasis and induced bladder pathologies,PLoS neglected tropical diseases,2017,NA,Experiment 6,Nigeria,Homo sapiens,Urine,UBERON:0001088,Urinary schistosomiasis,EFO:0007530,Pathology Only,Infection Only,Urogenital schistosomiasis infection,10,25,NA,16S,3,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 2,Figure S2B,30 April 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,WikiWorks",Differential abundance in the urine microbiome of persons with urogenital schistosomiasis infection without bladder pathology (infection-only) and pathology without schistosomiasis infection (pathology-only).,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Edwardsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Photorhabdus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter",3379134|1224|1236|135622|267888;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|1903412|635;3379134|1224|1236|91347|1903409|551;3379134|1224|1236|91347|1903414|29487;3379134|1224|28211|204458|76892|75;3379134|1224|1236|91347|543;1783272|1239|91061|1385|90964|1279;3379134|1224|28211|356|212791;3379134|976|117743|200644|2762318|59732;1783272|1239|91061|1385|186817|1386;3379134|1224|28216|80840|75682|29580;3379134|1224|1236|2887326|468|497;3379134|1224|1236|2887326|468;3379134|1224|1236|2887326|468|469,Complete,Svetlana up
bsdb:28793309/7/1,28793309,case-control,28793309,https://doi.org/10.1371/journal.pntd.0005826,NA,"Adebayo A.S., Suryavanshi M.V., Bhute S., Agunloye A.M., Isokpehi R.D., Anumudu C.I. , Shouche Y.S.",The microbiome in urogenital schistosomiasis and induced bladder pathologies,PLoS neglected tropical diseases,2017,NA,Experiment 7,Nigeria,Homo sapiens,Urine,UBERON:0001088,Urinary schistosomiasis,EFO:0007530,Non-Infected,Infected,Not infected with urogenital schistosomiasis.,24,46,NA,16S,3,Ion Torrent,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 1,Figure 7,1 May 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,Scholastica,WikiWorks","Predicted microbial biomarkers in urogenital schistosomiasis cases (infected) and controls
(non-infected).",decreased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Trabulsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Xenorhabdus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",1783272|1239|1737404|1737405|1570339|165779;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1257;1783272|201174|1760|85011|2062;3379134|1224|1236|91347|543|158851;1783272|1239|91061|186826|33958|46255;3379134|1224|1236|91347|1903414|626;3379134|1224|1236|91347|543;1783272|1239|91061|186826|33958,Complete,Svetlana up
bsdb:28793309/7/2,28793309,case-control,28793309,https://doi.org/10.1371/journal.pntd.0005826,NA,"Adebayo A.S., Suryavanshi M.V., Bhute S., Agunloye A.M., Isokpehi R.D., Anumudu C.I. , Shouche Y.S.",The microbiome in urogenital schistosomiasis and induced bladder pathologies,PLoS neglected tropical diseases,2017,NA,Experiment 7,Nigeria,Homo sapiens,Urine,UBERON:0001088,Urinary schistosomiasis,EFO:0007530,Non-Infected,Infected,Not infected with urogenital schistosomiasis.,24,46,NA,16S,3,Ion Torrent,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 2,Figure 7,1 May 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,Scholastica,WikiWorks","Predicted microbial biomarkers in urogenital schistosomiasis cases (infected) and controls
(non-infected).",increased,"k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales",3379134|976|117747|200666|84566;3379134|976|117747|200666;3379134|976|117747;3379134|976|117747|200666|84566|28453;3379134|1224|1236|135614|32033|40323;1783272|1239|91061|1385,Complete,Svetlana up
bsdb:28808302/1/1,28808302,prospective cohort,28808302,10.1038/s41598-017-08530-9,NA,"Zhu D., Xiao S., Yu J., Ai Q., He Y., Cheng C., Zhang Y. , Pan Y.",Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants,Scientific reports,2017,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Antibiotic free group (postnatal day 3),combination of penicillin and moxalactam group (postnatal day 3),"pre-term neonates given a treatment regimen of penicillin (10U kg-1, twice a day) combined with moxalactam (40 mg kg-1, twice a day)",12,12,NA,16S,34,Illumina,NA,"ANOVA,T-Test",0.05,FALSE,NA,"birth weight,delivery procedure,gestational age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Text,10 January 2021,Mst Afroza Parvin,"Chloe,WikiWorks",Composition Analysis of Microbiota,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Actinomycetota",3379134|976|200643|171549|815|816;3379134|976;1783272|1239|91061|186826|33958|1578;3379134|1224|28211|204457|41297|13687;1783272|201174,Complete,Chloe
bsdb:28808302/1/2,28808302,prospective cohort,28808302,10.1038/s41598-017-08530-9,NA,"Zhu D., Xiao S., Yu J., Ai Q., He Y., Cheng C., Zhang Y. , Pan Y.",Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants,Scientific reports,2017,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Antibiotic free group (postnatal day 3),combination of penicillin and moxalactam group (postnatal day 3),"pre-term neonates given a treatment regimen of penicillin (10U kg-1, twice a day) combined with moxalactam (40 mg kg-1, twice a day)",12,12,NA,16S,34,Illumina,NA,"ANOVA,T-Test",0.05,FALSE,NA,"birth weight,delivery procedure,gestational age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Text,10 January 2021,Mst Afroza Parvin,WikiWorks,Composition Analysis of Microbiota,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,1783272|1239|186801|186802|31979|1485,Complete,Chloe
bsdb:28808302/2/1,28808302,prospective cohort,28808302,10.1038/s41598-017-08530-9,NA,"Zhu D., Xiao S., Yu J., Ai Q., He Y., Cheng C., Zhang Y. , Pan Y.",Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants,Scientific reports,2017,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Antibiotic free group (postnatal day 3),piperacillin-tazobactam group (postnatal day 3),"pre-term neonates receiving piperacillin-tazobactam (75 mg kg-1, twice a day)",12,12,NA,16S,34,Illumina,NA,"ANOVA,T-Test",0.05,FALSE,NA,"birth weight,delivery procedure,gestational age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Text,10 January 2021,Mst Afroza Parvin,"Chloe,WikiWorks",Composition Analysis of Microbiota,increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota",1783272|201174;3379134|976,Complete,Chloe
bsdb:28808302/3/1,28808302,prospective cohort,28808302,10.1038/s41598-017-08530-9,NA,"Zhu D., Xiao S., Yu J., Ai Q., He Y., Cheng C., Zhang Y. , Pan Y.",Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants,Scientific reports,2017,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Antibiotic free group (postnatal day 7),combination of penicillin and moxalactam group (postnatal day 7),"pre-term neonates given a treatment regimen of penicillin (10U kg-1, twice a day) combined with moxalactam (40 mg kg-1, twice a day)",12,12,NA,16S,34,Illumina,NA,"ANOVA,T-Test",0.05,FALSE,NA,"birth weight,delivery procedure,gestational age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Text,10 January 2021,Mst Afroza Parvin,"Chloe,WikiWorks",Composition Analysis of Microbiota,increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|976;3379134|1224|1236|91347|543|1940338,Complete,Chloe
bsdb:28808302/4/1,28808302,prospective cohort,28808302,10.1038/s41598-017-08530-9,NA,"Zhu D., Xiao S., Yu J., Ai Q., He Y., Cheng C., Zhang Y. , Pan Y.",Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants,Scientific reports,2017,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Antibiotic free group (postnatal day 7),piperacillin-tazobactam group (postnatal day 7),"pre-term neonates receiving piperacillin-tazobactam (75 mg kg-1, twice a day)",12,12,NA,16S,34,Illumina,NA,"ANOVA,T-Test",0.05,FALSE,NA,"birth weight,delivery procedure,gestational age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Text,10 January 2021,Mst Afroza Parvin,WikiWorks,Composition Analysis of Microbiota,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",3379134|976|200643|171549|815|816;1783272|1239|91061|186826|81852|1350,Complete,Chloe
bsdb:28808302/4/2,28808302,prospective cohort,28808302,10.1038/s41598-017-08530-9,NA,"Zhu D., Xiao S., Yu J., Ai Q., He Y., Cheng C., Zhang Y. , Pan Y.",Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants,Scientific reports,2017,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Antibiotic free group (postnatal day 7),piperacillin-tazobactam group (postnatal day 7),"pre-term neonates receiving piperacillin-tazobactam (75 mg kg-1, twice a day)",12,12,NA,16S,34,Illumina,NA,"ANOVA,T-Test",0.05,FALSE,NA,"birth weight,delivery procedure,gestational age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Text,10 January 2021,Mst Afroza Parvin,WikiWorks,Composition Analysis of Microbiota,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,3379134|1224|1236|91347|543|570,Complete,Chloe
bsdb:28808302/5/1,28808302,prospective cohort,28808302,10.1038/s41598-017-08530-9,NA,"Zhu D., Xiao S., Yu J., Ai Q., He Y., Cheng C., Zhang Y. , Pan Y.",Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants,Scientific reports,2017,NA,Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,piperacillin-tazobactam group (postnatal day 3),combination of penicillin and moxalactam group (postnatal day 3),"pre-term neonates given a treatment regimen of penicillin (10U kg-1, twice a day) combined with moxalactam (40 mg kg-1, twice a day)",12,12,NA,16S,34,Illumina,NA,"ANOVA,T-Test",0.05,FALSE,NA,"birth weight,delivery procedure,gestational age,sex",NA,NA,NA,NA,unchanged,NA,NA,Signature 1,Text,30 March 2022,Chloe,"Chloe,WikiWorks",NA,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,1783272|1239|91061|186826|81852|1350,Complete,Chloe
bsdb:28808302/6/1,28808302,prospective cohort,28808302,10.1038/s41598-017-08530-9,NA,"Zhu D., Xiao S., Yu J., Ai Q., He Y., Cheng C., Zhang Y. , Pan Y.",Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants,Scientific reports,2017,NA,Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,piperacillin-tazobactam group (postnatal day 7),combination of penicillin and moxalactam group (postnatal day 7),"pre-term neonates given a treatment regimen of penicillin (10U kg-1, twice a day) combined with moxalactam (40 mg kg-1, twice a day)",12,12,NA,16S,34,Illumina,NA,"ANOVA,T-Test",0.05,FALSE,NA,"birth weight,delivery procedure,gestational age,sex",NA,NA,NA,NA,unchanged,NA,NA,Signature 1,Text,30 March 2022,Chloe,"Chloe,WikiWorks",NA,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,1783272|1239|186801|186802|31979|1485,Complete,Chloe
bsdb:28808691/1/1,28808691,laboratory experiment,28808691,https://doi.org/10.1128/msystems.00047-17,https://journals.asm.org/doi/10.1128/msystems.00047-17,"Yasuda K., Hsu T., Gallini C.A., Mclver L.J., Schwager E., Shi A., DuLong C.R., Schwager R.N., Abu-Ali G.S., Franzosa E.A., Garrett W.S., Huttenhower C. , Morgan X.C.",Fluoride Depletes Acidogenic Taxa in Oral but Not Gut Microbial Communities in Mice,mSystems,2017,"16S rRNA sequencing, fluoridation, fluoride, gut microbiome, mouse, oral microbiome, shotgun metagenomic sequencing",Experiment 1,United States of America,Mus musculus,"Feces,Oral cavity","UBERON:0001988,UBERON:0000167",Sampling site,EFO:0000688,Mice oral sample,Mice stool sample,Stool samples collected from experimental mice at different time points,NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table S1,20 January 2026,Fiddyhamma,Fiddyhamma,Differentially abundant bacterial genera by oral-stool biogeography in mice inferred from univariate analysis,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",3379134|976|200643|171549|2005473;3379134|976|200643|171549|815|816;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171550;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:28808691/1/2,28808691,laboratory experiment,28808691,https://doi.org/10.1128/msystems.00047-17,https://journals.asm.org/doi/10.1128/msystems.00047-17,"Yasuda K., Hsu T., Gallini C.A., Mclver L.J., Schwager E., Shi A., DuLong C.R., Schwager R.N., Abu-Ali G.S., Franzosa E.A., Garrett W.S., Huttenhower C. , Morgan X.C.",Fluoride Depletes Acidogenic Taxa in Oral but Not Gut Microbial Communities in Mice,mSystems,2017,"16S rRNA sequencing, fluoridation, fluoride, gut microbiome, mouse, oral microbiome, shotgun metagenomic sequencing",Experiment 1,United States of America,Mus musculus,"Feces,Oral cavity","UBERON:0001988,UBERON:0000167",Sampling site,EFO:0000688,Mice oral sample,Mice stool sample,Stool samples collected from experimental mice at different time points,NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table S1,20 January 2026,Fiddyhamma,Fiddyhamma,Differentially abundant bacterial genera by oral-stool biogeography in mice inferred from univariate analysis,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|1224|1236|135625|712;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:28808691/2/1,28808691,laboratory experiment,28808691,https://doi.org/10.1128/msystems.00047-17,https://journals.asm.org/doi/10.1128/msystems.00047-17,"Yasuda K., Hsu T., Gallini C.A., Mclver L.J., Schwager E., Shi A., DuLong C.R., Schwager R.N., Abu-Ali G.S., Franzosa E.A., Garrett W.S., Huttenhower C. , Morgan X.C.",Fluoride Depletes Acidogenic Taxa in Oral but Not Gut Microbial Communities in Mice,mSystems,2017,"16S rRNA sequencing, fluoridation, fluoride, gut microbiome, mouse, oral microbiome, shotgun metagenomic sequencing",Experiment 2,United States of America,Mus musculus,Oral cavity,UBERON:0000167,Treatment outcome measurement,EFO:0008383,Control,Low fluoride,Mice treated with fluoridated drinking water (4 parts per million (ppm)) for a period of 12 weeks.,7,7,NA,16S,4,Illumina,log transformation,MaAsLin2,0.2,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2A,C and Table S2",20 January 2026,Fiddyhamma,Fiddyhamma,Fluoride selectively depletes acidogenic anaerobes in the oral microbiota.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|976|200643|171549|815|816|820;3379134|1224|28216|80840|119060|32008;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:28808691/3/1,28808691,laboratory experiment,28808691,https://doi.org/10.1128/msystems.00047-17,https://journals.asm.org/doi/10.1128/msystems.00047-17,"Yasuda K., Hsu T., Gallini C.A., Mclver L.J., Schwager E., Shi A., DuLong C.R., Schwager R.N., Abu-Ali G.S., Franzosa E.A., Garrett W.S., Huttenhower C. , Morgan X.C.",Fluoride Depletes Acidogenic Taxa in Oral but Not Gut Microbial Communities in Mice,mSystems,2017,"16S rRNA sequencing, fluoridation, fluoride, gut microbiome, mouse, oral microbiome, shotgun metagenomic sequencing",Experiment 3,United States of America,Mus musculus,Oral cavity,UBERON:0000167,Treatment outcome measurement,EFO:0008383,Control,High fluoride,Mice treated with fluoridated drinking water (4 parts per million (ppm)) plus a daily gavage of fluoride similar to a dose ingested when swallowing dental fluoride products (2.25 µg of fluoride per day via gavage) for a period of 12 weeks.,7,7,NA,16S,4,Illumina,log transformation,MaAsLin2,0.2,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2D, Table S2",20 January 2026,Fiddyhamma,Fiddyhamma,Fluoride selectively depletes acidogenic anaerobes in the oral microbiota.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Ruminobacter,3379134|1224|1236|135624|83763|866,Complete,Svetlana up
bsdb:28808691/3/2,28808691,laboratory experiment,28808691,https://doi.org/10.1128/msystems.00047-17,https://journals.asm.org/doi/10.1128/msystems.00047-17,"Yasuda K., Hsu T., Gallini C.A., Mclver L.J., Schwager E., Shi A., DuLong C.R., Schwager R.N., Abu-Ali G.S., Franzosa E.A., Garrett W.S., Huttenhower C. , Morgan X.C.",Fluoride Depletes Acidogenic Taxa in Oral but Not Gut Microbial Communities in Mice,mSystems,2017,"16S rRNA sequencing, fluoridation, fluoride, gut microbiome, mouse, oral microbiome, shotgun metagenomic sequencing",Experiment 3,United States of America,Mus musculus,Oral cavity,UBERON:0000167,Treatment outcome measurement,EFO:0008383,Control,High fluoride,Mice treated with fluoridated drinking water (4 parts per million (ppm)) plus a daily gavage of fluoride similar to a dose ingested when swallowing dental fluoride products (2.25 µg of fluoride per day via gavage) for a period of 12 weeks.,7,7,NA,16S,4,Illumina,log transformation,MaAsLin2,0.2,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2A,B and Table S2",20 January 2026,Fiddyhamma,Fiddyhamma,Fluoride selectively depletes acidogenic anaerobes in the oral microbiota.,decreased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|200940|3031449|213115|194924|35832;3379134|1224|28216|80840|995019|40544;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:28808698/1/1,28808698,case-control,28808698,10.3290/j.cjdr.a38769,NA,"Deng K., Ouyang X.Y., Chu Y. , Zhang Q.",Subgingival Microbiome of Gingivitis in Chinese Undergraduates,The Chinese journal of dental research : the official journal of the Scientific Section of the Chinese Stomatological Association (CSA),2017,NA,Experiment 1,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Gingivitis,MONDO:0002508,healthy controls,gingivitis,Patients with gingivitis,12,54,3 months,16S,34,Illumina,centered log-ratio,ANOSIM,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,figure 3 and text,10 January 2021,Marianthi Thomatos,"Lwaldron,WikiWorks,ChiomaBlessing",Subgingival Microbiome of Gingivitis in Chinese undergraduates VS healthy controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales genomosp. P1,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Spirochaetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",3379134|976|200643|171549|241556;3379134|976;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|171551|836|837;3379134|976|200643|171549|171552|838|28131;3379134|203691;3379134|976|200643|171549|2005525|195950;3379134|203691|203692|136|2845253|157,Complete,Shaimaa Elsafoury
bsdb:28808698/1/2,28808698,case-control,28808698,10.3290/j.cjdr.a38769,NA,"Deng K., Ouyang X.Y., Chu Y. , Zhang Q.",Subgingival Microbiome of Gingivitis in Chinese Undergraduates,The Chinese journal of dental research : the official journal of the Scientific Section of the Chinese Stomatological Association (CSA),2017,NA,Experiment 1,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Gingivitis,MONDO:0002508,healthy controls,gingivitis,Patients with gingivitis,12,54,3 months,16S,34,Illumina,centered log-ratio,ANOSIM,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,figure 3 and text,10 January 2021,Marianthi Thomatos,"WikiWorks,ChiomaBlessing",Subgingival Microbiome of Gingivitis in Chinese undergraduates VS healthy controls,decreased,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,3379134|976|117743|200644|49546|1016,Complete,Shaimaa Elsafoury
bsdb:28843021/1/1,28843021,case-control,28843021,10.1002/mds.27105,https://pubmed.ncbi.nlm.nih.gov/28843021/,"Heintz-Buschart A., Pandey U., Wicke T., Sixel-Döring F., Janzen A., Sittig-Wiegand E., Trenkwalder C., Oertel W.H., Mollenhauer B. , Wilmes P.",The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder,Movement disorders : official journal of the Movement Disorder Society,2018,"16S rRNA gene amplicon sequencing, PD, RBD, genome reconstructions, nonmotor phenotype",Experiment 1,Germany,Homo sapiens,Nasal cavity,UBERON:0001707,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease Patients,"PD patients underwent deep clinical characterization, including the International Parkinson and Movement Disorder Society (MDS) Unified Parkinson's Disease rating Scale (MDS‐UPDRS I–III), assessment of autonomic dysfunction in Parkinson's disease (Scopa‐AUT) gastrointestinal part (Questions 1‐7), depression by Geriatric Depression Scale and Montgomery‐Åsberg Depression Scale (MADRS), cognition by Mini–Mental State Examination (MMSE) as well as Montréal Cognitive Assessment (MoCA), and sleepiness by Epworth Sleepiness Scale (ESS).",78,76,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Results of the differential analysis of the nasal microbiota,11 March 2023,Jacquelynshevin,"Jacquelynshevin,Fatima,WikiWorks","Summarized results of the differential analyses of the nasal microbiota at the family. Taxa with multiple‐testing adjusted P values below 0.05 (and an absolute log2 fold change > 1 for differential analyses) were defined as significantly differentially abundant or related to a continuous variable, respectively.",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae",1783272|1239|91061|186826|186828;3379134|1224|2008785|119069|206349;3379134|1224|28211|356|45401,Complete,Fatima
bsdb:28843021/1/2,28843021,case-control,28843021,10.1002/mds.27105,https://pubmed.ncbi.nlm.nih.gov/28843021/,"Heintz-Buschart A., Pandey U., Wicke T., Sixel-Döring F., Janzen A., Sittig-Wiegand E., Trenkwalder C., Oertel W.H., Mollenhauer B. , Wilmes P.",The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder,Movement disorders : official journal of the Movement Disorder Society,2018,"16S rRNA gene amplicon sequencing, PD, RBD, genome reconstructions, nonmotor phenotype",Experiment 1,Germany,Homo sapiens,Nasal cavity,UBERON:0001707,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease Patients,"PD patients underwent deep clinical characterization, including the International Parkinson and Movement Disorder Society (MDS) Unified Parkinson's Disease rating Scale (MDS‐UPDRS I–III), assessment of autonomic dysfunction in Parkinson's disease (Scopa‐AUT) gastrointestinal part (Questions 1‐7), depression by Geriatric Depression Scale and Montgomery‐Åsberg Depression Scale (MADRS), cognition by Mini–Mental State Examination (MMSE) as well as Montréal Cognitive Assessment (MoCA), and sleepiness by Epworth Sleepiness Scale (ESS).",78,76,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Results of the differential analysis of the nasal microbiota,11 March 2023,Jacquelynshevin,"Jacquelynshevin,Fatima,WikiWorks","Summarized results of the differential analyses of the nasal microbiota at the family. Taxa with multiple‐testing adjusted P values below 0.05 (and an absolute log2 fold change > 1 for differential analyses) were defined as significantly differentially abundant or related to a continuous variable, respectively.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae",1783272|1239|91061|1385|186817;1783272|1239|91061|1385;3379134|200940|3031449|213115|194924;1783272|1239|91061|1385|186820;1783272|201174|1760|85006|1268;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|75682,Complete,Fatima
bsdb:28843021/2/1,28843021,case-control,28843021,10.1002/mds.27105,https://pubmed.ncbi.nlm.nih.gov/28843021/,"Heintz-Buschart A., Pandey U., Wicke T., Sixel-Döring F., Janzen A., Sittig-Wiegand E., Trenkwalder C., Oertel W.H., Mollenhauer B. , Wilmes P.",The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder,Movement disorders : official journal of the Movement Disorder Society,2018,"16S rRNA gene amplicon sequencing, PD, RBD, genome reconstructions, nonmotor phenotype",Experiment 2,Germany,Homo sapiens,Nasal cavity,UBERON:0001707,REM sleep behavior disorder,EFO:0007462,Healthy Controls,idiopathic rapid eye movement sleep behavior disorder,Subjects with iRBD diagnosed according to the consensus criteria of the International RBD Study group and no signs for neurodegenerative disorder (by clinical examination and neuropsychological testing).,78,21,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Results of the differential analysis of the nasal microbiota,11 March 2023,Jacquelynshevin,"Jacquelynshevin,Fatima,WikiWorks","Summarized results of the differential analyses of the nasal microbiota at the family. Taxa with multiple‐testing adjusted P values below 0.05 (and an absolute log2 fold change > 1 for differential analyses) were defined as significantly differentially abundant or related to a continuous variable, respectively.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae",1783272|1239|91061|1385;3379134|200940|3031449|213115|194924;3379134|1224|28216|80840|75682,Complete,Fatima
bsdb:28843021/3/1,28843021,case-control,28843021,10.1002/mds.27105,https://pubmed.ncbi.nlm.nih.gov/28843021/,"Heintz-Buschart A., Pandey U., Wicke T., Sixel-Döring F., Janzen A., Sittig-Wiegand E., Trenkwalder C., Oertel W.H., Mollenhauer B. , Wilmes P.",The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder,Movement disorders : official journal of the Movement Disorder Society,2018,"16S rRNA gene amplicon sequencing, PD, RBD, genome reconstructions, nonmotor phenotype",Experiment 3,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease Patients,"PD patients underwent deep clinical characterization, including the International Parkinson and Movement Disorder Society (MDS) Unified Parkinson's Disease rating Scale (MDS‐UPDRS I–III), assessment of autonomic dysfunction in Parkinson's disease (Scopa‐AUT) gastrointestinal part (Questions 1‐7), depression by Geriatric Depression Scale and Montgomery‐Åsberg Depression Scale (MADRS), cognition by Mini–Mental State Examination (MMSE) as well as Montréal Cognitive Assessment (MoCA), and sleepiness by Epworth Sleepiness Scale (ESS).",78,76,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,intake of diabetes medication,NA,NA,NA,NA,NA,NA,Signature 1,Summarized results of the differential and regression analyses of the gut microbiota,14 March 2023,Jacquelynshevin,"Jacquelynshevin,Fatima,WikiWorks","Differential analyses of the gut microbiome at OTU level (D): The fold change values are displayed in the two innermost heatmaps in G. ** (confirmed by ANCOM) and bold P-values are displayed in Figure 2. Taxa with multiple‐testing adjusted P values below 0.05 (and an absolute log2 fold change > 1 for differential analyses) were defined as significantly differentially abundant or related to a continuous variable, respectively.",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|186802|216572|244127;;3379134|976|200643;1783272|201174|1760|85004|31953;1783272|1239|526524|526525|128827;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|946234;3384189|32066|203490|203491|203492;1783272|1239|186801|3085636|186803;1783272|201174|84998|84999|1643824|133925;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|3085636|186803|572511|1532,Complete,Fatima
bsdb:28843021/3/2,28843021,case-control,28843021,10.1002/mds.27105,https://pubmed.ncbi.nlm.nih.gov/28843021/,"Heintz-Buschart A., Pandey U., Wicke T., Sixel-Döring F., Janzen A., Sittig-Wiegand E., Trenkwalder C., Oertel W.H., Mollenhauer B. , Wilmes P.",The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder,Movement disorders : official journal of the Movement Disorder Society,2018,"16S rRNA gene amplicon sequencing, PD, RBD, genome reconstructions, nonmotor phenotype",Experiment 3,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease Patients,"PD patients underwent deep clinical characterization, including the International Parkinson and Movement Disorder Society (MDS) Unified Parkinson's Disease rating Scale (MDS‐UPDRS I–III), assessment of autonomic dysfunction in Parkinson's disease (Scopa‐AUT) gastrointestinal part (Questions 1‐7), depression by Geriatric Depression Scale and Montgomery‐Åsberg Depression Scale (MADRS), cognition by Mini–Mental State Examination (MMSE) as well as Montréal Cognitive Assessment (MoCA), and sleepiness by Epworth Sleepiness Scale (ESS).",78,76,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,intake of diabetes medication,NA,NA,NA,NA,NA,NA,Signature 2,Summarized results of the differential and regression analyses of the gut microbiota,14 March 2023,Jacquelynshevin,"Jacquelynshevin,Fatima,WikiWorks","Differential analyses of the gut microbiome at OTU level (D): The fold change values are displayed in the two innermost heatmaps in G. ** (confirmed by ANCOM) and bold P-values are displayed in Figure 2. Taxa with multiple‐testing adjusted P values below 0.05 (and an absolute log2 fold change > 1 for differential analyses) were defined as significantly differentially abundant or related to a continuous variable, respectively.",decreased,"k__Bacillati|p__Bacillota,,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",1783272|1239;;3379134|976|200643|171549|815|816;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958|1578;1783272|201174|84998|84999|1643824|133925;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171552;3379134|1224;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;3379134|1224|28216|80840|995019|40544,Complete,Fatima
bsdb:28843021/4/1,28843021,case-control,28843021,10.1002/mds.27105,https://pubmed.ncbi.nlm.nih.gov/28843021/,"Heintz-Buschart A., Pandey U., Wicke T., Sixel-Döring F., Janzen A., Sittig-Wiegand E., Trenkwalder C., Oertel W.H., Mollenhauer B. , Wilmes P.",The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder,Movement disorders : official journal of the Movement Disorder Society,2018,"16S rRNA gene amplicon sequencing, PD, RBD, genome reconstructions, nonmotor phenotype",Experiment 4,Germany,Homo sapiens,Feces,UBERON:0001988,REM sleep behavior disorder,EFO:0007462,Healthy Controls,idiopathic rapid eye movement sleep behavior disorder,Subjects with iRBD diagnosed according to the consensus criteria of the International RBD Study group and no signs for neurodegenerative disorder (by clinical examination and neuropsychological testing).,78,21,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,intake of diabetes medication,NA,NA,NA,NA,NA,NA,Signature 1,Summarized results of the differential and regression analyses of the gut microbiota:,14 March 2023,Jacquelynshevin,"Jacquelynshevin,Fatima,WikiWorks","Differential analyses of the gut microbiome at OTU level (D): The fold change values are displayed in the two innermost heatmaps in G. ** (confirmed by ANCOM) and bold P-values are displayed in Figure 2. Taxa with multiple‐testing adjusted P values below 0.05 (and an absolute log2 fold change > 1 for differential analyses) were defined as significantly differentially abundant or related to a continuous variable, respectively.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta",1783272|1239|186801|186802|216572|244127;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|216572|946234;1783272|201174|84998|1643822|1643826|644652;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|572511|1532,Complete,Fatima
bsdb:28843021/4/2,28843021,case-control,28843021,10.1002/mds.27105,https://pubmed.ncbi.nlm.nih.gov/28843021/,"Heintz-Buschart A., Pandey U., Wicke T., Sixel-Döring F., Janzen A., Sittig-Wiegand E., Trenkwalder C., Oertel W.H., Mollenhauer B. , Wilmes P.",The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder,Movement disorders : official journal of the Movement Disorder Society,2018,"16S rRNA gene amplicon sequencing, PD, RBD, genome reconstructions, nonmotor phenotype",Experiment 4,Germany,Homo sapiens,Feces,UBERON:0001988,REM sleep behavior disorder,EFO:0007462,Healthy Controls,idiopathic rapid eye movement sleep behavior disorder,Subjects with iRBD diagnosed according to the consensus criteria of the International RBD Study group and no signs for neurodegenerative disorder (by clinical examination and neuropsychological testing).,78,21,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,intake of diabetes medication,NA,NA,NA,NA,NA,NA,Signature 2,Summarized results of the differential and regression analyses of the gut microbiota,14 March 2023,Jacquelynshevin,"Jacquelynshevin,Fatima,WikiWorks","Differential analyses of the gut microbiome at OTU level (D): The fold change values are displayed in the two innermost heatmaps in G. ** (confirmed by ANCOM) and bold P-values are displayed in Figure 2. Taxa with multiple‐testing adjusted P values below 0.05 (and an absolute log2 fold change > 1 for differential analyses) were defined as significantly differentially abundant or related to a continuous variable, respectively.",decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota,,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanosphaera",1783272|1239|909932|1843488|909930;1783272|1239;;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976|200643|171549|1853231|574697;1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|909929|1843491|52225;1783272|201174|84998|84999|1643824|133925;1783272|1239|186801|186802|216572;3379134|1224|1236|135625|712;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|1224|28216|80840|995019|40544;3366610|28890|183925|2158|2159|2316,Complete,NA
bsdb:28844190/1/1,28844190,prospective cohort,28844190,10.1902/jop.2017.160808,NA,"Duan X., Wu T., Xu X., Chen D., Mo A., Lei Y., Cheng L., Man Y., Zhou X., Wang Y. , Yuan Q.",Smoking May Lead to Marginal Bone Loss Around Non-Submerged Implants During Bone Healing by Altering Salivary Microbiome: A Prospective Study,Journal of periodontology,2017,"Alveolar bone loss, dental implants, microbiota, smoking",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,non-smokers,smokers,patients who have smoked >10 cigarettes a day for at least 5 years.,10,10,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,"Figure 4, Table 2",13 April 2023,Chioma,"Chioma,Fatima,WikiWorks",Significant differences between groups using Mann-Whitney test,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] infirmum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__uncultured Lachnoanaerobaculum sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__uncultured Stomatobaculum sp.",1783272|1239|909932|1843489|31977|906|187326;3379134|976|200643|171549|171551|836|837;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|186801|3082720|543314|56774;1783272|1239|186801|3085636|186803|1164882|1662275;1783272|1239|186801|3085636|186803|1213720|1662277,Complete,Fatima
bsdb:28844190/1/2,28844190,prospective cohort,28844190,10.1902/jop.2017.160808,NA,"Duan X., Wu T., Xu X., Chen D., Mo A., Lei Y., Cheng L., Man Y., Zhou X., Wang Y. , Yuan Q.",Smoking May Lead to Marginal Bone Loss Around Non-Submerged Implants During Bone Healing by Altering Salivary Microbiome: A Prospective Study,Journal of periodontology,2017,"Alveolar bone loss, dental implants, microbiota, smoking",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,non-smokers,smokers,patients who have smoked >10 cigarettes a day for at least 5 years.,10,10,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,"Figure 4, Table 2",13 April 2023,Chioma,"Chioma,Fatima,WikiWorks",Significant differences between groups using Mann-Whitney test,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella morbi,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium asaccharolyticum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__uncultured Selenomonas sp.",1783272|1239|186801|3085636|186803|43996|43997;1783272|1239|186801|3085636|186803|265975|1501332;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|909932|909929|1843491|970;1783272|1239|909932|909929|1843491|970|159275,Complete,Fatima
bsdb:28852182/1/1,28852182,case-control,28852182,10.1038/s41598-017-10663-w,NA,"Mancabelli L., Milani C., Lugli G.A., Turroni F., Mangifesta M., Viappiani A., Ticinesi A., Nouvenne A., Meschi T., van Sinderen D. , Ventura M.",Unveiling the gut microbiota composition and functionality associated with constipation through metagenomic analyses,Scientific reports,2017,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy Subjects (HS),Functional constipation (FC),Study participants who reported to have been suffering from Functional constipation,79,68,1 week,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Table S4,23 March 2025,MyleeeA,MyleeeA,Differentially abundant taxa between Functional constipation (FC) and Healthy Subjects (HS).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter sp. CAG:196,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Cercidoideae|g__Cercis|s__Cercis gigantea (nom. inval.),k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae|g__Gelria,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Polaromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota",3379134|1224|1236|2887326|468|469|1262690;3379134|976;3379134|976|200643|171549|1853231|574697;33090|35493|3398|72025|3803|1978181|49800|183790;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|186802|186807|51514;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|68295|186814|189326;3379134|29547|3031852|213849|72293|209;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|186802|216572|596767;1783272|1239|186801|3085636|186803|1164882;1783272|1239|91061|186826|1300|1357;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|80840|75682|846;1783272|1239|186801|186802|216572|100175;3379134|976|200643|171549|171552|577309;1783272|1239|186801|186802|186807|2740;1783272|1239|909932|1843488|909930|33024;3379134|1224|28216|80840|80864|52972;1783272|1239|186801|186802|216572|1508657;1783272|1239|526524|526525|2810280|3025755;3379134|256845|1313211|278082|255528|172900;;1783272|1239|186801|186802;1783272|544448|31969;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|186807;3379134|976|200643|171549|171551;3379134|1224;3379134|1224|28211|204441|41295;3379134|74201;3379134|976|200643|171549;3379134|976,Complete,Svetlana up
bsdb:28852182/1/2,28852182,case-control,28852182,10.1038/s41598-017-10663-w,NA,"Mancabelli L., Milani C., Lugli G.A., Turroni F., Mangifesta M., Viappiani A., Ticinesi A., Nouvenne A., Meschi T., van Sinderen D. , Ventura M.",Unveiling the gut microbiota composition and functionality associated with constipation through metagenomic analyses,Scientific reports,2017,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy Subjects (HS),Functional constipation (FC),Study participants who reported to have been suffering from Functional constipation,79,68,1 week,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Table S4,23 March 2025,MyleeeA,MyleeeA,Differentially abundant taxa between Functional constipation (FC) and Healthy Subjects (HS).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Parvularculales|f__Parvularculaceae|g__Parvularcula,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Polaromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",1783272|1239|186801|3085636|186803|1427378;3379134|976|200643|171549|815|816;3379134|976|117743|200644|49546|237;3379134|200930|68337|191393|2945020|248038;3379134|1224|28211|255473|255474|208215;3379134|1224|28216|80840|80864|52972;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3082720|186804,Complete,Svetlana up
bsdb:28852182/2/1,28852182,case-control,28852182,10.1038/s41598-017-10663-w,NA,"Mancabelli L., Milani C., Lugli G.A., Turroni F., Mangifesta M., Viappiani A., Ticinesi A., Nouvenne A., Meschi T., van Sinderen D. , Ventura M.",Unveiling the gut microbiota composition and functionality associated with constipation through metagenomic analyses,Scientific reports,2017,NA,Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy Subjects (HS),Functional constipation (FC),Study participants who reported to have been suffering from Functional constipation,79,68,1  week,16S,3,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2,26 March 2025,MyleeeA,MyleeeA,Differentially abundant taxa between Functional constipation (FC) and Healthy Subjects (HS).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|171552|577309;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|186802|216572|1508657;3379134|976|200643|171549;1783272|544448|31969;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171551;1783272|1239|186801|186802|216572|707003;1783272|1239|186801|186802,Complete,Svetlana up
bsdb:28852182/2/2,28852182,case-control,28852182,10.1038/s41598-017-10663-w,NA,"Mancabelli L., Milani C., Lugli G.A., Turroni F., Mangifesta M., Viappiani A., Ticinesi A., Nouvenne A., Meschi T., van Sinderen D. , Ventura M.",Unveiling the gut microbiota composition and functionality associated with constipation through metagenomic analyses,Scientific reports,2017,NA,Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy Subjects (HS),Functional constipation (FC),Study participants who reported to have been suffering from Functional constipation,79,68,1  week,16S,3,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2,26 March 2025,MyleeeA,MyleeeA,Differentially abundant taxa between Functional constipation (FC) and Healthy Subjects (HS).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:28852861/1/1,28852861,case-control,28852861,10.1007/s00535-017-1384-4,https://doi.org/10.1007/s00535-017-1384-4,"Nishino K., Nishida A., Inoue R., Kawada Y., Ohno M., Sakai S., Inatomi O., Bamba S., Sugimoto M., Kawahara M., Naito Y. , Andoh A.",Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease,Journal of gastroenterology,2018,"16S rRNA, IBD, Mucosa-associated microbiome",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Non-IBD,CD,Patients with Crohn's disease activity index <150,14,26,NA,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 5(a),23 November 2022,Fatima,"Fatima,Aiyshaaaa,WikiWorks",Comparative analyses of the taxonomic composition of the microbial community at the genus level. Representative genera with significant differences between groups are presented.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Pseudomonadati|p__Bacteroidota",3379134|1224|1236|135625|712|713;3384189|32066|203490|203491|203492|180162;1783272|1239|186801|186802|31979|1485;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|561;1783272|1239|186801|3085636|186803|1164882;1783272|1239|186801|3085636|186803|2316020|33038;3379134|976,Complete,Atrayees
bsdb:28852861/1/2,28852861,case-control,28852861,10.1007/s00535-017-1384-4,https://doi.org/10.1007/s00535-017-1384-4,"Nishino K., Nishida A., Inoue R., Kawada Y., Ohno M., Sakai S., Inatomi O., Bamba S., Sugimoto M., Kawahara M., Naito Y. , Andoh A.",Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease,Journal of gastroenterology,2018,"16S rRNA, IBD, Mucosa-associated microbiome",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Non-IBD,CD,Patients with Crohn's disease activity index <150,14,26,NA,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 5(a),20 March 2023,Aiyshaaaa,"Aiyshaaaa,WikiWorks",Comparative analyses of the taxonomic composition of the microbial community at the genus level. Representative genera with significant differences between groups are presented.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|204475;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263|40518;3379134|1224|1236|72274|135621|286,Complete,Atrayees
bsdb:28852861/2/1,28852861,case-control,28852861,10.1007/s00535-017-1384-4,https://doi.org/10.1007/s00535-017-1384-4,"Nishino K., Nishida A., Inoue R., Kawada Y., Ohno M., Sakai S., Inatomi O., Bamba S., Sugimoto M., Kawahara M., Naito Y. , Andoh A.",Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease,Journal of gastroenterology,2018,"16S rRNA, IBD, Mucosa-associated microbiome",Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,NON-IBD controls,UC,The patient who is diagnosed from ulcerative colitis(UC).,14,43,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 5(b),20 March 2023,Aiyshaaaa,"Aiyshaaaa,WikiWorks",Comparative analyses of the taxonomic composition of the microbial community at the genus level. Representative genera with significant differences between groups are presented,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota",1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;3379134|1224|1236|91347|543|544;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|29465;1783272|1239,Complete,Atrayees
bsdb:28852861/2/2,28852861,case-control,28852861,10.1007/s00535-017-1384-4,https://doi.org/10.1007/s00535-017-1384-4,"Nishino K., Nishida A., Inoue R., Kawada Y., Ohno M., Sakai S., Inatomi O., Bamba S., Sugimoto M., Kawahara M., Naito Y. , Andoh A.",Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease,Journal of gastroenterology,2018,"16S rRNA, IBD, Mucosa-associated microbiome",Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,NON-IBD controls,UC,The patient who is diagnosed from ulcerative colitis(UC).,14,43,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 5(b),21 March 2023,Aiyshaaaa,"Aiyshaaaa,WikiWorks",Comparative analyses of the taxonomic composition of the microbial community at the genus level. Representative genera with significant differences between groups are presented.,decreased,"k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|203691|203692|1643686|143786|29521;3379134|29547|3031852|213849|72293|209;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|204475;3379134|1224|1236|72274|135621|286;1783272|1239|186801|3085636|186803|33042;3379134|976|200643|171549|171552|838,Complete,Atrayees
bsdb:28852861/3/1,28852861,case-control,28852861,10.1007/s00535-017-1384-4,https://doi.org/10.1007/s00535-017-1384-4,"Nishino K., Nishida A., Inoue R., Kawada Y., Ohno M., Sakai S., Inatomi O., Bamba S., Sugimoto M., Kawahara M., Naito Y. , Andoh A.",Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease,Journal of gastroenterology,2018,"16S rRNA, IBD, Mucosa-associated microbiome",Experiment 3,Japan,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,UC,CD,The patient who is diagnosed from Crohn's disease(CD).,43,26,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 5(c),21 March 2023,Aiyshaaaa,"Aiyshaaaa,WikiWorks",Comparative analyses of the taxonomic composition of the microbial community at the genus level. Representative genera with significant differences between groups are presented,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",3384189|32066|203490|203491|203492|180162;1783272|1239|186801|186802|31979|1485;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|1903414|581;1783272|1239|186801|3082720|186804|1257;1783272|1239|186801|3085636|186803|2316020|33038,Complete,Atrayees
bsdb:28852861/3/2,28852861,case-control,28852861,10.1007/s00535-017-1384-4,https://doi.org/10.1007/s00535-017-1384-4,"Nishino K., Nishida A., Inoue R., Kawada Y., Ohno M., Sakai S., Inatomi O., Bamba S., Sugimoto M., Kawahara M., Naito Y. , Andoh A.",Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease,Journal of gastroenterology,2018,"16S rRNA, IBD, Mucosa-associated microbiome",Experiment 3,Japan,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,UC,CD,The patient who is diagnosed from Crohn's disease(CD).,43,26,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 5(c),21 March 2023,Aiyshaaaa,"Aiyshaaaa,WikiWorks",Comparative analyses of the taxonomic composition of the microbial community at the genus level. Representative genera with significant differences between groups are presented.,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|186802|204475;3379134|1224|1236|91347|543|544;1783272|1239|186801|3085636|186803|841;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|216851,Complete,Atrayees
bsdb:28860468/1/1,28860468,prospective cohort,28860468,10.1038/s41598-017-09842-6,NA,"Di Paola M., Sani C., Clemente A.M., Iossa A., Perissi E., Castronovo G., Tanturli M., Rivero D., Cozzolino F., Cavalieri D., Carozzi F., De Filippo C. , Torcia M.G.",Characterization of cervico-vaginal microbiota in women developing persistent high-risk Human Papillomavirus infection,Scientific reports,2017,NA,Experiment 1,Italy,Homo sapiens,Vaginal fluid,UBERON:0036243,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+  determined through HR-HC2 assay,17,55,3 days,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,figure 6a,10 January 2021,Cynthia Anderson,WikiWorks,Metagenomic biomarker discovery by LEfSe analysis betweeen HPV+ and HPV- women,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",3384189|32066|203490|203491|1129771|168808;1783272|1239|909932|1843489|31977|906;1783272|1239|91061|186826|33958|1253;1783272|201174|1760|85006|85019|1696;3379134|1224|1236|72274|135621|286,Complete,Fatima Zohra
bsdb:28860468/1/2,28860468,prospective cohort,28860468,10.1038/s41598-017-09842-6,NA,"Di Paola M., Sani C., Clemente A.M., Iossa A., Perissi E., Castronovo G., Tanturli M., Rivero D., Cozzolino F., Cavalieri D., Carozzi F., De Filippo C. , Torcia M.G.",Characterization of cervico-vaginal microbiota in women developing persistent high-risk Human Papillomavirus infection,Scientific reports,2017,NA,Experiment 1,Italy,Homo sapiens,Vaginal fluid,UBERON:0036243,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+  determined through HR-HC2 assay,17,55,3 days,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,figure 6a,10 January 2021,Cynthia Anderson,WikiWorks,Metagenomic biomarker discovery by LEfSe analysis betweeen HPV+ and HPV- women,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Pseudoxanthomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Candidatus Melainabacteria|c__Vampirovibriophyceae|o__Vampirovibrionales|g__Vampirovibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Alkanindiges",3379134|1224|1236|135614|32033|83618;1783272|201174|1760|2037|2049|1654;1783272|1798710|3118680|2211217|213484;3379134|1224|1236|2887326|468|222991,Complete,Fatima Zohra
bsdb:28860468/2/1,28860468,prospective cohort,28860468,10.1038/s41598-017-09842-6,NA,"Di Paola M., Sani C., Clemente A.M., Iossa A., Perissi E., Castronovo G., Tanturli M., Rivero D., Cozzolino F., Cavalieri D., Carozzi F., De Filippo C. , Torcia M.G.",Characterization of cervico-vaginal microbiota in women developing persistent high-risk Human Papillomavirus infection,Scientific reports,2017,NA,Experiment 2,Italy,Homo sapiens,Vaginal fluid,UBERON:0036243,Human papilloma virus infection,EFO:0001668,HPV+ (clearance),HPV+ (persistance),HR-HPV+ persistence confirmed by HPV genotyping after 1 year,27,28,3 days,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,figure 6b,10 January 2021,Cynthia Anderson,WikiWorks,Metagenomic biomarker discovery by LEfSe analysis betweeen HPV+ (clearance) and HPV+ (persistence),increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|201174|84998|84999|1643824|1380;1783272|1239|186801|186802|216572|216851,Complete,Fatima Zohra
bsdb:28860468/2/2,28860468,prospective cohort,28860468,10.1038/s41598-017-09842-6,NA,"Di Paola M., Sani C., Clemente A.M., Iossa A., Perissi E., Castronovo G., Tanturli M., Rivero D., Cozzolino F., Cavalieri D., Carozzi F., De Filippo C. , Torcia M.G.",Characterization of cervico-vaginal microbiota in women developing persistent high-risk Human Papillomavirus infection,Scientific reports,2017,NA,Experiment 2,Italy,Homo sapiens,Vaginal fluid,UBERON:0036243,Human papilloma virus infection,EFO:0001668,HPV+ (clearance),HPV+ (persistance),HR-HPV+ persistence confirmed by HPV genotyping after 1 year,27,28,3 days,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,figure 6b,10 January 2021,Cynthia Anderson,"Atrayees,WikiWorks",Metagenomic biomarker discovery by LEfSe analysis betweeen HPV+ (clearance) and HPV+ (persistence),decreased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Rhodoferax,3379134|1224|28216|80840|80864|28065,Complete,Fatima Zohra
bsdb:28863139/1/1,28863139,case-control,28863139,10.1371/journal.pone.0183509,NA,"Aarts E., Ederveen T.H.A., Naaijen J., Zwiers M.P., Boekhorst J., Timmerman H.M., Smeekens S.P., Netea M.G., Buitelaar J.K., Franke B., van Hijum S.A.F.T. , Arias Vasquez A.",Gut microbiome in ADHD and its relation to neural reward anticipation,PloS one,2017,NA,Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Attention deficit hyperactivity disorder,EFO:0003888,Controls,ADHD,cases were diagnosed based on DSM-IV symptoms using the Schedule for Affective Disorders and Schizophrenia for School-Age Children,77,19,NA,16S,34,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.1,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Fatima Zohra,WikiWorks,Differential abundance of microbial taxa for ADHD cases versus healthy controls,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales",1783272|201174;1783272|201174|1760;1783272|201174|1760|85004;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|201174|84998|1643822|1643826|84111;1783272|201174|1760|85004|31953|1678|28026;1783272|201174|1760|85004|31953|1678|216816|1679;1783272|201174|1760|85004|31953|1678|1680;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|171551;3379134|976|200643|171549|171550;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|820;28221;3379134|200940|3031449|213115,Complete,Shaimaa Elsafoury
bsdb:28863139/1/2,28863139,case-control,28863139,10.1371/journal.pone.0183509,NA,"Aarts E., Ederveen T.H.A., Naaijen J., Zwiers M.P., Boekhorst J., Timmerman H.M., Smeekens S.P., Netea M.G., Buitelaar J.K., Franke B., van Hijum S.A.F.T. , Arias Vasquez A.",Gut microbiome in ADHD and its relation to neural reward anticipation,PloS one,2017,NA,Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Attention deficit hyperactivity disorder,EFO:0003888,Controls,ADHD,cases were diagnosed based on DSM-IV symptoms using the Schedule for Affective Disorders and Schizophrenia for School-Age Children,77,19,NA,16S,34,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.1,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 3,10 January 2021,Fatima Zohra,WikiWorks,Differential abundance of microbial taxa for ADHD cases versus healthy controls,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus",1783272|1239;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803|33042|33043;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3120394|3120654|35829;1783272|1239|186801|3085636|186803|33042,Complete,Shaimaa Elsafoury
bsdb:28870194/1/1,28870194,randomized controlled trial,28870194,10.1186/s12906-017-1948-0,NA,"Pinheiro I., Robinson L., Verhelst A., Marzorati M., Winkens B., den Abbeele P.V. , Possemiers S.",A yeast fermentate improves gastrointestinal discomfort and constipation by modulation of the gut microbiome: results from a randomized double-blind placebo-controlled pilot trial,BMC complementary and alternative medicine,2017,"Bacteroides, Bacteroidetes, Constipation, EpiCor fermentate, GI transit time, Gastrointestinal discomfort, Gut microbiome, Human study, Prevotella, Saccharomyces cerevisiae",Experiment 1,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Placebo Total cohort V1(Visit 1),Placebo Total cohort V2(Visit 2),Participants in total cohort at visit 2 (3-weeks after treatment) who received the corresponding testing product (placebo),40,40,2 months,16S,56,Illumina,relative abundances,ANOVA,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Additional file 7,19 March 2025,Munaa,"Munaa,Tosin,Anne-mariesharp",Microbial taxa fold-changes (V2/V1) in Placebo total cohort.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|186801|3085636|186803|572511;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803;1783272|1239|909932|1843489|31977,Complete,Svetlana up
bsdb:28870194/1/2,28870194,randomized controlled trial,28870194,10.1186/s12906-017-1948-0,NA,"Pinheiro I., Robinson L., Verhelst A., Marzorati M., Winkens B., den Abbeele P.V. , Possemiers S.",A yeast fermentate improves gastrointestinal discomfort and constipation by modulation of the gut microbiome: results from a randomized double-blind placebo-controlled pilot trial,BMC complementary and alternative medicine,2017,"Bacteroides, Bacteroidetes, Constipation, EpiCor fermentate, GI transit time, Gastrointestinal discomfort, Gut microbiome, Human study, Prevotella, Saccharomyces cerevisiae",Experiment 1,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Placebo Total cohort V1(Visit 1),Placebo Total cohort V2(Visit 2),Participants in total cohort at visit 2 (3-weeks after treatment) who received the corresponding testing product (placebo),40,40,2 months,16S,56,Illumina,relative abundances,ANOVA,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Additional file 7,19 April 2025,Anne-mariesharp,Anne-mariesharp,Microbial taxa fold-changes (V2/V1) in Placebo total cohort.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:28870194/2/1,28870194,randomized controlled trial,28870194,10.1186/s12906-017-1948-0,NA,"Pinheiro I., Robinson L., Verhelst A., Marzorati M., Winkens B., den Abbeele P.V. , Possemiers S.",A yeast fermentate improves gastrointestinal discomfort and constipation by modulation of the gut microbiome: results from a randomized double-blind placebo-controlled pilot trial,BMC complementary and alternative medicine,2017,"Bacteroides, Bacteroidetes, Constipation, EpiCor fermentate, GI transit time, Gastrointestinal discomfort, Gut microbiome, Human study, Prevotella, Saccharomyces cerevisiae",Experiment 2,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Placebo moderate subgroup V1 (Visit 1),Placebo moderate subgroup V2 (Visit 2),A subgroup of participants with moderate symptoms of gastrointestinal discomfort and constipation at visit 2 (3-weeks after treatment) who received the corresponding testing product (placebo),13,13,2 months,16S,56,Illumina,relative abundances,ANOVA,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Additional file 9,19 March 2025,Munaa,"Munaa,Tosin",Microbial taxa fold-changes (V2/V1) in Placebo moderate subgroup,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:28870194/2/2,28870194,randomized controlled trial,28870194,10.1186/s12906-017-1948-0,NA,"Pinheiro I., Robinson L., Verhelst A., Marzorati M., Winkens B., den Abbeele P.V. , Possemiers S.",A yeast fermentate improves gastrointestinal discomfort and constipation by modulation of the gut microbiome: results from a randomized double-blind placebo-controlled pilot trial,BMC complementary and alternative medicine,2017,"Bacteroides, Bacteroidetes, Constipation, EpiCor fermentate, GI transit time, Gastrointestinal discomfort, Gut microbiome, Human study, Prevotella, Saccharomyces cerevisiae",Experiment 2,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Placebo moderate subgroup V1 (Visit 1),Placebo moderate subgroup V2 (Visit 2),A subgroup of participants with moderate symptoms of gastrointestinal discomfort and constipation at visit 2 (3-weeks after treatment) who received the corresponding testing product (placebo),13,13,2 months,16S,56,Illumina,relative abundances,ANOVA,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Additional file 9,19 March 2025,Munaa,"Munaa,Tosin",Microbial taxa fold-changes (V2/V1) in Placebo moderate subgroup,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|976|200643|171549|2005519|397864;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:28870194/3/1,28870194,randomized controlled trial,28870194,10.1186/s12906-017-1948-0,NA,"Pinheiro I., Robinson L., Verhelst A., Marzorati M., Winkens B., den Abbeele P.V. , Possemiers S.",A yeast fermentate improves gastrointestinal discomfort and constipation by modulation of the gut microbiome: results from a randomized double-blind placebo-controlled pilot trial,BMC complementary and alternative medicine,2017,"Bacteroides, Bacteroidetes, Constipation, EpiCor fermentate, GI transit time, Gastrointestinal discomfort, Gut microbiome, Human study, Prevotella, Saccharomyces cerevisiae",Experiment 3,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Placebo Total cohort V1(Visit 1),Placebo Total cohort V3(Visit 3),Participants in total cohort at visit 3 (6-weeks after treatment) who received the corresponding testing product (placebo),40,40,2 months,16S,56,Illumina,relative abundances,ANOVA,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Additional file 7,19 April 2025,Anne-mariesharp,Anne-mariesharp,Microbial taxa fold-changes (V3/V1) in Placebo total cohort.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",1783272|1239|909932|1843488|909930;1783272|1239|186801|3085636|186803|572511,Complete,Svetlana up
bsdb:28870194/3/2,28870194,randomized controlled trial,28870194,10.1186/s12906-017-1948-0,NA,"Pinheiro I., Robinson L., Verhelst A., Marzorati M., Winkens B., den Abbeele P.V. , Possemiers S.",A yeast fermentate improves gastrointestinal discomfort and constipation by modulation of the gut microbiome: results from a randomized double-blind placebo-controlled pilot trial,BMC complementary and alternative medicine,2017,"Bacteroides, Bacteroidetes, Constipation, EpiCor fermentate, GI transit time, Gastrointestinal discomfort, Gut microbiome, Human study, Prevotella, Saccharomyces cerevisiae",Experiment 3,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Placebo Total cohort V1(Visit 1),Placebo Total cohort V3(Visit 3),Participants in total cohort at visit 3 (6-weeks after treatment) who received the corresponding testing product (placebo),40,40,2 months,16S,56,Illumina,relative abundances,ANOVA,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Additional file 7,19 April 2025,Anne-mariesharp,Anne-mariesharp,Microbial taxa fold-changes (V3/V1) in Placebo total cohort,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171551,Complete,Svetlana up
bsdb:28870194/4/1,28870194,randomized controlled trial,28870194,10.1186/s12906-017-1948-0,NA,"Pinheiro I., Robinson L., Verhelst A., Marzorati M., Winkens B., den Abbeele P.V. , Possemiers S.",A yeast fermentate improves gastrointestinal discomfort and constipation by modulation of the gut microbiome: results from a randomized double-blind placebo-controlled pilot trial,BMC complementary and alternative medicine,2017,"Bacteroides, Bacteroidetes, Constipation, EpiCor fermentate, GI transit time, Gastrointestinal discomfort, Gut microbiome, Human study, Prevotella, Saccharomyces cerevisiae",Experiment 4,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,EpiCor Total cohort V1(Visit 1),EpiCor Total cohort V2(Visit 2),Participants in total cohort at visit 2 (3-weeks after treatment) who received the corresponding testing product (EpiCor fermentate),39,39,2 months,16S,56,Illumina,relative abundances,ANOVA,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Additional file 7,19 April 2025,Anne-mariesharp,Anne-mariesharp,Microbial taxa fold-changes (V2/V1) in EpiCor total cohort.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:28870194/4/2,28870194,randomized controlled trial,28870194,10.1186/s12906-017-1948-0,NA,"Pinheiro I., Robinson L., Verhelst A., Marzorati M., Winkens B., den Abbeele P.V. , Possemiers S.",A yeast fermentate improves gastrointestinal discomfort and constipation by modulation of the gut microbiome: results from a randomized double-blind placebo-controlled pilot trial,BMC complementary and alternative medicine,2017,"Bacteroides, Bacteroidetes, Constipation, EpiCor fermentate, GI transit time, Gastrointestinal discomfort, Gut microbiome, Human study, Prevotella, Saccharomyces cerevisiae",Experiment 4,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,EpiCor Total cohort V1(Visit 1),EpiCor Total cohort V2(Visit 2),Participants in total cohort at visit 2 (3-weeks after treatment) who received the corresponding testing product (EpiCor fermentate),39,39,2 months,16S,56,Illumina,relative abundances,ANOVA,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Additional file 7,19 April 2025,Anne-mariesharp,Anne-mariesharp,Microbial taxa fold-changes (V2/V1) in EpiCor total cohort,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550;1783272|1239,Complete,Svetlana up
bsdb:28870194/5/1,28870194,randomized controlled trial,28870194,10.1186/s12906-017-1948-0,NA,"Pinheiro I., Robinson L., Verhelst A., Marzorati M., Winkens B., den Abbeele P.V. , Possemiers S.",A yeast fermentate improves gastrointestinal discomfort and constipation by modulation of the gut microbiome: results from a randomized double-blind placebo-controlled pilot trial,BMC complementary and alternative medicine,2017,"Bacteroides, Bacteroidetes, Constipation, EpiCor fermentate, GI transit time, Gastrointestinal discomfort, Gut microbiome, Human study, Prevotella, Saccharomyces cerevisiae",Experiment 5,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,EpiCor Total cohort V1(Visit 1),EpiCor Total cohort V3(Visit 3),Participants in total cohort at visit 3(6-weeks after treatment) who received the corresponding testing product (EpiCor fermentate),39,39,2 months,16S,56,Illumina,relative abundances,ANOVA,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Additional file 7,19 April 2025,Anne-mariesharp,Anne-mariesharp,Microbial taxa fold-changes (V3/V1) in EpiCor total cohort,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803;1783272|201174|84998|84999|84107;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:28870194/5/2,28870194,randomized controlled trial,28870194,10.1186/s12906-017-1948-0,NA,"Pinheiro I., Robinson L., Verhelst A., Marzorati M., Winkens B., den Abbeele P.V. , Possemiers S.",A yeast fermentate improves gastrointestinal discomfort and constipation by modulation of the gut microbiome: results from a randomized double-blind placebo-controlled pilot trial,BMC complementary and alternative medicine,2017,"Bacteroides, Bacteroidetes, Constipation, EpiCor fermentate, GI transit time, Gastrointestinal discomfort, Gut microbiome, Human study, Prevotella, Saccharomyces cerevisiae",Experiment 5,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,EpiCor Total cohort V1(Visit 1),EpiCor Total cohort V3(Visit 3),Participants in total cohort at visit 3(6-weeks after treatment) who received the corresponding testing product (EpiCor fermentate),39,39,2 months,16S,56,Illumina,relative abundances,ANOVA,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Additional file 7,19 April 2025,Anne-mariesharp,Anne-mariesharp,Microbial taxa fold-changes (V3/V1) in EpiCor total cohort,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:28870194/6/1,28870194,randomized controlled trial,28870194,10.1186/s12906-017-1948-0,NA,"Pinheiro I., Robinson L., Verhelst A., Marzorati M., Winkens B., den Abbeele P.V. , Possemiers S.",A yeast fermentate improves gastrointestinal discomfort and constipation by modulation of the gut microbiome: results from a randomized double-blind placebo-controlled pilot trial,BMC complementary and alternative medicine,2017,"Bacteroides, Bacteroidetes, Constipation, EpiCor fermentate, GI transit time, Gastrointestinal discomfort, Gut microbiome, Human study, Prevotella, Saccharomyces cerevisiae",Experiment 6,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Placebo Severe subgroup V1(Visit 1),Placebo Severe subgroup V2(Visit 2),A subgroup of participants with severe symptoms of gastrointestinal discomfort and constipation at visit 2 (3-weeks after treatment) who received the corresponding testing product (Placebo),27,27,2 months,16S,56,Illumina,relative abundances,ANOVA,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Additional file 8,19 April 2025,Anne-mariesharp,Anne-mariesharp,Microbial taxa fold-changes (V2/V1) in Severe subgroup (Placebo),increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",1783272|1239|909932|1843488|909930;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|572511;1783272|1239|909932|1843489|31977;1783272|1239|909932|1843489|31977|39948,Complete,Svetlana up
bsdb:28870194/6/2,28870194,randomized controlled trial,28870194,10.1186/s12906-017-1948-0,NA,"Pinheiro I., Robinson L., Verhelst A., Marzorati M., Winkens B., den Abbeele P.V. , Possemiers S.",A yeast fermentate improves gastrointestinal discomfort and constipation by modulation of the gut microbiome: results from a randomized double-blind placebo-controlled pilot trial,BMC complementary and alternative medicine,2017,"Bacteroides, Bacteroidetes, Constipation, EpiCor fermentate, GI transit time, Gastrointestinal discomfort, Gut microbiome, Human study, Prevotella, Saccharomyces cerevisiae",Experiment 6,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Placebo Severe subgroup V1(Visit 1),Placebo Severe subgroup V2(Visit 2),A subgroup of participants with severe symptoms of gastrointestinal discomfort and constipation at visit 2 (3-weeks after treatment) who received the corresponding testing product (Placebo),27,27,2 months,16S,56,Illumina,relative abundances,ANOVA,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Additional file 8,19 April 2025,Anne-mariesharp,Anne-mariesharp,Microbial taxa fold-changes (V2/V1) in Severe subgroup (Placebo),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:28870194/7/1,28870194,randomized controlled trial,28870194,10.1186/s12906-017-1948-0,NA,"Pinheiro I., Robinson L., Verhelst A., Marzorati M., Winkens B., den Abbeele P.V. , Possemiers S.",A yeast fermentate improves gastrointestinal discomfort and constipation by modulation of the gut microbiome: results from a randomized double-blind placebo-controlled pilot trial,BMC complementary and alternative medicine,2017,"Bacteroides, Bacteroidetes, Constipation, EpiCor fermentate, GI transit time, Gastrointestinal discomfort, Gut microbiome, Human study, Prevotella, Saccharomyces cerevisiae",Experiment 7,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Placebo Severe subgroup V1(Visit 1),Placebo Severe subgroup V3(Visit 3),A sub group of participants with severe symptoms of gastrointestinal discomfort and constipation at visit 3 (6-weeks after treatment) who received the corresponding testing product (Placebo),27,27,2 months,16S,56,Illumina,relative abundances,ANOVA,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Additional file 8,19 April 2025,Anne-mariesharp,Anne-mariesharp,Microbial taxa fold-changes (V3/V1) in Severe subgroup (Placebo),increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",1783272|1239|909932|1843488|909930;1783272|1239|909932|1843488|909930|904;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|1263;1783272|1239|909932|1843489|31977|39948,Complete,Svetlana up
bsdb:28870194/7/2,28870194,randomized controlled trial,28870194,10.1186/s12906-017-1948-0,NA,"Pinheiro I., Robinson L., Verhelst A., Marzorati M., Winkens B., den Abbeele P.V. , Possemiers S.",A yeast fermentate improves gastrointestinal discomfort and constipation by modulation of the gut microbiome: results from a randomized double-blind placebo-controlled pilot trial,BMC complementary and alternative medicine,2017,"Bacteroides, Bacteroidetes, Constipation, EpiCor fermentate, GI transit time, Gastrointestinal discomfort, Gut microbiome, Human study, Prevotella, Saccharomyces cerevisiae",Experiment 7,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Placebo Severe subgroup V1(Visit 1),Placebo Severe subgroup V3(Visit 3),A sub group of participants with severe symptoms of gastrointestinal discomfort and constipation at visit 3 (6-weeks after treatment) who received the corresponding testing product (Placebo),27,27,2 months,16S,56,Illumina,relative abundances,ANOVA,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Additional file 8,19 April 2025,Anne-mariesharp,Anne-mariesharp,Microbial taxa fold-changes (V3/V1) in Severe subgroup (Placebo),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:28870194/8/1,28870194,randomized controlled trial,28870194,10.1186/s12906-017-1948-0,NA,"Pinheiro I., Robinson L., Verhelst A., Marzorati M., Winkens B., den Abbeele P.V. , Possemiers S.",A yeast fermentate improves gastrointestinal discomfort and constipation by modulation of the gut microbiome: results from a randomized double-blind placebo-controlled pilot trial,BMC complementary and alternative medicine,2017,"Bacteroides, Bacteroidetes, Constipation, EpiCor fermentate, GI transit time, Gastrointestinal discomfort, Gut microbiome, Human study, Prevotella, Saccharomyces cerevisiae",Experiment 8,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,EpiCor Severe subgroup V1(Visit 1),EpiCor Severe subgroup V2(Visit 2),A subgroup of participants with severe symptoms of gastrointestinal discomfort and constipation at visit 2 (3-weeks after treatment) who received the corresponding testing product (EpiCor fermentate),27,27,2 months,16S,56,Illumina,relative abundances,ANOVA,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Additional file 8,19 April 2025,Anne-mariesharp,Anne-mariesharp,Microbial taxa fold-changes (V2/V1) in Severe subgroup (EpiCor),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes",3379134|976|200643|171549|815|816;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|207244,Complete,Svetlana up
bsdb:28870194/8/2,28870194,randomized controlled trial,28870194,10.1186/s12906-017-1948-0,NA,"Pinheiro I., Robinson L., Verhelst A., Marzorati M., Winkens B., den Abbeele P.V. , Possemiers S.",A yeast fermentate improves gastrointestinal discomfort and constipation by modulation of the gut microbiome: results from a randomized double-blind placebo-controlled pilot trial,BMC complementary and alternative medicine,2017,"Bacteroides, Bacteroidetes, Constipation, EpiCor fermentate, GI transit time, Gastrointestinal discomfort, Gut microbiome, Human study, Prevotella, Saccharomyces cerevisiae",Experiment 8,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,EpiCor Severe subgroup V1(Visit 1),EpiCor Severe subgroup V2(Visit 2),A subgroup of participants with severe symptoms of gastrointestinal discomfort and constipation at visit 2 (3-weeks after treatment) who received the corresponding testing product (EpiCor fermentate),27,27,2 months,16S,56,Illumina,relative abundances,ANOVA,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Additional file 8,19 April 2025,Anne-mariesharp,Anne-mariesharp,Microbial taxa fold-changes (V2/V1) in Severe subgroup (EpiCor),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171550,Complete,Svetlana up
bsdb:28870194/9/1,28870194,randomized controlled trial,28870194,10.1186/s12906-017-1948-0,NA,"Pinheiro I., Robinson L., Verhelst A., Marzorati M., Winkens B., den Abbeele P.V. , Possemiers S.",A yeast fermentate improves gastrointestinal discomfort and constipation by modulation of the gut microbiome: results from a randomized double-blind placebo-controlled pilot trial,BMC complementary and alternative medicine,2017,"Bacteroides, Bacteroidetes, Constipation, EpiCor fermentate, GI transit time, Gastrointestinal discomfort, Gut microbiome, Human study, Prevotella, Saccharomyces cerevisiae",Experiment 9,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,EpiCor Severe subgroup V1(Visit 1),EpiCor Severe subgroup V3 (Visit 3),A sub group of participants with severe symptoms of gastrointestinal discomfort and constipation at visit 3 (6-weeks after treatment) who received the corresponding testing product (EpiCor fermentate),27,27,2 months,16S,56,Illumina,relative abundances,ANOVA,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Additional file 8,19 April 2025,Anne-mariesharp,Anne-mariesharp,Microbial taxa fold-changes (V3/V1) in Severe subgroup (EpiCor),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:28870194/9/2,28870194,randomized controlled trial,28870194,10.1186/s12906-017-1948-0,NA,"Pinheiro I., Robinson L., Verhelst A., Marzorati M., Winkens B., den Abbeele P.V. , Possemiers S.",A yeast fermentate improves gastrointestinal discomfort and constipation by modulation of the gut microbiome: results from a randomized double-blind placebo-controlled pilot trial,BMC complementary and alternative medicine,2017,"Bacteroides, Bacteroidetes, Constipation, EpiCor fermentate, GI transit time, Gastrointestinal discomfort, Gut microbiome, Human study, Prevotella, Saccharomyces cerevisiae",Experiment 9,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,EpiCor Severe subgroup V1(Visit 1),EpiCor Severe subgroup V3 (Visit 3),A sub group of participants with severe symptoms of gastrointestinal discomfort and constipation at visit 3 (6-weeks after treatment) who received the corresponding testing product (EpiCor fermentate),27,27,2 months,16S,56,Illumina,relative abundances,ANOVA,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Additional file 8,19 April 2025,Anne-mariesharp,Anne-mariesharp,Microbial taxa fold-changes (V3/V1) in Severe subgroup (EpiCor),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota",3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572;1783272|1239,Complete,Svetlana up
bsdb:28870194/10/1,28870194,randomized controlled trial,28870194,10.1186/s12906-017-1948-0,NA,"Pinheiro I., Robinson L., Verhelst A., Marzorati M., Winkens B., den Abbeele P.V. , Possemiers S.",A yeast fermentate improves gastrointestinal discomfort and constipation by modulation of the gut microbiome: results from a randomized double-blind placebo-controlled pilot trial,BMC complementary and alternative medicine,2017,"Bacteroides, Bacteroidetes, Constipation, EpiCor fermentate, GI transit time, Gastrointestinal discomfort, Gut microbiome, Human study, Prevotella, Saccharomyces cerevisiae",Experiment 10,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Placebo moderate subgroup V1 (Visit 1),Placebo moderate subgroup V3 (Visit 3),A subgroup of participants with moderate symptoms of gastrointestinal discomfort and constipation at visit 3 (6-weeks after treatment) who received the corresponding testing product (placebo),13,13,2 months,16S,56,Illumina,relative abundances,ANOVA,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Additional file 9,21 April 2025,Tosin,Tosin,Microbial taxa fold-changes (V3/V1) in Placebo moderate subgroup,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:28870194/10/2,28870194,randomized controlled trial,28870194,10.1186/s12906-017-1948-0,NA,"Pinheiro I., Robinson L., Verhelst A., Marzorati M., Winkens B., den Abbeele P.V. , Possemiers S.",A yeast fermentate improves gastrointestinal discomfort and constipation by modulation of the gut microbiome: results from a randomized double-blind placebo-controlled pilot trial,BMC complementary and alternative medicine,2017,"Bacteroides, Bacteroidetes, Constipation, EpiCor fermentate, GI transit time, Gastrointestinal discomfort, Gut microbiome, Human study, Prevotella, Saccharomyces cerevisiae",Experiment 10,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Placebo moderate subgroup V1 (Visit 1),Placebo moderate subgroup V3 (Visit 3),A subgroup of participants with moderate symptoms of gastrointestinal discomfort and constipation at visit 3 (6-weeks after treatment) who received the corresponding testing product (placebo),13,13,2 months,16S,56,Illumina,relative abundances,ANOVA,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Additional file 9,21 April 2025,Tosin,Tosin,Microbial taxa fold-changes (V3/V1) in Placebo moderate subgroup,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|976|200643|171549|2005519|397864;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:28870194/11/1,28870194,randomized controlled trial,28870194,10.1186/s12906-017-1948-0,NA,"Pinheiro I., Robinson L., Verhelst A., Marzorati M., Winkens B., den Abbeele P.V. , Possemiers S.",A yeast fermentate improves gastrointestinal discomfort and constipation by modulation of the gut microbiome: results from a randomized double-blind placebo-controlled pilot trial,BMC complementary and alternative medicine,2017,"Bacteroides, Bacteroidetes, Constipation, EpiCor fermentate, GI transit time, Gastrointestinal discomfort, Gut microbiome, Human study, Prevotella, Saccharomyces cerevisiae",Experiment 11,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,EpiCor Moderate subgroup V1(Visit 1),EpiCor Moderate subgroup V2(Visit 2),A subgroup of participants with moderate symptoms of gastrointestinal discomfort and constipation at visit 2 (3-weeks after treatment) who received the corresponding testing product (EpiCor fermentate),12,12,2 months,16S,56,Illumina,relative abundances,ANOVA,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Additional file 9,21 April 2025,Tosin,Tosin,Microbial taxa fold-changes (V2/V1) in Epicor moderate subgroup,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:28870194/11/2,28870194,randomized controlled trial,28870194,10.1186/s12906-017-1948-0,NA,"Pinheiro I., Robinson L., Verhelst A., Marzorati M., Winkens B., den Abbeele P.V. , Possemiers S.",A yeast fermentate improves gastrointestinal discomfort and constipation by modulation of the gut microbiome: results from a randomized double-blind placebo-controlled pilot trial,BMC complementary and alternative medicine,2017,"Bacteroides, Bacteroidetes, Constipation, EpiCor fermentate, GI transit time, Gastrointestinal discomfort, Gut microbiome, Human study, Prevotella, Saccharomyces cerevisiae",Experiment 11,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,EpiCor Moderate subgroup V1(Visit 1),EpiCor Moderate subgroup V2(Visit 2),A subgroup of participants with moderate symptoms of gastrointestinal discomfort and constipation at visit 2 (3-weeks after treatment) who received the corresponding testing product (EpiCor fermentate),12,12,2 months,16S,56,Illumina,relative abundances,ANOVA,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Additional file 9,21 April 2025,Tosin,Tosin,Microbial taxa fold-changes (V2/V1) in Epicor moderate subgroup,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263,Complete,Svetlana up
bsdb:28870194/12/1,28870194,randomized controlled trial,28870194,10.1186/s12906-017-1948-0,NA,"Pinheiro I., Robinson L., Verhelst A., Marzorati M., Winkens B., den Abbeele P.V. , Possemiers S.",A yeast fermentate improves gastrointestinal discomfort and constipation by modulation of the gut microbiome: results from a randomized double-blind placebo-controlled pilot trial,BMC complementary and alternative medicine,2017,"Bacteroides, Bacteroidetes, Constipation, EpiCor fermentate, GI transit time, Gastrointestinal discomfort, Gut microbiome, Human study, Prevotella, Saccharomyces cerevisiae",Experiment 12,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,EpiCor Moderate subgroup V1(Visit 1),EpiCor Moderate subgroup V3(Visit 3),A subgroup of participants with moderate symptoms of gastrointestinal discomfort and constipation at visit 3 (6-weeks after treatment) who received the corresponding testing product (EpiCor fermentate),12,12,2 months,16S,56,Illumina,relative abundances,ANOVA,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Additional file 9,21 April 2025,Tosin,Tosin,Microbial taxa fold-changes (V3/V1) in Epicor moderate subgroup,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|74201|203494|48461|1647988|239934;1783272|201174|84998|84999|84107;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:28870194/12/2,28870194,randomized controlled trial,28870194,10.1186/s12906-017-1948-0,NA,"Pinheiro I., Robinson L., Verhelst A., Marzorati M., Winkens B., den Abbeele P.V. , Possemiers S.",A yeast fermentate improves gastrointestinal discomfort and constipation by modulation of the gut microbiome: results from a randomized double-blind placebo-controlled pilot trial,BMC complementary and alternative medicine,2017,"Bacteroides, Bacteroidetes, Constipation, EpiCor fermentate, GI transit time, Gastrointestinal discomfort, Gut microbiome, Human study, Prevotella, Saccharomyces cerevisiae",Experiment 12,Belgium,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,EpiCor Moderate subgroup V1(Visit 1),EpiCor Moderate subgroup V3(Visit 3),A subgroup of participants with moderate symptoms of gastrointestinal discomfort and constipation at visit 3 (6-weeks after treatment) who received the corresponding testing product (EpiCor fermentate),12,12,2 months,16S,56,Illumina,relative abundances,ANOVA,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Additional file 9,21 April 2025,Tosin,Tosin,Microbial taxa fold-changes (V3/V1) in Epicor moderate subgroup,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:28875948/1/1,28875948,case-control,28875948,10.1088/1752-7163/aa7c24,NA,"Seerangaiyan K., van Winkelhoff A.J., Harmsen H.J.M., Rossen J.W.A. , Winkel E.G.",The tongue microbiome in healthy subjects and patients with intra-oral halitosis,Journal of breath research,2017,NA,Experiment 1,Netherlands,Homo sapiens,Superior surface of tongue,UBERON:0007371,Halitosis,HP:0100812,Control,Oral Halitosis,"IOH patient group was selected based on an organoleptic score of >= 2 from the mouth and nose =< 1, having a VSC level > 160 ppb, and H2S > 4 nmol/ L (96 ppb) and CH3SH > 0.5 nmol/L (12 ppb) and a DPSI of =< 2",5,10,3 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Phyu Han,WikiWorks,Significant differentially abundant OTU of intr-aoral halitosis and Control,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|1224|1236|135625|712|416916|739;3379134|29547|3031852|213849|72294|194;3379134|976|200643|171549|2005525|195950;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3082720|186804|1257;1783272|1239|909932|909929|1843491|970;3384189|32066|203490|203491|1129771|32067;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|186802;1783272|1239|1737404|1737405|1570339|543311;3379134|203691|203692|136|2845253|157;3379134|976|117743|200644|49546|1016;3379134|1224|1236|135625|712|416916;3379134|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
bsdb:28875948/1/2,28875948,case-control,28875948,10.1088/1752-7163/aa7c24,NA,"Seerangaiyan K., van Winkelhoff A.J., Harmsen H.J.M., Rossen J.W.A. , Winkel E.G.",The tongue microbiome in healthy subjects and patients with intra-oral halitosis,Journal of breath research,2017,NA,Experiment 1,Netherlands,Homo sapiens,Superior surface of tongue,UBERON:0007371,Halitosis,HP:0100812,Control,Oral Halitosis,"IOH patient group was selected based on an organoleptic score of >= 2 from the mouth and nose =< 1, having a VSC level > 160 ppb, and H2S > 4 nmol/ L (96 ppb) and CH3SH > 0.5 nmol/L (12 ppb) and a DPSI of =< 2",5,10,3 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Phyu Han,"Merit,WikiWorks",Significant differentially abundant OTU of intra-oral halitosis and Control,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",3379134|1224|1236|135625|712|416916;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712|724|729;1783272|1239|186801|3085636|186803|437755;1783272|1239|186801|3085636|186803|265975;3379134|976|200643|171549|171552|838;1783272|201174|1760|85006|1268|32207|2047;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|186807|2740;3384189|32066|203490|203491|1129771|32067,Complete,Shaimaa Elsafoury
bsdb:28891262/1/1,28891262,case-control,28891262,10.1111/ene.13398,NA,"Mertsalmi T.H., Aho V.T.E., Pereira P.A.B., Paulin L., Pekkonen E., Auvinen P. , Scheperjans F.",More than constipation - bowel symptoms in Parkinson's disease and their connection to gut microbiota,European journal of neurology,2017,"Parkinson's disease, constipation, irritable bowel syndrome, microbiota, non-motor symptoms",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Irritable Bowel Syndrome negative (IBS-),Irritable Bowel Syndrome positive (IBS+),Parkinson’s Disease patients with Irritable Bowel Syndrome (IBS)-like symptoms.,56,18,1 month,16S,123,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,"body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,18 April 2024,Abiola-Salako,"Abiola-Salako,WikiWorks",Bacteria with significant differences in relative abundance between PD Patients with or without IBS-like symptoms,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|976|200643|171549|815|816;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552,Complete,ChiomaBlessing
bsdb:28903182/1/1,28903182,case-control,28903182,10.1016/j.biopha.2017.08.101,NA,"Ishaq H.M., Mohammad I.S., Guo H., Shahzad M., Hou Y.J., Ma C., Naseem Z., Wu X., Shi P. , Xu J.",Molecular estimation of alteration in intestinal microbial composition in Hashimoto's thyroiditis patients,Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie,2017,"DGGE, Gut microbiota, Hashimoto’s thyroiditis, Hyporthyroidism, Pyrosequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Hashimoto's thyroiditis,EFO:0003779,healthy controls,hashimoto's thyroiditis patients,"The Thyroid stimulating hormone(TSH) was higher than 5 μIU/ml, T4 was lower than 4.2 μg/dl, T3 was lower than 0.78 ng/ml, anti-thyroid peroxidase antibodies level was higher than 15 IU/ml, and anti-thyroglobulin antibodies was more than 30%",12,29,2 months,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,unchanged,Signature 1,Table 7,10 January 2021,Rimsha Azhar,WikiWorks,Hashimoto's thyroid gut microbial phylotypes from pyrosequencing,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus flavefaciens,1783272|1239|186801|186802|216572|1263|1265,Complete,NA
bsdb:28903182/1/2,28903182,case-control,28903182,10.1016/j.biopha.2017.08.101,NA,"Ishaq H.M., Mohammad I.S., Guo H., Shahzad M., Hou Y.J., Ma C., Naseem Z., Wu X., Shi P. , Xu J.",Molecular estimation of alteration in intestinal microbial composition in Hashimoto's thyroiditis patients,Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie,2017,"DGGE, Gut microbiota, Hashimoto’s thyroiditis, Hyporthyroidism, Pyrosequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Hashimoto's thyroiditis,EFO:0003779,healthy controls,hashimoto's thyroiditis patients,"The Thyroid stimulating hormone(TSH) was higher than 5 μIU/ml, T4 was lower than 4.2 μg/dl, T3 was lower than 0.78 ng/ml, anti-thyroid peroxidase antibodies level was higher than 15 IU/ml, and anti-thyroglobulin antibodies was more than 30%",12,29,2 months,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,unchanged,Signature 2,Table 7,10 January 2021,Rimsha Azhar,WikiWorks,Hashimoto's thyroid gut microbial phylotypes from pyrosequencing,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,1783272|1239|91061|186826|33958|1578|1596,Complete,NA
bsdb:28903469/1/1,28903469,prospective cohort,28903469,10.1093/femsec/fix099,NA,"Tanaka M., Korenori Y., Washio M., Kobayashi T., Momoda R., Kiyohara C., Kuroda A., Saito Y., Sonomoto K. , Nakayama J.",Signatures in the gut microbiota of Japanese infants who developed food allergies in early childhood,FEMS microbiology ecology,2017,"16S rRNA gene, Clostridium, fecal microbiota, food allergies, infant",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,non-allergy,infant with food allergy,infant with food allergy,27,14,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2, text",10 January 2021,Lucy Mellor,WikiWorks,Relative abundance of gut microbiota of infants at 2 months of age in food allergy (FA) and non-allergy (NA) groups,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|91061|186826|33958|1243;1783272|1239|91061|186826|33958|46255;1783272|1239|909932|1843489|31977|29465,Complete,NA
bsdb:28903469/1/2,28903469,prospective cohort,28903469,10.1093/femsec/fix099,NA,"Tanaka M., Korenori Y., Washio M., Kobayashi T., Momoda R., Kiyohara C., Kuroda A., Saito Y., Sonomoto K. , Nakayama J.",Signatures in the gut microbiota of Japanese infants who developed food allergies in early childhood,FEMS microbiology ecology,2017,"16S rRNA gene, Clostridium, fecal microbiota, food allergies, infant",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,non-allergy,infant with food allergy,infant with food allergy,27,14,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 4c, text",10 January 2021,Lucy Mellor,WikiWorks,Relative abundances of genera in infants at 1 year of age which were statistically signficant differences between the food allergy (FA) and non-allergy (NA) groups,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",3379134|1224|1236|91347|543;1783272|1239|186801|186802|31979|1485,Complete,NA
bsdb:28923537/1/1,28923537,prospective cohort,28923537,10.1016/j.neo.2017.08.004,https://pubmed.ncbi.nlm.nih.gov/28923537/,"Frankel A.E., Coughlin L.A., Kim J., Froehlich T.W., Xie Y., Frenkel E.P. , Koh A.Y.",Metagenomic Shotgun Sequencing and Unbiased Metabolomic Profiling Identify Specific Human Gut Microbiota and Metabolites Associated with Immune Checkpoint Therapy Efficacy in Melanoma Patients,"Neoplasia (New York, N.Y.)",2017,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non responders (Progressive disease),Responders,"Twenty-four patients showed RECIST response (19, 49%) or stable (5, 13%) disease to ICT, what we classify as responders in this study",16,23,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2, text",30 August 2022,Sharmilac,"Sharmilac,Aiyshaaaa,WikiWorks","MSS identifies specific bacterial species that are enriched in the gut microbiomes of melanoma patients who are responding to ICT therapy. Relative abundance of gut bacterial taxa as determined by MetaPhlAn analysis of MSS data generated from fecal specimens collected from melanoma patients prior to receiving ipilimumab/nivolumab, pembrolizumab, ipilimumab alone, or nivolumab alone.Differential taxonomic abundance was analyzed by linear discriminate analysis coupled with effect size measurements (LEfSe) projected as a histogram (A, C and E) or cladrogram (B, D and F). All listed bacterial groups were significantly (P b .05, Kruskal-Wallis test) enriched for their respective groups (responder versus progressive).",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania filiformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis",3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|818;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|186802|216572|216851|853;1783272|1239|526524|526525|128827|61170|61171;1783272|1239|91061|186826|1300|1301|1318,Complete,Peace Sandy
bsdb:28923537/1/2,28923537,prospective cohort,28923537,10.1016/j.neo.2017.08.004,https://pubmed.ncbi.nlm.nih.gov/28923537/,"Frankel A.E., Coughlin L.A., Kim J., Froehlich T.W., Xie Y., Frenkel E.P. , Koh A.Y.",Metagenomic Shotgun Sequencing and Unbiased Metabolomic Profiling Identify Specific Human Gut Microbiota and Metabolites Associated with Immune Checkpoint Therapy Efficacy in Melanoma Patients,"Neoplasia (New York, N.Y.)",2017,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non responders (Progressive disease),Responders,"Twenty-four patients showed RECIST response (19, 49%) or stable (5, 13%) disease to ICT, what we classify as responders in this study",16,23,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2, text",16 April 2023,Sharmilac,"Sharmilac,Peace Sandy,WikiWorks","MSS identifies specific bacterial species that are enriched in the gut microbiomes of melanoma patients who are responding to ICT therapy. Relative abundance of gut bacterial taxa as determined by MetaPhlAn analysis of MSS data generated from fecal specimens collected from melanoma patients prior to receiving ipilimumab/nivolumab, pembrolizumab, ipilimumab alone, or nivolumab alone.Differential taxonomic abundance was analyzed by linear discriminate analysis coupled with effect size measurements (LEfSe) projected as a histogram (A, C and E) or cladrogram (B, D and F). All listed bacterial groups were significantly (P b .05, Kruskal-Wallis test) enriched for their respective groups (responder versus progressive).",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces viscosus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc gasicomitatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc mesenteroides,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia exigua,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus",1783272|201174|1760|2037|2049|1654|1656;1783272|1239|1737404|1737405|1570339|165779|33037;3379134|976|200643|171549|815|816|28111;1783272|1239|91061|186826|33958|1578|1596;1783272|201174|84998|84999|1643824|2767353|1382;1783272|1239|91061|186826|33958|1243|115778;1783272|1239|91061|186826|33958|1243|1245;1783272|1239|1737404|1737405|1570339|162289;1783272|201174|1760|2037|2049|2529408|1660;1783272|201174|84998|1643822|1643826|84108|84109;1783272|1239|91061|186826|1300|1301|102684;1783272|1239|91061|186826|1300|1301|1309;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|1239|909932|1843488|909930;1783272|201174|84998|84999|1643824|1380;1783272|201174|1760|2037;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294;1783272|201174|1760|2037|2049|1654;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958;1783272|1239|1737404|1737405|1570339|162289,Complete,Peace Sandy
bsdb:28924229/1/1,28924229,case-control,28924229,10.1038/s41598-017-11779-9,NA,"Zhao H., Chu M., Huang Z., Yang X., Ran S., Hu B., Zhang C. , Liang J.",Variations in oral microbiota associated with oral cancer,Scientific reports,2017,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Oral squamous cell carcinoma,EFO:0000199,Controls,oral squamous cell carcinoma (OSCC),"subjects with oral squamous cell carcinoma and did not have detectable periodontal inflammation, visible carious lesions, oral mucosa disease or any sever systemic disorders such as diabetes, immune compromise or genetic diseases",40,40,2 weeks,16S,45,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,unchanged,NA,NA,Signature 1,"Figure 1c, Figure 3b, 3c, Text",10 January 2021,Utsav Patel,WikiWorks,Variations in oral microbiota associated with oral cancer,increased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota,k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Spirochaetota",1783272|544448|31969|2085|2092|2093;3379134|203691|203692|136|2845253|157;3379134|29547|3031852|213849|72294|194;3379134|1224|28216|206351|481|538;1783272|1239|909932|909929|1843491|82202;3379134|976|200643|171549|171552|1283313;3384189|32066|203490|203491|203492|848;1783272|1239|909932|909929|1843491|970;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3082720|186804|1257;1783272|1239|186801|3082720|3118655|44259;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3085636|186803|43996;1783272|1239|1737404|1737405|1570339|543311;3379134|976|117743|200644|49546|1016;1783272|1239|186801|3082720|186804;1783272|1239|186801|3085636|186803;3379134|976;3384189|32066;3379134|203691,Complete,Rimsha Azhar
bsdb:28924229/1/2,28924229,case-control,28924229,10.1038/s41598-017-11779-9,NA,"Zhao H., Chu M., Huang Z., Yang X., Ran S., Hu B., Zhang C. , Liang J.",Variations in oral microbiota associated with oral cancer,Scientific reports,2017,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Oral squamous cell carcinoma,EFO:0000199,Controls,oral squamous cell carcinoma (OSCC),"subjects with oral squamous cell carcinoma and did not have detectable periodontal inflammation, visible carious lesions, oral mucosa disease or any sever systemic disorders such as diabetes, immune compromise or genetic diseases",40,40,2 weeks,16S,45,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,unchanged,NA,NA,Signature 2,"Figure 1c, Figure 3b, 3c, Text",10 January 2021,Utsav Patel,WikiWorks,Variations in oral microbiota associated with oral cancer,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota",1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3085636|186803|1213720;1783272|1239|91061|186826|186828|117563;3379134|1224|28216|80840|119060|47670;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|1300|1301;1783272|201174|1760|85004|31953|196081;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|2037|2049|1654;1783272|201174;1783272|1239,Complete,Rimsha Azhar
bsdb:28932201/1/1,28932201,"cross-sectional observational, not case-control",28932201,10.3389/fphys.2017.00675,NA,"Zheng J., Xiao X., Zhang Q., Mao L., Yu M., Xu J. , Wang T.",The Placental Microbiota Is Altered among Subjects with Gestational Diabetes Mellitus: A Pilot Study,Frontiers in physiology,2017,"16S rRNA gene, clinical characteristics, gestational diabetes mellitus, microbiota, placenta",Experiment 1,China,Homo sapiens,Uterus,UBERON:0000995,Gestational diabetes,EFO:0004593,controls,Gestational diabetes mellitus,"GDM was diagnosed when the fasting plasma glucose ≥5.1 mmol/L or 1 h post-OGTT glycemia ≥10.0 mmol/L or 2 h post-OGTT glycemia ≥8.5 mmol/L, according to the criteria set by International Association of Diabetes and Pregnancy Study Groups (IADPSG)",10,10,9 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 2+ Figure 4+ Supplemental Table S2,10 January 2021,Fatima Zohra,WikiWorks,Phlotypes in placental microbiota significantly different between GDM and NDM groups,increased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Thauera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae",3379134|1224;3379134|1224|28216|206389|2008794|33057;3379134|1224|28216|80840;3379134|1224|28211|356;3379134|1224|28216|80840|506,Complete,Shaimaa Elsafoury
bsdb:28932201/1/2,28932201,"cross-sectional observational, not case-control",28932201,10.3389/fphys.2017.00675,NA,"Zheng J., Xiao X., Zhang Q., Mao L., Yu M., Xu J. , Wang T.",The Placental Microbiota Is Altered among Subjects with Gestational Diabetes Mellitus: A Pilot Study,Frontiers in physiology,2017,"16S rRNA gene, clinical characteristics, gestational diabetes mellitus, microbiota, placenta",Experiment 1,China,Homo sapiens,Uterus,UBERON:0000995,Gestational diabetes,EFO:0004593,controls,Gestational diabetes mellitus,"GDM was diagnosed when the fasting plasma glucose ≥5.1 mmol/L or 1 h post-OGTT glycemia ≥10.0 mmol/L or 2 h post-OGTT glycemia ≥8.5 mmol/L, according to the criteria set by International Association of Diabetes and Pregnancy Study Groups (IADPSG)",10,10,9 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 2+ Figure 4+ Supplemental Table S2,10 January 2021,Fatima Zohra,WikiWorks,Phlotypes in placental microbiota significantly different between GDM and NDM groups,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Armatimonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Brevibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Sulfuricellaceae|g__Sulfuricella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Dyella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Pseudomonadati|p__Acidobacteriota|c__Holophagae|o__Holophagales,k__Pseudomonadati|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales,k__Pseudomonadati|p__Ignavibacteriota|c__Ignavibacteria|o__Ignavibacteriales,k__Pseudomonadati|p__Chlorobiota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Acidobacteriota|c__Holophagae|o__Holophagales|f__Holophagaceae|g__Geothrix,k__Pseudomonadati|p__Ignavibacteriota|c__Ignavibacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae",3379134|976;1783272|67819;1783272|1239|91061|1385|186822|55080;3379134|1224|28216|32003|2772226|935200;1783272|1239|91061|186826|33958|1578;3379134|1224|1236|135614|1775411|231454;3379134|976|200643|171549;1783272|1239|526524|526525;3379134|57723|533205|574975;3379134|1224|2008785|119069;3379134|1134404|795747|795748;3379134|1090;3379134|976|200643;3379134|57723|533205|574975|574976|44675;3379134|1134404|795747;1783272|1239|91061|186826|33958;3379134|1224|2008785|119069|206349;1783272|1239|91061|1385|186822,Complete,Shaimaa Elsafoury
bsdb:28944067/1/1,28944067,case-control,28944067,10.1136/bmjgast-2017-000145,NA,"Hibberd A.A., Lyra A., Ouwehand A.C., Rolny P., Lindegren H., Cedgård L. , Wettergren Y.",Intestinal microbiota is altered in patients with colon cancer and modified by probiotic intervention,BMJ open gastroenterology,2017,"COLORECTAL CANCER, INTESTINAL MICROBIOLOGY, PROBIOTICS, TUMOUR MARKERS",Experiment 1,Sweden,Homo sapiens,Mucosa of ascending colon,UBERON:0004990,Colorectal cancer,EFO:0005842,control group,colon cancer patients,patients diagnosed with stage I-III colon cancer,14,12,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,"Table 2, supplemental table S1",10 January 2021,Fatima Zohra,"Fatima,Claregrieve1,WikiWorks",Microbiota alterations in colon cancer mucosa samples compared with non cancer control mucosa at colonoscopy,increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Methanobacteriati|p__Methanobacteriota,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Mycoplasmatota",3379134|976;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|31979|1485;1783272|1239|909932|1843489|31977|39948;3366610|28890;3384189|32066;3384189|32066|203490|203491|203492|848;3366610|28890|183925|2158|2159|2172;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|3082720|186804|1257;1783272|544448,Complete,Claregrieve1
bsdb:28944067/1/2,28944067,case-control,28944067,10.1136/bmjgast-2017-000145,NA,"Hibberd A.A., Lyra A., Ouwehand A.C., Rolny P., Lindegren H., Cedgård L. , Wettergren Y.",Intestinal microbiota is altered in patients with colon cancer and modified by probiotic intervention,BMJ open gastroenterology,2017,"COLORECTAL CANCER, INTESTINAL MICROBIOLOGY, PROBIOTICS, TUMOUR MARKERS",Experiment 1,Sweden,Homo sapiens,Mucosa of ascending colon,UBERON:0004990,Colorectal cancer,EFO:0005842,control group,colon cancer patients,patients diagnosed with stage I-III colon cancer,14,12,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 2,"Table 2, supplemental table S1",10 January 2021,Fatima Zohra,"Fatima,Claregrieve1,WikiWorks",Microbiota alterations in colon cancer mucosa compared with non cancer control mucosa at colonoscopy,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:28944067/2/1,28944067,case-control,28944067,10.1136/bmjgast-2017-000145,NA,"Hibberd A.A., Lyra A., Ouwehand A.C., Rolny P., Lindegren H., Cedgård L. , Wettergren Y.",Intestinal microbiota is altered in patients with colon cancer and modified by probiotic intervention,BMJ open gastroenterology,2017,"COLORECTAL CANCER, INTESTINAL MICROBIOLOGY, PROBIOTICS, TUMOUR MARKERS",Experiment 2,Sweden,Homo sapiens,Colon,UBERON:0001155,Colorectal cancer,EFO:0005842,control group,colon cancer patients (tumor samples),patients diagnosed with stage I-III colon cancer,14,12,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,"Table 2, supplemental table S1",10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Microbiota alterations in colon cancer tumor samples compared with non cancer control mucosa at colonoscopy,increased,"k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",3366610|28890|183925|2158|2159|2172;1783272|1239|186801|3082720|186804|1257;1783272|1239|909932|909929|1843491|970,Complete,Claregrieve1
bsdb:28944067/3/1,28944067,case-control,28944067,10.1136/bmjgast-2017-000145,NA,"Hibberd A.A., Lyra A., Ouwehand A.C., Rolny P., Lindegren H., Cedgård L. , Wettergren Y.",Intestinal microbiota is altered in patients with colon cancer and modified by probiotic intervention,BMJ open gastroenterology,2017,"COLORECTAL CANCER, INTESTINAL MICROBIOLOGY, PROBIOTICS, TUMOUR MARKERS",Experiment 3,Sweden,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,control group,colon cancer patients (fecal samples),patients diagnosed with stage I-III colon cancer,21,14,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Supppemental table S2, text",10 January 2021,Fatima Zohra,"Fatima,Claregrieve1,WikiWorks",Microbiota alterations in colon cancer fecal samples compared with non cancer control fecal samples at colonoscopy,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus",1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3082720|186804|1257,Complete,Claregrieve1
bsdb:28944067/3/2,28944067,case-control,28944067,10.1136/bmjgast-2017-000145,NA,"Hibberd A.A., Lyra A., Ouwehand A.C., Rolny P., Lindegren H., Cedgård L. , Wettergren Y.",Intestinal microbiota is altered in patients with colon cancer and modified by probiotic intervention,BMJ open gastroenterology,2017,"COLORECTAL CANCER, INTESTINAL MICROBIOLOGY, PROBIOTICS, TUMOUR MARKERS",Experiment 3,Sweden,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,control group,colon cancer patients (fecal samples),patients diagnosed with stage I-III colon cancer,21,14,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supppemental table S2,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Microbiota alterations in colon cancer fecal samples compared with non cancer control fecal samples at colonoscopy,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Mycoplasmatota",1783272|1239|186801|3085636|186803|841;1783272|544448,Complete,NA
bsdb:28968427/1/1,28968427,"cross-sectional observational, not case-control",28968427,10.1371/journal.pone.0185569,NA,"Brazier L., Elguero E., Koumavor C.K., Renaud N., Prugnolle F., Thomas F., Ategbo S., Engoba M., Obengui E.M., Leroy P., Durand F., Renaud P. , Becquart .",Evolution in fecal bacterial/viral composition in infants of two central African countries (Gabon and Republic of the Congo) during their first month of life,PloS one,2017,NA,Experiment 1,Gabon,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,vaginal delivery,two-day aged babies c-section,NA,7,8,NA,16S,3,Roche454,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,figure 4 &text,10 January 2021,Shaimaa Elsafoury,WikiWorks,"Signatures include bacterial genera with a read frequency higher than 5% in at least one child. Viruses were tested and not found in meconium samples. preterm, normal and postterm included",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina",3379134|1224|1236|91347|543|570;1783272|1239|186801|186802|31979|1266,Complete,Shaimaa Elsafoury
bsdb:28968427/3/1,28968427,"cross-sectional observational, not case-control",28968427,10.1371/journal.pone.0185569,NA,"Brazier L., Elguero E., Koumavor C.K., Renaud N., Prugnolle F., Thomas F., Ategbo S., Engoba M., Obengui E.M., Leroy P., Durand F., Renaud P. , Becquart .",Evolution in fecal bacterial/viral composition in infants of two central African countries (Gabon and Republic of the Congo) during their first month of life,PloS one,2017,NA,Experiment 3,Gabon,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,vaginal delivery,seven-day aged babies c-section,NA,7,8,NA,16S,3,Roche454,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,figure 4 &text,10 January 2021,Shaimaa Elsafoury,WikiWorks,"Signatures include bacterial genera with a read frequency higher than 5% in at least one child. Viruses were tested and not found in meconium samples. preterm, normal and postterm included",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina",3379134|1224|1236|91347|543|570;1783272|1239|186801|186802|31979|1266,Complete,Shaimaa Elsafoury
bsdb:28968427/4/1,28968427,"cross-sectional observational, not case-control",28968427,10.1371/journal.pone.0185569,NA,"Brazier L., Elguero E., Koumavor C.K., Renaud N., Prugnolle F., Thomas F., Ategbo S., Engoba M., Obengui E.M., Leroy P., Durand F., Renaud P. , Becquart .",Evolution in fecal bacterial/viral composition in infants of two central African countries (Gabon and Republic of the Congo) during their first month of life,PloS one,2017,NA,Experiment 4,Congo,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,vaginal delivery,seven-day aged babies c-section,NA,7,8,NA,16S,3,Roche454,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,figure 4 &text,10 January 2021,Shaimaa Elsafoury,WikiWorks,"Signatures include bacterial genera with a read frequency higher than 5% in at least one child. Viruses were tested and not found in meconium samples. preterm, normal and postterm included",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",3379134|976|200643|171549|815|816;1783272|201174|84998|84999|84107|102106,Complete,Shaimaa Elsafoury
bsdb:28970732/1/1,28970732,time series / longitudinal observational,28970732,10.3748/wjg.v23.i33.6164,NA,"Xie G., Zhou Q., Qiu C.Z., Dai W.K., Wang H.P., Li Y.H., Liao J.X., Lu X.G., Lin S.F., Ye J.H., Ma Z.Y. , Wang W.J.",Ketogenic diet poses a significant effect on imbalanced gut microbiota in infants with refractory epilepsy,World journal of gastroenterology,2017,"Cronobacter, Epilepsy, Gut microbiota, Ketogenic diet, Seizures",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Ketogenic diet,EFO:0009371,healthy controls,post-ketogenic diet (P2),pediatric patients with refractory epilepsy after ketogenic diet treatment,30,14,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 5,14 November 2024,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of P2 group compared to healthy controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Lactonifactor,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptoclostridiaceae|g__Peptoclostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",3379134|1224|1236|2887326|468|469;1783272|1239|91061|1385|186817|1386;1783272|1239|186801|186802|3085642|580596;3379134|1224|1236|91347|543|413496;1783272|201174|84998|1643822|1643826|84111;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|1300|1357;1783272|1239|186801|186802|31979|420345;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|3082720|3120161|1481960;3379134|1224|1236|72274|135621|286;1783272|1239|186801|186802|216572|1508657;1783272|1239|526524|526525|2810280|3025755,Complete,NA
bsdb:28970732/1/2,28970732,time series / longitudinal observational,28970732,10.3748/wjg.v23.i33.6164,NA,"Xie G., Zhou Q., Qiu C.Z., Dai W.K., Wang H.P., Li Y.H., Liao J.X., Lu X.G., Lin S.F., Ye J.H., Ma Z.Y. , Wang W.J.",Ketogenic diet poses a significant effect on imbalanced gut microbiota in infants with refractory epilepsy,World journal of gastroenterology,2017,"Cronobacter, Epilepsy, Gut microbiota, Ketogenic diet, Seizures",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Ketogenic diet,EFO:0009371,healthy controls,post-ketogenic diet (P2),pediatric patients with refractory epilepsy after ketogenic diet treatment,30,14,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Tables 4 & 5,15 November 2024,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of P2 group compared to healthy controls,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",1783272|201174|1760|2037|2049|1654;1783272|201174;1783272|201174|1760|85004|31953|1678;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|31979|1485;3379134|1224|1236|91347|543|561;1783272|1239|186801|186802|216572|216851;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|1506553,Complete,NA
bsdb:28970732/2/1,28970732,time series / longitudinal observational,28970732,10.3748/wjg.v23.i33.6164,NA,"Xie G., Zhou Q., Qiu C.Z., Dai W.K., Wang H.P., Li Y.H., Liao J.X., Lu X.G., Lin S.F., Ye J.H., Ma Z.Y. , Wang W.J.",Ketogenic diet poses a significant effect on imbalanced gut microbiota in infants with refractory epilepsy,World journal of gastroenterology,2017,"Cronobacter, Epilepsy, Gut microbiota, Ketogenic diet, Seizures",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Epilepsy,EFO:0000474,healthy controls,pre-ketogenic diet (P1),pediatric patients with refractory epilepsy before ketogenic diet treatment,30,14,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 5,16 November 2024,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of P1 group compared to healthy controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Lactonifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptoclostridiaceae|g__Peptoclostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",3379134|1224|1236|2887326|468|469;1783272|1239|91061|1385|186817|1386;1783272|1239|186801|186802|3085642|580596;3379134|1224|1236|91347|543|413496;3379134|976|200643|171549|2005520|156973;1783272|201174|84998|1643822|1643826|84111;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|1300|1357;1783272|1239|186801|186802|31979|420345;1783272|1239|186801|3082720|543314|86331;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|3082720|3120161|1481960;3379134|976|200643|171549|171551|836;3379134|1224|1236|72274|135621|286;3379134|1224|1236|2887326|468|497;3379134|1224|28216|80840|119060|48736;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810280|3025755,Complete,NA
bsdb:28970732/2/2,28970732,time series / longitudinal observational,28970732,10.3748/wjg.v23.i33.6164,NA,"Xie G., Zhou Q., Qiu C.Z., Dai W.K., Wang H.P., Li Y.H., Liao J.X., Lu X.G., Lin S.F., Ye J.H., Ma Z.Y. , Wang W.J.",Ketogenic diet poses a significant effect on imbalanced gut microbiota in infants with refractory epilepsy,World journal of gastroenterology,2017,"Cronobacter, Epilepsy, Gut microbiota, Ketogenic diet, Seizures",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Epilepsy,EFO:0000474,healthy controls,pre-ketogenic diet (P1),pediatric patients with refractory epilepsy before ketogenic diet treatment,30,14,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Tables 4 & 5,16 November 2024,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of P1 group compared to healthy controls,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",1783272|201174|1760|2037|2049|1654;1783272|201174|84998|84999|1643824|1380;3379134|976|200643|171549|815|816;3379134|976;1783272|201174|1760|85004|31953|1678;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|31979|1485;3379134|1224|1236|91347|543|561;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724,Complete,NA
bsdb:28970732/3/1,28970732,time series / longitudinal observational,28970732,10.3748/wjg.v23.i33.6164,NA,"Xie G., Zhou Q., Qiu C.Z., Dai W.K., Wang H.P., Li Y.H., Liao J.X., Lu X.G., Lin S.F., Ye J.H., Ma Z.Y. , Wang W.J.",Ketogenic diet poses a significant effect on imbalanced gut microbiota in infants with refractory epilepsy,World journal of gastroenterology,2017,"Cronobacter, Epilepsy, Gut microbiota, Ketogenic diet, Seizures",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Ketogenic diet,EFO:0009371,healthy controls and P1 group,post-ketogenic diet (P2),pediatric patients with refractory epilepsy after ketogenic diet treatment,44,14,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,16 November 2024,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of P2 group compared to healthy controls and P1 group,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Brochothrix,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptoclostridiaceae|g__Peptoclostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium",1783272|1239|91061|1385|186817;1783272|1239|91061|1385;1783272|1239|91061|1385|186817|1386;1783272|1239|91061|1385|186820|2755;1783272|201174|84998|1643822|1643826|84111;1783272|201174|84998|1643822|1643826;1783272|201174|84998|1643822;1783272|1239|91061|1385|186820;3379134|976|200643|171549|1853231|283168;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|3120161|1481960;1783272|1239|526524|526525|128827|123375,Complete,NA
bsdb:28970732/4/1,28970732,time series / longitudinal observational,28970732,10.3748/wjg.v23.i33.6164,NA,"Xie G., Zhou Q., Qiu C.Z., Dai W.K., Wang H.P., Li Y.H., Liao J.X., Lu X.G., Lin S.F., Ye J.H., Ma Z.Y. , Wang W.J.",Ketogenic diet poses a significant effect on imbalanced gut microbiota in infants with refractory epilepsy,World journal of gastroenterology,2017,"Cronobacter, Epilepsy, Gut microbiota, Ketogenic diet, Seizures",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Epilepsy,EFO:0000474,healthy controls and P2 group,pre-ketogenic diet (P1),pediatric patients with refractory epilepsy after ketogenic diet treatment,44,14,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,17 November 2024,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of P1 group compared to healthy controls and P2 group,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Myroides,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae",3379134|1224|1236|2887326|468|469;1783272|1239|91061;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|31979;3379134|1224|1236|91347|543|413496;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;3379134|1224|1236;1783272|1239|186801|3085636|186803|1649459;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|1506553;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|1300|1357;1783272|1239|186801|3082720|543314|86331;3379134|976|117743|200644|49546|76831;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|3082720|186804|1257;3379134|1224|1236|2887326|468|497;1783272|1239|186801|186802|216572|1508657;3379134|1224|28211|204457|41297;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810280|3025755;1783272|1239|91061|186826|33958|46255;1783272|1239|186801|3082720|543314,Complete,NA
bsdb:28970732/5/1,28970732,time series / longitudinal observational,28970732,10.3748/wjg.v23.i33.6164,NA,"Xie G., Zhou Q., Qiu C.Z., Dai W.K., Wang H.P., Li Y.H., Liao J.X., Lu X.G., Lin S.F., Ye J.H., Ma Z.Y. , Wang W.J.",Ketogenic diet poses a significant effect on imbalanced gut microbiota in infants with refractory epilepsy,World journal of gastroenterology,2017,"Cronobacter, Epilepsy, Gut microbiota, Ketogenic diet, Seizures",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Epilepsy,EFO:0000474,P1 and P2 groups,healthy controls,healthy infants,28,30,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,17 November 2024,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of healthy controls compared to P1 and P2 groups,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,p__Candidatus Saccharimonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;1783272|201174|1760;1783272|201174;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|1224|28216;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;3379134|1224|28216|80840;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294;3379134|29547|3031852|213849;95818;1783272|1239|186801|186802|31979|1485;3379134|29547|3031852;3379134|1224|1236|91347|543|561;1783272|1239|186801|186802|216572|216851;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712;3379134|1224|1236|135625;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;3379134|1224|28216|80840|995019|40544;3379134|1224|28216|80840|995019,Complete,NA
bsdb:28988196/1/1,28988196,case-control,28988196,10.1136/gutjnl-2017-314814,https://pubmed.ncbi.nlm.nih.gov/28988196/,"Flemer B., Warren R.D., Barrett M.P., Cisek K., Das A., Jeffery I.B., Hurley E., O'Riordain M., Shanahan F. , O'Toole P.W.",The oral microbiota in colorectal cancer is distinctive and predictive,Gut,2018,"colonic bacteria, colorectal cancer, colorectal cancer screening, diet, tumour markers",Experiment 1,Ireland,Homo sapiens,Oral cavity,UBERON:0000167,Colorectal cancer,EFO:0005842,Healthy Controls,Individuals with CRC,Individuals diagnosed with CRC,103,99,1 month,16S,34,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5(B),5 July 2022,Jeshudy,"Jeshudy,Atrayees,WikiWorks",Scatterplot of the colonic prevalence of bacterial OTUs associated with oral pathogen and biofilm CAGs.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|909932|1843489|31977|39948;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;1783272|1239|526524|526525|128827|123375;1783272|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:28988196/1/2,28988196,case-control,28988196,10.1136/gutjnl-2017-314814,https://pubmed.ncbi.nlm.nih.gov/28988196/,"Flemer B., Warren R.D., Barrett M.P., Cisek K., Das A., Jeffery I.B., Hurley E., O'Riordain M., Shanahan F. , O'Toole P.W.",The oral microbiota in colorectal cancer is distinctive and predictive,Gut,2018,"colonic bacteria, colorectal cancer, colorectal cancer screening, diet, tumour markers",Experiment 1,Ireland,Homo sapiens,Oral cavity,UBERON:0000167,Colorectal cancer,EFO:0005842,Healthy Controls,Individuals with CRC,Individuals diagnosed with CRC,103,99,1 month,16S,34,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5(B),5 July 2022,Jeshudy,"Jeshudy,Atrayees,Folakunmi,WikiWorks",Scatterplot of the colonic prevalence of bacterial OTUs associated with oral pathogen and biofilm CAGs.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|2037|2049|1654;3379134|1224|1236|135625|712|724;1783272|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:28988196/2/1,28988196,case-control,28988196,10.1136/gutjnl-2017-314814,https://pubmed.ncbi.nlm.nih.gov/28988196/,"Flemer B., Warren R.D., Barrett M.P., Cisek K., Das A., Jeffery I.B., Hurley E., O'Riordain M., Shanahan F. , O'Toole P.W.",The oral microbiota in colorectal cancer is distinctive and predictive,Gut,2018,"colonic bacteria, colorectal cancer, colorectal cancer screening, diet, tumour markers",Experiment 2,Ireland,Homo sapiens,Oral cavity,UBERON:0000167,Colorectal cancer,EFO:0005842,Healthy Controls,Individuals with CRC,Individuals diagnosed with CRC,103,99,1 month,16S,34,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,supplementary table 2,22 January 2024,Folakunmi,"Folakunmi,WikiWorks",Differentially abundant taxa in the oral microbiome between colorectal cancer patients and healthy controls by ANCOM,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|1224|1236|135625|712|724;1783272|1239|1737404|1737405|1570339|543311;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|1283313;1783272|1239|186801|3085636|186803|1164882;3379134|1224|28216|206351|481|482;1783272|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:28988196/3/1,28988196,case-control,28988196,10.1136/gutjnl-2017-314814,https://pubmed.ncbi.nlm.nih.gov/28988196/,"Flemer B., Warren R.D., Barrett M.P., Cisek K., Das A., Jeffery I.B., Hurley E., O'Riordain M., Shanahan F. , O'Toole P.W.",The oral microbiota in colorectal cancer is distinctive and predictive,Gut,2018,"colonic bacteria, colorectal cancer, colorectal cancer screening, diet, tumour markers",Experiment 3,Ireland,Homo sapiens,Oral cavity,UBERON:0000167,Colorectal cancer,EFO:0005842,Healthy Controls,Individuals with polyps,Individuals diagnosed with polyps,103,32,1 month,16S,34,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,supplementary table 2,22 January 2024,Folakunmi,"Folakunmi,WikiWorks",Differentially abundant taxa in the oral microbiome between colorectal cancer patients and healthy controls by ANCOM,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",1783272|1239|1737404|1737405|1570339|543311;1783272|1239|91061|186826|1300|1301;3384189|32066|203490|203491|1129771|32067,Complete,Folakunmi
bsdb:29017394/1/1,29017394,case-control,29017394,10.1080/09168451.2017.1383849,https://pubmed.ncbi.nlm.nih.gov/29017394/,"Inoue R., Sawai T., Sawai C., Nakatani M., Romero-Pérez G.A., Ozeki M., Nonomura K. , Tsukahara T.",A preliminary study of gut dysbiosis in children with food allergy,"Bioscience, biotechnology, and biochemistry",2017,"food allergy, gut dysbiosis, high throughput 16S rRNA gene sequencing",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,Healthy children,Food allergic children,"Children aged 18 months to 6 years diagnosed with food allergy based on clinical symptoms and oral food challenge tests, prior to receiving any treatment.",4,4,1 month,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 2,17 April 2025,Shulamite,Shulamite,Composition of gut microbiota of healthy and food allergic children. In mean relative abundance between groups are indicated with an asterisk (*).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|1224|28216|80840|995019|40544;1783272|1239|186801|3085636|186803|28050;1783272|1239|909932|1843489|31977|29465,Complete,KateRasheed
bsdb:29017394/1/2,29017394,case-control,29017394,10.1080/09168451.2017.1383849,https://pubmed.ncbi.nlm.nih.gov/29017394/,"Inoue R., Sawai T., Sawai C., Nakatani M., Romero-Pérez G.A., Ozeki M., Nonomura K. , Tsukahara T.",A preliminary study of gut dysbiosis in children with food allergy,"Bioscience, biotechnology, and biochemistry",2017,"food allergy, gut dysbiosis, high throughput 16S rRNA gene sequencing",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,Healthy children,Food allergic children,"Children aged 18 months to 6 years diagnosed with food allergy based on clinical symptoms and oral food challenge tests, prior to receiving any treatment.",4,4,1 month,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 2,17 April 2025,Shulamite,Shulamite,Composition of gut microbiota of healthy and food allergic children. In mean relative abundance between groups are indicated with an asterisk (*).,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|186803|189330,Complete,KateRasheed
bsdb:29023689/1/1,29023689,case-control,29023689,10.1002/ijc.31098,NA,"Liu H.X., Tao L.L., Zhang J., Zhu Y.G., Zheng Y., Liu D., Zhou M., Ke H., Shi M.M. , Qu J.M.",Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects,International journal of cancer,2018,"16S rRNA, bacteria, lower airway, lung cancer, microbiota",Experiment 1,China,Homo sapiens,Lung,UBERON:0002048,Lung cancer,MONDO:0008903,controls,cancerous site,diagnosis of lung cancer established by histological confirmation,18,24,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,decreased,NA,increased,NA,NA,Signature 1,Figure 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differentially abundant taxa between T (patients in cancerous site) and N (normal) groups,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|1760|85007;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:29023689/1/2,29023689,case-control,29023689,10.1002/ijc.31098,NA,"Liu H.X., Tao L.L., Zhang J., Zhu Y.G., Zheng Y., Liu D., Zhou M., Ke H., Shi M.M. , Qu J.M.",Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects,International journal of cancer,2018,"16S rRNA, bacteria, lower airway, lung cancer, microbiota",Experiment 1,China,Homo sapiens,Lung,UBERON:0002048,Lung cancer,MONDO:0008903,controls,cancerous site,diagnosis of lung cancer established by histological confirmation,18,24,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,decreased,NA,increased,NA,NA,Signature 2,Figure 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differentially abundant taxa between T (patients in cancerous site) and N (normal) groups,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",3379134|1224|1236|2887326|468;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:29023689/2/1,29023689,case-control,29023689,10.1002/ijc.31098,NA,"Liu H.X., Tao L.L., Zhang J., Zhu Y.G., Zheng Y., Liu D., Zhou M., Ke H., Shi M.M. , Qu J.M.",Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects,International journal of cancer,2018,"16S rRNA, bacteria, lower airway, lung cancer, microbiota",Experiment 2,China,Homo sapiens,Lung,UBERON:0002048,Lung cancer,MONDO:0008903,controls,paired contralateral non-cancerous site in lung cancer patients,paired contralateral non-cancerous site samples from patients with diagnosis of lung cancer established by histological confirmation,18,24,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differentially abundant taxa between TN (contralateral non-cancerous site) and N (normal) groups,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|976|117743|200644|49546|1016;3379134|976|117743|200644|49546;3379134|976|117743|200644;3379134|976|117743|200644|49546|237;3379134|1224|1236|135625|712|724;1783272|1239|91061|186826;3384189|32066|203490|203491|1129771|32067;3384189|32066|203490|203491|1129771;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481;3379134|1224|28216|206351;3379134|1224|1236|135625|712;3379134|1224|1236|135625;1783272|1239|909932|909929|1843491|970;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:29023689/2/2,29023689,case-control,29023689,10.1002/ijc.31098,NA,"Liu H.X., Tao L.L., Zhang J., Zhu Y.G., Zheng Y., Liu D., Zhou M., Ke H., Shi M.M. , Qu J.M.",Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects,International journal of cancer,2018,"16S rRNA, bacteria, lower airway, lung cancer, microbiota",Experiment 2,China,Homo sapiens,Lung,UBERON:0002048,Lung cancer,MONDO:0008903,controls,paired contralateral non-cancerous site in lung cancer patients,paired contralateral non-cancerous site samples from patients with diagnosis of lung cancer established by histological confirmation,18,24,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differentially abundant taxa between TN (contralateral non-cancerous site) and N (normal) groups,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales",3379134|1224|1236|2887326|468|469;1783272|1239|186801|3085636|186803;3379134|1224|1236|2887326|468;3379134|1224|1236|72274,Complete,Claregrieve1
bsdb:29023689/3/1,29023689,case-control,29023689,10.1002/ijc.31098,NA,"Liu H.X., Tao L.L., Zhang J., Zhu Y.G., Zheng Y., Liu D., Zhou M., Ke H., Shi M.M. , Qu J.M.",Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects,International journal of cancer,2018,"16S rRNA, bacteria, lower airway, lung cancer, microbiota",Experiment 3,China,Homo sapiens,Lung,UBERON:0002048,Sampling site,EFO:0000688,paired contralateral non-cancerous site (TN),cancerous site (T),patients with diagnosis of lung cancer established by histological confirmation,24,24,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 3,10 January 2021,Fatima Zohra,"WikiWorks,Folakunmi",Differentially abundant taxa between T (patients in cancerous site) and TN (contralateral non-cancerous site) groups,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,p__Candidatus Saccharimonadota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",1783272|1239|91061|1385;95818;1783272|1239|909932|1843489|31977|39948,Complete,Folakunmi
bsdb:29023689/4/1,29023689,case-control,29023689,10.1002/ijc.31098,NA,"Liu H.X., Tao L.L., Zhang J., Zhu Y.G., Zheng Y., Liu D., Zhou M., Ke H., Shi M.M. , Qu J.M.",Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects,International journal of cancer,2018,"16S rRNA, bacteria, lower airway, lung cancer, microbiota",Experiment 4,China,Homo sapiens,Lung,UBERON:0002048,Lung cancer,MONDO:0008903,control group with no antibiotics,cancerous site with no antibiotics,patients who have diagnosis of lung cancer established by histological confirmation,8,13,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,decreased,NA,increased,NA,NA,Signature 1,Supplemental Figure S1,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Significant bacterial difference between To (samples from cancerous site who received no antibiotics prior to 3 months) and No (normal samples who received no antibiotics),increased,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,3379134|976|117743|200644|49546|1016,Complete,Folakunmi
bsdb:29023689/4/2,29023689,case-control,29023689,10.1002/ijc.31098,NA,"Liu H.X., Tao L.L., Zhang J., Zhu Y.G., Zheng Y., Liu D., Zhou M., Ke H., Shi M.M. , Qu J.M.",Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects,International journal of cancer,2018,"16S rRNA, bacteria, lower airway, lung cancer, microbiota",Experiment 4,China,Homo sapiens,Lung,UBERON:0002048,Lung cancer,MONDO:0008903,control group with no antibiotics,cancerous site with no antibiotics,patients who have diagnosis of lung cancer established by histological confirmation,8,13,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,decreased,NA,increased,NA,NA,Signature 2,Supplemental Figure S1,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Significant bacterial difference between To (samples from cancerous site who received no antibiotics prior to 3 months) and No (normal samples who received no antibiotics),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,c__Deltaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Myxococcota|c__Myxococcia|o__Myxococcales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Hydrotalea",3379134|1224|28216|80840|80864;28221;3379134|1224|1236|2887326|468;3379134|2818505|32015|29;3379134|1224|28211|204455|31989|265;3379134|1224|28211|204455|31989;3379134|1224|28211|204455;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|72274;3379134|1224|28216|80840;3379134|1224|28211;3379134|976|1853228|1853229|563835;1783272|1239|186801;1783272|1239|186801|186802|1898207;3379134|976;3379134|976|1853228|1853229|563835|1004300,Complete,Folakunmi
bsdb:29023689/5/1,29023689,case-control,29023689,10.1002/ijc.31098,NA,"Liu H.X., Tao L.L., Zhang J., Zhu Y.G., Zheng Y., Liu D., Zhou M., Ke H., Shi M.M. , Qu J.M.",Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects,International journal of cancer,2018,"16S rRNA, bacteria, lower airway, lung cancer, microbiota",Experiment 5,China,Homo sapiens,Lung,UBERON:0002048,Lung cancer,MONDO:0008903,control group with no antibiotics (No),contralateral non-cancerous site with no antibiotics (TNo),contralateral non-cancerous site samples from lung cancer patients who received no antibiotics in  the prior three months,8,13,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,increased,NA,unchanged,NA,NA,Signature 1,supplementary figure 1,3 February 2024,Folakunmi,"Folakunmi,WikiWorks",Differentially abundant taxa between TNo (samples from the contralateral noncancerous site of lung cancer patients who received no antibiotics prior to 3 months) and No (control samples who received no antibiotics),increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|1239|91061;1783272|1239|91061|186826;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481;3379134|1224|28216|206351;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279,Complete,Folakunmi
bsdb:29023689/5/2,29023689,case-control,29023689,10.1002/ijc.31098,NA,"Liu H.X., Tao L.L., Zhang J., Zhu Y.G., Zheng Y., Liu D., Zhou M., Ke H., Shi M.M. , Qu J.M.",Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects,International journal of cancer,2018,"16S rRNA, bacteria, lower airway, lung cancer, microbiota",Experiment 5,China,Homo sapiens,Lung,UBERON:0002048,Lung cancer,MONDO:0008903,control group with no antibiotics (No),contralateral non-cancerous site with no antibiotics (TNo),contralateral non-cancerous site samples from lung cancer patients who received no antibiotics in  the prior three months,8,13,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,increased,NA,unchanged,NA,NA,Signature 2,supplementary figure 1,3 February 2024,Folakunmi,"Folakunmi,WikiWorks",Differentially abundant taxa between TNo (samples from the contralateral noncancerous site of lung cancer patients who received no antibiotics prior to 3 months) and No (control samples who received no antibiotics),decreased,"s__uncultured bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Hydrotalea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium",77133;1783272|1239|186801|3085636|186803|33042;3379134|1224|1236|2887326|468|469;3379134|1224|28211|204458|76892;3379134|1224|1236|2887326|468;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|1224|28216|80840;3379134|1224|1236|72274;3379134|1224|28211;3379134|976|1853228|1853229|563835|1004300;1783272|1239|186801|3085636|186803;1783272|1239|186801;1783272|1239|186801|186802|1898207,Complete,Folakunmi
bsdb:29023689/6/1,29023689,case-control,29023689,10.1002/ijc.31098,NA,"Liu H.X., Tao L.L., Zhang J., Zhu Y.G., Zheng Y., Liu D., Zhou M., Ke H., Shi M.M. , Qu J.M.",Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects,International journal of cancer,2018,"16S rRNA, bacteria, lower airway, lung cancer, microbiota",Experiment 6,China,Homo sapiens,Lung,UBERON:0002048,Sampling site,EFO:0000688,contralateral non-cancerous site with no antibiotics (TNo),Cancerous site with no antibiotics (To),cancerous site samples from lung cancer patients who received no antibiotics in  the prior three months,13,13,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,decreased,NA,unchanged,NA,NA,Signature 1,supplementary figure 1,4 February 2024,Folakunmi,"Folakunmi,WikiWorks",Differentially abundant taxa between TNo (samples from the contralateral noncancerous site of lung cancer patients who received no antibiotics prior to 3 months) and To (cancerous site samples of lung cancer patients who received no antibiotics prior to 3 months),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",1783272|201174|1760|85007|1653;1783272|1239|909932|1843488|909930;1783272|1239|909932|1843488|909930|33024,Complete,Folakunmi
bsdb:29031597/1/1,29031597,case-control,29031597,10.1016/j.jaci.2017.09.018,NA,"Goldman D.L., Chen Z., Shankar V., Tyberg M., Vicencio A. , Burk R.",Lower airway microbiota and mycobiota in children with severe asthma,The Journal of allergy and clinical immunology,2018,NA,Experiment 1,United States of America,Homo sapiens,Right lung middle lobe bronchiole,UBERON:0012068,Asthma,MONDO:0004979,non-asthma,severe asthma,severe asthma,11,15,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 1a, 1b",10 January 2021,Rimsha Azhar,"Fatima,Claregrieve1,WikiWorks",Differentially abundant genera between severe asthma and non-asthma patients,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Leucosporidiales|f__Leucosporidiaceae|g__Leucosporidium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Fungi|p__Ascomycota|c__Pneumocystomycetes|o__Pneumocystales|f__Pneumocystaceae|g__Pneumocystis,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Rhodotorula,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815|816;3379134|976|117743|200644|49546|1016;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|946234;4751|5204|162481|231212|1163720|5277;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;4751|4890|147553|37987|44281|4753;4751|5204|162481|231213|1799696|5533;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263,Complete,Claregrieve1
bsdb:29031597/1/2,29031597,case-control,29031597,10.1016/j.jaci.2017.09.018,NA,"Goldman D.L., Chen Z., Shankar V., Tyberg M., Vicencio A. , Burk R.",Lower airway microbiota and mycobiota in children with severe asthma,The Journal of allergy and clinical immunology,2018,NA,Experiment 1,United States of America,Homo sapiens,Right lung middle lobe bronchiole,UBERON:0012068,Asthma,MONDO:0004979,non-asthma,severe asthma,severe asthma,11,15,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 1a, 1b",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differentially abundant genera between severe asthma and non-asthma patients,decreased,"k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Cryptococcaceae|g__Cryptococcus,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Davidiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Fungi|p__Basidiomycota|c__Agaricostilbomycetes|o__Agaricostilbales|f__Agaricostilbaceae|g__Sterigmatomyces",4751|5204|155616|5234|1884633|5206;4751|4890|147541|2726946|452563|237557;3379134|1224|1236|91347|1903414|583;4751|5204|162480|48846|48847|5615,Complete,Claregrieve1
bsdb:29051531/1/1,29051531,case-control,29051531,10.1038/s41598-017-13601-y,NA,"Vogt N.M., Kerby R.L., Dill-McFarland K.A., Harding S.J., Merluzzi A.P., Johnson S.C., Carlsson C.M., Asthana S., Zetterberg H., Blennow K., Bendlin B.B. , Rey F.E.",Gut microbiome alterations in Alzheimer's disease,Scientific reports,2017,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healhty controls,Alzheimer's,NA,25,25,6 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,sex",NA,NA,decreased,decreased,unchanged,unchanged,NA,Signature 1,Figure 2+figure 1,10 January 2021,Fatima Zohra,"Kwekuamoo,Merit,WikiWorks",Bacterias differentially represented in faeces from AD participants compared to controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|91061|1385|539738|1378;1783272|1239|909932|1843488|909930|33024;3379134|200940|3031449|213115|194924|35832;3379134|976|200643|171549|171550;3379134|976|200643|171549,Complete,Shaimaa Elsafoury
bsdb:29051531/1/2,29051531,case-control,29051531,10.1038/s41598-017-13601-y,NA,"Vogt N.M., Kerby R.L., Dill-McFarland K.A., Harding S.J., Merluzzi A.P., Johnson S.C., Carlsson C.M., Asthana S., Zetterberg H., Blennow K., Bendlin B.B. , Rey F.E.",Gut microbiome alterations in Alzheimer's disease,Scientific reports,2017,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healhty controls,Alzheimer's,NA,25,25,6 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,sex",NA,NA,decreased,decreased,unchanged,unchanged,NA,Signature 2,Figure 2+figure 1,10 January 2021,Fatima Zohra,"Fatima,Kwekuamoo,WikiWorks",Bacterias differentially represented in faeces from AD participants compared to controls,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Bacillati|p__Bacillota|c__Clostridia,,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium",1783272|201174;1783272|201174|84998|1643822|1643826|447020;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|909932|1843489|31977|39948;1783272|1239;1783272|1239|186801|186802|541000;1783272|1239|186801|3082720|186804;1783272|1239|526524|526525|2810281;1783272|1239|186801;;1783272|1239|186801|3082720|543314|86331,Complete,Fatima
bsdb:29052232/1/1,29052232,case-control,29052232,10.1111/all.13331,NA,"Kim B.S., Lee E., Lee M.J., Kang M.J., Yoon J., Cho H.J., Park J., Won S., Lee S.Y. , Hong S.J.",Different functional genes of upper airway microbiome associated with natural course of childhood asthma,Allergy,2018,"airway, childhood asthma, function, microbiome",Experiment 1,South Korea,Homo sapiens,Nasopharynx,UBERON:0001728,Asthma,MONDO:0004979,healthy control,asthma,asthma,31,31,3 months,16S,123,Roche454,relative abundances,Dunn's test,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2,10 January 2021,Lucy Mellor,WikiWorks,Relative abundance of bacterial genera in patients with asthma and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|91061|1385|90964|1279;3379134|976|200643|171549|171552|838,Complete,Folakunmi
bsdb:29052232/1/2,29052232,case-control,29052232,10.1111/all.13331,NA,"Kim B.S., Lee E., Lee M.J., Kang M.J., Yoon J., Cho H.J., Park J., Won S., Lee S.Y. , Hong S.J.",Different functional genes of upper airway microbiome associated with natural course of childhood asthma,Allergy,2018,"airway, childhood asthma, function, microbiome",Experiment 1,South Korea,Homo sapiens,Nasopharynx,UBERON:0001728,Asthma,MONDO:0004979,healthy control,asthma,asthma,31,31,3 months,16S,123,Roche454,relative abundances,Dunn's test,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2,10 January 2021,Lucy Mellor,WikiWorks,Relative abundance of bacterial genera in patients with asthma and healthy controls,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,3379134|1224|1236|135625|712|724,Complete,Folakunmi
bsdb:29052232/2/1,29052232,case-control,29052232,10.1111/all.13331,NA,"Kim B.S., Lee E., Lee M.J., Kang M.J., Yoon J., Cho H.J., Park J., Won S., Lee S.Y. , Hong S.J.",Different functional genes of upper airway microbiome associated with natural course of childhood asthma,Allergy,2018,"airway, childhood asthma, function, microbiome",Experiment 2,South Korea,Homo sapiens,Nasopharynx,UBERON:0001728,Asthma,MONDO:0004979,healthy control,asthma remission,asthma remission,31,30,3 months,16S,123,Roche454,relative abundances,Dunn's test,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2,10 January 2021,Lucy Mellor,WikiWorks,Relative abundance of bacterial genera in patients with asthma remission and healthy controls,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas",3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|171552|838;1783272|1239|1737404|1737405|1570339|543311,Complete,Folakunmi
bsdb:29052232/2/2,29052232,case-control,29052232,10.1111/all.13331,NA,"Kim B.S., Lee E., Lee M.J., Kang M.J., Yoon J., Cho H.J., Park J., Won S., Lee S.Y. , Hong S.J.",Different functional genes of upper airway microbiome associated with natural course of childhood asthma,Allergy,2018,"airway, childhood asthma, function, microbiome",Experiment 2,South Korea,Homo sapiens,Nasopharynx,UBERON:0001728,Asthma,MONDO:0004979,healthy control,asthma remission,asthma remission,31,30,3 months,16S,123,Roche454,relative abundances,Dunn's test,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2,10 January 2021,Lucy Mellor,WikiWorks,Relative abundance of bacterial genera in patients with asthma remission and healthy controls,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,3379134|1224|1236|135625|712|724,Complete,Folakunmi
bsdb:29083504/1/1,29083504,case-control,29083504,https://doi.org/10.1002/hep.29623,https://pubmed.ncbi.nlm.nih.gov/29083504/,"Puri P., Liangpunsakul S., Christensen J.E., Shah V.H., Kamath P.S., Gores G.J., Walker S., Comerford M., Katz B., Borst A., Yu Q., Kumar D.P., Mirshahi F., Radaeva S., Chalasani N.P., Crabb D.W. , Sanyal A.J.",The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis,"Hepatology (Baltimore, Md.)",2018,NA,Experiment 1,United States of America,Homo sapiens,Blood,UBERON:0000178,"Hepatitis, Alcoholic",EFO:1001345,NAC,alcoholics,alcoholic hepatitis,20,56,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,figure 2B,10 January 2021,Fatima Zohra,"Lwaldron,WikiWorks",Differential group taxonomic features for non-alcohol consuming controls (NAC) and combined alcoholic group,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerocolumna,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|1224|28211|356|41294|374;1783272|201174|1760|85006|85023|33882;1783272|1239|186801|3085636|186803|1843210;1783272|201174|1760|85007|1653|1716;1783272|1239|186801|3082720|186804;1783272|1239|186801|3085636|186803,Complete,NA
bsdb:29083504/1/2,29083504,case-control,29083504,https://doi.org/10.1002/hep.29623,https://pubmed.ncbi.nlm.nih.gov/29083504/,"Puri P., Liangpunsakul S., Christensen J.E., Shah V.H., Kamath P.S., Gores G.J., Walker S., Comerford M., Katz B., Borst A., Yu Q., Kumar D.P., Mirshahi F., Radaeva S., Chalasani N.P., Crabb D.W. , Sanyal A.J.",The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis,"Hepatology (Baltimore, Md.)",2018,NA,Experiment 1,United States of America,Homo sapiens,Blood,UBERON:0000178,"Hepatitis, Alcoholic",EFO:1001345,NAC,alcoholics,alcoholic hepatitis,20,56,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,figure 2B,10 January 2021,Fatima Zohra,WikiWorks,Differential group taxonomic features for non-alcohol consuming controls (NAC) and combined alcoholic group,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Friedmanniella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Oceanobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillales Family X. Incertae Sedis|g__Thermicanus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Microvirga,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Rickettsiaceae|g__Rickettsia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Tepidimonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hydrogenophaga,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Caldimonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Hydrogenophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas",1783272|201174|1760|85007|85026|2053;1783272|201174|1760|85009|85015|1839;1783272|201174|1760|85009|85015|53387;1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171550|239759;3379134|976|117743|200644|49546|237;1783272|1239|91061|1385|186817|182709;1783272|1239|91061|1385|539003|94008;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|1263;3379134|1224|28211|356|119045|186650;3379134|1224|28211|204455|31989|265;3379134|1224|28211|766|775|780;3379134|1224|28216|80840|114248;3379134|1224|28216|80840|80864|12916;3379134|1224|28216|80840|80864|47420;3379134|1224|28216|80840|2975441|215579;3379134|1224|28216|80840|75682|29580;3379134|1224|2008785|119069|206349|70774;3379134|1224|1236|135624|84642|642,Complete,NA
bsdb:29083504/2/1,29083504,case-control,29083504,https://doi.org/10.1002/hep.29623,https://pubmed.ncbi.nlm.nih.gov/29083504/,"Puri P., Liangpunsakul S., Christensen J.E., Shah V.H., Kamath P.S., Gores G.J., Walker S., Comerford M., Katz B., Borst A., Yu Q., Kumar D.P., Mirshahi F., Radaeva S., Chalasani N.P., Crabb D.W. , Sanyal A.J.",The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis,"Hepatology (Baltimore, Md.)",2018,NA,Experiment 2,United States of America,Homo sapiens,Blood,UBERON:0000178,"Hepatitis, Alcoholic",EFO:1001345,NAC,HDC,alcoholic hepatitis,20,19,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,figure 3C,10 January 2021,Fatima Zohra,"Lwaldron,WikiWorks",differential group taxonomic features for non-alcohol consuming controls (NAC) and heavy drinking control (HDC),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Phenylobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|g__Rhodobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",3379134|1224|1236|2887326|468|469;1783272|1239|1737404|1737405|1570339|165779;3379134|1224|28211|356|41294|374;3379134|976|117743|200644|2762318|59732;1783272|201174|1760|85006|1268|57493;3384189|32066|203490|203491|1129771;1783272|201174|1760|85006|85023|33882;3379134|1224|28216|206351|481|482;3379134|1224|28211|204458|76892|20;1783272|201174|1760|85011|2062|1883;3379134|1224|28211|204455|1060;1783272|1239|186801|3082720|186804,Complete,NA
bsdb:29083504/2/2,29083504,case-control,29083504,https://doi.org/10.1002/hep.29623,https://pubmed.ncbi.nlm.nih.gov/29083504/,"Puri P., Liangpunsakul S., Christensen J.E., Shah V.H., Kamath P.S., Gores G.J., Walker S., Comerford M., Katz B., Borst A., Yu Q., Kumar D.P., Mirshahi F., Radaeva S., Chalasani N.P., Crabb D.W. , Sanyal A.J.",The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis,"Hepatology (Baltimore, Md.)",2018,NA,Experiment 2,United States of America,Homo sapiens,Blood,UBERON:0000178,"Hepatitis, Alcoholic",EFO:1001345,NAC,HDC,alcoholic hepatitis,20,19,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,figure 3C,10 January 2021,Fatima Zohra,WikiWorks,differential group taxonomic features for non-alcohol consuming controls (NAC) and heavy drinking control (HDC),decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Tepidimonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Pseudomonadati|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Hydrogenophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group",1783272|201174|1760|85007|85026|2053;1783272|201174|1760|85009|85015|1839;1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|171551;3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|838;3379134|976|117743|200644|49546|237;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|31979|1485;3379134|1224|28216|80840|114248;3379134|1224|28216|80840|80864|12916;3379134|1224|2008785|119069|206349|70774;3379134|1224|1236|72274|135621|351,Complete,NA
bsdb:29083504/3/1,29083504,case-control,29083504,https://doi.org/10.1002/hep.29623,https://pubmed.ncbi.nlm.nih.gov/29083504/,"Puri P., Liangpunsakul S., Christensen J.E., Shah V.H., Kamath P.S., Gores G.J., Walker S., Comerford M., Katz B., Borst A., Yu Q., Kumar D.P., Mirshahi F., Radaeva S., Chalasani N.P., Crabb D.W. , Sanyal A.J.",The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis,"Hepatology (Baltimore, Md.)",2018,NA,Experiment 3,United States of America,Homo sapiens,Blood,UBERON:0000178,"Hepatitis, Alcoholic",EFO:1001345,NAC,MAH,alcoholic hepatitis,20,18,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,figure 3C,10 January 2021,Fatima Zohra,"Lwaldron,WikiWorks",differential group taxonomic features for non-alcohol consuming controls (NAC) and moderate alcoholic hepatitis(MAH),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Curvibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium",1783272|1239|186801|3082720|186804;3379134|1224|1236|2887326|468|469;1783272|201174|1760|2037|2049|1654;1783272|1239|1737404|1737405|1570339|165779;3379134|1224|28211|356|41294|374;1783272|1239|91061|186826|186828;3379134|976|117743|200644|2762318|501783;1783272|201174|1760|85007|1653|1716;3379134|1224|28216|80840|80864|281915;1783272|1239|91061|186826|186828|117563;3379134|1224|28211|356|119045|407,Complete,NA
bsdb:29083504/3/2,29083504,case-control,29083504,https://doi.org/10.1002/hep.29623,https://pubmed.ncbi.nlm.nih.gov/29083504/,"Puri P., Liangpunsakul S., Christensen J.E., Shah V.H., Kamath P.S., Gores G.J., Walker S., Comerford M., Katz B., Borst A., Yu Q., Kumar D.P., Mirshahi F., Radaeva S., Chalasani N.P., Crabb D.W. , Sanyal A.J.",The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis,"Hepatology (Baltimore, Md.)",2018,NA,Experiment 3,United States of America,Homo sapiens,Blood,UBERON:0000178,"Hepatitis, Alcoholic",EFO:1001345,NAC,MAH,alcoholic hepatitis,20,18,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,figure 3C,10 January 2021,Fatima Zohra,WikiWorks,differential group taxonomic features for non-alcohol consuming controls (NAC) and moderate alcoholic hepatitis(MAH),decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Friedmanniella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Hydrogenophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group",1783272|201174|1760|85009|85015|1839;1783272|201174|1760|85009|85015|53387;1783272|201174|1760|2037;3379134|976|200643|171549;3379134|976|200643|171549|171551;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|976|117743|200644|49546|237;1783272|1239|91061|1385|186817|1386;1783272|1239|186801|186802|31979|1485;3379134|1224|28211|204457|41297;3379134|1224|28216|80840|75682|29580;3379134|1224|28216|80840;3379134|1224|2008785|119069|206349|70774;3379134|1224|1236|135624|84642;3379134|1224|1236|72274|135621|351,Complete,NA
bsdb:29083504/4/1,29083504,case-control,29083504,https://doi.org/10.1002/hep.29623,https://pubmed.ncbi.nlm.nih.gov/29083504/,"Puri P., Liangpunsakul S., Christensen J.E., Shah V.H., Kamath P.S., Gores G.J., Walker S., Comerford M., Katz B., Borst A., Yu Q., Kumar D.P., Mirshahi F., Radaeva S., Chalasani N.P., Crabb D.W. , Sanyal A.J.",The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis,"Hepatology (Baltimore, Md.)",2018,NA,Experiment 4,United States of America,Homo sapiens,Blood,UBERON:0000178,"Hepatitis, Alcoholic",EFO:1001345,NAC,SAH,alcoholic hepatitis,20,19,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,figure 3C,10 January 2021,Fatima Zohra,"Atrayees,WikiWorks",differential group taxonomic features for non-alcohol consuming controls (NAC) and severe alcoholic hepatitis(SAH),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Alloiococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Gillisia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae",1783272|201174|1760|2037|2049|1654;1783272|1239|91061|186826|186828|1651;1783272|201174|1760|85006|85020|43668;1783272|201174|1760|85007|1653|1716;3379134|976|117743|200644|49546|244698;1783272|201174|1760|85006|85023|33882;1783272|201174|1760|85008|28056,Complete,NA
bsdb:29083504/4/2,29083504,case-control,29083504,https://doi.org/10.1002/hep.29623,https://pubmed.ncbi.nlm.nih.gov/29083504/,"Puri P., Liangpunsakul S., Christensen J.E., Shah V.H., Kamath P.S., Gores G.J., Walker S., Comerford M., Katz B., Borst A., Yu Q., Kumar D.P., Mirshahi F., Radaeva S., Chalasani N.P., Crabb D.W. , Sanyal A.J.",The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis,"Hepatology (Baltimore, Md.)",2018,NA,Experiment 4,United States of America,Homo sapiens,Blood,UBERON:0000178,"Hepatitis, Alcoholic",EFO:1001345,NAC,SAH,alcoholic hepatitis,20,19,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,figure 3C,10 January 2021,Fatima Zohra,WikiWorks,differential group taxonomic features for non-alcohol consuming controls (NAC) and severe alcoholic hepatitis(SAH),decreased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia|o__Acidimicrobiales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae",1783272|201174|84992|84993;1783272|201174|1760|85006|85023;1783272|201174|1760|85009|85015|1839;1783272|201174|1760|2037;1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|171551;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550|239759;3379134|976|117743|200644|49546|237;3379134|976|1853228|1853229|563835;3379134|976|768503|768507|89373,Complete,NA
bsdb:29091972/1/1,29091972,prospective cohort,29091972,10.1371/journal.pone.0187307,NA,"Minato T., Maeda T., Fujisawa Y., Tsuji H., Nomoto K., Ohno K. , Hirayama M.",Progression of Parkinson's disease is associated with gut dysbiosis: Two-year follow-up study,PloS one,2017,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Disease staging,EFO:0000410,Stable Group at year 0,Deteriorated Group at year 0,The Deteriorated Group is the group of patients with significantly higher UPDRS(United Parkinson's Disease Rating Scale) score at year 0,18,18,NA,PCR,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,figure 1A,16 April 2024,Idiaru angela,"Idiaru angela,WikiWorks",Abundance of Bifidobacterium at year 0 in the deteriorated and stable groups.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Svetlana up
bsdb:29091972/2/1,29091972,prospective cohort,29091972,10.1371/journal.pone.0187307,NA,"Minato T., Maeda T., Fujisawa Y., Tsuji H., Nomoto K., Ohno K. , Hirayama M.",Progression of Parkinson's disease is associated with gut dysbiosis: Two-year follow-up study,PloS one,2017,NA,Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Timepoint,EFO:0000724,Parkinson's disease patients at year 0,Parkinson's disease patients at year 2,Patients with Parkinson's disease followed up after year 2,36,28,NA,PCR,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2 & supplementary Table 2,16 April 2024,Idiaru angela,"Idiaru angela,WikiWorks",Difference of bacterial counts between years 0 and 2 in Parkinson's disease patients,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,",1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549|815|816|817;1783272|201174|84998|84999|1643824|1380;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|81852|1350;,Complete,Svetlana up
bsdb:29091972/3/1,29091972,prospective cohort,29091972,10.1371/journal.pone.0187307,NA,"Minato T., Maeda T., Fujisawa Y., Tsuji H., Nomoto K., Ohno K. , Hirayama M.",Progression of Parkinson's disease is associated with gut dysbiosis: Two-year follow-up study,PloS one,2017,NA,Experiment 3,Japan,Homo sapiens,Feces,UBERON:0001988,Timepoint,EFO:0000724,Deteriorated Group at year 0,Deteriorated Group at year 2,The Deteriorated Group is the group of patients with significantly higher UPDRS(United Parkinson's Disease Rating Scale) score at year 2,18,11,NA,PCR,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2 & supplementary Table 2,18 April 2024,Idiaru angela,"Idiaru angela,WikiWorks",Difference of bacterial counts between years 0 and 2 in the Deteriorated group.,decreased,NA,NA,Complete,Svetlana up
bsdb:29091972/4/1,29091972,prospective cohort,29091972,10.1371/journal.pone.0187307,NA,"Minato T., Maeda T., Fujisawa Y., Tsuji H., Nomoto K., Ohno K. , Hirayama M.",Progression of Parkinson's disease is associated with gut dysbiosis: Two-year follow-up study,PloS one,2017,NA,Experiment 4,Japan,Homo sapiens,Feces,UBERON:0001988,Timepoint,EFO:0000724,Stable group at year 0,Stable group at year 2,The Stable Group is the group of patients with significantly lower UPDRS(United Parkinson's Disease Rating Scale) score at year 2,18,17,NA,PCR,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2 & supplementary Table 2,18 April 2024,Idiaru angela,"Idiaru angela,WikiWorks",Difference of bacterial counts between years 0 and 2 in the Stable group.,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",1783272|201174|84998|84999|1643824|1380;;3379134|976|200643|171549|815|816|817;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|81852|1350,Complete,Svetlana up
bsdb:29097493/2/1,29097493,prospective cohort,29097493,10.1126/science.aan4236,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5827966/,"Gopalakrishnan V., Spencer C.N., Nezi L., Reuben A., Andrews M.C., Karpinets T.V., Prieto P.A., Vicente D., Hoffman K., Wei S.C., Cogdill A.P., Zhao L., Hudgens C.W., Hutchinson D.S., Manzo T., Petaccia de Macedo M., Cotechini T., Kumar T., Chen W.S., Reddy S.M., Szczepaniak Sloane R., Galloway-Pena J., Jiang H., Chen P.L., Shpall E.J., Rezvani K., Alousi A.M., Chemaly R.F., Shelburne S., Vence L.M., Okhuysen P.C., Jensen V.B., Swennes A.G., McAllister F., Marcelo Riquelme Sanchez E., Zhang Y., Le Chatelier E., Zitvogel L., Pons N., Austin-Breneman J.L., Haydu L.E., Burton E.M., Gardner J.M., Sirmans E., Hu J., Lazar A.J., Tsujikawa T., Diab A., Tawbi H., Glitza I.C., Hwu W.J., Patel S.P., Woodman S.E., Amaria R.N., Davies M.A., Gershenwald J.E., Hwu P., Lee J.E., Zhang J., Coussens L.M., Cooper Z.A., Futreal P.A., Daniel C.R., Ajami N.J., Petrosino J.F., Tetzlaff M.T., Sharma P., Allison J.P., Jenq R.R. , Wargo J.A.",Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients,"Science (New York, N.Y.)",2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,Patients were classified as R if they achieved an objective response (complete or partial response or stable disease lasting at least 6 months),35,54,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,NA,NA,NA,increased,NA,Signature 1,Figure 2D,30 August 2022,Sharmilac,"Sharmilac,WikiWorks","(D) LDA scores computed for differentially-abundant taxa in the fecal microbiomes of R
(blue) and NR (red). Length indicates effect size associated with a taxon. p=0.05 for the
Kruskal-Wallis test; LDA score > 3.",increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__Ruminiclostridium hungatei,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",1783272|1239;1783272|1239|186801;1783272|1239|186801|186802|1898207;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|171551|836|1583331;1783272|1239|909932|1843489|31977;1783272|1239|186801|186802|216572|1508657|48256;1783272|1239|909932|1843488|909930|33024;1783272|1239|909932|1843488|909930|33024|33025;1783272|1239|1737404|1737405|1570339|162289;1783272|201174|1760|85006|1268;1783272|544448|31969;1783272|201174|1760|85006|1268|32207,Complete,Fatima
bsdb:29097493/2/2,29097493,prospective cohort,29097493,10.1126/science.aan4236,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5827966/,"Gopalakrishnan V., Spencer C.N., Nezi L., Reuben A., Andrews M.C., Karpinets T.V., Prieto P.A., Vicente D., Hoffman K., Wei S.C., Cogdill A.P., Zhao L., Hudgens C.W., Hutchinson D.S., Manzo T., Petaccia de Macedo M., Cotechini T., Kumar T., Chen W.S., Reddy S.M., Szczepaniak Sloane R., Galloway-Pena J., Jiang H., Chen P.L., Shpall E.J., Rezvani K., Alousi A.M., Chemaly R.F., Shelburne S., Vence L.M., Okhuysen P.C., Jensen V.B., Swennes A.G., McAllister F., Marcelo Riquelme Sanchez E., Zhang Y., Le Chatelier E., Zitvogel L., Pons N., Austin-Breneman J.L., Haydu L.E., Burton E.M., Gardner J.M., Sirmans E., Hu J., Lazar A.J., Tsujikawa T., Diab A., Tawbi H., Glitza I.C., Hwu W.J., Patel S.P., Woodman S.E., Amaria R.N., Davies M.A., Gershenwald J.E., Hwu P., Lee J.E., Zhang J., Coussens L.M., Cooper Z.A., Futreal P.A., Daniel C.R., Ajami N.J., Petrosino J.F., Tetzlaff M.T., Sharma P., Allison J.P., Jenq R.R. , Wargo J.A.",Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients,"Science (New York, N.Y.)",2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,Patients were classified as R if they achieved an objective response (complete or partial response or stable disease lasting at least 6 months),35,54,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,NA,NA,NA,increased,NA,Signature 2,Figure 2D,30 August 2022,Sharmilac,"Sharmilac,WikiWorks","(D) LDA scores computed for differentially-abundant taxa in the fecal microbiomes of R
(blue) and NR (red). Length indicates effect size associated with a taxon. p=0.05 for the
Kruskal-Wallis test; LDA score > 3.",decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella stercoris,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Oleidesulfovibrio|s__Oleidesulfovibrio alaskensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides mediterraneensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia",1783272|201174|84998|84999|84107|102106|147206;3379134|200940|3031449|213115|194924|2909705|58180;3379134|976|200643|171549|815|816|1841856;3379134|976|200643|171549|171552|838|470565;1783272|201174|1760|85004|31953|2701|2702;1783272|201174|1760|85004|31953|2701;3379134|976;3379134|976|200643|171549;3379134|976|200643,Complete,Fatima
bsdb:29097494/1/1,29097494,time series / longitudinal observational,29097494,10.1126/science.aan3706,NA,"Routy B., Le Chatelier E., Derosa L., Duong C.P.M., Alou M.T., Daillère R., Fluckiger A., Messaoudene M., Rauber C., Roberti M.P., Fidelle M., Flament C., Poirier-Colame V., Opolon P., Klein C., Iribarren K., Mondragón L., Jacquelot N., Qu B., Ferrere G., Clémenson C., Mezquita L., Masip J.R., Naltet C., Brosseau S., Kaderbhai C., Richard C., Rizvi H., Levenez F., Galleron N., Quinquis B., Pons N., Ryffel B., Minard-Colin V., Gonin P., Soria J.C., Deutsch E., Loriot Y., Ghiringhelli F., Zalcman G., Goldwasser F., Escudier B., Hellmann M.D., Eggermont A., Raoult D., Albiges L., Kroemer G. , Zitvogel L.",Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors,"Science (New York, N.Y.)",2018,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,"Non-small cell lung carcinoma,Renal cell carcinoma,Disease progression measurement","EFO:0003060,EFO:0000681,EFO:0008336",Non-Responders (progression or death),Responders (partial response or stable disease),"non-small cell lung carcinoma or renal carcinoma patients (all samples regardless of ampicillin, colistin, and streptomycin (ATB) anitbiotic treatment) that have been treated with PD-1 blockage with partial response or stable disease",36,42,NA,WMS,NA,Mass spectrometry,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2b,10 January 2021,William Lam,"WikiWorks,Folakunmi",Comparsion of partial response/ stable disease and progressive disease in fecal samples of all patients with non-small cell lung cell lung carcinoma (NSCLC) or renal cell carcinoma (RCC) reponse at 3 months of PD-1 monoclonal antibodies (mAB) treatment,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus|s__Cloacibacillus porcorum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|171550|239759|626932;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|29523;3384194|508458|649775|649776|649777|508459|1197717;1783272|1239|91061|186826|81852|1350|1352;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|186806|1730|142586;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171552|838;1783272|1239,Complete,Folakunmi
bsdb:29097494/1/2,29097494,time series / longitudinal observational,29097494,10.1126/science.aan3706,NA,"Routy B., Le Chatelier E., Derosa L., Duong C.P.M., Alou M.T., Daillère R., Fluckiger A., Messaoudene M., Rauber C., Roberti M.P., Fidelle M., Flament C., Poirier-Colame V., Opolon P., Klein C., Iribarren K., Mondragón L., Jacquelot N., Qu B., Ferrere G., Clémenson C., Mezquita L., Masip J.R., Naltet C., Brosseau S., Kaderbhai C., Richard C., Rizvi H., Levenez F., Galleron N., Quinquis B., Pons N., Ryffel B., Minard-Colin V., Gonin P., Soria J.C., Deutsch E., Loriot Y., Ghiringhelli F., Zalcman G., Goldwasser F., Escudier B., Hellmann M.D., Eggermont A., Raoult D., Albiges L., Kroemer G. , Zitvogel L.",Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors,"Science (New York, N.Y.)",2018,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,"Non-small cell lung carcinoma,Renal cell carcinoma,Disease progression measurement","EFO:0003060,EFO:0000681,EFO:0008336",Non-Responders (progression or death),Responders (partial response or stable disease),"non-small cell lung carcinoma or renal carcinoma patients (all samples regardless of ampicillin, colistin, and streptomycin (ATB) anitbiotic treatment) that have been treated with PD-1 blockage with partial response or stable disease",36,42,NA,WMS,NA,Mass spectrometry,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2b,10 January 2021,William Lam,"Atrayees,WikiWorks,Folakunmi",Comparsion of partial response/ stable disease and progressive disease in fecal samples of all patients with non-small cell lung cell lung carcinoma (NSCLC) or renal cell carcinoma (RCC) reponse at 3 months of PD-1 monoclonal antibodies (mAB) treatment,decreased,"k__Bacillati|p__Bacillota|s__Bacillota bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239|1879010;3379134|976|200643|171549|815|816|626929;3379134|976|200643|171549|815|816|291645;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|1898207;1783272|1239|186801|186802|31979|1485|1506;1783272|1239|186801|3085636|186803|2719313|208479;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|171552|838;3379134|1224;1783272|1239|186801|186802,Complete,Folakunmi
bsdb:29097494/2/1,29097494,time series / longitudinal observational,29097494,10.1126/science.aan3706,NA,"Routy B., Le Chatelier E., Derosa L., Duong C.P.M., Alou M.T., Daillère R., Fluckiger A., Messaoudene M., Rauber C., Roberti M.P., Fidelle M., Flament C., Poirier-Colame V., Opolon P., Klein C., Iribarren K., Mondragón L., Jacquelot N., Qu B., Ferrere G., Clémenson C., Mezquita L., Masip J.R., Naltet C., Brosseau S., Kaderbhai C., Richard C., Rizvi H., Levenez F., Galleron N., Quinquis B., Pons N., Ryffel B., Minard-Colin V., Gonin P., Soria J.C., Deutsch E., Loriot Y., Ghiringhelli F., Zalcman G., Goldwasser F., Escudier B., Hellmann M.D., Eggermont A., Raoult D., Albiges L., Kroemer G. , Zitvogel L.",Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors,"Science (New York, N.Y.)",2018,NA,Experiment 2,France,Homo sapiens,Feces,UBERON:0001988,"Non-small cell lung carcinoma,Renal cell carcinoma,Disease progression measurement","EFO:0003060,EFO:0000681,EFO:0008336",Progressive- Free- Survival more less than 30 days,Progressive -Free- Survival more than 30 days,"non-small cell lung carcinoma or renal carcinoma patients (excluding ampicillin, colistin, and streptomycin (ATB) anitbiotic treatment) that have been treated with PD-1 blockage with partial response or stable disease that are Progressive- Free- Survival greater than 3 months",100,100,NA,WMS,NA,Mass spectrometry,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2C,10 January 2021,William Lam,"Atrayees,WikiWorks,Folakunmi",Comparsion of patients with partial progressive survival free more than 3 months and less than 3 in fecal samples of patients (excluding those treated with antibiotics) with non-small cell lung cell lung carcinoma (NSCLC) or renal cell carcinoma (RCC) reponse at 3 months of PD-1 monoclonal antibodies (mAB) treatment,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|s__Bacillota bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:110,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759;1783272|1239;1783272|1239|1879010;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|291645;3379134|976|200643|171549|815|816|371601;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485|1506;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730|142586;1783272|1239|1263000;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|541000;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|41978;1783272|1239;1783272|1239|186801|186802,Complete,Folakunmi
bsdb:29097494/2/2,29097494,time series / longitudinal observational,29097494,10.1126/science.aan3706,NA,"Routy B., Le Chatelier E., Derosa L., Duong C.P.M., Alou M.T., Daillère R., Fluckiger A., Messaoudene M., Rauber C., Roberti M.P., Fidelle M., Flament C., Poirier-Colame V., Opolon P., Klein C., Iribarren K., Mondragón L., Jacquelot N., Qu B., Ferrere G., Clémenson C., Mezquita L., Masip J.R., Naltet C., Brosseau S., Kaderbhai C., Richard C., Rizvi H., Levenez F., Galleron N., Quinquis B., Pons N., Ryffel B., Minard-Colin V., Gonin P., Soria J.C., Deutsch E., Loriot Y., Ghiringhelli F., Zalcman G., Goldwasser F., Escudier B., Hellmann M.D., Eggermont A., Raoult D., Albiges L., Kroemer G. , Zitvogel L.",Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors,"Science (New York, N.Y.)",2018,NA,Experiment 2,France,Homo sapiens,Feces,UBERON:0001988,"Non-small cell lung carcinoma,Renal cell carcinoma,Disease progression measurement","EFO:0003060,EFO:0000681,EFO:0008336",Progressive- Free- Survival more less than 30 days,Progressive -Free- Survival more than 30 days,"non-small cell lung carcinoma or renal carcinoma patients (excluding ampicillin, colistin, and streptomycin (ATB) anitbiotic treatment) that have been treated with PD-1 blockage with partial response or stable disease that are Progressive- Free- Survival greater than 3 months",100,100,NA,WMS,NA,Mass spectrometry,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2C,10 January 2021,William Lam,"Atrayees,WikiWorks,Folakunmi",Comparsion of patients with partial progressive survival free more than 3 months and less than 3 in fecal samples of patients (excluding those treated with antibiotics) with non-small cell lung cell lung carcinoma (NSCLC) or renal cell carcinoma (RCC) reponse at 3 months of PD-1 monoclonal antibodies (mAB) treatment,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Bacillota|s__Bacillota bacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239|186801|186802|216572|244127|169435;1783272|1239|1879010;1783272|1239|526524|526525|128827;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|2005525|375288|823;1783272|1239|186801|186802,Complete,Folakunmi
bsdb:29097494/3/1,29097494,time series / longitudinal observational,29097494,10.1126/science.aan3706,NA,"Routy B., Le Chatelier E., Derosa L., Duong C.P.M., Alou M.T., Daillère R., Fluckiger A., Messaoudene M., Rauber C., Roberti M.P., Fidelle M., Flament C., Poirier-Colame V., Opolon P., Klein C., Iribarren K., Mondragón L., Jacquelot N., Qu B., Ferrere G., Clémenson C., Mezquita L., Masip J.R., Naltet C., Brosseau S., Kaderbhai C., Richard C., Rizvi H., Levenez F., Galleron N., Quinquis B., Pons N., Ryffel B., Minard-Colin V., Gonin P., Soria J.C., Deutsch E., Loriot Y., Ghiringhelli F., Zalcman G., Goldwasser F., Escudier B., Hellmann M.D., Eggermont A., Raoult D., Albiges L., Kroemer G. , Zitvogel L.",Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors,"Science (New York, N.Y.)",2018,NA,Experiment 3,France,Homo sapiens,Feces,UBERON:0001988,"Non-small cell lung carcinoma,Renal cell carcinoma,Disease progression measurement","EFO:0003060,EFO:0000681,EFO:0008336",Non-Responders,Responders,"non-small cell lung carcinoma or renal carcinoma patients (all samples regardless of ampicillin, colistin, and streptomycin (ATB) anitbiotic treatment) that have been treated with PD-1 blockage with partial response or stable disease",16,16,NA,WMS,NA,Mass spectrometry,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2g,10 January 2021,William Lam,WikiWorks,"Culturomics-based analyses of fecal samples in 16 Responders and 16 Non-Responders Non-Small Cell Lung Carcinoma patients (defined as the best clinical outcome) before PD-1 blockage immunotherapy, each commensal colony having been identified by mass spectrometry",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus haemolyticus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium aurimucosum",1783272|1239|91061|1385|90964|1279|1283;1783272|201174|1760|85007|1653|1716|169292,Complete,Folakunmi
bsdb:29102920/1/1,29102920,"cross-sectional observational, not case-control",29102920,10.1136/gutjnl-2017-314205,NA,"Ferreira R.M., Pereira-Marques J., Pinto-Ribeiro I., Costa J.L., Carneiro F., Machado J.C. , Figueiredo C.",Gastric microbial community profiling reveals a dysbiotic cancer-associated microbiota,Gut,2018,"Helicobacter pylori, bacterial infection, gastric carcinoma, gastritis",Experiment 1,Portugal,Homo sapiens,Stomach,UBERON:0000945,Gastric carcinoma,EFO:0000178,chronic gastritis,gastric carcinoma,gastric carcinoma,81,54,NA,16S,56,Ion Torrent,relative abundances,LEfSe,0.05,TRUE,4,age,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,"Figure 3, Figure S4",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differential microbial abundance between chronic gastritis and gastric carcinoma patients by LefSe,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter|s__Achromobacter sp.,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium|s__Phyllobacterium sp.,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus|s__Rhodococcus sp. (in: high G+C Gram-positive bacteria),k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales",3379134|1224|28216|80840|506|222|134375;1783272|201174;3379134|1224|28216|80840;3379134|976|117743|200644|2762318|59732|1871047;3379134|1224|1236|91347|543|544|1896336;1783272|1239|186801|186802|31979|1485|1506;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236;1783272|201174|1760|85007|85025;3379134|1224|28211|356|69277|28100|1871046;3379134|1224;3379134|1224|1236|72274|135621|286|306;1783272|201174|1760|85007|85025|1827|1831;3379134|1224|1236|135614|32033;3379134|1224|1236|135614,Complete,Claregrieve1
bsdb:29102920/1/2,29102920,"cross-sectional observational, not case-control",29102920,10.1136/gutjnl-2017-314205,NA,"Ferreira R.M., Pereira-Marques J., Pinto-Ribeiro I., Costa J.L., Carneiro F., Machado J.C. , Figueiredo C.",Gastric microbial community profiling reveals a dysbiotic cancer-associated microbiota,Gut,2018,"Helicobacter pylori, bacterial infection, gastric carcinoma, gastritis",Experiment 1,Portugal,Homo sapiens,Stomach,UBERON:0000945,Gastric carcinoma,EFO:0000178,chronic gastritis,gastric carcinoma,gastric carcinoma,81,54,NA,16S,56,Ion Torrent,relative abundances,LEfSe,0.05,TRUE,4,age,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,"Figure 3, Figure S4",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differential microbial abundance between chronic gastritis and gastric carcinoma patients by LefSe,decreased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota,k__Bacillati|p__Bacillota,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter sp.,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sp.",1783272|1239|91061;3379134|976|200643;3379134|976;3379134|29547|3031852|213849;3379134|29547;1783272|1239;3384189|32066;3384189|32066|203490;3379134|29547|3031852|213849|72293|209|218;3379134|29547|3031852|213849|72293;1783272|1239|91061|186826;3379134|1224|28216|206351|481|482|192066;3379134|1224|28216|206351;3379134|976|200643|171549|171552|838|59823;3379134|976|200643|171549|171552;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301|1306;1783272|1239|91061|1385|539738|1378|1966354,Complete,Claregrieve1
bsdb:29133803/1/1,29133803,"cross-sectional observational, not case-control",29133803,https://doi.org/10.1038/s41598-017-15554-8,https://www.nature.com/articles/s41598-017-15554-8.,"Mehta S.D., Pradhan A.K., Green S.J., Naqib A., Odoyo-June E., Gaydos C.A., Barry S., Landay A. , Bailey R.C.",Microbial Diversity of Genital Ulcers of HSV-2 Seropositive Women,Scientific reports,2017,NA,Experiment 1,Kenya,Homo sapiens,External female genitalia,UBERON:0005056,HSV2 virologic severity measurement,EFO:0009010,Women with HSV-2 PCR- Negative Ulcers,Women with HSV-2 PCR- Positive Ulcers,Patients were classified as having genital ulcers if detected using polymerase chain reaction (PCR),21,28,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.1,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Table 4,9 April 2025,Ese,Ese,Differentially abundant bacterial taxa in women with HSV-2 PCR positive ulcers,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",1783272|1239|1737404|1737405|1570339|165779;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|1239|909932|1843489|31977|39948,Complete,Svetlana up
bsdb:29133803/2/2,29133803,"cross-sectional observational, not case-control",29133803,https://doi.org/10.1038/s41598-017-15554-8,https://www.nature.com/articles/s41598-017-15554-8.,"Mehta S.D., Pradhan A.K., Green S.J., Naqib A., Odoyo-June E., Gaydos C.A., Barry S., Landay A. , Bailey R.C.",Microbial Diversity of Genital Ulcers of HSV-2 Seropositive Women,Scientific reports,2017,NA,Experiment 2,Kenya,Homo sapiens,External female genitalia,UBERON:0005056,HIV infection,EFO:0000764,HIV Negative Women,HIV Positive Women,Patients were classified as having HIV after undergoing HIV testing conducted according to Kenyan national guidelines.,18,30,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 4,14 April 2025,Ese,Ese,Differentially abundant bacterial taxa in HIV Positive Women,decreased,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,1783272|1239|1737404|1737405|1570339|150022,Complete,Svetlana up
bsdb:29152146/1/1,29152146,case-control,29152146,10.18632/oncotarget.21490,NA,"Wang H., Altemus J., Niazi F., Green H., Calhoun B.C., Sturgis C., Grobmyer S.R. , Eng C.","Breast tissue, oral and urinary microbiomes in breast cancer",Oncotarget,2017,"breast cancer, metagenomics, microbiome, oral, urine",Experiment 1,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,healthy controls,breast cancer patients,"Breast cancer patients eligible were over 18 years of age, female, had tumors greater than or equal to 2 cm in size, were undergoing mastectomy. Patients receiving neo-adjuvant therapy prior to surgery or with active clinical breast infection were excluded from the study.",24,39,NA,16S,34,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4: A) Breast Tissue,27 June 2025,Ecsharp,Ecsharp,Taxa Significantly Different in Cancer vs. Non-Cancer Samples by Wilcoxon Rank Sum,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria",3379134|1224|28216;1783272|1239|1737404|1737405|1570339|162289;3379134|1224|28216|80840|506;3379134|1224|1236|91347|543;3379134|1224|1236|91347;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85006|1268;3379134|1224|1236,Complete,NA
bsdb:29152146/1/2,29152146,case-control,29152146,10.18632/oncotarget.21490,NA,"Wang H., Altemus J., Niazi F., Green H., Calhoun B.C., Sturgis C., Grobmyer S.R. , Eng C.","Breast tissue, oral and urinary microbiomes in breast cancer",Oncotarget,2017,"breast cancer, metagenomics, microbiome, oral, urine",Experiment 1,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,healthy controls,breast cancer patients,"Breast cancer patients eligible were over 18 years of age, female, had tumors greater than or equal to 2 cm in size, were undergoing mastectomy. Patients receiving neo-adjuvant therapy prior to surgery or with active clinical breast infection were excluded from the study.",24,39,NA,16S,34,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 4: A) Breast Tissue,30 June 2025,Ecsharp,Ecsharp,Taxa Significantly Different in Cancer vs. Non-Cancer Samples by Wilcoxon Rank Sum,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae",1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;1783272|201174|84998|84999|1643824|1380;3379134|1224|28211|356|119045|407;3379134|1224|28211|356|119045;1783272|1239|186801|3085636|186803|43996;1783272|1239|91061|1385|539738,Complete,NA
bsdb:29152146/2/1,29152146,case-control,29152146,10.18632/oncotarget.21490,NA,"Wang H., Altemus J., Niazi F., Green H., Calhoun B.C., Sturgis C., Grobmyer S.R. , Eng C.","Breast tissue, oral and urinary microbiomes in breast cancer",Oncotarget,2017,"breast cancer, metagenomics, microbiome, oral, urine",Experiment 2,United States of America,Homo sapiens,Urine,UBERON:0001088,Breast cancer,MONDO:0007254,healthy controls,breast cancer patients,"Breast cancer patients eligible were over 18 years of age, female, had tumors greater than or equal to 2 cm in size, were undergoing mastectomy. Patients receiving neo-adjuvant therapy prior to surgery or with active clinical breast infection were excluded from the study.",19,46,NA,16S,34,Illumina,NA,LEfSe,0.05,FALSE,2,NA,menopause,NA,increased,NA,NA,NA,NA,Signature 1,Supplementary Table 4: B) Urine,30 June 2025,Ecsharp,Ecsharp,Taxa Significantly Different in Cancer vs. Non-Cancer Samples Independent of Menopausal Status,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|201174|1760|2037;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|1385|186818;1783272|201174|1760|85009|31957;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|1385;3379134|1224|28211;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279,Complete,NA
bsdb:29152146/3/1,29152146,case-control,29152146,10.18632/oncotarget.21490,NA,"Wang H., Altemus J., Niazi F., Green H., Calhoun B.C., Sturgis C., Grobmyer S.R. , Eng C.","Breast tissue, oral and urinary microbiomes in breast cancer",Oncotarget,2017,"breast cancer, metagenomics, microbiome, oral, urine",Experiment 3,United States of America,Homo sapiens,Urine,UBERON:0001088,Menopause,EFO:0003922,Premenopausal women,Peri/postmenopausal women,"Urine samples from patients with peri/postmenopausal menopausal status from the entire cohort, consisting of both cancer and healthy patients.",32,44,NA,16S,34,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplementary Table 4: B) Urine,30 June 2025,Ecsharp,Ecsharp,Taxa Significantly Different in Premenopausal vs. Peri/Postmenopausal Patient Samples by Wilcoxon Rank Sum,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Helcococcus,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Trueperella,s__bacterium PH2,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia",1783272|1239|91061|186826|186827|66831;1783272|1239|186801|186802|216572;1783272|1239|1737404|1737405|1737406;1783272|1239|1737404|1737405|1570339|162289;1783272|201174|1760|2037|2049;1783272|1239|186801;1783272|1239|186801|186802|1898207;1783272|1239|91061|186826|186827;1783272|201174|1760|2037;1783272|1239|186801|3085636|186803|33042;3379134|29547|3031852|213849;3379134|29547|3031852|213849|72294;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|186801|3085636|186803|572511;1783272|201174|1760|85009|31957;1783272|201174|1760|2037|2049|184869;1783272|1239|909932|1843489|31977|39948;3379134|976|200643|171549|171551;1783272|1239|1737404|1737405|1570339|31983;3379134|1224;3379134|976|200643;3379134|976|200643|171549;3379134|976;1783272|1239|909932|1843489|31977;1783272|201174|1760|2037|2049|76833;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|189330;1783272|201174|1760|2037|2049|1069494;239775;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;3379134|1224|1236|91347|1903414|583;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|841;1783272|1239|91061|186826|81852;1783272|201174;1783272|201174|1760|2037|2049|1654;3379134|200940|3031449|213115;3379134|200940|3031449|213115|194924;28221;3379134|200940|3031449|213115|194924|35832;1783272|1239|1737404|1737405|1570339|150022,Complete,NA
bsdb:29152146/3/2,29152146,case-control,29152146,10.18632/oncotarget.21490,NA,"Wang H., Altemus J., Niazi F., Green H., Calhoun B.C., Sturgis C., Grobmyer S.R. , Eng C.","Breast tissue, oral and urinary microbiomes in breast cancer",Oncotarget,2017,"breast cancer, metagenomics, microbiome, oral, urine",Experiment 3,United States of America,Homo sapiens,Urine,UBERON:0001088,Menopause,EFO:0003922,Premenopausal women,Peri/postmenopausal women,"Urine samples from patients with peri/postmenopausal menopausal status from the entire cohort, consisting of both cancer and healthy patients.",32,44,NA,16S,34,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Supplementary Table 4: B) Urine,30 June 2025,Ecsharp,Ecsharp,Taxa Significantly Different in Premenopausal vs. Peri/Postmenopausal Patient Samples by Wilcoxon Rank Sum,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958;1783272|1239|186801|3085636|186803|177971;1783272|1239|91061|186826;1783272|1239|91061;1783272|1239,Complete,NA
bsdb:29166320/1/1,29166320,time series / longitudinal observational,29166320,10.1249/MSS.0000000000001495,NA,"Allen J.M., Mailing L.J., Niemiro G.M., Moore R., Cook M.D., White B.A., Holscher H.D. , Woods J.A.",Exercise Alters Gut Microbiota Composition and Function in Lean and Obese Humans,Medicine and science in sports and exercise,2018,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Exercise,EFO:0000483,lean subjects,obese subjects,sedentary participants between 20 and 45 years of age with BMI > 30 (classified as obese),18,14,3 months,16S,4,Illumina,NA,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 2d,29 December 2022,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance between obese and lean participants after the 6 week exercise program,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",3379134|976|200643|171549|815|816;1783272|201174|84998|84999|84107|102106,Complete,Claregrieve1
bsdb:29166320/1/2,29166320,time series / longitudinal observational,29166320,10.1249/MSS.0000000000001495,NA,"Allen J.M., Mailing L.J., Niemiro G.M., Moore R., Cook M.D., White B.A., Holscher H.D. , Woods J.A.",Exercise Alters Gut Microbiota Composition and Function in Lean and Obese Humans,Medicine and science in sports and exercise,2018,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Exercise,EFO:0000483,lean subjects,obese subjects,sedentary participants between 20 and 45 years of age with BMI > 30 (classified as obese),18,14,3 months,16S,4,Illumina,NA,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 2d,29 December 2022,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance between obese and lean participants after the 6 week exercise program,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|28050,Complete,Claregrieve1
bsdb:29166320/2/1,29166320,time series / longitudinal observational,29166320,10.1249/MSS.0000000000001495,NA,"Allen J.M., Mailing L.J., Niemiro G.M., Moore R., Cook M.D., White B.A., Holscher H.D. , Woods J.A.",Exercise Alters Gut Microbiota Composition and Function in Lean and Obese Humans,Medicine and science in sports and exercise,2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Exercise,EFO:0000483,lean subjects,obese subjects,sedentary participants between 20 and 45 years of age with BMI >30 (classified as obese),18,14,3 months,16S,NA,Illumina,NA,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 2d,29 December 2022,Claregrieve1,"Claregrieve1,Lwaldron,WikiWorks",Differential abundance between obese and lean participants after the 6 week sedentary washout post-exercise program,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",1783272|1239|186801|3085636|186803|189330;1783272|201174|84998|84999|84107|102106,Complete,Claregrieve1
bsdb:29166320/2/2,29166320,time series / longitudinal observational,29166320,10.1249/MSS.0000000000001495,NA,"Allen J.M., Mailing L.J., Niemiro G.M., Moore R., Cook M.D., White B.A., Holscher H.D. , Woods J.A.",Exercise Alters Gut Microbiota Composition and Function in Lean and Obese Humans,Medicine and science in sports and exercise,2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Exercise,EFO:0000483,lean subjects,obese subjects,sedentary participants between 20 and 45 years of age with BMI >30 (classified as obese),18,14,3 months,16S,NA,Illumina,NA,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 2e,16 March 2023,Lwaldron,"Lwaldron,WikiWorks",Differential abundance between obese and lean participants after the 6 week sedentary washout post-exercise program,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|28050,Complete,NA
bsdb:29167295/1/1,29167295,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva P.T., Tun H.M., Konya T., Guttman D.S., Becker A.B., Mandhane P.J., Turvey S.E., Subbarao P., Sears M.R., Scott J.A. , Kozyrskyj A.L.",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,NA,Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma,maternal asthma/male caucasian infants,male caucasian infants born to mothers who had prenatal asthma,504,41,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 1a,10 January 2021,Lucy Mellor,"KathyWaldron,WikiWorks,Merit,ChiomaBlessing,Folakunmi",Linear discriminant analysis (LDA) plots for maternal prenatal atopic asthma for those who gave birth to male caucasian infants compared to no asthma group.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|1239|91061|186826|1300|1357;1783272|1239|909932|909929|1843491|158846;1783272|201174|1760|2037|2049|1654;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|1385|539738;1783272|1239|909932|909929|1843491|158846,Complete,Folakunmi
bsdb:29167295/1/2,29167295,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva P.T., Tun H.M., Konya T., Guttman D.S., Becker A.B., Mandhane P.J., Turvey S.E., Subbarao P., Sears M.R., Scott J.A. , Kozyrskyj A.L.",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,NA,Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma,maternal asthma/male caucasian infants,male caucasian infants born to mothers who had prenatal asthma,504,41,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 1a,10 January 2021,Lucy Mellor,"KathyWaldron,WikiWorks,ChiomaBlessing,Folakunmi",Linear discriminant analysis (LDA) plots for maternal prenatal atopic asthma for those who gave birth to male caucasian infants compared to no asthma group.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Trabulsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",3379134|1224|1236|91347|543|158851;1783272|1239|91061|186826|33958|1578,Complete,Folakunmi
bsdb:29167295/2/1,29167295,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva P.T., Tun H.M., Konya T., Guttman D.S., Becker A.B., Mandhane P.J., Turvey S.E., Subbarao P., Sears M.R., Scott J.A. , Kozyrskyj A.L.",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,NA,Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma,maternal asthma,female caucasian infants born to mothers who had prenatal asthma,430,46,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 1b,10 January 2021,Lucy Mellor,"KathyWaldron,WikiWorks,ChiomaBlessing,Folakunmi",Linear discriminant analysis (LDA) plots for maternal prenatal atopic asthma for those who gave birth to female caucasian infants compared to no asthma group.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|817;3379134|976|200643;3379134|976;3379134|1224|1236|72274|135621|286;3379134|1224|1236|72274|135621|286,Complete,Folakunmi
bsdb:29167295/2/2,29167295,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva P.T., Tun H.M., Konya T., Guttman D.S., Becker A.B., Mandhane P.J., Turvey S.E., Subbarao P., Sears M.R., Scott J.A. , Kozyrskyj A.L.",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,NA,Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma,maternal asthma,female caucasian infants born to mothers who had prenatal asthma,430,46,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 1b,10 January 2021,Lucy Mellor,"WikiWorks,Merit,ChiomaBlessing,Folakunmi",Linear discriminant analysis (LDA) plots for maternal prenatal atopic asthma for those who gave birth to female caucasian infants compared to no asthma group.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.",1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|186802|31979|1485|1506,Complete,Folakunmi
bsdb:29167295/4/1,29167295,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva P.T., Tun H.M., Konya T., Guttman D.S., Becker A.B., Mandhane P.J., Turvey S.E., Subbarao P., Sears M.R., Scott J.A. , Kozyrskyj A.L.",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,NA,Experiment 4,Canada,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma,maternal asthma/caucasian infants,mothers of caucasian infants who had prenatal asthma,721,74,NA,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table 2,10 January 2021,Lucy Mellor,WikiWorks,"Median relative abundance of dominant bacterial taxa at the phylum, family and genus levels in infant gut microbiota according to material prenatal asthma in caucasian infants",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578,Complete,Folakunmi
bsdb:29167295/5/1,29167295,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva P.T., Tun H.M., Konya T., Guttman D.S., Becker A.B., Mandhane P.J., Turvey S.E., Subbarao P., Sears M.R., Scott J.A. , Kozyrskyj A.L.",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,NA,Experiment 5,Canada,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma,maternal asthma/female infants,"prenatal asthma mothers of female infants who were vaginally delivered, breastfed, not exposed to maternal antibiotics",186,21,NA,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table S2,10 January 2021,Lucy Mellor,WikiWorks,"Median relative abundance of dominant bacterial taxa in infant gut microbiota according to material prenatal asthma in female infants, vaginally delivered, breastfed, not exposed to materal antibiotics during birth",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976;1783272|1239|186801|3085636|186803|189330,Complete,Folakunmi
bsdb:29167295/5/2,29167295,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva P.T., Tun H.M., Konya T., Guttman D.S., Becker A.B., Mandhane P.J., Turvey S.E., Subbarao P., Sears M.R., Scott J.A. , Kozyrskyj A.L.",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,NA,Experiment 5,Canada,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma,maternal asthma/female infants,"prenatal asthma mothers of female infants who were vaginally delivered, breastfed, not exposed to maternal antibiotics",186,21,NA,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table S2,10 January 2021,Lucy Mellor,WikiWorks,"Median relative abundance of dominant bacterial taxa in infant gut microbiota according to material prenatal asthma in female infants, vaginally delivered, breastfed, not exposed to materal antibiotics during birth",decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",1783272|1239;3379134|1224;3379134|1224|1236|91347|543,Complete,Folakunmi
bsdb:29167295/6/1,29167295,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva P.T., Tun H.M., Konya T., Guttman D.S., Becker A.B., Mandhane P.J., Turvey S.E., Subbarao P., Sears M.R., Scott J.A. , Kozyrskyj A.L.",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,NA,Experiment 6,Canada,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma,maternal asthma/caucasian infants/allergies,"prenatal asthma mothers of caucasian infants, who had allergies during pregnancy",429,64,NA,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table S3,10 January 2021,Lucy Mellor,WikiWorks,"Median relative abundance of dominant bacterial taxa at the phylum, family and genus levels in infant gut microbiota according to material prenatal asthma in caucasian mothers with allergies during pregnancy",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|906;3379134|1224|1236|91347|543,Complete,Folakunmi
bsdb:29167295/7/1,29167295,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva P.T., Tun H.M., Konya T., Guttman D.S., Becker A.B., Mandhane P.J., Turvey S.E., Subbarao P., Sears M.R., Scott J.A. , Kozyrskyj A.L.",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,NA,Experiment 7,Canada,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma,maternal asthma/caucasian infants/no allergies,"prenatal asthma mothers of caucasian infants, who had no allergies during pregnancy",278,10,NA,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table S3,10 January 2021,Lucy Mellor,WikiWorks,"Median relative abundance of dominant bacterial taxa at the phylum, family and genus levels in infant gut microbiota according to material prenatal asthma in caucasian mothers with no allergies during pregnancy",increased,"k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",3379134|74201;3379134|74201|203494|48461|203557;3379134|74201|203494|48461|1647988|239934,Complete,Folakunmi
bsdb:29167295/7/2,29167295,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva P.T., Tun H.M., Konya T., Guttman D.S., Becker A.B., Mandhane P.J., Turvey S.E., Subbarao P., Sears M.R., Scott J.A. , Kozyrskyj A.L.",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,NA,Experiment 7,Canada,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma,maternal asthma/caucasian infants/no allergies,"prenatal asthma mothers of caucasian infants, who had no allergies during pregnancy",278,10,NA,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table S3,10 January 2021,Lucy Mellor,WikiWorks,"Median relative abundance of dominant bacterial taxa at the phylum, family and genus levels in infant gut microbiota according to material prenatal asthma in caucasian mothers with no allergies during pregnancy",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",1783272|201174|1760|2037|2049;1783272|201174|1760|2037|2049|1654,Complete,Folakunmi
bsdb:29167295/8/1,29167295,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva P.T., Tun H.M., Konya T., Guttman D.S., Becker A.B., Mandhane P.J., Turvey S.E., Subbarao P., Sears M.R., Scott J.A. , Kozyrskyj A.L.",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,NA,Experiment 8,Canada,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma,overweight prenatal asthma caucasian mothers,"prenatal asthma mothers of caucasian infants, who were overweight/obese before pregnancy",291,33,NA,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table S3,27 February 2024,Folakunmi,"Folakunmi,WikiWorks","Median relative abundance of bacterial taxa at phylum, family and genus level in fecal microbiota at 3-4 months according to maternal asthma during pregnancy, restricted to Caucasian mothers and stratified by maternal pre-pregnancy weight",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|81850;1783272|1239|909932|1843489|31977|906,Complete,Folakunmi
bsdb:29172724/1/1,29172724,case-control,29172724,10.1080/02713683.2017.1406528,NA,"Ham B., Hwang H.B., Jung S.H., Chang S., Kang K.D. , Kwon M.J.",Distribution and Diversity of Ocular Microbial Communities in Diabetic Patients Compared with Healthy Subjects,Current eye research,2018,"Bacterial diversity, Bradyrhizobiaceae, Burkholderia, LFR analysis, Staphylococcus",Experiment 1,Republic of Korea,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Type II diabetes mellitus,MONDO:0005148,healthy controls,diabetic,Type 2 diabetic patients undergoing vitrectomy,16,9,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,NA,2.6,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 5,19 September 2023,Mary Bearkland,"Mary Bearkland,Peace Sandy,WikiWorks","Figure 5. Comparative analysis of the microbial communities of groups with and without diabetes at the phylum (A) and genus (B) levels using the linear
discriminant analysis (LDA) effect size (LEfSe) method. LDA scores (log 10) for the most prevalent taxa in diabetic patients are represented on the positive scale,
whereas LDA-negative scores indicate enriched taxa in the healthy controls.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Asticcacaulis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae,c__Deltaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfotomaculaceae|g__Desulfotomaculum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Desulfuromonadales|f__Desulfuromonadaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Desulfuromonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Idiomarinaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Marinobacteraceae|g__Marinobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Mycoplana,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Nesterenkonia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae|g__Rheinheimera,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|g__Rhodobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Saccharopolyspora,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Salinibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales,k__Metazoa|p__Chordata|c__Lepidosauria|o__Squamata|f__Viperidae|s__Crotalinae|g__Trimeresurus|s__Trimeresurus fasciatus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Wautersiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae",3379134|1224|1236|2887326|468|469;1783272|1239|91061|186826|186827;1783272|1239|91061|186826|186827|1375;3379134|1224|1236|135624;3379134|1224|28211|356|82115|357;3379134|1224|1236|135622|72275;3379134|1224|1236|135622;1783272|201174|1760|85006|1268|1663;3379134|1224|28211|204458|76892|76890;3379134|1224|28211|204441|2829815|191;1783272|201174|1760|85006|85019;1783272|201174|1760|85006|85019|1696;3379134|1224|28216|80840|119060|32008;3379134|1224|28216|80840|119060;3379134|1224|28216|80840;3379134|1224|1236|135613|1046;28221;1783272|1239|186801|186802|2937910|1562;3379134|200940|3031651|69541|213421;3379134|200940|3031651|69541;3379134|1224|1236;3379134|1224|1236|135619|28256;3379134|1224|1236|135619|28256|2745;3379134|1224|1236|135622|267893;1783272|201174|1760|85006|85021;3379134|1224|1236|72274|2887365|2742;1783272|201174|1760|85006|1268;1783272|201174|1760|85006|1268|1269;3379134|1224|1236|2887326|468;3379134|1224|28211|356|82115|13159;1783272|201174|1760|85006|1268|57494;3379134|1224|1236|135619;3379134|1224|28216|80840|75682;3379134|1224|28211|204455|31989;1783272|1239|186801|186802|186807;3379134|1224|28211|356|69277;3379134|1224|28211|356|69277|28100;1783272|1239|91061|1385|186818;3379134|1224|1236|72274;3379134|1224;1783272|201174|1760|85010|2070;3379134|1224|1236|135613|1046|67575;3379134|1224|28211|356|82115;3379134|1224|28211|204455|1060;3379134|1224|28211|204441|41295;1783272|201174|1760|85010|2070|1835;1783272|201174|1760|85006|85023|235888;1783272|1239|186801|68295;33208|7711|8504|8509|8689|8710|8764|342873;3379134|976|117743|200644|2762318|343873;3379134|1224|1236|135613|1046,Complete,Peace Sandy
bsdb:29172724/1/2,29172724,case-control,29172724,10.1080/02713683.2017.1406528,NA,"Ham B., Hwang H.B., Jung S.H., Chang S., Kang K.D. , Kwon M.J.",Distribution and Diversity of Ocular Microbial Communities in Diabetic Patients Compared with Healthy Subjects,Current eye research,2018,"Bacterial diversity, Bradyrhizobiaceae, Burkholderia, LFR analysis, Staphylococcus",Experiment 1,Republic of Korea,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Type II diabetes mellitus,MONDO:0005148,healthy controls,diabetic,Type 2 diabetic patients undergoing vitrectomy,16,9,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,NA,2.6,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 5,20 September 2023,Mary Bearkland,"Mary Bearkland,Boadiwaa,WikiWorks","Figure 5. Comparative analysis of the microbial communities of groups with and without diabetes at the phylum (A) and genus (B) levels using the linear
discriminant analysis (LDA) effect size (LEfSe) method. LDA scores (log 10) for the most prevalent taxa in diabetic patients are represented on the positive scale,
whereas LDA-negative scores indicate enriched taxa in the healthy controls.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Viridiplantae|p__Streptophyta,k__Bacillati|p__Cyanobacteriota",3379134|1224|28211;1783272|1239|91061|1385;1783272|1239|91061;1783272|1239;1783272|1239|186801|186802|31979;1783272|1117;3379134|1224|28211|356;3379134|1224|28211|356|41294;3379134|1224|28211|204457|41297|165696;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;33090|35493;1783272|1117,Complete,Peace Sandy
bsdb:29180991/1/1,29180991,case-control,29180991,10.3389/fmicb.2017.02222,NA,"Wang J., Wang Y., Zhang X., Liu J., Zhang Q., Zhao Y., Peng J., Feng Q., Dai J., Sun S., Zhao Y., Zhao L., Zhang Y., Hu Y. , Zhang M.",Gut Microbial Dysbiosis Is Associated with Altered Hepatic Functions and Serum Metabolites in Chronic Hepatitis B Patients,Frontiers in microbiology,2017,"16S rRNA gene sequencing, aromatic amino acids, chronic hepatitis B, gut sysbiosis, serum metabolomics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic hepatitis B virus infection,EFO:0004239,healthy controls,chronic hepatitis B patients,Chronic hepatitis B patients,22,85,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 2,10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differential microbial abundance between chronic hepatitis patients and controls,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|909932|909929|1843491|158846;1783272|201174|1760|2037|2049|1654;1783272|1239|186801|186802|31979|1485|1506;1783272|1239|186801|3085636|186803,Complete,Claregrieve1
bsdb:29180991/1/2,29180991,case-control,29180991,10.3389/fmicb.2017.02222,NA,"Wang J., Wang Y., Zhang X., Liu J., Zhang Q., Zhao Y., Peng J., Feng Q., Dai J., Sun S., Zhao Y., Zhao L., Zhang Y., Hu Y. , Zhang M.",Gut Microbial Dysbiosis Is Associated with Altered Hepatic Functions and Serum Metabolites in Chronic Hepatitis B Patients,Frontiers in microbiology,2017,"16S rRNA gene sequencing, aromatic amino acids, chronic hepatitis B, gut sysbiosis, serum metabolomics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic hepatitis B virus infection,EFO:0004239,healthy controls,chronic hepatitis B patients,Chronic hepatitis B patients,22,85,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table 2,10 January 2021,Rimsha Azhar,"Fatima,Claregrieve1,WikiWorks",Differential microbial abundance between chronic hepatitis patients and controls,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Asaccharobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|976|200643|171549|815|816;3379134|976|200643|171549|1853231|574697;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;3379134|1224|1236|91347|543;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|1898207;1783272|201174|84998|1643822|1643826|553372;1783272|201174|84998|84999|84107;3379134|1224|1236|91347|543|1940338;3379134|1224|1236|91347|543;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572,Complete,Claregrieve1
bsdb:29186529/1/1,29186529,randomized controlled trial,29186529,10.1093/infdis/jix604,NA,"de Gunzburg J., Ghozlane A., Ducher A., Le Chatelier E., Duval X., Ruppé E., Armand-Lefevre L., Sablier-Gallis F., Burdet C., Alavoine L., Chachaty E., Augustin V., Varastet M., Levenez F., Kennedy S., Pons N., Mentré F. , Andremont A.",Protection of the Human Gut Microbiome From Antibiotics,The Journal of infectious diseases,2018,"Clostridium difficile, antibiotics, fluoroquinolones, microbiome",Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Negative control group (CLT),moxifloxacin treated group (MXF),healthy male and female volunteers aged >18 years,8,14,3 months,WMS,NA,Mass spectrometry,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,"Supplementary table 3, Supplementary figure 1",10 January 2021,Mst Afroza Parvin,WikiWorks,A detailed analysis of the MGSs that differed significantly between treatment groups,increased,",k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",;1783272|1239|186801|3085636|186803|572511,Complete,NA
bsdb:29186529/1/2,29186529,randomized controlled trial,29186529,10.1093/infdis/jix604,NA,"de Gunzburg J., Ghozlane A., Ducher A., Le Chatelier E., Duval X., Ruppé E., Armand-Lefevre L., Sablier-Gallis F., Burdet C., Alavoine L., Chachaty E., Augustin V., Varastet M., Levenez F., Kennedy S., Pons N., Mentré F. , Andremont A.",Protection of the Human Gut Microbiome From Antibiotics,The Journal of infectious diseases,2018,"Clostridium difficile, antibiotics, fluoroquinolones, microbiome",Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Negative control group (CLT),moxifloxacin treated group (MXF),healthy male and female volunteers aged >18 years,8,14,3 months,WMS,NA,Mass spectrometry,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,"Supplementary table 3, Supplementary figure 1",10 January 2021,Mst Afroza Parvin,"Lwaldron,WikiWorks",A detailed analysis of the MGSs that differed significantly between treatment groups,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium|s__Cloacibacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549;3379134|976|200643|171549|2005519|397864|487174;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|28026;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|1955243;3379134|976|200643|171549|1853231|574697;3379134|976|200643|171549|1853231|574697|544645;1783272|1239|526524|526525|2810280|135858;3379134|976|117743|200644|2762318|501783|1913682;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|31979|1485|1506;1783272|1239|526524|526525|2810280|100883;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239;3379134|1224|1236|135625|712|724|729;1783272|1239|186801|3082720|186804|1505657|261299;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|1853231|283168|28118;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|459786|1945593;1783272|1239|186801|186802|541000;3379134|976|200643|171549|2005525|375288|823;3379134|1224|28216|80840|995019|577310|487175;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|91061|186826|1300|1301|1318,Complete,NA
bsdb:29186529/2/1,29186529,randomized controlled trial,29186529,10.1093/infdis/jix604,NA,"de Gunzburg J., Ghozlane A., Ducher A., Le Chatelier E., Duval X., Ruppé E., Armand-Lefevre L., Sablier-Gallis F., Burdet C., Alavoine L., Chachaty E., Augustin V., Varastet M., Levenez F., Kennedy S., Pons N., Mentré F. , Andremont A.",Protection of the Human Gut Microbiome From Antibiotics,The Journal of infectious diseases,2018,"Clostridium difficile, antibiotics, fluoroquinolones, microbiome",Experiment 2,France,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,moxifloxacin treated group (MXF),DAV132+moxifloxacin treated group (MXF+DAV132),healthy male and female volunteers aged >18 years,14,14,3 months,WMS,NA,Mass spectrometry,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,"Supplementary table 3, Supplementary figure 1",10 January 2021,Mst Afroza Parvin,WikiWorks,A detailed analysis of the MGSs that differed significantly between treatment groups,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium|s__Cloacibacterium sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp.,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis",3379134|976|200643|171549|2005525|375288|823;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|3085636|186803|841|360807;3379134|976|200643|171549|1853231|283168|28118;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|572511|1955243;1783272|1239|186801|186802|31979|1485|1506;1783272|1239;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|1263|40519;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|216851;3379134|1224|28216|80840|995019|577310|487175;3379134|976|117743|200644|2762318|501783|1913682;1783272|201174|1760|85004|31953|1678|1680;3379134|976|200643|171549|171550|239759|328813;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|459786|1945593;1783272|1239|526524|526525|2810280|100883;3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|1853231|574697|544645;1783272|1239|186801|186802|541000;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|1853231|574697;3379134|976|200643|171549|2005519|397864|487174;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|3085636|186803|189330|39486;3379134|1224|1236|135625|712|724|729;3379134|976|200643|171549|171550|239759|1288121,Complete,NA
bsdb:29186529/2/2,29186529,randomized controlled trial,29186529,10.1093/infdis/jix604,NA,"de Gunzburg J., Ghozlane A., Ducher A., Le Chatelier E., Duval X., Ruppé E., Armand-Lefevre L., Sablier-Gallis F., Burdet C., Alavoine L., Chachaty E., Augustin V., Varastet M., Levenez F., Kennedy S., Pons N., Mentré F. , Andremont A.",Protection of the Human Gut Microbiome From Antibiotics,The Journal of infectious diseases,2018,"Clostridium difficile, antibiotics, fluoroquinolones, microbiome",Experiment 2,France,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,moxifloxacin treated group (MXF),DAV132+moxifloxacin treated group (MXF+DAV132),healthy male and female volunteers aged >18 years,14,14,3 months,WMS,NA,Mass spectrometry,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 2,"Supplementary table 3, Supplementary figure 1",10 January 2021,Mst Afroza Parvin,WikiWorks,A detailed analysis of the MGSs that differed significantly between treatment groups,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,1783272|1239|186801|3085636|186803|572511,Complete,NA
bsdb:29186529/3/1,29186529,randomized controlled trial,29186529,10.1093/infdis/jix604,NA,"de Gunzburg J., Ghozlane A., Ducher A., Le Chatelier E., Duval X., Ruppé E., Armand-Lefevre L., Sablier-Gallis F., Burdet C., Alavoine L., Chachaty E., Augustin V., Varastet M., Levenez F., Kennedy S., Pons N., Mentré F. , Andremont A.",Protection of the Human Gut Microbiome From Antibiotics,The Journal of infectious diseases,2018,"Clostridium difficile, antibiotics, fluoroquinolones, microbiome",Experiment 3,France,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Negative control group (CLT),DAV132+moxifloxacin treated group (MXF+DAV132),healthy male and female volunteers aged >18 years,8,14,3 months,WMS,NA,Mass spectrometry,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,"Supplementary table 3, Supplementary figure 1",10 January 2021,Mst Afroza Parvin,WikiWorks,A detailed analysis of the MGSs that differed significantly between treatment groups,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239;1783272|1239|186801|3085636|186803,Complete,NA
bsdb:29186529/3/2,29186529,randomized controlled trial,29186529,10.1093/infdis/jix604,NA,"de Gunzburg J., Ghozlane A., Ducher A., Le Chatelier E., Duval X., Ruppé E., Armand-Lefevre L., Sablier-Gallis F., Burdet C., Alavoine L., Chachaty E., Augustin V., Varastet M., Levenez F., Kennedy S., Pons N., Mentré F. , Andremont A.",Protection of the Human Gut Microbiome From Antibiotics,The Journal of infectious diseases,2018,"Clostridium difficile, antibiotics, fluoroquinolones, microbiome",Experiment 3,France,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Negative control group (CLT),DAV132+moxifloxacin treated group (MXF+DAV132),healthy male and female volunteers aged >18 years,8,14,3 months,WMS,NA,Mass spectrometry,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,"Supplementary table 3, Supplementary figure 1",10 January 2021,Mst Afroza Parvin,WikiWorks,A detailed analysis of the MGSs that differed significantly between treatment groups,decreased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii",3379134|200940|3031449|213115|194924|35832|35833;1783272|201174|1760|85004|31953|1678|1680;1783272|1239|186801|3082720|186804|1505657|261299;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|186802|216572|946234|292800,Complete,NA
bsdb:29190829/1/1,29190829,case-control,29190829,10.1371/journal.pone.0188873,NA,"Thompson K.J., Ingle J.N., Tang X., Chia N., Jeraldo P.R., Walther-Antonio M.R., Kandimalla K.K., Johnson S., Yao J.Z., Harrington S.C., Suman V.J., Wang L., Weinshilboum R.L., Boughey J.C., Kocher J.P., Nelson H., Goetz M.P. , Kalari K.R.",A comprehensive analysis of breast cancer microbiota and host gene expression,PloS one,2017,NA,Experiment 1,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast carcinoma,EFO:0000305,Control,Breast Cancer,Patients with breast cancer,668,72,NA,16S,345,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3 +text,10 January 2021,Phyu Han,"Lwaldron,WikiWorks",Species compositions of the Breast Caner and Non-cancerous Adjacent tissues,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Alkalihalobacillus|s__Alkalihalobacillus alcalophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium|s__Brachybacterium muris,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Furfurilactobacillus|s__Furfurilactobacillus rossiae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycolicibacterium|s__Mycolicibacterium phlei,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycolicibacterium|s__Mycolicibacterium fortuitum",1783272|1239|91061|1385|186817|2675234|1445;1783272|201174|1760|85006|85020|43668|219301;1783272|1239|91061|186826|33958|2767882|231049;3379134|1224|1236|91347|543|590|28901;1783272|201174|1760|85007|1762|1866885|1771;1783272|201174|1760|85007|1762|1866885|1766,Complete,Fatima
bsdb:29190829/1/2,29190829,case-control,29190829,10.1371/journal.pone.0188873,NA,"Thompson K.J., Ingle J.N., Tang X., Chia N., Jeraldo P.R., Walther-Antonio M.R., Kandimalla K.K., Johnson S., Yao J.Z., Harrington S.C., Suman V.J., Wang L., Weinshilboum R.L., Boughey J.C., Kocher J.P., Nelson H., Goetz M.P. , Kalari K.R.",A comprehensive analysis of breast cancer microbiota and host gene expression,PloS one,2017,NA,Experiment 1,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast carcinoma,EFO:0000305,Control,Breast Cancer,Patients with breast cancer,668,72,NA,16S,345,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3 +text,10 January 2021,Phyu Han,"Lwaldron,WikiWorks",Species compositions of the Breast Caner and Non-cancerous Adjacent tissues,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter radioresistens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia pickettii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium|s__Microbacterium barkeri",3379134|1224|1236|2887326|468|469|40216;3379134|1224|1236|91347|543|561|562;3379134|1224|28216|80840|119060|48736|329;1783272|201174|1760|85006|85023|33882|33917,Complete,Fatima
bsdb:29196415/1/1,29196415,case-control,29196415,10.1158/0008-5472.CAN-17-1296,NA,"Peters B.A., Wu J., Pei Z., Yang L., Purdue M.P., Freedman N.D., Jacobs E.J., Gapstur S.M., Hayes R.B. , Ahn J.",Oral Microbiome Composition Reflects Prospective Risk for Esophageal Cancers,Cancer research,2017,NA,Experiment 1,United States of America,Homo sapiens,Mouth,UBERON:0000165,Esophageal cancer,MONDO:0007576,controls,Esophageal Adenocarcinoma (EAC),diagnosed with easophageal cancer anytime after oral wash sample collection,160,81,NA,16S,4,Illumina,NA,Logistic Regression,0.05,FALSE,NA,"age,race,sex","alcohol drinking,body mass index,smoking behavior",NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 1, Text",10 January 2021,Utsav Patel,WikiWorks,"Oral Microbiome composition and prospective risk for esophageal cancer, no significance for q-value",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia cardiffensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",3379134|976|200643|171549|2005525|195950|28112;1783272|201174|1760|2037|2049|2529408|181487;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|909929|1843491|970,Complete,Fatima Zohra
bsdb:29196415/1/2,29196415,case-control,29196415,10.1158/0008-5472.CAN-17-1296,NA,"Peters B.A., Wu J., Pei Z., Yang L., Purdue M.P., Freedman N.D., Jacobs E.J., Gapstur S.M., Hayes R.B. , Ahn J.",Oral Microbiome Composition Reflects Prospective Risk for Esophageal Cancers,Cancer research,2017,NA,Experiment 1,United States of America,Homo sapiens,Mouth,UBERON:0000165,Esophageal cancer,MONDO:0007576,controls,Esophageal Adenocarcinoma (EAC),diagnosed with easophageal cancer anytime after oral wash sample collection,160,81,NA,16S,4,Illumina,NA,Logistic Regression,0.05,FALSE,NA,"age,race,sex","alcohol drinking,body mass index,smoking behavior",NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 1, Text",10 January 2021,Utsav Patel,WikiWorks,"Oral Microbiome composition and prospective risk for esophageal cancer, no significance for q-value",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum umeaense,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sicca,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",3379134|976|200643|171549|171552|1283313;1783272|1239|186801|3085636|186803|265975;1783272|1239|526524|526525|128827|123375;3379134|1224|28216|206351|481|482;1783272|201174|1760|85007|1653|1716|61592;3379134|976|200643|171549|171552|2974257|425941;1783272|1239|91061|186826|1300|1301|1313;1783272|1239|186801|3085636|186803|1164882|617123;1783272|1239|186801|3085636|186803|265975|1501329;1783272|1239|526524|526525|128827|123375|102148;3379134|1224|28216|206351|481|482|484;3379134|1224|28216|206351|481|482|490;3379134|1224|1236|135625|712|724,Complete,Fatima Zohra
bsdb:29196415/2/1,29196415,case-control,29196415,10.1158/0008-5472.CAN-17-1296,NA,"Peters B.A., Wu J., Pei Z., Yang L., Purdue M.P., Freedman N.D., Jacobs E.J., Gapstur S.M., Hayes R.B. , Ahn J.",Oral Microbiome Composition Reflects Prospective Risk for Esophageal Cancers,Cancer research,2017,NA,Experiment 2,United States of America,Homo sapiens,Mouth,UBERON:0000165,Esophageal cancer,MONDO:0007576,controls,Esophageal Squamous cell carcinoma (ESCC),diagnosed with easophageal cancer anytime after oral wash sample collection,50,25,NA,16S,4,Illumina,NA,Logistic Regression,0.05,FALSE,NA,"age,race,sex","alcohol drinking,body mass index,smoking behavior",NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 1, Text",10 January 2021,Utsav Patel,WikiWorks,"Oral Microbiome composition and prospective risk for esophageal cancer, no significance for q-value",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria weaveri,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema vincentii",3379134|976|200643|171549|171552|2974257|425941;3379134|976|117743|200644|2762318|59735;3379134|1224|28216|206351|481|482|28091;3379134|203691|203692|136|2845253|157|69710,Complete,Fatima Zohra
bsdb:29196415/2/2,29196415,case-control,29196415,10.1158/0008-5472.CAN-17-1296,NA,"Peters B.A., Wu J., Pei Z., Yang L., Purdue M.P., Freedman N.D., Jacobs E.J., Gapstur S.M., Hayes R.B. , Ahn J.",Oral Microbiome Composition Reflects Prospective Risk for Esophageal Cancers,Cancer research,2017,NA,Experiment 2,United States of America,Homo sapiens,Mouth,UBERON:0000165,Esophageal cancer,MONDO:0007576,controls,Esophageal Squamous cell carcinoma (ESCC),diagnosed with easophageal cancer anytime after oral wash sample collection,50,25,NA,16S,4,Illumina,NA,Logistic Regression,0.05,FALSE,NA,"age,race,sex","alcohol drinking,body mass index,smoking behavior",NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 1, Text",10 January 2021,Utsav Patel,WikiWorks,"Oral Microbiome composition and prospective risk for esophageal cancer, no significance for q-value",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter aphrophilus",1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171552|838;3379134|1224|1236|135625|712|416916|732,Complete,Fatima Zohra
bsdb:29196767/1/1,29196767,case-control,29196767,10.1167/iovs.17-22957,NA,"Wen X., Miao L., Deng Y., Bible P.W., Hu X., Zou Y., Liu Y., Guo S., Liang J., Chen T., Peng G.H., Chen W., Liang L. , Wei L.",The Influence of Age and Sex on Ocular Surface Microbiota in Healthy Adults,Investigative ophthalmology & visual science,2017,NA,Experiment 1,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Age at assessment,EFO:0008007,Young,Old,Aged 47-84 years old,48,42,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 6,10 September 2023,Mary Bearkland,"Mary Bearkland,Peace Sandy,WikiWorks","FIGURE 6. The bacterial species with significant differences in relative
abundance between old and young groups. The LefSe program is used
to find the bacterial species that specifically distinguish the old (green)
from young (red) conjunctival microbiomes (LDA score > 3).",increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus prevotii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium aurimucosum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium jeikeium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium resistens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium urealyticum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium avidum,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus radiodurans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus luteus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria gonorrhoeae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria lactamica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Rubrivivax|s__Rubrivivax gelatinosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus haemolyticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus lugdunensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus warneri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudopneumoniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Anaplasmataceae|g__Wolbachia|s__Wolbachia pipientis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Anaplasmataceae|g__Wolbachia|s__Wolbachia sp.",1783272|1239|1737404|1737405|1570339|165779|33034;1783272|201174|1760|85007|1653|1716|169292;1783272|201174|1760|85007|1653|1716|38289;1783272|201174|1760|85007|1653|1716|258224;1783272|201174|1760|85007|1653|1716|43771;1783272|201174|1760|85009|31957|1912216|33010;3384194|1297|188787|118964|183710|1298|1299;3379134|1224|1236|91347|543|561|562;1783272|1239|1737404|1737405|1570339|150022|1260;3384189|32066|203490|203491|1129771|32067|40542;1783272|201174|1760|85006|1268|1269|1270;3379134|1224|28216|206351|481|482|485;3379134|1224|28216|206351|481|482|486;3379134|976|200643|171549|171552|838|28132;1783272|201174|1760|85006|1268|32207|2047;1783272|201174|1760|85006|1268|32207|43675;3379134|1224|28216|80840|2975441|28067|28068;1783272|1239|91061|1385|90964|1279|1283;1783272|1239|91061|1385|90964|1279|28035;1783272|1239|91061|1385|90964|1279|1292;1783272|1239|91061|186826|1300|1301|1302;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1313;1783272|1239|91061|186826|1300|1301|257758;1783272|1239|91061|186826|1300|1301|1305;1783272|1239|91061|186826|1300|1301|1306;3379134|1224|28211|766|942|953|955;3379134|1224|28211|766|942|953|956,Complete,Peace Sandy
bsdb:29196767/1/2,29196767,case-control,29196767,10.1167/iovs.17-22957,NA,"Wen X., Miao L., Deng Y., Bible P.W., Hu X., Zou Y., Liu Y., Guo S., Liang J., Chen T., Peng G.H., Chen W., Liang L. , Wei L.",The Influence of Age and Sex on Ocular Surface Microbiota in Healthy Adults,Investigative ophthalmology & visual science,2017,NA,Experiment 1,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Age at assessment,EFO:0008007,Young,Old,Aged 47-84 years old,48,42,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 6,10 September 2023,Mary Bearkland,"Mary Bearkland,WikiWorks","FIGURE 6. The bacterial species with significant differences in relative
abundance between old and young groups. The LefSe program is used
to find the bacterial species that specifically distinguish the old (green)
from young (red) conjunctival microbiomes (LDA score > 3).",decreased,"k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mycoplasmopsis|s__Mycoplasmopsis pulmonis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Pseudomonadati|p__Chlorobiota|c__Chlorobiia|o__Chlorobiales|f__Chlorobiaceae|g__Chlorobium|s__Chlorobium phaeobacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Listeria|s__Listeria monocytogenes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira murdochii,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|g__Candidatus Karelsulcia,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mycoplasmopsis|s__Mycoplasmopsis bovis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella|s__Brucella anthropi,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mesomycoplasma|s__Mesomycoplasma hyorhinis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes",1783272|544448|2790996|2895623|2767358|2107;1783272|1239|91061|186826|33958|1578|47770;3379134|1090|191410|191411|191412|1091|1096;1783272|1239|91061|1385|186820|1637|1639;1783272|1239|91061|186826|81852|1350|1351;3379134|203691|203692|1643686|143786|29521|84378;3379134|976|117743|200644|336809;1783272|544448|2790996|2895623|2767358|28903;3379134|1224|1236|72274|135621|286|287;3379134|1224|28211|356|118882|234|529;1783272|544448|2790996|2895623|2923352|2100;1783272|201174|1760|85009|31957|1912216|1747,Complete,Peace Sandy
bsdb:29196767/2/1,29196767,case-control,29196767,10.1167/iovs.17-22957,NA,"Wen X., Miao L., Deng Y., Bible P.W., Hu X., Zou Y., Liu Y., Guo S., Liang J., Chen T., Peng G.H., Chen W., Liang L. , Wei L.",The Influence of Age and Sex on Ocular Surface Microbiota in Healthy Adults,Investigative ophthalmology & visual science,2017,NA,Experiment 2,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Biological sex,PATO:0000047,Male,Female,Biological sex=female,42,48,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4a,24 September 2023,Mary Bearkland,"Mary Bearkland,Peace Sandy,WikiWorks","FIGURE 4. Sex-differences in conjunctival microbiome of healthy adults. Male and female groups,... while no significant difference is observed in Shannon diversity index (A).  (Note- no taxon were found to be decreased in females compared to males)",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus luteus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Diaphorobacter|s__[Acidovorax] ebreus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus haemolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii",3379134|1224|1236|91347|543|561|562;1783272|201174|1760|85006|1268|1269|1270;3379134|1224|28216|80840|80864|238749|721785;1783272|1239|91061|1385|90964|1279|1283;3379134|1224|1236|2887326|468|469|470,Complete,Peace Sandy
bsdb:29196767/2/2,29196767,case-control,29196767,10.1167/iovs.17-22957,NA,"Wen X., Miao L., Deng Y., Bible P.W., Hu X., Zou Y., Liu Y., Guo S., Liang J., Chen T., Peng G.H., Chen W., Liang L. , Wei L.",The Influence of Age and Sex on Ocular Surface Microbiota in Healthy Adults,Investigative ophthalmology & visual science,2017,NA,Experiment 2,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Biological sex,PATO:0000047,Male,Female,Biological sex=female,42,48,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4a,24 September 2023,Mary Bearkland,"Mary Bearkland,Peace Sandy,WikiWorks","FIGURE 4. Sex-differences in conjunctival microbiome of healthy adults. Male and female groups,... while no significant difference is observed in Shannon diversity index (A).  (Note- no taxon were found to be increased in females compared to males)",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis",1783272|201174|1760|85009|31957|1912216|1747;1783272|1239|91061|1385|90964|1279|1282,Complete,Peace Sandy
bsdb:29207565/1/1,29207565,time series / longitudinal observational,29207565,10.3390/genes8120364,NA,"Mueller N.T., Shin H., Pizoni A., Werlang I.C., Matte U., Goldani M.Z., Goldani H.A.S. , Dominguez-Bello M.G.","Delivery Mode and the Transition of Pioneering Gut-Microbiota Structure, Composition and Predicted Metabolic Function",Genes,2017,"cesarean section, microbial community, microbiome, microbiota, obesity",Experiment 1,Brazil,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,mecomium in vaginal delivery,transitional stool,cases are delivery or an elective C-section delivery between 38 and 42 weeks of gestation (confirmed by an ultrasound taken before the 20th week of pregnancy).,10,10,3 months,16S,4,Illumina,relative abundances,LEfSe,NA,FALSE,3,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Figure S2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Bacterial taxa comparisons in meconium and transitional stool by delivery mode.,increased,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,3379134|29547|3031852|213849|72293|209,Complete,Shaimaa Elsafoury
bsdb:29207565/1/2,29207565,time series / longitudinal observational,29207565,10.3390/genes8120364,NA,"Mueller N.T., Shin H., Pizoni A., Werlang I.C., Matte U., Goldani M.Z., Goldani H.A.S. , Dominguez-Bello M.G.","Delivery Mode and the Transition of Pioneering Gut-Microbiota Structure, Composition and Predicted Metabolic Function",Genes,2017,"cesarean section, microbial community, microbiome, microbiota, obesity",Experiment 1,Brazil,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,mecomium in vaginal delivery,transitional stool,cases are delivery or an elective C-section delivery between 38 and 42 weeks of gestation (confirmed by an ultrasound taken before the 20th week of pregnancy).,10,10,3 months,16S,4,Illumina,relative abundances,LEfSe,NA,FALSE,3,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,Figure S2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Bacterial taxa comparisons in meconium and transitional stool by delivery mode.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Hydrogenophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Geobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia",3379134|1224|1236|2887326|468|469;3379134|1224|2008785|119069|206349|70774;1783272|1239|91061|186826|1300|1301;3379134|1224|28211|204457|41297|13687;1783272|201174|1760|85007|1653|1716;1783272|201174|84995|84996|84997|42255;3379134|1224|28211|204457|3423717|165695;1783272|1239|91061|1385|3120669|129337;3379134|1224|28216|206351|481|482;1783272|1239|1737404|1737405|1570339|165779;3379134|1224|28211|356|119045|407;1783272|1239|909932|1843489|31977|29465;1783272|201174|1760|85006|1268|1269;1783272|1239|91061|186826|1300|1357;3379134|1224|28211|356|82115|357;3379134|1224|28211|356|212791;3379134|1224|28216|80840|75682|29580;3379134|1224|28216|80840|80864|80865,Complete,Shaimaa Elsafoury
bsdb:29207565/2/1,29207565,time series / longitudinal observational,29207565,10.3390/genes8120364,NA,"Mueller N.T., Shin H., Pizoni A., Werlang I.C., Matte U., Goldani M.Z., Goldani H.A.S. , Dominguez-Bello M.G.","Delivery Mode and the Transition of Pioneering Gut-Microbiota Structure, Composition and Predicted Metabolic Function",Genes,2017,"cesarean section, microbial community, microbiome, microbiota, obesity",Experiment 2,Brazil,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,mecomium in C-section delivery,transitional stool,cases are delivery or an elective C-section delivery between 38 and 42 weeks of gestation (confirmed by an ultrasound taken before the 20th week of pregnancy).,40,40,3 months,16S,4,Illumina,relative abundances,LEfSe,NA,FALSE,3,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Figure S2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Bacterial taxa comparisons in meconium and transitional stool by delivery mode.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|81852|1350,Complete,Shaimaa Elsafoury
bsdb:29207565/2/2,29207565,time series / longitudinal observational,29207565,10.3390/genes8120364,NA,"Mueller N.T., Shin H., Pizoni A., Werlang I.C., Matte U., Goldani M.Z., Goldani H.A.S. , Dominguez-Bello M.G.","Delivery Mode and the Transition of Pioneering Gut-Microbiota Structure, Composition and Predicted Metabolic Function",Genes,2017,"cesarean section, microbial community, microbiome, microbiota, obesity",Experiment 2,Brazil,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,mecomium in C-section delivery,transitional stool,cases are delivery or an elective C-section delivery between 38 and 42 weeks of gestation (confirmed by an ultrasound taken before the 20th week of pregnancy).,40,40,3 months,16S,4,Illumina,relative abundances,LEfSe,NA,FALSE,3,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,Figure S2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Bacterial taxa comparisons in meconium and transitional stool by delivery mode.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium",3379134|1224|1236|72274|135621|286;1783272|1239|91061|1385|186817|400634;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|186826|1300|1301;3379134|1224|28216|80840|119060|106589;3384189|32066|203490|203491|1129771|32067;1783272|201174|1760|2037|2049|1654;3384189|32066|203490|203491|203492|848;3379134|1224|28211|204457|41297|13687;1783272|201174|84995|84996|84997|42255;3379134|1224|1236|135619|28256|2745;3379134|203691|203692|136|2845253|157;3379134|1224|1236|135625|712|724;3379134|1224|28211|204458|76892|41275;3379134|1224|1236|135615|868|2717;3379134|1224|28211|204457|3423717|165695,Complete,Shaimaa Elsafoury
bsdb:29221120/1/1,29221120,case-control,29221120,10.18632/oncotarget.18820,NA,"Ren Z., Jiang J., Xie H., Li A., Lu H., Xu S., Zhou L., Zhang H., Cui G., Chen X., Liu Y., Wu L., Qin N., Sun R., Wang W., Li L., Wang W. , Zheng S.",Gut microbial profile analysis by MiSeq sequencing of pancreatic carcinoma patients in China,Oncotarget,2017,"MiSeq sequencing, alpha diversity, biomarkers, gut microbiota, pancreatic carcinoma",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Pancreatic carcinoma,EFO:0002618,healthy controls,pancreatic cancer,patients with pancreatic cancer diagnosed according to international guidelines by comprehensive consideration of clinical symptoms,57,85,2 months,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,"age,body mass index,sex",NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,Figure 4,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential abundance of fecal microbial communities between PC patients and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Paraliobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|909932|1843488|909930|904;3379134|1224|1236|135625|712|416916;3379134|29547|3031852|213849|72294|194;1783272|1239|526524|526525|2810280|135858;1783272|1239|909932|909929|1843491|82202;3379134|1224|1236|91347|543|413496;3379134|1224|1236|91347|543|547;3379134|976|200643|171549|171552|52228;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|33958|1578;3384189|32066|203490|203491|1129771|32067;1783272|1239|91061|1385|186817|200903;3379134|976|200643|171549|171552|838;1783272|1239|909932|909929|1843491|970;1783272|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:29221120/1/2,29221120,case-control,29221120,10.18632/oncotarget.18820,NA,"Ren Z., Jiang J., Xie H., Li A., Lu H., Xu S., Zhou L., Zhang H., Cui G., Chen X., Liu Y., Wu L., Qin N., Sun R., Wang W., Li L., Wang W. , Zheng S.",Gut microbial profile analysis by MiSeq sequencing of pancreatic carcinoma patients in China,Oncotarget,2017,"MiSeq sequencing, alpha diversity, biomarkers, gut microbiota, pancreatic carcinoma",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Pancreatic carcinoma,EFO:0002618,healthy controls,pancreatic cancer,patients with pancreatic cancer diagnosed according to international guidelines by comprehensive consideration of clinical symptoms,57,85,2 months,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,"age,body mass index,sex",NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,Figure 4,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential abundance of fecal microbial communities between PC patients and healthy controls,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Paraeggerthella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|216572|244127;1783272|201174|1760|85004|31953|1678;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|572511;3379134|1224|28211|204458|76892|41275;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|189330;1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|204475;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3082720|543314|86331;1783272|201174|84998|1643822|1643826|651554;3379134|1224|28216|80840|995019|577310;3379134|1224|1236|91347|1903414|583;3379134|1224|28211|356|82115|379;1783272|1239|186801|186802|216572|44748,Complete,Claregrieve1
bsdb:29221120/2/1,29221120,case-control,29221120,10.18632/oncotarget.18820,NA,"Ren Z., Jiang J., Xie H., Li A., Lu H., Xu S., Zhou L., Zhang H., Cui G., Chen X., Liu Y., Wu L., Qin N., Sun R., Wang W., Li L., Wang W. , Zheng S.",Gut microbial profile analysis by MiSeq sequencing of pancreatic carcinoma patients in China,Oncotarget,2017,"MiSeq sequencing, alpha diversity, biomarkers, gut microbiota, pancreatic carcinoma",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Pancreatic carcinoma,EFO:0002618,pancreatic head cancer without obstruction,pancreatic head cancer with obstruction,pancreatic head cancer with obstruction of common bile duct,32,22,2 months,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 5,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between pancreatic cancer patients with bile obstruction vs without obstruction,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Parasporobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|1224|28216|80840|80864|283;1783272|1239|91061|186826|186828|117563;1783272|1239|186801|3085636|186803|140625;3384189|32066|203490|203491|1129771|32067;1783272|1239|186801|3085636|186803|115543;1783272|1239|186801|3085636|186803|46205;1783272|1239|186801|186802|216572|1200657;1783272|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:29221120/2/2,29221120,case-control,29221120,10.18632/oncotarget.18820,NA,"Ren Z., Jiang J., Xie H., Li A., Lu H., Xu S., Zhou L., Zhang H., Cui G., Chen X., Liu Y., Wu L., Qin N., Sun R., Wang W., Li L., Wang W. , Zheng S.",Gut microbial profile analysis by MiSeq sequencing of pancreatic carcinoma patients in China,Oncotarget,2017,"MiSeq sequencing, alpha diversity, biomarkers, gut microbiota, pancreatic carcinoma",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Pancreatic carcinoma,EFO:0002618,pancreatic head cancer without obstruction,pancreatic head cancer with obstruction,pancreatic head cancer with obstruction of common bile duct,32,22,2 months,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 5,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between pancreatic cancer patients with bile obstruction vs without obstruction,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Anaerorhabdus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella",1783272|1239|526524|526525|128827|118966;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|620,Complete,Claregrieve1
bsdb:29230385/1/1,29230385,case-control,29230385,10.3389/fcimb.2017.00488,https://www.frontiersin.org/articles/10.3389/fcimb.2017.00488/full,"Wu P., Chen Y., Zhao J., Zhang G., Chen J., Wang J. , Zhang H.",Urinary Microbiome and Psychological Factors in Women with Overactive Bladder,Frontiers in cellular and infection microbiology,2017,"bacteria, depression, overactive bladder, psychology, urinary microbiome",Experiment 1,China,Homo sapiens,Female urethra,UBERON:0001334,Overactive bladder,EFO:1000781,Asymptomatic controls,Overactive Bladder (OAB) patients,"Adult patients aged 18 or above, diagnosed with OAB",25,30,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,decreased,decreased,NA,NA,Signature 1,Figure 4,4 October 2023,Ojotuleonalo,"Ojotuleonalo,WikiWorks",Urinary microbiomes that were significantly more increased in the samples of female patients with OAB (Over Active Bladder) compared to the control samples from asymptomatic women,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Helcococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus",1783272|1239|91061|1385|90964|1279;3384189|32066|203490|203491|1129771|168808;3379134|1224|1236|91347|1903414|583;1783272|1239|1737404|1737405|1570339|31983;1783272|1239|91061|1385|539738|1378;1783272|544448|31969|2085|2092|2093;1783272|1239|91061|186826|186827|1375,Complete,Folakunmi
bsdb:29230385/1/2,29230385,case-control,29230385,10.3389/fcimb.2017.00488,https://www.frontiersin.org/articles/10.3389/fcimb.2017.00488/full,"Wu P., Chen Y., Zhao J., Zhang G., Chen J., Wang J. , Zhang H.",Urinary Microbiome and Psychological Factors in Women with Overactive Bladder,Frontiers in cellular and infection microbiology,2017,"bacteria, depression, overactive bladder, psychology, urinary microbiome",Experiment 1,China,Homo sapiens,Female urethra,UBERON:0001334,Overactive bladder,EFO:1000781,Asymptomatic controls,Overactive Bladder (OAB) patients,"Adult patients aged 18 or above, diagnosed with OAB",25,30,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,decreased,decreased,NA,NA,Signature 2,Figure 4,4 October 2023,Ojotuleonalo,"Ojotuleonalo,WikiWorks",Urinary microbiomes that were significantly more decreased in the samples of female patients with OAB (Over Active Bladder) compared to the control samples from asymptomatic women,decreased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Jonquetella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma",1783272|1239|1737404|1737405|1570339|165779;3379134|29547|3031852|213849|72294|194;1783272|1239|909932|1843489|31977|39948;1783272|1239|91061|186826|81852|1350;1783272|1239|1737404|1737405|1570339|150022;3384189|32066|203490|203491|203492|848;3384194|508458|649775|649776|3029088|428711;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1357;3379134|1224|28211|204457|41297|165696;3379134|976|200643|171549|171552|838;3384194|508458|649775|649776|3029088|638847;1783272|544448|2790996|2790998|2129,Complete,Folakunmi
bsdb:29230385/2/1,29230385,case-control,29230385,10.3389/fcimb.2017.00488,https://www.frontiersin.org/articles/10.3389/fcimb.2017.00488/full,"Wu P., Chen Y., Zhao J., Zhang G., Chen J., Wang J. , Zhang H.",Urinary Microbiome and Psychological Factors in Women with Overactive Bladder,Frontiers in cellular and infection microbiology,2017,"bacteria, depression, overactive bladder, psychology, urinary microbiome",Experiment 2,China,Homo sapiens,Female urethra,NA,Anxiety,EFO:0005230,Overactive Bladder (OAB) without anxiety,Overactive Bladder (OAB) with anxiety,"Adult patients aged 18 or above, diagnosed with OAB and have anxiety",18,12,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,increased,increased,increased,increased,NA,NA,Signature 1,Figure 5C,8 October 2023,Ojotuleonalo,"Ojotuleonalo,Peace Sandy,Folakunmi,WikiWorks",Urinary microbiomes that were significantly more increased in the samples of female patients with OAB (Over Active Bladder) with anxiety compared to the samples of female patients with OAB without anxiety,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae|g__Alicyclobacillus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Helcococcus,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Leptolyngbyales|f__Leptolyngbyaceae|g__Leptolyngbya,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia",1783272|201174|1760|2037|2049|76833;1783272|1239|91061|1385|186823|29330;1783272|1239|1737404|1737405|1570339|162290;1783272|1239|1737404|1737405|1570339|31983;1783272|1117|3028117|3079749|1890438|47251;3379134|976|200643|171549|171551|836;3384189|32066|203490|203491|1129771|168808,Complete,Folakunmi
bsdb:29230385/2/2,29230385,case-control,29230385,10.3389/fcimb.2017.00488,https://www.frontiersin.org/articles/10.3389/fcimb.2017.00488/full,"Wu P., Chen Y., Zhao J., Zhang G., Chen J., Wang J. , Zhang H.",Urinary Microbiome and Psychological Factors in Women with Overactive Bladder,Frontiers in cellular and infection microbiology,2017,"bacteria, depression, overactive bladder, psychology, urinary microbiome",Experiment 2,China,Homo sapiens,Female urethra,NA,Anxiety,EFO:0005230,Overactive Bladder (OAB) without anxiety,Overactive Bladder (OAB) with anxiety,"Adult patients aged 18 or above, diagnosed with OAB and have anxiety",18,12,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,increased,increased,increased,increased,NA,NA,Signature 2,Figure 5C,8 October 2023,Ojotuleonalo,"Ojotuleonalo,Peace Sandy,Folakunmi,WikiWorks",Urinary microbiomes that were significantly more decreased in the samples of female patients with OAB (Over Active Bladder) with anxiety compared to the samples of female patients with OAB without anxiety.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Cryocola,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter",3379134|1224|28211|356|82115|357;3379134|1224|28216|80840|119060|32008;1783272|201174|84998|84999|84107|102106;1783272|201174|1760|85006|85023|205841;3366610|28890|183925|2158|2159|2172;3379134|1224|1236|2887326|468|497,Complete,Folakunmi
bsdb:29230385/3/1,29230385,case-control,29230385,10.3389/fcimb.2017.00488,https://www.frontiersin.org/articles/10.3389/fcimb.2017.00488/full,"Wu P., Chen Y., Zhao J., Zhang G., Chen J., Wang J. , Zhang H.",Urinary Microbiome and Psychological Factors in Women with Overactive Bladder,Frontiers in cellular and infection microbiology,2017,"bacteria, depression, overactive bladder, psychology, urinary microbiome",Experiment 3,China,Homo sapiens,Female urethra,UBERON:0001334,Depressive disorder,MONDO:0002050,Overactive Bladder (OAB) without depression,Overactive Bladder (OAB) with depression,"Adult patients aged 18 or above, diagnosed with OAB and have anxiety",16,14,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,increased,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 5D,18 January 2024,Folakunmi,"Folakunmi,WikiWorks",Urinary microbiomes that were significantly decreased in the samples of female patients with OAB (Over Active Bladder) with depression compared to the samples of female patients with OAB without depression,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sporobacterium|s__Sporobacterium sp. WAL 1855D",1783272|1239|186801|186802|31979|1485;1783272|201174|1760|2037|2049|76833;3379134|976|117747|200666|84566|84567;1783272|1239|186801|3085636|186803|100132|507843,Complete,Folakunmi
bsdb:29234019/1/1,29234019,case-control,29234019,10.1038/s41598-017-17351-9,NA,"Curty G., Costa R.L., Siqueira J.D., Meyrelles A.I., Machado E.S., Soares E.A. , Soares M.A.",Analysis of the cervical microbiome and potential biomarkers from postpartum HIV-positive women displaying cervical intraepithelial lesions,Scientific reports,2017,NA,Experiment 1,Brazil,Homo sapiens,Uterus,UBERON:0000995,Cervical glandular intraepithelial neoplasia,EFO:1000165,Normal tissue HIV patients,Cervical Intraepithelial Lesion HIV patients,Cases were identified by HIV rapid or ELISA test and subsequent Western blot following recommendations for HIV diagnosis by the Brazilian Ministry of Health. this were also patients with cervical intraepithelial lesions,42,38,NA,16S,3456,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Phyu Han,WikiWorks,Bacteria that presented higher relative abundance in cervical lesions using LEfse,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,1783272|1239|186801|3085636|186803|437755,Complete,Shaimaa Elsafoury
bsdb:29234019/2/1,29234019,case-control,29234019,10.1038/s41598-017-17351-9,NA,"Curty G., Costa R.L., Siqueira J.D., Meyrelles A.I., Machado E.S., Soares E.A. , Soares M.A.",Analysis of the cervical microbiome and potential biomarkers from postpartum HIV-positive women displaying cervical intraepithelial lesions,Scientific reports,2017,NA,Experiment 2,Brazil,Homo sapiens,Uterus,UBERON:0000995,Cervical glandular intraepithelial neoplasia,EFO:1000165,Normal tissue HIV patients,Cervical Intraepithelial Lesion HIV patients,Cases were identified by HIV rapid or ELISA test and subsequent Western blot following recommendations for HIV diagnosis by the Brazilian Ministry of Health.,42,38,NA,16S,3456,Illumina,relative abundances,LEfSe,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Shaimaa Elsafoury,"WikiWorks,Davvve",Bacteria that presented higher relative abundance in cervical lesions using LEfse protocol,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Caldimonas|s__Caldimonas thermodepolymerans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis",1783272|1239|91061|186826|186827|1375;1783272|201174|1760|85004|31953|1678|1681;3379134|1224|28216|80840|2975441|196013|215580;1783272|201174|1760|85004|31953|2701|2702,Complete,Shaimaa Elsafoury
bsdb:29276170/1/1,29276170,laboratory experiment,29276170,https://doi.org/10.1016/j.chom.2017.11.003,NA,"Zou J., Chassaing B., Singh V., Pellizzon M., Ricci M., Fythe M.D., Kumar M.V. , Gewirtz A.T.",Fiber-Mediated Nourishment of Gut Microbiota Protects against Diet-Induced Obesity by Restoring IL-22-Mediated Colonic Health,Cell host & microbe,2018,"germ-free mice, intestinal inflammation, metabolic syndrome, microbiota encroachment, short-chain fatty acids",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,High fat diet,EFO:0002757,High fat diet (HFD: 50 cell),High fat diet (HFD:200 Inul ),"High fat diet - [HFD] enriched with inulin increased gut epithelial proliferation, prevented colon atrophy",6,6,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S3D,6 October 2021,Lorakasselman,"Lorakasselman,Aiyshaaaa,Merit,Peace Sandy,WikiWorks",Taxonomic cladogram obtained from LEfSe analysis of 16S sequences by comparing HFD enrichment of inulin with standard HFD (50g cellulose),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;3379134|976|200643|171549|171550,Complete,Peace Sandy
bsdb:29276170/1/2,29276170,laboratory experiment,29276170,https://doi.org/10.1016/j.chom.2017.11.003,NA,"Zou J., Chassaing B., Singh V., Pellizzon M., Ricci M., Fythe M.D., Kumar M.V. , Gewirtz A.T.",Fiber-Mediated Nourishment of Gut Microbiota Protects against Diet-Induced Obesity by Restoring IL-22-Mediated Colonic Health,Cell host & microbe,2018,"germ-free mice, intestinal inflammation, metabolic syndrome, microbiota encroachment, short-chain fatty acids",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,High fat diet,EFO:0002757,High fat diet (HFD: 50 cell),High fat diet (HFD:200 Inul ),"High fat diet - [HFD] enriched with inulin increased gut epithelial proliferation, prevented colon atrophy",6,6,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S3D,7 October 2021,Chloe,"Chloe,Lorakasselman,Aiyshaaaa,Peace Sandy,WikiWorks",Taxonomic cladogram obtained from LEfSe analysis of 16S sequences by comparing HFD enrichment of Inulin with standard HFD,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061|1385;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|186807|51514;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301,Complete,Peace Sandy
bsdb:29276170/2/1,29276170,laboratory experiment,29276170,https://doi.org/10.1016/j.chom.2017.11.003,NA,"Zou J., Chassaing B., Singh V., Pellizzon M., Ricci M., Fythe M.D., Kumar M.V. , Gewirtz A.T.",Fiber-Mediated Nourishment of Gut Microbiota Protects against Diet-Induced Obesity by Restoring IL-22-Mediated Colonic Health,Cell host & microbe,2018,"germ-free mice, intestinal inflammation, metabolic syndrome, microbiota encroachment, short-chain fatty acids",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,High fat diet,EFO:0002757,Chow,High fat diet (HFD:200 Inul ),"High-fat diet - (HFD) enriched with inulin increased guy epithelial proliferation, prevented colon atrophy",6,6,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig S3 E,30 January 2024,Peace Sandy,"Peace Sandy,WikiWorks",D-E) Taxonomic cladogram obtained from LEfSe analysis of 16S sequences by comparing HFD enrichment of Inulin with standard HFD (D) or chow (E).,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum",1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|1300;1783272|1239|526524|526525|128827|174708,Complete,Peace Sandy
bsdb:29276170/2/2,29276170,laboratory experiment,29276170,https://doi.org/10.1016/j.chom.2017.11.003,NA,"Zou J., Chassaing B., Singh V., Pellizzon M., Ricci M., Fythe M.D., Kumar M.V. , Gewirtz A.T.",Fiber-Mediated Nourishment of Gut Microbiota Protects against Diet-Induced Obesity by Restoring IL-22-Mediated Colonic Health,Cell host & microbe,2018,"germ-free mice, intestinal inflammation, metabolic syndrome, microbiota encroachment, short-chain fatty acids",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,High fat diet,EFO:0002757,Chow,High fat diet (HFD:200 Inul ),"High-fat diet - (HFD) enriched with inulin increased guy epithelial proliferation, prevented colon atrophy",6,6,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig S3 E,30 January 2024,Peace Sandy,"Peace Sandy,WikiWorks",D-E) Taxonomic cladogram obtained from LEfSe analysis of 16S sequences by comparing HFD enrichment of inulin with standard HFD (D) or chow (E).,decreased,"k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Hymenochaetales|f__Rickenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium",4751|5204|155619|139380|1124673;3379134|976|200643|171549;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|526524|526525|2810281|191303;1783272|1239|526524|526525|2810281;1783272|1239|186801|186802|31979|49082;1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572;1783272|1239|186801|186802;1783272|1239|526524|526525|2810280|135858,Complete,Peace Sandy
bsdb:29302014/1/1,29302014,time series / longitudinal observational,29302014,10.1126/science.aao3290,https://pubmed.ncbi.nlm.nih.gov/29302014/,"Matson V., Fessler J., Bao R., Chongsuwat T., Zha Y., Alegre M.L., Luke J.J. , Gajewski T.F.",The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients,"Science (New York, N.Y.)",2018,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,NA,26,16,NA,16S,4,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1, text",28 July 2022,Sharmilac,"Sharmilac,Fatima,WikiWorks",Relative abundance of differentially abundant taxa in responders versus nonresponders;,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,1783272|201174|1760|85004|31953,Complete,Fatima
bsdb:29302014/2/1,29302014,time series / longitudinal observational,29302014,10.1126/science.aao3290,https://pubmed.ncbi.nlm.nih.gov/29302014/,"Matson V., Fessler J., Bao R., Chongsuwat T., Zha Y., Alegre M.L., Luke J.J. , Gajewski T.F.",The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients,"Science (New York, N.Y.)",2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,NA,26,16,NA,16S,4,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"text, Figure 2",24 August 2022,Fatima,"Fatima,WikiWorks",Quantitative PCR score representing aggregate data for the relative abundances of 10 species,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum",3379134|976|200643|171549|2005525|375288;1783272|1239|91061|186826|81852|1350|1352;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|1760|85004|31953|1678|1680;3379134|1224|1236|91347|543|570|573;1783272|1239|909932|1843489|31977|29465|29466;3379134|976|200643|171549|2005525|375288|46503;1783272|1239|91061|186826|33958|1578|1591;1783272|201174|1760|85004|31953|1678|216816,Complete,Fatima
bsdb:29302014/2/2,29302014,time series / longitudinal observational,29302014,10.1126/science.aao3290,https://pubmed.ncbi.nlm.nih.gov/29302014/,"Matson V., Fessler J., Bao R., Chongsuwat T., Zha Y., Alegre M.L., Luke J.J. , Gajewski T.F.",The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients,"Science (New York, N.Y.)",2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,NA,26,16,NA,16S,4,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"text, Figure 2",24 August 2022,Fatima,"Fatima,WikiWorks",Quantitative PCR score representing aggregate data for the relative abundances of 10 species,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis",1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|841|166486,Complete,Fatima
bsdb:29302014/3/1,29302014,time series / longitudinal observational,29302014,10.1126/science.aao3290,https://pubmed.ncbi.nlm.nih.gov/29302014/,"Matson V., Fessler J., Bao R., Chongsuwat T., Zha Y., Alegre M.L., Luke J.J. , Gajewski T.F.",The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients,"Science (New York, N.Y.)",2018,NA,Experiment 3,United States of America,Mus musculus,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,"Non-responders, group B","Responders, group A",Mouse with 16.SIY melanoma tumor growth,3,3,NA,16S,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,24 August 2022,Fatima,"Fatima,WikiWorks",Relative abundance in mouse groups A and b of key species validated for quantitative PCR,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae",1783272|201174|84998|84999|84107|102106|74426;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|91061|186826|33958|1578|1591;3379134|1224|1236|91347|543|570|573;3379134|976|200643|171549|2005525|375288|46503,Complete,Fatima
bsdb:29302014/3/2,29302014,time series / longitudinal observational,29302014,10.1126/science.aao3290,https://pubmed.ncbi.nlm.nih.gov/29302014/,"Matson V., Fessler J., Bao R., Chongsuwat T., Zha Y., Alegre M.L., Luke J.J. , Gajewski T.F.",The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients,"Science (New York, N.Y.)",2018,NA,Experiment 3,United States of America,Mus musculus,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,"Non-responders, group B","Responders, group A",Mouse with 16.SIY melanoma tumor growth,3,3,NA,16S,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,24 August 2022,Fatima,"Fatima,WikiWorks",Relative abundance in mouse groups A an B of key species validated for quantitative PCR scoring.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,1783272|1239|186801|3085636|186803|841|166486,Complete,Fatima
bsdb:29305057/1/1,29305057,"cross-sectional observational, not case-control",29305057,https://doi.org/10.1016/j.syapm.2017.11.008,NA,"Lim M.Y., Song E.J., Kim S.H., Lee J. , Nam Y.D.",Comparison of DNA extraction methods for human gut microbial community profiling,Systematic and applied microbiology,2018,"16S rRNA gene sequencing, Bead beating, DNA extraction, Gut microbiota, Human fecal sample",Experiment 1,Republic of Korea,Homo sapiens,Feces,UBERON:0001988,Nucleic acid extraction protocol,NA,No bead-beating method for TS kit,Bead-beating method for TS kit,Bead beating facilitates DNA recovery by lysing both Gram-negative and Gram-positive bacteria.,1,1,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Supplementary Fig. S7a,7 April 2025,Ameenatoloko,"Ameenatoloko,Montana-D","Differential microbial abundance between the no-bead-beating and bead-beating groups for the TS kit, as determined by LEfSe analysis.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|33042;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:29305057/1/2,29305057,"cross-sectional observational, not case-control",29305057,https://doi.org/10.1016/j.syapm.2017.11.008,NA,"Lim M.Y., Song E.J., Kim S.H., Lee J. , Nam Y.D.",Comparison of DNA extraction methods for human gut microbial community profiling,Systematic and applied microbiology,2018,"16S rRNA gene sequencing, Bead beating, DNA extraction, Gut microbiota, Human fecal sample",Experiment 1,Republic of Korea,Homo sapiens,Feces,UBERON:0001988,Nucleic acid extraction protocol,NA,No bead-beating method for TS kit,Bead-beating method for TS kit,Bead beating facilitates DNA recovery by lysing both Gram-negative and Gram-positive bacteria.,1,1,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Supplementary Fig. S7a,8 April 2025,Ameenatoloko,Ameenatoloko,"Differential microbial abundance between the no-bead-beating and bead-beating groups for the TS kit, as determined by LEfSe analysis.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales",3379134|976|200643|171549|815|816;3379134|976|200643|171549|815;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|976|200643|171549;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|119852;1783272|1239|526524|526525|128827|61170;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;3379134|1224|28216|80840|995019|40544;3379134|1224|28216|80840|506;3379134|1224|28216|80840,Complete,Svetlana up
bsdb:29305057/2/1,29305057,"cross-sectional observational, not case-control",29305057,https://doi.org/10.1016/j.syapm.2017.11.008,NA,"Lim M.Y., Song E.J., Kim S.H., Lee J. , Nam Y.D.",Comparison of DNA extraction methods for human gut microbial community profiling,Systematic and applied microbiology,2018,"16S rRNA gene sequencing, Bead beating, DNA extraction, Gut microbiota, Human fecal sample",Experiment 2,Republic of Korea,Homo sapiens,Feces,UBERON:0001988,Nucleic acid extraction protocol,NA,No bead-beating method for QS kit,Bead-beating method for QS kit,Bead beating facilitates DNA recovery by lysing both Gram-negative and Gram-positive bacteria.,1,1,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Supplementary Fig. S7b,8 April 2025,Ameenatoloko,"Ameenatoloko,Montana-D","Differential microbial abundance between the no-bead-beating and bead-beating groups for the QS kit, as determined by LEfSe analysis.",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|909932|1843488|909930|904;1783272|1239|186801|3085636|186803|207244;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|33042;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|186802|186807;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977,Complete,Svetlana up
bsdb:29305057/2/2,29305057,"cross-sectional observational, not case-control",29305057,https://doi.org/10.1016/j.syapm.2017.11.008,NA,"Lim M.Y., Song E.J., Kim S.H., Lee J. , Nam Y.D.",Comparison of DNA extraction methods for human gut microbial community profiling,Systematic and applied microbiology,2018,"16S rRNA gene sequencing, Bead beating, DNA extraction, Gut microbiota, Human fecal sample",Experiment 2,Republic of Korea,Homo sapiens,Feces,UBERON:0001988,Nucleic acid extraction protocol,NA,No bead-beating method for QS kit,Bead-beating method for QS kit,Bead beating facilitates DNA recovery by lysing both Gram-negative and Gram-positive bacteria.,1,1,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Supplementary Fig. S7b,8 April 2025,Ameenatoloko,Ameenatoloko,"Differential microbial abundance between the no-bead-beating and bead-beating groups for the QS kit, as determined by LEfSe analysis.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales",3379134|976|200643|171549|815|816;3379134|976|200643|171549|815;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|976|200643|171549;1783272|1239|186801|186802|216572|119852;1783272|1239|909932|1843488|909930|33024;3379134|1224|28216|80840|995019|40544;3379134|1224|28216|80840|506;3379134|1224|28216|80840;3379134|200940|3031449|213115|194924|35832;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|203557;3379134|74201|203494|48461,Complete,Svetlana up
bsdb:29307330/1/1,29307330,randomized controlled trial,29307330,10.1017/S0007114517003440,NA,"Healey G., Murphy R., Butts C., Brough L., Whelan K. , Coad J.","Habitual dietary fibre intake influences gut microbiota response to an inulin-type fructan prebiotic: a randomised, double-blind, placebo-controlled, cross-over, human intervention study",The British journal of nutrition,2018,"HDF high dietary fibre; LDF low dietary fibre, 16S rRNA gene sequencing, Gut microbiota, Habitual dietary fibres, Inulin-type fructan prebiotics, Responsiveness",Experiment 1,New Zealand,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Prebiotic,Placebo,placebo (control for prebiotic intake - representing lower fiber group),34,33,6 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Text, Table 4, Figure 5, and Figure 7",10 January 2021,Lora Kasselman,WikiWorks,Mean genus level changes after the prebiotic intervention between the low and high dietary fibre groups.,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|3085636|186803,Complete,Peace Sandy
bsdb:29307330/1/2,29307330,randomized controlled trial,29307330,10.1017/S0007114517003440,NA,"Healey G., Murphy R., Butts C., Brough L., Whelan K. , Coad J.","Habitual dietary fibre intake influences gut microbiota response to an inulin-type fructan prebiotic: a randomised, double-blind, placebo-controlled, cross-over, human intervention study",The British journal of nutrition,2018,"HDF high dietary fibre; LDF low dietary fibre, 16S rRNA gene sequencing, Gut microbiota, Habitual dietary fibres, Inulin-type fructan prebiotics, Responsiveness",Experiment 1,New Zealand,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Prebiotic,Placebo,placebo (control for prebiotic intake - representing lower fiber group),34,33,6 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Text, Table 4, Figure 5, and Figure 7",10 January 2021,Lora Kasselman,WikiWorks,Mean genus level changes after the prebiotic intervention between the low and high dietary fibre groups.,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|201174;1783272|201174|1760|85004|31953|1678,Complete,Peace Sandy
bsdb:29307330/2/1,29307330,randomized controlled trial,29307330,10.1017/S0007114517003440,NA,"Healey G., Murphy R., Butts C., Brough L., Whelan K. , Coad J.","Habitual dietary fibre intake influences gut microbiota response to an inulin-type fructan prebiotic: a randomised, double-blind, placebo-controlled, cross-over, human intervention study",The British journal of nutrition,2018,"HDF high dietary fibre; LDF low dietary fibre, 16S rRNA gene sequencing, Gut microbiota, Habitual dietary fibres, Inulin-type fructan prebiotics, Responsiveness",Experiment 2,New Zealand,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,prebiotic (inulin-type fructan) - in participants with low dietary fiber,placebo,placebo (control for prebiotic intake - representing lower fiber group),34,33,6 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Text, Table 4, Figure 5, and Figure 7",10 January 2021,Lora Kasselman,WikiWorks,Mean genus level changes after the prebiotic intervention between the low and high dietary fibre groups.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Peace Sandy
bsdb:29307330/3/1,29307330,randomized controlled trial,29307330,10.1017/S0007114517003440,NA,"Healey G., Murphy R., Butts C., Brough L., Whelan K. , Coad J.","Habitual dietary fibre intake influences gut microbiota response to an inulin-type fructan prebiotic: a randomised, double-blind, placebo-controlled, cross-over, human intervention study",The British journal of nutrition,2018,"HDF high dietary fibre; LDF low dietary fibre, 16S rRNA gene sequencing, Gut microbiota, Habitual dietary fibres, Inulin-type fructan prebiotics, Responsiveness",Experiment 3,New Zealand,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,prebiotic (inulin-type fructan) - in participants with high dietary fiber,placebo,placebo (control for prebiotic intake - representing lower fiber group),34,33,6 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Text, Table 4, Figure 5, and Figure 7",10 January 2021,Lora Kasselman,"WikiWorks,Peace Sandy",Mean genus level changes after the prebiotic intervention between the low and high dietary fibre groups.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803,Complete,Peace Sandy
bsdb:29307330/3/2,29307330,randomized controlled trial,29307330,10.1017/S0007114517003440,NA,"Healey G., Murphy R., Butts C., Brough L., Whelan K. , Coad J.","Habitual dietary fibre intake influences gut microbiota response to an inulin-type fructan prebiotic: a randomised, double-blind, placebo-controlled, cross-over, human intervention study",The British journal of nutrition,2018,"HDF high dietary fibre; LDF low dietary fibre, 16S rRNA gene sequencing, Gut microbiota, Habitual dietary fibres, Inulin-type fructan prebiotics, Responsiveness",Experiment 3,New Zealand,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,prebiotic (inulin-type fructan) - in participants with high dietary fiber,placebo,placebo (control for prebiotic intake - representing lower fiber group),34,33,6 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Text, Table 4, Figure 5, and Figure 7",10 January 2021,Lora Kasselman,WikiWorks,Mean genus level changes after the prebiotic intervention between the low and high dietary fibre groups.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Peace Sandy
bsdb:29307330/4/1,29307330,randomized controlled trial,29307330,10.1017/S0007114517003440,NA,"Healey G., Murphy R., Butts C., Brough L., Whelan K. , Coad J.","Habitual dietary fibre intake influences gut microbiota response to an inulin-type fructan prebiotic: a randomised, double-blind, placebo-controlled, cross-over, human intervention study",The British journal of nutrition,2018,"HDF high dietary fibre; LDF low dietary fibre, 16S rRNA gene sequencing, Gut microbiota, Habitual dietary fibres, Inulin-type fructan prebiotics, Responsiveness",Experiment 4,New Zealand,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Low dietary fiber,High dietary fiber,Placebo (control for prebiotic intake - representing lower fiber group),14,20,6 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 7,10 January 2021,Lora Kasselman,"WikiWorks,Peace Sandy","Mean genus level changes after the prebiotic intervention between the
low ( ) and high dietary fibre ( ) groups. * Significant change (P <0·05) as
analysed by a two-way repeated-measures ANOVA (blocked by participant)
and least significant difference test.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572,Complete,Peace Sandy
bsdb:29307330/4/2,29307330,randomized controlled trial,29307330,10.1017/S0007114517003440,NA,"Healey G., Murphy R., Butts C., Brough L., Whelan K. , Coad J.","Habitual dietary fibre intake influences gut microbiota response to an inulin-type fructan prebiotic: a randomised, double-blind, placebo-controlled, cross-over, human intervention study",The British journal of nutrition,2018,"HDF high dietary fibre; LDF low dietary fibre, 16S rRNA gene sequencing, Gut microbiota, Habitual dietary fibres, Inulin-type fructan prebiotics, Responsiveness",Experiment 4,New Zealand,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Low dietary fiber,High dietary fiber,Placebo (control for prebiotic intake - representing lower fiber group),14,20,6 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 7,21 February 2024,Peace Sandy,"Peace Sandy,WikiWorks",Mean genus level changes after the prebiotic intervention between the low ( ) and high dietary fibre ( ) groups. * Significant change (P <0·05) as analysed by a two-way repeated-measures ANOVA (blocked by participant) and least significant difference test.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Peace Sandy
bsdb:29313867/1/1,29313867,"cross-sectional observational, not case-control",29313867,NA,NA,"Di Pietro M., Filardo S., Porpora M.G., Recine N., Latino M.A. , Sessa R.",HPV/Chlamydia trachomatis co-infection: metagenomic analysis of cervical microbiota in asymptomatic women,The new microbiologica,2018,"Cervical microbiota, Chlamydia trachomatis, Coinfection, HPV, Metagenomic analysis",Experiment 1,Italy,Homo sapiens,Endocervix,UBERON:0000458,Chlamydia trachomatis infectious disease,EFO:0007205,healthy control,patient with chlamydia infection,patient with Chlamydia infection,7,7,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Cynthia Anderson,WikiWorks,LEfSe results on cervical microbiota in C. trachomatis-positive women compared to HPV-positive women or healthy controls.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus christensenii",1783272|1239|91061|186826|186827|1375;1783272|1239|91061|186826|186827;1783272|1239|91061|186826|186827|1375|87541,Complete,Fatima Zohra
bsdb:29313867/1/2,29313867,"cross-sectional observational, not case-control",29313867,NA,NA,"Di Pietro M., Filardo S., Porpora M.G., Recine N., Latino M.A. , Sessa R.",HPV/Chlamydia trachomatis co-infection: metagenomic analysis of cervical microbiota in asymptomatic women,The new microbiologica,2018,"Cervical microbiota, Chlamydia trachomatis, Coinfection, HPV, Metagenomic analysis",Experiment 1,Italy,Homo sapiens,Endocervix,UBERON:0000458,Chlamydia trachomatis infectious disease,EFO:0007205,healthy control,patient with chlamydia infection,patient with Chlamydia infection,7,7,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 3,10 January 2021,Cynthia Anderson,WikiWorks,LEfSe results on cervical microbiota in C. trachomatis-positive women compared to HPV-positive women or healthy controls.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli",1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958;1783272|1239;1783272|1239|91061,Complete,Fatima Zohra
bsdb:29313867/2/1,29313867,"cross-sectional observational, not case-control",29313867,NA,NA,"Di Pietro M., Filardo S., Porpora M.G., Recine N., Latino M.A. , Sessa R.",HPV/Chlamydia trachomatis co-infection: metagenomic analysis of cervical microbiota in asymptomatic women,The new microbiologica,2018,"Cervical microbiota, Chlamydia trachomatis, Coinfection, HPV, Metagenomic analysis",Experiment 2,Italy,Homo sapiens,Endocervix,UBERON:0000458,"Chlamydophila infectious disease,Human papilloma virus infection","EFO:1000863,EFO:0001668",HPV positive women,patient with chlamydia infection,patient with Chlamydia infection,7,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Cynthia Anderson,WikiWorks,LEfSe results on cervical microbiota in C. trachomatis-positive women compared to HPV-positive women or healthy controls.,increased,"k__Pseudomonadati|p__Chlamydiota,k__Pseudomonadati|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae,k__Pseudomonadati|p__Chlamydiota|c__Chlamydiia,k__Pseudomonadati|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales,k__Pseudomonadati|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia,k__Pseudomonadati|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia|s__Chlamydia trachomatis",3379134|204428;3379134|204428|204429|51291|809;3379134|204428|204429;3379134|204428|204429|51291;3379134|204428|204429|51291|809|810;3379134|204428|204429|51291|809|810|813,Complete,Fatima Zohra
bsdb:29313867/2/2,29313867,"cross-sectional observational, not case-control",29313867,NA,NA,"Di Pietro M., Filardo S., Porpora M.G., Recine N., Latino M.A. , Sessa R.",HPV/Chlamydia trachomatis co-infection: metagenomic analysis of cervical microbiota in asymptomatic women,The new microbiologica,2018,"Cervical microbiota, Chlamydia trachomatis, Coinfection, HPV, Metagenomic analysis",Experiment 2,Italy,Homo sapiens,Endocervix,UBERON:0000458,"Chlamydophila infectious disease,Human papilloma virus infection","EFO:1000863,EFO:0001668",HPV positive women,patient with chlamydia infection,patient with Chlamydia infection,7,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 3,10 January 2021,Cynthia Anderson,WikiWorks,LEfSe results on cervical microbiota in C. trachomatis-positive women compared to HPV-positive women or healthy controls.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota",1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|91061;1783272|1239|91061|186826;1783272|1239,Complete,Fatima Zohra
bsdb:29317709/1/1,29317709,"cross-sectional observational, not case-control",29317709,10.1038/s41598-017-18596-0,NA,"Hsieh Y.Y., Tung S.Y., Pan H.Y., Yen C.W., Xu H.W., Lin Y.J., Deng Y.F., Hsu W.T., Wu C.S. , Li C.",Increased Abundance of Clostridium and Fusobacterium in Gastric Microbiota of Patients with Gastric Cancer in Taiwan,Scientific reports,2018,NA,Experiment 1,Taiwan,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,patients diagnosed with gastritis,patients diagnosed with gastric cancer,Patients with gastric cancer,16,11,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Valentina Pineda,"Claregrieve1,WikiWorks",Bacteria specifically found in patients with gastric cancer compared with the average counts in gastritis specimens,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium colicanis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium canifelinum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis",1783272|1239|186801|186802|31979|1485|179628;3384189|32066|203490|203491|203492|848|285729;3384189|32066|203490|203491|203492|848|851;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|91061|186826|33958|2742598|1598;1783272|1239|909932|1843489|31977|906|187326;3379134|976|200643|171549|171552|838|28131;3379134|976|200643|171549|171552|2974251|28135;1783272|1239|91061|186826|1300|1301|1302;1783272|1239|91061|186826|1300|1301|1318,Complete,Claregrieve1
bsdb:29318631/1/1,29318631,case-control,29318631,10.1111/all.13389,NA,"Fazlollahi M., Chun Y., Grishin A., Wood R.A., Burks A.W., Dawson P., Jones S.M., Leung D.Y.M., Sampson H.A., Sicherer S.H. , Bunyavanich S.",Early-life gut microbiome and egg allergy,Allergy,2018,"egg allergy, egg sensitization, food allergy, microbiome, purine",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Egg allergy,EFO:0007248,healthy control,children with egg allergy,children with egg allergy (ages ranging from 3 to 16 months),75,66,NA,16S,4,Illumina,relative abundances,"LEfSe,Logistic Regression",0.05,FALSE,2,NA,"age,antibiotic,atopic eczema,breast feeding",NA,increased,increased,NA,NA,increased,Signature 1,"Figure 2b, text",10 January 2021,Lucy Mellor,WikiWorks,Bacterial genera significantly associated with egg allergy,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus",1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300|1357,Complete,Atrayees
bsdb:29318631/1/2,29318631,case-control,29318631,10.1111/all.13389,NA,"Fazlollahi M., Chun Y., Grishin A., Wood R.A., Burks A.W., Dawson P., Jones S.M., Leung D.Y.M., Sampson H.A., Sicherer S.H. , Bunyavanich S.",Early-life gut microbiome and egg allergy,Allergy,2018,"egg allergy, egg sensitization, food allergy, microbiome, purine",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Egg allergy,EFO:0007248,healthy control,children with egg allergy,children with egg allergy (ages ranging from 3 to 16 months),75,66,NA,16S,4,Illumina,relative abundances,"LEfSe,Logistic Regression",0.05,FALSE,2,NA,"age,antibiotic,atopic eczema,breast feeding",NA,increased,increased,NA,NA,increased,Signature 2,"Figure 2b, text",10 January 2021,Lucy Mellor,WikiWorks,Bacterial genera significantly associated with egg allergy,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,1783272|1239|91061|186826|33958|1243,Complete,Atrayees
bsdb:29318631/2/1,29318631,case-control,29318631,10.1111/all.13389,NA,"Fazlollahi M., Chun Y., Grishin A., Wood R.A., Burks A.W., Dawson P., Jones S.M., Leung D.Y.M., Sampson H.A., Sicherer S.H. , Bunyavanich S.",Early-life gut microbiome and egg allergy,Allergy,2018,"egg allergy, egg sensitization, food allergy, microbiome, purine",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Egg allergy,EFO:0007248,healthy control,children with egg sensitization,children with egg sensitization,40,101,NA,16S,4,Illumina,relative abundances,"LEfSe,Logistic Regression",0.05,FALSE,2,NA,"age,race",NA,increased,increased,NA,NA,increased,Signature 1,"Figure 5b, text",10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Bacterial genera significantly associated with egg sensitization,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|841;3379134|74201;1783272|1239,Complete,Atrayees
bsdb:29320965/1/1,29320965,case-control,29320965,10.1089/thy.2017.0395,NA,"Zhao F., Feng J., Li J., Zhao L., Liu Y., Chen H., Jin Y., Zhu B. , Wei Y.",Alterations of the Gut Microbiota in Hashimoto's Thyroiditis Patients,Thyroid : official journal of the American Thyroid Association,2018,"Hashimoto's thyroiditis, biomarker, clinical parameters, dysbiosis, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Hashimoto's thyroiditis,EFO:0003779,healthy controls,hashimoto's thyroiditis patients,"presence of euthyroidism, free thyroxine, and thyrotropin without hormonal therapy",27,50,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 2a, 2b, table 3",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Comparisons of the relative abundance using LEfSe analysis,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|189330;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|186806|1730|42322;1783272|1239;1783272|1239|186801|3085636|186803|1407607;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803;3379134|1224|1236|135625|712;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263|438033;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|186802|31979|1485,Complete,Atrayees
bsdb:29320965/1/2,29320965,case-control,29320965,10.1089/thy.2017.0395,NA,"Zhao F., Feng J., Li J., Zhao L., Liu Y., Chen H., Jin Y., Zhu B. , Wei Y.",Alterations of the Gut Microbiota in Hashimoto's Thyroiditis Patients,Thyroid : official journal of the American Thyroid Association,2018,"Hashimoto's thyroiditis, biomarker, clinical parameters, dysbiosis, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Hashimoto's thyroiditis,EFO:0003779,healthy controls,hashimoto's thyroiditis patients,"presence of euthyroidism, free thyroxine, and thyrotropin without hormonal therapy",27,50,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 2a, 2b, table 3",10 January 2021,Rimsha Azhar,WikiWorks,Comparisons of the relative abundance using LEfSe analysis,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Actinomycetota|c__Thermoleophilia|o__Gaiellales|f__Gaiellaceae|g__Gaiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Actinomycetota|c__Thermoleophilia|o__Gaiellales|f__Gaiellaceae,k__Pseudomonadati|p__Bacteroidota,k__Thermotogati|p__Synergistota",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|1283313;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3085636|186803|1506553;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|577309;1783272|201174|1497346|1154584|1154585|1154586;3379134|976|200643|171549|815;3379134|976|200643|171549|171552;3379134|976|200643|171549|171551;1783272|1239|909932|1843488|909930;1783272|201174|1497346|1154584|1154585;3379134|976;3384194|508458,Complete,Atrayees
bsdb:29321519/1/1,29321519,prospective cohort,29321519,10.1038/s41467-017-02573-2,NA,"Stokholm J., Blaser M.J., Thorsen J., Rasmussen M.A., Waage J., Vinding R.K., Schoos A.M., Kunøe A., Fink N.R., Chawes B.L., Bønnelykke K., Brejnrod A.D., Mortensen M.S., Al-Soud W.A., Sørensen S.J. , Bisgaard H.",Maturation of the gut microbiome and risk of asthma in childhood,Nature communications,2018,NA,Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma at 5 years old,child with asthma at 5 years old,"child with physician diagnosed asthma based on verified diary recordings of five episodes of troublesome lung symptoms within 6 months, exercise-induced symptoms, prolonged nocturnal cough, and/or persistent cough outside of common colds, need for intermittent rescue use of inhaled β2-agonist, response to a 3-month course of inhaled corticosteroids andrelapse upon ending treatment",531,58,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3,10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Relative abundances of bacterial genera in 1-year fecal samples associated with asthma at age 5 years in all children,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:29321519/1/2,29321519,prospective cohort,29321519,10.1038/s41467-017-02573-2,NA,"Stokholm J., Blaser M.J., Thorsen J., Rasmussen M.A., Waage J., Vinding R.K., Schoos A.M., Kunøe A., Fink N.R., Chawes B.L., Bønnelykke K., Brejnrod A.D., Mortensen M.S., Al-Soud W.A., Sørensen S.J. , Bisgaard H.",Maturation of the gut microbiome and risk of asthma in childhood,Nature communications,2018,NA,Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma at 5 years old,child with asthma at 5 years old,"child with physician diagnosed asthma based on verified diary recordings of five episodes of troublesome lung symptoms within 6 months, exercise-induced symptoms, prolonged nocturnal cough, and/or persistent cough outside of common colds, need for intermittent rescue use of inhaled β2-agonist, response to a 3-month course of inhaled corticosteroids andrelapse upon ending treatment",531,58,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3,10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Relative abundances of bacterial genera in 1-year fecal samples associated with asthma at age 5 years in all children,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|186801|3085636|186803|841;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|216572|216851;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|216572|1263;1783272|1239|909932|1843489|31977|39948;3379134|976|200643|171549|171552|838,Complete,Atrayees
bsdb:29321519/2/1,29321519,prospective cohort,29321519,10.1038/s41467-017-02573-2,NA,"Stokholm J., Blaser M.J., Thorsen J., Rasmussen M.A., Waage J., Vinding R.K., Schoos A.M., Kunøe A., Fink N.R., Chawes B.L., Bønnelykke K., Brejnrod A.D., Mortensen M.S., Al-Soud W.A., Sørensen S.J. , Bisgaard H.",Maturation of the gut microbiome and risk of asthma in childhood,Nature communications,2018,NA,Experiment 2,Denmark,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma at 5 years old,child with asthma at 5 years old among mothers with asthma,"child with physician diagnosed asthma based on verified diary recordings of five episodes of troublesome lung symptoms within 6 months, exercise-induced symptoms, prolonged nocturnal cough, and/or persistent cough outside of common colds, need for intermittent rescue use of inhaled β2-agonist, response to a 3-month course of inhaled corticosteroids andrelapse upon ending treatment and mother with asthma",122,25,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3,10 January 2021,Lucy Mellor,WikiWorks,Relative abundances of bacterial genera in 1-year fecal samples associated with asthma at age 5 years in children born to asthmatic mothers,increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,1783272|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:29321519/2/2,29321519,prospective cohort,29321519,10.1038/s41467-017-02573-2,NA,"Stokholm J., Blaser M.J., Thorsen J., Rasmussen M.A., Waage J., Vinding R.K., Schoos A.M., Kunøe A., Fink N.R., Chawes B.L., Bønnelykke K., Brejnrod A.D., Mortensen M.S., Al-Soud W.A., Sørensen S.J. , Bisgaard H.",Maturation of the gut microbiome and risk of asthma in childhood,Nature communications,2018,NA,Experiment 2,Denmark,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma at 5 years old,child with asthma at 5 years old among mothers with asthma,"child with physician diagnosed asthma based on verified diary recordings of five episodes of troublesome lung symptoms within 6 months, exercise-induced symptoms, prolonged nocturnal cough, and/or persistent cough outside of common colds, need for intermittent rescue use of inhaled β2-agonist, response to a 3-month course of inhaled corticosteroids andrelapse upon ending treatment and mother with asthma",122,25,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3,10 January 2021,Lucy Mellor,"WikiWorks,Suwaiba,Atrayees",Relative abundances of bacterial genera in 1-year fecal samples associated with asthma at age 5 years in children born to asthmatic mothers,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",3379134|976|200643|171549|171550|239759;1783272|201174|1760|85004|31953|1678;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|2005525|375288;1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|946234;3379134|74201|203494|48461|1647988|239934,Complete,Atrayees
bsdb:29321519/3/1,29321519,prospective cohort,29321519,10.1038/s41467-017-02573-2,NA,"Stokholm J., Blaser M.J., Thorsen J., Rasmussen M.A., Waage J., Vinding R.K., Schoos A.M., Kunøe A., Fink N.R., Chawes B.L., Bønnelykke K., Brejnrod A.D., Mortensen M.S., Al-Soud W.A., Sørensen S.J. , Bisgaard H.",Maturation of the gut microbiome and risk of asthma in childhood,Nature communications,2018,NA,Experiment 3,Denmark,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma at 5 years old,child with asthma at 5 years old among mothers without asthma,child with asthma at 5 years old among mothers without asthma,409,33,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3,20 July 2023,Atrayees,"Atrayees,WikiWorks",Relative abundances of bacterial genera in 1-year fecal samples associated with asthma at age 5 years in children born to non-asthmatic mothers,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",1783272|1239|909932|1843489|31977|29465;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|1263;3379134|74201|203494|48461|1647988|239934,Complete,Atrayees
bsdb:29321519/3/2,29321519,prospective cohort,29321519,10.1038/s41467-017-02573-2,NA,"Stokholm J., Blaser M.J., Thorsen J., Rasmussen M.A., Waage J., Vinding R.K., Schoos A.M., Kunøe A., Fink N.R., Chawes B.L., Bønnelykke K., Brejnrod A.D., Mortensen M.S., Al-Soud W.A., Sørensen S.J. , Bisgaard H.",Maturation of the gut microbiome and risk of asthma in childhood,Nature communications,2018,NA,Experiment 3,Denmark,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,no asthma at 5 years old,child with asthma at 5 years old among mothers without asthma,child with asthma at 5 years old among mothers without asthma,409,33,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3,20 July 2023,Atrayees,"Atrayees,WikiWorks",Relative abundances of bacterial genera in 1-year fecal samples associated with asthma at age 5 years in children born to non-asthmatic mothers,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor",1783272|1239|186801|186802|216572|216851;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|946234,Complete,Atrayees
bsdb:29327043/1/1,29327043,case-control,29327043,10.1001/jamaoncol.2017.4777,NA,"Hayes R.B., Ahn J., Fan X., Peters B.A., Ma Y., Yang L., Agalliu I., Burk R.D., Ganly I., Purdue M.P., Freedman N.D., Gapstur S.M. , Pei Z.",Association of Oral Microbiome With Risk for Incident Head and Neck Squamous Cell Cancer,JAMA oncology,2018,NA,Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Head and neck squamous cell carcinoma,EFO:0000181,controls,HNSCC,"histologically confirmed incident HNSCC including oral cavity, pharynx and larynx. (excluding salivary glands & nasopharynx)",254,129,NA,16S,34,Roche454,raw counts,DESeq2,0.1,TRUE,NA,"age,date,ethnic group,sex","age,alcohol drinking,sex,smoking behavior",NA,NA,NA,NA,unchanged,unchanged,Signature 1,Table 2,10 January 2021,Utsav Patel,"Claregrieve1,WikiWorks",Differential microbial abundance between controls and HNSCC patients,increased,k__Bacillati|p__Actinomycetota,1783272|201174,Complete,Fatima Zohra
bsdb:29327043/1/2,29327043,case-control,29327043,10.1001/jamaoncol.2017.4777,NA,"Hayes R.B., Ahn J., Fan X., Peters B.A., Ma Y., Yang L., Agalliu I., Burk R.D., Ganly I., Purdue M.P., Freedman N.D., Gapstur S.M. , Pei Z.",Association of Oral Microbiome With Risk for Incident Head and Neck Squamous Cell Cancer,JAMA oncology,2018,NA,Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Head and neck squamous cell carcinoma,EFO:0000181,controls,HNSCC,"histologically confirmed incident HNSCC including oral cavity, pharynx and larynx. (excluding salivary glands & nasopharynx)",254,129,NA,16S,34,Roche454,raw counts,DESeq2,0.1,TRUE,NA,"age,date,ethnic group,sex","age,alcohol drinking,sex,smoking behavior",NA,NA,NA,NA,unchanged,unchanged,Signature 2,Table 2,10 January 2021,Utsav Patel,"Claregrieve1,WikiWorks",Differential microbial abundance between controls and HNSCC patients,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena",3379134|1224|28216;3379134|976|117743|200644|49546|1016|327575;1783272|201174|1760|85007|1653|1716;3379134|1224|28216|206351|481|32257;3379134|976|200643|171549|171552|2974257|425941;1783272|1239|909932|909929|1843491|970|69823,Complete,Fatima Zohra
bsdb:29327043/2/1,29327043,case-control,29327043,10.1001/jamaoncol.2017.4777,NA,"Hayes R.B., Ahn J., Fan X., Peters B.A., Ma Y., Yang L., Agalliu I., Burk R.D., Ganly I., Purdue M.P., Freedman N.D., Gapstur S.M. , Pei Z.",Association of Oral Microbiome With Risk for Incident Head and Neck Squamous Cell Cancer,JAMA oncology,2018,NA,Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,Squamous cell carcinoma,EFO:0000707,controls,Larynx cancer cases,histologically confirmed incident HNSCC involving the larynx,254,58,NA,16S,34,Roche454,raw counts,DESeq2,0.1,TRUE,NA,"age,date,ethnic group,sex","age,alcohol drinking,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,"Table 2, Supplementary Table 6, Text",10 January 2021,Utsav Patel,"Claregrieve1,WikiWorks",Differential microbial abundance between controls and larynx cancer patients,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella denitrificans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis",1783272|1239|91061|186826|186827|46123;3379134|1224|28216;3379134|976|117743|200644|49546|1016;1783272|201174|1760|85007|1653|1716;3379134|1224|28216|206351|481|32257;3379134|1224|28216|206351|481|32257|502;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351;1783272|1239|91061|186826|1300|1301|1305,Complete,Fatima Zohra
bsdb:29327043/3/1,29327043,case-control,29327043,10.1001/jamaoncol.2017.4777,NA,"Hayes R.B., Ahn J., Fan X., Peters B.A., Ma Y., Yang L., Agalliu I., Burk R.D., Ganly I., Purdue M.P., Freedman N.D., Gapstur S.M. , Pei Z.",Association of Oral Microbiome With Risk for Incident Head and Neck Squamous Cell Cancer,JAMA oncology,2018,NA,Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Squamous cell carcinoma,EFO:0000707,controls,Pharynx cancer cases,histologically confirmed incident HNSCC involving the pharynx,254,30,NA,16S,34,Roche454,raw counts,DESeq2,0.1,TRUE,NA,"age,date,ethnic group,sex","age,alcohol drinking,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,"Table 2, Supplementary Table 6, Text",10 January 2021,Utsav Patel,"Claregrieve1,WikiWorks",Differential microbial abundance between controls and pharynx cancer patients,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella denticariosi",1783272|201174|1760|2037|2049|1654|544580;3379134|1224|28216;1783272|201174|1760|85007|1653|1716;3379134|1224|28216|206351|481|32257;3379134|1224|28216|206351;1783272|1239|909932|1843489|31977|29465|419208,Complete,Fatima Zohra
bsdb:29327043/4/1,29327043,case-control,29327043,10.1001/jamaoncol.2017.4777,NA,"Hayes R.B., Ahn J., Fan X., Peters B.A., Ma Y., Yang L., Agalliu I., Burk R.D., Ganly I., Purdue M.P., Freedman N.D., Gapstur S.M. , Pei Z.",Association of Oral Microbiome With Risk for Incident Head and Neck Squamous Cell Cancer,JAMA oncology,2018,NA,Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,Squamous cell carcinoma,EFO:0000707,controls,Oral cavity cancer cases,histologically confirmed incident HNSCC involving the oral cavity,254,41,NA,16S,34,Roche454,raw counts,DESeq2,0.1,TRUE,NA,"age,date,ethnic group,sex","age,alcohol drinking,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,"Table 2, Supplementary Table 6, Text",10 January 2021,Utsav Patel,"Claregrieve1,WikiWorks",Differential microbial abundance between controls and oral cavity cancer patients,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,1783272|201174|1760|2037|2049|1654,Complete,Fatima Zohra
bsdb:29327043/4/2,29327043,case-control,29327043,10.1001/jamaoncol.2017.4777,NA,"Hayes R.B., Ahn J., Fan X., Peters B.A., Ma Y., Yang L., Agalliu I., Burk R.D., Ganly I., Purdue M.P., Freedman N.D., Gapstur S.M. , Pei Z.",Association of Oral Microbiome With Risk for Incident Head and Neck Squamous Cell Cancer,JAMA oncology,2018,NA,Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,Squamous cell carcinoma,EFO:0000707,controls,Oral cavity cancer cases,histologically confirmed incident HNSCC involving the oral cavity,254,41,NA,16S,34,Roche454,raw counts,DESeq2,0.1,TRUE,NA,"age,date,ethnic group,sex","age,alcohol drinking,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 2,"Table 2, Supplementary Table 6, Text",10 January 2021,Utsav Patel,"Claregrieve1,WikiWorks",Differential microbial abundance between controls and oral cavity cancer patients,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sicca,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra",3379134|1224|28216|206351|481|482|490;1783272|1239|1737404|1737405|1570339|543311|33033,Complete,Fatima Zohra
bsdb:29352709/1/1,29352709,"cross-sectional observational, not case-control",29352709,10.1016/j.schres.2018.01.002,NA,"Shen Y., Xu J., Li Z., Huang Y., Yuan Y., Wang J., Zhang M., Hu S. , Liang Y.",Analysis of gut microbiota diversity and auxiliary diagnosis as a biomarker in patients with schizophrenia: A cross-sectional study,Schizophrenia research,2018,"16S rRNA sequencing, Biomarker, Brain-gut axis, Gut microbiota, Schizophrenia",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Healthy controls,Schizophrenia,The patients were examined and diagnosed according to the ICD-10 by two trained psychiatric physicians.,53,64,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure 4, S3",10 January 2021,Fatima Zohra,WikiWorks,"Microbial composition at phylum, genus and species level in healthy and schizophrenia cohorts",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|838;3379134|1224|1236;3379134|1224;3379134|1224|1236|135624;3379134|1224|1236|135624|83763|83770;3379134|1224|1236|91347|543;3379134|1224|1236|91347;3379134|1224|1236|135624|83763;3384189|32066|203490;3384189|32066;3384189|32066|203490|203491|203492;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491;1783272|1239|909932|1843489|31977;1783272|1239|909932|1843489|31977|906;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958;3379134|1224|1236|91347|543|544;1783272|1239|909932|1843488|909930|33024;1783272|1239|909932|1843488|909930|904;3379134|200940|3031449|213115|194924|872,Complete,Shaimaa Elsafoury
bsdb:29352709/1/2,29352709,"cross-sectional observational, not case-control",29352709,10.1016/j.schres.2018.01.002,NA,"Shen Y., Xu J., Li Z., Huang Y., Yuan Y., Wang J., Zhang M., Hu S. , Liang Y.",Analysis of gut microbiota diversity and auxiliary diagnosis as a biomarker in patients with schizophrenia: A cross-sectional study,Schizophrenia research,2018,"16S rRNA sequencing, Biomarker, Brain-gut axis, Gut microbiota, Schizophrenia",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Healthy controls,Schizophrenia,The patients were examined and diagnosed according to the ICD-10 by two trained psychiatric physicians.,53,64,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 4, S3",10 January 2021,Fatima Zohra,WikiWorks,"Microbial composition at phylum, genus and species level in healthy and schizophrenia cohorts",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|572511;3379134|1224|28216|80840|506;1783272|1239|186801|186802;1783272|1239|186801;1783272|1239;1783272|1239|186801|3085636|186803,Complete,Shaimaa Elsafoury
bsdb:29353409/1/1,29353409,case-control,29353409,10.1007/s00240-018-1037-y,NA,"Tang R., Jiang Y., Tan A., Ye J., Xian X., Xie Y., Wang Q., Yao Z. , Mo Z.",16S rRNA gene sequencing reveals altered composition of gut microbiota in individuals with kidney stones,Urolithiasis,2018,"16S rRNA, Biomarker, Gut microbiota, Nephrolithiasis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,"Urolithiasis,Nephrolithiasis","MONDO:0024647,EFO:0004253",healthy control,kidney stone group,patients with kidney stones,13,13,3 months,16S,4,Illumina,relative abundances,LEfSe,3,FALSE,3,"age,race",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 5,10 January 2021,Rimsha Azhar,"KathyWaldron,WikiWorks",LEfSe analysis based on OTU characterizes microbiome between the Kidney Stone group and HC group.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Boseaceae|g__Bosea,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Boseaceae|g__Bosea|s__Bosea thiooxidans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|s__Bacteroidaceae bacterium",3379134|1224|1236|2887326|468|469;3379134|976|200643|171549|171552|1283313;3379134|1224|28211|356|2831100|85413;3379134|1224|28211|356|2831100|85413|53254;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|186806|1730;1783272|1239|526524|526525|128827|1573534;1783272|1239|186801|3085636|186803|1506553;1783272|1239|909932|909929|1843491|158846;3379134|1224|1236|2887326|468;3379134|1224|1236|72274;3379134|1224|1236|72274|135621|286|287;3379134|1224|1236|91347|543|620;1783272|1239|186801|3085636|186803|2316020|33038;3379134|976|200643|171549|815|2212467,Complete,Atrayees
bsdb:29353409/1/2,29353409,case-control,29353409,10.1007/s00240-018-1037-y,NA,"Tang R., Jiang Y., Tan A., Ye J., Xian X., Xie Y., Wang Q., Yao Z. , Mo Z.",16S rRNA gene sequencing reveals altered composition of gut microbiota in individuals with kidney stones,Urolithiasis,2018,"16S rRNA, Biomarker, Gut microbiota, Nephrolithiasis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,"Urolithiasis,Nephrolithiasis","MONDO:0024647,EFO:0004253",healthy control,kidney stone group,patients with kidney stones,13,13,3 months,16S,4,Illumina,relative abundances,LEfSe,3,FALSE,3,"age,race",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 5,10 January 2021,Rimsha Azhar,WikiWorks,LEfSe analysis based on OTU characterizes microbiome between the Kidney Stone group and HC group.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Thalassospiraceae|g__Thalassospira,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter piscolens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter",1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3082768|990719;1783272|1239|909932|1843489|31977|39948;1783272|1239|526524|526525|128827|61170;3379134|1224|28211|204441|2844866|168934;3379134|1224|28211|204441|41295;3379134|1224|28211|204441;3379134|1224|28211;3384194|508458|649775|649776|3029088|638847;3384194|508458|649775|649776|3029088|638847|638849;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004;1783272|201174|1760|85004|31953;1783272|201174|1760;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|3085636|186803|841;3379134|976|200643|171549|171550|239759|328814;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171550|239759|328813;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|815|909656|310297;3379134|1224|1236|91347|543|547,Complete,Atrayees
bsdb:29353409/2/1,29353409,case-control,29353409,10.1007/s00240-018-1037-y,NA,"Tang R., Jiang Y., Tan A., Ye J., Xian X., Xie Y., Wang Q., Yao Z. , Mo Z.",16S rRNA gene sequencing reveals altered composition of gut microbiota in individuals with kidney stones,Urolithiasis,2018,"16S rRNA, Biomarker, Gut microbiota, Nephrolithiasis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,"Nephrolithiasis,Urolithiasis","EFO:0004253,MONDO:0024647",healthy control,kidney stone group,patients with kidney stones,13,13,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,race",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Table 2, Figure 2",10 January 2021,Rimsha Azhar,WikiWorks,List of genera that were significantly different between Kidney Stone group and HC group,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales",3379134|976|200643|171549|171552|1283313;1783272|1239|526524|526525|2810280|1505663;1783272|1239|186801|3085636|186803;1783272|1239|909932|1843488|909930|33024;1783272|1239|909932|909929|1843491|158846;3379134|1224|1236|2887326|468|469;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|620;3379134|1224|28216|80840|995019|40544;1783272|1239|526524|526525|128827;3379134|1224|1236|2887326|468;3379134|1224|1236|72274;1783272|1239|526524|526525,Complete,Atrayees
bsdb:29353409/2/2,29353409,case-control,29353409,10.1007/s00240-018-1037-y,NA,"Tang R., Jiang Y., Tan A., Ye J., Xian X., Xie Y., Wang Q., Yao Z. , Mo Z.",16S rRNA gene sequencing reveals altered composition of gut microbiota in individuals with kidney stones,Urolithiasis,2018,"16S rRNA, Biomarker, Gut microbiota, Nephrolithiasis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,"Nephrolithiasis,Urolithiasis","EFO:0004253,MONDO:0024647",healthy control,kidney stone group,patients with kidney stones,13,13,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,race",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Table 2, Figure 2",10 January 2021,Rimsha Azhar,WikiWorks,List of genera that were significantly different between Kidney Stone group and HC group,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|526524|526525|128827|1573535;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572|1263;3379134|1224|28216|80840|995019|577310;3379134|200940|3031449|213115|194924|35832,Complete,Atrayees
bsdb:29362454/1/1,29362454,"cross-sectional observational, not case-control",29362454,10.1038/s41598-018-19753-9,NA,"Da Silva H.E., Teterina A., Comelli E.M., Taibi A., Arendt B.M., Fischer S.E., Lou W. , Allard J.P.",Nonalcoholic fatty liver disease is associated with dysbiosis independent of body mass index and insulin resistance,Scientific reports,2018,NA,Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,Healthy control,NAFLD- [non alcoholic fatty liver disease],Adults with biopsy-proven steatosis and non-alcoholic fatty liver disease,28,39,6 months,PCR,NA,Illumina,NA,Metastats,0.05,TRUE,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,Signature 1,table 2,10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy",Taxa identified as differentially abundant in patients with nonalocholic fatty liver disease (NAFLD) compared to HC,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli",1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|91061,Complete,Peace Sandy
bsdb:29362454/1/2,29362454,"cross-sectional observational, not case-control",29362454,10.1038/s41598-018-19753-9,NA,"Da Silva H.E., Teterina A., Comelli E.M., Taibi A., Arendt B.M., Fischer S.E., Lou W. , Allard J.P.",Nonalcoholic fatty liver disease is associated with dysbiosis independent of body mass index and insulin resistance,Scientific reports,2018,NA,Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,Healthy control,NAFLD- [non alcoholic fatty liver disease],Adults with biopsy-proven steatosis and non-alcoholic fatty liver disease,28,39,6 months,PCR,NA,Illumina,NA,Metastats,0.05,TRUE,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,Signature 2,Table 2,10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy",Taxa identified as differentially abundant in patients with nonalocholic fatty liver disease (NAFLD) compared to HC,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|207244;1783272|1239;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|541000;3379134|976|200643|171549|171551;3379134|976|200643|171549|171550;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|841;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3085636|186803;1783272|1239|186801;3379134|976|200643|171549,Complete,Peace Sandy
bsdb:29375539/1/1,29375539,case-control,29375539,10.3389/fmicb.2017.02699,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5770402/,"Russo E., Bacci G., Chiellini C., Fagorzi C., Niccolai E., Taddei A., Ricci F., Ringressi M.N., Borrelli R., Melli F., Miloeva M., Bechi P., Mengoni A., Fani R. , Amedei A.",Preliminary Comparison of Oral and Intestinal Human Microbiota in Patients with Colorectal Cancer: A Pilot Study,Frontiers in microbiology,2017,"Fusobacterium nucleatum, colorectal cancer, gut microbiota, oral microbiota, quantitative polymerase chain reaction, taxonomic analysis",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Controls,Colorectal Cancer Patients,Italian patients aged 71-95 with colorectal adenocarcinoma confirmed by histological analysis undergoing surgical resections,10,10,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 7A,12 January 2022,Itslanapark,"Itslanapark,Peace Sandy,Atrayees,Folakunmi,WikiWorks","Linear discriminant analysis of association between sampling sites and microbial taxa. A linear discriminant analysis was performed using Lefse and
considering the three body sites sampled in this study, namely: biopsy (red), saliva (green), and stool (blue). (A) Different body sites showed a characteristic taxonomic
composition with major clades strongly associated with a particular site. Proteobacteria were mostly associated with biopsy samples whereas Fusobacteria and
Bacteroidetes were mainly associated with saliva and stool samples, respectively.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiales Family XVII. Incertae Sedis",3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643;1783272|1239|186801;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|186801|186802;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171551;3379134|976|200643|171549|171550;;1783272|1239|186801|186802|539000,Complete,Folakunmi
bsdb:29375539/2/1,29375539,case-control,29375539,10.3389/fmicb.2017.02699,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5770402/,"Russo E., Bacci G., Chiellini C., Fagorzi C., Niccolai E., Taddei A., Ricci F., Ringressi M.N., Borrelli R., Melli F., Miloeva M., Bechi P., Mengoni A., Fani R. , Amedei A.",Preliminary Comparison of Oral and Intestinal Human Microbiota in Patients with Colorectal Cancer: A Pilot Study,Frontiers in microbiology,2017,"Fusobacterium nucleatum, colorectal cancer, gut microbiota, oral microbiota, quantitative polymerase chain reaction, taxonomic analysis",Experiment 2,Italy,Homo sapiens,Saliva,UBERON:0001836,Colorectal cancer,EFO:0005842,Healthy Controls,Colorectal cancer Patients,Italian patients aged 71-95 with colorectal adenocarcinoma confirmed by histological analysis undergoing surgical resections.,10,10,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,NA,increased,decreased,NA,NA,NA,Signature 1,Figure 7A,25 January 2022,Itslanapark,"Itslanapark,Adanwa,Peace Sandy,Folakunmi,WikiWorks","Linear discriminant analysis of association between sampling sites and microbial taxa. A linear discriminant analysis was performed using Lefse and
considering the three body sites sampled in this study, namely: biopsy (red), saliva (green), and stool (blue). (A) Different body sites showed a characteristic taxonomic
composition with major clades strongly associated with a particular site. Proteobacteria were mostly associated with biopsy samples whereas Fusobacteria and
Bacteroidetes were mainly associated with saliva and stool samples, respectively.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,p__Candidatus Saccharimonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales",1783272|201174|1760|2037|2049;1783272|201174|1760|2037;1783272|201174;1783272|1239|91061|1385;1783272|1239|91061;3379134|1224|28216;3379134|976|117743|200644|49546;3379134|976|117743|200644;3384189|32066|203490;3384189|32066|203490|203491|1129771;1783272|201174|1760|85006|1268;1783272|201174|1760|85006;1783272|1239|909932;3379134|1224|28216|206351|481;3379134|1224|28216|206351;3379134|1224|1236|135625|712;3379134|976|200643|171549|171552;1783272|1239|909932|909929;1783272|1239|91061|186826|1300;1783272|1239|909932|1843489|31977;95818;1783272|1239|91061|186826,Complete,Folakunmi
bsdb:29375539/3/1,29375539,case-control,29375539,10.3389/fmicb.2017.02699,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5770402/,"Russo E., Bacci G., Chiellini C., Fagorzi C., Niccolai E., Taddei A., Ricci F., Ringressi M.N., Borrelli R., Melli F., Miloeva M., Bechi P., Mengoni A., Fani R. , Amedei A.",Preliminary Comparison of Oral and Intestinal Human Microbiota in Patients with Colorectal Cancer: A Pilot Study,Frontiers in microbiology,2017,"Fusobacterium nucleatum, colorectal cancer, gut microbiota, oral microbiota, quantitative polymerase chain reaction, taxonomic analysis",Experiment 3,Italy,Homo sapiens,Colorectum,UBERON:0012652,Colorectal cancer,EFO:0005842,Healthy Controls,Biopsy samples of colorectal cancer patients,Italian patients aged 71-95 with colorectal adenocarcinoma confirmed by histological analysis undergoing surgical resections.,10,10,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 1,Figure 7A,10 January 2024,Folakunmi,"Folakunmi,WikiWorks","Linear discriminant analysis of association between sampling sites and microbial taxa. A linear discriminant analysis was performed using Lefse and considering the three body sites sampled in this study, namely: biopsy, saliva, and stool.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,c__Deltaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria",1783272|1239|186801|3085636|186803;3384189|32066|203490|203491|203492;3379134|1224|28211|356;3379134|1224|28211;28221;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236,Complete,Folakunmi
bsdb:29388394/1/1,29388394,case-control,29388394,10.1111/ijpo.12262,NA,"López-Contreras B.E., Morán-Ramos S., Villarruel-Vázquez R., Macías-Kauffer L., Villamil-Ramírez H., León-Mimila P., Vega-Badillo J., Sánchez-Muñoz F., Llanos-Moreno L.E., Canizalez-Román A., Del Río-Navarro B., Ibarra-González I., Vela-Amieva M., Villarreal-Molina T., Ochoa-Leyva A., Aguilar-Salinas C.A. , Canizales-Quinteros S.",Composition of gut microbiota in obese and normal-weight Mexican school-age children and its association with metabolic traits,Pediatric obesity,2018,"Amino acids, Mexican children, gut microbiota, obesity",Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,pediatric normal weight,pediatric obese,"Obesity was defined as body mass index (BMI) ≥95th percentile, whereas NW was de- fined as BMI between the 15th and 75th percentiles for age and gender based on Centers for Disease Control and Prevention (CDC) reference data",67,71,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table S6,10 January 2021,Marianthi Thomatos,WikiWorks,Composition of gut microbiota in obese and normal-weight mexican school-age children,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|976|200643|171549|815|816|28111;3379134|976|200643|171549|815|816|85831;3379134|976|200643|171549|815|816|28116;1783272|1239|909932|1843489|31977|39948;3379134|976|200643|171549|815|816;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|186801|3085636|186803,Complete,Shaimaa Elsafoury
bsdb:29388394/1/2,29388394,case-control,29388394,10.1111/ijpo.12262,NA,"López-Contreras B.E., Morán-Ramos S., Villarruel-Vázquez R., Macías-Kauffer L., Villamil-Ramírez H., León-Mimila P., Vega-Badillo J., Sánchez-Muñoz F., Llanos-Moreno L.E., Canizalez-Román A., Del Río-Navarro B., Ibarra-González I., Vela-Amieva M., Villarreal-Molina T., Ochoa-Leyva A., Aguilar-Salinas C.A. , Canizales-Quinteros S.",Composition of gut microbiota in obese and normal-weight Mexican school-age children and its association with metabolic traits,Pediatric obesity,2018,"Amino acids, Mexican children, gut microbiota, obesity",Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,pediatric normal weight,pediatric obese,"Obesity was defined as body mass index (BMI) ≥95th percentile, whereas NW was de- fined as BMI between the 15th and 75th percentiles for age and gender based on Centers for Disease Control and Prevention (CDC) reference data",67,71,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table S6,10 January 2021,Marianthi Thomatos,WikiWorks,Composition of gut microbiota in obese and normal-weight mexican school-age children,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|186801|3082768|990719;3379134|976|200643|171549|815|909656|310297;3379134|1224|1236|91347|543;3379134|976|200643|171549|171550;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171552|2974265|363265;3379134|976|200643|171549|171552|2974251|165179;3379134|1224|28216|80840|995019|40544;3379134|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
bsdb:29388394/2/1,29388394,case-control,29388394,10.1111/ijpo.12262,NA,"López-Contreras B.E., Morán-Ramos S., Villarruel-Vázquez R., Macías-Kauffer L., Villamil-Ramírez H., León-Mimila P., Vega-Badillo J., Sánchez-Muñoz F., Llanos-Moreno L.E., Canizalez-Román A., Del Río-Navarro B., Ibarra-González I., Vela-Amieva M., Villarreal-Molina T., Ochoa-Leyva A., Aguilar-Salinas C.A. , Canizales-Quinteros S.",Composition of gut microbiota in obese and normal-weight Mexican school-age children and its association with metabolic traits,Pediatric obesity,2018,"Amino acids, Mexican children, gut microbiota, obesity",Experiment 2,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,female pediatric normal weight,female pediatric obese,"Obesity was defined as body mass index (BMI) ≥95th percentile, whereas NW was de- fined as BMI between the 15th and 75th percentiles for age and gender based on Centers for Disease Control and Prevention (CDC) reference data",29,29,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiota in obese and normal weight mexican school-age children,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,3379134|976|200643|171549|815|816|28111,Complete,Shaimaa Elsafoury
bsdb:29388394/2/2,29388394,case-control,29388394,10.1111/ijpo.12262,NA,"López-Contreras B.E., Morán-Ramos S., Villarruel-Vázquez R., Macías-Kauffer L., Villamil-Ramírez H., León-Mimila P., Vega-Badillo J., Sánchez-Muñoz F., Llanos-Moreno L.E., Canizalez-Román A., Del Río-Navarro B., Ibarra-González I., Vela-Amieva M., Villarreal-Molina T., Ochoa-Leyva A., Aguilar-Salinas C.A. , Canizales-Quinteros S.",Composition of gut microbiota in obese and normal-weight Mexican school-age children and its association with metabolic traits,Pediatric obesity,2018,"Amino acids, Mexican children, gut microbiota, obesity",Experiment 2,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,female pediatric normal weight,female pediatric obese,"Obesity was defined as body mass index (BMI) ≥95th percentile, whereas NW was de- fined as BMI between the 15th and 75th percentiles for age and gender based on Centers for Disease Control and Prevention (CDC) reference data",29,29,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Text,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiota in obese and normal weight mexican school-age children,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,3379134|976|200643|171549|1853231|283168,Complete,Shaimaa Elsafoury
bsdb:29388394/3/1,29388394,case-control,29388394,10.1111/ijpo.12262,NA,"López-Contreras B.E., Morán-Ramos S., Villarruel-Vázquez R., Macías-Kauffer L., Villamil-Ramírez H., León-Mimila P., Vega-Badillo J., Sánchez-Muñoz F., Llanos-Moreno L.E., Canizalez-Román A., Del Río-Navarro B., Ibarra-González I., Vela-Amieva M., Villarreal-Molina T., Ochoa-Leyva A., Aguilar-Salinas C.A. , Canizales-Quinteros S.",Composition of gut microbiota in obese and normal-weight Mexican school-age children and its association with metabolic traits,Pediatric obesity,2018,"Amino acids, Mexican children, gut microbiota, obesity",Experiment 3,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,male pediatric normal weight,male pediatric obese,"Obesity was defined as body mass index (BMI) ≥95th percentile, whereas NW was de- fined as BMI between the 15th and 75th percentiles for age and gender based on Centers for Disease Control and Prevention (CDC) reference data",38,42,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiota in obese and normal weight mexican school-age children,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,3379134|976|200643|171549|815|816|28111,Complete,Shaimaa Elsafoury
bsdb:29388394/3/2,29388394,case-control,29388394,10.1111/ijpo.12262,NA,"López-Contreras B.E., Morán-Ramos S., Villarruel-Vázquez R., Macías-Kauffer L., Villamil-Ramírez H., León-Mimila P., Vega-Badillo J., Sánchez-Muñoz F., Llanos-Moreno L.E., Canizalez-Román A., Del Río-Navarro B., Ibarra-González I., Vela-Amieva M., Villarreal-Molina T., Ochoa-Leyva A., Aguilar-Salinas C.A. , Canizales-Quinteros S.",Composition of gut microbiota in obese and normal-weight Mexican school-age children and its association with metabolic traits,Pediatric obesity,2018,"Amino acids, Mexican children, gut microbiota, obesity",Experiment 3,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,male pediatric normal weight,male pediatric obese,"Obesity was defined as body mass index (BMI) ≥95th percentile, whereas NW was de- fined as BMI between the 15th and 75th percentiles for age and gender based on Centers for Disease Control and Prevention (CDC) reference data",38,42,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Text,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiota in obese and normal weight mexican school-age children,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,3379134|976|200643|171549|815|909656|310297,Complete,Shaimaa Elsafoury
bsdb:29411528/1/1,29411528,"cross-sectional observational, not case-control",29411528,10.1111/jcmm.13508,NA,"Zhou Y., Ou Z., Tang X., Zhou Y., Xu H., Wang X., Li K., He J., Du Y., Wang H., Chen Y. , Nie Y.",Alterations in the gut microbiota of patients with acquired immune deficiency syndrome,Journal of cellular and molecular medicine,2018,"acquired immune deficiency syndrome, dysbiosis, highly active antiretroviral therapy, human immunodeficiency virus, microbiota, transmission route",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,healthy controls,HIV infected patients,patients infected with HIV,35,33,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,Figure 5b,10 January 2021,Fatima Zohra,"WikiWorks,ChiomaBlessing",Differentially abundant microbial taxa in HIV infected patients compared with healthy controls,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis",1783272|1239|91061;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;3379134|1224|1236;1783272|1239|186801|3085636|186803|1506553;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|2316020|33038;3379134|1224;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1343,Complete,Claregrieve1
bsdb:29411528/1/2,29411528,"cross-sectional observational, not case-control",29411528,10.1111/jcmm.13508,NA,"Zhou Y., Ou Z., Tang X., Zhou Y., Xu H., Wang X., Li K., He J., Du Y., Wang H., Chen Y. , Nie Y.",Alterations in the gut microbiota of patients with acquired immune deficiency syndrome,Journal of cellular and molecular medicine,2018,"acquired immune deficiency syndrome, dysbiosis, highly active antiretroviral therapy, human immunodeficiency virus, microbiota, transmission route",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,healthy controls,HIV infected patients,patients infected with HIV,35,33,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Figure 5b,10 January 2021,Fatima Zohra,"WikiWorks,ChiomaBlessing",Differentially abundant microbial taxa in HIV infected patients compared with healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|909932|1843488|909930;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976;1783272|1239|186801;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932;1783272|1239|186801|186802|541000;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|909932|909929;1783272|1239|186801|186802|216572|292632;1783272|1239|909932|1843489|31977,Complete,Claregrieve1
bsdb:29411528/2/1,29411528,"cross-sectional observational, not case-control",29411528,10.1111/jcmm.13508,NA,"Zhou Y., Ou Z., Tang X., Zhou Y., Xu H., Wang X., Li K., He J., Du Y., Wang H., Chen Y. , Nie Y.",Alterations in the gut microbiota of patients with acquired immune deficiency syndrome,Journal of cellular and molecular medicine,2018,"acquired immune deficiency syndrome, dysbiosis, highly active antiretroviral therapy, human immunodeficiency virus, microbiota, transmission route",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,healthy controls,HIV infected patients who are homosexual,homosexual patients infected with HIV,35,4,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6b,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between HIV+ patients who were infected through homosexual sex and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales",1783272|1239|91061;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|526524|526525|2810280|1505663;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|91061|186826,Complete,Claregrieve1
bsdb:29411528/2/2,29411528,"cross-sectional observational, not case-control",29411528,10.1111/jcmm.13508,NA,"Zhou Y., Ou Z., Tang X., Zhou Y., Xu H., Wang X., Li K., He J., Du Y., Wang H., Chen Y. , Nie Y.",Alterations in the gut microbiota of patients with acquired immune deficiency syndrome,Journal of cellular and molecular medicine,2018,"acquired immune deficiency syndrome, dysbiosis, highly active antiretroviral therapy, human immunodeficiency virus, microbiota, transmission route",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,healthy controls,HIV infected patients who are homosexual,homosexual patients infected with HIV,35,4,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6b,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between HIV+ patients who were infected through homosexual sex and healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales",1783272|1239|909932|1843488|909930;3379134|976|200643|171549;3379134|976;3379134|976|200643;1783272|1239|186801;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|909932;1783272|1239|186801|186802|541000;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|2974251|165179;3379134|976|200643|171549|171552;1783272|1239|909932|909929,Complete,Claregrieve1
bsdb:29411528/3/1,29411528,"cross-sectional observational, not case-control",29411528,10.1111/jcmm.13508,NA,"Zhou Y., Ou Z., Tang X., Zhou Y., Xu H., Wang X., Li K., He J., Du Y., Wang H., Chen Y. , Nie Y.",Alterations in the gut microbiota of patients with acquired immune deficiency syndrome,Journal of cellular and molecular medicine,2018,"acquired immune deficiency syndrome, dysbiosis, highly active antiretroviral therapy, human immunodeficiency virus, microbiota, transmission route",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,healthy controls,Intravenous drug abuse HIV patients,Intravenous drug abuse patients infected with HIV,35,3,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6b,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between HIV+ patients who were infected through intravenous drug use and healthy controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|2316020|33038,Complete,Claregrieve1
bsdb:29411528/4/1,29411528,"cross-sectional observational, not case-control",29411528,10.1111/jcmm.13508,NA,"Zhou Y., Ou Z., Tang X., Zhou Y., Xu H., Wang X., Li K., He J., Du Y., Wang H., Chen Y. , Nie Y.",Alterations in the gut microbiota of patients with acquired immune deficiency syndrome,Journal of cellular and molecular medicine,2018,"acquired immune deficiency syndrome, dysbiosis, highly active antiretroviral therapy, human immunodeficiency virus, microbiota, transmission route",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,heterosexual subjects with HIV,homosexual subjects with HIV,homosexual patients infected with HIV,26,4,1 month,16S,4,Illumina,relative abundances,Metastats,0.05,FALSE,3,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6d,10 January 2021,Fatima Zohra,"WikiWorks,ChiomaBlessing",Relative abundance bacteria with significance between heterosexual and homosexual subjects,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|186801|3085636|186803|1506553;3379134|976|200643|171549|2005525|375288;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:29411528/5/1,29411528,"cross-sectional observational, not case-control",29411528,10.1111/jcmm.13508,NA,"Zhou Y., Ou Z., Tang X., Zhou Y., Xu H., Wang X., Li K., He J., Du Y., Wang H., Chen Y. , Nie Y.",Alterations in the gut microbiota of patients with acquired immune deficiency syndrome,Journal of cellular and molecular medicine,2018,"acquired immune deficiency syndrome, dysbiosis, highly active antiretroviral therapy, human immunodeficiency virus, microbiota, transmission route",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,healthy control,HAART-treated HIV+ patients,HIV infected patients treated with highly active antiretroviral therapy (HAART),35,14,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 7c,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between HIV+ patients treated with HAART and healthy controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus",3379134|976|200643|171549|815|816|817;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|3085636|186803|1506553;3379134|1224|1236|91347|543|620;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|91061|186826|1300|1301|1308,Complete,Claregrieve1
bsdb:29411528/5/2,29411528,"cross-sectional observational, not case-control",29411528,10.1111/jcmm.13508,NA,"Zhou Y., Ou Z., Tang X., Zhou Y., Xu H., Wang X., Li K., He J., Du Y., Wang H., Chen Y. , Nie Y.",Alterations in the gut microbiota of patients with acquired immune deficiency syndrome,Journal of cellular and molecular medicine,2018,"acquired immune deficiency syndrome, dysbiosis, highly active antiretroviral therapy, human immunodeficiency virus, microbiota, transmission route",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,healthy control,HAART-treated HIV+ patients,HIV infected patients treated with highly active antiretroviral therapy (HAART),35,14,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 7c,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between HIV+ patients treated with HAART and healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|909932|1843488|909930;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976;3379134|976|200643;1783272|1239|186801;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932;1783272|1239|186801|186802|541000;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|909932|909929;1783272|1239|186801|186802|216572|292632;1783272|1239|909932|1843489|31977,Complete,Claregrieve1
bsdb:29411528/6/1,29411528,"cross-sectional observational, not case-control",29411528,10.1111/jcmm.13508,NA,"Zhou Y., Ou Z., Tang X., Zhou Y., Xu H., Wang X., Li K., He J., Du Y., Wang H., Chen Y. , Nie Y.",Alterations in the gut microbiota of patients with acquired immune deficiency syndrome,Journal of cellular and molecular medicine,2018,"acquired immune deficiency syndrome, dysbiosis, highly active antiretroviral therapy, human immunodeficiency virus, microbiota, transmission route",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,healthy control,HAART untreated,HIV infected patients not treated with HAART,35,19,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 7c,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between HIV+ patients who are HAART-treatment naive and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota",1783272|1239|91061;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;3379134|1224|1236;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;3379134|1224,Complete,Claregrieve1
bsdb:29434076/1/1,29434076,"cross-sectional observational, not case-control",29434076,10.1620/tjem.244.113,NA,"Hamada S., Masamune A., Nabeshima T. , Shimosegawa T.",Differences in Gut Microbiota Profiles between Autoimmune Pancreatitis and Chronic Pancreatitis,The Tohoku journal of experimental medicine,2018,"16S sequence, microbiome, next generation sequencing, pancreatic cancer, pancreatitis",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Chronic pancreatitis,EFO:0000342,chronic pancreatitis,autoimmune pancreatitis type 1,autoimmune pancreatitis type 1,8,12,NA,16S,45,Illumina,NA,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2, text",10 January 2021,Rimsha Azhar,"Claregrieve1,Atrayees,WikiWorks",Differential microbial abundance between patients with type 1 autoimmune pancreatitis (AIP) and chronic pancreatitis (CP),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium lacusfryxellense,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster lavalensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum lactatifermentans",3379134|976|200643|171549|815|816|28116;1783272|1239|186801|186802|31979|1485|205328;1783272|1239|186801|3085636|186803|2719313|460384;1783272|1239|91061|186826|1300|1301|113107;1783272|1239|91061|186826|1300|1301|1302;1783272|1239|186801|3085636|3118652|2039240|160404,Complete,Claregrieve1
bsdb:29459704/1/1,29459704,"cross-sectional observational, not case-control",29459704,10.1038/s41598-018-21657-7,NA,"Shi Y.C., Guo H., Chen J., Sun G., Ren R.R., Guo M.Z., Peng L.H. , Yang Y.S.",Initial meconium microbiome in Chinese neonates delivered naturally or by cesarean section,Scientific reports,2018,NA,Experiment 1,China,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,vaginal delivery,C-section,the first-pass meconium stools from within 24 h of delivery,8,10,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 1,10 January 2021,Shaimaa Elsafoury,"Fatima,WikiWorks",Comparison of the microbiome of vaginally delivered and C-section-delivered newborns,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas|s__Aeromonas veronii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus amyloliquefaciens,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus licheniformis,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales,k__Thermotogati|p__Deinococcota|c__Deinococci,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Thermotogati|p__Deinococcota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",3379134|1224|1236|135624|84642|642|654;3379134|1224|28211;1783272|1239|91061|1385|186817;1783272|1239|91061|1385;1783272|1239|91061;1783272|1239|91061|1385|186817|1386;1783272|1239|91061|1385|186817|1386|1390;1783272|1239|91061|1385|186817|1386|1402;3384194|1297|188787|118964|183710;3384194|1297|188787|118964;3384194|1297|188787;3384194|1297|188787|118964|183710|1298;3384194|1297;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239;3379134|976|200643|171549|815|909656|821;3379134|1224|1236|135614|32033|40323;3379134|1224|1236|135614|32033;3379134|1224|1236|135614;1783272|1239|186801|3085636|186803|1766253|39491,Complete,Fatima
bsdb:29459704/1/2,29459704,"cross-sectional observational, not case-control",29459704,10.1038/s41598-018-21657-7,NA,"Shi Y.C., Guo H., Chen J., Sun G., Ren R.R., Guo M.Z., Peng L.H. , Yang Y.S.",Initial meconium microbiome in Chinese neonates delivered naturally or by cesarean section,Scientific reports,2018,NA,Experiment 1,China,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,vaginal delivery,C-section,the first-pass meconium stools from within 24 h of delivery,8,10,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 1,10 January 2021,Shaimaa Elsafoury,WikiWorks,ComparisonofthemicrobiomesofvaginallydeliveredandC-section-deliverednewborns,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas testosteroni,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",1783272|201174|1760;1783272|201174;1783272|201174|1760|2037;1783272|201174|1760|85009|31957;3379134|1224|1236;1783272|201174|1760|85009|31957|1912216|1747;1783272|201174|1760|85009|31957|1743;3379134|1224|1236|72274;1783272|201174|1760|85010|2070;3379134|1224|28216|80840;3379134|1224|28216;3379134|1224|28216|80840|80864|283;3379134|1224|28216|80840|80864;3379134|1224|28216|80840|80864|283|285;3379134|1224|1236|72274|135621|286,Complete,Shaimaa Elsafoury
bsdb:29462324/1/1,29462324,laboratory experiment,29462324,10.1093/humrep/dex372,NA,"Yuan M., Li D., Zhang Z., Sun H., An M. , Wang G.",Endometriosis induces gut microbiota alterations in mice,"Human reproduction (Oxford, England)",2018,NA,Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Healthy mice,Mice who were injected with endometrial tissues,Researchers induced endometriosis models by intraperitoneal injection of endometrial tissues to mimic endometriosis formation in humans.,4,4,NA,16S,4,Illumina,raw counts,T-Test,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 4,8 August 2021,Samara.Khan,"Samara.Khan,Fatima,WikiWorks","Researchers used t-tests to calculate the differences in microbiota at the taxon level between the control and experimental groups.

The following bacterial taxa were more abundant in mice with simulated endometriosis than in mice without endometriosis.",increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella",1783272|201174;3379134|1224|28216|80840|506;3379134|1224|28216;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;3379134|1224|28216|80840;1783272|1239;3379134|1224|28216|80840|995019|577310,Complete,Fatima
bsdb:29462324/1/2,29462324,laboratory experiment,29462324,10.1093/humrep/dex372,NA,"Yuan M., Li D., Zhang Z., Sun H., An M. , Wang G.",Endometriosis induces gut microbiota alterations in mice,"Human reproduction (Oxford, England)",2018,NA,Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Healthy mice,Mice who were injected with endometrial tissues,Researchers induced endometriosis models by intraperitoneal injection of endometrial tissues to mimic endometriosis formation in humans.,4,4,NA,16S,4,Illumina,raw counts,T-Test,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 4,8 August 2021,Samara.Khan,"Samara.Khan,WikiWorks","Researchers used the LEfse method to determine the predominant microbiota in each sample. They then used t-tests to calculate the differences in microbiota at the taxon level between the control and experimental groups.

The following bacterial taxa were less abundant in mice with simulated endometriosis than in mice without endometriosis.",decreased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",3379134|976;3379134|976|200643;3379134|976|200643|171549,Complete,Fatima
bsdb:29462324/2/1,29462324,laboratory experiment,29462324,10.1093/humrep/dex372,NA,"Yuan M., Li D., Zhang Z., Sun H., An M. , Wang G.",Endometriosis induces gut microbiota alterations in mice,"Human reproduction (Oxford, England)",2018,NA,Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Healthy mice,Mice who were injected with endometrial tissues,Researchers induced endometriosis models by intraperitoneal injection of endometrial tissues to mimic endometriosis formation in humans.,4,4,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 4,14 March 2022,Fatima,"WikiWorks,Fatima",LDA coupled with effect size measurements identified the most differentially abundant taxa between the two groups,increased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Chloe
bsdb:29462324/2/2,29462324,laboratory experiment,29462324,10.1093/humrep/dex372,NA,"Yuan M., Li D., Zhang Z., Sun H., An M. , Wang G.",Endometriosis induces gut microbiota alterations in mice,"Human reproduction (Oxford, England)",2018,NA,Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Healthy mice,Mice who were injected with endometrial tissues,Researchers induced endometriosis models by intraperitoneal injection of endometrial tissues to mimic endometriosis formation in humans.,4,4,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 4,14 March 2022,Fatima,"WikiWorks,Fatima",LDA coupled with effect size measurements identified the most differentially abundant taxa between the two groups,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota",3379134|976|200643|171549|171552|1283313;3379134|976|200643;3379134|976|200643|171549;3379134|976,Complete,Chloe
bsdb:29470389/1/1,29470389,randomized controlled trial,29470389,10.3390/nu10020244,NA,"Bamberger C., Rossmeier A., Lechner K., Wu L., Waldmann E., Fischer S., Stark R.G., Altenhofer J., Henze K. , Parhofer K.G.","A Walnut-Enriched Diet Affects Gut Microbiome in Healthy Caucasian Subjects: A Randomized, Controlled Trial",Nutrients,2018,"butyric acid, cholesterol, diet, gut microbiome, lipids, nuts, prebiotic, probiotic, walnuts",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,after walnut diet,before walnut diet,before walnut consumption,135,135,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,"Figure 4b, 5a, and text",10 January 2021,Lora Kasselman,"WikiWorks,Atrayees",Most abundant Operational Taxonomic Units for both walnut and control phase at genus level. Significant different OTUs are marked with by using * and p-values. pvalues were calculated using a pairwise Fisher test.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|216572,Complete,Atrayees
bsdb:29470389/1/2,29470389,randomized controlled trial,29470389,10.3390/nu10020244,NA,"Bamberger C., Rossmeier A., Lechner K., Wu L., Waldmann E., Fischer S., Stark R.G., Altenhofer J., Henze K. , Parhofer K.G.","A Walnut-Enriched Diet Affects Gut Microbiome in Healthy Caucasian Subjects: A Randomized, Controlled Trial",Nutrients,2018,"butyric acid, cholesterol, diet, gut microbiome, lipids, nuts, prebiotic, probiotic, walnuts",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,after walnut diet,before walnut diet,before walnut consumption,135,135,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,"Figure 4b, 5a, and text",10 January 2021,Lora Kasselman,"WikiWorks,Atrayees",Most abundant Operational Taxonomic Units for both walnut and control phase at genus level. Significant different OTUs are marked with by using * and p-values. pvalues were calculated using a pairwise Fisher test.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",1783272|1239|186801|186802|541000;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511,Complete,Atrayees
bsdb:29470389/2/1,29470389,randomized controlled trial,29470389,10.3390/nu10020244,NA,"Bamberger C., Rossmeier A., Lechner K., Wu L., Waldmann E., Fischer S., Stark R.G., Altenhofer J., Henze K. , Parhofer K.G.","A Walnut-Enriched Diet Affects Gut Microbiome in Healthy Caucasian Subjects: A Randomized, Controlled Trial",Nutrients,2018,"butyric acid, cholesterol, diet, gut microbiome, lipids, nuts, prebiotic, probiotic, walnuts",Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,replace both,carbohydrate replacement (with walnuts),before walnut consumption,135,135,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,"age,body mass index,smoking behavior,triglycerides",NA,NA,NA,NA,NA,NA,Signature 1,5a and text,10 January 2021,Lora Kasselman,"WikiWorks,Atrayees",Most abundant Operational Taxonomic Units for both walnut and control phase at genus level. Significant different OTUs are marked with by using * and p-values. pvalues were calculated using a pairwise Fisher test.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|186801|186802|204475;1783272|1239|186801|3085636|186803|1407607;3379134|976|200643|171549|815|816,Complete,Atrayees
bsdb:29470389/3/1,29470389,randomized controlled trial,29470389,10.3390/nu10020244,NA,"Bamberger C., Rossmeier A., Lechner K., Wu L., Waldmann E., Fischer S., Stark R.G., Altenhofer J., Henze K. , Parhofer K.G.","A Walnut-Enriched Diet Affects Gut Microbiome in Healthy Caucasian Subjects: A Randomized, Controlled Trial",Nutrients,2018,"butyric acid, cholesterol, diet, gut microbiome, lipids, nuts, prebiotic, probiotic, walnuts",Experiment 3,Germany,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,fat replacement (with walnuts),replace both,before walnut consumption,135,135,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,"age,body mass index,smoking behavior,triglycerides",NA,NA,NA,NA,NA,NA,Signature 1,5a and text,10 January 2021,Lora Kasselman,"WikiWorks,Atrayees",Most abundant Operational Taxonomic Units for both walnut and control phase at genus level. Significant different OTUs are marked with by using * and p-values. pvalues were calculated using a pairwise Fisher test.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|186801|186802|204475;1783272|1239|186801|3085636|186803|1407607;3379134|976|200643|171549|815|816,Complete,Atrayees
bsdb:29483910/1/1,29483910,laboratory experiment,29483910,10.3389/fimmu.2018.00182,NA,"Groves H.T., Cuthbertson L., James P., Moffatt M.F., Cox M.J. , Tregoning J.S.",Respiratory Disease following Viral Lung Infection Alters the Murine Gut Microbiota,Frontiers in immunology,2018,"Bacteroidetes, Firmicutes, Mucin 5ac, gut microbiota, influenza, respiratory syncytial virus infections",Experiment 1,United Kingdom,Mus musculus,Feces,UBERON:0001988,Sampling time,EFO:0000689,Day 0,Day 7,Mice assessed 7 days after infection with respiratory syncytial virus (RSV),NA,NA,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 1,"Figure 2A&2B, within results text (The Composition of the Gut Microbiota Is Altered following Lung Infection, paragraph 2)",13 June 2021,Claregrieve1,"Claregrieve1,Folakunmi,WikiWorks",Differential abundance of gut microbiota of respiratory syncytial virus (RSV) infected mice between Day 0 and Day 7 of infection,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",1783272|1239;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958,Complete,Folakunmi
bsdb:29483910/1/2,29483910,laboratory experiment,29483910,10.3389/fimmu.2018.00182,NA,"Groves H.T., Cuthbertson L., James P., Moffatt M.F., Cox M.J. , Tregoning J.S.",Respiratory Disease following Viral Lung Infection Alters the Murine Gut Microbiota,Frontiers in immunology,2018,"Bacteroidetes, Firmicutes, Mucin 5ac, gut microbiota, influenza, respiratory syncytial virus infections",Experiment 1,United Kingdom,Mus musculus,Feces,UBERON:0001988,Sampling time,EFO:0000689,Day 0,Day 7,Mice assessed 7 days after infection with respiratory syncytial virus (RSV),NA,NA,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 2,"Figure 2A&2B, within results text (The Composition of the Gut Microbiota Is Altered following Lung Infection, paragraph 2)",13 June 2021,Claregrieve1,"Claregrieve1,Folakunmi,WikiWorks",Differential abundance of gut microbiota of respiratory syncytial virus (RSV) infected mice between Day 0 and Day 7 of infection,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",3379134|976|200643|171549|815;3379134|976|200643;3379134|976|200643|171549|2005473,Complete,Folakunmi
bsdb:29483910/2/1,29483910,laboratory experiment,29483910,10.3389/fimmu.2018.00182,NA,"Groves H.T., Cuthbertson L., James P., Moffatt M.F., Cox M.J. , Tregoning J.S.",Respiratory Disease following Viral Lung Infection Alters the Murine Gut Microbiota,Frontiers in immunology,2018,"Bacteroidetes, Firmicutes, Mucin 5ac, gut microbiota, influenza, respiratory syncytial virus infections",Experiment 2,United Kingdom,Mus musculus,Feces,UBERON:0001988,Sampling time,EFO:0000689,Day 0,Day 7,Day 7 of infection for mice infected with influenza virus (H1N1),NA,NA,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 1,"Figure 4C, 4D",16 June 2021,Claregrieve1,"Claregrieve1,Folakunmi,WikiWorks",Differential abundance of gut microbiota of influenza virus (H1N1) infected mice between Day 0 and Day 7 of infection,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Folakunmi
bsdb:29483910/2/2,29483910,laboratory experiment,29483910,10.3389/fimmu.2018.00182,NA,"Groves H.T., Cuthbertson L., James P., Moffatt M.F., Cox M.J. , Tregoning J.S.",Respiratory Disease following Viral Lung Infection Alters the Murine Gut Microbiota,Frontiers in immunology,2018,"Bacteroidetes, Firmicutes, Mucin 5ac, gut microbiota, influenza, respiratory syncytial virus infections",Experiment 2,United Kingdom,Mus musculus,Feces,UBERON:0001988,Sampling time,EFO:0000689,Day 0,Day 7,Day 7 of infection for mice infected with influenza virus (H1N1),NA,NA,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 2,"Figure 4C, 4D",16 June 2021,Claregrieve1,"Claregrieve1,Folakunmi,WikiWorks",Differential abundance of gut microbiota of influenza virus (H1N1) infected mice between Day 0 and Day 7 of infection,increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",3379134|976;3379134|976|200643|171549|2005473;3379134|976|200643|171549|171551,Complete,Folakunmi
bsdb:29483910/3/1,29483910,laboratory experiment,29483910,10.3389/fimmu.2018.00182,NA,"Groves H.T., Cuthbertson L., James P., Moffatt M.F., Cox M.J. , Tregoning J.S.",Respiratory Disease following Viral Lung Infection Alters the Murine Gut Microbiota,Frontiers in immunology,2018,"Bacteroidetes, Firmicutes, Mucin 5ac, gut microbiota, influenza, respiratory syncytial virus infections",Experiment 3,United Kingdom,Mus musculus,Feces,UBERON:0001988,Sampling time,EFO:0000689,Day 0,Day 7,Day 7 of infection for mice infected with phosphate-buffered saline (PBS).,NA,NA,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 1,"Figure 2A&2B, within results text (The Composition of the Gut Microbiota Is Altered following Lung Infection, paragraph 2)",26 January 2024,Folakunmi,"Folakunmi,WikiWorks",Differential abundance of gut microbiota of phosphate-buffered saline (PBS) infected mice between Day 0 and Day 7 of infection,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239;1783272|1239|186801|3085636|186803,Complete,Folakunmi
bsdb:29483910/3/2,29483910,laboratory experiment,29483910,10.3389/fimmu.2018.00182,NA,"Groves H.T., Cuthbertson L., James P., Moffatt M.F., Cox M.J. , Tregoning J.S.",Respiratory Disease following Viral Lung Infection Alters the Murine Gut Microbiota,Frontiers in immunology,2018,"Bacteroidetes, Firmicutes, Mucin 5ac, gut microbiota, influenza, respiratory syncytial virus infections",Experiment 3,United Kingdom,Mus musculus,Feces,UBERON:0001988,Sampling time,EFO:0000689,Day 0,Day 7,Day 7 of infection for mice infected with phosphate-buffered saline (PBS).,NA,NA,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 2,"Figure 2A&2B, within results text (The Composition of the Gut Microbiota Is Altered following Lung Infection, paragraph 2)",26 January 2024,Folakunmi,"Folakunmi,WikiWorks",Differential abundance of gut microbiota of phosphate-buffered saline (PBS) infected mice between Day 0 and Day 7 of infection,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,3379134|976|200643,Complete,Folakunmi
bsdb:29486796/1/1,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 1,Liberia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,Zero Soil Transmitted Helminth infection (Zero STH infection),High Soil Transmitted Helminth infection (High STH infection),High Soil Transmitted Helminth infection (High STH infection) refers to individuals found with eggs from Ascaris helminth; when their feces was measured by the Kato-Katz smear in eggs per gram (EPG).,48,26,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Table S5,1 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in the gut microbiota between infected and uninfected groups in Liberia (based on the presence of eggs in feces for Ascaris helminth).,decreased,",k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Cellulosilyticaceae|g__Cellulosilyticum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",;1783272|1239|186801|3085636|3018741|698776;1783272|1239|186801|186802;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|3085636|186803;3379134|1224|28216|80840;3379134|1224|28216;1783272|1239|186801|186802|216572|216851,Complete,Svetlana up
bsdb:29486796/1/2,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 1,Liberia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,Zero Soil Transmitted Helminth infection (Zero STH infection),High Soil Transmitted Helminth infection (High STH infection),High Soil Transmitted Helminth infection (High STH infection) refers to individuals found with eggs from Ascaris helminth; when their feces was measured by the Kato-Katz smear in eggs per gram (EPG).,48,26,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,Table S5,1 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in the gut microbiota between infected and uninfected groups in Liberia (based on the presence of eggs in feces for Ascaris helminth).,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Cyanobacteriota,k__Viridiplantae|p__Streptophyta,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia",1783272|1239|526524|526525|128827|123375;;1783272|1239|186801|3082720|543314|86331;1783272|201174|84998|84999|1643824|133925;1783272|1117;33090|35493;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;1783272|1239|526524|526525|128827|174708;1783272|1239|526524|526525|128827;1783272|1239|91061|186826;1783272|201174|84998|1643822|1643826|84111;3379134|1224;1783272|201174|84998|84999|84107;1783272|1239|186801|3082720|543314;1783272|201174|84998|84999;1783272|201174;3379134|1224|1236;1783272|201174|84992,Complete,Svetlana up
bsdb:29486796/2/1,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 2,Liberia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,Zero Soil Transmitted Helminth infection (Zero STH infection),High Soil Transmitted Helminth infection (High STH infection),High Soil Transmitted Helminth infection (High STH infection) refers to individuals found with eggs from any helminth; when their feces was measured by the Kato-Katz smear in eggs per gram (EPG).,48,26,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Table S5,1 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in the gut microbiota between infected and uninfected groups in Liberia (based on the presence of any helminth eggs in feces).,increased,",k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella",;1783272|1239;1783272|1239|186801|186802|204475;3379134|1224|28211|356|45401;3379134|1224|28211;3379134|1224|28211|356;3379134|1224;3379134|976|200643|171549|171551;1783272|201174|84998|1643822|1643826|84111;1783272|1239|526524|526525|128827;3379134|1224;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|292632;1783272|201174|84998|84999|1643824|133925,Complete,Svetlana up
bsdb:29486796/2/2,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 2,Liberia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,Zero Soil Transmitted Helminth infection (Zero STH infection),High Soil Transmitted Helminth infection (High STH infection),High Soil Transmitted Helminth infection (High STH infection) refers to individuals found with eggs from any helminth; when their feces was measured by the Kato-Katz smear in eggs per gram (EPG).,48,26,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,Table S5,1 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in the gut microbiota between infected and uninfected groups in Liberia (based on the presence of any helminth eggs in feces).,decreased,"k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Plesiomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Cellulosilyticaceae|g__Cellulosilyticum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Lawsonia,,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",3379134|203691|203692|136;3379134|1224|1236|91347|543|702;1783272|1239|186801|3085636|3018741|698776;1783272|1239|91061|1385|186818;1783272|1239|186801|186802;3379134|200940|3031449|213115|194924|41707;;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|216851;1783272|1239|91061|1385|186817|1386;1783272|1239|526524|526525|2810280|100883;3379134|1224|28216|80840|995019;1783272|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:29486796/3/1,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 3,Liberia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,Zero Soil Transmitted Helminth infection (Zero STH infection),High Soil Transmitted Helminth infection (High STH infection),"High Soil Transmitted Helminth infection (High STH infection) refers to individuals with CT≤ 28, when Ascaris qPCR was carried out.",48,26,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Table S5,1 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in the gut microbiota between infected and uninfected groups in Liberia (based on the CT value when Ascaris qPCR was carried out).,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Anaerorhabdus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerosphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Buttiauxella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfocurvus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kluyvera,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Pilibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Viridiplantae|p__Streptophyta,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Succinispira,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XII. Incertae Sedis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",1783272|1239|909932|1843488|909930;1783272|201174|84992;1783272|201174;1783272|1239|526524|526525|128827|174708;1783272|1239|526524|526525|128827|118966;1783272|1239|1737404|1737405|1570339|1273095;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|3082720|543314|109326;1783272|1239;3379134|1224|1236|91347|543|82976;1783272|1239|186801|3085636|186803|830;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;28221;3379134|200940|3031449|213115|194924|700595;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;1783272|201174|84998|1643822|1643826|84111;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|204475;1783272|1239|186801|186802|404402;3379134|1224|28211|356|45401;3379134|1224|28211|356;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|543|579;1783272|1239|91061|186826|1300|1357;1783272|1239|186801|3085636|186803|248744;1783272|1239|186801|3082720|543314|86331;3379134|1224|1236|91347|1903414|581;1783272|201174|84998|84999|1643824|133925;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|186802|216572|459786;1783272|1239|91061|186826|81852|337670;3379134|1224|1236|91347|543|160674;1783272|1239|186801|186802|216572|1263;1783272|201174|84998|1643822|1643826|84108;1783272|1239|526524|526525|128827|123375;33090|35493;1783272|1239|909932|1843488|909930|78119;1783272|1239|91061;1783272|1239;3379134|976;1783272|1239|91061|186826|186828;1783272|1239|186801|186802|543313;1783272|1239|186801|3082720|543314;1783272|201174|84998|84999|84107;3379134|1224|1236|91347|543;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|216572;1783272|1239|91061|186826|1300;1783272|1117;3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:29486796/3/2,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 3,Liberia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,Zero Soil Transmitted Helminth infection (Zero STH infection),High Soil Transmitted Helminth infection (High STH infection),"High Soil Transmitted Helminth infection (High STH infection) refers to individuals with CT≤ 28, when Ascaris qPCR was carried out.",48,26,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,Table S5,1 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in the gut microbiota between infected and uninfected groups in Liberia (based on the CT value when Ascaris qPCR was carried out).,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|s__Bacteroidetes oral taxon 274,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Ruminobacter",1783272|1239|909932|909929|1843491|52225;1783272|1239|186801|3085636|186803;1783272|1239|909932|1843489|31977;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|526524|526525|2810281|191303;3379134|976|200643|171549;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171552;3379134|976|200643;3379134|1224|28216|80840;1783272|1239|186801|3085636|186803|841;3379134|976;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|976|652708;3379134|1224|1236|135624|83763|866,Complete,Svetlana up
bsdb:29486796/4/1,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 4,Liberia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,Zero Soil Transmitted Helminth infection (Zero STH infection),High Soil Transmitted Helminth infection (High STH infection),"High Soil Transmitted Helminth infection (High STH infection) refers to individuals with CT≤ 28, when Necator qPCR was carried out.",48,26,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Table S5,2 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in the gut microbiota between infected and uninfected groups in Liberia (based on the CT value when Necator qPCR was carried out).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Coraliomargaritaceae|g__Coraliomargarita,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Cryobacterium,c__Deltaproteobacteria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Dermabacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfocurvus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae|g__Opitutus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Puniceicoccaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Sharpea,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax,,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Maritalea,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae",1783272|1239|186801|186802|216572|258514;1783272|201174|84992;1783272|201174;1783272|1239|186801|186802|216572|244127;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|1239|526524|526525|2810280|135858;1783272|201174|84998|84999|84107|102106;3379134|74201|414999|415001|3056371|442430;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|1760|85006|85023|69578;28221;1783272|201174|1760|85006|85020|36739;1783272|201174|1760|85006|85020;3379134|200940|3031449|213115|194924|700595;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;1783272|201174|84998|1643822|1643826|84111;3379134|1224|28211|356|212791;1783272|1239|91061|186826|81852;1783272|1239|186801|186802|216572|946234;1783272|1239|909932|1843489|31977|906;3379134|1224|1236|91347|1903414|581;1783272|201174|1760|85007|1762;1783272|201174|1760|85007|1762|1763;1783272|201174|84998|84999|1643824|133925;3379134|74201|414999|415000|134623;3379134|74201|414999;3379134|74201|414999|415000|134623|178440;1783272|1239|186801|186802|216572|459786;3379134|1224;3379134|74201|414999|415001|415002;3379134|74201|414999|415001;3379134|976|200643|171549|171550;1783272|1239|526524|526525|2810280|519427;3379134|1224|28216|80840|80864|34072;;1783272|1239|186801|3082720|543314;1783272|201174|84998|84999|84107;3379134|200940|3031449|213115|194924;3379134|1224|28211|356|45401;3379134|74201|414999;1783272|1239|186801|186802|216572;3379134|1224|28211|356|2831106|623276;3379134|976|117743|200644;1783272|1239|186801|3082720|543314,Complete,NA
bsdb:29486796/4/2,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 4,Liberia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,Zero Soil Transmitted Helminth infection (Zero STH infection),High Soil Transmitted Helminth infection (High STH infection),"High Soil Transmitted Helminth infection (High STH infection) refers to individuals with CT≤ 28, when Necator qPCR was carried out.",48,26,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,Table S5,2 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in the gut microbiota between infected and uninfected groups in Liberia (based on the CT value when Necator qPCR was carried out).,decreased,",k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|976;3379134|976|200643;3379134|976|200643|171549;1783272|1239|186801|3085636|186803;3379134|1224|1236|135625;3379134|1224|1236|135625|712;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803,Complete,NA
bsdb:29486796/5/1,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 5,Liberia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,Zero Soil Transmitted Helminth infection (Zero STH infection),High Soil Transmitted Helminth infection (High STH infection),"High Soil Transmitted Helminth infection (High STH infection) refers to individuals with CT≤ 28, when any helminth qPCR(quantitative real-time PCR) was carried out.",48,26,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Table S5,2 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in the gut microbiota between infected and uninfected groups in Liberia (based on the CT value when any helminth qPCR was carried out).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Buttiauxella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,p__Candidatus Saccharimonadota,p__Candidatus Saccharimonadota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Coraliomargaritaceae|g__Coraliomargarita,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfocurvus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XII. Incertae Sedis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Paraeggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Pilibacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Puniceicoccaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Viridiplantae|p__Streptophyta,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",1783272|1239|186801|186802|216572|258514;1783272|201174|84992;1783272|201174;1783272|1239|526524|526525|128827|174708;3379134|1224|28211;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|3082720|543314|109326;3379134|1224|1236|91347|543|82976;1783272|1239|186801|3085636|186803|830;95818;95818;1783272|201174|84998|84999|84107|102106;3379134|74201|414999|415001|3056371|442430;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;28221;3379134|200940|3031449|213115|194924|700595;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;1783272|201174|84998|1643822|1643826|84111;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|543313;1783272|1239|186801|3082720|543314;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|204475;3379134|1224|28211|356|45401;3379134|1224|28211|356;1783272|1239|91061|186826|1300|1357;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3082720|543314|86331;1783272|201174|84998|84999|1643824|133925;3379134|74201|414999;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|186802|216572|459786;1783272|201174|84998|1643822|1643826|651554;1783272|1239|186801|186802|186807|2740;1783272|1239|91061|186826|81852|337670;3379134|74201|414999|415001|415002;3379134|74201|414999|415001;3379134|1224|1236|91347|543|160674;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1200657;1783272|1239|186801|186802|216572|44748;33090|35493;1783272|1239|186801|186802|216572|292632;1783272|201174;1783272|1239|91061;1783272|1239;;1783272|201174|84998|84999|84107;1783272|1239|526524|526525|128827;1783272|1239|186801|186802;1783272|1239|91061|186826;1783272|1239|186801|186802|216572;3384194|508458|649775|649776|649777;1783272|1117;3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:29486796/5/2,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 5,Liberia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,Zero Soil Transmitted Helminth infection (Zero STH infection),High Soil Transmitted Helminth infection (High STH infection),"High Soil Transmitted Helminth infection (High STH infection) refers to individuals with CT≤ 28, when any helminth qPCR(quantitative real-time PCR) was carried out.",48,26,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,Table S5,2 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in the gut microbiota between infected and uninfected groups in Liberia (based on the CT value when any helminth qPCR was carried out).,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Ruminobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Plesiomonas",1783272|1239|91061|186826|186828|117563;1783272|1239|526524|526525|2810280|100883;1783272|1239|186801|3085636|186803;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|46205;1783272|1239|526524|526525|2810281|191303;3379134|976|200643|171549;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171552;3379134|976|200643;1783272|201174|1760|85006|1268|32207;3379134|976;1783272|201174|1760|85006|1268;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;;3379134|1224|1236|135624|83763|866;3379134|1224|1236|91347|543|702,Complete,Svetlana up
bsdb:29486796/6/1,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 6,Indonesia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,Zero Soil Transmitted Helminth infection (Zero STH infection),High Soil Transmitted Helminth infection (High STH infection),"High Soil Transmitted Helminth infection (High STH infection) refers to individuals with CT≤ 28, when any helminth qPCR(quantitative real-time PCR) was carried out.",43,78,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Table S5,2 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in the gut microbiota between infected and uninfected groups in Indonesia (based on the CT value when any helminth qPCR was carried out).,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Tepidibacteraceae|g__Sporacetigenium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetitomaculum,c__Deltaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella",1783272|1239|526524|526525|128827|123375;1783272|1239|909932|909929|1843491|82373;1783272|1239|909932|1843489|31977;1783272|1239|186801|3082720|3120162|360541;1783272|1239|186801|3085636|186803|31980;28221;3379134|976|200643;1783272|1239|909932|1843489|31977|39948;3379134|976;3379134|1224|1236|135624|83763|83770;3379134|1224|1236|135624|83763;1783272|1239|186801|3085636|186803|830;3379134|1224|1236|135624;1783272|1239|526524|526525|128827;1783272|1239|91061|186826|81852;3379134|200940|3031449|213115;3379134|200940|3031449|213115|194924;1783272|1239|909932;1783272|1239|909932|909929;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|216851;1783272|1239|91061|186826|33958;1783272|1239|526524|526525|128827|174708;3379134|200940|3031449|213115|194924|35832;1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|186802|216572|946234;1783272|1239|909932|909929;1783272|1239|909932|1843489|31977;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|186802|216572|1017280;1783272|1239|909932|1843489|31977|209879;3379134|1224|28216|80840|80864;1783272|201174|84998|84999|1643824|133925,Complete,Svetlana up
bsdb:29486796/6/2,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 6,Indonesia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,Zero Soil Transmitted Helminth infection (Zero STH infection),High Soil Transmitted Helminth infection (High STH infection),"High Soil Transmitted Helminth infection (High STH infection) refers to individuals with CT≤ 28, when any helminth qPCR(quantitative real-time PCR) was carried out.",43,78,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Table S5,2 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in the gut microbiota between infected and uninfected groups in Indonesia (based on the CT value when any helminth qPCR was carried out).,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Asaccharobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",1783272|201174|84998|1643822|1643826|553372;3379134|976|200643|171549|815;1783272|1239|186801|3085636|186803|572511;3379134|976|117743|200644|2762318|59732;1783272|201174|84998|1643822|1643826|84111;3379134|976|117743|200644|49546;3379134|976|117743|200644;3379134|976|117743;1783272|201174|84998|1643822|1643826|644652;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803;1783272|201174|1760|85007|85025;3379134|976|200643|171549|171552|577309;1783272|201174|1760|85007|85025|1827;3379134|1224|28216|80840|80864|34072;3379134|976|200643|171549;3379134|1224|28211|204457|335929;3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:29486796/7/1,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 7,Indonesia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,2008 - Uninfected,2010 - Uninfected,"2010 refers to individuals that were treated with anthelmintics or placebo in 2010, although they were not infected.",43,32,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,2 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance in the gut microbiota between uninfected individuals in Indonesia (2008-2010), treated with anthelmintics or placebo in 2010.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae",3379134|1224|28216;3379134|1224|28216|80840;3379134|1224|28216|80840|80864,Complete,Svetlana up
bsdb:29486796/7/2,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 7,Indonesia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,2008 - Uninfected,2010 - Uninfected,"2010 refers to individuals that were treated with anthelmintics or placebo in 2010, although they were not infected.",43,32,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S5,2 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance in the gut microbiota between uninfected individuals in Indonesia (2008-2010), treated with anthelmintics or placebo in 2010.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Afipia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax",3379134|1224|28211|356|41294|1033;3379134|976|117743|200644|2762318|59732;3379134|1224|28211|356|119045;3379134|1224|28211|356|119045|407;3379134|1224|28211|356|41294;1783272|201174|1760|85007|85025;3379134|976|117747|200666|84566|84567;3379134|1224|1236|72274|135621;3379134|1224|1236|72274|135621|286;3379134|1224|28211|356|82115;3379134|1224|28211|356|82115|379;1783272|201174|1760|85007|85025|1827;3379134|1224|28216|80840|80864|34072,Complete,Svetlana up
bsdb:29486796/8/1,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 8,Indonesia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,2008 - Uninfected,2010 - Uninfected,"2010 refers to individuals that were treated with placebo in 2010, although they were not infected.",43,16,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,2 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance in the gut microbiota between uninfected individuals in Indonesia (2008-2010), treated with placebo in 2010.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",3379134|1224|28216;3379134|1224|28216|80840;3379134|1224|28216|80840|80864;3379134|976|200643|171549,Complete,Svetlana up
bsdb:29486796/8/2,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 8,Indonesia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,2008 - Uninfected,2010 - Uninfected,"2010 refers to individuals that were treated with placebo in 2010, although they were not infected.",43,16,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S5,2 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance in the gut microbiota between uninfected individuals in Indonesia (2008-2010), treated with placebo in 2010.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Afipia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae",3379134|1224|28211|356|41294|1033;3379134|976|117743|200644|2762318|59732;3379134|976|117743|200644|49546;3379134|976|117743|200644;3379134|976|117743;1783272|1239|186801|186802|216572|596767;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;3379134|1224|1236|135614|32033;3379134|1224|1236|135614;3379134|1224|28211|356|119045;3379134|1224|28211|356|119045|407;3379134|1224|28211|356|41294;1783272|201174|1760|85007|85025;1783272|1239|186801|3085636|186803|265975;3379134|976|117747|200666|84566|84567;1783272|201174|1760|85009|31957;1783272|201174|1760|85009|31957|1743;3379134|1224|1236|72274|135621;3379134|1224|1236|72274;3379134|1224|1236|72274|135621|286;3379134|1224|28211|356|82115;3379134|1224|28211|356|82115|379;1783272|201174|1760|85007|85025|1827;3379134|976|117747|200666|84566;3379134|976|117747|200666;3379134|976|117747;3379134|1224|1236|135614|32033|40323;3379134|1224|28216|80840|80864|34072;1783272|1239|909932|1843489|31977|29465;3379134|1224|28211|356|41294;3379134|1224|28211|356;3379134|1224|1236|72274|135621,Complete,Svetlana up
bsdb:29486796/9/1,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 9,Indonesia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,2008 - Uninfected,2010 - Uninfected,2010 refers to individuals that were untreated and uninfected in year 2010 (time effect).,43,16,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,2 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in the gut microbiota between untreated uninfected individuals in Indonesia in the year 2008-2010 (time effect).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales",3379134|1224|28216|80840|80864;3379134|1224|28216;3379134|1224|28216|80840,Complete,Svetlana up
bsdb:29486796/9/2,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 9,Indonesia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,2008 - Uninfected,2010 - Uninfected,2010 refers to individuals that were untreated and uninfected in year 2010 (time effect).,43,16,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S5,2 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in the gut microbiota between untreated uninfected individuals in Indonesia in the year 2008-2010 (time effect).,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Afipia",3379134|1224|28211|356|82115;3379134|1224|28211|356|82115|379;3379134|1224|1236|72274|135621;3379134|1224|1236|72274|135621|286;3379134|1224|28211|356|41294;1783272|201174|1760|85007|85025;1783272|201174|1760|85007|85025|1827;3379134|976|117743|200644|2762318|59732;3379134|976|117747|200666|84566|84567;3379134|1224|28211|356|119045;3379134|1224|28211|356|119045|407;3379134|1224|28216|80840|80864|34072;3379134|1224|28211|356|41294|1033,Complete,Svetlana up
bsdb:29486796/10/1,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 10,Indonesia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,2008 - Uninfected,2010 - Uninfected,2010 refers to individuals that were treated with anthelmintics although they were not infected with STH species (treatment effect).,43,16,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,2 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance in the gut microbiota between uninfected individuals in Indonesia (2008-2010 ), treated with anthelmintics in 2010 (treatment effect).",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia",1783272|1239|91061|186826|81852|1350;3379134|976|117743|200644|49546;3379134|976|117743|200644;3379134|976|117743;3379134|1224|1236|72274;3379134|976|117747|200666|84566;3379134|976|117747|200666;3379134|976|117747,Complete,Svetlana up
bsdb:29486796/10/2,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 10,Indonesia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,2008 - Uninfected,2010 - Uninfected,2010 refers to individuals that were treated with anthelmintics although they were not infected with STH species (treatment effect).,43,16,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S5,2 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance in the gut microbiota between uninfected individuals in Indonesia (2008-2010), treated with anthelmintics in 2010 (treatment effect).",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum",3379134|1224|28211|356|118882;3379134|1224|28211|356|118882|528,Complete,Svetlana up
bsdb:29486796/11/2,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 11,Indonesia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,2010 - Treated with albendazole,2008 - Infected,2008 refers to the STH-infected individuals.,27,78,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Table S5,2 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in the gut microbiota between infected and uninfected individuals after treatment with albendazole.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Afipia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium",3379134|1224|28211|356|41294|1033;3379134|1224|28211|356|119045;3379134|1224|28211|356|119045|407;3379134|1224|28211|356|41294;1783272|201174|1760|85007|85025;3379134|976|117747|200666|84566|84567;3379134|1224|1236|72274|135621;3379134|1224|1236|72274|135621|286;1783272|201174|1760|85007|85025|1827;3379134|1224|28216|80840|80864|34072;3379134|1224|28216|80840|80864;3379134|1224|28216|80840;3379134|1224|28216;3379134|1224|28211|356|82115;3379134|1224|28211|356|82115|379;3379134|976|117743|200644|2762318|59732,Complete,Svetlana up
bsdb:29486796/12/1,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 12,Indonesia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,2010 - Treated with albendazole and dewormed,2008 - Infected,2008 refers to the STH-infected individuals.,27,78,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Table S5,2 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in the gut microbiota between infected and uninfected individuals after treatment with albendazole and deworming (deworming effect),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,c__Deltaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc",3379134|976|117747|200666|84566|28453;28221;3379134|976|200643|171549|1853231|574697;3379134|976|200643|171549|171552|558436;3379134|1224|28216|80840|995019;1783272|1239|91061|186826|33958|1243,Complete,Svetlana up
bsdb:29486796/13/1,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 13,Indonesia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,2010 - Self cleared individuals,2008 - Infected,2008 refers to individuals with STH infection.,8,78,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Table S5,2 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa among self-cleared individuals and uninfected individuals.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales,k__Thermotogati|p__Synergistota|c__Synergistia,k__Thermotogati|p__Synergistota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;3384194|508458|649775|649776;3384194|508458|649775;3384194|508458;1783272|201174|84998|84999|1643824|133925,Complete,Svetlana up
bsdb:29486796/14/1,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 14,Indonesia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,Uninfected (Zero STH infection),Heavy Infected (Ascaris),Heavy Infected (Ascaris) refers to individuals heavily infected with Ascaris helminth infection in 2008.,43,12,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Table S5,2 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa among uninfected individuals and individuals heavily infected with Ascaris helminth.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,c__Deltaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Tepidibacteraceae|g__Sporacetigenium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales",3379134|1224|28216|80840|80864;1783272|1239|909932|1843489|31977|209879;1783272|1239|909932|1843489|31977;1783272|1239|909932|909929;1783272|1239|526524|526525|128827|174708;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|216572|216851;1783272|1239|909932|909929;1783272|1239|909932;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;3379134|1224|1236|135624;3379134|1224|1236|135624|83763;3379134|1224|1236|135624|83763|83770;3379134|200940|3031449|213115|194924|872;3379134|976;1783272|1239|909932|1843489|31977|39948;28221;1783272|1239|186801|3082720|3120162|360541;1783272|1239|909932|1843489|31977;1783272|1239|909932|909929|1843491|82373;1783272|1239|186801|3082720|186804;;3379134|1224|28216|80840,Complete,Svetlana up
bsdb:29486796/14/2,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 14,Indonesia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,Uninfected (Zero STH infection),Heavy Infected (Ascaris),Heavy Infected (Ascaris) refers to individuals heavily infected with Ascaris helminth infection in 2008.,43,12,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Table S5,2 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa among uninfected individuals and individuals heavily infected with Ascaris helminth.,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria,k__Pseudomonadati|p__Lentisphaerota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Afipia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas",3379134|976;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|1239|91061|1385|539738|1378;3379134|976|117743|200644|2762318|59732;3379134|976|200643|171549;3379134|976|117743|200644|49546;3379134|976|117743|200644;3379134|976|117743;1783272|201174|84998|1643822|1643826|84111;1783272|201174|1760|85007|85025|1827;1783272|201174|1760|85007|85025;3379134|256845|1313211|278082|255528|172900;3379134|256845|1313211|278082;3379134|256845|1313211|278082|255528;3379134|256845|1313211;3379134|256845;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803;3379134|1224|28211|356|82115|379;1783272|1239|186801|3085636|186803|84036;3379134|1224|28211|356|41294|1033;3379134|1224|28216|80840|80864|34072;1783272|1239|91061|186826|1300;1783272|1239|1737404|1737405|1570339|543311,Complete,Svetlana up
bsdb:29486796/15/1,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 15,Indonesia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,Uninfected (Zero STH infection),Heavy Infected (Necator),Heavy Infected (Necator) refers to individuals heavily infected with Necator helminth infection in 2008.,43,12,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Table S5,3 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa among Indonesia uninfected individuals and individuals heavily infected with Necator helminth in 2008.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Kurthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Mangrovibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Tepidibacteraceae|g__Sporacetigenium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales",3379134|1224|1236|135624;1783272|1239|526524|526525|128827|174708;1783272|1239|909932|909929|1843491|82373;3379134|976|200643|171549;3379134|976|200643;3379134|976;1783272|1239|186801|186802|216572|946234;3379134|1224|1236|135625|712|724;1783272|1239|91061|1385|186818|1649;1783272|1239|186801|3085636|186803|140625;3379134|1224|1236|91347|543|451512;3379134|1224|1236|135625|712;3379134|1224|1236|135625;1783272|1239|186801|3082720|186804;1783272|1239|186801|186802|216572|1017280;1783272|1239|526524|526525|128827|123375;3379134|203691|203692|136|137;1783272|1239|186801|3082720|3120162|360541;3379134|1224|1236|135624|83763|83770;3379134|1224|1236|135624|83763;3379134|203691|203692|136|2845253|157;1783272|1239|526524|526525|2810281|191303;3379134|976;1783272|1239|91061|186826|33958;1783272|1239|909932|909929,Complete,Svetlana up
bsdb:29486796/15/2,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 15,Indonesia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,Uninfected (Zero STH infection),Heavy Infected (Necator),Heavy Infected (Necator) refers to individuals heavily infected with Necator helminth infection in 2008.,43,12,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Table S5,3 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa among Indonesia uninfected individuals and individuals heavily infected with Necator helminth in 2008.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Bacillota|c__Tissierellia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",3379134|1224|1236|72274;1783272|1239|186801|3085636|186803;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037;1783272|201174|1760|2037|2049;1783272|1239|1737404;3379134|976|200643|171549,Complete,Svetlana up
bsdb:29486796/16/1,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 16,Indonesia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,Uninfected (Zero STH infection),Heavy Infected (Trichuris),Heavy Infected (Trichuris) refers to individuals heavily infected with Trichuris helminth infection in 2008.,43,19,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Table S5,3 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa among Indonesia uninfected individuals and individuals heavily infected with Trichuris helminth in 2008.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,c__Deltaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Paraeggerthella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae|g__Tissierella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Bhargavaea",1783272|1239|91061|186826|81852|2737;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;3379134|1224|28216|206351;3379134|1224|28216|206351|481;1783272|1239|526524|526525|128827;3379134|1224|1236|135624;3379134|1224|1236|135624|83763|83770;3379134|1224|1236|135624|83763;3379134|200940|3031449|213115|194924|872;28221;3379134|1224|1236;1783272|201174|84998|1643822|1643826|651554;1783272|1239|526524|526525|128827|123375;1783272|1239|1737404|1737405|1737406|41273;1783272|1239|91061|1385|186818|941338,Complete,Svetlana up
bsdb:29486796/16/2,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 16,Indonesia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,Uninfected (Zero STH infection),Heavy Infected (Trichuris),Heavy Infected (Trichuris) refers to individuals heavily infected with Trichuris helminth infection in 2008.,43,19,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Table S5,3 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa among Indonesia uninfected individuals and individuals heavily infected with Trichuris helminth in 2008.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803;1783272|201174|1760|85007|85025|1827;3379134|976|117747|200666|84566;3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:29486796/17/1,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 17,Indonesia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,Self-cleared,Still-Infected,"Still-infected refers to baseline (2008) untreated, infected individuals who remained infected in 2010.",8,26,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Table S5,3 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differentially abundant taxa between baseline (2008) untreated, infected individuals who remained infected in 2010, and those who were free from the infection in 2010 without anthelmintic treatment (“self-cleared”).",increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,1783272|1239|909932|1843489|31977|39948,Complete,NA
bsdb:29486796/17/2,29486796,time series / longitudinal observational,29486796,10.1186/s40168-018-0416-5,NA,"Rosa B.A., Supali T., Gankpala L., Djuardi Y., Sartono E., Zhou Y., Fischer K., Martin J., Tyagi R., Bolay F.K., Fischer P.U., Yazdanbakhsh M. , Mitreva M.",Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia,Microbiome,2018,"16S rRNA gene, Helminth, Intestine, Metagenome, Microbiota, Nematode, Parasite",Experiment 17,Indonesia,Homo sapiens,Feces,UBERON:0001988,Helminthiasis,EFO:1001342,Self-cleared,Still-Infected,"Still-infected refers to baseline (2008) untreated, infected individuals who remained infected in 2010.",8,26,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Table S5,3 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differentially abundant taxa between baseline (2008) untreated, infected individuals who remained infected in 2010, and those who were free from the infection in 2010 without anthelmintic treatment (“self-cleared”).",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactovum",1783272|1239|186801|186802|186807|2740;3379134|1224|1236|2887326|468;3379134|1224|1236|2887326|468|469;1783272|1239|186801|186802|216572|292632;3379134|1224|28216|80840|80864|283;3379134|1224|28211|204455|31989|265;3379134|1224|28211|356|45401;1783272|1239|186801|186802|204475;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|186826|1300|303226,Complete,NA
bsdb:29489859/1/1,29489859,randomized controlled trial,29489859,10.1371/journal.pone.0192443,NA,"Glatz M., Jo J.H., Kennedy E.A., Polley E.C., Segre J.A., Simpson E.L. , Kong H.H.",Emollient use alters skin barrier and microbes in infants at risk for developing atopic dermatitis,PloS one,2018,NA,Experiment 1,United States of America,Homo sapiens,Skin of cheek,UBERON:0008803,Atopic eczema,EFO:0000274,no emollient use,emollient use,infant randomized to emollient therapy,9,10,NA,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 1,Figure 3b,10 January 2021,Lucy Mellor,WikiWorks,Relative abundance of Streptococcus salivarius in infants randomized to emollient and control in cheek sample,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,1783272|1239|91061|186826|1300|1301|1304,Complete,Claregrieve1
bsdb:29489859/2/1,29489859,randomized controlled trial,29489859,10.1371/journal.pone.0192443,NA,"Glatz M., Jo J.H., Kennedy E.A., Polley E.C., Segre J.A., Simpson E.L. , Kong H.H.",Emollient use alters skin barrier and microbes in infants at risk for developing atopic dermatitis,PloS one,2018,NA,Experiment 2,United States of America,Homo sapiens,Skin of forearm,UBERON:0003403,Atopic eczema,EFO:0000274,no emollient use,emollient use,infant randomized to emollient therapy,9,10,NA,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 1,Figure 3b,10 January 2021,Lucy Mellor,WikiWorks,Relative abundance of Streptococcus salivarius in infants randomized to emollient and control in dorsal forearm sample,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,1783272|1239|91061|186826|1300|1301|1304,Complete,Claregrieve1
bsdb:29489859/2/2,29489859,randomized controlled trial,29489859,10.1371/journal.pone.0192443,NA,"Glatz M., Jo J.H., Kennedy E.A., Polley E.C., Segre J.A., Simpson E.L. , Kong H.H.",Emollient use alters skin barrier and microbes in infants at risk for developing atopic dermatitis,PloS one,2018,NA,Experiment 2,United States of America,Homo sapiens,Skin of forearm,UBERON:0003403,Atopic eczema,EFO:0000274,no emollient use,emollient use,infant randomized to emollient therapy,9,10,NA,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 2,Figure 3b,10 January 2021,Lucy Mellor,WikiWorks,Relative abundance of Streptococcus salivarius in infants randomized to emollient and control in volar forearm sample,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,1783272|1239|91061|186826|1300|1301|1304,Complete,Claregrieve1
bsdb:29501802/1/1,29501802,case-control,29501802,10.1016/j.bbi.2018.02.016,NA,"Qian Y., Yang X., Xu S., Wu C., Song Y., Qin N., Chen S.D. , Xiao Q.",Alteration of the fecal microbiota in Chinese patients with Parkinson's disease,"Brain, behavior, and immunity",2018,"16S rRNA gene, Gut microbiota, Neurodegenerative disorder",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Participants with Parkinson's Disease,All PD patients eligible for this study were diagnosed with PD according to the UK Brain Bank criteria. Patients with IBS were excluded.,45,45,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,"age,body mass index,constipation,sex",NA,increased,increased,increased,NA,NA,Signature 1,Figure 3A.,15 January 2022,Fcuevas3,"Fcuevas3,Claregrieve1,WikiWorks",Taxonomic differences of fecal microbiota in PD and healthy groups,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Aquabacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Thermoproteati|p__Nitrososphaerota|c__Nitrososphaeria|o__Nitrososphaerales|f__Nitrososphaeraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Thermoproteati|p__Nitrososphaerota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Thermoproteati|p__Nitrososphaerota|c__Nitrososphaeria|o__Nitrososphaerales,k__Thermoproteati|p__Nitrososphaerota|c__Nitrososphaeria|o__Nitrososphaerales|f__Nitrososphaeraceae|g__Nitrososphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales",3379134|1224|1236|2887326|468|469;3379134|976|200643|171549|171550|239759;3379134|1224|28216|80840|92793;1783272|1239|186801|186802|3085642|580596;3379134|976|1853228|1853229|563835;1783272|1239|186801|186802|31979|1485;3379134|200940|3031449|213115|194924|872;1783272|1239|526524|526525|128827;1783272|1239|526524;1783272|1239;3379134|1224|1236|91347|543|570;3379134|1224|1236|2887326|468;1783275|651137|1643678|1033996|1033997;3379134|976|200643|171549|171552|577309;3379134|1224|28211|356|82115;3379134|976|200643|171549|171550;3379134|976|117747|200666;3379134|976|117747;3379134|1224|28211|204457|41297;3379134|1224|28211|204457;3379134|1224|28211|204457|41297|13687;1783275|651137;3379134|1224|1236|135614|32033;3379134|1224|1236|135614;3379134|200940|3031449|213115|194924|872;3379134|1224|28216|80840;1783275|651137|1643678|1033996;1783275|651137|1643678|1033996|1033997|497726;1783272|1239|186801|3085636|186803;3379134|1224|1236|72274,Complete,Claregrieve1
bsdb:29501802/1/2,29501802,case-control,29501802,10.1016/j.bbi.2018.02.016,NA,"Qian Y., Yang X., Xu S., Wu C., Song Y., Qin N., Chen S.D. , Xiao Q.",Alteration of the fecal microbiota in Chinese patients with Parkinson's disease,"Brain, behavior, and immunity",2018,"16S rRNA gene, Gut microbiota, Neurodegenerative disorder",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Participants with Parkinson's Disease,All PD patients eligible for this study were diagnosed with PD according to the UK Brain Bank criteria. Patients with IBS were excluded.,45,45,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,"age,body mass index,constipation,sex",NA,increased,increased,increased,NA,NA,Signature 2,Figure 3A.,22 January 2022,Fcuevas3,"Fcuevas3,WikiWorks",Taxonomic differences of fecal microbiota in PD and healthy groups.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium",1783272|201174|1760|2037;1783272|1239|91061|186826|81850;1783272|1239|91061|186826|33958|1578;3379134|976|117743|200644;3379134|976|117743;3379134|976|1853228|1853229|563835|504481,Complete,Claregrieve1
bsdb:29502926/1/1,29502926,case-control,29502926,10.1016/j.numecd.2018.01.004,NA,"Verduci E., Moretti F., Bassanini G., Banderali G., Rovelli V., Casiraghi M.C., Morace G., Borgo F. , Borghi E.",Phenylketonuric diet negatively impacts on butyrate production,"Nutrition, metabolism, and cardiovascular diseases : NMCD",2018,"Butyrate, Faecalibacterium prausnitzii, Phenylketonuria, Short chain fatty acids",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Phenylketonuria,MONDO:0009861,mild hyperphenylalaninemic with unrestricted diet,phenylketonuric with Phe-restricted diet,phenylketonuric patients with restricted (phenylalanine-free) diets,21,21,3 months,16S,23,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,10 January 2021,Aboud Ezzeddine,WikiWorks,"Microbial quantification, in phenylketonuric (PKU) and mild hyperphenylalaninemia (MHP) children, of Faecalibacterium prausnitzii, and Roseburia spp",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|841;1783272|1239|91061|186826|33958|1578,Complete,Atrayees
bsdb:29513935/1/1,29513935,"cross-sectional observational, not case-control",29513935,10.1002/art.40485,NA,"Lopez-Oliva I., Paropkari A.D., Saraswat S., Serban S., Yonel Z., Sharma P., de Pablo P., Raza K., Filer A., Chapple I., Dietrich T., Grant M.M. , Kumar P.S.",Dysbiotic Subgingival Microbial Communities in Periodontally Healthy Patients With Rheumatoid Arthritis,"Arthritis & rheumatology (Hoboken, N.J.)",2018,NA,Experiment 1,United Kingdom,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,healthy controls,Rheumatoid Arthritis,periodontally healthy patients with Rheumatoid Arthritis,19,22,3 months,16S,123456789,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplemental Table 1,10 November 2022,Tislam,"Tislam,Aiyshaaaa,Claregrieve1,WikiWorks",Differential microbial abundance between RA patients and controls,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia cardiffensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces dentalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces israelii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces johnsonii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces radicidentis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera geminata,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella rimae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium scardovii,k__Bacillati|p__Chloroflexota|c__Chloroflexia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Cryptobacterium|s__Cryptobacterium curtum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister sp.,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum orale,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum saburreum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hongkongensis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia shahii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia wadei,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma faucium,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma orale,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma salivarium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella uli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp. oral taxon 078,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Parascardovia|s__Parascardovia denticolens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella dentalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella maculosa,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oulorum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella oralis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium acidifaciens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas flueggei,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. oral taxon 136,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. oral taxon 140,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. oral taxon 143,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas noxia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia exigua,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus downei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella sp. oral taxon 808,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 346,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema parvum,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema socranskii,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema vincentii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp. oral taxon 780,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|s__Veillonellaceae bacterium oral taxon 132,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|s__Veillonellaceae bacterium oral taxon 145,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|s__Veillonellaceae bacterium oral taxon 148,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|s__Veillonellaceae bacterium oral taxon 150,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|s__Veillonellaceae bacterium oral taxon 155,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|s__Veillonellaceae bacterium oral taxon 483",1783272|201174|1760|2037|2049|2529408|181487;1783272|201174|1760|2037|2049|1654|272548;1783272|201174|1760|2037|2049|1654|1659;1783272|201174|1760|2037|2049|1654|544581;1783272|201174|1760|2037|2049|1654|1655;1783272|201174|1760|2037|2049|1654|544580;1783272|201174|1760|2037|2049|1654|111015;1783272|1239|909932|1843489|31977|906|156456;1783272|201174|84998|84999|1643824|2767353|1382;1783272|201174|84998|84999|1643824|2767353|1383;3379134|976|200643|171549|815;1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|1678|1689;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|158787;1783272|200795|32061;1783272|201174|84998|1643822|1643826|84162|84163;3379134|200940|3031451|3024411|213121|893;3379134|200940|3031449|213115|194924|872;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|909932|1843489|31977|39948|1955814;1783272|1239|526524|526525|128827;3384194|508458|649775|649776|3029087|1434006|651822;3384194|508458|649775|649776|3029087|1434006|2699746;1783272|1239|186801|3085636|186803|43994;1783272|1239|186801|3085636|186803|1164882|979627;1783272|1239|186801|3085636|186803|1164882|467210;1783272|1239|91061|186826|33958|2742598|1613;1783272|1239|91061|186826|33958|2742598|1598;3384189|32066|203490|203491|1129771|32067|554406;3384189|32066|203490|203491|1129771|32067|157691;3384189|32066|203490|203491|1129771|32067|157687;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843489|31977|906|187326;1783272|1239|909932|909929|1843491|52225;1783272|1239|186801|3085636|186803|437755;1783272|544448|2790996|2895623|2895509|56142;1783272|544448|2790996|2895623|2895509|2121;1783272|544448|2790996|2895623|2895509|2124;1783272|201174|84998|84999|1643824|133925;1783272|201174|84998|84999|1643824|133925|133926;1783272|1239|186801|3085636|186803|265975|652706;1783272|201174|1760|85004|31953|196082|78258;3379134|976|200643|171549|171552|838|52227;3379134|976|200643|171549|171552|838|28129;3379134|976|200643|171549|171552|838|470565;3379134|976|200643|171549|171552|2974251|439703;3379134|976|200643|171549|171552|2974251|28136;3379134|976|200643|171549|171552|2974257|28134;3379134|976|200643|171549|171552|2974251|228604;1783272|201174|1760|85009|31957|1743|556499;1783272|201174|1760|85004|31953|196081|230143;1783272|1239|909932|909929|1843491|970|135080;1783272|1239|909932|909929|1843491|970|713030;1783272|1239|909932|909929|1843491|970|671225;1783272|1239|909932|909929|1843491|970|712533;1783272|1239|909932|909929|1843491|970|135083;1783272|1239|909932|909929|1843491|970|69823;1783272|201174|84998|1643822|1643826|84108|84109;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|91061|186826|1300|1301|1317;3379134|976|200643|171549|2005525|195950|712711;95818|713049;3379134|203691|203692|136|2845253|157|138851;3379134|203691|203692|136|2845253|157|53419;3379134|203691|203692|136|2845253|157|69710;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|909932|1843489|31977|29465|671229;1783272|1239|909932|1843489|31977|713066;1783272|1239|909932|1843489|31977|713068;1783272|1239|909932|1843489|31977|713069;1783272|1239|909932|1843489|31977|671234;1783272|1239|909932|1843489|31977|671235;1783272|1239|909932|1843489|31977|713070,Complete,Claregrieve1
bsdb:29513935/1/2,29513935,"cross-sectional observational, not case-control",29513935,10.1002/art.40485,NA,"Lopez-Oliva I., Paropkari A.D., Saraswat S., Serban S., Yonel Z., Sharma P., de Pablo P., Raza K., Filer A., Chapple I., Dietrich T., Grant M.M. , Kumar P.S.",Dysbiotic Subgingival Microbial Communities in Periodontally Healthy Patients With Rheumatoid Arthritis,"Arthritis & rheumatology (Hoboken, N.J.)",2018,NA,Experiment 1,United Kingdom,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,healthy controls,Rheumatoid Arthritis,periodontally healthy patients with Rheumatoid Arthritis,19,22,3 months,16S,123456789,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 1,10 November 2022,Tislam,"Tislam,Claregrieve1,WikiWorks",Differential microbial abundance between RA patients and healthy controls,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter sp. oral taxon 408,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter sp. oral taxon 458,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter sp. oral taxon 513,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp. oral taxon 308,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Shouchella|s__Shouchella clausii,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella|s__Bergeyella sp. oral taxon 322,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga haemolytica,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella sp. oral taxon 164,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella sp. oral taxon 451,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella morbi,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas testosteroni,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfomicrobiaceae|g__Desulfomicrobium|s__Desulfomicrobium orale,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus italicus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus saccharolyticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus haemolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp. oral taxon 035,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp. oral taxon 036,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella|s__Johnsonella ignava,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella denitrificans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella sp. oral taxon 012,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella sp. oral taxon 459,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella kingae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Leptothrix|s__Leptothrix sp. oral taxon 025,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 212,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus|s__Lysinibacillus fusiformis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria bacilliformis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flava,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria meningitidis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria polysaccharea,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ottowia|s__Ottowia sp. oral taxon 894,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp. oral taxon 393,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus|s__Peptococcus sp. oral taxon 167,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|s__Peptostreptococcaceae bacterium oral taxon 106,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas catoniae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp. oral taxon 279,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp. oral taxon 284,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella shahii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas fluorescens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Stutzerimonas|s__Stutzerimonas stutzeri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Ectopseudomonas|s__Ectopseudomonas oleovorans,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus caprae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus warneri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus intermedius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pyogenes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Terrahaemophilus|s__Terrahaemophilus aromaticivorans,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp. oral taxon 250,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae",3379134|1224|1236|2887326|468|469|470;3379134|1224|1236|2887326|468|469|712104;3379134|1224|1236|135625|712|416916|712148;3379134|1224|1236|135625|712|416916|712150;3379134|1224|1236|135625|712|416916|739;3379134|976|200643|171549|171552|1283313|671218;3379134|976|200643|171549|171552|1283313|712462;1783272|1239|91061|1385|186817|2893057|79880;3379134|976|117743|200644|2762318|59735|712187;3379134|29547|3031852|213849|72294|194|204;3379134|976|117743|200644|49546|1016|45243;3379134|976|117743|200644|49546|1016|1019;1783272|1239|186801|3085636|186803|43996|712233;1783272|1239|186801|3085636|186803|43996|712234;1783272|1239|186801|3085636|186803|43996|43997;3379134|1224|28216|80840|80864|283|285;3379134|200940|3031449|213115|213116|898|132132;3379134|1224|28216|206351|481|538|539;1783272|1239|91061|186826|81852|1350|246144;1783272|1239|91061|186826|81852|1350|41997;1783272|1239|91061|1385|539738|1378|1379;1783272|1239|91061|1385|539738|1378|29391;1783272|1239|91061|1385|539738|1378|84135;1783272|1239|91061|186826|186828|117563|46124;3379134|1224|1236|135625|712|724|726;3379134|1224|1236|135625|712|724|712309;3379134|1224|1236|135625|712|724|712310;3379134|1224|1236|135625|712|724|727;3379134|1224|1236|135625|712|724|729;1783272|1239|186801|3085636|186803|43994|43995;3379134|1224|28216|206351|481|32257|505;3379134|1224|28216|206351|481|32257|502;3379134|1224|28216|206351|481|32257|712319;3379134|1224|28216|206351|481|32257|712320;3379134|1224|28216|206351|481|32257|504;1783272|1239|91061|186826|33958|1578|47770;1783272|1239|91061|186826|33958|1578|1596;3379134|1224|28216|80840|2975441|88|712353;3384189|32066|203490|203491|1129771|32067|712357;1783272|1239|91061|1385|186817|400634|28031;3379134|1224|28216|206351|481|482|267212;3379134|1224|28216|206351|481|482|34026;3379134|1224|28216|206351|481|482|484;3379134|1224|28216|206351|481|482|487;3379134|1224|28216|206351|481|482|489;3379134|1224|28216|80840|80864|219181|1658672;1783272|1239|1737404|1737405|1570339|543311|1944660;1783272|1239|1737404|1737405|1570339|543311|713008;1783272|1239|186801|186802|186807|2740|671215;1783272|1239|186801|3082720|186804|713019;3379134|976|200643|171549|171551|836|41976;3379134|976|200643|171549|171551|836|712438;3379134|976|200643|171549|171551|836|712439;3379134|976|200643|171549|171552|838|28131;3379134|976|200643|171549|171552|2974257|228603;1783272|201174|1760|85009|31957|1912216|1747;1783272|201174|1760|85006|1268|32207|2047;1783272|201174|1760|85006|1268|32207|43675;3379134|1224|1236|72274|135621|286|294;3379134|1224|1236|72274|135621|2901164|316;3379134|1224|1236|72274|135621|3236654|330;1783272|1239|91061|1385|90964|1279|29380;1783272|1239|91061|1385|90964|1279|1282;1783272|1239|91061|1385|90964|1279|1292;3379134|1224|1236|135614|32033|40323|40324;1783272|1239|91061|186826|1300|1301|113107;1783272|1239|91061|186826|1300|1301|1338;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|91061|186826|1300|1301|1314;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|1300|1301|1343;3379134|1224|1236|135625|712|217201|217202;3379134|203691|203692|136|2845253|157|712731;1783272|1239|909932|1843489|31977|29465|423477,Complete,Claregrieve1
bsdb:29518185/1/1,29518185,time series / longitudinal observational,29518185,10.1093/cid/ciy153,NA,"Hakim H., Dallas R., Wolf J., Tang L., Schultz-Cherry S., Darling V., Johnson C., Karlsson E.A., Chang T.C., Jeha S., Pui C.H., Sun Y., Pounds S., Hayden R.T., Tuomanen E. , Rosch J.W.",Gut Microbiome Composition Predicts Infection Risk During Chemotherapy in Children With Acute Lymphoblastic Leukemia,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2018,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,baseline,post-induction therapy,6 weeks of remission induction therapy,112,87,NA,16S,123,Illumina,relative abundances,Negative Binomial Regression,0.05,TRUE,NA,NA,"antibiotic exposure,demographics",NA,decreased,decreased,decreased,NA,NA,Signature 1,Supplemental Table S3,10 January 2021,William Lam,"WikiWorks,Atrayees",Change in gut microbiota diversity in acute lymphoblastic leukemia children from baseline to post induction,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",1783272|1239;1783272|1239|186801|186802|31979;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|33958,Complete,Atrayees
bsdb:29518185/1/2,29518185,time series / longitudinal observational,29518185,10.1093/cid/ciy153,NA,"Hakim H., Dallas R., Wolf J., Tang L., Schultz-Cherry S., Darling V., Johnson C., Karlsson E.A., Chang T.C., Jeha S., Pui C.H., Sun Y., Pounds S., Hayden R.T., Tuomanen E. , Rosch J.W.",Gut Microbiome Composition Predicts Infection Risk During Chemotherapy in Children With Acute Lymphoblastic Leukemia,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2018,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,baseline,post-induction therapy,6 weeks of remission induction therapy,112,87,NA,16S,123,Illumina,relative abundances,Negative Binomial Regression,0.05,TRUE,NA,NA,"antibiotic exposure,demographics",NA,decreased,decreased,decreased,NA,NA,Signature 2,Supplemental Table S3,10 January 2021,William Lam,"WikiWorks,Atrayees",Change in gut microbiota diversity in acute lymphoblastic leukemia children from baseline to post induction,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Verrucomicrobiota",1783272|1239|186801|186802|216572|216851|1971605;1783272|201174;3379134|74201,Complete,Atrayees
bsdb:29518185/2/1,29518185,time series / longitudinal observational,29518185,10.1093/cid/ciy153,NA,"Hakim H., Dallas R., Wolf J., Tang L., Schultz-Cherry S., Darling V., Johnson C., Karlsson E.A., Chang T.C., Jeha S., Pui C.H., Sun Y., Pounds S., Hayden R.T., Tuomanen E. , Rosch J.W.",Gut Microbiome Composition Predicts Infection Risk During Chemotherapy in Children With Acute Lymphoblastic Leukemia,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,baseline,post-consolidation therapy,8 weeks of consolidation,112,107,NA,16S,123,Illumina,relative abundances,Negative Binomial Regression,0.05,TRUE,NA,NA,"acute lymphoblastic leukemia,chemotherapy",NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Supplemental Table S3,10 January 2021,William Lam,"WikiWorks,Atrayees",Change in gut microbiota diversity in acute lymphoblastic leukemia children from baseline to postconsildation,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",1783272|1239;1783272|1239|91061|186826|33958,Complete,Atrayees
bsdb:29518185/2/2,29518185,time series / longitudinal observational,29518185,10.1093/cid/ciy153,NA,"Hakim H., Dallas R., Wolf J., Tang L., Schultz-Cherry S., Darling V., Johnson C., Karlsson E.A., Chang T.C., Jeha S., Pui C.H., Sun Y., Pounds S., Hayden R.T., Tuomanen E. , Rosch J.W.",Gut Microbiome Composition Predicts Infection Risk During Chemotherapy in Children With Acute Lymphoblastic Leukemia,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,baseline,post-consolidation therapy,8 weeks of consolidation,112,107,NA,16S,123,Illumina,relative abundances,Negative Binomial Regression,0.05,TRUE,NA,NA,"acute lymphoblastic leukemia,chemotherapy",NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Table 1, Figure 1 and  2, Supplemental Table S3",10 January 2021,William Lam,"WikiWorks,Atrayees",Change in gut microbiota diversity in acute lymphoblastic leukemia children from baseline to postconsildation,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Verrucomicrobiota",3379134|976;1783272|201174;3379134|74201,Complete,Atrayees
bsdb:29518185/3/1,29518185,time series / longitudinal observational,29518185,10.1093/cid/ciy153,NA,"Hakim H., Dallas R., Wolf J., Tang L., Schultz-Cherry S., Darling V., Johnson C., Karlsson E.A., Chang T.C., Jeha S., Pui C.H., Sun Y., Pounds S., Hayden R.T., Tuomanen E. , Rosch J.W.",Gut Microbiome Composition Predicts Infection Risk During Chemotherapy in Children With Acute Lymphoblastic Leukemia,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2018,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,baseline,post re-induction therapy,120 weeks of continuation phase with the last 17-20 weeks of reinduction II therapy,112,90,NA,16S,123,Illumina,relative abundances,Negative Binomial Regression,0.05,TRUE,NA,NA,"acute lymphoblastic leukemia,chemotherapy",NA,decreased,unchanged,decreased,NA,NA,Signature 1,Supplemental Table S3,10 January 2021,William Lam,"WikiWorks,Atrayees",Change in gut microbiota diversity in acute lymphoblastic leukemia children from baseline to post re-induction,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",1783272|1239;1783272|1239|186801|186802|31979;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|33958,Complete,Atrayees
bsdb:29518185/3/2,29518185,time series / longitudinal observational,29518185,10.1093/cid/ciy153,NA,"Hakim H., Dallas R., Wolf J., Tang L., Schultz-Cherry S., Darling V., Johnson C., Karlsson E.A., Chang T.C., Jeha S., Pui C.H., Sun Y., Pounds S., Hayden R.T., Tuomanen E. , Rosch J.W.",Gut Microbiome Composition Predicts Infection Risk During Chemotherapy in Children With Acute Lymphoblastic Leukemia,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2018,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,baseline,post re-induction therapy,120 weeks of continuation phase with the last 17-20 weeks of reinduction II therapy,112,90,NA,16S,123,Illumina,relative abundances,Negative Binomial Regression,0.05,TRUE,NA,NA,"acute lymphoblastic leukemia,chemotherapy",NA,decreased,unchanged,decreased,NA,NA,Signature 2,Supplemental Table S3,10 January 2021,William Lam,"WikiWorks,Atrayees",Change in gut microbiota diversity in acute lymphoblastic leukemia children from baseline to post re-induction,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Verrucomicrobiota",1783272|1239|186801|186802|541000;1783272|1239|186801|186802|216572|216851|1971605;1783272|201174;3379134|74201,Complete,Atrayees
bsdb:29518185/4/1,29518185,time series / longitudinal observational,29518185,10.1093/cid/ciy153,NA,"Hakim H., Dallas R., Wolf J., Tang L., Schultz-Cherry S., Darling V., Johnson C., Karlsson E.A., Chang T.C., Jeha S., Pui C.H., Sun Y., Pounds S., Hayden R.T., Tuomanen E. , Rosch J.W.",Gut Microbiome Composition Predicts Infection Risk During Chemotherapy in Children With Acute Lymphoblastic Leukemia,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2018,NA,Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,non-febrile neutropenia,febrile neutropenia,fever as an oral temperature more than 38.0°C persisting for more than 1 hour; neutropenia as an absolute neutrophil count less than or equal to 500 cells per microliter after baseline first sampled,47,65,NA,16S,123,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"acute lymphoblastic leukemia,chemotherapy",NA,unchanged,NA,NA,NA,NA,Signature 1,"Supplemental Table S6, Figure 5a",10 January 2021,William Lam,WikiWorks,Comparison of baseline diversity and composition between acute lymphoblastic leukemia children with and without febrile neutropenia occurring throughout therapy,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,Atrayees
bsdb:29518419/1/1,29518419,case-control,29518419,10.1016/j.jaci.2018.02.020,NA,"Fazlollahi M., Lee T.D., Andrade J., Oguntuyo K., Chun Y., Grishina G., Grishin A. , Bunyavanich S.",The nasal microbiome in asthma,The Journal of allergy and clinical immunology,2018,"16S rRNA sequencing, Nasal, asthma, microbiome, upper airway, upper respiratory tract",Experiment 1,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,healthy control,exacerbated asthma,physician-diagnosed current asthma presenting with an encounter diagnosis of asthma exacerbation,21,20,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 2,10 January 2021,Lucy Mellor,WikiWorks,Distinct bacterial composition in subjects with exacerbated asthma and healthy controls (phylum level),increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota",3379134|976;3379134|1224,Complete,Atrayees
bsdb:29518419/2/1,29518419,case-control,29518419,10.1016/j.jaci.2018.02.020,NA,"Fazlollahi M., Lee T.D., Andrade J., Oguntuyo K., Chun Y., Grishina G., Grishin A. , Bunyavanich S.",The nasal microbiome in asthma,The Journal of allergy and clinical immunology,2018,"16S rRNA sequencing, Nasal, asthma, microbiome, upper airway, upper respiratory tract",Experiment 2,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,healthy control,non-exacerbated asthma,"physician-diagnosed current asthma presenting for routine, non-urgent, asthma followup care.",21,31,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 2,10 January 2021,Lucy Mellor,WikiWorks,Distinct bacterial composition in subjects with non-exacerbated asthma and healthy controls (phyum level),increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota",3379134|976;3379134|1224,Complete,Atrayees
bsdb:29518419/3/1,29518419,case-control,29518419,10.1016/j.jaci.2018.02.020,NA,"Fazlollahi M., Lee T.D., Andrade J., Oguntuyo K., Chun Y., Grishina G., Grishin A. , Bunyavanich S.",The nasal microbiome in asthma,The Journal of allergy and clinical immunology,2018,"16S rRNA sequencing, Nasal, asthma, microbiome, upper airway, upper respiratory tract",Experiment 3,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,non-exacerbated asthma,exacerbated asthma,physician-diagnosed current asthma presenting with an encounter diagnosis of asthma exacerbation,31,20,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 3,10 January 2021,Victoria Goulbourne,WikiWorks,Linear discriminant analysis (LDA) demonstrated distinct bacterial genera enriched in exacerbated and non-exacerbated asthma,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Alkanindiges,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella",3379134|976|200643|171549|171552|838;3379134|1224|1236|2887326|468|222991;1783272|201174|1760|85004|31953|2701,Complete,Lucy Mellor
bsdb:29518419/3/2,29518419,case-control,29518419,10.1016/j.jaci.2018.02.020,NA,"Fazlollahi M., Lee T.D., Andrade J., Oguntuyo K., Chun Y., Grishina G., Grishin A. , Bunyavanich S.",The nasal microbiome in asthma,The Journal of allergy and clinical immunology,2018,"16S rRNA sequencing, Nasal, asthma, microbiome, upper airway, upper respiratory tract",Experiment 3,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,non-exacerbated asthma,exacerbated asthma,physician-diagnosed current asthma presenting with an encounter diagnosis of asthma exacerbation,31,20,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Figure 3,10 January 2021,Victoria Goulbourne,WikiWorks,Linear discriminant analysis (LDA) demonstrated distinct bacterial genera enriched in exacerbated and non-exacerbated asthma,decreased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,1783272|1239|909932|1843489|31977|39948,Complete,Lucy Mellor
bsdb:29518419/4/1,29518419,case-control,29518419,10.1016/j.jaci.2018.02.020,NA,"Fazlollahi M., Lee T.D., Andrade J., Oguntuyo K., Chun Y., Grishina G., Grishin A. , Bunyavanich S.",The nasal microbiome in asthma,The Journal of allergy and clinical immunology,2018,"16S rRNA sequencing, Nasal, asthma, microbiome, upper airway, upper respiratory tract",Experiment 4,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,healthy control,asthma,"physician-diagnosed current asthma presenting for routine, non-urgent, asthma followup care or with an encounter diagnosis of asthma exacerbation",21,51,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4, text",10 January 2021,Lucy Mellor,WikiWorks,Species differentially abundant between asthmatics and health controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Alkanindiges|s__Alkanindiges hongkongensis",3379134|976|200643|171549|171552|2974257|28127;1783272|1239|909932|1843489|31977|39948|218538;1783272|201174|1760|85004|31953|2701|2702;3379134|1224|1236|2887326|468|222991|208968,Complete,Atrayees
bsdb:29518419/5/1,29518419,case-control,29518419,10.1016/j.jaci.2018.02.020,NA,"Fazlollahi M., Lee T.D., Andrade J., Oguntuyo K., Chun Y., Grishina G., Grishin A. , Bunyavanich S.",The nasal microbiome in asthma,The Journal of allergy and clinical immunology,2018,"16S rRNA sequencing, Nasal, asthma, microbiome, upper airway, upper respiratory tract",Experiment 5,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,healthy control,asthma,"physician-diagnosed current asthma presenting for routine, non-urgent, asthma followup care or with an encounter diagnosis of asthma exacerbation",21,51,NA,16S,34,RT-qPCR,raw counts,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,10 January 2021,Victoria Goulbourne,WikiWorks,Difference in fold change between asthmatics and healthy controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis",3379134|976|200643|171549|171552|2974257|28127;1783272|201174|1760|85004|31953|2701|2702,Complete,Lucy Mellor
bsdb:29520144/1/1,29520144,case-control,29520144,10.2147/NDT.S159322,NA,"Chen J.J., Zheng P., Liu Y.Y., Zhong X.G., Wang H.Y., Guo Y.J. , Xie P.",Sex differences in gut microbiota in patients with major depressive disorder,Neuropsychiatric disease and treatment,2018,"MDD, biomarker, gut microbiota, major depressive disorder",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,Healthy Controls,depressed female,NA,24,24,NA,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,NA,demographics,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,10 January 2021,Fatima Zohra,WikiWorks,Sex differences in gut microbiota in female patients with major depressive disorder,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Asaccharobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",1783272|1239|186801|3085636|186803|572511;1783272|201174;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85004|31953|1678;1783272|201174|84998|1643822|1643826|553372;1783272|201174|84998|84999|1643824|1380;1783272|201174|84998|1643822|1643826|84111;1783272|201174|84998|1643822|1643826|644652;1783272|201174|84998|84999|1643824|133925;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|216851;3379134|200940|3031449|213115|194924|872;1783272|201174|84998|84999;1783272|1239|186801|3085636|186803;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;3379134|1224|1236|135625;3379134|1224|1236|135625|712;1783272|1239|186801|186802|186806;1783272|201174|84998|84999|84107,Complete,Shaimaa Elsafoury
bsdb:29520144/1/2,29520144,case-control,29520144,10.2147/NDT.S159322,NA,"Chen J.J., Zheng P., Liu Y.Y., Zhong X.G., Wang H.Y., Guo Y.J. , Xie P.",Sex differences in gut microbiota in patients with major depressive disorder,Neuropsychiatric disease and treatment,2018,"MDD, biomarker, gut microbiota, major depressive disorder",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,Healthy Controls,depressed female,NA,24,24,NA,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,NA,demographics,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5,10 January 2021,Fatima Zohra,WikiWorks,Sex differences in gut microbiota in female patients with major depressive disorder,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter",1783272|1239|186801|186802|404402;3379134|1224|28216|80840|995019|40544;3384194|508458|649775|649776|3029088|638847,Complete,Shaimaa Elsafoury
bsdb:29520144/2/1,29520144,case-control,29520144,10.2147/NDT.S159322,NA,"Chen J.J., Zheng P., Liu Y.Y., Zhong X.G., Wang H.Y., Guo Y.J. , Xie P.",Sex differences in gut microbiota in patients with major depressive disorder,Neuropsychiatric disease and treatment,2018,"MDD, biomarker, gut microbiota, major depressive disorder",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,Healthy Controls,depressed male,NA,20,20,yes,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,NA,demographics,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,10 January 2021,Fatima Zohra,"Fatima,WikiWorks",Sex differences in gut microbiota in male patients with major depressive disorder,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",1783272|201174|84998|84999|1643824|1380;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976|200643;1783272|1239|909932|1843489|31977|29465;1783272|1239|526524|526525|128827,Complete,Fatima
bsdb:29520144/2/2,29520144,case-control,29520144,10.2147/NDT.S159322,NA,"Chen J.J., Zheng P., Liu Y.Y., Zhong X.G., Wang H.Y., Guo Y.J. , Xie P.",Sex differences in gut microbiota in patients with major depressive disorder,Neuropsychiatric disease and treatment,2018,"MDD, biomarker, gut microbiota, major depressive disorder",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,Healthy Controls,depressed male,NA,20,20,yes,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,NA,demographics,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6,10 January 2021,Fatima Zohra,WikiWorks,Sex differences in gut microbiota in male patients with major depressive disorder,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter",1783272|201174|84998|84999|84107;1783272|1239|186801;1783272|201174|84998|1643822|1643826|644652;1783272|1239|186801|3082720|543314|109326;3384194|508458|649775|649776|3029088|638847,Complete,Shaimaa Elsafoury
bsdb:29525681/1/1,29525681,case-control,29525681,10.1016/j.intimp.2018.03.003,NA,"Wang X., Zhang L., Wang Y., Liu X., Zhang H., Liu Y., Shen N., Yang J. , Gai Z.",Gut microbiota dysbiosis is associated with Henoch-Schönlein Purpura in children,International immunopharmacology,2018,"Dysbiosis, Henoch-Schönlein Purpura, IgA, Microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Henoch-Schoenlein purpura,EFO:1000965,controls,Henoch-Schönlein Purpura,Henoch-Schönlein Purpura in children,70,85,NA,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 6b,10 January 2021,Rimsha Azhar,WikiWorks,The most differentially abundant taxa between Henoch-Schönlein Purpura (HSP) and controls,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",1783272|1239|909932|1843489|31977|29465;3384189|32066|203490;3384189|32066;3384189|32066|203490|203491;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|81852;1783272|1239|909932|1843489|31977;1783272|1239|909932|909929|1843491|158846;3379134|976|200643|171549|171551;3379134|976|200643|171549|2005525|375288,Complete,Claregrieve1
bsdb:29525681/1/2,29525681,case-control,29525681,10.1016/j.intimp.2018.03.003,NA,"Wang X., Zhang L., Wang Y., Liu X., Zhang H., Liu Y., Shen N., Yang J. , Gai Z.",Gut microbiota dysbiosis is associated with Henoch-Schönlein Purpura in children,International immunopharmacology,2018,"Dysbiosis, Henoch-Schönlein Purpura, IgA, Microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Henoch-Schoenlein purpura,EFO:1000965,controls,Henoch-Schönlein Purpura,Henoch-Schönlein Purpura in children,70,85,NA,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Figure 6b,10 January 2021,Rimsha Azhar,"Fatima,WikiWorks",The most differentially abundant taxa between Henoch-Schönlein Purpura (HSP) and controls,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",3379134|1224|28216|80840|506;3379134|1224|28216;3379134|1224|28216|80840;1783272|1239|186801|3082768|990719;1783272|1239|186801;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802;1783272|1239;3379134|1224|1236|135625|712|724;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803;3379134|1224|28216|80840|995019|577310;3379134|1224|1236|135625|712;3379134|1224|1236|135625;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|1766253|39491,Complete,Claregrieve1
bsdb:29538354/1/1,29538354,"cross-sectional observational, not case-control",29538354,10.1038/pr.2018.29,NA,"Tapiainen T., Paalanne N., Tejesvi M.V., Koivusaari P., Korpela K., Pokka T., Salo J., Kaukola T., Pirttilä A.M., Uhari M. , Renko M.",Maternal influence on the fetal microbiome in a population-based study of the first-pass meconium,Pediatric research,2018,NA,Experiment 1,Finland,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,vaginal delivery,C-section,Delivery via cesarean section,172,40,NA,16S,45,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 3,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Effect of delivery mode on the microbiome in the CS group compared to the vaginal delivery group,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,Shaimaa Elsafoury
bsdb:29538354/2/1,29538354,"cross-sectional observational, not case-control",29538354,10.1038/pr.2018.29,NA,"Tapiainen T., Paalanne N., Tejesvi M.V., Koivusaari P., Korpela K., Pokka T., Salo J., Kaukola T., Pirttilä A.M., Uhari M. , Renko M.",Maternal influence on the fetal microbiome in a population-based study of the first-pass meconium,Pediatric research,2018,NA,Experiment 2,Finland,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,Antimicrobials use during delivery (no),Antimicrobials use during delivery (yes),"Mothers who used antimicrobials during delivery (Cefuroxime (n= 31), penicillin (n= 28), piperacillin-tazobactam (n=2))",151,61,NA,16S,45,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 3,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Effect of antimicrobial use on the microbiome of the first stool in the group who received antimicrobials (YES) compared to those did not (NO),increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Shaimaa Elsafoury
bsdb:29538354/3/1,29538354,"cross-sectional observational, not case-control",29538354,10.1038/pr.2018.29,NA,"Tapiainen T., Paalanne N., Tejesvi M.V., Koivusaari P., Korpela K., Pokka T., Salo J., Kaukola T., Pirttilä A.M., Uhari M. , Renko M.",Maternal influence on the fetal microbiome in a population-based study of the first-pass meconium,Pediatric research,2018,NA,Experiment 3,Finland,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,Maternal consumption of probiotics (NO),Maternal consumption of probiotics (YES),Mothers who consumed probiotics (lactobacilli) during pregnancy,151,61,NA,16S,45,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 3,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Effect of probiotics on the microbiome in the group who consumed lactobacilli (YES) compared to the group who did not (NO),increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Shaimaa Elsafoury
bsdb:29538354/4/1,29538354,"cross-sectional observational, not case-control",29538354,10.1038/pr.2018.29,NA,"Tapiainen T., Paalanne N., Tejesvi M.V., Koivusaari P., Korpela K., Pokka T., Salo J., Kaukola T., Pirttilä A.M., Uhari M. , Renko M.",Maternal influence on the fetal microbiome in a population-based study of the first-pass meconium,Pediatric research,2018,NA,Experiment 4,Finland,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,Furry pets at home (NO),Furry pets at home (YES),Mothers who have furry pets at home during pregnancy,108,104,NA,16S,45,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"antimicrobial agent during labor,delivery procedure,probiotics during pregnancy",NA,increased,NA,NA,NA,increased,Signature 1,Table 4,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Effect of furry pets at home on the microbiome in the group who have furry pets at home (YES) compared to the group who don't have (NO),increased,"k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",3379134|976;1783272|1239|186801|186802|216572|216851,Complete,Shaimaa Elsafoury
bsdb:29538354/4/2,29538354,"cross-sectional observational, not case-control",29538354,10.1038/pr.2018.29,NA,"Tapiainen T., Paalanne N., Tejesvi M.V., Koivusaari P., Korpela K., Pokka T., Salo J., Kaukola T., Pirttilä A.M., Uhari M. , Renko M.",Maternal influence on the fetal microbiome in a population-based study of the first-pass meconium,Pediatric research,2018,NA,Experiment 4,Finland,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,Furry pets at home (NO),Furry pets at home (YES),Mothers who have furry pets at home during pregnancy,108,104,NA,16S,45,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"antimicrobial agent during labor,delivery procedure,probiotics during pregnancy",NA,increased,NA,NA,NA,increased,Signature 2,Table 4,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Effect of furry pets at home on the microbiome in the group who have furry pets at home (YES) compared to the group who don't have (NO),decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|1239;1783272|1239|91061|1385|90964|1279,Complete,Shaimaa Elsafoury
bsdb:29554907/1/1,29554907,time series / longitudinal observational,29554907,10.1186/s12941-018-0264-y,NA,"Zou Z.H., Liu D., Li H.D., Zhu D.P., He Y., Hou T. , Yu J.L.",Prenatal and postnatal antibiotic exposure influences the gut microbiota of preterm infants in neonatal intensive care units,Annals of clinical microbiology and antimicrobials,2018,"Anti-bacterial agents, Gastrointestinal microbiome, High-throughput nucleotide sequencing, Infant, premature, Intensive care unit, neonatal",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,prenatal antibiotic free group (PAF group),infants(14-d old) exposed to prenatal antibiotic therapy (PAT group),Pre-term infants,12,12,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,"Figure 1b, c; Figure 4a,b",10 January 2021,Mst Afroza Parvin,WikiWorks,LEfSe results on gut microbiomes of preterm infants,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinilabiliaceae|g__Saccharicrinis,k__Pseudomonadati|p__Campylobacterota,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales",3379134|976|200643|1970189|558415|1618113;3379134|29547;3379134|976|117743|200644,Complete,NA
bsdb:29554907/1/2,29554907,time series / longitudinal observational,29554907,10.1186/s12941-018-0264-y,NA,"Zou Z.H., Liu D., Li H.D., Zhu D.P., He Y., Hou T. , Yu J.L.",Prenatal and postnatal antibiotic exposure influences the gut microbiota of preterm infants in neonatal intensive care units,Annals of clinical microbiology and antimicrobials,2018,"Anti-bacterial agents, Gastrointestinal microbiome, High-throughput nucleotide sequencing, Infant, premature, Intensive care unit, neonatal",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,prenatal antibiotic free group (PAF group),infants(14-d old) exposed to prenatal antibiotic therapy (PAT group),Pre-term infants,12,12,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,"Figure 1b, c; Figure 4a,b",10 January 2021,Mst Afroza Parvin,WikiWorks,LEfSe results on gut microbiomes of preterm infants,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|1239|186801|186802;1783272|1239|186801;1783272|201174|1760|85004|31953|1678,Complete,NA
bsdb:29554907/2/1,29554907,time series / longitudinal observational,29554907,10.1186/s12941-018-0264-y,NA,"Zou Z.H., Liu D., Li H.D., Zhu D.P., He Y., Hou T. , Yu J.L.",Prenatal and postnatal antibiotic exposure influences the gut microbiota of preterm infants in neonatal intensive care units,Annals of clinical microbiology and antimicrobials,2018,"Anti-bacterial agents, Gastrointestinal microbiome, High-throughput nucleotide sequencing, Infant, premature, Intensive care unit, neonatal",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants exposed to antibiotic <=7day (L group),infants exposed to antibiotic >7day (H group),Pre-term infants,11,11,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 8,10 January 2021,Mst Afroza Parvin,WikiWorks,LEfSe analysis showed significant differences in microbial community structure between the H and L groups.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,3379134|1224|28216,Complete,NA
bsdb:29554907/2/2,29554907,time series / longitudinal observational,29554907,10.1186/s12941-018-0264-y,NA,"Zou Z.H., Liu D., Li H.D., Zhu D.P., He Y., Hou T. , Yu J.L.",Prenatal and postnatal antibiotic exposure influences the gut microbiota of preterm infants in neonatal intensive care units,Annals of clinical microbiology and antimicrobials,2018,"Anti-bacterial agents, Gastrointestinal microbiome, High-throughput nucleotide sequencing, Infant, premature, Intensive care unit, neonatal",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants exposed to antibiotic <=7day (L group),infants exposed to antibiotic >7day (H group),Pre-term infants,11,11,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 8,10 January 2021,Mst Afroza Parvin,WikiWorks,LEfSe analysis showed significant differences in microbial community structure between the H and L groups.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae",1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004;1783272|201174|1760|85004|31953,Complete,NA
bsdb:29562298/1/1,29562298,case-control,29562298,10.1093/rheumatology/key052,NA,"Mikuls T.R., Walker C., Qiu F., Yu F., Thiele G.M., Alfant B., Li E.C., Zhao L.Y., Wang G.P., Datta S. , Payne J.B.",The subgingival microbiome in patients with established rheumatoid arthritis,"Rheumatology (Oxford, England)",2018,"osteoarthritis, periodontitis, rheumatoid arthritis, subgingival microbiome",Experiment 1,NA,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Arthritis,EFO:0005856,Osteoarthritis (OA),Rheumatoid Arthritis (RA),Patients with Rheumatoid Arthritis,296,260,NA,16S,123,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,"comorbidity,marital status,race,smoking status",NA,unchanged,increased,unchanged,NA,unchanged,Signature 1,text,2 November 2022,Tislam,"Tislam,Peace Sandy,WikiWorks","Differential expression of OTUs between RA and OA patients based on periodontitis status 

Differential expression analysis conducted using two separate linear models: the first fitted with RA vs OA status, periodontitis status and the interaction between these factors (base model); and the second fitted with the same factors as the base model in addition to race, marital status and smoking (fully adjusted model). OTU: operational taxonomic unit; FDR: false discovery rate.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella multiformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp.",1783272|1239|186801|3085636|186803|43996;1783272|1239|186801|186802|1898207;1783272|1239|186801|3085636|186803;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838|282402;3379134|976|200643|171549|171552|838|59823;1783272|1239|909932|909929|1843491|970;3379134|203691|203692|136|2845253|157|166,Complete,Peace Sandy
bsdb:29563617/1/1,29563617,time series / longitudinal observational,29563617,10.1038/s41598-018-23389-0,NA,"Zhang H., Lu J., Lu Y., Cai Q., Liu H. , Xu C.",Cervical microbiome is altered in cervical intraepithelial neoplasia after loop electrosurgical excision procedure in china,Scientific reports,2018,NA,Experiment 1,China,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical glandular intraepithelial neoplasia,EFO:1000165,after loop electrosurgical excision procedure,before,Cervical intraepithelial neoplasia 2/3 patients who underwent Loop electrosurgical excision procedure(LEEP),26,26,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,unchanged,increased,Signature 1,Figure 4,10 January 2021,Cynthia Anderson,"Atrayees,WikiWorks",Histogram of the LDA scores was used to features differentially abundant between LEEP and no LEEP state.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia vaginalis",1783272|201174|1760;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;3379134|1224|28216|80840|119060;1783272|1239|186801;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;1783272|1239|186801|186802;1783272|201174|1760|85004|31953|2701|2702;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958|1578|33959;3384189|32066|203490|203491|1129771;1783272|201174|1760|85007;1783272|1239|186801|186802|541000;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171552|838|419005;3384189|32066|203490|203491|1129771|168808;1783272|1239|909932|1843489|31977|29465;3384189|32066|203490|203491|1129771|168808|187101,Complete,Fatima Zohra
bsdb:29563617/1/2,29563617,time series / longitudinal observational,29563617,10.1038/s41598-018-23389-0,NA,"Zhang H., Lu J., Lu Y., Cai Q., Liu H. , Xu C.",Cervical microbiome is altered in cervical intraepithelial neoplasia after loop electrosurgical excision procedure in china,Scientific reports,2018,NA,Experiment 1,China,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical glandular intraepithelial neoplasia,EFO:1000165,after loop electrosurgical excision procedure,before,Cervical intraepithelial neoplasia 2/3 patients who underwent Loop electrosurgical excision procedure(LEEP),26,26,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,unchanged,increased,Signature 2,Figure 4,10 January 2021,Cynthia Anderson,WikiWorks,Histogram of the LDA scores was used to features differentially abundant between LEEP and no LEEP state.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli",1783272|1239|91061|1385|90964|1279;3379134|1224|1236|2887326|468;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|526524|526525|128827;3379134|1224|28216|80840|119060|48736;1783272|201174|84998|84999;1783272|201174|84998|84999|84107;1783272|1239;1783272|1239|91061,Complete,Fatima Zohra
bsdb:29564487/1/1,29564487,case-control,29564487,10.1007/s00248-018-1176-2,NA,"Pulikkan J., Maji A., Dhakan D.B., Saxena R., Mohan B., Anto M.M., Agarwal N., Grace T. , Sharma V.K.",Gut Microbial Dysbiosis in Indian Children with Autism Spectrum Disorders,Microbial ecology,2018,"Autism spectrum disorder (ASD), Gastrointestinal symptoms, Gut microbial dysbiosis, Gut-brain axis, Indian children",Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Healthy controls,Children with Autism Spectrum Disorder (ASD),"Diagnosis of all the cases was carried out using a CARS (Childhood Autism Rating Scale) score, DSM-5 approved AIIMS-modified INDT-ASD (INCLEN Diagnostic Tool for Autism Spectrum Disorder), and the ISAA (Indian Scale for Assessment of Autism) tool",24,30,1 month,16S,3,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 3, Supplementary Table S8-9",5 December 2024,AlishaM,"AlishaM,WikiWorks",Families and genera showing significant variations between ASD and healthy children identified using Wilcoxon rank sum test,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae",1783272|201174|1760|85004|31953;1783272|1239|91061|186826|33958;1783272|1239|909932|1843489|31977;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|909929|1843491|52225;1783272|1239|526524|526525|128827;1783272|1239|91061|186826|81852;3379134|200940|3031449|213115|194924;3379134|203691|203692|136|137,Complete,NA
bsdb:29564487/1/2,29564487,case-control,29564487,10.1007/s00248-018-1176-2,NA,"Pulikkan J., Maji A., Dhakan D.B., Saxena R., Mohan B., Anto M.M., Agarwal N., Grace T. , Sharma V.K.",Gut Microbial Dysbiosis in Indian Children with Autism Spectrum Disorders,Microbial ecology,2018,"Autism spectrum disorder (ASD), Gastrointestinal symptoms, Gut microbial dysbiosis, Gut-brain axis, Indian children",Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Healthy controls,Children with Autism Spectrum Disorder (ASD),"Diagnosis of all the cases was carried out using a CARS (Childhood Autism Rating Scale) score, DSM-5 approved AIIMS-modified INDT-ASD (INCLEN Diagnostic Tool for Autism Spectrum Disorder), and the ISAA (Indian Scale for Assessment of Autism) tool",24,30,1 month,16S,3,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 3, Supplementary Table S8-9",5 December 2024,AlishaM,"AlishaM,WikiWorks",Families and genera showing significant variations between ASD and healthy children identified using Wilcoxon rank sum test,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,3379134|976|200643|171549|1853231|283168,Complete,NA
bsdb:29564487/2/1,29564487,case-control,29564487,10.1007/s00248-018-1176-2,NA,"Pulikkan J., Maji A., Dhakan D.B., Saxena R., Mohan B., Anto M.M., Agarwal N., Grace T. , Sharma V.K.",Gut Microbial Dysbiosis in Indian Children with Autism Spectrum Disorders,Microbial ecology,2018,"Autism spectrum disorder (ASD), Gastrointestinal symptoms, Gut microbial dysbiosis, Gut-brain axis, Indian children",Experiment 2,India,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Healthy controls,Children with Autism Spectrum Disorder (ASD),"Diagnosis of all the cases was carried out using a CARS (Childhood Autism Rating Scale) score, DSM-5 approved AIIMS-modified INDT-ASD (INCLEN Diagnostic Tool for Autism Spectrum Disorder), and the ISAA (Indian Scale for Assessment of Autism) tool",24,30,1 month,16S,3,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Supplementary Figure S4, Supplementary Table S11",6 December 2024,AlishaM,"AlishaM,WikiWorks",Discriminatory genera using LefSe,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera",1783272|201174|1760|85004|31953|1678;1783272|1239|909932|909929|1843491|52225;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|906,Complete,NA
bsdb:29576948/1/1,29576948,case-control,29576948,10.7717/peerj.4458,NA,"Wu Y., Chi X., Zhang Q., Chen F. , Deng X.",Characterization of the salivary microbiome in people with obesity,PeerJ,2018,"Body-Mass Index, High-throughput nucleotide sequencing, Microbiome, Obesity, Oral microbiome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Obesity,EFO:0001073,controls,Obesity group,obesity group (BMI ≥30),29,33,3 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 2,10 January 2021,Rimsha Azhar,"Lwaldron,WikiWorks",Differentially abundant taxa between people with obesity and normal weight control,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",3379134|976|200643|171549;3379134|976|200643;3379134|1224|1236|135615|868;1783272|1239|91061|186826|186828;1783272|1239|186801|3085636|186803|43996;3379134|1224|28216|80840|80864;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|91061|186826|186828|117563;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|186802|186807;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|526524|526525|128827|123375;3379134|1224|28211|356|335928;1783272|1239|186801|3082720|186804,Complete,Shaimaa Elsafoury
bsdb:29576948/1/2,29576948,case-control,29576948,10.7717/peerj.4458,NA,"Wu Y., Chi X., Zhang Q., Chen F. , Deng X.",Characterization of the salivary microbiome in people with obesity,PeerJ,2018,"Body-Mass Index, High-throughput nucleotide sequencing, Microbiome, Obesity, Oral microbiome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Obesity,EFO:0001073,controls,Obesity group,obesity group (BMI ≥30),29,33,3 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 2,10 January 2021,Rimsha Azhar,WikiWorks,Differentially abundant taxa between people with obesity and normal weight control,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",3379134|1224|1236;3379134|976|117743;3379134|1224|1236|135625;3379134|1224|28216|80840;3379134|976|117743|200644;1783272|201174|1760|85007;3379134|1224|1236|135615;3379134|1224|1236|135614;3379134|1224|1236|135625|712;3379134|1224|28216|80840|119060;3379134|976|117743|200644|49546;1783272|201174|1760|85007|1653;3379134|1224|1236|135625|712|724;3379134|1224|1236|135615|868|2717;1783272|1239|91061|1385|90964;3379134|976|117743|200644|49546|1016;3379134|1224|28216|80840|119060|47670;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|135614|32033|40323,Complete,Shaimaa Elsafoury
bsdb:29580894/1/1,29580894,"cross-sectional observational, not case-control",29580894,10.1016/j.bbr.2018.03.036,NA,"Jiang H.Y., Zhou Y.Y., Zhou G.L., Li Y.C., Yuan J., Li X.H. , Ruan B.",Gut microbiota profiles in treatment-naïve children with attention deficit hyperactivity disorder,Behavioural brain research,2018,"Gut-brain axis, Hyperactivity, Inattention, Microbiome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Attention deficit hyperactivity disorder,EFO:0003888,healthy control,ADHD,Treatment-Naive Children diagnosed with ADHD,32,51,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 1d , Figure S8",10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy","(d) LEfSe identified the most differentially abundant taxons between HC and ADHD groups at genus level. Taxonomic cladogram obtained from LEfSe analysis of 16S sequences (relative
abundance > 0.5%). HC-enriched taxa are indicated with a positive LDA score (green), and taxa enriched in ADHD have a negative score (red). Only taxa meeting an
LDA significant threshold > 2 are shown 

LEfSe identified the most differentially abundant taxons between HC and ADHD groups at family level. Taxonomic cladogram obtained from LEfSe analysis of 16S sequences (relative abundance >0.5%). (Red) ADHD taxa; (Green) taxa enriched in HCs. HC-enriched taxa are indicated with a positive LDA score (green), and taxa enriched in ADHD have a negative score (red). Only taxa meeting an LDA significant threshold >2 are shown.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae",3379134|1224|1236|2887326|468|469;1783272|1239|186801|3082768|990719|990721;1783272|1239|526524|526525|2810280|100883;1783272|1239|526524|526525|128827|1573534;1783272|1239|186801|186802|186807;1783272|1239|186801|3082720|186804;1783272|201174|84998|84999|84107|1473205;3379134|1224|1236|135614|32033|40323;1783272|1239|186801|3082720|186804|1505652;3379134|1224|1236|2887326|468;3379134|1224|1236|135614|32033,Complete,Peace Sandy
bsdb:29580894/1/2,29580894,"cross-sectional observational, not case-control",29580894,10.1016/j.bbr.2018.03.036,NA,"Jiang H.Y., Zhou Y.Y., Zhou G.L., Li Y.C., Yuan J., Li X.H. , Ruan B.",Gut microbiota profiles in treatment-naïve children with attention deficit hyperactivity disorder,Behavioural brain research,2018,"Gut-brain axis, Hyperactivity, Inattention, Microbiome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Attention deficit hyperactivity disorder,EFO:0003888,healthy control,ADHD,Treatment-Naive Children diagnosed with ADHD,32,51,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure1, Figure S8",10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy","d) LEfSe identified the most differentially abundant taxons between HC and ADHD groups at genus level. Taxonomic cladogram obtained from LEfSe analysis of 16S sequences (relative abundance > 0.5%). HC-enriched taxa are indicated with a positive LDA score (green), and taxa enriched in ADHD have a negative score (red). Only taxa meeting an LDA significant threshold > 2 are shown

LEfSe identified the most differentially abundant taxons between HC and ADHD groups at family level. Taxonomic cladogram obtained from LEfSe analysis of 16S sequences (relative abundance >0.5%). (Red) ADHD taxa; (Green) taxa enriched in HCs. HC-enriched taxa are indicated with a positive LDA score (green), and taxa enriched in ADHD have a negative score (red). Only taxa meeting an LDA significant threshold >2 are shown.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",3379134|1224|28216|80840|506;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|28050|39485;3379134|1224|28216|80840|995019|40544;1783272|1239|909932|1843488|909930|904;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3085636|186803|1506577,Complete,Peace Sandy
bsdb:29592876/1/1,29592876,time series / longitudinal observational,29592876,10.1182/bloodadvances.2018017731,NA,"DeFilipp Z., Peled J.U., Li S., Mahabamunuge J., Dagher Z., Slingerland A.E., Del Rio C., Valles B., Kempner M.E., Smith M., Brown J., Dey B.R., El-Jawahri A., McAfee S.L., Spitzer T.R., Ballen K.K., Sung A.D., Dalton T.E., Messina J.A., Dettmer K., Liebisch G., Oefner P., Taur Y., Pamer E.G., Holler E., Mansour M.K., van den Brink M.R.M., Hohmann E., Jenq R.R. , Chen Y.B.",Third-party fecal microbiota transplantation following allo-HCT reconstitutes microbiome diversity,Blood advances,2018,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,patients post allogenic hematopoietic cell transplant/pre Fecal Microbiota Transplant,patients preallogenic hematopoietic cell transplant,patients who received Fecal Microbiome Transplant,5,13,2 days,16S,45,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,"HLA match,acute graft vs. host disease,age,history of GI,transplant conditioning",NA,NA,NA,NA,increased,NA,Signature 1,Figure 4B,10 January 2021,Nadine Ulysse,WikiWorks,Third-party fecal microbiota transplantation (FMT) may restore intestinal microbiome diversity after allogeneic hematopoietic cell transplantation (allo-HCT),increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,1783272|1239|186801|186802,Complete,Rimsha Azhar
bsdb:29592876/2/1,29592876,time series / longitudinal observational,29592876,10.1182/bloodadvances.2018017731,NA,"DeFilipp Z., Peled J.U., Li S., Mahabamunuge J., Dagher Z., Slingerland A.E., Del Rio C., Valles B., Kempner M.E., Smith M., Brown J., Dey B.R., El-Jawahri A., McAfee S.L., Spitzer T.R., Ballen K.K., Sung A.D., Dalton T.E., Messina J.A., Dettmer K., Liebisch G., Oefner P., Taur Y., Pamer E.G., Holler E., Mansour M.K., van den Brink M.R.M., Hohmann E., Jenq R.R. , Chen Y.B.",Third-party fecal microbiota transplantation following allo-HCT reconstitutes microbiome diversity,Blood advances,2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,post fecal mircobiota day 180,post allogenic hematopoietic cell transplant/ pre Fecal microbiota transplant,patients who received Fecal Microbiome Transplant,5,13,2 days,16S,45,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,"HLA match,acute graft vs. host disease,age,history of GI,transplant conditioning",NA,NA,NA,NA,unchanged,NA,Signature 1,Figure 4B,10 January 2021,Nadine Ulysse,WikiWorks,Third-party fecal microbiota transplantation (FMT) may restore intestinal microbiome diversity after allogeneic hematopoietic cell transplantation (allo-HCT),decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,1783272|1239|186801|186802,Complete,Rimsha Azhar
bsdb:29592876/3/1,29592876,time series / longitudinal observational,29592876,10.1182/bloodadvances.2018017731,NA,"DeFilipp Z., Peled J.U., Li S., Mahabamunuge J., Dagher Z., Slingerland A.E., Del Rio C., Valles B., Kempner M.E., Smith M., Brown J., Dey B.R., El-Jawahri A., McAfee S.L., Spitzer T.R., Ballen K.K., Sung A.D., Dalton T.E., Messina J.A., Dettmer K., Liebisch G., Oefner P., Taur Y., Pamer E.G., Holler E., Mansour M.K., van den Brink M.R.M., Hohmann E., Jenq R.R. , Chen Y.B.",Third-party fecal microbiota transplantation following allo-HCT reconstitutes microbiome diversity,Blood advances,2018,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,post fecal mircobiota day 7,post allogenic hematopoietic cell transplant/ pre Fecal microbiota transplant,patients who received Fecal Microbiome Transplant,5,13,2 days,16S,45,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,"HLA match,acute graft vs. host disease,age,history of GI,transplant conditioning",NA,NA,NA,NA,decreased,NA,Signature 1,Figure 5,10 January 2021,Nadine Ulysse,WikiWorks,Third-party fecal microbiota transplantation (FMT) may restore intestinal microbiome diversity after allogeneic hematopoietic cell transplantation (allo-HCT),decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,1783272|1239|186801|186802,Complete,Rimsha Azhar
bsdb:29592876/4/1,29592876,time series / longitudinal observational,29592876,10.1182/bloodadvances.2018017731,NA,"DeFilipp Z., Peled J.U., Li S., Mahabamunuge J., Dagher Z., Slingerland A.E., Del Rio C., Valles B., Kempner M.E., Smith M., Brown J., Dey B.R., El-Jawahri A., McAfee S.L., Spitzer T.R., Ballen K.K., Sung A.D., Dalton T.E., Messina J.A., Dettmer K., Liebisch G., Oefner P., Taur Y., Pamer E.G., Holler E., Mansour M.K., van den Brink M.R.M., Hohmann E., Jenq R.R. , Chen Y.B.",Third-party fecal microbiota transplantation following allo-HCT reconstitutes microbiome diversity,Blood advances,2018,NA,Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,post fecal mircobiota day 30,post allogenic hematopoietic cell transplant/ pre Fecal microbiota transplant,patients who received Fecal Microbiome Transplant,5,13,2 days,16S,45,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,"HLA match,acute graft vs. host disease,age,history of GI,transplant conditioning",NA,NA,NA,NA,decreased,NA,Signature 1,Figure 5,10 January 2021,Nadine Ulysse,WikiWorks,Third-party fecal microbiota transplantation (FMT) may restore intestinal microbiome diversity after allogeneic hematopoietic cell transplantation (allo-HCT),decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,1783272|1239|186801|186802,Complete,Rimsha Azhar
bsdb:29596446/1/1,29596446,"cross-sectional observational, not case-control",29596446,10.1371/journal.pone.0194171,NA,"Barengolts E., Green S.J., Eisenberg Y., Akbar A., Reddivari B., Layden B.T., Dugas L. , Chlipala G.","Gut microbiota varies by opioid use, circulating leptin and oxytocin in African American men with diabetes and high burden of chronic disease",PloS one,2018,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Metaformin negative among Opoid negative,Metaformin positive,"Opioid use was defined as “Yes” if during review of medical record two parameters were present: 1) the participant was under care of psychiatric care professional, and 2) psychiatric care professional established the diagnosis of opioid use disorder as official diagnosis in medical record",34,21,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Yaseen Javaid,WikiWorks,the interactive influence of metformin and opioids on gut microbiota in the subgroup with diabetes.,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Shaimaa Elsafoury
bsdb:29596446/1/2,29596446,"cross-sectional observational, not case-control",29596446,10.1371/journal.pone.0194171,NA,"Barengolts E., Green S.J., Eisenberg Y., Akbar A., Reddivari B., Layden B.T., Dugas L. , Chlipala G.","Gut microbiota varies by opioid use, circulating leptin and oxytocin in African American men with diabetes and high burden of chronic disease",PloS one,2018,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Metaformin negative among Opoid negative,Metaformin positive,"Opioid use was defined as “Yes” if during review of medical record two parameters were present: 1) the participant was under care of psychiatric care professional, and 2) psychiatric care professional established the diagnosis of opioid use disorder as official diagnosis in medical record",34,21,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 4,10 January 2021,Yaseen Javaid,WikiWorks,the interactive influence of metformin and opioids on gut microbiota in the subgroup with diabetes.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,3379134|976|200643|171549|815|816|47678,Complete,Shaimaa Elsafoury
bsdb:29596446/2/1,29596446,"cross-sectional observational, not case-control",29596446,10.1371/journal.pone.0194171,NA,"Barengolts E., Green S.J., Eisenberg Y., Akbar A., Reddivari B., Layden B.T., Dugas L. , Chlipala G.","Gut microbiota varies by opioid use, circulating leptin and oxytocin in African American men with diabetes and high burden of chronic disease",PloS one,2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Metaformin negative among Opoid positive,Metaformin positive,"Opioid use was defined as “Yes” if during review of medical record two parameters were present: 1) the participant was under care of psychiatric care professional, and 2) psychiatric care professional established the diagnosis of opioid use disorder as official diagnosis in medical record",35,9,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,the interactive influence of metformin and opioids on gut microbiota in the subgroup with diabetes.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
bsdb:29596446/2/2,29596446,"cross-sectional observational, not case-control",29596446,10.1371/journal.pone.0194171,NA,"Barengolts E., Green S.J., Eisenberg Y., Akbar A., Reddivari B., Layden B.T., Dugas L. , Chlipala G.","Gut microbiota varies by opioid use, circulating leptin and oxytocin in African American men with diabetes and high burden of chronic disease",PloS one,2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Metaformin negative among Opoid positive,Metaformin positive,"Opioid use was defined as “Yes” if during review of medical record two parameters were present: 1) the participant was under care of psychiatric care professional, and 2) psychiatric care professional established the diagnosis of opioid use disorder as official diagnosis in medical record",35,9,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,the interactive influence of metformin and opioids on gut microbiota in the subgroup with diabetes.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Shaimaa Elsafoury
bsdb:29596446/3/1,29596446,"cross-sectional observational, not case-control",29596446,10.1371/journal.pone.0194171,NA,"Barengolts E., Green S.J., Eisenberg Y., Akbar A., Reddivari B., Layden B.T., Dugas L. , Chlipala G.","Gut microbiota varies by opioid use, circulating leptin and oxytocin in African American men with diabetes and high burden of chronic disease",PloS one,2018,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,opoid negative among Metaformin negative,Opoid positive,"Opioid use was defined as “Yes” if during review of medical record two parameters were present: 1) the participant was under care of psychiatric care professional, and 2) psychiatric care professional established the diagnosis of opioid use disorder as official diagnosis in medical record",34,35,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,the interactive influence of metformin and opioids on gut microbiota in the subgroup with diabetes.,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Shaimaa Elsafoury
bsdb:29596446/3/2,29596446,"cross-sectional observational, not case-control",29596446,10.1371/journal.pone.0194171,NA,"Barengolts E., Green S.J., Eisenberg Y., Akbar A., Reddivari B., Layden B.T., Dugas L. , Chlipala G.","Gut microbiota varies by opioid use, circulating leptin and oxytocin in African American men with diabetes and high burden of chronic disease",PloS one,2018,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,opoid negative among Metaformin negative,Opoid positive,"Opioid use was defined as “Yes” if during review of medical record two parameters were present: 1) the participant was under care of psychiatric care professional, and 2) psychiatric care professional established the diagnosis of opioid use disorder as official diagnosis in medical record",34,35,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,the interactive influence of metformin and opioids on gut microbiota in the subgroup with diabetes.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
bsdb:29608253/1/1,29608253,"cross-sectional observational, not case-control",29608253,10.1002/cam4.1471,NA,"Zhang C., Liu Y., Gao W., Pan Y., Gao Y., Shen J. , Xiong H.",The direct and indirect association of cervical microbiota with the risk of cervical intraepithelial neoplasia,Cancer medicine,2018,"16sRNA, HPV, cervical intraepithelial neoplasia, cervical microbiota, next-generation sequencing",Experiment 1,China,Homo sapiens,Uterus,UBERON:0000995,Cervical glandular intraepithelial neoplasia,EFO:1000165,Cervical Intraepithelial Neoplasis -1,Cervical Intraepithelial Neoplasis +2,NA,126,40,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Phyu Han,WikiWorks,LEfSe showing the differences in the 18 most abundant species according to Cervical Intraepithelial Neoplasia (CIN) status,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter ureolyticus",1783272|1239|91061|186826|33958|1578|47770;3379134|976|200643|171549|815|816|817;1783272|1239|91061|186826|1300|1301|1311;3379134|29547|3031852|213849|72294|194|827,Complete,Shaimaa Elsafoury
bsdb:29608253/1/2,29608253,"cross-sectional observational, not case-control",29608253,10.1002/cam4.1471,NA,"Zhang C., Liu Y., Gao W., Pan Y., Gao Y., Shen J. , Xiong H.",The direct and indirect association of cervical microbiota with the risk of cervical intraepithelial neoplasia,Cancer medicine,2018,"16sRNA, HPV, cervical intraepithelial neoplasia, cervical microbiota, next-generation sequencing",Experiment 1,China,Homo sapiens,Uterus,UBERON:0000995,Cervical glandular intraepithelial neoplasia,EFO:1000165,Cervical Intraepithelial Neoplasis -1,Cervical Intraepithelial Neoplasis +2,NA,126,40,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Phyu Han,WikiWorks,LEfSe showing the differences in the 18 most abundant species according to Cervical Intraepithelial Neoplasia (CIN) status,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium|s__Photobacterium damselae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus jensenii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae",3379134|1224|1236|135623|641|657|38293;1783272|1239|91061|186826|33958|1578|109790;1783272|201174|84998|84999|1643824|2767327|82135,Complete,Shaimaa Elsafoury
bsdb:29608253/2/1,29608253,"cross-sectional observational, not case-control",29608253,10.1002/cam4.1471,NA,"Zhang C., Liu Y., Gao W., Pan Y., Gao Y., Shen J. , Xiong H.",The direct and indirect association of cervical microbiota with the risk of cervical intraepithelial neoplasia,Cancer medicine,2018,"16sRNA, HPV, cervical intraepithelial neoplasia, cervical microbiota, next-generation sequencing",Experiment 2,China,Homo sapiens,Uterus,UBERON:0000995,Cervical glandular intraepithelial neoplasia,EFO:1000165,HPV -ve among pateints with Cervical Intraepithelial Neoplasia different severity status,HPV +ve,NA,130,36,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,LEfSe showing the differences in the 18 most abundant species according to HPV infection,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Stutzerimonas|s__Stutzerimonas stutzeri,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius",1783272|1239|91061|186826|1300|1301|1311;3379134|976|200643|171549|815|816|817;3379134|1224|1236|72274|135621|2901164|316;1783272|1239|186801|3082720|186804|1257|1261,Complete,Shaimaa Elsafoury
bsdb:29608253/2/2,29608253,"cross-sectional observational, not case-control",29608253,10.1002/cam4.1471,NA,"Zhang C., Liu Y., Gao W., Pan Y., Gao Y., Shen J. , Xiong H.",The direct and indirect association of cervical microbiota with the risk of cervical intraepithelial neoplasia,Cancer medicine,2018,"16sRNA, HPV, cervical intraepithelial neoplasia, cervical microbiota, next-generation sequencing",Experiment 2,China,Homo sapiens,Uterus,UBERON:0000995,Cervical glandular intraepithelial neoplasia,EFO:1000165,HPV -ve among pateints with Cervical Intraepithelial Neoplasia different severity status,HPV +ve,NA,130,36,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,LEfSe showing the differences in the 18 most abundant species according to HPV infection,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus delbrueckii,1783272|1239|91061|186826|33958|1578|1584,Complete,Shaimaa Elsafoury
bsdb:29624747/1/1,29624747,case-control,29624747,10.1111/pai.12904,NA,"Kourosh A., Luna R.A., Balderas M., Nance C., Anagnostou A., Devaraj S. , Davis C.M.",Fecal microbiome signatures are different in food-allergic children compared to siblings and healthy children,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2018,"T regulatory cells, environment, food allergy, genetics, microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,healthy control,child with food allergy,child with food allergy,21,22,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 3, Figure 4, Figure 5",10 January 2021,Lucy Mellor,"WikiWorks,Merit,Atrayees",Differentially abundant operational taxonomic units (OTUs) obsereved between food-allergic children and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes",1783272|1239|186801|186802|216572|216851|1971605;1783272|1239|186801|186802|216572|459786|351091,Complete,Atrayees
bsdb:29624747/1/2,29624747,case-control,29624747,10.1111/pai.12904,NA,"Kourosh A., Luna R.A., Balderas M., Nance C., Anagnostou A., Devaraj S. , Davis C.M.",Fecal microbiome signatures are different in food-allergic children compared to siblings and healthy children,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2018,"T regulatory cells, environment, food allergy, genetics, microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,healthy control,child with food allergy,child with food allergy,21,22,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 3, Figure 4, Figure 5",10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Differentially abundant operational taxonomic units (OTUs) obsereved between food-allergic children and healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae",1783272|1239|186801|3085636|186803|572511|1955243;3379134|1224|1236|135625|712|724|729,Complete,Atrayees
bsdb:29624747/2/1,29624747,case-control,29624747,10.1111/pai.12904,NA,"Kourosh A., Luna R.A., Balderas M., Nance C., Anagnostou A., Devaraj S. , Davis C.M.",Fecal microbiome signatures are different in food-allergic children compared to siblings and healthy children,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2018,"T regulatory cells, environment, food allergy, genetics, microbiome",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,healthy sibling,child with food allergy,child with food allergy,25,22,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 3, Figure 4, Figure 5",10 January 2021,Lucy Mellor,"WikiWorks,Merit,Atrayees",Differentially abundant operational taxonomic units (OTUs) obsereved between food-allergic children and their siblings,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.",1783272|1239|186801|186802|216572|459786|351091;1783272|1239|186801|186802|216572|216851|1971605,Complete,Atrayees
bsdb:29624747/2/2,29624747,case-control,29624747,10.1111/pai.12904,NA,"Kourosh A., Luna R.A., Balderas M., Nance C., Anagnostou A., Devaraj S. , Davis C.M.",Fecal microbiome signatures are different in food-allergic children compared to siblings and healthy children,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2018,"T regulatory cells, environment, food allergy, genetics, microbiome",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,healthy sibling,child with food allergy,child with food allergy,25,22,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 3, Figure 4, Figure 5",10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Differentially abundant operational taxonomic units (OTUs) obsereved between food-allergic children and their siblings,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp.",3379134|1224|1236|135625|712|724|729;1783272|1239|186801|3085636|186803|572511|1955243;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|171550|239759|1872444,Complete,Atrayees
bsdb:29624747/3/1,29624747,case-control,29624747,10.1111/pai.12904,NA,"Kourosh A., Luna R.A., Balderas M., Nance C., Anagnostou A., Devaraj S. , Davis C.M.",Fecal microbiome signatures are different in food-allergic children compared to siblings and healthy children,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2018,"T regulatory cells, environment, food allergy, genetics, microbiome",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,healthy control,healthy sibling,sibling with no food allergy,21,25,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 3, Figure 4, Figure 5",10 January 2021,Lucy Mellor,WikiWorks,Differentially abundant operational taxonomic units (OTUs) obsereved between non-food-allergic siblings and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp.",1783272|1239|186801|186802|216572|459786|351091;1783272|1239|186801|186802|216572|216851|1971605;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|171550|239759|1872444,Complete,Atrayees
bsdb:29624747/3/2,29624747,case-control,29624747,10.1111/pai.12904,NA,"Kourosh A., Luna R.A., Balderas M., Nance C., Anagnostou A., Devaraj S. , Davis C.M.",Fecal microbiome signatures are different in food-allergic children compared to siblings and healthy children,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2018,"T regulatory cells, environment, food allergy, genetics, microbiome",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,healthy control,healthy sibling,sibling with no food allergy,21,25,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 3, Figure 4, Figure 5",10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Differentially abundant operational taxonomic units (OTUs) obsereved between non-food-allergic siblings and healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae",1783272|1239|186801|3085636|186803|572511|1955243;3379134|1224|1236|135625|712|724|729,Complete,Atrayees
bsdb:29624747/4/1,29624747,case-control,29624747,10.1111/pai.12904,NA,"Kourosh A., Luna R.A., Balderas M., Nance C., Anagnostou A., Devaraj S. , Davis C.M.",Fecal microbiome signatures are different in food-allergic children compared to siblings and healthy children,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2018,"T regulatory cells, environment, food allergy, genetics, microbiome",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,<7 years,7-18 years,child age 7-18,26,42,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text,10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Differentially abundant taxons in children <7 years compared to children 7-18 years,increased,"k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes",3379134|976;1783272|1239|186801|186802|216572|459786|351091,Complete,Atrayees
bsdb:29624747/4/2,29624747,case-control,29624747,10.1111/pai.12904,NA,"Kourosh A., Luna R.A., Balderas M., Nance C., Anagnostou A., Devaraj S. , Davis C.M.",Fecal microbiome signatures are different in food-allergic children compared to siblings and healthy children,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2018,"T regulatory cells, environment, food allergy, genetics, microbiome",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,<7 years,7-18 years,child age 7-18,26,42,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Text,10 January 2021,Lucy Mellor,WikiWorks,Differentially abundant taxons in children <7 years compared to children 7-18 years,decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",1783272|1239;3379134|1224;1783272|1239|526524|526525|128827;1783272|1239|186801|3085636|186803;1783272|1239|186801|3082720|186804,Complete,Atrayees
bsdb:29625474/1/1,29625474,case-control,29625474,10.1167/iovs.17-22677,NA,"Huang X., Ye Z., Cao Q., Su G., Wang Q., Deng J., Zhou C., Kijlstra A. , Yang P.",Gut Microbiota Composition and Fecal Metabolic Phenotype in Patients With Acute Anterior Uveitis,Investigative ophthalmology & visual science,2018,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Anterior uveitis,EFO:1000811,N (Healthy Controls),AAU (Acute Anterior Uveitis Patients),Patients diagnosed with Acute Anterior Uveitis (AAU),40,38,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,ethnic group,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Figure 2, 3",16 July 2025,Anne-mariesharp,Anne-mariesharp,Taxa difference between AAU patients and healthy controls,increased,",k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Thermotogati|p__Deinococcota|c__Deinococci,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Pseudoxanthomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Tissierellia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",;3379134|1224|28216|80840|119060|32008;3384194|1297|188787;3379134|1224|1236|135619|28256;3379134|1224|1236|135619|28256|2745;1783272|1239|909932;3379134|1224|1236|135619;3379134|976|200643|171549|171552|577309;3379134|1224|1236|135614|32033|83618;1783272|1239|909932|909929;1783272|1239|909932|909929|1843491|970;1783272|1239|1737404;1783272|1239|909932|1843489|31977|29465,Complete,KateRasheed
bsdb:29625474/1/2,29625474,case-control,29625474,10.1167/iovs.17-22677,NA,"Huang X., Ye Z., Cao Q., Su G., Wang Q., Deng J., Zhou C., Kijlstra A. , Yang P.",Gut Microbiota Composition and Fecal Metabolic Phenotype in Patients With Acute Anterior Uveitis,Investigative ophthalmology & visual science,2018,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Anterior uveitis,EFO:1000811,N (Healthy Controls),AAU (Acute Anterior Uveitis Patients),Patients diagnosed with Acute Anterior Uveitis (AAU),40,38,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,ethnic group,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Figure 2, 3",16 July 2025,Anne-mariesharp,Anne-mariesharp,Taxa difference between AAU patients and healthy controls,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Chelativorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Desemzia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Halanaerobiales|f__Halanaerobiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Halanaerobiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Halanaerobiales|f__Halanaerobiaceae|g__Halocella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Methanobacteriati|p__Methanobacteriota,k__Methanobacteriati|p__Methanobacteriota|c__Methanomicrobia|o__Methanomicrobiales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Pusillimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Sporosarcina,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Symbiobacteriaceae|g__Symbiobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Thermosediminibacterales|f__Tepidanaerobacteraceae|g__Tepidanaerobacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tepidimicrobiaceae|g__Tepidimicrobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Ureibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family III. Incertae Sedis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Symbiobacteriaceae",3379134|1224|28216|80840|506;;3379134|976|200643|171549|2005519|397864;1783272|1239|186801|3085636|186803|572511;1783272|1239|91061|186826|186828;1783272|1239|91061|1385|186818;3379134|1224|28211|356|69277|449972;1783272|1239|186801|186802|31979|1485;1783272|1239|91061|186826|186828|82800;3379134|200940|3024418|213118;3379134|200940|3031451|3024411|213121;3379134|200940|3031451|3024411|213121|893;1783272|1239|186801|3085636|186803|189330;1783272|1239|526524|526525|128827;1783272|1239|91061|186826|186828|117563;1783272|1239|186801|53433|972;1783272|1239|186801|53433;1783272|1239|186801|53433|972|46466;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803;3366610|28890;3366610|28890|224756|2191;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|3082720|186804;3379134|1224|1236|72274|135621;3379134|1224|1236|72274|135621|286;3379134|1224|28216|80840|506|305976;1783272|1239|186801|3085636|186803|841;1783272|1239|91061|1385|186818|1569;1783272|1239|186801|186802|543349|2733;1783272|1239|186801|2770089|2770092|499228;1783272|1239|1737404|1737405|2992719|285105;1783272|1239|91061|1385|186818|160795;1783272|1239|186801|186802|1689146;1783272|1239|186801|186802|543349,Complete,KateRasheed
bsdb:29625474/2/1,29625474,case-control,29625474,10.1167/iovs.17-22677,NA,"Huang X., Ye Z., Cao Q., Su G., Wang Q., Deng J., Zhou C., Kijlstra A. , Yang P.",Gut Microbiota Composition and Fecal Metabolic Phenotype in Patients With Acute Anterior Uveitis,Investigative ophthalmology & visual science,2018,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Anterior uveitis,EFO:1000811,N (Healthy Controls),AAU (Acute Anterior Uveitis Patients),Patients diagnosed with Acute Anterior Uveitis (AAU),40,38,3 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,"age,ethnic group,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table S1,16 July 2025,Anne-mariesharp,Anne-mariesharp,List of significantly different gut microbiota between AAU patients and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|909932;1783272|1239|909932|909929;1783272|1239|909932|1843489|31977|29465,Complete,KateRasheed
bsdb:29625474/2/2,29625474,case-control,29625474,10.1167/iovs.17-22677,NA,"Huang X., Ye Z., Cao Q., Su G., Wang Q., Deng J., Zhou C., Kijlstra A. , Yang P.",Gut Microbiota Composition and Fecal Metabolic Phenotype in Patients With Acute Anterior Uveitis,Investigative ophthalmology & visual science,2018,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Anterior uveitis,EFO:1000811,N (Healthy Controls),AAU (Acute Anterior Uveitis Patients),Patients diagnosed with Acute Anterior Uveitis (AAU),40,38,3 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,"age,ethnic group,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table S1,16 July 2025,Anne-mariesharp,"Anne-mariesharp,Poornima,Ese",List of significantly different gut microbiota between AAU patients and healthy controls,decreased,",k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia glucerasea,k__Thermotogati|p__Deinococcota|c__Deinococci,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|s__Peptostreptococcaceae bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Pseudoxanthomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Pusillimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|s__Selenomonadales bacterium Marseille-P2399,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas dianae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Sporosarcina,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Symbiobacteriaceae|g__Symbiobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales,k__Methanobacteriati|p__Methanobacteriota",;1783272|1239|186801|3085636|186803|572511|536633;3384194|1297|188787;3379134|200940|3024418|213118;1783272|1239|91061|186826|186828|117563;1783272|1239|186801|3085636|186803|1898203;1783272|1239|909932;3379134|1224|1236|135619;3379134|976|200643|171549|171552|577309;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1904861;3379134|1224|1236|135614|32033|83618;3379134|1224|28216|80840|506|305976;1783272|1239|186801|3085636|186803|841;1783272|1239|909932|909929|1806836;1783272|1239|909932|909929|1843491|970|135079;1783272|1239|91061|1385|186818|1569;1783272|1239|186801|186802|543349|2733;3379134|200940|3031451|3024411;3366610|28890,Complete,KateRasheed
bsdb:29625474/3/1,29625474,case-control,29625474,10.1167/iovs.17-22677,NA,"Huang X., Ye Z., Cao Q., Su G., Wang Q., Deng J., Zhou C., Kijlstra A. , Yang P.",Gut Microbiota Composition and Fecal Metabolic Phenotype in Patients With Acute Anterior Uveitis,Investigative ophthalmology & visual science,2018,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,"Anterior uveitis,Ankylosing spondylitis","EFO:0003898,EFO:1000811",Healthy Controls,AAU+ AS+ (Acute Anterior Uveitis Patients with Ankylosing Spondylitis),Patients diagnosed with Acute Anterior Uveitis (AAU) and Ankylosing Spondylitis (AS),40,17,3 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,"age,ethnic group,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S2,16 July 2025,Anne-mariesharp,Anne-mariesharp,"List of significantly different gut microbiota between AAU+
AS+ patients and healthy controls",increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,1783272|1239|909932|1843489|31977|29465,Complete,KateRasheed
bsdb:29625474/3/2,29625474,case-control,29625474,10.1167/iovs.17-22677,NA,"Huang X., Ye Z., Cao Q., Su G., Wang Q., Deng J., Zhou C., Kijlstra A. , Yang P.",Gut Microbiota Composition and Fecal Metabolic Phenotype in Patients With Acute Anterior Uveitis,Investigative ophthalmology & visual science,2018,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,"Anterior uveitis,Ankylosing spondylitis","EFO:0003898,EFO:1000811",Healthy Controls,AAU+ AS+ (Acute Anterior Uveitis Patients with Ankylosing Spondylitis),Patients diagnosed with Acute Anterior Uveitis (AAU) and Ankylosing Spondylitis (AS),40,17,3 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,"age,ethnic group,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S2,16 July 2025,Anne-mariesharp,Anne-mariesharp,"List of significantly different gut microbiota between AAU+
AS+ patients and healthy controls",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea",3379134|976|200643|171549|1853231|283168;1783272|1239|186801|3085636|186803|189330,Complete,KateRasheed
bsdb:29625474/4/1,29625474,case-control,29625474,10.1167/iovs.17-22677,NA,"Huang X., Ye Z., Cao Q., Su G., Wang Q., Deng J., Zhou C., Kijlstra A. , Yang P.",Gut Microbiota Composition and Fecal Metabolic Phenotype in Patients With Acute Anterior Uveitis,Investigative ophthalmology & visual science,2018,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Anterior uveitis,EFO:1000811,Healthy Controls,AAU+ AS- (Acute Anterior Uveitis Patients without Ankylosing Spondylitis),Patients diagnosed with Acute Anterior Uveitis (AAU) and who do not have Ankylosing Spondylitis (AS),40,21,3 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,"age,ethnic group,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S3,16 July 2025,Anne-mariesharp,Anne-mariesharp,"List of significantly different gut microbiota between AAU+
AS- patients and healthy controls",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella",1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|2005519|397864,Complete,KateRasheed
bsdb:29625474/5/1,29625474,case-control,29625474,10.1167/iovs.17-22677,NA,"Huang X., Ye Z., Cao Q., Su G., Wang Q., Deng J., Zhou C., Kijlstra A. , Yang P.",Gut Microbiota Composition and Fecal Metabolic Phenotype in Patients With Acute Anterior Uveitis,Investigative ophthalmology & visual science,2018,NA,Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Anterior uveitis,EFO:1000811,HLA-B27- (Human Leukocyte Antigen B27 negative) patients,HLA-B27+ (Human Leukocyte Antigen B27 positive) patients,Acute Anterior Uveitis patients that tested positive for Human Leukocyte Antigen B27 (HLA-B27),8,28,3 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S4,16 July 2025,Anne-mariesharp,Anne-mariesharp,List of significantly different gut microbiota between HLA-B27+ patients and HLA-B27- patients,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|201174|84998|84999|84107|102106,Complete,KateRasheed
bsdb:29632427/1/1,29632427,case-control,29632427,10.3748/wjg.v24.i13.1464,NA,"Ma H.Q., Yu T.T., Zhao X.J., Zhang Y. , Zhang H.J.",Fecal microbial dysbiosis in Chinese patients with inflammatory bowel disease,World journal of gastroenterology,2018,"16S ribosomal DNA, Chinese, Crohn’s disease, Microbial dysbiosis, Ulcerative colitis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Healthy controls,Patients with Crohn's disease,"Patients with Crohn's disease (11 with as active disease defined by CDAI > 150, 4 with inactive disease)",29,15,3 months,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,decreased,unchanged,NA,NA,Signature 1,Table 2,20 October 2022,Claregrieve1,"Claregrieve1,Suwaiba,WikiWorks",Differential microbial abundance between Crohn's patients and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,s__unidentified rumen bacterium RFN20",1783272|1239|91061|186826|186827|46123;3379134|1224|1236|91347|543|561;3379134|1224;1783272|1239|186801|186802|186806|113286;70463,Complete,Claregrieve1
bsdb:29632427/1/2,29632427,case-control,29632427,10.3748/wjg.v24.i13.1464,NA,"Ma H.Q., Yu T.T., Zhao X.J., Zhang Y. , Zhang H.J.",Fecal microbial dysbiosis in Chinese patients with inflammatory bowel disease,World journal of gastroenterology,2018,"16S ribosomal DNA, Chinese, Crohn’s disease, Microbial dysbiosis, Ulcerative colitis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Healthy controls,Patients with Crohn's disease,"Patients with Crohn's disease (11 with as active disease defined by CDAI > 150, 4 with inactive disease)",29,15,3 months,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,decreased,unchanged,NA,NA,Signature 2,Table 2,20 October 2022,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between Crohn's patients and healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis",1783272|1239|186801|186802|3085642|580596;1783272|1239|909932|909929|1843491|52225;3379134|1224|1236|135625|712|724;3379134|256845|1313211|278082|255528|172900,Complete,Claregrieve1
bsdb:29632427/2/1,29632427,case-control,29632427,10.3748/wjg.v24.i13.1464,NA,"Ma H.Q., Yu T.T., Zhao X.J., Zhang Y. , Zhang H.J.",Fecal microbial dysbiosis in Chinese patients with inflammatory bowel disease,World journal of gastroenterology,2018,"16S ribosomal DNA, Chinese, Crohn’s disease, Microbial dysbiosis, Ulcerative colitis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Healthy controls,Patients with ulcerative colitis,Patients with ulcerative colitis,29,14,3 months,16S,4,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Table 2,20 October 2022,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between ulcerative colitis patients and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Schwartzia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Spirochaetota",1783272|1239|91061|186826|186828|117563;1783272|1239|186801|3082720|186804|1257;1783272|1239|909932|909929|1843491|55506;3379134|976|117743|200644|49546|1016;3379134|1224;3379134|1224|1236|91347|543|561;3379134|1224|28216|80840|75682|29580;3379134|29547|3031852|213849|72294|194;1783272|201174|1760|2037|2049|1654;1783272|201174|84998|1643822|1643826|84111;1783272|201174|1760|85007|1653|1716;3379134|203691,Complete,Claregrieve1
bsdb:29632427/2/2,29632427,case-control,29632427,10.3748/wjg.v24.i13.1464,NA,"Ma H.Q., Yu T.T., Zhao X.J., Zhang Y. , Zhang H.J.",Fecal microbial dysbiosis in Chinese patients with inflammatory bowel disease,World journal of gastroenterology,2018,"16S ribosomal DNA, Chinese, Crohn’s disease, Microbial dysbiosis, Ulcerative colitis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Healthy controls,Patients with ulcerative colitis,Patients with ulcerative colitis,29,14,3 months,16S,4,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,Table 2,20 October 2022,Claregrieve1,"Claregrieve1,Merit,WikiWorks",Differential microbial abundance between ulcerative colitis patients and healthy controls,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Pseudomonadati|p__Lentisphaerota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|1853231|574697;3379134|200940|3031449|213115|194924|872;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|3085636|186803|140625;3379134|256845;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|909929|1843491|52225;3379134|1224|28216|80840|75682|846;3379134|976|200643|171549|171552|838;3384194|508458|649775|649776|3029088|638847;3384194|508458|649775|649776|649777|2753;3379134|256845|1313211|278082|255528|172900;3379134|976|200643|171549|171552|838|59823,Complete,Claregrieve1
bsdb:29632427/3/1,29632427,case-control,29632427,10.3748/wjg.v24.i13.1464,NA,"Ma H.Q., Yu T.T., Zhao X.J., Zhang Y. , Zhang H.J.",Fecal microbial dysbiosis in Chinese patients with inflammatory bowel disease,World journal of gastroenterology,2018,"16S ribosomal DNA, Chinese, Crohn’s disease, Microbial dysbiosis, Ulcerative colitis",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Patients with ulcerative colitis,Patients with Crohn's disease,Patients with Crohn's disease,14,15,3 months,16S,4,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,20 October 2022,Claregrieve1,"Claregrieve1,Suwaiba,Merit,WikiWorks",Differential abundance between patients with ulcerative colitis vs Crohn's disease,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia",1783272|1239|91061|186826|186827|46123|46125;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|186806|113286;1783272|201174|84998|1643822|1643826|84108,Complete,Claregrieve1
bsdb:29632427/3/2,29632427,case-control,29632427,10.3748/wjg.v24.i13.1464,NA,"Ma H.Q., Yu T.T., Zhao X.J., Zhang Y. , Zhang H.J.",Fecal microbial dysbiosis in Chinese patients with inflammatory bowel disease,World journal of gastroenterology,2018,"16S ribosomal DNA, Chinese, Crohn’s disease, Microbial dysbiosis, Ulcerative colitis",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Patients with ulcerative colitis,Patients with Crohn's disease,Patients with Crohn's disease,14,15,3 months,16S,4,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,20 October 2022,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance between patients with ulcerative colitis vs Crohn's disease,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propioniferax|s__Propioniferax innocua,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium",1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|437755;1783272|1239|91061|1385|90964|1279;3379134|976|117743|200644|49546|1016;3379134|1224|1236|135625|712|724;3379134|1224|28216|80840|75682|29580;3379134|1224|1236|135615|868|2717;3379134|1224|28216|80840|119060|47670;1783272|201174|1760|85009|31957|53456|1753;3379134|1224|1236|135622|267890|22;1783272|201174|1760|85007|1653|1716,Complete,Claregrieve1
bsdb:29659737/1/1,29659737,time series / longitudinal observational,29659737,https://doi.org/10.1093/cid/ciy265,NA,"Wood L.F., Brown B.P., Lennard K., Karaoz U., Havyarimana E., Passmore J.S., Hesseling A.C., Edlefsen P.T., Kuhn L., Mulder N., Brodie E.L., Sodora D.L. , Jaspan H.B.",Feeding-Related Gut Microbial Composition Associates With Peripheral T-Cell Activation and Mucosal Gene Expression in African Infants,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2018,NA,Experiment 1,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV mother to child transmission,EFO:0004595,Non-exclusively breastfed (NEBF) infants at 6 weeks,Exclusively breastfed (EBF) infants at 6 weeks.,EBF infants defined as infants fed breast milk only (except for prescribed medicine) from birth to the study visit(6 weeks).,55,44,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text: Gut Microbiota Is Altered by Feeding Modality- At 6 weeks, EBF infants had lower relative abundance of Streptococcus luteciae and supplementary Figure 2",20 October 2024,Adwan,"Adwan,Tosin,WikiWorks",Specific taxa differentially abundant in (exclusively breastfed) EBF versus (non-exclusively breastfed) NEBF infants at 6 Weeks. This study represents the gut microbial composition changes observed in non-exclusively breastfed (NEBF) infants compared to exclusively breastfed (EBF) infants.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus lutetiensis,1783272|1239|91061|186826|1300|1301|150055,Complete,Svetlana up
bsdb:29659737/2/1,29659737,time series / longitudinal observational,29659737,https://doi.org/10.1093/cid/ciy265,NA,"Wood L.F., Brown B.P., Lennard K., Karaoz U., Havyarimana E., Passmore J.S., Hesseling A.C., Edlefsen P.T., Kuhn L., Mulder N., Brodie E.L., Sodora D.L. , Jaspan H.B.",Feeding-Related Gut Microbial Composition Associates With Peripheral T-Cell Activation and Mucosal Gene Expression in African Infants,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2018,NA,Experiment 2,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV mother to child transmission,EFO:0004595,Non-exclusively breastfed (NEBF) infants at 14 weeks.,Exclusively breastfed (EBF) infants at 14 weeks.,EBF infants defined as infants fed breast milk only (except for prescribed medicine) from birth to the study visit(14 weeks).,67,17,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text: Gut Microbiota Is Altered by Feeding Modality-  (At 14 weeks, EBF infants had higher relative abundance of Streptococcus lactarius, as well as Actinomyces and Atopobium) and Supplementary Figure 2.",22 October 2024,Tosin,"Tosin,WikiWorks",Specific taxa differentially abundant in (exclusively breastfed) EBF versus (non-exclusively breastfed) NEBF infants at 14 Weeks. This study represents the gut microbial composition changes observed in non-exclusively breastfed (NEBF) infants compared to exclusively breastfed (EBF) infants.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus lactarius",1783272|201174|1760|2037|2049|1654;1783272|201174|84998|84999|1643824|1380;1783272|1239|91061|186826|1300|1301|684066,Complete,Svetlana up
bsdb:29659737/2/2,29659737,time series / longitudinal observational,29659737,https://doi.org/10.1093/cid/ciy265,NA,"Wood L.F., Brown B.P., Lennard K., Karaoz U., Havyarimana E., Passmore J.S., Hesseling A.C., Edlefsen P.T., Kuhn L., Mulder N., Brodie E.L., Sodora D.L. , Jaspan H.B.",Feeding-Related Gut Microbial Composition Associates With Peripheral T-Cell Activation and Mucosal Gene Expression in African Infants,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2018,NA,Experiment 2,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV mother to child transmission,EFO:0004595,Non-exclusively breastfed (NEBF) infants at 14 weeks.,Exclusively breastfed (EBF) infants at 14 weeks.,EBF infants defined as infants fed breast milk only (except for prescribed medicine) from birth to the study visit(14 weeks).,67,17,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Text: Gut Microbiota Is Altered by Feeding Modality- At 14 weeks, EBF infants had lower relative abundance of two Bacteroides OTUs and supplementary Figure 2.",22 October 2024,Tosin,"Tosin,WikiWorks",Specific taxa differentially abundant in (exclusively breastfed) EBF versus (non-exclusively breastfed) NEBF infants at 14 Weeks. This study represents the gut microbial composition changes observed in non-exclusively breastfed (NEBF) infants compared to exclusively breastfed (EBF) infants.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:29659737/3/1,29659737,time series / longitudinal observational,29659737,https://doi.org/10.1093/cid/ciy265,NA,"Wood L.F., Brown B.P., Lennard K., Karaoz U., Havyarimana E., Passmore J.S., Hesseling A.C., Edlefsen P.T., Kuhn L., Mulder N., Brodie E.L., Sodora D.L. , Jaspan H.B.",Feeding-Related Gut Microbial Composition Associates With Peripheral T-Cell Activation and Mucosal Gene Expression in African Infants,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2018,NA,Experiment 3,South Africa,Homo sapiens,Feces,UBERON:0001988,Cell activation,GO:0001775,Infants with Low HL-ADR (Human Leukocyte Antigen - DR isotype) expression on CD4 + T-cell,Infants with High HL-ADR (Human Leukocyte Antigen - DR isotype) expression on CD4 + T-cell,Infants with high CD4+HLA-DR+ T-cell frequency,NA,NA,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,24 October 2024,Tosin,"Tosin,WikiWorks","Gut microbial composition partially explains peripheral blood CD4+ T-cell activation. Significantly differentially abundant OTUs merged at the lowest taxonomic level in infants with high HLA-DR expression vs those with low HLA-DR expression, as computed by DeSeq2.",increased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,3379134|74201|203494|48461|1647988|239934|239935,Complete,Svetlana up
bsdb:29659737/3/2,29659737,time series / longitudinal observational,29659737,https://doi.org/10.1093/cid/ciy265,NA,"Wood L.F., Brown B.P., Lennard K., Karaoz U., Havyarimana E., Passmore J.S., Hesseling A.C., Edlefsen P.T., Kuhn L., Mulder N., Brodie E.L., Sodora D.L. , Jaspan H.B.",Feeding-Related Gut Microbial Composition Associates With Peripheral T-Cell Activation and Mucosal Gene Expression in African Infants,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2018,NA,Experiment 3,South Africa,Homo sapiens,Feces,UBERON:0001988,Cell activation,GO:0001775,Infants with Low HL-ADR (Human Leukocyte Antigen - DR isotype) expression on CD4 + T-cell,Infants with High HL-ADR (Human Leukocyte Antigen - DR isotype) expression on CD4 + T-cell,Infants with high CD4+HLA-DR+ T-cell frequency,NA,NA,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4B,24 October 2024,Tosin,"Tosin,WikiWorks","Gut microbial composition partially explains peripheral blood CD4+ T-cell activation. Significantly differentially abundant OTUs merged at the lowest taxonomic level in infants with high HLA-DR expression vs those with low HLA-DR expression, as computed by DeSeq2.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus lactarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Pantoea agglomerans",1783272|1239|91061|186826|1300|1301;1783272|201174|1760|85004|31953|1678|1681;1783272|1239|91061|186826|1300|1301|684066;1783272|1239|91061|1385|539738;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|91347|1903409|53335|549,Complete,Svetlana up
bsdb:29665823/1/1,29665823,laboratory experiment,29665823,10.1186/s12989-018-0252-6,NA,"Wang W., Zhou J., Chen M., Huang X., Xie X., Li W., Cao Q., Kan H., Xu Y. , Ying Z.",Exposure to concentrated ambient PM<sub>2.5</sub> alters the composition of gut microbiota in a murine model,Particle and fibre toxicology,2018,"Diabetes, Glucose homeostatic, Gut microbiota, PM2.5",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Air pollution,ENVO:02500037,mice exposed to PM 2.5 (CAP),mice exposed to filtered air (FA),male C57Bl/6 J mice exposed to PM2.5 (CAP),10,10,NA,16S,4,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,increased,increased,increased,NA,unchanged,Signature 1,Figure 4 & text,10 January 2021,Zyaijah Bailey,"Claregrieve1,WikiWorks",The differential taxa between FA- and CAP-exposed mice,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma sualvi,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella|s__Rikenella microfusus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium DW52",1783272|1239|186801|3085636|186803|248744;1783272|544448|31969|2085|2092|2093;1783272|544448|31969|2085|2092;1783272|544448|31969|2085;3379134|976|200643|171549|171550;3379134|976|200643|171549|171550|239759|214856;1783272|544448|2790996|2895623|2895509|2125;3379134|976|200643|171549|171550|28138|28139;1783272|1239|186801|3085636|186803|1837329,Complete,Claregrieve1
bsdb:29665823/1/2,29665823,laboratory experiment,29665823,10.1186/s12989-018-0252-6,NA,"Wang W., Zhou J., Chen M., Huang X., Xie X., Li W., Cao Q., Kan H., Xu Y. , Ying Z.",Exposure to concentrated ambient PM<sub>2.5</sub> alters the composition of gut microbiota in a murine model,Particle and fibre toxicology,2018,"Diabetes, Glucose homeostatic, Gut microbiota, PM2.5",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Air pollution,ENVO:02500037,mice exposed to PM 2.5 (CAP),mice exposed to filtered air (FA),male C57Bl/6 J mice exposed to PM2.5 (CAP),10,10,NA,16S,4,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,increased,increased,increased,NA,unchanged,Signature 2,Figure 4 & text,10 January 2021,Zyaijah Bailey,"Claregrieve1,WikiWorks",The differential taxa between FA- and CAP-exposed mice,decreased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. 001,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 10-1,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. Culture Jar-56,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter hepaticus",3379134|29547|3031852|213849;3379134|29547;3379134|29547|3031852|213849|72293|209;3379134|29547|3031852|213849|72293;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|31979|1485|1970093;1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|186803|1235800;1783272|1239|186801|186802|31979|1485|1003360;1783272|1239|186801|186802|216572|100175;1783272|1239|526524|526525|128827|174708;1783272|1239|526524|526525|2810281|191303;3379134|29547|3031852|213849|72293|209|32025,Complete,Claregrieve1
bsdb:29685174/1/1,29685174,"cross-sectional observational, not case-control",29685174,10.1186/s40168-018-0448-x,NA,"Fan X., Peters B.A., Jacobs E.J., Gapstur S.M., Purdue M.P., Freedman N.D., Alekseyenko A.V., Wu J., Yang L., Pei Z., Hayes R.B. , Ahn J.",Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults,Microbiome,2018,"16s rRNA genes, Alcohol consumption, Large population-based study, Oral microbiome",Experiment 1,United States of America,Homo sapiens,Mouth,UBERON:0000165,Alcohol drinking,EFO:0004329,Non-drinkers,Moderate drinkers,"> 0 but ≤ 1 drinks per day, on average, for women, and > 0 but ≤ 2 drinks per day, on average, for men",270,614,NA,16S,34,Roche454,raw counts,DESeq2,NA,TRUE,NA,NA,"age,body mass index,education level,race,sex,smoking status",NA,NA,NA,NA,increased,increased,Signature 1,Figure 3a,15 March 2023,Brian,"Brian,Suwaiba,Atrayees,WikiWorks",Heatmap of fold changes and the correlations of the taxa related to alcohol drinking level,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|171552|838;3379134|976|117743|200644|2762318|59735;1783272|201174|1760|85007|1653|1716;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|1129771|32067;3379134|1224|1236|135625|712;3379134|1224|1236|135625|712|416916;3379134|1224|1236|135615|868|2717;3379134|1224|28216|206351|481|538;3379134|1224|28216|206351|481|32257;3379134|1224|28216|206351|481|482;3379134|976|200643|171549,Complete,Atrayees
bsdb:29685174/1/2,29685174,"cross-sectional observational, not case-control",29685174,10.1186/s40168-018-0448-x,NA,"Fan X., Peters B.A., Jacobs E.J., Gapstur S.M., Purdue M.P., Freedman N.D., Alekseyenko A.V., Wu J., Yang L., Pei Z., Hayes R.B. , Ahn J.",Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults,Microbiome,2018,"16s rRNA genes, Alcohol consumption, Large population-based study, Oral microbiome",Experiment 1,United States of America,Homo sapiens,Mouth,UBERON:0000165,Alcohol drinking,EFO:0004329,Non-drinkers,Moderate drinkers,"> 0 but ≤ 1 drinks per day, on average, for women, and > 0 but ≤ 2 drinks per day, on average, for men",270,614,NA,16S,34,Roche454,raw counts,DESeq2,NA,TRUE,NA,NA,"age,body mass index,education level,race,sex,smoking status",NA,NA,NA,NA,increased,increased,Signature 2,Figure 3a,15 March 2023,Brian,"Brian,Suwaiba,WikiWorks",Heat map fold changes and the correlations of the taxa related to alcohol drinking level,decreased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans",1783272|1239|91061;1783272|1239|91061|186826|186828|117563|46124;1783272|1239|91061|186826|186828|117563|137732,Complete,Atrayees
bsdb:29685174/2/1,29685174,"cross-sectional observational, not case-control",29685174,10.1186/s40168-018-0448-x,NA,"Fan X., Peters B.A., Jacobs E.J., Gapstur S.M., Purdue M.P., Freedman N.D., Alekseyenko A.V., Wu J., Yang L., Pei Z., Hayes R.B. , Ahn J.",Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults,Microbiome,2018,"16s rRNA genes, Alcohol consumption, Large population-based study, Oral microbiome",Experiment 2,United States of America,Homo sapiens,Mouth,UBERON:0000165,Alcohol drinking,EFO:0004329,Non-drinkers,Heavy drinkers,Women and men who had greater than one or two drinks per day respectively,270,160,NA,16S,34,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,education level,race,sex,smoking status",NA,NA,NA,NA,increased,increased,Signature 1,Figure 3a,24 March 2023,Suwaiba,"Suwaiba,Atrayees,WikiWorks",Heatmap fold changes and the correlations of the taxa related to alcohol drinking level,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049|1654|55565;3379134|1224|1236|135625|712|416916;3379134|976|117743|200644|2762318|59735;1783272|1239|186801|3085636|186803|1164882;3384189|32066|203490|203491|1129771|32067;3379134|1224|28216|206351|481|482;3379134|1224|1236|135625|712;1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|2005525|195950;1783272|1239|91061|186826|186828|117563|137732;3379134|976|200643|171549,Complete,Atrayees
bsdb:29685174/2/2,29685174,"cross-sectional observational, not case-control",29685174,10.1186/s40168-018-0448-x,NA,"Fan X., Peters B.A., Jacobs E.J., Gapstur S.M., Purdue M.P., Freedman N.D., Alekseyenko A.V., Wu J., Yang L., Pei Z., Hayes R.B. , Ahn J.",Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults,Microbiome,2018,"16s rRNA genes, Alcohol consumption, Large population-based study, Oral microbiome",Experiment 2,United States of America,Homo sapiens,Mouth,UBERON:0000165,Alcohol drinking,EFO:0004329,Non-drinkers,Heavy drinkers,Women and men who had greater than one or two drinks per day respectively,270,160,NA,16S,34,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,education level,race,sex,smoking status",NA,NA,NA,NA,increased,increased,Signature 2,Figure 3a,24 March 2023,Suwaiba,"Suwaiba,WikiWorks",Heatmap of fold changes and the correlations of the taxa related to alcohol drinking level,decreased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans",1783272|1239|91061;1783272|1239|91061|186826;1783272|1239|91061|186826|186828|117563|46124;1783272|1239|91061|186826|186828|117563|137732,Complete,Atrayees
bsdb:29685174/4/1,29685174,"cross-sectional observational, not case-control",29685174,10.1186/s40168-018-0448-x,NA,"Fan X., Peters B.A., Jacobs E.J., Gapstur S.M., Purdue M.P., Freedman N.D., Alekseyenko A.V., Wu J., Yang L., Pei Z., Hayes R.B. , Ahn J.",Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults,Microbiome,2018,"16s rRNA genes, Alcohol consumption, Large population-based study, Oral microbiome",Experiment 4,United States of America,Homo sapiens,Mouth,UBERON:0000165,Alcohol drinking,EFO:0004329,Non-drinkers,Beer drinkers,Alcohol drinkers who drink beer exclusively,270,39,NA,16S,34,Roche454,raw counts,DESeq2,0.1,TRUE,NA,NA,"age,alcohol drinking,body mass index,education level,race,sex,smoking status",NA,increased,NA,NA,NA,increased,Signature 1,Figure 4a,24 March 2023,Suwaiba,"Suwaiba,WikiWorks",Heatmap of fold changes of correlations of the taxa related to alcohol drinking type,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Parascardovia",3379134|1224|1236|135625|712|416916;1783272|201174|1760|85004|31953|196082,Complete,Atrayees
bsdb:29685174/4/2,29685174,"cross-sectional observational, not case-control",29685174,10.1186/s40168-018-0448-x,NA,"Fan X., Peters B.A., Jacobs E.J., Gapstur S.M., Purdue M.P., Freedman N.D., Alekseyenko A.V., Wu J., Yang L., Pei Z., Hayes R.B. , Ahn J.",Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults,Microbiome,2018,"16s rRNA genes, Alcohol consumption, Large population-based study, Oral microbiome",Experiment 4,United States of America,Homo sapiens,Mouth,UBERON:0000165,Alcohol drinking,EFO:0004329,Non-drinkers,Beer drinkers,Alcohol drinkers who drink beer exclusively,270,39,NA,16S,34,Roche454,raw counts,DESeq2,0.1,TRUE,NA,NA,"age,alcohol drinking,body mass index,education level,race,sex,smoking status",NA,increased,NA,NA,NA,increased,Signature 2,Figure 4a,25 March 2023,Suwaiba,"Suwaiba,WikiWorks",Heatmap of fold changes and the correlations of the taxa related to alcohol drinking type,decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum",1783272|1239;3379134|976;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803|265975;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|1213720,Complete,Atrayees
bsdb:29685174/5/1,29685174,"cross-sectional observational, not case-control",29685174,10.1186/s40168-018-0448-x,NA,"Fan X., Peters B.A., Jacobs E.J., Gapstur S.M., Purdue M.P., Freedman N.D., Alekseyenko A.V., Wu J., Yang L., Pei Z., Hayes R.B. , Ahn J.",Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults,Microbiome,2018,"16s rRNA genes, Alcohol consumption, Large population-based study, Oral microbiome",Experiment 5,United States of America,Homo sapiens,Mouth,UBERON:0000165,Alcohol drinking,EFO:0004329,Non-drinkers,Liquor drinkers,Alcohol drinkers who exclusively drank liquor,270,26,NA,16S,34,Roche454,raw counts,DESeq2,0.1,TRUE,NA,NA,"age,alcohol drinking,body mass index,education level,race,sex,smoking status",NA,increased,NA,NA,NA,increased,Signature 1,Figure 4a,25 March 2023,Suwaiba,"Suwaiba,WikiWorks",Heatmap of fold changes and correlations of the taxa related to alcohol drinking type,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171552|838,Complete,Atrayees
bsdb:29685174/5/2,29685174,"cross-sectional observational, not case-control",29685174,10.1186/s40168-018-0448-x,NA,"Fan X., Peters B.A., Jacobs E.J., Gapstur S.M., Purdue M.P., Freedman N.D., Alekseyenko A.V., Wu J., Yang L., Pei Z., Hayes R.B. , Ahn J.",Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults,Microbiome,2018,"16s rRNA genes, Alcohol consumption, Large population-based study, Oral microbiome",Experiment 5,United States of America,Homo sapiens,Mouth,UBERON:0000165,Alcohol drinking,EFO:0004329,Non-drinkers,Liquor drinkers,Alcohol drinkers who exclusively drank liquor,270,26,NA,16S,34,Roche454,raw counts,DESeq2,0.1,TRUE,NA,NA,"age,alcohol drinking,body mass index,education level,race,sex,smoking status",NA,increased,NA,NA,NA,increased,Signature 2,Figure 4a,25 March 2023,Suwaiba,"Suwaiba,WikiWorks",Heatmap fold changes and correlations of taxa related to alcohol drinking type,decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Parascardovia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum",1783272|1239;3379134|976;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|3085636|186803|265975;1783272|201174|1760|85004|31953|196082;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|1213720,Complete,Atrayees
bsdb:29687353/1/1,29687353,case-control,29687353,10.1007/s00430-018-0542-5,NA,"Allali I., Boukhatem N., Bouguenouch L., Hardi H., Boudouaya H.A., Cadenas M.B., Ouldim K., Amzazi S., Azcarate-Peril M.A. , Ghazal H.",Gut microbiome of Moroccan colorectal cancer patients,Medical microbiology and immunology,2018,"16S rRNA sequencing, Bacterial community, Colorectal cancer, Gut microbiome composition, Moroccan population",Experiment 1,Morocco,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy control,colorectal cancer,untreated colorectal cancer patients,12,11,3 months,16S,12,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,"age,diet,region","body mass index,family history of cancer,sex",NA,NA,NA,NA,NA,unchanged,Signature 1,Table 2 and text,10 January 2021,Lora Kasselman,"Claregrieve1,WikiWorks",Differential microbial taxa between controls and CRC patients,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium",3379134|74201|203494|48461|1647988|239934;3379134|200940|3031449|213115|194924|35832;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|186807|51514;3379134|200940|3031449|213115|194924;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|541000;3379134|1224|28216|80840|75682|846;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836;1783272|1239|186801|186802|216572|1263;1783272|1239|909932|909929|1843491|970;1783272|1239|186801|3085636|186803;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|186806|1730,Complete,Claregrieve1
bsdb:29687353/1/2,29687353,case-control,29687353,10.1007/s00430-018-0542-5,NA,"Allali I., Boukhatem N., Bouguenouch L., Hardi H., Boudouaya H.A., Cadenas M.B., Ouldim K., Amzazi S., Azcarate-Peril M.A. , Ghazal H.",Gut microbiome of Moroccan colorectal cancer patients,Medical microbiology and immunology,2018,"16S rRNA sequencing, Bacterial community, Colorectal cancer, Gut microbiome composition, Moroccan population",Experiment 1,Morocco,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy control,colorectal cancer,untreated colorectal cancer patients,12,11,3 months,16S,12,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,"age,diet,region","body mass index,family history of cancer,sex",NA,NA,NA,NA,NA,unchanged,Signature 2,Table 2 and text,10 January 2021,Lora Kasselman,"Claregrieve1,WikiWorks",Differential microbial taxa between controls and CRC patients,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella",1783272|1239|909932|909929|1843491|158846;3379134|1224|28211|356|41294;1783272|1239|909932|909929|1843491|52225,Complete,Claregrieve1
bsdb:29738477/1/1,29738477,time series / longitudinal observational,29738477,10.3390/nu10050576,NA,"Klimenko N.S., Tyakht A.V., Popenko A.S., Vasiliev A.S., Altukhov I.A., Ischenko D.S., Shashkova T.I., Efimova D.A., Nikogosov D.A., Osipenko D.A., Musienko S.V., Selezneva K.S., Baranova A., Kurilshikov A.M., Toshchakov S.M., Korzhenkov A.A., Samarov N.I., Shevchenko M.A., Tepliuk A.V. , Alexeev D.G.",Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science Project,Nutrients,2018,"16S rRNA metagenomics, citizen science, gut microbiota, intervention, microbiome stability, personalized diet, responders",Experiment 1,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,"high vegetable, fruit, grain","Low vegetable, fruit, grains,",low fiber,215,215,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1 and Figure 2,10 January 2021,Lora Kasselman,WikiWorks,"Figure 1. Associations of the microbial taxa with long-term dietary habits and other factors from the questionnaire (n = 207 subjects). Analysis was performed for the baseline samples at taxonomic levels from species to phyla. Rows are sorted in alphabetic order. Cell color denotes the value of the linear model coefficient from the MaAsLin analysis. All significant associations (FDR adjusted p < 0.1) are marked with one of the symbols (&, #, @): “&”. Figure 2. Major changes in the gut community structure of the volunteers after following the dietary
recommendations. Red branches of the cladogram denote the taxa that were increased in abundance,
while the blue ones—decreased. Significance criterion: p < 0.05 in metagenomeSeq model and log10 of
the effect size >2 in LEfSe method (n = 430 paired samples).",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",3379134|976|200643|171549|815;3379134|976|200643|171549|171551;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572;1783272|1239|909932|1843488|909930;1783272|1239|909932|1843489|31977;3379134|1224|28216|80840|995019;3379134|200940|3031449|213115|194924;1783272|1239|91061|186826|33958,Complete,NA
bsdb:29738477/1/2,29738477,time series / longitudinal observational,29738477,10.3390/nu10050576,NA,"Klimenko N.S., Tyakht A.V., Popenko A.S., Vasiliev A.S., Altukhov I.A., Ischenko D.S., Shashkova T.I., Efimova D.A., Nikogosov D.A., Osipenko D.A., Musienko S.V., Selezneva K.S., Baranova A., Kurilshikov A.M., Toshchakov S.M., Korzhenkov A.A., Samarov N.I., Shevchenko M.A., Tepliuk A.V. , Alexeev D.G.",Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science Project,Nutrients,2018,"16S rRNA metagenomics, citizen science, gut microbiota, intervention, microbiome stability, personalized diet, responders",Experiment 1,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,"high vegetable, fruit, grain","Low vegetable, fruit, grains,",low fiber,215,215,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1 and Figure 2,10 January 2021,Lora Kasselman,WikiWorks,"Figure 1. Associations of the microbial taxa with long-term dietary habits and other factors from the questionnaire (n = 207 subjects). Analysis was performed for the baseline samples at taxonomic levels from species to phyla. Rows are sorted in alphabetic order. Cell color denotes the value of the linear model coefficient from the MaAsLin analysis. All significant associations (FDR adjusted p < 0.1) are marked with one of the symbols (&, #, @): “&”. Figure 2. Major changes in the gut community structure of the volunteers after following the dietary
recommendations. Red branches of the cladogram denote the taxa that were increased in abundance,
while the blue ones—decreased. Significance criterion: p < 0.05 in metagenomeSeq model and log10 of
the effect size >2 in LEfSe method (n = 430 paired samples).",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|459786;3366610|28890|183925|2158|2159;1783272|201174|1760|85004|31953;1783272|201174|84998|84999|84107;1783272|1239|91061|1385|90964;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|1300;1783272|1239|186801|3082768|424536;1783272|1239|186801|186802|31979;1783272|1239|526524|526525|128827;1783272|1239;3379134|1224|28211|204457|41297;3379134|1224|1236|91347|543;3379134|74201|203494|48461|203557,Complete,NA
bsdb:29738477/2/1,29738477,time series / longitudinal observational,29738477,10.3390/nu10050576,NA,"Klimenko N.S., Tyakht A.V., Popenko A.S., Vasiliev A.S., Altukhov I.A., Ischenko D.S., Shashkova T.I., Efimova D.A., Nikogosov D.A., Osipenko D.A., Musienko S.V., Selezneva K.S., Baranova A., Kurilshikov A.M., Toshchakov S.M., Korzhenkov A.A., Samarov N.I., Shevchenko M.A., Tepliuk A.V. , Alexeev D.G.",Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science Project,Nutrients,2018,"16S rRNA metagenomics, citizen science, gut microbiota, intervention, microbiome stability, personalized diet, responders",Experiment 2,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,before dietary intervention,two weeks after a dietry intervention,NA,215,215,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S8,10 January 2021,Shaimaa Elsafoury,WikiWorks,"Сhanges in relative abundance of microbial taxa after dietary intervention. The analysis was performed using metagenomeSeq. For each taxon, the columns “Beta” and “Eff. size” contain the values of linear model coefficient and effect size calculated using LEfSe.",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|186802|404402|404403;1783272|201174|84998|1643822|1643826|84111;1783272|1239|91061|186826|1300|1357|1358;1783272|201174|1760|85004|31953|1678|216816|1679;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|1300|1301;3379134|74201|203494|48461|203557;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|81852;3379134|74201|203494;3379134|74201|203494|48461;1783272|1239|186801|3085636|186803|189330|88431;3379134|74201;3379134|1224|28211;1783272|1239|186801|186802|186806|1730;1783272|1239|91061;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|31979;1783272|1239|186801|186802;1783272|1239|186801;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953;1783272|1239|186801|3085636|186803|572511,Complete,Shaimaa Elsafoury
bsdb:29738477/2/2,29738477,time series / longitudinal observational,29738477,10.3390/nu10050576,NA,"Klimenko N.S., Tyakht A.V., Popenko A.S., Vasiliev A.S., Altukhov I.A., Ischenko D.S., Shashkova T.I., Efimova D.A., Nikogosov D.A., Osipenko D.A., Musienko S.V., Selezneva K.S., Baranova A., Kurilshikov A.M., Toshchakov S.M., Korzhenkov A.A., Samarov N.I., Shevchenko M.A., Tepliuk A.V. , Alexeev D.G.",Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science Project,Nutrients,2018,"16S rRNA metagenomics, citizen science, gut microbiota, intervention, microbiome stability, personalized diet, responders",Experiment 2,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,before dietary intervention,two weeks after a dietry intervention,NA,215,215,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S8,10 January 2021,Shaimaa Elsafoury,"Fatima,WikiWorks","Сhanges in relative abundance of microbial taxa after dietary intervention. The analysis was performed using metagenomeSeq. For each taxon, the columns “Beta” and “Eff. size” contain the values of linear model coefficient and effect size calculated using LEfSe.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum",3379134|976|200643|171549|815|816|626929;3379134|976|200643|171549|815|816|28111;28221;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|91061|186826|33958;1783272|1239|909932|1843488|909930|33024|626940;3379134|976|200643|171549|815|909656|310297;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|186802|216572|1263;1783272|201174|84998|1643822|1643826|84108;1783272|201174|84998|1643822|1643826|84108|572010;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977;1783272|1239|186801|3085636|186803|2316020|46228;1783272|1239|186801|186802|216572|39492,Complete,Fatima
bsdb:29740427/1/1,29740427,prospective cohort,29740427,10.3389/fimmu.2018.00669,NA,"Han L., Jin H., Zhou L., Zhang X., Fan Z., Dai M., Lin Q., Huang F., Xuan L., Zhang H. , Liu Q.",Intestinal Microbiota at Engraftment Influence Acute Graft-Versus-Host Disease <i>via</i> the Treg/Th17 Balance in Allo-HSCT Recipients,Frontiers in immunology,2018,"acute graft-versus-host disease, allogeneic hematopoietic stem cell transplantation, histone acetylation, immune homeostasis, intestinal microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Graft versus host disease,MONDO:0013730,Grades 0-I (non-acute graft-host disease),Grades II-IV (acute graft-host-disease),patients diagnoised with acute graft-versus-host disease (aGVHD),49,32,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 1,"Figure 3a, b and text",10 January 2021,William Lam,WikiWorks,Differences of intestinal microbiota at engraftment between acute graft-verse-house disease (aGVHD) and non-acute graft-versus host disease (non-aGVHD) patients,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota",3379134|976|200643|171549|171551;3379134|1224|1236|91347|543;3379134|1224|1236|91347;3379134|1224|1236;3379134|1224,Complete,Atrayees
bsdb:29740427/1/2,29740427,prospective cohort,29740427,10.3389/fimmu.2018.00669,NA,"Han L., Jin H., Zhou L., Zhang X., Fan Z., Dai M., Lin Q., Huang F., Xuan L., Zhang H. , Liu Q.",Intestinal Microbiota at Engraftment Influence Acute Graft-Versus-Host Disease <i>via</i> the Treg/Th17 Balance in Allo-HSCT Recipients,Frontiers in immunology,2018,"acute graft-versus-host disease, allogeneic hematopoietic stem cell transplantation, histone acetylation, immune homeostasis, intestinal microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Graft versus host disease,MONDO:0013730,Grades 0-I (non-acute graft-host disease),Grades II-IV (acute graft-host-disease),patients diagnoised with acute graft-versus-host disease (aGVHD),49,32,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 2,"Figure 3a, b and text",10 January 2021,William Lam,WikiWorks,Differences of intestinal microbiota at engraftment between acute graft-verse-house disease (aGVHD) and non-acute graft-versus host disease (non-aGVHD) patients,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",1783272|1239|186801|186802|186806;1783272|1239|186801|3085636|186803;1783272|1239|186801|3082720|186804;1783272|1239|186801|186802|541000;1783272|1239|186801|186802;1783272|1239|186801;1783272|1239|526524|526525|128827;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|572511,Complete,Atrayees
bsdb:29740427/2/1,29740427,prospective cohort,29740427,10.3389/fimmu.2018.00669,NA,"Han L., Jin H., Zhou L., Zhang X., Fan Z., Dai M., Lin Q., Huang F., Xuan L., Zhang H. , Liu Q.",Intestinal Microbiota at Engraftment Influence Acute Graft-Versus-Host Disease <i>via</i> the Treg/Th17 Balance in Allo-HSCT Recipients,Frontiers in immunology,2018,"acute graft-versus-host disease, allogeneic hematopoietic stem cell transplantation, histone acetylation, immune homeostasis, intestinal microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Graft versus host disease,MONDO:0013730,standard conditioning,intensified conditioning,patients diagnoised with grade II to IV acute graft-versus-host disease (aGVHD) undergoing intense conditioning,19,13,NA,16S,4,Illumina,NA,NA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,increased,NA,Signature 1,"Figure 5a, b, c, d",10 January 2021,William Lam,WikiWorks,Differences in the intestinal microbiota (diversity and composition) are associated with conditioning intensity in allogeneic hematopoietic stem cell transplant (allo-HSCT) patients,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|541000,Complete,Atrayees
bsdb:29740427/3/1,29740427,prospective cohort,29740427,10.3389/fimmu.2018.00669,NA,"Han L., Jin H., Zhou L., Zhang X., Fan Z., Dai M., Lin Q., Huang F., Xuan L., Zhang H. , Liu Q.",Intestinal Microbiota at Engraftment Influence Acute Graft-Versus-Host Disease <i>via</i> the Treg/Th17 Balance in Allo-HSCT Recipients,Frontiers in immunology,2018,"acute graft-versus-host disease, allogeneic hematopoietic stem cell transplantation, histone acetylation, immune homeostasis, intestinal microbiota",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Graft versus host disease,MONDO:0013730,no b-lactum antibiotics,b-lactum antibiotics,"patients diagnoised with grade II to IV acute graft-versus-host disease (aGVHD) undergoing intense conditioning treated with b-lactum (include carbapenem, cephalosporin, and b-lactam-b-lactamase combinations.)",48,31,NA,16S,4,Illumina,NA,NA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 1,"Figure 4 a, b, d",10 January 2021,William Lam,WikiWorks,Differences in the intestinal microbiota (diversity and composition) are associated with Beta-Lactum antibiotic in allogeneic hematopoietic stem cell transplant (allo-HSCT) patients,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,1783272|1239|186801|3085636|186803,Complete,Atrayees
bsdb:29740427/4/1,29740427,prospective cohort,29740427,10.3389/fimmu.2018.00669,NA,"Han L., Jin H., Zhou L., Zhang X., Fan Z., Dai M., Lin Q., Huang F., Xuan L., Zhang H. , Liu Q.",Intestinal Microbiota at Engraftment Influence Acute Graft-Versus-Host Disease <i>via</i> the Treg/Th17 Balance in Allo-HSCT Recipients,Frontiers in immunology,2018,"acute graft-versus-host disease, allogeneic hematopoietic stem cell transplantation, histone acetylation, immune homeostasis, intestinal microbiota",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Graft versus host disease,MONDO:0013730,no vancomycin antibiotics,vancomycin antibiotics,patients diagnoised with grade II to IV acute graft-versus-host disease (aGVHD) undergoing intense conditioning treated with vancomycin,59,20,NA,16S,4,Illumina,NA,NA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 1,"Figure 4 a, b, d",10 January 2021,William Lam,WikiWorks,Differences in the intestinal microbiota (diversity and composition) are associated with Vancomycin antibiotic in allogeneic hematopoietic stem cell transplant (allo-HSCT) patients,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,Atrayees
bsdb:29756631/1/1,29756631,case-control,29756631,10.2340/00015555-2968,NA,"Deng Y., Wang H., Zhou J., Mou Y., Wang G. , Xiong X.",Patients with Acne Vulgaris Have a Distinct Gut Microbiota in Comparison with Healthy Controls,Acta dermato-venereologica,2018,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Acne,EFO:0003894,Healthy control group,Acne vulgaris group,"Patients with mild, moderate, severe and very severe acne",43,43,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 3A,6 March 2024,Scholastica,"Scholastica,ChiomaBlessing,WikiWorks",Bacterial taxa significantly enriched in acne samples (AS) compared to healthy control samples (CS),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota",3379134|976|200643|171549;3379134|976|200643;3379134|976,Complete,ChiomaBlessing
bsdb:29756631/1/2,29756631,case-control,29756631,10.2340/00015555-2968,NA,"Deng Y., Wang H., Zhou J., Mou Y., Wang G. , Xiong X.",Patients with Acne Vulgaris Have a Distinct Gut Microbiota in Comparison with Healthy Controls,Acta dermato-venereologica,2018,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Acne,EFO:0003894,Healthy control group,Acne vulgaris group,"Patients with mild, moderate, severe and very severe acne",43,43,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Figure 3A,6 March 2024,Scholastica,"Scholastica,ChiomaBlessing,WikiWorks",Bacterial taxa significantly abundant in acne samples (AS) compared to healthy control samples (CS),decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Oceanobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|91061|186826|186827;1783272|1239|91061|186826|186827|1375;1783272|1239|186801|3082720|3118656|114627;1783272|1239|91061|1385|186817;1783272|1239|91061|1385;1783272|1239|91061|1385|186817|1386;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|1239|91061|186826|186828;1783272|1239|91061|186826|186828|2747;1783272|1239|186801;1783272|1239|186801|186802|31979;28221;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;3379134|1224|28211|356|212791;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|204475;1783272|1239|91061|186826|186828|117563;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|1385|186817|400634;1783272|1239|91061|1385|186817|182709;3379134|1224|28216|80840|75682|846;1783272|1239|91061|1385|186822;1783272|1239|91061|1385|186822|44249;3379134|976|200643|171549|171552|577309;1783272|1239|91061|1385|186818;1783272|1239|186801|186802|216572|1263;1783272|1239;1783272|1239|186801|186802;1783272|1239|186801|186802|216572,Complete,ChiomaBlessing
bsdb:29758946/1/1,29758946,case-control,29758946,http://dx.doi. 438 org/10.3233/JAD-180176,NA,"Zhuang Z.Q., Shen L.L., Li W.W., Fu X., Zeng F., Gui L., Lü Y., Cai M., Zhu C., Tan Y.L., Zheng P., Li H.Y., Zhu J., Zhou H.D., Bu X.L. , Wang Y.J.",Gut Microbiota is Altered in Patients with Alzheimer's Disease,Journal of Alzheimer's disease : JAD,2018,"16S ribosomal RNA sequencing, Alzheimer’s disease, amyloid-β peptide, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healthy controls,Alzheimer's disease,Patients with active Alzheimer's disease,43,43,6 months,16S,34,Illumina,relative abundances,LEfSe,0.01,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 4 B,26 March 2024,Temitayo,"Temitayo,Peace Sandy,WikiWorks","Differences of bacterial taxa between AD and control group b) Histogram of the LDA scores for different abundant genera. Positive LDA scores indicate the enrichment of taxa
in AD group (red) relative to control group (green), and negative LDA scores indicate the depletion of taxa in AD group relative to control group. Box shows statistically significant different bacteria",increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella|s__Ezakiella coagulans,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas bennonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__uncultured Bacteroides sp.",1783272|201174;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|3082768|424536;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|33042|33043;1783272|1239|1737404|1582879|46507;1783272|201174|84998|1643822|1643826|644652|471189;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171551|836|501496;3379134|976|200643|171549|171552|838;3379134|1224|28211|204441|41295;3379134|1224|28211|204441;1783272|1239|186801|186802|31979|1266;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|216572|292632;3379134|976|200643|171549|815|816|162156,Complete,Peace Sandy
bsdb:29758946/1/2,29758946,case-control,29758946,http://dx.doi. 438 org/10.3233/JAD-180176,NA,"Zhuang Z.Q., Shen L.L., Li W.W., Fu X., Zeng F., Gui L., Lü Y., Cai M., Zhu C., Tan Y.L., Zheng P., Li H.Y., Zhu J., Zhou H.D., Bu X.L. , Wang Y.J.",Gut Microbiota is Altered in Patients with Alzheimer's Disease,Journal of Alzheimer's disease : JAD,2018,"16S ribosomal RNA sequencing, Alzheimer’s disease, amyloid-β peptide, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healthy controls,Alzheimer's disease,Patients with active Alzheimer's disease,43,43,6 months,16S,34,Illumina,relative abundances,LEfSe,0.01,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 4 B,26 March 2024,Temitayo,"Temitayo,Peace Sandy,WikiWorks","Differences of bacterial taxa between AD and control group b) Histogram of the LDA scores for different abundant genera. Positive LDA scores indicate the enrichment of taxa in AD group (red) relative to control group (green), and negative LDA scores indicate the depletion of taxa in AD group relative to control group. Box shows statistically significant different bacteria",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium varium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 10-1,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,s__uncultured bacterium,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus grandis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella secunda",1783272|1239|186801|3085636|186803|207244|105841;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|85831;1783272|1239|186801|3085636|186803|572511;3384194|1297|188787|118964;3384194|1297|188787|118964|183710|1298;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|216572|946234|292800;3384189|32066|203490|203491|203492|848|856;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|1898203;1783272|1239|186801|3085636|186803|1235800;1783272|1239|909932;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|909656|310297;1783272|1239|909932|909929;1783272|201174|84998|1643822|1643826|84108;1783272|1239|186801|3085636|186803|1213720;1783272|1239|526524|526525|2810280|3025755|1547;3379134|1224|1236|135623|641|662;3379134|1224|1236|135623|641;3379134|1224|1236|135623;1783272|1239|186801|186802|216572|1263;77133;3384194|1297|188787|118964|183710|1298|57498;3379134|1224|28216|80840|995019|577310|626947,Complete,Peace Sandy
bsdb:29764499/1/1,29764499,"cross-sectional observational, not case-control",29764499,10.1186/s40168-018-0472-x,NA,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum,Microbiome,2018,"Bacterial species, Body mass index, Gestational diabetes, Gestational hyperglycaemia, Glycaemic traits, Gut microbiota, Pregnancy",Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic  pregnancy,gestational diabetes mellitus (GDM) pregnancy,Women with gestational diabetes mellitus (GDM) pregnancy (third trimester) during the first visit,157,50,2 months,16S,12,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,FIG 2 (B),18 October 2024,Rahila,"Rahila,WikiWorks",Taxonomic biomarkers of gestational diabetes during 3rd trimester of pregnancy identified by linear discriminant analysis (LDA) using LEfSe .,increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",1783272|201174|84992;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037;1783272|201174;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;3379134|200940|3031449|213115|194924|872;1783272|1239|91061|186826|186828|117563;1783272|1239|91061|186826|33958|1243;1783272|201174|1760|85006|1268;1783272|1239|186801|3082720|543314|86331;33090|35493|3398|72025|3803|3814|508215;1783272|1239|91061|186826|33958,Complete,Svetlana up
bsdb:29764499/1/2,29764499,"cross-sectional observational, not case-control",29764499,10.1186/s40168-018-0472-x,NA,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum,Microbiome,2018,"Bacterial species, Body mass index, Gestational diabetes, Gestational hyperglycaemia, Glycaemic traits, Gut microbiota, Pregnancy",Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic  pregnancy,gestational diabetes mellitus (GDM) pregnancy,Women with gestational diabetes mellitus (GDM) pregnancy (third trimester) during the first visit,157,50,2 months,16S,12,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,FIG 2 (B),18 October 2024,Rahila,"Rahila,WikiWorks",Taxonomic biomarkers of gestational diabetes during 3rd trimester of pregnancy identified by linear discriminant analysis (LDA) using LEfSe .,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia",1783272|1239|186801|3085636|186803|653683;1783272|1239|186801|3120394|3120654|35829;1783272|1239|186801|3085636|186803|248744,Complete,Svetlana up
bsdb:29764499/2/1,29764499,"cross-sectional observational, not case-control",29764499,10.1186/s40168-018-0472-x,NA,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum,Microbiome,2018,"Bacterial species, Body mass index, Gestational diabetes, Gestational hyperglycaemia, Glycaemic traits, Gut microbiota, Pregnancy",Experiment 2,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Previous normoglycaemic  pregnancy,Previous GDM pregnancy,Women with gestational diabetes mellitus (GDM) pregnancy Postpartum (average of nine months) during second visit,82,43,2 months,16S,12,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 2 (D),18 October 2024,Rahila,"Rahila,WikiWorks",Taxonomic biomarkers of gestational diabetes during postpartum pregnancy identified by linear discriminant analysis (LDA) using LEfSe .,increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfitobacteriaceae|g__Dehalobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella",1783272|201174|84992;1783272|201174;1783272|1239|186801|186802|31979;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|1239|186801|186802|2937909|56112;3379134|1224|1236|91347|1903412|568;1783272|1239|186801|186802|404402;1783272|201174|84998|84999|1643824|133925,Complete,Svetlana up
bsdb:29764499/2/2,29764499,"cross-sectional observational, not case-control",29764499,10.1186/s40168-018-0472-x,NA,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum,Microbiome,2018,"Bacterial species, Body mass index, Gestational diabetes, Gestational hyperglycaemia, Glycaemic traits, Gut microbiota, Pregnancy",Experiment 2,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Previous normoglycaemic  pregnancy,Previous GDM pregnancy,Women with gestational diabetes mellitus (GDM) pregnancy Postpartum (average of nine months) during second visit,82,43,2 months,16S,12,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,FIG 2 (D),18 October 2024,Rahila,"Rahila,WikiWorks",Taxonomic biomarkers of gestational diabetes during postpartum pregnancy identified by linear discriminant analysis (LDA) using LEfSe .,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales",3384189|32066|203490|203491|203492;3384189|32066|203490|203491|203492|848;3379134|1224|1236|72274,Complete,Svetlana up
bsdb:29764499/3/1,29764499,"cross-sectional observational, not case-control",29764499,10.1186/s40168-018-0472-x,NA,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum,Microbiome,2018,"Bacterial species, Body mass index, Gestational diabetes, Gestational hyperglycaemia, Glycaemic traits, Gut microbiota, Pregnancy",Experiment 3,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Preceding normoglycaemic  pregnancy,Preceding gestational diabetes mellitus (GDM) pregnancy,Women with gestational diabetes mellitus (GDM) during third trimester pregnancy within  genus-level OTUs,79,43,2 months,16S,12,Illumina,raw counts,Wald Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,18 October 2024,Rahila,"Rahila,WikiWorks",Operational taxonomic units differentially abundant in women with and without gestational diabetes during third trimester pregnancy at the genus level,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|572511,Complete,Svetlana up
bsdb:29764499/3/2,29764499,"cross-sectional observational, not case-control",29764499,10.1186/s40168-018-0472-x,NA,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum,Microbiome,2018,"Bacterial species, Body mass index, Gestational diabetes, Gestational hyperglycaemia, Glycaemic traits, Gut microbiota, Pregnancy",Experiment 3,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Preceding normoglycaemic  pregnancy,Preceding gestational diabetes mellitus (GDM) pregnancy,Women with gestational diabetes mellitus (GDM) during third trimester pregnancy within  genus-level OTUs,79,43,2 months,16S,12,Illumina,raw counts,Wald Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S5,18 October 2024,Rahila,"Rahila,WikiWorks",Operational taxonomic units differentially abundant in women with and without gestational diabetes during third trimester pregnancy at the genus level,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Isobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",3379134|976|200643|171549|815|816;1783272|1239|91061|186826|186828|142587;3379134|1224|28216|80840|995019|40544;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|1392389;1783272|1239|186801|3120394|3120654|35829;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|186802|216572|216851,Complete,Svetlana up
bsdb:29764499/4/1,29764499,"cross-sectional observational, not case-control",29764499,10.1186/s40168-018-0472-x,NA,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum,Microbiome,2018,"Bacterial species, Body mass index, Gestational diabetes, Gestational hyperglycaemia, Glycaemic traits, Gut microbiota, Pregnancy",Experiment 4,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Previous normoglycaemic  pregnancy,Previous gestational diabetes mellitus (GDM) pregnancy,Women with gestational diabetes mellitus (GDM) average of 8.8 months  postpartum pregnancy within  genus-level OTUs,79,43,2 months,16S,12,Illumina,raw counts,Wald Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,18 October 2024,Rahila,"Rahila,WikiWorks,Poornima,Ese",Operational taxonomic units differentially abundant in women with and without gestational diabetes at postpartum pregnancy at the genus level,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax|s__Anaerovorax odorimutans,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Asaccharobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Cellulosibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Fusibacteraceae|g__Fusibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phreatobacteraceae|g__Phreatobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pseudocitrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Salinihabitans,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia sp.,k__Methanobacteriati|p__Methanobacteriota|c__Halobacteria|o__Halobacteriales|f__Natrialbaceae|g__Natrarchaeobaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|186801|3120394|3120654|35829;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|3082720|543314|109326;1783272|1239|186801|3082720|543314|109326|109327;1783272|201174|84998|1643822|1643826|553372;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|3085642|580596|2049021;1783272|1239|186801|3085636|186803|830;1783272|1239|186801|186802|216572|1246649;1783272|1239|186801|3082768|990719|990721;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|189330;3379134|1224|1236|91347|543|561;1783272|1239|186801|186802|216572|216851;1783272|1239|526524|526525|128827|1573534;1783272|1239|186801|186802|3679999|76008;1783272|1239|526524|526525|128827|61170;1783272|201174|84998|84999|1643824|133925;3379134|976|200643|171549|171552|577309|2049036;3379134|1224|28216|80840|995019|577310;3379134|1224|28211|356|2843305|1632780;3379134|976|200643|171549|171552|838;3379134|1224|1236|91347|543|1504576;1783272|1239|186801|186802|216572|1017280;1783272|1239|186801|3085636|186803|841;3379134|1224|28211|204455|2854170|1398404;1783272|201174|84998|84999|84107|1473205;3379134|1224|1236|91347|543|620;1783272|201174|84998|1643822|1643826|84108|2049041;3366610|28890|183963|2235|1644061|2765402;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|171551|836;1783272|1239|186801|186802|1392389;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:29764499/4/2,29764499,"cross-sectional observational, not case-control",29764499,10.1186/s40168-018-0472-x,NA,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum,Microbiome,2018,"Bacterial species, Body mass index, Gestational diabetes, Gestational hyperglycaemia, Glycaemic traits, Gut microbiota, Pregnancy",Experiment 4,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Previous normoglycaemic  pregnancy,Previous gestational diabetes mellitus (GDM) pregnancy,Women with gestational diabetes mellitus (GDM) average of 8.8 months  postpartum pregnancy within  genus-level OTUs,79,43,2 months,16S,12,Illumina,raw counts,Wald Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S5,18 October 2024,Rahila,"Rahila,WikiWorks",Operational taxonomic units differentially abundant in women with and without gestational diabetes at postpartum pregnancy at the genus level,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Isobaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|186828|142587;3379134|976|200643|171549|815|816;1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|186802|216572|216851,Complete,Svetlana up
bsdb:29764499/5/1,29764499,"cross-sectional observational, not case-control",29764499,10.1186/s40168-018-0472-x,NA,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum,Microbiome,2018,"Bacterial species, Body mass index, Gestational diabetes, Gestational hyperglycaemia, Glycaemic traits, Gut microbiota, Pregnancy",Experiment 5,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normal pre-pregnancy BMI,Overweight pre-pregnancy BMI,Pregnant women that shows overweight pre-pregnancy BMI,61,67,2 months,16S,12,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Figure S12,19 October 2024,Rahila,"Rahila,WikiWorks","Taxonomic biomarkers of overweight  down to genus level
identified by linear discriminant analysis (LDA) using LEfSe.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551|836,Complete,Svetlana up
bsdb:29764499/5/2,29764499,"cross-sectional observational, not case-control",29764499,10.1186/s40168-018-0472-x,NA,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum,Microbiome,2018,"Bacterial species, Body mass index, Gestational diabetes, Gestational hyperglycaemia, Glycaemic traits, Gut microbiota, Pregnancy",Experiment 5,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normal pre-pregnancy BMI,Overweight pre-pregnancy BMI,Pregnant women that shows overweight pre-pregnancy BMI,61,67,2 months,16S,12,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Figure S12,19 October 2024,Rahila,"Rahila,WikiWorks","Taxonomic biomarkers of overweight  down to genus level
identified by linear discriminant analysis (LDA) using LEfSe.",decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",3379134|74201|203494|48461|203557;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201;3379134|74201|203494|48461|1647988|239934;1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|186802|216572|253238;1783272|1239|186801|186802|216572|459786,Complete,Svetlana up
bsdb:29764499/6/1,29764499,"cross-sectional observational, not case-control",29764499,10.1186/s40168-018-0472-x,NA,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum,Microbiome,2018,"Bacterial species, Body mass index, Gestational diabetes, Gestational hyperglycaemia, Glycaemic traits, Gut microbiota, Pregnancy",Experiment 6,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normal pre-pregnancy BMI,obesity pre-pregnancy BMI,Pregnant women that shows obesity pre-pregnancy BMI,61,58,2 months,16S,12,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Figure S12,19 October 2024,Rahila,"Rahila,WikiWorks",Taxonomic biomarkers of Obesity down to genus level identified by linear discriminant analysis (LDA) using LEfSe.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus",3379134|976|200643|171549|171551|836;1783272|1239|909932|1843488|909930|904,Complete,Svetlana up
bsdb:29764499/6/2,29764499,"cross-sectional observational, not case-control",29764499,10.1186/s40168-018-0472-x,NA,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum,Microbiome,2018,"Bacterial species, Body mass index, Gestational diabetes, Gestational hyperglycaemia, Glycaemic traits, Gut microbiota, Pregnancy",Experiment 6,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normal pre-pregnancy BMI,obesity pre-pregnancy BMI,Pregnant women that shows obesity pre-pregnancy BMI,61,58,2 months,16S,12,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Figure S12,19 October 2024,Rahila,"Rahila,WikiWorks",Taxonomic biomarkers of Obesity down to genus level identified by linear discriminant analysis (LDA) using LEfSe.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",1783272|1239|186801|186802|216572|253238;1783272|1239|186801|186802|216572|44748;1783272|201174|84998|1643822|1643826|84111;1783272|1239|526524|526525|128827,Complete,Svetlana up
bsdb:29764499/7/1,29764499,"cross-sectional observational, not case-control",29764499,10.1186/s40168-018-0472-x,NA,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum,Microbiome,2018,"Bacterial species, Body mass index, Gestational diabetes, Gestational hyperglycaemia, Glycaemic traits, Gut microbiota, Pregnancy",Experiment 7,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Lean women,Overweight women,Women with Overweight  body mass index during third trimester of pregnancy,61,67,2 months,16S,12,Illumina,raw counts,Wald Test,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Table S10,19 October 2024,Rahila,"Rahila,WikiWorks",Operational taxonomic units differentially abundant in pregnant women between Overweight and  Lean pre-pregnancy body mass index,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,1783272|1239|186801|186802|216572|216851,Complete,Svetlana up
bsdb:29764499/7/2,29764499,"cross-sectional observational, not case-control",29764499,10.1186/s40168-018-0472-x,NA,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum,Microbiome,2018,"Bacterial species, Body mass index, Gestational diabetes, Gestational hyperglycaemia, Glycaemic traits, Gut microbiota, Pregnancy",Experiment 7,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Lean women,Overweight women,Women with Overweight  body mass index during third trimester of pregnancy,61,67,2 months,16S,12,Illumina,raw counts,Wald Test,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Table S10,19 October 2024,Rahila,"Rahila,WikiWorks",Operational taxonomic units differentially abundant in pregnant women between Overweight and  Lean pre-pregnancy body mass index,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,1783272|1239|186801|186802|216572|459786,Complete,Svetlana up
bsdb:29764499/8/1,29764499,"cross-sectional observational, not case-control",29764499,10.1186/s40168-018-0472-x,NA,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum,Microbiome,2018,"Bacterial species, Body mass index, Gestational diabetes, Gestational hyperglycaemia, Glycaemic traits, Gut microbiota, Pregnancy",Experiment 8,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Lean women,Obese women,Women with Obesity during third trimester of pregnancy,61,58,2 months,16S,12,Illumina,raw counts,Wald Test,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Table S10,19 October 2024,Rahila,"Rahila,WikiWorks",Operational taxonomic units differentially abundant in pregnant women between Obese and Lean pre-pregnancy body mass index,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|526524|526525|128827;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|216851,Complete,Svetlana up
bsdb:29764499/8/2,29764499,"cross-sectional observational, not case-control",29764499,10.1186/s40168-018-0472-x,NA,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum,Microbiome,2018,"Bacterial species, Body mass index, Gestational diabetes, Gestational hyperglycaemia, Glycaemic traits, Gut microbiota, Pregnancy",Experiment 8,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Lean women,Obese women,Women with Obesity during third trimester of pregnancy,61,58,2 months,16S,12,Illumina,raw counts,Wald Test,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Table S10,19 October 2024,Rahila,"Rahila,WikiWorks",Operational taxonomic units differentially abundant in pregnant women between Obese and Lean pre-pregnancy body mass index,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma",3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|100175;1783272|1239|186801|186802|216572|44748;1783272|544448|31969|186332|186333|2152,Complete,Svetlana up
bsdb:29764499/9/1,29764499,"cross-sectional observational, not case-control",29764499,10.1186/s40168-018-0472-x,NA,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum,Microbiome,2018,"Bacterial species, Body mass index, Gestational diabetes, Gestational hyperglycaemia, Glycaemic traits, Gut microbiota, Pregnancy",Experiment 9,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic adjusting for pre-pregnancy BMI,GDM adjusting for pre-pregnancy BMI,Pregnant women with GDM adjusted for pre-pregnancy BMI,143,43,2 months,16S,12,Illumina,raw counts,Wald Test,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Table S11.,19 October 2024,Rahila,"Rahila,WikiWorks","Operational taxonomic units differentially abundant in pregnant women with GDM and
normal glucose regulation adjusted for pre-pregnancy BMI",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|1239|186801|186802|216572|244127;1783272|1239|186801|186802|216572|216851,Complete,Svetlana up
bsdb:29764499/9/2,29764499,"cross-sectional observational, not case-control",29764499,10.1186/s40168-018-0472-x,NA,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum,Microbiome,2018,"Bacterial species, Body mass index, Gestational diabetes, Gestational hyperglycaemia, Glycaemic traits, Gut microbiota, Pregnancy",Experiment 9,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic adjusting for pre-pregnancy BMI,GDM adjusting for pre-pregnancy BMI,Pregnant women with GDM adjusted for pre-pregnancy BMI,143,43,2 months,16S,12,Illumina,raw counts,Wald Test,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Table S11.,19 October 2024,Rahila,"Rahila,WikiWorks","Operational taxonomic units differentially abundant in pregnant women with GDM and
normal glucose regulation adjusted for pre-pregnancy BMI",decreased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:29764499/10/1,29764499,"cross-sectional observational, not case-control",29764499,10.1186/s40168-018-0472-x,NA,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum,Microbiome,2018,"Bacterial species, Body mass index, Gestational diabetes, Gestational hyperglycaemia, Glycaemic traits, Gut microbiota, Pregnancy",Experiment 10,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic weight gain during pregnancy,GDM weight gain during pregnancy,Women weight gain during pregnancy adjusted for pre-pregnancy BMI and gestational age,143,43,2 months,16S,12,Illumina,raw counts,Wald Test,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Table S12,19 October 2024,Rahila,"Rahila,WikiWorks",Operational taxonomic units associated with weight gain during pregnancy adjusted for pre-pregnancy BMI and gestational age,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Tardiphaga",1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|186802|216572|216851;3379134|1224|28211|356|41294|1395974,Complete,Svetlana up
bsdb:29764499/10/2,29764499,"cross-sectional observational, not case-control",29764499,10.1186/s40168-018-0472-x,NA,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum,Microbiome,2018,"Bacterial species, Body mass index, Gestational diabetes, Gestational hyperglycaemia, Glycaemic traits, Gut microbiota, Pregnancy",Experiment 10,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic weight gain during pregnancy,GDM weight gain during pregnancy,Women weight gain during pregnancy adjusted for pre-pregnancy BMI and gestational age,143,43,2 months,16S,12,Illumina,raw counts,Wald Test,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Table S12,19 October 2024,Rahila,"Rahila,WikiWorks",Operational taxonomic units associated with weight gain during pregnancy adjusted for pre-pregnancy BMI and gestational age,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|44748;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:29765068/1/1,29765068,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P., Barnes D., Goulder A., Cui H., Roe D.J., Chase D.M. , Herbst-Kralovetz M.M.","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 1,United States of America,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ determined by the Linear Array HPV Genotyping Tests,20,31,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Enrichment in bacterial taxa in the HPV+ group when compared to HPV-negative control prior to adjusting,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens",3379134|976|200643|171549|171552|838;3384189|32066|203490|203491|1129771|168808|40543,Complete,Fatima Zohra
bsdb:29765068/1/2,29765068,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P., Barnes D., Goulder A., Cui H., Roe D.J., Chase D.M. , Herbst-Kralovetz M.M.","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 1,United States of America,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ determined by the Linear Array HPV Genotyping Tests,20,31,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Enrichment in bacterial taxa in the HPV+ group when compared to HPV-negative control prior to adjusting,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus lactolyticus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria|s__Fenollaria massiliensis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus mulieris,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus grossensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus",1783272|201174|1760|2037|2049|1654;1783272|1239|1737404|1737405|1570339|165779|33032;1783272|201174|1760|85004|31953|1678;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|1686313|938288;3384189|32066|203490|203491|203492|848|851;1783272|201174|1760|85004|31953|2701;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|1596;1783272|201174|1760|2037|2049|2050|2052;1783272|1239|1737404|1737405|1570339|162289|1465756;1783272|1239|91061|186826|1300|1301|1328,Complete,Fatima Zohra
bsdb:29765068/2/1,29765068,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P., Barnes D., Goulder A., Cui H., Roe D.J., Chase D.M. , Herbst-Kralovetz M.M.","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 2,United States of America,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,low grade dysplasia,low grade dysplasia confirmed by histology of colonoscopy-directed biopsy,20,12,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Enrichment in bacterial taxa in the low grade dysplasia  group when compared to HPV-negative control prior to adjusting,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemelliphila|s__Gemelliphila asaccharolytica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus mulieris,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens",1783272|201174|84998|84999|1643824|2767327|82135;1783272|1239|91061|1385|539738|3076174|502393;1783272|201174|1760|2037|2049|2050|2052;1783272|1239|1737404|1737405|1570339|543311;3384189|32066|203490|203491|1129771|168808|40543,Complete,Fatima Zohra
bsdb:29765068/2/2,29765068,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P., Barnes D., Goulder A., Cui H., Roe D.J., Chase D.M. , Herbst-Kralovetz M.M.","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 2,United States of America,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,low grade dysplasia,low grade dysplasia confirmed by histology of colonoscopy-directed biopsy,20,12,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Enrichment in bacterial taxa in the low grade dysplasia group when compared to HPV-negative control prior to adjusting,decreased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter ureolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Aedoeadaptatus|s__Aedoeadaptatus coxii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus duerdenii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus grossensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus",1783272|1239|1737404|1737405|1570339|165779|1287640;3379134|1224|1236|91347|1903410|71655;3379134|29547|3031852|213849|72294|194|827;3379134|1224|1236|91347|543|561;1783272|1239|1737404|1737405|1570339|150022|1260;3384189|32066|203490|203491|203492|848|851;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|47770;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|1737404|1737405|1570339|2981628|755172;1783272|1239|1737404|1737405|1570339|162289|507750;1783272|1239|1737404|1737405|1570339|162289|1465756;3379134|1224|1236|91347|543|620;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1328,Complete,Fatima Zohra
bsdb:29765068/3/1,29765068,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P., Barnes D., Goulder A., Cui H., Roe D.J., Chase D.M. , Herbst-Kralovetz M.M.","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 3,United States of America,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,high grade dysplasia,high grade dysplasia confirmed by histology of colonoscopy-directed biopsy,20,27,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Enrichment in bacterial taxa in the high grade dysplasia group when compared to HPV-negative control prior to adjusting,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae",1783272|201174|84998|84999|1643824|1380;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|1643824|2767327|82135;1783272|201174|1760|85004|31953|2701;3379134|976|200643|171549|171552|2974257|28127;1783272|1239|909932|1843489|31977|906;1783272|1239|1737404|1737405|1570339|543311;3379134|976|200643|171549|171552|838|419005;1783272|1239|186801|3085636|186803|177971;3384189|32066|203490|203491|1129771|168808;3384189|32066|203490|203491|1129771|168808|40543;1783272|1239|91061|186826|1300|1301|1311,Complete,Fatima Zohra
bsdb:29765068/3/2,29765068,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P., Barnes D., Goulder A., Cui H., Roe D.J., Chase D.M. , Herbst-Kralovetz M.M.","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 3,United States of America,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,high grade dysplasia,high grade dysplasia confirmed by histology of colonoscopy-directed biopsy,20,27,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Enrichment in bacterial taxa in the high grade dysplasia group when compared to HPV-negative control prior to adjusting,decreased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus lactolyticus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister propionicifaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria|s__Fenollaria massiliensis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Aedoeadaptatus|s__Aedoeadaptatus coxii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus duerdenii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus grossensis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella corporis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma",1783272|1239|1737404|1737405|1570339|165779|33032;1783272|1239|1737404|1737405|1570339|165779|1287640;1783272|201174|1760|85004|31953|1678;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|39948|308994;1783272|1239|186801|186802|1686313|938288;1783272|1239|1737404|1737405|1570339|150022|1260;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|1737404|1737405|1570339|2981628|755172;1783272|1239|1737404|1737405|1570339|162289|507750;1783272|1239|1737404|1737405|1570339|162289|1465756;1783272|1239|1737404|1737405|1570339|162289|33031;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838|28125;3379134|976|200643|171549|171552|838|28128;3379134|976|200643|171549|171552|838|28130;1783272|1239|91061|186826|1300|1301;1783272|544448|2790996|2790998|2129,Complete,Fatima Zohra
bsdb:29765068/4/1,29765068,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P., Barnes D., Goulder A., Cui H., Roe D.J., Chase D.M. , Herbst-Kralovetz M.M.","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 4,United States of America,Homo sapiens,Vagina,UBERON:0000996,Cervical cancer,MONDO:0002974,HPV-,invasive cervical carcinoma,invasive cervical carcinoma confirmed by histology of colonoscopy-directed biopsy,20,10,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Enrichment in bacterial taxa in the invasive cervical carcinoma group when compared to HPV-negative control prior to adjusting,increased,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,3384189|32066|203490|203491|1129771|168808|40543,Complete,Fatima Zohra
bsdb:29765068/4/2,29765068,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P., Barnes D., Goulder A., Cui H., Roe D.J., Chase D.M. , Herbst-Kralovetz M.M.","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 4,United States of America,Homo sapiens,Vagina,UBERON:0000996,Cervical cancer,MONDO:0002974,HPV-,invasive cervical carcinoma,invasive cervical carcinoma confirmed by histology of colonoscopy-directed biopsy,20,10,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Enrichment in bacterial taxa in the invasive cervical carcinoma group when compared to HPV-negative control prior to adjusting,decreased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus lactolyticus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister propionicifaciens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria|s__Fenollaria massiliensis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Aedoeadaptatus|s__Aedoeadaptatus coxii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus duerdenii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus grossensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella corporis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Winkia|s__Winkia neuii|s__Winkia neuii subsp. anitrata",1783272|1239|1737404|1737405|1570339|165779|33032;1783272|201174|1760|85004|31953|1678;3379134|1224|1236|91347|1903410|71655;1783272|201174|1760|85007|1653|1716;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|39948|308994;3379134|1224|1236|91347|543|561;1783272|1239|186801|186802|1686313|938288;3384189|32066|203490|203491|203492|848|851;1783272|1239|186801|186802|404402;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|47770;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|1737404|1737405|1570339|2981628|755172;1783272|1239|1737404|1737405|1570339|162289|507750;1783272|1239|1737404|1737405|1570339|162289|1465756;3379134|976|200643|171549|171552|838|28125;3379134|976|200643|171549|171552|838|28128;3379134|1224|1236|91347|543|620;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1328;1783272|544448|2790996|2790998|2129;1783272|201174|1760|2037|2049|2692118|33007|29318,Complete,Fatima Zohra
bsdb:29765068/5/1,29765068,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P., Barnes D., Goulder A., Cui H., Roe D.J., Chase D.M. , Herbst-Kralovetz M.M.","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 5,United States of America,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ determined by the Linear Array HPV Genotyping Tests,20,31,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,ethnic group",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing","Enrichment in bacterial taxa in the HPV+ group when compared to HPV-negative control after adjusting for age, BMI and ethnicity",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella",1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|906;1783272|201174|84998|84999|1643824|133925;1783272|1239|186801|3082720|186804|1257|1261;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|177971,Complete,Fatima Zohra
bsdb:29765068/5/2,29765068,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P., Barnes D., Goulder A., Cui H., Roe D.J., Chase D.M. , Herbst-Kralovetz M.M.","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 5,United States of America,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ determined by the Linear Array HPV Genotyping Tests,20,31,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,ethnic group",NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing","Enrichment in bacterial taxa in the HPV+ group when compared to HPV-negative control after adjusting for age, BMI and ethnicity",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus grossensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia",1783272|1239|91061|186826|186827|1375;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|1737404|1737405|1570339|165779|1287640;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|2701;3379134|976|200643|171549|171552|2974257|386414;1783272|1239|1737404|1737405|1570339|162289|1465756;3379134|976|200643|171549|171552|838|28125,Complete,Fatima Zohra
bsdb:29765068/6/1,29765068,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P., Barnes D., Goulder A., Cui H., Roe D.J., Chase D.M. , Herbst-Kralovetz M.M.","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 6,United States of America,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,low grade dysplasia,low grade dysplasia confirmed by histology of colonoscopy-directed biopsy,20,12,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,ethnic group",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing","Enrichment in bacterial taxa in the low grade dysplasia group when compared to HPV-negative control after adjusting for age, BMI and ethnicity",increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus lactolyticus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemelliphila|s__Gemelliphila asaccharolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus mulieris,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Winkia|s__Winkia neuii|s__Winkia neuii subsp. anitrata",1783272|1239|1737404|1737405|1570339|165779|33032;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|31979|1485;1783272|1239|909932|1843489|31977|39948;1783272|1239|91061|1385|539738|3076174|502393;3379134|976|200643|171549|171552|2974257|28127;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|91061|186826|33958|1578|147802;1783272|201174|1760|2037|2049|2050|2052;1783272|1239|186801|3082720|186804|1257|1261;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|419005;3379134|976|200643|171549|171552|838|28130;3384189|32066|203490|203491|1129771|168808;3384189|32066|203490|203491|1129771|168808|40543;1783272|201174|1760|2037|2049|2692118|33007|29318,Complete,Fatima Zohra
bsdb:29765068/6/2,29765068,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P., Barnes D., Goulder A., Cui H., Roe D.J., Chase D.M. , Herbst-Kralovetz M.M.","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 6,United States of America,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,low grade dysplasia,low grade dysplasia confirmed by histology of colonoscopy-directed biopsy,20,12,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,ethnic group",NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing","Enrichment in bacterial taxa in the low grade dysplasia group when compared to HPV-negative control after adjusting for age, BMI and ethnicity",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Aedoeadaptatus|s__Aedoeadaptatus coxii",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|47770;1783272|1239|1737404|1737405|1570339|2981628|755172,Complete,Fatima Zohra
bsdb:29765068/7/1,29765068,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P., Barnes D., Goulder A., Cui H., Roe D.J., Chase D.M. , Herbst-Kralovetz M.M.","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 7,United States of America,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,high grade dysplasia,high grade dysplasia confirmed by histology of colonoscopy-directed biopsy,20,27,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,ethnic group",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing","Enrichment in bacterial taxa in the high grade dysplasia group when compared to HPV-negative control after adjusting for age, BMI and ethnicity",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens",1783272|1239|186801|186802|31979|1485;1783272|201174|1760|85004|31953|2701;1783272|1239|91061|186826|33958|1578|147802;1783272|1239|909932|1843489|31977|906;1783272|1239|1737404|1737405|1570339|543311;3379134|976|200643|171549|171552|838|419005;1783272|1239|186801|3085636|186803|177971;3384189|32066|203490|203491|1129771|168808;3384189|32066|203490|203491|1129771|168808|40543,Complete,Fatima Zohra
bsdb:29765068/7/2,29765068,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P., Barnes D., Goulder A., Cui H., Roe D.J., Chase D.M. , Herbst-Kralovetz M.M.","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 7,United States of America,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,high grade dysplasia,high grade dysplasia confirmed by histology of colonoscopy-directed biopsy,20,27,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,ethnic group",NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Cynthia Anderson,"Fatima,WikiWorks,ChiomaBlessing","Enrichment in bacterial taxa in the high grade dysplasia group when compared to HPV-negative control after adjusting for age, BMI and ethnicity",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinotignum|s__Actinotignum schaalii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus lactolyticus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter ureolyticus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium coyleae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella|s__Ezakiella coagulans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria|s__Fenollaria massiliensis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Aedoeadaptatus|s__Aedoeadaptatus coxii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus duerdenii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus grossensis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia",1783272|201174|1760|2037|2049|1653174|59505;1783272|1239|91061|186826|186827|1375;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|1737404|1737405|1570339|165779|33032;1783272|1239|1737404|1737405|1570339|165779|1287640;1783272|201174|1760|85004|31953|1678;3379134|29547|3031852|213849|72294|194|827;1783272|201174|1760|85007|1653|1716|53374;1783272|1239|909932|1843489|31977|39948;1783272|1239|1737404|1582879|46507;1783272|1239|186801|186802|1686313|938288;1783272|1239|1737404|1737405|1570339|162290;1783272|201174|1760|85004|31953|2701;1783272|1239|186801|186802|404402;3379134|976|200643|171549|171552|2974257|28127;3379134|976|200643|171549|171552|2974257|386414;1783272|1239|1737404|1737405|1570339|2981628|755172;1783272|1239|1737404|1737405|1570339|162289|507750;1783272|1239|1737404|1737405|1570339|162289|1465756;1783272|1239|1737404|1737405|1570339|162289|33031;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838|28125,Complete,Fatima Zohra
bsdb:29765068/8/1,29765068,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P., Barnes D., Goulder A., Cui H., Roe D.J., Chase D.M. , Herbst-Kralovetz M.M.","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 8,United States of America,Homo sapiens,Vagina,UBERON:0000996,Cervical cancer,MONDO:0002974,HPV-,invasive cervical carcinoma,invasive cervical carcinoma confirmed by histology of colonoscopy-directed biopsy,20,10,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,ethnic group",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Cynthia Anderson,"Cynthia Anderson,Lwaldron,WikiWorks,ChiomaBlessing","Enrichment in bacterial taxa in the invasive cervical carcinoma group when compared to HPV-negative control after adjusting for age, BMI, and ethnicity",decreased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus grossensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia",1783272|1239|1737404|1737405|1570339|165779;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|2701;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|47770;1783272|1239|186801|3085636|186803|437755;1783272|1239|1737404|1737405|1570339|162289|1465756;3379134|976|200643|171549|171552|838|28125,Complete,Fatima
bsdb:29765068/9/1,29765068,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P., Barnes D., Goulder A., Cui H., Roe D.J., Chase D.M. , Herbst-Kralovetz M.M.","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 9,United States of America,Homo sapiens,Vagina,UBERON:0000996,"Human papilloma virus infection,Cervical cancer","EFO:0001668,MONDO:0002974",abnormal pH,normal pH,"HPV+ determined by the Linear Array HPV Genotyping Tests, low grade dysplasia,high grade dysplasia, invasive cervical carcinoma confirmed by histology of colonoscopy-directed biopsy,",20,74,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Enrichment in bacterial taxa in patients with abnormal pH vs. normal pH,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma hominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus mulieris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella montpellierensis",1783272|201174|84998|84999|1643824|1380;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|31979|1485;1783272|1239|91061|186826|81852|1350;3384189|32066|203490|203491|203492|848|851;1783272|201174|1760|85004|31953|2701;1783272|1239|91061|1385|539738|1378;1783272|1239|909932|1843489|31977|906;1783272|544448|2790996|2895623|2895509|2098;1783272|201174|1760|2037|2049|2050|2052;1783272|1239|186801|3085636|186803|437755;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|419005;3379134|976|200643|171549|171552|838|28130;1783272|1239|186801|3085636|186803|177971;3384189|32066|203490|203491|1129771|168808;3384189|32066|203490|203491|1129771|168808|40543;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1311;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|187328,Complete,Fatima Zohra
bsdb:29765068/9/2,29765068,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P., Barnes D., Goulder A., Cui H., Roe D.J., Chase D.M. , Herbst-Kralovetz M.M.","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 9,United States of America,Homo sapiens,Vagina,UBERON:0000996,"Human papilloma virus infection,Cervical cancer","EFO:0001668,MONDO:0002974",abnormal pH,normal pH,"HPV+ determined by the Linear Array HPV Genotyping Tests, low grade dysplasia,high grade dysplasia, invasive cervical carcinoma confirmed by histology of colonoscopy-directed biopsy,",20,74,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Enrichment in bacterial taxa in patients with abnormal pH vs. normal pH,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella",3379134|1224|1236|91347|1903410|71655;1783272|1239|186801|186802|31979|1485;3379134|1224|1236|91347|543|561;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|1596;3379134|1224|1236|91347|543|620,Complete,Fatima Zohra
bsdb:29765068/10/1,29765068,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P., Barnes D., Goulder A., Cui H., Roe D.J., Chase D.M. , Herbst-Kralovetz M.M.","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 10,United States of America,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,non-Hispanic,Hispanic,"HPV+ determined by the Linear Array HPV Genotyping Tests, low grade dysplasia,high grade dysplasia, invasive cervical carcinoma confirmed by histology of colonoscopy-directed biopsy,",53,47,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Enrichment in bacterial taxa in Hispanic vs. non-Hispanic group,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus mulieris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella montpellierensis",1783272|1239|91061|186826|186827|1375;1783272|201174|84998|84999|1643824|1380;1783272|1239|91061|186826|81852|1350;1783272|201174|84998|84999|1643824|2767327|82135;1783272|201174|1760|85004|31953|2701;1783272|1239|909932|1843489|31977|906;1783272|201174|1760|2037|2049|2050|2052;1783272|1239|186801|3085636|186803|437755;3379134|976|200643|171549|171551|836;1783272|1239|186801|3085636|186803|177971;3384189|32066|203490|203491|1129771|168808;3384189|32066|203490|203491|1129771|168808|40543;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|187328,Complete,Fatima Zohra
bsdb:29765068/10/2,29765068,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P., Barnes D., Goulder A., Cui H., Roe D.J., Chase D.M. , Herbst-Kralovetz M.M.","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,NA,Experiment 10,United States of America,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,non-Hispanic,Hispanic,"HPV+ determined by the Linear Array HPV Genotyping Tests, low grade dysplasia,high grade dysplasia, invasive cervical carcinoma confirmed by histology of colonoscopy-directed biopsy,",53,47,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Enrichment in bacterial taxa in Hispanic vs. non-Hispanic group,decreased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri",1783272|1239|1737404|1737405|1570339|165779|33037;3379134|976|200643|171549|171552|2974257|28127;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|1596,Complete,Fatima Zohra
bsdb:29771400/1/NA,29771400,"cross-sectional observational, not case-control",29771400,10.26355/eurrev_201805_14899,NA,"Wang X.M., Ma Z.Y. , Song N.","Inflammatory cytokines IL-6, IL-10, IL-13, TNF-α and peritoneal fluid flora were associated with infertility in patients with endometriosis",European review for medical and pharmacological sciences,2018,NA,Experiment 1,China,Homo sapiens,Uterovesical pouch,UBERON:0011049,Endometriosis,EFO:0001065,Non-endometriosis patients with infertility,Endometriosis patients with infertility,Patients were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).,30,55,NA,16S,45,Ion Torrent,NA,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:29774014/1/1,29774014,case-control,29774014,10.3389/fmicb.2018.00862,NA,"Yang C.Y., Yeh Y.M., Yu H.Y., Chin C.Y., Hsu C.W., Liu H., Huang P.J., Hu S.N., Liao C.T., Chang K.P. , Chang Y.L.",Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging,Frontiers in microbiology,2018,"16S rRNA sequencing, cancer progression, community dysbiosis, complexity, oral microbiome",Experiment 1,Taiwan,Homo sapiens,Mouth,UBERON:0000165,Squamous cell carcinoma,EFO:0000707,healthy controls,Stage 4,OSCC  confirmed by biopsy and pathological findings,51,90,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,NA,NA,unchanged,Signature 1,Figure 5,10 January 2021,Utsav Patel,"WikiWorks,Atrayees,ChiomaBlessing",Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging in Stage 4 group compared to healthy control group,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia|s__Alloscardovia omnicolens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera geminata,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Prevotella heparinolytica,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus",3379134|1224|1236|135625|712|416916|739;3379134|976|200643|171549|171552|1283313|1872471;1783272|201174|1760|85004|31953|419014|419015;1783272|1239|909932|1843489|31977|906|156456;3379134|976|200643|171549|815|816|28113;3379134|29547|3031852|213849|72294|194|824;3379134|29547|3031852|213849|72294|194|205;1783272|1239|909932|909929|1843491|82202;1783272|1239|909932|1843489|31977|39948|39950;3379134|1224|28216|206351|481|538|539;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|3082720|3118655|44259|143361;3384189|32066|203490|203491|203492|848|860;1783272|1239|91061|186826|186828|117563|137732;3379134|1224|1236|135625|712|724|727;3384189|32066|203490|203491|1129771|32067|104608;3379134|1224|28216|206351|481|482|495;3379134|1224|28216|206351|481|482|1107316;1783272|1239|186801|3085636|186803|265975|1969407;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171551|836|1924944;1783272|1239|909932|909929|1843491|970|2053611;1783272|1239|909932|909929|1843491|970|69823;1783272|1239|91061|186826|1300|1301|76860,Complete,Atrayees
bsdb:29774014/1/2,29774014,case-control,29774014,10.3389/fmicb.2018.00862,NA,"Yang C.Y., Yeh Y.M., Yu H.Y., Chin C.Y., Hsu C.W., Liu H., Huang P.J., Hu S.N., Liao C.T., Chang K.P. , Chang Y.L.",Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging,Frontiers in microbiology,2018,"16S rRNA sequencing, cancer progression, community dysbiosis, complexity, oral microbiome",Experiment 1,Taiwan,Homo sapiens,Mouth,UBERON:0000165,Squamous cell carcinoma,EFO:0000707,healthy controls,Stage 4,OSCC  confirmed by biopsy and pathological findings,51,90,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,NA,NA,unchanged,Signature 2,Figure 5,10 January 2021,Utsav Patel,"WikiWorks,Atrayees,ChiomaBlessing",Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging in Stage 4 group compared to healthy control group,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces gerencseriae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Pseudoleptotrichia|s__Pseudoleptotrichia goodfellowii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia georgiae",1783272|201174|1760|2037|2049|1654|52769;1783272|1239|91061|186826|186828|117563|46124;3379134|976|200643|171549|171552|2974257|425941;3379134|976|200643|171549|171552|838|28132;3384189|32066|203490|203491|1129771|2755140|157692;1783272|201174|1760|2037|2049|2529408|52768,Complete,Atrayees
bsdb:29774014/2/1,29774014,case-control,29774014,10.3389/fmicb.2018.00862,NA,"Yang C.Y., Yeh Y.M., Yu H.Y., Chin C.Y., Hsu C.W., Liu H., Huang P.J., Hu S.N., Liao C.T., Chang K.P. , Chang Y.L.",Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging,Frontiers in microbiology,2018,"16S rRNA sequencing, cancer progression, community dysbiosis, complexity, oral microbiome",Experiment 2,Taiwan,Homo sapiens,Mouth,UBERON:0000165,Squamous cell carcinoma,EFO:0000707,healthy controls,Stage 1,OSCC  confirmed by biopsy and pathological findings,51,41,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,increased,Signature 1,Supplementary Figure 5A,10 January 2021,Utsav Patel,"WikiWorks,ChiomaBlessing",Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging  in Stage 1 group compared to healthy control group,increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus",3379134|29547|3031852|213849|72294|194|205;1783272|1239|186801|3082720|3118655|44259|143361;3384189|32066|203490|203491|203492|848|860;1783272|1239|91061|186826|186828|117563|137732;3379134|1224|1236|135625|712|724|727;3379134|1224|28216|206351|481|482|1107316;1783272|1239|1737404|1737405|1570339|543311|33033;3379134|976|200643|171549|171551|836|1924944;1783272|1239|91061|186826|1300|1301|76860,Complete,ChiomaBlessing
bsdb:29774014/2/2,29774014,case-control,29774014,10.3389/fmicb.2018.00862,NA,"Yang C.Y., Yeh Y.M., Yu H.Y., Chin C.Y., Hsu C.W., Liu H., Huang P.J., Hu S.N., Liao C.T., Chang K.P. , Chang Y.L.",Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging,Frontiers in microbiology,2018,"16S rRNA sequencing, cancer progression, community dysbiosis, complexity, oral microbiome",Experiment 2,Taiwan,Homo sapiens,Mouth,UBERON:0000165,Squamous cell carcinoma,EFO:0000707,healthy controls,Stage 1,OSCC  confirmed by biopsy and pathological findings,51,41,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,increased,Signature 2,Supplementary Figure 5A,10 January 2021,Utsav Patel,"WikiWorks,ChiomaBlessing",Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging in Stage 1 group compared to healthy control group,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula",3379134|1224|1236|135625|712|724|729;3379134|976|200643|171549|171551|836|1583331;3379134|976|200643|171549|171552|838|28132;1783272|201174|1760|2037|2049|2529408|1660;1783272|1239|909932|1843489|31977|29465|29466,Complete,ChiomaBlessing
bsdb:29774014/3/1,29774014,case-control,29774014,10.3389/fmicb.2018.00862,NA,"Yang C.Y., Yeh Y.M., Yu H.Y., Chin C.Y., Hsu C.W., Liu H., Huang P.J., Hu S.N., Liao C.T., Chang K.P. , Chang Y.L.",Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging,Frontiers in microbiology,2018,"16S rRNA sequencing, cancer progression, community dysbiosis, complexity, oral microbiome",Experiment 3,Taiwan,Homo sapiens,Mouth,UBERON:0000165,Squamous cell carcinoma,EFO:0000707,healthy controls,Stage 2 & 3,OSCC  confirmed by biopsy and pathological findings,51,66,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,NA,NA,increased,Signature 1,Supplementary Figure 5B,10 January 2021,Utsav Patel,"WikiWorks,ChiomaBlessing",Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging in Stages 2 & 3 group compared to healthy control group,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera geminata,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus",3379134|1224|1236|135625|712|416916|739;1783272|1239|909932|1843489|31977|906|156456;3379134|29547|3031852|213849|72294|194|824;3379134|29547|3031852|213849|72294|194|205;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3082720|3118655|44259|143361;3384189|32066|203490|203491|203492|848|860;1783272|1239|91061|186826|186828|117563|137732;3379134|1224|1236|135625|712|724|727;1783272|1239|1737404|1737405|1570339|543311|33033;3379134|976|200643|171549|171551|836|1924944;1783272|1239|909932|909929|1843491|970|69823;1783272|1239|91061|186826|1300|1301|76860,Complete,ChiomaBlessing
bsdb:29774014/3/2,29774014,case-control,29774014,10.3389/fmicb.2018.00862,NA,"Yang C.Y., Yeh Y.M., Yu H.Y., Chin C.Y., Hsu C.W., Liu H., Huang P.J., Hu S.N., Liao C.T., Chang K.P. , Chang Y.L.",Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging,Frontiers in microbiology,2018,"16S rRNA sequencing, cancer progression, community dysbiosis, complexity, oral microbiome",Experiment 3,Taiwan,Homo sapiens,Mouth,UBERON:0000165,Squamous cell carcinoma,EFO:0000707,healthy controls,Stage 2 & 3,OSCC  confirmed by biopsy and pathological findings,51,66,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,NA,NA,increased,Signature 2,Supplementary Figure 5B,10 January 2021,Utsav Patel,"WikiWorks,ChiomaBlessing",Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging in Stages 2 & 3 group compared to healthy control group,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,p__Candidatus Absconditibacteriota|s__SR1 bacterium oral taxon 875",3379134|1224|1236|135625|712|724|729;3379134|976|200643|171549|171551|836|1583331;3379134|976|200643|171549|171552|838|28132;1783272|201174|1760|2037|2049|2529408|1660;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|909932|1843489|31977|29465|29466;221235|1226342,Complete,ChiomaBlessing
bsdb:29776865/1/1,29776865,case-control,29776865,10.1016/j.parkreldis.2018.05.007,https://pubmed.ncbi.nlm.nih.gov/29776865/,"Lin A., Zheng W., He Y., Tang W., Wei X., He R., Huang W., Su Y., Huang Y., Zhou H. , Xie H.",Gut microbiota in patients with Parkinson's disease in southern China,Parkinsonism & related disorders,2018,"16S rRNA next-generation-sequencing, Clinical motor phenotype, Gut microbiota, Parkinson's disease",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Controls,Parkinson's disease,"Patient diagnosed by a movement disorder specialist according to the 2015 Clinical Diagnostic Criteria for Parkinson's disease, from the International Parkinson and Movement Disorder Society, and were receiving the medications to treat PD at the time of this study.",45,75,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,1 February 2023,Jacquelynshevin,"Jacquelynshevin,WikiWorks",Specific microbial differences in taxa between PD and control in LEFSe and its adjusted P values.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae",1783272|1239|91061|186826|186827;1783272|201174|1760|85004|31953;3379134|200940|3031449|213115|194924;1783272|1239|186801|186802|186806,Complete,Fatima
bsdb:29776865/1/2,29776865,case-control,29776865,10.1016/j.parkreldis.2018.05.007,https://pubmed.ncbi.nlm.nih.gov/29776865/,"Lin A., Zheng W., He Y., Tang W., Wei X., He R., Huang W., Su Y., Huang Y., Zhou H. , Xie H.",Gut microbiota in patients with Parkinson's disease in southern China,Parkinsonism & related disorders,2018,"16S rRNA next-generation-sequencing, Clinical motor phenotype, Gut microbiota, Parkinson's disease",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Controls,Parkinson's disease,"Patient diagnosed by a movement disorder specialist according to the 2015 Clinical Diagnostic Criteria for Parkinson's disease, from the International Parkinson and Movement Disorder Society, and were receiving the medications to treat PD at the time of this study.",45,75,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,1 February 2023,Jacquelynshevin,"Jacquelynshevin,Aleru002,WikiWorks",Specific microbial differences in taxa between PD and control in LEFSe and its adjusted P values.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Methanobacteriati|p__Methanobacteriota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomonadales|f__Hyphomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Idiomarinaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae",1783272|201174|1760|2037|2049;1783272|1239;1783272|201174|1760|85006|85019;3379134|1224|28211|356|118882;3379134|1224|28216|80840|80864;3366610|28890;1783272|1239|91061|1385|539738;3379134|1224|1236|135619|28256;3379134|1224|28211|2800060|69657;3379134|1224|1236|135622|267893;1783272|201174|1760|85006|85021;1783272|1239|186801|3085636|186803;3366610|28890|183925|2158|2159;3379134|1224|28211|356|119045;1783272|201174|1760|85006|1268;1783272|544448;3379134|1224|1236|135625|712;3379134|1224|28211|204457|41297;1783272|1239|91061|186826|1300;3379134|1224|1236|135614|32033,Complete,Fatima
bsdb:29776865/2/1,29776865,case-control,29776865,10.1016/j.parkreldis.2018.05.007,https://pubmed.ncbi.nlm.nih.gov/29776865/,"Lin A., Zheng W., He Y., Tang W., Wei X., He R., Huang W., Su Y., Huang Y., Zhou H. , Xie H.",Gut microbiota in patients with Parkinson's disease in southern China,Parkinsonism & related disorders,2018,"16S rRNA next-generation-sequencing, Clinical motor phenotype, Gut microbiota, Parkinson's disease",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,PD duration less than 5 years,PD duration more than 5 years,"Patients with PD were classified into two groups according to disease duration: at least five years and less than five years.. Patients with PD were diagnosed by a movement disorder specialist according to the 2015 Clinical Diagnostic Criteria for Parkinson's disease, from the International Parkinson and Movement Disorder Society, and were receiving the medications to treat PD at the time of this study.",44,30,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,9 February 2023,Jacquelynshevin,"Jacquelynshevin,WikiWorks",Taxa identified as significant difference between clinical phenotypes.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",3379134|1224|1236|135625|712|416916;3379134|200930|68337|191393|191394;3379134|200930|68337|191393|2945020|248038;3379134|976|200643|171549|171550,Complete,Fatima
bsdb:29776865/2/2,29776865,case-control,29776865,10.1016/j.parkreldis.2018.05.007,https://pubmed.ncbi.nlm.nih.gov/29776865/,"Lin A., Zheng W., He Y., Tang W., Wei X., He R., Huang W., Su Y., Huang Y., Zhou H. , Xie H.",Gut microbiota in patients with Parkinson's disease in southern China,Parkinsonism & related disorders,2018,"16S rRNA next-generation-sequencing, Clinical motor phenotype, Gut microbiota, Parkinson's disease",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,PD duration less than 5 years,PD duration more than 5 years,"Patients with PD were classified into two groups according to disease duration: at least five years and less than five years.. Patients with PD were diagnosed by a movement disorder specialist according to the 2015 Clinical Diagnostic Criteria for Parkinson's disease, from the International Parkinson and Movement Disorder Society, and were receiving the medications to treat PD at the time of this study.",44,30,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,9 February 2023,Jacquelynshevin,"Jacquelynshevin,WikiWorks",Taxa identified as significant difference between clinical phenotypes.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,3379134|1224|28211|356|69277|28100,Complete,Fatima
bsdb:29776865/3/1,29776865,case-control,29776865,10.1016/j.parkreldis.2018.05.007,https://pubmed.ncbi.nlm.nih.gov/29776865/,"Lin A., Zheng W., He Y., Tang W., Wei X., He R., Huang W., Su Y., Huang Y., Zhou H. , Xie H.",Gut microbiota in patients with Parkinson's disease in southern China,Parkinsonism & related disorders,2018,"16S rRNA next-generation-sequencing, Clinical motor phenotype, Gut microbiota, Parkinson's disease",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Late-onset PD,Early-onset PD,Parkinson's disease patient with age of onset less than 50.,51,23,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 3,9 February 2023,Jacquelynshevin,"Jacquelynshevin,WikiWorks",Taxa identified as significant difference between clinical phenotypes.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",3379134|1224|28216|80840|506;1783272|1239|91061|186826|186827|66831;1783272|1239|186801|186802|216572|216851;3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|1300|1357;3379134|1224|28216|80840|995019|40544;3379134|1224|1236|135625|712;1783272|1239|186801|186802|31979|1485,Complete,Fatima
bsdb:29776865/3/2,29776865,case-control,29776865,10.1016/j.parkreldis.2018.05.007,https://pubmed.ncbi.nlm.nih.gov/29776865/,"Lin A., Zheng W., He Y., Tang W., Wei X., He R., Huang W., Su Y., Huang Y., Zhou H. , Xie H.",Gut microbiota in patients with Parkinson's disease in southern China,Parkinsonism & related disorders,2018,"16S rRNA next-generation-sequencing, Clinical motor phenotype, Gut microbiota, Parkinson's disease",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Late-onset PD,Early-onset PD,Parkinson's disease patient with age of onset less than 50.,51,23,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 3,9 February 2023,Jacquelynshevin,"Jacquelynshevin,WikiWorks",Taxa identified as significant difference between clinical phenotypes.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas",1783272|1239|186801|186802|216572|244127;3379134|1224|28216|80840|80864|283,Complete,Fatima
bsdb:29776865/4/1,29776865,case-control,29776865,10.1016/j.parkreldis.2018.05.007,https://pubmed.ncbi.nlm.nih.gov/29776865/,"Lin A., Zheng W., He Y., Tang W., Wei X., He R., Huang W., Su Y., Huang Y., Zhou H. , Xie H.",Gut microbiota in patients with Parkinson's disease in southern China,Parkinsonism & related disorders,2018,"16S rRNA next-generation-sequencing, Clinical motor phenotype, Gut microbiota, Parkinson's disease",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Non-tremor dominant PD,Tremor dominant PD,Parkinson's disease patient with tremor dominant motor symptoms.,56,18,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 3,9 February 2023,Jacquelynshevin,"Jacquelynshevin,WikiWorks",Taxa identified as significant difference between clinical phenotypes.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae",1783272|1239|186801|186802|216572|244127;3384189|32066|203490|203491|1129771,Complete,Fatima
bsdb:29776865/4/2,29776865,case-control,29776865,10.1016/j.parkreldis.2018.05.007,https://pubmed.ncbi.nlm.nih.gov/29776865/,"Lin A., Zheng W., He Y., Tang W., Wei X., He R., Huang W., Su Y., Huang Y., Zhou H. , Xie H.",Gut microbiota in patients with Parkinson's disease in southern China,Parkinsonism & related disorders,2018,"16S rRNA next-generation-sequencing, Clinical motor phenotype, Gut microbiota, Parkinson's disease",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Non-tremor dominant PD,Tremor dominant PD,Parkinson's disease patient with tremor dominant motor symptoms.,56,18,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 3,9 February 2023,Jacquelynshevin,"Jacquelynshevin,WikiWorks",Taxa identified as significant difference between clinical phenotypes.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,1783272|1239|186801|3085636|186803|841,Complete,Fatima
bsdb:29783199/1/1,29783199,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu E.A., Comba I.Y., Cho T., Engen P.A., Yazıcı C., Soberanes S., Hamanaka R.B., Niğdelioğlu R., Meliton A.Y., Ghio A.J., Budinger G.R.S. , Mutlu G.M.",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,"Air pollution, Feces, Gastrointestinal, Intestine, Microbiota",Experiment 1,United States of America,Mus musculus,Small intestine,UBERON:0002108,Air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,relative abundances,LEfSe,0.05,FALSE,5,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure S3,10 January 2021,Zyaijah Bailey,"Lwaldron,WikiWorks,Merit",Histograms of relative abundance of selected statistically differentially abundant genera in the small intestine.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",3379134|976|200643|171549;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826;3379134|976|200643|171549|815;3379134|976|200643|171549,Complete,ChiomaBlessing
bsdb:29783199/1/2,29783199,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu E.A., Comba I.Y., Cho T., Engen P.A., Yazıcı C., Soberanes S., Hamanaka R.B., Niğdelioğlu R., Meliton A.Y., Ghio A.J., Budinger G.R.S. , Mutlu G.M.",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,"Air pollution, Feces, Gastrointestinal, Intestine, Microbiota",Experiment 1,United States of America,Mus musculus,Small intestine,UBERON:0002108,Air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,relative abundances,LEfSe,0.05,FALSE,5,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Figure S3,10 January 2021,Zyaijah Bailey,"Lwaldron,WikiWorks",Histograms of relative abundance of selected statistically differentially abundant genera in the small intestine.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|186827,Complete,ChiomaBlessing
bsdb:29783199/2/1,29783199,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu E.A., Comba I.Y., Cho T., Engen P.A., Yazıcı C., Soberanes S., Hamanaka R.B., Niğdelioğlu R., Meliton A.Y., Ghio A.J., Budinger G.R.S. , Mutlu G.M.",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,"Air pollution, Feces, Gastrointestinal, Intestine, Microbiota",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,relative abundances,LEfSe,0.05,FALSE,5,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure S6,10 January 2021,Zyaijah Bailey,"Atrayees,WikiWorks,Merit",Individual abundance histograms of bacterial lineages changing particularly in the fecal samples,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Hymenochaetales|f__Rickenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|s__Bacteroidaceae bacterium",3379134|976|200643|171549;1783272|1239|186801|3085636|186803;4751|5204|155619|139380|1124673;1783272|1239|186801|3085636|186803|28050;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2030927;3379134|976|200643|171549|815|2212467,Complete,ChiomaBlessing
bsdb:29783199/2/2,29783199,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu E.A., Comba I.Y., Cho T., Engen P.A., Yazıcı C., Soberanes S., Hamanaka R.B., Niğdelioğlu R., Meliton A.Y., Ghio A.J., Budinger G.R.S. , Mutlu G.M.",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,"Air pollution, Feces, Gastrointestinal, Intestine, Microbiota",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,relative abundances,LEfSe,0.05,FALSE,5,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Figure S6,10 January 2021,Zyaijah Bailey,WikiWorks,Individual abundance histograms of bacterial lineages changing particularly in the fecal samples,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",3379134|976|200643|171549|815|816;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|33958|1578;1783272|1239|526524|526525|2810281|191303,Complete,ChiomaBlessing
bsdb:29783199/3/1,29783199,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu E.A., Comba I.Y., Cho T., Engen P.A., Yazıcı C., Soberanes S., Hamanaka R.B., Niğdelioğlu R., Meliton A.Y., Ghio A.J., Budinger G.R.S. , Mutlu G.M.",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,"Air pollution, Feces, Gastrointestinal, Intestine, Microbiota",Experiment 3,United States of America,Mus musculus,Caecum,UBERON:0001153,Air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,relative abundances,LEfSe,0.05,FALSE,5,NA,NA,NA,unchanged,unchanged,NA,NA,increased,Signature 1,Figure S4,10 January 2021,Zyaijah Bailey,"WikiWorks,Rukky",Histograms of relative abundance of selected statistically differentially abundant genera in the cecum.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|s__Rikenellaceae bacterium",3379134|976|200643|171549|2030927;3379134|976|200643|171549|171550|2049048,Complete,Rukky
bsdb:29783199/3/2,29783199,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu E.A., Comba I.Y., Cho T., Engen P.A., Yazıcı C., Soberanes S., Hamanaka R.B., Niğdelioğlu R., Meliton A.Y., Ghio A.J., Budinger G.R.S. , Mutlu G.M.",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,"Air pollution, Feces, Gastrointestinal, Intestine, Microbiota",Experiment 3,United States of America,Mus musculus,Caecum,UBERON:0001153,Air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,relative abundances,LEfSe,0.05,FALSE,5,NA,NA,NA,unchanged,unchanged,NA,NA,increased,Signature 2,Figure S4,10 January 2021,WikiWorks,"Atrayees,WikiWorks,Merit",Histograms of relative abundance of selected statistically differentially abundant genera in the cecum.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|s__Bacteroidaceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",3379134|976|200643|171549|815;3379134|976|200643|171549|815|2212467;3379134|976|200643|171549;3379134|976|200643|171549|2030927;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;1783272|1239|526524|526525|2810281|191303,Complete,ChiomaBlessing
bsdb:29783199/4/1,29783199,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu E.A., Comba I.Y., Cho T., Engen P.A., Yazıcı C., Soberanes S., Hamanaka R.B., Niğdelioğlu R., Meliton A.Y., Ghio A.J., Budinger G.R.S. , Mutlu G.M.",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,"Air pollution, Feces, Gastrointestinal, Intestine, Microbiota",Experiment 4,United States of America,Mus musculus,Stomach,UBERON:0000945,Air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,relative abundances,LEfSe,0.05,FALSE,5,NA,NA,NA,unchanged,unchanged,NA,NA,increased,Signature 1,Figure S2,10 January 2021,Zyaijah Bailey,"Lwaldron,WikiWorks",Histograms of relative abundance of selected statistically differentially abundant genera in the stomach,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",1783272|1239|91061|186826|33958;3379134|976|200643|171549,Complete,ChiomaBlessing
bsdb:29783199/4/2,29783199,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu E.A., Comba I.Y., Cho T., Engen P.A., Yazıcı C., Soberanes S., Hamanaka R.B., Niğdelioğlu R., Meliton A.Y., Ghio A.J., Budinger G.R.S. , Mutlu G.M.",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,"Air pollution, Feces, Gastrointestinal, Intestine, Microbiota",Experiment 4,United States of America,Mus musculus,Stomach,UBERON:0000945,Air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,relative abundances,LEfSe,0.05,FALSE,5,NA,NA,NA,unchanged,unchanged,NA,NA,increased,Signature 2,Figure S2,10 January 2021,Zyaijah Bailey,WikiWorks,Histograms of relative abundance of selected statistically differentially abundant genera in the stomach,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,ChiomaBlessing
bsdb:29783199/5/1,29783199,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu E.A., Comba I.Y., Cho T., Engen P.A., Yazıcı C., Soberanes S., Hamanaka R.B., Niğdelioğlu R., Meliton A.Y., Ghio A.J., Budinger G.R.S. , Mutlu G.M.",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,"Air pollution, Feces, Gastrointestinal, Intestine, Microbiota",Experiment 5,United States of America,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,relative abundances,LEfSe,0.05,FALSE,5,NA,NA,NA,increased,unchanged,NA,NA,increased,Signature 1,Figure S5,10 January 2021,Zyaijah Bailey,"WikiWorks,Merit",Histograms of relative abundance of selected statistically differentially abundant genera in the colon,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|1869337;3379134|976|200643|171549|2005525|375288,Complete,ChiomaBlessing
bsdb:29783199/5/2,29783199,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu E.A., Comba I.Y., Cho T., Engen P.A., Yazıcı C., Soberanes S., Hamanaka R.B., Niğdelioğlu R., Meliton A.Y., Ghio A.J., Budinger G.R.S. , Mutlu G.M.",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,"Air pollution, Feces, Gastrointestinal, Intestine, Microbiota",Experiment 5,United States of America,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,relative abundances,LEfSe,0.05,FALSE,5,NA,NA,NA,increased,unchanged,NA,NA,increased,Signature 2,Figure S5,10 January 2021,Zyaijah Bailey,"WikiWorks,Merit",Histograms of relative abundance of selected statistically differentially abundant genera in the colon,decreased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",1783272|544448|31969|186332|186333|2086;1783272|1239|186801|186802|31979|1485;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|31979;1783272|1239|186801;1783272|1239|186801|186802|1898207;1783272|1239|186801;1783272|1239|186801|186802|31979,Complete,ChiomaBlessing
bsdb:29783199/6/1,29783199,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu E.A., Comba I.Y., Cho T., Engen P.A., Yazıcı C., Soberanes S., Hamanaka R.B., Niğdelioğlu R., Meliton A.Y., Ghio A.J., Budinger G.R.S. , Mutlu G.M.",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,"Air pollution, Feces, Gastrointestinal, Intestine, Microbiota",Experiment 6,United States of America,Mus musculus,"Feces,Stomach,Caecum,Small intestine,Colon","UBERON:0001153,UBERON:0001155,UBERON:0001988,UBERON:0000945,UBERON:0002108",Air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,relative abundances,LEfSe,0.05,FALSE,5,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure 5,10 January 2021,Zyaijah Bailey,"Atrayees,WikiWorks",LEfSe analysis of all samples revealed genera altered with PM exposure throughout the GI tract,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|1385|90964|1279;1783272|1239|91061,Complete,Atrayees
bsdb:29783199/6/2,29783199,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu E.A., Comba I.Y., Cho T., Engen P.A., Yazıcı C., Soberanes S., Hamanaka R.B., Niğdelioğlu R., Meliton A.Y., Ghio A.J., Budinger G.R.S. , Mutlu G.M.",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,"Air pollution, Feces, Gastrointestinal, Intestine, Microbiota",Experiment 6,United States of America,Mus musculus,"Feces,Stomach,Caecum,Small intestine,Colon","UBERON:0001153,UBERON:0001155,UBERON:0001988,UBERON:0000945,UBERON:0002108",Air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,relative abundances,LEfSe,0.05,FALSE,5,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Figure 5,10 January 2021,Zyaijah Bailey,"Atrayees,WikiWorks",LEfSe analysis of all samples revealed genera altered with PM exposure throughout the GI tract,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",1783272|1239|91061|186826|33958;3379134|976|200643|171549|171550;3379134|976|200643|171549,Complete,Atrayees
bsdb:29791775/1/1,29791775,case-control,29791775,10.1111/1471-0528.15299,NA,"Tabatabaei N., Eren A.M., Barreiro L.B., Yotova V., Dumaine A., Allard C. , Fraser W.D.",Vaginal microbiome in early pregnancy and subsequent risk of spontaneous preterm birth: a case-control study,BJOG : an international journal of obstetrics and gynaecology,2019,"16S rRNA, Lactobacillus, bacterial vaginosis, preterm birth, vaginal microbiome",Experiment 1,Canada,Homo sapiens,Vagina,UBERON:0000996,Premature birth,EFO:0003917,mothers whose newborns were delivered at ≥37 getastional weeks,mothers whose newborns were delivered at <34 gestational week,NA,365,17,NA,16S,4,Illumina,relative abundances,NLMIXED,0.05,TRUE,NA,NA,"body mass index,ethnic group,maternal age,parity,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,Table 2 & S2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Vaginal microbial oligotype differential relative abundance composition between pregnant women who had early (<34 weeks of gestation) preterm versus full term (≥37 weeks gestation) deliveries,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia solanacearum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|1239|91061|186826|33958|1578|1596;1783272|1239|91061|186826|33958|1578|33959;1783272|201174|1760|85004|31953|1678|216816|1679;1783272|201174|1760|85004|31953|1678|1685;1783272|1239|91061|186826|33958|1578|1579;1783272|1239|91061|186826|33958|1578|47770;1783272|1239|91061|186826|33958|1578|147802;3379134|1224|28216|80840|119060|48736|305;1783272|201174|1760|85004|31953|1678,Complete,Atrayees
bsdb:29791788/1/1,29791788,case-control,29791788,10.1111/jam.13929,NA,"Jugé R., Rouaud-Tinguely P., Breugnot J., Servaes K., Grimaldi C., Roth M.P., Coppin H. , Closs B.",Shift in skin microbiota of Western European women across aging,Journal of applied microbiology,2018,"16S rRNA gene sequencing, Western European women, age-related changes, alpha diversity, beta diversity, microbiota, skin",Experiment 1,France,Homo sapiens,Skin of body,UBERON:0002097,Age,EFO:0000246,younger age,older age European women,aging,17,17,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,unchanged,NA,NA,unchanged,Signature 1,"Figure 4, Figure S1, Figure s2",10 January 2021,Rimsha Azhar,WikiWorks,Taxonomic analysis of forehead microbiota using LEfSe between older and younger european women,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota",1783272|201174|1760|85006|1268|1663;3384189|32066|203490|203491|1129771|168808;3379134|1224|1236|2887326|468;3379134|1224|1236|72274;1783272|201174|1760|85007|1653|1716;3379134|1224|1236|135619|28256;3379134|1224|1236|135619|28256|2745;3379134|1224|1236|135619;3379134|1224|28216|206351|481;3379134|1224|28216|206351;3379134|1224|28216;3379134|1224,Complete,NA
bsdb:29791788/1/2,29791788,case-control,29791788,10.1111/jam.13929,NA,"Jugé R., Rouaud-Tinguely P., Breugnot J., Servaes K., Grimaldi C., Roth M.P., Coppin H. , Closs B.",Shift in skin microbiota of Western European women across aging,Journal of applied microbiology,2018,"16S rRNA gene sequencing, Western European women, age-related changes, alpha diversity, beta diversity, microbiota, skin",Experiment 1,France,Homo sapiens,Skin of body,UBERON:0002097,Age,EFO:0000246,younger age,older age European women,aging,17,17,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,unchanged,NA,NA,unchanged,Signature 2,"Figure 4, Figure S1, Figure s2",10 January 2021,Rimsha Azhar,WikiWorks,Taxonomic analysis of forehead microbiota using  LEfSe between older and younger european women,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales",1783272|201174|1760|85009|31957;1783272|201174|1760|85009|31957|1743;1783272|201174|1760|85009,Complete,NA
bsdb:29793531/1/1,29793531,laboratory experiment,29793531,10.1186/s40168-018-0476-6,NA,"Robertson R.C., Kaliannan K., Strain C.R., Ross R.P., Stanton C. , Kang J.X.",Maternal omega-3 fatty acids regulate offspring obesity through persistent modulation of gut microbiota,Microbiome,2018,"Maternal diet, Microbiome, Microbiota, Obesity, n-3 PUFA",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,foster mother fat1 pre HFD,foster mother wild-type pre HFD,fat-1 mice: with a balanced tissue n-6/n-3 ratio (~ 1:1) and wild-type (WT) mice: with a high n-6/ n-3 ratio similar to the Western diet (> 10:1).,15,9,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2.4,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text, Figure S4",10 January 2021,Marianthi Thomatos,WikiWorks,"Pre-High fat diet (HFD) and Post-HF diet differential abundance in offspring according to foster mother genotype at lactation, wild type (WT) or fat-1 (balanced tissue n-6/n-3)",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|31979;1783272|1239|526524|526525|2810281|191303;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|186807;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|186802|216572|946234;1783272|1239|526524|526525;1783272|1239|526524;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802|541000;1783272|1239|186801|186802|3085642|580596;3379134|976|200643|171549|2005525|375288;1783272|1239;1783272|1239|186801;1783272|1239|186801|186802,Complete,Shaimaa Elsafoury
bsdb:29793531/1/2,29793531,laboratory experiment,29793531,10.1186/s40168-018-0476-6,NA,"Robertson R.C., Kaliannan K., Strain C.R., Ross R.P., Stanton C. , Kang J.X.",Maternal omega-3 fatty acids regulate offspring obesity through persistent modulation of gut microbiota,Microbiome,2018,"Maternal diet, Microbiome, Microbiota, Obesity, n-3 PUFA",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,foster mother fat1 pre HFD,foster mother wild-type pre HFD,fat-1 mice: with a balanced tissue n-6/n-3 ratio (~ 1:1) and wild-type (WT) mice: with a high n-6/ n-3 ratio similar to the Western diet (> 10:1).,15,9,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2.4,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Text, Figure S4",10 January 2021,Marianthi Thomatos,WikiWorks,"Pre-High fat diet (HFD) and Post-HF diet differential abundance in offspring according to foster mother genotype at lactation, wild type (WT) or fat-1 (balanced tissue n-6/n-3)",decreased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas",3379134|976;3379134|976|200643;3379134|976|200643|171549;3379134|29547|3031852|213849;3379134|29547;3379134|1224;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;28221;3379134|200940|3031449|213115;3379134|976|200643|171549|171550;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|2005519|397864;3379134|29547|3031852|213849|72293;3379134|29547|3031852|213849|72293|209;3379134|200940|3031449|213115|194924;3379134|976|200643|171549|1853231|283168;3379134|200940|3031449|213115|194924|872;1783272|1239|526524|526525|128827|174708;3379134|976|200643|171549|171550|28138;95818|2093818|2093825|2171986|1331051,Complete,Shaimaa Elsafoury
bsdb:29793531/2/1,29793531,laboratory experiment,29793531,10.1186/s40168-018-0476-6,NA,"Robertson R.C., Kaliannan K., Strain C.R., Ross R.P., Stanton C. , Kang J.X.",Maternal omega-3 fatty acids regulate offspring obesity through persistent modulation of gut microbiota,Microbiome,2018,"Maternal diet, Microbiome, Microbiota, Obesity, n-3 PUFA",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,foster mother fat1 post HFD,foster mother wild-type post HFD,fat-1 mice: with a balanced tissue n-6/n-3 ratio (~ 1:1) and wild-type (WT) mice: with a high n-6/ n-3 ratio similar to the Western diet (> 10:1).,15,9,NA,16S,34,Illumina,NA,LEfSe,0.05,TRUE,2.4,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text, Figure S4",10 January 2021,Marianthi Thomatos,WikiWorks,"Pre-High fat diet (HFD) and Post-HF diet differential abundance in offspring according to foster mother genotype at lactation, wild type (WT) or fat-1 (balanced tissue n-6/n-3)",increased,"k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Lentisphaerales|f__Lentisphaeraceae|g__Lentisphaera,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria",3379134|256845|1313211|278082|255528|172900;3379134|256845|1313211|278081|566277|256846;3379134|256845|1313211|278082|255528;1783272|1239|526524|526525|128827;3379134|256845|1313211|278082;1783272|1239|186801|186802|31979|1485;1783272|1239|526524|526525;1783272|1239|526524;3379134|976|200643|171549|171550|28138;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|946234;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|186802|186807;1783272|1239|91061|186826;1783272|1239|91061;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802|541000;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;1783272|1239;1783272|1239|186801;1783272|1239|186801|186802;3379134|256845|1313211,Complete,Shaimaa Elsafoury
bsdb:29793531/2/2,29793531,laboratory experiment,29793531,10.1186/s40168-018-0476-6,NA,"Robertson R.C., Kaliannan K., Strain C.R., Ross R.P., Stanton C. , Kang J.X.",Maternal omega-3 fatty acids regulate offspring obesity through persistent modulation of gut microbiota,Microbiome,2018,"Maternal diet, Microbiome, Microbiota, Obesity, n-3 PUFA",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,foster mother fat1 post HFD,foster mother wild-type post HFD,fat-1 mice: with a balanced tissue n-6/n-3 ratio (~ 1:1) and wild-type (WT) mice: with a high n-6/ n-3 ratio similar to the Western diet (> 10:1).,15,9,NA,16S,34,Illumina,NA,LEfSe,0.05,TRUE,2.4,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Text, Figure S4",10 January 2021,Marianthi Thomatos,WikiWorks,"Pre-High fat diet (HFD) and Post-HF diet differential abundance in offspring according to foster mother genotype at lactation, wild type (WT) or fat-1 (balanced tissue n-6/n-3)",decreased,"k__Pseudomonadati|p__Campylobacterota,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Pseudomonadota,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas",3379134|29547;3379134|29547|3031852|213849;3379134|1224;28221;3379134|200940|3031449|213115;3379134|29547|3031852|213849|72293;3379134|29547|3031852|213849|72293|209;3379134|200940|3031449|213115|194924;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976|200643|171549|1853231|283168;95818|2093818|2093825|2171986|1331051,Complete,Shaimaa Elsafoury
bsdb:29804833/1/1,29804833,laboratory experiment,29804833,10.1016/j.cell.2018.04.027,NA,"Olson C.A., Vuong H.E., Yano J.M., Liang Q.Y., Nusbaum D.J. , Hsiao E.Y.",The Gut Microbiota Mediates the Anti-Seizure Effects of the Ketogenic Diet,Cell,2018,"6-Hz seizures, Akkermansia, GGsTop, Kcna1, Parabacteroides, epilepsy, gamma-glutamyl transpeptidase, ketogenic diet, microbiome, microbiota",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,control diet (CD) group day 14,ketogenic diet (KD) group day 14,specific-pathogen free (SPF) mice after 14 days of ketogenic diet treatment,9,9,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S1D,12 December 2024,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of KD group compared to CD group after 14 days of treatment,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|526524|526525|128827;3379134|1224|28216|80840|995019|40544,Complete,NA
bsdb:29804833/1/2,29804833,laboratory experiment,29804833,10.1016/j.cell.2018.04.027,NA,"Olson C.A., Vuong H.E., Yano J.M., Liang Q.Y., Nusbaum D.J. , Hsiao E.Y.",The Gut Microbiota Mediates the Anti-Seizure Effects of the Ketogenic Diet,Cell,2018,"6-Hz seizures, Akkermansia, GGsTop, Kcna1, Parabacteroides, epilepsy, gamma-glutamyl transpeptidase, ketogenic diet, microbiome, microbiota",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,control diet (CD) group day 14,ketogenic diet (KD) group day 14,specific-pathogen free (SPF) mice after 14 days of ketogenic diet treatment,9,9,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S1D,12 December 2024,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of KD group compared to CD group after 14 days of treatment,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",1783272|1239|526524|526525|128827|174708;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|216816;3379134|200940|3031449|213115|194924|872,Complete,NA
bsdb:29804833/2/1,29804833,laboratory experiment,29804833,10.1016/j.cell.2018.04.027,NA,"Olson C.A., Vuong H.E., Yano J.M., Liang Q.Y., Nusbaum D.J. , Hsiao E.Y.",The Gut Microbiota Mediates the Anti-Seizure Effects of the Ketogenic Diet,Cell,2018,"6-Hz seizures, Akkermansia, GGsTop, Kcna1, Parabacteroides, epilepsy, gamma-glutamyl transpeptidase, ketogenic diet, microbiome, microbiota",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,control diet (CD) group day 8,ketogenic diet (KD) group day 8,specific-pathogen free (SPF) mice after 8 days of ketogenic diet treatment,9,9,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S1D,5 January 2025,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of KD group compared to CD group after 8 days of treatment,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|526524|526525|128827;3379134|976|200643|171549|2005525|375288,Complete,NA
bsdb:29804833/2/2,29804833,laboratory experiment,29804833,10.1016/j.cell.2018.04.027,NA,"Olson C.A., Vuong H.E., Yano J.M., Liang Q.Y., Nusbaum D.J. , Hsiao E.Y.",The Gut Microbiota Mediates the Anti-Seizure Effects of the Ketogenic Diet,Cell,2018,"6-Hz seizures, Akkermansia, GGsTop, Kcna1, Parabacteroides, epilepsy, gamma-glutamyl transpeptidase, ketogenic diet, microbiome, microbiota",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,control diet (CD) group day 8,ketogenic diet (KD) group day 8,specific-pathogen free (SPF) mice after 8 days of ketogenic diet treatment,9,9,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S1D,5 January 2025,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of KD group compared to CD group after 8 days of treatment,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",1783272|1239|526524|526525|128827|174708;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|216816;3379134|200940|3031449|213115|194924|872,Complete,NA
bsdb:29804833/3/1,29804833,laboratory experiment,29804833,10.1016/j.cell.2018.04.027,NA,"Olson C.A., Vuong H.E., Yano J.M., Liang Q.Y., Nusbaum D.J. , Hsiao E.Y.",The Gut Microbiota Mediates the Anti-Seizure Effects of the Ketogenic Diet,Cell,2018,"6-Hz seizures, Akkermansia, GGsTop, Kcna1, Parabacteroides, epilepsy, gamma-glutamyl transpeptidase, ketogenic diet, microbiome, microbiota",Experiment 3,United States of America,Mus musculus,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,control diet (CD) group day 4,ketogenic diet (KD) group day 4,specific-pathogen free (SPF) mice after 4 days of ketogenic diet treatment,9,9,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S1D,5 January 2025,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of KD group compared to CD group after 4 days of treatment,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|526524|526525|128827;3379134|976|200643|171549|2005525|375288,Complete,NA
bsdb:29804833/3/2,29804833,laboratory experiment,29804833,10.1016/j.cell.2018.04.027,NA,"Olson C.A., Vuong H.E., Yano J.M., Liang Q.Y., Nusbaum D.J. , Hsiao E.Y.",The Gut Microbiota Mediates the Anti-Seizure Effects of the Ketogenic Diet,Cell,2018,"6-Hz seizures, Akkermansia, GGsTop, Kcna1, Parabacteroides, epilepsy, gamma-glutamyl transpeptidase, ketogenic diet, microbiome, microbiota",Experiment 3,United States of America,Mus musculus,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,control diet (CD) group day 4,ketogenic diet (KD) group day 4,specific-pathogen free (SPF) mice after 4 days of ketogenic diet treatment,9,9,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S1D,5 January 2025,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of KD group compared to CD group after 4 days of treatment,decreased,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,3379134|200940|3031449|213115|194924|872,Complete,NA
bsdb:29804833/4/1,29804833,laboratory experiment,29804833,10.1016/j.cell.2018.04.027,NA,"Olson C.A., Vuong H.E., Yano J.M., Liang Q.Y., Nusbaum D.J. , Hsiao E.Y.",The Gut Microbiota Mediates the Anti-Seizure Effects of the Ketogenic Diet,Cell,2018,"6-Hz seizures, Akkermansia, GGsTop, Kcna1, Parabacteroides, epilepsy, gamma-glutamyl transpeptidase, ketogenic diet, microbiome, microbiota",Experiment 4,United States of America,Mus musculus,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,Kcna1−/− control diet (CD) group,Kcna1−/− ketogenic diet (KD) group,"Kcna1−/− SPF mice treated with Abx or vehicle for 1 week, gavaged with vehicle or A. muciniphila and Parabacteroides, and fed KD or CD for 3 weeks. Kcna1−/− group is used to mimic a gene mutation in humans that causes neurological problems such as epilepsy.",21,21,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5B,2 March 2025,Kavyaayala,Kavyaayala,Fecal microbiome of Kcna1−/− KD group mice compared to Kcna1−/− CD group mice,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|2005525|375288,Complete,NA
bsdb:29808701/1/1,29808701,"cross-sectional observational, not case-control",29808701,10.1089/AID.2017.0200,NA,"Lewy T., Hong B.Y., Weiser B., Burger H., Tremain A., Weinstock G., Anastos K. , George M.D.","Oral Microbiome in HIV-Infected Women: Shifts in the Abundance of Pathogenic and Beneficial Bacteria Are Associated with Aging, HIV Load, CD4 Count, and Antiretroviral Therapy",AIDS research and human retroviruses,2019,"HIV, aging, disease progression, opportunistic infection, oral microbiome, saliva",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,HIV infection,EFO:0000764,Age-matched HIV-uninfected women,HIV-positive women who have been taking ART for more than 1 year,HIV-positive women who have been taking antiretroviral therapy (ART) for more than 1 year,3,3,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplementary Figure S3,10 January 2021,Michael Lutete,"WikiWorks,Atrayees",Differences in abundance of salivary bacteria between HIV uninfected women and HIV-positive women on ART,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella",1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|3085636|186803|437755,Complete,Folakunmi
bsdb:29808701/2/1,29808701,"cross-sectional observational, not case-control",29808701,10.1089/AID.2017.0200,NA,"Lewy T., Hong B.Y., Weiser B., Burger H., Tremain A., Weinstock G., Anastos K. , George M.D.","Oral Microbiome in HIV-Infected Women: Shifts in the Abundance of Pathogenic and Beneficial Bacteria Are Associated with Aging, HIV Load, CD4 Count, and Antiretroviral Therapy",AIDS research and human retroviruses,2019,"HIV, aging, disease progression, opportunistic infection, oral microbiome, saliva",Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,"HIV infection,Oral candidiasis","EFO:0007406,EFO:0000764",Age-matched HIV-uninfected womenn,HIV-positive women with oral candidiasis,HIV-positive women with oral candidiasis,3,3,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplementary Figure S3,10 January 2021,Michael Lutete,"WikiWorks,Atrayees",Differences in abundance of salivary bacteria between HIV uninfected women and HIV-positive women coinfected with oral candidiasis,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|3085636|186803,Complete,Folakunmi
bsdb:29808701/3/1,29808701,"cross-sectional observational, not case-control",29808701,10.1089/AID.2017.0200,NA,"Lewy T., Hong B.Y., Weiser B., Burger H., Tremain A., Weinstock G., Anastos K. , George M.D.","Oral Microbiome in HIV-Infected Women: Shifts in the Abundance of Pathogenic and Beneficial Bacteria Are Associated with Aging, HIV Load, CD4 Count, and Antiretroviral Therapy",AIDS research and human retroviruses,2019,"HIV, aging, disease progression, opportunistic infection, oral microbiome, saliva",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Age,EFO:0000246,HIV uninfected women who are less than 35 years of age,HIV uninfected women who are 50 years of age or older,HIV-negative women who are 50 years of age or older,4,4,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplementary Figure S3,10 January 2021,Michael Lutete,"WikiWorks,Atrayees",Differences in abundance of salivary bacteria between young HIV uninfected women and old HIV uninfected women,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella",1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|3085636|186803|437755,Complete,Folakunmi
bsdb:29808701/4/1,29808701,"cross-sectional observational, not case-control",29808701,10.1089/AID.2017.0200,NA,"Lewy T., Hong B.Y., Weiser B., Burger H., Tremain A., Weinstock G., Anastos K. , George M.D.","Oral Microbiome in HIV-Infected Women: Shifts in the Abundance of Pathogenic and Beneficial Bacteria Are Associated with Aging, HIV Load, CD4 Count, and Antiretroviral Therapy",AIDS research and human retroviruses,2019,"HIV, aging, disease progression, opportunistic infection, oral microbiome, saliva",Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,"Coinfection,Age","EFO:0010716,EFO:0000246",young HIV-infected group without coinfection,aging HIV-infected women with coinfections,"aging HIV-infected women with coinfections; Hairy leukoplakia, oral candida, kaposi's sarcoma, HPV",4,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 5,24 August 2023,Atrayees,"Atrayees,Folakunmi,WikiWorks",LEfSe was performed to identify statistically different bacterial taxa in their relative abundance between young adult HIV-infected women versus aging HIV-infected women with coinfection.,increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum|s__Mucispirillum schaedleri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,",3379134|200940|3031449|213115|194924|872|885;1783272|1239|91061|186826|33958|1578|1591;1783272|1239|91061|186826|33958|2742598|1598;3379134|200930|68337|191393|2945020|248038|248039;3379134|976|200643|171549|1853231|283168|1965233;1783272|1239|91061|186826|186827;1783272|1239|186801|186802|31979;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1357|44273;1783272|1239|186801|186802|216572|119852;,Complete,Folakunmi
bsdb:29808701/4/2,29808701,"cross-sectional observational, not case-control",29808701,10.1089/AID.2017.0200,NA,"Lewy T., Hong B.Y., Weiser B., Burger H., Tremain A., Weinstock G., Anastos K. , George M.D.","Oral Microbiome in HIV-Infected Women: Shifts in the Abundance of Pathogenic and Beneficial Bacteria Are Associated with Aging, HIV Load, CD4 Count, and Antiretroviral Therapy",AIDS research and human retroviruses,2019,"HIV, aging, disease progression, opportunistic infection, oral microbiome, saliva",Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,"Coinfection,Age","EFO:0010716,EFO:0000246",young HIV-infected group without coinfection,aging HIV-infected women with coinfections,"aging HIV-infected women with coinfections; Hairy leukoplakia, oral candida, kaposi's sarcoma, HPV",4,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 5,24 August 2023,Atrayees,"Atrayees,WikiWorks",LEfSe was performed to identify statistically different bacterial taxa in their relative abundance between young adult HIV-infected women versus aging HIV-infected women with coinfection.,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia|s__Bulleidia sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Mycoplasmatota",1783272|1239|526524|526525|128827|123375|102148;1783272|1239|526524|526525|128827|118747|2704657;1783272|1239|909932|1843489|31977|29465|29466;1783272|544448,Complete,Folakunmi
bsdb:29851662/1/NA,29851662,time series / longitudinal observational,29851662,10.1097/QAD.0000000000001811,NA,"Presti R.M., Handley S.A., Droit L., Ghannoum M., Jacobson M., Shiboski C.H., Webster-Cyriaque J., Brown T., Yin M.T. , Overton E.T.",Alterations in the oral microbiome in HIV-infected participants after antiretroviral therapy administration are influenced by immune status,"AIDS (London, England)",2018,NA,Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Viral load,EFO:0010125,High viral load at baseline,Low viral load at baseline,Participants with viral load less than 100 000 copies/ml at baseline,9,26,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:29851662/2/1,29851662,time series / longitudinal observational,29851662,10.1097/QAD.0000000000001811,NA,"Presti R.M., Handley S.A., Droit L., Ghannoum M., Jacobson M., Shiboski C.H., Webster-Cyriaque J., Brown T., Yin M.T. , Overton E.T.",Alterations in the oral microbiome in HIV-infected participants after antiretroviral therapy administration are influenced by immune status,"AIDS (London, England)",2018,NA,Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,Response to antiviral drug,EFO:0010123,Baseline samples,Week 24 samples,Saliva samples after 24 weeks of antiretroviral therapy,35,35,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2 :Table S1,16 October 2023,MyleeeA,"MyleeeA,WikiWorks",Bacterial taxa differentially abundant in saliva prior to and following 24 weeks of antiretroviral therapy,increased,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema lecithinolyticum,3379134|203691|203692|136|2845253|157|53418,Complete,Folakunmi
bsdb:29851662/2/2,29851662,time series / longitudinal observational,29851662,10.1097/QAD.0000000000001811,NA,"Presti R.M., Handley S.A., Droit L., Ghannoum M., Jacobson M., Shiboski C.H., Webster-Cyriaque J., Brown T., Yin M.T. , Overton E.T.",Alterations in the oral microbiome in HIV-infected participants after antiretroviral therapy administration are influenced by immune status,"AIDS (London, England)",2018,NA,Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,Response to antiviral drug,EFO:0010123,Baseline samples,Week 24 samples,Saliva samples after 24 weeks of antiretroviral therapy,35,35,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2, Table S1",16 October 2023,MyleeeA,"MyleeeA,Folakunmi,WikiWorks",Bacterial taxa differentially abundant in saliva prior to and following 24 weeks of antiretroviral therapy,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum|s__Muribaculum intestinale,3379134|976|200643|171549|2005473|1918540|1796646,Complete,Folakunmi
bsdb:29851662/4/1,29851662,time series / longitudinal observational,29851662,10.1097/QAD.0000000000001811,NA,"Presti R.M., Handley S.A., Droit L., Ghannoum M., Jacobson M., Shiboski C.H., Webster-Cyriaque J., Brown T., Yin M.T. , Overton E.T.",Alterations in the oral microbiome in HIV-infected participants after antiretroviral therapy administration are influenced by immune status,"AIDS (London, England)",2018,NA,Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,CD4-positive T-lymphocyte count,EFO:0010105,week 24 CD4+ low samples,week 24 CD4+ high samples,samples with high CD4+ at Week 24 following Anti Retroviral Therapy,35,35,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"Figure 3, Table S2",16 October 2023,MyleeeA,"MyleeeA,Folakunmi,WikiWorks",The effect of CD4+ T-cell counts on the salivary bacterial microbiome: Differential abundance of bacterial taxa in CD4+ low vs. CD4+ high patient saliva.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,3379134|1224|1236|135625|712|724|729,Complete,Folakunmi
bsdb:29859859/1/1,29859859,time series / longitudinal observational,29859859,10.1016/j.schres.2018.05.017,NA,"Yuan X., Zhang P., Wang Y., Liu Y., Li X., Kumar B.U., Hei G., Lv L., Huang X.F., Fan X. , Song X.","Changes in metabolism and microbiota after 24-week risperidone treatment in drug naïve, normal weight patients with first episode schizophrenia",Schizophrenia research,2018,"Metabolism, Microbiota, Schizophrenia",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy controls,schizophrenia,Drug-naive first-episode schizophrenia patients,41,41,1 month,16S,NA,RT-qPCR,raw counts,T-Test,0.05,FALSE,NA,NA,"age,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,table 2,10 January 2021,Fatima Zohra,WikiWorks,comparison of fecal bacteria between schizophrenic patients and controls,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|201174|1760|85004|31953|1678;3379134|1224|1236|91347|543|561|562;1783272|1239|91061|186826|33958|1578,Complete,Atrayees
bsdb:29859859/1/2,29859859,time series / longitudinal observational,29859859,10.1016/j.schres.2018.05.017,NA,"Yuan X., Zhang P., Wang Y., Liu Y., Li X., Kumar B.U., Hei G., Lv L., Huang X.F., Fan X. , Song X.","Changes in metabolism and microbiota after 24-week risperidone treatment in drug naïve, normal weight patients with first episode schizophrenia",Schizophrenia research,2018,"Metabolism, Microbiota, Schizophrenia",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy controls,schizophrenia,Drug-naive first-episode schizophrenia patients,41,41,1 month,16S,NA,RT-qPCR,raw counts,T-Test,0.05,FALSE,NA,NA,"age,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 2,table 2,27 June 2023,Atrayees,"Atrayees,WikiWorks",comparison of fecal bacteria between schizophrenic patients and controls,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,1783272|1239|186801|3085636|186803|572511|1532,Complete,Atrayees
bsdb:29874201/1/1,29874201,prospective cohort,29874201,10.1097/QAI.0000000000001693,NA,"Arnbjerg C.J., Vestad B., Hov J.R., Pedersen K.K., Jespersen S., Johannesen H.H., Holm K., Halvorsen B., Fallentin E., Hansen A.E., Lange T., Kjær A., Trøseid M., Fischer B.M. , Nielsen S.D.",Effect of Lactobacillus rhamnosus GG Supplementation on Intestinal Inflammation Assessed by PET/MRI Scans and Gut Microbiota Composition in HIV-Infected Individuals,Journal of acquired immune deficiency syndromes (1999),2018,NA,Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,baseline,combination antiretroviral therapy treated individuals after taking LGG probiotic for 8 weeks,Persons with HIV,27,27,2 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,"Text, Supplementary Figure 3",10 January 2021,Michael Lutete,WikiWorks,Effect of Probiotic LGG on Gut Microbiota Composition,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3085636|186803,Complete,Claregrieve1
bsdb:29874201/1/2,29874201,prospective cohort,29874201,10.1097/QAI.0000000000001693,NA,"Arnbjerg C.J., Vestad B., Hov J.R., Pedersen K.K., Jespersen S., Johannesen H.H., Holm K., Halvorsen B., Fallentin E., Hansen A.E., Lange T., Kjær A., Trøseid M., Fischer B.M. , Nielsen S.D.",Effect of Lactobacillus rhamnosus GG Supplementation on Intestinal Inflammation Assessed by PET/MRI Scans and Gut Microbiota Composition in HIV-Infected Individuals,Journal of acquired immune deficiency syndromes (1999),2018,NA,Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,baseline,combination antiretroviral therapy treated individuals after taking LGG probiotic for 8 weeks,Persons with HIV,27,27,2 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,"Text, Supplementary Figure 3",10 January 2021,Michael Lutete,WikiWorks,Effect of Probiotic LGG on Gut Microbiota Composition,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",3379134|1224|1236|91347|543;1783272|1239|526524|526525|128827,Complete,Claregrieve1
bsdb:29874201/3/1,29874201,prospective cohort,29874201,10.1097/QAI.0000000000001693,NA,"Arnbjerg C.J., Vestad B., Hov J.R., Pedersen K.K., Jespersen S., Johannesen H.H., Holm K., Halvorsen B., Fallentin E., Hansen A.E., Lange T., Kjær A., Trøseid M., Fischer B.M. , Nielsen S.D.",Effect of Lactobacillus rhamnosus GG Supplementation on Intestinal Inflammation Assessed by PET/MRI Scans and Gut Microbiota Composition in HIV-Infected Individuals,Journal of acquired immune deficiency syndromes (1999),2018,NA,Experiment 3,Denmark,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,individuals with no change in uptake,individuals with decreased F-2-fluoro-2-deoxy-D-glucose (F-FDG) uptake on positron emission tomography (PET)/magnetic resonance imaging (MRI),Persons with HIV,7,5,2 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,"Text, Figure 2",10 January 2021,Michael Lutete,WikiWorks,Changes in relative abundance of Enterobacteriaceae after LGG supplementation in responders and nonresponders,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,Claregrieve1
bsdb:29885665/1/1,29885665,case-control,29885665,10.1186/s40168-018-0487-3,NA,"Durack J., Huang Y.J., Nariya S., Christian L.S., Ansel K.M., Beigelman A., Castro M., Dyer A.M., Israel E., Kraft M., Martin R.J., Mauger D.T., Rosenberg S.R., King T.S., White S.R., Denlinger L.C., Holguin F., Lazarus S.C., Lugogo N., Peters S.P., Smith L.J., Wechsler M.E., Lynch S.V. , Boushey H.A.",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,"Adult asthma, Atopy, Bronchial microbiota, Corynebacterium, Eosinophilic inflammation, Induced sputum microbiota, Lower airways, Moraxella, Nasal microbiota, Oral microbiota, Upper airways",Experiment 1,United States of America,Homo sapiens,"Bronchus,External nose","UBERON:0002185,UBERON:0007827",Atopic asthma,EFO:0010638,bronchial brush specimens,nasal brush speciments,nasal brush specimen type,27,27,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 1,Figure 3,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between paired bronchial brush (BB) and nasal brush (NB) specimen types,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Alloiococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|1239|91061|186826|186828|1651;1783272|201174|1760|85007|1653|1716;3379134|1224|1236|2887326|468|475;1783272|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:29885665/1/2,29885665,case-control,29885665,10.1186/s40168-018-0487-3,NA,"Durack J., Huang Y.J., Nariya S., Christian L.S., Ansel K.M., Beigelman A., Castro M., Dyer A.M., Israel E., Kraft M., Martin R.J., Mauger D.T., Rosenberg S.R., King T.S., White S.R., Denlinger L.C., Holguin F., Lazarus S.C., Lugogo N., Peters S.P., Smith L.J., Wechsler M.E., Lynch S.V. , Boushey H.A.",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,"Adult asthma, Atopy, Bronchial microbiota, Corynebacterium, Eosinophilic inflammation, Induced sputum microbiota, Lower airways, Moraxella, Nasal microbiota, Oral microbiota, Upper airways",Experiment 1,United States of America,Homo sapiens,"Bronchus,External nose","UBERON:0002185,UBERON:0007827",Atopic asthma,EFO:0010638,bronchial brush specimens,nasal brush speciments,nasal brush specimen type,27,27,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 2,Figure 3,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between paired bronchial brush (BB) and nasal brush (NB) specimen types,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|1760|2037|2049|1654;3384189|32066|203490|203491|1129771|32067;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:29885665/2/1,29885665,case-control,29885665,10.1186/s40168-018-0487-3,NA,"Durack J., Huang Y.J., Nariya S., Christian L.S., Ansel K.M., Beigelman A., Castro M., Dyer A.M., Israel E., Kraft M., Martin R.J., Mauger D.T., Rosenberg S.R., King T.S., White S.R., Denlinger L.C., Holguin F., Lazarus S.C., Lugogo N., Peters S.P., Smith L.J., Wechsler M.E., Lynch S.V. , Boushey H.A.",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,"Adult asthma, Atopy, Bronchial microbiota, Corynebacterium, Eosinophilic inflammation, Induced sputum microbiota, Lower airways, Moraxella, Nasal microbiota, Oral microbiota, Upper airways",Experiment 2,United States of America,Homo sapiens,"Bronchus,Mouth","UBERON:0002185,UBERON:0000165",Atopic asthma,EFO:0010638,bronchial brush specimens,oral wash specimens,oral wash specimen type,27,27,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,unchanged,increased,NA,NA,NA,increased,Signature 1,Figure 3,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between paired bronchial brush (BB) and oral wash (OW) specimen types,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|1760|2037|2049|1654;3384189|32066|203490|203491|1129771|32067;1783272|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:29885665/2/2,29885665,case-control,29885665,10.1186/s40168-018-0487-3,NA,"Durack J., Huang Y.J., Nariya S., Christian L.S., Ansel K.M., Beigelman A., Castro M., Dyer A.M., Israel E., Kraft M., Martin R.J., Mauger D.T., Rosenberg S.R., King T.S., White S.R., Denlinger L.C., Holguin F., Lazarus S.C., Lugogo N., Peters S.P., Smith L.J., Wechsler M.E., Lynch S.V. , Boushey H.A.",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,"Adult asthma, Atopy, Bronchial microbiota, Corynebacterium, Eosinophilic inflammation, Induced sputum microbiota, Lower airways, Moraxella, Nasal microbiota, Oral microbiota, Upper airways",Experiment 2,United States of America,Homo sapiens,"Bronchus,Mouth","UBERON:0002185,UBERON:0000165",Atopic asthma,EFO:0010638,bronchial brush specimens,oral wash specimens,oral wash specimen type,27,27,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,unchanged,increased,NA,NA,NA,increased,Signature 2,Figure 3,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between paired bronchial brush (BB) and oral wash (OW) specimen types,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|201174|1760|85007|1653|1716;3379134|1224|1236|2887326|468|475;3379134|976|200643|171549|171552|838;1783272|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:29885665/3/1,29885665,case-control,29885665,10.1186/s40168-018-0487-3,NA,"Durack J., Huang Y.J., Nariya S., Christian L.S., Ansel K.M., Beigelman A., Castro M., Dyer A.M., Israel E., Kraft M., Martin R.J., Mauger D.T., Rosenberg S.R., King T.S., White S.R., Denlinger L.C., Holguin F., Lazarus S.C., Lugogo N., Peters S.P., Smith L.J., Wechsler M.E., Lynch S.V. , Boushey H.A.",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,"Adult asthma, Atopy, Bronchial microbiota, Corynebacterium, Eosinophilic inflammation, Induced sputum microbiota, Lower airways, Moraxella, Nasal microbiota, Oral microbiota, Upper airways",Experiment 3,United States of America,Homo sapiens,"Sputum,External nose","UBERON:0007311,UBERON:0007827",Atopic asthma,EFO:0010638,nasal brush specimens,induced sputum specimens,induced sputum specimen type,27,27,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,increased,increased,NA,NA,NA,increased,Signature 1,Figure 3,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks,OdigiriGreat",Differential microbial abundance between paired Nasal brush (NB) and induced sputum (IS) specimen types,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|1760|2037|2049|1654;3384189|32066|203490|203491|1129771|32067;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:29885665/3/2,29885665,case-control,29885665,10.1186/s40168-018-0487-3,NA,"Durack J., Huang Y.J., Nariya S., Christian L.S., Ansel K.M., Beigelman A., Castro M., Dyer A.M., Israel E., Kraft M., Martin R.J., Mauger D.T., Rosenberg S.R., King T.S., White S.R., Denlinger L.C., Holguin F., Lazarus S.C., Lugogo N., Peters S.P., Smith L.J., Wechsler M.E., Lynch S.V. , Boushey H.A.",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,"Adult asthma, Atopy, Bronchial microbiota, Corynebacterium, Eosinophilic inflammation, Induced sputum microbiota, Lower airways, Moraxella, Nasal microbiota, Oral microbiota, Upper airways",Experiment 3,United States of America,Homo sapiens,"Sputum,External nose","UBERON:0007311,UBERON:0007827",Atopic asthma,EFO:0010638,nasal brush specimens,induced sputum specimens,induced sputum specimen type,27,27,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,increased,increased,NA,NA,NA,increased,Signature 2,Figure 3,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks,OdigiriGreat",Differential microbial abundance between paired Nasal brush (NB) and induced sputum (IS) specimen types,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Alloiococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|1239|91061|186826|186828|1651;1783272|201174|1760|85007|1653|1716;3379134|1224|1236|2887326|468|475;1783272|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:29885665/4/1,29885665,case-control,29885665,10.1186/s40168-018-0487-3,NA,"Durack J., Huang Y.J., Nariya S., Christian L.S., Ansel K.M., Beigelman A., Castro M., Dyer A.M., Israel E., Kraft M., Martin R.J., Mauger D.T., Rosenberg S.R., King T.S., White S.R., Denlinger L.C., Holguin F., Lazarus S.C., Lugogo N., Peters S.P., Smith L.J., Wechsler M.E., Lynch S.V. , Boushey H.A.",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,"Adult asthma, Atopy, Bronchial microbiota, Corynebacterium, Eosinophilic inflammation, Induced sputum microbiota, Lower airways, Moraxella, Nasal microbiota, Oral microbiota, Upper airways",Experiment 4,United States of America,Homo sapiens,"Mouth,External nose","UBERON:0000165,UBERON:0007827",Atopic asthma,EFO:0010638,nasal brush specimens,oral wash specimens,oral wash specimen type,27,27,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,increased,increased,NA,NA,NA,increased,Signature 1,Figure 3,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between paired nasal brush (NB) and oral wash (OW) specimen types,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|1760|2037|2049|1654;3384189|32066|203490|203491|1129771|32067;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:29885665/4/2,29885665,case-control,29885665,10.1186/s40168-018-0487-3,NA,"Durack J., Huang Y.J., Nariya S., Christian L.S., Ansel K.M., Beigelman A., Castro M., Dyer A.M., Israel E., Kraft M., Martin R.J., Mauger D.T., Rosenberg S.R., King T.S., White S.R., Denlinger L.C., Holguin F., Lazarus S.C., Lugogo N., Peters S.P., Smith L.J., Wechsler M.E., Lynch S.V. , Boushey H.A.",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,"Adult asthma, Atopy, Bronchial microbiota, Corynebacterium, Eosinophilic inflammation, Induced sputum microbiota, Lower airways, Moraxella, Nasal microbiota, Oral microbiota, Upper airways",Experiment 4,United States of America,Homo sapiens,"Mouth,External nose","UBERON:0000165,UBERON:0007827",Atopic asthma,EFO:0010638,nasal brush specimens,oral wash specimens,oral wash specimen type,27,27,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,increased,increased,NA,NA,NA,increased,Signature 2,Figure 3,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between paired nasal brush (NB) and oral wash (OW) specimen types,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Alloiococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|1239|91061|186826|186828|1651;1783272|201174|1760|85007|1653|1716;3379134|1224|1236|2887326|468|475;1783272|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:29885665/5/1,29885665,case-control,29885665,10.1186/s40168-018-0487-3,NA,"Durack J., Huang Y.J., Nariya S., Christian L.S., Ansel K.M., Beigelman A., Castro M., Dyer A.M., Israel E., Kraft M., Martin R.J., Mauger D.T., Rosenberg S.R., King T.S., White S.R., Denlinger L.C., Holguin F., Lazarus S.C., Lugogo N., Peters S.P., Smith L.J., Wechsler M.E., Lynch S.V. , Boushey H.A.",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,"Adult asthma, Atopy, Bronchial microbiota, Corynebacterium, Eosinophilic inflammation, Induced sputum microbiota, Lower airways, Moraxella, Nasal microbiota, Oral microbiota, Upper airways",Experiment 5,United States of America,Homo sapiens,"Sputum,Mouth","UBERON:0007311,UBERON:0000165",Atopic asthma,EFO:0010638,induced sputum specimens,oral wash specimens,oral wash specimen type,27,27,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between paired induced sputum (IS) and oral wash (OW) specimen types,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,1783272|201174|1760|2037|2049|1654,Complete,Claregrieve1
bsdb:29885665/5/2,29885665,case-control,29885665,10.1186/s40168-018-0487-3,NA,"Durack J., Huang Y.J., Nariya S., Christian L.S., Ansel K.M., Beigelman A., Castro M., Dyer A.M., Israel E., Kraft M., Martin R.J., Mauger D.T., Rosenberg S.R., King T.S., White S.R., Denlinger L.C., Holguin F., Lazarus S.C., Lugogo N., Peters S.P., Smith L.J., Wechsler M.E., Lynch S.V. , Boushey H.A.",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,"Adult asthma, Atopy, Bronchial microbiota, Corynebacterium, Eosinophilic inflammation, Induced sputum microbiota, Lower airways, Moraxella, Nasal microbiota, Oral microbiota, Upper airways",Experiment 5,United States of America,Homo sapiens,"Sputum,Mouth","UBERON:0007311,UBERON:0000165",Atopic asthma,EFO:0010638,induced sputum specimens,oral wash specimens,oral wash specimen type,27,27,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between paired induced sputum (IS) and oral wash (OW) specimen types,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|201174|1760|85007|1653|1716;3379134|976|200643|171549|171552|838;1783272|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:29885665/6/1,29885665,case-control,29885665,10.1186/s40168-018-0487-3,NA,"Durack J., Huang Y.J., Nariya S., Christian L.S., Ansel K.M., Beigelman A., Castro M., Dyer A.M., Israel E., Kraft M., Martin R.J., Mauger D.T., Rosenberg S.R., King T.S., White S.R., Denlinger L.C., Holguin F., Lazarus S.C., Lugogo N., Peters S.P., Smith L.J., Wechsler M.E., Lynch S.V. , Boushey H.A.",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,"Adult asthma, Atopy, Bronchial microbiota, Corynebacterium, Eosinophilic inflammation, Induced sputum microbiota, Lower airways, Moraxella, Nasal microbiota, Oral microbiota, Upper airways",Experiment 6,United States of America,Homo sapiens,"Bronchus,Sputum","UBERON:0007311,UBERON:0002185",Atopic asthma,EFO:0010638,bronchial brush specimens,induced sputum specimens,induced sputum specimen type,27,27,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,unchanged,increased,NA,NA,NA,increased,Signature 1,Figure 3,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between paired bronchial brush (BB) and induced sputum (IS) specimen types,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3384189|32066|203490|203491|1129771|32067;1783272|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:29885665/7/1,29885665,case-control,29885665,10.1186/s40168-018-0487-3,NA,"Durack J., Huang Y.J., Nariya S., Christian L.S., Ansel K.M., Beigelman A., Castro M., Dyer A.M., Israel E., Kraft M., Martin R.J., Mauger D.T., Rosenberg S.R., King T.S., White S.R., Denlinger L.C., Holguin F., Lazarus S.C., Lugogo N., Peters S.P., Smith L.J., Wechsler M.E., Lynch S.V. , Boushey H.A.",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,"Adult asthma, Atopy, Bronchial microbiota, Corynebacterium, Eosinophilic inflammation, Induced sputum microbiota, Lower airways, Moraxella, Nasal microbiota, Oral microbiota, Upper airways",Experiment 7,United States of America,Homo sapiens,External nose,UBERON:0007827,Atopic asthma,EFO:0010638,healthy controls,atopic asthma subjects,subjects with atopic asthma,11,22,3 months,16S,4,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S6B,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks,Chloe",Asthmatic subjects showed significant enrichment in a number of specific Staphylococcus taxa in NB samples compared to HCs.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hydrogenophaga,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae",1783272|1239|91061|1385|90964|1279;3379134|1224|28216|206351|481;1783272|201174|1760|85007|1653|1716;3379134|1224|28216|80840|80864|47420;1783272|1239|91061|1385|90964|1279|1282;1783272|1239|91061|1385|186818,Complete,Claregrieve1
bsdb:29901485/1/1,29901485,"cross-sectional observational, not case-control",29901485,10.1097/PSY.0000000000000614.,https://pubmed.ncbi.nlm.nih.gov/29901485/,"Carson T.L., Wang F., Cui X., Jackson B.E., Van Der Pol W.J., Lefkowitz E.J., Morrow C. , Baskin M.L.","Associations Between Race, Perceived Psychological Stress, and the Gut Microbiota in a Sample of Generally Healthy Black and White Women: A Pilot Study on the Role of Race and Perceived Psychological Stress",Psychosomatic medicine,2018,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,White Women,Black Women,Healthy non-Hispanic black females (age ≥19 years),33,47,3 months,16S,4,Illumina,NA,PERMANOVA,0.05,TRUE,NA,NA,"age,body mass index,diet,waist circumference",NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table 3,29 June 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1,WikiWorks",Racial comparisons of the average abundance of selected colorectal cancer-associated genera.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,Claregrieve1
bsdb:29904624/1/1,29904624,case-control,29904624,10.3389/fcimb.2018.00167,NA,"Wu P., Zhang G., Zhao J., Chen J., Chen Y., Huang W., Zhong J. , Zeng J.",Profiling the Urinary Microbiota in Male Patients With Bladder Cancer in China,Frontiers in cellular and infection microbiology,2018,"extracellular matrix, inflammation, microbiota, urinary bladder neoplasms, urinary tract",Experiment 1,China,Homo sapiens,Urine,UBERON:0001088,Bladder carcinoma,NA,Non-neoplastic (controls),Bladder cancer,Male patients with bladder cancer,18,31,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 1,Figure 4B,7 April 2024,Ayibatari,"Ayibatari,Scholastica,WikiWorks",Microbial taxa associated with bladder cancer (red) versus non-cancer group (green),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baylyi,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Atopostipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Candidatus Limnoluna,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Geobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales,k__Bacillati|p__Actinomycetota|c__Rubrobacteria,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium",3379134|1224|1236|2887326|468|469;3379134|1224|1236|2887326|468|469|202950;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|91061|186826|186828|292480;1783272|201174|1760|85006|85023|507002;1783272|1239|91061|186826|186828;1783272|1239|91061|1385|3120669|129337;3379134|1224|28211|766;33090|35493|3398|72025|3803|3814|508215;1783272|201174|84995|84996|84997|42255;1783272|201174|84995|84996|84997;1783272|201174|84995|84996;1783272|201174|84995;3379134|976|117747|200666|84566;3379134|976|117747|200666|84566|28453,Complete,Svetlana up
bsdb:29904624/1/2,29904624,case-control,29904624,10.3389/fcimb.2018.00167,NA,"Wu P., Zhang G., Zhao J., Chen J., Chen Y., Huang W., Zhong J. , Zeng J.",Profiling the Urinary Microbiota in Male Patients With Bladder Cancer in China,Frontiers in cellular and infection microbiology,2018,"extracellular matrix, inflammation, microbiota, urinary bladder neoplasms, urinary tract",Experiment 1,China,Homo sapiens,Urine,UBERON:0001088,Bladder carcinoma,NA,Non-neoplastic (controls),Bladder cancer,Male patients with bladder cancer,18,31,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 2,Figure 4B,7 April 2024,Ayibatari,"Ayibatari,Scholastica,WikiWorks",Microbial taxa associated with bladder cancer (red) versus non-cancer group (green),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Roseomonadaceae|g__Roseomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",3379134|1224|28211|3120395|433;3379134|976|200643;3379134|1224|28216|80840|119060;1783272|1239|186801|186802|186806|1730|39497;3379134|1224|1236|91347|1903414|583;3379134|1224|28211|204441;3379134|1224|28211|3120395|3385906|125216;3379134|1224|1236|91347|1903411|613;3379134|976|200643|171549|2005473,Complete,Svetlana up
bsdb:29904624/2/1,29904624,case-control,29904624,10.3389/fcimb.2018.00167,NA,"Wu P., Zhang G., Zhao J., Chen J., Chen Y., Huang W., Zhong J. , Zeng J.",Profiling the Urinary Microbiota in Male Patients With Bladder Cancer in China,Frontiers in cellular and infection microbiology,2018,"extracellular matrix, inflammation, microbiota, urinary bladder neoplasms, urinary tract",Experiment 2,China,Homo sapiens,Urine,UBERON:0001088,Disease recurrence,EFO:0004952,Lower risk of recurrence (LER),Higher risk of recurrence (HER),"Male bladder cancer patients stratified into the higher risk of recurrence group (HER, recurrence score of EORTC ≥ 5) based on European Organization for Research and Treatment of Cancer (EORTC) scoring system",16,10,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 1,Supplementary Figure 4B,7 April 2024,Ayibatari,"Ayibatari,Scholastica,WikiWorks","Microbial taxa associated with high risk of recurrence (HER, red) versus low risk of recurrence (LER, green)",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacillati|p__Chloroflexota|c__Chloroflexia|o__Chloroflexales,k__Bacillati|p__Chloroflexota|c__Chloroflexia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Porphyrobacter",3379134|1224|1236|135624|84642;3379134|1224|1236|135624;3379134|1224|1236|135624|84642|642;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|29547|3031852|213849|72294;3379134|29547|3031852|213849;1783272|200795|32061|32064;1783272|200795|32061;1783272|201174|1760|85006|85020;3379134|29547|3031852;3379134|1224|28211|204457|335929;1783272|1239|186801|186802|216572|216851;1783272|1239|91061|1385|539738|1378;3379134|1224|28216|80840|75682|963;1783272|201174|1760|85009|85015;3379134|1224|28211|204457|335929|1111,Complete,Svetlana up
bsdb:29904624/2/2,29904624,case-control,29904624,10.3389/fcimb.2018.00167,NA,"Wu P., Zhang G., Zhao J., Chen J., Chen Y., Huang W., Zhong J. , Zeng J.",Profiling the Urinary Microbiota in Male Patients With Bladder Cancer in China,Frontiers in cellular and infection microbiology,2018,"extracellular matrix, inflammation, microbiota, urinary bladder neoplasms, urinary tract",Experiment 2,China,Homo sapiens,Urine,UBERON:0001088,Disease recurrence,EFO:0004952,Lower risk of recurrence (LER),Higher risk of recurrence (HER),"Male bladder cancer patients stratified into the higher risk of recurrence group (HER, recurrence score of EORTC ≥ 5) based on European Organization for Research and Treatment of Cancer (EORTC) scoring system",16,10,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 2,Supplementary Figure 4B,7 April 2024,Ayibatari,"Ayibatari,Scholastica,WikiWorks","Microbial taxa associated with high risk of recurrence (HER, red) versus low risk of recurrence (LER, green)",decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:29904624/3/1,29904624,case-control,29904624,10.3389/fcimb.2018.00167,NA,"Wu P., Zhang G., Zhao J., Chen J., Chen Y., Huang W., Zhong J. , Zeng J.",Profiling the Urinary Microbiota in Male Patients With Bladder Cancer in China,Frontiers in cellular and infection microbiology,2018,"extracellular matrix, inflammation, microbiota, urinary bladder neoplasms, urinary tract",Experiment 3,China,Homo sapiens,Urine,UBERON:0001088,Disease progression measurement,EFO:0008336,Lower risk of progression (LEP),Higher risk of progression (HEP),"Male bladder cancer patients stratified into the higher risk of progression group (HEP, progression score of EORTC ≥ 7) based on European Organization for Research and Treatment of Cancer (EORTC) scoring system",15,11,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 1,Supplementary Figure 5B,7 April 2024,Ayibatari,"Ayibatari,Scholastica,WikiWorks","Microbial taxa associated with high risk of progression (HEP, red) versus low risk of progression (LEP, green)",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Chloroflexota|c__Chloroflexia|o__Chloroflexales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Marmoricola,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Porphyrobacter",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|200795|32061|32064;1783272|201174|1760|85006|85020;3379134|1224|28211|204457|335929;1783272|201174|1760|85009|85015|86795;1783272|201174|1760|85006|1268;1783272|201174|1760|85009|85015;3379134|1224|28211|204457|335929|1111,Complete,Svetlana up
bsdb:29904624/3/2,29904624,case-control,29904624,10.3389/fcimb.2018.00167,NA,"Wu P., Zhang G., Zhao J., Chen J., Chen Y., Huang W., Zhong J. , Zeng J.",Profiling the Urinary Microbiota in Male Patients With Bladder Cancer in China,Frontiers in cellular and infection microbiology,2018,"extracellular matrix, inflammation, microbiota, urinary bladder neoplasms, urinary tract",Experiment 3,China,Homo sapiens,Urine,UBERON:0001088,Disease progression measurement,EFO:0008336,Lower risk of progression (LEP),Higher risk of progression (HEP),"Male bladder cancer patients stratified into the higher risk of progression group (HEP, progression score of EORTC ≥ 7) based on European Organization for Research and Treatment of Cancer (EORTC) scoring system",15,11,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 2,Supplementary Figure 5B,7 April 2024,Ayibatari,"Ayibatari,Scholastica,WikiWorks","Microbial taxa associated with high risk of progression (HEP, red) versus low risk of progression (LEP, green)",decreased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__uncultured Corynebacterium sp.",1783272|1239|91061;1783272|1239;1783272|1117;1783272|1239|91061|186826;1783272|201174|1760|85007|1653|1716|159447,Complete,Svetlana up
bsdb:29909506/1/1,29909506,time series / longitudinal observational,29909506,10.1186/s13568-018-0629-9,NA,"Bang S.J., Kim G., Lim M.Y., Song E.J., Jung D.H., Kum J.S., Nam Y.D., Park C.S. , Seo D.H.",The influence of in vitro pectin fermentation on the human fecal microbiome,AMB Express,2018,"Fecal microbiota, Fermentation, Pectin, Prebiotic, Short chain fatty acids",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,late pectin incubation time,early pectin incubation time,before/early pectin incubation,3,3,6 months,16S,12,Ion Torrent,relative abundances,Linear Regression,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4 and text,10 January 2021,Lora Kasselman,WikiWorks,Significantly changed taxa according to pectin incubation time (q value < 0.1),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|201174|1760|85004|31953|1678;1783272|201174|84998|84999|84107;1783272|1239|526524|526525|2810280|100883;1783272|1239|186801|3082720|186804;3379134|1224|28216|80840|75682|846;1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|31979;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|3085636|186803|33042;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|2005525|375288;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3085636|186803|841;3379134|976|200643|171549|171550;3379134|976|200643|171549|815|816,Complete,Folakunmi
bsdb:29909506/1/2,29909506,time series / longitudinal observational,29909506,10.1186/s13568-018-0629-9,NA,"Bang S.J., Kim G., Lim M.Y., Song E.J., Jung D.H., Kum J.S., Nam Y.D., Park C.S. , Seo D.H.",The influence of in vitro pectin fermentation on the human fecal microbiome,AMB Express,2018,"Fecal microbiota, Fermentation, Pectin, Prebiotic, Short chain fatty acids",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,late pectin incubation time,early pectin incubation time,before/early pectin incubation,3,3,6 months,16S,12,Ion Torrent,relative abundances,Linear Regression,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4 and text,10 January 2021,Lora Kasselman,WikiWorks,Significantly changed taxa according to pectin incubation time (q value < 0.1),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",1783272|1239|186801|3085636|186803|28050;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|31979|1485;3379134|1224|28216|80840;3379134|976|200643|171549,Complete,Folakunmi
bsdb:29920927/1/1,29920927,prospective cohort,29920927,10.1111/ajt.14974,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301138/,"Lee J.R., Magruder M., Zhang L., Westblade L.F., Satlin M.J., Robertson A., Edusei E., Crawford C., Ling L., Taur Y., Schluter J., Lubetzky M., Dadhania D., Pamer E. , Suthanthiran M.",Gut microbiota dysbiosis and diarrhea in kidney transplant recipients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2019,"complication: medical/metabolic, diarrhea, gut microbiota, kidney disease, kidney transplantation/nephrology, microbiomics, translational research/science",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Controls (No Diarrhea Group),Diarrhea Group,Kidney transplant recipients that developed post-transplant diarrhea within the first 3 months after transplantation,46,18,NA,16S,45,Illumina,relative abundances,Mann-Whitney (Wilcoxon),NA,NA,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Figure 2, Table 2",29 March 2023,Ufuoma Ejite,"Ufuoma Ejite,Atrayees,WikiWorks",Differential microbial abundance between Controls and Diarrhea group,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus",1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|526524|526525|2810280|100883;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|33042,Complete,Atrayees
bsdb:29920927/1/2,29920927,prospective cohort,29920927,10.1111/ajt.14974,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301138/,"Lee J.R., Magruder M., Zhang L., Westblade L.F., Satlin M.J., Robertson A., Edusei E., Crawford C., Ling L., Taur Y., Schluter J., Lubetzky M., Dadhania D., Pamer E. , Suthanthiran M.",Gut microbiota dysbiosis and diarrhea in kidney transplant recipients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2019,"complication: medical/metabolic, diarrhea, gut microbiota, kidney disease, kidney transplantation/nephrology, microbiomics, translational research/science",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Controls (No Diarrhea Group),Diarrhea Group,Kidney transplant recipients that developed post-transplant diarrhea within the first 3 months after transplantation,46,18,NA,16S,45,Illumina,relative abundances,Mann-Whitney (Wilcoxon),NA,NA,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 2,29 March 2023,Ufuoma Ejite,"Ufuoma Ejite,WikiWorks",Differential microbial abundance between Controls and Diarrhea group,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|561;1783272|1239|186801|3085636|186803|1506553,Complete,Atrayees
bsdb:29920927/2/1,29920927,prospective cohort,29920927,10.1111/ajt.14974,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301138/,"Lee J.R., Magruder M., Zhang L., Westblade L.F., Satlin M.J., Robertson A., Edusei E., Crawford C., Ling L., Taur Y., Schluter J., Lubetzky M., Dadhania D., Pamer E. , Suthanthiran M.",Gut microbiota dysbiosis and diarrhea in kidney transplant recipients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2019,"complication: medical/metabolic, diarrhea, gut microbiota, kidney disease, kidney transplantation/nephrology, microbiomics, translational research/science",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Antibiotic-excluded Controls (No Diarrhea Group),Antibiotic-excluded Diarrhea Group,Antibiotic-excluded diarrheal group; Kidney transplant recipients that developed post-transplant diarrhea within the first 3 months after transplantation,46,13,NA,16S,45,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,antibiotic exposure,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S2,18 April 2023,Ufuoma Ejite,"Ufuoma Ejite,Atrayees,WikiWorks",Differential microbial abundance between Antibiotic-excluded Controls and Antibiotic-excluded Diarrhea group,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus",1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|1407607;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|1508657;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|204475;1783272|1239|526524|526525|2810280|100883,Complete,Atrayees
bsdb:29920927/2/2,29920927,prospective cohort,29920927,10.1111/ajt.14974,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301138/,"Lee J.R., Magruder M., Zhang L., Westblade L.F., Satlin M.J., Robertson A., Edusei E., Crawford C., Ling L., Taur Y., Schluter J., Lubetzky M., Dadhania D., Pamer E. , Suthanthiran M.",Gut microbiota dysbiosis and diarrhea in kidney transplant recipients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2019,"complication: medical/metabolic, diarrhea, gut microbiota, kidney disease, kidney transplantation/nephrology, microbiomics, translational research/science",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Antibiotic-excluded Controls (No Diarrhea Group),Antibiotic-excluded Diarrhea Group,Antibiotic-excluded diarrheal group; Kidney transplant recipients that developed post-transplant diarrhea within the first 3 months after transplantation,46,13,NA,16S,45,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,antibiotic exposure,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S2,18 April 2023,Ufuoma Ejite,"Ufuoma Ejite,Atrayees,WikiWorks",Differential microbial abundance between Antibiotic-excluded Controls and Antibiotic-excluded Diarrhea group,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|186801|3085636|186803|1506553;3379134|1224|1236|91347|543|561;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|3085636|186803|572511;1783272|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:29920927/3/1,29920927,prospective cohort,29920927,10.1111/ajt.14974,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301138/,"Lee J.R., Magruder M., Zhang L., Westblade L.F., Satlin M.J., Robertson A., Edusei E., Crawford C., Ling L., Taur Y., Schluter J., Lubetzky M., Dadhania D., Pamer E. , Suthanthiran M.",Gut microbiota dysbiosis and diarrhea in kidney transplant recipients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2019,"complication: medical/metabolic, diarrhea, gut microbiota, kidney disease, kidney transplantation/nephrology, microbiomics, translational research/science",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,1000 mg/day MMF Dosage No Diarrhea Group,2000 mg/day MMF Dosage No Diarrhea Group,2000 mg/day MMF Dosage administered to the No Diarrhea Group,21,25,NA,16S,45,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,intake of diabetes medication,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S4,19 April 2023,Ufuoma Ejite,"Ufuoma Ejite,Atrayees,WikiWorks",Differential microbial abundance between 1000 mg/day MMF Dosage No Diarrhea Group and 2000 mg/day MMF Dosage No Diarrhea Group,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes",1783272|1239|526524|526525|128827;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3082720|186804|1505657;1783272|1239|186801|186802|186806|1730;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|207244,Complete,Atrayees
bsdb:29920927/3/2,29920927,prospective cohort,29920927,10.1111/ajt.14974,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301138/,"Lee J.R., Magruder M., Zhang L., Westblade L.F., Satlin M.J., Robertson A., Edusei E., Crawford C., Ling L., Taur Y., Schluter J., Lubetzky M., Dadhania D., Pamer E. , Suthanthiran M.",Gut microbiota dysbiosis and diarrhea in kidney transplant recipients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2019,"complication: medical/metabolic, diarrhea, gut microbiota, kidney disease, kidney transplantation/nephrology, microbiomics, translational research/science",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,1000 mg/day MMF Dosage No Diarrhea Group,2000 mg/day MMF Dosage No Diarrhea Group,2000 mg/day MMF Dosage administered to the No Diarrhea Group,21,25,NA,16S,45,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,intake of diabetes medication,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S4,6 June 2023,Atrayees,"Atrayees,WikiWorks",Differential microbial abundance between 1000 mg/day MMF Dosage No Diarrhea Group and 2000 mg/day MMF Dosage No Diarrhea Group,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger",1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|186802|204475,Complete,Atrayees
bsdb:29920927/4/1,29920927,prospective cohort,29920927,10.1111/ajt.14974,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301138/,"Lee J.R., Magruder M., Zhang L., Westblade L.F., Satlin M.J., Robertson A., Edusei E., Crawford C., Ling L., Taur Y., Schluter J., Lubetzky M., Dadhania D., Pamer E. , Suthanthiran M.",Gut microbiota dysbiosis and diarrhea in kidney transplant recipients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2019,"complication: medical/metabolic, diarrhea, gut microbiota, kidney disease, kidney transplantation/nephrology, microbiomics, translational research/science",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,1000 mg/day MMF Dosage No Diarrhea Group,1000 mg/day MMF Dosage Diarrhea Group,1000 mg/day MMF Dosage administered to the Diarrhea Group,21,4,NA,16S,45,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,intake of diabetes medication,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,19 April 2023,Ufuoma Ejite,"Ufuoma Ejite,Atrayees,WikiWorks",Differential microbial abundance between 1000 mg/day MMF Dosage No Diarrhea Group and 1000 mg/day MMF Dosage Diarrhea Group,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|186802|204475;1783272|1239|186801|3085636|186803|33042;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3082720|186804|1505657,Complete,Atrayees
bsdb:29920927/4/2,29920927,prospective cohort,29920927,10.1111/ajt.14974,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301138/,"Lee J.R., Magruder M., Zhang L., Westblade L.F., Satlin M.J., Robertson A., Edusei E., Crawford C., Ling L., Taur Y., Schluter J., Lubetzky M., Dadhania D., Pamer E. , Suthanthiran M.",Gut microbiota dysbiosis and diarrhea in kidney transplant recipients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2019,"complication: medical/metabolic, diarrhea, gut microbiota, kidney disease, kidney transplantation/nephrology, microbiomics, translational research/science",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,1000 mg/day MMF Dosage No Diarrhea Group,1000 mg/day MMF Dosage Diarrhea Group,1000 mg/day MMF Dosage administered to the Diarrhea Group,21,4,NA,16S,45,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,intake of diabetes medication,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S5,19 April 2023,Ufuoma Ejite,"Ufuoma Ejite,Atrayees,WikiWorks",Differential microbial abundance between 1000 mg/day MMF Dosage No Diarrhea Group and 1000 mg/day MMF Dosage Diarrhea Group,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus",1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|561;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|1506553;1783272|1239|526524|526525|2810280|100883,Complete,Atrayees
bsdb:29920927/5/1,29920927,prospective cohort,29920927,10.1111/ajt.14974,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301138/,"Lee J.R., Magruder M., Zhang L., Westblade L.F., Satlin M.J., Robertson A., Edusei E., Crawford C., Ling L., Taur Y., Schluter J., Lubetzky M., Dadhania D., Pamer E. , Suthanthiran M.",Gut microbiota dysbiosis and diarrhea in kidney transplant recipients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2019,"complication: medical/metabolic, diarrhea, gut microbiota, kidney disease, kidney transplantation/nephrology, microbiomics, translational research/science",Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,2000 mg/day MMF Dosage No Diarrhea Group,2000 mg/day MMF Dosage Diarrhea Group,2000 mg/day MMF Dosage administered to the Diarrhea Group,25,13,NA,16S,45,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,intake of diabetes medication,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S6,19 April 2023,Ufuoma Ejite,"Ufuoma Ejite,Atrayees,WikiWorks",Differential microbial abundance between 2000 mg/day MMF Dosage No Diarrhea Group and 2000 mg/day MMF Dosage Diarrhea Group,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|459786;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|204475;1783272|1239|526524|526525|2810280|100883;1783272|1239|526524|526525|2810280|3025755,Complete,Atrayees
bsdb:29920927/5/2,29920927,prospective cohort,29920927,10.1111/ajt.14974,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301138/,"Lee J.R., Magruder M., Zhang L., Westblade L.F., Satlin M.J., Robertson A., Edusei E., Crawford C., Ling L., Taur Y., Schluter J., Lubetzky M., Dadhania D., Pamer E. , Suthanthiran M.",Gut microbiota dysbiosis and diarrhea in kidney transplant recipients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2019,"complication: medical/metabolic, diarrhea, gut microbiota, kidney disease, kidney transplantation/nephrology, microbiomics, translational research/science",Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,2000 mg/day MMF Dosage No Diarrhea Group,2000 mg/day MMF Dosage Diarrhea Group,2000 mg/day MMF Dosage administered to the Diarrhea Group,25,13,NA,16S,45,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,intake of diabetes medication,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S6,19 April 2023,Ufuoma Ejite,"Ufuoma Ejite,Atrayees,WikiWorks",Differential microbial abundance between 2000 mg/day MMF Dosage No Diarrhea Group and 2000 mg/day MMF Dosage Diarrhea Group,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter",1783272|1239|91061|186826|81852|1350;1783272|1239|186801|3085636|186803|1506553;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3082720|186804|1505657,Complete,Atrayees
bsdb:29920927/6/1,29920927,prospective cohort,29920927,10.1111/ajt.14974,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301138/,"Lee J.R., Magruder M., Zhang L., Westblade L.F., Satlin M.J., Robertson A., Edusei E., Crawford C., Ling L., Taur Y., Schluter J., Lubetzky M., Dadhania D., Pamer E. , Suthanthiran M.",Gut microbiota dysbiosis and diarrhea in kidney transplant recipients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2019,"complication: medical/metabolic, diarrhea, gut microbiota, kidney disease, kidney transplantation/nephrology, microbiomics, translational research/science",Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Pre-Diarrheal specimens,Diarrheal specimens,Diarrheal specimens,14,14,NA,16S,45,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S7,7 June 2023,Atrayees,"Atrayees,WikiWorks",Relative abundance of taxa in Diarrheal specimens,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea",1783272|1239|186801|186802|204475;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803|207244;1783272|1239|526524|526525|2810280|3025755;1783272|1239|526524|526525|2810280|100883;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|1508657;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|33042;3379134|1224|1236|91347|543|561;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|189330,Complete,Atrayees
bsdb:29920927/6/2,29920927,prospective cohort,29920927,10.1111/ajt.14974,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301138/,"Lee J.R., Magruder M., Zhang L., Westblade L.F., Satlin M.J., Robertson A., Edusei E., Crawford C., Ling L., Taur Y., Schluter J., Lubetzky M., Dadhania D., Pamer E. , Suthanthiran M.",Gut microbiota dysbiosis and diarrhea in kidney transplant recipients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2019,"complication: medical/metabolic, diarrhea, gut microbiota, kidney disease, kidney transplantation/nephrology, microbiomics, translational research/science",Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Pre-Diarrheal specimens,Diarrheal specimens,Diarrheal specimens,14,14,NA,16S,45,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S7,7 June 2023,Atrayees,"Atrayees,WikiWorks",Relative abundance of taxa in Diarrheal specimens,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|1506553,Complete,Atrayees
bsdb:29920927/7/1,29920927,prospective cohort,29920927,10.1111/ajt.14974,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301138/,"Lee J.R., Magruder M., Zhang L., Westblade L.F., Satlin M.J., Robertson A., Edusei E., Crawford C., Ling L., Taur Y., Schluter J., Lubetzky M., Dadhania D., Pamer E. , Suthanthiran M.",Gut microbiota dysbiosis and diarrhea in kidney transplant recipients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2019,"complication: medical/metabolic, diarrhea, gut microbiota, kidney disease, kidney transplantation/nephrology, microbiomics, translational research/science",Experiment 7,United States of America,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,First Diarrheal Specimens Time-Matched Fecal Specimens from the No Diarrhea Group,First Diarrheal Specimens in the Diarrhea group,First Diarrheal Specimens in the Diarrhea group,46,18,NA,16S,45,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.15,NA,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Table S1,7 June 2023,Atrayees,"Atrayees,WikiWorks",Relative abundance of taxa in the Diarrhea Group,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|1508657;1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549|815|816;1783272|1239|526524|526525|2810280|100883;1783272|1239|186801|186802|204475;1783272|1239|526524|526525|2810280|3025755;1783272|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:29920927/7/2,29920927,prospective cohort,29920927,10.1111/ajt.14974,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301138/,"Lee J.R., Magruder M., Zhang L., Westblade L.F., Satlin M.J., Robertson A., Edusei E., Crawford C., Ling L., Taur Y., Schluter J., Lubetzky M., Dadhania D., Pamer E. , Suthanthiran M.",Gut microbiota dysbiosis and diarrhea in kidney transplant recipients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2019,"complication: medical/metabolic, diarrhea, gut microbiota, kidney disease, kidney transplantation/nephrology, microbiomics, translational research/science",Experiment 7,United States of America,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,First Diarrheal Specimens Time-Matched Fecal Specimens from the No Diarrhea Group,First Diarrheal Specimens in the Diarrhea group,First Diarrheal Specimens in the Diarrhea group,46,18,NA,16S,45,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.15,NA,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Table S1,7 June 2023,Atrayees,"Atrayees,WikiWorks",Relative abundance of taxa in the Diarrhea Group,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter",1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|561;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3082720|186804|1505657,Complete,Atrayees
bsdb:29922272/1/1,29922272,case-control,29922272,10.3389/fmicb.2018.01210,NA,"Del Chierico F., Abbatini F., Russo A., Quagliariello A., Reddel S., Capoccia D., Caccamo R., Ginanni Corradini S., Nobili V., De Peppo F., Dallapiccola B., Leonetti F., Silecchia G. , Putignani L.",Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns,Frontiers in microbiology,2018,"bacterial markers, dysbiosis, gut microbiota, metabolic pathways, obesity",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control adult,obese adolescent,Adolescents who are obese,25,12,2 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Table 2,10 January 2021,Marianthi Thomatos,"WikiWorks,ChiomaBlessing",Gut microbiota markers in Obese adolescents compared to the Adult control group.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",1783272|201174|1760|2037|2049|1654;1783272|1239|186801|186802|31979;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|1760|85009|31957|1912216|1747;1783272|1239|186801|186802|216572|216851|853,Complete,Shaimaa Elsafoury
bsdb:29922272/1/2,29922272,case-control,29922272,10.3389/fmicb.2018.01210,NA,"Del Chierico F., Abbatini F., Russo A., Quagliariello A., Reddel S., Capoccia D., Caccamo R., Ginanni Corradini S., Nobili V., De Peppo F., Dallapiccola B., Leonetti F., Silecchia G. , Putignani L.",Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns,Frontiers in microbiology,2018,"bacterial markers, dysbiosis, gut microbiota, metabolic pathways, obesity",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control adult,obese adolescent,Adolescents who are obese,25,12,2 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Table 2,10 January 2021,Marianthi Thomatos,"WikiWorks,ChiomaBlessing",Gut microbiota markers in Obese adolescents compared to the Adult control group.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,1783272|1239|186801|186802|216572|119852,Complete,Shaimaa Elsafoury
bsdb:29922272/2/1,29922272,case-control,29922272,10.3389/fmicb.2018.01210,NA,"Del Chierico F., Abbatini F., Russo A., Quagliariello A., Reddel S., Capoccia D., Caccamo R., Ginanni Corradini S., Nobili V., De Peppo F., Dallapiccola B., Leonetti F., Silecchia G. , Putignani L.",Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns,Frontiers in microbiology,2018,"bacterial markers, dysbiosis, gut microbiota, metabolic pathways, obesity",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control adolescent,obese adult,Adults who are obese,20,12,2 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Table 2,10 January 2021,Marianthi Thomatos,"WikiWorks,ChiomaBlessing",Gut microbiota markers in Obese adults compared to the Adolescents control group.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|186801|186802|31979;1783272|201174|1760|85009|31957|1912216|1747;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|1300|1301,Complete,Shaimaa Elsafoury
bsdb:29922272/2/2,29922272,case-control,29922272,10.3389/fmicb.2018.01210,NA,"Del Chierico F., Abbatini F., Russo A., Quagliariello A., Reddel S., Capoccia D., Caccamo R., Ginanni Corradini S., Nobili V., De Peppo F., Dallapiccola B., Leonetti F., Silecchia G. , Putignani L.",Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns,Frontiers in microbiology,2018,"bacterial markers, dysbiosis, gut microbiota, metabolic pathways, obesity",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control adolescent,obese adult,Adults who are obese,20,12,2 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Table 2,10 January 2021,Marianthi Thomatos,"WikiWorks,ChiomaBlessing",Gut microbiota markers in Obese adults compared to the Adolescents control group.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|2005519;1783272|1239|186801|186802|216572|119852,Complete,Shaimaa Elsafoury
bsdb:29922272/3/1,29922272,case-control,29922272,10.3389/fmicb.2018.01210,NA,"Del Chierico F., Abbatini F., Russo A., Quagliariello A., Reddel S., Capoccia D., Caccamo R., Ginanni Corradini S., Nobili V., De Peppo F., Dallapiccola B., Leonetti F., Silecchia G. , Putignani L.",Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns,Frontiers in microbiology,2018,"bacterial markers, dysbiosis, gut microbiota, metabolic pathways, obesity",Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control adult,control adolescent,NA,12,12,2 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Table 2,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiota markers in obese adolescent and adult patterns: age-dependent differential patterns,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae",1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|2005519,Complete,Shaimaa Elsafoury
bsdb:29922272/3/2,29922272,case-control,29922272,10.3389/fmicb.2018.01210,NA,"Del Chierico F., Abbatini F., Russo A., Quagliariello A., Reddel S., Capoccia D., Caccamo R., Ginanni Corradini S., Nobili V., De Peppo F., Dallapiccola B., Leonetti F., Silecchia G. , Putignani L.",Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns,Frontiers in microbiology,2018,"bacterial markers, dysbiosis, gut microbiota, metabolic pathways, obesity",Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control adult,control adolescent,NA,12,12,2 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Table 2,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiota markers in obese adolescent and adult patterns: age-dependent differential patterns,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|1300|1301,Complete,Shaimaa Elsafoury
bsdb:29922272/4/1,29922272,case-control,29922272,10.3389/fmicb.2018.01210,NA,"Del Chierico F., Abbatini F., Russo A., Quagliariello A., Reddel S., Capoccia D., Caccamo R., Ginanni Corradini S., Nobili V., De Peppo F., Dallapiccola B., Leonetti F., Silecchia G. , Putignani L.",Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns,Frontiers in microbiology,2018,"bacterial markers, dysbiosis, gut microbiota, metabolic pathways, obesity",Experiment 4,Italy,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,obese adult,obese adolescent,Adolescents who are obese,20,25,2 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table S4,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Gut microbiota markers in Obese adolescents compared to the Obese adult group.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",1783272|201174|1760|2037|2049|1654;1783272|201174;1783272|201174|84998|1643822|1643826|447020;1783272|1239;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|186802|216572|216851|853,Complete,Shaimaa Elsafoury
bsdb:29922272/5/1,29922272,case-control,29922272,10.3389/fmicb.2018.01210,NA,"Del Chierico F., Abbatini F., Russo A., Quagliariello A., Reddel S., Capoccia D., Caccamo R., Ginanni Corradini S., Nobili V., De Peppo F., Dallapiccola B., Leonetti F., Silecchia G. , Putignani L.",Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns,Frontiers in microbiology,2018,"bacterial markers, dysbiosis, gut microbiota, metabolic pathways, obesity",Experiment 5,Italy,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control adolescent,obese adolescent,Adolescents who are obese,12,25,2 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Table S4,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Gut microbiota markers in Obese adolescents compared to the Adolescents control group.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula",1783272|201174|1760|2037|2049|1654;1783272|201174;1783272|201174|84998|1643822|1643826|447020;1783272|1239;1783272|1239|186801|186802|31979;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|1760|85009|31957|1912216|1747;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465|29466,Complete,Shaimaa Elsafoury
bsdb:29922272/5/2,29922272,case-control,29922272,10.3389/fmicb.2018.01210,NA,"Del Chierico F., Abbatini F., Russo A., Quagliariello A., Reddel S., Capoccia D., Caccamo R., Ginanni Corradini S., Nobili V., De Peppo F., Dallapiccola B., Leonetti F., Silecchia G. , Putignani L.",Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns,Frontiers in microbiology,2018,"bacterial markers, dysbiosis, gut microbiota, metabolic pathways, obesity",Experiment 5,Italy,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control adolescent,obese adolescent,Adolescents who are obese,12,25,2 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Table S4,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Gut microbiota markers in Obese adolescents compared to the Adolescents control group.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",3379134|976|200643|171549|815|816|47678;3379134|976;3379134|976|200643|171549|2005519;1783272|1239|186801|186802|216572|119852,Complete,Shaimaa Elsafoury
bsdb:29922272/6/1,29922272,case-control,29922272,10.3389/fmicb.2018.01210,NA,"Del Chierico F., Abbatini F., Russo A., Quagliariello A., Reddel S., Capoccia D., Caccamo R., Ginanni Corradini S., Nobili V., De Peppo F., Dallapiccola B., Leonetti F., Silecchia G. , Putignani L.",Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns,Frontiers in microbiology,2018,"bacterial markers, dysbiosis, gut microbiota, metabolic pathways, obesity",Experiment 6,Italy,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control adult,obese adult,Adults who are obese,12,20,2 months,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table S4,10 January 2021,Shaimaa Elsafoury,"WikiWorks,ChiomaBlessing",Gut microbiota markers in Obese adults compared to the Adults control group.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",1783272|201174|1760|85009|31957|1912216|1747;1783272|1239|186801|186802|216572|216851|853,Complete,Shaimaa Elsafoury
bsdb:29926167/1/1,29926167,"cross-sectional observational, not case-control",29926167,https://doi.org/10.1007/s00535-018-1488-5,https://dx.doi.org/10.1007/s00535-018-1488-5,"Takagi T., Naito Y., Inoue R., Kashiwagi S., Uchiyama K., Mizushima K., Tsuchiya S., Dohi O., Yoshida N., Kamada K., Ishikawa T., Handa O., Konishi H., Okuda K., Tsujimoto Y., Ohnogi H. , Itoh Y.","Differences in gut microbiota associated with age, sex, and stool consistency in healthy Japanese subjects",Journal of gastroenterology,2019,"16S rRNA, Bristol stool scale, Gut microbiota",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Biological sex,PATO:0000047,Male,Female,Female subjects investigated for gut microbiota,138,139,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 4,11 April 2025,Anne-mariesharp,"Anne-mariesharp,Montana-D",Significantly different genera of gut microbiota between male and female subjects,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|186802|186806|264995;1783272|1239|186801|186802|216572|244127;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3082768|990719|990721;1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|2005519,Complete,KateRasheed
bsdb:29926167/1/2,29926167,"cross-sectional observational, not case-control",29926167,https://doi.org/10.1007/s00535-018-1488-5,https://dx.doi.org/10.1007/s00535-018-1488-5,"Takagi T., Naito Y., Inoue R., Kashiwagi S., Uchiyama K., Mizushima K., Tsuchiya S., Dohi O., Yoshida N., Kamada K., Ishikawa T., Handa O., Konishi H., Okuda K., Tsujimoto Y., Ohnogi H. , Itoh Y.","Differences in gut microbiota associated with age, sex, and stool consistency in healthy Japanese subjects",Journal of gastroenterology,2019,"16S rRNA, Bristol stool scale, Gut microbiota",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Biological sex,PATO:0000047,Male,Female,Female subjects investigated for gut microbiota,138,139,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 4,11 April 2025,Montana-D,"Montana-D,Anne-mariesharp",Significantly different genera of gut microbiota between male and female subjects.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|91061|186826|186827|46123;1783272|201174|1760|2037|2049|1654;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|186806|1730;3384189|32066|203490|203491|203492|848;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|909929|1843491|52225;1783272|1239|186801|3085636|186803|437755;1783272|1239|186801|3085636|186803|265975;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|171552|838,Complete,KateRasheed
bsdb:29926167/2/1,29926167,"cross-sectional observational, not case-control",29926167,https://doi.org/10.1007/s00535-018-1488-5,https://dx.doi.org/10.1007/s00535-018-1488-5,"Takagi T., Naito Y., Inoue R., Kashiwagi S., Uchiyama K., Mizushima K., Tsuchiya S., Dohi O., Yoshida N., Kamada K., Ishikawa T., Handa O., Konishi H., Okuda K., Tsujimoto Y., Ohnogi H. , Itoh Y.","Differences in gut microbiota associated with age, sex, and stool consistency in healthy Japanese subjects",Journal of gastroenterology,2019,"16S rRNA, Bristol stool scale, Gut microbiota",Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Abnormal stool composition,HP:0031685,Loose (stool in males),Intermediate (stool in males),Stool consistency (in males) classified as Intermediate using the Bristol stool scale (BSS),43,86,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 8A,11 April 2025,Anne-mariesharp,Anne-mariesharp,Significantly different genera of microbial communities among each stool consistency group for males according to the BSS (Bristol Stool Scale),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572,Complete,KateRasheed
bsdb:29926167/2/2,29926167,"cross-sectional observational, not case-control",29926167,https://doi.org/10.1007/s00535-018-1488-5,https://dx.doi.org/10.1007/s00535-018-1488-5,"Takagi T., Naito Y., Inoue R., Kashiwagi S., Uchiyama K., Mizushima K., Tsuchiya S., Dohi O., Yoshida N., Kamada K., Ishikawa T., Handa O., Konishi H., Okuda K., Tsujimoto Y., Ohnogi H. , Itoh Y.","Differences in gut microbiota associated with age, sex, and stool consistency in healthy Japanese subjects",Journal of gastroenterology,2019,"16S rRNA, Bristol stool scale, Gut microbiota",Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Abnormal stool composition,HP:0031685,Loose (stool in males),Intermediate (stool in males),Stool consistency (in males) classified as Intermediate using the Bristol stool scale (BSS),43,86,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 8A,11 April 2025,Anne-mariesharp,Anne-mariesharp,Significantly different genera of microbial communities among each stool consistency group for males according to the BSS (Bristol Stool Scale),decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",3384189|32066|203490|203491|203492|848;3379134|200940|3031449|213115|194924|35832,Complete,KateRasheed
bsdb:29926167/3/1,29926167,"cross-sectional observational, not case-control",29926167,https://doi.org/10.1007/s00535-018-1488-5,https://dx.doi.org/10.1007/s00535-018-1488-5,"Takagi T., Naito Y., Inoue R., Kashiwagi S., Uchiyama K., Mizushima K., Tsuchiya S., Dohi O., Yoshida N., Kamada K., Ishikawa T., Handa O., Konishi H., Okuda K., Tsujimoto Y., Ohnogi H. , Itoh Y.","Differences in gut microbiota associated with age, sex, and stool consistency in healthy Japanese subjects",Journal of gastroenterology,2019,"16S rRNA, Bristol stool scale, Gut microbiota",Experiment 3,Japan,Homo sapiens,Feces,UBERON:0001988,Abnormal stool composition,HP:0031685,Loose (stool in Males),Hard (stool in Males),Stool consistency (in males) classified as Hard using the Bristol stool scale (BSS),43,9,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 8A,11 April 2025,Montana-D,"Montana-D,Anne-mariesharp",Significantly different genera of microbial communities among each stool consistency group for males according to their BSS (Bristol Scale Score),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572,Complete,KateRasheed
bsdb:29926167/4/1,29926167,"cross-sectional observational, not case-control",29926167,https://doi.org/10.1007/s00535-018-1488-5,https://dx.doi.org/10.1007/s00535-018-1488-5,"Takagi T., Naito Y., Inoue R., Kashiwagi S., Uchiyama K., Mizushima K., Tsuchiya S., Dohi O., Yoshida N., Kamada K., Ishikawa T., Handa O., Konishi H., Okuda K., Tsujimoto Y., Ohnogi H. , Itoh Y.","Differences in gut microbiota associated with age, sex, and stool consistency in healthy Japanese subjects",Journal of gastroenterology,2019,"16S rRNA, Bristol stool scale, Gut microbiota",Experiment 4,Japan,Homo sapiens,Feces,UBERON:0001988,Abnormal stool composition,HP:0031685,Intermediate (stool in Males),Hard (stool in Males),Stool consistency (in males) classified as Hard using the Bristol stool scale (BSS),86,9,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 8A,11 April 2025,Montana-D,"Montana-D,Anne-mariesharp",Significantly different genera of microbial communities among each stool consistency group for males according to their BSS (Bristol Scale Score),increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,1783272|1239|186801|186802|216572|119852,Complete,KateRasheed
bsdb:29926167/5/2,29926167,"cross-sectional observational, not case-control",29926167,https://doi.org/10.1007/s00535-018-1488-5,https://dx.doi.org/10.1007/s00535-018-1488-5,"Takagi T., Naito Y., Inoue R., Kashiwagi S., Uchiyama K., Mizushima K., Tsuchiya S., Dohi O., Yoshida N., Kamada K., Ishikawa T., Handa O., Konishi H., Okuda K., Tsujimoto Y., Ohnogi H. , Itoh Y.","Differences in gut microbiota associated with age, sex, and stool consistency in healthy Japanese subjects",Journal of gastroenterology,2019,"16S rRNA, Bristol stool scale, Gut microbiota",Experiment 5,Japan,Homo sapiens,Feces,UBERON:0001988,Abnormal stool composition,HP:0031685,Loose (stool in Females),Intermediate (stool in Females),Stool consistency (in females) classified as intermediate using the Bristol stool scale (BSS),32,80,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 8B,11 April 2025,Montana-D,Montana-D,Significantly different genera of microbial communities among each stool consistency group for females according to the BSS (Bristol Scale Score),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia",3379134|1224|1236|135625|712|724;3379134|1224|1236|91347|1903411|613,Complete,KateRasheed
bsdb:29926167/6/1,29926167,"cross-sectional observational, not case-control",29926167,https://doi.org/10.1007/s00535-018-1488-5,https://dx.doi.org/10.1007/s00535-018-1488-5,"Takagi T., Naito Y., Inoue R., Kashiwagi S., Uchiyama K., Mizushima K., Tsuchiya S., Dohi O., Yoshida N., Kamada K., Ishikawa T., Handa O., Konishi H., Okuda K., Tsujimoto Y., Ohnogi H. , Itoh Y.","Differences in gut microbiota associated with age, sex, and stool consistency in healthy Japanese subjects",Journal of gastroenterology,2019,"16S rRNA, Bristol stool scale, Gut microbiota",Experiment 6,Japan,Homo sapiens,Feces,UBERON:0001988,Abnormal stool composition,HP:0031685,Loose (stool in females),Hard (stool in females),Stool consistency (in females) classified as hard using the Bristol stool scale (BSS),32,27,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 8B,11 April 2025,Anne-mariesharp,Anne-mariesharp,Significantly different genera of microbial communities among each stool consistency group for females according to the BSS (Bristol Stool Scale),increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",3379134|29547|3031852|213849|72294|194;1783272|1239|526524|526525|2810281|191303,Complete,KateRasheed
bsdb:29926167/7/1,29926167,"cross-sectional observational, not case-control",29926167,https://doi.org/10.1007/s00535-018-1488-5,https://dx.doi.org/10.1007/s00535-018-1488-5,"Takagi T., Naito Y., Inoue R., Kashiwagi S., Uchiyama K., Mizushima K., Tsuchiya S., Dohi O., Yoshida N., Kamada K., Ishikawa T., Handa O., Konishi H., Okuda K., Tsujimoto Y., Ohnogi H. , Itoh Y.","Differences in gut microbiota associated with age, sex, and stool consistency in healthy Japanese subjects",Journal of gastroenterology,2019,"16S rRNA, Bristol stool scale, Gut microbiota",Experiment 7,Japan,Homo sapiens,Feces,UBERON:0001988,Abnormal stool composition,HP:0031685,Intermediate (stool in Females),Hard (stool in Females),Stool consistency (in females) classified as Hard using the Bristol stool scale (BSS),80,27,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 8B,11 April 2025,Anne-mariesharp,Anne-mariesharp,Significantly different genera of microbial communities among each stool consistency group for females according to the BSS (Bristol Stool Scale),increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",1783272|201174|84998|1643822|1643826|447020;3379134|29547|3031852|213849|72294|194;1783272|1239|526524|526525|2810281|191303,Complete,KateRasheed
bsdb:29926167/8/1,29926167,"cross-sectional observational, not case-control",29926167,https://doi.org/10.1007/s00535-018-1488-5,https://dx.doi.org/10.1007/s00535-018-1488-5,"Takagi T., Naito Y., Inoue R., Kashiwagi S., Uchiyama K., Mizushima K., Tsuchiya S., Dohi O., Yoshida N., Kamada K., Ishikawa T., Handa O., Konishi H., Okuda K., Tsujimoto Y., Ohnogi H. , Itoh Y.","Differences in gut microbiota associated with age, sex, and stool consistency in healthy Japanese subjects",Journal of gastroenterology,2019,"16S rRNA, Bristol stool scale, Gut microbiota",Experiment 8,Japan,Homo sapiens,Feces,UBERON:0001988,Biological sex,PATO:0000047,Male (20 - 39years),Female (20 - 39years),Female subjects within the age group of 20 - 39years,19,28,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Supplementary Figure 4a,17 April 2025,Montana-D,"Montana-D,Anne-mariesharp",Significantly differential taxa between males and females within the age range (20-39),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239|186801|186802|186806|264995;1783272|201174|1760|85004|31953|1678;3379134|29547|3031852|213849|72294|194;1783272|1239|186801|186802|216572|1263,Complete,KateRasheed
bsdb:29926167/8/2,29926167,"cross-sectional observational, not case-control",29926167,https://doi.org/10.1007/s00535-018-1488-5,https://dx.doi.org/10.1007/s00535-018-1488-5,"Takagi T., Naito Y., Inoue R., Kashiwagi S., Uchiyama K., Mizushima K., Tsuchiya S., Dohi O., Yoshida N., Kamada K., Ishikawa T., Handa O., Konishi H., Okuda K., Tsujimoto Y., Ohnogi H. , Itoh Y.","Differences in gut microbiota associated with age, sex, and stool consistency in healthy Japanese subjects",Journal of gastroenterology,2019,"16S rRNA, Bristol stool scale, Gut microbiota",Experiment 8,Japan,Homo sapiens,Feces,UBERON:0001988,Biological sex,PATO:0000047,Male (20 - 39years),Female (20 - 39years),Female subjects within the age group of 20 - 39years,19,28,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Supplementary Figure 4a,17 April 2025,Montana-D,"Montana-D,Anne-mariesharp",Significantly differential taxa between males and females within the age range (20-39),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium",3379134|1224|1236|91347|543|561;1783272|1239|186801|3085636|186803|265975,Complete,KateRasheed
bsdb:29926167/9/1,29926167,"cross-sectional observational, not case-control",29926167,https://doi.org/10.1007/s00535-018-1488-5,https://dx.doi.org/10.1007/s00535-018-1488-5,"Takagi T., Naito Y., Inoue R., Kashiwagi S., Uchiyama K., Mizushima K., Tsuchiya S., Dohi O., Yoshida N., Kamada K., Ishikawa T., Handa O., Konishi H., Okuda K., Tsujimoto Y., Ohnogi H. , Itoh Y.","Differences in gut microbiota associated with age, sex, and stool consistency in healthy Japanese subjects",Journal of gastroenterology,2019,"16S rRNA, Bristol stool scale, Gut microbiota",Experiment 9,Japan,Homo sapiens,Feces,UBERON:0001988,Biological sex,PATO:0000047,Male (40 - 59years),Female (40 - 59years),Female subjects within the age group of 40 - 59years,51,49,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Supplementary Figure 4b,18 April 2025,Anne-mariesharp,Anne-mariesharp,Significant differential taxa between males and females of age range (40 - 59 years),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae|g__Defluviitalea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239|186801|186802|216572|52784;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|1185407|1185408;1783272|1239|186801|186802|186807|51514;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|171551|836;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802,Complete,KateRasheed
bsdb:29926167/9/2,29926167,"cross-sectional observational, not case-control",29926167,https://doi.org/10.1007/s00535-018-1488-5,https://dx.doi.org/10.1007/s00535-018-1488-5,"Takagi T., Naito Y., Inoue R., Kashiwagi S., Uchiyama K., Mizushima K., Tsuchiya S., Dohi O., Yoshida N., Kamada K., Ishikawa T., Handa O., Konishi H., Okuda K., Tsujimoto Y., Ohnogi H. , Itoh Y.","Differences in gut microbiota associated with age, sex, and stool consistency in healthy Japanese subjects",Journal of gastroenterology,2019,"16S rRNA, Bristol stool scale, Gut microbiota",Experiment 9,Japan,Homo sapiens,Feces,UBERON:0001988,Biological sex,PATO:0000047,Male (40 - 59years),Female (40 - 59years),Female subjects within the age group of 40 - 59years,51,49,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Supplementary Figure 4b,18 April 2025,Anne-mariesharp,"Anne-mariesharp,Montana-D",Significant differential taxa between males and females of age range (40 - 59 years),decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|909932|909929|1843491|158846;3379134|976|200643|171549|171552|838,Complete,KateRasheed
bsdb:29926167/10/1,29926167,"cross-sectional observational, not case-control",29926167,https://doi.org/10.1007/s00535-018-1488-5,https://dx.doi.org/10.1007/s00535-018-1488-5,"Takagi T., Naito Y., Inoue R., Kashiwagi S., Uchiyama K., Mizushima K., Tsuchiya S., Dohi O., Yoshida N., Kamada K., Ishikawa T., Handa O., Konishi H., Okuda K., Tsujimoto Y., Ohnogi H. , Itoh Y.","Differences in gut microbiota associated with age, sex, and stool consistency in healthy Japanese subjects",Journal of gastroenterology,2019,"16S rRNA, Bristol stool scale, Gut microbiota",Experiment 10,Japan,Homo sapiens,Feces,UBERON:0001988,Biological sex,PATO:0000047,Male (60 years or above),Female (60 years or above),Female subjects that are 60 years or above,69,61,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 1,Supplementary Figure 4C,17 April 2025,Montana-D,"Montana-D,Anne-mariesharp",Significantly abundant taxa between males and females of age range (60 or above),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",3379134|976|200643|171549|815|816;1783272|201174|84998|1643822|1643826|84111;1783272|1239|526524|526525|128827|61170;1783272|1239|526524|526525|2810281|191303,Complete,KateRasheed
bsdb:29926167/10/2,29926167,"cross-sectional observational, not case-control",29926167,https://doi.org/10.1007/s00535-018-1488-5,https://dx.doi.org/10.1007/s00535-018-1488-5,"Takagi T., Naito Y., Inoue R., Kashiwagi S., Uchiyama K., Mizushima K., Tsuchiya S., Dohi O., Yoshida N., Kamada K., Ishikawa T., Handa O., Konishi H., Okuda K., Tsujimoto Y., Ohnogi H. , Itoh Y.","Differences in gut microbiota associated with age, sex, and stool consistency in healthy Japanese subjects",Journal of gastroenterology,2019,"16S rRNA, Bristol stool scale, Gut microbiota",Experiment 10,Japan,Homo sapiens,Feces,UBERON:0001988,Biological sex,PATO:0000047,Male (60 years or above),Female (60 years or above),Female subjects that are 60 years or above,69,61,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 2,Supplementary Figure 4C,17 April 2025,Montana-D,"Montana-D,Anne-mariesharp",Significantly abundant taxa between males and females of age range (60 or above),decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Pseudomonadati|p__Bacteroidota",1783272|201174|1760|2037|2049|1654;3379134|200940|3031449|213115|194924|872;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3085636|186803|437755;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|171552|838;1783272|201174|84998|1643822|1643826|84108;3379134|976,Complete,KateRasheed
bsdb:29935270/1/1,29935270,case-control,29935270,10.1016/j.anaerobe.2018.06.009,NA,"Adamberg K., Adamberg S., Ernits K., Larionova A., Voor T., Jaagura M., Visnapuu T. , Alamäe T.","Composition and metabolism of fecal microbiota from normal and overweight children are differentially affected by melibiose, raffinose and raffinose-derived fructans",Anaerobe,2018,"Bacteroides, Candidate prebiotic, Dietary fiber, Fructooligosaccharides, Levan, Levansucrase, Short-chain fatty acids",Experiment 1,Estonia,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight children,overweight children,"overweight, but otherwise healthy children (7-12 years)",9,9,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3, Table S2, text",10 January 2021,Mst Afroza Parvin,"WikiWorks,Merit,Atrayees,Folakunmi",Composition of fecal pools used as inocula according to dominant taxa classified at the phylum or species level.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus equinus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus timonensis",1783272|1239|186801|3085636|186803|1766253|39491;1783272|201174|1760|85004|31953|1678|1681;1783272|1239|186801|3085636|186803|33042;1783272|1239|91061|186826|1300|1301|1335;1783272|1239|186801|3085636|186803|3342669|45851;1783272|1239|1737404|1737405|1570339|162289|1268254,Complete,Folakunmi
bsdb:29935270/1/2,29935270,case-control,29935270,10.1016/j.anaerobe.2018.06.009,NA,"Adamberg K., Adamberg S., Ernits K., Larionova A., Voor T., Jaagura M., Visnapuu T. , Alamäe T.","Composition and metabolism of fecal microbiota from normal and overweight children are differentially affected by melibiose, raffinose and raffinose-derived fructans",Anaerobe,2018,"Bacteroides, Candidate prebiotic, Dietary fiber, Fructooligosaccharides, Levan, Levansucrase, Short-chain fatty acids",Experiment 1,Estonia,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight children,overweight children,"overweight, but otherwise healthy children (7-12 years)",9,9,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3, Table S2",10 January 2021,Mst Afroza Parvin,"WikiWorks,Folakunmi,Scholastica,Welile",Composition of fecal pools used as inocula according to dominant taxa classified at the phylum or species level.,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanosphaera|s__Methanosphaera stadtmanae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia|s__Senegalimassilia anaerobia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__uncultured Lachnoclostridium sp.",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759|1288121;1783272|1239|186801|3085636|186803|207244|649756;3379134|976|200643|171549|815|816|246787;3379134|976|200643|171549|815|816|28111;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|2005519|397864|487174;1783272|201174|1760|85004|31953|1678|28025;3379134|200940|3031449|213115|194924|35832|35833;3366610|28890|183925|2158|2159|2316|2317;3379134|976|200643|171549|171552|577309|454154;3379134|976|200643|171549|815|909656|821;1783272|201174|84998|84999|84107|1473205|1473216;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|1506553|1586779,Complete,Folakunmi
bsdb:29935270/2/1,29935270,case-control,29935270,10.1016/j.anaerobe.2018.06.009,NA,"Adamberg K., Adamberg S., Ernits K., Larionova A., Voor T., Jaagura M., Visnapuu T. , Alamäe T.","Composition and metabolism of fecal microbiota from normal and overweight children are differentially affected by melibiose, raffinose and raffinose-derived fructans",Anaerobe,2018,"Bacteroides, Candidate prebiotic, Dietary fiber, Fructooligosaccharides, Levan, Levansucrase, Short-chain fatty acids",Experiment 2,Estonia,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Adults,Overweight children,"overweight, but otherwise healthy children (7-12 years)",9,7,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3, Table S2",10 January 2021,Mst Afroza Parvin,"WikiWorks,Merit,Folakunmi",Composition of fecal pools used as inocula according to dominant taxa classified at the phylum or species level.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium mitsuokai,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__Eubacteriales Family XIII. Incertae Sedis bacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Wegman et al. 2014),k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus equinus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus timonensis",1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|526524|526525|2810280|135858|100886;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|1898207;1783272|1239|186801|186802|31979|1485|1506;1783272|1239|186801|3085636|186803|1506553;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3082720|543314|2137877;1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|186802|216572|1263|1160721;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|91061|186826|1300|1301|1335;1783272|1239|1737404|1737405|1570339|162289|1268254,Complete,Folakunmi
bsdb:29935270/2/2,29935270,case-control,29935270,10.1016/j.anaerobe.2018.06.009,NA,"Adamberg K., Adamberg S., Ernits K., Larionova A., Voor T., Jaagura M., Visnapuu T. , Alamäe T.","Composition and metabolism of fecal microbiota from normal and overweight children are differentially affected by melibiose, raffinose and raffinose-derived fructans",Anaerobe,2018,"Bacteroides, Candidate prebiotic, Dietary fiber, Fructooligosaccharides, Levan, Levansucrase, Short-chain fatty acids",Experiment 2,Estonia,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Adults,Overweight children,"overweight, but otherwise healthy children (7-12 years)",9,7,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3, Table S2",10 January 2021,Mst Afroza Parvin,"WikiWorks,Folakunmi",Composition of fecal pools used as inocula according to dominant taxa classified at the phylum or species level.,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia|s__Senegalimassilia anaerobia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae",1783272|201174|84998|84999|84107|1473205|1473216;1783272|1239|186801|3085636|186803|33042|33043;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3082768|990719,Complete,Folakunmi
bsdb:29935270/3/1,29935270,case-control,29935270,10.1016/j.anaerobe.2018.06.009,NA,"Adamberg K., Adamberg S., Ernits K., Larionova A., Voor T., Jaagura M., Visnapuu T. , Alamäe T.","Composition and metabolism of fecal microbiota from normal and overweight children are differentially affected by melibiose, raffinose and raffinose-derived fructans",Anaerobe,2018,"Bacteroides, Candidate prebiotic, Dietary fiber, Fructooligosaccharides, Levan, Levansucrase, Short-chain fatty acids",Experiment 3,Estonia,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Adults,normal weight children,healthy children with normal weight (7-12 years),7,9,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3, Table S2",30 January 2024,Folakunmi,"Folakunmi,Joan Chuks,WikiWorks",Composition of fecal pools used as inocula according to dominant taxa classified at the species level.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium mitsuokai,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanosphaera|s__Methanosphaera stadtmanae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Wegman et al. 2014),k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Succiniclasticum,s__rumen bacterium NK4A214,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp.",1783272|201174|84998|1643822|1643826|447020|446660;3379134|976|200643|171549|815|816|338188;3379134|976|200643|171549|815|816|818;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|28025;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|526524|526525|2810280|135858|100886;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|1737404|1737405|1570339|150022|1260;1783272|1239|186801|3082720|186804|1505657|261299;3366610|28890|183925|2158|2159|2316|2317;3379134|976|200643|171549|815|909656|310298;3379134|976|200643|171549|815|909656|204516;1783272|1239|186801|186802|216572|1263|1160721;1783272|1239|909932|1843488|909930|40840;877428;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|1506553|2028282,Complete,Folakunmi
bsdb:29935270/3/2,29935270,case-control,29935270,10.1016/j.anaerobe.2018.06.009,NA,"Adamberg K., Adamberg S., Ernits K., Larionova A., Voor T., Jaagura M., Visnapuu T. , Alamäe T.","Composition and metabolism of fecal microbiota from normal and overweight children are differentially affected by melibiose, raffinose and raffinose-derived fructans",Anaerobe,2018,"Bacteroides, Candidate prebiotic, Dietary fiber, Fructooligosaccharides, Levan, Levansucrase, Short-chain fatty acids",Experiment 3,Estonia,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Adults,normal weight children,healthy children with normal weight (7-12 years),7,9,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3, Table S2",30 January 2024,Folakunmi,"Folakunmi,Joan Chuks,WikiWorks",Composition of fecal pools used as inocula according to dominant taxa classified at the species level.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium",1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|186802|216572|1263|40519;3379134|976|200643|171549|171552|1283313;1783272|1239|526524|526525|128827|331630,Complete,Folakunmi
bsdb:29950689/1/1,29950689,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters B.A., Shapiro J.A., Church T.R., Miller G., Trinh-Shevrin C., Yuen E., Friedlander C., Hayes R.B. , Ahn J.",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight,obese,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m2",211,142,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,unchanged,NA,NA,NA,decreased,Signature 1,Supplemental Table 4,10 January 2021,Marianthi Thomatos,"Merit,WikiWorks",Taxonomic sginature of obesity in a large study of American adults,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|201174|1760|2037|2049;1783272|201174|1760|2037;1783272|1239|526524|526525|128827|2749846|31971;1783272|1239|91061;3379134|976|200643|171549|815|816|28116;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|33042;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|186801|186802;3379134|1224|1236;1783272|1239|186801|3085636|186803|140625;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|541000;3379134|1224;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977,Complete,Shaimaa Elsafoury
bsdb:29950689/1/2,29950689,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters B.A., Shapiro J.A., Church T.R., Miller G., Trinh-Shevrin C., Yuen E., Friedlander C., Hayes R.B. , Ahn J.",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight,obese,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m2",211,142,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,unchanged,NA,NA,NA,decreased,Signature 2,Supplemental Table 4,10 January 2021,Marianthi Thomatos,"Merit,WikiWorks",Taxonomic sginature of obesity in a large study of American adults,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|186807|51514;1783272|1239|186801|3085636|186803|189330;1783272|1239|526524|526525|128827;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|541000;3379134|976|200643|171549|2005525|375288;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|976|200643|171549|171550,Complete,Shaimaa Elsafoury
bsdb:29950689/2/1,29950689,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters B.A., Shapiro J.A., Church T.R., Miller G., Trinh-Shevrin C., Yuen E., Friedlander C., Hayes R.B. , Ahn J.",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight,overweight,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m2",211,246,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Table 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Taxonomic sginature of obesity in a large study of American adults,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",3379134|976|200643|171549|815|816;1783272|1239|91061;1783272|1239|91061|186826;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|140625;1783272|1239|186801|186802|541000;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|1263;3379134|200940|3031449|213115|194924|35832,Complete,Shaimaa Elsafoury
bsdb:29950689/2/2,29950689,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters B.A., Shapiro J.A., Church T.R., Miller G., Trinh-Shevrin C., Yuen E., Friedlander C., Hayes R.B. , Ahn J.",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight,overweight,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m2",211,246,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplemental Table 4,10 January 2021,Shaimaa Elsafoury,"Merit,WikiWorks",Taxonomic sginature of obesity in a large study of American adults,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|186807|51514;1783272|1239|526524|526525|128827;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|541000;3379134|976|200643|171549|2005525|375288,Complete,Shaimaa Elsafoury
bsdb:29950689/3/1,29950689,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters B.A., Shapiro J.A., Church T.R., Miller G., Trinh-Shevrin C., Yuen E., Friedlander C., Hayes R.B. , Ahn J.",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight men,obese men,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m2",80,70,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 5,10 January 2021,Marianthi Thomatos,WikiWorks,Taxonomic sginature of obesity in a large study of American adults,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria",3379134|976|200643|171549|2005525|375288|823;1783272|1239|91061;1783272|1239|91061|186826;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|541000;1783272|1239|909932|1843489|31977;3379134|1224;3379134|1224|1236,Complete,Shaimaa Elsafoury
bsdb:29950689/3/2,29950689,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters B.A., Shapiro J.A., Church T.R., Miller G., Trinh-Shevrin C., Yuen E., Friedlander C., Hayes R.B. , Ahn J.",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight men,obese men,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m2",80,70,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table 5,10 January 2021,Marianthi Thomatos,"Merit,WikiWorks",Taxonomic sginature of obesity in a large study of American adults,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae",1783272|1239|186801|186802|31979;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;1783272|1239|186801|186802|186807|51514;1783272|1239|186801|186802|216572|1263;1783272|1239|1737404|1737405|1737406,Complete,Shaimaa Elsafoury
bsdb:29950689/4/1,29950689,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters B.A., Shapiro J.A., Church T.R., Miller G., Trinh-Shevrin C., Yuen E., Friedlander C., Hayes R.B. , Ahn J.",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,NA,Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight men,overweight men,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m3",80,171,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 5,10 January 2021,Shaimaa Elsafoury,WikiWorks,Taxonomic sginature of obesity in a large study of American adults,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium",3379134|976|200643|171549|815|816;1783272|1239|91061;1783272|1239|91061|186826;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|140625,Complete,Shaimaa Elsafoury
bsdb:29950689/4/2,29950689,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters B.A., Shapiro J.A., Church T.R., Miller G., Trinh-Shevrin C., Yuen E., Friedlander C., Hayes R.B. , Ahn J.",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,NA,Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight men,overweight men,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m3",80,171,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table 5,10 January 2021,Shaimaa Elsafoury,"Merit,WikiWorks",Taxonomic sginature of obesity in a large study of American adults,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Thermotogati|p__Synergistota|c__Synergistia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",1783272|1239|186801|3082768|990719;3379134|1224|28216|80840;1783272|1239|186801|186802|31979;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;1783272|1239|186801|186802|186807|51514;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|186802|216572|1263;3384194|508458|649775;1783272|1239|1737404|1737405|1737406;1783272|1239|186801|3085636|186803|2316020|33038,Complete,Shaimaa Elsafoury
bsdb:29950689/5/1,29950689,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters B.A., Shapiro J.A., Church T.R., Miller G., Trinh-Shevrin C., Yuen E., Friedlander C., Hayes R.B. , Ahn J.",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,NA,Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight women,obese women,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m5",131,72,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 5,10 January 2021,Marianthi Thomatos,WikiWorks,Taxonomic sginature of obesity in a large study of American adults,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239|91061;1783272|1239|91061|186826;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|186803|140625;3379134|1224;3379134|1224|28216|80840;3379134|1224|1236;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|1737404|1737405|1737406;1783272|1239|186801|186802|216572|1263,Complete,Shaimaa Elsafoury
bsdb:29950689/5/2,29950689,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters B.A., Shapiro J.A., Church T.R., Miller G., Trinh-Shevrin C., Yuen E., Friedlander C., Hayes R.B. , Ahn J.",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,NA,Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight women,obese women,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m5",131,72,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table 5,10 January 2021,Marianthi Thomatos,"Merit,WikiWorks",Taxonomic sginature of obesity in a large study of American adults,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium",1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|186807|51514;1783272|1239|186801;1783272|1239|186801|186802|1898207,Complete,Shaimaa Elsafoury
bsdb:29950689/6/1,29950689,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters B.A., Shapiro J.A., Church T.R., Miller G., Trinh-Shevrin C., Yuen E., Friedlander C., Hayes R.B. , Ahn J.",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,NA,Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight women,overweight women,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m7",131,75,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 5,10 January 2021,Shaimaa Elsafoury,WikiWorks,Taxonomic sginature of obesity in a large study of American adults,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",1783272|1239|91061;1783272|1239|91061|186826;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|140625;3379134|1224;3379134|1224|28216|80840;3379134|1224|1236;3379134|1224|1236|91347;3379134|1224|1236|91347|543,Complete,Shaimaa Elsafoury
bsdb:29950689/6/2,29950689,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters B.A., Shapiro J.A., Church T.R., Miller G., Trinh-Shevrin C., Yuen E., Friedlander C., Hayes R.B. , Ahn J.",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,NA,Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight women,overweight women,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m7",131,75,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table 5,10 January 2021,Shaimaa Elsafoury,"Merit,WikiWorks",Taxonomic sginature of obesity in a large study of American adults,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia",1783272|1239|186801|186802|31979;1783272|1239|186801,Complete,Shaimaa Elsafoury
bsdb:29955075/1/1,29955075,"cross-sectional observational, not case-control",29955075,10.1038/s41598-018-27980-3,NA,"Tuominen H., Rautava S., Syrjänen S., Collado M.C. , Rautava J.","HPV infection and bacterial microbiota in the placenta, uterine cervix and oral mucosa",Scientific reports,2018,NA,Experiment 1,Finland,Homo sapiens,Placenta,UBERON:0001987,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ placenta sample determined by PCR and genotyped with Multimetrix,26,13,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 1 + text,10 January 2021,Cynthia Anderson,WikiWorks,The bacterial microbiota in placenta samples negative and positive for HPV DNA,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners",1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|544448|2790996|2790998|2129;1783272|1239|91061|186826|33958|1578|147802,Complete,Fatima Zohra
bsdb:29955075/2/1,29955075,"cross-sectional observational, not case-control",29955075,10.1038/s41598-018-27980-3,NA,"Tuominen H., Rautava S., Syrjänen S., Collado M.C. , Rautava J.","HPV infection and bacterial microbiota in the placenta, uterine cervix and oral mucosa",Scientific reports,2018,NA,Experiment 2,Finland,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ cervical sample determined by PCR and genotyped with Multimetrix,30,9,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2 + text,10 January 2021,Cynthia Anderson,WikiWorks,The bacterial microbiota in cervical samples negative and positive for HPV DNA,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners",1783272|1239|91061|186826|33958|1578;1783272|544448|2790996|2790998|2129;1783272|1239|91061|186826|33958|1578|147802,Complete,Fatima Zohra
bsdb:29955075/2/2,29955075,"cross-sectional observational, not case-control",29955075,10.1038/s41598-018-27980-3,NA,"Tuominen H., Rautava S., Syrjänen S., Collado M.C. , Rautava J.","HPV infection and bacterial microbiota in the placenta, uterine cervix and oral mucosa",Scientific reports,2018,NA,Experiment 2,Finland,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ cervical sample determined by PCR and genotyped with Multimetrix,30,9,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2 + text,10 January 2021,Cynthia Anderson,WikiWorks,The bacterial microbiota in cervical samples negative and positive for HPV DNA,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus",1783272|1239|186801|3082720|186804;1783272|1239|91061|186826|81852;3379134|1224|1236|135625|712|724;1783272|1239|186801|3082720|186804|1257,Complete,Fatima Zohra
bsdb:29955075/3/1,29955075,"cross-sectional observational, not case-control",29955075,10.1038/s41598-018-27980-3,NA,"Tuominen H., Rautava S., Syrjänen S., Collado M.C. , Rautava J.","HPV infection and bacterial microbiota in the placenta, uterine cervix and oral mucosa",Scientific reports,2018,NA,Experiment 3,Finland,Homo sapiens,Mouth,UBERON:0000165,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ oral sample determined by PCR and genotyped with Multimetrix,26,13,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Figure 3 + text,10 January 2021,Cynthia Anderson,WikiWorks,The bacterial microbiota in oral samples negative and positive for HPV DNA,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia",1783272|201174|1760|85004|31953;1783272|1239|1737404|1737405|1570339|150022,Complete,Fatima Zohra
bsdb:29955075/3/2,29955075,"cross-sectional observational, not case-control",29955075,10.1038/s41598-018-27980-3,NA,"Tuominen H., Rautava S., Syrjänen S., Collado M.C. , Rautava J.","HPV infection and bacterial microbiota in the placenta, uterine cervix and oral mucosa",Scientific reports,2018,NA,Experiment 3,Finland,Homo sapiens,Mouth,UBERON:0000165,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ oral sample determined by PCR and genotyped with Multimetrix,26,13,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Figure 3 + text,10 January 2021,Cynthia Anderson,WikiWorks,The bacterial microbiota in oral samples negative and positive for HPV DNA,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,3379134|1224|1236|135625|712|724,Complete,Fatima Zohra
bsdb:29971220/1/1,29971220,"cross-sectional observational, not case-control",29971220,10.3389/fcimb.2018.00202,NA,"Gao J.J., Zhang Y., Gerhard M., Mejias-Luque R., Zhang L., Vieth M., Ma J.L., Bajbouj M., Suchanek S., Liu W.D., Ulm K., Quante M., Li Z.X., Zhou T., Schmid R., Classen M., Li W.Q., You W.C. , Pan K.F.",Association Between Gut Microbiota and <i>Helicobacter pylori</i>-Related Gastric Lesions in a High-Risk Population of Gastric Cancer,Frontiers in cellular and infection microbiology,2018,"16S ribosomal RNA gene sequencing, Helicobacter pylori, gastric lesions, gut microbiota, microbial diversity",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,non-current H.pylori infection,current H.pylori infection,patients with H.pylori infection (bacteria were histologically detected in any one of the biopsies or it was positively indicated by C-UBT),23,24,NA,16S,4,Illumina,NA,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure S2D,10 January 2021,Fatima Zohra,"Fatima,Claregrieve1,WikiWorks",differential microbial abundance between current or non-current H.Pylori infection subjects,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",1783272|1239|91061|1385|539738|1378;1783272|1239|526524|526525|128827,Complete,Claregrieve1
bsdb:29971220/1/2,29971220,"cross-sectional observational, not case-control",29971220,10.3389/fcimb.2018.00202,NA,"Gao J.J., Zhang Y., Gerhard M., Mejias-Luque R., Zhang L., Vieth M., Ma J.L., Bajbouj M., Suchanek S., Liu W.D., Ulm K., Quante M., Li Z.X., Zhou T., Schmid R., Classen M., Li W.Q., You W.C. , Pan K.F.",Association Between Gut Microbiota and <i>Helicobacter pylori</i>-Related Gastric Lesions in a High-Risk Population of Gastric Cancer,Frontiers in cellular and infection microbiology,2018,"16S ribosomal RNA gene sequencing, Helicobacter pylori, gastric lesions, gut microbiota, microbial diversity",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,non-current H.pylori infection,current H.pylori infection,patients with H.pylori infection (bacteria were histologically detected in any one of the biopsies or it was positively indicated by C-UBT),23,24,NA,16S,4,Illumina,NA,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure S2D,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",differential microbial abundance between current or non-current H.Pylori infection subjects,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax|s__Acidovorax facilis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus|s__Rhodococcus erythropolis",3379134|1224|28216|80840|80864|12916;3379134|1224|28216|80840|80864|12916|12917;1783272|201174|1760|85007|85025;1783272|201174|1760|85007|85025|1827;1783272|201174|1760|85007|85025|1827|1833,Complete,Claregrieve1
bsdb:29971220/2/1,29971220,"cross-sectional observational, not case-control",29971220,10.3389/fcimb.2018.00202,NA,"Gao J.J., Zhang Y., Gerhard M., Mejias-Luque R., Zhang L., Vieth M., Ma J.L., Bajbouj M., Suchanek S., Liu W.D., Ulm K., Quante M., Li Z.X., Zhou T., Schmid R., Classen M., Li W.Q., You W.C. , Pan K.F.",Association Between Gut Microbiota and <i>Helicobacter pylori</i>-Related Gastric Lesions in a High-Risk Population of Gastric Cancer,Frontiers in cellular and infection microbiology,2018,"16S ribosomal RNA gene sequencing, Helicobacter pylori, gastric lesions, gut microbiota, microbial diversity",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,past H.pylori infection,current H.pylori infection patients,patients with H.pylori infection (bacteria were histologically detected in any one of the biopsies or it was positively indicated by C-UBT),8,24,NA,16S,4,Illumina,NA,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2D,10 January 2021,Fatima Zohra,"Fatima,Claregrieve1,WikiWorks",differential microbial abundance between current and past H.Pylori infection subjects,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|1224|28216|80840|506;3379134|976|200643|171549;3379134|976|200643|171549|815|816|820;3379134|976;3379134|976|200643;3379134|1224|28216;3379134|1224|28216|80840;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|2974251|165179;3379134|976|200643|171549|171552;3379134|1224|28216|80840|995019|40544,Complete,Claregrieve1
bsdb:29971220/3/1,29971220,"cross-sectional observational, not case-control",29971220,10.3389/fcimb.2018.00202,NA,"Gao J.J., Zhang Y., Gerhard M., Mejias-Luque R., Zhang L., Vieth M., Ma J.L., Bajbouj M., Suchanek S., Liu W.D., Ulm K., Quante M., Li Z.X., Zhou T., Schmid R., Classen M., Li W.Q., You W.C. , Pan K.F.",Association Between Gut Microbiota and <i>Helicobacter pylori</i>-Related Gastric Lesions in a High-Risk Population of Gastric Cancer,Frontiers in cellular and infection microbiology,2018,"16S ribosomal RNA gene sequencing, Helicobacter pylori, gastric lesions, gut microbiota, microbial diversity",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,H.pylori negative,past H.pylori infection,subjects with evidence of past H.pylori infection but no current infection,15,8,NA,16S,4,Illumina,NA,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2D,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",differential microbial abundance between past H.Pylori infection subjects and individuals who are H.Pylori negative,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",3379134|976|200643|171549;3379134|976|200643|171549|815|816|28111;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|820;3379134|976;3379134|976|200643;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|815|909656|310298;3379134|976|200643|171549|171551,Complete,Claregrieve1
bsdb:29971220/4/1,29971220,"cross-sectional observational, not case-control",29971220,10.3389/fcimb.2018.00202,NA,"Gao J.J., Zhang Y., Gerhard M., Mejias-Luque R., Zhang L., Vieth M., Ma J.L., Bajbouj M., Suchanek S., Liu W.D., Ulm K., Quante M., Li Z.X., Zhou T., Schmid R., Classen M., Li W.Q., You W.C. , Pan K.F.",Association Between Gut Microbiota and <i>Helicobacter pylori</i>-Related Gastric Lesions in a High-Risk Population of Gastric Cancer,Frontiers in cellular and infection microbiology,2018,"16S ribosomal RNA gene sequencing, Helicobacter pylori, gastric lesions, gut microbiota, microbial diversity",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,normal,gastritis cases,subjects with gastric lesions (gastritis),7,18,NA,16S,4,Illumina,NA,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4,10 January 2021,Fatima Zohra,"Claregrieve1,Rukky,WikiWorks",differential microbial abundance between gastritis and non-gastritis (normal) subjects,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|s__Mollicutes bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae sp. B_A14,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium EM3",1783272|1239|186801|186802|216572|244127;1783272|1239|91061;1783272|1239;1783272|1239|186801;1783272|1239|186801|3085636|186803|189330;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;3379134|1224|1236;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|877420;1783272|1239|91061|186826;1783272|544448|31969|37628;1783272|1239|186801|186802|541000;1783272|1239|186801|186802|216572|2485925;1783272|1239|186801|186802|216572|3023528;3379134|1224|1236|91347|543|620;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|216572|2807717,Complete,Claregrieve1
bsdb:29971220/4/2,29971220,"cross-sectional observational, not case-control",29971220,10.3389/fcimb.2018.00202,NA,"Gao J.J., Zhang Y., Gerhard M., Mejias-Luque R., Zhang L., Vieth M., Ma J.L., Bajbouj M., Suchanek S., Liu W.D., Ulm K., Quante M., Li Z.X., Zhou T., Schmid R., Classen M., Li W.Q., You W.C. , Pan K.F.",Association Between Gut Microbiota and <i>Helicobacter pylori</i>-Related Gastric Lesions in a High-Risk Population of Gastric Cancer,Frontiers in cellular and infection microbiology,2018,"16S ribosomal RNA gene sequencing, Helicobacter pylori, gastric lesions, gut microbiota, microbial diversity",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,normal,gastritis cases,subjects with gastric lesions (gastritis),7,18,NA,16S,4,Illumina,NA,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",differential microbial abundance between gastritis and non-gastritis (normal) subjects,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia",3379134|976|200643|171549;3379134|976;3379134|976|200643,Complete,Claregrieve1
bsdb:29971220/5/1,29971220,"cross-sectional observational, not case-control",29971220,10.3389/fcimb.2018.00202,NA,"Gao J.J., Zhang Y., Gerhard M., Mejias-Luque R., Zhang L., Vieth M., Ma J.L., Bajbouj M., Suchanek S., Liu W.D., Ulm K., Quante M., Li Z.X., Zhou T., Schmid R., Classen M., Li W.Q., You W.C. , Pan K.F.",Association Between Gut Microbiota and <i>Helicobacter pylori</i>-Related Gastric Lesions in a High-Risk Population of Gastric Cancer,Frontiers in cellular and infection microbiology,2018,"16S ribosomal RNA gene sequencing, Helicobacter pylori, gastric lesions, gut microbiota, microbial diversity",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,normal,subjects with metaplasia,subjects with metaplasia,7,22,NA,16S,4,Illumina,NA,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks,Merit",differential microbial abundance between subjects with metaplasia and normal subjects,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium",1783272|1239;1783272|1239|186801;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|189330;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|3085636|186803|1506553;3379134|1224|1236;1783272|1239|186801|3085636|186803;1783272|1239|186801|3082720|186804;3379134|1224;1783272|1239|186801|3082720|186804|1501226;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|1898207,Complete,Claregrieve1
bsdb:29971220/5/2,29971220,"cross-sectional observational, not case-control",29971220,10.3389/fcimb.2018.00202,NA,"Gao J.J., Zhang Y., Gerhard M., Mejias-Luque R., Zhang L., Vieth M., Ma J.L., Bajbouj M., Suchanek S., Liu W.D., Ulm K., Quante M., Li Z.X., Zhou T., Schmid R., Classen M., Li W.Q., You W.C. , Pan K.F.",Association Between Gut Microbiota and <i>Helicobacter pylori</i>-Related Gastric Lesions in a High-Risk Population of Gastric Cancer,Frontiers in cellular and infection microbiology,2018,"16S ribosomal RNA gene sequencing, Helicobacter pylori, gastric lesions, gut microbiota, microbial diversity",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,normal,subjects with metaplasia,subjects with metaplasia,7,22,NA,16S,4,Illumina,NA,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",differential microbial abundance between subjects with metaplasia and normal subjects,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia",3379134|976|200643|171549;3379134|976;3379134|976|200643,Complete,Claregrieve1
bsdb:29971220/6/1,29971220,"cross-sectional observational, not case-control",29971220,10.3389/fcimb.2018.00202,NA,"Gao J.J., Zhang Y., Gerhard M., Mejias-Luque R., Zhang L., Vieth M., Ma J.L., Bajbouj M., Suchanek S., Liu W.D., Ulm K., Quante M., Li Z.X., Zhou T., Schmid R., Classen M., Li W.Q., You W.C. , Pan K.F.",Association Between Gut Microbiota and <i>Helicobacter pylori</i>-Related Gastric Lesions in a High-Risk Population of Gastric Cancer,Frontiers in cellular and infection microbiology,2018,"16S ribosomal RNA gene sequencing, Helicobacter pylori, gastric lesions, gut microbiota, microbial diversity",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,subjects with gastritis,subjects with metaplasia,subjects with metaplasia,18,22,NA,16S,4,Illumina,NA,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",differential microbial abundance between gastritis and metaplastia subjects,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236;3379134|1224,Complete,Claregrieve1
bsdb:29971220/6/2,29971220,"cross-sectional observational, not case-control",29971220,10.3389/fcimb.2018.00202,NA,"Gao J.J., Zhang Y., Gerhard M., Mejias-Luque R., Zhang L., Vieth M., Ma J.L., Bajbouj M., Suchanek S., Liu W.D., Ulm K., Quante M., Li Z.X., Zhou T., Schmid R., Classen M., Li W.Q., You W.C. , Pan K.F.",Association Between Gut Microbiota and <i>Helicobacter pylori</i>-Related Gastric Lesions in a High-Risk Population of Gastric Cancer,Frontiers in cellular and infection microbiology,2018,"16S ribosomal RNA gene sequencing, Helicobacter pylori, gastric lesions, gut microbiota, microbial diversity",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,subjects with gastritis,subjects with metaplasia,subjects with metaplasia,18,22,NA,16S,4,Illumina,NA,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks,Merit",differential microbial abundance between gastritis and metaplastia subjects,decreased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium",1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|1898207,Complete,Claregrieve1
bsdb:29988340/1/1,29988340,"cross-sectional observational, not case-control",29988340,10.3389/fmicb.2018.01250,NA,"Gao X., Zhang M., Xue J., Huang J., Zhuang R., Zhou X., Zhang H., Fu Q. , Hao Y.",Body Mass Index Differences in the Gut Microbiota Are Gender Specific,Frontiers in microbiology,2018,"16S rRNA, Chinese, gender, gut microbiota, obesity",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Sex design,EFO:0001752,male,female,NA,259,292,2 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,age,NA,increased,NA,unchanged,unchanged,increased,Signature 1,supplementry figure S2,10 January 2021,Marianthi Thomatos,WikiWorks,Differences in body mass index  and gut microbiota by Gender,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,1783272|1239|186801|186802|216572|1263,Complete,Shaimaa Elsafoury
bsdb:29988340/2/1,29988340,"cross-sectional observational, not case-control",29988340,10.3389/fmicb.2018.01250,NA,"Gao X., Zhang M., Xue J., Huang J., Zhuang R., Zhou X., Zhang H., Fu Q. , Hao Y.",Body Mass Index Differences in the Gut Microbiota Are Gender Specific,Frontiers in microbiology,2018,"16S rRNA, Chinese, gender, gut microbiota, obesity",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,female normal weight,female obese,NA,168,20,2 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,age,NA,unchanged,NA,unchanged,unchanged,increased,Signature 1,Text + fig 2B,10 January 2021,Marianthi Thomatos,WikiWorks,Differences in body mass index and gut microbiota by Gender,decreased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,1783272|1239|909932|1843488|909930|33024,Complete,Shaimaa Elsafoury
bsdb:29988340/3/1,29988340,"cross-sectional observational, not case-control",29988340,10.3389/fmicb.2018.01250,NA,"Gao X., Zhang M., Xue J., Huang J., Zhuang R., Zhou X., Zhang H., Fu Q. , Hao Y.",Body Mass Index Differences in the Gut Microbiota Are Gender Specific,Frontiers in microbiology,2018,"16S rRNA, Chinese, gender, gut microbiota, obesity",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,male normal weight,male obese,NA,93,38,2 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,age,NA,unchanged,NA,unchanged,unchanged,unchanged,Signature 1,Text + fig 2B,10 January 2021,Marianthi Thomatos,WikiWorks,Differences in body mass index and gut microbiota by Gender,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",3379134|976|200643|171549|1853231|574697;3384189|32066|203490|203491|203492|848,Complete,Shaimaa Elsafoury
bsdb:29988340/4/1,29988340,"cross-sectional observational, not case-control",29988340,10.3389/fmicb.2018.01250,NA,"Gao X., Zhang M., Xue J., Huang J., Zhuang R., Zhou X., Zhang H., Fu Q. , Hao Y.",Body Mass Index Differences in the Gut Microbiota Are Gender Specific,Frontiers in microbiology,2018,"16S rRNA, Chinese, gender, gut microbiota, obesity",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight,obese,NA,261,58,2 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,age,NA,unchanged,NA,unchanged,unchanged,unchanged,Signature 1,Text + fig 2B,10 January 2021,Marianthi Thomatos,WikiWorks,Differences in body mass index and gut microbiota by Gender,increased,"k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",3384189|32066;3384189|32066|203490|203491|203492|848,Complete,Shaimaa Elsafoury
bsdb:30001426/1/1,30001426,case-control,30001426,10.1371/journal.pone.0200728,NA,"Prehn-Kristensen A., Zimmermann A., Tittmann L., Lieb W., Schreiber S., Baving L. , Fischer A.",Reduced microbiome alpha diversity in young patients with ADHD,PloS one,2018,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Attention deficit hyperactivity disorder,EFO:0003888,controls,ADHD males,NA,17,14,NA,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,figure 3,10 January 2021,Fatima Zohra,WikiWorks,Differential abundance of taxa in male ADHD and healthy controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|1224|28216|206351|481;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|815|816,Complete,NA
bsdb:30001426/1/2,30001426,case-control,30001426,10.1371/journal.pone.0200728,NA,"Prehn-Kristensen A., Zimmermann A., Tittmann L., Lieb W., Schreiber S., Baving L. , Fischer A.",Reduced microbiome alpha diversity in young patients with ADHD,PloS one,2018,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Attention deficit hyperactivity disorder,EFO:0003888,controls,ADHD males,NA,17,14,NA,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,figure 3,10 January 2021,Fatima Zohra,WikiWorks,Differential abundance of taxa in male ADHD and healthy controls,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|976|200643|171549|171552;1783272|1239|186801|3082768|424536;3379134|976|200643|171549|171551;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|2005525|375288,Complete,NA
bsdb:30006660/1/1,30006660,case-control,30006660,10.1007/s10096-018-3322-7,NA,"Paalanne N., Husso A., Salo J., Pieviläinen O., Tejesvi M.V., Koivusaari P., Pirttilä A.M., Pokka T., Mattila S., Jyrkäs J., Turpeinen A., Uhari M., Renko M. , Tapiainen T.",Intestinal microbiome as a risk factor for urinary tract infections in children,European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology,2018,NA,Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Urinary tract infection,EFO:0003103,healthy controls,urinary tract infection,urinary tract infection,69,37,NA,16S,45,Ion Torrent,relative abundances,LEfSe,3,FALSE,3,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2,10 January 2021,Rimsha Azhar,WikiWorks,Comaprison between UTI patients and Health controls using linear discriminant analysis,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania massiliensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Priestia|s__Priestia flexa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus dispar,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia glucerasea",3379134|1224|1236|91347|543|547;1783272|1239|526524|526525|128827|61170|1468449;1783272|1239|91061|1385|186817|2800373|86664;1783272|1239|186801|3085636|186803|2719313|333367;1783272|1239|91061|186826|81852|1350|44009;1783272|1239|186801|3085636|186803|572511|536633,Complete,Atrayees
bsdb:30006660/1/2,30006660,case-control,30006660,10.1007/s10096-018-3322-7,NA,"Paalanne N., Husso A., Salo J., Pieviläinen O., Tejesvi M.V., Koivusaari P., Pirttilä A.M., Pokka T., Mattila S., Jyrkäs J., Turpeinen A., Uhari M., Renko M. , Tapiainen T.",Intestinal microbiome as a risk factor for urinary tract infections in children,European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology,2018,NA,Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Urinary tract infection,EFO:0003103,healthy controls,urinary tract infection,urinary tract infection,69,37,NA,16S,45,Ion Torrent,relative abundances,LEfSe,3,FALSE,3,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2,10 January 2021,Rimsha Azhar,"Fatima,WikiWorks",Comaprison between UTI patients and Health controls using linear discriminant analysis,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium tertium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia|s__Massilia aurea,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia lituseburensis",1783272|1239|186801|186802|31979|1485|1559;1783272|1239|909932|1843489|31977|39948;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|1737404|1737405|1570339|150022|1260;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712|724|729;3379134|1224|28216|80840|75682|149698;3379134|1224|28216|80840|75682;3379134|1224|1236|135625|712;3379134|1224|1236|135625;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171552|2974257|386414;3379134|1224|28216|80840|75682|149698|373040;1783272|1239|186801|3082720|186804|1501226|1537,Complete,Atrayees
bsdb:30007242/1/1,30007242,time series / longitudinal observational,30007242,10.1016/j.eplepsyres.2018.06.015,NA,"Zhang Y., Zhou S., Zhou Y., Yu L., Zhang L. , Wang Y.",Altered gut microbiome composition in children with refractory epilepsy after ketogenic diet,Epilepsy research,2018,"Children, Gut microbiota, Ketogenic diet, Refractory epilepsy",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,pre-ketogenic diet,post-ketogenic diet,children with intractable epilepsy after ketogenic diet treatment,20,20,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 2,20 November 2024,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of post-ketogenic diet group compared to pre-ketogenic diet group,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota",3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976,Complete,NA
bsdb:30007242/1/2,30007242,time series / longitudinal observational,30007242,10.1016/j.eplepsyres.2018.06.015,NA,"Zhang Y., Zhou S., Zhou Y., Yu L., Zhang L. , Wang Y.",Altered gut microbiome composition in children with refractory epilepsy after ketogenic diet,Epilepsy research,2018,"Children, Gut microbiota, Ketogenic diet, Refractory epilepsy",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,pre-ketogenic diet,post-ketogenic diet,children with intractable epilepsy after ketogenic diet treatment,20,20,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 2,20 November 2024,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of post-ketogenic diet group compared to pre-ketogenic diet group,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leucobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",3379134|1224|1236|2887326|468|469;1783272|201174|1760|2037;1783272|201174|1760;1783272|201174;1783272|1239;3379134|1224|28216|80840|119060;1783272|1239|186801;3379134|976|200643|171549|2005519|1348911;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803;1783272|201174|1760|85006|85023|55968;1783272|201174|1760|85006|85023;3379134|1224|1236|2887326|468;1783272|1239|186801|186802|216572;3379134|1224|1236|72274|135621;3379134|1224|1236|72274;3379134|1224|1236|72274|135621|286,Complete,NA
bsdb:30007242/2/1,30007242,time series / longitudinal observational,30007242,10.1016/j.eplepsyres.2018.06.015,NA,"Zhang Y., Zhou S., Zhou Y., Yu L., Zhang L. , Wang Y.",Altered gut microbiome composition in children with refractory epilepsy after ketogenic diet,Epilepsy research,2018,"Children, Gut microbiota, Ketogenic diet, Refractory epilepsy",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,post-ketogenic diet responders,post-ketogenic diet nonresponders,Nonresponders are patients classified as having less than 50% of seizure frequency reduction after ketogenic diet treatment. This particular group refers to the samples taken from nonresponders post-treatment.,10,10,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,25 November 2024,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of post-ketogenic diet nonresponders compared to post-ketogenic diet responders,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|1760;1783272|201174;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|1239|186801|3085636|186803|189330;1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803|1407607;1783272|201174|84998|1643822|1643826|644652;3379134|29547|3031852|213849|72293|209;3379134|29547|3031852|213849|72293;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171550;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301,Complete,NA
bsdb:30029052/1/1,30029052,"cross-sectional observational, not case-control",30029052,10.1016/j.jpsychires.2018.07.007,NA,"Jiang H.Y., Zhang X., Yu Z.H., Zhang Z., Deng M., Zhao J.H. , Ruan B.",Altered gut microbiota profile in patients with generalized anxiety disorder,Journal of psychiatric research,2018,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,healthy controls,treatment active Generalized Anxiety disorder,The active state of GAD was defined as a baseline Hamilton Anxiety Rating Scale HAMA score ≥14 upon admission to the hospital. The remissive state was defined as a HAMA score < 7 after 3 months of treatment.,36,40,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,"age,body mass index,sex",NA,NA,unchanged,NA,unchanged,NA,decreased,Signature 1,Figure 1,10 January 2021,Fatima Zohra,WikiWorks,Comparison of relative abundance at the bacterial phylum and genus levels between healthy controls and generalized anxiety disorder groups,increased,"k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Bacteroidota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia",3384189|32066;3379134|976;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|2316020|33038;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|946234;3384189|32066|203490;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;1783272|1239|186801|3085636|186803|1432051;1783272|1239|526524|526525|2810280|1505663;1783272|1239|186801|186802|31979|1485|1522;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643,Complete,Shaimaa Elsafoury
bsdb:30029052/1/2,30029052,"cross-sectional observational, not case-control",30029052,10.1016/j.jpsychires.2018.07.007,NA,"Jiang H.Y., Zhang X., Yu Z.H., Zhang Z., Deng M., Zhao J.H. , Ruan B.",Altered gut microbiota profile in patients with generalized anxiety disorder,Journal of psychiatric research,2018,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,healthy controls,treatment active Generalized Anxiety disorder,The active state of GAD was defined as a baseline Hamilton Anxiety Rating Scale HAMA score ≥14 upon admission to the hospital. The remissive state was defined as a HAMA score < 7 after 3 months of treatment.,36,40,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,"age,body mass index,sex",NA,NA,unchanged,NA,unchanged,NA,decreased,Signature 2,Figure 1,10 January 2021,Fatima Zohra,"Lwaldron,WikiWorks",Comparison of relative abundance at the bacterial phylum and genus levels between healthy controls and generalized anxiety disorder groups,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",3379134|1224|28216|80840|506;3379134|1224|28216;3379134|200940|3031449|213115|194924|35832;3379134|1224|28216|80840;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3082768|990719;1783272|1239|186801;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;28221;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|541000;1783272|1239|186801|186802|186807;1783272|1239|186801|3085636|186803|46205;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263|438033;1783272|1239|186801|186802|216572|292632;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|3085636|186803|1766253|39491,Complete,Fatima
bsdb:30029052/2/1,30029052,"cross-sectional observational, not case-control",30029052,10.1016/j.jpsychires.2018.07.007,NA,"Jiang H.Y., Zhang X., Yu Z.H., Zhang Z., Deng M., Zhao J.H. , Ruan B.",Altered gut microbiota profile in patients with generalized anxiety disorder,Journal of psychiatric research,2018,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,healthy controls,treatment naiive Generalized Anxiety disorder,The active state of GAD was defined as a baseline Hamilton Anxiety Rating Scale HAMA score ≥14 upon admission to the hospital. The remissive state was defined as a HAMA score < 7 after 3 months of treatment.,17,12,2 months,16S,34,Illumina,NA,LEfSe,0.05,TRUE,2,"age,body mass index,sex",NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Comparison of relative abundance at the bacterial phylum and genus levels between healthy controls and treatment naiive generalized anxiety disorder groups,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota",1783272|1239|91061|186826|33958|1578;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|2316020|33038;3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|620;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|1224|1236|91347|543;3379134|1224|1236|91347;3379134|976|200643|171549|2005525|375288;1783272|1239|91061|186826|33958;1783272|1239|526524|526525|2810280|1505663;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|186802|31979|1485|1522;1783272|1239|186801|186802|216572|946234;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066,Complete,Shaimaa Elsafoury
bsdb:30029052/2/2,30029052,"cross-sectional observational, not case-control",30029052,10.1016/j.jpsychires.2018.07.007,NA,"Jiang H.Y., Zhang X., Yu Z.H., Zhang Z., Deng M., Zhao J.H. , Ruan B.",Altered gut microbiota profile in patients with generalized anxiety disorder,Journal of psychiatric research,2018,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,healthy controls,treatment naiive Generalized Anxiety disorder,The active state of GAD was defined as a baseline Hamilton Anxiety Rating Scale HAMA score ≥14 upon admission to the hospital. The remissive state was defined as a HAMA score < 7 after 3 months of treatment.,17,12,2 months,16S,34,Illumina,NA,LEfSe,0.05,TRUE,2,"age,body mass index,sex",NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 2,10 January 2021,Shaimaa Elsafoury,"Fatima,WikiWorks",Comparison of relative abundance at the bacterial phylum and genus levels between healthy controls and treatment naiive generalized anxiety disorder groups,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",1783272|1239|186801|186802|216572|244127;3379134|976|200643|171549|2005519|397864;1783272|1239|186801|186802|3085642|580596;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|3082768|990719;1783272|1239|186801;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|186801|186802|216572|216851;1783272|1239;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|437755;1783272|1239|186801|186802|541000;3379134|1224|28216|80840|75682|846;3379134|1224|28216|80840|75682;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|186802|186807;1783272|1239|186801|186802|186807|2740;3379134|976|200643|171549|171552;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263|438033;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|3085636|186803|1766253|39491,Complete,Fatima
bsdb:30042470/1/1,30042470,"cross-sectional observational, not case-control",30042470,https://doi.org/10.1038/s41372-018-0172-1,NA,"Imoto N., Morita H., Amanuma F., Maruyama H., Watanabe S. , Hashiguchi N.",Maternal antimicrobial use at delivery has a stronger impact than mode of delivery on bifidobacterial colonization in infants: a pilot study,Journal of perinatology : official journal of the California Perinatal Association,2018,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,without (non-Abx) use of maternal antimicrobial agents at delivery,infants with (Abx),Healthy infants,14,19,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 1,Table 2,10 January 2021,Mst Afroza Parvin,WikiWorks,Relative abundance of the six most common bacterial genera in all infants (n = 33) and in those with and without use of maternal antibiotics and with Cesarean or vaginal delivery,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,NA
bsdb:30042470/2/1,30042470,"cross-sectional observational, not case-control",30042470,https://doi.org/10.1038/s41372-018-0172-1,NA,"Imoto N., Morita H., Amanuma F., Maruyama H., Watanabe S. , Hashiguchi N.",Maternal antimicrobial use at delivery has a stronger impact than mode of delivery on bifidobacterial colonization in infants: a pilot study,Journal of perinatology : official journal of the California Perinatal Association,2018,NA,Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Healthy infant not exposed to maternal antimicrobial,Healthy infant  exposed to maternal antimicrobial,"An infant or baby is the very young offspring of human beings. A newborn is, in colloquial use, an infant who is only hours, days, or up to one month old.",14,19,NA,16S,234,Illumina,relative abundances,"T-Test,ANOSIM,Spearman Correlation,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 1,NA,11 March 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,WikiWorks",NA,NA,NA,NA,Complete,NA
bsdb:30042470/2/2,30042470,"cross-sectional observational, not case-control",30042470,https://doi.org/10.1038/s41372-018-0172-1,NA,"Imoto N., Morita H., Amanuma F., Maruyama H., Watanabe S. , Hashiguchi N.",Maternal antimicrobial use at delivery has a stronger impact than mode of delivery on bifidobacterial colonization in infants: a pilot study,Journal of perinatology : official journal of the California Perinatal Association,2018,NA,Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Healthy infant not exposed to maternal antimicrobial,Healthy infant  exposed to maternal antimicrobial,"An infant or baby is the very young offspring of human beings. A newborn is, in colloquial use, an infant who is only hours, days, or up to one month old.",14,19,NA,16S,234,Illumina,relative abundances,"T-Test,ANOSIM,Spearman Correlation,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 2,NA,11 March 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,WikiWorks",NA,NA,NA,NA,Complete,NA
bsdb:30051546/1/1,30051546,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A., Mörkl S., Kashofer K., Halwachs B., Dalkner N., Bengesser S., Birner A., Fellendorf F., Platzer M., Queissner R., Schütze G., Schwarz M.J., Moll N., Holzer P., Holl A.K., Kapfhammer H.P., Gorkiewicz G. , Reininghaus E.Z.",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,"16S rRNA gene, bipolar disorder, diversity, gut microbiota, gut-brain axis, illness duration, inflammation, metabolic syndrome, oxidative stress, tryptophan",Experiment 1,Austria,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,Controls,Bipolar disorder,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,10,32,1 month,16S,12,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 3,10 January 2021,Fatima Zohra,WikiWorks,Differentially abundant features of Bipolar disorder individuals in comparison to HC,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia",1783272|201174;1783272|201174|84998|84999;1783272|201174|84998|84999|84107;1783272|201174|84998,Complete,Shaimaa Elsafoury
bsdb:30051546/1/2,30051546,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A., Mörkl S., Kashofer K., Halwachs B., Dalkner N., Bengesser S., Birner A., Fellendorf F., Platzer M., Queissner R., Schütze G., Schwarz M.J., Moll N., Holzer P., Holl A.K., Kapfhammer H.P., Gorkiewicz G. , Reininghaus E.Z.",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,"16S rRNA gene, bipolar disorder, diversity, gut microbiota, gut-brain axis, illness duration, inflammation, metabolic syndrome, oxidative stress, tryptophan",Experiment 1,Austria,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,Controls,Bipolar disorder,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,10,32,1 month,16S,12,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table 3,10 January 2021,Fatima Zohra,WikiWorks,Differentially abundant features of Bipolar disorder individuals in comparison to HC,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|1239|186801|186802|541000;1783272|1239|186801|186802|216572|216851,Complete,Shaimaa Elsafoury
bsdb:30051546/2/1,30051546,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A., Mörkl S., Kashofer K., Halwachs B., Dalkner N., Bengesser S., Birner A., Fellendorf F., Platzer M., Queissner R., Schütze G., Schwarz M.J., Moll N., Holzer P., Holl A.K., Kapfhammer H.P., Gorkiewicz G. , Reininghaus E.Z.",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,"16S rRNA gene, bipolar disorder, diversity, gut microbiota, gut-brain axis, illness duration, inflammation, metabolic syndrome, oxidative stress, tryptophan",Experiment 2,Austria,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,low IL-6,Bipolar patients with high IL-6,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,NA,NA,1 month,16S,12,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text (results),10 January 2021,Fatima Zohra,WikiWorks,Microbiota composition in relation to inflammatory markers among bipolar patients,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061|186826;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301,Complete,Shaimaa Elsafoury
bsdb:30051546/3/1,30051546,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A., Mörkl S., Kashofer K., Halwachs B., Dalkner N., Bengesser S., Birner A., Fellendorf F., Platzer M., Queissner R., Schütze G., Schwarz M.J., Moll N., Holzer P., Holl A.K., Kapfhammer H.P., Gorkiewicz G. , Reininghaus E.Z.",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,"16S rRNA gene, bipolar disorder, diversity, gut microbiota, gut-brain axis, illness duration, inflammation, metabolic syndrome, oxidative stress, tryptophan",Experiment 3,Austria,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,low total cholesterol,Bipolar patients with high total cholesterol,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,NA,NA,1 month,16S,12,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text (results),10 January 2021,Fatima Zohra,WikiWorks,Microbiota composition in relation to lipid levels among bipolar patients,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,1783272|1239|186801|186802|31979,Complete,Shaimaa Elsafoury
bsdb:30051546/4/1,30051546,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A., Mörkl S., Kashofer K., Halwachs B., Dalkner N., Bengesser S., Birner A., Fellendorf F., Platzer M., Queissner R., Schütze G., Schwarz M.J., Moll N., Holzer P., Holl A.K., Kapfhammer H.P., Gorkiewicz G. , Reininghaus E.Z.",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,"16S rRNA gene, bipolar disorder, diversity, gut microbiota, gut-brain axis, illness duration, inflammation, metabolic syndrome, oxidative stress, tryptophan",Experiment 4,Austria,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,low LDL,Bipolar patients with high LDL,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,NA,NA,1 month,16S,12,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text (results),10 January 2021,Shaimaa Elsafoury,WikiWorks,Microbiota composition in relation to lipid levels among bipolar patients,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
bsdb:30051546/5/1,30051546,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A., Mörkl S., Kashofer K., Halwachs B., Dalkner N., Bengesser S., Birner A., Fellendorf F., Platzer M., Queissner R., Schütze G., Schwarz M.J., Moll N., Holzer P., Holl A.K., Kapfhammer H.P., Gorkiewicz G. , Reininghaus E.Z.",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,"16S rRNA gene, bipolar disorder, diversity, gut microbiota, gut-brain axis, illness duration, inflammation, metabolic syndrome, oxidative stress, tryptophan",Experiment 5,Austria,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,low TRP,Bipolar patients with high TRP,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,NA,NA,1 month,16S,12,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text (results),10 January 2021,Fatima Zohra,WikiWorks,Microbiota composition in relation to tryptophan metabolites among bipolar patients,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958;1783272|201174|84998|84999|84107;1783272|1239|186801|186802|31979,Complete,Shaimaa Elsafoury
bsdb:30051546/6/1,30051546,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A., Mörkl S., Kashofer K., Halwachs B., Dalkner N., Bengesser S., Birner A., Fellendorf F., Platzer M., Queissner R., Schütze G., Schwarz M.J., Moll N., Holzer P., Holl A.K., Kapfhammer H.P., Gorkiewicz G. , Reininghaus E.Z.",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,"16S rRNA gene, bipolar disorder, diversity, gut microbiota, gut-brain axis, illness duration, inflammation, metabolic syndrome, oxidative stress, tryptophan",Experiment 6,Austria,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,low TBARS level,Bipolar patients with high TBARS level,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,NA,NA,1 month,16S,12,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text (results),10 January 2021,Fatima Zohra,WikiWorks,Microbiota composition in relation to markers of oxidative stress among bipolar patients,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,1783272|1239|186801|186802|186806|1730,Complete,Shaimaa Elsafoury
bsdb:30051546/7/1,30051546,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A., Mörkl S., Kashofer K., Halwachs B., Dalkner N., Bengesser S., Birner A., Fellendorf F., Platzer M., Queissner R., Schütze G., Schwarz M.J., Moll N., Holzer P., Holl A.K., Kapfhammer H.P., Gorkiewicz G. , Reininghaus E.Z.",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,"16S rRNA gene, bipolar disorder, diversity, gut microbiota, gut-brain axis, illness duration, inflammation, metabolic syndrome, oxidative stress, tryptophan",Experiment 7,Austria,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,low MDA level,Bipolar patients with high MDA level,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,NA,NA,1 month,16S,12,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text (results),10 January 2021,Fatima Zohra,WikiWorks,Microbiota composition in relation to markers of oxidative stress among bipolar patients,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,1783272|1239|186801|186802|216572|216851,Complete,Shaimaa Elsafoury
bsdb:30051546/8/1,30051546,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A., Mörkl S., Kashofer K., Halwachs B., Dalkner N., Bengesser S., Birner A., Fellendorf F., Platzer M., Queissner R., Schütze G., Schwarz M.J., Moll N., Holzer P., Holl A.K., Kapfhammer H.P., Gorkiewicz G. , Reininghaus E.Z.",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,"16S rRNA gene, bipolar disorder, diversity, gut microbiota, gut-brain axis, illness duration, inflammation, metabolic syndrome, oxidative stress, tryptophan",Experiment 8,Austria,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,low BMI,Bipolar patients with high BMI,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,NA,NA,1 month,16S,12,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text (results),10 January 2021,Fatima Zohra,WikiWorks,Microbiota composition in relation to BMI among bipolar patients,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958;1783272|1239|91061,Complete,Shaimaa Elsafoury
bsdb:30051546/9/1,30051546,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A., Mörkl S., Kashofer K., Halwachs B., Dalkner N., Bengesser S., Birner A., Fellendorf F., Platzer M., Queissner R., Schütze G., Schwarz M.J., Moll N., Holzer P., Holl A.K., Kapfhammer H.P., Gorkiewicz G. , Reininghaus E.Z.",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,"16S rRNA gene, bipolar disorder, diversity, gut microbiota, gut-brain axis, illness duration, inflammation, metabolic syndrome, oxidative stress, tryptophan",Experiment 9,Austria,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,no metabolic syndrome,Bipolar patients with metabolic syndrome,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,NA,NA,1 month,16S,12,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text (results),10 January 2021,Fatima Zohra,WikiWorks,Microbiota composition in relation to metabolic syndrome among bipolar patients,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|201174|84998|84999|84107,Complete,Shaimaa Elsafoury
bsdb:30051546/10/1,30051546,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A., Mörkl S., Kashofer K., Halwachs B., Dalkner N., Bengesser S., Birner A., Fellendorf F., Platzer M., Queissner R., Schütze G., Schwarz M.J., Moll N., Holzer P., Holl A.K., Kapfhammer H.P., Gorkiewicz G. , Reininghaus E.Z.",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,"16S rRNA gene, bipolar disorder, diversity, gut microbiota, gut-brain axis, illness duration, inflammation, metabolic syndrome, oxidative stress, tryptophan",Experiment 10,Austria,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,healthier bipolar patients,Bipolar patients with depressive syndrome,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,NA,NA,1 month,16S,12,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text (results),10 January 2021,Fatima Zohra,WikiWorks,Microbiota composition in relation to depressive syndrome among bipolar patients,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,Shaimaa Elsafoury
bsdb:30051546/10/2,30051546,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A., Mörkl S., Kashofer K., Halwachs B., Dalkner N., Bengesser S., Birner A., Fellendorf F., Platzer M., Queissner R., Schütze G., Schwarz M.J., Moll N., Holzer P., Holl A.K., Kapfhammer H.P., Gorkiewicz G. , Reininghaus E.Z.",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,"16S rRNA gene, bipolar disorder, diversity, gut microbiota, gut-brain axis, illness duration, inflammation, metabolic syndrome, oxidative stress, tryptophan",Experiment 10,Austria,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,healthier bipolar patients,Bipolar patients with depressive syndrome,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,NA,NA,1 month,16S,12,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,text (results),10 January 2021,Fatima Zohra,WikiWorks,Microbiota composition in relation to depressive syndrome among bipolar patients,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|186803|841,Complete,Shaimaa Elsafoury
bsdb:30051546/11/1,30051546,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A., Mörkl S., Kashofer K., Halwachs B., Dalkner N., Bengesser S., Birner A., Fellendorf F., Platzer M., Queissner R., Schütze G., Schwarz M.J., Moll N., Holzer P., Holl A.K., Kapfhammer H.P., Gorkiewicz G. , Reininghaus E.Z.",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,"16S rRNA gene, bipolar disorder, diversity, gut microbiota, gut-brain axis, illness duration, inflammation, metabolic syndrome, oxidative stress, tryptophan",Experiment 11,Austria,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,Controls,Bipolar disorder,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,10,27,1 month,16S,12,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 1,10 January 2021,Fatima Zohra,WikiWorks,Differentially abundant features of Bipolar disorder individuals in comparison to HC after exclusion obese and diabetic patients,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia",1783272|201174;1783272|201174|84998|84999;1783272|201174|84998|84999|84107;1783272|201174|84998,Complete,Shaimaa Elsafoury
bsdb:30051546/11/2,30051546,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A., Mörkl S., Kashofer K., Halwachs B., Dalkner N., Bengesser S., Birner A., Fellendorf F., Platzer M., Queissner R., Schütze G., Schwarz M.J., Moll N., Holzer P., Holl A.K., Kapfhammer H.P., Gorkiewicz G. , Reininghaus E.Z.",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,"16S rRNA gene, bipolar disorder, diversity, gut microbiota, gut-brain axis, illness duration, inflammation, metabolic syndrome, oxidative stress, tryptophan",Experiment 11,Austria,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,Controls,Bipolar disorder,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,10,27,1 month,16S,12,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 1,10 January 2021,Fatima Zohra,WikiWorks,Differentially abundant features of Bipolar disorder individuals in comparison to HC after exclusion obese and diabetic patients,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|1239|186801|186802|541000;1783272|1239|186801|186802|216572|216851,Complete,Shaimaa Elsafoury
bsdb:30054546/1/1,30054546,case-control,30054546,https://doi.org/10.1038/s41598-018-29730-x,NA,"Vallès Y., Inman C.K., Peters B.A., Ali R., Wareth L.A., Abdulle A., Alsafar H., Anouti F.A., Dhaheri A.A., Galani D., Haji M., Hamiz A.A., Hosani A.A., Houqani M.A., Junaibi A.A., Kazim M., Kirchhoff T., Mahmeed W.A., Maskari F.A., Alnaeemi A., Oumeziane N., Ramasamy R., Schmidt A.M., Weitzman M., Zaabi E.A., Sherman S., Hayes R.B. , Ahn J.",Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study,Scientific reports,2018,NA,Experiment 1,United Arab Emirates,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Nonsmokers,Cigarette Smokers,People consuming tobacco in the form of cigarettes (CS),225,33,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,increased,NA,increased,Signature 1,Table 2,17 March 2023,Adi13,"Adi13,ChiomaBlessing,WikiWorks","Differentially abundant taxa at selected taxonomical levels by type of tobacco use, compared to nonsmokers",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes|s__uncultured Synergistes sp.",1783272|201174|84998|84999|1643824|1380;1783272|201174|1760|85004|31953|1678;3379134|29547|3031852|213849|72294|194;1783272|1239|909932|1843489|31977|39948;3379134|1224|28211|356|212791;1783272|1239|909932|1843489|31977|906;1783272|544448|31969|2085|2092|2093;3379134|976|200643|171549|2005523|346096;3379134|976|200643|171549|171552|838;3379134|203691|203692|136|2845253|157;3384194|508458|649775|649776|649777|2753|290252,Complete,Claregrieve1
bsdb:30054546/1/2,30054546,case-control,30054546,https://doi.org/10.1038/s41598-018-29730-x,NA,"Vallès Y., Inman C.K., Peters B.A., Ali R., Wareth L.A., Abdulle A., Alsafar H., Anouti F.A., Dhaheri A.A., Galani D., Haji M., Hamiz A.A., Hosani A.A., Houqani M.A., Junaibi A.A., Kazim M., Kirchhoff T., Mahmeed W.A., Maskari F.A., Alnaeemi A., Oumeziane N., Ramasamy R., Schmidt A.M., Weitzman M., Zaabi E.A., Sherman S., Hayes R.B. , Ahn J.",Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study,Scientific reports,2018,NA,Experiment 1,United Arab Emirates,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Nonsmokers,Cigarette Smokers,People consuming tobacco in the form of cigarettes (CS),225,33,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,increased,NA,increased,Signature 2,Table 2,17 March 2023,Adi13,"Adi13,WikiWorks","Differentially abundant taxa at selected taxonomical levels by type of tobacco use, compared to nonsmokers",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",3379134|976|200643|171549|171551|836;3379134|976|117743|200644|49546|1016;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|81852|2737;1783272|1239|186801|3082720|186804|1257;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|1129771|32067;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|206351|481|538;3379134|1224|28216|206351|481|482;3379134|1224|1236|135615|868|2717;3379134|1224|1236|135625|712|713;3379134|1224|1236|135625|712|416916;3379134|1224|1236|135625|712|724,Complete,Claregrieve1
bsdb:30054546/2/1,30054546,case-control,30054546,https://doi.org/10.1038/s41598-018-29730-x,NA,"Vallès Y., Inman C.K., Peters B.A., Ali R., Wareth L.A., Abdulle A., Alsafar H., Anouti F.A., Dhaheri A.A., Galani D., Haji M., Hamiz A.A., Hosani A.A., Houqani M.A., Junaibi A.A., Kazim M., Kirchhoff T., Mahmeed W.A., Maskari F.A., Alnaeemi A., Oumeziane N., Ramasamy R., Schmidt A.M., Weitzman M., Zaabi E.A., Sherman S., Hayes R.B. , Ahn J.",Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study,Scientific reports,2018,NA,Experiment 2,United Arab Emirates,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Nonsmokers,Dokha Smokers,People consuming tobacco in the form of dokha (DS),225,16,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplemental. Table S2,18 March 2023,Adi13,"Adi13,ChiomaBlessing,WikiWorks","Differentially abundant taxa at selected taxonomical levels by type of tobacco use, compared to nonsmokers",increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Claregrieve1
bsdb:30054546/2/2,30054546,case-control,30054546,https://doi.org/10.1038/s41598-018-29730-x,NA,"Vallès Y., Inman C.K., Peters B.A., Ali R., Wareth L.A., Abdulle A., Alsafar H., Anouti F.A., Dhaheri A.A., Galani D., Haji M., Hamiz A.A., Hosani A.A., Houqani M.A., Junaibi A.A., Kazim M., Kirchhoff T., Mahmeed W.A., Maskari F.A., Alnaeemi A., Oumeziane N., Ramasamy R., Schmidt A.M., Weitzman M., Zaabi E.A., Sherman S., Hayes R.B. , Ahn J.",Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study,Scientific reports,2018,NA,Experiment 2,United Arab Emirates,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Nonsmokers,Dokha Smokers,People consuming tobacco in the form of dokha (DS),225,16,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplemental. Table S2,18 March 2023,Adi13,"Adi13,ChiomaBlessing,WikiWorks","Differentially abundant taxa at selected taxonomical levels by type of tobacco use, compared to nonsmokers",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",3379134|1224|28216|80840|119060|47670;3379134|976|200643|171549|171551|836,Complete,Claregrieve1
bsdb:30054546/3/2,30054546,case-control,30054546,https://doi.org/10.1038/s41598-018-29730-x,NA,"Vallès Y., Inman C.K., Peters B.A., Ali R., Wareth L.A., Abdulle A., Alsafar H., Anouti F.A., Dhaheri A.A., Galani D., Haji M., Hamiz A.A., Hosani A.A., Houqani M.A., Junaibi A.A., Kazim M., Kirchhoff T., Mahmeed W.A., Maskari F.A., Alnaeemi A., Oumeziane N., Ramasamy R., Schmidt A.M., Weitzman M., Zaabi E.A., Sherman S., Hayes R.B. , Ahn J.",Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study,Scientific reports,2018,NA,Experiment 3,United Arab Emirates,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Nonsmokers,Shisha Smokers,People consuming tobacco in the form of shisha (SS),225,15,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplemental. Table S2,18 March 2023,Adi13,"Adi13,ChiomaBlessing,WikiWorks","Differentially abundant taxa at selected taxonomical levels by type of tobacco use, compared to nonsmokers",decreased,"p__Candidatus Altimarinota|s__Candidatus Gracilibacteria bacterium GN02-872,k__Bacillati|p__Cyanobacteriota,p__Candidatus Absconditibacteriota|s__candidate division SR1 bacterium",363464|1912928;1783272|1117;221235|2044938,Complete,Claregrieve1
bsdb:30054546/4/1,30054546,case-control,30054546,https://doi.org/10.1038/s41598-018-29730-x,NA,"Vallès Y., Inman C.K., Peters B.A., Ali R., Wareth L.A., Abdulle A., Alsafar H., Anouti F.A., Dhaheri A.A., Galani D., Haji M., Hamiz A.A., Hosani A.A., Houqani M.A., Junaibi A.A., Kazim M., Kirchhoff T., Mahmeed W.A., Maskari F.A., Alnaeemi A., Oumeziane N., Ramasamy R., Schmidt A.M., Weitzman M., Zaabi E.A., Sherman S., Hayes R.B. , Ahn J.",Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study,Scientific reports,2018,NA,Experiment 4,United Arab Emirates,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Nonsmokers,Mutiple Smokers,"People consuming tobacco in multiple forms out of cigarettes (CS), dokha (DS) and shisha (SS)",225,41,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental. Table S2,18 March 2023,Adi13,"Adi13,ChiomaBlessing,WikiWorks","Differentially abundant taxa at selected taxonomical levels by type of tobacco use, compared to nonsmokers",increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes|s__uncultured Synergistes sp.",3379134|29547|3031852|213849|72294|194;3379134|1224|28211|356|212791;1783272|544448|31969|2085|2092|2093;3379134|976|200643|171549|2005523|346096;3379134|203691|203692|136|2845253|157;3384194|508458|649775|649776|649777|2753|290252,Complete,Claregrieve1
bsdb:30054546/4/2,30054546,case-control,30054546,https://doi.org/10.1038/s41598-018-29730-x,NA,"Vallès Y., Inman C.K., Peters B.A., Ali R., Wareth L.A., Abdulle A., Alsafar H., Anouti F.A., Dhaheri A.A., Galani D., Haji M., Hamiz A.A., Hosani A.A., Houqani M.A., Junaibi A.A., Kazim M., Kirchhoff T., Mahmeed W.A., Maskari F.A., Alnaeemi A., Oumeziane N., Ramasamy R., Schmidt A.M., Weitzman M., Zaabi E.A., Sherman S., Hayes R.B. , Ahn J.",Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study,Scientific reports,2018,NA,Experiment 4,United Arab Emirates,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Nonsmokers,Mutiple Smokers,"People consuming tobacco in multiple forms out of cigarettes (CS), dokha (DS) and shisha (SS)",225,41,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental. Table S2,18 March 2023,Adi13,"Adi13,ChiomaBlessing,WikiWorks","Differentially abundant taxa at selected taxonomical levels by type of tobacco use, compared to nonsmokers",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus",3379134|1224|1236|135625|712|713;3379134|1224|28216|206351|481|538;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135625|712|724;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|206351|481|482;1783272|1239|91061|186826|81852|2737,Complete,Claregrieve1
bsdb:30054546/5/1,30054546,case-control,30054546,https://doi.org/10.1038/s41598-018-29730-x,NA,"Vallès Y., Inman C.K., Peters B.A., Ali R., Wareth L.A., Abdulle A., Alsafar H., Anouti F.A., Dhaheri A.A., Galani D., Haji M., Hamiz A.A., Hosani A.A., Houqani M.A., Junaibi A.A., Kazim M., Kirchhoff T., Mahmeed W.A., Maskari F.A., Alnaeemi A., Oumeziane N., Ramasamy R., Schmidt A.M., Weitzman M., Zaabi E.A., Sherman S., Hayes R.B. , Ahn J.",Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study,Scientific reports,2018,NA,Experiment 5,United Arab Emirates,Homo sapiens,Saliva,UBERON:0001836,Cotinine measurement,EFO:0007813,Cotinine negative,Cotinine positive,Subjects with positive cotinine result,225,22,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental. Table S4,5 December 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differentially abundant taxa at all taxonomical levels in the contrasts between cotinine positive versus cotinine negative.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae,k__Bacillati|p__Cyanobacteriota,p__Candidatus Altimarinota|s__Candidatus Gracilibacteria bacterium GN02-872,k__Pseudomonadati|p__Pseudomonadota,p__Candidatus Absconditibacteriota|s__candidate division SR1 bacterium",3379134|1224|1236|135625|712|416916;3379134|976|117743|200644|49546|1016;3379134|1224|1236|135615|868|2717;3379134|1224|28216|206351|481|538;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135625|712|724;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|206351|481|482;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836;1783272|201174|1760|85006|1268|32207;3379134|976|117743|200644|2762318;1783272|1117;363464|1912928;3379134|1224;221235|2044938,Complete,ChiomaBlessing
bsdb:30054546/5/2,30054546,case-control,30054546,https://doi.org/10.1038/s41598-018-29730-x,NA,"Vallès Y., Inman C.K., Peters B.A., Ali R., Wareth L.A., Abdulle A., Alsafar H., Anouti F.A., Dhaheri A.A., Galani D., Haji M., Hamiz A.A., Hosani A.A., Houqani M.A., Junaibi A.A., Kazim M., Kirchhoff T., Mahmeed W.A., Maskari F.A., Alnaeemi A., Oumeziane N., Ramasamy R., Schmidt A.M., Weitzman M., Zaabi E.A., Sherman S., Hayes R.B. , Ahn J.",Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study,Scientific reports,2018,NA,Experiment 5,United Arab Emirates,Homo sapiens,Saliva,UBERON:0001836,Cotinine measurement,EFO:0007813,Cotinine negative,Cotinine positive,Subjects with positive cotinine result,225,22,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental. Table S4,5 December 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differentially abundant taxa at all taxonomical levels in the contrasts between cotinine positive versus cotinine negative.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes|s__uncultured Synergistes sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia",1783272|201174|1760|85004|31953|1678;3379134|29547|3031852|213849|72294|194;3379134|200940|3031451|3024411|213121|893;1783272|1239|186801|3082720|3118655|44259;1783272|1239|909932|1843489|31977|906;1783272|544448|31969|2085|2092|2093;3379134|976|200643|171549|2005523|346096;3379134|203691|203692|136|2845253|157;3384194|508458|649775|649776|649777|2753|290252;3379134|976|200643|171549|171552|577309;3379134|203691|203692,Complete,ChiomaBlessing
bsdb:30054546/8/1,30054546,case-control,30054546,https://doi.org/10.1038/s41598-018-29730-x,NA,"Vallès Y., Inman C.K., Peters B.A., Ali R., Wareth L.A., Abdulle A., Alsafar H., Anouti F.A., Dhaheri A.A., Galani D., Haji M., Hamiz A.A., Hosani A.A., Houqani M.A., Junaibi A.A., Kazim M., Kirchhoff T., Mahmeed W.A., Maskari F.A., Alnaeemi A., Oumeziane N., Ramasamy R., Schmidt A.M., Weitzman M., Zaabi E.A., Sherman S., Hayes R.B. , Ahn J.",Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study,Scientific reports,2018,NA,Experiment 8,United Arab Emirates,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Shisha,CIigarettes,People consuming tobacco in the form of cigarettes (CS),15,33,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplemental. Table S3,11 December 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differentially abundant taxa at all taxonomical levels between Cigarettes and Shisha,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae",3379134|1224|1236|135625|712|713;1783272|1239|186801|3085636|186803|830;3379134|976|117743|200644|49546|1016;3379134|1224|28216|80840|80864;3384189|32066|203490;1783272|1239|91061|1385|539738;3379134|976|117743|200644|2762318,Complete,ChiomaBlessing
bsdb:30054546/8/2,30054546,case-control,30054546,https://doi.org/10.1038/s41598-018-29730-x,NA,"Vallès Y., Inman C.K., Peters B.A., Ali R., Wareth L.A., Abdulle A., Alsafar H., Anouti F.A., Dhaheri A.A., Galani D., Haji M., Hamiz A.A., Hosani A.A., Houqani M.A., Junaibi A.A., Kazim M., Kirchhoff T., Mahmeed W.A., Maskari F.A., Alnaeemi A., Oumeziane N., Ramasamy R., Schmidt A.M., Weitzman M., Zaabi E.A., Sherman S., Hayes R.B. , Ahn J.",Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study,Scientific reports,2018,NA,Experiment 8,United Arab Emirates,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Shisha,CIigarettes,People consuming tobacco in the form of cigarettes (CS),15,33,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplemental. Table S3,11 December 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differentially abundant taxa at all taxonomical levels between Cigarettes and Shisha,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes|s__uncultured Synergistes sp.,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma",3379134|976|200643|171549|2005523|346096;3379134|203691|203692|136|2845253|157;3384194|508458|649775|649776|649777|2753|290252;1783272|544448|31969|2085|2092|2093,Complete,ChiomaBlessing
bsdb:30054546/9/1,30054546,case-control,30054546,https://doi.org/10.1038/s41598-018-29730-x,NA,"Vallès Y., Inman C.K., Peters B.A., Ali R., Wareth L.A., Abdulle A., Alsafar H., Anouti F.A., Dhaheri A.A., Galani D., Haji M., Hamiz A.A., Hosani A.A., Houqani M.A., Junaibi A.A., Kazim M., Kirchhoff T., Mahmeed W.A., Maskari F.A., Alnaeemi A., Oumeziane N., Ramasamy R., Schmidt A.M., Weitzman M., Zaabi E.A., Sherman S., Hayes R.B. , Ahn J.",Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study,Scientific reports,2018,NA,Experiment 9,United Arab Emirates,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Shisha,Dokha,People consuming tobacco in the form of Dokha,15,16,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplemental. Table S3,11 December 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differentially abundant taxa at all taxonomical levels between Dokha and Shisha,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae",3379134|1224|1236|135625|712|713;3379134|976|117743|200644|2762318;1783272|1239|91061|1385|539738,Complete,ChiomaBlessing
bsdb:30065718/1/1,30065718,"cross-sectional observational, not case-control",30065718,10.3389/fmicb.2018.01603,NA,"Dong L., Yin J., Zhao J., Ma S.R., Wang H.R., Wang M., Chen W. , Wei W.Q.",Microbial Similarity and Preference for Specific Sites in Healthy Oral Cavity and Esophagus,Frontiers in microbiology,2018,"16S rRNA gene sequencing, esophagus, microbial preference, microbial similarity, oral cavity",Experiment 1,China,Homo sapiens,"Oral cavity,Esophagus","UBERON:0000167,UBERON:0001043",Health study participation,EFO:0010130,Oral cavity,Esophagus,"Healthy individual who are esophageal disease-free, confirmed by endoscopic examination and then biopsy-based pathological diagnosis if necessary.",27,27,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,increased,decreased,NA,NA,Signature 1,"Figure 3, Supplementary Figure S1",2 May 2024,Scholastica,"Scholastica,WikiWorks",Microbial taxa significantly different in the oral cavity compared to the esophagus with LDA score >2 using LEfse analysis,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Phenylobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Pseudomonadati|p__Bacteroidota|c__Saprospiria|o__Saprospirales|f__Saprospiraceae|g__Saprospira,k__Pseudomonadati|p__Bacteroidota|c__Saprospiria|o__Saprospirales,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",3379134|1224|28211|3120395|433;3379134|1224|1236|2887326|468|469;3379134|1224|1236|135625|712|713;1783272|1239|526524|526525|128827|174708;3379134|1224|28211;1783272|1239|91061|1385|186817;1783272|1239|91061|1385;1783272|1239|91061;1783272|1239;1783272|1239|186801|3085636|186803|572511;3379134|1224|28211|356|41294|374;3379134|1224|28211|356|118882;3379134|1224|28211|204458|76892;3379134|1224|28211|204458;3379134|976|1853228|1853229|563835;3379134|976|117743|200644|2762318|59732;1783272|1239|186801|3085636|186803|33042;3379134|1224|28211|356|212791;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236;1783272|1239|91061|1385|539738;3379134|1224|28211|356;1783272|201174|1760|85006|85021;1783272|1239|91061|186826;3379134|1224|1236|135614|32033;3379134|1224|1236|135614;3379134|1224|28211|356|119045;3379134|1224|28211|356|119045|407;3379134|1224|28211|356|41294;3379134|1224|28211|204457|41297|165696;3379134|1224|28211|356|118882|528;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|75682;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|1224|28211|204458|76892|20;1783272|201174|1760|85009|31957|1743;3379134|1224|1236|72274|135621;3379134|1224|1236|72274;3379134|1224|1236|72274|135621|286;3379134|1224|28216|80840|119060|48736;3379134|1224|28211|204441|41295;3379134|1224|28211|204441;3379134|976|1937959|1936988|89374|1007;3379134|976|1937959|1936988;3379134|976|1853228|1853229|563835|504481;3379134|1224|28211|204457|3423717|165695;3379134|1224|28211|204457|41297;3379134|1224|28211|204457;3379134|1224|28211|204457|41297|13687;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|135614|32033|40323;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;3379134|1224|28211|3120395|433;3379134|1224|28211|356|41294;3379134|1224|28211|204458|76892;3379134|1224|1236|91347|543;3379134|1224|28211|356|119045;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|75682;3379134|1224|28211|204441|41295;3379134|976|200643|171549|2005473,Complete,Svetlana up
bsdb:30065718/1/2,30065718,"cross-sectional observational, not case-control",30065718,10.3389/fmicb.2018.01603,NA,"Dong L., Yin J., Zhao J., Ma S.R., Wang H.R., Wang M., Chen W. , Wei W.Q.",Microbial Similarity and Preference for Specific Sites in Healthy Oral Cavity and Esophagus,Frontiers in microbiology,2018,"16S rRNA gene sequencing, esophagus, microbial preference, microbial similarity, oral cavity",Experiment 1,China,Homo sapiens,"Oral cavity,Esophagus","UBERON:0000167,UBERON:0001043",Health study participation,EFO:0010130,Oral cavity,Esophagus,"Healthy individual who are esophageal disease-free, confirmed by endoscopic examination and then biopsy-based pathological diagnosis if necessary.",27,27,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,increased,decreased,NA,NA,Signature 2,"Figure 3, Supplementary Figure S1",2 May 2024,Scholastica,"Scholastica,WikiWorks",Microbial taxa significantly different in the oral cavity compared to the esophagus with LDA score >2 using LEfse analysis,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,p__Candidatus Saccharimonadota",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;1783272|201174;3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|1224|28216;3379134|1224|1236|135615|868;3379134|1224|1236|135615;3379134|1224|1236|135615|868|2717;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481;3379134|1224|28216|206351;3379134|976|200643|171549|2005523|346096;1783272|1239|909932|909929|1843491|970;95818,Complete,Svetlana up
bsdb:30065718/2/1,30065718,"cross-sectional observational, not case-control",30065718,10.3389/fmicb.2018.01603,NA,"Dong L., Yin J., Zhao J., Ma S.R., Wang H.R., Wang M., Chen W. , Wei W.Q.",Microbial Similarity and Preference for Specific Sites in Healthy Oral Cavity and Esophagus,Frontiers in microbiology,2018,"16S rRNA gene sequencing, esophagus, microbial preference, microbial similarity, oral cavity",Experiment 2,China,Homo sapiens,Oral cavity,UBERON:0000167,Health study participation,EFO:0010130,Saliva and tongue dorsum,Supragingival plaque,Supragingival plaque samples of healthy individual confirmed free of periodontal diseases and no incident caries at the time of sampling by a dentist.,27,27,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 1,Figure 5,4 May 2024,Scholastica,"Scholastica,WikiWorks",Significantly higher relative abundance in the supragingival plaques compared to other two sites,increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia,k__Pseudomonadati|p__Spirochaetota",3379134|976;3379134|29547|3031852;3379134|976|117743;3384189|32066;3384189|32066|203490;3379134|203691|203692;3379134|203691,Complete,Svetlana up
bsdb:30065718/3/1,30065718,"cross-sectional observational, not case-control",30065718,10.3389/fmicb.2018.01603,NA,"Dong L., Yin J., Zhao J., Ma S.R., Wang H.R., Wang M., Chen W. , Wei W.Q.",Microbial Similarity and Preference for Specific Sites in Healthy Oral Cavity and Esophagus,Frontiers in microbiology,2018,"16S rRNA gene sequencing, esophagus, microbial preference, microbial similarity, oral cavity",Experiment 3,China,Homo sapiens,Oral cavity,UBERON:0000167,Health study participation,EFO:0010130,Tongue dorsum and supragingival plaque,Saliva,Saliva samples of healthy individual confirmed free of periodontal diseases and no incident caries at the time of sampling by a dentist.,27,27,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,4 May 2024,Scholastica,"Scholastica,WikiWorks",Significantly higher relative abundance in the saliva compared to other two sites,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Thermotogati|p__Synergistota|c__Synergistia,k__Thermotogati|p__Synergistota",3379134|976|200643;1783272|201174|84998;3384194|508458|649775;3384194|508458,Complete,Svetlana up
bsdb:30065718/4/1,30065718,"cross-sectional observational, not case-control",30065718,10.3389/fmicb.2018.01603,NA,"Dong L., Yin J., Zhao J., Ma S.R., Wang H.R., Wang M., Chen W. , Wei W.Q.",Microbial Similarity and Preference for Specific Sites in Healthy Oral Cavity and Esophagus,Frontiers in microbiology,2018,"16S rRNA gene sequencing, esophagus, microbial preference, microbial similarity, oral cavity",Experiment 4,China,Homo sapiens,Oral cavity,UBERON:0000167,Health study participation,EFO:0010130,Supragingival plaque and Saliva,Tongue dorsum,Tongue dorsum samples of healthy individual confirmed free of periodontal diseases and no incident caries at the time of sampling by a dentist.,27,27,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,4 May 2024,Scholastica,"Scholastica,WikiWorks",Significantly higher relative abundance in the tongue dorsum compared to other two sites,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia",1783272|1239|526524;1783272|1239|186801,Complete,Svetlana up
bsdb:30065719/1/1,30065719,case-control,30065719,10.3389/fmicb.2018.01607,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6057110/,"Deng X., Li Z., Li G., Li B., Jin X. , Lyu G.",Comparison of Microbiota in Patients Treated by Surgery or Chemotherapy by 16S rRNA Sequencing Reveals Potential Biomarkers for Colorectal Cancer Therapy,Frontiers in microbiology,2018,"16S rRNA sequencing, bacterial diversity, chemotherapy, colorectal cancer, surgery",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy individuals,CRC patients,patients diagnosed with colorectal cancer,33,31,NA,16S,45,Illumina,relative abundances,PERMANOVA,0.001,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,11 February 2022,Itslanapark,"Itslanapark,Rimsha,WikiWorks",crc patients after chemotherapy,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus flavefaciens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Viridiplantae|p__Streptophyta,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Pseudomonadati|p__Bacteroidota|s__uncultured Bacteroidota bacterium",3379134|1224|1236|135625|712|713;3379134|1224|28216|80840|506;1783272|1239|186801|3085636|186803|207244;1783272|1239|91061;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|820;3379134|976;3379134|976|200643;1783272|1239|186801|3085636|186803|572511|33035;3379134|1224|1236|91347|543|544;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|1898207;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|33042;1783272|1117;1783272|1239|186801|3085636|186803|189330;3379134|1224|1236|91347|1903409|551;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826;3384189|32066|203490|203491|1129771|32067;3384189|32066|203490|203491|1129771;3379134|1224|28216|206351|481|482;1783272|1239|186801|3085636|186803|265975;3379134|1224|1236|135625;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|186801|186802|216572|1263|1265;1783272|1239|909932|909929|1843491|970;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;33090|35493;3379134|1224|28216|80840|995019|40544;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|909932|1843489|31977;1783272|1239|186801|3085636|186803|2316020|33038;3379134|976|152509,Complete,Rimsha
bsdb:30077182/1/1,30077182,"case-control,laboratory experiment",30077182,https://doi.org/10.1186/s40168-018-0520-6,NA,"Ye Z., Zhang N., Wu C., Zhang X., Wang Q., Huang X., Du L., Cao Q., Tang J., Zhou C., Hou S., He Y., Xu Q., Xiong X., Kijlstra A., Qin N. , Yang P.",A metagenomic study of the gut microbiome in Behcet's disease,Microbiome,2018,"Behcet’s disease, Fecal microbiota transplant, Gut microbiome, Metagenomic analysis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Behcet's syndrome,EFO:0003780,Healthy Control,Untreated active Behcet's disease (BD) patients,"Active BD was defined according to  presence of active intraocular inflammation 
(case-control)",52,24,1 month,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2a,8 March 2024,Fiddyhamma,"Fiddyhamma,Welile,ChiomaBlessing,WikiWorks",Differentially abundant genera in Behcet's disease subjects compared to healthy controls.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes ihumii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. HGB5,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum|s__Azospirillum sp. CAG:239,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:770,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila sp. 4_1_30,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella sp. 4_8_47FAA,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella sp. CAG:166,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:202,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:240,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:83,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp. CAG:815,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. KLE 1728,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. KLE 1745,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium VE202-24,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium cv2,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|o__Crassvirales|f__Intestiviridae|s__Crudevirinae|g__Carjivirus|s__Carjivirus communis",3379134|976|200643|171549|171550|239759|1470347;3379134|976|200643|171549|171550|239759|908612;3379134|1224|28211|204441|2829815|191|1262705;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|28111;3379134|976|200643|171549|815|816|1262751;3379134|200940|3031449|213115|194924|35832|693988;3379134|200940|3031449|213115|194924|35832|35833;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|84998|84999|84107|102106|742722;1783272|201174|84998|84999|84107|102106|1262850;1783272|1239|186801|186802|186806|1730|1262884;1783272|1239|1263013;1783272|1239|1262992;3384189|32066|203490|203491|203492|848|1262901;1783272|1239|909932|909929|1843491|52225|52226;1783272|1239|186801|186802|216572|459786|1226322;1783272|1239|186801|186802|216572|459786|1226323;1783272|1239|186801|186802|216572|1232459;3379134|976|200643|171549|171552|577309|454154;3379134|976|200643|171549|815|909656|387090;1783272|1239|186801|186802|216572|1627893;2731360|2731618|2731619|1978007|2942964|2942972|2948652|2955582,Complete,ChiomaBlessing
bsdb:30077182/1/2,30077182,"case-control,laboratory experiment",30077182,https://doi.org/10.1186/s40168-018-0520-6,NA,"Ye Z., Zhang N., Wu C., Zhang X., Wang Q., Huang X., Du L., Cao Q., Tang J., Zhou C., Hou S., He Y., Xu Q., Xiong X., Kijlstra A., Qin N. , Yang P.",A metagenomic study of the gut microbiome in Behcet's disease,Microbiome,2018,"Behcet’s disease, Fecal microbiota transplant, Gut microbiome, Metagenomic analysis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Behcet's syndrome,EFO:0003780,Healthy Control,Untreated active Behcet's disease (BD) patients,"Active BD was defined according to  presence of active intraocular inflammation 
(case-control)",52,24,1 month,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2a,8 March 2024,Fiddyhamma,"Fiddyhamma,ChiomaBlessing,WikiWorks",Differentially abundant genera in Behcet's disease subjects compared to healthy controls.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acidocellaceae|g__Acidiphilium|s__Acidiphilium sp. CAG:727,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. CAG:268,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp. CAG:528,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:1024,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:127,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:349,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:813,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp. CAG:782,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:38,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Methanobacteriati|p__Methanobacteriota|c__Methanomicrobia|o__Methanomicrobiales|f__Methanomicrobiaceae|g__Methanoculleus|s__Methanoculleus sp. CAG:1088,k__Methanobacteriati|p__Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomethylophilaceae|g__Methanomethylophilus|s__Methanomethylophilus alvi,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter piscolens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp. CAG:314",3379134|1224|28211|3120395|3385905|522|1262689;3379134|976|200643|171549|171550|239759|1262693;1783272|1239|186801|186802|216572|244127|1262700;1783272|1239|186801|186802|31979|1485|1262770;1783272|1239|186801|186802|31979|1485|1262774;1783272|1239|186801|186802|31979|1485|1262797;1783272|1239|186801|186802|31979|1485|1262843;1783272|1239|186801|3085636|186803|33042|1262863;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|186801|186802|186806|1730|1262889;3384189|32066|203490|203491|203492|848|850;1783272|1239|909932|1843489|31977|906|907;3366610|28890|224756|2191|2194|45989|1262903;3366610|2283796|183967|1235850|2517203|1291539|1291540;3384194|508458|649775|649776|3029088|638847|638849;1783272|1239|186801|186802|216572|292632|1262970,Complete,ChiomaBlessing
bsdb:30077182/3/1,30077182,"case-control,laboratory experiment",30077182,https://doi.org/10.1186/s40168-018-0520-6,NA,"Ye Z., Zhang N., Wu C., Zhang X., Wang Q., Huang X., Du L., Cao Q., Tang J., Zhou C., Hou S., He Y., Xu Q., Xiong X., Kijlstra A., Qin N. , Yang P.",A metagenomic study of the gut microbiome in Behcet's disease,Microbiome,2018,"Behcet’s disease, Fecal microbiota transplant, Gut microbiome, Metagenomic analysis",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Healthy Control feces treated group,Behcet's disease (BD) feces treated group,B10RIII mice (mice undergoing autoimmune uveitis) colonized with untreated BD patients stool samples (experimental),4,4,NA,NA,NA,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Supplementary Figure S1c, Supplementary Table S9",8 March 2024,Fiddyhamma,"Fiddyhamma,ChiomaBlessing,WikiWorks",Abundance of altered genera	in Behcet's disease (BD) patients’ feces treated group compared to healthy control feces treated mice,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171552|1283313;1783272|1239|186801|186802|216572|52784;3379134|200940|3031449|213115|194924|35832;3379134|976|200643|171549|1853231|574697;3379134|976|200643|171549|2005519|1348911;3379134|200930|68337|191393|2945020|248038;3379134|976|200643|171549|171552|577309,Complete,ChiomaBlessing
bsdb:30077182/3/2,30077182,"case-control,laboratory experiment",30077182,https://doi.org/10.1186/s40168-018-0520-6,NA,"Ye Z., Zhang N., Wu C., Zhang X., Wang Q., Huang X., Du L., Cao Q., Tang J., Zhou C., Hou S., He Y., Xu Q., Xiong X., Kijlstra A., Qin N. , Yang P.",A metagenomic study of the gut microbiome in Behcet's disease,Microbiome,2018,"Behcet’s disease, Fecal microbiota transplant, Gut microbiome, Metagenomic analysis",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Healthy Control feces treated group,Behcet's disease (BD) feces treated group,B10RIII mice (mice undergoing autoimmune uveitis) colonized with untreated BD patients stool samples (experimental),4,4,NA,NA,NA,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Supplementary Figure S1c, Supplementary Table S9",8 March 2024,Fiddyhamma,"Fiddyhamma,ChiomaBlessing,WikiWorks",Abundance of altered genera	in Behcet's disease (BD) patients’ feces treated group compared to healthy control feces treated mice,decreased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,1783272|201174|84998|84999|84107|102106,Complete,ChiomaBlessing
bsdb:30077182/4/1,30077182,"case-control,laboratory experiment",30077182,https://doi.org/10.1186/s40168-018-0520-6,NA,"Ye Z., Zhang N., Wu C., Zhang X., Wang Q., Huang X., Du L., Cao Q., Tang J., Zhou C., Hou S., He Y., Xu Q., Xiong X., Kijlstra A., Qin N. , Yang P.",A metagenomic study of the gut microbiome in Behcet's disease,Microbiome,2018,"Behcet’s disease, Fecal microbiota transplant, Gut microbiome, Metagenomic analysis",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Behcet's syndrome,EFO:0003780,Healthy Control,Untreated active Behcet's disease (BD) patients,"Active BD was defined according to  presence of active intraocular inflammation 
(case-control)",52,24,1 month,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental. Table S3,29 March 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Enriched/ depleted species in Behcet's disease subjects compared to healthy controls,increased,"k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Clavicipitaceae|g__Atkinsonella|s__Atkinsonella texensis,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Clavicipitaceae|g__Epichloe|s__Epichloe aotearoae,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Botryosphaeriales|f__Botryosphaeriaceae|g__Macrophomina|s__Macrophomina phaseolina,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas sp. Leaf70,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Diaporthales|f__Diaporthaceae|g__Diaporthe|s__Diaporthe ampelina,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Glomerellaceae|g__Colletotrichum|s__Colletotrichum higginsianum,k__Fungi|p__Ascomycota|c__Orbiliomycetes|o__Orbiliales|f__Orbiliaceae|g__Drechslerella|s__Drechslerella stenobrocha,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Hypocreaceae|g__Trichoderma|s__Trichoderma parareesei,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Chaetothyriales|f__Herpotrichiellaceae|g__Cladophialophora|s__Cladophialophora psammophila,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Glomerellaceae|g__Colletotrichum|s__Colletotrichum orbiculare,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas rhizophila,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. ph3,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida parapsilosis,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Clavicipitaceae|g__Claviceps|s__Claviceps paspali,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium argentoratense,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Chaetothyriales|f__Herpotrichiellaceae|g__Exophiala|s__Exophiala mesophila,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Pichiales|f__Pichiaceae|g__Ogataea|s__Ogataea methanolica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Shiraiaceae|g__Shiraia|s__Shiraia sp. slf14,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Sordariaceae|g__Neurospora|s__Neurospora crassa",4751|4890|147550|5125|34397|40612|51582;4751|4890|147550|5125|34397|5112|170559;4751|4890|147541|451869|45131|35724|35725;3379134|1224|1236|135614|32033|40323|1736233;4751|4890|147550|5114|767018|36922|1214573;4751|4890|147550|1028384|681950|5455|80884;4751|4890|189478|189479|47021|314126|314127;4751|4890|147550|5125|5129|5543|858221;4751|4890|147545|34395|43219|82105|1182553;4751|4890|147550|1028384|681950|5455|5465;3379134|1224|1236|135614|32033|40323|216778;1783272|201174|1760|2037|2049|1654|1118058;4751|4890|3239874|2916678|766764|5475|5480;4751|4890|147550|5125|34397|5110|40601;1783272|201174|1760|85007|1653|1716|42817;4751|4890|147545|34395|43219|5583|212818;4751|4890|3239874|3243775|1156497|461281|1156966;1783272|201174|1760|2037|2049|1654|55565;3379134|1224|1236|135614|32033|40323|40324;4751|4890|147541|92860|224418|224419|665115;4751|4890|147550|5139|5148|5140|5141,Complete,ChiomaBlessing
bsdb:30077182/4/2,30077182,"case-control,laboratory experiment",30077182,https://doi.org/10.1186/s40168-018-0520-6,NA,"Ye Z., Zhang N., Wu C., Zhang X., Wang Q., Huang X., Du L., Cao Q., Tang J., Zhou C., Hou S., He Y., Xu Q., Xiong X., Kijlstra A., Qin N. , Yang P.",A metagenomic study of the gut microbiome in Behcet's disease,Microbiome,2018,"Behcet’s disease, Fecal microbiota transplant, Gut microbiome, Metagenomic analysis",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Behcet's syndrome,EFO:0003780,Healthy Control,Untreated active Behcet's disease (BD) patients,"Active BD was defined according to  presence of active intraocular inflammation 
(case-control)",52,24,1 month,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental. Table S3,29 March 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Enriched/ depleted species in Behcet's disease subjects compared to healthy controls,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter sp. CAG:196,s__Epichloe glyceriae",3379134|1224|1236|2887326|468|469|1262690;79591,Complete,ChiomaBlessing
bsdb:30081953/1/1,30081953,case-control,30081953,10.1186/s40168-018-0515-3,NA,"Zhu J., Liao M., Yao Z., Liang W., Li Q., Liu J., Yang H., Ji Y., Wei W., Tan A., Liang S., Chen Y., Lin H., Zhu X., Huang S., Tian J., Tang R., Wang Q. , Mo Z.",Breast cancer in postmenopausal women is associated with an altered gut metagenome,Microbiome,2018,"Breast cancer, Gut microbiota, Immunity, Metabolism, Metagenomic analyses",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,controls,Postmenopausal breast cancer patients,Postmenopausal breast cancer patients,46,44,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,unchanged,Signature 1,Table 2 and Supplementary Table S4,10 January 2021,Rimsha Azhar,WikiWorks,Relative abundance of the different species between postmenopausal breast cancer patients and postmenopausal healthy controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella sonnei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus|s__Proteus mirabilis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella boydii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio cholerae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia fergusonii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella flexneri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter johnsonii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia|s__Providencia rettgeri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus gallinarum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia|s__Erwinia amylovora,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Bruguierivoracaceae|g__Sodalis|s__Sodalis glossinidius,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter radioresistens,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium varium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia|s__Yersinia enterocolitica,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella|s__Shewanella putrefaciens",3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|543|620|624;3379134|1224|1236|91347|1903414|583|584;3379134|1224|1236|91347|543|620|621;3379134|1224|1236|135623|641|662|666;3379134|1224|1236|91347|543|561|564;3379134|1224|1236|91347|543|620|623;3379134|1224|1236|2887326|468|469|470;3379134|1224|1236|2887326|468|469|40214;3379134|1224|1236|91347|1903414|586|587;1783272|1239|91061|186826|33958|2742598|97478;3379134|976|200643|171549|171551|836|281920;3384189|32066|203490|203491|203492|848|851;3379134|1224|1236|91347|543|544|545;3379134|200940|3031449|213115|194924|872|901;1783272|1239|91061|186826|81852|1350|1353;3379134|1224|1236|91347|543|590|28901;3379134|1224|1236|91347|1903409|551|552;3379134|1224|1236|91347|2812006|84565|63612;3379134|1224|1236|2887326|468|469|40216;3384189|32066|203490|203491|203492|848|856;1783272|1239|909932|1843488|909930|904|187327;3379134|976|200643|171549|171552|838|419005;3379134|1224|1236|91347|1903411|629|630;1783272|1239|1737404|1737405|1570339|165779|33037;3379134|1224|1236|135622|267890|22|24,Complete,Fatima Zohra
bsdb:30081953/1/2,30081953,case-control,30081953,10.1186/s40168-018-0515-3,NA,"Zhu J., Liao M., Yao Z., Liang W., Li Q., Liu J., Yang H., Ji Y., Wei W., Tan A., Liang S., Chen Y., Lin H., Zhu X., Huang S., Tian J., Tang R., Wang Q. , Mo Z.",Breast cancer in postmenopausal women is associated with an altered gut metagenome,Microbiome,2018,"Breast cancer, Gut microbiota, Immunity, Metabolism, Metagenomic analyses",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,controls,Postmenopausal breast cancer patients,Postmenopausal breast cancer patients,46,44,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,unchanged,Signature 2,Table 2 and Supplementary Table S4,10 January 2021,Rimsha Azhar,WikiWorks,Relative abundance of the different species between postmenopausal breast cancer patients and postmenopausal healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia albertii,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella|s__Brucella melitensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus vaginalis",1783272|1239|186801|3085636|186803|28050|39485;3379134|1224|1236|91347|543|561|208962;3379134|29547|3031852|213849|72294|194|199;1783272|1239|186801|3085636|186803|841|360807;3379134|1224|28211|356|118882|234|29459;1783272|1239|91061|186826|33958|2742598|1633,Complete,Fatima Zohra
bsdb:30088332/1/1,30088332,case-control,30088332,10.1002/mbo3.678,NA,"Lun H., Yang W., Zhao S., Jiang M., Xu M., Liu F. , Wang Y.",Altered gut microbiota and microbial biomarkers associated with chronic kidney disease,MicrobiologyOpen,2019,"chronic kidney disease, gut microbiota, hemodialysis, intestinal dysbiosis, microbial biomarker",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,healthy controls,chronic kidney disease,patients with chronic kidney disease,24,49,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3b,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Comparison of gut bacteria between the HC and chronic kidney disease groups,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum",3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976;3379134|976|200643;1783272|201174|84998|1643822|1643826|84111;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|526524|526525|2810280|1505663;3379134|1224|1236|91347|543|561;1783272|1239|186801|186802|216572|946234;3379134|1224|1236;1783272|1239|91061|186826|81850;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3085636|186803|1769710;3379134|1224|1236|91347|543|620;1783272|1239|91061|186826|33958|46255;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|186802|31979|1485|1522,Complete,Claregrieve1
bsdb:30088332/1/2,30088332,case-control,30088332,10.1002/mbo3.678,NA,"Lun H., Yang W., Zhao S., Jiang M., Xu M., Liu F. , Wang Y.",Altered gut microbiota and microbial biomarkers associated with chronic kidney disease,MicrobiologyOpen,2019,"chronic kidney disease, gut microbiota, hemodialysis, intestinal dysbiosis, microbial biomarker",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,healthy controls,chronic kidney disease,patients with chronic kidney disease,24,49,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3b,10 January 2021,Fatima Zohra,WikiWorks,Comparison of gut bacteria between the HC and chronic kidney disease groups,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota",1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|186802|541000;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3082720|186804;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|3085636|186803|28050;1783272|1239|91061|186826|186828|2747;1783272|1239|186801|3085636|186803|1766253|39491;3379134|976|200643|171549|171552;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|909929;1783272|1239|909932;1783272|1239|909932|1843489|31977;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239,Complete,Claregrieve1
bsdb:30089174/1/1,30089174,case-control,30089174,10.1371/journal.pone.0201768,NA,"Ho E.X.P., Cheung C.M.G., Sim S., Chu C.W., Wilm A., Lin C.B., Mathur R., Wong D., Chan C.M., Bhagarva M., Laude A., Lim T.H., Wong T.Y., Cheng C.Y., Davila S. , Hibberd M.",Human pharyngeal microbiota in age-related macular degeneration,PloS one,2018,NA,Experiment 1,Singapore,Homo sapiens,Throat,UBERON:0000341,Age-related macular degeneration,EFO:0001365,Control,AMD(Age-related macular degeneration)-positive,Patients with Age-related macular degeneration,386,245,NA,16S,3456,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 2,27 June 2025,Anne-mariesharp,Anne-mariesharp,DESeq2 differential abundance analysis expressed as Log2FC comparison of AMD-positive samples and control samples.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,1783272|1239|91061|1385|539738|1378,Complete,KateRasheed
bsdb:30089174/1/2,30089174,case-control,30089174,10.1371/journal.pone.0201768,NA,"Ho E.X.P., Cheung C.M.G., Sim S., Chu C.W., Wilm A., Lin C.B., Mathur R., Wong D., Chan C.M., Bhagarva M., Laude A., Lim T.H., Wong T.Y., Cheng C.Y., Davila S. , Hibberd M.",Human pharyngeal microbiota in age-related macular degeneration,PloS one,2018,NA,Experiment 1,Singapore,Homo sapiens,Throat,UBERON:0000341,Age-related macular degeneration,EFO:0001365,Control,AMD(Age-related macular degeneration)-positive,Patients with Age-related macular degeneration,386,245,NA,16S,3456,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 2,27 June 2025,Anne-mariesharp,Anne-mariesharp,DESeq2 differential abundance analysis expressed as Log2FC comparison of AMD-positive samples and control samples.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,KateRasheed
bsdb:30089174/2/1,30089174,case-control,30089174,10.1371/journal.pone.0201768,NA,"Ho E.X.P., Cheung C.M.G., Sim S., Chu C.W., Wilm A., Lin C.B., Mathur R., Wong D., Chan C.M., Bhagarva M., Laude A., Lim T.H., Wong T.Y., Cheng C.Y., Davila S. , Hibberd M.",Human pharyngeal microbiota in age-related macular degeneration,PloS one,2018,NA,Experiment 2,Singapore,Homo sapiens,Throat,UBERON:0000341,Age-related macular degeneration,EFO:0001365,Control ( - ),AMD(Age-related macular degeneration)-positive ( + ),Patients with Age-related macular degeneration,386,245,NA,16S,3456,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,unchanged,NA,NA,Signature 1,"Figure 3, Supplementary Table 4",27 June 2025,Anne-mariesharp,Anne-mariesharp,Relative abundances of significant genera between case (Age-related macular degeneration - positive) and control samples,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:30089174/2/2,30089174,case-control,30089174,10.1371/journal.pone.0201768,NA,"Ho E.X.P., Cheung C.M.G., Sim S., Chu C.W., Wilm A., Lin C.B., Mathur R., Wong D., Chan C.M., Bhagarva M., Laude A., Lim T.H., Wong T.Y., Cheng C.Y., Davila S. , Hibberd M.",Human pharyngeal microbiota in age-related macular degeneration,PloS one,2018,NA,Experiment 2,Singapore,Homo sapiens,Throat,UBERON:0000341,Age-related macular degeneration,EFO:0001365,Control ( - ),AMD(Age-related macular degeneration)-positive ( + ),Patients with Age-related macular degeneration,386,245,NA,16S,3456,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,unchanged,NA,NA,Signature 2,"Figure 3, Supplementary Table 4",27 June 2025,Anne-mariesharp,Anne-mariesharp,Relative abundances of significant genera between case (Age-related macular degeneration - positive) and control samples,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",3379134|976|200643|171549|171552|838;3384189|32066|203490|203491|1129771|32067,Complete,KateRasheed
bsdb:30089174/3/1,30089174,case-control,30089174,10.1371/journal.pone.0201768,NA,"Ho E.X.P., Cheung C.M.G., Sim S., Chu C.W., Wilm A., Lin C.B., Mathur R., Wong D., Chan C.M., Bhagarva M., Laude A., Lim T.H., Wong T.Y., Cheng C.Y., Davila S. , Hibberd M.",Human pharyngeal microbiota in age-related macular degeneration,PloS one,2018,NA,Experiment 3,Singapore,Homo sapiens,Throat,UBERON:0000341,Microbiome,EFO:0004982,Rest (The rest of the study population),High Prevotella,Subjects with high relative abundance of Prevotella,604,27,NA,16S,3456,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 2,27 June 2025,Anne-mariesharp,Anne-mariesharp,Microbial genera significantly associated with high Prevotella relative abundance.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella",1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|171551|836;1783272|1239|91061|186826|186828|117563;1783272|1239|91061|1385|539738|1378,Complete,KateRasheed
bsdb:30089174/4/1,30089174,case-control,30089174,10.1371/journal.pone.0201768,NA,"Ho E.X.P., Cheung C.M.G., Sim S., Chu C.W., Wilm A., Lin C.B., Mathur R., Wong D., Chan C.M., Bhagarva M., Laude A., Lim T.H., Wong T.Y., Cheng C.Y., Davila S. , Hibberd M.",Human pharyngeal microbiota in age-related macular degeneration,PloS one,2018,NA,Experiment 4,Singapore,Homo sapiens,Throat,UBERON:0000341,Microbiome,EFO:0004982,Rest (The rest of the study population),High Gemella,Subjects with high relative abundance of Gemella,610,21,NA,16S,3456,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 3,27 June 2025,Anne-mariesharp,Anne-mariesharp,Microbial genera significantly associated with high Gemella relative abundance.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",3379134|1224|1236|135625|712|416916;1783272|1239|186801|3082720|3118655|44259;3379134|1224|1236|135625|712|724,Complete,KateRasheed
bsdb:30089174/4/2,30089174,case-control,30089174,10.1371/journal.pone.0201768,NA,"Ho E.X.P., Cheung C.M.G., Sim S., Chu C.W., Wilm A., Lin C.B., Mathur R., Wong D., Chan C.M., Bhagarva M., Laude A., Lim T.H., Wong T.Y., Cheng C.Y., Davila S. , Hibberd M.",Human pharyngeal microbiota in age-related macular degeneration,PloS one,2018,NA,Experiment 4,Singapore,Homo sapiens,Throat,UBERON:0000341,Microbiome,EFO:0004982,Rest (The rest of the study population),High Gemella,Subjects with high relative abundance of Gemella,610,21,NA,16S,3456,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 3,27 June 2025,Anne-mariesharp,Anne-mariesharp,Microbial genera significantly associated with high Gemella relative abundance.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976|200643|171549|171552|838;1783272|1239|909932|1843489|31977|29465,Complete,KateRasheed
bsdb:30089174/5/1,30089174,case-control,30089174,10.1371/journal.pone.0201768,NA,"Ho E.X.P., Cheung C.M.G., Sim S., Chu C.W., Wilm A., Lin C.B., Mathur R., Wong D., Chan C.M., Bhagarva M., Laude A., Lim T.H., Wong T.Y., Cheng C.Y., Davila S. , Hibberd M.",Human pharyngeal microbiota in age-related macular degeneration,PloS one,2018,NA,Experiment 5,Singapore,Homo sapiens,Throat,UBERON:0000341,Age-related macular degeneration,EFO:0001365,Control ( - ),L-AMD(Late Age-related macular degeneration)-positive,Patients with late-stage Age-related macular degeneration,386,165,NA,16S,3456,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4, Supplementary Table 6",27 June 2025,Anne-mariesharp,Anne-mariesharp,Relative abundances of significant genera between controls and individuals with late AMD(Age-related macular degeneration),increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella",1783272|1239|91061|186826|1300|1301;1783272|1239|91061|1385|539738|1378,Complete,KateRasheed
bsdb:30089174/5/2,30089174,case-control,30089174,10.1371/journal.pone.0201768,NA,"Ho E.X.P., Cheung C.M.G., Sim S., Chu C.W., Wilm A., Lin C.B., Mathur R., Wong D., Chan C.M., Bhagarva M., Laude A., Lim T.H., Wong T.Y., Cheng C.Y., Davila S. , Hibberd M.",Human pharyngeal microbiota in age-related macular degeneration,PloS one,2018,NA,Experiment 5,Singapore,Homo sapiens,Throat,UBERON:0000341,Age-related macular degeneration,EFO:0001365,Control ( - ),L-AMD(Late Age-related macular degeneration)-positive,Patients with late-stage Age-related macular degeneration,386,165,NA,16S,3456,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 4, Supplementary Table 6",27 June 2025,Anne-mariesharp,Anne-mariesharp,Relative abundances of significant genera between controls and individuals with late AMD(Age-related macular degeneration),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",3379134|976|200643|171549|171552|838;3384189|32066|203490|203491|1129771|32067,Complete,KateRasheed
bsdb:30089174/6/1,30089174,case-control,30089174,10.1371/journal.pone.0201768,NA,"Ho E.X.P., Cheung C.M.G., Sim S., Chu C.W., Wilm A., Lin C.B., Mathur R., Wong D., Chan C.M., Bhagarva M., Laude A., Lim T.H., Wong T.Y., Cheng C.Y., Davila S. , Hibberd M.",Human pharyngeal microbiota in age-related macular degeneration,PloS one,2018,NA,Experiment 6,Singapore,Homo sapiens,Throat,UBERON:0000341,Age-related macular degeneration,EFO:0001365,Control (Healthy participants),Case (Age-related macular degeneration patients),Patients with Age-related macular degeneration greater than 60years,180,192,NA,16S,3456,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 5,27 June 2025,Anne-mariesharp,Anne-mariesharp,Association between microbial genera and AMD status in individuals >60 years. Genera with significantly different relative abundances in case/control conditions are shown.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:30089174/6/2,30089174,case-control,30089174,10.1371/journal.pone.0201768,NA,"Ho E.X.P., Cheung C.M.G., Sim S., Chu C.W., Wilm A., Lin C.B., Mathur R., Wong D., Chan C.M., Bhagarva M., Laude A., Lim T.H., Wong T.Y., Cheng C.Y., Davila S. , Hibberd M.",Human pharyngeal microbiota in age-related macular degeneration,PloS one,2018,NA,Experiment 6,Singapore,Homo sapiens,Throat,UBERON:0000341,Age-related macular degeneration,EFO:0001365,Control (Healthy participants),Case (Age-related macular degeneration patients),Patients with Age-related macular degeneration greater than 60years,180,192,NA,16S,3456,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 5,27 June 2025,Anne-mariesharp,Anne-mariesharp,Association between microbial genera and AMD status in individuals >60 years. Genera with significantly different relative abundances in case/control conditions are shown.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",3379134|976|200643|171549|171552|838;3384189|32066|203490|203491|1129771|32067,Complete,KateRasheed
bsdb:30089174/7/1,30089174,case-control,30089174,10.1371/journal.pone.0201768,NA,"Ho E.X.P., Cheung C.M.G., Sim S., Chu C.W., Wilm A., Lin C.B., Mathur R., Wong D., Chan C.M., Bhagarva M., Laude A., Lim T.H., Wong T.Y., Cheng C.Y., Davila S. , Hibberd M.",Human pharyngeal microbiota in age-related macular degeneration,PloS one,2018,NA,Experiment 7,Singapore,Homo sapiens,Throat,UBERON:0000341,Age-related macular degeneration,EFO:0001365,Control ( - ) (Healthy participants),Case ( + ) (Age-related macular degeneration patients),Patients with Age-related macular degeneration,20,20,NA,PCR,NA,NA,relative abundances,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,"age,sex",NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 5,27 June 2025,Anne-mariesharp,Anne-mariesharp,Differential abundance of selected microbial genera between disease groups based on qPCR-derived copy numbers,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:30089174/7/2,30089174,case-control,30089174,10.1371/journal.pone.0201768,NA,"Ho E.X.P., Cheung C.M.G., Sim S., Chu C.W., Wilm A., Lin C.B., Mathur R., Wong D., Chan C.M., Bhagarva M., Laude A., Lim T.H., Wong T.Y., Cheng C.Y., Davila S. , Hibberd M.",Human pharyngeal microbiota in age-related macular degeneration,PloS one,2018,NA,Experiment 7,Singapore,Homo sapiens,Throat,UBERON:0000341,Age-related macular degeneration,EFO:0001365,Control ( - ) (Healthy participants),Case ( + ) (Age-related macular degeneration patients),Patients with Age-related macular degeneration,20,20,NA,PCR,NA,NA,relative abundances,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,"age,sex",NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 5,27 June 2025,Anne-mariesharp,Anne-mariesharp,Differential abundance of selected microbial genera between disease groups based on qPCR-derived copy numbers,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,KateRasheed
bsdb:30117171/1/1,30117171,"cross-sectional observational, not case-control,prospective cohort",30117171,10.1002/pros.23713,NA,"Alanee S., El-Zawahry A., Dynda D., Dabaja A., McVary K., Karr M. , Braundmeier-Fleming A.",A prospective study to examine the association of the urinary and fecal microbiota with prostate cancer diagnosis after transrectal biopsy of the prostate using 16sRNA gene analysis,The Prostate,2019,"benign prostate, microbiota, prostate cancer",Experiment 1,United States of America,Homo sapiens,Urine,UBERON:0001088,prostate cancer,NA,controls,prostate cancer patients,the association of urinary and fecal microbiota with prostate cancer diagnosis,16,14,28 days,16S,345,Illumina,NA,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Table 1, Text",10 January 2021,Rimsha Azhar,"WikiWorks,Atrayees",Significant differential OTU frequencies in urine samples of patients with or without prostate cancer,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,Atrayees
bsdb:30117171/1/2,30117171,"cross-sectional observational, not case-control,prospective cohort",30117171,10.1002/pros.23713,NA,"Alanee S., El-Zawahry A., Dynda D., Dabaja A., McVary K., Karr M. , Braundmeier-Fleming A.",A prospective study to examine the association of the urinary and fecal microbiota with prostate cancer diagnosis after transrectal biopsy of the prostate using 16sRNA gene analysis,The Prostate,2019,"benign prostate, microbiota, prostate cancer",Experiment 1,United States of America,Homo sapiens,Urine,UBERON:0001088,prostate cancer,NA,controls,prostate cancer patients,the association of urinary and fecal microbiota with prostate cancer diagnosis,16,14,28 days,16S,345,Illumina,NA,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Table 1, text",26 June 2023,Atrayees,"Atrayees,WikiWorks",Significant differential OTU frequencies in urine samples of patients with or without prostate cancer,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|186802|216572|258514,Complete,Atrayees
bsdb:30122883/1/1,30122883,case-control,30122883,10.3748/wjg.v24.i30.3448,NA,"Zhao Y., Mao Y.F., Tang Y.S., Ni M.Z., Liu Q.H., Wang Y., Feng Q., Peng J.H. , Hu Y.Y.",Altered oral microbiota in chronic hepatitis B patients with different tongue coatings,World journal of gastroenterology,2018,"16S rRNA gene sequencing, Chronic hepatitis B, Metabolomics, Microbiota, Tongue diagnosis",Experiment 1,China,Homo sapiens,Tongue,UBERON:0001723,Chronic hepatitis B virus infection,EFO:0004239,healthy controls,chronic hepatitis B yellow tongue coating patients,"patients diagnosed with chronic hepatitis B per ""The Guidelines for the Prevention and Treatment of Chronic Hepatitis B (2010 version)"" with a yellow tongue coating",22,28,3 months,16S,3,Ion Torrent,NA,Metastats,0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Figure 2B, Figure 3A",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differentially abundant taxa between chronic hepatitis B yellow tongue coating patients and healthy controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|28216|80840|119060;3379134|1224|1236|135615|868;3379134|1224|28216|80840|80864;3379134|1224|28216|80840|80864|283;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481;3379134|1224,Complete,Claregrieve1
bsdb:30122883/1/2,30122883,case-control,30122883,10.3748/wjg.v24.i30.3448,NA,"Zhao Y., Mao Y.F., Tang Y.S., Ni M.Z., Liu Q.H., Wang Y., Feng Q., Peng J.H. , Hu Y.Y.",Altered oral microbiota in chronic hepatitis B patients with different tongue coatings,World journal of gastroenterology,2018,"16S rRNA gene sequencing, Chronic hepatitis B, Metabolomics, Microbiota, Tongue diagnosis",Experiment 1,China,Homo sapiens,Tongue,UBERON:0001723,Chronic hepatitis B virus infection,EFO:0004239,healthy controls,chronic hepatitis B yellow tongue coating patients,"patients diagnosed with chronic hepatitis B per ""The Guidelines for the Prevention and Treatment of Chronic Hepatitis B (2010 version)"" with a yellow tongue coating",22,28,3 months,16S,3,Ion Torrent,NA,Metastats,0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Figure 2B, Figure 3A",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differentially abundant taxa between chronic hepatitis B yellow tongue coating patients and healthy controls,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptoclostridiaceae|g__Peptoclostridium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia",1783272|201174|1760|85004|31953;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294;95818|2093818|2093825|2171986|1331051;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|3120161|1481960;1783272|201174|1760|85004|31953|196081,Complete,Claregrieve1
bsdb:30122883/2/1,30122883,case-control,30122883,10.3748/wjg.v24.i30.3448,NA,"Zhao Y., Mao Y.F., Tang Y.S., Ni M.Z., Liu Q.H., Wang Y., Feng Q., Peng J.H. , Hu Y.Y.",Altered oral microbiota in chronic hepatitis B patients with different tongue coatings,World journal of gastroenterology,2018,"16S rRNA gene sequencing, Chronic hepatitis B, Metabolomics, Microbiota, Tongue diagnosis",Experiment 2,China,Homo sapiens,Tongue,UBERON:0001723,Chronic hepatitis B virus infection,EFO:0004239,chronic hepatitis B white tongue coating patients,chronic hepatitis B yellow tongue coating patients,"patients diagnosed with chronic hepatitis B per ""The Guidelines for the Prevention and Treatment of Chronic Hepatitis B (2010 version)"" with a yellow tongue coating",25,28,3 months,16S,3,Ion Torrent,NA,Metastats,0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Figure 2B, Figure 3A",10 January 2021,Rimsha Azhar,"Fatima,Claregrieve1,WikiWorks",Differentially abundant taxa between chronic hepatitis B yellow and white tongue coating patients,increased,"p__Candidatus Altimarinota,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota",363464;1783272|544448|31969|2085|2092|2093;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481;3379134|1224,Complete,Claregrieve1
bsdb:30122883/2/2,30122883,case-control,30122883,10.3748/wjg.v24.i30.3448,NA,"Zhao Y., Mao Y.F., Tang Y.S., Ni M.Z., Liu Q.H., Wang Y., Feng Q., Peng J.H. , Hu Y.Y.",Altered oral microbiota in chronic hepatitis B patients with different tongue coatings,World journal of gastroenterology,2018,"16S rRNA gene sequencing, Chronic hepatitis B, Metabolomics, Microbiota, Tongue diagnosis",Experiment 2,China,Homo sapiens,Tongue,UBERON:0001723,Chronic hepatitis B virus infection,EFO:0004239,chronic hepatitis B white tongue coating patients,chronic hepatitis B yellow tongue coating patients,"patients diagnosed with chronic hepatitis B per ""The Guidelines for the Prevention and Treatment of Chronic Hepatitis B (2010 version)"" with a yellow tongue coating",25,28,3 months,16S,3,Ion Torrent,NA,Metastats,0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Figure 2B, Figure 3A",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differentially abundant taxa between chronic hepatitis B yellow and white tongue coating patients,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|976;1783272|1239|186801|3085636|186803|43996;3379134|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:30122883/3/1,30122883,case-control,30122883,10.3748/wjg.v24.i30.3448,NA,"Zhao Y., Mao Y.F., Tang Y.S., Ni M.Z., Liu Q.H., Wang Y., Feng Q., Peng J.H. , Hu Y.Y.",Altered oral microbiota in chronic hepatitis B patients with different tongue coatings,World journal of gastroenterology,2018,"16S rRNA gene sequencing, Chronic hepatitis B, Metabolomics, Microbiota, Tongue diagnosis",Experiment 3,China,Homo sapiens,Tongue,UBERON:0001723,Chronic hepatitis B virus infection,EFO:0004239,healthy controls,chronic hepatitis B white tongue coating patients,"patients diagnosed with chronic hepatitis B per ""The Guidelines for the Prevention and Treatment of Chronic Hepatitis B (2010 version)"" with a white tongue coating",22,25,3 months,16S,3,Ion Torrent,NA,Metastats,0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Figure 2B, Figure 3A",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differentially abundant taxa between healthy controls and chronic hepatitis B white tongue coating patients,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",3379134|976|117743|200644|2762318|59735;1783272|1239|526524|526525|128827|118747;1783272|1239|909932|909929|1843491|82202;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836,Complete,Claregrieve1
bsdb:30122883/3/2,30122883,case-control,30122883,10.3748/wjg.v24.i30.3448,NA,"Zhao Y., Mao Y.F., Tang Y.S., Ni M.Z., Liu Q.H., Wang Y., Feng Q., Peng J.H. , Hu Y.Y.",Altered oral microbiota in chronic hepatitis B patients with different tongue coatings,World journal of gastroenterology,2018,"16S rRNA gene sequencing, Chronic hepatitis B, Metabolomics, Microbiota, Tongue diagnosis",Experiment 3,China,Homo sapiens,Tongue,UBERON:0001723,Chronic hepatitis B virus infection,EFO:0004239,healthy controls,chronic hepatitis B white tongue coating patients,"patients diagnosed with chronic hepatitis B per ""The Guidelines for the Prevention and Treatment of Chronic Hepatitis B (2010 version)"" with a white tongue coating",22,25,3 months,16S,3,Ion Torrent,NA,Metastats,0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Figure 2B, Figure 3A",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differentially abundant taxa between healthy controls and chronic hepatitis B white tongue coating patients,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Alysiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;3379134|1224|28216|206351|481|194195;3379134|1224|1236|135615|868;1783272|544448|31969|2085|2092;1783272|1239|186801|186802|186806|113286;1783272|201174|1760|85004|31953|196081,Complete,Claregrieve1
bsdb:30123780/1/1,30123780,case-control,30123780,10.3389/fcimb.2018.00267,NA,"Lim Y., Fukuma N., Totsika M., Kenny L., Morrison M. , Punyadeera C.",The Performance of an Oral Microbiome Biomarker Panel in Predicting Oral Cavity and Oropharyngeal Cancers,Frontiers in cellular and infection microbiology,2018,"biomarker, oral cancer, oral microbiome, oral rinse, saliva",Experiment 1,Australia,Homo sapiens,Mouth,UBERON:0000165,Head and neck carcinoma,MONDO:0002038,High-risk individuals,OCC & OPC,Newly diagnosed OCC(Oral Cavity Cancer) and OPC (Oropharyngeal Cancer),11,32,NA,16S,678,Illumina,NA,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Figure 1B, Supp. Table 2, Text",10 January 2021,Utsav Patel,WikiWorks,The Performance of an Oral Microbiome in Predicting Oral Cavity and Oropharyngeal Cancers,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia",3379134|976|200643|171549|2005523|346096;1783272|201174|1760|85007|1653|1716;3379134|976|200643|171549|171551|836;1783272|201174|1760|2037|2049|1654;3379134|1224|1236|135625|712|713;3379134|976|117743|200644|49546|1016;3384189|32066|203490|203491|203492|848;3379134|1224|1236|135625|712|416916;3379134|1224|28216|80840|119060|47670,Complete,Atrayees
bsdb:30123780/2/1,30123780,case-control,30123780,10.3389/fcimb.2018.00267,NA,"Lim Y., Fukuma N., Totsika M., Kenny L., Morrison M. , Punyadeera C.",The Performance of an Oral Microbiome Biomarker Panel in Predicting Oral Cavity and Oropharyngeal Cancers,Frontiers in cellular and infection microbiology,2018,"biomarker, oral cancer, oral microbiome, oral rinse, saliva",Experiment 2,Australia,Homo sapiens,Mouth,UBERON:0000165,Head and neck carcinoma,MONDO:0002038,Normal Healthy Controls,OCC & OPC,Newly diagnosed OCC(Oral Cavity Cancer) and OPC (Oropharyngeal Cancer),20,31,NA,16S,678,Illumina,NA,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Supp. Table 2, Text",10 January 2021,Utsav Patel,"WikiWorks,Atrayees",The Performance of an Oral Microbiome in Predicting Oral Cavity and Oropharyngeal Cancers,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,1783272|1239|186801|3085636|186803|265975,Complete,Atrayees
bsdb:30123780/2/2,30123780,case-control,30123780,10.3389/fcimb.2018.00267,NA,"Lim Y., Fukuma N., Totsika M., Kenny L., Morrison M. , Punyadeera C.",The Performance of an Oral Microbiome Biomarker Panel in Predicting Oral Cavity and Oropharyngeal Cancers,Frontiers in cellular and infection microbiology,2018,"biomarker, oral cancer, oral microbiome, oral rinse, saliva",Experiment 2,Australia,Homo sapiens,Mouth,UBERON:0000165,Head and neck carcinoma,MONDO:0002038,Normal Healthy Controls,OCC & OPC,Newly diagnosed OCC(Oral Cavity Cancer) and OPC (Oropharyngeal Cancer),20,31,NA,16S,678,Illumina,NA,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,"Figure 1B, Supp. Table 2, Text",10 January 2021,Utsav Patel,WikiWorks,The Performance of an Oral Microbiome in Predicting Oral Cavity and Oropharyngeal Cancers,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga",1783272|201174|1760|85006|1268|32207;3379134|1224|1236|135625|712|724;1783272|201174|1760|85007|1653|1716;3379134|976|200643|171549|2005523|346096;3379134|976|200643|171549|171551|836;3379134|976|117743|200644|49546|1016,Complete,Atrayees
bsdb:30131575/1/1,30131575,"cross-sectional observational, not case-control",30131575,10.1038/s41598-018-30428-3,NA,"Berni Canani R., De Filippis F., Nocerino R., Paparo L., Di Scala C., Cosenza L., Della Gatta G., Calignano A., De Caro C., Laiola M., Gilbert J.A. , Ercolini D.",Gut microbiota composition and butyrate production in children affected by non-IgE-mediated cow's milk allergy,Scientific reports,2018,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,healthy controls,non-IgE mediated cow's milk allergy,"children aged 1-26 months with a diagnosis of non-IgE mediated cow's milk allergy based on clinical history, negative result of skin prick test, and/or negative level of IgE serum-specific anti-cow's milk proteins",23,23,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Supplemental Table S1,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between cow's milk allergy non IgE patients at diagnosis and healthy controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979|1266,Complete,Claregrieve1
bsdb:30131575/2/1,30131575,"cross-sectional observational, not case-control",30131575,10.1038/s41598-018-30428-3,NA,"Berni Canani R., De Filippis F., Nocerino R., Paparo L., Di Scala C., Cosenza L., Della Gatta G., Calignano A., De Caro C., Laiola M., Gilbert J.A. , Ercolini D.",Gut microbiota composition and butyrate production in children affected by non-IgE-mediated cow's milk allergy,Scientific reports,2018,NA,Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,infant with non-IgE-mediated cow's milk allergy at diagnosis,infant with non-IgE-mediated cow's milk allergy treated with EHCF,infant with non-IgE mediated cow's milk allergy treated with EHCF,23,9,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Supplemental Table S1,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between non-IgE-Mediated cow's milk allergy patients treated with EHCF and non-IgE mediated cow's milk allergy patients at diagnosis,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",3379134|976|200643|171549|815|816;3379134|976|200643|171549|171550|239759,Complete,Claregrieve1
bsdb:30131575/3/1,30131575,"cross-sectional observational, not case-control",30131575,10.1038/s41598-018-30428-3,NA,"Berni Canani R., De Filippis F., Nocerino R., Paparo L., Di Scala C., Cosenza L., Della Gatta G., Calignano A., De Caro C., Laiola M., Gilbert J.A. , Ercolini D.",Gut microbiota composition and butyrate production in children affected by non-IgE-mediated cow's milk allergy,Scientific reports,2018,NA,Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,infant with non-IgE-mediated cow's milk allergy at diagnosis,infant with non-IgE-mediated cow's milk allergy treated with EHCF+LGG,infant with non-IgE mediated cow's milk allergy treated with EHCF+LGG,23,14,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Supplemental Table S1,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between non-IgE-Mediated cow's milk allergy patients treated with EHCF + LGG and non-IgE mediated cow's milk allergy patients at diagnosis,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816,Complete,Claregrieve1
bsdb:30131575/3/2,30131575,"cross-sectional observational, not case-control",30131575,10.1038/s41598-018-30428-3,NA,"Berni Canani R., De Filippis F., Nocerino R., Paparo L., Di Scala C., Cosenza L., Della Gatta G., Calignano A., De Caro C., Laiola M., Gilbert J.A. , Ercolini D.",Gut microbiota composition and butyrate production in children affected by non-IgE-mediated cow's milk allergy,Scientific reports,2018,NA,Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,infant with non-IgE-mediated cow's milk allergy at diagnosis,infant with non-IgE-mediated cow's milk allergy treated with EHCF+LGG,infant with non-IgE mediated cow's milk allergy treated with EHCF+LGG,23,14,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Supplementary Table S1,31 December 2022,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between non-IgE-Mediated cow's milk allergy patients treated with EHCF + LGG and non-IgE mediated cow's milk allergy patients at diagnosis,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,1783272|201174|1760|85011|2062|1883,Complete,Claregrieve1
bsdb:30131575/4/1,30131575,"cross-sectional observational, not case-control",30131575,10.1038/s41598-018-30428-3,NA,"Berni Canani R., De Filippis F., Nocerino R., Paparo L., Di Scala C., Cosenza L., Della Gatta G., Calignano A., De Caro C., Laiola M., Gilbert J.A. , Ercolini D.",Gut microbiota composition and butyrate production in children affected by non-IgE-mediated cow's milk allergy,Scientific reports,2018,NA,Experiment 4,Italy,Homo sapiens,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,infant with non-IgE-mediated cow's milk allergy treated with EHCF,infant with non-IgE-mediated cow's milk allergy treated with EHCF+LGG,infant with non-IgE mediated cow's milk allergy treated with EHCF+LGG,9,14,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Supplemental Table S1,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between non-IgE-Mediated cow's milk allergy patients treated with EHCF + LGG and non-IgE mediated cow's milk allergy patients treated with EHCF,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239|186801|3085636|186803|28050;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572|1263,Complete,Claregrieve1
bsdb:30131575/4/2,30131575,"cross-sectional observational, not case-control",30131575,10.1038/s41598-018-30428-3,NA,"Berni Canani R., De Filippis F., Nocerino R., Paparo L., Di Scala C., Cosenza L., Della Gatta G., Calignano A., De Caro C., Laiola M., Gilbert J.A. , Ercolini D.",Gut microbiota composition and butyrate production in children affected by non-IgE-mediated cow's milk allergy,Scientific reports,2018,NA,Experiment 4,Italy,Homo sapiens,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,infant with non-IgE-mediated cow's milk allergy treated with EHCF,infant with non-IgE-mediated cow's milk allergy treated with EHCF+LGG,infant with non-IgE mediated cow's milk allergy treated with EHCF+LGG,9,14,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Supplemental Table S1,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks",Differential microbial abundance between non-IgE-Mediated cow's milk allergy treated with EHCF + LGG and non-IgE mediated cow's milk allergy treated with EHCF,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;1783272|1239|909932|1843489|31977|39948,Complete,Claregrieve1
bsdb:30139999/1/1,30139999,randomized controlled trial,30139999,10.1038/s41598-018-30783-1,NA,"Gurry T., Gibbons S.M., Nguyen L.T.T., Kearney S.M., Ananthakrishnan A., Jiang X., Duvallet C., Kassam Z. , Alm E.J.",Predictability and persistence of prebiotic dietary supplementation in a healthy human cohort,Scientific reports,2018,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,day 6 of PECTIN spike-in,day 3 of PECTIN spike-in,before pectin spike-in,9,9,6 months,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,"age,body mass index",NA,NA,NA,NA,NA,NA,Signature 1,Figure 1b and text,10 January 2021,Lora Kasselman,WikiWorks,"OTUs that showed statistically significant (DESeq. 2, FDR < 0.1) differential abundance on day 6 compared to day 3 in response to particular spike-ins. Mean relative abundances are computed across all participants and then converted to Z-scores across timepoints, to illustrate relative changes through time. - PECTIN",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|841;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|186802|541000;1783272|1239|186801|186802|216572|216851|853,Complete,NA
bsdb:30139999/2/1,30139999,randomized controlled trial,30139999,10.1038/s41598-018-30783-1,NA,"Gurry T., Gibbons S.M., Nguyen L.T.T., Kearney S.M., Ananthakrishnan A., Jiang X., Duvallet C., Kassam Z. , Alm E.J.",Predictability and persistence of prebiotic dietary supplementation in a healthy human cohort,Scientific reports,2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,day 6 of INULIN spike-in,day 3 of INULIN spike-in,before pectin spike-in,9,9,6 months,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,"age,body mass index",NA,NA,NA,NA,NA,NA,Signature 1,Figure 1b and text,10 January 2021,Lora Kasselman,WikiWorks,"OTUs that showed statistically significant (DESeq. 2, FDR < 0.1) differential abundance on day 6 compared to day 3 in response to particular spike-ins. Mean relative abundances are computed across all participants and then converted to Z-scores across timepoints, to illustrate relative changes through time. - INULIN",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",1783272|1239|186801|3085636|186803;3379134|976|200643|171549|815|816|820;1783272|1239|186801|186802|216572|216851|853,Complete,NA
bsdb:30153231/1/1,30153231,case-control,30153231,10.1097/INF.0000000000002174,NA,"Kelly M.S., Surette M.G., Smieja M., Rossi L., Luinstra K., Steenhoff A.P., Goldfarb D.M., Pernica J.M., Arscott-Mills T., Boiditswe S., Mazhani T., Rawls J.F., Cunningham C.K., Shah S.S., Feemster K.A. , Seed P.C.",Pneumococcal Colonization and the Nasopharyngeal Microbiota of Children in Botswana,The Pediatric infectious disease journal,2018,NA,Experiment 1,Botswana,Homo sapiens,Nasopharynx,UBERON:0001728,Pneumonia,EFO:0003106,negative,S.pneumoniae positive,clinical pneumonnia,74,96,NA,16S,3,Illumina,NA,Logistic Regression,0.05,FALSE,NA,"date,primary care clinic",age,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3,10 January 2021,Fatima Zohra,WikiWorks,Relative abundance of highly abundant genera by S. pneumoniae colonization,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|1224|1236|2887326|468|475;1783272|1239|91061|186826|1300|1301,Complete,NA
bsdb:30153231/1/2,30153231,case-control,30153231,10.1097/INF.0000000000002174,NA,"Kelly M.S., Surette M.G., Smieja M., Rossi L., Luinstra K., Steenhoff A.P., Goldfarb D.M., Pernica J.M., Arscott-Mills T., Boiditswe S., Mazhani T., Rawls J.F., Cunningham C.K., Shah S.S., Feemster K.A. , Seed P.C.",Pneumococcal Colonization and the Nasopharyngeal Microbiota of Children in Botswana,The Pediatric infectious disease journal,2018,NA,Experiment 1,Botswana,Homo sapiens,Nasopharynx,UBERON:0001728,Pneumonia,EFO:0003106,negative,S.pneumoniae positive,clinical pneumonnia,74,96,NA,16S,3,Illumina,NA,Logistic Regression,0.05,FALSE,NA,"date,primary care clinic",age,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3,10 January 2021,Fatima Zohra,WikiWorks,Relative abundance of highly abundant genera by S. pneumoniae colonization,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|201174|1760|85007|1653|1716;1783272|1239|91061|1385|90964|1279,Complete,NA
bsdb:30154758/1/1,30154758,laboratory experiment,30154758,https://doi.org/10.3389/fmicb.2018.01665,NA,"Wang H., Ji Y., Yin C., Deng M., Tang T., Deng B., Ren W., Deng J., Yin Y. , Tan C.",Differential Analysis of Gut Microbiota Correlated With Oxidative Stress in Sows With High or Low Litter Performance During Lactation,Frontiers in microbiology,2018,"gut microbiota, lactation, litter performance, oxidative stress, sows",Experiment 1,China,Sus scrofa domesticus,Feces,UBERON:0001988,Pregnancy,EFO:0002950,High litter performance sows at G109,Low litter performance sows at G109,Low litter performance sows group at day 109 of gestation,10,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,increased,increased,decreased,NA,unchanged,Signature 1,Figure 4B,14 April 2024,Scholastica,"Scholastica,WikiWorks",Differences in fecal microbiota in day 109 of gestation of high litter performance sows compared to day 109 of gestation of low litter performance sows,increased,"k__Pseudomonadati|p__Candidatus Electryoneota|c__Candidatus Tariuqbacteria|o__Candidatus Tariuqbacterales,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|3031806|3075765|3075766;1783272|1117;1783272|1239|909932|1843488|909930|33024;1783272|1239|526524|526525|2810281|191303;1783272|1239|526524|526525|2810281;1783272|1239|909932|1843489|31977,Complete,Svetlana up
bsdb:30154758/1/2,30154758,laboratory experiment,30154758,https://doi.org/10.3389/fmicb.2018.01665,NA,"Wang H., Ji Y., Yin C., Deng M., Tang T., Deng B., Ren W., Deng J., Yin Y. , Tan C.",Differential Analysis of Gut Microbiota Correlated With Oxidative Stress in Sows With High or Low Litter Performance During Lactation,Frontiers in microbiology,2018,"gut microbiota, lactation, litter performance, oxidative stress, sows",Experiment 1,China,Sus scrofa domesticus,Feces,UBERON:0001988,Pregnancy,EFO:0002950,High litter performance sows at G109,Low litter performance sows at G109,Low litter performance sows group at day 109 of gestation,10,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,increased,increased,decreased,NA,unchanged,Signature 2,Figure 4B,14 April 2024,Scholastica,"Scholastica,WikiWorks",Differences in fecal microbiota in day 109 of gestation of high litter performance sows compared to day 109 of gestation of low litter performance sows,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:30154758/2/1,30154758,laboratory experiment,30154758,https://doi.org/10.3389/fmicb.2018.01665,NA,"Wang H., Ji Y., Yin C., Deng M., Tang T., Deng B., Ren W., Deng J., Yin Y. , Tan C.",Differential Analysis of Gut Microbiota Correlated With Oxidative Stress in Sows With High or Low Litter Performance During Lactation,Frontiers in microbiology,2018,"gut microbiota, lactation, litter performance, oxidative stress, sows",Experiment 2,China,Sus scrofa domesticus,Feces,UBERON:0001988,Maternal milk,XCO:0000415,High litter performance sows at L21,Low litter performance sows at L21,Low litter performance sows group at day 21 of lactation (L21),10,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,increased,increased,decreased,NA,unchanged,Signature 1,Figure 4E,15 April 2024,Scholastica,"Scholastica,WikiWorks",Differences in fecal microbiota in day 21 of lactation of high litter performance sows compared to day 21 of lactation of low litter performance sows,increased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239|186801;1783272|1239|186801|186802,Complete,Svetlana up
bsdb:30154758/2/2,30154758,laboratory experiment,30154758,https://doi.org/10.3389/fmicb.2018.01665,NA,"Wang H., Ji Y., Yin C., Deng M., Tang T., Deng B., Ren W., Deng J., Yin Y. , Tan C.",Differential Analysis of Gut Microbiota Correlated With Oxidative Stress in Sows With High or Low Litter Performance During Lactation,Frontiers in microbiology,2018,"gut microbiota, lactation, litter performance, oxidative stress, sows",Experiment 2,China,Sus scrofa domesticus,Feces,UBERON:0001988,Maternal milk,XCO:0000415,High litter performance sows at L21,Low litter performance sows at L21,Low litter performance sows group at day 21 of lactation (L21),10,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,increased,increased,decreased,NA,unchanged,Signature 2,Figure 4E,15 April 2024,Scholastica,"Scholastica,WikiWorks,Tosin",Differences in fecal microbiota in day 21 of lactation of high litter performance sows compared to day 21 of lactation of low litter performance sows,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|s__Enterococcaceae bacterium RF39",1783272|1239|186801|3085636|186803|33042;1783272|544448|31969;1783272|544448;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;1783272|544448|31969;1783272|1239|91061|186826|81852|423410,Complete,Svetlana up
bsdb:30154758/3/1,30154758,laboratory experiment,30154758,https://doi.org/10.3389/fmicb.2018.01665,NA,"Wang H., Ji Y., Yin C., Deng M., Tang T., Deng B., Ren W., Deng J., Yin Y. , Tan C.",Differential Analysis of Gut Microbiota Correlated With Oxidative Stress in Sows With High or Low Litter Performance During Lactation,Frontiers in microbiology,2018,"gut microbiota, lactation, litter performance, oxidative stress, sows",Experiment 3,China,Sus scrofa domesticus,Feces,UBERON:0001988,Pregnancy,EFO:0002950,Day 109 of gestation (G109) of H group,Day 21 of lactation (L21) of H group,Day 21 of lactation (L21) of high litter performance sows group,10,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 4H,14 April 2024,Scholastica,"Scholastica,WikiWorks,Tosin",Differences in fecal microbiota in day 109 of gestation (G109) compared to day 21 of lactation (L21) of high litter performance sows,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|s__Enterococcaceae bacterium RF39",1783272|1239|91061|186826|33958;1783272|544448|31969;1783272|544448;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3082720|543314|86331;1783272|1239|91061|186826|81852|423410,Complete,Svetlana up
bsdb:30154758/3/2,30154758,laboratory experiment,30154758,https://doi.org/10.3389/fmicb.2018.01665,NA,"Wang H., Ji Y., Yin C., Deng M., Tang T., Deng B., Ren W., Deng J., Yin Y. , Tan C.",Differential Analysis of Gut Microbiota Correlated With Oxidative Stress in Sows With High or Low Litter Performance During Lactation,Frontiers in microbiology,2018,"gut microbiota, lactation, litter performance, oxidative stress, sows",Experiment 3,China,Sus scrofa domesticus,Feces,UBERON:0001988,Pregnancy,EFO:0002950,Day 109 of gestation (G109) of H group,Day 21 of lactation (L21) of H group,Day 21 of lactation (L21) of high litter performance sows group,10,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 4H,14 April 2024,Scholastica,"Scholastica,WikiWorks",Differences in fecal microbiota in day 109 of gestation (G109) compared to day 21 of lactation (L21) of high litter performance sows,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Propionicimonas,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae",3379134|1224|1236|135624;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|1224|1236;1783272|201174|1760|85009|85015;1783272|201174|1760|85009|85015|236052;3379134|1224;3379134|1224|1236|135624|83763|83770;3379134|1224|1236|135624|83763;1783272|201174|84998|84999|84107;3379134|29547|3031852|213849|72293,Complete,Svetlana up
bsdb:30154758/4/1,30154758,laboratory experiment,30154758,https://doi.org/10.3389/fmicb.2018.01665,NA,"Wang H., Ji Y., Yin C., Deng M., Tang T., Deng B., Ren W., Deng J., Yin Y. , Tan C.",Differential Analysis of Gut Microbiota Correlated With Oxidative Stress in Sows With High or Low Litter Performance During Lactation,Frontiers in microbiology,2018,"gut microbiota, lactation, litter performance, oxidative stress, sows",Experiment 4,China,Sus scrofa domesticus,Feces,UBERON:0001988,Pregnancy,EFO:0002950,Day 109 of gestation (G109) of L group,Day 21 of lactation (L21) of L group,Day 21 of lactation (L21) of low litter performance sows group,10,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 4K,14 April 2024,Scholastica,"Scholastica,WikiWorks",Differences in fecal microbiota in day 109 of gestation (G109) compared to day 21 of lactation (L21) of low litter performance sows,decreased,"k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Propionicimonas,k__Pseudomonadati|p__Pseudomonadota,k__Viridiplantae|p__Streptophyta,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1117;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236;1783272|1239|186801|3085636|186803;1783272|201174|1760|85009|85015;1783272|1239|909932|1843488|909930|33024;1783272|201174|1760|85009|85015|236052;3379134|1224;33090|35493;1783272|1239|909932|1843489|31977;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:30157754/1/1,30157754,case-control,30157754,10.1186/s12866-018-1232-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6114884/,"Zhang Y., Yu X., Yu E., Wang N., Cai Q., Shuai Q., Yan F., Jiang L., Wang H., Liu J., Chen Y., Li Z. , Jiang Q.",Changes in gut microbiota and plasma inflammatory factors across the stages of colorectal tumorigenesis: a case-control study,BMC microbiology,2018,"Colorectal cancer (CRC), Correlation analysis, Gut microbiota, Plasma inflammatory factors",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy controls,CRC patients,patients diagnosed with colorectal cancer,130,130,6 months,16S,34,Illumina,NA,Zero-Inflated Beta Regression,0.05,TRUE,NA,"age,sex","age,alcohol drinking,body mass index,sex,smoking status",NA,unchanged,NA,unchanged,NA,NA,Signature 1,Table S1,20 January 2022,Itslanapark,"Itslanapark,Claregrieve1,Atrayees,WikiWorks",CRC-associated microbiota in CRC patients compared with controls,increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter rectus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Metazoa|p__Chordata|c__Actinopteri|o__Cyprinodontiformes|f__Nothobranchiidae|g__Scriptaphyosemion|s__Scriptaphyosemion liberiense,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",3379134|29547|3031852|213849|72294|194|203;1783272|1239|909932|1843489|31977|39948|39950;1783272|201174|84998|1643822|1643826|84111|84112;3384189|32066|203490|203491|203492|848|851;1783272|1239|91061|1385|539738|1378|29391;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|1239|186801|3082720|186804|1257|341694;3379134|976|200643|171549|171551|836|28123;33208|7711|186623|28738|405002|129983|60404;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|186801|3085636|186803|1506553|29347;1783272|1239|186801|3085636|186803|2941495|1512;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Claregrieve1
bsdb:30157754/1/2,30157754,case-control,30157754,10.1186/s12866-018-1232-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6114884/,"Zhang Y., Yu X., Yu E., Wang N., Cai Q., Shuai Q., Yan F., Jiang L., Wang H., Liu J., Chen Y., Li Z. , Jiang Q.",Changes in gut microbiota and plasma inflammatory factors across the stages of colorectal tumorigenesis: a case-control study,BMC microbiology,2018,"Colorectal cancer (CRC), Correlation analysis, Gut microbiota, Plasma inflammatory factors",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy controls,CRC patients,patients diagnosed with colorectal cancer,130,130,6 months,16S,34,Illumina,NA,Zero-Inflated Beta Regression,0.05,TRUE,NA,"age,sex","age,alcohol drinking,body mass index,sex,smoking status",NA,unchanged,NA,unchanged,NA,NA,Signature 2,Table S1,20 January 2022,Itslanapark,"Itslanapark,Claregrieve1,Aiyshaaaa,WikiWorks",CRC-associated microbiota in CRC patients compared with controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum desmolans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris",1783272|1239|186801|186802|3085642|2048137|39484;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|186801|3085636|186803|572511|871665;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|186801|3085636|186803|2316020|46228,Complete,Claregrieve1
bsdb:30157953/1/1,30157953,prospective cohort,30157953,10.1186/s40168-018-0531-3,NA,"Shanahan E.R., Shah A., Koloski N., Walker M.M., Talley N.J., Morrison M. , Holtmann G.J.",Influence of cigarette smoking on the human duodenal mucosa-associated microbiota,Microbiome,2018,"Cigarettes, Duodenum, Microbiome, Mucosa, Small intestine, Smoking",Experiment 1,Australia,Homo sapiens,Small intestine,UBERON:0002108,Smoking behavior,EFO:0004318,never smoked,"patients with FD, ID,or CD who currently smoked","patient with FD,ID or CD with who previously or currently smokes",41,61,2 months,16S,678,Illumina,centered log-ratio,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Figure 3& Text,10 January 2021,Zyaijah Bailey,WikiWorks,Linear discriminant analysis effect size (LEfSe) method to identify bacterial OTUs that are associated with smoking status.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|85006|1268|32207;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:30157953/2/1,30157953,prospective cohort,30157953,10.1186/s40168-018-0531-3,NA,"Shanahan E.R., Shah A., Koloski N., Walker M.M., Talley N.J., Morrison M. , Holtmann G.J.",Influence of cigarette smoking on the human duodenal mucosa-associated microbiota,Microbiome,2018,"Cigarettes, Duodenum, Microbiome, Mucosa, Small intestine, Smoking",Experiment 2,Australia,Homo sapiens,Small intestine,UBERON:0002108,Smoking behavior,EFO:0004318,never smoked,"patients with FD, ID,or CD who currently smokes","patient with FD,ID or CD with who previously or currently smokes",41,61,2 months,16S,678,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 3 & Text,10 January 2021,Zyaijah Bailey,WikiWorks,Linear discriminant analysis effect size (LEfSe) method to identify bacterial OTUs that are associated with smoking status.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|838,Complete,Atrayees
bsdb:30188331/1/1,30188331,"cross-sectional observational, not case-control",30188331,10.1097/GME.0000000000001202,NA,"Yoshikata R., Myint K.Z., Ohta H. , Ishigaki Y.","Inter-relationship between diet, lifestyle habits, gut microflora, and the equol-producer phenotype: baseline findings from a placebo-controlled intervention trial","Menopause (New York, N.Y.)",2019,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,"Equol producer (""healhtier"" diet)","Equol NON producer (""unhealthier"" diet)",cross sectional,45,13,NA,16S,3,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Table 2, Table 3, and text",10 January 2021,Lora Kasselman,WikiWorks,TABLE 2. Comparisons of microbial results between equol producers and nonproducers,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,NA
bsdb:30188331/2/1,30188331,"cross-sectional observational, not case-control",30188331,10.1097/GME.0000000000001202,NA,"Yoshikata R., Myint K.Z., Ohta H. , Ishigaki Y.","Inter-relationship between diet, lifestyle habits, gut microflora, and the equol-producer phenotype: baseline findings from a placebo-controlled intervention trial","Menopause (New York, N.Y.)",2019,NA,Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,"Equol producer (""healhtier"" diet)","Equol NON producer (""unhealthier"" diet)",cross sectional,45,13,NA,16S,3,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Table 2, Table 3, and text",10 January 2021,Lora Kasselman,WikiWorks,TABLE 2. Comparisons of microbial results between equol producers and nonproducers,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,NA
bsdb:30204780/1/1,30204780,case-control,30204780,10.1371/journal.pone.0203503,NA,"Wang T., Yu L., Xu C., Pan K., Mo M., Duan M., Zhang Y. , Xiong H.",Chronic fatigue syndrome patients have alterations in their oral microbiome composition and function,PloS one,2018,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Chronic fatigue syndrome,EFO:0004540,Healthy controls,Chronic Fatigue patients,NA,45,46,2 months for healthy control only,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,body mass index,sex",NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 3b,10 January 2021,Shaimaa Elsafoury,"Fatima,WikiWorks",LEfSe analysis identified the most differentially abundant taxa between healthy controls and CFS patients.Only taxa with LDA > 3 are shown.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Alkalibacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella",1783272|1239|91061|1385|186817|331654;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294;3379134|29547|3031852|213849;3379134|29547;3384189|32066;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378,Complete,Fatima
bsdb:30204780/1/2,30204780,case-control,30204780,10.1371/journal.pone.0203503,NA,"Wang T., Yu L., Xu C., Pan K., Mo M., Duan M., Zhang Y. , Xiong H.",Chronic fatigue syndrome patients have alterations in their oral microbiome composition and function,PloS one,2018,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Chronic fatigue syndrome,EFO:0004540,Healthy controls,Chronic Fatigue patients,NA,45,46,2 months for healthy control only,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,body mass index,sex",NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 3b,10 January 2021,Shaimaa Elsafoury,WikiWorks,LEfSe analysis identified the most differentially abundant taxa between healthy controls and CFS patients.Only taxa with LDA > 3 are shown.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",3379134|1224|1236;1783272|1239|909932|1843489|31977;1783272|1239|909932;1783272|1239|909932|909929;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836;3379134|1224|1236|2887326|468|475;3379134|1224|1236|72274|135621|351;3379134|1224|1236|72274|135621|286,Complete,Shaimaa Elsafoury
bsdb:30224347/1/1,30224347,case-control,30224347,10.2337/dc18-0253,NA,"Leiva-Gea I., Sánchez-Alcoholado L., Martín-Tejedor B., Castellano-Castillo D., Moreno-Indias I., Urda-Cardona A., Tinahones F.J., Fernández-García J.C. , Queipo-Ortuño M.I.",Gut Microbiota Differs in Composition and Functionality Between Children With Type 1 Diabetes and MODY2 and Healthy Control Subjects: A Case-Control Study,Diabetes care,2018,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Type I diabetes mellitus,MONDO:0005147,maturity-onset diabetes of the young 2 (MODY2) and healthy Controls,Type I Diabetics,"type 1 diabetes was diagnosed according to the criteria of the American Diabetes Association and the positivity of at least two persistent, confirmed anti-islet autoantibodies (anti-insulin autoantibodies, GAD autoantibodies, or tyrosine phosphatase autoantibodies). MODY2 children were diagnosed by suggestive clinical history, negative anti-islet autoantibodies, and positive genetic testing. Healthy control subjects were children with negative anti-islet autoantibodies,",28,15,3 months,16S,23,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,breastfeeding duration,delivery procedure,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Text,10 January 2021,Yaseen Javaid,WikiWorks,"differentially abundant taxa of the fecal microbiota in type 1 diabetes, MODY2, and healthy controls",increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|976;3379134|976|200643|171549|815;3379134|976|200643|171549|171550;3379134|1224|1236|91347|543;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|541000;1783272|1239|909932|1843489|31977;1783272|1239|91061|186826|1300;3379134|976|200643|171549|815|816;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300|1301;3379134|1224|1236|91347|543|547;3379134|1224|28216|80840|995019|40544,Complete,Shaimaa Elsafoury
bsdb:30224347/1/2,30224347,case-control,30224347,10.2337/dc18-0253,NA,"Leiva-Gea I., Sánchez-Alcoholado L., Martín-Tejedor B., Castellano-Castillo D., Moreno-Indias I., Urda-Cardona A., Tinahones F.J., Fernández-García J.C. , Queipo-Ortuño M.I.",Gut Microbiota Differs in Composition and Functionality Between Children With Type 1 Diabetes and MODY2 and Healthy Control Subjects: A Case-Control Study,Diabetes care,2018,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Type I diabetes mellitus,MONDO:0005147,maturity-onset diabetes of the young 2 (MODY2) and healthy Controls,Type I Diabetics,"type 1 diabetes was diagnosed according to the criteria of the American Diabetes Association and the positivity of at least two persistent, confirmed anti-islet autoantibodies (anti-insulin autoantibodies, GAD autoantibodies, or tyrosine phosphatase autoantibodies). MODY2 children were diagnosed by suggestive clinical history, negative anti-islet autoantibodies, and positive genetic testing. Healthy control subjects were children with negative anti-islet autoantibodies,",28,15,3 months,16S,23,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,breastfeeding duration,delivery procedure,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Text,10 January 2021,Yaseen Javaid,WikiWorks,"differentially abundant taxa of the fecal microbiota in type 1 diabetes, MODY2, and healthy controls",decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota",1783272|1239;1783272|201174,Complete,Shaimaa Elsafoury
bsdb:30224347/2/1,30224347,case-control,30224347,10.2337/dc18-0253,NA,"Leiva-Gea I., Sánchez-Alcoholado L., Martín-Tejedor B., Castellano-Castillo D., Moreno-Indias I., Urda-Cardona A., Tinahones F.J., Fernández-García J.C. , Queipo-Ortuño M.I.",Gut Microbiota Differs in Composition and Functionality Between Children With Type 1 Diabetes and MODY2 and Healthy Control Subjects: A Case-Control Study,Diabetes care,2018,NA,Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Type I diabetes mellitus,MONDO:0005147,healthy Controls,Type I Diabetics and maturity-onset diabetes of the young 2 (MODY2),"type 1 diabetes was diagnosed according to the criteria of the American Diabetes Association and the positivity of at least two persistent, confirmed anti-islet autoantibodies (anti-insulin autoantibodies, GAD autoantibodies, or tyrosine phosphatase autoantibodies). MODY2 children were diagnosed by suggestive clinical history, negative anti-islet autoantibodies, and positive genetic testing. Healthy control subjects were children with negative anti-islet autoantibodies,",13,30,3 months,16S,23,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,breastfeeding duration,delivery procedure,race,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,Text,10 January 2021,Shaimaa Elsafoury,WikiWorks,"differentially abundant taxa of the fecal microbiota in type 1 diabetes, MODY2, and healthy controls",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|216572|216851,Complete,Shaimaa Elsafoury
bsdb:30228282/1/1,30228282,case-control,30228282,10.1038/s41598-018-32219-2,NA,"Zhang M., Ma W., Zhang J., He Y. , Wang J.",Analysis of gut microbiota profiles and microbe-disease associations in children with autism spectrum disorders in China,Scientific reports,2018,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autism,EFO:0003758,typically developing controls,autism,diagnosed with autistic spectrum disorder according to DSM-5 (Diagnostic and Statistical Manual of Mental Disorders-5th Edition),6,35,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Fatima Zohra,WikiWorks,The bacterial abundance at the level of phylum and genus in autistic and typically developing children with significant difference,increased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Shaimaa Elsafoury
bsdb:30228282/1/2,30228282,case-control,30228282,10.1038/s41598-018-32219-2,NA,"Zhang M., Ma W., Zhang J., He Y. , Wang J.",Analysis of gut microbiota profiles and microbe-disease associations in children with autism spectrum disorders in China,Scientific reports,2018,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autism,EFO:0003758,typically developing controls,autism,diagnosed with autistic spectrum disorder according to DSM-5 (Diagnostic and Statistical Manual of Mental Disorders-5th Edition),6,35,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 2,10 January 2021,Fatima Zohra,WikiWorks,The bacterial abundance at the level of phylum and genus in autistic and typically developing children with significant difference,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus",1783272|1239;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|91347|543|561;1783272|201174|1760|2037|2049|1654;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|526524|526525|128827|118747;1783272|1239|1737404|1737405|1570339|162289,Complete,Shaimaa Elsafoury
bsdb:30231060/1/1,30231060,"cross-sectional observational, not case-control",30231060,10.1371/journal.pone.0202278,NA,"Beyer K., Zaura E., Brandt B.W., Buijs M.J., Brun J.G., Crielaard W. , Bolstad A.I.",Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health,PloS one,2018,NA,Experiment 1,Norway,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,Rheumatoid Arthritis (RA) Remission,Active (RA) Rheumatoid Arthritis,Individuals with active rheumatoid arthritis (RA),28,60,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Figure 3, text",2 November 2022,Tislam,"Tislam,Peace Sandy,WikiWorks","(B) Differentially discriminatory OTUs (N = 21) by RA disease activity status, as identified by linear discriminant analysis effect size (LEfSe) analysis. Active RA = grey bars; RA remission = black bars.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85007|1653|1716;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Peace Sandy
bsdb:30231060/1/2,30231060,"cross-sectional observational, not case-control",30231060,10.1371/journal.pone.0202278,NA,"Beyer K., Zaura E., Brandt B.W., Buijs M.J., Brun J.G., Crielaard W. , Bolstad A.I.",Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health,PloS one,2018,NA,Experiment 1,Norway,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,Rheumatoid Arthritis (RA) Remission,Active (RA) Rheumatoid Arthritis,Individuals with active rheumatoid arthritis (RA),28,60,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,"Figure 2, text",2 November 2022,Tislam,"Tislam,WikiWorks","(B) Differentially discriminatory OTUs (N = 21) by RA disease activity status, as identified by linear discriminant analysis effect size (LEfSe) analysis. Active RA = grey bars; RA remission = black bars.",decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",1783272|201174|84998|84999|1643824|1380;1783272|1239|186801|186802|1898207;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|265975;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171550;1783272|1239|909932|909929|1843491|970,Complete,Peace Sandy
bsdb:30231060/2/1,30231060,"cross-sectional observational, not case-control",30231060,10.1371/journal.pone.0202278,NA,"Beyer K., Zaura E., Brandt B.W., Buijs M.J., Brun J.G., Crielaard W. , Bolstad A.I.",Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health,PloS one,2018,NA,Experiment 2,Norway,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,No prednisolone,Prednisolone,Individuals who received prednisolone,57,21,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,S4F Table,20 January 2024,Peace Sandy,"Peace Sandy,WikiWorks","Significantly discriminatory OTUs between the microbiome sample clusters (use - and non-use of prednisolone). From the 552 OTUs, 19 discriminated significantly use and non-use of prednisolone (LDA >2, p<0.05, LEfSe). Prednisolone (N=21)=black dots; no prednisolone (N=57)=grey dots.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",3379134|1224|28216|206351|481|32257;3379134|976|117743|200644|49546|1016;1783272|1239|91061|186826|1300|1301;3379134|1224|1236|135615|868|2717;1783272|1239|909932|909929|1843491|970,Complete,Peace Sandy
bsdb:30231060/2/2,30231060,"cross-sectional observational, not case-control",30231060,10.1371/journal.pone.0202278,NA,"Beyer K., Zaura E., Brandt B.W., Buijs M.J., Brun J.G., Crielaard W. , Bolstad A.I.",Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health,PloS one,2018,NA,Experiment 2,Norway,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,No prednisolone,Prednisolone,Individuals who received prednisolone,57,21,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,S4F Table,20 January 2024,Peace Sandy,"Peace Sandy,WikiWorks","Significantly discriminatory OTUs between the microbiome sample clusters (use - and non-use of prednisolone). From the 552 OTUs, 19 discriminated significantly use and non-use of prednisolone (LDA >2, p<0.05, LEfSe). Prednisolone (N=21)=black dots; no prednisolone (N=57)=grey dots.",decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__Eubacteriales Family XIII. Incertae Sedis bacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",1783272|201174|84998|84999|1643824|1380;1783272|1239|186801|3082720|543314|2137877;1783272|201174|84998|84999|84107;1783272|1239|186801|3085636|1185407;1783272|1239|909932|1843489|31977|39948;3384194|508458|649775|649776|3029087|1434006;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3082720|543314|86331;3379134|976|200643|171549|171552|838;3379134|203691|203692|136|2845253|157,Complete,Peace Sandy
bsdb:30231060/3/1,30231060,"cross-sectional observational, not case-control",30231060,10.1371/journal.pone.0202278,NA,"Beyer K., Zaura E., Brandt B.W., Buijs M.J., Brun J.G., Crielaard W. , Bolstad A.I.",Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health,PloS one,2018,NA,Experiment 3,Norway,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,Never Smokers,Former Smokers,Former Smokers,29,35,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,S4A,20 January 2024,Peace Sandy,"Peace Sandy,WikiWorks","S4A Table. Significantly discriminatory OTUs between the microbiome sample clusters (Smoking status). From the 552 OTUs, 37 discriminated significantly between smoking status (LDA >2, p<0.05, LEfSe). Never smokers (N=29)=green bars; former smokers (N=35)=blue bars; current smokers (N=14)=red bars.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",1783272|201174|1760|2037|2049|1654;3379134|1224|1236|135625|712|416916;3379134|976|117743|200644|2762318|59735;3379134|976|117743|200644|49546|1016;3379134|1224|1236|135615|868|2717;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135625|712|724;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|206351|481|482,Complete,Peace Sandy
bsdb:30231060/3/2,30231060,"cross-sectional observational, not case-control",30231060,10.1371/journal.pone.0202278,NA,"Beyer K., Zaura E., Brandt B.W., Buijs M.J., Brun J.G., Crielaard W. , Bolstad A.I.",Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health,PloS one,2018,NA,Experiment 3,Norway,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,Never Smokers,Former Smokers,Former Smokers,29,35,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,S4A Table,20 January 2024,Peace Sandy,"Peace Sandy,WikiWorks","S4A Table. Significantly discriminatory OTUs between the microbiome sample clusters (Smoking status). From the 552 OTUs, 37 discriminated significantly between smoking status (LDA >2, p<0.05, LEfSe). Never smokers (N=29)=green bars; former smokers (N=35)=blue bars; current smokers (N=14)=red bars.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",1783272|201174|1760|2037|2049|76833;3379134|1224|1236|135615|868|2717;3384189|32066|203490|203491|1129771|32067;3379134|1224|28216|206351|481|482,Complete,Peace Sandy
bsdb:30231060/4/1,30231060,"cross-sectional observational, not case-control",30231060,10.1371/journal.pone.0202278,NA,"Beyer K., Zaura E., Brandt B.W., Buijs M.J., Brun J.G., Crielaard W. , Bolstad A.I.",Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health,PloS one,2018,NA,Experiment 4,Norway,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,Never Smokers,Current Smokers,Current Smokers,29,14,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,S4A Table,20 January 2024,Peace Sandy,"Peace Sandy,WikiWorks","S4A Table. Significantly discriminatory OTUs between the microbiome sample clusters (Smoking status). From the 552 OTUs, 37 discriminated significantly between smoking status (LDA >2, p<0.05, LEfSe). Never smokers (N=29)=green bars; former smokers (N=35)=blue bars; current smokers (N=14)=red bars.",increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3384189|32066|203490|203491|203492|848;3384194|508458|649775|649776|649777;3384194|508458|649775|649776|3029087|1434006;3379134|976|200643|171549|2005523|346096;1783272|201174|1760|2037|2049|1654;3379134|203691|203692|136|2845253|157;3379134|976|200643|171549|2005525|195950;1783272|1239|909932|909929|1843491|970;1783272|544448|31969|2085|2092|2093;1783272|1239|186801|3085636|1185407;1783272|1239|186801|3082720|543314|86331;3379134|976|200643|171549|171552|838,Complete,Peace Sandy
bsdb:30231060/4/2,30231060,"cross-sectional observational, not case-control",30231060,10.1371/journal.pone.0202278,NA,"Beyer K., Zaura E., Brandt B.W., Buijs M.J., Brun J.G., Crielaard W. , Bolstad A.I.",Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health,PloS one,2018,NA,Experiment 4,Norway,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,Never Smokers,Current Smokers,Current Smokers,29,14,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,S4A Table,20 January 2024,Peace Sandy,"Peace Sandy,WikiWorks","S4A Table. Significantly discriminatory OTUs between the microbiome sample clusters (Smoking status). From the 552 OTUs, 37 discriminated significantly between smoking status (LDA >2, p<0.05, LEfSe). Never smokers (N=29)=green bars; former smokers (N=35)=blue bars; current smokers (N=14)=red bars.",decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium",3384189|32066|203490|203491|1129771|32067;1783272|201174|1760|2037|2049|76833;3379134|1224|28216|206351|481|482;3379134|1224|1236|135615|868|2717,Complete,Peace Sandy
bsdb:30231060/5/1,30231060,"cross-sectional observational, not case-control",30231060,10.1371/journal.pone.0202278,NA,"Beyer K., Zaura E., Brandt B.W., Buijs M.J., Brun J.G., Crielaard W. , Bolstad A.I.",Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health,PloS one,2018,NA,Experiment 5,Norway,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,Former Smokers,Current Smokers,Current Smokers,35,14,3 Months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,S4A Table,20 January 2024,Peace Sandy,"Peace Sandy,WikiWorks","S4A Table. Significantly discriminatory OTUs between the microbiome sample clusters (Smoking status). From the 552 OTUs, 37 discriminated significantly between smoking status (LDA >2, p<0.05, LEfSe). Never smokers (N=29)=green bars; former smokers (N=35)=blue bars; current smokers (N=14)=red bars.",increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3384189|32066|203490|203491|203492|848;3384194|508458|649775|649776|649777;3384194|508458|649775|649776|3029087|1434006;3379134|976|200643|171549|2005523|346096;1783272|201174|1760|2037|2049|1654;3379134|203691|203692|136|2845253|157;3379134|976|200643|171549|2005525|195950;1783272|1239|909932|909929|1843491|970;1783272|544448|31969|2085|2092|2093;1783272|1239|186801|3085636|1185407;1783272|1239|186801|3082720|543314|86331;3379134|976|200643|171549|171552|838,Complete,Peace Sandy
bsdb:30231060/5/2,30231060,"cross-sectional observational, not case-control",30231060,10.1371/journal.pone.0202278,NA,"Beyer K., Zaura E., Brandt B.W., Buijs M.J., Brun J.G., Crielaard W. , Bolstad A.I.",Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health,PloS one,2018,NA,Experiment 5,Norway,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,Former Smokers,Current Smokers,Current Smokers,35,14,3 Months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,S4A Table,20 January 2024,Peace Sandy,"Peace Sandy,WikiWorks","S4A Table. Significantly discriminatory OTUs between the microbiome sample clusters (Smoking status). From the 552 OTUs, 37 discriminated significantly between smoking status (LDA >2, p<0.05, LEfSe). Never smokers (N=29)=green bars; former smokers (N=35)=blue bars; current smokers (N=14)=red bars.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella",3379134|1224|28216|206351|481|482;1783272|201174|1760|85007|1653|1716;3379134|1224|1236|135625|712|724;3379134|976|117743|200644|49546|1016;3379134|1224|1236|135625|712|416916;3379134|1224|28216|80840|119060|47670;3379134|1224|1236|135615|868|2717;1783272|1239|91061|1385|539738|1378;1783272|201174|1760|2037|2049|1654;3379134|976|117743|200644|2762318|59735,Complete,Peace Sandy
bsdb:30237489/1/1,30237489,case-control,30237489,10.1038/s41424-018-0048-x,NA,"Dong T., Chen T., White R.A., Wang X., Hu W., Liang Y., Zhang Y., Lu C., Chen M., Aase H. , Xia Y.",Meconium microbiome associates with the development of neonatal jaundice,Clinical and translational gastroenterology,2018,NA,Experiment 1,China,Homo sapiens,Meconium,UBERON:0007109,Neonatal jaundice,EFO:1000739,control,cesarean infants with jaundice,cesarean infants with jaundice,160,141,Currently on antibiotics,16S,3,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,"alcohol drinking,birth weight,gestational age,gestational diabetes,maternal age,preterm premature rupture of the membranes,sex,smoking behavior",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,LDA Score (log10) between control and case groups in cesarean infants with jaundice,increased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,3379134|1224|28216|80840|119060|106589,Complete,Shaimaa Elsafoury
bsdb:30237489/1/2,30237489,case-control,30237489,10.1038/s41424-018-0048-x,NA,"Dong T., Chen T., White R.A., Wang X., Hu W., Liang Y., Zhang Y., Lu C., Chen M., Aase H. , Xia Y.",Meconium microbiome associates with the development of neonatal jaundice,Clinical and translational gastroenterology,2018,NA,Experiment 1,China,Homo sapiens,Meconium,UBERON:0007109,Neonatal jaundice,EFO:1000739,control,cesarean infants with jaundice,cesarean infants with jaundice,160,141,Currently on antibiotics,16S,3,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,"alcohol drinking,birth weight,gestational age,gestational diabetes,maternal age,preterm premature rupture of the membranes,sex,smoking behavior",NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,LDA Score (log10) between control and case groups in cesarean infants with jaundice,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum|s__Bifidobacterium pseudolongum subsp. globosum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales",1783272|1239|186801|186802|31979;3379134|1224|1236|135625|712;1783272|201174|1760|85004|31953|1678|1694|1690;3379134|1224|1236|135625,Complete,Shaimaa Elsafoury
bsdb:30237489/2/1,30237489,case-control,30237489,10.1038/s41424-018-0048-x,NA,"Dong T., Chen T., White R.A., Wang X., Hu W., Liang Y., Zhang Y., Lu C., Chen M., Aase H. , Xia Y.",Meconium microbiome associates with the development of neonatal jaundice,Clinical and translational gastroenterology,2018,NA,Experiment 2,China,Homo sapiens,Meconium,UBERON:0007109,Neonatal jaundice,EFO:1000739,control,infants with jaundice,infants with jaundice,160,141,Currently on antibiotics,16S,3,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,"alcohol drinking,birth weight,feeding practices,gestational age,gestational diabetes,maternal age,mode of birth,preterm premature rupture of the membranes,sex,smoking behavior",NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Figure 2,10 January 2021,Rimsha Azhar,WikiWorks,LDA Score (log10) between control and case groups in all infants,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,1783272|1239|186801|186802|31979|1485|1502,Complete,Shaimaa Elsafoury
bsdb:30237489/2/2,30237489,case-control,30237489,10.1038/s41424-018-0048-x,NA,"Dong T., Chen T., White R.A., Wang X., Hu W., Liang Y., Zhang Y., Lu C., Chen M., Aase H. , Xia Y.",Meconium microbiome associates with the development of neonatal jaundice,Clinical and translational gastroenterology,2018,NA,Experiment 2,China,Homo sapiens,Meconium,UBERON:0007109,Neonatal jaundice,EFO:1000739,control,infants with jaundice,infants with jaundice,160,141,Currently on antibiotics,16S,3,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,"alcohol drinking,birth weight,feeding practices,gestational age,gestational diabetes,maternal age,mode of birth,preterm premature rupture of the membranes,sex,smoking behavior",NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Figure 2,10 January 2021,Rimsha Azhar,WikiWorks,LDA Score (log10) between control and case groups in all infants,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300|1301,Complete,Shaimaa Elsafoury
bsdb:30239655/1/1,30239655,"cross-sectional observational, not case-control",30239655,10.1093/ecco-jcc/jjy136,NA,"Kiernan M.G., Coffey J.C., McDermott K., Cotter P.D., Cabrera-Rubio R., Kiely P.A. , Dunne C.P.",The Human Mesenteric Lymph Node Microbiome Differentiates Between Crohn's Disease and Ulcerative Colitis,Journal of Crohn's & colitis,2019,NA,Experiment 1,Ireland,Homo sapiens,Mesenteric lymph node,UBERON:0002509,Inflammatory bowel disease,EFO:0003767,Ulcerative colitis,Crohn's disease,histopathologivally diagnosed ulcerative colitis and crohn's disease,8,5,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,increased,NA,NA,increased,Signature 1,Figure 3B,10 January 2021,Fatima Zohra,WikiWorks,Abundance of phyla in MLN of crohn's disease (CD) and ulcerative colitis (UC) patients,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,Rimsha Azhar
bsdb:30239655/2/1,30239655,"cross-sectional observational, not case-control",30239655,10.1093/ecco-jcc/jjy136,NA,"Kiernan M.G., Coffey J.C., McDermott K., Cotter P.D., Cabrera-Rubio R., Kiely P.A. , Dunne C.P.",The Human Mesenteric Lymph Node Microbiome Differentiates Between Crohn's Disease and Ulcerative Colitis,Journal of Crohn's & colitis,2019,NA,Experiment 2,Ireland,Homo sapiens,Mesenteric lymph node,UBERON:0002509,Inflammatory bowel disease,EFO:0003767,Ulcerative colitis,Crohn's disease,histopathologivally diagnosed ulcerative colitis and crohn's disease,8,5,NA,16S,34,Illumina,raw counts,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,increased,NA,NA,increased,Signature 1,Figure 3B,10 January 2021,Fatima Zohra,WikiWorks,Abundance of phyla in MLN of crohn's disease (CD) and ulcerative colitis (UC) patients,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Rimsha Azhar
bsdb:30249275/1/1,30249275,"cross-sectional observational, not case-control",30249275,10.1186/s40168-018-0557-6.,https://pubmed.ncbi.nlm.nih.gov/30249275/,"He Y., Wu W., Wu S., Zheng H.M., Li P., Sheng H.F., Chen M.X., Chen Z.H., Ji G.Y., Zheng Z.D., Mujagond P., Chen X.J., Rong Z.H., Chen P., Lyu L.Y., Wang X., Xu J.B., Wu C.B., Yu N., Xu Y.J., Yin J., Raes J., Ma W.J. , Zhou H.W.","Linking gut microbiota, metabolic syndrome and economic status based on a population-level analysis",Microbiome,2018,"16S rRNA gene sequencing, Economic status, Epidemiology, Faecal microbiome, Guangdong Gut Microbiome Project, Metabolic syndrome, Population level survey",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,NA,underdeveloped cities vs developed cities,"7009 Individuals' fecal samples from underdeveloped cities with GDP/capita of 22.1K to 25.3K CNY, and those from developed cities with GDP/capita of 149.5K to 136.1K CNY. (continuous variables)",NA,7009,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,geographic area,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4a,23 June 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks","Associations between OTUs and host economic status. a Stacked plot showing the number of OTUs that are positively associated with income or spending (continuous variables).

Colors correspond to taxonomies in the legend.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|976|200643|171549|815|816;3379134|1224|28216;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|1263;1783272|1239|909932|1843489|31977,Complete,NA
bsdb:30249275/1/2,30249275,"cross-sectional observational, not case-control",30249275,10.1186/s40168-018-0557-6.,https://pubmed.ncbi.nlm.nih.gov/30249275/,"He Y., Wu W., Wu S., Zheng H.M., Li P., Sheng H.F., Chen M.X., Chen Z.H., Ji G.Y., Zheng Z.D., Mujagond P., Chen X.J., Rong Z.H., Chen P., Lyu L.Y., Wang X., Xu J.B., Wu C.B., Yu N., Xu Y.J., Yin J., Raes J., Ma W.J. , Zhou H.W.","Linking gut microbiota, metabolic syndrome and economic status based on a population-level analysis",Microbiome,2018,"16S rRNA gene sequencing, Economic status, Epidemiology, Faecal microbiome, Guangdong Gut Microbiome Project, Metabolic syndrome, Population level survey",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,NA,underdeveloped cities vs developed cities,"7009 Individuals' fecal samples from underdeveloped cities with GDP/capita of 22.1K to 25.3K CNY, and those from developed cities with GDP/capita of 149.5K to 136.1K CNY. (continuous variables)",NA,7009,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,geographic area,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4a,23 June 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks",Associations between OTUs and host economic status. A Stacked plot showing the number of OTUs that are negatively associated with income or spending (continuous variables). Colors correspond to taxonomies in the legend.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239|186801|186802|31979;3379134|1224|1236;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|1263,Complete,NA
bsdb:30257444/1/1,30257444,"cross-sectional observational, not case-control",30257444,10.3390/microorganisms6040098,NA,"Kashtanova D.A., Tkacheva O.N., Doudinskaya E.N., Strazhesko I.D., Kotovskaya Y.V., Popenko A.S., Tyakht A.V. , Alexeev D.G.",Gut Microbiota in Patients with Different Metabolic Statuses: Moscow Study,Microorganisms,2018,"cardiovascular risk factors, diet, glucose metabolism, gut microbiota, metabolic status",Experiment 1,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,low BMI,High BMI,NA,69,23,3 months,16S,34,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiota in patients with obesity,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|1224|1236|91347|1903411|613;3379134|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
bsdb:30257444/2/1,30257444,"cross-sectional observational, not case-control",30257444,10.3390/microorganisms6040098,NA,"Kashtanova D.A., Tkacheva O.N., Doudinskaya E.N., Strazhesko I.D., Kotovskaya Y.V., Popenko A.S., Tyakht A.V. , Alexeev D.G.",Gut Microbiota in Patients with Different Metabolic Statuses: Moscow Study,Microorganisms,2018,"cardiovascular risk factors, diet, glucose metabolism, gut microbiota, metabolic status",Experiment 2,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,non-abdominal obesity,Abdominal obesity,NA,39,53,3 months,16S,34,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiota in patients with obesity,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|1224|1236|91347|1903411|613;3379134|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
bsdb:30257444/2/2,30257444,"cross-sectional observational, not case-control",30257444,10.3390/microorganisms6040098,NA,"Kashtanova D.A., Tkacheva O.N., Doudinskaya E.N., Strazhesko I.D., Kotovskaya Y.V., Popenko A.S., Tyakht A.V. , Alexeev D.G.",Gut Microbiota in Patients with Different Metabolic Statuses: Moscow Study,Microorganisms,2018,"cardiovascular risk factors, diet, glucose metabolism, gut microbiota, metabolic status",Experiment 2,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,non-abdominal obesity,Abdominal obesity,NA,39,53,3 months,16S,34,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 2,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiota in patients with obesity,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,1783272|1239|186801|186802|216572|119852,Complete,Shaimaa Elsafoury
bsdb:30261302/1/1,30261302,"cross-sectional observational, not case-control",30261302,10.1016/j.bbi.2018.09.026,NA,"Coello K., Hansen T.H., Sørensen N., Munkholm K., Kessing L.V., Pedersen O. , Vinberg M.",Gut microbiota composition in patients with newly diagnosed bipolar disorder and their unaffected first-degree relatives,"Brain, behavior, and immunity",2019,"Bipolar disorder, Gut microbiota, Microbiota, Newly diagnosed, Unaffected relatives",Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,healthy controls,bipolar disorder patients,NA,77,113,NA,16S,34,Illumina,relative abundances,Fisher's Exact Test,0.05,TRUE,NA,NA,"age,physical activity,sex,smoking behavior,waist circumference",NA,unchanged,NA,NA,NA,unchanged,Signature 1,"table 2, figure3",10 January 2021,Fatima Zohra,"WikiWorks,Folakunmi",gut microbiota composition in patients with newly diagnosed bipolar and healthy controls,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,1783272|1239|186801|186802|216572|946234,Complete,Folakunmi
bsdb:30261302/2/1,30261302,"cross-sectional observational, not case-control",30261302,10.1016/j.bbi.2018.09.026,NA,"Coello K., Hansen T.H., Sørensen N., Munkholm K., Kessing L.V., Pedersen O. , Vinberg M.",Gut microbiota composition in patients with newly diagnosed bipolar disorder and their unaffected first-degree relatives,"Brain, behavior, and immunity",2019,"Bipolar disorder, Gut microbiota, Microbiota, Newly diagnosed, Unaffected relatives",Experiment 2,Denmark,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,unaffected relatives,bipolar disorder patients,Healthy first degree relatives of bipolar disorder patients,39,113,NA,16S,34,Illumina,relative abundances,Fisher's Exact Test,0.05,TRUE,NA,NA,"age,physical activity,sex,smoking behavior,waist circumference",NA,unchanged,NA,NA,NA,unchanged,Signature 1,"table 2, figure3",21 February 2024,Folakunmi,"Folakunmi,WikiWorks",Gut microbiota composition in patients with newly diagnosed bipolar and their unaffected first degree relatives,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,1783272|1239|186801|186802|216572|946234,Complete,Folakunmi
bsdb:30263008/1/1,30263008,case-control,30263008,10.7150/ijbs.24151,NA,"Ishaq H.M., Mohammad I.S., Shahzad M., Ma C., Raza M.A., Wu X., Guo H., Shi P. , Xu J.",Molecular Alteration Analysis of Human Gut Microbial Composition in Graves' disease Patients,International journal of biological sciences,2018,"DGGE, GD, Gut microbiota, High-throughput sequencing, Hyperthyroidism, Ophthalmopathy",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,healthy controls,graves disease,graves' disease patients,11,27,2 months,16S,34,Illumina,raw counts,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,"Fig 5, Fig6, Table 6,7 and text",10 January 2021,Rimsha Azhar,WikiWorks,Gut microbial composition differences between Graves' disease and control at different levels,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella|s__Morganella morganii",3379134|976|200643|171549|171552;3379134|1224|1236|135625|712;3379134|976|200643|171549|171552|838;3379134|1224|1236|135625|712|724;3379134|29547|3031852|213849|72294|194|204;1783272|1239|909932|1843489|31977|29465|1926307;3379134|1224|1236|91347|1903414|581|582,Complete,Folakunmi
bsdb:30263008/1/2,30263008,case-control,30263008,10.7150/ijbs.24151,NA,"Ishaq H.M., Mohammad I.S., Shahzad M., Ma C., Raza M.A., Wu X., Guo H., Shi P. , Xu J.",Molecular Alteration Analysis of Human Gut Microbial Composition in Graves' disease Patients,International journal of biological sciences,2018,"DGGE, GD, Gut microbiota, High-throughput sequencing, Hyperthyroidism, Ophthalmopathy",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,healthy controls,graves disease,graves' disease patients,11,27,2 months,16S,34,Illumina,raw counts,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,"Fig 5, Fig6, Table 6,7 and text",10 January 2021,Rimsha Azhar,"WikiWorks,Folakunmi",Gut microbial composition differences between Graves' disease and control at different levels,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550|239759|1872444;3379134|1224|1236|91347|543;1783272|1239|186801|186802|216572|216851;1783272|1239|91061|186826|33958|1578|1596;3379134|976|200643|171549|171550;1783272|1239|909932|1843489|31977;1783272|1239|909932|1843489|31977|39948,Complete,Folakunmi
bsdb:30267022/1/1,30267022,case-control,30267022,10.1038/s41598-018-32730-6,NA,"Gao X., Jia R., Xie L., Kuang L., Feng L. , Wan C.",A study of the correlation between obesity and intestinal flora in school-age children,Scientific reports,2018,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,controls,obese children,School children meeting WHO diagnostic criteria for obesity,38,39,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,decreased,increased,NA,decreased,Signature 1,"Table2, Table 3",10 January 2021,Mst Afroza Parvin,"Claregrieve1,WikiWorks",Comparisons of relative abundance of gut bacteria between the obesity and control groups at the level of Phylum & Species,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister histaminiformans,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter|s__Oxalobacter formigenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum",1783272|1239|909932|1843489|31977|39948|209880;3379134|976;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|909932|909929|1843491|158846|437897;3379134|1224|28216|80840|75682|846|847;3379134|976|200643|171549|2005525|375288|823;3379134|1224|28216|80840|995019|577310|487175;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|171552|2974265|363265;1783272|1239|186801|3085636|186803|2941495|1512,Complete,Claregrieve1
bsdb:30267022/1/2,30267022,case-control,30267022,10.1038/s41598-018-32730-6,NA,"Gao X., Jia R., Xie L., Kuang L., Feng L. , Wan C.",A study of the correlation between obesity and intestinal flora in school-age children,Scientific reports,2018,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,controls,obese children,School children meeting WHO diagnostic criteria for obesity,38,39,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,decreased,increased,NA,decreased,Signature 2,"Table2, Table 3, text",10 January 2021,Mst Afroza Parvin,"Lwaldron,Claregrieve1,WikiWorks",Comparisons of relative abundance of gut bacteria between the obesity and control groups at the level of Phylum & Species,decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes butyraticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia luti,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,p__Candidatus Saccharimonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus cecorum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Lactonifactor|s__Lactonifactor longoviformis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalispora|s__Faecalispora sporosphaeroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] sulci",1783272|201174;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171552|1283313|671218;1783272|1239|186801|3085636|186803|207244|645466;1783272|1239|186801|3085636|186803|207244|105841;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|818;1783272|1239|186801|3085636|186803|572511|89014;1783272|1239|186801|3085636|186803|572511|418240;95818;1783272|1239|91061|186826|81852|1350|44008;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|186801|186802|216572|216851|853;1783272|1239;1783272|201174|84998|1643822|1643826|644652|471189;1783272|1239|186801|186802|31979|420345|341220;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|91061|186826|1300|1301|76860;1783272|1239|91061|186826|1300|1301|1304;3379134|74201;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|186802|216572|3115229|1549;1783272|1239|186801|3082720|543314|143393,Complete,Claregrieve1
bsdb:30268819/1/1,30268819,"cross-sectional observational, not case-control",30268819,10.1016/j.schres.2018.09.014,NA,"Nguyen T.T., Kosciolek T., Maldonado Y., Daly R.E., Martin A.S., McDonald D., Knight R. , Jeste D.V.",Differences in gut microbiome composition between persons with chronic schizophrenia and healthy comparison subjects,Schizophrenia research,2019,"Bacteria, Gut-brain axis, Microbes, Phylum, Probiotics, Psychosis",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,non-psychiatric controls,schizophrenia,outpatients with schizophrenia or schizoaffective disorder,25,25,NA,16S,4,Illumina,NA,Kruskall-Wallis,0.01,TRUE,NA,demographics,"age,antimicrobial agent,body mass index,race,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2+ Supplemental Table S2,10 January 2021,Fatima Zohra,WikiWorks,Differentially abundant genera in schizophrenia and non-psychiatric controls,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",1783272|1239|1737404|1737405|1570339|165779;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803|572511,Complete,Atrayees
bsdb:30268819/1/2,30268819,"cross-sectional observational, not case-control",30268819,10.1016/j.schres.2018.09.014,NA,"Nguyen T.T., Kosciolek T., Maldonado Y., Daly R.E., Martin A.S., McDonald D., Knight R. , Jeste D.V.",Differences in gut microbiome composition between persons with chronic schizophrenia and healthy comparison subjects,Schizophrenia research,2019,"Bacteria, Gut-brain axis, Microbes, Phylum, Probiotics, Psychosis",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,non-psychiatric controls,schizophrenia,outpatients with schizophrenia or schizoaffective disorder,25,25,NA,16S,4,Illumina,NA,Kruskall-Wallis,0.01,TRUE,NA,demographics,"age,antimicrobial agent,body mass index,race,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2+ Supplemental Table S2,10 January 2021,Fatima Zohra,WikiWorks,Differentially abundant genera in schizophrenia and non-psychiatric controls,decreased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae",3379134|1224;3379134|1224|1236|135625|712|724;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|186802|31979|1485;3379134|1224|1236|135625|712|724|729,Complete,Atrayees
bsdb:30279332/1/1,30279332,randomized controlled trial,30279332,10.3390/nu10101402,NA,"Hess J., Wang Q., Gould T. , Slavin J.",Impact of Agaricus bisporus Mushroom Consumption on Gut Health Markers in Healthy Adults,Nutrients,2018,"fiber, gut health, laxation, microbiota, mushrooms, prebiotic",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,mushroom,Meat,NA,16,16,3 months,16S,123,Illumina,raw counts,Linear Regression,0.004,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 9 and text,10 January 2021,Lora Kasselman,WikiWorks,Percent abundance across 5 days of fecal collection for identified abundant bacterial taxa (mushroom diet vs meat diet),increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea",1783272|1239;1783272|1239|186801|3085636|186803|189330,Complete,Shaimaa Elsafoury
bsdb:30279332/1/2,30279332,randomized controlled trial,30279332,10.3390/nu10101402,NA,"Hess J., Wang Q., Gould T. , Slavin J.",Impact of Agaricus bisporus Mushroom Consumption on Gut Health Markers in Healthy Adults,Nutrients,2018,"fiber, gut health, laxation, microbiota, mushrooms, prebiotic",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,mushroom,Meat,NA,16,16,3 months,16S,123,Illumina,raw counts,Linear Regression,0.004,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 9 and text,10 January 2021,Lora Kasselman,WikiWorks,Percent abundance across 5 days of fecal collection for identified abundant bacterial taxa (mushroom diet vs meat diet),decreased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|976;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|207244;3379134|1224|28216|80840|995019|40544,Complete,Shaimaa Elsafoury
bsdb:30280027/1/1,30280027,case-control,30280027,10.7717/peerj.5649,NA,"Zhou Z., Ling G., Ding N., Xun Z., Zhu C., Hua H. , Chen X.",Molecular analysis of oral microflora in patients with primary Sjögren's syndrome by using high-throughput sequencing,PeerJ,2018,"Core microbiome, Dental caries, High-throughput sequencing, Oral microflora, Primary Sjögren’s syndrome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Sjogren syndrome,EFO:0000699,Controls,PSS,Patients with Sjogren syndrome,23,22,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"age,sex",NA,decreased,decreased,unchanged,NA,decreased,NA,Signature 1,Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,Comparison of microbiota using LDA score by LEfSe analysis between primary sjogres patients(PSS) and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota",1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|909929;1783272|1239|909932|1843489|31977;3379134|1224|1236;3379134|1224,Complete,Shaimaa Elsafoury
bsdb:30280027/1/2,30280027,case-control,30280027,10.7717/peerj.5649,NA,"Zhou Z., Ling G., Ding N., Xun Z., Zhu C., Hua H. , Chen X.",Molecular analysis of oral microflora in patients with primary Sjögren's syndrome by using high-throughput sequencing,PeerJ,2018,"Core microbiome, Dental caries, High-throughput sequencing, Oral microflora, Primary Sjögren’s syndrome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Sjogren syndrome,EFO:0000699,Controls,PSS,Patients with Sjogren syndrome,23,22,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"age,sex",NA,decreased,decreased,unchanged,NA,decreased,NA,Signature 2,Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,Comparison of microbiota using LDA score by LEfSe analysis between primary sjogres patients(PSS) and healthy controls,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Actinomycetota",1783272|201174|1760|2037|2049|1654;3379134|1224|1236|135625|712|724;3379134|1224|28216|206351|481|482;1783272|201174|1760|85006|1268|32207;3379134|976|200643|171549|171551|836;1783272|1239|186801|3082720|186804|1257;3379134|1224|28216;1783272|201174|1760|2037|2049;3379134|1224|1236|135625|712;3379134|1224|28216|206351|481;3379134|1224|28216|206351;1783272|201174|1760|85006|1268;3379134|976|200643|171549|171551;1783272|201174|1760|2037;3384189|32066|203490;3384189|32066;3384189|32066|203490|203491;1783272|1239|186801;1783272|1239|186801|186802;3379134|1224|1236|135625;1783272|201174,Complete,Shaimaa Elsafoury
bsdb:30291996/1/1,30291996,"cross-sectional observational, not case-control",30291996,10.1016/j.eplepsyres.2018.09.013,NA,"Peng A., Qiu X., Lai W., Li W., Zhang L., Zhu X., He S., Duan J. , Chen L.",Altered composition of the gut microbiome in patients with drug-resistant epilepsy,Epilepsy research,2018,"Drug-resistant epilepsy, Epilepsy, Microbiome, Microbiota, Ruminococcus",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Epilepsy,EFO:0000474,Drug sensitive epilepsy,Drug resistant epilepsy,Drug resistant epilepsy patients were defined according to the 2015 International League Against Epilepsy (ILAE),49,42,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,increased,NA,NA,Signature 1,Figure 2,16 December 2021,Fatima,"Fatima,WikiWorks",Lefse analysis showing microbiome differences in patients with drug sensitive epilepsy and  drug sensitive epilepsy,decreased,",k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella",;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976;3379134|976|200643;3379134|976|200643|171549|2005519|397864,Complete,Lwaldron
bsdb:30291996/1/2,30291996,"cross-sectional observational, not case-control",30291996,10.1016/j.eplepsyres.2018.09.013,NA,"Peng A., Qiu X., Lai W., Li W., Zhang L., Zhu X., He S., Duan J. , Chen L.",Altered composition of the gut microbiome in patients with drug-resistant epilepsy,Epilepsy research,2018,"Drug-resistant epilepsy, Epilepsy, Microbiome, Microbiota, Ruminococcus",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Epilepsy,EFO:0000474,Drug sensitive epilepsy,Drug resistant epilepsy,Drug resistant epilepsy patients were defined according to the 2015 International League Against Epilepsy (ILAE),49,42,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,increased,NA,NA,Signature 2,Figure 2,16 December 2021,Fatima,"Fatima,WikiWorks",Lefse analysis showing microbiome differences among drug resistance and drug sensitive epilepsy,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,,k__Methanobacteriati|p__Methanobacteriota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,p__Candidatus Saccharimonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales",1783272|1239|526524;3379134|1224|1236|2887326|468;1783272|1239;1783272|1239|186801|3085636|186803;1783272|1239|909932;1783272|1239|909932|909929;1783272|1239|186801|3085636|186803|841;1783272|1239|909932|1843488|909930|33024;1783272|1239|909932|1843488|909930;3366610|28890|183925;3366610|28890|183925|2158|2159;3366610|28890|183925|2158|2159|2172;3366610|28890|183925|2158;3384189|32066;3384189|32066|203490;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|33042;3379134|1224|28216|206351;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481;;3366610|28890;3379134|74201|203494|48461;3379134|74201;3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|203557;3379134|74201|203494;1783272|1239|186801|186802|204475;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|171552|577309;1783272|1239|526524|526525|2810280|100883;3379134|1224|28216|80840|80864|80865;95818;1783272|1239|186801|3085636|186803|189330;1783272|1239|526524|526525|128827|61170;1783272|1239|526524|526525|128827;1783272|201174|84998|84999|1643824|1380;1783272|1239|526524|526525,Complete,Fatima
bsdb:30291996/2/NA,30291996,"cross-sectional observational, not case-control",30291996,10.1016/j.eplepsyres.2018.09.013,NA,"Peng A., Qiu X., Lai W., Li W., Zhang L., Zhu X., He S., Duan J. , Chen L.",Altered composition of the gut microbiome in patients with drug-resistant epilepsy,Epilepsy research,2018,"Drug-resistant epilepsy, Epilepsy, Microbiome, Microbiota, Ruminococcus",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Epilepsy,EFO:0000474,Healthy controls,Drug resistant epilepsy,Drug sensitive epilepsy patients were defined according to the 2015 International League Against Epilepsy (ILAE),65,49,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:30292647/1/1,30292647,case-control,30292647,10.1016/j.resmic.2018.09.002,NA,"Zeng B., Lai Z., Sun L., Zhang Z., Yang J., Li Z., Lin J. , Zhang Z.",Structural and functional profiles of the gut microbial community in polycystic ovary syndrome with insulin resistance (IR-PCOS): a pilot study,Research in microbiology,2019,"Gut microbial community, Insulin resistance, Polycystic ovary syndrome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,HC - Healthy Controls,NIR-PCOS - NIR(Non-Insulin Resistance),NIR-PCOS - PCOS without insulin resistance,8,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy","Identification of the bacterial taxa with statistically significant difference between groups using LEfSe software. LEfSe was performed in pairwise manner for HC vs. NIR-PCOS (A), HC vs. IR-PCOS (B) and NIR-PCOS vs. IR-PCOS (C). Cladograms show the taxonomic hierarchical structure and the circles from the inside to the outside indicate kingdom, phyla, class, order, family, genus. Taxa enriched in HC, NIR-PCOS and IR-PCOS group are colored by green, blue and red respectively (LDA > 2.0 and P < 0.05), relative abundance of these biomarkers are showed in the histogram (mean and standard deviation values are plotted) under the corresponding cladogram.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803,Complete,Peace Sandy
bsdb:30292647/1/2,30292647,case-control,30292647,10.1016/j.resmic.2018.09.002,NA,"Zeng B., Lai Z., Sun L., Zhang Z., Yang J., Li Z., Lin J. , Zhang Z.",Structural and functional profiles of the gut microbial community in polycystic ovary syndrome with insulin resistance (IR-PCOS): a pilot study,Research in microbiology,2019,"Gut microbial community, Insulin resistance, Polycystic ovary syndrome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,HC - Healthy Controls,NIR-PCOS - NIR(Non-Insulin Resistance),NIR-PCOS - PCOS without insulin resistance,8,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 3,10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy","Identification of the bacterial taxa with statistically significant difference between groups using LEfSe software. LEfSe was performed in pairwise manner for HC vs. NIR-PCOS (A), HC vs. IR-PCOS (B) and NIR-PCOS vs. IR-PCOS (C). Cladograms show the taxonomic hierarchical structure and the circles from the inside to the outside indicate kingdom, phyla, class, order, family, genus. Taxa enriched in HC, NIR-PCOS and IR-PCOS group are colored by green, blue and red respectively (LDA > 2.0 and P < 0.05), relative abundance of these biomarkers are showed in the histogram (mean and standard deviation values are plotted) under the corresponding cladogram.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552,Complete,Peace Sandy
bsdb:30292647/2/1,30292647,case-control,30292647,10.1016/j.resmic.2018.09.002,NA,"Zeng B., Lai Z., Sun L., Zhang Z., Yang J., Li Z., Lin J. , Zhang Z.",Structural and functional profiles of the gut microbial community in polycystic ovary syndrome with insulin resistance (IR-PCOS): a pilot study,Research in microbiology,2019,"Gut microbial community, Insulin resistance, Polycystic ovary syndrome",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,HC - Healthy Controls,IR-PCOS IR-(Insulin Resistance),PCOS with Insulin resistance,8,9,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy","Identification of the bacterial taxa with statistically significant difference between groups using LEfSe software. LEfSe was performed in pairwise manner for HC vs. NIR-PCOS (A), HC vs. IR-PCOS (B) and NIR-PCOS vs. IR-PCOS (C). Cladograms show the taxonomic hierarchical structure and the circles from the inside to the outside indicate kingdom, phyla, class, order, family, genus. Taxa enriched in HC, NIR-PCOS and IR-PCOS group are colored by green, blue and red respectively (LDA > 2.0 and P < 0.05), relative abundance of these biomarkers are showed in the histogram (mean and standard deviation values are plotted) under the corresponding cladogram.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|28050,Complete,Peace Sandy
bsdb:30292647/2/2,30292647,case-control,30292647,10.1016/j.resmic.2018.09.002,NA,"Zeng B., Lai Z., Sun L., Zhang Z., Yang J., Li Z., Lin J. , Zhang Z.",Structural and functional profiles of the gut microbial community in polycystic ovary syndrome with insulin resistance (IR-PCOS): a pilot study,Research in microbiology,2019,"Gut microbial community, Insulin resistance, Polycystic ovary syndrome",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,HC - Healthy Controls,IR-PCOS IR-(Insulin Resistance),PCOS with Insulin resistance,8,9,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 3,10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy","Identification of the bacterial taxa with statistically significant difference between groups using LEfSe software. LEfSe was performed in pairwise manner for HC vs. NIR-PCOS (A), HC vs. IR-PCOS (B) and NIR-PCOS vs. IR-PCOS (C). Cladograms show the taxonomic hierarchical structure and the circles from the inside to the outside indicate kingdom, phyla, class, order, family, genus. Taxa enriched in HC, NIR-PCOS and IR-PCOS group are colored by green, blue and red respectively (LDA > 2.0 and P < 0.05), relative abundance of these biomarkers are showed in the histogram (mean and standard deviation values are plotted) under the corresponding cladogram.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552,Complete,Peace Sandy
bsdb:30292647/3/1,30292647,case-control,30292647,10.1016/j.resmic.2018.09.002,NA,"Zeng B., Lai Z., Sun L., Zhang Z., Yang J., Li Z., Lin J. , Zhang Z.",Structural and functional profiles of the gut microbial community in polycystic ovary syndrome with insulin resistance (IR-PCOS): a pilot study,Research in microbiology,2019,"Gut microbial community, Insulin resistance, Polycystic ovary syndrome",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,NIR-PCOS - NIR(Non-Insulin Resistance),IR-PCOS IR-(Insulin Resistance),PCOS with Insulin Resistance,8,9,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3,10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy","Identification of the bacterial taxa with statistically significant difference between groups using LEfSe software. LEfSe was performed in pairwise manner for HC vs. NIR-PCOS (A), HC vs. IR-PCOS (B) and NIR-PCOS vs. IR-PCOS (C). Cladograms show the taxonomic hierarchical structure and the circles from the inside to the outside indicate kingdom, phyla, class, order, family, genus. Taxa enriched in HC, NIR-PCOS and IR-PCOS group are colored by green, blue and red respectively (LDA > 2.0 and P < 0.05), relative abundance of these biomarkers are showed in the histogram (mean and standard deviation values are plotted) under the corresponding cladogram.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia",3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643,Complete,Peace Sandy
bsdb:30292647/3/2,30292647,case-control,30292647,10.1016/j.resmic.2018.09.002,NA,"Zeng B., Lai Z., Sun L., Zhang Z., Yang J., Li Z., Lin J. , Zhang Z.",Structural and functional profiles of the gut microbial community in polycystic ovary syndrome with insulin resistance (IR-PCOS): a pilot study,Research in microbiology,2019,"Gut microbial community, Insulin resistance, Polycystic ovary syndrome",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,NIR-PCOS - NIR(Non-Insulin Resistance),IR-PCOS IR-(Insulin Resistance),PCOS with Insulin Resistance,8,9,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 3,10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy","Identification of the bacterial taxa with statistically significant difference between groups using LEfSe software. LEfSe was performed in pairwise manner for HC vs. NIR-PCOS (A), HC vs. IR-PCOS (B) and NIR-PCOS vs. IR-PCOS (C). Cladograms show the taxonomic hierarchical structure and the circles from the inside to the outside indicate kingdom, phyla, class, order, family, genus. Taxa enriched in HC, NIR-PCOS and IR-PCOS group are colored by green, blue and red respectively (LDA > 2.0 and P < 0.05), relative abundance of these biomarkers are showed in the histogram (mean and standard deviation values are plotted) under the corresponding cladogram.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota",1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803;1783272|1239,Complete,Peace Sandy
bsdb:30300382/1/1,30300382,case-control,30300382,10.1371/journal.pone.0204674,NA,"Yue Q., Yin F.T., Zhang Q., Yuan C., Ye M.Y., Wang X.L., Li J.J. , Gan Y.H.",Carious status and supragingival plaque microbiota in hemodialysis patients,PloS one,2018,NA,Experiment 1,China,Homo sapiens,Gingiva,UBERON:0001828,Chronic kidney disease,EFO:0003884,healthy controls,Chronic kidney disease,chronic kidney disease patients undergoing hemodialysis,30,30,1 month,16S,34,Illumina,relative abundances,Metastats,0.05,FALSE,NA,"age,sex,smoking behavior",NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between CKD patients and healthy controls,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|201174|1760|2037|2049|1654;3379134|976|117743|200644|2762318|59735;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|33958|1578,Complete,Claregrieve1
bsdb:30300382/1/2,30300382,case-control,30300382,10.1371/journal.pone.0204674,NA,"Yue Q., Yin F.T., Zhang Q., Yuan C., Ye M.Y., Wang X.L., Li J.J. , Gan Y.H.",Carious status and supragingival plaque microbiota in hemodialysis patients,PloS one,2018,NA,Experiment 1,China,Homo sapiens,Gingiva,UBERON:0001828,Chronic kidney disease,EFO:0003884,healthy controls,Chronic kidney disease,chronic kidney disease patients undergoing hemodialysis,30,30,1 month,16S,34,Illumina,relative abundances,Metastats,0.05,FALSE,NA,"age,sex,smoking behavior",NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between CKD patients and healthy controls,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|171551|836,Complete,Claregrieve1
bsdb:30300382/2/1,30300382,case-control,30300382,10.1371/journal.pone.0204674,NA,"Yue Q., Yin F.T., Zhang Q., Yuan C., Ye M.Y., Wang X.L., Li J.J. , Gan Y.H.",Carious status and supragingival plaque microbiota in hemodialysis patients,PloS one,2018,NA,Experiment 2,China,Homo sapiens,Gingiva,UBERON:0001828,Chronic kidney disease,EFO:0003884,healthy controls,Chronic kidney disease,chronic kidney disease patients undergoing hemodialysis,30,30,1 month,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex,smoking behavior",NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 4,10 January 2021,Fatima Zohra,"Claregrieve1,Atrayees,WikiWorks",Differential microbial abundance between CKD patients and healthy controls,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter curvus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sobrinus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] infirmum",1783272|201174|1760|2037|2049|1654|1655;3379134|29547|3031852|213849|72294|194|200;3379134|976|117743|200644|49546|1016|44737;1783272|1239|91061|186826|33958|2767887|1624;1783272|1239|91061|186826|33958|2742598|1613;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|91061|186826|1300|1301|1309;1783272|1239|91061|186826|1300|1301|1310;1783272|1239|186801|3082720|543314|56774,Complete,Claregrieve1
bsdb:30300382/2/2,30300382,case-control,30300382,10.1371/journal.pone.0204674,NA,"Yue Q., Yin F.T., Zhang Q., Yuan C., Ye M.Y., Wang X.L., Li J.J. , Gan Y.H.",Carious status and supragingival plaque microbiota in hemodialysis patients,PloS one,2018,NA,Experiment 2,China,Homo sapiens,Gingiva,UBERON:0001828,Chronic kidney disease,EFO:0003884,healthy controls,Chronic kidney disease,chronic kidney disease patients undergoing hemodialysis,30,30,1 month,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex,smoking behavior",NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 4,15 July 2022,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between CKD patients and healthy controls,decreased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|s__Acholeplasmatales bacterium canine oral taxon 172,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga haemolytica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus haemolyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella|s__Johnsonella ignava,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. GHG17,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp. CM12,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella genomosp. P6,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral clone GU027,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Pseudoleptotrichia|s__Pseudoleptotrichia goodfellowii",1783272|544448|31969|186329|1151604;3379134|976|117743|200644|49546|1016|45243;3379134|1224|1236|135625|712|724|726;1783272|1239|186801|3085636|186803|43994|43995;3379134|1224|28216|206351|481|482|742463;1783272|1239|186801|3085636|186803|265975|936567;3379134|976|200643|171549|171552|838|239138;3379134|976|200643|171549|171552|838|28131;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552|2974257|425941;3379134|976|200643|171549|171552|838|242668;3384189|32066|203490|203491|1129771|2755140|157692,Complete,Claregrieve1
bsdb:30300382/4/1,30300382,case-control,30300382,10.1371/journal.pone.0204674,NA,"Yue Q., Yin F.T., Zhang Q., Yuan C., Ye M.Y., Wang X.L., Li J.J. , Gan Y.H.",Carious status and supragingival plaque microbiota in hemodialysis patients,PloS one,2018,NA,Experiment 4,China,Homo sapiens,Gingiva,UBERON:0001828,Chronic kidney disease,EFO:0003884,healthy controls,Chronic kidney disease,chronic kidney disease patients undergoing hemodialysis,30,30,1 month,16S,3456,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex,smoking behavior",NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 5,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential abundance of Streptococcus mutans in supragingival plaque measured by quantitative real-time PCR between kidney disease patients and healthy controls,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,1783272|1239|91061|186826|1300|1301|1309,Complete,Claregrieve1
bsdb:30301893/1/1,30301893,meta-analysis,30301893,10.1038/s41467-018-06473-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6177445/#Sec1title,"Ho N.T., Li F., Lee-Sarwar K.A., Tun H.M., Brown B.P., Pannaraj P.S., Bender J.M., Azad M.B., Thompson A.L., Weiss S.T., Azcarate-Peril M.A., Litonjua A.A., Kozyrskyj A.L., Jaspan H.B., Aldrovandi G.M. , Kuhn L.",Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations,Nature communications,2018,NA,Experiment 1,Bangladesh,Homo sapiens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,Exclusive Breast Feeding (EBF),Non_Exclusive Breast Feeding (Non-EBF),Infants who was feed breast milk with either formula or solid.,138,178,NA,16S,4,Illumina,relative abundances,Random Forest Analysis,0.05,TRUE,NA,NA,"age,sex",NA,increased,unchanged,NA,NA,unchanged,Signature 1,"Table 11, Table 2, Table 3",2 October 2024,Shulamite,"Shulamite,Peace Sandy,WikiWorks",Gut bacterial taxa with differential relative abundances from 6 months to 2 years of age between infants with duration of exclusive breastfeeding >2 months vs. ≤2 months from birth.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|81852|1350,Complete,Peace Sandy
bsdb:30301893/1/2,30301893,meta-analysis,30301893,10.1038/s41467-018-06473-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6177445/#Sec1title,"Ho N.T., Li F., Lee-Sarwar K.A., Tun H.M., Brown B.P., Pannaraj P.S., Bender J.M., Azad M.B., Thompson A.L., Weiss S.T., Azcarate-Peril M.A., Litonjua A.A., Kozyrskyj A.L., Jaspan H.B., Aldrovandi G.M. , Kuhn L.",Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations,Nature communications,2018,NA,Experiment 1,Bangladesh,Homo sapiens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,Exclusive Breast Feeding (EBF),Non_Exclusive Breast Feeding (Non-EBF),Infants who was feed breast milk with either formula or solid.,138,178,NA,16S,4,Illumina,relative abundances,Random Forest Analysis,0.05,TRUE,NA,NA,"age,sex",NA,increased,unchanged,NA,NA,unchanged,Signature 2,"Table 11, Table 2, Table 3",8 October 2024,Shulamite,"Shulamite,Rahila,Peace Sandy,WikiWorks",Gut bacterial taxa with differential relative abundances from 6 months to 2 years of age between infants with duration of exclusive breastfeeding >2 months vs. ≤2 months from birth.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|3085636|186803|572511;1783272|1239|526524|526525|2810280|135858;1783272|201174|84998|84999|84107|102106;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|31979;1783272|201174|84998|84999|84107;1783272|1239|186801|3085636|186803,Complete,Peace Sandy
bsdb:30301893/2/1,30301893,meta-analysis,30301893,10.1038/s41467-018-06473-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6177445/#Sec1title,"Ho N.T., Li F., Lee-Sarwar K.A., Tun H.M., Brown B.P., Pannaraj P.S., Bender J.M., Azad M.B., Thompson A.L., Weiss S.T., Azcarate-Peril M.A., Litonjua A.A., Kozyrskyj A.L., Jaspan H.B., Aldrovandi G.M. , Kuhn L.",Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations,Nature communications,2018,NA,Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,Increasing Exclusive Breast Feeding (EBF),Reduced exclusivity of beast feeding to none breastfeeding,Introducing other foods or liquids while still breastfeeding,86,48,NA,16S,4,Illumina,relative abundances,Random Forest Analysis,0.005,TRUE,NA,NA,age,NA,increased,increased,NA,NA,NA,Signature 1,"Table 3, Table 2",3 October 2024,Shulamite,"Shulamite,Rahila,Peace Sandy,WikiWorks","Meta-analysis of five studies that included a non-breastfeeding group for gut bacterial taxa with trend in relative abundance across exclusive breastfeeding, nonexclusive breastfeeding and non breastfeeding groups.",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.",3379134|74201|203494|48461|1647988|239934;1783272|1239;3379134|976|200643;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|186806|1730;3379134|74201;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979|1485;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|186802|186806|1730|142586,Complete,Peace Sandy
bsdb:30301893/2/2,30301893,meta-analysis,30301893,10.1038/s41467-018-06473-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6177445/#Sec1title,"Ho N.T., Li F., Lee-Sarwar K.A., Tun H.M., Brown B.P., Pannaraj P.S., Bender J.M., Azad M.B., Thompson A.L., Weiss S.T., Azcarate-Peril M.A., Litonjua A.A., Kozyrskyj A.L., Jaspan H.B., Aldrovandi G.M. , Kuhn L.",Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations,Nature communications,2018,NA,Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,Increasing Exclusive Breast Feeding (EBF),Reduced exclusivity of beast feeding to none breastfeeding,Introducing other foods or liquids while still breastfeeding,86,48,NA,16S,4,Illumina,relative abundances,Random Forest Analysis,0.005,TRUE,NA,NA,age,NA,increased,increased,NA,NA,NA,Signature 2,"Table 3, Table 2",3 October 2024,Shulamite,"Shulamite,Peace Sandy,WikiWorks","Meta-analysis of five studies that included a non-breastfeeding group for gut bacterial taxa with trend in relative abundance across exclusive breastfeeding, nonexclusive breastfeeding and non breastfeeding groups.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",3379134|1224|1236|135625|712|724;1783272|1239|91061|1385|90964|1279,Complete,Peace Sandy
bsdb:30301893/3/1,30301893,meta-analysis,30301893,10.1038/s41467-018-06473-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6177445/#Sec1title,"Ho N.T., Li F., Lee-Sarwar K.A., Tun H.M., Brown B.P., Pannaraj P.S., Bender J.M., Azad M.B., Thompson A.L., Weiss S.T., Azcarate-Peril M.A., Litonjua A.A., Kozyrskyj A.L., Jaspan H.B., Aldrovandi G.M. , Kuhn L.",Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations,Nature communications,2018,NA,Experiment 3,Haiti,Homo sapiens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,"Exclusively Breastfeeding (EBF), Vaginally Born and C-section Born","Non-Exclusive Breastfeeding (Non-EBF), Vaginally Born and C-section Born",Infants fed with breast milk plus  solid or formula,37,11,NA,16S,4,Illumina,relative abundances,Random Forest Analysis,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,"Table 2, Table 3.",3 October 2024,Shulamite,"Shulamite,Peace Sandy,WikiWorks","Meta-analysis of all seven included studies for gut bacterial taxa
with differential relative abundances between non-exclusively breastfed vs. exclusively
breastfed infants ≤6 months of age.

Meta-analysis of five studies that included a non-breastfeeding
group for gut bacterial taxa with trend in relative abundance across exclusive
breastfeeding, non-exclusive breastfeeding and non-breastfeeding groups.",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Verrucomicrobiota",3379134|74201|203494|48461|1647988|239934;1783272|1239;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|186806|1730;3379134|74201,Complete,Peace Sandy
bsdb:30301893/3/2,30301893,meta-analysis,30301893,10.1038/s41467-018-06473-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6177445/#Sec1title,"Ho N.T., Li F., Lee-Sarwar K.A., Tun H.M., Brown B.P., Pannaraj P.S., Bender J.M., Azad M.B., Thompson A.L., Weiss S.T., Azcarate-Peril M.A., Litonjua A.A., Kozyrskyj A.L., Jaspan H.B., Aldrovandi G.M. , Kuhn L.",Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations,Nature communications,2018,NA,Experiment 3,Haiti,Homo sapiens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,"Exclusively Breastfeeding (EBF), Vaginally Born and C-section Born","Non-Exclusive Breastfeeding (Non-EBF), Vaginally Born and C-section Born",Infants fed with breast milk plus  solid or formula,37,11,NA,16S,4,Illumina,relative abundances,Random Forest Analysis,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 2,Table 2 and Table 3,19 November 2024,Peace Sandy,"Peace Sandy,WikiWorks","Meta-analysis of all seven included studies for gut bacterial taxa with differential relative abundances between non-exclusively breastfed vs. exclusively breastfed infants ≤6 months of age.

Meta-analysis of five studies that included a non-breastfeeding group for gut bacterial taxa with trend in relative abundance across exclusive breastfeeding, non-exclusive breastfeeding and non-breastfeeding groups.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",3379134|1224|1236|135625|712|724;1783272|1239|91061|1385|90964|1279,Complete,NA
bsdb:30301893/3/3,30301893,meta-analysis,30301893,10.1038/s41467-018-06473-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6177445/#Sec1title,"Ho N.T., Li F., Lee-Sarwar K.A., Tun H.M., Brown B.P., Pannaraj P.S., Bender J.M., Azad M.B., Thompson A.L., Weiss S.T., Azcarate-Peril M.A., Litonjua A.A., Kozyrskyj A.L., Jaspan H.B., Aldrovandi G.M. , Kuhn L.",Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations,Nature communications,2018,NA,Experiment 3,Haiti,Homo sapiens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,"Exclusively Breastfeeding (EBF), Vaginally Born and C-section Born","Non-Exclusive Breastfeeding (Non-EBF), Vaginally Born and C-section Born",Infants fed with breast milk plus  solid or formula,37,11,NA,16S,4,Illumina,relative abundances,Random Forest Analysis,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 3,Table 3 and Table 2,19 November 2024,Peace Sandy,"Peace Sandy,WikiWorks","Meta-analysis of all seven included studies for gut bacterial taxa with differential relative abundances between non-exclusively breastfed vs. exclusively breastfed infants ≤6 months of age.

Meta-analysis of five studies that included a non-breastfeeding group for gut bacterial taxa with trend in relative abundance across exclusive breastfeeding, non-exclusive breastfeeding and non-breastfeeding groups.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",3379134|1224|1236|135625|712|724;1783272|1239|91061|1385|90964|1279,Complete,NA
bsdb:30301893/3/4,30301893,meta-analysis,30301893,10.1038/s41467-018-06473-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6177445/#Sec1title,"Ho N.T., Li F., Lee-Sarwar K.A., Tun H.M., Brown B.P., Pannaraj P.S., Bender J.M., Azad M.B., Thompson A.L., Weiss S.T., Azcarate-Peril M.A., Litonjua A.A., Kozyrskyj A.L., Jaspan H.B., Aldrovandi G.M. , Kuhn L.",Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations,Nature communications,2018,NA,Experiment 3,Haiti,Homo sapiens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,"Exclusively Breastfeeding (EBF), Vaginally Born and C-section Born","Non-Exclusive Breastfeeding (Non-EBF), Vaginally Born and C-section Born",Infants fed with breast milk plus  solid or formula,37,11,NA,16S,4,Illumina,relative abundances,Random Forest Analysis,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 4,Table 2 and Table 3,19 November 2024,Peace Sandy,"Peace Sandy,WikiWorks","Meta-analysis of all seven included studies for gut bacterial taxa with differential relative abundances between non-exclusively breastfed vs. exclusively breastfed infants ≤6 months of age.

Meta-analysis of five studies that included a non-breastfeeding group for gut bacterial taxa with trend in relative abundance across exclusive breastfeeding, non-exclusive breastfeeding and non-breastfeeding groups.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",3379134|1224|1236|135625|712|724;1783272|1239|91061|1385|90964|1279,Complete,NA
bsdb:30301893/4/1,30301893,meta-analysis,30301893,10.1038/s41467-018-06473-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6177445/#Sec1title,"Ho N.T., Li F., Lee-Sarwar K.A., Tun H.M., Brown B.P., Pannaraj P.S., Bender J.M., Azad M.B., Thompson A.L., Weiss S.T., Azcarate-Peril M.A., Litonjua A.A., Kozyrskyj A.L., Jaspan H.B., Aldrovandi G.M. , Kuhn L.",Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations,Nature communications,2018,NA,Experiment 4,South Africa,Homo sapiens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,Exclusive Breastfeeding (EBF),Non-Exclusive Breastfeeding (Non-EBF),Infants fed with breast milk plus solid or formula,86,57,NA,16S,4,Illumina,relative abundances,Random Forest Analysis,0.05,TRUE,NA,NA,NA,NA,NA,increased,NA,NA,NA,Signature 1,"Table 2, Table 3.",5 October 2024,Shulamite,"Shulamite,Rahila,Peace Sandy,WikiWorks","Meta-analysis of all seven included studies for gut bacterial taxa with differential relative abundances between non-exclusively breastfed vs. exclusively breastfed infants ≤6 months of age.

Meta-analysis of five studies that included a non-breastfeeding group for gut bacterial taxa with trend in relative abundance across exclusive breastfeeding, non-exclusive breastfeeding and non-breastfeeding groups.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Verrucomicrobiota",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|186806|1730;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843489|31977|29465;3379134|74201|203494|48461|1647988|239934;1783272|1239;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|33042;3379134|74201,Complete,Peace Sandy
bsdb:30301893/4/2,30301893,meta-analysis,30301893,10.1038/s41467-018-06473-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6177445/#Sec1title,"Ho N.T., Li F., Lee-Sarwar K.A., Tun H.M., Brown B.P., Pannaraj P.S., Bender J.M., Azad M.B., Thompson A.L., Weiss S.T., Azcarate-Peril M.A., Litonjua A.A., Kozyrskyj A.L., Jaspan H.B., Aldrovandi G.M. , Kuhn L.",Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations,Nature communications,2018,NA,Experiment 4,South Africa,Homo sapiens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,Exclusive Breastfeeding (EBF),Non-Exclusive Breastfeeding (Non-EBF),Infants fed with breast milk plus solid or formula,86,57,NA,16S,4,Illumina,relative abundances,Random Forest Analysis,0.05,TRUE,NA,NA,NA,NA,NA,increased,NA,NA,NA,Signature 2,"Table 2, Table 3.",19 November 2024,Peace Sandy,"Peace Sandy,WikiWorks","Meta-analysis of all seven included studies for gut bacterial taxa with differential relative abundances between non-exclusively breastfed vs. exclusively breastfed infants ≤6 months of age.

Meta-analysis of five studies that included a non-breastfeeding group for gut bacterial taxa with trend in relative abundance across exclusive breastfeeding, non-exclusive breastfeeding and non-breastfeeding groups.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",3379134|1224|1236|135625|712|724;1783272|1239|91061|1385|90964|1279,Complete,Peace Sandy
bsdb:30301893/5/1,30301893,meta-analysis,30301893,10.1038/s41467-018-06473-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6177445/#Sec1title,"Ho N.T., Li F., Lee-Sarwar K.A., Tun H.M., Brown B.P., Pannaraj P.S., Bender J.M., Azad M.B., Thompson A.L., Weiss S.T., Azcarate-Peril M.A., Litonjua A.A., Kozyrskyj A.L., Jaspan H.B., Aldrovandi G.M. , Kuhn L.",Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations,Nature communications,2018,NA,Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,Increasing Exclusive Breast Feeding (EBF),Reduced exclusivity of beast feeding to none breastfeeding,Exclusive breastfeeding to infants were reduced.,150,68,NA,16S,4,Illumina,relative abundances,Random Forest Analysis,0.005,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 7,4 October 2024,Shulamite,"Shulamite,WikiWorks",Meta-analysis stratified by mode of delivery for gut bacterial taxa with differential relative abundances between non-exclusively breastfed vs. exclusively breastfed infants ≤6 months of age.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",1783272|1239|909932|1843488|909930|904;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|815|816;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|31979;3379134|1224|1236|135625|712|416916;1783272|1239|91061|186826|1300|1357;1783272|1239|186801|3085636|186803|572511,Complete,Peace Sandy
bsdb:30301893/5/3,30301893,meta-analysis,30301893,10.1038/s41467-018-06473-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6177445/#Sec1title,"Ho N.T., Li F., Lee-Sarwar K.A., Tun H.M., Brown B.P., Pannaraj P.S., Bender J.M., Azad M.B., Thompson A.L., Weiss S.T., Azcarate-Peril M.A., Litonjua A.A., Kozyrskyj A.L., Jaspan H.B., Aldrovandi G.M. , Kuhn L.",Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations,Nature communications,2018,NA,Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,Increasing Exclusive Breast Feeding (EBF),Reduced exclusivity of beast feeding to none breastfeeding,Exclusive breastfeeding to infants were reduced.,150,68,NA,16S,4,Illumina,relative abundances,Random Forest Analysis,0.005,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 3,Table 7,8 October 2024,Shulamite,"Shulamite,Rahila,WikiWorks",Meta-analysis stratified by mode of delivery for gut bacterial taxa with differential relative abundances between non-exclusively breastfed vs. exclusively breastfed infants ≤6 months of age.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",1783272|1239|186801|186802|216572|244127;1783272|1239|909932|1843488|909930|33024;3379134|1224|1236|91347|1903414|583;3379134|1224;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|91347|543,Complete,Peace Sandy
bsdb:30301893/6/1,30301893,meta-analysis,30301893,10.1038/s41467-018-06473-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6177445/#Sec1title,"Ho N.T., Li F., Lee-Sarwar K.A., Tun H.M., Brown B.P., Pannaraj P.S., Bender J.M., Azad M.B., Thompson A.L., Weiss S.T., Azcarate-Peril M.A., Litonjua A.A., Kozyrskyj A.L., Jaspan H.B., Aldrovandi G.M. , Kuhn L.",Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations,Nature communications,2018,NA,Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,Exclusive BreastFeeding (EBF),Non-Exclusive Breastfeeding (Non-EBF),Infants fed with breast milk plus solid or formula.,38,66,NA,16S,345,Roche454,relative abundances,NA,0.005,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 6,4 October 2024,Shulamite,"Shulamite,WikiWorks",Meta-analysis of six studies without data from VDAART trial study for gut bacterial taxa with differential relative abundances between non-exclusively breastfed vs. exclusively breastfed infants ≤6 months of age (sensitivity analysis).,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|909932|1843488|909930|904;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|186806|1730;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843489|31977|29465,Complete,Peace Sandy
bsdb:30301893/7/1,30301893,meta-analysis,30301893,10.1038/s41467-018-06473-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6177445/#Sec1title,"Ho N.T., Li F., Lee-Sarwar K.A., Tun H.M., Brown B.P., Pannaraj P.S., Bender J.M., Azad M.B., Thompson A.L., Weiss S.T., Azcarate-Peril M.A., Litonjua A.A., Kozyrskyj A.L., Jaspan H.B., Aldrovandi G.M. , Kuhn L.",Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations,Nature communications,2018,NA,Experiment 7,United States of America,Homo sapiens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,Increasing Exclusive Breast Feeding (EBF),Reduced exclusivity of beast feeding to none breastfeeding,NA,12,8,NA,16S,12,Illumina,relative abundances,Random Forest Analysis,0.005,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Table 4,6 October 2024,Shulamite,"Shulamite,Rahila,WikiWorks",Meta-analysis of six studies without data from North Carolina study for gut bacterial taxa with differential relative abundances between non-exclusivelybreastfed vs. exclusively breastfed infants ≤6 months of age (sensitivity analysis).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|186802|31979;1783272|1239|186801|186802;3379134|976|200643,Complete,Peace Sandy
bsdb:30314304/1/1,30314304,prospective cohort,30314304,10.3390/nu10101481,NA,"Díaz M., Guadamuro L., Espinosa-Martos I., Mancabelli L., Jiménez S., Molinos-Norniella C., Pérez-Solis D., Milani C., Rodríguez J.M., Ventura M., Bousoño C., Gueimonde M., Margolles A., Díaz J.J. , Delgado S.",Microbiota and Derived Parameters in Fecal Samples of Infants with Non-IgE Cow's Milk Protein Allergy under a Restricted Diet,Nutrients,2018,"cow’s milk protein, fecal microbiota, non-IgE mediated allergy, protein hydrolyzed formulas, tolerance acquisition",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,infant with non-IgE-mediated cow's milk allergy non-tolerant to cow's milk protein,infant with non-IgE-mediated cow's milk allergy tolerant to cow's milk protein,infant with non-IgE mediated cow's milk allergy tolerant to cow's milk after a period of six months dairy-free diet,3,14,1 month,16S,34,Illumina,relative abundances,Metastats,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,10 January 2021,Lucy Mellor,WikiWorks,"Significant differences in fecal microbial abundances (%) between tolerant and non-tolerant infants with non-IgE mediated cow’s milk protein allergy (NIM-CMPA) after
a period with a diet free of cow’s milk protein (CMP)",increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|201174;1783272|201174|1760|85004|31953;1783272|201174|84998|84999|84107;1783272|201174|1760|85004|31953|1678,Complete,Atrayees
bsdb:30314304/2/1,30314304,prospective cohort,30314304,10.3390/nu10101481,NA,"Díaz M., Guadamuro L., Espinosa-Martos I., Mancabelli L., Jiménez S., Molinos-Norniella C., Pérez-Solis D., Milani C., Rodríguez J.M., Ventura M., Bousoño C., Gueimonde M., Margolles A., Díaz J.J. , Delgado S.",Microbiota and Derived Parameters in Fecal Samples of Infants with Non-IgE Cow's Milk Protein Allergy under a Restricted Diet,Nutrients,2018,"cow’s milk protein, fecal microbiota, non-IgE mediated allergy, protein hydrolyzed formulas, tolerance acquisition",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,healthy control,infant with non-IgE-mediated cow's milk allergy,"infant with cow's milk protein allergy confirmed by a negative skin prick test, values lower than 0.35 kU/L cow’s milk-specific IgE determined in their blood, and a clear positive standardized oral challenge (SOC), performed under medical supervision",10,17,1 month,16S,34,Illumina,relative abundances,Metastats,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2, text",10 January 2021,Lucy Mellor,"WikiWorks,Atrayees",Differences in relative abundances (%) of sequences in fecal samples of infants with non-IgE mediated cow’s milk protein allergy (NIM-CMPA) and non-allergic control infants,increased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,1783272|201174|84998|84999|84107,Complete,Atrayees
bsdb:30314304/2/2,30314304,prospective cohort,30314304,10.3390/nu10101481,NA,"Díaz M., Guadamuro L., Espinosa-Martos I., Mancabelli L., Jiménez S., Molinos-Norniella C., Pérez-Solis D., Milani C., Rodríguez J.M., Ventura M., Bousoño C., Gueimonde M., Margolles A., Díaz J.J. , Delgado S.",Microbiota and Derived Parameters in Fecal Samples of Infants with Non-IgE Cow's Milk Protein Allergy under a Restricted Diet,Nutrients,2018,"cow’s milk protein, fecal microbiota, non-IgE mediated allergy, protein hydrolyzed formulas, tolerance acquisition",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,healthy control,infant with non-IgE-mediated cow's milk allergy,"infant with cow's milk protein allergy confirmed by a negative skin prick test, values lower than 0.35 kU/L cow’s milk-specific IgE determined in their blood, and a clear positive standardized oral challenge (SOC), performed under medical supervision",10,17,1 month,16S,34,Illumina,relative abundances,Metastats,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2,10 January 2021,Lucy Mellor,WikiWorks,Differences in relative abundances (%) of sequences in fecal samples of infants with non-IgE mediated cow’s milk protein allergy (NIM-CMPA) and non-allergic control infants,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|976;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816,Complete,Atrayees
bsdb:30341386/1/1,30341386,time series / longitudinal observational,30341386,10.1038/s41598-018-33750-y,NA,"Arokiyaraj S., Seo S.S., Kwon M., Lee J.K. , Kim M.K.","Association of cervical microbial community with persistence, clearance and negativity of Human Papillomavirus in Korean women: a longitudinal study",Scientific reports,2018,NA,Experiment 1,South Korea,Homo sapiens,Uterus,UBERON:0000995,Human papilloma virus infection,EFO:0001668,HPV clearance,HPV persistent,"HPV DNA was detected using the Digene HC2 high-risk DNA test (Qiagen, Gaithersburg, MD, USA) with signal amplification and chemiluminescence for 13 types of HR-HPV scored in RLU/PC. A positive result indicated a concentration of 1 pg/ml or higher than the RLU/cutoff ratio (RLU of the specimen/mean RLU of 2 positive controls).",15,16,NA,16S,NA,Roche454,relative abundances,LEfSe,0.05,FALSE,2,NA,"age,contraception,menopause,smoking behavior",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 2,10 January 2021,Phyu Han,WikiWorks,Mulivariate odd ratios of species according to different types of HPV,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides johnsonii,3379134|976|200643|171549|2005525|375288|387661,Complete,Shaimaa Elsafoury
bsdb:30341386/2/1,30341386,time series / longitudinal observational,30341386,10.1038/s41598-018-33750-y,NA,"Arokiyaraj S., Seo S.S., Kwon M., Lee J.K. , Kim M.K.","Association of cervical microbial community with persistence, clearance and negativity of Human Papillomavirus in Korean women: a longitudinal study",Scientific reports,2018,NA,Experiment 2,South Korea,Homo sapiens,Uterus,UBERON:0000995,Human papilloma virus infection,EFO:0001668,HPV negative,HPV clearance,"HPV DNA was detected using the Digene HC2 high-risk DNA test (Qiagen, Gaithersburg, MD, USA) with signal amplification and chemiluminescence for 13 types of HR-HPV scored in RLU/PC. A positive result indicated a concentration of 1 pg/ml or higher than the RLU/cutoff ratio (RLU of the specimen/mean RLU of 2 positive controls).",10,15,NA,16S,NA,Roche454,NA,LEfSe,0.05,FALSE,2,NA,"age,contraception,menopause,smoking behavior",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 2,10 January 2021,Phyu Han,WikiWorks,Mulivariate odd ratios of species according to different types of HPV,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma urealyticum",1783272|201174|1760|85004|31953|2701|2702;1783272|544448|2790996|2790998|2129|2130,Complete,Shaimaa Elsafoury
bsdb:30341386/3/1,30341386,time series / longitudinal observational,30341386,10.1038/s41598-018-33750-y,NA,"Arokiyaraj S., Seo S.S., Kwon M., Lee J.K. , Kim M.K.","Association of cervical microbial community with persistence, clearance and negativity of Human Papillomavirus in Korean women: a longitudinal study",Scientific reports,2018,NA,Experiment 3,South Korea,Homo sapiens,Uterus,UBERON:0000995,Human papilloma virus infection,EFO:0001668,HPV presistent and clearance,HPV negative,"HPV DNA was detected using the Digene HC2 high-risk DNA test (Qiagen, Gaithersburg, MD, USA) with signal amplification and chemiluminescence for 13 types of HR-HPV scored in RLU/PC. A positive result indicated a concentration of 1 pg/ml or higher than the RLU/cutoff ratio (RLU of the specimen/mean RLU of 2 positive controls).",31,10,NA,16S,NA,Roche454,NA,LEfSe,0.05,FALSE,2,NA,"age,contraception,menopause,smoking behavior",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 2,10 January 2021,Phyu Han,WikiWorks,Mulivariate odd ratios of species according to different types of HPV,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,1783272|1239|91061|186826|33958|1578|47770,Complete,Shaimaa Elsafoury
bsdb:30341386/4/1,30341386,time series / longitudinal observational,30341386,10.1038/s41598-018-33750-y,NA,"Arokiyaraj S., Seo S.S., Kwon M., Lee J.K. , Kim M.K.","Association of cervical microbial community with persistence, clearance and negativity of Human Papillomavirus in Korean women: a longitudinal study",Scientific reports,2018,NA,Experiment 4,South Korea,Homo sapiens,Uterus,UBERON:0000995,Human papilloma virus infection,EFO:0001668,HPV presistent and negative,HPV clearance,"HPV DNA was detected using the Digene HC2 high-risk DNA test (Qiagen, Gaithersburg, MD, USA) with signal amplification and chemiluminescence for 13 types of HR-HPV scored in RLU/PC. A positive result indicated a concentration of 1 pg/ml or higher than the RLU/cutoff ratio (RLU of the specimen/mean RLU of 2 positive controls).",26,15,NA,16S,NA,Roche454,NA,LEfSe,0.05,FALSE,2,NA,"age,contraception,menopause,smoking behavior",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Mulivariate odd ratios of species according to different types of HPV,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,1783272|1239|186801|3085636|186803|28050|39485,Complete,Shaimaa Elsafoury
bsdb:30342346/1/1,30342346,case-control,30342346,10.1016/j.intimp.2018.10.017,NA,"Chen B., Wang J., Wang Y., Zhang J., Zhao C., Shen N., Yang J., Gai Z. , Zhang L.",Oral microbiota dysbiosis and its association with Henoch-Schönlein Purpura in children,International immunopharmacology,2018,"Dysbiosis, Henoch-Schönlein Purpura, Immunoglobulin, Oral microbiota",Experiment 1,China,Homo sapiens,Mouth,UBERON:0000165,Henoch-Schoenlein purpura,EFO:1000965,controls,Henoch-Schönlein Purpura,Henoch-Schönlein Purpura in children,66,98,1 month,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,"age,sex",NA,NA,increased,NA,NA,NA,increased,Signature 1,"Figure 6b, 6c",10 January 2021,Rimsha Azhar,WikiWorks,"Histogram of the LDA scores computed for different abundance levels between children with HSP and healthy children, as detected by the LEfSe tool",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",3379134|1224|28216|206351;3379134|1224|28216|206351|481;3379134|1224|28216|206351|481|482;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932;1783272|1239|909932|1843489;1783272|1239|909932|1843489|31977;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|976;3379134|976|200643;3379134|976|200643|171549,Complete,NA
bsdb:30342346/1/2,30342346,case-control,30342346,10.1016/j.intimp.2018.10.017,NA,"Chen B., Wang J., Wang Y., Zhang J., Zhao C., Shen N., Yang J., Gai Z. , Zhang L.",Oral microbiota dysbiosis and its association with Henoch-Schönlein Purpura in children,International immunopharmacology,2018,"Dysbiosis, Henoch-Schönlein Purpura, Immunoglobulin, Oral microbiota",Experiment 1,China,Homo sapiens,Mouth,UBERON:0000165,Henoch-Schoenlein purpura,EFO:1000965,controls,Henoch-Schönlein Purpura,Henoch-Schönlein Purpura in children,66,98,1 month,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,"age,sex",NA,NA,increased,NA,NA,NA,increased,Signature 2,"Figure 6b, 6c",10 January 2021,Rimsha Azhar,WikiWorks,"Histogram of the LDA scores computed for different abundance levels between children with HSP and healthy children, as detected by the LEfSe tool",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|1236|135625|712|724;3379134|1224|1236|135625;3379134|1224|1236|135625|712;3379134|1224|28211;3379134|1224|1236|2887326|468|469;3379134|1224|1236|2887326|468;3379134|1224|1236|72274;3379134|1224|1236;3379134|1224,Complete,NA
bsdb:30355393/1/1,30355393,"cross-sectional observational, not case-control",30355393,10.1017/S0007114518002465,NA,"Lin D., Peters B.A., Friedlander C., Freiman H.J., Goedert J.J., Sinha R., Miller G., Bernstein M.A., Hayes R.B. , Ahn J.",Association of dietary fibre intake and gut microbiota in adults,The British journal of nutrition,2018,"FC fold change, NCI National Cancer Institute, NYU New York University, Cross-sectional studies, Dietary fibre intake, Epidemiology, Gut microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,low quartile of TOTAL fiber intake,Higher quartile of TOTAL fiber intake,Subjects who had a higher total fiber intake,76,75,NA,16S,34,"Illumina,Roche454",raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex,smoking status",NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 2, Supplemental Table 1",10 January 2021,Lora Kasselman,"Claregrieve1,WikiWorks,ChiomaBlessing",Forest plot of the fold change of microbial abundance in both New York University and National Cancer Institute study populations with significant association with higher fibre intake subjects,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",1783272|201174|1760|2037|2049|1654;1783272|1239|526524|526525|128827|2749846|31971;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|119852,Complete,Claregrieve1
bsdb:30355393/1/2,30355393,"cross-sectional observational, not case-control",30355393,10.1017/S0007114518002465,NA,"Lin D., Peters B.A., Friedlander C., Freiman H.J., Goedert J.J., Sinha R., Miller G., Bernstein M.A., Hayes R.B. , Ahn J.",Association of dietary fibre intake and gut microbiota in adults,The British journal of nutrition,2018,"FC fold change, NCI National Cancer Institute, NYU New York University, Cross-sectional studies, Dietary fibre intake, Epidemiology, Gut microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,low quartile of TOTAL fiber intake,Higher quartile of TOTAL fiber intake,Subjects who had a higher total fiber intake,76,75,NA,16S,34,"Illumina,Roche454",raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex,smoking status",NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 2, Supplemental Table 1",10 January 2021,Lora Kasselman,"Claregrieve1,Merit,WikiWorks,ChiomaBlessing,Davvve",Forest plot of the fold change of microbial abundance in both New York University and National Cancer Institute study populations with significant association with higher fibre intake subjects.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|186802|31979,Complete,Claregrieve1
bsdb:30355393/2/1,30355393,"cross-sectional observational, not case-control",30355393,10.1017/S0007114518002465,NA,"Lin D., Peters B.A., Friedlander C., Freiman H.J., Goedert J.J., Sinha R., Miller G., Bernstein M.A., Hayes R.B. , Ahn J.",Association of dietary fibre intake and gut microbiota in adults,The British journal of nutrition,2018,"FC fold change, NCI National Cancer Institute, NYU New York University, Cross-sectional studies, Dietary fibre intake, Epidemiology, Gut microbiome",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,low fiber intake from FRUITS/ VEGETABLES,Higher fiber intake from FRUITS/ VEGETABLES,Subjects who had a higher fiber intake from FRUITS/ VEGETABLES,76,75,"no ""long term"" antibiotics use",16S,34,"Illumina,Roche454",raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex,smoking status",NA,unchanged,NA,NA,NA,NA,Signature 1,"Supplemental Table 2, Figure 3",28 October 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Taxonomy-based Meta-analysis to evaluate taxa abundance by higher fibre intake from FRUIT/ VEGETABLE  in the NCI and NYU study population,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii",1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549|815|816|820;1783272|201174|84998|84999;1783272|1239|91061|186826;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|1263|40518,Complete,Folakunmi
bsdb:30355393/2/2,30355393,"cross-sectional observational, not case-control",30355393,10.1017/S0007114518002465,NA,"Lin D., Peters B.A., Friedlander C., Freiman H.J., Goedert J.J., Sinha R., Miller G., Bernstein M.A., Hayes R.B. , Ahn J.",Association of dietary fibre intake and gut microbiota in adults,The British journal of nutrition,2018,"FC fold change, NCI National Cancer Institute, NYU New York University, Cross-sectional studies, Dietary fibre intake, Epidemiology, Gut microbiome",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,low fiber intake from FRUITS/ VEGETABLES,Higher fiber intake from FRUITS/ VEGETABLES,Subjects who had a higher fiber intake from FRUITS/ VEGETABLES,76,75,"no ""long term"" antibiotics use",16S,34,"Illumina,Roche454",raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex,smoking status",NA,unchanged,NA,NA,NA,NA,Signature 2,Supplemental Table 2,28 October 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Taxonomy-based Meta-analysis to evaluate taxa abundance by higher fibre intake from FRUIT/ VEGETABLE  in the NCI and NYU study population,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,1783272|1239|186801|3082720|186804,Complete,Folakunmi
bsdb:30355393/3/1,30355393,"cross-sectional observational, not case-control",30355393,10.1017/S0007114518002465,NA,"Lin D., Peters B.A., Friedlander C., Freiman H.J., Goedert J.J., Sinha R., Miller G., Bernstein M.A., Hayes R.B. , Ahn J.",Association of dietary fibre intake and gut microbiota in adults,The British journal of nutrition,2018,"FC fold change, NCI National Cancer Institute, NYU New York University, Cross-sectional studies, Dietary fibre intake, Epidemiology, Gut microbiome",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,low fiber intake from BEANS,Higher fiber intake from BEANS,Subjects who had a higher fiber intake from BEANS,76,75,"no ""long term"" antibiotics use",16S,34,"Illumina,Roche454",raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex,smoking status",NA,unchanged,NA,NA,NA,NA,Signature 1,"Supplemental Table 4, Figure 3",28 October 2023,ChiomaBlessing,"ChiomaBlessing,Folakunmi,WikiWorks",Taxonomy-based Meta-analysis to evaluate taxa abundance by higher fibre intake from BEANS in the NCI and NYU study population,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853,Complete,Folakunmi
bsdb:30355393/3/2,30355393,"cross-sectional observational, not case-control",30355393,10.1017/S0007114518002465,NA,"Lin D., Peters B.A., Friedlander C., Freiman H.J., Goedert J.J., Sinha R., Miller G., Bernstein M.A., Hayes R.B. , Ahn J.",Association of dietary fibre intake and gut microbiota in adults,The British journal of nutrition,2018,"FC fold change, NCI National Cancer Institute, NYU New York University, Cross-sectional studies, Dietary fibre intake, Epidemiology, Gut microbiome",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,low fiber intake from BEANS,Higher fiber intake from BEANS,Subjects who had a higher fiber intake from BEANS,76,75,"no ""long term"" antibiotics use",16S,34,"Illumina,Roche454",raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex,smoking status",NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 3, supplementary table 4",28 October 2023,ChiomaBlessing,"ChiomaBlessing,Folakunmi,WikiWorks",Heatmap analysis representing fold changes of taxa in higher fiber intake from BEANS in the meta-analysis of NCI and NYU study populations,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae",1783272|201174|1760|2037;1783272|1239|526524|526525|128827|2749846|31971;3379134|976|200643|171549|815|816;28221;3379134|200940|3031449|213115;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|1853231;1783272|1239|186801|186802|216572|1263;3379134|200940|3031449|213115|194924,Complete,Folakunmi
bsdb:30355393/4/1,30355393,"cross-sectional observational, not case-control",30355393,10.1017/S0007114518002465,NA,"Lin D., Peters B.A., Friedlander C., Freiman H.J., Goedert J.J., Sinha R., Miller G., Bernstein M.A., Hayes R.B. , Ahn J.",Association of dietary fibre intake and gut microbiota in adults,The British journal of nutrition,2018,"FC fold change, NCI National Cancer Institute, NYU New York University, Cross-sectional studies, Dietary fibre intake, Epidemiology, Gut microbiome",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,low fiber intake from GRAINS,Higher fiber intake from GRAINS,Subjects who had a higher fiber intake from GRAINS,76,75,"no ""long term"" antibiotics use",16S,34,"Illumina,Roche454",raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex,smoking status",NA,unchanged,NA,NA,NA,NA,Signature 1,Supplemental. Table 3,28 October 2023,ChiomaBlessing,"ChiomaBlessing,Folakunmi,WikiWorks",Taxonomy-based Meta-analysis to evaluate taxa abundance by higher fibre intake from GRAINS in the NCI and NYU study population,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|186803,Complete,Folakunmi
bsdb:30365522/1/1,30365522,"cross-sectional observational, not case-control",30365522,10.1371/journal.pone.0206366,NA,"Romano-Keeler J., Shilts M.H., Tovchigrechko A., Wang C., Brucker R.M., Moore D.J., Fonnesbeck C., Meng S., Correa H., Lovvorn H.N., Tang Y.W., Hooper L., Bordenstein S.R., Das S.R. , Weitkamp J.H.",Distinct mucosal microbial communities in infants with surgical necrotizing enterocolitis correlate with age and antibiotic exposure,PloS one,2018,NA,Experiment 1,United States of America,Homo sapiens,Mucosa of small intestine,UBERON:0001204,Necrotizing enterocolitis,EFO:0003928,non-NEC,NEC,infants who underwent intestinal resection at <180 days of age with NEC,14,10,NA,16S,123,Roche454,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Figure 5,10 January 2021,Fatima Zohra,WikiWorks,Comparison of the abundance of tissue bacterial genera between infants with or without necrotizing enterocolitis (NEC),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|1239|186801|186802|31979|1485;1783272|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:30365522/1/2,30365522,"cross-sectional observational, not case-control",30365522,10.1371/journal.pone.0206366,NA,"Romano-Keeler J., Shilts M.H., Tovchigrechko A., Wang C., Brucker R.M., Moore D.J., Fonnesbeck C., Meng S., Correa H., Lovvorn H.N., Tang Y.W., Hooper L., Bordenstein S.R., Das S.R. , Weitkamp J.H.",Distinct mucosal microbial communities in infants with surgical necrotizing enterocolitis correlate with age and antibiotic exposure,PloS one,2018,NA,Experiment 1,United States of America,Homo sapiens,Mucosa of small intestine,UBERON:0001204,Necrotizing enterocolitis,EFO:0003928,non-NEC,NEC,infants who underwent intestinal resection at <180 days of age with NEC,14,10,NA,16S,123,Roche454,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,Figure 5,23 December 2022,Claregrieve1,"Claregrieve1,WikiWorks",Comparison of the abundance of tissue bacterial genera between infants with or without necrotizing enterocolitis (NEC),decreased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae|g__Alicyclobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium",3379134|29547|3031852|213849|2808963|28196;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|91061|1385|186823|29330;1783272|201174|1760|2037|2049|1654;3379134|1224|1236|72274|135621|286;3379134|976|117743|200644|2762318|59732;3379134|1224|28216|80840|80864|283;1783272|201174|1760|2037;3379134|976|1853228|1853229|563835;3379134|976;1783272|1239|91061|186826|1300|1301;;1783272|201174|1760|85007|1653|1716,Complete,Claregrieve1
bsdb:30365522/3/1,30365522,"cross-sectional observational, not case-control",30365522,10.1371/journal.pone.0206366,NA,"Romano-Keeler J., Shilts M.H., Tovchigrechko A., Wang C., Brucker R.M., Moore D.J., Fonnesbeck C., Meng S., Correa H., Lovvorn H.N., Tang Y.W., Hooper L., Bordenstein S.R., Das S.R. , Weitkamp J.H.",Distinct mucosal microbial communities in infants with surgical necrotizing enterocolitis correlate with age and antibiotic exposure,PloS one,2018,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Necrotizing enterocolitis,EFO:0003928,non-NEC,NEC,infants who underwent intestinal resection at <180 days of age with NEC,14,10,NA,16S,1234,Roche454,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,10 January 2021,Fatima Zohra,WikiWorks,Comparison of the abundance of tissue bacterial genera between infants with or without necrotizing enterocolitis (NEC) after adjusting,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:30366118/1/1,30366118,case-control,30366118,10.1016/j.anaerobe.2018.10.009,NA,"Maya-Lucas O., Murugesan S., Nirmalkar K., Alcaraz L.D., Hoyo-Vadillo C., Pizano-Zárate M.L. , García-Mena J.",The gut microbiome of Mexican children affected by obesity,Anaerobe,2019,"Cholesterol, Gut microbiome, High-throughput sequencing, Mexican children, Obesity, Triglycerides",Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Normal weight children,Obese children,Obese children aged between 9 and 11 years-old,10,10,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 4A,10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing","Differentially abundant bacterial genera, families, or species in obese children compared to normal weight children.",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|909929|1843491|158846,Complete,ChiomaBlessing
bsdb:30366118/1/2,30366118,case-control,30366118,10.1016/j.anaerobe.2018.10.009,NA,"Maya-Lucas O., Murugesan S., Nirmalkar K., Alcaraz L.D., Hoyo-Vadillo C., Pizano-Zárate M.L. , García-Mena J.",The gut microbiome of Mexican children affected by obesity,Anaerobe,2019,"Cholesterol, Gut microbiome, High-throughput sequencing, Mexican children, Obesity, Triglycerides",Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Normal weight children,Obese children,Obese children aged between 9 and 11 years-old,10,10,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 4A,10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing","Differentially abundant bacterial genera, families, or species in obese children compared to normal weight children.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales,k__Thermoproteati|p__Thermoproteota|c__Thermoprotei|o__Desulfurococcales|f__Desulfurococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 7_1_58FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA",1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|207244|649756;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816|674529;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|291644;3379134|976|200643|171549|815|816|371601;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|3085636|186803|3569723|410072;28221;3379134|200940|3024418|213118;1783275|28889|183924|114380|2272;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|2719313|358743;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|909932|1843489|31977|29465|29466;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;1783272|1239|186801|3085636|186803|658087;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|1263|457412,Complete,ChiomaBlessing
bsdb:30366816/1/1,30366816,"cross-sectional observational, not case-control",30366816,10.1016/j.ebiom.2018.10.037,NA,"Moon J.Y., Zolnik C.P., Wang Z., Qiu Y., Usyk M., Wang T., Kizer J.R., Landay A.L., Kurland I.J., Anastos K., Kaplan R.C., Burk R.D. , Qi Q.","Gut microbiota and plasma metabolites associated with diabetes in women with, or at high risk for, HIV infection",EBioMedicine,2018,"Diabetes, Gut microbiota, HIV, Metabolite",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,"HIV infection,Diabetes mellitus","EFO:0000764,EFO:0000400",Women without diabetes,Women with diabetes,Women with or at high risk for HIV infection who have diabetes,26,22,NA,16S,4,Illumina,raw counts,Linear Regression,0.1,TRUE,NA,NA,"HIV infection,age",NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,"Text, Figure 2, Table 2",10 January 2021,Michael Lutete,"Claregrieve1,WikiWorks",Differentially abundant genera by diabetes status in women with HIV or at high risk for HIV,decreased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia",1783272|1239|1737404|1737405|1570339|165779;1783272|1239|1737404|1737405|1570339|150022;3384189|32066|203490|203491|1129771|168808;1783272|201174|84998|1643822|1643826|447020,Complete,Claregrieve1
bsdb:30395655/1/1,30395655,time series / longitudinal observational,30395655,10.1371/journal.pone.0207016,NA,"Tuominen H., Rautava S., Collado M.C., Syrjänen S. , Rautava J.",HPV infection and bacterial microbiota in breast milk and infant oral mucosa,PloS one,2018,NA,Experiment 1,Finland,Homo sapiens,Mouth,UBERON:0000165,"Age,Human papilloma virus infection","EFO:0000246,EFO:0001668",at birth,two months,infants with HPV infection at 2 months of age,13,22,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 1,"Figure 2D, text",10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between samples at birth and after 2 months,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia",1783272|201174|1760|85006|1268;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|39778;3379134|976|117743|200644|2762318;3379134|1224|1236|135625|712|724;1783272|1239|1737404|1737405|1570339|165779|1872515;1783272|1239|1737404|1737405|1570339|150022,Complete,Claregrieve1
bsdb:30395655/1/2,30395655,time series / longitudinal observational,30395655,10.1371/journal.pone.0207016,NA,"Tuominen H., Rautava S., Collado M.C., Syrjänen S. , Rautava J.",HPV infection and bacterial microbiota in breast milk and infant oral mucosa,PloS one,2018,NA,Experiment 1,Finland,Homo sapiens,Mouth,UBERON:0000165,"Age,Human papilloma virus infection","EFO:0000246,EFO:0001668",at birth,two months,infants with HPV infection at 2 months of age,13,22,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 2,"Figure 2D, text",10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between samples at birth and after 2 months,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae",3379134|1224|28211|356|82115|357;3379134|976|200643|171549|815|816;3379134|1224|28216|80840|80864|80865;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|906;1783272|201174|1760|85009|31957|1743;3379134|1224|1236|72274|135621|286;1783272|1239|91061|1385|90964|1279;1783272|1239|1737404|1737405|1737406,Complete,Claregrieve1
bsdb:30395655/2/1,30395655,time series / longitudinal observational,30395655,10.1371/journal.pone.0207016,NA,"Tuominen H., Rautava S., Collado M.C., Syrjänen S. , Rautava J.",HPV infection and bacterial microbiota in breast milk and infant oral mucosa,PloS one,2018,NA,Experiment 2,Finland,Homo sapiens,Mouth,UBERON:0000165,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,infants that were positive for HPV infection,21,14,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 5F,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between HPV+ and HPV- infants,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma",1783272|1239|91061|1385|186817|400634;1783272|544448|2790996|2790998|2129,Complete,Claregrieve1
bsdb:30395655/2/2,30395655,time series / longitudinal observational,30395655,10.1371/journal.pone.0207016,NA,"Tuominen H., Rautava S., Collado M.C., Syrjänen S. , Rautava J.",HPV infection and bacterial microbiota in breast milk and infant oral mucosa,PloS one,2018,NA,Experiment 2,Finland,Homo sapiens,Mouth,UBERON:0000165,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,infants that were positive for HPV infection,21,14,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 5F,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between HPV+ and HPV- infants,decreased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,1783272|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:30395655/3/1,30395655,time series / longitudinal observational,30395655,10.1371/journal.pone.0207016,NA,"Tuominen H., Rautava S., Collado M.C., Syrjänen S. , Rautava J.",HPV infection and bacterial microbiota in breast milk and infant oral mucosa,PloS one,2018,NA,Experiment 3,Finland,Homo sapiens,Mouth,UBERON:0000165,Human papilloma virus infection,EFO:0001668,HPV- at two months,HPV+ at two months,HPV+ infants at two months,17,5,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,decreased,Signature 1,text,10 January 2021,Fatima Zohra,WikiWorks,effect of age on infant oral HPV infection and bacterial microbiota,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",1783272|1239|909932|1843489|31977;1783272|1239|909932|1843489|31977|29465|39778,Complete,Claregrieve1
bsdb:30405010/1/1,30405010,case-control,30405010,https://doi.org/10.3390/ijerph15112479,https://www.mdpi.com/1660-4601/15/11/2479,"Rodríguez-Rabassa M., López P., Rodríguez-Santiago R.E., Cases A., Felici M., Sánchez R., Yamamura Y. , Rivera-Amill V.",Cigarette Smoking Modulation of Saliva Microbial Composition and Cytokine Levels,International journal of environmental research and public health,2018,"cytokines, microbiome, saliva, smoking, tobacco",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Non-smokers,Smokers,Current smokers.,16,18,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,13 March 2023,Dupe,"Dupe,Mcarlson,Peace Sandy,WikiWorks",Differential LEfSe-associated bacteria between the smoker and nonsmoker groups.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Alloiococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Budviciaceae|g__Leminorella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Necropsobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Thermoproteati|p__Candidatus Bathyarchaeota",3379134|1224|1236|135625|712|713;1783272|1239|91061|186826|186828|1651;3379134|976|200643|171549|815;1783272|1239|526524|526525|128827|118747;3379134|976|117743|200644|2762318|59732;1783272|1239|526524|526525|128827|1647;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|91347|1903416|82980;3379134|1224|1236|135625|712|908284;3379134|1224|1236|91347|1903411|613;3379134|1224|28216|80840|995019|40544;1783275|928852,Complete,Mcarlson
bsdb:30405010/1/2,30405010,case-control,30405010,https://doi.org/10.3390/ijerph15112479,https://www.mdpi.com/1660-4601/15/11/2479,"Rodríguez-Rabassa M., López P., Rodríguez-Santiago R.E., Cases A., Felici M., Sánchez R., Yamamura Y. , Rivera-Amill V.",Cigarette Smoking Modulation of Saliva Microbial Composition and Cytokine Levels,International journal of environmental research and public health,2018,"cytokines, microbiome, saliva, smoking, tobacco",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Non-smokers,Smokers,Current smokers.,16,18,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,13 March 2023,Dupe,"Dupe,Mcarlson,Peace Sandy,WikiWorks",Differential LEfSe-associated bacteria between the smoker and nonsmoker groups.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae|g__Pilimelia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter",1783272|1239|91061|186826|186827|46123;1783272|201174|1760|2037|2049|1654;3379134|976|117743|200644|49546|1016;1783272|201174|1760|85007|1653|1716;1783272|1239|186801|3082720|3118655|44259;1783272|1239|91061|186826|186828|117563;3384189|32066|203490|203491|1129771|32067;1783272|1239|186801|3082720|543314|86331;1783272|201174|1760|85008|28056|53370;1783272|1239|909932|909929|1843491|970;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|2005525|195950;3379134|1224|1236|2887326|468|469,Complete,Mcarlson
bsdb:30405584/1/1,30405584,"cross-sectional observational, not case-control",30405584,10.3389/fmicb.2018.02533,NA,"Godoy-Vitorino F., Romaguera J., Zhao C., Vargas-Robles D., Ortiz-Morales G., Vázquez-Sánchez F., Sanchez-Vázquez M., de la Garza-Casillas M., Martinez-Ferrer M., White J.R., Bittinger K., Dominguez-Bello M.G. , Blaser M.J.",Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population,Frontiers in microbiology,2018,"16S rRNA, ITS2, cervical cancer, cervicovaginal microbiota, fungi",Experiment 1,United States of America,Homo sapiens,Vagina,UBERON:0000996,"Cervical glandular intraepithelial neoplasia,Human papilloma virus infection","EFO:1000165,EFO:0001668",Atypical Squamous Cells of Undetermined Significance,Low Grade Squamous Intraepithelial Lesion,low grade squamous intraepithelial lesion,6,18,2 months,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 1,Figure 8,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Fungal biomarker signatures in Low Grade Squamous Intraepithelial Lesion compared to Atypical Squamous Cells of Undetermined Significance (in the 58 introitus samples),decreased,"k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae",4751|4890|4891|4892|4893|4930;4751|5204|162481|231213|1799696,Complete,Fatima Zohra
bsdb:30405584/2/1,30405584,"cross-sectional observational, not case-control",30405584,10.3389/fmicb.2018.02533,NA,"Godoy-Vitorino F., Romaguera J., Zhao C., Vargas-Robles D., Ortiz-Morales G., Vázquez-Sánchez F., Sanchez-Vázquez M., de la Garza-Casillas M., Martinez-Ferrer M., White J.R., Bittinger K., Dominguez-Bello M.G. , Blaser M.J.",Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population,Frontiers in microbiology,2018,"16S rRNA, ITS2, cervical cancer, cervicovaginal microbiota, fungi",Experiment 2,United States of America,Homo sapiens,Vagina,UBERON:0000996,"Cervical glandular intraepithelial neoplasia,Human papilloma virus infection","EFO:1000165,EFO:0001668",Low risk-HPV,High risk-HPV,High risk-HPV,3,27,2 months,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 1,Figure 8,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Fungal biomarker signatures in high risk-HPV group compared to low risk-HPV group (in the 58 introitus samples),increased,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,4751|5204|1538075|162474|742845|55193,Complete,Fatima
bsdb:30405584/2/2,30405584,"cross-sectional observational, not case-control",30405584,10.3389/fmicb.2018.02533,NA,"Godoy-Vitorino F., Romaguera J., Zhao C., Vargas-Robles D., Ortiz-Morales G., Vázquez-Sánchez F., Sanchez-Vázquez M., de la Garza-Casillas M., Martinez-Ferrer M., White J.R., Bittinger K., Dominguez-Bello M.G. , Blaser M.J.",Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population,Frontiers in microbiology,2018,"16S rRNA, ITS2, cervical cancer, cervicovaginal microbiota, fungi",Experiment 2,United States of America,Homo sapiens,Vagina,UBERON:0000996,"Cervical glandular intraepithelial neoplasia,Human papilloma virus infection","EFO:1000165,EFO:0001668",Low risk-HPV,High risk-HPV,High risk-HPV,3,27,2 months,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 2,Figure 8,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Fungal biomarker signatures in high risk-HPV group compared to low risk-HPV group (in the 58 introitus samples),decreased,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae,4751|5204|162481|231213|1799696,Complete,Fatima
bsdb:30405584/3/1,30405584,"cross-sectional observational, not case-control",30405584,10.3389/fmicb.2018.02533,NA,"Godoy-Vitorino F., Romaguera J., Zhao C., Vargas-Robles D., Ortiz-Morales G., Vázquez-Sánchez F., Sanchez-Vázquez M., de la Garza-Casillas M., Martinez-Ferrer M., White J.R., Bittinger K., Dominguez-Bello M.G. , Blaser M.J.",Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population,Frontiers in microbiology,2018,"16S rRNA, ITS2, cervical cancer, cervicovaginal microbiota, fungi",Experiment 3,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,"Cervical glandular intraepithelial neoplasia,Human papilloma virus infection","EFO:1000165,EFO:0001668",Atypical Squamous Cells of Undetermined Significance,Low Grade Squamous Intraepithelial Lesion,low grade squamus intraepithelial lesion,6,18,2 months,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 8,10 January 2021,Cynthia Anderson,"ChiomaBlessing,WikiWorks",Fungal biomarker signatures in Low Grade Squamous Intraepithelial Lesion compared to Atypical Squamous Cells of Undetermined Significance (in the 55 cervical samples),decreased,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae,4751|5204|162481|231213|1799696,Complete,Fatima Zohra
bsdb:30405584/4/1,30405584,"cross-sectional observational, not case-control",30405584,10.3389/fmicb.2018.02533,NA,"Godoy-Vitorino F., Romaguera J., Zhao C., Vargas-Robles D., Ortiz-Morales G., Vázquez-Sánchez F., Sanchez-Vázquez M., de la Garza-Casillas M., Martinez-Ferrer M., White J.R., Bittinger K., Dominguez-Bello M.G. , Blaser M.J.",Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population,Frontiers in microbiology,2018,"16S rRNA, ITS2, cervical cancer, cervicovaginal microbiota, fungi",Experiment 4,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,"Cervical glandular intraepithelial neoplasia,Human papilloma virus infection","EFO:1000165,EFO:0001668",Low risk-HPV,High risk-HPV,High risk-HPV,3,27,2 months,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 8,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Fungal biomarker signatures in Low Grade Squamous Intraepithelial Lesion compared to Atypical Squamous Cells of Undetermined Significance (in 55 cervical samples),increased,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,4751|5204|1538075|162474|742845|55193,Complete,Fatima Zohra
bsdb:30405584/4/2,30405584,"cross-sectional observational, not case-control",30405584,10.3389/fmicb.2018.02533,NA,"Godoy-Vitorino F., Romaguera J., Zhao C., Vargas-Robles D., Ortiz-Morales G., Vázquez-Sánchez F., Sanchez-Vázquez M., de la Garza-Casillas M., Martinez-Ferrer M., White J.R., Bittinger K., Dominguez-Bello M.G. , Blaser M.J.",Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population,Frontiers in microbiology,2018,"16S rRNA, ITS2, cervical cancer, cervicovaginal microbiota, fungi",Experiment 4,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,"Cervical glandular intraepithelial neoplasia,Human papilloma virus infection","EFO:1000165,EFO:0001668",Low risk-HPV,High risk-HPV,High risk-HPV,3,27,2 months,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Figure 8,10 January 2021,Cynthia Anderson,"WikiWorks,ChiomaBlessing",Fungal biomarker signatures in Low Grade Squamous Intraepithelial Lesion compared to Atypical Squamous Cells of Undetermined Significance (in 55 cervical samples),decreased,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae,4751|5204|162481|231213|1799696,Complete,Fatima Zohra
bsdb:30412600/1/1,30412600,meta-analysis,30412600,10.1371/journal.pone.0207002,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6226189/,"Shah M.S., DeSantis T., Yamal J.M., Weir T., Ryan E.P., Cope J.L. , Hollister E.B.",Re-purposing 16S rRNA gene sequence data from within case paired tumor biopsy and tumor-adjacent biopsy or fecal samples to identify microbial markers for colorectal cancer,PloS one,2018,NA,Experiment 1,United States of America,Homo sapiens,"Colorectal mucosa,Feces","UBERON:0013067,UBERON:0001988",Colorectal cancer,EFO:0005842,Healthy tumor-adjacent biopsy,CRC tumor biopsy,Colorectal tumor tissues,294,294,1 - 3 months,16S,NA,"Illumina,Roche454",raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2A, Result text",11 March 2024,Scholastica,"Scholastica,WikiWorks","Pairwise differences in CRC tumor vs. healthy adjacent tissue. Boxplots indicate the distribution of the relative abundances of various taxa and corresponding lines connect paired samples, depicting the direction of change in relative abundance of statistically significantly different families between CRC tumor biopsy samples and adjacent non-affected tissue microbiome(n = 294 pairs, 588 samples)",increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota",3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|1129771|32067;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;1783272|1239|91061|186826|1300|1301;1783272|201174,Complete,NA
bsdb:30412600/1/2,30412600,meta-analysis,30412600,10.1371/journal.pone.0207002,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6226189/,"Shah M.S., DeSantis T., Yamal J.M., Weir T., Ryan E.P., Cope J.L. , Hollister E.B.",Re-purposing 16S rRNA gene sequence data from within case paired tumor biopsy and tumor-adjacent biopsy or fecal samples to identify microbial markers for colorectal cancer,PloS one,2018,NA,Experiment 1,United States of America,Homo sapiens,"Colorectal mucosa,Feces","UBERON:0013067,UBERON:0001988",Colorectal cancer,EFO:0005842,Healthy tumor-adjacent biopsy,CRC tumor biopsy,Colorectal tumor tissues,294,294,1 - 3 months,16S,NA,"Illumina,Roche454",raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2A, Result text",11 March 2024,Scholastica,"Scholastica,WikiWorks","Description: Pairwise differences in CRC tumor vs. healthy adjacent tissue. Boxplots indicate the distribution of the relative abundances of various taxa and corresponding lines connect paired samples, depicting the direction of change in relative abundance of statistically significantly different families between CRC tumor biopsy samples and adjacent non-affected tissue microbiome(n = 294 pairs, 588 samples)",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572,Complete,NA
bsdb:30412600/2/1,30412600,meta-analysis,30412600,10.1371/journal.pone.0207002,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6226189/,"Shah M.S., DeSantis T., Yamal J.M., Weir T., Ryan E.P., Cope J.L. , Hollister E.B.",Re-purposing 16S rRNA gene sequence data from within case paired tumor biopsy and tumor-adjacent biopsy or fecal samples to identify microbial markers for colorectal cancer,PloS one,2018,NA,Experiment 2,United States of America,Homo sapiens,"Feces,Colorectal mucosa","UBERON:0001988,UBERON:0013067",Colorectal cancer,EFO:0005842,Tumor biopsy,Fecal samples,Fecal samples from the same colorectal case,42,42,1 - 3 months,16S,NA,"Illumina,Roche454",raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2B, Result text",11 March 2024,Scholastica,"Scholastica,WikiWorks","Pairwise differences in tumor biopsy fecal samples. Boxplots indicate the distribution of the relative abundances of various taxa and corresponding lines connect paired samples, depicting the direction of change in relative abundance of statistically significantly different families between CRC tumor biopsy and fecal samples (n = 42 pairs, 84 samples)",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|572511;1783272|201174|1760|85004|31953|1678,Complete,NA
bsdb:30412600/2/2,30412600,meta-analysis,30412600,10.1371/journal.pone.0207002,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6226189/,"Shah M.S., DeSantis T., Yamal J.M., Weir T., Ryan E.P., Cope J.L. , Hollister E.B.",Re-purposing 16S rRNA gene sequence data from within case paired tumor biopsy and tumor-adjacent biopsy or fecal samples to identify microbial markers for colorectal cancer,PloS one,2018,NA,Experiment 2,United States of America,Homo sapiens,"Feces,Colorectal mucosa","UBERON:0001988,UBERON:0013067",Colorectal cancer,EFO:0005842,Tumor biopsy,Fecal samples,Fecal samples from the same colorectal case,42,42,1 - 3 months,16S,NA,"Illumina,Roche454",raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2B, Result text",11 March 2024,Scholastica,"Scholastica,WikiWorks","Pairwise differences in tumor biopsy fecal samples. Boxplots indicate the distribution of the relative abundances of various taxa and corresponding lines connect paired samples, depicting the direction of change in relative abundance of statistically significantly different families between CRC tumor biopsy and fecal samples (n = 42 pairs, 84 samples)",decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",3384189|32066|203490|203491|203492|848;1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|171552|838;1783272|1239|91061|1385|90964|1279,Complete,NA
bsdb:30416659/1/1,30416659,case-control,30416659,NA,NA,"Zhang W.Q., Zhao S.K., Luo J.W., Dong X.P., Hao Y.T., Li H., Shan L., Zhou Y., Shi H.B., Zhang Z.Y., Peng C.L. , Zhao X.G.",Alterations of fecal bacterial communities in patients with lung cancer,American journal of translational research,2018,"16S rRNA gene sequencing, Lung cancer, carcinogenesis, gut bacteria, microbial dysbiosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Lung cancer,MONDO:0008903,healthy volunteers,lung cancer patients,lung cancer patients with a definite postoperative pathological diagnosis,41,41,1 year,16S,12,Illumina,NA,Metastats,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 4,10 January 2021,Fatima Zohra,WikiWorks,Significant differences of the predominant taxa from lung cancer patients and healthy volunteers,increased,"k__Pseudomonadati|p__Bacteroidota,k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",3379134|976;3384189|32066;3379134|976|200643|171549|815|816;1783272|1239|909932|1843489|31977|29465;3384189|32066|203490|203491|203492|848;1783272|1239|909932|1843488|909930|33024,Complete,Claregrieve1
bsdb:30416659/1/2,30416659,case-control,30416659,NA,NA,"Zhang W.Q., Zhao S.K., Luo J.W., Dong X.P., Hao Y.T., Li H., Shan L., Zhou Y., Shi H.B., Zhang Z.Y., Peng C.L. , Zhao X.G.",Alterations of fecal bacterial communities in patients with lung cancer,American journal of translational research,2018,"16S rRNA gene sequencing, Lung cancer, carcinogenesis, gut bacteria, microbial dysbiosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Lung cancer,MONDO:0008903,healthy volunteers,lung cancer patients,lung cancer patients with a definite postoperative pathological diagnosis,41,41,1 year,16S,12,Illumina,NA,Metastats,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 4,10 January 2021,Fatima Zohra,WikiWorks,Significant differences of the predominant taxa from lung cancer patients and healthy volunteers,decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kluyvera,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella",1783272|1239;3379134|1224|1236|91347|543|579;1783272|1239|186801|186802|216572|216851;3379134|1224|1236|91347|543|547;1783272|1239|909932|1843489|31977|39948;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|620,Complete,Claregrieve1
bsdb:30416659/2/1,30416659,case-control,30416659,NA,NA,"Zhang W.Q., Zhao S.K., Luo J.W., Dong X.P., Hao Y.T., Li H., Shan L., Zhou Y., Shi H.B., Zhang Z.Y., Peng C.L. , Zhao X.G.",Alterations of fecal bacterial communities in patients with lung cancer,American journal of translational research,2018,"16S rRNA gene sequencing, Lung cancer, carcinogenesis, gut bacteria, microbial dysbiosis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Lung cancer,MONDO:0008903,healthy volunteers,lung cancer patients,lung cancer patients with a definite postoperative pathological diagnosis,41,41,1 year,16S,12,Illumina,relative abundances,LEfSe,0.05,TRUE,4,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 5,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential abundance of fecal microbiota from patients with lung cancer and healthy volunteers,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|976|200643|171549;3379134|976;3379134|976|200643;3384189|32066;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066|203490|203491|203492|848;3379134|1224|1236|91347|543|570;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|171552;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816,Complete,Claregrieve1
bsdb:30416659/2/2,30416659,case-control,30416659,NA,NA,"Zhang W.Q., Zhao S.K., Luo J.W., Dong X.P., Hao Y.T., Li H., Shan L., Zhou Y., Shi H.B., Zhang Z.Y., Peng C.L. , Zhao X.G.",Alterations of fecal bacterial communities in patients with lung cancer,American journal of translational research,2018,"16S rRNA gene sequencing, Lung cancer, carcinogenesis, gut bacteria, microbial dysbiosis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Lung cancer,MONDO:0008903,healthy volunteers,lung cancer patients,lung cancer patients with a definite postoperative pathological diagnosis,41,41,1 year,16S,12,Illumina,relative abundances,LEfSe,0.05,TRUE,4,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 5,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential abundance of fecal microbiota from patients with lung cancer and healthy volunteers,decreased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium",1783272|1239|186801;1783272|1239|909932|1843489|31977|39948;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|561;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239;3379134|1224|1236;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|541000;3379134|1224;3379134|1224|1236|91347|543|620;1783272|1239|186801|186802|1898207,Complete,Claregrieve1
bsdb:30418043/1/1,30418043,case-control,30418043,10.1556/030.65.2018.045,NA,"Muleviciene A., D'Amico F., Turroni S., Candela M. , Jankauskiene A.",Iron deficiency anemia-related gut microbiota dysbiosis in infants and young children: A pilot study,Acta microbiologica et immunologica Hungarica,2018,"children, dysbiosis, gut microbiota, infants, iron deficiency anemia",Experiment 1,Lithuania,Homo sapiens,Feces,UBERON:0001988,Iron deficiency anemia,HP:0001891,healthy control,iron deficiency anemia,infants and young children with iron deficiency anemia,10,10,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,Discriminant species-level taxa between iron deficiency anemia (IDA) infants and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium neonatale",1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|186801|186802|31979|1485|137838,Complete,ChiomaBlessing
bsdb:30418043/1/2,30418043,case-control,30418043,10.1556/030.65.2018.045,NA,"Muleviciene A., D'Amico F., Turroni S., Candela M. , Jankauskiene A.",Iron deficiency anemia-related gut microbiota dysbiosis in infants and young children: A pilot study,Acta microbiologica et immunologica Hungarica,2018,"children, dysbiosis, gut microbiota, infants, iron deficiency anemia",Experiment 1,Lithuania,Homo sapiens,Feces,UBERON:0001988,Iron deficiency anemia,HP:0001891,healthy control,iron deficiency anemia,infants and young children with iron deficiency anemia,10,10,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,Discriminant species-level taxa between iron deficiency anemia (IDA) infants and healthy controls,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|3085636|186803|189330|39486;1783272|201174|1760|85004|31953|1678|1681;1783272|1239|909932|1843489|31977|39948,Complete,ChiomaBlessing
bsdb:30446559/1/1,30446559,time series / longitudinal observational,30446559,https://doi.org/10.1128/AEM.02479-18,NA,"Parris D.J., Morgan M.M. , Stewart F.J.",Feeding Rapidly Alters Microbiome Composition and Gene Transcription in the Clownfish Gut,Applied and environmental microbiology,2019,"digestion, diurnal, feeding, food-associated microbes, gut microbiome dynamics",Experiment 1,Georgia,Premnas biaculeatus,Digestive tract,UBERON:0001555,Diet,EFO:0002755,Pre-fed group at 1100 h,Post-fed group at 1230 h,The post-fed group consists of fish fed at 1230 hours. (1.5 hours postfeeding),17,18,NA,16S,34,Illumina,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplemental Table S2,6 March 2024,Muqtadirat,"Muqtadirat,Victoria,WikiWorks",The table shows the diverse microbial groups that fluctuated in abundance over the 2-day sampling period.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Anoxybacillus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Azoarcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Balneolota|c__Balneolia|o__Balneolales|f__Balneolaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Beijerinckiaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Cryomorphaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Geobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hydrogenophaga,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Moritellaceae|g__Moritella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Streptosporangiales|f__Nocardiopsidaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Idiomarinaceae|g__Pseudidiomarina,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Psychrilyobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Psychromonadaceae|g__Psychromonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Roseinatronobacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Sporanaerobacteraceae|g__Sporanaerobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Sporosarcina,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tepidimicrobiaceae|g__Tepidimicrobium,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Ureibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Virgibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia",3379134|1224|28216|80840|506;1783272|1239|91061|1385|3120669|150247;3379134|29547|3031852|213849|2808963|28196;3379134|1224|28216|206389|2008794|12960;1783272|1239|91061|1385;1783272|1239|91061|1385|186817|1386;3379134|976|200643|171549;3379134|1936987|1853221|1853223|1813606;3379134|1224|28211|356|45404;3384189|32066|203490|203491|203492|180162;3379134|1224|1236|135613|1046;3379134|1224|1236|91347|543|544;3379134|976|117743|200644|246874;3379134|1224|1236|91347|1903409|551;1783272|1239|186801|186802;1783272|1239|91061|1385|3120669|129337;3379134|1224|28216|80840|80864|47420;1783272|1239|91061|1385|90964|227979;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|33958|1243;3379134|1224|1236|135622|267891|58050;1783272|201174|1760|85012|83676;3379134|74201|414999;3379134|1224|28211|204455|31989|265;3379134|1224|1236|135625|712;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1257;3379134|1224|1236|135623|641|657;1783272|1239|91061|1385|186818;3379134|976|200643|171549|171552|838;3379134|1224|1236|91347|1903414|583;3379134|1224|1236|135622|267893|2800384;3384189|32066|203490|203491|203492|623282;3379134|1224|1236|2887326|468|497;3379134|1224|1236|135622|267894|67572;3379134|1224|28211|204455|31989|119541;1783272|1239|1737404|1737405|2992718|165812;1783272|1239|91061|1385|186818|1569;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;1783272|1239|1737404|1737405|2992719|285105;3384194|1297|188787|68933|188786|270;1783272|1239|91061|1385|186818|160795;1783272|1239|91061|186826|81852|2737;1783272|1239|909932|1843489|31977;3379134|1224|1236|135623|641;1783272|1239|91061|1385|186817|84406;3379134|1224|1236|135614|32033;3379134|1224|1236|91347|1903411|629,Complete,Chloe
bsdb:30446559/1/2,30446559,time series / longitudinal observational,30446559,https://doi.org/10.1128/AEM.02479-18,NA,"Parris D.J., Morgan M.M. , Stewart F.J.",Feeding Rapidly Alters Microbiome Composition and Gene Transcription in the Clownfish Gut,Applied and environmental microbiology,2019,"digestion, diurnal, feeding, food-associated microbes, gut microbiome dynamics",Experiment 1,Georgia,Premnas biaculeatus,Digestive tract,UBERON:0001555,Diet,EFO:0002755,Pre-fed group at 1100 h,Post-fed group at 1230 h,The post-fed group consists of fish fed at 1230 hours. (1.5 hours postfeeding),17,18,NA,16S,34,Illumina,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Supplemental Table S2,7 March 2024,Muqtadirat,"Muqtadirat,Victoria,WikiWorks",The table shows the diverse microbial groups that fluctuated in abundance over the 2-day sampling period.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales,3379134|1224|1236|135622,Complete,Chloe
bsdb:30446559/4/1,30446559,time series / longitudinal observational,30446559,https://doi.org/10.1128/AEM.02479-18,NA,"Parris D.J., Morgan M.M. , Stewart F.J.",Feeding Rapidly Alters Microbiome Composition and Gene Transcription in the Clownfish Gut,Applied and environmental microbiology,2019,"digestion, diurnal, feeding, food-associated microbes, gut microbiome dynamics",Experiment 4,Georgia,Premnas biaculeatus,Digestive tract,UBERON:0001555,Diet,EFO:0002755,Pre-fed group at 1100 h,Post-fed group at 2000 h,The post-fed group consists of fish fed at 2000 hours. (9 hours post-feeding),17,17,NA,16S,34,Illumina,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplemental Table S2,12 April 2024,Victoria,"Victoria,WikiWorks",The table shows the diverse microbial groups that fluctuated in abundance over the 2-day sampling period.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Anoxybacillus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Azoarcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Balneolota|c__Balneolia|o__Balneolales|f__Balneolaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Beijerinckiaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Geobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hydrogenophaga,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Moritellaceae|g__Moritella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Streptosporangiales|f__Nocardiopsidaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Idiomarinaceae|g__Pseudidiomarina,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Psychrilyobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Psychromonadaceae|g__Psychromonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Roseinatronobacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Sporanaerobacteraceae|g__Sporanaerobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Sporosarcina,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tepidimicrobiaceae|g__Tepidimicrobium,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Ureibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Virgibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae",3379134|1224|28216|80840|506;1783272|1239|91061|1385|3120669|150247;3379134|29547|3031852|213849|2808963|28196;3379134|1224|28216|206389|2008794|12960;1783272|1239|91061|1385;1783272|1239|91061|1385|186817|1386;3379134|976|200643|171549;3379134|1936987|1853221|1853223|1813606;3379134|1224|28211|356|45404;3384189|32066|203490|203491|203492|180162;3379134|1224|1236|135613|1046;3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|1903409|551;1783272|1239|186801|186802;1783272|1239|91061|1385|3120669|129337;3379134|1224|28216|80840|80864|47420;1783272|1239|91061|1385|90964|227979;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|33958|1243;3379134|1224|1236|135622|267891|58050;1783272|201174|1760|85012|83676;3379134|1224|28211|204455|31989|265;3379134|1224|1236|135625|712;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1257;3379134|1224|1236|135623|641|657;1783272|1239|91061|1385|186818;3379134|976|200643|171549|171552|838;3379134|1224|1236|91347|1903414|583;3379134|1224|1236|135622|267893|2800384;3384189|32066|203490|203491|203492|623282;3379134|1224|1236|2887326|468|497;3379134|1224|1236|135622|267894|67572;3379134|1224|28211|204455|31989|119541;1783272|1239|1737404|1737405|2992718|165812;1783272|1239|91061|1385|186818|1569;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;1783272|1239|1737404|1737405|2992719|285105;3384194|1297|188787|68933|188786|270;1783272|1239|91061|1385|186818|160795;1783272|1239|91061|186826|81852|2737;1783272|1239|909932|1843489|31977;3379134|1224|1236|135623|641;1783272|1239|91061|1385|186817|84406;3379134|1224|1236|91347|1903411|629;3379134|1224|1236|135614|32033,Complete,Chloe
bsdb:30446559/4/2,30446559,time series / longitudinal observational,30446559,https://doi.org/10.1128/AEM.02479-18,NA,"Parris D.J., Morgan M.M. , Stewart F.J.",Feeding Rapidly Alters Microbiome Composition and Gene Transcription in the Clownfish Gut,Applied and environmental microbiology,2019,"digestion, diurnal, feeding, food-associated microbes, gut microbiome dynamics",Experiment 4,Georgia,Premnas biaculeatus,Digestive tract,UBERON:0001555,Diet,EFO:0002755,Pre-fed group at 1100 h,Post-fed group at 2000 h,The post-fed group consists of fish fed at 2000 hours. (9 hours post-feeding),17,17,NA,16S,34,Illumina,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Supplemental Table S2,12 April 2024,Victoria,"Victoria,WikiWorks",The table shows the diverse microbial groups that fluctuated in abundance over the 2-day sampling period.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Cryomorphaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|1224|1236|135622;3379134|976|117743|200644|246874;3379134|74201|414999;1783272|1239|91061|186826|1300|1301,Complete,Chloe
bsdb:30459320/1/1,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 1,"Ghana,United States of America",Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Obese Ghanaians(GO) + Obese Americans(UO) + Lean Americans(UL),Lean Ghanaians (GL),Participants in the Lean Ghanaians (GL) group were women from Ghana with body mass index (BMI) < 25 kg/m2,71,29,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3F and Table S4,15 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","Fold change difference of the average abundance of all phenotypic differences (i.e., African American women and obese Ghanaians) versus lean Ghanaians.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens",1783272|1239|186801|186802|31979;1783272|201174|84998|84999|84107;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171552;1783272|1239|186801|186802|216572|1263|40519;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|909932|1843489|31977;1783272|1239|186801|186802;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802;1783272|1239;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572|1263;;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|28050;1783272|201174|84998|84999|84107|102106|74426,Complete,Svetlana up
bsdb:30459320/1/2,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 1,"Ghana,United States of America",Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Obese Ghanaians(GO) + Obese Americans(UO) + Lean Americans(UL),Lean Ghanaians (GL),Participants in the Lean Ghanaians (GL) group were women from Ghana with body mass index (BMI) < 25 kg/m2,71,29,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3F and Table S4,15 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","Fold change difference of the average abundance of all phenotypic differences (i.e., African American women and obese Ghanaians) versus lean Ghanaians.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|820;3379134|200940|3031449|213115|194924|35832;3379134|200940|3031449|213115|194924;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572|216851|853;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;1783272|1239|186801|186802|216572|1263;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Svetlana up
bsdb:30459320/2/1,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 2,Ghana,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Lean Ghanaians (GL),Obese Ghanaians(GO),Participants in the Obese Ghanaians (GO) group were women from Ghana with body mass index (BMI) > 25 kg/m2.,29,21,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,age,NA,unchanged,unchanged,NA,unchanged,NA,Signature 1,Table S4,18 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","Sequences with significantly different levels across the groups: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese)",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:30459320/2/2,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 2,Ghana,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Lean Ghanaians (GL),Obese Ghanaians(GO),Participants in the Obese Ghanaians (GO) group were women from Ghana with body mass index (BMI) > 25 kg/m2.,29,21,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,age,NA,unchanged,unchanged,NA,unchanged,NA,Signature 2,Table S4,18 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","Sequences with significantly different levels across the groups: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese)",decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota,,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239;;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171550,Complete,Svetlana up
bsdb:30459320/3/1,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 3,"Ghana,United States of America",Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Obese Ghanaians(GO),Obese Americans (UO),Participants in the Obese Americans (UO) group were women from America with body mass index (BMI) > 25 kg/m2.,21,37,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,age,NA,decreased,decreased,NA,decreased,NA,Signature 1,Table S4,18 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","Sequences with significantly different levels across the groups: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese)",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|820;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|31979|1485;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572|216851|853;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|1263;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Svetlana up
bsdb:30459320/3/2,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 3,"Ghana,United States of America",Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Obese Ghanaians(GO),Obese Americans (UO),Participants in the Obese Americans (UO) group were women from America with body mass index (BMI) > 25 kg/m2.,21,37,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,age,NA,decreased,decreased,NA,decreased,NA,Signature 2,Table S4,18 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","Sequences with significantly different levels across the groups: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese)",decreased,"k__Bacillati|p__Bacillota,,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",1783272|1239;;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|84998|84999|84107;1783272|1239|909932|1843489|31977|39948;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572;3379134|1224|1236|135625|712;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|40519;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|526524|526525|2810281|191303,Complete,Svetlana up
bsdb:30459320/4/1,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Lean Americans (UL),Obese Americans(UO),Participants in the Obese Americans (UO) group were women from America with body mass index (BMI) > 25 kg/m2.,13,37,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,age,NA,unchanged,unchanged,NA,unchanged,NA,Signature 1,Table S4,18 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","Sequences with significantly different levels across the groups: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese)",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri",3379134|976|200643|171549|815|816;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|186802;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171552|2974251|165179,Complete,Svetlana up
bsdb:30459320/4/2,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Lean Americans (UL),Obese Americans(UO),Participants in the Obese Americans (UO) group were women from America with body mass index (BMI) > 25 kg/m2.,13,37,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,age,NA,unchanged,unchanged,NA,unchanged,NA,Signature 2,Table S4,18 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","Sequences with significantly different levels across the groups: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese).",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:30459320/5/1,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 5,"Ghana,United States of America",Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Lean Ghanaians(GL),Lean Americans (UL),Participants in the Lean Americans (UL) group were women from America with body mass index (BMI) < 25 kg/m2.,29,13,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,age,NA,decreased,decreased,NA,decreased,NA,Signature 1,Table S4,18 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","Sequences with significantly different levels across the groups: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese).",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|820;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|31979|1485;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572|216851|853;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|1263;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Svetlana up
bsdb:30459320/5/2,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 5,"Ghana,United States of America",Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Lean Ghanaians(GL),Lean Americans (UL),Participants in the Lean Americans (UL) group were women from America with body mass index (BMI) < 25 kg/m2.,29,13,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,age,NA,decreased,decreased,NA,decreased,NA,Signature 2,Table S4,18 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","Sequences with significantly different levels across the groups: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese).",decreased,"k__Bacillati|p__Bacillota,,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",1783272|1239;;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|84998|84999|84107;1783272|1239|909932|1843489|31977|39948;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572;3379134|1224|1236|135625|712;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|40519;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|526524|526525|2810281|191303,Complete,Svetlana up
bsdb:30459320/6/1,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 6,"Ghana,United States of America",Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Ghana Women (GL + GO),American Women (UL + UO),Participants in the American Women (UL + UO) group were women from America who were both lean and obese.,50,50,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,age,NA,decreased,decreased,NA,decreased,NA,Signature 1,Table S4,18 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","Sequences with significantly different levels across the groups: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese).",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|820;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|31979|1485;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572|216851|853;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|1263;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Svetlana up
bsdb:30459320/6/2,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 6,"Ghana,United States of America",Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Ghana Women (GL + GO),American Women (UL + UO),Participants in the American Women (UL + UO) group were women from America who were both lean and obese.,50,50,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,age,NA,decreased,decreased,NA,decreased,NA,Signature 2,Table S4,18 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","Sequences with significantly different levels across the groups: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese).",decreased,"k__Bacillati|p__Bacillota,,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",1783272|1239;;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|84998|84999|84107;1783272|1239|909932|1843489|31977|39948;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572;3379134|1224|1236|135625|712;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|40519;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|526524|526525|2810281|191303,Complete,Svetlana up
bsdb:30459320/7/1,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 7,"Ghana,United States of America",Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,All Lean Women (UL + GL),All Obese Women (UO + GO),Participants in the All Obese Women (UO + GO) group were women from both America and Ghana with body mass index (BMI) > 25 kg/m2.,42,58,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,age,NA,unchanged,unchanged,NA,unchanged,NA,Signature 1,Table S4,18 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","Sequences with significantly different levels across the groups: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese).",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Svetlana up
bsdb:30459320/7/2,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 7,"Ghana,United States of America",Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,All Lean Women (UL + GL),All Obese Women (UO + GO),Participants in the All Obese Women (UO + GO) group were women from both America and Ghana with body mass index (BMI) > 25 kg/m2.,42,58,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,age,NA,unchanged,unchanged,NA,unchanged,NA,Signature 2,Table S4,18 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","Sequences with significantly different levels across the groups: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese).",decreased,",k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|820;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:30459320/8/1,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 8,Ghana,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,Lean Ghanaians (GL) humanized mice,Obese Ghanaians(GO) humanized mice,"Mice humanized by fecal samples from participants in the Obese Ghanaians (GO) group, defined as women from Ghana with a body mass index (BMI) > 25 kg/m².",4,4,NA,16S,4,Illumina,raw counts,Linear Regression,0.001,FALSE,NA,NA,age,NA,unchanged,unchanged,NA,unchanged,NA,Signature 1,Table S15,20 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","Sequences with significantly different levels across the groups in the Murine samples: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese).",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis",1783272|1239|186801|186802;3379134|976|200643|171549|2005525|375288|823,Complete,Svetlana up
bsdb:30459320/10/1,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 10,"Ghana,United States of America",Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Obese Ghanaians(GO),Obese Americans (UO),Participants in the Obese Americans (UO) group were women from America with body mass index (BMI) > 25 kg/m2.,21,37,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,age,NA,decreased,decreased,NA,decreased,NA,Signature 1,Table S16,24 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","Human-murine co-abundance: Ghana0: Ghana lean, Ghana1: Ghana obese, USA0=USA lean, and USA1=USA obese",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|820;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:30459320/10/2,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 10,"Ghana,United States of America",Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Obese Ghanaians(GO),Obese Americans (UO),Participants in the Obese Americans (UO) group were women from America with body mass index (BMI) > 25 kg/m2.,21,37,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,age,NA,decreased,decreased,NA,decreased,NA,Signature 2,Table S16,24 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","Human-murine co-abundance: Ghana0: Ghana lean, Ghana1: Ghana obese, USA0=USA lean, and USA1=USA obese",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium celatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella",3379134|976|200643|171549|171552|2974251|165179;1783272|1239|186801|186802;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485|36834;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|52784;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|909932|1843489|31977|39948;1783272|201174|84998|84999|84107;3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|543|570,Complete,Svetlana up
bsdb:30459320/11/1,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 11,"Ghana,United States of America",Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,Lean Ghanaians(GL) humanized mice,Lean Americans (UL) humanized mice,"Mice humanized by fecal samples from participants in the Lean Americans (UL) group, defined as women from America with a body mass index (BMI) < 25 kg/m².",4,4,NA,16S,4,Illumina,raw counts,Linear Regression,0.001,FALSE,NA,NA,age,NA,unchanged,unchanged,NA,unchanged,NA,Signature 1,Table S15,20 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","Sequences with significantly different levels across the groups in the Murine samples: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese).",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",1783272|1239|186801|186802;1783272|1239|91061|186826|33958|2767887|1623;3379134|976|200643|171549|2005525|375288|823;3379134|1224|28216|80840|995019|40544,Complete,Svetlana up
bsdb:30459320/12/1,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 12,"United States of America,Ghana",Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,Lean Ghana (GL) humanized mice,Obese Americans(UO) humanized mice,"Mice humanized by fecal samples from participants in the Obese Americans (GO) group, defined as women from America with a body mass index (BMI) < 25 kg/m².",4,4,NA,16S,4,Illumina,raw counts,Linear Regression,0.001,FALSE,NA,NA,age,NA,unchanged,unchanged,NA,unchanged,NA,Signature 1,Table S15,20 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","Sequences with significantly different levels across the groups in the Murine samples: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese).",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",1783272|1239|186801|186802;3379134|1224|28216|80840|995019|40544,Complete,Svetlana up
bsdb:30459320/13/1,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 13,"Ghana,United States of America",Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,Ghana Women (GL + GO) humanized mice,American Women (UL + UO) humanized mice,Mice humanized by fecal samples from the African American women groups (UL + UO).,8,8,NA,16S,4,Illumina,raw counts,Linear Regression,0.001,FALSE,NA,NA,age,NA,unchanged,unchanged,NA,unchanged,NA,Signature 1,Table S15,20 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","Sequences with significantly different levels across the groups in the Murine samples: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese).",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis",1783272|1239|186801|186802;3379134|976|200643|171549|2005525|375288|823,Complete,Svetlana up
bsdb:30459320/14/1,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 14,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Lean Americans (UL),Obese Americans(UO),Participants in the Obese Americans (UO) group were women from America with body mass index (BMI) > 25 kg/m2.,13,37,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,age,NA,unchanged,unchanged,NA,unchanged,NA,Signature 1,Table S16,24 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","Human-murine co-abundance: Ghana0: Ghana lean, Ghana1: Ghana obese, USA0=USA lean, and USA1=USA obese",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus",1783272|201174|84998|84999|84107|102106|74426;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171552|2974251|165179;3379134|976|200643|171549|815|816;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803|33042,Complete,Svetlana up
bsdb:30459320/14/2,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 14,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Lean Americans (UL),Obese Americans(UO),Participants in the Obese Americans (UO) group were women from America with body mass index (BMI) > 25 kg/m2.,13,37,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,age,NA,unchanged,unchanged,NA,unchanged,NA,Signature 2,Table S16,24 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","Human-murine co-abundance: Ghana0: Ghana lean, Ghana1: Ghana obese, USA0=USA lean, and USA1=USA obese",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,1783272|1239|186801|186802|216572|119852,Complete,Svetlana up
bsdb:30459320/15/1,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 15,"Ghana,United States of America",Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,(Obese Ghanaians(GO) + Obese Americans(UO) + Lean Americans(UL)) humanized mice,Lean Ghanaians (GL) humanized mice,"Mice humanized by fecal samples from participants in the Lean Ghanaians (GL) group, defined as women from Ghana with a body mass index (BMI) < 25 kg/m².",12,4,NA,16S,4,Illumina,raw counts,Linear Regression,0.001,FALSE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Table S15,20 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","Sequences with significantly different levels across the groups in the Murine samples: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese).",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",1783272|1239|186801|186802;3379134|976|200643|171549|2005525|375288|823;3379134|1224|28216|80840|995019|40544,Complete,Svetlana up
bsdb:30459320/16/1,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 16,"Ghana,United States of America",Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Lean Ghanaians(GL),Lean Americans (UL),Participants in the Lean Americans (UL) group were women from America with body mass index (BMI) < 25 kg/m2.,29,13,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,age,NA,decreased,decreased,NA,decreased,NA,Signature 1,Table S16,24 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","Human-murine co-abundance: Ghana0: Ghana lean, Ghana1: Ghana obese, USA0=USA lean, and USA1=USA obese",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus pullicaecorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|3085642|580596|501571;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572|1263;3379134|200940|3031449|213115|194924|35832,Complete,Svetlana up
bsdb:30459320/16/2,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 16,"Ghana,United States of America",Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Lean Ghanaians(GL),Lean Americans (UL),Participants in the Lean Americans (UL) group were women from America with body mass index (BMI) < 25 kg/m2.,29,13,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,age,NA,decreased,decreased,NA,decreased,NA,Signature 2,Table S16,24 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","Human-murine co-abundance: Ghana0: Ghana lean, Ghana1: Ghana obese, USA0=USA lean, and USA1=USA obese",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium celatum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",1783272|1239|186801|186802|216572|52784;1783272|1239|186801|186802|31979|1485|36834;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|84998|84999|84107;1783272|1239|909932|1843489|31977|39948;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802;3379134|1224|1236|91347|543|570;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|1263|40519;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|186801|186802|31979,Complete,Svetlana up
bsdb:30459320/17/1,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 17,"Ghana,United States of America",Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Ghana Women (GL + GO),American Women (UL + UO),Participants in the American Women (UL + UO) group were women from America who were both lean and obese.,50,50,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,age,NA,decreased,decreased,NA,decreased,NA,Signature 1,Table S16,24 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","Human-murine co-abundance: Ghana0: Ghana lean, Ghana1: Ghana obese, USA0=USA lean, and USA1=USA obese",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|1263;3379134|200940|3031449|213115|194924|35832,Complete,Svetlana up
bsdb:30459320/17/2,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 17,"Ghana,United States of America",Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Ghana Women (GL + GO),American Women (UL + UO),Participants in the American Women (UL + UO) group were women from America who were both lean and obese.,50,50,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,age,NA,decreased,decreased,NA,decreased,NA,Signature 2,Table S16,24 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","Human-murine co-abundance: Ghana0: Ghana lean, Ghana1: Ghana obese, USA0=USA lean, and USA1=USA obese",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium celatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella",3379134|976|200643|171549|171552|2974251|165179;1783272|1239|186801|186802;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485|36834;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|52784;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|909932|1843489|31977|39948;1783272|201174|84998|84999|84107;1783272|201174|84998|84999|84107|102106|74426;3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|543|570,Complete,Svetlana up
bsdb:30459320/18/1,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 18,"Ghana,United States of America",Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,All Lean Women (UL + GL),All Obese Women (UO + GO),Participants in the All Obese Women (UO + GO) group were women from both America and Ghana with body mass index (BMI) > 25 kg/m2.,42,58,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,age,NA,unchanged,unchanged,NA,unchanged,NA,Signature 1,Table S16,24 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","Human-murine co-abundance: Ghana0: Ghana lean, Ghana1: Ghana obese, USA0=USA lean, and USA1=USA obese",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus pullicaecorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|3085642|580596|501571;1783272|1239|186801|186802|216572|1263;1783272|201174|84998|84999|84107|102106|74426,Complete,Svetlana up
bsdb:30459320/18/2,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 18,"Ghana,United States of America",Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,All Lean Women (UL + GL),All Obese Women (UO + GO),Participants in the All Obese Women (UO + GO) group were women from both America and Ghana with body mass index (BMI) > 25 kg/m2.,42,58,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,age,NA,unchanged,unchanged,NA,unchanged,NA,Signature 2,Table S16,24 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","Human-murine co-abundance: Ghana0: Ghana lean, Ghana1: Ghana obese, USA0=USA lean, and USA1=USA obese",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|186802;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:30459320/19/1,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 19,"Ghana,United States of America",Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Obese Ghanaians(GO) + Obese Americans(UO) + Lean Americans(UL),Lean Ghanaians (GL),Participants in the Lean Ghanaians (GL) group were women from Ghana with body mass index (BMI) < 25 kg/m2,71,29,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Table S16,24 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","Human-murine co-abundance: Ghana0: Ghana lean, Ghana1: Ghana obese, USA0=USA lean, and USA1=USA obese",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium celatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella",3379134|976|200643|171549|171552|2974251|165179;1783272|1239|186801|186802;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485|36834;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|52784;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|909932|1843489|31977|39948;1783272|201174|84998|84999|84107;1783272|201174|84998|84999|84107|102106|74426;3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|543|570,Complete,Svetlana up
bsdb:30459320/19/2,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 19,"Ghana,United States of America",Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Obese Ghanaians(GO) + Obese Americans(UO) + Lean Americans(UL),Lean Ghanaians (GL),Participants in the Lean Ghanaians (GL) group were women from Ghana with body mass index (BMI) < 25 kg/m2,71,29,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 2,Table S16,24 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","Human-murine co-abundance: Ghana0: Ghana lean, Ghana1: Ghana obese, USA0=USA lean, and USA1=USA obese",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus pullicaecorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|820;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|3085642|580596|501571;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|216851|853,Complete,Svetlana up
bsdb:30459320/20/1,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 20,"Ghana,United States of America",Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Lean Ghanaian women (GL),Obese American women(UO),"Participants in the Obese Americans (GO) group, defined as women from America with a body mass index (BMI) < 25 kg/m².",29,37,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,age,NA,unchanged,unchanged,NA,unchanged,NA,Signature 1,Table S16,24 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","Human-murine co-abundance: Ghana0: Ghana lean, Ghana1: Ghana obese, USA0=USA lean, and USA1=USA obese",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus pullicaecorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|820;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|3085642|580596|501571;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|216572|1263,Complete,Svetlana up
bsdb:30459320/20/2,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 20,"Ghana,United States of America",Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Lean Ghanaian women (GL),Obese American women(UO),"Participants in the Obese Americans (GO) group, defined as women from America with a body mass index (BMI) < 25 kg/m².",29,37,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,age,NA,unchanged,unchanged,NA,unchanged,NA,Signature 2,Table S16,24 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","Human-murine co-abundance: Ghana0: Ghana lean, Ghana1: Ghana obese, USA0=USA lean, and USA1=USA obese",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium celatum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri",1783272|1239|186801|186802|216572|52784;1783272|1239|186801|186802|31979|1485|36834;1783272|201174|84998|84999|84107;1783272|1239|909932|1843489|31977|39948;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802;3379134|1224|1236|91347|543|570;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|1263|40519;3379134|976|200643|171549|171552|2974251|165179,Complete,Svetlana up
bsdb:30459320/21/1,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 21,Ghana,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,Lean Ghanaians (GL) humanized mice,Obese Ghanaians(GO) humanized mice,"Mice humanized by fecal samples from participants in the Obese Ghanaians (GO) group, defined as women from Ghana with a body mass index (BMI) > 25 kg/m².",4,4,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,age,NA,unchanged,unchanged,NA,unchanged,NA,Signature 1,Table S16,24 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","Human-murine co-abundance: Ghana0: Ghana lean, Ghana1: Ghana obese, USA0=USA lean, and USA1=USA obese",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis",3379134|976|200643|171549|815|816|85831;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958|2767887|1623;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|1263;3379134|1224|28216|80840|995019|40544;3379134|976|200643|171549|2005525|375288|823,Complete,Svetlana up
bsdb:30459320/21/2,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 21,Ghana,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,Lean Ghanaians (GL) humanized mice,Obese Ghanaians(GO) humanized mice,"Mice humanized by fecal samples from participants in the Obese Ghanaians (GO) group, defined as women from Ghana with a body mass index (BMI) > 25 kg/m².",4,4,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,age,NA,unchanged,unchanged,NA,unchanged,NA,Signature 2,Table S16,24 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","Human-murine co-abundance: Ghana0: Ghana lean, Ghana1: Ghana obese, USA0=USA lean, and USA1=USA obese",decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,3379134|976|200643|171549|815|816|47678,Complete,Svetlana up
bsdb:30459320/22/1,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 22,"Ghana,United States of America",Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,Obese Ghanaians(GO),Obese Americans (UO),Mice humanized by fecal samples from participants in the Obese Americans (UO) group defined as women from America with body mass index (BMI) > 25 kg/m2.,4,4,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,age,NA,decreased,decreased,NA,decreased,NA,Signature 1,Table S16,24 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","Human-murine co-abundance: Ghana0: Ghana lean, Ghana1: Ghana obese, USA0=USA lean, and USA1=USA obese",increased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,3379134|1224|28216|80840|995019|40544,Complete,Svetlana up
bsdb:30459320/22/2,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 22,"Ghana,United States of America",Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,Obese Ghanaians(GO),Obese Americans (UO),Mice humanized by fecal samples from participants in the Obese Americans (UO) group defined as women from America with body mass index (BMI) > 25 kg/m2.,4,4,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,age,NA,decreased,decreased,NA,decreased,NA,Signature 2,Table S16,24 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","Human-murine co-abundance: Ghana0: Ghana lean, Ghana1: Ghana obese, USA0=USA lean, and USA1=USA obese",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae|g__Defluviitalea|s__Defluviitalea saccharophila,1783272|1239|186801|3085636|1185407|1185408|879970,Complete,Svetlana up
bsdb:30459320/23/1,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 23,"Ghana,United States of America",Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,Lean Ghanaians(GL) humanized mice,Lean Americans (UL) humanized mice,"Mice humanized by fecal samples from participants in the Lean Americans (UL) group, defined as women from America with a body mass index (BMI) < 25 kg/m².",4,4,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,age,NA,unchanged,unchanged,NA,unchanged,NA,Signature 1,Table S16,24 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","Human-murine co-abundance: Ghana0: Ghana lean, Ghana1: Ghana obese, USA0=USA lean, and USA1=USA obese",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|976|200643|171549|815|816|85831;1783272|1239|186801|186802;1783272|1239|91061|186826|33958|2767887|1623;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|1263;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:30459320/23/2,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 23,"Ghana,United States of America",Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,Lean Ghanaians(GL) humanized mice,Lean Americans (UL) humanized mice,"Mice humanized by fecal samples from participants in the Lean Americans (UL) group, defined as women from America with a body mass index (BMI) < 25 kg/m².",4,4,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,age,NA,unchanged,unchanged,NA,unchanged,NA,Signature 2,Table S16,24 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","Human-murine co-abundance: Ghana0: Ghana lean, Ghana1: Ghana obese, USA0=USA lean, and USA1=USA obese",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae|g__Defluviitalea|s__Defluviitalea saccharophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239|186801|3085636|1185407|1185408|879970;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|186802,Complete,Svetlana up
bsdb:30459320/24/1,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 24,"Ghana,United States of America",Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,Lean Ghana (GL) humanized mice,Obese Americans(UO) humanized mice,"Mice humanized by fecal samples from participants in the Obese Americans (GO) group, defined as women from America with a body mass index (BMI) < 25 kg/m².",4,4,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,age,NA,unchanged,unchanged,NA,unchanged,NA,Signature 1,Table S16,24 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","Human-murine co-abundance: Ghana0: Ghana lean, Ghana1: Ghana obese, USA0=USA lean, and USA1=USA obese",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis",3379134|976|200643|171549|815|816|85831;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171550;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|33958|2767887|1623,Complete,Svetlana up
bsdb:30459320/24/2,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 24,"Ghana,United States of America",Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,Lean Ghana (GL) humanized mice,Obese Americans(UO) humanized mice,"Mice humanized by fecal samples from participants in the Obese Americans (GO) group, defined as women from America with a body mass index (BMI) < 25 kg/m².",4,4,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,age,NA,unchanged,unchanged,NA,unchanged,NA,Signature 2,Table S16,24 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","Human-murine co-abundance: Ghana0: Ghana lean, Ghana1: Ghana obese, USA0=USA lean, and USA1=USA obese",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae|g__Defluviitalea|s__Defluviitalea saccharophila,1783272|1239|186801|3085636|1185407|1185408|879970,Complete,Svetlana up
bsdb:30459320/25/1,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 25,"Ghana,United States of America",Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,Ghana Women (GL + GO) humanized mice,American Women (UL + UO) humanized mice,Mice humanized by fecal samples from the African American women groups (UL + UO).,8,8,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,age,NA,unchanged,unchanged,NA,unchanged,NA,Signature 1,Table S16,24 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","Human-murine co-abundance: Ghana0: Ghana lean, Ghana1: Ghana obese, USA0=USA lean, and USA1=USA obese",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis",3379134|976|200643|171549|815|816|85831;3379134|976|200643|171549|2005525|375288|823;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958|2767887|1623,Complete,Svetlana up
bsdb:30459320/25/2,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 25,"Ghana,United States of America",Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,Ghana Women (GL + GO) humanized mice,American Women (UL + UO) humanized mice,Mice humanized by fecal samples from the African American women groups (UL + UO).,8,8,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,age,NA,unchanged,unchanged,NA,unchanged,NA,Signature 2,Table S16,24 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","Human-murine co-abundance: Ghana0: Ghana lean, Ghana1: Ghana obese, USA0=USA lean, and USA1=USA obese",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae|g__Defluviitalea|s__Defluviitalea saccharophila",1783272|1239|186801|186802;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|1185407|1185408|879970,Complete,Svetlana up
bsdb:30459320/26/1,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 26,United States of America,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,Lean Americans (UL),Obese Americans(UO),Mice humanized by fecal samples from participants in the Obese Americans (UO) group defined as women from America with body mass index (BMI) > 25 kg/m2.,4,4,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,age,NA,unchanged,unchanged,NA,unchanged,NA,Signature 1,Table S16,24 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","Human-murine co-abundance: Ghana0: Ghana lean, Ghana1: Ghana obese, USA0=USA lean, and USA1=USA obese",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239|186801|3085636|186803|2316020|33038;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802,Complete,Svetlana up
bsdb:30459320/26/2,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 26,United States of America,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,Lean Americans (UL),Obese Americans(UO),Mice humanized by fecal samples from participants in the Obese Americans (UO) group defined as women from America with body mass index (BMI) > 25 kg/m2.,4,4,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,age,NA,unchanged,unchanged,NA,unchanged,NA,Signature 2,Table S16,24 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","Human-murine co-abundance: Ghana0: Ghana lean, Ghana1: Ghana obese, USA0=USA lean, and USA1=USA obese",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,1783272|1239|186801|186802,Complete,Svetlana up
bsdb:30459320/27/1,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 27,"Ghana,United States of America",Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,(Obese Ghanaians(GO) + Obese Americans(UO) + Lean Americans(UL)) humanized mice,Lean Ghanaians (GL) humanized mice,"Mice humanized by fecal samples from participants in the Lean Ghanaians (GL) group, defined as women from Ghana with a body mass index (BMI) < 25 kg/m².",12,4,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Table S16,24 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","Human-murine co-abundance: Ghana0: Ghana lean, Ghana1: Ghana obese, USA0=USA lean, and USA1=USA obese",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae|g__Defluviitalea|s__Defluviitalea saccharophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",3379134|976|200643|171549|815|816|47678;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|1185407|1185408|879970;1783272|1239|186801|186802|216572|119852,Complete,Svetlana up
bsdb:30459320/27/2,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 27,"Ghana,United States of America",Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,(Obese Ghanaians(GO) + Obese Americans(UO) + Lean Americans(UL)) humanized mice,Lean Ghanaians (GL) humanized mice,"Mice humanized by fecal samples from participants in the Lean Ghanaians (GL) group, defined as women from Ghana with a body mass index (BMI) < 25 kg/m².",12,4,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 2,Table S16,24 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","Human-murine co-abundance: Ghana0: Ghana lean, Ghana1: Ghana obese, USA0=USA lean, and USA1=USA obese",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis",3379134|976|200643|171549|815|816|85831;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171550;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|33958|2767887|1623,Complete,Svetlana up
bsdb:30459320/28/1,30459320,"cross-sectional observational, not case-control",30459320,10.1038/s41598-018-35230-9,https://pubmed.ncbi.nlm.nih.gov/30459320/,"Dugas L.R., Bernabé B.P., Priyadarshini M., Fei N., Park S.J., Brown L., Plange-Rhule J., Nelson D., Toh E.C., Gao X., Dong Q., Sun J., Kliethermes S., Gottel N., Luke A., Gilbert J.A. , Layden B.T.",Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women,Scientific reports,2018,NA,Experiment 28,"Ghana,United States of America",Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,All Lean Women (UL + GL) humanized mice,All Obese Women (UO + GO) humanized mice,Mice humanized by fecal samples from participants in the All Obese Women (UO + GO) group defined as women from both America and Ghana with body mass index (BMI) > 25 kg/m2.,8,8,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,age,NA,unchanged,unchanged,NA,unchanged,NA,Signature 1,Table S16,24 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","Human-murine co-abundance: Ghana0: Ghana lean, Ghana1: Ghana obese, USA0=USA lean, and USA1=USA obese",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis",3379134|976|200643|171549|815|816|85831;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|33958|2767887|1623,Complete,Svetlana up
bsdb:30459400/1/1,30459400,case-control,30459400,10.1038/s41598-018-35473-6,NA,"Chen B., Zhao Y., Li S., Yang L., Wang H., Wang T., Bin Shi Z., Gai X., Heng C., Zhang J., Yang L. , Zhang .",Variations in oral microbiome profiles in rheumatoid arthritis and osteoarthritis with potential biomarkers for arthritis screening,Scientific reports,2018,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,"Osteoarthritis,Rheumatoid arthritis","MONDO:0005178,EFO:0000685",healthy controls,arthritis patient,arthritis,155,177,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,"Figure 2, text",16 August 2021,Tislam,"Tislam,WikiWorks","(c) Histogram of the LDA scores, where the LDA score indicates the effective size and ranking of each differentially abundant taxon (LDA > 2).",increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3384189|32066|203490|203491|203492|848;3379134|1224|28216|80840|119060|47670;3384189|32066|203490|203491|1129771|32067;1783272|1239|91061|186826|186828|117563;1783272|201174|1760|2037|2049|1654;1783272|1239|91061|186826|1300|1301;1783272|201174|1760|85006|1268|32207;3379134|1224|1236|135625|712|724;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|909932|1843489|31977|29465;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838|28132;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|838,Complete,Chloe
bsdb:30459400/1/2,30459400,case-control,30459400,10.1038/s41598-018-35473-6,NA,"Chen B., Zhao Y., Li S., Yang L., Wang H., Wang T., Bin Shi Z., Gai X., Heng C., Zhang J., Yang L. , Zhang .",Variations in oral microbiome profiles in rheumatoid arthritis and osteoarthritis with potential biomarkers for arthritis screening,Scientific reports,2018,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,"Osteoarthritis,Rheumatoid arthritis","MONDO:0005178,EFO:0000685",healthy controls,arthritis patient,arthritis,155,177,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,"Figure 2, text",16 August 2021,Tislam,"Tislam,WikiWorks","(c) Histogram of the LDA scores, where the LDA score indicates the effective size and ranking of each differentially abundant taxon (LDA > 2).",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Wautersiella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas|s__Brevundimonas diminuta,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas yabuuchiae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Mycoplana",3379134|1224|1236|2887326|468|469;3379134|976|117743|200644|2762318|59732;3379134|1224|1236|72274|135621|286;3379134|1224|28211|356|212791;3379134|1224|1236|135614|32033|40323;3379134|1224|28211|204457|41297|13687;3379134|976|117743|200644|2762318|343873;3379134|1224|28211|204458|76892|41275|293;3379134|976|200643|171549|815|816;3379134|1224|28216|80840|80864|283;3379134|1224|28211|204457|41297|13687|172044;3379134|1224|28211|356|82115|13159,Complete,Chloe
bsdb:30459400/2/1,30459400,case-control,30459400,10.1038/s41598-018-35473-6,NA,"Chen B., Zhao Y., Li S., Yang L., Wang H., Wang T., Bin Shi Z., Gai X., Heng C., Zhang J., Yang L. , Zhang .",Variations in oral microbiome profiles in rheumatoid arthritis and osteoarthritis with potential biomarkers for arthritis screening,Scientific reports,2018,NA,Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,"Osteoarthritis,Rheumatoid arthritis","MONDO:0005178,EFO:0000685",Osteoarthritis,rheumatoid arthritis,patient with rheumatoid arthritis,67,110,NA,16S,NA,Illumina,NA,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2, text",17 August 2021,Tislam,"Tislam,WikiWorks","c) Histogram of the LDA scores, where
the LDA score indicates the efective size and ranking of each diferentially abundant taxon (LDA>2).",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",3379134|1224|1236|135625|712|724|735;3379134|1224|1236|135625|712|713;3379134|1224|1236|135625|712|416916;3379134|976|200643|171549|171552|1283313|76122;3384189|32066|203490|203491|203492|848;1783272|1239|909932|1843489|31977|29465;3379134|976|200643|171549|171552|838;1783272|1239|909932|1843489|31977|29465|39778;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712|724|729;3379134|1224|28216|206351|481|482|28449;3379134|1224|28216|206351|481|482,Complete,Chloe
bsdb:30459400/2/2,30459400,case-control,30459400,10.1038/s41598-018-35473-6,NA,"Chen B., Zhao Y., Li S., Yang L., Wang H., Wang T., Bin Shi Z., Gai X., Heng C., Zhang J., Yang L. , Zhang .",Variations in oral microbiome profiles in rheumatoid arthritis and osteoarthritis with potential biomarkers for arthritis screening,Scientific reports,2018,NA,Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,"Osteoarthritis,Rheumatoid arthritis","MONDO:0005178,EFO:0000685",Osteoarthritis,rheumatoid arthritis,patient with rheumatoid arthritis,67,110,NA,16S,NA,Illumina,NA,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2,17 August 2021,Tislam,"Tislam,WikiWorks","(c) Histogram of the LDA scores, where the LDA score indicates the efective size and ranking of each diferentially abundant taxon (LDA>2).",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia",1783272|1239|91061|186826|1300|1301;1783272|201174|1760|2037|2049|1654;3379134|1224|28216|80840|119060|47670;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|186826|186828|117563;1783272|201174|1760|85006|1268|32207|2047;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|91061|186826|186827|46123,Complete,Chloe
bsdb:30463989/1/1,30463989,time series / longitudinal observational,30463989,10.1158/1940-6207.CAPR-18-0233,NA,"Ritu W., Enqi W., Zheng S., Wang J., Ling Y. , Wang Y.","Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women","Cancer prevention research (Philadelphia, Pa.)",2019,NA,Experiment 1,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,Baseline HPV-,Baseline HPV+,HPV+ confirmed by HPV assay and genotyping,43,90,2 weeks,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,unchanged,NA,unchanged,Signature 1,Figure 3,10 January 2021,Cynthia Anderson,WikiWorks,Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status,increased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma",1783272|544448|31969;1783272|544448;1783272|544448|31969|2085;1783272|544448|31969|2085|2092;1783272|544448|2790996|2790998|2129,Complete,Fatima Zohra
bsdb:30463989/1/2,30463989,time series / longitudinal observational,30463989,10.1158/1940-6207.CAPR-18-0233,NA,"Ritu W., Enqi W., Zheng S., Wang J., Ling Y. , Wang Y.","Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women","Cancer prevention research (Philadelphia, Pa.)",2019,NA,Experiment 1,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,Baseline HPV-,Baseline HPV+,HPV+ confirmed by HPV assay and genotyping,43,90,2 weeks,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,unchanged,NA,unchanged,Signature 2,figure 3,10 January 2021,Cynthia Anderson,"WikiWorks,Merit",Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae,k__Thermotogati|p__Deinococcota|c__Deinococci,k__Thermotogati|p__Deinococcota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Ectothiorhodospiraceae,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Rickettsiella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales",3379134|1224|1236|118969|118968;3384194|1297|188787;3384194|1297;3379134|1224|1236|135613|72276;1783272|1239|1737404|1582879;1783272|1239|186801|186802|216572|216851;3384189|32066|203490|203491|203492;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|186820;3379134|1224|1236|118969|118968|873565;3384189|32066|203490|203491,Complete,Fatima Zohra
bsdb:30463989/2/1,30463989,time series / longitudinal observational,30463989,10.1158/1940-6207.CAPR-18-0233,NA,"Ritu W., Enqi W., Zheng S., Wang J., Ling Y. , Wang Y.","Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women","Cancer prevention research (Philadelphia, Pa.)",2019,NA,Experiment 2,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,no new acquisition of HPV within a year,new acquisition of HPV within a year,New HPV-type acquisition confirmed by HPV assay and genotyping,109,24,2 weeks,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,figure 3,10 January 2021,Cynthia Anderson,WikiWorks,Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,1783272|201174|1760|2037|2049|1654,Complete,Fatima Zohra
bsdb:30463989/3/1,30463989,time series / longitudinal observational,30463989,10.1158/1940-6207.CAPR-18-0233,NA,"Ritu W., Enqi W., Zheng S., Wang J., Ling Y. , Wang Y.","Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women","Cancer prevention research (Philadelphia, Pa.)",2019,NA,Experiment 3,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,with at least one HPV type cleared in a year,without any HPV type cleared,No HPV-type cleared confirmed by HPV assay and genotyping,75,15,2 weeks,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,figure 3,10 January 2021,Cynthia Anderson,WikiWorks,Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales",3379134|1224|28211|204455|31989;3379134|1224|28211|204455,Complete,Fatima Zohra
bsdb:30463989/4/1,30463989,time series / longitudinal observational,30463989,10.1158/1940-6207.CAPR-18-0233,NA,"Ritu W., Enqi W., Zheng S., Wang J., Ling Y. , Wang Y.","Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women","Cancer prevention research (Philadelphia, Pa.)",2019,NA,Experiment 4,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ confirmed by HPV assay and genotyping,43,90,2 weeks,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,figure 3,10 January 2021,Cynthia Anderson,WikiWorks,Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status at the OTU level,increased,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma parvum,1783272|544448|2790996|2790998|2129|134821,Complete,Fatima Zohra
bsdb:30463989/4/2,30463989,time series / longitudinal observational,30463989,10.1158/1940-6207.CAPR-18-0233,NA,"Ritu W., Enqi W., Zheng S., Wang J., Ling Y. , Wang Y.","Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women","Cancer prevention research (Philadelphia, Pa.)",2019,NA,Experiment 4,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ confirmed by HPV assay and genotyping,43,90,2 weeks,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,figure 3,10 January 2021,Cynthia Anderson,WikiWorks,Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status at the OTU level,decreased,"k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella|s__Ezakiella massiliensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa",1783272|1239|1737404|1582879|1852374;3379134|1224|1236|72274|135621|286|287,Complete,Fatima Zohra
bsdb:30463989/5/1,30463989,time series / longitudinal observational,30463989,10.1158/1940-6207.CAPR-18-0233,NA,"Ritu W., Enqi W., Zheng S., Wang J., Ling Y. , Wang Y.","Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women","Cancer prevention research (Philadelphia, Pa.)",2019,NA,Experiment 5,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,no new acquisition of HPV within a year,new acquisition of HPV within a year,New HPV-type acquisition confirmed by HPV assay and genotyping,109,24,2 weeks,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,figure 3,10 January 2021,Cynthia Anderson,WikiWorks,Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status at the OTU level,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oulorum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus",3379134|976|200643|171549|171552|1283313|76122;3379134|976|200643|171549|171552|838|28133;3379134|976|200643|171549|171552|2974251|28136;1783272|1239|909932|1843489|31977|39948|218538,Complete,Fatima Zohra
bsdb:30463989/6/1,30463989,time series / longitudinal observational,30463989,10.1158/1940-6207.CAPR-18-0233,NA,"Ritu W., Enqi W., Zheng S., Wang J., Ling Y. , Wang Y.","Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women","Cancer prevention research (Philadelphia, Pa.)",2019,NA,Experiment 6,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,with any HPV type cleared in a year,without any HPV type cleared,No HPV-type cleared confirmed by HPV assay and genotyping,75,15,2 weeks,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,figure 3,10 January 2021,Cynthia Anderson,WikiWorks,Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status at the OTU level,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemelliphila|s__Gemelliphila asaccharolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Pseudomonadati|p__Myxococcota|o__Polyangiales|f__Labilitrichaceae|g__Labilithrix|s__Labilithrix luteola,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnotalea|s__Lachnotalea glycerini",1783272|1239|91061|1385|539738|3076174|502393;3379134|976|200643|171549|171552|838|419005;3379134|2818505|3031712|1524216|1524217|1391654;1783272|1239|186801|3085636|186803|1763508|1763509,Complete,Fatima Zohra
bsdb:30463989/7/1,30463989,time series / longitudinal observational,30463989,10.1158/1940-6207.CAPR-18-0233,NA,"Ritu W., Enqi W., Zheng S., Wang J., Ling Y. , Wang Y.","Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women","Cancer prevention research (Philadelphia, Pa.)",2019,NA,Experiment 7,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,no HPV type persisted,at least one HPV type persisted,Any HPV-type persisted confirmed by HPV assay and genotyping,64,29,2 weeks,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,figure 3,10 January 2021,Cynthia Anderson,WikiWorks,Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status at the OTU level,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Microvirga|s__Microvirga lupini,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus radiopugnans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerobacterium|s__Anaerobacterium chartisolvens",3379134|976|200643|171549|171552|2974257|386414;3379134|1224|28211|356|119045|186650|420324;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|186801|3085636|186803|3569723|410072;3384194|1297|188787|118964|183710|1298|1182571;1783272|1239|186801|186802|216572|1486725|1297424,Complete,Fatima Zohra
bsdb:30463989/7/2,30463989,time series / longitudinal observational,30463989,10.1158/1940-6207.CAPR-18-0233,NA,"Ritu W., Enqi W., Zheng S., Wang J., Ling Y. , Wang Y.","Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women","Cancer prevention research (Philadelphia, Pa.)",2019,NA,Experiment 7,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,no HPV type persisted,at least one HPV type persisted,Any HPV-type persisted confirmed by HPV assay and genotyping,64,29,2 weeks,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,figure 3,10 January 2021,Cynthia Anderson,WikiWorks,Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status at the OTU level,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus delbrueckii,1783272|1239|91061|186826|33958|1578|1584,Complete,Fatima Zohra
bsdb:30466372/1/1,30466372,laboratory experiment,30466372,10.1080/1028415X.2018.1537169,NA,"Reichelt A.C., Loughman A., Bernard A., Raipuria M., Abbott K.N., Dachtler J., Van T.T.H. , Moore R.J.","An intermittent hypercaloric diet alters gut microbiota, prefrontal cortical gene expression and social behaviours in rats",Nutritional neuroscience,2018,"Adolescence, Diet, Memory, Microbiota, Obesity, Social interaction",Experiment 1,Australia,Rattus norvegicus,Feces,UBERON:0001988,Obesity,EFO:0001073,control rats,Rats fed  HFHS,NA,8,8,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 3a & 3b,10 January 2021,Marianthi Thomatos,WikiWorks,Relative abundance of rats fed high fat and high surgar diet (HFHS) VS. Controls,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum",1783272|1239|186801|3085636|186803|572511;1783272|201174|1760|85004|31953|1678;1783272|1239|909932|1843488|909930|33024;1783272|1239|526524|526525|128827|174708,Complete,Shaimaa Elsafoury
bsdb:30478001/1/1,30478001,randomized controlled trial,30478001,10.1016/j.ebiom.2018.11.035,NA,"Wei S., Mortensen M.S., Stokholm J., Brejnrod A.D., Thorsen J., Rasmussen M.A., Trivedi U., Bisgaard H. , Sørensen S.J.","Short- and long-term impacts of azithromycin treatment on the gut microbiota in children: A double-blind, randomized, placebo-controlled trial",EBioMedicine,2018,"Antibiotics, Asthma, Azithromycin, Children, Gut microbiota, RCT",Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Azithromycin,CHEBI:2955,The group given a placebo,The group given an azithromycin oral solution,"1-3-year-olds diagnosed with recurrent asthma-like symptoms from the COPSAC2010 cohort. Exclusion criteria included macrolide allergy, heart, liver, neurological, kidney disease, and or one or more clinical signs of pneumonia. Participants were prescribed a 3-day course of oral azithromycin solution of 10mg/kg per day.",33,39,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Supplementary table 2,24 September 2021,Gina,"Gina,WikiWorks",Short term effects: the relative abundance of significant taxa between groups at different phylogenetic levels.,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__uncultured Bifidobacterium sp.",1783272|201174;1783272|201174|1760|85004;1783272|1239;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678|165187,Complete,NA
bsdb:30478001/1/2,30478001,randomized controlled trial,30478001,10.1016/j.ebiom.2018.11.035,NA,"Wei S., Mortensen M.S., Stokholm J., Brejnrod A.D., Thorsen J., Rasmussen M.A., Trivedi U., Bisgaard H. , Sørensen S.J.","Short- and long-term impacts of azithromycin treatment on the gut microbiota in children: A double-blind, randomized, placebo-controlled trial",EBioMedicine,2018,"Antibiotics, Asthma, Azithromycin, Children, Gut microbiota, RCT",Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Azithromycin,CHEBI:2955,The group given a placebo,The group given an azithromycin oral solution,"1-3-year-olds diagnosed with recurrent asthma-like symptoms from the COPSAC2010 cohort. Exclusion criteria included macrolide allergy, heart, liver, neurological, kidney disease, and or one or more clinical signs of pneumonia. Participants were prescribed a 3-day course of oral azithromycin solution of 10mg/kg per day.",33,39,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Supplementary table 2,24 September 2021,Gina,"Gina,WikiWorks",Short term effect: the relative abundance of significant taxa between groups at different phylogenetic levels.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor",1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|946234,Complete,NA
bsdb:30483228/1/1,30483228,case-control,30483228,10.3389/fmicb.2018.02682,NA,"Guo C., Li Y., Wang P., Li Y., Qiu C., Li M., Wang D., Zhao R., Li D., Wang Y., Li S., Dai W. , Zhang L.",Alterations of Gut Microbiota in Cholestatic Infants and Their Correlation With Hepatic Function,Frontiers in microbiology,2018,"16S rRNA, bacterial biomarkers, co-abundance network, hepatic function, infantile cholestasis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Extrahepatic cholestasis,EFO:1000933,healthy infants,cholestasis infants,NA,37,43,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 2+ text,10 January 2021,Christina Brown,WikiWorks,Differentially abundundant gut microbiota in cholestatic infants vs healthy infants,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|1385|90964|1279;1783272|1239|909932|1843489|31977|906;3379134|1224|28211|356|69277|28100;1783272|1239|909932|909929|1843491|158846,Complete,Shaimaa Elsafoury
bsdb:30483228/1/2,30483228,case-control,30483228,10.3389/fmicb.2018.02682,NA,"Guo C., Li Y., Wang P., Li Y., Qiu C., Li M., Wang D., Zhao R., Li D., Wang Y., Li S., Dai W. , Zhang L.",Alterations of Gut Microbiota in Cholestatic Infants and Their Correlation With Hepatic Function,Frontiers in microbiology,2018,"16S rRNA, bacterial biomarkers, co-abundance network, hepatic function, infantile cholestasis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Extrahepatic cholestasis,EFO:1000933,healthy infants,cholestasis infants,NA,37,43,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 2 + text,10 January 2021,Christina Brown,WikiWorks,Differentially abundundant gut microbiota in cholestatic infants vs healthy infants,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|207244;1783272|201174|84998|84999|84107|102106,Complete,Shaimaa Elsafoury
bsdb:30488079/1/1,30488079,time series / longitudinal observational,30488079,10.11622/smedj.2018152,https://pubmed.ncbi.nlm.nih.gov/30488079/,"Koo S.H., Deng J., Ang D.S.W., Hsiang J.C., Lee L.S., Aazmi S., Mohamed E.H.M., Yang H., Yap S.Y., Teh L.K., Salleh M.Z., Lee E.J.D. , Ang T.L.",Effects of proton pump inhibitor on the human gut microbiome profile in multi-ethnic groups in Singapore,Singapore medical journal,2019,"gastroesophageal reflux disease, gastrointestinal microbiome, omeprazole",Experiment 1,Singapore,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Day 1 participants,Day 7 participants,The day participants stopped the course of Omeprazole at therapeutic dose (20mg daily),34,34,1 month,16S,34,Illumina,relative abundances,"Kruskall-Wallis,LEfSe",0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,increased,Signature 1,Fig 5a (3rd Cladogram),6 March 2024,Deacme,"Deacme,ChiomaBlessing,WikiWorks",Significant taxa abundance in participants at Day 7 after a course of Omeprazole (20 mg) compared to Day 1,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella montpellierensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Lelliottia|s__Lelliottia amnigena,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter ludwigii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella denticariosi,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella|s__Johnsonella ignava,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia",1783272|1239|91061;1783272|1239|186801|3085636|186803|43994;1783272|1239|91061|186826;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|909932|1843489|31977|29465|187328;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|91061|186826|1300|1301|1343;1783272|1239|91061|186826|33958|2767887|1624;3379134|1224|1236|91347|543|1330545|61646;3379134|1224|1236|91347|543|547|299767;3379134|1224|1236|91347|543|547;3379134|1224|1236|135625|712|724|729;3379134|1224|1236|135625|712;3379134|1224|1236|135625;1783272|1239|909932|1843489|31977|29465|419208;1783272|1239|186801|3085636|186803|43994|43995;3379134|976|200643|171549|171552|838|28125,Complete,ChiomaBlessing
bsdb:30488079/1/2,30488079,time series / longitudinal observational,30488079,10.11622/smedj.2018152,https://pubmed.ncbi.nlm.nih.gov/30488079/,"Koo S.H., Deng J., Ang D.S.W., Hsiang J.C., Lee L.S., Aazmi S., Mohamed E.H.M., Yang H., Yap S.Y., Teh L.K., Salleh M.Z., Lee E.J.D. , Ang T.L.",Effects of proton pump inhibitor on the human gut microbiome profile in multi-ethnic groups in Singapore,Singapore medical journal,2019,"gastroesophageal reflux disease, gastrointestinal microbiome, omeprazole",Experiment 1,Singapore,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Day 1 participants,Day 7 participants,The day participants stopped the course of Omeprazole at therapeutic dose (20mg daily),34,34,1 month,16S,34,Illumina,relative abundances,"Kruskall-Wallis,LEfSe",0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,increased,Signature 2,Fig 5a (3rd Cladogram),6 March 2024,Deacme,"Deacme,ChiomaBlessing,WikiWorks",Significant taxa abundance in participants at Day 7 after a course of Omeprazole (20 mg) compared to Day 1,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella tanakaei,k__Bacillati|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria",1783272|201174|84998|84999|84107|102106|626935;1783272|1239|186801|68295;3379134|1224|1236|91347|543;3379134|1224|1236|91347;3379134|1224|1236,Complete,ChiomaBlessing
bsdb:30488079/3/1,30488079,time series / longitudinal observational,30488079,10.11622/smedj.2018152,https://pubmed.ncbi.nlm.nih.gov/30488079/,"Koo S.H., Deng J., Ang D.S.W., Hsiang J.C., Lee L.S., Aazmi S., Mohamed E.H.M., Yang H., Yap S.Y., Teh L.K., Salleh M.Z., Lee E.J.D. , Ang T.L.",Effects of proton pump inhibitor on the human gut microbiome profile in multi-ethnic groups in Singapore,Singapore medical journal,2019,"gastroesophageal reflux disease, gastrointestinal microbiome, omeprazole",Experiment 3,Singapore,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Day 7,Day 14,The day that marked the 7th day after participants stopped the course of Omeprazole at therapeutic dose (20mg daily),34,34,1 month,16S,34,Illumina,relative abundances,"LEfSe,Kruskall-Wallis",0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Fig 5a (2nd Cladogram),7 March 2024,Deacme,"Deacme,ChiomaBlessing,WikiWorks",Significant taxa abundance in participants at Day 14 after they stopped the course of Omeprazole (20 mg) compared to Day 7,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae",1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|186802|216572|244127|169435;3379134|976|200643|171549;3379134|976|200643;1783272|1239|526524|526525|2810281|191303;1783272|1239|526524|526525|2810281,Complete,ChiomaBlessing
bsdb:30488079/3/2,30488079,time series / longitudinal observational,30488079,10.11622/smedj.2018152,https://pubmed.ncbi.nlm.nih.gov/30488079/,"Koo S.H., Deng J., Ang D.S.W., Hsiang J.C., Lee L.S., Aazmi S., Mohamed E.H.M., Yang H., Yap S.Y., Teh L.K., Salleh M.Z., Lee E.J.D. , Ang T.L.",Effects of proton pump inhibitor on the human gut microbiome profile in multi-ethnic groups in Singapore,Singapore medical journal,2019,"gastroesophageal reflux disease, gastrointestinal microbiome, omeprazole",Experiment 3,Singapore,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Day 7,Day 14,The day that marked the 7th day after participants stopped the course of Omeprazole at therapeutic dose (20mg daily),34,34,1 month,16S,34,Illumina,relative abundances,"LEfSe,Kruskall-Wallis",0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Fig 5a (2nd cladogram),7 March 2024,Deacme,"Deacme,ChiomaBlessing,WikiWorks",Significant taxa abundance in participants at Day 14 after they stopped the course of Omeprazole (20 mg) compared to Day 7,decreased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia|s__Erwinia billingiae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Lelliottia|s__Lelliottia amnigena,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Mannheimia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella denticariosi,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella montpellierensis,k__Bacillati|p__Chloroflexota|c__Caldilineae|o__Caldilineales|f__Caldilineaceae,k__Bacillati|p__Chloroflexota|c__Caldilineae|o__Caldilineales|f__Caldilineaceae|g__Caldilinea,k__Bacillati|p__Chloroflexota|c__Caldilineae|o__Caldilineales,k__Bacillati|p__Chloroflexota|c__Anaerolineae,k__Bacillati|p__Chloroflexota|c__Caldilineae|o__Caldilineales|f__Caldilineaceae|g__Caldilinea|s__Caldilinea tarbellica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella|s__Johnsonella ignava,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter soli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Mannheimia|s__Mannheimia caviae",1783272|1239|91061;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|1903409|551;3379134|1224|1236|91347|1903409|551|182337;3379134|1224|1236;3379134|1224|1236|135625|712|724|729;1783272|1239|91061|186826;3379134|1224|1236|91347|543|1330545|61646;3379134|1224|1236|135625|712|75984;3379134|1224|1236|135625|712;3379134|1224|1236|135625;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843489|31977|29465|419208;1783272|1239|909932|1843489|31977|29465|187328;1783272|200795|475962|475963|475964;1783272|200795|475962|475963|475964|233191;1783272|200795|475962|475963;1783272|200795|292625;1783272|200795|475962|475963|475964|233191|859243;1783272|1239|91061|186826|33958|2767887|1624;1783272|1239|186801|3085636|186803|43994|43995;1783272|1239|186801|3085636|186803|43994;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|909932|1843489|31977|29465|29466;3379134|1224|1236|91347|543|547|885040;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712|75984|879276,Complete,ChiomaBlessing
bsdb:30488079/4/1,30488079,time series / longitudinal observational,30488079,10.11622/smedj.2018152,https://pubmed.ncbi.nlm.nih.gov/30488079/,"Koo S.H., Deng J., Ang D.S.W., Hsiang J.C., Lee L.S., Aazmi S., Mohamed E.H.M., Yang H., Yap S.Y., Teh L.K., Salleh M.Z., Lee E.J.D. , Ang T.L.",Effects of proton pump inhibitor on the human gut microbiome profile in multi-ethnic groups in Singapore,Singapore medical journal,2019,"gastroesophageal reflux disease, gastrointestinal microbiome, omeprazole",Experiment 4,Singapore,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Chinese participants,Indian participants,Participants who belong to the Indian ethnic group,12,10,1 month,16S,34,Illumina,relative abundances,"Kruskall-Wallis,LEfSe",0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Fig 5b (1st cladogram),7 March 2024,Deacme,"Deacme,ChiomaBlessing,WikiWorks",Significant taxa abundance in participants of Indian descent compared to participants of Chinese descent,increased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix,1783272|1239|526524|526525|128827|1647,Complete,ChiomaBlessing
bsdb:30488079/4/2,30488079,time series / longitudinal observational,30488079,10.11622/smedj.2018152,https://pubmed.ncbi.nlm.nih.gov/30488079/,"Koo S.H., Deng J., Ang D.S.W., Hsiang J.C., Lee L.S., Aazmi S., Mohamed E.H.M., Yang H., Yap S.Y., Teh L.K., Salleh M.Z., Lee E.J.D. , Ang T.L.",Effects of proton pump inhibitor on the human gut microbiome profile in multi-ethnic groups in Singapore,Singapore medical journal,2019,"gastroesophageal reflux disease, gastrointestinal microbiome, omeprazole",Experiment 4,Singapore,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Chinese participants,Indian participants,Participants who belong to the Indian ethnic group,12,10,1 month,16S,34,Illumina,relative abundances,"Kruskall-Wallis,LEfSe",0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Fig 5b (1st cladogram),7 March 2024,Deacme,"Deacme,ChiomaBlessing,WikiWorks",Significant taxa abundance in participants of Indian descent compared to participants of Chinese descent,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium naviforme",1783272|1239|186801|186802|216572|244127|169435;3379134|74201|203494|48461|203557;3379134|74201|203494|48461|1647988|239934|239935;3379134|74201|203494|48461;3384189|32066|203490|203491|203492|848|77917,Complete,ChiomaBlessing
bsdb:30488079/6/1,30488079,time series / longitudinal observational,30488079,10.11622/smedj.2018152,https://pubmed.ncbi.nlm.nih.gov/30488079/,"Koo S.H., Deng J., Ang D.S.W., Hsiang J.C., Lee L.S., Aazmi S., Mohamed E.H.M., Yang H., Yap S.Y., Teh L.K., Salleh M.Z., Lee E.J.D. , Ang T.L.",Effects of proton pump inhibitor on the human gut microbiome profile in multi-ethnic groups in Singapore,Singapore medical journal,2019,"gastroesophageal reflux disease, gastrointestinal microbiome, omeprazole",Experiment 6,Singapore,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Indian participants,Malay participants,Participants who belong to the Malay ethnic group,10,12,1 month,16S,34,Illumina,relative abundances,"Kruskall-Wallis,LEfSe",0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Fig 5b (1st cladogram),7 March 2024,Deacme,"Deacme,ChiomaBlessing,WikiWorks",Significant taxa abundance in participants of Malay descent compared to participants of Indian descent,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella stercoricanis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella granulomatis",3379134|1224|28216|80840|995019|40544|234908;3379134|1224|1236|91347|543|570|39824,Complete,ChiomaBlessing
bsdb:30488079/7/1,30488079,time series / longitudinal observational,30488079,10.11622/smedj.2018152,https://pubmed.ncbi.nlm.nih.gov/30488079/,"Koo S.H., Deng J., Ang D.S.W., Hsiang J.C., Lee L.S., Aazmi S., Mohamed E.H.M., Yang H., Yap S.Y., Teh L.K., Salleh M.Z., Lee E.J.D. , Ang T.L.",Effects of proton pump inhibitor on the human gut microbiome profile in multi-ethnic groups in Singapore,Singapore medical journal,2019,"gastroesophageal reflux disease, gastrointestinal microbiome, omeprazole",Experiment 7,Singapore,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Male participants,Female participants,Participants who identify with the female gender,16,18,1 month,16S,34,Illumina,relative abundances,"Kruskall-Wallis,LEfSe",0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Fig 5c,7 March 2024,Deacme,"Deacme,ChiomaBlessing,WikiWorks",Significant taxa abundance in Female participants compared to Male participants,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium|s__Sphingobacterium shayense",1783272|1239|909932|1843488|909930|904|187327;3379134|976|200643|171549|815|816|626929;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|371601;3379134|976|200643|171549|171552|2974257|28127;3379134|976|117747|200666|84566;3379134|976|117747|200666;3379134|976|117747;3379134|976|117747|200666|84566|28453;3379134|976|117747|200666|84566|28453|626343,Complete,ChiomaBlessing
bsdb:30488079/7/2,30488079,time series / longitudinal observational,30488079,10.11622/smedj.2018152,https://pubmed.ncbi.nlm.nih.gov/30488079/,"Koo S.H., Deng J., Ang D.S.W., Hsiang J.C., Lee L.S., Aazmi S., Mohamed E.H.M., Yang H., Yap S.Y., Teh L.K., Salleh M.Z., Lee E.J.D. , Ang T.L.",Effects of proton pump inhibitor on the human gut microbiome profile in multi-ethnic groups in Singapore,Singapore medical journal,2019,"gastroesophageal reflux disease, gastrointestinal microbiome, omeprazole",Experiment 7,Singapore,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Male participants,Female participants,Participants who identify with the female gender,16,18,1 month,16S,34,Illumina,relative abundances,"Kruskall-Wallis,LEfSe",0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Fig 5c,7 March 2024,Deacme,"Deacme,ChiomaBlessing,WikiWorks",Significant taxa abundance in Female participants compared to Male participants,decreased,"k__Bacillati|p__Chloroflexota|c__Anaerolineae,k__Bacillati|p__Chloroflexota|c__Caldilineae|o__Caldilineales|f__Caldilineaceae|g__Caldilinea,k__Bacillati|p__Chloroflexota|c__Caldilineae|o__Caldilineales|f__Caldilineaceae|g__Caldilinea|s__Caldilinea tarbellica,k__Bacillati|p__Chloroflexota|c__Caldilineae|o__Caldilineales|f__Caldilineaceae,k__Bacillati|p__Chloroflexota|c__Caldilineae|o__Caldilineales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium naviforme",1783272|200795|292625;1783272|200795|475962|475963|475964|233191;1783272|200795|475962|475963|475964|233191|859243;1783272|200795|475962|475963|475964;1783272|200795|475962|475963;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|3085636|186803|265975|237576;3384189|32066|203490|203491|203492|848|77917,Complete,ChiomaBlessing
bsdb:30497517/1/1,30497517,"cross-sectional observational, not case-control",30497517,10.1186/s40168-018-0588-z,NA,"Lam T.H., Verzotto D., Brahma P., Ng A.H.Q., Hu P., Schnell D., Tiesman J., Kong R., Ton T.M.U., Li J., Ong M., Lu Y., Swaile D., Liu P., Liu J. , Nagarajan N.",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,NA,Experiment 1,Philippines,Homo sapiens,Skin of body,UBERON:0002097,Body odor measurement,EFO:0008386,head of child,head of teenager,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure S3, S4",10 January 2021,Rimsha Azhar,"WikiWorks,Davvve,ChiomaBlessing",Significant microbial genera and species associated with teen head VS child head,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes",1783272|201174|1760|85009|31957|1912216;1783272|201174|1760|85009|31957|1912216|1747,Complete,Shaimaa Elsafoury
bsdb:30497517/1/2,30497517,"cross-sectional observational, not case-control",30497517,10.1186/s40168-018-0588-z,NA,"Lam T.H., Verzotto D., Brahma P., Ng A.H.Q., Hu P., Schnell D., Tiesman J., Kong R., Ton T.M.U., Li J., Ong M., Lu Y., Swaile D., Liu P., Liu J. , Nagarajan N.",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,NA,Experiment 1,Philippines,Homo sapiens,Skin of body,UBERON:0002097,Body odor measurement,EFO:0008386,head of child,head of teenager,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure S3, S4",10 January 2021,Rimsha Azhar,"WikiWorks,Davvve,ChiomaBlessing",Significant microbial genera and species associated with teen head VS child head,decreased,"k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia globosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis",4751|5204|1538075|162474|742845|55193;4751|5204|1538075|162474|742845|55193|76773;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|1385|90964|1279|1282;1783272|1239|91061|1385|90964|1279|1290,Complete,Shaimaa Elsafoury
bsdb:30497517/2/1,30497517,"cross-sectional observational, not case-control",30497517,10.1186/s40168-018-0588-z,NA,"Lam T.H., Verzotto D., Brahma P., Ng A.H.Q., Hu P., Schnell D., Tiesman J., Kong R., Ton T.M.U., Li J., Ong M., Lu Y., Swaile D., Liu P., Liu J. , Nagarajan N.",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,NA,Experiment 2,Philippines,Homo sapiens,Skin of body,UBERON:0002097,Body odor measurement,EFO:0008386,child neck,teen neck,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure S3, S4",10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Significant microbial genera and species associated with teen neck VS child neck,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia globosa",1783272|201174|1760|85009|31957|1912216;1783272|201174|1760|85009|31957|1912216|1747;4751|5204|1538075|162474|742845|55193;4751|5204|1538075|162474|742845|55193|76773,Complete,Shaimaa Elsafoury
bsdb:30497517/2/2,30497517,"cross-sectional observational, not case-control",30497517,10.1186/s40168-018-0588-z,NA,"Lam T.H., Verzotto D., Brahma P., Ng A.H.Q., Hu P., Schnell D., Tiesman J., Kong R., Ton T.M.U., Li J., Ong M., Lu Y., Swaile D., Liu P., Liu J. , Nagarajan N.",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,NA,Experiment 2,Philippines,Homo sapiens,Skin of body,UBERON:0002097,Body odor measurement,EFO:0008386,child neck,teen neck,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure S3, S4",10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Significant microbial genera and species associated with teen neck VS child neck,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis",1783272|1239|91061|1385|90964|1279;1783272|1239|91061|1385|90964|1279|1290,Complete,Shaimaa Elsafoury
bsdb:30497517/3/1,30497517,"cross-sectional observational, not case-control",30497517,10.1186/s40168-018-0588-z,NA,"Lam T.H., Verzotto D., Brahma P., Ng A.H.Q., Hu P., Schnell D., Tiesman J., Kong R., Ton T.M.U., Li J., Ong M., Lu Y., Swaile D., Liu P., Liu J. , Nagarajan N.",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,NA,Experiment 3,Philippines,Homo sapiens,Skin of body,UBERON:0002097,Body odor measurement,EFO:0008386,child underarm,teen underarm,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure S3, S4",10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Significant microbial genera and species associated with teen underarm VS child underarm,increased,"k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia globosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis",4751|5204|1538075|162474|742845|55193|76773;1783272|1239|91061|1385|90964|1279|1282,Complete,Shaimaa Elsafoury
bsdb:30497517/3/2,30497517,"cross-sectional observational, not case-control",30497517,10.1186/s40168-018-0588-z,NA,"Lam T.H., Verzotto D., Brahma P., Ng A.H.Q., Hu P., Schnell D., Tiesman J., Kong R., Ton T.M.U., Li J., Ong M., Lu Y., Swaile D., Liu P., Liu J. , Nagarajan N.",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,NA,Experiment 3,Philippines,Homo sapiens,Skin of body,UBERON:0002097,Body odor measurement,EFO:0008386,child underarm,teen underarm,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure S3, S4",10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Significant microbial genera and species associated with teen underarm VS child underarm,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,1783272|1239|91061|1385|90964|1279|1290,Complete,Shaimaa Elsafoury
bsdb:30497517/4/1,30497517,"cross-sectional observational, not case-control",30497517,10.1186/s40168-018-0588-z,NA,"Lam T.H., Verzotto D., Brahma P., Ng A.H.Q., Hu P., Schnell D., Tiesman J., Kong R., Ton T.M.U., Li J., Ong M., Lu Y., Swaile D., Liu P., Liu J. , Nagarajan N.",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,NA,Experiment 4,Philippines,Homo sapiens,Skin of body,UBERON:0002097,Body odor measurement,EFO:0008386,after excercise,Children Neck before,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1& S3,10 January 2021,Shaimaa Elsafoury,WikiWorks,List of microbes at the genus level that show significant correlation with odor intensity in at least one age group,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,Shaimaa Elsafoury
bsdb:30497517/4/2,30497517,"cross-sectional observational, not case-control",30497517,10.1186/s40168-018-0588-z,NA,"Lam T.H., Verzotto D., Brahma P., Ng A.H.Q., Hu P., Schnell D., Tiesman J., Kong R., Ton T.M.U., Li J., Ong M., Lu Y., Swaile D., Liu P., Liu J. , Nagarajan N.",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,NA,Experiment 4,Philippines,Homo sapiens,Skin of body,UBERON:0002097,Body odor measurement,EFO:0008386,after excercise,Children Neck before,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1& S3,10 January 2021,Shaimaa Elsafoury,WikiWorks,List of microbes at the genus level that show significant correlation with odor intensity in at least one age group,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,1783272|201174|1760|85009|31957|1912216,Complete,Shaimaa Elsafoury
bsdb:30497517/5/1,30497517,"cross-sectional observational, not case-control",30497517,10.1186/s40168-018-0588-z,NA,"Lam T.H., Verzotto D., Brahma P., Ng A.H.Q., Hu P., Schnell D., Tiesman J., Kong R., Ton T.M.U., Li J., Ong M., Lu Y., Swaile D., Liu P., Liu J. , Nagarajan N.",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,NA,Experiment 5,Philippines,Homo sapiens,Skin of body,UBERON:0002097,Body odor measurement,EFO:0008386,after excercise,teen underarm before,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1& S3,10 January 2021,Shaimaa Elsafoury,WikiWorks,List of microbes at the genus level that show significant correlation with odor intensity in at least one age group,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,3379134|1224|28211|204455|31989|265,Complete,Shaimaa Elsafoury
bsdb:30497517/6/1,30497517,"cross-sectional observational, not case-control",30497517,10.1186/s40168-018-0588-z,NA,"Lam T.H., Verzotto D., Brahma P., Ng A.H.Q., Hu P., Schnell D., Tiesman J., Kong R., Ton T.M.U., Li J., Ong M., Lu Y., Swaile D., Liu P., Liu J. , Nagarajan N.",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,NA,Experiment 6,Philippines,Homo sapiens,Skin of body,UBERON:0002097,Body odor measurement,EFO:0008386,after excercise,teen Neck before,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1& S3,10 January 2021,Shaimaa Elsafoury,WikiWorks,List of microbes at the genus level that show significant correlation with odor intensity in at least one age group,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,3379134|1224|1236|2887326|468|469,Complete,Shaimaa Elsafoury
bsdb:30508628/1/1,30508628,case-control,30508628,10.1016/j.micpath.2018.11.051,NA,"Xu J., Xiang C., Zhang C., Xu B., Wu J., Wang R., Yang Y., Shi L., Zhang J. , Zhan Z.",Microbial biomarkers of common tongue coatings in patients with gastric cancer,Microbial pathogenesis,2019,"Gastric cancer, Microbiome, Tongue coating",Experiment 1,China,Homo sapiens,Tongue,UBERON:0001723,Gastric cancer,MONDO:0001056,other coatings,white-thin tongue coating GC patient,gastric cancer with different tongue coatings,90,25,1 month,16S,345,RT-qPCR,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 1,10 January 2021,Rimsha Azhar,"WikiWorks,Atrayees",LEfSe analysis of microbial taxa from tongue coating in GC patients,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Phaeosphaeriaceae|g__Ampelomyces",3379134|1224|28216|80840|119060|47670;3379134|976|117743|200644|49546|1016|327575;4751|4890|147541|92860|5020|50729,Complete,Atrayees
bsdb:30508628/1/2,30508628,case-control,30508628,10.1016/j.micpath.2018.11.051,NA,"Xu J., Xiang C., Zhang C., Xu B., Wu J., Wang R., Yang Y., Shi L., Zhang J. , Zhan Z.",Microbial biomarkers of common tongue coatings in patients with gastric cancer,Microbial pathogenesis,2019,"Gastric cancer, Microbiome, Tongue coating",Experiment 1,China,Homo sapiens,Tongue,UBERON:0001723,Gastric cancer,MONDO:0001056,other coatings,white-thin tongue coating GC patient,gastric cancer with different tongue coatings,90,25,1 month,16S,345,RT-qPCR,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table 1,10 January 2021,Rimsha Azhar,"WikiWorks,Atrayees",LEfSe analysis of microbial taxa from tongue coating in GC patients,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium|s__Fusarium equiseti",1783272|1239|186801|3085636|186803|1213720;1783272|1239|909932|1843489|31977|906|187326;1783272|1239|186801|186802|186806|1730|142586;4751|5204|162481|231213;4751|4890|147550|5125|110618|5506|61235,Complete,Atrayees
bsdb:30508628/2/1,30508628,case-control,30508628,10.1016/j.micpath.2018.11.051,NA,"Xu J., Xiang C., Zhang C., Xu B., Wu J., Wang R., Yang Y., Shi L., Zhang J. , Zhan Z.",Microbial biomarkers of common tongue coatings in patients with gastric cancer,Microbial pathogenesis,2019,"Gastric cancer, Microbiome, Tongue coating",Experiment 2,China,Homo sapiens,Tongue,UBERON:0001723,Gastric cancer,MONDO:0001056,other coatings,white-thick tongue coating GC patient,gastric cancer with different tongue coatings,72,43,1 month,16S,345,RT-qPCR,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 2,10 January 2021,Rimsha Azhar,"WikiWorks,Atrayees",LEfSe analysis of microbial taxa from tongue coating in GC patients,increased,"p__Candidatus Saccharimonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella maculosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum",95818;1783272|1239|186801|186802|541000;1783272|1239|909932|1843489|31977|906|187326;1783272|1239|909932|909929|1843491|970|69823;3379134|976|200643|171549|171552|2974251|439703;1783272|1239|186801|3082720|543314|35518,Complete,Atrayees
bsdb:30508628/2/2,30508628,case-control,30508628,10.1016/j.micpath.2018.11.051,NA,"Xu J., Xiang C., Zhang C., Xu B., Wu J., Wang R., Yang Y., Shi L., Zhang J. , Zhan Z.",Microbial biomarkers of common tongue coatings in patients with gastric cancer,Microbial pathogenesis,2019,"Gastric cancer, Microbiome, Tongue coating",Experiment 2,China,Homo sapiens,Tongue,UBERON:0001723,Gastric cancer,MONDO:0001056,other coatings,white-thick tongue coating GC patient,gastric cancer with different tongue coatings,72,43,1 month,16S,345,RT-qPCR,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table 2,10 January 2021,Rimsha Azhar,"WikiWorks,Atrayees",LEfSe analysis of microbial taxa from tongue coating in GC patients,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter ursingii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales",3379134|1224|1236|2887326|468|469|108980;1783272|1239|91061|186826|33958|2767887|1624;4751|4890|147550|5125,Complete,Atrayees
bsdb:30508628/3/1,30508628,case-control,30508628,10.1016/j.micpath.2018.11.051,NA,"Xu J., Xiang C., Zhang C., Xu B., Wu J., Wang R., Yang Y., Shi L., Zhang J. , Zhan Z.",Microbial biomarkers of common tongue coatings in patients with gastric cancer,Microbial pathogenesis,2019,"Gastric cancer, Microbiome, Tongue coating",Experiment 3,China,Homo sapiens,Tongue,UBERON:0001723,Gastric cancer,MONDO:0001056,other coatings,yellow-thick tongue coating GC patient,gastric cancer with different tongue coatings,95,20,1 month,16S,345,RT-qPCR,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 4,10 January 2021,Rimsha Azhar,"WikiWorks,Atrayees",LEfSe analysis of microbial taxa from tongue coating in GC patients,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Marinobacteraceae|g__Marinobacter|s__Marinobacter sp. NP39,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae",1783272|1239|186801|186802|541000;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|206351|481|482;1783272|1239|186801|3082720|186804|1257;1783272|1239|91061|1385|539738|1378|84135;3379134|976|117743|200644|49546|1016|1019;3379134|1224|1236|135625|712|724|729;3379134|1224|1236|72274|2887365|2742|479370;3379134|1224|28216|80840|119060,Complete,Atrayees
bsdb:30508628/4/1,30508628,case-control,30508628,10.1016/j.micpath.2018.11.051,NA,"Xu J., Xiang C., Zhang C., Xu B., Wu J., Wang R., Yang Y., Shi L., Zhang J. , Zhan Z.",Microbial biomarkers of common tongue coatings in patients with gastric cancer,Microbial pathogenesis,2019,"Gastric cancer, Microbiome, Tongue coating",Experiment 4,China,Homo sapiens,Tongue,UBERON:0001723,Gastric cancer,MONDO:0001056,other coatings,yellow-thin coating GC patient,gastric cancer with yellow thin coating,88,27,1 month,16S,345,RT-qPCR,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 3,18 August 2023,Atrayees,"Atrayees,WikiWorks",LEfSe analysis of microbial taxa from tongue coating in GC patients,decreased,"k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Cladosporium|s__Cladosporium halotolerans,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Hypocreaceae|g__Trichoderma",4751|4890|147541|2726946|452563|5498|1052096;4751|4890|147550|5125|5129|5543,Complete,Atrayees
bsdb:30513082/1/1,30513082,"cross-sectional observational, not case-control",30513082,10.1371/journal.pbio.2006842,https://pubmed.ncbi.nlm.nih.gov/30513082/,"Brooks A.W., Priya S., Blekhman R. , Bordenstein S.R.",Gut microbiota diversity across ethnicities in the United States,PLoS biology,2018,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Caucasians,Asian Pacific,Asian Pacific sampled from the American Gut Project (AGP) data set,1237,88,2 weeks,16S,345,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,decreased,decreased,NA,NA,Signature 1,Figure 4,7 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1,WikiWorks",Differential microbial abundance between Caucasian and Asian Pacific subjects,increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,1783272|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:30513082/1/2,30513082,"cross-sectional observational, not case-control",30513082,10.1371/journal.pbio.2006842,https://pubmed.ncbi.nlm.nih.gov/30513082/,"Brooks A.W., Priya S., Blekhman R. , Bordenstein S.R.",Gut microbiota diversity across ethnicities in the United States,PLoS biology,2018,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Caucasians,Asian Pacific,Asian Pacific sampled from the American Gut Project (AGP) data set,1237,88,2 weeks,16S,345,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,decreased,decreased,NA,NA,Signature 2,Figure 4,7 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1,WikiWorks",Differential microbial abundance between Caucasian and Asian Pacific subjects,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239|186801|3082768|990719;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|1853231;1783272|1239|186801|186802|186807;3379134|976|200643|171549|171550;3379134|74201|203494|48461|203557;3379134|256845|1313211|278082|255528;1783272|201174|84998|84999|84107;1783272|1239|186801|186802,Complete,Atrayees
bsdb:30513082/2/1,30513082,"cross-sectional observational, not case-control",30513082,10.1371/journal.pbio.2006842,https://pubmed.ncbi.nlm.nih.gov/30513082/,"Brooks A.W., Priya S., Blekhman R. , Bordenstein S.R.",Gut microbiota diversity across ethnicities in the United States,PLoS biology,2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Caucasians,Hispanic,Hispanics sampled from the American Gut Project (AGP) data set,1237,37,2 weeks,16S,345,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,sex",NA,increased,increased,increased,NA,NA,Signature 1,Figure 4,7 July 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks","Ethnicity-associated taxa match between the HMP and AGP. Bar plots depict the log10 transformed relative abundance for individuals possessing the respective
taxon within each ethnicity, ubiquity appears above (AGP) or below (HMP) bars, and the 25th and 75th percentiles are shown with extending whiskers. Mann–Whitney
U tests evaluate differences in abundance and ubiquity for all individuals between pairs of ethnicities.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|1853231;1783272|1239|186801|186802|186807;3379134|976|200643|171549|171550;1783272|1239|909932|1843489|31977|29465;3379134|256845|1313211|278082|255528;1783272|1239|186801|186802;1783272|201174|84998|84999|84107,Complete,ChiomaBlessing
bsdb:30513082/2/2,30513082,"cross-sectional observational, not case-control",30513082,10.1371/journal.pbio.2006842,https://pubmed.ncbi.nlm.nih.gov/30513082/,"Brooks A.W., Priya S., Blekhman R. , Bordenstein S.R.",Gut microbiota diversity across ethnicities in the United States,PLoS biology,2018,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Caucasians,Hispanic,Hispanics sampled from the American Gut Project (AGP) data set,1237,37,2 weeks,16S,345,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,sex",NA,increased,increased,increased,NA,NA,Signature 2,Figure 4,7 July 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks","Ethnicity-associated taxa match between the HMP and AGP. Bar plots depict the log10 transformed relative abundance for individuals possessing the respective
taxon within each ethnicity, ubiquity appears above (AGP) or below (HMP) bars, and the 25th and 75th percentiles are shown with extending whiskers. Mann–Whitney
U tests evaluate differences in abundance and ubiquity for all individuals between pairs of ethnicities; f",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",1783272|1239|186801|3082768|990719;3379134|74201|203494|48461|203557,Complete,ChiomaBlessing
bsdb:30513082/3/1,30513082,"cross-sectional observational, not case-control",30513082,10.1371/journal.pbio.2006842,https://pubmed.ncbi.nlm.nih.gov/30513082/,"Brooks A.W., Priya S., Blekhman R. , Bordenstein S.R.",Gut microbiota diversity across ethnicities in the United States,PLoS biology,2018,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Caucasians,African Americans,African Americans sampled from the American Gut Project (AGP) data set,1237,13,2 weeks,16S,345,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,decreased,decreased,NA,NA,Signature 1,Figure 4,7 July 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks","Ethnicity-associated taxa match between the HMP and AGP. Bar plots depict the log10 transformed relative abundance for individuals possessing the respective
taxon within each ethnicity, ubiquity appears above (AGP) or below (HMP) bars, and the 25th and 75th percentiles are shown with extending whiskers. Mann–Whitney
U tests evaluate differences in abundance and ubiquity for all individuals between pairs of ethnicities; f",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter",1783272|1239|186801|186802|186807;1783272|1239|909932|1843489|31977|29465;3379134|256845|1313211|278082|255528;3379134|976|200643|171549|1853231;3379134|976|200643|171549|1853231|283168,Complete,ChiomaBlessing
bsdb:30513082/3/2,30513082,"cross-sectional observational, not case-control",30513082,10.1371/journal.pbio.2006842,https://pubmed.ncbi.nlm.nih.gov/30513082/,"Brooks A.W., Priya S., Blekhman R. , Bordenstein S.R.",Gut microbiota diversity across ethnicities in the United States,PLoS biology,2018,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Caucasians,African Americans,African Americans sampled from the American Gut Project (AGP) data set,1237,13,2 weeks,16S,345,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,decreased,decreased,NA,NA,Signature 2,Figure 4,7 July 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks","Ethnicity-associated taxa match between the HMP and AGP. Bar plots depict the log10 transformed relative abundance for individuals possessing the respective
taxon within each ethnicity, ubiquity appears above (AGP) or below (HMP) bars, and the 25th and 75th percentiles are shown with extending whiskers. Mann–Whitney
U tests evaluate differences in abundance and ubiquity for all individuals between pairs of ethnicities.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",1783272|1239|186801|3082768|990719;1783272|1239|186801|186802;3379134|74201|203494|48461|203557;3379134|976|200643|171549|171550;1783272|201174|84998|84999|84107,Complete,ChiomaBlessing
bsdb:30513082/4/1,30513082,"cross-sectional observational, not case-control",30513082,10.1371/journal.pbio.2006842,https://pubmed.ncbi.nlm.nih.gov/30513082/,"Brooks A.W., Priya S., Blekhman R. , Bordenstein S.R.",Gut microbiota diversity across ethnicities in the United States,PLoS biology,2018,NA,Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Caucasians,Asian Pacific,Asian Pacific sampled from Human Microbiome Project (HMP) data set,211,34,2 weeks,16S,345,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,decreased,decreased,NA,NA,Signature 1,Figure 4,7 July 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks","Ethnicity-associated taxa match between the HMP and AGP. Bar plots depict the log10 transformed relative abundance for individuals possessing the respective
taxon within each ethnicity, ubiquity appears above (AGP) or below (HMP) bars, and the 25th and 75th percentiles are shown with extending whiskers. Mann–Whitney
U tests evaluate differences in abundance and ubiquity for all individuals between pairs of ethnicities.",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae",1783272|1239|909932|1843489|31977|29465;3379134|256845|1313211|278082|255528,Complete,ChiomaBlessing
bsdb:30513082/4/2,30513082,"cross-sectional observational, not case-control",30513082,10.1371/journal.pbio.2006842,https://pubmed.ncbi.nlm.nih.gov/30513082/,"Brooks A.W., Priya S., Blekhman R. , Bordenstein S.R.",Gut microbiota diversity across ethnicities in the United States,PLoS biology,2018,NA,Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Caucasians,Asian Pacific,Asian Pacific sampled from Human Microbiome Project (HMP) data set,211,34,2 weeks,16S,345,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,decreased,decreased,NA,NA,Signature 2,Figure 4,7 July 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks","Ethnicity-associated taxa match between the HMP and AGP. Bar plots depict the log10 transformed relative abundance for individuals possessing the respective
taxon within each ethnicity, ubiquity appears above (AGP) or below (HMP) bars, and the 25th and 75th percentiles are shown with extending whiskers. Mann–Whitney
U tests evaluate differences in abundance and ubiquity for all individuals between pairs of ethnicities.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",1783272|1239|186801|186802|186807;1783272|1239|186801|3082768|990719;1783272|1239|186801|186802;3379134|74201|203494|48461|203557;3379134|976|200643|171549|1853231;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|171550;1783272|201174|84998|84999|84107,Complete,ChiomaBlessing
bsdb:30513082/5/1,30513082,"cross-sectional observational, not case-control",30513082,10.1371/journal.pbio.2006842,https://pubmed.ncbi.nlm.nih.gov/30513082/,"Brooks A.W., Priya S., Blekhman R. , Bordenstein S.R.",Gut microbiota diversity across ethnicities in the United States,PLoS biology,2018,NA,Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Caucasians,Hispanics,Hispanics sampled from Human Microbiome Project (HMP) data set,211,43,2 weeks,16S,345,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,sex",NA,increased,increased,increased,NA,NA,Signature 1,Figure 4,8 July 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks","Ethnicity-associated taxa match between the HMP and AGP. Bar plots depict the log10 transformed relative abundance for individuals possessing the respective
taxon within each ethnicity, ubiquity appears above (AGP) or below (HMP) bars, and the 25th and 75th percentiles are shown with extending whiskers. Mann–Whitney
U tests evaluate differences in abundance and ubiquity for all individuals between pairs of ethnicities.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae",1783272|1239|186801|186802|186807;1783272|1239|186801|3082768|990719;1783272|1239|909932|1843489|31977|29465;3379134|256845|1313211|278082|255528,Complete,ChiomaBlessing
bsdb:30513082/5/2,30513082,"cross-sectional observational, not case-control",30513082,10.1371/journal.pbio.2006842,https://pubmed.ncbi.nlm.nih.gov/30513082/,"Brooks A.W., Priya S., Blekhman R. , Bordenstein S.R.",Gut microbiota diversity across ethnicities in the United States,PLoS biology,2018,NA,Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Caucasians,Hispanics,Hispanics sampled from Human Microbiome Project (HMP) data set,211,43,2 weeks,16S,345,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,sex",NA,increased,increased,increased,NA,NA,Signature 2,Figure 4,8 July 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks","Ethnicity-associated taxa match between the HMP and AGP. Bar plots depict the log10 transformed relative abundance for individuals possessing the respective
taxon within each ethnicity, ubiquity appears above (AGP) or below (HMP) bars, and the 25th and 75th percentiles are shown with extending whiskers. Mann–Whitney
U tests evaluate differences in abundance and ubiquity for all individuals between pairs of ethnicities.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",1783272|1239|186801|186802;3379134|74201|203494|48461|203557;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|1853231;3379134|976|200643|171549|171550;1783272|201174|84998|84999|84107,Complete,ChiomaBlessing
bsdb:30513082/6/1,30513082,"cross-sectional observational, not case-control",30513082,10.1371/journal.pbio.2006842,https://pubmed.ncbi.nlm.nih.gov/30513082/,"Brooks A.W., Priya S., Blekhman R. , Bordenstein S.R.",Gut microbiota diversity across ethnicities in the United States,PLoS biology,2018,NA,Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Caucasians,African Americans,African Americans sampled from Human Microbiome Project (HMP) data set,211,10,2 weeks,16S,345,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,decreased,decreased,NA,NA,Signature 1,Figure 4,8 July 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks","Ethnicity-associated taxa match between the HMP and AGP. Bar plots depict the log10 transformed relative abundance for individuals possessing the respective
taxon within each ethnicity, ubiquity appears above (AGP) or below (HMP) bars, and the 25th and 75th percentiles are shown with extending whiskers. Mann–Whitney
U tests evaluate differences in abundance and ubiquity for all individuals between pairs of ethnicities.",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",1783272|1239|909932|1843489|31977|29465;3379134|976|200643|171549|1853231;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|171550;1783272|201174|84998|84999|84107,Complete,ChiomaBlessing
bsdb:30513082/6/2,30513082,"cross-sectional observational, not case-control",30513082,10.1371/journal.pbio.2006842,https://pubmed.ncbi.nlm.nih.gov/30513082/,"Brooks A.W., Priya S., Blekhman R. , Bordenstein S.R.",Gut microbiota diversity across ethnicities in the United States,PLoS biology,2018,NA,Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Caucasians,African Americans,African Americans sampled from Human Microbiome Project (HMP) data set,211,10,2 weeks,16S,345,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,decreased,decreased,NA,NA,Signature 2,Figure 4,8 July 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks","Ethnicity-associated taxa match between the HMP and AGP. Bar plots depict the log10 transformed relative abundance for individuals possessing the respective
taxon within each ethnicity, ubiquity appears above (AGP) or below (HMP) bars, and the 25th and 75th percentiles are shown with extending whiskers. Mann–Whitney
U tests evaluate differences in abundance and ubiquity for all individuals between pairs of ethnicities.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae",1783272|1239|186801|186802|186807;1783272|1239|186801|3082768|990719;1783272|1239|186801|186802;3379134|74201|203494|48461|203557;3379134|256845|1313211|278082|255528,Complete,ChiomaBlessing
bsdb:30518941/1/1,30518941,case-control,30518941,10.1038/s41598-018-35877-4,NA,"Kaur U.S., Shet A., Rajnala N., Gopalan B.P., Moar P., D H., Singh B.P., Chaturvedi R. , Tandon R.",High Abundance of genus Prevotella in the gut of perinatally HIV-infected children is associated with IP-10 levels despite therapy,Scientific reports,2018,NA,Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,uninfected age-matched controls,Perinatally HIV-infected children,Perinatally HIV-infected children,14,29,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,age,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,"Text, Figure 1, Figure 3, Table S1",10 January 2021,Michael Lutete,WikiWorks,Perinatally HIV-infected children show a distinct pattern of gut microbiota compared to uninfected controls,increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Spirochaetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales",3379134|976;3379134|203691;3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|838;1783272|1239|909932|1843489|31977|906;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|909932|909929|1843491|970;1783272|1239|186801|186802|31979|1485;3384189|32066|203490|203491|1129771;3384189|32066|203490|203491|1129771|32067;3379134|1224|1236|91347|1903409|53335;3379134|1224|1236|135624|84642;3384189|32066;3384189|32066|203490;3384189|32066|203490|203491,Complete,Atrayees
bsdb:30518941/1/2,30518941,case-control,30518941,10.1038/s41598-018-35877-4,NA,"Kaur U.S., Shet A., Rajnala N., Gopalan B.P., Moar P., D H., Singh B.P., Chaturvedi R. , Tandon R.",High Abundance of genus Prevotella in the gut of perinatally HIV-infected children is associated with IP-10 levels despite therapy,Scientific reports,2018,NA,Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,uninfected age-matched controls,Perinatally HIV-infected children,Perinatally HIV-infected children,14,29,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,age,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,"Text, Figure 1, Figure 3, Table S1",10 January 2021,Michael Lutete,"Aiyshaaaa,WikiWorks,Merit",Perinatally HIV-infected children show a distinct pattern of gut microbiota compared to uninfected controls,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Chloroflexota|c__Anaerolineae,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria,k__Pseudomonadati|p__Lentisphaerota,k__Bacillati|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae|g__Longilinea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Prosthecobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales",1783272|201174;1783272|200795|292625;1783272|1239;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979;1783272|1117;1783272|1239|186801|186802|186807|51514;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803;3379134|256845|1313211;3379134|256845;1783272|200795|292625|292629|292628|475961;1783272|1239|186801|186802|541000;3379134|74201|203494|48461|203557|48463;3379134|1224|28211|766;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|1263;3379134|256845|1313211|278082|255528;3379134|256845|1313211|278082,Complete,Atrayees
bsdb:30524957/1/1,30524957,case-control,30524957,10.3389/fonc.2018.00520,NA,"Yang J., Mu X., Wang Y., Zhu D., Zhang J., Liang C., Chen B., Wang J., Zhao C., Zuo Z., Heng X., Zhang C. , Zhang L.",Dysbiosis of the Salivary Microbiome Is Associated With Non-smoking Female Lung Cancer and Correlated With Immunocytochemistry Markers,Frontiers in oncology,2018,"biomarker, dysbiosis, lung cancer, non-smoking female patient, salivary microbiome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Lung cancer,MONDO:0008903,healthy controls,non-smoking female lung cancer patients,female and have confirmed diagnosis of non-small-cell lung cancer,172,75,NA,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,sex,smoking status",NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 5,10 January 2021,Rimsha Azhar,"WikiWorks,Claregrieve1",Differentially abundant taxa between lung cancer and control groups,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Blastomonadaceae|g__Blastomonas,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Rhodocyclaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales",3379134|1224|28211|204457|3423720|150203;3379134|976|117743|200644;3379134|976|117743;3379134|1224|28216|80840|75682|963;3379134|1224|28216|80840|75682;3379134|1224;3379134|1224|28216|206389|75787;3379134|1224|28211|204457|41297;3379134|1224|28211|204457;3379134|1224|28211|204457|41297|13687;3379134|976|117743|200644|2762318;3379134|1224|28216|206389,Complete,Claregrieve1
bsdb:30524957/1/2,30524957,case-control,30524957,10.3389/fonc.2018.00520,NA,"Yang J., Mu X., Wang Y., Zhu D., Zhang J., Liang C., Chen B., Wang J., Zhao C., Zuo Z., Heng X., Zhang C. , Zhang L.",Dysbiosis of the Salivary Microbiome Is Associated With Non-smoking Female Lung Cancer and Correlated With Immunocytochemistry Markers,Frontiers in oncology,2018,"biomarker, dysbiosis, lung cancer, non-smoking female patient, salivary microbiome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Lung cancer,MONDO:0008903,healthy controls,non-smoking female lung cancer patients,female and have confirmed diagnosis of non-small-cell lung cancer,172,75,NA,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,sex,smoking status",NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Figure 5,10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differentially abundant taxa between lung cancer and control groups,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Bacteroidota",3379134|1224|1236|2887326|468|469;1783272|1239|91061;3379134|976;3379134|1224|28216;3379134|1224|28216|80840;3379134|976|117743|200644|2762318|59732;3379134|1224|28216|80840|80864;3379134|1224|28216|80840|80864|283;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239;1783272|1239|91061|186826;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;3379134|1224|1236|135614|32033;3379134|1224|1236|135614;3379134|1224|1236|72274|135621;3379134|976,Complete,Claregrieve1
bsdb:30534614/1/1,30534614,time series / longitudinal observational,30534614,10.1038/s42003-018-0221-5,NA,"Rampelli S., Guenther K., Turroni S., Wolters M., Veidebaum T., Kourides Y., Molnár D., Lissner L., Benitez-Paez A., Sanz Y., Fraterman A., Michels N., Brigidi P., Candela M. , Ahrens W.",Pre-obese children's dysbiotic gut microbiome and unhealthy diets may predict the development of obesity,Communications biology,2018,NA,Experiment 1,"Cyprus,Estonia,Germany,Hungary,Sweden",Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight,obese,children aged 2-9 years,34,36,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 1,Table 2,10 January 2021,Mst Afroza Parvin,WikiWorks,Microbial taxa significantly different across the four groups of children,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|841,Complete,NA
bsdb:30534614/1/2,30534614,time series / longitudinal observational,30534614,10.1038/s42003-018-0221-5,NA,"Rampelli S., Guenther K., Turroni S., Wolters M., Veidebaum T., Kourides Y., Molnár D., Lissner L., Benitez-Paez A., Sanz Y., Fraterman A., Michels N., Brigidi P., Candela M. , Ahrens W.",Pre-obese children's dysbiotic gut microbiome and unhealthy diets may predict the development of obesity,Communications biology,2018,NA,Experiment 1,"Cyprus,Estonia,Germany,Hungary,Sweden",Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight,obese,children aged 2-9 years,34,36,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 2,Table 2,10 January 2021,Mst Afroza Parvin,WikiWorks,Microbial taxa significantly different across the four groups of children,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",3379134|976|200643|171549|171552;1783272|1239|186801|3082768|990719;1783272|1239|1737404|1737405|1737406;1783272|201174|84998|1643822|1643826|84108;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|119852,Complete,NA
bsdb:30534614/2/1,30534614,time series / longitudinal observational,30534614,10.1038/s42003-018-0221-5,NA,"Rampelli S., Guenther K., Turroni S., Wolters M., Veidebaum T., Kourides Y., Molnár D., Lissner L., Benitez-Paez A., Sanz Y., Fraterman A., Michels N., Brigidi P., Candela M. , Ahrens W.",Pre-obese children's dysbiotic gut microbiome and unhealthy diets may predict the development of obesity,Communications biology,2018,NA,Experiment 2,"Cyprus,Estonia,Germany,Hungary,Sweden",Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,before onset of obesity,after onset of obesity,children aged 2-9 years,36,36,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 1,Table 2,10 January 2021,Mst Afroza Parvin,WikiWorks,Microbial taxa significantly different across the four groups of children,increased,"k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|1224;1783272|1239|526524|526525|2810280|135858;3379134|1224|28216|80840|506;3379134|1224|28216|80840|995019|40544,Complete,NA
bsdb:30534614/2/2,30534614,time series / longitudinal observational,30534614,10.1038/s42003-018-0221-5,NA,"Rampelli S., Guenther K., Turroni S., Wolters M., Veidebaum T., Kourides Y., Molnár D., Lissner L., Benitez-Paez A., Sanz Y., Fraterman A., Michels N., Brigidi P., Candela M. , Ahrens W.",Pre-obese children's dysbiotic gut microbiome and unhealthy diets may predict the development of obesity,Communications biology,2018,NA,Experiment 2,"Cyprus,Estonia,Germany,Hungary,Sweden",Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,before onset of obesity,after onset of obesity,children aged 2-9 years,36,36,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 2,Table 2,10 January 2021,Mst Afroza Parvin,WikiWorks,Microbial taxa significantly different across the four groups of children,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239|91061|186826|33958;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|541000;1783272|1239|186801|186802|216572|1263,Complete,NA
bsdb:30535886/1/1,30535886,case-control,30535886,10.1007/s10620-018-5411-y,NA,"Qi Y.F., Sun J.N., Ren L.F., Cao X.L., Dong J.H., Tao K., Guan X.M., Cui Y.N. , Su W.","Intestinal Microbiota Is Altered in Patients with Gastric Cancer from Shanxi Province, China",Digestive diseases and sciences,2019,"Cellular immunity, Gastric cancer, Intestinal microbiota, Shanxi Province",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Gastric adenocarcinoma,EFO:0000503,healthy controls,Gastric cancer,gastric carcinoma confirmed by pathological examination,88,116,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Fatima Zohra,WikiWorks,Most differentially abundant taxa between healthy controls and gastric cancer patients,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|1224|1236;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224;3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|838;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|620;1783272|1239|91061;1783272|1239|91061|186826;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|171551;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|171550;3379134|976|200643|171549|171550|239759;1783272|201174|1760;1783272|201174;1783272|1239|909932|1843489|31977|29465;1783272|201174|1760|85004;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|3082768|990719;3379134|976|200643|171549|2005525|375288,Complete,Shaimaa Elsafoury
bsdb:30535886/1/2,30535886,case-control,30535886,10.1007/s10620-018-5411-y,NA,"Qi Y.F., Sun J.N., Ren L.F., Cao X.L., Dong J.H., Tao K., Guan X.M., Cui Y.N. , Su W.","Intestinal Microbiota Is Altered in Patients with Gastric Cancer from Shanxi Province, China",Digestive diseases and sciences,2019,"Cellular immunity, Gastric cancer, Intestinal microbiota, Shanxi Province",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Gastric adenocarcinoma,EFO:0000503,healthy controls,Gastric cancer,gastric carcinoma confirmed by pathological examination,88,116,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Fatima Zohra,WikiWorks,Most differentially abundant taxa between healthy controls and gastric cancer patients,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",1783272|1239|186801|186802;1783272|1239|186801;1783272|1239;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|186802|541000;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|1506553,Complete,Shaimaa Elsafoury
bsdb:30535886/2/1,30535886,case-control,30535886,10.1007/s10620-018-5411-y,NA,"Qi Y.F., Sun J.N., Ren L.F., Cao X.L., Dong J.H., Tao K., Guan X.M., Cui Y.N. , Su W.","Intestinal Microbiota Is Altered in Patients with Gastric Cancer from Shanxi Province, China",Digestive diseases and sciences,2019,"Cellular immunity, Gastric cancer, Intestinal microbiota, Shanxi Province",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Gastric adenocarcinoma,EFO:0000503,healthy controls,Gastric cancer,gastric carcinoma confirmed by pathological examination,48,48,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary figure 3,10 January 2021,Fatima Zohra,WikiWorks,Most differentially abundant taxa between healthy controls and gastric cancer patients who are age and sex matched,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae",1783272|1239|526524|526525|128827|1729679;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236;3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|838;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|620;1783272|1239|91061;1783272|1239|91061|186826;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|201174|1760;1783272|201174;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958;3379134|976|200643|171549|171550;3379134|976|200643|171549|171550|239759;1783272|201174|1760|85004;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|3082768|990719,Complete,Shaimaa Elsafoury
bsdb:30535886/2/2,30535886,case-control,30535886,10.1007/s10620-018-5411-y,NA,"Qi Y.F., Sun J.N., Ren L.F., Cao X.L., Dong J.H., Tao K., Guan X.M., Cui Y.N. , Su W.","Intestinal Microbiota Is Altered in Patients with Gastric Cancer from Shanxi Province, China",Digestive diseases and sciences,2019,"Cellular immunity, Gastric cancer, Intestinal microbiota, Shanxi Province",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Gastric adenocarcinoma,EFO:0000503,healthy controls,Gastric cancer,gastric carcinoma confirmed by pathological examination,48,48,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary figure 3,10 January 2021,Fatima Zohra,WikiWorks,Most differentially abundant taxa between healthy controls and gastric cancer patients who are age and sex matched,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",3379134|1224|28216|80840;3379134|1224|28216;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|1506553,Complete,Shaimaa Elsafoury
bsdb:30541450/1/1,30541450,"cross-sectional observational, not case-control",30541450,10.1186/s12866-018-1362-x,NA,"Whisner C.M., Maldonado J., Dente B., Krajmalnik-Brown R. , Bruening M.","Diet, physical activity and screen time but not body mass index are associated with the gut microbiome of a diverse cohort of college students living in university housing: a cross-sectional study",BMC microbiology,2018,"Adolescence, Diet, Lifestyle behaviors, Microbiome, Microbiota, Obesity, Pediatric, Physical activity",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,high dietary fiber,low,BMI ≥ 30.0 kg/m2 was considered obese,68,68,2-3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,Text and figure 4,10 January 2021,Marianthi Thomatos,WikiWorks,Relative abundance of fiber intake in a cohort of diverse cohort of first year college students living in university housing,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",3379134|976|200643|171549|2005519;3379134|1224|28211;1783272|1239|186801|186802|216572|1263,Complete,Shaimaa Elsafoury
bsdb:30541450/1/2,30541450,"cross-sectional observational, not case-control",30541450,10.1186/s12866-018-1362-x,NA,"Whisner C.M., Maldonado J., Dente B., Krajmalnik-Brown R. , Bruening M.","Diet, physical activity and screen time but not body mass index are associated with the gut microbiome of a diverse cohort of college students living in university housing: a cross-sectional study",BMC microbiology,2018,"Adolescence, Diet, Lifestyle behaviors, Microbiome, Microbiota, Obesity, Pediatric, Physical activity",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,high dietary fiber,low,BMI ≥ 30.0 kg/m2 was considered obese,68,68,2-3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 2,Text and figure 4,10 January 2021,Marianthi Thomatos,WikiWorks,Relative abundance of fiber intake in a cohort of diverse cohort of first year college students living in university housing,decreased,k__Bacillati|p__Mycoplasmatota,1783272|544448,Complete,Shaimaa Elsafoury
bsdb:30541450/2/1,30541450,"cross-sectional observational, not case-control",30541450,10.1186/s12866-018-1362-x,NA,"Whisner C.M., Maldonado J., Dente B., Krajmalnik-Brown R. , Bruening M.","Diet, physical activity and screen time but not body mass index are associated with the gut microbiome of a diverse cohort of college students living in university housing: a cross-sectional study",BMC microbiology,2018,"Adolescence, Diet, Lifestyle behaviors, Microbiome, Microbiota, Obesity, Pediatric, Physical activity",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,hight moderate to vigrous physical activity,low,BMI ≥ 30.0 kg/m2 was considered obese,68,68,2-3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text and figure 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Relative abundance of fiber intake in a cohort of diverse cohort of first year college students living in university housing,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales",3379134|1224|1236|91347|543;3379134|1224|1236|91347,Complete,Shaimaa Elsafoury
bsdb:30541450/2/2,30541450,"cross-sectional observational, not case-control",30541450,10.1186/s12866-018-1362-x,NA,"Whisner C.M., Maldonado J., Dente B., Krajmalnik-Brown R. , Bruening M.","Diet, physical activity and screen time but not body mass index are associated with the gut microbiome of a diverse cohort of college students living in university housing: a cross-sectional study",BMC microbiology,2018,"Adolescence, Diet, Lifestyle behaviors, Microbiome, Microbiota, Obesity, Pediatric, Physical activity",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,hight moderate to vigrous physical activity,low,BMI ≥ 30.0 kg/m2 was considered obese,68,68,2-3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Text and figure 4,10 January 2021,Shaimaa Elsafoury,"Merit,WikiWorks,Lwaldron,Iram jamshed,Folakunmi",Relative abundance of fiber intake in a cohort of diverse cohort of first year college students living in university housing,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171552|577309,Complete,Shaimaa Elsafoury
bsdb:30542916/1/1,30542916,time series / longitudinal observational,30542916,10.1007/s00284-018-1610-1,NA,"Guo R., Liu H., Li X., Yang Q., Jia L., Zheng Y. , Li W.",Subgingival Microbial Changes During the First 3 Months of Fixed Appliance Treatment in Female Adult Patients,Current microbiology,2019,NA,Experiment 1,China,Homo sapiens,Dental plaque,UBERON:0016482,Gingival disease,EFO:0009670,before,1 month after the placement of the brackets,subgingial microbial changes during fixed appliance treatment,10,10,1 month,16S,34,Illumina,NA,Metastats,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 1,Figure 5,10 January 2021,Rimsha Azhar,WikiWorks,Relative abundance of microbiota that showed statistically significant differences among three different time points,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga",3379134|1224|1236|135625|712|713;3379134|976|117743|200644|49546|1016,Complete,NA
bsdb:30542916/2/1,30542916,time series / longitudinal observational,30542916,10.1007/s00284-018-1610-1,NA,"Guo R., Liu H., Li X., Yang Q., Jia L., Zheng Y. , Li W.",Subgingival Microbial Changes During the First 3 Months of Fixed Appliance Treatment in Female Adult Patients,Current microbiology,2019,NA,Experiment 2,China,Homo sapiens,Dental plaque,UBERON:0016482,Gingival disease,EFO:0009670,before,3 months after the placement of the brackets,subgingial microbial changes during fixed appliance treatment,10,10,1 month,16S,34,Illumina,NA,Metastats,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 1,Figure 5,10 January 2021,Rimsha Azhar,WikiWorks,Relative abundance of microbiota that showed statistically significant differences among three different time points,increased,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,3379134|976|117743|200644|49546|1016,Complete,NA
bsdb:30542916/2/2,30542916,time series / longitudinal observational,30542916,10.1007/s00284-018-1610-1,NA,"Guo R., Liu H., Li X., Yang Q., Jia L., Zheng Y. , Li W.",Subgingival Microbial Changes During the First 3 Months of Fixed Appliance Treatment in Female Adult Patients,Current microbiology,2019,NA,Experiment 2,China,Homo sapiens,Dental plaque,UBERON:0016482,Gingival disease,EFO:0009670,before,3 months after the placement of the brackets,subgingial microbial changes during fixed appliance treatment,10,10,1 month,16S,34,Illumina,NA,Metastats,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 2,Figure 5,10 January 2021,Rimsha Azhar,"Fatima,WikiWorks",Relative abundance of microbiota that showed statistically significant differences among three different time points,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis|s__Streptococcus oralis subsp. tigurinus",1783272|1239|91061|186826|186828|117563;1783272|1239|91061|186826|1300|1301|1303|1077464,Complete,NA
bsdb:30545401/1/1,30545401,case-control,30545401,10.1186/s40168-018-0603-4,NA,"Forbes J.D., Chen C.Y., Knox N.C., Marrie R.A., El-Gabalawy H., de Kievit T., Alfa M., Bernstein C.N. , Van Domselaar G.",A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?,Microbiome,2018,"16S rRNA gene amplicon sequencing, Bacteria, Gut microbiota, Immune-mediated inflammatory disease, Inflammatory bowel disease, Machine learning classifiers, Multiple sclerosis, Rheumatoid arthritis, Taxonomic biomarkers",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,healthy controls,crohn's disease,patients with immune-mediated inflammatory disease (IMID),23,20,2 months,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Table 2,10 January 2021,Fatima Zohra,"Fatima,WikiWorks,Merit,ChiomaBlessing",Abundant taxa in Crohn's disease patients microbiota relative to healthy controls (HC),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|201174|1760|2037|2049|1654;1783272|1239;1783272|1239|186801|3085636|186803|572511;1783272|1239|91061|186826|186828;1783272|201174|84998|1643822|1643826|84111;1783272|1239|526524|526525|128827|1573536;1783272|1239|91061|1385|539738|1378;1783272|1239|186801|3082720|186804|1505657;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803,Complete,Fatima
bsdb:30545401/1/2,30545401,case-control,30545401,10.1186/s40168-018-0603-4,NA,"Forbes J.D., Chen C.Y., Knox N.C., Marrie R.A., El-Gabalawy H., de Kievit T., Alfa M., Bernstein C.N. , Van Domselaar G.",A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?,Microbiome,2018,"16S rRNA gene amplicon sequencing, Bacteria, Gut microbiota, Immune-mediated inflammatory disease, Inflammatory bowel disease, Machine learning classifiers, Multiple sclerosis, Rheumatoid arthritis, Taxonomic biomarkers",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,healthy controls,crohn's disease,patients with immune-mediated inflammatory disease (IMID),23,20,2 months,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Table 2,10 January 2021,Fatima Zohra,"Fatima,WikiWorks,ChiomaBlessing",Abundant taxa in Crohn's disease patients microbiota relative to healthy controls (HC),decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Asaccharobacter,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|201174|84998|1643822|1643826|553372;1783272|1239|186801;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|33042;1783272|201174|84998|84999|84107;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|204475;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|186802|216572|292632;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|216572,Complete,Fatima
bsdb:30545401/2/1,30545401,case-control,30545401,10.1186/s40168-018-0603-4,NA,"Forbes J.D., Chen C.Y., Knox N.C., Marrie R.A., El-Gabalawy H., de Kievit T., Alfa M., Bernstein C.N. , Van Domselaar G.",A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?,Microbiome,2018,"16S rRNA gene amplicon sequencing, Bacteria, Gut microbiota, Immune-mediated inflammatory disease, Inflammatory bowel disease, Machine learning classifiers, Multiple sclerosis, Rheumatoid arthritis, Taxonomic biomarkers",Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,healthy controls,ulcerative colitis,patients with immune-mediated inflammatory disease (IMID),23,19,2 months,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Table 2,10 January 2021,Fatima Zohra,"Fatima,WikiWorks,Merit,ChiomaBlessing",Abundant taxa in Ulcerative colitis patients microbiota relative to healthy controls (HC),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|201174|1760|2037|2049|1654;1783272|1239|186801|186802|186806|264995;1783272|201174|1760|85004|31953|1678;1783272|201174|84998|1643822|1643826|84111;1783272|1239|526524|526525|128827|1573536;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803,Complete,Fatima
bsdb:30545401/2/2,30545401,case-control,30545401,10.1186/s40168-018-0603-4,NA,"Forbes J.D., Chen C.Y., Knox N.C., Marrie R.A., El-Gabalawy H., de Kievit T., Alfa M., Bernstein C.N. , Van Domselaar G.",A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?,Microbiome,2018,"16S rRNA gene amplicon sequencing, Bacteria, Gut microbiota, Immune-mediated inflammatory disease, Inflammatory bowel disease, Machine learning classifiers, Multiple sclerosis, Rheumatoid arthritis, Taxonomic biomarkers",Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,healthy controls,ulcerative colitis,patients with immune-mediated inflammatory disease (IMID),23,19,2 months,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Table 2,10 January 2021,Fatima Zohra,"WikiWorks,ChiomaBlessing",Abundant taxa in Ulcerative colitis patients microbiota relative to healthy controls (HC),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter",1783272|1239|186801|186802|204475;1783272|201174|84998|1643822|1643826|644652;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|44748,Complete,Fatima
bsdb:30545401/3/1,30545401,case-control,30545401,10.1186/s40168-018-0603-4,NA,"Forbes J.D., Chen C.Y., Knox N.C., Marrie R.A., El-Gabalawy H., de Kievit T., Alfa M., Bernstein C.N. , Van Domselaar G.",A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?,Microbiome,2018,"16S rRNA gene amplicon sequencing, Bacteria, Gut microbiota, Immune-mediated inflammatory disease, Inflammatory bowel disease, Machine learning classifiers, Multiple sclerosis, Rheumatoid arthritis, Taxonomic biomarkers",Experiment 3,Canada,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,healthy controls,multiple sceloris,patients with immune-mediated inflammatory disease (IMID),23,19,2 months,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Table 2,10 January 2021,Fatima Zohra,"WikiWorks,Merit,ChiomaBlessing",Abundant taxa in Multiple sclerosis patients microbiota relative to healthy controls (HC),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",1783272|201174|1760|2037|2049|1654;1783272|1239|186801|186802|186806|264995;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|1643822|1643826|84111;1783272|1239|526524|526525|128827|1573536;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810281|191303,Complete,Fatima
bsdb:30545401/3/2,30545401,case-control,30545401,10.1186/s40168-018-0603-4,NA,"Forbes J.D., Chen C.Y., Knox N.C., Marrie R.A., El-Gabalawy H., de Kievit T., Alfa M., Bernstein C.N. , Van Domselaar G.",A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?,Microbiome,2018,"16S rRNA gene amplicon sequencing, Bacteria, Gut microbiota, Immune-mediated inflammatory disease, Inflammatory bowel disease, Machine learning classifiers, Multiple sclerosis, Rheumatoid arthritis, Taxonomic biomarkers",Experiment 3,Canada,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,healthy controls,multiple sceloris,patients with immune-mediated inflammatory disease (IMID),23,19,2 months,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Table 2,10 January 2021,Fatima Zohra,"WikiWorks,ChiomaBlessing",Abundant taxa in Multiple sclerosis patients microbiota relative to healthy controls (HC),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sporobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",1783272|1239|186801|186802|3085642|580596;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|204475;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|100132;1783272|1239|186801|186802|216572|292632,Complete,Fatima
bsdb:30545401/4/1,30545401,case-control,30545401,10.1186/s40168-018-0603-4,NA,"Forbes J.D., Chen C.Y., Knox N.C., Marrie R.A., El-Gabalawy H., de Kievit T., Alfa M., Bernstein C.N. , Van Domselaar G.",A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?,Microbiome,2018,"16S rRNA gene amplicon sequencing, Bacteria, Gut microbiota, Immune-mediated inflammatory disease, Inflammatory bowel disease, Machine learning classifiers, Multiple sclerosis, Rheumatoid arthritis, Taxonomic biomarkers",Experiment 4,Canada,Homo sapiens,Feces,UBERON:0001988,Rheumatoid arthritis,EFO:0000685,healthy controls,arthiritis,patients with immune-mediated inflammatory disease (IMID),23,21,2 months,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Table 2,10 January 2021,Fatima Zohra,"Fatima,WikiWorks,Merit,ChiomaBlessing",Abundant taxa in Rheumatoid arthritis patients microbiota relative to healthy controls (HC),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|201174|1760|2037|2049|1654;1783272|1239;1783272|201174|84998|1643822|1643826|84111;1783272|1239|526524|526525|128827|1573536;1783272|1239|91061|1385|539738|1378;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803,Complete,Fatima
bsdb:30545401/4/2,30545401,case-control,30545401,10.1186/s40168-018-0603-4,NA,"Forbes J.D., Chen C.Y., Knox N.C., Marrie R.A., El-Gabalawy H., de Kievit T., Alfa M., Bernstein C.N. , Van Domselaar G.",A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?,Microbiome,2018,"16S rRNA gene amplicon sequencing, Bacteria, Gut microbiota, Immune-mediated inflammatory disease, Inflammatory bowel disease, Machine learning classifiers, Multiple sclerosis, Rheumatoid arthritis, Taxonomic biomarkers",Experiment 4,Canada,Homo sapiens,Feces,UBERON:0001988,Rheumatoid arthritis,EFO:0000685,healthy controls,arthiritis,patients with immune-mediated inflammatory disease (IMID),23,21,2 months,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Table 2,10 January 2021,Fatima Zohra,"WikiWorks,ChiomaBlessing",Abundant taxa in Rheumatoid arthritis patients microbiota relative to healthy controls (HC),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",1783272|1239|186801|186802|186806|264995;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|204475;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|186802|216572|292632,Complete,Fatima
bsdb:30547792/1/1,30547792,laboratory experiment,30547792,10.1186/s12931-018-0959-9,https://pubmed.ncbi.nlm.nih.gov/30547792/,"Zhang R., Chen L., Cao L., Li K.J., Huang Y., Luan X.Q. , Li G.",Effects of smoking on the lower respiratory tract microbiome in mice,Respiratory research,2018,"Inflammation, Lower respiratory tract, Mice, Microbiome, Smoking",Experiment 1,China,Mus musculus,Lung,UBERON:0002048,Smoking behavior,EFO:0004318,Non-smoking,Smoking,Male Kunming mice exposed to smoking for 2h per day for 90 days.,20,20,NA,16S,45,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 10,14 March 2023,Sophy,"Sophy,Aiyshaaaa,Claregrieve1,WikiWorks",Differential microbial abundance between the smoking and non-smoking mice,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Acidobacteriota|c__Blastocatellia|o__Blastocatellales|f__Blastocatellaceae|g__Blastocatella,k__Pseudomonadati|p__Acidobacteriota|c__Blastocatellia|o__Blastocatellales,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Spirosomataceae|g__Dyadobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Chloroflexota|c__Ktedonobacteria|o__Ktedonobacterales|f__Ktedonobacteraceae,k__Bacillati|p__Chloroflexota|c__Ktedonobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Nitrosomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Planomicrobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Sporolactobacillaceae|g__Pullulanibacillus,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Sporolactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Trichococcus",3379134|976|200643|171549|171552|1283313;3379134|57723|1562566|1748771|1748772|1281902;3379134|57723|1562566|1748771;3379134|976|768503|768507|2896860|120831;3379134|1224|1236|91347|543|1940338;1783272|200795|388447|388448|388449;1783272|200795|388447;1783272|1239|91061|186826|1300|1357;1783272|544448|31969;1783272|544448;3379134|1224|28216|32003|206379;3379134|1224|28216|32003;3379134|1224|28216|80840|75682;3379134|976|117747|200666|84566|84567;1783272|1239|91061|1385|186818|162291;3379134|976|200643|171549|171551|836;3379134|1224|1236|91347|1903414|583;1783272|1239|91061|1385|186821|475230;3379134|976|117747|200666|84566;1783272|1239|91061|1385|186821;1783272|1239|186801|186802|216572|292632;1783272|1239|91061|186826|186828|82802,Complete,Claregrieve1
bsdb:30547792/1/2,30547792,laboratory experiment,30547792,10.1186/s12931-018-0959-9,https://pubmed.ncbi.nlm.nih.gov/30547792/,"Zhang R., Chen L., Cao L., Li K.J., Huang Y., Luan X.Q. , Li G.",Effects of smoking on the lower respiratory tract microbiome in mice,Respiratory research,2018,"Inflammation, Lower respiratory tract, Mice, Microbiome, Smoking",Experiment 1,China,Mus musculus,Lung,UBERON:0002048,Smoking behavior,EFO:0004318,Non-smoking,Smoking,Male Kunming mice exposed to smoking for 2h per day for 90 days.,20,20,NA,16S,45,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 10,23 April 2023,Sophy,"Sophy,Claregrieve1,WikiWorks",Differential microbial abundance between the smoking and non-smoking mice,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Brevibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Desulfuromonadales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Diaphorobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Geobacterales|f__Geobacteraceae|g__Geobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kluyvera,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Nesterenkonia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella",1783272|201174|1760|85006|85020|43668;1783272|1239|91061|1385|186822|55080;3379134|1224|28216|80840|119060;3379134|200940|3031651|69541;3379134|1224|28216|80840|80864|238749;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|200940|3031651|3031668|213422|28231;3379134|1224|1236|91347|543|579;1783272|1239|91061|186826|81850;1783272|1239|91061|186826|33958|1578;3379134|1224|28211|356|69277|68287;1783272|201174|1760|85006|1268|57494;3379134|1224|1236|135619;1783272|1239|909932|1843488|909930|33024;3379134|1224|28211|356|69277;3379134|1224|28216|80840|119060|48736;3379134|1224|1236|91347|543|160674,Complete,Claregrieve1
bsdb:30547792/2/1,30547792,laboratory experiment,30547792,10.1186/s12931-018-0959-9,https://pubmed.ncbi.nlm.nih.gov/30547792/,"Zhang R., Chen L., Cao L., Li K.J., Huang Y., Luan X.Q. , Li G.",Effects of smoking on the lower respiratory tract microbiome in mice,Respiratory research,2018,"Inflammation, Lower respiratory tract, Mice, Microbiome, Smoking",Experiment 2,China,Mus musculus,Lung,UBERON:0002048,Smoking behavior,EFO:0004318,Non-smoking,Smoking,Male Kunming mice exposed to smoking for 2h per day for 90 days.,20,20,NA,16S,45,Illumina,relative abundances,Mann-Whitney (Wilcoxon),NA,NA,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 2,29 May 2023,Atrayees,"Atrayees,ChiomaBlessing,WikiWorks",Differentially abundant taxon in the smoking and the non-smoking groups.,increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia|o__Acidimicrobiales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Methanobacteriati|p__Thermoplasmatota|c__Thermoplasmata|o__Candidatus Thermoprofundales,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Spirosomataceae|g__Dyadobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Jatrophihabitantales|f__Jatrophihabitantaceae|g__Jatrophihabitans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Macrococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Planomicrobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Pseudochrobactrum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Sporolactobacillaceae|g__Pullulanibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Trichococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Planctomycetales|f__Planctomycetaceae|s__uncultured Planctomycetaceae bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",1783272|201174|84992|84993;3379134|976|200643|171549|171552|1283313;3366610|2283796|183967|347538;3379134|976|768503|768507|2896860|120831;1783272|201174|1760|2805415|2805416|1434010;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|1385|90964|69965;1783272|1239|186801|3085636|186803|248744;3379134|976|200643|171549|2005523|346096;3379134|976|117747|200666|84566|84567;1783272|1239|91061|1385|186818|162291;3379134|976|200643|171549|171551|836;3379134|1224|1236|91347|1903414|583;3379134|1224|28211|356|118882|354349;1783272|1239|91061|1385|186821|475230;1783272|1239|186801|186802|216572|292632;1783272|1239|91061|186826|186828|82802;3379134|1224|28211|204458|76892;3379134|203682|203683|112|126|100233;3379134|1224|1236|91347|543|1940338,Complete,Atrayees
bsdb:30547792/2/2,30547792,laboratory experiment,30547792,10.1186/s12931-018-0959-9,https://pubmed.ncbi.nlm.nih.gov/30547792/,"Zhang R., Chen L., Cao L., Li K.J., Huang Y., Luan X.Q. , Li G.",Effects of smoking on the lower respiratory tract microbiome in mice,Respiratory research,2018,"Inflammation, Lower respiratory tract, Mice, Microbiome, Smoking",Experiment 2,China,Mus musculus,Lung,UBERON:0002048,Smoking behavior,EFO:0004318,Non-smoking,Smoking,Male Kunming mice exposed to smoking for 2h per day for 90 days.,20,20,NA,16S,45,Illumina,relative abundances,Mann-Whitney (Wilcoxon),NA,NA,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 2,29 May 2023,Atrayees,"Atrayees,ChiomaBlessing,Chinelsy,WikiWorks",Differentially abundant taxon in the smoking and the non-smoking groups.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Brevibacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Catenisphaera,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Diaphorobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Geobacterales|f__Geobacteraceae|g__Geobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kluyvera,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Nesterenkonia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paucimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Variibacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|s__uncultured Phyllobacteriaceae bacterium",1783272|201174|1760|85006|85020|43668;1783272|1239|91061|1385|186822|55080;1783272|1239|526524|526525|128827|1774107;1783272|201174|1760|85007|1653|1716;3379134|1224|28216|80840|80864|238749;3379134|1224|1236|91347|543|547;3379134|200940|3031651|3031668|213422|28231;1783272|1239|91061|1385|90964|227979;3379134|1224|1236|91347|543|579;1783272|1239|91061|186826|33958|1578;3379134|1224|28211|356|69277|68287;3379134|200930|68337|191393|2945020|248038;1783272|201174|1760|85006|1268|57494;3379134|1224|1236|135625|712|745;3379134|1224|28216|80840|119060|157932;3379134|1224|1236|91347|543|160674;3379134|1224|28211|356|41294|1649510;3379134|1224|28211|356|69277|257462,Complete,Atrayees
bsdb:30548192/1/1,30548192,case-control,30548192,10.1111/1462-2920.14498,NA,"Jin Y., Liu Y., Zhao L., Zhao F., Feng J., Li S., Chen H., Sun J., Zhu B., Geng R. , Wei Y.",Gut microbiota in patients after surgical treatment for colorectal cancer,Environmental microbiology,2019,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,postoperation patients,Carcinoma patients,The adenoma and carcinoma patients were diagnosed by colonoscopic examination and histopathological review of biopsies. Postoperative patients were classified as having NDA or CIT by follow-up surveillance colonoscopy and biopsies,47,15,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Supplemental Figure 5 and Table S2,10 January 2021,Rimsha Azhar,WikiWorks,The relative abundance of genus in carcinoma and postoperative patients,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|171552|838;1783272|1239|1737404|1737405|1570339|150022;3379134|1224|28216|80840|119060|48736;1783272|201174|84998|84999|1643824|1380;1783272|1239|186801|186802|404402;3379134|976|200643|171549|171552|1283313;1783272|201174|1760|85007|1653|1716;1783272|1239|526524|526525|2810280|135858;1783272|1239|526524|526525|128827|1573535;1783272|1239|1737404|1737405|1570339|543311;3379134|1224|1236|72274|135621|286;1783272|1239|91061|1385|539738|1378;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836;1783272|1239|91061|186826|33958|46255;1783272|1239|91061|186826|186828|117563;1783272|201174|1760|2037|2049|1654,Complete,Shaimaa Elsafoury
bsdb:30548192/1/2,30548192,case-control,30548192,10.1111/1462-2920.14498,NA,"Jin Y., Liu Y., Zhao L., Zhao F., Feng J., Li S., Chen H., Sun J., Zhu B., Geng R. , Wei Y.",Gut microbiota in patients after surgical treatment for colorectal cancer,Environmental microbiology,2019,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,postoperation patients,Carcinoma patients,The adenoma and carcinoma patients were diagnosed by colonoscopic examination and histopathological review of biopsies. Postoperative patients were classified as having NDA or CIT by follow-up surveillance colonoscopy and biopsies,47,15,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Supplemental Figure 5 and Table S2,10 January 2021,Rimsha Azhar,WikiWorks,The relative abundance of genus in carcinoma and postoperative patients,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Parascardovia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",3384189|32066|203490|203491|1129771|32067;1783272|201174|1760|85004|31953|196082;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85006|85023|33882;1783272|201174|1760|85007|2805586|1847725;1783272|1239|526524|526525|128827|1573534;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|1506577;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|2316020|33038,Complete,Shaimaa Elsafoury
bsdb:30548192/2/1,30548192,case-control,30548192,10.1111/1462-2920.14498,NA,"Jin Y., Liu Y., Zhao L., Zhao F., Feng J., Li S., Chen H., Sun J., Zhu B., Geng R. , Wei Y.",Gut microbiota in patients after surgical treatment for colorectal cancer,Environmental microbiology,2019,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,CIT(cleain intestine),NDA(new dev. adenoma),The adenoma and carcinoma patients were diagnosed by colonoscopic examination and histopathological review of biopsies. Postoperative patients were classified as having NDA or CIT by follow-up surveillance colonoscopy and biopsies,26,21,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,2.5,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 1,Figure 4 and Table B,10 January 2021,Rimsha Azhar,WikiWorks,LEfSe identified differene in abundace between NDA and CIT,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium",1783272|1239|91061|186826|186827|46123;1783272|201174|84998|84999|1643824|1380;3379134|1224|1236|91347|1903414|581;3379134|976|200643|171549|171552|838;1783272|1239|526524|526525|128827|123375,Complete,Shaimaa Elsafoury
bsdb:30548192/2/2,30548192,case-control,30548192,10.1111/1462-2920.14498,NA,"Jin Y., Liu Y., Zhao L., Zhao F., Feng J., Li S., Chen H., Sun J., Zhu B., Geng R. , Wei Y.",Gut microbiota in patients after surgical treatment for colorectal cancer,Environmental microbiology,2019,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,CIT(cleain intestine),NDA(new dev. adenoma),The adenoma and carcinoma patients were diagnosed by colonoscopic examination and histopathological review of biopsies. Postoperative patients were classified as having NDA or CIT by follow-up surveillance colonoscopy and biopsies,26,21,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,2.5,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 2,Figure 4 and Table B,10 January 2021,Rimsha Azhar,WikiWorks,LEfSe identified differene in abundace between NDA and CIT,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus",3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|33042;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|3085636|186803|437755;1783272|1239|186801|186802|216572|459786;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|216572|244127,Complete,Shaimaa Elsafoury
bsdb:30551387/1/1,30551387,laboratory experiment,30551387,10.1016/j.biopha.2018.11.013,NA,"Liu D., Lin L., Lin Y., Zhong Y., Zhang S., Liu W., Zou B., Liao Q. , Xie Z.",Zengye decoction induces alterations to metabolically active gut microbiota in aged constipated rats,Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie,2019,"16s rRNA, Constipation, Gut microbiome, Metabolism, Zengye decoction",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,Combination of Control and Recovery group,ZYD (Zengye decoction) group,Aged constipated rats treated with Zengye decoction (ZYD),20,10,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,29 March 2025,Tosin,Tosin,Differentially abundant microbial cladogram obtained by LEfSe (B),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|s__Enterococcaceae bacterium RF39",1783272|1239|186801|186802|31979|1485;1783272|1239|526524|526525|128827|61170;1783272|544448|31969;3379134|1224|1236|2887326|468;1783272|544448;1783272|1239|909932|1843488|909930|33024;3379134|1224|1236|72274;3379134|976|200643|171549|171550;1783272|1239|909932|1843489|31977;1783272|1239|91061|186826|81852|423410,Complete,Svetlana up
bsdb:30551387/2/1,30551387,laboratory experiment,30551387,10.1016/j.biopha.2018.11.013,NA,"Liu D., Lin L., Lin Y., Zhong Y., Zhang S., Liu W., Zou B., Liao Q. , Xie Z.",Zengye decoction induces alterations to metabolically active gut microbiota in aged constipated rats,Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie,2019,"16s rRNA, Constipation, Gut microbiome, Metabolism, Zengye decoction",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,Combination of Recovery group and ZYD (Zengye decoction) group,Control group,Aged constipated rats in the control group,20,10,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,30 March 2025,Tosin,Tosin,Differentially abundant microbial cladogram obtained by LEfSe (B),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Oligella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus",1783272|201174|1760|2037;3379134|1224|1236|135624|84642;3379134|1224|1236|135624;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;1783272|1239|186801|186802|186807|51514;3379134|1224|1236|135614|32033;3379134|1224|1236|135614;3379134|1224|28216|80840|506|90243;3379134|1224|28216|80840|75682|846;3379134|1224|28216|80840|75682;3379134|1224|1236|2887326|468|497;1783272|1239|186801|3085636|186803|841;1783272|1239|526524|526525|2810281|191303;1783272|1239|526524|526525|2810281;1783272|1239|91061|186826|81852|2737,Complete,Svetlana up
bsdb:30551387/3/1,30551387,laboratory experiment,30551387,10.1016/j.biopha.2018.11.013,NA,"Liu D., Lin L., Lin Y., Zhong Y., Zhang S., Liu W., Zou B., Liao Q. , Xie Z.",Zengye decoction induces alterations to metabolically active gut microbiota in aged constipated rats,Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie,2019,"16s rRNA, Constipation, Gut microbiome, Metabolism, Zengye decoction",Experiment 3,China,Rattus norvegicus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,Combination of Control group and ZYD (Zengye decoction) group,Recovery group,Aged constipated rats in the recovery group,20,10,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,30 March 2025,Tosin,"Tosin,KateRasheed",Differentially abundant microbial cladogram obtained by LEfSe (B),increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales,k__Pseudomonadati|p__Deferribacterota,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres",3379134|29547|3031852|213849;3379134|200930|68337|191393|191394;3379134|200930|68337|191393;3379134|200930;3379134|200940|3031449|213115|194924|872;3379134|29547|3031852;3379134|29547|3031852|213849|72293;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;3379134|200930|68337|191393|2945020|248038;3379134|976|200643|171549|171552|838;3379134|200930|68337,Complete,Svetlana up
bsdb:30551387/4/1,30551387,laboratory experiment,30551387,10.1016/j.biopha.2018.11.013,NA,"Liu D., Lin L., Lin Y., Zhong Y., Zhang S., Liu W., Zou B., Liao Q. , Xie Z.",Zengye decoction induces alterations to metabolically active gut microbiota in aged constipated rats,Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie,2019,"16s rRNA, Constipation, Gut microbiome, Metabolism, Zengye decoction",Experiment 4,China,Rattus norvegicus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,Control group,Recovery group,Aged constipated rats in the recovery group,10,10,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 5,30 March 2025,Tosin,Tosin,"Comparison of relative abundance at the phylum, family and genus levels among the three groups",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,s__bacterium AF12,k__Pseudomonadati|p__Deferribacterota",1783272|1239|186801|3082768|990719;3379134|200940|3031449|213115|194924|872;3379134|29547|3031852|213849|72293;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171550;1729795;3379134|200930,Complete,Svetlana up
bsdb:30551387/4/2,30551387,laboratory experiment,30551387,10.1016/j.biopha.2018.11.013,NA,"Liu D., Lin L., Lin Y., Zhong Y., Zhang S., Liu W., Zou B., Liao Q. , Xie Z.",Zengye decoction induces alterations to metabolically active gut microbiota in aged constipated rats,Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie,2019,"16s rRNA, Constipation, Gut microbiome, Metabolism, Zengye decoction",Experiment 4,China,Rattus norvegicus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,Control group,Recovery group,Aged constipated rats in the recovery group,10,10,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 5,30 March 2025,Tosin,Tosin,"Comparison of relative abundance at the phylum, family and genus levels among the three groups",decreased,"k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Oligella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium",1783272|544448;3379134|1224|28216|80840|75682;1783272|1239|909932|1843489|31977;1783272|1239|526524|526525|2810281;3379134|1224|1236|135624|84642;3379134|1224|28216|80840|75682|846;3379134|1224|28216|80840|506|90243;1783272|1239|186801|3085636|186803|841;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|31979|1485;1783272|1239|526524|526525|2810281|191303;1783272|201174|1760|85007|1653|1716,Complete,Svetlana up
bsdb:30551387/5/1,30551387,laboratory experiment,30551387,10.1016/j.biopha.2018.11.013,NA,"Liu D., Lin L., Lin Y., Zhong Y., Zhang S., Liu W., Zou B., Liao Q. , Xie Z.",Zengye decoction induces alterations to metabolically active gut microbiota in aged constipated rats,Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie,2019,"16s rRNA, Constipation, Gut microbiome, Metabolism, Zengye decoction",Experiment 5,China,Rattus norvegicus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,Recovery group,ZYD (Zengye decoction) group,Aged constipated rats treated with Zengye decoction (ZYD),10,10,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 5,30 March 2025,Tosin,Tosin,"Comparison of relative abundance at the phylum, family and genus levels among the three groups",increased,"k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Oligella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|544448;3379134|1224|28216|80840|75682;1783272|1239|909932|1843489|31977;1783272|1239|186801|186802|31979;3379134|1224|1236|135624|84642;3379134|1224|28216|80840|75682|846;3379134|1224|28216|80840|506|90243;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:30551387/5/2,30551387,laboratory experiment,30551387,10.1016/j.biopha.2018.11.013,NA,"Liu D., Lin L., Lin Y., Zhong Y., Zhang S., Liu W., Zou B., Liao Q. , Xie Z.",Zengye decoction induces alterations to metabolically active gut microbiota in aged constipated rats,Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie,2019,"16s rRNA, Constipation, Gut microbiome, Metabolism, Zengye decoction",Experiment 5,China,Rattus norvegicus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,Recovery group,ZYD (Zengye decoction) group,Aged constipated rats treated with Zengye decoction (ZYD),10,10,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 5,30 March 2025,Tosin,Tosin,"Comparison of relative abundance at the phylum, family and genus levels among the three groups",decreased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,s__bacterium AF12,k__Pseudomonadati|p__Deferribacterota",3379134|29547|3031852|213849|72293;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;3379134|976|200643|171549|171550;1729795;3379134|200930,Complete,Svetlana up
bsdb:30558669/1/1,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 1,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Cluster 1 and Cluster 3,Cluster 2,"The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella.

This group consists of esotypes that are dominated by Streptococcus (Streptococcus mitis/oralis/pneumoniae).",NA,NA,2 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,"Additional file 1, sheet 6",16 May 2024,Fiddyhamma,"Fiddyhamma,Victoria,Ifeanyisam,WikiWorks",The taxonomic differences across clusters in 16S rRNA amplicon data using LEfSe analysis.,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota",1783272|1239|91061;1783272|1239|91061|186826;3379134|976|200643|171549|171551|836;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|1385;1783272|1239,Complete,Svetlana up
bsdb:30558669/2/1,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 2,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Cluster 1 and Cluster 2,Cluster 3,"The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella.

This group consists of esotypes that are dominated by by Prevotella (Prevotella melaninogenica and Prevotella pallens), and to a lesser extent Veillonella.",NA,NA,2 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,"Additional file 1, sheet 6",16 May 2024,Fiddyhamma,"Fiddyhamma,Victoria,Ifeanyisam,WikiWorks",The taxonomic differences across clusters in 16S rRNA amplicon data using LEfSe analysis.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;1783272|201174;1783272|201174|84998|84999|1643824|1380;3379134|976|200643|171549;3379134|976|200643;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|1239|91061|186826|186828|117563;3379134|1224|28216|206351|481|32257;1783272|1239|186801|3085636|186803|1164882;1783272|1239|186801|3085636|186803;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3082720|543314|86331;1783272|1239|909932;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|909932|909929;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977;1783272|1239|91061|186826|186828;1783272|1239|186801|3085636|186803;1783272|1239|909932|1843489|31977;1783272|201174|84992;3379134|976;3379134|976|200643|171549|171552,Complete,Svetlana up
bsdb:30558669/3/1,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 3,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Cluster 2 and Cluster 3,Cluster 1,"The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. This group consists of esotypes that are dominated by by Prevotella (Prevotella melaninogenica and Prevotella pallens), and to a lesser extent Veillonella.",NA,NA,2 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,"Additional file 1, sheet 6",16 May 2024,Fiddyhamma,"Fiddyhamma,Victoria,Ifeanyisam,WikiWorks",The taxonomic differences across clusters in 16S rRNA amplicon data using LEfSe analysis.	  ,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:30558669/4/1,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 4,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Cluster 1 and Cluster 3,Cluster 2,The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. This group consists of esotypes that are dominated by Streptococcus (Streptococcus mitis/oralis/pneumoniae).,NA,NA,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,"Additional file 1, sheet 7",25 May 2024,Fiddyhamma,"Fiddyhamma,Victoria,Ifeanyisam,WikiWorks",The taxonomic differences across clusters in MetaPhlan2 output from shotgun sequencing data using LEfSe analysis. ,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota",1783272|1239|91061;1783272|1239,Complete,Svetlana up
bsdb:30558669/5/1,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 5,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Cluster 1 and Cluster 2,Cluster 3,"The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. This group consists of esotypes that are dominated by by Prevotella (Prevotella melaninogenica and Prevotella pallens), and to a lesser extent Veillonella.",NA,NA,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,"Additional file 1, sheet 7",29 May 2024,Fiddyhamma,"Fiddyhamma,Victoria,Ifeanyisam,WikiWorks",The taxonomic differences across clusters in MetaPhlan2 output from shotgun sequencing data using LEfSe analysis.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella veroralis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota",3379134|976|200643|171549;3379134|976|200643;1783272|1239|909932;3379134|976|200643|171549|171552|838|470565;3379134|976|200643|171549|171552|838|60133;3379134|976|200643|171549|171552|838|28137;1783272|1239|909932|909929;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977;1783272|1239|909932|1843489|31977|29465;3379134|976,Complete,Svetlana up
bsdb:30558669/6/1,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 6,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Cluster 2 and Cluster 3,Cluster 1,"The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. This group consists of esotypes that are dominated by by Prevotella (Prevotella melaninogenica and Prevotella pallens), and to a lesser extent Veillonella.",NA,NA,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,"Additional file 1, sheet 7",29 May 2024,Fiddyhamma,"Fiddyhamma,Victoria,Ifeanyisam,WikiWorks",The taxonomic differences across clusters in MetaPhlan2 output from shotgun sequencing data using LEfSe analysis.,increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",1783272|201174|84992;1783272|201174|1760|2037;1783272|201174;3379134|976|117743|200644|49546|1016;3379134|976|117743|200644|49546;3379134|976|117743|200644;3379134|976|117743;3379134|1224|1236;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712|724|729;1783272|201174|1760|85006|1268;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|1224;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|186828|117563;1783272|201174|1760|85006|1268|32207,Complete,Svetlana up
bsdb:30558669/7/1,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 7,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Normal esophagus),GERD (Gastroesophageal reflux disease),This group consists of patients with Gastroesophageal reflux disease.,59,29,2 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, sheet 4",16 August 2024,Fiddyhamma,"Fiddyhamma,Victoria,WikiWorks",The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Acetoanaerobium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae",1783272|1239|186801|3082720|3118655|186831;3379134|29547|3031852|213849|72294|194;1783272|1239|186801|3082720|3118655|44259;3379134|976|117743|200644|49546,Complete,Svetlana up
bsdb:30558669/7/2,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 7,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Normal esophagus),GERD (Gastroesophageal reflux disease),This group consists of patients with Gastroesophageal reflux disease.,59,29,2 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Additional file 3, sheet 4",17 August 2024,Victoria,"Victoria,Fiddyhamma,WikiWorks",The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|1940338;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:30558669/8/1,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 8,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal,Gastroesophageal reflux disease GERD(within subjects classified as PPI NO),This group consists of patients with Gastroesophageal reflux disease(within subjects classified as PPI NO),59,19,2 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, sheet 4",18 August 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Acetoanaerobium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",1783272|1239|186801|3082720|3118655|186831;3379134|29547|3031852|213849|72294|194;3379134|1224|1236|135615|868|2717;1783272|1239|186801|3082720|3118655|44259;3384189|32066|203490|203491|1129771|32067;3379134|1224|28216|206351|481;3379134|1224|28216|206351;3379134|976|200643|171549|171552|838;3379134|1224;33090|35493|3398|72025|3803|3814|508215;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|186802;3379134|976|117743|200644|49546;3379134|1224|1236|135625|712,Complete,Svetlana up
bsdb:30558669/8/2,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 8,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal,Gastroesophageal reflux disease GERD(within subjects classified as PPI NO),This group consists of patients with Gastroesophageal reflux disease(within subjects classified as PPI NO),59,19,2 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Additional file 3, sheet 4",18 August 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|909932|909929|1843491|82202;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|1940338;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3085636|186803|265975;3379134|976|200643|171549|171552|838;1783272|201174|84998|1643822|1643826|84108;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;3379134|976|200643|171549;1783272|1239|909932|1843489|31977,Complete,Svetlana up
bsdb:30558669/9/1,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 9,Australia,Homo sapiens,Esophagus,UBERON:0001043,Barrett's esophagus,EFO:0000280,Normal,Barrett’s Esophagus (BE),This group consists of patients with Barrett’s Esophagus,59,12,2 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, sheet 4",18 August 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",3379134|976|117743|200644|49546|1016;3384189|32066|203490|203491|1129771|32067,Complete,Svetlana up
bsdb:30558669/10/1,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 10,Australia,Homo sapiens,Esophagus,UBERON:0001043,Barrett's esophagus,EFO:0000280,Gastroesophageal reflux disease (GERD),Barrett’s Esophagus (BE),This group consists of patients with Barrett’s Esophagus,29,12,2 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, sheet 4",18 August 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga",3379134|1224|28216|80840;3379134|976|117743|200644|49546|1016,Complete,Svetlana up
bsdb:30558669/10/2,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 10,Australia,Homo sapiens,Esophagus,UBERON:0001043,Barrett's esophagus,EFO:0000280,Gastroesophageal reflux disease (GERD),Barrett’s Esophagus (BE),This group consists of patients with Barrett’s Esophagus,29,12,2 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Additional file 3, sheet 4",18 August 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,3379134|976|200643|171549|171552|1283313,Complete,Svetlana up
bsdb:30558669/11/1,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 11,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Gastroesophageal reflux disease (GERD),Glandular mucosa (GM),This group consists of patients with Glandular mucosa,29,14,2 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, sheet 4",18 August 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans",3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|1200657,Complete,Svetlana up
bsdb:30558669/11/2,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 11,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Gastroesophageal reflux disease (GERD),Glandular mucosa (GM),This group consists of patients with Glandular mucosa,29,14,2 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Additional file 3, sheet 4",18 August 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Acetoanaerobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|186801|3082720|3118655|186831;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|909932|1843489|31977,Complete,Svetlana up
bsdb:30558669/12/1,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 12,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Normal,Glandular mucosa (GM),This group consists of patients with Glandular mucosa,59,14,2 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, sheet 4",18 August 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552,Complete,Svetlana up
bsdb:30558669/12/2,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 12,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Normal,Glandular mucosa (GM),This group consists of patients with Glandular mucosa,59,14,2 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Additional file 3, sheet 4",18 August 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|976|200643|171549|171552;1783272|1239|909932|1843489|31977,Complete,Svetlana up
bsdb:30558669/13/1,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 13,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Normal esophagus),GERD (Gastroesophageal reflux disease),This group consists of patients with Gastroesophageal reflux disease.,59,29,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, sheet 5",18 August 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",The differences across disease subgroups using LEfSe analysis (Shotgun MetaPhlan2 data).,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria macacae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria meningitidis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella micans,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema medium,k__Fusobacteriati|p__Fusobacteriota",3384189|32066|203490|203491;3384189|32066|203490;3379134|1224|1236|135625|712|724|729;3379134|1224|28216|206351|481|482|496;3379134|1224|28216|206351|481|482|487;3379134|976|200643|171549|171552|838|28131;3379134|976|200643|171549|171552|838|189723;3379134|203691|203692|136|2845253|157|58231;3384189|32066,Complete,Svetlana up
bsdb:30558669/14/1,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 14,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Normal esophagus),GERD (Gastroesophageal reflux disease)within subjects classified as PPI NO,This group consists of patients with Gastroesophageal reflux disease(within subjects classified as PPI NO),59,19,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, sheet 5",18 August 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",The differences across disease subgroups using LEfSe analysis (Shotgun MetaPhlan2 data).,increased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria meningitidis,3379134|1224|28216|206351|481|482|487,Complete,Svetlana up
bsdb:30558669/14/2,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 14,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Normal esophagus),GERD (Gastroesophageal reflux disease)within subjects classified as PPI NO,This group consists of patients with Gastroesophageal reflux disease(within subjects classified as PPI NO),59,19,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Additional file 3, sheet 5",18 August 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",The differences across disease subgroups using LEfSe analysis (Shotgun MetaPhlan2 data).,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843489|31977|906|187326;3379134|976|200643|171549|171552|838|60133;1783272|201174|1760|85006|1268|32207,Complete,Svetlana up
bsdb:30558669/15/1,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 15,Australia,Homo sapiens,Esophagus,UBERON:0001043,Barrett's esophagus,EFO:0000280,Normal,Barrett’s Esophagus (BE),This group consists of patients with Barrett’s Esophagus,59,12,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, sheet 5",18 August 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",The differences across disease subgroups using LEfSe analysis (Shotgun MetaPhlan2 data).,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp. oral taxon 780,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella",1783272|1239|91061|186826|1300|1301|1305;1783272|1239|909932|1843489|31977|29465|671229;1783272|1239|91061|1385|539738|1378,Complete,Svetlana up
bsdb:30558669/16/1,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 16,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Normal,Glandular mucosa (GM),This group consists of patients with Glandular mucosa,59,14,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, sheet 5",24 September 2024,Fiddyhamma,"Fiddyhamma,Ifeanyisam,WikiWorks",The differences across disease subgroups using LEfSe analysis (Shotgun MetaPhlan2 data).,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera geminata,k__Shotokuvirae|p__Cossaviricota|c__Papovaviricetes|o__Zurhausenvirales|f__Papillomaviridae|s__Firstpapillomavirinae|g__Betapapillomavirus,k__Shotokuvirae|p__Cossaviricota|c__Papovaviricetes|o__Zurhausenvirales|f__Papillomaviridae|s__Firstpapillomavirinae|g__Betapapillomavirus|s__Betapapillomavirus 3,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus|s__Desulfobulbus sp. oral taxon 041,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia|s__Eggerthia catenaformis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium necrophorum,k__Shotokuvirae|p__Cossaviricota|c__Papovaviricetes|o__Zurhausenvirales|f__Papillomaviridae|s__Firstpapillomavirinae|g__Gammapapillomavirus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter pylori,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella oralis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria cinerea,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Shotokuvirae|p__Cossaviricota|c__Papovaviricetes|o__Zurhausenvirales|f__Papillomaviridae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella multiformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema socranskii,k__Shotokuvirae|p__Cossaviricota|c__Papovaviricetes|o__Zurhausenvirales|f__Papillomaviridae|s__Firstpapillomavirinae|g__Gammapapillomavirus|s__Gammapapillomavirus 13,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Pseudomonadati|p__Bacteroidota|s__Bacteroidetes bacterium oral taxon 272",1783272|1239|91061|186826|186827|46123;1783272|1239|91061|186826|186827|46123|46125;1783272|1239|91061|186826|186827;1783272|1239|909932|1843489|31977|156454;1783272|1239|909932|1843489|31977|906|156456;2732092|2732415|2732421|2732533|151340|2169595|333922;2732092|2732415|2732421|2732533|151340|2169595|333922|334207;3379134|1224|28216|80840|119060|32008;28221;3379134|200940|3024418|213118;3379134|200940|3031451|3024411|213121;3379134|200940|3031451|3024411|213121|893;3379134|200940|3031451|3024411|213121|893|712258;1783272|1239|526524|526525|2810280|1279384;1783272|1239|526524|526525|2810280|1279384|31973;3384189|32066|203490|203491|203492|848|859;2732092|2732415|2732421|2732533|151340|2169595|325455;3379134|29547|3031852|213849|72293|209;3379134|29547|3031852|213849|72293|209|210;3379134|29547|3031852|213849|72293;3379134|976|200643|171549|171552|2974257|28134;3379134|1224|28216|206351|481|482|483;3379134|1224|28216|206351|481|482|484;2732092|2732415|2732421|2732533|151340;3379134|976|200643|171549|171552|838|282402;1783272|1239|91061|186826|1300|1301|113107;1783272|1239|91061|186826|1300|1301|1302;3379134|203691|203692|136|2845253|157|53419;2732092|2732415|2732421|2732533|151340|2169595|325455|1513258;3379134|1224|28216|80840|119060|32008;3379134|976|651591,Complete,Svetlana up
bsdb:30558669/17/1,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 17,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,GERD(Gastroesophageal reflux disease),Glandular mucosa (GM),This group consists of patients with Glandular mucosa,29,14,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, sheet 5",24 September 2024,Fiddyhamma,"Fiddyhamma,Ifeanyisam,WikiWorks",The differences across disease subgroups using LEfSe analysis (Shotgun MetaPhlan2 data).,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter aphrophilus,k__Shotokuvirae|p__Cossaviricota|c__Papovaviricetes|o__Zurhausenvirales|f__Papillomaviridae|s__Firstpapillomavirinae|g__Betapapillomavirus,k__Shotokuvirae|p__Cossaviricota|c__Papovaviricetes|o__Zurhausenvirales|f__Papillomaviridae|s__Firstpapillomavirinae|g__Betapapillomavirus|s__Betapapillomavirus 3,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia|s__Eggerthia catenaformis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium necrophorum,k__Shotokuvirae|p__Cossaviricota|c__Papovaviricetes|o__Zurhausenvirales|f__Papillomaviridae|s__Firstpapillomavirinae|g__Gammapapillomavirus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter pylori,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella oralis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria cinerea,k__Shotokuvirae|p__Cossaviricota|c__Papovaviricetes|o__Zurhausenvirales|f__Papillomaviridae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas noxia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Shotokuvirae|p__Cossaviricota|c__Papovaviricetes|o__Zurhausenvirales|f__Papillomaviridae|s__Firstpapillomavirinae|g__Gammapapillomavirus|s__Gammapapillomavirus 13,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Pseudomonadati|p__Bacteroidota|s__Bacteroidetes bacterium oral taxon 272",1783272|1239|91061|186826|186827|46123;1783272|1239|91061|186826|186827|46123|46125;1783272|1239|91061|186826|186827;3379134|1224|1236|135625|712|416916|732;2732092|2732415|2732421|2732533|151340|2169595|333922;2732092|2732415|2732421|2732533|151340|2169595|333922|334207;1783272|1239|526524|526525|2810280|1279384;1783272|1239|526524|526525|2810280|1279384|31973;3384189|32066|203490|203491|203492|848|859;2732092|2732415|2732421|2732533|151340|2169595|325455;3379134|29547|3031852|213849|72293|209;3379134|29547|3031852|213849|72293|209|210;3379134|29547|3031852|213849|72293;3379134|976|200643|171549|171552|2974257|28134;3379134|1224|28216|206351|481|32257;3379134|1224|28216|206351|481|482|483;2732092|2732415|2732421|2732533|151340;1783272|1239|909932|909929|1843491|970|135083;1783272|1239|91061|186826|1300|1301|1302;2732092|2732415|2732421|2732533|151340|2169595|325455|1513258;3379134|1224|28216|206351|481|32257;3379134|976|651591,Complete,Svetlana up
bsdb:30558669/17/2,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 17,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,GERD(Gastroesophageal reflux disease),Glandular mucosa (GM),This group consists of patients with Glandular mucosa,29,14,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Additional file 3, sheet 5",3 January 2025,Fiddyhamma,"Fiddyhamma,WikiWorks",The differences across disease subgroups using LEfSe analysis (Shotgun MetaPhlan2 data).,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,3379134|976|200643|171549|171551|836|837,Complete,Svetlana up
bsdb:30558669/18/1,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 18,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Cluster 1),GERD(Gastroesophageal reflux disease) (Cluster 1),This group consists of patients with Gastroesophageal reflux disease.,NA,NA,2 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, sheet 6",24 September 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",Differences across normal subjects and GERD patients in each clusters using LEfSe analysis,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae",1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;3379134|976|117743|200644|49546,Complete,Svetlana up
bsdb:30558669/18/2,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 18,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Cluster 1),GERD(Gastroesophageal reflux disease) (Cluster 1),This group consists of patients with Gastroesophageal reflux disease.,NA,NA,2 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Additional file 3, sheet 6",24 September 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",Differences across normal subjects and GERD patients in each clusters using LEfSe analysis,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:30558669/19/1,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 19,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Cluster 2),GERD(Gastroesophageal reflux disease) (Cluster 2),This group consists of patients with Gastroesophageal reflux disease.,NA,NA,2 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, sheet 6",24 September 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",Differences across normal subjects and GERD patients in each clusters using LEfSe analysis,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Brachymonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",3379134|1224|28216|80840|80864|28219;1783272|201174|1760|85007|1653|1716;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|186801|3082720|3118655|44259;3384189|32066|203490|203491|1129771;3379134|1224|28216|206351|481|482;1783272|1239|186801|3085636|186803|265975;3379134|976|200643|171549|171552|838;1783272|1239|909932|909929|1843491|970;1783272|1239|526524|526525|128827|123375;1783272|1239|909932|1843489|31977|29465;1783272|201174|1760|2037;1783272|1239;3379134|1224|1236|135625|712,Complete,Svetlana up
bsdb:30558669/19/2,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 19,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Cluster 2),GERD(Gastroesophageal reflux disease) (Cluster 2),This group consists of patients with Gastroesophageal reflux disease.,NA,NA,2 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Additional file 3, sheet 6",24 September 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",Differences across normal subjects and GERD patients in each clusters using LEfSe analysis,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",3379134|1224|1236;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|976|200643|171549|171552|838;3379134|1224|1236|135625|712,Complete,Svetlana up
bsdb:30558669/21/1,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 21,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Cluster 1),GERD(Gastroesophageal reflux disease) (Cluster 1),This group consists of patients with Gastroesophageal reflux disease.,NA,NA,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, sheet 7",24 September 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",Differences across normal subjects and GERD patients in each clusters using LEfSe analysis,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella",3379134|976|200643|171549|171552|1283313|76122;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|186806|1730;3379134|976|200643|171549|171552|1283313,Complete,Svetlana up
bsdb:30558669/21/2,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 21,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Cluster 1),GERD(Gastroesophageal reflux disease) (Cluster 1),This group consists of patients with Gastroesophageal reflux disease.,NA,NA,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Additional file 3, sheet 7",24 September 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",Differences across normal subjects and GERD patients in each clusters using LEfSe analysis,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,3379134|976|200643|171549|171552|1283313,Complete,Svetlana up
bsdb:30558669/22/1,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 22,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Cluster 2),GERD(Gastroesophageal reflux disease) (Cluster 2),This group consists of patients with Gastroesophageal reflux disease.,NA,NA,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, sheet 7",24 September 2024,Fiddyhamma,"Fiddyhamma,Ifeanyisam,WikiWorks",Differences across normal subjects and GERD patients in each clusters using LEfSe analysis,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota,,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia wadei,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] infirmum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__Eubacteriales Family XIII. Incertae Sedis bacterium",1783272|201174|1760|2037;1783272|201174;;1783272|1239|186801|3082720|543314;3384189|32066|203490|203491|1129771|32067;3384189|32066|203490|203491|1129771|32067|157687;3384189|32066|203490|203491|1129771;1783272|201174|1760|85006|1268;3379134|976|200643|171549|171552|838|28129;3379134|976|200643|171549|171552|838|28133;33090|35493|3398|72025|3803|3814|508215;1783272|201174|1760|85006|1268|32207|43675;3379134|976|200643|171549|171552|2974251|28135;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|1300|1301|1343;1783272|1239|186801|3082720|543314|56774;3384189|32066|203490|203491|1129771|32067;1783272|1239|186801|3082720|543314|2137877,Complete,Svetlana up
bsdb:30558669/22/2,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 22,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Cluster 2),GERD(Gastroesophageal reflux disease) (Cluster 2),This group consists of patients with Gastroesophageal reflux disease.,NA,NA,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Additional file 3, sheet 7",24 September 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",Differences across normal subjects and GERD patients in each clusters using LEfSe analysis,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,3379134|1224|1236|135625|712|724|735,Complete,Svetlana up
bsdb:30558669/23/1,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 23,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Cluster 3),GERD(Gastroesophageal reflux disease) (Cluster 3),This group consists of patients with Gastroesophageal reflux disease.,NA,NA,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Additional file 3, sheet 7",24 September 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",Differences across normal subjects and GERD patients in each clusters using LEfSe analysis,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria macacae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria meningitidis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Pasteuriaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema medium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales",1783272|1239|91061|1385;3379134|1224|1236;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712|724|729;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481|482|496;3379134|1224|28216|206351|481|482|487;3379134|1224|28216|206351|481;3379134|1224|28216|206351;3379134|1224|1236|135625;1783272|1239|91061|1385|538998;3379134|1224;3379134|203691|203692|136|2845253|157|58231;1783272|1239|91061|1385,Complete,Svetlana up
bsdb:30558669/23/2,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 23,Australia,Homo sapiens,Esophagus,UBERON:0001043,Gastroesophageal reflux disease,EFO:0003948,Normal (Cluster 3),GERD(Gastroesophageal reflux disease) (Cluster 3),This group consists of patients with Gastroesophageal reflux disease.,NA,NA,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Additional file 3, sheet 7",24 September 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",Differences across normal subjects and GERD patients in each clusters using LEfSe analysis,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",1783272|201174|84998|84999|1643824|1380;3379134|976|200643|171549;3379134|976|200643;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998|84999|1643824|2767353|1382;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552,Complete,Svetlana up
bsdb:30558669/24/1,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 24,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Subjects with normal esophagus on PPI-No,Subjects with normal esophagus on PPI-Yes,This group consists of patients with normal esophagus,NA,NA,2 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Additional figure 3 A,24 September 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",Microbial taxa identified using LEfSe analysis to be differentially abundant between subjects on PPI as compared to subjects not on PPI,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella dentalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis",3379134|976|200643|171549|171552|838|52227;1783272|1239|91061|186826|1300|1301|1343,Complete,Svetlana up
bsdb:30558669/24/2,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 24,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Subjects with normal esophagus on PPI-No,Subjects with normal esophagus on PPI-Yes,This group consists of patients with normal esophagus,NA,NA,2 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Additional figure 3A,24 September 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",Microbial taxa identified using LEfSe analysis to be differentially abundant between subjects on PPI as compared to subjects not on PPI,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae",1783272|1239|186801|3082720|186804|1257;3379134|1224|1236|135625|712|724|727;3379134|976|200643|171549|171552|2974251|228604,Complete,Svetlana up
bsdb:30558669/25/1,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 25,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Subjects with GERD on PPI-No,Subjects with GERD on PPI-Yes,This group consists of patients with gastroesophageal reflux disease,NA,NA,2 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Additional figure 3B,24 September 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",Microbial taxa identified using LEfSe analysis to be differentially abundant between subjects on PPI as compared to subjects not on PPI,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum longum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",1783272|201174|1760|2037|2049|1654|55565;3379134|976|200643|171549|171552|1283313;1783272|1239|91061|1385|539738|1378|29391;1783272|1239|186801|3085636|186803;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843489|31977|906|187326;1783272|1239|909932;3379134|976|200643|171549|171552|838|470565;3379134|976|200643|171549|171552|838|60133;3379134|976|200643|171549|171552|2974251|228604;1783272|1239|909932|909929;1783272|1239|186801|3085636|186803|1213720;1783272|1239|186801|3085636|186803|1213720|796942;1783272|1239|91061|186826|1300|1301|76860;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977;1783272|201174|1760|85006|1268|32207,Complete,Svetlana up
bsdb:30558669/25/2,30558669,prospective cohort,30558669,https://doi.org/10.1186/s40168-018-0611-4,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4,"Deshpande N.P., Riordan S.M., Castaño-Rodríguez N., Wilkins M.R. , Kaakoush N.O.","Signatures within the esophageal microbiome are associated with host genetics, age, and disease",Microbiome,2018,"Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms",Experiment 25,Australia,Homo sapiens,Esophagus,UBERON:0001043,Esophageal adenocarcinoma,EFO:0000478,Subjects with GERD on PPI-No,Subjects with GERD on PPI-Yes,This group consists of patients with gastroesophageal reflux disease,NA,NA,2 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Additional figure 3B,24 September 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",Microbial taxa identified using LEfSe analysis to be differentially abundant between subjects on PPI as compared to subjects not on PPI,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria meningitidis,3379134|1224|28216|206351|481|482|487,Complete,Svetlana up
bsdb:30562947/1/1,30562947,laboratory experiment,30562947,10.3390/ijms19124079,NA,"Ishii C., Nakanishi Y., Murakami S., Nozu R., Ueno M., Hioki K., Aw W., Hirayama A., Soga T., Ito M., Tomita M. , Fukuda S.",A Metabologenomic Approach Reveals Changes in the Intestinal Environment of Mice Fed on American Diet,International journal of molecular sciences,2018,"American diet, CE-TOFMS, intestinal microbiota, metabologenomics, metabolome, microbiome, multi-omics, next-generation sequencing",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Methionine measurement,EFO:0009771,mice fed control rodent diet.,mice fed American Diet,"C57BL/6J mice fed an American diet (AD), which contained higher amounts of fat and fiber",6,5,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table 2,10 January 2021,Tahiya Begum,"Claregrieve1,WikiWorks",Increased abundance of microbial taxa in AD mice compared with control mice,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiales Family XVII. Incertae Sedis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus",1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|171552;1783272|1239|186801|186802|539000;1783272|1239|91061|1385|186817;1783272|1239|91061|1385|186817|1386;1783272|1239|91061|186826|1300|1357,Complete,Claregrieve1
bsdb:30562947/1/2,30562947,laboratory experiment,30562947,10.3390/ijms19124079,NA,"Ishii C., Nakanishi Y., Murakami S., Nozu R., Ueno M., Hioki K., Aw W., Hirayama A., Soga T., Ito M., Tomita M. , Fukuda S.",A Metabologenomic Approach Reveals Changes in the Intestinal Environment of Mice Fed on American Diet,International journal of molecular sciences,2018,"American diet, CE-TOFMS, intestinal microbiota, metabologenomics, metabolome, microbiome, multi-omics, next-generation sequencing",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Methionine measurement,EFO:0009771,mice fed control rodent diet.,mice fed American Diet,"C57BL/6J mice fed an American diet (AD), which contained higher amounts of fat and fiber",6,5,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Table 2,10 January 2021,Tahiya Begum,"Claregrieve1,WikiWorks",Decreased abundance of microbial taxa in AD mice compared with control mice,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|526524|526525|128827;1783272|1239|186801|186802|186806|1730|142586;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;3379134|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:30564225/1/1,30564225,laboratory experiment,30564225,10.3389/fmicb.2018.03002,NA,"Liu J., Chang R., Zhang X., Wang Z., Wen J. , Zhou T.",Non-isoflavones Diet Incurred Metabolic Modifications Induced by Constipation in Rats via Targeting Gut Microbiota,Frontiers in microbiology,2018,"constipation, intestinal microbiota, isoflavones, metabolism, β-glucosidase",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Response to diet,EFO:0010757,CNISO (Control Non-Isoflavones),NISO (Non-Isoflavones),"Rats of experimental group that were fed with non-isoflavones diet obtained from Trophic Animal Feed High-tech Co., Ltd. (Nantong, China) for 1 week",6,6,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Figure 4A, 5A",6 May 2025,Anne-mariesharp,Anne-mariesharp,Differential abundance of intestinal microbiota between CNISO AND NISO groups at phylum and genus levels,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|1853231|574697;1783272|201174|84998|84999|84107|102106;3379134|200940|3031449|213115|194924|872;1783272|1239|91061|1385|539738|1378;3379134|976|200643|171549|171552|577309;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3085636|186803|841,Complete,KateRasheed
bsdb:30564225/1/2,30564225,laboratory experiment,30564225,10.3389/fmicb.2018.03002,NA,"Liu J., Chang R., Zhang X., Wang Z., Wen J. , Zhou T.",Non-isoflavones Diet Incurred Metabolic Modifications Induced by Constipation in Rats via Targeting Gut Microbiota,Frontiers in microbiology,2018,"constipation, intestinal microbiota, isoflavones, metabolism, β-glucosidase",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Response to diet,EFO:0010757,CNISO (Control Non-Isoflavones),NISO (Non-Isoflavones),"Rats of experimental group that were fed with non-isoflavones diet obtained from Trophic Animal Feed High-tech Co., Ltd. (Nantong, China) for 1 week",6,6,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"Figure 4A, 5A",6 May 2025,Anne-mariesharp,Anne-mariesharp,Differential abundance of intestinal microbiota between CNISO AND NISO groups at phylum and genus levels,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,p__Candidatus Saccharimonadota,p__Candidatus Saccharimonadota,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Viridiplantae|p__Streptophyta,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,s__unidentified",1783272|1239|186801|3085636|186803|1427378;1783272|201174|84998|1643822|1643826|447020;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171552|1283313;1783272|544448|31969|186332|186333|2086;3379134|976|200643|171549|2005519|397864;1783272|201174|1760|85004|31953|1678;95818;95818;1783272|1117;1783272|1239|186801|186802|1392389;1783272|1239|91061|186826|33958|1578;1783272|544448;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|171552|838;33090|35493;1783272|1239|909932|1843489|31977|29465;32644,Complete,KateRasheed
bsdb:30565661/1/1,30565661,case-control,30565661,10.1002/ijc.32007,NA,"Feng J., Zhao F., Sun J., Lin B., Zhao L., Liu Y., Jin Y., Li S., Li A. , Wei Y.",Alterations in the gut microbiota and metabolite profiles of thyroid carcinoma patients,International journal of cancer,2019,"clinical parameter, gut microbiota, metabolite, predictive model, thyroid carcinoma",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Thyroid carcinoma,EFO:0002892,healthy controls,patients with thyroid carcinoma,at least one solid lesion identified by thyroid ultrasonagraphy,35,30,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,"age,body mass index,sex",NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure 2a,10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differential microbial abundance between healthy controls and thyroid carcinoma patients,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Thermoproteati|p__Candidatus Bathyarchaeota,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. 001,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium ND3006,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|207244;1783275|928852;1783272|1239|186801|3082768|990719;1783272|1239|186801|3085636|186803|33042;3379134|1224|1236|91347|543;1783272|1239|526524|526525|128827;3379134|1224|1236|91347|543|561;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|42322;1783272|1239;1783272|1239|186801|3082720|186804|1505657;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3082720|186804;3379134|1224;3379134|976|200643|171549|171550;3379134|1224|1236|91347|543|620;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|292632;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|31979|1485|1970093;1783272|1239|91061|186826|1300|1357;1783272|1239|186801|3085636|186803|1410629;3379134|976|200643|171549|171550|239759,Complete,Claregrieve1
bsdb:30565661/1/2,30565661,case-control,30565661,10.1002/ijc.32007,NA,"Feng J., Zhao F., Sun J., Lin B., Zhao L., Liu Y., Jin Y., Li S., Li A. , Wei Y.",Alterations in the gut microbiota and metabolite profiles of thyroid carcinoma patients,International journal of cancer,2019,"clinical parameter, gut microbiota, metabolite, predictive model, thyroid carcinoma",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Thyroid carcinoma,EFO:0002892,healthy controls,patients with thyroid carcinoma,at least one solid lesion identified by thyroid ultrasonagraphy,35,30,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,"age,body mass index,sex",NA,NA,increased,increased,NA,NA,increased,Signature 2,Figure 2a,10 January 2021,Rimsha Azhar,"Lwaldron,Claregrieve1,WikiWorks",Differential microbial abundance between healthy controls and thyroid carcinoma patients,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|909932|1843488|909930;3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976;1783272|1239|186801|3085636|186803|1506553;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|186803,Complete,Claregrieve1
bsdb:30568265/1/1,30568265,"cross-sectional observational, not case-control",30568265,10.1038/s41366-018-0290-z,https://pubmed.ncbi.nlm.nih.gov/30568265/,"Karvonen A.M., Sordillo J.E., Gold D.R., Bacharier L.B., O'Connor G.T., Zeiger R.S., Beigelman A., Weiss S.T. , Litonjua A.A.",Gut microbiota and overweight in 3-year old children,International journal of obesity (2005),2019,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control babies at the age of 3,overweight/obese babies,NA,356,146,1 week,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,education level",NA,unchanged,NA,NA,NA,NA,Signature 1,Table 3 & 4,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiota in overweight 3 year old children,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|841,Complete,Shaimaa Elsafoury
bsdb:30568265/1/2,30568265,"cross-sectional observational, not case-control",30568265,10.1038/s41366-018-0290-z,https://pubmed.ncbi.nlm.nih.gov/30568265/,"Karvonen A.M., Sordillo J.E., Gold D.R., Bacharier L.B., O'Connor G.T., Zeiger R.S., Beigelman A., Weiss S.T. , Litonjua A.A.",Gut microbiota and overweight in 3-year old children,International journal of obesity (2005),2019,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,control babies at the age of 3,overweight/obese babies,NA,356,146,1 week,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,education level",NA,unchanged,NA,NA,NA,NA,Signature 2,Table 3 & 4,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiota in overweight 3 year old children,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,3379134|976|200643|171549|2005525|375288,Complete,Shaimaa Elsafoury
bsdb:30576008/1/1,30576008,case-control,30576008,10.1002/mds.27581,NA,"Barichella M., Severgnini M., Cilia R., Cassani E., Bolliri C., Caronni S., Ferri V., Cancello R., Ceccarani C., Faierman S., Pinelli G., De Bellis G., Zecca L., Cereda E., Consolandi C. , Pezzoli G.",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,"MSA, PD, PSP, Parkinson-s disease, clinical features, gut-brain axis, multiple system atrophy, progressive supranuclear palsy",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with idiopathic parkinson's disease,Patients with idiopathic parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,193,1 month,16S,34,Illumina,NA,Negative Binomial Regression,0.05,NA,NA,"age,body mass index,geographic area","age,alcohol drinking,breast feeding,constipation,sex,smoking status",NA,NA,increased,NA,NA,increased,Signature 1,"Supplementary table 3, Signature 1 is for increased abundance in those with Parkinson's",19 September 2021,Fcuevas3,"Fcuevas3,Fatima,Atrayees,WikiWorks",Analysis of relative taxa abundance in controls and different disease groups.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacillati|p__Bacillota,k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Tarzettaceae|g__Paurocotylis|s__Paurocotylis pila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",3379134|74201|203494|48461|1647988|239934;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3082768|424536;3379134|1224|1236|91347|543;3379134|1224;3379134|74201|203494|48461|203557;1783272|1239;4751|4890|147549|5185|3434657|47200|47201;3379134|976|200643|171549|171551;3379134|1224|1236|91347|543|561,Complete,Atrayees
bsdb:30576008/1/2,30576008,case-control,30576008,10.1002/mds.27581,NA,"Barichella M., Severgnini M., Cilia R., Cassani E., Bolliri C., Caronni S., Ferri V., Cancello R., Ceccarani C., Faierman S., Pinelli G., De Bellis G., Zecca L., Cereda E., Consolandi C. , Pezzoli G.",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,"MSA, PD, PSP, Parkinson-s disease, clinical features, gut-brain axis, multiple system atrophy, progressive supranuclear palsy",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with idiopathic parkinson's disease,Patients with idiopathic parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,193,1 month,16S,34,Illumina,NA,Negative Binomial Regression,0.05,NA,NA,"age,body mass index,geographic area","age,alcohol drinking,breast feeding,constipation,sex,smoking status",NA,NA,increased,NA,NA,increased,Signature 2,"Supplementary table 3,",28 September 2021,Fcuevas3,"Fcuevas3,Atrayees,WikiWorks",Analysis of relative taxa abundance in controls and different disease groups.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572;1783272|1239;1783272|1239|186801|186802|216572|216851,Complete,Atrayees
bsdb:30576008/2/1,30576008,case-control,30576008,10.1002/mds.27581,NA,"Barichella M., Severgnini M., Cilia R., Cassani E., Bolliri C., Caronni S., Ferri V., Cancello R., Ceccarani C., Faierman S., Pinelli G., De Bellis G., Zecca L., Cereda E., Consolandi C. , Pezzoli G.",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,"MSA, PD, PSP, Parkinson-s disease, clinical features, gut-brain axis, multiple system atrophy, progressive supranuclear palsy",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,the trend over Parkinson's disease progression,Patients with idiopathic Parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,193,NA,16S,34,Illumina,relative abundances,Negative Binomial Regression,0.05,NA,NA,"age,body mass index,geographic area","age,breast feeding,constipation,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,"Supplementary table 4, Signature 1 is for increased taxa abundance in different groups of Parkinson's disease patients.",20 September 2021,Fcuevas3,"Fcuevas3,WikiWorks",Analysis of relative taxa abundance in different groups of Parkinson’s disease patients.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",3379134|74201|203494|48461|1647988|239934;1783272|1239|91061|186826|81850;1783272|1239|91061|186826|33958|1578;3379134|74201;3379134|74201|203494|48461|203557,Complete,Atrayees
bsdb:30576008/2/2,30576008,case-control,30576008,10.1002/mds.27581,NA,"Barichella M., Severgnini M., Cilia R., Cassani E., Bolliri C., Caronni S., Ferri V., Cancello R., Ceccarani C., Faierman S., Pinelli G., De Bellis G., Zecca L., Cereda E., Consolandi C. , Pezzoli G.",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,"MSA, PD, PSP, Parkinson-s disease, clinical features, gut-brain axis, multiple system atrophy, progressive supranuclear palsy",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,the trend over Parkinson's disease progression,Patients with idiopathic Parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,193,NA,16S,34,Illumina,relative abundances,Negative Binomial Regression,0.05,NA,NA,"age,body mass index,geographic area","age,breast feeding,constipation,smoking status",NA,NA,NA,NA,NA,NA,Signature 2,"Supplementary table 4, Signature 2 is for decreased taxa abundance in different groups of Parkinson's disease patients.",28 September 2021,Fcuevas3,"Fcuevas3,Atrayees,WikiWorks",Analysis of relative taxa abundance in different groups of Parkinson’s disease patients.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,1783272|1239|186801|3085636|186803,Complete,Atrayees
bsdb:30576008/3/1,30576008,case-control,30576008,10.1002/mds.27581,NA,"Barichella M., Severgnini M., Cilia R., Cassani E., Bolliri C., Caronni S., Ferri V., Cancello R., Ceccarani C., Faierman S., Pinelli G., De Bellis G., Zecca L., Cereda E., Consolandi C. , Pezzoli G.",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,"MSA, PD, PSP, Parkinson-s disease, clinical features, gut-brain axis, multiple system atrophy, progressive supranuclear palsy",Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with MSA(multiple system atrophy) disease,Patients diagnosed with synucleinopathy multiple system atrophy (MSA),113,22,NA,16S,34,Illumina,relative abundances,Negative Binomial Regression,0.05,NA,NA,"age,body mass index,geographic area","age,alcohol drinking,breast feeding,constipation,sex,smoking status",NA,NA,increased,NA,NA,increased,Signature 1,Supplementary table 3,30 September 2021,Fcuevas3,"Fcuevas3,Atrayees,WikiWorks",Analysis of relative taxa abundance in controls and different disease groups.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Metazoa|p__Chordata|c__Actinopteri|o__Cichliformes|f__Cichlidae|s__Astronotinae|g__Chaetobranchopsis,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",3379134|74201|203494|48461|1647988|239934;1783272|1239|91061|186826|33958;3379134|74201;3379134|74201|203494|48461|203557;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300;1783272|1239|186801|3082768|990719;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953;33208|7711|186623|1489911|8113|318552|74107;1783272|201174;1783272|201174|84998|84999|84107,Complete,Atrayees
bsdb:30576008/3/2,30576008,case-control,30576008,10.1002/mds.27581,NA,"Barichella M., Severgnini M., Cilia R., Cassani E., Bolliri C., Caronni S., Ferri V., Cancello R., Ceccarani C., Faierman S., Pinelli G., De Bellis G., Zecca L., Cereda E., Consolandi C. , Pezzoli G.",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,"MSA, PD, PSP, Parkinson-s disease, clinical features, gut-brain axis, multiple system atrophy, progressive supranuclear palsy",Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with MSA(multiple system atrophy) disease,Patients diagnosed with synucleinopathy multiple system atrophy (MSA),113,22,NA,16S,34,Illumina,relative abundances,Negative Binomial Regression,0.05,NA,NA,"age,body mass index,geographic area","age,alcohol drinking,breast feeding,constipation,sex,smoking status",NA,NA,increased,NA,NA,increased,Signature 2,Supplementary table 3,30 September 2021,Fcuevas3,"Fcuevas3,Atrayees,WikiWorks",Analysis of relative taxa abundance in controls and different disease groups.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|171552;1783272|1239;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803,Complete,Atrayees
bsdb:30576008/4/1,30576008,case-control,30576008,10.1002/mds.27581,NA,"Barichella M., Severgnini M., Cilia R., Cassani E., Bolliri C., Caronni S., Ferri V., Cancello R., Ceccarani C., Faierman S., Pinelli G., De Bellis G., Zecca L., Cereda E., Consolandi C. , Pezzoli G.",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,"MSA, PD, PSP, Parkinson-s disease, clinical features, gut-brain axis, multiple system atrophy, progressive supranuclear palsy",Experiment 4,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with PSP(progressive supranuclear palsy) disease,Patients diagnosed with tauopathy progressive supranuclear palsy (PSP),113,22,NA,16S,34,Illumina,relative abundances,Negative Binomial Regression,0.05,NA,NA,"age,body mass index,geographic area","age,alcohol drinking,breast feeding,constipation,sex,smoking status",NA,NA,increased,NA,NA,increased,Signature 1,"Supplementary table 3, Signature 1 is for increased abundance in those with PSP",30 September 2021,Fcuevas3,"Fcuevas3,Atrayees,WikiWorks",Analysis of relative taxa abundance in controls and different disease groups,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3082768|424536;1783272|1239|186801|186802|216572|119852;3379134|74201;3379134|74201|203494|48461|203557;3379134|1224;3379134|1224|1236|91347|543,Complete,Atrayees
bsdb:30576008/4/2,30576008,case-control,30576008,10.1002/mds.27581,NA,"Barichella M., Severgnini M., Cilia R., Cassani E., Bolliri C., Caronni S., Ferri V., Cancello R., Ceccarani C., Faierman S., Pinelli G., De Bellis G., Zecca L., Cereda E., Consolandi C. , Pezzoli G.",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,"MSA, PD, PSP, Parkinson-s disease, clinical features, gut-brain axis, multiple system atrophy, progressive supranuclear palsy",Experiment 4,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with PSP(progressive supranuclear palsy) disease,Patients diagnosed with tauopathy progressive supranuclear palsy (PSP),113,22,NA,16S,34,Illumina,relative abundances,Negative Binomial Regression,0.05,NA,NA,"age,body mass index,geographic area","age,alcohol drinking,breast feeding,constipation,sex,smoking status",NA,NA,increased,NA,NA,increased,Signature 2,Supplementary table 3,30 September 2021,Fcuevas3,"Fcuevas3,Atrayees,WikiWorks",Analysis of relative taxa abundance in controls and different disease groups,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|841;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|216851,Complete,Atrayees
bsdb:30576008/5/1,30576008,case-control,30576008,10.1002/mds.27581,NA,"Barichella M., Severgnini M., Cilia R., Cassani E., Bolliri C., Caronni S., Ferri V., Cancello R., Ceccarani C., Faierman S., Pinelli G., De Bellis G., Zecca L., Cereda E., Consolandi C. , Pezzoli G.",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,"MSA, PD, PSP, Parkinson-s disease, clinical features, gut-brain axis, multiple system atrophy, progressive supranuclear palsy",Experiment 5,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with De-novo Parkinson's disease,Patients with de novo Parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,39,NA,16S,34,Illumina,relative abundances,Negative Binomial Regression,0.05,NA,NA,"age,body mass index,geographic area","age,alcohol drinking,breast feeding,constipation,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary table 4,30 September 2021,Fcuevas3,"Fcuevas3,Atrayees,WikiWorks",Analysis of relative taxa abundance in different groups of Parkinson’s disease patients.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,1783272|1239|186801|3085636|186803,Complete,Atrayees
bsdb:30576008/6/1,30576008,case-control,30576008,10.1002/mds.27581,NA,"Barichella M., Severgnini M., Cilia R., Cassani E., Bolliri C., Caronni S., Ferri V., Cancello R., Ceccarani C., Faierman S., Pinelli G., De Bellis G., Zecca L., Cereda E., Consolandi C. , Pezzoli G.",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,"MSA, PD, PSP, Parkinson-s disease, clinical features, gut-brain axis, multiple system atrophy, progressive supranuclear palsy",Experiment 6,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's disease,patients with early Parkinson's disease,Patients with early Parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,57,NA,16S,34,Illumina,relative abundances,Negative Binomial Regression,0.05,NA,NA,"age,body mass index,geographic area","age,alcohol drinking,breast feeding,constipation,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,"Supplementary table 4, Signature 1 is for increased taxa abundance among patients with early Parkinson's",30 September 2021,Fcuevas3,"Fcuevas3,Atrayees,WikiWorks",Analysis of relative taxa abundance in different groups of Parkinson’s disease patients,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3082768|424536;3379134|1224|1236|91347|543;3379134|74201;3379134|74201|203494|48461|203557;3379134|1224;1783272|1239|186801|186802|216572|119852,Complete,Atrayees
bsdb:30576008/6/2,30576008,case-control,30576008,10.1002/mds.27581,NA,"Barichella M., Severgnini M., Cilia R., Cassani E., Bolliri C., Caronni S., Ferri V., Cancello R., Ceccarani C., Faierman S., Pinelli G., De Bellis G., Zecca L., Cereda E., Consolandi C. , Pezzoli G.",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,"MSA, PD, PSP, Parkinson-s disease, clinical features, gut-brain axis, multiple system atrophy, progressive supranuclear palsy",Experiment 6,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's disease,patients with early Parkinson's disease,Patients with early Parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,57,NA,16S,34,Illumina,relative abundances,Negative Binomial Regression,0.05,NA,NA,"age,body mass index,geographic area","age,alcohol drinking,breast feeding,constipation,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 2,"Supplementary table 4, Signature 2 is for decreased taxa abundance among participants with early Parkinson's",30 September 2021,Fcuevas3,"Fcuevas3,Atrayees,WikiWorks",Analysis of relative taxa abundance in different groups of Parkinson’s disease patients.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|216851;1783272|1239;1783272|1239|186801|3085636|186803|841,Complete,Atrayees
bsdb:30576008/7/1,30576008,case-control,30576008,10.1002/mds.27581,NA,"Barichella M., Severgnini M., Cilia R., Cassani E., Bolliri C., Caronni S., Ferri V., Cancello R., Ceccarani C., Faierman S., Pinelli G., De Bellis G., Zecca L., Cereda E., Consolandi C. , Pezzoli G.",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,"MSA, PD, PSP, Parkinson-s disease, clinical features, gut-brain axis, multiple system atrophy, progressive supranuclear palsy",Experiment 7,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with mid stage Parkinson's,Patients with mid stage Parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,53,NA,16S,34,Illumina,relative abundances,Negative Binomial Regression,0.05,NA,NA,"age,body mass index,geographic area","age,alcohol drinking,breast feeding,constipation,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary table 4,30 September 2021,Fcuevas3,"Fcuevas3,Atrayees,WikiWorks",Analysis of relative taxa abundance in different groups of Parkinson’s disease patients,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3082768|424536;3379134|1224|1236|91347|543;3379134|1224;3379134|74201;3379134|74201|203494|48461|203557;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953;3379134|976|200643|171549|171551;3379134|976|200643|171549|2005525|375288,Complete,Atrayees
bsdb:30576008/7/2,30576008,case-control,30576008,10.1002/mds.27581,NA,"Barichella M., Severgnini M., Cilia R., Cassani E., Bolliri C., Caronni S., Ferri V., Cancello R., Ceccarani C., Faierman S., Pinelli G., De Bellis G., Zecca L., Cereda E., Consolandi C. , Pezzoli G.",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,"MSA, PD, PSP, Parkinson-s disease, clinical features, gut-brain axis, multiple system atrophy, progressive supranuclear palsy",Experiment 7,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with mid stage Parkinson's,Patients with mid stage Parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,53,NA,16S,34,Illumina,relative abundances,Negative Binomial Regression,0.05,NA,NA,"age,body mass index,geographic area","age,alcohol drinking,breast feeding,constipation,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 2,Supplementary table 4,30 September 2021,Fcuevas3,"Fcuevas3,Atrayees,WikiWorks",Analysis of relative taxa abundance in different groups of Parkinson’s disease patients,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|1239|186801|3085636|186803;1783272|1239;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|216851,Complete,Atrayees
bsdb:30576008/8/1,30576008,case-control,30576008,10.1002/mds.27581,NA,"Barichella M., Severgnini M., Cilia R., Cassani E., Bolliri C., Caronni S., Ferri V., Cancello R., Ceccarani C., Faierman S., Pinelli G., De Bellis G., Zecca L., Cereda E., Consolandi C. , Pezzoli G.",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,"MSA, PD, PSP, Parkinson-s disease, clinical features, gut-brain axis, multiple system atrophy, progressive supranuclear palsy",Experiment 8,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with advanced stage Parkinson's,Patients with advanced stage Parkinson&#039;s disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,44,NA,16S,34,Illumina,relative abundances,Negative Binomial Regression,0.05,NA,NA,"age,body mass index,geographic area","age,alcohol drinking,breast feeding,constipation,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,"Supplementary table 4, Signature 1 is for increased taxa abundance among those with advanced Parkinson's",30 September 2021,Fcuevas3,"Fcuevas3,Atrayees,WikiWorks",Analysis of relative taxa abundance in different groups of Parkinson’s disease patients,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",3379134|74201|203494|48461|1647988|239934;3379134|1224|1236|91347|543;3379134|1224;3379134|74201;3379134|74201|203494|48461|203557;3379134|1224|1236|91347|543|561;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958;1783272|1239|186801|3082768|990719;3379134|976|200643|171549|2005525|375288;1783272|201174;1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549|171551;1783272|201174|1760|85004|31953;1783272|201174|84998|84999|84107,Complete,Atrayees
bsdb:30576008/8/2,30576008,case-control,30576008,10.1002/mds.27581,NA,"Barichella M., Severgnini M., Cilia R., Cassani E., Bolliri C., Caronni S., Ferri V., Cancello R., Ceccarani C., Faierman S., Pinelli G., De Bellis G., Zecca L., Cereda E., Consolandi C. , Pezzoli G.",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,"MSA, PD, PSP, Parkinson-s disease, clinical features, gut-brain axis, multiple system atrophy, progressive supranuclear palsy",Experiment 8,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with advanced stage Parkinson's,Patients with advanced stage Parkinson&#039;s disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,44,NA,16S,34,Illumina,relative abundances,Negative Binomial Regression,0.05,NA,NA,"age,body mass index,geographic area","age,alcohol drinking,breast feeding,constipation,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 2,"Supplementary table 4, Signature 2 is for decreased taxa abundance among those with advanced Parkinson's",30 September 2021,Fcuevas3,"Fcuevas3,Atrayees,WikiWorks",Analysis of relative taxa abundance in different groups of Parkinson’s disease patients,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572,Complete,Atrayees
bsdb:30581271/1/1,30581271,case-control,30581271,10.3748/wjg.v24.i46.5223,NA,"Rojas-Feria M., Romero-García T., Fernández Caballero-Rico J.Á., Pastor Ramírez H., Avilés-Recio M., Castro-Fernandez M., Chueca Porcuna N., Romero-Gόmez M., García F., Grande L. , Del Campo J.A.",Modulation of faecal metagenome in Crohn's disease: Role of microRNAs as biomarkers,World journal of gastroenterology,2018,"Bacteroidetes, Crohn’s disease, Dysbiosis, Firmicutes, microRNAs",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,healthy control,crohn's disease,new-onset adult crohn's disease (CD) patients,16,13,10 weeks,16S,123,Illumina,NA,Chi-Square,0.05,FALSE,NA,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,"figure 2, 3, 4",10 January 2021,Fatima Zohra,WikiWorks,Significant difference between control group and crohn's disease,decreased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Entomoplasmatales|f__Entomoplasmataceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfohalobiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Entomoplasmatales|f__Entomoplasmataceae|g__Mesoplasma,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfonauticaceae|g__Desulfonauticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio",1783272|1239|186801;1783272|1239|186801|186802|541000;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|186806;3379134|976|200643|171549|171550;1783272|544448|31969|186328|33925;3379134|200940|3031449|213115|213117;1783272|201174|1760|85007|1653;1783272|544448|31969|2085|2092;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|841;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|186806|1730;1783272|544448|31969|186328|33925|46239;3379134|200940|3031449|213115|2956789|206664;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171550|28138;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3085636|186803|830,Complete,Fatima
bsdb:30584008/1/1,30584008,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X., Shao L., Liu X., Ji F., Mei Y., Cheng Y., Liu F., Yan C., Li L. , Ling Z.",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 1,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,normal tissues,peritumoral tissues,gastric cancer,230,247,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,decreased,decreased,decreased,NA,decreased,Signature 1,"Figure 2a, 2c, 2f",10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Differentially abundant taxa between peritumoral tissues and normal tissues,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae|g__Aquabacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|74201|203494|48461|1647988|239934|239935;3379134|1224|28211|356|335928|45402;3379134|976|200643|171549|815|816|817;3379134|1224|1236|135619|28256;3379134|1224|1236|135619|28256|2745;3379134|29547|3031852|213849|72293|209;3379134|29547|3031852|213849|72293;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;3379134|1224|28211|356|119045|407;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1257;3379134|1224;1783272|1239|909932|909929|1843491|970;3379134|1224|1236|135622|267890|22;3379134|1224|1236|135622|267890;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977,Complete,Claregrieve1
bsdb:30584008/1/2,30584008,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X., Shao L., Liu X., Ji F., Mei Y., Cheng Y., Liu F., Yan C., Li L. , Ling Z.",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 1,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,normal tissues,peritumoral tissues,gastric cancer,230,247,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,decreased,decreased,decreased,NA,decreased,Signature 2,"Figure 2a, 2c, 2f",10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Differentially abundant taxa between peritumoral tissues and normal tissues,decreased,"k__Pseudomonadati|p__Acidobacteriota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus cereus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Chloroflexota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas",3379134|57723;1783272|1239|91061|1385|186817;1783272|1239;1783272|1239|91061|1385|186817|1386;1783272|1239|91061|1385|186817|1386|1396;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976;1783272|200795;1783272|201174|1760|85007|1653|1716;3379134|1224|1236|91347|543;1783272|1239|186801|186802|216572|216851;3384189|32066;3384189|32066|203490|203491|203492|848;1783272|1239|186801|186802|541000;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171551;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|201174|1760|85009|31957|1743;3379134|1224|1236|72274|135621|286;3379134|976|200643|171549|171552|2974251|165179;3379134|1224|28211|204457|41297;3379134|1224|28211|204457|41297|13687,Complete,Claregrieve1
bsdb:30584008/2/1,30584008,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X., Shao L., Liu X., Ji F., Mei Y., Cheng Y., Liu F., Yan C., Li L. , Ling Z.",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 2,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,peritumoral tissues,tumoral tissues,gastric cancer,247,229,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,increased,decreased,increased,NA,unchanged,Signature 1,"Figure 2a, 2c, 2f",10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Differentially abundant taxa between tumoral tissues and peritumoral tissues,increased,"k__Pseudomonadati|p__Acidobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus cereus,k__Bacillati|p__Chloroflexota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus",3379134|57723;3379134|1224|1236|72274|135621|351;1783272|1239|91061|1385|186817|1386;1783272|1239|91061|1385|186817|1386|1396;1783272|200795;3379134|1224|1236|91347|543;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552;1783272|201174|1760|85009|31957|1743;3379134|1224|1236|72274|135621|286;1783272|1239|91061|186826|1300|1301|1328,Complete,Claregrieve1
bsdb:30584008/2/2,30584008,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X., Shao L., Liu X., Ji F., Mei Y., Cheng Y., Liu F., Yan C., Li L. , Ling Z.",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 2,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,peritumoral tissues,tumoral tissues,gastric cancer,247,229,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,increased,decreased,increased,NA,unchanged,Signature 2,"Figure 2a, 2c, 2f",10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Differentially abundant taxa between tumoral tissues and peritumoral tissues,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter pylori,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas",1783272|1239|186801|186802|216572|216851;3379134|1224|1236|135619|28256;3379134|1224|1236|135619|28256|2745;3379134|29547|3031852|213849|72293|209|210;1783272|1239|186801|186802|541000;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171551;3379134|1224;3379134|1224|1236|135622|267890|22;3379134|1224|1236|135622|267890;3379134|976|117747|200666|84566;3379134|1224|28211|204457|41297|13687,Complete,Claregrieve1
bsdb:30584008/3/1,30584008,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X., Shao L., Liu X., Ji F., Mei Y., Cheng Y., Liu F., Yan C., Li L. , Ling Z.",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 3,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,normal tissues,tumoral tissues,gastric cancer,230,229,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,decreased,decreased,decreased,NA,decreased,Signature 1,"Figure 2a, 2c, 2f",10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Differentially abundant taxa between tumoral tissues and normal tissues,increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|201174;3379134|74201|203494|48461|1647988|239934|239935;1783272|1239;1783272|1239|91061|1385|186817|1386;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85009|31957|1912216|1747;3384189|32066;3384189|32066|203490|203491|203492|848;3379134|1224|1236|135619|28256|2745;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171552|838|28132;1783272|201174|1760|85009|31957|1743;1783272|1239|909932|909929|1843491|970;3379134|1224|1236|135622|267890|22;3379134|1224|1236|135622|267890;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|909932|1843489|31977,Complete,Claregrieve1
bsdb:30584008/3/2,30584008,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X., Shao L., Liu X., Ji F., Mei Y., Cheng Y., Liu F., Yan C., Li L. , Ling Z.",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 3,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,normal tissues,tumoral tissues,gastric cancer,230,229,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,decreased,decreased,decreased,NA,decreased,Signature 2,"Figure 2a, 2c, 2f",10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Differentially abundant taxa between tumoral tissues and normal tissues,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter pylori,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas",3379134|1224|1236|72274|135621|351;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|820;3379134|29547|3031852|213849|72293|209;3379134|29547|3031852|213849|72293|209|210;3379134|29547|3031852|213849|72293;3379134|1224;3379134|1224|1236|72274|135621|286;3379134|976|200643|171549|171552|2974251|165179;3379134|1224|28211|204457|41297|13687,Complete,Claregrieve1
bsdb:30584008/4/1,30584008,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X., Shao L., Liu X., Ji F., Mei Y., Cheng Y., Liu F., Yan C., Li L. , Ling Z.",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 4,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,early stage normal,early stage tumor,gastric cancer,112,116,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,unchanged,decreased,unchanged,NA,NA,Signature 1,"Figure 4k, 4l, 4m, 4n",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Early-stage gastric microbiota between normal and tumor samples,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus",1783272|201174|1760|85009|31957|1912216|1747;1783272|1239|91061|186826|1300|1301|1328,Complete,Claregrieve1
bsdb:30584008/4/2,30584008,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X., Shao L., Liu X., Ji F., Mei Y., Cheng Y., Liu F., Yan C., Li L. , Ling Z.",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 4,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,early stage normal,early stage tumor,gastric cancer,112,116,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,unchanged,decreased,unchanged,NA,NA,Signature 2,"Figure 4k, 4l, 4m, 4n",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Early-stage gastric microbiota between normal and tumor samples,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas yabuuchiae",3379134|976|200643|171549|171552|2974251|165179;3379134|1224|28211|204457|41297|13687|172044,Complete,Claregrieve1
bsdb:30584008/5/1,30584008,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X., Shao L., Liu X., Ji F., Mei Y., Cheng Y., Liu F., Yan C., Li L. , Ling Z.",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 5,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,early stage normal,early stage peritumor,gastric cancer,112,118,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,decreased,decreased,unchanged,NA,NA,Signature 1,"Figure 4k, 4l, 4m, 4n",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Early-stage gastric microbiota in normal and peritumor samples,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas yabuuchiae,3379134|1224|28211|204457|41297|13687|172044,Complete,Claregrieve1
bsdb:30584008/6/1,30584008,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X., Shao L., Liu X., Ji F., Mei Y., Cheng Y., Liu F., Yan C., Li L. , Ling Z.",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 6,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,late stage normal,late stage tumor,gastric cancer,118,113,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,decreased,decreased,unchanged,NA,NA,Signature 1,"Figure 4k, 4l, 4m, 4n",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Late-stage gastric microbiota in normal and tumor samples,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus",1783272|201174|1760|85009|31957|1912216|1747;1783272|1239|91061|186826|1300|1301|1328,Complete,Claregrieve1
bsdb:30584008/8/1,30584008,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X., Shao L., Liu X., Ji F., Mei Y., Cheng Y., Liu F., Yan C., Li L. , Ling Z.",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 8,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,late stage normal,late stage peritumor,gastric cancer,118,129,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,decreased,decreased,decreased,NA,NA,Signature 1,"Figure 4k, 4l, 4m, 4n",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",late-stage gastric microbiota in normal vs peritumor samples,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,3379134|976|200643|171549|171552|2974251|165179,Complete,Claregrieve1
bsdb:30584008/9/1,30584008,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X., Shao L., Liu X., Ji F., Mei Y., Cheng Y., Liu F., Yan C., Li L. , Ling Z.",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 9,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,normal HP-,normal HP+,normal samples that are H. Pylori positive,64,166,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,"age,sex",NA,decreased,decreased,decreased,NA,NA,Signature 1,"Figure 5l, Supp FigS9",10 January 2021,Rimsha Azhar,WikiWorks,Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in normal microhabitat,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|28216|80840;3379134|1224|28216|80840|75682|149698;3379134|1224|28216|80840|75682;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85007|1653;1783272|201174|1760|2037|2049;1783272|201174|1760|2037|2049|1654;3379134|1224|28211|356|119045|407;3379134|1224|28211|356|119045;1783272|1239|186801|3085636|186803;3379134|1224|28211|204457;3379134|1224|28211|204457|41297|13687;3379134|1224|28211|204457|41297;3379134|1224|28211;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;3379134|29547|3031852|213849|72293;3379134|29547|3031852|213849|72293|209;3379134|29547|3031852|213849;3379134|29547;3379134|1224,Complete,Claregrieve1
bsdb:30584008/9/2,30584008,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X., Shao L., Liu X., Ji F., Mei Y., Cheng Y., Liu F., Yan C., Li L. , Ling Z.",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 9,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,normal HP-,normal HP+,normal samples that are H. Pylori positive,64,166,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,"age,sex",NA,decreased,decreased,decreased,NA,NA,Signature 2,"Figure 5, Supp FigS9",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in normal microhabitat,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|909932|1843488|909930;3379134|1224|1236|135622;3379134|1224|28216;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239;1783272|1239|186801|186802|204475;3379134|1224|1236|135619|28256;3379134|1224|1236|135619|28256|2745;3379134|1224|1236|135619;1783272|1239|186801|186802|541000;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;3379134|1224|1236|135622|267890|22;3379134|1224|1236|135622|267890;1783272|1239|186801|3085636|186803,Complete,Claregrieve1
bsdb:30584008/10/1,30584008,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X., Shao L., Liu X., Ji F., Mei Y., Cheng Y., Liu F., Yan C., Li L. , Ling Z.",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 10,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,peritumor HP-,peritumor HP+,peritumor samples that are H. Pylori positive,65,182,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,"age,sex",NA,decreased,unchanged,decreased,NA,NA,Signature 1,Figure S10,10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in peritumor microhabitat,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillales Family X. Incertae Sedis",1783272|1239|91061|1385|186817;1783272|1239|91061|1385;1783272|1239|91061|1385|186817|1386;3379134|29547|3031852|213849;3379134|29547;1783272|1239|91061|1385|539738|1378;3379134|29547|3031852|213849|72293|209;3379134|29547|3031852|213849|72293;3379134|1224;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|1385|539003,Complete,Claregrieve1
bsdb:30584008/10/2,30584008,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X., Shao L., Liu X., Ji F., Mei Y., Cheng Y., Liu F., Yan C., Li L. , Ling Z.",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 10,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,peritumor HP-,peritumor HP+,peritumor samples that are H. Pylori positive,65,182,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,"age,sex",NA,decreased,unchanged,decreased,NA,NA,Signature 2,Figure S10,10 January 2021,Rimsha Azhar,WikiWorks,Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in peritumor microhabitat,decreased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",1783272|1239|186801;1783272|1239|909932|1843488|909930|33024;1783272|1239|909932|1843488|909930;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|541000;1783272|1239|186801|186802|204475;1783272|1239|909932|909929|1843491|158846;1783272|1239|91061|1385|186817|1386;1783272|1239|91061|186826;3379134|976|200643|171549|2005525|375288,Complete,Claregrieve1
bsdb:30584008/11/1,30584008,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X., Shao L., Liu X., Ji F., Mei Y., Cheng Y., Liu F., Yan C., Li L. , Ling Z.",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 11,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,tumor HP-,tumor HP+,tumor samples that are H. Pylori positive,77,152,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,"age,sex",NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure S11,10 January 2021,Rimsha Azhar,WikiWorks,Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in tumor microhabitat,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota",1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|1224|28211|204458;3379134|1224|28211|204458|76892;3379134|1224|28211|204458|76892|41275;3379134|1224|28211|356;3379134|1224|28211;1783272|1239|186801|3085636|186803|572511;3379134|1224|28216|80840;3379134|1224|28216|80840|75682|149698;3379134|1224|28211|204457;3379134|976|117747|200666|84566;3379134|1224|28211|204457|41297|165696;3379134|29547|3031852|213849|72293;3379134|29547|3031852|213849|72293|209;3379134|29547|3031852|213849;3379134|29547,Complete,Claregrieve1
bsdb:30584008/11/2,30584008,"cross-sectional observational, not case-control",30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X., Shao L., Liu X., Ji F., Mei Y., Cheng Y., Liu F., Yan C., Li L. , Ling Z.",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,"Gastric cancer, Gastric microbiota, Helicobacter pylori, Stomach microhabitat, Tumor microenvironment",Experiment 11,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,tumor HP-,tumor HP+,tumor samples that are H. Pylori positive,77,152,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,"age,sex",NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure S11,10 January 2021,Rimsha Azhar,WikiWorks,Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in tumor microhabitat,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|1236|2887326|468|469;3379134|1224|1236|2887326|468;1783272|1239|186801|186802|216572|1263;3379134|1224|1236|72274|135621|286;3379134|1224|1236|72274|135621|351;3379134|1224|1236|72274;3379134|1224|28216;3379134|1224|28211|356|118882;3379134|1224|28211|204457|41297|13687;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953;3379134|1224,Complete,Claregrieve1
bsdb:30584306/1/1,30584306,case-control,30584306,10.2147/NDT.S188340,NA,"Huang Y., Shi X., Li Z., Shen Y., Shi X., Wang L., Li G., Yuan Y., Wang J., Zhang Y., Zhao L., Zhang M., Kang Y. , Liang Y.",Possible association of Firmicutes in the gut microbiota of patients with major depressive disorder,Neuropsychiatric disease and treatment,2018,"Firmicutes, brain–gut axis, depression, gut microbiota, short-chain fatty acids",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,controls,MDD,NA,27,27,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Fig 1, fig 3b, figure 4",10 January 2021,Fatima Zohra,WikiWorks,Differential abundance of firmicutes in patients with major depressive disorder,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella",3379134|1224|28216|80840|75682|846;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|526524|526525|128827|118747;3379134|1224|1236|72274|135621|286;1783272|1239|186801|3082720|186804|1257;1783272|1239|91061|1385|539738|1378,Complete,Atrayees
bsdb:30584306/1/2,30584306,case-control,30584306,10.2147/NDT.S188340,NA,"Huang Y., Shi X., Li Z., Shen Y., Shi X., Wang L., Li G., Yuan Y., Wang J., Zhang Y., Zhao L., Zhang M., Kang Y. , Liang Y.",Possible association of Firmicutes in the gut microbiota of patients with major depressive disorder,Neuropsychiatric disease and treatment,2018,"Firmicutes, brain–gut axis, depression, gut microbiota, short-chain fatty acids",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,controls,MDD,NA,27,27,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"Fig 1, fig 3b, figure 4",10 January 2021,Fatima Zohra,WikiWorks,Differential abundance of firmicutes in patients with major depressive disorder,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea",1783272|1239;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|541000;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|186803|189330,Complete,Atrayees
bsdb:30619212/1/1,30619212,case-control,30619212,10.3389/fmicb.2018.03146,NA,"Coretti L., Paparo L., Riccio M.P., Amato F., Cuomo M., Natale A., Borrelli L., Corrado G., Comegna M., Buommino E., Castaldo G., Bravaccio C., Chiariotti L., Berni Canani R. , Lembo F.",Gut Microbiota Features in Young Children With Autism Spectrum Disorders,Frontiers in microbiology,2018,"ASD, Bifidobacterium longum, Faecalibacterium prausnitzii, butyrate, gut microbiome, propionate, short chain fatty acids",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Healthy controls,Children with Autism Spectrum Disorder (ASD),Diagnosis of autism spectrum disorder was made according to the Diagnostic and Statistical Manual of Mental Disorders - Fifth Edition (DSM-5),14,11,1 month,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,NA,NA,age,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 2,29 November 2024,AlishaM,"AlishaM,WikiWorks",Taxonomic differences of gut microbiota between healthy controls and ASD groups,increased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia",3379134|1224;3379134|976|200643,Complete,NA
bsdb:30619212/1/2,30619212,case-control,30619212,10.3389/fmicb.2018.03146,NA,"Coretti L., Paparo L., Riccio M.P., Amato F., Cuomo M., Natale A., Borrelli L., Corrado G., Comegna M., Buommino E., Castaldo G., Bravaccio C., Chiariotti L., Berni Canani R. , Lembo F.",Gut Microbiota Features in Young Children With Autism Spectrum Disorders,Frontiers in microbiology,2018,"ASD, Bifidobacterium longum, Faecalibacterium prausnitzii, butyrate, gut microbiome, propionate, short chain fatty acids",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Healthy controls,Children with Autism Spectrum Disorder (ASD),Diagnosis of autism spectrum disorder was made according to the Diagnostic and Statistical Manual of Mental Disorders - Fifth Edition (DSM-5),14,11,1 month,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,NA,NA,age,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 2,29 November 2024,AlishaM,"AlishaM,WikiWorks",Taxonomic differences of gut microbiota between healthy controls and ASD groups,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae",1783272|201174;1783272|1239|91061|186826|1300;1783272|201174|84998|84999|84107;1783272|201174|1760|85004|31953;1783272|201174|1760|2037|2049,Complete,NA
bsdb:30619212/2/1,30619212,case-control,30619212,10.3389/fmicb.2018.03146,NA,"Coretti L., Paparo L., Riccio M.P., Amato F., Cuomo M., Natale A., Borrelli L., Corrado G., Comegna M., Buommino E., Castaldo G., Bravaccio C., Chiariotti L., Berni Canani R. , Lembo F.",Gut Microbiota Features in Young Children With Autism Spectrum Disorders,Frontiers in microbiology,2018,"ASD, Bifidobacterium longum, Faecalibacterium prausnitzii, butyrate, gut microbiome, propionate, short chain fatty acids",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Healthy controls,Children with Autism Spectrum Disorder (ASD),Diagnosis of autism spectrum disorder was made according to the Diagnostic and Statistical Manual of Mental Disorders - Fifth Edition (DSM-5),14,11,1 month,16S,34,Illumina,relative abundances,"LEfSe,Metastats",0.05,TRUE,2,age,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Table 3, Supplementary Table S1",29 November 2024,AlishaM,"AlishaM,WikiWorks",Comparison of relative abundances of each OTU identified in ASD patients and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;3379134|976|200643|171549|815;3379134|1224|1236|91347|543;3379134|1224|1236|135625|712;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171551,Complete,NA
bsdb:30619212/2/2,30619212,case-control,30619212,10.3389/fmicb.2018.03146,NA,"Coretti L., Paparo L., Riccio M.P., Amato F., Cuomo M., Natale A., Borrelli L., Corrado G., Comegna M., Buommino E., Castaldo G., Bravaccio C., Chiariotti L., Berni Canani R. , Lembo F.",Gut Microbiota Features in Young Children With Autism Spectrum Disorders,Frontiers in microbiology,2018,"ASD, Bifidobacterium longum, Faecalibacterium prausnitzii, butyrate, gut microbiome, propionate, short chain fatty acids",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Healthy controls,Children with Autism Spectrum Disorder (ASD),Diagnosis of autism spectrum disorder was made according to the Diagnostic and Statistical Manual of Mental Disorders - Fifth Edition (DSM-5),14,11,1 month,16S,34,Illumina,relative abundances,"LEfSe,Metastats",0.05,TRUE,2,age,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Figure 3, Supplementary Table S1",29 November 2024,AlishaM,"AlishaM,WikiWorks",Comparison of relative abundances of each OTU identified in ASD patients and healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae",1783272|1239|91061|1385|539738;1783272|1239|186801|3085636|186803;1783272|201174|1760|2037|2049;1783272|1239|91061|186826|1300;1783272|201174|84998|84999|84107;1783272|1239|91061|186826|186827;1783272|201174|1760|85007|1653;1783272|201174|1760|85004|31953,Complete,NA
bsdb:30619779/1/1,30619779,case-control,30619779,10.3389/fcimb.2018.00433,NA,"Hu Y.L., Pang W., Huang Y., Zhang Y. , Zhang C.J.",The Gastric Microbiome Is Perturbed in Advanced Gastric Adenocarcinoma Identified Through Shotgun Metagenomics,Frontiers in cellular and infection microbiology,2018,"gastric adenocarcinoma, human, inflammation, microbiome, shotgun metagenomics",Experiment 1,China,Homo sapiens,Stomach,UBERON:0000945,Gastric adenocarcinoma,EFO:0000503,Superficial gastritis (SG),Gastric adenocarcinoma (GC),SG patients with mild to moderate epigastric discomfort. The disgnosis of malignancy was based on patological analysis of tissue biopsies,5,6,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,"age,body mass index,sex",NA,NA,unchanged,NA,NA,NA,decreased,Signature 1,Figure 2A and Figure 2B,10 January 2021,Rimsha Azhar,"WikiWorks,Peace Sandy",Taxonomic changes in GC microbiome. (A) Cladogram of the gastric microbial taxa associated with GC and SG. GC-enriched taxa are colored in red and SG-enriched taxa are in green. (B) Histogram of the linear discriminant analysis (LDA) scores for differentially abundant taxonomic features between GC and SG groups. Significance obtained by LDA effect size (LEfSe) at p < 0.05 (Kruksal–Wallis test) and LDAscore>2.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sicca,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae",3379134|1224|1236|135625|712|416916;3379134|976|200643|171549|171552|1283313;3379134|1224|1236;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481|482|490;3379134|1224|1236|135625|712;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|91061|186826|1300|1301|1313;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836|28124;3379134|1224|1236|135625|712|416916|739;3379134|1224|28216|206351|481,Complete,Peace Sandy
bsdb:30619779/1/2,30619779,case-control,30619779,10.3389/fcimb.2018.00433,NA,"Hu Y.L., Pang W., Huang Y., Zhang Y. , Zhang C.J.",The Gastric Microbiome Is Perturbed in Advanced Gastric Adenocarcinoma Identified Through Shotgun Metagenomics,Frontiers in cellular and infection microbiology,2018,"gastric adenocarcinoma, human, inflammation, microbiome, shotgun metagenomics",Experiment 1,China,Homo sapiens,Stomach,UBERON:0000945,Gastric adenocarcinoma,EFO:0000503,Superficial gastritis (SG),Gastric adenocarcinoma (GC),SG patients with mild to moderate epigastric discomfort. The disgnosis of malignancy was based on patological analysis of tissue biopsies,5,6,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,"age,body mass index,sex",NA,NA,unchanged,NA,NA,NA,decreased,Signature 2,Figure 2A and Figure 2B,10 January 2021,Rimsha Azhar,"WikiWorks,Peace Sandy,MyleeeA",Taxonomic changes in GC microbiome. (A) Cladogram of the gastric microbial taxa associated with GC and SG. GC-enriched taxa are colored in red and SG-enriched taxa are in green. (B) Histogram of the linear discriminant analysis (LDA) scores for differentially abundant taxonomic features between GC and SG groups. Significance obtained by LDA effect size (LEfSe) at p < 0.05 (Kruksal–Wallis test) and LDAscore>2.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Blastomonadaceae|g__Blastomonas,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium|s__Sphingobium yanoikuyae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] infirmum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium|s__Sphingobium xenophagum",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049|1654|55565;3379134|1224|28211;1783272|201174|84998|84999|1643824|1380;1783272|201174|1760|85004|31953;3379134|1224|28211|204457|3423720|150203;1783272|201174|84998|84999|84107;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|561|1884818;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|201174|84998|84999|1643824|2767353|1382;1783272|1239|186801|3085636|186803|265975|237576;3379134|976|200643|171549|171552|838|28129;3379134|976|200643|171549|171552|838|28129;1783272|201174|1760|85006|1268|32207|43675;3379134|1224|28211|204457|3423717|165695;3379134|1224|28211|204457|3423717|165695|13690;3379134|1224|28211|204457|41297;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|91061|186826|1300|1301|113107;1783272|1239|91061|186826|1300|1301|45634;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1305;1783272|1239|186801|3082720|543314|56774;3379134|1224|28211|204457|3423717|165695|121428,Complete,Peace Sandy
bsdb:30631088/1/1,30631088,"cross-sectional observational, not case-control",30631088,http://dx.doi.org/10.1038/s41598-018-37208-z,NA,"Jana Mittelstrass, Joy Bergelson, Mathew W. Horton",Characterizing both bacteria and fungi improves understanding of the Arabidopsis root microbiome,Scientific reports,2019,"Arabidopsis thaliana, bacteria, fungi, microbiome, roots, leaves, field experiment",Experiment 1,United States of America,Arabidopsis thaliana,Accessory nerve root,UBERON:0014615,Root,PO:0009005,Control group (Leaves),Test group (Roots),"The leaf microbiome, representing the microbial communities associated with the leaves of the Arabidopsis plants.",4,4,NA,16S,567,Roche454,raw counts,Linear Regression,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Table 1,6 October 2023,Spykelionel,"Spykelionel,Peace Sandy,WikiWorks","The top 10 differentially enriched genera from each kingdom and their preferred habitats. 
The estimates (coefficients) and P - values are from a generalized linear (Poisson) model, fit to determine the effect of the factor organ while taking into account differences in sequencing effort among samples. Note: the ‘Unassigned’ categories include diverse taxa, which themselves may be differentially enriched (or depleted) in the root relative to the leaf microbiome.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Fungi|p__Mucoromycota|c__Mortierellomycetes|o__Mortierellales|f__Mortierellaceae|g__Mortierella,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales|g__Tetracladium",3379134|1224|28216|80840|75682|149698;4751|1913637|2212732|214503|4854|4855;4751|4890|147548|5178|164535,Complete,Peace Sandy
bsdb:30631088/1/2,30631088,"cross-sectional observational, not case-control",30631088,http://dx.doi.org/10.1038/s41598-018-37208-z,NA,"Jana Mittelstrass, Joy Bergelson, Mathew W. Horton",Characterizing both bacteria and fungi improves understanding of the Arabidopsis root microbiome,Scientific reports,2019,"Arabidopsis thaliana, bacteria, fungi, microbiome, roots, leaves, field experiment",Experiment 1,United States of America,Arabidopsis thaliana,Accessory nerve root,UBERON:0014615,Root,PO:0009005,Control group (Leaves),Test group (Roots),"The leaf microbiome, representing the microbial communities associated with the leaves of the Arabidopsis plants.",4,4,NA,16S,567,Roche454,raw counts,Linear Regression,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 2,Table 1,6 October 2023,Spykelionel,"Spykelionel,Peace Sandy,WikiWorks","The top 10 differentially enriched genera from each kingdom and their preferred habitats. The estimates (coefficients) and P - values are from a generalized linear (Poisson) model, fit to determine the effect of the factor organ while taking into account differences in sequencing effort among samples. Note: the ‘Unassigned’ categories include diverse taxa, which themselves may be differentially enriched (or depleted) in the root relative to the leaf microbiome.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Pleosporaceae|g__Alternaria,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales|f__Discinellaceae|g__Articulospora,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Cladosporium,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Plectosphaerellaceae|g__Plectosphaerella",3379134|1224|28216|80840|75682|29580;3379134|1224|1236|72274|135621|286;4751|4890|147541|92860|28556|5598;4751|4890|147548|5178|2794838|253308;4751|4890|147541|2726946|452563|5498;4751|4890|147550|1028384|1033978|40657,Complete,Peace Sandy
bsdb:30633889/1/1,30633889,prospective cohort,30633889,10.1016/j.trsl.2018.12.005,NA,"Brown R.G., Al-Memar M., Marchesi J.R., Lee Y.S., Smith A., Chan D., Lewis H., Kindinger L., Terzidou V., Bourne T., Bennett P.R. , MacIntyre D.A.",Establishment of vaginal microbiota composition in early pregnancy and its association with subsequent preterm prelabor rupture of the fetal membranes,Translational research : the journal of laboratory and clinical medicine,2019,NA,Experiment 1,United Kingdom,Homo sapiens,Vagina,UBERON:0000996,Preterm premature rupture of the membranes,MONDO:0012511,controls,PPROM,(PPROM) preterm premature rupture of the membranes,36,60,9 months,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,"body mass index,ethnic group,gestational age,maternal age",NA,NA,NA,NA,NA,unchanged,NA,Signature 1,Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,The effect size for each of the differentially abundant species was estimated using LDA,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus tetradius,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",1783272|1239|1737404|1737405|1570339|165779;1783272|201174|1760|2037|2049;1783272|1239|909932|1843489|31977|39948|309120;1783272|1239|909932|1843489|31977|39948;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|1737404|1737405|1570339|165779|33036;1783272|1239|1737404|1737405|1570339;1783272|1239|1737404|1737405|1570339|543311;3379134|976|200643|171549|171552|838|28125;3379134|976|200643|171549|171552|2974257|386414;1783272|1239|909932|1843489|31977;1783272|1239|909932;3384189|32066|203490|203491;3384189|32066;1783272|1239|186801|3085636|186803|43996;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171552;3379134|976|200643|171549;3379134|976;3379134|976|200643|171549|171552|838;3379134|976|200643;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802;1783272|1239|186801;1783272|1239|91061|186826|1300,Complete,Atrayees
bsdb:30633889/1/2,30633889,prospective cohort,30633889,10.1016/j.trsl.2018.12.005,NA,"Brown R.G., Al-Memar M., Marchesi J.R., Lee Y.S., Smith A., Chan D., Lewis H., Kindinger L., Terzidou V., Bourne T., Bennett P.R. , MacIntyre D.A.",Establishment of vaginal microbiota composition in early pregnancy and its association with subsequent preterm prelabor rupture of the fetal membranes,Translational research : the journal of laboratory and clinical medicine,2019,NA,Experiment 1,United Kingdom,Homo sapiens,Vagina,UBERON:0000996,Preterm premature rupture of the membranes,MONDO:0012511,controls,PPROM,(PPROM) preterm premature rupture of the membranes,36,60,9 months,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,"body mass index,ethnic group,gestational age,maternal age",NA,NA,NA,NA,NA,unchanged,NA,Signature 2,Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,The effect size for each of the differentially abundant species was estimated using LDA,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus vaginalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota",1783272|1239|91061|186826|33958|2742598|1633;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061;1783272|1239,Complete,Atrayees
bsdb:30641975/1/1,30641975,"cross-sectional observational, not case-control",30641975,10.3390/microorganisms7010017,https://pubmed.ncbi.nlm.nih.gov/30641975/,"Bowyer R.C.E., Jackson M.A., Le Roy C.I., Ni Lochlainn M., Spector T.D., Dowd J.B. , Steves C.J.",Socioeconomic Status and the Gut Microbiome: A TwinsUK Cohort Study,Microorganisms,2019,"SES, microbiome, microbiota, sociobiome, socioeconomic status",Experiment 1,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,"Higher SES (income= > £25,000)","lower SES (income<£25,000)","Lower socioeconomic status(SES) with higher deprivation by income <£25,000",457,342,NA,16S,4,Illumina,NA,edgeR,0.05,TRUE,NA,NA,"age,body mass index,diet",NA,decreased,decreased,decreased,NA,NA,Signature 1,Figure 2A; Tabel 2,10 June 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks","Differential abundance of OTUs with socioeconomic variables and covariates. DeSeq2 calculated the differential abundance of OTUs in: (A). Between the lowest and highest levels of deprivation for education, income, and the IMD, and in models adjusted for age, Body Mass Index (BMI), health deficit (FI), and diet (HEI).
 Table 2. Summary of taxa assigned to OTUs found to be differentially abundant between the most-deprived and least-deprived measures of socioeconomic status in at least two models. Only taxa with multiple OTUs assigned to it, or with multiple SES factors associated with it, and with q-value <, 0.01 are discussed. OTUs relatively enriched in the least deprived compared to the highest for each SES variable are indicated with (+); those enriched in the most deprived compared to the least indicated with (−); where multiple directions of association were observed, this is indicated with (+/−).",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales",3379134|1224|1236|91347;1783272|1239|526524|526525;1783272|1239|91061|186826,Complete,NA
bsdb:30641975/1/2,30641975,"cross-sectional observational, not case-control",30641975,10.3390/microorganisms7010017,https://pubmed.ncbi.nlm.nih.gov/30641975/,"Bowyer R.C.E., Jackson M.A., Le Roy C.I., Ni Lochlainn M., Spector T.D., Dowd J.B. , Steves C.J.",Socioeconomic Status and the Gut Microbiome: A TwinsUK Cohort Study,Microorganisms,2019,"SES, microbiome, microbiota, sociobiome, socioeconomic status",Experiment 1,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,"Higher SES (income= > £25,000)","lower SES (income<£25,000)","Lower socioeconomic status(SES) with higher deprivation by income <£25,000",457,342,NA,16S,4,Illumina,NA,edgeR,0.05,TRUE,NA,NA,"age,body mass index,diet",NA,decreased,decreased,decreased,NA,NA,Signature 2,Figure 2A; Table 2,10 June 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks","Differential abundance of OTUs with socioeconomic variables and covariates. DeSeq2 calculated the differential abundance of OTUs in: (A). Between the lowest and highest levels of deprivation for education, income, and the IMD, and in models adjusted for age, Body Mass Index (BMI), health deficit (FI), and diet (HEI).
Table 2. Summary of taxa assigned to OTUs found to be differentially abundant between the most-deprived and least-deprived measures of socioeconomic status
in at least two models. Only taxa with multiple OTUs assigned to it, or with multiple SES factors associated with it, and with q-value <, 0.01 are discussed. OTUs
relatively enriched in the least deprived compared to the highest for each SES variable are indicated with (+); those enriched in the most deprived compared to the least
indicated with (−); where multiple directions of association were observed, this is indicated with (+/−).",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",1783272|1239|186801|186802;3379134|74201|203494|48461;3379134|976|200643|171549|171550,Complete,NA
bsdb:30643289/1/1,30643289,laboratory experiment,30643289,10.1038/s41591-018-0324-z,NA,"Feehley T., Plunkett C.H., Bao R., Choi Hong S.M., Culleen E., Belda-Ferre P., Campbell E., Aitoro R., Nocerino R., Paparo L., Andrade J., Antonopoulos D.A., Berni Canani R. , Nagler C.R.",Healthy infants harbor intestinal bacteria that protect against food allergy,Nature medicine,2019,NA,Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,healthy Infants-colonised mice,cow’s milk allergic (CMA) infants-colonized mice,Germ-free mice colonised with human feces from cow’s milk allergic (CMA) infant donors,8,9,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,mode of birth,sex",NA,unchanged,unchanged,NA,NA,NA,NA,Signature 1,Figure 2e,10 January 2021,Lucy Mellor,"WikiWorks,Atrayees,Joan Chuks",LEfSe analysis of genera that are differentially abundant in cow milk allergy-colonized mice compared to healthy infant-colonized mice,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979;1783272|1239|526524|526525|2810280|100883;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802;1783272|1239|186801|186802|541000;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|2005519;1783272|1239|186801|186802;1783272|1239|186801|186802|216572,Complete,Atrayees
bsdb:30643289/1/2,30643289,laboratory experiment,30643289,10.1038/s41591-018-0324-z,NA,"Feehley T., Plunkett C.H., Bao R., Choi Hong S.M., Culleen E., Belda-Ferre P., Campbell E., Aitoro R., Nocerino R., Paparo L., Andrade J., Antonopoulos D.A., Berni Canani R. , Nagler C.R.",Healthy infants harbor intestinal bacteria that protect against food allergy,Nature medicine,2019,NA,Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Milk allergic reaction,EFO:0007369,healthy Infants-colonised mice,cow’s milk allergic (CMA) infants-colonized mice,Germ-free mice colonised with human feces from cow’s milk allergic (CMA) infant donors,8,9,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,mode of birth,sex",NA,unchanged,unchanged,NA,NA,NA,NA,Signature 2,Figure 2e,10 January 2021,Lucy Mellor,"WikiWorks,Atrayees,Joan Chuks",LEfSe analysis of genera that are differentially abundant in cow milk allergy-colonized mice compared to healthy infant-colonized mice,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|590;1783272|1239|91061|186826|1300|1301;3379134|1224|1236|91347|543;1783272|1239|186801|3085636|186803,Complete,Atrayees
bsdb:30644740/1/1,30644740,randomized controlled trial,30644740,10.1021/acs.jafc.8b05408,NA,"Brasili E., Hassimotto N.M.A., Del Chierico F., Marini F., Quagliariello A., Sciubba F., Miccheli A., Putignani L. , Lajolo F.",Daily Consumption of Orange Juice from Citrus sinensis L. Osbeck cv. Cara Cara and cv. Bahia Differently Affects Gut Microbiota Profiling as Unveiled by an Integrated Meta-Omics Approach,Journal of agricultural and food chemistry,2019,"1H NMR-based metabolomics, Clostridia, gut microbiota, pyrosequencing, “Bahia” orange juice, “Cara Cara” orange juice",Experiment 1,Brazil,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Time 0 days controls,Time 7 days,NA,21,21,currently on antibiotics,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,unchanged,Signature 1,"Table 1, Table 2, Table S2",10 January 2021,Lora Kasselman,WikiWorks,"Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|171551,Complete,Shaimaa Elsafoury
bsdb:30644740/2/1,30644740,randomized controlled trial,30644740,10.1021/acs.jafc.8b05408,NA,"Brasili E., Hassimotto N.M.A., Del Chierico F., Marini F., Quagliariello A., Sciubba F., Miccheli A., Putignani L. , Lajolo F.",Daily Consumption of Orange Juice from Citrus sinensis L. Osbeck cv. Cara Cara and cv. Bahia Differently Affects Gut Microbiota Profiling as Unveiled by an Integrated Meta-Omics Approach,Journal of agricultural and food chemistry,2019,"1H NMR-based metabolomics, Clostridia, gut microbiota, pyrosequencing, “Bahia” orange juice, “Cara Cara” orange juice",Experiment 2,Brazil,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Time 0 days Cara Cara,Time 7 days,NA,21,21,currently on antibiotics,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,"Table 1, Table 2, Table S3",10 January 2021,Lora Kasselman,"Aiyshaaaa,WikiWorks,Merit","Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups",increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",1783272|1239|1737404|1737405|1737406;1783272|1239|186801;1783272|1239|909932|1843489|31977;3379134|976|200643|171549|1853231;1783272|1239|186801|186802|31979,Complete,Shaimaa Elsafoury
bsdb:30644740/2/2,30644740,randomized controlled trial,30644740,10.1021/acs.jafc.8b05408,NA,"Brasili E., Hassimotto N.M.A., Del Chierico F., Marini F., Quagliariello A., Sciubba F., Miccheli A., Putignani L. , Lajolo F.",Daily Consumption of Orange Juice from Citrus sinensis L. Osbeck cv. Cara Cara and cv. Bahia Differently Affects Gut Microbiota Profiling as Unveiled by an Integrated Meta-Omics Approach,Journal of agricultural and food chemistry,2019,"1H NMR-based metabolomics, Clostridia, gut microbiota, pyrosequencing, “Bahia” orange juice, “Cara Cara” orange juice",Experiment 2,Brazil,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Time 0 days Cara Cara,Time 7 days,NA,21,21,currently on antibiotics,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,"Table 1, Table 2, Table S4",10 January 2021,Lora Kasselman,WikiWorks,"Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups",decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,3379134|976|200643|171549|1853231|283168,Complete,Shaimaa Elsafoury
bsdb:30644740/3/1,30644740,randomized controlled trial,30644740,10.1021/acs.jafc.8b05408,NA,"Brasili E., Hassimotto N.M.A., Del Chierico F., Marini F., Quagliariello A., Sciubba F., Miccheli A., Putignani L. , Lajolo F.",Daily Consumption of Orange Juice from Citrus sinensis L. Osbeck cv. Cara Cara and cv. Bahia Differently Affects Gut Microbiota Profiling as Unveiled by an Integrated Meta-Omics Approach,Journal of agricultural and food chemistry,2019,"1H NMR-based metabolomics, Clostridia, gut microbiota, pyrosequencing, “Bahia” orange juice, “Cara Cara” orange juice",Experiment 3,Brazil,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Time 0 days Bahia,Time 7 days,NA,21,21,currently on antibiotics,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,"Table 1, Table 2, Table S5",10 January 2021,Lora Kasselman,"WikiWorks,Merit","Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae",1783272|1239|909932|1843489|31977;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|1737404|1737405|1737406;3379134|976|200643|171549|1853231,Complete,Shaimaa Elsafoury
bsdb:30644740/4/1,30644740,randomized controlled trial,30644740,10.1021/acs.jafc.8b05408,NA,"Brasili E., Hassimotto N.M.A., Del Chierico F., Marini F., Quagliariello A., Sciubba F., Miccheli A., Putignani L. , Lajolo F.",Daily Consumption of Orange Juice from Citrus sinensis L. Osbeck cv. Cara Cara and cv. Bahia Differently Affects Gut Microbiota Profiling as Unveiled by an Integrated Meta-Omics Approach,Journal of agricultural and food chemistry,2019,"1H NMR-based metabolomics, Clostridia, gut microbiota, pyrosequencing, “Bahia” orange juice, “Cara Cara” orange juice",Experiment 4,Brazil,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,controls at time 7,Cara Cara,NA,21,21,currently on antibiotics,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 1, Table 2, Table S7",10 January 2021,Lora Kasselman,WikiWorks,"Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas",3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005519;1783272|1239|526524|526525|128827|2749846|31971;1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|541000;1783272|1239|186801|186802|216572|244127;3379134|1224|1236|91347|543;3379134|976|200643|171549|1853231|574697,Complete,Shaimaa Elsafoury
bsdb:30644740/4/2,30644740,randomized controlled trial,30644740,10.1021/acs.jafc.8b05408,NA,"Brasili E., Hassimotto N.M.A., Del Chierico F., Marini F., Quagliariello A., Sciubba F., Miccheli A., Putignani L. , Lajolo F.",Daily Consumption of Orange Juice from Citrus sinensis L. Osbeck cv. Cara Cara and cv. Bahia Differently Affects Gut Microbiota Profiling as Unveiled by an Integrated Meta-Omics Approach,Journal of agricultural and food chemistry,2019,"1H NMR-based metabolomics, Clostridia, gut microbiota, pyrosequencing, “Bahia” orange juice, “Cara Cara” orange juice",Experiment 4,Brazil,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,controls at time 7,Cara Cara,NA,21,21,currently on antibiotics,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Table 1, Table 2, Table S8",10 January 2021,Lora Kasselman,WikiWorks,"Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,1783272|1239|186801|3082768|990719,Complete,Shaimaa Elsafoury
bsdb:30644740/5/1,30644740,randomized controlled trial,30644740,10.1021/acs.jafc.8b05408,NA,"Brasili E., Hassimotto N.M.A., Del Chierico F., Marini F., Quagliariello A., Sciubba F., Miccheli A., Putignani L. , Lajolo F.",Daily Consumption of Orange Juice from Citrus sinensis L. Osbeck cv. Cara Cara and cv. Bahia Differently Affects Gut Microbiota Profiling as Unveiled by an Integrated Meta-Omics Approach,Journal of agricultural and food chemistry,2019,"1H NMR-based metabolomics, Clostridia, gut microbiota, pyrosequencing, “Bahia” orange juice, “Cara Cara” orange juice",Experiment 5,Brazil,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,controls at time 7,Bahia,NA,21,21,currently on antibiotics,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 1, Table 2, Table S9",10 January 2021,Lora Kasselman,WikiWorks,"Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus",1783272|201174|84998|1643822|1643826|447020;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|541000;1783272|1239|186801|186802|216572|244127,Complete,Shaimaa Elsafoury
bsdb:30644740/6/1,30644740,randomized controlled trial,30644740,10.1021/acs.jafc.8b05408,NA,"Brasili E., Hassimotto N.M.A., Del Chierico F., Marini F., Quagliariello A., Sciubba F., Miccheli A., Putignani L. , Lajolo F.",Daily Consumption of Orange Juice from Citrus sinensis L. Osbeck cv. Cara Cara and cv. Bahia Differently Affects Gut Microbiota Profiling as Unveiled by an Integrated Meta-Omics Approach,Journal of agricultural and food chemistry,2019,"1H NMR-based metabolomics, Clostridia, gut microbiota, pyrosequencing, “Bahia” orange juice, “Cara Cara” orange juice",Experiment 6,Brazil,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Bahia at time 7,Cara Cara,NA,21,21,currently on antibiotics,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 1, Table 2, Table S11",10 January 2021,Lora Kasselman,WikiWorks,"Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups",increased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus,1783272|1239|526524|526525|128827|2749846|31971,Complete,Shaimaa Elsafoury
bsdb:30656437/1/1,30656437,time series / longitudinal observational,30656437,10.1186/s11671-018-2834-5,NA,"Mao Z., Li Y., Dong T., Zhang L., Zhang Y., Li S., Hu H., Sun C. , Xia Y.",Exposure to Titanium Dioxide Nanoparticles During Pregnancy Changed Maternal Gut Microbiota and Increased Blood Glucose of Rat,Nanoscale research letters,2019,"Gut microbiota, Increased fasting blood glucose, Pregnancy exposure, TiO2 NPs",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Titanium dioxide nanoparticle,CHEBI:51050,control pregnant rats at gestational day 10,pregnant rats exposed to titanium dioxide nanoparticles,The female rats were daily gavage administrated with 5 mg/kg bw/day of TiO2 NPs from the 5th to 18th day after pregnancy.,4,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 4,10 January 2021,Yaseen Javaid,WikiWorks,Exposure to Titanium Dioxide Nanoparticles During Pregnancy Changed Maternal Gut Microbiota of preganat rats,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,1783272|1239|186801|186802,Complete,Shaimaa Elsafoury
bsdb:30656437/1/2,30656437,time series / longitudinal observational,30656437,10.1186/s11671-018-2834-5,NA,"Mao Z., Li Y., Dong T., Zhang L., Zhang Y., Li S., Hu H., Sun C. , Xia Y.",Exposure to Titanium Dioxide Nanoparticles During Pregnancy Changed Maternal Gut Microbiota and Increased Blood Glucose of Rat,Nanoscale research letters,2019,"Gut microbiota, Increased fasting blood glucose, Pregnancy exposure, TiO2 NPs",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Titanium dioxide nanoparticle,CHEBI:51050,control pregnant rats at gestational day 10,pregnant rats exposed to titanium dioxide nanoparticles,The female rats were daily gavage administrated with 5 mg/kg bw/day of TiO2 NPs from the 5th to 18th day after pregnancy.,4,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 4,10 January 2021,Yaseen Javaid,"Fatima,WikiWorks",Exposure to Titanium Dioxide Nanoparticles During Pregnancy Changed Maternal Gut Microbiota of preganat rats,decreased,k__Pseudomonadati|p__Acidobacteriota|c__Terriglobia|o__Terriglobales|f__Acidobacteriaceae|s__bacterium Ellin6075,3379134|57723|204432|204433|204434|234266,Complete,Fatima
bsdb:30669509/1/1,30669509,randomized controlled trial,30669509,10.3390/ijms20020433,NA,"Jalanka J., Major G., Murray K., Singh G., Nowak A., Kurtz C., Silos-Santiago I., Johnston J.M., de Vos W.M. , Spiller R.",The Effect of Psyllium Husk on Intestinal Microbiota in Constipated Patients and Healthy Controls,International journal of molecular sciences,2019,"constipation, ispaghula, microbiome, prebiotics, transit",Experiment 1,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,healthy participants at  baseline,healthy participants following high dose of Psyllium supplementation,Participants were given 7-14g of Psyllium per day for 7days,8,8,1 month,16S,45,Illumina,raw counts,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,23 March 2025,Ese,Ese,Taxonomic differences of fecal microbiota in healthy adults,increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,1783272|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:30669509/1/2,30669509,randomized controlled trial,30669509,10.3390/ijms20020433,NA,"Jalanka J., Major G., Murray K., Singh G., Nowak A., Kurtz C., Silos-Santiago I., Johnston J.M., de Vos W.M. , Spiller R.",The Effect of Psyllium Husk on Intestinal Microbiota in Constipated Patients and Healthy Controls,International journal of molecular sciences,2019,"constipation, ispaghula, microbiome, prebiotics, transit",Experiment 1,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,healthy participants at  baseline,healthy participants following high dose of Psyllium supplementation,Participants were given 7-14g of Psyllium per day for 7days,8,8,1 month,16S,45,Illumina,raw counts,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2,23 March 2025,Ese,Ese,Taxonomic differences of fecal microbiota in healthy adults,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,1783272|1239|186801|186802|216572|292632,Complete,Folakunmi
bsdb:30669509/2/1,30669509,randomized controlled trial,30669509,10.3390/ijms20020433,NA,"Jalanka J., Major G., Murray K., Singh G., Nowak A., Kurtz C., Silos-Santiago I., Johnston J.M., de Vos W.M. , Spiller R.",The Effect of Psyllium Husk on Intestinal Microbiota in Constipated Patients and Healthy Controls,International journal of molecular sciences,2019,"constipation, ispaghula, microbiome, prebiotics, transit",Experiment 2,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,constipated patients at baseline,constipated participants following Psyllium supplementation,Constipated participants were given 21g of Psyllium per day for 7days,16,16,1 month,16S,45,Illumina,raw counts,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,23 March 2025,Ese,Ese,Taxonomic differences of fecal microbiota in constipated participants,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|28050;1783272|1239|909932|1843488|909930|33024;3379134|1224|28216|80840|995019|40544;1783272|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:30669509/2/2,30669509,randomized controlled trial,30669509,10.3390/ijms20020433,NA,"Jalanka J., Major G., Murray K., Singh G., Nowak A., Kurtz C., Silos-Santiago I., Johnston J.M., de Vos W.M. , Spiller R.",The Effect of Psyllium Husk on Intestinal Microbiota in Constipated Patients and Healthy Controls,International journal of molecular sciences,2019,"constipation, ispaghula, microbiome, prebiotics, transit",Experiment 2,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,constipated patients at baseline,constipated participants following Psyllium supplementation,Constipated participants were given 21g of Psyllium per day for 7days,16,16,1 month,16S,45,Illumina,raw counts,Negative Binomial Regression,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,23 March 2025,Ese,Ese,Taxonomic differences of fecal microbiota in constipated participants,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella sp.,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Coriobacterium|s__uncultured Coriobacterium sp.",1783272|1239|186801|3082768|990719|990721|1935934;1783272|201174|84998|84999|84107|33870|286136,Complete,Folakunmi
bsdb:30669509/3/1,30669509,randomized controlled trial,30669509,10.3390/ijms20020433,NA,"Jalanka J., Major G., Murray K., Singh G., Nowak A., Kurtz C., Silos-Santiago I., Johnston J.M., de Vos W.M. , Spiller R.",The Effect of Psyllium Husk on Intestinal Microbiota in Constipated Patients and Healthy Controls,International journal of molecular sciences,2019,"constipation, ispaghula, microbiome, prebiotics, transit",Experiment 3,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,healthy participants at baseline,constipated participants at baseline,"Participants suffering from chronic constipation, which was defined by meeting the Rome III criteria for either functional constipation or constipation-predominant irritable bowel syndrome.",8,16,1 month,16S,45,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,25 March 2025,Ese,Ese,Taxonomic differences of fecal microbiota in constipated patients and healthy patients,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella sp.,k__Bacillati|p__Bacillota|c__Clostridia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Coriobacterium|s__uncultured Coriobacterium sp.",1783272|201174|1760|2037|2049|1654;1783272|201174|84998|1643822|1643826|447020;1783272|1239|186801|3082768|990719|990721|1935934;1783272|1239|186801;3379134|200940|3031449|213115|194924|872;1783272|1239|526524|526525|128827;1783272|201174|1760|85007|85025|1827;1783272|201174|84998|84999|84107|33870|286136,Complete,Folakunmi
bsdb:30669509/3/2,30669509,randomized controlled trial,30669509,10.3390/ijms20020433,NA,"Jalanka J., Major G., Murray K., Singh G., Nowak A., Kurtz C., Silos-Santiago I., Johnston J.M., de Vos W.M. , Spiller R.",The Effect of Psyllium Husk on Intestinal Microbiota in Constipated Patients and Healthy Controls,International journal of molecular sciences,2019,"constipation, ispaghula, microbiome, prebiotics, transit",Experiment 3,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,healthy participants at baseline,constipated participants at baseline,"Participants suffering from chronic constipation, which was defined by meeting the Rome III criteria for either functional constipation or constipation-predominant irritable bowel syndrome.",8,16,1 month,16S,45,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,26 March 2025,Ese,Ese,Taxonomic differences of fecal microbiota in constipated patients and healthy patients,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",1783272|1239|186801|3085636|186803|28050;3379134|1224|28216|80840|995019|40544,Complete,Folakunmi
bsdb:30669548/1/1,30669548,"cross-sectional observational, not case-control",30669548,10.3390/ijms20020438,NA,"Chávez-Carbajal A., Nirmalkar K., Pérez-Lizaur A., Hernández-Quiroz F., Ramírez-Del-Alto S., García-Mena J. , Hernández-Guerrero C.",Gut Microbiota and Predicted Metabolic Pathways in a Sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome,International journal of molecular sciences,2019,"16S rDNA, Mexican women, gut microbiota, high-throughput DNA sequencing, ion torrent, metabolic syndrome, obesity",Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight,obese,"the guidelines from the American Heart Association was used to diagnose metabolic syndrome, which must adhere to at least three of the five following parameters; 1. Elevated waist circumference: waist circumference of ≥80, 2. Elevated Triglycerides ≥150 mg/dL, 3. Reduced HDL- Cholesterol <50 mg/dL, 4. Elevated Blood pressure; systolic ≥130 mm Hg and/or diastolic ≥85 mm Hg and 5. Elevated Fasting blood glucose ≥100 mg/dL. On the other hand, the women with just OB were identified using body mass index (BMI) as follows: normal rank was considered 18.5–24.99 kg/m2, the rank for obese class I was 30–34.99 kg/m2, obese class II 35–39.99 kg/m2, and obese class III greater than or equal to 40 kg/m2.",25,17,3 months,16S,3,Ion Torrent,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,unchanged,Signature 1,Text + figure 1 + Table S1 + Table S2  Table S7,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiota in a sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|33042,Complete,Shaimaa Elsafoury
bsdb:30669548/1/2,30669548,"cross-sectional observational, not case-control",30669548,10.3390/ijms20020438,NA,"Chávez-Carbajal A., Nirmalkar K., Pérez-Lizaur A., Hernández-Quiroz F., Ramírez-Del-Alto S., García-Mena J. , Hernández-Guerrero C.",Gut Microbiota and Predicted Metabolic Pathways in a Sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome,International journal of molecular sciences,2019,"16S rDNA, Mexican women, gut microbiota, high-throughput DNA sequencing, ion torrent, metabolic syndrome, obesity",Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight,obese,"the guidelines from the American Heart Association was used to diagnose metabolic syndrome, which must adhere to at least three of the five following parameters; 1. Elevated waist circumference: waist circumference of ≥80, 2. Elevated Triglycerides ≥150 mg/dL, 3. Reduced HDL- Cholesterol <50 mg/dL, 4. Elevated Blood pressure; systolic ≥130 mm Hg and/or diastolic ≥85 mm Hg and 5. Elevated Fasting blood glucose ≥100 mg/dL. On the other hand, the women with just OB were identified using body mass index (BMI) as follows: normal rank was considered 18.5–24.99 kg/m2, the rank for obese class I was 30–34.99 kg/m2, obese class II 35–39.99 kg/m2, and obese class III greater than or equal to 40 kg/m2.",25,17,3 months,16S,3,Ion Torrent,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,unchanged,Signature 2,Text + figure 1 + Table S1 + Table S2  Table S7,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiota in a sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",3379134|976|200643|171549|815|816;1783272|1239|526524|526525|128827,Complete,Shaimaa Elsafoury
bsdb:30669548/2/1,30669548,"cross-sectional observational, not case-control",30669548,10.3390/ijms20020438,NA,"Chávez-Carbajal A., Nirmalkar K., Pérez-Lizaur A., Hernández-Quiroz F., Ramírez-Del-Alto S., García-Mena J. , Hernández-Guerrero C.",Gut Microbiota and Predicted Metabolic Pathways in a Sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome,International journal of molecular sciences,2019,"16S rDNA, Mexican women, gut microbiota, high-throughput DNA sequencing, ion torrent, metabolic syndrome, obesity",Experiment 2,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight,obese + metabolic syndrome,"the guidelines from the American Heart Association was used to diagnose metabolic syndrome, which must adhere to at least three of the five following parameters; 1. Elevated waist circumference: waist circumference of ≥80, 2. Elevated Triglycerides ≥150 mg/dL, 3. Reduced HDL- Cholesterol <50 mg/dL, 4. Elevated Blood pressure; systolic ≥130 mm Hg and/or diastolic ≥85 mm Hg and 5. Elevated Fasting blood glucose ≥100 mg/dL. On the other hand, the women with just OB were identified using body mass index (BMI) as follows: normal rank was considered 18.5–24.99 kg/m2, the rank for obese class I was 30–34.99 kg/m2, obese class II 35–39.99 kg/m2, and obese class III greater than or equal to 40 kg/m2.",25,25,3 months,16S,3,Ion Torrent,NA,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,unchanged,Signature 1,Text + figure 1 + Table S1 + Table S2  Table S7,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiota in a sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|33042,Complete,Shaimaa Elsafoury
bsdb:30669548/2/2,30669548,"cross-sectional observational, not case-control",30669548,10.3390/ijms20020438,NA,"Chávez-Carbajal A., Nirmalkar K., Pérez-Lizaur A., Hernández-Quiroz F., Ramírez-Del-Alto S., García-Mena J. , Hernández-Guerrero C.",Gut Microbiota and Predicted Metabolic Pathways in a Sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome,International journal of molecular sciences,2019,"16S rDNA, Mexican women, gut microbiota, high-throughput DNA sequencing, ion torrent, metabolic syndrome, obesity",Experiment 2,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight,obese + metabolic syndrome,"the guidelines from the American Heart Association was used to diagnose metabolic syndrome, which must adhere to at least three of the five following parameters; 1. Elevated waist circumference: waist circumference of ≥80, 2. Elevated Triglycerides ≥150 mg/dL, 3. Reduced HDL- Cholesterol <50 mg/dL, 4. Elevated Blood pressure; systolic ≥130 mm Hg and/or diastolic ≥85 mm Hg and 5. Elevated Fasting blood glucose ≥100 mg/dL. On the other hand, the women with just OB were identified using body mass index (BMI) as follows: normal rank was considered 18.5–24.99 kg/m2, the rank for obese class I was 30–34.99 kg/m2, obese class II 35–39.99 kg/m2, and obese class III greater than or equal to 40 kg/m2.",25,25,3 months,16S,3,Ion Torrent,NA,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,unchanged,Signature 2,Text + figure 1 + Table S1 + Table S2  Table S7,10 January 2021,Marianthi Thomatos,WikiWorks,Gut microbiota in a sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",3379134|976|200643|171549|815|816;1783272|1239|526524|526525|128827,Complete,Shaimaa Elsafoury
bsdb:30674011/1/1,30674011,"cross-sectional observational, not case-control",30674011,10.1007/s40618-019-1010-9,NA,"Shi T.T., Xin Z., Hua L., Zhao R.X., Yang Y.L., Wang H., Zhang S., Liu W. , Xie R.R.",Alterations in the intestinal microbiota of patients with severe and active Graves' orbitopathy: a cross-sectional study,Journal of endocrinological investigation,2019,"16S rRNA gene, Graves’ orbitopathy (GO), Gut microbiota, Thyrotropin receptor antibody (TRAb)",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Graves ophthalmopathy,EFO:1001466,Healthy controls,graves orbitopathy,"The diagnosis of GO was established according to the EUGOGO Guidelines. The active GO was defined by a clinical activity score (CAS)≥3/7, and the severe GO was defined by NOSPECS score≥IV. CT or MRI was used to exclude any orbital space-occupying disease such as tumor or extraocular myositis.",32,33,1 month,16S,4,Ion Torrent,relative abundances,Metastats,0.05,FALSE,NA,"age,sex",NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,"Figure 4a, 4b, 4c",10 January 2021,Rimsha Azhar,"Rimsha,Fatima,LGeistlinger,WikiWorks","Comparison of the bacterial abundance at the phylum, genus and species levels in patients with graves' orbitopathy and healthy controls",increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|976;3379134|976|200643|171549|171552|2974251|165179;3379134|976|200643|171549|171552,Complete,Fatima
bsdb:30674011/1/2,30674011,"cross-sectional observational, not case-control",30674011,10.1007/s40618-019-1010-9,NA,"Shi T.T., Xin Z., Hua L., Zhao R.X., Yang Y.L., Wang H., Zhang S., Liu W. , Xie R.R.",Alterations in the intestinal microbiota of patients with severe and active Graves' orbitopathy: a cross-sectional study,Journal of endocrinological investigation,2019,"16S rRNA gene, Graves’ orbitopathy (GO), Gut microbiota, Thyrotropin receptor antibody (TRAb)",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Graves ophthalmopathy,EFO:1001466,Healthy controls,graves orbitopathy,"The diagnosis of GO was established according to the EUGOGO Guidelines. The active GO was defined by a clinical activity score (CAS)≥3/7, and the severe GO was defined by NOSPECS score≥IV. CT or MRI was used to exclude any orbital space-occupying disease such as tumor or extraocular myositis.",32,33,1 month,16S,4,Ion Torrent,relative abundances,Metastats,0.05,FALSE,NA,"age,sex",NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 2,"Figure 4a, 4b, 4c",10 January 2021,Rimsha Azhar,"Rimsha,Fatima,WikiWorks","Comparison of the bacterial abundance at the phylum, genus and species levels in patients with graves' orbitopathy and healthy controls",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Marseillibacter|s__Marseillibacter massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",3379134|976|200643|171549|171550|239759|328814;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|1853231|574697;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|186802|186806|1730|39496;1783272|1239;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|216572|1930587|1852369;3379134|976|200643|171549|815|909656|204516;1783272|1239|186801|186802|216572|1263,Complete,Fatima
bsdb:30674011/2/1,30674011,"cross-sectional observational, not case-control",30674011,10.1007/s40618-019-1010-9,NA,"Shi T.T., Xin Z., Hua L., Zhao R.X., Yang Y.L., Wang H., Zhang S., Liu W. , Xie R.R.",Alterations in the intestinal microbiota of patients with severe and active Graves' orbitopathy: a cross-sectional study,Journal of endocrinological investigation,2019,"16S rRNA gene, Graves’ orbitopathy (GO), Gut microbiota, Thyrotropin receptor antibody (TRAb)",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Graves ophthalmopathy,EFO:1001466,healthy controls,graves orbitopathy,severe and active graves' orbitopathy,32,33,1 month,16S,4,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,Figure 5b,10 January 2021,Rimsha Azhar,"Fatima,WikiWorks",Difference between the intestinal microbiome of patients with graves' orbitopathy and healthy controls by LEfSE,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|976|200643|171549;3379134|976;3379134|976|200643;3379134|976|200643|171549|171552|2974251|165179;3379134|976|200643|171549|171552;3379134|976|200643|171549|171552,Complete,Fatima
bsdb:30674011/2/2,30674011,"cross-sectional observational, not case-control",30674011,10.1007/s40618-019-1010-9,NA,"Shi T.T., Xin Z., Hua L., Zhao R.X., Yang Y.L., Wang H., Zhang S., Liu W. , Xie R.R.",Alterations in the intestinal microbiota of patients with severe and active Graves' orbitopathy: a cross-sectional study,Journal of endocrinological investigation,2019,"16S rRNA gene, Graves’ orbitopathy (GO), Gut microbiota, Thyrotropin receptor antibody (TRAb)",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Graves ophthalmopathy,EFO:1001466,healthy controls,graves orbitopathy,severe and active graves' orbitopathy,32,33,1 month,16S,4,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 2,Figure 5b,10 January 2021,Rimsha Azhar,"Fatima,WikiWorks",Difference between the intestinal microbiome of patients with graves' orbitopathy and healthy controls by LEfSE,increased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801;1783272|1239|186801|186802;1783272|1239;1783272|1239|186801|3085636|186803,Complete,Fatima
bsdb:30675188/1/1,30675188,"cross-sectional observational, not case-control",30675188,10.1186/s13099-018-0281-6,NA,"Liu Q., Li F., Zhuang Y., Xu J., Wang J., Mao X., Zhang Y. , Liu X.",Alteration in gut microbiota associated with hepatitis B and non-hepatitis virus related hepatocellular carcinoma,Gut pathogens,2019,"Dysbiosis, Gut microbiome, HBV, Hepatocellular carcinoma, Liver cancer",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Hepatocellular carcinoma,EFO:0000182,healthy controls,non-HBV non-HCV related HCC,HCC patients whose disease is not related to hepatitis B/hepatitis virus,33,22,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,NA,Signature 1,Figure 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between healthy controls and non-hepatitis virus related hepatocellular carcinoma patients,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,1783272|1239|186801|186802|216572|244127,Complete,Claregrieve1
bsdb:30675188/1/2,30675188,"cross-sectional observational, not case-control",30675188,10.1186/s13099-018-0281-6,NA,"Liu Q., Li F., Zhuang Y., Xu J., Wang J., Mao X., Zhang Y. , Liu X.",Alteration in gut microbiota associated with hepatitis B and non-hepatitis virus related hepatocellular carcinoma,Gut pathogens,2019,"Dysbiosis, Gut microbiome, HBV, Hepatocellular carcinoma, Liver cancer",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Hepatocellular carcinoma,EFO:0000182,healthy controls,non-HBV non-HCV related HCC,HCC patients whose disease is not related to hepatitis B/hepatitis virus,33,22,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,NA,Signature 2,Figure 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance comparing healthy controls to non-hepatitis virus related hepatocellular carcinoma patients,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;1783272|1239|909932|909929|1843491|158846,Complete,Claregrieve1
bsdb:30675188/2/1,30675188,"cross-sectional observational, not case-control",30675188,10.1186/s13099-018-0281-6,NA,"Liu Q., Li F., Zhuang Y., Xu J., Wang J., Mao X., Zhang Y. , Liu X.",Alteration in gut microbiota associated with hepatitis B and non-hepatitis virus related hepatocellular carcinoma,Gut pathogens,2019,"Dysbiosis, Gut microbiome, HBV, Hepatocellular carcinoma, Liver cancer",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Hepatocellular carcinoma,EFO:0000182,healthy controls,HBV-related HCC patients,HBV-related HCC patients,33,35,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance comparing healthy controls to HBV-related hepatocellular carcinoma patients,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|186801|186802|216572|244127;1783272|1239|186801|186802|541000;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:30675188/3/1,30675188,"cross-sectional observational, not case-control",30675188,10.1186/s13099-018-0281-6,NA,"Liu Q., Li F., Zhuang Y., Xu J., Wang J., Mao X., Zhang Y. , Liu X.",Alteration in gut microbiota associated with hepatitis B and non-hepatitis virus related hepatocellular carcinoma,Gut pathogens,2019,"Dysbiosis, Gut microbiome, HBV, Hepatocellular carcinoma, Liver cancer",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Hepatocellular carcinoma,EFO:0000182,HBV related HCC patients,non-HBV non-HCV patients,HCC patients whose disease is not related to hepatitis B/hepatitis virus,35,22,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between HBV-related hepatocellular carcinoma patients and non-hepatitis virus related HCC patients,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Buchnera,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",3379134|1224|1236|91347|1903409|32199;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|3085636|186803|28050;1783272|1239|909932|1843488|909930|33024,Complete,Claregrieve1
bsdb:30696838/1/1,30696838,case-control,30696838,10.1038/s41598-018-36709-1,NA,"Ajibola O., Rowan A.D., Ogedengbe C.O., Mshelia M.B., Cabral D.J., Eze A.A., Obaro S. , Belenky P.",Urogenital schistosomiasis is associated with signatures of microbiome dysbiosis in Nigerian adolescents,Scientific reports,2019,NA,Experiment 1,Nigeria,Homo sapiens,Feces,UBERON:0001988,Schistosomiasis,EFO:1001475,Schistosomiasis negative,Schistosomiasis positive,Schistosomiasis positive are adolescents within the age of 11-15years that have been infected by Schistosoma.,25,24,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 3(Figs. 3),16 October 2024,KateRasheed,"KateRasheed,WikiWorks",Significant abundance of taxa in the infected adolescents.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|s__uncultured Coriobacteriaceae bacterium,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia",3379134|1224|1236|2887326|468|469;3379134|976|200643|171549|171552|1283313;1783272|201174|1760|85004|31953;28221;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;1783272|1239|909932|1843489|31977|39948;3384189|32066|203490|203491;3384189|32066|203490;3379134|1224|1236|135625|712|724;1783272|1239|909932|1843489|31977|906;3379134|1224|1236|2887326|468;1783272|1239|909932;1783272|201174|84998|84999|1643824|133925;3379134|1224|1236|135625|712;3379134|1224|1236|135625;1783272|1239|186801|186802|186807;1783272|1239|186801|186802|186807|2740;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|1224|1236|72274;1783272|201174|1760;3379134|1224;1783272|1239|909932|909929;1783272|1239|909932|1843489|31977;1783272|201174|84998|84999|84107|331632;1783272|201174|84992,Complete,Svetlana up
bsdb:30696838/1/2,30696838,case-control,30696838,10.1038/s41598-018-36709-1,NA,"Ajibola O., Rowan A.D., Ogedengbe C.O., Mshelia M.B., Cabral D.J., Eze A.A., Obaro S. , Belenky P.",Urogenital schistosomiasis is associated with signatures of microbiome dysbiosis in Nigerian adolescents,Scientific reports,2019,NA,Experiment 1,Nigeria,Homo sapiens,Feces,UBERON:0001988,Schistosomiasis,EFO:1001475,Schistosomiasis negative,Schistosomiasis positive,Schistosomiasis positive are adolescents within the age of 11-15years that have been infected by Schistosoma.,25,24,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 3(Figs. 3),16 October 2024,KateRasheed,"KateRasheed,WikiWorks",Significant abundance of taxa in the infected adolescents.,decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacillati|p__Candidatus Melainabacteria,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|s__uncultured Mollicutes bacterium,k__Bacillati|p__Mycoplasmatota|s__uncultured Mycoplasmatota bacterium,s__uncultured rumen bacterium,s__uncultured bacterium",1783272|1239;3379134|1224|28216;1783272|1798710|1906119;1783272|1798710;1783272|1239|186801;1783272|1239|186801|186802|31979|1485;1783272|1117;1783272|1239|186801|186802;1783272|544448|31969;1783272|544448;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171551;1783272|1239|186801|186802|216572|292632;1783272|1239|526524|526525|128827|331630;1783272|544448|31969|220137;1783272|544448|658143;136703;77133,Complete,Svetlana up
bsdb:30701077/1/1,30701077,time series / longitudinal observational,30701077,10.1038/s41522-018-0073-2,NA,"Lindefeldt M., Eng A., Darban H., Bjerkner A., Zetterström C.K., Allander T., Andersson B., Borenstein E., Dahlin M. , Prast-Nielsen S.",The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with severe epilepsy,NPJ biofilms and microbiomes,2019,NA,Experiment 1,Sweden,Homo sapiens,Feces,UBERON:0001988,Epilepsy,EFO:0000474,before keto diet,after keto diet,children with therapy resistent inoperabe epilepsy or a diagnosis of a neorometablic disorder in which KD is recommended,12,12,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3,10 January 2021,Fatima Zohra,"WikiWorks,Folakunmi,Chloe",Statistical changes at all taxonomic levels during dietary interventaion (keto diet) using LEFse method,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",1783272|201174;1783272|1239|186801|3085636|186803|1766253|39491;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|909932|1843489|31977|39948,Complete,Folakunmi
bsdb:30701077/1/2,30701077,time series / longitudinal observational,30701077,10.1038/s41522-018-0073-2,NA,"Lindefeldt M., Eng A., Darban H., Bjerkner A., Zetterström C.K., Allander T., Andersson B., Borenstein E., Dahlin M. , Prast-Nielsen S.",The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with severe epilepsy,NPJ biofilms and microbiomes,2019,NA,Experiment 1,Sweden,Homo sapiens,Feces,UBERON:0001988,Epilepsy,EFO:0000474,before keto diet,after keto diet,children with therapy resistent inoperabe epilepsy or a diagnosis of a neorometablic disorder in which KD is recommended,12,12,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3,10 January 2021,Fatima Zohra,"WikiWorks,Chloe",Statistical changes at all taxonomic levels during dietary interventaion (keto diet) using LEFse method,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|561|562;3379134|1224|1236;3379134|1224,Complete,Folakunmi
bsdb:30707176/1/1,30707176,case-control,30707176,10.1097/CM9.0000000000000086,NA,"Bai W., Chen S., Tang C.S., Qi J.G., Cui Q.H., Xu M., Du J.B. , Jin H.F.",Gut microbiota analysis and its significance in vasovagal syncope in children,Chinese medical journal,2019,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Syncope,HP:0001279,healthy children,children with vasovagal syncope,children ages 5-18 who meet diagnostic criteria for vasovagal syncope,20,20,2 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 3,10 January 2021,Shaimaa Elsafoury,"Claregrieve1,WikiWorks",Differential microbial abundance between controls and children with VVS,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,1783272|1239|186801|186802|541000,Complete,Claregrieve1
bsdb:30711862/1/1,30711862,randomized controlled trial,30711862,10.1016/j.nut.2018.10.038,NA,"Xie X., He Y., Li H., Yu D., Na L., Sun T., Zhang D., Shi X., Xia Y., Jiang T., Rong S., Yang S., Ma X. , Xu G.",Effects of prebiotics on immunologic indicators and intestinal microbiota structure in perioperative colorectal cancer patients,"Nutrition (Burbank, Los Angeles County, Calif.)",2019,"Colorectal cancer, Immune system, Intestinal microbiota, Operation, Prebiotics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,"Nutraceutical,Colorectal cancer","CHEBI:50733,EFO:0005842",colorectal cancer patients who didn't take prebiotics (preoperative fecal sample),colorectal cancer patients who took prebiotics (preoperative fecal sample),"Patients with radiologic and pathologic diagnosis of CRC (preoperatively). Patients in the intervention group (prebiotic group) received a daily oral dose of 30 g prebiotic supplement (Hangzhou Niuqu Biotech Co., Hainengbo, China) containing fructooligosaccharide (25%), xylooligosaccharide (25%), polydextrose (25%), and resistant dextrin (25%) for 7 d from hospitalization to the day before the operation.",20,18,6 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Table 4; Table 3,3 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1,WikiWorks",Differential microbial abundance between patients who took prebiotics and patients who did not,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",3379134|976|200643|171549|815|816;1783272|1239|91061|186826|81852|1350,Complete,Claregrieve1
bsdb:30711862/1/2,30711862,randomized controlled trial,30711862,10.1016/j.nut.2018.10.038,NA,"Xie X., He Y., Li H., Yu D., Na L., Sun T., Zhang D., Shi X., Xia Y., Jiang T., Rong S., Yang S., Ma X. , Xu G.",Effects of prebiotics on immunologic indicators and intestinal microbiota structure in perioperative colorectal cancer patients,"Nutrition (Burbank, Los Angeles County, Calif.)",2019,"Colorectal cancer, Immune system, Intestinal microbiota, Operation, Prebiotics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,"Nutraceutical,Colorectal cancer","CHEBI:50733,EFO:0005842",colorectal cancer patients who didn't take prebiotics (preoperative fecal sample),colorectal cancer patients who took prebiotics (preoperative fecal sample),"Patients with radiologic and pathologic diagnosis of CRC (preoperatively). Patients in the intervention group (prebiotic group) received a daily oral dose of 30 g prebiotic supplement (Hangzhou Niuqu Biotech Co., Hainengbo, China) containing fructooligosaccharide (25%), xylooligosaccharide (25%), polydextrose (25%), and resistant dextrin (25%) for 7 d from hospitalization to the day before the operation.",20,18,6 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Table 4; Table 3,3 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1,WikiWorks",Differential microbial abundance between patients who took prebiotics and patients who did not,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Claregrieve1
bsdb:30711862/2/1,30711862,randomized controlled trial,30711862,10.1016/j.nut.2018.10.038,NA,"Xie X., He Y., Li H., Yu D., Na L., Sun T., Zhang D., Shi X., Xia Y., Jiang T., Rong S., Yang S., Ma X. , Xu G.",Effects of prebiotics on immunologic indicators and intestinal microbiota structure in perioperative colorectal cancer patients,"Nutrition (Burbank, Los Angeles County, Calif.)",2019,"Colorectal cancer, Immune system, Intestinal microbiota, Operation, Prebiotics",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,"Colorectal cancer,Nutraceutical","EFO:0005842,CHEBI:50733",colorectal cancer patients non-prebiotic (preoperative),colorectal cancer patients non-prebiotic (postoperative),Patients with radiologic and pathologic diagnosis of CRC who underwent radical resection (post-operative samples) and did not take prebiotics pre-surgery.,20,20,no treatment with antibiotics within 6 mo before surgery,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Table 5,3 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1,WikiWorks",Differential microbial abundance between the pre- and postoperative timepoints in patients who did not take prebiotics,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,Claregrieve1
bsdb:30711862/2/2,30711862,randomized controlled trial,30711862,10.1016/j.nut.2018.10.038,NA,"Xie X., He Y., Li H., Yu D., Na L., Sun T., Zhang D., Shi X., Xia Y., Jiang T., Rong S., Yang S., Ma X. , Xu G.",Effects of prebiotics on immunologic indicators and intestinal microbiota structure in perioperative colorectal cancer patients,"Nutrition (Burbank, Los Angeles County, Calif.)",2019,"Colorectal cancer, Immune system, Intestinal microbiota, Operation, Prebiotics",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,"Colorectal cancer,Nutraceutical","EFO:0005842,CHEBI:50733",colorectal cancer patients non-prebiotic (preoperative),colorectal cancer patients non-prebiotic (postoperative),Patients with radiologic and pathologic diagnosis of CRC who underwent radical resection (post-operative samples) and did not take prebiotics pre-surgery.,20,20,no treatment with antibiotics within 6 mo before surgery,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Table 5,3 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1,WikiWorks",Differential microbial abundance between the pre- and postoperative timepoints in patients who did not take prebiotics,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061|1385|186817|1386;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:30711862/3/1,30711862,randomized controlled trial,30711862,10.1016/j.nut.2018.10.038,NA,"Xie X., He Y., Li H., Yu D., Na L., Sun T., Zhang D., Shi X., Xia Y., Jiang T., Rong S., Yang S., Ma X. , Xu G.",Effects of prebiotics on immunologic indicators and intestinal microbiota structure in perioperative colorectal cancer patients,"Nutrition (Burbank, Los Angeles County, Calif.)",2019,"Colorectal cancer, Immune system, Intestinal microbiota, Operation, Prebiotics",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,"Nutraceutical,Colorectal cancer","CHEBI:50733,EFO:0005842",colorectal cancer patients who took prebiotics (preoperative fecal sample),colorectal cancer patients who took prebiotics (postoperative fecal sample),Patients with radiologic and pathologic diagnosis of CRC who underwent radical resection (post-operative samples) and took prebiotics pre-surgery.,18,18,no treatment with antibiotics within 6 mo before surgery,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Table 5; Figure 3,3 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1,WikiWorks",Differential microbial abundance between the pre- and postoperative timepoints in patients who took prebiotics,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",1783272|1239|91061|1385|186817|1386;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|1940338,Complete,Claregrieve1
bsdb:30711862/3/2,30711862,randomized controlled trial,30711862,10.1016/j.nut.2018.10.038,NA,"Xie X., He Y., Li H., Yu D., Na L., Sun T., Zhang D., Shi X., Xia Y., Jiang T., Rong S., Yang S., Ma X. , Xu G.",Effects of prebiotics on immunologic indicators and intestinal microbiota structure in perioperative colorectal cancer patients,"Nutrition (Burbank, Los Angeles County, Calif.)",2019,"Colorectal cancer, Immune system, Intestinal microbiota, Operation, Prebiotics",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,"Nutraceutical,Colorectal cancer","CHEBI:50733,EFO:0005842",colorectal cancer patients who took prebiotics (preoperative fecal sample),colorectal cancer patients who took prebiotics (postoperative fecal sample),Patients with radiologic and pathologic diagnosis of CRC who underwent radical resection (post-operative samples) and took prebiotics pre-surgery.,18,18,no treatment with antibiotics within 6 mo before surgery,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Table 5; Figure 3,3 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1,WikiWorks",Differential microbial abundance between the pre- and postoperative timepoints in patients who took prebiotics,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,Claregrieve1
bsdb:30714640/1/1,30714640,case-control,30714640,10.1002/jcla.22842,NA,"Qiu J., Zhou H., Jing Y. , Dong C.",Association between blood microbiome and type 2 diabetes mellitus: A nested case-control study,Journal of clinical laboratory analysis,2019,"16S ribosomal RNA, blood microbiome, nested case-control study, type 2 diabetes mellitus",Experiment 1,China,Homo sapiens,Blood,UBERON:0000178,Type II diabetes mellitus,MONDO:0005148,controls,Type-2 DM cases,NA,100,50,2 months,16S,56,Illumina,raw counts,T-Test,0.05,FALSE,NA,"age,sex","alcohol drinking,blood pressure,body mass index,smoking behavior,total cholesterol measurement,triglycerides",NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table 5,10 January 2021,Yaseen Javaid,WikiWorks,Association between blood microbiome and type 2 diabetes mellitus: A nested case-control study. (all the bacteria either have zero mean or not detectable in both groups except Aquabacterium),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Cellulomonadaceae|g__Actinotalea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alishewanella,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Pseudoclavibacter",1783272|201174|1760|85006|85016|458839;3379134|1224|1236|135622|72275|111142;3379134|976|1853228|1853229|563835|504481;1783272|201174|1760|85006|85023|255204,Complete,Shaimaa Elsafoury
bsdb:30714640/1/2,30714640,case-control,30714640,10.1002/jcla.22842,NA,"Qiu J., Zhou H., Jing Y. , Dong C.",Association between blood microbiome and type 2 diabetes mellitus: A nested case-control study,Journal of clinical laboratory analysis,2019,"16S ribosomal RNA, blood microbiome, nested case-control study, type 2 diabetes mellitus",Experiment 1,China,Homo sapiens,Blood,UBERON:0000178,Type II diabetes mellitus,MONDO:0005148,controls,Type-2 DM cases,NA,100,50,2 months,16S,56,Illumina,raw counts,T-Test,0.05,FALSE,NA,"age,sex","alcohol drinking,blood pressure,body mass index,smoking behavior,total cholesterol measurement,triglycerides",NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Table 5,10 January 2021,Yaseen Javaid,WikiWorks,Association between blood microbiome and type 2 diabetes mellitus: A nested case-control study. (all the bacteria either have zero mean or not detectable in both groups except Aquabacterium),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Aquabacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Pseudonocardia",3379134|1224|28216|80840|92793;3379134|1224|1236|135614|32033|338;1783272|201174|1760|85010|2070|1847,Complete,Shaimaa Elsafoury
bsdb:30714640/2/1,30714640,case-control,30714640,10.1002/jcla.22842,NA,"Qiu J., Zhou H., Jing Y. , Dong C.",Association between blood microbiome and type 2 diabetes mellitus: A nested case-control study,Journal of clinical laboratory analysis,2019,"16S ribosomal RNA, blood microbiome, nested case-control study, type 2 diabetes mellitus",Experiment 2,China,Homo sapiens,Blood,UBERON:0000178,Type II diabetes mellitus,MONDO:0005148,carier of pathogens controls,Type-2 DM cariers of pathogens,The non-carrier meant that the individual did not have sequence read for the specific pathogen.,NA,NA,2 months,16S,56,Illumina,raw counts,T-Test,0.05,FALSE,NA,"age,sex","alcohol drinking,blood pressure,body mass index,smoking behavior,total cholesterol measurement,triglycerides",NA,NA,NA,NA,NA,NA,Signature 1,Table 6,10 January 2021,Shaimaa Elsafoury,WikiWorks,Associations between blood microbiome and the subsequent risk of Type-2 diabetes mellitus,increased,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium,3379134|976|1853228|1853229|563835|504481,Complete,Shaimaa Elsafoury
bsdb:30714640/2/2,30714640,case-control,30714640,10.1002/jcla.22842,NA,"Qiu J., Zhou H., Jing Y. , Dong C.",Association between blood microbiome and type 2 diabetes mellitus: A nested case-control study,Journal of clinical laboratory analysis,2019,"16S ribosomal RNA, blood microbiome, nested case-control study, type 2 diabetes mellitus",Experiment 2,China,Homo sapiens,Blood,UBERON:0000178,Type II diabetes mellitus,MONDO:0005148,carier of pathogens controls,Type-2 DM cariers of pathogens,The non-carrier meant that the individual did not have sequence read for the specific pathogen.,NA,NA,2 months,16S,56,Illumina,raw counts,T-Test,0.05,FALSE,NA,"age,sex","alcohol drinking,blood pressure,body mass index,smoking behavior,total cholesterol measurement,triglycerides",NA,NA,NA,NA,NA,NA,Signature 2,Table 6,10 January 2021,Shaimaa Elsafoury,WikiWorks,Associations between blood microbiome and the subsequent risk of Type-2 diabetes mellitus,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
bsdb:30728029/1/1,30728029,time series / longitudinal observational,30728029,10.1186/s12905-019-0727-0,NA,"Wiik J., Sengpiel V., Kyrgiou M., Nilsson S., Mitra A., Tanbo T., Monceyron Jonassen C., Møller Tannæs T. , Sjøborg K.","Cervical microbiota in women with cervical intra-epithelial neoplasia, prior to and after local excisional treatment, a Norwegian cohort study",BMC women's health,2019,"CIN, Cervical Intraepithelial Neoplasia, HPV, Human papillomavirus, LEEP, Lactobacillus, Vaginal microbiota",Experiment 1,Norway,Homo sapiens,Endocervix,UBERON:0000458,Cervical glandular intraepithelial neoplasia,EFO:1000165,normal,LEEP group before procedure,women with suspected high grade cervical dysplasia planning for their first Loop Electrosurgical Excision Procedure,100,89,NA,16S,NA,RT-qPCR,NA,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 5,10 January 2021,Cynthia Anderson,"Claregrieve1,WikiWorks",Differential abundance of cervical microbiota in the LEEP group and the Reference group,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma parvum,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma hominis",1783272|201174|1760|85004|31953|2701|2702;1783272|544448|2790996|2790998|2129|134821;1783272|544448|2790996|2895623|2895509|2098,Complete,Claregrieve1
bsdb:30728029/2/1,30728029,time series / longitudinal observational,30728029,10.1186/s12905-019-0727-0,NA,"Wiik J., Sengpiel V., Kyrgiou M., Nilsson S., Mitra A., Tanbo T., Monceyron Jonassen C., Møller Tannæs T. , Sjøborg K.","Cervical microbiota in women with cervical intra-epithelial neoplasia, prior to and after local excisional treatment, a Norwegian cohort study",BMC women's health,2019,"CIN, Cervical Intraepithelial Neoplasia, HPV, Human papillomavirus, LEEP, Lactobacillus, Vaginal microbiota",Experiment 2,Norway,Homo sapiens,Endocervix,UBERON:0000458,Cervical glandular intraepithelial neoplasia,EFO:1000165,normal,LEEP group before procedure,women with suspected high grade cervical dysplasia planning for their first Loop Electrosurgical Excision Procedure,99,89,NA,16S,NA,RT-qPCR,NA,Logistic Regression,0.05,FALSE,NA,NA,"age,contraception,marital status,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,Table 5,10 January 2021,Cynthia Anderson,"Claregrieve1,WikiWorks",Differential abundance of cervical microbiota in the LEEP group and the Reference group,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma parvum",1783272|201174|1760|85004|31953|2701|2702;1783272|544448|2790996|2790998|2129|134821,Complete,Claregrieve1
bsdb:30728029/3/1,30728029,time series / longitudinal observational,30728029,10.1186/s12905-019-0727-0,NA,"Wiik J., Sengpiel V., Kyrgiou M., Nilsson S., Mitra A., Tanbo T., Monceyron Jonassen C., Møller Tannæs T. , Sjøborg K.","Cervical microbiota in women with cervical intra-epithelial neoplasia, prior to and after local excisional treatment, a Norwegian cohort study",BMC women's health,2019,"CIN, Cervical Intraepithelial Neoplasia, HPV, Human papillomavirus, LEEP, Lactobacillus, Vaginal microbiota",Experiment 3,Norway,Homo sapiens,Endocervix,UBERON:0000458,Cervical glandular intraepithelial neoplasia,EFO:1000165,normal,LEEP group before procedure (age <46),women <46 years old with suspected high grade cervical dysplasia planning for their first Loop Electrosurgical Excision Procedure,48,75,NA,16S,NA,RT-qPCR,NA,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 1,10 January 2021,Cynthia Anderson,"Claregrieve1,WikiWorks",Differential abundance of the cervical microbiota in the LEEP group and the Reference group in women aged < 46 years,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma hominis,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma parvum",1783272|201174|1760|85004|31953|2701|2702;1783272|544448|2790996|2895623|2895509|2098;1783272|544448|2790996|2790998|2129|134821,Complete,Claregrieve1
bsdb:30728029/4/1,30728029,time series / longitudinal observational,30728029,10.1186/s12905-019-0727-0,NA,"Wiik J., Sengpiel V., Kyrgiou M., Nilsson S., Mitra A., Tanbo T., Monceyron Jonassen C., Møller Tannæs T. , Sjøborg K.","Cervical microbiota in women with cervical intra-epithelial neoplasia, prior to and after local excisional treatment, a Norwegian cohort study",BMC women's health,2019,"CIN, Cervical Intraepithelial Neoplasia, HPV, Human papillomavirus, LEEP, Lactobacillus, Vaginal microbiota",Experiment 4,Norway,Homo sapiens,Endocervix,UBERON:0000458,Cervical glandular intraepithelial neoplasia,EFO:1000165,normal,LEEP group before procedure,women <46 years old with suspected high grade cervical dysplasia planning for their first Loop Electrosurgical Excision Procedure,48,75,NA,16S,NA,RT-qPCR,NA,Logistic Regression,0.05,FALSE,NA,NA,"age,contraception,marital status,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 1,10 January 2021,Cynthia Anderson,"Claregrieve1,WikiWorks",Differential abundance of cervical microbiota in the LEEP group and the Reference group in women aged < 46 years,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma parvum",1783272|201174|1760|85004|31953|2701|2702;1783272|544448|2790996|2790998|2129|134821,Complete,Claregrieve1
bsdb:30728029/5/1,30728029,time series / longitudinal observational,30728029,10.1186/s12905-019-0727-0,NA,"Wiik J., Sengpiel V., Kyrgiou M., Nilsson S., Mitra A., Tanbo T., Monceyron Jonassen C., Møller Tannæs T. , Sjøborg K.","Cervical microbiota in women with cervical intra-epithelial neoplasia, prior to and after local excisional treatment, a Norwegian cohort study",BMC women's health,2019,"CIN, Cervical Intraepithelial Neoplasia, HPV, Human papillomavirus, LEEP, Lactobacillus, Vaginal microbiota",Experiment 5,Norway,Homo sapiens,Endocervix,UBERON:0000458,Cervical glandular intraepithelial neoplasia,EFO:1000165,normal,LEEP group 6 months post-procedure,women 6 months after Loop Electrosurgical Excision Procedure,100,77,NA,16S,NA,RT-qPCR,NA,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 2,10 January 2021,Cynthia Anderson,"Claregrieve1,WikiWorks",Differential abundance between the cervical microbiota six months post treatment in the LEEP group and the cervical microbiota in the Reference group,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma hominis,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma parvum",1783272|201174|1760|85004|31953|2701|2702;1783272|544448|2790996|2895623|2895509|2098;1783272|544448|2790996|2790998|2129|134821,Complete,Claregrieve1
bsdb:30728029/6/1,30728029,time series / longitudinal observational,30728029,10.1186/s12905-019-0727-0,NA,"Wiik J., Sengpiel V., Kyrgiou M., Nilsson S., Mitra A., Tanbo T., Monceyron Jonassen C., Møller Tannæs T. , Sjøborg K.","Cervical microbiota in women with cervical intra-epithelial neoplasia, prior to and after local excisional treatment, a Norwegian cohort study",BMC women's health,2019,"CIN, Cervical Intraepithelial Neoplasia, HPV, Human papillomavirus, LEEP, Lactobacillus, Vaginal microbiota",Experiment 6,Norway,Homo sapiens,Endocervix,UBERON:0000458,Cervical glandular intraepithelial neoplasia,EFO:1000165,normal,LEEP group 12 months post-procedure,women 12 months after Loop Electrosurgical Excision Procedure,100,72,NA,16S,NA,RT-qPCR,NA,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 3,10 January 2021,Cynthia Anderson,"Claregrieve1,WikiWorks",Differential abundance between cervical microbiota 12 months post treatment in the LEEP group and the cervical microbiota in the Reference group,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma hominis,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma parvum",1783272|201174|1760|85004|31953|2701|2702;1783272|544448|2790996|2895623|2895509|2098;1783272|544448|2790996|2790998|2129|134821,Complete,Claregrieve1
bsdb:30737418/1/1,30737418,case-control,30737418,10.1038/s41598-018-38031-2,NA,"Zhou B., Sun C., Huang J., Xia M., Guo E., Li N., Lu H., Shan W., Wu Y., Li Y., Xu X., Weng D., Meng L., Hu J., Gao Q., Ma D. , Chen G.",The biodiversity Composition of Microbiome in Ovarian Carcinoma Patients,Scientific reports,2019,NA,Experiment 1,China,Homo sapiens,Uterus,UBERON:0000995,Ovarian cancer,MONDO:0008170,normal tissue,ovarian cancer,women diagnosed with high grade ovarian cancer,25,25,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,decreased,NA,unchanged,NA,NA,Signature 1,"Figure 2, Fig S3",10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy","LEfSe was performed to identify the most differentially abundant taxons between ovarian cancer tissues and normal distal fallopian tube tissues.  

(A,C) Histogram of the LDA scores for differentially abundant phyla and genera, respectively. Only taxa meeting an LDA significant threshold of 3.5 are shown. *P < 0.05; **P < 0.01; ***P < 0.001.",increased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Caldimonas,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Faucicola|s__Faucicola osloensis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium|s__Sphingobium yanoikuyae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia|s__Providencia vermicola,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter lwoffii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas azotifigens",3379134|1224;3379134|1224|28211|356|212791;3379134|1224|28216|80840|80864|283;1783272|1239|91061|1385|90964|1279;3379134|1224|28211|204457|3423717|165695;3379134|1224|28211|356|119045|407;3379134|1224|28216|80840|119060|106589;3379134|1224|1236|91347|1903414|586;3379134|1224|28216|80840|2975441|196013;3379134|976|1853228|1853229|563835|504481;3379134|1224|28216|80840|80864|12916;3379134|1224|28211|204457|41297|13687;3379134|1224|1236|2887326|468|469;3379134|1224|1236|2887326|468|1604696|34062;3379134|1224|28211|204457|3423717|165695|13690;3379134|1224|1236|91347|1903414|586|333965;3379134|1224|1236|2887326|468|469|28090;3379134|1224|28211|204457|41297|13687|330920,Complete,Peace Sandy
bsdb:30737418/1/2,30737418,case-control,30737418,10.1038/s41598-018-38031-2,NA,"Zhou B., Sun C., Huang J., Xia M., Guo E., Li N., Lu H., Shan W., Wu Y., Li Y., Xu X., Weng D., Meng L., Hu J., Gao Q., Ma D. , Chen G.",The biodiversity Composition of Microbiome in Ovarian Carcinoma Patients,Scientific reports,2019,NA,Experiment 1,China,Homo sapiens,Uterus,UBERON:0000995,Ovarian cancer,MONDO:0008170,normal tissue,ovarian cancer,women diagnosed with high grade ovarian cancer,25,25,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,decreased,NA,unchanged,NA,NA,Signature 2,"Figure 2, Fig S3",10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy","LEfSe was performed to identify the most differentially abundant taxons between ovarian cancer tissues and normal distal fallopian tube tissues.

(A,C) Histogram of the LDA scores for differentially abundant phyla and genera, respectively. Only taxa meeting an LDA significant threshold of 3.5 are shown. *P < 0.05; **P < 0.01; ***P < 0.001.",decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Acidobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Pseudolactococcus|s__Pseudolactococcus piscium",1783272|1239;1783272|201174;3379134|57723;1783272|1239|186801|186802|216572|236752;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|1300|3436058|1364,Complete,Peace Sandy
bsdb:30764497/2/1,30764497,case-control,30764497,10.3390/nu11020337,NA,"Plaza-Díaz J., Gómez-Fernández A., Chueca N., Torre-Aguilar M.J., Gil Á., Perez-Navero J.L., Flores-Rojas K., Martín-Borreguero P., Solis-Urra P., Ruiz-Ojeda F.J., Garcia F. , Gil-Campos M.",Autism Spectrum Disorder (ASD) with and without Mental Regression is Associated with Changes in the Fecal Microbiota,Nutrients,2019,"autism spectrum disorder, children, intestinal microbiota, nutrients",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Autism,EFO:0003758,healthy controls,children with autism non-mental regression (ANMR),Children between 2-6 years old with an agreed clinical diagnosis of autism per the ICD 10th Edition for ASD and DSM-5 who did not have development regression during the first two years of life.,57,30,NA,16S,34,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 2, Figure 2 & Table 3",10 January 2021,Shaimaa Elsafoury,"Claregrieve1,WikiWorks",Relative abundances of bacteria in fecal microbiota of children with ANMR ASD and healthy children.,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",1783272|201174;1783272|201174|1760;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|2719313|208479;1783272|201174|1760|85006|85023;1783272|1239|186801|68295|186814;1783272|1239|91061|186826|81852|1350,Complete,Claregrieve1
bsdb:30764497/3/1,30764497,case-control,30764497,10.3390/nu11020337,NA,"Plaza-Díaz J., Gómez-Fernández A., Chueca N., Torre-Aguilar M.J., Gil Á., Perez-Navero J.L., Flores-Rojas K., Martín-Borreguero P., Solis-Urra P., Ruiz-Ojeda F.J., Garcia F. , Gil-Campos M.",Autism Spectrum Disorder (ASD) with and without Mental Regression is Associated with Changes in the Fecal Microbiota,Nutrients,2019,"autism spectrum disorder, children, intestinal microbiota, nutrients",Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Autism,EFO:0003758,healthy controls,children with autism mental regression (AMR),Children between 2-6 years old with an agreed clinical diagnosis of autism per the ICD 10th Edition for ASD and DSM-5 who had development regression during the first two years of life.,57,18,NA,16S,34,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 2, Figure 2 & Table 3",10 January 2021,Shaimaa Elsafoury,"Claregrieve1,WikiWorks",Relative abundances of bacteria in fecal microbiota of children with AMR ASD and healthy children.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae",1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|91061|186826|81852|1350;1783272|201174|1760|85006|85023;3379134|1224;1783272|1239|186801|68295|186814,Complete,Claregrieve1
bsdb:30764497/4/1,30764497,case-control,30764497,10.3390/nu11020337,NA,"Plaza-Díaz J., Gómez-Fernández A., Chueca N., Torre-Aguilar M.J., Gil Á., Perez-Navero J.L., Flores-Rojas K., Martín-Borreguero P., Solis-Urra P., Ruiz-Ojeda F.J., Garcia F. , Gil-Campos M.",Autism Spectrum Disorder (ASD) with and without Mental Regression is Associated with Changes in the Fecal Microbiota,Nutrients,2019,"autism spectrum disorder, children, intestinal microbiota, nutrients",Experiment 4,Spain,Homo sapiens,Feces,UBERON:0001988,Autism,EFO:0003758,healthy controls,children with autism spectrum disorders (ASD),Children between 2-6 years old with an agreed clinical diagnosis of autism per the ICD 10th Edition for ASD and DSM-5,57,48,NA,16S,34,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,10 January 2021,Shaimaa Elsafoury,"Claregrieve1,WikiWorks",Relative abundances of bacteria in fecal microbiota of children with ASD (AMR or ANMR) and healthy children.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfohalobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Thermoactinomycetaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae",1783272|1239|91061|1385|186817;1783272|201174|1760|85004|31953;1783272|201174|1760|85007|1653;3379134|200940|3031449|213115|213117;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|526524|526525|128827;1783272|201174|1760|85006|85023;1783272|1239|91061|1385|186824;3384189|32066|203490|203491|203492,Complete,Claregrieve1
bsdb:30764497/4/2,30764497,case-control,30764497,10.3390/nu11020337,NA,"Plaza-Díaz J., Gómez-Fernández A., Chueca N., Torre-Aguilar M.J., Gil Á., Perez-Navero J.L., Flores-Rojas K., Martín-Borreguero P., Solis-Urra P., Ruiz-Ojeda F.J., Garcia F. , Gil-Campos M.",Autism Spectrum Disorder (ASD) with and without Mental Regression is Associated with Changes in the Fecal Microbiota,Nutrients,2019,"autism spectrum disorder, children, intestinal microbiota, nutrients",Experiment 4,Spain,Homo sapiens,Feces,UBERON:0001988,Autism,EFO:0003758,healthy controls,children with autism spectrum disorders (ASD),Children between 2-6 years old with an agreed clinical diagnosis of autism per the ICD 10th Edition for ASD and DSM-5,57,48,NA,16S,34,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1,10 January 2021,Shaimaa Elsafoury,WikiWorks,Relative abundances of bacteria in fecal microbiota of children with ASD (AMR or ANMR) and healthy children.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,1783272|1239|186801|3085636|186803,Complete,Claregrieve1
bsdb:30775438/1/1,30775438,case-control,30775438,10.1126/sciadv.aau8317,NA,"Zheng P., Zeng B., Liu M., Chen J., Pan J., Han Y., Liu Y., Cheng K., Zhou C., Wang H., Zhou X., Gui S., Perry S.W., Wong M.L., Licinio J., Wei H. , Xie P.",The gut microbiome from patients with schizophrenia modulates the glutamate-glutamine-GABA cycle and schizophrenia-relevant behaviors in mice,Science advances,2019,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,HC: individuals without a psychiatric diagnosis of schizophrenia,SCZ: individuals with a psychiatric diagnosis of schizophrenia,"individuals with schizophrenia diagnosed by Structured Psychiatric Interview using Diagnostic and Statistical Manual of Mental Disorders, 4th Edition (DSM-IV)",69,63,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,NA,NA,decreased,decreased,NA,decreased,Signature 1,Table S2A,23 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,WikiWorks",Up-regulated relative abundance of operational taxonomic units in individuals with schizophrenia compared to normal controls.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__uncultured Acidaminococcus sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia|s__Alloscardovia omnicolens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina|s__uncultured Sarcina sp.,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,s__metagenome,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium anhuiense,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__uncultured Alloprevotella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__uncultured Prevotella sp.,s__human gut metagenome,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__uncultured Dialister sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",1783272|1239|909932|1843488|909930|904|352152;3379134|1224|28216|80840|995019|40544|40545;1783272|201174|1760|85004|31953|419014|419015;3379134|976|200643|171549|815|816|246787;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979|1266|200448;1783272|201174|84998|84999|1643824|1380;256318;3379134|976|117743|200644|49546|237|459526;3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|171552|1283313|1283315;3379134|976|200643|171549|171552|838|159272;408170;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|909932|1843489|31977|39948|278064;1783272|1239|909932|1843489|31977|906|907;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843489|31977|29465;3379134|74201|203494|48461|1647988|239934,Complete,Svetlana up
bsdb:30775438/1/2,30775438,case-control,30775438,10.1126/sciadv.aau8317,NA,"Zheng P., Zeng B., Liu M., Chen J., Pan J., Han Y., Liu Y., Cheng K., Zhou C., Wang H., Zhou X., Gui S., Perry S.W., Wong M.L., Licinio J., Wei H. , Xie P.",The gut microbiome from patients with schizophrenia modulates the glutamate-glutamine-GABA cycle and schizophrenia-relevant behaviors in mice,Science advances,2019,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,HC: individuals without a psychiatric diagnosis of schizophrenia,SCZ: individuals with a psychiatric diagnosis of schizophrenia,"individuals with schizophrenia diagnosed by Structured Psychiatric Interview using Diagnostic and Statistical Manual of Mental Disorders, 4th Edition (DSM-IV)",69,63,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,NA,NA,decreased,decreased,NA,decreased,Signature 2,Table S2A,24 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,WikiWorks",Down-regulated relative abundance of operational taxonomic units in individuals with schizophrenia compared to normal controls.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,p__Candidatus Saccharimonadota|s__Candidatus Saccharibacteria bacterium UB2523,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella stercoris,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella|s__Raoultella ornithinolytica,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Liu et al. 2021),k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral clone DR034,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral clone FR058,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,p__Candidatus Saccharimonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__uncultured Citrobacter sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__uncultured Dorea sp.,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__uncultured Granulicatella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__uncultured Hafnia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__uncultured Lachnoclostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|s__uncultured Mollicutes bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__uncultured Ruminiclostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__uncultured Ruminococcus RM2,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__uncultured Ruminococcus sp.",3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|28111;95818|1516129;1783272|201174|84998|84999|84107|102106|147206;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|91061|1385|539738|1378|84135;3379134|1224|1236|135625|712|724|729;1783272|1239|186801|3085636|186803|877420;3379134|976|200643|171549|1853231|283168|28118;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|815|909656|204516;3379134|1224|1236|91347|543|160674|54291;1783272|1239|186801|186802|216572|3068309;1783272|1239|186801|186802|216572|1263|3062497;1783272|1239|91061|186826|1300|1301|1304;95818|163602;95818|175646;1783272|1239|186801|3085636|186803|2316020|33039;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005519|397864;1783272|1239|186801|3085636|186803|572511;95818;1783272|1239|186801|3085636|186803|33042;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|1407607;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803;3379134|1224|28211|356|119045|407;1783272|1239|91061|186826|1300|1301;3379134|1224|1236|91347|543|544|200446;1783272|1239|186801|3085636|186803|189330|286138;1783272|1239|526524|526525|128827|331630;1783272|1239|91061|186826|186828|117563|316089;3379134|1224|1236|91347|1903412|568|374604;1783272|1239|186801|3085636|186803|1506553|1586779;1783272|1239|186801|3085636|186803|297314;1783272|544448|31969|220137;1783272|1239|186801|186802|216572|707003;1783272|1239|186801|186802|216572|1508657|1757166;1783272|1239|186801|186802|216572|1263|129703;1783272|1239|186801|186802|216572|1263|165186,Complete,Svetlana up
bsdb:30778155/1/1,30778155,prospective cohort,30778155,10.1038/s41598-019-39700-6,https://pubmed.ncbi.nlm.nih.gov/30778155/,"Ata B., Yildiz S., Turkgeldi E., Brocal V.P., Dinleyici E.C., Moya A. , Urman B.","The Endobiota Study: Comparison of Vaginal, Cervical and Gut Microbiota Between Women with Stage 3/4 Endometriosis and Healthy Controls",Scientific reports,2019,NA,Experiment 1,Turkey,Homo sapiens,"Vaginal fluid,Feces,Endocervix","UBERON:0000458,UBERON:0036243,UBERON:0001988",Endometriosis,EFO:0001065,Healthy controls,Stage 3/4 endometriosis patients,Women with histology-proven stage 3/4 endometriosis,14,14,2 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 1,24 June 2021,Samara.Khan,"Samara.Khan,Peace Sandy,WikiWorks",Diferences between microbiota in women with endometriosis and healthy controls.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma",1783272|201174|1760|85004|31953|2701;3379134|1224|1236|91347|543|1940338;3379134|976|200643|171549|171552|1283313;1783272|1239|91061|186826|1300|1301;1783272|544448|2790996|2790998|2129,Complete,Peace Sandy
bsdb:30778155/1/2,30778155,prospective cohort,30778155,10.1038/s41598-019-39700-6,https://pubmed.ncbi.nlm.nih.gov/30778155/,"Ata B., Yildiz S., Turkgeldi E., Brocal V.P., Dinleyici E.C., Moya A. , Urman B.","The Endobiota Study: Comparison of Vaginal, Cervical and Gut Microbiota Between Women with Stage 3/4 Endometriosis and Healthy Controls",Scientific reports,2019,NA,Experiment 1,Turkey,Homo sapiens,"Vaginal fluid,Feces,Endocervix","UBERON:0000458,UBERON:0036243,UBERON:0001988",Endometriosis,EFO:0001065,Healthy controls,Stage 3/4 endometriosis patients,Women with histology-proven stage 3/4 endometriosis,14,14,2 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 1,5 February 2024,Peace Sandy,"Peace Sandy,WikiWorks",Diferences between microbiota in women with endometriosis and healthy controls.,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella",3384189|32066|203490|203491|1129771|168808;3379134|976|200643|171549|171552|838;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|906;1783272|201174|1760|85004|31953|2701;3379134|976|200643|171549|2005519|397864,Complete,Peace Sandy
bsdb:30778376/1/1,30778376,"cross-sectional observational, not case-control",30778376,10.3389/fcimb.2019.00004,NA,"Zeng X., Gao X., Peng Y., Wu Q., Zhu J., Tan C., Xia G., You C., Xu R., Pan S., Zhou H., He Y. , Yin J.",Higher Risk of Stroke Is Correlated With Increased Opportunistic Pathogen Load and Reduced Levels of Butyrate-Producing Bacteria in the Gut,Frontiers in cellular and infection microbiology,2019,"16S rRNA, fecal, microbiota, short-chain fatty acids, stroke risk",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Low Risk (LR) and Medium Risk (MR),High Risk (HR),"The high-risk (HR) group comprised of participants with three or more risk factors. The risk factors Include Hypertension, Atrial fibrillation,  Diabetes mellitus, Dyslipidemias, Smoking, Physical inactivity, Overweight and Family history of stroke.",105,36,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,Figure 2C,26 October 2024,MyleeeA,"MyleeeA,WikiWorks",Differentially Abundant taxa between the Low Risk (LR)/Medium Risk (MR) and High Risk (HR) groups  determined using linear discriminant analysis effect size (LEfSe) analysis,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",3379134|1224|1236|91347;3379134|1224|1236|91347|543,Complete,Svetlana up
bsdb:30778376/2/1,30778376,"cross-sectional observational, not case-control",30778376,10.3389/fcimb.2019.00004,NA,"Zeng X., Gao X., Peng Y., Wu Q., Zhu J., Tan C., Xia G., You C., Xu R., Pan S., Zhou H., He Y. , Yin J.",Higher Risk of Stroke Is Correlated With Increased Opportunistic Pathogen Load and Reduced Levels of Butyrate-Producing Bacteria in the Gut,Frontiers in cellular and infection microbiology,2019,"16S rRNA, fecal, microbiota, short-chain fatty acids, stroke risk",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Low Risk (LR) and High Risk (HR),Medium Risk (MR),"The Medium-risk (MR) group comprised of participants with less than three risk factors and chronic diseases. The risk factors Include Hypertension, Atrial fibrillation, Diabetes mellitus, Dyslipidemias, Smoking, Physical inactivity, Overweight and Family history of stroke.",87,54,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,Figure 2C,26 October 2024,MyleeeA,"MyleeeA,WikiWorks",Differentially Abundant taxa between the Low Risk (LR)/High Risk (HR) and Medium Risk (MR) groups determined using linear discriminant analysis effect size (LEfSe) analysis,increased,"k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Plesiomonas",3384194|508458|649775|649776|649777|508459;1783272|1239|186801|186802|31979|1485;3379134|1224|1236|91347|543|702,Complete,Svetlana up
bsdb:30778376/3/1,30778376,"cross-sectional observational, not case-control",30778376,10.3389/fcimb.2019.00004,NA,"Zeng X., Gao X., Peng Y., Wu Q., Zhu J., Tan C., Xia G., You C., Xu R., Pan S., Zhou H., He Y. , Yin J.",Higher Risk of Stroke Is Correlated With Increased Opportunistic Pathogen Load and Reduced Levels of Butyrate-Producing Bacteria in the Gut,Frontiers in cellular and infection microbiology,2019,"16S rRNA, fecal, microbiota, short-chain fatty acids, stroke risk",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,High Risk (HR) and Medium Risk (MR),Low Risk (LR),"The Low-risk (LR) group comprised of participants with less than three risk factors without chronic diseases. The risk factors Include Hypertension, Atrial fibrillation, Diabetes mellitus, Dyslipidemias, Smoking, Physical inactivity, Overweight and Family history of stroke.",90,51,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,Figure 2C,26 October 2024,MyleeeA,"MyleeeA,KateRasheed,WikiWorks",Differentially Abundant taxa between the High Risk (HR)/Medium Risk (MR) and Low Risk (LR) groups determined using linear discriminant analysis effect size (LEfSe) analysis,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|s__Streptococcaceae bacterium RF32",3379134|1224|1236|135625|712|416916;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803|841;1783272|1239|91061|186826|1300|423432,Complete,Svetlana up
bsdb:30778376/4/1,30778376,"cross-sectional observational, not case-control",30778376,10.3389/fcimb.2019.00004,NA,"Zeng X., Gao X., Peng Y., Wu Q., Zhu J., Tan C., Xia G., You C., Xu R., Pan S., Zhou H., He Y. , Yin J.",Higher Risk of Stroke Is Correlated With Increased Opportunistic Pathogen Load and Reduced Levels of Butyrate-Producing Bacteria in the Gut,Frontiers in cellular and infection microbiology,2019,"16S rRNA, fecal, microbiota, short-chain fatty acids, stroke risk",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Low Risk (LR) and Medium Risk (MR) Without Medication use,High Risk (HR) Without Medication use,"The high-risk (HR) group comprised of participants with three or more risk factors without medication use. The risk factors Include Hypertension, Atrial fibrillation, Diabetes mellitus, Dyslipidemias, Smoking, Physical inactivity, Overweight and Family history of stroke.",56,7,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Supplementary Figure 5,26 October 2024,MyleeeA,"MyleeeA,WikiWorks",Differentially Abundant taxa between the Low Risk (LR)/Medium Risk (MR) and High Risk (HR) groups Without medication use determined using linear discriminant analysis effect size (LEfSe) analysis.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum,k__Methanobacteriati|p__Thermoplasmatota|c__Thermoplasmata,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Pseudoxanthomonas,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,c__Deltaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria",1783272|201174|1760|2037|2049;3379134|976|200643|171549|171551|836;3379134|976|117747|200666|84566|28453;1783272|201174|1760|2037|2049|76833;3366610|2283796|183967;3379134|1224|1236|91347|543|160674;3379134|1224|1236|135614|32033|83618;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;28221;3379134|1224|28216|80840;3379134|1224|28216,Complete,Svetlana up
bsdb:30778376/5/1,30778376,"cross-sectional observational, not case-control",30778376,10.3389/fcimb.2019.00004,NA,"Zeng X., Gao X., Peng Y., Wu Q., Zhu J., Tan C., Xia G., You C., Xu R., Pan S., Zhou H., He Y. , Yin J.",Higher Risk of Stroke Is Correlated With Increased Opportunistic Pathogen Load and Reduced Levels of Butyrate-Producing Bacteria in the Gut,Frontiers in cellular and infection microbiology,2019,"16S rRNA, fecal, microbiota, short-chain fatty acids, stroke risk",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Low Risk (LR) and High Risk (HR) Without Medication use,Medium Risk (MR) Without Medication use,"The Medium-risk (MR) group comprised of participants with less than three risk factors, chronic diseases and without medication use. The risk factors Include Hypertension, Atrial fibrillation, Diabetes mellitus, Dyslipidemias, Smoking, Physical inactivity, Overweight and Family history of stroke.",51,12,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Supplementary Figure 5,26 October 2024,MyleeeA,"MyleeeA,WikiWorks",Differentially Abundant taxa between the Low Risk (LR)/High Risk (HR) and Medium Risk (MR) groups Without medication use determined using linear discriminant analysis effect size (LEfSe) analysis,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Plesiomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|909932|909929|1843491|52225;3379134|1224|1236|91347|543|702;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:30778376/6/1,30778376,"cross-sectional observational, not case-control",30778376,10.3389/fcimb.2019.00004,NA,"Zeng X., Gao X., Peng Y., Wu Q., Zhu J., Tan C., Xia G., You C., Xu R., Pan S., Zhou H., He Y. , Yin J.",Higher Risk of Stroke Is Correlated With Increased Opportunistic Pathogen Load and Reduced Levels of Butyrate-Producing Bacteria in the Gut,Frontiers in cellular and infection microbiology,2019,"16S rRNA, fecal, microbiota, short-chain fatty acids, stroke risk",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,High Risk (HR) and Medium Risk (MR) Without Medication use,Low Risk (LR) Without Medication use,"The Low-risk (LR) group comprised of participants with less than three risk factors without chronic diseases and medication use. The risk factors Include Hypertension, Atrial fibrillation, Diabetes mellitus, Dyslipidemias, Smoking, Physical inactivity, Overweight and Family history of stroke.",19,44,3 Months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Supplementary Figure 5,26 October 2024,MyleeeA,"MyleeeA,WikiWorks",Differentially Abundant taxa between the High Risk (HR)/Medium Risk (MR) and Low Risk (LR) groups Without medication use determined using linear discriminant analysis effect size (LEfSe) analysis,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3082720|186804,Complete,Svetlana up
bsdb:30778376/7/1,30778376,"cross-sectional observational, not case-control",30778376,10.3389/fcimb.2019.00004,NA,"Zeng X., Gao X., Peng Y., Wu Q., Zhu J., Tan C., Xia G., You C., Xu R., Pan S., Zhou H., He Y. , Yin J.",Higher Risk of Stroke Is Correlated With Increased Opportunistic Pathogen Load and Reduced Levels of Butyrate-Producing Bacteria in the Gut,Frontiers in cellular and infection microbiology,2019,"16S rRNA, fecal, microbiota, short-chain fatty acids, stroke risk",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Low Risk (LR) and Medium Risk (MR) With Medication use,High Risk (HR) With  Medication use,"The high-risk (HR) group comprised of participants with three or more risk factors with medication use. The risk factors Include Hypertension, Atrial fibrillation, Diabetes mellitus, Dyslipidemias, Smoking, Physical inactivity, Overweight and Family history of stroke.",49,29,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Supplementary Figure 6,26 October 2024,MyleeeA,"MyleeeA,WikiWorks",Differentially Abundant taxa between the Low Risk (LR)/Medium Risk (MR) and High Risk (HR) groups With medication use determined using linear discriminant analysis effect size (LEfSe) analysis.,increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,1783272|1239|909932|1843489|31977,Complete,Svetlana up
bsdb:30778376/8/1,30778376,"cross-sectional observational, not case-control",30778376,10.3389/fcimb.2019.00004,NA,"Zeng X., Gao X., Peng Y., Wu Q., Zhu J., Tan C., Xia G., You C., Xu R., Pan S., Zhou H., He Y. , Yin J.",Higher Risk of Stroke Is Correlated With Increased Opportunistic Pathogen Load and Reduced Levels of Butyrate-Producing Bacteria in the Gut,Frontiers in cellular and infection microbiology,2019,"16S rRNA, fecal, microbiota, short-chain fatty acids, stroke risk",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Low Risk (LR) and High Risk (HR) With Medication use,Medium Risk (MR) With Medication use,"The Medium-risk (MR) group comprised of participants with less than three risk factors, chronic diseases and with medication use. The risk factors Include Hypertension, Atrial fibrillation, Diabetes mellitus, Dyslipidemias, Smoking, Physical inactivity, Overweight and Family history of stroke.",36,42,3 Months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Supplementary Figure 6,26 October 2024,MyleeeA,"MyleeeA,WikiWorks",Differentially Abundant taxa between the Low Risk (LR)/High Risk (HR) and Medium Risk (MR) groups With medication use determined using linear discriminant analysis effect size (LEfSe) analysis,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,1783272|1239|186801|186802|216572|119852,Complete,Svetlana up
bsdb:30778376/9/1,30778376,"cross-sectional observational, not case-control",30778376,10.3389/fcimb.2019.00004,NA,"Zeng X., Gao X., Peng Y., Wu Q., Zhu J., Tan C., Xia G., You C., Xu R., Pan S., Zhou H., He Y. , Yin J.",Higher Risk of Stroke Is Correlated With Increased Opportunistic Pathogen Load and Reduced Levels of Butyrate-Producing Bacteria in the Gut,Frontiers in cellular and infection microbiology,2019,"16S rRNA, fecal, microbiota, short-chain fatty acids, stroke risk",Experiment 9,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,High Risk (HR) and Medium Risk (MR) With Medication use,Low Risk (LR) With Medication use,"The Low-risk (LR) group comprised of participants with less than three risk factors with chronic diseases and medication use. The risk factors Include Hypertension, Atrial fibrillation, Diabetes mellitus, Dyslipidemias, Smoking, Physical inactivity, Overweight and Family history of stroke.",71,7,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Supplementary Figure 6,26 October 2024,MyleeeA,"MyleeeA,KateRasheed,WikiWorks",Differentially Abundant taxa between the High Risk (HR)/Medium Risk (MR) and Low Risk (LR) groups With medication use determined using linear discriminant analysis effect size (LEfSe) analysis,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hylemonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|s__Streptococcaceae bacterium RF32",3379134|1224|1236|135625|712|416916;1783272|1239|186801|3085636|186803|572511;3379134|1224|28216|80840|80864|232523;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;1783272|1239|91061|1385|186817|400634;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803|841;1783272|1239|91061|186826|81852|2737;1783272|1239|91061|186826|1300|423432,Complete,Svetlana up
bsdb:30778376/10/1,30778376,"cross-sectional observational, not case-control",30778376,10.3389/fcimb.2019.00004,NA,"Zeng X., Gao X., Peng Y., Wu Q., Zhu J., Tan C., Xia G., You C., Xu R., Pan S., Zhou H., He Y. , Yin J.",Higher Risk of Stroke Is Correlated With Increased Opportunistic Pathogen Load and Reduced Levels of Butyrate-Producing Bacteria in the Gut,Frontiers in cellular and infection microbiology,2019,"16S rRNA, fecal, microbiota, short-chain fatty acids, stroke risk",Experiment 10,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Low Risk (LR) and Medium Risk (MR),High Risk (HR),"The high-risk (HR) group comprised of participants with three or more risk factors. The risk factors Include Hypertension, Atrial fibrillation, Diabetes mellitus, Dyslipidemias, Smoking, Physical inactivity, Overweight and Family history of stroke.",103,36,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Supplementary Figure 2G,26 October 2024,MyleeeA,"MyleeeA,WikiWorks",Differentially Abundant taxa between the Low Risk (LR)/Medium Risk (MR) and High Risk (HR) groups determined using linear discriminant analysis effect size (LEfSe) analysis. DADA2 sequencing was used.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia",3379134|1224|1236|91347|543|561;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;3384189|32066|203490|203491|203492|180162;3379134|1224|1236|91347|1903411|613,Complete,Svetlana up
bsdb:30778376/11/1,30778376,"cross-sectional observational, not case-control",30778376,10.3389/fcimb.2019.00004,NA,"Zeng X., Gao X., Peng Y., Wu Q., Zhu J., Tan C., Xia G., You C., Xu R., Pan S., Zhou H., He Y. , Yin J.",Higher Risk of Stroke Is Correlated With Increased Opportunistic Pathogen Load and Reduced Levels of Butyrate-Producing Bacteria in the Gut,Frontiers in cellular and infection microbiology,2019,"16S rRNA, fecal, microbiota, short-chain fatty acids, stroke risk",Experiment 11,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Low Risk (LR) and High Risk (HR),Medium Risk (MR),"The Medium-risk (MR) group comprised of participants with less than three risk factors and chronic diseases. The risk factors Include Hypertension, Atrial fibrillation, Diabetes mellitus, Dyslipidemias, Smoking, Physical inactivity, Overweight and Family history of stroke.",87,52,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Supplementary Figure 2G,26 October 2024,MyleeeA,"MyleeeA,WikiWorks",Differentially Abundant taxa between the Low Risk (LR)/High Risk (HR) and Medium Risk (MR) groups determined using linear discriminant analysis effect size (LEfSe) analysis. DADA2 sequencing was used.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Plesiomonas,3379134|1224|1236|91347|543|702,Complete,Svetlana up
bsdb:30778376/13/1,30778376,"cross-sectional observational, not case-control",30778376,10.3389/fcimb.2019.00004,NA,"Zeng X., Gao X., Peng Y., Wu Q., Zhu J., Tan C., Xia G., You C., Xu R., Pan S., Zhou H., He Y. , Yin J.",Higher Risk of Stroke Is Correlated With Increased Opportunistic Pathogen Load and Reduced Levels of Butyrate-Producing Bacteria in the Gut,Frontiers in cellular and infection microbiology,2019,"16S rRNA, fecal, microbiota, short-chain fatty acids, stroke risk",Experiment 13,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Low Risk (LR),High Risk (HR),"The high-risk (HR) group comprised of participants with three or more risk factors. The risk factors Include Hypertension, Atrial fibrillation, Diabetes mellitus, Dyslipidemias, Smoking, Physical inactivity, Overweight and Family history of stroke.",51,36,3 months,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 4E,1 November 2024,MyleeeA,"MyleeeA,WikiWorks","The relative abundance of butyrate and lactate-producing bacteria in the gut, between the High Risk (HR) and Low Risk (LR) groups.",increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,Svetlana up
bsdb:30778376/13/2,30778376,"cross-sectional observational, not case-control",30778376,10.3389/fcimb.2019.00004,NA,"Zeng X., Gao X., Peng Y., Wu Q., Zhu J., Tan C., Xia G., You C., Xu R., Pan S., Zhou H., He Y. , Yin J.",Higher Risk of Stroke Is Correlated With Increased Opportunistic Pathogen Load and Reduced Levels of Butyrate-Producing Bacteria in the Gut,Frontiers in cellular and infection microbiology,2019,"16S rRNA, fecal, microbiota, short-chain fatty acids, stroke risk",Experiment 13,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Low Risk (LR),High Risk (HR),"The high-risk (HR) group comprised of participants with three or more risk factors. The risk factors Include Hypertension, Atrial fibrillation, Diabetes mellitus, Dyslipidemias, Smoking, Physical inactivity, Overweight and Family history of stroke.",51,36,3 months,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,"Figure 3A, 3B, 3D, 3E",1 November 2024,MyleeeA,"MyleeeA,KateRasheed,WikiWorks","The relative abundance of butyrate and lactate-producing bacteria in the gut, between the High Risk (HR) and Low Risk (LR) groups.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|216851,Complete,Svetlana up
bsdb:30778376/14/1,30778376,"cross-sectional observational, not case-control",30778376,10.3389/fcimb.2019.00004,NA,"Zeng X., Gao X., Peng Y., Wu Q., Zhu J., Tan C., Xia G., You C., Xu R., Pan S., Zhou H., He Y. , Yin J.",Higher Risk of Stroke Is Correlated With Increased Opportunistic Pathogen Load and Reduced Levels of Butyrate-Producing Bacteria in the Gut,Frontiers in cellular and infection microbiology,2019,"16S rRNA, fecal, microbiota, short-chain fatty acids, stroke risk",Experiment 14,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Low Risk (LR),High Risk (HR),"The high-risk (HR) group comprised of participants with three or more risk factors. The risk factors Include Hypertension, Atrial fibrillation, Diabetes mellitus, Dyslipidemias, Smoking, Physical inactivity, Overweight and Family history of stroke.",41,31,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Supplementary Figure 1G,28 October 2024,Princess Ben,"Princess Ben,MyleeeA,WikiWorks",Differentially Abundant taxa in the High Risk (HR) compared to Low Risk (LR) groups were determined using linear discriminant analysis effect size (LEfSe) analysis.,increased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Plesiomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes",3379134|1224;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236;1783272|1239|909932|1843489|31977;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;1783272|1239|909932|1843489|31977|906;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3082768|990719|990721;3379134|1224|28211|356|119045|407;3379134|1224|28216|80840|80864|80865;1783272|1239|91061|186826|33958|1243;3379134|1224|1236|91347|543|702;1783272|1239|186801|3085636|186803|207244,Complete,Svetlana up
bsdb:30778376/14/2,30778376,"cross-sectional observational, not case-control",30778376,10.3389/fcimb.2019.00004,NA,"Zeng X., Gao X., Peng Y., Wu Q., Zhu J., Tan C., Xia G., You C., Xu R., Pan S., Zhou H., He Y. , Yin J.",Higher Risk of Stroke Is Correlated With Increased Opportunistic Pathogen Load and Reduced Levels of Butyrate-Producing Bacteria in the Gut,Frontiers in cellular and infection microbiology,2019,"16S rRNA, fecal, microbiota, short-chain fatty acids, stroke risk",Experiment 14,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Low Risk (LR),High Risk (HR),"The high-risk (HR) group comprised of participants with three or more risk factors. The risk factors Include Hypertension, Atrial fibrillation, Diabetes mellitus, Dyslipidemias, Smoking, Physical inactivity, Overweight and Family history of stroke.",41,31,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Supplementary Figure 1G,1 November 2024,MyleeeA,"MyleeeA,WikiWorks",Differentially Abundant taxa in the High Risk (HR) compared to Low Risk (LR) groups were determined using linear discriminant analysis effect size (LEfSe) analysis.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium",1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|216851;3379134|74201;3379134|74201|203494|48461;3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|203557;3379134|74201|203494;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|841;3379134|1224|28211|204457|41297|13687;1783272|1239|186801|3085636|186803|140625,Complete,Svetlana up
bsdb:30778376/15/1,30778376,"cross-sectional observational, not case-control",30778376,10.3389/fcimb.2019.00004,NA,"Zeng X., Gao X., Peng Y., Wu Q., Zhu J., Tan C., Xia G., You C., Xu R., Pan S., Zhou H., He Y. , Yin J.",Higher Risk of Stroke Is Correlated With Increased Opportunistic Pathogen Load and Reduced Levels of Butyrate-Producing Bacteria in the Gut,Frontiers in cellular and infection microbiology,2019,"16S rRNA, fecal, microbiota, short-chain fatty acids, stroke risk",Experiment 15,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Low Risk (LR),Medium Risk (MR),"The Medium-risk (MR) group comprised of participants with less than three risk factors and chronic diseases. The risk factors Include Hypertension, Atrial fibrillation, Diabetes mellitus, Dyslipidemias, Smoking, Physical inactivity, Overweight and Family history of stroke.",51,54,3 months,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4G,1 November 2024,MyleeeA,"MyleeeA,WikiWorks","The relative abundance of butyrate and lactate-producing bacteria in the gut, between the Medium Risk (MR) and Low Risk (LR) groups.",increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,1783272|1239|909932|1843489|31977,Complete,Svetlana up
bsdb:30778376/15/2,30778376,"cross-sectional observational, not case-control",30778376,10.3389/fcimb.2019.00004,NA,"Zeng X., Gao X., Peng Y., Wu Q., Zhu J., Tan C., Xia G., You C., Xu R., Pan S., Zhou H., He Y. , Yin J.",Higher Risk of Stroke Is Correlated With Increased Opportunistic Pathogen Load and Reduced Levels of Butyrate-Producing Bacteria in the Gut,Frontiers in cellular and infection microbiology,2019,"16S rRNA, fecal, microbiota, short-chain fatty acids, stroke risk",Experiment 15,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Low Risk (LR),Medium Risk (MR),"The Medium-risk (MR) group comprised of participants with less than three risk factors and chronic diseases. The risk factors Include Hypertension, Atrial fibrillation, Diabetes mellitus, Dyslipidemias, Smoking, Physical inactivity, Overweight and Family history of stroke.",51,54,3 months,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3E,1 November 2024,MyleeeA,"MyleeeA,KateRasheed,WikiWorks","The relative abundance of butyrate and lactate-producing bacteria in the gut, between the Medium Risk (MR) and Low Risk (LR) groups.",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,1783272|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:30778376/16/1,30778376,"cross-sectional observational, not case-control",30778376,10.3389/fcimb.2019.00004,NA,"Zeng X., Gao X., Peng Y., Wu Q., Zhu J., Tan C., Xia G., You C., Xu R., Pan S., Zhou H., He Y. , Yin J.",Higher Risk of Stroke Is Correlated With Increased Opportunistic Pathogen Load and Reduced Levels of Butyrate-Producing Bacteria in the Gut,Frontiers in cellular and infection microbiology,2019,"16S rRNA, fecal, microbiota, short-chain fatty acids, stroke risk",Experiment 16,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Medium Risk (LR) and High Risk (HR),Low Risk,Low Risk refers to participants without chronic diseases.,88,51,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Supplementary Figure 2G,7 January 2025,KateRasheed,"KateRasheed,WikiWorks",Differentially Abundant taxa between the High Risk (HR)/Medium Risk (MR) and Low Risk (LR) groups determined using linear discriminant analysis effect size (LEfSe) analysis. DADA2 sequencing was used.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:30782659/1/1,30782659,case-control,30782659,10.1128/mBio.02785-18,NA,"Klein C., Gonzalez D., Samwel K., Kahesa C., Mwaiselage J., Aluthge N., Fernando S., West J.T., Wood C. , Angeletti P.C.","Relationship between the Cervical Microbiome, HIV Status, and Precancerous Lesions",mBio,2019,"16S RNA, cervical cancer, deep sequencing, human immunodeficiency virus, human papillomavirus, microbiome",Experiment 1,United Republic of Tanzania,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,negative for intraepithelial lesion or malignancy,high-grade squamous intraepithelial lesions,high-grade squamous intraepithelial lesions (HSIL) comfirmed by Pap smear,23,45,NA,16S,4,Illumina,relative abundances,LEfSe,0.1,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,figure 6a,10 January 2021,Cynthia Anderson,WikiWorks,LEfSe linear discriminant analysis (LDA) scores between unmatched high-grade squamous intraepithelial lesions (HSIL) and negative for intraepithelial lesion (NILM),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae",3379134|1224|1236|72274|135621|351;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|72274;1783272|544448;1783272|544448|31969|2085;1783272|1239|91061|1385|90964,Complete,Fatima Zohra
bsdb:30782659/1/2,30782659,case-control,30782659,10.1128/mBio.02785-18,NA,"Klein C., Gonzalez D., Samwel K., Kahesa C., Mwaiselage J., Aluthge N., Fernando S., West J.T., Wood C. , Angeletti P.C.","Relationship between the Cervical Microbiome, HIV Status, and Precancerous Lesions",mBio,2019,"16S RNA, cervical cancer, deep sequencing, human immunodeficiency virus, human papillomavirus, microbiome",Experiment 1,United Republic of Tanzania,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,negative for intraepithelial lesion or malignancy,high-grade squamous intraepithelial lesions,high-grade squamous intraepithelial lesions (HSIL) comfirmed by Pap smear,23,45,NA,16S,4,Illumina,relative abundances,LEfSe,0.1,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,figure 6a,10 January 2021,Cynthia Anderson,WikiWorks,LEfSe linear discriminant analysis (LDA) scores between unmatched high-grade squamous intraepithelial lesions (HSIL) and negative for intraepithelial lesion (NILM),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia",3379134|1224|1236;1783272|1239|1737404|1737405|1570339|150022,Complete,Fatima Zohra
bsdb:30782659/2/1,30782659,case-control,30782659,10.1128/mBio.02785-18,NA,"Klein C., Gonzalez D., Samwel K., Kahesa C., Mwaiselage J., Aluthge N., Fernando S., West J.T., Wood C. , Angeletti P.C.","Relationship between the Cervical Microbiome, HIV Status, and Precancerous Lesions",mBio,2019,"16S RNA, cervical cancer, deep sequencing, human immunodeficiency virus, human papillomavirus, microbiome",Experiment 2,United Republic of Tanzania,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,negative for intraepithelial lesion or malignancy,high-grade squamous intraepithelial lesions,high-grade squamous intraepithelial lesions (HSIL) comfirmed by Pap smear,4,4,NA,16S,4,Illumina,relative abundances,LEfSe,0.1,TRUE,NA,age,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,figure 6b,10 January 2021,Cynthia Anderson,WikiWorks,LEfSe linear discriminant analysis (LDA) scores between matched high-grade squamous intraepithelial lesions (HSIL) and negative for intraepithelial lesion (NILM),increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales",1783272|1239|91061|186826|1300|1301;1783272|1239|1737404|1737405|1570339|543311;1783272|544448;1783272|544448|31969;1783272|544448|31969|2085,Complete,Fatima Zohra
bsdb:30782659/2/2,30782659,case-control,30782659,10.1128/mBio.02785-18,NA,"Klein C., Gonzalez D., Samwel K., Kahesa C., Mwaiselage J., Aluthge N., Fernando S., West J.T., Wood C. , Angeletti P.C.","Relationship between the Cervical Microbiome, HIV Status, and Precancerous Lesions",mBio,2019,"16S RNA, cervical cancer, deep sequencing, human immunodeficiency virus, human papillomavirus, microbiome",Experiment 2,United Republic of Tanzania,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,negative for intraepithelial lesion or malignancy,high-grade squamous intraepithelial lesions,high-grade squamous intraepithelial lesions (HSIL) comfirmed by Pap smear,4,4,NA,16S,4,Illumina,relative abundances,LEfSe,0.1,TRUE,NA,age,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,figure 6b,10 January 2021,Cynthia Anderson,WikiWorks,LEfSe linear discriminant analysis (LDA) scores between matched high-grade squamous intraepithelial lesions (HSIL) and negative for intraepithelial lesion (NILM),decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia",1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578|147802;1783272|1239|91061;1783272|1239|91061|186826;1783272|1239|1737404|1737405|1570339|150022,Complete,Fatima Zohra
bsdb:30782659/3/1,30782659,case-control,30782659,10.1128/mBio.02785-18,NA,"Klein C., Gonzalez D., Samwel K., Kahesa C., Mwaiselage J., Aluthge N., Fernando S., West J.T., Wood C. , Angeletti P.C.","Relationship between the Cervical Microbiome, HIV Status, and Precancerous Lesions",mBio,2019,"16S RNA, cervical cancer, deep sequencing, human immunodeficiency virus, human papillomavirus, microbiome",Experiment 3,United Republic of Tanzania,Homo sapiens,Uterine cervix,UBERON:0000002,HIV infection,EFO:0000764,HIV-,HIV+,HIV+ comfirmed by Standard Diagnostics HIV-1/2 3.0 detection kit,95,39,NA,16S,4,Illumina,relative abundances,LEfSe,0.1,TRUE,NA,NA,NA,NA,NA,increased,NA,NA,NA,Signature 1,figure 6c,10 January 2021,Cynthia Anderson,"WikiWorks,Merit",LEfSe linear discriminant analysis (LDA) scores.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales,k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus",1783272|201174|1760|2037|2049;1783272|201174|1760|2037;1783272|1239|91061|186826|186827|1375;3379134|1224|28211;1783272|1239;1783272|201174|1760|85004|31953;1783272|1239|91061|186826|186828;1783272|1239|186801;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724|727;1783272|544448|31969;1783272|1239|186801|3085636|186803|437755;1783272|544448|31969|2085|2092;1783272|544448|31969|2085;1783272|544448;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1257;1783272|1239|186801|3082720|186804|1257|1261;3379134|1224|28211|356|82115;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1328,Complete,Fatima Zohra
bsdb:30782659/3/2,30782659,case-control,30782659,10.1128/mBio.02785-18,NA,"Klein C., Gonzalez D., Samwel K., Kahesa C., Mwaiselage J., Aluthge N., Fernando S., West J.T., Wood C. , Angeletti P.C.","Relationship between the Cervical Microbiome, HIV Status, and Precancerous Lesions",mBio,2019,"16S RNA, cervical cancer, deep sequencing, human immunodeficiency virus, human papillomavirus, microbiome",Experiment 3,United Republic of Tanzania,Homo sapiens,Uterine cervix,UBERON:0000002,HIV infection,EFO:0000764,HIV-,HIV+,HIV+ comfirmed by Standard Diagnostics HIV-1/2 3.0 detection kit,95,39,NA,16S,4,Illumina,relative abundances,LEfSe,0.1,TRUE,NA,NA,NA,NA,NA,increased,NA,NA,NA,Signature 2,figure 6c,10 January 2021,Cynthia Anderson,WikiWorks,LEfSe linear discriminant analysis (LDA) scores.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|201174|1760|2037|2049|28263;1783272|544448|2790996|2790998|2129;1783272|1239|91061|186826|33958|2742598|1598;1783272|201174|1760;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678,Complete,Fatima Zohra
bsdb:30791484/1/1,30791484,"cross-sectional observational, not case-control",30791484,10.3390/nu11020433,NA,"Iino C., Shimoyama T., Iino K., Yokoyama Y., Chinda D., Sakuraba H., Fukuda S. , Nakaji S.",Daidzein Intake Is Associated with Equol Producing Status through an Increase in the Intestinal Bacteria Responsible for Equol Production,Nutrients,2019,"Asaccharobacter celatus, Slackia isoflavoniconvertens, daidzein, equol, gut microbiota",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,equol,NA,equol non-producers,equol producers,The equol production status was defined by a urinary log 10 - transformed equol/daidzein ratio of −1.75 or more as described previously,586,458,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Relative abundance of species (percentage of the total bacterial 16sRNA).,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens|s__Adlercreutzia equolifaciens subsp. celatus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens",1783272|201174|84998|1643822|1643826|447020|446660|394340;1783272|201174|84998|1643822|1643826|84108|572010,Complete,Atrayees
bsdb:30794590/1/1,30794590,"cross-sectional observational, not case-control",30794590,10.1371/journal.pone.0212406,NA,"Saito K., Koido S., Odamaki T., Kajihara M., Kato K., Horiuchi S., Adachi S., Arakawa H., Yoshida S., Akasu T., Ito Z., Uchiyama K., Saruta M., Xiao J.Z., Sato N. , Ohkusa T.",Metagenomic analyses of the gut microbiota associated with colorectal adenoma,PloS one,2019,NA,Experiment 1,Japan,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,Healthy,Intramucosal CRC,Intramucosal CRC is in its earliest stage (stage 0) and is also known as carcinoma in situ or intramucosal carcinoma. Intramucosal CRC has not yet grown beyond the inner mucosal layer of the colorectum,10,24,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 4B, Figure 7",4 July 2022,Jeshudy,"Jeshudy,Atrayees,WikiWorks",Characterization of microbiomes in intramucosal CRC patients and healthy subjects.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium perfoetens",1783272|1239|909932|909929|1843491|158846;3379134|1224|28211|204457|3423717|165695;3384189|32066|203490|203491|203492|848|860;3384189|32066|203490|203491|203492|848|852,Complete,Atrayees
bsdb:30794590/1/2,30794590,"cross-sectional observational, not case-control",30794590,10.1371/journal.pone.0212406,NA,"Saito K., Koido S., Odamaki T., Kajihara M., Kato K., Horiuchi S., Adachi S., Arakawa H., Yoshida S., Akasu T., Ito Z., Uchiyama K., Saruta M., Xiao J.Z., Sato N. , Ohkusa T.",Metagenomic analyses of the gut microbiota associated with colorectal adenoma,PloS one,2019,NA,Experiment 1,Japan,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,Healthy,Intramucosal CRC,Intramucosal CRC is in its earliest stage (stage 0) and is also known as carcinoma in situ or intramucosal carcinoma. Intramucosal CRC has not yet grown beyond the inner mucosal layer of the colorectum,10,24,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 4B, Figure 7",4 July 2022,Jeshudy,"Jeshudy,Atrayees,WikiWorks",Characterization of microbiomes in intramucosal CRC patients and healthy subjects.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium varium",3379134|1224|1236|135625|712|713;3384189|32066|203490|203491|203492|848;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;1783272|201174|1760|2037|2049|1654;3384189|32066|203490;3384189|32066|203490|203491;3384189|32066|203490|203491|203492;3384189|32066|203490|203491|203492|848|856,Complete,Atrayees
bsdb:30794590/2/1,30794590,"cross-sectional observational, not case-control",30794590,10.1371/journal.pone.0212406,NA,"Saito K., Koido S., Odamaki T., Kajihara M., Kato K., Horiuchi S., Adachi S., Arakawa H., Yoshida S., Akasu T., Ito Z., Uchiyama K., Saruta M., Xiao J.Z., Sato N. , Ohkusa T.",Metagenomic analyses of the gut microbiota associated with colorectal adenoma,PloS one,2019,NA,Experiment 2,Japan,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,CRA (colorectal adenoma),Intramucosal CRC,Intramucosal CRC is in its earliest stage (stage 0) and is also known as carcinoma in situ or intramucosal carcinoma. Intramucosal CRC has not yet grown beyond the inner mucosal layer of the colorectum,47,24,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 8B,4 July 2022,Jeshudy,"Jeshudy,WikiWorks",Characterization of microbiomes in patients with CRA and intramucosal CRC by LEfSe analysis and LDA. Histogram of the LDA scores (log10) computed for features that were differentially abundant in patients with CRA and intramucosal CRC.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae",3379134|976|200643|171549|1853231|574697;1783272|201174|84998|84999|84107|102106;1783272|1239|909932|909929|1843491|52225;28221;3379134|200940|3031449|213115;3384194|508458|649775|649776|649777;3379134|1224|28216|80840|80864|283;3379134|200940|3031449|213115|194924,Complete,Atrayees
bsdb:30794590/2/2,30794590,"cross-sectional observational, not case-control",30794590,10.1371/journal.pone.0212406,NA,"Saito K., Koido S., Odamaki T., Kajihara M., Kato K., Horiuchi S., Adachi S., Arakawa H., Yoshida S., Akasu T., Ito Z., Uchiyama K., Saruta M., Xiao J.Z., Sato N. , Ohkusa T.",Metagenomic analyses of the gut microbiota associated with colorectal adenoma,PloS one,2019,NA,Experiment 2,Japan,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,CRA (colorectal adenoma),Intramucosal CRC,Intramucosal CRC is in its earliest stage (stage 0) and is also known as carcinoma in situ or intramucosal carcinoma. Intramucosal CRC has not yet grown beyond the inner mucosal layer of the colorectum,47,24,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 8B, Figure 9",4 July 2022,Jeshudy,"Jeshudy,Atrayees,WikiWorks",Characterization of microbiomes in patients with CRA and intramucosal CRC by LEfSe analysis and LDA. Histogram of the LDA scores (log10) computed for features that were differentially abundant in patients with CRA and intramucosal CRC.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|909932|909929|1843491|158846;1783272|1239|526524|526525|128827;1783272|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:30794590/3/1,30794590,"cross-sectional observational, not case-control",30794590,10.1371/journal.pone.0212406,NA,"Saito K., Koido S., Odamaki T., Kajihara M., Kato K., Horiuchi S., Adachi S., Arakawa H., Yoshida S., Akasu T., Ito Z., Uchiyama K., Saruta M., Xiao J.Z., Sato N. , Ohkusa T.",Metagenomic analyses of the gut microbiota associated with colorectal adenoma,PloS one,2019,NA,Experiment 3,Japan,Homo sapiens,Intestine,UBERON:0000160,Colorectal adenoma,EFO:0005406,Healthy,CRA (colorectal adenoma),"Colorectal adenoma, as diagnosed after a complete colonoscopic exampination",10,47,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Figure 2B, Figure 6",4 July 2022,Jeshudy,"Jeshudy,Atrayees,WikiWorks",Characterization of microbiomes in CRA patients and healthy subjects by LEfSe analysis and LDA. (A) Taxonomic representation of statistically and biologically consistent differences in CRA and healthy subjects. (B) Histogram of the LDA scores (log10) computed for features with differential abundance in CRA patients and healthy subjects.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium varium",1783272|1239|186801|3085636|186803|140625;3379134|976|200643|171549|1853231|574697;3379134|1224|1236|91347|543|590;3379134|1224|28216|80840|80864|283;3379134|1224|1236|2887326|468;3384189|32066|203490|203491|203492|848|856,Complete,Atrayees
bsdb:30794590/3/2,30794590,"cross-sectional observational, not case-control",30794590,10.1371/journal.pone.0212406,NA,"Saito K., Koido S., Odamaki T., Kajihara M., Kato K., Horiuchi S., Adachi S., Arakawa H., Yoshida S., Akasu T., Ito Z., Uchiyama K., Saruta M., Xiao J.Z., Sato N. , Ohkusa T.",Metagenomic analyses of the gut microbiota associated with colorectal adenoma,PloS one,2019,NA,Experiment 3,Japan,Homo sapiens,Intestine,UBERON:0000160,Colorectal adenoma,EFO:0005406,Healthy,CRA (colorectal adenoma),"Colorectal adenoma, as diagnosed after a complete colonoscopic exampination",10,47,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Figure 2B, Figure 6",4 July 2022,Jeshudy,"Jeshudy,Atrayees,WikiWorks",Characterization of microbiomes in CRA patients and healthy subjects by LEfSe analysis and LDA. Histogram of the LDA scores (log10) computed for features with differential abundance in CRA patients and healthy subjects.,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae",1783272|201174|84998|84999|1643824|1380;1783272|1239|1737404|1737405|1570339|543311;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492|848|860;3384189|32066|203490|203491|203492|848|851;3384189|32066|203490;3384189|32066|203490|203491;3384189|32066|203490|203491|203492,Complete,Atrayees
bsdb:30800106/1/1,30800106,case-control,30800106,https://doi.org/10.3389/fmicb.2019.00164,NA,"Bodkhe R., Shetty S.A., Dhotre D.P., Verma A.K., Bhatia K., Mishra A., Kaur G., Pande P., Bangarusamy D.K., Santosh B.P., Perumal R.C., Ahuja V., Shouche Y.S. , Makharia G.K.",Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls,Frontiers in microbiology,2019,"H. pylori, butyrate, celiac, duodenal microbiota, gluten, gut microbiota",Experiment 1,India,Homo sapiens,Duodenum,UBERON:0002114,Celiac disease,EFO:0001060,Disease Control (DC),First-degree relatives (FDRs) of celiac disease (CeD) patients,First-degree relatives (FDRs) of celiac disease (CeD) patients genetically susceptible to celiac disease (CeD),14,13,NA,16S,4,Illumina,raw counts,DESeq2,0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3A,30 March 2024,Temi,"Temi,Scholastica,WikiWorks",Comparison of differential abundance of microbial ASVs in duodenal microbiota of disease control (DC) group versus First-degree relatives (FDRs),increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Methanobacteriati|p__Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|171552|838;1783272|1239|1737404|1737405|1570339|543311;3366610|2283796|183967|1235850|1577788|1080709;1783272|1239|909932|1843489|31977|906;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3082720|186804|1505657;3379134|29547|3031852|213849|72293|209;1783272|1239|91061|186826|186828|117563;1783272|1239|91061|1385|539738|1378;1783272|1239|186801|186802|186806|1730;1783272|1239|526524|526525|2810280|135858;1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|207244;1783272|201174|1760|2037|2049|1654,Complete,Svetlana up
bsdb:30800106/1/2,30800106,case-control,30800106,https://doi.org/10.3389/fmicb.2019.00164,NA,"Bodkhe R., Shetty S.A., Dhotre D.P., Verma A.K., Bhatia K., Mishra A., Kaur G., Pande P., Bangarusamy D.K., Santosh B.P., Perumal R.C., Ahuja V., Shouche Y.S. , Makharia G.K.",Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls,Frontiers in microbiology,2019,"H. pylori, butyrate, celiac, duodenal microbiota, gluten, gut microbiota",Experiment 1,India,Homo sapiens,Duodenum,UBERON:0002114,Celiac disease,EFO:0001060,Disease Control (DC),First-degree relatives (FDRs) of celiac disease (CeD) patients,First-degree relatives (FDRs) of celiac disease (CeD) patients genetically susceptible to celiac disease (CeD),14,13,NA,16S,4,Illumina,raw counts,DESeq2,0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3A,30 March 2024,Temi,"Temi,Scholastica,WikiWorks",Comparison of differential abundance of microbial ASVs in duodenal microbiota of disease control (DC) group versus First-degree relatives (FDRs),decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Methanobacteriati|p__Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella",1783272|1239|526524|526525|2810281|191303;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|1263;3379134|1224|1236|2887326|468|475;3366610|2283796|183967|1235850|1577788|1080709;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3082720|186804|1505657;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|2005519|397864,Complete,NA
bsdb:30800106/2/1,30800106,case-control,30800106,https://doi.org/10.3389/fmicb.2019.00164,NA,"Bodkhe R., Shetty S.A., Dhotre D.P., Verma A.K., Bhatia K., Mishra A., Kaur G., Pande P., Bangarusamy D.K., Santosh B.P., Perumal R.C., Ahuja V., Shouche Y.S. , Makharia G.K.",Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls,Frontiers in microbiology,2019,"H. pylori, butyrate, celiac, duodenal microbiota, gluten, gut microbiota",Experiment 2,India,Homo sapiens,Duodenum,UBERON:0002114,Celiac disease,EFO:0001060,First-degree relatives (FDRs) of celiac disease (CeD) patients,Celiac disease (CeD),Patients with celiac disease (CeD),13,16,NA,16S,4,Illumina,raw counts,DESeq2,0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3B,29 May 2024,Scholastica,"Scholastica,WikiWorks",Comparison of differential abundance of microbial ASVs in duodenal microbiota of celiac disease versus disease control (DC) group,increased,"k__Methanobacteriati|p__Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",3366610|2283796|183967|1235850|1577788|1080709;1783272|1239|909932|1843489|31977|906;1783272|1239|91061|186826|33958|1578;3379134|29547|3031852|213849|72293|209;1783272|1239|186801|186802|186806|1730;1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|3085636|186803|572511;3379134|74201|203494|48461|1647988|239934,Complete,Svetlana up
bsdb:30800106/2/2,30800106,case-control,30800106,https://doi.org/10.3389/fmicb.2019.00164,NA,"Bodkhe R., Shetty S.A., Dhotre D.P., Verma A.K., Bhatia K., Mishra A., Kaur G., Pande P., Bangarusamy D.K., Santosh B.P., Perumal R.C., Ahuja V., Shouche Y.S. , Makharia G.K.",Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls,Frontiers in microbiology,2019,"H. pylori, butyrate, celiac, duodenal microbiota, gluten, gut microbiota",Experiment 2,India,Homo sapiens,Duodenum,UBERON:0002114,Celiac disease,EFO:0001060,First-degree relatives (FDRs) of celiac disease (CeD) patients,Celiac disease (CeD),Patients with celiac disease (CeD),13,16,NA,16S,4,Illumina,raw counts,DESeq2,0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3B,29 May 2024,Scholastica,"Scholastica,WikiWorks",Comparison of differential abundance of microbial ASVs in duodenal microbiota of celiac disease versus disease control (DC) group,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Methanobacteriati|p__Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",1783272|1239|526524|526525|2810281|191303;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|1263;1783272|1239|1737404|1737405|1570339|543311;3366610|2283796|183967|1235850|1577788|1080709;1783272|1239|186801|3082720|186804|1505657;1783272|1239|91061|186826|186828|117563;1783272|1239|91061|1385|539738|1378;1783272|1239|186801|186802|186806|1730;1783272|1239|526524|526525|2810280|135858;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|207244;1783272|201174|1760|2037|2049|1654,Complete,Svetlana up
bsdb:30800106/3/1,30800106,case-control,30800106,https://doi.org/10.3389/fmicb.2019.00164,NA,"Bodkhe R., Shetty S.A., Dhotre D.P., Verma A.K., Bhatia K., Mishra A., Kaur G., Pande P., Bangarusamy D.K., Santosh B.P., Perumal R.C., Ahuja V., Shouche Y.S. , Makharia G.K.",Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls,Frontiers in microbiology,2019,"H. pylori, butyrate, celiac, duodenal microbiota, gluten, gut microbiota",Experiment 3,India,Homo sapiens,Duodenum,UBERON:0002114,Celiac disease,EFO:0001060,Disease Control (DC),Celiac disease (CeD),Patients with celiac disease (CeD),14,16,NA,16S,4,Illumina,raw counts,DESeq2,0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3C,29 May 2024,Scholastica,"Scholastica,WikiWorks",Comparison of differential abundance of microbial ASVs in duodenal microbiota of disease control (DC)  versus celiac disease (CeD) patients,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Methanobacteriati|p__Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",3379134|976|200643|171549|171552|838;3366610|2283796|183967|1235850|1577788|1080709;1783272|1239|909932|1843489|31977|906;1783272|1239|91061|186826|33958|1578;3379134|29547|3031852|213849|72293|209;1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|3085636|186803|572511,Complete,Svetlana up
bsdb:30800106/3/2,30800106,case-control,30800106,https://doi.org/10.3389/fmicb.2019.00164,NA,"Bodkhe R., Shetty S.A., Dhotre D.P., Verma A.K., Bhatia K., Mishra A., Kaur G., Pande P., Bangarusamy D.K., Santosh B.P., Perumal R.C., Ahuja V., Shouche Y.S. , Makharia G.K.",Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls,Frontiers in microbiology,2019,"H. pylori, butyrate, celiac, duodenal microbiota, gluten, gut microbiota",Experiment 3,India,Homo sapiens,Duodenum,UBERON:0002114,Celiac disease,EFO:0001060,Disease Control (DC),Celiac disease (CeD),Patients with celiac disease (CeD),14,16,NA,16S,4,Illumina,raw counts,DESeq2,0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3C,29 May 2024,Scholastica,"Scholastica,WikiWorks",Comparison of differential abundance of microbial ASVs in duodenal microbiota of disease control (DC) versus celiac disease (CeD) patients,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Methanobacteriati|p__Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella",1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|216572|1263;3379134|1224|1236|2887326|468|475;3366610|2283796|183967|1235850|1577788|1080709;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3082720|186804|1505657;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|2005519|397864,Complete,Svetlana up
bsdb:30800106/4/1,30800106,case-control,30800106,https://doi.org/10.3389/fmicb.2019.00164,NA,"Bodkhe R., Shetty S.A., Dhotre D.P., Verma A.K., Bhatia K., Mishra A., Kaur G., Pande P., Bangarusamy D.K., Santosh B.P., Perumal R.C., Ahuja V., Shouche Y.S. , Makharia G.K.",Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls,Frontiers in microbiology,2019,"H. pylori, butyrate, celiac, duodenal microbiota, gluten, gut microbiota",Experiment 4,India,Homo sapiens,Feces,UBERON:0001988,Celiac disease,EFO:0001060,Disease Control (DC),First-degree relatives (FDRs) of celiac disease (CeD) patients,Fecal samples of first-degree relatives (FDRs) of celiac disease (CeD) patients genetically susceptible to celiac disease (CeD),23,15,NA,16S,4,Illumina,raw counts,DESeq2,0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 5A,29 May 2024,Scholastica,"Scholastica,WikiWorks",Comparison of differential abundance of microbial ASVs in fecal microbiota of disease control (DC) group versus First-degree relatives (FDRs),increased,k__Methanobacteriati|p__Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus,3366610|2283796|183967|1235850|1577788|1080709,Complete,Svetlana up
bsdb:30800106/4/2,30800106,case-control,30800106,https://doi.org/10.3389/fmicb.2019.00164,NA,"Bodkhe R., Shetty S.A., Dhotre D.P., Verma A.K., Bhatia K., Mishra A., Kaur G., Pande P., Bangarusamy D.K., Santosh B.P., Perumal R.C., Ahuja V., Shouche Y.S. , Makharia G.K.",Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls,Frontiers in microbiology,2019,"H. pylori, butyrate, celiac, duodenal microbiota, gluten, gut microbiota",Experiment 4,India,Homo sapiens,Feces,UBERON:0001988,Celiac disease,EFO:0001060,Disease Control (DC),First-degree relatives (FDRs) of celiac disease (CeD) patients,Fecal samples of first-degree relatives (FDRs) of celiac disease (CeD) patients genetically susceptible to celiac disease (CeD),23,15,NA,16S,4,Illumina,raw counts,DESeq2,0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 5A,29 May 2024,Scholastica,"Scholastica,WikiWorks",Comparison of differential abundance of microbial ASVs in fecal microbiota of disease control (DC) group versus First-degree relatives (FDRs),decreased,"k__Methanobacteriati|p__Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",3366610|2283796|183967|1235850|1577788|1080709;1783272|1239|91061|186826|33958|1578;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|189330;3379134|74201|203494|48461|1647988|239934,Complete,Svetlana up
bsdb:30800106/5/1,30800106,case-control,30800106,https://doi.org/10.3389/fmicb.2019.00164,NA,"Bodkhe R., Shetty S.A., Dhotre D.P., Verma A.K., Bhatia K., Mishra A., Kaur G., Pande P., Bangarusamy D.K., Santosh B.P., Perumal R.C., Ahuja V., Shouche Y.S. , Makharia G.K.",Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls,Frontiers in microbiology,2019,"H. pylori, butyrate, celiac, duodenal microbiota, gluten, gut microbiota",Experiment 5,India,Homo sapiens,Feces,UBERON:0001988,Celiac disease,EFO:0001060,Disease Control (DC),First-degree relatives (FDRs) of celiac disease (CeD) patients,First-degree relatives (FDRs) of celiac disease (CeD) patients genetically susceptible to celiac disease (CeD),23,15,NA,16S,4,Illumina,raw counts,DESeq2,0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 5B,29 May 2024,Scholastica,"Scholastica,WikiWorks",Comparison of differential abundance of microbial ASVs in fecal microbiota of celiac disease versus disease control (DC) group,increased,"k__Methanobacteriati|p__Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",3366610|2283796|183967|1235850|1577788|1080709;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:30800106/5/2,30800106,case-control,30800106,https://doi.org/10.3389/fmicb.2019.00164,NA,"Bodkhe R., Shetty S.A., Dhotre D.P., Verma A.K., Bhatia K., Mishra A., Kaur G., Pande P., Bangarusamy D.K., Santosh B.P., Perumal R.C., Ahuja V., Shouche Y.S. , Makharia G.K.",Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls,Frontiers in microbiology,2019,"H. pylori, butyrate, celiac, duodenal microbiota, gluten, gut microbiota",Experiment 5,India,Homo sapiens,Feces,UBERON:0001988,Celiac disease,EFO:0001060,Disease Control (DC),First-degree relatives (FDRs) of celiac disease (CeD) patients,First-degree relatives (FDRs) of celiac disease (CeD) patients genetically susceptible to celiac disease (CeD),23,15,NA,16S,4,Illumina,raw counts,DESeq2,0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 5B,29 May 2024,Scholastica,"Scholastica,WikiWorks",Comparison of differential abundance of microbial ASVs in fecal microbiota of celiac disease versus disease control (DC) group,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Methanobacteriati|p__Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",1783272|1239|91061|186826|33958|1253;3366610|2283796|183967|1235850|1577788|1080709;1783272|1239|186801|3082720|186804|1505657;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|572511,Complete,Svetlana up
bsdb:30800106/6/1,30800106,case-control,30800106,https://doi.org/10.3389/fmicb.2019.00164,NA,"Bodkhe R., Shetty S.A., Dhotre D.P., Verma A.K., Bhatia K., Mishra A., Kaur G., Pande P., Bangarusamy D.K., Santosh B.P., Perumal R.C., Ahuja V., Shouche Y.S. , Makharia G.K.",Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls,Frontiers in microbiology,2019,"H. pylori, butyrate, celiac, duodenal microbiota, gluten, gut microbiota",Experiment 6,India,Homo sapiens,Feces,UBERON:0001988,Celiac disease,EFO:0001060,First-degree relatives (FDRs) of celiac disease (CeD) patients,Celiac disease (CeD),Patients with celiac disease (CeD),15,21,NA,16S,4,Illumina,raw counts,DESeq2,0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 5C,29 May 2024,Scholastica,"Scholastica,WikiWorks",Comparison of differential abundance of microbial ASVs in fecal microbiota of disease control (DC) versus celiac disease (CeD) patients,increased,"k__Methanobacteriati|p__Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",3366610|2283796|183967|1235850|1577788|1080709;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:30800106/6/2,30800106,case-control,30800106,https://doi.org/10.3389/fmicb.2019.00164,NA,"Bodkhe R., Shetty S.A., Dhotre D.P., Verma A.K., Bhatia K., Mishra A., Kaur G., Pande P., Bangarusamy D.K., Santosh B.P., Perumal R.C., Ahuja V., Shouche Y.S. , Makharia G.K.",Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls,Frontiers in microbiology,2019,"H. pylori, butyrate, celiac, duodenal microbiota, gluten, gut microbiota",Experiment 6,India,Homo sapiens,Feces,UBERON:0001988,Celiac disease,EFO:0001060,First-degree relatives (FDRs) of celiac disease (CeD) patients,Celiac disease (CeD),Patients with celiac disease (CeD),15,21,NA,16S,4,Illumina,raw counts,DESeq2,0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 5C,29 May 2024,Scholastica,"Scholastica,WikiWorks",Comparison of differential abundance of microbial ASVs in fecal microbiota of disease control (DC) versus celiac disease (CeD) patients,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Methanobacteriati|p__Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",3379134|976|200643|171549|171552|838;3366610|2283796|183967|1235850|1577788|1080709;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|189330;3379134|74201|203494|48461|1647988|239934,Complete,Svetlana up
bsdb:30800111/1/1,30800111,laboratory experiment,30800111,https://doi.org/10.3389/fmicb.2019.00175,NA,"Zhang F., Ma T., Cui P., Tamadon A., He S., Huo C., Yierfulati G., Xu X., Hu W., Li X., Shao L.R., Guo H., Feng Y. , Xu C.","Diversity of the Gut Microbiota in Dihydrotestosterone-Induced PCOS Rats and the Pharmacologic Effects of Diane-35, Probiotics, and Berberine",Frontiers in microbiology,2019,"DHT, Diane-35, PCOS, berberine, gut microbiota, probiotics",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Control,HFD (High fat diet),"Female Wistar rats of 21 days fed a high-fat chow, energy%: 60% from fat, 20% from carbohydrates and 20% from protein, 5.24 kcal/g (Research Diets, D12492).",6,6,NA,16S,34,Illumina,relative abundances,ANOVA,0.01,FALSE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Figure 5D,6 June 2025,Anne-mariesharp,Anne-mariesharp,The abundance of Spirochaetaceae at the family level.,decreased,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,3379134|203691|203692|136|137,Complete,KateRasheed
bsdb:30800111/2/1,30800111,laboratory experiment,30800111,https://doi.org/10.3389/fmicb.2019.00175,NA,"Zhang F., Ma T., Cui P., Tamadon A., He S., Huo C., Yierfulati G., Xu X., Hu W., Li X., Shao L.R., Guo H., Feng Y. , Xu C.","Diversity of the Gut Microbiota in Dihydrotestosterone-Induced PCOS Rats and the Pharmacologic Effects of Diane-35, Probiotics, and Berberine",Frontiers in microbiology,2019,"DHT, Diane-35, PCOS, berberine, gut microbiota, probiotics",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control,DHT (Dihydrotestosterone),"Female Wistar rats of 21 days fed with standard chow, energy%: 10.3% from fat, 65.5% from carbohydrate and 24.2% from protein, 3.52kcal/g (Shanghai SLAC Laboratory Animal) and implanted subcutaneously with slow-release Dihydrotestosterone (15 mg, 75-day release) silicone tubes at 21 days old to induce Polycystic ovary syndrome",6,6,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 5D,6 June 2025,Anne-mariesharp,Anne-mariesharp,The abundance of Spirochaetaceae at the family level.,decreased,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,3379134|203691|203692|136|137,Complete,KateRasheed
bsdb:30800111/3/1,30800111,laboratory experiment,30800111,https://doi.org/10.3389/fmicb.2019.00175,NA,"Zhang F., Ma T., Cui P., Tamadon A., He S., Huo C., Yierfulati G., Xu X., Hu W., Li X., Shao L.R., Guo H., Feng Y. , Xu C.","Diversity of the Gut Microbiota in Dihydrotestosterone-Induced PCOS Rats and the Pharmacologic Effects of Diane-35, Probiotics, and Berberine",Frontiers in microbiology,2019,"DHT, Diane-35, PCOS, berberine, gut microbiota, probiotics",Experiment 3,China,Rattus norvegicus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control,DHT (Dihydrotestosterone) + Berberine,"DHT-induced PCOS rats treated with Berberine daily, starting 7 weeks after DHT implantation",6,6,NA,16S,34,Illumina,relative abundances,ANOVA,0.01,FALSE,NA,NA,NA,NA,decreased,decreased,increased,NA,decreased,Signature 1,Figure 5D,6 June 2025,Anne-mariesharp,Anne-mariesharp,The abundance of Spirochaetaceae at the family level.,decreased,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,3379134|203691|203692|136|137,Complete,KateRasheed
bsdb:30800111/4/1,30800111,laboratory experiment,30800111,https://doi.org/10.3389/fmicb.2019.00175,NA,"Zhang F., Ma T., Cui P., Tamadon A., He S., Huo C., Yierfulati G., Xu X., Hu W., Li X., Shao L.R., Guo H., Feng Y. , Xu C.","Diversity of the Gut Microbiota in Dihydrotestosterone-Induced PCOS Rats and the Pharmacologic Effects of Diane-35, Probiotics, and Berberine",Frontiers in microbiology,2019,"DHT, Diane-35, PCOS, berberine, gut microbiota, probiotics",Experiment 4,China,Rattus norvegicus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Control,HFD (High fat diet),"Female Wistar rats of 21 days fed a high-fat chow, energy%: 60% from fat, 20% from carbohydrates and 20% from protein, 5.24 kcal/g (Research Diets, D12492).",6,6,NA,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,"Figure 6A, Supplementary figure 2A",6 June 2025,Anne-mariesharp,Anne-mariesharp,Different fecal microbiota in rats at the genus level,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|3068309,Complete,KateRasheed
bsdb:30800111/4/2,30800111,laboratory experiment,30800111,https://doi.org/10.3389/fmicb.2019.00175,NA,"Zhang F., Ma T., Cui P., Tamadon A., He S., Huo C., Yierfulati G., Xu X., Hu W., Li X., Shao L.R., Guo H., Feng Y. , Xu C.","Diversity of the Gut Microbiota in Dihydrotestosterone-Induced PCOS Rats and the Pharmacologic Effects of Diane-35, Probiotics, and Berberine",Frontiers in microbiology,2019,"DHT, Diane-35, PCOS, berberine, gut microbiota, probiotics",Experiment 4,China,Rattus norvegicus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Control,HFD (High fat diet),"Female Wistar rats of 21 days fed a high-fat chow, energy%: 60% from fat, 20% from carbohydrates and 20% from protein, 5.24 kcal/g (Research Diets, D12492).",6,6,NA,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,"Figure 6A, Supplementary figure 2A",8 July 2025,Anne-mariesharp,Anne-mariesharp,Different fecal microbiota in rats at the genus level,decreased,NA,NA,Complete,KateRasheed
bsdb:30800111/5/1,30800111,laboratory experiment,30800111,https://doi.org/10.3389/fmicb.2019.00175,NA,"Zhang F., Ma T., Cui P., Tamadon A., He S., Huo C., Yierfulati G., Xu X., Hu W., Li X., Shao L.R., Guo H., Feng Y. , Xu C.","Diversity of the Gut Microbiota in Dihydrotestosterone-Induced PCOS Rats and the Pharmacologic Effects of Diane-35, Probiotics, and Berberine",Frontiers in microbiology,2019,"DHT, Diane-35, PCOS, berberine, gut microbiota, probiotics",Experiment 5,China,Rattus norvegicus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control,DHT (Dihydrotestosterone),"Female Wistar rats of 21 days fed with standard chow, energy%: 10.3% from fat, 65.5% from carbohydrate and 24.2% from protein, 3.52kcal/g (Shanghai SLAC Laboratory Animal) and implanted subcutaneously with slow-release Dihydrotestosterone (15 mg, 75-day release) silicone tubes at 21 days old to induce Polycystic ovary syndrome",6,6,NA,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 6B, Supplementary figure 2B",6 June 2025,Anne-mariesharp,Anne-mariesharp,Different fecal microbiota in rats at the genus level,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,KateRasheed
bsdb:30800111/5/2,30800111,laboratory experiment,30800111,https://doi.org/10.3389/fmicb.2019.00175,NA,"Zhang F., Ma T., Cui P., Tamadon A., He S., Huo C., Yierfulati G., Xu X., Hu W., Li X., Shao L.R., Guo H., Feng Y. , Xu C.","Diversity of the Gut Microbiota in Dihydrotestosterone-Induced PCOS Rats and the Pharmacologic Effects of Diane-35, Probiotics, and Berberine",Frontiers in microbiology,2019,"DHT, Diane-35, PCOS, berberine, gut microbiota, probiotics",Experiment 5,China,Rattus norvegicus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control,DHT (Dihydrotestosterone),"Female Wistar rats of 21 days fed with standard chow, energy%: 10.3% from fat, 65.5% from carbohydrate and 24.2% from protein, 3.52kcal/g (Shanghai SLAC Laboratory Animal) and implanted subcutaneously with slow-release Dihydrotestosterone (15 mg, 75-day release) silicone tubes at 21 days old to induce Polycystic ovary syndrome",6,6,NA,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Supplementary figure 2B,8 July 2025,Anne-mariesharp,Anne-mariesharp,Different fecal microbiota in rats at the genus level,decreased,NA,NA,Complete,KateRasheed
bsdb:30800111/6/1,30800111,laboratory experiment,30800111,https://doi.org/10.3389/fmicb.2019.00175,NA,"Zhang F., Ma T., Cui P., Tamadon A., He S., Huo C., Yierfulati G., Xu X., Hu W., Li X., Shao L.R., Guo H., Feng Y. , Xu C.","Diversity of the Gut Microbiota in Dihydrotestosterone-Induced PCOS Rats and the Pharmacologic Effects of Diane-35, Probiotics, and Berberine",Frontiers in microbiology,2019,"DHT, Diane-35, PCOS, berberine, gut microbiota, probiotics",Experiment 6,China,Rattus norvegicus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control,DHT (Dihydrotestosterone) + Diane-35,"DHT-induced PCOS rats treated with Diane-35 daily, starting 7 weeks after DHT implantation",6,6,NA,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Supplementary Figure 2C,13 June 2025,Amaanarif,"Amaanarif,Anne-mariesharp",Different fecal microbiota in rats at the genus level,increased,NA,NA,Complete,KateRasheed
bsdb:30800111/7/1,30800111,laboratory experiment,30800111,https://doi.org/10.3389/fmicb.2019.00175,NA,"Zhang F., Ma T., Cui P., Tamadon A., He S., Huo C., Yierfulati G., Xu X., Hu W., Li X., Shao L.R., Guo H., Feng Y. , Xu C.","Diversity of the Gut Microbiota in Dihydrotestosterone-Induced PCOS Rats and the Pharmacologic Effects of Diane-35, Probiotics, and Berberine",Frontiers in microbiology,2019,"DHT, Diane-35, PCOS, berberine, gut microbiota, probiotics",Experiment 7,China,Rattus norvegicus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control,DHT (Dihydrotestosterone) + Probiotics,"DHT-induced PCOS rats treated with Probiotics daily, starting 7 weeks after DHT implantation",6,6,NA,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Supplementary Figure 2D,13 June 2025,Amaanarif,"Amaanarif,Anne-mariesharp",Different fecal microbiota in rats at the genus level,decreased,NA,NA,Complete,KateRasheed
bsdb:30800111/8/1,30800111,laboratory experiment,30800111,https://doi.org/10.3389/fmicb.2019.00175,NA,"Zhang F., Ma T., Cui P., Tamadon A., He S., Huo C., Yierfulati G., Xu X., Hu W., Li X., Shao L.R., Guo H., Feng Y. , Xu C.","Diversity of the Gut Microbiota in Dihydrotestosterone-Induced PCOS Rats and the Pharmacologic Effects of Diane-35, Probiotics, and Berberine",Frontiers in microbiology,2019,"DHT, Diane-35, PCOS, berberine, gut microbiota, probiotics",Experiment 8,China,Rattus norvegicus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control,DHT (Dihydrotestosterone) + Berberine,"DHT-induced PCOS rats treated with Berberine daily, starting 7 weeks after DHT implantation",6,6,NA,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,increased,NA,decreased,Signature 1,"Figure 6E, Supplementary Figure 2E",8 July 2025,Anne-mariesharp,Anne-mariesharp,Different fecal microbiota in rats at the genus level,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",1783272|1239|186801|3085636|186803|572511;1783272|1239|909932|1843488|909930|33024;1783272|1239|526524|526525|2810280|3025755,Complete,KateRasheed
bsdb:30800111/8/2,30800111,laboratory experiment,30800111,https://doi.org/10.3389/fmicb.2019.00175,NA,"Zhang F., Ma T., Cui P., Tamadon A., He S., Huo C., Yierfulati G., Xu X., Hu W., Li X., Shao L.R., Guo H., Feng Y. , Xu C.","Diversity of the Gut Microbiota in Dihydrotestosterone-Induced PCOS Rats and the Pharmacologic Effects of Diane-35, Probiotics, and Berberine",Frontiers in microbiology,2019,"DHT, Diane-35, PCOS, berberine, gut microbiota, probiotics",Experiment 8,China,Rattus norvegicus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control,DHT (Dihydrotestosterone) + Berberine,"DHT-induced PCOS rats treated with Berberine daily, starting 7 weeks after DHT implantation",6,6,NA,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,increased,NA,decreased,Signature 2,"Figure 6E, Supplementary Figure 2E",8 July 2025,Anne-mariesharp,Anne-mariesharp,Different fecal microbiota in rats at the genus level,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|186802|216572|3068309;1783272|1239|186801|186802|216572,Complete,KateRasheed
bsdb:30804895/1/1,30804895,time series / longitudinal observational,30804895,10.3389/fmicb.2019.00054,NA,"Qin T., Zhang F., Zhou H., Ren H., Du Y., Liang S., Wang F., Cheng L., Xie X., Jin A., Wu Y., Zhao J. , Xu J.",High-Level PM2.5/PM10 Exposure Is Associated With Alterations in the Human Pharyngeal Microbiota Composition,Frontiers in microbiology,2019,"PM2.5/PM10, microbiome composition, pharynx, respiratory pathogen, smoking",Experiment 1,China,Homo sapiens,Cavity of pharynx,UBERON:0001731,Air pollution,ENVO:02500037,pre-smog swabs,post-smog swabs,Vendors in an open-air farer's market who worked in the same place and were exposed to smog over the same business hours,83,83,NA,16S,34,Illumina,relative abundances,LEfSe,0.001,TRUE,4,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 1,Figure S3,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Histogram of unique biomarker bacteria in each group as analyzed by linear discriminant analysis effect size (LefSe),increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Bacilli,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",1783272|1239|909932|1843489|31977;1783272|1239|91061;3384189|32066|203490|203491|1129771|32067,Complete,Claregrieve1
bsdb:30804895/1/2,30804895,time series / longitudinal observational,30804895,10.3389/fmicb.2019.00054,NA,"Qin T., Zhang F., Zhou H., Ren H., Du Y., Liang S., Wang F., Cheng L., Xie X., Jin A., Wu Y., Zhao J. , Xu J.",High-Level PM2.5/PM10 Exposure Is Associated With Alterations in the Human Pharyngeal Microbiota Composition,Frontiers in microbiology,2019,"PM2.5/PM10, microbiome composition, pharynx, respiratory pathogen, smoking",Experiment 1,China,Homo sapiens,Cavity of pharynx,UBERON:0001731,Air pollution,ENVO:02500037,pre-smog swabs,post-smog swabs,Vendors in an open-air farer's market who worked in the same place and were exposed to smog over the same business hours,83,83,NA,16S,34,Illumina,relative abundances,LEfSe,0.001,TRUE,4,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 2,Figure S3,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Histogram of unique biomarker bacteria in each group as analyzed by linear discriminant analysis effect size (LefSe),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|1224|28216;3379134|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:30813950/1/1,30813950,prospective cohort,30813950,10.1186/s40168-019-0645-2,NA,"Iszatt N., Janssen S., Lenters V., Dahl C., Stigum H., Knight R., Mandal S., Peddada S., González A., Midtvedt T. , Eggesbø M.",Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month,Microbiome,2019,"Birth cohort, Breast milk, Infant gut microbiome, Short-chain fatty acids, Toxicants",Experiment 1,Norway,Homo sapiens,Feces,UBERON:0001988,Environmental exposure measurement,EFO:0008360,one-month age infants exposed to low chemical breast milk (<20th percentile),one-month age infants exposed to high chemical breast milk,infants with high chemical exposure (≥ 80th percentile breast milk toxicant exposure),45,45,2 weeks,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,gestational age,NA,increased,NA,NA,NA,NA,Signature 1,Figure 2,10 January 2021,Shaimaa Elsafoury,"Fatima,LGeistlinger,WikiWorks",Differentially abundant sequences in the high vs. low chemical exposure groups.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",1783272|1239|186801|186802|31979|1485;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|1300,Complete,Claregrieve1
bsdb:30813950/1/2,30813950,prospective cohort,30813950,10.1186/s40168-019-0645-2,NA,"Iszatt N., Janssen S., Lenters V., Dahl C., Stigum H., Knight R., Mandal S., Peddada S., González A., Midtvedt T. , Eggesbø M.",Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month,Microbiome,2019,"Birth cohort, Breast milk, Infant gut microbiome, Short-chain fatty acids, Toxicants",Experiment 1,Norway,Homo sapiens,Feces,UBERON:0001988,Environmental exposure measurement,EFO:0008360,one-month age infants exposed to low chemical breast milk (<20th percentile),one-month age infants exposed to high chemical breast milk,infants with high chemical exposure (≥ 80th percentile breast milk toxicant exposure),45,45,2 weeks,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,gestational age,NA,increased,NA,NA,NA,NA,Signature 2,Figure 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differentially abundant sequences in the high vs. low chemical exposure groups.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:30838178/1/1,30838178,prospective cohort,30838178,10.3389/fcimb.2019.00028,NA,"Nearing J.T., Connors J., Whitehouse S., Van Limbergen J., Macdonald T., Kulkarni K. , Langille M.G.I.",Infectious Complications Are Associated With Alterations in the Gut Microbiome in Pediatric Patients With Acute Lymphoblastic Leukemia,Frontiers in cellular and infection microbiology,2019,"cancer, clinical, genomics, infection, leukemia, metagenomics, microbiome",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,non-infectious complications (NIC),Infectious complications (IC),Infectious complications (IC) in the past 6 months of Acute Lymphoblastic Leukemia treatment,7,9,2 weeks,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 1,"Figure 3, Supp. Figure 10-12",10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential microbial abundance between patients who experienced infectious complications and those who did not,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Methanobacteriati|p__Methanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",3379134|976|200643|171549|815;1783272|201174|1760|85004|31953;1783272|1239|186801|186802|186806;3366610|28890;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|541000;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550;3379134|976;1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549|815|816;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|216851,Complete,Claregrieve1
bsdb:30838178/1/2,30838178,prospective cohort,30838178,10.3389/fcimb.2019.00028,NA,"Nearing J.T., Connors J., Whitehouse S., Van Limbergen J., Macdonald T., Kulkarni K. , Langille M.G.I.",Infectious Complications Are Associated With Alterations in the Gut Microbiome in Pediatric Patients With Acute Lymphoblastic Leukemia,Frontiers in cellular and infection microbiology,2019,"cancer, clinical, genomics, infection, leukemia, metagenomics, microbiome",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,non-infectious complications (NIC),Infectious complications (IC),Infectious complications (IC) in the past 6 months of Acute Lymphoblastic Leukemia treatment,7,9,2 weeks,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 2,Figure 3a,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential microbial abundance between patients who experienced infectious complications and those who did not,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter|s__Achromobacter sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium|s__Agrobacterium tumefaciens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas|s__Brevundimonas diminuta,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Bordetella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|28216|80840|506|222|134375;3379134|1224|28211|356|82115|357;3379134|1224|28211|356|82115|357|358;3379134|1224|28216|80840|506|507;3379134|1224|28211|204458|76892|41275|293;3379134|1224|28211|204458|76892|41275;3379134|1224|28216|80840|506|517;3379134|1224|28211|204458|76892;3379134|1224|28211|356|82115;3379134|1224|28216|80840|506;3379134|1224|28216|80840|119060;3379134|1224,Complete,Claregrieve1
bsdb:30841606/1/1,30841606,case-control,30841606,10.3390/cancers11030309,NA,"Kwon M., Seo S.S., Kim M.K., Lee D.O. , Lim M.C.",Compositional and Functional Differences between Microbiota and Cervical Carcinogenesis as Identified by Shotgun Metagenomic Sequencing,Cancers,2019,"cervical cancer, cervical intraepithelial neoplasia, microbiome, shotgun metagenomic sequencing",Experiment 1,South Korea,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical glandular intraepithelial neoplasia,EFO:1000165,normal controls,cervical intraepithelial neoplasia cases,women with histology proven CIN2/3,18,17,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 1,10 January 2021,Cynthia Anderson,"Cynthia Anderson,LGeistlinger,WikiWorks","Microbial compositions among normal group, cervical intraepithelial neoplasia 2 or 3, and cervical cancer",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Thermotogati|p__Thermotogota|c__Thermotogae|o__Thermotogales|f__Thermotogaceae|g__Pseudothermotoga,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Anaplasmataceae|g__Wolbachia",1783272|1239|186801|3082720|3118656|114627;3384194|200918|188708|2419|188709|1643951;3379134|1224|28211|766|942|953,Complete,Claregrieve1
bsdb:30841606/1/2,30841606,case-control,30841606,10.3390/cancers11030309,NA,"Kwon M., Seo S.S., Kim M.K., Lee D.O. , Lim M.C.",Compositional and Functional Differences between Microbiota and Cervical Carcinogenesis as Identified by Shotgun Metagenomic Sequencing,Cancers,2019,"cervical cancer, cervical intraepithelial neoplasia, microbiome, shotgun metagenomic sequencing",Experiment 1,South Korea,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical glandular intraepithelial neoplasia,EFO:1000165,normal controls,cervical intraepithelial neoplasia cases,women with histology proven CIN2/3,18,17,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 1,10 January 2021,Cynthia Anderson,WikiWorks,"Microbial compositions among normal group, cervical intraepithelial neoplasia 2 or 3, and cervical cancer",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae|g__Pseudoalteromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter",3379134|1224|1236|135622|267888|53246;3379134|1224|1236|2887326|468|497,Complete,Claregrieve1
bsdb:30841606/2/1,30841606,case-control,30841606,10.3390/cancers11030309,NA,"Kwon M., Seo S.S., Kim M.K., Lee D.O. , Lim M.C.",Compositional and Functional Differences between Microbiota and Cervical Carcinogenesis as Identified by Shotgun Metagenomic Sequencing,Cancers,2019,"cervical cancer, cervical intraepithelial neoplasia, microbiome, shotgun metagenomic sequencing",Experiment 2,South Korea,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical cancer,MONDO:0002974,normal control,cervical cancer,histology proven cervical cancer,18,12,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 1,10 January 2021,Cynthia Anderson,WikiWorks,"Microbial compositions among normal group, cervical intraepithelial neoplasia 2 or 3, and cervical cancer",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Thermotogati|p__Thermotogota|c__Thermotogae|o__Thermotogales|f__Thermotogaceae|g__Pseudothermotoga,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Anaplasmataceae|g__Wolbachia",1783272|1239|186801|3082720|3118656|114627;3384194|200918|188708|2419|188709|1643951;3379134|1224|28211|766|942|953,Complete,Claregrieve1
bsdb:30841606/2/2,30841606,case-control,30841606,10.3390/cancers11030309,NA,"Kwon M., Seo S.S., Kim M.K., Lee D.O. , Lim M.C.",Compositional and Functional Differences between Microbiota and Cervical Carcinogenesis as Identified by Shotgun Metagenomic Sequencing,Cancers,2019,"cervical cancer, cervical intraepithelial neoplasia, microbiome, shotgun metagenomic sequencing",Experiment 2,South Korea,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical cancer,MONDO:0002974,normal control,cervical cancer,histology proven cervical cancer,18,12,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 1,10 January 2021,Cynthia Anderson,"Cynthia Anderson,LGeistlinger,WikiWorks","Microbial compositions among normal group, cervical intraepithelial neoplasia 2 or 3, and cervical cancer",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae|g__Candidatus Endolissoclinum",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|1385|90964|1279;3379134|1224|28211|204441|41295|1263978,Complete,Claregrieve1
bsdb:30845942/7/1,30845942,time series / longitudinal observational,30845942,10.1186/s12920-019-0494-7,NA,"Biagi E., Zama D., Rampelli S., Turroni S., Brigidi P., Consolandi C., Severgnini M., Picotti E., Gasperini P., Merli P., Decembrino N., Zecca M., Cesaro S., Faraci M., Prete A., Locatelli F., Pession A., Candela M. , Masetti R.",Early gut microbiota signature of aGvHD in children given allogeneic hematopoietic cell transplantation for hematological disorders,BMC medical genomics,2019,"16S rRNA gene sequencing, Acute graft-versus-host disease, Alloreactivity, Gut microbiota, Hematopoietic stem cell transplantation, Pediatric patients",Experiment 7,Italy,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,Non-Acute graft vs. host disease (non-aGvHD) : pre-Hematopoietic Stem Cell Transplantation (pre-HSCT) sample,Non-Acute graft vs. host disease (non-aGvHD) : Engraftment sample,"Fecal samples were obtained from patients during Hematopoietic Stem Cell Transplantation (HSCT). Following transplantation, the patients didn't develop gastrointestinal Acute graft vs. host disease (non-aGvHD).",16,16,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3c and Supplementary Table 1,9 December 2025,Firdaws,Firdaws,Log2 fold changes of the main discriminant genera between pre-Hematopoietic Stem Cell Transplantation (pre-HSCT) and engraftment samples in subjects who did not develop acute Graft-versus-Host Disease (non-aGvHD).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|3085636|186803|841,Complete,KateRasheed
bsdb:30845942/8/1,30845942,time series / longitudinal observational,30845942,10.1186/s12920-019-0494-7,NA,"Biagi E., Zama D., Rampelli S., Turroni S., Brigidi P., Consolandi C., Severgnini M., Picotti E., Gasperini P., Merli P., Decembrino N., Zecca M., Cesaro S., Faraci M., Prete A., Locatelli F., Pession A., Candela M. , Masetti R.",Early gut microbiota signature of aGvHD in children given allogeneic hematopoietic cell transplantation for hematological disorders,BMC medical genomics,2019,"16S rRNA gene sequencing, Acute graft-versus-host disease, Alloreactivity, Gut microbiota, Hematopoietic stem cell transplantation, Pediatric patients",Experiment 8,Italy,Homo sapiens,Feces,UBERON:0001988,Acute graft vs. host disease,EFO:0004599,Acute graft vs. host disease I-II grade at a skin level (Skin aGvHD) : pre-Hematopoietic Stem Cell Transplantation (pre-HSCT) sample,Acute graft vs. host disease I-II grade at a skin level (Skin aGvHD) : Engraftment sample.,"Fecal samples were obtained from patients during Hematopoietic Stem Cell Transplantation (HSCT). Following transplantation, the patients developed Acute graft vs. host disease I-II grade involving the skin (Skin aGvHD)",13,13,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3d and Supplementary Table 1,9 December 2025,Firdaws,Firdaws,Log2 fold changes of the main discriminant genera between pre-Hematopoietic Stem Cell Transplantation (pre-HSCT) and engraftment samples in subjects who developed acute Graft-versus-Host Disease I-II grade only involving the skin (skin-aGvHD).,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263,Complete,KateRasheed
bsdb:30854760/1/1,30854760,case-control,30854760,10.1111/1471-0528.15600,NA,"Brown R.G., Chan D., Terzidou V., Lee Y.S., Smith A., Marchesi J.R., MacIntyre D.A. , Bennett P.R.",Prospective observational study of vaginal microbiota pre- and post-rescue cervical cerclage,BJOG : an international journal of obstetrics and gynaecology,2019,"Infection, preterm birth, rescue cerclage, vaginal microbiome",Experiment 1,United Kingdom,Homo sapiens,Vagina,UBERON:0000996,Cervical cerclage,NCIT:C102763,Vaginal microbiome of asymptomatic women prior to cerclage,Vaginal microbiome of symptomatic women prior ro cerclage,NA,13,7,NA,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Cladogram describing differentially abundant vaginal microbial clades and nodes observed between asymptomatic women and those with symptoms as identified using LEfSe analysis,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudopneumoniae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella",1783272|1239|91061|186826|1300|1301|257758;3379134|976|200643|171549|171552|838|28130;1783272|201174|1760|85004|31953|2701|2702;1783272|201174|1760|85004|31953|2701,Complete,NA
bsdb:30854760/1/2,30854760,case-control,30854760,10.1111/1471-0528.15600,NA,"Brown R.G., Chan D., Terzidou V., Lee Y.S., Smith A., Marchesi J.R., MacIntyre D.A. , Bennett P.R.",Prospective observational study of vaginal microbiota pre- and post-rescue cervical cerclage,BJOG : an international journal of obstetrics and gynaecology,2019,"Infection, preterm birth, rescue cerclage, vaginal microbiome",Experiment 1,United Kingdom,Homo sapiens,Vagina,UBERON:0000996,Cervical cerclage,NCIT:C102763,Vaginal microbiome of asymptomatic women prior to cerclage,Vaginal microbiome of symptomatic women prior ro cerclage,NA,13,7,NA,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2,10 January 2021,Shaimaa Elsafoury,WikiWorks,Cladogram describing differentially abundant vaginal microbial clades and nodes observed between asymptomatic women and those with symptoms as identified using LEfSe analysis,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,1783272|1239|91061|186826|33958|1578|47770,Complete,NA
bsdb:30860574/1/1,30860574,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y., Jin S., Wang J., Zhang L., Mu Y., Huang K., Zhao B., Zhang K., Cui Y. , Li S.",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,"Bifidobacterium, 16S rRNA gene sequencing, childhood eczema, diversity, gut microbiome, qPCR",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0-3 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,raw counts,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3a,10 January 2021,Lucy Mellor,WikiWorks,Significantly diverse bacterial communities between healthy and eczema groups in age groups 0-3 years,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia",1783272|1239|186801|3085636|186803|841;3379134|1224|1236|91347|1903409|551,Complete,Lwaldron
bsdb:30860574/1/2,30860574,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y., Jin S., Wang J., Zhang L., Mu Y., Huang K., Zhao B., Zhang K., Cui Y. , Li S.",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,"Bifidobacterium, 16S rRNA gene sequencing, childhood eczema, diversity, gut microbiome, qPCR",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0-3 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,raw counts,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3a,10 January 2021,Lucy Mellor,WikiWorks,Significantly diverse bacterial communities between healthy and eczema groups in age groups 0-3 years,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter",1783272|201174|1760|85004|31953|1678;3379134|1224|1236|91347|543|547,Complete,Lwaldron
bsdb:30860574/2/1,30860574,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y., Jin S., Wang J., Zhang L., Mu Y., Huang K., Zhao B., Zhang K., Cui Y. , Li S.",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,"Bifidobacterium, 16S rRNA gene sequencing, childhood eczema, diversity, gut microbiome, qPCR",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0-3 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3b,10 January 2021,Lucy Mellor,"Lwaldron,WikiWorks",Significantly diverse bacterial communities between healthy and eczema groups in age groups 0-3 years,increased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium neonatale",1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|186801|186802|31979|1485|137838,Complete,Lwaldron
bsdb:30860574/2/2,30860574,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y., Jin S., Wang J., Zhang L., Mu Y., Huang K., Zhao B., Zhang K., Cui Y. , Li S.",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,"Bifidobacterium, 16S rRNA gene sequencing, childhood eczema, diversity, gut microbiome, qPCR",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0-3 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3b,10 January 2021,Lucy Mellor,WikiWorks,Significantly diverse bacterial communities between healthy and eczema groups in age groups 0-3 years,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Pseudomonadati|p__Pseudomonadota",1783272|201174;1783272|201174|1760;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678|216816|1679;3379134|1224,Complete,Lwaldron
bsdb:30860574/3/1,30860574,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y., Jin S., Wang J., Zhang L., Mu Y., Huang K., Zhao B., Zhang K., Cui Y. , Li S.",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,"Bifidobacterium, 16S rRNA gene sequencing, childhood eczema, diversity, gut microbiome, qPCR",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0-0.5 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,raw counts,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3c,10 January 2021,Lucy Mellor,WikiWorks,Significantly diverse bacterial communities between healthy and eczema groups in age group 0-0.5 years,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,3379134|1224|1236|91347|1903409|551,Complete,Lwaldron
bsdb:30860574/3/2,30860574,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y., Jin S., Wang J., Zhang L., Mu Y., Huang K., Zhao B., Zhang K., Cui Y. , Li S.",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,"Bifidobacterium, 16S rRNA gene sequencing, childhood eczema, diversity, gut microbiome, qPCR",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0-0.5 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,raw counts,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3c,10 January 2021,Lucy Mellor,WikiWorks,Significantly diverse bacterial communities between healthy and eczema groups in age group 0-0.5 years,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|28050,Complete,Lwaldron
bsdb:30860574/4/1,30860574,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y., Jin S., Wang J., Zhang L., Mu Y., Huang K., Zhao B., Zhang K., Cui Y. , Li S.",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,"Bifidobacterium, 16S rRNA gene sequencing, childhood eczema, diversity, gut microbiome, qPCR",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0-0.5 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3d,10 January 2021,Lucy Mellor,WikiWorks,Significantly diverse bacterial communities between healthy and eczema groups in age group 0-0.5 years,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis",1783272|1239|909932|1843489|31977|29465|29466;3379134|976|200643|171549|815|816|817,Complete,Lwaldron
bsdb:30860574/4/2,30860574,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y., Jin S., Wang J., Zhang L., Mu Y., Huang K., Zhao B., Zhang K., Cui Y. , Li S.",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,"Bifidobacterium, 16S rRNA gene sequencing, childhood eczema, diversity, gut microbiome, qPCR",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0-0.5 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3d,10 January 2021,Lucy Mellor,WikiWorks,Significantly diverse bacterial communities between healthy and eczema groups in age group 0-0.5 years,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,1783272|201174|1760|85004|31953|1678|1681,Complete,Lwaldron
bsdb:30860574/5/1,30860574,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y., Jin S., Wang J., Zhang L., Mu Y., Huang K., Zhao B., Zhang K., Cui Y. , Li S.",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,"Bifidobacterium, 16S rRNA gene sequencing, childhood eczema, diversity, gut microbiome, qPCR",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0.5-1 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,raw counts,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3e,10 January 2021,Lucy Mellor,WikiWorks,Significantly diverse bacterial communities between healthy and eczema groups in age group 0.5-1 years,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,3379134|1224|1236|91347|1903409|551,Complete,Lwaldron
bsdb:30860574/5/2,30860574,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y., Jin S., Wang J., Zhang L., Mu Y., Huang K., Zhao B., Zhang K., Cui Y. , Li S.",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,"Bifidobacterium, 16S rRNA gene sequencing, childhood eczema, diversity, gut microbiome, qPCR",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0.5-1 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,raw counts,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3e,10 January 2021,Lucy Mellor,WikiWorks,Significantly diverse bacterial communities between healthy and eczema groups in age group 0.5-1 years,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter",1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|1300|1301;3379134|29547|3031852|213849|72294|194,Complete,Lwaldron
bsdb:30860574/6/1,30860574,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y., Jin S., Wang J., Zhang L., Mu Y., Huang K., Zhao B., Zhang K., Cui Y. , Li S.",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,"Bifidobacterium, 16S rRNA gene sequencing, childhood eczema, diversity, gut microbiome, qPCR",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0.5-1 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3f,10 January 2021,Lucy Mellor,WikiWorks,Significantly diverse bacterial communities between healthy and eczema groups in age group 0.5-1 years,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|201174;1783272|201174|1760;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678|216816|1679;3379134|1224|1236|91347|543|547,Complete,Lwaldron
bsdb:30860574/7/1,30860574,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y., Jin S., Wang J., Zhang L., Mu Y., Huang K., Zhao B., Zhang K., Cui Y. , Li S.",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,"Bifidobacterium, 16S rRNA gene sequencing, childhood eczema, diversity, gut microbiome, qPCR",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 1-2 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,raw counts,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3g,10 January 2021,Lucy Mellor,"WikiWorks,Merit",Significantly diverse bacterial communities between healthy and eczema groups in age group 1-2 years,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|85004|31953|1678;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Lwaldron
bsdb:30860574/8/1,30860574,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y., Jin S., Wang J., Zhang L., Mu Y., Huang K., Zhao B., Zhang K., Cui Y. , Li S.",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,"Bifidobacterium, 16S rRNA gene sequencing, childhood eczema, diversity, gut microbiome, qPCR",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 1-2 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3h,10 January 2021,Lucy Mellor,WikiWorks,Significantly diverse bacterial communities between healthy and eczema groups in age group 1-2 years,decreased,k__Bacillati|p__Actinomycetota,1783272|201174,Complete,Lwaldron
bsdb:30860574/9/1,30860574,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y., Jin S., Wang J., Zhang L., Mu Y., Huang K., Zhao B., Zhang K., Cui Y. , Li S.",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,"Bifidobacterium, 16S rRNA gene sequencing, childhood eczema, diversity, gut microbiome, qPCR",Experiment 9,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 2-3 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,raw counts,T-Test,0.05,FALSE,NA,age,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3i,10 January 2021,Lucy Mellor,WikiWorks,Significantly diverse bacterial communities between healthy and eczema groups in age group 2-3 years,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",1783272|201174|1760|85004|31953|1678;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;3379134|200940|3031449|213115|194924|35832,Complete,Lwaldron
bsdb:30860574/10/1,30860574,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y., Jin S., Wang J., Zhang L., Mu Y., Huang K., Zhao B., Zhang K., Cui Y. , Li S.",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,"Bifidobacterium, 16S rRNA gene sequencing, childhood eczema, diversity, gut microbiome, qPCR",Experiment 10,China,Homo sapiens,Feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 2-3 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,age,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3j,10 January 2021,Lucy Mellor,WikiWorks,Significantly diverse bacterial communities between healthy and eczema groups in age group 2-3 years,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota",1783272|1239|186801|3085636|186803;1783272|201174;1783272|201174|1760;1783272|201174|1760|85004;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;3379134|1224,Complete,Lwaldron
bsdb:30866773/1/1,30866773,time series / longitudinal observational,30866773,10.1080/22221751.2018.1563458,NA,"Yang L., Hao Y., Hu J., Kelly D., Li H., Brown S., Tasker C., Roche N.E., Chang T.L. , Pei Z.",Differential effects of depot medroxyprogesterone acetate administration on vaginal microbiome in Hispanic White and Black women,Emerging microbes & infections,2019,"HIV acquisition, Vaginal microbiome, bacterial vaginosis-associated bacteria, depot medroxyprogesterone acetate, network",Experiment 1,United States of America,Homo sapiens,Vagina,UBERON:0000996,Medroxyprogesterone acetate,CHEBI:6716,depot medroxyprogesterone acetate vaginal microbiome (visit 2) among black participants,naive black participants (baseline visit),participants who had not yet been given the medroxyprogesterone acetate treatment at baseline,16,16,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.2,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differential genera between naive and DMPA-treated vaginal microbiomes in Hispanic White and Black women,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:30866773/2/1,30866773,time series / longitudinal observational,30866773,10.1080/22221751.2018.1563458,NA,"Yang L., Hao Y., Hu J., Kelly D., Li H., Brown S., Tasker C., Roche N.E., Chang T.L. , Pei Z.",Differential effects of depot medroxyprogesterone acetate administration on vaginal microbiome in Hispanic White and Black women,Emerging microbes & infections,2019,"HIV acquisition, Vaginal microbiome, bacterial vaginosis-associated bacteria, depot medroxyprogesterone acetate, network",Experiment 2,United States of America,Homo sapiens,Vagina,UBERON:0000996,Medroxyprogesterone acetate,CHEBI:6716,black naive vaginal microbiome (baseline visit ),white naiive vaginal microbiome (baseline),white participants at baseline,16,9,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.2,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3,10 January 2021,Shaimaa Elsafoury,"Claregrieve1,WikiWorks",Differential genera between Hispanic White and Black women at baseline,increased,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,1783272|1239|1737404|1737405|1570339|150022,Complete,Claregrieve1
bsdb:30866773/2/2,30866773,time series / longitudinal observational,30866773,10.1080/22221751.2018.1563458,NA,"Yang L., Hao Y., Hu J., Kelly D., Li H., Brown S., Tasker C., Roche N.E., Chang T.L. , Pei Z.",Differential effects of depot medroxyprogesterone acetate administration on vaginal microbiome in Hispanic White and Black women,Emerging microbes & infections,2019,"HIV acquisition, Vaginal microbiome, bacterial vaginosis-associated bacteria, depot medroxyprogesterone acetate, network",Experiment 2,United States of America,Homo sapiens,Vagina,UBERON:0000996,Medroxyprogesterone acetate,CHEBI:6716,black naive vaginal microbiome (baseline visit ),white naiive vaginal microbiome (baseline),white participants at baseline,16,9,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.2,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3,10 January 2021,Shaimaa Elsafoury,"Claregrieve1,WikiWorks",Differential genera between Hispanic White and Black women at baseline,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella",1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|177971,Complete,Claregrieve1
bsdb:30866773/3/1,30866773,time series / longitudinal observational,30866773,10.1080/22221751.2018.1563458,NA,"Yang L., Hao Y., Hu J., Kelly D., Li H., Brown S., Tasker C., Roche N.E., Chang T.L. , Pei Z.",Differential effects of depot medroxyprogesterone acetate administration on vaginal microbiome in Hispanic White and Black women,Emerging microbes & infections,2019,"HIV acquisition, Vaginal microbiome, bacterial vaginosis-associated bacteria, depot medroxyprogesterone acetate, network",Experiment 3,United States of America,Homo sapiens,Vagina,UBERON:0000996,Medroxyprogesterone acetate,CHEBI:6716,black participants after using depot medroxyprogesterone (visit 2),white participants after using depot medroxyprogesterone (visit 2),white participants at visit 2,16,9,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.2,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,decreased,Signature 1,Figure 3,10 January 2021,Shaimaa Elsafoury,"Claregrieve1,WikiWorks",Differential genera between Hispanic White and Black women at visit 2,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Claregrieve1
bsdb:30866773/3/2,30866773,time series / longitudinal observational,30866773,10.1080/22221751.2018.1563458,NA,"Yang L., Hao Y., Hu J., Kelly D., Li H., Brown S., Tasker C., Roche N.E., Chang T.L. , Pei Z.",Differential effects of depot medroxyprogesterone acetate administration on vaginal microbiome in Hispanic White and Black women,Emerging microbes & infections,2019,"HIV acquisition, Vaginal microbiome, bacterial vaginosis-associated bacteria, depot medroxyprogesterone acetate, network",Experiment 3,United States of America,Homo sapiens,Vagina,UBERON:0000996,Medroxyprogesterone acetate,CHEBI:6716,black participants after using depot medroxyprogesterone (visit 2),white participants after using depot medroxyprogesterone (visit 2),white participants at visit 2,16,9,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.2,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,decreased,Signature 2,Figure 3,10 January 2021,Shaimaa Elsafoury,"Claregrieve1,WikiWorks",Differential genera between Hispanic White and Black women at visit 2,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia",1783272|1239|186801|186802|31979|1485;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378;3379134|976|200643|171549|171552|838;3384189|32066|203490|203491|1129771|168808,Complete,Claregrieve1
bsdb:30866773/4/1,30866773,time series / longitudinal observational,30866773,10.1080/22221751.2018.1563458,NA,"Yang L., Hao Y., Hu J., Kelly D., Li H., Brown S., Tasker C., Roche N.E., Chang T.L. , Pei Z.",Differential effects of depot medroxyprogesterone acetate administration on vaginal microbiome in Hispanic White and Black women,Emerging microbes & infections,2019,"HIV acquisition, Vaginal microbiome, bacterial vaginosis-associated bacteria, depot medroxyprogesterone acetate, network",Experiment 4,United States of America,Homo sapiens,Vagina,UBERON:0000996,Medroxyprogesterone acetate,CHEBI:6716,black participants after using depot medroxyprogesterone (visit 3),white participants after using depot medroxyprogesterone (visit 3),white participants at visit 3,16,9,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.2,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,unchanged,Signature 1,Figure 3,10 January 2021,Shaimaa Elsafoury,"Claregrieve1,WikiWorks",Differentially abundant genera between Hispanic White and Black women at visit 3,increased,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,1783272|1239|1737404|1737405|1570339|150022,Complete,Claregrieve1
bsdb:30866773/4/2,30866773,time series / longitudinal observational,30866773,10.1080/22221751.2018.1563458,NA,"Yang L., Hao Y., Hu J., Kelly D., Li H., Brown S., Tasker C., Roche N.E., Chang T.L. , Pei Z.",Differential effects of depot medroxyprogesterone acetate administration on vaginal microbiome in Hispanic White and Black women,Emerging microbes & infections,2019,"HIV acquisition, Vaginal microbiome, bacterial vaginosis-associated bacteria, depot medroxyprogesterone acetate, network",Experiment 4,United States of America,Homo sapiens,Vagina,UBERON:0000996,Medroxyprogesterone acetate,CHEBI:6716,black participants after using depot medroxyprogesterone (visit 3),white participants after using depot medroxyprogesterone (visit 3),white participants at visit 3,16,9,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.2,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,unchanged,Signature 2,Figure 3,10 January 2021,Shaimaa Elsafoury,"Claregrieve1,WikiWorks",Differentially abundant genera between Hispanic White and Black women at visit 3,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|91061|186826|186827|1375;1783272|1239|909932|1843489|31977|906;3379134|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:30867711/1/1,30867711,case-control,30867711,10.3892/etm.2019.7200,NA,"Wang F.G., Bai R.X., Yan W.M., Yan M., Dong L.Y. , Song M.M.","Differential composition of gut microbiota among healthy volunteers, morbidly obese patients and post-bariatric surgery patients",Experimental and therapeutic medicine,2019,"Roux-en-Y gastric bypass, bariatric surgery, gut microbiota, morbid obesity, sleeve gastrectomy, type 2 diabetes mellitus",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,healthy controls,obese patients prior to Sleeve gastrectomy SG0,obese patients had a body mass index (BMI) of >28 kg/m2.,20,19,3 months,16S,4,Ion Torrent,NA,Kruskall-Wallis,0.05,FALSE,4,"age,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table 3,10 January 2021,Marianthi Thomatos,WikiWorks,Differential composition of gut microbiota among healthy volunteers and morbidly obese patients before recieving sleeve gastrectomy,increased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|186802|541000;3384189|32066|203490|203491|203492|848|850;1783272|1239|186801|3082720|186804,Complete,Shaimaa Elsafoury
bsdb:30867711/2/1,30867711,case-control,30867711,10.3892/etm.2019.7200,NA,"Wang F.G., Bai R.X., Yan W.M., Yan M., Dong L.Y. , Song M.M.","Differential composition of gut microbiota among healthy volunteers, morbidly obese patients and post-bariatric surgery patients",Experimental and therapeutic medicine,2019,"Roux-en-Y gastric bypass, bariatric surgery, gut microbiota, morbid obesity, sleeve gastrectomy, type 2 diabetes mellitus",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,healthy controls,Roux-en-Y gastric bypass (RYGB),obese patients had a body mass index (BMI) of >28 kg/m2.,20,7,3 months,16S,4,Ion Torrent,NA,Kruskall-Wallis,0.05,FALSE,4,"age,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differential composition of gut microbiota among healthy volunteers and morbidly obese patients before recieving Roux-en-Y gastric bypass,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera",1783272|201174|1760|85004;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3082720|186804;1783272|1239|909932|1843489|31977|906,Complete,Shaimaa Elsafoury
bsdb:30867711/3/1,30867711,case-control,30867711,10.3892/etm.2019.7200,NA,"Wang F.G., Bai R.X., Yan W.M., Yan M., Dong L.Y. , Song M.M.","Differential composition of gut microbiota among healthy volunteers, morbidly obese patients and post-bariatric surgery patients",Experimental and therapeutic medicine,2019,"Roux-en-Y gastric bypass, bariatric surgery, gut microbiota, morbid obesity, sleeve gastrectomy, type 2 diabetes mellitus",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,obese patients prior to Sleeve gastrectomy SG0,obese patients three months after Sleeve gastrectomy SG3,obese patients had a body mass index (BMI) of >28 kg/m2.,19,8,3 months,16S,4,Ion Torrent,NA,Kruskall-Wallis,0.05,FALSE,4,"age,sex",NA,NA,increased,increased,NA,NA,increased,Signature 1,Table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differential composition of gut microbiota among healthy volunteers and morbidly obese patients before recieving sleeve gastrectomy,decreased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii",1783272|1239|91061;1783272|1239|91061|186826;1783272|1239|91061|186826|1300;3379134|976|200643|171549|171550;3379134|976|200643|171549|171550|239759;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1308;3379134|976|200643|171549|171551;3379134|976|200643|171549|171550|239759|214856,Complete,Shaimaa Elsafoury
bsdb:30867711/4/1,30867711,case-control,30867711,10.3892/etm.2019.7200,NA,"Wang F.G., Bai R.X., Yan W.M., Yan M., Dong L.Y. , Song M.M.","Differential composition of gut microbiota among healthy volunteers, morbidly obese patients and post-bariatric surgery patients",Experimental and therapeutic medicine,2019,"Roux-en-Y gastric bypass, bariatric surgery, gut microbiota, morbid obesity, sleeve gastrectomy, type 2 diabetes mellitus",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,patients prior to Roux-en-Y gastric bypass RYGB0,obese patients 3 moths after Roux-en-Y gastric bypass RYGB3,obese patients had a body mass index (BMI) of >28 kg/m2.,7,3,3 months,16S,4,Ion Torrent,NA,Kruskall-Wallis,0.05,FALSE,4,"age,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differential composition of gut microbiota among healthy volunteers and morbidly obese patients before recieving Roux-en-Y gastric bypass,increased,"k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|1239|909932;1783272|1239|909932|909929;1783272|1239|186801|186802|216572|216851,Complete,Shaimaa Elsafoury
bsdb:30867711/4/2,30867711,case-control,30867711,10.3892/etm.2019.7200,NA,"Wang F.G., Bai R.X., Yan W.M., Yan M., Dong L.Y. , Song M.M.","Differential composition of gut microbiota among healthy volunteers, morbidly obese patients and post-bariatric surgery patients",Experimental and therapeutic medicine,2019,"Roux-en-Y gastric bypass, bariatric surgery, gut microbiota, morbid obesity, sleeve gastrectomy, type 2 diabetes mellitus",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,patients prior to Roux-en-Y gastric bypass RYGB0,obese patients 3 moths after Roux-en-Y gastric bypass RYGB3,obese patients had a body mass index (BMI) of >28 kg/m2.,7,3,3 months,16S,4,Ion Torrent,NA,Kruskall-Wallis,0.05,FALSE,4,"age,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differential composition of gut microbiota among healthy volunteers and morbidly obese patients before recieving Roux-en-Y gastric bypass,decreased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus",1783272|1239|91061;1783272|1239|91061|186826;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1308,Complete,Shaimaa Elsafoury
bsdb:30894059/1/1,30894059,"cross-sectional observational, not case-control",30894059,10.1080/19490976.2019.1580097,NA,"Bjørkhaug S.T., Aanes H., Neupane S.P., Bramness J.G., Malvik S., Henriksen C., Skar V., Medhus A.W. , Valeur J.",Characterization of gut microbiota composition and functions in patients with chronic alcohol overconsumption,Gut microbes,2019,"Clostridium, Faecalibacterium, Holdemania, Nutritional screening, PICRUSt, Proteobacteria, Sutterella, short-chain fatty acids",Experiment 1,Norway,Homo sapiens,Feces,UBERON:0001988,Alcohol drinking,EFO:0004329,controls,alcohol overconsumers,subjects with ongoing or recent history of alcohol overconsumption of more than 20 or 40 g of alcohol per day,18,24,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 2, 3",10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential abundance of microbiota between patients with alcohol overconsumption and controls,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",1783272|1239|186801|186802|31979|1485;1783272|1239|526524|526525|128827|61170;3379134|1224;3379134|1224|28216|80840|995019|40544,Complete,Claregrieve1
bsdb:30894059/1/2,30894059,"cross-sectional observational, not case-control",30894059,10.1080/19490976.2019.1580097,NA,"Bjørkhaug S.T., Aanes H., Neupane S.P., Bramness J.G., Malvik S., Henriksen C., Skar V., Medhus A.W. , Valeur J.",Characterization of gut microbiota composition and functions in patients with chronic alcohol overconsumption,Gut microbes,2019,"Clostridium, Faecalibacterium, Holdemania, Nutritional screening, PICRUSt, Proteobacteria, Sutterella, short-chain fatty acids",Experiment 1,Norway,Homo sapiens,Feces,UBERON:0001988,Alcohol drinking,EFO:0004329,controls,alcohol overconsumers,subjects with ongoing or recent history of alcohol overconsumption of more than 20 or 40 g of alcohol per day,18,24,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 2, 3",10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential abundance of microbiota between patients with alcohol overconsumption and controls,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,1783272|1239|186801|186802|216572|216851,Complete,Claregrieve1
bsdb:30894059/2/1,30894059,"cross-sectional observational, not case-control",30894059,10.1080/19490976.2019.1580097,NA,"Bjørkhaug S.T., Aanes H., Neupane S.P., Bramness J.G., Malvik S., Henriksen C., Skar V., Medhus A.W. , Valeur J.",Characterization of gut microbiota composition and functions in patients with chronic alcohol overconsumption,Gut microbes,2019,"Clostridium, Faecalibacterium, Holdemania, Nutritional screening, PICRUSt, Proteobacteria, Sutterella, short-chain fatty acids",Experiment 2,Norway,Homo sapiens,Feces,UBERON:0001988,Alcohol drinking,EFO:0004329,controls,alcohol overconsumers,NA,18,24,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4a,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differentially abundant taxa between alcohol overconsumers and controls,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae",1783272|1239|909932|1843488|909930|904;1783272|201174|1760|2037;3379134|1224|28216|80840|506;1783272|1239|526524|526525|128827|118747;1783272|1239|186801|186802|31979|1485;3379134|200940|3031449|213115;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|186801|3085636|186803|2383;3379134|1224|1236|91347|543|561;1783272|1239|526524|526525|128827|61170;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803;1783272|1239|909932|909929|1843491|158846;1783272|201174|1760|85006|1268;3379134|1224|1236|91347|1903414|581;3379134|1224;1783272|201174|1760|85006|1268|32207;3379134|1224|28216|80840|995019|40544;1783272|1239|1737404|1737405|1737406,Complete,Claregrieve1
bsdb:30894059/2/2,30894059,"cross-sectional observational, not case-control",30894059,10.1080/19490976.2019.1580097,NA,"Bjørkhaug S.T., Aanes H., Neupane S.P., Bramness J.G., Malvik S., Henriksen C., Skar V., Medhus A.W. , Valeur J.",Characterization of gut microbiota composition and functions in patients with chronic alcohol overconsumption,Gut microbes,2019,"Clostridium, Faecalibacterium, Holdemania, Nutritional screening, PICRUSt, Proteobacteria, Sutterella, short-chain fatty acids",Experiment 2,Norway,Homo sapiens,Feces,UBERON:0001988,Alcohol drinking,EFO:0004329,controls,alcohol overconsumers,NA,18,24,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4a,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differentially abundant taxa between alcohol overconsumers and controls,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinatimonas",1783272|201174;1783272|201174|84998|1643822|1643826|447020;1783272|1239|186801;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|186801|186802|216572|216851;1783272|1239|909932|909929|1843491|52225;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|3085636|186803|265975;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|135624|83763|674963,Complete,Claregrieve1
bsdb:30894560/1/1,30894560,randomized controlled trial,30894560,https://doi.org/10.1038/s41598-018-38216-9,https://www.nature.com/articles/s41598-018-38216-9,"Zhang L., Ouyang Y., Li H., Shen L., Ni Y., Fang Q., Wu G., Qian L., Xiao Y., Zhang J., Yin P., Panagiotou G., Xu G., Ye J. , Jia W.",Metabolic phenotypes and the gut microbiota in response to dietary resistant starch type 2 in normal-weight subjects: a randomized crossover trial,Scientific reports,2019,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Control starch intake (CS),Resistant starch intake (RS),These are the participants that consumed 40 g/day of high-amylose maize resistant starch type 2 for 4 weeks during the intervention phase.,NA,NA,3 weeks,16S,3,Roche454,log transformation,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3A,10 October 2025,Lindy,Lindy,Differentially abundant bacterial taxa identified after resistant starch type 2 (RS2) supplementation compared with control starch (CS) in healthy humans (adults).,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,1783272|1239|186801|186802|216572|3068309,Complete,KateRasheed
bsdb:30894560/1/2,30894560,randomized controlled trial,30894560,https://doi.org/10.1038/s41598-018-38216-9,https://www.nature.com/articles/s41598-018-38216-9,"Zhang L., Ouyang Y., Li H., Shen L., Ni Y., Fang Q., Wu G., Qian L., Xiao Y., Zhang J., Yin P., Panagiotou G., Xu G., Ye J. , Jia W.",Metabolic phenotypes and the gut microbiota in response to dietary resistant starch type 2 in normal-weight subjects: a randomized crossover trial,Scientific reports,2019,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Control starch intake (CS),Resistant starch intake (RS),These are the participants that consumed 40 g/day of high-amylose maize resistant starch type 2 for 4 weeks during the intervention phase.,NA,NA,3 weeks,16S,3,Roche454,log transformation,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 3A,11 October 2025,Lindy,Lindy,Differentially abundant bacterial taxa identified were significantly decreased after resistant starch type 2 (RS2) supplementation compared with control starch (CS) in healthy humans (adults).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|189330;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050|39485;3379134|976|200643|171549|171552|577309;1783272|1239|909932|1843488|909930|33024,Complete,KateRasheed
bsdb:30895172/1/1,30895172,case-control,30895172,10.3389/fcimb.2019.00040,NA,"Ma B., Liang J., Dai M., Wang J., Luo J., Zhang Z. , Jing J.",Altered Gut Microbiota in Chinese Children With Autism Spectrum Disorders,Frontiers in cellular and infection microbiology,2019,"16S rRNA, Chinese children, autism spectrum disorder, case control, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Neurotypical children,Children with Autism Spectrum Disorder (ASD),Diagnosed with ASD according to DSM-5 (Diagnostic and Statistical Manual of Mental Disorders - 5th Edition),45,45,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,NA,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Tables 2-3, S5-7",14 November 2024,AlishaM,"AlishaM,WikiWorks","Species, classes, order, family and genera presenting significant differences between NT and ASD groups",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis",3379134|1224|1236|135625|712;3379134|976|200643|171549|171552|1283313;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|909656|821;3379134|1224|1236|135625|712|724|729;1783272|1239|186801|3085636|186803|2719313|1531,Complete,NA
bsdb:30895172/1/2,30895172,case-control,30895172,10.3389/fcimb.2019.00040,NA,"Ma B., Liang J., Dai M., Wang J., Luo J., Zhang Z. , Jing J.",Altered Gut Microbiota in Chinese Children With Autism Spectrum Disorders,Frontiers in cellular and infection microbiology,2019,"16S rRNA, Chinese children, autism spectrum disorder, case control, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Neurotypical children,Children with Autism Spectrum Disorder (ASD),Diagnosed with ASD according to DSM-5 (Diagnostic and Statistical Manual of Mental Disorders - 5th Edition),45,45,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,NA,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Tables 2-3, S5-7",14 November 2024,AlishaM,"AlishaM,WikiWorks","Species, classes, order, family and genera presenting significant differences between NT and ASD groups",decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",1783272|1239|909932|1843489|31977;3379134|1224|1236|91347|543;1783272|1239|909932|1843488|909930;3379134|200940|3031449|213115|194924;1783272|1239|91061|186826|33958;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|3085636|186803|1506553;3379134|1224|1236|91347|543|1940338;1783272|1239|909932|1843488|909930|33024;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|186802|216572;1783272|201174|84998|1643822|1643826|84111;3379134|976|200643|171549|1853231|283168;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803;3379134|200940|3031449|213115|194924|35832,Complete,NA
bsdb:30895172/2/1,30895172,case-control,30895172,10.3389/fcimb.2019.00040,NA,"Ma B., Liang J., Dai M., Wang J., Luo J., Zhang Z. , Jing J.",Altered Gut Microbiota in Chinese Children With Autism Spectrum Disorders,Frontiers in cellular and infection microbiology,2019,"16S rRNA, Chinese children, autism spectrum disorder, case control, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Neurotypical children,Children with Autism Spectrum Disorder (ASD),Diagnosed with ASD according to DSM-5 (Diagnostic and Statistical Manual of Mental Disorders - 5th Edition),45,45,3 months,16S,34,Illumina,relative abundances,Linear Regression,0.05,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Tables 2-3, S6-7",14 November 2024,AlishaM,"AlishaM,WikiWorks","Species, classes, order, family and genera presenting significant differences between NT and ASD groups",increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,1783272|1239|186801|3085636|186803|2719313|1531,Complete,NA
bsdb:30904962/1/1,30904962,case-control,30904962,10.1186/s13568-019-0763-z,NA,"Wang Z., Wang Q., Zhao J., Gong L., Zhang Y., Wang X. , Yuan Z.",Altered diversity and composition of the gut microbiome in patients with cervical cancer,AMB Express,2019,"16S rRNA, Cervical cancer, Deep sequencing, Gut microbiota",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Cervical cancer,MONDO:0002974,healthy controls,cervical cancer,pathology confirmed cervical cancer patients,5,8,2 months,16S,4,Illumina,raw counts,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between patients with cervical cancer and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio",1783272|1239|186801|3085636|186803|189330;3379134|1224|1236|91347|1903414|581;3379134|1224|1236|91347|1903414|583;1783272|1239|186801|186802|216572|1263;3379134|1224|1236|135622|267890|22;3379134|1224|1236|135624|83763|83770,Complete,Claregrieve1
bsdb:30904962/1/2,30904962,case-control,30904962,10.1186/s13568-019-0763-z,NA,"Wang Z., Wang Q., Zhao J., Gong L., Zhang Y., Wang X. , Yuan Z.",Altered diversity and composition of the gut microbiome in patients with cervical cancer,AMB Express,2019,"16S rRNA, Cervical cancer, Deep sequencing, Gut microbiota",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Cervical cancer,MONDO:0002974,healthy controls,cervical cancer,pathology confirmed cervical cancer patients,5,8,2 months,16S,4,Illumina,raw counts,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Table 3,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between patients with cervical cancer and healthy controls,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",3379134|1224|1236|135619|28256|2745;1783272|1239|909932|1843488|909930|33024,Complete,Claregrieve1
bsdb:30904962/2/1,30904962,case-control,30904962,10.1186/s13568-019-0763-z,NA,"Wang Z., Wang Q., Zhao J., Gong L., Zhang Y., Wang X. , Yuan Z.",Altered diversity and composition of the gut microbiome in patients with cervical cancer,AMB Express,2019,"16S rRNA, Cervical cancer, Deep sequencing, Gut microbiota",Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Cervical cancer,MONDO:0002974,healthy controls,cervical cancer patients,pathology confirmed cervical cancer patients,5,8,2 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,age,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,"Figure 4, Table 3, Figure 5",10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between patients with cervical cancer and healthy controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans",3379134|976|200643|171549|815|816|46506;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|561|562;3379134|1224|1236;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|909656|310297;3379134|1224;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|360807,Complete,Claregrieve1
bsdb:30904962/2/2,30904962,case-control,30904962,10.1186/s13568-019-0763-z,NA,"Wang Z., Wang Q., Zhao J., Gong L., Zhang Y., Wang X. , Yuan Z.",Altered diversity and composition of the gut microbiome in patients with cervical cancer,AMB Express,2019,"16S rRNA, Cervical cancer, Deep sequencing, Gut microbiota",Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Cervical cancer,MONDO:0002974,healthy controls,cervical cancer patients,pathology confirmed cervical cancer patients,5,8,2 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,age,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,"Figure 4, Table 3, Figure 5",10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differential microbial abundance between patients with cervical cancer and healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales",1783272|1239|909932|1843488|909930;1783272|1239|909932;1783272|1239|909932|1843488|909930|33024;1783272|1239|909932|909929,Complete,Claregrieve1
bsdb:30919073/1/1,30919073,time series / longitudinal observational,30919073,10.1007/s00277-019-03599-w,NA,"Ames N.J., Barb J.J., Ranucci A., Kim H., Mudra S.E., Cashion A.K., Townsley D.M., Childs R., Paster B.J., Faller L.L. , Wallen G.R.",The oral microbiome of patients undergoing treatment for severe aplastic anemia: a pilot study,Annals of hematology,2019,"Immunosuppression and hematopoietic stem cell transplant, Oral microbiome, Tongue brushings",Experiment 1,United States of America,Homo sapiens,Tongue,UBERON:0001723,Severe aplastic anemia,EFO:0006927,baseline,hematopoietic stem cell transplantation engraftment,"In HSCT patients, The first sample was obtained before transplant conditioning treatment. The second specimen was collected at engraftment, defined as two absolute neutrophil counts of greater than 500 per microliter for at least 2 days. The final specimen collection occurred at the participant’s scheduled clinic visit approximately 100 days following transplant.",4,4,NA,16S,2345678,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,figure 8a,10 January 2021,Shaimaa Elsafoury,"WikiWorks,Atrayees,Folakunmi",Statistically significant bacteria as determined by Lefse analysis for hematopoietic stem cell transplantation patients between the baseline timepoint and engraftment timepoint,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces lingnae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp.",3379134|1224|1236|135625|712|724|729;1783272|201174|1760|85006|1268|32207|43675;1783272|201174|1760|2037|2049|1654|114702;1783272|1239|91061|1385|539738|1378|84135;1783272|1239|186801|3085636|186803|265975|237576;3379134|976|200643|171549|171552|838|28129;1783272|1239|91061|1385|539738|1378|1379;3379134|1224|28216|206351|481|482;3384189|32066|203490|203491|203492|848|860;1783272|1239|186801|3085636|186803|1213720;3379134|976|200643|171549|171552|2974257|425941;3379134|976|200643|171549|171551|836|1924944,Complete,NA
bsdb:30919073/2/1,30919073,time series / longitudinal observational,30919073,10.1007/s00277-019-03599-w,NA,"Ames N.J., Barb J.J., Ranucci A., Kim H., Mudra S.E., Cashion A.K., Townsley D.M., Childs R., Paster B.J., Faller L.L. , Wallen G.R.",The oral microbiome of patients undergoing treatment for severe aplastic anemia: a pilot study,Annals of hematology,2019,"Immunosuppression and hematopoietic stem cell transplant, Oral microbiome, Tongue brushings",Experiment 2,United States of America,Homo sapiens,Tongue,UBERON:0001723,Severe aplastic anemia,EFO:0006927,baseline,hematopoietic stem cell transplantation engraftment,"In HSCT patients, The first sample was obtained before transplant conditioning treatment. The second specimen was collected at engraftment, defined as two absolute neutrophil counts of greater than 500 per microliter for at least 2 days. The final specimen collection occurred at the participant’s scheduled clinic visit approximately 100 days following transplant.",4,4,NA,16S,3456789,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 8&7,10 January 2021,Shaimaa Elsafoury,WikiWorks,Statistically significant bacteria as determined by Lefse analysis for (a) hematopoietic stem cell transplantation and (b) immunosuppressive therapy group.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces lingnae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis",3379134|1224|1236|135625|712|724|729;1783272|201174|1760|2037|2049|1654|114702;1783272|1239|91061|1385|539738|1378|84135;1783272|1239|186801|3085636|186803|265975|237576;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|2974257|425941,Complete,NA
bsdb:30919073/3/1,30919073,time series / longitudinal observational,30919073,10.1007/s00277-019-03599-w,NA,"Ames N.J., Barb J.J., Ranucci A., Kim H., Mudra S.E., Cashion A.K., Townsley D.M., Childs R., Paster B.J., Faller L.L. , Wallen G.R.",The oral microbiome of patients undergoing treatment for severe aplastic anemia: a pilot study,Annals of hematology,2019,"Immunosuppression and hematopoietic stem cell transplant, Oral microbiome, Tongue brushings",Experiment 3,United States of America,Homo sapiens,Tongue,UBERON:0001723,Severe aplastic anemia,EFO:0006927,engraftment,hematopoietic stem cell transplantation 100 days after the transplant,"In HSCT patients, The first sample was obtained before transplant conditioning treatment. The second specimen was collected at engraftment, defined as two absolute neutrophil counts of greater than 500 per microliter for at least 2 days. The final specimen collection occurred at the participant’s scheduled clinic visit approximately 100 days following transplant.",4,4,NA,16S,2345678,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 8&7,10 January 2021,Shaimaa Elsafoury,WikiWorks,Statistically significant bacteria as determined by Lefse analysis for (a) hematopoietic stem cell transplantation and (b) immunosuppressive therapy group.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis",3379134|1224|1236|135625|712|724|729;1783272|1239|91061|1385|539738|1378|84135,Complete,NA
bsdb:30919073/4/1,30919073,time series / longitudinal observational,30919073,10.1007/s00277-019-03599-w,NA,"Ames N.J., Barb J.J., Ranucci A., Kim H., Mudra S.E., Cashion A.K., Townsley D.M., Childs R., Paster B.J., Faller L.L. , Wallen G.R.",The oral microbiome of patients undergoing treatment for severe aplastic anemia: a pilot study,Annals of hematology,2019,"Immunosuppression and hematopoietic stem cell transplant, Oral microbiome, Tongue brushings",Experiment 4,United States of America,Homo sapiens,Tongue,UBERON:0001723,Severe aplastic anemia,EFO:0006927,engraftment,hematopoietic stem cell transplantation 100 days after the transplant,"In HSCT patients, The first sample was obtained before transplant conditioning treatment. The second specimen was collected at engraftment, defined as two absolute neutrophil counts of greater than 500 per microliter for at least 2 days. The final specimen collection occurred at the participant’s scheduled clinic visit approximately 100 days following transplant.",4,4,NA,16S,3456789,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 8&7,10 January 2021,Shaimaa Elsafoury,WikiWorks,Statistically significant bacteria as determined by Lefse analysis for (a) hematopoietic stem cell transplantation and (b) immunosuppressive therapy group.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,1783272|201174|1760|85006|1268|32207|43675,Complete,NA
bsdb:30927646/1/1,30927646,case-control,30927646,10.1016/j.jpsychires.2019.03.017,NA,"Rong H., Xie X.H., Zhao J., Lai W.T., Wang M.B., Xu D., Liu Y.H., Guo Y.Y., Xu S.X., Deng W.F., Yang Q.F., Xiao L., Zhang Y.L., He F.S., Wang S. , Liu T.B.","Similarly in depression, nuances of gut microbiota: Evidences from a shotgun metagenomics sequencing study on major depressive disorder versus bipolar disorder with current major depressive episode patients",Journal of psychiatric research,2019,"Bipolar disorder, Diversity, G(m) coefficient, Gut microbiota, Major depressive disorder, Shotgun metagenomics sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,controls,MDD,NA,30,31,1 month,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,unchanged,NA,Signature 1,"Figure 1, Table 2, figure 3",10 January 2021,Fatima Zohra,WikiWorks,Comparison of bacterial abundance of major depressive disorder and healthy controls,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium",1783272|1239;1783272|201174;1783272|1239|186801|186802|31979|1485;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|216572|459786;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|909929|1843491|970;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843488|909930|904;3379134|1224|1236|91347|543;3379134|976|200643|171549|171552|838;3379134|1224|1236|91347|543|561|562;1783272|1239|909932|1843489|31977|906|907;1783272|1239|186801|186802|216572|459786|351091;1783272|201174|1760|85004|31953|1678|1680;3379134|976|200643|171549|171552|838|28132;1783272|201174|1760|85004|31953|1678|1689,Complete,NA
bsdb:30927646/1/2,30927646,case-control,30927646,10.1016/j.jpsychires.2019.03.017,NA,"Rong H., Xie X.H., Zhao J., Lai W.T., Wang M.B., Xu D., Liu Y.H., Guo Y.Y., Xu S.X., Deng W.F., Yang Q.F., Xiao L., Zhang Y.L., He F.S., Wang S. , Liu T.B.","Similarly in depression, nuances of gut microbiota: Evidences from a shotgun metagenomics sequencing study on major depressive disorder versus bipolar disorder with current major depressive episode patients",Journal of psychiatric research,2019,"Bipolar disorder, Diversity, G(m) coefficient, Gut microbiota, Major depressive disorder, Shotgun metagenomics sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,controls,MDD,NA,30,31,1 month,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,unchanged,NA,Signature 2,"Figure 1, Table 2, figure 3",10 January 2021,Fatima Zohra,WikiWorks,Comparison of bacterial abundance of major depressive disorder and healthy controls,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae",3379134|976;3379134|976|200643|171549|815|816;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|2005525|195950;3379134|1224|1236|135625|712|724|729,Complete,NA
bsdb:30927646/2/1,30927646,case-control,30927646,10.1016/j.jpsychires.2019.03.017,NA,"Rong H., Xie X.H., Zhao J., Lai W.T., Wang M.B., Xu D., Liu Y.H., Guo Y.Y., Xu S.X., Deng W.F., Yang Q.F., Xiao L., Zhang Y.L., He F.S., Wang S. , Liu T.B.","Similarly in depression, nuances of gut microbiota: Evidences from a shotgun metagenomics sequencing study on major depressive disorder versus bipolar disorder with current major depressive episode patients",Journal of psychiatric research,2019,"Bipolar disorder, Diversity, G(m) coefficient, Gut microbiota, Major depressive disorder, Shotgun metagenomics sequencing",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,healthy controls,bipolar,NA,30,30,1 month,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,unchanged,NA,Signature 1,"Figure 1, Table 2, figure 3",10 January 2021,Fatima Zohra,WikiWorks,Comparison of bacterial abundance of bipolar disorder with major depressive disorder and healthy controls,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides helcogenes",3379134|976;3379134|976|200643|171549|815|816;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|2005525|195950;3379134|976|200643|171549|815|816|290053,Complete,NA
bsdb:30936547/1/1,30936547,"case-control,meta-analysis",30936547,10.1038/s41591-019-0406-6,NA,"Wirbel J., Pyl P.T., Kartal E., Zych K., Kashani A., Milanese A., Fleck J.S., Voigt A.Y., Palleja A., Ponnudurai R., Sunagawa S., Coelho L.P., Schrotz-King P., Vogtmann E., Habermann N., Niméus E., Thomas A.M., Manghi P., Gandini S., Serrano D., Mizutani S., Shiroma H., Shiba S., Shibata T., Yachida S., Yamada T., Waldron L., Naccarati A., Segata N., Sinha R., Ulrich C.M., Brenner H., Arumugam M., Bork P. , Zeller G.",Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer,Nature medicine,2019,NA,Experiment 1,"Austria,China,France,Germany,Italy,Japan,United States of America",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,controls,colorectal cancer,Colorectal cancer cases from eight independent studies,392,386,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 1 (species) and extended data fig. 4 (genera),26 June 2021,Lwaldron,"Lwaldron,WikiWorks",Species and genera enriched in CRC vs controls,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium animalis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium vincentii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|s__Peptostreptococcaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",1783272|1239|1737404|1737405|1570339|165779;1783272|1239|1737404|1737405|1570339|165779|1287640;1783272|1239|186801|186802|216572|244127|1872531;1783272|1239|186801|186802|1898207;1783272|1239|909932|1843489|31977|39948|1955814;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|186802|186806|1730;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492|848|851;3384189|32066|203490|203491|203492|848|76859;3384189|32066|203490|203491|203492|848|155615;3384189|32066|203490|203491|203492|848|68766;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|1385|539738|1378|29391;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|3085636|186803|1649459|154046;1783272|1239|186801|3085636|186803|1506553;3384189|32066|203490|203491|1129771|32067;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|1239|1737404|1737405|1570339|543311|1944660;1783272|1239|186801|3082720|186804|1904861;1783272|1239|186801|3082720|186804|1257;1783272|1239|186801|3082720|186804|1257|341694;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171551|836|28123;3379134|976|200643|171549|171551|836|322095;3379134|976|200643|171549|171551|836|281920;3379134|976|200643|171549|171552|838|28131;3379134|976|200643|171549|171552|838|28133;1783272|1239|526524|526525|128827|123375;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|216572|292632|2053618;1783272|1239|186801|3085636|186803|2941495|1512;1783272|1239|186801|3085636|186803|2316020|33039,Complete,NA
bsdb:30936547/1/2,30936547,"case-control,meta-analysis",30936547,10.1038/s41591-019-0406-6,NA,"Wirbel J., Pyl P.T., Kartal E., Zych K., Kashani A., Milanese A., Fleck J.S., Voigt A.Y., Palleja A., Ponnudurai R., Sunagawa S., Coelho L.P., Schrotz-King P., Vogtmann E., Habermann N., Niméus E., Thomas A.M., Manghi P., Gandini S., Serrano D., Mizutani S., Shiroma H., Shiba S., Shibata T., Yachida S., Yamada T., Waldron L., Naccarati A., Segata N., Sinha R., Ulrich C.M., Brenner H., Arumugam M., Bork P. , Zeller G.",Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer,Nature medicine,2019,NA,Experiment 1,"Austria,China,France,Germany,Italy,Japan,United States of America",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,controls,colorectal cancer,Colorectal cancer cases from eight independent studies,392,386,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Extended Data Fig. 4,5 July 2021,Lwaldron,"Lwaldron,WikiWorks",Genera enriched in CRC vs controls,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",1783272|1239|1737404|1737405|1570339|165779;1783272|1239|186801|186802|186806|1730;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|3085636|186803|1506553;3384189|32066|203490|203491|1129771|32067;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836;1783272|1239|526524|526525|128827|123375;1783272|1239|186801|186802|216572|292632,Complete,NA
bsdb:30936547/1/3,30936547,"case-control,meta-analysis",30936547,10.1038/s41591-019-0406-6,NA,"Wirbel J., Pyl P.T., Kartal E., Zych K., Kashani A., Milanese A., Fleck J.S., Voigt A.Y., Palleja A., Ponnudurai R., Sunagawa S., Coelho L.P., Schrotz-King P., Vogtmann E., Habermann N., Niméus E., Thomas A.M., Manghi P., Gandini S., Serrano D., Mizutani S., Shiroma H., Shiba S., Shibata T., Yachida S., Yamada T., Waldron L., Naccarati A., Segata N., Sinha R., Ulrich C.M., Brenner H., Arumugam M., Bork P. , Zeller G.",Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer,Nature medicine,2019,NA,Experiment 1,"Austria,China,France,Germany,Italy,Japan,United States of America",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,controls,colorectal cancer,Colorectal cancer cases from eight independent studies,392,386,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 3,Fig. 1,5 July 2021,Lwaldron,"Lwaldron,WikiWorks",Species enriched in CRC vs controls,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium animalis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium vincentii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|s__Peptostreptococcaceae bacterium",1783272|1239|1737404|1737405|1570339|165779|1287640;1783272|1239|186801|186802|216572|244127|1872531;1783272|1239|909932|1843489|31977|39948|1955814;1783272|1239|186801|3085636|186803|2719313|208479;3384189|32066|203490|203491|203492|848|851;3384189|32066|203490|203491|203492|848|76859;3384189|32066|203490|203491|203492|848|155615;3384189|32066|203490|203491|203492|848|68766;1783272|1239|91061|1385|539738|1378|29391;1783272|1239|186801|3085636|186803|1649459|154046;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|1239|1737404|1737405|1570339|543311|1944660;1783272|1239|186801|3082720|186804|1257|341694;3379134|976|200643|171549|171551|836|28123;3379134|976|200643|171549|171551|836|322095;3379134|976|200643|171549|171551|836|281920;3379134|976|200643|171549|171552|838|28131;3379134|976|200643|171549|171552|838|28133;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|186801|186802|216572|292632|2053618;1783272|1239|186801|3085636|186803|2941495|1512;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|186802|1898207;1783272|1239|186801|3082720|186804|1904861,Complete,NA
bsdb:30936548/1/1,30936548,"case-control,meta-analysis",30936548,10.1038/s41591-019-0405-7,NA,"Thomas A.M., Manghi P., Asnicar F., Pasolli E., Armanini F., Zolfo M., Beghini F., Manara S., Karcher N., Pozzi C., Gandini S., Serrano D., Tarallo S., Francavilla A., Gallo G., Trompetto M., Ferrero G., Mizutani S., Shiroma H., Shiba S., Shibata T., Yachida S., Yamada T., Wirbel J., Schrotz-King P., Ulrich C.M., Brenner H., Arumugam M., Bork P., Zeller G., Cordero F., Dias-Neto E., Setubal J.C., Tett A., Pardini B., Rescigno M., Waldron L., Naccarati A. , Segata N.",Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation,Nature medicine,2019,NA,Experiment 1,"Austria,Canada,China,France,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,controls,colorectal cancer cases,colorectal cancer cases,308,313,NA,WMS,NA,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Extended Data Fig. 4,26 June 2021,Lwaldron,"Lwaldron,WikiWorks",taxonomic meta-analysis of CRC cases vs controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila sp.,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter ureolyticus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio desulfuricans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium limosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium necrophorum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 3_1_57FAA_CT1,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella rimae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus harei,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia cardiffensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia exigua,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia sp.,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus dysgalactiae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gallolyticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis|s__Streptococcus oralis subsp. tigurinus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] infirmum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|171552|1283313|76122;1783272|1239|1737404|1737405|1570339|165779|1287640;1783272|1239|1737404|1737405|1570339|165779|33037;1783272|1239|186801|186802|216572|244127|1872531;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|291644;3379134|200940|3031449|213115|194924|35832|1929485;3379134|200940|3031449|213115|194924|35832|35833;3379134|29547|3031852|213849|72294|194|824;3379134|29547|3031852|213849|72294|194|204;3379134|29547|3031852|213849|72294|194|827;3379134|200940|3031449|213115|194924|872|876;3379134|1224|28216|206351|481|538|539;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|186806|1730|1736;1783272|1239|186801|186802|216572|946234|292800;3384189|32066|203490|203491|203492|848|850;3384189|32066|203490|203491|203492|848|859;3384189|32066|203490|203491|203492|848|851;1783272|1239|91061|1385|539738|1378|29391;1783272|1239|91061|186826|186828|117563|46124;1783272|1239|186801|3085636|186803|658086;1783272|201174|84998|84999|1643824|2767353|1383;3384189|32066|203490|203491|1129771|32067|104608;3366610|28890|183925|2158|2159|2172|2173;3366610|28890|183925|2158|2159|2172|66852;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|1239|1737404|1737405|1570339|543311|1944660;1783272|1239|1737404|1737405|1570339|162289|54005;1783272|1239|186801|3082720|186804|1257|1261;1783272|1239|186801|3082720|186804|1257|1262;1783272|1239|186801|3082720|186804|1257|341694;3379134|976|200643|171549|171551|836|28123;3379134|976|200643|171549|171551|836|322095;3379134|976|200643|171549|171551|836|281920;3379134|976|200643|171549|171552|838|28131;1783272|201174|1760|2037|2049|2529408|181487;1783272|1239|909932|909929|1843491|970|69823;1783272|201174|84998|1643822|1643826|84108|84109;1783272|201174|84998|1643822|1643826|84108|2049041;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|91061|186826|1300|1301|76860;1783272|1239|91061|186826|1300|1301|1334;1783272|1239|91061|186826|1300|1301|315405;1783272|1239|91061|186826|1300|1301|1303|1077464;1783272|1239|186801|3085636|186803|2941495|1512;1783272|1239|186801|3082720|543314|56774;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Lwaldron
bsdb:30936548/1/2,30936548,"case-control,meta-analysis",30936548,10.1038/s41591-019-0405-7,NA,"Thomas A.M., Manghi P., Asnicar F., Pasolli E., Armanini F., Zolfo M., Beghini F., Manara S., Karcher N., Pozzi C., Gandini S., Serrano D., Tarallo S., Francavilla A., Gallo G., Trompetto M., Ferrero G., Mizutani S., Shiroma H., Shiba S., Shibata T., Yachida S., Yamada T., Wirbel J., Schrotz-King P., Ulrich C.M., Brenner H., Arumugam M., Bork P., Zeller G., Cordero F., Dias-Neto E., Setubal J.C., Tett A., Pardini B., Rescigno M., Waldron L., Naccarati A. , Segata N.",Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation,Nature medicine,2019,NA,Experiment 1,"Austria,Canada,China,France,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,controls,colorectal cancer cases,colorectal cancer cases,308,313,NA,WMS,NA,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 2,Extended Data Fig. 4,26 June 2021,Lwaldron,"Lwaldron,WikiWorks",taxonomic meta-analysis of CRC cases vs controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 1_1_57FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum",1783272|1239|186801|3085636|186803|658081;1783272|1239|186801|186802|216572|1263|457412;3379134|1224|1236|72274|135621|286|306;1783272|201174|1760|85004|31953|1678|216816|1679;1783272|1239|186801|3085636|186803|2569097|39488;1783272|201174|84998|1643822|1643826|447020|446660;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|841|166486;1783272|201174|84998|1643822|1643826|644652|471189;1783272|201174|1760|85004|31953|1678|1686,Complete,Lwaldron
bsdb:30936548/1/3,30936548,"case-control,meta-analysis",30936548,10.1038/s41591-019-0405-7,NA,"Thomas A.M., Manghi P., Asnicar F., Pasolli E., Armanini F., Zolfo M., Beghini F., Manara S., Karcher N., Pozzi C., Gandini S., Serrano D., Tarallo S., Francavilla A., Gallo G., Trompetto M., Ferrero G., Mizutani S., Shiroma H., Shiba S., Shibata T., Yachida S., Yamada T., Wirbel J., Schrotz-King P., Ulrich C.M., Brenner H., Arumugam M., Bork P., Zeller G., Cordero F., Dias-Neto E., Setubal J.C., Tett A., Pardini B., Rescigno M., Waldron L., Naccarati A. , Segata N.",Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation,Nature medicine,2019,NA,Experiment 1,"Austria,Canada,China,France,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,controls,colorectal cancer cases,colorectal cancer cases,308,313,NA,WMS,NA,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 3,Extended Data Fig. 5,26 June 2021,Lwaldron,"Lwaldron,WikiWorks",putative oral species in CRC cases vs controls,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] infirmum,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis|s__Streptococcus oralis subsp. tigurinus",3384189|32066|203490|203491|203492|848|851;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|1239|91061|1385|539738|1378|29391;1783272|1239|186801|3082720|186804|1257|341694;1783272|1239|526524|526525|128827|123375|102148;3379134|976|200643|171549|171552|838|28131;1783272|1239|91061|186826|1300|1301|76860;1783272|1239|91061|186826|186828|117563|46124;3379134|1224|28216|206351|481|538|539;3379134|29547|3031852|213849|72294|194|204;3379134|976|200643|171549|171552|1283313|76122;1783272|1239|186801|3082720|543314|56774;3379134|29547|3031852|213849|72294|194|824;3379134|976|200643|171549|171552|838|28133;1783272|1239|91061|186826|1300|1301|1303|1077464,Complete,Lwaldron
bsdb:30936548/1/4,30936548,"case-control,meta-analysis",30936548,10.1038/s41591-019-0405-7,NA,"Thomas A.M., Manghi P., Asnicar F., Pasolli E., Armanini F., Zolfo M., Beghini F., Manara S., Karcher N., Pozzi C., Gandini S., Serrano D., Tarallo S., Francavilla A., Gallo G., Trompetto M., Ferrero G., Mizutani S., Shiroma H., Shiba S., Shibata T., Yachida S., Yamada T., Wirbel J., Schrotz-King P., Ulrich C.M., Brenner H., Arumugam M., Bork P., Zeller G., Cordero F., Dias-Neto E., Setubal J.C., Tett A., Pardini B., Rescigno M., Waldron L., Naccarati A. , Segata N.",Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation,Nature medicine,2019,NA,Experiment 1,"Austria,Canada,China,France,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,controls,colorectal cancer cases,colorectal cancer cases,308,313,NA,WMS,NA,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 4,Extended Data Fig. 5,26 June 2021,Lwaldron,"Lwaldron,WikiWorks",putative oral species in CRC cases vs controls,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis",1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|1300|1301|113107,Complete,Lwaldron
bsdb:30936882/1/1,30936882,case-control,30936882,10.3389/fimmu.2019.00533,NA,"Ling Z., Shao L., Liu X., Cheng Y., Yan C., Mei Y., Ji F. , Liu X.",Regulatory T Cells and Plasmacytoid Dendritic Cells Within the Tumor Microenvironment in Gastric Cancer Are Correlated With Gastric Microbiota Dysbiosis: A Preliminary Study,Frontiers in immunology,2019,"Tregs (Regulatory T cells), gastric cancer, microbiota (microorganism), pDCs, tumor microenvironment",Experiment 1,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,normal,gastric cancer peritumor group,gastric cancer,60,61,1 month,16S,34,Illumina,relative abundances,LEfSe,2,TRUE,2,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,LEfSe identifies the taxa with the greatest differences in abundance among the three stomach microhabitats,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae",3379134|1224|1236|135619;3379134|1224|1236|135619|28256|2745;3379134|1224|1236|135619|28256;3379134|1224|1236|135622|267890;3379134|1224|1236|135622|267890|22;3379134|1224|1236|135622;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|81852;3379134|1224|28211|204458|76892|41275;1783272|201174|1760|85006|1268|1663;1783272|201174|1760|85007|1762|1763;1783272|201174|1760|85007|1762,Complete,Atrayees
bsdb:30936882/1/2,30936882,case-control,30936882,10.3389/fimmu.2019.00533,NA,"Ling Z., Shao L., Liu X., Cheng Y., Yan C., Mei Y., Ji F. , Liu X.",Regulatory T Cells and Plasmacytoid Dendritic Cells Within the Tumor Microenvironment in Gastric Cancer Are Correlated With Gastric Microbiota Dysbiosis: A Preliminary Study,Frontiers in immunology,2019,"Tregs (Regulatory T cells), gastric cancer, microbiota (microorganism), pDCs, tumor microenvironment",Experiment 1,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,normal,gastric cancer peritumor group,gastric cancer,60,61,1 month,16S,34,Illumina,relative abundances,LEfSe,2,TRUE,2,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,LEfSe identifies the taxa with the greatest differences in abundance among the three stomach microhabitats,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Legionellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Legionellaceae|g__Legionella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales",3379134|1224|28216|80840|119060|106589;3379134|1224|28216|80840|119060;3379134|976|200643|171549|171551;3379134|1224|1236|118969|444;3379134|1224|1236|118969|444|445;3379134|1224|1236|118969,Complete,Atrayees
bsdb:30936882/2/1,30936882,case-control,30936882,10.3389/fimmu.2019.00533,NA,"Ling Z., Shao L., Liu X., Cheng Y., Yan C., Mei Y., Ji F. , Liu X.",Regulatory T Cells and Plasmacytoid Dendritic Cells Within the Tumor Microenvironment in Gastric Cancer Are Correlated With Gastric Microbiota Dysbiosis: A Preliminary Study,Frontiers in immunology,2019,"Tregs (Regulatory T cells), gastric cancer, microbiota (microorganism), pDCs, tumor microenvironment",Experiment 2,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,peritumor,gastric cancer tumor group,gastric cancer,61,59,1 month,16S,34,Illumina,relative abundances,LEfSe,2,TRUE,2,NA,NA,NA,increased,NA,increased,NA,unchanged,Signature 1,Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,LEfSe identifies the taxa with the greatest differences in abundance among the three stomach microhabitats,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",1783272|1239|91061;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|81852;1783272|1239|909932|909929|1843491|970;3379134|1224|1236|135619;3379134|1224|1236|135619|28256|2745;3379134|1224|1236|135619|28256;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004;3379134|1224|1236|91347|543;3379134|1224|1236|91347;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|171550;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|541000;1783272|1239|186801|3085636|186803|841;1783272|1239|909932|1843489|31977|906;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;1783272|1239|186801|3085636|186803|572511,Complete,Atrayees
bsdb:30936882/2/2,30936882,case-control,30936882,10.3389/fimmu.2019.00533,NA,"Ling Z., Shao L., Liu X., Cheng Y., Yan C., Mei Y., Ji F. , Liu X.",Regulatory T Cells and Plasmacytoid Dendritic Cells Within the Tumor Microenvironment in Gastric Cancer Are Correlated With Gastric Microbiota Dysbiosis: A Preliminary Study,Frontiers in immunology,2019,"Tregs (Regulatory T cells), gastric cancer, microbiota (microorganism), pDCs, tumor microenvironment",Experiment 2,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,peritumor,gastric cancer tumor group,gastric cancer,61,59,1 month,16S,34,Illumina,relative abundances,LEfSe,2,TRUE,2,NA,NA,NA,increased,NA,increased,NA,unchanged,Signature 2,Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,LEfSe identifies the taxa with the greatest differences in abundance among the three stomach microhabitats,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|28211|356|82115|379;3379134|1224|28211|356|82115;3379134|976;1783272|1239|909932|909929|1843491|158846;3379134|1224|1236|135622|267890;3379134|1224|1236|135622|267890|22;3379134|1224|1236|135622;1783272|201174|1760|85007|1762|1763;1783272|201174|1760|85007|1762;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;3379134|1224,Complete,Atrayees
bsdb:30936882/3/1,30936882,case-control,30936882,10.3389/fimmu.2019.00533,NA,"Ling Z., Shao L., Liu X., Cheng Y., Yan C., Mei Y., Ji F. , Liu X.",Regulatory T Cells and Plasmacytoid Dendritic Cells Within the Tumor Microenvironment in Gastric Cancer Are Correlated With Gastric Microbiota Dysbiosis: A Preliminary Study,Frontiers in immunology,2019,"Tregs (Regulatory T cells), gastric cancer, microbiota (microorganism), pDCs, tumor microenvironment",Experiment 3,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,normal,gastric cancer tumor group,gastric cancer,60,59,1 month,16S,34,Illumina,relative abundances,LEfSe,2,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,decreased,Signature 1,Figure 3,10 January 2021,Rimsha Azhar,"Lwaldron,WikiWorks",LEfSe identifies the taxa with the greatest differences in abundance among the three stomach microhabitats,increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Aquabacterium,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae,k__Pseudomonadati|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales,k__Pseudomonadati|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Hydrogenophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|201174;3379134|1224|1236|135622;3379134|1224|28216|80840|92793;1783272|1239|91061;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;3379134|1224|28216|80840;1783272|1239|91061|186826|186828;1783272|1239|186801|3085636|186803|33042;1783272|1239|909932|1843489|31977|39948;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239;1783272|1239|91061|1385|539738|1378;1783272|1239|186801|186802|204475;1783272|1239|91061|186826|186828|117563;3379134|1224|2008785|119069|206349;3379134|1224|2008785|119069;3379134|1224|2008785|119069|206349|70774;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;3379134|1224|28216|80840|75682|149698;3379134|1224|28211|356|119045;3379134|1224|28211|356|119045|407;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481;3379134|1224|28216|206351;1783272|1239|186801|186802|541000;3379134|1224|28216|80840|75682;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1257;1783272|201174|1760|85009|31957;1783272|201174|1760|85009|31957|1743;1783272|1239|186801|3085636|186803|841;1783272|201174|84995|84996|84997|42255;1783272|201174|84995|84996|84997;1783272|201174|84995|84996;1783272|1239|186801|186802|216572|1263;3379134|1224|1236|135622|267890|22;3379134|1224|1236|135622|267890;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977,Complete,Atrayees
bsdb:30936882/3/2,30936882,case-control,30936882,10.3389/fimmu.2019.00533,NA,"Ling Z., Shao L., Liu X., Cheng Y., Yan C., Mei Y., Ji F. , Liu X.",Regulatory T Cells and Plasmacytoid Dendritic Cells Within the Tumor Microenvironment in Gastric Cancer Are Correlated With Gastric Microbiota Dysbiosis: A Preliminary Study,Frontiers in immunology,2019,"Tregs (Regulatory T cells), gastric cancer, microbiota (microorganism), pDCs, tumor microenvironment",Experiment 3,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,normal,gastric cancer tumor group,gastric cancer,60,59,1 month,16S,34,Illumina,relative abundances,LEfSe,2,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,decreased,Signature 2,Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,LEfSe identifies the taxa with the greatest differences in abundance among the three stomach microhabitats,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",3379134|976;3379134|976|200643|171549|171551;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85007|1653;3379134|1224|28216|80840|119060;3379134|1224|28216|80840|119060|106589;1783272|201174|1760|2037|2049;1783272|201174|1760|2037|2049|1654;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279,Complete,Atrayees
bsdb:30940469/1/1,30940469,"cross-sectional observational, not case-control",30940469,10.1016/j.resmic.2019.03.003,NA,"Shin J.H., Park Y.H., Sim M., Kim S.A., Joung H. , Shin D.M.",Serum level of sex steroid hormone is associated with diversity and profiles of human gut microbiome,Research in microbiology,2019,"Estradiol, Gut microbiota, Sex differences, Sex steroid hormone, Testosterone",Experiment 1,Republic of Korea,Homo sapiens,Feces,UBERON:0001988,Testosterone measurement,EFO:0004908,Low testosterone group of men,High testosterone group of men,Men with high (tertile3; >4.55 ng/ml) levels of serum testosterone concentration,10,10,6 months,16S,12,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.1,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3B,11 October 2025,Tosin,Tosin,Significant abundant taxa between low and high testosterone groups of men,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",3379134|1224|1236|2887326|468|469;1783272|1239|186801|3085636|186803|189330;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|186802|216572|1263,Complete,NA
bsdb:30940469/2/1,30940469,"cross-sectional observational, not case-control",30940469,10.1016/j.resmic.2019.03.003,NA,"Shin J.H., Park Y.H., Sim M., Kim S.A., Joung H. , Shin D.M.",Serum level of sex steroid hormone is associated with diversity and profiles of human gut microbiome,Research in microbiology,2019,"Estradiol, Gut microbiota, Sex differences, Sex steroid hormone, Testosterone",Experiment 2,Republic of Korea,Homo sapiens,Feces,UBERON:0001988,Estradiol measurement,EFO:0004697,Low estradiol group of women,High estradiol group of women,Women with high (tertile3; >60.0 pg/ml) levels of serum estradiol concentration,9,9,6 months,16S,12,Ion Torrent,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 4B,11 October 2025,Tosin,Tosin,Significant abundant taxa between low and high estradiol groups of women,increased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,NA
bsdb:30940469/2/2,30940469,"cross-sectional observational, not case-control",30940469,10.1016/j.resmic.2019.03.003,NA,"Shin J.H., Park Y.H., Sim M., Kim S.A., Joung H. , Shin D.M.",Serum level of sex steroid hormone is associated with diversity and profiles of human gut microbiome,Research in microbiology,2019,"Estradiol, Gut microbiota, Sex differences, Sex steroid hormone, Testosterone",Experiment 2,Republic of Korea,Homo sapiens,Feces,UBERON:0001988,Estradiol measurement,EFO:0004697,Low estradiol group of women,High estradiol group of women,Women with high (tertile3; >60.0 pg/ml) levels of serum estradiol concentration,9,9,6 months,16S,12,Ion Torrent,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 4B,11 October 2025,Tosin,Tosin,Significant abundant taxa between low and high estradiol groups of women,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,NA
bsdb:30940469/3/1,30940469,"cross-sectional observational, not case-control",30940469,10.1016/j.resmic.2019.03.003,NA,"Shin J.H., Park Y.H., Sim M., Kim S.A., Joung H. , Shin D.M.",Serum level of sex steroid hormone is associated with diversity and profiles of human gut microbiome,Research in microbiology,2019,"Estradiol, Gut microbiota, Sex differences, Sex steroid hormone, Testosterone",Experiment 3,Republic of Korea,Homo sapiens,Feces,UBERON:0001988,Estradiol measurement,EFO:0004697,Low estradiol group of women,High estradiol group of women,Women with high (tertile3; >60.0 pg/ml) levels of serum estradiol concentration,9,9,6 months,16S,12,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.1,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 5A,11 October 2025,Tosin,Tosin,Significant abundant taxa between low and high estradiol groups of women,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia",3379134|976|200643|171549|1853231|574697;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|186802|186807|51514;1783272|201174|84998|1643822|1643826|84108,Complete,NA
bsdb:30944164/1/1,30944164,randomized controlled trial,30944164,10.1126/scitranslmed.aav0537,NA,"Bourke C.D., Gough E.K., Pimundu G., Shonhai A., Berejena C., Terry L., Baumard L., Choudhry N., Karmali Y., Bwakura-Dangarembizi M., Musiime V., Lutaakome J., Kekitiinwa A., Mutasa K., Szubert A.J., Spyer M.J., Deayton J.R., Glass M., Geum H.M., Pardieu C., Gibb D.M., Klein N., Edens T.J., Walker A.S., Manges A.R. , Prendergast A.J.",Cotrimoxazole reduces systemic inflammation in HIV infection by altering the gut microbiome and immune activation,Science translational medicine,2019,NA,Experiment 1,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,"HIV infection,Antimicrobial agent","CHEBI:33281,EFO:0000764",stop cotrimoxazole prophylaxis,continue cotrimoxazole prophylaxis,HIV-positive and antiretroviral therapy (ART) treated children who were randomized to continue taking cotrimoxazole prophylaxis,36,36,NA,WMS,NA,Illumina,NA,Zero-Inflated Beta Regression,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 1,"Text, Figure S3, Figure S2",10 January 2021,Michael Lutete,"WikiWorks,Atrayees",Bacterial species from stool samples that differ between HIV-positive ART-treated Zimbabwean children randomized to continue versus stop cotrimoxazole prophylaxis based on protein families,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides johnsonii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis",3379134|976|200643|171549|815|816|371601;3379134|1224|1236|91347|543|561|562;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|2005525|375288|328812;3379134|976|200643|171549|2005525|375288|387661;1783272|1239|186801|3085636|186803|841|166486;3379134|976|200643|171549|171550|239759|2585118,Complete,Atrayees
bsdb:30944164/1/2,30944164,randomized controlled trial,30944164,10.1126/scitranslmed.aav0537,NA,"Bourke C.D., Gough E.K., Pimundu G., Shonhai A., Berejena C., Terry L., Baumard L., Choudhry N., Karmali Y., Bwakura-Dangarembizi M., Musiime V., Lutaakome J., Kekitiinwa A., Mutasa K., Szubert A.J., Spyer M.J., Deayton J.R., Glass M., Geum H.M., Pardieu C., Gibb D.M., Klein N., Edens T.J., Walker A.S., Manges A.R. , Prendergast A.J.",Cotrimoxazole reduces systemic inflammation in HIV infection by altering the gut microbiome and immune activation,Science translational medicine,2019,NA,Experiment 1,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,"HIV infection,Antimicrobial agent","CHEBI:33281,EFO:0000764",stop cotrimoxazole prophylaxis,continue cotrimoxazole prophylaxis,HIV-positive and antiretroviral therapy (ART) treated children who were randomized to continue taking cotrimoxazole prophylaxis,36,36,NA,WMS,NA,Illumina,NA,Zero-Inflated Beta Regression,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 2,"Text, Figure S3",10 January 2021,Michael Lutete,"Claregrieve1,WikiWorks,Atrayees",Bacterial species from stool samples that differ between HIV-positive ART-treated Zimbabwean children randomized to continue versus stop cotrimoxazole prophylaxis based on protein families,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis",3379134|1224|1236|135625|712|724|729;1783272|1239|526524|526525|128827|1573535|1735;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|186801|186802|216572|216851|853;1783272|1239|91061|186826|1300|1301|1304;3379134|976|200643|171549|171550|239759|328813;1783272|1239|186801|3082720|186804|1505657|261299;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|91061|186826|1300|1301|1309;1783272|1239|91061|186826|1300|1301|1343,Complete,Atrayees
bsdb:30962186/1/1,30962186,"cross-sectional observational, not case-control",30962186,10.2215/CJN.12161018,NA,"Shah N.B., Allegretti A.S., Nigwekar S.U., Kalim S., Zhao S., Lelouvier B., Servant F., Serena G., Thadhani R.I., Raj D.S. , Fasano A.",Blood Microbiome Profile in CKD : A Pilot Study,Clinical journal of the American Society of Nephrology : CJASN,2019,"Blood microbiome, Cross-Sectional Studies, DNA, Bacterial, Ribosomal, Dysbiosis, Endotoxemia, Enterobacteriaceae, Metagenomics, Microbiota, Permeability, Pilot Projects, Polymerase Chain Reaction, Proteobacteria, Pseudomonadaceae, Renal Insufficiency, Chronic, Sequence Analysis, chronic kidney disease, glomerular filtration rate",Experiment 1,United States of America,Homo sapiens,Blood,UBERON:0000178,Chronic kidney disease,EFO:0003884,controls,CKD,NA,20,20,currently on antibiotics,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,age,"age,body mass index,hyperlipidemia,hypertension,immunosuppressant use measurement,leukocyte",NA,NA,decreased,NA,NA,NA,Signature 1,Figure 3 and Table 2,10 January 2021,Rimsha Azhar,"Lwaldron,WikiWorks",Linear discriminant analysis Effect Size (LEfSe) showing microbiome differences between groups at various taxonomic levels.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae|g__Hyphomicrobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Legionellaceae|g__Legionella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Legionellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Flectobacillaceae|g__Pseudarcicella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia|s__Yersinia intermedia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales",3379134|1224|28211|3120395|433;3379134|1224|1236|2887326|468|469;3379134|1224|1236|72274|135621|351;1783272|1239|91061|1385|186817|1386;3379134|976|1853228|1853229|563835;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236;3379134|1224|28211|356|45401;3379134|1224|28211|356|45401|81;3379134|1224|1236|118969|444|445;3379134|1224|1236|118969|444;3379134|1224|1236|118969;3379134|1224|1236|135614|32033|68;1783272|1239|186801|3082720|186804;3379134|1224;3379134|976|768503|768507|3141701|1664383;3379134|1224|1236|72274|135621|286;3379134|976|1853228|1853229|563835|504481;3379134|1224|1236|91347|1903411|613;3379134|1224|1236|91347|1903411|629;3379134|1224|1236|91347|1903411|629|631;3379134|1224|28211|204441,Complete,Shaimaa Elsafoury
bsdb:30962186/1/2,30962186,"cross-sectional observational, not case-control",30962186,10.2215/CJN.12161018,NA,"Shah N.B., Allegretti A.S., Nigwekar S.U., Kalim S., Zhao S., Lelouvier B., Servant F., Serena G., Thadhani R.I., Raj D.S. , Fasano A.",Blood Microbiome Profile in CKD : A Pilot Study,Clinical journal of the American Society of Nephrology : CJASN,2019,"Blood microbiome, Cross-Sectional Studies, DNA, Bacterial, Ribosomal, Dysbiosis, Endotoxemia, Enterobacteriaceae, Metagenomics, Microbiota, Permeability, Pilot Projects, Polymerase Chain Reaction, Proteobacteria, Pseudomonadaceae, Renal Insufficiency, Chronic, Sequence Analysis, chronic kidney disease, glomerular filtration rate",Experiment 1,United States of America,Homo sapiens,Blood,UBERON:0000178,Chronic kidney disease,EFO:0003884,controls,CKD,NA,20,20,currently on antibiotics,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,age,"age,body mass index,hyperlipidemia,hypertension,immunosuppressant use measurement,leukocyte",NA,NA,decreased,NA,NA,NA,Signature 2,Figure 3 and Table 2,10 January 2021,Rimsha Azhar,"Fatima,Lwaldron,WikiWorks",Linear discriminant analysis Effect Size (LEfSe) showing microbiome differences between groups at various taxonomic levels.,decreased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia|o__Acidimicrobiales|f__Acidimicrobiaceae,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia|o__Acidimicrobiales,k__Pseudomonadati|p__Acidobacteriota|c__Terriglobia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Aurantimicrobium,k__Pseudomonadati|p__Acidobacteriota|c__Terriglobia|o__Bryobacterales|f__Bryobacteraceae|g__Bryobacter,k__Pseudomonadati|p__Acidobacteriota|c__Terriglobia|o__Bryobacterales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae,k__Metazoa|p__Arthropoda|c__Insecta|o__Grylloblattodea|f__Grylloblattidae|g__Galloisiana|s__Galloisiana yuasai,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Microscillaceae,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Fulvivirgaceae|g__Ohtaekwangia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",1783272|201174|84992|84993|84994;1783272|201174|84992|84993;3379134|57723|204432;1783272|201174|1760|85006|85023|1705353;3379134|57723|204432|332160|1962910|911113;3379134|57723|204432|332160;1783272|201174|1760|85007|1653|1716;3379134|200940|3031451|3024411|213121;33208|6656|50557|58557|244939|73579|378494;1783272|1239|186801|3085636|186803;3379134|976|768503|768507|1937962;3379134|976|768503|768507|2762286|1210119;3379134|1224|28211|204455|31989|265;3379134|1224|28211|204457|41297|13687;3379134|1224|1236|135614|32033|40323;1783272|1239|186801|3085636|186803|1506577,Complete,Shaimaa Elsafoury
bsdb:30972048/1/1,30972048,"cross-sectional observational, not case-control",30972048,10.3389/fmicb.2019.00598,NA,"Liu Y., Qin S., Song Y., Feng Y., Lv N., Xue Y., Liu F., Wang S., Zhu B., Ma J. , Yang H.",The Perturbation of Infant Gut Microbiota Caused by Cesarean Delivery Is Partially Restored by Exclusive Breastfeeding,Frontiers in microbiology,2019,"breastfeeding, delivery mode, early life, gut microbiome, infant, postnatal antibiotic exposure",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,vaginal born children,cesarean born,cesarean delivery,60,34,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 1C and Text,10 January 2021,Yaseen Javaid,"Merit,WikiWorks",The Perturbation of Infant Gut Microbiota Caused by Cesarean Delivery Is Partially Restored by Exclusive Breastfeeding,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Amylolactobacillus|s__Amylolactobacillus amylophilus,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales",1783272|1239|91061|186826|33958|2767876|1603;1783272|1239;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|1898207;1783272|1239|186801|186802;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|909932;1783272|1239|909932|909929;1783272|1239|909932|1843489,Complete,Rimsha Azhar
bsdb:30972048/1/2,30972048,"cross-sectional observational, not case-control",30972048,10.3389/fmicb.2019.00598,NA,"Liu Y., Qin S., Song Y., Feng Y., Lv N., Xue Y., Liu F., Wang S., Zhu B., Ma J. , Yang H.",The Perturbation of Infant Gut Microbiota Caused by Cesarean Delivery Is Partially Restored by Exclusive Breastfeeding,Frontiers in microbiology,2019,"breastfeeding, delivery mode, early life, gut microbiome, infant, postnatal antibiotic exposure",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,vaginal born children,cesarean born,cesarean delivery,60,34,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 1C and Text,10 January 2021,Yaseen Javaid,WikiWorks,The Perturbation of Infant Gut Microbiota Caused by Cesarean Delivery Is Partially Restored by Exclusive Breastfeeding,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|201174;1783272|201174|1760|85004;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678,Complete,Rimsha Azhar
bsdb:30972048/2/1,30972048,"cross-sectional observational, not case-control",30972048,10.3389/fmicb.2019.00598,NA,"Liu Y., Qin S., Song Y., Feng Y., Lv N., Xue Y., Liu F., Wang S., Zhu B., Ma J. , Yang H.",The Perturbation of Infant Gut Microbiota Caused by Cesarean Delivery Is Partially Restored by Exclusive Breastfeeding,Frontiers in microbiology,2019,"breastfeeding, delivery mode, early life, gut microbiome, infant, postnatal antibiotic exposure",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,cesarean born and breastfed,cesarean born and mixed-fed,cesarean delivery and mixed-fed,24,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3d and Text,10 January 2021,Rimsha Azhar,WikiWorks,Enriched taxa of different level from cesarean born breastfed infants and from cesarean born mixed-fed infants,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977;1783272|1239|909932;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350,Complete,Rimsha Azhar
bsdb:30972048/2/2,30972048,"cross-sectional observational, not case-control",30972048,10.3389/fmicb.2019.00598,NA,"Liu Y., Qin S., Song Y., Feng Y., Lv N., Xue Y., Liu F., Wang S., Zhu B., Ma J. , Yang H.",The Perturbation of Infant Gut Microbiota Caused by Cesarean Delivery Is Partially Restored by Exclusive Breastfeeding,Frontiers in microbiology,2019,"breastfeeding, delivery mode, early life, gut microbiome, infant, postnatal antibiotic exposure",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Cesarean section,EFO:0009636,cesarean born and breastfed,cesarean born and mixed-fed,cesarean delivery and mixed-fed,24,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3d and Text,10 January 2021,Rimsha Azhar,WikiWorks,Enriched taxa of different level from cesarean born breastfed infants and from cesarean born mixed-fed infants,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",1783272|1239|186801|3085636|186803|1506577;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|171552,Complete,Rimsha Azhar
bsdb:30982856/1/1,30982856,prospective cohort,30982856,10.1093/ajcn/nqz006,https://pubmed.ncbi.nlm.nih.gov/30982856/,"Ford S.L., Lohmann P., Preidis G.A., Gordon P.S., O'Donnell A., Hagan J., Venkatachalam A., Balderas M., Luna R.A. , Hair A.B.",Improved feeding tolerance and growth are linked to increased gut microbial community diversity in very-low-birth-weight infants fed mother's own milk compared with donor breast milk,The American journal of clinical nutrition,2019,"breast milk, donor milk, feeding intolerance, growth, microbiota, neonate, premature infant, very low birth weight",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Maternal milk,XCO:0000415,DM (Donor's Milk),MOM (Mother's own milk),Mother's own milk group consists of infants who drank at least >50% of mother's own milk. Any less and they were placed in the other cohort.,43,74,NA,16S,4,Illumina,relative abundances,Logistic Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,FIGURE 2C and FIGURE 2 D,29 June 2022,Uyokeeswaran,"Uyokeeswaran,Peace Sandy,WikiWorks","(C) When comparing longitudinal changes across samples from all study subjects, increasing relative abundance of Proteobacteria was observed. There were no significant differences observed at the phylum level during the first 2 wk of life. By week 4, microbiota from the MOM cohort had significantly higher abundance of Actinobacteria (P = 0.032) and decreased abundance of Firmicutes (P = 0.011). (D) By week 4, microbiota from the MOM cohort had significantly increased abundance of Bacteroides (P = 0.046), Bifidobacterium (P = 0.026), and Enterococcus (P < 0.001) in comparison to the DM cohort. DM infants had significantly higher abundance of Staphylococcus (P = 0.014). DM, donor human milk; MOM, mother's own milk; PCoA, principal coordinates analysis.",increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",1783272|201174;3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|81852|1350,Complete,Peace Sandy
bsdb:30982856/1/2,30982856,prospective cohort,30982856,10.1093/ajcn/nqz006,https://pubmed.ncbi.nlm.nih.gov/30982856/,"Ford S.L., Lohmann P., Preidis G.A., Gordon P.S., O'Donnell A., Hagan J., Venkatachalam A., Balderas M., Luna R.A. , Hair A.B.",Improved feeding tolerance and growth are linked to increased gut microbial community diversity in very-low-birth-weight infants fed mother's own milk compared with donor breast milk,The American journal of clinical nutrition,2019,"breast milk, donor milk, feeding intolerance, growth, microbiota, neonate, premature infant, very low birth weight",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Maternal milk,XCO:0000415,DM (Donor's Milk),MOM (Mother's own milk),Mother's own milk group consists of infants who drank at least >50% of mother's own milk. Any less and they were placed in the other cohort.,43,74,NA,16S,4,Illumina,relative abundances,Logistic Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Figure 2C and Figure 2D,29 June 2022,Uyokeeswaran,"Uyokeeswaran,Peace Sandy,WikiWorks","(C) When comparing longitudinal changes across samples from all study subjects, increasing relative abundance of Proteobacteria was observed. There were no significant differences observed at the phylum level during the first 2 wk of life. By week 4, microbiota from the MOM cohort had significantly higher abundance of Actinobacteria (P = 0.032) and decreased abundance of Firmicutes (P = 0.011). (D) By week 4, microbiota from the MOM cohort had significantly increased abundance of Bacteroides (P = 0.046), Bifidobacterium (P = 0.026), and Enterococcus (P < 0.001) in comparison to the DM cohort. DM infants had significantly higher abundance of Staphylococcus (P = 0.014). DM, donor human milk; MOM, mother's own milk; PCoA, principal coordinates analysis.",decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|1239;1783272|1239|91061|1385|90964|1279,Complete,Peace Sandy
bsdb:30986570/1/1,30986570,"cross-sectional observational, not case-control",30986570,10.1016/j.pvr.2019.04.006,NA,"Onywera H., Williamson A.L., Mbulawa Z.Z.A., Coetzee D. , Meiring T.L.",The cervical microbiota in reproductive-age South African women with and without human papillomavirus infection,"Papillomavirus research (Amsterdam, Netherlands)",2019,"African, Cervical microbiota, High-risk HPV (HR-HPV), Potential biomarkers, Reproductive-age",Experiment 1,South Africa,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,low risk hpv,high risk hpv,High risk HPV infection confirmed through HPV genotyping test,57,30,NA,16S,34,Illumina,relative abundances,LEfSe,0.2,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,figure 4,10 January 2021,Cynthia Anderson,WikiWorks,Potential biomarkers for high-risk HPV by LefSe,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Coriobacterium,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota",3379134|1224|1236|72274|135621|351;1783272|1239|91061|186826|186827;1783272|201174|84998|84999;1783272|201174|84998|84999|84107|33870;1783272|201174;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;3384189|32066|203490|203491;3384189|32066,Complete,Fatima Zohra
bsdb:30986570/1/2,30986570,"cross-sectional observational, not case-control",30986570,10.1016/j.pvr.2019.04.006,NA,"Onywera H., Williamson A.L., Mbulawa Z.Z.A., Coetzee D. , Meiring T.L.",The cervical microbiota in reproductive-age South African women with and without human papillomavirus infection,"Papillomavirus research (Amsterdam, Netherlands)",2019,"African, Cervical microbiota, High-risk HPV (HR-HPV), Potential biomarkers, Reproductive-age",Experiment 1,South Africa,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,low risk hpv,high risk hpv,High risk HPV infection confirmed through HPV genotyping test,57,30,NA,16S,34,Illumina,relative abundances,LEfSe,0.2,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,figure 4,10 January 2021,Cynthia Anderson,WikiWorks,Potential biomarkers for high-risk HPV by LefSe,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae",3379134|1224|1236|135625;3379134|1224|1236|135625|712;3379134|1224|1236|135625|712|724;3379134|1224|28211;3379134|1224|1236;3379134|1224|1236|72274;3379134|1224|28211|356|69277|28100;3379134|1224|28211|356;3379134|1224|28211|356|69277,Complete,Fatima Zohra
bsdb:30986570/2/1,30986570,"cross-sectional observational, not case-control",30986570,10.1016/j.pvr.2019.04.006,NA,"Onywera H., Williamson A.L., Mbulawa Z.Z.A., Coetzee D. , Meiring T.L.",The cervical microbiota in reproductive-age South African women with and without human papillomavirus infection,"Papillomavirus research (Amsterdam, Netherlands)",2019,"African, Cervical microbiota, High-risk HPV (HR-HPV), Potential biomarkers, Reproductive-age",Experiment 2,South Africa,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,no HPV,HPV,HPV infection confirmed through HPV genotyping test,50,37,NA,16S,34,Illumina,relative abundances,LEfSe,0.2,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,supplemental figure 2,10 January 2021,Cynthia Anderson,WikiWorks,Potential biomarkers for HPV by LefSe.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales,k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella",3379134|1224|28211;3379134|1224|28211|766;1783272|201174|1760;1783272|201174|1760|85004;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|2701,Complete,Fatima Zohra
bsdb:30986570/2/2,30986570,"cross-sectional observational, not case-control",30986570,10.1016/j.pvr.2019.04.006,NA,"Onywera H., Williamson A.L., Mbulawa Z.Z.A., Coetzee D. , Meiring T.L.",The cervical microbiota in reproductive-age South African women with and without human papillomavirus infection,"Papillomavirus research (Amsterdam, Netherlands)",2019,"African, Cervical microbiota, High-risk HPV (HR-HPV), Potential biomarkers, Reproductive-age",Experiment 2,South Africa,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,no HPV,HPV,HPV infection confirmed through HPV genotyping test,50,37,NA,16S,34,Illumina,relative abundances,LEfSe,0.2,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,supplemental figure 2,10 January 2021,Cynthia Anderson,WikiWorks,Potential biomarkers for HPV by LefSe.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas veronii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales",3379134|1224|1236;3379134|1224|1236|135625;3379134|1224|1236|135625|712;3379134|1224|1236|72274;3379134|29547|3031852|213849;3379134|29547;3379134|1224|1236|72274|135621|286;3379134|1224|1236|72274|135621|286|76761;3379134|1224|1236|72274|135621|351;3379134|1224|28211|356;3379134|1224|28211|356|69277;3379134|1224|28211|356|69277|28100;3379134|1224|28211|204458|76892;3379134|1224|28211|204458,Complete,Fatima Zohra
bsdb:30988420/1/1,30988420,time series / longitudinal observational,30988420,10.1038/s41598-019-42652-6,NA,"Rashidi A., Kaiser T., Shields-Cutler R., Graiziger C., Holtan S.G., Rehman T.U., Wasko J., Weisdorf D.J., Dunny G., Khoruts A. , Staley C.",Dysbiosis patterns during re-induction/salvage versus induction chemotherapy for acute leukemia,Scientific reports,2019,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Leukemia,EFO:0000565,repeat therapy,induction,acute leukemia patients undergoing chemotherapy,7,13,NA,16S,4,Illumina,relative abundances,LEfSe,0.01,TRUE,4,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2b,10 January 2021,Fatima Zohra,"WikiWorks,Claregrieve1",Composition of microbial communities during induction and repeat therapy in leukemia patients,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|216572|1263,Complete,Claregrieve1
bsdb:30988420/1/2,30988420,time series / longitudinal observational,30988420,10.1038/s41598-019-42652-6,NA,"Rashidi A., Kaiser T., Shields-Cutler R., Graiziger C., Holtan S.G., Rehman T.U., Wasko J., Weisdorf D.J., Dunny G., Khoruts A. , Staley C.",Dysbiosis patterns during re-induction/salvage versus induction chemotherapy for acute leukemia,Scientific reports,2019,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Leukemia,EFO:0000565,repeat therapy,induction,acute leukemia patients undergoing chemotherapy,7,13,NA,16S,4,Illumina,relative abundances,LEfSe,0.01,TRUE,4,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2b,10 January 2021,Fatima Zohra,"WikiWorks,Claregrieve1",Composition of microbial communities during induction and repeat therapy in leukemia patients,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|2037|2049|1654;1783272|201174|84998|1643822|1643826|84111;1783272|1239|91061|186826|81852|1350;1783272|1239|526524|526525|128827|1573536;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572|292632;1783272|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:31001490/1/1,31001490,case-control,31001490,10.3389/fcimb.2019.00090,NA,"Hu Y., Feng Y., Wu J., Liu F., Zhang Z., Hao Y., Liang S., Li B., Li J., Lv N., Xu Y., Zhu B. , Sun Z.",The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients,Frontiers in cellular and infection microbiology,2019,"human gut microbiota, metabolic potential, metagenomic sequencing, microbial diversity, tuberculosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,healthy controls,Tuberculosis (TB) patients,"patients diagnosed with TB by assessing symptoms, including the results of acid-fast bacilli (AFB) smear microscopy, culture, the T-SPOT.TB test and a chest radiograph.",31,30,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"Figure 2A, Text (results)",10 January 2021,Yu Wang,"WikiWorks,Peace Sandy","(A) Differentially abundant species between the C and P groups. P-values for all differentially abundant species between groups are plotted above (Wilcoxon rank-sum test, FDR < 0.1, respectively). Species (present in at least 10% samples) with mean relative abundances of more than 0.001 were considered.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus",1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|33042,Complete,Peace Sandy
bsdb:31001490/1/2,31001490,case-control,31001490,10.3389/fcimb.2019.00090,NA,"Hu Y., Feng Y., Wu J., Liu F., Zhang Z., Hao Y., Liang S., Li B., Li J., Lv N., Xu Y., Zhu B. , Sun Z.",The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients,Frontiers in cellular and infection microbiology,2019,"human gut microbiota, metabolic potential, metagenomic sequencing, microbial diversity, tuberculosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,healthy controls,Tuberculosis (TB) patients,"patients diagnosed with TB by assessing symptoms, including the results of acid-fast bacilli (AFB) smear microscopy, culture, the T-SPOT.TB test and a chest radiograph.",31,30,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,"Figure 2A, Text (results)",10 January 2021,Yu Wang,"Lwaldron,WikiWorks,Peace Sandy","(A) Differentially abundant species between the C and P groups. P-values for all differentially abundant species between groups are plotted above (Wilcoxon rank-sum test, FDR < 0.1, respectively). Species (present in at least 10% samples) with mean relative abundances of more than 0.001 were considered.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp. ART55/1,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas rupellensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris",1783272|1239|186801|3085636|186803|1766253|39491;3379134|74201|203494|48461|1647988|239934|239935;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|216816|1679;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|186801|3085636|186803|572511|40520;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|33042|2049024;1783272|1239|186801|3085636|186803|33042|751585;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330|88431;3379134|1224|1236|135625|712|724|729;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|909932|909929|1843491|158846|437897;1783272|1239|909932|909929|1843491|158846|158847;1783272|1239|909932|909929|1843491|158846|491921;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|841|360807;3379134|1224|28216|80840|995019|40544|40545;1783272|1239|186801|3085636|186803|2316020|46228,Complete,Peace Sandy
bsdb:31006170/1/1,31006170,prospective cohort,31006170,10.1111/1471-0528.15799,NA,"Coker M.O., Hoen A.G., Dade E., Lundgren S., Li Z., Wong A.D., Zens M.S., Palys T.J., Morrison H.G., Sogin M.L., Baker E.R., Karagas M.R. , Madan J.C.",Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study,BJOG : an international journal of obstetrics and gynaecology,2020,"Gut, infant, intestinal microbiota, intrapartum antibiotics, neonate",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants (6-weeks) to mothers unexposed to  intrapartum antibiotic,infants(6-weeks) to mothers exposed to intrapartum antibiotic,vaginally delivered at full-term (>37 weeks of gestation),179,87,NA,16S,45,Illumina,relative abundances,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,"Table S1, Figure S2 & Text",10 January 2021,Mst Afroza Parvin,"WikiWorks,Atrayees",MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|186806|113286;1783272|201174|1760|2037|2049|184869;1783272|1239|909932|1843489|31977|29465|39778,Complete,Atrayees
bsdb:31006170/1/2,31006170,prospective cohort,31006170,10.1111/1471-0528.15799,NA,"Coker M.O., Hoen A.G., Dade E., Lundgren S., Li Z., Wong A.D., Zens M.S., Palys T.J., Morrison H.G., Sogin M.L., Baker E.R., Karagas M.R. , Madan J.C.",Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study,BJOG : an international journal of obstetrics and gynaecology,2020,"Gut, infant, intestinal microbiota, intrapartum antibiotics, neonate",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants (6-weeks) to mothers unexposed to  intrapartum antibiotic,infants(6-weeks) to mothers exposed to intrapartum antibiotic,vaginally delivered at full-term (>37 weeks of gestation),179,87,NA,16S,45,Illumina,relative abundances,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,"Table S1, Figure S2 & Text",10 January 2021,Mst Afroza Parvin,"WikiWorks,Atrayees",MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263,Complete,Atrayees
bsdb:31006170/2/1,31006170,prospective cohort,31006170,10.1111/1471-0528.15799,NA,"Coker M.O., Hoen A.G., Dade E., Lundgren S., Li Z., Wong A.D., Zens M.S., Palys T.J., Morrison H.G., Sogin M.L., Baker E.R., Karagas M.R. , Madan J.C.",Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study,BJOG : an international journal of obstetrics and gynaecology,2020,"Gut, infant, intestinal microbiota, intrapartum antibiotics, neonate",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants (1-year) to mothers unexposed to  intrapartum antibiotic,infants(1-year) to mothers exposed to intrapartum antibiotic,vaginally delivered at full-term (>37 weeks of gestation),179,87,NA,16S,45,Illumina,relative abundances,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Table S1,10 January 2021,Mst Afroza Parvin,"WikiWorks,Atrayees",MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|186806|113286;1783272|201174|1760|2037|2049|184869;1783272|1239|909932|1843489|31977|29465|39778,Complete,Atrayees
bsdb:31006170/2/2,31006170,prospective cohort,31006170,10.1111/1471-0528.15799,NA,"Coker M.O., Hoen A.G., Dade E., Lundgren S., Li Z., Wong A.D., Zens M.S., Palys T.J., Morrison H.G., Sogin M.L., Baker E.R., Karagas M.R. , Madan J.C.",Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study,BJOG : an international journal of obstetrics and gynaecology,2020,"Gut, infant, intestinal microbiota, intrapartum antibiotics, neonate",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants (1-year) to mothers unexposed to  intrapartum antibiotic,infants(1-year) to mothers exposed to intrapartum antibiotic,vaginally delivered at full-term (>37 weeks of gestation),179,87,NA,16S,45,Illumina,relative abundances,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Table S1,10 January 2021,Mst Afroza Parvin,"WikiWorks,Atrayees",MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|841,Complete,Atrayees
bsdb:31006170/3/1,31006170,prospective cohort,31006170,10.1111/1471-0528.15799,NA,"Coker M.O., Hoen A.G., Dade E., Lundgren S., Li Z., Wong A.D., Zens M.S., Palys T.J., Morrison H.G., Sogin M.L., Baker E.R., Karagas M.R. , Madan J.C.",Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study,BJOG : an international journal of obstetrics and gynaecology,2020,"Gut, infant, intestinal microbiota, intrapartum antibiotics, neonate",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants (6-weeks) to mothers unexposed to  antibiotic,infants(6-weeks) to mothers exposed to  antibiotic penicillin,vaginally delivered at full-term (>37 weeks of gestation),179,55,NA,16S,45,Illumina,relative abundances,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,"text, Figure 3",10 January 2021,Mst Afroza Parvin,"WikiWorks,Atrayees",MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|28116;1783272|201174|1760|85004|31953|1678,Complete,Atrayees
bsdb:31006170/4/1,31006170,prospective cohort,31006170,10.1111/1471-0528.15799,NA,"Coker M.O., Hoen A.G., Dade E., Lundgren S., Li Z., Wong A.D., Zens M.S., Palys T.J., Morrison H.G., Sogin M.L., Baker E.R., Karagas M.R. , Madan J.C.",Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study,BJOG : an international journal of obstetrics and gynaecology,2020,"Gut, infant, intestinal microbiota, intrapartum antibiotics, neonate",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants (1-year) to mothers unexposed to  antibiotic,infants(1-year) to mothers exposed to the penicillin group,vaginally delivered at full-term (>37 weeks of gestation),179,55,NA,16S,45,Illumina,relative abundances,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,"Table S1, Figure S2 & Text, Figure 1, Figure 3",10 January 2021,Mst Afroza Parvin,WikiWorks,MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|2316020|33038,Complete,Atrayees
bsdb:31006170/4/2,31006170,prospective cohort,31006170,10.1111/1471-0528.15799,NA,"Coker M.O., Hoen A.G., Dade E., Lundgren S., Li Z., Wong A.D., Zens M.S., Palys T.J., Morrison H.G., Sogin M.L., Baker E.R., Karagas M.R. , Madan J.C.",Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study,BJOG : an international journal of obstetrics and gynaecology,2020,"Gut, infant, intestinal microbiota, intrapartum antibiotics, neonate",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants (1-year) to mothers unexposed to  antibiotic,infants(1-year) to mothers exposed to the penicillin group,vaginally delivered at full-term (>37 weeks of gestation),179,55,NA,16S,45,Illumina,relative abundances,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,"Text, Figure 3",10 January 2021,Mst Afroza Parvin,"WikiWorks,Atrayees",MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|817;1783272|1239|186801|186802|31979|1485;1783272|1239|909932|909929|1843491|158846;1783272|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:31006170/5/1,31006170,prospective cohort,31006170,10.1111/1471-0528.15799,NA,"Coker M.O., Hoen A.G., Dade E., Lundgren S., Li Z., Wong A.D., Zens M.S., Palys T.J., Morrison H.G., Sogin M.L., Baker E.R., Karagas M.R. , Madan J.C.",Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study,BJOG : an international journal of obstetrics and gynaecology,2020,"Gut, infant, intestinal microbiota, intrapartum antibiotics, neonate",Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants (6-weeks) to mothers unexposed to  antibiotic,infants(6-weeks) to mothers exposed to multi-class antibiotics,vaginally delivered at full-term (>37 weeks of gestation),179,12,NA,16S,45,Illumina,relative abundances,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,increased,NA,unchanged,NA,NA,Signature 1,"Text, Figure 3",10 January 2021,Mst Afroza Parvin,"WikiWorks,Atrayees",MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).,increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,1783272|1239|909932|1843489|31977|29465|39778,Complete,Atrayees
bsdb:31006170/6/1,31006170,prospective cohort,31006170,10.1111/1471-0528.15799,NA,"Coker M.O., Hoen A.G., Dade E., Lundgren S., Li Z., Wong A.D., Zens M.S., Palys T.J., Morrison H.G., Sogin M.L., Baker E.R., Karagas M.R. , Madan J.C.",Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study,BJOG : an international journal of obstetrics and gynaecology,2020,"Gut, infant, intestinal microbiota, intrapartum antibiotics, neonate",Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants to mothers unexposed to intrapartum antibiotic,infants to mothers exposed to cephalosporins,NA,179,14,NA,16S,45,Illumina,relative abundances,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"text, figure 3",10 August 2023,Atrayees,"Atrayees,WikiWorks",Taxa that are significantly associated with maternal antibiotic exposure (unexposed infants as the reference group).,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Atrayees
bsdb:31006170/6/2,31006170,prospective cohort,31006170,10.1111/1471-0528.15799,NA,"Coker M.O., Hoen A.G., Dade E., Lundgren S., Li Z., Wong A.D., Zens M.S., Palys T.J., Morrison H.G., Sogin M.L., Baker E.R., Karagas M.R. , Madan J.C.",Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study,BJOG : an international journal of obstetrics and gynaecology,2020,"Gut, infant, intestinal microbiota, intrapartum antibiotics, neonate",Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants to mothers unexposed to intrapartum antibiotic,infants to mothers exposed to cephalosporins,NA,179,14,NA,16S,45,Illumina,relative abundances,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Text, Figure 3",10 August 2023,Atrayees,"Atrayees,WikiWorks",Taxa that are significantly associated with maternal antibiotic exposure (unexposed infants as the reference group).,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,3379134|976|200643|171549|815|816|817,Complete,Atrayees
bsdb:31026576/1/1,31026576,prospective cohort,31026576,10.1016/j.jtho.2019.04.007,"https://pubmed.ncbi.nlm.nih.gov/31026576/#:~:text=Patients_With_NSCLC-,The_Diversity_of_Gut_Microbiome_is_Associated_With_Favorable_Responses,(8):1378-1389.","Jin Y., Dong H., Xia L., Yang Y., Zhu Y., Shen Y., Zheng H., Yao C., Wang Y. , Lu S.",The Diversity of Gut Microbiome is Associated With Favorable Responses to Anti-Programmed Death 1 Immunotherapy in Chinese Patients With NSCLC,Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer,2019,"Advanced NSCLC, Clinical benefit, Gut microbiota, Nivolumab, Systemic immune signatures",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,Patients in this study were defined as responder (R) (with partial response or stable disease),14,23,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,NA,NA,NA,NA,NA,increased,NA,NA,increased,NA,Signature 1,"Figures 3a,b & c",25 July 2022,Sharmilac,"Sharmilac,WikiWorks","Comparison of gut microbiota composition between responders (R) and non responders (NR). (A) Heatmap of seven bacterial genera with statistically differential abundance in R (n ¼ 13) and NR (n ¼ 12) at baseline. (B) Histogram of two representative differentially abundant genera at baseline. (C) Histogram of Bifidobacterium longum and Prevotella copri at baseline (left) and T1 timepoint (right). Statistical analysis was performed by Mann-Whitney test. **p < 0.01, * p < 0.05.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella",3379134|976|200643|171549|171550|239759|28117;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|3085636|186803|140625;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171552|2974251|165179;3379134|1224|1236|91347|543|620,Complete,Fatima
bsdb:31026576/1/2,31026576,prospective cohort,31026576,10.1016/j.jtho.2019.04.007,"https://pubmed.ncbi.nlm.nih.gov/31026576/#:~:text=Patients_With_NSCLC-,The_Diversity_of_Gut_Microbiome_is_Associated_With_Favorable_Responses,(8):1378-1389.","Jin Y., Dong H., Xia L., Yang Y., Zhu Y., Shen Y., Zheng H., Yao C., Wang Y. , Lu S.",The Diversity of Gut Microbiome is Associated With Favorable Responses to Anti-Programmed Death 1 Immunotherapy in Chinese Patients With NSCLC,Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer,2019,"Advanced NSCLC, Clinical benefit, Gut microbiota, Nivolumab, Systemic immune signatures",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,Patients in this study were defined as responder (R) (with partial response or stable disease),14,23,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,NA,NA,NA,NA,NA,increased,NA,NA,increased,NA,Signature 2,"Figure 3a,b,c",25 July 2022,Sharmilac,"Sharmilac,WikiWorks","Comparison of gut microbiota composition between responders (R) and non responders (NR). (A) Heatmap of seven bacterial genera with statistically differential abundance in R (n ¼ 13) and NR (n ¼ 12) at baseline. (B) Histogram of two representative differentially abundant genera at baseline. (C) Histogram of Bifidobacterium longum and Prevotella copri at baseline (left) and T1 timepoint (right). Statistical analysis was performed by Mann-Whitney test. **p < 0.01, * p < 0.05.",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,1783272|1239|186801|186802|216572|1263,Complete,Fatima
bsdb:31037294/1/1,31037294,laboratory experiment,31037294,10.1093/humrep/dez041,NA,"Chadchan S.B., Cheng M., Parnell L.A., Yin Y., Schriefer A., Mysorekar I.U. , Kommagani R.",Antibiotic therapy with metronidazole reduces endometriosis disease progression in mice: a potential role for gut microbiota,"Human reproduction (Oxford, England)",2019,"endometriosis, gut bacteria, inflammation, metronidazole, microbiome",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Non-endo mice,Endo mice,Uterine tissue was transplanted onto the peritoneal wall in order to induce endometriosis in these mice.,5,5,NA,16S,NA,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 3,9 August 2021,Samara.Khan,"Samara.Khan,Claregrieve1,WikiWorks",Differential microbial abundance between non-endo and endo mice: fecal samples from mice with simulated endometriosis had higher levels of Bacteroidetes and Firmicutes than non-endo mice. The bacteroides genera was absent in non-endo mice but present in endo mice.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,Claregrieve1
bsdb:31048728/1/1,31048728,laboratory experiment,31048728,10.1038/s41598-019-43280-w,https://doi.org/10.1038/s41598-019-43280-w,"Lee S., La T.M., Lee H.J., Choi I.S., Song C.S., Park S.Y., Lee J.B. , Lee S.W.",Characterization of microbial communities in the chicken oviduct and the origin of chicken embryo gut microbiota,Scientific reports,2019,NA,Experiment 1,South Korea,Gallus gallus,Oviduct,UBERON:0000993,Developmental stage,EFO:0000399,Immature hen magnum sample (23 weeks-old),Mature hen magnum sample,Magnum samples of 34 weeks-old laying SPF hens,8,16,NA,16S,23456789,Ion Torrent,centered log-ratio,ANCOM,0.05,NA,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 2.,11 March 2024,KwennB,"KwennB,Ayibatari,Rahila,Folakunmi,WikiWorks",ANCOM differential abundance mature and immature hen magnum groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",3379134|976|117743|200644|49546|237;1783272|1239|909932|909929|1843491|158846,Complete,Folakunmi
bsdb:31048728/1/2,31048728,laboratory experiment,31048728,10.1038/s41598-019-43280-w,https://doi.org/10.1038/s41598-019-43280-w,"Lee S., La T.M., Lee H.J., Choi I.S., Song C.S., Park S.Y., Lee J.B. , Lee S.W.",Characterization of microbial communities in the chicken oviduct and the origin of chicken embryo gut microbiota,Scientific reports,2019,NA,Experiment 1,South Korea,Gallus gallus,Oviduct,UBERON:0000993,Developmental stage,EFO:0000399,Immature hen magnum sample (23 weeks-old),Mature hen magnum sample,Magnum samples of 34 weeks-old laying SPF hens,8,16,NA,16S,23456789,Ion Torrent,centered log-ratio,ANCOM,0.05,NA,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 2.,13 March 2024,KwennB,"KwennB,Ayibatari,Rahila,Folakunmi,WikiWorks",ANCOM differential abundance between the mature and immature hen magnum groups.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae",3379134|1224|28211|356|41294|374;3379134|1224|28211|356|41294;1783272|201174|1760|85007|85025,Complete,Folakunmi
bsdb:31053143/1/1,31053143,"cross-sectional observational, not case-control",31053143,10.1186/s12970-019-0290-y,NA,"Jang L.G., Choi G., Kim S.W., Kim B.Y., Lee S. , Park H.",The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,Journal of the International Society of Sports Nutrition,2019,"Body builder, Dietary fiber, Distance runner, Gut microbiota",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,distance runners (high carb),body builders (high protein),NA,15,15,6 months,16S,34,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3 and Text,10 January 2021,Lora Kasselman,WikiWorks,The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae",1783272|1239|186801|3085636|186803|572511|418240;3379134|1224|1236|91347|543|547|550,Complete,Shaimaa Elsafoury
bsdb:31053143/1/2,31053143,"cross-sectional observational, not case-control",31053143,10.1186/s12970-019-0290-y,NA,"Jang L.G., Choi G., Kim S.W., Kim B.Y., Lee S. , Park H.",The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,Journal of the International Society of Sports Nutrition,2019,"Body builder, Dietary fiber, Distance runner, Gut microbiota",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,distance runners (high carb),body builders (high protein),NA,15,15,6 months,16S,34,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3 and Text,10 January 2021,Lora Kasselman,WikiWorks,The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus",1783272|201174|1760|85004|31953|1678|1680;1783272|1239|186801|186802|216572|1263|40519;3379134|976|200643|171549|815|816|47678;3379134|1224|1236|91347|543|561|562;1783272|201174|1760|85004|31953|1678;3379134|1224|1236|91347|543|561;1783272|1239|91061|186826|1300|1357,Complete,Shaimaa Elsafoury
bsdb:31053143/2/1,31053143,"cross-sectional observational, not case-control",31053143,10.1186/s12970-019-0290-y,NA,"Jang L.G., Choi G., Kim S.W., Kim B.Y., Lee S. , Park H.",The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,Journal of the International Society of Sports Nutrition,2019,"Body builder, Dietary fiber, Distance runner, Gut microbiota",Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,control,body builders (high protein),NA,15,15,6 months,16S,34,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3 and Text,10 January 2021,Lora Kasselman,WikiWorks,The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella",3379134|1224|28216|80840|995019|40544;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|31979|1485;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|1432051,Complete,Shaimaa Elsafoury
bsdb:31053143/2/2,31053143,"cross-sectional observational, not case-control",31053143,10.1186/s12970-019-0290-y,NA,"Jang L.G., Choi G., Kim S.W., Kim B.Y., Lee S. , Park H.",The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,Journal of the International Society of Sports Nutrition,2019,"Body builder, Dietary fiber, Distance runner, Gut microbiota",Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,control,body builders (high protein),NA,15,15,6 months,16S,34,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3 and Text,10 January 2021,Lora Kasselman,WikiWorks,The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Latilactobacillus|s__Latilactobacillus sakei,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc",1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|3085636|186803|2569097|39488;3379134|976|200643|171549|815|816|46506;1783272|1239|186801|186802|216572|1263|40519;1783272|201174|1760|85004|31953|1678|216816|1679;3379134|1224|1236|91347|543|561|562;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|2767885|1599;3379134|1224|28216|80840|995019|577310;1783272|1239|91061|186826|33958|1243,Complete,Shaimaa Elsafoury
bsdb:31053143/3/1,31053143,"cross-sectional observational, not case-control",31053143,10.1186/s12970-019-0290-y,NA,"Jang L.G., Choi G., Kim S.W., Kim B.Y., Lee S. , Park H.",The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,Journal of the International Society of Sports Nutrition,2019,"Body builder, Dietary fiber, Distance runner, Gut microbiota",Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,control,distance runners (high carb),NA,15,15,6 months,16S,34,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3 and Text,10 January 2021,Lora Kasselman,WikiWorks,The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,increased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,3379134|1224|28216|80840|995019|40544,Complete,Shaimaa Elsafoury
bsdb:31053143/3/2,31053143,"cross-sectional observational, not case-control",31053143,10.1186/s12970-019-0290-y,NA,"Jang L.G., Choi G., Kim S.W., Kim B.Y., Lee S. , Park H.",The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,Journal of the International Society of Sports Nutrition,2019,"Body builder, Dietary fiber, Distance runner, Gut microbiota",Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,control,distance runners (high carb),NA,15,15,6 months,16S,34,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3 and Text,10 January 2021,Lora Kasselman,WikiWorks,The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella confusa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc",3379134|1224|1236|91347|543|547|550;1783272|1239|91061|186826|33958|46255|1583;1783272|1239|186801|186802|31979|1485|1522;3379134|976|200643|171549|815|816|47678;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|3085636|186803|572511;3379134|1224|1236|91347|543|547;1783272|1239|91061|186826|33958|46255;1783272|1239|91061|186826|33958|1243,Complete,Shaimaa Elsafoury
bsdb:31063846/1/1,31063846,"cross-sectional observational, not case-control",31063846,https://doi.org/10.1016/j.bbi.2019.05.008,https://www.sciencedirect.com/science/article/pii/S0889159118307190,"Liu P., Wu L., Peng G., Han Y., Tang R., Ge J., Zhang L., Jia L., Yue S., Zhou K., Li L., Luo B. , Wang B.",Altered microbiomes distinguish Alzheimer's disease from amnestic mild cognitive impairment and health in a Chinese cohort,"Brain, behavior, and immunity",2019,"Alzheimer’s disease, Amnestic mild cognitive impairment, Microbiome marker",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,healthy controls,Alzheimer’s disease,Patients with dementia stage of alzheimer's disease.,32,33,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,Figure 2,12 March 2023,Sophy,"Sophy,Aiyshaaaa,Claregrieve1,WikiWorks",Differential microbial abundance between Alzheimers patients and healthy controls,decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. (in: firmicutes),k__Bacillati|p__Bacillota|c__Clostridia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",1783272|1239;3379134|976|200643;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|1898207;3379134|976|200643|171549;1783272|1239|91061|1385|186817|1386|1409;1783272|1239|186801;3379134|1224|1236|91347|543,Complete,Claregrieve1
bsdb:31063846/1/2,31063846,"cross-sectional observational, not case-control",31063846,https://doi.org/10.1016/j.bbi.2019.05.008,https://www.sciencedirect.com/science/article/pii/S0889159118307190,"Liu P., Wu L., Peng G., Han Y., Tang R., Ge J., Zhang L., Jia L., Yue S., Zhou K., Li L., Luo B. , Wang B.",Altered microbiomes distinguish Alzheimer's disease from amnestic mild cognitive impairment and health in a Chinese cohort,"Brain, behavior, and immunity",2019,"Alzheimer’s disease, Amnestic mild cognitive impairment, Microbiome marker",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,healthy controls,Alzheimer’s disease,Patients with dementia stage of alzheimer's disease.,32,33,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 2,Figure 2,12 March 2023,Sophy,"Sophy,Aiyshaaaa,Claregrieve1,WikiWorks",Differential microbial abundance between Alzheimers patients and healthy controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",3379134|1224|1236;3379134|1224;3379134|1224|1236|91347;3379134|1224|1236|91347|543,Complete,Claregrieve1
bsdb:31063846/2/1,31063846,"cross-sectional observational, not case-control",31063846,https://doi.org/10.1016/j.bbi.2019.05.008,https://www.sciencedirect.com/science/article/pii/S0889159118307190,"Liu P., Wu L., Peng G., Han Y., Tang R., Ge J., Zhang L., Jia L., Yue S., Zhou K., Li L., Luo B. , Wang B.",Altered microbiomes distinguish Alzheimer's disease from amnestic mild cognitive impairment and health in a Chinese cohort,"Brain, behavior, and immunity",2019,"Alzheimer’s disease, Amnestic mild cognitive impairment, Microbiome marker",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,healthy controls,aMCI patients,Patients with amnestic mild cognitive impairment of alzheimer's disease.,32,32,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 2,25 March 2023,Sophy,"Sophy,Claregrieve1,WikiWorks",Differential microbial abundance between aMCI patients and healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|572511,Complete,Claregrieve1
bsdb:31063846/2/2,31063846,"cross-sectional observational, not case-control",31063846,https://doi.org/10.1016/j.bbi.2019.05.008,https://www.sciencedirect.com/science/article/pii/S0889159118307190,"Liu P., Wu L., Peng G., Han Y., Tang R., Ge J., Zhang L., Jia L., Yue S., Zhou K., Li L., Luo B. , Wang B.",Altered microbiomes distinguish Alzheimer's disease from amnestic mild cognitive impairment and health in a Chinese cohort,"Brain, behavior, and immunity",2019,"Alzheimer’s disease, Amnestic mild cognitive impairment, Microbiome marker",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,healthy controls,aMCI patients,Patients with amnestic mild cognitive impairment of alzheimer's disease.,32,32,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 2,25 March 2023,Sophy,"Sophy,Claregrieve1,WikiWorks",Differential microbial abundance between aMCI patients and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|909932|1843489|31977;3379134|976|200643;3379134|976|200643|171549;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816,Complete,Claregrieve1
bsdb:31063846/3/1,31063846,"cross-sectional observational, not case-control",31063846,https://doi.org/10.1016/j.bbi.2019.05.008,https://www.sciencedirect.com/science/article/pii/S0889159118307190,"Liu P., Wu L., Peng G., Han Y., Tang R., Ge J., Zhang L., Jia L., Yue S., Zhou K., Li L., Luo B. , Wang B.",Altered microbiomes distinguish Alzheimer's disease from amnestic mild cognitive impairment and health in a Chinese cohort,"Brain, behavior, and immunity",2019,"Alzheimer’s disease, Amnestic mild cognitive impairment, Microbiome marker",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Alzheimers patients in dementia stage,aMCI patients,Patients with amnestic mild cognitive impairment of alzheimer's disease.,33,32,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 2,25 March 2023,Sophy,"Sophy,Aiyshaaaa,Claregrieve1,WikiWorks",Differential microbial abundance between Alzheimers patients with dementia and aMCI patients,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236;3379134|1224,Complete,Claregrieve1
bsdb:31063846/3/2,31063846,"cross-sectional observational, not case-control",31063846,https://doi.org/10.1016/j.bbi.2019.05.008,https://www.sciencedirect.com/science/article/pii/S0889159118307190,"Liu P., Wu L., Peng G., Han Y., Tang R., Ge J., Zhang L., Jia L., Yue S., Zhou K., Li L., Luo B. , Wang B.",Altered microbiomes distinguish Alzheimer's disease from amnestic mild cognitive impairment and health in a Chinese cohort,"Brain, behavior, and immunity",2019,"Alzheimer’s disease, Amnestic mild cognitive impairment, Microbiome marker",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Alzheimers patients in dementia stage,aMCI patients,Patients with amnestic mild cognitive impairment of alzheimer's disease.,33,32,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 2,25 March 2023,Sophy,"Sophy,Claregrieve1,WikiWorks",Differential microbial abundance between Alzheimers patients with dementia and aMCI patients,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|186801|186802|31979;1783272|1239|186801|186802|216572|1263;1783272|1239|186801;3379134|976|200643;1783272|1239|186801|186802|1898207;3379134|976|200643|171549;1783272|1239|186801|186802|216572;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816,Complete,Claregrieve1
bsdb:31064831/1/1,31064831,time series / longitudinal observational,31064831,10.1128/mBio.00632-19,NA,"Haran J.P., Bhattarai S.K., Foley S.E., Dutta P., Ward D.V., Bucci V. , McCormick B.A.",Alzheimer's Disease Microbiome Is Associated with Dysregulation of the Anti-Inflammatory P-Glycoprotein Pathway,mBio,2019,"Alzheimer’s Disease, dementia, elderly, gut-brain axis, intestinal homeostasis, intestinal microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,No Dementia (Controls),Alzheimer's Disease (AD) patients,Elders with Alzheimer's Disease,51,24,NA,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,16 December 2024,AaishahM,"AaishahM,WikiWorks",Relative abundance of bacterial taxa in AD patients and controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|1853231|283168;1783272|201174|84998|84999|84107|102106,Complete,NA
bsdb:31064831/1/2,31064831,time series / longitudinal observational,31064831,10.1128/mBio.00632-19,NA,"Haran J.P., Bhattarai S.K., Foley S.E., Dutta P., Ward D.V., Bucci V. , McCormick B.A.",Alzheimer's Disease Microbiome Is Associated with Dysregulation of the Anti-Inflammatory P-Glycoprotein Pathway,mBio,2019,"Alzheimer’s Disease, dementia, elderly, gut-brain axis, intestinal homeostasis, intestinal microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,No Dementia (Controls),Alzheimer's Disease (AD) patients,Elders with Alzheimer's Disease,51,24,NA,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S2,16 December 2024,AaishahM,"AaishahM,WikiWorks",Relative abundance of bacterial taxa in AD patients and controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|841,Complete,NA
bsdb:31064831/2/1,31064831,time series / longitudinal observational,31064831,10.1128/mBio.00632-19,NA,"Haran J.P., Bhattarai S.K., Foley S.E., Dutta P., Ward D.V., Bucci V. , McCormick B.A.",Alzheimer's Disease Microbiome Is Associated with Dysregulation of the Anti-Inflammatory P-Glycoprotein Pathway,mBio,2019,"Alzheimer’s Disease, dementia, elderly, gut-brain axis, intestinal homeostasis, intestinal microbiome",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,No Dementia (Controls),Other Dementia Types,Elders with other Dementia types,51,33,NA,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,16 December 2024,AaishahM,"AaishahM,WikiWorks",Relative abundance of bacterial taxa in those with other Dementia types and controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|1853231|283168,Complete,NA
bsdb:31064831/2/2,31064831,time series / longitudinal observational,31064831,10.1128/mBio.00632-19,NA,"Haran J.P., Bhattarai S.K., Foley S.E., Dutta P., Ward D.V., Bucci V. , McCormick B.A.",Alzheimer's Disease Microbiome Is Associated with Dysregulation of the Anti-Inflammatory P-Glycoprotein Pathway,mBio,2019,"Alzheimer’s Disease, dementia, elderly, gut-brain axis, intestinal homeostasis, intestinal microbiome",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,No Dementia (Controls),Other Dementia Types,Elders with other Dementia types,51,33,NA,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2,16 December 2024,AaishahM,"AaishahM,WikiWorks",Relative abundance of bacterial taxa in those with other Dementia types and controls,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|201174|84998|84999|84107|102106;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|841,Complete,NA
bsdb:31065547/1/1,31065547,case-control,31065547,10.3389/fcimb.2019.00112,NA,"Zhuang H., Cheng L., Wang Y., Zhang Y.K., Zhao M.F., Liang G.D., Zhang M.C., Li Y.G., Zhao J.B., Gao Y.N., Zhou Y.J. , Liu S.L.",Dysbiosis of the Gut Microbiome in Lung Cancer,Frontiers in cellular and infection microbiology,2019,"16S rRNA, biomarkers, gut microbiota, lung cancer, microbial diversity, next generation sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Lung cancer,MONDO:0008903,controls,lung cancer,lung cancer patients,30,30,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 3, Supplementary Figure S3",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differential microbial abundance between lung cancer patients and healthy controls by LefSe,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Macrococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;1783272|201174|84998|84999|1643824|1380;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|526524|526525|2810280|1505663;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|186802|1392389;1783272|1239|91061|1385|90964|69965;3379134|1224|1236|91347|543|160674;1783272|1239|91061|1385|90964,Complete,Claregrieve1
bsdb:31065547/1/2,31065547,case-control,31065547,10.3389/fcimb.2019.00112,NA,"Zhuang H., Cheng L., Wang Y., Zhang Y.K., Zhao M.F., Liang G.D., Zhang M.C., Li Y.G., Zhao J.B., Gao Y.N., Zhou Y.J. , Liu S.L.",Dysbiosis of the Gut Microbiome in Lung Cancer,Frontiers in cellular and infection microbiology,2019,"16S rRNA, biomarkers, gut microbiota, lung cancer, microbial diversity, next generation sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Lung cancer,MONDO:0008903,controls,lung cancer,lung cancer patients,30,30,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 3, Supplementary Figure S3",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Differential microbial abundance between lung cancer patients and healthy controls by LefSe,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alteromonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lentibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",1783272|201174|1760;1783272|201174|84998|1643822|1643826|447020;3379134|1224|1236|135622|72275;3379134|1224|1236|135622;3379134|1224|1236|135622|72275|226;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|31979;1783272|201174|84998|84999|84107|102106;3379134|976|200643|171549|2005519|1348911;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|28050;1783272|1239|91061|1385|186817|175304;1783272|1239|186801|3085636|186803|437755;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|3082720|186804|1257;1783272|1239|186801|3085636|186803|46205;1783272|1239|186801|186802|216572|1508657;3379134|1224|28216|80840|995019|40544,Complete,Claregrieve1
bsdb:31065565/1/1,31065565,time series / longitudinal observational,31065565,10.1093/ofid/ofz173,NA,"Galloway-Peña J.R., Peterson C.B., Malik F., Sahasrabhojane P.V., Shah D.P., Brumlow C.E., Carlin L.G., Chemaly R.F., Im J.S., Rondon G., Felix E., Veillon L., Lorenzi P.L., Alousi A.M., Jenq R.R., Kontoyiannis D.P., Shpall E.J., Shelburne S.A. , Okhuysen P.C.","Fecal Microbiome, Metabolites, and Stem Cell Transplant Outcomes: A Single-Center Pilot Study",Open forum infectious diseases,2019,"butyrate, graft-vs-host disease (GVHD), hematopoietic stem cell transplant (HSCT), indole, microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,healthy volunteers,hematopoietic stem cell transplant recipients,patients undergoing T cell repleted allogeneic hematopoietic stem cell transplantation,18,50,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"Text, Figure 1",10 January 2021,Nadine Ulysse,WikiWorks,Clinical and Microbime Predictors of Acute GastroIntestinal Graft-vs- Host Disease,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,1783272|1239|91061|186826|81852|1350,Complete,Fatima Zohra
bsdb:31065565/1/2,31065565,time series / longitudinal observational,31065565,10.1093/ofid/ofz173,NA,"Galloway-Peña J.R., Peterson C.B., Malik F., Sahasrabhojane P.V., Shah D.P., Brumlow C.E., Carlin L.G., Chemaly R.F., Im J.S., Rondon G., Felix E., Veillon L., Lorenzi P.L., Alousi A.M., Jenq R.R., Kontoyiannis D.P., Shpall E.J., Shelburne S.A. , Okhuysen P.C.","Fecal Microbiome, Metabolites, and Stem Cell Transplant Outcomes: A Single-Center Pilot Study",Open forum infectious diseases,2019,"butyrate, graft-vs-host disease (GVHD), hematopoietic stem cell transplant (HSCT), indole, microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,healthy volunteers,hematopoietic stem cell transplant recipients,patients undergoing T cell repleted allogeneic hematopoietic stem cell transplantation,18,50,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,"Text, Figure 1",10 January 2021,Nadine Ulysse,WikiWorks,Clinical and Microbime Predictors of Acute GastroIntestinal Graft-vs- Host Disease,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",1783272|1239|186801|3085636|186803|46205;1783272|1239|186801|186802|216572|292632,Complete,Fatima Zohra
bsdb:31065565/2/1,31065565,time series / longitudinal observational,31065565,10.1093/ofid/ofz173,NA,"Galloway-Peña J.R., Peterson C.B., Malik F., Sahasrabhojane P.V., Shah D.P., Brumlow C.E., Carlin L.G., Chemaly R.F., Im J.S., Rondon G., Felix E., Veillon L., Lorenzi P.L., Alousi A.M., Jenq R.R., Kontoyiannis D.P., Shpall E.J., Shelburne S.A. , Okhuysen P.C.","Fecal Microbiome, Metabolites, and Stem Cell Transplant Outcomes: A Single-Center Pilot Study",Open forum infectious diseases,2019,"butyrate, graft-vs-host disease (GVHD), hematopoietic stem cell transplant (HSCT), indole, microbiome",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,low fecal butyrate levels,high fecal butyrate levels,patients undergoing T cell repleted allogeneic hematopoietic stem cell transplantation,50,50,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text, Figure 3, Supplemental figure 2",10 January 2021,Nadine Ulysse,WikiWorks,Differences in fecal metabolites among hemapoietic stem cell transplant (HSCT) recipients at baseline,increased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|186802|541000;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|572511;1783272|1239|526524;1783272|1239|526524|526525;1783272|1239|526524|526525|128827;1783272|1239|186801|3085636|186803|46205;1783272|1239|526524|526525|2810280|1505663,Complete,Fatima Zohra
bsdb:31065565/2/2,31065565,time series / longitudinal observational,31065565,10.1093/ofid/ofz173,NA,"Galloway-Peña J.R., Peterson C.B., Malik F., Sahasrabhojane P.V., Shah D.P., Brumlow C.E., Carlin L.G., Chemaly R.F., Im J.S., Rondon G., Felix E., Veillon L., Lorenzi P.L., Alousi A.M., Jenq R.R., Kontoyiannis D.P., Shpall E.J., Shelburne S.A. , Okhuysen P.C.","Fecal Microbiome, Metabolites, and Stem Cell Transplant Outcomes: A Single-Center Pilot Study",Open forum infectious diseases,2019,"butyrate, graft-vs-host disease (GVHD), hematopoietic stem cell transplant (HSCT), indole, microbiome",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,low fecal butyrate levels,high fecal butyrate levels,patients undergoing T cell repleted allogeneic hematopoietic stem cell transplantation,50,50,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Text, Figure 3, Supplemental figure 2",10 January 2021,Nadine Ulysse,WikiWorks,Differences in fecal metabolites among hemapoietic stem cell transplant (HSCT) recipients at baseline,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|81852;1783272|1239|91061|186826;1783272|1239|91061,Complete,Fatima Zohra
bsdb:31067473/1/1,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 1,Canada,Mus musculus,Feces,UBERON:0001988,Phenotype,EFO:0000651,JAX group,JAX-CH group,Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).,12,16,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,increased,Signature 1,Figure 3D,15 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.,increased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",1783272|544448|31969|186332|186333|2086;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|186807|51514;1783272|1239|91061|186826|33958|1578;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:31067473/1/2,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 1,Canada,Mus musculus,Feces,UBERON:0001988,Phenotype,EFO:0000651,JAX group,JAX-CH group,Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).,12,16,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,increased,Signature 2,Figure 3D,15 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|1239|526524|526525|128827|174708;1783272|201174|1760|85004|31953|1678,Complete,Svetlana up
bsdb:31067473/2/1,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 2,Canada,Mus musculus,Feces,UBERON:0001988,Phenotype,EFO:0000651,TAC group,TAC-CH group,Samples taken from co-housed mice from Taconic Farms (TAC-CH).,12,16,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,increased,Signature 1,Figure 3E,15 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|3082720|3030910;1783272|1239|186801|186802|31979|1485;3379134|976|200643|171549|2005473;1783272|1239|186801|186802|216572|119852;1783272|1239|526524|526525|2810281|191303,Complete,Svetlana up
bsdb:31067473/2/2,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 2,Canada,Mus musculus,Feces,UBERON:0001988,Phenotype,EFO:0000651,TAC group,TAC-CH group,Samples taken from co-housed mice from Taconic Farms (TAC-CH).,12,16,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,increased,Signature 2,Figure 3E,15 April 2024,Aleru Divine,"Aleru Divine,WikiWorks,Scholastica",LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|201174|84998|1643822|1643826|447020;1783272|1239|186801|186802|31979|49082;1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171550;1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:31067473/3/1,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 3,Canada,Mus musculus,Feces,UBERON:0001988,Phenotype,EFO:0000651,TAC-CH group,JAX-CH group,Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).,16,16,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 3B,15 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe plots showing differential taxa (family level) in co-housed mice.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",1783272|1239|186801|3082720|3030910;1783272|1239|526524|526525|2810281;3379134|74201|203494|48461|203557,Complete,Svetlana up
bsdb:31067473/3/2,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 3,Canada,Mus musculus,Feces,UBERON:0001988,Phenotype,EFO:0000651,TAC-CH group,JAX-CH group,Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).,16,16,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 3B,15 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe plots showing differential taxa (family level) in co-housed mice.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:31067473/4/1,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 4,Canada,Mus musculus,Colon,UBERON:0001155,Phenotype,EFO:0000651,JAX group,JAX-CH group,Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).,12,16,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 3I,15 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|186807|51514;1783272|1239|91061|186826|33958|1578;3379134|200930|68337|191393|2945020|248038;3379134|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:31067473/4/2,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 4,Canada,Mus musculus,Colon,UBERON:0001155,Phenotype,EFO:0000651,JAX group,JAX-CH group,Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).,12,16,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 3I,15 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|201174|84998|1643822|1643826|447020;1783272|1239|526524|526525|128827|174708;1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549|2005473;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|1263,Complete,Svetlana up
bsdb:31067473/5/1,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 5,Canada,Mus musculus,Colon,UBERON:0001155,Phenotype,EFO:0000651,TAC group,TAC-CH group,Samples taken from co-housed mice from Taconic Farms (TAC-CH).,12,16,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,increased,NA,unchanged,NA,increased,Signature 1,Figure 3J,15 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,1783272|1239|186801|3085636|186803|33042,Complete,Svetlana up
bsdb:31067473/5/2,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 5,Canada,Mus musculus,Colon,UBERON:0001155,Phenotype,EFO:0000651,TAC group,TAC-CH group,Samples taken from co-housed mice from Taconic Farms (TAC-CH).,12,16,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,increased,NA,unchanged,NA,increased,Signature 2,Figure 3J,15 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:31067473/6/1,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 6,Canada,Mus musculus,Colon,UBERON:0001155,Phenotype,EFO:0000651,TAC-CH group,JAX-CH group,Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).,16,16,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,increased,Signature 1,Figure 3G,15 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe plots showing differential taxa (family level) in co-housed mice.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",1783272|1239|186801|3082720|3030910;1783272|1239|186801|186802|216572;1783272|1239|526524|526525|2810281;3379134|74201|203494|48461|203557,Complete,Svetlana up
bsdb:31067473/6/2,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 6,Canada,Mus musculus,Colon,UBERON:0001155,Phenotype,EFO:0000651,TAC-CH group,JAX-CH group,Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).,16,16,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,increased,Signature 2,Figure 3G,15 April 2024,Aleru Divine,"Aleru Divine,WikiWorks,Tosin",LEfSe plots showing differential taxa (family level) in co-housed mice.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|s__Enterococcaceae bacterium RF39",3379134|976|200643|171549|171551;1783272|1239|91061|186826|81852|423410,Complete,Svetlana up
bsdb:31067473/7/1,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 7,Canada,Mus musculus,Ileum,UBERON:0002116,Phenotype,EFO:0000651,JAX group,JAX-CH group,Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).,12,16,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 3N,15 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|186807|51514;3379134|200930|68337|191393|2945020|248038;3379134|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:31067473/7/2,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 7,Canada,Mus musculus,Ileum,UBERON:0002116,Phenotype,EFO:0000651,JAX group,JAX-CH group,Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).,12,16,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 3N,15 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|1239|526524|526525|128827|174708;1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549|2005473;3379134|976|200643|171549|171550;1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:31067473/8/1,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 8,Canada,Mus musculus,Ileum,UBERON:0002116,Phenotype,EFO:0000651,TAC group,TAC-CH group,Samples taken from co-housed mice from Taconic Farms (TAC-CH).,12,16,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,increased,Signature 1,Figure 3O,15 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.,increased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,1783272|1239|526524|526525|2810281|191303,Complete,Svetlana up
bsdb:31067473/8/2,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 8,Canada,Mus musculus,Ileum,UBERON:0002116,Phenotype,EFO:0000651,TAC group,TAC-CH group,Samples taken from co-housed mice from Taconic Farms (TAC-CH).,12,16,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,increased,Signature 2,Figure 3O,15 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,3379134|1224|1236,Complete,Svetlana up
bsdb:31067473/9/1,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 9,Canada,Mus musculus,Ileum,UBERON:0002116,Phenotype,EFO:0000651,TAC-CH group,JAX-CH group,Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).,16,16,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 3L,15 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe plots showing differential taxa (family level) in co-housed mice.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",1783272|1239|186801|186802|216572;1783272|1239|526524|526525|2810281;3379134|74201|203494|48461|203557,Complete,Svetlana up
bsdb:31067473/10/1,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 10,Canada,Mus musculus,"Feces,Colon","UBERON:0001988,UBERON:0001155",Phenotype,EFO:0000651,JAX-CH colon group,JAX-CH fecal pellets group,Samples taken from the fecal pellets of co-housed mice from Jackson Laboratory (JAX-CH).,16,16,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S3,15 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe plots comparing differentiating taxa (family/ genus) in colon and pellet compartments of co-housed mice from Jackson Laboratory (JAX-CH).,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",1783272|201174|84998|1643822|1643826|447020;3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|186803|207244;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|31979;1783272|1239|526524|526525|128827;1783272|1239|91061|186826|33958|1578;3379134|1224|28211|766;1783272|1239|526524|526525|2810281|191303,Complete,Svetlana up
bsdb:31067473/10/2,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 10,Canada,Mus musculus,"Feces,Colon","UBERON:0001988,UBERON:0001155",Phenotype,EFO:0000651,JAX-CH colon group,JAX-CH fecal pellets group,Samples taken from the fecal pellets of co-housed mice from Jackson Laboratory (JAX-CH).,16,16,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S3,15 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe plots comparing differentiating taxa (family/ genus) in colon and pellet compartments of co-housed mice from Jackson Laboratory (JAX-CH).,decreased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.",1783272|544448|31969|186332|186333|2086;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|186807|51514;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|41978,Complete,Svetlana up
bsdb:31067473/11/1,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 11,Canada,Mus musculus,"Feces,Colon","UBERON:0001988,UBERON:0001155",Phenotype,EFO:0000651,TAC-CH colon group,TAC-CH fecal pellets group,Samples taken from the fecal pellets of co-housed mice from Taconic Farms (TAC-CH).,16,16,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S3,15 April 2024,Aleru Divine,"Aleru Divine,WikiWorks,Tosin",LEfSe plots comparing differentiating taxa (family/ genus) in colon and pellet compartments of co-housed mice from Taconic Farms (TAC-CH).,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|s__Enterococcaceae bacterium RF39",1783272|201174|84998|1643822|1643826|447020;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|31979;1783272|1239|526524|526525|128827;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|2005473;3379134|976|200643|171549|2005525|375288;3379134|1224|28211|766;1783272|1239|91061|186826|81852|423410,Complete,Svetlana up
bsdb:31067473/11/2,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 11,Canada,Mus musculus,"Feces,Colon","UBERON:0001988,UBERON:0001155",Phenotype,EFO:0000651,TAC-CH colon group,TAC-CH fecal pellets group,Samples taken from the fecal pellets of co-housed mice from Taconic Farms (TAC-CH).,16,16,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S3,15 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe plots comparing differentiating taxa (family/ genus) in colon and pellet compartments of co-housed mice from Taconic Farms (TAC-CH).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus",1783272|1239|186801|186802;3379134|200930|68337|191393|2945020|248038;1783272|544448|31969|186332|186333|2086;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|41978;1783272|1239|186801|3085636|186803|33042,Complete,Svetlana up
bsdb:31067473/12/1,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 12,Canada,Mus musculus,Feces,UBERON:0001988,Phenotype,EFO:0000651,P1 TAC group,P1 JAX group,Fecal pellet samples of the parental generation (P1) of Jackson Laboratory (JAX) mice.,4,4,NA,16S,4,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 6 and S7,15 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|1643822|1643826|447020;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:31067473/12/2,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 12,Canada,Mus musculus,Feces,UBERON:0001988,Phenotype,EFO:0000651,P1 TAC group,P1 JAX group,Fecal pellet samples of the parental generation (P1) of Jackson Laboratory (JAX) mice.,4,4,NA,16S,4,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 6 and S7,15 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus|s__Candidatus Arthromitus sp. SFB-mouse,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979|49082|49118;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:31067473/13/NA,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 13,Canada,Mus musculus,Feces,UBERON:0001988,Phenotype,EFO:0000651,P1 JAX group,F1 mJAX group,Fecal pellet samples from the maternal F1-generation of Jackson Laboratory (mJAX) mice.,4,15,NA,16S,4,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,increased,NA,increased,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:31067473/14/NA,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 14,Canada,Mus musculus,Feces,UBERON:0001988,Phenotype,EFO:0000651,P1 TAC group,F1 mTAC group,Fecal pellet samples from the maternal F1-generation of Taconic farms (mTAC) mice.,4,15,NA,16S,4,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:31067473/15/1,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 15,Canada,Mus musculus,Feces,UBERON:0001988,Phenotype,EFO:0000651,F1 mTAC group,F1 mJAX group,Fecal pellet samples from the maternal F1-generation of Jackson Laboratory (mJAX) mice.,15,15,NA,16S,4,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 6 and S7,15 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in F1 mJAX and mTAC mice,increased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,3379134|74201|203494|48461|1647988|239934,Complete,Svetlana up
bsdb:31067473/16/1,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 16,Canada,Mus musculus,Colon,UBERON:0001155,Phenotype,EFO:0000651,P1 TAC group,P1 JAX group,Colon samples of the parental generation (P1) of Jackson Laboratory (JAX) mice.,4,4,NA,16S,4,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 6 and S7,15 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|186802|31979|1485;1783272|544448|31969|186332|186333|2086;1783272|201174|1760|85004|31953|1678;3379134|1224|1236|2887326|468|469;3379134|976|200643|171549|171550;3379134|976|200643|171549|2005473,Complete,Svetlana up
bsdb:31067473/16/2,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 16,Canada,Mus musculus,Colon,UBERON:0001155,Phenotype,EFO:0000651,P1 TAC group,P1 JAX group,Colon samples of the parental generation (P1) of Jackson Laboratory (JAX) mice.,4,4,NA,16S,4,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 6 and S7,15 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus|s__Candidatus Arthromitus sp. SFB-mouse,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea",3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979|49082|49118;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|186802|186807|51514;1783272|1239|186801|3085636|186803|189330,Complete,Svetlana up
bsdb:31067473/17/NA,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 17,Canada,Mus musculus,Colon,UBERON:0001155,Phenotype,EFO:0000651,P1 JAX group,F1 mJAX group,Colon samples from the maternal F1-generation of Jackson Laboratory (mJAX) mice.,4,15,NA,16S,4,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:31067473/18/NA,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 18,Canada,Mus musculus,Colon,UBERON:0001155,Phenotype,EFO:0000651,P1 TAC group,F1 mTAC group,Colon samples from the maternal F1-generation of Taconic farms (mTAC) mice.,4,15,NA,16S,4,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,increased,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:31067473/19/1,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 19,Canada,Mus musculus,Colon,UBERON:0001155,Phenotype,EFO:0000651,F1 mTAC group,F1 mJAX group,Colon samples from the maternal F1-generation of Jackson Laboratory (mJAX) mice.,15,15,NA,16S,4,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,decreased,Signature 1,Figure 6 and S7,15 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|2005473,Complete,Svetlana up
bsdb:31067473/19/2,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 19,Canada,Mus musculus,Colon,UBERON:0001155,Phenotype,EFO:0000651,F1 mTAC group,F1 mJAX group,Colon samples from the maternal F1-generation of Jackson Laboratory (mJAX) mice.,15,15,NA,16S,4,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,decreased,Signature 2,Figure 6 and S7,15 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus|s__Candidatus Arthromitus sp. SFB-mouse,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium",1783272|1239|186801|186802|31979|49082|49118;1783272|1239|186801|186802|186807|51514,Complete,Svetlana up
bsdb:31067473/20/1,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 20,Canada,Mus musculus,Ileum,UBERON:0002116,Phenotype,EFO:0000651,P1 TAC group,P1 JAX group,Ileum samples of the parental generation (P1) of Jackson Laboratory (JAX) mice.,4,4,NA,16S,4,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 6 and S7,16 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|1643822|1643826|447020;1783272|544448|31969|186332|186333|2086,Complete,Svetlana up
bsdb:31067473/20/2,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 20,Canada,Mus musculus,Ileum,UBERON:0002116,Phenotype,EFO:0000651,P1 TAC group,P1 JAX group,Ileum samples of the parental generation (P1) of Jackson Laboratory (JAX) mice.,4,4,NA,16S,4,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 6 and S7,16 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus|s__Candidatus Arthromitus sp. SFB-mouse,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium",3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979|49082|49118;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|186802|186807|51514,Complete,Svetlana up
bsdb:31067473/21/NA,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 21,Canada,Mus musculus,Ileum,UBERON:0002116,Phenotype,EFO:0000651,P1 JAX group,F1 mJAX group,Ileum samples from the maternal F1-generation of Jackson Laboratory (mJAX) mice.,4,15,NA,16S,4,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:31067473/22/NA,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 22,Canada,Mus musculus,Ileum,UBERON:0002116,Phenotype,EFO:0000651,P1 TAC group,F1 mTAC group,Ileum samples from the maternal F1-generation of Taconic farms (mTAC) mice.,4,15,NA,16S,4,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:31067473/23/1,31067473,laboratory experiment,31067473,https://doi.org/10.1016/j.celrep.2019.04.023,NA,"Robertson S.J., Lemire P., Maughan H., Goethel A., Turpin W., Bedrani L., Guttman D.S., Croitoru K., Girardin S.E. , Philpott D.J.",Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models,Cell reports,2019,"co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse",Experiment 23,Canada,Mus musculus,Ileum,UBERON:0002116,Phenotype,EFO:0000651,F1 mTAC group,F1 mJAX group,Ileum samples from the maternal F1-generation of Jackson Laboratory (mJAX) mice.,15,15,NA,16S,4,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 6 and S7,16 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice.,increased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,3379134|74201|203494|48461|1647988|239934,Complete,Svetlana up
bsdb:31076212/1/1,31076212,case-control,31076212,https://doi.org/10.1016/j.annepidem.2019.03.005,NA,"Beghini F., Renson A., Zolnik C.P., Geistlinger L., Usyk M., Moody T.U., Thorpe L., Dowd J.B., Burk R., Segata N., Jones H.E. , Waldron L.",Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study,Annals of epidemiology,2019,"16S, Human microbiome, Microbiota, Oral health, RNA, Ribosomal, Smoking, Tobacco",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Tobacco smoke exposure measurement,EFO:0009115,Never smokers,Current cigarette smokers,"Participants who reported smoking more than 100 cigarettes in their lifetime, smoking a cigarette in the last 5 days, and not using any alternative tobacco product in the last 5 days (the 90 with highest measured serum cotinine were selected)",43,86,NA,16S,4,Illumina,NA,edgeR,0.05,TRUE,NA,NA,"age,diabetes mellitus,education level,physical activity,race,sex",NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Supplementary Fig. 4 , Supplementary Fig. 5",28 March 2023,Atrayees,"Atrayees,Peace Sandy,WikiWorks","Differentially abundant OTUs, taxonomically assigned to 28 different genera identified between current cigarette smokers and never smokers. 

Differentially abundant microbes found in the current smokers and the never smokers at the phylum level (obtained by crude differential analysis).",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|1236|135625|712|713;3379134|976|117743|200644|2762318|59735;1783272|201174|1760|85004|31953|1678;3379134|1224|1236|135615|868|2717;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|1164882;1783272|1239|91061|186826|1300|1357;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171551|836;1783272|1239|91061|186826|1300|1301;3379134|1224,Complete,Peace Sandy
bsdb:31076212/1/2,31076212,case-control,31076212,https://doi.org/10.1016/j.annepidem.2019.03.005,NA,"Beghini F., Renson A., Zolnik C.P., Geistlinger L., Usyk M., Moody T.U., Thorpe L., Dowd J.B., Burk R., Segata N., Jones H.E. , Waldron L.",Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study,Annals of epidemiology,2019,"16S, Human microbiome, Microbiota, Oral health, RNA, Ribosomal, Smoking, Tobacco",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Tobacco smoke exposure measurement,EFO:0009115,Never smokers,Current cigarette smokers,"Participants who reported smoking more than 100 cigarettes in their lifetime, smoking a cigarette in the last 5 days, and not using any alternative tobacco product in the last 5 days (the 90 with highest measured serum cotinine were selected)",43,86,NA,16S,4,Illumina,NA,edgeR,0.05,TRUE,NA,NA,"age,diabetes mellitus,education level,physical activity,race,sex",NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Supplementary Fig. 4 , Supplementary Fig. 5",28 March 2023,Atrayees,"Atrayees,Peace Sandy,WikiWorks","Differentially abundant OTUs, taxonomically assigned to 28 different genera identified between current cigarette smokers and never smokers. 

Differentially abundant microbes found in the current smokers and the never smokers at the phylum level (obtained by crude differential analysis).",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Thermotogati|p__Synergistota,k__Bacillati|p__Actinomycetota,p__Candidatus Saccharimonadota,k__Pseudomonadati|p__Spirochaetota",3379134|976|200643|171549|171552|1283313;1783272|1239|909932|1843489|31977|156454;3379134|29547|3031852|213849|72294|194;3384194|508458|649775|649776|3029087|1434006;1783272|1239|91061|186826|33958|1578;3384189|32066|203490|203491|1129771|32067;1783272|1239|909932|1843489|31977|906;3379134|976|200643|171549|2005473;3379134|976|200643|171549|171552|838;3379134|1224|1236|72274|135621|286;1783272|201174|1760|85006|1268|32207;3379134|203691|203692|136|2845253|157;1783272|1239|909932|1843489|31977|29465;3384194|508458;1783272|201174;95818;3379134|203691,Complete,Peace Sandy
bsdb:31076212/2/1,31076212,case-control,31076212,https://doi.org/10.1016/j.annepidem.2019.03.005,NA,"Beghini F., Renson A., Zolnik C.P., Geistlinger L., Usyk M., Moody T.U., Thorpe L., Dowd J.B., Burk R., Segata N., Jones H.E. , Waldron L.",Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study,Annals of epidemiology,2019,"16S, Human microbiome, Microbiota, Oral health, RNA, Ribosomal, Smoking, Tobacco",Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,Tobacco smoke exposure measurement,EFO:0009115,Never Smokers,Alternative Tobacco Smokers,"Participants who used e-cigarettes, hookah, and/or 
cigar or cigarillo but not cigarettes",43,49,NA,16S,4,Illumina,NA,edgeR,0.05,TRUE,NA,NA,"age,diabetes mellitus,education level,physical activity,race,sex",NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Text,4 January 2024,Peace Sandy,"Peace Sandy,WikiWorks","Differential abundance of OTUs from participants who used e-cigarettes, hookah, and/or 
cigar or cigarillo but not cigarettes",increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota",1783272|201174;1783272|1239;3379134|1224,Complete,Lwaldron
bsdb:31076212/2/2,31076212,case-control,31076212,https://doi.org/10.1016/j.annepidem.2019.03.005,NA,"Beghini F., Renson A., Zolnik C.P., Geistlinger L., Usyk M., Moody T.U., Thorpe L., Dowd J.B., Burk R., Segata N., Jones H.E. , Waldron L.",Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study,Annals of epidemiology,2019,"16S, Human microbiome, Microbiota, Oral health, RNA, Ribosomal, Smoking, Tobacco",Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,Tobacco smoke exposure measurement,EFO:0009115,Never Smokers,Alternative Tobacco Smokers,"Participants who used e-cigarettes, hookah, and/or 
cigar or cigarillo but not cigarettes",43,49,NA,16S,4,Illumina,NA,edgeR,0.05,TRUE,NA,NA,"age,diabetes mellitus,education level,physical activity,race,sex",NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Text,4 January 2024,Peace Sandy,"Peace Sandy,WikiWorks","Differential abundance of OTUs from participants who used e-cigarettes, hookah, and/or 
cigar/cigarillo but not cigarettes",decreased,"k__Pseudomonadati|p__Bacteroidota,s__uncultured bacterium",3379134|976;77133,Complete,Lwaldron
bsdb:31076212/3/1,31076212,case-control,31076212,https://doi.org/10.1016/j.annepidem.2019.03.005,NA,"Beghini F., Renson A., Zolnik C.P., Geistlinger L., Usyk M., Moody T.U., Thorpe L., Dowd J.B., Burk R., Segata N., Jones H.E. , Waldron L.",Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study,Annals of epidemiology,2019,"16S, Human microbiome, Microbiota, Oral health, RNA, Ribosomal, Smoking, Tobacco",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Tobacco smoke exposure measurement,EFO:0009115,Never Smokers,participants who only smoked hookah,participants who only smoked hookah,43,28,NA,16S,4,Illumina,NA,edgeR,0.05,TRUE,NA,NA,"age,diabetes mellitus,education level,physical activity,race,sex",NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Text,5 January 2024,Peace Sandy,"Peace Sandy,WikiWorks","In those who only smoked hookah (n = 28), genera Porphyromonas, Leptotrichia, 
Streptobacillus, Fusobacterium, and an uncultured bacterium from Saccharibacteria were 
depleted.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,s__uncultured bacterium",3379134|976|200643|171549|171551|836;3384189|32066|203490|203491|1129771|32067;3384189|32066|203490|203491|1129771|34104;3384189|32066|203490|203491|203492|848;77133,Complete,Lwaldron
bsdb:31078141/1/1,31078141,time series / longitudinal observational,31078141,10.1186/s40168-019-0687-5,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6511141/pdf/40168_2019_Article_687.pdf,"Rocafort M., Noguera-Julian M., Rivera J., Pastor L., Guillén Y., Langhorst J., Parera M., Mandomando I., Carrillo J., Urrea V., Rodríguez C., Casadellà M., Calle M.L., Clotet B., Blanco J., Naniche D. , Paredes R.",Evolution of the gut microbiome following acute HIV-1 infection,Microbiome,2019,"AIDS, HIV-1, HIV-1 pathogenesis, Microbiome, acute HIV-1 infection",Experiment 1,Mozambique,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV-1-negative individuals,Recently HIV-1 infected individuals,"Individuals with recent HIV infection (RHI), defined as a negative or indeterminate rapid test serology (first test negative or first test positive and second test negative) and positive HIV-1 viremia",54,49,NA,16S,34,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,"age,body mass index",NA,NA,unchanged,unchanged,unchanged,NA,increased,Signature 1,Figure 2,8 January 2022,Joyessa,"Joyessa,Claregrieve1,WikiWorks",Differential microbial abundance between recently HIV-1 infected and HIV-negative individuals,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,1783272|1239|186801|3085636|186803|189330,Complete,Claregrieve1
bsdb:31078141/1/2,31078141,time series / longitudinal observational,31078141,10.1186/s40168-019-0687-5,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6511141/pdf/40168_2019_Article_687.pdf,"Rocafort M., Noguera-Julian M., Rivera J., Pastor L., Guillén Y., Langhorst J., Parera M., Mandomando I., Carrillo J., Urrea V., Rodríguez C., Casadellà M., Calle M.L., Clotet B., Blanco J., Naniche D. , Paredes R.",Evolution of the gut microbiome following acute HIV-1 infection,Microbiome,2019,"AIDS, HIV-1, HIV-1 pathogenesis, Microbiome, acute HIV-1 infection",Experiment 1,Mozambique,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV-1-negative individuals,Recently HIV-1 infected individuals,"Individuals with recent HIV infection (RHI), defined as a negative or indeterminate rapid test serology (first test negative or first test positive and second test negative) and positive HIV-1 viremia",54,49,NA,16S,34,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,"age,body mass index",NA,NA,unchanged,unchanged,unchanged,NA,increased,Signature 2,Figure 2,8 January 2022,Joyessa,"Joyessa,Claregrieve1,WikiWorks",Differential microbial abundance between recently HIV-1 infected and HIV-negative individuals,increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,1783272|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:31087436/1/1,31087436,"cross-sectional observational, not case-control",31087436,10.1111/aji.13147,NA,"Akiyama K., Nishioka K., Khan K.N., Tanaka Y., Mori T., Nakaya T. , Kitawaki J.",Molecular detection of microbial colonization in cervical mucus of women with and without endometriosis,"American journal of reproductive immunology (New York, N.Y. : 1989)",2019,"cervical mucus, endometriosis, metagenomic analysis, microbiota",Experiment 1,Japan,Homo sapiens,Uterine cervix,UBERON:0000002,Endometriosis,EFO:0001065,Women scheduled for laparoscopic surgery for benign uterine/ ovarian conditions,Stage 3/4 endometriosis patients,Women were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).,39,30,6 months,16S,56,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 1,Figure 4,8 August 2021,Samara.Khan,"Samara.Khan,WikiWorks",Enterobactericeae and streptococcus were significantly higher in the cervical mucus of the endometriosis group than the control group.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|1224|1236|91347|543;1783272|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:31100891/1/1,31100891,case-control,31100891,10.3390/jcm8050693,NA,"Jeong Y., Kim J.W., You H.J., Park S.J., Lee J., Ju J.H., Park M.S., Jin H., Cho M.L., Kwon B., Park S.H. , Ji G.E.",Gut Microbial Composition and Function Are Altered in Patients with Early Rheumatoid Arthritis,Journal of clinical medicine,2019,"Collinsella, autoimmune disease, dysbiosis, gut microbiome, microbial diversity, rheumatoid arthritis",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Rheumatoid arthritis,EFO:0000685,female healthy control,female with early RA,female early rheumatoid arthritis patients,25,29,NA,16S,NA,Illumina,relative abundances,LEfSe,0.1,TRUE,3,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,"Figure 3, text",30 November 2021,Tislam,"Tislam,Claregrieve1,WikiWorks",Differential microbial abundance between RA patients and controls,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia",1783272|201174;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|186801|186802|186806|1730;1783272|1239|91061|186826|33958|1243;3384194|508458|649775|649776|649777;1783272|1239|526524,Complete,Claregrieve1
bsdb:31100891/1/2,31100891,case-control,31100891,10.3390/jcm8050693,NA,"Jeong Y., Kim J.W., You H.J., Park S.J., Lee J., Ju J.H., Park M.S., Jin H., Cho M.L., Kwon B., Park S.H. , Ji G.E.",Gut Microbial Composition and Function Are Altered in Patients with Early Rheumatoid Arthritis,Journal of clinical medicine,2019,"Collinsella, autoimmune disease, dysbiosis, gut microbiome, microbial diversity, rheumatoid arthritis",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Rheumatoid arthritis,EFO:0000685,female healthy control,female with early RA,female early rheumatoid arthritis patients,25,29,NA,16S,NA,Illumina,relative abundances,LEfSe,0.1,TRUE,3,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,"Figure 3, text",30 November 2021,Tislam,"Tislam,Claregrieve1,WikiWorks",Differential microbial abundance between RA patients and controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota",3379134|976|200643|171549;3379134|976|200643;3379134|976,Complete,Claregrieve1
bsdb:31109865/1/1,31109865,case-control,31109865,10.1016/j.job.2019.03.003,NA,"Takahashi Y., Park J., Hosomi K., Yamada T., Kobayashi A., Yamaguchi Y., Iketani S., Kunisawa J., Mizuguchi K., Maeda N. , Ohshima T.",Analysis of oral microbiota in Japanese oral cancer patients using 16S rRNA sequencing,Journal of oral biosciences,2019,"Bacteria, Epidemiology, Metagenomics, Microbiota, Mouth neoplasms",Experiment 1,Japan,Homo sapiens,Saliva,UBERON:0001836,Squamous cell carcinoma,EFO:0000707,noncancer individuals,Oral Squamous Cell Cancer patients,All diagnoses of oral squamous cell carcinoma were confirmed by biopsy and pathological findings.The control group was defined as individuals without any diagnosed mucosal diseases and other cancers and these individuals were over the age of 40.,80,60,1 month,16S,34,Illumina,raw counts,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 1,"Fig 1,3 and Text",10 January 2021,Utsav Patel,WikiWorks,Oral microbiota in japanese oral cancer patients vs. noncancer individuals: a case-control study,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga",1783272|1239|186801|3082720|186804|1257;3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|171552|1283313;3379134|976|117743|200644|49546|1016,Complete,Shaimaa Elsafoury
bsdb:31109865/1/2,31109865,case-control,31109865,10.1016/j.job.2019.03.003,NA,"Takahashi Y., Park J., Hosomi K., Yamada T., Kobayashi A., Yamaguchi Y., Iketani S., Kunisawa J., Mizuguchi K., Maeda N. , Ohshima T.",Analysis of oral microbiota in Japanese oral cancer patients using 16S rRNA sequencing,Journal of oral biosciences,2019,"Bacteria, Epidemiology, Metagenomics, Microbiota, Mouth neoplasms",Experiment 1,Japan,Homo sapiens,Saliva,UBERON:0001836,Squamous cell carcinoma,EFO:0000707,noncancer individuals,Oral Squamous Cell Cancer patients,All diagnoses of oral squamous cell carcinoma were confirmed by biopsy and pathological findings.The control group was defined as individuals without any diagnosed mucosal diseases and other cancers and these individuals were over the age of 40.,80,60,1 month,16S,34,Illumina,raw counts,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 2,"Fig 1,3 and Text",10 January 2021,Utsav Patel,WikiWorks,Oral microbiota in japanese oral cancer patients vs. noncancer individuals: a case-control study,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",1783272|201174|1760|85006|1268|32207;3379134|1224|1236|135625|712|724,Complete,Shaimaa Elsafoury
bsdb:31126003/1/1,31126003,"cross-sectional observational, not case-control",31126003,10.1016/j.envpol.2018.12.083,NA,"Li X., Sun Y., An Y., Wang R., Lin H., Liu M., Li S., Ma M. , Xiao C.",Air pollution during the winter period and respiratory tract microbial imbalance in a healthy young population in Northeastern China,"Environmental pollution (Barking, Essex : 1987)",2019,"Air pollution, Airborne particulate matter, Coal burning, Oropharyngeal microbiota, Respiratory tract diseases",Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,Air pollution,ENVO:02500037,lightly poluuted region (A),moderately polluted region (B),"paticipants lived in any of those regions for more than 2 years. region A: (lightly polluted region of PM 2.5), region B: (moderately polluted region of PM 2.5) and region C: (heavily polluted region of PM 2.5)",35,40,3 months,16S,3,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"age,body height,body weight,sex,vital capacity",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3, 4, 5, 6",10 January 2021,Rimsha Azhar,WikiWorks,"Abundance analysis of the dominant bacterial taxa of A (lightly polluted region of PM 2.5), B (moderately polluted region of PM 2.5) and C (heavily polluted region of PM 2.5)",increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",1783272|1239;1783272|201174;1783272|1239|186801;1783272|201174|1760;1783272|1239|186801|186802;1783272|201174|1760|2037;1783272|1239|186801|3085636|186803;1783272|201174|1760|85006|1268;1783272|201174|1760|2037|2049;1783272|1239|186801|186802|541000;1783272|201174|1760|85006|1268|32207;1783272|1239|186801|3085636|186803|265975;3379134|1224|28216|206351|481|482;1783272|201174|1760|2037|2049|1654,Complete,Shaimaa Elsafoury
bsdb:31126003/1/2,31126003,"cross-sectional observational, not case-control",31126003,10.1016/j.envpol.2018.12.083,NA,"Li X., Sun Y., An Y., Wang R., Lin H., Liu M., Li S., Ma M. , Xiao C.",Air pollution during the winter period and respiratory tract microbial imbalance in a healthy young population in Northeastern China,"Environmental pollution (Barking, Essex : 1987)",2019,"Air pollution, Airborne particulate matter, Coal burning, Oropharyngeal microbiota, Respiratory tract diseases",Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,Air pollution,ENVO:02500037,lightly poluuted region (A),moderately polluted region (B),"paticipants lived in any of those regions for more than 2 years. region A: (lightly polluted region of PM 2.5), region B: (moderately polluted region of PM 2.5) and region C: (heavily polluted region of PM 2.5)",35,40,3 months,16S,3,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"age,body height,body weight,sex,vital capacity",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3, 4, 5, 6",10 January 2021,Rimsha Azhar,"Merit,WikiWorks","Abundance analysis of the dominant bacterial taxa of A (lightly polluted region of PM 2.5), B (moderately polluted region of PM 2.5) and C (heavily polluted region of PM 2.5)",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|976|117743|200644;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;3384189|32066|203490|203491|203492|848;3379134|1224|1236|2887326|468|475;3379134|1224|1236|2887326|468;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|1224|1236|72274;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977,Complete,Shaimaa Elsafoury
bsdb:31126003/2/1,31126003,"cross-sectional observational, not case-control",31126003,10.1016/j.envpol.2018.12.083,NA,"Li X., Sun Y., An Y., Wang R., Lin H., Liu M., Li S., Ma M. , Xiao C.",Air pollution during the winter period and respiratory tract microbial imbalance in a healthy young population in Northeastern China,"Environmental pollution (Barking, Essex : 1987)",2019,"Air pollution, Airborne particulate matter, Coal burning, Oropharyngeal microbiota, Respiratory tract diseases",Experiment 2,China,Homo sapiens,Throat,UBERON:0000341,Air pollution,ENVO:02500037,lightly poluuted region (A),heavily polluted region (C),"paticipants lived in any of those regions for more than 2 years. region A: (lightly polluted region of PM 2.5), region B: (moderately polluted region of PM 2.5) and region C: (heavily polluted region of PM 2.5)",35,39,3 months,16S,3,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"age,body height,body weight,sex,vital capacity",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3, 4, 5, 6",10 January 2021,Rimsha Azhar,WikiWorks,"Abundance analysis of the dominant bacterial taxa of A (lightly polluted region of PM 2.5), B (moderately polluted region of PM 2.5) and C (heavily polluted region of PM 2.5)",increased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239;3379134|1224;1783272|201174;1783272|1239|186801;1783272|1239|186801|186802|541000;3379134|1224|1236;3379134|1224|28211;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803,Complete,Shaimaa Elsafoury
bsdb:31126003/2/2,31126003,"cross-sectional observational, not case-control",31126003,10.1016/j.envpol.2018.12.083,NA,"Li X., Sun Y., An Y., Wang R., Lin H., Liu M., Li S., Ma M. , Xiao C.",Air pollution during the winter period and respiratory tract microbial imbalance in a healthy young population in Northeastern China,"Environmental pollution (Barking, Essex : 1987)",2019,"Air pollution, Airborne particulate matter, Coal burning, Oropharyngeal microbiota, Respiratory tract diseases",Experiment 2,China,Homo sapiens,Throat,UBERON:0000341,Air pollution,ENVO:02500037,lightly poluuted region (A),heavily polluted region (C),"paticipants lived in any of those regions for more than 2 years. region A: (lightly polluted region of PM 2.5), region B: (moderately polluted region of PM 2.5) and region C: (heavily polluted region of PM 2.5)",35,39,3 months,16S,3,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"age,body height,body weight,sex,vital capacity",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3, 4, 5, 6",10 January 2021,Rimsha Azhar,"Merit,WikiWorks","Abundance analysis of the dominant bacterial taxa of A (lightly polluted region of PM 2.5), B (moderately polluted region of PM 2.5) and C (heavily polluted region of PM 2.5)",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849;3379134|976|117743|200644|49546|1016;3379134|976|117743|200644|49546;3379134|976|117743|200644;3379134|976|117743;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;3384189|32066|203490|203491|203492|848;3379134|1224|1236|2887326|468|475;3379134|1224|1236|2887326|468;3379134|1224|28216|206351;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977,Complete,Shaimaa Elsafoury
bsdb:31126003/3/1,31126003,"cross-sectional observational, not case-control",31126003,10.1016/j.envpol.2018.12.083,NA,"Li X., Sun Y., An Y., Wang R., Lin H., Liu M., Li S., Ma M. , Xiao C.",Air pollution during the winter period and respiratory tract microbial imbalance in a healthy young population in Northeastern China,"Environmental pollution (Barking, Essex : 1987)",2019,"Air pollution, Airborne particulate matter, Coal burning, Oropharyngeal microbiota, Respiratory tract diseases",Experiment 3,China,Homo sapiens,Throat,UBERON:0000341,Air pollution,ENVO:02500037,moderately poluuted region (B),heavily polluted region (C),"paticipants lived in any of those regions for more than 2 years. region A: (lightly polluted region of PM 2.5), region B: (moderately polluted region of PM 2.5) and region C: (heavily polluted region of PM 2.5)",40,39,3 months,16S,3,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"age,body height,body weight,sex,vital capacity",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3, 4, 5, 6",10 January 2021,Rimsha Azhar,WikiWorks,"Abundance analysis of the dominant bacterial taxa of A (lightly polluted region of PM 2.5), B (moderately polluted region of PM 2.5) and C (heavily polluted region of PM 2.5)",increased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales",3379134|1224;3379134|1224|1236;3379134|1224|28211;3379134|1224|1236|72274,Complete,Shaimaa Elsafoury
bsdb:31126003/3/2,31126003,"cross-sectional observational, not case-control",31126003,10.1016/j.envpol.2018.12.083,NA,"Li X., Sun Y., An Y., Wang R., Lin H., Liu M., Li S., Ma M. , Xiao C.",Air pollution during the winter period and respiratory tract microbial imbalance in a healthy young population in Northeastern China,"Environmental pollution (Barking, Essex : 1987)",2019,"Air pollution, Airborne particulate matter, Coal burning, Oropharyngeal microbiota, Respiratory tract diseases",Experiment 3,China,Homo sapiens,Throat,UBERON:0000341,Air pollution,ENVO:02500037,moderately poluuted region (B),heavily polluted region (C),"paticipants lived in any of those regions for more than 2 years. region A: (lightly polluted region of PM 2.5), region B: (moderately polluted region of PM 2.5) and region C: (heavily polluted region of PM 2.5)",40,39,3 months,16S,3,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"age,body height,body weight,sex,vital capacity",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3, 4, 5, 6",10 January 2021,Rimsha Azhar,WikiWorks,"Abundance analysis of the dominant bacterial taxa of A (lightly polluted region of PM 2.5), B (moderately polluted region of PM 2.5) and C (heavily polluted region of PM 2.5)",decreased,"k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",3384189|32066;1783272|201174|1760;3384189|32066|203490;1783272|201174|1760|2037;3384189|32066|203490|203491;3379134|1224|28216|206351;3379134|29547|3031852|213849;1783272|201174|1760|85006|1268;3384189|32066|203490|203491|203492;3379134|1224|28216|206351|481;3384189|32066|203490|203491|1129771;1783272|201174|1760|2037|2049;1783272|201174|1760|85006|1268|32207;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|265975;1783272|201174|1760|2037|2049|1654;3379134|29547|3031852|213849|72294|194;3379134|1224|28216|206351|481|482,Complete,Shaimaa Elsafoury
bsdb:31138779/1/1,31138779,laboratory experiment,31138779,10.1038/s41419-019-1638-6,NA,"Lv J., Jia Y., Li J., Kuai W., Li Y., Guo F., Xu X., Zhao Z., Lv J. , Li Z.",Gegen Qinlian decoction enhances the effect of PD-1 blockade in colorectal cancer with microsatellite stability by remodelling the gut microbiota and the tumour microenvironment,Cell death & disease,2019,NA,Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,non-GQD,low-dose GQD (300 mg/kg),"BALB/c mice (male, ~20 g, aged 5 weeks) were fed adaptively for 1 week under specific pathogen-free conditions with food and water provided ad libitum.  Then the mice were
orally gavaged with 300 mg/kg Gegen Qinlian decoction (GQD), a classical
traditional Chinese medicine (TCM) formula, once a day for 10 days.  The mouse colorectal carcinoma cell line CT26  (~2.5 × 106 cells/mouse) were transplanted subcutaneously
into the left axillary region of each mouse and allowed ~1 week to establish tumours.",20,23,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3c,4 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1,WikiWorks",Differential microbial abundance between the GQD (300 mg/kg) vs. the non-GQD groups based on the Wilcoxon rank-sum test.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium CIEAF 012,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus|s__Proteus mirabilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas",1783272|1239|526524|526525|128827|1470349;1783272|1239|186801|186802|1159214;1783272|1239|91061|186826|33958|1578;3379134|1224|1236|91347|1903414|583|584;1783272|1239|186801|186802|31979|1485|1522;1783272|1239|526524|526525|128827;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|3085636|186803|841;95818|2093818|2093825|2171986|1331051,Complete,Claregrieve1
bsdb:31138779/1/2,31138779,laboratory experiment,31138779,10.1038/s41419-019-1638-6,NA,"Lv J., Jia Y., Li J., Kuai W., Li Y., Guo F., Xu X., Zhao Z., Lv J. , Li Z.",Gegen Qinlian decoction enhances the effect of PD-1 blockade in colorectal cancer with microsatellite stability by remodelling the gut microbiota and the tumour microenvironment,Cell death & disease,2019,NA,Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,non-GQD,low-dose GQD (300 mg/kg),"BALB/c mice (male, ~20 g, aged 5 weeks) were fed adaptively for 1 week under specific pathogen-free conditions with food and water provided ad libitum.  Then the mice were
orally gavaged with 300 mg/kg Gegen Qinlian decoction (GQD), a classical
traditional Chinese medicine (TCM) formula, once a day for 10 days.  The mouse colorectal carcinoma cell line CT26  (~2.5 × 106 cells/mouse) were transplanted subcutaneously
into the left axillary region of each mouse and allowed ~1 week to establish tumours.",20,23,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 3c,4 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1,WikiWorks",Differential microbial abundance between the GQD (300 mg/kg) vs. the non-GQD groups based on the Wilcoxon rank-sum test.,decreased,"p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus sp.,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__uncultured Oscillibacter sp.",95818|2093818|2093825|2171986|1331051;1783272|1239|186801|186802|186807;1783272|1239|91061|1385|90964|1279|29387;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|186802|216572|459786|876091,Complete,Claregrieve1
bsdb:31138779/2/1,31138779,laboratory experiment,31138779,10.1038/s41419-019-1638-6,NA,"Lv J., Jia Y., Li J., Kuai W., Li Y., Guo F., Xu X., Zhao Z., Lv J. , Li Z.",Gegen Qinlian decoction enhances the effect of PD-1 blockade in colorectal cancer with microsatellite stability by remodelling the gut microbiota and the tumour microenvironment,Cell death & disease,2019,NA,Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,non-GQD,low-dose GQD (300 mg/kg),"BALB/c mice (male, ~20 g, aged 5 weeks) were fed adaptively for 1 week under specific pathogen-free conditions with food and water provided ad libitum.  Then the mice were orally lavaged with 300 mg/kg Gegen Qinlian decoction (GQD), a classical
traditional Chinese medicine (TCM) formula, once a day for 10 days.  The mouse colorectal carcinoma cell line CT26  (~2.5 × 106 cells/mouse) were transplanted subcutaneously into the left axillary region of each mouse and allowed ~1 week to establish tumours.",20,23,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3d,4 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1,WikiWorks",Differential microbial abundance between the GQD (300 mg/kg) vs. the non-GQD groups based on LefSe analysis (LDA > 2),increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium CIEAF 012,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus murinus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus|s__Proteus mirabilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__uncultured Roseburia sp.",1783272|1239|526524|526525|128827|1470349;1783272|1239|186801|186802|1159214;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|91061|186826|33958|2767887|1622;3379134|1224|1236|91347|1903414|583;3379134|1224|1236|91347|1903414|583|584;1783272|1239|186801|186802|31979|1485|1522;1783272|1239|526524|526525|128827;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|3085636|186803|841|512314,Complete,Claregrieve1
bsdb:31138779/2/2,31138779,laboratory experiment,31138779,10.1038/s41419-019-1638-6,NA,"Lv J., Jia Y., Li J., Kuai W., Li Y., Guo F., Xu X., Zhao Z., Lv J. , Li Z.",Gegen Qinlian decoction enhances the effect of PD-1 blockade in colorectal cancer with microsatellite stability by remodelling the gut microbiota and the tumour microenvironment,Cell death & disease,2019,NA,Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,non-GQD,low-dose GQD (300 mg/kg),"BALB/c mice (male, ~20 g, aged 5 weeks) were fed adaptively for 1 week under specific pathogen-free conditions with food and water provided ad libitum.  Then the mice were orally lavaged with 300 mg/kg Gegen Qinlian decoction (GQD), a classical
traditional Chinese medicine (TCM) formula, once a day for 10 days.  The mouse colorectal carcinoma cell line CT26  (~2.5 × 106 cells/mouse) were transplanted subcutaneously into the left axillary region of each mouse and allowed ~1 week to establish tumours.",20,23,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 3D,4 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1,WikiWorks",Differential microbial abundance between the GQD (300 mg/kg) vs. the non-GQD groups based on LefSe analysis (LDA > 2),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__uncultured Bacteroidales bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,p__Candidatus Saccharimonadota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp.",3379134|976|200643|171549|194843;3379134|1224|1236;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|186801|186802|186807;1783272|1239|91061|1385;1783272|1239|91061|1385|90964|1279;95818|2093818|2093825|2171986|1331051;95818;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|186802|216572|459786|1945593,Complete,Claregrieve1
bsdb:31138779/3/1,31138779,laboratory experiment,31138779,10.1038/s41419-019-1638-6,NA,"Lv J., Jia Y., Li J., Kuai W., Li Y., Guo F., Xu X., Zhao Z., Lv J. , Li Z.",Gegen Qinlian decoction enhances the effect of PD-1 blockade in colorectal cancer with microsatellite stability by remodelling the gut microbiota and the tumour microenvironment,Cell death & disease,2019,NA,Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,control,low-dose GQD (300 mg/kg) + PD-1,"BALB/c mice (male, ~20 g, aged 5 weeks) were fed adaptively for 1 week under specific pathogen-free conditions with food and water provided ad libitum.  Then the mice were orally gavaged with 300 mg/kg Gegen Qinlian decoction (GQD), a classical traditional Chinese medicine (TCM) formula, once a day for 10 days.  The mouse colorectal carcinoma cell line CT26  (~2.5 × 106 cells/mouse) were transplanted subcutaneously into the left axillary region of each mouse and allowed ~1 week to establish tumours.  When the tumours reached a size of 50mm3, the mice were intraperitoneally (i.p.) injected with 250 μg of anti-mouse PD-1 mAb.  The mice in the control group were administered the same volume of PBS. All mice were injected five times at 3-day intervals with antimouse PD-1 mAb or PBS",11,12,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 4f,13 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1,WikiWorks",Differential microbial abundance between the GQD (300 mg/kg) + PD-1 group vs. the control group based on the Wilcoxon rank-sum test.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__uncultured Eubacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Mycoplasmatota|c__Mollicutes",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549;3379134|976|200643|171549|815|816|85831;1783272|1239|526524|526525|128827|1470349;1783272|1239|186801|186802|1898207;1783272|1239|186801|3085636|186803|1898203;1783272|1239|186801|186802|186807;3379134|976|200643|171549|171552;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|186802|186806|1730|165185;1783272|1239|186801|186802|216572|707003;1783272|1239|186801|186802|186806|1730|39497;1783272|544448|31969,Complete,Claregrieve1
bsdb:31138779/3/2,31138779,laboratory experiment,31138779,10.1038/s41419-019-1638-6,NA,"Lv J., Jia Y., Li J., Kuai W., Li Y., Guo F., Xu X., Zhao Z., Lv J. , Li Z.",Gegen Qinlian decoction enhances the effect of PD-1 blockade in colorectal cancer with microsatellite stability by remodelling the gut microbiota and the tumour microenvironment,Cell death & disease,2019,NA,Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,control,low-dose GQD (300 mg/kg) + PD-1,"BALB/c mice (male, ~20 g, aged 5 weeks) were fed adaptively for 1 week under specific pathogen-free conditions with food and water provided ad libitum.  Then the mice were orally gavaged with 300 mg/kg Gegen Qinlian decoction (GQD), a classical traditional Chinese medicine (TCM) formula, once a day for 10 days.  The mouse colorectal carcinoma cell line CT26  (~2.5 × 106 cells/mouse) were transplanted subcutaneously into the left axillary region of each mouse and allowed ~1 week to establish tumours.  When the tumours reached a size of 50mm3, the mice were intraperitoneally (i.p.) injected with 250 μg of anti-mouse PD-1 mAb.  The mice in the control group were administered the same volume of PBS. All mice were injected five times at 3-day intervals with antimouse PD-1 mAb or PBS",11,12,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Fig 4f,14 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1,WikiWorks",Differential microbial abundance between GQD(300mg/kg)+PD-1 group and control group,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__uncultured Bacteroidales bacterium,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas|s__uncultured Candidatus Saccharimonas sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__uncultured Coprococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__uncultured Eubacteriales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__uncultured Ruminiclostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium",1783272|1239|186801|186802|216572|244127|1872531;1783272|201174|1760|85004|31953|1678|28025;95818|2093818|2093825|2171986|1331051;1783272|1239|186801|3085636|186803|841|2049040;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|194843;95818|2093818|2093825|2171986|1331051|1983405;1783272|1239|186801|3085636|186803|33042|458253;1783272|1239|186801|186802|172733;1783272|1239|186801|186802|216572|1508657|1757166;1783272|1239|186801|186802|216572|2485925;1783272|1239|186801|186802|1898207,Complete,Claregrieve1
bsdb:31138779/4/1,31138779,laboratory experiment,31138779,10.1038/s41419-019-1638-6,NA,"Lv J., Jia Y., Li J., Kuai W., Li Y., Guo F., Xu X., Zhao Z., Lv J. , Li Z.",Gegen Qinlian decoction enhances the effect of PD-1 blockade in colorectal cancer with microsatellite stability by remodelling the gut microbiota and the tumour microenvironment,Cell death & disease,2019,NA,Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,control,low-dose GQD (300 mg/kg),"BALB/c mice (male, ~20 g, aged 5 weeks) were fed adaptively for 1 week under specific pathogen-free conditions with food and water provided ad libitum.  Then the mice were orally gavaged with 300 mg/kg Gegen Qinlian decoction (GQD), a classical traditional Chinese medicine (TCM) formula, once a day for 10 days.  The mouse colorectal carcinoma cell line CT26  (~2.5 × 106 cells/mouse) were transplanted subcutaneously into the left axillary region of each mouse and allowed ~1 week to establish tumours.  When the tumours reached a size of 50mm3, the mice were intraperitoneally (i.p.) injected with 250 μg of anti-mouse PD-1 mAb.  The mice in the control group were administered the same volume of PBS. All mice were injected five times at 3-day intervals with antimouse PD-1 mAb or PBS",11,12,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Supp fig S6D,15 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1,WikiWorks",Differential microbial abundance between GQD(300mg/kg) treated mice and controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|186801|3085636|186803|1649459;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;1783272|201174|84998|84999|84107,Complete,Claregrieve1
bsdb:31138779/4/2,31138779,laboratory experiment,31138779,10.1038/s41419-019-1638-6,NA,"Lv J., Jia Y., Li J., Kuai W., Li Y., Guo F., Xu X., Zhao Z., Lv J. , Li Z.",Gegen Qinlian decoction enhances the effect of PD-1 blockade in colorectal cancer with microsatellite stability by remodelling the gut microbiota and the tumour microenvironment,Cell death & disease,2019,NA,Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,control,low-dose GQD (300 mg/kg),"BALB/c mice (male, ~20 g, aged 5 weeks) were fed adaptively for 1 week under specific pathogen-free conditions with food and water provided ad libitum.  Then the mice were orally gavaged with 300 mg/kg Gegen Qinlian decoction (GQD), a classical traditional Chinese medicine (TCM) formula, once a day for 10 days.  The mouse colorectal carcinoma cell line CT26  (~2.5 × 106 cells/mouse) were transplanted subcutaneously into the left axillary region of each mouse and allowed ~1 week to establish tumours.  When the tumours reached a size of 50mm3, the mice were intraperitoneally (i.p.) injected with 250 μg of anti-mouse PD-1 mAb.  The mice in the control group were administered the same volume of PBS. All mice were injected five times at 3-day intervals with antimouse PD-1 mAb or PBS",11,12,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,supp fig S6,15 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1,WikiWorks",Differential microbial abundance between GQD(300mg/kg) treated mice and controls,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Thermoproteati|p__Thermoproteota|c__Thermoprotei|o__Desulfurococcales|f__Desulfurococcaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] brachy,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|201174;1783272|544448|31969|186332|186333|2086;1783272|544448|31969|186332|186333;1783272|544448|31969|186332;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3082768|990719;1783272|1239|186801|3085636|186803|33042;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;28221;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115;1783275|28889|183924|114380|2272;1783272|201174|84998|1643822|1643826|580024;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|3082720|543314|35517;3379134|976|200643|171549;1783272|1239|186801|3082768|990719;1783272|1239|186801|3085636|186803,Complete,Claregrieve1
bsdb:31138779/5/1,31138779,laboratory experiment,31138779,10.1038/s41419-019-1638-6,NA,"Lv J., Jia Y., Li J., Kuai W., Li Y., Guo F., Xu X., Zhao Z., Lv J. , Li Z.",Gegen Qinlian decoction enhances the effect of PD-1 blockade in colorectal cancer with microsatellite stability by remodelling the gut microbiota and the tumour microenvironment,Cell death & disease,2019,NA,Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,control,PD-1 group,"BALB/c mice (male, ~20 g, aged 5 weeks) were fed adaptively for 1 week under specific pathogen-free conditions with food and water provided ad libitum.  Then the mice were orally gavaged with 300 mg/kg Gegen Qinlian decoction (GQD), a classical traditional Chinese medicine (TCM) formula, once a day for 10 days.  The mouse colorectal carcinoma cell line CT26  (~2.5 × 106 cells/mouse) were transplanted subcutaneously into the left axillary region of each mouse and allowed ~1 week to establish tumours.  When the tumours reached a size of 50mm3, the mice were intraperitoneally (i.p.) injected with 250 μg of anti-mouse PD-1 mAb.  The mice in the control group were administered the same volume of PBS. All mice were injected five times at 3-day intervals with antimouse PD-1 mAb or PBS",11,9,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,supp fig S6,17 September 2022,Mary Bearkland,"Mary Bearkland,WikiWorks",Supplementary Figure S6:  (E) LDA scores computed for differentially abundant taxa in the faecal microbiomes of mice from each group.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Mycoplasmatota",1783272|201174|84998|1643822|1643826|447020;1783272|544448|31969|186332|186333|2086;1783272|544448|31969|186332|186333;1783272|544448|31969|186332;1783272|1239|526524|526525|2810280|1505663;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|3085636|186803|1649459;1783272|544448|31969;1783272|544448,Complete,Claregrieve1
bsdb:31138779/5/2,31138779,laboratory experiment,31138779,10.1038/s41419-019-1638-6,NA,"Lv J., Jia Y., Li J., Kuai W., Li Y., Guo F., Xu X., Zhao Z., Lv J. , Li Z.",Gegen Qinlian decoction enhances the effect of PD-1 blockade in colorectal cancer with microsatellite stability by remodelling the gut microbiota and the tumour microenvironment,Cell death & disease,2019,NA,Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,control,PD-1 group,"BALB/c mice (male, ~20 g, aged 5 weeks) were fed adaptively for 1 week under specific pathogen-free conditions with food and water provided ad libitum.  Then the mice were orally gavaged with 300 mg/kg Gegen Qinlian decoction (GQD), a classical traditional Chinese medicine (TCM) formula, once a day for 10 days.  The mouse colorectal carcinoma cell line CT26  (~2.5 × 106 cells/mouse) were transplanted subcutaneously into the left axillary region of each mouse and allowed ~1 week to establish tumours.  When the tumours reached a size of 50mm3, the mice were intraperitoneally (i.p.) injected with 250 μg of anti-mouse PD-1 mAb.  The mice in the control group were administered the same volume of PBS. All mice were injected five times at 3-day intervals with antimouse PD-1 mAb or PBS",11,9,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,supp fig S6,17 September 2022,Mary Bearkland,"Mary Bearkland,WikiWorks",Supplementary Figure S6:  (E) LDA scores computed for differentially abundant taxa in the faecal microbiomes of mice from each group.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota",1783272|1239|186801|186802|216572|459786;1783272|1239,Complete,Claregrieve1
bsdb:31138779/6/1,31138779,laboratory experiment,31138779,10.1038/s41419-019-1638-6,NA,"Lv J., Jia Y., Li J., Kuai W., Li Y., Guo F., Xu X., Zhao Z., Lv J. , Li Z.",Gegen Qinlian decoction enhances the effect of PD-1 blockade in colorectal cancer with microsatellite stability by remodelling the gut microbiota and the tumour microenvironment,Cell death & disease,2019,NA,Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,control,low dose 300 mg/kg GQD + PD-1 group,"BALB/c mice (male, ~20 g, aged 5 weeks) were fed adaptively for 1 week under specific pathogen-free conditions with food and water provided ad libitum.  Then the mice were orally gavaged with 300 mg/kg Gegen Qinlian decoction (GQD), a classical traditional Chinese medicine (TCM) formula, once a day for 10 days.  The mouse colorectal carcinoma cell line CT26  (~2.5 × 106 cells/mouse) were transplanted subcutaneously into the left axillary region of each mouse and allowed ~1 week to establish tumours.  When the tumours reached a size of 50mm3, the mice were intraperitoneally (i.p.) injected with 250 μg of anti-mouse PD-1 mAb.  The mice in the control group were administered the same volume of PBS. All mice were injected five times at 3-day intervals with antimouse PD-1 mAb or PBS",11,12,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,supp fig S6,17 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1,WikiWorks",Differentially abundant taxa between control mice and mice treated with 300mg/kg GQD + PD-1,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|526524|526525|128827|1470349;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|1508657;3379134|976|200643|171549|171552;1783272|1239|186801|186802|541000,Complete,Claregrieve1
bsdb:31138779/6/2,31138779,laboratory experiment,31138779,10.1038/s41419-019-1638-6,NA,"Lv J., Jia Y., Li J., Kuai W., Li Y., Guo F., Xu X., Zhao Z., Lv J. , Li Z.",Gegen Qinlian decoction enhances the effect of PD-1 blockade in colorectal cancer with microsatellite stability by remodelling the gut microbiota and the tumour microenvironment,Cell death & disease,2019,NA,Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,control,low dose 300 mg/kg GQD + PD-1 group,"BALB/c mice (male, ~20 g, aged 5 weeks) were fed adaptively for 1 week under specific pathogen-free conditions with food and water provided ad libitum.  Then the mice were orally gavaged with 300 mg/kg Gegen Qinlian decoction (GQD), a classical traditional Chinese medicine (TCM) formula, once a day for 10 days.  The mouse colorectal carcinoma cell line CT26  (~2.5 × 106 cells/mouse) were transplanted subcutaneously into the left axillary region of each mouse and allowed ~1 week to establish tumours.  When the tumours reached a size of 50mm3, the mice were intraperitoneally (i.p.) injected with 250 μg of anti-mouse PD-1 mAb.  The mice in the control group were administered the same volume of PBS. All mice were injected five times at 3-day intervals with antimouse PD-1 mAb or PBS",11,12,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supp fig S6,17 September 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1,WikiWorks",Differentially abundant taxa between control mice and mice treated with 300mg/kg GQD + PD-1,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,p__Candidatus Saccharimonadota",1783272|1239|186801|186802|216572|244127;3379134|976|200643|171549;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;95818,Complete,Claregrieve1
bsdb:31141234/1/1,31141234,case-control,31141234,10.1111/1346-8138.14933,NA,"Shapiro J., Cohen N.A., Shalev V., Uzan A., Koren O. , Maharshak N.",Psoriatic patients have a distinct structural and functional fecal microbiota compared with controls,The Journal of dermatology,2019,"bacteria, inflammation, metabolome, microbiota, psoriasis",Experiment 1,Israel,Homo sapiens,Feces,UBERON:0001988,Psoriasis,EFO:0000676,healthy controls,psoriasis,patients with active psoriatic disease diagnosed by a senior dermatologist,22,24,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,"age,comorbidity,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4,10 January 2021,Rimsha Azhar,WikiWorks,Comparison of genera signatures between psoriatic patients and the control participants,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|216851;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3082768|990719|990721;1783272|201174|1760|2037|2049|1654;1783272|201174|84998|84999|84107|102106,Complete,NA
bsdb:31141234/1/2,31141234,case-control,31141234,10.1111/1346-8138.14933,NA,"Shapiro J., Cohen N.A., Shalev V., Uzan A., Koren O. , Maharshak N.",Psoriatic patients have a distinct structural and functional fecal microbiota compared with controls,The Journal of dermatology,2019,"bacteria, inflammation, metabolome, microbiota, psoriasis",Experiment 1,Israel,Homo sapiens,Feces,UBERON:0001988,Psoriasis,EFO:0000676,healthy controls,psoriasis,patients with active psoriatic disease diagnosed by a senior dermatologist,22,24,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,"age,comorbidity,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4,10 January 2021,Rimsha Azhar,WikiWorks,Comparison of genera signatures between psoriatic patients and the control participants,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",3379134|976|200643|171549|1853231|574697;3379134|200940|3031449|213115|194924|35832;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|838;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|3085636|186803|28050;3379134|976|200643|171549|171552|577309,Complete,NA
bsdb:31141574/1/1,31141574,laboratory experiment,31141574,10.1371/journal.pone.0217553,NA,"Deshpande N.G., Saxena J., Pesaresi T.G., Carrell C.D., Ashby G.B., Liao M.K. , Freeman L.R.",High fat diet alters gut microbiota but not spatial working memory in early middle-aged Sprague Dawley rats,PloS one,2019,NA,Experiment 1,United States of America,Rattus norvegicus,Feces,UBERON:0001988,Diet,EFO:0002755,low fat diet,high fat diet,"High fat diet rats were fed (20% protein, 35% carbohydrate, 45% fat by calories).  Controls or low fat diet were fed (20% protein, 70% carbohydrate, 10% fat by calories) for eight weeks.",6,6,NA,16S,NA,Roche454,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 1,10 January 2021,Lora Kasselman,WikiWorks,Mean relative abundances for gut genera and p-value for differences between high-fat and control animals are listed. Class and phylum are indicated as well,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|186828|117563;1783272|1239|186801|186802|216572|1486725;1783272|1239|186801|3082720|543314|109326;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572|100175;1783272|1239|186801|186802|216572|1017280;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|3085636|186803|1506577;1783272|1239|526524|526525|2810280|1505663;1783272|1239|526524|526525|128827|61170;1783272|201174|1760|85006|1268|32207;1783272|201174|84998|1643822|1643826|447020;1783272|201174|84998|84999|84107|102106,Complete,Shaimaa Elsafoury
bsdb:31141574/1/2,31141574,laboratory experiment,31141574,10.1371/journal.pone.0217553,NA,"Deshpande N.G., Saxena J., Pesaresi T.G., Carrell C.D., Ashby G.B., Liao M.K. , Freeman L.R.",High fat diet alters gut microbiota but not spatial working memory in early middle-aged Sprague Dawley rats,PloS one,2019,NA,Experiment 1,United States of America,Rattus norvegicus,Feces,UBERON:0001988,Diet,EFO:0002755,low fat diet,high fat diet,"High fat diet rats were fed (20% protein, 35% carbohydrate, 45% fat by calories).  Controls or low fat diet were fed (20% protein, 70% carbohydrate, 10% fat by calories) for eight weeks.",6,6,NA,16S,NA,Roche454,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 1,10 January 2021,Lora Kasselman,WikiWorks,Mean relative abundances for gut genera and p-value for differences between high-fat and control animals are listed. Class and phylum are indicated as well,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella",3379134|1224|1236|91347|543|544;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|588605,Complete,Shaimaa Elsafoury
bsdb:31151886/1/1,31151886,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A., Jones H.E., Beghini F., Segata N., Zolnik C.P., Usyk M., Moody T.U., Thorpe L., Burk R., Waldron L. , Dowd J.B.",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,College graduate or more,Less than High school diploma,Less than High school diploma,87,65,NA,16S,4,Illumina,relative abundances,edgeR,0.01,TRUE,NA,NA,education level,NA,NA,unchanged,NA,NA,NA,Signature 1,Spreadsheet,13 April 2023,Kelvin Joseph,"Kelvin Joseph,Atrayees,WikiWorks",The relative abundance of selected species based on education level.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,3379134|976|200643|171549|171552|1283313,Complete,Atrayees
bsdb:31151886/1/2,31151886,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A., Jones H.E., Beghini F., Segata N., Zolnik C.P., Usyk M., Moody T.U., Thorpe L., Burk R., Waldron L. , Dowd J.B.",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,College graduate or more,Less than High school diploma,Less than High school diploma,87,65,NA,16S,4,Illumina,relative abundances,edgeR,0.01,TRUE,NA,NA,education level,NA,NA,unchanged,NA,NA,NA,Signature 2,Spreadsheet,15 June 2023,Atrayees,"Atrayees,WikiWorks",The relative abundance of selected species based on education level.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|976|200643|171549|171551|836;3379134|29547|3031852|213849|72294|194;3379134|976|200643|171549|171552|838;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|3082720|3118655|44259;1783272|201174|1760|85004|31953|196081;1783272|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:31151886/2/1,31151886,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A., Jones H.E., Beghini F., Segata N., Zolnik C.P., Usyk M., Moody T.U., Thorpe L., Burk R., Waldron L. , Dowd J.B.",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,College graduate or more,Some college or associate's degree,Some college or associate's degree,87,67,NA,16S,4,Illumina,relative abundances,edgeR,0.01,TRUE,NA,NA,education level,NA,NA,unchanged,NA,NA,NA,Signature 1,Spreadsheet,1 May 2023,Kelvin Joseph,"Kelvin Joseph,Atrayees,WikiWorks",The relative abundance of selected species based on education level.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,1783272|201174|1760|85007|1653|1716,Complete,Atrayees
bsdb:31151886/2/2,31151886,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A., Jones H.E., Beghini F., Segata N., Zolnik C.P., Usyk M., Moody T.U., Thorpe L., Burk R., Waldron L. , Dowd J.B.",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,College graduate or more,Some college or associate's degree,Some college or associate's degree,87,67,NA,16S,4,Illumina,relative abundances,edgeR,0.01,TRUE,NA,NA,education level,NA,NA,unchanged,NA,NA,NA,Signature 2,Spreadsheet,2 May 2023,Kelvin Joseph,"Kelvin Joseph,Atrayees,WikiWorks",The relative abundance of selected species based on education level.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|85004|31953|196081;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|171552|1283313;1783272|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:31151886/3/1,31151886,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A., Jones H.E., Beghini F., Segata N., Zolnik C.P., Usyk M., Moody T.U., Thorpe L., Burk R., Waldron L. , Dowd J.B.",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Cigarette smokers,Alternative smokers,Alternative smokers,86,72,NA,16S,4,Illumina,relative abundances,edgeR,0.01,TRUE,NA,NA,smoking status,NA,NA,unchanged,NA,NA,NA,Signature 1,Spreadsheet,2 May 2023,Kelvin Joseph,"Kelvin Joseph,Atrayees,WikiWorks",The relative abundance of selected species in cigarette smokers and alternate smokers,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum",1783272|1239|909932|1843489|31977|156454;3379134|1224|1236|72274|135621|286;1783272|1239|91061|186826|1300|1301;1783272|201174|1760|85004|31953|419014;1783272|201174|1760|2037|2049|1654;1783272|1239|186801|3085636|186803|1213720,Complete,Atrayees
bsdb:31151886/3/2,31151886,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A., Jones H.E., Beghini F., Segata N., Zolnik C.P., Usyk M., Moody T.U., Thorpe L., Burk R., Waldron L. , Dowd J.B.",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Cigarette smokers,Alternative smokers,Alternative smokers,86,72,NA,16S,4,Illumina,relative abundances,edgeR,0.01,TRUE,NA,NA,smoking status,NA,NA,unchanged,NA,NA,NA,Signature 2,Spreadsheet,2 May 2023,Kelvin Joseph,"Kelvin Joseph,Atrayees,WikiWorks",The relative abundance of selected species in cigarette smokers and alternate smokers,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella",3384189|32066|203490|203491|203492|848;3379134|1224|28216|206351|481|482;3384189|32066|203490|203491|1129771|34104;3379134|976|200643|171549|171551|836;3379134|976|117743|200644|2762318|59735;3379134|1224|28216|80840|119060|47670;3379134|1224|1236|135615|868|2717;1783272|1239|91061|1385|539738|1378;3379134|976|200643|171549|171552|1283313,Complete,Atrayees
bsdb:31151886/4/1,31151886,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A., Jones H.E., Beghini F., Segata N., Zolnik C.P., Usyk M., Moody T.U., Thorpe L., Burk R., Waldron L. , Dowd J.B.",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Cigarette smokers,Former smokers,Former smokers,86,43,NA,16S,4,Illumina,relative abundances,edgeR,0.01,TRUE,NA,NA,smoking status,NA,NA,unchanged,NA,NA,NA,Signature 1,Spreadsheet,2 May 2023,Kelvin Joseph,"Kelvin Joseph,Atrayees,WikiWorks",The relative abundance of selected species in cigarette smokers and former smokers,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|171552|1283313;3379134|29547|3031852|213849|72294|194;3379134|976|200643|171549|171552|838;3379134|1224|1236|72274|135621|286,Complete,Atrayees
bsdb:31151886/4/2,31151886,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A., Jones H.E., Beghini F., Segata N., Zolnik C.P., Usyk M., Moody T.U., Thorpe L., Burk R., Waldron L. , Dowd J.B.",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Cigarette smokers,Former smokers,Former smokers,86,43,NA,16S,4,Illumina,relative abundances,edgeR,0.01,TRUE,NA,NA,smoking status,NA,NA,unchanged,NA,NA,NA,Signature 2,Spreadsheet,15 June 2023,Atrayees,"Atrayees,WikiWorks",The relative abundance of selected species in cigarette smokers and former smokers,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga",3379134|1224|28216|206351|481|482;3379134|976|117743|200644|2762318|59735;3379134|1224|28216|80840|119060|47670;3379134|1224|1236|135625|712|724;1783272|1239|186801|186802|186807|2740;3379134|976|117743|200644|49546|1016,Complete,Atrayees
bsdb:31151886/5/1,31151886,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A., Jones H.E., Beghini F., Segata N., Zolnik C.P., Usyk M., Moody T.U., Thorpe L., Burk R., Waldron L. , Dowd J.B.",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 5,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Cigarette smokers,Never smokers,Never smokers,86,43,NA,16S,4,Illumina,relative abundances,edgeR,0.01,TRUE,NA,NA,smoking status,NA,NA,unchanged,NA,NA,NA,Signature 1,Spreadsheet,15 June 2023,Atrayees,"Atrayees,WikiWorks",The relative abundance of selected species in cigarette smokers and never smokers,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3085636|186803|1213720;3379134|976|200643|171549|171552|838;3379134|29547|3031852|213849|72294|194;3384189|32066|203490|203491|1129771|32067;1783272|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:31151886/5/2,31151886,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A., Jones H.E., Beghini F., Segata N., Zolnik C.P., Usyk M., Moody T.U., Thorpe L., Burk R., Waldron L. , Dowd J.B.",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 5,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Cigarette smokers,Never smokers,Never smokers,86,43,NA,16S,4,Illumina,relative abundances,edgeR,0.01,TRUE,NA,NA,smoking status,NA,NA,unchanged,NA,NA,NA,Signature 2,Spreadsheet,15 June 2023,Atrayees,"Atrayees,WikiWorks",The relative abundance of selected species in cigarette smokers and never smokers,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus",3379134|1224|28216|206351|481|482;3379134|976|117743|200644|2762318|59735;1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|171551|836;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|1300|1357;3379134|1224|1236|135625|712|724;3379134|1224|28216|80840|119060|47670;1783272|201174|1760|85004|31953|1678;3379134|1224|1236|135625|712|713,Complete,Atrayees
bsdb:31151886/6/1,31151886,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A., Jones H.E., Beghini F., Segata N., Zolnik C.P., Usyk M., Moody T.U., Thorpe L., Burk R., Waldron L. , Dowd J.B.",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 6,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Cigarette smokers,Secondhand smokers,Secondhand smokers,86,38,NA,16S,4,Illumina,relative abundances,edgeR,0.01,TRUE,NA,NA,smoking status,NA,NA,unchanged,NA,NA,NA,Signature 1,Spreadsheet,15 June 2023,Atrayees,"Atrayees,WikiWorks",The relative abundance of selected species in cigarette smokers and secondhand smokers,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",1783272|1239|909932|1843489|31977|29465;3384189|32066|203490|203491|1129771|32067;1783272|1239|91061|186826|33958|1578;33090|35493|3398|72025|3803|3814|508215;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|156454;1783272|201174|1760|2037|2049|1654,Complete,Atrayees
bsdb:31151886/6/2,31151886,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A., Jones H.E., Beghini F., Segata N., Zolnik C.P., Usyk M., Moody T.U., Thorpe L., Burk R., Waldron L. , Dowd J.B.",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 6,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Cigarette smokers,Secondhand smokers,Secondhand smokers,86,38,NA,16S,4,Illumina,relative abundances,edgeR,0.01,TRUE,NA,NA,smoking status,NA,NA,unchanged,NA,NA,NA,Signature 2,Spreadsheet,15 June 2023,Atrayees,"Atrayees,WikiWorks",The relative abundance of selected species in cigarette smokers and secondhand smokers,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|976|117743|200644|2762318|59735;1783272|1239|186801|3082720|186804|1257;1783272|1239|91061|1385|539738|1378;3379134|976|200643|171549|171552|1283313;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|838,Complete,Atrayees
bsdb:31151886/7/1,31151886,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A., Jones H.E., Beghini F., Segata N., Zolnik C.P., Usyk M., Moody T.U., Thorpe L., Burk R., Waldron L. , Dowd J.B.",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 7,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Non-Hispanic white,Asian,Asian,97,22,NA,16S,4,Illumina,relative abundances,edgeR,0.01,TRUE,NA,NA,race,NA,NA,unchanged,NA,NA,NA,Signature 1,Spreadsheet,15 June 2023,Atrayees,"Atrayees,WikiWorks",The relative abundance of selected species in Non-Hispanic whites and Asians.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,3379134|976|200643|171549|171552|1283313,Complete,Atrayees
bsdb:31151886/8/1,31151886,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A., Jones H.E., Beghini F., Segata N., Zolnik C.P., Usyk M., Moody T.U., Thorpe L., Burk R., Waldron L. , Dowd J.B.",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 8,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Non-Hispanic white,Hispanic,Hispanics,97,71,NA,16S,4,Illumina,relative abundances,edgeR,0.01,TRUE,NA,NA,race,NA,NA,unchanged,NA,NA,NA,Signature 1,Spreadsheet,15 June 2023,Atrayees,"Atrayees,WikiWorks",The relative abundance of selected species in Non-Hispanic whites and Hispanics,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171551|836;3379134|29547|3031852|213849|72294|194;1783272|1239|186801|3082720|3118655|44259;3379134|203691|203692|136|2845253|157;3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|171552|1283313;1783272|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:31151886/9/1,31151886,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A., Jones H.E., Beghini F., Segata N., Zolnik C.P., Usyk M., Moody T.U., Thorpe L., Burk R., Waldron L. , Dowd J.B.",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 9,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Non-Hispanic white,Non-Hispanic black,Non-Hispanic black,97,75,NA,16S,4,Illumina,relative abundances,edgeR,0.01,TRUE,NA,NA,race,NA,NA,unchanged,NA,NA,NA,Signature 1,Spreadsheet,15 June 2023,Atrayees,"Atrayees,WikiWorks",The relative abundance of selected species in Non-Hispanic whites and Non-Hispanic blacks,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus",1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|135615|868|2717;3384189|32066|203490|203491|1129771|34104,Complete,Atrayees
bsdb:31151886/9/2,31151886,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A., Jones H.E., Beghini F., Segata N., Zolnik C.P., Usyk M., Moody T.U., Thorpe L., Burk R., Waldron L. , Dowd J.B.",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 9,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Non-Hispanic white,Non-Hispanic black,Non-Hispanic black,97,75,NA,16S,4,Illumina,relative abundances,edgeR,0.01,TRUE,NA,NA,race,NA,NA,unchanged,NA,NA,NA,Signature 2,Spreadsheet,15 June 2023,Atrayees,"Atrayees,WikiWorks",The relative abundance of selected species in Non-Hispanic whites and Non-Hispanic blacks,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Acholeplasma,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",3379134|976|200643|171549|171552|838;3379134|29547|3031852|213849|72294|194;1783272|201174|84998|84999|1643824|1380;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|156454;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3082720|3118655|44259;3379134|976|200643|171549|171552|1283313;1783272|544448|31969|186329|2146|2147;3379134|976|200643|171549|171551|836,Complete,Atrayees
bsdb:31151886/10/1,31151886,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A., Jones H.E., Beghini F., Segata N., Zolnik C.P., Usyk M., Moody T.U., Thorpe L., Burk R., Waldron L. , Dowd J.B.",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 10,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Males,Females,Females,132,150,NA,16S,4,Illumina,relative abundances,edgeR,0.01,TRUE,NA,NA,sex,NA,NA,unchanged,NA,NA,NA,Signature 1,Spreadsheet,15 June 2023,Atrayees,"Atrayees,WikiWorks",The relative abundance of selected species in males and females,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",3379134|1224|1236|135625|712|713;3379134|203691|203692|136|2845253|157;3379134|976|200643|171549|171551|836,Complete,Atrayees
bsdb:31151886/11/1,31151886,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A., Jones H.E., Beghini F., Segata N., Zolnik C.P., Usyk M., Moody T.U., Thorpe L., Burk R., Waldron L. , Dowd J.B.",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 11,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,age group 20-29,age group 35-64,age group 35-64,70,NA,NA,16S,4,Illumina,relative abundances,edgeR,0.01,TRUE,NA,NA,age,NA,NA,unchanged,NA,NA,NA,Signature 1,Spreadsheet,15 June 2023,Atrayees,"Atrayees,WikiWorks",The relative abundance of selected species in age group 20-29 and age group 35-64,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus",3379134|976|200643|171549|171551|836;3379134|1224|1236|72274|135621|286;3379134|976|200643|171549|171552|1283313;1783272|201174|84998|84999|1643824|1380;3384189|32066|203490|203491|1129771|32067;3384189|32066|203490|203491|203492|848;3379134|1224|1236|135625|712|713,Complete,Atrayees
bsdb:31151886/11/2,31151886,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A., Jones H.E., Beghini F., Segata N., Zolnik C.P., Usyk M., Moody T.U., Thorpe L., Burk R., Waldron L. , Dowd J.B.",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 11,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,age group 20-29,age group 35-64,age group 35-64,70,NA,NA,16S,4,Illumina,relative abundances,edgeR,0.01,TRUE,NA,NA,age,NA,NA,unchanged,NA,NA,NA,Signature 2,Spreadsheet,15 June 2023,Atrayees,"Atrayees,WikiWorks",The relative abundance of selected species in age group 20-29 and age group 35-64,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|33958|1578;3384189|32066|203490|203491|1129771|32067,Complete,Atrayees
bsdb:31151886/12/1,31151886,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A., Jones H.E., Beghini F., Segata N., Zolnik C.P., Usyk M., Moody T.U., Thorpe L., Burk R., Waldron L. , Dowd J.B.",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 12,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,age group 20-29,age group 65 and over,age group 65 and over,70,NA,NA,16S,4,Illumina,relative abundances,edgeR,0.01,TRUE,NA,NA,age,NA,NA,unchanged,NA,NA,NA,Signature 1,Spreadsheet,15 June 2023,Atrayees,"Atrayees,WikiWorks",The relative abundance of selected species in age group 20-29 and age group 65 and over,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella",3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|171552|838;1783272|1239|186801|3082720|3118655|44259;3384189|32066|203490|203491|1129771|32067;3379134|203691|203692|136|2845253|157;3379134|976|200643|171549|171551|836;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|3085636|186803|43996;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3082720|186804|1257;3379134|1224|1236|135625|712|724;3379134|976|117743|200644|2762318|59735,Complete,Atrayees
bsdb:31151886/12/2,31151886,"cross-sectional observational, not case-control",31151886,https://doi.org/10.1016/j.annepidem.2019.03.006,https://pubmed.ncbi.nlm.nih.gov/31151886/,"Renson A., Jones H.E., Beghini F., Segata N., Zolnik C.P., Usyk M., Moody T.U., Thorpe L., Burk R., Waldron L. , Dowd J.B.",Sociodemographic variation in the oral microbiome,Annals of epidemiology,2019,"Demographics, Health disparities, Oral microbiome, Social epidemiology",Experiment 12,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,age group 20-29,age group 65 and over,age group 65 and over,70,NA,NA,16S,4,Illumina,relative abundances,edgeR,0.01,TRUE,NA,NA,age,NA,NA,unchanged,NA,NA,NA,Signature 2,Spreadsheet,15 June 2023,Atrayees,"Atrayees,WikiWorks",The relative abundance of selected species in age group 20-29 and age group 65 and over,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1301;33090|35493|3398|72025|3803|3814|508215;1783272|1239|91061|186826|1300|1357;3379134|976|117743|200644|49546|1016;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|196081;1783272|1239|909932|1843489|31977|156454,Complete,Atrayees
bsdb:31152265/1/1,31152265,case-control,31152265,10.1007/s10096-019-03598-9,NA,"Zheng Y., Wang Q., Ma L., Chen Y., Gao Y., Zhang G., Cui S., Liang H., He C. , Song L.",Alterations in the skin microbiome are associated with disease severity and treatment in the perioral zone of the skin of infants with atopic dermatitis,European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology,2019,"Atopic dermatitis, Bacterial diversity, Perioral skin, Prevotella melaninogenica",Experiment 1,China,Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,healthy control,severe atopic dermatitis,child with severe atopic dermatitis based on eczema area and severity index (EASI) local rating method,20,20,1 month,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,decreased,increased,NA,decreased,Signature 1,"Table 2, Table 3",10 January 2021,Lucy Mellor,WikiWorks,Different genera of average relative abundance >=0.1% in healthy and severe atopic dermatitis groups,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Alloiococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Tepidimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium simulans,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas yabuuchiae",1783272|1239|91061|1385|90964|1279;1783272|201174|1760|85007|85025|1827;1783272|1239|91061|186826|186828|1651;3379134|1224|28216|80840|114248;1783272|1239|91061|1385|90964|1279|1280;1783272|201174|1760|85007|1653|1716|146827;3379134|1224|28211|204457|41297|13687|172044,Complete,Folakunmi
bsdb:31152265/1/2,31152265,case-control,31152265,10.1007/s10096-019-03598-9,NA,"Zheng Y., Wang Q., Ma L., Chen Y., Gao Y., Zhang G., Cui S., Liang H., He C. , Song L.",Alterations in the skin microbiome are associated with disease severity and treatment in the perioral zone of the skin of infants with atopic dermatitis,European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology,2019,"Atopic dermatitis, Bacterial diversity, Perioral skin, Prevotella melaninogenica",Experiment 1,China,Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,healthy control,severe atopic dermatitis,child with severe atopic dermatitis based on eczema area and severity index (EASI) local rating method,20,20,1 month,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,decreased,increased,NA,decreased,Signature 2,"Table 2, Table 3",10 January 2021,Lucy Mellor,"WikiWorks,Folakunmi",Different genera of average relative abundance >=0.1% in healthy and severe atopic dermatitis groups,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Limnobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella",3379134|1224|28211|356|82115|357;1783272|201174|84998|84999|1643824|1380;3379134|976|200643|171549|171552|2974257|425941;3384189|32066|203490|203491|1129771|32067;3379134|1224|28216|80840|119060|131079;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|28132;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|186828|117563,Complete,Folakunmi
bsdb:31153098/1/1,31153098,case-control,31153098,10.1016/j.archoralbio.2019.05.025,NA,"Farina R., Severi M., Carrieri A., Miotto E., Sabbioni S., Trombelli L. , Scapoli C.",Whole metagenomic shotgun sequencing of the subgingival microbiome of diabetics and non-diabetics with different periodontal conditions,Archives of oral biology,2019,"Biofilms, Dental plaque, Gingival sulcus, Metagenomics, Microbiota, Periodontal pocket, Periodontitis",Experiment 1,Italy,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Periodontitis,EFO:0000649,Individuals without Periodontitis,Periodontitis patients,Patients affected by moderate to severe periodontitis,6,6,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,15 January 2026,Tosin,Tosin,Bacteria genera/species with a nominal significantly difference 0.01 level at White’s non-parametric t-test applied to compare relative abundance between the two groups (patients with and without periodontitis).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae|s__Anaerolineaceae bacterium oral taxon 439,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ottowia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ottowia|s__Ottowia sp. oral taxon 894,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Bacillati|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae|g__Anaerolinea",3379134|1224|1236|135625|712|416916;1783272|200795|292625|292629|292628|1889813;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|39948|39950;3379134|1224|28216|80840|80864|219181;3379134|1224|28216|80840|80864|219181|1658672;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|1737404|1737405|1570339|543311|33033;3379134|976|200643|171549|171551|836|28123;1783272|200795|292625|292629|292628|233189,Complete,KateRasheed
bsdb:31153098/1/2,31153098,case-control,31153098,10.1016/j.archoralbio.2019.05.025,NA,"Farina R., Severi M., Carrieri A., Miotto E., Sabbioni S., Trombelli L. , Scapoli C.",Whole metagenomic shotgun sequencing of the subgingival microbiome of diabetics and non-diabetics with different periodontal conditions,Archives of oral biology,2019,"Biofilms, Dental plaque, Gingival sulcus, Metagenomics, Microbiota, Periodontal pocket, Periodontitis",Experiment 1,Italy,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Periodontitis,EFO:0000649,Individuals without Periodontitis,Periodontitis patients,Patients affected by moderate to severe periodontitis,6,6,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 4,29 January 2026,Tosin,Tosin,Bacteria genera/species with a nominal significantly difference 0.01 level at White’s non-parametric t-test applied to compare relative abundance between the two groups (patients with and without periodontitis).,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microcella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. Chiba101,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microcella|s__Microcella alkaliphila,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris",1783272|201174|1760|85006|85023|337004;1783272|201174|1760|2037|2049|1654|1851395;1783272|201174|1760|85006|85023|337004|279828;1783272|201174|1760|2037|2049|1654|544580,Complete,KateRasheed
bsdb:31153098/2/1,31153098,case-control,31153098,10.1016/j.archoralbio.2019.05.025,NA,"Farina R., Severi M., Carrieri A., Miotto E., Sabbioni S., Trombelli L. , Scapoli C.",Whole metagenomic shotgun sequencing of the subgingival microbiome of diabetics and non-diabetics with different periodontal conditions,Archives of oral biology,2019,"Biofilms, Dental plaque, Gingival sulcus, Metagenomics, Microbiota, Periodontal pocket, Periodontitis",Experiment 2,Italy,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Periodontitis,EFO:0000649,Type 2 diabetes mellitus and periodontitis negative patients (T2D - P-),Type 2 diabetes mellitus negative and periodontitis positive patients (T2D - P+),Patients affected by moderate to severe periodontitis but not type 2 Diabetes Mellitus (T2D). They had a number of sites with periodontitis ≥ 5mm varying between 28 - 49%.,3,3,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,15 January 2026,Tosin,Tosin,Bacterial genera and species showing nominal significance at p ≤ 0.01 based on White’s non-parametric t-test comparing relative abundances between type 2 diabetes mellitus–negative/periodontitis-negative and type 2 diabetes mellitus–negative/periodontitis-positive patients.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae|s__Anaerolineaceae bacterium oral taxon 439,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter rectus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacillati|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae|g__Anaerolinea",3379134|1224|1236|135625|712|416916;1783272|200795|292625|292629|292628|1889813;3379134|29547|3031852|213849|72294|194|203;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171551|836|837;1783272|200795|292625|292629|292628|233189,Complete,KateRasheed
bsdb:31153098/2/2,31153098,case-control,31153098,10.1016/j.archoralbio.2019.05.025,NA,"Farina R., Severi M., Carrieri A., Miotto E., Sabbioni S., Trombelli L. , Scapoli C.",Whole metagenomic shotgun sequencing of the subgingival microbiome of diabetics and non-diabetics with different periodontal conditions,Archives of oral biology,2019,"Biofilms, Dental plaque, Gingival sulcus, Metagenomics, Microbiota, Periodontal pocket, Periodontitis",Experiment 2,Italy,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Periodontitis,EFO:0000649,Type 2 diabetes mellitus and periodontitis negative patients (T2D - P-),Type 2 diabetes mellitus negative and periodontitis positive patients (T2D - P+),Patients affected by moderate to severe periodontitis but not type 2 Diabetes Mellitus (T2D). They had a number of sites with periodontitis ≥ 5mm varying between 28 - 49%.,3,3,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 4,18 January 2026,Tosin,Tosin,Bacterial genera and species showing nominal significance at p ≤ 0.01 based on White’s non-parametric t-test comparing relative abundances between type 2 diabetes mellitus–negative/periodontitis-negative and type 2 diabetes mellitus–negative/periodontitis-positive patients.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microcella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microcella|s__Microcella alkaliphila",1783272|201174|1760|85006|85023|337004;1783272|201174|1760|85006|85023|337004|279828,Complete,KateRasheed
bsdb:31153098/3/1,31153098,case-control,31153098,10.1016/j.archoralbio.2019.05.025,NA,"Farina R., Severi M., Carrieri A., Miotto E., Sabbioni S., Trombelli L. , Scapoli C.",Whole metagenomic shotgun sequencing of the subgingival microbiome of diabetics and non-diabetics with different periodontal conditions,Archives of oral biology,2019,"Biofilms, Dental plaque, Gingival sulcus, Metagenomics, Microbiota, Periodontal pocket, Periodontitis",Experiment 3,Italy,Homo sapiens,Subgingival dental plaque,UBERON:0016484,"Periodontitis,Type II diabetes mellitus","EFO:0000649,MONDO:0005148",Type 2 diabetes mellitus positive and periodontitis negative patients (T2D + P -),Type 2 diabetes mellitus positive and periodontitis positive patients (T2D + P +),Patients affected by both moderate to severe periodontitis and type 2 Diabetes Mellitus (T2D). They had a number of sites with periodontitis ≥ 5mm varying between 30 - 44%.,3,3,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,18 January 2026,Tosin,Tosin,Bacterial genera and species showing nominal significance at p ≤ 0.01 based on White’s non-parametric t-test comparing relative abundances between type 2 diabetes mellitus–positive/periodontitis-negative and type 2 diabetes mellitus–positive/periodontitis-positive patients.,increased,"k__Bacillati|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae|s__Anaerolineaceae bacterium oral taxon 439,k__Bacillati|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae|g__Anaerolinea,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 212,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema maltophilum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes",1783272|200795|292625|292629|292628|1889813;1783272|200795|292625|292629|292628|233189;1783272|1239|909932|1843489|31977|39948;3384189|32066|203490|203491|1129771|32067|712357;3379134|203691|203692|136|2845253|157|51160;1783272|1239|909932|1843489|31977|39948|39950,Complete,KateRasheed
bsdb:31153098/3/2,31153098,case-control,31153098,10.1016/j.archoralbio.2019.05.025,NA,"Farina R., Severi M., Carrieri A., Miotto E., Sabbioni S., Trombelli L. , Scapoli C.",Whole metagenomic shotgun sequencing of the subgingival microbiome of diabetics and non-diabetics with different periodontal conditions,Archives of oral biology,2019,"Biofilms, Dental plaque, Gingival sulcus, Metagenomics, Microbiota, Periodontal pocket, Periodontitis",Experiment 3,Italy,Homo sapiens,Subgingival dental plaque,UBERON:0016484,"Periodontitis,Type II diabetes mellitus","EFO:0000649,MONDO:0005148",Type 2 diabetes mellitus positive and periodontitis negative patients (T2D + P -),Type 2 diabetes mellitus positive and periodontitis positive patients (T2D + P +),Patients affected by both moderate to severe periodontitis and type 2 Diabetes Mellitus (T2D). They had a number of sites with periodontitis ≥ 5mm varying between 30 - 44%.,3,3,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 4,29 January 2026,Tosin,Tosin,Bacterial genera and species showing nominal significance at p ≤ 0.01 based on White’s non-parametric t-test comparing relative abundances between type 2 diabetes mellitus–positive/periodontitis-negative and type 2 diabetes mellitus–positive/periodontitis-positive patients.,decreased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis",3379134|29547|3031852|213849|72294|194;1783272|201174|1760|85006|1268|32207|2047;3379134|29547|3031852|213849|72294|194|824,Complete,KateRasheed
bsdb:31153098/4/1,31153098,case-control,31153098,10.1016/j.archoralbio.2019.05.025,NA,"Farina R., Severi M., Carrieri A., Miotto E., Sabbioni S., Trombelli L. , Scapoli C.",Whole metagenomic shotgun sequencing of the subgingival microbiome of diabetics and non-diabetics with different periodontal conditions,Archives of oral biology,2019,"Biofilms, Dental plaque, Gingival sulcus, Metagenomics, Microbiota, Periodontal pocket, Periodontitis",Experiment 4,Italy,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Type II diabetes mellitus,MONDO:0005148,Individuals without type 2 diabetes mellitus (T2D),Individuals with type 2 diabetes mellitus (T2D),Patients affected by type 2 Diabetes Mellitus (T2D),6,6,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,18 January 2026,Tosin,Tosin,Bacterial genera and species showing nominal significance at p ≤ 0.01 based on White’s non-parametric t-test comparing relative abundances between individuals with/without type 2 diabetes mellitus (T2D).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Ornithobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Ornithobacterium|s__Ornithobacterium rhinotracheale",1783272|1239|186801|3082720|3118655|44259;3379134|976|117743|200644|2762318|28250;1783272|1239|186801|3082720|3118655|44259|143361;3379134|976|117743|200644|2762318|28250|28251,Complete,KateRasheed
bsdb:31153098/5/1,31153098,case-control,31153098,10.1016/j.archoralbio.2019.05.025,NA,"Farina R., Severi M., Carrieri A., Miotto E., Sabbioni S., Trombelli L. , Scapoli C.",Whole metagenomic shotgun sequencing of the subgingival microbiome of diabetics and non-diabetics with different periodontal conditions,Archives of oral biology,2019,"Biofilms, Dental plaque, Gingival sulcus, Metagenomics, Microbiota, Periodontal pocket, Periodontitis",Experiment 5,Italy,Homo sapiens,Subgingival dental plaque,UBERON:0016484,"Periodontitis,Type II diabetes mellitus","EFO:0000649,MONDO:0005148",Type 2 diabetes mellitus negative and periodontitis positive patients (T2D - P +),Type 2 diabetes mellitus positive and periodontitis positive patients (T2D + P +),Patients affected by both moderate to severe periodontitis and type 2 Diabetes Mellitus (T2D). They had a number of sites with periodontitis ≥ 5mm varying between 30 - 44%.,3,3,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,18 January 2026,Tosin,Tosin,Bacterial genera and species showing nominal significance at p ≤ 0.01 based on White’s non-parametric t-test comparing relative abundances between type 2 diabetes mellitus–negative/periodontitis-positive and type 2 diabetes mellitus–positive/periodontitis-positive patients.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes",1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|39948|39950,Complete,KateRasheed
bsdb:31153098/5/2,31153098,case-control,31153098,10.1016/j.archoralbio.2019.05.025,NA,"Farina R., Severi M., Carrieri A., Miotto E., Sabbioni S., Trombelli L. , Scapoli C.",Whole metagenomic shotgun sequencing of the subgingival microbiome of diabetics and non-diabetics with different periodontal conditions,Archives of oral biology,2019,"Biofilms, Dental plaque, Gingival sulcus, Metagenomics, Microbiota, Periodontal pocket, Periodontitis",Experiment 5,Italy,Homo sapiens,Subgingival dental plaque,UBERON:0016484,"Periodontitis,Type II diabetes mellitus","EFO:0000649,MONDO:0005148",Type 2 diabetes mellitus negative and periodontitis positive patients (T2D - P +),Type 2 diabetes mellitus positive and periodontitis positive patients (T2D + P +),Patients affected by both moderate to severe periodontitis and type 2 Diabetes Mellitus (T2D). They had a number of sites with periodontitis ≥ 5mm varying between 30 - 44%.,3,3,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 4,18 January 2026,Tosin,Tosin,Bacterial genera and species showing nominal significance at p ≤ 0.01 based on White’s non-parametric t-test comparing relative abundances between type 2 diabetes mellitus–negative/periodontitis-positive and type 2 diabetes mellitus–positive/periodontitis-positive patients.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp. OMZ 838",1783272|1239|186801|3082720|3118655|44259;1783272|1239|186801|3082720|3118655|44259|143361;3379134|203691|203692|136|2845253|157|1539298,Complete,KateRasheed
bsdb:31171880/1/1,31171880,case-control,31171880,10.1038/s41591-019-0458-7,NA,"Yachida S., Mizutani S., Shiroma H., Shiba S., Nakajima T., Sakamoto T., Watanabe H., Masuda K., Nishimoto Y., Kubo M., Hosoda F., Rokutan H., Matsumoto M., Takamaru H., Yamada M., Matsuda T., Iwasaki M., Yamaji T., Yachida T., Soga T., Kurokawa K., Toyoda A., Ogura Y., Hayashi T., Hatakeyama M., Nakagama H., Saito Y., Fukuda S., Shibata T. , Yamada T.",Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer,Nature medicine,2019,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy control (normal and a few polyps),stage I/II (SI/II),stage I and II CRCs,251,111,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.005,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2B,12 June 2022,Jeshudy,"Jeshudy,WikiWorks","Species abundances were assessed for significant elevation or depletion (P< 0.005; one-sided Mann–Whitney U test) in each of the four stages, MP (n= 67), S0 (n= 73), SI/II (n= 111) and SIII/IV (n= 74), compared to the healthy controls (n= 251).",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei",1783272|201174|84998|84999|84107|102106|74426;3384189|32066|203490|203491|203492|848|851;1783272|1239|91061|1385|539738|1378|29391;1783272|201174|84998|84999|1643824|2767353|1382;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|1239|186801|3082720|186804|1257|1261;1783272|1239|186801|3082720|186804|1257|341694;3379134|976|200643|171549|171551|836|281920;1783272|201174|1760|2037|2049|2529408|1660;1783272|1239|526524|526525|128827|123375|102148,Complete,Atrayees
bsdb:31171880/1/2,31171880,case-control,31171880,10.1038/s41591-019-0458-7,NA,"Yachida S., Mizutani S., Shiroma H., Shiba S., Nakajima T., Sakamoto T., Watanabe H., Masuda K., Nishimoto Y., Kubo M., Hosoda F., Rokutan H., Matsumoto M., Takamaru H., Yamada M., Matsuda T., Iwasaki M., Yamaji T., Yachida T., Soga T., Kurokawa K., Toyoda A., Ogura Y., Hayashi T., Hatakeyama M., Nakagama H., Saito Y., Fukuda S., Shibata T. , Yamada T.",Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer,Nature medicine,2019,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy control (normal and a few polyps),stage I/II (SI/II),stage I and II CRCs,251,111,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.005,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2B,12 June 2022,Jeshudy,"Jeshudy,WikiWorks","Species abundances were assessed for significant elevation or depletion (P< 0.005; one-sided Mann–Whitney U test) in each of the four stages, MP (n= 67), S0 (n= 73), SI/II (n= 111) and SIII/IV (n= 74), compared to the healthy controls (n= 251).",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira multipara",1783272|201174|1760|85004|31953|1678|216816|1679;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|28050|28051,Complete,Atrayees
bsdb:31171880/2/1,31171880,case-control,31171880,10.1038/s41591-019-0458-7,NA,"Yachida S., Mizutani S., Shiroma H., Shiba S., Nakajima T., Sakamoto T., Watanabe H., Masuda K., Nishimoto Y., Kubo M., Hosoda F., Rokutan H., Matsumoto M., Takamaru H., Yamada M., Matsuda T., Iwasaki M., Yamaji T., Yachida T., Soga T., Kurokawa K., Toyoda A., Ogura Y., Hayashi T., Hatakeyama M., Nakagama H., Saito Y., Fukuda S., Shibata T. , Yamada T.",Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer,Nature medicine,2019,NA,Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy control (normal and a few polyps),stage III/IV (SIII/IV),stage III and IV CRCs,251,74,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.005,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2B,12 June 2022,Jeshudy,"Jeshudy,WikiWorks",Phylum distribution of the number of species that are either elevated or depleted in each of the four stages compared to the healthy controls.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Fructilactobacillus|s__Fructilactobacillus sanfranciscensis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Oleidesulfovibrio|s__Oleidesulfovibrio vietnamensis",1783272|201174|84998|84999|84107|102106|74426;1783272|201174|84998|84999|1643824|2767353|1382;1783272|201174|1760|2037|2049|2529408|1660;1783272|1239|526524|526525|128827|123375|102148;3379134|976|200643|171549|171551|836|281920;3384189|32066|203490|203491|203492|848|851;1783272|1239|909932|909929|1843491|970|69823;1783272|1239|91061|1385|539738|1378|29391;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|91061|186826|33958|2767881|1625;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3082720|186804|1257|1261;1783272|1239|186801|3082720|186804|1257|341694;3379134|200940|3031449|213115|194924|35832|35833;3379134|200940|3031449|213115|194924|2909705|201571,Complete,Atrayees
bsdb:31171880/2/2,31171880,case-control,31171880,10.1038/s41591-019-0458-7,NA,"Yachida S., Mizutani S., Shiroma H., Shiba S., Nakajima T., Sakamoto T., Watanabe H., Masuda K., Nishimoto Y., Kubo M., Hosoda F., Rokutan H., Matsumoto M., Takamaru H., Yamada M., Matsuda T., Iwasaki M., Yamaji T., Yachida T., Soga T., Kurokawa K., Toyoda A., Ogura Y., Hayashi T., Hatakeyama M., Nakagama H., Saito Y., Fukuda S., Shibata T. , Yamada T.",Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer,Nature medicine,2019,NA,Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy control (normal and a few polyps),stage III/IV (SIII/IV),stage III and IV CRCs,251,74,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.005,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2B,12 June 2022,Jeshudy,"Jeshudy,WikiWorks","Species abundances were assessed for significant elevation or depletion (P< 0.005; one-sided Mann–Whitney U test) in each of the four stages, MP (n= 67), S0 (n= 73), SI/II (n= 111) and SIII/IV (n= 74), compared to the healthy controls (n= 251).",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira multipara",1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|28050|28051,Complete,Atrayees
bsdb:31171880/3/1,31171880,case-control,31171880,10.1038/s41591-019-0458-7,NA,"Yachida S., Mizutani S., Shiroma H., Shiba S., Nakajima T., Sakamoto T., Watanabe H., Masuda K., Nishimoto Y., Kubo M., Hosoda F., Rokutan H., Matsumoto M., Takamaru H., Yamada M., Matsuda T., Iwasaki M., Yamaji T., Yachida T., Soga T., Kurokawa K., Toyoda A., Ogura Y., Hayashi T., Hatakeyama M., Nakagama H., Saito Y., Fukuda S., Shibata T. , Yamada T.",Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer,Nature medicine,2019,NA,Experiment 3,Japan,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy control (normal and a few polyps),S0,stage 0/pTis CRC (S0),251,73,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.005,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2B,12 June 2022,Jeshudy,"Jeshudy,WikiWorks","Species abundances were assessed for significant elevation or depletion (P< 0.005; one-sided Mann–Whitney U test) in each of the four stages, MP (n= 67), S0 (n= 73), SI/II (n= 111) and SIII/IV (n= 74), compared to the healthy controls (n= 251).",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces viscosus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Fructilactobacillus|s__Fructilactobacillus sanfranciscensis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio longreachensis",1783272|201174|84998|84999|1643824|2767353|1382;1783272|201174|84998|84999|84107|102106|74426;3379134|976|200643|171549|171551|836|281920;3384189|32066|203490|203491|203492|848|851;1783272|201174|1760|2037|2049|1654|1656;1783272|201174|1760|2037|2049|2529408|1660;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|909932|1843488|909930|33024|626940;1783272|1239|91061|1385|539738|1378|29391;1783272|1239|91061|186826|33958|2767881|1625;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|1239|186801|3082720|186804|1257|341694;3379134|200940|3031449|213115|194924|872|29505,Complete,Atrayees
bsdb:31171880/3/2,31171880,case-control,31171880,10.1038/s41591-019-0458-7,NA,"Yachida S., Mizutani S., Shiroma H., Shiba S., Nakajima T., Sakamoto T., Watanabe H., Masuda K., Nishimoto Y., Kubo M., Hosoda F., Rokutan H., Matsumoto M., Takamaru H., Yamada M., Matsuda T., Iwasaki M., Yamaji T., Yachida T., Soga T., Kurokawa K., Toyoda A., Ogura Y., Hayashi T., Hatakeyama M., Nakagama H., Saito Y., Fukuda S., Shibata T. , Yamada T.",Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer,Nature medicine,2019,NA,Experiment 3,Japan,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy control (normal and a few polyps),S0,stage 0/pTis CRC (S0),251,73,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.005,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2B,12 June 2022,Jeshudy,"Jeshudy,WikiWorks","Species abundances were assessed for significant elevation or depletion (P< 0.005; one-sided Mann–Whitney U test) in each of the four stages, MP (n= 67), S0 (n= 73), SI/II (n= 111) and SIII/IV (n= 74), compared to the healthy controls (n= 251).",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira multipara,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens",1783272|201174|1760|85004|31953|1678|216816|1679;1783272|1239|186801|3085636|186803|28050|28051;1783272|1239|186801|3085636|186803|28050|39485,Complete,Atrayees
bsdb:31171880/4/1,31171880,case-control,31171880,10.1038/s41591-019-0458-7,NA,"Yachida S., Mizutani S., Shiroma H., Shiba S., Nakajima T., Sakamoto T., Watanabe H., Masuda K., Nishimoto Y., Kubo M., Hosoda F., Rokutan H., Matsumoto M., Takamaru H., Yamada M., Matsuda T., Iwasaki M., Yamaji T., Yachida T., Soga T., Kurokawa K., Toyoda A., Ogura Y., Hayashi T., Hatakeyama M., Nakagama H., Saito Y., Fukuda S., Shibata T. , Yamada T.",Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer,Nature medicine,2019,NA,Experiment 4,Japan,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy control (normal and a few polyps),MP,"multiple polypoid adenomas with low- grade dysplasia (MP, more than three adenomas, mostly more than five adenomas)",251,67,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.005,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2B,12 June 2022,Jeshudy,"Jeshudy,WikiWorks","Species abundances were assessed for significant elevation or depletion (P< 0.005; one-sided Mann–Whitney U test) in each of the four stages, MP (n= 67), S0 (n= 73), SI/II (n= 111) and SIII/IV (n= 74), compared to the healthy controls (n= 251).",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Oleidesulfovibrio|s__Oleidesulfovibrio vietnamensis",1783272|201174|84998|84999|1643824|2767353|1382;3384189|32066|203490|203491|203492|848|851;1783272|201174|1760|2037|2049|2529408|1660;1783272|1239|909932|1843488|909930|33024|626940;1783272|1239|909932|909929|1843491|970|69823;3379134|200940|3031449|213115|194924|2909705|201571,Complete,Atrayees
bsdb:31171880/4/2,31171880,case-control,31171880,10.1038/s41591-019-0458-7,NA,"Yachida S., Mizutani S., Shiroma H., Shiba S., Nakajima T., Sakamoto T., Watanabe H., Masuda K., Nishimoto Y., Kubo M., Hosoda F., Rokutan H., Matsumoto M., Takamaru H., Yamada M., Matsuda T., Iwasaki M., Yamaji T., Yachida T., Soga T., Kurokawa K., Toyoda A., Ogura Y., Hayashi T., Hatakeyama M., Nakagama H., Saito Y., Fukuda S., Shibata T. , Yamada T.",Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer,Nature medicine,2019,NA,Experiment 4,Japan,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy control (normal and a few polyps),MP,"multiple polypoid adenomas with low- grade dysplasia (MP, more than three adenomas, mostly more than five adenomas)",251,67,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.005,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2B,12 June 2022,Jeshudy,"Jeshudy,WikiWorks","Species abundances were assessed for significant elevation or depletion (P< 0.005; one-sided Mann–Whitney U test) in each of the four stages, MP (n= 67), S0 (n= 73), SI/II (n= 111) and SIII/IV (n= 74), compared to the healthy controls (n= 251).",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira multipara,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens",1783272|201174|1760|85004|31953|1678|216816|1679;1783272|1239|186801|3085636|186803|28050|28051;1783272|1239|186801|3085636|186803|28050|39485,Complete,Atrayees
bsdb:31174953/1/1,31174953,case-control,31174953,10.1016/j.parkreldis.2019.06.003,NA,"Pietrucci D., Cerroni R., Unida V., Farcomeni A., Pierantozzi M., Mercuri N.B., Biocca S., Stefani A. , Desideri A.",Dysbiosis of gut microbiota in a selected population of Parkinson's patients,Parkinsonism & related disorders,2019,"16S rRNA, Dysbiosis, Functional pathways, Gut microbiota, Parkinson's disease, Predictors",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls (HC),Parkinson's disease (PD),"Patients with severe and active Parkinson disease.
Recruited patients had a diagnosis of idiopathic PD according to the UK Parkinson's Disease Society Brain Bank criteria with a disease duration (measured as the time following the first diagnosis) longer than 6 months",72,80,1 month,16S,34,Illumina,relative abundances,"Linear Regression,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,"age,sex",NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Supplementary Table S7A,8 March 2024,Mojisayo Awolesi,"Mojisayo Awolesi,Welile,Fiddyhamma,Scholastica,WikiWorks",Significantly abundant bacterial families and genera in Parkinson's disease versus healthy controls (HC) detected by two methods (Generalized Linear Models and Wilcoxon-Mann-Withney test),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|1300|1357;3379134|1224|1236|91347|543|590;3379134|1224|1236|91347|543|620;3379134|1224|1236|91347|543,Complete,Svetlana up
bsdb:31174953/1/2,31174953,case-control,31174953,10.1016/j.parkreldis.2019.06.003,NA,"Pietrucci D., Cerroni R., Unida V., Farcomeni A., Pierantozzi M., Mercuri N.B., Biocca S., Stefani A. , Desideri A.",Dysbiosis of gut microbiota in a selected population of Parkinson's patients,Parkinsonism & related disorders,2019,"16S rRNA, Dysbiosis, Functional pathways, Gut microbiota, Parkinson's disease, Predictors",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls (HC),Parkinson's disease (PD),"Patients with severe and active Parkinson disease.
Recruited patients had a diagnosis of idiopathic PD according to the UK Parkinson's Disease Society Brain Bank criteria with a disease duration (measured as the time following the first diagnosis) longer than 6 months",72,80,1 month,16S,34,Illumina,relative abundances,"Linear Regression,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,"age,sex",NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Supplementary Table S7A,8 March 2024,Mojisayo Awolesi,"Mojisayo Awolesi,Welile,Fiddyhamma,Scholastica,WikiWorks",Significantly abundant bacterial families and genera in Parkinson's disease versus healthy controls (HC) detected by two methods (Generalized Linear Models and Wilcoxon-Mann-Withney test),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:31174953/2/1,31174953,case-control,31174953,10.1016/j.parkreldis.2019.06.003,NA,"Pietrucci D., Cerroni R., Unida V., Farcomeni A., Pierantozzi M., Mercuri N.B., Biocca S., Stefani A. , Desideri A.",Dysbiosis of gut microbiota in a selected population of Parkinson's patients,Parkinsonism & related disorders,2019,"16S rRNA, Dysbiosis, Functional pathways, Gut microbiota, Parkinson's disease, Predictors",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls (HC),Parkinson's disease (excluding iCOMT users),Patients with Parkinson's disease (PD) excluding eight patients taking catechol-O-methyl transferase (COMT) inhibitors,72,72,1 month,16S,34,Illumina,relative abundances,"Linear Regression,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table S7B,12 April 2024,Fiddyhamma,"Fiddyhamma,Scholastica,WikiWorks",Significantly abundant bacterial families and genera in Parkinson's disease (excluding iCOMT users) versus healthy controls detected by two methods (Generalized Linear Models and Wilcoxon-Mann-Withney test),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;3379134|1224|1236|91347|543,Complete,Svetlana up
bsdb:31174953/2/2,31174953,case-control,31174953,10.1016/j.parkreldis.2019.06.003,NA,"Pietrucci D., Cerroni R., Unida V., Farcomeni A., Pierantozzi M., Mercuri N.B., Biocca S., Stefani A. , Desideri A.",Dysbiosis of gut microbiota in a selected population of Parkinson's patients,Parkinsonism & related disorders,2019,"16S rRNA, Dysbiosis, Functional pathways, Gut microbiota, Parkinson's disease, Predictors",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls (HC),Parkinson's disease (excluding iCOMT users),Patients with Parkinson's disease (PD) excluding eight patients taking catechol-O-methyl transferase (COMT) inhibitors,72,72,1 month,16S,34,Illumina,relative abundances,"Linear Regression,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table S7B,12 April 2024,Fiddyhamma,"Fiddyhamma,Scholastica,WikiWorks",Significantly abundant bacterial families and genera in Parkinson's disease (excluding iCOMT users) versus healthy controls detected by two methods (Generalized Linear Models and Wilcoxon-Mann-Withney test),decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:31182740/1/1,31182740,"cross-sectional observational, not case-control",31182740,10.1038/s41598-019-44674-6,NA,"Corrêa J.D., Fernandes G.R., Calderaro D.C., Mendonça S.M.S., Silva J.M., Albiero M.L., Cunha F.Q., Xiao E., Ferreira G.A., Teixeira A.L., Mukherjee C., Leys E.J., Silva T.A. , Graves D.T.",Oral microbial dysbiosis linked to worsened periodontal condition in rheumatoid arthritis patients,Scientific reports,2019,NA,Experiment 1,Brazil,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Periodontitis,EFO:0000649,patients with no rheumatoid arthritis,patients with rheumatoid arthritis,patients with rheumatoid arthritis,20,21,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,"age,sex",NA,NA,increased,NA,increased,NA,increased,Signature 1,"Figure 3b, text",29 July 2021,Tislam,"Tislam,Fatima,WikiWorks",OTUs with different relative abundance based on LEfSe among subjects with periodontitis,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter actinomycetemcomitans,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium timidum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella dentalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella multisaccharivorax,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas artemidis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter sp.",3379134|1224|1236|135625|712|416916|714;1783272|1239|186801|3082720|543314|86331|35519;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|1239|1737404|1737405|1570339|162289|33031;3379134|976|200643|171549|171552|838|52227;3379134|976|200643|171549|171552|838|470565;3379134|976|200643|171549|171552|52228|310514;3379134|976|200643|171549|171552|2974251|228604;3379134|1224|1236|72274|135621|286|287;1783272|1239|909932|909929|1843491|970|671224;3379134|1224|1236|135625|712|416916|1872413,Complete,Fatima
bsdb:31182740/1/2,31182740,"cross-sectional observational, not case-control",31182740,10.1038/s41598-019-44674-6,NA,"Corrêa J.D., Fernandes G.R., Calderaro D.C., Mendonça S.M.S., Silva J.M., Albiero M.L., Cunha F.Q., Xiao E., Ferreira G.A., Teixeira A.L., Mukherjee C., Leys E.J., Silva T.A. , Graves D.T.",Oral microbial dysbiosis linked to worsened periodontal condition in rheumatoid arthritis patients,Scientific reports,2019,NA,Experiment 1,Brazil,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Periodontitis,EFO:0000649,patients with no rheumatoid arthritis,patients with rheumatoid arthritis,patients with rheumatoid arthritis,20,21,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,"age,sex",NA,NA,increased,NA,increased,NA,increased,Signature 2,"Figure 3b, text",29 July 2021,Tislam,"Tislam,Fatima,WikiWorks",OTUs with different relative abundance based on LEfSe among subjects with periodontitis,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella marshii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia meyeri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp.",3379134|976|200643|171549|171552|2974257|189722;1783272|201174|1760|2037|2049|2529408|52773;1783272|1239|91061|186826|1300|1301|1328;3379134|203691|203692|136|2845253|157|166,Complete,Fatima
bsdb:31182740/2/1,31182740,"cross-sectional observational, not case-control",31182740,10.1038/s41598-019-44674-6,NA,"Corrêa J.D., Fernandes G.R., Calderaro D.C., Mendonça S.M.S., Silva J.M., Albiero M.L., Cunha F.Q., Xiao E., Ferreira G.A., Teixeira A.L., Mukherjee C., Leys E.J., Silva T.A. , Graves D.T.",Oral microbial dysbiosis linked to worsened periodontal condition in rheumatoid arthritis patients,Scientific reports,2019,NA,Experiment 2,Brazil,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,patients with no rheumatoid arthritis,patients with rheumatoid arthritis,patients with rheumatoid arthritis,27,21,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,"age,sex",NA,NA,increased,NA,increased,NA,increased,Signature 1,"Figure 3a, text",29 July 2021,Tislam,"Tislam,Fatima,WikiWorks",Differential abundance based on LEfSe among subjects without periodontitis,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera geminata,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella rimae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia shahii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia wadei,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium neglectum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium timidum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella buccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella dentalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella maculosa,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella multisaccharivorax,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oulorum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella shahii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas flueggei,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas noxia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. oral clone DO042,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella sp. oral taxon 808",3379134|976|200643|171549|171552|1283313|671218;1783272|1239|909932|1843489|31977|906|156456;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|1689;3379134|976|117743|200644|49546|1016|1018;1783272|201174|1760|85007|1653|1716|43768;1783272|201174|84998|84999|1643824|2767353|1383;3384189|32066|203490|203491|1129771|32067|157688;3384189|32066|203490|203491|1129771|32067|157691;3384189|32066|203490|203491|1129771|32067|157687;1783272|1239|909932|909929|1843491|52225;1783272|1239|186801|3082720|543314|86331|114528;1783272|1239|186801|3082720|543314|86331|35519;3379134|976|200643|171549|171552|2974251|28126;3379134|976|200643|171549|171552|838|52227;3379134|976|200643|171549|171552|838|28129;3379134|976|200643|171549|171552|838|470565;3379134|976|200643|171549|171552|2974251|439703;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552|52228|310514;3379134|976|200643|171549|171552|838|28133;3379134|976|200643|171549|171552|2974251|28136;3379134|976|200643|171549|171552|838|60133;3379134|976|200643|171549|171552|2974251|228604;3379134|976|200643|171549|171552|2974257|228603;3379134|1224|1236|72274|135621|286|287;1783272|201174|1760|85004|31953|196081|230143;1783272|1239|909932|909929|1843491|970|135080;1783272|1239|909932|909929|1843491|970|135083;1783272|1239|909932|909929|1843491|970|163583;1783272|1239|909932|909929|1843491|970|69823;3379134|976|200643|171549|2005525|195950|712711,Complete,NA
bsdb:31182740/2/2,31182740,"cross-sectional observational, not case-control",31182740,10.1038/s41598-019-44674-6,NA,"Corrêa J.D., Fernandes G.R., Calderaro D.C., Mendonça S.M.S., Silva J.M., Albiero M.L., Cunha F.Q., Xiao E., Ferreira G.A., Teixeira A.L., Mukherjee C., Leys E.J., Silva T.A. , Graves D.T.",Oral microbial dysbiosis linked to worsened periodontal condition in rheumatoid arthritis patients,Scientific reports,2019,NA,Experiment 2,Brazil,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,patients with no rheumatoid arthritis,patients with rheumatoid arthritis,patients with rheumatoid arthritis,27,21,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,"age,sex",NA,NA,increased,NA,increased,NA,increased,Signature 2,"Figure 3, text",29 July 2021,Tislam,"Tislam,WikiWorks",subjects without periodontitis,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia|s__Delftia tsuruhatensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles|s__Roseateles puraquae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella pleuritidis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral clone BR014,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter piscolens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia meyeri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral clone ASCB04",3379134|1224|28216|80840|80864|80865|180282;1783272|1239|91061|186826|186828|117563|137732;3379134|1224|28216|206351|481|32257|505;3379134|1224|28216|80840|2975441|93681|431059;3379134|976|200643|171549|171552|2974257|407975;3379134|976|200643|171549|171552|838|163559;3384194|508458|649775|649776|3029088|638847|638849;1783272|201174|1760|85006|1268|32207|172042;1783272|201174|1760|2037|2049|2529408|52773;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|91061|186826|1300|1301|325787,Complete,NA
bsdb:31199220/1/1,31199220,case-control,31199220,10.1099/jmm.0.001003,NA,"Karabudak S., Ari O., Durmaz B., Dal T., Basyigit T., Kalcioglu M.T. , Durmaz R.",Analysis of the effect of smoking on the buccal microbiome using next-generation sequencing technology,Journal of medical microbiology,2019,"buccal microbiome, metagenomic analysis, next-generation sequencing, smoking",Experiment 1,Turkey,Homo sapiens,Buccal mucosa,UBERON:0006956,Smoking behavior,EFO:0004318,non-smokers,smokers,"Participants who smoke cigarettes that fulfilled the inclusion criteria for good health: no use of antibiotics in the past 3 months, no respiratory infections, no oral aphthous lesions on buccal mucosa, and absence of dental problems",20,20,3 months,16S,23456789,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table 2,10 January 2021,Victoria Goulbourne,WikiWorks,Comparison of statistically significant differences between smoker and non-smoker groups at genus and species levels,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica",1783272|201174|1760|2037|2049|1654;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|1300|1301|113107;3379134|976|200643|171549|171552|2974251|228604;3379134|976|200643|171549|171552|838|28132;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|909932|1843489|31977|29465|39777,Complete,Claregrieve1
bsdb:31200089/1/1,31200089,case-control,31200089,10.1016/j.neulet.2019.134297,https://pubmed.ncbi.nlm.nih.gov/31200089/,"Li F., Wang P., Chen Z., Sui X., Xie X. , Zhang J.",Alteration of the fecal microbiota in North-Eastern Han Chinese population with sporadic Parkinson's disease,Neuroscience letters,2019,"16S rRNA gene, Gut microbiome, Microbiota–gut–brain axis, Parkinson’s disease, Pathogenesis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease Patients,Patients with sporadic PD and over 65 age.,10,10,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,4 May 2023,Jacquelynshevin,"Jacquelynshevin,Chloe,WikiWorks","The histogram of the LDA scores presents species whose abundance
showed significant differences between the heathy controls and PD patients in
the fecal samples. The length of each bin, namely, the LDA score. A p-value
of < 0.05 and a score ≥ 2.0 were considered significant in KW rank sum test
and Wilcox tests, respectively. The horizontal straight line in the panel indicated the group means, and the dotted line indicated the group medians.",increased,",k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota",;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|186802|216572|596767;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|171551;1783272|1239|186801|186802|216572|292632;3379134|74201|203494|48461|203557;3379134|74201|203494;3379134|74201|203494|48461;3379134|74201,Complete,Atrayees
bsdb:31200089/1/2,31200089,case-control,31200089,10.1016/j.neulet.2019.134297,https://pubmed.ncbi.nlm.nih.gov/31200089/,"Li F., Wang P., Chen Z., Sui X., Xie X. , Zhang J.",Alteration of the fecal microbiota in North-Eastern Han Chinese population with sporadic Parkinson's disease,Neuroscience letters,2019,"16S rRNA gene, Gut microbiome, Microbiota–gut–brain axis, Parkinson’s disease, Pathogenesis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease Patients,Patients with sporadic PD and over 65 age.,10,10,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5,4 May 2023,Jacquelynshevin,"Jacquelynshevin,Chloe,WikiWorks","The histogram of the LDA scores presents species whose abundance showed significant differences between the heathy controls and PD patients in the fecal samples. The length of each bin, namely, the LDA score. A p-value of < 0.05 and a score ≥ 2.0 were considered significant in KW rank sum test and Wilcox tests, respectively. The horizontal straight line in the panel indicated the group means, and the dotted line indicated the group medians.",decreased,",k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",;1783272|1239|909932|1843489|31977|209879;3379134|976|200643|171549;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;1783272|1239|526524|526525|128827|1573535;1783272|1239|91061|186826|33958;3379134|976|200643|171549|171552;1783272|1239|186801|3085636|186803|1506577,Complete,Atrayees
bsdb:31201284/1/1,31201284,"cross-sectional observational, not case-control",31201284,10.1136/gutjnl-2018-317836,NA,"Wei Y., Li Y., Yan L., Sun C., Miao Q., Wang Q., Xiao X., Lian M., Li B., Chen Y., Zhang J., Li Y., Huang B., Li Y., Cao Q., Fan Z., Chen X., Fang J.Y., Gershwin M.E., Tang R. , Ma X.",Alterations of gut microbiome in autoimmune hepatitis,Gut,2020,"autoimmune hepatitis, intestinal microbiology",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autoimmune Hepatitis,EFO:0005676,healthy controls,autoimmune hepatits cases,The diagnosis of AIH was made if patients conformed with (1) 1999 revised International Autoimmune Hepatitis Group (IAIHG) score ≥10 and/or (2) 2008 IAIHG simplified AIH score ≥6 and/or (3) histological features indicative of AIH.,98,91,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 2,25 February 2021,Valentina,"Valentina,Fiddyhamma,WikiWorks",LDA effect size analysis of 11 genera was significantly different between AIH and the control group.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|39778,Complete,Atrayees
bsdb:31201284/1/2,31201284,"cross-sectional observational, not case-control",31201284,10.1136/gutjnl-2018-317836,NA,"Wei Y., Li Y., Yan L., Sun C., Miao Q., Wang Q., Xiao X., Lian M., Li B., Chen Y., Zhang J., Li Y., Huang B., Li Y., Cao Q., Fan Z., Chen X., Fang J.Y., Gershwin M.E., Tang R. , Ma X.",Alterations of gut microbiome in autoimmune hepatitis,Gut,2020,"autoimmune hepatitis, intestinal microbiology",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autoimmune Hepatitis,EFO:0005676,healthy controls,autoimmune hepatits cases,The diagnosis of AIH was made if patients conformed with (1) 1999 revised International Autoimmune Hepatitis Group (IAIHG) score ≥10 and/or (2) 2008 IAIHG simplified AIH score ≥6 and/or (3) histological features indicative of AIH.,98,91,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Figure 2,3 March 2021,Valentina,"Valentina,Atrayees,WikiWorks",LDA effect size analysis of taxa that was significantly different between AIH and the control group.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572,Complete,Atrayees
bsdb:31201890/1/1,31201890,"cross-sectional observational, not case-control",31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K., Durack J., Valladares R., Fadrosh D.W., Lin D.L., Calatroni A., LeBeau P.K., Tran H.T., Fujimura K.E., LaMere B., Merana G., Lynch K., Cohen R.T., Pongracic J., Khurana Hershey G.K., Kercsmar C.M., Gill M., Liu A.H., Kim H., Kattan M., Teach S.J., Togias A., Boushey H.A., Gern J.E., Jackson D.J. , Lynch S.V.",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,"16S rRNA, Microbiota, Moraxella species, Staphylococcus species, airway, asthma, exacerbation, rhinovirus",Experiment 1,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,children who did not experience asthma exacerbation,Children who experienced exacerbation,"children who experienced exacerbation of their asthma (physician-prescribed use of systemic corticosteroids for asthma symptoms, hospitalization for asthma, or both)",346,67,NA,16S,4,Illumina,relative abundances,Zero-Inflated Beta Regression,0.15,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Table E5,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between children with exacerbation and children without,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,3379134|1224|1236|135625|712|724,Complete,Claregrieve1
bsdb:31201890/2/1,31201890,"cross-sectional observational, not case-control",31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K., Durack J., Valladares R., Fadrosh D.W., Lin D.L., Calatroni A., LeBeau P.K., Tran H.T., Fujimura K.E., LaMere B., Merana G., Lynch K., Cohen R.T., Pongracic J., Khurana Hershey G.K., Kercsmar C.M., Gill M., Liu A.H., Kim H., Kattan M., Teach S.J., Togias A., Boushey H.A., Gern J.E., Jackson D.J. , Lynch S.V.",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,"16S rRNA, Microbiota, Moraxella species, Staphylococcus species, airway, asthma, exacerbation, rhinovirus",Experiment 2,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,Samples with no rhinovirus infection,Samples with any rhinovirus infection,Samples with rhinovirus infection assessed by using quantitative PCR and partial sequencing to identify viral strain type,1883,1239,NA,16S,4,Illumina,relative abundances,Zero-Inflated Beta Regression,0.15,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Table E5,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between samples with rhinovirus and samples without,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:31201890/2/2,31201890,"cross-sectional observational, not case-control",31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K., Durack J., Valladares R., Fadrosh D.W., Lin D.L., Calatroni A., LeBeau P.K., Tran H.T., Fujimura K.E., LaMere B., Merana G., Lynch K., Cohen R.T., Pongracic J., Khurana Hershey G.K., Kercsmar C.M., Gill M., Liu A.H., Kim H., Kattan M., Teach S.J., Togias A., Boushey H.A., Gern J.E., Jackson D.J. , Lynch S.V.",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,"16S rRNA, Microbiota, Moraxella species, Staphylococcus species, airway, asthma, exacerbation, rhinovirus",Experiment 2,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,Samples with no rhinovirus infection,Samples with any rhinovirus infection,Samples with rhinovirus infection assessed by using quantitative PCR and partial sequencing to identify viral strain type,1883,1239,NA,16S,4,Illumina,relative abundances,Zero-Inflated Beta Regression,0.15,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 2,Table E5,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between samples with rhinovirus and samples without,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:31201890/3/1,31201890,"cross-sectional observational, not case-control",31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K., Durack J., Valladares R., Fadrosh D.W., Lin D.L., Calatroni A., LeBeau P.K., Tran H.T., Fujimura K.E., LaMere B., Merana G., Lynch K., Cohen R.T., Pongracic J., Khurana Hershey G.K., Kercsmar C.M., Gill M., Liu A.H., Kim H., Kattan M., Teach S.J., Togias A., Boushey H.A., Gern J.E., Jackson D.J. , Lynch S.V.",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,"16S rRNA, Microbiota, Moraxella species, Staphylococcus species, airway, asthma, exacerbation, rhinovirus",Experiment 3,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,Samples that were RV-A negative-,Samples with rhinovirus-A (RV-A),Samples with rhinovirus-A,1883,386,NA,16S,4,Illumina,relative abundances,Zero-Inflated Beta Regression,0.15,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Table E5,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between samples with rhinovirus-A and samples with no rhinovirus detected,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:31201890/3/2,31201890,"cross-sectional observational, not case-control",31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K., Durack J., Valladares R., Fadrosh D.W., Lin D.L., Calatroni A., LeBeau P.K., Tran H.T., Fujimura K.E., LaMere B., Merana G., Lynch K., Cohen R.T., Pongracic J., Khurana Hershey G.K., Kercsmar C.M., Gill M., Liu A.H., Kim H., Kattan M., Teach S.J., Togias A., Boushey H.A., Gern J.E., Jackson D.J. , Lynch S.V.",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,"16S rRNA, Microbiota, Moraxella species, Staphylococcus species, airway, asthma, exacerbation, rhinovirus",Experiment 3,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,Samples that were RV-A negative-,Samples with rhinovirus-A (RV-A),Samples with rhinovirus-A,1883,386,NA,16S,4,Illumina,relative abundances,Zero-Inflated Beta Regression,0.15,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 2,Table E5,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between samples with rhinovirus-A and samples with no rhinovirus detected,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:31201890/5/1,31201890,"cross-sectional observational, not case-control",31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K., Durack J., Valladares R., Fadrosh D.W., Lin D.L., Calatroni A., LeBeau P.K., Tran H.T., Fujimura K.E., LaMere B., Merana G., Lynch K., Cohen R.T., Pongracic J., Khurana Hershey G.K., Kercsmar C.M., Gill M., Liu A.H., Kim H., Kattan M., Teach S.J., Togias A., Boushey H.A., Gern J.E., Jackson D.J. , Lynch S.V.",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,"16S rRNA, Microbiota, Moraxella species, Staphylococcus species, airway, asthma, exacerbation, rhinovirus",Experiment 5,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,children who did not experience exacerbation,Children who experienced exacerbation,"children who experienced exacerbation of their asthma (physician-prescribed use of systemic corticosteroids for asthma symptoms, hospitalization for asthma, or both)",346,67,NA,16S,4,Illumina,relative abundances,Zero-Inflated Beta Regression,0.15,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table I,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between children with exacerbation and children without,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,3379134|1224|1236|2887326|468|475,Complete,Claregrieve1
bsdb:31201890/5/2,31201890,"cross-sectional observational, not case-control",31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K., Durack J., Valladares R., Fadrosh D.W., Lin D.L., Calatroni A., LeBeau P.K., Tran H.T., Fujimura K.E., LaMere B., Merana G., Lynch K., Cohen R.T., Pongracic J., Khurana Hershey G.K., Kercsmar C.M., Gill M., Liu A.H., Kim H., Kattan M., Teach S.J., Togias A., Boushey H.A., Gern J.E., Jackson D.J. , Lynch S.V.",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,"16S rRNA, Microbiota, Moraxella species, Staphylococcus species, airway, asthma, exacerbation, rhinovirus",Experiment 5,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,children who did not experience exacerbation,Children who experienced exacerbation,"children who experienced exacerbation of their asthma (physician-prescribed use of systemic corticosteroids for asthma symptoms, hospitalization for asthma, or both)",346,67,NA,16S,4,Illumina,relative abundances,Zero-Inflated Beta Regression,0.15,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table I,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between children with exacerbation and children without,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Alloiococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|1239|91061|186826|186828|1651;1783272|201174|1760|85007|1653|1716;3379134|1224|1236|135625|712|724;1783272|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:31201890/7/1,31201890,"cross-sectional observational, not case-control",31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K., Durack J., Valladares R., Fadrosh D.W., Lin D.L., Calatroni A., LeBeau P.K., Tran H.T., Fujimura K.E., LaMere B., Merana G., Lynch K., Cohen R.T., Pongracic J., Khurana Hershey G.K., Kercsmar C.M., Gill M., Liu A.H., Kim H., Kattan M., Teach S.J., Togias A., Boushey H.A., Gern J.E., Jackson D.J. , Lynch S.V.",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,"16S rRNA, Microbiota, Moraxella species, Staphylococcus species, airway, asthma, exacerbation, rhinovirus",Experiment 7,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,samples with no rhinovirus infection,samples with any rhinovirus infection,samples with rhinovirus infection,1883,1239,NA,16S,4,Illumina,relative abundances,Zero-Inflated Beta Regression,0.15,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table I,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between samples with any viral infection and samples without,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:31201890/7/2,31201890,"cross-sectional observational, not case-control",31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K., Durack J., Valladares R., Fadrosh D.W., Lin D.L., Calatroni A., LeBeau P.K., Tran H.T., Fujimura K.E., LaMere B., Merana G., Lynch K., Cohen R.T., Pongracic J., Khurana Hershey G.K., Kercsmar C.M., Gill M., Liu A.H., Kim H., Kattan M., Teach S.J., Togias A., Boushey H.A., Gern J.E., Jackson D.J. , Lynch S.V.",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,"16S rRNA, Microbiota, Moraxella species, Staphylococcus species, airway, asthma, exacerbation, rhinovirus",Experiment 7,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,samples with no rhinovirus infection,samples with any rhinovirus infection,samples with rhinovirus infection,1883,1239,NA,16S,4,Illumina,relative abundances,Zero-Inflated Beta Regression,0.15,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table I,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between samples with any viral infection and samples without,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:31201890/8/1,31201890,"cross-sectional observational, not case-control",31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K., Durack J., Valladares R., Fadrosh D.W., Lin D.L., Calatroni A., LeBeau P.K., Tran H.T., Fujimura K.E., LaMere B., Merana G., Lynch K., Cohen R.T., Pongracic J., Khurana Hershey G.K., Kercsmar C.M., Gill M., Liu A.H., Kim H., Kattan M., Teach S.J., Togias A., Boushey H.A., Gern J.E., Jackson D.J. , Lynch S.V.",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,"16S rRNA, Microbiota, Moraxella species, Staphylococcus species, airway, asthma, exacerbation, rhinovirus",Experiment 8,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,Rhinovirus-negative samples,Samples with rhinovirus A,Samples with rhinovirus A present,1883,386,NA,16S,4,Illumina,relative abundances,Zero-Inflated Beta Regression,0.15,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table I,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between samples infected with rhinovirus-A and samples with no rhinovirus detected,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:31201890/8/2,31201890,"cross-sectional observational, not case-control",31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K., Durack J., Valladares R., Fadrosh D.W., Lin D.L., Calatroni A., LeBeau P.K., Tran H.T., Fujimura K.E., LaMere B., Merana G., Lynch K., Cohen R.T., Pongracic J., Khurana Hershey G.K., Kercsmar C.M., Gill M., Liu A.H., Kim H., Kattan M., Teach S.J., Togias A., Boushey H.A., Gern J.E., Jackson D.J. , Lynch S.V.",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,"16S rRNA, Microbiota, Moraxella species, Staphylococcus species, airway, asthma, exacerbation, rhinovirus",Experiment 8,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Asthma,MONDO:0004979,Rhinovirus-negative samples,Samples with rhinovirus A,Samples with rhinovirus A present,1883,386,NA,16S,4,Illumina,relative abundances,Zero-Inflated Beta Regression,0.15,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table I,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between samples infected with rhinovirus-A and samples with no rhinovirus detected,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,Claregrieve1
bsdb:31205521/1/1,31205521,case-control,31205521,10.7150/jca.28077,NA,"Zhang W., Luo J., Dong X., Zhao S., Hao Y., Peng C., Shi H., Zhou Y., Shan L., Sun Q., Li Y. , Zhao X.",Salivary Microbial Dysbiosis is Associated with Systemic Inflammatory Markers and Predicted Oral Metabolites in Non-Small Cell Lung Cancer Patients,Journal of Cancer,2019,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Lung cancer,MONDO:0008903,Healthy controls,NSCLC,Newly diagnosed NSCLC (non-small cell lung cancer) patients,20,39,6 months,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"age,body mass index,sex",NA,NA,increased,unchanged,increased,NA,unchanged,Signature 1,Figure 3 (B),10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy","(b) Histogram of the linear discriminant analysis (LDA) scores for differentially abundant bacterial
taxa between non-small cell lung cancer patients and healthy controls. Only taxa meeting an LDA significant threshold > 4.0 are shown. Red (HC) indicates the healthy controls, and green (NSCLC), non-small cell lung cancer group",increased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia",3379134|1224;3379134|1224|28216;3379134|1224|28216|80840;1783272|1239|91061;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826;3379134|1224|28216|80840|119060;3379134|1224|28216|80840|119060|47670,Complete,Peace Sandy
bsdb:31205521/1/2,31205521,case-control,31205521,10.7150/jca.28077,NA,"Zhang W., Luo J., Dong X., Zhao S., Hao Y., Peng C., Shi H., Zhou Y., Shan L., Sun Q., Li Y. , Zhao X.",Salivary Microbial Dysbiosis is Associated with Systemic Inflammatory Markers and Predicted Oral Metabolites in Non-Small Cell Lung Cancer Patients,Journal of Cancer,2019,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Lung cancer,MONDO:0008903,Healthy controls,NSCLC,Newly diagnosed NSCLC (non-small cell lung cancer) patients,20,39,6 months,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"age,body mass index,sex",NA,NA,increased,unchanged,increased,NA,unchanged,Signature 2,Figure 3 (B),10 January 2021,Fatima Zohra,"WikiWorks,Peace Sandy","(b) Histogram of the linear discriminant analysis (LDA) scores for differentially abundant bacterial taxa between non-small cell lung cancer patients and healthy controls. Only taxa meeting an LDA significant threshold > 4.0 are shown. Red (HC) indicates the healthy controls, and green (NSCLC), non-small cell lung cancer group",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",3379134|976|200643|171549|171551;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552;3379134|976;3379134|976|200643;3379134|976|200643|171549,Complete,Peace Sandy
bsdb:31206804/1/1,31206804,case-control,31206804,10.1111/pai.13096,NA,"Chiu C.Y., Cheng M.L., Chiang M.H., Kuo Y.L., Tsai M.H., Chiu C.C. , Lin G.",Gut microbial-derived butyrate is inversely associated with IgE responses to allergens in childhood asthma,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2019,"Clostridium spp., asthma, butyrate, histidine, mite-specific IgE, β-alanine",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,healthy control,asthma,child age 4-7 years with physician diagnosed asthma,24,34,1 month,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2a, Text (Association between gut metabolites and microbiota for rhinitis and asthma)",10 January 2021,Lucy Mellor,"WikiWorks,Folakunmi",Differential expression of genera of bacteria between children with asthma and health controls,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239|186801|186802|31979|1485;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|561;1783272|1239|186801|186802|186806|1730;1783272|1239|91061|186826|33958|1578,Complete,Folakunmi
bsdb:31206804/1/2,31206804,case-control,31206804,10.1111/pai.13096,NA,"Chiu C.Y., Cheng M.L., Chiang M.H., Kuo Y.L., Tsai M.H., Chiu C.C. , Lin G.",Gut microbial-derived butyrate is inversely associated with IgE responses to allergens in childhood asthma,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2019,"Clostridium spp., asthma, butyrate, histidine, mite-specific IgE, β-alanine",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Asthma,MONDO:0004979,healthy control,asthma,child age 4-7 years with physician diagnosed asthma,24,34,1 month,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2a, Text (Association between gut metabolites and microbiota for rhinitis and asthma)",10 January 2021,Lucy Mellor,"WikiWorks,Folakunmi",Differential expression of genera of bacteria between children with asthma and health controls,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|841,Complete,Folakunmi
bsdb:31206804/2/1,31206804,case-control,31206804,10.1111/pai.13096,NA,"Chiu C.Y., Cheng M.L., Chiang M.H., Kuo Y.L., Tsai M.H., Chiu C.C. , Lin G.",Gut microbial-derived butyrate is inversely associated with IgE responses to allergens in childhood asthma,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2019,"Clostridium spp., asthma, butyrate, histidine, mite-specific IgE, β-alanine",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Allergic rhinitis,EFO:0005854,healthy control,allergic rhinitis,child age 4-7 years with physician diagnosed allergic rhinitis,24,27,1 month,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2a, Text",10 January 2021,Lucy Mellor,WikiWorks,Differential expression of genera of bacteria between children with allergic rhinitis and health controls,increased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,1783272|201174|84998|1643822|1643826|447020,Complete,Folakunmi
bsdb:31206804/2/2,31206804,case-control,31206804,10.1111/pai.13096,NA,"Chiu C.Y., Cheng M.L., Chiang M.H., Kuo Y.L., Tsai M.H., Chiu C.C. , Lin G.",Gut microbial-derived butyrate is inversely associated with IgE responses to allergens in childhood asthma,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2019,"Clostridium spp., asthma, butyrate, histidine, mite-specific IgE, β-alanine",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Allergic rhinitis,EFO:0005854,healthy control,allergic rhinitis,child age 4-7 years with physician diagnosed allergic rhinitis,24,27,1 month,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2a, Text",10 January 2021,Lucy Mellor,"WikiWorks,Folakunmi",Differential expression of genera of bacteria between children with allergic rhinitis and health controls,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea",1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|189330,Complete,Folakunmi
bsdb:31211854/1/1,31211854,case-control,31211854,10.1111/sji.12799,NA,"Huang S., Mao J., Zhou L., Xiong X. , Deng Y.",The imbalance of gut microbiota and its correlation with plasma inflammatory cytokines in pemphigus vulgaris patients,Scandinavian journal of immunology,2019,"cytokines, gut microbiota, pemphigus vulgaris",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Pemphigus vulgaris,EFO:0004719,healthy control,Pemphigus vulgaris (PV)  Patients,Patients with pemphigus vulgaris,14,18,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 2b,10 January 2021,Lucy Mellor,"Chloe,WikiWorks",Bacterial taxa difference between pemphigus vulgaris (PV) patients and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",1783272|1239|91061|186826|186827|46123;1783272|1239|91061|186826|186827;1783272|1239|91061;1783272|1239|91061|186826|186828;1783272|1239|526524|526525|2810280|100883;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|186801|186802|216572|946234;3379134|1224|1236;1783272|1239|91061|186826|186828|117563;1783272|1239|91061|186826;1783272|1239|91061|186826|1300;3379134|1224|1236|91347|543|1940338,Complete,Chloe
bsdb:31211854/1/2,31211854,case-control,31211854,10.1111/sji.12799,NA,"Huang S., Mao J., Zhou L., Xiong X. , Deng Y.",The imbalance of gut microbiota and its correlation with plasma inflammatory cytokines in pemphigus vulgaris patients,Scandinavian journal of immunology,2019,"cytokines, gut microbiota, pemphigus vulgaris",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Pemphigus vulgaris,EFO:0004719,healthy control,Pemphigus vulgaris (PV)  Patients,Patients with pemphigus vulgaris,14,18,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 2b,10 January 2021,Lucy Mellor,"WikiWorks,Merit",Bacterial taxa difference between pemphigus vulgaris (PV) patients and healthy controls,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus",3379134|1224|28211;3379134|1224|28216;3379134|1224|28216|80840;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|33042,Complete,Chloe
bsdb:31215600/1/1,31215600,"cross-sectional observational, not case-control",31215600,10.1590/1678-7757-2018-0635,NA,"Yokoi A., Ekuni D., Hata H., Yamane-Takeuchi M., Maruyama T., Yamanaka R. , Morita M.",Relationship between acetaldehyde concentration in mouth air and characteristics of microbiota of tongue dorsum in Japanese healthy adults: a cross-sectional study,Journal of applied oral science : revista FOB,2019,NA,Experiment 1,Japan,Homo sapiens,Mouth,UBERON:0000165,Acetaldehyde,CHEBI:15343,low acetaldehyde concentration group,high acetaldehyde concentration group,"The Sensor Gas Chromatograph SGEA-P2 (FIS Inc., Itami, Japan) was used to measure acetaldehyde concentrations in mouth air.",6,6,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Difference in relative abundance of tongue microbiome between High acetaldehyde concentration group and Low acetaldehyde concentration group.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens",1783272|1239|91061|1385|539738|1378|84135;1783272|1239|909932|1843489|31977|29465|29466;3379134|1224|28216|206351|481|482|484,Complete,NA
bsdb:31215600/1/2,31215600,"cross-sectional observational, not case-control",31215600,10.1590/1678-7757-2018-0635,NA,"Yokoi A., Ekuni D., Hata H., Yamane-Takeuchi M., Maruyama T., Yamanaka R. , Morita M.",Relationship between acetaldehyde concentration in mouth air and characteristics of microbiota of tongue dorsum in Japanese healthy adults: a cross-sectional study,Journal of applied oral science : revista FOB,2019,NA,Experiment 1,Japan,Homo sapiens,Mouth,UBERON:0000165,Acetaldehyde,CHEBI:15343,low acetaldehyde concentration group,high acetaldehyde concentration group,"The Sensor Gas Chromatograph SGEA-P2 (FIS Inc., Itami, Japan) was used to measure acetaldehyde concentrations in mouth air.",6,6,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Shaimaa Elsafoury,WikiWorks,Difference in relative abundance of tongue microbiome between High acetaldehyde concentration group and Low acetaldehyde concentration group.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola",1783272|1239|91061|186826|1300|1301|1318;3379134|976|200643|171549|171552|838|470565,Complete,NA
bsdb:31219947/1/1,31219947,case-control,31219947,10.1097/j.pain.0000000000001640,NA,"Minerbi A., Gonzalez E., Brereton N.J.B., Anjarkouchian A., Dewar K., Fitzcharles M.A., Chevalier S. , Shir Y.",Altered microbiome composition in individuals with fibromyalgia,Pain,2019,NA,Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Fibromyalgia,EFO:0005687,Unrelated control (UC) group,Fibromyalgia patient (FM) group,"Individuals with fibromyalgia (FM), a prevalent syndrome, characterised by chronic widespread pain, fatigue, and impaired sleep, that is challenging to diagnose and difficult to treat",48,77,2 months,16S,56,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3A, 3B, Supplementary table DA OTUS (FM vs UC)",27 November 2025,Tosin,Tosin,Significant differentially abundant operational taxonomic units (OTUs) between the Fibromyalgia (FM) individuals and unrelated controls (UC) using differential expression analysis for sequencing data version 2 (DESeq2),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum desmolans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hydrogenotrophica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia massiliensis (ex Liu et al. 2021),k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella tayi,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",1783272|1239|186801|3120394|3120654|35829;1783272|1239|186801|186802|3085642|2048137|39484;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550|239759|328813;1783272|1239;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511|53443;1783272|1239|186801|3085636|186803|572511|3062492;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107;1783272|1239|186801|3085636|186803|1432051|1720294;1783272|1239|186801|3085636|186803|1432051|1432052;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|1649459|154046;1783272|1239|186801|186802|1392389|1297617;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|46503;1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|186801|3085636|186803|1506553|29347;1783272|1239|186801|3085636|186803|572511,Complete,KateRasheed
bsdb:31219947/1/2,31219947,case-control,31219947,10.1097/j.pain.0000000000001640,NA,"Minerbi A., Gonzalez E., Brereton N.J.B., Anjarkouchian A., Dewar K., Fitzcharles M.A., Chevalier S. , Shir Y.",Altered microbiome composition in individuals with fibromyalgia,Pain,2019,NA,Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Fibromyalgia,EFO:0005687,Unrelated control (UC) group,Fibromyalgia patient (FM) group,"Individuals with fibromyalgia (FM), a prevalent syndrome, characterised by chronic widespread pain, fatigue, and impaired sleep, that is challenging to diagnose and difficult to treat",48,77,2 months,16S,56,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3A, 3B, Supplementary table DA OTUS (FM vs UC)",27 November 2025,Allan,"Allan,Tosin",Significant differentially abundant operational taxonomic units (OTUs) between the Fibromyalgia (FM) individuals and unrelated controls (UC) using differential expression analysis for sequencing data version 2 (DESeq2),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri",3379134|976|200643|171549|815|816|820;1783272|1239|186801|3085636|186803|572511|871665;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712|724|729;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171552|2974251|165179,Complete,KateRasheed
bsdb:31221587/1/1,31221587,case-control,31221587,10.1016/j.ebiom.2019.05.064,NA,"Aho V.T.E., Pereira P.A.B., Voutilainen S., Paulin L., Pekkonen E., Auvinen P. , Scheperjans F.",Gut microbiota in Parkinson's disease: Temporal stability and relations to disease progression,EBioMedicine,2019,"Disease progression, Gut microbiota, Gut-brain-axis, Parkinson's disease",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls at baseline,Participants with Parkinson's Disease at baseline,Patients with Parkinson's disease at baseline.,64,64,NA,16S,34,Illumina,raw counts,"ANCOM,DESeq2",0.05,TRUE,NA,"age,sex","body mass index,irritable bowel syndrome",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Table 8, Supplemental. Table S4C",2 February 2023,Fcuevas3,"Fcuevas3,Folakunmi,ChiomaBlessing,WikiWorks","Taxa that are differentially abundant between control and PD groups, according to ANCOM and DESeq2 at Baseline",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia",3379134|976|200643|171549|171550|239759;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3082720|186804|1501226,Complete,ChiomaBlessing
bsdb:31221587/1/2,31221587,case-control,31221587,10.1016/j.ebiom.2019.05.064,NA,"Aho V.T.E., Pereira P.A.B., Voutilainen S., Paulin L., Pekkonen E., Auvinen P. , Scheperjans F.",Gut microbiota in Parkinson's disease: Temporal stability and relations to disease progression,EBioMedicine,2019,"Disease progression, Gut microbiota, Gut-brain-axis, Parkinson's disease",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls at baseline,Participants with Parkinson's Disease at baseline,Patients with Parkinson's disease at baseline.,64,64,NA,16S,34,Illumina,raw counts,"ANCOM,DESeq2",0.05,TRUE,NA,"age,sex","body mass index,irritable bowel syndrome",NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,"Table 8, Supplemental. Table S4C",2 February 2023,Fcuevas3,"Fcuevas3,Folakunmi,ChiomaBlessing,WikiWorks","Taxa that are differentially abundant between control and PD groups, according to ANCOM and DESeq2 at Baseline",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|1853231|574697;3379134|976|200643|171549|171551;3379134|976|200643|171549|171552|838;1783272|1239|909932|1843489|31977;1783272|1239|909932|1843489|31977|39948,Complete,ChiomaBlessing
bsdb:31221587/2/1,31221587,case-control,31221587,10.1016/j.ebiom.2019.05.064,NA,"Aho V.T.E., Pereira P.A.B., Voutilainen S., Paulin L., Pekkonen E., Auvinen P. , Scheperjans F.",Gut microbiota in Parkinson's disease: Temporal stability and relations to disease progression,EBioMedicine,2019,"Disease progression, Gut microbiota, Gut-brain-axis, Parkinson's disease",Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Stable PD patients at follow up,Progressed PD patients at follow up,"Patients with progressed Parkinson's disease, defined based
on between-timepoint change in Unified Parkinson's Disease Rating
Scale (UPDRS) I-III sum and total medication load calculated using the
Levodopa Equivalent Dose (LED).",41,15,NA,16S,34,Illumina,raw counts,"ANCOM,DESeq2",0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Table 9: Follow up.,2 February 2023,Fcuevas3,"Fcuevas3,Folakunmi,ChiomaBlessing,WikiWorks",Summary of differential abundance results contrasting follow-up progressed and stable PD patients,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|201174|1760|85004|31953|1678;1783272|544448|31969|186332|186333;1783272|544448|31969|186332|186333|2152;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802,Complete,ChiomaBlessing
bsdb:31221587/2/2,31221587,case-control,31221587,10.1016/j.ebiom.2019.05.064,NA,"Aho V.T.E., Pereira P.A.B., Voutilainen S., Paulin L., Pekkonen E., Auvinen P. , Scheperjans F.",Gut microbiota in Parkinson's disease: Temporal stability and relations to disease progression,EBioMedicine,2019,"Disease progression, Gut microbiota, Gut-brain-axis, Parkinson's disease",Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Stable PD patients at follow up,Progressed PD patients at follow up,"Patients with progressed Parkinson's disease, defined based
on between-timepoint change in Unified Parkinson's Disease Rating
Scale (UPDRS) I-III sum and total medication load calculated using the
Levodopa Equivalent Dose (LED).",41,15,NA,16S,34,Illumina,raw counts,"ANCOM,DESeq2",0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,Table 9: Follow-up,10 January 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Summary of differential abundance results contrasting follow-up progressed and stable PD patients,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",3379134|976|200643|171549|171552|838;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3085636|186803|33042;3379134|200940|3031449|213115|194924|872,Complete,ChiomaBlessing
bsdb:31221587/3/1,31221587,case-control,31221587,10.1016/j.ebiom.2019.05.064,NA,"Aho V.T.E., Pereira P.A.B., Voutilainen S., Paulin L., Pekkonen E., Auvinen P. , Scheperjans F.",Gut microbiota in Parkinson's disease: Temporal stability and relations to disease progression,EBioMedicine,2019,"Disease progression, Gut microbiota, Gut-brain-axis, Parkinson's disease",Experiment 3,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls at time of follow-up,Participants with Parkinson's Disease at time of follow-up,Participants with Parkinson's Disease at time of follow-up,64,64,NA,16S,34,Illumina,raw counts,"ANCOM,DESeq2",0.05,TRUE,NA,"age,sex","body mass index,irritable bowel syndrome",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Table 8, Supplemental. Table S4C",2 February 2023,Fcuevas3,"Fcuevas3,Folakunmi,ChiomaBlessing,WikiWorks","Taxa that are differentially abundant between control and PD groups, according to ANCOM and DESeq2 at Follow-up.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia",1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3082720|186804|1501226,Complete,ChiomaBlessing
bsdb:31221587/3/2,31221587,case-control,31221587,10.1016/j.ebiom.2019.05.064,NA,"Aho V.T.E., Pereira P.A.B., Voutilainen S., Paulin L., Pekkonen E., Auvinen P. , Scheperjans F.",Gut microbiota in Parkinson's disease: Temporal stability and relations to disease progression,EBioMedicine,2019,"Disease progression, Gut microbiota, Gut-brain-axis, Parkinson's disease",Experiment 3,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls at time of follow-up,Participants with Parkinson's Disease at time of follow-up,Participants with Parkinson's Disease at time of follow-up,64,64,NA,16S,34,Illumina,raw counts,"ANCOM,DESeq2",0.05,TRUE,NA,"age,sex","body mass index,irritable bowel syndrome",NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,"Table 8, Supplemental. Table S4C",2 February 2023,Fcuevas3,"Fcuevas3,Folakunmi,ChiomaBlessing,WikiWorks","Taxa that are differentially abundant between control and PD groups, according to ANCOM and DESeq2 at Follow-up.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Puniceicoccaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|976|200643|171549|815|816;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|74201|414999|415001|415002;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|171551;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977,Complete,ChiomaBlessing
bsdb:31221587/4/1,31221587,case-control,31221587,10.1016/j.ebiom.2019.05.064,NA,"Aho V.T.E., Pereira P.A.B., Voutilainen S., Paulin L., Pekkonen E., Auvinen P. , Scheperjans F.",Gut microbiota in Parkinson's disease: Temporal stability and relations to disease progression,EBioMedicine,2019,"Disease progression, Gut microbiota, Gut-brain-axis, Parkinson's disease",Experiment 4,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Tremor-dominant phenotype (TD) at baseline,Postural instability and gait difficulty (PIGD) phenotype at baseline,Parkinson's disease patients with PIGD phenotype at baseline.,21,28,NA,16S,34,Illumina,raw counts,"ANCOM,DESeq2",0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Table S8 (B) in supplementary results.,16 October 2023,Folakunmi,"Folakunmi,ChiomaBlessing,MyleeeA,WikiWorks",Differential abundance comparison results for disease phenotype (TD vs PIGD; within the PD patient group) at baseline.,decreased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,c__Deltaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|544448|31969|186332|186333;1783272|544448|31969|186332|186333|2152;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|1432051;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|1940338;1783272|1239|91061|186826|1300|1357;3379134|976|200643|171549|171552|838;28221;1783272|1239|186801|3085636|186803,Complete,ChiomaBlessing
bsdb:31221587/4/2,31221587,case-control,31221587,10.1016/j.ebiom.2019.05.064,NA,"Aho V.T.E., Pereira P.A.B., Voutilainen S., Paulin L., Pekkonen E., Auvinen P. , Scheperjans F.",Gut microbiota in Parkinson's disease: Temporal stability and relations to disease progression,EBioMedicine,2019,"Disease progression, Gut microbiota, Gut-brain-axis, Parkinson's disease",Experiment 4,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Tremor-dominant phenotype (TD) at baseline,Postural instability and gait difficulty (PIGD) phenotype at baseline,Parkinson's disease patients with PIGD phenotype at baseline.,21,28,NA,16S,34,Illumina,raw counts,"ANCOM,DESeq2",0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,Table S8 (B) in supplementary results.,16 October 2023,Folakunmi,"Folakunmi,ChiomaBlessing,WikiWorks",Differential abundance comparison results for disease phenotype (TD vs PIGD; within the PD patient group) at baseline.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|830;1783272|1239|186801|186802|204475;1783272|1239|909932|1843488|909930;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802;,Complete,ChiomaBlessing
bsdb:31221587/5/1,31221587,case-control,31221587,10.1016/j.ebiom.2019.05.064,NA,"Aho V.T.E., Pereira P.A.B., Voutilainen S., Paulin L., Pekkonen E., Auvinen P. , Scheperjans F.",Gut microbiota in Parkinson's disease: Temporal stability and relations to disease progression,EBioMedicine,2019,"Disease progression, Gut microbiota, Gut-brain-axis, Parkinson's disease",Experiment 5,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Tremor-dominant phenotype (TD) at follow-up,Postural instability and gait difficulty (PIGD) phenotype at follow-up,Parkinson's disease patients with PIGD phenotype at follow-up,20,35,NA,16S,34,Illumina,raw counts,"ANCOM,DESeq2",0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Table S8 (B) in supplementary results.,16 October 2023,Folakunmi,"Folakunmi,Peace Sandy,Hodan Issah,ChiomaBlessing,WikiWorks",Differential abundance comparison results for disease phenotype (TD vs PIGD; within the PD patient group) at follow-up,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia",3379134|976|200643|171549|2005519|397864;1783272|1239|91061|186826|1300|1357;1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171551;1783272|544448|31969|186332|186333;1783272|544448|31969|186332|186333|2152;1783272|1239|186801|186802;1783272|1239|186801,Complete,ChiomaBlessing
bsdb:31221587/5/2,31221587,case-control,31221587,10.1016/j.ebiom.2019.05.064,NA,"Aho V.T.E., Pereira P.A.B., Voutilainen S., Paulin L., Pekkonen E., Auvinen P. , Scheperjans F.",Gut microbiota in Parkinson's disease: Temporal stability and relations to disease progression,EBioMedicine,2019,"Disease progression, Gut microbiota, Gut-brain-axis, Parkinson's disease",Experiment 5,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Tremor-dominant phenotype (TD) at follow-up,Postural instability and gait difficulty (PIGD) phenotype at follow-up,Parkinson's disease patients with PIGD phenotype at follow-up,20,35,NA,16S,34,Illumina,raw counts,"ANCOM,DESeq2",0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,Table S8 (B) in supplementary results.,16 October 2023,Folakunmi,"Folakunmi,WikiWorks",Differential abundance comparison results for disease phenotype (TD vs PIGD; within the PD patient group),increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|186802|216572,Complete,ChiomaBlessing
bsdb:31221587/6/1,31221587,case-control,31221587,10.1016/j.ebiom.2019.05.064,NA,"Aho V.T.E., Pereira P.A.B., Voutilainen S., Paulin L., Pekkonen E., Auvinen P. , Scheperjans F.",Gut microbiota in Parkinson's disease: Temporal stability and relations to disease progression,EBioMedicine,2019,"Disease progression, Gut microbiota, Gut-brain-axis, Parkinson's disease",Experiment 6,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Stable PD patients at baseline,Progressed PD patients at baseline,"Patients with progressed Parkinson's disease, defined based
on between-timepoint change in Unified Parkinson's Disease Rating
Scale (UPDRS) I-III sum and total medication load calculated using the
Levodopa Equivalent Dose (LED).",41,15,NA,16S,34,Illumina,raw counts,DESeq2,0.05,FALSE,NA,"age,sex",NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Table 9: Baseline,11 January 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Summary of differential abundance results contrasting follow-up progressed and stable PD patients,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803,Complete,ChiomaBlessing
bsdb:31221587/6/2,31221587,case-control,31221587,10.1016/j.ebiom.2019.05.064,NA,"Aho V.T.E., Pereira P.A.B., Voutilainen S., Paulin L., Pekkonen E., Auvinen P. , Scheperjans F.",Gut microbiota in Parkinson's disease: Temporal stability and relations to disease progression,EBioMedicine,2019,"Disease progression, Gut microbiota, Gut-brain-axis, Parkinson's disease",Experiment 6,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Stable PD patients at baseline,Progressed PD patients at baseline,"Patients with progressed Parkinson's disease, defined based
on between-timepoint change in Unified Parkinson's Disease Rating
Scale (UPDRS) I-III sum and total medication load calculated using the
Levodopa Equivalent Dose (LED).",41,15,NA,16S,34,Illumina,raw counts,DESeq2,0.05,FALSE,NA,"age,sex",NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,Table 9: Baseline,11 January 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Summary of differential abundance results contrasting follow-up progressed and stable PD patients,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",3379134|976|200643|171549|171552|838;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3085636|186803|33042;3379134|200940|3031449|213115|194924|872,Complete,ChiomaBlessing
bsdb:31226994/1/1,31226994,prospective cohort,31226994,10.1186/s12941-019-0318-9,NA,"Zhang M., Differding M.K., Benjamin-Neelon S.E., Østbye T., Hoyo C. , Mueller N.T.",Association of prenatal antibiotics with measures of infant adiposity and the gut microbiome,Annals of clinical microbiology and antimicrobials,2019,"Antibiotic, Child health, Gut microbiome, Pediatric obesity, Pregnancy, Prenatal exposure",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,3-month old infants not exposed to antibiotics during the second trimester,3-month-old infants exposed to antibiotics in the second trimester,infants born after 28 weeks gestation with no congenital abnormalities who were exposed to antibiotics during the second trimester,56,12,NA,16S,4,Illumina,NA,Beta Binomial Regression,0.05,TRUE,NA,NA,"body mass index,education level,household income,marital status,maternal age,race,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1, Table S2",10 January 2021,Mst Afroza Parvin,"Claregrieve1,WikiWorks",Differential microbial abundance between infants who were and were not exposed to antibiotics in the second trimester,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",1783272|1239|186801|3085636|186803|1407607;1783272|1239|91061|186826|81852|1350,Complete,Claregrieve1
bsdb:31226994/1/2,31226994,prospective cohort,31226994,10.1186/s12941-019-0318-9,NA,"Zhang M., Differding M.K., Benjamin-Neelon S.E., Østbye T., Hoyo C. , Mueller N.T.",Association of prenatal antibiotics with measures of infant adiposity and the gut microbiome,Annals of clinical microbiology and antimicrobials,2019,"Antibiotic, Child health, Gut microbiome, Pediatric obesity, Pregnancy, Prenatal exposure",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,3-month old infants not exposed to antibiotics during the second trimester,3-month-old infants exposed to antibiotics in the second trimester,infants born after 28 weeks gestation with no congenital abnormalities who were exposed to antibiotics during the second trimester,56,12,NA,16S,4,Illumina,NA,Beta Binomial Regression,0.05,TRUE,NA,NA,"body mass index,education level,household income,marital status,maternal age,race,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 1, Table S2",15 July 2022,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between infants who were and were not exposed to antibiotics in the second trimester,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium neonatale,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus antri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979|1485|137838;3379134|1224|1236|91347|543;1783272|1239|91061|186826|33958|2742598|227943;3379134|1224|1236|135625|712;1783272|201174|1760|2037|2049|2529408|1660;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:31226994/3/1,31226994,prospective cohort,31226994,10.1186/s12941-019-0318-9,NA,"Zhang M., Differding M.K., Benjamin-Neelon S.E., Østbye T., Hoyo C. , Mueller N.T.",Association of prenatal antibiotics with measures of infant adiposity and the gut microbiome,Annals of clinical microbiology and antimicrobials,2019,"Antibiotic, Child health, Gut microbiome, Pediatric obesity, Pregnancy, Prenatal exposure",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,12-month-old infants not exposed to antibiotics during the second trimester,12-month-old infants exposed to antibiotics during the second trimester,infants born after 28 weeks gestation with no congenital abnormalities who were exposed to antibiotics during the second trimester,40,10,NA,16S,4,Illumina,NA,Beta Binomial Regression,0.05,TRUE,NA,NA,"body mass index,education level,household income,marital status,maternal age,race,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1, Table S2",10 January 2021,Mst Afroza Parvin,"Claregrieve1,WikiWorks",Differential microbial abundance between infants who were and were not exposed to antibiotics in the second trimester,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803;1783272|1239|186801|3082720|186804;1783272|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:31226994/3/2,31226994,prospective cohort,31226994,10.1186/s12941-019-0318-9,NA,"Zhang M., Differding M.K., Benjamin-Neelon S.E., Østbye T., Hoyo C. , Mueller N.T.",Association of prenatal antibiotics with measures of infant adiposity and the gut microbiome,Annals of clinical microbiology and antimicrobials,2019,"Antibiotic, Child health, Gut microbiome, Pediatric obesity, Pregnancy, Prenatal exposure",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,12-month-old infants not exposed to antibiotics during the second trimester,12-month-old infants exposed to antibiotics during the second trimester,infants born after 28 weeks gestation with no congenital abnormalities who were exposed to antibiotics during the second trimester,40,10,NA,16S,4,Illumina,NA,Beta Binomial Regression,0.05,TRUE,NA,NA,"body mass index,education level,household income,marital status,maternal age,race,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 1, Table S2",10 January 2021,Mst Afroza Parvin,"Claregrieve1,WikiWorks",Differential microbial abundance between infants who were and were not exposed to antibiotics in the second trimester,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485;3379134|1224|1236|91347|543;1783272|1239|186801|186802|204475;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3082720|186804;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|423477,Complete,Claregrieve1
bsdb:31231345/1/1,31231345,case-control,31231345,10.3389/fmicb.2019.01261,NA,"Chen X.H., Wang A., Chu A.N., Gong Y.H. , Yuan Y.",Mucosa-Associated Microbiota in Gastric Cancer Tissues Compared With Non-cancer Tissues,Frontiers in microbiology,2019,"16S rDNA, cancer microenvironment, gastric cancer, microbiota, risk",Experiment 1,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,adjacent normal tissue,cancer tissue,gastric cancer patients who underwent subtotal gastrectomy,62,62,1 month,16S,45,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure 3,10 January 2021,Valentina Pineda,WikiWorks,Differential bacteria between non-cancerous tissues and cancerous tissues in Gastric Cancer Patients by LEfSe analysis,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacillati|p__Actinomycetota|c__Thermoleophilia,k__Pseudomonadati|p__Acidobacteriota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Bacillati|p__Bacillota",3379134|1224|28211|356;1783272|201174|1497346;3379134|57723;1783272|1239|909932|909929|1843491|970;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|2974251|28135;1783272|1239|186801|3085636|186803|1164882;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|909929;1783272|1239|909932;1783272|1239|909932|1843489|31977;1783272|1239|186801|3082720|186804|1257;1783272|1239|186801|3085636|186803;3379134|1224|28211|204457|41297|13687;1783272|201174;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171552|838|28129;3379134|1224|1236|2887326|468|469;3379134|1224|1236|2887326|468;3379134|976|200643|171549|171552;3379134|1224|1236|2887326|468|469|470;1783272|1239|186801|186802;1783272|1239|186801;1783272|1239|91061|1385|186817;1783272|1239|91061|1385|186817|1386;3379134|976|200643|171549;3379134|976|200643;1783272|1239|91061;3379134|976;1783272|1239|91061|1385;3379134|1224|1236|72274|135621|286|287;1783272|1239,Complete,Folakunmi
bsdb:31231345/1/2,31231345,case-control,31231345,10.3389/fmicb.2019.01261,NA,"Chen X.H., Wang A., Chu A.N., Gong Y.H. , Yuan Y.",Mucosa-Associated Microbiota in Gastric Cancer Tissues Compared With Non-cancer Tissues,Frontiers in microbiology,2019,"16S rDNA, cancer microenvironment, gastric cancer, microbiota, risk",Experiment 1,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,adjacent normal tissue,cancer tissue,gastric cancer patients who underwent subtotal gastrectomy,62,62,1 month,16S,45,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Figure3,10 January 2021,Valentina Pineda,WikiWorks,Differential bacteria between non-cancerous tissues and cancerous tissues in Gastric Cancer Patients by LEfSe analysis,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter pylori,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia marcescens,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Niveispirillum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Levilactobacillus|s__Levilactobacillus brevis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales",3379134|1224|1236|91347|543;3379134|1224|1236|91347;3379134|1224|1236|91347|1903411|613;3379134|29547|3031852|213849|72293|209|210;3379134|29547|3031852|213849|72293;3379134|29547|3031852|213849|72293|209;3379134|1224|1236|91347|1903411|613|615;3379134|29547|3031852|213849;3379134|29547;3379134|1224|28211|204441|2829815|1543704;3379134|1224|28211|204441|41295;3379134|1224|28211|204441;1783272|1239|91061|186826|33958|2767886|1580;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|1300|1357|1358;3379134|1224|1236|135614,Complete,Folakunmi
bsdb:31231345/2/1,31231345,case-control,31231345,10.3389/fmicb.2019.01261,NA,"Chen X.H., Wang A., Chu A.N., Gong Y.H. , Yuan Y.",Mucosa-Associated Microbiota in Gastric Cancer Tissues Compared With Non-cancer Tissues,Frontiers in microbiology,2019,"16S rDNA, cancer microenvironment, gastric cancer, microbiota, risk",Experiment 2,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,H-pylori sequencing negative,H-pylori sequencing positive,H-pylori sequencing positive non-cancerous samples while studying the correlation between non-cancerous tissue microbiota and gastric cancer risk factors,44,18,1 month,16S,45,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,supplementary figure 2,29 February 2024,Folakunmi,"Folakunmi,KateRasheed,WikiWorks",Differential bacteria between H.pylori-sequencing positive and H.pylori-sequencing negative non-cancer samples by LEfSe analysis,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alishewanella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Atopostipes,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota",1783272|201174|1760|2037|2049|1654|55565;1783272|201174|1760|2037|2049|1654|1655;3379134|1224|1236|135625|712|416916;3379134|1224|1236|135622|72275|111142;3379134|1224|1236|135622|72275;1783272|1239|91061|186826|186828|292480;1783272|1239|91061;1783272|1239,Complete,Folakunmi
bsdb:31231345/2/2,31231345,case-control,31231345,10.3389/fmicb.2019.01261,NA,"Chen X.H., Wang A., Chu A.N., Gong Y.H. , Yuan Y.",Mucosa-Associated Microbiota in Gastric Cancer Tissues Compared With Non-cancer Tissues,Frontiers in microbiology,2019,"16S rDNA, cancer microenvironment, gastric cancer, microbiota, risk",Experiment 2,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,H-pylori sequencing negative,H-pylori sequencing positive,H-pylori sequencing positive non-cancerous samples while studying the correlation between non-cancerous tissue microbiota and gastric cancer risk factors,44,18,1 month,16S,45,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,supplementary figure 2,29 February 2024,Folakunmi,"Folakunmi,KateRasheed,WikiWorks",Differential bacteria between H.pylori-sequencing positive and H.pylori-sequencing negative non-cancer samples by LEfSe analysis,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae",3379134|1224|1236;3379134|976|200643|171549|171552|838|28131;3379134|976|200643|171549|171552;3379134|1224|1236|72274|135621;3379134|1224|1236|72274;3379134|1224;3379134|1224|1236|72274|135621|286;3379134|1224|1236|72274|135621|286|287;3379134|1224|28211|204457|41297,Complete,Folakunmi
bsdb:31231345/3/1,31231345,case-control,31231345,10.3389/fmicb.2019.01261,NA,"Chen X.H., Wang A., Chu A.N., Gong Y.H. , Yuan Y.",Mucosa-Associated Microbiota in Gastric Cancer Tissues Compared With Non-cancer Tissues,Frontiers in microbiology,2019,"16S rDNA, cancer microenvironment, gastric cancer, microbiota, risk",Experiment 3,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,adjacent normal tissue,cancer tissue,gastric cancer patients who underwent subtotal gastrectomy,62,62,1 month,16S,45,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,supplementary table S5,29 February 2024,Folakunmi,"Folakunmi,WikiWorks",Significantly differential bacteria identified among the top 20 abundant genera of the cancer  and non-cancer groups,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.",3379134|1224|1236|2887326|468|469;1783272|1239|91061|1385|186817|1386;3379134|976|200643|171549|815|816;3379134|1224|28211|204457|41297|13687;1783272|1239|186801|3082720|186804|1257;1783272|1239|91061|186826|1300|1301;3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|171552|838|59823,Complete,Folakunmi
bsdb:31231345/3/2,31231345,case-control,31231345,10.3389/fmicb.2019.01261,NA,"Chen X.H., Wang A., Chu A.N., Gong Y.H. , Yuan Y.",Mucosa-Associated Microbiota in Gastric Cancer Tissues Compared With Non-cancer Tissues,Frontiers in microbiology,2019,"16S rDNA, cancer microenvironment, gastric cancer, microbiota, risk",Experiment 3,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,adjacent normal tissue,cancer tissue,gastric cancer patients who underwent subtotal gastrectomy,62,62,1 month,16S,45,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,supplementary table S5,29 February 2024,Folakunmi,"Folakunmi,WikiWorks",Significantly differential bacteria identified among the top 20 abundant genera of the cancer and non-cancer groups,decreased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",3379134|29547|3031852|213849|72293|209;1783272|1239|91061|186826|33958|1578,Complete,Folakunmi
bsdb:31245306/1/1,31245306,case-control,31245306,10.3389/fcimb.2019.00206,NA,"Li F., Wang M., Wang J., Li R. , Zhang Y.",Alterations to the Gut Microbiota and Their Correlation With Inflammatory Factors in Chronic Kidney Disease,Frontiers in cellular and infection microbiology,2019,"16S rDNA deep sequencing, Akkermansia, chronic kidney disease, gut microbiota, inflammatory factors",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,healthy controls,chronic kidney disease patients,individuals diagnosed with chronic kidney disease because they exhibited an effective glomerular filtration rate of <60mL/min for a 3 month period,22,50,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 2a,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Taxonomic differences in fecal microbiota exhibited by patients with chronic kidney disease compared with healthy controls,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",1783272|201174;1783272|201174|1760|2037;1783272|201174|1760;3379134|976|200643|171549|171552|1283313;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;3379134|200940|3031449|213115|194924|872;3379134|1224|28211|356|119045;3379134|1224|28211|356|119045|407;3379134|976|200643|171549|171552|577309,Complete,Claregrieve1
bsdb:31245306/1/2,31245306,case-control,31245306,10.3389/fcimb.2019.00206,NA,"Li F., Wang M., Wang J., Li R. , Zhang Y.",Alterations to the Gut Microbiota and Their Correlation With Inflammatory Factors in Chronic Kidney Disease,Frontiers in cellular and infection microbiology,2019,"16S rDNA deep sequencing, Akkermansia, chronic kidney disease, gut microbiota, inflammatory factors",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,healthy controls,chronic kidney disease patients,individuals diagnosed with chronic kidney disease because they exhibited an effective glomerular filtration rate of <60mL/min for a 3 month period,22,50,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 2a,10 January 2021,Fatima Zohra,"Lwaldron,Claregrieve1,WikiWorks",Taxonomic differences in fecal microbiota exhibited by patients with chronic kidney disease compared with healthy controls,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres,k__Pseudomonadati|p__Deferribacterota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Pseudomonadati|p__Campylobacterota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Parvibacter,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes,k__Thermotogati|p__Synergistota,k__Thermotogati|p__Synergistota|c__Synergistia,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales",3379134|74201|203494|48461|1647988|239934;1783272|1239|526524|526525|128827|174708;1783272|1239|91061;3379134|1224|28216;3379134|1224|28216|80840;3379134|29547|3031852|213849;3379134|200930|68337|191393|191394;3379134|200930|68337|191393;3379134|200930|68337;3379134|200930;1783272|201174|84998|1643822|1643826|580024;3379134|29547;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|186806|1730;3379134|29547|3031852|213849|72293|209;3379134|29547|3031852|213849|72293;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|33958|1243;1783272|201174|1760|85006|1268;3379134|200930|68337|191393|2945020|248038;1783272|201174|84998|84999|1643824|133925;1783272|1239|186801|3085636|186803|265975;3379134|1224|28216|80840|995019|577310;1783272|201174|84998|84999|84107|1427376;3384194|508458|649775|649776|3029088|638847;1783272|201174|1760|85006|1268|32207;3379134|1224|28216|80840|995019;3384194|508458|649775|649776|649777;3384194|508458|649775|649776;3384194|508458|649775|649776|649777|2753;3384194|508458;3384194|508458|649775;3379134|74201;3379134|74201|203494|48461|203557;3379134|74201|203494;3379134|74201|203494|48461,Complete,Claregrieve1
bsdb:31247001/1/1,31247001,case-control,31247001,10.1371/journal.pone.0218252,NA,"Mihaila D., Donegan J., Barns S., LaRocca D., Du Q., Zheng D., Vidal M., Neville C., Uhlig R. , Middleton F.A.",The oral microbiome of early stage Parkinson's disease and its relationship with functional measures of motor and non-motor function,PloS one,2019,NA,Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Parkinson's disease,MONDO:0005180,Healthy age-sex matched controls without Parkinson's disease.,Participants with early stage Parkinson's Disease.,Subjects included in the Parkinson’s disease (PD) group had been previously diagnosed by a neurologist and met the general diagnostic criteria for early PD.,36,48,NA,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 4,29 November 2021,Fcuevas3,"Fcuevas3,Claregrieve1,Atrayees,WikiWorks",Significantly changed microbiota in early stage PD.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida dubliniensis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga canimorsus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae|g__Cellulosimicrobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Clavibacter|s__Clavibacter michiganensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Metazoa|p__Chordata|c__Actinopteri|o__Gerreiformes|f__Gerreidae|g__Gerres|s__Gerres decacanthus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus|s__Lactiplantibacillus plantarum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Parascardovia|s__Parascardovia denticolens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia inopinata,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Torulaspora|s__Torulaspora delbrueckii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Clavibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Parascardovia",1783272|201174|1760|85004|31953|1678|28025;1783272|201174|1760|85004|31953|1678|1689;1783272|201174|1760|85004|31953|1678|216816;4751|4890|3239874|2916678|766764|5475|5476;4751|4890|3239874|2916678|766764|5475|42374;3379134|976|117743|200644|49546|1016|28188;1783272|201174|1760|85006|85017|157920;1783272|201174|1760|85006|85023|1573|28447;1783272|201174|1760|85004|31953|2701|2702;33208|7711|186623|2024538|274463|274464|581038;1783272|1239|91061|186826|33958|2767842|1590;1783272|1239|91061|186826|33958|1578|1579;1783272|1239|91061|186826|33958|2767887|1623;1783272|1239|91061|186826|33958|2767887|1624;1783272|1239|91061|186826|33958|2742598|1613;1783272|1239|91061|186826|33958|2742598|1598;3379134|1224|28211|356|119045|407;1783272|201174|1760|85004|31953|196082|78258;1783272|201174|1760|85007|85025|1827;1783272|201174|1760|85004|31953|196081|78259;1783272|1239|91061|186826|1300|1301|1309;4751|4890|4891|4892|4893|4948|4950;3379134|1224|28211|356|118882|234;4751|4890|3239874|2916678|766764|5475;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85006|85023|1573;1783272|201174|1760|85004|31953|2701;1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85004|31953|196082,Complete,Atrayees
bsdb:31247001/1/2,31247001,case-control,31247001,10.1371/journal.pone.0218252,NA,"Mihaila D., Donegan J., Barns S., LaRocca D., Du Q., Zheng D., Vidal M., Neville C., Uhlig R. , Middleton F.A.",The oral microbiome of early stage Parkinson's disease and its relationship with functional measures of motor and non-motor function,PloS one,2019,NA,Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Parkinson's disease,MONDO:0005180,Healthy age-sex matched controls without Parkinson's disease.,Participants with early stage Parkinson's Disease.,Subjects included in the Parkinson’s disease (PD) group had been previously diagnosed by a neurologist and met the general diagnostic criteria for early PD.,36,48,NA,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 4. Significantly changed microbiota in early stage PD.,29 November 2021,Fcuevas3,"Fcuevas3,Atrayees,WikiWorks",Significantly changed microbiota in early stage PD.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Priestia|s__Priestia megaterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Buchnera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|g__Candidatus Azobacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|g__Candidatus Azobacteroides|s__Candidatus Azobacteroides pseudotrichonymphae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium sp. IHB B 17019,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|s__Flavobacteriaceae bacterium 3519-10,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Halobacillus|s__Halobacillus mangrovi,s__Streptococcus phage PhiSpn_200,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Wenyingzhuangia|s__Wenyingzhuangia fucanilytica,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter ureolyticus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Wenyingzhuangia",1783272|1239|91061|1385|186817|2800373|1404;3379134|1224|1236|91347|1903409|32199;3379134|976|200643|171549|511434;3379134|976|200643|171549|511434|511435;3379134|976|117743|200644|2762318|59732|1721091;3379134|976|117743|200644|49546|531844;1783272|1239|91061|1385|186817|45667|402384;890041;3379134|976|117743|200644|49546|1518147|1790137;3379134|29547|3031852|213849|72294|194|827;3379134|976|117743|200644|49546|1518147,Complete,Atrayees
bsdb:31248424/1/1,31248424,case-control,31248424,10.1186/s12974-019-1528-y,NA,"Lin C.H., Chen C.C., Chiang H.L., Liou J.M., Chang C.M., Lu T.P., Chuang E.Y., Tai Y.C., Cheng C., Lin H.Y. , Wu M.S.",Altered gut microbiota and inflammatory cytokine responses in patients with Parkinson's disease,Journal of neuroinflammation,2019,"Cytokines, Dysbiosis, Gut microbiome, Neuroinflammation, Parkinson’s disease",Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls without Parkinson's disease,Participants with Parkinson's Disease,PD was diagnosed according to the United Kingdom PD Society Brain Bank clinical diagnostic criteria.,77,80,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex","age,diet,sex",NA,increased,unchanged,NA,NA,increased,Signature 1,Figure 3A,22 January 2022,Fcuevas3,"Fcuevas3,WikiWorks",Taxonomic differences of fecal microbiota in PD and control groups,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales",3379134|976|200643|171549|171551;3379134|976|200643|171549|2005525|375288;3379134|74201;3379134|74201|203494|48461|203557;3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461;3379134|976|200643|171549|1853231;3379134|976|200643|171549|171550;3379134|976|200643|171549|1853231|574697;3379134|200930|68337|191393|191394;3379134|1224|28211;1783272|1239|909932|1843489|31977|29465;1783272|1239|526524;1783272|1239|526524|526525;1783272|1239|526524|526525|128827;3379134|976|200643|171549|1853231|283168;1783272|544448;3379134|200930|68337|191393|2945020|248038;3379134|200930|68337;3379134|200940|3031449|213115|194924|35832;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81850;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|33958|1578;1783272|544448|31969;3379134|1224|28211|356,Complete,Rimsha
bsdb:31248424/1/2,31248424,case-control,31248424,10.1186/s12974-019-1528-y,NA,"Lin C.H., Chen C.C., Chiang H.L., Liou J.M., Chang C.M., Lu T.P., Chuang E.Y., Tai Y.C., Cheng C., Lin H.Y. , Wu M.S.",Altered gut microbiota and inflammatory cytokine responses in patients with Parkinson's disease,Journal of neuroinflammation,2019,"Cytokines, Dysbiosis, Gut microbiome, Neuroinflammation, Parkinson’s disease",Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls without Parkinson's disease,Participants with Parkinson's Disease,PD was diagnosed according to the United Kingdom PD Society Brain Bank clinical diagnostic criteria.,77,80,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex","age,diet,sex",NA,increased,unchanged,NA,NA,increased,Signature 2,Figure 3A.,22 January 2022,Fcuevas3,"Fcuevas3,Rimsha,WikiWorks",Taxonomic differences of fecal microbiota in PD and control groups,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552,Complete,Rimsha
bsdb:31248424/2/1,31248424,case-control,31248424,10.1186/s12974-019-1528-y,NA,"Lin C.H., Chen C.C., Chiang H.L., Liou J.M., Chang C.M., Lu T.P., Chuang E.Y., Tai Y.C., Cheng C., Lin H.Y. , Wu M.S.",Altered gut microbiota and inflammatory cytokine responses in patients with Parkinson's disease,Journal of neuroinflammation,2019,"Cytokines, Dysbiosis, Gut microbiome, Neuroinflammation, Parkinson’s disease",Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Participants with Parkinson's Disease with non-tremor subtypes,Participants with Parkinson's Disease with tremor subtypes,Participants with Parkinson's Disease with tremor subtypes.,33,47,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex","age,diet,sex",NA,increased,NA,NA,NA,increased,Signature 1,Figure 4A.,22 January 2022,Fcuevas3,"Fcuevas3,Rimsha,WikiWorks",Taxonomic differences of fecal microbiota in non tremor and tremor groups.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__Eubacteriales Family XIII. Incertae Sedis bacterium,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801;1783272|1239|186801|3082720|543314|2137877;1783272|1239;3379134|74201;3379134|74201|203494|48461|203557;3379134|74201|203494;3379134|74201|203494|48461,Complete,Rimsha
bsdb:31248424/2/2,31248424,case-control,31248424,10.1186/s12974-019-1528-y,NA,"Lin C.H., Chen C.C., Chiang H.L., Liou J.M., Chang C.M., Lu T.P., Chuang E.Y., Tai Y.C., Cheng C., Lin H.Y. , Wu M.S.",Altered gut microbiota and inflammatory cytokine responses in patients with Parkinson's disease,Journal of neuroinflammation,2019,"Cytokines, Dysbiosis, Gut microbiome, Neuroinflammation, Parkinson’s disease",Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Participants with Parkinson's Disease with non-tremor subtypes,Participants with Parkinson's Disease with tremor subtypes,Participants with Parkinson's Disease with tremor subtypes.,33,47,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex","age,diet,sex",NA,increased,NA,NA,NA,increased,Signature 2,Figure 4A.,22 January 2022,Fcuevas3,"Fcuevas3,Rimsha,WikiWorks",Taxonomic differences of fecal microbiota in PD and control groups,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|1224|28216|80840|506;3379134|976|200643|171549;3379134|976;3379134|976|200643;3379134|1224|28216|80840|119060|106589;3379134|200940|3031449|213115|194924|872;3379134|976|117743|200644|49546|237;1783272|1239|186801|3082720|543314|86331;1783272|201174|1760|85009|31957|1743;3379134|1224|28216|80840|995019|40544,Complete,Rimsha
bsdb:31250341/1/1,31250341,case-control,31250341,10.1007/s11684-019-0695-7,NA,"Zhang H., Chang Y., Zheng Q., Zhang R., Hu C. , Jia W.",Altered intestinal microbiota associated with colorectal cancer,Frontiers of medicine,2019,"Devosia, Eubacterium, colorectal cancer (CRC), gut microbiota, intestinal",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy controls,colorectal cancer,diagnosed only with colorectal cancer with endoscopy,14,9,1 month,16S,6,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,"Figure 3, Supplementary table 2, table 2",10 January 2021,Fatima Zohra,WikiWorks,Altered intestinal microbiota associated with colorectal cancer,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Devosia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium",3379134|1224|28211|356|45401;3379134|1224|28211|356|2831106|46913;3379134|1224|28211|356;3379134|1224|28211;1783272|1239|91061|1385|186822|44249;1783272|1239|91061|1385|186822;3379134|976|117743|200644|2762318|59732,Complete,Atrayees
bsdb:31250341/1/2,31250341,case-control,31250341,10.1007/s11684-019-0695-7,NA,"Zhang H., Chang Y., Zheng Q., Zhang R., Hu C. , Jia W.",Altered intestinal microbiota associated with colorectal cancer,Frontiers of medicine,2019,"Devosia, Eubacterium, colorectal cancer (CRC), gut microbiota, intestinal",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy controls,colorectal cancer,diagnosed only with colorectal cancer with endoscopy,14,9,1 month,16S,6,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,"Figure 3, Supplementary table 2, table 2",10 January 2021,Fatima Zohra,WikiWorks,Altered intestinal microbiota associated with colorectal cancer,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia",3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|31979;28221;3379134|200940|3031449|213115;1783272|1239|186801|186802|186806|1730;3379134|1224|1236|91347|543|570;3384189|32066|203490|203491|1129771|32067;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3082720|543314|86331;3379134|1224|1236|91347|1903411|613,Complete,Atrayees
bsdb:31281534/1/1,31281534,case-control,31281534,10.7150/thno.35186,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6592169/,"Yang Y., Misra B.B., Liang L., Bi D., Weng W., Wu W., Cai S., Qin H., Goel A., Li X. , Ma Y.",Integrated microbiome and metabolome analysis reveals a novel interplay between commensal bacteria and metabolites in colorectal cancer,Theranostics,2019,"biomarkers, colorectal cancer, gut, metabolomics, microbiome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy controls,Colorectal Cancer patients,patients diagnosed with colorectal cancer,50,50,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,increased,unchanged,NA,NA,Signature 1,Figure 2(b),20 February 2022,Itslanapark,"Itslanapark,Aiyshaaaa,Davvve,Peace Sandy,WikiWorks",The differences in abundance between the H group and the CRC groups.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Lentisphaerales|f__Lentisphaeraceae|g__Lentisphaera,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria",3379134|74201|203494|48461|1647988|239934;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|1940338;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;3384189|32066|203490|203491|203492|848;3379134|256845|1313211|278081|566277|256846;1783272|1239|1737404|1737405|1570339|543311;3379134|976|200643|171549|171551|836;3379134|1224|1236|72274;3379134|1224;3379134|1224|1236,Complete,Peace Sandy
bsdb:31281534/1/2,31281534,case-control,31281534,10.7150/thno.35186,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6592169/,"Yang Y., Misra B.B., Liang L., Bi D., Weng W., Wu W., Cai S., Qin H., Goel A., Li X. , Ma Y.",Integrated microbiome and metabolome analysis reveals a novel interplay between commensal bacteria and metabolites in colorectal cancer,Theranostics,2019,"biomarkers, colorectal cancer, gut, metabolomics, microbiome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy controls,Colorectal Cancer patients,patients diagnosed with colorectal cancer,50,50,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,increased,unchanged,NA,NA,Signature 2,Figure 2(b),20 February 2022,Itslanapark,"Itslanapark,Aiyshaaaa,Davvve,Peace Sandy,WikiWorks",The differences in abundance between the H group and the CRC groups.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium oxidoreducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Solibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",1783272|1239|909932|1843488|909930;1783272|201174;1783272|1239;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|1732;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|995019|577310;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3085636|186803|46205;1783272|1239|186801|3082720|186804|1501226;1783272|1239|909932|909929;1783272|1239|91061|1385|186818|648800;1783272|1239|186801|186802|216572|292632,Complete,Peace Sandy
bsdb:31289031/1/1,31289031,case-control,31289031,10.1182/bloodadvances.2019032276,NA,"Pianko M.J., Devlin S.M., Littmann E.R., Chansakul A., Mastey D., Salcedo M., Fontana E., Ling L., Tavitian E., Slingerland J.B., Slingerland A.E., Clurman A., Gomes A.L.C., Taur Y., Pamer E.G., Peled J.U., van den Brink M.R.M., Landgren O. , Lesokhin A.M.",Minimal residual disease negativity in multiple myeloma is associated with intestinal microbiota composition,Blood advances,2019,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,Minimal Residual Disease+ (positivity) with Allogenic Stem Cell Transplant,Minimal Residual Disease- (negativity) with Allogenic Stem Cell Transplant,Patients with multiple myeloma (MM) who achieve minimal residual disease (MRD) negativity (MRD-) after upfront treatment,18,16,NA,16S,45,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 1,Figure 1a,10 January 2021,William Lam,WikiWorks,Linear discriminant analysis (LDA) effect size analysis of microbiota differentially associated with MRD status with subclass of autologous stem cell transplantation (ASCT),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens|s__Ethanoligenens harbinense,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter|s__Sporobacter termitidis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter",1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|186802|216572|253238|253239;1783272|1239|186801|186802|216572|253238;1783272|1239|186801|186802|216572|44748|44749;1783272|1239|186801|186802|216572|44748,Complete,Atrayees
bsdb:31289031/1/2,31289031,case-control,31289031,10.1182/bloodadvances.2019032276,NA,"Pianko M.J., Devlin S.M., Littmann E.R., Chansakul A., Mastey D., Salcedo M., Fontana E., Ling L., Tavitian E., Slingerland J.B., Slingerland A.E., Clurman A., Gomes A.L.C., Taur Y., Pamer E.G., Peled J.U., van den Brink M.R.M., Landgren O. , Lesokhin A.M.",Minimal residual disease negativity in multiple myeloma is associated with intestinal microbiota composition,Blood advances,2019,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,Minimal Residual Disease+ (positivity) with Allogenic Stem Cell Transplant,Minimal Residual Disease- (negativity) with Allogenic Stem Cell Transplant,Patients with multiple myeloma (MM) who achieve minimal residual disease (MRD) negativity (MRD-) after upfront treatment,18,16,NA,16S,45,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 2,Figure 1a,10 January 2021,William Lam,WikiWorks,Linear discriminant analysis (LDA) effect size analysis of microbiota differentially associated with MRD status with subclass of autologous stem cell transplantation (ASCT),decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces israelii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas nexilis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus equinus",1783272|201174|1760|2037|2049|1654|1659;1783272|201174|1760|2037|2049|1654|1655;1783272|201174|1760|85006;1783272|201174|1760|85006|1268;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|2047;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|186801|3085636|186803|2005355|29361;1783272|1239|91061|186826|1300|1301|1335,Complete,Atrayees
bsdb:31289031/2/1,31289031,case-control,31289031,10.1182/bloodadvances.2019032276,NA,"Pianko M.J., Devlin S.M., Littmann E.R., Chansakul A., Mastey D., Salcedo M., Fontana E., Ling L., Tavitian E., Slingerland J.B., Slingerland A.E., Clurman A., Gomes A.L.C., Taur Y., Pamer E.G., Peled J.U., van den Brink M.R.M., Landgren O. , Lesokhin A.M.",Minimal residual disease negativity in multiple myeloma is associated with intestinal microbiota composition,Blood advances,2019,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,Minimal Residual Disease+ (positivity) with Allogenic Stem Cell Transplant,Minimal Residual Disease- (negativity) with Allogenic Stem Cell Transplant,Patients with multiple myeloma (MM) who achieve minimal residual disease (MRD) negativity (MRD-) after upfront treatment,18,16,NA,16S,45,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Figure 1b,10 January 2021,William Lam,"WikiWorks,Atrayees",Relative abundance of genera Eubacterium and Faecalibacterium by MRD status,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|216851,Complete,Atrayees
bsdb:31289031/3/1,31289031,case-control,31289031,10.1182/bloodadvances.2019032276,NA,"Pianko M.J., Devlin S.M., Littmann E.R., Chansakul A., Mastey D., Salcedo M., Fontana E., Ling L., Tavitian E., Slingerland J.B., Slingerland A.E., Clurman A., Gomes A.L.C., Taur Y., Pamer E.G., Peled J.U., van den Brink M.R.M., Landgren O. , Lesokhin A.M.",Minimal residual disease negativity in multiple myeloma is associated with intestinal microbiota composition,Blood advances,2019,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,Minimal Residual Disease+ (positivity) with Allogenic Stem Cell Transplant,Minimal Residual Disease- (negativity) with Allogenic Stem Cell Transplant,Patients with multiple myeloma (MM) who achieve minimal residual disease (MRD) negativity (MRD-) after upfront treatment,18,16,NA,16S,45,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Figure 1c,10 January 2021,William Lam,WikiWorks,Forest plots showing effect of covariates on relative abundance of E hallii and F prausnitzii,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,1783272|1239|186801|186802|216572|216851|853,Complete,Atrayees
bsdb:31289031/4/1,31289031,case-control,31289031,10.1182/bloodadvances.2019032276,NA,"Pianko M.J., Devlin S.M., Littmann E.R., Chansakul A., Mastey D., Salcedo M., Fontana E., Ling L., Tavitian E., Slingerland J.B., Slingerland A.E., Clurman A., Gomes A.L.C., Taur Y., Pamer E.G., Peled J.U., van den Brink M.R.M., Landgren O. , Lesokhin A.M.",Minimal residual disease negativity in multiple myeloma is associated with intestinal microbiota composition,Blood advances,2019,NA,Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,female,males,Patients with multiple myeloma (MM) who achieve minimal residual disease (MRD) negativity (MRD-) after upfront treatment,18,16,NA,16S,45,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Figure 1c,10 January 2021,William Lam,WikiWorks,Forest plots showing effect of covariates on relative abundance of E hallii and F prausnitzii,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,1783272|1239|186801|186802|216572|216851|853,Complete,Atrayees
bsdb:31289031/5/1,31289031,case-control,31289031,10.1182/bloodadvances.2019032276,NA,"Pianko M.J., Devlin S.M., Littmann E.R., Chansakul A., Mastey D., Salcedo M., Fontana E., Ling L., Tavitian E., Slingerland J.B., Slingerland A.E., Clurman A., Gomes A.L.C., Taur Y., Pamer E.G., Peled J.U., van den Brink M.R.M., Landgren O. , Lesokhin A.M.",Minimal residual disease negativity in multiple myeloma is associated with intestinal microbiota composition,Blood advances,2019,NA,Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,Minimal Residual Disease+ (positivity) with Allogenic Stem Cell Transplant,Minimal Residual Disease- (negativity) with Allogenic Stem Cell Transplant,Patients with multiple myeloma (MM) who achieve minimal residual disease (MRD) negativity (MRD-) after upfront treatment,18,16,NA,16S,45,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Figure 1c,10 January 2021,William Lam,WikiWorks,Forest plots showing effect of covariates on relative abundance of E hallii and F prausnitzii,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,1783272|1239|186801|3085636|186803|2569097|39488,Complete,Atrayees
bsdb:31289031/6/1,31289031,case-control,31289031,10.1182/bloodadvances.2019032276,NA,"Pianko M.J., Devlin S.M., Littmann E.R., Chansakul A., Mastey D., Salcedo M., Fontana E., Ling L., Tavitian E., Slingerland J.B., Slingerland A.E., Clurman A., Gomes A.L.C., Taur Y., Pamer E.G., Peled J.U., van den Brink M.R.M., Landgren O. , Lesokhin A.M.",Minimal residual disease negativity in multiple myeloma is associated with intestinal microbiota composition,Blood advances,2019,NA,Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,Age greater than 65 years old,Age less than 65 years old,Patients with multiple myeloma (MM) who achieve minimal residual disease (MRD) negativity (MRD-) after upfront treatment,18,16,NA,16S,45,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Figure 1c,10 January 2021,William Lam,WikiWorks,Forest plots showing effect of covariates on relative abundance of E hallii and F prausnitzii,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,1783272|1239|186801|3085636|186803|2569097|39488,Complete,Atrayees
bsdb:31334130/1/1,31334130,case-control,31334130,10.3389/fcimb.2019.00205,NA,"Wang L., Yin G., Guo Y., Zhao Y., Zhao M., Lai Y., Sui P., Shi T., Guo W. , Huang Z.",Variations in Oral Microbiota Composition Are Associated With a Risk of Throat Cancer,Frontiers in cellular and infection microbiology,2019,"16S rRNA gene, early diagnosis, microbiome, next-generation sequencing, oral health, throat cancer",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Head and neck carcinoma,MONDO:0002038,Healthy controls,Throat cancer,"throat cancer including cancer of oropharynx, hypopharynx, nasopharynx and larynx",29,32,6 months,16S,3,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,"Figure 2, Figure 3, Text",10 January 2021,Utsav Patel,WikiWorks,Variations in oral microbiota composition associated with a risk of Throat Cancer,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales",3379134|1224|1236|72274|135621|286;3379134|1224|1236|135625|712|416916;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|1508657;3379134|1224|28216|80840|119060|47670;3379134|976|200643|171549|815|909656;3379134|976|200643|171549|815|816;3379134|976|200643|171549|171552;3379134|1224|1236|72274|135621|351;3379134|976|200643|171549|815;3379134|1224|28216|80840|119060;3379134|1224|28216|80840;3379134|1224|28211;3379134|1224|28211|766,Complete,Fatima Zohra
bsdb:31334130/1/2,31334130,case-control,31334130,10.3389/fcimb.2019.00205,NA,"Wang L., Yin G., Guo Y., Zhao Y., Zhao M., Lai Y., Sui P., Shi T., Guo W. , Huang Z.",Variations in Oral Microbiota Composition Are Associated With a Risk of Throat Cancer,Frontiers in cellular and infection microbiology,2019,"16S rRNA gene, early diagnosis, microbiome, next-generation sequencing, oral health, throat cancer",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Head and neck carcinoma,MONDO:0002038,Healthy controls,Throat cancer,"throat cancer including cancer of oropharynx, hypopharynx, nasopharynx and larynx",29,32,6 months,16S,3,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,"Figure 2, Figure 3, Text",10 January 2021,Utsav Patel,"Lwaldron,WikiWorks",Variations in oral microbiota composition associated with a risk of Throat Cancer,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,p__Candidatus Altimarinota,p__Candidatus Saccharimonadota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Campylobacterota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|1224|1236|135625|712|713;1783272|1239|186801|3082720|543314|109326;3379134|976|117743|200644|2762318|59735;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294;3379134|29547|3031852|213849;363464;95818;1783272|1239|186801;1783272|201174|1760|85007|1653;1783272|201174|1760|85007;1783272|201174|1760|85007|1653|1716;3379134|29547;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730;3384189|32066;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066|203490|203491|203492|848;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|1506553;3384189|32066|203490|203491|1129771|32067;3384189|32066|203490|203491|1129771;3379134|1224|1236|2887326|468|475;3379134|1224|1236|2887326|468;1783272|1239|909932;3379134|1224|28216|206351|481|482;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|841;1783272|201174|1760|85006|1268|32207;1783272|1239|909932|909929;1783272|1239|909932|909929|1843491|970;3379134|203691|203692|136|137;3379134|203691|203692|136;3379134|203691|203692;3379134|203691|203692|136|2845253|157;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977,Complete,Fatima
bsdb:31334130/2/1,31334130,case-control,31334130,10.3389/fcimb.2019.00205,NA,"Wang L., Yin G., Guo Y., Zhao Y., Zhao M., Lai Y., Sui P., Shi T., Guo W. , Huang Z.",Variations in Oral Microbiota Composition Are Associated With a Risk of Throat Cancer,Frontiers in cellular and infection microbiology,2019,"16S rRNA gene, early diagnosis, microbiome, next-generation sequencing, oral health, throat cancer",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Head and neck carcinoma,MONDO:0002038,Vocal cord polyp,Cancer,"throat cancer including cancer of oropharynx, hypopharynx, nasopharynx and larynx",9,32,6 months,16S,3,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure 2, Figure 3, Text",10 January 2021,Utsav Patel,WikiWorks,Variations in oral microbiota composition associated with a risk of Throat Cancer,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group",3379134|1224|1236|91347|543|547;3379134|1224|1236|135625|712|416916;3379134|1224|1236|72274|135621|286;3379134|1224|1236|72274|135621|351,Complete,Fatima Zohra
bsdb:31334130/2/2,31334130,case-control,31334130,10.3389/fcimb.2019.00205,NA,"Wang L., Yin G., Guo Y., Zhao Y., Zhao M., Lai Y., Sui P., Shi T., Guo W. , Huang Z.",Variations in Oral Microbiota Composition Are Associated With a Risk of Throat Cancer,Frontiers in cellular and infection microbiology,2019,"16S rRNA gene, early diagnosis, microbiome, next-generation sequencing, oral health, throat cancer",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Head and neck carcinoma,MONDO:0002038,Vocal cord polyp,Cancer,"throat cancer including cancer of oropharynx, hypopharynx, nasopharynx and larynx",9,32,6 months,16S,3,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 2, Figure 3, Text",10 January 2021,Utsav Patel,WikiWorks,Variations in oral microbiota composition associated with a risk of Throat Cancer,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,p__Candidatus Saccharimonadota,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Lentimicrobiaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,p__Candidatus Altimarinota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales",3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|171552|838;1783272|1239|186801|3082720|3118655|44259;3379134|1224|1236|135625|712|713;3379134|29547|3031852|213849|72293|209;3379134|976|200643|171549|171550;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3082720|543314|109326;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|3085636|186803|43994;3384189|32066|203490;3384189|32066;3384189|32066|203490|203491;3384189|32066|203490|203491|203492;3384189|32066|203490|203491|1129771;1783272|1239|186801|3082720|186804;95818;3379134|976|117747|200666;3379134|976|117747;3379134|976|200643|171549|1840213;3379134|29547|3031852|213849|72293;363464;3379134|1224|28211|204458|76892;3379134|1224|28211|204458;1783272|1239|186801|3085636|1185407;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115,Complete,Fatima Zohra
bsdb:31337439/1/1,31337439,prospective cohort,31337439,10.1186/s40425-019-0650-9,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6651993/,"Zheng Y., Wang T., Tu X., Huang Y., Zhang H., Tan D., Jiang W., Cai S., Zhao P., Song R., Li P., Qin N. , Fang W.",Gut microbiome affects the response to anti-PD-1 immunotherapy in patients with hepatocellular carcinoma,Journal for immunotherapy of cancer,2019,"Anti-PD-1 immunotherapy, Gut microbiome, Hepatocellular carcinoma",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,"Responders (R, n = 3) were defined by radiographic evidence as complete or partial response, or stable disease lasting for at least six months.",5,3,NA,WMS,NA,BGISEQ-500 Sequencing,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,"text, Figure 2A, Figure S4",3 September 2022,Sharmilac,"Sharmilac,Fatima,WikiWorks","Meta-analysis of the bacteria significantly enriched in R and NR. a Heatmap showing the relative abundance of R-enriched and NR-enriched bacterial species, as identified by LEfSe.
Differentially abundant genera (a) and species (b) between R and NR, identified by LEfSe.",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Liberibacter|s__Candidatus Liberibacter brunswickensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium ulcerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 7_1_58FAA,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus oris,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus vaginalis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Pseudomonadati|p__Rhodothermota|c__Rhodothermia|o__Rhodothermales|f__Salinibacteraceae|g__Salinibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|186802|216572|244127|169435;3379134|976|200643|171549|815|816|246787;1783272|201174|1760|85004|31953|1678|1689;1783272|1239|186801|3085636|186803|572511|40520;3379134|1224|28211|356|82115|34019|1968796;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|186801|3085636|186803|189330|39486;3384189|32066|203490|203491|203492|848|861;1783272|1239|186801|3085636|186803|658087;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|91061|186826|33958|2742598|97478;1783272|1239|91061|186826|33958|2742598|1632;1783272|1239|91061|186826|33958|2742598|1633;1783272|1239|909932|1843489|31977|906|187326;1783272|1239|186801|186802|216572|1263|40518;3379134|1853220|1853222|1853224|1853225|146918;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|186801|186802|216572|292632;1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|216572|1263;3379134|74201|203494|48461|1647988|239934;1783272|1239|909932|1843489|31977|39948;1783272|201174|1760|85004|31953|196081,Complete,Fatima
bsdb:31337439/1/2,31337439,prospective cohort,31337439,10.1186/s40425-019-0650-9,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6651993/,"Zheng Y., Wang T., Tu X., Huang Y., Zhang H., Tan D., Jiang W., Cai S., Zhao P., Song R., Li P., Qin N. , Fang W.",Gut microbiome affects the response to anti-PD-1 immunotherapy in patients with hepatocellular carcinoma,Journal for immunotherapy of cancer,2019,"Anti-PD-1 immunotherapy, Gut microbiome, Hepatocellular carcinoma",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,"Responders (R, n = 3) were defined by radiographic evidence as complete or partial response, or stable disease lasting for at least six months.",5,3,NA,WMS,NA,BGISEQ-500 Sequencing,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,increased,Signature 2,"text, Figure 2A",3 September 2022,Sharmilac,"Sharmilac,Fatima,Aiyshaaaa,WikiWorks","Meta-analysis of the bacteria significantly enriched in R and NR. a Heatmap showing the relative abundance of R-enriched and NR-enriched bacterial species, as identified by LEfSe.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter aphrophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fluxus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Bartonellaceae|g__Bartonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Bordetella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia albertii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium varium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus pittmaniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Cellvibrio",3379134|1224|1236|135625|712|416916|732;3379134|976|200643|171549|815|816|28111;3379134|976|200643|171549|815|816|626930;3379134|976|200643|171549|815|816|291645;3379134|976|200643|171549|815|816|820;3379134|1224|28211|356|772|773;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|1681;3379134|1224|28216|80840|506|517;3379134|1224|1236|91347|543|561|208962;3384189|32066|203490|203491|203492|848|856;3379134|1224|1236|135625|712|724|249188;3379134|1224|1236|91347|543|570|548;1783272|1239|91061|186826|33958|2767887|1624;1783272|1239|909932|1843489|31977|906|907;1783272|1239|526524|526525|2810281|191303;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843489|31977|29465|39778;1783272|201174|1760|85009|31957;3379134|1224|1236|1706369|1706371|10,Complete,Fatima
bsdb:31337807/1/1,31337807,prospective cohort,31337807,10.1038/s41598-019-46964-5,NA,"Tapiainen T., Koivusaari P., Brinkac L., Lorenzi H.A., Salo J., Renko M., Pruikkonen H., Pokka T., Li W., Nelson K., Pirttilä A.M. , Tejesvi M.V.",Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants,Scientific reports,2019,NA,Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control group,Postnatal antibiotic group (2-day old infant),"Term, vaginally delivered infants",47,29,NA,16S,45,Ion Torrent,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure 5, Figure 3",10 January 2021,Mst Afroza Parvin,"WikiWorks,Atrayees",The relative abundances of the bacterial genera and phyla mainly explaining the observed phylum level changes after perinatal antibiotic exposure,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota",1783272|1239|91061|186826|33958|1578;1783272|1239,Complete,Atrayees
bsdb:31337807/1/2,31337807,prospective cohort,31337807,10.1038/s41598-019-46964-5,NA,"Tapiainen T., Koivusaari P., Brinkac L., Lorenzi H.A., Salo J., Renko M., Pruikkonen H., Pokka T., Li W., Nelson K., Pirttilä A.M. , Tejesvi M.V.",Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants,Scientific reports,2019,NA,Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control group,Postnatal antibiotic group (2-day old infant),"Term, vaginally delivered infants",47,29,NA,16S,45,Ion Torrent,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 5, Figure 3",10 January 2021,Mst Afroza Parvin,"WikiWorks,Atrayees",The relative abundances of the bacterial genera and phyla mainly explaining the observed phylum level changes after perinatal antibiotic exposure,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,Atrayees
bsdb:31337807/2/1,31337807,prospective cohort,31337807,10.1038/s41598-019-46964-5,NA,"Tapiainen T., Koivusaari P., Brinkac L., Lorenzi H.A., Salo J., Renko M., Pruikkonen H., Pokka T., Li W., Nelson K., Pirttilä A.M. , Tejesvi M.V.",Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants,Scientific reports,2019,NA,Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control group,IAP group (4-day old infant),"Term, vaginally delivered infants",47,44,NA,16S,45,Ion Torrent,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 5,10 January 2021,Mst Afroza Parvin,WikiWorks,The relative abundances of the bacterial genera mainly explaining the observed phylum level changes after perinatal antibiotic exposure,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,Atrayees
bsdb:31337807/3/1,31337807,prospective cohort,31337807,10.1038/s41598-019-46964-5,NA,"Tapiainen T., Koivusaari P., Brinkac L., Lorenzi H.A., Salo J., Renko M., Pruikkonen H., Pokka T., Li W., Nelson K., Pirttilä A.M. , Tejesvi M.V.",Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants,Scientific reports,2019,NA,Experiment 3,Finland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control group,IAP group (6-month old infant),"Term, vaginally delivered infants",47,44,NA,16S,45,Ion Torrent,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure 5, Figure 3",10 January 2021,Mst Afroza Parvin,"WikiWorks,Atrayees",The relative abundances of the bacterial genera and phyla mainly explaining the observed phylum level changes after perinatal antibiotic exposure,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota",1783272|1239|186801|186802|31979|1485;1783272|1239,Complete,Atrayees
bsdb:31337807/3/2,31337807,prospective cohort,31337807,10.1038/s41598-019-46964-5,NA,"Tapiainen T., Koivusaari P., Brinkac L., Lorenzi H.A., Salo J., Renko M., Pruikkonen H., Pokka T., Li W., Nelson K., Pirttilä A.M. , Tejesvi M.V.",Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants,Scientific reports,2019,NA,Experiment 3,Finland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control group,IAP group (6-month old infant),"Term, vaginally delivered infants",47,44,NA,16S,45,Ion Torrent,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 3, Figure 5",6 July 2023,Atrayees,"Atrayees,WikiWorks",The relative abundances of the bacterial genera and phyla mainly explaining the observed phylum level changes after perinatal antibiotic exposure,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,3379134|976|200643,Complete,Atrayees
bsdb:31337807/4/1,31337807,prospective cohort,31337807,10.1038/s41598-019-46964-5,NA,"Tapiainen T., Koivusaari P., Brinkac L., Lorenzi H.A., Salo J., Renko M., Pruikkonen H., Pokka T., Li W., Nelson K., Pirttilä A.M. , Tejesvi M.V.",Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants,Scientific reports,2019,NA,Experiment 4,Finland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control group,IAP+postnatal antibiotic group (2-day old infant),"Term, vaginally delivered infants",47,29,NA,16S,45,Ion Torrent,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 5,10 January 2021,Mst Afroza Parvin,WikiWorks,The relative abundances of the bacterial genera mainly explaining the observed phylum level changes after perinatal antibiotic exposure,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Atrayees
bsdb:31337807/4/2,31337807,prospective cohort,31337807,10.1038/s41598-019-46964-5,NA,"Tapiainen T., Koivusaari P., Brinkac L., Lorenzi H.A., Salo J., Renko M., Pruikkonen H., Pokka T., Li W., Nelson K., Pirttilä A.M. , Tejesvi M.V.",Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants,Scientific reports,2019,NA,Experiment 4,Finland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control group,IAP+postnatal antibiotic group (2-day old infant),"Term, vaginally delivered infants",47,29,NA,16S,45,Ion Torrent,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 5, Figure 3",10 January 2021,Mst Afroza Parvin,"WikiWorks,Atrayees",The relative abundances of the bacterial genera and phyla mainly explaining the observed phylum level changes after perinatal antibiotic exposure,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia",3379134|976|200643|171549|815|816;3379134|976|200643,Complete,Atrayees
bsdb:31337807/5/1,31337807,prospective cohort,31337807,10.1038/s41598-019-46964-5,NA,"Tapiainen T., Koivusaari P., Brinkac L., Lorenzi H.A., Salo J., Renko M., Pruikkonen H., Pokka T., Li W., Nelson K., Pirttilä A.M. , Tejesvi M.V.",Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants,Scientific reports,2019,NA,Experiment 5,Finland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control group,IAP+postnatal antibiotic group (4-day old infant),"Term, vaginally delivered infants",47,29,NA,16S,45,Ion Torrent,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 5,10 January 2021,Mst Afroza Parvin,WikiWorks,The relative abundances of the bacterial genera mainly explaining the observed phylum level changes after perinatal antibiotic exposure,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,Atrayees
bsdb:31337807/6/1,31337807,prospective cohort,31337807,10.1038/s41598-019-46964-5,NA,"Tapiainen T., Koivusaari P., Brinkac L., Lorenzi H.A., Salo J., Renko M., Pruikkonen H., Pokka T., Li W., Nelson K., Pirttilä A.M. , Tejesvi M.V.",Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants,Scientific reports,2019,NA,Experiment 6,Finland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control group,IAP+postnatal antibiotic group (6-month old infant),"Term, vaginally delivered infants",47,29,NA,16S,45,Ion Torrent,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 5,10 January 2021,Mst Afroza Parvin,WikiWorks,The relative abundances of the bacterial genera mainly explaining the observed phylum level changes after perinatal antibiotic exposure,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,1783272|1239|186801|186802|31979|1485,Complete,Atrayees
bsdb:31337807/6/2,31337807,prospective cohort,31337807,10.1038/s41598-019-46964-5,NA,"Tapiainen T., Koivusaari P., Brinkac L., Lorenzi H.A., Salo J., Renko M., Pruikkonen H., Pokka T., Li W., Nelson K., Pirttilä A.M. , Tejesvi M.V.",Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants,Scientific reports,2019,NA,Experiment 6,Finland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control group,IAP+postnatal antibiotic group (6-month old infant),"Term, vaginally delivered infants",47,29,NA,16S,45,Ion Torrent,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 3, Figure 5",6 July 2023,Atrayees,"Atrayees,WikiWorks",The relative abundances of the bacterial genera mainly explaining the observed phylum level changes after perinatal antibiotic exposure,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,3379134|976|200643,Complete,Atrayees
bsdb:31339887/1/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 1,"United States of America,South Africa,Ghana",Homo sapiens,Feces,UBERON:0001988,Risk factor,EFO:0003919,Non-Cardiometabolic Risk (CMD),Cardiometabolic Risk (CMD),"Participants in the CMD group had Cardiometabolic Risk (CM) risk defined as at least 3 CM risk factors from five: waist circumference, elevated blood pressure, elevated blood fasting glucose, elevated triglyceride and low HDL concentration in USA, RSA, and Ghana",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,NA,NA,NA,NA,Signature 1,Figure 2D,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific gut bacterial taxa are differentially abundant (in relative terms) between study sites with and without elevated CM risk (only significantly differential exact sequence variants (ESVs) with relative abundance ≥ 1% in at least one group shown.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:31339887/1/2,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 1,"United States of America,South Africa,Ghana",Homo sapiens,Feces,UBERON:0001988,Risk factor,EFO:0003919,Non-Cardiometabolic Risk (CMD),Cardiometabolic Risk (CMD),"Participants in the CMD group had Cardiometabolic Risk (CM) risk defined as at least 3 CM risk factors from five: waist circumference, elevated blood pressure, elevated blood fasting glucose, elevated triglyceride and low HDL concentration in USA, RSA, and Ghana",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,NA,NA,NA,NA,Signature 2,Figure 2D,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific gut bacterial taxa are differentially abundant (in relative terms) between study sites with and without elevated CM risk (only significantly differential exact sequence variants (ESVs) with relative abundance ≥ 1% in at least one group shown.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",1783272|1239|186801|186802|31979;3379134|976|200643|171549|171552|838;1783272|1239|186801|3082720|186804,Complete,Svetlana up
bsdb:31339887/2/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 2,"Ghana,South Africa,United States of America",Homo sapiens,Saliva,UBERON:0001836,Risk factor,EFO:0003919,Non-Cardiometabolic Risk (CMD),Cardiometabolic Risk (CMD),"Participants in the CMD group had Cardiometabolic Risk (CM) risk defined as at least 3 CM risk factors from five: waist circumference, elevated blood pressure, elevated blood fasting glucose, elevated triglyceride and low HDL concentration in USA, RSA, and Ghana",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3C,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific oral bacterial taxa are differentially abundant (in relative terms) between study sites with and without elevated CM risk (only significantly differential exact sequence variants (ESVs) with relative abundance ≥ 1% in at least one group shown.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976|200643|171549|171552|838;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:31339887/2/2,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 2,"Ghana,South Africa,United States of America",Homo sapiens,Saliva,UBERON:0001836,Risk factor,EFO:0003919,Non-Cardiometabolic Risk (CMD),Cardiometabolic Risk (CMD),"Participants in the CMD group had Cardiometabolic Risk (CM) risk defined as at least 3 CM risk factors from five: waist circumference, elevated blood pressure, elevated blood fasting glucose, elevated triglyceride and low HDL concentration in USA, RSA, and Ghana",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3C,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific oral bacterial taxa are differentially abundant (in relative terms) between study sites with and without elevated CM risk (only significantly differential exact sequence variants (ESVs) with relative abundance ≥ 1% in at least one group shown.,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",3384189|32066|203490|203491|203492|848;3379134|1224|1236|135625|712|724;1783272|201174|1760|85006|1268|32207,Complete,Svetlana up
bsdb:31339887/3/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 3,Jamaica,Homo sapiens,Feces,UBERON:0001988,Hyperglycemia,HP:0003074,Non-hyperglycemia,Hyperglycemia,Participants from Jamaica with elevated fasting blood glucose.,NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,NA,NA,NA,NA,Signature 1,Figure S7b,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific gut bacterial exact sequences variances (ESV) are differentially abundant between hyperglycemic and non-hyperglycemic participants from Jamaica.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:31339887/4/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 4,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Waist circumference,EFO:0004342,Low waist circumference (Male),High waist circumference (Male),"Male participants from all countries (Jamaica, Ghana, South Africa and United States of America) with high waist circumference.",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure S6a,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific gut bacterial exact sequences variances (ESV) are differentially abundant between low waist and high waist circumference in male participants in all countries.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:31339887/4/2,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 4,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Waist circumference,EFO:0004342,Low waist circumference (Male),High waist circumference (Male),"Male participants from all countries (Jamaica, Ghana, South Africa and United States of America) with high waist circumference.",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure S6a,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific gut bacterial exact sequences variances (ESV) are differentially abundant between low waist and high waist circumference in male participants in all countries.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|1224|1236|91347|543;3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:31339887/5/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 5,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Waist circumference,EFO:0004342,Low waist circumference (male and female),High waist circumference (male and female),"All(male and female) participants from all countries (Jamaica, Ghana, South Africa and United States of America) with high waist circumference.",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure S6b,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific gut bacterial exact sequences variances (ESV) are differentially abundant between low waist and high waist circumference in all participants in all countries.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,1783272|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:31339887/5/2,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 5,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Waist circumference,EFO:0004342,Low waist circumference (male and female),High waist circumference (male and female),"All(male and female) participants from all countries (Jamaica, Ghana, South Africa and United States of America) with high waist circumference.",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure S6b,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific gut bacterial exact sequences variances (ESV) are differentially abundant between low waist and high waist circumference in all participants in all countries.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|186801|186802|31979;3379134|1224|1236|91347|543;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:31339887/6/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 6,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Waist circumference,EFO:0004342,Low waist circumference (female),High waist circumference (female),"Female participants from all countries (Jamaica, Ghana, South Africa and United States of America) with high waist circumference.",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure S6c,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific gut bacterial exact sequences variances (ESV) are differentially abundant between low waist and high waist circumference in female participants in all countries.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,1783272|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:31339887/6/2,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 6,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Waist circumference,EFO:0004342,Low waist circumference (female),High waist circumference (female),"Female participants from all countries (Jamaica, Ghana, South Africa and United States of America) with high waist circumference.",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure S6c,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific gut bacterial exact sequences variances (ESV) are differentially abundant between low waist and high waist circumference in female participants in all countries.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",3379134|1224|1236|91347|543;1783272|1239|186801|186802|216572|119852,Complete,Svetlana up
bsdb:31339887/7/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 7,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Hypertension,EFO:0000537,Non-hypertension (male and female),Hypertension (male and female),"All(male and female) participants from all countries (Jamaica, Ghana, South Africa and United States of America) with elevated blood pressure (hypertention).",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure S6d,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific gut bacterial exact sequences variances (ESV) are differentially abundant between non-hypertensive and hypertensive participants in all countries.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,Svetlana up
bsdb:31339887/8/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 8,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Hypertension,EFO:0000537,Non-hypertension (male),Hypertension (male),"Male participants from all countries (Jamaica, Ghana, South Africa and United States of America) with elevated blood pressure (Hypertension).",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure S6e,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific gut bacterial exact sequences variances (ESV) are differentially abundant between non-hypertensive and hypertensive male participants in all countries.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,1783272|1239|186801|186802|216572|216851,Complete,Svetlana up
bsdb:31339887/9/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 9,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Hypertension,EFO:0000537,Non-hypertension (female),Hypertension (female),"Female participants from all countries (Jamaica, Ghana, South Africa and United States of America) with elevated blood pressure (hypertension).",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure S6f,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific gut bacterial exact sequences variances (ESV) are differentially abundant between non-hypertensive and hypertensive female participants in all countries.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,1783272|1239|186801|186802|31979,Complete,Svetlana up
bsdb:31339887/9/2,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 9,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Hypertension,EFO:0000537,Non-hypertension (female),Hypertension (female),"Female participants from all countries (Jamaica, Ghana, South Africa and United States of America) with elevated blood pressure (hypertension).",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure S6f,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific gut bacterial exact sequences variances (ESV) are differentially abundant between non-hypertensive and hypertensive female participants in all countries.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3082720|186804,Complete,Svetlana up
bsdb:31339887/10/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 10,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Hyperglycemia,HP:0003074,Non-hyperglycemia (male and female),Hyperglycemia (male and female),"All(male and female) participants from all countries (Jamaica, Ghana, South Africa and United States of America) with elevated fasted blood glucose (Hyperglycemia).",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure S6g,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific gut bacterial exact sequences variances (ESV) are differentially abundant between non-hyperglycemic and hyperglycemic participants in all countries.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,Svetlana up
bsdb:31339887/11/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 11,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Hyperglycemia,HP:0003074,Non-hyperglycemia (female),Hyperglycemia (female),"Female participants from all countries (Jamaica, Ghana, South Africa and United States of America) with elevated fasted blood glucose (hyperglycemia)",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure S6h,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific gut bacterial exact sequences variances (ESV) are differentially abundant between non-hyperglycemic and hyperglycemic female participants in all countries.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,Svetlana up
bsdb:31339887/11/2,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 11,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Hyperglycemia,HP:0003074,Non-hyperglycemia (female),Hyperglycemia (female),"Female participants from all countries (Jamaica, Ghana, South Africa and United States of America) with elevated fasted blood glucose (hyperglycemia)",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure S6h,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific gut bacterial exact sequences variances (ESV) are differentially abundant between non-hyperglycemic and hyperglycemic female participants in all countries.,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|526524|526525|128827;1783272|1239|909932|1843489|31977,Complete,Svetlana up
bsdb:31339887/12/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 12,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Hypertriglyceridemia,EFO:0004211,Non-hypertriglyceridemia (male and female),Hypertriglyceridemia (male and female),"All(male and female) participants from all countries (Jamaica, Ghana, South Africa and United States of America) with Hypertriglyceridemia.",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure S6i,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific gut bacterial exact sequences variances (ESV) are differentially abundant between non-hypertriglyceridemic and hypertriglyceridemic participants in all countries.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:31339887/13/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 13,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Hypertriglyceridemia,EFO:0004211,Non-hypertriglyceridemia (female),Hypertriglyceridemia (female),"Female participants from all countries (Jamaica, Ghana, South Africa and United States of America) with Hypertriglyceridemia.",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure S6j,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific gut bacterial exact sequences variances (ESV) are differentially abundant between non-hypertriglyceridemic and hypertriglyceridemic female participants in all countries.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",1783272|1239|186801|3085636|186803|33042;3379134|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:31339887/13/2,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 13,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Hypertriglyceridemia,EFO:0004211,Non-hypertriglyceridemia (female),Hypertriglyceridemia (female),"Female participants from all countries (Jamaica, Ghana, South Africa and United States of America) with Hypertriglyceridemia.",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure S6j,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific gut bacterial exact sequences variances (ESV) are differentially abundant between non-hypertriglyceridemic and hypertriglyceridemic female participants in all countries.,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:31339887/14/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 14,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,HDL cholesterol,CHEBI:47775,HIGH high-density lipoprotein (male and female),LOW high-density lipoprotein (male and female),"All(male and female) participants from all countries (Jamaica, Ghana, South Africa and United States of America) with LOW high-density lipoprotein (HDL) concentration.",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure S6k,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific gut bacterial exact sequences variances (ESV) are differentially abundant between low HDL and high HDL levels in all participants in all countries.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,Svetlana up
bsdb:31339887/15/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 15,South Africa,Homo sapiens,Feces,UBERON:0001988,Waist circumference,EFO:0004342,Low waist circumference,High waist circumference,All participants from South Africa with high waist circumference.,NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure S7a,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific gut bacterial exact sequences variances (ESV) are differentially abundant between high waist and low waist circumference groups in participants from South Africa.,increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,1783272|1239|909932|1843489|31977|39948,Complete,Svetlana up
bsdb:31339887/16/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 16,South Africa,Homo sapiens,Feces,UBERON:0001988,Hypertriglyceridemia,EFO:0004211,Non-hypertriglyceridemia,Hypertriglyceridemia,Participants from South Africa who had hypertriglyceridemia.,NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure S7c,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific gut bacterial exact sequences variances (ESV) are differentially abundant between non-hyperglyceridemic and hyperglyceridemic participants from South Africa.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,1783272|1239|186801|186802|216572|119852,Complete,Svetlana up
bsdb:31339887/17/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 17,South Africa,Homo sapiens,Feces,UBERON:0001988,HDL cholesterol,CHEBI:47775,HIGH high-density lipoprotein (HDL),LOW high-density lipoprotein (HDL),All participants from South Africa with LOW high-density lipoprotein (HDL) concentration.,NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure S7d,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific gut bacterial exact sequences variances (ESV) are differentially abundant between low HDL and high HDL levels in participants from South Africa.,increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,1783272|1239|909932|1843489|31977|906,Complete,Svetlana up
bsdb:31339887/18/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 18,"Ghana,South Africa,Jamaica,United States of America",Homo sapiens,Saliva,UBERON:0001836,Waist circumference,EFO:0004342,Low waist circumference (male and female),High waist circumference (male and female),"All (male and female) participants from all countries (Jamaica, Ghana, South Africa and United States of America) with high waist circumference.",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure S18a,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific oral bacterial exact sequences variances (ESV) are differentially abundant between high waist and low waist circumference groups in participants from all countries.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:31339887/18/2,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 18,"Ghana,South Africa,Jamaica,United States of America",Homo sapiens,Saliva,UBERON:0001836,Waist circumference,EFO:0004342,Low waist circumference (male and female),High waist circumference (male and female),"All (male and female) participants from all countries (Jamaica, Ghana, South Africa and United States of America) with high waist circumference.",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure S18a,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific oral bacterial exact sequences variances (ESV) are differentially abundant between high waist and low waist circumference groups in participants from all countries.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|201174|1760|85006|1268|32207;3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:31339887/19/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 19,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Saliva,UBERON:0001836,Waist circumference,EFO:0004342,Low waist circumference (male),High waist circumference (male),"Male participants from all countries (Jamaica, Ghana, South Africa and United States of America) with high waist circumference.",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure S18b,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific oral bacterial exact sequences variances (ESV) are differentially abundant between high waist and low waist circumference groups in male participants from all countries.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|976|200643|171549|171552|838;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:31339887/19/2,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 19,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Saliva,UBERON:0001836,Waist circumference,EFO:0004342,Low waist circumference (male),High waist circumference (male),"Male participants from all countries (Jamaica, Ghana, South Africa and United States of America) with high waist circumference.",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure S18b,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific oral bacterial exact sequences variances (ESV) are differentially abundant between high waist and low waist circumference groups in male participants from all countries.,decreased,NA,NA,Complete,Svetlana up
bsdb:31339887/20/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 20,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Saliva,UBERON:0001836,Waist circumference,EFO:0004342,Low waist circumference (female),High waist circumference (female),"Female participants from all countries (Jamaica, Ghana, South Africa and United States of America) with high waist circumference.",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure S18c,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific oral bacterial exact sequences variances (ESV) are differentially abundant between high waist and low waist circumference groups in female participants from all countries.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:31339887/20/2,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 20,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Saliva,UBERON:0001836,Waist circumference,EFO:0004342,Low waist circumference (female),High waist circumference (female),"Female participants from all countries (Jamaica, Ghana, South Africa and United States of America) with high waist circumference.",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure S18c,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific oral bacterial exact sequences variances (ESV) are differentially abundant between high waist and low waist circumference groups in female participants from all countries.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,1783272|201174|1760|85006|1268|32207,Complete,Svetlana up
bsdb:31339887/21/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 21,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Saliva,UBERON:0001836,Hypertension,EFO:0000537,Non-hypertension (male and female),Hypertension (male and female),"All (male and female) participants from all countries (Jamaica, Ghana, South Africa and United States of America) with elevated blood pressure (hypertension).",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure S18d,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific oral bacterial exact sequences variances (ESV) are differentially abundant between non-hypertensive and hypertensive participants in all countries.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976|200643|171549|171552|838;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:31339887/21/2,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 21,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Saliva,UBERON:0001836,Hypertension,EFO:0000537,Non-hypertension (male and female),Hypertension (male and female),"All (male and female) participants from all countries (Jamaica, Ghana, South Africa and United States of America) with elevated blood pressure (hypertension).",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure S18d,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific oral bacterial exact sequences variances (ESV) are differentially abundant between non-hypertensive and hypertensive participants in all countries.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",1783272|201174|1760|85006|1268|32207;3379134|1224|28216|206351|481|482,Complete,Svetlana up
bsdb:31339887/22/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 22,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Saliva,UBERON:0001836,Hypertension,EFO:0000537,Non-hypertension (male),Hypertension (male),"Male participants from all countries (Jamaica, Ghana, South Africa and United States of America) with elevated blood pressure (hypertension).",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure S18e,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific oral bacterial exact sequences variances (ESV) are differentially abundant between non-hypertensive and hypertensive male participants in all countries.,increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:31339887/22/2,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 22,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Saliva,UBERON:0001836,Hypertension,EFO:0000537,Non-hypertension (male),Hypertension (male),"Male participants from all countries (Jamaica, Ghana, South Africa and United States of America) with elevated blood pressure (hypertension).",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure S18e,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific oral bacterial exact sequences variances (ESV) are differentially abundant between non-hypertensive and hypertensive male participants in all countries.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,3379134|1224|28216|206351|481|482,Complete,Svetlana up
bsdb:31339887/23/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 23,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Saliva,UBERON:0001836,Hypertension,EFO:0000537,Non-hypertension (female),Hypertension (female),"Female participants from all countries (Jamaica, Ghana, South Africa and United States of America) with elevated blood pressure (hypertension).",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure S18f,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific oral bacterial exact sequences variances (ESV) are differentially abundant between non-hypertensive and hypertensive female participants in all countries.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:31339887/23/2,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 23,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Saliva,UBERON:0001836,Hypertension,EFO:0000537,Non-hypertension (female),Hypertension (female),"Female participants from all countries (Jamaica, Ghana, South Africa and United States of America) with elevated blood pressure (hypertension).",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure S18f,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific oral bacterial exact sequences variances (ESV) are differentially abundant between non-hypertensive and hypertensive female participants in all countries.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,1783272|201174|1760|85006|1268|32207,Complete,Svetlana up
bsdb:31339887/24/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 24,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Saliva,UBERON:0001836,Hypertriglyceridemia,EFO:0004211,Non-Hypertriglyceridemia (female),Hypertriglyceridemia (female),"Female participants from all countries (Jamaica, Ghana, South Africa and United States of America) with hypertriglyceridemia.",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure S18g,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific oral bacterial exact sequences variances (ESV) are differentially abundant between non-hypertriglyceridemic and hypertriglyceridemic female participants in all countries.,increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:31339887/24/2,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 24,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Saliva,UBERON:0001836,Hypertriglyceridemia,EFO:0004211,Non-Hypertriglyceridemia (female),Hypertriglyceridemia (female),"Female participants from all countries (Jamaica, Ghana, South Africa and United States of America) with hypertriglyceridemia.",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure S18g,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific oral bacterial exact sequences variances (ESV) are differentially abundant between non-hypertriglyceridemic and hypertriglyceridemic female participants in all countries.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,3379134|1224|28216|206351|481|482,Complete,Svetlana up
bsdb:31339887/25/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 25,"South Africa,Ghana,Jamaica,United States of America",Homo sapiens,Saliva,UBERON:0001836,HDL cholesterol,CHEBI:47775,HIGH high-density lipoprotein (male),LOW high-density lipoprotein (male),"Male participants from all countries (Jamaica, Ghana, South Africa and United States of America) with LOW high-density lipoprotein (HDL) concentration.",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure S18h,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific oral bacterial exact sequences variances (ESV) are differentially abundant between low HDL and high HDL levels in male participants from all countries.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:31339887/26/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 26,United States of America,Homo sapiens,Saliva,UBERON:0001836,Waist circumference,EFO:0004342,Low waist circumference,High waist circumference,All participants from the United States of America with high waist circumference.,NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure S19a,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific oral bacterial exact sequences variances (ESV) are differentially abundant between high waist and low waist circumference groups in all participants from the United States of America.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|1224|1236|135625|712|724;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:31339887/26/2,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 26,United States of America,Homo sapiens,Saliva,UBERON:0001836,Waist circumference,EFO:0004342,Low waist circumference,High waist circumference,All participants from the United States of America with high waist circumference.,NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,Figure S19a,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific oral bacterial exact sequences variances (ESV) are differentially abundant between high waist and low waist circumference groups in all participants from the United States of America.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,3379134|976|200643|171549|171551|836,Complete,Svetlana up
bsdb:31339887/27/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 27,United States of America,Homo sapiens,Saliva,UBERON:0001836,Hyperglycemia,HP:0003074,Non-hyperglycemia,Hyperglycemia,All participants from all countries the United States of America with elevated fasting plasma glucose (hyperglycemia),NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure S19b,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific oral bacterial exact sequences variances (ESV) are differentially abundant between hyperglycemic and non-hyperglycemic participants from the United States of America.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,3379134|1224|1236|135625|712|724,Complete,Svetlana up
bsdb:31339887/28/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 28,Ghana,Homo sapiens,Saliva,UBERON:0001836,Hypertriglyceridemia,EFO:0004211,Non-hypertriglyceridemia,Hypertriglyceridemia,Participants from Ghana with hypertriglyceridemia.,NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure S19c,29 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific oral bacterial exact sequences variances (ESV) are differentially abundant between non-hypertriglyceridemic and hypertriglyceridemic female participants from Ghana.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,3379134|1224|1236|135625|712,Complete,Svetlana up
bsdb:31339887/29/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 29,Ghana,Homo sapiens,Saliva,UBERON:0001836,Waist circumference,EFO:0004342,Low waist circumference,High waist circumference,All participants from Ghana with high waist circumference.,NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure S19a,13 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific oral bacterial exact sequences variances (ESV) are differentially abundant between high waist and low waist circumference groups in all participants from Ghana.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:31339887/30/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 30,South Africa,Homo sapiens,Saliva,UBERON:0001836,Waist circumference,EFO:0004342,Low waist circumference,High waist circumference,All participants from South Africa with high waist circumference.,NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure S19a,13 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific oral bacterial exact sequences variances (ESV) are differentially abundant between high waist and low waist circumference groups in all participants from South Africa.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:31339887/31/1,31339887,"cross-sectional observational, not case-control",31339887,10.1371/journal.pone.0215262,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215262#pone-0215262-g003,"Fei N., Bernabé B.P., Lie L., Baghdan D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Gottel N., Riesen W., Korte W., Luke A., Kliethermes S.A., Layden B.T., Gilbert J.A. , Dugas L.R.",The human microbiota is associated with cardiometabolic risk across the epidemiologic transition,PloS one,2019,NA,Experiment 31,Ghana,Homo sapiens,Feces,UBERON:0001988,Waist circumference,EFO:0004342,Low waist circumference,High waist circumference,All participants from Ghana with high waist circumference.,NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure S7a,13 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Specific gut bacterial exact sequences variances (ESV) are differentially abundant between high waist and low waist circumference groups in participants from Ghana.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,1783272|1239|186801|3085636|186803|572511,Complete,Svetlana up
bsdb:31354427/1/1,31354427,case-control,31354427,10.3389/fnmol.2019.00171,https://www.frontiersin.org/articles/10.3389/fnmol.2019.00171/full,"Li C., Cui L., Yang Y., Miao J., Zhao X., Zhang J., Cui G. , Zhang Y.",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,"Akkermansia, Lactobacillus, Parkinson’s disease, dysbiosis, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls(HC),patients with parkinson's disease,The patients who have been diagnosed with Parkinson's Disease(PD). Parkinson’s disease (PD) is a common neurodegenerative disorder characterized by motor and non-motor symptoms.,48,51,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,4,"age,body mass index",NA,NA,increased,decreased,increased,NA,decreased,Signature 1,Figure 3,18 October 2021,Fcuevas3,"Fcuevas3,Lwaldron,Aiyshaaaa,WikiWorks","Using LEfSe analysis we identified one class, four orders, three families, and two genera that showed significant different abundances between the PD and control groups",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572,Complete,Fatima
bsdb:31354427/1/2,31354427,case-control,31354427,10.3389/fnmol.2019.00171,https://www.frontiersin.org/articles/10.3389/fnmol.2019.00171/full,"Li C., Cui L., Yang Y., Miao J., Zhao X., Zhang J., Cui G. , Zhang Y.",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,"Akkermansia, Lactobacillus, Parkinson’s disease, dysbiosis, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls(HC),patients with parkinson's disease,The patients who have been diagnosed with Parkinson's Disease(PD). Parkinson’s disease (PD) is a common neurodegenerative disorder characterized by motor and non-motor symptoms.,48,51,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,4,"age,body mass index",NA,NA,increased,decreased,increased,NA,decreased,Signature 2,Figure 3,18 October 2021,Fcuevas3,"Fcuevas3,Lwaldron,Aiyshaaaa,WikiWorks","Using LEfSe analysis we identified one class, four orders, three families, and two genera that showed significant different abundances between the PD and control groups.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",1783272|1239|91061;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|2005473,Complete,Fatima
bsdb:31354427/2/1,31354427,case-control,31354427,10.3389/fnmol.2019.00171,https://www.frontiersin.org/articles/10.3389/fnmol.2019.00171/full,"Li C., Cui L., Yang Y., Miao J., Zhao X., Zhang J., Cui G. , Zhang Y.",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,"Akkermansia, Lactobacillus, Parkinson’s disease, dysbiosis, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease subjects,"Patients who had been diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,raw counts,T-Test,0.05,NA,NA,"age,body mass index",NA,NA,increased,decreased,increased,NA,decreased,Signature 1,FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.,24 May 2023,Fcuevas3,"Fcuevas3,WikiWorks","2A. Phylum, increased abundances.",increased,k__Pseudomonadati|p__Verrucomicrobiota,3379134|74201,Complete,Fatima
bsdb:31354427/2/2,31354427,case-control,31354427,10.3389/fnmol.2019.00171,https://www.frontiersin.org/articles/10.3389/fnmol.2019.00171/full,"Li C., Cui L., Yang Y., Miao J., Zhao X., Zhang J., Cui G. , Zhang Y.",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,"Akkermansia, Lactobacillus, Parkinson’s disease, dysbiosis, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease subjects,"Patients who had been diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,raw counts,T-Test,0.05,NA,NA,"age,body mass index",NA,NA,increased,decreased,increased,NA,decreased,Signature 2,FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.,24 May 2023,Fcuevas3,"Fcuevas3,WikiWorks",2B. Class. Increased abundances.,increased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia",1783272|1239|186801;1783272|1239|909932;3379134|74201|203494,Complete,Fatima
bsdb:31354427/2/3,31354427,case-control,31354427,10.3389/fnmol.2019.00171,https://www.frontiersin.org/articles/10.3389/fnmol.2019.00171/full,"Li C., Cui L., Yang Y., Miao J., Zhao X., Zhang J., Cui G. , Zhang Y.",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,"Akkermansia, Lactobacillus, Parkinson’s disease, dysbiosis, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease subjects,"Patients who had been diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,raw counts,T-Test,0.05,NA,NA,"age,body mass index",NA,NA,increased,decreased,increased,NA,decreased,Signature 3,FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.,25 May 2023,Fcuevas3,"Fcuevas3,WikiWorks","2B. Class, decreased abundances.",decreased,k__Bacillati|p__Bacillota|c__Bacilli,1783272|1239|91061,Complete,Fatima
bsdb:31354427/2/4,31354427,case-control,31354427,10.3389/fnmol.2019.00171,https://www.frontiersin.org/articles/10.3389/fnmol.2019.00171/full,"Li C., Cui L., Yang Y., Miao J., Zhao X., Zhang J., Cui G. , Zhang Y.",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,"Akkermansia, Lactobacillus, Parkinson’s disease, dysbiosis, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease subjects,"Patients who had been diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,raw counts,T-Test,0.05,NA,NA,"age,body mass index",NA,NA,increased,decreased,increased,NA,decreased,Signature 4,FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.,25 May 2023,Fcuevas3,"Fcuevas3,WikiWorks","2C. Order, increased abundances.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales",1783272|1239|186801|186802;1783272|1239|909932|909929;3379134|74201|203494|48461,Complete,Fatima
bsdb:31354427/2/5,31354427,case-control,31354427,10.3389/fnmol.2019.00171,https://www.frontiersin.org/articles/10.3389/fnmol.2019.00171/full,"Li C., Cui L., Yang Y., Miao J., Zhao X., Zhang J., Cui G. , Zhang Y.",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,"Akkermansia, Lactobacillus, Parkinson’s disease, dysbiosis, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease subjects,"Patients who had been diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,raw counts,T-Test,0.05,NA,NA,"age,body mass index",NA,NA,increased,decreased,increased,NA,decreased,Signature 5,FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.,25 May 2023,Fcuevas3,"Fcuevas3,WikiWorks","2C. Order, decreased abundances.",decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,1783272|1239|91061|186826,Complete,Fatima
bsdb:31354427/2/6,31354427,case-control,31354427,10.3389/fnmol.2019.00171,https://www.frontiersin.org/articles/10.3389/fnmol.2019.00171/full,"Li C., Cui L., Yang Y., Miao J., Zhao X., Zhang J., Cui G. , Zhang Y.",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,"Akkermansia, Lactobacillus, Parkinson’s disease, dysbiosis, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease subjects,"Patients who had been diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,raw counts,T-Test,0.05,NA,NA,"age,body mass index",NA,NA,increased,decreased,increased,NA,decreased,Signature 6,FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.,25 May 2023,Fcuevas3,"Fcuevas3,WikiWorks","2D. Family, increased abundances.",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",1783272|1239|909932|1843488|909930;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171551;3379134|976|200643|171549|171550;1783272|1239|909932|1843489|31977;3379134|74201|203494|48461|203557,Complete,Fatima
bsdb:31354427/2/7,31354427,case-control,31354427,10.3389/fnmol.2019.00171,https://www.frontiersin.org/articles/10.3389/fnmol.2019.00171/full,"Li C., Cui L., Yang Y., Miao J., Zhao X., Zhang J., Cui G. , Zhang Y.",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,"Akkermansia, Lactobacillus, Parkinson’s disease, dysbiosis, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease subjects,"Patients who had been diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,raw counts,T-Test,0.05,NA,NA,"age,body mass index",NA,NA,increased,decreased,increased,NA,decreased,Signature 7,FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.,25 May 2023,Fcuevas3,"Fcuevas3,Fatima,WikiWorks","2D. Family, decreased abundances.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",1783272|1239|91061|186826|33958;3379134|976|200643|171549|2005473,Complete,Fatima
bsdb:31354427/2/8,31354427,case-control,31354427,10.3389/fnmol.2019.00171,https://www.frontiersin.org/articles/10.3389/fnmol.2019.00171/full,"Li C., Cui L., Yang Y., Miao J., Zhao X., Zhang J., Cui G. , Zhang Y.",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,"Akkermansia, Lactobacillus, Parkinson’s disease, dysbiosis, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease subjects,"Patients who had been diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,raw counts,T-Test,0.05,NA,NA,"age,body mass index",NA,NA,increased,decreased,increased,NA,decreased,Signature 8,FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests,25 May 2023,Fcuevas3,"Fcuevas3,WikiWorks","2E. Genus, increased abundances.",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;3366610|28890|183925|2158|2159|2172;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263,Complete,Fatima
bsdb:31354427/2/9,31354427,case-control,31354427,10.3389/fnmol.2019.00171,https://www.frontiersin.org/articles/10.3389/fnmol.2019.00171/full,"Li C., Cui L., Yang Y., Miao J., Zhao X., Zhang J., Cui G. , Zhang Y.",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,"Akkermansia, Lactobacillus, Parkinson’s disease, dysbiosis, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease subjects,"Patients who had been diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,raw counts,T-Test,0.05,NA,NA,"age,body mass index",NA,NA,increased,decreased,increased,NA,decreased,Signature 9,FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests,25 May 2023,Fcuevas3,"Fcuevas3,WikiWorks","2E. Genus, decreased abundances.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1301,Complete,Fatima
bsdb:31354427/2/10,31354427,case-control,31354427,10.3389/fnmol.2019.00171,https://www.frontiersin.org/articles/10.3389/fnmol.2019.00171/full,"Li C., Cui L., Yang Y., Miao J., Zhao X., Zhang J., Cui G. , Zhang Y.",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,"Akkermansia, Lactobacillus, Parkinson’s disease, dysbiosis, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease subjects,"Patients who had been diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,raw counts,T-Test,0.05,NA,NA,"age,body mass index",NA,NA,increased,decreased,increased,NA,decreased,Signature 10,FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.,25 May 2023,Fcuevas3,"Fcuevas3,WikiWorks","2F. Species, increased abundances.",increased,"k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",3366610|28890|183925|2158|2159|2172|2173;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Fatima
bsdb:31354427/2/11,31354427,case-control,31354427,10.3389/fnmol.2019.00171,https://www.frontiersin.org/articles/10.3389/fnmol.2019.00171/full,"Li C., Cui L., Yang Y., Miao J., Zhao X., Zhang J., Cui G. , Zhang Y.",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,"Akkermansia, Lactobacillus, Parkinson’s disease, dysbiosis, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease subjects,"Patients who had been diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,raw counts,T-Test,0.05,NA,NA,"age,body mass index",NA,NA,increased,decreased,increased,NA,decreased,Signature 11,FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests,25 May 2023,Fcuevas3,"Fcuevas3,WikiWorks","2F. Species, decreased abundances.",decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,1783272|1239|91061|186826|33958|1578|1596,Complete,Fatima
bsdb:31358825/1/1,31358825,case-control,31358825,10.1038/s41598-019-45588-z,NA,"Yang T.W., Lee W.H., Tu S.J., Huang W.C., Chen H.M., Sun T.H., Tsai M.C., Wang C.C., Chen H.Y., Huang C.C., Shiu B.H., Yang T.L., Huang H.T., Chou Y.P., Chou C.H., Huang Y.R., Sun Y.R., Liang C., Lin F.M., Ho S.Y., Chen W.L., Yang S.F., Ueng K.C., Huang H.D., Huang C.N., Jong Y.J. , Lin C.C.",Enterotype-based Analysis of Gut Microbiota along the Conventional Adenoma-Carcinoma Colorectal Cancer Pathway,Scientific reports,2019,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,controls,CRC,CRC positive during colonoscopy,104,62,2 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,"Figure 4A, Text",10 January 2021,Lora Kasselman,"Claregrieve1,WikiWorks",Differential microbial abundance between controls and colorectal cancer patients,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",3379134|1224|1236|135624|84642|642;3384189|32066|203490|203491|203492|848,Complete,Claregrieve1
bsdb:31358825/1/2,31358825,case-control,31358825,10.1038/s41598-019-45588-z,NA,"Yang T.W., Lee W.H., Tu S.J., Huang W.C., Chen H.M., Sun T.H., Tsai M.C., Wang C.C., Chen H.Y., Huang C.C., Shiu B.H., Yang T.L., Huang H.T., Chou Y.P., Chou C.H., Huang Y.R., Sun Y.R., Liang C., Lin F.M., Ho S.Y., Chen W.L., Yang S.F., Ueng K.C., Huang H.D., Huang C.N., Jong Y.J. , Lin C.C.",Enterotype-based Analysis of Gut Microbiota along the Conventional Adenoma-Carcinoma Colorectal Cancer Pathway,Scientific reports,2019,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,controls,CRC,CRC positive during colonoscopy,104,62,2 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 2,"Figure 4A, Text",10 January 2021,Lora Kasselman,"Claregrieve1,WikiWorks",Differential microbial abundance between controls and colorectal cancer patients,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",3379134|976|200643|171549|815|816;3379134|200940|3031449|213115|194924|35832;3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543|413496;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803|841,Complete,NA
bsdb:31370796/1/1,31370796,prospective cohort,31370796,10.1186/s12879-019-4279-6,NA,"Chen Y., Hong Z., Wang W., Gu L., Gao H., Qiu L. , Di W.",Association between the vaginal microbiome and high-risk human papillomavirus infection in pregnant Chinese women,BMC infectious diseases,2019,"High-risk human papillomavirus, Pregnancy, Vaginal microbiome",Experiment 1,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Human papilloma virus infection,EFO:0001668,non pregnant no HPV,non pregnant high risk HPV,non pregnant high risk HPV confirmed using HPV genotyping kit,30,19,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure 5,10 January 2021,Cynthia Anderson,WikiWorks,The unique taxa and microbiomarkers for different groups,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus",1783272|201174|1760|85004|31953|1678;3379134|976;1783272|1239|91061|1385;1783272|1239|91061|1385|186817;1783272|1239|91061|1385|186817|1386,Complete,Fatima Zohra
bsdb:31370796/1/2,31370796,prospective cohort,31370796,10.1186/s12879-019-4279-6,NA,"Chen Y., Hong Z., Wang W., Gu L., Gao H., Qiu L. , Di W.",Association between the vaginal microbiome and high-risk human papillomavirus infection in pregnant Chinese women,BMC infectious diseases,2019,"High-risk human papillomavirus, Pregnancy, Vaginal microbiome",Experiment 1,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Human papilloma virus infection,EFO:0001668,non pregnant no HPV,non pregnant high risk HPV,non pregnant high risk HPV confirmed using HPV genotyping kit,30,19,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Figure 5,10 January 2021,Cynthia Anderson,WikiWorks,The unique taxa and microbiomarkers for different groups,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958;1783272|1239|91061|186826,Complete,Fatima Zohra
bsdb:31370796/2/1,31370796,prospective cohort,31370796,10.1186/s12879-019-4279-6,NA,"Chen Y., Hong Z., Wang W., Gu L., Gao H., Qiu L. , Di W.",Association between the vaginal microbiome and high-risk human papillomavirus infection in pregnant Chinese women,BMC infectious diseases,2019,"High-risk human papillomavirus, Pregnancy, Vaginal microbiome",Experiment 2,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Human papilloma virus infection,EFO:0001668,pregnant no HPV,pregnant high risk HPV,pregnant high risk HPV confirmed using HPV genotyping kit,48,38,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 5,10 January 2021,Cynthia Anderson,WikiWorks,The unique taxa and microbiomarkers for different groups,increased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax",3379134|1224;3379134|1224|28216;3379134|1224|28216|80840|80864;3379134|1224|28216|80840;3379134|1224|28216|80840|80864|12916,Complete,Fatima Zohra
bsdb:31370796/2/2,31370796,prospective cohort,31370796,10.1186/s12879-019-4279-6,NA,"Chen Y., Hong Z., Wang W., Gu L., Gao H., Qiu L. , Di W.",Association between the vaginal microbiome and high-risk human papillomavirus infection in pregnant Chinese women,BMC infectious diseases,2019,"High-risk human papillomavirus, Pregnancy, Vaginal microbiome",Experiment 2,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Human papilloma virus infection,EFO:0001668,pregnant no HPV,pregnant high risk HPV,pregnant high risk HPV confirmed using HPV genotyping kit,48,38,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 5,10 January 2021,Cynthia Anderson,WikiWorks,The unique taxa and microbiomarkers for different groups,decreased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061;1783272|1239|186801|3085636|186803;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301,Complete,Fatima Zohra
bsdb:31379800/1/1,31379800,"cross-sectional observational, not case-control",31379800,10.3389/fmicb.2019.01664,NA,"Ma X., Chi C., Fan L., Dong B., Shao X., Xie S., Li M. , Xue W.",The Microbiome of Prostate Fluid Is Associated With Prostate Cancer,Frontiers in microbiology,2019,"cancer, microbiome, prostate, prostate cancer, prostatic fluid",Experiment 1,China,Homo sapiens,Prostate gland secretion,UBERON:0004796,Prostate carcinoma,EFO:0001663,non-prostate cancer,prostate cancer,Prostate cancer  commonest male malignant tumors determined by pathology of prostate biopsy,27,32,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,increased,NA,unchanged,Signature 1,Figure 5,10 January 2021,Rimsha Azhar,"WikiWorks,Peace Sandy",Analysis of the specific microbial species differences. (A) The differences in microbial species between the two groups were explored.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Geobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061|186826|186828|2747;1783272|1239|91061|1385|3120669|129337;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|1300|1301,Complete,Peace Sandy
bsdb:31379800/1/2,31379800,"cross-sectional observational, not case-control",31379800,10.3389/fmicb.2019.01664,NA,"Ma X., Chi C., Fan L., Dong B., Shao X., Xie S., Li M. , Xue W.",The Microbiome of Prostate Fluid Is Associated With Prostate Cancer,Frontiers in microbiology,2019,"cancer, microbiome, prostate, prostate cancer, prostatic fluid",Experiment 1,China,Homo sapiens,Prostate gland secretion,UBERON:0004796,Prostate carcinoma,EFO:0001663,non-prostate cancer,prostate cancer,Prostate cancer  commonest male malignant tumors determined by pathology of prostate biopsy,27,32,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,increased,NA,unchanged,Signature 2,Figure 5,10 January 2021,Rimsha Azhar,"WikiWorks,Peace Sandy",Analysis of the specific microbial species differences. (A) The differences in microbial species between the two groups were explored.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus",1783272|1239|186801|3082720|3118656|114627;3379134|1224|1236|91347|543|413496;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|1385|186822|44249,Complete,Peace Sandy
bsdb:31391545/1/1,31391545,laboratory experiment,31391545,10.1038/s41380-019-0475-4,NA,"Zhu F., Guo R., Wang W., Ju Y., Wang Q., Ma Q., Sun Q., Fan Y., Xie Y., Yang Z., Jie Z., Zhao B., Xiao L., Yang L., Zhang T., Liu B., Guo L., He X., Chen Y., Chen C., Gao C., Xu X., Yang H., Wang J., Dang Y., Madsen L., Brix S., Kristiansen K., Jia H. , Ma X.",Transplantation of microbiota from drug-free patients with schizophrenia causes schizophrenia-like abnormal behaviors and dysregulated kynurenine metabolism in mice,Molecular psychiatry,2020,NA,Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Healthy Control Mice (HC Mice),Schizophrenia Mice (SCZ Mice),"Schizophrenia Mice (SCZ Mice) refers to mice whose gut microbiome was depleted by oral gavage of a cocktail of antibiotics and then re-constructed with gut microbiota from SCZ patients, that is, they were colonized with fecal microbiota of SCZ patients.",25,25,NA,WMS,NA,BGISEQ-500 Sequencing,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 5,8 November 2024,KateRasheed,"KateRasheed,WikiWorks",Significantly differentially enriched mOTUs between SCZ mice and HC mice.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium ulcerans,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania filiformis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D16,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|186801|186802|216572|244127|169435;3384189|32066|203490|203491|203492|848|861;1783272|1239|526524|526525|128827|61170|61171;3379134|1224|1236|91347|543|570|573;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|2005525|375288|46503;1783272|1239|186801|186802|216572|1017280|106588;1783272|1239|186801|186802|216572|552398;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|3085636|186803|1506553|29347;3379134|976|200643|171549|815|816|28111;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:31391545/1/2,31391545,laboratory experiment,31391545,10.1038/s41380-019-0475-4,NA,"Zhu F., Guo R., Wang W., Ju Y., Wang Q., Ma Q., Sun Q., Fan Y., Xie Y., Yang Z., Jie Z., Zhao B., Xiao L., Yang L., Zhang T., Liu B., Guo L., He X., Chen Y., Chen C., Gao C., Xu X., Yang H., Wang J., Dang Y., Madsen L., Brix S., Kristiansen K., Jia H. , Ma X.",Transplantation of microbiota from drug-free patients with schizophrenia causes schizophrenia-like abnormal behaviors and dysregulated kynurenine metabolism in mice,Molecular psychiatry,2020,NA,Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Healthy Control Mice (HC Mice),Schizophrenia Mice (SCZ Mice),"Schizophrenia Mice (SCZ Mice) refers to mice whose gut microbiome was depleted by oral gavage of a cocktail of antibiotics and then re-constructed with gut microbiota from SCZ patients, that is, they were colonized with fecal microbiota of SCZ patients.",25,25,NA,WMS,NA,BGISEQ-500 Sequencing,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 5,8 November 2024,KateRasheed,"KateRasheed,WikiWorks",Significantly differentially enriched mOTUs between SCZ mice and HC mice.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sp. oral taxon 329,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium 1_7_47FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. HGF2,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio sp. 3_1_syn3,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter hepaticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mycoplasmopsis|s__Mycoplasmopsis pulmonis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] hylemonae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella xylaniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis|s__Victivallis vadensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis",3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|626929;3379134|976|200643|171549|815|816|46506;3379134|976|200643|171549|815|816|820;3379134|976|117743|200644|49546|1016|706435;1783272|1239|186801|186802|457421;1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|186801|186802|31979|1485|908340;1783272|1239|526524|526525|2810280|100883|100884;3379134|200940|3031449|213115|194924|872|457398;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|3085636|186803|2719313|208479;3379134|1224|1236|91347|543|561|562;3379134|29547|3031852|213849|72293|209|32025;3379134|1224|1236|91347|543|570|571;1783272|1239|91061|186826|33958|1578|33959;1783272|544448|2790996|2895623|2767358|2107;3379134|1224|28216|80840|995019|577310|487175;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|186801|3085636|186803|1506553|89153;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171552|577309|454155;3379134|976|200643|171549|815|816|329854;3379134|256845|1313211|278082|255528|172900|172901;3379134|1224|1236|91347|543|544|1639133,Complete,Svetlana up
bsdb:31428073/1/1,31428073,case-control,31428073,10.3389/fmicb.2019.01780,NA,"Kageyama S., Takeshita T., Takeuchi K., Asakawa M., Matsumi R., Furuta M., Shibata Y., Nagai K., Ikebe M., Morita M., Masuda M., Toh Y., Kiyohara Y., Ninomiya T. , Yamashita Y.",Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers,Frontiers in microbiology,2019,"colorectal cancer, digestive tract cancer, esophageal cancer, gastric cancer, oral microbiota, pharyngeal cancer, saliva, tongue cancer",Experiment 1,Japan,Homo sapiens,Saliva,UBERON:0001836,Digestive system cancer,MONDO:0002516,controls,digestive tract cancer patients,"patients with digestive tract cancers (tongue/pharynx, esophagus, stomach and/or large intestine)",118,59,1 month,16S,12,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,increased,increased,unchanged,NA,NA,Signature 1,"Figure 3, Figure S1",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Bacterial species corresponding to the differentially abundant OTUs between digestive tract cancer patients and control subjects,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|85007|1653|1716;3384189|32066|203490|203491|203492|848;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481|482|495;3379134|976|200643|171549|171551|836|837;1783272|201174|1760|2037|2049|2529408|1660;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1305;1783272|1239|91061|186826|1300|1301|1306;1783272|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:31428073/1/2,31428073,case-control,31428073,10.3389/fmicb.2019.01780,NA,"Kageyama S., Takeshita T., Takeuchi K., Asakawa M., Matsumi R., Furuta M., Shibata Y., Nagai K., Ikebe M., Morita M., Masuda M., Toh Y., Kiyohara Y., Ninomiya T. , Yamashita Y.",Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers,Frontiers in microbiology,2019,"colorectal cancer, digestive tract cancer, esophageal cancer, gastric cancer, oral microbiota, pharyngeal cancer, saliva, tongue cancer",Experiment 1,Japan,Homo sapiens,Saliva,UBERON:0001836,Digestive system cancer,MONDO:0002516,controls,digestive tract cancer patients,"patients with digestive tract cancers (tongue/pharynx, esophagus, stomach and/or large intestine)",118,59,1 month,16S,12,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,increased,increased,unchanged,NA,NA,Signature 2,"Figure 3, Figure S1",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Bacterial species corresponding to the differentially abundant OTUs between digestive tract cancer patients and control subjects,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei",1783272|201174|1760|2037|2049|1654|55565;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171551|836|1583331;3379134|976|200643|171549|171551|836|1924944;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|28132;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|2047;1783272|1239|526524|526525|128827|123375|102148,Complete,Claregrieve1
bsdb:31428073/2/1,31428073,case-control,31428073,10.3389/fmicb.2019.01780,NA,"Kageyama S., Takeshita T., Takeuchi K., Asakawa M., Matsumi R., Furuta M., Shibata Y., Nagai K., Ikebe M., Morita M., Masuda M., Toh Y., Kiyohara Y., Ninomiya T. , Yamashita Y.",Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers,Frontiers in microbiology,2019,"colorectal cancer, digestive tract cancer, esophageal cancer, gastric cancer, oral microbiota, pharyngeal cancer, saliva, tongue cancer",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Tongue neoplasm,EFO:0003871,controls,tongue/pharyngeal cancer patients,patients with tongue/pharyngeal cancer,26,13,1 month,16S,12,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,increased,increased,unchanged,NA,NA,Signature 1,"Figure S3, Figure 5",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Bacterial species corresponding to the differentially abundant OTUs between tongue/pharyngeal cancer patients and control subjects,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis",3379134|1224|1236|135625|712|416916|739;1783272|201174|1760|85007|1653|1716;3384189|32066|203490|203491|1129771|32067;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171551|836|837;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1305,Complete,Claregrieve1
bsdb:31428073/2/2,31428073,case-control,31428073,10.3389/fmicb.2019.01780,NA,"Kageyama S., Takeshita T., Takeuchi K., Asakawa M., Matsumi R., Furuta M., Shibata Y., Nagai K., Ikebe M., Morita M., Masuda M., Toh Y., Kiyohara Y., Ninomiya T. , Yamashita Y.",Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers,Frontiers in microbiology,2019,"colorectal cancer, digestive tract cancer, esophageal cancer, gastric cancer, oral microbiota, pharyngeal cancer, saliva, tongue cancer",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Tongue neoplasm,EFO:0003871,controls,tongue/pharyngeal cancer patients,patients with tongue/pharyngeal cancer,26,13,1 month,16S,12,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,increased,increased,unchanged,NA,NA,Signature 2,"Figure S3, Figure 5",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Bacterial species corresponding to the differentially abundant OTUs between tongue/pharyngeal cancer patients and control subjects,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis",3379134|976|200643|171549|171552|838|28132;1783272|201174|1760|85006|1268|32207|2047;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|113107,Complete,Claregrieve1
bsdb:31428073/3/1,31428073,case-control,31428073,10.3389/fmicb.2019.01780,NA,"Kageyama S., Takeshita T., Takeuchi K., Asakawa M., Matsumi R., Furuta M., Shibata Y., Nagai K., Ikebe M., Morita M., Masuda M., Toh Y., Kiyohara Y., Ninomiya T. , Yamashita Y.",Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers,Frontiers in microbiology,2019,"colorectal cancer, digestive tract cancer, esophageal cancer, gastric cancer, oral microbiota, pharyngeal cancer, saliva, tongue cancer",Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Esophageal cancer,MONDO:0007576,controls,esophageal cancer patients,patients with esophageal cancer,24,12,1 month,16S,12,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,increased,increased,increased,NA,NA,Signature 1,"Figure S3, Figure 5",10 January 2021,WikiWorks,"Claregrieve1,WikiWorks",Bacterial species corresponding to the differentially abundant OTUs between esophageal cancer patients and control subjects,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.",3379134|1224|1236|135625|712|416916|739;1783272|201174|1760|85007|1653|1716;3384189|32066|203490|203491|1129771|32067|157688;3384189|32066|203490|203491|1129771|32067|104608;1783272|1239|909932|1843489|31977|906|187326;3379134|976|200643|171549|171551|836|837;1783272|1239|91061|186826|1300|1301|1306,Complete,Claregrieve1
bsdb:31428073/3/2,31428073,case-control,31428073,10.3389/fmicb.2019.01780,NA,"Kageyama S., Takeshita T., Takeuchi K., Asakawa M., Matsumi R., Furuta M., Shibata Y., Nagai K., Ikebe M., Morita M., Masuda M., Toh Y., Kiyohara Y., Ninomiya T. , Yamashita Y.",Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers,Frontiers in microbiology,2019,"colorectal cancer, digestive tract cancer, esophageal cancer, gastric cancer, oral microbiota, pharyngeal cancer, saliva, tongue cancer",Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Esophageal cancer,MONDO:0007576,controls,esophageal cancer patients,patients with esophageal cancer,24,12,1 month,16S,12,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,increased,increased,increased,NA,NA,Signature 2,"Figure S3, Figure 5",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Bacterial species corresponding to the differentially abundant OTUs between esophageal cancer patients and control subjects,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis",1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549|171552|838|28132;1783272|201174|1760|85006|1268|32207|2047;1783272|1239|91061|186826|1300|1301;3379134|1224|28216|206351|481|482;1783272|1239|91061|186826|1300|1301|113107,Complete,Claregrieve1
bsdb:31428073/4/1,31428073,case-control,31428073,10.3389/fmicb.2019.01780,NA,"Kageyama S., Takeshita T., Takeuchi K., Asakawa M., Matsumi R., Furuta M., Shibata Y., Nagai K., Ikebe M., Morita M., Masuda M., Toh Y., Kiyohara Y., Ninomiya T. , Yamashita Y.",Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers,Frontiers in microbiology,2019,"colorectal cancer, digestive tract cancer, esophageal cancer, gastric cancer, oral microbiota, pharyngeal cancer, saliva, tongue cancer",Experiment 4,China,Homo sapiens,Saliva,UBERON:0001836,Colorectal cancer,EFO:0005842,controls,colorectal cancer patients,patients with colorectal cancer,48,24,1 month,16S,12,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure S3, Figure 5",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Bacterial species corresponding to the differentially abundant OTUs between colorectal cancer patients and control subjects,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces paraguayensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis",1783272|201174|1760|85007|1653|1716;1783272|1239|909932|1843489|31977|906|187326;3379134|1224|28216|206351|481|482;1783272|1239|186801|3085636|186803|265975|237576;3379134|976|200643|171549|171551|836|837;3379134|976|200643|171549|171552|838|59823;1783272|201174|1760|2037|2049|2529408|1660;1783272|201174|1760|85011|2062|1883|68251;1783272|1239|91061|186826|1300|1301|1318,Complete,Claregrieve1
bsdb:31428073/4/2,31428073,case-control,31428073,10.3389/fmicb.2019.01780,NA,"Kageyama S., Takeshita T., Takeuchi K., Asakawa M., Matsumi R., Furuta M., Shibata Y., Nagai K., Ikebe M., Morita M., Masuda M., Toh Y., Kiyohara Y., Ninomiya T. , Yamashita Y.",Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers,Frontiers in microbiology,2019,"colorectal cancer, digestive tract cancer, esophageal cancer, gastric cancer, oral microbiota, pharyngeal cancer, saliva, tongue cancer",Experiment 4,China,Homo sapiens,Saliva,UBERON:0001836,Colorectal cancer,EFO:0005842,controls,colorectal cancer patients,patients with colorectal cancer,48,24,1 month,16S,12,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure S3, Figure 5",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Bacterial species corresponding to the differentially abundant OTUs between colorectal cancer patients and control subjects,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|976|200643|171549|171551|836|1583331;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552|838|59823;1783272|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:31428073/5/1,31428073,case-control,31428073,10.3389/fmicb.2019.01780,NA,"Kageyama S., Takeshita T., Takeuchi K., Asakawa M., Matsumi R., Furuta M., Shibata Y., Nagai K., Ikebe M., Morita M., Masuda M., Toh Y., Kiyohara Y., Ninomiya T. , Yamashita Y.",Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers,Frontiers in microbiology,2019,"colorectal cancer, digestive tract cancer, esophageal cancer, gastric cancer, oral microbiota, pharyngeal cancer, saliva, tongue cancer",Experiment 5,China,Homo sapiens,Saliva,UBERON:0001836,Gastric cancer,MONDO:0001056,controls,gastric cancer patients,patients with gastric cancer,20,10,1 month,16S,12,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure S3, Figure 5",10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",Bacterial species corresponding to the differentially abundant OTUs between gastric cancer patients and control subjects,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3384189|32066|203490|203491|203492|848|860;1783272|1239|91061|1385|539738|1378|84135;3379134|1224|1236|135625|712|724|729;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171551|836|837;1783272|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:31428073/5/2,31428073,case-control,31428073,10.3389/fmicb.2019.01780,NA,"Kageyama S., Takeshita T., Takeuchi K., Asakawa M., Matsumi R., Furuta M., Shibata Y., Nagai K., Ikebe M., Morita M., Masuda M., Toh Y., Kiyohara Y., Ninomiya T. , Yamashita Y.",Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers,Frontiers in microbiology,2019,"colorectal cancer, digestive tract cancer, esophageal cancer, gastric cancer, oral microbiota, pharyngeal cancer, saliva, tongue cancer",Experiment 5,China,Homo sapiens,Saliva,UBERON:0001836,Gastric cancer,MONDO:0001056,controls,gastric cancer patients,patients with gastric cancer,20,10,1 month,16S,12,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure S3, Figure 5",10 January 2021,WikiWorks,"Claregrieve1,WikiWorks",Bacterial species corresponding to the differentially abundant OTUs between gastric cancer patients and control subjects,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171551|836|1924944;3379134|976|200643|171549|171552|838;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:31434623/1/1,31434623,case-control,31434623,10.1016/j.jalz.2019.07.002,NA,"Li B., He Y., Ma J., Huang P., Du J., Cao L., Wang Y., Xiao Q., Tang H. , Chen S.",Mild cognitive impairment has similar alterations as Alzheimer's disease in gut microbiota,Alzheimer's & dementia : the journal of the Alzheimer's Association,2019,"16S rRNA gene, Alzheimer's disease, Amyloid, Fecal microbiota, Mild cognitive impairment",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Normal Controls,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,30,30,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2A + Figure S1A,11 December 2024,AaishahM,"AaishahM,WikiWorks",Taxonomic differences of fecal microbiota in patients with AD and normal controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia",3379134|1224|1236|2887326|468|469;1783272|201174;3379134|74201|203494|48461|1647988|239934;1783272|1239|91061;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|186801|3085636|186803|189330;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;3379134|74201|203494|48461|203557;3379134|74201|203494|48461;3379134|74201|203494,Complete,NA
bsdb:31434623/1/2,31434623,case-control,31434623,10.1016/j.jalz.2019.07.002,NA,"Li B., He Y., Ma J., Huang P., Du J., Cao L., Wang Y., Xiao Q., Tang H. , Chen S.",Mild cognitive impairment has similar alterations as Alzheimer's disease in gut microbiota,Alzheimer's & dementia : the journal of the Alzheimer's Association,2019,"16S rRNA gene, Alzheimer's disease, Amyloid, Fecal microbiota, Mild cognitive impairment",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Normal Controls,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,30,30,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2A + Figure S1A,11 December 2024,AaishahM,"AaishahM,WikiWorks",Taxonomic differences of fecal microbiota in patients with AD and normal controls,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|1224|1236|135624;3379134|1224|28216|80840|506;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976|200643|171549|2005519|397864;3379134|1224|28216;3379134|1224|28216|80840;3379134|976|200643|171549|1853231|574697;3379134|1224|1236|135625|712|724;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|577309;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|976|200643|171549|171551;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|1224|28211|204441|41295;3379134|1224|28211|204441;3379134|1224|1236|135624|83763|83770;3379134|1224|1236|135624|83763;3379134|1224|28216|80840|995019|40544,Complete,NA
bsdb:31434623/2/1,31434623,case-control,31434623,10.1016/j.jalz.2019.07.002,NA,"Li B., He Y., Ma J., Huang P., Du J., Cao L., Wang Y., Xiao Q., Tang H. , Chen S.",Mild cognitive impairment has similar alterations as Alzheimer's disease in gut microbiota,Alzheimer's & dementia : the journal of the Alzheimer's Association,2019,"16S rRNA gene, Alzheimer's disease, Amyloid, Fecal microbiota, Mild cognitive impairment",Experiment 2,China,Homo sapiens,Blood,UBERON:0000178,Alzheimer's disease,MONDO:0004975,Normal Controls,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,30,30,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2B + Figure S1B,11 December 2024,AaishahM,"AaishahM,WikiWorks",Taxonomic differences of blood microbiota in patients with AD and normal controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Glutamicibacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Pelagibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Sterolibacteriaceae|g__Sulfuritalea,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Vibrionimonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|28216|80840|80864|12916;3379134|1224|1236|91347|543|561;1783272|201174|1760|85006|1268|1742989;3379134|1224|28211|356|2831106|1082930;1783272|201174|1760|85009|31957|1743;3379134|1224|1236|72274|135621|286;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|135614|32033|40323;3379134|1224|28216|32003|2008793|1054211;3379134|976|1853228|1853229|563835|1649511;1783272|201174|1760|85009|31957;1783272|201174|1760|85009;3379134|976|1853228|1853229|563835;3379134|976|117747|200666;3379134|976|117747;1783272|1239|91061|1385|90964;1783272|1239|91061|1385;1783272|1239|91061;3379134|1224|28211|356|45401;3379134|1224|28211|204457|41297;3379134|1224|28211|204457;3379134|1224|28216|80840|80864;3379134|1224|28216|80840;3379134|1224|28216;3379134|1224|1236|72274|135621;3379134|1224|1236|72274;3379134|1224|1236|135614|32033;3379134|1224|1236;3379134|1224,Complete,NA
bsdb:31434623/2/2,31434623,case-control,31434623,10.1016/j.jalz.2019.07.002,NA,"Li B., He Y., Ma J., Huang P., Du J., Cao L., Wang Y., Xiao Q., Tang H. , Chen S.",Mild cognitive impairment has similar alterations as Alzheimer's disease in gut microbiota,Alzheimer's & dementia : the journal of the Alzheimer's Association,2019,"16S rRNA gene, Alzheimer's disease, Amyloid, Fecal microbiota, Mild cognitive impairment",Experiment 2,China,Homo sapiens,Blood,UBERON:0000178,Alzheimer's disease,MONDO:0004975,Normal Controls,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,30,30,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2B + Figure S1B,11 December 2024,AaishahM,"AaishahM,WikiWorks",Taxonomic differences of blood microbiota in patients with AD and normal controls,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leucobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Nesterenkonia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomonadales|f__Hyphomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae",3379134|1224|28216|80840|506|222;3379134|1224|1236|2887326|468|469|470;3379134|1224|28211|204458|76892|41275;3379134|1224|1236|91347|543|547;3379134|1224|1236|135619|28256|2745;1783272|201174|1760|85006|85023|55968;3379134|1224|28211|356|119045|407;1783272|201174|1760|85006|1268|57494;3379134|1224|28211|356|118882|528;3379134|1224|1236|91347|1903411|613;1783272|201174|1760|85006|85023;1783272|201174|1760|85006;1783272|201174;3379134|1224|28211|204458|76892;3379134|1224|28211|2800060|69657;3379134|1224|28211|204458;3379134|1224|28211|356|118882;3379134|1224|28211|356|119045;3379134|1224|28211|356|69277;3379134|1224|28211|356;3379134|1224|28211|204455|31989;3379134|1224|28211|204455;3379134|1224|28211|204441;3379134|1224|28211;3379134|1224|28216|80840|506;3379134|1224|1236|135619|28256;3379134|1224|1236|135619|135620;3379134|1224|1236|2887326|468,Complete,NA
bsdb:31434623/3/1,31434623,case-control,31434623,10.1016/j.jalz.2019.07.002,NA,"Li B., He Y., Ma J., Huang P., Du J., Cao L., Wang Y., Xiao Q., Tang H. , Chen S.",Mild cognitive impairment has similar alterations as Alzheimer's disease in gut microbiota,Alzheimer's & dementia : the journal of the Alzheimer's Association,2019,"16S rRNA gene, Alzheimer's disease, Amyloid, Fecal microbiota, Mild cognitive impairment",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Normal Controls,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,30,30,NA,16S,34,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,"age,body mass index,constipation",NA,NA,NA,NA,NA,NA,Signature 1,Table 2,11 December 2024,AaishahM,"AaishahM,WikiWorks",Generalized linear model for significant genera in AD patients and normal controls,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea",1783272|1239|186801|3085636|186803|572511;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|189330,Complete,NA
bsdb:31434623/3/2,31434623,case-control,31434623,10.1016/j.jalz.2019.07.002,NA,"Li B., He Y., Ma J., Huang P., Du J., Cao L., Wang Y., Xiao Q., Tang H. , Chen S.",Mild cognitive impairment has similar alterations as Alzheimer's disease in gut microbiota,Alzheimer's & dementia : the journal of the Alzheimer's Association,2019,"16S rRNA gene, Alzheimer's disease, Amyloid, Fecal microbiota, Mild cognitive impairment",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Normal Controls,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,30,30,NA,16S,34,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,"age,body mass index,constipation",NA,NA,NA,NA,NA,NA,Signature 2,Table 2,11 December 2024,AaishahM,"AaishahM,WikiWorks",Generalized linear model for significant genera in AD patients and normal controls,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|40544;3379134|976|200643|171549|171552|577309,Complete,NA
bsdb:31434623/4/1,31434623,case-control,31434623,10.1016/j.jalz.2019.07.002,NA,"Li B., He Y., Ma J., Huang P., Du J., Cao L., Wang Y., Xiao Q., Tang H. , Chen S.",Mild cognitive impairment has similar alterations as Alzheimer's disease in gut microbiota,Alzheimer's & dementia : the journal of the Alzheimer's Association,2019,"16S rRNA gene, Alzheimer's disease, Amyloid, Fecal microbiota, Mild cognitive impairment",Experiment 4,China,Homo sapiens,Blood,UBERON:0000178,Alzheimer's disease,MONDO:0004975,Normal Controls,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,30,30,NA,16S,34,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,"age,body mass index,constipation",NA,NA,NA,NA,NA,NA,Signature 1,Table 2,11 December 2024,AaishahM,"AaishahM,WikiWorks",Generalized linear model for significant genera in AD patients and normal controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Glutamicibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium",3379134|1224|28216|80840|80864|12916;3379134|1224|1236|91347|543|561;1783272|201174|1760|85006|1268|1742989;3379134|1224|1236|72274|135621|286;1783272|201174|1760|85009|31957|1743,Complete,NA
bsdb:31434623/4/2,31434623,case-control,31434623,10.1016/j.jalz.2019.07.002,NA,"Li B., He Y., Ma J., Huang P., Du J., Cao L., Wang Y., Xiao Q., Tang H. , Chen S.",Mild cognitive impairment has similar alterations as Alzheimer's disease in gut microbiota,Alzheimer's & dementia : the journal of the Alzheimer's Association,2019,"16S rRNA gene, Alzheimer's disease, Amyloid, Fecal microbiota, Mild cognitive impairment",Experiment 4,China,Homo sapiens,Blood,UBERON:0000178,Alzheimer's disease,MONDO:0004975,Normal Controls,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,30,30,NA,16S,34,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,"age,body mass index,constipation",NA,NA,NA,NA,NA,NA,Signature 2,Table 2,11 December 2024,AaishahM,"AaishahM,WikiWorks",Generalized linear model for significant genera in AD patients and normal controls,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leucobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum",3379134|1224|1236|2887326|468|469;3379134|1224|1236|135619|28256|2745;1783272|201174|1760|85006|85023|55968;3379134|1224|28211|356|118882|528,Complete,NA
bsdb:31434623/5/1,31434623,case-control,31434623,10.1016/j.jalz.2019.07.002,NA,"Li B., He Y., Ma J., Huang P., Du J., Cao L., Wang Y., Xiao Q., Tang H. , Chen S.",Mild cognitive impairment has similar alterations as Alzheimer's disease in gut microbiota,Alzheimer's & dementia : the journal of the Alzheimer's Association,2019,"16S rRNA gene, Alzheimer's disease, Amyloid, Fecal microbiota, Mild cognitive impairment",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Normal Controls,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,30,30,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,13 December 2024,AaishahM,"AaishahM,WikiWorks",Relative abundance comparing AD patients and controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",3379134|1224|1236|91347|543|561;1783272|1239|91061|186826|33958|1578,Complete,NA
bsdb:31434623/5/2,31434623,case-control,31434623,10.1016/j.jalz.2019.07.002,NA,"Li B., He Y., Ma J., Huang P., Du J., Cao L., Wang Y., Xiao Q., Tang H. , Chen S.",Mild cognitive impairment has similar alterations as Alzheimer's disease in gut microbiota,Alzheimer's & dementia : the journal of the Alzheimer's Association,2019,"16S rRNA gene, Alzheimer's disease, Amyloid, Fecal microbiota, Mild cognitive impairment",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Normal Controls,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,30,30,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,13 December 2024,AaishahM,"AaishahM,WikiWorks",Relative abundance comparing AD patients and controls,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,NA
bsdb:31434623/6/1,31434623,case-control,31434623,10.1016/j.jalz.2019.07.002,NA,"Li B., He Y., Ma J., Huang P., Du J., Cao L., Wang Y., Xiao Q., Tang H. , Chen S.",Mild cognitive impairment has similar alterations as Alzheimer's disease in gut microbiota,Alzheimer's & dementia : the journal of the Alzheimer's Association,2019,"16S rRNA gene, Alzheimer's disease, Amyloid, Fecal microbiota, Mild cognitive impairment",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Normal Controls,Mild Cognitive Impairment (MCI),Patients with mild cognitive impairment,30,30,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,13 December 2024,AaishahM,"AaishahM,WikiWorks",Relative abundance comparing MCI patients and controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",3379134|1224|1236|91347|543|561;1783272|1239|91061|186826|33958|1578,Complete,NA
bsdb:31434623/6/2,31434623,case-control,31434623,10.1016/j.jalz.2019.07.002,NA,"Li B., He Y., Ma J., Huang P., Du J., Cao L., Wang Y., Xiao Q., Tang H. , Chen S.",Mild cognitive impairment has similar alterations as Alzheimer's disease in gut microbiota,Alzheimer's & dementia : the journal of the Alzheimer's Association,2019,"16S rRNA gene, Alzheimer's disease, Amyloid, Fecal microbiota, Mild cognitive impairment",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Normal Controls,Mild Cognitive Impairment (MCI),Patients with mild cognitive impairment,30,30,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,13 December 2024,AaishahM,"AaishahM,WikiWorks",Relative abundance comparing MCI patients and controls,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,NA
bsdb:31434623/7/1,31434623,case-control,31434623,10.1016/j.jalz.2019.07.002,NA,"Li B., He Y., Ma J., Huang P., Du J., Cao L., Wang Y., Xiao Q., Tang H. , Chen S.",Mild cognitive impairment has similar alterations as Alzheimer's disease in gut microbiota,Alzheimer's & dementia : the journal of the Alzheimer's Association,2019,"16S rRNA gene, Alzheimer's disease, Amyloid, Fecal microbiota, Mild cognitive impairment",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Normal Controls,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,30,30,NA,16S,34,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S1,13 December 2024,AaishahM,"AaishahM,WikiWorks",Differences of the fecal microbiota at all levels between AD and normal controls,increased,"k__Bacillati|p__Actinomycetota,p__Candidatus Saccharimonadota,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174;95818;3379134|74201;1783272|1239|91061;1783272|1239|186801;1783272|201174|84998;1783272|1239|526524;3379134|74201|203494;1783272|201174|1760|85004;1783272|1239|186801|186802;1783272|201174|84998|84999;1783272|1239|526524|526525;1783272|1239|91061|186826;3379134|74201|203494|48461;1783272|201174|1760|85004|31953;1783272|201174|84998|84999|84107;1783272|1239|526524|526525|128827;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|1300;3379134|74201|203494|48461|203557;3379134|74201|203494|48461|1647988|239934;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|189330;1783272|201174|84998|1643822|1643826|84111;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1301,Complete,NA
bsdb:31434623/7/2,31434623,case-control,31434623,10.1016/j.jalz.2019.07.002,NA,"Li B., He Y., Ma J., Huang P., Du J., Cao L., Wang Y., Xiao Q., Tang H. , Chen S.",Mild cognitive impairment has similar alterations as Alzheimer's disease in gut microbiota,Alzheimer's & dementia : the journal of the Alzheimer's Association,2019,"16S rRNA gene, Alzheimer's disease, Amyloid, Fecal microbiota, Mild cognitive impairment",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Normal Controls,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,30,30,NA,16S,34,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S1,13 December 2024,AaishahM,"AaishahM,WikiWorks",Differences of the fecal microbiota at all levels between AD and normal controls,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|976|200643;3379134|1224|28216;3379134|976|200643|171549;3379134|1224|28216|80840;3379134|1224|1236|135625;3379134|1224|28216|80840|506;3379134|976|200643|171549|815;3379134|1224|1236|135625|712;3379134|976|200643|171549|171551;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;3379134|976|200643|171549|1853231|574697;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|28050;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|171552|838,Complete,NA
bsdb:31434623/8/1,31434623,case-control,31434623,10.1016/j.jalz.2019.07.002,NA,"Li B., He Y., Ma J., Huang P., Du J., Cao L., Wang Y., Xiao Q., Tang H. , Chen S.",Mild cognitive impairment has similar alterations as Alzheimer's disease in gut microbiota,Alzheimer's & dementia : the journal of the Alzheimer's Association,2019,"16S rRNA gene, Alzheimer's disease, Amyloid, Fecal microbiota, Mild cognitive impairment",Experiment 8,China,Homo sapiens,Blood,UBERON:0000178,Alzheimer's disease,MONDO:0004975,Normal Controls,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,30,30,NA,16S,34,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S2,13 December 2024,AaishahM,"AaishahM,WikiWorks",Differences of the blood microbiota at all levels between AD and normal controls,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Glutamicibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Legionellaceae|g__Legionella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Pelagibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Skermanella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Sterolibacteriaceae|g__Sulfuritalea,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Vibrionimonas",1783272|1239|91061;3379134|1224|28216;3379134|1224|1236;3379134|976|117747;1783272|1239|91061|1385;3379134|1224|28216|80840;1783272|201174|1760|85009;3379134|1224|1236|72274;3379134|976|117747|200666;3379134|1224|28216|80840|80864;3379134|1224|28211|356|45401;1783272|201174|1760|85009|31957;3379134|1224|1236|72274|135621;3379134|1224|28211|204457|41297;1783272|1239|91061|1385|90964;3379134|1224|1236|135614|32033;3379134|1224|28216|80840|80864|12916;1783272|1239|186801|3085636|186803|572511;3379134|1224|1236|91347|543|561;1783272|201174|1760|85006|1268|1742989;3379134|1224|1236|118969|444|445;3379134|1224|28211|204457|41297|165696;3379134|1224|28211|356|2831106|1082930;1783272|201174|1760|85009|31957|1743;3379134|1224|1236|72274|135621|286;3379134|1224|28211|204441|2829815|204447;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|135614|32033|40323;3379134|1224|28216|32003|2008793|1054211;3379134|976|1853228|1853229|563835|1649511,Complete,NA
bsdb:31434623/8/2,31434623,case-control,31434623,10.1016/j.jalz.2019.07.002,NA,"Li B., He Y., Ma J., Huang P., Du J., Cao L., Wang Y., Xiao Q., Tang H. , Chen S.",Mild cognitive impairment has similar alterations as Alzheimer's disease in gut microbiota,Alzheimer's & dementia : the journal of the Alzheimer's Association,2019,"16S rRNA gene, Alzheimer's disease, Amyloid, Fecal microbiota, Mild cognitive impairment",Experiment 8,China,Homo sapiens,Blood,UBERON:0000178,Alzheimer's disease,MONDO:0004975,Normal Controls,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,30,30,NA,16S,34,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S2,13 December 2024,AaishahM,"AaishahM,WikiWorks",Differences of the blood microbiota at all levels between AD and normal controls,decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leucobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Sterolibacteriaceae|g__Methyloversatilis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Nesterenkonia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Undibacterium",1783272|201174;3379134|1224|28211;3379134|1224|28211|204458;1783272|201174|1760|85006;3379134|1224|1236|135619;3379134|1224|28211|356;3379134|1224|28211|204455;3379134|1224|28211|204441;3379134|1224|28216|80840|506;3379134|1224|28211|356|118882;3379134|1224|28211|204458|76892;3379134|1224|1236|135619|28256;3379134|1224|1236|2887326|468;3379134|1224|28216|80840|75682;3379134|1224|28211|356|69277;3379134|1224|28211|204455|31989;3379134|1224|28211|204441|41295;3379134|1224|28211|204458|76892|41275;3379134|1224|1236|91347|543|547;3379134|1224|1236|135619|28256|2745;1783272|201174|1760|85006|85023|55968;3379134|1224|28216|32003|2008793|378210;1783272|201174|1760|85006|1268|57494;3379134|1224|28211|356|118882|528;3379134|1224|1236|2887326|468|497;3379134|1224|1236|91347|1903411|613;3379134|1224|28216|80840|75682|401469,Complete,NA
bsdb:31440136/1/1,31440136,case-control,31440136,10.3389/fnins.2019.00839,NA,"Gorecki A.M., Preskey L., Bakeberg M.C., Kenna J.E., Gildenhuys C., MacDougall G., Dunlop S.A., Mastaglia F.L., Akkari P.A., Koengten F. , Anderton R.S.",Altered Gut Microbiome in Parkinson's Disease and the Influence of Lipopolysaccharide in a Human α-Synuclein Over-Expressing Mouse Model,Frontiers in neuroscience,2019,"Gammaproteobacteria, Parkinson’s disease, Thy1-αSyn, gastrointestinal, lipopolysaccharide, microbiome",Experiment 1,Australia,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Participants with idiopathic Parkinson's Disease and mild symptoms.,"All patients were confirmed to have idiopathic Parkinson’s disease by a movement disorders neurologist, in accordance with the United Kingdom Brain Bank criteria and mild symptoms.",7,7,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1.,22 January 2022,Fcuevas3,"Fcuevas3,WikiWorks","Mean class abundance in people with Parkinson’s disease and healthy controls, specifically control vs. mild PD.",increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,3379134|1224|1236,Complete,Claregrieve1
bsdb:31440136/2/1,31440136,case-control,31440136,10.3389/fnins.2019.00839,NA,"Gorecki A.M., Preskey L., Bakeberg M.C., Kenna J.E., Gildenhuys C., MacDougall G., Dunlop S.A., Mastaglia F.L., Akkari P.A., Koengten F. , Anderton R.S.",Altered Gut Microbiome in Parkinson's Disease and the Influence of Lipopolysaccharide in a Human α-Synuclein Over-Expressing Mouse Model,Frontiers in neuroscience,2019,"Gammaproteobacteria, Parkinson’s disease, Thy1-αSyn, gastrointestinal, lipopolysaccharide, microbiome",Experiment 2,Australia,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Participants with mild PD,Participants with severe PD,"All patients were confirmed to have idiopathic Parkinson’s disease by a movement disorders neurologist, in accordance with the United Kingdom Brain Bank criteria and severe symptoms.",7,7,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1.,22 January 2022,Fcuevas3,"Fcuevas3,WikiWorks",Mean class abundance in people with mild and severe Parkinson’s disease.,increased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,3379134|74201|203494,Complete,Claregrieve1
bsdb:31456752/1/1,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Control (Constipation mice without treatment),CMB1 (Constipation mice treated with CMB1 with adhesion properties),"This group was intragastrically administered 0.25 mL of normal saline solution containing 4 × 10^10 CFU/mL CMB1(Combined multiple strains of Bifidobacterium with adhesion property), respectively, daily for 2 weeks and loperamide (0.25 mL) intragastrically from day 15 to day 17 to induce constipation.",8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,increased,NA,NA,increased,Signature 1,"Fig. 3, 4 & 5",8 April 2025,Joiejoie,"Joiejoie,Mautin",Relative abundance (%) of fecal microbial taxa at the genus level in constipated mice fed CMB,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae",1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|171552|838;3379134|29547|3031852|213849|72293,Complete,KateRasheed
bsdb:31456752/1/2,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Control (Constipation mice without treatment),CMB1 (Constipation mice treated with CMB1 with adhesion properties),"This group was intragastrically administered 0.25 mL of normal saline solution containing 4 × 10^10 CFU/mL CMB1(Combined multiple strains of Bifidobacterium with adhesion property), respectively, daily for 2 weeks and loperamide (0.25 mL) intragastrically from day 15 to day 17 to induce constipation.",8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,increased,NA,NA,increased,Signature 2,"Fig. 3, 4 & 5",21 April 2025,Joiejoie,"Joiejoie,Anne-mariesharp",Relative abundance (%) of fecal microbial taxa at the genus level in constipated mice fed CMB,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",3379134|976|200643|171549|171550|239759;1783272|544448|31969|186332|186333|2086;1783272|1239|186801|186802|31979|1485;1783272|1239|526524|526525|2810280|100883;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|44748;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|459786,Complete,KateRasheed
bsdb:31456752/2/1,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Control ( Constipation mice without treatment ),CMB2 (Constipation mice treated with CMB2 with no adhesion properties),"This group was intragastrically administered 0.25 mL of normal saline solution containing 4 × 10^10 CFU/mL CMB2(Combined multiple strains of Bifidobacterium with no adhesion property), respectively, daily for 2 weeks and loperamide (0.25 mL) intragastrically from day 15 to day 17 to induce constipation.",8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,"Fig. 3, 4 & 5",8 April 2025,Joiejoie,"Joiejoie,Mautin,Anne-mariesharp",Relative abundance (%) of fecal microbial taxa at the genus level in constipated mice fed CMB,increased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter",1783272|544448|31969|186332|186333|2086;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|44748,Complete,KateRasheed
bsdb:31456752/2/2,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Control ( Constipation mice without treatment ),CMB2 (Constipation mice treated with CMB2 with no adhesion properties),"This group was intragastrically administered 0.25 mL of normal saline solution containing 4 × 10^10 CFU/mL CMB2(Combined multiple strains of Bifidobacterium with no adhesion property), respectively, daily for 2 weeks and loperamide (0.25 mL) intragastrically from day 15 to day 17 to induce constipation.",8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 2,"Fig. 3, 4 & 5",21 April 2025,Joiejoie,"Joiejoie,Anne-mariesharp",Relative abundance (%) of fecal microbial taxa at the genus level in constipated mice fed CMB,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",1783272|1239|186801|186802|31979|1485;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3085636|186803;1783272|1239|526524|526525|2810280|100883;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|44748;1783272|1239|526524|526525|2810281|191303;3379134|29547|3031852|213849|72293;3379134|976|200643|171549|171550|239759,Complete,KateRasheed
bsdb:31456752/3/1,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Normal (Healthy mice),CMB1 (Constipation mice treated with CMB1 with adhesion properties),"This group was intragastrically administered 0.25 mL of normal saline solution containing 4 × 10^10 CFU/mL CMB1(Combined multiple strains of Bifidobacterium with adhesion property), respectively, daily for 2 weeks and loperamide (0.25 mL) intragastrically from day 15 to day 17 to induce constipation.",8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,"Fig. 3, 4 & 5",8 April 2025,Joiejoie,"Joiejoie,Mautin",Relative abundance (%) of fecal microbial taxa at the genus level in constipated mice fed CMB,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae",1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|1578;3379134|29547|3031852|213849|72293,Complete,KateRasheed
bsdb:31456752/3/2,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Normal (Healthy mice),CMB1 (Constipation mice treated with CMB1 with adhesion properties),"This group was intragastrically administered 0.25 mL of normal saline solution containing 4 × 10^10 CFU/mL CMB1(Combined multiple strains of Bifidobacterium with adhesion property), respectively, daily for 2 weeks and loperamide (0.25 mL) intragastrically from day 15 to day 17 to induce constipation.",8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,"Fig. 3, 4 & 5",21 April 2025,Joiejoie,"Joiejoie,Anne-mariesharp",Relative abundance (%) of fecal microbial taxa at the genus level in constipated mice fed CMB,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|976|200643|171549|171550|239759;1783272|544448|31969|186332|186333|2086;1783272|1239|186801|186802|31979|1485;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|44748;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3085636|186803,Complete,KateRasheed
bsdb:31456752/4/1,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Normal (Healthy mice),CMB2 (Constipation mice treated with CMB2 with no adhesion properties),"This group was intragastrically administered 0.25 mL of normal saline solution containing 4 × 10^10 CFU/mL CMB2(Combined multiple strains of Bifidobacterium with no adhesion property), respectively, daily for 2 weeks and loperamide (0.25 mL) intragastrically from day 15 to day 17 to induce constipation.",8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,"Fig. 3, 4 & 5",8 April 2025,Joiejoie,"Joiejoie,Mautin,Anne-mariesharp",Relative abundance (%) of fecal microbial taxa at the genus level in constipated mice fed CMB,increased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",1783272|544448|31969|186332|186333|2086;1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549|1853231|283168;3379134|29547|3031852|213849|72293;3379134|976|200643|171549|171550|239759,Complete,KateRasheed
bsdb:31456752/4/2,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Normal (Healthy mice),CMB2 (Constipation mice treated with CMB2 with no adhesion properties),"This group was intragastrically administered 0.25 mL of normal saline solution containing 4 × 10^10 CFU/mL CMB2(Combined multiple strains of Bifidobacterium with no adhesion property), respectively, daily for 2 weeks and loperamide (0.25 mL) intragastrically from day 15 to day 17 to induce constipation.",8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,"Fig. 3, 4 & 5",21 April 2025,Joiejoie,"Joiejoie,Anne-mariesharp",Relative abundance (%) of fecal microbial taxa at the genus level in constipated mice fed CMB,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter",3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958|1578;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|44748,Complete,KateRasheed
bsdb:31456752/5/1,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,CMB2 (Constipation mice treated with CMB2 with no adhesion properties),CMB1 (Constipation mice treated with CMB1 with adhesion properties),"This group was intragastrically administered 0.25 mL of normal saline solution containing 4 × 10^10 CFU/mL CMB1(Combined multiple strains of Bifidobacterium with adhesion property), respectively, daily for 2 weeks and loperamide (0.25 mL) intragastrically from day 15 to day 17 to induce constipation.",8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,increased,NA,NA,increased,Signature 1,"Fig. 3, 4 & 5",8 April 2025,Joiejoie,"Joiejoie,Mautin",Relative abundance (%) of fecal microbial taxa at the genus level in constipated mice fed CMB,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae",1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|33958|1578;3379134|29547|3031852|213849|72293,Complete,KateRasheed
bsdb:31456752/5/2,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,CMB2 (Constipation mice treated with CMB2 with no adhesion properties),CMB1 (Constipation mice treated with CMB1 with adhesion properties),"This group was intragastrically administered 0.25 mL of normal saline solution containing 4 × 10^10 CFU/mL CMB1(Combined multiple strains of Bifidobacterium with adhesion property), respectively, daily for 2 weeks and loperamide (0.25 mL) intragastrically from day 15 to day 17 to induce constipation.",8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,increased,NA,NA,increased,Signature 2,"Fig. 3, 4 & 5",21 April 2025,Joiejoie,"Joiejoie,Anne-mariesharp",Relative abundance (%) of fecal microbial taxa at the genus level in constipated mice fed CMB,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter",3379134|976|200643|171549|171550|239759;1783272|544448|31969|186332|186333|2086;1783272|1239|186801|186802|31979|1485;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|44748,Complete,KateRasheed
bsdb:31456752/6/1,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Normal (Healthy mice),Control (Constipation mice without treatment),This group were given 0.25 mL normal saline (NS) using intragastric administration once a day for 17 days and loperamide (0.25 mL) intragastrically from day 15 to day 17 to induce constipation.,8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,"Fig. 3, 4 & 5",8 April 2025,Joiejoie,"Joiejoie,Mautin,Anne-mariesharp",Relative abundance (%) of fecal microbial taxa at the genus level in constipated mice fed CMB,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae",3379134|976|200643|171549|171550|239759;1783272|544448|31969|186332|186333|2086;1783272|1239|186801|186802|31979|1485;1783272|1239|526524|526525|2810280|100883;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|216572|44748;1783272|1239|526524|526525|2810281|191303;3379134|29547|3031852|213849|72293,Complete,KateRasheed
bsdb:31456752/6/2,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Normal (Healthy mice),Control (Constipation mice without treatment),This group were given 0.25 mL normal saline (NS) using intragastric administration once a day for 17 days and loperamide (0.25 mL) intragastrically from day 15 to day 17 to induce constipation.,8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,"Fig. 3, 4 & 5",21 April 2025,Joiejoie,"Joiejoie,Anne-mariesharp",Relative abundance (%) of fecal microbial taxa at the genus level in constipated mice fed CMB,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|33958|1578,Complete,KateRasheed
bsdb:31456752/7/1,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 7,China,Mus musculus,Caecum,UBERON:0001153,Constipation,HP:0002019,Control (Constipation mice without treatment),CMB1 (Constipation mice treated with CMB1 with adhesion properties),"The CMB1 group was intragastrically administered 0.25 mL of normal saline solution containing 4 × 10^10 CFU/mL CMB1(Combined multiple strains of Bifidobacterium with adhesion property), respectively, daily for 2 weeks and loperamide (0.25 mL) intragastrically from day 15 to day 17 to induce constipation.",8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,increased,NA,NA,increased,Signature 1,"Fig. 6, 7 & 8",8 April 2025,Joiejoie,"Joiejoie,Mautin,Anne-mariesharp",Relative abundance (%) of caecal microbial taxa at the genus level in constipated mice fed CMB.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|186807|51514;1783272|1239|186801|3085636|186803|189330;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|2005473,Complete,KateRasheed
bsdb:31456752/7/2,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 7,China,Mus musculus,Caecum,UBERON:0001153,Constipation,HP:0002019,Control (Constipation mice without treatment),CMB1 (Constipation mice treated with CMB1 with adhesion properties),"The CMB1 group was intragastrically administered 0.25 mL of normal saline solution containing 4 × 10^10 CFU/mL CMB1(Combined multiple strains of Bifidobacterium with adhesion property), respectively, daily for 2 weeks and loperamide (0.25 mL) intragastrically from day 15 to day 17 to induce constipation.",8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,increased,NA,NA,increased,Signature 2,"Fig. 6, 7 & 8",21 April 2025,Joiejoie,"Joiejoie,Anne-mariesharp",Relative abundance (%) of caecal microbial taxa at the genus level in constipated mice fed CMB.,decreased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",1783272|544448|31969|186332|186333|2086;3379134|976|200643|171549|2005525|375288,Complete,KateRasheed
bsdb:31456752/8/1,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 8,China,Mus musculus,Caecum,UBERON:0001153,Constipation,HP:0002019,Control (Constipation mice without treatment),CMB2 (Constipation mice treated with CMB2 with no adhesion properties),"This group was intragastrically administered 0.25 mL of normal saline solution containing 4 × 10^10 CFU/mL CMB2(Combined multiple strains of Bifidobacterium with no adhesion property), respectively, daily for 2 weeks and loperamide (0.25 mL) intragastrically from day 15 to day 17 to induce constipation.",8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,"Fig. 6, 7 & 8",8 April 2025,Joiejoie,"Joiejoie,Mautin,Anne-mariesharp",Relative abundance (%) of caecal microbial taxa at the genus level in constipated mice fed CMB.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|31979|1485;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|1853231|283168;3379134|200930|68337|191393|2945020|248038,Complete,KateRasheed
bsdb:31456752/8/2,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 8,China,Mus musculus,Caecum,UBERON:0001153,Constipation,HP:0002019,Control (Constipation mice without treatment),CMB2 (Constipation mice treated with CMB2 with no adhesion properties),"This group was intragastrically administered 0.25 mL of normal saline solution containing 4 × 10^10 CFU/mL CMB2(Combined multiple strains of Bifidobacterium with no adhesion property), respectively, daily for 2 weeks and loperamide (0.25 mL) intragastrically from day 15 to day 17 to induce constipation.",8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 2,"Fig. 6, 7 & 8",21 April 2025,Joiejoie,"Joiejoie,Anne-mariesharp",Relative abundance (%) of caecal microbial taxa at the genus level in constipated mice fed CMB.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma",1783272|1239|186801|186802|186807|51514;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|3085636|186803|189330;3379134|976|200643|171549|171550|28138;3379134|29547|3031852|213849|72293;3379134|976|200643|171549|2005525|375288;1783272|544448|31969|186332|186333|2086,Complete,KateRasheed
bsdb:31456752/9/1,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 9,China,Mus musculus,Caecum,UBERON:0001153,Constipation,HP:0002019,Normal (Healthy mice),CMB1 (Constipation mice treated with CMB1 with adhesion properties),"This group was intragastrically administered 0.25 mL of normal saline solution containing 4 × 10^10 CFU/mL CMB1(Combined multiple strains of Bifidobacterium with adhesion property), respectively, daily for 2 weeks and loperamide (0.25 mL) intragastrically from day 15 to day 17 to induce constipation.",8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,"Fig. 6, 7 & 8",8 April 2025,Joiejoie,"Joiejoie,Mautin,Anne-mariesharp",Relative abundance (%) of caecal microbial taxa at the genus level in constipated mice fed CMB.,increased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",1783272|544448|31969|186332|186333|2086;3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|186807|51514;3379134|200940|3031449|213115|194924|872;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|2005473,Complete,KateRasheed
bsdb:31456752/9/2,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 9,China,Mus musculus,Caecum,UBERON:0001153,Constipation,HP:0002019,Normal (Healthy mice),CMB1 (Constipation mice treated with CMB1 with adhesion properties),"This group was intragastrically administered 0.25 mL of normal saline solution containing 4 × 10^10 CFU/mL CMB1(Combined multiple strains of Bifidobacterium with adhesion property), respectively, daily for 2 weeks and loperamide (0.25 mL) intragastrically from day 15 to day 17 to induce constipation.",8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 2,"Fig. 6, 7 & 8",21 April 2025,Joiejoie,"Joiejoie,Anne-mariesharp",Relative abundance (%) of caecal microbial taxa at the genus level in constipated mice fed CMB.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|171550|28138;3379134|976|200643|171549|1853231|283168;3379134|200930|68337|191393|2945020|248038;3379134|29547|3031852|213849|72293;3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|186803,Complete,KateRasheed
bsdb:31456752/10/1,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 10,China,Mus musculus,Caecum,UBERON:0001153,Constipation,HP:0002019,Normal (Healthy mice),CMB2 (Constipation mice treated with CMB2 with no adhesion properties),"This group was intragastrically administered 0.25 mL of normal saline solution containing 4 × 10^10 CFU/mL CMB2(Combined multiple strains of Bifidobacterium with no adhesion property), respectively, daily for 2 weeks and loperamide (0.25 mL) intragastrically from day 15 to day 17 to induce constipation.",8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,"Fig. 6, 7 & 8",12 April 2025,Joiejoie,"Joiejoie,Mautin,Anne-mariesharp",Relative abundance (%) of caecal microbial taxa at the genus level in constipated mice fed CMB.,increased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",1783272|544448|31969|186332|186333|2086;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|2005473,Complete,KateRasheed
bsdb:31456752/10/2,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 10,China,Mus musculus,Caecum,UBERON:0001153,Constipation,HP:0002019,Normal (Healthy mice),CMB2 (Constipation mice treated with CMB2 with no adhesion properties),"This group was intragastrically administered 0.25 mL of normal saline solution containing 4 × 10^10 CFU/mL CMB2(Combined multiple strains of Bifidobacterium with no adhesion property), respectively, daily for 2 weeks and loperamide (0.25 mL) intragastrically from day 15 to day 17 to induce constipation.",8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,"Fig. 6, 7 & 8",21 April 2025,Joiejoie,"Joiejoie,Anne-mariesharp",Relative abundance (%) of caecal microbial taxa at the genus level in constipated mice fed CMB.,decreased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",3379134|200940|3031449|213115|194924|872;1783272|1239|186801|3085636|186803|189330;3379134|976|200643|171549|171550|28138;3379134|29547|3031852|213849|72293;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|31979|1485,Complete,KateRasheed
bsdb:31456752/11/1,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 11,China,Mus musculus,Caecum,UBERON:0001153,Constipation,HP:0002019,CMB2 (Constipation mice treated with CMB2 with no adhesion properties),CMB1 (Constipation mice treated with CMB1 with adhesion properties),"This group was intragastrically administered 0.25 mL of normal saline solution containing 4 × 10^10 CFU/mL CMB1(Combined multiple strains of Bifidobacterium with adhesion property), respectively, daily for 2 weeks and loperamide (0.25 mL) intragastrically from day 15 to day 17 to induce constipation.",8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,increased,Signature 1,"Fig. 6, 7 & 8",12 April 2025,Joiejoie,"Joiejoie,Mautin,Anne-mariesharp",Relative abundance (%) of caecal microbial taxa at the genus level in constipated mice fed CMB.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|186807|51514;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|3085636|186803|189330;3379134|976|200643|171549|171550|28138;1783272|1239|186801|186802|216572|1263;3379134|29547|3031852|213849|72293;3379134|976|200643|171549|2005473,Complete,KateRasheed
bsdb:31456752/11/2,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 11,China,Mus musculus,Caecum,UBERON:0001153,Constipation,HP:0002019,CMB2 (Constipation mice treated with CMB2 with no adhesion properties),CMB1 (Constipation mice treated with CMB1 with adhesion properties),"This group was intragastrically administered 0.25 mL of normal saline solution containing 4 × 10^10 CFU/mL CMB1(Combined multiple strains of Bifidobacterium with adhesion property), respectively, daily for 2 weeks and loperamide (0.25 mL) intragastrically from day 15 to day 17 to induce constipation.",8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,increased,Signature 2,"Fig. 6, 7 & 8",21 April 2025,Joiejoie,"Joiejoie,Anne-mariesharp",Relative abundance (%) of caecal microbial taxa at the genus level in constipated mice fed CMB.,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",3379134|74201|203494|48461|1647988|239934;1783272|201174|1760|85004|31953|1678;3379134|200930|68337|191393|2945020|248038;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|119852,Complete,KateRasheed
bsdb:31456752/12/1,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 12,China,Mus musculus,Caecum,UBERON:0001153,Constipation,HP:0002019,Normal (Healthy mice),Control (Constipation mice without treatment),This group were given 0.25 mL normal saline (NS) using intragastric administration once a day for 17 days and loperamide (0.25 mL) intragastrically from day 15 to day 17 to induce constipation.,8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,"Fig. 6, 7 & 8",12 April 2025,Joiejoie,"Joiejoie,Mautin,Anne-mariesharp",Relative abundance (%) of caecal microbial taxa at the genus level in constipated mice fed CMB.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",1783272|201174|84998|1643822|1643826|447020;1783272|544448|31969|186332|186333|2086;1783272|1239|186801|186802|186807|51514;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005473,Complete,KateRasheed
bsdb:31456752/12/2,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 12,China,Mus musculus,Caecum,UBERON:0001153,Constipation,HP:0002019,Normal (Healthy mice),Control (Constipation mice without treatment),This group were given 0.25 mL normal saline (NS) using intragastric administration once a day for 17 days and loperamide (0.25 mL) intragastrically from day 15 to day 17 to induce constipation.,8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,"Fig. 6, 7 & 8",21 April 2025,Joiejoie,"Joiejoie,Anne-mariesharp",Relative abundance (%) of caecal microbial taxa at the genus level in constipated mice fed CMB.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|171550|28138;3379134|976|200643|171549|1853231|283168;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|216572|119852;3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|186803,Complete,KateRasheed
bsdb:31456752/13/1,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 13,China,Mus musculus,"Feces,Caecum","UBERON:0001153,UBERON:0001988",Sampling site,EFO:0000688,Normal (Healthy mice) (fecal sample),C-Normal (Healthy mice) (cecal sample),These are healthy mice that were given 0.25 mL normal saline (NS) using intragastric administration once a day for 17 days.,8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 9,10,11",12 April 2025,Joiejoie,"Joiejoie,Mautin",The genus-level comparison of fecal samples and caecum content samples.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|186802|31979|1485;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|171550|28138;1783272|1239|186801|186802|216572|1263;3379134|29547|3031852|213849|72293;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|189330,Complete,KateRasheed
bsdb:31456752/13/2,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 13,China,Mus musculus,"Feces,Caecum","UBERON:0001153,UBERON:0001988",Sampling site,EFO:0000688,Normal (Healthy mice) (fecal sample),C-Normal (Healthy mice) (cecal sample),These are healthy mice that were given 0.25 mL normal saline (NS) using intragastric administration once a day for 17 days.,8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 9,10,11",23 April 2025,Mautin,Mautin,The genus-level comparison of fecal samples and caecum content samples,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter",1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|1853231|283168,Complete,KateRasheed
bsdb:31456752/14/1,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 14,China,Mus musculus,"Feces,Caecum","UBERON:0001988,UBERON:0001153",Sampling site,EFO:0000688,Control (Constipation mice without treatment) (fecal sample),C-Control (Constipation mice without treatment) (cecal sample),This group were given 0.25 mL normal saline (NS) using intragastric administration once a day for 17 days and loperamide (0.25 mL) intragastrically from day 15 to day 17 to induce constipation.,8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 9,10,11",12 April 2025,Joiejoie,"Joiejoie,Mautin",The genus-level comparison of fecal samples and caecum content samples.,increased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",1783272|544448|31969|186332|186333|2086;1783272|1239|186801|3085636|186803|189330;3379134|29547|3031852|213849|72293;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171550|28138;1783272|1239|186801|186802|216572|1263;3379134|74201|203494|48461|1647988|239934,Complete,KateRasheed
bsdb:31456752/14/2,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 14,China,Mus musculus,"Feces,Caecum","UBERON:0001988,UBERON:0001153",Sampling site,EFO:0000688,Control (Constipation mice without treatment) (fecal sample),C-Control (Constipation mice without treatment) (cecal sample),This group were given 0.25 mL normal saline (NS) using intragastric administration once a day for 17 days and loperamide (0.25 mL) intragastrically from day 15 to day 17 to induce constipation.,8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 9,10,11",23 April 2025,Mautin,Mautin,The genus-level comparison of fecal samples and caecum content samples,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter",1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|1853231|283168,Complete,KateRasheed
bsdb:31456752/15/1,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 15,China,Mus musculus,"Feces,Caecum","UBERON:0001153,UBERON:0001988",Sampling site,EFO:0000688,CMB1 (Constipation mice treated with CMB1 with adhesion properties) (fecal sample),C-CMB1 (Constipation mice treated with CMB1 with adhesion properties) (cecal sample),"This group was intragastrically administered 0.25 mL of normal saline solution containing 4 × 10^10 CFU/mL CMB1(Combined multiple strains of Bifidobacterium with adhesion property), respectively, daily for 2 weeks and loperamide (0.25 mL) intragastrically from day 15 to day 17 to induce constipation.",8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 9,10,11",12 April 2025,Joiejoie,"Joiejoie,Mautin",The genus-level comparison of fecal samples and caecum content samples.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea",3379134|74201|203494|48461|1647988|239934;1783272|544448|31969|186332|186333|2086;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979|1485;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171550|28138;1783272|1239|186801|186802|216572|1263;3379134|29547|3031852|213849|72293;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|189330,Complete,KateRasheed
bsdb:31456752/15/2,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 15,China,Mus musculus,"Feces,Caecum","UBERON:0001153,UBERON:0001988",Sampling site,EFO:0000688,CMB1 (Constipation mice treated with CMB1 with adhesion properties) (fecal sample),C-CMB1 (Constipation mice treated with CMB1 with adhesion properties) (cecal sample),"This group was intragastrically administered 0.25 mL of normal saline solution containing 4 × 10^10 CFU/mL CMB1(Combined multiple strains of Bifidobacterium with adhesion property), respectively, daily for 2 weeks and loperamide (0.25 mL) intragastrically from day 15 to day 17 to induce constipation.",8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 9,10,11",23 April 2025,Mautin,Mautin,The genus-level comparison of fecal samples and caecum content samples.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter",1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|1853231|283168,Complete,KateRasheed
bsdb:31456752/16/1,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 16,China,Mus musculus,"Feces,Caecum","UBERON:0001153,UBERON:0001988",Sampling site,EFO:0000688,CMB2  (Constipation mice treated with CMB2 with no adhesion properties) (fecal sample),C-CMB2 (Constipation mice treated with CMB2 with no adhesion properties) (cecal sample),"This group was intragastrically administered 0.25 mL of normal saline solution containing 4 × 10^10 CFU/mL CMB2(Combined multiple strains of Bifidobacterium with no adhesion property), respectively, daily for 2 weeks and loperamide (0.25 mL) intragastrically from day 15 to day 17 to induce constipation.",8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 9,10,11",12 April 2025,Joiejoie,"Joiejoie,Mautin",The genus-level comparison of fecal samples and caecum content samples.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae",3379134|74201|203494|48461|1647988|239934;1783272|544448|31969|186332|186333|2086;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|189330;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171550|28138;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803;3379134|29547|3031852|213849|72293,Complete,KateRasheed
bsdb:31456752/16/2,31456752,laboratory experiment,31456752,10.3389/fmicb.2019.01721,NA,"Wang L., Chen C., Cui S., Lee Y.K., Wang G., Zhao J., Zhang H. , Chen W.",Adhesive <i>Bifidobacterium</i> Induced Changes in Cecal Microbiome Alleviated Constipation in Mice,Frontiers in microbiology,2019,"Bifidobacterium, SCFAs, adhesion properties, constipation, gut microbiota",Experiment 16,China,Mus musculus,"Feces,Caecum","UBERON:0001153,UBERON:0001988",Sampling site,EFO:0000688,CMB2  (Constipation mice treated with CMB2 with no adhesion properties) (fecal sample),C-CMB2 (Constipation mice treated with CMB2 with no adhesion properties) (cecal sample),"This group was intragastrically administered 0.25 mL of normal saline solution containing 4 × 10^10 CFU/mL CMB2(Combined multiple strains of Bifidobacterium with no adhesion property), respectively, daily for 2 weeks and loperamide (0.25 mL) intragastrically from day 15 to day 17 to induce constipation.",8,8,NA,16S,4,Illumina,log transformation,ANOVA,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 9,10,11",23 April 2025,Mautin,Mautin,The genus-level comparison of fecal samples and caecum content samples.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter",1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|1853231|283168,Complete,KateRasheed
bsdb:31456756/1/1,31456756,laboratory experiment,31456756,10.3389/fmicb.2019.01767,NA,"Hu C., Li F., Duan Y., Yin Y. , Kong X.",Dietary Supplementation With Leucine or in Combination With Arginine Decreases Body Fat Weight and Alters Gut Microbiota Composition in Finishing Pigs,Frontiers in microbiology,2019,"arginine, colon, dietary supplementation, glutamic acid, leucine, microbiota, short-chain fatty acid",Experiment 1,China,Sus scrofa domesticus,Colon,UBERON:0001155,Diet measurement,EFO:0008111,"Combination of Leu_Glu (1.00% Leucine + 1.00% Glutamic acid), Leu_Arg ( 1.00% Leucine + 1.00% Arginine) and BD (basal diet)",Leu (Leucine) group,Pigs fed a basal diet supplemented with 1.00% Leucine + 1.37% alanine (Leu group),36,12,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 8A and 8B,5 May 2025,Tosin,Tosin,Taxonomic differences of colonic microbiota among the four groups. Comparison of relative abundance at the phylum (A) and genus (B) levels between the four groups.,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia",1783272|201174;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;1783272|201174|84998|1643822|1643826|84108,Complete,KateRasheed
bsdb:31456756/2/1,31456756,laboratory experiment,31456756,10.3389/fmicb.2019.01767,NA,"Hu C., Li F., Duan Y., Yin Y. , Kong X.",Dietary Supplementation With Leucine or in Combination With Arginine Decreases Body Fat Weight and Alters Gut Microbiota Composition in Finishing Pigs,Frontiers in microbiology,2019,"arginine, colon, dietary supplementation, glutamic acid, leucine, microbiota, short-chain fatty acid",Experiment 2,China,Sus scrofa domesticus,Colon,UBERON:0001155,Diet measurement,EFO:0008111,"Combination of Leu (Leucine), Leu_Glu (1.00% Leucine + 1.00% Glutamic acid) and Leu_Arg (1.00% Leucine + 1.00% Arginine)",BD (Basal diet),"The pigs in the control group were fed a basal diet supplemented with 2.05% alanine (isonitrogenous control, BD group)",36,12,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 8B,6 May 2025,Tosin,Tosin,Taxonomic differences of colonic microbiota among the four groups. Comparison of relative abundance at the genus (B) level between the four groups.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium",1783272|1239|186801|3085636|186803|653683;3379134|976|117743|200644|49546|237,Complete,KateRasheed
bsdb:31456756/3/1,31456756,laboratory experiment,31456756,10.3389/fmicb.2019.01767,NA,"Hu C., Li F., Duan Y., Yin Y. , Kong X.",Dietary Supplementation With Leucine or in Combination With Arginine Decreases Body Fat Weight and Alters Gut Microbiota Composition in Finishing Pigs,Frontiers in microbiology,2019,"arginine, colon, dietary supplementation, glutamic acid, leucine, microbiota, short-chain fatty acid",Experiment 3,China,Sus scrofa domesticus,Colon,UBERON:0001155,Diet measurement,EFO:0008111,"Combination of Leu (Leucine), Leu_Glu (1.00% Leucine + 1.00% Glutamic acid) and Leu_Arg (1.00% Leucine + 1.00% Arginine)",BD (Basal diet),"The pigs in the control group were fed a basal diet supplemented with 2.05% alanine (isonitrogenous control, BD group)",36,12,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 8C,6 May 2025,Tosin,Tosin,Linear discriminant analysis (LDA) scores for the enriched microbiota among the four groups,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter",3379134|976|117743|200644|49546|237;1783272|1239|186801|3085636|186803|653683,Complete,KateRasheed
bsdb:31456756/4/1,31456756,laboratory experiment,31456756,10.3389/fmicb.2019.01767,NA,"Hu C., Li F., Duan Y., Yin Y. , Kong X.",Dietary Supplementation With Leucine or in Combination With Arginine Decreases Body Fat Weight and Alters Gut Microbiota Composition in Finishing Pigs,Frontiers in microbiology,2019,"arginine, colon, dietary supplementation, glutamic acid, leucine, microbiota, short-chain fatty acid",Experiment 4,China,Sus scrofa domesticus,Colon,UBERON:0001155,Diet measurement,EFO:0008111,"Combination of Leu_Glu (1.00% Leucine + 1.00% Glutamic acid), Leu_Arg ( 1.00% Leucine + 1.00% Arginine) and BD (basal diet)",Leu (Leucine) group,Pigs fed a basal diet supplemented with 1.00% Leucine + 1.37% alanine (Leu group),36,12,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 8C,6 May 2025,Tosin,Tosin,Linear discriminant analysis (LDA) scores for the enriched microbiota among the four groups,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia",1783272|201174;1783272|201174|84992;1783272|201174|84998|84999;1783272|201174|84998|84999|84107;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|1643822|1643826|84108,Complete,KateRasheed
bsdb:31456756/5/1,31456756,laboratory experiment,31456756,10.3389/fmicb.2019.01767,NA,"Hu C., Li F., Duan Y., Yin Y. , Kong X.",Dietary Supplementation With Leucine or in Combination With Arginine Decreases Body Fat Weight and Alters Gut Microbiota Composition in Finishing Pigs,Frontiers in microbiology,2019,"arginine, colon, dietary supplementation, glutamic acid, leucine, microbiota, short-chain fatty acid",Experiment 5,China,Sus scrofa domesticus,Colon,UBERON:0001155,Diet measurement,EFO:0008111,"Combination of Leu (Leucine), Leu_Arg ( 1.00% Leucine + 1.00% Arginine) and BD (basal diet) groups",Leu_ Glu (1.00% Leucine + 1.00% Glutamic acid) group,Pigs fed a basal diet supplemented with 1.00% Leucine + 1.00% glutamic acid (Leu_Glu group),36,12,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 8C,6 May 2025,Tosin,Tosin,Linear discriminant analysis (LDA) scores for the enriched microbiota among four groups,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Catenisphaera,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",1783272|1239|526524|526525|128827|1774107;3379134|1224|1236|2887326|468;1783272|1239|186801|186802|216572|119852;3379134|1224|1236|72274;1783272|1239|909932|909929|1843491|970,Complete,KateRasheed
bsdb:31463790/1/1,31463790,case-control,31463790,10.1007/s12275-019-9127-2,NA,"Li Z., Gong Y., Chen S., Li S., Zhang Y., Zhong H., Wang Z., Chen Y., Deng Q., Jiang Y., Li L., Fu M. , Yi G.",Comparative portrayal of ocular surface microbe with and without dry eye,"Journal of microbiology (Seoul, Korea)",2019,"16S rRNA gene sequencing, dry eye, meibomian gland dysfunction, ocular surface bacteria",Experiment 1,China,Homo sapiens,Conjunctiva,UBERON:0001811,Dry eye syndrome,EFO:1000906,healthy controls,Dry Eye,"Patients with Dry Eye  (with or without Meibomian Gland Disease).  
Subjects were considered to have DE if a positive
dry eye survey OSDI ≥ 13 was recorded in addition
to a positive score in one or more tests (tear break-up time
≤ 10; osmolarity ≥ 308 mOsm/L or interocular difference > 8
mOsm/L; ocular surface staining > 5 corneal spots, > 9 conjunctival
spots, or lid margin ≥ 2 mm length, and 25% width).",54,35,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,Figure 4,9 September 2023,Mary Bearkland,"Mary Bearkland,Peace Sandy,Folakunmi,WikiWorks","Taxa listed according to their linear discriminant analysis (LDA)
values determined from comparisons between the DE patients and NDE
subjects as computed by the use of the LEfSe algorithm.",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,3379134|976|200643,Complete,Folakunmi
bsdb:31463790/1/2,31463790,case-control,31463790,10.1007/s12275-019-9127-2,NA,"Li Z., Gong Y., Chen S., Li S., Zhang Y., Zhong H., Wang Z., Chen Y., Deng Q., Jiang Y., Li L., Fu M. , Yi G.",Comparative portrayal of ocular surface microbe with and without dry eye,"Journal of microbiology (Seoul, Korea)",2019,"16S rRNA gene sequencing, dry eye, meibomian gland dysfunction, ocular surface bacteria",Experiment 1,China,Homo sapiens,Conjunctiva,UBERON:0001811,Dry eye syndrome,EFO:1000906,healthy controls,Dry Eye,"Patients with Dry Eye  (with or without Meibomian Gland Disease).  
Subjects were considered to have DE if a positive
dry eye survey OSDI ≥ 13 was recorded in addition
to a positive score in one or more tests (tear break-up time
≤ 10; osmolarity ≥ 308 mOsm/L or interocular difference > 8
mOsm/L; ocular surface staining > 5 corneal spots, > 9 conjunctival
spots, or lid margin ≥ 2 mm length, and 25% width).",54,35,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 2,Figure 4,9 September 2023,Mary Bearkland,"Mary Bearkland,Folakunmi,WikiWorks","Taxa listed according to their linear discriminant analysis (LDA)
values determined from comparisons between the DE patients and NDE
subjects as computed by the use of the LEfSe algorithm.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas plecoglossicida",3379134|1224|1236;3379134|1224|1236|72274|135621;3379134|1224;3379134|1224|1236|72274|135621|286;3379134|1224|1236|72274|135621|286|70775,Complete,Folakunmi
bsdb:31463790/2/1,31463790,case-control,31463790,10.1007/s12275-019-9127-2,NA,"Li Z., Gong Y., Chen S., Li S., Zhang Y., Zhong H., Wang Z., Chen Y., Deng Q., Jiang Y., Li L., Fu M. , Yi G.",Comparative portrayal of ocular surface microbe with and without dry eye,"Journal of microbiology (Seoul, Korea)",2019,"16S rRNA gene sequencing, dry eye, meibomian gland dysfunction, ocular surface bacteria",Experiment 2,China,Homo sapiens,Conjunctiva,UBERON:0001811,Dry eye syndrome,EFO:1000906,Non-MGD,MGD,Patients with Dry Eye with Meibomian Gland Disease,10,25,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 6,9 September 2023,Mary Bearkland,"Mary Bearkland,Folakunmi,WikiWorks",Taxa listed according to their linear discriminant analysis (LDA) values determined from comparisons between the MGD patients and NMGD subjects in DE group as computed by the use of the LEfSe algorithm.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus pumilus",1783272|1239|91061|1385|186817;1783272|1239|91061|1385;1783272|1239|91061;1783272|1239|91061|1385|186817|1386|1408,Complete,Folakunmi
bsdb:31463790/2/2,31463790,case-control,31463790,10.1007/s12275-019-9127-2,NA,"Li Z., Gong Y., Chen S., Li S., Zhang Y., Zhong H., Wang Z., Chen Y., Deng Q., Jiang Y., Li L., Fu M. , Yi G.",Comparative portrayal of ocular surface microbe with and without dry eye,"Journal of microbiology (Seoul, Korea)",2019,"16S rRNA gene sequencing, dry eye, meibomian gland dysfunction, ocular surface bacteria",Experiment 2,China,Homo sapiens,Conjunctiva,UBERON:0001811,Dry eye syndrome,EFO:1000906,Non-MGD,MGD,Patients with Dry Eye with Meibomian Gland Disease,10,25,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 6,9 September 2023,Mary Bearkland,"Mary Bearkland,Aleru002,Folakunmi,WikiWorks",Taxa listed according to their linear discriminant analysis (LDA) values determined from comparisons between the MGD patients and NMGD subjects in DE group as computed by the use of LEfSe algorithm.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Thermomonas",3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|216572;3379134|1224|1236|135614|32033|141948,Complete,Folakunmi
bsdb:31464899/1/1,31464899,case-control,31464899,10.1097/MD.0000000000016626,NA,"Liang W., Yang Y., Wang H., Wang H., Yu X., Lu Y., Shen S. , Teng L.",Gut microbiota shifts in patients with gastric cancer in perioperative period,Medicine,2019,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,controls,gastric cancer,gastric cancer patients,22,20,1 month,16S,NA,Illumina,raw counts,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,increased,unchanged,NA,increased,Signature 1,"Figure 2, Sup. figure 2A, Sup. figure 2B",10 January 2021,Valentina Pineda,WikiWorks,Comparision of gut microbiota between Gastric Cancer patients and Healthy Controls,increased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales",3379134|1224;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|620;1783272|1239|186801|186802|31979|1485;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236;3379134|1224|1236|91347,Complete,Claregrieve1
bsdb:31464899/1/2,31464899,case-control,31464899,10.1097/MD.0000000000016626,NA,"Liang W., Yang Y., Wang H., Wang H., Yu X., Lu Y., Shen S. , Teng L.",Gut microbiota shifts in patients with gastric cancer in perioperative period,Medicine,2019,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,controls,gastric cancer,gastric cancer patients,22,20,1 month,16S,NA,Illumina,raw counts,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,increased,unchanged,NA,increased,Signature 2,"Figure 2, Sup. figure 2A, Sup. figure 2B",10 January 2021,Valentina Pineda,WikiWorks,Comparision of gut microbiota between Gastric Cancer patients and Healthy Controls,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",3379134|976;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976|200643|171549,Complete,Claregrieve1
bsdb:31464899/2/1,31464899,case-control,31464899,10.1097/MD.0000000000016626,NA,"Liang W., Yang Y., Wang H., Wang H., Yu X., Lu Y., Shen S. , Teng L.",Gut microbiota shifts in patients with gastric cancer in perioperative period,Medicine,2019,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,healthy gastric cancer (post surgery),gastric cancer,gastric cancer patients,6,20,1 month,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 5,10 January 2021,Valentina Pineda,WikiWorks,LEfSe analysis of enriched bacterial taxa in gut microbiota between gastric cancer group and healthy gastric cancer group,increased,"k__Thermotogati|p__Synergistota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella",3384194|508458;1783272|1239|186801|3085636|186803;3379134|1224|1236|91347|543|570,Complete,Claregrieve1
bsdb:31464899/2/2,31464899,case-control,31464899,10.1097/MD.0000000000016626,NA,"Liang W., Yang Y., Wang H., Wang H., Yu X., Lu Y., Shen S. , Teng L.",Gut microbiota shifts in patients with gastric cancer in perioperative period,Medicine,2019,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,healthy gastric cancer (post surgery),gastric cancer,gastric cancer patients,6,20,1 month,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 5,10 January 2021,Valentina Pineda,WikiWorks,LEfSe analysis of enriched bacterial taxa in gut microbiota between gastric cancer group and healthy gastric cancer group,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,p__Candidatus Saccharimonadota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|74201|203494;3379134|74201|203494|48461;3379134|74201|203494|48461|203557;3379134|74201;3379134|74201|203494|48461|1647988|239934;3379134|1224|1236|91347|543|620;95818;1783272|1239|909932|909929;1783272|1239|909932;1783272|1239|909932|1843489|31977;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|39948;3379134|976|200643|171549|171552,Complete,Claregrieve1
bsdb:31477562/1/1,31477562,randomized controlled trial,31477562,10.1016/j.ebiom.2019.08.032,NA,"Nagpal R., Neth B.J., Wang S., Craft S. , Yadav H.",Modified Mediterranean-ketogenic diet modulates gut microbiome and short-chain fatty acids in association with Alzheimer's disease markers in subjects with mild cognitive impairment,EBioMedicine,2019,"Alzheimer, Dementia, Diet, High fat, Ketogenic, Microbiota, Nutrition, Short-chain fatty acids",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Cognitive Normal,Mild Cognitive Impairment,Participants diagnosed with early Mild Cognitive Impairment (diagnosed using ADNI-2 criteria) randomly assigned to either a modified Mediterranean-ketogenic diet (MMKD) or an American heart association diet (AHAD) group,6,11,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Fig. 1d-n and Result text,10 March 2024,MyleeeA,"MyleeeA,Welile,Scholastica,WikiWorks",Differences in the gut microbiome between subjects clinically diagnosed with mild cognitive impairment (MCI) versus cognitively normal (CN) counterparts.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota",1783272|1239|186801|3085636|186803|33042;3379134|1224|1236|91347|543;1783272|1239|909932|1843488|909930|33024;3379134|1224,Complete,Svetlana up
bsdb:31477562/1/2,31477562,randomized controlled trial,31477562,10.1016/j.ebiom.2019.08.032,NA,"Nagpal R., Neth B.J., Wang S., Craft S. , Yadav H.",Modified Mediterranean-ketogenic diet modulates gut microbiome and short-chain fatty acids in association with Alzheimer's disease markers in subjects with mild cognitive impairment,EBioMedicine,2019,"Alzheimer, Dementia, Diet, High fat, Ketogenic, Microbiota, Nutrition, Short-chain fatty acids",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Cognitive Normal,Mild Cognitive Impairment,Participants diagnosed with early Mild Cognitive Impairment (diagnosed using ADNI-2 criteria) randomly assigned to either a modified Mediterranean-ketogenic diet (MMKD) or an American heart association diet (AHAD) group,6,11,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Fig. 1d-n and Result text,10 March 2024,MyleeeA,"MyleeeA,Scholastica,WikiWorks",Differences in the gut microbiome between subjects clinically diagnosed with mild cognitive impairment (MCI) versus cognitively normal (CN) counterparts.,decreased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,1783272|1239|909932|1843489|31977|39948,Complete,Svetlana up
bsdb:31477562/2/1,31477562,randomized controlled trial,31477562,10.1016/j.ebiom.2019.08.032,NA,"Nagpal R., Neth B.J., Wang S., Craft S. , Yadav H.",Modified Mediterranean-ketogenic diet modulates gut microbiome and short-chain fatty acids in association with Alzheimer's disease markers in subjects with mild cognitive impairment,EBioMedicine,2019,"Alzheimer, Dementia, Diet, High fat, Ketogenic, Microbiota, Nutrition, Short-chain fatty acids",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Post American heart association diet (AHAD) in MCI,Post modified Mediterranean-ketogenic diet (MMKD) in MCI,Participants diagnosed with early mild cognitive impairment (MCI) at endpoint of the modified Mediterranean-ketogenic diet (MMKD) intervention,11,11,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Fig. 4 and Text,12 March 2024,MyleeeA,"MyleeeA,Scholastica,WikiWorks",Significant bacterial taxa at endpoint American heart association diet (Post-AHAD) intervention compared to endpoint modified Mediterranean-ketogenic diet (Post-MMKD) intervention,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678,Complete,Svetlana up
bsdb:31477562/3/1,31477562,randomized controlled trial,31477562,10.1016/j.ebiom.2019.08.032,NA,"Nagpal R., Neth B.J., Wang S., Craft S. , Yadav H.",Modified Mediterranean-ketogenic diet modulates gut microbiome and short-chain fatty acids in association with Alzheimer's disease markers in subjects with mild cognitive impairment,EBioMedicine,2019,"Alzheimer, Dementia, Diet, High fat, Ketogenic, Microbiota, Nutrition, Short-chain fatty acids",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Post American heart association diet (AHAD) in CN and MCI,Post modified Mediterranean-ketogenic diet (MMKD) in CN and MCI,All Participants including cognitively normal (CN) and those diagnosed with early mild cognitive impairment (MCI) at endpoint of the modified Mediterranean-ketogenic diet (MMKD) intervention,17,17,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Fig. 4,12 March 2024,MyleeeA,"MyleeeA,Scholastica,WikiWorks",Significant bacterial taxa at endpoint American heart association diet (Post-AHAD) intervention compared to endpoint modified Mediterranean-ketogenic diet (Post-MMKD) intervention,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678,Complete,Svetlana up
bsdb:31477562/4/1,31477562,randomized controlled trial,31477562,10.1016/j.ebiom.2019.08.032,NA,"Nagpal R., Neth B.J., Wang S., Craft S. , Yadav H.",Modified Mediterranean-ketogenic diet modulates gut microbiome and short-chain fatty acids in association with Alzheimer's disease markers in subjects with mild cognitive impairment,EBioMedicine,2019,"Alzheimer, Dementia, Diet, High fat, Ketogenic, Microbiota, Nutrition, Short-chain fatty acids",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Pre modified Mediterranean-ketogenic diet (MMKD) in CN and MCI,Post modified Mediterranean-ketogenic diet (MMKD) in CN and MCI,All Participants including cognitively normal (CN) and those diagnosed with early mild cognitive impairment (MCI) at endpoint of the modified Mediterranean-ketogenic diet (MMKD) intervention,17,17,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Suppl. Fig.4.,17 March 2024,MyleeeA,"MyleeeA,Scholastica,WikiWorks",Lefse analysis showing bacterial taxa contributing to the microbiome difference at baseline (pre) compared to endpoint (post) modified Mediterranean-ketogenic diet (MMKD),increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,1783272|1239|91061|186826|1300|1357,Complete,Svetlana up
bsdb:31477562/4/2,31477562,randomized controlled trial,31477562,10.1016/j.ebiom.2019.08.032,NA,"Nagpal R., Neth B.J., Wang S., Craft S. , Yadav H.",Modified Mediterranean-ketogenic diet modulates gut microbiome and short-chain fatty acids in association with Alzheimer's disease markers in subjects with mild cognitive impairment,EBioMedicine,2019,"Alzheimer, Dementia, Diet, High fat, Ketogenic, Microbiota, Nutrition, Short-chain fatty acids",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Pre modified Mediterranean-ketogenic diet (MMKD) in CN and MCI,Post modified Mediterranean-ketogenic diet (MMKD) in CN and MCI,All Participants including cognitively normal (CN) and those diagnosed with early mild cognitive impairment (MCI) at endpoint of the modified Mediterranean-ketogenic diet (MMKD) intervention,17,17,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Suppl. Fig.4.,28 May 2024,Scholastica,"Scholastica,WikiWorks",Lefse analysis showing bacterial taxa contributing to the microbiome difference at baseline (pre) compared to endpoint (post) modified Mediterranean-ketogenic diet (MMKD),decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|201174;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678,Complete,Svetlana up
bsdb:31481657/1/1,31481657,case-control,31481657,10.1038/s41598-019-48768-z,NA,"Newman T.M., Krishnan L.P., Lee J. , Adami G.R.",Microbiomic differences at cancer-prone oral mucosa sites with marijuana usage,Scientific reports,2019,NA,Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Cannabis use,EFO:0007585,controls (lateral border of tongue),marijuana usage group,"using marijuana on 20 or more days in the past month associated with a distinct oral microbiota at the most common sites of HNSCC, the lateral border of the tongue",19,20,1 month,16S,123,Illumina,relative abundances,LEfSe,NA,FALSE,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3,10 January 2021,Utsav Patel,"WikiWorks,Atrayees,ChiomaBlessing",Abundant taxa at the lateral border of the tongue in the marijuana usage group VS controls,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Boseaceae|g__Bosea,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Boseaceae|g__Bosea|s__Bosea vestrisii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia|s__Delftia acidovorans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Leptothrix,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica",1783272|201174|1760|2037|2049|1654|55565;3379134|1224|28211|356|2831100|85413;3379134|1224|28211|356|2831100|85413|151416;3379134|1224|28216|80840|80864;3379134|1224|28216|80840|80864|80865;3379134|1224|28216|80840|80864|80865|80866;3379134|1224|28216|80840|2975441|88;1783272|201174|1760|85006|1268;1783272|1239|186801|3082720|543314|86331;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|909932|1843489|31977|29465|39777,Complete,Atrayees
bsdb:31481657/1/2,31481657,case-control,31481657,10.1038/s41598-019-48768-z,NA,"Newman T.M., Krishnan L.P., Lee J. , Adami G.R.",Microbiomic differences at cancer-prone oral mucosa sites with marijuana usage,Scientific reports,2019,NA,Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Cannabis use,EFO:0007585,controls (lateral border of tongue),marijuana usage group,"using marijuana on 20 or more days in the past month associated with a distinct oral microbiota at the most common sites of HNSCC, the lateral border of the tongue",19,20,1 month,16S,123,Illumina,relative abundances,LEfSe,NA,FALSE,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3,10 January 2021,Utsav Patel,"WikiWorks,Atrayees,ChiomaBlessing",Abundant taxa at the lateral border of the tongue in the marijuana usage group VS controls,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella|s__Bergeyella sp.,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",3379134|976;3379134|976|117743|200644|2762318|59735;3379134|976|117743|200644|2762318|59735|1962306;3379134|976|117743|200644|49546|1016;3379134|976|117743|200644|49546;3379134|976|117743|200644;3379134|976|117743;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|171552|2974257|425941;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836,Complete,Atrayees
bsdb:31481657/2/1,31481657,case-control,31481657,10.1038/s41598-019-48768-z,NA,"Newman T.M., Krishnan L.P., Lee J. , Adami G.R.",Microbiomic differences at cancer-prone oral mucosa sites with marijuana usage,Scientific reports,2019,NA,Experiment 2,United States of America,Homo sapiens,Pharynx,UBERON:0006562,Cannabis use,EFO:0007585,controls (oral pharynx),marijuana usage group,"using marijuana on 20 or more days in the past month associated with a distinct oral microbiota at the most common sites of HNSCC, the oral pharynx.",19,20,1 month,16S,123,Illumina,relative abundances,LEfSe,NA,FALSE,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3,10 January 2021,Utsav Patel,"WikiWorks,Atrayees,ChiomaBlessing",Abundant taxa at the oral pharynx in the marijuana usage group VS controls,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales",1783272|1239|186801|3082720|543314|86331;1783272|1239|909932;1783272|1239|186801|186802|541000;1783272|1239|909932|909929|1843491;1783272|1239|909932|909929;1783272|1239|909932|909929|1843491|970;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977;1783272|1239|909932|1843489,Complete,Atrayees
bsdb:31481657/2/2,31481657,case-control,31481657,10.1038/s41598-019-48768-z,NA,"Newman T.M., Krishnan L.P., Lee J. , Adami G.R.",Microbiomic differences at cancer-prone oral mucosa sites with marijuana usage,Scientific reports,2019,NA,Experiment 2,United States of America,Homo sapiens,Pharynx,UBERON:0006562,Cannabis use,EFO:0007585,controls (oral pharynx),marijuana usage group,"using marijuana on 20 or more days in the past month associated with a distinct oral microbiota at the most common sites of HNSCC, the oral pharynx.",19,20,1 month,16S,123,Illumina,relative abundances,LEfSe,NA,FALSE,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3,10 January 2021,Utsav Patel,"WikiWorks,Atrayees,ChiomaBlessing",Abundant taxa at the oral pharynx in the marijuana usage group VS controls,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|976|117743|200644|2762318|59735;1783272|1239|91061|186826;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:31481657/3/1,31481657,case-control,31481657,10.1038/s41598-019-48768-z,NA,"Newman T.M., Krishnan L.P., Lee J. , Adami G.R.",Microbiomic differences at cancer-prone oral mucosa sites with marijuana usage,Scientific reports,2019,NA,Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Cannabis use,EFO:0007585,controls (lateral border of tongue),marijuana usage group,"using marijuana on 20 or more days in the past month associated with a distinct oral microbiota at the most common sites of HNSCC, the lateral border of the tongue",19,20,1 month,16S,123,Illumina,raw counts,DESeq2,NA,TRUE,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,table 1,10 January 2021,Utsav Patel,"WikiWorks,Atrayees,ChiomaBlessing",DESeq2 differentiation of taxa on the genus level at the lateral border of tongue in the marijuana usage group VS controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Boseaceae|g__Bosea,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Leptothrix,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",3379134|1224|28211|356|2831100|85413;3379134|1224|28216|80840|80864|80865;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|80840|2975441|88;3379134|1224|1236|72274|135621|286;1783272|201174|1760|85006|1268|32207,Complete,Atrayees
bsdb:31481657/3/2,31481657,case-control,31481657,10.1038/s41598-019-48768-z,NA,"Newman T.M., Krishnan L.P., Lee J. , Adami G.R.",Microbiomic differences at cancer-prone oral mucosa sites with marijuana usage,Scientific reports,2019,NA,Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Cannabis use,EFO:0007585,controls (lateral border of tongue),marijuana usage group,"using marijuana on 20 or more days in the past month associated with a distinct oral microbiota at the most common sites of HNSCC, the lateral border of the tongue",19,20,1 month,16S,123,Illumina,raw counts,DESeq2,NA,TRUE,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Table 1,10 January 2021,Utsav Patel,"WikiWorks,Atrayees,ChiomaBlessing",DESeq2 differentiation of taxa on the genus level at the lateral border of tongue in the marijuana usage group VS controls,decreased,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,3379134|976|117743|200644|2762318|59735,Complete,Atrayees
bsdb:31481657/4/1,31481657,case-control,31481657,10.1038/s41598-019-48768-z,NA,"Newman T.M., Krishnan L.P., Lee J. , Adami G.R.",Microbiomic differences at cancer-prone oral mucosa sites with marijuana usage,Scientific reports,2019,NA,Experiment 4,United States of America,Homo sapiens,Pharynx,UBERON:0006562,Cannabis use,EFO:0007585,controls (oral pharynx),marijuana usage group,"using marijuana on 20 or more days in the past month associated with a distinct oral microbiota at the most common sites of HNSCC, the oral pharynx.",19,20,1 month,16S,123,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Table 1,24 July 2023,Atrayees,"Atrayees,ChiomaBlessing,WikiWorks",DESeq2 differentiation of taxa on the genus level at the oral pharynx in the marijuana usage group VS controls,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171552|838;1783272|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:31481657/4/2,31481657,case-control,31481657,10.1038/s41598-019-48768-z,NA,"Newman T.M., Krishnan L.P., Lee J. , Adami G.R.",Microbiomic differences at cancer-prone oral mucosa sites with marijuana usage,Scientific reports,2019,NA,Experiment 4,United States of America,Homo sapiens,Pharynx,UBERON:0006562,Cannabis use,EFO:0007585,controls (oral pharynx),marijuana usage group,"using marijuana on 20 or more days in the past month associated with a distinct oral microbiota at the most common sites of HNSCC, the oral pharynx.",19,20,1 month,16S,123,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Table 1,24 July 2023,Atrayees,"Atrayees,ChiomaBlessing,WikiWorks",DESeq2 differentiation of taxa on the genus level at the oral pharynx in the marijuana usage group VS controls,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus",3379134|976|117743|200644|2762318|59735;1783272|1239|91061|1385|186817|400634,Complete,Atrayees
bsdb:31489128/1/1,31489128,prospective cohort,31489128,10.1080/20002297.2019.1650597,NA,"Yang Y., Cai Q., Zheng W., Steinwandel M., Blot W.J., Shu X.O. , Long J.",Oral microbiome and obesity in a large study of low-income and African-American populations,Journal of oral microbiology,2019,"16S rRNA gene sequencing; Southern Community Cohort Study; Probiotic taxa, Oral microbiome, obesity",Experiment 1,United States of America,Homo sapiens,Mouth,UBERON:0000165,Obesity,EFO:0001073,obese,non-obese,"participants who were selected for four nested case-control studies to investigate the oral microbiome and those diagnosed after mouth rinse sample colection with type 2 diabetes, lung cancer, upper aero-digestive tract cancer, and colorectal cancer",647,969,1 year,16S,4,Illumina,NA,Logistic Regression,0.05,TRUE,NA,"age,race,sex,smoking status","age,alcohol drinking,number of teeth measurement,race,sex,smoking behavior",NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table 2,10 January 2021,Victoria Goulbourne,WikiWorks,Probiotic bacterial taxa showing a significantly higher prevelance in non-obese than obese individuals,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium scardovii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium subtile,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus panis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus ultunensis",1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|216816|1679;1783272|201174|1760|85004|31953|1678|158787;1783272|201174|1760|85004|31953|1678|77635;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|2742598|1613;1783272|1239|91061|186826|33958|2742598|47493;1783272|1239|91061|186826|33958|1578|227945,Complete,NA
bsdb:31489128/2/1,31489128,prospective cohort,31489128,10.1080/20002297.2019.1650597,NA,"Yang Y., Cai Q., Zheng W., Steinwandel M., Blot W.J., Shu X.O. , Long J.",Oral microbiome and obesity in a large study of low-income and African-American populations,Journal of oral microbiology,2019,"16S rRNA gene sequencing; Southern Community Cohort Study; Probiotic taxa, Oral microbiome, obesity",Experiment 2,United States of America,Homo sapiens,Mouth,UBERON:0000165,Obesity,EFO:0001073,non-obese,obese,"participants who were selected for four nested case-control studies to investigate the oral microbiome and those diagnosed after mouth rinse sample colection with type 2 diabetes, lung cancer, upper aero-digestive tract cancer, and colorectal cancer",969,647,1 year,16S,4,Illumina,NA,Logistic Regression,0.05,TRUE,NA,"age,race,sex,smoking behavior","age,alcohol drinking,number of teeth measurement,race,sex,smoking behavior",NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table 3,10 January 2021,Victoria Goulbourne,"Atrayees,WikiWorks",Common bacterial taxa showing a significantly higher prevelance in obese than in non-obese individuals,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus",1783272|201174|1760|2037|2049|1654|29317;1783272|1239|91061|186826|186828;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563;1783272|1239|91061|186826|186828|117563|46124;1783272|1239|91061|186826|1300|1301|45634,Complete,NA
bsdb:31489128/2/2,31489128,prospective cohort,31489128,10.1080/20002297.2019.1650597,NA,"Yang Y., Cai Q., Zheng W., Steinwandel M., Blot W.J., Shu X.O. , Long J.",Oral microbiome and obesity in a large study of low-income and African-American populations,Journal of oral microbiology,2019,"16S rRNA gene sequencing; Southern Community Cohort Study; Probiotic taxa, Oral microbiome, obesity",Experiment 2,United States of America,Homo sapiens,Mouth,UBERON:0000165,Obesity,EFO:0001073,non-obese,obese,"participants who were selected for four nested case-control studies to investigate the oral microbiome and those diagnosed after mouth rinse sample colection with type 2 diabetes, lung cancer, upper aero-digestive tract cancer, and colorectal cancer",969,647,1 year,16S,4,Illumina,NA,Logistic Regression,0.05,TRUE,NA,"age,race,sex,smoking behavior","age,alcohol drinking,number of teeth measurement,race,sex,smoking behavior",NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Table 4,10 January 2021,Victoria Goulbourne,"Atrayees,WikiWorks",Rare taxa showing a significantly higher prevelance in obese or non-obese individuals,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter sp. oral taxon 512",1783272|201174|1760|85004|31953|419014;1783272|1239|909932|1843489|31977|156454;3379134|1224|1236|135625|712|416916|712149,Complete,NA
bsdb:31500892/1/1,31500892,case-control,31500892,10.1016/j.ygyno.2019.09.002,NA,"Sims T.T., Colbert L.E., Zheng J., Delgado Medrano A.Y., Hoffman K.L., Ramondetta L., Jazaeri A., Jhingran A., Schmeler K.M., Daniel C.R. , Klopp A.",Gut microbial diversity and genus-level differences identified in cervical cancer patients versus healthy controls,Gynecologic oncology,2019,"Cervical cancer, Gut microbiota, Gynecologic cancer, Microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Cervical cancer,MONDO:0002974,healthy controls,cervical cancer patient,patients with biopsy-proven carcinoma of the cervix,46,42,1 month- controls only,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 4A,10 January 2021,Cynthia Anderson,WikiWorks,The fecal microbiota of individuals with cervical cancer statistically significantly different from that of healthy individuals,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171551|836;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|1506553;3379134|1224|28216|80840|995019|40544;1783272|1239|526524|526525|2810280|1505663;1783272|1239|186801|3085636|186803|437755;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|216572|459786;1783272|1239|91061|186826|1300|1301,Complete,Fatima Zohra
bsdb:31500892/1/2,31500892,case-control,31500892,10.1016/j.ygyno.2019.09.002,NA,"Sims T.T., Colbert L.E., Zheng J., Delgado Medrano A.Y., Hoffman K.L., Ramondetta L., Jazaeri A., Jhingran A., Schmeler K.M., Daniel C.R. , Klopp A.",Gut microbial diversity and genus-level differences identified in cervical cancer patients versus healthy controls,Gynecologic oncology,2019,"Cervical cancer, Gut microbiota, Gynecologic cancer, Microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Cervical cancer,MONDO:0002974,healthy controls,cervical cancer patient,patients with biopsy-proven carcinoma of the cervix,46,42,1 month- controls only,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 4A,10 January 2021,Cynthia Anderson,"Fatima,WikiWorks",The fecal microbiota of individuals with cervical cancer statistically significantly different from that of healthy individuals,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas",3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3082768|990719;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|561;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3082720|186804|1505657;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3082720|186804|1501226;3379134|1224|1236|91347|543|620;3379134|976|200643|171549|1853231|574697,Complete,Fatima Zohra
bsdb:31500892/2/1,31500892,case-control,31500892,10.1016/j.ygyno.2019.09.002,NA,"Sims T.T., Colbert L.E., Zheng J., Delgado Medrano A.Y., Hoffman K.L., Ramondetta L., Jazaeri A., Jhingran A., Schmeler K.M., Daniel C.R. , Klopp A.",Gut microbial diversity and genus-level differences identified in cervical cancer patients versus healthy controls,Gynecologic oncology,2019,"Cervical cancer, Gut microbiota, Gynecologic cancer, Microbiome",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Cervical cancer,MONDO:0002974,healthy controls,cervical cancer patient,patients with biopsy-proven carcinoma of the cervix,46,42,1 month- controls only,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,age,NA,increased,NA,NA,NA,NA,Signature 1,Figure 4B,10 January 2021,Cynthia Anderson,WikiWorks,The fecal microbiota of individuals with cervical cancer statistically significantly different from that of healthy individuals after adjusting for age,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella",3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171551|836;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|1506553;1783272|1239|526524|526525|2810280|1505663;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|437755,Complete,Fatima Zohra
bsdb:31500892/2/2,31500892,case-control,31500892,10.1016/j.ygyno.2019.09.002,NA,"Sims T.T., Colbert L.E., Zheng J., Delgado Medrano A.Y., Hoffman K.L., Ramondetta L., Jazaeri A., Jhingran A., Schmeler K.M., Daniel C.R. , Klopp A.",Gut microbial diversity and genus-level differences identified in cervical cancer patients versus healthy controls,Gynecologic oncology,2019,"Cervical cancer, Gut microbiota, Gynecologic cancer, Microbiome",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Cervical cancer,MONDO:0002974,healthy controls,cervical cancer patient,patients with biopsy-proven carcinoma of the cervix,46,42,1 month- controls only,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,age,NA,increased,NA,NA,NA,NA,Signature 2,Figure 4B,10 January 2021,Cynthia Anderson,WikiWorks,The fecal microbiota of individuals with cervical cancer statistically significantly different from that of healthy individuals after adjusting for age,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|171550|239759,Complete,Fatima Zohra
bsdb:31500892/3/1,31500892,case-control,31500892,10.1016/j.ygyno.2019.09.002,NA,"Sims T.T., Colbert L.E., Zheng J., Delgado Medrano A.Y., Hoffman K.L., Ramondetta L., Jazaeri A., Jhingran A., Schmeler K.M., Daniel C.R. , Klopp A.",Gut microbial diversity and genus-level differences identified in cervical cancer patients versus healthy controls,Gynecologic oncology,2019,"Cervical cancer, Gut microbiota, Gynecologic cancer, Microbiome",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Cervical cancer,MONDO:0002974,healthy controls,cervical cancer patient,patients with biopsy-proven carcinoma of the cervix,46,42,1 month- controls only,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,race,NA,increased,NA,NA,NA,NA,Signature 1,Figure 4C,10 January 2021,Cynthia Anderson,WikiWorks,The fecal microbiota of individuals with cervical cancer statistically significantly different from that of healthy individuals after adjusting for race,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella",3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171551|836;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|1506553;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810280|1505663;1783272|1239|186801|3085636|186803|437755,Complete,Fatima Zohra
bsdb:31500892/3/2,31500892,case-control,31500892,10.1016/j.ygyno.2019.09.002,NA,"Sims T.T., Colbert L.E., Zheng J., Delgado Medrano A.Y., Hoffman K.L., Ramondetta L., Jazaeri A., Jhingran A., Schmeler K.M., Daniel C.R. , Klopp A.",Gut microbial diversity and genus-level differences identified in cervical cancer patients versus healthy controls,Gynecologic oncology,2019,"Cervical cancer, Gut microbiota, Gynecologic cancer, Microbiome",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Cervical cancer,MONDO:0002974,healthy controls,cervical cancer patient,patients with biopsy-proven carcinoma of the cervix,46,42,1 month- controls only,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,race,NA,increased,NA,NA,NA,NA,Signature 2,Figure 4C,10 January 2021,Cynthia Anderson,WikiWorks,The fecal microbiota of individuals with cervical cancer statistically significantly different from that of healthy individuals after adjusting for race,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",1783272|1239|186801|3082720|186804|1505657;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|207244;3379134|1224|1236|91347|543|547;3379134|976|200643|171549|171550|239759,Complete,Fatima Zohra
bsdb:31502207/1/1,31502207,case-control,31502207,10.1007/s40257-019-00471-5,https://pubmed.ncbi.nlm.nih.gov/31502207/,"Rainer B.M., Thompson K.G., Antonescu C., Florea L., Mongodin E.F., Bui J., Fischer A.H., Pasieka H.B., Garza L.A., Kang S. , Chien A.L.",Characterization and Analysis of the Skin Microbiota in Rosacea: A Case-Control Study,American journal of clinical dermatology,2020,NA,Experiment 1,United States of America,Homo sapiens,"Skin of cheek,External nose","UBERON:0008803,UBERON:0007827",Rosacea,EFO:1000760,Healthy controls,Participants with papulopustular rosacea (PPR),Participants with rosacea included individuals with diagnosed papulopustular rosacea (PPR): severity of rosacea assessed using the National Rosacea Society clinical grading system ranged from mild to moderate,19,19,2 months,16S,34,Illumina,NA,Metastats,0.05,TRUE,NA,"age,race,sex",NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Table 1,30 May 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1,WikiWorks",Differential microbial abundance between papulopustular rosacea (PPR) patients and healthy controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter ureolyticus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium kroppenstedtii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Gleimia|s__Gleimia europaea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia",3379134|976|200643|171549|171552|1283313|76122;3379134|29547|3031852|213849|72294|194|827;1783272|201174|1760|85007|1653|1716|161879;1783272|201174|1760|2037|2049|2692113|66228;3379134|976|200643|171549|171552|838|28131,Complete,Claregrieve1
bsdb:31502207/1/2,31502207,case-control,31502207,10.1007/s40257-019-00471-5,https://pubmed.ncbi.nlm.nih.gov/31502207/,"Rainer B.M., Thompson K.G., Antonescu C., Florea L., Mongodin E.F., Bui J., Fischer A.H., Pasieka H.B., Garza L.A., Kang S. , Chien A.L.",Characterization and Analysis of the Skin Microbiota in Rosacea: A Case-Control Study,American journal of clinical dermatology,2020,NA,Experiment 1,United States of America,Homo sapiens,"Skin of cheek,External nose","UBERON:0008803,UBERON:0007827",Rosacea,EFO:1000760,Healthy controls,Participants with papulopustular rosacea (PPR),Participants with rosacea included individuals with diagnosed papulopustular rosacea (PPR): severity of rosacea assessed using the National Rosacea Society clinical grading system ranged from mild to moderate,19,19,2 months,16S,34,Illumina,NA,Metastats,0.05,TRUE,NA,"age,race,sex",NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Table 1,30 May 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1,WikiWorks",Differential microbial abundance between papulopustular rosacea (PPR) patients and healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Anoxybacillus|s__Anoxybacillus kestanbolensis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae|g__Azorhizobium|s__Azorhizobium doebereinerae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium granulosum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas|s__Dysgonomonas gade,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia|s__Providencia stuartii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella|s__Shewanella algae",1783272|1239|91061|1385|3120669|150247|227476;3379134|1224|28211|356|335928|6|281091;1783272|201174|1760|85009|31957|1912216|33011;3379134|976|200643|171549|2005520|156973|156974;3379134|1224|1236|91347|1903414|586|588;3379134|1224|1236|135622|267890|22|38313,Complete,Claregrieve1
bsdb:31502207/2/1,31502207,case-control,31502207,10.1007/s40257-019-00471-5,https://pubmed.ncbi.nlm.nih.gov/31502207/,"Rainer B.M., Thompson K.G., Antonescu C., Florea L., Mongodin E.F., Bui J., Fischer A.H., Pasieka H.B., Garza L.A., Kang S. , Chien A.L.",Characterization and Analysis of the Skin Microbiota in Rosacea: A Case-Control Study,American journal of clinical dermatology,2020,NA,Experiment 2,United States of America,Homo sapiens,"External nose,Skin of cheek","UBERON:0007827,UBERON:0008803",Rosacea,EFO:1000760,Healthy controls,Participants with erythematotelangiectatic rosacea,Participants with rosacea included individuals with diagnosed erythematotelangiectatic rosacea (ETR): severity of rosacea assessed using the National Rosacea Society clinical grading system ranged from mild to moderate,19,19,2 months,16S,34,Illumina,NA,Metastats,0.05,TRUE,NA,"age,race,sex",NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Table 1,3 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1,WikiWorks",Differential microbial abundance in erythematotelangiectatic rosacea (ETR) patients compared to healthy controls,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae|g__Azorhizobium|s__Azorhizobium doebereinerae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia|s__Providencia stuartii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Roseomonadaceae|g__Roseomonas|s__Roseomonas mucosa,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella|s__Shewanella algae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",3379134|1224|28211|356|335928|6|281091;3379134|976|200643|171549|171551|836|28124;3379134|1224|1236|91347|1903414|586|588;3379134|1224|28211|3120395|3385906|125216|207340;3379134|1224|1236|135622|267890|22|38313;1783272|1239|186801|3085636|186803|2316020|33038,Complete,Claregrieve1
bsdb:31528836/1/1,31528836,randomized controlled trial,31528836,10.1093/cdn/nzz079,NA,"Dhillon J., Li Z. , Ortiz R.M.",Almond Snacking for 8 wk Increases Alpha-Diversity of the Gastrointestinal Microbiome and Decreases <i>Bacteroides fragilis</i> Abundance Compared with an Isocaloric Snack in College Freshmen,Current developments in nutrition,2019,"ANCOM, adolescence, amplicon sequence variants, cardiovascular, functional foods, gut, metabolism, minority, nutrients, nuts",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,higher fiber (almonds) - at baseline,"lower fiber (cracker), at baseline",students eating crackers,38,35,NA,16S,45,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,unchanged,NA,decreased,Signature 1,Table 1,10 January 2021,Lora Kasselman,"WikiWorks,Atrayees",ANCOM results of selected taxa prevalent in at least 25% of the samples obtained from college freshmen in the almond and cracker groups at baseline,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,3379134|976|200643|171549|815|816|817,Complete,NA
bsdb:31528836/2/1,31528836,randomized controlled trial,31528836,10.1093/cdn/nzz079,NA,"Dhillon J., Li Z. , Ortiz R.M.",Almond Snacking for 8 wk Increases Alpha-Diversity of the Gastrointestinal Microbiome and Decreases <i>Bacteroides fragilis</i> Abundance Compared with an Isocaloric Snack in College Freshmen,Current developments in nutrition,2019,"ANCOM, adolescence, amplicon sequence variants, cardiovascular, functional foods, gut, metabolism, minority, nutrients, nuts",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,higher fiber (almonds) - 8 wk after intervention,lower fiber (cracker) - 8 wk after intervention,students eating crackers,38,35,NA,16S,45,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,unchanged,NA,decreased,Signature 1,Table 1,10 January 2021,Lora Kasselman,"Lwaldron,WikiWorks,Atrayees",ANCOM results of selected taxa prevalent in at least 25% of the samples obtained from college freshmen in the almond and cracker groups 8 wk after the intervention,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Mycoplasmatota|c__Mollicutes",1783272|1239|186801|3085636|186803|28050;1783272|544448|31969,Complete,NA
bsdb:31528836/2/2,31528836,randomized controlled trial,31528836,10.1093/cdn/nzz079,NA,"Dhillon J., Li Z. , Ortiz R.M.",Almond Snacking for 8 wk Increases Alpha-Diversity of the Gastrointestinal Microbiome and Decreases <i>Bacteroides fragilis</i> Abundance Compared with an Isocaloric Snack in College Freshmen,Current developments in nutrition,2019,"ANCOM, adolescence, amplicon sequence variants, cardiovascular, functional foods, gut, metabolism, minority, nutrients, nuts",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,higher fiber (almonds) - 8 wk after intervention,lower fiber (cracker) - 8 wk after intervention,students eating crackers,38,35,NA,16S,45,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,unchanged,NA,decreased,Signature 2,Table 1,10 January 2021,Lora Kasselman,"Lwaldron,WikiWorks,Atrayees",ANCOM results of selected taxa prevalent in at least 25% of the samples obtained from college freshmen in the almond and cracker groups 8 wk after the intervention,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|1853231|574697;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|2005473,Complete,NA
bsdb:31528836/3/1,31528836,randomized controlled trial,31528836,10.1093/cdn/nzz079,NA,"Dhillon J., Li Z. , Ortiz R.M.",Almond Snacking for 8 wk Increases Alpha-Diversity of the Gastrointestinal Microbiome and Decreases <i>Bacteroides fragilis</i> Abundance Compared with an Isocaloric Snack in College Freshmen,Current developments in nutrition,2019,"ANCOM, adolescence, amplicon sequence variants, cardiovascular, functional foods, gut, metabolism, minority, nutrients, nuts",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,higher fiber (almonds),lower fiber (cracker),students eating crackers,35,38,NA,16S,45,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,10 January 2021,Lora Kasselman,WikiWorks,ANCOM results of selected taxa prevalent in at least 25% of the samples obtained from college freshmen in the almond and cracker groups at baseline and 8 wk after the intervention,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,3379134|1224|28216|80840|995019|40544,Complete,NA
bsdb:31530647/1/1,31530647,"cross-sectional observational, not case-control",31530647,10.1128/mSystems.00289-19,NA,"Tarallo S., Ferrero G., Gallo G., Francavilla A., Clerico G., Realis Luc A., Manghi P., Thomas A.M., Vineis P., Segata N., Pardini B., Naccarati A. , Cordero F.",Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples,mSystems,2019,"gut microbiome, human stool samples, microRNAs, small RNAs",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls,Colorectal cancer (CRC),Patients diagnosed with colorectal carcinoma,24,29,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental. Table S1B,12 January 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differences in fecal microbiome among healthy and carcinoma (CRC) patients,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum",3379134|976|200643|171549|815|816|329854;1783272|201174|1760|85004|31953|1678|1680;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|186802|216572|292632;1783272|201174|1760|85004|31953|1678|216816,Complete,ChiomaBlessing
bsdb:31530647/1/2,31530647,"cross-sectional observational, not case-control",31530647,10.1128/mSystems.00289-19,NA,"Tarallo S., Ferrero G., Gallo G., Francavilla A., Clerico G., Realis Luc A., Manghi P., Thomas A.M., Vineis P., Segata N., Pardini B., Naccarati A. , Cordero F.",Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples,mSystems,2019,"gut microbiome, human stool samples, microRNAs, small RNAs",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls,Colorectal cancer (CRC),Patients diagnosed with colorectal carcinoma,24,29,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental. Table S1B,12 January 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differences in fecal microbiome among healthy and carcinoma (CRC) patients,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella|s__Morganella morganii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum",3379134|1224|1236|91347|1903414|581|582;3379134|1224|1236|91347|543|570|571;3379134|1224|1236|91347|543|561|562;3379134|976|200643|171549|171552|2974265|363265;1783272|1239|186801|3085636|186803|2941495|1512,Complete,ChiomaBlessing
bsdb:31530647/2/1,31530647,"cross-sectional observational, not case-control",31530647,10.1128/mSystems.00289-19,NA,"Tarallo S., Ferrero G., Gallo G., Francavilla A., Clerico G., Realis Luc A., Manghi P., Thomas A.M., Vineis P., Segata N., Pardini B., Naccarati A. , Cordero F.",Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples,mSystems,2019,"gut microbiome, human stool samples, microRNAs, small RNAs",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls,Adenomas,Patients diagnosed with colorectal adenomas,24,27,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental. Table S1B,1 August 2022,Jeshudy,"Jeshudy,ChiomaBlessing,WikiWorks",Differences in fecal microbiome among healthy and adenoma patients,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|3085636|186803|28050|39485,Complete,ChiomaBlessing
bsdb:31530647/3/1,31530647,"cross-sectional observational, not case-control",31530647,10.1128/mSystems.00289-19,NA,"Tarallo S., Ferrero G., Gallo G., Francavilla A., Clerico G., Realis Luc A., Manghi P., Thomas A.M., Vineis P., Segata N., Pardini B., Naccarati A. , Cordero F.",Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples,mSystems,2019,"gut microbiome, human stool samples, microRNAs, small RNAs",Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Adenoma,Carcinoma (CRC),Patients diagnosed with colorectal carcinoma,27,29,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental. Table S1B,12 January 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differences in fecal microbiome among adenoma and carcinoma (CRC) patients,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,3379134|976|200643|171549|1853231|283168|28118,Complete,ChiomaBlessing
bsdb:31530647/3/2,31530647,"cross-sectional observational, not case-control",31530647,10.1128/mSystems.00289-19,NA,"Tarallo S., Ferrero G., Gallo G., Francavilla A., Clerico G., Realis Luc A., Manghi P., Thomas A.M., Vineis P., Segata N., Pardini B., Naccarati A. , Cordero F.",Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples,mSystems,2019,"gut microbiome, human stool samples, microRNAs, small RNAs",Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Adenoma,Carcinoma (CRC),Patients diagnosed with colorectal carcinoma,27,29,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental. Table S1B,12 January 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differences in fecal microbiome among adenoma and carcinoma (CRC) patients,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens",1783272|201174|1760|85004|31953|1678|1686;1783272|201174|84998|84999|84107|102106|74426,Complete,ChiomaBlessing
bsdb:31534227/1/1,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 1,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Delivery measurement,EFO:0006922,Vaginal mode of delivery during neonatal (early) transmission - Transmission,Caesarean section (CS) mode of delivery during neonatal (early) transmission - Transmission,Babies delivered by caesarean section who underwent maternal transmission of gastrointestinal bacteria,35,24,NA,WMS,NA,Illumina,relative abundances,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 3a,23 April 2025,Ameenatoloko,"Ameenatoloko,Victoria,KateRasheed","Maternal microbial strain transmission frequencies between vaginally and caesarean-delivered babies, longitudinally sampled during the neonatal (early) period.",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",1783272|1239|91061|186826|1300|1301|1304;1783272|1239|186801|3085636|186803|2316020|33039,Complete,KateRasheed
bsdb:31534227/1/2,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 1,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Delivery measurement,EFO:0006922,Vaginal mode of delivery during neonatal (early) transmission - Transmission,Caesarean section (CS) mode of delivery during neonatal (early) transmission - Transmission,Babies delivered by caesarean section who underwent maternal transmission of gastrointestinal bacteria,35,24,NA,WMS,NA,Illumina,relative abundances,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 3a,6 May 2025,Ameenatoloko,"Ameenatoloko,Victoria,KateRasheed","Maternal microbial strain transmission frequencies between vaginally and caesarean delivered babies, longitudinally sampled during the neonatal (early) period.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus",3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|815|816|371601;1783272|201174|1760|85004|31953|1678|1681;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|28026;1783272|201174|84998|84999|84107|102106|74426;3379134|1224|1236|91347|543|561|562;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|821;1783272|1239|91061|186826|1300|1301|1308,Complete,KateRasheed
bsdb:31534227/2/1,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 2,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Delivery measurement,EFO:0006922,Vaginal mode of delivery during infancy (late) transmission - Transmission,Caesarean section (CS) mode of delivery during infancy (late) transmission - Transmission,Babies delivered by caesarean section who underwent infancy (late) maternal transmission of gastrointestinal bacteria,35,24,NA,WMS,NA,Illumina,relative abundances,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 3a,24 April 2025,Ameenatoloko,"Ameenatoloko,Victoria,KateRasheed","Maternal microbial strain transmission frequencies between vaginally and caesarean-delivered babies, longitudinally sampled during the infancy (late) period.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius",1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|3085636|186803|572511|418240;3379134|1224|1236|91347|543|561|562;1783272|1239|91061|186826|1300|1301|1304,Complete,KateRasheed
bsdb:31534227/2/2,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 2,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Delivery measurement,EFO:0006922,Vaginal mode of delivery during infancy (late) transmission - Transmission,Caesarean section (CS) mode of delivery during infancy (late) transmission - Transmission,Babies delivered by caesarean section who underwent infancy (late) maternal transmission of gastrointestinal bacteria,35,24,NA,WMS,NA,Illumina,relative abundances,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 3a,25 April 2025,Ameenatoloko,"Ameenatoloko,Victoria,KateRasheed","Maternal microbial strain transmission frequencies between vaginally and caesarean-delivered babies, longitudinally sampled during the infancy (late) period.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|815|816|371601;1783272|201174|1760|85004|31953|1678|1681;1783272|201174|1760|85004|31953|1678|28026;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|186802|216572|216851|853;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|821;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|186801|3085636|186803|2316020|33039,Complete,KateRasheed
bsdb:31534227/3/1,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 3,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Delivery measurement,EFO:0006922,Babies delivered vaginally in the early neonatal period - Transmission,Babies delivered by caesarean section (CS) in the early neonatal period - Transmission,"Maternal strain transmission across 178 mother-baby pairs (vaginal: 112, C-section: 66) sampled at least once during the early neonatal period.",112,66,NA,WMS,NA,Illumina,relative abundances,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Extended Data Fig. 4, Fig. S6",25 April 2025,Ameenatoloko,"Ameenatoloko,Victoria",Transmission of maternal microbial strains during the early neonatal period.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis",1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|1300|1301|1343,Complete,KateRasheed
bsdb:31534227/3/2,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 3,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Delivery measurement,EFO:0006922,Babies delivered vaginally in the early neonatal period - Transmission,Babies delivered by caesarean section (CS) in the early neonatal period - Transmission,"Maternal strain transmission across 178 mother-baby pairs (vaginal: 112, C-section: 66) sampled at least once during the early neonatal period.",112,66,NA,WMS,NA,Illumina,relative abundances,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Extended Data Fig. 4, Fig. S6",6 May 2025,Ameenatoloko,"Ameenatoloko,Victoria",Transmission of maternal microbial strains during the early neonatal period.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus",3379134|976|200643|171549|815|816|820;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|91061|186826|1300|1301|1343;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|28026;1783272|201174|1760|85004|31953|1678|1681;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|84998|84999|84107|102106|74426;3379134|1224|1236|91347|543|561|562;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|371601;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|821,Complete,KateRasheed
bsdb:31534227/4/1,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 4,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Delivery measurement,EFO:0006922,Babies delivered vaginally,Babies delivered by caesarean section,Babies delivered by caesarean section were deprived of maternally transmitted commensal bacteria but had a substantially higher relative abundance of opportunistic pathogens commonly associated with the hospital environment.,606,596,NA,WMS,NA,Illumina,relative abundances,"Fisher's Exact Test,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 4a,25 April 2025,Ameenatoloko,Ameenatoloko,Extensive and frequent colonization of babies delivered by caesarean section with diverse opportunistic pathogens.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens",1783272|1239|91061|186826|81852|1350|1351;1783272|1239|91061|186826|81852|1350|1352;3379134|1224|1236|91347|543|547|550;3379134|1224|1236|91347|543|570|573;3379134|1224|1236|91347|543|570|571;1783272|1239|186801|186802|31979|1485|1502,Complete,KateRasheed
bsdb:31534227/5/1,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 5,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Delivery measurement,EFO:0006922,Babies delivered vaginally sampled during the neonatal period on day 4,Babies delivered by caesarean section sampled during the neonatal period on day 4,Babies delivered by caesarean section were deprived of maternally transmitted commensal bacteria but had a substantially higher relative abundance of opportunistic pathogens commonly associated with the hospital environment.,157,153,NA,WMS,NA,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),Fisher's Exact Test",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Extended Data Fig. 5a,7 May 2025,Ameenatoloko,"Ameenatoloko,KateRasheed",Frequency and abundance of opportunistic pathogens in the neonatal gut microbiota.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium",1783272|1239|186801|186802|31979|1485|1502;3379134|1224|1236|91347|543|547|550;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|91061|186826|81852|1350|1352,Complete,KateRasheed
bsdb:31534227/6/1,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 6,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Delivery measurement,EFO:0006922,Babies delivered vaginally sampled during the neonatal period on day 7,Babies delivered by caesarean section sampled during the neonatal period on day 7,Babies delivered by caesarean section were deprived of maternally transmitted commensal bacteria but had a substantially higher relative abundance of opportunistic pathogens commonly associated with the hospital environment.,280,252,NA,WMS,NA,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),Fisher's Exact Test",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Extended Data Fig. 5a,7 May 2025,Ameenatoloko,Ameenatoloko,Frequency and abundance of opportunistic pathogens in the neonatal gut microbiota.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis",3379134|1224|1236|91347|543|570|573;3379134|1224|1236|91347|543|570|571;3379134|1224|1236|91347|543|547|550;1783272|1239|186801|186802|31979|1485|1502;1783272|1239|91061|186826|81852|1350|1352;1783272|1239|91061|186826|81852|1350|1351,Complete,KateRasheed
bsdb:31534227/7/1,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 7,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Delivery measurement,EFO:0006922,Babies delivered vaginally sampled during the neonatal period on day 21,Babies delivered by caesarean section sampled during the neonatal period on day 21,Babies delivered by caesarean section were deprived of maternally transmitted commensal bacteria but had a substantially higher relative abundance of opportunistic pathogens commonly associated with the hospital environment.,147,178,NA,WMS,NA,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),Fisher's Exact Test",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Extended Data Fig. 5a,7 May 2025,Ameenatoloko,Ameenatoloko,Frequency and abundance of opportunistic pathogens in the neonatal gut microbiota.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae",1783272|1239|186801|186802|31979|1485|1502;1783272|1239|91061|186826|81852|1350|1351;3379134|1224|1236|91347|543|547|550;1783272|1239|91061|186826|81852|1350|1352;3379134|1224|1236|91347|543|570|571;3379134|1224|1236|91347|543|570|573,Complete,KateRasheed
bsdb:31534227/8/1,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 8,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Antibiotic_mother_labour_Intrapartum antibiotic prophylaxis - for vaginal delivery (day 4),No Antibiotic_mother_labour_Intrapartum antibiotic prophylaxis - for vaginal delivery (day 4),Mothers who did not receive Intrapartum antibiotic prophylaxis (IAP) during labour.,23,NA,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,antibiotic,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,10 May 2025,Ameenatoloko,Ameenatoloko,Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,1783272|201174|1760|85004|31953|1678|1685,Complete,KateRasheed
bsdb:31534227/8/2,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 8,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Antibiotic_mother_labour_Intrapartum antibiotic prophylaxis - for vaginal delivery (day 4),No Antibiotic_mother_labour_Intrapartum antibiotic prophylaxis - for vaginal delivery (day 4),Mothers who did not receive Intrapartum antibiotic prophylaxis (IAP) during labour.,23,NA,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,antibiotic,NA,NA,NA,NA,NA,NA,Signature 2,Table S5,10 May 2025,Ameenatoloko,Ameenatoloko,Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,1783272|201174|1760|85004|31953|1678|1681,Complete,KateRasheed
bsdb:31534227/9/1,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 9,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,No Abx_mother_prior_birth on day 4;[where Abx is antibiotics],Abx_mother_prior_birth on day 4; [where Abx is antibiotics],Postnatal antibiotics were administered to mothers before their baby/babies were born.,NA,NA,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,antibiotic,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,10 May 2025,Ameenatoloko,Ameenatoloko,Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,3379134|1224|1236|91347|543|561|562,Complete,KateRasheed
bsdb:31534227/10/1,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 10,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,No Breastfeeding_status on day 4,Breastfeeding_status on day 4,Babies that were breastfed during the neonatal period (≤1 month).,NA,NA,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,breast feeding,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,10 May 2025,Ameenatoloko,Ameenatoloko,Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus lugdunensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis",1783272|1239|91061|1385|90964|1279|28035;3379134|1224|1236|135625|712|724|729;1783272|1239|91061|1385|90964|1279|1282,Complete,KateRasheed
bsdb:31534227/10/2,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 10,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,No Breastfeeding_status on day 4,Breastfeeding_status on day 4,Babies that were breastfed during the neonatal period (≤1 month).,NA,NA,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,breast feeding,NA,NA,NA,NA,NA,NA,Signature 2,Table S5,10 May 2025,Ameenatoloko,Ameenatoloko,Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus",1783272|201174|1760|85004|31953|1678|1681;1783272|1239|186801|186802|31979|1485|1502;1783272|1239|91061|186826|1300|1301|1308,Complete,KateRasheed
bsdb:31534227/11/1,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 11,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Delivery measurement,EFO:0006922,Deliveries by caesarean section on day 4,Vaginal deliveries on day 4,Babies that were delivered through the vagina.,NA,NA,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,delivery procedure,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,10 May 2025,Ameenatoloko,Ameenatoloko,Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli",3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|820;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|84998|84999|84107|102106|74426;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|821;1783272|201174|1760|85004|31953|1678|1681;3379134|1224|1236|91347|543|561|562,Complete,KateRasheed
bsdb:31534227/11/2,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 11,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Delivery measurement,EFO:0006922,Deliveries by caesarean section on day 4,Vaginal deliveries on day 4,Babies that were delivered through the vagina.,NA,NA,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,delivery procedure,NA,NA,NA,NA,NA,NA,Signature 2,Table S5,10 May 2025,Ameenatoloko,Ameenatoloko,Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa",1783272|1239|186801|186802|31979|1485|1502;3379134|1224|1236|91347|543|547|550;1783272|1239|91061|186826|81852|1350|1351;3379134|1224|1236|135625|712|724|729;1783272|1239|91061|1385|90964|1279|1282;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|909932|1843489|31977|29465|29466;1783272|201174|1760|85006|1268|32207|43675,Complete,KateRasheed
bsdb:31534227/12/1,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 12,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Place of residence measurement,EFO:0009583,"The Barking, Havering and Redbridge University Hospitals NHS Trust and the University College London Hospitals NHS Foundation Trust (BHR + UCLH) on day 4",The University Hospitals Leicester NHS Trust (LEI) on day 4,Babies born in the University Hospitals Leicester NHS Trust (LEI) from May 2014 to December 2017.,NA,NA,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,10 May 2025,Ameenatoloko,Ameenatoloko,Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans",1783272|1239|91061|186826|81852|1350|1351;1783272|1239|91061|1385|539738|1378|1379,Complete,KateRasheed
bsdb:31534227/13/1,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 13,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,"No Abx_mother_labour_IAP on day 7 for vaginal delivery[where Abx is antibiotics, and IAP is Intrapartum antibiotic prophylaxis]","Abx_mother_labour_IAP on day 7 for vaginal delivery; [where Abx is antibiotics, and IAP is Intrapartum antibiotic prophylaxis]",Mothers who received Intrapartum antibiotic prophylaxis (IAP) during labour.,NA,NA,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,antibiotic,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,10 May 2025,Ameenatoloko,Ameenatoloko,Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,1783272|201174|1760|85004|31953|1678|216816,Complete,KateRasheed
bsdb:31534227/14/1,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 14,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,No Breastfeeding_status on day 7,Breastfeeding_status on day 7,Babies that were breastfed during the neonatal period (≤1 month).,NA,NA,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,breast feeding,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,10 May 2025,Ameenatoloko,Ameenatoloko,Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis",1783272|1239|91061|1385|539738|1378|1379;3379134|1224|1236|135625|712|724|729;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|91061|1385|90964|1279|1282,Complete,KateRasheed
bsdb:31534227/14/2,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 14,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,No Breastfeeding_status on day 7,Breastfeeding_status on day 7,Babies that were breastfed during the neonatal period (≤1 month).,NA,NA,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,breast feeding,NA,NA,NA,NA,NA,NA,Signature 2,Table S5,10 May 2025,Ameenatoloko,Ameenatoloko,Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus",3379134|1224|1236|91347|543|570|571;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1343;1783272|1239|91061|186826|1300|1301|1308,Complete,KateRasheed
bsdb:31534227/15/1,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 15,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Delivery measurement,EFO:0006922,Deliveries by caesarean section on day 7,Vaginal deliveries on day 7,Babies that were born vaginally.,NA,NA,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,delivery procedure,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,10 May 2025,Ameenatoloko,Ameenatoloko,Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum",1783272|201174|1760|85004|31953|1678|1685;3379134|1224|1236|91347|543|561|562;1783272|1239|91061|1385|90964|1279|1290;3379134|976|200643|171549|2005525|375288|823;1783272|201174|84998|84999|84107|102106|74426;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|815|909656|357276;1783272|201174|1760|85004|31953|1678|1681;1783272|201174|1760|85004|31953|1678|216816,Complete,KateRasheed
bsdb:31534227/15/2,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 15,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Delivery measurement,EFO:0006922,Deliveries by caesarean section on day 7,Vaginal deliveries on day 7,Babies that were born vaginally.,NA,NA,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,delivery procedure,NA,NA,NA,NA,NA,NA,Signature 2,Table S5,10 May 2025,Ameenatoloko,Ameenatoloko,Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae",1783272|1239|186801|186802|31979|1485|1502;3379134|1224|1236|91347|543|547|550;3379134|1224|1236|91347|543|570|571;3379134|1224|1236|91347|543|570|573;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|91061|186826|81852|1350|1351;3379134|1224|1236|135625|712|724|729,Complete,KateRasheed
bsdb:31534227/17/1,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 17,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,No Abx_Baby_after_discharge on day 21,Abx_Baby_after_discharge on day 21,Antibiotics were given to babies in the neonatal period after discharge.,NA,NA,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,antibiotic,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,10 May 2025,Ameenatoloko,Ameenatoloko,Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,1783272|201174|1760|85006|1268|32207|43675,Complete,KateRasheed
bsdb:31534227/18/1,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 18,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,"Abx_mother_labour_IAP on day 21 for vaginal delivery[where Abx is antibiotics, and IAP is Intrapartum antibiotic prophylaxis]","No Abx_mother_labour_IAP on day 21 for vaginal delivery[where Abx is antibiotics, and IAP is Intrapartum antibiotic prophylaxis]",Mothers who did not receive antibiotics during labour.,NA,NA,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,antibiotic,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,10 May 2025,Ameenatoloko,Ameenatoloko,Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,1783272|201174|1760|85004|31953|1678|1681,Complete,KateRasheed
bsdb:31534227/18/2,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 18,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,"Abx_mother_labour_IAP on day 21 for vaginal delivery[where Abx is antibiotics, and IAP is Intrapartum antibiotic prophylaxis]","No Abx_mother_labour_IAP on day 21 for vaginal delivery[where Abx is antibiotics, and IAP is Intrapartum antibiotic prophylaxis]",Mothers who did not receive antibiotics during labour.,NA,NA,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,antibiotic,NA,NA,NA,NA,NA,NA,Signature 2,Table S5,16 September 2025,KateRasheed,KateRasheed,Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,1783272|201174|1760|85004|31953|1678|1681,Complete,KateRasheed
bsdb:31534227/20/1,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 20,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,No Abx_mother_prior_birth on day 21,Abx_mother_prior_birth on day 21,Postnatal antibiotics were administered to mothers before their baby/babies were born.,NA,NA,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,antibiotic,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,10 May 2025,Ameenatoloko,Ameenatoloko,Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,3379134|1224|1236|91347|543|561|562,Complete,KateRasheed
bsdb:31534227/21/1,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 21,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,No Breastfeeding_status on day 21,Breastfeeding_status on day 21,Babies that were breastfed during the neonatal period (≤1 month).,NA,NA,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,breast feeding,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,10 May 2025,Ameenatoloko,Ameenatoloko,Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium avidum",3379134|1224|1236|135625|712|724|729;1783272|1239|91061|1385|90964|1279|1282;1783272|1239|91061|186826|1300|1301|1303;1783272|201174|1760|85009|31957|1912216|33010,Complete,KateRasheed
bsdb:31534227/21/2,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 21,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,No Breastfeeding_status on day 21,Breastfeeding_status on day 21,Babies that were breastfed during the neonatal period (≤1 month).,NA,NA,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,breast feeding,NA,NA,NA,NA,NA,NA,Signature 2,Table S5,10 May 2025,Ameenatoloko,Ameenatoloko,Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna",1783272|1239|91061|186826|81852|1350|1351;1783272|1239|186801|3082720|186804|1505657|261299;3379134|1224|1236|91347|543|570|571;1783272|1239|91061|186826|1300|1301|1343;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|1737404|1737405|1570339|150022|1260,Complete,KateRasheed
bsdb:31534227/22/1,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 22,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Delivery measurement,EFO:0006922,Deliveries by caesarean section on day 21,Vaginal deliveries on day 21,Babies that were born vaginally.,NA,NA,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,delivery procedure,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,10 May 2025,Ameenatoloko,Ameenatoloko,Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus",3379134|976|200643|171549|815|909656|357276;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|1681;3379134|976|200643|171549|815|816|820;1783272|201174|84998|84999|84107|102106|74426;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|909656|821,Complete,KateRasheed
bsdb:31534227/22/2,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 22,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Delivery measurement,EFO:0006922,Deliveries by caesarean section on day 21,Vaginal deliveries on day 21,Babies that were born vaginally.,NA,NA,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,delivery procedure,NA,NA,NA,NA,NA,NA,Signature 2,Table S5,10 May 2025,Ameenatoloko,Ameenatoloko,Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca",1783272|201174|1760|85004|31953|1678|1689;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|186801|186802|31979|1485|1502;1783272|1239|91061|186826|81852|1350|1352;1783272|1239|91061|186826|1300|1301|1318;3379134|1224|1236|91347|543|570|571,Complete,KateRasheed
bsdb:31534227/23/1,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 23,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Sex design,EFO:0001752,Female gender on day 21,Male gender on day 21,Male newborn baby/babies.,NA,NA,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,sex,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,10 May 2025,Ameenatoloko,Ameenatoloko,Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,1783272|1239|91061|1385|90964|1279|1290,Complete,KateRasheed
bsdb:31534227/24/1,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 24,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Place of residence measurement,EFO:0009583,"The Barking, Havering and Redbridge University Hospitals NHS Trust and the University College London Hospitals NHS Foundation Trust (BHR + UCLH) on day 21",The University Hospitals Leicester NHS Trust (LEI) on day 21,Babies born in the University Hospitals Leicester NHS Trust (LEI) from May 2014 to December 2017.,NA,NA,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,10 May 2025,Ameenatoloko,Ameenatoloko,Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula",3379134|1224|1236|91347|543|570|573;1783272|1239|909932|1843489|31977|29465|29466,Complete,KateRasheed
bsdb:31534227/25/1,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 25,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,No Breastfeeding_status at infancy,Breastfeeding_status at infancy,Babies who were breastfed during infancy (at 4 to 12 months of age).,NA,NA,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,breast feeding,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,10 May 2025,Ameenatoloko,Ameenatoloko,Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus peroris,1783272|1239|91061|186826|1300|1301|68891,Complete,KateRasheed
bsdb:31534227/25/2,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 25,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,No Breastfeeding_status at infancy,Breastfeeding_status at infancy,Babies who were breastfed during infancy (at 4 to 12 months of age).,NA,NA,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,breast feeding,NA,NA,NA,NA,NA,NA,Signature 2,Table S5,10 May 2025,Ameenatoloko,Ameenatoloko,Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum",1783272|1239|186801|3085636|186803|207244|105841;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|28116;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|3085636|186803|1649459|154046;3379134|976|200643|171549|2005525|375288|46503;1783272|1239|186801|3085636|186803|2941495|1512,Complete,KateRasheed
bsdb:31534227/26/1,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 26,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Delivery measurement,EFO:0006922,Deliveries by caesarean section at infancy,Vaginal deliveries at infancy,Babies that were born vaginally and later sampled at infancy between 4 to 12 months of their lives.,NA,NA,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,delivery procedure,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,10 May 2025,Ameenatoloko,Ameenatoloko,Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae",3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|815|816|47678,Complete,KateRasheed
bsdb:31534227/27/1,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 27,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,No Abx_mother_prior_birth for the mother,Abx_mother_prior_birth for the mother,Postnatal Antibiotics were administered to mothers before their baby/babies were born.,NA,NA,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,antibiotic,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,10 May 2025,Ameenatoloko,Ameenatoloko,Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.,increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,1783272|1239|909932|1843489|31977|29465|29466,Complete,KateRasheed
bsdb:31534227/28/1,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 28,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Place of residence measurement,EFO:0009583,"The Barking, Havering and Redbridge University Hospitals NHS Trust and the University College London Hospitals NHS Foundation Trust (BHR + UCLH)  for the mother",The University Hospitals Leicester NHS Trust (LEI) for the mother,Mothers who gave birth in the University Hospitals Leicester NHS Trust (LEI) from May 2014 to December 2017.,NA,NA,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,10 May 2025,Ameenatoloko,Ameenatoloko,Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,1783272|201174|1760|85004|31953|1678|28025,Complete,KateRasheed
bsdb:31534227/29/1,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 29,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,No Abx_mother_after_hospital on day 21,Abx_mother_after_hospital on day 21,Antibiotics were given to mothers after they left the hospital where they gave birth.,NA,NA,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,antibiotic,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,10 May 2025,Ameenatoloko,Ameenatoloko,Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,3379134|1224|1236|91347|543|570|573,Complete,KateRasheed
bsdb:31534227/30/1,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 30,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Delivery measurement,EFO:0006922,Vaginal mode of delivery during neonatal (early) transmission - No Transmission,Caesarean section (CS) mode of delivery during neonatal (early) transmission - No Transmission,Babies delivered by caesarean section who did not undergo maternal transmission of gastrointestinal bacteria,35,24,NA,WMS,NA,Illumina,relative abundances,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 3A,16 September 2025,KateRasheed,KateRasheed,"No transmission in maternal microbial strain frequencies between vaginally and caesarean delivered babies, longitudinally sampled during the neonatal (early) period.",increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,1783272|201174|1760|85004|31953|1678|216816,Complete,KateRasheed
bsdb:31534227/30/2,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 30,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Delivery measurement,EFO:0006922,Vaginal mode of delivery during neonatal (early) transmission - No Transmission,Caesarean section (CS) mode of delivery during neonatal (early) transmission - No Transmission,Babies delivered by caesarean section who did not undergo maternal transmission of gastrointestinal bacteria,35,24,NA,WMS,NA,Illumina,relative abundances,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 3A,16 September 2025,KateRasheed,KateRasheed,"No transmission in maternal microbial strain frequencies between vaginally and caesarean delivered babies, longitudinally sampled during the neonatal (early) period.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",3379134|976|200643|171549|815|909656|821;3379134|1224|1236|91347|543|561|562;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|186801|3085636|186803|2316020|33039,Complete,KateRasheed
bsdb:31534227/31/1,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 31,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Delivery measurement,EFO:0006922,Vaginal mode of delivery during infancy (late) transmission - No Transmission,Caesarean section (CS) mode of delivery during infancy (late) transmission - No Transmission,Babies delivered by caesarean section who did not undergo infancy (late) maternal transmission of gastrointestinal bacteria,35,24,NA,WMS,NA,Illumina,relative abundances,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 3A,16 September 2025,KateRasheed,KateRasheed,"No transmission in maternal microbial strain frequencies between vaginally and caesarean delivered babies, longitudinally sampled during the infancy (late) period.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum",3379134|1224|1236|91347|543|561|562;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|1760|85004|31953|1678|1681,Complete,KateRasheed
bsdb:31534227/31/2,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 31,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Delivery measurement,EFO:0006922,Vaginal mode of delivery during infancy (late) transmission - No Transmission,Caesarean section (CS) mode of delivery during infancy (late) transmission - No Transmission,Babies delivered by caesarean section who did not undergo infancy (late) maternal transmission of gastrointestinal bacteria,35,24,NA,WMS,NA,Illumina,relative abundances,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 3A,16 September 2025,KateRasheed,KateRasheed,"No transmission in maternal microbial strain frequencies between vaginally and caesarean delivered babies, longitudinally sampled during the infancy (late) period.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae",3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|371601;3379134|976|200643|171549|815|816|28116;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803|572511|418240,Complete,KateRasheed
bsdb:31534227/32/1,31534227,time series / longitudinal observational,31534227,https://doi.org/10.1038/s41586-019-1560-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC6894937/,"Shao Y., Forster S.C., Tsaliki E., Vervier K., Strang A., Simpson N., Kumar N., Stares M.D., Rodger A., Brocklehurst P., Field N. , Lawley T.D.",Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,Nature,2019,NA,Experiment 32,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Delivery measurement,EFO:0006922,Babies delivered vaginally in the early neonatal period - No Transmission,Babies delivered by caesarean section (CS) in the early neonatal period - No Transmission,"Babies without maternal strain transmission across 178 mother-baby pairs (vaginal: 112, C-section: 66) sampled at least once during the early neonatal period.",112,66,NA,WMS,NA,Illumina,relative abundances,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Extended Data Fig. 4,16 September 2025,KateRasheed,KateRasheed,"No transmission in maternal microbial strain frequencies between vaginally and caesarean delivered babies, at least once during the early neonatal period.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis",3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|815|816|820;3379134|1224|1236|91347|543|561|562;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|371601;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|1681;1783272|201174|1760|85004|31953|1678|1680;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|91061|186826|1300|1301|1343,Complete,KateRasheed
bsdb:31555603/1/1,31555603,"cross-sectional observational, not case-control",31555603,10.3389/fcimb.2019.00294,NA,"Zhou Y., Wang L., Pei F., Ji M., Zhang F., Sun Y., Zhao Q., Hong Y., Wang X., Tian J. , Wang Y.",Patients With LR-HPV Infection Have a Distinct Vaginal Microbiota in Comparison With Healthy Controls,Frontiers in cellular and infection microbiology,2019,"16S RNA sequencing, condyloma acuminatum, low-risk HPV, sexually transmitted infections, vaginal microbiome",Experiment 1,China,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,negative control,low risk HPV,LR-HPV+ according to results of screening,20,42,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,increased,NA,NA,Signature 1,Figure 4B,10 January 2021,Cynthia Anderson,"Lwaldron,WikiWorks,Merit",Comparisons of vaginal bacteria between the NC and HPV-LR groups,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Pseudomonadati|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae,k__Pseudomonadati|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales,k__Pseudomonadati|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Hydrogenophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;3379134|976|200643|171549|171550|239759;1783272|201174|1760|85004|31953|1678;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|572511;3379134|1224|28216|80840|119060;3379134|976|200643|171549|1853231|574697;1783272|1239|186801;1783272|1239|186801|186802|31979|1485;3379134|1224|28216|80840|80864;3379134|976|200643|171549|2005519|1348911;1783272|1239|186801|3085636|186803|33042;1783272|1239|909932|1843489|31977|39948;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803|1407607;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;1783272|1239|186801|186802|204475;3379134|1224|2008785|119069|206349;3379134|1224|2008785|119069;3379134|1224|2008785|119069|206349|70774;1783272|1239|186801|3085636|186803;3384189|32066|203490|203491|1129771;1783272|1239|909932|1843489|31977|906;1783272|544448|31969;1783272|544448;1783272|1239|186801|186802|541000;3379134|1224|1236|135625|712|745;3379134|1224|1236|135625|712;3379134|1224|1236|135625;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1257;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171550;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1200657;3384189|32066|203490|203491|1129771|168808;3379134|1224|28216|80840|995019|40544;3379134|1224|28216|80840|995019,Complete,Fatima
bsdb:31555603/1/2,31555603,"cross-sectional observational, not case-control",31555603,10.3389/fcimb.2019.00294,NA,"Zhou Y., Wang L., Pei F., Ji M., Zhang F., Sun Y., Zhao Q., Hong Y., Wang X., Tian J. , Wang Y.",Patients With LR-HPV Infection Have a Distinct Vaginal Microbiota in Comparison With Healthy Controls,Frontiers in cellular and infection microbiology,2019,"16S RNA sequencing, condyloma acuminatum, low-risk HPV, sexually transmitted infections, vaginal microbiome",Experiment 1,China,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,negative control,low risk HPV,LR-HPV+ according to results of screening,20,42,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,increased,NA,NA,Signature 2,Figure 4B,10 January 2021,Cynthia Anderson,"WikiWorks,Merit",Comparisons of vaginal bacteria between the NC and HPV-LR groups,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter,k__Thermoproteati|p__Nitrososphaerota|c__Nitrososphaeria|o__Nitrososphaerales|f__Nitrososphaeraceae|g__Nitrososphaera,k__Thermoproteati|p__Nitrososphaerota|c__Nitrososphaeria|o__Nitrososphaerales|f__Nitrososphaeraceae,k__Thermoproteati|p__Nitrososphaerota|c__Nitrososphaeria|o__Nitrososphaerales,k__Thermoproteati|p__Nitrososphaerota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae",3379134|1224|1236|135624;3379134|1224|1236|72274|135621|351;3379134|1224|1236;3379134|29547|3031852|213849|72293|209;3379134|29547|3031852|213849|72293;3379134|1224|1236|135614|32033|68;1783275|651137|1643678|1033996|1033997|497726;1783275|651137|1643678|1033996|1033997;1783275|651137|1643678|1033996;1783275|651137;3379134|1224|1236|72274;3379134|1224|1236|135624|83763;3379134|1224|1236|72274|135621,Complete,Fatima Zohra
bsdb:31559135/1/1,31559135,laboratory experiment,31559135,10.1002/advs.201900972,NA,"Li X., Sun H., Li B., Zhang X., Cui J., Yun J., Yang Y., Zhang L., Meng Q., Wu S., Duan J., Yang H., Wu J., Sun Z., Zou Y. , Chen R.",Probiotics Ameliorate Colon Epithelial Injury Induced by Ambient Ultrafine Particles Exposure,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2019,"Lactobacillus, air pollution, colonic epithelium, gut microbiota, ultrafine particles",Experiment 1,China,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,mice exposed to FRA,Diesel exhaust particle (DEP) exposed mice,mice exposed to Diesel exhaust particles (DEP),30,37,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2C & text,10 January 2021,Zyaijah Bailey,WikiWorks,LEfSe histogram of fecal microbiota profiling from DEPs group (fecal samples from male n = 20 and female n = 17) and FRA group (fecal samples from male n = 15 and female n = 15) following 7‐day exposure.,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239|91061;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578,Complete,NA
bsdb:31559135/1/2,31559135,laboratory experiment,31559135,10.1002/advs.201900972,NA,"Li X., Sun H., Li B., Zhang X., Cui J., Yun J., Yang Y., Zhang L., Meng Q., Wu S., Duan J., Yang H., Wu J., Sun Z., Zou Y. , Chen R.",Probiotics Ameliorate Colon Epithelial Injury Induced by Ambient Ultrafine Particles Exposure,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2019,"Lactobacillus, air pollution, colonic epithelium, gut microbiota, ultrafine particles",Experiment 1,China,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,mice exposed to FRA,Diesel exhaust particle (DEP) exposed mice,mice exposed to Diesel exhaust particles (DEP),30,37,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2C & text,10 January 2021,Zyaijah Bailey,"Aiyshaaaa,WikiWorks,Merit",LEfSe histogram of fecal microbiota profiling from DEPs group (fecal samples from male n = 20 and female n = 17) and FRA group (fecal samples from male n = 15 and female n = 15) following 7‐day exposure.,decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",1783272|1239;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|1898207;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|31979|1485|1506;3379134|976|200643|171549,Complete,NA
bsdb:31561385/1/1,31561385,case-control,31561385,https://doi.org/10.3233%2FJPD-191693,NA,"Vidal-Martinez G., Chin B., Camarillo C., Herrera G.V., Yang B., Sarosiek I. , Perez R.G.","A Pilot Microbiota Study in Parkinson's Disease Patients versus Control Subjects, and Effects of FTY720 and FTY720-Mitoxy Therapies in Parkinsonian and Multiple System Atrophy Mouse Models",Journal of Parkinson's disease,2020,"FTY720, FTY720-Mitoxy, Microbiota, Parkinson’s disease, multiple system atrophy, transgenic mouse models",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson’s disease,Patients diagnosed with Parkinson’s disease (confirmed by a neurologist) between 35 and 95 years of age.,13,9,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1 (Column A),8 March 2024,Flo,"Flo,Scholastica,WikiWorks",Relative abundance of gut microbial taxa in pilot studies of human PD.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|203557,Complete,Chloe
bsdb:31561385/2/1,31561385,case-control,31561385,https://doi.org/10.3233%2FJPD-191693,NA,"Vidal-Martinez G., Chin B., Camarillo C., Herrera G.V., Yang B., Sarosiek I. , Perez R.G.","A Pilot Microbiota Study in Parkinson's Disease Patients versus Control Subjects, and Effects of FTY720 and FTY720-Mitoxy Therapies in Parkinsonian and Multiple System Atrophy Mouse Models",Journal of Parkinson's disease,2020,"FTY720, FTY720-Mitoxy, Microbiota, Parkinson’s disease, multiple system atrophy, transgenic mouse models",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Wild Type mice,Parkinsonian mice,10-month old transgenic (Tg) parkinsonian mice that expresses A53T mutant human alpha-synuclein (a-Syn) in neurons,2,5,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1 (column B),8 March 2024,Flo,"Flo,Scholastica,WikiWorks",Relative abundance of relevant taxa in Wild Type compared to Parkinsonian mice,increased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Chloe
bsdb:31563898/1/1,31563898,case-control,31563898,10.1136/jech-2019-212474,NA,"Yang Y., Zheng W., Cai Q.Y., Shrubsole M.J., Pei Z., Brucker R., Steinwandel M.D., Bordenstein S.R., Li Z., Blot W.J., Shu X.O. , Long J.",Cigarette smoking and oral microbiota in low-income and African-American populations,Journal of epidemiology and community health,2019,"African-American, European-American, cigarette smoking, oral microbiota",Experiment 1,United States of America,Homo sapiens,Mouth,UBERON:0000165,Smoking status measurement,EFO:0006527,Never-Smokers,Current-Smokers,"Participants with a smoking history were chosen based on four nested-control cases for incident cases of upper-aerodigestive tract cancer, type 2 diabetes, lung cancer, and colorectal cancer.",547,592,1 year,16S,4,Illumina,relative abundances,Logistic Regression,0.05,FALSE,NA,"age,alcohol drinking,body mass index,oral hygiene,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 2,3,and 4",14 March 2023,Nnadichioma,"Nnadichioma,Atrayees,Aiyshaaaa,Merit,WikiWorks",Higher prevalence of probiotic bacterial taxa among current-smokers than among never-smokers and former-smokers and Individual taxa showing a differential prevalence between current-smokers and never-smokers,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus oris,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus panis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 313,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 057,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces lingnae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola",1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|47770;1783272|1239|91061|186826|33958|1578|1596;1783272|201174|84998|84999|1643824|2767353|1382;1783272|1239|91061|186826|33958|2742598|1613;1783272|1239|91061|186826|33958|2742598|1632;1783272|1239|91061|186826|33958|2742598|47493;1783272|1239|91061|186826|33958|2742598|1598;1783272|201174;1783272|201174|1760|2037|2049;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049|1654|55565;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|2037|2049|2529408|1660;1783272|201174|84998|84999|84107;1783272|201174|1760|85006|1268|32207|43675;1783272|201174|84998|84999|1643824|1380;3379134|976|200643|171549|171552|838|652722;1783272|1239|91061|186826|1300|1301|712621;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843489|31977|906|187326;1783272|201174|1760|2037|2049|1654|114702;1783272|1239|91061|186826|33958;3379134|203691|203692|136|2845253|157|158,Complete,Atrayees
bsdb:31563898/1/2,31563898,case-control,31563898,10.1136/jech-2019-212474,NA,"Yang Y., Zheng W., Cai Q.Y., Shrubsole M.J., Pei Z., Brucker R., Steinwandel M.D., Bordenstein S.R., Li Z., Blot W.J., Shu X.O. , Long J.",Cigarette smoking and oral microbiota in low-income and African-American populations,Journal of epidemiology and community health,2019,"African-American, European-American, cigarette smoking, oral microbiota",Experiment 1,United States of America,Homo sapiens,Mouth,UBERON:0000165,Smoking status measurement,EFO:0006527,Never-Smokers,Current-Smokers,"Participants with a smoking history were chosen based on four nested-control cases for incident cases of upper-aerodigestive tract cancer, type 2 diabetes, lung cancer, and colorectal cancer.",547,592,1 year,16S,4,Illumina,relative abundances,Logistic Regression,0.05,FALSE,NA,"age,alcohol drinking,body mass index,oral hygiene,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3 and 4,14 March 2023,Nnadichioma,"Nnadichioma,Aiyshaaaa,Atrayees,WikiWorks",Individual taxa showing a differential relative abundance between current-smokers and never-smokers and former-smokers and Individual taxa showing a differential prevalence between current-smokers and never-smokers,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella denitrificans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] infirmum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum umeaense,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria pharyngis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus paraphrohaemolyticus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus",3379134|1224|28216|80840|119060;3379134|1224|1236|135615|868|2717;1783272|1239|91061|186826|81852|1350;3379134|1224|28216|206351|481|32257;3379134|1224|28216|206351|481|32257|502;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481|482|1107316;3379134|1224|28216|206351|481;3379134|976|200643|171549|171552|2974257|425941;3379134|976|117743|200644|49546|1016|1019;1783272|1239|186801|3085636|186803;1783272|1239|186801|3082720|543314|56774;1783272|1239|186801|3085636|186803|1164882|617123;3379134|1224;3379134|1224|28216|206351|481|482|29434;3379134|1224|28216|206351|481|482|28449;3379134|1224|1236|135625|712;3379134|1224|1236|135625|712|416916;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712|724|735;3379134|1224|1236|135625|712|724|736;3379134|976|117743|200644|49546;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|1300|1301|45634,Complete,Atrayees
bsdb:31563898/2/1,31563898,case-control,31563898,10.1136/jech-2019-212474,NA,"Yang Y., Zheng W., Cai Q.Y., Shrubsole M.J., Pei Z., Brucker R., Steinwandel M.D., Bordenstein S.R., Li Z., Blot W.J., Shu X.O. , Long J.",Cigarette smoking and oral microbiota in low-income and African-American populations,Journal of epidemiology and community health,2019,"African-American, European-American, cigarette smoking, oral microbiota",Experiment 2,United States of America,Homo sapiens,Mouth,UBERON:0000165,Smoking status measurement,EFO:0006527,Never-Smokers,Former-Smokers,"Participants with a smoking history were chosen based on four nested-control cases for incident cases of upper-aerodigestive tract cancer, type 2 diabetes, lung cancer, and colorectal cancer.",547,477,1 year,16S,4,Illumina,relative abundances,Logistic Regression,0.05,FALSE,NA,"age,alcohol drinking,body mass index,oral hygiene,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 2,3,and 4",28 March 2023,Nnadichioma,"Nnadichioma,Aiyshaaaa,Merit,Atrayees,WikiWorks",Higher prevalence of probiotic bacterial taxa among current-smokers than among never-smokers and former-smokers and Individual taxa showing a differential relative abundance between current-smokers and never-smokers,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus oris,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus panis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 057,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces lingnae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae",1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|91061|186826|33958|1578|47770;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|91061|186826|33958|2742598|1613;1783272|1239|91061|186826|33958|2742598|1632;1783272|1239|91061|186826|33958|2742598|47493;1783272|1239|91061|186826|33958|2742598|1598;1783272|1239|91061|186826|1300|1301|712621;1783272|201174|1760|2037|2049;1783272|201174;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|43675;3379134|1224|1236|135625|712|724|735;1783272|1239|91061|186826|1300|1301|45634;1783272|201174|1760|2037|2049|1654|114702;1783272|201174|1760|85004|31953,Complete,Atrayees
bsdb:31563898/2/2,31563898,case-control,31563898,10.1136/jech-2019-212474,NA,"Yang Y., Zheng W., Cai Q.Y., Shrubsole M.J., Pei Z., Brucker R., Steinwandel M.D., Bordenstein S.R., Li Z., Blot W.J., Shu X.O. , Long J.",Cigarette smoking and oral microbiota in low-income and African-American populations,Journal of epidemiology and community health,2019,"African-American, European-American, cigarette smoking, oral microbiota",Experiment 2,United States of America,Homo sapiens,Mouth,UBERON:0000165,Smoking status measurement,EFO:0006527,Never-Smokers,Former-Smokers,"Participants with a smoking history were chosen based on four nested-control cases for incident cases of upper-aerodigestive tract cancer, type 2 diabetes, lung cancer, and colorectal cancer.",547,477,1 year,16S,4,Illumina,relative abundances,Logistic Regression,0.05,FALSE,NA,"age,alcohol drinking,body mass index,oral hygiene,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,"Table 2, 3 and 4",28 March 2023,Nnadichioma,"Nnadichioma,Aiyshaaaa,Atrayees,WikiWorks",Individual taxa showing a differential relative abundance between current-smokers and never-smokers,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella denitrificans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum umeaense,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 070,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] infirmum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria pharyngis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus paraphrohaemolyticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus",3379134|976|117743|200644|49546|1016|1019;3379134|1224|1236|135615|868|2717;1783272|1239|91061|186826|81852|1350;3379134|1224|28216|206351|481|32257|502;1783272|1239|186801|3085636|186803|1164882|617123;1783272|1239|186801|3085636|186803;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|206351|481|482|1107316;1783272|1239|91061|186826|1300|1301|671226;3379134|203691|203692|136|2845253|157|158;1783272|1239|186801|3082720|543314|56774;3379134|1224|28216|80840|119060;3379134|1224|28216|206351|481|32257;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|81850;1783272|201174|1760|2037|2049|1654|55565;1783272|201174|84998|84999|84107;1783272|201174|84998|84999|1643824|1380;1783272|201174|84998|84999|1643824|2767353|1382;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712|416916;3379134|1224;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481;3379134|1224|28216|206351|481|482|29434;3379134|1224|28216|206351|481|482|28449;3379134|1224|1236|135625|712;3379134|1224|1236|135625|712|724|736;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|1300|1301|45634,Complete,Atrayees
bsdb:31563898/3/1,31563898,case-control,31563898,10.1136/jech-2019-212474,NA,"Yang Y., Zheng W., Cai Q.Y., Shrubsole M.J., Pei Z., Brucker R., Steinwandel M.D., Bordenstein S.R., Li Z., Blot W.J., Shu X.O. , Long J.",Cigarette smoking and oral microbiota in low-income and African-American populations,Journal of epidemiology and community health,2019,"African-American, European-American, cigarette smoking, oral microbiota",Experiment 3,United States of America,Homo sapiens,Mouth,UBERON:0000165,Smoking status measurement,EFO:0006527,Former-Smokers,Current-Smokers,"Participants with a smoking history were chosen based on four nested-control cases for incident cases of upper-aerodigestive tract cancer, type 2 diabetes, lung cancer, and colorectal cancer.",477,592,1 year,16S,4,Illumina,relative abundances,Logistic Regression,0.05,FALSE,NA,"age,alcohol drinking,body mass index,oral hygiene,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 2, 3, and 4",28 March 2023,Nnadichioma,"Nnadichioma,Aiyshaaaa,Atrayees,WikiWorks",Higher prevalence of probiotic bacterial taxa among current-smokers than among never-smokers and former-smokers and Individual taxa showing a differential relative abundance between current-smokers and never-smokers,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces lingnae,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus oris,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus panis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 313,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 057,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 070,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049|1654|55565;1783272|201174|1760|2037|2049|1654|114702;1783272|201174;1783272|201174|84998|84999|1643824|1380;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|91061|186826|33958|1578|47770;1783272|1239|91061|186826|33958|1578|1596;1783272|201174|84998|84999|1643824|2767353|1382;1783272|1239|91061|186826|33958|2742598|1613;1783272|1239|91061|186826|33958|2742598|1632;1783272|1239|91061|186826|33958|2742598|47493;1783272|1239|91061|186826|33958|2742598|1598;1783272|1239|909932|1843489|31977|906|187326;3379134|976|200643|171549|171552|838|652722;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300|1301|712621;1783272|1239|91061|186826|1300|1301|671226;3379134|203691|203692|136|2845253|157|158;1783272|1239|91061|186826|33958;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85006|1268|32207;1783272|1239|909932|1843489|31977|906;1783272|1239|91061|186826|33958|1578,Complete,Atrayees
bsdb:31563898/3/2,31563898,case-control,31563898,10.1136/jech-2019-212474,NA,"Yang Y., Zheng W., Cai Q.Y., Shrubsole M.J., Pei Z., Brucker R., Steinwandel M.D., Bordenstein S.R., Li Z., Blot W.J., Shu X.O. , Long J.",Cigarette smoking and oral microbiota in low-income and African-American populations,Journal of epidemiology and community health,2019,"African-American, European-American, cigarette smoking, oral microbiota",Experiment 3,United States of America,Homo sapiens,Mouth,UBERON:0000165,Smoking status measurement,EFO:0006527,Former-Smokers,Current-Smokers,"Participants with a smoking history were chosen based on four nested-control cases for incident cases of upper-aerodigestive tract cancer, type 2 diabetes, lung cancer, and colorectal cancer.",477,592,1 year,16S,4,Illumina,relative abundances,Logistic Regression,0.05,FALSE,NA,"age,alcohol drinking,body mass index,oral hygiene,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3 and 4,28 March 2023,Nnadichioma,"Nnadichioma,Aiyshaaaa,Merit,Atrayees,WikiWorks",Individual taxa showing a differential relative abundance between current-smokers and never-smokers,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus paraphrohaemolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella denitrificans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum umeaense,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria pharyngis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria pharyngis|s__Neisseria pharyngis subsp. flava,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] infirmum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium",3379134|1224|1236|135625|712|416916;3379134|976|117743|200644|49546|1016|1019;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135625|712|724|735;3379134|1224|1236|135625|712|724|736;3379134|1224|28216|206351|481|32257|502;1783272|1239|186801|3085636|186803|1164882|617123;1783272|1239|186801|3085636|186803;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481|482|495;3379134|1224|28216|206351|481|482|1107316;3379134|1224|28216|206351|481|482|29434;3379134|1224|28216|206351|481|482|29434|47658;3379134|976|200643|171549|171552|2974257|425941;3379134|1224;1783272|1239|91061|186826|1300|1301|45634;1783272|1239|186801|3082720|543314|56774;3379134|1224|28216|206351|481;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712;3379134|976|117743|200644|49546;3379134|1224|28216|80840|119060;3379134|1224|28216|206351|481|32257;3379134|1224|1236|135615|868|2717,Complete,Atrayees
bsdb:31573753/1/1,31573753,case-control,31573753,10.1111/1471-0528.15972,NA,"Al-Memar M., Bobdiwala S., Fourie H., Mannino R., Lee Y.S., Smith A., Marchesi J.R., Timmerman D., Bourne T., Bennett P.R. , MacIntyre D.A.",The association between vaginal bacterial composition and miscarriage: a nested case-control study,BJOG : an international journal of obstetrics and gynaecology,2020,"First trimester miscarriage, second trimester miscarriage, vaginal bacteria, vaginal microbiome",Experiment 1,United Kingdom,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Spontaneous abortion,EFO:1001255,Viable control pregnancy,First or second-trimester miscarriage,NA,81,77,NA,16S,12,Illumina,NA,Chi-Square,0.05,NA,NA,"age,body mass index,gestational age",NA,NA,NA,NA,NA,increased,increased,Signature 1,Figure 2A,14 October 2021,Titas,"Titas,WikiWorks",NA,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,1783272|1239|91061|186826|33958|1578|1591,Complete,Fatima
bsdb:31573753/2/1,31573753,case-control,31573753,10.1111/1471-0528.15972,NA,"Al-Memar M., Bobdiwala S., Fourie H., Mannino R., Lee Y.S., Smith A., Marchesi J.R., Timmerman D., Bourne T., Bennett P.R. , MacIntyre D.A.",The association between vaginal bacterial composition and miscarriage: a nested case-control study,BJOG : an international journal of obstetrics and gynaecology,2020,"First trimester miscarriage, second trimester miscarriage, vaginal bacteria, vaginal microbiome",Experiment 2,United Kingdom,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Spontaneous abortion,EFO:1001255,Viable control pregnancy,First trimester miscarriage,NA,81,64,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,2D,14 October 2021,Titas,"Titas,WikiWorks",NA,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,1783272|1239|91061|186826|33958|1578|1591,Complete,Fatima
bsdb:31573753/2/2,31573753,case-control,31573753,10.1111/1471-0528.15972,NA,"Al-Memar M., Bobdiwala S., Fourie H., Mannino R., Lee Y.S., Smith A., Marchesi J.R., Timmerman D., Bourne T., Bennett P.R. , MacIntyre D.A.",The association between vaginal bacterial composition and miscarriage: a nested case-control study,BJOG : an international journal of obstetrics and gynaecology,2020,"First trimester miscarriage, second trimester miscarriage, vaginal bacteria, vaginal microbiome",Experiment 2,United Kingdom,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Spontaneous abortion,EFO:1001255,Viable control pregnancy,First trimester miscarriage,NA,81,64,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2D + interpretation,14 October 2021,Titas,"Titas,WikiWorks",Samples deplete of Lactobacillus spp. display increased richness and diversity and colonization by potential pathogens.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",3379134|976|200643|171549|171552|838|59823;1783272|1239|91061|186826|1300|1301;1783272|1239|1737404|1737405|1570339|162289;1783272|544448|2790996|2790998|2129;1783272|1239|909932|1843489|31977|39948,Complete,Fatima
bsdb:31573753/3/1,31573753,case-control,31573753,10.1111/1471-0528.15972,NA,"Al-Memar M., Bobdiwala S., Fourie H., Mannino R., Lee Y.S., Smith A., Marchesi J.R., Timmerman D., Bourne T., Bennett P.R. , MacIntyre D.A.",The association between vaginal bacterial composition and miscarriage: a nested case-control study,BJOG : an international journal of obstetrics and gynaecology,2020,"First trimester miscarriage, second trimester miscarriage, vaginal bacteria, vaginal microbiome",Experiment 3,United Kingdom,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Spontaneous abortion,EFO:1001255,missed miscarriage,complete/incomplete miscarriage,"A missed miscarriage is when a baby has died in the womb, but the mother hasn't had any symptoms, such as bleeding or pain.
A complete miscarriage has taken place when all the pregnancy tissue has left your uterus.",61,13,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,14 October 2021,Titas,"Titas,Fatima,WikiWorks",Vaginal microbiota composition on the basis of incomplete and/or complete miscarriages,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,1783272|1239|91061|186826|33958|1578|1591,Complete,Fatima
bsdb:31575935/1/1,31575935,"cross-sectional observational, not case-control",31575935,10.1038/s41598-019-50410-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6773718/,"Ceccarani C., Foschi C., Parolin C., D'Antuono A., Gaspari V., Consolandi C., Laghi L., Camboni T., Vitali B., Severgnini M. , Marangoni A.",Diversity of vaginal microbiome and metabolome during genital infections,Scientific reports,2019,NA,Experiment 1,Italy,Homo sapiens,Vagina,UBERON:0000996,Chlamydia trachomatis infectious disease,EFO:0007205,Healthy Controls,Chlamydia trachomatis,‘Chlamydia’ (CT) (detection of C. trachomatis DNA by Versant CT/GC DNA 1.0 Assay),21,20,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table 2,9 March 2023,Danyab56,"Danyab56,Aiyshaaaa,Claregrieve1,WikiWorks",Differential microbial abundance between controls and chlamydia subjects,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|1239|91061|186826|186827;1783272|1239|91061|186826|186827|1375;1783272|201174|1760|85004|31953|419014;1783272|201174|84998|84999|1643824|1380;1783272|201174|1760|85004|31953;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107;1783272|1239|909932|1843489|31977|39948;3379134|1224|1236|91347|543|561;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803|841;3384189|32066|203490|203491|1129771|168808;1783272|1239|91061|186826|1300|1301;1783272|544448|2790996|2790998|2129;1783272|1239|909932|1843489|31977;1783272|201174|84998|84999|84107;1783272|1239|186801|3085636|186803;1783272|201174|1760|85004|31953|1678,Complete,Claregrieve1
bsdb:31575935/2/1,31575935,"cross-sectional observational, not case-control",31575935,10.1038/s41598-019-50410-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6773718/,"Ceccarani C., Foschi C., Parolin C., D'Antuono A., Gaspari V., Consolandi C., Laghi L., Camboni T., Vitali B., Severgnini M. , Marangoni A.",Diversity of vaginal microbiome and metabolome during genital infections,Scientific reports,2019,NA,Experiment 2,Italy,Homo sapiens,Vagina,UBERON:0000996,Vulvovaginal candidiasis,EFO:0007543,Healthy Controls,Vulvovaginal candidiasis,vulvovaginal candidiasis (VVC),21,18,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table 2,9 March 2023,Danyab56,"Danyab56,Aiyshaaaa,Claregrieve1,WikiWorks",Differential microbial abundance between controls and vulvovaginal candidiasis subjects,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578,Complete,Claregrieve1
bsdb:31575935/2/2,31575935,"cross-sectional observational, not case-control",31575935,10.1038/s41598-019-50410-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6773718/,"Ceccarani C., Foschi C., Parolin C., D'Antuono A., Gaspari V., Consolandi C., Laghi L., Camboni T., Vitali B., Severgnini M. , Marangoni A.",Diversity of vaginal microbiome and metabolome during genital infections,Scientific reports,2019,NA,Experiment 2,Italy,Homo sapiens,Vagina,UBERON:0000996,Vulvovaginal candidiasis,EFO:0007543,Healthy Controls,Vulvovaginal candidiasis,vulvovaginal candidiasis (VVC),21,18,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Table 2,9 March 2023,Danyab56,"Danyab56,Aiyshaaaa,Claregrieve1,WikiWorks",Differential microbial abundance between controls and vulvovaginal candidiasis subjects,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",1783272|201174|1760|2037|2049;1783272|201174;1783272|201174|1760|85004|31953|419014;1783272|201174|84998|84999|1643824|1380;3379134|976|200643;1783272|201174|1760|85004|31953;1783272|1239|186801|3085636|186803|572511;1783272|201174|84998|84999|84107;1783272|1239|909932|1843489|31977|39948;3379134|1224|1236|91347|543|561;1783272|1239|186801|186802|216572|216851;1783272|1239|1737404|1737405|1570339|150022;1783272|201174|1760|85004|31953|2701;1783272|1239|186801|3085636|186803;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|186802|216572;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|186801|3085636|186803|841;1783272|1239|91061|186826|1300|1301;1783272|1239|1737404|1737405|1737406;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977;3379134|1224|1236|135614|32033|338;1783272|201174|84998|84999|84107,Complete,Claregrieve1
bsdb:31575935/3/1,31575935,"cross-sectional observational, not case-control",31575935,10.1038/s41598-019-50410-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6773718/,"Ceccarani C., Foschi C., Parolin C., D'Antuono A., Gaspari V., Consolandi C., Laghi L., Camboni T., Vitali B., Severgnini M. , Marangoni A.",Diversity of vaginal microbiome and metabolome during genital infections,Scientific reports,2019,NA,Experiment 3,Italy,Homo sapiens,Vagina,UBERON:0000996,Bacterial vaginosis,EFO:0003932,Healthy Controls,bacterial vaginosis,bacterial vaginosis (BV),21,20,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,unchanged,Signature 1,Table 2,9 March 2023,Danyab56,"Danyab56,Aiyshaaaa,Claregrieve1,WikiWorks",Differential microbial abundance between controls and bacterial vaginosis subjects,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578,Complete,Claregrieve1
bsdb:31575935/3/2,31575935,"cross-sectional observational, not case-control",31575935,10.1038/s41598-019-50410-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6773718/,"Ceccarani C., Foschi C., Parolin C., D'Antuono A., Gaspari V., Consolandi C., Laghi L., Camboni T., Vitali B., Severgnini M. , Marangoni A.",Diversity of vaginal microbiome and metabolome during genital infections,Scientific reports,2019,NA,Experiment 3,Italy,Homo sapiens,Vagina,UBERON:0000996,Bacterial vaginosis,EFO:0003932,Healthy Controls,bacterial vaginosis,bacterial vaginosis (BV),21,20,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,unchanged,Signature 2,Table 2,9 March 2023,Danyab56,"Danyab56,Aiyshaaaa,Claregrieve1,WikiWorks",Differential microbial abundance between controls and bacterial vaginosis subjects,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Caryophyllales|f__Cactaceae|s__Cactoideae|g__Rebutia|s__Rebutia arenacea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Metazoa|p__Platyhelminthes|c__Rhabditophora|o__Rhabdocoela|f__Typhloplanidae,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",1783272|201174|1760|2037|2049;1783272|1239|91061|186826|186827;1783272|1239|91061|186826|186827|1375;1783272|201174|84998|84999|1643824|1380;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107;1783272|1239|909932|1843489|31977|39948;1783272|201174|1760|85004|31953|2701;1783272|1239|91061|1385|539738|1378;1783272|1239|186801|3085636|186803;3384189|32066|203490|203491|1129771;1783272|1239|909932|1843489|31977|906;1783272|201174|1760|2037|2049|2050;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;33090|35493|3398|3524|3593|186265|432459|1001126;1783272|1239|186801|3085636|186803|841;3384189|32066|203490|203491|1129771|168808;1783272|1239|1737404|1737405|1737406;33208|6157|147100|27901|27902;1783272|544448|2790996|2790998|2129;1783272|1239|909932|1843489|31977;1783272|201174|84998|84999|84107,Complete,Claregrieve1
bsdb:31583533/1/1,31583533,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E., Kamilari E., Savkov D., Sergeev A., Zakharova I., Vogazianos P., Tomazou M., Antoniades A. , Shammas C.",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,"Antibiotics, Azithromycin, Lactulose, Microbiome, Prebiotics",Experiment 1,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,azithromycin-lactulose treated (day 0),azithromycin-lactulose treated (day 18),"administered a single daily dosage of 10 mg/kg body weight azithromycin in addition with 20 mg/kg body weight lactulose per day, as powder for oral suspension.",42,42,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,2 December 2021,Mmarin,"Mmarin,WikiWorks","AZ azithromycin. A and L represent higher mean relative abundance for the azithromycin only and azitrhomycin + lactulose groups, respectively Arrows point up or down indicate an increase or increase compared to the relative abundance at day 0, respectively",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|1224|1236|91347|543|547;3379134|976|200643|171549|171552|838,Complete,Folakunmi
bsdb:31583533/1/2,31583533,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E., Kamilari E., Savkov D., Sergeev A., Zakharova I., Vogazianos P., Tomazou M., Antoniades A. , Shammas C.",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,"Antibiotics, Azithromycin, Lactulose, Microbiome, Prebiotics",Experiment 1,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,azithromycin-lactulose treated (day 0),azithromycin-lactulose treated (day 18),"administered a single daily dosage of 10 mg/kg body weight azithromycin in addition with 20 mg/kg body weight lactulose per day, as powder for oral suspension.",42,42,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,2 December 2021,Mmarin,"Mmarin,WikiWorks","AZ azithromycin. A and L represent higher mean relative abundance for the azithromycin only and azitrhomycin + lactulose groups, respectively Arrows point up or down indicate an increase or increase compared to the relative abundance at day 0, respectively",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239|186801|3085636|186803|207244;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263,Complete,Folakunmi
bsdb:31583533/2/1,31583533,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E., Kamilari E., Savkov D., Sergeev A., Zakharova I., Vogazianos P., Tomazou M., Antoniades A. , Shammas C.",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,"Antibiotics, Azithromycin, Lactulose, Microbiome, Prebiotics",Experiment 2,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,azithromycin treated (day 0),azithromycin treated (day 18),"administered 10 mg/kg body weight per day of azithromycin, as powder for oral suspension.",42,42,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,3 December 2021,Mmarin,"Mmarin,WikiWorks","Arrows point up or down indicate an increase or increase compared to the relative abundance at day 0, respectively",decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,3379134|1224|1236|91347|543|547,Complete,Folakunmi
bsdb:31583533/2/2,31583533,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E., Kamilari E., Savkov D., Sergeev A., Zakharova I., Vogazianos P., Tomazou M., Antoniades A. , Shammas C.",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,"Antibiotics, Azithromycin, Lactulose, Microbiome, Prebiotics",Experiment 2,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,azithromycin treated (day 0),azithromycin treated (day 18),"administered 10 mg/kg body weight per day of azithromycin, as powder for oral suspension.",42,42,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,3 December 2021,Mmarin,"Mmarin,WikiWorks","Arrows point up or down indicate an increase or increase compared to the relative abundance at day 0, respectively",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira",1783272|201174|84998|1643822|1643826|447020;1783272|1239|186801|3085636|186803|28050,Complete,Folakunmi
bsdb:31583533/3/1,31583533,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E., Kamilari E., Savkov D., Sergeev A., Zakharova I., Vogazianos P., Tomazou M., Antoniades A. , Shammas C.",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,"Antibiotics, Azithromycin, Lactulose, Microbiome, Prebiotics",Experiment 3,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,azithromycin treated (day 0),azithromycin treated (day 60),"administered 10 mg/kg body weight per day of azithromycin, as powder for oral suspension.",42,42,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,3 December 2021,Mmarin,"Mmarin,WikiWorks","Arrows point up or down indicate an increase or increase compared to the relative abundance at day 0, respectively",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|1224|1236|91347|543|547;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|171552|838;3379134|1224|28216|80840|995019|40544,Complete,Folakunmi
bsdb:31583533/3/2,31583533,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E., Kamilari E., Savkov D., Sergeev A., Zakharova I., Vogazianos P., Tomazou M., Antoniades A. , Shammas C.",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,"Antibiotics, Azithromycin, Lactulose, Microbiome, Prebiotics",Experiment 3,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,azithromycin treated (day 0),azithromycin treated (day 60),"administered 10 mg/kg body weight per day of azithromycin, as powder for oral suspension.",42,42,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,3 December 2021,Mmarin,"Mmarin,WikiWorks","Arrows point up or down indicate an increase or increase compared to the relative abundance at day 0, respectively",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|84998|1643822|1643826|447020;1783272|1239|186801|3082720|3118656|114627;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:31583533/4/1,31583533,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E., Kamilari E., Savkov D., Sergeev A., Zakharova I., Vogazianos P., Tomazou M., Antoniades A. , Shammas C.",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,"Antibiotics, Azithromycin, Lactulose, Microbiome, Prebiotics",Experiment 4,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,azithromycin treated (0-18),azithromycin-lactulose treated (0-18),"administered a single daily dosage of 10 mg/kg body weight azithromycin in addition with 20 mg/kg body weight lactulose per day, as powder for oral suspension.",42,42,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 1,Table 1,3 December 2021,Mmarin,"Mmarin,Folakunmi,WikiWorks","AZ azithromycin. A and L represent higher mean relative abundance for the azithromycin only and azitrhomycin + lactulose groups, respectively Arrows point up or down indicate an increase or increase compared to the relative abundance at day 0, respectively

(day 18)",increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,1783272|1239|186801|3085636|186803|207244,Complete,Folakunmi
bsdb:31583533/4/2,31583533,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E., Kamilari E., Savkov D., Sergeev A., Zakharova I., Vogazianos P., Tomazou M., Antoniades A. , Shammas C.",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,"Antibiotics, Azithromycin, Lactulose, Microbiome, Prebiotics",Experiment 4,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,azithromycin treated (0-18),azithromycin-lactulose treated (0-18),"administered a single daily dosage of 10 mg/kg body weight azithromycin in addition with 20 mg/kg body weight lactulose per day, as powder for oral suspension.",42,42,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 2,Table 1,3 December 2021,Mmarin,"Mmarin,Folakunmi,WikiWorks","AZ azithromycin. A and L represent higher mean relative abundance for the azithromycin only and azitrhomycin + lactulose groups, respectively Arrows point up or down indicate an increase or increase compared to the relative abundance at day 0, respectively

(day 60)",increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:31583533/5/1,31583533,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E., Kamilari E., Savkov D., Sergeev A., Zakharova I., Vogazianos P., Tomazou M., Antoniades A. , Shammas C.",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,"Antibiotics, Azithromycin, Lactulose, Microbiome, Prebiotics",Experiment 5,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,azithromycin treated (0-60),azithromycin-lactulose treated (0-60),"patients administered a single daily dosage of 10 mg/kg body weight azithromycin in addition with 20 mg/kg body weight lactulose per day, as powder for oral suspension.",42,42,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 1,Table 1,20 February 2024,Folakunmi,"Folakunmi,WikiWorks",Significant differences in relative abundance between groups and time points,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,3379134|976|200643|171549|2005520|156973,Complete,Folakunmi
bsdb:31583533/5/2,31583533,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E., Kamilari E., Savkov D., Sergeev A., Zakharova I., Vogazianos P., Tomazou M., Antoniades A. , Shammas C.",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,"Antibiotics, Azithromycin, Lactulose, Microbiome, Prebiotics",Experiment 5,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,azithromycin treated (0-60),azithromycin-lactulose treated (0-60),"patients administered a single daily dosage of 10 mg/kg body weight azithromycin in addition with 20 mg/kg body weight lactulose per day, as powder for oral suspension.",42,42,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 2,Table 1,20 February 2024,Folakunmi,"Folakunmi,WikiWorks",Significant differences in relative abundance between groups and time points,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|186801|3082720|3118656|114627;1783272|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:31583533/6/1,31583533,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E., Kamilari E., Savkov D., Sergeev A., Zakharova I., Vogazianos P., Tomazou M., Antoniades A. , Shammas C.",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,"Antibiotics, Azithromycin, Lactulose, Microbiome, Prebiotics",Experiment 6,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,azithromycin treated at day 18,azithromycin-lactulose at day 18,"patients administered a single daily dosage of 10 mg/kg body weight azithromycin in addition with 20 mg/kg body weight lactulose per day, as powder for oral suspension.",42,42,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 1,Table 1,20 February 2024,Folakunmi,"Folakunmi,WikiWorks",Significant differences in relative abundance between groups at day 18 time point,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera",1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|1853231|574697;1783272|1239|526524|526525|2810280|100883;1783272|1239|526524|526525|128827|1647;1783272|1239|909932|1843489|31977|906,Complete,Folakunmi
bsdb:31583533/7/1,31583533,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E., Kamilari E., Savkov D., Sergeev A., Zakharova I., Vogazianos P., Tomazou M., Antoniades A. , Shammas C.",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,"Antibiotics, Azithromycin, Lactulose, Microbiome, Prebiotics",Experiment 7,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,azithromycin treated at day 60,azithromycin-lactulose at day 60,"patients administered a single daily dosage of 10 mg/kg body weight azithromycin in addition with 20 mg/kg body weight lactulose per day, as powder for oral suspension.",42,42,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 1,Table 1,20 February 2024,Folakunmi,"Folakunmi,WikiWorks",Significant differences in relative abundance between groups at day 20 time point,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,3379134|976|200643|171549|2005520|156973,Complete,Folakunmi
bsdb:31583533/7/2,31583533,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E., Kamilari E., Savkov D., Sergeev A., Zakharova I., Vogazianos P., Tomazou M., Antoniades A. , Shammas C.",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,"Antibiotics, Azithromycin, Lactulose, Microbiome, Prebiotics",Experiment 7,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,azithromycin treated at day 60,azithromycin-lactulose at day 60,"patients administered a single daily dosage of 10 mg/kg body weight azithromycin in addition with 20 mg/kg body weight lactulose per day, as powder for oral suspension.",42,42,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 2,Table 1,20 February 2024,Folakunmi,"Folakunmi,WikiWorks",Significant differences in relative abundance between groups at day 20 time point,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|186801|3082720|3118656|114627;1783272|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:31583533/8/NA,31583533,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E., Kamilari E., Savkov D., Sergeev A., Zakharova I., Vogazianos P., Tomazou M., Antoniades A. , Shammas C.",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,"Antibiotics, Azithromycin, Lactulose, Microbiome, Prebiotics",Experiment 8,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,azithromycin-lactulose treated (day 0),azithromycin-lactulose treated (day 60),"administered a single daily dosage of 10 mg/kg body weight azithromycin in addition with 20 mg/kg body weight lactulose per day, as powder for oral suspension.",42,42,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:31594229/1/1,31594229,case-control,31594229,10.3233/JAD-190587,NA,"Liu X.X., Jiao B., Liao X.X., Guo L.N., Yuan Z.H., Wang X., Xiao X.W., Zhang X.Y., Tang B.S. , Shen L.",Analysis of Salivary Microbiome in Patients with Alzheimer's Disease,Journal of Alzheimer's disease : JAD,2019,"16S rRNA, APOE, Alzheimer’s disease, oral microbiome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,Healthy controls,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,39,39,1 month,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 2,1 December 2024,AaishahM,"AaishahM,WikiWorks",Relative abundance of bacterial phyla,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,3379134|1224|1236|2887326|468|475,Complete,NA
bsdb:31594229/2/1,31594229,case-control,31594229,10.3233/JAD-190587,NA,"Liu X.X., Jiao B., Liao X.X., Guo L.N., Yuan Z.H., Wang X., Xiao X.W., Zhang X.Y., Tang B.S. , Shen L.",Analysis of Salivary Microbiome in Patients with Alzheimer's Disease,Journal of Alzheimer's disease : JAD,2019,"16S rRNA, APOE, Alzheimer’s disease, oral microbiome",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,APOE ε4(-),APOE ε4(+),Patients who are APOE ε4 positive,16,23,1 month,16S,34,Illumina,relative abundances,Metastats,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 3,2 December 2024,AaishahM,"AaishahM,WikiWorks",Metastats analysis of taxa in AD patients with different APOE phenotype,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus",1783272|201174|1760|2037|2049;1783272|201174|1760|2037|2049|1654;3379134|1224|1236|135625|712|713,Complete,NA
bsdb:31594229/3/1,31594229,case-control,31594229,10.3233/JAD-190587,NA,"Liu X.X., Jiao B., Liao X.X., Guo L.N., Yuan Z.H., Wang X., Xiao X.W., Zhang X.Y., Tang B.S. , Shen L.",Analysis of Salivary Microbiome in Patients with Alzheimer's Disease,Journal of Alzheimer's disease : JAD,2019,"16S rRNA, APOE, Alzheimer’s disease, oral microbiome",Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,Healthy controls,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,39,39,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 4A + Figure 4B,2 December 2024,AaishahM,"AaishahM,WikiWorks",LEfSe results on saliva microbiome,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Sphaerochaetaceae|g__Sphaerochaeta,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae",1783272|1239|91061|1385|539738|1378;3379134|1224|28216|206351|481|32257;3384189|32066|203490|203491|1129771|32067;1783272|1239|186801|3082720|543314|86331;3379134|1224|1236|2887326|468|475;3379134|203691|203692|136|2791015|399320;3384189|32066|203490|203491|1129771;1783272|1239|186801|186802|186806,Complete,NA
bsdb:31594229/3/2,31594229,case-control,31594229,10.3233/JAD-190587,NA,"Liu X.X., Jiao B., Liao X.X., Guo L.N., Yuan Z.H., Wang X., Xiao X.W., Zhang X.Y., Tang B.S. , Shen L.",Analysis of Salivary Microbiome in Patients with Alzheimer's Disease,Journal of Alzheimer's disease : JAD,2019,"16S rRNA, APOE, Alzheimer’s disease, oral microbiome",Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,Healthy controls,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,39,39,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 4A + Figure 4B,2 December 2024,AaishahM,"AaishahM,WikiWorks",LEfSe results on saliva microbiome,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae",1783272|201174|1760|85006|1268|32207;1783272|201174;1783272|201174|1760|2037;1783272|201174|1760|85006|1268,Complete,NA
bsdb:31594229/4/1,31594229,case-control,31594229,10.3233/JAD-190587,NA,"Liu X.X., Jiao B., Liao X.X., Guo L.N., Yuan Z.H., Wang X., Xiao X.W., Zhang X.Y., Tang B.S. , Shen L.",Analysis of Salivary Microbiome in Patients with Alzheimer's Disease,Journal of Alzheimer's disease : JAD,2019,"16S rRNA, APOE, Alzheimer’s disease, oral microbiome",Experiment 4,China,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,APOE ε4(-),APOE ε4(+),Patients who are APOE ε4 positive,16,23,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 4C + Figure 4D,2 December 2024,AaishahM,"AaishahM,WikiWorks",LEfSe results on saliva microbiome,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfomicrobiaceae|g__Desulfomicrobium",1783272|1239|91061|186826|186827|46123;1783272|1239|91061|186826|186827;3379134|200940|3031449|213115|213116|898,Complete,NA
bsdb:31594229/4/2,31594229,case-control,31594229,10.3233/JAD-190587,NA,"Liu X.X., Jiao B., Liao X.X., Guo L.N., Yuan Z.H., Wang X., Xiao X.W., Zhang X.Y., Tang B.S. , Shen L.",Analysis of Salivary Microbiome in Patients with Alzheimer's Disease,Journal of Alzheimer's disease : JAD,2019,"16S rRNA, APOE, Alzheimer’s disease, oral microbiome",Experiment 4,China,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,APOE ε4(-),APOE ε4(+),Patients who are APOE ε4 positive,16,23,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 4C,2 December 2024,AaishahM,"AaishahM,WikiWorks",LEfSe results on saliva microbiome,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,3379134|1224|1236|135625|712|713,Complete,NA
bsdb:31595156/1/1,31595156,case-control,31595156,10.7150/ijbs.35980,NA,"Liu F., Li J., Guan Y., Lou Y., Chen H., Xu M., Deng D., Chen J., Ni B., Zhao L., Li H., Sang H. , Cai X.",Dysbiosis of the Gut Microbiome is associated with Tumor Biomarkers in Lung Cancer,International journal of biological sciences,2019,"16SrRNAsequencing, Carcinoembryonic antigen, Cytokeratin 19 fragment, Fecal, Gut microbiome, Lung cancer, Neuron specific enolase",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Lung cancer,MONDO:0008903,healthy control,lung cancer group,newly diagnosed lung cancer patients by histopathology and computed tomography,16,30,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,Figure 3B,10 January 2021,Fatima Zohra,WikiWorks,Comparison of relative abundant microbiome at family level between cancer groups and healthy controls,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,1783272|1239|186801|3085636|186803,Complete,Claregrieve1
bsdb:31595156/2/1,31595156,case-control,31595156,10.7150/ijbs.35980,NA,"Liu F., Li J., Guan Y., Lou Y., Chen H., Xu M., Deng D., Chen J., Ni B., Zhao L., Li H., Sang H. , Cai X.",Dysbiosis of the Gut Microbiome is associated with Tumor Biomarkers in Lung Cancer,International journal of biological sciences,2019,"16SrRNAsequencing, Carcinoembryonic antigen, Cytokeratin 19 fragment, Fecal, Gut microbiome, Lung cancer, Neuron specific enolase",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Lung cancer,MONDO:0008903,controls + other lung cancer groups,CEA group,newly diagnosed lung cancer patients who are CEA-positive,35,11,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,Figure 3B,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Comparison of relatively abundant microbiota between CEA group and other study groups,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",3379134|976|200643|171549|815;1783272|1239|91061|186826|1300,Complete,Claregrieve1
bsdb:31595156/3/1,31595156,case-control,31595156,10.7150/ijbs.35980,NA,"Liu F., Li J., Guan Y., Lou Y., Chen H., Xu M., Deng D., Chen J., Ni B., Zhao L., Li H., Sang H. , Cai X.",Dysbiosis of the Gut Microbiome is associated with Tumor Biomarkers in Lung Cancer,International journal of biological sciences,2019,"16SrRNAsequencing, Carcinoembryonic antigen, Cytokeratin 19 fragment, Fecal, Gut microbiome, Lung cancer, Neuron specific enolase",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Lung cancer,MONDO:0008903,controls + other lung cancer groups,NSE group,newly diagnosed lung cancer patients who are NSE positive,37,9,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,Figure 3B,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Differentially abundant microbiota between NSE group and the other study groups,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",3379134|1224|1236|91347|543;3384189|32066|203490|203491|203492;3379134|74201|203494|48461|203557,Complete,Claregrieve1
bsdb:31595156/4/1,31595156,case-control,31595156,10.7150/ijbs.35980,NA,"Liu F., Li J., Guan Y., Lou Y., Chen H., Xu M., Deng D., Chen J., Ni B., Zhao L., Li H., Sang H. , Cai X.",Dysbiosis of the Gut Microbiome is associated with Tumor Biomarkers in Lung Cancer,International journal of biological sciences,2019,"16SrRNAsequencing, Carcinoembryonic antigen, Cytokeratin 19 fragment, Fecal, Gut microbiome, Lung cancer, Neuron specific enolase",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Lung cancer,MONDO:0008903,healthy controls,CYF group,newly diagnosed lung cancer patients who are CYFRA positive,16,10,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,Figure 3B,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks",Relative microbial abundance between CYF group and healthy controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",3379134|1224|1236|91347|543;3384189|32066|203490|203491|203492;3379134|74201|203494|48461|203557,Complete,Claregrieve1
bsdb:31595156/5/1,31595156,case-control,31595156,10.7150/ijbs.35980,NA,"Liu F., Li J., Guan Y., Lou Y., Chen H., Xu M., Deng D., Chen J., Ni B., Zhao L., Li H., Sang H. , Cai X.",Dysbiosis of the Gut Microbiome is associated with Tumor Biomarkers in Lung Cancer,International journal of biological sciences,2019,"16SrRNAsequencing, Carcinoembryonic antigen, Cytokeratin 19 fragment, Fecal, Gut microbiome, Lung cancer, Neuron specific enolase",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Lung cancer,MONDO:0008903,healthy controls + other lung cancer groups,CYF group,newly diagnosed lung cancer patients who are CYFRA positive,36,10,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,Figure 3B,11 November 2022,Claregrieve1,"Claregrieve1,WikiWorks",Relative microbial abundance between CYF group and other study groups,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|976|200643|171549|171552;1783272|1239|909932|1843489|31977,Complete,Claregrieve1
bsdb:31609493/1/1,31609493,prospective cohort,31609493,doi:10.1111/jgh.14868,NA,"Burt AD, Fujishiro M, Hattori S, Hirooka Y, Honda T, Nakamura M, Singh R, Yamamoto K, Yamamura T, Zorron Cheng Tao Pu L",Microbiota profile is different for early and invasive colorectal cancer and is consistent throughout the colon,Journal of Gastroenterology and Hepatology,2020,"colonoscopy, colorectal neoplasms, fusobacterium nucleatum, gastrointestinal microbiome, microbiota",Experiment 1,Japan,Homo sapiens,Colon,UBERON:0001155,Colorectal cancer,EFO:0005842,Early cancer group,Invasive cancer group,Patients undergoing ESD procedure for colorectal cancer,11,14,NA,16S,34,Illumina,NA,Welch's T-Test,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1, Figure 5, Figure 4",24 May 2022,Jeshudy,"Jeshudy,Fatima,WikiWorks",Figure 1: Fusobacterium genera profile for invasive (YES) and early (NO) colorectal cancer.,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium vincentii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.",3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492|848|155615;3384189|32066|203490|203491|203492|848|68766,Complete,Fatima
bsdb:31609493/1/2,31609493,prospective cohort,31609493,doi:10.1111/jgh.14868,NA,"Burt AD, Fujishiro M, Hattori S, Hirooka Y, Honda T, Nakamura M, Singh R, Yamamoto K, Yamamura T, Zorron Cheng Tao Pu L",Microbiota profile is different for early and invasive colorectal cancer and is consistent throughout the colon,Journal of Gastroenterology and Hepatology,2020,"colonoscopy, colorectal neoplasms, fusobacterium nucleatum, gastrointestinal microbiome, microbiota",Experiment 1,Japan,Homo sapiens,Colon,UBERON:0001155,Colorectal cancer,EFO:0005842,Early cancer group,Invasive cancer group,Patients undergoing ESD procedure for colorectal cancer,11,14,NA,16S,34,Illumina,NA,Welch's T-Test,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2, Figure 3",9 July 2022,Jeshudy,"Jeshudy,Fatima,WikiWorks",Oribacterium parvum profile for invasive (YES) and early (NO) colorectal cancer (colon samples).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium",1783272|1239|186801|3085636|186803|265975|1501329;1783272|1239|186801|186802|1898207,Complete,Fatima
bsdb:31611994/1/1,31611994,case-control,31611994,10.3892/ol.2019.10841,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6781660/,"Sheng Q., Du H., Cheng X., Cheng X., Tang Y., Pan L., Wang Q. , Lin J.",Characteristics of fecal gut microbiota in patients with colorectal cancer at different stages and different sites,Oncology letters,2019,"16S rRNA sequencing, bioinformatics analysis, colorectal cancer, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Controls,CRC,"The CRC patients were selected according to the criteria of no other health complications, no family history of CRC or recurrence of CRC, and no radiotherapy and chemotherapy prior to surgical resection. Patients were then classified according to postoperative clinical data using the tumor-node-metastasis (TNM) staging system for malignant tumors.",30,67,3 months,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,"age,sex",NA,NA,increased,unchanged,increased,NA,NA,Signature 1,Figure 5,21 February 2022,Itslanapark,"Itslanapark,WikiWorks",Comparison of relative abundance of genera in fecal samples of patients with CRC and healthy controls.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum",3379134|976|200643|171549|171552|838;1783272|201174|84998|84999|84107|102106;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|3082720|186804|1257;1783272|1239|186801|3085636|186803|1164882,Complete,Rimsha
bsdb:31611994/1/2,31611994,case-control,31611994,10.3892/ol.2019.10841,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6781660/,"Sheng Q., Du H., Cheng X., Cheng X., Tang Y., Pan L., Wang Q. , Lin J.",Characteristics of fecal gut microbiota in patients with colorectal cancer at different stages and different sites,Oncology letters,2019,"16S rRNA sequencing, bioinformatics analysis, colorectal cancer, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Controls,CRC,"The CRC patients were selected according to the criteria of no other health complications, no family history of CRC or recurrence of CRC, and no radiotherapy and chemotherapy prior to surgical resection. Patients were then classified according to postoperative clinical data using the tumor-node-metastasis (TNM) staging system for malignant tumors.",30,67,3 months,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,"age,sex",NA,NA,increased,unchanged,increased,NA,NA,Signature 2,Figure 5,21 February 2022,Itslanapark,"Itslanapark,WikiWorks",Comparison of relative abundance of genera in fecal samples of patients with CRC and healthy controls.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter",3379134|1224|1236|91347|543|413496;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|216572|44748,Complete,Rimsha
bsdb:31619666/1/1,31619666,case-control,31619666,10.1038/s41467-019-12253-y,NA,"Fyhrquist N., Muirhead G., Prast-Nielsen S., Jeanmougin M., Olah P., Skoog T., Jules-Clement G., Feld M., Barrientos-Somarribas M., Sinkko H., van den Bogaard E.H., Zeeuwen P.L.J.M., Rikken G., Schalkwijk J., Niehues H., Däubener W., Eller S.K., Alexander H., Pennino D., Suomela S., Tessas I., Lybeck E., Baran A.M., Darban H., Gangwar R.S., Gerstel U., Jahn K., Karisola P., Yan L., Hansmann B., Katayama S., Meller S., Bylesjö M., Hupé P., Levi-Schaffer F., Greco D., Ranki A., Schröder J.M., Barker J., Kere J., Tsoka S., Lauerma A., Soumelis V., Nestle F.O., Homey B., Andersson B. , Alenius H.",Microbe-host interplay in atopic dermatitis and psoriasis,Nature communications,2019,NA,Experiment 1,"Finland,Germany,United Kingdom",Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,healthy control,adult with atopic dermatitis,adult with moderate-to-severe chronic atopic dermatitis,115,82,2 weeks,16S,NA,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 1c,10 January 2021,Lucy Mellor,"WikiWorks,Folakunmi",Differentially abundant OTUs among adults with atopic dermatitis (AD) and healthy controls,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,1783272|1239|91061|1385|90964|1279|1280,Complete,Folakunmi
bsdb:31619666/1/2,31619666,case-control,31619666,10.1038/s41467-019-12253-y,NA,"Fyhrquist N., Muirhead G., Prast-Nielsen S., Jeanmougin M., Olah P., Skoog T., Jules-Clement G., Feld M., Barrientos-Somarribas M., Sinkko H., van den Bogaard E.H., Zeeuwen P.L.J.M., Rikken G., Schalkwijk J., Niehues H., Däubener W., Eller S.K., Alexander H., Pennino D., Suomela S., Tessas I., Lybeck E., Baran A.M., Darban H., Gangwar R.S., Gerstel U., Jahn K., Karisola P., Yan L., Hansmann B., Katayama S., Meller S., Bylesjö M., Hupé P., Levi-Schaffer F., Greco D., Ranki A., Schröder J.M., Barker J., Kere J., Tsoka S., Lauerma A., Soumelis V., Nestle F.O., Homey B., Andersson B. , Alenius H.",Microbe-host interplay in atopic dermatitis and psoriasis,Nature communications,2019,NA,Experiment 1,"Finland,Germany,United Kingdom",Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,healthy control,adult with atopic dermatitis,adult with moderate-to-severe chronic atopic dermatitis,115,82,2 weeks,16S,NA,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 1c,10 January 2021,Lucy Mellor,"WikiWorks,Folakunmi",Differentially abundant OTUs among adults with atopic dermatitis (AD) and healthy controls,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles|s__Roseateles sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus sp.",3379134|1224|28216|80840|119060|32008|36773;1783272|201174|1760|85009|31957|1912216|1747;1783272|1239|1737404|1737405|1570339|150022|1981334;1783272|1239|91061|186826|33958|1578|1591;3379134|1224|28216|80840|2975441|93681|1909303;1783272|1239|91061|1385|90964|1279|29387,Complete,Folakunmi
bsdb:31619666/2/1,31619666,case-control,31619666,10.1038/s41467-019-12253-y,NA,"Fyhrquist N., Muirhead G., Prast-Nielsen S., Jeanmougin M., Olah P., Skoog T., Jules-Clement G., Feld M., Barrientos-Somarribas M., Sinkko H., van den Bogaard E.H., Zeeuwen P.L.J.M., Rikken G., Schalkwijk J., Niehues H., Däubener W., Eller S.K., Alexander H., Pennino D., Suomela S., Tessas I., Lybeck E., Baran A.M., Darban H., Gangwar R.S., Gerstel U., Jahn K., Karisola P., Yan L., Hansmann B., Katayama S., Meller S., Bylesjö M., Hupé P., Levi-Schaffer F., Greco D., Ranki A., Schröder J.M., Barker J., Kere J., Tsoka S., Lauerma A., Soumelis V., Nestle F.O., Homey B., Andersson B. , Alenius H.",Microbe-host interplay in atopic dermatitis and psoriasis,Nature communications,2019,NA,Experiment 2,"Finland,Germany,United Kingdom",Homo sapiens,Skin of body,UBERON:0002097,Psoriasis,EFO:0000676,healthy control,adult with psoriasis,adult with psoriasis,115,119,2 weeks,16S,NA,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 1c,10 January 2021,Lucy Mellor,"WikiWorks,Folakunmi",Differentially abundant OTUs among adults with psoriasis (PSO) and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium kroppenstedtii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium simulans,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae",1783272|1239|1737404|1737405|1570339|165779|1872515;1783272|201174|1760|85007|1653|1716|161879;1783272|201174|1760|85007|1653|1716|146827;1783272|1239|1737404|1737405|1570339|150022|1981334;3379134|1224|28216|206351|481,Complete,Folakunmi
bsdb:31619666/2/2,31619666,case-control,31619666,10.1038/s41467-019-12253-y,NA,"Fyhrquist N., Muirhead G., Prast-Nielsen S., Jeanmougin M., Olah P., Skoog T., Jules-Clement G., Feld M., Barrientos-Somarribas M., Sinkko H., van den Bogaard E.H., Zeeuwen P.L.J.M., Rikken G., Schalkwijk J., Niehues H., Däubener W., Eller S.K., Alexander H., Pennino D., Suomela S., Tessas I., Lybeck E., Baran A.M., Darban H., Gangwar R.S., Gerstel U., Jahn K., Karisola P., Yan L., Hansmann B., Katayama S., Meller S., Bylesjö M., Hupé P., Levi-Schaffer F., Greco D., Ranki A., Schröder J.M., Barker J., Kere J., Tsoka S., Lauerma A., Soumelis V., Nestle F.O., Homey B., Andersson B. , Alenius H.",Microbe-host interplay in atopic dermatitis and psoriasis,Nature communications,2019,NA,Experiment 2,"Finland,Germany,United Kingdom",Homo sapiens,Skin of body,UBERON:0002097,Psoriasis,EFO:0000676,healthy control,adult with psoriasis,adult with psoriasis,115,119,2 weeks,16S,NA,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 1c,10 January 2021,Lucy Mellor,"WikiWorks,Folakunmi",Differentially abundant OTUs among adults with psoriasis (PSO) and healthy controls,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles|s__Roseateles sp.",3379134|1224|28216|80840|119060|32008|36773;1783272|1239|91061|186826|33958|1578|1591;3379134|1224|28216|80840|2975441|93681|1909303,Complete,Folakunmi
bsdb:31619666/4/1,31619666,case-control,31619666,10.1038/s41467-019-12253-y,NA,"Fyhrquist N., Muirhead G., Prast-Nielsen S., Jeanmougin M., Olah P., Skoog T., Jules-Clement G., Feld M., Barrientos-Somarribas M., Sinkko H., van den Bogaard E.H., Zeeuwen P.L.J.M., Rikken G., Schalkwijk J., Niehues H., Däubener W., Eller S.K., Alexander H., Pennino D., Suomela S., Tessas I., Lybeck E., Baran A.M., Darban H., Gangwar R.S., Gerstel U., Jahn K., Karisola P., Yan L., Hansmann B., Katayama S., Meller S., Bylesjö M., Hupé P., Levi-Schaffer F., Greco D., Ranki A., Schröder J.M., Barker J., Kere J., Tsoka S., Lauerma A., Soumelis V., Nestle F.O., Homey B., Andersson B. , Alenius H.",Microbe-host interplay in atopic dermatitis and psoriasis,Nature communications,2019,NA,Experiment 4,"Finland,Germany,United Kingdom",Homo sapiens,Skin of body,UBERON:0002097,Atopic eczema,EFO:0000274,healthy control,adults with psoriasis,adult with moderate-to-severe chronic plaque-type psoriasis,115,119,2 weeks,16S,NA,Roche454,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon),Spearman Correlation",0.01,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,supplementary table 2,26 February 2024,Folakunmi,"Folakunmi,WikiWorks",Abundant OTUs that were significantly associated with disease and also significantly associated with a confounded effect.,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium kroppenstedtii",1783272|1239|1737404|1737405|1570339|150022|1981334;3379134|1224|28211|356|41294|374|376;1783272|201174|1760|85007|1653|1716|1720;1783272|201174|1760|85007|1653|1716|161879,Complete,Folakunmi
bsdb:31619731/1/1,31619731,"cross-sectional observational, not case-control",31619731,10.1038/s41598-019-51142-8,NA,"Cook R.R., Fulcher J.A., Tobin N.H., Li F., Lee D.J., Woodward C., Javanbakht M., Brookmeyer R., Shoptaw S., Bolan R., Aldrovandi G.M. , Gorbach P.M.",Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men,Scientific reports,2019,NA,Experiment 1,United States of America,Homo sapiens,Rectum,UBERON:0001052,"HIV infection,Methamphetamine dependence","EFO:0000764,EFO:0004701",HIV-positive non-MA users,HIV-positive MA users,HIV-positive Men who have sex with men (MSM) who self-reported methamphetamine (MA) use in the past six months,81,101,NA,16S,4,Illumina,NA,Negative Binomial Regression,0.1,TRUE,NA,NA,"HIV/AIDS pre-exposure prophylaxis,age,alcohol drinking,antibiotic,antiretroviral therapy,cannabis use,ethnic group,homelessness,number of sex partners,receptive anal intercourse frequency,sexually transmitted infection,smoking behavior,substance use",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Text, Supplementary Table S2, Figure 3",10 January 2021,Michael Lutete,"Claregrieve1,WikiWorks",Differential abundance of bacterial genera between HIV+ methamphetamine users and non-users,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Mannheimia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus",1783272|201174|1760|2037|2049|1654;3379134|1224|1236|135625|712|75984;1783272|1239|909932|1843489|31977|909928;3384189|32066|203490|203491|1129771|34104,Complete,Claregrieve1
bsdb:31619731/2/1,31619731,"cross-sectional observational, not case-control",31619731,10.1038/s41598-019-51142-8,NA,"Cook R.R., Fulcher J.A., Tobin N.H., Li F., Lee D.J., Woodward C., Javanbakht M., Brookmeyer R., Shoptaw S., Bolan R., Aldrovandi G.M. , Gorbach P.M.",Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men,Scientific reports,2019,NA,Experiment 2,United States of America,Homo sapiens,Rectum,UBERON:0001052,Methamphetamine dependence,EFO:0004701,non-users,Methamphetamine users,MSM who self-reported methamphetamine (MA) use in the past six months,225,156,NA,16S,4,Illumina,NA,Negative Binomial Regression,0.1,TRUE,NA,NA,"HIV/AIDS pre-exposure prophylaxis,age,alcohol drinking,antibiotic,antiretroviral therapy,cannabis use,ethnic group,homelessness,number of sex partners,receptive anal intercourse frequency,sexually transmitted infection,smoking behavior,substance use",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Text, Supplementary Table S2",10 January 2021,Michael Lutete,WikiWorks,Differential abundance of bacterial genera between MA users and non-users,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium",1783272|1239|1737404|1737405|1570339|1161127;3379134|1224|1236|135625|712|724;1783272|1239|186801|186802|186806|1730;1783272|1239|909932|1843489|31977|29465;1783272|201174|1760|85007|85029|37914;1783272|1239|91061|186826|1300|1301;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|1737404|1737405|1570339|150022;1783272|201174|1760|85007|1653|1716;3384189|32066|203490|203491|203492|848;1783272|1239|1737404|1737405|1570339|162289;3379134|976|200643|171549|171551|836;1783272|1239|186801|3082720|186804|1257;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|186801|3082720|543314|86331,Complete,Claregrieve1
bsdb:31619731/2/2,31619731,"cross-sectional observational, not case-control",31619731,10.1038/s41598-019-51142-8,NA,"Cook R.R., Fulcher J.A., Tobin N.H., Li F., Lee D.J., Woodward C., Javanbakht M., Brookmeyer R., Shoptaw S., Bolan R., Aldrovandi G.M. , Gorbach P.M.",Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men,Scientific reports,2019,NA,Experiment 2,United States of America,Homo sapiens,Rectum,UBERON:0001052,Methamphetamine dependence,EFO:0004701,non-users,Methamphetamine users,MSM who self-reported methamphetamine (MA) use in the past six months,225,156,NA,16S,4,Illumina,NA,Negative Binomial Regression,0.1,TRUE,NA,NA,"HIV/AIDS pre-exposure prophylaxis,age,alcohol drinking,antibiotic,antiretroviral therapy,cannabis use,ethnic group,homelessness,number of sex partners,receptive anal intercourse frequency,sexually transmitted infection,smoking behavior,substance use",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Text, Supplementary Table S2",10 January 2021,Michael Lutete,WikiWorks,Differential abundance of bacterial genera between MA users and non-users,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella",1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|171552|1283313,Complete,Claregrieve1
bsdb:31619731/3/1,31619731,"cross-sectional observational, not case-control",31619731,10.1038/s41598-019-51142-8,NA,"Cook R.R., Fulcher J.A., Tobin N.H., Li F., Lee D.J., Woodward C., Javanbakht M., Brookmeyer R., Shoptaw S., Bolan R., Aldrovandi G.M. , Gorbach P.M.",Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men,Scientific reports,2019,NA,Experiment 3,United States of America,Homo sapiens,Rectum,UBERON:0001052,Methamphetamine dependence,EFO:0004701,MSM who did not test positive on MA urine drug screening,MSM who tested positive on MA urine drug screening,MSM who tested positive for methamphetamine (MA) use in a urine drug screening,329,52,NA,16S,4,Illumina,NA,Negative Binomial Regression,0.1,TRUE,NA,NA,"HIV/AIDS pre-exposure prophylaxis,age,alcohol drinking,antibiotic,antiretroviral therapy,cannabis use,ethnic group,homelessness,number of sex partners,receptive anal intercourse frequency,sexually transmitted infection,smoking behavior,substance use",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Supplementary Figure S6, Results within text (Page 5, under subheading ""Dose-response analysis of bacterial counts on increasing frequency of MA use""",10 January 2021,Michael Lutete,"WikiWorks,ChiomaBlessing",Sensitivity analysis using urine toxicology screening to define MA use,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",1783272|1239|1737404|1737405|1570339|165779;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85007|85029|37914;1783272|1239|186801|186802|186806|1730;1783272|1239|1737404|1737405|1570339|150022;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3082720|543314|86331;1783272|1239|1737404|1737405|1570339|1161127;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836,Complete,Claregrieve1
bsdb:31619731/3/2,31619731,"cross-sectional observational, not case-control",31619731,10.1038/s41598-019-51142-8,NA,"Cook R.R., Fulcher J.A., Tobin N.H., Li F., Lee D.J., Woodward C., Javanbakht M., Brookmeyer R., Shoptaw S., Bolan R., Aldrovandi G.M. , Gorbach P.M.",Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men,Scientific reports,2019,NA,Experiment 3,United States of America,Homo sapiens,Rectum,UBERON:0001052,Methamphetamine dependence,EFO:0004701,MSM who did not test positive on MA urine drug screening,MSM who tested positive on MA urine drug screening,MSM who tested positive for methamphetamine (MA) use in a urine drug screening,329,52,NA,16S,4,Illumina,NA,Negative Binomial Regression,0.1,TRUE,NA,NA,"HIV/AIDS pre-exposure prophylaxis,age,alcohol drinking,antibiotic,antiretroviral therapy,cannabis use,ethnic group,homelessness,number of sex partners,receptive anal intercourse frequency,sexually transmitted infection,smoking behavior,substance use",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Text, Supplementary Figure 4-6",10 January 2021,Michael Lutete,WikiWorks,Sensitivity analysis using urine toxicology screening to define MA use,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Lentisphaerota|c__Oligosphaeria|o__Oligosphaerales|f__Oligosphaeraceae|g__Oligosphaera,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|31979|1485;1783272|1239|91061|186826|33958|1578;3379134|256845|1313207|1313208|1313209|1313210;3379134|1224|1236|135624|83763|83770,Complete,Claregrieve1
bsdb:31619731/4/1,31619731,"cross-sectional observational, not case-control",31619731,10.1038/s41598-019-51142-8,NA,"Cook R.R., Fulcher J.A., Tobin N.H., Li F., Lee D.J., Woodward C., Javanbakht M., Brookmeyer R., Shoptaw S., Bolan R., Aldrovandi G.M. , Gorbach P.M.",Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men,Scientific reports,2019,NA,Experiment 4,United States of America,Homo sapiens,Rectum,UBERON:0001052,Methamphetamine dependence,EFO:0004701,HIV-positive men who have sex with men who did not test positive in a methamphetamine drug screening,HIV-positive men who have sex with men who tested positive in a methamphetamine drug screening,HIV-positive Men who have sex with men (MSM) who tested positive in a methamphetamine (MA) drug screening,81,21,NA,16S,4,Illumina,NA,Negative Binomial Regression,0.1,TRUE,NA,NA,"HIV/AIDS pre-exposure prophylaxis,age,alcohol drinking,antibiotic,antiretroviral therapy,cannabis use,ethnic group,homelessness,number of sex partners,receptive anal intercourse frequency,sexually transmitted infection,smoking behavior,substance use",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Text, Supplementary Figure 4-6",10 January 2021,Michael Lutete,"Claregrieve1,WikiWorks",Differential microbial abundance between MA+ and MA- stratified by HIV (Using urine toxicology screening to define MA use in HIV-positive MSM),increased,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,3384189|32066|203490|203491|1129771|34104,Complete,Claregrieve1
bsdb:31619731/4/2,31619731,"cross-sectional observational, not case-control",31619731,10.1038/s41598-019-51142-8,NA,"Cook R.R., Fulcher J.A., Tobin N.H., Li F., Lee D.J., Woodward C., Javanbakht M., Brookmeyer R., Shoptaw S., Bolan R., Aldrovandi G.M. , Gorbach P.M.",Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men,Scientific reports,2019,NA,Experiment 4,United States of America,Homo sapiens,Rectum,UBERON:0001052,Methamphetamine dependence,EFO:0004701,HIV-positive men who have sex with men who did not test positive in a methamphetamine drug screening,HIV-positive men who have sex with men who tested positive in a methamphetamine drug screening,HIV-positive Men who have sex with men (MSM) who tested positive in a methamphetamine (MA) drug screening,81,21,NA,16S,4,Illumina,NA,Negative Binomial Regression,0.1,TRUE,NA,NA,"HIV/AIDS pre-exposure prophylaxis,age,alcohol drinking,antibiotic,antiretroviral therapy,cannabis use,ethnic group,homelessness,number of sex partners,receptive anal intercourse frequency,sexually transmitted infection,smoking behavior,substance use",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Text, Supplementary Figure 4-6",10 January 2021,Michael Lutete,"Claregrieve1,WikiWorks",Differential microbial abundance between MA+ and MA- in HIv+ patients (Using urine toxicology screening to define MA use in HIV-positive MSM),decreased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,3379134|1224|28216|80840|75682|846,Complete,Claregrieve1
bsdb:31619731/5/1,31619731,"cross-sectional observational, not case-control",31619731,10.1038/s41598-019-51142-8,NA,"Cook R.R., Fulcher J.A., Tobin N.H., Li F., Lee D.J., Woodward C., Javanbakht M., Brookmeyer R., Shoptaw S., Bolan R., Aldrovandi G.M. , Gorbach P.M.",Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men,Scientific reports,2019,NA,Experiment 5,United States of America,Homo sapiens,Rectum,UBERON:0001052,Methamphetamine dependence,EFO:0004701,HIV-negative MSM who did not test positive in a MA drug screening,HIV-negative MSM who tested positive in a MA drug screening,HIV-negative Men who have sex with men (MSM) who tested positive in a methamphetamine (MA) drug screening,248,31,NA,16S,4,Illumina,NA,Negative Binomial Regression,0.1,TRUE,NA,NA,"HIV/AIDS pre-exposure prophylaxis,age,alcohol drinking,antibiotic,antiretroviral therapy,cannabis use,ethnic group,homelessness,number of sex partners,receptive anal intercourse frequency,sexually transmitted infection,smoking behavior,substance use",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Supplementary Figure S6,10 January 2021,Michael Lutete,"Claregrieve1,WikiWorks,ChiomaBlessing",Differential microbial abundance between MA+ and MA- in HIV- men,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,1783272|1239|186801|186802|31979|1485,Complete,Claregrieve1
bsdb:31619731/5/2,31619731,"cross-sectional observational, not case-control",31619731,10.1038/s41598-019-51142-8,NA,"Cook R.R., Fulcher J.A., Tobin N.H., Li F., Lee D.J., Woodward C., Javanbakht M., Brookmeyer R., Shoptaw S., Bolan R., Aldrovandi G.M. , Gorbach P.M.",Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men,Scientific reports,2019,NA,Experiment 5,United States of America,Homo sapiens,Rectum,UBERON:0001052,Methamphetamine dependence,EFO:0004701,HIV-negative MSM who did not test positive in a MA drug screening,HIV-negative MSM who tested positive in a MA drug screening,HIV-negative Men who have sex with men (MSM) who tested positive in a methamphetamine (MA) drug screening,248,31,NA,16S,4,Illumina,NA,Negative Binomial Regression,0.1,TRUE,NA,NA,"HIV/AIDS pre-exposure prophylaxis,age,alcohol drinking,antibiotic,antiretroviral therapy,cannabis use,ethnic group,homelessness,number of sex partners,receptive anal intercourse frequency,sexually transmitted infection,smoking behavior,substance use",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Supplementary Figure S6,10 January 2021,Michael Lutete,"Claregrieve1,WikiWorks,ChiomaBlessing",Differential microbial abundance between MA+ and MA- in HIV- men,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",3379134|976|200643|171549|2005519|397864;1783272|1239|91061|186826|186828|117563;3384189|32066|203490|203491|1129771|168808;3384189|32066|203490|203491|1129771|34104;1783272|1239|186801|186802|216572|292632,Complete,Claregrieve1
bsdb:31620923/1/1,31620923,prospective cohort,31620923,10.1007/s11357-019-00098-8,NA,"Singh H., Torralba M.G., Moncera K.J., DiLello L., Petrini J., Nelson K.E. , Pieper R.",Gastro-intestinal and oral microbiome signatures associated with healthy aging,GeroScience,2019,"16S rRNA, Akkermansia, Chronic disease, Gut microbiome, Healthy aging, Longevity, Metagenomic analysis, Oral microbiome, Streptococcus",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Age,EFO:0000246,healthy aging (HA),non-healthy aging (NHA),"participants aged 70–82 who had a medical history linked to one or more of the following major disease categories: cancer, acute or chronic cardiovascular disease, acute or chronic pulmonary disease, chronic liver disease, diabetes and diabetic complications, and stroke or neurodegenerative disorder.",33,32,6 weeks,16S,123,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Figure 2, Supplemental File S2",10 January 2021,Yu Wang,"WikiWorks,Claregrieve1",Oral cavity microbiomes diversity and taxonomic differences between healthy aging (HA) and non-healthy aging (NHA) cohorts,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|201174|1760|85006|1268|32207;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85004|31953|1678,Complete,Claregrieve1
bsdb:31620923/1/2,31620923,prospective cohort,31620923,10.1007/s11357-019-00098-8,NA,"Singh H., Torralba M.G., Moncera K.J., DiLello L., Petrini J., Nelson K.E. , Pieper R.",Gastro-intestinal and oral microbiome signatures associated with healthy aging,GeroScience,2019,"16S rRNA, Akkermansia, Chronic disease, Gut microbiome, Healthy aging, Longevity, Metagenomic analysis, Oral microbiome, Streptococcus",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Age,EFO:0000246,healthy aging (HA),non-healthy aging (NHA),"participants aged 70–82 who had a medical history linked to one or more of the following major disease categories: cancer, acute or chronic cardiovascular disease, acute or chronic pulmonary disease, chronic liver disease, diabetes and diabetic complications, and stroke or neurodegenerative disorder.",33,32,6 weeks,16S,123,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"Figure 2, Supplemental File S2",10 January 2021,Yu Wang,"WikiWorks,Claregrieve1",Oral cavity microbiomes diversity and taxonomic differences between healthy aging (HA) and non-healthy aging (NHA) cohorts,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptoclostridiaceae|g__Peptoclostridium,p__Candidatus Absconditibacteriota|s__candidate division SR1 bacterium",3379134|976|117743|200644|49546|1016;3384189|32066|203490|203491|203492|848;3379134|1224|1236|135625|712|724;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|2005525|195950;3379134|203691|203692|136|2845253|157;3379134|1224|28216|206351|481|538;3379134|1224|28216|80840|119060|47670;1783272|1239|186801|3085636|186803|43994;3379134|1224|1236|135615|868|2717;3379134|1224|28216|80840|80864|283;1783272|1239|186801|3082720|3118655|44259;3384189|32066|203490|203491|203492|848|68766;1783272|201174|1760|85009|31957|1743;3379134|1224|1236|135625|712|724|740;1783272|201174|1760|85007|1653|1716;3379134|976|200643|171549|171551|836;1783272|1239|186801|3082720|3120161|1481960;221235|2044938,Complete,Claregrieve1
bsdb:31620923/2/1,31620923,prospective cohort,31620923,10.1007/s11357-019-00098-8,NA,"Singh H., Torralba M.G., Moncera K.J., DiLello L., Petrini J., Nelson K.E. , Pieper R.",Gastro-intestinal and oral microbiome signatures associated with healthy aging,GeroScience,2019,"16S rRNA, Akkermansia, Chronic disease, Gut microbiome, Healthy aging, Longevity, Metagenomic analysis, Oral microbiome, Streptococcus",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,healthy aging (HA),non-healthy aging (NHA),"participants aged 70–82 who had a medical history linked to one or more of the following major disease categories: cancer, acute or chronic cardiovascular disease, acute or chronic pulmonary disease, chronic liver disease, diabetes and diabetic complications, and stroke or neurodegenerative disorder.",33,32,6 weeks,16S,123,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Figure 4a, Figure 5, Supplemental File S2",10 January 2021,Yu Wang,"WikiWorks,Claregrieve1",Gut microbiomes diversity and taxonomic differences between healthy aging (HA) and non-healthy aging (NHA) cohorts,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",3379134|1224|1236|91347|543|561;1783272|1239|91061|186826|33958|1578;3379134|1224|1236|91347|543|620;1783272|1239|91061|186826|1300|1301;1783272|544448|31969;1783272|1239|186801|186802|1898207;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|3085636|186803|46205;1783272|1239|186801|186802|216572|1508657,Complete,Claregrieve1
bsdb:31620923/2/2,31620923,prospective cohort,31620923,10.1007/s11357-019-00098-8,NA,"Singh H., Torralba M.G., Moncera K.J., DiLello L., Petrini J., Nelson K.E. , Pieper R.",Gastro-intestinal and oral microbiome signatures associated with healthy aging,GeroScience,2019,"16S rRNA, Akkermansia, Chronic disease, Gut microbiome, Healthy aging, Longevity, Metagenomic analysis, Oral microbiome, Streptococcus",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,healthy aging (HA),non-healthy aging (NHA),"participants aged 70–82 who had a medical history linked to one or more of the following major disease categories: cancer, acute or chronic cardiovascular disease, acute or chronic pulmonary disease, chronic liver disease, diabetes and diabetic complications, and stroke or neurodegenerative disorder.",33,32,6 weeks,16S,123,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Figure 4a, Figure 5, Supplemental File S2",10 January 2021,Yu Wang,"WikiWorks,Claregrieve1",Gut microbiomes diversity and taxonomic differences between healthy aging (HA) and non-healthy aging (NHA) cohorts,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__Eubacteriales Family XIII. Incertae Sedis bacterium",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|815|816;1783272|1239|526524|526525|128827;1783272|1239|186801|3085636|186803;1783272|201174|84998|1643822|1643826|84108;1783272|1239|186801|3082720|543314|2137877,Complete,Claregrieve1
bsdb:31637220/1/1,31637220,"cross-sectional observational, not case-control",31637220,10.3389/fcimb.2019.00339,NA,"Kolbe A.R., Castro-Nallar E., Preciado D. , Pérez-Losada M.",Altered Middle Ear Microbiome in Children With Chronic Otitis Media With Effusion and Respiratory Illnesses,Frontiers in cellular and infection microbiology,2019,"amplicon sequence variants, asthma, bronchiolitis, middle ear microbiome, otitis media",Experiment 1,United States of America,Homo sapiens,Middle ear,NA,Lower respiratory tract disease,EFO:0009433,Chronic Otitis Media With Effusion (COME) without asthma or bronchiolitis,Chronic Otitis Media With Effusion (COME) with asthma or bronchiolitis,"Children from 3 to 176 months of age, with Chronic Otitis Media With Effusion (COME) with a history of lower airway disease (i.e., asthma or bronchiolitis),  defined by a history of pulmonary physician-diagnosed asthma; documented chronic wheezing being treated with a daily respiratory inhaler; or PCR (+) for rhinovirus bronchiolitis diagnosis.",37,13,2 weeks,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 5,6 May 2024,Scholastica,"Scholastica,WikiWorks","Differentially abundant genera/species (p-adjusted < 0.05) in middle ear fluid (MEF) of patients with lower airway disease diagnosis (i.e., asthma or bronchiolitis) compared to those without.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella",3379134|1224|1236|135625|712|724;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|2887326|468|475,Complete,Svetlana up
bsdb:31637220/1/2,31637220,"cross-sectional observational, not case-control",31637220,10.3389/fcimb.2019.00339,NA,"Kolbe A.R., Castro-Nallar E., Preciado D. , Pérez-Losada M.",Altered Middle Ear Microbiome in Children With Chronic Otitis Media With Effusion and Respiratory Illnesses,Frontiers in cellular and infection microbiology,2019,"amplicon sequence variants, asthma, bronchiolitis, middle ear microbiome, otitis media",Experiment 1,United States of America,Homo sapiens,Middle ear,NA,Lower respiratory tract disease,EFO:0009433,Chronic Otitis Media With Effusion (COME) without asthma or bronchiolitis,Chronic Otitis Media With Effusion (COME) with asthma or bronchiolitis,"Children from 3 to 176 months of age, with Chronic Otitis Media With Effusion (COME) with a history of lower airway disease (i.e., asthma or bronchiolitis),  defined by a history of pulmonary physician-diagnosed asthma; documented chronic wheezing being treated with a daily respiratory inhaler; or PCR (+) for rhinovirus bronchiolitis diagnosis.",37,13,2 weeks,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,decreased,NA,NA,NA,decreased,Signature 2,Figure 5,6 May 2024,Scholastica,"Scholastica,WikiWorks","Differentially abundant genera/species (p-adjusted < 0.05) in middle ear fluid (MEF) of patients with lower airway disease diagnosis (i.e., asthma or bronchiolitis) compared to those without.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Alloiococcus|s__Alloiococcus otitis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium otitidis",1783272|1239|91061|186826|186828|1651|1652;1783272|201174|1760|85007|1653|1716|29321,Complete,Svetlana up
bsdb:31672155/1/1,31672155,"cross-sectional observational, not case-control",31672155,10.1186/s13059-019-1831-z,https://pubmed.ncbi.nlm.nih.gov/31672155/,"Kaplan R.C., Wang Z., Usyk M., Sotres-Alvarez D., Daviglus M.L., Schneiderman N., Talavera G.A., Gellman M.D., Thyagarajan B., Moon J.Y., Vázquez-Baeza Y., McDonald D., Williams-Nguyen J.S., Wu M.C., North K.E., Shaffer J., Sollecito C.C., Qi Q., Isasi C.R., Wang T., Knight R. , Burk R.D.","Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity",Genome biology,2019,"Epidemiology, Hispanic population, Microbiome, Mycobiome, Obesity",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Individuals with a healthy body mass index,Obese individuals,Individuals who had a class II or class III obesity,293,294,6 months,16S,4,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,decreased,NA,NA,NA,NA,Signature 1,Table S4,17 March 2023,Ombati,"Ombati,Chloe,Atrayees,WikiWorks","Association of genus level 16S data with obesity, adjusted for age, sex, field
center, and Hispanic background. This involved the identification of bacterial and fungal taxa associated with birthplace, relocation, and obesity.",decreased,"k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",3384194|508458|649775|649776|649777|508459;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572;1783272|1239|186801|186802;1783272|201174|84998|84999|84107;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|186802|216572|119852;1783272|201174|84998|1643822|1643826|84111;3379134|976|200643|171549|171550;1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|186803|572511;3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988|239934,Complete,Atrayees
bsdb:31672155/1/2,31672155,"cross-sectional observational, not case-control",31672155,10.1186/s13059-019-1831-z,https://pubmed.ncbi.nlm.nih.gov/31672155/,"Kaplan R.C., Wang Z., Usyk M., Sotres-Alvarez D., Daviglus M.L., Schneiderman N., Talavera G.A., Gellman M.D., Thyagarajan B., Moon J.Y., Vázquez-Baeza Y., McDonald D., Williams-Nguyen J.S., Wu M.C., North K.E., Shaffer J., Sollecito C.C., Qi Q., Isasi C.R., Wang T., Knight R. , Burk R.D.","Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity",Genome biology,2019,"Epidemiology, Hispanic population, Microbiome, Mycobiome, Obesity",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Individuals with a healthy body mass index,Obese individuals,Individuals who had a class II or class III obesity,293,294,6 months,16S,4,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,decreased,NA,NA,NA,NA,Signature 2,Table S4,8 June 2023,Atrayees,"Atrayees,WikiWorks","Association of genus level 16S data with obesity, adjusted for age, sex, field center, and Hispanic background. This involved the identification of bacterial and fungal taxa associated with birthplace, relocation, and obesity.",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|909932|1843488|909930|904;1783272|1239|909932|1843489|31977|906;1783272|1239|526524|526525|2810280|135858;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:31672155/2/1,31672155,"cross-sectional observational, not case-control",31672155,10.1186/s13059-019-1831-z,https://pubmed.ncbi.nlm.nih.gov/31672155/,"Kaplan R.C., Wang Z., Usyk M., Sotres-Alvarez D., Daviglus M.L., Schneiderman N., Talavera G.A., Gellman M.D., Thyagarajan B., Moon J.Y., Vázquez-Baeza Y., McDonald D., Williams-Nguyen J.S., Wu M.C., North K.E., Shaffer J., Sollecito C.C., Qi Q., Isasi C.R., Wang T., Knight R. , Burk R.D.","Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity",Genome biology,2019,"Epidemiology, Hispanic population, Microbiome, Mycobiome, Obesity",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Early age,Later age,NA,1674,1674,6 months,16S,4,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,"age,race,sex",NA,decreased,NA,NA,NA,NA,Signature 1,Table S5,28 March 2023,Ombati,"Ombati,Atrayees,WikiWorks","Association of genus level 16S data with age at relocation among Latin American born individuals, adjusted for age, sex, field center and Hispanic background.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",1783272|1239|186801|186802;3379134|976|200643|171549|1853231|574697;3379134|1224|1236|135625|712|724;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|216851;3379134|1224|1236|91347|543|570;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|577309;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|140625;3379134|200940|3031449|213115|194924|872;3379134|976|200643|171549|2005519;1783272|1239|91061|186826|33958;1783272|544448|31969|186332|186333;1783272|1239|186801|186802|216572;1783272|201174|84998|84999|84107;1783272|1239|186801|3082768|990719;3379134|1224|1236|91347|543,Complete,Atrayees
bsdb:31672155/2/2,31672155,"cross-sectional observational, not case-control",31672155,10.1186/s13059-019-1831-z,https://pubmed.ncbi.nlm.nih.gov/31672155/,"Kaplan R.C., Wang Z., Usyk M., Sotres-Alvarez D., Daviglus M.L., Schneiderman N., Talavera G.A., Gellman M.D., Thyagarajan B., Moon J.Y., Vázquez-Baeza Y., McDonald D., Williams-Nguyen J.S., Wu M.C., North K.E., Shaffer J., Sollecito C.C., Qi Q., Isasi C.R., Wang T., Knight R. , Burk R.D.","Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity",Genome biology,2019,"Epidemiology, Hispanic population, Microbiome, Mycobiome, Obesity",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Early age,Later age,NA,1674,1674,6 months,16S,4,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,"age,race,sex",NA,decreased,NA,NA,NA,NA,Signature 2,Table S5,12 June 2023,Atrayees,"Atrayees,WikiWorks","Association of genus level 16S data with age at relocation among Latin American born individuals, adjusted for age, sex, field center and Hispanic background.",decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium",1783272|1239|526524|526525|2810280|100883;3379134|976|200643|171549|815|816;1783272|1239|909932|1843488|909930|904;3379134|1224|28216|80840|995019|40544;1783272|1239|526524|526525|128827|61170;1783272|201174|1760|85004|31953|1678;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|186802|216572|119852;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|244127;1783272|201174|84998|1643822|1643826|447020;1783272|1239|186801|186802|186806|1730,Complete,Atrayees
bsdb:31672155/4/1,31672155,"cross-sectional observational, not case-control",31672155,10.1186/s13059-019-1831-z,https://pubmed.ncbi.nlm.nih.gov/31672155/,"Kaplan R.C., Wang Z., Usyk M., Sotres-Alvarez D., Daviglus M.L., Schneiderman N., Talavera G.A., Gellman M.D., Thyagarajan B., Moon J.Y., Vázquez-Baeza Y., McDonald D., Williams-Nguyen J.S., Wu M.C., North K.E., Shaffer J., Sollecito C.C., Qi Q., Isasi C.R., Wang T., Knight R. , Burk R.D.","Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity",Genome biology,2019,"Epidemiology, Hispanic population, Microbiome, Mycobiome, Obesity",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,USB (US born),LAB,Latin American Born,225,1532,6 months,16S,4,Illumina,raw counts,Linear Regression,0.05,NA,NA,NA,age,NA,decreased,NA,NA,NA,NA,Signature 1,Table S7,28 March 2023,Ombati,"Ombati,Atrayees,WikiWorks",Fungal taxa that differ after comparing those born in the mainland USA versus those born in Latin America.,decreased,"k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Phaffomycetales|f__Phaffomycetaceae|g__Cyberlindnera|s__Cyberlindnera jadinii,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Phaffomycetales|f__Phaffomycetaceae|g__Cyberlindnera,k__Fungi|p__Basidiomycota|c__Agaricomycetes,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Penicillium|s__Penicillium roqueforti,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Mycenaceae|g__Panellus,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Kluyveromyces|s__Kluyveromyces marxianus,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Pleosporaceae|g__Alternaria|s__Alternaria rosae,k__Fungi|p__Basidiomycota|c__Agaricomycetes|f__Xenasmatellaceae|g__Xenasmatella|s__Xenasmatella ardosiaca,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Cladosporium|s__Cladosporium salinae,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Corticiales|f__Corticiaceae|g__Erythricium|s__Erythricium laetum,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Corticiales|f__Corticiaceae|g__Erythricium",4751|4890|4891|3243778|115784|604195|4903;4751|4890|4891|3243778|115784|604195;4751|5204|155619;4751|4890|147545|5042|1131492|5073|5082;4751|5204|155619|5338|2024004|5635;4751|4890|4891|4892|4893|4910|4911;4751|4890|147541|92860|28556|5598|1187941;4751|5204|155619|3118719|301415|467934;4751|4890|147541|2726946|452563|5498|1052097;4751|5204|155619|452338|5304|264095|264096;4751|5204|155619|452338|5304|264095,Complete,Atrayees
bsdb:31672155/4/2,31672155,"cross-sectional observational, not case-control",31672155,10.1186/s13059-019-1831-z,https://pubmed.ncbi.nlm.nih.gov/31672155/,"Kaplan R.C., Wang Z., Usyk M., Sotres-Alvarez D., Daviglus M.L., Schneiderman N., Talavera G.A., Gellman M.D., Thyagarajan B., Moon J.Y., Vázquez-Baeza Y., McDonald D., Williams-Nguyen J.S., Wu M.C., North K.E., Shaffer J., Sollecito C.C., Qi Q., Isasi C.R., Wang T., Knight R. , Burk R.D.","Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity",Genome biology,2019,"Epidemiology, Hispanic population, Microbiome, Mycobiome, Obesity",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,USB (US born),LAB,Latin American Born,225,1532,6 months,16S,4,Illumina,raw counts,Linear Regression,0.05,NA,NA,NA,age,NA,decreased,NA,NA,NA,NA,Signature 2,Table S7,13 June 2023,Atrayees,"Atrayees,WikiWorks",Fungal taxa that differ after comparing those born in the mainland USA versus those born in Latin America.,increased,"k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Cystofilobasidiaceae|g__Cystofilobasidium,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Kurtzmaniella|s__[Candida] railenensis",4751|5204|155616|90883|165808|5410;4751|4890|3239874|2916678|766764|549703|45579,Complete,Atrayees
bsdb:31672155/5/1,31672155,"cross-sectional observational, not case-control",31672155,10.1186/s13059-019-1831-z,https://pubmed.ncbi.nlm.nih.gov/31672155/,"Kaplan R.C., Wang Z., Usyk M., Sotres-Alvarez D., Daviglus M.L., Schneiderman N., Talavera G.A., Gellman M.D., Thyagarajan B., Moon J.Y., Vázquez-Baeza Y., McDonald D., Williams-Nguyen J.S., Wu M.C., North K.E., Shaffer J., Sollecito C.C., Qi Q., Isasi C.R., Wang T., Knight R. , Burk R.D.","Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity",Genome biology,2019,"Epidemiology, Hispanic population, Microbiome, Mycobiome, Obesity",Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Individuals with a healthy body mass index,Individuals who were obese,Individuals with class II or class III obesity,293,294,6 months,16S,4,Illumina,raw counts,Linear Regression,NA,TRUE,NA,NA,"age,sex",NA,decreased,NA,NA,NA,NA,Signature 1,Table S8,28 March 2023,Ombati,"Ombati,Atrayees,WikiWorks","Association of genus level ITS1 data with obesity, adjusted for age, sex, field
center, and Hispanic background. Only one met Pvalue < 0.05.",decreased,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Debaryomyces|s__Debaryomyces sp.,4751|4890|3239874|2916678|766764|4958|1853546,Complete,Atrayees
bsdb:31672155/6/2,31672155,"cross-sectional observational, not case-control",31672155,10.1186/s13059-019-1831-z,https://pubmed.ncbi.nlm.nih.gov/31672155/,"Kaplan R.C., Wang Z., Usyk M., Sotres-Alvarez D., Daviglus M.L., Schneiderman N., Talavera G.A., Gellman M.D., Thyagarajan B., Moon J.Y., Vázquez-Baeza Y., McDonald D., Williams-Nguyen J.S., Wu M.C., North K.E., Shaffer J., Sollecito C.C., Qi Q., Isasi C.R., Wang T., Knight R. , Burk R.D.","Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity",Genome biology,2019,"Epidemiology, Hispanic population, Microbiome, Mycobiome, Obesity",Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Early age,Later age,Individuals who had relocated to the USA at a younger age( 18 and below),1674,1674,6 months,16S,4,Illumina,raw counts,Linear Regression,NA,TRUE,NA,NA,"age,sex",NA,decreased,NA,NA,NA,NA,Signature 2,Table S9,8 June 2023,Atrayees,"Atrayees,WikiWorks","Association of genus level ITS1 data with age at relocation among Latin
American-born individuals, adjusted for age, sex, field center, and Hispanic background",increased,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida,4751|4890|3239874|2916678|766764|5475,Complete,Atrayees
bsdb:31674052/1/1,31674052,case-control,31674052,10.1111/jgh.14910,NA,"Yang M., Zhang L., Hong G., Li Y., Li G., Qian W., Xiong H., Bai T., Song J. , Hou X.",Duodenal and rectal mucosal microbiota related to small intestinal bacterial overgrowth in diarrhea-predominant irritable bowel syndrome,Journal of gastroenterology and hepatology,2020,"glucose hydrogen breath test, irritable bowel syndrome, microbial dysbiosis index, mucosal-associated microbiota, small intestinal bacterial overgrowth",Experiment 1,China,Homo sapiens,Duodenal mucosa,UBERON:0000320,Small intestine enteropathy,EFO:0009705,IBS.sibo-,IBS.sibo+,duodenal mucosa samples of patients with typical clinical symptoms and normal colonoscopy presentation fulfilling the Rome III diagnostic criteria with SIBO,43,34,3 months,16S,123,Roche454,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,increased,NA,NA,NA,Signature 1,Figure S3,30 July 2022,Jeshudy,"Jeshudy,WikiWorks",Enriched genera in duodenal mucosa obtained from LEfSe.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Nevskiales|f__Nevskiaceae|g__Nevskia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",1783272|201174|1760|85006|1268|1663;1783272|1239|91061|186826|186828|2747;1783272|1239|91061|186826|33958|1243;3379134|1224|28211|356|41294|374;3379134|1224|1236|1775403|568386|64001;1783272|1239|91061|186826|1300|1357;3379134|1224|1236|72274|135621|286,Complete,Folakunmi
bsdb:31674052/1/2,31674052,case-control,31674052,10.1111/jgh.14910,NA,"Yang M., Zhang L., Hong G., Li Y., Li G., Qian W., Xiong H., Bai T., Song J. , Hou X.",Duodenal and rectal mucosal microbiota related to small intestinal bacterial overgrowth in diarrhea-predominant irritable bowel syndrome,Journal of gastroenterology and hepatology,2020,"glucose hydrogen breath test, irritable bowel syndrome, microbial dysbiosis index, mucosal-associated microbiota, small intestinal bacterial overgrowth",Experiment 1,China,Homo sapiens,Duodenal mucosa,UBERON:0000320,Small intestine enteropathy,EFO:0009705,IBS.sibo-,IBS.sibo+,duodenal mucosa samples of patients with typical clinical symptoms and normal colonoscopy presentation fulfilling the Rome III diagnostic criteria with SIBO,43,34,3 months,16S,123,Roche454,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,increased,NA,NA,NA,Signature 2,Figure S3B,30 July 2022,Jeshudy,"Jeshudy,Folakunmi,WikiWorks",Enriched genera in duodenal mucosa obtained from LEfSe.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces purpurascens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium",3379134|1224|28216|80840|506|222;3379134|1224|28211|356|82115|357;1783272|201174|1760|85006|85019|1696;3379134|1224|28211|204458|76892|41275;1783272|201174|1760|85006|85023|33882;1783272|201174|1760|85006|1268|1269;3379134|1224|28211|356|118882|528;1783272|1239|91061|1385|186822|44249;1783272|201174|1760|85009|31957|1743;3379134|1224|28211|356|82115|379;3379134|976|117747|200666|84566|28453;3379134|1224|28211|204457|3423717|165695;1783272|201174|1760|85011|2062|1883|1924;1783272|201174|1760|85007|1653|1716,Complete,Folakunmi
bsdb:31674052/3/1,31674052,case-control,31674052,10.1111/jgh.14910,NA,"Yang M., Zhang L., Hong G., Li Y., Li G., Qian W., Xiong H., Bai T., Song J. , Hou X.",Duodenal and rectal mucosal microbiota related to small intestinal bacterial overgrowth in diarrhea-predominant irritable bowel syndrome,Journal of gastroenterology and hepatology,2020,"glucose hydrogen breath test, irritable bowel syndrome, microbial dysbiosis index, mucosal-associated microbiota, small intestinal bacterial overgrowth",Experiment 3,China,Homo sapiens,Mucosa of rectum,UBERON:0003346,Small intestine enteropathy,EFO:0009705,IBS.sibo-,IBS.sibo+,rectal mucosa samples of patients with typical clinical symptoms and normal colonoscopy presentation fulfilling the Rome III diagnostic criteria; with SIBO,43,34,3 months,16S,123,Roche454,relative abundances,LEfSe,0.05,NA,2,NA,"age,body mass index,sex",NA,NA,decreased,NA,NA,NA,Signature 1,figure 3B,8 February 2024,Folakunmi,"Folakunmi,WikiWorks",Differentially abundant taxa in rectal mucosa between SIBO- IBS-D patients and  SIBO+ IBS-D patients.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Modestobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Geobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Helcococcus",1783272|1239|909932|909929|1843491|82373;1783272|1239|91061|186826|186828|2747;1783272|1239|91061|186826|81852|1350;1783272|201174|1760|1643682|85030|88138;1783272|1239|91061|1385|3120669|129337;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85009|31957|1743;1783272|1239|1737404|1737405|1570339|31983,Complete,Folakunmi
bsdb:31674052/3/2,31674052,case-control,31674052,10.1111/jgh.14910,NA,"Yang M., Zhang L., Hong G., Li Y., Li G., Qian W., Xiong H., Bai T., Song J. , Hou X.",Duodenal and rectal mucosal microbiota related to small intestinal bacterial overgrowth in diarrhea-predominant irritable bowel syndrome,Journal of gastroenterology and hepatology,2020,"glucose hydrogen breath test, irritable bowel syndrome, microbial dysbiosis index, mucosal-associated microbiota, small intestinal bacterial overgrowth",Experiment 3,China,Homo sapiens,Mucosa of rectum,UBERON:0003346,Small intestine enteropathy,EFO:0009705,IBS.sibo-,IBS.sibo+,rectal mucosa samples of patients with typical clinical symptoms and normal colonoscopy presentation fulfilling the Rome III diagnostic criteria; with SIBO,43,34,3 months,16S,123,Roche454,relative abundances,LEfSe,0.05,NA,2,NA,"age,body mass index,sex",NA,NA,decreased,NA,NA,NA,Signature 2,figure 3B,8 February 2024,Folakunmi,"Folakunmi,WikiWorks",Differentially abundant taxa in rectal mucosa between SIBO- IBS-D patients and SIBO+ IBS-D patients.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Janibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium",3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|572511;1783272|1239|91061|1385|90964|1279;1783272|201174|1760|85006|85021|53457;3379134|1224|1236|91347|543|544;3379134|976|200643|171549|1853231|283168;3379134|1224|28211|356|119045|407;3384194|1297|188787|118964|183710|1298;3379134|1224|28211|356|82115|357;3379134|976|117747|200666|84566|28453,Complete,Folakunmi
bsdb:31674052/4/1,31674052,case-control,31674052,10.1111/jgh.14910,NA,"Yang M., Zhang L., Hong G., Li Y., Li G., Qian W., Xiong H., Bai T., Song J. , Hou X.",Duodenal and rectal mucosal microbiota related to small intestinal bacterial overgrowth in diarrhea-predominant irritable bowel syndrome,Journal of gastroenterology and hepatology,2020,"glucose hydrogen breath test, irritable bowel syndrome, microbial dysbiosis index, mucosal-associated microbiota, small intestinal bacterial overgrowth",Experiment 4,China,Homo sapiens,Duodenum,UBERON:0002114,Small intestine enteropathy,EFO:0009705,HC.sibo-,HC.sibo+,duodenal fluid samples of healthy controls (with no IBS) with SIBO,12,7,3 months,16S,123,Roche454,relative abundances,Chi-Square,0.05,NA,NA,NA,"age,body mass index,sex",NA,NA,unchanged,NA,NA,NA,Signature 1,Table S1,30 July 2022,Jeshudy,"Jeshudy,WikiWorks",Comparisons of microbial composition at the phylum level between SIBO+ and SIBO- IBS-D patients and healthy individuals.,increased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Folakunmi
bsdb:31674052/5/1,31674052,case-control,31674052,10.1111/jgh.14910,NA,"Yang M., Zhang L., Hong G., Li Y., Li G., Qian W., Xiong H., Bai T., Song J. , Hou X.",Duodenal and rectal mucosal microbiota related to small intestinal bacterial overgrowth in diarrhea-predominant irritable bowel syndrome,Journal of gastroenterology and hepatology,2020,"glucose hydrogen breath test, irritable bowel syndrome, microbial dysbiosis index, mucosal-associated microbiota, small intestinal bacterial overgrowth",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Small intestine enteropathy,EFO:0009705,IBS.sibo-,IBS.sibo+,Feces samples of patients with typical clinical symptoms and normal colonoscopy presentation fulfilling the Rome III diagnostic criteria; with SIBO,43,34,3 months,16S,123,Roche454,relative abundances,Chi-Square,0.05,NA,NA,NA,"age,body mass index,sex",NA,NA,unchanged,NA,NA,NA,Signature 1,Table S1,30 July 2022,Jeshudy,"Jeshudy,WikiWorks",Comparisons of microbial composition at the phylum level between SIBO+ and SIBO- IBS-D patients and healthy individuals.,increased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Folakunmi
bsdb:31676759/1/1,31676759,prospective cohort,31676759,10.1038/s41467-019-12989-7,NA,"Thorsen J., Rasmussen M.A., Waage J., Mortensen M., Brejnrod A., Bønnelykke K., Chawes B.L., Brix S., Sørensen S.J., Stokholm J. , Bisgaard H.",Infant airway microbiota and topical immune perturbations in the origins of childhood asthma,Nature communications,2019,NA,Experiment 1,Denmark,Homo sapiens,Hypopharynx,UBERON:0001051,Asthma,MONDO:0004979,healthy control,child with asthma at age 6,"asthma at age 6 years diagnosed using a pre-defined validated quantitative symptom algorithm based on parental registration of troublesome lung symptoms on structured daily diary cards from birth, verified by study pediatricians at each clinic visit",438,135,NA,16S,4,Illumina,NA,Cox Proportional-Hazards Regression,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Supplemental Table 1,10 January 2021,Lucy Mellor,"Claregrieve1,WikiWorks","Associations between log-relative abundances at one month and asthma development by age six years, assessed with Cox proportional hazards regression",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976|200643|171549|171552|838;1783272|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:31678982/1/1,31678982,case-control,31678982,10.12659/MSM.919988,NA,"Zhang B., Gu J., Liu J., Huang B. , Li J.",Fecal Microbiota Taxonomic Shifts in Chinese Multiple Myeloma Patients Analyzed by Quantitative Polimerase Chain Reaction (QPCR) and 16S rRNA High-Throughput Sequencing,Medical science monitor : international medical journal of experimental and clinical research,2019,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Multiple myeloma,EFO:0001378,healthy control,Multiple Myeloma patient,"patient diagnosis with multiple myeloma and no other disease validated to affect intestinal microbial including digestive disease like liver cirrhosis, liver cancer, inflammatory bowel disease, and irritable bowel syndrome; systemic disease like diabetes and hypertension and thyroid disease; no treatment including antibiotics, chemotherapy, plasma exchange or bone marrow transplant; no cold, fever or other infections within 3 months before sampling with administrated antibacterial drugs, gastrointestinal motility drugs or micro-ecological conditioning agents like eating and living habit change 1 week before sampling",17,40,3 months,16S,34,Illumina,raw counts,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,Table 6 & text,10 January 2021,William Lam,"WikiWorks,Atrayees",Comparison of Intestinal Microbial between the Multiple Myeloma group and healthy control at the phylum level,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,Atrayees
bsdb:31678982/1/2,31678982,case-control,31678982,10.12659/MSM.919988,NA,"Zhang B., Gu J., Liu J., Huang B. , Li J.",Fecal Microbiota Taxonomic Shifts in Chinese Multiple Myeloma Patients Analyzed by Quantitative Polimerase Chain Reaction (QPCR) and 16S rRNA High-Throughput Sequencing,Medical science monitor : international medical journal of experimental and clinical research,2019,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Multiple myeloma,EFO:0001378,healthy control,Multiple Myeloma patient,"patient diagnosis with multiple myeloma and no other disease validated to affect intestinal microbial including digestive disease like liver cirrhosis, liver cancer, inflammatory bowel disease, and irritable bowel syndrome; systemic disease like diabetes and hypertension and thyroid disease; no treatment including antibiotics, chemotherapy, plasma exchange or bone marrow transplant; no cold, fever or other infections within 3 months before sampling with administrated antibacterial drugs, gastrointestinal motility drugs or micro-ecological conditioning agents like eating and living habit change 1 week before sampling",17,40,3 months,16S,34,Illumina,raw counts,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,Table 6 & text,10 January 2021,William Lam,"WikiWorks,Atrayees",Comparison of Intestinal Microbial between the Multiple Myeloma group and healthy control at the phylum level,decreased,k__Bacillati|p__Actinomycetota,1783272|201174,Complete,Atrayees
bsdb:31678982/2/1,31678982,case-control,31678982,10.12659/MSM.919988,NA,"Zhang B., Gu J., Liu J., Huang B. , Li J.",Fecal Microbiota Taxonomic Shifts in Chinese Multiple Myeloma Patients Analyzed by Quantitative Polimerase Chain Reaction (QPCR) and 16S rRNA High-Throughput Sequencing,Medical science monitor : international medical journal of experimental and clinical research,2019,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Multiple myeloma,EFO:0001378,healthy control,Multiple Myeloma patient,"patient diagnosis with multiple myeloma and no other disease validated to affect intestinal microbial including digestive disease like liver cirrhosis, liver cancer, inflammatory bowel disease, and irritable bowel syndrome; systemic disease like diabetes and hypertension and thyroid disease; no treatment including antibiotics, chemotherapy, plasma exchange or bone marrow transplant; no cold, fever or other infections within 3 months before sampling with administrated antibacterial drugs, gastrointestinal motility drugs or micro-ecological conditioning agents like eating and living habit change 1 week before sampling",17,40,3 months,16S,34,Illumina,relative abundances,LEfSe,2,FALSE,2,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,Figure 3a,10 January 2021,William Lam,WikiWorks,Intestinal Microbial taxonomic differences were detected based on Operational Taxonomic Unit between Multiple Myeloma group and healthy controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter|s__Cronobacter sakazakii",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|1224;1783272|1239|526524|526525|2810281|191303;3379134|1224|1236|91347|543|413496;3379134|1224|1236|91347|543|413496|28141,Complete,Atrayees
bsdb:31678982/2/2,31678982,case-control,31678982,10.12659/MSM.919988,NA,"Zhang B., Gu J., Liu J., Huang B. , Li J.",Fecal Microbiota Taxonomic Shifts in Chinese Multiple Myeloma Patients Analyzed by Quantitative Polimerase Chain Reaction (QPCR) and 16S rRNA High-Throughput Sequencing,Medical science monitor : international medical journal of experimental and clinical research,2019,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Multiple myeloma,EFO:0001378,healthy control,Multiple Myeloma patient,"patient diagnosis with multiple myeloma and no other disease validated to affect intestinal microbial including digestive disease like liver cirrhosis, liver cancer, inflammatory bowel disease, and irritable bowel syndrome; systemic disease like diabetes and hypertension and thyroid disease; no treatment including antibiotics, chemotherapy, plasma exchange or bone marrow transplant; no cold, fever or other infections within 3 months before sampling with administrated antibacterial drugs, gastrointestinal motility drugs or micro-ecological conditioning agents like eating and living habit change 1 week before sampling",17,40,3 months,16S,34,Illumina,relative abundances,LEfSe,2,FALSE,2,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,Figure 3a,10 January 2021,William Lam,WikiWorks,Intestinal Microbial taxonomic differences were detected based on Operational Taxonomic Unit between Multiple Myeloma group and healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus",1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|186802|186806|1730;1783272|201174|84998;1783272|201174|84998|84999;1783272|201174|84998|84999|84107;1783272|1239|186801|3085636|186803|207244;1783272|201174|84998|1643822|1643826|84108;1783272|1239|526524|526525|2810280|135858;3379134|1224|28211|204441|41295;3379134|1224|28211;3379134|1224|28211|204441;1783272|1239|909932|1843488|909930|904,Complete,Atrayees
bsdb:31678982/3/1,31678982,case-control,31678982,10.12659/MSM.919988,NA,"Zhang B., Gu J., Liu J., Huang B. , Li J.",Fecal Microbiota Taxonomic Shifts in Chinese Multiple Myeloma Patients Analyzed by Quantitative Polimerase Chain Reaction (QPCR) and 16S rRNA High-Throughput Sequencing,Medical science monitor : international medical journal of experimental and clinical research,2019,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Multiple myeloma,EFO:0001378,healthy control,Multiple Myeloma patient,"patient diagnosis with multiple myeloma and no other disease validated to affect intestinal microbial including digestive disease like liver cirrhosis, liver cancer, inflammatory bowel disease, and irritable bowel syndrome; systemic disease like diabetes and hypertension and thyroid disease; no treatment including antibiotics, chemotherapy, plasma exchange or bone marrow transplant; no cold, fever or other infections within 3 months before sampling with administrated antibacterial drugs, gastrointestinal motility drugs or micro-ecological conditioning agents like eating and living habit change 1 week before sampling",17,40,3 months,16S,34,Illumina,relative abundances,Metastats,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 7 and text,10 January 2021,William Lam,"WikiWorks,Atrayees","Genus with significant difference between Multiple Myeloma group and healthy control group was selected, followed by ordering according to the abundance in the intestinal tract of MM patients",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Solanales|f__Solanaceae|s__Nicotianoideae|g__Nicotiana|s__Nicotiana otophora,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|841;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843488|909930|904;1783272|1239|526524|526525|128827|1472649;1783272|1239|186801|3085636|186803|830;33090|35493|3398|4069|4070|424554|4085|4091;1783272|1239|526524|526525|128827|174708,Complete,Atrayees
bsdb:31678982/3/2,31678982,case-control,31678982,10.12659/MSM.919988,NA,"Zhang B., Gu J., Liu J., Huang B. , Li J.",Fecal Microbiota Taxonomic Shifts in Chinese Multiple Myeloma Patients Analyzed by Quantitative Polimerase Chain Reaction (QPCR) and 16S rRNA High-Throughput Sequencing,Medical science monitor : international medical journal of experimental and clinical research,2019,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Multiple myeloma,EFO:0001378,healthy control,Multiple Myeloma patient,"patient diagnosis with multiple myeloma and no other disease validated to affect intestinal microbial including digestive disease like liver cirrhosis, liver cancer, inflammatory bowel disease, and irritable bowel syndrome; systemic disease like diabetes and hypertension and thyroid disease; no treatment including antibiotics, chemotherapy, plasma exchange or bone marrow transplant; no cold, fever or other infections within 3 months before sampling with administrated antibacterial drugs, gastrointestinal motility drugs or micro-ecological conditioning agents like eating and living habit change 1 week before sampling",17,40,3 months,16S,34,Illumina,relative abundances,Metastats,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 7 & text,4 July 2023,Atrayees,"Atrayees,WikiWorks","Genus with significant difference between Multiple Myeloma group and healthy control group was selected, followed by ordering according to the abundance in the intestinal tract of MM patients",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptoclostridiaceae|g__Peptoclostridium,1783272|1239|186801|3082720|3120161|1481960,Complete,Atrayees
bsdb:31678982/4/1,31678982,case-control,31678982,10.12659/MSM.919988,NA,"Zhang B., Gu J., Liu J., Huang B. , Li J.",Fecal Microbiota Taxonomic Shifts in Chinese Multiple Myeloma Patients Analyzed by Quantitative Polimerase Chain Reaction (QPCR) and 16S rRNA High-Throughput Sequencing,Medical science monitor : international medical journal of experimental and clinical research,2019,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Multiple myeloma,EFO:0001378,healthy relatives control,Multiple Myeloma patient,"patient diagnosis with multiple myeloma and no other disease validated to affect intestinal microbial including digestive disease like liver cirrhosis, liver cancer, inflammatory bowel disease, and irritable bowel syndrome; systemic disease like diabetes and hypertension and thyroid disease; no treatment including antibiotics, chemotherapy, plasma exchange or bone marrow transplant; no cold, fever or other infections within 3 months before sampling with administrated antibacterial drugs, gastrointestinal motility drugs or micro-ecological conditioning agents like eating and living habit change 1 week before sampling",21,21,3 months,16S,34,RT-qPCR,relative abundances,Metastats,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 8 and text,10 January 2021,William Lam,"WikiWorks,Atrayees",Intestinal Microbial detection in Multiple Myeloma patients and their family members using Quantitative Reverse Transcription Polymerase Chain Reaction,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum",3379134|1224|1236|72274|135621|286|287;1783272|1239|186801|186802|216572|1535,Complete,Atrayees
bsdb:31682463/1/1,31682463,"cross-sectional observational, not case-control",31682463,10.1164/rccm.201905-1016OC,https://pubmed.ncbi.nlm.nih.gov/31682463/,"Yang L., Dunlap D.G., Qin S., Fitch A., Li K., Koch C.D., Nouraie M., DeSensi R., Ho K.S., Martinson J.J., Methé B. , Morris A.",Alterations in Oral Microbiota in HIV Are Related to Decreased Pulmonary Function,American journal of respiratory and critical care medicine,2020,"HIV, lung function, microbiome, saliva, stool",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,HIV infection,EFO:0000764,HIV-uninfected individuals,HIV+ individuals,People with HIV,93,75,5 days,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 1 D,15 December 2021,Joyessa,"Joyessa,Claregrieve1,WikiWorks",Differential abundance in saliva of HIV- individuals vs HIV+ individuals,decreased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,p__Candidatus Absconditibacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. 2-3,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio sp.",3379134|29547|3031852|213849|72294|194;3379134|976|117743|200644|49546|1016;3384189|32066|203490|203491|203492|848;3379134|1224|28216|206351|481|482;1783272|1239|186801|3085636|186803|265975;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|2005525|195950;221235;3379134|1224|28216|206351|481;3379134|976|200643|171549|171552|838|1486938;1783272|1239|186801|3085636|186803|830|28121,Complete,Claregrieve1
bsdb:31682463/1/2,31682463,"cross-sectional observational, not case-control",31682463,10.1164/rccm.201905-1016OC,https://pubmed.ncbi.nlm.nih.gov/31682463/,"Yang L., Dunlap D.G., Qin S., Fitch A., Li K., Koch C.D., Nouraie M., DeSensi R., Ho K.S., Martinson J.J., Methé B. , Morris A.",Alterations in Oral Microbiota in HIV Are Related to Decreased Pulmonary Function,American journal of respiratory and critical care medicine,2020,"HIV, lung function, microbiome, saliva, stool",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,HIV infection,EFO:0000764,HIV-uninfected individuals,HIV+ individuals,People with HIV,93,75,5 days,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 1 D,16 December 2021,Joyessa,"Joyessa,Claregrieve1,WikiWorks",Differential microbial abundance in saliva of HIV- individuals vs HIV+ individuals,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:31682463/2/1,31682463,"cross-sectional observational, not case-control",31682463,10.1164/rccm.201905-1016OC,https://pubmed.ncbi.nlm.nih.gov/31682463/,"Yang L., Dunlap D.G., Qin S., Fitch A., Li K., Koch C.D., Nouraie M., DeSensi R., Ho K.S., Martinson J.J., Methé B. , Morris A.",Alterations in Oral Microbiota in HIV Are Related to Decreased Pulmonary Function,American journal of respiratory and critical care medicine,2020,"HIV, lung function, microbiome, saliva, stool",Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,"Nicotine dependence,Smoking behavior","EFO:0003768,EFO:0004318",HIV+ non-smokers,HIV+ smokers,People with HIV who currently smoke cigarettes,26,23,5 days,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 2E,15 December 2021,Joyessa,"Joyessa,Claregrieve1,WikiWorks",Differential bacterial abundance in oral samples from HIV+ individuals by smoking status,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",3379134|976|200643|171549|171552|1283313;3379134|976|117743|200644|2762318|59735;3379134|29547|3031852|213849|72294|194;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|43994;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|838;3379134|1224|28216|206351|481;3379134|1224|1236|135625|712,Complete,Claregrieve1
bsdb:31682463/2/2,31682463,"cross-sectional observational, not case-control",31682463,10.1164/rccm.201905-1016OC,https://pubmed.ncbi.nlm.nih.gov/31682463/,"Yang L., Dunlap D.G., Qin S., Fitch A., Li K., Koch C.D., Nouraie M., DeSensi R., Ho K.S., Martinson J.J., Methé B. , Morris A.",Alterations in Oral Microbiota in HIV Are Related to Decreased Pulmonary Function,American journal of respiratory and critical care medicine,2020,"HIV, lung function, microbiome, saliva, stool",Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,"Nicotine dependence,Smoking behavior","EFO:0003768,EFO:0004318",HIV+ non-smokers,HIV+ smokers,People with HIV who currently smoke cigarettes,26,23,5 days,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 2E,16 December 2021,Joyessa,"Joyessa,Claregrieve1,WikiWorks",Differential bacterial abundance in oral samples from HIV+ individuals by smoking status,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|84998|84999|1643824|1380;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:31682463/3/1,31682463,"cross-sectional observational, not case-control",31682463,10.1164/rccm.201905-1016OC,https://pubmed.ncbi.nlm.nih.gov/31682463/,"Yang L., Dunlap D.G., Qin S., Fitch A., Li K., Koch C.D., Nouraie M., DeSensi R., Ho K.S., Martinson J.J., Methé B. , Morris A.",Alterations in Oral Microbiota in HIV Are Related to Decreased Pulmonary Function,American journal of respiratory and critical care medicine,2020,"HIV, lung function, microbiome, saliva, stool",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Abnormality on pulmonary function testing,HP:0030878,HIV+ patients with normal DLCO,HIV+ patients with reduced DLCO,HIV+ patients with DLCO% predicted <80%,38,37,5 days,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3 I,16 December 2021,Joyessa,"Joyessa,Claregrieve1,WikiWorks",Differential microbial abundance between reduced DLCO HIV+ patients and normal DLCO HIV+ patients,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:31682463/3/2,31682463,"cross-sectional observational, not case-control",31682463,10.1164/rccm.201905-1016OC,https://pubmed.ncbi.nlm.nih.gov/31682463/,"Yang L., Dunlap D.G., Qin S., Fitch A., Li K., Koch C.D., Nouraie M., DeSensi R., Ho K.S., Martinson J.J., Methé B. , Morris A.",Alterations in Oral Microbiota in HIV Are Related to Decreased Pulmonary Function,American journal of respiratory and critical care medicine,2020,"HIV, lung function, microbiome, saliva, stool",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Abnormality on pulmonary function testing,HP:0030878,HIV+ patients with normal DLCO,HIV+ patients with reduced DLCO,HIV+ patients with DLCO% predicted <80%,38,37,5 days,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 3I,16 December 2021,Joyessa,"Joyessa,Claregrieve1,Merit,WikiWorks",Differential microbial abundance between reduced DLCO HIV+ patients and normal DLCO HIV+ patients,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp.,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales",3379134|976|200643|171549|171552|1283313;3379134|976|117743|200644|49546|1016;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|1164882;1783272|1239|1737404|1737405|1570339|543311;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|1213720;3379134|1224|28216|206351|481;3379134|976|200643|171549|171552;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481|482|192066;3379134|1224|28216|206351|481;3379134|1224|28216|206351;1783272|1239|1737404|1737405|1570339|543311|1944660;3384189|32066|203490|203491|203492;3384189|32066|203490|203491,Complete,Claregrieve1
bsdb:31686318/1/1,31686318,laboratory experiment,31686318,10.1007/s11427-019-9540-y,NA,"Li J., Rui J., Li Y., Tang N., Zhan S., Jiang J. , Li X.",Ambient temperature alters body size and gut microbiota of Xenopus tropicalis,Science China. Life sciences,2020,"Xenopus tropicalis, body size, gut microbiota, temperature, thermal adaptation",Experiment 1,China,Xenopus tropicalis,Midgut,UBERON:0001045,Temperature,EFO:0001702,Cool Gut,Warm Gut,Xenopus tropicalis gut microbiota response to warm environmental conditions,23,28,NA,16S,45,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table S4 (Genus level),12 October 2023,Chikamso,"Chikamso,Peace Sandy,Folakunmi,WikiWorks",Different abundance of gut microbiota between warm (group 1) and cool (group 0) environment (Warm Gut vs. Cool Gut),increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Thalassospiraceae|g__Thalassospira",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|186802|216572|244127;1783272|1239|526524|526525|2810280|100883;3379134|976|200643|171549|2005525|375288;3379134|1224|28211|204441|2844866|168934,Complete,Folakunmi
bsdb:31686318/1/2,31686318,laboratory experiment,31686318,10.1007/s11427-019-9540-y,NA,"Li J., Rui J., Li Y., Tang N., Zhan S., Jiang J. , Li X.",Ambient temperature alters body size and gut microbiota of Xenopus tropicalis,Science China. Life sciences,2020,"Xenopus tropicalis, body size, gut microbiota, temperature, thermal adaptation",Experiment 1,China,Xenopus tropicalis,Midgut,UBERON:0001045,Temperature,EFO:0001702,Cool Gut,Warm Gut,Xenopus tropicalis gut microbiota response to warm environmental conditions,23,28,NA,16S,45,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Table S4 (Genus level),12 October 2023,Chikamso,"Chikamso,OdigiriGreat,Chinelsy,Peace Sandy,Folakunmi,WikiWorks",Different abundance of gut microbiota between warm (group 1) and cool (group 0) environment (Warm Gut vs. Cool Gut),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Anoxybacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium",3379134|1224|1236|91347|543|544;1783272|1239|91061|1385|3120669|150247;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|3085636|186803|653683;1783272|1239|186801|3082720|186804|1501226;3379134|1224|1236|2887326|468|469;3379134|1224|28216|80840|75682|29580,Complete,Folakunmi
bsdb:31696774/1/1,31696774,prospective cohort,31696774,10.1080/19490976.2019.1681861,https://pubmed.ncbi.nlm.nih.gov/31696774/,"Astbury S., Atallah E., Vijay A., Aithal G.P., Grove J.I. , Valdes A.M.",Lower gut microbiome diversity and higher abundance of proinflammatory genus <i>Collinsella</i> are associated with biopsy-proven nonalcoholic steatohepatitis,Gut microbes,2020,"Collinsella, Fatty liver, cirrhosis, microbiome, nonalcoholic steatohepatitis",Experiment 1,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic steatohepatitis,EFO:1001249,Healthy controls,Individuals diagnosed with  Nonalcoholic steatohepatitis (without cirrhosis),"Individuals diagnosed with  Nonalcoholic steatohepatitis (without cirrhosis); The Fatty Liver Inhibition of Progression (FLIP) Consortium algorithm was used as a diagnostic indicator where the histological diagnosis of NASH requires the presence of steatosis, ballooning, and lobular inflammation",76,40,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 4,11 August 2021,Madhubani Dey,"Madhubani Dey,WikiWorks",Increased abundance of bacterial communities in individuals diagnosed with Nonalcoholic steatohepatitis (without cirrhosis),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae",1783272|201174|1760|2037|2049|1654;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|1898203;3379134|1224|28211|204441|41295,Complete,Atrayees
bsdb:31696774/1/2,31696774,prospective cohort,31696774,10.1080/19490976.2019.1681861,https://pubmed.ncbi.nlm.nih.gov/31696774/,"Astbury S., Atallah E., Vijay A., Aithal G.P., Grove J.I. , Valdes A.M.",Lower gut microbiome diversity and higher abundance of proinflammatory genus <i>Collinsella</i> are associated with biopsy-proven nonalcoholic steatohepatitis,Gut microbes,2020,"Collinsella, Fatty liver, cirrhosis, microbiome, nonalcoholic steatohepatitis",Experiment 1,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic steatohepatitis,EFO:1001249,Healthy controls,Individuals diagnosed with  Nonalcoholic steatohepatitis (without cirrhosis),"Individuals diagnosed with  Nonalcoholic steatohepatitis (without cirrhosis); The Fatty Liver Inhibition of Progression (FLIP) Consortium algorithm was used as a diagnostic indicator where the histological diagnosis of NASH requires the presence of steatosis, ballooning, and lobular inflammation",76,40,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 4,11 August 2021,Madhubani Dey,"Madhubani Dey,Merit,WikiWorks",Decreased abundance of bacterial communities in individuals diagnosed with Nonalcoholic steatohepatitis (without cirrhosis),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptoclostridiaceae|g__Peptoclostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005519|397864;3379134|200940|3031449|213115|194924|872;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|2485925;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|577309;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|3082720|3120161|1481960;3379134|976|200643|171549|171551;1783272|1239|186801|3082720|186804|1505652;3379134|976|200643|171549|1853231,Complete,Atrayees
bsdb:31696774/2/1,31696774,prospective cohort,31696774,10.1080/19490976.2019.1681861,https://pubmed.ncbi.nlm.nih.gov/31696774/,"Astbury S., Atallah E., Vijay A., Aithal G.P., Grove J.I. , Valdes A.M.",Lower gut microbiome diversity and higher abundance of proinflammatory genus <i>Collinsella</i> are associated with biopsy-proven nonalcoholic steatohepatitis,Gut microbes,2020,"Collinsella, Fatty liver, cirrhosis, microbiome, nonalcoholic steatohepatitis",Experiment 2,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic steatohepatitis,EFO:1001249,Healthy controls,Individuals diagnosed with Nonalcoholic steatohepatitis (NASH) with cirrhosis,"Individuals diagnosed with Nonalcoholic steatohepatitis (NASH) with cirrhosis; The Fatty Liver Inhibition of Progression (FLIP) Consortium algorithm was used as a diagnostic indicator where the histological diagnosis of NASH requires the presence of steatosis, ballooning, and lobular inflammation; Fibrosis was scored following the CRN grading system54 by a single pathologist.",76,25,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 4,11 August 2021,Madhubani Dey,"Madhubani Dey,WikiWorks",Increased abundance of bacterial communities in individuals diagnosed with Nonalcoholic steatohepatitis (NASH) with cirrhosis,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",1783272|201174|1760|2037|2049|1654;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|3085636|186803|1506553,Complete,Atrayees
bsdb:31696774/2/2,31696774,prospective cohort,31696774,10.1080/19490976.2019.1681861,https://pubmed.ncbi.nlm.nih.gov/31696774/,"Astbury S., Atallah E., Vijay A., Aithal G.P., Grove J.I. , Valdes A.M.",Lower gut microbiome diversity and higher abundance of proinflammatory genus <i>Collinsella</i> are associated with biopsy-proven nonalcoholic steatohepatitis,Gut microbes,2020,"Collinsella, Fatty liver, cirrhosis, microbiome, nonalcoholic steatohepatitis",Experiment 2,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic steatohepatitis,EFO:1001249,Healthy controls,Individuals diagnosed with Nonalcoholic steatohepatitis (NASH) with cirrhosis,"Individuals diagnosed with Nonalcoholic steatohepatitis (NASH) with cirrhosis; The Fatty Liver Inhibition of Progression (FLIP) Consortium algorithm was used as a diagnostic indicator where the histological diagnosis of NASH requires the presence of steatosis, ballooning, and lobular inflammation; Fibrosis was scored following the CRN grading system54 by a single pathologist.",76,25,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 4,11 August 2021,Madhubani Dey,"Madhubani Dey,Merit,WikiWorks",Decreased abundance of bacterial communities in individuals diagnosed with Nonalcoholic steatohepatitis (NASH) with cirrhosis,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptoclostridiaceae|g__Peptoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__Ruminiclostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3082720|3120161|1481960;1783272|1239|186801|186802|216572|1508657|2053608;1783272|1239|186801|3082720|186804|1505652;3379134|976|200643|171549|171551;3379134|976|200643|171549|1853231,Complete,Atrayees
bsdb:31699813/1/1,31699813,"cross-sectional observational, not case-control",31699813,10.1136/annrheumdis-2019-215743,NA,"Kishikawa T., Maeda Y., Nii T., Motooka D., Matsumoto Y., Matsushita M., Matsuoka H., Yoshimura M., Kawada S., Teshigawara S., Oguro E., Okita Y., Kawamoto K., Higa S., Hirano T., Narazaki M., Ogata A., Saeki Y., Nakamura S., Inohara H., Kumanogoh A., Takeda K. , Okada Y.",Metagenome-wide association study of gut microbiome revealed novel aetiology of rheumatoid arthritis in the Japanese population,Annals of the rheumatic diseases,2020,"autoimmune diseases, gene polymorphism, rheumatoid arthritis",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Rheumatoid arthritis,EFO:0000685,healthy controls,rheumatoid arthritis,Patients with RA,42,82,3 months,WMS,NA,Illumina,relative abundances,PERMANOVA,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 1,15 March 2023,Nice25,"Nice25,WikiWorks",Taxonomic differences of fecal microbiota in RA and healthy groups.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella corporis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella marshii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii",1783272|201174|1760|85004|31953|2701;1783272|201174|1760|85004|31953|2701|2702;3379134|976|200643|171549|171551|836|322095;3379134|976|200643|171549|171552|838|419005;3379134|976|200643|171549|171552|838|28128;3379134|976|200643|171549|171552|838|28129;3379134|976|200643|171549|171552|838|28130;3379134|976|200643|171549|171552|2974257|189722;3379134|976|200643|171549|815|909656|671267,Complete,Claregrieve1
bsdb:31705027/1/1,31705027,case-control,31705027,10.1038/s41598-019-52894-z,NA,"Ventura R.E., Iizumi T., Battaglia T., Liu M., Perez-Perez G.I., Herbert J. , Blaser M.J.",Gut microbiome of treatment-naïve MS patients of different ethnicities early in disease course,Scientific reports,2019,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Relapsing-remitting multiple sclerosis,EFO:0003929,Healthy Controls,Caucasian Americans (CA),Individuals diagnosed with relapsing-remitting multiple sclerosis (MS) who were Caucasian Americans,15,15,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,ethnic group,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2D,3 October 2024,MyleeeA,"MyleeeA,WikiWorks",Differential abundance of taxa in Caucasian MS and control samples.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",3379134|74201|203494|48461;3379134|74201;3379134|74201|203494|48461|203557;3379134|74201|203494;1783272|1239|186801|186802|31979|1485;3379134|74201|203494|48461|1647988|239934,Complete,ChiomaBlessing
bsdb:31705027/2/1,31705027,case-control,31705027,10.1038/s41598-019-52894-z,NA,"Ventura R.E., Iizumi T., Battaglia T., Liu M., Perez-Perez G.I., Herbert J. , Blaser M.J.",Gut microbiome of treatment-naïve MS patients of different ethnicities early in disease course,Scientific reports,2019,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Relapsing-remitting multiple sclerosis,EFO:0003929,Healthy Controls,Hispanic Americans (HA),Individuals diagnosed with relapsing-remitting multiple sclerosis (MS) who were Hispanic Americans by Ethnicity,15,16,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,ethnic group,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2E,4 October 2024,MyleeeA,"MyleeeA,WikiWorks",Differential abundance of taxa's that were significantly enriched in Hispanic MS and control samples using linear discriminant analysis (LDA) score of differences by LDA effect size (LEfSe),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485;1783272|1239|91061;1783272|1239|186801|3085636|186803|189330;1783272|1239|526524|526525|128827|61170;1783272|201174|84998|1643822|1643826|447020,Complete,ChiomaBlessing
bsdb:31705027/2/2,31705027,case-control,31705027,10.1038/s41598-019-52894-z,NA,"Ventura R.E., Iizumi T., Battaglia T., Liu M., Perez-Perez G.I., Herbert J. , Blaser M.J.",Gut microbiome of treatment-naïve MS patients of different ethnicities early in disease course,Scientific reports,2019,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Relapsing-remitting multiple sclerosis,EFO:0003929,Healthy Controls,Hispanic Americans (HA),Individuals diagnosed with relapsing-remitting multiple sclerosis (MS) who were Hispanic Americans by Ethnicity,15,16,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,ethnic group,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2E,4 October 2024,MyleeeA,"MyleeeA,WikiWorks",Differential abundance of taxa's that were significantly enriched in Hispanic MS and control samples using linear discriminant analysis (LDA) score of differences by LDA effect size (LEfSe),decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|28050;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|201174|84998|1643822|1643826|84108;3379134|976|200643|171549|2005473,Complete,ChiomaBlessing
bsdb:31705027/3/1,31705027,case-control,31705027,10.1038/s41598-019-52894-z,NA,"Ventura R.E., Iizumi T., Battaglia T., Liu M., Perez-Perez G.I., Herbert J. , Blaser M.J.",Gut microbiome of treatment-naïve MS patients of different ethnicities early in disease course,Scientific reports,2019,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Relapsing-remitting multiple sclerosis,EFO:0003929,Healthy Controls,African Americans (AA),Individuals diagnosed with relapsing-remitting multiple sclerosis (MS) who were African Americans by Ethnicity,14,14,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,ethnic group,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2F,4 October 2024,MyleeeA,"MyleeeA,WikiWorks",Differential abundance of taxa's that were significantly enriched in African American MS and control samples using linear discriminant analysis (LDA) score of differences by LDA effect size (LEfSe),increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia",1783272|201174|84998|1643822|1643826|447020;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998,Complete,ChiomaBlessing
bsdb:31705027/4/1,31705027,case-control,31705027,10.1038/s41598-019-52894-z,NA,"Ventura R.E., Iizumi T., Battaglia T., Liu M., Perez-Perez G.I., Herbert J. , Blaser M.J.",Gut microbiome of treatment-naïve MS patients of different ethnicities early in disease course,Scientific reports,2019,NA,Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Relapsing-remitting multiple sclerosis,EFO:0003929,Healthy Controls,Multiple Sclerosis (MS),"All treatment-naïve Multiple Sclerosis subjects who were diagnosed within 6 months of the specimen collection. They subjects included Caucasian American, Hispanic American and African American.",24,24,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,ethnic group",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,4 October 2024,MyleeeA,"MyleeeA,WikiWorks",Differential abundance of taxa in the Multiple Sclerosis and control subjects from Whole Genome Sequencing (WGS) analysis as determined by LDA effect size (LEfSe).,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis|s__Anaerofustis stercorihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. KLE 1755,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 2_2_44A,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 6_1_45,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. 3_1_31,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 3_1_57FAA_CT1,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 5_1_57FAA,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp. 4_3_54A2FAA,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] methylpentosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas nexilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum",1783272|201174|84998|1643822|1643826|447020|446660;3379134|976|200643|171549|171550|239759|328813;1783272|1239|186801|186802|186806|264995|214853;1783272|1239|186801|186802|216572|244127|169435;1783272|1239|186801|3085636|186803|572511|33035;1783272|1239|186801|186802|31979|1485|1226325;1783272|1239|909932|1843489|31977|39948|218538;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|3085636|186803|2719313|333367;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|2719313|358743;1783272|1239|186801|3085636|186803|2719313|1531;1783272|1239|526524|526525|128827|457422;1783272|1239|526524|526525|128827|469614;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|186806|1730|457402;1783272|201174|1760|85004|31953|2701|2702;1783272|201174|84998|1643822|1643826|644652|471189;3379134|976|200643|171549|171552|2974257|386414;1783272|1239|186801|3085636|186803|1649459|154046;1783272|1239|186801|3082720|186804|1505657|261299;1783272|1239|186801|3085636|186803|658086;1783272|1239|186801|3085636|186803|658085;1783272|1239|91061|186826|1300|1357|1358;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3082720|186804|1257|1261;3379134|976|200643|171549|171551|836|28123;3379134|976|200643|171549|171551|836|281920;3379134|976|200643|171549|171552|838|28125;3379134|976|200643|171549|171552|838|28130;1783272|1239|186801|186802|216572|1263|457412;1783272|1239|91061|186826|1300|1301|1309;1783272|1239|186801|186802|216572|292632|665956;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|186801|186802|31979|1485|1522;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|186802|216572|84026;1783272|1239|186801|3085636|186803|2005355|29361;1783272|1239|186801|3085636|186803|2941495|1512,Complete,ChiomaBlessing
bsdb:31705027/4/2,31705027,case-control,31705027,10.1038/s41598-019-52894-z,NA,"Ventura R.E., Iizumi T., Battaglia T., Liu M., Perez-Perez G.I., Herbert J. , Blaser M.J.",Gut microbiome of treatment-naïve MS patients of different ethnicities early in disease course,Scientific reports,2019,NA,Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Relapsing-remitting multiple sclerosis,EFO:0003929,Healthy Controls,Multiple Sclerosis (MS),"All treatment-naïve Multiple Sclerosis subjects who were diagnosed within 6 months of the specimen collection. They subjects included Caucasian American, Hispanic American and African American.",24,24,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,ethnic group",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,4 October 2024,MyleeeA,"MyleeeA,WikiWorks",Differential abundance of taxa in the Multiple Sclerosis and control subjects from Whole Genome Sequencing (WGS) analysis as determined by LDA effect size (LEfSe).,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium 1_1_47,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis",3379134|1224|28216|80840|469610;3379134|1224|1236|135625|712|724|729;3379134|976|200643|171549|171550|239759|1288121;3379134|976|200643|171549|815|816|371601;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|2005519|397864|487174,Complete,ChiomaBlessing
bsdb:31719139/1/3,31719139,"cross-sectional observational, not case-control",31719139,https://doi.org/10.1128/msystems.00438-19,https://pubmed.ncbi.nlm.nih.gov/31719139/,"Gupta A., Dhakan D.B., Maji A., Saxena R., P K V.P., Mahajan S., Pulikkan J., Kurian J., Gomez A.M., Scaria J., Amato K.R., Sharma A.K. , Sharma V.K.","Association of Flavonifractor plautii, a Flavonoid-Degrading Bacterium, with the Gut Microbiome of Colorectal Cancer Patients in India",mSystems,2019,"Flavonifractor plautii, biomarkers, colorectal cancer, gut microbiome",Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy control,Colorectal cancer patients,Indians who are colorectal cancer patients,30,30,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 3,"Text, Figure 2, Table S3",27 March 2023,Atrayees,"Atrayees,Claregrieve1,WikiWorks",Species observed to be significantly associated with CRC or healthy samples.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter hominis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus gallinarum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus vaginalis,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|815|816|28111;3379134|29547|3031852|213849|72294|194|76517;3379134|1224|1236|91347|543|544|545;1783272|1239|91061|186826|81852|1350|1353;1783272|1239|91061|1385|539738|1378|29391;3379134|1224|1236|91347|543|570|571;1783272|1239|91061|186826|33958|2742598|1633;3366610|28890|183925|2158|2159|2172|2173;3379134|976|200643|171549|1853231|283168|28118;3379134|1224|28216|80840|995019|577310|487175;3379134|976|200643|171549|171551|836|281920;3379134|976|200643|171549|171552|838|28125;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|91061|186826|1300|1301|1305;3379134|976|200643|171549|815|816|626929;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|329854;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|216572|946234|292800;3379134|976|200643|171549|2005525|375288|823;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|186801|3082720|186804|1257|341694,Complete,Claregrieve1
bsdb:31719139/1/4,31719139,"cross-sectional observational, not case-control",31719139,https://doi.org/10.1128/msystems.00438-19,https://pubmed.ncbi.nlm.nih.gov/31719139/,"Gupta A., Dhakan D.B., Maji A., Saxena R., P K V.P., Mahajan S., Pulikkan J., Kurian J., Gomez A.M., Scaria J., Amato K.R., Sharma A.K. , Sharma V.K.","Association of Flavonifractor plautii, a Flavonoid-Degrading Bacterium, with the Gut Microbiome of Colorectal Cancer Patients in India",mSystems,2019,"Flavonifractor plautii, biomarkers, colorectal cancer, gut microbiome",Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy control,Colorectal cancer patients,Indians who are colorectal cancer patients,30,30,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 4,"Text, Figure 2, Table S3",27 March 2023,Atrayees,"Atrayees,Claregrieve1,WikiWorks",Species observed to be significantly associated with CRC or healthy samples,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus fermentans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas testosteroni,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium varium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus pittmaniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus amylovorus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema succinifaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",1783272|1239|909932|1843488|909930|904|905;3379134|976|200643|171549|171550|239759|28117;1783272|1239|186801|3085636|186803|2569097|39488;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|820;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|1689;1783272|1239|186801|3085636|186803|3342669|45851;3379134|1224|28216|80840|80864|283|285;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|189330|88431;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|186802|186806|1730|39496;3384189|32066|203490|203491|203492|848|856;3379134|1224|1236|135625|712|724|249188;1783272|1239|91061|186826|33958|1578|1604;1783272|1239|909932|909929|1843491|52225|52226;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|91061|186826|1300|1301|68892;3379134|203691|203692|136|2845253|157|167;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|186802|216572|216851|853;1783272|1239|91061|186826|33958|2767887|1623;1783272|1239|909932|1843489|31977|906|907;1783272|1239|186801|3085636|186803|1766253|39491,Complete,Claregrieve1
bsdb:31727922/1/1,31727922,"cross-sectional observational, not case-control",31727922,10.1038/s41598-019-53041-4,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6856127/,"Half E., Keren N., Reshef L., Dorfman T., Lachter I., Kluger Y., Reshef N., Knobler H., Maor Y., Stein A., Konikoff F.M. , Gophna U.",Fecal microbiome signatures of pancreatic cancer patients,Scientific reports,2019,NA,Experiment 1,Israel,Homo sapiens,Feces,UBERON:0001988,Pancreatic carcinoma,EFO:0002618,Healthy control,Pancreatic cancer patients,Patients presenting with pancreatic cancer. The diagnosis was verified by histological samples obtained by EUS or by postoperative pathological assessment.,13,30,2 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2a,4 February 2021,Yu Wang,"Yu Wang,Fatima,Claregrieve1,WikiWorks",Bacterial taxa identified by LEfSe as differential between PC patients and healthy control subjects.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549;1783272|1239|909932|1843489|31977|906;3379134|976|200643|171549|1853231|283168;1783272|1239|909932|1843489|31977;1783272|1239|186801|3085636|186803|1898203,Complete,Claregrieve1
bsdb:31727922/1/2,31727922,"cross-sectional observational, not case-control",31727922,10.1038/s41598-019-53041-4,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6856127/,"Half E., Keren N., Reshef L., Dorfman T., Lachter I., Kluger Y., Reshef N., Knobler H., Maor Y., Stein A., Konikoff F.M. , Gophna U.",Fecal microbiome signatures of pancreatic cancer patients,Scientific reports,2019,NA,Experiment 1,Israel,Homo sapiens,Feces,UBERON:0001988,Pancreatic carcinoma,EFO:0002618,Healthy control,Pancreatic cancer patients,Patients presenting with pancreatic cancer. The diagnosis was verified by histological samples obtained by EUS or by postoperative pathological assessment.,13,30,2 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2a,4 February 2021,Yu Wang,"Yu Wang,Fatima,Claregrieve1,WikiWorks",Bacterial taxa identified by LEfSe as differential between PC patients and healthy control subjects.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,s__uncultured bacterium",1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|541000;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|31979|1485|1506;1783272|1239|186801|186802|216572|2485925;77133,Complete,Claregrieve1
bsdb:31727922/3/1,31727922,"cross-sectional observational, not case-control",31727922,10.1038/s41598-019-53041-4,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6856127/,"Half E., Keren N., Reshef L., Dorfman T., Lachter I., Kluger Y., Reshef N., Knobler H., Maor Y., Stein A., Konikoff F.M. , Gophna U.",Fecal microbiome signatures of pancreatic cancer patients,Scientific reports,2019,NA,Experiment 3,Israel,Homo sapiens,Feces,UBERON:0001988,Pancreatic carcinoma,EFO:0002618,NBO PC,BO PC,Bile duct-obstructed pancreatic cancer patients.,16,11,2 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3b,4 February 2021,Yu Wang,"Yu Wang,Fatima,WikiWorks",Taxa identified by LEfSe as differentiating between BO PC and NBO PC patients.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,1783272|1239|186801|3085636|186803|572511,Complete,Claregrieve1
bsdb:31727922/3/2,31727922,"cross-sectional observational, not case-control",31727922,10.1038/s41598-019-53041-4,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6856127/,"Half E., Keren N., Reshef L., Dorfman T., Lachter I., Kluger Y., Reshef N., Knobler H., Maor Y., Stein A., Konikoff F.M. , Gophna U.",Fecal microbiome signatures of pancreatic cancer patients,Scientific reports,2019,NA,Experiment 3,Israel,Homo sapiens,Feces,UBERON:0001988,Pancreatic carcinoma,EFO:0002618,NBO PC,BO PC,Bile duct-obstructed pancreatic cancer patients.,16,11,2 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3b,4 February 2021,Yu Wang,"Yu Wang,Fatima,Claregrieve1,WikiWorks",Taxa identified by LEfSe as differentiating between BO PC and NBO PC patients.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|909932|909929;1783272|1239|909932|1843489|31977;3379134|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:31727922/4/1,31727922,"cross-sectional observational, not case-control",31727922,10.1038/s41598-019-53041-4,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6856127/,"Half E., Keren N., Reshef L., Dorfman T., Lachter I., Kluger Y., Reshef N., Knobler H., Maor Y., Stein A., Konikoff F.M. , Gophna U.",Fecal microbiome signatures of pancreatic cancer patients,Scientific reports,2019,NA,Experiment 4,Israel,Homo sapiens,Feces,UBERON:0001988,Pancreatic carcinoma,EFO:0002618,Healthy control,NBO PC,Non-Bile duct-obstructed pancreatic cancer patients.,13,16,2 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3c,4 February 2021,Yu Wang,"Yu Wang,Fatima,Claregrieve1,WikiWorks",Taxa identified by LEfSe as differentiating between healthy controls and non bile-duct obstructed pancreatic cancer patients.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. 001,k__Bacillati|p__Mycoplasmatota|c__Mollicutes",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|541000;1783272|1239|186801|186802|31979|1485|1970093;1783272|544448|31969,Complete,Claregrieve1
bsdb:31727922/4/2,31727922,"cross-sectional observational, not case-control",31727922,10.1038/s41598-019-53041-4,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6856127/,"Half E., Keren N., Reshef L., Dorfman T., Lachter I., Kluger Y., Reshef N., Knobler H., Maor Y., Stein A., Konikoff F.M. , Gophna U.",Fecal microbiome signatures of pancreatic cancer patients,Scientific reports,2019,NA,Experiment 4,Israel,Homo sapiens,Feces,UBERON:0001988,Pancreatic carcinoma,EFO:0002618,Healthy control,NBO PC,Non-Bile duct-obstructed pancreatic cancer patients.,13,16,2 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3c,4 February 2021,Yu Wang,"Claregrieve1,Fatima,Yu Wang,WikiWorks",Taxa identified by LEfSe as differentiating between healthy controls and non bile-duct obstructed pancreatic cancer patients.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549,Complete,Claregrieve1
bsdb:31729407/1/1,31729407,time series / longitudinal observational,31729407,10.1038/s41598-019-53073-w,NA,"Laheij A.M.G.A., Raber-Durlacher J.E., Koppelmans R.G.A., Huysmans M.D.N.J.M., Potting C., van Leeuwen S.J.M., Hazenberg M.D., Brennan M.T., von Bültzingslöwen I., Johansson J.E., de Soet J.J., Haverman T.M., Buijs M.J., Brandt B.W., Rozema F.R., Blijlevens N.M.A. , Zaura E.",Microbial changes in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients,Scientific reports,2019,NA,Experiment 1,Netherlands,Homo sapiens,Mouth,UBERON:0000165,Oral mucositis,EFO:1001904,no ulcerative oral mucositis,ulcerative oral mucositis,patient developed uclerative oral mucositis,31,20,NA,16S,4,RT-qPCR,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,10 January 2021,William Lam,WikiWorks,Minimum entropy decomposition nodes (MEDs) that significantly discriminate multiple myeloma patients that did not develop uclerative oral mucositis and patients that did develop uclerative oral mucositis before auto stem cell transplant identified by LEfSe,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|1385|90964|1279;3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|171552|838,Complete,Atrayees
bsdb:31729407/1/2,31729407,time series / longitudinal observational,31729407,10.1038/s41598-019-53073-w,NA,"Laheij A.M.G.A., Raber-Durlacher J.E., Koppelmans R.G.A., Huysmans M.D.N.J.M., Potting C., van Leeuwen S.J.M., Hazenberg M.D., Brennan M.T., von Bültzingslöwen I., Johansson J.E., de Soet J.J., Haverman T.M., Buijs M.J., Brandt B.W., Rozema F.R., Blijlevens N.M.A. , Zaura E.",Microbial changes in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients,Scientific reports,2019,NA,Experiment 1,Netherlands,Homo sapiens,Mouth,UBERON:0000165,Oral mucositis,EFO:1001904,no ulcerative oral mucositis,ulcerative oral mucositis,patient developed uclerative oral mucositis,31,20,NA,16S,4,RT-qPCR,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,10 January 2021,William Lam,WikiWorks,Minimum entropy decomposition nodes (MEDs) that significantly discriminate multiple myeloma patients that did not develop uclerative oral mucositis and patients that did develop uclerative oral mucositis before auto stem cell transplant identified by LEfSe,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",1783272|1239|91061|186826|1300|1301;1783272|201174|1760|2037|2049|1654,Complete,Atrayees
bsdb:31729407/2/1,31729407,time series / longitudinal observational,31729407,10.1038/s41598-019-53073-w,NA,"Laheij A.M.G.A., Raber-Durlacher J.E., Koppelmans R.G.A., Huysmans M.D.N.J.M., Potting C., van Leeuwen S.J.M., Hazenberg M.D., Brennan M.T., von Bültzingslöwen I., Johansson J.E., de Soet J.J., Haverman T.M., Buijs M.J., Brandt B.W., Rozema F.R., Blijlevens N.M.A. , Zaura E.",Microbial changes in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients,Scientific reports,2019,NA,Experiment 2,Netherlands,Homo sapiens,Mouth,UBERON:0000165,Oral mucositis,EFO:1001904,one and two weeks after stem cell transplant,pre- and three month after auto stem cell transplant,patient developed uclerative oral mucositis,31,20,NA,16S,4,RT-qPCR,relative abundances,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,text,10 January 2021,William Lam,"WikiWorks,Atrayees",Based on principle component analysis asses taxa were responsible for the observed microbial shifts over time in non-uclerative oral mucositis group,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp.",1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843489|31977|29465|39778;1783272|201174|1760|2037|2049|1654|29317;1783272|201174|1760|2037|2049|1654|55565;3379134|976|200643|171549|171552|838;3384189|32066|203490|203491|1129771|32067;1783272|1239|909932|1843489|31977|906|187326;1783272|1239|909932|1843489|31977|29465|1926307,Complete,Atrayees
bsdb:31729407/2/2,31729407,time series / longitudinal observational,31729407,10.1038/s41598-019-53073-w,NA,"Laheij A.M.G.A., Raber-Durlacher J.E., Koppelmans R.G.A., Huysmans M.D.N.J.M., Potting C., van Leeuwen S.J.M., Hazenberg M.D., Brennan M.T., von Bültzingslöwen I., Johansson J.E., de Soet J.J., Haverman T.M., Buijs M.J., Brandt B.W., Rozema F.R., Blijlevens N.M.A. , Zaura E.",Microbial changes in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients,Scientific reports,2019,NA,Experiment 2,Netherlands,Homo sapiens,Mouth,UBERON:0000165,Oral mucositis,EFO:1001904,one and two weeks after stem cell transplant,pre- and three month after auto stem cell transplant,patient developed uclerative oral mucositis,31,20,NA,16S,4,RT-qPCR,relative abundances,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,text,10 January 2021,William Lam,"WikiWorks,Atrayees",Based on principle component analysis asses taxa were responsible for the observed microbial shifts over time in non-uclerative oral mucositis group,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|2742598|1613;1783272|201174|1760|85004|31953|196081|230143,Complete,Atrayees
bsdb:31729407/3/1,31729407,time series / longitudinal observational,31729407,10.1038/s41598-019-53073-w,NA,"Laheij A.M.G.A., Raber-Durlacher J.E., Koppelmans R.G.A., Huysmans M.D.N.J.M., Potting C., van Leeuwen S.J.M., Hazenberg M.D., Brennan M.T., von Bültzingslöwen I., Johansson J.E., de Soet J.J., Haverman T.M., Buijs M.J., Brandt B.W., Rozema F.R., Blijlevens N.M.A. , Zaura E.",Microbial changes in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients,Scientific reports,2019,NA,Experiment 3,Netherlands,Homo sapiens,Mouth,UBERON:0000165,Oral mucositis,EFO:1001904,one and two weeks after stem cell transplant,pre- and three month after auto stem cell transplant,patient developed uclerative oral mucositis,31,20,NA,16S,4,RT-qPCR,relative abundances,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,text,10 January 2021,William Lam,"WikiWorks,Atrayees",Based on principle component analysis asses taxa were responsible for the observed microbial shifts over time in uclerative oral mucositis group,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis",1783272|1239|91061|186826|1300|1301|113107;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843489|31977|29465|39778;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049|1654|55565;1783272|1239|91061|1385|539738|1378|1379;1783272|1239|91061|1385|539738|1378|29391;1783272|1239|91061|1385|539738|1378|84135,Complete,Atrayees
bsdb:31729407/3/2,31729407,time series / longitudinal observational,31729407,10.1038/s41598-019-53073-w,NA,"Laheij A.M.G.A., Raber-Durlacher J.E., Koppelmans R.G.A., Huysmans M.D.N.J.M., Potting C., van Leeuwen S.J.M., Hazenberg M.D., Brennan M.T., von Bültzingslöwen I., Johansson J.E., de Soet J.J., Haverman T.M., Buijs M.J., Brandt B.W., Rozema F.R., Blijlevens N.M.A. , Zaura E.",Microbial changes in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients,Scientific reports,2019,NA,Experiment 3,Netherlands,Homo sapiens,Mouth,UBERON:0000165,Oral mucositis,EFO:1001904,one and two weeks after stem cell transplant,pre- and three month after auto stem cell transplant,patient developed uclerative oral mucositis,31,20,NA,16S,4,RT-qPCR,relative abundances,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,text,10 January 2021,William Lam,"WikiWorks,Atrayees",Based on principle component analysis asses taxa were responsible for the observed microbial shifts over time in uclerative oral mucositis group,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus caprae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus warneri,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis",1783272|1239|91061|1385|90964|1279|1280;1783272|1239|91061|1385|90964|1279|29380;1783272|1239|91061|1385|90964|1279|1282;1783272|1239|91061|1385|90964|1279|1292;1783272|201174|1760|85004|31953|196081|230143;1783272|1239|91061|186826|81852|1350|1351,Complete,Atrayees
bsdb:31729407/4/1,31729407,time series / longitudinal observational,31729407,10.1038/s41598-019-53073-w,NA,"Laheij A.M.G.A., Raber-Durlacher J.E., Koppelmans R.G.A., Huysmans M.D.N.J.M., Potting C., van Leeuwen S.J.M., Hazenberg M.D., Brennan M.T., von Bültzingslöwen I., Johansson J.E., de Soet J.J., Haverman T.M., Buijs M.J., Brandt B.W., Rozema F.R., Blijlevens N.M.A. , Zaura E.",Microbial changes in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients,Scientific reports,2019,NA,Experiment 4,Netherlands,Homo sapiens,Mouth,UBERON:0000165,Oral mucositis,EFO:1001904,low or no fungi load,0.1% or higher fungi load,patient developed uclerative oral mucositis,31,20,NA,16S,4,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text,10 January 2021,William Lam,"WikiWorks,Atrayees",Principle component analysis of salivary microbial profiles based on fungal load relative to bacterial 16s rDNA,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|201174|1760|85004|31953|196081;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|33958|1578,Complete,Atrayees
bsdb:31729407/4/2,31729407,time series / longitudinal observational,31729407,10.1038/s41598-019-53073-w,NA,"Laheij A.M.G.A., Raber-Durlacher J.E., Koppelmans R.G.A., Huysmans M.D.N.J.M., Potting C., van Leeuwen S.J.M., Hazenberg M.D., Brennan M.T., von Bültzingslöwen I., Johansson J.E., de Soet J.J., Haverman T.M., Buijs M.J., Brandt B.W., Rozema F.R., Blijlevens N.M.A. , Zaura E.",Microbial changes in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients,Scientific reports,2019,NA,Experiment 4,Netherlands,Homo sapiens,Mouth,UBERON:0000165,Oral mucositis,EFO:1001904,low or no fungi load,0.1% or higher fungi load,patient developed uclerative oral mucositis,31,20,NA,16S,4,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,text,10 January 2021,William Lam,"WikiWorks,Atrayees",Principle component analysis of salivary microbial profiles based on fungal load relative to bacterial 16s rDNA,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|909932|1843489|31977|29465;1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549|171552|838;3384189|32066|203490|203491|1129771|32067;1783272|1239|909932|1843489|31977|906;1783272|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:31735171/1/1,31735171,case-control,31735171,10.1186/s12887-019-1782-2,NA,"Li W., Zhu Y., Liao Q., Wang Z. , Wan C.",Characterization of gut microbiota in children with pulmonary tuberculosis,BMC pediatrics,2019,"16SrDNA, Children, Gut microbiota, Pulmonary tuberculosis",Experiment 1,NA,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,Healthy controls,PTB patients,Positive smear/culture or clinical‐radiological diagnosis per national guidelines,18,18,1 month,16S,34,Illumina,relative abundances,"T-Test,Mann-Whitney (Wilcoxon)",0.05,NA,NA,"age,sex design",antibiotic exposure,NA,increased,NA,increased,NA,NA,Signature 1,"Fig. 2, Fig. 3, Fig. 4",13 June 2025,Nuerteye,Nuerteye,"Fig 2: Family‐level barplots 
Fig 3: Genus‐level barplots 
Fig 4: Species‐level barplots",increased,NA,NA,Complete,NA
bsdb:31735171/1/2,31735171,case-control,31735171,10.1186/s12887-019-1782-2,NA,"Li W., Zhu Y., Liao Q., Wang Z. , Wan C.",Characterization of gut microbiota in children with pulmonary tuberculosis,BMC pediatrics,2019,"16SrDNA, Children, Gut microbiota, Pulmonary tuberculosis",Experiment 1,NA,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,Healthy controls,PTB patients,Positive smear/culture or clinical‐radiological diagnosis per national guidelines,18,18,1 month,16S,34,Illumina,relative abundances,"T-Test,Mann-Whitney (Wilcoxon)",0.05,NA,NA,"age,sex design",antibiotic exposure,NA,increased,NA,increased,NA,NA,Signature 2,"Fig. 2, Fig. 3, Fig. 4",13 June 2025,Nuerteye,Nuerteye,"Fig 2: Family‐level barplots 
Fig 3: Genus‐level barplots 
Fig 4: Species‐level barplots",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|1263,Complete,NA
bsdb:31738825/1/1,31738825,case-control,31738825,10.1167/iovs.19-27719,NA,"Dong X., Wang Y., Wang W., Lin P. , Huang Y.",Composition and Diversity of Bacterial Community on the Ocular Surface of Patients With Meibomian Gland Dysfunction,Investigative ophthalmology & visual science,2019,NA,Experiment 1,China,Homo sapiens,"Margin of eyelid,Conjunctival sac","UBERON:0034772,UBERON:0005908",Dry eye syndrome,EFO:1000906,Healthy controls,Meibomian Gland Dysfunction (MGD) Groups,Patients with diagnosis of  Meibomian Gland Dysfunction MGD,42,47,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Fig 3,16 October 2023,Mary Bearkland,"Mary Bearkland,Peace Sandy,WikiWorks","LEfSe analysis of the normal control group and the MGD groups. (B) Linear discriminant analysis scoring of biomarkers corresponding to (A), computed by the LEfSe tool. When the score of a taxon was >4.0 with P < 0.01, it was listed in the histogram, which showed all the biomarkers found from the domain to species level. “p”, “c”, “o”, “f”, “g”, and “s” referred to phylum, class, order, family, genus, and species, respectively. At the genus level, the biomarkers were Staphylococcus and Sphingomonas in the patients with MGD, and Corynebacterium in the controls. The length of the histogram represented the linear discriminate analysis values of the different taxa.",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas melonis",1783272|1239|91061|1385;1783272|1239|91061;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|1385|90964;1783272|1239;1783272|1239|91061|1385|90964|1279|1282;3379134|1224|28211|204457|41297|13687;3379134|1224|28211|204457|41297;3379134|1224|28211|204457;3379134|1224|28211|204457|41297|13687|152682,Complete,Peace Sandy
bsdb:31738825/1/2,31738825,case-control,31738825,10.1167/iovs.19-27719,NA,"Dong X., Wang Y., Wang W., Lin P. , Huang Y.",Composition and Diversity of Bacterial Community on the Ocular Surface of Patients With Meibomian Gland Dysfunction,Investigative ophthalmology & visual science,2019,NA,Experiment 1,China,Homo sapiens,"Margin of eyelid,Conjunctival sac","UBERON:0034772,UBERON:0005908",Dry eye syndrome,EFO:1000906,Healthy controls,Meibomian Gland Dysfunction (MGD) Groups,Patients with diagnosis of  Meibomian Gland Dysfunction MGD,42,47,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Fig 3,16 October 2023,Mary Bearkland,"Mary Bearkland,Peace Sandy,WikiWorks","LEfSe analysis of the normal control group and the MGD groups. (B) Linear discriminant analysis scoring of biomarkers corresponding to (A), computed by the LEfSe tool. When the score of a taxon was >4.0 with P < 0.01, it was listed in the histogram, which showed all the biomarkers found from the domain to species level. “p”, “c”, “o”, “f”, “g”, and “s” referred to phylum, class, order, family, genus, and species, respectively. At the genus level, the biomarkers were Staphylococcus and Sphingomonas in the patients with MGD, and Corynebacterium in the controls. The length of the histogram represented the linear discriminate analysis values of the different taxa.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium",1783272|201174|1760|85007|1653|1716;1783272|201174|1760|2037;1783272|201174;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716,Complete,Peace Sandy
bsdb:31749298/1/1,31749298,"cross-sectional observational, not case-control",31749298,10.1111/1471-0528.15981,NA,"Borgogna J.C., Shardell M.D., Santori E.K., Nelson T.M., Rath J.M., Glover E.D., Ravel J., Gravitt P.E., Yeoman C.J. , Brotman R.M.",The vaginal metabolome and microbiota of cervical HPV-positive and HPV-negative women: a cross-sectional analysis,BJOG : an international journal of obstetrics and gynaecology,2020,"16S rRNA gene amplicon sequencing, human papillomavirus, vaginal metabolome, vaginal microbiota",Experiment 1,United States of America,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ confirmed using Roche Linear Array HPV Genotyping Test,13,26,1 month,16S,123,Roche454,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,supplemental figure 3,10 January 2021,Cynthia Anderson,WikiWorks,The association between vaginal taxa and detection status as identified by LEfSE,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium|s__Atopobium sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus christensenii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus asaccharolyticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus vaginalis",1783272|201174|1760|85004|31953|2701|2702;1783272|201174|84998|1643822|1643826|84111;1783272|1239|91061|1385|539738|1378;1783272|201174|84998|84999|1643824|1380|1872650;1783272|1239|909932|1843489|31977;1783272|1239|91061|186826|186827|1375|87541;1783272|1239|1737404|1737405|1570339|162289|1258;1783272|1239|91061|186826|33958|2742598|1633,Complete,Fatima Zohra
bsdb:31749298/1/2,31749298,"cross-sectional observational, not case-control",31749298,10.1111/1471-0528.15981,NA,"Borgogna J.C., Shardell M.D., Santori E.K., Nelson T.M., Rath J.M., Glover E.D., Ravel J., Gravitt P.E., Yeoman C.J. , Brotman R.M.",The vaginal metabolome and microbiota of cervical HPV-positive and HPV-negative women: a cross-sectional analysis,BJOG : an international journal of obstetrics and gynaecology,2020,"16S rRNA gene amplicon sequencing, human papillomavirus, vaginal metabolome, vaginal microbiota",Experiment 1,United States of America,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ confirmed using Roche Linear Array HPV Genotyping Test,13,26,1 month,16S,123,Roche454,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,supplemental figure 3,10 January 2021,Cynthia Anderson,WikiWorks,The association between vaginal taxa and detection status as identified by LEfSE,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus jensenii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus",1783272|201174|1760|85004|31953;1783272|201174|84998|84999|1643824|2767327|82135;1783272|1239|91061|186826|33958|1578|109790;1783272|1239|91061|186826|33958|1578|47770,Complete,Fatima Zohra
bsdb:31752810/1/1,31752810,"cross-sectional observational, not case-control",31752810,10.1186/s12903-019-0947-6,NA,"Xi R., Wang R., Wang Y., Xiang Z., Su Z., Cao Z., Xu X., Zheng X. , Li J.",Comparative analysis of the oral microbiota between iron-deficiency anaemia (IDA) patients and healthy individuals by high-throughput sequencing,BMC oral health,2019,"High-throughput sequencing, Infective endocarditis, Iron-deficiency anaemia, Oral microbiota",Experiment 1,China,Homo sapiens,Dental plaque,UBERON:0016482,Iron deficiency anemia,HP:0001891,healthy control,iron deficiency anemia,patients with iron deficiency anemia,24,24,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,decreased,unchanged,decreased,NA,NA,Signature 1,"Figure 3b, 4b, Table S2",10 January 2021,Rimsha Azhar,WikiWorks,Comparison of bacterial taxonomy (>1% relative abundance) of samples between healthy controls and iron deficiency anemia (IDA) patients,increased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239;3379134|1224|1236|2887326|468|475;1783272|1239|91061|186826|1300|1357;3379134|1224|1236|72274|135621|286;1783272|1239|91061|186826|81852|1350;1783272|201174|1760|85006|1268|57493;1783272|1239|91061|186826|33958|1578,Complete,Claregrieve1
bsdb:31752810/1/2,31752810,"cross-sectional observational, not case-control",31752810,10.1186/s12903-019-0947-6,NA,"Xi R., Wang R., Wang Y., Xiang Z., Su Z., Cao Z., Xu X., Zheng X. , Li J.",Comparative analysis of the oral microbiota between iron-deficiency anaemia (IDA) patients and healthy individuals by high-throughput sequencing,BMC oral health,2019,"High-throughput sequencing, Infective endocarditis, Iron-deficiency anaemia, Oral microbiota",Experiment 1,China,Homo sapiens,Dental plaque,UBERON:0016482,Iron deficiency anemia,HP:0001891,healthy control,iron deficiency anemia,patients with iron deficiency anemia,24,24,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,decreased,unchanged,decreased,NA,NA,Signature 2,"Figure 3b, 4b, Table S2",10 January 2021,Rimsha Azhar,WikiWorks,Comparison of bacterial taxonomy (>1% relative abundance) of samples between healthy controls and iron deficiency anemia (IDA) patients,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium",1783272|201174;1783272|201174|1760|85007|1653|1716;3379134|1224|28216|206351|481|482;3379134|1224|1236|135625|712|416916;3379134|1224|1236|135615|868|2717,Complete,Folakunmi
bsdb:31752810/2/1,31752810,"cross-sectional observational, not case-control",31752810,10.1186/s12903-019-0947-6,NA,"Xi R., Wang R., Wang Y., Xiang Z., Su Z., Cao Z., Xu X., Zheng X. , Li J.",Comparative analysis of the oral microbiota between iron-deficiency anaemia (IDA) patients and healthy individuals by high-throughput sequencing,BMC oral health,2019,"High-throughput sequencing, Infective endocarditis, Iron-deficiency anaemia, Oral microbiota",Experiment 2,China,Homo sapiens,Dental plaque,UBERON:0016482,Iron deficiency anemia,HP:0001891,healthy control,iron deficiency anemia,patients with iron deficiency anemia,24,24,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3.5,"age,sex",NA,NA,decreased,unchanged,decreased,NA,NA,Signature 1,Figure 5b,10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",LEfSe analysis of samples between healthy controls and iron deficiency anemia (IDA) patients,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae",1783272|1239|91061;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239;1783272|201174|1760|85006|1268|57493;1783272|1239|91061|186826;1783272|1239|91061|186826|1300|1357;3379134|1224|1236|2887326|468|475;3379134|1224|1236|2887326|468;1783272|1239|186801|3082720|186804;3379134|1224|1236|72274;3379134|1224|1236|72274|135621|286;1783272|1239|91061|186826|1300;3379134|1224|1236|72274|135621,Complete,Claregrieve1
bsdb:31752810/2/2,31752810,"cross-sectional observational, not case-control",31752810,10.1186/s12903-019-0947-6,NA,"Xi R., Wang R., Wang Y., Xiang Z., Su Z., Cao Z., Xu X., Zheng X. , Li J.",Comparative analysis of the oral microbiota between iron-deficiency anaemia (IDA) patients and healthy individuals by high-throughput sequencing,BMC oral health,2019,"High-throughput sequencing, Infective endocarditis, Iron-deficiency anaemia, Oral microbiota",Experiment 2,China,Homo sapiens,Dental plaque,UBERON:0016482,Iron deficiency anemia,HP:0001891,healthy control,iron deficiency anemia,patients with iron deficiency anemia,24,24,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3.5,"age,sex",NA,NA,decreased,unchanged,decreased,NA,NA,Signature 2,Figure 5b,10 January 2021,Rimsha Azhar,WikiWorks,LEfSe analysis of samples between healthy controls and iron deficiency anemia (IDA) patients,decreased,"k__Pseudomonadati|p__Campylobacterota,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Caldimonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes",3379134|29547;3379134|29547|3031852|213849;3379134|29547|3031852|213849|72294;3379134|29547|3031852|213849|72294|194;3379134|1224|1236|135615|868;3379134|1224|1236|135615;3379134|1224|1236|135615|868|2717;1783272|201174|1760|85006|1268|32207;3379134|1224|1236|135625|712|416916;3379134|1224|28216|80840|2975441|215579;3379134|1224|28216|80840;3379134|976|117743|200644|49546|1016;3379134|976|117743;3379134|976|117743|200644|49546;3379134|976|117743|200644;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481;3379134|1224|28216|206351;3379134|1224|28216;1783272|201174|1760|85007;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;1783272|201174;1783272|201174|1760,Complete,Claregrieve1
bsdb:31752810/3/1,31752810,"cross-sectional observational, not case-control",31752810,10.1186/s12903-019-0947-6,NA,"Xi R., Wang R., Wang Y., Xiang Z., Su Z., Cao Z., Xu X., Zheng X. , Li J.",Comparative analysis of the oral microbiota between iron-deficiency anaemia (IDA) patients and healthy individuals by high-throughput sequencing,BMC oral health,2019,"High-throughput sequencing, Infective endocarditis, Iron-deficiency anaemia, Oral microbiota",Experiment 3,China,Homo sapiens,Dental plaque,UBERON:0016482,Iron deficiency anemia,HP:0001891,iron deficiency anemia moderate,iron deficiency anemia severe,iron defiency anemia,16,8,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3.5,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5d,10 January 2021,Rimsha Azhar,WikiWorks,LEfSe analysis of samples between iron deficiency anemia moderate (IDA_m) and iron deficiency anemia severe (IDA_s) patients,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Porphyrobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales",1783272|201174|1760|85006|1268|57493;3379134|1224|28211|204457|335929|1111;1783272|201174|1760|85004|31953;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|1385|90964;3379134|1224|1236|2887326|468|475;3379134|1224|1236|2887326|468;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|81852;3379134|1224|1236|72274|135621|286;3379134|1224|1236|72274|135621|351;1783272|1239;3379134|1224|1236;1783272|1239|91061|186826|1300|1357;3379134|1224|1236|72274,Complete,Claregrieve1
bsdb:31752810/3/2,31752810,"cross-sectional observational, not case-control",31752810,10.1186/s12903-019-0947-6,NA,"Xi R., Wang R., Wang Y., Xiang Z., Su Z., Cao Z., Xu X., Zheng X. , Li J.",Comparative analysis of the oral microbiota between iron-deficiency anaemia (IDA) patients and healthy individuals by high-throughput sequencing,BMC oral health,2019,"High-throughput sequencing, Infective endocarditis, Iron-deficiency anaemia, Oral microbiota",Experiment 3,China,Homo sapiens,Dental plaque,UBERON:0016482,Iron deficiency anemia,HP:0001891,iron deficiency anemia moderate,iron deficiency anemia severe,iron defiency anemia,16,8,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3.5,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5d,10 January 2021,Rimsha Azhar,WikiWorks,LEfSe analysis of samples between iron deficiency anemia moderate (IDA_m) and iron deficiency anemia severe (IDA_s) patients,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae",3379134|1224|1236|135625;3379134|1224|1236|135625|712;3379134|1224|28216|206351;3379134|1224|28216|206351|481,Complete,Claregrieve1
bsdb:31753468/1/1,31753468,laboratory experiment,31753468,10.1016/j.envres.2019.108913,NA,"Fitch M.N., Phillippi D., Zhang Y., Lucero J., Pandey R.S., Liu J., Brower J., Allen M.S., Campen M.J., McDonald J.D. , Lund A.K.","Effects of inhaled air pollution on markers of integrity, inflammation, and microbiota profiles of the intestines in Apolipoprotein E knockout mice",Environmental research,2020,"Air pollution, Inflammation, Intestine epithelial barrier, Microbiome",Experiment 1,United States of America,Mus musculus,Small intestine,UBERON:0002108,Air pollution,ENVO:02500037,mice exposed to Filtered Air,mice exposed to MVE,male ApoE−/- mice exposed to  mixed diesel and gasoline engine emissions (MVE) or Wood Smoke (WS),20,20,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 10 & text,10 January 2021,Zyaijah Bailey,"WikiWorks,Atrayees","Effects of inhaled filtered air (FA), wood-smoke (WS), and mixed diesel and gasoline vehicle exhaust (MVE) on the relative abundance of gastrointestinal bacteria at the (A) phylum level, and (B) genus level in ApoE−/-mice.",increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota",1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|31979|1485;1783272|1239,Complete,Atrayees
bsdb:31753468/1/2,31753468,laboratory experiment,31753468,10.1016/j.envres.2019.108913,NA,"Fitch M.N., Phillippi D., Zhang Y., Lucero J., Pandey R.S., Liu J., Brower J., Allen M.S., Campen M.J., McDonald J.D. , Lund A.K.","Effects of inhaled air pollution on markers of integrity, inflammation, and microbiota profiles of the intestines in Apolipoprotein E knockout mice",Environmental research,2020,"Air pollution, Inflammation, Intestine epithelial barrier, Microbiome",Experiment 1,United States of America,Mus musculus,Small intestine,UBERON:0002108,Air pollution,ENVO:02500037,mice exposed to Filtered Air,mice exposed to MVE,male ApoE−/- mice exposed to  mixed diesel and gasoline engine emissions (MVE) or Wood Smoke (WS),20,20,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 10 & text,10 January 2021,Zyaijah Bailey,"Claregrieve1,WikiWorks","Effects of inhaled filtered air (FA), wood-smoke (WS), and mixed diesel and gasoline vehicle exhaust (MVE) on the relative abundance of gastrointestinal bacteria at the (A) phylum level, and (B) genus level in ApoE−/-mice.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|3085636|186803,Complete,Atrayees
bsdb:31753468/2/1,31753468,laboratory experiment,31753468,10.1016/j.envres.2019.108913,NA,"Fitch M.N., Phillippi D., Zhang Y., Lucero J., Pandey R.S., Liu J., Brower J., Allen M.S., Campen M.J., McDonald J.D. , Lund A.K.","Effects of inhaled air pollution on markers of integrity, inflammation, and microbiota profiles of the intestines in Apolipoprotein E knockout mice",Environmental research,2020,"Air pollution, Inflammation, Intestine epithelial barrier, Microbiome",Experiment 2,United States of America,Mus musculus,Small intestine,UBERON:0002108,Air pollution,ENVO:02500037,mice exposed to Filtered Air,mice exposed to WS,male ApoE−/- mice exposed to  mixed diesel and gasoline engine emissions (MVE) or Wood Smoke (WS),20,20,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 10 & text,10 January 2021,Zyaijah Bailey,"Claregrieve1,WikiWorks","Effects of inhaled filtered air (FA), wood-smoke (WS), and mixed diesel and gasoline vehicle exhaust (MVE) on the relative abundance of gastrointestinal bacteria at the (A) phylum level, and (B) genus level in ApoE−/-mice.",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,3379134|976|200643|171549,Complete,Atrayees
bsdb:31753468/2/2,31753468,laboratory experiment,31753468,10.1016/j.envres.2019.108913,NA,"Fitch M.N., Phillippi D., Zhang Y., Lucero J., Pandey R.S., Liu J., Brower J., Allen M.S., Campen M.J., McDonald J.D. , Lund A.K.","Effects of inhaled air pollution on markers of integrity, inflammation, and microbiota profiles of the intestines in Apolipoprotein E knockout mice",Environmental research,2020,"Air pollution, Inflammation, Intestine epithelial barrier, Microbiome",Experiment 2,United States of America,Mus musculus,Small intestine,UBERON:0002108,Air pollution,ENVO:02500037,mice exposed to Filtered Air,mice exposed to WS,male ApoE−/- mice exposed to  mixed diesel and gasoline engine emissions (MVE) or Wood Smoke (WS),20,20,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 10 & text,10 January 2021,Zyaijah Bailey,"Claregrieve1,WikiWorks","Effects of inhaled filtered air (FA), wood-smoke (WS), and mixed diesel and gasoline vehicle exhaust (MVE) on the relative abundance of gastrointestinal bacteria at the (A) phylum level, and (B) genus level in ApoE−/-mice.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|186802|31979|1485;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|3085636|186803,Complete,Atrayees
bsdb:31759120/1/1,31759120,laboratory experiment,31759120,10.1016/j.ygeno.2019.11.011,NA,"Kumar H., Park W., Lim D., Srikanth K., Kim J.M., Jia X.Z., Han J.L., Hanotte O., Park J.E. , Oyola S.O.",Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes,Genomics,2020,"Antibiotic resistant gene., CAZy, Indigenous chicken, KEGG, LEfSe, Microbiome, eggNOG",Experiment 1,Ethiopia,Gallus gallus,Caecum,UBERON:0001153,Restricted to specific location,MONDO:0045042,Amhara (AM) highland region,Afar (AF) lowland region,"Afar (AF) is a low altitude region known for active volcanic eruptions and receives relatively limited rainfall (Dulecha, 730 m above sea level).",5,5,NA,WMS,NA,Illumina,relative abundances,LEfSe,NA,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S2,6 November 2024,Tosin,"Tosin,WikiWorks","Taxonomic annotation of microorganisms in AF (Afar: lowland) and AM (Amhara: highland) regions through Linear Discriminant Analysis, identifying taxa with significant differences between the two regions.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. CHKCI003,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caecimuris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 3_1_13,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:443,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:661,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:714,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella sp. An22,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pullorum|s__Bifidobacterium pullorum subsp. saeculare,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter secundus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter|s__Cronobacter sakazakii,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Desulfuromonadales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Indolivaga|s__Indolivaga capnocytophagoides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor sp. An92,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Geobacterales|f__Geobacteraceae|g__Geobacter,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Geobacterales|f__Geobacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp. CAG:409,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola barnesiae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P2-180,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum variabile,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__[Eubacterium] cellulosolvens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__uncultured Bacteroides sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas|s__uncultured Dysgonomonas sp.",3379134|976|200643|171549|171550|239759|1780376;3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|815|816|1796613;3379134|976|200643|171549|815|816|28111;3379134|976|200643|171549|815|816|457389;3379134|976|200643|171549|815|816|1262739;3379134|976|200643|171549|815|816|1262746;3379134|976|200643|171549|815|816|1262749;3379134|976|200643|171549|2005519|397864|1965590;1783272|201174|1760|85004|31953|1678|78448|78257;3379134|976|200643|171549|2005519|1348911;3379134|976|200643|171549|2005519|1348911|1501392;3379134|1224|1236|91347|543|413496;3379134|1224|1236|91347|543|413496|28141;3379134|200940|3031651|69541;3379134|976|200643|171549|2005520;3379134|976|200643|171549|2005520|156973;3379134|976|200643|171549|2005520|3680098|45254;1783272|1239|186801|186802|216572|946234|1965666;3379134|200940|3031651|3031668|213422|28231;3379134|200940|3031651|3031668|213422;3379134|976|200643|171549|2005525|375288|1262913;3379134|976|200643|171549|815|909656|376804;3379134|976|200643|171549|815|909656|310298;3379134|976|200643|171549|815|909656|310298;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|171552|838|2024224;1783272|1239|186801|186802|216572|292632|214851;1783272|1239|186801|186802|186806|1730|29322;3379134|976|200643|171549|815|816|162156;3379134|976|200643|171549|2005520|156973|206096,Complete,Svetlana up
bsdb:31759120/1/2,31759120,laboratory experiment,31759120,10.1016/j.ygeno.2019.11.011,NA,"Kumar H., Park W., Lim D., Srikanth K., Kim J.M., Jia X.Z., Han J.L., Hanotte O., Park J.E. , Oyola S.O.",Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes,Genomics,2020,"Antibiotic resistant gene., CAZy, Indigenous chicken, KEGG, LEfSe, Microbiome, eggNOG",Experiment 1,Ethiopia,Gallus gallus,Caecum,UBERON:0001153,Restricted to specific location,MONDO:0045042,Amhara (AM) highland region,Afar (AF) lowland region,"Afar (AF) is a low altitude region known for active volcanic eruptions and receives relatively limited rainfall (Dulecha, 730 m above sea level).",5,5,NA,WMS,NA,Illumina,relative abundances,LEfSe,NA,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S2,8 November 2024,Tosin,"Tosin,WikiWorks","Taxonomic annotation of microorganisms in AF (Afar: lowland) and AM (Amhara: highland) regions through Linear Discriminant Analysis, identifying taxa with significant differences between the two regions.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. An54,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 3_1_40A,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. An279,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:1060,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:462,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:702,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|s__Bacteroidia bacterium 43-41,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. An46,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium 59_14,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium CHKCI006,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. An121,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. An122,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. An192,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. HUN102,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. An58,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. An77,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania filiformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. An138,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides johnsonii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp. Marseille-P3160,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1058,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1124,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1185,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:617,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:924,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter rarus",3379134|976|200643|171549|171550|239759|1965645;3379134|976|200643|171549|815|816|246787;3379134|976|200643|171549|815|816|28111;3379134|976|200643|171549|815|816|469593;3379134|976|200643|171549|815|816|1965620;3379134|976|200643|171549|815|816|1262734;3379134|976|200643|171549|815|816|1262740;3379134|976|200643|171549|815|816|1262747;3379134|976|200643|1895720;1783272|1239|186801|3085636|186803|572511|33035;1783272|1239|186801|3085636|186803|572511|1965636;3379134|1224|28216|80840|119060|32008;3379134|1224|28216|80840|119060;3379134|1224|28216|80840;1783272|1239|186801|186802|1897049;1783272|1239|186801|186802|1780379;1783272|1239|186801|3085636|186803|2719313|358743;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|216851|1965550;1783272|1239|186801|186802|216572|216851|1965551;1783272|1239|186801|186802|216572|216851|1965581;3379134|976|200643|171549|171552|838|1392486;1783272|1239|186801|186802|216572|216851|1965648;1783272|1239|186801|186802|216572|216851|1965655;1783272|1239|526524|526525|128827|61170;1783272|1239|526524|526525|128827|61170|61171;1783272|1239|186801|3085636|186803|1506553|1965560;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843489|31977|906|907;1783272|1239|909932;3379134|976|200643|171549|2005525|375288|387661;3379134|976|200643|171549|2005525|375288|1917887;3379134|976|200643|171549|171552|838|1262918;3379134|976|200643|171549|171552|838|1262920;3379134|976|200643|171549|171552|838|1262921;3379134|976|200643|171549|171552|838|1262933;3379134|976|200643|171549|171552|838|1262938;1783272|1239|909932|1843489;3379134|976|200643|171549|171552|558436|1676614,Complete,Svetlana up
bsdb:31759120/2/1,31759120,laboratory experiment,31759120,10.1016/j.ygeno.2019.11.011,NA,"Kumar H., Park W., Lim D., Srikanth K., Kim J.M., Jia X.Z., Han J.L., Hanotte O., Park J.E. , Oyola S.O.",Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes,Genomics,2020,"Antibiotic resistant gene., CAZy, Indigenous chicken, KEGG, LEfSe, Microbiome, eggNOG",Experiment 2,Ethiopia,Gallus gallus,Caecum,UBERON:0001153,Restricted to specific location,MONDO:0045042,Amhara (AM) highland region,Afar (AF) lowland region,"Afar (AF) is a low altitude region known for active volcanic eruptions and receives relatively limited rainfall (Dulecha, 730 m above sea level).",5,5,NA,WMS,NA,Illumina,relative abundances,Metastats,NA,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S1,9 November 2024,Tosin,"Tosin,WikiWorks",Taxa differentially abundant between AM(Amhara: highland region) and AF(Afar: lowland region).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:661,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter secundus",3379134|976|200643|171549|815|816|1262746;3379134|976|200643|171549|2005519|1348911|1501392,Complete,Svetlana up
bsdb:31759120/2/2,31759120,laboratory experiment,31759120,10.1016/j.ygeno.2019.11.011,NA,"Kumar H., Park W., Lim D., Srikanth K., Kim J.M., Jia X.Z., Han J.L., Hanotte O., Park J.E. , Oyola S.O.",Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes,Genomics,2020,"Antibiotic resistant gene., CAZy, Indigenous chicken, KEGG, LEfSe, Microbiome, eggNOG",Experiment 2,Ethiopia,Gallus gallus,Caecum,UBERON:0001153,Restricted to specific location,MONDO:0045042,Amhara (AM) highland region,Afar (AF) lowland region,"Afar (AF) is a low altitude region known for active volcanic eruptions and receives relatively limited rainfall (Dulecha, 730 m above sea level).",5,5,NA,WMS,NA,Illumina,relative abundances,Metastats,NA,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S1,9 November 2024,Tosin,"Tosin,WikiWorks",Taxa differentially abundant between AM(Amhara: highland region) and AF(Afar: lowland region).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. An51A,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:462,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium CHKCI006,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. An121",3379134|976|200643|171549|815|816|1965640;3379134|976|200643|171549|815|816|1262740;1783272|1239|186801|186802|1780379;1783272|1239|186801|186802|216572|216851|1965550,Complete,Svetlana up
bsdb:31764438/1/1,31764438,case-control,31764438,10.1097/MPG.0000000000002461,NA,"Kansal S., Catto-Smith A.G., Boniface K., Thomas S., Cameron D.J., Oliver M., Alex G., Kirkwood C.D. , Wagner J.",Variation of Gut Mucosal Microbiome With Anti-Saccharomyces cerevisiae Antibody Status in Pediatric Crohn Disease,Journal of pediatric gastroenterology and nutrition,2019,NA,Experiment 1,Australia,Homo sapiens,Ileum,UBERON:0002116,Crohn's disease,EFO:0000384,crohn disease ASCA negative patients,crohn disease ASCA positive patients,Crohn disease anti-Saccharomyces cerevisiae antibody status,39,38,3 months,16S,2,Non-quantitative PCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 1,10 January 2021,Rimsha Azhar,WikiWorks,Bacterial species significantly associated with Crohn disease Anti-Saccharomyces cerevisiae antibody status (ASCA) positive patients and CD ASCA-negative patients,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,1783272|1239|186801|3085636|186803|2316020|33039,Complete,Atrayees
bsdb:31764438/1/2,31764438,case-control,31764438,10.1097/MPG.0000000000002461,NA,"Kansal S., Catto-Smith A.G., Boniface K., Thomas S., Cameron D.J., Oliver M., Alex G., Kirkwood C.D. , Wagner J.",Variation of Gut Mucosal Microbiome With Anti-Saccharomyces cerevisiae Antibody Status in Pediatric Crohn Disease,Journal of pediatric gastroenterology and nutrition,2019,NA,Experiment 1,Australia,Homo sapiens,Ileum,UBERON:0002116,Crohn's disease,EFO:0000384,crohn disease ASCA negative patients,crohn disease ASCA positive patients,Crohn disease anti-Saccharomyces cerevisiae antibody status,39,38,3 months,16S,2,Non-quantitative PCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 1,10 January 2021,Rimsha Azhar,WikiWorks,Bacterial species significantly associated with Crohn disease Anti-Saccharomyces cerevisiae antibody status (ASCA) positive patients and CD ASCA-negative patients,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",3379134|1224|1236|91347|543|547|550;1783272|1239|186801|186802|216572|216851|853,Complete,Atrayees
bsdb:31771977/1/1,31771977,prospective cohort,31771977,10.1128/mSystems.00639-19,https://pubmed.ncbi.nlm.nih.gov/31771977/,"Yang Y., Zheng W., Cai Q., Shrubsole M.J., Pei Z., Brucker R., Steinwandel M., Bordenstein S.R., Li Z., Blot W.J., Shu X.O. , Long J.",Racial Differences in the Oral Microbiome: Data from Low-Income Populations of African Ancestry and European Ancestry,mSystems,2019,"oral microbiome, racial difference",Experiment 1,United States of America,Homo sapiens,Oral opening,UBERON:0000166,Ethnic group,EFO:0001799,European Americans (EA),African Americans (AA),"Mouth rinse samples of 1,058 African Americans, with about 57% population with low SES of annual household income < $15,000.",558,1058,1 year,16S,4,Illumina,NA,Logistic Regression,0.05,TRUE,NA,NA,"age,alcohol drinking,body mass index,household income,sex,smoking status",NA,NA,NA,NA,NA,increased,Signature 1,Table 2; Figure 3,11 July 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks","TABLE 2 Significantly higher abundance of Bacteroidetes and lower abundance of Actinobacteria and Firmicutes among African-Americans
FIG 3 Thirteen common bacterial taxa showing a significant differential abundance between AAs and EAs in linear regression analyses.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838|28129;1783272|1239|186801|3082720|186804,Complete,NA
bsdb:31771977/1/2,31771977,prospective cohort,31771977,10.1128/mSystems.00639-19,https://pubmed.ncbi.nlm.nih.gov/31771977/,"Yang Y., Zheng W., Cai Q., Shrubsole M.J., Pei Z., Brucker R., Steinwandel M., Bordenstein S.R., Li Z., Blot W.J., Shu X.O. , Long J.",Racial Differences in the Oral Microbiome: Data from Low-Income Populations of African Ancestry and European Ancestry,mSystems,2019,"oral microbiome, racial difference",Experiment 1,United States of America,Homo sapiens,Oral opening,UBERON:0000166,Ethnic group,EFO:0001799,European Americans (EA),African Americans (AA),"Mouth rinse samples of 1,058 African Americans, with about 57% population with low SES of annual household income < $15,000.",558,1058,1 year,16S,4,Illumina,NA,Logistic Regression,0.05,TRUE,NA,NA,"age,alcohol drinking,body mass index,household income,sex,smoking status",NA,NA,NA,NA,NA,increased,Signature 2,Table 2; Figure 3,11 July 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks","TABLE 2 Significantly higher abundance of Bacteroidetes and lower abundance of Actinobacteria and Firmicutes among African-Americans 
FIG 3 Thirteen common bacterial taxa showing a significant differential abundance between AAs and EAs in linear regression analyses.",decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 057",1783272|201174;1783272|1239|91061|186826|186828;1783272|1239|91061|186826|186828|117563;1783272|1239|91061|186826|186828|117563|46124;1783272|201174|1760|85006|1268;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300|1301|45634;1783272|1239|91061|186826|1300|1301|712621,Complete,NA
bsdb:31794002/1/1,31794002,"cross-sectional observational, not case-control",31794002,10.1093/ntr/ntz220,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7364824/pdf/ntz220.pdf,"Nolan-Kenney R., Wu F., Hu J., Yang L., Kelly D., Li H., Jasmine F., Kibriya M.G., Parvez F., Shaheen I., Sarwar G., Ahmed A., Eunus M., Islam T., Pei Z., Ahsan H. , Chen Y.",The Association Between Smoking and Gut Microbiome in Bangladesh,Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco,2020,NA,Experiment 1,Bangladesh,Homo sapiens,Feces,UBERON:0001988,"Nicotine dependence,Smoking behavior","EFO:0003768,EFO:0004318",Never smokers,Current Smokers,Current smokers of cigarettes and bidis were categorized as current smokers,151,62,1 month,16S,34,Illumina,relative abundances,"Beta Binomial Regression,Logistic Regression",0.05,TRUE,NA,NA,"age,body mass index,education level,sex",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 3,4 January 2022,Joyessa,"Joyessa,Aiyshaaaa,Peace Sandy,ChiomaBlessing,WikiWorks",Relative Abundances or Presence/ Absence of significant taxa in current smokers compared to never-smokers.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia",1783272|1239|526524|526525|2810280|135858;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524,Complete,ChiomaBlessing
bsdb:31794002/2/1,31794002,"cross-sectional observational, not case-control",31794002,10.1093/ntr/ntz220,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7364824/pdf/ntz220.pdf,"Nolan-Kenney R., Wu F., Hu J., Yang L., Kelly D., Li H., Jasmine F., Kibriya M.G., Parvez F., Shaheen I., Sarwar G., Ahmed A., Eunus M., Islam T., Pei Z., Ahsan H. , Chen Y.",The Association Between Smoking and Gut Microbiome in Bangladesh,Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco,2020,NA,Experiment 2,Bangladesh,Homo sapiens,Feces,UBERON:0001988,"Nicotine dependence,Smoking behavior","EFO:0003768,EFO:0004318",Never smokers,Current Smokers,"Current smokers of cigarettes and bidis were categorized as current smokers, further assessed their association with packs of cigarettes smoked",151,62,1 month,16S,34,Illumina,relative abundances,"Beta Binomial Regression,Logistic Regression",0.05,TRUE,NA,NA,"age,body mass index,education level,sex",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 5,2 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Relative Abundances or Presence/ Absence of Significant Bacterial Taxa Associated With One Increase in Packs Smoked,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella",1783272|1239|526524|526525;1783272|1239|186801|3082720|186804;1783272|201174|84998|1643822|1643826|84108;1783272|1239|526524|526525|2810280|135858;1783272|201174|84998|84999|84107|102106;1783272|1239|909932|909929|1843491|52225,Complete,ChiomaBlessing
bsdb:31808612/1/1,31808612,case-control,31808612,10.1111/jcmm.14880,NA,"Sun Q., Xu X., Zhang J., Sun M., Tian Q., Li Q., Cao W., Zhang X., Wang H., Liu J., Zhang J., Meng X., Wu L., Song M., Liu H., Wang W. , Wang Y.",Association of suboptimal health status with intestinal microbiota in Chinese youths,Journal of cellular and molecular medicine,2020,"16S rRNA, LEfSe analysis, intestinal microbiota, random forest tree, suboptimal health status",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Health trait,EFO:0007652,healthy controls,suboptimal health status,subjects with SHSQ-25 (SHS score >= 35),50,50,2 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,increased,unchanged,increased,NA,unchanged,Signature 1,Figure 5,10 January 2021,Rimsha Azhar,"Claregrieve1,WikiWorks",LDA score of LEfSe analysis between suboptimal health status (SHS) and control group,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae",3379134|976|117743|200644|2762318|59732;1783272|1117;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|541000;1783272|1239|186801|186802|186807;3379134|976|200643|171549|171550;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;3379134|74201;1783272|1239|186801|186802|1898207;3384189|32066|203490|203491|203492,Complete,Claregrieve1
bsdb:31808612/1/2,31808612,case-control,31808612,10.1111/jcmm.14880,NA,"Sun Q., Xu X., Zhang J., Sun M., Tian Q., Li Q., Cao W., Zhang X., Wang H., Liu J., Zhang J., Meng X., Wu L., Song M., Liu H., Wang W. , Wang Y.",Association of suboptimal health status with intestinal microbiota in Chinese youths,Journal of cellular and molecular medicine,2020,"16S rRNA, LEfSe analysis, intestinal microbiota, random forest tree, suboptimal health status",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Health trait,EFO:0007652,healthy controls,suboptimal health status,subjects with SHSQ-25 (SHS score >= 35),50,50,2 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,increased,unchanged,increased,NA,unchanged,Signature 2,Figure 5,10 January 2021,Rimsha Azhar,WikiWorks,LDA score of LEfSe analysis between suboptimal health status (SHS) and control group,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|1224|1236|91347|1903414|581;3379134|1224|28216|80840|119060|48736;3379134|1224|28216;3379134|1224|28216|80840|506;3379134|1224|28216|80840|995019|40544,Complete,Claregrieve1
bsdb:31815177/1/1,31815177,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S., Schwiertz A., Unger M.M., Becker A., Faßbender K., Ratering S., Kohl M., Schnell S., Schäfer K.H. , Egert M.",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease Patients,Patients with Parkinson's Disease.,25,34,NA,16S,45,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Table 2 and Text,16 March 2024,FaithAlexander,"FaithAlexander,WikiWorks",16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Parkinson's Disease Patients and Healthy Controls.,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|3082720|186804,Complete,Peace Sandy
bsdb:31815177/1/2,31815177,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S., Schwiertz A., Unger M.M., Becker A., Faßbender K., Ratering S., Kohl M., Schnell S., Schäfer K.H. , Egert M.",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease Patients,Patients with Parkinson's Disease.,25,34,NA,16S,45,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,Table 2 and Text,16 March 2024,FaithAlexander,"FaithAlexander,WikiWorks",16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Parkinson's Disease Patients and Healthy controls.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607,Complete,Peace Sandy
bsdb:31815177/2/1,31815177,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S., Schwiertz A., Unger M.M., Becker A., Faßbender K., Ratering S., Kohl M., Schnell S., Schäfer K.H. , Egert M.",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Male Parkinson's disease Patients,Female Parkinson's disease Patients,Female Patients with Parkinson's disease,23,11,NA,16S,45,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Table 2 and Text,16 March 2024,FaithAlexander,"FaithAlexander,WikiWorks",16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Male Parkinson's disease Patients and Female Parkinson's disease Patients.,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|3082720|186804,Complete,Peace Sandy
bsdb:31815177/2/2,31815177,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S., Schwiertz A., Unger M.M., Becker A., Faßbender K., Ratering S., Kohl M., Schnell S., Schäfer K.H. , Egert M.",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Male Parkinson's disease Patients,Female Parkinson's disease Patients,Female Patients with Parkinson's disease,23,11,NA,16S,45,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,Table 2 and Text,16 March 2024,FaithAlexander,"FaithAlexander,WikiWorks",16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Male Parkinson's Disease Patients and Female Parkinson's Disease Patients.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,1783272|1239|186801|186802|216572|216851,Complete,Peace Sandy
bsdb:31815177/3/1,31815177,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S., Schwiertz A., Unger M.M., Becker A., Faßbender K., Ratering S., Kohl M., Schnell S., Schäfer K.H. , Egert M.",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 3,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Calprotectin Negative Controls,Parkinson's Disease Patients with elevated Calprotectin levels,Parkinson's Disease Patients with elevated levels of Fecal Calprotectin,22,14,NA,16S,45,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Table 2 and Text,16 March 2024,FaithAlexander,"FaithAlexander,WikiWorks",16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Parkinson's Disease Patients with elevated levels of fecal Calprotectin and Calprotectin Negative Healthy Controls.,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",1783272|1239|1737404|1737405|1570339|150022;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|3082720|186804,Complete,Peace Sandy
bsdb:31815177/3/2,31815177,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S., Schwiertz A., Unger M.M., Becker A., Faßbender K., Ratering S., Kohl M., Schnell S., Schäfer K.H. , Egert M.",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 3,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Calprotectin Negative Controls,Parkinson's Disease Patients with elevated Calprotectin levels,Parkinson's Disease Patients with elevated levels of Fecal Calprotectin,22,14,NA,16S,45,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,Table 2 and Text,16 March 2024,FaithAlexander,"FaithAlexander,WikiWorks",16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Parkinson's Disease Patients with elevated levels of fecal Calprotectin  and Calprotectin Negative Healthy Controls.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607,Complete,Peace Sandy
bsdb:31815177/4/1,31815177,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S., Schwiertz A., Unger M.M., Becker A., Faßbender K., Ratering S., Kohl M., Schnell S., Schäfer K.H. , Egert M.",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 4,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Calprotectin positive Parkinson's Disease Patients,Parkinson's Disease Patients with normal Calprotectin levels,Patients with Parkinson's disease that had normal Calprotectin levels..,14,14,NA,16S,45,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Table 2 and Text,16 March 2024,FaithAlexander,"FaithAlexander,WikiWorks",16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Parkinson's Disease Patients with normal Calprotectin levels and Calprotectin positive Parkinson's Disease Patients',increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,1783272|1239|186801|186802|216572|216851,Complete,Peace Sandy
bsdb:31815177/4/2,31815177,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S., Schwiertz A., Unger M.M., Becker A., Faßbender K., Ratering S., Kohl M., Schnell S., Schäfer K.H. , Egert M.",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 4,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Calprotectin positive Parkinson's Disease Patients,Parkinson's Disease Patients with normal Calprotectin levels,Patients with Parkinson's disease that had normal Calprotectin levels..,14,14,NA,16S,45,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,Table 2 and Text,16 March 2024,FaithAlexander,"FaithAlexander,WikiWorks",16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Parkinson's Disease Patients with normal Calprotectin levels and Calprotectin positive Parkinson's Disease Patients.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301,Complete,Peace Sandy
bsdb:31815177/5/1,31815177,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S., Schwiertz A., Unger M.M., Becker A., Faßbender K., Ratering S., Kohl M., Schnell S., Schäfer K.H. , Egert M.",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 5,Germany,Homo sapiens,Feces,UBERON:0001988,Phenotypic sex,NA,Male Healthy Controls,Female Healthy Controls,Healthy Control persons who were of the female gender,11,14,NA,16S,45,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Table 2 and Text,17 March 2024,FaithAlexander,"FaithAlexander,WikiWorks",16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Male Healthy Controls and Female Healthy Controls.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678,Complete,Peace Sandy
bsdb:31815177/6/1,31815177,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S., Schwiertz A., Unger M.M., Becker A., Faßbender K., Ratering S., Kohl M., Schnell S., Schäfer K.H. , Egert M.",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 6,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Female Parkinson's Disease Patients,Male Parkinson's Disease Patients,Parkinson's Disease Patients of the Male Gender,11,23,NA,16S,45,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Table 2 and Text,17 March 2024,FaithAlexander,"FaithAlexander,WikiWorks",16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Male Parkinson's disease Patients and Female Parkinson's disease Patients.,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,1783272|201174|1760|85004|31953,Complete,Peace Sandy
bsdb:31815177/7/1,31815177,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S., Schwiertz A., Unger M.M., Becker A., Faßbender K., Ratering S., Kohl M., Schnell S., Schäfer K.H. , Egert M.",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 7,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Normal Calprotectin levels Parkinson's Disease Patients,Parkinson's disease Patients with Normal Calprotectin levels.,25,14,NA,16S,45,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Table 2 and Text,17 March 2024,FaithAlexander,"FaithAlexander,WikiWorks",16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Parkinson's disease Patients with normal Calprotectin levels and Healthy Controls.,increased,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,1783272|1239|1737404|1737405|1570339|162289,Complete,Peace Sandy
bsdb:31815177/9/NA,31815177,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S., Schwiertz A., Unger M.M., Becker A., Faßbender K., Ratering S., Kohl M., Schnell S., Schäfer K.H. , Egert M.",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 9,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease Patients not treated with L-dopa,Parkinson's disease Patients who were not treated with L-dopa.,25,10,NA,16S,45,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:31815177/10/NA,31815177,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S., Schwiertz A., Unger M.M., Becker A., Faßbender K., Ratering S., Kohl M., Schnell S., Schäfer K.H. , Egert M.",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 10,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Parkinson's disease Patients treated with L-dopa,Parkinson's Disease Patients not treated with L-dopa,Parkinson's disease Patients who were not treated with L-dopa.,24,10,NA,16S,45,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:31815177/11/1,31815177,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S., Schwiertz A., Unger M.M., Becker A., Faßbender K., Ratering S., Kohl M., Schnell S., Schäfer K.H. , Egert M.",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 11,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's disease Patients treated with entacapone,Parkinson's disease patients who were treated with entacapone.,25,11,NA,16S,45,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Table 2 and Text,17 March 2024,FaithAlexander,"FaithAlexander,WikiWorks",16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Parkinson's disease Patients treated with entacapone and Healthy Controls.,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] brachy",1783272|1239|1737404|1737405|1570339|165779;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|3082720|186804;1783272|1239|186801|3085636|186803|1769710;1783272|1239|186801|3082720|543314|35517,Complete,Peace Sandy
bsdb:31815177/11/2,31815177,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S., Schwiertz A., Unger M.M., Becker A., Faßbender K., Ratering S., Kohl M., Schnell S., Schäfer K.H. , Egert M.",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 11,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's disease Patients treated with entacapone,Parkinson's disease patients who were treated with entacapone.,25,11,NA,16S,45,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,Table 2 and Text,17 March 2024,FaithAlexander,"FaithAlexander,WikiWorks",16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Parkinson's disease Patients treated with entacapone and Healthy Controls.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|1263|438033,Complete,Peace Sandy
bsdb:31815177/12/1,31815177,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S., Schwiertz A., Unger M.M., Becker A., Faßbender K., Ratering S., Kohl M., Schnell S., Schäfer K.H. , Egert M.",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 12,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's disease Patients with HR Phenotype,Parkinson's disease Patients with a Hypokinetic-rigid phenotype.,25,15,NA,16S,45,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Table 2 and Text,17 March 2024,FaithAlexander,"FaithAlexander,WikiWorks",16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Parkinson's disease Patients with Hypokinetic-rigid [HR] Phenotype and Healthy Controls.,increased,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,1783272|1239|1737404|1737405|1570339|162289,Complete,Peace Sandy
bsdb:31815177/12/2,31815177,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S., Schwiertz A., Unger M.M., Becker A., Faßbender K., Ratering S., Kohl M., Schnell S., Schäfer K.H. , Egert M.",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 12,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's disease Patients with HR Phenotype,Parkinson's disease Patients with a Hypokinetic-rigid phenotype.,25,15,NA,16S,45,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,Table 2 and Text,17 March 2024,FaithAlexander,"FaithAlexander,WikiWorks",16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Parkinson's disease Patients with Hypokinetic-rigid [HR] Phenotype and Healthy Controls.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,1783272|1239|186801|186802|216572|216851,Complete,Peace Sandy
bsdb:31815177/14/1,31815177,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S., Schwiertz A., Unger M.M., Becker A., Faßbender K., Ratering S., Kohl M., Schnell S., Schäfer K.H. , Egert M.",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 14,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's disease Patients with HY Stage of 1 to 2.5,Parkinson's disease Patients with Hoehn-Yahr [HY] Stage of 1 to 2.5.,25,18,NA,16S,45,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Table 2 and Text,17 March 2024,FaithAlexander,"FaithAlexander,WikiWorks",16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Parkinson's disease Patients with Hoehn-Yahr [HY] Stage of 1 to 2.5 and Healthy Controls.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus",1783272|1239|186801|186802|216572|216851;1783272|1239|1737404|1737405|1570339|162289,Complete,Peace Sandy
bsdb:31815177/15/1,31815177,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S., Schwiertz A., Unger M.M., Becker A., Faßbender K., Ratering S., Kohl M., Schnell S., Schäfer K.H. , Egert M.",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 15,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's disease Patients with HY Stage of 3 to 4,Parkinson's disease Patients with Hoehn-Yahr [HY] Stage of 3 to 4.,25,16,NA,16S,45,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Table 2 and Text,17 March 2024,FaithAlexander,"FaithAlexander,Peace Sandy,WikiWorks",16S rRNA analysis showing the differences in the relative abundance of microbiota composition between Parkinson's disease Patients with Hoehn-Yahr [HY] Stage 3 to 4 and Healthy Controls.,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|186802|216572|216851,Complete,Peace Sandy
bsdb:31815177/16/NA,31815177,case-control,31815177,10.1038/s41531-019-0100-x,NA,"Weis S., Schwiertz A., Unger M.M., Becker A., Faßbender K., Ratering S., Kohl M., Schnell S., Schäfer K.H. , Egert M.",Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota,NPJ Parkinson's disease,2019,"Constipation, Parkinson's disease",Experiment 16,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Parkinson's disease Patients with HY Stage of 1 to 2.5,Parkinson's disease Patients with HY Stage of 3 to 4,Parkinson's disease Patients with Hoehn-Yahr [HY] Stage of 3 to 4.,18,16,NA,16S,45,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:31824239/1/1,31824239,case-control,31824239,10.3389/fnins.2019.01184,NA,"Jin M., Li J., Liu F., Lyu N., Wang K., Wang L., Liang S., Tao H., Zhu B. , Alkasir R.",Analysis of the Gut Microflora in Patients With Parkinson's Disease,Frontiers in neuroscience,2019,"16S rRNA gene, Illumina MiSeq, Parkinson's disease, Prevotella, Turicibacter, gut microflora",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,NPD group: patients suffering with suffering with with PD for less than 1 year and before treatment.,New Parkinson's disease patients: patients suffering with with PD for less than 1 year and before treatment.,68,13,3 months,16S,NA,Illumina,NA,Metastats,0.05,FALSE,NA,"age,life style",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3. Genus level comparison among NPD samples.,29 November 2021,Fcuevas3,"Fcuevas3,Rimsha,WikiWorks",Genus-level comparison among NPD samples collected at different times.,increased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,1783272|1239|526524|526525|2810281|191303,Complete,Rimsha
bsdb:31824239/1/2,31824239,case-control,31824239,10.3389/fnins.2019.01184,NA,"Jin M., Li J., Liu F., Lyu N., Wang K., Wang L., Liang S., Tao H., Zhu B. , Alkasir R.",Analysis of the Gut Microflora in Patients With Parkinson's Disease,Frontiers in neuroscience,2019,"16S rRNA gene, Illumina MiSeq, Parkinson's disease, Prevotella, Turicibacter, gut microflora",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,NPD group: patients suffering with suffering with with PD for less than 1 year and before treatment.,New Parkinson's disease patients: patients suffering with with PD for less than 1 year and before treatment.,68,13,3 months,16S,NA,Illumina,NA,Metastats,0.05,FALSE,NA,"age,life style",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,FIGURE 3,29 November 2021,Fcuevas3,"Fcuevas3,Rimsha,WikiWorks",Genus-level comparison among NPD samples collected at different times.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|976|200643|171549|171552|577309;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300|1301,Complete,Rimsha
bsdb:31824239/2/1,31824239,case-control,31824239,10.3389/fnins.2019.01184,NA,"Jin M., Li J., Liu F., Lyu N., Wang K., Wang L., Liang S., Tao H., Zhu B. , Alkasir R.",Analysis of the Gut Microflora in Patients With Parkinson's Disease,Frontiers in neuroscience,2019,"16S rRNA gene, Illumina MiSeq, Parkinson's disease, Prevotella, Turicibacter, gut microflora",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,NPD group: patients suffering with PD for less than 1 year and 5 days after treatment.,New Parkinson's disease patients: patients suffering with PD for less than 1 year and samples taken 5 days after treatment.,68,13,3 months,16S,NA,Illumina,NA,Metastats,0.01,NA,NA,"age,life style",NA,NA,increased,unchanged,increased,NA,NA,Signature 1,FIGURE 3.,29 November 2021,Fcuevas3,"Fcuevas3,Rimsha,WikiWorks",Genus-level comparison among NPD samples collected at different times.,increased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,1783272|1239|526524|526525|2810281|191303,Complete,Rimsha
bsdb:31824239/3/1,31824239,case-control,31824239,10.3389/fnins.2019.01184,NA,"Jin M., Li J., Liu F., Lyu N., Wang K., Wang L., Liang S., Tao H., Zhu B. , Alkasir R.",Analysis of the Gut Microflora in Patients With Parkinson's Disease,Frontiers in neuroscience,2019,"16S rRNA gene, Illumina MiSeq, Parkinson's disease, Prevotella, Turicibacter, gut microflora",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,NPD group: patients suffering with PD for less than 1 year and 14 days after treatment.,New Parkinson's disease patients: patients suffering with PD for less than 1 year and samples taken 14 days after treatment.,68,13,3 months,16S,NA,Illumina,NA,Metastats,0.05,NA,NA,"age,life style",NA,NA,increased,unchanged,increased,NA,NA,Signature 1,FIGURE 3.,29 November 2021,Fcuevas3,"Fcuevas3,Rimsha,WikiWorks",Genus-level comparison among NPD samples collected at different times.,increased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,1783272|1239|526524|526525|2810281|191303,Complete,Rimsha
bsdb:31824239/3/2,31824239,case-control,31824239,10.3389/fnins.2019.01184,NA,"Jin M., Li J., Liu F., Lyu N., Wang K., Wang L., Liang S., Tao H., Zhu B. , Alkasir R.",Analysis of the Gut Microflora in Patients With Parkinson's Disease,Frontiers in neuroscience,2019,"16S rRNA gene, Illumina MiSeq, Parkinson's disease, Prevotella, Turicibacter, gut microflora",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,NPD group: patients suffering with PD for less than 1 year and 14 days after treatment.,New Parkinson's disease patients: patients suffering with PD for less than 1 year and samples taken 14 days after treatment.,68,13,3 months,16S,NA,Illumina,NA,Metastats,0.05,NA,NA,"age,life style",NA,NA,increased,unchanged,increased,NA,NA,Signature 2,FIGURE 3.,29 November 2021,Fcuevas3,"Fcuevas3,Rimsha,WikiWorks",Genus-level comparison among NPD samples collected at different times.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,1783272|1239|186801|186802|216572|1263,Complete,Rimsha
bsdb:31824447/1/1,31824447,laboratory experiment,31824447,10.3389/fmicb.2019.02620,NA,"Lu J., Zhang X., Liu Y., Cao H., Han Q., Xie B., Fan L., Li X., Hu J., Yang G. , Shi X.","Effect of Fermented Corn-Soybean Meal on Serum Immunity, the Expression of Genes Related to Gut Immunity, Gut Microbiota, and Bacterial Metabolites in Grower-Finisher Pigs",Frontiers in microbiology,2019,"corn-soybean meal, fermented feed, immunity, metabolite, microbiota, pig",Experiment 1,China,Sus scrofa domesticus,Colon,UBERON:0001155,Response to diet,EFO:0010757,UF (Unfermented feed/control group),FF (Fermented feed group),Group fed with fermented complete commercial soybean meal (FF),6,6,NA,16S,45,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Table 6, Table 8",5 May 2025,Tosin,Tosin,Relative abundance of microbial phylum and Family (percentage) in the colon of pigs in the FF and control groups.,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",1783272|201174;1783272|1239;1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171550,Complete,KateRasheed
bsdb:31824447/1/2,31824447,laboratory experiment,31824447,10.3389/fmicb.2019.02620,NA,"Lu J., Zhang X., Liu Y., Cao H., Han Q., Xie B., Fan L., Li X., Hu J., Yang G. , Shi X.","Effect of Fermented Corn-Soybean Meal on Serum Immunity, the Expression of Genes Related to Gut Immunity, Gut Microbiota, and Bacterial Metabolites in Grower-Finisher Pigs",Frontiers in microbiology,2019,"corn-soybean meal, fermented feed, immunity, metabolite, microbiota, pig",Experiment 1,China,Sus scrofa domesticus,Colon,UBERON:0001155,Response to diet,EFO:0010757,UF (Unfermented feed/control group),FF (Fermented feed group),Group fed with fermented complete commercial soybean meal (FF),6,6,NA,16S,45,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Table 6, Table 8",5 May 2025,Tosin,Tosin,Relative abundance of microbial phylum and family (percentage) in the colon of pigs in the FF and control groups.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Fibrobacterota|c__Fibrobacteria|o__Fibrobacterales|f__Fibrobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Verrucomicrobiota,k__Methanobacteriati|p__Thermoplasmatota|c__Thermoplasmata|o__Thermoplasmatales",1783272|1239|909932|1843488|909930;3379134|1224|28216|80840|506;1783272|544448|31969|186332|186333;3379134|976|200643|171549|815;3379134|976;1783272|1239|526524|526525|128827;3379134|65842|204430|218872|204431;1783272|1239|186801|3085636|186803;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171552;3379134|1224;3379134|1224|28211|204441|41295;1783272|1239|91061|186826|1300;3379134|1224|1236|135624|83763;1783272|1239|909932|1843489|31977;3379134|74201;3366610|2283796|183967|2301,Complete,KateRasheed
bsdb:31824447/2/1,31824447,laboratory experiment,31824447,10.3389/fmicb.2019.02620,NA,"Lu J., Zhang X., Liu Y., Cao H., Han Q., Xie B., Fan L., Li X., Hu J., Yang G. , Shi X.","Effect of Fermented Corn-Soybean Meal on Serum Immunity, the Expression of Genes Related to Gut Immunity, Gut Microbiota, and Bacterial Metabolites in Grower-Finisher Pigs",Frontiers in microbiology,2019,"corn-soybean meal, fermented feed, immunity, metabolite, microbiota, pig",Experiment 2,China,Sus scrofa domesticus,Duodenum,UBERON:0002114,Response to diet,EFO:0010757,UF (Unfermented feed/control group),FF (Fermented feed group),Group fed with fermented complete commercial soybean meal (FF),6,6,NA,16S,45,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Table 5, Table 7",5 May 2025,Tosin,Tosin,Relative abundance of microbial phylum and family (percentage) in the duodenum of pigs in the FF and control groups.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Verrucomicrobiota",1783272|1239|909932|1843488|909930;3379134|976;3379134|74201,Complete,KateRasheed
bsdb:31834952/1/1,31834952,"cross-sectional observational, not case-control",31834952,10.1111/myc.13046,https://pubmed.ncbi.nlm.nih.gov/31834952/,"Han S.H., Lee J.S., Song K.H., Choe Y.B., Ahn K.J. , Lee Y.W.",Differences in foot skin microbiomes between patients with type 2 diabetes and healthy individuals,Mycoses,2020,"Trichophyton rubrum, biodiversity, diabetes mellitus, microbiome",Experiment 1,South Korea,Homo sapiens,"Skin of sole of pes,Interdigital space","UBERON:0036252,UBERON:0013778",Type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,"Type 2 Diabetes Mellitus patients diagnosed by an endocrinologist at Konkuk University Medical Center, Seoul, Korea",18,17,concomitant systemic (within four weeks of enrolment) or topical (within two weeks of enrolment) treatments,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,unchanged,NA,decreased,Signature 1,Table 2,7 June 2021,Madhubani Dey,"Madhubani Dey,Atrayees,WikiWorks",Decrease in the abundance of fungal species in Diabetes Mellitus patients,decreased,"k__Fungi|p__Ascomycota|c__Dothideomycetes,k__Fungi|p__Basidiomycota|c__Agaricomycetes,k__Fungi|p__Ascomycota,k__Fungi|p__Ascomycota|c__Leotiomycetes,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Capnodiales,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Pleosporaceae,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales|f__Stereaceae,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Omphalotaceae,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Pleosporaceae|g__Alternaria,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Cladosporium,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Didymellaceae|g__Ascochyta,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae|g__Mycosphaerella,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Pleosporaceae|g__Stemphylium,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales|f__Stereaceae|g__Stereum,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Cladosporium|s__Cladosporium flabelliforme,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Pleosporaceae|g__Alternaria|s__Alternaria alternata,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Didymellaceae|g__Ascochyta|s__Ascochyta herbicola,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Cladosporium|s__Cladosporium herbarum,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida parapsilosis",4751|4890|147541;4751|5204|155619;4751|4890;4751|4890|147548;4751|4890|147541|92860;4751|4890|147541|134362;4751|5204|155619|5338;4751|5204|155619|452342;4751|4890|147541|92860|28556;4751|4890|147541|2726946|452563;4751|4890|147541|2726947|93133;4751|5204|155619|452342|103376;4751|5204|155619|5338|72117;4751|4890|147541|92860|28556|5598;4751|4890|147541|2726946|452563|5498;4751|4890|147541|92860|683158|5453;4751|4890|147541|2726947|93133|41254;4751|4890|147541|92860|28556|95729;4751|5204|155619|452342|103376|5644;4751|4890|147541|2726946|452563|5498|887091;4751|4890|147541|92860|28556|5598|5599;4751|4890|147541|92860|683158|5453|749840;4751|4890|147541|2726946|452563|5498|29918;4751|4890|3239874|2916678|766764|5475|5480,Complete,Atrayees
bsdb:31834952/1/2,31834952,"cross-sectional observational, not case-control",31834952,10.1111/myc.13046,https://pubmed.ncbi.nlm.nih.gov/31834952/,"Han S.H., Lee J.S., Song K.H., Choe Y.B., Ahn K.J. , Lee Y.W.",Differences in foot skin microbiomes between patients with type 2 diabetes and healthy individuals,Mycoses,2020,"Trichophyton rubrum, biodiversity, diabetes mellitus, microbiome",Experiment 1,South Korea,Homo sapiens,"Skin of sole of pes,Interdigital space","UBERON:0036252,UBERON:0013778",Type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,"Type 2 Diabetes Mellitus patients diagnosed by an endocrinologist at Konkuk University Medical Center, Seoul, Korea",18,17,concomitant systemic (within four weeks of enrolment) or topical (within two weeks of enrolment) treatments,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,unchanged,NA,decreased,Signature 2,Table 2,7 June 2021,Madhubani Dey,"Madhubani Dey,Atrayees,WikiWorks",Increase in the abundance of fungal species in Diabetes Mellitus patients,increased,"k__Fungi|p__Basidiomycota|c__Malasseziomycetes,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Onygenales|f__Arthrodermataceae|g__Trichophyton|s__Trichophyton rubrum,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta",4751|5204|1538075;4751|5204|1538075|162474;4751|4890|147545|33183|34384|5550|5551;4751|5204|1538075|162474|742845|55193|76775,Complete,Atrayees
bsdb:31836795/1/1,31836795,case-control,31836795,10.1038/s41598-019-55667-w,NA,"Wang Q., Rao Y., Guo X., Liu N., Liu S., Wen P., Li S. , Li Y.",Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma,Scientific reports,2019,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Esophageal squamous cell carcinoma,EFO:0005922,Healthy controls,Oesophageal cancer,"patients with oesophageal cancer diagnosed by electronic gastroscopy and histopathology, with no related surgery, radiotherapy or chemotherapy for oesophageal cancer before sampling",21,20,1 month,16S,34,Illumina,relative abundances,Metastats,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 5,10 January 2021,Utsav Patel,"WikiWorks,Folakunmi",Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma (ESCC),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium",1783272|201174|1760|2037|2049|1654;1783272|201174|84998|84999|1643824|1380;3379134|1224|1236|135615|868|2717,Complete,Folakunmi
bsdb:31836795/1/2,31836795,case-control,31836795,10.1038/s41598-019-55667-w,NA,"Wang Q., Rao Y., Guo X., Liu N., Liu S., Wen P., Li S. , Li Y.",Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma,Scientific reports,2019,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Esophageal squamous cell carcinoma,EFO:0005922,Healthy controls,Oesophageal cancer,"patients with oesophageal cancer diagnosed by electronic gastroscopy and histopathology, with no related surgery, radiotherapy or chemotherapy for oesophageal cancer before sampling",21,20,1 month,16S,34,Illumina,relative abundances,Metastats,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 5,10 January 2021,Utsav Patel,"WikiWorks,Folakunmi",Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma (ESCC),decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|171551|836,Complete,Folakunmi
bsdb:31836795/2/1,31836795,case-control,31836795,10.1038/s41598-019-55667-w,NA,"Wang Q., Rao Y., Guo X., Liu N., Liu S., Wen P., Li S. , Li Y.",Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma,Scientific reports,2019,NA,Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Esophageal squamous cell carcinoma,EFO:0005922,Healthy controls,Oesophageal cancer,"patients with oesophageal cancer diagnosed by electronic gastroscopy and histopathology, with no related surgery, radiotherapy or chemotherapy for oesophageal cancer before sampling",21,20,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 6,10 January 2021,Utsav Patel,"WikiWorks,Folakunmi",Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma (ESCC),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|201174|84998|84999|1643824;1783272|201174|84998|84999|1643824|1380;1783272|201174|84998|84999;1783272|201174|84998,Complete,Folakunmi
bsdb:31836795/2/2,31836795,case-control,31836795,10.1038/s41598-019-55667-w,NA,"Wang Q., Rao Y., Guo X., Liu N., Liu S., Wen P., Li S. , Li Y.",Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma,Scientific reports,2019,NA,Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Esophageal squamous cell carcinoma,EFO:0005922,Healthy controls,Oesophageal cancer,"patients with oesophageal cancer diagnosed by electronic gastroscopy and histopathology, with no related surgery, radiotherapy or chemotherapy for oesophageal cancer before sampling",21,20,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 6,10 January 2021,Utsav Patel,"WikiWorks,Folakunmi",Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma (ESCC),decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",3384189|32066|203490|203491|203492;3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836,Complete,Folakunmi
bsdb:31837420/1/1,31837420,laboratory experiment,31837420,https://doi.org/10.1016/j.nbd.2019.104704,NA,"Yang D., Zhao D., Shah S.Z.A., Wu W., Lai M., Zhang X., Li J., Guan Z., Zhao H., Li W., Gao H., Zhou X. , Yang L.",Implications of gut microbiota dysbiosis and metabolic changes in prion disease,Neurobiology of disease,2020,"Metabolomics, Microbiome, Multi-omics analysis, Prion infection, Short chain fatty acids",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Prion disease,EFO:0004720,Healthy Control (C),Prion-infected mice (R),Prion-infected mice,25,12,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Fig. 2B,18 March 2024,Ikehdarlington,"Ikehdarlington,Scholastica,WikiWorks",Differentially abundant bacterial taxa in prion-infected groups versus healthy control groups.,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota",1783272|1239|91061;3379134|29547|3031852|213849;3379134|29547|3031852;3379134|29547|3031852|213849|72293|209;3379134|29547|3031852|213849|72293;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;3379134|1224,Complete,Svetlana up
bsdb:31837420/1/2,31837420,laboratory experiment,31837420,https://doi.org/10.1016/j.nbd.2019.104704,NA,"Yang D., Zhao D., Shah S.Z.A., Wu W., Lai M., Zhang X., Li J., Guan Z., Zhao H., Li W., Gao H., Zhou X. , Yang L.",Implications of gut microbiota dysbiosis and metabolic changes in prion disease,Neurobiology of disease,2020,"Metabolomics, Microbiome, Multi-omics analysis, Prion infection, Short chain fatty acids",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Prion disease,EFO:0004720,Healthy Control (C),Prion-infected mice (R),Prion-infected mice,25,12,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 2,Fig. 2B,18 March 2024,Ikehdarlington,"Ikehdarlington,Scholastica,WikiWorks",Differentially abundant bacterial taxa in prion-infected groups versus healthy control groups.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,p__Candidatus Saccharimonadota,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|976|200643|171549|171552|1283313;95818;95818|2093818|2093825|2171986|1331051;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|707003;3379134|976|200643|171549|171552,Complete,Svetlana up
bsdb:31841737/1/1,31841737,"cross-sectional observational, not case-control",31841737,10.1016/j.jneuroim.2019.577126,NA,"Shi Z., Qiu Y., Wang J., Fang Y., Zhang Y., Chen H., Du Q., Zhao Z., Yan C., Yang M. , Zhou H.",Dysbiosis of gut microbiota in patients with neuromyelitis optica spectrum disorders: A cross sectional study,Journal of neuroimmunology,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Neuromyelitis optica,EFO:0004256,healthy controls,neuromyelitis optica spectrum disorder,Each patient met the 2015 international diagnostic criteria for NMOSD and tested positive for serum AQP4-IgG using cell-based assays,20,20,currently on antibiotics,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 3,10 January 2021,Rimsha Azhar,WikiWorks,Abundance of gut microbiota between the NMOSD and HS groups,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224;3379134|1224|1236;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|620;1783272|1239|91061;1783272|1239|91061|1385;1783272|1239|91061|186826;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|186802|216572|1486725;1783272|1239|909932|1843489|31977|156454;1783272|1239|186801|186802|216572|946234;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300,Complete,Atrayees
bsdb:31841737/1/2,31841737,"cross-sectional observational, not case-control",31841737,10.1016/j.jneuroim.2019.577126,NA,"Shi Z., Qiu Y., Wang J., Fang Y., Zhang Y., Chen H., Du Q., Zhao Z., Yan C., Yang M. , Zhou H.",Dysbiosis of gut microbiota in patients with neuromyelitis optica spectrum disorders: A cross sectional study,Journal of neuroimmunology,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Neuromyelitis optica,EFO:0004256,healthy controls,neuromyelitis optica spectrum disorder,Each patient met the 2015 international diagnostic criteria for NMOSD and tested positive for serum AQP4-IgG using cell-based assays,20,20,currently on antibiotics,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 3, text",10 January 2021,Rimsha Azhar,"WikiWorks,Atrayees",Abundance of gut microbiota between the NMOSD and HS groups,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|1224|28216|80840|995019|40544;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|171552;1783272|1239|186801|186802;1783272|1239|186801;3379134|976|200643|171549|171552|838,Complete,Atrayees
bsdb:31842923/1/1,31842923,case-control,31842923,10.1186/s12969-019-0387-5,NA,"Grevich S., Lee P., Leroux B., Ringold S., Darveau R., Henstorf G., Berg J., Kim A., Velan E., Kelly J., Baltuck C., Reeves A., Leahey H., Hager K., Brittnacher M., Hayden H., Miller S., McLean J. , Stevens A.",Oral health and plaque microbial profile in juvenile idiopathic arthritis,Pediatric rheumatology online journal,2019,"Gingivitis, Juvenile idiopathic arthritis, Microbiota, Oral health",Experiment 1,United States of America,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Arthritis,EFO:0005856,healthy controls,Juvenile Idiopathic Arthritis,Juvenile Idiopathic Arthritis,11,85,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,Signature 1,"Figure 2, text",10 November 2022,Tislam,"Tislam,WikiWorks",c Linear discriminant analysis (LDA) through the LefSe tool. Enriched microbial communities between the two groups with a two log-fold difference or greater are shown in the LEfSe plot. d Bacteria genera found to be significantly different between the polyarticular JIA and healthy control groups.*p-value < 0.05,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85007|1653|1716;3384189|32066|203490|203491|1129771|32067;1783272|201174|1760|2037|2049,Complete,Atrayees
bsdb:31842923/1/2,31842923,case-control,31842923,10.1186/s12969-019-0387-5,NA,"Grevich S., Lee P., Leroux B., Ringold S., Darveau R., Henstorf G., Berg J., Kim A., Velan E., Kelly J., Baltuck C., Reeves A., Leahey H., Hager K., Brittnacher M., Hayden H., Miller S., McLean J. , Stevens A.",Oral health and plaque microbial profile in juvenile idiopathic arthritis,Pediatric rheumatology online journal,2019,"Gingivitis, Juvenile idiopathic arthritis, Microbiota, Oral health",Experiment 1,United States of America,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Arthritis,EFO:0005856,healthy controls,Juvenile Idiopathic Arthritis,Juvenile Idiopathic Arthritis,11,85,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,Signature 2,"Figure 2, text",10 November 2022,Tislam,"Tislam,Atrayees,WikiWorks",c Linear discriminant analysis (LDA) through the LefSe tool. Enriched microbial communities between the two groups with a two log-fold difference or greater are shown in the LEfSe plot. d Bacteria genera found to be significantly different between the polyarticular JIA and healthy control groups.*p-value < 0.05,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella",1783272|1239|91061|186826|1300|1301;3379134|1224|1236|135625|712|724|729;3384189|32066|203490|203491|1129771|32067;3379134|1224|1236|135625|712|724;3379134|1224|28216|206351|481|32257,Complete,Atrayees
bsdb:31844128/2/1,31844128,"cross-sectional observational, not case-control",31844128,10.1038/s41598-019-55720-8,NA,"Walsh D.M., Hokenstad A.N., Chen J., Sung J., Jenkins G.D., Chia N., Nelson H., Mariani A. , Walther-Antonio M.R.S.",Postmenopause as a key factor in the composition of the Endometrial Cancer Microbiome (ECbiome),Scientific reports,2019,NA,Experiment 2,United States of America,Homo sapiens,Lower part of vagina,UBERON:0015243,Endometrial cancer,MONDO:0011962,Benign,Endometrial cancer,Patients undergoing hysterectomy for endometrial cancer,67,57,2 weeks,16S,345,Illumina,relative abundances,Wald Test,0.1,TRUE,NA,NA,"body mass index,menopause,vaginal pH",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4 + Table S2,10 January 2021,Fatima Zohra,"WikiWorks,ChiomaBlessing",Bacterial OTUs differentially enriched among patients with endometrial cancer compared to Benign patients,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,ChiomaBlessing
bsdb:31844128/2/2,31844128,"cross-sectional observational, not case-control",31844128,10.1038/s41598-019-55720-8,NA,"Walsh D.M., Hokenstad A.N., Chen J., Sung J., Jenkins G.D., Chia N., Nelson H., Mariani A. , Walther-Antonio M.R.S.",Postmenopause as a key factor in the composition of the Endometrial Cancer Microbiome (ECbiome),Scientific reports,2019,NA,Experiment 2,United States of America,Homo sapiens,Lower part of vagina,UBERON:0015243,Endometrial cancer,MONDO:0011962,Benign,Endometrial cancer,Patients undergoing hysterectomy for endometrial cancer,67,57,2 weeks,16S,345,Illumina,relative abundances,Wald Test,0.1,TRUE,NA,NA,"body mass index,menopause,vaginal pH",NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4 + Table S2,10 January 2021,Fatima Zohra,"WikiWorks,ChiomaBlessing",Bacterial OTUs differentially enriched among patients with endometrial cancer compared to Benign patients,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049|28263;3379134|29547|3031852|213849|72294|194;1783272|1239|1737404|1737405|1570339|150022;3384189|32066|203490|203491|203492|848;1783272|1239|1737404|1737405|1570339|162290;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|186807|2740;1783272|1239|1737404|1737405|1570339|162289;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|201174|1760|2037|2049|184869;1783272|1239|1737404|1737405|1570339|165779,Complete,ChiomaBlessing
bsdb:31869338/1/1,31869338,"cross-sectional observational, not case-control",31869338,10.1371/journal.pone.0225622,https://pubmed.ncbi.nlm.nih.gov/31869338/,"Cram J.A., Fiore-Gartland A.J., Srinivasan S., Karuna S., Pantaleo G., Tomaras G.D., Fredricks D.N. , Kublin J.G.",Human gut microbiota is associated with HIV-reactive immunoglobulin at baseline and following HIV vaccination,PloS one,2019,NA,Experiment 1,United States of America,Homo sapiens,Mucosa of rectum,UBERON:0003346,Response to vaccine,EFO:0004645,healthy controls,Vaccinated participants,Participants who were vaccinated,16,20,NA,16S,34,Roche454,NA,Logistic Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig 4.,15 October 2023,Chinelsy,"Chinelsy,WikiWorks",The microbiota vary between participants and can be described by weighted UniFrac axis 1 (MDS1). Variations along this axis are evident at the family level within certain classes and orders.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",3379134|976|200643|171549|815;3379134|976|200643|171549|171551;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550;1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|186806;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|186807;1783272|1239|1737404|1737405|1570339;1783272|1239|186801|3082720|186804,Complete,Chinelsy
bsdb:31873965/1/1,31873965,time series / longitudinal observational,31873965,10.1002/cncr.32641,NA,"Rashidi A., Kaiser T., Graiziger C., Holtan S.G., Rehman T.U., Weisdorf D.J., Dunny G.M., Khoruts A. , Staley C.",Gut dysbiosis during antileukemia chemotherapy versus allogeneic hematopoietic cell transplantation,Cancer,2020,"dysbiosis, leukemia, microbiota, transplantation",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Leukemia,EFO:0000565,Allogeneic Hematopoetic Stem Cell Transplant,Acute anti-leukemia treatment,Patients with leukemia who underwent intensive chemotherapy (any regimen involving 4 weeks or more of hospitalization) that did not have allo-HCT,20,20,NA,16S,4,Illumina,relative abundances,LEfSe,0.01,TRUE,4,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Text,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential microbial abundance between patients with acute leukemia treated with antileukemia regimens compared with allogeneic hematopoeitic stem cell transplant,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",3379134|976|200643|171549|815|816;3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|186802|216572|216851,Complete,Claregrieve1
bsdb:31873965/1/2,31873965,time series / longitudinal observational,31873965,10.1002/cncr.32641,NA,"Rashidi A., Kaiser T., Graiziger C., Holtan S.G., Rehman T.U., Weisdorf D.J., Dunny G.M., Khoruts A. , Staley C.",Gut dysbiosis during antileukemia chemotherapy versus allogeneic hematopoietic cell transplantation,Cancer,2020,"dysbiosis, leukemia, microbiota, transplantation",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Leukemia,EFO:0000565,Allogeneic Hematopoetic Stem Cell Transplant,Acute anti-leukemia treatment,Patients with leukemia who underwent intensive chemotherapy (any regimen involving 4 weeks or more of hospitalization) that did not have allo-HCT,20,20,NA,16S,4,Illumina,relative abundances,LEfSe,0.01,TRUE,4,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Text,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential microbial abundance between patients with acute leukemia treated with antileukemia regimens compared with allogeneic hematopoeitic stem cell transplant,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,1783272|1239|186801|186802|31979|1485,Complete,Claregrieve1
bsdb:31884727/1/1,31884727,laboratory experiment,31884727,10.1002/mbo3.982,NA,"Song Y. , Gyarmati P.",Microbiota changes in a pediatric acute lymphocytic leukemia mouse model,MicrobiologyOpen,2020,"high-throughput sequencing, leukemia, metagenomics, microbiota",Experiment 1,United States of America,Mus musculus,Small intestine,UBERON:0002108,Acute lymphoblastic leukemia,EFO:0000220,Healthy Control,Fecal bacterial composition in small intestines of leukemia mice,Three-week old female mice induced leukemia using lymphomblasts from pediatric acture lymphocytic leukemia patients from ATCC,8,8,NA,16S,4,MGISEQ-2000,NA,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 4a, 4b and text",10 January 2021,William Lam,"WikiWorks,Peace Sandy",Relative abundances (a) and the ratio of relative abundances (b) of the bacterial microbiota between the fecal compositions in the small intestine of control and leukemic mice,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium|s__Dehalobacterium formicoaceticum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",3379134|74201|203494|48461|1647988|239934;1783272|544448|31969|186332|186333|2086;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|830;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|186807|51514|51515;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572|1263,Complete,Peace Sandy
bsdb:31884727/1/2,31884727,laboratory experiment,31884727,10.1002/mbo3.982,NA,"Song Y. , Gyarmati P.",Microbiota changes in a pediatric acute lymphocytic leukemia mouse model,MicrobiologyOpen,2020,"high-throughput sequencing, leukemia, metagenomics, microbiota",Experiment 1,United States of America,Mus musculus,Small intestine,UBERON:0002108,Acute lymphoblastic leukemia,EFO:0000220,Healthy Control,Fecal bacterial composition in small intestines of leukemia mice,Three-week old female mice induced leukemia using lymphomblasts from pediatric acture lymphocytic leukemia patients from ATCC,8,8,NA,16S,4,MGISEQ-2000,NA,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 4a, 4b and text",10 January 2021,William Lam,"WikiWorks,Peace Sandy",Relative abundances (a) and the ratio of relative abundances (b) of the bacterial microbiota between the fecal compositions in the small intestine of control and leukemic mice,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",1783272|201174|84998|1643822|1643826|447020;1783272|1239|91061|186826|33958|1578;1783272|1239|526524|526525|2810281|191303,Complete,Peace Sandy
bsdb:31884727/2/1,31884727,laboratory experiment,31884727,10.1002/mbo3.982,NA,"Song Y. , Gyarmati P.",Microbiota changes in a pediatric acute lymphocytic leukemia mouse model,MicrobiologyOpen,2020,"high-throughput sequencing, leukemia, metagenomics, microbiota",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,Healthy Control,Fecal bacterial composition of leukemia mice,Three-week old female mice induced leukemia using lymphomblasts from pediatric acture lymphocytic leukemia patients from ATCC,8,8,NA,16S,4,MGISEQ-2000,NA,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,text (subset of Figure 2),7 March 2024,Lwaldron,"Lwaldron,WikiWorks",Increased relative abundance in leukemic mice compared to control mice,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus",1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;3379134|1224|28216|80840|119060|48736;1783272|1239|91061|186826|1300|1357,Complete,NA
bsdb:31884727/2/2,31884727,laboratory experiment,31884727,10.1002/mbo3.982,NA,"Song Y. , Gyarmati P.",Microbiota changes in a pediatric acute lymphocytic leukemia mouse model,MicrobiologyOpen,2020,"high-throughput sequencing, leukemia, metagenomics, microbiota",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,Healthy Control,Fecal bacterial composition of leukemia mice,Three-week old female mice induced leukemia using lymphomblasts from pediatric acture lymphocytic leukemia patients from ATCC,8,8,NA,16S,4,MGISEQ-2000,NA,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2,7 March 2024,Lwaldron,"Lwaldron,WikiWorks",Decreased relative abundance in leukemic mice compared to control mice. I skipped the middle part of Figure 2 where the two groups look almost the same.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85011|2062|1883;1783272|1239|186801|186802|31979;3384189|32066|203490|203491|203492|848;1783272|1239|526524|526525|2810281|191303;3379134|74201|203494|48461|1647988|239934,Complete,NA
bsdb:31887116/1/NA,31887116,laboratory experiment,31887116,10.1371/journal.pone.0226835,NA,"Hantschel J., Weis S., Schäfer K.H., Menger M.D., Kohl M., Egert M. , Laschke M.W.",Effect of endometriosis on the fecal bacteriota composition of mice during the acute phase of lesion formation,PloS one,2019,NA,Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Sham(Healthy controls),Endometriosis mice,Mice for whom endometrial tissue was transplanted into the peritoneal cavity to simulate endometriosis. The sample was taken 3 days before the transplantation of uterine tissue fragments,6,8,NA,16S,45,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:31887116/2/NA,31887116,laboratory experiment,31887116,10.1371/journal.pone.0226835,NA,"Hantschel J., Weis S., Schäfer K.H., Menger M.D., Kohl M., Egert M. , Laschke M.W.",Effect of endometriosis on the fecal bacteriota composition of mice during the acute phase of lesion formation,PloS one,2019,NA,Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Sham(Healthy controls),Endometriosis mice,Mice for whom endometrial tissue was transplanted into the peritoneal cavity to simulate endometriosis. The sample was taken 7 days after the induction of endometriosis (after EI).,8,8,NA,16S,45,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:31887116/3/NA,31887116,laboratory experiment,31887116,10.1371/journal.pone.0226835,NA,"Hantschel J., Weis S., Schäfer K.H., Menger M.D., Kohl M., Egert M. , Laschke M.W.",Effect of endometriosis on the fecal bacteriota composition of mice during the acute phase of lesion formation,PloS one,2019,NA,Experiment 3,United States of America,Mus musculus,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Sham(Healthy controls),Endometriosis mice,Mice for whom endometrial tissue was transplanted into the peritoneal cavity to simulate endometriosis. The sample was taken 21 days after the induction of endometriosis (after EI).,7,5,NA,16S,45,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:31891538/1/1,31891538,case-control,31891538,10.1152/ajpendo.00266.2019,https://pubmed.ncbi.nlm.nih.gov/31891538/,"Xu Y., Zhang M., Zhang J., Sun Z., Ran L., Ban Y., Wang B., Hou X., Zhai S., Ren L., Wang M. , Hu J.",Differential intestinal and oral microbiota features associated with gestational diabetes and maternal inflammation,American journal of physiology. Endocrinology and metabolism,2020,"16S rRNA, gestational diabetes mellitus, intestinal microbiota, oral microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Healthy controls,Individuals with gestational diabetes,Individuals with gestational diabetes at third trimester during pregnancy,31,30,2 weeks,16S,34,Illumina,relative abundances,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 1 D,27 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1,Davvve,WikiWorks",Differential microbial abundance between individuals diagnosed with gestational diabetes and healthy controls.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales",3379134|1224|1236;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712;3379134|1224|1236|135625,Complete,Claregrieve1
bsdb:31891538/1/2,31891538,case-control,31891538,10.1152/ajpendo.00266.2019,https://pubmed.ncbi.nlm.nih.gov/31891538/,"Xu Y., Zhang M., Zhang J., Sun Z., Ran L., Ban Y., Wang B., Hou X., Zhai S., Ren L., Wang M. , Hu J.",Differential intestinal and oral microbiota features associated with gestational diabetes and maternal inflammation,American journal of physiology. Endocrinology and metabolism,2020,"16S rRNA, gestational diabetes mellitus, intestinal microbiota, oral microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Healthy controls,Individuals with gestational diabetes,Individuals with gestational diabetes at third trimester during pregnancy,31,30,2 weeks,16S,34,Illumina,relative abundances,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 1 D,27 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1,Davvve,WikiWorks",Differential microbial abundance between individuals diagnosed with gestational diabetes and healthy controls.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",3379134|976|200643|171549|171550|239759;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171550,Complete,Claregrieve1
bsdb:31891538/2/1,31891538,case-control,31891538,10.1152/ajpendo.00266.2019,https://pubmed.ncbi.nlm.nih.gov/31891538/,"Xu Y., Zhang M., Zhang J., Sun Z., Ran L., Ban Y., Wang B., Hou X., Zhai S., Ren L., Wang M. , Hu J.",Differential intestinal and oral microbiota features associated with gestational diabetes and maternal inflammation,American journal of physiology. Endocrinology and metabolism,2020,"16S rRNA, gestational diabetes mellitus, intestinal microbiota, oral microbiota",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Gestational diabetes,EFO:0004593,Healthy controls,Individuals with gestational diabetes,Individuals with gestational diabetes at third trimester during pregnancy,31,30,2 weeks,16S,34,Illumina,relative abundances,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,2,NA,NA,NA,unchanged,decreased,unchanged,NA,NA,Signature 1,Figure 2D,9 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1,WikiWorks",Differential microbial abundance between individuals diagnosed with gestational diabetes and healthy controls,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|909932|909929|1843491|970,Complete,Claregrieve1
bsdb:31891538/2/2,31891538,case-control,31891538,10.1152/ajpendo.00266.2019,https://pubmed.ncbi.nlm.nih.gov/31891538/,"Xu Y., Zhang M., Zhang J., Sun Z., Ran L., Ban Y., Wang B., Hou X., Zhai S., Ren L., Wang M. , Hu J.",Differential intestinal and oral microbiota features associated with gestational diabetes and maternal inflammation,American journal of physiology. Endocrinology and metabolism,2020,"16S rRNA, gestational diabetes mellitus, intestinal microbiota, oral microbiota",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Gestational diabetes,EFO:0004593,Healthy controls,Individuals with gestational diabetes,Individuals with gestational diabetes at third trimester during pregnancy,31,30,2 weeks,16S,34,Illumina,relative abundances,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,2,NA,NA,NA,unchanged,decreased,unchanged,NA,NA,Signature 2,Figure 2D,27 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1,WikiWorks",Differential microbial abundance between individuals diagnosed with gestational diabetes and healthy controls,decreased,"k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc",3384189|32066;3384189|32066|203490|203491|203492;3384189|32066|203490;1783272|1239|186801|3085636|186803|1164882;1783272|1239|91061|186826|33958;3384189|32066|203490|203491|1129771|32067;3384189|32066|203490|203491|1129771;1783272|1239|91061|186826|33958|1243,Complete,Claregrieve1
bsdb:31905907/1/1,31905907,"cross-sectional observational, not case-control",31905907,10.3390/ijerph17010256,https://pubmed.ncbi.nlm.nih.gov/31905907/,"Al-Zyoud W., Hajjo R., Abu-Siniyeh A. , Hajjaj S.",Salivary Microbiome and Cigarette Smoking: A First of Its Kind Investigation in Jordan,International journal of environmental research and public health,2019,"16S rRNA, Jordan, bioinformatics, microbiome, microbiota, next-generation sequencing, operational taxonomic unit (OTU), saliva, smoking",Experiment 1,Jordan,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Non-smokers,Smokers,Smoking subjects who smoked at least one cigarette per day.,51,49,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,3,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,"Table 3, 4",3 April 2023,Khadeeejah,"Khadeeejah,Atrayees,Claregrieve1,WikiWorks",Differential microbial abundance between non-smokers versus smokers (regardless of gender).,increased,"k__Bacillati|p__Bacillota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239;3384189|32066|203490;3379134|976|200643|171549|171552|838;3379134|1224;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:31905907/1/2,31905907,"cross-sectional observational, not case-control",31905907,10.3390/ijerph17010256,https://pubmed.ncbi.nlm.nih.gov/31905907/,"Al-Zyoud W., Hajjo R., Abu-Siniyeh A. , Hajjaj S.",Salivary Microbiome and Cigarette Smoking: A First of Its Kind Investigation in Jordan,International journal of environmental research and public health,2019,"16S rRNA, Jordan, bioinformatics, microbiome, microbiota, next-generation sequencing, operational taxonomic unit (OTU), saliva, smoking",Experiment 1,Jordan,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Non-smokers,Smokers,Smoking subjects who smoked at least one cigarette per day.,51,49,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,3,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,"Table 3, 4",3 April 2023,Khadeeejah,"Khadeeejah,Atrayees,Claregrieve1,WikiWorks",Differential microbial abundance between non-smokers versus smokers (regardless of gender).,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,3379134|1224|28216|206351|481|482,Complete,Claregrieve1
bsdb:31905907/2/1,31905907,"cross-sectional observational, not case-control",31905907,10.3390/ijerph17010256,https://pubmed.ncbi.nlm.nih.gov/31905907/,"Al-Zyoud W., Hajjo R., Abu-Siniyeh A. , Hajjaj S.",Salivary Microbiome and Cigarette Smoking: A First of Its Kind Investigation in Jordan,International journal of environmental research and public health,2019,"16S rRNA, Jordan, bioinformatics, microbiome, microbiota, next-generation sequencing, operational taxonomic unit (OTU), saliva, smoking",Experiment 2,Jordan,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Non-smokers,Smokers,Smoker subjects smoked at least one cigarette per day.,51,49,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,"Figure 7, Table 5",30 May 2023,Atrayees,"Atrayees,Claregrieve1,WikiWorks",Differential microbial abundance between non-smokers versus smokers by LefSe,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. (in: firmicutes)",1783272|201174|1760|2037|2049|1654;1783272|201174|84998|84999|1643824|1380;1783272|1239|909932|1843489|31977|906;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|1385|186817|1386|1409,Complete,Claregrieve1
bsdb:31905907/2/2,31905907,"cross-sectional observational, not case-control",31905907,10.3390/ijerph17010256,https://pubmed.ncbi.nlm.nih.gov/31905907/,"Al-Zyoud W., Hajjo R., Abu-Siniyeh A. , Hajjaj S.",Salivary Microbiome and Cigarette Smoking: A First of Its Kind Investigation in Jordan,International journal of environmental research and public health,2019,"16S rRNA, Jordan, bioinformatics, microbiome, microbiota, next-generation sequencing, operational taxonomic unit (OTU), saliva, smoking",Experiment 2,Jordan,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Non-smokers,Smokers,Smoker subjects smoked at least one cigarette per day.,51,49,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,"Figure 7, Table 5",30 May 2023,Atrayees,"Atrayees,Claregrieve1,WikiWorks",Differential microbial abundance between non-smokers versus smokers by LefSe,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Pseudomonadati|p__Pseudomonadota",3379134|976|117743|200644|2762318|59735;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135625|712|724;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|2005525|195950;3384189|32066|203490;3379134|1224,Complete,Claregrieve1
bsdb:31916654/1/1,31916654,case-control,31916654,10.1111/odi.13277,NA,"Belstrøm D., Eiberg J.M., Enevold C., Grande M.A., Jensen C.A.J., Skov L. , Hansen P.R.",Salivary microbiota and inflammation-related proteins in patients with psoriasis,Oral diseases,2020,"inflammation, microbiota, periodontitis, psoriasis, saliva",Experiment 1,Denmark,Homo sapiens,Saliva,UBERON:0001836,Psoriasis,EFO:0000676,orally healthy individuals,Psoriasis patient,NA,52,27,3 months,16S,123,Illumina,relative abundances,LEfSe,1e-4,TRUE,2,NA,NA,unchanged,NA,unchanged,NA,NA,unchanged,Signature 1,Figure 2(b),30 March 2023,Ellajessica,"Ellajessica,Aiyshaaaa,WikiWorks",Using Linear discriminant effect size analysis. Linear discriminant analysis score expressed as (log 10) of significant bacterial taxa between healthy controls and Psoriasis.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter sp.,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria perflava,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa",3379134|1224|1236|135625|712|416916|1872413;3379134|976|117743|200644|49546|1016|44737;3379134|1224|1236|135625|712|724|729;3379134|1224|28216|206351|481|482|33053;1783272|1239|1737404|1737405|1570339|162289|33031;3379134|976|200643|171549|171552|838|28132;1783272|201174|1760|85006|1268|32207|43675,Complete,Atrayees
bsdb:31916654/1/2,31916654,case-control,31916654,10.1111/odi.13277,NA,"Belstrøm D., Eiberg J.M., Enevold C., Grande M.A., Jensen C.A.J., Skov L. , Hansen P.R.",Salivary microbiota and inflammation-related proteins in patients with psoriasis,Oral diseases,2020,"inflammation, microbiota, periodontitis, psoriasis, saliva",Experiment 1,Denmark,Homo sapiens,Saliva,UBERON:0001836,Psoriasis,EFO:0000676,orally healthy individuals,Psoriasis patient,NA,52,27,3 months,16S,123,Illumina,relative abundances,LEfSe,1e-4,TRUE,2,NA,NA,unchanged,NA,unchanged,NA,NA,unchanged,Signature 2,Figure 2(b),30 March 2023,Ellajessica,"Ellajessica,Aiyshaaaa,WikiWorks",Using Linear discriminant effect size analysis. Linear discriminant analysis score expressed as (log 10) of significant bacterial taxa between healthy controls and Psoriasis.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria macacae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sobrinus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp.",1783272|201174|1760|2037|2049|1654|29317;1783272|201174|1760|85009|31957|2801844|1750;3379134|976|117743|200644|49546|1016|44737;1783272|1239|91061|186826|33958|1578|1596;3379134|1224|28216|206351|481|482|496;1783272|1239|91061|186826|1300|1301|1309;1783272|1239|91061|186826|1300|1301|1310;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843489|31977|29465|1926307,Complete,Atrayees
bsdb:31916654/2/1,31916654,case-control,31916654,10.1111/odi.13277,NA,"Belstrøm D., Eiberg J.M., Enevold C., Grande M.A., Jensen C.A.J., Skov L. , Hansen P.R.",Salivary microbiota and inflammation-related proteins in patients with psoriasis,Oral diseases,2020,"inflammation, microbiota, periodontitis, psoriasis, saliva",Experiment 2,Denmark,Homo sapiens,Saliva,UBERON:0001836,Psoriasis,EFO:0000676,periodntitis,Psoriasis,Individuals who have been diagnosed with Psoriasis.,27,58,3 months,16S,123,Illumina,relative abundances,LEfSe,0.001,TRUE,2,NA,NA,unchanged,NA,unchanged,NA,NA,unchanged,Signature 1,Figure 2(a),24 April 2023,Aiyshaaaa,"Aiyshaaaa,WikiWorks",Using Linear discriminant effect size analysis. Linear discriminant analysis score expressed as (log 10) of significant bacterial taxa between Periodontitis (P) versus Psoriasis (PS).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio sp.,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sp.,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella denitrificans,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia shahii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium neglectum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria perflava,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.",3379134|1224|1236|135625|712|416916|1872413;1783272|1239|186801|3085636|186803|830|28121;3379134|29547|3031852|213849|72294|194|199;3379134|976|117743|200644|49546|1016|44737;3384189|32066|203490|203491|203492|848|68766;1783272|1239|91061|1385|539738|1378|29391;3379134|1224|28216|206351|481|32257|502;3384189|32066|203490|203491|1129771|32067|157691;3384189|32066|203490|203491|1129771|32067|104608;1783272|1239|186801|3082720|543314|86331|114528;3379134|1224|28216|206351|481|482|33053;3379134|1224|28216|206351|481|482|28449;3379134|976|200643|171549|171551|836|1924944;3379134|976|200643|171549|171552|838|60133;3379134|976|200643|171549|171552|838|59823;1783272|1239|91061|186826|1300|1301|1306,Complete,Atrayees
bsdb:31916654/2/2,31916654,case-control,31916654,10.1111/odi.13277,NA,"Belstrøm D., Eiberg J.M., Enevold C., Grande M.A., Jensen C.A.J., Skov L. , Hansen P.R.",Salivary microbiota and inflammation-related proteins in patients with psoriasis,Oral diseases,2020,"inflammation, microbiota, periodontitis, psoriasis, saliva",Experiment 2,Denmark,Homo sapiens,Saliva,UBERON:0001836,Psoriasis,EFO:0000676,periodntitis,Psoriasis,Individuals who have been diagnosed with Psoriasis.,27,58,3 months,16S,123,Illumina,relative abundances,LEfSe,0.001,TRUE,2,NA,NA,unchanged,NA,unchanged,NA,NA,unchanged,Signature 2,Figure 2(a),24 April 2023,Aiyshaaaa,"Aiyshaaaa,WikiWorks",Using Linear discriminant effect size analysis. Linear discriminant analysis score expressed as (log 10) of significant bacterial taxa between Periodontitis (P) versus Psoriasis (PS).,decreased,"k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium sp.,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium naviforme,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp.,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus|s__Desulfobulbus sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium timidum,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma faucium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella pleuritidis,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema socranskii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa",3384194|508458|649775|649776|3029087|1434006|2699746;3379134|203691|203692|136|2845253|157|158;3384189|32066|203490|203491|203492|848|77917;3379134|203691|203692|136|2845253|157|166;3384194|508458|649775|649776|3029087|1434006|651822;1783272|1239|91061|186826|1300|1301|76860;3379134|976|200643|171549|171551|836|837;1783272|201174|1760|85006|1268|32207|2047;3379134|200940|3031451|3024411|213121|893|895;3379134|976|200643|171549|2005525|195950|28112;1783272|1239|186801|3082720|543314|86331|35519;1783272|544448|2790996|2895623|2895509|56142;3379134|976|200643|171549|171552|2974257|407975;3379134|203691|203692|136|2845253|157|53419;3384189|32066|203490|203491|203492|848;1783272|1239|91061|186826|1300|1301|1309;1783272|1239|186801|3082720|3118655|44259|143361;3379134|976|200643|171549|171552|838|28131;3379134|976|200643|171549|171551|836|28124;1783272|201174|1760|2037|2049|2529408|1660;1783272|201174|1760|85006|1268|32207|43675,Complete,Atrayees
bsdb:31916654/3/1,31916654,case-control,31916654,10.1111/odi.13277,NA,"Belstrøm D., Eiberg J.M., Enevold C., Grande M.A., Jensen C.A.J., Skov L. , Hansen P.R.",Salivary microbiota and inflammation-related proteins in patients with psoriasis,Oral diseases,2020,"inflammation, microbiota, periodontitis, psoriasis, saliva",Experiment 3,Denmark,Homo sapiens,Saliva,UBERON:0001836,Periodontitis,EFO:0000649,orally healthy individuals,Periodontitis patients,Patients who have been diagnosed with periodontitis,52,27,3 months,16S,123,Illumina,NA,LEfSe,0.001,TRUE,2,NA,NA,unchanged,NA,unchanged,NA,NA,unchanged,Signature 1,Figure 2(c),31 May 2023,Atrayees,"Atrayees,WikiWorks",Using Linear discriminant effect size analysis. Linear discriminant analysis score expressed as (log 10) of significant bacterial taxa between healthy controls versus Periodontitis (P).,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia|s__Bulleidia extructa,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus|s__Desulfobulbus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium sp.,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella pleuritidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus ultunensis,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma faucium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium timidum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|s__Peptostreptococcaceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella dentalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema lecithinolyticum,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema socranskii,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp.",1783272|201174|1760|2037|2049|1654|544580;3379134|976|200643|171549|171552|1283313|76122;1783272|1239|526524|526525|128827|118747|118748;3379134|29547|3031852|213849|72294|194|205;1783272|1239|186801|186802|1898207;3379134|200940|3031451|3024411|213121|893|895;1783272|1239|186801|3082720|3118655|44259|143361;3384194|508458|649775|649776|3029087|1434006|651822;3384194|508458|649775|649776|3029087|1434006|2699746;3384189|32066|203490|203491|203492|848|851;3384189|32066|203490|203491|203492|848|68766;3379134|1224|1236|135625|712|724|729;3379134|976|200643|171549|171552|2974257|407975;1783272|1239|91061|186826|33958|1578|227945;1783272|544448|2790996|2895623|2895509|56142;1783272|1239|186801|3082720|543314|86331|35519;1783272|1239|186801|3082720|186804|1904861;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|171551|836|837;3379134|976|200643|171549|171552|838|52227;3379134|976|200643|171549|171552|838|28131;3379134|976|200643|171549|171552|838|59823;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|2047;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|91061|186826|1300|1301|76860;3379134|976|200643|171549|2005525|195950|28112;3379134|203691|203692|136|2845253|157|59892;3379134|203691|203692|136|2845253|157|158;3379134|203691|203692|136|2845253|157|53418;3379134|203691|203692|136|2845253|157|53419;3379134|203691|203692|136|2845253|157|166,Complete,Atrayees
bsdb:31916654/3/2,31916654,case-control,31916654,10.1111/odi.13277,NA,"Belstrøm D., Eiberg J.M., Enevold C., Grande M.A., Jensen C.A.J., Skov L. , Hansen P.R.",Salivary microbiota and inflammation-related proteins in patients with psoriasis,Oral diseases,2020,"inflammation, microbiota, periodontitis, psoriasis, saliva",Experiment 3,Denmark,Homo sapiens,Saliva,UBERON:0001836,Periodontitis,EFO:0000649,orally healthy individuals,Periodontitis patients,Patients who have been diagnosed with periodontitis,52,27,3 months,16S,123,Illumina,NA,LEfSe,0.001,TRUE,2,NA,NA,unchanged,NA,unchanged,NA,NA,unchanged,Signature 2,Figure 2(c),31 May 2023,Atrayees,"Atrayees,WikiWorks",Using Linear discriminant effect size analysis. Linear discriminant analysis score expressed as (log 10) of significant bacterial taxa between healthy controls versus Periodontitis (P).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella denticariosi,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella saccharolytica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella sp. (in: b-proteobacteria),k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ottowia|s__Ottowia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium neglectum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus durans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium vescum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria macacae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola",3379134|976|117743|200644|49546|1016|1017;1783272|1239|91061|186826|186828|117563|137732;1783272|1239|909932|1843489|31977|29465|419208;3379134|1224|28216|206351|481|482|192066;1783272|1239|186801|3085636|186803|1898203;3384189|32066|203490|203491|1129771|32067|104608;3379134|976|200643|171549|171552|2974257|633701;1783272|1239|909932|909929|1843491|52225|2049034;3379134|1224|28216|206351|481|32257|2020713;3379134|1224|28216|80840|80864|219181|1898956;1783272|1239|186801|3082720|543314|86331|114528;3384189|32066|203490|203491|1129771|32067|40542;1783272|201174|1760|85009|31957|2801844|1750;3379134|1224|1236|135625|712|416916|1872413;1783272|1239|91061|186826|81852|1350|53345;1783272|1239|186801|186802|216572|2485925;3379134|1224|28216|206351|481|482|1107316;1783272|1239|186801|3082720|543314|86331|86333;1783272|1239|526524|526525|128827|123375|102148;3379134|1224|28216|206351|481|482|496;3379134|976|200643|171549|171552|838|470565,Complete,Atrayees
bsdb:31917273/1/1,31917273,case-control,31917273,10.1016/j.micpath.2019.103943,https://pubmed.ncbi.nlm.nih.gov/31917273/,"Yuan X., Wang L., Meng D., Wu L., Wang X., Zhang D., Luo Z., Pang Y. , Liu G.",The impact of NBUVB on microbial community profiling in the lesional skin of vitiligo subjects,Microbial pathogenesis,2020,"16S rRNA, Bacterial diversity, Cutaneous microbiome, Vitiligo",Experiment 1,China,Homo sapiens,Skin of body,UBERON:0002097,Vitiligo,EFO:0004208,Vitiligo patients before narrowband UV (NBUVB) light irradiation in normal skin (NF group),Vitiligo patients after NBUVB irradiation on normal skin (NB group),"Vitiligo patients after NBUVB irradiation on normal skin (NB group); Vitiligo patients recruited from Weifang Medical University Hospital, Shandong, China, from February 2018 to January 2019.",15,15,6 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 1,"within results text (Alterations in the composition of cutaneous microbiota associated with vitiligo at the phylum level, lines 7-9)",24 April 2023,Atrayees,"Atrayees,Folakunmi,WikiWorks",Relative abundance of predominant bacteria at phylum and genus level in the NF and NB groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Cyanobacteriota",3379134|976|200643;1783272|1117,Complete,Folakunmi
bsdb:31917273/1/2,31917273,case-control,31917273,10.1016/j.micpath.2019.103943,https://pubmed.ncbi.nlm.nih.gov/31917273/,"Yuan X., Wang L., Meng D., Wu L., Wang X., Zhang D., Luo Z., Pang Y. , Liu G.",The impact of NBUVB on microbial community profiling in the lesional skin of vitiligo subjects,Microbial pathogenesis,2020,"16S rRNA, Bacterial diversity, Cutaneous microbiome, Vitiligo",Experiment 1,China,Homo sapiens,Skin of body,UBERON:0002097,Vitiligo,EFO:0004208,Vitiligo patients before narrowband UV (NBUVB) light irradiation in normal skin (NF group),Vitiligo patients after NBUVB irradiation on normal skin (NB group),"Vitiligo patients after NBUVB irradiation on normal skin (NB group); Vitiligo patients recruited from Weifang Medical University Hospital, Shandong, China, from February 2018 to January 2019.",15,15,6 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 2,"within results text (Alterations in the composition of cutaneous microbiota associated with vitiligo at the phylum level, lines 7-9)",2 February 2024,Folakunmi,"Folakunmi,WikiWorks",Relative abundance of predominant bacteria at phylum and genus level in the NF and NB groups.,decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota",1783272|201174;3379134|1224,Complete,Folakunmi
bsdb:31917273/2/1,31917273,case-control,31917273,10.1016/j.micpath.2019.103943,https://pubmed.ncbi.nlm.nih.gov/31917273/,"Yuan X., Wang L., Meng D., Wu L., Wang X., Zhang D., Luo Z., Pang Y. , Liu G.",The impact of NBUVB on microbial community profiling in the lesional skin of vitiligo subjects,Microbial pathogenesis,2020,"16S rRNA, Bacterial diversity, Cutaneous microbiome, Vitiligo",Experiment 2,China,Homo sapiens,Skin of body,UBERON:0002097,Vitiligo,EFO:0004208,Normal skin of Vitiligo patients before narrowband UV (NBUVB) light irradiation (NF group),Lesional skin of Vitiligo patients after NBUVB irradiation (DB group),"Lesional skin of Vitiligo patients after NBUVB irradiation (DB group); Vitiligo patients recruited from Weifang Medical University Hospital, Shandong, China, from February 2018 to January 2019.",15,15,6 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"within results text (Alterations in the composition of cutaneous microbiota associated with vitiligo at the phylum level, lines 9-11)",2 February 2024,Folakunmi,"Folakunmi,WikiWorks",Relative abundance of predominant bacteria at phylum and genus level in the NF and DB groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Pseudomonadota",3379134|976|200643;3379134|1224,Complete,Folakunmi
bsdb:31917273/2/2,31917273,case-control,31917273,10.1016/j.micpath.2019.103943,https://pubmed.ncbi.nlm.nih.gov/31917273/,"Yuan X., Wang L., Meng D., Wu L., Wang X., Zhang D., Luo Z., Pang Y. , Liu G.",The impact of NBUVB on microbial community profiling in the lesional skin of vitiligo subjects,Microbial pathogenesis,2020,"16S rRNA, Bacterial diversity, Cutaneous microbiome, Vitiligo",Experiment 2,China,Homo sapiens,Skin of body,UBERON:0002097,Vitiligo,EFO:0004208,Normal skin of Vitiligo patients before narrowband UV (NBUVB) light irradiation (NF group),Lesional skin of Vitiligo patients after NBUVB irradiation (DB group),"Lesional skin of Vitiligo patients after NBUVB irradiation (DB group); Vitiligo patients recruited from Weifang Medical University Hospital, Shandong, China, from February 2018 to January 2019.",15,15,6 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"within results text (Alterations in the composition of cutaneous microbiota associated with vitiligo at the phylum level, lines 9-11)",2 February 2024,Folakunmi,"Folakunmi,WikiWorks",Relative abundance of predominant bacteria at phylum and genus level in the NF and DB groups.,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota",1783272|1239;1783272|201174,Complete,Folakunmi
bsdb:31917273/3/1,31917273,case-control,31917273,10.1016/j.micpath.2019.103943,https://pubmed.ncbi.nlm.nih.gov/31917273/,"Yuan X., Wang L., Meng D., Wu L., Wang X., Zhang D., Luo Z., Pang Y. , Liu G.",The impact of NBUVB on microbial community profiling in the lesional skin of vitiligo subjects,Microbial pathogenesis,2020,"16S rRNA, Bacterial diversity, Cutaneous microbiome, Vitiligo",Experiment 3,China,Homo sapiens,Skin of body,UBERON:0002097,Vitiligo,EFO:0004208,Lesional skin of Vitiligo patients before irradiation (DF group),Lesional skin of Vitiligo patients after NBUVB irradiation (DB group),"Lesional skin of Vitiligo patients after NBUVB irradiation (DB group); Vitiligo patients recruited from Weifang Medical University Hospital, Shandong, China, from February 2018 to January 2019.",15,15,6 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,decreased,Signature 1,"within results text (Alterations in the composition of cutaneous microbiota associated with vitiligo at the phylum level, lines 12-14)",2 February 2024,Folakunmi,"Folakunmi,WikiWorks",Relative abundance of predominant bacteria at phylum and genus level in the DF and DB groups.,increased,"k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Actinomycetota",3379134|1224;1783272|201174,Complete,Folakunmi
bsdb:31917273/3/2,31917273,case-control,31917273,10.1016/j.micpath.2019.103943,https://pubmed.ncbi.nlm.nih.gov/31917273/,"Yuan X., Wang L., Meng D., Wu L., Wang X., Zhang D., Luo Z., Pang Y. , Liu G.",The impact of NBUVB on microbial community profiling in the lesional skin of vitiligo subjects,Microbial pathogenesis,2020,"16S rRNA, Bacterial diversity, Cutaneous microbiome, Vitiligo",Experiment 3,China,Homo sapiens,Skin of body,UBERON:0002097,Vitiligo,EFO:0004208,Lesional skin of Vitiligo patients before irradiation (DF group),Lesional skin of Vitiligo patients after NBUVB irradiation (DB group),"Lesional skin of Vitiligo patients after NBUVB irradiation (DB group); Vitiligo patients recruited from Weifang Medical University Hospital, Shandong, China, from February 2018 to January 2019.",15,15,6 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,decreased,Signature 2,"within results text (Alterations in the composition of cutaneous microbiota associated with vitiligo at the phylum level, lines 12-14)",2 February 2024,Folakunmi,"Folakunmi,WikiWorks",Relative abundance of predominant bacteria at phylum and genus level in the DF and DB groups.,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Folakunmi
bsdb:31934770/1/1,31934770,"cross-sectional observational, not case-control",31934770,10.1089/chi.2019.0280,NA,"Da Silva C.C., Monteil M.A. , Davis E.M.",Overweight and Obesity in Children Are Associated with an Abundance of Firmicutes and Reduction of Bifidobacterium in Their Gastrointestinal Microbiota,Childhood obesity (Print),2020,"bifidobacterium, children, firmicutes, gut, microbiome, obesity",Experiment 1,Trinidad and Tobago,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal,overweight/obesity,school aged children (6-14 years),30,21,3 months,16S,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Table 2 & 3,10 January 2021,Mst Afroza Parvin,WikiWorks,The Relative Abundance (%) of the Most Dominant Bacterial Families & genus from Stool Samples at Varying Demographic and Anthropometric Measure,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,NA
bsdb:31934770/1/2,31934770,"cross-sectional observational, not case-control",31934770,10.1089/chi.2019.0280,NA,"Da Silva C.C., Monteil M.A. , Davis E.M.",Overweight and Obesity in Children Are Associated with an Abundance of Firmicutes and Reduction of Bifidobacterium in Their Gastrointestinal Microbiota,Childhood obesity (Print),2020,"bifidobacterium, children, firmicutes, gut, microbiome, obesity",Experiment 1,Trinidad and Tobago,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal,overweight/obesity,school aged children (6-14 years),30,21,3 months,16S,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,Table 2 & 3,10 January 2021,Mst Afroza Parvin,WikiWorks,The Relative Abundance (%) of the Most Dominant Bacterial Families & genus from Stool Samples at Varying Demographic and Anthropometric Measure,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678,Complete,NA
bsdb:31935575/1/1,31935575,laboratory experiment,31935575,10.1016/j.chemosphere.2020.125879,NA,"Liu W., Zhou Y., Yong Li Y., Qin L., Yu R., Li Y., Chen Y. , Xu .",Effects of PM<sub>2.5</sub> exposure during gestation on maternal gut microbiota and pregnancy outcomes,Chemosphere,2020,"Gut microbiota, PM(2.5), Pregnancy outcomes, Short chain fatty acids",Experiment 1,China,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,mice exposed suspension from extracts of “blank” filter,mice exposed to Pm 2.5 suspension,exposed to PM2.5 suspension,12,12,NA,16S,34,Illumina,relative abundances,LEfSe,2,FALSE,2,NA,NA,NA,increased,unchanged,increased,NA,unchanged,Signature 1,"Figure 4a, text",10 January 2021,Zyaijah Bailey,"Lwaldron,WikiWorks,Merit","the most differentially abundant taxa between the two groups were identified through the LDA score which was generated from LEfSe analysis (phylum to genus: p, phylum; c, class; o, order; f, family; g, genus)",increased,"c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Pseudomonadota,p__candidate phylum NAG2,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp.,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.",28221;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;1783272|1239|186801|186802|216572|946234;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;3384189|32066|203490|203491|203492|848;1783272|1239|186801|186802|216572|459786;3379134|1224;1448937;1783272|1239|186801|186802|216572|459786|1945593;3384189|32066|203490|203491|203492|848|68766,Complete,Atrayees
bsdb:31935575/1/2,31935575,laboratory experiment,31935575,10.1016/j.chemosphere.2020.125879,NA,"Liu W., Zhou Y., Yong Li Y., Qin L., Yu R., Li Y., Chen Y. , Xu .",Effects of PM<sub>2.5</sub> exposure during gestation on maternal gut microbiota and pregnancy outcomes,Chemosphere,2020,"Gut microbiota, PM(2.5), Pregnancy outcomes, Short chain fatty acids",Experiment 1,China,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,mice exposed suspension from extracts of “blank” filter,mice exposed to Pm 2.5 suspension,exposed to PM2.5 suspension,12,12,NA,16S,34,Illumina,relative abundances,LEfSe,2,FALSE,2,NA,NA,NA,increased,unchanged,increased,NA,unchanged,Signature 2,"Figure 4a, text",10 January 2021,Zyaijah Bailey,"WikiWorks,Atrayees,Merit","the most differentially abundant taxa between the two groups were identified through the LDA score which was generated from LEfSe analysis (phylum to genus: p, phylum; c, class; o, order; f, family; g, genus)",decreased,"k__Pseudomonadati|p__Acidobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres,k__Pseudomonadati|p__Deferribacterota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Gemmatimonadota|c__Gemmatimonadia|o__Gemmatimonadales|f__Gemmatimonadaceae,k__Pseudomonadati|p__Gemmatimonadota|c__Gemmatimonadia|o__Gemmatimonadales,k__Pseudomonadati|p__Gemmatimonadota|c__Gemmatimonadia,k__Pseudomonadati|p__Gemmatimonadota,k__Pseudomonadati|p__Gemmatimonadota|c__Gemmatimonadia|o__Gemmatimonadales|f__Gemmatimonadaceae|g__Gemmatimonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leucobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.",3379134|57723;3379134|1224|1236|72274|135621|351;1783272|1239|91061|1385;1783272|1239|91061;1783272|1239|91061|1385|186817|1386;3379134|200930|68337|191393|191394;3379134|200930|68337|191393;3379134|200930|68337;3379134|200930;3379134|1224|28216|80840|80864|80865;3379134|1224|1236;3379134|142182|219685|219686|219687;3379134|142182|219685|219686;3379134|142182|219685;3379134|142182;3379134|142182|219685|219686|219687|173479;1783272|201174|1760|85006|85023|55968;1783272|201174|1760|85006|85023;3379134|200930|68337|191393|2945020|248038;3379134|976|200643|171549|1853231|283168;3379134|1224|1236|72274;3379134|1224|1236|72274|135621|286;1783272|1239|909932|909929|1843491|970;3379134|1224|28211|204457;3379134|1224|28211|204457|41297|13687;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|1853231;1783272|1239|91061|186826|1300|1301|1306,Complete,Atrayees
bsdb:31951695/1/NA,31951695,prospective cohort,31951695,10.21101/cejph.a5393,NA,"Parco S., Benericetti G., Vascotto F. , Palmisciano G.",Microbiome and diversity indices during blood stem cells transplantation - new perspectives?,Central European journal of public health,2019,"blood stem cells transplantation, graft versus host disease, oral and gut microbiome",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,pre- allogeneic hematopoietic stem cell transplant,post- allogeneic hematopoietic stem cell transplant,children between 3 and 10 years of age that have undergone allogeneic hematopoeitic stem cell transplantation and hospitalized at Institute for Maternal and Child Health of Trieste,5,5,NA,16S,123,Ion Torrent,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:31954395/1/1,31954395,case-control,31954395,10.1186/s13048-019-0603-4,NA,"Wang Q., Zhao L., Han L., Fu G., Tuo X., Ma S., Li Q., Wang Y., Liang D., Tang M., Sun C., Wang Q., Song Q. , Li Q.",The differential distribution of bacteria between cancerous and noncancerous ovarian tissues in situ,Journal of ovarian research,2020,"16S rRNA sequencing, Bacteria, KEGG, Lipopolysaccharide, Ovarian cancer",Experiment 1,China,Homo sapiens,Uterus,UBERON:0000995,Ovarian cancer,MONDO:0008170,controls,ovarian cancer,preliminary diagnosis of suspected ovarian cancer and undergoing laparotomy,10,6,2 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure 3, Table 2",10 January 2021,Fatima Zohra,"Lwaldron,WikiWorks,LGeistlinger",Differential relative abundance of taxa in ovarian communities between patients in cancer an control group.,increased,"k__Pseudomonadati|p__Aquificota,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Planctomycetales,k__Pseudomonadati|p__Planctomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Verrucomicrobiota|c__Spartobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae,k__Bacillati|p__Chloroflexota|c__Ktedonobacteria|o__Thermogemmatisporales|f__Thermogemmatisporaceae",3379134|200783;3379134|29547|3031852|213849;3379134|1224|1236|91347;3366610|28890|183925|2158|2159;3366610|28890|183925|2158;1783272|201174|1760|85006|85023;3379134|1224|1236|2887326|468;3379134|203682|203683|112;3379134|203682;3379134|1224|1236|72274;3379134|74201|134549;1783272|1239|91061|1385|90964;3384194|1297|188787|68933|188786;1783272|200795|388447|768667|768668,Complete,Lwaldron
bsdb:31954395/1/2,31954395,case-control,31954395,10.1186/s13048-019-0603-4,NA,"Wang Q., Zhao L., Han L., Fu G., Tuo X., Ma S., Li Q., Wang Y., Liang D., Tang M., Sun C., Wang Q., Song Q. , Li Q.",The differential distribution of bacteria between cancerous and noncancerous ovarian tissues in situ,Journal of ovarian research,2020,"16S rRNA sequencing, Bacteria, KEGG, Lipopolysaccharide, Ovarian cancer",Experiment 1,China,Homo sapiens,Uterus,UBERON:0000995,Ovarian cancer,MONDO:0008170,controls,ovarian cancer,preliminary diagnosis of suspected ovarian cancer and undergoing laparotomy,10,6,2 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 3, Table 2",10 January 2021,Fatima Zohra,WikiWorks,Differential relative abundance of taxa in ovarian communities between patients in cancer an control group,decreased,"k__Thermoproteati|p__Thermoproteota,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia,k__Methanobacteriati|p__Methanobacteriota|c__Halobacteria|o__Halobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Methanobacteriati|p__Methanobacteriota|c__Archaeoglobi|o__Archaeoglobales|f__Archaeoglobaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Methanobacteriati|p__Methanobacteriota|c__Methanomicrobia|o__Methanomicrobiales|f__Methanocorpusculaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Methanobacteriati|p__Methanobacteriota|c__Halobacteria|o__Halobacteriales|f__Haloferacaceae|g__Haloferax",1783275|28889;3379134|976|117747;3366610|28890|183963|2235;3379134|976|117743|200644|49546;3366610|28890|183980|2231|2232;3384189|32066|203490|203491|1129771;3366610|28890|224756|2191|88404;1783272|201174|1760|1643682|85030;1783272|1239|91061|1385|186822|44249;3366610|28890|183963|2235|1644056|2251,Complete,Lwaldron
bsdb:31973685/1/1,31973685,"cross-sectional observational, not case-control",31973685,10.1080/19490976.2020.1712985,https://pubmed.ncbi.nlm.nih.gov/31973685/,"Moran-Ramos S., Lopez-Contreras B.E., Villarruel-Vazquez R., Ocampo-Medina E., Macias-Kauffer L., Martinez-Medina J.N., Villamil-Ramirez H., León-Mimila P., Del Rio-Navarro B.E., Ibarra-Gonzalez I., Vela-Amieva M., Gomez-Perez F.J., Velazquez-Cruz R., Salmeron J., Reyes-Castillo Z., Aguilar-Salinas C. , Canizales-Quinteros S.",Environmental and intrinsic factors shaping gut microbiota composition and diversity and its relation to metabolic health in children and early adolescents: A population-based study,Gut microbes,2020,"adolescents, children, co-abundance groups, diversity, enterotypes, gut microbiota, obesity",Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,lower monthly household income,higher monthly household income,higher monthly household income,NA,NA,6 months,16S,4,Illumina,relative abundances,PERMANOVA,0.05,TRUE,NA,NA,"age,antibiotic exposure,household income,sex",NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Table  1, text",23 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Atrayees,WikiWorks",Taxa significantly associated with monthly household income.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus",1783272|201174|84998|1643822|1643826|84111|84112;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|171550;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|186802|216572|119852;1783272|1239|526524|526525|128827|2749846|31971,Complete,Atrayees
bsdb:31973685/1/2,31973685,"cross-sectional observational, not case-control",31973685,10.1080/19490976.2020.1712985,https://pubmed.ncbi.nlm.nih.gov/31973685/,"Moran-Ramos S., Lopez-Contreras B.E., Villarruel-Vazquez R., Ocampo-Medina E., Macias-Kauffer L., Martinez-Medina J.N., Villamil-Ramirez H., León-Mimila P., Del Rio-Navarro B.E., Ibarra-Gonzalez I., Vela-Amieva M., Gomez-Perez F.J., Velazquez-Cruz R., Salmeron J., Reyes-Castillo Z., Aguilar-Salinas C. , Canizales-Quinteros S.",Environmental and intrinsic factors shaping gut microbiota composition and diversity and its relation to metabolic health in children and early adolescents: A population-based study,Gut microbes,2020,"adolescents, children, co-abundance groups, diversity, enterotypes, gut microbiota, obesity",Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,lower monthly household income,higher monthly household income,higher monthly household income,NA,NA,6 months,16S,4,Illumina,relative abundances,PERMANOVA,0.05,TRUE,NA,NA,"age,antibiotic exposure,household income,sex",NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Table 1, text",23 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Atrayees,WikiWorks",taxa significantly associated with monthly household income.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|838;1783272|1239|909932|1843489|31977,Complete,Atrayees
bsdb:31976177/1/1,31976177,case-control,31976177,10.7717/peerj.8317,NA,"Chen X., Sun H., Jiang F., Shen Y., Li X., Hu X., Shen X. , Wei P.",Alteration of the gut microbiota associated with childhood obesity by 16S rRNA gene sequencing,PeerJ,2020,"16S rRNA gene sequencing, Alpha diversity, Bacterial compositions, Beta Diversity, Childhood obesity, Gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight children,obese children,volunteers between the ages of 6-11 years old who were determined to be obese by BMI,23,28,1 month,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,decreased,decreased,NA,decreased,Signature 1,"Figure 2, Text",10 January 2021,Mst Afroza Parvin,"Claregrieve1,WikiWorks",Relative abundance of microbial taxa in normal weight group vs obese group,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",1783272|1239|186801|186802|216572|216851;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|28050;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843488|909930|33024,Complete,Claregrieve1
bsdb:31976177/1/2,31976177,case-control,31976177,10.7717/peerj.8317,NA,"Chen X., Sun H., Jiang F., Shen Y., Li X., Hu X., Shen X. , Wei P.",Alteration of the gut microbiota associated with childhood obesity by 16S rRNA gene sequencing,PeerJ,2020,"16S rRNA gene sequencing, Alpha diversity, Bacterial compositions, Beta Diversity, Childhood obesity, Gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight children,obese children,volunteers between the ages of 6-11 years old who were determined to be obese by BMI,23,28,1 month,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,decreased,decreased,NA,decreased,Signature 2,"Figure 2, Text",10 January 2021,Mst Afroza Parvin,"Claregrieve1,WikiWorks",Relative abundance of microbial taxa in normal weight group vs obese group,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572|119852,Complete,Claregrieve1
bsdb:31976177/2/1,31976177,case-control,31976177,10.7717/peerj.8317,NA,"Chen X., Sun H., Jiang F., Shen Y., Li X., Hu X., Shen X. , Wei P.",Alteration of the gut microbiota associated with childhood obesity by 16S rRNA gene sequencing,PeerJ,2020,"16S rRNA gene sequencing, Alpha diversity, Bacterial compositions, Beta Diversity, Childhood obesity, Gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight children,obese children,volunteers between the ages of 6-11 years old who were determined to be obese by BMI,23,28,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,decreased,decreased,NA,decreased,Signature 1,Figure 5,10 January 2021,Mst Afroza Parvin,"Lwaldron,Claregrieve1,WikiWorks",Relative abundance of microbial taxa in normal weight group vs obese group,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetitomaculum|s__Acetitomaculum ruminis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Pasteuriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] colinum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae",1783272|1239|186801|3085636|186803|31980|2382;3379134|1224|1236|135625|712|713;3379134|1224|1236|135625|712|416916;3379134|1224|28216|80840|506;1783272|1239|91061;3379134|1224|28216;3379134|1224|28216|80840;3379134|29547|3031852|213849|72294|194;1783272|1239|91061|186826|186828;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485|1502;1783272|1239|526524|526525|128827|2749846|31971;3384189|32066;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066|203490|203491|203492|848;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712|724|727;3379134|1224|1236|135625|712|724|729;1783272|1239|186801|3085636|186803|28050;1783272|1239|91061|186826;3384189|32066|203490|203491|1129771;1783272|1239|909932|909929|1843491|158846;1783272|201174|1760|85006|1268;3379134|1224|1236|135625;1783272|1239|91061|1385|538998;1783272|1239|186801|3082720|186804;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|815|909656|387090;3379134|976|200643|171549|171552|2974251|165179;3379134|1224;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;3379134|1224|28216|80840|995019|40544;1783272|1239|526524|526525|2810281|191303;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|186801|3085636|186803|1506577|36835;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|526524|526525|2810281,Complete,Claregrieve1
bsdb:31976177/2/2,31976177,case-control,31976177,10.7717/peerj.8317,NA,"Chen X., Sun H., Jiang F., Shen Y., Li X., Hu X., Shen X. , Wei P.",Alteration of the gut microbiota associated with childhood obesity by 16S rRNA gene sequencing,PeerJ,2020,"16S rRNA gene sequencing, Alpha diversity, Bacterial compositions, Beta Diversity, Childhood obesity, Gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight children,obese children,volunteers between the ages of 6-11 years old who were determined to be obese by BMI,23,28,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,decreased,decreased,NA,decreased,Signature 2,Figure 5,10 January 2021,Mst Afroza Parvin,"Lwaldron,Claregrieve1,WikiWorks,Merit",Relative abundance of microbial taxa in normal weight group vs obese group,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae|g__Defluviitalea,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Hathewaya,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter|s__Oxalobacter formigenes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles|s__Roseateles saccharophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Rickettsiella|s__Rickettsiella massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii",1783272|201174;1783272|201174|84998|1643822|1643826|447020;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550|239759|626932;1783272|1239|186801|186802|216572|244127;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|2005519;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|1680;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|186801|3085636|1185407|1185408;28221;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|31979|1769729;1783272|1239|526524|526525|128827|61170;1783272|544448|31969;1783272|544448;1783272|1239|186801|186802|216572|119852;3379134|1224|28216|80840|75682|846;3379134|1224|28216|80840|75682|846|847;3379134|1224|28216|80840|75682;3379134|1224|28216|80840|2975441|93681|304;1783272|1239|186801|186802|186807;3379134|976|200643|171549|171552|838;3379134|1224|1236|118969|118968|59195|676517;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|44748;1783272|1239|91061|186826|1300|1301|1302,Complete,Claregrieve1
bsdb:31990790/1/1,31990790,prospective cohort,31990790,10.1097/CMR.0000000000000656,https://journals.lww.com/melanomaresearch/Fulltext/2020/06000/Gut_microbial_species_and_metabolic_pathways.2.aspx,"Wind T.T., Gacesa R., Vich Vila A., de Haan J.J., Jalving M., Weersma R.K. , Hospers G.A.P.",Gut microbial species and metabolic pathways associated with response to treatment with immune checkpoint inhibitors in metastatic melanoma,Melanoma research,2020,NA,Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,"Melanoma patients with a confirmed response, defined as a complete response, partial response (PR) or stable disease (SD) according to RECIST 12 weeks after start of therapy that was ongoing at the next radiological evaluation, were labelled ‘responder’. In order to include late responders in our analysis, patients with progressive disease (PD) on the first radiological evaluation but a response at the second radiological evaluation compared to baseline were also labelled ‘responder’.",13,12,NA,WMS,NA,Illumina,NA,Fisher's Exact Test,0.05,TRUE,NA,NA,"age,antibiotic exposure,body mass index,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3,1 September 2022,Sharmilac,"Sharmilac,Claregrieve1,WikiWorks",Differentially abundant taxa in responders vs non-responders (FDR cut-off = 0.05),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 2_1_58FAA,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|815|816|28111;3379134|976|200643|171549|815|816|818;3379134|200940|3031449|213115|194924|872|901;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|186806|1730|39496;3379134|1224|1236|135625|712|724|729;1783272|1239|526524|526525|128827|1573535|1735;1783272|1239|186801|3085636|186803|658082;1783272|1239|909932|1843488|909930|33024|626940;3379134|976|200643|171549|815|909656|204516;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|186802|216572|39492;1783272|1239|186801|3085636|186803|2316020|33038;3379134|200940|3031449|213115|194924|35832;3379134|1224|1236;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543;1783272|1239|909932|1843488|909930;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843488|909930|33024,Complete,Claregrieve1
bsdb:31990790/1/2,31990790,prospective cohort,31990790,10.1097/CMR.0000000000000656,https://journals.lww.com/melanomaresearch/Fulltext/2020/06000/Gut_microbial_species_and_metabolic_pathways.2.aspx,"Wind T.T., Gacesa R., Vich Vila A., de Haan J.J., Jalving M., Weersma R.K. , Hospers G.A.P.",Gut microbial species and metabolic pathways associated with response to treatment with immune checkpoint inhibitors in metastatic melanoma,Melanoma research,2020,NA,Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,"Melanoma patients with a confirmed response, defined as a complete response, partial response (PR) or stable disease (SD) according to RECIST 12 weeks after start of therapy that was ongoing at the next radiological evaluation, were labelled ‘responder’. In order to include late responders in our analysis, patients with progressive disease (PD) on the first radiological evaluation but a response at the second radiological evaluation compared to baseline were also labelled ‘responder’.",13,12,NA,WMS,NA,Illumina,NA,Fisher's Exact Test,0.05,TRUE,NA,NA,"age,antibiotic exposure,body mass index,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3,1 September 2022,Sharmilac,"Sharmilac,Claregrieve1,WikiWorks",Differentially abundant taxa in responders vs non-responders (FDR cut-off = 0.05),decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp. ART55/1,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 21_3,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 2_2_44A,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania filiformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 7_1_58FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 8_1_57FAA,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759|1288121;3379134|976|200643|171549|815|816|246787;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|46506;3379134|976|200643|171549|815|816|371601;3379134|976|200643|171549|2005519|397864|487174;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|3085636|186803|33042|751585;1783272|1239|526524|526525|128827|658657;1783272|1239|526524|526525|128827|457422;1783272|1239|186801|186802|186806|1730|39490;1783272|1239|526524|526525|128827|61170|61171;1783272|1239|186801|3085636|186803|658087;1783272|1239|186801|3085636|186803|665951;3379134|976|200643|171549|171552|577309|454154;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|186801|186802|216572|1263|40519;1783272|201174|1760|2037|2049|2529408|1660;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1343;1783272|1239|186801|3085636|186803|2316020|46228;1783272|201174|84998|1643822|1643826|84111;1783272|201174|84998|84999|1643824|133925;1783272|1239|186801|3082720|186804;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|171552|838;1783272|201174|84998|1643822|1643826|84111;1783272|1239|91061|186826|1300;3379134|976|200643|171549|171552,Complete,Claregrieve1
bsdb:32009325/1/1,32009325,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park Y.M., Lee S.Y., Kang M.J., Kim B.S., Lee M.J., Jung S.S., Yoon J.S., Cho H.J., Lee E., Yang S.I., Seo J.H., Kim H.B., Suh D.I., Shin Y.H., Kim K.W., Ahn K. , Hong S.J.","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,"Dermatitis, atopic, gastrointestinal microbiome, infant, metabolomics, metagenome",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy control,infant with transient atopic dermatitis,infant with transient atopic dermatitis,84,22,NA,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2a, Text",10 January 2021,Lucy Mellor,WikiWorks,Phylum level relative abundance of gut microbiota in infants with transient atopic dermatitis (AD) and healthy controls,increased,k__Bacillati|p__Actinomycetota,1783272|201174,Complete,Folakunmi
bsdb:32009325/1/2,32009325,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park Y.M., Lee S.Y., Kang M.J., Kim B.S., Lee M.J., Jung S.S., Yoon J.S., Cho H.J., Lee E., Yang S.I., Seo J.H., Kim H.B., Suh D.I., Shin Y.H., Kim K.W., Ahn K. , Hong S.J.","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,"Dermatitis, atopic, gastrointestinal microbiome, infant, metabolomics, metagenome",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy control,infant with transient atopic dermatitis,infant with transient atopic dermatitis,84,22,NA,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2b, Text",10 January 2021,Lucy Mellor,WikiWorks,Genus level relative abundance of gut microbiota in infants with transient atopic dermatitis (AD) and healthy controls,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",1783272|201174|1760|85004|31953|1678;3379134|74201|203494|48461|1647988|239934,Complete,Folakunmi
bsdb:32009325/2/1,32009325,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park Y.M., Lee S.Y., Kang M.J., Kim B.S., Lee M.J., Jung S.S., Yoon J.S., Cho H.J., Lee E., Yang S.I., Seo J.H., Kim H.B., Suh D.I., Shin Y.H., Kim K.W., Ahn K. , Hong S.J.","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,"Dermatitis, atopic, gastrointestinal microbiome, infant, metabolomics, metagenome",Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy controls,infants with persistent atopic dermatitis,infant with persistent atopic dermatitis,84,26,NA,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2b, Text",10 January 2021,Lucy Mellor,WikiWorks,Genus level relative abundance of gut microbiota in infants with persistent atopic dermatitis (AD) and healthy controls,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:32009325/2/2,32009325,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park Y.M., Lee S.Y., Kang M.J., Kim B.S., Lee M.J., Jung S.S., Yoon J.S., Cho H.J., Lee E., Yang S.I., Seo J.H., Kim H.B., Suh D.I., Shin Y.H., Kim K.W., Ahn K. , Hong S.J.","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,"Dermatitis, atopic, gastrointestinal microbiome, infant, metabolomics, metagenome",Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy controls,infants with persistent atopic dermatitis,infant with persistent atopic dermatitis,84,26,NA,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2b, Text",10 January 2021,Lucy Mellor,WikiWorks,Genus level relative abundance of gut microbiota in infants with persistent atopic dermatitis (AD) and healthy controls,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,1783272|1239|186801|186802|31979|1485,Complete,Folakunmi
bsdb:32009325/3/1,32009325,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park Y.M., Lee S.Y., Kang M.J., Kim B.S., Lee M.J., Jung S.S., Yoon J.S., Cho H.J., Lee E., Yang S.I., Seo J.H., Kim H.B., Suh D.I., Shin Y.H., Kim K.W., Ahn K. , Hong S.J.","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,"Dermatitis, atopic, gastrointestinal microbiome, infant, metabolomics, metagenome",Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,transient atopic dermatitis,infants with persistent atopic dermatitis,infant with persistent atopic dermatitis,22,26,NA,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2b, Text",10 January 2021,Lucy Mellor,WikiWorks,Genus level relative abundance of gut microbiota in infants with persistent atopic dermatitis (AD) and transient atopic dermatitis,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:32009325/3/2,32009325,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park Y.M., Lee S.Y., Kang M.J., Kim B.S., Lee M.J., Jung S.S., Yoon J.S., Cho H.J., Lee E., Yang S.I., Seo J.H., Kim H.B., Suh D.I., Shin Y.H., Kim K.W., Ahn K. , Hong S.J.","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,"Dermatitis, atopic, gastrointestinal microbiome, infant, metabolomics, metagenome",Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,transient atopic dermatitis,infants with persistent atopic dermatitis,infant with persistent atopic dermatitis,22,26,NA,16S,123,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2b, Text",10 January 2021,Lucy Mellor,WikiWorks,Genus level relative abundance of gut microbiota in infants with persistent atopic dermatitis (AD) and transient atopic dermatitis,decreased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,3379134|74201|203494|48461|1647988|239934,Complete,Folakunmi
bsdb:32009325/4/1,32009325,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park Y.M., Lee S.Y., Kang M.J., Kim B.S., Lee M.J., Jung S.S., Yoon J.S., Cho H.J., Lee E., Yang S.I., Seo J.H., Kim H.B., Suh D.I., Shin Y.H., Kim K.W., Ahn K. , Hong S.J.","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,"Dermatitis, atopic, gastrointestinal microbiome, infant, metabolomics, metagenome",Experiment 4,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy controls,infants with persistent atopic dermatitis,infant with persistent atopic dermatitis,84,26,NA,16S,123,Roche454,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Figure S1a,10 January 2021,Lucy Mellor,WikiWorks,LEfSe analysis of the infant gut microbiota in healthy controls and persistent AD subjects,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus",1783272|1239|91061;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300;1783272|1239|91061|186826;1783272|1239|186801|3082720|186804|1505657;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|171551;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3082720|186804|1505652;1783272|1239|186801|3082720|186804|1501226;1783272|1239|91061|186826|186828|117563;1783272|1239|91061|186826|186827;1783272|1239|526524|526525|2810280|100883,Complete,Folakunmi
bsdb:32009325/4/2,32009325,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park Y.M., Lee S.Y., Kang M.J., Kim B.S., Lee M.J., Jung S.S., Yoon J.S., Cho H.J., Lee E., Yang S.I., Seo J.H., Kim H.B., Suh D.I., Shin Y.H., Kim K.W., Ahn K. , Hong S.J.","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,"Dermatitis, atopic, gastrointestinal microbiome, infant, metabolomics, metagenome",Experiment 4,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy controls,infants with persistent atopic dermatitis,infant with persistent atopic dermatitis,84,26,NA,16S,123,Roche454,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplemental Figure S1a,10 January 2021,Lucy Mellor,"WikiWorks,Merit",LEfSe analysis of the infant gut microbiota in healthy controls and persistent AD subjects,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kosakonia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pseudocitrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;3379134|1224|1236|91347|543|544;1783272|1239|526524|526525|2810280|100883;1783272|201174|84998|1643822|1643826|84111;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|1330547;3379134|1224|1236|91347|543|1504576;3379134|1224|1236|91347|543|160674;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|1898207;1783272|1239|186801|186802|31979|1485,Complete,Folakunmi
bsdb:32009325/5/1,32009325,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park Y.M., Lee S.Y., Kang M.J., Kim B.S., Lee M.J., Jung S.S., Yoon J.S., Cho H.J., Lee E., Yang S.I., Seo J.H., Kim H.B., Suh D.I., Shin Y.H., Kim K.W., Ahn K. , Hong S.J.","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,"Dermatitis, atopic, gastrointestinal microbiome, infant, metabolomics, metagenome",Experiment 5,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,transient atopic dermatitis,infants with persistent atopic dermatitis,infant with persistent atopic dermatitis,22,26,before sample collection,16S,123,Roche454,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Figure S1b,10 January 2021,Lucy Mellor,"WikiWorks,Merit,Folakunmi",LEfSe analysis of the infant gut microbiota in transient AD and persistent AD subjects,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter",1783272|1239;1783272|1239|526524|526525|2810280|100883;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|216851;3379134|1224|1236|2887326|468;1783272|1239|186801|186802|541000;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;3379134|1224|1236|72274|135621;3379134|1224|1236|72274;1783272|1239|186801|3082720|186804|1501226;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;3379134|1224|1236|2887326|468|469,Complete,Folakunmi
bsdb:32009325/5/2,32009325,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park Y.M., Lee S.Y., Kang M.J., Kim B.S., Lee M.J., Jung S.S., Yoon J.S., Cho H.J., Lee E., Yang S.I., Seo J.H., Kim H.B., Suh D.I., Shin Y.H., Kim K.W., Ahn K. , Hong S.J.","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,"Dermatitis, atopic, gastrointestinal microbiome, infant, metabolomics, metagenome",Experiment 5,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,transient atopic dermatitis,infants with persistent atopic dermatitis,infant with persistent atopic dermatitis,22,26,before sample collection,16S,123,Roche454,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplemental Figure S1b,10 January 2021,Lucy Mellor,"WikiWorks,Merit",LEfSe analysis of the infant gut microbiota in transient AD and persistent AD subjects,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kosakonia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Verrucomicrobium",3379134|74201|203494|48461|1647988|239934;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|1330547;3379134|1224|1236|91347|543|160674;3379134|74201|203494;3379134|74201|203494|48461;3379134|74201;3379134|74201|203494|48461|203557|2735,Complete,Folakunmi
bsdb:32009325/6/1,32009325,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park Y.M., Lee S.Y., Kang M.J., Kim B.S., Lee M.J., Jung S.S., Yoon J.S., Cho H.J., Lee E., Yang S.I., Seo J.H., Kim H.B., Suh D.I., Shin Y.H., Kim K.W., Ahn K. , Hong S.J.","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,"Dermatitis, atopic, gastrointestinal microbiome, infant, metabolomics, metagenome",Experiment 6,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy control,infant with transient atopic dermatitis,infant with transient atopic dermatitis,84,22,before sample collection,16S,123,Roche454,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Figure S1c,10 January 2021,Lucy Mellor,"Fatima,WikiWorks,Folakunmi",LEfSe analysis of the infant gut microbiota in healthy controls and transient AD subjects,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|201174;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678,Complete,Folakunmi
bsdb:32009325/6/2,32009325,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park Y.M., Lee S.Y., Kang M.J., Kim B.S., Lee M.J., Jung S.S., Yoon J.S., Cho H.J., Lee E., Yang S.I., Seo J.H., Kim H.B., Suh D.I., Shin Y.H., Kim K.W., Ahn K. , Hong S.J.","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,"Dermatitis, atopic, gastrointestinal microbiome, infant, metabolomics, metagenome",Experiment 6,South Korea,Homo sapiens,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,healthy control,infant with transient atopic dermatitis,infant with transient atopic dermatitis,84,22,before sample collection,16S,123,Roche454,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplemental Figure S1c,10 January 2021,Lucy Mellor,WikiWorks,LEfSe analysis of the infant gut microbiota in healthy controls and transient AD subjects,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales",1783272|201174|1760|85006|1268;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006,Complete,Folakunmi
bsdb:32010111/1/1,32010111,laboratory experiment,32010111,10.3389/fmicb.2019.03067,https://pmc.ncbi.nlm.nih.gov/articles/PMC6974438/,"Geng S., Yang L., Cheng F., Zhang Z., Li J., Liu W., Li Y., Chen Y., Bao Y., Chen L., Fei Z., Li X., Hou J., Lin Y., Liu Z., Zhang S., Wang H., Zhang Q., Wang H., Wang X. , Zhang J.",Gut Microbiota Are Associated With Psychological Stress-Induced Defections in Intestinal and Blood-Brain Barriers,Frontiers in microbiology,2019,"blood–brain barrier, communication box, dysbiosis, gut microbiota, intestinal barrier, psychological stress, tight junction",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Response to stress,GO:0006950,Control group,Psychological-stress model group,Rats that received psychological stress stimulation through the communication box system for 28 days.,6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Fig. 4E and F,6 May 2025,Shulamite,Shulamite,"Results of LEfSe analysis and key taxa found by LDA analysis (multigroup comparison strategy: one-against-all, LDA > 2, P < 0.05).",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Catenisphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XII. Incertae Sedis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Globicatella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",1783272|1239|909932|1843488|909930;1783272|1239|91061|186826|186827;1783272|1239|909932|1843489|31977|209879;1783272|1239|526524|526525|128827|174708;1783272|1239|186801|3082720|543314;1783272|1239|91061|1385;3379134|976|200643|171549;1783272|1239|526524|526525|128827|1774107;1783272|1239|186801|3085636|186803|33042;1783272|201174|84998|84999|84107;3379134|200940|3031449|213115|194924|872;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|186801|186802|543313;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186827|13075;1783272|1239|526524|526525|128827|1573535;1783272|1239|909932;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|186802|186807|2740;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171552;1783272|1239|909932|909929;3379134|203691|203692|136|2845253|157;3379134|976|200643|171549;1783272|1239|526524|526525|128827,Complete,KateRasheed
bsdb:32010111/1/2,32010111,laboratory experiment,32010111,10.3389/fmicb.2019.03067,https://pmc.ncbi.nlm.nih.gov/articles/PMC6974438/,"Geng S., Yang L., Cheng F., Zhang Z., Li J., Liu W., Li Y., Chen Y., Bao Y., Chen L., Fei Z., Li X., Hou J., Lin Y., Liu Z., Zhang S., Wang H., Zhang Q., Wang H., Wang X. , Zhang J.",Gut Microbiota Are Associated With Psychological Stress-Induced Defections in Intestinal and Blood-Brain Barriers,Frontiers in microbiology,2019,"blood–brain barrier, communication box, dysbiosis, gut microbiota, intestinal barrier, psychological stress, tight junction",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Response to stress,GO:0006950,Control group,Psychological-stress model group,Rats that received psychological stress stimulation through the communication box system for 28 days.,6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,increased,Signature 2,Fig. 4E and F,7 May 2025,Shulamite,"Shulamite,Victoria,KateRasheed","Results of LEfSe analysis and key taxa found by LDA analysis (multigroup comparison strategy: one-against-all, LDA > 2, P < 0.05).",decreased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__[Bacteroides] pectinophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",3379134|200940|3031449|213115|194924|35832;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802;1783272|1239|526524|526525|128827|1573534;1783272|1239|186801|186802|1392389;1783272|544448|31969|2085|2092|2093;1783272|544448|31969|2085|2092;1783272|544448|31969|2085;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|186807;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1501226;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|186802|384638;1783272|1239|186801|186802,Complete,KateRasheed
bsdb:32010563/1/1,32010563,prospective cohort,32010563,10.21037/tlcr.2019.10.23,NA,"Katayama Y., Yamada T., Shimamoto T., Iwasaku M., Kaneko Y., Uchino J. , Takayama K.",The role of the gut microbiome on the efficacy of immune checkpoint inhibitors in Japanese responder patients with advanced non-small cell lung cancer,Translational lung cancer research,2019,"Immunotherapy, gut microbiome, non-small cell lung cancer (NSCLC), retrospective analysis",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,We defined responder (R) (partial response to ICI treatment) or non-responder (NR) (stable or progressive disease after ICI treatment at the time of first clinical evaluation) according to the RECIST 1.1 evaluation.,11,6,NA,16S,12,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2,2 September 2022,Sharmilac,"Sharmilac,Fatima,WikiWorks",The differential abundant taxa in the gut microbiomes of R (green) and NR (red) was analyzed by linear discriminate analysis coupled with effect size measurements (LEfSe),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",1783272|1239|186801|186802|31979|1485;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|84036;1783272|1239|91061|186826|33958,Complete,Fatima
bsdb:32010563/1/2,32010563,prospective cohort,32010563,10.21037/tlcr.2019.10.23,NA,"Katayama Y., Yamada T., Shimamoto T., Iwasaku M., Kaneko Y., Uchino J. , Takayama K.",The role of the gut microbiome on the efficacy of immune checkpoint inhibitors in Japanese responder patients with advanced non-small cell lung cancer,Translational lung cancer research,2019,"Immunotherapy, gut microbiome, non-small cell lung cancer (NSCLC), retrospective analysis",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,We defined responder (R) (partial response to ICI treatment) or non-responder (NR) (stable or progressive disease after ICI treatment at the time of first clinical evaluation) according to the RECIST 1.1 evaluation.,11,6,NA,16S,12,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2,2 September 2022,Sharmilac,"Sharmilac,Fatima,WikiWorks",The differential abundant taxa in the gut microbiomes of R (green) and NR (red) was analyzed by linear discriminate analysis coupled with effect size measurements (LEfSe),decreased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",3379134|200940|3031449|213115|194924|35832;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|40544;3379134|1224|28211;3379134|1224|28216|80840|506;3379134|1224|28216;3379134|1224|28216|80840;3379134|976|200643|171549|171551,Complete,Fatima
bsdb:32011017/1/1,32011017,prospective cohort,32011017,10.1111/ppe.12623,NA,"Kortekangas E., Kamng'ona A.W., Fan Y.M., Cheung Y.B., Ashorn U., Matchado A., Poelman B., Maleta K., Dewey K.G. , Ashorn P.",Environmental exposures and child and maternal gut microbiota in rural Malawi,Paediatric and perinatal epidemiology,2020,"child health, environment, gut microbiota, seasons, socio-economic factors",Experiment 1,Malawi,Homo sapiens,Feces,UBERON:0001988,Sampling time,EFO:0000689,samples taken in dry/hot or rainy season,samples taken in dry/cold season,samples taken in the dry/cold season,NA,NA,NA,16S,4,Illumina,NA,Zero-Inflated Beta Regression,0.05,TRUE,NA,NA,"antibiotic exposure,delivery procedure,education level,marital status,maternal age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,20 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1,WikiWorks",Differential abundance between samples from dry/cold season vs samples from dry/hot or rainy season,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus porcinus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301|1340;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|541000;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|1898207;1783272|1239|186801|186802|216572|216851,Complete,Claregrieve1
bsdb:32011017/1/2,32011017,prospective cohort,32011017,10.1111/ppe.12623,NA,"Kortekangas E., Kamng'ona A.W., Fan Y.M., Cheung Y.B., Ashorn U., Matchado A., Poelman B., Maleta K., Dewey K.G. , Ashorn P.",Environmental exposures and child and maternal gut microbiota in rural Malawi,Paediatric and perinatal epidemiology,2020,"child health, environment, gut microbiota, seasons, socio-economic factors",Experiment 1,Malawi,Homo sapiens,Feces,UBERON:0001988,Sampling time,EFO:0000689,samples taken in dry/hot or rainy season,samples taken in dry/cold season,samples taken in the dry/cold season,NA,NA,NA,16S,4,Illumina,NA,Zero-Inflated Beta Regression,0.05,TRUE,NA,NA,"antibiotic exposure,delivery procedure,education level,marital status,maternal age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,20 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Claregrieve1,WikiWorks",Differential abundance between samples from dry/cold season vs samples from dry/hot or rainy season,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron",3379134|1224|1236|91347|543|547;1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|186802|1898207;1783272|1239|186801|186802|31979|1485;1783272|1239|91061|186826|186828|117563|46124;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|815|816|817;1783272|1239|186801|186802|216572|1263;3379134|1224|1236|91347|543;3379134|976|200643|171549|815|816|818,Complete,Claregrieve1
bsdb:32012716/1/1,32012716,prospective cohort,32012716,10.3390/microorganisms8020179,NA,"Wong W.S.W., Sabu P., Deopujari V., Levy S., Shah A.A., Clemency N., Provenzano M., Saadoon R., Munagala A., Baker R., Baveja R., Mueller N.T., Dominguez-Bello M.G., Huddleston K., Niederhuber J.E. , Hourigan S.K.",Prenatal and Peripartum Exposure to Antibiotics and Cesarean Section Delivery Are Associated with Differences in Diversity and Composition of the Infant Meconium Microbiome,Microorganisms,2020,"antibiotics, delivery mode, infant, microbiome, neonate, pediatrics",Experiment 1,United States of America,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,vaginal delivery,C-section,"meconium defined as the first stool passed, other than meconium staining of amniotic fluid.",62,43,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,increased,NA,unchanged,Signature 1,Figure 4 & text,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differentially abundant OTUs(FDR< 0.05) according to deliverymode,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Pseudoscardovia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Meiothermus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Chelatococcaceae|g__Chelatococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Tepidimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Leptothrix,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Rubrivivax,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Anoxybacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium",1783272|1239|909932|1843489|31977|29465;3379134|1224|28211|356|119045|407;3379134|1224|1236|91347|543|544;1783272|1239|91061|1385|90964|1279;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|186826|1300|1301;3379134|1224|28216|80840|80864|12916;1783272|201174|1760|85009|31957|1743;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|2887326|468|469;3379134|1224|28211|356|41294|374;3379134|1224|28216|80840|80864|80865;1783272|201174|1760|85004|31953|1302778;1783272|1239|91061|186826|33958|1578;3379134|1224|28216|80840|506|222;3384194|1297|188787|68933|188786|65551;3379134|1224|28211|356|2036754|28209;3379134|1224|1236|135614|32033|40323;3379134|1224|28216|80840|114248;3379134|1224|1236|135625|712|724;3379134|1224|28216|80840|2975441|88;3379134|1224|28216|80840|80864|283;3379134|1224|28216|80840|2975441|28067;3379134|976|1853228|1853229|563835|504481;1783272|1239|91061|186826|1300|1357;3379134|1224|1236|91347|543|547;1783272|1239|91061|1385|3120669|150247;3379134|1224|28211|356|82115|357,Complete,NA
bsdb:32012716/1/2,32012716,prospective cohort,32012716,10.3390/microorganisms8020179,NA,"Wong W.S.W., Sabu P., Deopujari V., Levy S., Shah A.A., Clemency N., Provenzano M., Saadoon R., Munagala A., Baker R., Baveja R., Mueller N.T., Dominguez-Bello M.G., Huddleston K., Niederhuber J.E. , Hourigan S.K.",Prenatal and Peripartum Exposure to Antibiotics and Cesarean Section Delivery Are Associated with Differences in Diversity and Composition of the Infant Meconium Microbiome,Microorganisms,2020,"antibiotics, delivery mode, infant, microbiome, neonate, pediatrics",Experiment 1,United States of America,Homo sapiens,Meconium,UBERON:0007109,Cesarean section,EFO:0009636,vaginal delivery,C-section,"meconium defined as the first stool passed, other than meconium staining of amniotic fluid.",62,43,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,increased,NA,unchanged,Signature 2,Figure 4 & text,10 January 2021,Shaimaa Elsafoury,WikiWorks,Differentially abundant OTUs(FDR< 0.05) according to deliverymode,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Trabulsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|1224|1236|91347|543|561;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979|1485;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|543|158851;3379134|1224|1236|91347|543|620;1783272|1239|91061|1385|90964|1279;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|186826|1300|1301,Complete,NA
bsdb:32021942/1/1,32021942,"cross-sectional observational, not case-control",32021942,10.1016/j.heliyon.2020.e03311,NA,"Mondo E., Barone M., Soverini M., D'Amico F., Cocchi M., Petrulli C., Mattioli M., Marliani G., Candela M. , Accorsi P.A.",Gut microbiome structure and adrenocortical activity in dogs with aggressive and phobic behavioral disorders,Heliyon,2020,"Aggressive dogs, Animal behavior, Behavioral disorders, Biological sciences, Endocrinology, Hormones, Microbiology, Microbiome, Phobic dogs, Veterinary medicine",Experiment 1,Italy,Canis lupus familiaris,Feces,UBERON:0001988,Behavior or behavioral disorder measurement,EFO:0004782,Normal and Phobic behavior,Aggressive behavior,Dogs presenting aggressive  behavior.,31,11,NA,16S,34,Illumina,relative abundances,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3,12 April 2025,Asoler2004,Asoler2004,Canine gut microbiome profile of the behavior groups aggressive (Group 1) vs. normal and phobic (Group 0).,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",1783272|1239|526524|526525|2810280|135858;1783272|1239|909932|909929|1843491|158846,Complete,ChiomaBlessing
bsdb:32021942/2/1,32021942,"cross-sectional observational, not case-control",32021942,10.1016/j.heliyon.2020.e03311,NA,"Mondo E., Barone M., Soverini M., D'Amico F., Cocchi M., Petrulli C., Mattioli M., Marliani G., Candela M. , Accorsi P.A.",Gut microbiome structure and adrenocortical activity in dogs with aggressive and phobic behavioral disorders,Heliyon,2020,"Aggressive dogs, Animal behavior, Behavioral disorders, Biological sciences, Endocrinology, Hormones, Microbiology, Microbiome, Phobic dogs, Veterinary medicine",Experiment 2,Italy,Canis lupus familiaris,Feces,UBERON:0001988,Behavior or behavioral disorder measurement,EFO:0004782,Normal behavior,Aggressive behavior,Dogs with aggressive behavior disorder.,18,11,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure S1,14 April 2025,Asoler2004,Asoler2004,Canine gut microbiome profile of the behavior groups aggressive (Group 1) vs. normal (Group 0).,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|186802|186806|1730;1783272|1239|909932|909929|1843491|158846,Complete,ChiomaBlessing
bsdb:32021942/2/2,32021942,"cross-sectional observational, not case-control",32021942,10.1016/j.heliyon.2020.e03311,NA,"Mondo E., Barone M., Soverini M., D'Amico F., Cocchi M., Petrulli C., Mattioli M., Marliani G., Candela M. , Accorsi P.A.",Gut microbiome structure and adrenocortical activity in dogs with aggressive and phobic behavioral disorders,Heliyon,2020,"Aggressive dogs, Animal behavior, Behavioral disorders, Biological sciences, Endocrinology, Hormones, Microbiology, Microbiome, Phobic dogs, Veterinary medicine",Experiment 2,Italy,Canis lupus familiaris,Feces,UBERON:0001988,Behavior or behavioral disorder measurement,EFO:0004782,Normal behavior,Aggressive behavior,Dogs with aggressive behavior disorder.,18,11,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure S1,24 April 2025,Asoler2004,Asoler2004,Canine gut microbiome profile of the behavior groups aggressive (Group 1) vs. normal (Group 0).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|976|200643|171549|815|816;1783272|1239|526524|526525|2810280|100883;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|3082720|186804|1257;3379134|1224|28216|80840|995019|40544,Complete,ChiomaBlessing
bsdb:32021942/3/1,32021942,"cross-sectional observational, not case-control",32021942,10.1016/j.heliyon.2020.e03311,NA,"Mondo E., Barone M., Soverini M., D'Amico F., Cocchi M., Petrulli C., Mattioli M., Marliani G., Candela M. , Accorsi P.A.",Gut microbiome structure and adrenocortical activity in dogs with aggressive and phobic behavioral disorders,Heliyon,2020,"Aggressive dogs, Animal behavior, Behavioral disorders, Biological sciences, Endocrinology, Hormones, Microbiology, Microbiome, Phobic dogs, Veterinary medicine",Experiment 3,Italy,Canis lupus familiaris,Feces,UBERON:0001988,Behavior or behavioral disorder measurement,EFO:0004782,Phobic behavior,Aggressive behavior,Dogs with aggressive behavior disorder.,13,11,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure S1,14 April 2025,Asoler2004,Asoler2004,Canine gut microbiome profile of the behavior groups aggressive (Group 1) vs. phobic (Group 0).,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",1783272|1239|526524|526525|2810280|135858;1783272|1239|909932|909929|1843491|158846,Complete,ChiomaBlessing
bsdb:32021942/3/2,32021942,"cross-sectional observational, not case-control",32021942,10.1016/j.heliyon.2020.e03311,NA,"Mondo E., Barone M., Soverini M., D'Amico F., Cocchi M., Petrulli C., Mattioli M., Marliani G., Candela M. , Accorsi P.A.",Gut microbiome structure and adrenocortical activity in dogs with aggressive and phobic behavioral disorders,Heliyon,2020,"Aggressive dogs, Animal behavior, Behavioral disorders, Biological sciences, Endocrinology, Hormones, Microbiology, Microbiome, Phobic dogs, Veterinary medicine",Experiment 3,Italy,Canis lupus familiaris,Feces,UBERON:0001988,Behavior or behavioral disorder measurement,EFO:0004782,Phobic behavior,Aggressive behavior,Dogs with aggressive behavior disorder.,13,11,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure S1,24 April 2025,Asoler2004,Asoler2004,Canine gut microbiome profile of the behavior groups aggressive (Group 1) vs. phobic (Group 0).,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium,1783272|1239|186801|3085636|186803|2383,Complete,ChiomaBlessing
bsdb:32024079/1/1,32024079,"cross-sectional observational, not case-control",32024079,https://doi.org/10.3390/jcm9020386,NA,"Swarte J.C., Douwes R.M., Hu S., Vich Vila A., Eisenga M.F., van Londen M., Gomes-Neto A.W., Weersma R.K., Harmsen H.J.M. , Bakker S.J.L.",Characteristics and Dysbiosis of the Gut Microbiome in Renal Transplant Recipients,Journal of clinical medicine,2020,"16S rRNA sequencing, Proteobacteria, butyrate-producing bacteria, diarrhea, gut microbiome, gut microbiota, immunosuppressive medication, kidney transplantation, renal transplant recipient",Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Renal transplant outcome measurement,EFO:0005199,Healthy controls,RTR (Renal Transplant Recipients),These are renal transplant recipients that were at least one year post transplantation,105,139,NA,16S,45,Illumina,arcsine square-root,MaAsLin2,0.1,TRUE,NA,NA,"age,body mass index,sex,smoking behavior",NA,decreased,NA,NA,NA,unchanged,Signature 1,Figure 4 & Table S1,19 April 2025,Agatha,"Agatha,Montana-D,Victoria",Significantly differential abundant taxa between RTRs and healthy controls.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia para-adiacens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia glucerasea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Caloramator,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales|f__Desulfococcaceae|g__Desulfonema,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Gracilibacteraceae|g__Gracilibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hespellia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria,k__Pseudomonadati|p__Lentisphaerota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus vaginalis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Parasporobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae|g__Rhodospirillum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Succiniclasticum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Vallitaleaceae|g__Vallitalea,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus peroris,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Metazoa|p__Arthropoda|c__Insecta|o__Lepidoptera|f__Hesperiidae|s__Trapezitinae|g__Dispar,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfotomaculaceae|g__Desulfotomaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae",1783272|1239|91061|186826|186827|46123|191553;1783272|1239|909932|1843488|909930|904;1783272|1239|91061|186826|186827;1783272|1239|186801|186802|186806|264995;1783272|1239|91061;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|871665;1783272|1239|186801|3085636|186803|572511|536633;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|186802|31979|44258;1783272|1239|91061|186826|186828;1783272|1239|526524|526525|2810280|135858;1783272|1239|526524|526525|2810280|100883;3379134|1224|28216|80840|80864|80865;3379134|200940|3024418|213118|2931039|45654;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|91061|186826|81852;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|186806|1730;1783272|1239|526524|526525|128827|1573534;1783272|1239|1737404|1737405|1570339|150022;3379134|1224|1236;1783272|1239|186801|186802|541019|342658;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|241189;1783272|1239|526524|526525|128827|61170;3379134|1224|1236|91347|543|570|573;1783272|1239|186801|3085636|186803|1506553;3379134|256845|1313211;3379134|256845;1783272|1239|91061|186826|33958|2742598|1633;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3085636|186803|115543;3379134|1224|1236|135625|712;3379134|1224|1236|135625;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|909932|1843488|909930|33024;3379134|1224|28211|204441|41295|1081;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|186801|186802|216572|1263;1783272|201174|1760|2037|2049|2529408|1660;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|909932|1843488|909930|40840;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|3085636|2603322|1348611;1783272|1239|909932|1843489|31977|29465;3379134|256845|1313211|278082|255528;3379134|256845|1313211|278082;1783272|1239|186801|3085636|186803|1506553|29347;1783272|1239|186801|3085636|186803|572511|1322;3379134|1224|28216|80840|995019|40544;3379134|1224|28216|80840|506;1783272|1239|186801|3085636|186803|2719313|1531;1783272|201174|1760|2037;1783272|1239|526524|526525|128827|123375;1783272|1239|91061|186826|1300|1301|1313;1783272|1239|526524|526525|2810280|100883|100884;3379134|1224|1236|91347|543;3379134|1224|1236|91347;1783272|201174|1760|2037|2049|1654;3379134|1224;1783272|1239|186801|3082768|990719|990721;1783272|1239|91061|186826|1300|1301|68891;1783272|1239|186801|186802|216572|596767;1783272|1239|186801|186802|186806;1783272|201174|1760|2037|2049;33208|6656|50557|7088|40093|328868|509375;33090|35493|3398|72025|3803|3814|508215;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|186801|186802|2937910|1562;1783272|1239|186801|186802|216572|1200657;1783272|201174|1760|85006|1268,Complete,KateRasheed
bsdb:32024079/1/2,32024079,"cross-sectional observational, not case-control",32024079,https://doi.org/10.3390/jcm9020386,NA,"Swarte J.C., Douwes R.M., Hu S., Vich Vila A., Eisenga M.F., van Londen M., Gomes-Neto A.W., Weersma R.K., Harmsen H.J.M. , Bakker S.J.L.",Characteristics and Dysbiosis of the Gut Microbiome in Renal Transplant Recipients,Journal of clinical medicine,2020,"16S rRNA sequencing, Proteobacteria, butyrate-producing bacteria, diarrhea, gut microbiome, gut microbiota, immunosuppressive medication, kidney transplantation, renal transplant recipient",Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Renal transplant outcome measurement,EFO:0005199,Healthy controls,RTR (Renal Transplant Recipients),These are renal transplant recipients that were at least one year post transplantation,105,139,NA,16S,45,Illumina,arcsine square-root,MaAsLin2,0.1,TRUE,NA,NA,"age,body mass index,sex,smoking behavior",NA,decreased,NA,NA,NA,unchanged,Signature 2,Figure 4 & Table S1,22 April 2025,Agatha,"Agatha,Montana-D,Victoria",Significantly differential abundant taxa between RTRS and healthy controls.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Asaccharospora,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella viscericola,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum|s__Bifidobacterium catenulatum subsp. kashiwanohense,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium ruminantium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia|s__Bulleidia extructa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio fibrisolvens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Caldimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Caloramator|s__Caloramator mitchellensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella hongkongensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium disporicum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium|s__Dehalobacterium formicoaceticum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Desulfofundulus|s__Desulfofundulus kuznetsovii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus casseliflavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium|s__Lachnobacterium bovis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora saccharolytica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Paeniclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter|s__Papillibacter cinnamivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia ilealis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus champanellensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia cocleata,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] polysaccharolyticum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] infirmum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaeromicropila|s__Anaeromicropila populeti,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Thermohalobacteraceae|g__Brassicibacter|s__Brassicibacter mesophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Thermotaleaceae|g__Thermotalea|s__Thermotalea metallivorans,k__Metazoa|p__Arthropoda|c__Insecta|o__Coleoptera|f__Staphylinidae|s__Oxytelinae|g__Coprophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus|s__Alkaliphilus transvaalensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium cadaveris,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Heliobacteriaceae|g__Heliophilum|s__Heliophilum fasciatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfitobacteriaceae|g__Desulfosporosinus|s__Desulfosporosinus burensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Proteinivoracaceae|g__Anaerobranca,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Heliobacteriaceae|g__Heliophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Asaccharospora|s__Asaccharospora irregularis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium rangiferina,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio|s__Acetivibrio ethanolgignens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lutisporales|f__Lutisporaceae|g__Lutispora|s__Lutispora thermophila,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Obesumbacterium",1783272|1239|909932|1843488|909930|904;1783272|201174;1783272|1239|186801|3085636|186803|1766253|39491;3379134|976|200643|171549|171552|1283313|671218;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|186801|3085636|186803|207244;1783272|1239|909932|909929|1843491|82373;1783272|1239|186801|3082720|186804|1505660;1783272|1239|91061|1385;3379134|976|200643|171549|2005519|397864|397865;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|1686|630129;1783272|201174|1760|85004|31953|1678|78346;3379134|1224|1236|91347|1903410|71655;1783272|1239|526524|526525|128827|118747|118748;1783272|1239|186801|3085636|186803|830|831;3379134|1224|28216|80840|2975441|196013;1783272|1239|186801|186802|31979|44258|908809;1783272|1239|186801|3085636|186803|2383;1783272|1239|186801|3082768|990719|990721|270498;3379134|1224|1236|91347|543|544;1783272|1239|186801|186802|31979|1485|84024;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|33042|33043;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|186801|186802|186807|51514;1783272|1239|186801|186802|186807|51514|51515;1783272|1239|186801|186802|186807|2282741|58135;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|91061|186826|81852|1350|37734;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|946234|292800;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;3384189|32066|203490|203491|203492|848;1783272|1239|186801|186802|204475|745368;1783272|1239|526524|526525|128827|1573535;1783272|1239|526524|526525|128827|1573535|1735;1783272|1239|186801|186802|404402|404403;1783272|1239|186801|3085636|186803|140625;1783272|1239|186801|3085636|186803|140625|140626;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|2719231|84030;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|33958|1243;1783272|1239|91061|186826|33958|2767887|1623;1783272|1239|91061|1385|186817|400634;1783272|1239|909932|909929|1843491|52225;1783272|1239|186801|3082720|543314|86331;3379134|1224|1236|2887326|468;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|75682|846;1783272|1239|186801|3082720|186804|1849828;1783272|1239|186801|186802|216572|100175|100176;1783272|1239|186801|186802|186807;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|1017280|106588;1783272|1239|186801|3082720|186804|1501226|1115758;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|1263|1161942;3379134|1224|1236|91347|543|590;1783272|1239|909932|909929|1843491|970;1783272|201174|84998|1643822|1643826|84108;1783272|201174|84998|1643822|1643826|84108|572010;1783272|1239|91061|1385|90964;1783272|1239|186801|3085636|186803|84036;1783272|1239|526524|526525|2810280|3025755|69824;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|3085636|186803|1506553|29364;1783272|1239|186801|3082720|543314|56774;1783272|1239|186801|186802|216572|39492;1783272|1239|186801|3085636|186803|3024823|37658;1783272|1239|1737404|1737405|2848916|1433991|745119;1783272|1239|186801|3082720|3118657|648799|520762;33208|6656|50557|7041|29026|82877|1006423;1783272|1239|186801|3082720|3118656|114627|114628;1783272|1239|186801|186802|31979|1485|1529;1783272|1239|186801|186802|31984|150818|35700;1783272|1239|186801|186802|2937909|79206|1037382;1783272|1239|186801|186802|1491775|42447;1783272|1239|186801|186802|31984|150818;1783272|1239|186801|3082720|186804|1505660|29359;1783272|1239|186801|186802|186806|1730|469803;1783272|1239|186801|3120394|3120654|35829|290052;1783272|1239|186801|3120427|3120708|667112|288966;3379134|1224|1236|91347|1903412|82982,Complete,KateRasheed
bsdb:32024712/1/1,32024712,"cross-sectional observational, not case-control",32024712,10.1128/mSphere.00798-19,https://pubmed.ncbi.nlm.nih.gov/32024712/,"Annavajhala M.K., Khan S.D., Sullivan S.B., Shah J., Pass L., Kister K., Kunen H., Chiang V., Monnot G.C., Ricupero C.L., Mazur R.A., Gordon P., de Jong A., Wadhwa S., Yin M.T., Demmer R.T. , Uhlemann A.C.",Oral and Gut Microbial Diversity and Immune Regulation in Patients with HIV on Antiretroviral Therapy,mSphere,2020,"HIV, antiretroviral agents, antiretroviral therapy, immune dysfunction, immune system activation, mycobiome, oral microbiome",Experiment 1,United States of America,Homo sapiens,"Oral cavity,Feces","UBERON:0000167,UBERON:0001988",HIV infection,EFO:0000764,PLWH >50 years old with no/mild periodontitis,PLWH >50 years old with severe periodontitis,Patients with severe periodontal disease,4,22,3 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,race,sex",NA,unchanged,decreased,NA,NA,NA,Signature 1,Table S5 and Table S6,18 January 2023,Jacquelynshevin,"Jacquelynshevin,Peace Sandy,WikiWorks","Differentially abundant fungal taxa in saliva and subgingival plaque from patients with severe vs. no/mild periodontal disease (DESeq2, p<0.05, padj (FDR)<0.05)",increased,"k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida parapsilosis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",4751|4890|3239874|2916678|766764|5475|5476;4751|4890|3239874|2916678|766764|5475|5480;3379134|976|200643|171549|171552|838;3384189|32066|203490|203491|203492|848;1783272|201174|1760|85006|1268|32207;3379134|1224|28216|206351|481|32257;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|3085636|186803|437755;1783272|1239|91061|186826|1300|1301;3379134|1224|1236|135625|712|724,Complete,Peace Sandy
bsdb:32024712/1/2,32024712,"cross-sectional observational, not case-control",32024712,10.1128/mSphere.00798-19,https://pubmed.ncbi.nlm.nih.gov/32024712/,"Annavajhala M.K., Khan S.D., Sullivan S.B., Shah J., Pass L., Kister K., Kunen H., Chiang V., Monnot G.C., Ricupero C.L., Mazur R.A., Gordon P., de Jong A., Wadhwa S., Yin M.T., Demmer R.T. , Uhlemann A.C.",Oral and Gut Microbial Diversity and Immune Regulation in Patients with HIV on Antiretroviral Therapy,mSphere,2020,"HIV, antiretroviral agents, antiretroviral therapy, immune dysfunction, immune system activation, mycobiome, oral microbiome",Experiment 1,United States of America,Homo sapiens,"Oral cavity,Feces","UBERON:0000167,UBERON:0001988",HIV infection,EFO:0000764,PLWH >50 years old with no/mild periodontitis,PLWH >50 years old with severe periodontitis,Patients with severe periodontal disease,4,22,3 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,race,sex",NA,unchanged,decreased,NA,NA,NA,Signature 2,Table S5 and Table S6,24 January 2023,Jacquelynshevin,"Jacquelynshevin,Peace Sandy,WikiWorks","Differentially abundant fungal taxa in saliva and subgingival plaque from patients with severe vs. no/mild periodontal disease (DESeq2, p<0.05, padj (FDR)<0.05)",decreased,"k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida dubliniensis,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Debaryomyces|s__Debaryomyces hansenii,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Pleosporaceae|g__Exserohilum|s__Exserohilum turcicum,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Tausonia|s__Tausonia pullulans,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",4751|4890|3239874|2916678|766764|5475|42374;4751|4890|3239874|2916678|766764|4958|4959;4751|4890|147541|92860|28556|91493|93612;4751|5204|155616|90883|1851551|415704|82525;4751|4890|4891|4892|4893|4930|4932;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843489|31977|29465,Complete,Peace Sandy
bsdb:32039051/1/1,32039051,case-control,32039051,10.3389/fcimb.2019.00475,NA,"Tong Y., Zheng L., Qing P., Zhao H., Li Y., Su L., Zhang Q., Zhao Y., Luo Y. , Liu Y.",Oral Microbiota Perturbations Are Linked to High Risk for Rheumatoid Arthritis,Frontiers in cellular and infection microbiology,2019,"anti-citrullinated protein autoantibodies, dysbiosis, high risk, oral microbiome, rheumatoid arthritis",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,Healthy controls,Pre - High risk Patients,"Pre, “pre-clinical” at risk for RA individuals; RF, rheumatoid factor; ACPA,
anti-citrullinated protein antibodies;",23,29,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,"age,ethnic group,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"Figure 3B, text",16 August 2021,Tislam,"Tislam,Atrayees,Peace Sandy,WikiWorks","FIGURE 3  LEfSe analysis revealed the specific taxa changes in high-risk individuals (Pre) and RA patients. LefSe analysis was applied to identify differentially abundant taxa and for which the LDA scores more than 3 are shown (B). LefSe, the LDA effect size. *p < 0.05; **p < 0.01; and ***p < 0.001.",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella",1783272|1239|91061|1385;1783272|1239|91061|1385|539738|1378,Complete,Peace Sandy
bsdb:32039051/1/2,32039051,case-control,32039051,10.3389/fcimb.2019.00475,NA,"Tong Y., Zheng L., Qing P., Zhao H., Li Y., Su L., Zhang Q., Zhao Y., Luo Y. , Liu Y.",Oral Microbiota Perturbations Are Linked to High Risk for Rheumatoid Arthritis,Frontiers in cellular and infection microbiology,2019,"anti-citrullinated protein autoantibodies, dysbiosis, high risk, oral microbiome, rheumatoid arthritis",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,Healthy controls,Pre - High risk Patients,"Pre, “pre-clinical” at risk for RA individuals; RF, rheumatoid factor; ACPA,
anti-citrullinated protein antibodies;",23,29,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,"age,ethnic group,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 2,"Figure 3, text",17 August 2021,Tislam,"Tislam,Peace Sandy,WikiWorks","FIGURE 3 LEfSe analysis revealed the specific taxa changes in high-risk individuals (Pre) and RA patients. LefSe analysis was applied to identify differentially abundant taxa and for which the LDA scores more than 3 are shown (B). LefSe, the LDA effect size. *p < 0.05; **p < 0.01; and ***p < 0.001.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia",1783272|1239|186801|3082720|3118655|44259;3379134|1224|1236;3379134|1224|1236|135625|712|724;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836;3379134|1224|1236|72274;3379134|1224;3379134|203691|203692|136|137|146;3379134|203691|203692|136|137;3379134|203691|203692|136;3379134|203691|203692,Complete,Peace Sandy
bsdb:32039051/2/1,32039051,case-control,32039051,10.3389/fcimb.2019.00475,NA,"Tong Y., Zheng L., Qing P., Zhao H., Li Y., Su L., Zhang Q., Zhao Y., Luo Y. , Liu Y.",Oral Microbiota Perturbations Are Linked to High Risk for Rheumatoid Arthritis,Frontiers in cellular and infection microbiology,2019,"anti-citrullinated protein autoantibodies, dysbiosis, high risk, oral microbiome, rheumatoid arthritis",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,Healthy controls,Rheumatoid Arthritis,Patients with Rheumatoid Arthritis,23,27,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,"age,ethnic group,sex",NA,NA,increased,NA,NA,NA,decreased,Signature 1,"Figure 3, text",21 January 2024,Peace Sandy,"Peace Sandy,WikiWorks","FIGURE 3 LEfSe analysis revealed the specific taxa changes in high-risk individuals (Pre) and RA patients. LefSe analysis was applied to identify differentially abundant taxa and for which the LDA scores more than 3 are shown (B). LefSe, the LDA effect size. *p < 0.05; **p < 0.01; and ***p < 0.001.",increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium",1783272|1239;1783272|1239|909932;1783272|1239|909932|909929;1783272|1239|909932|1843489|31977;1783272|201174;1783272|201174|1760|2037;1783272|201174|1760|2037|2049;1783272|201174|1760|2037|2049|1654;95818|2093818|2093825;3379134|203691|203692|136|2845253|157;1783272|1239|909932|909929|1843491|970;3379134|976|200643|171549|171552|838;1783272|1239|909932|1843489|31977|906;1783272|201174|84998|84999;1783272|201174|84998|84999|1643824;1783272|201174|84998|84999|1643824|1380,Complete,Peace Sandy
bsdb:32039051/2/2,32039051,case-control,32039051,10.3389/fcimb.2019.00475,NA,"Tong Y., Zheng L., Qing P., Zhao H., Li Y., Su L., Zhang Q., Zhao Y., Luo Y. , Liu Y.",Oral Microbiota Perturbations Are Linked to High Risk for Rheumatoid Arthritis,Frontiers in cellular and infection microbiology,2019,"anti-citrullinated protein autoantibodies, dysbiosis, high risk, oral microbiome, rheumatoid arthritis",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,Healthy controls,Rheumatoid Arthritis,Patients with Rheumatoid Arthritis,23,27,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,"age,ethnic group,sex",NA,NA,increased,NA,NA,NA,decreased,Signature 2,"Figure 3, text",21 January 2024,Peace Sandy,"Peace Sandy,WikiWorks","FIGURE 3 LEfSe analysis revealed the specific taxa changes in high-risk individuals (Pre) and RA patients. LefSe analysis was applied to identify differentially abundant taxa and for which the LDA scores more than 3 are shown (B). LefSe, the LDA effect size. *p < 0.05; **p < 0.01; and ***p < 0.001.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta",1783272|1239|186801|3082720|3118655|44259;3379134|1224|1236;3379134|1224|1236|135625|712|724;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836;3379134|1224|1236|72274;3379134|1224;3379134|203691|203692|136|137;3379134|203691|203692|136;3379134|203691|203692;3379134|203691|203692|136|137|146,Complete,Peace Sandy
bsdb:32039051/3/1,32039051,case-control,32039051,10.3389/fcimb.2019.00475,NA,"Tong Y., Zheng L., Qing P., Zhao H., Li Y., Su L., Zhang Q., Zhao Y., Luo Y. , Liu Y.",Oral Microbiota Perturbations Are Linked to High Risk for Rheumatoid Arthritis,Frontiers in cellular and infection microbiology,2019,"anti-citrullinated protein autoantibodies, dysbiosis, high risk, oral microbiome, rheumatoid arthritis",Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,Rheumatoid Arthritis,Pre - High risk Patients,"Pre, “pre-clinical” at risk for RA individuals; RF, rheumatoid factor; ACPA, anti-citrullinated protein antibodies;",27,29,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,"age,ethnic group,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"Figure 3, text",21 January 2024,Peace Sandy,"Peace Sandy,WikiWorks","FIGURE 3 LEfSe analysis revealed the specific taxa changes in high-risk individuals (Pre) and RA patients. LefSe analysis was applied to identify differentially abundant taxa and for which the LDA scores more than 3 are shown (B). LefSe, the LDA effect size. *p < 0.05; **p < 0.01; and ***p < 0.001.",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella",1783272|1239|91061|1385;1783272|1239|91061|1385|539738|1378,Complete,Peace Sandy
bsdb:32039051/3/2,32039051,case-control,32039051,10.3389/fcimb.2019.00475,NA,"Tong Y., Zheng L., Qing P., Zhao H., Li Y., Su L., Zhang Q., Zhao Y., Luo Y. , Liu Y.",Oral Microbiota Perturbations Are Linked to High Risk for Rheumatoid Arthritis,Frontiers in cellular and infection microbiology,2019,"anti-citrullinated protein autoantibodies, dysbiosis, high risk, oral microbiome, rheumatoid arthritis",Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,Rheumatoid Arthritis,Pre - High risk Patients,"Pre, “pre-clinical” at risk for RA individuals; RF, rheumatoid factor; ACPA, anti-citrullinated protein antibodies;",27,29,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,"age,ethnic group,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 2,"Figure 3, text",21 January 2024,Peace Sandy,"Peace Sandy,WikiWorks","FIGURE 3 LEfSe analysis revealed the specific taxa changes in high-risk individuals (Pre) and RA patients. LefSe analysis was applied to identify differentially abundant taxa and for which the LDA scores more than 3 are shown (B). LefSe, the LDA effect size. *p < 0.05; **p < 0.01; and ***p < 0.001.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Bacillota,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes,,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;1783272|201174;1783272|201174|84998|84999|1643824;1783272|1239;95818|2093818|2093825;1783272|201174|84998|84999;1783272|1239|909932|1843489|31977|906;1783272|1239|909932;;3379134|976|200643|171549|171552|838;1783272|1239|909932|909929;1783272|1239|909932|909929|1843491|970;3379134|203691|203692|136|2845253|157;1783272|1239|909932|1843489|31977;1783272|201174|84998|84999|1643824|1380,Complete,Peace Sandy
bsdb:32040443/1/1,32040443,"cross-sectional observational, not case-control",32040443,10.18632/aging.102775,https://pubmed.ncbi.nlm.nih.gov/32040443/,"Chen J.J., He S., Fang L., Wang B., Bai S.J., Xie J., Zhou C.J., Wang W. , Xie P.",Age-specific differential changes on gut microbiota composition in patients with major depressive disorder,Aging,2020,"Actinobacteria, Bacteroidetes, Firmicutes, gut microbiota, major depressive disorder",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Young Healthy Controls(aged 18-29 years),Middle-aged HC (aged 30-59 years),Subjects without major depressive disorder between the ages of 30 to 59 years.,27,44,NA,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 9 & Figure 10(A),7 April 2023,Aiyshaaaa,"Aiyshaaaa,Claregrieve1,WikiWorks",Differential microbial abundance by LefSe between young HCs and middle-aged HCs,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,1783272|1239|186801|3082720|543314,Complete,Claregrieve1
bsdb:32040443/1/2,32040443,"cross-sectional observational, not case-control",32040443,10.18632/aging.102775,https://pubmed.ncbi.nlm.nih.gov/32040443/,"Chen J.J., He S., Fang L., Wang B., Bai S.J., Xie J., Zhou C.J., Wang W. , Xie P.",Age-specific differential changes on gut microbiota composition in patients with major depressive disorder,Aging,2020,"Actinobacteria, Bacteroidetes, Firmicutes, gut microbiota, major depressive disorder",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Young Healthy Controls(aged 18-29 years),Middle-aged HC (aged 30-59 years),Subjects without major depressive disorder between the ages of 30 to 59 years.,27,44,NA,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 9 & Figure 10(A),7 April 2023,Aiyshaaaa,"Aiyshaaaa,Claregrieve1,WikiWorks",Differential microbial abundance by LefSe between young HCs and middle-aged HCs,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|91061|186826|186828;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;1783272|1239|91061|186826|186828|117563;1783272|1239|909932|909929|1843491|158846;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:32040443/2/1,32040443,"cross-sectional observational, not case-control",32040443,10.18632/aging.102775,https://pubmed.ncbi.nlm.nih.gov/32040443/,"Chen J.J., He S., Fang L., Wang B., Bai S.J., Xie J., Zhou C.J., Wang W. , Xie P.",Age-specific differential changes on gut microbiota composition in patients with major depressive disorder,Aging,2020,"Actinobacteria, Bacteroidetes, Firmicutes, gut microbiota, major depressive disorder",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Young MDD (aged 18-29 years),Middle-aged MDD (aged 30-59 years),Individuals who have been diagnosed with Major Depressive Disorder(MDD) between the ages of 30-59 years.,25,45,NA,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 9 & Figure 10(B),7 April 2023,Aiyshaaaa,"Aiyshaaaa,Claregrieve1,WikiWorks",Differential microbial abundance by LefSe between young MDDs and middle-aged MDDs,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",1783272|1239|186801|3085636|186803|207244;1783272|201174|84998|1643822|1643826|84111;1783272|201174|84998|1643822|1643826|644652;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;1783272|1239|186801|3082720|186804;1783272|1239|526524|526525|2810281|191303,Complete,Claregrieve1
bsdb:32040443/2/2,32040443,"cross-sectional observational, not case-control",32040443,10.18632/aging.102775,https://pubmed.ncbi.nlm.nih.gov/32040443/,"Chen J.J., He S., Fang L., Wang B., Bai S.J., Xie J., Zhou C.J., Wang W. , Xie P.",Age-specific differential changes on gut microbiota composition in patients with major depressive disorder,Aging,2020,"Actinobacteria, Bacteroidetes, Firmicutes, gut microbiota, major depressive disorder",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Young MDD (aged 18-29 years),Middle-aged MDD (aged 30-59 years),Individuals who have been diagnosed with Major Depressive Disorder(MDD) between the ages of 30-59 years.,25,45,NA,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 9 & Figure 10(B),7 April 2023,Aiyshaaaa,"Aiyshaaaa,Claregrieve1,WikiWorks",Differential microbial abundance by LefSe between young MDDs and middle-aged MDDs,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|909932|1843488|909930;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|909932|1843489|31977,Complete,Claregrieve1
bsdb:32040443/3/1,32040443,"cross-sectional observational, not case-control",32040443,10.18632/aging.102775,https://pubmed.ncbi.nlm.nih.gov/32040443/,"Chen J.J., He S., Fang L., Wang B., Bai S.J., Xie J., Zhou C.J., Wang W. , Xie P.",Age-specific differential changes on gut microbiota composition in patients with major depressive disorder,Aging,2020,"Actinobacteria, Bacteroidetes, Firmicutes, gut microbiota, major depressive disorder",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Middle-aged HC (aged 30-59 years),Middle-aged MDD (aged 30-59 years),Individuals who have been diagnosed with Major Depressive Disorder(MDD) between the ages of 30-59 years.,44,45,Not specified,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 7,30 May 2023,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance by LefSe between middle-aged HCs and MDDs,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",3379134|1224|28216|80840|995019;1783272|1239|909932|1843488|909930;3379134|976|200643|171549|815;3379134|976|200643|171549|171552;1783272|1239|186801|3082720|543314|109326;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|186802|216572|459786;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3085636|186803|33042;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|216851,Complete,Claregrieve1
bsdb:32040443/3/2,32040443,"cross-sectional observational, not case-control",32040443,10.18632/aging.102775,https://pubmed.ncbi.nlm.nih.gov/32040443/,"Chen J.J., He S., Fang L., Wang B., Bai S.J., Xie J., Zhou C.J., Wang W. , Xie P.",Age-specific differential changes on gut microbiota composition in patients with major depressive disorder,Aging,2020,"Actinobacteria, Bacteroidetes, Firmicutes, gut microbiota, major depressive disorder",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Middle-aged HC (aged 30-59 years),Middle-aged MDD (aged 30-59 years),Individuals who have been diagnosed with Major Depressive Disorder(MDD) between the ages of 30-59 years.,44,45,Not specified,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 7,30 May 2023,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance by LefSe between middle-aged HCs and MDDs,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__Eubacteriales Family XIII. Incertae Sedis bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",1783272|1239|186801|3085636|186803;1783272|201174|84998|84999|84107;1783272|1239|91061|186826|1300;1783272|1239|186801|186802|186806;1783272|201174|1760|2037|2049;1783272|1239|186801|3082720|543314|2137877;1783272|1239|186801|3085636|186803|207244;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|1300|1301;1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|186806|1730;1783272|201174|1760|2037|2049|1654,Complete,Claregrieve1
bsdb:32040443/4/1,32040443,"cross-sectional observational, not case-control",32040443,10.18632/aging.102775,https://pubmed.ncbi.nlm.nih.gov/32040443/,"Chen J.J., He S., Fang L., Wang B., Bai S.J., Xie J., Zhou C.J., Wang W. , Xie P.",Age-specific differential changes on gut microbiota composition in patients with major depressive disorder,Aging,2020,"Actinobacteria, Bacteroidetes, Firmicutes, gut microbiota, major depressive disorder",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Young HC (aged 18-29 years),Young MDD (aged 18-29 years),Individuals who have been diagnosed with Major Depressive Disorder(MDD) between the ages of 18-29 years.,27,25,Not specified,16S,345,Roche454,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 6,30 May 2023,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance by LefSe between young HCs and MDDs,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.",1783272|1239|186801|186802|31979;1783272|1239|186801|3082720|186804;1783272|1239|186801|186802|216572|2485925;1783272|1239|186801|186802|31979|1485|1506,Complete,ChiomaBlessing
bsdb:32046455/2/1,32046455,"cross-sectional observational, not case-control",32046455,10.1007/s43032-019-00113-5,NA,"Perrotta A.R., Borrelli G.M., Martins C.O., Kallas E.G., Sanabani S.S., Griffith L.G., Alm E.J. , Abrao M.S.",The Vaginal Microbiome as a Tool to Predict rASRM Stage of Disease in Endometriosis: a Pilot Study,"Reproductive sciences (Thousand Oaks, Calif.)",2020,"Diagnosis, Endometriosis, Microbiome, Pathogenesis, Vaginal microbiome",Experiment 2,Brazil,Homo sapiens,Vagina,UBERON:0000996,Endometriosis,EFO:0001065,patients with rASRM stages 1 - 2,patients with rASRM stages 3 - 4,Patients with vaginal and rectal microbiome profiles and their association to severity of endometriosis (rASRM) stages 3 - 4,12,8,3 months,16S,4,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 3B,13 July 2023,Atrayees,"Atrayees,ChiomaBlessing,WikiWorks","Correlations of OTU abundance with stage of disease, showing abundance in stages 3 - 4 compared to stages 1 - 2",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|1224|1236|135625|712|724;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171551|836;1783272|1239|91061|186826|1300|1301,Complete,ChiomaBlessing
bsdb:32046455/2/2,32046455,"cross-sectional observational, not case-control",32046455,10.1007/s43032-019-00113-5,NA,"Perrotta A.R., Borrelli G.M., Martins C.O., Kallas E.G., Sanabani S.S., Griffith L.G., Alm E.J. , Abrao M.S.",The Vaginal Microbiome as a Tool to Predict rASRM Stage of Disease in Endometriosis: a Pilot Study,"Reproductive sciences (Thousand Oaks, Calif.)",2020,"Diagnosis, Endometriosis, Microbiome, Pathogenesis, Vaginal microbiome",Experiment 2,Brazil,Homo sapiens,Vagina,UBERON:0000996,Endometriosis,EFO:0001065,patients with rASRM stages 1 - 2,patients with rASRM stages 3 - 4,Patients with vaginal and rectal microbiome profiles and their association to severity of endometriosis (rASRM) stages 3 - 4,12,8,3 months,16S,4,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 3B,13 July 2023,Atrayees,"Atrayees,ChiomaBlessing,WikiWorks","Correlations of OTU abundance with stage of disease, showing abundance in stages 3 - 4 compared to stages 1 - 2",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Tissierellia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum",3379134|1224|28216|80840|80864|12916;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|909932|1843489|31977|39948;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|404402;1783272|1239|91061|186826|33958|1578;1783272|1239|1737404|1737405|1570339|162289;3379134|1224|28211|356|69277|28100;3379134|976|200643|171549|171552|838;1783272|201174|1760|85009|31957|1743;3379134|1224|28211|204457|41297|13687;1783272|1239|91061|186826|1300|1301;1783272|1239|1737404;1783272|201174|1760|2037|2049|184869,Complete,ChiomaBlessing
bsdb:32056780/1/1,32056780,prospective cohort,32056780,10.1016/j.jad.2019.12.020,NA,"Madan A., Thompson D., Fowler J.C., Ajami N.J., Salas R., Frueh B.C., Bradshaw M.R., Weinstein B.L., Oldham J.M. , Petrosino J.F.",The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness,Journal of affective disorders,2020,"Anxiety, Depression, Microbiome, Microbiota, Outcomes, Serious mental illness",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,mild depression,severe depression,"Patients in this group were diagnosed with severe depression
(The primary patient-reported outcome measures used in this study were the Patient Health Questionnaire – 9 (PHQ-9) and the Patient Health Questionnaire – Generalized Anxiety Disorder screener (GAD-7); they were used to quantify depression severity).",NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1A and 1B,10 January 2021,WikiWorks,"WikiWorks,Merit,ChiomaBlessing",Significant bacterial biomarkers among individuals with severe depression VS individuals with mild depression at admission,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 1_4_56FAA",1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|186802|216572|1263|41978;1783272|1239|186801|3085636|186803|658655,Complete,ChiomaBlessing
bsdb:32056780/1/2,32056780,prospective cohort,32056780,10.1016/j.jad.2019.12.020,NA,"Madan A., Thompson D., Fowler J.C., Ajami N.J., Salas R., Frueh B.C., Bradshaw M.R., Weinstein B.L., Oldham J.M. , Petrosino J.F.",The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness,Journal of affective disorders,2020,"Anxiety, Depression, Microbiome, Microbiota, Outcomes, Serious mental illness",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,mild depression,severe depression,"Patients in this group were diagnosed with severe depression
(The primary patient-reported outcome measures used in this study were the Patient Health Questionnaire – 9 (PHQ-9) and the Patient Health Questionnaire – Generalized Anxiety Disorder screener (GAD-7); they were used to quantify depression severity).",NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1A and 1B,10 January 2021,Fatima Zohra,"WikiWorks,Rukky,ChiomaBlessing,Joan Chuks",Significant bacterial biomarkers among individuals with severe depression VS individuals with mild depression at admission,decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter|s__Oxalobacter formigenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",1783272|201174;3379134|976|200643|171549|171550|239759|1288121;1783272|201174|1760|85004|31953|1678|1680;3379134|1224|28216|80840|75682|846|847;1783272|1239|186801|186802|216572|707003,Complete,Rukky
bsdb:32056780/2/1,32056780,prospective cohort,32056780,10.1016/j.jad.2019.12.020,NA,"Madan A., Thompson D., Fowler J.C., Ajami N.J., Salas R., Frueh B.C., Bradshaw M.R., Weinstein B.L., Oldham J.M. , Petrosino J.F.",The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness,Journal of affective disorders,2020,"Anxiety, Depression, Microbiome, Microbiota, Outcomes, Serious mental illness",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Unipolar depression,EFO:0003761,mild depression,moderate depression,Patients in this group were diagnosed with moderate depression (The primary patient-reported outcome measures used in this study were the Patient Health Questionnaire – 9 (PHQ-9) and the Patient Health Questionnaire – Generalized Anxiety Disorder screener (GAD-7); they were used to quantify depression severity).,NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1A and 1B,10 January 2021,Fatima Zohra,"WikiWorks,ChiomaBlessing",Significant bacterial biomarkers among individuals with moderate depression VS individuals with mild depression at admission,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum",1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|186802|216572|946234;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|186801|3085636|186803|2941495|1512,Complete,ChiomaBlessing
bsdb:32056780/3/1,32056780,prospective cohort,32056780,10.1016/j.jad.2019.12.020,NA,"Madan A., Thompson D., Fowler J.C., Ajami N.J., Salas R., Frueh B.C., Bradshaw M.R., Weinstein B.L., Oldham J.M. , Petrosino J.F.",The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness,Journal of affective disorders,2020,"Anxiety, Depression, Microbiome, Microbiota, Outcomes, Serious mental illness",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,mild anxiety,severe anxiety,Patients in this group were diagnosed with severe anxiety (The primary patient-reported outcome measures used in this study were the Patient Health Questionnaire – 9 (PHQ-9) and the Patient Health Questionnaire – Generalized Anxiety Disorder screener (GAD-7); they were used to quantify anxiety severity).,NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1C and 1D,10 January 2021,Fatima Zohra,"WikiWorks,Atrayees,ChiomaBlessing",Significant bacterial biomarkers among individuals with severe anxiety VS individuals with mild anxiety at admission,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 1_4_56FAA",1783272|1239|91061|186826|1300|1301|1328;1783272|1239|186801|3085636|186803|658655,Complete,ChiomaBlessing
bsdb:32056780/3/2,32056780,prospective cohort,32056780,10.1016/j.jad.2019.12.020,NA,"Madan A., Thompson D., Fowler J.C., Ajami N.J., Salas R., Frueh B.C., Bradshaw M.R., Weinstein B.L., Oldham J.M. , Petrosino J.F.",The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness,Journal of affective disorders,2020,"Anxiety, Depression, Microbiome, Microbiota, Outcomes, Serious mental illness",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,mild anxiety,severe anxiety,Patients in this group were diagnosed with severe anxiety (The primary patient-reported outcome measures used in this study were the Patient Health Questionnaire – 9 (PHQ-9) and the Patient Health Questionnaire – Generalized Anxiety Disorder screener (GAD-7); they were used to quantify anxiety severity).,NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1C and 1D,10 January 2021,Fatima Zohra,"WikiWorks,Merit,ChiomaBlessing",Significant bacterial biomarkers among individuals with severe anxiety VS individuals with mild anxiety at admission,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.",1783272|201174|1760;1783272|201174;1783272|1239|186801|3085636|186803|1766253|39491;3379134|976|200643|171549|171550|239759|28117;1783272|1239;1783272|201174|1760|85004|31953|1678|1680;1783272|1239|186801;1783272|1239|186801|3085636|186803|3570277|116085;1783272|201174|1760|85007|1653;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730|39496;1783272|201174|1760|85007|2805586|1847725;1783272|201174|1760|85007;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|186802|216572|1263|41978,Complete,ChiomaBlessing
bsdb:32056780/4/1,32056780,prospective cohort,32056780,10.1016/j.jad.2019.12.020,NA,"Madan A., Thompson D., Fowler J.C., Ajami N.J., Salas R., Frueh B.C., Bradshaw M.R., Weinstein B.L., Oldham J.M. , Petrosino J.F.",The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness,Journal of affective disorders,2020,"Anxiety, Depression, Microbiome, Microbiota, Outcomes, Serious mental illness",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,mild anxiety,moderate anxiety,Patients in this group were diagnosed with moderate anxiety (The primary patient-reported outcome measures used in this study were the Patient Health Questionnaire – 9 (PHQ-9) and the Patient Health Questionnaire – Generalized Anxiety Disorder screener (GAD-7); they were used to quantify anxiety severity).,NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1C and 1D,10 January 2021,Fatima Zohra,"WikiWorks,Atrayees,ChiomaBlessing",Significant bacterial biomarkers among individuals with moderate anxiety VS individuals with mild anxiety at admission,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 1_1_57FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium 1_7_47FAA,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella",1783272|1239|91061|186826|1300|1357|1358;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|3085636|186803|658081;1783272|1239|186801|186802|457421;1783272|201174|84998|1643822|1643826|84111,Complete,ChiomaBlessing
bsdb:32056780/5/1,32056780,prospective cohort,32056780,10.1016/j.jad.2019.12.020,NA,"Madan A., Thompson D., Fowler J.C., Ajami N.J., Salas R., Frueh B.C., Bradshaw M.R., Weinstein B.L., Oldham J.M. , Petrosino J.F.",The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness,Journal of affective disorders,2020,"Anxiety, Depression, Microbiome, Microbiota, Outcomes, Serious mental illness",Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Remission,EFO:0009785,No,Yes,Participants who achieved remission from depression at discharge,NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A and 3B,20 February 2024,ChiomaBlessing,"ChiomaBlessing,Joan Chuks,WikiWorks",Significant bacterial biomarkers among participants who achieved remission from depression (YES) VS participants who did not achieve remission from depression at discharge (NO),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",1783272|1239|186801|3085636|186803|1766253|39491;3379134|1224|28216|80840|506;1783272|1239;3379134|976|200643|171549|815|816|291645;3379134|1224|28216;3379134|1224|28216|80840;1783272|1239|186801;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;1783272|1239|909932;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|186802|186807;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|186802|216572|3068309;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|909932|909929;1783272|1239|186801|186802|216572|707003,Complete,ChiomaBlessing
bsdb:32056780/5/2,32056780,prospective cohort,32056780,10.1016/j.jad.2019.12.020,NA,"Madan A., Thompson D., Fowler J.C., Ajami N.J., Salas R., Frueh B.C., Bradshaw M.R., Weinstein B.L., Oldham J.M. , Petrosino J.F.",The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness,Journal of affective disorders,2020,"Anxiety, Depression, Microbiome, Microbiota, Outcomes, Serious mental illness",Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Remission,EFO:0009785,No,Yes,Participants who achieved remission from depression at discharge,NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3A and 3B,20 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Significant bacterial biomarkers among participants who achieved remission from depression (YES) VS participants who did not achieve remission from depression at discharge (NO),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Domibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hydrogenotrophica,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",1783272|1239|186801|186802|216572|1263|41978;1783272|1239|91061|1385;1783272|1239|91061|1385|186818;1783272|1239|91061|1385|186817|1433999;3379134|1224|1236|72274;3379134|1224|1236|72274|135621;3379134|1224|1236|72274|135621|286;3379134|1224|1236|91347|543;3379134|1224|1236|91347;3379134|1224|1236;1783272|1239|186801|3085636|186803|572511|53443;1783272|1239|186801|3082720|186804|1505657|261299;1783272|1239|186801|3085636|186803|2316020|33038;3379134|1224|1236|91347|543|561,Complete,ChiomaBlessing
bsdb:32056780/6/1,32056780,prospective cohort,32056780,10.1016/j.jad.2019.12.020,NA,"Madan A., Thompson D., Fowler J.C., Ajami N.J., Salas R., Frueh B.C., Bradshaw M.R., Weinstein B.L., Oldham J.M. , Petrosino J.F.",The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness,Journal of affective disorders,2020,"Anxiety, Depression, Microbiome, Microbiota, Outcomes, Serious mental illness",Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Remission,EFO:0009785,No,Yes,Participants who achieved remission from anxiety at discharge,NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3C and 3D,20 February 2024,ChiomaBlessing,"ChiomaBlessing,Joan Chuks,WikiWorks",Significant bacterial biomarkers among participants who achieved remission from anxiety (YES) VS participants who did not achieve remission from anxiety at discharge (NO),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 8_1_57FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",1783272|1239|186801|3085636|186803|1766253|39491;3379134|1224|28216|80840|506;1783272|1239;3379134|1224|28216;3379134|1224|28216|80840;1783272|1239|186801;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|1185407;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803|665951;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|186801|186802|216572|1263|41978;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|216572|707003,Complete,ChiomaBlessing
bsdb:32056780/6/2,32056780,prospective cohort,32056780,10.1016/j.jad.2019.12.020,NA,"Madan A., Thompson D., Fowler J.C., Ajami N.J., Salas R., Frueh B.C., Bradshaw M.R., Weinstein B.L., Oldham J.M. , Petrosino J.F.",The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness,Journal of affective disorders,2020,"Anxiety, Depression, Microbiome, Microbiota, Outcomes, Serious mental illness",Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Remission,EFO:0009785,No,Yes,Participants who achieved remission from anxiety at discharge,NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3C and 3D,20 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Significant bacterial biomarkers among participants who achieved remission from anxiety (YES) VS participants who did not achieve remission from anxiety at discharge (NO),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hydrogenotrophica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 21_3,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 1_1_57FAA,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Bacilli",3379134|976|200643|171549|815|816|291645;1783272|1239|186801|3085636|186803|572511|53443;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|526524|526525|128827|658657;3379134|1224|1236|91347|543|1940338;3379134|1224|1236;1783272|1239|186801|3082720|186804|1505657|261299;1783272|1239|186801|3085636|186803|658081;3379134|1224;1783272|1239|91061|186826|1300|1301|1304;3379134|1224|1236|91347|543|561;1783272|1239|91061,Complete,ChiomaBlessing
bsdb:32065949/1/1,32065949,case-control,32065949,10.1016/j.jpsychires.2020.02.005,NA,"Ma X., Asif H., Dai L., He Y., Zheng W., Wang D., Ren H., Tang J., Li C., Jin K., Li Z. , Chen X.",Alteration of the gut microbiome in first-episode drug-naïve and chronic medicated schizophrenia correlate with regional brain volumes,Journal of psychiatric research,2020,"Brain, Gut microbiome, Schizophrenia, Structural MRI",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy controls,FSCZ,first-episode drug naive schizophrenia (FSCZ) diagnosed according to the DSM IV criteria and PANSS having illness duration <=12 months and no treatment with antipsychotic medications before,69,40,1 month,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,demographics,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3,10 January 2021,Fatima Zohra,"WikiWorks,Atrayees","Compositional differences in gut microbiota between first-episode drug naive schizophrenia (FSCZ), anti-psychotic treated schizophrenia (TSCZ) patients and healthy controls (HC)",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",1783272|1239|186801|3082768|990719;3379134|1224|1236|91347|543;3379134|256845|1313211|278082|255528;1783272|1239|91061|186826|81852;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|620;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|81852|1350,Complete,Atrayees
bsdb:32065949/1/2,32065949,case-control,32065949,10.1016/j.jpsychires.2020.02.005,NA,"Ma X., Asif H., Dai L., He Y., Zheng W., Wang D., Ren H., Tang J., Li C., Jin K., Li Z. , Chen X.",Alteration of the gut microbiome in first-episode drug-naïve and chronic medicated schizophrenia correlate with regional brain volumes,Journal of psychiatric research,2020,"Brain, Gut microbiome, Schizophrenia, Structural MRI",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy controls,FSCZ,first-episode drug naive schizophrenia (FSCZ) diagnosed according to the DSM IV criteria and PANSS having illness duration <=12 months and no treatment with antipsychotic medications before,69,40,1 month,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,demographics,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3,10 January 2021,Fatima Zohra,"Atrayees,WikiWorks","Compositional differences in gut microbiota between first-episode drug naive schizophrenia (FSCZ), anti-psychotic treated schizophrenia (TSCZ) patients and healthy controls (HC)",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|1224|1236|135625|712;3379134|1224|1236|135624|83763;1783272|1239|526524|526525|2810281;1783272|1239|186801|3082720|186804;3384189|32066|203490|203491|203492|848;1783272|1239|909932|1843489|31977|906;3379134|1224|1236|135625|712|713;1783272|1239|909932|1843489|31977,Complete,Atrayees
bsdb:32065949/2/1,32065949,case-control,32065949,10.1016/j.jpsychires.2020.02.005,NA,"Ma X., Asif H., Dai L., He Y., Zheng W., Wang D., Ren H., Tang J., Li C., Jin K., Li Z. , Chen X.",Alteration of the gut microbiome in first-episode drug-naïve and chronic medicated schizophrenia correlate with regional brain volumes,Journal of psychiatric research,2020,"Brain, Gut microbiome, Schizophrenia, Structural MRI",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy controls,TSCZ,"first-episode drug naive schizophrenia(FSCZ) diagnosed according to the DSM IV criteria and PANSS having illness duration <=12 months and no treatment with antipsycotic medications before, anti-psycotic treated schizophrenia (TSCZ) having illness duration >12 months and received antipsychotic treatment for at least past 3 months",69,85,1 month,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,demographics,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 3,10 January 2021,Fatima Zohra,WikiWorks,"Compositional differences in gut microbiota between first-episode drug naive schizophrenia (FSCZ), anti-psychotic treated schizophrenia (TSCZ) patients and healthy controls (HC)",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|186801|3082768|990719;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|33958;3379134|1224|1236|91347|543|561;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|33958|1578;3379134|1224|1236|91347|543|620;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:32065949/2/2,32065949,case-control,32065949,10.1016/j.jpsychires.2020.02.005,NA,"Ma X., Asif H., Dai L., He Y., Zheng W., Wang D., Ren H., Tang J., Li C., Jin K., Li Z. , Chen X.",Alteration of the gut microbiome in first-episode drug-naïve and chronic medicated schizophrenia correlate with regional brain volumes,Journal of psychiatric research,2020,"Brain, Gut microbiome, Schizophrenia, Structural MRI",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy controls,TSCZ,"first-episode drug naive schizophrenia(FSCZ) diagnosed according to the DSM IV criteria and PANSS having illness duration <=12 months and no treatment with antipsycotic medications before, anti-psycotic treated schizophrenia (TSCZ) having illness duration >12 months and received antipsychotic treatment for at least past 3 months",69,85,1 month,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,demographics,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 3,10 January 2021,Fatima Zohra,"Aiyshaaaa,WikiWorks,Atrayees","Compositional differences in gut microbiota between first-episode drug naive schizophrenia (FSCZ), anti-psychotic treated schizophrenia (TSCZ) patients and healthy controls (HC)",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera",3379134|1224|1236|135625|712;1783272|1239|526524|526525|2810281;3379134|1224|1236|135625|712|713;1783272|1239|909932|1843489|31977|906,Complete,Atrayees
bsdb:32065949/3/1,32065949,case-control,32065949,10.1016/j.jpsychires.2020.02.005,NA,"Ma X., Asif H., Dai L., He Y., Zheng W., Wang D., Ren H., Tang J., Li C., Jin K., Li Z. , Chen X.",Alteration of the gut microbiome in first-episode drug-naïve and chronic medicated schizophrenia correlate with regional brain volumes,Journal of psychiatric research,2020,"Brain, Gut microbiome, Schizophrenia, Structural MRI",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,FSCZ,TSCZ,"first-episode drug naive schizophrenia(FSCZ) diagnosed according to the DSM IV criteria and PANSS having illness duration <=12 months and no treatment with antipsycotic medications before, anti-psycotic treated schizophrenia (TSCZ) having illness duration >12 months and received antipsychotic treatment for at least past 3 months",40,85,1 month,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,demographics,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 3,10 January 2021,Fatima Zohra,WikiWorks,"Compositional differences in gut microbiota between first-episode drug naive schizophrenia (FSCZ), anti-psychotic treated schizophrenia (TSCZ) patients and healthy controls (HC)",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|186801|3082720|186804;1783272|1239|909932|1843489|31977;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|33958;3379134|1224|1236|91347|543|561;3384189|32066|203490|203491|203492|848;1783272|1239|909932|1843489|31977|906;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|33958|1578;3379134|1224|1236|91347|543|620;1783272|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:32065949/3/2,32065949,case-control,32065949,10.1016/j.jpsychires.2020.02.005,NA,"Ma X., Asif H., Dai L., He Y., Zheng W., Wang D., Ren H., Tang J., Li C., Jin K., Li Z. , Chen X.",Alteration of the gut microbiome in first-episode drug-naïve and chronic medicated schizophrenia correlate with regional brain volumes,Journal of psychiatric research,2020,"Brain, Gut microbiome, Schizophrenia, Structural MRI",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,FSCZ,TSCZ,"first-episode drug naive schizophrenia(FSCZ) diagnosed according to the DSM IV criteria and PANSS having illness duration <=12 months and no treatment with antipsycotic medications before, anti-psycotic treated schizophrenia (TSCZ) having illness duration >12 months and received antipsychotic treatment for at least past 3 months",40,85,1 month,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,demographics,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 3,10 January 2021,Fatima Zohra,WikiWorks,"Compositional differences in gut microbiota between first-episode drug naive schizophrenia (FSCZ), anti-psychotic treated schizophrenia (TSCZ) patients and healthy controls (HC)",decreased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,1783272|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:32073296/1/1,32073296,time series / longitudinal observational,32073296,https://doi.org/10.3920/BM2019.0039,NA,"Ozkul C., Yalinay M. , Karakan T.",Structural changes in gut microbiome after Ramadan fasting: a pilot study,Beneficial microbes,2020,"Ramadan fasting, gut microbiota, intermittent fasting, microbiome",Experiment 1,Turkey,Homo sapiens,Feces,UBERON:0001988,Fasting,EFO:0002756,adults before fasting,adults after fasting,Healthy adults who were on Ramadan fast with a fasting period of approximately 17H per day for 29 days.,9,9,2 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure S2,13 March 2023,Barakat Dindi,"Barakat Dindi,Chloe,WikiWorks",LeFSe analysis and Linear discriminant effect size showing the differential abundance of discriminative taxa at the two-time points I.e before and after fasting.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales",3379134|74201|203494|48461|1647988|239934;1783272|1239|526524|526525|128827|174708;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|3085642|580596;1783272|1239|909932|1843489|31977|39948;1783272|1239|526524;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|216851;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3085636|186803|841;3379134|74201|203494;1783272|1239|526524|526525,Complete,Atrayees
bsdb:32073296/1/2,32073296,time series / longitudinal observational,32073296,https://doi.org/10.3920/BM2019.0039,NA,"Ozkul C., Yalinay M. , Karakan T.",Structural changes in gut microbiome after Ramadan fasting: a pilot study,Beneficial microbes,2020,"Ramadan fasting, gut microbiota, intermittent fasting, microbiome",Experiment 1,Turkey,Homo sapiens,Feces,UBERON:0001988,Fasting,EFO:0002756,adults before fasting,adults after fasting,Healthy adults who were on Ramadan fast with a fasting period of approximately 17H per day for 29 days.,9,9,2 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Figure S2,13 March 2023,Barakat Dindi,"Barakat Dindi,Chloe,WikiWorks",LeFSe analysis and Linear discriminant effect size showing the differential abundance of discriminative taxa at the two-time points I.e before and after fasting.,decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Pseudomonadati|p__Pseudomonadota",1783272|1239;3379134|74152|641853;3379134|74152|641853|641854|641876;3379134|74152|641853|641854;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852|1350;1783272|1239|526524;3379134|1224|1236|91347|543|561;1783272|1239|186801|186802;1783272|1239|91061|186826;1783272|544448|31969;3379134|1224,Complete,Atrayees
bsdb:32079430/1/1,32079430,case-control,32079430,10.2217/fmb-2019-0283,NA,"Guo M., Yao J., Yang F., Liu W., Bai H., Ma J., Ma X., Zhang J., Fang Y., Miao Y., Sun J., Zhang Y. , Zhao H.",The composition of intestinal microbiota and its association with functional constipation of the elderly patients,Future microbiology,2020,"16s rRNA gene sequencing, functional constipation, intestinal microbiota composition, the elderly",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Heathy volunteers,Functional constipation (FC) group,Patients with functional constipation (FC),48,61,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,age,NA,NA,NA,NA,NA,NA,increased,Signature 1,Figure 3B,31 March 2025,Tosin,Tosin,The intestinal microbiota composition between functional constipation patients and healthy controls at the genus level,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae|g__Rheinheimera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|976|200643|171549|815|816;3379134|976|200643|171549|1853231|574697;3379134|29547|3031852|213849|72294|194;1783272|1239|186801|3085636|186803|2383;1783272|1239|186801|186802|31979|1485;3379134|1224|1236|135613|1046|67575;3379134|1224|28216|80840|995019|40544,Complete,Svetlana up
bsdb:32079430/1/2,32079430,case-control,32079430,10.2217/fmb-2019-0283,NA,"Guo M., Yao J., Yang F., Liu W., Bai H., Ma J., Ma X., Zhang J., Fang Y., Miao Y., Sun J., Zhang Y. , Zhao H.",The composition of intestinal microbiota and its association with functional constipation of the elderly patients,Future microbiology,2020,"16s rRNA gene sequencing, functional constipation, intestinal microbiota composition, the elderly",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Heathy volunteers,Functional constipation (FC) group,Patients with functional constipation (FC),48,61,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,age,NA,NA,NA,NA,NA,NA,increased,Signature 2,Figure 3B,1 April 2025,Tosin,Tosin,The intestinal microbiota composition between functional constipation patients and healthy controls at the genus level,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Edwardsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|74201|203494|48461|1647988|239934;1783272|1239|526524|526525|128827|174708;1783272|201174|84998|84999|1643824|1380;1783272|1239|186801|186802|186807|51514;3384194|1297|188787|118964|183710|1298;3379134|1224|1236|91347|1903412|635;3379134|1224|1236|91347|543|561;1783272|1239|91061|186826|1300|1357;3379134|976|200643|171549|171552|838;3379134|1224|1236|72274|135621|286;3379134|1224|28211|204457|41297|13687;3384194|1297|188787|68933|188786|270;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:32079430/2/1,32079430,case-control,32079430,10.2217/fmb-2019-0283,NA,"Guo M., Yao J., Yang F., Liu W., Bai H., Ma J., Ma X., Zhang J., Fang Y., Miao Y., Sun J., Zhang Y. , Zhao H.",The composition of intestinal microbiota and its association with functional constipation of the elderly patients,Future microbiology,2020,"16s rRNA gene sequencing, functional constipation, intestinal microbiota composition, the elderly",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Heathy volunteers,Functional constipation (FC) group,Patients with functional constipation (FC),48,61,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,NA,NA,NA,NA,increased,Signature 1,Figure 4,1 April 2025,Tosin,Tosin,The comparison of different intestinal microbiota species between functional constipation patients and healthy controls based on the classification level tree,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales",3379134|1224|28216|80840|506;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|1224|28216;3379134|200940|3031449|213115|194924|35832;3379134|1224|28216|80840;3379134|976|200643|171549|1853231|574697;3379134|1224|1236|91347|543|547;1783272|1239|186801|3085636|186803|28050;3379134|256845|1313211;3379134|976|200643|171549|2005473;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|1853231;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|186807;3379134|976|200643|171549|171550;3379134|1224|28216|80840|995019|40544;3379134|256845|1313211|278082|255528;3379134|256845|1313211|278082,Complete,Svetlana up
bsdb:32079430/2/2,32079430,case-control,32079430,10.2217/fmb-2019-0283,NA,"Guo M., Yao J., Yang F., Liu W., Bai H., Ma J., Ma X., Zhang J., Fang Y., Miao Y., Sun J., Zhang Y. , Zhao H.",The composition of intestinal microbiota and its association with functional constipation of the elderly patients,Future microbiology,2020,"16s rRNA gene sequencing, functional constipation, intestinal microbiota composition, the elderly",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Heathy volunteers,Functional constipation (FC) group,Patients with functional constipation (FC),48,61,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,NA,NA,NA,NA,increased,Signature 2,Figure 4,1 April 2025,Tosin,Tosin,The comparison of different intestinal microbiota species between functional constipation patients and healthy controls based on the classification level tree,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Viridiplantae|p__Streptophyta,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacillati|p__Cyanobacteriota",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;3379134|1224|1236|135624|84642;3379134|1224|1236|135624;3379134|74201|203494|48461|1647988|239934;1783272|201174|84998|84999|1643824|1380;1783272|1239|91061;1783272|1239|526524|526525|128827|118747;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|186801|3085636|186803|189330;1783272|201174|84998|1643822|1643826|84111;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|1903409|551;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;3379134|1224|1236|91347|543|561;1783272|1239|186801|186802|186806|1730;3379134|1224|1236;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1357;3379134|1224|1236|2887326|468;3379134|1224|1236|91347|1903414|583;3379134|1224|1236|72274|135621;3379134|1224|1236|72274;3379134|1224|1236|72274|135621|286;3379134|1224|1236|91347|1903411|613;3379134|1224|28211|204457|41297;3379134|1224|28211|204457;3379134|1224|28211|204457|41297|13687;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;33090|35493;3384194|1297|188787|68933|188786;3384194|1297|188787|68933;3384194|1297|188787|68933|188786|270;1783272|1239|909932|1843489|31977|29465;3379134|74201|203494|48461|203557;3379134|74201|203494|48461;3379134|74201|203494;1783272|1117,Complete,Svetlana up
bsdb:32083132/1/1,32083132,"cross-sectional observational, not case-control",32083132,10.1155/2020/7828392,https://pubmed.ncbi.nlm.nih.gov/32083132/,"Liu W., Zhang R., Shu R., Yu J., Li H., Long H., Jin S., Li S., Hu Q., Yao F., Zhou C., Huang Q., Hu X., Chen M., Hu W., Wang Q., Fang S. , Wu Q.",Study of the Relationship between Microbiome and Colorectal Cancer Susceptibility Using 16SrRNA Sequencing,BioMed research international,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Controls (HC),Colorectal Cancer (CC),Patients who visited the department of gastroenterology of Tianyou hospital of Wuhan from January 2017 to December 2017 and received colonoscopy and histopathological examination were recruited to the study. Patients with colorectal adenocarcinoma were recorded as the colorectal cancer (CC) group.,42,51,2 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,Table 4,9 December 2021,Itslanapark,"Itslanapark,WikiWorks",Difference analysis at the phylum level between Colorectal Cancer and Healthy Controls. Wilcoxon tests were used to analyze differences in the abundance between the two groups. Significant differences were evaluated by False Discovery Rate.,increased,"k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Spirochaetota,k__Thermotogati|p__Synergistota",3384189|32066;3379134|1224;3379134|203691;3384194|508458,Complete,Fatima
bsdb:32083132/1/2,32083132,"cross-sectional observational, not case-control",32083132,10.1155/2020/7828392,https://pubmed.ncbi.nlm.nih.gov/32083132/,"Liu W., Zhang R., Shu R., Yu J., Li H., Long H., Jin S., Li S., Hu Q., Yao F., Zhou C., Huang Q., Hu X., Chen M., Hu W., Wang Q., Fang S. , Wu Q.",Study of the Relationship between Microbiome and Colorectal Cancer Susceptibility Using 16SrRNA Sequencing,BioMed research international,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Controls (HC),Colorectal Cancer (CC),Patients who visited the department of gastroenterology of Tianyou hospital of Wuhan from January 2017 to December 2017 and received colonoscopy and histopathological examination were recruited to the study. Patients with colorectal adenocarcinoma were recorded as the colorectal cancer (CC) group.,42,51,2 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,Table 4,10 December 2021,Itslanapark,"Itslanapark,WikiWorks",Difference analysis at the phylum level between Colorectal Cancer and Healthy Controls. Wilcoxon tests were used to analyze differences in the abundance between the two groups. Significant differences were evaluated by False Discovery Rate.,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Fatima
bsdb:32093640/1/1,32093640,time series / longitudinal observational,32093640,10.1186/s12885-020-6654-5,NA,"Chua L.L., Rajasuriar R., Lim Y.A.L., Woo Y.L., Loke P. , Ariffin H.","Temporal changes in gut microbiota profile in children with acute lymphoblastic leukemia prior to commencement-, during-, and post-cessation of chemotherapy",BMC cancer,2020,"Bacteroides, Bacteroidetes, Chemotherapy, Childhood acute lymphoblastic leukemia, Microbiome, Microbiota dysbiosis",Experiment 1,Malaysia,Homo sapiens,Feces,UBERON:0001988,Leukemia,EFO:0000565,healthy control,Acute Lymphoblastic Leukemia diagnosis and Pre- Chemotherapy treatment,children (ages 2-6 years old) diagnosed with and treated for Acute Lymphoblastic Leukemia,7,7,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,"age,ethnic group",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a,10 January 2021,William Lam,WikiWorks,Differentially abundant bacteria were identified between Acute Lymphoblastic Leukemia (ALL) patients pre-chemotherapy and healthy controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis",3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|815|816|817,Complete,NA
bsdb:32093640/1/2,32093640,time series / longitudinal observational,32093640,10.1186/s12885-020-6654-5,NA,"Chua L.L., Rajasuriar R., Lim Y.A.L., Woo Y.L., Loke P. , Ariffin H.","Temporal changes in gut microbiota profile in children with acute lymphoblastic leukemia prior to commencement-, during-, and post-cessation of chemotherapy",BMC cancer,2020,"Bacteroides, Bacteroidetes, Chemotherapy, Childhood acute lymphoblastic leukemia, Microbiome, Microbiota dysbiosis",Experiment 1,Malaysia,Homo sapiens,Feces,UBERON:0001988,Leukemia,EFO:0000565,healthy control,Acute Lymphoblastic Leukemia diagnosis and Pre- Chemotherapy treatment,children (ages 2-6 years old) diagnosed with and treated for Acute Lymphoblastic Leukemia,7,7,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,"age,ethnic group",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3a,10 January 2021,William Lam,WikiWorks,Differentially abundant bacteria were identified between Acute Lymphoblastic Leukemia (ALL) patients pre-chemotherapy and healthy controls,decreased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",3379134|29547|3031852|213849|72294|194;1783272|1239|909932|1843489|31977;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85004|31953|1678;1783272|201174|84998|84999|1643824|1380;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|91061|1385|90964|1279;3379134|976|200643|171549|171552|838;1783272|1239|1737404|1737405|1570339|165779;3379134|976|200643|171549|171551|836,Complete,NA
bsdb:32093640/1/3,32093640,time series / longitudinal observational,32093640,10.1186/s12885-020-6654-5,NA,"Chua L.L., Rajasuriar R., Lim Y.A.L., Woo Y.L., Loke P. , Ariffin H.","Temporal changes in gut microbiota profile in children with acute lymphoblastic leukemia prior to commencement-, during-, and post-cessation of chemotherapy",BMC cancer,2020,"Bacteroides, Bacteroidetes, Chemotherapy, Childhood acute lymphoblastic leukemia, Microbiome, Microbiota dysbiosis",Experiment 1,Malaysia,Homo sapiens,Feces,UBERON:0001988,Leukemia,EFO:0000565,healthy control,Acute Lymphoblastic Leukemia diagnosis and Pre- Chemotherapy treatment,children (ages 2-6 years old) diagnosed with and treated for Acute Lymphoblastic Leukemia,7,7,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,"age,ethnic group",NA,NA,NA,NA,NA,NA,NA,Signature 3,Figure 3b,10 January 2021,William Lam,WikiWorks,Differentially abundant bacteria were identified between Acute Lymphoblastic Leukemia (ALL) patients post-chemotherapy and healthy controls,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,NA
bsdb:32093640/1/4,32093640,time series / longitudinal observational,32093640,10.1186/s12885-020-6654-5,NA,"Chua L.L., Rajasuriar R., Lim Y.A.L., Woo Y.L., Loke P. , Ariffin H.","Temporal changes in gut microbiota profile in children with acute lymphoblastic leukemia prior to commencement-, during-, and post-cessation of chemotherapy",BMC cancer,2020,"Bacteroides, Bacteroidetes, Chemotherapy, Childhood acute lymphoblastic leukemia, Microbiome, Microbiota dysbiosis",Experiment 1,Malaysia,Homo sapiens,Feces,UBERON:0001988,Leukemia,EFO:0000565,healthy control,Acute Lymphoblastic Leukemia diagnosis and Pre- Chemotherapy treatment,children (ages 2-6 years old) diagnosed with and treated for Acute Lymphoblastic Leukemia,7,7,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,"age,ethnic group",NA,NA,NA,NA,NA,NA,NA,Signature 4,Figure 3b,10 January 2021,William Lam,WikiWorks,Differentially abundant bacteria were identified between Acute Lymphoblastic Leukemia (ALL) patients post-chemotherapy and healthy controls,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium",1783272|201174|84998|84999|1643824|1380;3379134|976|200643|171549|815|816;3379134|976|200643|171549|171552|838;3384189|32066|203490|203491|203492|848;1783272|201174|1760|85007|1653|1716,Complete,NA
bsdb:32101664/1/1,32101664,prospective cohort,32101664,10.1056/NEJMoa1900623,NA,"Peled J.U., Gomes A.L.C., Devlin S.M., Littmann E.R., Taur Y., Sung A.D., Weber D., Hashimoto D., Slingerland A.E., Slingerland J.B., Maloy M., Clurman A.G., Stein-Thoeringer C.K., Markey K.A., Docampo M.D., Burgos da Silva M., Khan N., Gessner A., Messina J.A., Romero K., Lew M.V., Bush A., Bohannon L., Brereton D.G., Fontana E., Amoretti L.A., Wright R.J., Armijo G.K., Shono Y., Sanchez-Escamilla M., Castillo Flores N., Alarcon Tomas A., Lin R.J., Yáñez San Segundo L., Shah G.L., Cho C., Scordo M., Politikos I., Hayasaka K., Hasegawa Y., Gyurkocza B., Ponce D.M., Barker J.N., Perales M.A., Giralt S.A., Jenq R.R., Teshima T., Chao N.J., Holler E., Xavier J.B., Pamer E.G. , van den Brink M.R.M.",Microbiota as Predictor of Mortality in Allogeneic Hematopoietic-Cell Transplantation,The New England journal of medicine,2020,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,Survivors,Mortality,Patients in the MSK cohort (Cohort 1) who died within the follow-up period.,464,240,NA,16S,45,Illumina,log transformation,Cox Proportional-Hazards Regression,NA,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Supplementary Figure S8, Supplementary Table S9",7 November 2025,Blegodwin,Blegodwin,Bacterial taxa associated with increased mortality risk (positive effect size) at MSK day 7-21.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia|s__Alloscardovia omnicolens,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hydrogenotrophica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Dickeya|s__Dickeya chrysanthemi,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter ludwigii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster lavalensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus mundtii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus rivorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium limosum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania filiformis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Massilimicrobiota|s__Massilimicrobiota timonensis,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|s__Peptostreptococcaceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Pseudolactococcus|s__Pseudolactococcus piscium,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula",1783272|1239|91061|186826|186827|46123|46125;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550|239759|28117;1783272|201174|1760|85004|31953|419014|419015;1783272|1239|91061|1385;1783272|1239|91061;1783272|1239;3379134|976|200643|171549;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|818;1783272|201174|1760|85004|31953|1678|1689;1783272|1239|186801|3085636|186803|572511|53443;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|830;1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|526524|526525|2810280|100883;3379134|1224|1236|91347|1903410|204037|556;3379134|1224|1236|91347|543|547|299767;1783272|1239|186801|3085636|186803|2719313|358742;1783272|1239|186801|3085636|186803|2719313|1531;1783272|1239|186801|3085636|186803|2719313|460384;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|81852|1350|53346;1783272|1239|91061|186826|81852|1350|762845;1783272|1239|186801|186802|186806|1730|1736;3379134|1224|1236|135625|712|724|729;1783272|1239|526524|526525|128827|61170|61171;3379134|1224|1236|91347|543|570|571;1783272|1239|91061|186826|33958|1578|1579;1783272|1239|91061|186826|33958|2767887|1624;1783272|1239|526524|526525|128827|1924110|1776392;1783272|544448|31969|2085|2092|2093;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|46503;3379134|1224|28216|80840|995019|577310|487175;1783272|1239|186801|3082720|186804|1904861;3379134|976|200643|171549|171552|838|28132;1783272|1239|91061|186826|1300|3436058|1364;3379134|1224;1783272|1239|186801|186802|216572|1263;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|91061|186826|1300|1301|1309;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|29466,Complete,NA
bsdb:32101664/1/2,32101664,prospective cohort,32101664,10.1056/NEJMoa1900623,NA,"Peled J.U., Gomes A.L.C., Devlin S.M., Littmann E.R., Taur Y., Sung A.D., Weber D., Hashimoto D., Slingerland A.E., Slingerland J.B., Maloy M., Clurman A.G., Stein-Thoeringer C.K., Markey K.A., Docampo M.D., Burgos da Silva M., Khan N., Gessner A., Messina J.A., Romero K., Lew M.V., Bush A., Bohannon L., Brereton D.G., Fontana E., Amoretti L.A., Wright R.J., Armijo G.K., Shono Y., Sanchez-Escamilla M., Castillo Flores N., Alarcon Tomas A., Lin R.J., Yáñez San Segundo L., Shah G.L., Cho C., Scordo M., Politikos I., Hayasaka K., Hasegawa Y., Gyurkocza B., Ponce D.M., Barker J.N., Perales M.A., Giralt S.A., Jenq R.R., Teshima T., Chao N.J., Holler E., Xavier J.B., Pamer E.G. , van den Brink M.R.M.",Microbiota as Predictor of Mortality in Allogeneic Hematopoietic-Cell Transplantation,The New England journal of medicine,2020,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,Survivors,Mortality,Patients in the MSK cohort (Cohort 1) who died within the follow-up period.,464,240,NA,16S,45,Illumina,log transformation,Cox Proportional-Hazards Regression,NA,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Supplementary Figure S8, Supplementary Table S9",7 November 2025,Blegodwin,Blegodwin,Bacterial taxa associated with reduced mortality risk (negative effect size) at MSK day 7-21.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum|s__Actinobaculum massiliense,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia luti,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium paraputrificum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. Culture-54,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. ID5,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium tertium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium pseudogenitalium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Drancourtella|s__Drancourtella massiliensis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus gallinarum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalispora|s__Faecalispora sporosphaeroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Fructilactobacillus|s__Fructilactobacillus fructivorans,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora algidixylanolytica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus|s__Lactiplantibacillus plantarum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella rimae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lentilactobacillus|s__Lentilactobacillus buchneri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus animalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter faecis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium neglectum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Parascardovia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus|s__Pediococcus acidilactici,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium freudenreichii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia inopinata,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus lutetiensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter|s__Terrisporobacter glycolicus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia saccharogumia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella confusa,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",1783272|201174|1760|2037|2049|76833|202789;1783272|201174|1760|2037|2049|1654|55565;1783272|201174;3379134|74201|203494|48461|1647988|239934|239935;3379134|1224|28211;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|186801|3085636|186803|207244|105841;1783272|201174|1760|85009|31957|2801844|1750;1783272|201174|84998|84999|1643824|1380;1783272|1239|91061|1385|186817;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|46506;3379134|976|200643|171549|815|816|820;1783272|1239|186801|3085636|186803|572511|871665;1783272|1239|186801|3085636|186803|572511|89014;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|31979|1485|29363;1783272|1239|186801|186802|31979|1485|1502;1783272|1239|186801|186802|31979|1485|1003352;1783272|1239|186801|186802|31979|1485|320882;1783272|1239|186801|186802|31979|1485|1559;1783272|1239|526524|526525|2810280;1783272|1239|186801|3085636|186803|3569723|410072;1783272|201174|84998|84999|84107;1783272|201174|1760|85007|1653|1716|38303;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|186802|216572|1903506|1632013;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|91061|186826|81852|1350|1353;1783272|1239|526524|526525;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|216572|3115229|1549;1783272|1239|91061|186826|33958|2767881|1614;3384189|32066;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492|848|851;1783272|1239|91061|1385|539738|1378|1379;1783272|1239|91061|186826|186828|117563|46124;1783272|1239|526524|526525|128827|1573535|1735;1783272|1239|186801|3085636|186803|1649459|154046;1783272|1239|186801|3082720|186804|1505657|261299;1783272|1239|186801|3085636|186803|2719231|94868;1783272|1239|91061|186826|33958|2767842|1590;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|91061|186826|1300|1357;1783272|201174|84998|84999|1643824|2767353|1383;1783272|1239|91061|186826|33958|2767893|1581;1783272|1239|91061|186826|33958|2767887|1605;1783272|1239|91061|186826|33958|2742598|1613;1783272|1239|91061|186826|33958|2742598|1598;1783272|1239|186801|3085636|186803|2316020|592978;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843489|31977|906|187326;1783272|1239|186801|3082720|543314|86331|114528;1783272|1239|186801|186802|216572|119852;1783272|201174|1760|85004|31953|196082;1783272|1239|91061|186826|33958|1253|1254;1783272|1239|186801|3082720|186804;1783272|1239|909932|1843488|909930|33024|33025;1783272|201174|1760|85009|31957|1743;1783272|201174|1760|85009|31957|1743|1744;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|301302;1783272|201174|1760|85006|1268|32207|2047;1783272|1239|186801|186802|216572|1263;1783272|201174|1760|85004|31953|196081|78259;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301|150055;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|186801|3082720|186804|1505652|36841;1783272|1239|526524|526525|2810280|3025755|341225;1783272|1239|526524|526525|2810280|3025755|29348;1783272|1239|526524|526525|2810281|191303|154288;1783272|1239|91061|186826|33958|46255|1583;1783272|1239|186801|3082720|186804,Complete,NA
bsdb:32105635/1/1,32105635,"cross-sectional observational, not case-control",32105635,10.1016/j.isci.2020.100884,NA,"Pushalkar S., Paul B., Li Q., Yang J., Vasconcelos R., Makwana S., González J.M., Shah S., Xie C., Janal M.N., Queiroz E., Bederoff M., Leinwand J., Solarewicz J., Xu F., Aboseria E., Guo Y., Aguallo D., Gomez C., Kamer A., Shelley D., Aphinyanaphongs Y., Barber C., Gordon T., Corby P., Li X. , Saxena D.",Electronic Cigarette Aerosol Modulates the Oral Microbiome and Increases Risk of Infection,iScience,2020,"In Vitro Toxicology, Microbiome, Oral Microbiology",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,non-smokers,e-cigarette smokers,"participants who were 21 years or older, healthy, diagnosed with periodontal disease, and current e-cigarette smokers",39,40,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure S2,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between e-cig smokers and never smokers,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum orale,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus|s__Peptococcus sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri",3384189|32066|203490|203491|203492|848|860;3384189|32066|203490|203491|203492|848|68766;1783272|1239|186801|3085636|186803|1164882|979627;3379134|1224|28216|80840|119060|47670|47671;1783272|1239|186801|3085636|186803|265975|1501329;1783272|1239|186801|186802|186807|2740|2049038;3379134|976|200643|171549|171552|838|59823;1783272|1239|91061|186826|1300|1301|1303;3379134|976|200643|171549|171551|836|1583331,Complete,Claregrieve1
bsdb:32105635/1/2,32105635,"cross-sectional observational, not case-control",32105635,10.1016/j.isci.2020.100884,NA,"Pushalkar S., Paul B., Li Q., Yang J., Vasconcelos R., Makwana S., González J.M., Shah S., Xie C., Janal M.N., Queiroz E., Bederoff M., Leinwand J., Solarewicz J., Xu F., Aboseria E., Guo Y., Aguallo D., Gomez C., Kamer A., Shelley D., Aphinyanaphongs Y., Barber C., Gordon T., Corby P., Li X. , Saxena D.",Electronic Cigarette Aerosol Modulates the Oral Microbiome and Increases Risk of Infection,iScience,2020,"In Vitro Toxicology, Microbiome, Oral Microbiology",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,non-smokers,e-cigarette smokers,"participants who were 21 years or older, healthy, diagnosed with periodontal disease, and current e-cigarette smokers",39,40,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Figure S2,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between e-cig smokers and never smokers,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia|s__Alloscardovia omnicolens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria bacilliformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella multisaccharivorax,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas artemidis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas dianae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia exigua,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus capitis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|s__uncultured Bacteroidota bacterium",1783272|201174|1760|85004|31953|419014|419015;1783272|1239|186801|186802;1783272|1239|186801|3082720|3118655|44259|143361;3384194|508458|649775|649776|3029087|1434006|651822;3384189|32066|203490|203491|203492|848|851;1783272|1239|91061|186826|1300|1357|1358;1783272|1239|909932|909929|1843491|52225|2049034;3379134|1224|28216|206351|481|482|267212;1783272|1239|186801|3085636|186803|265975|1969407;1783272|1239|1737404|1737405|1570339|543311|33033;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|171551|836|281920;3379134|976|200643|171549|171552|52228|310514;3379134|976|200643|171549|171552|2974251|28135;3379134|976|200643|171549|171552|838|59823;1783272|1239|909932|909929|1843491|970|671224;1783272|1239|909932|909929|1843491|970|135079;1783272|201174|84998|1643822|1643826|84108|84109;1783272|1239|91061|1385|90964|1279|29388;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|909932|1843489|31977;3379134|976|152509,Complete,Claregrieve1
bsdb:32105635/2/1,32105635,"cross-sectional observational, not case-control",32105635,10.1016/j.isci.2020.100884,NA,"Pushalkar S., Paul B., Li Q., Yang J., Vasconcelos R., Makwana S., González J.M., Shah S., Xie C., Janal M.N., Queiroz E., Bederoff M., Leinwand J., Solarewicz J., Xu F., Aboseria E., Guo Y., Aguallo D., Gomez C., Kamer A., Shelley D., Aphinyanaphongs Y., Barber C., Gordon T., Corby P., Li X. , Saxena D.",Electronic Cigarette Aerosol Modulates the Oral Microbiome and Increases Risk of Infection,iScience,2020,"In Vitro Toxicology, Microbiome, Oral Microbiology",Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,never smokers,cigarette smokers,"participants who were 21 years or older, healthy, diagnosed with periodontal disease, and current smokers",39,40,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure S2,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between cigarette smokers and never smokers,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces gerencseriae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga haemolytica,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella morbi,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus haemolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum orale,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ottowia|s__Ottowia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus|s__Peptococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae",1783272|1239|91061|186826|186827|46123|46125;1783272|201174|1760|2037|2049|1654|52769;3379134|976|117743|200644|49546|1016|1017;3379134|976|117743|200644|49546|1016|45243;3379134|976|117743|200644|49546|1016|327575;3379134|976|117743|200644|49546|1016|1019;3379134|1224|1236|135615|868|2717|2718;1783272|1239|186801|3085636|186803|43996|43997;1783272|201174|1760|85007|1653|1716|61592;3379134|1224|28216|206351|481|538|539;3384189|32066|203490|203491|203492|848|860;1783272|1239|91061|186826|186828|117563|137732;3379134|1224|1236|135625|712|724|726;3379134|1224|1236|135625|712|724|735;3379134|1224|1236|135625|712|724|740;1783272|1239|186801|3085636|186803|1164882|979627;3379134|1224|28216|80840|119060|47670|47671;3379134|1224|28216|206351|481|482|1107316;3379134|1224|28216|206351|481|482|192066;1783272|1239|186801|3085636|186803|265975|1501329;1783272|1239|186801|186802|541000;3379134|1224|28216|80840|80864|219181|1898956;1783272|1239|186801|186802|186807|2740|2049038;1783272|1239|186801|3082720|186804|1257|341694;3379134|976|200643|171549|171551|836|1583331;3379134|976|200643|171549|171552|838|59823;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|909932|1843489|31977|29465|423477,Complete,Claregrieve1
bsdb:32105635/2/2,32105635,"cross-sectional observational, not case-control",32105635,10.1016/j.isci.2020.100884,NA,"Pushalkar S., Paul B., Li Q., Yang J., Vasconcelos R., Makwana S., González J.M., Shah S., Xie C., Janal M.N., Queiroz E., Bederoff M., Leinwand J., Solarewicz J., Xu F., Aboseria E., Guo Y., Aguallo D., Gomez C., Kamer A., Shelley D., Aphinyanaphongs Y., Barber C., Gordon T., Corby P., Li X. , Saxena D.",Electronic Cigarette Aerosol Modulates the Oral Microbiome and Increases Risk of Infection,iScience,2020,"In Vitro Toxicology, Microbiome, Oral Microbiology",Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,never smokers,cigarette smokers,"participants who were 21 years or older, healthy, diagnosed with periodontal disease, and current smokers",39,40,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure S2,10 January 2021,Victoria Goulbourne,"Lwaldron,Claregrieve1,WikiWorks",Differential microbial abundance between cigarette smokers and never smokers,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces lingnae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia|s__Alloscardovia omnicolens,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus|s__Desulfobulbus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella sp.,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella maculosa,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella multisaccharivorax,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella oralis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oulorum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella veroralis,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter piscolens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas artemidis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas dianae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia exigua,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema maltophilum,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|201174|1760|2037|2049|1654|114702;1783272|201174|1760|85004|31953|419014|419015;3379134|200940|3031451|3024411|213121|893|895;1783272|1239|186801|186802;1783272|1239|186801|3082720|3118655|44259|143361;3384194|508458|649775|649776|3029087|1434006|651822;3384189|32066|203490|203491|203492|848|851;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|91061|186826|1300|1357|1358;1783272|1239|909932|1843489|31977|906|187326;1783272|1239|909932|1843489|31977|906|2023260;1783272|1239|909932|909929|1843491|52225|2049034;1783272|544448|31969;1783272|1239|186801|3085636|186803|265975|1969407;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|1239|1737404|1737405|1570339|162289|33031;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|171551|836|281920;3379134|976|200643|171549|171552|838|28129;3379134|976|200643|171549|171552|838|28131;3379134|976|200643|171549|171552|2974251|439703;3379134|976|200643|171549|171552|52228|310514;3379134|976|200643|171549|171552|2974257|28134;3379134|976|200643|171549|171552|2974251|28135;3379134|976|200643|171549|171552|2974251|28136;3379134|976|200643|171549|171552|838|59823;3379134|976|200643|171549|171552|838|28137;3384194|508458|649775|649776|3029088|638847|638849;1783272|201174|1760|85004|31953|196081|230143;1783272|1239|909932|909929|1843491|970|671224;1783272|1239|909932|909929|1843491|970|135079;1783272|201174|84998|1643822|1643826|84108|84109;1783272|1239|91061|186826|1300|1301|1318;3379134|203691|203692|136|2845253|157|158;3379134|203691|203692|136|2845253|157|51160;3379134|203691|203692|136|2845253|157|166;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|909932|1843489|31977|29465|1926307;1783272|1239|909932|1843489|31977,Complete,Claregrieve1
bsdb:32105635/3/1,32105635,"cross-sectional observational, not case-control",32105635,10.1016/j.isci.2020.100884,NA,"Pushalkar S., Paul B., Li Q., Yang J., Vasconcelos R., Makwana S., González J.M., Shah S., Xie C., Janal M.N., Queiroz E., Bederoff M., Leinwand J., Solarewicz J., Xu F., Aboseria E., Guo Y., Aguallo D., Gomez C., Kamer A., Shelley D., Aphinyanaphongs Y., Barber C., Gordon T., Corby P., Li X. , Saxena D.",Electronic Cigarette Aerosol Modulates the Oral Microbiome and Increases Risk of Infection,iScience,2020,"In Vitro Toxicology, Microbiome, Oral Microbiology",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,cigarette smoker,E-cigarette smoker,"participants who were 21 years or older, healthy, diagnosed with periodontal disease, and current e-cigarette users",40,40,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure S2,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between cigarette smokers and e-cigarette smokers,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga haemolytica,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella morbi,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus haemolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus|s__Peptococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae",3379134|976|117743|200644|49546|1016|1017;3379134|976|117743|200644|49546|1016|45243;3379134|976|117743|200644|49546|1016|1019;3379134|1224|1236|135615|868|2717|2718;1783272|1239|186801|3085636|186803|43996|43997;1783272|201174|1760|85007|1653|1716|61592;3379134|1224|28216|206351|481|538|539;3384189|32066|203490|203491|203492|848|860;3379134|1224|1236|135625|712|724|726;3379134|1224|1236|135625|712|724|740;3379134|1224|28216|80840|119060|47670|47671;3379134|1224|28216|206351|481|482|1107316;3379134|1224|28216|206351|481|482|192066;1783272|1239|186801|186802|541000;1783272|1239|186801|186802|186807|2740|2049038;1783272|1239|186801|3082720|186804|1257|341694;3379134|976|200643|171549|171551|836|1583331;3379134|976|200643|171549|171552|838|59823;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|909932|1843489|31977|29465|423477,Complete,Claregrieve1
bsdb:32105635/3/2,32105635,"cross-sectional observational, not case-control",32105635,10.1016/j.isci.2020.100884,NA,"Pushalkar S., Paul B., Li Q., Yang J., Vasconcelos R., Makwana S., González J.M., Shah S., Xie C., Janal M.N., Queiroz E., Bederoff M., Leinwand J., Solarewicz J., Xu F., Aboseria E., Guo Y., Aguallo D., Gomez C., Kamer A., Shelley D., Aphinyanaphongs Y., Barber C., Gordon T., Corby P., Li X. , Saxena D.",Electronic Cigarette Aerosol Modulates the Oral Microbiome and Increases Risk of Infection,iScience,2020,"In Vitro Toxicology, Microbiome, Oral Microbiology",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,cigarette smoker,E-cigarette smoker,"participants who were 21 years or older, healthy, diagnosed with periodontal disease, and current e-cigarette users",40,40,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure S2,10 January 2021,Victoria Goulbourne,"Claregrieve1,WikiWorks",Differential microbial abundance between cigarette smokers and e-cigarette smokers,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces lingnae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia|s__Alloscardovia omnicolens,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales|f__Desulfobacteraceae|g__Desulfobotulus|s__Desulfobotulus sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis",1783272|201174|1760|2037|2049|1654|114702;1783272|201174|1760|85004|31953|419014|419015;3379134|200940|3024418|213118|213119|48001|1940337;1783272|1239|909932|1843489|31977|906|187326;3379134|976|200643|171549|171552|838|59823;1783272|1239|91061|186826|1300|1301|1318,Complete,Claregrieve1
bsdb:32106294/1/1,32106294,case-control,32106294,10.1167/iovs.61.2.47,NA,"Deng Y., Wen X., Hu X., Zou Y., Zhao C., Chen X., Miao L., Li X., Deng X., Bible P.W., Ke H., Situ J., Guo S., Liang J., Chen T., Zou B., Liu Y., Chen W., Wu K., Zhang M., Jin Z.B., Liang L. , Wei L.","Geographic Difference Shaped Human Ocular Surface Metagenome of Young Han Chinese From Beijing, Wenzhou, and Guangzhou Cities",Investigative ophthalmology & visual science,2020,NA,Experiment 1,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Health study participation,EFO:0010130,Guangzhou healthy volunteers,Bejing healthy volunteers,Healthy nonsmokers from Bejing,48,20,6 months,WMS,NA,Illumina,relative abundances,LEfSe,NA,NA,3,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 4,1 October 2023,Mary Bearkland,"Mary Bearkland,Peace Sandy,WikiWorks",Figure 4: The characteristics of Guangzhou and Beijing conjunctival microbiome (A). The LDA effect size program was used to find the bacterial species which significantly distinguished Beijing (green) and Guangzhou (red) microbiomes (LDA score >3).,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus cereus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella|s__Brucella anthropi,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Cereibacter|s__Cereibacter sphaeroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium aurimucosum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium jeikeium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium urealyticum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia|s__Delftia acidovorans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia|s__Delftia sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia|s__Gordonia polyisoprenivorans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Kytococcaceae|g__Kytococcus|s__Kytococcus sedentarius,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus luteus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria meningitidis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia pickettii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium|s__Rhizobium sp.",1783272|1239|91061|1385|186817|1386|1396;3379134|1224|28211|356|118882|234|529;3379134|1224|28211|204455|31989|1653176|1063;1783272|201174|1760|85007|1653|1716|169292;1783272|201174|1760|85007|1653|1716|38289;1783272|201174|1760|85007|1653|1716|43771;3379134|1224|28216|80840|80864|80865|80866;3379134|1224|28216|80840|80864|80865|1886637;1783272|1239|91061|186826|81852|1350|1351;3379134|1224|1236|91347|543|561|562;1783272|201174|1760|85007|85026|2053|84595;1783272|201174|1760|85006|2805426|57499|1276;1783272|201174|1760|85006|1268|1269|1270;3379134|1224|28216|206351|481|482|487;3379134|976|200643|171549|171551|836|837;3379134|1224|1236|72274|135621|286|287;3379134|1224|28216|80840|119060|48736|329;3379134|1224|28211|356|82115|379|391,Complete,Peace Sandy
bsdb:32106294/1/2,32106294,case-control,32106294,10.1167/iovs.61.2.47,NA,"Deng Y., Wen X., Hu X., Zou Y., Zhao C., Chen X., Miao L., Li X., Deng X., Bible P.W., Ke H., Situ J., Guo S., Liang J., Chen T., Zou B., Liu Y., Chen W., Wu K., Zhang M., Jin Z.B., Liang L. , Wei L.","Geographic Difference Shaped Human Ocular Surface Metagenome of Young Han Chinese From Beijing, Wenzhou, and Guangzhou Cities",Investigative ophthalmology & visual science,2020,NA,Experiment 1,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Health study participation,EFO:0010130,Guangzhou healthy volunteers,Bejing healthy volunteers,Healthy nonsmokers from Bejing,48,20,6 months,WMS,NA,Illumina,relative abundances,LEfSe,NA,NA,3,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 4,1 October 2023,Mary Bearkland,"Mary Bearkland,WikiWorks",Figure 4: The characteristics of Guangzhou and Beijing conjunctival microbiome (A). The LDA effect size program was used to find the bacterial species which significantly distinguished Beijing (green) and Guangzhou (red) microbiomes (LDA score >3).,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Listeria|s__Listeria monocytogenes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Ectopseudomonas|s__Ectopseudomonas mendocina,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira murdochii,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|g__Candidatus Karelsulcia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mycoplasmopsis|s__Mycoplasmopsis bovis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax|s__Acidovorax sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Diaphorobacter|s__[Acidovorax] ebreus,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mesomycoplasma|s__Mesomycoplasma hyorhinis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes",1783272|1239|91061|1385|186820|1637|1639;3379134|1224|1236|72274|135621|3236654|300;3379134|203691|203692|1643686|143786|29521|84378;3379134|976|117743|200644|336809;3379134|1224|1236|135614|32033|40323|40324;1783272|544448|2790996|2895623|2767358|28903;3379134|1224|28216|80840|80864|12916|1872122;3379134|1224|28216|80840|80864|238749|721785;1783272|544448|2790996|2895623|2923352|2100;1783272|201174|1760|85009|31957|1912216|1747,Complete,Peace Sandy
bsdb:32111156/1/1,32111156,case-control,32111156,10.1186/s12866-020-01734-6,NA,"Xie J., Huang J.S., Huang X.J., Peng J.M., Yu Z., Yuan Y.Q., Xiao K.F. , Guo J.N.",Profiling the urinary microbiome in men with calcium-based kidney stones,BMC microbiology,2020,"Calcium-based, Kidney stone, Microbiome, Renal pelvis, Urine",Experiment 1,China,Homo sapiens,Urinary bladder,UBERON:0001255,Nephrolithiasis,EFO:0004253,HB group - Bladder urine from healthy controls.,KB group - Bladder urine from kidney stone patients.,Bladder urine collected from nephrolithiasis (Kidney stone) patients.,21,22,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,decreased,decreased,increased,NA,decreased,Signature 1,Fig. 5A & 5B,22 March 2024,Victoria,"Victoria,WikiWorks","A Cladogram and LEfSe analyses of microbiomes among HB (red), KB (green), and KP (blue) groups. Taxa in graph were with LDA score threshold > 2.0 and statistically significant (p < 0.05).",increased,"k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Dyella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rahnella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingopyxidaceae|g__Sphingopyxis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Aminobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae",3379134|976;1783272|1239;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|186807;3379134|1224|1236|135614|1775411|231454;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;3379134|1224|1236|91347|1903411|34037;1783272|1239|186801|186802|186807|2740;3379134|1224|28211|204457|3423718|165697;3379134|1224|28211|356|69277|31988;1783272|1239|91061|1385|186822|44249;3379134|976|200643|171549|171551;3379134|1224|1236|135624;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|1853231,Complete,Peace Sandy
bsdb:32111156/1/2,32111156,case-control,32111156,10.1186/s12866-020-01734-6,NA,"Xie J., Huang J.S., Huang X.J., Peng J.M., Yu Z., Yuan Y.Q., Xiao K.F. , Guo J.N.",Profiling the urinary microbiome in men with calcium-based kidney stones,BMC microbiology,2020,"Calcium-based, Kidney stone, Microbiome, Renal pelvis, Urine",Experiment 1,China,Homo sapiens,Urinary bladder,UBERON:0001255,Nephrolithiasis,EFO:0004253,HB group - Bladder urine from healthy controls.,KB group - Bladder urine from kidney stone patients.,Bladder urine collected from nephrolithiasis (Kidney stone) patients.,21,22,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,decreased,decreased,increased,NA,decreased,Signature 2,Fig. 5A & 5B,22 March 2024,Victoria,"Victoria,WikiWorks","A Cladogram and LEfSe analyses of microbiomes among HB (red), KB (green) and KP (blue) groups. Taxa in graph were with LDA score threshold > 2.0 and statistically significant (p < 0.05)",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae",3379134|1224|1236|2887326|468;3379134|1224|1236|2887326|468|469;3379134|1224|1236|72274;3379134|1224|1236;3379134|1224;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492,Complete,Peace Sandy
bsdb:32111156/2/1,32111156,case-control,32111156,10.1186/s12866-020-01734-6,NA,"Xie J., Huang J.S., Huang X.J., Peng J.M., Yu Z., Yuan Y.Q., Xiao K.F. , Guo J.N.",Profiling the urinary microbiome in men with calcium-based kidney stones,BMC microbiology,2020,"Calcium-based, Kidney stone, Microbiome, Renal pelvis, Urine",Experiment 2,China,Homo sapiens,Renal pelvis/ureter,UBERON:0036295,Nephrolithiasis,EFO:0004253,KB group - Bladder urine from kidney stone patients.,KP group - Renal pelvis urine from kidney stone patients.,Renal pelvis urine collected from nephrolithiasis (Kidney stone) patients.,22,22,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 5A & 5B,22 March 2024,Victoria,"Victoria,WikiWorks","A Cladogram and LEfSe analyses of microbiomes among HB (red), KB (green) and KP (blue) groups. Taxa in graph were with LDA score threshold > 2.0 and statistically significant (p < 0.05)",increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales",3384189|32066|203490|203491|203492;3384189|32066|203490|203491|203492|848;3379134|1224;3379134|1224|1236;3379134|1224|1236|2887326|468;3379134|1224|1236|2887326|468|469;3379134|1224|1236|72274,Complete,Peace Sandy
bsdb:32111156/2/2,32111156,case-control,32111156,10.1186/s12866-020-01734-6,NA,"Xie J., Huang J.S., Huang X.J., Peng J.M., Yu Z., Yuan Y.Q., Xiao K.F. , Guo J.N.",Profiling the urinary microbiome in men with calcium-based kidney stones,BMC microbiology,2020,"Calcium-based, Kidney stone, Microbiome, Renal pelvis, Urine",Experiment 2,China,Homo sapiens,Renal pelvis/ureter,UBERON:0036295,Nephrolithiasis,EFO:0004253,KB group - Bladder urine from kidney stone patients.,KP group - Renal pelvis urine from kidney stone patients.,Renal pelvis urine collected from nephrolithiasis (Kidney stone) patients.,22,22,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 5A & 5B,22 March 2024,Victoria,"Victoria,WikiWorks","A Cladogram and LEfSe analyses of microbiomes among HB (red), KB (green) and KP (blue) groups. Taxa in graph were with LDA score threshold > 2.0 and statistically significant (p < 0.05)",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Anoxybacillus",1783272|201174|1760|2037;1783272|1239|91061|1385|3120669|150247,Complete,Peace Sandy
bsdb:32115690/1/1,32115690,time series / longitudinal observational,32115690,10.1002/ijc.32942,NA,"De Pietri S., Ingham A.C., Frandsen T.L., Rathe M., Krych L., Castro-Mejía J.L., Nielsen D.S., Nersting J., Wehner P.S., Schmiegelow K., Hasle H., Pamp S.J. , Müller K.",Gastrointestinal toxicity during induction treatment for childhood acute lymphoblastic leukemia: The impact of the gut microbiota,International journal of cancer,2020,"C-reactive protein, acute lymphoblastic leukemia, citrulline, gastrointestinal toxicity, microbiota, mucositis",Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Acute lymphoblastic leukemia,EFO:0000220,baseline,induction chemotherapy,children (ages 1-18 years old) newly diagnosed with Acute Lymphoblastic Leukemia and undergoing induction chemotherapy according to the Nordic Society of Paediatric Haematology and Oncology (NOPHO) post initiation of induction chemotherapy,32,51,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential microbial abundance between baseline and Day 15 of induction chemotherapy,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.,1783272|1239|91061|186826|81852|1350|35783,Complete,Claregrieve1
bsdb:32123200/1/1,32123200,case-control,32123200,10.1038/s41598-020-60674-3,NA,"Rullo J., Far P.M., Quinn M., Sharma N., Bae S., Irrcher I. , Sharma S.",Local oral and nasal microbiome diversity in age-related macular degeneration,Scientific reports,2020,NA,Experiment 1,Canada,Homo sapiens,Nasal cavity mucosa,UBERON:0001826,Age-related macular degeneration,EFO:0001365,Controls,Nasal Cases,Nasal samples collected from treatment-naïve patients with newly diagnosed neovascular AMD (Age-related Macular Degeneration),5,13,NA,16S,4,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,11 August 2025,Anne-mariesharp,Anne-mariesharp,Log2fold change in the relative abundance of operational taxonomic units of cases over controls.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae",1783272|201174|1760|2037|2049|1654|29317;1783272|201174|1760|2037|2049;3379134|1224|28216|80840;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|1300|1301|1306;1783272|1239|909932|1843489|31977|29465|1926307;3379134|1224|1236|72274|135621,Complete,KateRasheed
bsdb:32123200/1/2,32123200,case-control,32123200,10.1038/s41598-020-60674-3,NA,"Rullo J., Far P.M., Quinn M., Sharma N., Bae S., Irrcher I. , Sharma S.",Local oral and nasal microbiome diversity in age-related macular degeneration,Scientific reports,2020,NA,Experiment 1,Canada,Homo sapiens,Nasal cavity mucosa,UBERON:0001826,Age-related macular degeneration,EFO:0001365,Controls,Nasal Cases,Nasal samples collected from treatment-naïve patients with newly diagnosed neovascular AMD (Age-related Macular Degeneration),5,13,NA,16S,4,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,11 August 2025,Anne-mariesharp,Anne-mariesharp,Log2fold change in the relative abundance of operational taxonomic units of cases over controls.,decreased,k__Bacillati|p__Bacillota|c__Clostridia,1783272|1239|186801,Complete,KateRasheed
bsdb:32123200/2/1,32123200,case-control,32123200,10.1038/s41598-020-60674-3,NA,"Rullo J., Far P.M., Quinn M., Sharma N., Bae S., Irrcher I. , Sharma S.",Local oral and nasal microbiome diversity in age-related macular degeneration,Scientific reports,2020,NA,Experiment 2,Canada,Homo sapiens,Buccal mucosa,UBERON:0006956,Age-related macular degeneration,EFO:0001365,Controls,Oral Cases,Oral samples collected from treatment-naïve patients with newly diagnosed neovascular AMD (Age-related Macular Degeneration),5,13,NA,16S,4,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,11 August 2025,Anne-mariesharp,Anne-mariesharp,Log2fold change in the relative abundance of operational taxonomic units of cases over controls.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus sp.,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus sp.,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae",1783272|201174|1760|2037|2049|1654|29317;1783272|201174;1783272|1239|1737404|1737405|1570339|165779|1872515;3379134|29547|3031852|213849|72294|194|205;1783272|1239|1737404|1737405|1570339|150022|1981334;1783272|1239|1737404|1737405|1570339|162289;3379134|976|200643|171549|171552|838;1783272|201174|1760|85009|31957|1743|1977903;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|1385|90964|1279|29387;1783272|1239;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85009|31957,Complete,KateRasheed
bsdb:32123200/2/2,32123200,case-control,32123200,10.1038/s41598-020-60674-3,NA,"Rullo J., Far P.M., Quinn M., Sharma N., Bae S., Irrcher I. , Sharma S.",Local oral and nasal microbiome diversity in age-related macular degeneration,Scientific reports,2020,NA,Experiment 2,Canada,Homo sapiens,Buccal mucosa,UBERON:0006956,Age-related macular degeneration,EFO:0001365,Controls,Oral Cases,Oral samples collected from treatment-naïve patients with newly diagnosed neovascular AMD (Age-related Macular Degeneration),5,13,NA,16S,4,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,11 August 2025,Anne-mariesharp,Anne-mariesharp,Log2fold change in the relative abundance of operational taxonomic units of cases over controls.,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli",3384189|32066|203490|203491|203492|848;1783272|1239|91061,Complete,KateRasheed
bsdb:32143621/1/1,32143621,case-control,32143621,10.1186/s12934-020-01319-y,NA,"Gallardo-Becerra L., Cornejo-Granados F., García-López R., Valdez-Lara A., Bikel S., Canizales-Quinteros S., López-Contreras B.E., Mendoza-Vargas A., Nielsen H. , Ochoa-Leyva A.","Metatranscriptomic analysis to define the Secrebiome, and 16S rRNA profiling of the gut microbiome in obesity and metabolic syndrome of Mexican children",Microbial cell factories,2020,"AAR, CAZY, Metabolic syndrome, Metatranscriptome, Metatranscriptomics, Microbiome, Microbiota, Obesity, Secrebiome, Secretome",Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Normal weight (NW),Obese children (O),Obesity was defined by body mass index (BMI) ≥ 95th percentile. Children in the O group were selected so that they did not have more than one trait matching the metabolic syndrome traits.,10,10,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,1,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure 2,10 January 2021,Mst Afroza Parvin,"WikiWorks,ChiomaBlessing",Differentially abundant taxa in obese (O) children compared to normal weight (NW) children,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",1783272|201174|1760|85004|31953|1678|1680;1783272|1239|186801|186802|216572|216851|853;3379134|976|200643|171549|171551|836,Complete,ChiomaBlessing
bsdb:32143621/1/2,32143621,case-control,32143621,10.1186/s12934-020-01319-y,NA,"Gallardo-Becerra L., Cornejo-Granados F., García-López R., Valdez-Lara A., Bikel S., Canizales-Quinteros S., López-Contreras B.E., Mendoza-Vargas A., Nielsen H. , Ochoa-Leyva A.","Metatranscriptomic analysis to define the Secrebiome, and 16S rRNA profiling of the gut microbiome in obesity and metabolic syndrome of Mexican children",Microbial cell factories,2020,"AAR, CAZY, Metabolic syndrome, Metatranscriptome, Metatranscriptomics, Microbiome, Microbiota, Obesity, Secrebiome, Secretome",Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Normal weight (NW),Obese children (O),Obesity was defined by body mass index (BMI) ≥ 95th percentile. Children in the O group were selected so that they did not have more than one trait matching the metabolic syndrome traits.,10,10,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,1,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Figure 2,10 January 2021,Mst Afroza Parvin,"WikiWorks,ChiomaBlessing",Differentially abundant taxa in obese (O) children compared to normal weight (NW) children,decreased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,1783272|1239|909932|1843488|909930|33024,Complete,ChiomaBlessing
bsdb:32143621/2/1,32143621,case-control,32143621,10.1186/s12934-020-01319-y,NA,"Gallardo-Becerra L., Cornejo-Granados F., García-López R., Valdez-Lara A., Bikel S., Canizales-Quinteros S., López-Contreras B.E., Mendoza-Vargas A., Nielsen H. , Ochoa-Leyva A.","Metatranscriptomic analysis to define the Secrebiome, and 16S rRNA profiling of the gut microbiome in obesity and metabolic syndrome of Mexican children",Microbial cell factories,2020,"AAR, CAZY, Metabolic syndrome, Metatranscriptome, Metatranscriptomics, Microbiome, Microbiota, Obesity, Secrebiome, Secretome",Experiment 2,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Normal weight (NW),Obesity with metabolic syndrome (OMS),"OMS were defined by the presence of waist circumference > 75th by age and gender, and at least two of the following metabolic traits: (1) triglycerides > 1.1 mmol/L (100 mg/dL); (2) HDL cholesterol < 1.3 mmol/L (50 mg/dL), (3) glucose > 6.1 mmol/L (110 mg/dL) and (4) systolic blood pressure > 90th percentile for gender, age, and height.",10,7,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,1,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure 2,10 January 2021,Mst Afroza Parvin,"WikiWorks,ChiomaBlessing",Differentially abundant taxa in Obesity with metabolic syndrome (OMS) children compared to normal weight (NW) children,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Caldimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota",1783272|1239|91061;1783272|1239|526524|526525|2810280|135858;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|3085636|186803|33042;1783272|201174|84998|84999|84107;1783272|201174|84998;1783272|1239|526524|526525|128827;3379134|1224;3379134|1224|28216|80840|2975441|196013;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802;1783272|1239,Complete,ChiomaBlessing
bsdb:32143621/2/2,32143621,case-control,32143621,10.1186/s12934-020-01319-y,NA,"Gallardo-Becerra L., Cornejo-Granados F., García-López R., Valdez-Lara A., Bikel S., Canizales-Quinteros S., López-Contreras B.E., Mendoza-Vargas A., Nielsen H. , Ochoa-Leyva A.","Metatranscriptomic analysis to define the Secrebiome, and 16S rRNA profiling of the gut microbiome in obesity and metabolic syndrome of Mexican children",Microbial cell factories,2020,"AAR, CAZY, Metabolic syndrome, Metatranscriptome, Metatranscriptomics, Microbiome, Microbiota, Obesity, Secrebiome, Secretome",Experiment 2,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Normal weight (NW),Obesity with metabolic syndrome (OMS),"OMS were defined by the presence of waist circumference > 75th by age and gender, and at least two of the following metabolic traits: (1) triglycerides > 1.1 mmol/L (100 mg/dL); (2) HDL cholesterol < 1.3 mmol/L (50 mg/dL), (3) glucose > 6.1 mmol/L (110 mg/dL) and (4) systolic blood pressure > 90th percentile for gender, age, and height.",10,7,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,1,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Figure 2,10 January 2021,Mst Afroza Parvin,"WikiWorks,ChiomaBlessing",Differentially abundant taxa in Obesity with metabolic syndrome (OMS) children compared to normal weight (NW) children,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,3379134|976|200643|171549,Complete,ChiomaBlessing
bsdb:32150591/1/2,32150591,case-control,32150591,10.1371/journal.ppat.1008348,NA,"Oku S., Takeshita T., Futatsuki T., Kageyama S., Asakawa M., Mori Y., Miyamoto T., Hata J., Ninomiya T., Kashiwazaki H. , Yamashita Y.",Disrupted tongue microbiota and detection of nonindigenous bacteria on the day of allogeneic hematopoietic stem cell transplantation,PLoS pathogens,2020,NA,Experiment 1,Japan,Homo sapiens,Tongue,UBERON:0001723,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,community-dwelling controls,allogeneic-hematopoietic stem cell transplant,patient ages 36-69 years old undergoing allogeneic- hematopoietic stem cell transplantation,164,45,NA,16S,12,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Fig. 2,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential abundances of predominant bacterial genera in the tongue microbiota of community-dwelling adults and allogeneic-hematopoietic stem cell transplantation patients,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|976|200643|171549|171552|1283313;3379134|1224|1236|135625|712|724;3384189|32066|203490|203491|1129771|32067;3379134|1224|28216|206351|481|482;1783272|1239|186801|3085636|186803|265975;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:32152391/1/1,32152391,case-control,32152391,https://doi.org/10.1038/s41598-020-60794-w,NA,"Kittipibul T., Puangsricharern V. , Chatsuwan T.",Comparison of the ocular microbiome between chronic Stevens-Johnson syndrome patients and healthy subjects,Scientific reports,2020,NA,Experiment 1,Thailand,Homo sapiens,Conjunctival sac,UBERON:0005908,Stevens-Johnson syndrome,EFO:0004276,healthy controls,Stevens-Johnson Syndrome,Stevens-Johnson Syndrome patients,20,20,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 1,24 September 2023,Mary Bearkland,"Mary Bearkland,WikiWorks","Figure 1. Significant difference of taxa abundance. This figure represents the significant difference of taxonomic
level of each genus comparing between SJS patients and healthy subjects. We analyzed the proportion of each
genus by Mann-Whitney U test. The p-value less than 0.05 was defined as statistically significant difference.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Salinivibrio,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae|g__Pseudoalteromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Thermomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|216851;3379134|1224|1236|135623|641|51366;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|33042;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|33958|1578;3384189|32066|203490|203491|203492|848;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|91061|1385|186817|1386;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171552|577309;3379134|1224|1236|2887326|468|469;1783272|1239|186801|186802|216572|1263;1783272|1239|909932|909929|1843491|158846;3379134|976|200643|171549|1853231|283168;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|135622|267888|53246;3379134|1224|1236|91347|1903409|551;3379134|1224|1236|72274|135621|286;1783272|201174|84998|84999|84107|102106;3366610|28890|183925|2158|2159|2172;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|135614|32033|141948;1783272|1239|186801|3085636|186803|841;1783272|1239|526524|526525|2810281|191303,Complete,Peace Sandy
bsdb:32152391/1/2,32152391,case-control,32152391,https://doi.org/10.1038/s41598-020-60794-w,NA,"Kittipibul T., Puangsricharern V. , Chatsuwan T.",Comparison of the ocular microbiome between chronic Stevens-Johnson syndrome patients and healthy subjects,Scientific reports,2020,NA,Experiment 1,Thailand,Homo sapiens,Conjunctival sac,UBERON:0005908,Stevens-Johnson syndrome,EFO:0004276,healthy controls,Stevens-Johnson Syndrome,Stevens-Johnson Syndrome patients,20,20,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 1,24 September 2023,Mary Bearkland,"Mary Bearkland,WikiWorks","Figure 1. Significant difference of taxa abundance. This figure represents the significant difference of taxonomic
level of each genus comparing between SJS patients and healthy subjects. We analyzed the proportion of each
genus by Mann-Whitney U test. The p-value less than 0.05 was defined as statistically significant difference.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Cohaesibacteraceae|g__Cohaesibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Fusibacteraceae|g__Fusibacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Tenacibaculum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Piscirickettsiaceae|g__Methylophaga,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio",3379134|1224|1236|135622|267890|22;3379134|1224|28211|356|655351|655352;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|3679999|76008;3379134|976|117743|200644|49546|104267;3379134|1224|1236|72273|135616|40222;3384189|32066|203490|203491|203492|180162;3379134|29547|3031852|213849|2808963|28196;3379134|1224|1236|135623|641|662,Complete,Peace Sandy
bsdb:32158702/1/1,32158702,case-control,32158702,10.3389/fcimb.2020.00063,https://pubmed.ncbi.nlm.nih.gov/32158702/,"Doumatey A.P., Adeyemo A., Zhou J., Lei L., Adebamowo S.N., Adebamowo C. , Rotimi C.N.",Gut Microbiome Profiles Are Associated With Type 2 Diabetes in Urban Africans,Frontiers in cellular and infection microbiology,2020,"16S V4 rRNA sequencing, gut microbiome, microbial composition, type 2 diabetes, urban Africans",Experiment 1,Nigeria,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,"Individuals diagnosed with Type 2 Diabetes Mellitus; The definition of T2D was based on the American Diabetes Association (ADA) criteria: a fasting plasma glucose concentration (FPG) ≥ 126 mg/dl (7.0 mmol/l) or a 2-h post-load value in the oral glucose tolerance test ≥ 200 mg/dl (11.1 mmol/l) on more than one occasion. Alternatively, a diagnosis of T2D was accepted if an individual was on pharmacological treatment for T2D, and a review of clinical records indicated adequate justification for that therapy.",193,98,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,"Table 3, Table 4",27 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1,WikiWorks",Differential microbial abundance between controls and individuals with Type 2 Diabetes,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Cellulosilyticaceae|g__Cellulosilyticum|s__Cellulosilyticum ruminicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium butyricum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium paraputrificum,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",1783272|1239|186801|3085636|3018741|698776|425254;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485|1492;1783272|1239|186801|186802|31979|1485|29363;1783272|1239;1783272|1239|186801|3082720|186804,Complete,Claregrieve1
bsdb:32158702/1/2,32158702,case-control,32158702,10.3389/fcimb.2020.00063,https://pubmed.ncbi.nlm.nih.gov/32158702/,"Doumatey A.P., Adeyemo A., Zhou J., Lei L., Adebamowo S.N., Adebamowo C. , Rotimi C.N.",Gut Microbiome Profiles Are Associated With Type 2 Diabetes in Urban Africans,Frontiers in cellular and infection microbiology,2020,"16S V4 rRNA sequencing, gut microbiome, microbial composition, type 2 diabetes, urban Africans",Experiment 1,Nigeria,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,"Individuals diagnosed with Type 2 Diabetes Mellitus; The definition of T2D was based on the American Diabetes Association (ADA) criteria: a fasting plasma glucose concentration (FPG) ≥ 126 mg/dl (7.0 mmol/l) or a 2-h post-load value in the oral glucose tolerance test ≥ 200 mg/dl (11.1 mmol/l) on more than one occasion. Alternatively, a diagnosis of T2D was accepted if an individual was on pharmacological treatment for T2D, and a review of clinical records indicated adequate justification for that therapy.",193,98,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,"Table 3, Table 4",15 August 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1,WikiWorks",Differential microbial abundance between controls and individuals with Type 2 Diabetes,increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Methanobacteriati|p__Methanobacteriota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter|s__Terrisporobacter glycolicus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris",3379134|976;3379134|200940|3031449|213115|194924|872|901;3366610|28890;3379134|976|200643|171549|171552|838;1783272|1239|186801|3082720|186804|1505652|36841;1783272|1239|186801|3085636|186803|2316020|46228,Complete,Claregrieve1
bsdb:32161568/1/1,32161568,case-control,32161568,10.3389/fneur.2020.00137,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7052381/,"Ren T., Gao Y., Qiu Y., Jiang S., Zhang Q., Zhang J., Wang L., Zhang Y., Wang L. , Nie K.",Gut Microbiota Altered in Mild Cognitive Impairment Compared With Normal Cognition in Sporadic Parkinson's Disease,Frontiers in neurology,2020,"Parkinson's disease, cognition impairment, gut micro biome, high throughput sequencing, short fatty acids",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy spouses and Parkinson's disease patients with mild cognitive impairment,Parkinson's disease patients with normal cognition,"All patients eligible for this study were diagnosed for PD according to the UK Brain Bank criteria. Cognition abilities were estimated using the Mini-Mental State Examination (MMSE) and Montreal Cognitive Assessment (MoCA), and the scores were obtained from two other neuropsychological tests in each of the five cognitive domains.",26,14,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,"age,body mass index,constipation,education level,sex",NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure S3,20 May 2023,Jacquelynshevin,"Jacquelynshevin,WikiWorks","Alteration in the taxa between PD-MCI, PD-NC and healthy groups(LDA)",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales",1783272|1239|186801|186802;1783272|1239|186801;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171551;1783272|1239|186801|186802|216572|707003;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|572511;1783272|201174;1783272|1239|186801|3082768|990719;3379134|976|200643|171549|2005525|375288|328812;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|186801|3085636|186803|572511|33035;1783272|201174|84998|84999|84107;1783272|201174|84998;1783272|201174|84998|84999,Complete,Atrayees
bsdb:32161568/2/1,32161568,case-control,32161568,10.3389/fneur.2020.00137,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7052381/,"Ren T., Gao Y., Qiu Y., Jiang S., Zhang Q., Zhang J., Wang L., Zhang Y., Wang L. , Nie K.",Gut Microbiota Altered in Mild Cognitive Impairment Compared With Normal Cognition in Sporadic Parkinson's Disease,Frontiers in neurology,2020,"Parkinson's disease, cognition impairment, gut micro biome, high throughput sequencing, short fatty acids",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy spouses and Parkinson's disease patients with normal cognition,Parkinson's disease patients with mild cognitive impairment,"All patients eligible for this study were diagnosed for PD according to the UK Brain Bank criteria. Cognition abilities were estimated using the Mini-Mental State Examination (MMSE) and Montreal Cognitive Assessment (MoCA), and the scores were obtained from two other neuropsychological tests in each of the five cognitive domains.",27,13,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,"age,body mass index,constipation,education level,sex",NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure S3,20 May 2023,Jacquelynshevin,"Jacquelynshevin,WikiWorks","Alteration in the taxa between PD-MCI, PD-NC and healthy groups(LDA)",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. N15.MGS-57,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus",3379134|976|200643|171549|171550;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|1263|1637508;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|543|570|573;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|3085636|186803|2316020|33039;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|1853231|283168|28118,Complete,Atrayees
bsdb:32161568/3/1,32161568,case-control,32161568,10.3389/fneur.2020.00137,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7052381/,"Ren T., Gao Y., Qiu Y., Jiang S., Zhang Q., Zhang J., Wang L., Zhang Y., Wang L. , Nie K.",Gut Microbiota Altered in Mild Cognitive Impairment Compared With Normal Cognition in Sporadic Parkinson's Disease,Frontiers in neurology,2020,"Parkinson's disease, cognition impairment, gut micro biome, high throughput sequencing, short fatty acids",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy spouses,Parkinson's disease patients with mild cognitive impairment and Parkinson's disease patients with normal cognition,"All patients eligible for this study were diagnosed for PD according to the UK Brain Bank criteria. Cognition abilities were estimated using the Mini-Mental State Examination (MMSE) and Montreal Cognitive Assessment (MoCA), and the scores were obtained from two other neuropsychological tests in each of the five cognitive domains.",13,27,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,"age,body mass index,constipation,education level,sex",NA,increased,increased,increased,NA,NA,Signature 1,Figure S3,20 May 2023,Jacquelynshevin,"Jacquelynshevin,WikiWorks","Alteration in the taxa between PD-MCI, PD-NC and healthy groups(LDA)",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota",3379134|976|200643|171549;3379134|976|200643;1783272|1239|909932|1843489|31977|906|187326;1783272|1239|909932|1843489|31977|29465;3379134|976,Complete,Atrayees
bsdb:32169076/1/1,32169076,"cross-sectional observational, not case-control",32169076,10.1186/s12967-020-02291-2,NA,"Murugesan S., Al Ahmad S.F., Singh P., Saadaoui M., Kumar M. , Al Khodor S.",Profiling the Salivary microbiome of the Qatari population,Journal of translational medicine,2020,"16S rRNA gene sequencing, Dysbiosis, Oral health, Qatar Biobank, Qatari, Saliva",Experiment 1,Qatar,Homo sapiens,Saliva,UBERON:0001836,Sex design,EFO:0001752,Males,Females,NA,555,442,NA,16S,123,Illumina,relative abundances,LEfSe,2,NA,2,NA,"age,sex,smoking status",NA,unchanged,unchanged,unchanged,NA,increased,Signature 1,Figure 1c,31 March 2023,Suwaiba,"Suwaiba,Atrayees,WikiWorks",Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in males (green) and females (red),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Bacteroidota",3379134|976|117743|200644|2762318|59735;3379134|976|200643|171549|2005525|195950;3379134|976,Complete,Atrayees
bsdb:32169076/1/2,32169076,"cross-sectional observational, not case-control",32169076,10.1186/s12967-020-02291-2,NA,"Murugesan S., Al Ahmad S.F., Singh P., Saadaoui M., Kumar M. , Al Khodor S.",Profiling the Salivary microbiome of the Qatari population,Journal of translational medicine,2020,"16S rRNA gene sequencing, Dysbiosis, Oral health, Qatar Biobank, Qatari, Saliva",Experiment 1,Qatar,Homo sapiens,Saliva,UBERON:0001836,Sex design,EFO:0001752,Males,Females,NA,555,442,NA,16S,123,Illumina,relative abundances,LEfSe,2,NA,2,NA,"age,sex,smoking status",NA,unchanged,unchanged,unchanged,NA,increased,Signature 2,Figure 1c,31 March 2023,Suwaiba,"Suwaiba,Atrayees,WikiWorks",Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in males (green) and females (red),increased,"k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Spirochaetota",3379134|203691|203692|136|2845253|157;1783272|544448|31969|2085|2092|2093;1783272|201174|1760|85007|1653|1716;3379134|203691,Complete,Atrayees
bsdb:32169076/2/1,32169076,"cross-sectional observational, not case-control",32169076,10.1186/s12967-020-02291-2,NA,"Murugesan S., Al Ahmad S.F., Singh P., Saadaoui M., Kumar M. , Al Khodor S.",Profiling the Salivary microbiome of the Qatari population,Journal of translational medicine,2020,"16S rRNA gene sequencing, Dysbiosis, Oral health, Qatar Biobank, Qatari, Saliva",Experiment 2,Qatar,Homo sapiens,Saliva,UBERON:0001836,Aging,GO:0007568,Adults,Elderly,People older than 65years of age,979,18,NA,16S,123,Illumina,relative abundances,LEfSe,0.007,NA,2,NA,"age,sex",NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 2c,31 March 2023,Suwaiba,"Suwaiba,Atrayees,ChiomaBlessing,WikiWorks",Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in Elderly (green) and Adults (red).,increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,p__Candidatus Saccharimonadota",3379134|976;3379134|976|200643|171549|171552|838;3379134|203691|203692|136|137|146;3379134|203691|203692|136|2845253|157;95818,Complete,Atrayees
bsdb:32169076/2/2,32169076,"cross-sectional observational, not case-control",32169076,10.1186/s12967-020-02291-2,NA,"Murugesan S., Al Ahmad S.F., Singh P., Saadaoui M., Kumar M. , Al Khodor S.",Profiling the Salivary microbiome of the Qatari population,Journal of translational medicine,2020,"16S rRNA gene sequencing, Dysbiosis, Oral health, Qatar Biobank, Qatari, Saliva",Experiment 2,Qatar,Homo sapiens,Saliva,UBERON:0001836,Aging,GO:0007568,Adults,Elderly,People older than 65years of age,979,18,NA,16S,123,Illumina,relative abundances,LEfSe,0.007,NA,2,NA,"age,sex",NA,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 2c,31 March 2023,Suwaiba,"Suwaiba,Atrayees,Peace Sandy,WikiWorks",Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in Elderly (green) and Adults (red).,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,p__Candidatus Saccharimonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Nanosynbacterales|f__Candidatus Nanosynbacteraceae|g__Candidatus Nanosynbacter|s__Candidatus Nanosynbacter sp. TM7-053",1783272|1239|91061|186826|186827|46123;1783272|201174|1760|2037|2049|1654;1783272|201174;3379134|1224|1236|135625|712|416916;1783272|1239|909932|1843489|31977|156454;1783272|1239;3379134|29547|3031852|213849|72294|194;95818;1783272|1239|186801|3085636|186803|43996;1783272|1239|909932|1843489|31977|39948;3379134|1224|28216|206351|481|538;3384189|32066;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;3379134|1224|28216|206351|481|32257;1783272|1239|186801|3085636|186803|1164882;3379134|1224|28216|80840|119060|47670;3384189|32066|203490|203491|1129771|32067;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|3082720|186804;3379134|1224;1783272|201174|1760|85006|1268|32207;1783272|1239|909932|909929|1843491|970;1783272|1239|186801|3085636|186803|1213720;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;95818|2093818|2093819|2093822|2093823|2902634,Complete,Atrayees
bsdb:32169076/3/1,32169076,"cross-sectional observational, not case-control",32169076,10.1186/s12967-020-02291-2,NA,"Murugesan S., Al Ahmad S.F., Singh P., Saadaoui M., Kumar M. , Al Khodor S.",Profiling the Salivary microbiome of the Qatari population,Journal of translational medicine,2020,"16S rRNA gene sequencing, Dysbiosis, Oral health, Qatar Biobank, Qatari, Saliva",Experiment 3,Qatar,Homo sapiens,Saliva,UBERON:0001836,Gingival bleeding,HP:0000225,Participants without gingivitis bleeding,Participants with gingival bleeding,Participants reported suffering from a bleeding gum,913,84,NA,16S,123,Illumina,relative abundances,LEfSe,2,NA,2,"age,sex",NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,Figure 3c,31 March 2023,Suwaiba,"Suwaiba,WikiWorks",Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that did not report bleeding (green) and the participants that reported bleeding gums (red),increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|976;3379134|976|117743|200644|49546|1016;3379134|976|200643|171549|171552|838,Complete,Atrayees
bsdb:32169076/3/2,32169076,"cross-sectional observational, not case-control",32169076,10.1186/s12967-020-02291-2,NA,"Murugesan S., Al Ahmad S.F., Singh P., Saadaoui M., Kumar M. , Al Khodor S.",Profiling the Salivary microbiome of the Qatari population,Journal of translational medicine,2020,"16S rRNA gene sequencing, Dysbiosis, Oral health, Qatar Biobank, Qatari, Saliva",Experiment 3,Qatar,Homo sapiens,Saliva,UBERON:0001836,Gingival bleeding,HP:0000225,Participants without gingivitis bleeding,Participants with gingival bleeding,Participants reported suffering from a bleeding gum,913,84,NA,16S,123,Illumina,relative abundances,LEfSe,2,NA,2,"age,sex",NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,Figure 3c,31 March 2023,Suwaiba,"Suwaiba,Atrayees,Peace Sandy,WikiWorks",Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that did not report bleeding (green) and the participants that reported bleeding gums (red),decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota,p__Candidatus Saccharimonadota,k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Nanosynbacterales|f__Candidatus Nanosynbacteraceae|g__Candidatus Nanosynbacter|s__Candidatus Nanosynbacter featherlites",1783272|201174;3379134|976|200643|171549|171552|1283313;1783272|1239;95818;3384189|32066;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;3379134|1224|28216|80840|119060|47670;3384189|32066|203490|203491|1129771|32067;1783272|1239|909932|1843489|31977|906;3379134|1224|28216|206351|481|482;3379134|1224;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;95818|2093818|2093819|2093822|2093823|2572088,Complete,Atrayees
bsdb:32169076/4/1,32169076,"cross-sectional observational, not case-control",32169076,10.1186/s12967-020-02291-2,NA,"Murugesan S., Al Ahmad S.F., Singh P., Saadaoui M., Kumar M. , Al Khodor S.",Profiling the Salivary microbiome of the Qatari population,Journal of translational medicine,2020,"16S rRNA gene sequencing, Dysbiosis, Oral health, Qatar Biobank, Qatari, Saliva",Experiment 4,Qatar,Homo sapiens,Saliva,UBERON:0001836,Oral ulcer,HP:0000155,Participants without oral ulcers,Participants with oral ulcers,Participants who reported suffering from oral ulcers,960,37,NA,16S,123,Illumina,relative abundances,LEfSe,2,NA,2,"age,sex",NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,Figure 4c,31 March 2023,Suwaiba,"Suwaiba,WikiWorks",Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that did not report any mouth ulcer (green) and the participants that reported having mouth ulcers (red),increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|976;3379134|976|117743|200644|49546|1016;3379134|976|200643|171549|171552|838,Complete,Atrayees
bsdb:32169076/4/2,32169076,"cross-sectional observational, not case-control",32169076,10.1186/s12967-020-02291-2,NA,"Murugesan S., Al Ahmad S.F., Singh P., Saadaoui M., Kumar M. , Al Khodor S.",Profiling the Salivary microbiome of the Qatari population,Journal of translational medicine,2020,"16S rRNA gene sequencing, Dysbiosis, Oral health, Qatar Biobank, Qatari, Saliva",Experiment 4,Qatar,Homo sapiens,Saliva,UBERON:0001836,Oral ulcer,HP:0000155,Participants without oral ulcers,Participants with oral ulcers,Participants who reported suffering from oral ulcers,960,37,NA,16S,123,Illumina,relative abundances,LEfSe,2,NA,2,"age,sex",NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,Figure 4c,31 March 2023,Suwaiba,"Suwaiba,WikiWorks",Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that did not report any mouth ulcer (green) and the participants that reported having mouth ulcers (red),decreased,"k__Bacillati|p__Bacillota,k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Actinomycetota",1783272|1239;3384189|32066;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;3384189|32066|203490|203491|1129771|32067;1783272|1239|909932|1843489|31977|906;3379134|1224|28216|206351|481|482;3379134|1224;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;1783272|201174,Complete,Atrayees
bsdb:32169076/5/1,32169076,"cross-sectional observational, not case-control",32169076,10.1186/s12967-020-02291-2,NA,"Murugesan S., Al Ahmad S.F., Singh P., Saadaoui M., Kumar M. , Al Khodor S.",Profiling the Salivary microbiome of the Qatari population,Journal of translational medicine,2020,"16S rRNA gene sequencing, Dysbiosis, Oral health, Qatar Biobank, Qatari, Saliva",Experiment 5,Qatar,Homo sapiens,Saliva,UBERON:0001836,Dentures,EFO:0010078,Participants without dentures,Participants with dentures,Participants who reported using dentures,861,136,NA,16S,123,Illumina,relative abundances,LEfSe,2,NA,2,"age,sex",NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,Figure 5c,31 March 2023,Suwaiba,"Suwaiba,Atrayees,WikiWorks",Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that did not use dentures (green) and the participants that reported using dentures (red),increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter",1783272|201174;3379134|1224;3379134|1224|28216|206351|481|482;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|186806|113286,Complete,Atrayees
bsdb:32169076/5/2,32169076,"cross-sectional observational, not case-control",32169076,10.1186/s12967-020-02291-2,NA,"Murugesan S., Al Ahmad S.F., Singh P., Saadaoui M., Kumar M. , Al Khodor S.",Profiling the Salivary microbiome of the Qatari population,Journal of translational medicine,2020,"16S rRNA gene sequencing, Dysbiosis, Oral health, Qatar Biobank, Qatari, Saliva",Experiment 5,Qatar,Homo sapiens,Saliva,UBERON:0001836,Dentures,EFO:0010078,Participants without dentures,Participants with dentures,Participants who reported using dentures,861,136,NA,16S,123,Illumina,relative abundances,LEfSe,2,NA,2,"age,sex",NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,Figure 5c,31 March 2023,Suwaiba,"Suwaiba,Atrayees,WikiWorks",Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that did not use dentures (green) and the participants that reported using dentures (red),decreased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|29547|3031852|213849|72294|194;1783272|1239|186801|186802|216572,Complete,Atrayees
bsdb:32169076/6/1,32169076,"cross-sectional observational, not case-control",32169076,10.1186/s12967-020-02291-2,NA,"Murugesan S., Al Ahmad S.F., Singh P., Saadaoui M., Kumar M. , Al Khodor S.",Profiling the Salivary microbiome of the Qatari population,Journal of translational medicine,2020,"16S rRNA gene sequencing, Dysbiosis, Oral health, Qatar Biobank, Qatari, Saliva",Experiment 6,Qatar,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Non-smokers,Smokers,Participants classified as smokers,733,264,NA,16S,123,Illumina,relative abundances,LEfSe,2,NA,2,NA,NA,NA,decreased,unchanged,decreased,NA,NA,Signature 1,Figure 6c,31 March 2023,Suwaiba,"Suwaiba,WikiWorks",Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in smokers (green) and non- smokers (red),increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|976;3379134|976|200643|171549|171552|838,Complete,Atrayees
bsdb:32169076/6/2,32169076,"cross-sectional observational, not case-control",32169076,10.1186/s12967-020-02291-2,NA,"Murugesan S., Al Ahmad S.F., Singh P., Saadaoui M., Kumar M. , Al Khodor S.",Profiling the Salivary microbiome of the Qatari population,Journal of translational medicine,2020,"16S rRNA gene sequencing, Dysbiosis, Oral health, Qatar Biobank, Qatari, Saliva",Experiment 6,Qatar,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Non-smokers,Smokers,Participants classified as smokers,733,264,NA,16S,123,Illumina,relative abundances,LEfSe,2,NA,2,NA,NA,NA,decreased,unchanged,decreased,NA,NA,Signature 2,Figure 6c,31 March 2023,Suwaiba,"Suwaiba,WikiWorks",Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in smokers (green) and non- smokers (red),decreased,"k__Pseudomonadati|p__Pseudomonadota,k__Thermotogati|p__Synergistota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|1224;3384194|508458;1783272|1239|91061|186826|1300|1357;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|1385|539738|1378;3379134|976|117743|200644|49546|1016;1783272|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:32169076/7/1,32169076,"cross-sectional observational, not case-control",32169076,10.1186/s12967-020-02291-2,NA,"Murugesan S., Al Ahmad S.F., Singh P., Saadaoui M., Kumar M. , Al Khodor S.",Profiling the Salivary microbiome of the Qatari population,Journal of translational medicine,2020,"16S rRNA gene sequencing, Dysbiosis, Oral health, Qatar Biobank, Qatari, Saliva",Experiment 7,Qatar,Homo sapiens,Saliva,UBERON:0001836,Coffee consumption,EFO:0004330,Non-coffee drinkers,Coffee drinkers,Participants considered coffee drinkers,887,110,NA,16S,123,Illumina,relative abundances,LEfSe,2,NA,2,NA,"age,sex",NA,increased,increased,increased,NA,NA,Signature 1,Figure 7c,31 March 2023,Suwaiba,"Suwaiba,Atrayees,WikiWorks",Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that do not drink coffee (green) and the participants that are considered coffee drinkers (red),increased,"p__Candidatus Saccharimonadota,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",95818;1783272|201174;3379134|1224;1783272|1239;3379134|1224|28216|80840|119060|47670;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:32169076/7/2,32169076,"cross-sectional observational, not case-control",32169076,10.1186/s12967-020-02291-2,NA,"Murugesan S., Al Ahmad S.F., Singh P., Saadaoui M., Kumar M. , Al Khodor S.",Profiling the Salivary microbiome of the Qatari population,Journal of translational medicine,2020,"16S rRNA gene sequencing, Dysbiosis, Oral health, Qatar Biobank, Qatari, Saliva",Experiment 7,Qatar,Homo sapiens,Saliva,UBERON:0001836,Coffee consumption,EFO:0004330,Non-coffee drinkers,Coffee drinkers,Participants considered coffee drinkers,887,110,NA,16S,123,Illumina,relative abundances,LEfSe,2,NA,2,NA,"age,sex",NA,increased,increased,increased,NA,NA,Signature 2,Figure 7c,31 March 2023,Suwaiba,"Suwaiba,WikiWorks",Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that do not drink coffee (green) and the participants that are considered coffee drinkers (red),decreased,"k__Pseudomonadati|p__Bacteroidota,k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|976;3384189|32066;3379134|976|200643|171549|171552|838,Complete,Atrayees
bsdb:32169076/8/1,32169076,"cross-sectional observational, not case-control",32169076,10.1186/s12967-020-02291-2,NA,"Murugesan S., Al Ahmad S.F., Singh P., Saadaoui M., Kumar M. , Al Khodor S.",Profiling the Salivary microbiome of the Qatari population,Journal of translational medicine,2020,"16S rRNA gene sequencing, Dysbiosis, Oral health, Qatar Biobank, Qatari, Saliva",Experiment 8,Qatar,Homo sapiens,Saliva,UBERON:0001836,Tea consumption measurement,EFO:0010091,Non tea drinkers,Tea drinkers,Participants considered tea drinkers,229,768,NA,16S,123,Illumina,relative abundances,LEfSe,2,NA,2,NA,NA,NA,increased,increased,increased,NA,increased,Signature 1,Figure 8c,31 March 2023,Suwaiba,"Suwaiba,WikiWorks",Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. Features with LDA scores ≥ 2 are presented,decreased,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,3379134|976|117743|200644|49546|1016,Complete,Atrayees
bsdb:32192080/1/1,32192080,case-control,32192080,10.3390/diagnostics10030163,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151170/,"Hernandes C., Silveira P., Rodrigues Sereia A.F., Christoff A.P., Mendes H., Valter de Oliveira L.F. , Podgaec S.","Microbiome Profile of Deep Endometriosis Patients: Comparison of Vaginal Fluid, Endometrium and Lesion","Diagnostics (Basel, Switzerland)",2020,"16S rRNA, endometriosis, microbiome, next generation sequencing (NGS), pathogenesis, vaginal fluid",Experiment 1,Brazil,Homo sapiens,Vagina,UBERON:0000996,Endometriosis,EFO:0001065,Control group,Vaginal Fluid,"Vaginal samples were collected and processed for the evaluation of
their bacterial profile:",11,21,1 month,16S,34,Illumina,raw counts,DESeq2,0,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 4B,1 July 2021,Samara.Khan,"Samara.Khan,WikiWorks",There was increased abundance of gemella and streptococcus when comparing the vaginal fluid of endometriosis patients to healthy controls,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|1300|1301,Complete,Peace Sandy
bsdb:32192080/1/2,32192080,case-control,32192080,10.3390/diagnostics10030163,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151170/,"Hernandes C., Silveira P., Rodrigues Sereia A.F., Christoff A.P., Mendes H., Valter de Oliveira L.F. , Podgaec S.","Microbiome Profile of Deep Endometriosis Patients: Comparison of Vaginal Fluid, Endometrium and Lesion","Diagnostics (Basel, Switzerland)",2020,"16S rRNA, endometriosis, microbiome, next generation sequencing (NGS), pathogenesis, vaginal fluid",Experiment 1,Brazil,Homo sapiens,Vagina,UBERON:0000996,Endometriosis,EFO:0001065,Control group,Vaginal Fluid,"Vaginal samples were collected and processed for the evaluation of
their bacterial profile:",11,21,1 month,16S,34,Illumina,raw counts,DESeq2,0,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 4B,1 July 2021,Samara.Khan,"Samara.Khan,WikiWorks","There was decreased abundance of aerococcus in vaginal fluid of endometriosis patients compared to healthy controls. Atopobium, which is normally found in the lower female reproductive tract, was completely absent in vaginal fluid of endometriosis patients.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium",1783272|1239|91061|186826|186827|1375;1783272|201174|84998|84999|1643824|1380,Complete,Peace Sandy
bsdb:32192080/2/1,32192080,case-control,32192080,10.3390/diagnostics10030163,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151170/,"Hernandes C., Silveira P., Rodrigues Sereia A.F., Christoff A.P., Mendes H., Valter de Oliveira L.F. , Podgaec S.","Microbiome Profile of Deep Endometriosis Patients: Comparison of Vaginal Fluid, Endometrium and Lesion","Diagnostics (Basel, Switzerland)",2020,"16S rRNA, endometriosis, microbiome, next generation sequencing (NGS), pathogenesis, vaginal fluid",Experiment 2,Brazil,Homo sapiens,Uterus,UBERON:0000995,Endometriosis,EFO:0001065,Control group,Eutopic Endometrium Samples,"Eutopic Endometrium samples were collected and processed for the evaluation of
their bacterial profile:",11,18,1 month,16S,34,Illumina,raw counts,DESeq2,0,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 4B,1 July 2021,Samara.Khan,"Samara.Khan,WikiWorks",There was increased abundance of bifidobacterium when comparing the endometrial lining of endometriosis patients to healthy controls,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Peace Sandy
bsdb:32192080/2/2,32192080,case-control,32192080,10.3390/diagnostics10030163,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151170/,"Hernandes C., Silveira P., Rodrigues Sereia A.F., Christoff A.P., Mendes H., Valter de Oliveira L.F. , Podgaec S.","Microbiome Profile of Deep Endometriosis Patients: Comparison of Vaginal Fluid, Endometrium and Lesion","Diagnostics (Basel, Switzerland)",2020,"16S rRNA, endometriosis, microbiome, next generation sequencing (NGS), pathogenesis, vaginal fluid",Experiment 2,Brazil,Homo sapiens,Uterus,UBERON:0000995,Endometriosis,EFO:0001065,Control group,Eutopic Endometrium Samples,"Eutopic Endometrium samples were collected and processed for the evaluation of
their bacterial profile:",11,18,1 month,16S,34,Illumina,raw counts,DESeq2,0,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 4B,1 July 2021,Samara.Khan,"Samara.Khan,WikiWorks","There was decreased abundance of atopobium, mobiluncus, campylobacter, chromohalobacter, and alcanivorax when comparing the endometrial lining of endometriosis patients to healthy controls",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Alcanivoracaceae|g__Alcanivorax,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Chromohalobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus",3379134|1224|1236|135619|224372|59753;1783272|201174|84998|84999|1643824|1380;3379134|29547|3031852|213849|72294|194;3379134|1224|1236|135619|28256|42054;1783272|201174|1760|2037|2049|2050,Complete,Peace Sandy
bsdb:32192080/3/1,32192080,case-control,32192080,10.3390/diagnostics10030163,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151170/,"Hernandes C., Silveira P., Rodrigues Sereia A.F., Christoff A.P., Mendes H., Valter de Oliveira L.F. , Podgaec S.","Microbiome Profile of Deep Endometriosis Patients: Comparison of Vaginal Fluid, Endometrium and Lesion","Diagnostics (Basel, Switzerland)",2020,"16S rRNA, endometriosis, microbiome, next generation sequencing (NGS), pathogenesis, vaginal fluid",Experiment 3,Brazil,Homo sapiens,Uterus,UBERON:0000995,Endometriosis,EFO:0001065,Controls group,endometriotic lesion samples,"endometriotic lesion samples  collected and processed for the evaluation of
their bacterial profile:",11,8,1 month,16S,34,Illumina,raw counts,DESeq2,0,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 4B,1 July 2021,Samara.Khan,"Samara.Khan,WikiWorks","When comparing tissue from endometrial lesions to tissue from endometrium of healthy controls, the following species were increased: aerococcus, staphylococcus, sphingomonas, alishewanella, pseudomonas, and enterococcus",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alishewanella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",1783272|1239|91061|186826|186827|1375;1783272|1239|91061|1385|90964|1279;3379134|1224|28211|204457|41297|13687;3379134|1224|1236|135622|72275|111142;3379134|1224|1236|72274|135621|286;1783272|1239|91061|186826|81852|1350,Complete,Peace Sandy
bsdb:32192080/3/2,32192080,case-control,32192080,10.3390/diagnostics10030163,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151170/,"Hernandes C., Silveira P., Rodrigues Sereia A.F., Christoff A.P., Mendes H., Valter de Oliveira L.F. , Podgaec S.","Microbiome Profile of Deep Endometriosis Patients: Comparison of Vaginal Fluid, Endometrium and Lesion","Diagnostics (Basel, Switzerland)",2020,"16S rRNA, endometriosis, microbiome, next generation sequencing (NGS), pathogenesis, vaginal fluid",Experiment 3,Brazil,Homo sapiens,Uterus,UBERON:0000995,Endometriosis,EFO:0001065,Controls group,endometriotic lesion samples,"endometriotic lesion samples  collected and processed for the evaluation of
their bacterial profile:",11,8,1 month,16S,34,Illumina,raw counts,DESeq2,0,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 4B,1 July 2021,Samara.Khan,"Samara.Khan,WikiWorks","When comparing tissue from endometrial lesions to tissue from endometrium of healthy controls, the following species were decreased: prevotella, atopobium, afipia, mobiluncus, campylobacter, and facklamia",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Afipia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia",3379134|976|200643|171549|171552|838;1783272|201174|84998|84999|1643824|1380;3379134|1224|28211|356|41294|1033;1783272|201174|1760|2037|2049|2050;3379134|29547|3031852|213849|72294|194;1783272|1239|91061|186826|186827|66831,Complete,Peace Sandy
bsdb:32214153/1/1,32214153,case-control,32214153,10.1038/s41598-020-62224-3,https://pubmed.ncbi.nlm.nih.gov/32214153/,"Li Q., Chang Y., Zhang K., Chen H., Tao S. , Zhang Z.",Implication of the gut microbiome composition of type 2 diabetic patients from northern China,Scientific reports,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,Individuals diagnosed with Type 2 Diabetes Mellitus; T2D subjects were required to meet the following inclusion criteria: (i) fasting blood glucose test (FBG) 7 mmol/L or greater and/or 2-h fasting oral glucose tolerance test (OGTT) 11.1 mmol/L or greater35; (ii) no previously received pharmacologic treatment; and (iii) body mass index (BMI) > 18.0 kg/m2.,40,20,2 months,16S,45,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,NA,Signature 1,Figure 2b,5 July 2021,Madhubani Dey,"Madhubani Dey,Atrayees,WikiWorks",Decreased abundance of bacterial communities in individuals with Type 2 Diabetes compared to healthy controls,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",3379134|74201|203494|48461|1647988|239934;1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|216572|216851,Complete,Atrayees
bsdb:32214153/1/2,32214153,case-control,32214153,10.1038/s41598-020-62224-3,https://pubmed.ncbi.nlm.nih.gov/32214153/,"Li Q., Chang Y., Zhang K., Chen H., Tao S. , Zhang Z.",Implication of the gut microbiome composition of type 2 diabetic patients from northern China,Scientific reports,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,Individuals diagnosed with Type 2 Diabetes Mellitus; T2D subjects were required to meet the following inclusion criteria: (i) fasting blood glucose test (FBG) 7 mmol/L or greater and/or 2-h fasting oral glucose tolerance test (OGTT) 11.1 mmol/L or greater35; (ii) no previously received pharmacologic treatment; and (iii) body mass index (BMI) > 18.0 kg/m2.,40,20,2 months,16S,45,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,NA,Signature 2,Figure 2b,5 July 2021,Madhubani Dey,"Madhubani Dey,WikiWorks",Increased abundance of bacterial communities in individuals with Type 2 Diabetes compared to healthy controls,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|186801|3085636|186803|189330;3384189|32066|203490|203491|203492|848;1783272|1239;1783272|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:32214382/1/1,32214382,time series / longitudinal observational,32214382,10.1371/journal.ppat.1008376,NA,"Usyk M., Zolnik C.P., Castle P.E., Porras C., Herrero R., Gradissimo A., Gonzalez P., Safaeian M., Schiffman M. , Burk R.D.",Cervicovaginal microbiome and natural history of HPV in a longitudinal study,PLoS pathogens,2020,NA,Experiment 1,Costa Rica,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV (clearance),Visit 1 HPV (progression),HPV progression to CIN2+ lesion diagnosis,70,33,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,Merit",Bacteria associated with progression to CIN2+ identified using LEfSe,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus christensenii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus prevotii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter canadensis,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter ureolyticus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium atypicum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella bergensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Methylophilaceae|g__Methylobacillus|s__Methylobacillus flagellatus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Methylophilaceae|g__Methylobacillus|s__Methylobacillus glycogenes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria gonorrhoeae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus harei,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus indolicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas bennonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella veroralis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia meyeri,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas leidyi,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema pallidum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella montpellierensis",1783272|1239|91061|186826|186827|1375|87541;1783272|1239|1737404|1737405|1570339|165779|33034;1783272|201174|1760|85004|31953|1678|1681;1783272|201174|1760|85004|31953|1678|216816|1679;1783272|1239|186801|3085636|186803|572511|1322;3379134|29547|3031852|213849|72294|194|449520;3379134|29547|3031852|213849|72294|194|827;1783272|201174|1760|85007|1653|1716|191610;1783272|201174|1760|85004|31953|2701|2702;3379134|976|200643|171549|171552|52228|242750;3379134|1224|28216|32003|32011|404|405;3379134|1224|28216|32003|32011|404|406;3379134|1224|28216|206351|481|482|485;1783272|1239|1737404|1737405|1570339|162289|54005;1783272|1239|1737404|1737405|1570339|162289|33030;3379134|976|200643|171549|171551|836|501496;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552|838|28137;1783272|201174|1760|2037|2049|2529408|52773;1783272|201174|1760|2037|2049|2529408|1660;3379134|1224|28211|204457|41297|13687|68569;3379134|203691|203692|136|2845253|157|160;1783272|1239|909932|1843489|31977|29465|187328,Complete,Fatima Zohra
bsdb:32214382/1/2,32214382,time series / longitudinal observational,32214382,10.1371/journal.ppat.1008376,NA,"Usyk M., Zolnik C.P., Castle P.E., Porras C., Herrero R., Gradissimo A., Gonzalez P., Safaeian M., Schiffman M. , Burk R.D.",Cervicovaginal microbiome and natural history of HPV in a longitudinal study,PLoS pathogens,2020,NA,Experiment 1,Costa Rica,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV (clearance),Visit 1 HPV (progression),HPV progression to CIN2+ lesion diagnosis,70,33,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Cynthia Anderson,WikiWorks,Bacteria associated with progression to CIN2+ identified using LEfSe,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella paludivivens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners",3379134|976|200643|171549|171552|2974251|185294;1783272|1239|91061|186826|33958|1578|147802,Complete,Fatima Zohra
bsdb:32214382/2/1,32214382,time series / longitudinal observational,32214382,10.1371/journal.ppat.1008376,NA,"Usyk M., Zolnik C.P., Castle P.E., Porras C., Herrero R., Gradissimo A., Gonzalez P., Safaeian M., Schiffman M. , Burk R.D.",Cervicovaginal microbiome and natural history of HPV in a longitudinal study,PLoS pathogens,2020,NA,Experiment 2,Costa Rica,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV (clearance),Visit 2 HPV (progression),HPV progression to CIN2+ lesion diagnosis,69,33,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 4,10 January 2021,Cynthia Anderson,WikiWorks,Bacteria associated with progression to CIN2+ identified using LEfSe,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas circumdentaria,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus prevotii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus harei,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella bergeri,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium gleum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus",3379134|976|200643|171549|171552|838|419005;3379134|976|200643|171549|171551|836|29524;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|1239|909932|1843489|31977|39948|487173;1783272|1239|1737404|1737405|1570339|165779|33034;1783272|1239|1737404|1737405|1570339|162289|54005;1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|91061|1385|539738|1378|84136;3379134|976|117743|200644|2762318|59732|250;1783272|1239|186801|3085636|186803|33042|33043,Complete,Fatima Zohra
bsdb:32214382/2/2,32214382,time series / longitudinal observational,32214382,10.1371/journal.ppat.1008376,NA,"Usyk M., Zolnik C.P., Castle P.E., Porras C., Herrero R., Gradissimo A., Gonzalez P., Safaeian M., Schiffman M. , Burk R.D.",Cervicovaginal microbiome and natural history of HPV in a longitudinal study,PLoS pathogens,2020,NA,Experiment 2,Costa Rica,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV (clearance),Visit 2 HPV (progression),HPV progression to CIN2+ lesion diagnosis,69,33,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 4,10 January 2021,Cynthia Anderson,"WikiWorks,Atrayees",Bacteria associated with progression to CIN2+ identified using LEfSe,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces johnsonii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium|s__Atopobium minutum,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio|s__Acetivibrio clariflavus",1783272|201174|1760|2037|2049|1654|544581;1783272|201174|84998|84999|1643824|1380|1381;1783272|1239|186801|3120394|3120654|35829|288965,Complete,Fatima Zohra
bsdb:32235826/1/1,32235826,case-control,32235826,10.1038/s41467-020-15457-9,https://www.nature.com/articles/s41467-020-15457-9,"Zhu F., Ju Y., Wang W., Wang Q., Guo R., Ma Q., Sun Q., Fan Y., Xie Y., Yang Z., Jie Z., Zhao B., Xiao L., Yang L., Zhang T., Feng J., Guo L., He X., Chen Y., Chen C., Gao C., Xu X., Yang H., Wang J., Dang Y., Madsen L., Brix S., Kristiansen K., Jia H. , Ma X.",Metagenome-wide association of gut microbiome features for schizophrenia,Nature communications,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Healthy controls,"Schizophrenic patients (ARSCZ, FESCZ)","Only acutely relapsed schizophrenic (ARSCZ) and first-episode schizophrenic (FESCZ) patients were recruited in this study. The current episode of ARSCZ patients was required to happen in the last three months. ARSCZ patients were free of treatment for at least six months. The current episode of FESCZ patients was required to happen in the last year. FESCZ patients did not take any antipsychotics, or their accumulative dosages of antipsychotics intake were much less than the effective dosage (generally less than 100 mg chlorpromazine equivalents in the last two weeks based on the transformation method).",81,90,1 month,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"alcohol drinking,demographics,diet,smoking status,socioeconomic status",NA,NA,increased,NA,NA,NA,increased,Signature 1,Supplementary Data 5A,22 September 2021,Titas,"Titas,Atrayees,Chloe,WikiWorks",Significantly decreased gut mOTU between schizophrenia patients and healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius",1783272|1239|91061|186826|33958|1578|1579;1783272|1239|186801|186802|31979|1485|1502;3379134|976|200643|171549|815|909656|310297,Complete,Chloe
bsdb:32235826/1/2,32235826,case-control,32235826,10.1038/s41467-020-15457-9,https://www.nature.com/articles/s41467-020-15457-9,"Zhu F., Ju Y., Wang W., Wang Q., Guo R., Ma Q., Sun Q., Fan Y., Xie Y., Yang Z., Jie Z., Zhao B., Xiao L., Yang L., Zhang T., Feng J., Guo L., He X., Chen Y., Chen C., Gao C., Xu X., Yang H., Wang J., Dang Y., Madsen L., Brix S., Kristiansen K., Jia H. , Ma X.",Metagenome-wide association of gut microbiome features for schizophrenia,Nature communications,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Healthy controls,"Schizophrenic patients (ARSCZ, FESCZ)","Only acutely relapsed schizophrenic (ARSCZ) and first-episode schizophrenic (FESCZ) patients were recruited in this study. The current episode of ARSCZ patients was required to happen in the last three months. ARSCZ patients were free of treatment for at least six months. The current episode of FESCZ patients was required to happen in the last year. FESCZ patients did not take any antipsychotics, or their accumulative dosages of antipsychotics intake were much less than the effective dosage (generally less than 100 mg chlorpromazine equivalents in the last two weeks based on the transformation method).",81,90,1 month,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"alcohol drinking,demographics,diet,smoking status,socioeconomic status",NA,NA,increased,NA,NA,NA,increased,Signature 2,Supplementary Data 5A,23 September 2021,Titas,"Titas,Chloe,WikiWorks",Significantly increased gut mOTU between schizophrenia patients and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum",1783272|1239|909932|1843488|909930|904|187327;3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|91061|186826|81852|1350|1352;1783272|1239|91061|186826|33958|2742598|1613;1783272|1239|186801|186802|216572|1017280|106588;1783272|1239|91061|186826|1300|1301|1343;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|186801|186802|216572|39492,Complete,Chloe
bsdb:32235826/2/1,32235826,case-control,32235826,10.1038/s41467-020-15457-9,https://www.nature.com/articles/s41467-020-15457-9,"Zhu F., Ju Y., Wang W., Wang Q., Guo R., Ma Q., Sun Q., Fan Y., Xie Y., Yang Z., Jie Z., Zhao B., Xiao L., Yang L., Zhang T., Feng J., Guo L., He X., Chen Y., Chen C., Gao C., Xu X., Yang H., Wang J., Dang Y., Madsen L., Brix S., Kristiansen K., Jia H. , Ma X.",Metagenome-wide association of gut microbiome features for schizophrenia,Nature communications,2020,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Healthy controls at baseline,Schizophrenic patients (38 participant subsample) at baseline,"38 participants with schizophrenia selected for followup. Only acutely relapsed schizophrenic (ARSCZ) and first-episode schizophrenic (FESCZ) patients were recruited in this study. The current episode of ARSCZ patients was required to happen in the last three months. ARSCZ patients were free of treatment for at least six months. The current episode of FESCZ patients was required to happen in the last year. FESCZ patients did not take any antipsychotics, or their accumulative dosages of antipsychotics intake were much less than the effective dosage (generally less than 100 mg chlorpromazine equivalents in the last two weeks based on the transformation method).",81,38,1 month,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"alcohol drinking,demographics,diet,smoking status,socioeconomic status",NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Data 10,3 January 2024,Chloe,"Chloe,WikiWorks",Taxa decreased in schizophrenic subsample compared to healthy controls,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,1783272|1239|186801|186802|216572|39492,Complete,Chloe
bsdb:32235826/3/1,32235826,case-control,32235826,10.1038/s41467-020-15457-9,https://www.nature.com/articles/s41467-020-15457-9,"Zhu F., Ju Y., Wang W., Wang Q., Guo R., Ma Q., Sun Q., Fan Y., Xie Y., Yang Z., Jie Z., Zhao B., Xiao L., Yang L., Zhang T., Feng J., Guo L., He X., Chen Y., Chen C., Gao C., Xu X., Yang H., Wang J., Dang Y., Madsen L., Brix S., Kristiansen K., Jia H. , Ma X.",Metagenome-wide association of gut microbiome features for schizophrenia,Nature communications,2020,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Baseline Healthy controls,3 Month Follow-up Schizophrenic patients (38 participant subsample),"38 participants with schizophrenia selected for followup at 3 months. Only acutely relapsed schizophrenic (ARSCZ) and first-episode schizophrenic (FESCZ) patients were recruited in this study. The current episode of ARSCZ patients was required to happen in the last three months. ARSCZ patients were free of treatment for at least six months. The current episode of FESCZ patients was required to happen in the last year. FESCZ patients did not take any antipsychotics, or their accumulative dosages of antipsychotics intake were much less than the effective dosage (generally less than 100 mg chlorpromazine equivalents in the last two weeks based on the transformation method).",81,38,1 month,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"alcohol drinking,demographics,diet,smoking status,socioeconomic status",NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Data 10,3 January 2024,Chloe,"Chloe,WikiWorks",Baseline healthy controls compared to 3 month Follow up schizophrenia (38 samples),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter|s__Caulobacter segnis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter|s__Caulobacter vibrioides,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__[Bacteroides] pectinophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella variicola,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cancerogenus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius",3379134|1224|28211|204458|76892|75|88688;3379134|1224|28211|204458|76892|75|155892;1783272|1239|186801|3082720|186804|1257|341694;3379134|1224|1236|91347|543|570|548;1783272|1239|186801|186802|384638;1783272|1239|186801|186802|216572|39492;3379134|1224|1236|91347|543|570|244366;3379134|74201|203494|48461|1647988|239934|239935;3379134|1224|1236|91347|543|547|158836;3379134|1224|1236|91347|543|547|550;3379134|976|200643|171549|171550|239759|328814;3379134|1224|1236|91347|543|547|69218;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|815|909656|310297,Complete,Chloe
bsdb:32235826/3/2,32235826,case-control,32235826,10.1038/s41467-020-15457-9,https://www.nature.com/articles/s41467-020-15457-9,"Zhu F., Ju Y., Wang W., Wang Q., Guo R., Ma Q., Sun Q., Fan Y., Xie Y., Yang Z., Jie Z., Zhao B., Xiao L., Yang L., Zhang T., Feng J., Guo L., He X., Chen Y., Chen C., Gao C., Xu X., Yang H., Wang J., Dang Y., Madsen L., Brix S., Kristiansen K., Jia H. , Ma X.",Metagenome-wide association of gut microbiome features for schizophrenia,Nature communications,2020,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Baseline Healthy controls,3 Month Follow-up Schizophrenic patients (38 participant subsample),"38 participants with schizophrenia selected for followup at 3 months. Only acutely relapsed schizophrenic (ARSCZ) and first-episode schizophrenic (FESCZ) patients were recruited in this study. The current episode of ARSCZ patients was required to happen in the last three months. ARSCZ patients were free of treatment for at least six months. The current episode of FESCZ patients was required to happen in the last year. FESCZ patients did not take any antipsychotics, or their accumulative dosages of antipsychotics intake were much less than the effective dosage (generally less than 100 mg chlorpromazine equivalents in the last two weeks based on the transformation method).",81,38,1 month,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"alcohol drinking,demographics,diet,smoking status,socioeconomic status",NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Data 10,3 January 2024,Chloe,"Chloe,WikiWorks",Decreased in participants with schizophrenia at 3 months compared to baseline controls,decreased,"s__butyrate-producing bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__butyrate-producing bacterium SS3/4",2811711;1783272|1239|186801|186802|216572|1263|457412;1783272|1239|186801|186802|245014,Complete,Chloe
bsdb:32235826/4/1,32235826,case-control,32235826,10.1038/s41467-020-15457-9,https://www.nature.com/articles/s41467-020-15457-9,"Zhu F., Ju Y., Wang W., Wang Q., Guo R., Ma Q., Sun Q., Fan Y., Xie Y., Yang Z., Jie Z., Zhao B., Xiao L., Yang L., Zhang T., Feng J., Guo L., He X., Chen Y., Chen C., Gao C., Xu X., Yang H., Wang J., Dang Y., Madsen L., Brix S., Kristiansen K., Jia H. , Ma X.",Metagenome-wide association of gut microbiome features for schizophrenia,Nature communications,2020,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Antipsychotic drug,CHEBI:35476,Baseline Schizophrenic patients (38 participant subsample),3 Month Follow-up Schizophrenic patients (38 participant subsample),Alterations in abundance of mOTUs in the gut of SCZ patients after 3-month antipsychotics treatment,38,38,1 month,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"alcohol drinking,demographics,diet,smoking status,socioeconomic status",NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Data 11,3 January 2024,Chloe,"Chloe,WikiWorks",Increased in 3 month follow-up schizophrenia patients treated with antipsychotics compared to baseline,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes",3379134|1224|1236|91347|543|547|550;3379134|1224|1236|91347|543|570|548,Complete,ChiomaBlessing
bsdb:32236123/1/1,32236123,"cross-sectional observational, not case-control",32236123,10.1371/journal.pone.0228574,NA,"Stennett C.A., Dyer T.V., He X., Robinson C.K., Ravel J., Ghanem K.G. , Brotman R.M.",A cross-sectional pilot study of birth mode and vaginal microbiota in reproductive-age women,PloS one,2020,NA,Experiment 1,United States of America,Homo sapiens,Vaginal fluid,UBERON:0036243,Bacterial vaginosis,EFO:0003932,vaginal delivery,cesarean section,women reported birth by C-section,117,27,1 month,PCR,NA,Illumina,relative abundances,LEfSe,NA,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,1 June 2023,Danyab56,"Danyab56,WikiWorks","The bacterial taxa with the highest effect sizes (linear discriminant analysis [LDA] scores > 4) reflect marked abundance in one birth mode group and not in the other. Three taxa were differentially abundant at this level, with P. bivia being more abundant in C-section-delivered group and L. jensenii and L. iners being more abundant in the vaginally-delivered group. However, these differences were not statistically significant (0.05 < p < 0.30).",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,3379134|976|200643|171549|171552|838|28125,Complete,Fatima
bsdb:32236123/1/2,32236123,"cross-sectional observational, not case-control",32236123,10.1371/journal.pone.0228574,NA,"Stennett C.A., Dyer T.V., He X., Robinson C.K., Ravel J., Ghanem K.G. , Brotman R.M.",A cross-sectional pilot study of birth mode and vaginal microbiota in reproductive-age women,PloS one,2020,NA,Experiment 1,United States of America,Homo sapiens,Vaginal fluid,UBERON:0036243,Bacterial vaginosis,EFO:0003932,vaginal delivery,cesarean section,women reported birth by C-section,117,27,1 month,PCR,NA,Illumina,relative abundances,LEfSe,NA,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2,1 June 2023,Danyab56,"Danyab56,WikiWorks","The bacterial taxa with the highest effect sizes (linear discriminant analysis [LDA] scores > 4) reflect marked abundance in one birth mode group and not in the other. Three taxa were differentially abundant at this level, with P. bivia being more abundant in C-section-delivered group and L. jensenii and L. iners being more abundant in the vaginally-delivered group. However, these differences were not statistically significant (0.05 < p < 0.30).",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus jensenii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners",1783272|1239|91061|186826|33958|1578|109790;1783272|1239|91061|186826|33958|1578|147802,Complete,Fatima
bsdb:32237205/1/1,32237205,"cross-sectional observational, not case-control",32237205,10.1002/cam4.3027,NA,"Tsementzi D., Pena-Gonzalez A., Bai J., Hu Y.J., Patel P., Shelton J., Dolan M., Arluck J., Khanna N., Conrad L., Scott I., Eng T.Y., Konstantinidis K.T. , Bruner D.W.",Comparison of vaginal microbiota in gynecologic cancer patients pre- and post-radiation therapy and healthy women,Cancer medicine,2020,"16S rRNA gene, gynecologic cancer, postmenopausal women, radiation therapy, vaginal microbiota",Experiment 1,United States of America,Homo sapiens,Vagina,UBERON:0000996,female reproductive organ cancer,NA,Healthy controls,Cancer Pre-Rt (Pre-Radiation Therapy),Postmenopausal women (naturally or due to hysterectomy) with endometrial or cervical cancer Prior to treatment with radiotherapy with or without surgery and/or chemotherapy,69,20,1 month,16S,4,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,unchanged,increased,increased,NA,NA,NA,Signature 1,Figure 1A and B,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks,MyleeeA",Differentially abundant bacterial genera between the Healthy and Cancer Pre-RT group,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,p__Parabasalia|o__Trichomonadida|f__Trichomonadidae|g__Trichomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Criibacterium|s__Criibacterium bergeronii",1783272|1239|1737404|1737405|1570339|165779;1783272|1239|909932|1843489|31977|39948;1783272|1239|1737404|1582879;3384189|32066|203490|203491|203492|848;1783272|201174|1760|2037|2049|2050;1783272|1239|186801|3085636|186803|437755;1783272|544448|31969|2085|2092|2093;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3384189|32066|203490|203491|1129771|168808;3379134|29547|3031852|213849|72294|194;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3085636|186803|177971;5719|37104|181550|5721;1783272|1239|186801|3082720|3118655|1937664|1871336,Complete,Claregrieve1
bsdb:32237205/1/2,32237205,"cross-sectional observational, not case-control",32237205,10.1002/cam4.3027,NA,"Tsementzi D., Pena-Gonzalez A., Bai J., Hu Y.J., Patel P., Shelton J., Dolan M., Arluck J., Khanna N., Conrad L., Scott I., Eng T.Y., Konstantinidis K.T. , Bruner D.W.",Comparison of vaginal microbiota in gynecologic cancer patients pre- and post-radiation therapy and healthy women,Cancer medicine,2020,"16S rRNA gene, gynecologic cancer, postmenopausal women, radiation therapy, vaginal microbiota",Experiment 1,United States of America,Homo sapiens,Vagina,UBERON:0000996,female reproductive organ cancer,NA,Healthy controls,Cancer Pre-Rt (Pre-Radiation Therapy),Postmenopausal women (naturally or due to hysterectomy) with endometrial or cervical cancer Prior to treatment with radiotherapy with or without surgery and/or chemotherapy,69,20,1 month,16S,4,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,unchanged,increased,increased,NA,NA,NA,Signature 2,Figure 1A and B,10 January 2021,Fatima Zohra,"Claregrieve1,WikiWorks,MyleeeA",Differentially abundant bacterial genera between the Healthy and Cancer Pre-RT group,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|171550|239759,Complete,Claregrieve1
bsdb:32237205/2/1,32237205,"cross-sectional observational, not case-control",32237205,10.1002/cam4.3027,NA,"Tsementzi D., Pena-Gonzalez A., Bai J., Hu Y.J., Patel P., Shelton J., Dolan M., Arluck J., Khanna N., Conrad L., Scott I., Eng T.Y., Konstantinidis K.T. , Bruner D.W.",Comparison of vaginal microbiota in gynecologic cancer patients pre- and post-radiation therapy and healthy women,Cancer medicine,2020,"16S rRNA gene, gynecologic cancer, postmenopausal women, radiation therapy, vaginal microbiota",Experiment 2,United States of America,Homo sapiens,Vagina,UBERON:0000996,female reproductive organ cancer,NA,Healthy controls,Women with gynecological cancer,Postmenopausal women (naturally or due to hysterectomy) with endometrial or cervical cancer treated with radiotherapy with or without surgery and/or chemotherapy,69,65,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a and 4,24 February 2025,Tosin,"Tosin,Victoria",Differentially abundant bacterial operational taxonomic units between healthy and cancer groups.,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,p__Parabasalia|o__Trichomonadida|f__Trichomonadidae|g__Trichomonas,k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus",1783272|1239|1737404|1737405|1570339|165779;1783272|1239|909932|1843489|31977|39948;1783272|1239|1737404|1582879;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|1129771;1783272|201174|1760|2037|2049|2050;1783272|1239|186801|3085636|186803|437755;1783272|544448|31969|2085|2092|2093;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3384189|32066|203490|203491|1129771|168808;5719|37104|181550|5721;3384189|32066;1783272|1239|186801|186802|186807|2740,Complete,KateRasheed
bsdb:32237205/2/2,32237205,"cross-sectional observational, not case-control",32237205,10.1002/cam4.3027,NA,"Tsementzi D., Pena-Gonzalez A., Bai J., Hu Y.J., Patel P., Shelton J., Dolan M., Arluck J., Khanna N., Conrad L., Scott I., Eng T.Y., Konstantinidis K.T. , Bruner D.W.",Comparison of vaginal microbiota in gynecologic cancer patients pre- and post-radiation therapy and healthy women,Cancer medicine,2020,"16S rRNA gene, gynecologic cancer, postmenopausal women, radiation therapy, vaginal microbiota",Experiment 2,United States of America,Homo sapiens,Vagina,UBERON:0000996,female reproductive organ cancer,NA,Healthy controls,Women with gynecological cancer,Postmenopausal women (naturally or due to hysterectomy) with endometrial or cervical cancer treated with radiotherapy with or without surgery and/or chemotherapy,69,65,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3a and 4,24 February 2025,Tosin,"Tosin,Victoria",Differentially abundant bacterial operational taxonomic units between healthy and cancer groups.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|177971;3379134|976|200643|171549|171550|239759;3379134|74201|203494|48461|1647988|239934,Complete,KateRasheed
bsdb:32237205/3/1,32237205,"cross-sectional observational, not case-control",32237205,10.1002/cam4.3027,NA,"Tsementzi D., Pena-Gonzalez A., Bai J., Hu Y.J., Patel P., Shelton J., Dolan M., Arluck J., Khanna N., Conrad L., Scott I., Eng T.Y., Konstantinidis K.T. , Bruner D.W.",Comparison of vaginal microbiota in gynecologic cancer patients pre- and post-radiation therapy and healthy women,Cancer medicine,2020,"16S rRNA gene, gynecologic cancer, postmenopausal women, radiation therapy, vaginal microbiota",Experiment 3,United States of America,Homo sapiens,Vagina,UBERON:0000996,female reproductive organ cancer,NA,Pre-RT GynCa groups (Gynecologic cancer patients Pre-radiation therapy).,Post-RT GynCa groups (Gynecologic cancer patients post-radiation therapy).,Postmenopausal women with Gynecologic cancer post-radiation therapy.,65,25,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,unchanged,increased,decreased,NA,NA,NA,Signature 1,Figure 3b,24 February 2025,Tosin,Tosin,Differentially abundant bacterial operational taxonomic units between pre- and post-RT (radiation therapy) vaginal microbiomes.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136",3379134|976|200643|171549|171550|239759;3379134|1224|1236|91347|543;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171552|838;3379134|1224|1236|72274|135621|286;1783272|1239|186801|3085636|186803|877420,Complete,KateRasheed
bsdb:32237205/3/2,32237205,"cross-sectional observational, not case-control",32237205,10.1002/cam4.3027,NA,"Tsementzi D., Pena-Gonzalez A., Bai J., Hu Y.J., Patel P., Shelton J., Dolan M., Arluck J., Khanna N., Conrad L., Scott I., Eng T.Y., Konstantinidis K.T. , Bruner D.W.",Comparison of vaginal microbiota in gynecologic cancer patients pre- and post-radiation therapy and healthy women,Cancer medicine,2020,"16S rRNA gene, gynecologic cancer, postmenopausal women, radiation therapy, vaginal microbiota",Experiment 3,United States of America,Homo sapiens,Vagina,UBERON:0000996,female reproductive organ cancer,NA,Pre-RT GynCa groups (Gynecologic cancer patients Pre-radiation therapy).,Post-RT GynCa groups (Gynecologic cancer patients post-radiation therapy).,Postmenopausal women with Gynecologic cancer post-radiation therapy.,65,25,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,unchanged,increased,decreased,NA,NA,NA,Signature 2,Figure 3b,24 February 2025,Tosin,Tosin,Differentially abundant bacterial operational taxonomic units between pre- and post-RT vaginal microbiomes.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|1224|28216|80840|995019|40544;1783272|1239|186801|186802|216572,Complete,KateRasheed
bsdb:32237205/4/1,32237205,"cross-sectional observational, not case-control",32237205,10.1002/cam4.3027,NA,"Tsementzi D., Pena-Gonzalez A., Bai J., Hu Y.J., Patel P., Shelton J., Dolan M., Arluck J., Khanna N., Conrad L., Scott I., Eng T.Y., Konstantinidis K.T. , Bruner D.W.",Comparison of vaginal microbiota in gynecologic cancer patients pre- and post-radiation therapy and healthy women,Cancer medicine,2020,"16S rRNA gene, gynecologic cancer, postmenopausal women, radiation therapy, vaginal microbiota",Experiment 4,United States of America,Homo sapiens,Vagina,UBERON:0000996,"Genital neoplasm, female",NA,Healthy cohort (HC),Cancer Cohort,Postmenopausal women with gynecological cancer (GynCa),69,65,1 month,16S,4,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 2B,27 February 2025,MyleeeA,MyleeeA,Phylum level abundance between Cancer cohort and Healthy cohort at p≤0.05 using Welch two sample t-test.,increased,"k__Pseudomonadati|p__Bacteroidota,k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Campylobacterota",3379134|976;3384189|32066;1783272|544448;3379134|29547,Complete,KateRasheed
bsdb:32237205/4/2,32237205,"cross-sectional observational, not case-control",32237205,10.1002/cam4.3027,NA,"Tsementzi D., Pena-Gonzalez A., Bai J., Hu Y.J., Patel P., Shelton J., Dolan M., Arluck J., Khanna N., Conrad L., Scott I., Eng T.Y., Konstantinidis K.T. , Bruner D.W.",Comparison of vaginal microbiota in gynecologic cancer patients pre- and post-radiation therapy and healthy women,Cancer medicine,2020,"16S rRNA gene, gynecologic cancer, postmenopausal women, radiation therapy, vaginal microbiota",Experiment 4,United States of America,Homo sapiens,Vagina,UBERON:0000996,"Genital neoplasm, female",NA,Healthy cohort (HC),Cancer Cohort,Postmenopausal women with gynecological cancer (GynCa),69,65,1 month,16S,4,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 2B,27 February 2025,MyleeeA,MyleeeA,Phylum level abundance between Cancer cohort and Healthy cohort at p≤0.05 using Welch two sample t-test.,decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Actinomycetota",1783272|1239;3379134|1224;1783272|201174,Complete,KateRasheed
bsdb:32241904/1/1,32241904,case-control,32241904,10.1136/gutjnl-2019-319766,NA,"Wang X., Yang S., Li S., Zhao L., Hao Y., Qin J., Zhang L., Zhang C., Bian W., Zuo L., Gao X., Zhu B., Lei X.G., Gu Z., Cui W., Xu X., Li Z., Zhu B., Li Y., Chen S., Guo H., Zhang H., Sun J., Zhang M., Hui Y., Zhang X., Liu X., Sun B., Wang L., Qiu Q., Zhang Y., Li X., Liu W., Xue R., Wu H., Shao D., Li J., Zhou Y., Li S., Yang R., Pedersen O.B., Yu Z., Ehrlich S.D. , Ren F.",Aberrant gut microbiota alters host metabolome and impacts renal failure in humans and rodents,Gut,2020,"bile acid, enteric bacterial microflora",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Kidney disease,EFO:0003086,Healthy Controls,End Stage Renal Disease (ESRD),"Patients diagnosed with End stage Renal Disease (ESRD) according to the Kidney Disease: 
Improving Global Outcomes Clinical Practice guidelines and were undergoing stable haemodialysis (1–3 times per week).",69,223,1 month,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 2B,2 May 2025,MyleeeA,MyleeeA,Differentially abundant Species between patients with End stage Renal disease (ESRD) and healthy controls.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. YL32,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA",3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|171550|239759|328814;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|1322;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|186802|216572|946234;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|1506553|1834196;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|186802|216572|1263|457412,Complete,KateRasheed
bsdb:32241904/1/2,32241904,case-control,32241904,10.1136/gutjnl-2019-319766,NA,"Wang X., Yang S., Li S., Zhao L., Hao Y., Qin J., Zhang L., Zhang C., Bian W., Zuo L., Gao X., Zhu B., Lei X.G., Gu Z., Cui W., Xu X., Li Z., Zhu B., Li Y., Chen S., Guo H., Zhang H., Sun J., Zhang M., Hui Y., Zhang X., Liu X., Sun B., Wang L., Qiu Q., Zhang Y., Li X., Liu W., Xue R., Wu H., Shao D., Li J., Zhou Y., Li S., Yang R., Pedersen O.B., Yu Z., Ehrlich S.D. , Ren F.",Aberrant gut microbiota alters host metabolome and impacts renal failure in humans and rodents,Gut,2020,"bile acid, enteric bacterial microflora",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Kidney disease,EFO:0003086,Healthy Controls,End Stage Renal Disease (ESRD),"Patients diagnosed with End stage Renal Disease (ESRD) according to the Kidney Disease: 
Improving Global Outcomes Clinical Practice guidelines and were undergoing stable haemodialysis (1–3 times per week).",69,223,1 month,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 2B,2 May 2025,MyleeeA,MyleeeA,Differentially abundant Species between patients with End stage Renal disease (ESRD) and healthy controls.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Liu et al. 2021)",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|1506553;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|186801|186802|216572|1263|3062497,Complete,KateRasheed
bsdb:32245419/1/1,32245419,case-control,32245419,https://doi.org/10.1186/s12866-020-01733-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-020-01733-7,"Yu F.Y., Wang Q.Q., Li M., Cheng Y.H., Cheng Y.L., Zhou Y., Yang X., Zhang F., Ge X., Zhao B. , Ren X.Y.",Dysbiosis of saliva microbiome in patients with oral lichen planus,BMC microbiology,2020,"16S rDNA, High-throughput sequencing, Oral lichen planus, Salivary microbiome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Oral lichen planus,EFO:0008517,Healthy Control,Oral lichen planus (both erosive and non-erosive ),"Oral lichen planus (OLP) is a common oral mucosal disease with or without accompanying lesions in skin, nails, eyes, or urogenital tissue",10,20,NA,16S,4,Illumina,relative abundances,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,"Table 5, Supplemental figure (Excel sheet) and Text",25 March 2024,Fiddyhamma,"Fiddyhamma,Scholastica,WikiWorks",The differential taxa of bacteria in oral lichen planus (OLP) patients with and without erosive lesions (E and NE) versus control group,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Altererythrobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium",3379134|1224|28211|204457|335929|361177;1783272|201174|1760|85006|1268|1663;1783272|1239|909932|1843489|31977|906;1783272|201174|1760|2037|2049|2050;1783272|1239|186801|3085636|186803|265975,Complete,Svetlana up
bsdb:32245419/1/2,32245419,case-control,32245419,https://doi.org/10.1186/s12866-020-01733-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-020-01733-7,"Yu F.Y., Wang Q.Q., Li M., Cheng Y.H., Cheng Y.L., Zhou Y., Yang X., Zhang F., Ge X., Zhao B. , Ren X.Y.",Dysbiosis of saliva microbiome in patients with oral lichen planus,BMC microbiology,2020,"16S rDNA, High-throughput sequencing, Oral lichen planus, Salivary microbiome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Oral lichen planus,EFO:0008517,Healthy Control,Oral lichen planus (both erosive and non-erosive ),"Oral lichen planus (OLP) is a common oral mucosal disease with or without accompanying lesions in skin, nails, eyes, or urogenital tissue",10,20,NA,16S,4,Illumina,relative abundances,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,"Table 5, Supplemental figure (Excel sheet) and Text",25 March 2024,Fiddyhamma,"Fiddyhamma,Scholastica,WikiWorks",The differential taxa of bacteria in oral lichen planus (OLP) patients with and without erosive lesions (E and NE) versus control group,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Acholeplasma,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Crocinitomicaceae|g__Fluviicola,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Sterolibacteriaceae|g__Sulfuritalea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",1783272|1239|91061|186826|186827|46123;1783272|544448|31969|186329|2146|2147;3379134|1224|1236|135625|712|416916;3379134|976|200643|171549|815|816;3379134|1224|28216|206351|481|538;1783272|1239|1737404|1582879;3379134|976|117743|200644|1853230|332102;3384189|32066|203490|203491|1129771|32067;3379134|1224|28216|206351|481|482;3379134|976|1853228|1853229|563835|504481;3379134|1224|28216|32003|2008793|1054211;3379134|976|200643|171549|2005525|195950;1783272|1239|186801|186802|216572|707003,Complete,Svetlana up
bsdb:32245419/2/NA,32245419,case-control,32245419,https://doi.org/10.1186/s12866-020-01733-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-020-01733-7,"Yu F.Y., Wang Q.Q., Li M., Cheng Y.H., Cheng Y.L., Zhou Y., Yang X., Zhang F., Ge X., Zhao B. , Ren X.Y.",Dysbiosis of saliva microbiome in patients with oral lichen planus,BMC microbiology,2020,"16S rDNA, High-throughput sequencing, Oral lichen planus, Salivary microbiome",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Oral lichen planus,EFO:0008517,OLP patients without erosive lesions (NE),Patients with oral aphthous ulcer (RAU/U),"Recurrent aphthous ulceration (RAU) is a common oral mucosal disease also characterized by multiple oral ulcers, a feature similar to erosive OLP but different from OLP in the pattern of the clinical lesions and the pathogenesis mechanism",10,10,NA,16S,4,Illumina,relative abundances,NA,0.05,FALSE,NA,NA,NA,NA,increased,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:32245419/3/NA,32245419,case-control,32245419,https://doi.org/10.1186/s12866-020-01733-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-020-01733-7,"Yu F.Y., Wang Q.Q., Li M., Cheng Y.H., Cheng Y.L., Zhou Y., Yang X., Zhang F., Ge X., Zhao B. , Ren X.Y.",Dysbiosis of saliva microbiome in patients with oral lichen planus,BMC microbiology,2020,"16S rDNA, High-throughput sequencing, Oral lichen planus, Salivary microbiome",Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Oral lichen planus,EFO:0008517,Healthy control,Patients with oral aphthous ulcer (U/RAU),"Recurrent aphthous ulceration (RAU) is a common oral mucosal disease also characterized by multiple oral ulcers, a feature similar to erosive OLP but different from OLP in the pattern of the clinical lesions and the pathogenesis mechanism",10,10,NA,16S,4,Illumina,relative abundances,NA,0.05,FALSE,NA,NA,NA,NA,increased,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:32245419/4/1,32245419,case-control,32245419,https://doi.org/10.1186/s12866-020-01733-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-020-01733-7,"Yu F.Y., Wang Q.Q., Li M., Cheng Y.H., Cheng Y.L., Zhou Y., Yang X., Zhang F., Ge X., Zhao B. , Ren X.Y.",Dysbiosis of saliva microbiome in patients with oral lichen planus,BMC microbiology,2020,"16S rDNA, High-throughput sequencing, Oral lichen planus, Salivary microbiome",Experiment 4,China,Homo sapiens,Saliva,UBERON:0001836,Oral lichen planus,EFO:0008517,Healthy control,OLP patients with erosive lesions (E),Erosive OLP is a common oral mucosal disease characterized by multiple oral ulcers in its clinical presentation with chronic and painful ulceration of the skin and mucosal surfaces,10,10,NA,16S,4,Illumina,relative abundances,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Table 4 and Text,25 March 2024,Fiddyhamma,"Fiddyhamma,Scholastica,WikiWorks",The differential taxa of bacteria in oral lichen planus (OLP) patients with erosive lesions (E) versus control group,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia",1783272|1239|186801|3085636|186803|265975;3379134|203691|203692|136;3379134|203691|203692,Complete,Svetlana up
bsdb:32245419/4/2,32245419,case-control,32245419,https://doi.org/10.1186/s12866-020-01733-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-020-01733-7,"Yu F.Y., Wang Q.Q., Li M., Cheng Y.H., Cheng Y.L., Zhou Y., Yang X., Zhang F., Ge X., Zhao B. , Ren X.Y.",Dysbiosis of saliva microbiome in patients with oral lichen planus,BMC microbiology,2020,"16S rDNA, High-throughput sequencing, Oral lichen planus, Salivary microbiome",Experiment 4,China,Homo sapiens,Saliva,UBERON:0001836,Oral lichen planus,EFO:0008517,Healthy control,OLP patients with erosive lesions (E),Erosive OLP is a common oral mucosal disease characterized by multiple oral ulcers in its clinical presentation with chronic and painful ulceration of the skin and mucosal surfaces,10,10,NA,16S,4,Illumina,relative abundances,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Table 4 and Text,25 March 2024,Fiddyhamma,"Fiddyhamma,Scholastica,WikiWorks",The differential taxa of bacteria in oral lichen planus (OLP) patients with erosive lesions (E) versus control group,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",1783272|1239|91061|186826|186827|46123;1783272|1239|91061|186826|186827;3379134|1224|1236|135625|712|724;3379134|1224|28216|206351|481|482,Complete,Svetlana up
bsdb:32245419/5/1,32245419,case-control,32245419,https://doi.org/10.1186/s12866-020-01733-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-020-01733-7,"Yu F.Y., Wang Q.Q., Li M., Cheng Y.H., Cheng Y.L., Zhou Y., Yang X., Zhang F., Ge X., Zhao B. , Ren X.Y.",Dysbiosis of saliva microbiome in patients with oral lichen planus,BMC microbiology,2020,"16S rDNA, High-throughput sequencing, Oral lichen planus, Salivary microbiome",Experiment 5,China,Homo sapiens,Saliva,UBERON:0001836,Oral lichen planus,EFO:0008517,Healthy control,OLP patients without erosive lesions (NE),"Non-erosive OLP is a common oral mucosal disease without accompanying lesions in skin, nails, eyes, or urogenital tissue",10,10,NA,16S,4,Illumina,relative abundances,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Table 4 and Text,25 March 2024,Fiddyhamma,"Fiddyhamma,Scholastica,WikiWorks",The differential taxa of bacteria in oral lichen planus (OLP) patients without erosive lesions (NE) versus control group,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium",3379134|1224|1236|135625|712|724;3379134|1224|28216|206351|481|482;1783272|1239|186801|3085636|186803|265975,Complete,Svetlana up
bsdb:32245419/5/2,32245419,case-control,32245419,https://doi.org/10.1186/s12866-020-01733-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-020-01733-7,"Yu F.Y., Wang Q.Q., Li M., Cheng Y.H., Cheng Y.L., Zhou Y., Yang X., Zhang F., Ge X., Zhao B. , Ren X.Y.",Dysbiosis of saliva microbiome in patients with oral lichen planus,BMC microbiology,2020,"16S rDNA, High-throughput sequencing, Oral lichen planus, Salivary microbiome",Experiment 5,China,Homo sapiens,Saliva,UBERON:0001836,Oral lichen planus,EFO:0008517,Healthy control,OLP patients without erosive lesions (NE),"Non-erosive OLP is a common oral mucosal disease without accompanying lesions in skin, nails, eyes, or urogenital tissue",10,10,NA,16S,4,Illumina,relative abundances,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Table 4 and Text,25 March 2024,Fiddyhamma,"Fiddyhamma,Scholastica,WikiWorks",The differential taxa of bacteria in oral lichen planus (OLP) patients without erosive lesions (NE) versus control group,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia",1783272|1239|91061|186826|186827|46123;1783272|1239|91061|186826|186827;3379134|203691|203692|136;3379134|203691|203692,Complete,Svetlana up
bsdb:32245419/6/NA,32245419,case-control,32245419,https://doi.org/10.1186/s12866-020-01733-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-020-01733-7,"Yu F.Y., Wang Q.Q., Li M., Cheng Y.H., Cheng Y.L., Zhou Y., Yang X., Zhang F., Ge X., Zhao B. , Ren X.Y.",Dysbiosis of saliva microbiome in patients with oral lichen planus,BMC microbiology,2020,"16S rDNA, High-throughput sequencing, Oral lichen planus, Salivary microbiome",Experiment 6,China,Homo sapiens,Saliva,UBERON:0001836,Oral lichen planus,EFO:0008517,Patients with oral aphthous ulcer (U/RAU),OLP patients with erosive lesions (E),Erosive OLP is a common oral mucosal disease characterized by multiple oral ulcers in its clinical presentation with chronic and painful ulceration of the skin and mucosal surfaces,10,10,NA,16S,4,Illumina,relative abundances,NA,0.05,FALSE,NA,NA,NA,NA,increased,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:32245419/7/1,32245419,case-control,32245419,https://doi.org/10.1186/s12866-020-01733-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-020-01733-7,"Yu F.Y., Wang Q.Q., Li M., Cheng Y.H., Cheng Y.L., Zhou Y., Yang X., Zhang F., Ge X., Zhao B. , Ren X.Y.",Dysbiosis of saliva microbiome in patients with oral lichen planus,BMC microbiology,2020,"16S rDNA, High-throughput sequencing, Oral lichen planus, Salivary microbiome",Experiment 7,China,Homo sapiens,Saliva,UBERON:0001836,Oral lichen planus,EFO:0008517,OLP patients without erosive lesions (NE),OLP patients with erosive lesions (E),Erosive OLP is a common oral mucosal disease characterized by multiple oral ulcers in its clinical presentation with chronic and painful ulceration of the skin and mucosal surfaces,10,10,NA,16S,4,Illumina,relative abundances,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Table 4 and Text,25 March 2024,Fiddyhamma,"Fiddyhamma,Scholastica,WikiWorks",The differential taxa of bacteria in oral lichen planus (OLP) patients with (E) compared to patients without (NE) erosive lesions,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia",1783272|1239|91061|186826|186827|46123;1783272|1239|91061|186826|186827;3379134|203691|203692|136;3379134|203691|203692,Complete,Svetlana up
bsdb:32245419/7/2,32245419,case-control,32245419,https://doi.org/10.1186/s12866-020-01733-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-020-01733-7,"Yu F.Y., Wang Q.Q., Li M., Cheng Y.H., Cheng Y.L., Zhou Y., Yang X., Zhang F., Ge X., Zhao B. , Ren X.Y.",Dysbiosis of saliva microbiome in patients with oral lichen planus,BMC microbiology,2020,"16S rDNA, High-throughput sequencing, Oral lichen planus, Salivary microbiome",Experiment 7,China,Homo sapiens,Saliva,UBERON:0001836,Oral lichen planus,EFO:0008517,OLP patients without erosive lesions (NE),OLP patients with erosive lesions (E),Erosive OLP is a common oral mucosal disease characterized by multiple oral ulcers in its clinical presentation with chronic and painful ulceration of the skin and mucosal surfaces,10,10,NA,16S,4,Illumina,relative abundances,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Table 4 and Text,25 March 2024,Fiddyhamma,"Fiddyhamma,Scholastica,WikiWorks",The differential taxa of bacteria in oral lichen planus (OLP) patients with (E) compared to patients without (NE) erosive lesions,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium",3379134|1224|1236|135625|712|724;3379134|1224|28216|206351|481|482;1783272|1239|186801|3085636|186803|265975,Complete,Svetlana up
bsdb:32251484/1/1,32251484,laboratory experiment,32251484,10.1371/journal.pone.0230932,NA,"Tam A., Filho F.S.L., Ra S.W., Yang J., Leung J.M., Churg A., Wright J.L. , Sin D.D.",Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome,PloS one,2020,NA,Experiment 1,Canada,Mus musculus,Caecum,UBERON:0001153,Air pollution,ENVO:02500037,all other mice,male mice exposed to cigarette smoke,male mice exposed to smoke,50,8,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,3.5,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 1,Figure 7,10 January 2021,Zyaijah Bailey,"Claregrieve1,WikiWorks,Merit",Differentially abundant taxa in the smoke-exposed male mice versus all other mice,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Nanobdellati|p__Candidatus Aenigmatarchaeota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;1783276|743724;3379134|1224|28211|204441;3379134|74201|203494;3379134|74201,Complete,Claregrieve1
bsdb:32251484/2/1,32251484,laboratory experiment,32251484,10.1371/journal.pone.0230932,NA,"Tam A., Filho F.S.L., Ra S.W., Yang J., Leung J.M., Churg A., Wright J.L. , Sin D.D.",Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome,PloS one,2020,NA,Experiment 2,Canada,Mus musculus,Caecum,UBERON:0001153,Air pollution,ENVO:02500037,all other mice,female mice exposed to cigarette smoke,female mice exposed to cigarette smoke,48,10,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,3.5,NA,NA,decreased,increased,NA,NA,NA,increased,Signature 1,Figure 7,10 January 2021,Zyaijah Bailey,"Claregrieve1,WikiWorks",Differentially abundant taxa in the smoke-exposed female mice versus all other mice,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005473,Complete,Claregrieve1
bsdb:32251484/3/1,32251484,laboratory experiment,32251484,10.1371/journal.pone.0230932,NA,"Tam A., Filho F.S.L., Ra S.W., Yang J., Leung J.M., Churg A., Wright J.L. , Sin D.D.",Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome,PloS one,2020,NA,Experiment 3,Canada,Mus musculus,Caecum,UBERON:0001153,Air pollution,ENVO:02500037,all other mice,ovariectomized female mice exposed to cigarette smoke,ovariectomized female mice exposed to smoke,48,10,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,3.5,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 1,Figure 7,10 January 2021,Zyaijah Bailey,"Claregrieve1,WikiWorks,Merit",Differentially abundant taxa in the smoke-exposed ovariectomized female mice versus all other mice,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.",1783272|1239|186801|3085636|186803|830;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550|28138;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|59823,Complete,Claregrieve1
bsdb:32251484/4/1,32251484,laboratory experiment,32251484,10.1371/journal.pone.0230932,NA,"Tam A., Filho F.S.L., Ra S.W., Yang J., Leung J.M., Churg A., Wright J.L. , Sin D.D.",Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome,PloS one,2020,NA,Experiment 4,Canada,Mus musculus,Caecum,UBERON:0001153,Air pollution,ENVO:02500037,control,mice exposed to smoke,"male, female or ovariectomized females mice exposed to smoke",30,28,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,3.5,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 1,Figure 2,10 January 2021,Zyaijah Bailey,"Claregrieve1,WikiWorks,Merit",Differential microbial taxa between the control and smoke-exposed groups,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988|239934|1872421;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|459786;3379134|74201|203494;3379134|74201|203494|48461;3379134|74201,Complete,Claregrieve1
bsdb:32251484/4/2,32251484,laboratory experiment,32251484,10.1371/journal.pone.0230932,NA,"Tam A., Filho F.S.L., Ra S.W., Yang J., Leung J.M., Churg A., Wright J.L. , Sin D.D.",Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome,PloS one,2020,NA,Experiment 4,Canada,Mus musculus,Caecum,UBERON:0001153,Air pollution,ENVO:02500037,control,mice exposed to smoke,"male, female or ovariectomized females mice exposed to smoke",30,28,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,3.5,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 2,Figure 2,10 January 2021,Zyaijah Bailey,"Claregrieve1,Atrayees,WikiWorks,Merit",Differential microbial taxa between the control and smoke-exposed groups,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__uncultured Bacteroidales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira sp.",3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|2005473;3379134|976|200643|171549|171550;3379134|976|200643|171549|194843;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|2049031,Complete,Claregrieve1
bsdb:32252632/1/1,32252632,"cross-sectional observational, not case-control",32252632,10.1186/s12866-020-01759-x,NA,"Onywera H., Williamson A.L., Cozzuto L., Bonnin S., Mbulawa Z.Z.A., Coetzee D., Ponomarenko J. , Meiring T.L.",The penile microbiota of Black South African men: relationship with human papillomavirus and HIV infection,BMC microbiology,2020,"HIV, Human papillomavirus (HPV), Microbiota, Penile",Experiment 1,South Africa,Homo sapiens,Skin of penis,UBERON:0001331,Human papillomavirus,NCBITAXON:10566,High-Risk HPV Negative (HR-HPV Negative),High-Risk HPV Positive (HR-HPV Positive),High-Risk HPV Positive (HR-HPV Positive) refers to individuals infected with Human Papillomavirus.,81,102,NA,16S,34,Illumina,relative abundances,LEfSe,0.2,TRUE,3,NA,NA,unchanged,unchanged,NA,unchanged,unchanged,NA,Signature 1,Fig. 5,4 November 2024,KateRasheed,"KateRasheed,WikiWorks",Significant differentially abundant taxa between HR-HPV positive and negative individuals.,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|1737404|1737405|1570339|162289;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802;3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:32252632/1/2,32252632,"cross-sectional observational, not case-control",32252632,10.1186/s12866-020-01759-x,NA,"Onywera H., Williamson A.L., Cozzuto L., Bonnin S., Mbulawa Z.Z.A., Coetzee D., Ponomarenko J. , Meiring T.L.",The penile microbiota of Black South African men: relationship with human papillomavirus and HIV infection,BMC microbiology,2020,"HIV, Human papillomavirus (HPV), Microbiota, Penile",Experiment 1,South Africa,Homo sapiens,Skin of penis,UBERON:0001331,Human papillomavirus,NCBITAXON:10566,High-Risk HPV Negative (HR-HPV Negative),High-Risk HPV Positive (HR-HPV Positive),High-Risk HPV Positive (HR-HPV Positive) refers to individuals infected with Human Papillomavirus.,81,102,NA,16S,34,Illumina,relative abundances,LEfSe,0.2,TRUE,3,NA,NA,unchanged,unchanged,NA,unchanged,unchanged,NA,Signature 2,Fig. 5,4 November 2024,KateRasheed,"KateRasheed,WikiWorks",Significant differentially abundant taxa between HR-HPV positive and negative individuals.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales",1783272|201174|1760|85006|85019;1783272|201174|1760|2037,Complete,Svetlana up
bsdb:32252632/2/1,32252632,"cross-sectional observational, not case-control",32252632,10.1186/s12866-020-01759-x,NA,"Onywera H., Williamson A.L., Cozzuto L., Bonnin S., Mbulawa Z.Z.A., Coetzee D., Ponomarenko J. , Meiring T.L.",The penile microbiota of Black South African men: relationship with human papillomavirus and HIV infection,BMC microbiology,2020,"HIV, Human papillomavirus (HPV), Microbiota, Penile",Experiment 2,South Africa,Homo sapiens,Skin of penis,UBERON:0001331,Human papillomavirus,NCBITAXON:10566,HR-HPV-uninfected in HIV-negative,HR-HPV-infected in HIV-negative,HR-HPV-infected in HIV-negative refers to the presence of High-Risk Human papillomavirus (HPV) in men that are not infected with HIV.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.2,TRUE,3,NA,NA,unchanged,unchanged,NA,unchanged,unchanged,NA,Signature 1,Additional file 5: Figure S3,4 November 2024,KateRasheed,"KateRasheed,WikiWorks",Significant differentially abundant taxa between HR-HPV-infected in HIV-negative and HR-HPV-uninfected in HIV-negative individuals.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium",1783272|201174|1760|2037;1783272|201174|1760|85006|85019|1696;1783272|201174|1760|85006|85020|43668,Complete,Svetlana up
bsdb:32252632/4/1,32252632,"cross-sectional observational, not case-control",32252632,10.1186/s12866-020-01759-x,NA,"Onywera H., Williamson A.L., Cozzuto L., Bonnin S., Mbulawa Z.Z.A., Coetzee D., Ponomarenko J. , Meiring T.L.",The penile microbiota of Black South African men: relationship with human papillomavirus and HIV infection,BMC microbiology,2020,"HIV, Human papillomavirus (HPV), Microbiota, Penile",Experiment 4,South Africa,Homo sapiens,Skin of penis,UBERON:0001331,Human papillomavirus,NCBITAXON:10566,Non-Corynebacterium-dominated microbiota (Diverse penile microbiota (CSTs 2-5)),Corynebacterium-dominated penile microbiota (CST-1),Corynebacterium-dominated penile microbiota (CST-1) refers to men who had less HR-HPV.,111,127,NA,16S,34,Illumina,relative abundances,LEfSe,0.2,TRUE,2,NA,NA,decreased,decreased,NA,decreased,decreased,NA,Signature 1,Additional file 3: Table S2,4 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in men with Corynebacterium-dominated versus diverse penile microbiota.,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Dermabacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Eremococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|g__Exiguobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Pseudoclavibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Salinicoccus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Tessaracoccus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli,,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Nosocomiicoccus",1783272|1239|1737404|1737405|1570339|165779;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|201174|1760|85006|85020|43668;1783272|201174|1760|85006|85019|1696;1783272|1239|186801|186802|31979|1485;1783272|201174|1760|85007|1653|1716;3379134|1224|28216|80840|80864|80865;1783272|201174|1760|85006|85020|36739;3379134|1224|28211|356|212791;1783272|1239|91061|186826|186827|171412;1783272|1239|91061|1385|33986;1783272|1239|91061|186826|186827|66831;1783272|1239|186801|186802|204475;1783272|1239|91061|1385|90964|227979;1783272|1239|186801|3085636|186803;3379134|1224|28216|80840|75682|149698;3379134|1224|28211|356|119045|407;3379134|1224|28216|206351|481|482;1783272|201174|1760|85009|31957|1743;1783272|201174|1760|85006|85023|255204;3379134|1224|1236|2887326|468|497;1783272|1239|186801|3085636|186803|841;1783272|1239|91061|1385|90964|45669;3379134|1224|28211|204457|41297|13687;1783272|1239|91061|1385|90964|1279;1783272|201174|1760|85009|31957|72763;1783272|201174|1760|2037;1783272|1239|91061|1385;1783272|1239|91061;;1783272|201174|1760|85006|85020;3379134|1224|28216|206351|481;1783272|201174|1760|85007|85025;3379134|1224|28216|80840|75682;1783272|1239|91061|1385|186818;3379134|1224|28211|204457|41297;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|489909,Complete,Svetlana up
bsdb:32252632/4/2,32252632,"cross-sectional observational, not case-control",32252632,10.1186/s12866-020-01759-x,NA,"Onywera H., Williamson A.L., Cozzuto L., Bonnin S., Mbulawa Z.Z.A., Coetzee D., Ponomarenko J. , Meiring T.L.",The penile microbiota of Black South African men: relationship with human papillomavirus and HIV infection,BMC microbiology,2020,"HIV, Human papillomavirus (HPV), Microbiota, Penile",Experiment 4,South Africa,Homo sapiens,Skin of penis,UBERON:0001331,Human papillomavirus,NCBITAXON:10566,Non-Corynebacterium-dominated microbiota (Diverse penile microbiota (CSTs 2-5)),Corynebacterium-dominated penile microbiota (CST-1),Corynebacterium-dominated penile microbiota (CST-1) refers to men who had less HR-HPV.,111,127,NA,16S,34,Illumina,relative abundances,LEfSe,0.2,TRUE,2,NA,NA,decreased,decreased,NA,decreased,decreased,NA,Signature 2,Additional file 3: Table S2,4 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in men with Corynebacterium-dominated versus diverse penile microbiota.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Tissierellia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae",3379134|1224|1236|135624|84642|642;1783272|201174|1760|2037|2049|28263;1783272|201174|84998|84999|1643824|1380;3379134|976|200643|171549|815|816;3379134|1224|28211|356|118882|234;3379134|29547|3031852|213849|72294|194;3379134|1224|1236|91347|543|544;1783272|1239|909932|1843489|31977|39948;1783272|1239|1737404|1737405|1570339|150022;1783272|201174|1760|85004|31953|2701;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;3379134|976|200643|171549|171552|52228;1783272|1239|186801|186802|404402;1783272|201174|1760|85006|1268|57493;1783272|201174|1760|85006|1268|1269;1783272|201174|1760|2037|2049|2050;1783272|1239|1737404|1737405|1570339|1161127;1783272|544448|31969|2085|2092|2093;1783272|1239|909932|1843489|31977|909928;1783272|201174|84998|84999|1643824|133925;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|186802|186807|2740;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3379134|1224|1236|72274|135621|286;3384194|508458|649775|649776|3029088|638847;1783272|1239|186801|186802|216572|1200657;3384189|32066|203490|203491|1129771|168808;1783272|1239|91061|186826|1300|1301;3379134|1224|28216|80840|995019|40544;1783272|1239|1737404;1783272|201174|1760|2037|2049|184869;1783272|1239|91061|186826|186827;1783272|1239;3379134|976|200643|171549;3379134|976;1783272|201174|84998|84999|84107;1783272|1239|186801|186802;1783272|201174|1760|85006|1268;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171551;3379134|976|200643|171549|171552;1783272|1239|909932|1843489|31977;3379134|1224|28211|356|118882,Complete,Svetlana up
bsdb:32258202/1/1,32258202,"cross-sectional observational, not case-control",32258202,10.1093/ofid/ofz463,NA,"Fulcher J.A., Li F., Cook R.R., Zabih S., Louie A., Okochi H., Tobin N.H., Gandhi M., Shoptaw S., Gorbach P.M. , Aldrovandi G.M.",Rectal Microbiome Alterations Associated With Oral Human Immunodeficiency Virus Pre-Exposure Prophylaxis,Open forum infectious diseases,2019,"men who have sex with men (MSM), pre-exposure prophylaxis (PrEP), rectal microbiome",Experiment 1,United States of America,Homo sapiens,Rectum,UBERON:0001052,HIV/AIDS pre-exposure prophylaxis,GSSO:001787,HIV-negative MSM not on PrEP,HIV-negative MSM on PrEP,HIV-negative Men who have sex with men (MSM) on HIV pre-exposure prophylaxis (PrEP),37,37,NA,16S,4,Illumina,raw counts,Linear Regression,0.1,TRUE,NA,"age,alcohol drinking,anal intercourse,drug dependence,ethnic group,marijuana,nicotine dependence,obesity,race",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 1, Figure 2, Text",10 January 2021,Michael Lutete,WikiWorks,Pre-exposure prophylaxis use associates with differential abundance of specific bacterial genera,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella",1783272|1239|91061|186826|1300|1301;3384189|32066|203490|203491|203492|848;1783272|1239|909932|909929|1843491|52225,Complete,NA
bsdb:32258202/1/2,32258202,"cross-sectional observational, not case-control",32258202,10.1093/ofid/ofz463,NA,"Fulcher J.A., Li F., Cook R.R., Zabih S., Louie A., Okochi H., Tobin N.H., Gandhi M., Shoptaw S., Gorbach P.M. , Aldrovandi G.M.",Rectal Microbiome Alterations Associated With Oral Human Immunodeficiency Virus Pre-Exposure Prophylaxis,Open forum infectious diseases,2019,"men who have sex with men (MSM), pre-exposure prophylaxis (PrEP), rectal microbiome",Experiment 1,United States of America,Homo sapiens,Rectum,UBERON:0001052,HIV/AIDS pre-exposure prophylaxis,GSSO:001787,HIV-negative MSM not on PrEP,HIV-negative MSM on PrEP,HIV-negative Men who have sex with men (MSM) on HIV pre-exposure prophylaxis (PrEP),37,37,NA,16S,4,Illumina,raw counts,Linear Regression,0.1,TRUE,NA,"age,alcohol drinking,anal intercourse,drug dependence,ethnic group,marijuana,nicotine dependence,obesity,race",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 1, Figure 2, Text",10 January 2021,Michael Lutete,WikiWorks,Pre-exposure prophylaxis use associates with differential abundance of specific bacterial genera,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella",3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|620,Complete,NA
bsdb:32258202/2/1,32258202,"cross-sectional observational, not case-control",32258202,10.1093/ofid/ofz463,NA,"Fulcher J.A., Li F., Cook R.R., Zabih S., Louie A., Okochi H., Tobin N.H., Gandhi M., Shoptaw S., Gorbach P.M. , Aldrovandi G.M.",Rectal Microbiome Alterations Associated With Oral Human Immunodeficiency Virus Pre-Exposure Prophylaxis,Open forum infectious diseases,2019,"men who have sex with men (MSM), pre-exposure prophylaxis (PrEP), rectal microbiome",Experiment 2,United States of America,Homo sapiens,Rectum,UBERON:0001052,HIV/AIDS pre-exposure prophylaxis,GSSO:001787,HIV-negative MSM not on PrEP,HIV-negative MSM on PrEP,HIV-negative Men who have sex with men (MSM) on HIV pre-exposure prophylaxis (PrEP),37,37,NA,16S,4,Illumina,raw counts,NA,0.05,TRUE,NA,"age,alcohol drinking,anal intercourse,drug dependence,ethnic group,marijuana,nicotine dependence,obesity,race",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 2, Text",10 January 2021,Michael Lutete,WikiWorks,Pre-exposure prophylaxis use associates with differential abundance of specific bacterial genera,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,NA
bsdb:32274300/1/1,32274300,case-control,32274300,10.1002/advs.201902862,NA,"Zheng P., Yang J., Li Y., Wu J., Liang W., Yin B., Tan X., Huang Y., Chai T., Zhang H., Duan J., Zhou J., Sun Z., Chen X., Marwari S., Lai J., Huang T., Du Y., Zhang P., Perry S.W., Wong M.L., Licinio J., Hu S., Xie P. , Wang G.",Gut Microbial Signatures Can Discriminate Unipolar from Bipolar Depression,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2020,"bipolar disorder, gut microbiome, major depressive disorder, microbiota–gut–brain axis, unipolar depression",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Mood disorder,EFO:0004247,healthy controls (HCs),bipolar disorder (BD),Participants who suffer from depressive episodes of bipolar disorder (BD),217,217,1 month,16S,34,Illumina,NA,LEfSe,0.05,NA,2.5,"age,body mass index,sex",NA,NA,unchanged,decreased,NA,unchanged,NA,Signature 1,Supplementary file: Figure. S4b.,29 October 2023,Chinelsy,"Chinelsy,ChiomaBlessing,Idiaru angela,WikiWorks",Discriminative OTUs observed in the pairwise comparisons between bipolar disorder (BD) and healthy controls (HC).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces plicatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__Tyzzerella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",3379134|976|200643|171549|815|816;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|1643822|1643826|84111;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|1506553;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|186802|216572;3379134|1224|1236|72274|135621|286;1783272|1239|91061|186826|1300|1301;1783272|201174|1760|85011|2062|1883|1922;1783272|1239|186801|186802|216572|292632;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|3085636|186803|1506577|2053632;1783272|1239|186801|186802|31979|1485,Complete,ChiomaBlessing
bsdb:32274300/2/1,32274300,case-control,32274300,10.1002/advs.201902862,NA,"Zheng P., Yang J., Li Y., Wu J., Liang W., Yin B., Tan X., Huang Y., Chai T., Zhang H., Duan J., Zhou J., Sun Z., Chen X., Marwari S., Lai J., Huang T., Du Y., Zhang P., Perry S.W., Wong M.L., Licinio J., Hu S., Xie P. , Wang G.",Gut Microbial Signatures Can Discriminate Unipolar from Bipolar Depression,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2020,"bipolar disorder, gut microbiome, major depressive disorder, microbiota–gut–brain axis, unipolar depression",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Mood disorder,EFO:0004247,healthy controls (HCs),Major depressive disorder (MDD),Participants who suffer from depressive episodes from major depressive disorder (MDD),217,165,1 month,16S,34,Illumina,NA,LEfSe,0.05,NA,2.5,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,unchanged,NA,Signature 1,Supplementary file: Figure. S4a.,29 October 2023,Chinelsy,"Chinelsy,ChiomaBlessing,WikiWorks","Discriminative OTUs observed in the pairwise comparisons between major 
depressive disorder (MDD) and healthy controls (HC).",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.",3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|544;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|91061;1783272|1239|186801|186802|216572|1263|41978,Complete,ChiomaBlessing
bsdb:32274300/2/2,32274300,case-control,32274300,10.1002/advs.201902862,NA,"Zheng P., Yang J., Li Y., Wu J., Liang W., Yin B., Tan X., Huang Y., Chai T., Zhang H., Duan J., Zhou J., Sun Z., Chen X., Marwari S., Lai J., Huang T., Du Y., Zhang P., Perry S.W., Wong M.L., Licinio J., Hu S., Xie P. , Wang G.",Gut Microbial Signatures Can Discriminate Unipolar from Bipolar Depression,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2020,"bipolar disorder, gut microbiome, major depressive disorder, microbiota–gut–brain axis, unipolar depression",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Mood disorder,EFO:0004247,healthy controls (HCs),Major depressive disorder (MDD),Participants who suffer from depressive episodes from major depressive disorder (MDD),217,165,1 month,16S,34,Illumina,NA,LEfSe,0.05,NA,2.5,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,unchanged,NA,Signature 2,Supplementary file: Figure. S4a.,14 December 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Discriminative OTUs observed in the pairwise comparisons between major depressive disorder (MDD) and healthy controls (HC).,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,ChiomaBlessing
bsdb:32274300/3/1,32274300,case-control,32274300,10.1002/advs.201902862,NA,"Zheng P., Yang J., Li Y., Wu J., Liang W., Yin B., Tan X., Huang Y., Chai T., Zhang H., Duan J., Zhou J., Sun Z., Chen X., Marwari S., Lai J., Huang T., Du Y., Zhang P., Perry S.W., Wong M.L., Licinio J., Hu S., Xie P. , Wang G.",Gut Microbial Signatures Can Discriminate Unipolar from Bipolar Depression,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2020,"bipolar disorder, gut microbiome, major depressive disorder, microbiota–gut–brain axis, unipolar depression",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Mood disorder,EFO:0004247,bipolar disorder (BD),Major depressive disorder (MDD),Participants who suffer from depressive episodes from major depressive disorder (MDD),217,165,1 month,16S,34,Illumina,NA,LEfSe,0.05,NA,2.5,"age,body mass index",NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary file: Figure. S4c.,29 October 2023,Chinelsy,"Chinelsy,ChiomaBlessing,WikiWorks",Discriminative OTUs observed in the pairwise comparisons between major depressive disorder (MDD) and bipolar disorder (BD).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp.",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|3085636|186803|2569097|39488;3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|201174|84998|1643822|1643826|84111;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3082720|186804;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810280|3025755;3379134|976|200643|171549|171552|838|59823;1783272|1239|186801|3085636|186803|33042|2049024,Complete,ChiomaBlessing
bsdb:32274300/3/2,32274300,case-control,32274300,10.1002/advs.201902862,NA,"Zheng P., Yang J., Li Y., Wu J., Liang W., Yin B., Tan X., Huang Y., Chai T., Zhang H., Duan J., Zhou J., Sun Z., Chen X., Marwari S., Lai J., Huang T., Du Y., Zhang P., Perry S.W., Wong M.L., Licinio J., Hu S., Xie P. , Wang G.",Gut Microbial Signatures Can Discriminate Unipolar from Bipolar Depression,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2020,"bipolar disorder, gut microbiome, major depressive disorder, microbiota–gut–brain axis, unipolar depression",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Mood disorder,EFO:0004247,bipolar disorder (BD),Major depressive disorder (MDD),Participants who suffer from depressive episodes from major depressive disorder (MDD),217,165,1 month,16S,34,Illumina,NA,LEfSe,0.05,NA,2.5,"age,body mass index",NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary file: Figure. S4c.,29 October 2023,Chinelsy,"Chinelsy,ChiomaBlessing,WikiWorks",Discriminative OTUs observed in the pairwise comparisons between major depressive disorder (MDD) and bipolar disorder (BD).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.",1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|1239|909932|1843489|31977|39948;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1506553;1783272|1239|909932|1843488|909930|33024;3379134|1224|1236|72274|135621|286;1783272|1239|186801|3082720|186804|1501226;1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|171552|838|59823,Complete,ChiomaBlessing
bsdb:32277499/1/1,32277499,laboratory experiment,32277499,10.1111/pim.12721,NA,"Nyangahu D.D., Darby M., Havyarimana E., Brown B.P., Horsnell W. , Jaspan H.B.",Preconception helminth infection alters offspring microbiota and immune subsets in a mouse model,Parasite immunology,2020,"Nippostrongylus brasiliensis, CD4 T lymphocytes, Cell, animal model, parasite, tools and techniques",Experiment 1,South Africa,Mus musculus,Feces,UBERON:0001988,"Helminthiasis, animal",MONDO:0025082,Pregnant NvM,Pregnant NbM,Pregnant NbM are those previously infected with 500L3 Nippostrongylus brasiliensis (N brasiliensis) during pregnancy.,NA,NA,NA,16S,6,Illumina,centered log-ratio,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Figure 1D, S1",20 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant bacteria at different taxonomy level,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae",1783272|1239|91061|186826|186827;3379134|1224|28216|80840|506;1783272|1239|91061|1385;3379134|1224|28216|80840;1783272|1239|91061|186826|81852;3379134|976|117747|200666|84566;3379134|976|117747|200666;1783272|1239|91061|1385|90964,Complete,Svetlana up
bsdb:32277499/1/2,32277499,laboratory experiment,32277499,10.1111/pim.12721,NA,"Nyangahu D.D., Darby M., Havyarimana E., Brown B.P., Horsnell W. , Jaspan H.B.",Preconception helminth infection alters offspring microbiota and immune subsets in a mouse model,Parasite immunology,2020,"Nippostrongylus brasiliensis, CD4 T lymphocytes, Cell, animal model, parasite, tools and techniques",Experiment 1,South Africa,Mus musculus,Feces,UBERON:0001988,"Helminthiasis, animal",MONDO:0025082,Pregnant NvM,Pregnant NbM,Pregnant NbM are those previously infected with 500L3 Nippostrongylus brasiliensis (N brasiliensis) during pregnancy.,NA,NA,NA,16S,6,Illumina,centered log-ratio,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Figure 1D, S1",20 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant bacteria at different taxonomy level,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales",3379134|976|200643|171549|815;1783272|1239|526524|526525|128827;3379134|1224|1236|135625|712;3379134|976|200643|171549|171552;3379134|1224|1236|135625;1783272|1239|526524|526525,Complete,Svetlana up
bsdb:32277499/2/1,32277499,laboratory experiment,32277499,10.1111/pim.12721,NA,"Nyangahu D.D., Darby M., Havyarimana E., Brown B.P., Horsnell W. , Jaspan H.B.",Preconception helminth infection alters offspring microbiota and immune subsets in a mouse model,Parasite immunology,2020,"Nippostrongylus brasiliensis, CD4 T lymphocytes, Cell, animal model, parasite, tools and techniques",Experiment 2,South Africa,Mus musculus,Milk,UBERON:0001913,"Helminthiasis, animal",MONDO:0025082,NvM breastmilk (Naive Mothers),NbM breastmilk (Nippostrongylus brasiliensis Mothers),"NbM breastmilk refers to the breastmilk pellets from the stomachs of 14-day-old pups born to NbM.

NbM - (Nippostrongylus brasiliensis Mothers) refers to the group of maternal mice that were previously infected with 500L3 larvae of Nippostrongylus brasiliensis. The infection was treated and cleared with ivermectin.",5,5,NA,16S,6,Illumina,centered log-ratio,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2D,21 October 2024,Prolific,"Prolific,WikiWorks",The breastmilk microbiota signatures were derived from breastmilk samples collected from the stomachs of 14-day-old pups born to mothers with and without preconception Nippostrongylus brasiliensis infections.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae",3379134|1224|1236|91347|543;3379134|1224|1236|72274|135621,Complete,Svetlana up
bsdb:32277499/2/2,32277499,laboratory experiment,32277499,10.1111/pim.12721,NA,"Nyangahu D.D., Darby M., Havyarimana E., Brown B.P., Horsnell W. , Jaspan H.B.",Preconception helminth infection alters offspring microbiota and immune subsets in a mouse model,Parasite immunology,2020,"Nippostrongylus brasiliensis, CD4 T lymphocytes, Cell, animal model, parasite, tools and techniques",Experiment 2,South Africa,Mus musculus,Milk,UBERON:0001913,"Helminthiasis, animal",MONDO:0025082,NvM breastmilk (Naive Mothers),NbM breastmilk (Nippostrongylus brasiliensis Mothers),"NbM breastmilk refers to the breastmilk pellets from the stomachs of 14-day-old pups born to NbM.

NbM - (Nippostrongylus brasiliensis Mothers) refers to the group of maternal mice that were previously infected with 500L3 larvae of Nippostrongylus brasiliensis. The infection was treated and cleared with ivermectin.",5,5,NA,16S,6,Illumina,centered log-ratio,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2D,21 October 2024,Prolific,"Prolific,WikiWorks",The breastmilk microbiota signatures were derived from breastmilk samples collected from the stomachs of 14-day-old pups born to mothers with and without preconception Nippostrongylus brasiliensis infections,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae",1783272|1239|91061|186826|186827;1783272|1239|91061|1385|186817;1783272|201174|1760|85007|1653;1783272|1239|91061|1385|186818,Complete,Svetlana up
bsdb:32277499/3/1,32277499,laboratory experiment,32277499,10.1111/pim.12721,NA,"Nyangahu D.D., Darby M., Havyarimana E., Brown B.P., Horsnell W. , Jaspan H.B.",Preconception helminth infection alters offspring microbiota and immune subsets in a mouse model,Parasite immunology,2020,"Nippostrongylus brasiliensis, CD4 T lymphocytes, Cell, animal model, parasite, tools and techniques",Experiment 3,South Africa,Mus musculus,Feces,UBERON:0001988,"Helminthiasis, animal",MONDO:0025082,NvM pups,NbM pups,NbM pups are the babies given birth to by the NbM mothers.,NA,NA,NA,16S,6,Illumina,centered log-ratio,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 3D,21 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant bacteria at different taxonomy level,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae",1783272|1239|526524|526525|128827;1783272|201174|84998|84999|84107;1783272|201174|1760|85006|1268;3379134|1224|28216|80840|80864,Complete,Svetlana up
bsdb:32277499/3/2,32277499,laboratory experiment,32277499,10.1111/pim.12721,NA,"Nyangahu D.D., Darby M., Havyarimana E., Brown B.P., Horsnell W. , Jaspan H.B.",Preconception helminth infection alters offspring microbiota and immune subsets in a mouse model,Parasite immunology,2020,"Nippostrongylus brasiliensis, CD4 T lymphocytes, Cell, animal model, parasite, tools and techniques",Experiment 3,South Africa,Mus musculus,Feces,UBERON:0001988,"Helminthiasis, animal",MONDO:0025082,NvM pups,NbM pups,NbM pups are the babies given birth to by the NbM mothers.,NA,NA,NA,16S,6,Illumina,centered log-ratio,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 3D,21 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant bacteria at different taxonomy level,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae",1783272|1239|186801|186802|31979;3379134|1224|1236|91347|543;1783272|201174|1760|85007|1653;1783272|1239|91061|186826|186828,Complete,Svetlana up
bsdb:32277499/4/1,32277499,laboratory experiment,32277499,10.1111/pim.12721,NA,"Nyangahu D.D., Darby M., Havyarimana E., Brown B.P., Horsnell W. , Jaspan H.B.",Preconception helminth infection alters offspring microbiota and immune subsets in a mouse model,Parasite immunology,2020,"Nippostrongylus brasiliensis, CD4 T lymphocytes, Cell, animal model, parasite, tools and techniques",Experiment 4,South Africa,Mus musculus,Spleen,UBERON:0002106,"Helminthiasis, animal",MONDO:0025082,Low CD4+CD44hi Group,High CD4+CD44hi Group,High refers to the CD4 + CD44hi frequency around the mean of samples from NbM pups.,7,6,NA,16S,6,Illumina,centered log-ratio,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5H,22 October 2024,Prolific,"Prolific,KateRasheed,WikiWorks",Differential abundance of microbiota in the  CD4 + CD44hi frequency around the mean of samples from NbM pups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter",3379134|976|200643|171549|2005519|1348911;1783272|201174|84998|1643822|1643826|644652,Complete,Svetlana up
bsdb:32277499/4/2,32277499,laboratory experiment,32277499,10.1111/pim.12721,NA,"Nyangahu D.D., Darby M., Havyarimana E., Brown B.P., Horsnell W. , Jaspan H.B.",Preconception helminth infection alters offspring microbiota and immune subsets in a mouse model,Parasite immunology,2020,"Nippostrongylus brasiliensis, CD4 T lymphocytes, Cell, animal model, parasite, tools and techniques",Experiment 4,South Africa,Mus musculus,Spleen,UBERON:0002106,"Helminthiasis, animal",MONDO:0025082,Low CD4+CD44hi Group,High CD4+CD44hi Group,High refers to the CD4 + CD44hi frequency around the mean of samples from NbM pups.,7,6,NA,16S,6,Illumina,centered log-ratio,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5H,22 October 2024,Prolific,"Prolific,KateRasheed,WikiWorks",Differential abundance of microbiota in the  CD4 + CD44hi frequency around the mean of samples from NbM pups.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mobilitalea",1783272|1239|91061|186826|186827|1375;1783272|1239|186801|3085636|186803|1649471,Complete,Svetlana up
bsdb:32280686/1/1,32280686,case-control,32280686,10.1155/2020/2948282,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7114766/,"Liu X., Cheng Y., Shao L. , Ling Z.",Alterations of the Predominant Fecal Microbiota and Disruption of the Gut Mucosal Barrier in Patients with Early-Stage Colorectal Cancer,BioMed research international,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy controls,colorectal cancer patients,diagnosed with primary early-stage CRC (aged 46-75 years old) between January 2011 and March 2012,45,53,1 month,16S,NA,RT-qPCR,relative abundances,T-Test,0.05,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure1,16 February 2022,Fatima,"Fatima,WikiWorks",Quantitative real-time PCR analysis of the fecal abundant bacteria in patients with colorectal cancer,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum",3379134|1224|1236|91347|543;3384189|32066|203490|203491|203492|848|851,Complete,Fatima
bsdb:32280686/1/2,32280686,case-control,32280686,10.1155/2020/2948282,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7114766/,"Liu X., Cheng Y., Shao L. , Ling Z.",Alterations of the Predominant Fecal Microbiota and Disruption of the Gut Mucosal Barrier in Patients with Early-Stage Colorectal Cancer,BioMed research international,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy controls,colorectal cancer patients,diagnosed with primary early-stage CRC (aged 46-75 years old) between January 2011 and March 2012,45,53,1 month,16S,NA,RT-qPCR,relative abundances,T-Test,0.05,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure1,16 February 2022,Fatima,"Fatima,WikiWorks",Quantitative real-time PCR analysis of the fecal abundant bacteria in patients with colorectal cancer,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.",1783272|1239|91061|186826|33958|1578|1591;1783272|201174|1760|85004|31953|1678|41200;1783272|1239|186801|186802|31979|1485|1506,Complete,Fatima
bsdb:32295867/1/2,32295867,time series / longitudinal observational,32295867,10.1128/mSphere.00048-20,NA,"Robinson S., Peterson C.B., Sahasrabhojane P., Ajami N.J., Shelburne S.A., Kontoyiannis D.P. , Galloway-Peña J.R.",Observational Cohort Study of Oral Mycobiome and Interkingdom Interactions over the Course of Induction Therapy for Leukemia,mSphere,2020,"Malassezia, induction chemotherapy, interkingdom interactions, leukemia, mycobiome",Experiment 1,United States of America,Homo sapiens,Mouth,UBERON:0000165,Acute myeloid leukemia,EFO:0000222,Low Intensity Chemotherapy,High Intensity Chemotherapy,Acute Myeloid Leukemia patients receiving low-intensity remission induction chemotherapy at a later timepoint T6,11,28,NA,ITS / ITS2,NA,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 2,Figure 4,10 January 2021,William Lam,"Atrayees,WikiWorks,Folakunmi,ChiomaBlessing",Significantly enriched taxa in patients who received high-intensity chemotherapies compared to those who received low-intensity chemotherapy,decreased,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,4751|5204|1538075|162474|742845|55193,Complete,ChiomaBlessing
bsdb:32295867/2/1,32295867,time series / longitudinal observational,32295867,10.1128/mSphere.00048-20,NA,"Robinson S., Peterson C.B., Sahasrabhojane P., Ajami N.J., Shelburne S.A., Kontoyiannis D.P. , Galloway-Peña J.R.",Observational Cohort Study of Oral Mycobiome and Interkingdom Interactions over the Course of Induction Therapy for Leukemia,mSphere,2020,"Malassezia, induction chemotherapy, interkingdom interactions, leukemia, mycobiome",Experiment 2,United States of America,Homo sapiens,Mouth,UBERON:0000165,Acute myeloid leukemia,EFO:0000222,Patients without bacterial infections at T3,Patients with bacterial infections at T3,Acute Myeloid Leukemia patients that experienced microbiologically defined bacterial infections during remission induction chemotherapy at midpoint timepoint T3,30,9,NA,ITS / ITS2,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S2 + Figure 6,10 January 2021,William Lam,"Atrayees,WikiWorks,Folakunmi,ChiomaBlessing",Differential abundance among acute leukemia patients who had infections during induction chemotherapy compared to those who did not experience infections at midpoint time point (T3),increased,"k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales,k__Fungi|p__Ascomycota|c__Saccharomycetes",4751|4890|3239874|2916678|766764|1535326;4751|4890|3239874|2916678|766764;4751|4890|4891|4892;4751|4890|4891,Complete,ChiomaBlessing
bsdb:32295867/3/1,32295867,time series / longitudinal observational,32295867,10.1128/mSphere.00048-20,NA,"Robinson S., Peterson C.B., Sahasrabhojane P., Ajami N.J., Shelburne S.A., Kontoyiannis D.P. , Galloway-Peña J.R.",Observational Cohort Study of Oral Mycobiome and Interkingdom Interactions over the Course of Induction Therapy for Leukemia,mSphere,2020,"Malassezia, induction chemotherapy, interkingdom interactions, leukemia, mycobiome",Experiment 3,United States of America,Homo sapiens,Mouth,UBERON:0000165,Acute myeloid leukemia,EFO:0000222,Patients with no bacterial infections at T6,Patients with bacterial infections at T6,Acute Myeloid Leukemia patients that experience microbiologically defined bacterial infections during remission induction chemotherapy at endpoint timepoint T6,30,9,NA,ITS / ITS2,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6 + Figure S3,1 December 2023,Folakunmi,"Folakunmi,ChiomaBlessing,WikiWorks",Differential abundance among acute leukemia patients who had infections during induction chemotherapy compared to those who did not experience infections at a later time point (T6),decreased,"k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae,k__Fungi|p__Ascomycota|c__Sordariomycetes,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales,k__Fungi",4751|4890|147550|5125|110618|5506;4751|4890|147550|5125|110618;4751|4890|147550;4751|4890|147550|5125;4751,Complete,ChiomaBlessing
bsdb:32295867/4/1,32295867,time series / longitudinal observational,32295867,10.1128/mSphere.00048-20,NA,"Robinson S., Peterson C.B., Sahasrabhojane P., Ajami N.J., Shelburne S.A., Kontoyiannis D.P. , Galloway-Peña J.R.",Observational Cohort Study of Oral Mycobiome and Interkingdom Interactions over the Course of Induction Therapy for Leukemia,mSphere,2020,"Malassezia, induction chemotherapy, interkingdom interactions, leukemia, mycobiome",Experiment 4,United States of America,Homo sapiens,Mouth,UBERON:0000165,Antimicrobial agent,CHEBI:33281,Patients who did not receive Amphotericin B,Patients who received Amphotericin B,Acute Myeloid Leukemia patients who received amphotericin B.,66,6,NA,ITS / ITS2,NA,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,1 December 2023,Folakunmi,"Folakunmi,ChiomaBlessing,WikiWorks",Effect of amphotericin B on the composition of the oral fungal community at T6 in those who received amphotericin B compared to those who did not,increased,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium,4751|4890|147550|5125|110618|5506,Complete,ChiomaBlessing
bsdb:32299442/1/1,32299442,"cross-sectional observational, not case-control",32299442,10.1186/s12941-020-00356-0,NA,"Wei W., Zhang X., Tang H., Zeng L. , Wu R.",Microbiota composition and distribution along the female reproductive tract of women with endometriosis,Annals of clinical microbiology and antimicrobials,2020,"16S rRNA gene amplicon sequencing, Endometriosis, Microbial community composition, Microbial distribution",Experiment 1,China,Homo sapiens,"Lower part of vagina,Upper part of vagina,Cervical mucus","UBERON:0003974,UBERON:0000316,UBERON:0015243",Endometriosis,EFO:0001065,Controls Subject undergoing laparoscopic surgery for benign tumors,Endometriosis patients,Women with endometriosis,14,36,6 months,16S,45,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 2,8 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","The signature OTUs identified in the different sites of female reproductive tract were shown, including a vagina (CL), b posterior vaginal fornix (CU), c cervical mucus (CV), d endometrium (ET) and e peritoneal fluid (PF). Blue bar and purple bar note higher abundancy were occurred in EMS patients and healthy women, representatively. The signature OTUs were defined by Wilcoxon-rank sum test with p value < 0.05",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas viridiflava,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leucobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae|g__Hyphomicrobium",1783272|1239|91061|186826|33958|1578|147802;1783272|1239|91061|186826|81852|2737;1783272|201174|1760|85006|1268|1663;3379134|1224|1236|72274|135621|286|33069;3379134|1224|28211|204457|3423717|165695;3379134|1224|28216|80840|80864;3379134|1224|28216|80840|80864|80865;3379134|976|200643|171549|2005520|156973;3379134|1224|1236|72274|135621;1783272|1239|526524|526525|128827;3379134|1224|28211|204458|76892;3379134|1224|28211|204455|31989|265;3379134|1224|1236|135622|267890|22;3379134|1224|1236|72274|135621|286|306;1783272|201174|1760|85006|1268;3379134|1224|1236|2887326|468|469;1783272|1239|91061|186826|81852|1350;1783272|201174|1760|85006|85023|55968;1783272|1239|91061|1385|186822|44249;3379134|1224|1236|72274|135621|286;1783272|1239|1737404|1737405|1737406;3379134|1224|28211|356|45401|81,Complete,Peace Sandy
bsdb:32299442/1/2,32299442,"cross-sectional observational, not case-control",32299442,10.1186/s12941-020-00356-0,NA,"Wei W., Zhang X., Tang H., Zeng L. , Wu R.",Microbiota composition and distribution along the female reproductive tract of women with endometriosis,Annals of clinical microbiology and antimicrobials,2020,"16S rRNA gene amplicon sequencing, Endometriosis, Microbial community composition, Microbial distribution",Experiment 1,China,Homo sapiens,"Lower part of vagina,Upper part of vagina,Cervical mucus","UBERON:0003974,UBERON:0000316,UBERON:0015243",Endometriosis,EFO:0001065,Controls Subject undergoing laparoscopic surgery for benign tumors,Endometriosis patients,Women with endometriosis,14,36,6 months,16S,45,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 2,8 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","The signature OTUs identified in the different sites of female reproductive tract were shown, including a vagina (CL), b posterior vaginal fornix (CU), c cervical mucus (CV), d endometrium (ET) and e peritoneal fluid (PF). Blue bar and purple bar note higher abundancy were occurred in EMS patients and healthy women, representatively. The signature OTUs were defined by Wilcoxon-rank sum test with p value < 0.05",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella corporis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus casseliflavus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Macrococcoides|s__Macrococcoides caseolyticum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium|s__Sphingobacterium multivorum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Anaplasmataceae|g__Wolbachia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Agromyces,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",1783272|1239|91061|186826|186827|1375;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|33958|1578|1591;3384189|32066|203490|203491|1129771;1783272|201174|1760|2037|2049|2050;1783272|201174|84998|84999|84107;3379134|1224|1236|135614|1775411;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|909932|1843489|31977|906;3379134|976|200643|171549|171552|838|28128;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|186802;1783272|1239|91061|186826|81852|1350|37734;3379134|1224|28211|356;1783272|1239|186801|186802|216572|119852;1783272|1239|91061|1385|90964|3076173|69966;3379134|1224|1236|72274|135621;3379134|976|117747|200666|84566|28453|28454;1783272|201174|1760|85006|1268|1663;3379134|1224|1236|91347|543;3379134|1224|1236|2887326|468|469;3379134|1224|28211|766|942|953;1783272|201174|1760|85006|85023|33877;3379134|1224|28216|80840|995019|40544,Complete,Peace Sandy
bsdb:32312186/1/1,32312186,case-control,32312186,10.1080/19490976.2020.1747329,NA,"Dan Z., Mao X., Liu Q., Guo M., Zhuang Y., Liu Z., Chen K., Chen J., Xu R., Tang J., Qin L., Gu B., Liu K., Su C., Zhang F., Xia Y., Hu Z. , Liu X.",Altered gut microbial profile is associated with abnormal metabolism activity of Autism Spectrum Disorder,Gut microbes,2020,"16s rRNA, ASD, gut microbiota, metabolism, metagenomics, neurotransmitter",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Typically developing individuals,Children with Autism Spectrum Disorder (ASD),"Diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition",143,143,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,"age,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 1,Figure 1 f-g,11 December 2024,AlishaM,"AlishaM,WikiWorks",Bacterial taxa differentially abundant between TD and ASD,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides",3379134|1224|28216;3379134|1224|28216|80840|506;3379134|1224|28216|80840;3379134|1224|28216|80840|995019|577310;3379134|1224|1236|91347|543|1940338;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953;1783272|1239|909932|1843489|31977|39948;1783272|201174;3379134|1224;1783272|1239|186801|3082720|186804|1870884,Complete,NA
bsdb:32312186/1/2,32312186,case-control,32312186,10.1080/19490976.2020.1747329,NA,"Dan Z., Mao X., Liu Q., Guo M., Zhuang Y., Liu Z., Chen K., Chen J., Xu R., Tang J., Qin L., Gu B., Liu K., Su C., Zhang F., Xia Y., Hu Z. , Liu X.",Altered gut microbial profile is associated with abnormal metabolism activity of Autism Spectrum Disorder,Gut microbes,2020,"16s rRNA, ASD, gut microbiota, metabolism, metagenomics, neurotransmitter",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Typically developing individuals,Children with Autism Spectrum Disorder (ASD),"Diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition",143,143,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,"age,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 2,Figure 1 f-g,11 December 2024,AlishaM,"AlishaM,WikiWorks",Bacterial taxa differentially abundant between TD and ASD,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",3379134|976|200643;3379134|976|200643|171549;3379134|976|200643|171549|171552;1783272|1239|909932|909929|1843491|158846,Complete,NA
bsdb:32312186/2/1,32312186,case-control,32312186,10.1080/19490976.2020.1747329,NA,"Dan Z., Mao X., Liu Q., Guo M., Zhuang Y., Liu Z., Chen K., Chen J., Xu R., Tang J., Qin L., Gu B., Liu K., Su C., Zhang F., Xia Y., Hu Z. , Liu X.",Altered gut microbial profile is associated with abnormal metabolism activity of Autism Spectrum Disorder,Gut microbes,2020,"16s rRNA, ASD, gut microbiota, metabolism, metagenomics, neurotransmitter",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Typically developing individuals,Children with constipated Autism Spectrum Disorder (C-ASD),"Diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition",30,30,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,increased,NA,NA,NA,increased,Signature 1,"Figure 3F, Table S6",12 December 2024,AlishaM,"AlishaM,WikiWorks",Relative abundance of species enriched in TD versus C-ASD,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus cereus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium Barb7,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecichinchillae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fluxus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides helcogenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:144,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:443,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:462,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:598,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:633,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:702,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:875,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. HMSC073E02,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides timonensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella viscericola,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium botulinum,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Chroococcales|f__Aphanothecaceae|g__Crocosphaera|s__Crocosphaera watsonii,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium limosum,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium columnare,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella bergensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella pleuritidis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium A2,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides gordonii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp. CAG:409,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella xylaniphila,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter|s__Pedobacter panaciterrae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola barnesiae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola salanitronis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas cangingivalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella fusca,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1058,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1185,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:279,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:755,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:891,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. MSX73,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 306,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio|s__Pseudobutyrivibrio ruminis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella maculosa,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas ruminantium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus suis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella parvirubra,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter rarus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__uncultured Bacteroides sp.",3379134|976|200643|171549|171552|1283313|671218;3379134|976|200643|171549|171552|1283313|76122;1783272|1239|91061|1385|186817|1386|1396;3379134|976|200643|171549|1633203;3379134|976|200643|171549|815|816|85831;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|626929;3379134|976|200643|171549|815|816|871325;3379134|976|200643|171549|815|816|626930;3379134|976|200643|171549|815|816|290053;3379134|976|200643|171549|815|816|291644;3379134|976|200643|171549|815|816|1262736;3379134|976|200643|171549|815|816|1262739;3379134|976|200643|171549|815|816|1262740;3379134|976|200643|171549|815|816|1262743;3379134|976|200643|171549|815|816|1262744;3379134|976|200643|171549|815|816|1262747;3379134|976|200643|171549|815|816|1262752;3379134|976|200643|171549|815|816|1739517;3379134|976|200643|171549|815|816|46506;3379134|976|200643|171549|815|816|46506;3379134|976|200643|171549|815|816|1470345;3379134|976|200643|171549|2005519|397864|397865;3379134|29547|3031852|213849|72294|194|824;1783272|1239|186801|186802|31979|1485|1491;1783272|1117|3028117|1118|1890450|263510|263511;3379134|200940|3031449|213115|194924|872|901;1783272|1239|186801|186802|186806|1730|1736;3379134|976|117743|200644|49546|237|996;3379134|976|200643|171549|171552|52228|242750;3379134|976|200643|171549|171552|2974257|425941;3379134|976|200643|171549|171552|2974257|407975;1783272|1239|186801|3085636|186803|397290;3379134|976|200643|171549|171552|2974265|363265;3379134|976|200643|171549|2005525|375288|574930;3379134|976|200643|171549|2005525|375288|1262913;3379134|976|200643|171549|171552|577309|454155;3379134|976|117747|200666|84566|84567|363849;1783272|1239|909932|1843488|909930|33024|626940;3379134|976|200643|171549|815|909656|376804;3379134|976|200643|171549|815|909656|387090;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|909656|376805;3379134|976|200643|171549|171551|836|36874;3379134|976|200643|171549|171551|836|837;3379134|976|200643|171549|171552|838|419005;3379134|976|200643|171549|171552|838|28129;3379134|976|200643|171549|171552|838|589436;3379134|976|200643|171549|171552|838|470565;3379134|976|200643|171549|171552|838|60133;3379134|976|200643|171549|171552|838|1262918;3379134|976|200643|171549|171552|838|1262921;3379134|976|200643|171549|171552|838|1262924;3379134|976|200643|171549|171552|838|1262935;3379134|976|200643|171549|171552|838|1262937;3379134|976|200643|171549|171552|838|1032506;3379134|976|200643|171549|171552|838|712461;1783272|1239|186801|3085636|186803|46205|46206;3379134|1224|1236|72274|135621|286|287;3379134|976|200643|171549|171552|2974251|439703;3379134|976|200643|171549|171552|2974251|228604;1783272|1239|909932|909929|1843491|970|971;1783272|1239|91061|186826|1300|1301|1307;3379134|1224|28216|80840|995019|40544|437898;3379134|976|200643|171549|171552|558436|1676614;3379134|976|200643|171549|815|816|162156,Complete,NA
bsdb:32312186/3/1,32312186,case-control,32312186,10.1080/19490976.2020.1747329,NA,"Dan Z., Mao X., Liu Q., Guo M., Zhuang Y., Liu Z., Chen K., Chen J., Xu R., Tang J., Qin L., Gu B., Liu K., Su C., Zhang F., Xia Y., Hu Z. , Liu X.",Altered gut microbial profile is associated with abnormal metabolism activity of Autism Spectrum Disorder,Gut microbes,2020,"16s rRNA, ASD, gut microbiota, metabolism, metagenomics, neurotransmitter",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Typically developing individuals,Children with Autism Spectrum Disorder (ASD),"Diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition",143,143,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S3,16 December 2024,AlishaM,"AlishaM,WikiWorks",Operational taxonomic units with significantly different relative abundance between ASD and TD group.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Diaphorobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Uruburuella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella",1783272|1239|909932|1843489|31977|906;3379134|1224|28216|80840|80864|283;3379134|1224|1236|91347|543;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|186806|1730|39497;3379134|1224|1236|91347|1903414|581;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|46205;1783272|1239|186801|3085636|186803|830;3379134|1224|1236|135625|712|724;1783272|1239|91061|1385|186817|1386;3379134|1224|28216|80840|80864|238749;1783272|1239|91061|186826|186828|117563;1783272|1239|186801|3082720|186804|1505657;1783272|1239|186801|186802|216572|292632;3379134|976|200643|171549|171551;1783272|1798710|1906119;3379134|1224|28216|206351|481|299568;1783272|201174|1760|85004|31953|1678;1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|186802|216572|1508657;1783272|201174|84998|84999|84107|102106;1783272|1239|526524|526525|2810281|191303;3384189|32066|203490|203491|203492|180162;1783272|201174|84998|84999|84107;1783272|1239|186801|3085636|186803|189330;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|209879;1783272|1239|91061|186826|33958|46255;1783272|1239|91061|1385|539738|1378;1783272|1239|909932|909929|1843491|52225;1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|186802|186806|1730|39496;3379134|1224|28211|204457|41297;1783272|201174|84998|1643822|1643826|644652;1783272|1239|1737404|1582879,Complete,NA
bsdb:32312186/3/2,32312186,case-control,32312186,10.1080/19490976.2020.1747329,NA,"Dan Z., Mao X., Liu Q., Guo M., Zhuang Y., Liu Z., Chen K., Chen J., Xu R., Tang J., Qin L., Gu B., Liu K., Su C., Zhang F., Xia Y., Hu Z. , Liu X.",Altered gut microbial profile is associated with abnormal metabolism activity of Autism Spectrum Disorder,Gut microbes,2020,"16s rRNA, ASD, gut microbiota, metabolism, metagenomics, neurotransmitter",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Typically developing individuals,Children with Autism Spectrum Disorder (ASD),"Diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition",143,143,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S3,16 December 2024,AlishaM,"AlishaM,WikiWorks",Operational taxonomic units with significantly different relative abundance between ASD and TD group,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Anoxybacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Caproiciproducens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Brevibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Succiniclasticum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",3379134|976|200643|171549|171552|1283313;3384194|1297|188787|68933|188786|270;3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|577309;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3085636|186803|28050;3379134|976|200643|171549;3379134|1224|1236|135619|28256|2745;1783272|1239|186801|3085636|186803|28050|39485;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|186802|1392389;3379134|976|200643|171549|1853231|283168;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|3082768|990719;1783272|1239|91061|1385|3120669|150247;3379134|1224|28211|204441|41295;3379134|1224|28216|80840;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549;1783272|1239|186801|3085636|186803|1506577;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802|3082771|1738645;1783272|1239|909932|1843489|31977|156454;1783272|1239|526524|526525|128827|61170;1783272|1239|91061|1385|186822|55080;1783272|1239|186801|186802;3379134|1224|1236|2887326|468|469;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|216572|119852;3379134|1224|1236|2887326|468|497;3379134|976|200643|171549|171551;1783272|1239|909932|1843488|909930|40840;3379134|1224|1236|135614|32033|40323,Complete,NA
bsdb:32312186/4/1,32312186,case-control,32312186,10.1080/19490976.2020.1747329,NA,"Dan Z., Mao X., Liu Q., Guo M., Zhuang Y., Liu Z., Chen K., Chen J., Xu R., Tang J., Qin L., Gu B., Liu K., Su C., Zhang F., Xia Y., Hu Z. , Liu X.",Altered gut microbial profile is associated with abnormal metabolism activity of Autism Spectrum Disorder,Gut microbes,2020,"16s rRNA, ASD, gut microbiota, metabolism, metagenomics, neurotransmitter",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Typically developing individuals,Children with non-constipated Autism Spectrum Disorder (NC-ASD),"Diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition",86,86,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S4,16 December 2024,AlishaM,"AlishaM,WikiWorks","Operational taxonomic units, phylum and genus with significantly different relative abundance between NC-ASD and TD group",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Uruburuella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Cyanobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Pseudomonadati|p__Pseudomonadota",1783272|1239|186801|3085636|186803|207244;1783272|1239|91061|1385|186817|1386;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|830;1783272|1798710|1906119;1783272|1239|526524|526525|2810280|135858;3379134|1224|28216|80840|80864|283;1783272|1239|186801|3085636|186803|189330;3379134|1224|28216|206351|481|538;1783272|1239|186801|186802|186806|1730|39497;3384189|32066|203490|203491|203492|848;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;1783272|1239|186801|3082720|186804|1505657;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803;1783272|1239|909932|1843489|31977|906;3379134|1224|1236|91347|1903414|581;1783272|1239|186801|186802|216572|292632;1783272|1239|526524|526525|2810281|191303;3379134|1224|28216|206351|481|299568;1783272|1239|91061|186826|33958|46255;3379134|1224|1236|91347|543;1783272|1117;3384189|32066|203490;3379134|1224,Complete,NA
bsdb:32312186/4/2,32312186,case-control,32312186,10.1080/19490976.2020.1747329,NA,"Dan Z., Mao X., Liu Q., Guo M., Zhuang Y., Liu Z., Chen K., Chen J., Xu R., Tang J., Qin L., Gu B., Liu K., Su C., Zhang F., Xia Y., Hu Z. , Liu X.",Altered gut microbial profile is associated with abnormal metabolism activity of Autism Spectrum Disorder,Gut microbes,2020,"16s rRNA, ASD, gut microbiota, metabolism, metagenomics, neurotransmitter",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Typically developing individuals,Children with non-constipated Autism Spectrum Disorder (NC-ASD),"Diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition",86,86,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S4,16 December 2024,AlishaM,"AlishaM,WikiWorks","Operational taxonomic units, phylum and genus with significantly different relative abundance between NC-ASD and TD group",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Anoxybacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Caproiciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia",3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|1283313;1783272|1239|186801|3085636|186803|28050;1783272|1239|909932|1843488|909930|33024;3384194|1297|188787|68933|188786|270;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|171552;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|3085636|186803|2316020|33039;3379134|976|200643|171549|171550|239759;1783272|1239|909932|1843489|31977|39948;3379134|1224|28211|204441|41295;3379134|976|200643|171549;3379134|1224|1236|135619|28256|2745;3379134|976|200643|171549|171552|577309;1783272|1239|909932|909929|1843491|158846;3379134|976|200643|171549|1853231|574697;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803|1769710;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|119852;1783272|1239|91061|1385|3120669|150247;3379134|1224|28216|80840;1783272|1239|186801|3085636|186803|1506577;1783272|201174|84998|1643822|1643826|84108;1783272|1239|186801|186802;1783272|1239|186801|186802|3082771|1738645;1783272|1239|186801|186802|216572|596767;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|526524|526525|128827;3379134|1224|1236|135614|32033|40323;1783272|1239|909932|1843489|31977|156454;1783272|1239|1737404|1737405|1570339|162289;3379134|976|200643|171549|171552|838;3379134|976|200643,Complete,NA
bsdb:32320621/1/1,32320621,prospective cohort,32320621,10.1164/rccm.201911-2202OC,NA,"Mac Aogáin M., Lau K.J.X., Cai Z., Kumar Narayana J., Purbojati R.W., Drautz-Moses D.I., Gaultier N.E., Jaggi T.K., Tiew P.Y., Ong T.H., Siyue Koh M., Lim Yick Hou A., Abisheganaden J.A., Tsaneva-Atanasova K., Schuster S.C. , Chotirmall S.H.",Metagenomics Reveals a Core Macrolide Resistome Related to Microbiota in Chronic Respiratory Disease,American journal of respiratory and critical care medicine,2020,"antimicrobial resistance, macrolides, metagenomics, resistome, respiratory disease",Experiment 1,Singapore,Homo sapiens,Sputum,UBERON:0007311,Respiratory system disease,EFO:0000684,Non-diseased/ healthy individuals (ND),Diseased individuals (D),"Patients with a range of chronic respiratory disease states (severe asthma, chronic obstructive pulmonary disease- COPD, and bronchiectasis)",13,41,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,decreased,unchanged,NA,NA,Signature 1,Supplemental. fig. E3D and Supplemental fig. E3E,22 October 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential microbial abundance between diseased (D) and nondiseased (ND)/ healthy individuals,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa",1783272|201174|1760|85009|31957|2801844;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85007|1653|1716;3379134|1224|1236|91347|543|561;3379134|1224|1236|135625|712|724;3379134|1224|1236|91347|543|570;1783272|1239|91061|1385|186822|44249;3379134|1224|1236|72274|135621|286;3379134|1224|1236|2887326|468|497;3379134|976|200643|171549|2005525|195950;1783272|201174|1760|85006|1268|32207|43675,Complete,NA
bsdb:32320621/1/2,32320621,prospective cohort,32320621,10.1164/rccm.201911-2202OC,NA,"Mac Aogáin M., Lau K.J.X., Cai Z., Kumar Narayana J., Purbojati R.W., Drautz-Moses D.I., Gaultier N.E., Jaggi T.K., Tiew P.Y., Ong T.H., Siyue Koh M., Lim Yick Hou A., Abisheganaden J.A., Tsaneva-Atanasova K., Schuster S.C. , Chotirmall S.H.",Metagenomics Reveals a Core Macrolide Resistome Related to Microbiota in Chronic Respiratory Disease,American journal of respiratory and critical care medicine,2020,"antimicrobial resistance, macrolides, metagenomics, resistome, respiratory disease",Experiment 1,Singapore,Homo sapiens,Sputum,UBERON:0007311,Respiratory system disease,EFO:0000684,Non-diseased/ healthy individuals (ND),Diseased individuals (D),"Patients with a range of chronic respiratory disease states (severe asthma, chronic obstructive pulmonary disease- COPD, and bronchiectasis)",13,41,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,decreased,unchanged,NA,NA,Signature 2,Supplemental. fig. E3D and Supplemental fig. E3E,22 October 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential microbial abundance between diseased (D) and nondiseased (ND)/ healthy individuals,decreased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfomicrobiaceae|g__Desulfomicrobium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|1737404|1737405|1570339|543311;1783272|544448|31969|2085|2092|2093;1783272|1239|909932|909929|1843491|970;1783272|1239|909932|1843489|31977|39948;3384189|32066|203490|203491|1129771|32067;1783272|1239|186801|3082720|543314|86331;1783272|201174|84998|84999|1643824|1380;3379134|1224|1236|135625|712|416916;1783272|1239|526524|526525|128827|123375;1783272|201174|84998|84999|1643824|133925;1783272|1239|186801|3085636|186803|43996;3379134|1224|28216|80840|119060|47670;1783272|201174|1760|2037|2049|76833;3379134|29547|3031852|213849|72294|194;1783272|1239|186801|3085636|186803|1164882;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171552|1283313;1783272|1239|186801|186802|31979|1485;3379134|200940|3031449|213115|213116|898;3384189|32066|203490|203491|203492|848;3379134|203691|203692|136|2845253|157;3379134|976|200643|171549|171552|838,Complete,NA
bsdb:32332850/1/1,32332850,time series / longitudinal observational,32332850,10.1038/s41467-020-15856-y,NA,"Mitra A., MacIntyre D.A., Ntritsos G., Smith A., Tsilidis K.K., Marchesi J.R., Bennett P.R., Moscicki A.B. , Kyrgiou M.",The vaginal microbiota associates with the regression of untreated cervical intraepithelial neoplasia 2 lesions,Nature communications,2020,NA,Experiment 1,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical glandular intraepithelial neoplasia,EFO:1000165,CIN regression,CIN non-regression,"histology proven CIN2, no regression after 12 months",42,45,NA,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,10 January 2021,Cynthia Anderson,WikiWorks,LEfSe analysis identified baseline vaginal microbiota biomarkers associated with clinical outcomes at 12 months follow-up,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Actinomycetota|c__Actinomycetes",3379134|976|200643|171549|171552|2974257|386414;1783272|1239|909932;1783272|1239|909932|909929;1783272|201174|84998|84999;1783272|1239|186801|186802;1783272|201174|84998|84999|1643824|1380;1783272|201174|84998|84999|1643824|2767327|82135;1783272|201174|84998|84999|84107;3384189|32066;3384189|32066|203490|203491|1129771|168808;3384189|32066|203490|203491|1129771;1783272|1239|909932|1843489|31977;1783272|1239|909932|1843489|31977|906;3384189|32066|203490;3384189|32066|203490|203491;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171552|838;3379134|976;3379134|976|200643;3379134|976|200643|171549|171552;3379134|976|200643|171549;1783272|201174|1760,Complete,Fatima Zohra
bsdb:32332850/1/2,32332850,time series / longitudinal observational,32332850,10.1038/s41467-020-15856-y,NA,"Mitra A., MacIntyre D.A., Ntritsos G., Smith A., Tsilidis K.K., Marchesi J.R., Bennett P.R., Moscicki A.B. , Kyrgiou M.",The vaginal microbiota associates with the regression of untreated cervical intraepithelial neoplasia 2 lesions,Nature communications,2020,NA,Experiment 1,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical glandular intraepithelial neoplasia,EFO:1000165,CIN regression,CIN non-regression,"histology proven CIN2, no regression after 12 months",42,45,NA,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5,10 January 2021,Cynthia Anderson,WikiWorks,LEfSe analysis identified baseline vaginal microbiota biomarkers associated with clinical outcomes at 12 months follow-up,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota",1783272|1239|91061|186826;1783272|1239|91061;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239,Complete,Fatima Zohra
bsdb:32332850/2/1,32332850,time series / longitudinal observational,32332850,10.1038/s41467-020-15856-y,NA,"Mitra A., MacIntyre D.A., Ntritsos G., Smith A., Tsilidis K.K., Marchesi J.R., Bennett P.R., Moscicki A.B. , Kyrgiou M.",The vaginal microbiota associates with the regression of untreated cervical intraepithelial neoplasia 2 lesions,Nature communications,2020,NA,Experiment 2,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical glandular intraepithelial neoplasia,EFO:1000165,CIN regression,CIN non-regression,"histology proven CIN2, no regression after 12 months",42,45,NA,16S,12,Illumina,raw counts,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,unchanged,increased,Signature 1,Figure 4,10 January 2021,Cynthia Anderson,WikiWorks,Outcomes at 12-month follow-up according to baseline VMB composition at baseline,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis",3379134|976|200643|171549|171552|2974257|386414;1783272|201174|1760|85004|31953|2701|2702,Complete,Fatima Zohra
bsdb:32332850/4/1,32332850,time series / longitudinal observational,32332850,10.1038/s41467-020-15856-y,NA,"Mitra A., MacIntyre D.A., Ntritsos G., Smith A., Tsilidis K.K., Marchesi J.R., Bennett P.R., Moscicki A.B. , Kyrgiou M.",The vaginal microbiota associates with the regression of untreated cervical intraepithelial neoplasia 2 lesions,Nature communications,2020,NA,Experiment 4,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical glandular intraepithelial neoplasia,EFO:1000165,CIN regression,CIN non-regression,"histology proven CIN2, no regression after 24 months among women with no regression after 12 months",21,14,NA,16S,12,Illumina,raw counts,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,unchanged,unchanged,Signature 1,Supplementary Figure 3,10 January 2021,Cynthia Anderson,WikiWorks,Supplementary Figure 3. Outcomes at 24 months according to VMB composition at 12 months in a subgroup of 35 women with ongoing disease,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus christensenii,1783272|1239|91061|186826|186827|1375|87541,Complete,Fatima Zohra
bsdb:32334937/1/1,32334937,"cross-sectional observational, not case-control",32334937,10.1016/j.schres.2020.03.010,NA,"Yolken R., Prandovszky E., Severance E.G., Hatfield G. , Dickerson F.",The oropharyngeal microbiome is altered in individuals with schizophrenia and mania,Schizophrenia research,2020,"Depression, Immunity, Mania, Microbiome, Schizophrenia",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy controls,schizophrenia,"patients met DSM-IV criteria for schizophrenia, mania participants with symptoms of mania or hypermania could have diagnosis of Bipolar I disorder, single manic episode, most recent episode, mixed Bipolar II episode, most recent episode mixed,or Schizoaffective disorder., bipolar type (manic, hypomanic or mixed state)",85,121,NA,16S,34,Illumina,relative abundances,Wald Test,0.05,TRUE,NA,NA,"age,body mass index,race,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2, figure 3, figure 4, figure 5, figure 6",10 January 2021,Fatima Zohra,WikiWorks,"Levels of oral microbiome compared to controls adjusted for age, sex, race, cigarette smoking and BMI among individuals with schizophrenia and mania",increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:32334937/1/2,32334937,"cross-sectional observational, not case-control",32334937,10.1016/j.schres.2020.03.010,NA,"Yolken R., Prandovszky E., Severance E.G., Hatfield G. , Dickerson F.",The oropharyngeal microbiome is altered in individuals with schizophrenia and mania,Schizophrenia research,2020,"Depression, Immunity, Mania, Microbiome, Schizophrenia",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy controls,schizophrenia,"patients met DSM-IV criteria for schizophrenia, mania participants with symptoms of mania or hypermania could have diagnosis of Bipolar I disorder, single manic episode, most recent episode, mixed Bipolar II episode, most recent episode mixed,or Schizoaffective disorder., bipolar type (manic, hypomanic or mixed state)",85,121,NA,16S,34,Illumina,relative abundances,Wald Test,0.05,TRUE,NA,NA,"age,body mass index,race,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2, figure 3, figure 4, figure 5, figure 6",10 January 2021,Fatima Zohra,"WikiWorks,Atrayees","Levels of oral microbiome compared to controls adjusted for age, sex, race, cigarette smoking and BMI among individuals with schizophrenia and mania",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae",3379134|1224|28216|206351|481|482|28449;3379134|976|200643|171549|171552|838;3379134|976|117743|200644|2762318,Complete,Atrayees
bsdb:32334937/2/1,32334937,"cross-sectional observational, not case-control",32334937,10.1016/j.schres.2020.03.010,NA,"Yolken R., Prandovszky E., Severance E.G., Hatfield G. , Dickerson F.",The oropharyngeal microbiome is altered in individuals with schizophrenia and mania,Schizophrenia research,2020,"Depression, Immunity, Mania, Microbiome, Schizophrenia",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy controls,mania,"patients met DSM-IV criteria for schizophrenia, mania participants with symptoms of mania or hypermania could have diagnosis of Bipolar I disorder, single manic episode, most recent episode, mixed Bipolar II episode, most recent episode mixed,or Schizoaffective disorder., bipolar type (manic, hypomanic or mixed state)",85,62,NA,16S,34,Illumina,relative abundances,Wald Test,0.05,TRUE,NA,NA,"age,body mass index,race,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2, figure 3, figure 4, figure 5, figure 6",10 January 2021,Fatima Zohra,WikiWorks,"Levels of oral microbiome compared to controls adjusted for age, sex, race, cigarette smoking and BMI among individuals with schizophrenia and mania",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Caldimonas",1783272|1239|91061|186826|1300|1301;3379134|1224|28216|80840|2975441|215579,Complete,Atrayees
bsdb:32334937/2/2,32334937,"cross-sectional observational, not case-control",32334937,10.1016/j.schres.2020.03.010,NA,"Yolken R., Prandovszky E., Severance E.G., Hatfield G. , Dickerson F.",The oropharyngeal microbiome is altered in individuals with schizophrenia and mania,Schizophrenia research,2020,"Depression, Immunity, Mania, Microbiome, Schizophrenia",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy controls,mania,"patients met DSM-IV criteria for schizophrenia, mania participants with symptoms of mania or hypermania could have diagnosis of Bipolar I disorder, single manic episode, most recent episode, mixed Bipolar II episode, most recent episode mixed,or Schizoaffective disorder., bipolar type (manic, hypomanic or mixed state)",85,62,NA,16S,34,Illumina,relative abundances,Wald Test,0.05,TRUE,NA,NA,"age,body mass index,race,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2, figure 3, figure 4, figure 5, figure 6",10 January 2021,Fatima Zohra,"WikiWorks,Atrayees","Levels of oral microbiome compared to controls adjusted for age, sex, race, cigarette smoking and BMI among individuals with schizophrenia and mania",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae",3379134|1224|28216|206351|481|482|28449;3379134|976|200643|171549|171552|838;3379134|976|117743|200644|2762318,Complete,Atrayees
bsdb:32341759/1/1,32341759,"cross-sectional observational, not case-control",32341759,10.1080/20002297.2020.1742527,NA,"Sato N., Kakuta M., Uchino E., Hasegawa T., Kojima R., Kobayashi W., Sawada K., Tamura Y., Tokuda I., Imoto S., Nakaji S., Murashita K., Yanagita M. , Okuno Y.",The relationship between cigarette smoking and the tongue microbiome in an East Asian population,Journal of oral microbiology,2020,"East Asia, Oral cavity, cigarette smoking, microbiome, tongue",Experiment 1,Japan,Homo sapiens,Tongue,UBERON:0001723,Smoking behavior,EFO:0004318,never smokers,current smokers,participants who underwent tongue-coating analysis in 2016 and 2017,384,144,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,alcohol drinking,body mass index,dental caries,number of teeth measurement,peridontal microbiome,sex",NA,decreased,NA,decreased,NA,decreased,Signature 1,Figure 3(a),10 January 2021,Victoria Goulbourne,"WikiWorks,Atrayees",The result of comparison of bacterial abundance at the genus level,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma",1783272|201174|1760|85006|1268|32207;1783272|1239|91061|186826|1300|1301;1783272|201174|84998|84999|1643824|1380;1783272|1239|909932|1843489|31977|906;1783272|201174|1760|85007|1653|1716;3379134|976|200643|171549|2005523|346096;1783272|1239|186801|3082720|543314|109326;3379134|976|200643|171549|2005525|195950;1783272|1239|186801|3082720|3118655|44259;1783272|544448|31969|2085|2092|2093,Complete,Atrayees
bsdb:32341759/1/2,32341759,"cross-sectional observational, not case-control",32341759,10.1080/20002297.2020.1742527,NA,"Sato N., Kakuta M., Uchino E., Hasegawa T., Kojima R., Kobayashi W., Sawada K., Tamura Y., Tokuda I., Imoto S., Nakaji S., Murashita K., Yanagita M. , Okuno Y.",The relationship between cigarette smoking and the tongue microbiome in an East Asian population,Journal of oral microbiology,2020,"East Asia, Oral cavity, cigarette smoking, microbiome, tongue",Experiment 1,Japan,Homo sapiens,Tongue,UBERON:0001723,Smoking behavior,EFO:0004318,never smokers,current smokers,participants who underwent tongue-coating analysis in 2016 and 2017,384,144,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,alcohol drinking,body mass index,dental caries,number of teeth measurement,peridontal microbiome,sex",NA,decreased,NA,decreased,NA,decreased,Signature 2,Figure 3(a),10 January 2021,Victoria Goulbourne,"WikiWorks,Atrayees",The result of comparison of bacterial abundance at the genus level,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella",1783272|1239|186801|186802|186807|2740;3379134|976|117743|200644|49546|1016;3379134|1224|28216|206351|481|482;3379134|1224|1236|135615|868|2717;3379134|1224|28216|80840|119060|47670;1783272|1239|186801|3082720|186804|1257;1783272|1239|186801|3085636|186803|43996;3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|171551|836;1783272|1239|186801|3085636|186803|1164882;3384189|32066|203490|203491|1129771|32067;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|186802|186806|1730;3379134|29547|3031852|213849|72294|194;1783272|1239|526524|526525|128827|123375;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|1213720;1783272|1239|91061|1385|539738|1378,Complete,Atrayees
bsdb:32353108/1/1,32353108,case-control,32353108,10.1182/bloodadvances.2020001531,NA,"Payen M., Nicolis I., Robin M., Michonneau D., Delannoye J., Mayeur C., Kapel N., Berçot B., Butel M.J., Le Goff J., Socié G. , Rousseau C.",Functional and phylogenetic alterations in gut microbiome are linked to graft-versus-host disease severity,Blood advances,2020,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Graft versus host disease,MONDO:0013730,controls,Severe acute graft-versus-host-disease,patients who are diagnosed with severe gut acute graft- versus-host disease (between standard stage greater or equal to 2 and less than or equal to 4),35,35,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,NA,decreased,decreased,NA,decreased,Signature 1,Figure 2B,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential relative abundance between controls and severe acute graft-versus- host disease patients.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.",1783272|1239|91061|186826|1300|1357;3379134|1224|28216|80840|119060|47670;3379134|1224|1236|135614|32033|40323;3379134|1224|1236|135614|32033;3379134|1224|1236|135614;3379134|976|200643|171549|171552|838|59823,Complete,Claregrieve1
bsdb:32353108/1/2,32353108,case-control,32353108,10.1182/bloodadvances.2020001531,NA,"Payen M., Nicolis I., Robin M., Michonneau D., Delannoye J., Mayeur C., Kapel N., Berçot B., Butel M.J., Le Goff J., Socié G. , Rousseau C.",Functional and phylogenetic alterations in gut microbiome are linked to graft-versus-host disease severity,Blood advances,2020,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Graft versus host disease,MONDO:0013730,controls,Severe acute graft-versus-host-disease,patients who are diagnosed with severe gut acute graft- versus-host disease (between standard stage greater or equal to 2 and less than or equal to 4),35,35,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,NA,decreased,decreased,NA,decreased,Signature 2,Figure 2B,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential relative abundance between controls and severe acute graft-versus- host disease patients.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas",3379134|1224|28211;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801;1783272|1239|526524|526525|2810280|1505663;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|946234;1783272|1239|91061|1385|539738|1378;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|541000;3379134|1224|28211|204441;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3085636|186803|1769710,Complete,Claregrieve1
bsdb:32353108/2/1,32353108,case-control,32353108,10.1182/bloodadvances.2020001531,NA,"Payen M., Nicolis I., Robin M., Michonneau D., Delannoye J., Mayeur C., Kapel N., Berçot B., Butel M.J., Le Goff J., Socié G. , Rousseau C.",Functional and phylogenetic alterations in gut microbiome are linked to graft-versus-host disease severity,Blood advances,2020,NA,Experiment 2,France,Homo sapiens,Feces,UBERON:0001988,Graft versus host disease,MONDO:0013730,controls,Severe acute graft-versus-host-disease,patients who are diagnosed with severe gut acute graft- versus-host disease (between standard stage greater or equal to 2 and less than or equal to 3),35,35,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,decreased,decreased,NA,decreased,Signature 1,Figure 2C,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential relative abundance between controls and severe acute graft-versus-host disease patients.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|1224|1236|135614|32033|40323;3379134|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:32353108/2/2,32353108,case-control,32353108,10.1182/bloodadvances.2020001531,NA,"Payen M., Nicolis I., Robin M., Michonneau D., Delannoye J., Mayeur C., Kapel N., Berçot B., Butel M.J., Le Goff J., Socié G. , Rousseau C.",Functional and phylogenetic alterations in gut microbiome are linked to graft-versus-host disease severity,Blood advances,2020,NA,Experiment 2,France,Homo sapiens,Feces,UBERON:0001988,Graft versus host disease,MONDO:0013730,controls,Severe acute graft-versus-host-disease,patients who are diagnosed with severe gut acute graft- versus-host disease (between standard stage greater or equal to 2 and less than or equal to 3),35,35,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,decreased,decreased,NA,decreased,Signature 2,Figure 2C,10 January 2021,William Lam,"Claregrieve1,WikiWorks",Differential relative abundance between controls and severe acute graft-versus- host disease patients.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|3085636|186803|572511;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|186801|186802|216572|216851|1946507;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|1769710;1783272|1239|186801|186802|541000,Complete,Claregrieve1
bsdb:32370168/1/1,32370168,case-control,32370168,10.3390/cancers12051142,NA,"Clos-Garcia M., Garcia K., Alonso C., Iruarrizaga-Lejarreta M., D'Amato M., Crespo A., Iglesias A., Cubiella J., Bujanda L. , Falcón-Pérez J.M.",Integrative Analysis of Fecal Metagenomics and Metabolomics in Colorectal Cancer,Cancers,2020,"integration, metabolomics, microbiome, multiomics, omics, omics integration",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy controls,CRC patients,patients with gastrointestinal symptoms referred for colonoscopy,77,89,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4B,2 January 2022,Itslanapark,"Itslanapark,WikiWorks",Difference analysis at genus level between Colorectal Cancer patients and Healthy Controls.,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",3384189|32066|203490|203491|203492|848;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|91061|1385|90964|1279,Complete,Rimsha
bsdb:32370168/1/2,32370168,case-control,32370168,10.3390/cancers12051142,NA,"Clos-Garcia M., Garcia K., Alonso C., Iruarrizaga-Lejarreta M., D'Amato M., Crespo A., Iglesias A., Cubiella J., Bujanda L. , Falcón-Pérez J.M.",Integrative Analysis of Fecal Metagenomics and Metabolomics in Colorectal Cancer,Cancers,2020,"integration, metabolomics, microbiome, multiomics, omics, omics integration",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy controls,CRC patients,patients with gastrointestinal symptoms referred for colonoscopy,77,89,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4B,2 January 2022,Itslanapark,"Itslanapark,WikiWorks",Difference analysis at genus level between Colorectal Cancer patients and Healthy Controls.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|33042;1783272|1239|91061|186826|1300|1301,Complete,Rimsha
bsdb:32370168/2/1,32370168,case-control,32370168,10.3390/cancers12051142,NA,"Clos-Garcia M., Garcia K., Alonso C., Iruarrizaga-Lejarreta M., D'Amato M., Crespo A., Iglesias A., Cubiella J., Bujanda L. , Falcón-Pérez J.M.",Integrative Analysis of Fecal Metagenomics and Metabolomics in Colorectal Cancer,Cancers,2020,"integration, metabolomics, microbiome, multiomics, omics, omics integration",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,adenoma patients,CRC patients,patients with gastrointestinal symptoms referred for colonoscopy,65,89,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4C,15 May 2022,Rimsha,"Rimsha,WikiWorks",Difference analysis at genus level between Colorectal Cancer patients and adenoma patients.,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|1239|1737404|1737405|1570339|543311;1783272|1239|91061|1385|90964|1279,Complete,Rimsha
bsdb:32370168/2/2,32370168,case-control,32370168,10.3390/cancers12051142,NA,"Clos-Garcia M., Garcia K., Alonso C., Iruarrizaga-Lejarreta M., D'Amato M., Crespo A., Iglesias A., Cubiella J., Bujanda L. , Falcón-Pérez J.M.",Integrative Analysis of Fecal Metagenomics and Metabolomics in Colorectal Cancer,Cancers,2020,"integration, metabolomics, microbiome, multiomics, omics, omics integration",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,adenoma patients,CRC patients,patients with gastrointestinal symptoms referred for colonoscopy,65,89,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4C,15 May 2022,Rimsha,"Rimsha,WikiWorks",Difference analysis at genus level between Colorectal Cancer patients and adenoma patients.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia",1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|572511;1783272|201174|84998|1643822|1643826|447020,Complete,Rimsha
bsdb:32380969/1/1,32380969,time series / longitudinal observational,32380969,10.1186/s12887-020-02067-z,NA,"Zwittink R.D., van Zoeren-Grobben D., Renes I.B., van Lingen R.A., Norbruis O.F., Martin R., Groot Jebbink L.J., Knol J. , Belzer C.",Dynamics of the bacterial gut microbiota in preterm and term infants after intravenous amoxicillin/ceftazidime treatment,BMC pediatrics,2020,"Antibiotics, Gut microbiota, Infant, Next generation sequencing, Preterm",Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control (no treatment) - week 1,infants who received short-term or long-term antibiotic treatment - week 1,infants born between 32-42 weeks of gestation and admitted to the hospital (level III neonatal intensive care or level II neonatal ward) who received short-term antibiotics (<3 days) or longterm antibiotics (>5 days),28,35,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Text,10 January 2021,Mst Afroza Parvin,WikiWorks,"Differences in gut microbiota composition between infants receiving no, short or long antibiotic treatment",increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Claregrieve1
bsdb:32380969/1/2,32380969,time series / longitudinal observational,32380969,10.1186/s12887-020-02067-z,NA,"Zwittink R.D., van Zoeren-Grobben D., Renes I.B., van Lingen R.A., Norbruis O.F., Martin R., Groot Jebbink L.J., Knol J. , Belzer C.",Dynamics of the bacterial gut microbiota in preterm and term infants after intravenous amoxicillin/ceftazidime treatment,BMC pediatrics,2020,"Antibiotics, Gut microbiota, Infant, Next generation sequencing, Preterm",Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control (no treatment) - week 1,infants who received short-term or long-term antibiotic treatment - week 1,infants born between 32-42 weeks of gestation and admitted to the hospital (level III neonatal intensive care or level II neonatal ward) who received short-term antibiotics (<3 days) or longterm antibiotics (>5 days),28,35,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Text,10 January 2021,Mst Afroza Parvin,WikiWorks,"Differences in gut microbiota composition between infants receiving no, short or long antibiotic treatment",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|1224|1236|91347|543|561;1783272|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:32380969/2/1,32380969,time series / longitudinal observational,32380969,10.1186/s12887-020-02067-z,NA,"Zwittink R.D., van Zoeren-Grobben D., Renes I.B., van Lingen R.A., Norbruis O.F., Martin R., Groot Jebbink L.J., Knol J. , Belzer C.",Dynamics of the bacterial gut microbiota in preterm and term infants after intravenous amoxicillin/ceftazidime treatment,BMC pediatrics,2020,"Antibiotics, Gut microbiota, Infant, Next generation sequencing, Preterm",Experiment 2,Netherlands,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control(no treatment) - week 2,infants received long-term(>5days) antibiotic treatment - week 2,"infants born between 32-42 weeks of gestation and admitted to the hospital (level III neonatal intensive care or level II neonatal ward) who received >5 days antibiotics, week 2 timepoint",28,13,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Text,10 January 2021,Mst Afroza Parvin,"WikiWorks,Claregrieve1","Differences in gut microbiota composition between infants receiving no, short or long antibiotic treatment",increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,1783272|1239|91061|186826|81852|1350,Complete,Claregrieve1
bsdb:32380969/3/1,32380969,time series / longitudinal observational,32380969,10.1186/s12887-020-02067-z,NA,"Zwittink R.D., van Zoeren-Grobben D., Renes I.B., van Lingen R.A., Norbruis O.F., Martin R., Groot Jebbink L.J., Knol J. , Belzer C.",Dynamics of the bacterial gut microbiota in preterm and term infants after intravenous amoxicillin/ceftazidime treatment,BMC pediatrics,2020,"Antibiotics, Gut microbiota, Infant, Next generation sequencing, Preterm",Experiment 3,Netherlands,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants received short-term (<3days) antibiotic treatment - week 1,infants received long-term (>5days) antibiotic treatment - week 1,"infants born between 32-42 weeks of gestation and admitted to the hospital (level III neonatal intensive care or level II neonatal ward) who received longterm (>5 days) antibiotics, first post-natal week timepoint",22,13,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Text,24 May 2023,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between infants who received short-term and long-term antibiotics,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,1783272|1239|186801|186802|31979|1485|1506,Complete,Claregrieve1
bsdb:32380969/3/2,32380969,time series / longitudinal observational,32380969,10.1186/s12887-020-02067-z,NA,"Zwittink R.D., van Zoeren-Grobben D., Renes I.B., van Lingen R.A., Norbruis O.F., Martin R., Groot Jebbink L.J., Knol J. , Belzer C.",Dynamics of the bacterial gut microbiota in preterm and term infants after intravenous amoxicillin/ceftazidime treatment,BMC pediatrics,2020,"Antibiotics, Gut microbiota, Infant, Next generation sequencing, Preterm",Experiment 3,Netherlands,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,infants received short-term (<3days) antibiotic treatment - week 1,infants received long-term (>5days) antibiotic treatment - week 1,"infants born between 32-42 weeks of gestation and admitted to the hospital (level III neonatal intensive care or level II neonatal ward) who received longterm (>5 days) antibiotics, first post-natal week timepoint",22,13,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Text,24 May 2023,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between infants who received short-term and long-term antibiotics,increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,1783272|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:32381601/1/1,32381601,case-control,32381601,10.1681/ASN.2019101131,https://jasn.asnjournals.org/content/31/6/1358.abstract,"Denburg M.R., Koepsell K., Lee J.J., Gerber J., Bittinger K. , Tasian G.E.",Perturbations of the Gut Microbiome and Metabolome in Children with Calcium Oxalate Kidney Stone Disease,Journal of the American Society of Nephrology : JASN,2020,"intestine, kidney stones, metabolism, pediatric nephrology",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Nephrolithiasis,EFO:0004253,Healthy Controls,Patients with kidney stones,The patients suffering from Kidney Stones (nephrolithiasis) are individuals with incident and recurrent kidney stones consisting of 100% calcium (of which at least 50% was calcium oxalate) that spontaneously passed or were removed surgically within the prior 3 years.,44,44,3 months,WMS,NA,Illumina,relative abundances,T-Test,0.05,TRUE,NA,"age,race,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 1,figure 1,26 March 2023,Blessing Kaz,"Blessing Kaz,Aiyshaaaa,Atrayees,WikiWorks",The relative abundance of bacterial taxa among participants with kidney stone disease.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea|s__Faecalitalea cylindroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus champanellensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens|s__Ethanoligenens harbinense,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium limosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus albus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio proteoclasticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus suis,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema succinifaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Mageeibacillus|s__Mageeibacillus indolicus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Nitratidesulfovibrio|s__Nitratidesulfovibrio vulgaris,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pyogenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium botulinum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio desulfuricans,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia heliotrinireducens,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter jejuni,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis",1783272|1239|186801|3085636|186803|841|301301;1783272|1239|526524|526525|128827|1573534|39483;1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|459786|351091;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|1263|1161942;1783272|1239|91061|186826|81852|1350|1352;1783272|1239|186801|186802|216572|253238|253239;1783272|1239|186801|186802|186806|1730|1736;1783272|1239|186801|186802|216572|1263|1264;1783272|1239|186801|3085636|186803|830|43305;1783272|1239|91061|186826|1300|1301|1307;3379134|203691|203692|136|2845253|157|167;1783272|1239|186801|186802|216572|1637257|884684;3379134|200940|3031449|213115|194924|2802295|881;1783272|1239|91061|186826|1300|1301|1314;1783272|1239|186801|186802|31979|1485|1491;3379134|200940|3031449|213115|194924|872|876;1783272|201174|84998|1643822|1643826|84108|84110;3379134|29547|3031852|213849|72294|194|197;1783272|1239|91061|186826|81852|1350|1351;3379134|29547|3031852|213849|72294|194|195;1783272|1239|186801|186802|31979|1485|1502;1783272|201174|1760|85004|31953|1678|28025,Complete,Atrayees
bsdb:32401750/1/1,32401750,case-control,32401750,10.1371/journal.pntd.0008230,NA,"Namasivayam S., Diarra B., Diabate S., Sarro Y.D.S., Kone A., Kone B., Tolofoudie M., Baya B., Diakite M.T., Kodio O., Cohen K., Holl J., Achenbach C.J., Chatterjee S., Murphy R.L., Bishai W., Diallo S., Sher A. , Maiga M.",Patients infected with Mycobacterium africanum versus Mycobacterium tuberculosis possess distinct intestinal microbiota,PLoS neglected tropical diseases,2020,NA,Experiment 1,Mali,Homo sapiens,"Sputum,Feces","UBERON:0007311,UBERON:0001988",Pulmonary tuberculosis,EFO:1000049,Mycobacterium africanum (MAF),Mycobacterium tuberculosis (MTB),composed of newly infected active pulmonary tuberculosis patients defined by positive sputum culture,20,21,NA,16S,1234,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 2A-C,2 August 2025,Nuerteye,Nuerteye,"Alterations in the composition of the intestinal microbiome of MAF- and MTB-infected patients at the time of diagnosis. a. Relative abundances of the five most prominent phyla are compared between the three groups.  b-c. LEfSe analyses were performed to identify differentially abundant families in the two infection groups, MAF and MTB, compared to the healthy participants (b) and between the two infection groups (c). Taxa are filtered for p < 0.05 and linear discriminant analysis (LDA) score > 2.",increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Puniceicoccaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Heliobacteriaceae",3384189|32066|203490|203491|203492;3379134|74201|414999|415001|415002;1783272|1239|186801|186802|31984,Complete,NA
bsdb:32401750/1/2,32401750,case-control,32401750,10.1371/journal.pntd.0008230,NA,"Namasivayam S., Diarra B., Diabate S., Sarro Y.D.S., Kone A., Kone B., Tolofoudie M., Baya B., Diakite M.T., Kodio O., Cohen K., Holl J., Achenbach C.J., Chatterjee S., Murphy R.L., Bishai W., Diallo S., Sher A. , Maiga M.",Patients infected with Mycobacterium africanum versus Mycobacterium tuberculosis possess distinct intestinal microbiota,PLoS neglected tropical diseases,2020,NA,Experiment 1,Mali,Homo sapiens,"Sputum,Feces","UBERON:0007311,UBERON:0001988",Pulmonary tuberculosis,EFO:1000049,Mycobacterium africanum (MAF),Mycobacterium tuberculosis (MTB),composed of newly infected active pulmonary tuberculosis patients defined by positive sputum culture,20,21,NA,16S,1234,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 2A-C,2 August 2025,Nuerteye,Nuerteye,"Alterations in the composition of the intestinal microbiome of MAF- and MTB-infected patients at the time of diagnosis. a. Relative abundances of the five most prominent phyla are compared between the three groups.  b-c. LEfSe analyses were performed to identify differentially abundant families in the two infection groups, MAF and MTB, compared to the healthy participants (b) and between the two infection groups (c). Taxa are filtered for p < 0.05 and linear discriminant analysis (LDA) score > 2.",decreased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,1783272|201174|84998|84999|84107,Complete,NA
bsdb:32401750/2/1,32401750,case-control,32401750,10.1371/journal.pntd.0008230,NA,"Namasivayam S., Diarra B., Diabate S., Sarro Y.D.S., Kone A., Kone B., Tolofoudie M., Baya B., Diakite M.T., Kodio O., Cohen K., Holl J., Achenbach C.J., Chatterjee S., Murphy R.L., Bishai W., Diallo S., Sher A. , Maiga M.",Patients infected with Mycobacterium africanum versus Mycobacterium tuberculosis possess distinct intestinal microbiota,PLoS neglected tropical diseases,2020,NA,Experiment 2,Mali,Homo sapiens,"Sputum,Feces","UBERON:0007311,UBERON:0001988",Pulmonary tuberculosis,EFO:1000049,Healthy controls,Mycobacterium tuberculosis (MTB),composed of newly infected active pulmonary tuberculosis patients defined by positive sputum culture,10,21,NA,16S,1234,Illumina,NA,LEfSe,0.05,NA,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 2A-C,2 August 2025,Nuerteye,Nuerteye,"Alterations in the composition of the intestinal microbiome of MAF- and MTB-infected patients at the time of diagnosis. a. Relative abundances of the five most prominent phyla are compared between the three groups. b-c. LEfSe analyses were performed to identify differentially abundant families in the two infection groups, MAF and MTB, compared to the healthy participants (b) and between the two infection groups (c). Taxa are filtered for p < 0.05 and linear discriminant analysis (LDA) score > 2.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",3379134|976|200643|171549|171552;3379134|976|200643|171549|2005473;1783272|1239|909932|1843489|31977;3379134|1224|1236|135624|83763;1783272|1239|186801|186802|31979,Complete,NA
bsdb:32401750/3/1,32401750,case-control,32401750,10.1371/journal.pntd.0008230,NA,"Namasivayam S., Diarra B., Diabate S., Sarro Y.D.S., Kone A., Kone B., Tolofoudie M., Baya B., Diakite M.T., Kodio O., Cohen K., Holl J., Achenbach C.J., Chatterjee S., Murphy R.L., Bishai W., Diallo S., Sher A. , Maiga M.",Patients infected with Mycobacterium africanum versus Mycobacterium tuberculosis possess distinct intestinal microbiota,PLoS neglected tropical diseases,2020,NA,Experiment 3,Mali,Homo sapiens,"Sputum,Feces","UBERON:0007311,UBERON:0001988",Pulmonary tuberculosis,EFO:1000049,Healthy controls,Mycobacterium africanum (MAF),consist of active pulmonary tuberculosis patients defined by positive sputum culture who received anti tuberculosis treatment (ATT) two months after.,10,20,NA,16S,1234,Illumina,NA,LEfSe,0.05,NA,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 2A-C,2 August 2025,Nuerteye,Nuerteye,"Alterations in the composition of the intestinal microbiome of MAF- and MTB-infected patients at the time of diagnosis. a. Relative abundances of the five most prominent phyla are compared between the three groups. b-c. LEfSe analyses were performed to identify differentially abundant families in the two infection groups, MAF and MTB, compared to the healthy participants (b) and between the two infection groups (c). Taxa are filtered for p < 0.05 and linear discriminant analysis (LDA) score > 2.",increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,NA
bsdb:32401750/4/1,32401750,case-control,32401750,10.1371/journal.pntd.0008230,NA,"Namasivayam S., Diarra B., Diabate S., Sarro Y.D.S., Kone A., Kone B., Tolofoudie M., Baya B., Diakite M.T., Kodio O., Cohen K., Holl J., Achenbach C.J., Chatterjee S., Murphy R.L., Bishai W., Diallo S., Sher A. , Maiga M.",Patients infected with Mycobacterium africanum versus Mycobacterium tuberculosis possess distinct intestinal microbiota,PLoS neglected tropical diseases,2020,NA,Experiment 4,Mali,Homo sapiens,"Sputum,Feces","UBERON:0007311,UBERON:0001988",Pulmonary tuberculosis,EFO:1000049,Mycobacterium africanum plus anti tuberculosis treatment (MAF+HRZE),Mycobacterium tuberculosis plus anti tuberculosis treatment (MTB+HRZE),composed of newly infected active pulmonary tuberculosis patients defined by positive sputum culture who received anti tuberculosis treatment for the first two months.,20,21,NA,16S,1234,Illumina,NA,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3C,6 August 2025,Nuerteye,Nuerteye,Perturbation in the intestinal microbiome composition due to HRZE treatment in both MAF and MTB infection.  c. Pairwise LEfSe comparisons were performed between the three groups to identify differentially abundant families. Taxa are filtered for p <0.05 and LDA score > 2.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",1783272|201174|1760|85004|31953;1783272|1239|91061|186826|1300;1783272|201174|84998|84999|84107,Complete,NA
bsdb:32401750/5/1,32401750,case-control,32401750,10.1371/journal.pntd.0008230,NA,"Namasivayam S., Diarra B., Diabate S., Sarro Y.D.S., Kone A., Kone B., Tolofoudie M., Baya B., Diakite M.T., Kodio O., Cohen K., Holl J., Achenbach C.J., Chatterjee S., Murphy R.L., Bishai W., Diallo S., Sher A. , Maiga M.",Patients infected with Mycobacterium africanum versus Mycobacterium tuberculosis possess distinct intestinal microbiota,PLoS neglected tropical diseases,2020,NA,Experiment 5,Mali,Homo sapiens,"Sputum,Feces","UBERON:0007311,UBERON:0001988",Pulmonary tuberculosis,EFO:1000049,Healthy controls,Mycobacterium africanum plus anti tuberculosis treatment (MAF+HRZE),composed of newly infected active pulmonary tuberculosis patients defined by positive sputum culture who received HRZE treatment,10,20,NA,16S,1234,Illumina,NA,LEfSe,0.05,NA,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3C,6 August 2025,Nuerteye,Nuerteye,"Perturbation in the intestinal microbiome composition due to HRZE treatment in both MAF and MTB infection. c. Pairwise LEfSe comparisons
were performed between the three groups to identify differentially abundant families. Taxa are filtered for p <0.05 and LDA score > 2.",increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,1783272|1239|186801|3082720|186804,Complete,NA
bsdb:32401750/5/2,32401750,case-control,32401750,10.1371/journal.pntd.0008230,NA,"Namasivayam S., Diarra B., Diabate S., Sarro Y.D.S., Kone A., Kone B., Tolofoudie M., Baya B., Diakite M.T., Kodio O., Cohen K., Holl J., Achenbach C.J., Chatterjee S., Murphy R.L., Bishai W., Diallo S., Sher A. , Maiga M.",Patients infected with Mycobacterium africanum versus Mycobacterium tuberculosis possess distinct intestinal microbiota,PLoS neglected tropical diseases,2020,NA,Experiment 5,Mali,Homo sapiens,"Sputum,Feces","UBERON:0007311,UBERON:0001988",Pulmonary tuberculosis,EFO:1000049,Healthy controls,Mycobacterium africanum plus anti tuberculosis treatment (MAF+HRZE),composed of newly infected active pulmonary tuberculosis patients defined by positive sputum culture who received HRZE treatment,10,20,NA,16S,1234,Illumina,NA,LEfSe,0.05,NA,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 3C,6 August 2025,Nuerteye,Nuerteye,"Perturbation in the intestinal microbiome composition due to HRZE treatment in both MAF and MTB infection. c. Pairwise LEfSe comparisons
were performed between the three groups to identify differentially abundant families. Taxa are filtered for p <0.05 and LDA score > 2.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae",3379134|976|200643|171549|2005473;1783272|1239|186801|186802|186807;3379134|976|200643|171549|171550;3379134|1224|1236|135624|83763;1783272|1239|186801|3082768|990719;1783272|201174|1760|2037|2049;3379134|200940|3031449|213115|194924;3379134|1224|28216|80840|119060;1783272|201174|84998|1643822|1643826;3379134|74201|203494|48461|1647988;1783272|1239|186801|3085636|1185407,Complete,NA
bsdb:32401750/6/1,32401750,case-control,32401750,10.1371/journal.pntd.0008230,NA,"Namasivayam S., Diarra B., Diabate S., Sarro Y.D.S., Kone A., Kone B., Tolofoudie M., Baya B., Diakite M.T., Kodio O., Cohen K., Holl J., Achenbach C.J., Chatterjee S., Murphy R.L., Bishai W., Diallo S., Sher A. , Maiga M.",Patients infected with Mycobacterium africanum versus Mycobacterium tuberculosis possess distinct intestinal microbiota,PLoS neglected tropical diseases,2020,NA,Experiment 6,Mali,Homo sapiens,"Sputum,Feces","UBERON:0007311,UBERON:0001988",Pulmonary tuberculosis,EFO:1000049,Healthy controls,Mycobacterium tuberculosis plus anti tuberculosis treatment (MAF+HRZE)),consist of active pulmonary tuberculosis patients defined by positive sputum culture who received anti tuberculosis treatment (ATT) two months after.,10,21,NA,16S,1234,Illumina,NA,LEfSe,0.05,NA,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3C,6 August 2025,Nuerteye,Nuerteye,"Perturbation in the intestinal microbiome composition due to HRZE treatment in both MAF and MTB infection. c. Pairwise LEfSe comparisons
were performed between the three groups to identify differentially abundant families. Taxa are filtered for p <0.05 and LDA score > 2.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae",3379134|976|200643|171549|2005473;3379134|976|200643|171549|171550;3379134|1224|1236|135624|83763;1783272|1239|186801|3082768|990719;3379134|200940|3031449|213115|194924;3379134|74152|641853|641854|641876;1783272|1239|186801|186802|186807;3379134|976|200643|1970189|1573805,Complete,NA
bsdb:32415070/1/1,32415070,case-control,32415070,10.1038/s41467-020-16222-8,NA,"Vujkovic-Cvijin I., Sortino O., Verheij E., Sklar J., Wit F.W., Kootstra N.A., Sellers B., Brenchley J.M., Ananworanich J., Loeff M.S.V., Belkaid Y., Reiss P. , Sereti I.",HIV-associated gut dysbiosis is independent of sexual practice and correlates with noncommunicable diseases,Nature communications,2020,NA,Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV-seronegative controls,Persons with HIV (PWH),chronically HIV-infected people with suppressed viremia on antiretroviral therapy (ART),80,80,NA,16S,4,Illumina,NA,NA,0.05,TRUE,NA,"age,birth country,body mass index,sex,sexual preference",NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Supplementary Table 4,1 January 2023,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between seronegative controls and persons with HIV,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Gracilibacteraceae|g__Gracilibacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter",1783272|1239|186801|186802|541019|342658;1783272|201174|84998|1643822|1643826|84108|572010;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|1898207;1783272|1239|186801|186802|31979|1485|1506;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|216572|44748,Complete,Claregrieve1
bsdb:32415070/1/2,32415070,case-control,32415070,10.1038/s41467-020-16222-8,NA,"Vujkovic-Cvijin I., Sortino O., Verheij E., Sklar J., Wit F.W., Kootstra N.A., Sellers B., Brenchley J.M., Ananworanich J., Loeff M.S.V., Belkaid Y., Reiss P. , Sereti I.",HIV-associated gut dysbiosis is independent of sexual practice and correlates with noncommunicable diseases,Nature communications,2020,NA,Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV-seronegative controls,Persons with HIV (PWH),chronically HIV-infected people with suppressed viremia on antiretroviral therapy (ART),80,80,NA,16S,4,Illumina,NA,NA,0.05,TRUE,NA,"age,birth country,body mass index,sex,sexual preference",NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Supplementary Table 4,6 January 2023,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between seronegative controls and persons with HIV,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia",1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|186802|31979|1485;3379134|200940|3031449|213115|194924|35832|35833,Complete,Claregrieve1
bsdb:32425919/1/1,32425919,laboratory experiment,32425919,10.3389/fmicb.2020.00814,NA,"Xu X., Lv J., Guo F., Li J., Jia Y., Jiang D., Wang N., Zhang C., Kong L., Liu Y., Zhang Y., Lv J. , Li Z.",Gut Microbiome Influences the Efficacy of PD-1 Antibody Immunotherapy on MSS-Type Colorectal Cancer via Metabolic Pathway,Frontiers in microbiology,2020,"MSS-type CRC, PD-1 antibody, gut microbiota, immunotherapy, metabolic pathway",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control,Coli,Group 1 mice were treated with colistin (2 mg/ml) in sterile drinking water (Coli group).  Mice (in all groups) were then subcutaneously injected into the right axillary with 0.25 live CT26 tumor cells.,13,14,NA,16S,4,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,supp fig 1B,17 September 2022,Mary Bearkland,"Mary Bearkland,Atrayees,WikiWorks",Supplementary Figure 1.Compositional differences in the gut microbiome are associated with responses to PD-1 antibody immunotherapy  (B) Bar plot of compositional differences at genus level in the gut microbiome of three groups of mice by one-way ANOVA.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|1508657;3379134|976|200643|171549|2005525|375288;1783272|1239|526524|526525|128827,Complete,Atrayees
bsdb:32425919/1/2,32425919,laboratory experiment,32425919,10.3389/fmicb.2020.00814,NA,"Xu X., Lv J., Guo F., Li J., Jia Y., Jiang D., Wang N., Zhang C., Kong L., Liu Y., Zhang Y., Lv J. , Li Z.",Gut Microbiome Influences the Efficacy of PD-1 Antibody Immunotherapy on MSS-Type Colorectal Cancer via Metabolic Pathway,Frontiers in microbiology,2020,"MSS-type CRC, PD-1 antibody, gut microbiota, immunotherapy, metabolic pathway",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control,Coli,Group 1 mice were treated with colistin (2 mg/ml) in sterile drinking water (Coli group).  Mice (in all groups) were then subcutaneously injected into the right axillary with 0.25 live CT26 tumor cells.,13,14,NA,16S,4,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,supp fig 1B,17 September 2022,Mary Bearkland,"Mary Bearkland,Atrayees,WikiWorks",Supplementary Figure 1.Compositional differences in the gut microbiome are associated with responses to PD-1 antibody immunotherapy  (B) Bar plot of compositional differences at genus level in the gut microbiome of three groups of mice by one-way ANOVA.,decreased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",3379134|200940|3031449|213115|194924|872;1783272|1239|186801|3085636|186803;3379134|976|200643|171549;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|186802,Complete,Atrayees
bsdb:32425919/2/1,32425919,laboratory experiment,32425919,10.3389/fmicb.2020.00814,NA,"Xu X., Lv J., Guo F., Li J., Jia Y., Jiang D., Wang N., Zhang C., Kong L., Liu Y., Zhang Y., Lv J. , Li Z.",Gut Microbiome Influences the Efficacy of PD-1 Antibody Immunotherapy on MSS-Type Colorectal Cancer via Metabolic Pathway,Frontiers in microbiology,2020,"MSS-type CRC, PD-1 antibody, gut microbiota, immunotherapy, metabolic pathway",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control,Vanc,"Group 1 mice were treated with vancomycin alone (0.25 mg/ml) in sterile drinking
water (Vanc group).  Mice (in all groups) were then subcutaneously injected into the right axillary with 0.25 live CT26 tumor cells.",13,14,NA,16S,4,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,supp fig 1B,17 September 2022,Mary Bearkland,"Mary Bearkland,Merit,Atrayees,WikiWorks",Supplementary Figure 1(B) Bar plot of compositional differences at genus level in the gut microbiome of three groups of mice by one-way ANOVA.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",3379134|74201|203494|48461|1647988|239934;3379134|1224|1236|91347|543|1940338;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|171552;1783272|1239|186801|3085636|186803|841;3379134|1224|1236|91347|543;1783272|1239|91061|186826;1783272|1239|186801|186802,Complete,Atrayees
bsdb:32425919/2/2,32425919,laboratory experiment,32425919,10.3389/fmicb.2020.00814,NA,"Xu X., Lv J., Guo F., Li J., Jia Y., Jiang D., Wang N., Zhang C., Kong L., Liu Y., Zhang Y., Lv J. , Li Z.",Gut Microbiome Influences the Efficacy of PD-1 Antibody Immunotherapy on MSS-Type Colorectal Cancer via Metabolic Pathway,Frontiers in microbiology,2020,"MSS-type CRC, PD-1 antibody, gut microbiota, immunotherapy, metabolic pathway",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control,Vanc,"Group 1 mice were treated with vancomycin alone (0.25 mg/ml) in sterile drinking
water (Vanc group).  Mice (in all groups) were then subcutaneously injected into the right axillary with 0.25 live CT26 tumor cells.",13,14,NA,16S,4,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,supp fig 1B,17 September 2022,Mary Bearkland,"Mary Bearkland,Atrayees,WikiWorks",Supplementary Figure 1(B) Bar plot of compositional differences at genus level in the gut microbiome of three groups of mice by one-way ANOVA.,decreased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",3379134|200940|3031449|213115|194924|872;1783272|1239|186801|3085636|186803;3379134|976|200643|171549;1783272|1239|526524|526525|128827,Complete,Atrayees
bsdb:32425919/3/1,32425919,laboratory experiment,32425919,10.3389/fmicb.2020.00814,NA,"Xu X., Lv J., Guo F., Li J., Jia Y., Jiang D., Wang N., Zhang C., Kong L., Liu Y., Zhang Y., Lv J. , Li Z.",Gut Microbiome Influences the Efficacy of PD-1 Antibody Immunotherapy on MSS-Type Colorectal Cancer via Metabolic Pathway,Frontiers in microbiology,2020,"MSS-type CRC, PD-1 antibody, gut microbiota, immunotherapy, metabolic pathway",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Coli,Vanc,"Group 1 mice were treated with vancomycin alone (0.25 mg/ml) in sterile drinking
water (Vanc group).  Mice (in all groups) were then subcutaneously injected into the right axillary with 0.25 live CT26 tumor cells.",14,14,NA,16S,4,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,supp fig 1B,18 September 2022,Mary Bearkland,"Mary Bearkland,Merit,Atrayees,WikiWorks",Supplementary Figure 1 (B) Bar plot of compositional differences at genus level in the gut microbiome of three groups of mice by one-way ANOVA.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",3379134|74201|203494|48461|1647988|239934;3379134|1224|1236|91347|543|1940338;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|171552;1783272|1239|186801|3085636|186803|841;3379134|1224|1236|91347|543;1783272|1239|186801|186802|216572|1508657,Complete,Atrayees
bsdb:32425919/3/2,32425919,laboratory experiment,32425919,10.3389/fmicb.2020.00814,NA,"Xu X., Lv J., Guo F., Li J., Jia Y., Jiang D., Wang N., Zhang C., Kong L., Liu Y., Zhang Y., Lv J. , Li Z.",Gut Microbiome Influences the Efficacy of PD-1 Antibody Immunotherapy on MSS-Type Colorectal Cancer via Metabolic Pathway,Frontiers in microbiology,2020,"MSS-type CRC, PD-1 antibody, gut microbiota, immunotherapy, metabolic pathway",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Coli,Vanc,"Group 1 mice were treated with vancomycin alone (0.25 mg/ml) in sterile drinking
water (Vanc group).  Mice (in all groups) were then subcutaneously injected into the right axillary with 0.25 live CT26 tumor cells.",14,14,NA,16S,4,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 2,supp fig 1B,18 September 2022,Mary Bearkland,"Mary Bearkland,Atrayees,WikiWorks",Supplementary Figure 1 (B) Bar plot of compositional differences at genus level in the gut microbiome of three groups of mice by one-way ANOVA.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|976|200643|171549|815|816;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|216572|1508657;3379134|200940|3031449|213115|194924|872;3379134|976|200643|171549;1783272|1239|186801|3085636|186803,Complete,Atrayees
bsdb:32425919/4/1,32425919,laboratory experiment,32425919,10.3389/fmicb.2020.00814,NA,"Xu X., Lv J., Guo F., Li J., Jia Y., Jiang D., Wang N., Zhang C., Kong L., Liu Y., Zhang Y., Lv J. , Li Z.",Gut Microbiome Influences the Efficacy of PD-1 Antibody Immunotherapy on MSS-Type Colorectal Cancer via Metabolic Pathway,Frontiers in microbiology,2020,"MSS-type CRC, PD-1 antibody, gut microbiota, immunotherapy, metabolic pathway",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control,Coli,Group 1 mice were treated with colistin (2 mg/ml) in sterile drinking water (Coli group).  Mice (in all groups) were then subcutaneously injected into the right axillary with 0.25 live CT26 tumor cells.,6,7,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,supp fig 2,18 September 2022,Mary Bearkland,"Mary Bearkland,WikiWorks",Bar plot of compositional differences at species level in the Control vs. Coli,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|s__Bacteroidaceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,s__uncultured prokaryote",3379134|976|200643|171549|815|2212467;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|371601;3379134|976|200643|171549|2005525|375288|1869337;3379134|976|200643|171549;198431,Complete,Atrayees
bsdb:32425919/4/2,32425919,laboratory experiment,32425919,10.3389/fmicb.2020.00814,NA,"Xu X., Lv J., Guo F., Li J., Jia Y., Jiang D., Wang N., Zhang C., Kong L., Liu Y., Zhang Y., Lv J. , Li Z.",Gut Microbiome Influences the Efficacy of PD-1 Antibody Immunotherapy on MSS-Type Colorectal Cancer via Metabolic Pathway,Frontiers in microbiology,2020,"MSS-type CRC, PD-1 antibody, gut microbiota, immunotherapy, metabolic pathway",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control,Coli,Group 1 mice were treated with colistin (2 mg/ml) in sterile drinking water (Coli group).  Mice (in all groups) were then subcutaneously injected into the right axillary with 0.25 live CT26 tumor cells.,6,7,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,supp fig 2,18 September 2022,Mary Bearkland,"Mary Bearkland,Merit,Atrayees,WikiWorks",Bar plot of compositional differences at species level in the Control vs. Coli,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides oleiciplenus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:530,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:633,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,s__uncultured bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:462",3379134|976|200643|171549|815|816|626931;3379134|976|200643|171549|815|816|1262741;3379134|976|200643|171549|815|816|1262744;3379134|976|200643|171549|2005525|375288|328812;3379134|976|200643|171549|815|909656|204516;3379134|976|200643|171549|815|909656|671267;77133;3379134|976|200643|171549|815|816|1262740,Complete,Atrayees
bsdb:32425919/5/1,32425919,laboratory experiment,32425919,10.3389/fmicb.2020.00814,NA,"Xu X., Lv J., Guo F., Li J., Jia Y., Jiang D., Wang N., Zhang C., Kong L., Liu Y., Zhang Y., Lv J. , Li Z.",Gut Microbiome Influences the Efficacy of PD-1 Antibody Immunotherapy on MSS-Type Colorectal Cancer via Metabolic Pathway,Frontiers in microbiology,2020,"MSS-type CRC, PD-1 antibody, gut microbiota, immunotherapy, metabolic pathway",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control,Vanc,Group 1 mice were treated with  vancomycin alone (0.25 mg/ml) in sterile drinking water (Vanc group)  Mice (in all groups) were then subcutaneously injected into the right axillary with 0.25 live CT26 tumor cells.,6,7,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,supp fig 2,20 September 2022,Mary Bearkland,"Mary Bearkland,WikiWorks",Bar plot of compositional differences at species level in the Control vs. Coli groups of mice before PD-1 antibody treatment by one-way ANOVA.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 2_1_33B,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter rarus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|74201|203494|48461|1647988|239934|239935;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|815|816|469589;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|171552|558436|1676614;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005525|375288,Complete,Atrayees
bsdb:32425919/5/2,32425919,laboratory experiment,32425919,10.3389/fmicb.2020.00814,NA,"Xu X., Lv J., Guo F., Li J., Jia Y., Jiang D., Wang N., Zhang C., Kong L., Liu Y., Zhang Y., Lv J. , Li Z.",Gut Microbiome Influences the Efficacy of PD-1 Antibody Immunotherapy on MSS-Type Colorectal Cancer via Metabolic Pathway,Frontiers in microbiology,2020,"MSS-type CRC, PD-1 antibody, gut microbiota, immunotherapy, metabolic pathway",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control,Vanc,Group 1 mice were treated with  vancomycin alone (0.25 mg/ml) in sterile drinking water (Vanc group)  Mice (in all groups) were then subcutaneously injected into the right axillary with 0.25 live CT26 tumor cells.,6,7,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,supp fig 2,21 September 2022,Mary Bearkland,"Mary Bearkland,WikiWorks",Bar plot of compositional differences at species level in the  Control vs. Vanc group of mice before PD-1 antibody treatment by one-way ANOVA.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:927,k__Bacillati|p__Bacillota|s__Firmicutes bacterium ASF500,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium A4,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1031,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:873",3379134|976|200643|171549|815|816|1262753;1783272|1239|1378168;1783272|1239|186801|3085636|186803|397291;3379134|976|200643|171549|815|909656|204516;3379134|976|200643|171549|171552|838|1262917;3379134|976|200643|171549|171552|838|1262936,Complete,Atrayees
bsdb:32425919/6/1,32425919,laboratory experiment,32425919,10.3389/fmicb.2020.00814,NA,"Xu X., Lv J., Guo F., Li J., Jia Y., Jiang D., Wang N., Zhang C., Kong L., Liu Y., Zhang Y., Lv J. , Li Z.",Gut Microbiome Influences the Efficacy of PD-1 Antibody Immunotherapy on MSS-Type Colorectal Cancer via Metabolic Pathway,Frontiers in microbiology,2020,"MSS-type CRC, PD-1 antibody, gut microbiota, immunotherapy, metabolic pathway",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,coli,Vanc,Group 1 mice were treated with  vancomycin alone (0.25 mg/ml) in sterile drinking water (Vanc group)  Mice (in all groups) were then subcutaneously injected into the right axillary with 0.25 live CT26 tumor cells.,7,7,NA,WMS,NA,Illumina,relative abundances,ANOVA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,supp fig 2,21 September 2022,Mary Bearkland,"Mary Bearkland,WikiWorks",Bar plot of compositional differences at species level in the  Vanc vs.Coli groups of mice before PD-1 antibody treatment by one-way ANOVA.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:485,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis",3379134|976|200643|171549|171552|838|1262927;3379134|976|200643|171549|2005525|375288|823;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|2005525|375288;3379134|74201|203494|48461|1647988|239934|239935;3379134|1224|28216|80840|995019|577310|487175,Complete,Atrayees
bsdb:32425919/6/2,32425919,laboratory experiment,32425919,10.3389/fmicb.2020.00814,NA,"Xu X., Lv J., Guo F., Li J., Jia Y., Jiang D., Wang N., Zhang C., Kong L., Liu Y., Zhang Y., Lv J. , Li Z.",Gut Microbiome Influences the Efficacy of PD-1 Antibody Immunotherapy on MSS-Type Colorectal Cancer via Metabolic Pathway,Frontiers in microbiology,2020,"MSS-type CRC, PD-1 antibody, gut microbiota, immunotherapy, metabolic pathway",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,coli,Vanc,Group 1 mice were treated with  vancomycin alone (0.25 mg/ml) in sterile drinking water (Vanc group)  Mice (in all groups) were then subcutaneously injected into the right axillary with 0.25 live CT26 tumor cells.,7,7,NA,WMS,NA,Illumina,relative abundances,ANOVA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,supp fig 2,21 September 2022,Mary Bearkland,"Mary Bearkland,WikiWorks",Bar plot of compositional differences at species level in the Vanc vs.Coli groups of mice before PD-1 antibody treatment by one-way ANOVA.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:927,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1031,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:873,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:279,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium A4,k__Bacillati|p__Bacillota|s__Firmicutes bacterium ASF500",3379134|976|200643|171549|815|816|1262753;3379134|976|200643|171549|171552|838|1262917;3379134|976|200643|171549|171552|838|1262936;3379134|976|200643|171549|171552|838|1262924;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|3085636|186803|397291;1783272|1239|1378168,Complete,Atrayees
bsdb:32429742/1/1,32429742,"cross-sectional observational, not case-control",32429742,10.1089/chi.2019.0312,NA,"Aguilar T., Nava G.M., Olvera-Ramírez A.M., Ronquillo D., Camacho M., Zavala G.A., Caamaño M.C., Acevedo-Whitehouse K., Rosado J.L. , García O.P.",Gut Bacterial Families Are Associated with Body Composition and Metabolic Risk Markers in School-Aged Children in Rural Mexico,Childhood obesity (Print),2020,"bacterial families, children, metabolic markers, microbiota, obesity",Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight children,obese,School-aged children,56,16,4 months,16S,NA,RT-qPCR,relative abundances,ANOVA,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Figure A1,10 January 2021,Mst Afroza Parvin,WikiWorks,"Comparison of mean (ANOVA) between anthropometrical and biochemical variables and their association with the main bacterial families studied. (A) Comparison between normal weight, overweight, and obesity according to BMI for age.",increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,1783272|1239|91061|186826|33958,Complete,Atrayees
bsdb:32429742/1/2,32429742,"cross-sectional observational, not case-control",32429742,10.1089/chi.2019.0312,NA,"Aguilar T., Nava G.M., Olvera-Ramírez A.M., Ronquillo D., Camacho M., Zavala G.A., Caamaño M.C., Acevedo-Whitehouse K., Rosado J.L. , García O.P.",Gut Bacterial Families Are Associated with Body Composition and Metabolic Risk Markers in School-Aged Children in Rural Mexico,Childhood obesity (Print),2020,"bacterial families, children, metabolic markers, microbiota, obesity",Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,normal weight children,obese,School-aged children,56,16,4 months,16S,NA,RT-qPCR,relative abundances,ANOVA,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 2,Figure A1,10 January 2021,Mst Afroza Parvin,WikiWorks,"Comparison of mean (ANOVA) between anthropometrical and biochemical variables and their association with the main bacterial families studied. (A) Comparison between normal weight, overweight, and obesity according to BMI for age.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|976|200643|171549|815;3379134|976|200643|171549|171551;3379134|976|200643|171549|171552,Complete,Atrayees
bsdb:32437658/1/1,32437658,"laboratory experiment,time series / longitudinal observational",32437658,https://doi.org/10.1016/j.cell.2020.04.027,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7293577/,"Ang Q.Y., Alexander M., Newman J.C., Tian Y., Cai J., Upadhyay V., Turnbaugh J.A., Verdin E., Hall K.D., Leibel R.L., Ravussin E., Rosenbaum M., Patterson A.D. , Turnbaugh P.J.",Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells,Cell,2020,"Th17 cells, adipose tissue, bifidobacteria, intestinal immunity, ketogenic diet, ketone bodies, ketone ester, microbiome, β-hydroxybutyrate",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,Overweight/Obese Men on Baseline Diet (BD),Overweight/Obese Men on Ketogenic Diet (KD),Overweight or class I Obese non-diabetic men who consumed an isocaloric ketogenic diet for 4weeks,17,17,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1E,21 November 2022,Fatima,"Fatima,Lwaldron,Joan Chuks,WikiWorks","Bacterial taxa identified by DESeq2 as differentially abundant in Overweight/class I Obese non-diabetic Men, who consumed an isocaloric ketogenic diet for 4weeks Versus the same Overweight/class I Obese non-diabetic Men on Baseline Diet for 4weeks.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|g__Negativibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. 1-8,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",3379134|1224|1236|91347|543|1940338;1783272|1239|526524|526525|128827|1573534;1783272|1239|186801|186802|216572|946234;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3082720|186804|1505657;1783272|1239|186801|186802|1392389;1783272|1239|909932|909929|1843491|158846;1783272|1239|1980693;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|171552|838|1486937;1783272|1239|526524|526525|2810280|3025755,Complete,NA
bsdb:32437658/1/2,32437658,"laboratory experiment,time series / longitudinal observational",32437658,https://doi.org/10.1016/j.cell.2020.04.027,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7293577/,"Ang Q.Y., Alexander M., Newman J.C., Tian Y., Cai J., Upadhyay V., Turnbaugh J.A., Verdin E., Hall K.D., Leibel R.L., Ravussin E., Rosenbaum M., Patterson A.D. , Turnbaugh P.J.",Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells,Cell,2020,"Th17 cells, adipose tissue, bifidobacteria, intestinal immunity, ketogenic diet, ketone bodies, ketone ester, microbiome, β-hydroxybutyrate",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,Overweight/Obese Men on Baseline Diet (BD),Overweight/Obese Men on Ketogenic Diet (KD),Overweight or class I Obese non-diabetic men who consumed an isocaloric ketogenic diet for 4weeks,17,17,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1E,14 March 2024,Joan Chuks,"Joan Chuks,WikiWorks","Bacterial taxa identified by DESeq2 as differentially abundant in Overweight/class I Obese non-diabetic Men, who consumed an isocaloric ketogenic diet for 4weeks Versus the same Overweight/class I Obese non-diabetic Men on Baseline Diet for 4weeks.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|207244;1783272|201174|1760|85004|31953|1678;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|1263|41978,Complete,NA
bsdb:32437658/2/1,32437658,"laboratory experiment,time series / longitudinal observational",32437658,https://doi.org/10.1016/j.cell.2020.04.027,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7293577/,"Ang Q.Y., Alexander M., Newman J.C., Tian Y., Cai J., Upadhyay V., Turnbaugh J.A., Verdin E., Hall K.D., Leibel R.L., Ravussin E., Rosenbaum M., Patterson A.D. , Turnbaugh P.J.",Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells,Cell,2020,"Th17 cells, adipose tissue, bifidobacteria, intestinal immunity, ketogenic diet, ketone bodies, ketone ester, microbiome, β-hydroxybutyrate",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,Mice fed on High-fat Diet (HFD),Mice fed on Ketogenic Diet (KD),"Wild-type C57BL/6J mice of both sexes, between age 5 - 10 weeks, fed on ketogenic diet for 3 weeks.",6,6,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,diet,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3G + Figure S4F + Figure 5I,17 March 2024,Joan Chuks,"Joan Chuks,WikiWorks",Bacterial taxa identified by DESeq2 as differentially abundant in Wild-type and Mucin 2( Muc2-/-) deficient Mice fed on Ketogenic Diet(KD) Versus the Mice fed on High-Fat Diet (HFD).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus",1783272|1239|186801|3085636|186803|1427378;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|31979|1485|1506;1783272|201174|84998|1643822|1643826|580024;1783272|1239|186801|186802;1783272|1239|186801|186802|1392389;3379134|200930|68337|191393|2945020|248038;1783272|1239|526524|526525|128827|1470349,Complete,NA
bsdb:32437658/2/2,32437658,"laboratory experiment,time series / longitudinal observational",32437658,https://doi.org/10.1016/j.cell.2020.04.027,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7293577/,"Ang Q.Y., Alexander M., Newman J.C., Tian Y., Cai J., Upadhyay V., Turnbaugh J.A., Verdin E., Hall K.D., Leibel R.L., Ravussin E., Rosenbaum M., Patterson A.D. , Turnbaugh P.J.",Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells,Cell,2020,"Th17 cells, adipose tissue, bifidobacteria, intestinal immunity, ketogenic diet, ketone bodies, ketone ester, microbiome, β-hydroxybutyrate",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,Mice fed on High-fat Diet (HFD),Mice fed on Ketogenic Diet (KD),"Wild-type C57BL/6J mice of both sexes, between age 5 - 10 weeks, fed on ketogenic diet for 3 weeks.",6,6,NA,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,diet,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3G + Figure S4F,17 March 2024,Joan Chuks,"Joan Chuks,WikiWorks",Bacterial taxa identified by DESeq2 as differentially abundant in Wild-type and Mucin 2( Muc2-/-) deficient Mice fed on Ketogenic Diet(KD) Versus Wild-type and Mucin 2( Muc2-/-) deficient Mice fed on High-Fat Diet (HFD).,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136",1783272|201174|1760|85004|31953|1678;1783272|1239|526524|526525|128827|1937008;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|248744;3379134|976|200643|171549|2005473;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3085636|186803|877420,Complete,NA
bsdb:32437658/3/1,32437658,"laboratory experiment,time series / longitudinal observational",32437658,https://doi.org/10.1016/j.cell.2020.04.027,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7293577/,"Ang Q.Y., Alexander M., Newman J.C., Tian Y., Cai J., Upadhyay V., Turnbaugh J.A., Verdin E., Hall K.D., Leibel R.L., Ravussin E., Rosenbaum M., Patterson A.D. , Turnbaugh P.J.",Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells,Cell,2020,"Th17 cells, adipose tissue, bifidobacteria, intestinal immunity, ketogenic diet, ketone bodies, ketone ester, microbiome, β-hydroxybutyrate",Experiment 3,United States of America,Mus musculus,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,Mice fed on High-fat Diet (HFD-control),Mice fed High-fat Diet + Ketone Ester (HFD-KE),"C57BL/6J mice fed on High-fat diet that was supplemented with a synthetic Ketone ester(KE), beta-hydroxybutyrate(bHB).",NA,NA,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,diet,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5I + Figure 5M,19 March 2024,Joan Chuks,"Joan Chuks,WikiWorks","Bacterial taxa identified by DESeq2 as differentially abundant in C57BL/6J mice fed on High-fat diet supplemented with Ketone ester(KE), beta-hydroxybutyrate(bHB) Versus Mice fed on only High-Fat Diet (HFD).",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|186801|3085636|186803|1427378;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|838,Complete,NA
bsdb:32437658/3/2,32437658,"laboratory experiment,time series / longitudinal observational",32437658,https://doi.org/10.1016/j.cell.2020.04.027,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7293577/,"Ang Q.Y., Alexander M., Newman J.C., Tian Y., Cai J., Upadhyay V., Turnbaugh J.A., Verdin E., Hall K.D., Leibel R.L., Ravussin E., Rosenbaum M., Patterson A.D. , Turnbaugh P.J.",Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells,Cell,2020,"Th17 cells, adipose tissue, bifidobacteria, intestinal immunity, ketogenic diet, ketone bodies, ketone ester, microbiome, β-hydroxybutyrate",Experiment 3,United States of America,Mus musculus,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,Mice fed on High-fat Diet (HFD-control),Mice fed High-fat Diet + Ketone Ester (HFD-KE),"C57BL/6J mice fed on High-fat diet that was supplemented with a synthetic Ketone ester(KE), beta-hydroxybutyrate(bHB).",NA,NA,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,diet,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5M,19 March 2024,Joan Chuks,"Joan Chuks,WikiWorks","Bacterial taxa identified by DESeq2 as differentially abundant in C57BL/6J mice fed on High-fat diet supplemented with Ketone ester(KE), beta-hydroxybutyrate(bHB) Versus Mice fed on only High-Fat Diet (HFD).",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",1783272|201174|1760|85004|31953|1678;1783272|201174|84998|84999|84107|102106;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|1940338;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810281|191303,Complete,NA
bsdb:32442562/1/1,32442562,case-control,32442562,10.1053/j.gastro.2020.05.048,NA,"Zuo T., Zhang F., Lui G.C.Y., Yeoh Y.K., Li A.Y.L., Zhan H., Wan Y., Chung A.C.K., Cheung C.P., Chen N., Lai C.K.C., Chen Z., Tso E.Y.K., Fung K.S.C., Chan V., Ling L., Joynt G., Hui D.S.C., Chan F.K.L., Chan P.K.S. , Ng S.C.",Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization,Gastroenterology,2020,"Bacteria, Coronavirus, Fecal Nucleic Acid, Gut Microbiome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,"Uninfected controls, pneumonia patients, antibiotics treated COVID-19 patients",Antibiotic-naive COVID-19 patients,"COVID-19 patients hospitalized with SARS-CoV-2 infection confirmed by 2 consecutive RT-PCR tests, not treated with antibiotics",29,7,NA,WMS,NA,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,comorbidity,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 2,2 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance of microbial taxa between antibiotic-naive COVID-19 patients and healthy controls,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces viscosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii",1783272|201174|1760|2037|2049|1654|1656;1783272|1239|186801|3085636|186803|1649459|154046;3379134|976|200643|171549|815|816|291645,Complete,Chloe
bsdb:32442562/1/2,32442562,case-control,32442562,10.1053/j.gastro.2020.05.048,NA,"Zuo T., Zhang F., Lui G.C.Y., Yeoh Y.K., Li A.Y.L., Zhan H., Wan Y., Chung A.C.K., Cheung C.P., Chen N., Lai C.K.C., Chen Z., Tso E.Y.K., Fung K.S.C., Chan V., Ling L., Joynt G., Hui D.S.C., Chan F.K.L., Chan P.K.S. , Ng S.C.",Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization,Gastroenterology,2020,"Bacteria, Coronavirus, Fecal Nucleic Acid, Gut Microbiome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,"Uninfected controls, pneumonia patients, antibiotics treated COVID-19 patients",Antibiotic-naive COVID-19 patients,"COVID-19 patients hospitalized with SARS-CoV-2 infection confirmed by 2 consecutive RT-PCR tests, not treated with antibiotics",29,7,NA,WMS,NA,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,comorbidity,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 2,11 August 2021,Chloe,"Chloe,WikiWorks",Differential abundance of microbial taxa between antibiotic-naive COVID-19 patients and healthy controls,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,1783272|1239|186801|186802|186806|1730|39496,Complete,Chloe
bsdb:32442562/2/1,32442562,case-control,32442562,10.1053/j.gastro.2020.05.048,NA,"Zuo T., Zhang F., Lui G.C.Y., Yeoh Y.K., Li A.Y.L., Zhan H., Wan Y., Chung A.C.K., Cheung C.P., Chen N., Lai C.K.C., Chen Z., Tso E.Y.K., Fung K.S.C., Chan V., Ling L., Joynt G., Hui D.S.C., Chan F.K.L., Chan P.K.S. , Ng S.C.",Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization,Gastroenterology,2020,"Bacteria, Coronavirus, Fecal Nucleic Acid, Gut Microbiome",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,"Antibiotic-naive COVID-19 patients, pneumonia patients, uninfected controls",Antibiotic-treated COVID-19 patients,"COVID-19 patients hospitalized with SARS-CoV-2 infection confirmed by 2 consecutive RT-PCR tests, treated with antibiotics",28,8,NA,WMS,NA,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,comorbidity,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 2,2 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance of microbial taxa between antibiotic-naive and antibiotic-treated COVID-19 patients,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 5_1_63FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum",1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|658089;1783272|1239|186801|186802|186806|1730|39496,Complete,Chloe
bsdb:32442562/3/1,32442562,case-control,32442562,10.1053/j.gastro.2020.05.048,NA,"Zuo T., Zhang F., Lui G.C.Y., Yeoh Y.K., Li A.Y.L., Zhan H., Wan Y., Chung A.C.K., Cheung C.P., Chen N., Lai C.K.C., Chen Z., Tso E.Y.K., Fung K.S.C., Chan V., Ling L., Joynt G., Hui D.S.C., Chan F.K.L., Chan P.K.S. , Ng S.C.",Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization,Gastroenterology,2020,"Bacteria, Coronavirus, Fecal Nucleic Acid, Gut Microbiome",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,"Uninfected controls, COVID-19 patients",Pneumonia controls,Patients hospitalized with community-acquired pneumonia,30,6,NA,WMS,NA,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,comorbidity,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 2,2 July 2021,Claregrieve1,"Claregrieve1,Chloe,WikiWorks",Differential abundance of microbial taxa between healthy controls and pneumonia controls,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 5_1_63FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum",1783272|1239|526524|526525|2810280|100883;1783272|1239|91061|186826|81852|1350|1352;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|186801|3085636|186803|658089;1783272|1239|186801|186802|186806|1730|39496,Complete,Chloe
bsdb:32449092/1/1,32449092,"cross-sectional observational, not case-control",32449092,10.1007/s40618-020-01298-2,NA,"Shi T.T., Xin Z., Hua L., Wang H., Zhao R.X., Yang Y.L., Xie R.R., Liu H.Y. , Yang J.K.",Comparative assessment of gut microbial composition and function in patients with Graves' disease and Graves' orbitopathy,Journal of endocrinological investigation,2021,"16S rRNA gene, Graves’ disease, Graves’ orbitopathy, Gut microbiota, Metabolic functions",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Healthy subjects,Graves’ disease (GD),Patients diagnosed with Graves’ disease (GD),32,30,1 month,16S,4,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 5B and 6B,24 July 2025,Aleru Divine,Aleru Divine,Comparison of the changes in the structure of the fecal microbiota profile,increased,"k__Thermotogati|p__Deinococcota,k__Bacillati|p__Chloroflexota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3384194|1297;1783272|200795;1783272|1239|526524|526525|128827;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803;1783272|1239|186801|3082720|186804|1505657;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|171552,Complete,NA
bsdb:32449092/1/2,32449092,"cross-sectional observational, not case-control",32449092,10.1007/s40618-020-01298-2,NA,"Shi T.T., Xin Z., Hua L., Wang H., Zhao R.X., Yang Y.L., Xie R.R., Liu H.Y. , Yang J.K.",Comparative assessment of gut microbial composition and function in patients with Graves' disease and Graves' orbitopathy,Journal of endocrinological investigation,2021,"16S rRNA gene, Graves’ disease, Graves’ orbitopathy, Gut microbiota, Metabolic functions",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Healthy subjects,Graves’ disease (GD),Patients diagnosed with Graves’ disease (GD),32,30,1 month,16S,4,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 5B and 6B,24 July 2025,Aleru Divine,Aleru Divine,Comparison of the changes in the structure of the fecal microbiota profile,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|186801|186802|216572|292632;3379134|200940|3031449|213115|194924|35832;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|815|816,Complete,NA
bsdb:32449092/2/1,32449092,"cross-sectional observational, not case-control",32449092,10.1007/s40618-020-01298-2,NA,"Shi T.T., Xin Z., Hua L., Wang H., Zhao R.X., Yang Y.L., Xie R.R., Liu H.Y. , Yang J.K.",Comparative assessment of gut microbial composition and function in patients with Graves' disease and Graves' orbitopathy,Journal of endocrinological investigation,2021,"16S rRNA gene, Graves’ disease, Graves’ orbitopathy, Gut microbiota, Metabolic functions",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Graves ophthalmopathy,EFO:1001466,Healthy subjects,Graves’ ophthalmopathy (GO),Patients diagnosed with Graves’ ophthalmopathy (GO),32,33,1 month,16S,4,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure A and 6A,24 July 2025,Aleru Divine,Aleru Divine,Comparison of the changes in the structure of the fecal microbiota profile.,increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|976;3379134|976|200643|171549|171552,Complete,NA
bsdb:32449092/2/2,32449092,"cross-sectional observational, not case-control",32449092,10.1007/s40618-020-01298-2,NA,"Shi T.T., Xin Z., Hua L., Wang H., Zhao R.X., Yang Y.L., Xie R.R., Liu H.Y. , Yang J.K.",Comparative assessment of gut microbial composition and function in patients with Graves' disease and Graves' orbitopathy,Journal of endocrinological investigation,2021,"16S rRNA gene, Graves’ disease, Graves’ orbitopathy, Gut microbiota, Metabolic functions",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Graves ophthalmopathy,EFO:1001466,Healthy subjects,Graves’ ophthalmopathy (GO),Patients diagnosed with Graves’ ophthalmopathy (GO),32,33,1 month,16S,4,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure A and 6A,24 July 2025,Aleru Divine,Aleru Divine,Comparison of the changes in the structure of the fecal microbiota profile.,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",1783272|1239;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|3085642|580596;1783272|201174|84998|84999|84107|102106,Complete,NA
bsdb:32449092/3/1,32449092,"cross-sectional observational, not case-control",32449092,10.1007/s40618-020-01298-2,NA,"Shi T.T., Xin Z., Hua L., Wang H., Zhao R.X., Yang Y.L., Xie R.R., Liu H.Y. , Yang J.K.",Comparative assessment of gut microbial composition and function in patients with Graves' disease and Graves' orbitopathy,Journal of endocrinological investigation,2021,"16S rRNA gene, Graves’ disease, Graves’ orbitopathy, Gut microbiota, Metabolic functions",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,"Graves disease,Graves ophthalmopathy","EFO:0004237,EFO:1001466",Graves’ ophthalmopathy (GO),Graves’ disease (GD),Patients diagnosed with Graves’ disease (GD),33,30,1 month,16S,4,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 5C and 6C,24 July 2025,Aleru Divine,Aleru Divine,Comparison of the changes in the structure of the fecal microbiota profile.,increased,"k__Thermotogati|p__Deinococcota,k__Bacillati|p__Chloroflexota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",3384194|1297;1783272|200795;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3082720|186804|1505657;1783272|1239|909932|1843488|909930|33024,Complete,NA
bsdb:32449092/3/2,32449092,"cross-sectional observational, not case-control",32449092,10.1007/s40618-020-01298-2,NA,"Shi T.T., Xin Z., Hua L., Wang H., Zhao R.X., Yang Y.L., Xie R.R., Liu H.Y. , Yang J.K.",Comparative assessment of gut microbial composition and function in patients with Graves' disease and Graves' orbitopathy,Journal of endocrinological investigation,2021,"16S rRNA gene, Graves’ disease, Graves’ orbitopathy, Gut microbiota, Metabolic functions",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,"Graves disease,Graves ophthalmopathy","EFO:0004237,EFO:1001466",Graves’ ophthalmopathy (GO),Graves’ disease (GD),Patients diagnosed with Graves’ disease (GD),33,30,1 month,16S,4,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 5C and 6C,24 July 2025,Aleru Divine,Aleru Divine,Comparison of the changes in the structure of the fecal microbiota profile,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",1783272|1239|186801|186802|216572|292632;3379134|200940|3031449|213115|194924|35832,Complete,NA
bsdb:32466801/1/1,32466801,case-control,32466801,10.1186/s40168-020-00854-5,NA,"Jian X., Zhu Y., Ouyang J., Wang Y., Lei Q., Xia J., Guan Y., Zhang J., Guo J., He Y., Wang J., Li J., Lin J., Su M., Li G., Wu M., Qiu L., Xiang J., Xie L., Jia W. , Zhou W.",Alterations of gut microbiome accelerate multiple myeloma progression by increasing the relative abundances of nitrogen-recycling bacteria,Microbiome,2020,"Fecal microbiota transplantation, Gut microbiome, Multiple myeloma, Nitrogen-recycling bacteria",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Multiple myeloma,EFO:0001378,healthy control,multiple myeloma patients,newly diagnosed multiple myeloma patients,18,19,NA,16S,12,RT-qPCR,raw counts,DESeq2,0.05,TRUE,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplemental table S2,10 January 2021,William Lam,WikiWorks,The differential species and subspecies identified by DESeq2 (abs(log2(fold change)) > 1 and adjusted P < 0.05) enriched in multiple myeloma patients and healthy controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella variicola,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter ruminicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella fusca,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella|s__Raoultella ornithinolytica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter aphrophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter asburiae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes",3379134|1224|1236|91347|543|570|573;3379134|1224|1236|91347|543|570|244366;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|91061|186826|1300|1301|1302;3379134|1224|1236|91347|543|547|550;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1304;1783272|201174|1760|85004|31953|1678|1689;3379134|1224|1236|91347|543|544|546;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|91061|186826|1300|1301|28037;3379134|1224|1236|91347|543|570|548;3379134|976|200643|171549|171552|558436|839;3379134|976|200643|171549|171552|838|589436;1783272|1239|91061|186826|1300|1301|1328;3379134|976|200643|171549|171552|838|28132;1783272|1239|186801|186802|1392389|1297617;1783272|1239|91061|186826|1300|1301|1313;3379134|1224|1236|91347|543|160674|54291;1783272|201174|1760|85004|31953|1678|1680;3379134|1224|1236|135625|712|416916|732;3379134|1224|1236|91347|543|547|61645;1783272|1239|909932|1843489|31977|906|907;1783272|1239|186801|186802|216572|459786|351091,Complete,Claregrieve1
bsdb:32466801/1/2,32466801,case-control,32466801,10.1186/s40168-020-00854-5,NA,"Jian X., Zhu Y., Ouyang J., Wang Y., Lei Q., Xia J., Guan Y., Zhang J., Guo J., He Y., Wang J., Li J., Lin J., Su M., Li G., Wu M., Qiu L., Xiang J., Xie L., Jia W. , Zhou W.",Alterations of gut microbiome accelerate multiple myeloma progression by increasing the relative abundances of nitrogen-recycling bacteria,Microbiome,2020,"Fecal microbiota transplantation, Gut microbiome, Multiple myeloma, Nitrogen-recycling bacteria",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Multiple myeloma,EFO:0001378,healthy control,multiple myeloma patients,newly diagnosed multiple myeloma patients,18,19,NA,16S,12,RT-qPCR,raw counts,DESeq2,0.05,TRUE,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 2,Supplemental table S2,10 January 2021,William Lam,WikiWorks,The differential species and subspecies identified by DESeq2 (abs(log2(Fold Change)) > 1 and adjusted P < 0.05) enriched in multiple myeloma patients and healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pasteurianus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium phytofermentans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium baratii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium saccharobutylicum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio proteoclasticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio hungatei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium saccharoperbutylacetonicum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Herbinix|s__Herbinix luporum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium beijerinckii,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Paraclostridium|s__Paraclostridium sordellii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium botulinum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium butyricum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum|s__Bifidobacterium catenulatum subsp. kashiwanohense,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium varium",1783272|1239|91061|186826|1300|1301|197614;1783272|1239|186801|3085636|186803|1506553|66219;1783272|1239|186801|186802|31979|1485|1561;1783272|1239|186801|186802|31979|1485|169679;1783272|1239|186801|3085636|186803|830|43305;1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|186801|3085636|186803|830|185008;3379134|976|200643|171549|815|816|246787;1783272|1239|186801|186802|31979|1485|36745;3379134|976|200643|171549|2005525|375288|1869337;3379134|976|200643|171549|815|816|28116;1783272|1239|186801|3085636|186803|1663717|1679721;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|2005525|375288|823;1783272|1239|186801|3085636|186803|28050|39485;3379134|976|200643|171549|815|816|47678;1783272|201174|1760|85004|31953|1678|1686;1783272|1239|186801|186802|31979|1485|1520;1783272|1239|186801|3082720|186804|1849822|1505;1783272|1239|186801|186802|31979|1485|1491;1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|909932|909929|1843491|158846|158847;1783272|1239|186801|186802|31979|1485|1492;1783272|201174|1760|85004|31953|1678|1686|630129;1783272|201174|1760|85004|31953|1678|28026;3384189|32066|203490|203491|203492|848|856,Complete,Claregrieve1
bsdb:32466801/2/1,32466801,case-control,32466801,10.1186/s40168-020-00854-5,NA,"Jian X., Zhu Y., Ouyang J., Wang Y., Lei Q., Xia J., Guan Y., Zhang J., Guo J., He Y., Wang J., Li J., Lin J., Su M., Li G., Wu M., Qiu L., Xiang J., Xie L., Jia W. , Zhou W.",Alterations of gut microbiome accelerate multiple myeloma progression by increasing the relative abundances of nitrogen-recycling bacteria,Microbiome,2020,"Fecal microbiota transplantation, Gut microbiome, Multiple myeloma, Nitrogen-recycling bacteria",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Multiple myeloma,EFO:0001378,healthy controls,multiple myeloma patients,newly diagnosed multiple myeloma patients,18,19,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 1,"Figure 2b, text",10 January 2021,William Lam,"Claregrieve1,WikiWorks",Nitrogen- recycling bacteria species with differential abundance in multiple myeloma patients and healthy controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella variicola,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella|s__Raoultella ornithinolytica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis",3379134|1224|1236|91347|543|544|546;3379134|1224|1236|91347|543|547|550;3379134|1224|1236|91347|543|570|548;3379134|1224|1236|91347|543|570|573;3379134|1224|1236|91347|543|570|244366;3379134|1224|1236|91347|543|160674|54291;1783272|1239|91061|186826|1300|1301|1302;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|91061|186826|1300|1301|1313;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|1300|1301|28037,Complete,Claregrieve1
bsdb:32466801/2/2,32466801,case-control,32466801,10.1186/s40168-020-00854-5,NA,"Jian X., Zhu Y., Ouyang J., Wang Y., Lei Q., Xia J., Guan Y., Zhang J., Guo J., He Y., Wang J., Li J., Lin J., Su M., Li G., Wu M., Qiu L., Xiang J., Xie L., Jia W. , Zhou W.",Alterations of gut microbiome accelerate multiple myeloma progression by increasing the relative abundances of nitrogen-recycling bacteria,Microbiome,2020,"Fecal microbiota transplantation, Gut microbiome, Multiple myeloma, Nitrogen-recycling bacteria",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Multiple myeloma,EFO:0001378,healthy controls,multiple myeloma patients,newly diagnosed multiple myeloma patients,18,19,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 2,"Figure 2b, text",10 January 2021,William Lam,"Claregrieve1,WikiWorks",Nitrogen- recycling bacteria species with differential abundance in multiple myeloma patients and healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora saccharolytica,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium butyricum",1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|186801|3085636|186803|2719231|84030;1783272|1239|186801|186802|31979|1485|1492,Complete,Claregrieve1
bsdb:32468338/1/1,32468338,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu A.H., Tseng C., Vigen C., Yu Y., Cozen W., Garcia A.A. , Spicer D.",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,"Age at menarche, HER2 status, Microbiome, Tumor characteristics",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,HER2 Positive Breast Carcinoma,EFO:1000294,Her2 negative tumor,Her2 positive tumor,Breast cancer patients with Her2 positive tumors (human epidermal growth factor receptive 2 positive),25,12,1 week,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 3,29 June 2021,Itslanapark,"Itslanapark,WikiWorks",Mean ratio estimates found using zero-inflated negative binomial model of taxa abundance by HER2 status,increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,1783272|1239|909932|1843488|909930|904,Complete,Claregrieve1
bsdb:32468338/1/2,32468338,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu A.H., Tseng C., Vigen C., Yu Y., Cozen W., Garcia A.A. , Spicer D.",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,"Age at menarche, HER2 status, Microbiome, Tumor characteristics",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,HER2 Positive Breast Carcinoma,EFO:1000294,Her2 negative tumor,Her2 positive tumor,Breast cancer patients with Her2 positive tumors (human epidermal growth factor receptive 2 positive),25,12,1 week,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 3,30 June 2021,Itslanapark,"Itslanapark,Claregrieve1,WikiWorks","Mean ratio estimates found using zero-inflated negative binomial model of taxa abundance by ER, PR, and HER2 status",decreased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae",3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3082768|424536,Complete,Claregrieve1
bsdb:32468338/2/1,32468338,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu A.H., Tseng C., Vigen C., Yu Y., Cozen W., Garcia A.A. , Spicer D.",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,"Age at menarche, HER2 status, Microbiome, Tumor characteristics",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Age at menarche,EFO:0004703,early age at menarche (≤11),later age at menarche (≥12),breast cancer patients with age at menarche being over 12 years old,11,26,1 week,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,increased,NA,NA,NA,Signature 1,Table 5,7 July 2021,Itslanapark,"Itslanapark,Claregrieve1,WikiWorks","Mean estimate ratios gound using a zero-inflated negative binomial model of taxa abundances by age group, menarche age and parity.",increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,3379134|1224|1236|91347|543|561,Complete,Claregrieve1
bsdb:32468338/2/2,32468338,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu A.H., Tseng C., Vigen C., Yu Y., Cozen W., Garcia A.A. , Spicer D.",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,"Age at menarche, HER2 status, Microbiome, Tumor characteristics",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Age at menarche,EFO:0004703,early age at menarche (≤11),later age at menarche (≥12),breast cancer patients with age at menarche being over 12 years old,11,26,1 week,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,increased,NA,NA,NA,Signature 2,Table 5,7 July 2021,Itslanapark,"Itslanapark,WikiWorks","Mean estimate ratios found using a zero-inflated negative binomial model of taxa abundances by age group, menarche age and parity.",decreased,"k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",3366610|28890|183925|2158|2159|2172;1783272|1239|186801|186802|216572|1263,Complete,Claregrieve1
bsdb:32468338/3/1,32468338,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu A.H., Tseng C., Vigen C., Yu Y., Cozen W., Garcia A.A. , Spicer D.",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,"Age at menarche, HER2 status, Microbiome, Tumor characteristics",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Estrogen receptor status,EFO:0005512,ER+,ER-,breast cancer patients with negative Estrogen Receptor status,9,28,1 week,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 3,5 July 2021,Itslanapark,"Itslanapark,WikiWorks","Mean ratio estimates obtained by zero-inflated negative binomial model of taxa abundances by estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2 status.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|1224|1236|135625|712|724;1783272|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:32468338/5/1,32468338,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu A.H., Tseng C., Vigen C., Yu Y., Cozen W., Garcia A.A. , Spicer D.",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,"Age at menarche, HER2 status, Microbiome, Tumor characteristics",Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,Grade Low (I/II),Grade High (III),breast cancer patients with grade high level tumors (Grade III),14,23,1 week,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 4,7 July 2021,Itslanapark,"Itslanapark,WikiWorks",Mean estimate ratios found using zero- inflated negative binomial model of taxa abundances by grade and stage of breast cancer.,increased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,1783272|201174|84998|1643822|1643826|84111,Complete,Claregrieve1
bsdb:32468338/5/2,32468338,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu A.H., Tseng C., Vigen C., Yu Y., Cozen W., Garcia A.A. , Spicer D.",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,"Age at menarche, HER2 status, Microbiome, Tumor characteristics",Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,Grade Low (I/II),Grade High (III),breast cancer patients with grade high level tumors (Grade III),14,23,1 week,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 4,7 July 2021,Itslanapark,"Itslanapark,WikiWorks",Mean estimate ratios found using zero- inflated negative binomial model of taxa abundances by grade and stage of breast cancer.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes",1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|207244,Complete,Claregrieve1
bsdb:32468338/6/1,32468338,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu A.H., Tseng C., Vigen C., Yu Y., Cozen W., Garcia A.A. , Spicer D.",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,"Age at menarche, HER2 status, Microbiome, Tumor characteristics",Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Breast cancer stage,EFO:0005607,Stage Low (I/II),Stage High (III),Breast cancer patients with high stage progression of breast cancer (Stage III).,22,15,1 week,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 4,7 July 2021,Itslanapark,"Itslanapark,WikiWorks",Mean estimate ratios found using zero- inflated negative binomial model of taxa abundances by grade and stage of breast cancer.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",1783272|1239|186801|186802|31979|1485;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|135625|712|724,Complete,Claregrieve1
bsdb:32468338/6/2,32468338,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu A.H., Tseng C., Vigen C., Yu Y., Cozen W., Garcia A.A. , Spicer D.",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,"Age at menarche, HER2 status, Microbiome, Tumor characteristics",Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Breast cancer stage,EFO:0005607,Stage Low (I/II),Stage High (III),Breast cancer patients with high stage progression of breast cancer (Stage III).,22,15,1 week,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 4,7 July 2021,Itslanapark,"Itslanapark,WikiWorks",Mean estimate ratios found using zero- inflated negative binomial model of taxa abundances by grade and stage of breast cancer.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium",1783272|1239|909932|1843488|909930|904;1783272|1239|526524|526525|2810280|135858,Complete,Claregrieve1
bsdb:32468338/7/1,32468338,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu A.H., Tseng C., Vigen C., Yu Y., Cozen W., Garcia A.A. , Spicer D.",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,"Age at menarche, HER2 status, Microbiome, Tumor characteristics",Experiment 7,United States of America,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Age 50+,Age ≤50,Breast cancer patients whose age is ≤50 years old.,17,20,1 week,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.001,FALSE,NA,NA,"ethnic group,race",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 5,7 July 2021,Itslanapark,"Itslanapark,WikiWorks","Mean estimate ratios found using a zero-inflated negative binomial model of taxa abundances by age group, menarche age and parity.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus",1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;3379134|1224|1236|91347|543;1783272|1239|91061|186826|1300|1357,Complete,Claregrieve1
bsdb:32468338/8/1,32468338,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu A.H., Tseng C., Vigen C., Yu Y., Cozen W., Garcia A.A. , Spicer D.",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,"Age at menarche, HER2 status, Microbiome, Tumor characteristics",Experiment 8,United States of America,Homo sapiens,Feces,UBERON:0001988,Parous,EFO:0002947,Parous,Nulliparous,Breast cancer patients who are nulliparous (have had no live births.),29,8,1 week,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 5,7 July 2021,Itslanapark,"Itslanapark,WikiWorks","Mean estimate ratios found using a zero-inflated negative binomial model of taxa abundances by age group, menarche age and parity.",decreased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,1783272|1239|526524|526525|2810280|135858,Complete,Claregrieve1
bsdb:32468338/9/1,32468338,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu A.H., Tseng C., Vigen C., Yu Y., Cozen W., Garcia A.A. , Spicer D.",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,"Age at menarche, HER2 status, Microbiome, Tumor characteristics",Experiment 9,United States of America,Homo sapiens,Feces,UBERON:0001988,Body mass index,EFO:0004340,BMI<25,BMI≥25,Breast cancer patients with a high body mass index (BMI≥25),9,28,1 week,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 6,7 July 2021,Itslanapark,"Itslanapark,WikiWorks","Mean estimate ratios found using a zero-inflated negative binomial model of taxa abundances by BMI, total body fat, and physical activity.",increased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,3379134|74201|203494|48461|1647988|239934,Complete,Claregrieve1
bsdb:32468338/10/1,32468338,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu A.H., Tseng C., Vigen C., Yu Y., Cozen W., Garcia A.A. , Spicer D.",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,"Age at menarche, HER2 status, Microbiome, Tumor characteristics",Experiment 10,United States of America,Homo sapiens,Feces,UBERON:0001988,Body fat percentage,EFO:0007800,TBF≤46%,TBF>46%,Breast cancer patients with a total body fat percentage ≥46%.,25,12,1 week,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Table 6,7 July 2021,Itslanapark,"Itslanapark,WikiWorks","Mean estimate ratios found using a zero-inflated negative binomial model of taxa abundances by BMI, total body fat, and physical activity.",increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,1783272|1239|186801|186802|31979,Complete,Claregrieve1
bsdb:32468338/10/2,32468338,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu A.H., Tseng C., Vigen C., Yu Y., Cozen W., Garcia A.A. , Spicer D.",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,"Age at menarche, HER2 status, Microbiome, Tumor characteristics",Experiment 10,United States of America,Homo sapiens,Feces,UBERON:0001988,Body fat percentage,EFO:0007800,TBF≤46%,TBF>46%,Breast cancer patients with a total body fat percentage ≥46%.,25,12,1 week,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Table 6,7 July 2021,Itslanapark,"Itslanapark,WikiWorks","Mean estimate ratios found using a zero-inflated negative binomial model of taxa abundances by BMI, total body fat, and physical activity.",decreased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,1783272|201174|84998|84999|84107,Complete,Claregrieve1
bsdb:32473086/1/1,32473086,"cross-sectional observational, not case-control",32473086,10.1002/jpen.1861,NA,"Tan C., Wu Q., Wang H., Gao X., Xu R., Cui Z., Zhu J., Zeng X., Zhou H., He Y. , Yin J.",Dysbiosis of Gut Microbiota and Short-Chain Fatty Acids in Acute Ischemic Stroke and the Subsequent Risk for Poor Functional Outcomes,JPEN. Journal of parenteral and enteral nutrition,2021,"dysbiosis, functional outcome, gut microbiota, ischemic stroke, short-chain fatty acids",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Ischemic stroke,HP:0002140,Healthy control group (HC),Acute ischemic stroke (AIS),All acute ischemic stroke patients with ischemic stroke onset within 48 hours.,92,140,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2D,22 October 2024,InimfonD,"InimfonD,MyleeeA,WikiWorks",The difference between the gut microbiota of patients with acute ischemic stroke and healthy controls by LEfSE,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|1224|28216|80840|506;3379134|976|200643|171549|815;1783272|1239|186801|3085636|186803;3379134|1224|1236|2887326|468;3379134|1224|1236|135625|712;3379134|976|200643|171549|171552,Complete,Folakunmi
bsdb:32473086/2/1,32473086,"cross-sectional observational, not case-control",32473086,10.1002/jpen.1861,NA,"Tan C., Wu Q., Wang H., Gao X., Xu R., Cui Z., Zhu J., Zeng X., Zhou H., He Y. , Yin J.",Dysbiosis of Gut Microbiota and Short-Chain Fatty Acids in Acute Ischemic Stroke and the Subsequent Risk for Poor Functional Outcomes,JPEN. Journal of parenteral and enteral nutrition,2021,"dysbiosis, functional outcome, gut microbiota, ischemic stroke, short-chain fatty acids",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Ischemic stroke,HP:0002140,Healthy control/moderate AIS/ severe AIS,Mild acute ischemic stroke,Ischemic stroke Patients with a  NIHSS score < 5 points,154,78,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,figure 2D,23 October 2024,InimfonD,"InimfonD,Rahila,WikiWorks",These taxons show an increased abundance in mild acute ischemic patients as compared to the moderate/severe AIS patients and healthy controls by LEfSE,increased,"k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae",3379134|200930|68337|191393|191394;3379134|29547|3031852|213849|72293;1783272|1239|91061|186826|81850;1783272|201174|1760|85006|1268;3379134|1224|28211|356|41294,Complete,Folakunmi
bsdb:32473086/3/1,32473086,"cross-sectional observational, not case-control",32473086,10.1002/jpen.1861,NA,"Tan C., Wu Q., Wang H., Gao X., Xu R., Cui Z., Zhu J., Zeng X., Zhou H., He Y. , Yin J.",Dysbiosis of Gut Microbiota and Short-Chain Fatty Acids in Acute Ischemic Stroke and the Subsequent Risk for Poor Functional Outcomes,JPEN. Journal of parenteral and enteral nutrition,2021,"dysbiosis, functional outcome, gut microbiota, ischemic stroke, short-chain fatty acids",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Ischemic stroke,HP:0002140,Healthy control/mild AIS/ severe AIS,Moderate acute ischemic stroke,Ischemic stroke Patients with a  NIHSS score between 5 and 15 points,185,47,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2D,23 October 2024,InimfonD,"InimfonD,WikiWorks",These taxons are increased in moderate AIS as compared to healthy control/mild AIS/severe AIS,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae",3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|526524|526525|128827;3366610|28890|183925|2158|2159;1783272|201174|1760|85007|1653;1783272|1239|186801|186802|186806,Complete,Folakunmi
bsdb:32473086/4/1,32473086,"cross-sectional observational, not case-control",32473086,10.1002/jpen.1861,NA,"Tan C., Wu Q., Wang H., Gao X., Xu R., Cui Z., Zhu J., Zeng X., Zhou H., He Y. , Yin J.",Dysbiosis of Gut Microbiota and Short-Chain Fatty Acids in Acute Ischemic Stroke and the Subsequent Risk for Poor Functional Outcomes,JPEN. Journal of parenteral and enteral nutrition,2021,"dysbiosis, functional outcome, gut microbiota, ischemic stroke, short-chain fatty acids",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Ischemic stroke,HP:0002140,Healthy control/mild AIS/ moderate AIS,Severe acute ischemic stroke,Ischemic stroke Patients with a NIHSS score >15 points,217,15,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,figure 2D,23 October 2024,InimfonD,"InimfonD,WikiWorks",These taxa show increase in severe AIS compared to healthy control/mild AIS/moderate AIS by LEfSE,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae",3379134|976|200643|171549|171551;1783272|544448|31969|2085|2092;3379134|1224|28211|356|69277;1783272|1239|91061|186826|186828;1783272|1239|91061|1385|90964,Complete,Folakunmi
bsdb:32473086/5/1,32473086,"cross-sectional observational, not case-control",32473086,10.1002/jpen.1861,NA,"Tan C., Wu Q., Wang H., Gao X., Xu R., Cui Z., Zhu J., Zeng X., Zhou H., He Y. , Yin J.",Dysbiosis of Gut Microbiota and Short-Chain Fatty Acids in Acute Ischemic Stroke and the Subsequent Risk for Poor Functional Outcomes,JPEN. Journal of parenteral and enteral nutrition,2021,"dysbiosis, functional outcome, gut microbiota, ischemic stroke, short-chain fatty acids",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Ischemic stroke,HP:0002140,Healthy control group (HC),Acute ischemic stroke (AIS),All acute ischemic stroke patients with ischemic stroke onset within 48 hours.,92,140,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,27 October 2024,InimfonD,"InimfonD,Rahila,MyleeeA,WikiWorks",Comparison of the abundance of short-chain fatty acid-producing gut microbiota between healthy controls and Acute Ischemic Stroke patients according to taxonomic classification and LEfSe analysis.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",3379134|74201|203494|48461|1647988|239934;3379134|1224|1236|91347|543;1783272|1239|91061|186826|33958;3379134|976|200643|171549|171551,Complete,Folakunmi
bsdb:32473086/5/2,32473086,"cross-sectional observational, not case-control",32473086,10.1002/jpen.1861,NA,"Tan C., Wu Q., Wang H., Gao X., Xu R., Cui Z., Zhu J., Zeng X., Zhou H., He Y. , Yin J.",Dysbiosis of Gut Microbiota and Short-Chain Fatty Acids in Acute Ischemic Stroke and the Subsequent Risk for Poor Functional Outcomes,JPEN. Journal of parenteral and enteral nutrition,2021,"dysbiosis, functional outcome, gut microbiota, ischemic stroke, short-chain fatty acids",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Ischemic stroke,HP:0002140,Healthy control group (HC),Acute ischemic stroke (AIS),All acute ischemic stroke patients with ischemic stroke onset within 48 hours.,92,140,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,27 October 2024,InimfonD,"InimfonD,MyleeeA,WikiWorks",Comparison of the abundance of short-chain fatty acid-producing microbiota in healthy controls versus acute ischemic stroke patients according to taxonomic classification and LEfSe analysis.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|841,Complete,Folakunmi
bsdb:32473086/6/1,32473086,"cross-sectional observational, not case-control",32473086,10.1002/jpen.1861,NA,"Tan C., Wu Q., Wang H., Gao X., Xu R., Cui Z., Zhu J., Zeng X., Zhou H., He Y. , Yin J.",Dysbiosis of Gut Microbiota and Short-Chain Fatty Acids in Acute Ischemic Stroke and the Subsequent Risk for Poor Functional Outcomes,JPEN. Journal of parenteral and enteral nutrition,2021,"dysbiosis, functional outcome, gut microbiota, ischemic stroke, short-chain fatty acids",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Stroke outcome severity measurement,EFO:0009603,Moderate Acute ischemic stroke (AIS),Mild  (AIS),Acute ischemic stroke Patients with National Institutes of Health Stroke Scale (NIHSS) score < 5 points,47,78,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,27 October 2024,InimfonD,"InimfonD,Rahila,MyleeeA,WikiWorks",Comparison of the abundance of short-chain fatty acid-producing gut microbiota between moderate and mild acute ischemic patients according to taxonomic classification and LEfSe analysis.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,1783272|1239|186801|3085636|186803|841,Complete,Folakunmi
bsdb:32473086/6/2,32473086,"cross-sectional observational, not case-control",32473086,10.1002/jpen.1861,NA,"Tan C., Wu Q., Wang H., Gao X., Xu R., Cui Z., Zhu J., Zeng X., Zhou H., He Y. , Yin J.",Dysbiosis of Gut Microbiota and Short-Chain Fatty Acids in Acute Ischemic Stroke and the Subsequent Risk for Poor Functional Outcomes,JPEN. Journal of parenteral and enteral nutrition,2021,"dysbiosis, functional outcome, gut microbiota, ischemic stroke, short-chain fatty acids",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Stroke outcome severity measurement,EFO:0009603,Moderate Acute ischemic stroke (AIS),Mild  (AIS),Acute ischemic stroke Patients with National Institutes of Health Stroke Scale (NIHSS) score < 5 points,47,78,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,27 October 2024,InimfonD,"InimfonD,Rahila,MyleeeA,WikiWorks",Comparison of the abundance of short-chain fatty acid-producing gut microbiota between moderate and mild acute ischemic patients according to taxonomic classification and LEfSe analysis.,decreased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,3379134|74201|203494|48461|1647988|239934,Complete,Folakunmi
bsdb:32473086/7/1,32473086,"cross-sectional observational, not case-control",32473086,10.1002/jpen.1861,NA,"Tan C., Wu Q., Wang H., Gao X., Xu R., Cui Z., Zhu J., Zeng X., Zhou H., He Y. , Yin J.",Dysbiosis of Gut Microbiota and Short-Chain Fatty Acids in Acute Ischemic Stroke and the Subsequent Risk for Poor Functional Outcomes,JPEN. Journal of parenteral and enteral nutrition,2021,"dysbiosis, functional outcome, gut microbiota, ischemic stroke, short-chain fatty acids",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Stroke outcome severity measurement,EFO:0009603,Mild Acute ischemic stroke (AIS),Severe Acute Ischemic Stroke (AIS),Acute ischemic stroke Patients with National Institutes of Health Stroke Scale (NIHSS) score > 15 points,78,15,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,27 October 2024,InimfonD,"InimfonD,MyleeeA,WikiWorks",Comparison of the abundance of short-chain fatty acid-producing gut microbiota in severe acute ischemic stroke patients versus mild ischemic stroke patients according to taxonomic classification and LEfSe analysis”,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,1783272|1239|186801|3085636|186803|841,Complete,Folakunmi
bsdb:32482258/1/1,32482258,case-control,32482258,10.1016/j.fertnstert.2020.01.027,NA,"Chu W., Han Q., Xu J., Wang J., Sun Y., Li W., Chen Z.J. , Du Y.",Metagenomic analysis identified microbiome alterations and pathological association between intestinal microbiota and polycystic ovary syndrome,Fertility and sterility,2020,"Gut microbiota, KEGG orthologue, metagenomic sequencing, pathophysiologic progress, polycystic ovary syndrome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control group,Polycystic ovary syndrome group (PCOS),Patients diagnosed with Polycystic ovary syndrome group (PCOS).,14,14,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,18 June 2025,Victoria,Victoria,Linear discrimination analysis (LDA) effect size (LEfSe). Histogram of the LDA scores computed for differentially abundant species between the polycystic ovary syndrome (PCOS) and control groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. D20,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:353,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp. 1_1_43,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp. 4_1_40B,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella sonnei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella boydii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella flexneri,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|s__Enterobacteria phage SfV,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella sp. PAMC 28760,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella genomosp. SF-2015,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella dysenteriae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas kerstersii",3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|815|816|585543;3379134|1224|1236|91347|543|561|562;3379134|976|200643|171549|815|816|817;1783272|1239|186801|186802|216572|1263|1262955;3379134|1224|1236|91347|543|561|457400;3379134|1224|1236|91347|543|561|457401;3379134|1224|1236|91347|543|620|624;3379134|1224|1236|91347|543|620|621;3379134|1224|1236|91347|543|620|623;2731360|2731618|2731619|55884;3379134|1224|1236|91347|543|620|1813821;3379134|1224|1236|91347|543|620|1776082;3379134|1224|1236|91347|543|620|622;3379134|1224|28216|80840|80864|283|225992,Complete,KateRasheed
bsdb:32482258/1/2,32482258,case-control,32482258,10.1016/j.fertnstert.2020.01.027,NA,"Chu W., Han Q., Xu J., Wang J., Sun Y., Li W., Chen Z.J. , Du Y.",Metagenomic analysis identified microbiome alterations and pathological association between intestinal microbiota and polycystic ovary syndrome,Fertility and sterility,2020,"Gut microbiota, KEGG orthologue, metagenomic sequencing, pathophysiologic progress, polycystic ovary syndrome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control group,Polycystic ovary syndrome group (PCOS),Patients diagnosed with Polycystic ovary syndrome group (PCOS).,14,14,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1,18 June 2025,Victoria,Victoria,Linear discrimination analysis (LDA) effect size (LEfSe). Histogram of the LDA scores computed for differentially abundant species between the polycystic ovary syndrome (PCOS) and control groups.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hydrogenotrophica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:20,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella sp. 6_1_58FAA_CT1,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides gallinarum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis",1783272|1239|186801|3085636|186803|572511|53443;3379134|976|200643|171549|815|816|1262738;3379134|976|200643|171549|2005525|195950|665949;3379134|976|200643|171549|815|816|376806;3379134|1224|1236|91347|543|570|573;3379134|976|200643|171549|2005519|397864|487174;1783272|1239|186801|186802|216572|216851|853;3379134|976|200643|171549|171550|239759|2585118;3379134|976|200643|171549|815|909656|204516,Complete,KateRasheed
bsdb:32482258/2/1,32482258,case-control,32482258,10.1016/j.fertnstert.2020.01.027,NA,"Chu W., Han Q., Xu J., Wang J., Sun Y., Li W., Chen Z.J. , Du Y.",Metagenomic analysis identified microbiome alterations and pathological association between intestinal microbiota and polycystic ovary syndrome,Fertility and sterility,2020,"Gut microbiota, KEGG orthologue, metagenomic sequencing, pathophysiologic progress, polycystic ovary syndrome",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control group,Polycystic ovary syndrome group (PCOS),Patients diagnosed with Polycystic ovary syndrome group (PCOS).,14,14,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Figure 3 (B & D),18 June 2025,Victoria,"Victoria,Tosin",Comparison between the PCOS-enriched and control-enriched relative abundance of genus and species-level microbes ranked in descending order in the control group and the PCOS group.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. D20,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|s__Enterobacteria phage SfI,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|g__Lambdavirus|s__Lambdavirus HK629,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|g__Lambdavirus|s__Lambdavirus HK630,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|s__Escherichia phage TL-2011b,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp. 1_1_43,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp. 4_1_40B,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp. KTE172,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp. TW10509,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kluyvera,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|g__Lambdavirus,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|g__Lederbergvirus,k__Metazoa|p__Arthropoda|c__Insecta|o__Hemiptera|f__Diaspididae|g__Morganella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Metazoa|p__Chordata|c__Amphibia|o__Caudata|f__Proteidae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Riemerella|s__Riemerella anatipestifer,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella boydii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella dysenteriae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella flexneri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella genomosp. SF-2015,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|s__Shigella phage SfIV,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella sonnei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella sp. PAMC 28760,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|g__Uetakevirus,k__Metazoa|p__Arthropoda|c__Insecta|o__Mantodea|f__Amelidae|g__Yersinia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter",3379134|1224|1236|135624|84642|642;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|585543;2731360|2731618|2731619;3379134|1224|1236|91347|543|544;3379134|1224|28216|80840|80864|283;3379134|1224|1236|91347|543|413496;2731360|2731618|2731619|1225789;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|561|562;2731360|2731618|2731619|186765|2169968;2731360|2731618|2731619|186765|2169969;2731360|2731618|2731619|1124654;3379134|1224|1236|91347|543|561|457400;3379134|1224|1236|91347|543|561|457401;3379134|1224|1236|91347|543|561|1279005;3379134|1224|1236|91347|543|561|754332;3384189|32066|203490|203491|203492|848;3379134|1224|1236|91347|543|579;2731360|2731618|2731619|186765;2731360|2731618|2731619|186794;33208|6656|50557|7524|30080|108061;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|46503;33208|7711|8292|8293|166053|210425;3379134|1224|1236|72274|135621|286;3379134|976|117743|200644|2762318|34084|34085;3379134|1224|1236|91347|543|590;3379134|1224|1236|91347|543|620;3379134|1224|1236|91347|543|620|621;3379134|1224|1236|91347|543|620|622;3379134|1224|1236|91347|543|620|623;3379134|1224|1236|91347|543|620|1776082;2731360|2731618|2731619|1407493;3379134|1224|1236|91347|543|620|624;3379134|1224|1236|91347|543|620|1813821;2731360|2731618|2731619|542960;33208|6656|50557|7504|2901306|444888;3379134|1224|1236|91347|543|547,Complete,KateRasheed
bsdb:32482258/2/2,32482258,case-control,32482258,10.1016/j.fertnstert.2020.01.027,NA,"Chu W., Han Q., Xu J., Wang J., Sun Y., Li W., Chen Z.J. , Du Y.",Metagenomic analysis identified microbiome alterations and pathological association between intestinal microbiota and polycystic ovary syndrome,Fertility and sterility,2020,"Gut microbiota, KEGG orthologue, metagenomic sequencing, pathophysiologic progress, polycystic ovary syndrome",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control group,Polycystic ovary syndrome group (PCOS),Patients diagnosed with Polycystic ovary syndrome group (PCOS).,14,14,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Figure 3 (A & C),18 June 2025,Victoria,"Victoria,Tosin",Comparison between the PCOS-enriched and control-enriched relative abundance of genus and species-level microbes ranked in descending order in the control group and the PCOS group.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium Bact_01,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides gallinarum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:20,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hydrogenotrophica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|g__Candidatus Hemicellulosilyticus|s__Candidatus Hemicellulosilyticus sp. F083,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium UC5.1-2G4,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium CHKCI006,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus sp. 8_2_54BFAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp. AGR2135,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium A2,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium oral taxon 500,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia|s__Marvinbryantia formatexigens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sp. MJR8396C,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter laneus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp. HGS0025,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|g__Punavirus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:380,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|s__Spirochaetales bacterium Spiro_06,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella sp. 6_1_58FAA_CT1",3379134|976|200643|171549|171550|239759|2585118;3379134|976|200643|171549|1674815;3379134|976|200643|171549|815|816|376806;3379134|976|200643|171549|815|816|1262738;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|2005519|397864|487174;1783272|1239|186801|3085636|186803|572511|53443;3379134|976|200643|171549|3443719|1768114;1783272|1239|186801|1697791;1783272|1239|186801|186802|1780379;1783272|1239|526524|526525|2810280|100883|469597;1783272|1239|186801|3085636|186803|189330|1280669;1783272|1239|186801|186802|216572|216851|853;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|543|570|573;1783272|1239|186801|3085636|186803|397290;1783272|1239|186801|3085636|186803|712991;1783272|1239|186801|3085636|186803|248744;1783272|1239|186801|3085636|186803|248744|168384;1783272|1239|909932|1843489|31977|906|1603888;3379134|976|200643|171549|1853231|283168|626933;3379134|976|200643|171549|2005525|375288|1078087;3379134|976|200643|171549|815|909656|204516;2731360|2731618|2731619|186789;1783272|1239|186801|3085636|186803|841|1262946;1783272|1239|186801|186802|216572|1263|438033;3379134|203691|203692|136|1674862;3379134|976|200643|171549|2005525|195950;3379134|976|200643|171549|2005525|195950|665949,Complete,KateRasheed
bsdb:32488167/1/1,32488167,prospective cohort,32488167,10.1038/s41396-020-0686-3,https://pubmed.ncbi.nlm.nih.gov/32488167/,"Rasmussen M.A., Thorsen J., Dominguez-Bello M.G., Blaser M.J., Mortensen M.S., Brejnrod A.D., Shah S.A., Hjelmsø M.H., Lehtimäki J., Trivedi U., Bisgaard H., Sørensen S.J. , Stokholm J.",Ecological succession in the vaginal microbiota during pregnancy and birth,The ISME journal,2020,NA,Experiment 1,United States of America,Homo sapiens,Vagina,UBERON:0000996,Gestational age,EFO:0005112,Week 24,Week 36,gestational age of 36 weeks,56,57,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 3,28 October 2021,Joyessa,"Joyessa,Fatima,Claregrieve1,WikiWorks",Differentially abundant vaginal taxa at genus level between Week 24 vs. Week 36.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella",3379134|1224|1236|2887326|468|475;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|81852|1350;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|1385|539738|1378,Complete,Claregrieve1
bsdb:32488167/1/2,32488167,prospective cohort,32488167,10.1038/s41396-020-0686-3,https://pubmed.ncbi.nlm.nih.gov/32488167/,"Rasmussen M.A., Thorsen J., Dominguez-Bello M.G., Blaser M.J., Mortensen M.S., Brejnrod A.D., Shah S.A., Hjelmsø M.H., Lehtimäki J., Trivedi U., Bisgaard H., Sørensen S.J. , Stokholm J.",Ecological succession in the vaginal microbiota during pregnancy and birth,The ISME journal,2020,NA,Experiment 1,United States of America,Homo sapiens,Vagina,UBERON:0000996,Gestational age,EFO:0005112,Week 24,Week 36,gestational age of 36 weeks,56,57,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 3,28 October 2021,Joyessa,"Joyessa,Fatima,Claregrieve1,WikiWorks",Differentially abundant vaginal taxa at genus level between Week 24 vs. Week 36.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Claregrieve1
bsdb:32488167/2/1,32488167,prospective cohort,32488167,10.1038/s41396-020-0686-3,https://pubmed.ncbi.nlm.nih.gov/32488167/,"Rasmussen M.A., Thorsen J., Dominguez-Bello M.G., Blaser M.J., Mortensen M.S., Brejnrod A.D., Shah S.A., Hjelmsø M.H., Lehtimäki J., Trivedi U., Bisgaard H., Sørensen S.J. , Stokholm J.",Ecological succession in the vaginal microbiota during pregnancy and birth,The ISME journal,2020,NA,Experiment 2,United States of America,Homo sapiens,Vagina,UBERON:0000996,Gestational age,EFO:0005112,36,Birth,birth timepoint,57,57,NA,16S,4,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3,15 November 2021,Joyessa,"Joyessa,Claregrieve1,WikiWorks",Differentially abundant microbial taxa between the 36 week timepoint and birth timepoint,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|1760|85007|1653|1716;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|2887326|468|475;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:32488167/2/2,32488167,prospective cohort,32488167,10.1038/s41396-020-0686-3,https://pubmed.ncbi.nlm.nih.gov/32488167/,"Rasmussen M.A., Thorsen J., Dominguez-Bello M.G., Blaser M.J., Mortensen M.S., Brejnrod A.D., Shah S.A., Hjelmsø M.H., Lehtimäki J., Trivedi U., Bisgaard H., Sørensen S.J. , Stokholm J.",Ecological succession in the vaginal microbiota during pregnancy and birth,The ISME journal,2020,NA,Experiment 2,United States of America,Homo sapiens,Vagina,UBERON:0000996,Gestational age,EFO:0005112,36,Birth,birth timepoint,57,57,NA,16S,4,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3,30 August 2022,Claregrieve1,"Claregrieve1,WikiWorks",Differentially abundant microbial taxa between the 36 week timepoint and birth timepoint,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Claregrieve1
bsdb:32497191/1/1,32497191,"cross-sectional observational, not case-control",32497191,https://doi.org/10.1093/cid/ciaa709,NA,"Gu S., Chen Y., Wu Z., Chen Y., Gao H., Lv L., Guo F., Zhang X., Luo R., Huang C., Lu H., Zheng B., Zhang J., Yan R., Zhang H., Jiang H., Xu Q., Guo J., Gong Y., Tang L. , Li L.",Alterations of the Gut Microbiota in Patients With Coronavirus Disease 2019 or H1N1 Influenza,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2020,"COVID-19, H1N1, biomarker, dysbiosis, intestinal microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 cases,viral COVID-19 infections confirmed by real-time reverse-transcription polymerase chain reaction,30,30,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3.5,"age,body mass index,sex",NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 3a,3 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differences in microbial composition between patients with coronavirus disease 2019 and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",1783272|1239|91061|186826|1300|1301;1783272|201174|1760|85006|1268|32207;1783272|1239|909932|1843489|31977|29465;1783272|1239|526524|526525|2810280|1505663;1783272|201174|1760|2037|2049|1654,Complete,Fatima
bsdb:32497191/1/2,32497191,"cross-sectional observational, not case-control",32497191,https://doi.org/10.1093/cid/ciaa709,NA,"Gu S., Chen Y., Wu Z., Chen Y., Gao H., Lv L., Guo F., Zhang X., Luo R., Huang C., Lu H., Zheng B., Zhang J., Yan R., Zhang H., Jiang H., Xu Q., Guo J., Gong Y., Tang L. , Li L.",Alterations of the Gut Microbiota in Patients With Coronavirus Disease 2019 or H1N1 Influenza,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2020,"COVID-19, H1N1, biomarker, dysbiosis, intestinal microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 cases,viral COVID-19 infections confirmed by real-time reverse-transcription polymerase chain reaction,30,30,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3.5,"age,body mass index,sex",NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 3a,3 June 2021,Claregrieve1,"Claregrieve1,Fatima,WikiWorks",Differences in microbial composition between patients with coronavirus disease 2019 and healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3082720|186804|1505657;3379134|1224|1236|91347|543|570;1783272|1239|186801|3082720|186804|1501226;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|186802|31979|1485,Complete,Fatima
bsdb:32497191/2/1,32497191,"cross-sectional observational, not case-control",32497191,https://doi.org/10.1093/cid/ciaa709,NA,"Gu S., Chen Y., Wu Z., Chen Y., Gao H., Lv L., Guo F., Zhang X., Luo R., Huang C., Lu H., Zheng B., Zhang J., Yan R., Zhang H., Jiang H., Xu Q., Guo J., Gong Y., Tang L. , Li L.",Alterations of the Gut Microbiota in Patients With Coronavirus Disease 2019 or H1N1 Influenza,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2020,"COVID-19, H1N1, biomarker, dysbiosis, intestinal microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Influenza A (H1N1),EFO:1001488,Healthy controls,H1N1 cases,H1N1 patients with viral infection confirmed by real-time reverse-transcription polymerase chain reaction hospitalized between January 2018 and March 2019 with severe disease at time of admission,30,24,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3.5,"age,body mass index,sex",NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Supplementary Figure 2,3 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Comparison of estimated fecal microbiome phylotypes in H1N1 patients and healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3082720|186804|1501226;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|2569097|39488;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|1263|41978,Complete,NA
bsdb:32497191/2/2,32497191,"cross-sectional observational, not case-control",32497191,https://doi.org/10.1093/cid/ciaa709,NA,"Gu S., Chen Y., Wu Z., Chen Y., Gao H., Lv L., Guo F., Zhang X., Luo R., Huang C., Lu H., Zheng B., Zhang J., Yan R., Zhang H., Jiang H., Xu Q., Guo J., Gong Y., Tang L. , Li L.",Alterations of the Gut Microbiota in Patients With Coronavirus Disease 2019 or H1N1 Influenza,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2020,"COVID-19, H1N1, biomarker, dysbiosis, intestinal microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Influenza A (H1N1),EFO:1001488,Healthy controls,H1N1 cases,H1N1 patients with viral infection confirmed by real-time reverse-transcription polymerase chain reaction hospitalized between January 2018 and March 2019 with severe disease at time of admission,30,24,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3.5,"age,body mass index,sex",NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Supplementary Figure 2,3 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Comparison of estimated fecal microbiome phylotypes in H1N1 patients and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus",1783272|1239|91061|186826|81852|1350;3379134|976|200643|171549|171552|838;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|1737404|1737405|1570339|162289,Complete,NA
bsdb:32497191/3/1,32497191,"cross-sectional observational, not case-control",32497191,https://doi.org/10.1093/cid/ciaa709,NA,"Gu S., Chen Y., Wu Z., Chen Y., Gao H., Lv L., Guo F., Zhang X., Luo R., Huang C., Lu H., Zheng B., Zhang J., Yan R., Zhang H., Jiang H., Xu Q., Guo J., Gong Y., Tang L. , Li L.",Alterations of the Gut Microbiota in Patients With Coronavirus Disease 2019 or H1N1 Influenza,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2020,"COVID-19, H1N1, biomarker, dysbiosis, intestinal microbiota",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,H1N1 patients,COVID-19 patients,viral COVID-19 infections confirmed by real-time reverse-transcription polymerase chain reaction,24,30,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3.5,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 4a,3 June 2021,Claregrieve1,"Claregrieve1,Fatima,WikiWorks",Differences in microbiota composition between COVID-19 patients and H1N1 patients,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|207244;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803;1783272|201174|1760|85006|1268|32207;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|186802|31979|1485,Complete,Fatima
bsdb:32497191/3/2,32497191,"cross-sectional observational, not case-control",32497191,https://doi.org/10.1093/cid/ciaa709,NA,"Gu S., Chen Y., Wu Z., Chen Y., Gao H., Lv L., Guo F., Zhang X., Luo R., Huang C., Lu H., Zheng B., Zhang J., Yan R., Zhang H., Jiang H., Xu Q., Guo J., Gong Y., Tang L. , Li L.",Alterations of the Gut Microbiota in Patients With Coronavirus Disease 2019 or H1N1 Influenza,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2020,"COVID-19, H1N1, biomarker, dysbiosis, intestinal microbiota",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,H1N1 patients,COVID-19 patients,viral COVID-19 infections confirmed by real-time reverse-transcription polymerase chain reaction,24,30,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3.5,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 4a,3 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differences in microbiota composition between COVID-19 patients and H1N1 patients,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",3379134|976|200643|171549|171552|838;1783272|1239|1737404|1582879;3379134|74201|203494|48461|1647988|239934;1783272|1239|1737404|1737405|1570339|1161127;3379134|976|200643|171549|171551|836,Complete,Fatima
bsdb:32517799/1/1,32517799,case-control,32517799,10.1186/s12915-020-00775-7,NA,"Baldini F., Hertel J., Sandt E., Thinnes C.C., Neuberger-Castillo L., Pavelka L., Betsou F., Krüger R. , Thiele I.",Parkinson's disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions,BMC biology,2020,"Computational modelling, Gut microbiome, Metabolic modelling, Parkinson’s disease, Transsulfuration pathway",Experiment 1,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Participants with typical PD,"PD patients were defined as typical PD, according to the inclusion criteria by the United Kingdom Parkinson’s Disease Society Brain Bank Clinical Diagnostic Criteria.",162,147,6 months,16S,34,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,"age,sex","age,body mass index,constipation,sex",NA,unchanged,NA,NA,NA,increased,Signature 1,Figure 2 and Figure 3,22 January 2022,Fcuevas3,"Fcuevas3,Aiyshaaaa,Peace Sandy,WikiWorks","Boxplots of seven significantly changed species in PD vs. controls (FDR < 0.05). Significance levels were determined using multivariable semi-parametrical fractional regressions with the group variable (PD vs. control) as a predictor of interest, including age, gender, BMI, and technical variables (total read counts and sequencing run (batch)) as covariates. FDR, false discovery rate

Boxplots of eight significantly changed genera in PD vs. controls (FDR < 0.05). Significance levels were determined using multivariable semi-parametrical fractional regressions with the group variable (PD vs. control) as a predictor of interest, including age, gender, BMI, and technical variables (total read counts and sequencing run (batch)) as covariates. FDR, false discovery rate",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella minuta,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|186802|216572|244127|169435;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|3082768|990719|990721|626937;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|909932|1843488|909930|904,Complete,Peace Sandy
bsdb:32517799/1/2,32517799,case-control,32517799,10.1186/s12915-020-00775-7,NA,"Baldini F., Hertel J., Sandt E., Thinnes C.C., Neuberger-Castillo L., Pavelka L., Betsou F., Krüger R. , Thiele I.",Parkinson's disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions,BMC biology,2020,"Computational modelling, Gut microbiome, Metabolic modelling, Parkinson’s disease, Transsulfuration pathway",Experiment 1,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Participants with typical PD,"PD patients were defined as typical PD, according to the inclusion criteria by the United Kingdom Parkinson’s Disease Society Brain Bank Clinical Diagnostic Criteria.",162,147,6 months,16S,34,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,"age,sex","age,body mass index,constipation,sex",NA,unchanged,NA,NA,NA,increased,Signature 2,Figure 2 and Figure 3,22 January 2022,Fcuevas3,"Fcuevas3,Aiyshaaaa,Peace Sandy,WikiWorks","Boxplots of seven significantly changed species in PD vs. controls (FDR < 0.05). Significance levels were determined using multivariable semi-parametrical fractional regressions with the group variable (PD vs. control) as a predictor of interest, including age, gender, BMI, and technical variables (total read counts and sequencing run (batch)) as covariates. FDR, false discovery rate

Boxplots of eight significantly changed genera in PD vs. controls (FDR < 0.05). Significance levels were determined using multivariable semi-parametrical fractional regressions with the group variable (PD vs. control) as a predictor of interest, including age, gender, BMI, and technical variables (total read counts and sequencing run (batch)) as covariates. FDR, false discovery rate",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis",1783272|1239|186801|3085636|186803|841|166486;1783272|1239|526524|526525|2810281|191303;1783272|1239|526524|526525|2810281|191303|154288,Complete,Peace Sandy
bsdb:32544691/1/1,32544691,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W., Zhou Y., Qin Y., Li Y., Yu L., Li R., Chen Y. , Xu Y.",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,"Gut microbiota, Lipoproteins, Offspring, PM(2.5), Sex-specific",Experiment 1,China,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 3,ICR male mice exposed to PM 2.5,ICR mice exposed to PM 2.5 air,8,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,unchanged,Signature 1,Figure 7a & text,10 January 2021,Zyaijah Bailey,WikiWorks,"LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",1783272|1239|186801|3085636|186803|841;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171550,Complete,Atrayees
bsdb:32544691/1/2,32544691,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W., Zhou Y., Qin Y., Li Y., Yu L., Li R., Chen Y. , Xu Y.",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,"Gut microbiota, Lipoproteins, Offspring, PM(2.5), Sex-specific",Experiment 1,China,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 3,ICR male mice exposed to PM 2.5,ICR mice exposed to PM 2.5 air,8,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,unchanged,Signature 2,Figure 7a & text,10 January 2021,Zyaijah Bailey,"Lwaldron,WikiWorks","LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",1783272|1239|91061|186826|186827;1783272|1239|91061|186826|186827|66831;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481;3379134|1224|28216|206351;1783272|1239|91061|1385|90964;3379134|1224|1236|91347|543|1940338,Complete,Atrayees
bsdb:32544691/4/1,32544691,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W., Zhou Y., Qin Y., Li Y., Yu L., Li R., Chen Y. , Xu Y.",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,"Gut microbiota, Lipoproteins, Offspring, PM(2.5), Sex-specific",Experiment 4,China,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 35,ICR male mice exposed to PM 2.5,ICR mice exposed to PM 2.5,8,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,unchanged,Signature 1,Figure 7d& text,10 January 2021,Zyaijah Bailey,"WikiWorks,Atrayees","LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300,Complete,Atrayees
bsdb:32544691/4/2,32544691,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W., Zhou Y., Qin Y., Li Y., Yu L., Li R., Chen Y. , Xu Y.",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,"Gut microbiota, Lipoproteins, Offspring, PM(2.5), Sex-specific",Experiment 4,China,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 35,ICR male mice exposed to PM 2.5,ICR mice exposed to PM 2.5,8,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,unchanged,Signature 2,Figure 7d & text,8 August 2023,Atrayees,"Atrayees,WikiWorks","LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus",3379134|976|200643|171549|815|816;3379134|200940|3031449|213115|194924|872;3379134|976|200643|171549|815;1783272|1239|186801|186802|216572|244127,Complete,Atrayees
bsdb:32544691/5/2,32544691,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W., Zhou Y., Qin Y., Li Y., Yu L., Li R., Chen Y. , Xu Y.",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,"Gut microbiota, Lipoproteins, Offspring, PM(2.5), Sex-specific",Experiment 5,China,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 10,ICR female mice exposed to PM 2.5,ICR mice exposed to PM 2.5,8,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,Signature 2,Figure 7f & text,10 January 2021,Zyaijah Bailey,"WikiWorks,Atrayees,Merit","LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998|1643822|1643826|580024;3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|838,Complete,Atrayees
bsdb:32544691/6/1,32544691,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W., Zhou Y., Qin Y., Li Y., Yu L., Li R., Chen Y. , Xu Y.",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,"Gut microbiota, Lipoproteins, Offspring, PM(2.5), Sex-specific",Experiment 6,China,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 21,ICR female mice exposed to PM 2.5,ICR mice exposed to PM 2.5,8,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,increased,Signature 1,Figure 7g & text,10 January 2021,Zyaijah Bailey,"WikiWorks,Rukky","LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",increased,"c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes sp.",28221;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;3379134|74201|203494|48461|203557;3379134|74201|203494;3379134|74201|203494|48461;3379134|74201;1783272|1239|186801|3085636|186803|207244|1872530,Complete,Atrayees
bsdb:32544691/6/2,32544691,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W., Zhou Y., Qin Y., Li Y., Yu L., Li R., Chen Y. , Xu Y.",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,"Gut microbiota, Lipoproteins, Offspring, PM(2.5), Sex-specific",Experiment 6,China,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 21,ICR female mice exposed to PM 2.5,ICR mice exposed to PM 2.5,8,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,increased,Signature 2,Figure 7g & text,10 January 2021,Zyaijah Bailey,"Aiyshaaaa,WikiWorks,Merit,Atrayees","LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Viridiplantae|p__Streptophyta",1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;33090|35493,Complete,Atrayees
bsdb:32544691/7/1,32544691,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W., Zhou Y., Qin Y., Li Y., Yu L., Li R., Chen Y. , Xu Y.",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,"Gut microbiota, Lipoproteins, Offspring, PM(2.5), Sex-specific",Experiment 7,China,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 35,ICR female mice exposed to PM 2.5,ICR mice exposed to PM 2.5,8,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,Signature 1,Figure 7h & text,10 January 2021,Zyaijah Bailey,WikiWorks,"LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,1783272|1239|186801|186802|541000,Complete,Atrayees
bsdb:32544691/7/2,32544691,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W., Zhou Y., Qin Y., Li Y., Yu L., Li R., Chen Y. , Xu Y.",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,"Gut microbiota, Lipoproteins, Offspring, PM(2.5), Sex-specific",Experiment 7,China,Mus musculus,Colon,UBERON:0001155,Air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 35,ICR female mice exposed to PM 2.5,ICR mice exposed to PM 2.5,8,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,Signature 2,Figure 7h & text,10 January 2021,Zyaijah Bailey,"WikiWorks,Merit,Atrayees","LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239|186801|3082720|186804;1783272|1239|186801|186802|31979|1485,Complete,Atrayees
bsdb:32546712/1/1,32546712,"cross-sectional observational, not case-control",32546712,10.1038/s41598-020-66607-4,NA,"Tango C.N., Seo S.S., Kwon M., Lee D.O., Chang H.K. , Kim M.K.",Taxonomic and Functional Differences in Cervical Microbiome Associated with Cervical Cancer Development,Scientific reports,2020,NA,Experiment 1,South Korea,Homo sapiens,Uterine cervix,UBERON:0000002,"Cervical glandular intraepithelial neoplasia,Cervical cancer","EFO:1000165,MONDO:0002974",Healthy controls,CIN2/3-CC,patients diagnosed with CIN2/3 or cervical cancer during screening of the cervical tract,50,42,3 months,16S,NA,Roche454,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 1,figure 2,10 January 2021,Cynthia Anderson,"WikiWorks,Peace Sandy",Diferences in relative abundances of microbial taxa (genus and species) between groups by LEfSe analysis,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium striatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter|s__Enhydrobacter aerosaccus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus fornicalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Latilactobacillus|s__Latilactobacillus sakei,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia|s__Massilia alkalitolerans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus luteus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella koreensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella",1783272|201174|1760|85007|1653|1716|43770;1783272|201174|1760|85009|31957|1912216;1783272|201174|1760|85009|31957|1912216|1747;3379134|1224|28211|356|212791;3379134|1224|28211|356|212791|225324;3384189|32066|203490|203491|203492|848|851;1783272|1239|91061|186826|33958|1578|88164;1783272|1239|91061|186826|33958|2767885|1599;3379134|1224|28216|80840|75682|149698|286638;1783272|201174|1760|85006|1268|1269;1783272|201174|1760|85006|1268|1269|1270;3379134|976|200643|171549|171552|838|419005;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1313;1783272|1239|91061|186826|33958|46255;1783272|1239|91061|186826|33958|46255|165096;1783272|1239|909932|1843489|31977|29465;1783272|1239|1737404|1737405|1570339;3379134|1224|1236|72274|135621|286;3379134|1224|1236|91347|543;1783272|201174|1760|85007|1653|1716;3379134|1224|28216|80840|75682|149698;1783272|544448|2790996|2790998|2129;3379134|1224|28211|204457|41297|13687;1783272|1239|186801|3085636|186803;1783272|201174|1760|85004|31953|2701,Complete,Peace Sandy
bsdb:32546712/1/2,32546712,"cross-sectional observational, not case-control",32546712,10.1038/s41598-020-66607-4,NA,"Tango C.N., Seo S.S., Kwon M., Lee D.O., Chang H.K. , Kim M.K.",Taxonomic and Functional Differences in Cervical Microbiome Associated with Cervical Cancer Development,Scientific reports,2020,NA,Experiment 1,South Korea,Homo sapiens,Uterine cervix,UBERON:0000002,"Cervical glandular intraepithelial neoplasia,Cervical cancer","EFO:1000165,MONDO:0002974",Healthy controls,CIN2/3-CC,patients diagnosed with CIN2/3 or cervical cancer during screening of the cervical tract,50,42,3 months,16S,NA,Roche454,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 2,figure 2,3 February 2024,Peace Sandy,"Peace Sandy,WikiWorks",Diferences in relative abundances of microbial taxa (genus and species) between groups by LEfSe analysis,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,1783272|201174|1760|85004|31953|2701,Complete,Peace Sandy
bsdb:32552447/1/1,32552447,case-control,32552447,10.1080/22221751.2020.1783188,NA,"Hu Y., Cheng M., Liu B., Dong J., Sun L., Yang J., Yang F., Chen X. , Jin Q.",Metagenomic analysis of the lung microbiome in pulmonary tuberculosis - a pilot study,Emerging microbes & infections,2020,"16S rDNA, Lung microbiome, bronchoalveolar lavage, metagenomic analysis, tuberculosis",Experiment 1,China,Homo sapiens,Lung,UBERON:0002048,Pulmonary tuberculosis,EFO:1000049,Mycobacterium tuberculosis (MTB−),Mycobacterium tuberculosis (MTB+),"Mycobacterium tuberculosis (MTB) detected by smear, culture, PCR, or GeneXpert.",30,30,NA,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,Figure 2,5 July 2025,Nuerteye,Nuerteye,Average relative taxon abundance comparisons between the MTB+ and MTB- groups at the genus level.,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium tuberculosis,1783272|201174|1760|85007|1762|1763|1773,Complete,NA
bsdb:32552447/1/2,32552447,case-control,32552447,10.1080/22221751.2020.1783188,NA,"Hu Y., Cheng M., Liu B., Dong J., Sun L., Yang J., Yang F., Chen X. , Jin Q.",Metagenomic analysis of the lung microbiome in pulmonary tuberculosis - a pilot study,Emerging microbes & infections,2020,"16S rDNA, Lung microbiome, bronchoalveolar lavage, metagenomic analysis, tuberculosis",Experiment 1,China,Homo sapiens,Lung,UBERON:0002048,Pulmonary tuberculosis,EFO:1000049,Mycobacterium tuberculosis (MTB−),Mycobacterium tuberculosis (MTB+),"Mycobacterium tuberculosis (MTB) detected by smear, culture, PCR, or GeneXpert.",30,30,NA,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Figure 2,5 July 2025,Nuerteye,Nuerteye,Average relative taxon abundance comparisons between the MTB+ and MTB- groups at the genus level.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|171552|838;3379134|1224|28216|206351|481|482;1783272|1239|909932|909929|1843491|970;1783272|201174|1760|85004|31953|1678,Complete,NA
bsdb:32557853/1/1,32557853,"case-control,meta-analysis",32557853,10.1002/mds.28119,NA,"Nishiwaki H., Ito M., Ishida T., Hamaguchi T., Maeda T., Kashihara K., Tsuboi Y., Ueyama J., Shimamura T., Mori H., Kurokawa K., Katsuno M., Hirayama M. , Ohno K.",Meta-Analysis of Gut Dysbiosis in Parkinson's Disease,Movement disorders : official journal of the Movement Disorder Society,2020,"Parkinson's disease, confounding factors, gut microbiota, meta-analysis, pathway analysis",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's disease patients,Patients with parkinson’s disease (PD); a neurodegenerative disorder characterized primarily by loss of dopamine neurons in the substantia nigra.,137,223,1 month,16S,34,Illumina,relative abundances,"ANCOM,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Supporting Information Tables S5a and S5b,8 January 2026,Firdaws,Firdaws,Differentially abundant bacterial genera and families altered in Parkinson's disease in the Japanese dataset.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572;1783272|1239|186801|3082720|543314,Complete,NA
bsdb:32557853/1/2,32557853,"case-control,meta-analysis",32557853,10.1002/mds.28119,NA,"Nishiwaki H., Ito M., Ishida T., Hamaguchi T., Maeda T., Kashihara K., Tsuboi Y., Ueyama J., Shimamura T., Mori H., Kurokawa K., Katsuno M., Hirayama M. , Ohno K.",Meta-Analysis of Gut Dysbiosis in Parkinson's Disease,Movement disorders : official journal of the Movement Disorder Society,2020,"Parkinson's disease, confounding factors, gut microbiota, meta-analysis, pathway analysis",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's disease patients,Patients with parkinson’s disease (PD); a neurodegenerative disorder characterized primarily by loss of dopamine neurons in the substantia nigra.,137,223,1 month,16S,34,Illumina,relative abundances,"ANCOM,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Supporting Information Tables S5a and S5b,9 January 2026,Firdaws,Firdaws,Differentially abundant bacterial genera and families altered in Parkinson's disease in the Japanese dataset.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|841,Complete,NA
bsdb:32557853/2/1,32557853,"case-control,meta-analysis",32557853,10.1002/mds.28119,NA,"Nishiwaki H., Ito M., Ishida T., Hamaguchi T., Maeda T., Kashihara K., Tsuboi Y., Ueyama J., Shimamura T., Mori H., Kurokawa K., Katsuno M., Hirayama M. , Ohno K.",Meta-Analysis of Gut Dysbiosis in Parkinson's Disease,Movement disorders : official journal of the Movement Disorder Society,2020,"Parkinson's disease, confounding factors, gut microbiota, meta-analysis, pathway analysis",Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls (Dataset 1),Parkinson's disease patients (Dataset 1),"Dataset 1 comprised patients with Parkinson’s disease (PD), including both individuals receiving a catechol-O-methyltransferase (COMT) inhibitor and those not receiving one.",136,218,1 month,16S,34,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,FALSE,NA,"age,sex","age,body mass index,constipation,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supporting Information Table 10 and Figure 2,13 January 2026,Firdaws,Firdaws,Generalized linear model (GLM) analysis of the Japanese dataset for 25 bacterial taxa identified by meta-analysis of five datasets.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;1783272|1239|186801|3082768|990719|990721;3384194|508458|649775|649776|649777,Complete,NA
bsdb:32557853/2/2,32557853,"case-control,meta-analysis",32557853,10.1002/mds.28119,NA,"Nishiwaki H., Ito M., Ishida T., Hamaguchi T., Maeda T., Kashihara K., Tsuboi Y., Ueyama J., Shimamura T., Mori H., Kurokawa K., Katsuno M., Hirayama M. , Ohno K.",Meta-Analysis of Gut Dysbiosis in Parkinson's Disease,Movement disorders : official journal of the Movement Disorder Society,2020,"Parkinson's disease, confounding factors, gut microbiota, meta-analysis, pathway analysis",Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls (Dataset 1),Parkinson's disease patients (Dataset 1),"Dataset 1 comprised patients with Parkinson’s disease (PD), including both individuals receiving a catechol-O-methyltransferase (COMT) inhibitor and those not receiving one.",136,218,1 month,16S,34,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,FALSE,NA,"age,sex","age,body mass index,constipation,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supporting Information Table 10 and Figure 2,13 January 2026,Firdaws,Firdaws,Generalized linear model (GLM) analysis of the Japanese dataset for 25 bacterial taxa identified by meta-analysis of five datasets.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|841,Complete,NA
bsdb:32557853/3/1,32557853,"case-control,meta-analysis",32557853,10.1002/mds.28119,NA,"Nishiwaki H., Ito M., Ishida T., Hamaguchi T., Maeda T., Kashihara K., Tsuboi Y., Ueyama J., Shimamura T., Mori H., Kurokawa K., Katsuno M., Hirayama M. , Ohno K.",Meta-Analysis of Gut Dysbiosis in Parkinson's Disease,Movement disorders : official journal of the Movement Disorder Society,2020,"Parkinson's disease, confounding factors, gut microbiota, meta-analysis, pathway analysis",Experiment 3,Japan,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls (Dataset 1),Parkinson's disease patients (Dataset 1),"Dataset 1 comprised patients with Parkinson’s disease (PD), including both individuals receiving a catechol-O-methyltransferase (COMT) inhibitor and those not receiving one.",136,218,1 month,16S,34,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,FALSE,NA,"age,sex","age,body mass index,constipation,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supporting Information Figure S2 and Supporting Information Table S6,24 January 2026,Fiddyhamma,Fiddyhamma,Generalized linear model (GLM) analysis of our dataset for 23 bacterial taxa significantly changed in Parkinson’s disease (PD) in the Japanese dataset.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|171550;1783272|1239|186801|3082720|543314;1783272|1239|186801|186802|216572,Complete,NA
bsdb:32557853/3/2,32557853,"case-control,meta-analysis",32557853,10.1002/mds.28119,NA,"Nishiwaki H., Ito M., Ishida T., Hamaguchi T., Maeda T., Kashihara K., Tsuboi Y., Ueyama J., Shimamura T., Mori H., Kurokawa K., Katsuno M., Hirayama M. , Ohno K.",Meta-Analysis of Gut Dysbiosis in Parkinson's Disease,Movement disorders : official journal of the Movement Disorder Society,2020,"Parkinson's disease, confounding factors, gut microbiota, meta-analysis, pathway analysis",Experiment 3,Japan,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls (Dataset 1),Parkinson's disease patients (Dataset 1),"Dataset 1 comprised patients with Parkinson’s disease (PD), including both individuals receiving a catechol-O-methyltransferase (COMT) inhibitor and those not receiving one.",136,218,1 month,16S,34,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,FALSE,NA,"age,sex","age,body mass index,constipation,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supporting Information Figure S2 and Supporting Information Table S6,24 January 2026,Fiddyhamma,Fiddyhamma,Generalized linear model (GLM) analysis of our dataset for 23 bacterial taxa significantly changed in Parkinson’s disease (PD) in the Japanese dataset.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|841,Complete,NA
bsdb:32557853/4/1,32557853,"case-control,meta-analysis",32557853,10.1002/mds.28119,NA,"Nishiwaki H., Ito M., Ishida T., Hamaguchi T., Maeda T., Kashihara K., Tsuboi Y., Ueyama J., Shimamura T., Mori H., Kurokawa K., Katsuno M., Hirayama M. , Ohno K.",Meta-Analysis of Gut Dysbiosis in Parkinson's Disease,Movement disorders : official journal of the Movement Disorder Society,2020,"Parkinson's disease, confounding factors, gut microbiota, meta-analysis, pathway analysis",Experiment 4,Japan,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls (Dataset 2),Parkinson's disease patients (Dataset 2),Patients with parkinson’s disease (PD) in dataset 2 not taking a catechol-O-methyl transferase (COMT) inhibitor,136,151,1 month,16S,34,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,FALSE,NA,"age,sex","age,body mass index,constipation,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supporting Information Figure S2 and Supporting Information Table S6,23 January 2026,Fiddyhamma,Fiddyhamma,Generalized linear model (GLM) analysis of our dataset for 23 bacterial taxa significantly changed in Parkinson’s disease (PD) in the Japanese dataset.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|171550;1783272|1239|186801|3082720|543314;1783272|1239|186801|186802|216572,Complete,NA
bsdb:32557853/4/2,32557853,"case-control,meta-analysis",32557853,10.1002/mds.28119,NA,"Nishiwaki H., Ito M., Ishida T., Hamaguchi T., Maeda T., Kashihara K., Tsuboi Y., Ueyama J., Shimamura T., Mori H., Kurokawa K., Katsuno M., Hirayama M. , Ohno K.",Meta-Analysis of Gut Dysbiosis in Parkinson's Disease,Movement disorders : official journal of the Movement Disorder Society,2020,"Parkinson's disease, confounding factors, gut microbiota, meta-analysis, pathway analysis",Experiment 4,Japan,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls (Dataset 2),Parkinson's disease patients (Dataset 2),Patients with parkinson’s disease (PD) in dataset 2 not taking a catechol-O-methyl transferase (COMT) inhibitor,136,151,1 month,16S,34,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,FALSE,NA,"age,sex","age,body mass index,constipation,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supporting Information Figure S2 and Supporting Information Table S6,23 January 2026,Fiddyhamma,Fiddyhamma,Generalized linear model (GLM) analysis of our dataset for 23 bacterial taxa significantly changed in Parkinson’s disease (PD) in the Japanese dataset.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|841,Complete,NA
bsdb:32557853/7/1,32557853,"case-control,meta-analysis",32557853,10.1002/mds.28119,NA,"Nishiwaki H., Ito M., Ishida T., Hamaguchi T., Maeda T., Kashihara K., Tsuboi Y., Ueyama J., Shimamura T., Mori H., Kurokawa K., Katsuno M., Hirayama M. , Ohno K.",Meta-Analysis of Gut Dysbiosis in Parkinson's Disease,Movement disorders : official journal of the Movement Disorder Society,2020,"Parkinson's disease, confounding factors, gut microbiota, meta-analysis, pathway analysis",Experiment 7,Japan,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls (Dataset 2),Parkinson's disease patients (Dataset 2),Patients with parkinson’s disease (PD) in dataset 2 not taking a catechol-O-methyl transferase (COMT) inhibitor,136,151,1 month,16S,34,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,FALSE,NA,"age,sex","age,body mass index,constipation,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supporting Information Table 10 and Figure 2,14 January 2026,Firdaws,Firdaws,Generalized linear model (GLM) analysis of the Japanese dataset for 25 bacterial taxa identified by meta-analysis of five datasets.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;1783272|1239|186801|3082768|990719|990721;3384194|508458|649775|649776|649777,Complete,NA
bsdb:32557853/7/2,32557853,"case-control,meta-analysis",32557853,10.1002/mds.28119,NA,"Nishiwaki H., Ito M., Ishida T., Hamaguchi T., Maeda T., Kashihara K., Tsuboi Y., Ueyama J., Shimamura T., Mori H., Kurokawa K., Katsuno M., Hirayama M. , Ohno K.",Meta-Analysis of Gut Dysbiosis in Parkinson's Disease,Movement disorders : official journal of the Movement Disorder Society,2020,"Parkinson's disease, confounding factors, gut microbiota, meta-analysis, pathway analysis",Experiment 7,Japan,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls (Dataset 2),Parkinson's disease patients (Dataset 2),Patients with parkinson’s disease (PD) in dataset 2 not taking a catechol-O-methyl transferase (COMT) inhibitor,136,151,1 month,16S,34,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,FALSE,NA,"age,sex","age,body mass index,constipation,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supporting Information Table 10 and Figure 2,14 January 2026,Firdaws,Firdaws,Generalized linear model (GLM) analysis of the Japanese dataset for 25 bacterial taxa identified by meta-analysis of five datasets.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|841,Complete,NA
bsdb:32557853/11/1,32557853,"case-control,meta-analysis",32557853,10.1002/mds.28119,NA,"Nishiwaki H., Ito M., Ishida T., Hamaguchi T., Maeda T., Kashihara K., Tsuboi Y., Ueyama J., Shimamura T., Mori H., Kurokawa K., Katsuno M., Hirayama M. , Ohno K.",Meta-Analysis of Gut Dysbiosis in Parkinson's Disease,Movement disorders : official journal of the Movement Disorder Society,2020,"Parkinson's disease, confounding factors, gut microbiota, meta-analysis, pathway analysis",Experiment 11,"Japan,United States of America,Finland,Russian Federation,Germany",Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's disease patients,Patients with parkinson’s disease (PD); a neurodegenerative disorder characterized primarily by loss of dopamine neurons in the substantia nigra.,475,649,NA,16S,34,Illumina,relative abundances,Meta-Analysis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1 and Supporting Information Table S8,17 January 2026,Fiddyhamma,Fiddyhamma,Bacterial taxa at the genus and family levels that were changed homogenously in Parkinson’s disease (PD) in five datasets,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|s__uncultured Thermoanaerobacterales bacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae",1783272|1239|186801|3085636|186803|1649459;3379134|74201|203494|48461|1647988|239934;1783272|1239|526524|526525|2810280|100883;1783272|1239|186801|3082768|990719|990721;3379134|976|200643|171549|2005525|375288;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|216572|596767;1783272|1239|186801|68295|157468;1783272|1239|526524|526525|128827;1783272|1239|91061|186826|33958;3379134|74201|203494|48461|1647988;3379134|976|200643|171549|2005525;3384194|508458|649775|649776|649777;1783272|201174|84998|1643822|1643826,Complete,NA
bsdb:32557853/11/2,32557853,"case-control,meta-analysis",32557853,10.1002/mds.28119,NA,"Nishiwaki H., Ito M., Ishida T., Hamaguchi T., Maeda T., Kashihara K., Tsuboi Y., Ueyama J., Shimamura T., Mori H., Kurokawa K., Katsuno M., Hirayama M. , Ohno K.",Meta-Analysis of Gut Dysbiosis in Parkinson's Disease,Movement disorders : official journal of the Movement Disorder Society,2020,"Parkinson's disease, confounding factors, gut microbiota, meta-analysis, pathway analysis",Experiment 11,"Japan,United States of America,Finland,Russian Federation,Germany",Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's disease patients,Patients with parkinson’s disease (PD); a neurodegenerative disorder characterized primarily by loss of dopamine neurons in the substantia nigra.,475,649,NA,16S,34,Illumina,relative abundances,Meta-Analysis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1 and Supporting Information Table S8,17 January 2026,Fiddyhamma,Fiddyhamma,Bacterial taxa at the genus and family levels that were changed homogenously in Parkinson’s disease (PD) in five datasets,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|216851;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712,Complete,NA
bsdb:32565704/1/1,32565704,case-control,32565704,10.1016/j.sjbs.2020.04.040,NA,"Liu X., Tian K., Ma X., Wang S., Luo C. , Du Q.",Analysis of subgingival microbiome of periodontal disease and rheumatoid arthritis in Chinese: A case-control study,Saudi journal of biological sciences,2020,"Microbial diversity, Microbiome, Periodontitis, Rheumatoid arthritis, Spirochaetes",Experiment 1,China,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Rheumatoid arthritis,EFO:0000685,healthy controls,rheumatoid arthritis patients,rheumatoid arthritis patients RA,44,54,3 months,16S,4,Illumina,relative abundances,"T-Test,Mann-Whitney (Wilcoxon)",0.05,NA,NA,NA,NA,NA,increased,unchanged,unchanged,NA,NA,Signature 1,"Figure 5, 6, 7",14 March 2023,Sophy,"Sophy,Atrayees,WikiWorks","Different relative abundance of bacterial taxonomy profiles of RA, PD and control group",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|976|200643;3379134|203691|203692|136|137;3379134|203691|203692|136;3379134|203691|203692;3379134|203691|203692|136|2845253|157;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838,Complete,Atrayees
bsdb:32565704/1/2,32565704,case-control,32565704,10.1016/j.sjbs.2020.04.040,NA,"Liu X., Tian K., Ma X., Wang S., Luo C. , Du Q.",Analysis of subgingival microbiome of periodontal disease and rheumatoid arthritis in Chinese: A case-control study,Saudi journal of biological sciences,2020,"Microbial diversity, Microbiome, Periodontitis, Rheumatoid arthritis, Spirochaetes",Experiment 1,China,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Rheumatoid arthritis,EFO:0000685,healthy controls,rheumatoid arthritis patients,rheumatoid arthritis patients RA,44,54,3 months,16S,4,Illumina,relative abundances,"T-Test,Mann-Whitney (Wilcoxon)",0.05,NA,NA,NA,NA,NA,increased,unchanged,unchanged,NA,NA,Signature 2,"Figure 6, 7",14 March 2023,Sophy,"Sophy,Atrayees,WikiWorks",The profile of periodontal pathogens in RA and PE groups compared with controls (*P < 0.05).,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|2005525|195950,Complete,Atrayees
bsdb:32565704/2/1,32565704,case-control,32565704,10.1016/j.sjbs.2020.04.040,NA,"Liu X., Tian K., Ma X., Wang S., Luo C. , Du Q.",Analysis of subgingival microbiome of periodontal disease and rheumatoid arthritis in Chinese: A case-control study,Saudi journal of biological sciences,2020,"Microbial diversity, Microbiome, Periodontitis, Rheumatoid arthritis, Spirochaetes",Experiment 2,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Periodontitis,EFO:0000649,rheumatoid arthritis patients,periodontal disease patients,periodontal disease patients PA,54,45,3 months,16S,4,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),T-Test",0.05,NA,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 7,29 May 2023,Atrayees,"Atrayees,WikiWorks",Profile of periodontal pathogens in RA and PE groups compared with controls,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,Atrayees
bsdb:32565704/2/2,32565704,case-control,32565704,10.1016/j.sjbs.2020.04.040,NA,"Liu X., Tian K., Ma X., Wang S., Luo C. , Du Q.",Analysis of subgingival microbiome of periodontal disease and rheumatoid arthritis in Chinese: A case-control study,Saudi journal of biological sciences,2020,"Microbial diversity, Microbiome, Periodontitis, Rheumatoid arthritis, Spirochaetes",Experiment 2,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Periodontitis,EFO:0000649,rheumatoid arthritis patients,periodontal disease patients,periodontal disease patients PA,54,45,3 months,16S,4,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),T-Test",0.05,NA,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 6, 7",29 May 2023,Atrayees,"Atrayees,WikiWorks",Profile of periodontal pathogens in RA and PE groups compared with controls,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",3379134|976|200643|171549|171552|838;3379134|203691|203692|136|2845253|157;3379134|976|200643|171549|2005525|195950;3379134|976|200643|171549|171551|836,Complete,Atrayees
bsdb:32566740/1/1,32566740,case-control,32566740,10.1038/s41531-020-0112-6,NA,"Wallen Z.D., Appah M., Dean M.N., Sesler C.L., Factor S.A., Molho E., Zabetian C.P., Standaert D.G. , Payami H.",Characterizing dysbiosis of gut microbiome in PD: evidence for overabundance of opportunistic pathogens,NPJ Parkinson's disease,2020,"Genomics, Parkinson's disease",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls free of neurological disease,Participants with Parkinson's Disease,"Dataset 1. Participants with Parkinson's Disease, diagnosed by a movement disorder specialist using UK Brain Bank criteria.",136,212,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,"age,alcohol drinking,body mass index,constipation,geographic area,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2.,22 January 2022,Fcuevas3,"Fcuevas3,Claregrieve1,WikiWorks",Differential abundances of microbial taxa between healthy controls and PD patients,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:32566740/1/2,32566740,case-control,32566740,10.1038/s41531-020-0112-6,NA,"Wallen Z.D., Appah M., Dean M.N., Sesler C.L., Factor S.A., Molho E., Zabetian C.P., Standaert D.G. , Payami H.",Characterizing dysbiosis of gut microbiome in PD: evidence for overabundance of opportunistic pathogens,NPJ Parkinson's disease,2020,"Genomics, Parkinson's disease",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls free of neurological disease,Participants with Parkinson's Disease,"Dataset 1. Participants with Parkinson's Disease, diagnosed by a movement disorder specialist using UK Brain Bank criteria.",136,212,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,"age,alcohol drinking,body mass index,constipation,geographic area,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 2.,22 January 2022,Fcuevas3,"Fcuevas3,Claregrieve1,WikiWorks",Differential abundances of microbial taxa between healthy controls and PD patients,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|3085636|186803|841,Complete,Claregrieve1
bsdb:32566740/2/1,32566740,case-control,32566740,10.1038/s41531-020-0112-6,NA,"Wallen Z.D., Appah M., Dean M.N., Sesler C.L., Factor S.A., Molho E., Zabetian C.P., Standaert D.G. , Payami H.",Characterizing dysbiosis of gut microbiome in PD: evidence for overabundance of opportunistic pathogens,NPJ Parkinson's disease,2020,"Genomics, Parkinson's disease",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control free of neurological disease.,Participants with Parkinson's Disease,Dataset 2. PD was diagnosed by a movement disorder specialist using UK Brain Bank criteria,184,323,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"age,alcohol drinking,body mass index,constipation,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2.,22 January 2022,Fcuevas3,"Fcuevas3,WikiWorks",Differential abundances of 15 PD-associated genera replicated in two datasets.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|201174|1760|85007|1653|1716;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|1578,Complete,Claregrieve1
bsdb:32566740/2/2,32566740,case-control,32566740,10.1038/s41531-020-0112-6,NA,"Wallen Z.D., Appah M., Dean M.N., Sesler C.L., Factor S.A., Molho E., Zabetian C.P., Standaert D.G. , Payami H.",Characterizing dysbiosis of gut microbiome in PD: evidence for overabundance of opportunistic pathogens,NPJ Parkinson's disease,2020,"Genomics, Parkinson's disease",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control free of neurological disease.,Participants with Parkinson's Disease,Dataset 2. PD was diagnosed by a movement disorder specialist using UK Brain Bank criteria,184,323,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"age,alcohol drinking,body mass index,constipation,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 2.,22 January 2022,Fcuevas3,"Fcuevas3,WikiWorks",Differential abundances of 15 PD-associated genera replicated in two datasets.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|28050,Complete,Claregrieve1
bsdb:32591968/1/1,32591968,case-control,32591968,http://dx.doi.org/10.1007/s10620-020-06415-y,NA,"Wu Z.F., Zou K., Wu G.N., Jin Z.J., Xiang C.J., Xu S., Wang Y.H., Wu X.Y., Chen C., Xu Z., Li W.S., Yao X.Q., Zhang J.F. , Liu F.K.",A Comparison of Tumor-Associated and Non-Tumor-Associated Gastric Microbiota in Gastric Cancer Patients,Digestive diseases and sciences,2021,"Carcinogenesis, Gastric cancer, Microbiota, Stomach",Experiment 1,China,Homo sapiens,Gastric pit,UBERON:0000424,Gastric cancer,MONDO:0001056,Superficial gastritis,Gastric cancer (GC),Gastric microbiome in paired tumor and paracancerous tissue samples from GC patients undergoing surgical treatment,64,96,1 month,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,increased,NA,NA,Signature 1,Figure 2B,14 October 2023,Chikamso,"Chikamso,ChiomaBlessing,WikiWorks",Cladogram representation of the gastric microbiota taxa associated with superficial gastritis (group 0) an gastric cancer (group1),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Rudaea,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales",3379134|1224|1236|135624|84642;3379134|1224|1236|135624|84642|642;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849;3379134|29547;3379134|976|1853228|1853229|563835;3379134|976|1853228|1853229;1783272|1239|186801;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802;3379134|29547|3031852|213849|72293|209;3379134|29547|3031852|213849|72293;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85007;1783272|201174|1760|85007|85025;3379134|976|200643|171549|171552|838;3379134|1224|1236|135614|1775411;1783272|201174|1760|85007|85025|1827;3379134|1224|1236|135614|1775411|886360;3379134|976|1853228|1853229|563835|504481;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;3379134|1224|1236|135614,Complete,ChiomaBlessing
bsdb:32591968/1/2,32591968,case-control,32591968,http://dx.doi.org/10.1007/s10620-020-06415-y,NA,"Wu Z.F., Zou K., Wu G.N., Jin Z.J., Xiang C.J., Xu S., Wang Y.H., Wu X.Y., Chen C., Xu Z., Li W.S., Yao X.Q., Zhang J.F. , Liu F.K.",A Comparison of Tumor-Associated and Non-Tumor-Associated Gastric Microbiota in Gastric Cancer Patients,Digestive diseases and sciences,2021,"Carcinogenesis, Gastric cancer, Microbiota, Stomach",Experiment 1,China,Homo sapiens,Gastric pit,UBERON:0000424,Gastric cancer,MONDO:0001056,Superficial gastritis,Gastric cancer (GC),Gastric microbiome in paired tumor and paracancerous tissue samples from GC patients undergoing surgical treatment,64,96,1 month,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,increased,NA,NA,Signature 2,Figure 2B,14 October 2023,Chikamso,"Chikamso,ChiomaBlessing,WikiWorks",Cladogram representation of the gastric microbiota taxa associated with superficial gastritis (group 0) and gastric cancer (group 1).,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,p__Candidatus Altimarinota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;1783272|201174;3379134|976|200643|171549|171552|1283313;1783272|201174|1760|85006|1268|1663;3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|1224|28216;3379134|1224|28211|356|41294|374;3379134|1224|28211|204458|76892|41275;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294;363464;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066|203490|203491|203492|848;3379134|1224|1236|135625|712|724;3379134|1224|28211|356;3384189|32066|203490|203491|1129771|32067;1783272|201174|1760|85006|1268;1783272|201174|1760|85006;1783272|1239|909932;3379134|1224|28216|206351|481|482;3379134|1224|1236|135625|712;3379134|1224|1236|135625;;3379134|1224|28211|356|69277|28100;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|1224|28211|356|82115;33090|35493|3398|72025|3803|3814|508215;1783272|1239|909932|909929;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977;3379134|1224|28211|356|335928,Complete,ChiomaBlessing
bsdb:32591968/2/1,32591968,case-control,32591968,http://dx.doi.org/10.1007/s10620-020-06415-y,NA,"Wu Z.F., Zou K., Wu G.N., Jin Z.J., Xiang C.J., Xu S., Wang Y.H., Wu X.Y., Chen C., Xu Z., Li W.S., Yao X.Q., Zhang J.F. , Liu F.K.",A Comparison of Tumor-Associated and Non-Tumor-Associated Gastric Microbiota in Gastric Cancer Patients,Digestive diseases and sciences,2021,"Carcinogenesis, Gastric cancer, Microbiota, Stomach",Experiment 2,China,Homo sapiens,Gastric pit,UBERON:0000424,Gastric cancer,MONDO:0001056,non-tumor tissues of gastric cancer patients,tumor tissues of gastric cancer patients,Gastric microbiome in tumor tissue samples from GC patients undergoing surgical treatment,78,18,1 month,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Supplementary figure 3A,22 October 2023,Chikamso,"Chikamso,WikiWorks",Differential bacteria between the tumor and non-tumor tissues of gastric cancer patients by LEfSe analysis (LDA scores >3.0),decreased,"k__Bacillati|p__Actinomycetota|c__Nitriliruptoria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales",1783272|201174|908620;3379134|1224|28211|356|69277|68287;3379134|1224|28211|356|41294|374;3379134|1224|28211|356|335928;3379134|1224|1236|2887326|468;3379134|1224|28211|356|82115;3379134|1224|1236|72274;3379134|1224|28211|356,Complete,ChiomaBlessing
bsdb:32591968/2/2,32591968,case-control,32591968,http://dx.doi.org/10.1007/s10620-020-06415-y,NA,"Wu Z.F., Zou K., Wu G.N., Jin Z.J., Xiang C.J., Xu S., Wang Y.H., Wu X.Y., Chen C., Xu Z., Li W.S., Yao X.Q., Zhang J.F. , Liu F.K.",A Comparison of Tumor-Associated and Non-Tumor-Associated Gastric Microbiota in Gastric Cancer Patients,Digestive diseases and sciences,2021,"Carcinogenesis, Gastric cancer, Microbiota, Stomach",Experiment 2,China,Homo sapiens,Gastric pit,UBERON:0000424,Gastric cancer,MONDO:0001056,non-tumor tissues of gastric cancer patients,tumor tissues of gastric cancer patients,Gastric microbiome in tumor tissue samples from GC patients undergoing surgical treatment,78,18,1 month,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Supplementary figure 3A,22 October 2023,Chikamso,"Chikamso,WikiWorks",Differential bacteria between the tumor and non-tumor tissues of gastric cancer patients by LEfSe analysis (LDA >3.0),increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Fusobacteriati|p__Fusobacteriota",1783272|1239|91061;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066|203490|203491|203492|848;1783272|1239|91061|186826;3379134|1224|28216|206351|481;3384189|32066,Complete,ChiomaBlessing
bsdb:32596386/1/1,32596386,"laboratory experiment,time series / longitudinal observational",32596386,10.1155/2020/8456596,NA,"Chen Y., Fang L., Chen S., Zhou H., Fan Y., Lin L., Li J., Xu J., Chen Y., Ma Y. , Chen Y.",Gut Microbiome Alterations Precede Cerebral Amyloidosis and Microglial Pathology in a Mouse Model of Alzheimer's Disease,BioMed research international,2020,NA,Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Wild-type (WT),APP/PS1,"Alzheimer's Disease (AD) mouse model 
1-month-old",14,21,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table S2,6 October 2024,AaishahM,"AaishahM,WikiWorks",Significantly different taxa between WT and AD (APP/PS1) mice,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,NA
bsdb:32596386/2/1,32596386,"laboratory experiment,time series / longitudinal observational",32596386,10.1155/2020/8456596,NA,"Chen Y., Fang L., Chen S., Zhou H., Fan Y., Lin L., Li J., Xu J., Chen Y., Ma Y. , Chen Y.",Gut Microbiome Alterations Precede Cerebral Amyloidosis and Microglial Pathology in a Mouse Model of Alzheimer's Disease,BioMed research international,2020,NA,Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Wild-type (WT),APP/PS1,"Alzheimer's Disease (AD) mouse model
2-month-old",17,24,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,increased,unchanged,NA,unchanged,Signature 1,Table S2,6 October 2024,AaishahM,"AaishahM,WikiWorks",Significantly different taxa between WT and AD (APP/PS1) mice,increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",1783272|201174;3379134|74201|203494|48461|1647988|239934;1783272|1239|526524|526525|128827|174708;3379134|976|200643|171549|171552|1283313;1783272|201174|1760|85004|31953|1678;1783272|1239|526524|526525|128827;3379134|976|200643|171549|171552;3379134|74201|203494|48461|203557;3379134|74201;1783272|1239|526524|526525|2810280|3025755,Complete,NA
bsdb:32596386/3/1,32596386,"laboratory experiment,time series / longitudinal observational",32596386,10.1155/2020/8456596,NA,"Chen Y., Fang L., Chen S., Zhou H., Fan Y., Lin L., Li J., Xu J., Chen Y., Ma Y. , Chen Y.",Gut Microbiome Alterations Precede Cerebral Amyloidosis and Microglial Pathology in a Mouse Model of Alzheimer's Disease,BioMed research international,2020,NA,Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Wild-type (WT),APP/PS1,"Alzheimer's Disease (AD) mouse model
3-month-old",17,24,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table S2,17 December 2024,AaishahM,"AaishahM,WikiWorks",Significantly different taxa between WT and AD (APP/PS1) mice,increased,NA,NA,Complete,NA
bsdb:32596386/3/2,32596386,"laboratory experiment,time series / longitudinal observational",32596386,10.1155/2020/8456596,NA,"Chen Y., Fang L., Chen S., Zhou H., Fan Y., Lin L., Li J., Xu J., Chen Y., Ma Y. , Chen Y.",Gut Microbiome Alterations Precede Cerebral Amyloidosis and Microglial Pathology in a Mouse Model of Alzheimer's Disease,BioMed research international,2020,NA,Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Wild-type (WT),APP/PS1,"Alzheimer's Disease (AD) mouse model
3-month-old",17,24,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table S2,17 December 2024,AaishahM,"AaishahM,WikiWorks",Significantly different taxa between WT and AD (APP/PS1) mice,decreased,NA,NA,Complete,NA
bsdb:32596386/4/1,32596386,"laboratory experiment,time series / longitudinal observational",32596386,10.1155/2020/8456596,NA,"Chen Y., Fang L., Chen S., Zhou H., Fan Y., Lin L., Li J., Xu J., Chen Y., Ma Y. , Chen Y.",Gut Microbiome Alterations Precede Cerebral Amyloidosis and Microglial Pathology in a Mouse Model of Alzheimer's Disease,BioMed research international,2020,NA,Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Wild-type (WT),APP/PS1,"Alzheimer's Disease (AD) mouse model
6-month-old",31,34,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table S2,9 October 2024,AaishahM,"AaishahM,WikiWorks",Significantly different taxa between WT and AD (APP/PS1) mice,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|186803|572511;3379134|1224|1236|91347|543;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3085636|186803|1506577;3379134|74201|203494|48461|203557;3379134|74201;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|1940338,Complete,NA
bsdb:32596386/4/2,32596386,"laboratory experiment,time series / longitudinal observational",32596386,10.1155/2020/8456596,NA,"Chen Y., Fang L., Chen S., Zhou H., Fan Y., Lin L., Li J., Xu J., Chen Y., Ma Y. , Chen Y.",Gut Microbiome Alterations Precede Cerebral Amyloidosis and Microglial Pathology in a Mouse Model of Alzheimer's Disease,BioMed research international,2020,NA,Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Wild-type (WT),APP/PS1,"Alzheimer's Disease (AD) mouse model
6-month-old",31,34,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table S2,9 October 2024,AaishahM,"AaishahM,WikiWorks",Significantly different taxa between WT and AD (APP/PS1) mice,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|1940338;3379134|976|200643|171549|171550,Complete,NA
bsdb:32596386/5/1,32596386,"laboratory experiment,time series / longitudinal observational",32596386,10.1155/2020/8456596,NA,"Chen Y., Fang L., Chen S., Zhou H., Fan Y., Lin L., Li J., Xu J., Chen Y., Ma Y. , Chen Y.",Gut Microbiome Alterations Precede Cerebral Amyloidosis and Microglial Pathology in a Mouse Model of Alzheimer's Disease,BioMed research international,2020,NA,Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Wild-type (WT),APP/PS1,"Alzheimer's Disease (AD) mouse model
9-month-old",18,18,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 1,Table S2,9 October 2024,AaishahM,"AaishahM,WikiWorks",Significantly different taxa between WT and AD (APP/PS1) mice,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__Desulfovibrionaceae bacterium,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Pseudomonadota",3379134|74201|203494|48461|1647988|239934;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924|2049043;3379134|74201|203494|48461|203557;3379134|74201;3379134|1224,Complete,NA
bsdb:32596386/5/2,32596386,"laboratory experiment,time series / longitudinal observational",32596386,10.1155/2020/8456596,NA,"Chen Y., Fang L., Chen S., Zhou H., Fan Y., Lin L., Li J., Xu J., Chen Y., Ma Y. , Chen Y.",Gut Microbiome Alterations Precede Cerebral Amyloidosis and Microglial Pathology in a Mouse Model of Alzheimer's Disease,BioMed research international,2020,NA,Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Wild-type (WT),APP/PS1,"Alzheimer's Disease (AD) mouse model
9-month-old",18,18,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 2,Table S2,9 October 2024,AaishahM,"AaishahM,WikiWorks",Significantly different taxa between WT and AD(APP/PS1) mice,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Atopostipes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae",3379134|976|200643|171549|171550|239759;1783272|1239|91061|186826|186828|292480;1783272|1239|91061|186826|186828,Complete,NA
bsdb:32596386/6/1,32596386,"laboratory experiment,time series / longitudinal observational",32596386,10.1155/2020/8456596,NA,"Chen Y., Fang L., Chen S., Zhou H., Fan Y., Lin L., Li J., Xu J., Chen Y., Ma Y. , Chen Y.",Gut Microbiome Alterations Precede Cerebral Amyloidosis and Microglial Pathology in a Mouse Model of Alzheimer's Disease,BioMed research international,2020,NA,Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,"A combination of groups WT 2m, 3m, 6m, 9m",WT 1m,Wild-type mouse 1-month-old,83,14,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure S3 A,24 October 2024,AaishahM,"AaishahM,WikiWorks",Differentially represented bacterial taxa of WT,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",3379134|976|200643|171549;3379134|976|200643;3379134|976;1783272|1239|186801|186802|31979|49082;1783272|1239|186801|186802|31979,Complete,NA
bsdb:32596386/7/1,32596386,"laboratory experiment,time series / longitudinal observational",32596386,10.1155/2020/8456596,NA,"Chen Y., Fang L., Chen S., Zhou H., Fan Y., Lin L., Li J., Xu J., Chen Y., Ma Y. , Chen Y.",Gut Microbiome Alterations Precede Cerebral Amyloidosis and Microglial Pathology in a Mouse Model of Alzheimer's Disease,BioMed research international,2020,NA,Experiment 7,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,"A combination of groups WT 1m, 3m, 6m, 9m",WT 2m,Wild-type mouse 2-month-old,80,17,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,increased,unchanged,NA,unchanged,Signature 1,Figure S3 A,24 October 2024,AaishahM,"AaishahM,WikiWorks",Differentially represented bacterial taxa of WT,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__uncultured Muribaculaceae bacterium",3379134|976|200643|171549|2005473;3379134|976|200643|171549|2005473|2301481,Complete,NA
bsdb:32596386/8/1,32596386,"laboratory experiment,time series / longitudinal observational",32596386,10.1155/2020/8456596,NA,"Chen Y., Fang L., Chen S., Zhou H., Fan Y., Lin L., Li J., Xu J., Chen Y., Ma Y. , Chen Y.",Gut Microbiome Alterations Precede Cerebral Amyloidosis and Microglial Pathology in a Mouse Model of Alzheimer's Disease,BioMed research international,2020,NA,Experiment 8,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,"A combination of groups WT 1m, 2m, 6m, 9m",WT 3m,Wild-type mouse 3-month-old,80,17,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure S3 A,24 October 2024,AaishahM,"AaishahM,WikiWorks",Differentially represented bacterial taxa of WT,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",1783272|1239;1783272|1239|186801|186802|3085642|580596;3379134|200930|68337|191393|191394;3379134|200930|68337|191393;3379134|200930|68337;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|297314;1783272|1239|186801|186802|216572|707003,Complete,NA
bsdb:32596386/9/1,32596386,"laboratory experiment,time series / longitudinal observational",32596386,10.1155/2020/8456596,NA,"Chen Y., Fang L., Chen S., Zhou H., Fan Y., Lin L., Li J., Xu J., Chen Y., Ma Y. , Chen Y.",Gut Microbiome Alterations Precede Cerebral Amyloidosis and Microglial Pathology in a Mouse Model of Alzheimer's Disease,BioMed research international,2020,NA,Experiment 9,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,"A combination of groups WT 1m, 2m, 3m, 9m",WT 6m,Wild-type mouse 6-month-old,66,31,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure S3 A,24 October 2024,AaishahM,"AaishahM,WikiWorks",Differentially represented bacterial taxa of WT,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|s__uncultured Peptococcaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae",3379134|976|200643|171549|171552|1283313;1783272|1239|526524|526525|128827|174708;1783272|1239|186801|186802|186807|329911;1783272|1239|186801|186802|186807,Complete,NA
bsdb:32596386/10/1,32596386,"laboratory experiment,time series / longitudinal observational",32596386,10.1155/2020/8456596,NA,"Chen Y., Fang L., Chen S., Zhou H., Fan Y., Lin L., Li J., Xu J., Chen Y., Ma Y. , Chen Y.",Gut Microbiome Alterations Precede Cerebral Amyloidosis and Microglial Pathology in a Mouse Model of Alzheimer's Disease,BioMed research international,2020,NA,Experiment 10,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,"A combination of groups WT 1m, 2m, 3m, 6m",WT 9m,Wild-type mouse 9-month-old,79,18,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 1,Figure S3 A,25 October 2024,AaishahM,"AaishahM,WikiWorks",Differentially represented bacterial taxa of WT,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacillati|p__Candidatus Melainabacteria,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales|s__uncultured Gastranaerophilales bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|74201|203494|48461|1647988|239934;1783272|1798710|1906119;1783272|1798710;1783272|1117;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|186801|3085636|186803|1506553;3379134|1224|28211|204441|41295;3379134|1224|28211|204441;3379134|74201|203494|48461|203557;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201;1783272|1798710|1906119|3076055;3379134|976|200643|171549|171552,Complete,NA
bsdb:32596386/11/1,32596386,"laboratory experiment,time series / longitudinal observational",32596386,10.1155/2020/8456596,NA,"Chen Y., Fang L., Chen S., Zhou H., Fan Y., Lin L., Li J., Xu J., Chen Y., Ma Y. , Chen Y.",Gut Microbiome Alterations Precede Cerebral Amyloidosis and Microglial Pathology in a Mouse Model of Alzheimer's Disease,BioMed research international,2020,NA,Experiment 11,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,"A combination of groups APP/PS1 2m, 3m, 6m, 9m",APP/PS1 1m,Alzheimer's Disease (AD) mouse model 1-month-old,100,21,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure S3 B,25 October 2024,AaishahM,"AaishahM,WikiWorks",Differentially represented bacterial taxa of APP/PS1 1m,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979|49082;1783272|1239|186801|186802|31979;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|1940338;3379134|1224|1236;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|171550,Complete,NA
bsdb:32596386/12/1,32596386,"laboratory experiment,time series / longitudinal observational",32596386,10.1155/2020/8456596,NA,"Chen Y., Fang L., Chen S., Zhou H., Fan Y., Lin L., Li J., Xu J., Chen Y., Ma Y. , Chen Y.",Gut Microbiome Alterations Precede Cerebral Amyloidosis and Microglial Pathology in a Mouse Model of Alzheimer's Disease,BioMed research international,2020,NA,Experiment 12,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,"A combination of groups APP/PS1 1m, 3m, 6m, 9m",APP/PS1 2m,Alzheimer's Disease (AD) mouse model 2-month-old,97,24,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,increased,unchanged,NA,unchanged,Signature 1,Figure S3 B,25 October 2024,AaishahM,"AaishahM,WikiWorks",Differentially represented bacterial taxa of APP/PS1 2m,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__uncultured Muribaculaceae bacterium",1783272|1239|91061|1385|90964|1279;1783272|1239|91061|1385|90964;1783272|1239|91061|1385;3379134|976|200643|171549|2005473;3379134|976|200643|171549|2005473|2301481,Complete,NA
bsdb:32596386/13/1,32596386,"laboratory experiment,time series / longitudinal observational",32596386,10.1155/2020/8456596,NA,"Chen Y., Fang L., Chen S., Zhou H., Fan Y., Lin L., Li J., Xu J., Chen Y., Ma Y. , Chen Y.",Gut Microbiome Alterations Precede Cerebral Amyloidosis and Microglial Pathology in a Mouse Model of Alzheimer's Disease,BioMed research international,2020,NA,Experiment 13,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,"A combination of groups APP/PS1 1m, 2m, 6m, 9m",APP/PS1 3m,Alzheimer's Disease (AD) mouse model 3-month-old,97,24,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure S3 B,25 October 2024,AaishahM,"AaishahM,WikiWorks",Differentially represented bacterial taxa of APP/PS1 3m,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",1783272|1239|186801|186802|216572|244127;1783272|1239|186801|3085636|186803|572511;3379134|200930|68337|191393|191394;3379134|200930|68337|191393;3379134|200930|68337;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3085636|186803|297314;1783272|1239|186801|186802|216572|707003,Complete,NA
bsdb:32596386/14/1,32596386,"laboratory experiment,time series / longitudinal observational",32596386,10.1155/2020/8456596,NA,"Chen Y., Fang L., Chen S., Zhou H., Fan Y., Lin L., Li J., Xu J., Chen Y., Ma Y. , Chen Y.",Gut Microbiome Alterations Precede Cerebral Amyloidosis and Microglial Pathology in a Mouse Model of Alzheimer's Disease,BioMed research international,2020,NA,Experiment 14,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,"A combination of groups APP/PS1 1m, 2m, 3m, 9m",APP/PS1 6m,Alzheimer's Disease (AD) mouse model 6-month-old,87,34,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure S3 B,25 October 2024,AaishahM,"AaishahM,WikiWorks",Differentially represented bacterial taxa of APP/PS1 6m,increased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,1783272|1239|526524|526525|128827|174708,Complete,NA
bsdb:32596386/15/1,32596386,"laboratory experiment,time series / longitudinal observational",32596386,10.1155/2020/8456596,NA,"Chen Y., Fang L., Chen S., Zhou H., Fan Y., Lin L., Li J., Xu J., Chen Y., Ma Y. , Chen Y.",Gut Microbiome Alterations Precede Cerebral Amyloidosis and Microglial Pathology in a Mouse Model of Alzheimer's Disease,BioMed research international,2020,NA,Experiment 15,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,"A combination of groups APP/PS1 1m, 2m, 3m, 6m",APP/PS1 9m,Alzheimer's Disease (AD) mouse model 9-month-old,103,18,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 1,Figure S3 B,25 October 2024,AaishahM,"AaishahM,WikiWorks",Differentially represented bacterial taxa of APP/PS1 9m,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacillati|p__Cyanobacteriota,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales|s__uncultured Gastranaerophilales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|s__uncultured Peptococcaceae bacterium",1783272|201174;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1798710|1906119;1783272|1117;28221;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|186802|186807;3379134|1224;3379134|1224|28211|204441|41295;3379134|1224|28211|204441;1783272|1239|526524|526525|2810281|191303;1783272|1798710|1906119|3076055;1783272|1239|186801|186802|186807|329911,Complete,NA
bsdb:32604882/1/1,32604882,"cross-sectional observational, not case-control",32604882,10.3390/microorganisms8060961,NA,"Amaruddin A.I., Hamid F., Koopman J.P.R., Muhammad M., Brienen E.A., van Lieshout L., Geelen A.R., Wahyuni S., Kuijper E.J., Sartono E., Yazdanbakhsh M. , Zwittink R.D.","The Bacterial Gut Microbiota of Schoolchildren from High and Low Socioeconomic Status: A Study in an Urban Area of Makassar, Indonesia",Microorganisms,2020,"gut microbiota, intestinal parasites, nutritional status, schoolchildren, socioeconomic status",Experiment 1,Indonesia,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,Children of low SES,Children of high SES,"High SES school is located in the city centre and is considered of high status, with a majority of the parents working as high-skilled workers or professionals with higher education.",66,74,NA,16S,34,Illumina,relative abundances,PERMANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 1,Figure 1C.,5 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Peace Sandy,WikiWorks",Figure 1C. Differential abundance of bacterial taxa between high and low SES children. Taxa with Benjamini–Hochberg corrected p-value below 0.05 are shown.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|1239|526524|526525|128827;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|28050|2049031;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|186806|1730;1783272|201174|84998|84999|1643824;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678,Complete,Peace Sandy
bsdb:32604882/1/2,32604882,"cross-sectional observational, not case-control",32604882,10.3390/microorganisms8060961,NA,"Amaruddin A.I., Hamid F., Koopman J.P.R., Muhammad M., Brienen E.A., van Lieshout L., Geelen A.R., Wahyuni S., Kuijper E.J., Sartono E., Yazdanbakhsh M. , Zwittink R.D.","The Bacterial Gut Microbiota of Schoolchildren from High and Low Socioeconomic Status: A Study in an Urban Area of Makassar, Indonesia",Microorganisms,2020,"gut microbiota, intestinal parasites, nutritional status, schoolchildren, socioeconomic status",Experiment 1,Indonesia,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,Children of low SES,Children of high SES,"High SES school is located in the city centre and is considered of high status, with a majority of the parents working as high-skilled workers or professionals with higher education.",66,74,NA,16S,34,Illumina,relative abundances,PERMANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 2,Figure 1C.,5 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Peace Sandy,WikiWorks",Figure 1C. Differential abundance of bacterial taxa between high and low SES children. Taxa with Benjamini–Hochberg corrected p-value below 0.05 are shown.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__Eubacteriales Family XIII. Incertae Sedis bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella",3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|3082720|543314|2137877;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|186802|31979;3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|2005473;1783272|201174|84998|1643822|1643826;1783272|201174|84998|1643822|1643826|580024;1783272|201174|84998|84999|1643824;1783272|201174|84998|84999|1643824|2082587,Complete,Peace Sandy
bsdb:32630754/2/1,32630754,time series / longitudinal observational,32630754,https://doi.org/10.3390/ani10071127,NA,"Kim D.H., Kim M.H., Kim S.B., Son J.K., Lee J.H., Joo S.S., Gu B.H., Park T., Park B.Y. , Kim E.T.",Differential Dynamics of the Ruminal Microbiome of Jersey Cows in a Heat Stress Environment,Animals : an open access journal from MDPI,2020,"Holstein, Jersey, KEGG pathways, heat stress, ruminal microbiome",Experiment 2,Republic of Korea,Bos taurus,Rumen,UBERON:0007365,Ruminative stress response,EFO:0009857,Jersey cows under normal condition,Jersey cows under heat stress condition,"Jersey cows under heat stress condition. The measurement of the respiration rate and rectal temperature in May was considered as the normal condition, while  measurement of the respiration rate and rectal temperature in August was considered the heat stress condition.",8,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,NA,increased,NA,NA,Signature 1,figure 4C,23 October 2023,Folakunmi,"Folakunmi,ChiomaBlessing,WikiWorks",Differentially abundant taxa in Jersey cows under heat stress condition compared to Jersey cows under normal conditions,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus cereus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium botulinum,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Tissierellia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas|s__Xanthomonas arboricola",1783272|1239|91061|1385|186817|1386|1396;1783272|1239|91061|1385|186817|1386;3379134|203691|203692|1643686|143786;3379134|203691|203692|1643686;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|31979|1485|1491;1783272|1117;3379134|29547|3031852;3379134|976|117743;3384189|32066|203490;1783272|544448|31969;1783272|544448|31969|2085;1783272|544448;3379134|976|117747;1783272|1239|91061|1385|90964|1279;1783272|1239|1737404;3379134|1224|1236|135614|32033|338|56448,Complete,ChiomaBlessing
bsdb:32630754/2/2,32630754,time series / longitudinal observational,32630754,https://doi.org/10.3390/ani10071127,NA,"Kim D.H., Kim M.H., Kim S.B., Son J.K., Lee J.H., Joo S.S., Gu B.H., Park T., Park B.Y. , Kim E.T.",Differential Dynamics of the Ruminal Microbiome of Jersey Cows in a Heat Stress Environment,Animals : an open access journal from MDPI,2020,"Holstein, Jersey, KEGG pathways, heat stress, ruminal microbiome",Experiment 2,Republic of Korea,Bos taurus,Rumen,UBERON:0007365,Ruminative stress response,EFO:0009857,Jersey cows under normal condition,Jersey cows under heat stress condition,"Jersey cows under heat stress condition. The measurement of the respiration rate and rectal temperature in May was considered as the normal condition, while  measurement of the respiration rate and rectal temperature in August was considered the heat stress condition.",8,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,NA,increased,NA,NA,Signature 2,figure 4C + 4A,24 October 2023,Folakunmi,"Folakunmi,ChiomaBlessing,WikiWorks",Differentially abundant taxa in Jersey cows under heat stress condition compared to Jersey cows under normal conditions,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Anaerorhabdus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium WCE2004",1783272|201174|1760;1783272|201174;1783272|201174|1760|85004;1783272|201174|84998;1783272|1239|186801|186802;1783272|201174|1760|85011;1783272|201174|1760|85008;3379134|1224|1236|72274|135621|286;1783272|201174|1760|85010;1783272|201174|1760|85011|2062|1883;1783272|1239|526524|526525|128827|118966;3379134|976|200643|171549|1945890,Complete,ChiomaBlessing
bsdb:32640977/1/1,32640977,"cross-sectional observational, not case-control",32640977,10.1186/s12866-020-01883-8,NA,"Halboub E., Al-Ak'hali M.S., Alamir A.H., Homeida H.E., Baraniya D., Chen T. , Al-Hebshi N.N.",Tongue microbiome of smokeless tobacco users,BMC microbiology,2020,"Microbiota, Mouth neoplasms, Rothia mucilaginosa, high-throughput nucleotide sequencing, Tobacco, Tongue",Experiment 1,Saudi Arabia,Homo sapiens,Tongue,UBERON:0001723,Smoking behavior,EFO:0004318,non-shammah users,shammah users,participants who used shammah daily for at least one year without a period of cessation and those who had no history of shammah use,23,29,3 months,16S,123,Illumina,relative abundances,LEfSe,0.015,TRUE,NA,sex,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 3 a & b,10 January 2021,Victoria Goulbourne,WikiWorks,Differentially abundant taxa,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia meyeri,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia|s__Alloscardovia omnicolens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus gastricus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus pittmaniae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flava,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hongkongensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata",1783272|1239|91061|186826|1300|1301;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85004|31953|419014;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300|1301|1306;1783272|201174|1760|2037|2049|2529408|52773;1783272|201174|1760|85004|31953|419014|419015;1783272|1239|91061|186826|33958|2742598|227942;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|91061|186826|1300|1301|1343;3379134|1224|1236|135625|712|724|249188;3379134|1224|28216|206351|481|482|484;1783272|1239|909932|1843489|31977|29465|29466;3379134|1224|28216|206351|481|482|34026;3384189|32066|203490|203491|1129771|32067|554406;1783272|201174|1760|2037|2049|1654|29317;1783272|1239|91061|186826|1300|1301|1305;3379134|1224|28216|206351|481|482|495,Complete,Atrayees
bsdb:32640977/1/2,32640977,"cross-sectional observational, not case-control",32640977,10.1186/s12866-020-01883-8,NA,"Halboub E., Al-Ak'hali M.S., Alamir A.H., Homeida H.E., Baraniya D., Chen T. , Al-Hebshi N.N.",Tongue microbiome of smokeless tobacco users,BMC microbiology,2020,"Microbiota, Mouth neoplasms, Rothia mucilaginosa, high-throughput nucleotide sequencing, Tobacco, Tongue",Experiment 1,Saudi Arabia,Homo sapiens,Tongue,UBERON:0001723,Smoking behavior,EFO:0004318,non-shammah users,shammah users,participants who used shammah daily for at least one year without a period of cessation and those who had no history of shammah use,23,29,3 months,16S,123,Illumina,relative abundances,LEfSe,0.015,TRUE,NA,sex,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 3 a & b,10 January 2021,Victoria Goulbourne,WikiWorks,Differentially abundant taxa,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium asaccharolyticum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Pseudomonadati|p__Myxococcota|c__Myxococcia|o__Myxococcales|f__Archangiaceae|g__Archangium",3379134|1224|28216|206351|481|538;1783272|1239|186801|3082720|186804|1257;1783272|1239|186801|3085636|186803|265975;3379134|1224|28216|206351|481|538|539;1783272|1239|91061|186826|1300|1301|1306;1783272|1239|186801|3085636|186803|265975|1501332;1783272|1239|186801|3085636|186803|265975|237576;3384189|32066|203490|203491|1129771|32067|104608;3379134|2818505|32015|29|39|47,Complete,Atrayees
bsdb:32656096/1/1,32656096,"cross-sectional observational, not case-control",32656096,10.3389/fcimb.2020.00286,NA,"Yang Q., Wang Y., Wei X., Zhu J., Wang X., Xie X. , Lu W.",The Alterations of Vaginal Microbiome in HPV16 Infection as Identified by Shotgun Metagenomic Sequencing,Frontiers in cellular and infection microbiology,2020,"HPV infection, cervical cancer, metabolism, shotgun metagenomic sequencing, vaginal microbiome",Experiment 1,China,Homo sapiens,Vaginal fluid,UBERON:0036243,Human papilloma virus infection,EFO:0001668,Healthy control,HPV-16+,Patients with HPV-16 positive without lesion confirmed by HPV genotyping assay,25,27,1 month,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 3(B),21 March 2021,Cynthia Anderson,"Cynthia Anderson,Peace Sandy,WikiWorks",Vaginal microbiome as HPV16-infection markers. (B) Histogram of the LDA scores computed for species differentially abundant between HPV16-positive women and controls. The LDA scores (log10) > 2 are listed,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus tetradius,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium|s__Atopobium deltae,k__Pseudomonadati|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia|s__Chlamydia trachomatis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemelliphila|s__Gemelliphila asaccharolytica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Kytococcaceae|g__Kytococcus|s__Kytococcus sedentarius,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Mageeibacillus|s__Mageeibacillus indolicus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus curtisii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Nocardia|s__Nocardia brevicatena,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella uli,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus|s__Paracoccus denitrificans,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter|s__Pedobacter panaciterrae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus harei,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella corporis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia turicensis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces auratus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Stutzerimonas|s__Stutzerimonas stutzeri,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella montpellierensis,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter oralis,k__Fungi|p__Microsporidia|f__Enterocytozoonidae|g__Enterocytozoon|s__Enterocytozoon bieneusi,k__Fungi|p__Basidiomycota|c__Pucciniomycetes|o__Pucciniales|f__Melampsoraceae|g__Melampsora|s__Melampsora laricis-populina,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae,k__Fungi|p__Basidiomycota|c__Ustilaginomycetes|o__Ustilaginales|g__Kalmanozyma|s__Kalmanozyma brasiliensis,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces mikatae,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Thelebolales|f__Thelebolaceae|g__Pseudogymnoascus,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces kudriavzevii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Shotokuvirae|p__Cossaviricota|c__Papovaviricetes|o__Zurhausenvirales|f__Papillomaviridae|s__Firstpapillomavirinae|g__Alphapapillomavirus|s__Alphapapillomavirus 14",1783272|1239|1737404|1737405|1570339|165779|33036;1783272|201174|84998|84999|1643824|1380|1393034;3379134|204428|204429|51291|809|810|813;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|909932|1843489|31977|39948|309120;3384189|32066|203490|203491|203492|848|851;1783272|201174|1760|85004|31953|2701|2702;1783272|1239|91061|1385|539738|3076174|502393;1783272|201174|1760|85006|2805426|57499|1276;1783272|1239|186801|186802|216572|1637257|884684;1783272|201174|1760|2037|2049|2050|2051;1783272|201174|1760|85007|85025|1817|37327;1783272|201174|84998|84999|1643824|133925|133926;3379134|1224|28211|204455|31989|265|266;1783272|1239|1737404|1737405|1570339|543311|33033;3379134|976|117747|200666|84566|84567|363849;1783272|1239|1737404|1737405|1570339|162289|54005;1783272|1239|1737404|1737405|1570339|162289|33031;1783272|1239|186801|3082720|186804|1257|1261;3379134|976|200643|171549|171552|838|419005;3379134|976|200643|171549|171552|838|28125;3379134|976|200643|171549|171552|838|28128;3379134|976|200643|171549|171552|838|28130;3379134|976|200643|171549|171552|838|28132;1783272|201174|1760|2037|2049|2529408|131111;1783272|1239|526524|526525|128827|123375|102148;1783272|201174|1760|85011|2062|1883|114687;3379134|1224|1236|72274|135621|2901164|316;1783272|1239|909932|1843489|31977|29465|187328;3366610|28890|183925|2158|2159|2172|66851;4751|6029|27970|27971|31281;4751|5204|162484|5258|5259|5260|203908;4751|4890|4891|4892|4893|4930|252598;4751|5204|5257|5267|1804794|1392244;4751|5204|1538075|162474|742845|55193|76775;4751|4890|3239874|2916678|766764|5475|5476;4751|4890|4891|4892|4893|4930|114525;4751|4890|147548|292491|46451|78156;4751|4890|4891|4892|4893|4930|4932;4751|4890|4891|4892|4893|4930|114524;3379134|1224|1236|91347|543;1783272|1239|91061|186826|33958|1578;2732092|2732415|2732421|2732533|151340|2169595|333750|931244,Complete,Peace Sandy
bsdb:32656096/1/2,32656096,"cross-sectional observational, not case-control",32656096,10.3389/fcimb.2020.00286,NA,"Yang Q., Wang Y., Wei X., Zhu J., Wang X., Xie X. , Lu W.",The Alterations of Vaginal Microbiome in HPV16 Infection as Identified by Shotgun Metagenomic Sequencing,Frontiers in cellular and infection microbiology,2020,"HPV infection, cervical cancer, metabolism, shotgun metagenomic sequencing, vaginal microbiome",Experiment 1,China,Homo sapiens,Vaginal fluid,UBERON:0036243,Human papilloma virus infection,EFO:0001668,Healthy control,HPV-16+,Patients with HPV-16 positive without lesion confirmed by HPV genotyping assay,25,27,1 month,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 3 (B),25 January 2024,Peace Sandy,"Peace Sandy,WikiWorks",Vaginal microbiome as HPV16-infection markers. (B) Histogram of the LDA scores computed for species differentially abundant between HPV16-positive women and controls. The LDA scores (log10) > 2 are listed,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp. 1140_ESPC,k__Shotokuvirae|p__Cossaviricota|c__Papovaviricetes|o__Zurhausenvirales|f__Papillomaviridae|s__Firstpapillomavirinae|g__Alphapapillomavirus,k__Fungi|p__Microsporidia|g__Mitosporidium|s__Mitosporidium daphniae,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Nakaseomyces|s__Nakaseomyces glabratus,k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Mucor|s__Mucor ambiguus,k__Fungi|p__Microsporidia|f__Nosematidae|g__Nosema|s__Nosema bombycis",1783272|1239|91061|186826|81852|1350|1579349;2732092|2732415|2732421|2732533|151340|2169595|333750;4751|6029|1633384|1485682;4751|4890|4891|4892|4893|374468|5478;4751|1913637|2212703|4827|34489|4830|91626;4751|6029|27974|27977|27978,Complete,Peace Sandy
bsdb:32665329/1/1,32665329,"cross-sectional observational, not case-control",32665329,10.1128/mSystems.00450-20,NA,"Zhao C., Wei Z., Yang J., Zhang J., Yu C., Yang A., Zhang M., Zhang L., Wang Y., Mu X., Heng X., Yang H., Gai Z., Wang X. , Zhang L.",Characterization of the Vaginal Microbiome in Women with Infertility and Its Potential Correlation with Hormone Stimulation during <i>In Vitro</i> Fertilization Surgery,mSystems,2020,"in vitro fertilization, infertility, ovulation induction, vaginal microbiome",Experiment 1,China,Homo sapiens,Vagina,UBERON:0000996,Female infertility,EFO:0008560,"Group A-I, group O and group N-O",Group B-I,Patient samples from women suffering from secondary infertility collected during the first 3 days of the follicular phase,100,30,1 month,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S1,25 June 2025,Aleru Divine,Aleru Divine,"The most differentially abundant taxa between the four groups (A-I, B-I, N-O, and O groups).",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales,k__Bacillati|p__Mycoplasmatota",1783272|1239|91061|186826|186827;1783272|1239|91061|186826|186827|1375;1783272|1239|91061|1385|186817;1783272|1239|91061|1385;1783272|1239|91061|1385|186817|1386;1783272|201174|1760|85006|85020|43668;3379134|1224|28211|356|41294|374;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|909932|1843489|31977|906;1783272|544448|31969;1783272|544448|31969|2085|2092|2093;1783272|544448|31969|2085|2092;1783272|544448|31969|2085;1783272|544448,Complete,NA
bsdb:32665329/2/1,32665329,"cross-sectional observational, not case-control",32665329,10.1128/mSystems.00450-20,NA,"Zhao C., Wei Z., Yang J., Zhang J., Yu C., Yang A., Zhang M., Zhang L., Wang Y., Mu X., Heng X., Yang H., Gai Z., Wang X. , Zhang L.",Characterization of the Vaginal Microbiome in Women with Infertility and Its Potential Correlation with Hormone Stimulation during <i>In Vitro</i> Fertilization Surgery,mSystems,2020,"in vitro fertilization, infertility, ovulation induction, vaginal microbiome",Experiment 2,China,Homo sapiens,Vagina,UBERON:0000996,Female infertility,EFO:0008560,"Group B-I, group O and group N-O",Group A-I,patient samples from women suffering from secondary infertility collected after gonadotropin-releasing hormone [GnRH] agonist and recombinant human chorionic gonadotropin [r-hCG] administration,122,8,1 month,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S1,25 June 2025,Aleru Divine,Aleru Divine,"The most differentially abundant taxa between the four groups (A-I, B-I, N-O, and O groups).",increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota,,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Nevskiales|f__Nevskiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Steroidobacterales|f__Steroidobacteraceae|g__Steroidobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Vitreoscilla",1783272|201174;1783272|201174|84998|84999|1643824|1380;1783272|1239;;1783272|1239|91061|1385|186818;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|91061|1385|186817|400634;1783272|201174|1760|85008|28056;3379134|1224|1236|1775403|568386;3379134|1224|1236|3060226|2689614|469322;3379134|1224|28216|206351|481|59,Complete,NA
bsdb:32665329/3/1,32665329,"cross-sectional observational, not case-control",32665329,10.1128/mSystems.00450-20,NA,"Zhao C., Wei Z., Yang J., Zhang J., Yu C., Yang A., Zhang M., Zhang L., Wang Y., Mu X., Heng X., Yang H., Gai Z., Wang X. , Zhang L.",Characterization of the Vaginal Microbiome in Women with Infertility and Its Potential Correlation with Hormone Stimulation during <i>In Vitro</i> Fertilization Surgery,mSystems,2020,"in vitro fertilization, infertility, ovulation induction, vaginal microbiome",Experiment 3,China,Homo sapiens,Vagina,UBERON:0000996,Female infertility,EFO:0008560,"Group A-I, group B-I and group N-O",Group O,Patient samples from healthy women during the first 3 days of the ovulation period,88,42,1 month,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S1,25 June 2025,Aleru Divine,Aleru Divine,"The most differentially abundant taxa between the four groups (A-I, B-I, N-O, and O groups).",increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Chitinophaga,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Roseomonadaceae|g__Roseomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae|g__Spirosoma,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Viridiplantae|p__Streptophyta,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,p__Candidatus Absconditibacteriota|s__candidate division SR1 bacterium",1783272|201174|84992;3379134|1224|28211|204441|2829815|191;3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|1224|28216;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;3379134|976|1853228|1853229|563835|79328;1783272|1117;1783272|1239|186801|186802|216572|216851;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;1783272|1239|186801|3085636|186803;3384189|32066|203490|203491|1129771;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481;3379134|1224|28216|206351;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|1224|28211|3120395|3385906|125216;1783272|1239|909932|909929|1843491|970;1783272|1239|186801|3085636|186803|177971;3384189|32066|203490|203491|1129771|168808;3379134|976|768503|768507|89373|107;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;33090|35493;1783272|544448|2790996|2790998|2129;221235|2044938,Complete,NA
bsdb:32665329/4/1,32665329,"cross-sectional observational, not case-control",32665329,10.1128/mSystems.00450-20,NA,"Zhao C., Wei Z., Yang J., Zhang J., Yu C., Yang A., Zhang M., Zhang L., Wang Y., Mu X., Heng X., Yang H., Gai Z., Wang X. , Zhang L.",Characterization of the Vaginal Microbiome in Women with Infertility and Its Potential Correlation with Hormone Stimulation during <i>In Vitro</i> Fertilization Surgery,mSystems,2020,"in vitro fertilization, infertility, ovulation induction, vaginal microbiome",Experiment 4,China,Homo sapiens,Vagina,UBERON:0000996,Female infertility,EFO:0008560,"Group A-I, group B-I and group O",Group N-O,Patient samples from healthy women during 3 days of the nonovulation period [follicular phase],80,50,1 month,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S1,25 June 2025,Aleru Divine,Aleru Divine,"The most differentially abundant taxa between the four groups (A-I, B-I, N-O, and O groups).",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Aneurinibacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Wautersiella",3379134|1224|1236|2887326|468|469;1783272|1239|91061|1385|186822|55079;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|1224|28216|80840;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|186801|186802;3379134|1224|1236;3379134|1224|1236|135625|712|724;3379134|1224|1236|2887326|468;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|1224|1236|135623|641|657;3379134|1224|1236|91347|1903414|583;3379134|1224|1236|72274|135621;3379134|1224|1236|72274;3379134|1224;3379134|1224|1236|72274|135621|286;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977;3379134|1224|1236|135623|641;3379134|1224|1236|135623;3379134|976|117743|200644|2762318|343873,Complete,NA
bsdb:32673387/1/1,32673387,case-control,32673387,10.1167/iovs.61.8.22,NA,"Zhao F., Zhang D., Ge C., Zhang L., Reinach P.S., Tian X., Tao C., Zhao Z., Zhao C., Fu W., Zeng C. , Chen W.",Metagenomic Profiling of Ocular Surface Microbiome Changes in Meibomian Gland Dysfunction,Investigative ophthalmology & visual science,2020,NA,Experiment 1,China,Homo sapiens,Meibum,UBERON:0019315,Meibomian cyst,EFO:0007363,Healthy Control (HCs),Meibomian gland dysfunction (MGD),Patients diagnosed with Meibomian gland dysfunction (MGD),15,61,6 months,WMS,NA,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,NA,Signature 1,Table 1 and Supplementary Figure S2D,5 November 2024,Rahila,"Rahila,Aleru Divine,WikiWorks",Pathogens with differential incidences in meibum between MGD patients and healthy controls (p<0.05),increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus licheniformis,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter coli,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter jejuni,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia globosa,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas fluorescens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas protegens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia pickettii,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|g__Yarrowia|s__Yarrowia lipolytica",1783272|1239|91061|1385|186817|1386|1402;3379134|29547|3031852|213849|72294|194|195;3379134|29547|3031852|213849|72294|194|197;1783272|1239|91061|186826|81852|1350|1352;3379134|1224|1236|91347|543|561|562;4751|5204|1538075|162474|742845|55193|76773;3379134|1224|1236|72274|135621|286|287;3379134|1224|1236|72274|135621|286|294;3379134|1224|1236|72274|135621|286|380021;3379134|1224|28216|80840|119060|48736|329;4751|4890|3239873|3243772|4951|4952,Complete,Svetlana up
bsdb:32673387/1/2,32673387,case-control,32673387,10.1167/iovs.61.8.22,NA,"Zhao F., Zhang D., Ge C., Zhang L., Reinach P.S., Tian X., Tao C., Zhao Z., Zhao C., Fu W., Zeng C. , Chen W.",Metagenomic Profiling of Ocular Surface Microbiome Changes in Meibomian Gland Dysfunction,Investigative ophthalmology & visual science,2020,NA,Experiment 1,China,Homo sapiens,Meibum,UBERON:0019315,Meibomian cyst,EFO:0007363,Healthy Control (HCs),Meibomian gland dysfunction (MGD),Patients diagnosed with Meibomian gland dysfunction (MGD),15,61,6 months,WMS,NA,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,NA,Signature 2,Table 1 and Supplementary Figure S2D,21 January 2025,Aleru Divine,"Aleru Divine,WikiWorks",Pathogens with differential incidences in meibum between MGD patients and healthy controls (p<0.05),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas mosselii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas testosteroni,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia marcescens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sicca,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria meningitidis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Roseomonadaceae|g__Roseomonas|s__Roseomonas gilardii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus capitis",3379134|1224|1236|72274|135621|286|78327;3379134|1224|1236|91347|543|547;3379134|1224|28216|80840|80864|283|285;3379134|1224|1236|91347|1903411|613|615;3379134|1224|1236|135614|32033|40323|40324;3379134|1224|28216|206351|481|482|490;3379134|1224|28216|206351|481|482|487;3379134|1224|28211|3120395|3385906|125216|257708;1783272|1239|91061|1385|90964|1279|29388,Complete,Svetlana up
bsdb:32673387/2/1,32673387,case-control,32673387,10.1167/iovs.61.8.22,NA,"Zhao F., Zhang D., Ge C., Zhang L., Reinach P.S., Tian X., Tao C., Zhao Z., Zhao C., Fu W., Zeng C. , Chen W.",Metagenomic Profiling of Ocular Surface Microbiome Changes in Meibomian Gland Dysfunction,Investigative ophthalmology & visual science,2020,NA,Experiment 2,China,Homo sapiens,Meibum,UBERON:0019315,Meibomian cyst,EFO:0007363,Healthy Control (HCs),Meibomian gland dysfunction (MGD),Patients diagnosed with Meibomian gland dysfunction (MGD),15,61,6 months,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,NA,Signature 1,Supplementary Table S4,21 January 2025,Aleru Divine,"Aleru Divine,WikiWorks",Comparison of significant changes at the different taxonomic levels in meibum microbiomes of patients with MGD.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acidocellaceae|g__Acidiphilium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax|s__Acidovorax sp. KKS102,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter guillouiae,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae|g__Actinoplanes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae|g__Actinoplanes|s__Actinoplanes friuliensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas|s__Aeromonas media,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae|g__Alicyclobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae|g__Alicyclobacillus|s__Alicyclobacillus herbarius,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomicrobiaceae|g__Allosphingosinicella|s__Allosphingosinicella indica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Amycolatopsis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Aneurinibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Aneurinibacillus|s__Aneurinibacillus sp. XH2,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Anoxybacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Aurantiacibacter|s__Aurantiacibacter gangjinensis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus licheniformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus smithii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. oral taxon F28,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium elkanii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium sp. BTAi1,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium sp. OHSU_III,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium|s__Brevibacterium siliguriense,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella|s__Brucella anthropi,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter coli,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter jejuni,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium sp. StRB126,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Collimonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Collimonas|s__Collimonas arenae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Collimonas|s__Collimonas fungivorans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium aurimucosum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium callunae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium camporealensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium diphtheriae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium epidermidicanis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium glutamicum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium imitans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium jeikeium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium phocae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium riegelii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium simulans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. ATCC 6931,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium striatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium timonense,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium urealyticum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium ureicelerivorans,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Croceicoccus|s__Croceicoccus marinus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium avidum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Cytobacillus|s__Cytobacillus oceanisediminis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia|s__Delftia sp. HK171,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Dermabacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Dermabacter|s__Dermabacter vaginalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Desulfofundulus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Desulfofundulus|s__Desulfofundulus kuznetsovii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Erythrobacter|s__Erythrobacter neustonensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Fictibacillaceae|g__Fictibacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Friedmanniella|s__Friedmanniella luteola,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Geobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Geobacillus|s__Geobacillus genomosp. 3,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Geobacillus|s__Geobacillus sp. 12AMOR1,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Geobacillus|s__Geobacillus sp. GHH01,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Geobacillus|s__Geobacillus sp. LC300,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Geobacillus|s__Geobacillus sp. WCH70,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Geobacillus|s__Geobacillus sp. Y4.1MC1,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Geobacillus|s__Geobacillus subterraneus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Geobacillus|s__Geobacillus thermodenitrificans,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Geobacillus|s__Geobacillus thermoleovorans,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Halalkalibacterium (ex Joshi et al. 2022)|s__Halalkalibacterium halodurans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum|s__Herbaspirillum autotrophicum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum|s__Herbaspirillum frisingense,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum|s__Herbaspirillum hiltneri,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium|s__Janthinobacterium sp. LM6,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria|s__Kocuria flava,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria|s__Kocuria turfanensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae|g__Kyrpidia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae|g__Kyrpidia|s__Kyrpidia tusciae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lentibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lentibacillus|s__Lentibacillus amyloliquefaciens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium|s__Mesorhizobium opportunistum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium|s__Methylobacterium aquaticum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium|s__Methylobacterium nodulans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium kansasii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Thermoactinomycetaceae|g__Novibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Thermoactinomycetaceae|g__Novibacillus|s__Novibacillus thermophilus,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Oceanithermus|s__Oceanithermus profundus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus xylanexedens,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Parageobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Parageobacillus|s__Parageobacillus thermoglucosidasius,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter|s__Pedobacter cryoconitis,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter|s__Pedobacter heparinus,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter|s__Pedobacter sp. PACM 27299,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter|s__Pedobacter steynii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Porphyrobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Pseudodesulfovibrio|s__Pseudodesulfovibrio aespoeensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas yamanorum,k__Thermotogati|p__Thermotogota|c__Thermotogae|o__Thermotogales|f__Thermotogaceae|g__Pseudothermotoga|s__Pseudothermotoga lettingae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Rhizorhabdaceae|g__Rhizorhabdus|s__Rhizorhabdus wittichii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcoides|s__Rhodococcoides fascians,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus|s__Rhodococcus sp. PBTS 1,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter|s__Rubrobacter radiotolerans,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter|s__Rubrobacter xylanophilus,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|g__Samunavirus,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|g__Samunavirus|s__Samunavirus SM1,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Shouchella|s__Shouchella lehensis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium|s__Sphingobium baderi,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium|s__Sphingobium chlorophenolicum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium|s__Sphingobium chungbukense,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium|s__Sphingobium cloacae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium|s__Sphingobium indicum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium|s__Sphingobium sp. EP60837,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium|s__Sphingobium sp. MI1205,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium|s__Sphingobium sp. RAC03,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium|s__Sphingobium sp. SYK-6,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium|s__Sphingobium sp. TKS,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium|s__Sphingobium sp. YBL2,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas echinoides,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas koreensis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas melonis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas panacis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas paucimobilis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas sanxanigenens,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas sp. 007,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas sp. 037,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas sp. 664,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas sp. KC8,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas sp. LK11,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas sp. LM7,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas sp. MM-1,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas sp. NIC1,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas sp. NX-3,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas sp. SL9,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas taxi,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingopyxidaceae|g__Sphingopyxis|s__Sphingopyxis fribergensis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingopyxidaceae|g__Sphingopyxis|s__Sphingopyxis granuli,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces sp. CFMR 7,k__Pseudomonadati|p__Aquificota|c__Aquificia|o__Aquificales|f__Hydrogenothermaceae|g__Sulfurihydrogenibium,k__Pseudomonadati|p__Aquificota|c__Aquificia|o__Aquificales|f__Hydrogenothermaceae|g__Sulfurihydrogenibium|s__Sulfurihydrogenibium sp. YO3AOP1,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Terribacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Terribacillus|s__Terribacillus aidingensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Thermincolaceae|g__Thermincola,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Thermincolaceae|g__Thermincola|s__Thermincola potens,k__Bacillati|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae|g__Thermoanaerobacterium,k__Bacillati|p__Chloroflexota|c__Chloroflexia|o__Candidatus Thermobaculales|f__Candidatus Thermobaculaceae|g__Thermobaculum,k__Bacillati|p__Chloroflexota|c__Chloroflexia|o__Candidatus Thermobaculales|f__Candidatus Thermobaculaceae|g__Thermobaculum|s__Thermobaculum terrenum,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus|s__Thermus scotoductus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Ureibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Ureibacillus|s__Ureibacillus thermosphaericus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae|g__Xylanimonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae|g__Xylanimonas|s__Xylanimonas cellulosilytica,s__cotton phyllosphere bacterium M,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|s__uncultured Alphaproteobacteria bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas|s__uncultured Halomonas sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__uncultured Sphingomonas sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|s__uncultured beta proteobacterium,s__uncultured organism,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas hengshuiensis",3379134|1224|28211|3120395|3385905|522;3379134|1224|28216|80840|80864|12916|358220;3379134|1224|1236|2887326|468|469|106649;1783272|201174;1783272|201174|1760|85008|28056|1865;1783272|201174|1760|85008|28056|1865|196914;3379134|1224|1236|135624|84642|642|651;1783272|1239|91061|1385|186823|29330;1783272|1239|91061|1385|186823|29330|122960;3379134|1224|28211|204457|3423713|2823232|941907;1783272|201174|1760|85010|2070|1813;1783272|1239|91061|1385|186822|55079;1783272|1239|91061|1385|186822|55079|1450761;1783272|1239|91061|1385|3120669|150247;3379134|1224|28211|204457|335929|2800681|502682;3379134|1224|28211|204441|2829815|191;1783272|1239|91061|1385|186817|1386;1783272|1239|91061|1385|186817|1386|1402;1783272|1239|91061|1385|186817|1386|1479;1783272|1239|91061|1385|186817|1386|712180;3379134|1224|28211|356|41294|374;3379134|1224|28211|356|41294|374|29448;3379134|1224|28211|356|41294|374|288000;3379134|1224|28211|356|41294|374|1297865;1783272|201174|1760|85006|85019|1696;1783272|201174|1760|85006|85019|1696|1136497;3379134|1224|28211|356|118882|234|529;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294|194|195;3379134|29547|3031852|213849|72294|194|197;3379134|976|117743|200644|2762318|59732|878220;3379134|1224|28216|80840|75682|202907;3379134|1224|28216|80840|75682|202907|279058;3379134|1224|28216|80840|75682|202907|158899;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85007|1653|1716|169292;1783272|201174|1760|85007|1653|1716|1721;1783272|201174|1760|85007|1653|1716|161896;1783272|201174|1760|85007|1653|1716|1717;1783272|201174|1760|85007|1653|1716|1050174;1783272|201174|1760|85007|1653|1716|1718;1783272|201174|1760|85007|1653|1716|156978;1783272|201174|1760|85007|1653|1716|38289;1783272|201174|1760|85007|1653|1716|161895;1783272|201174|1760|85007|1653|1716|156976;1783272|201174|1760|85007|1653|1716|146827;1783272|201174|1760|85007|1653|1716|1487956;1783272|201174|1760|85007|1653|1716|43770;1783272|201174|1760|85007|1653|1716|441500;1783272|201174|1760|85007|1653|1716|43771;1783272|201174|1760|85007|1653|1716|401472;3379134|1224|28211|204457|335929|1295327|450378;1783272|201174|1760|85009|31957|1912216;1783272|201174|1760|85009|31957|1912216|33010;1783272|1239|91061|1385|186817|2675230|665099;3379134|1224|28216|80840|80864|80865|1920191;1783272|201174|1760|85006|85020|36739;1783272|201174|1760|85006|85020|36739|1630135;1783272|1239|186801|186802|186807|2282741;1783272|1239|186801|186802|186807|2282741|58135;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|81852|1350|1352;3379134|1224|28211|204457|335929|1041|1112;1783272|1239|91061|1385|3120697|1329200;1783272|201174|1760|85009|85015|53387|546871;1783272|1239|91061|1385|3120669|129337;1783272|1239|91061|1385|3120669|129337|1921421;1783272|1239|91061|1385|3120669|129337|1629723;1783272|1239|91061|1385|3120669|129337|1233873;1783272|1239|91061|1385|3120669|129337|1519377;1783272|1239|91061|1385|3120669|129337|471223;1783272|1239|91061|1385|3120669|129337|581103;1783272|1239|91061|1385|3120669|129337|129338;1783272|1239|91061|1385|3120669|129337|33940;1783272|1239|91061|1385|3120669|129337|33941;1783272|1239|91061|1385|186817|2893055|86665;3379134|1224|28216|80840|75682|963;3379134|1224|28216|80840|75682|963|180195;3379134|1224|28216|80840|75682|963|92645;3379134|1224|28216|80840|75682|963|341045;3379134|1224|28216|80840|75682|29580|1938606;1783272|201174|1760|85006|1268|57493|446860;1783272|201174|1760|85006|1268|57493|388357;1783272|1239|91061|1385|186823|1129704;1783272|1239|91061|1385|186823|1129704|33943;1783272|1239|91061|1385|186817|175304;1783272|1239|91061|1385|186817|175304|1472767;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843489|31977|906|907;3379134|1224|28211|356|69277|68287|593909;3379134|1224|28211|356|119045|407|270351;3379134|1224|28211|356|119045|407|114616;1783272|201174|1760|85007|1762|1763|1768;1783272|1239|91061|1385|186824|1677050;1783272|1239|91061|1385|186824|1677050|1471761;3384194|1297|188787|68933|188786|208447|187137;3379134|1224|28211|356|118882|528;1783272|1239|91061|1385|186822|44249|528191;1783272|1239|91061|1385|3120669|1906945;1783272|1239|91061|1385|3120669|1906945|1426;3379134|976|117747|200666|84566|84567;3379134|976|117747|200666|84566|84567|188932;3379134|976|117747|200666|84566|84567|984;3379134|976|117747|200666|84566|84567|1727164;3379134|976|117747|200666|84566|84567|430522;3379134|1224|28211|204457|335929|1111;1783272|201174|1760|85009|31957|1743;3379134|200940|3031449|213115|194924|2035811|182210;3379134|1224|1236|72274|135621|286|515393;3384194|200918|188708|2419|188709|1643951|177758;3379134|1224|28211|204457|3423714|1649486|160791;1783272|201174|1760|85007|85025|3259750|1828;1783272|201174|1760|85007|85025|1827|1653478;1783272|201174|84995|84996|84997|42255;1783272|201174|84995|84996|84997|42255|42256;1783272|201174|84995|84996|84997|42255|49319;2731360|2731618|2731619|2560221;2731360|2731618|2731619|2560221|2560683;1783272|1239|91061|1385|186817|2893057|300825;3379134|1224|28211|204457|3423717|165695;3379134|1224|28211|204457|3423717|165695|1332080;3379134|1224|28211|204457|3423717|165695|46429;3379134|1224|28211|204457|3423717|165695|56193;3379134|1224|28211|204457|3423717|165695|120107;3379134|1224|28211|204457|3423717|165695|332055;3379134|1224|28211|204457|3423717|165695|1855519;3379134|1224|28211|204457|3423717|165695|407020;3379134|1224|28211|204457|3423717|165695|1843368;3379134|1224|28211|204457|3423717|165695|627192;3379134|1224|28211|204457|3423717|165695|1315974;3379134|1224|28211|204457|3423717|165695|484429;3379134|1224|28211|204457|41297|13687;3379134|1224|28211|204457|41297|13687|59803;3379134|1224|28211|204457|41297|13687|93064;3379134|1224|28211|204457|41297|13687|152682;3379134|1224|28211|204457|41297|13687|1560345;3379134|1224|28211|204457|41297|13687|13689;3379134|1224|28211|204457|41297|13687|397260;3379134|1224|28211|204457|41297|13687|28214;3379134|1224|28211|204457|41297|13687|1130907;3379134|1224|28211|204457|41297|13687|1130911;3379134|1224|28211|204457|41297|13687|1130970;3379134|1224|28211|204457|41297|13687|1030157;3379134|1224|28211|204457|41297|13687|1390395;3379134|1224|28211|204457|41297|13687|1938607;3379134|1224|28211|204457|41297|13687|745310;3379134|1224|28211|204457|41297|13687|1961362;3379134|1224|28211|204457|41297|13687|863935;3379134|1224|28211|204457|41297|13687|1221575;3379134|1224|28211|204457|41297|13687|1549858;3379134|1224|28211|204457|3423718|165697|1515612;3379134|1224|28211|204457|3423718|165697|267128;1783272|201174|1760|85011|2062|1883;1783272|201174|1760|85011|2062|1883|1649184;3379134|200783|187857|32069|224027|212790;3379134|200783|187857|32069|224027|212790|436114;1783272|1239|91061|1385|186817|459532;1783272|1239|91061|1385|186817|459532|586416;1783272|1239|186801|186802|2937911|278993;1783272|1239|186801|186802|2937911|278993|863643;1783272|1239|186801|68295|186814|28895;1783272|200795|32061|3399777|3399778|262406;1783272|200795|32061|3399777|3399778|262406|166501;3384194|1297|188787|68933|188786|270|37636;1783272|1239|91061|1385|186818|160795;1783272|1239|91061|1385|186818|160795|51173;1783272|201174|1760|85006|85017|186188;1783272|201174|1760|85006|85017|186188|186189;378824;3379134|1224|28211|91750;3379134|1224|1236|135619|28256|2745|173971;3379134|1224|28211|204457|41297|13687|158754;3379134|1224|28216|86027;155900;3379134|1224|28211|204457|41297|13687|1609977,Complete,Svetlana up
bsdb:32673387/2/2,32673387,case-control,32673387,10.1167/iovs.61.8.22,NA,"Zhao F., Zhang D., Ge C., Zhang L., Reinach P.S., Tian X., Tao C., Zhao Z., Zhao C., Fu W., Zeng C. , Chen W.",Metagenomic Profiling of Ocular Surface Microbiome Changes in Meibomian Gland Dysfunction,Investigative ophthalmology & visual science,2020,NA,Experiment 2,China,Homo sapiens,Meibum,UBERON:0019315,Meibomian cyst,EFO:0007363,Healthy Control (HCs),Meibomian gland dysfunction (MGD),Patients diagnosed with Meibomian gland dysfunction (MGD),15,61,6 months,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,NA,Signature 2,Supplementary Table S4,21 January 2025,Aleru Divine,"Aleru Divine,WikiWorks",Comparison of significant changes at the different taxonomic levels in meibum microbiomes of patients with MGD.,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Diaphorobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria gonorrhoeae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola salanitronis,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas alkylphenolica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas asplenii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas azotoformans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas brassicacearum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas brenneri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas chlororaphis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas fluorescens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas glycinae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas granadensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas rhodesiae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. A214,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. B10,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. DR 5-09,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas tolaasii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas veronii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas viridiflava,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Roseomonadaceae|g__Roseomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus capitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xylella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas synxantha,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas orientalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas extremaustralis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas poae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas reinekei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas trivialis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas libanensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas cedrina,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Metapseudomonas|s__Metapseudomonas resinovorans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. bs2935,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. WCS374,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas koreensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas extremorientalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas mucidolens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas antarctica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas lini,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. GR 6-02,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__uncultured Pseudomonas sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas corrugata,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas prosekii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas simiae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas izuensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas agarici,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas vancouverensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas frederiksbergensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas arsenicoxydans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas thivervalensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas cichorii,s__Agaricus bisporus virus X",3379134|976;3379134|1224|28216|80840|80864|238749;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481|482|485;3379134|976|200643|171549|815|909656|376805;3379134|1224;3379134|1224|1236|72274|135621|286;3379134|1224|1236|72274|135621|286|287;3379134|1224|1236|72274|135621|286|237609;3379134|1224|1236|72274|135621|286|53407;3379134|1224|1236|72274|135621|286|47878;3379134|1224|1236|72274|135621|286|930166;3379134|1224|1236|72274|135621|286|129817;3379134|1224|1236|72274|135621|286|587753;3379134|1224|1236|72274|135621|286|294;3379134|1224|1236|72274|135621|286|1785145;3379134|1224|1236|72274|135621|286|1421430;3379134|1224|1236|72274|135621|286|76760;3379134|1224|1236|72274|135621|286|1855331;3379134|1224|1236|72274|135621|286|118613;3379134|1224|1236|72274|135621|286|1534110;3379134|1224|1236|72274|135621|286|29442;3379134|1224|1236|72274|135621|286|76761;3379134|1224|1236|72274|135621|286|33069;3379134|1224|28211|3120395|3385906|125216;1783272|1239|91061|1385|90964|1279|29388;1783272|1239|91061|186826|1300|1301|1304;3379134|1224|1236|135623|641|662;3379134|1224|1236|135614|32033|2370;3379134|1224|1236|72274|135621|286|47883;3379134|1224|1236|72274|135621|286|76758;3379134|1224|1236|72274|135621|286|359110;3379134|1224|1236|72274|135621|286|200451;3379134|1224|1236|72274|135621|286|395598;3379134|1224|1236|72274|135621|286|200450;3379134|1224|1236|72274|135621|286|75588;3379134|1224|1236|72274|135621|286|651740;3379134|1224|1236|72274|135621|3236656|53412;3379134|1224|1236|72274|135621|286|1761895;3379134|1224|1236|72274|135621|286|1495331;3379134|1224|1236|72274|135621|286|198620;3379134|1224|1236|72274|135621|286|169669;3379134|1224|1236|72274|135621|286|46679;3379134|1224|1236|72274|135621|286|219572;3379134|1224|1236|72274|135621|286|163011;3379134|1224|1236|72274|135621|286|1659194;3379134|1224|1236|72274|135621|286|114707;3379134|1224|1236|72274|135621|286|47879;3379134|1224|1236|72274|135621|286|1148509;3379134|1224|1236|72274|135621|286|321846;3379134|1224|1236|72274|135621|286|2684212;3379134|1224|1236|72274|135621|286|46677;3379134|1224|1236|72274|135621|286|95300;3379134|1224|1236|72274|135621|286|104087;3379134|1224|1236|72274|135621|286|702115;3379134|1224|1236|72274|135621|286|86265;3379134|1224|1236|72274|135621|286|36746;181522,Complete,Svetlana up
bsdb:32673387/3/1,32673387,case-control,32673387,10.1167/iovs.61.8.22,NA,"Zhao F., Zhang D., Ge C., Zhang L., Reinach P.S., Tian X., Tao C., Zhao Z., Zhao C., Fu W., Zeng C. , Chen W.",Metagenomic Profiling of Ocular Surface Microbiome Changes in Meibomian Gland Dysfunction,Investigative ophthalmology & visual science,2020,NA,Experiment 3,China,Homo sapiens,Skin of eyelid,UBERON:0001457,Meibomian cyst,EFO:0007363,Healthy Control (HCs),Meibomian gland dysfunction (MGD),Patients diagnosed with Meibomian gland dysfunction (MGD),15,61,6 months,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,NA,Signature 1,Supplementary Table S4,21 January 2025,Aleru Divine,"Aleru Divine,WikiWorks",Comparison of significant changes at the different taxonomic levels in the eyelid skin microbiomes of patients with MGD.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces pacaensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae|g__Alicyclobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae|g__Alicyclobacillus|s__Alicyclobacillus herbarius,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Altererythrobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Amycolatopsis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Aurantiacibacter|s__Aurantiacibacter gangjinensis,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus licheniformis,k__Shotokuvirae|p__Cossaviricota|c__Papovaviricetes|o__Zurhausenvirales|f__Papillomaviridae|s__Firstpapillomavirinae|g__Betapapillomavirus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Boseaceae|g__Bosea,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Boseaceae|g__Bosea|s__Bosea vaviloviae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium sp. BTAi1,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium|s__Brevibacterium siliguriense,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas|s__Brevundimonas subvibrioides,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter coli,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter jejuni,k__Pseudomonadati|p__Chlamydiota,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium gallinarum,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium sp. StRB126,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium argentoratense,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium aurimucosum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium diphtheriae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium glutamicum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium humireducens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium imitans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium jeikeium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium phocae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium simulans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium singulare,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. ATCC 6931,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium striatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium timonense,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium urealyticum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Croceicoccus|s__Croceicoccus marinus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium avidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium modestum,k__Bacillati|p__Cyanobacteriota,k__Thermotogati|p__Deinococcota,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus actinosclerus,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus proteolyticus,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus radiodurans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus|s__Dermacoccus nishinomiyaensis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Elizabethkingia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Elizabethkingia|s__Elizabethkingia anophelis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Filimonas|s__Filimonas lacunae,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Flavisolibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria|s__Kocuria flava,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lentibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lentibacillus|s__Lentibacillus amyloliquefaciens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Microlunatus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Microvirga,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Thermoactinomycetaceae|g__Novibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Thermoactinomycetaceae|g__Novibacillus|s__Novibacillus thermophilus,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Oceanithermus|s__Oceanithermus profundus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ottowia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ottowia|s__Ottowia sp. oral taxon 894,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus xylanexedens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Parageobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Parageobacillus|s__Parageobacillus thermoglucosidasius,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Pauljensenia|s__Pauljensenia hongkongensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella scopos,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium freudenreichii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Rhizorhabdaceae|g__Rhizorhabdus|s__Rhizorhabdus wittichii,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter|s__Rubrobacter radiotolerans,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter|s__Rubrobacter xylanophilus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium|s__Sphingobium chungbukense,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium|s__Sphingobium sp. EP60837,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium|s__Sphingobium sp. YBL2,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas echinoides,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas hengshuiensis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas panacis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas sp. 007,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas sp. 664,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas sp. LM7,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas sp. SL9,k__Pseudomonadati|p__Spirochaetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus haemolyticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus saprophyticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus intermedius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 064,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus suis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Tessaracoccus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Trueperella|s__Trueperella pyogenes,s__cotton phyllosphere bacterium M,s__uncultured organism,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kineosporiales|f__Kineosporiaceae|g__Kineococcus,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Chroococcidiopsidales|f__Chroococcidiopsidaceae|g__Chroococcidiopsis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Streptosporangiales|f__Thermomonosporaceae|g__Thermomonospora,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Filimonas,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Oceanithermus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium indologenes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium|s__Microbacterium aurum,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Elizabethkingia|s__Elizabethkingia bruuniana,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Tessaracoccus|s__Tessaracoccus aquimaris,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. VT 162,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus deserti,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kineosporiales|f__Kineosporiaceae|g__Kineococcus|s__Kineococcus radiotolerans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus urinaeequi,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus gobiensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Tessaracoccus|s__Tessaracoccus flavescens,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Microvirga|s__Microvirga ossetica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium casei,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Boseaceae|g__Bosea|s__Bosea sp. AS-1,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus puniceus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium flavescens,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Paraurantiacibacter|s__Paraurantiacibacter namhicola,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Flavisolibacter|s__Flavisolibacter tropicus,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium|s__Sphingobacterium sp. PM2-P1-29,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Boseaceae|g__Bosea|s__Bosea sp. RAC05,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Citromicrobium|s__Citromicrobium sp. JL477,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus maricopensis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Altererythrobacter|s__Altererythrobacter epoxidivorans,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingopyxidaceae|g__Sphingopyxis|s__Sphingopyxis macrogoltabida,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Streptosporangiales|f__Thermomonosporaceae|g__Thermomonospora|s__Thermomonospora curvata,s__uncultured bacterium PGSL07,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Paracidovorax|s__Paracidovorax citrulli",3379134|1224|1236|2887326|468|469|470;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049|1654|1655;1783272|201174|1760|2037|2049|1654|544580;1783272|201174|1760|2037|2049|1654|1852377;1783272|1239|91061|186826|186827|1375;1783272|1239|91061|1385|186823|29330;1783272|1239|91061|1385|186823|29330|122960;3379134|1224|28211|204457|335929|361177;1783272|201174|1760|85010|2070|1813;1783272|201174|1760|2037|2049|28263;3379134|1224|28211|204457|335929|2800681|502682;1783272|1239;1783272|1239|91061|1385|186817|1386|1402;2732092|2732415|2732421|2732533|151340|2169595|333922;3379134|1224|28211|356|2831100|85413;3379134|1224|28211|356|2831100|85413|1526658;3379134|1224|28211|356|41294|374|288000;1783272|201174|1760|85006|85019|1696;1783272|201174|1760|85006|85019|1696|1136497;3379134|1224|28211|204458|76892|41275|74313;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294|194|195;3379134|29547|3031852|213849|72294|194|197;3379134|204428;3379134|976|117743|200644|2762318|59732|1324352;3379134|976|117743|200644|2762318|59732|878220;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85007|1653|1716|42817;1783272|201174|1760|85007|1653|1716|169292;1783272|201174|1760|85007|1653|1716|1717;1783272|201174|1760|85007|1653|1716|1718;1783272|201174|1760|85007|1653|1716|1223514;1783272|201174|1760|85007|1653|1716|156978;1783272|201174|1760|85007|1653|1716|38289;1783272|201174|1760|85007|1653|1716|161895;1783272|201174|1760|85007|1653|1716|146827;1783272|201174|1760|85007|1653|1716|161899;1783272|201174|1760|85007|1653|1716|1487956;1783272|201174|1760|85007|1653|1716|43770;1783272|201174|1760|85007|1653|1716|441500;1783272|201174|1760|85007|1653|1716|43771;3379134|1224|28211|204457|335929|1295327|450378;1783272|201174|1760|85009|31957|1912216|33010;1783272|201174|1760|85009|31957|1912216|2559073;1783272|1117;3384194|1297;3384194|1297|188787|118964|183710|1298;3384194|1297|188787|118964|183710|1298|1768108;3384194|1297|188787|118964|183710|1298|55148;3384194|1297|188787|118964|183710|1298|1299;1783272|201174|1760|85006|145357|57495|1274;3379134|976|117743|200644|2762318|308865;3379134|976|117743|200644|2762318|308865|1117645;1783272|1239|91061|186826|81852|1350|1352;3379134|976|1853228|1853229|563835|649460|477680;3379134|976|1853228|1853229|563835|398041;1783272|201174|1760|85006|1268|57493|446860;1783272|1239|91061|1385|186817|175304;1783272|1239|91061|1385|186817|175304|1472767;1783272|201174|1760|85006|85023|33882;1783272|201174|1760|85009|31957|29404;3379134|1224|28211|356|119045|186650;1783272|1239|91061|1385|186824|1677050;1783272|1239|91061|1385|186824|1677050|1471761;3384194|1297|188787|68933|188786|208447|187137;3379134|1224|28216|80840|80864|219181;3379134|1224|28216|80840|80864|219181|1658672;1783272|1239|91061|1385|186822|44249|528191;3379134|1224|1236|91347|1903409|53335;1783272|1239|91061|1385|3120669|1906945;1783272|1239|91061|1385|3120669|1906945|1426;1783272|201174|1760|2037|2049|2740557|178339;3379134|976|200643|171549|171552|838|589437;1783272|201174|1760|85009|31957|1743;1783272|201174|1760|85009|31957|1743|1744;3379134|1224|28211|204457|3423714|1649486|160791;1783272|201174|84995|84996|84997|42255;1783272|201174|84995|84996|84997|42255|42256;1783272|201174|84995|84996|84997|42255|49319;3379134|1224|28211|204457|3423717|165695|56193;3379134|1224|28211|204457|3423717|165695|1855519;3379134|1224|28211|204457|3423717|165695|484429;3379134|1224|28211|204457|41297|13687|59803;3379134|1224|28211|204457|41297|13687|1609977;3379134|1224|28211|204457|41297|13687|1560345;3379134|1224|28211|204457|41297|13687|1130907;3379134|1224|28211|204457|41297|13687|1130970;3379134|1224|28211|204457|41297|13687|1938607;3379134|1224|28211|204457|41297|13687|1221575;3379134|203691;1783272|1239|91061|1385|90964|1279|1283;1783272|1239|91061|1385|90964|1279|29385;1783272|1239|91061|186826|1300|1301|45634;1783272|1239|91061|186826|1300|1301|1302;1783272|1239|91061|186826|1300|1301|1338;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|91061|186826|1300|1301|712624;1783272|1239|91061|186826|1300|1301|1307;1783272|201174|1760|85009|31957|72763;1783272|201174|1760|2037|2049|1069494|1661;378824;155900;1783272|201174|1760|622452|83778|33981;1783272|1117|3028117|1890505|1890528|54298;1783272|201174|1760|85012|2012|2019;3379134|976|1853228|1853229|563835|649460;3384194|1297|188787|68933|188786|208447;3379134|976|117743|200644|2762318|59732|253;1783272|201174|1760|85006|85023|33882|36805;3379134|976|117743|200644|2762318|308865|1756149;1783272|201174|1760|85009|31957|72763|1332264;1783272|1239|91061|186826|1300|1301|1419814;3384194|1297|188787|118964|183710|1298|310783;1783272|201174|1760|622452|83778|33981|131568;1783272|1239|91061|186826|186827|1375|51665;3384194|1297|188787|118964|183710|1298|502394;1783272|201174|1760|85009|31957|72763|399497;3379134|1224|28211|356|119045|186650|1882682;1783272|201174|1760|85007|1653|1716|160386;3379134|1224|28211|356|2831100|85413|2015316;3384194|1297|188787|118964|183710|1298|1182568;1783272|201174|1760|85007|1653|1716|28028;3379134|1224|28211|204457|335929|2800682|645517;3379134|976|1853228|1853229|563835|398041|1492898;3379134|976|117747|200666|84566|28453|403776;3379134|1224|28211|356|2831100|85413|1842539;3379134|1224|28211|204457|41297|72173|1634516;3384194|1297|188787|118964|183710|1298|309887;3379134|1224|28211|204457|335929|361177|361183;3379134|1224|28211|204457|3423718|165697|33050;1783272|201174|1760|85012|2012|2019|2020;1298972;3379134|1224|28216|80840|80864|3051137|80869,Complete,Svetlana up
bsdb:32673387/3/2,32673387,case-control,32673387,10.1167/iovs.61.8.22,NA,"Zhao F., Zhang D., Ge C., Zhang L., Reinach P.S., Tian X., Tao C., Zhao Z., Zhao C., Fu W., Zeng C. , Chen W.",Metagenomic Profiling of Ocular Surface Microbiome Changes in Meibomian Gland Dysfunction,Investigative ophthalmology & visual science,2020,NA,Experiment 3,China,Homo sapiens,Skin of eyelid,UBERON:0001457,Meibomian cyst,EFO:0007363,Healthy Control (HCs),Meibomian gland dysfunction (MGD),Patients diagnosed with Meibomian gland dysfunction (MGD),15,61,6 months,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,NA,Signature 2,Supplementary Table S4,21 January 2025,Aleru Divine,"Aleru Divine,WikiWorks",Comparison of significant changes at the different taxonomic levels in the eyelid skin microbiomes of patients with MGD.,decreased,"k__Pseudomonadati|p__Candidatus Cloacimonadota,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Rhodopseudomonas",3379134|456828;1783272|544448;3379134|1224;3379134|1224|28211|356|41294|1073,Complete,Svetlana up
bsdb:32675252/1/1,32675252,prospective cohort,32675252,10.1136/ijgc-2020-001547,NA,"Sims T.T., Biegert G.W.G., Ramogola-Masire D., Ngoni K., Solley T., Ning M.S., El Alam M.B., Mezzari M., Petrosino J., Zetola N.M., Schmeler K.M., Colbert L.E., Klopp A.H. , Grover S.",Tumor microbial diversity and compositional differences among women in Botswana with high-grade cervical dysplasia and cervical cancer,International journal of gynecological cancer : official journal of the International Gynecological Cancer Society,2020,"cervical cancer, cervix uteri, gynecology, uterine cervical neoplasms",Experiment 1,Botswana,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical cancer,MONDO:0002974,Cervical Dysplasia,Cervical Cancer patients,Patients diagnosed with moderate or poorly differentiated squamous cell cancer of the cervix.,21,10,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 2G,15 November 2024,MyleeeA,"MyleeeA,WikiWorks",Differentially abundant taxa between cervical cancer patients and cervical dysplasia patients using LefSe analysis.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Caldimonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales,k__Thermotogati|p__Synergistota|c__Synergistia,k__Thermotogati|p__Synergistota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales",3379134|976|200643|171549|171552|1283313;3379134|1224|28216|80840|119060;3379134|1224|28216|80840|2975441|196013;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;3379134|1224|1236;1783272|1239|186801|186802|216572;3379134|1224;3384194|508458|649775|649776|649777;3384194|508458|649775|649776;3384194|508458|649775;3384194|508458;3379134|1224|28216|80840,Complete,Svetlana up
bsdb:32675252/1/2,32675252,prospective cohort,32675252,10.1136/ijgc-2020-001547,NA,"Sims T.T., Biegert G.W.G., Ramogola-Masire D., Ngoni K., Solley T., Ning M.S., El Alam M.B., Mezzari M., Petrosino J., Zetola N.M., Schmeler K.M., Colbert L.E., Klopp A.H. , Grover S.",Tumor microbial diversity and compositional differences among women in Botswana with high-grade cervical dysplasia and cervical cancer,International journal of gynecological cancer : official journal of the International Gynecological Cancer Society,2020,"cervical cancer, cervix uteri, gynecology, uterine cervical neoplasms",Experiment 1,Botswana,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical cancer,MONDO:0002974,Cervical Dysplasia,Cervical Cancer patients,Patients diagnosed with moderate or poorly differentiated squamous cell cancer of the cervix.,21,10,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 2G,15 November 2024,MyleeeA,"MyleeeA,WikiWorks",Differentially abundant taxa between cervical cancer patients and cervical dysplasia patients using LefSe analysis.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira",1783272|1239|186801;1783272|1239;1783272|1239|186801|3085636|186803|28050,Complete,Svetlana up
bsdb:32675252/2/1,32675252,prospective cohort,32675252,10.1136/ijgc-2020-001547,NA,"Sims T.T., Biegert G.W.G., Ramogola-Masire D., Ngoni K., Solley T., Ning M.S., El Alam M.B., Mezzari M., Petrosino J., Zetola N.M., Schmeler K.M., Colbert L.E., Klopp A.H. , Grover S.",Tumor microbial diversity and compositional differences among women in Botswana with high-grade cervical dysplasia and cervical cancer,International journal of gynecological cancer : official journal of the International Gynecological Cancer Society,2020,"cervical cancer, cervix uteri, gynecology, uterine cervical neoplasms",Experiment 2,Botswana,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical cancer,MONDO:0002974,HIV Negative,HIV Positive,HIV positive cervical dysplasia and cervical cancer patient’s,7,24,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 1E,15 November 2024,MyleeeA,"MyleeeA,WikiWorks",Differentially abundant taxa between cervical cancer patients and cervical dysplasia HIV positive and negative patients using LefSe analysis.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales",1783272|1239|526524;1783272|1239|526524|526525;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|216572|1508657;1783272|1239|91061;1783272|1239|91061|186826,Complete,Svetlana up
bsdb:32675252/2/2,32675252,prospective cohort,32675252,10.1136/ijgc-2020-001547,NA,"Sims T.T., Biegert G.W.G., Ramogola-Masire D., Ngoni K., Solley T., Ning M.S., El Alam M.B., Mezzari M., Petrosino J., Zetola N.M., Schmeler K.M., Colbert L.E., Klopp A.H. , Grover S.",Tumor microbial diversity and compositional differences among women in Botswana with high-grade cervical dysplasia and cervical cancer,International journal of gynecological cancer : official journal of the International Gynecological Cancer Society,2020,"cervical cancer, cervix uteri, gynecology, uterine cervical neoplasms",Experiment 2,Botswana,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical cancer,MONDO:0002974,HIV Negative,HIV Positive,HIV positive cervical dysplasia and cervical cancer patient’s,7,24,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 1E,15 November 2024,MyleeeA,"MyleeeA,WikiWorks",Differentially abundant taxa between cervical cancer patients and cervical dysplasia HIV positive and negative patients using LefSe analysis.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,1783272|1239|186801|3082720|3118655|44259,Complete,Svetlana up
bsdb:32681566/1/1,32681566,laboratory experiment,32681566,10.1111/aji.13307,NA,"Ni Z., Sun S., Bi Y., Ding J., Cheng W., Yu J., Zhou L., Li M. , Yu C.",Correlation of fecal metabolomics and gut microbiota in mice with endometriosis,"American journal of reproductive immunology (New York, N.Y. : 1989)",2020,"endometriosis, intestines, metabolomics, microbiota",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Non-endo mice,Endo mice,Endometriosis was induced in female mice via transplantation of endometrial fragments.,6,6,NA,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3 and Results section,9 August 2021,Samara.Khan,"Samara.Khan,Claregrieve1,WikiWorks",Differential microbial abundance of mice with simulated endometriosis compared to controls.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|1432051;1783272|1239|526524|526525|128827|1573534;1783272|1239;1783272|201174|84998|1643822|1643826|644652;1783272|1239|186801|3085636|186803|877420;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|171552;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|1506577,Complete,Claregrieve1
bsdb:32681566/1/2,32681566,laboratory experiment,32681566,10.1111/aji.13307,NA,"Ni Z., Sun S., Bi Y., Ding J., Cheng W., Yu J., Zhou L., Li M. , Yu C.",Correlation of fecal metabolomics and gut microbiota in mice with endometriosis,"American journal of reproductive immunology (New York, N.Y. : 1989)",2020,"endometriosis, intestines, metabolomics, microbiota",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Non-endo mice,Endo mice,Endometriosis was induced in female mice via transplantation of endometrial fragments.,6,6,NA,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 3,9 August 2021,Samara.Khan,"Samara.Khan,Claregrieve1,WikiWorks",Differential microbial abundance of mice with simulated endometriosis compared to controls.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Pseudomonadati|p__Verrucomicrobiota",3379134|74201|203494|48461|1647988|239934;1783272|1239|526524|526525|128827|174708;3379134|1224|1236|91347|543|544;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|577310;3379134|1224;3379134|976|200643|171549|171550|28138;3379134|74201,Complete,Claregrieve1
bsdb:32690030/1/1,32690030,case-control,32690030,10.1186/s12877-020-01644-2,NA,"Stadlbauer V., Engertsberger L., Komarova I., Feldbacher N., Leber B., Pichler G., Fink N., Scarpatetti M., Schippinger W., Schmidt R. , Horvath A.","Dysbiosis, gut barrier dysfunction and inflammation in dementia: a pilot study",BMC geriatrics,2020,"Butyrate producer, Cognitive function, Diversity, Gut barrier, Inflammation, Microbiome",Experiment 1,Austria,Homo sapiens,Feces,UBERON:0001988,Dementia,MONDO:0001627,"Control, mild, and moderate dementia",Severe dementia,MMSE 0-9: The Mini-Mental State Examination [19] and the clock drawing test [20] were used to quantify cognitive function. We classified cognitive dysfunction according to the German S3-guideline on Dementia 2016 as MMSE 0–9: severe; MMSE 10–19: moderate; MMSE 20–26: mild; MMSE 27–30: no dementia [21].,NA,NA,1 month,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,"age,sex",NA,NA,NA,unchanged,unchanged,NA,NA,Signature 1,Figure 4A,28 March 2022,Lwaldron,"Lwaldron,WikiWorks",4a Features selected by Linear discriminant analysis Effect Size (LEfSe) to discriminate between dementia different stages of cognitive dysfunction and controls. Right-hand bar showing biomarkers of severe dementia.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. Marseille-P3371,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819",3379134|976|200643|171549|815|816|2778071;3379134|976|200643|171549|815|816|820;1783272|1239|186801|3085636|186803|2719313|1531;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|3085636|186803|1432051;3379134|1224|1236|91347|543;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|186801|3085636|186803|1769710;1783272|1239|186801|3085636|186803|1769710|2021466;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|186801|3085636|186803|84036;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|3082720|543314|35518;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|91061|186826|1300|1301|1308;1783272|201174|1760|2037|2049;3379134|1224|1236|91347;1783272|201174|1760|2037;1783272|1239|186801|186802|3082771|1924093|1944639;1783272|1239|186801|186802|216572|2485925;1783272|1239|186801|186802|216572|216851|1946507,Complete,Lwaldron
bsdb:32690030/2/1,32690030,case-control,32690030,10.1186/s12877-020-01644-2,NA,"Stadlbauer V., Engertsberger L., Komarova I., Feldbacher N., Leber B., Pichler G., Fink N., Scarpatetti M., Schippinger W., Schmidt R. , Horvath A.","Dysbiosis, gut barrier dysfunction and inflammation in dementia: a pilot study",BMC geriatrics,2020,"Butyrate producer, Cognitive function, Diversity, Gut barrier, Inflammation, Microbiome",Experiment 2,Austria,Homo sapiens,Feces,UBERON:0001988,Dementia,MONDO:0001627,Controls without cognitive impairments,Patients with dementia,"Participants with any level of dementia (mild, moderate, severe).",18,23,1 month,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,"age,sex",NA,NA,NA,unchanged,unchanged,NA,NA,Signature 1,3a,15 March 2022,Maryemzaki,"Maryemzaki,Lwaldron,WikiWorks",Differentially abundant taxa between any level of dementia vs controls,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|186801|186802|1898207;1783272|1239|186801|3085636|186803|2719313|1531;1783272|1239|186801|3085636|186803|1506553;3379134|976|200643|171549|815|909656|357276;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Lwaldron
bsdb:32690030/2/2,32690030,case-control,32690030,10.1186/s12877-020-01644-2,NA,"Stadlbauer V., Engertsberger L., Komarova I., Feldbacher N., Leber B., Pichler G., Fink N., Scarpatetti M., Schippinger W., Schmidt R. , Horvath A.","Dysbiosis, gut barrier dysfunction and inflammation in dementia: a pilot study",BMC geriatrics,2020,"Butyrate producer, Cognitive function, Diversity, Gut barrier, Inflammation, Microbiome",Experiment 2,Austria,Homo sapiens,Feces,UBERON:0001988,Dementia,MONDO:0001627,Controls without cognitive impairments,Patients with dementia,"Participants with any level of dementia (mild, moderate, severe).",18,23,1 month,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,"age,sex",NA,NA,NA,unchanged,unchanged,NA,NA,Signature 2,Figure 3a,15 March 2022,Maryemzaki,"Maryemzaki,Lwaldron,WikiWorks",Differentially abundant taxa between any level of dementia vs controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium MC_35,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|1766253|2021311;1783272|1239|186801|3085636|186803|1755642;1783272|1239|186801|3085636|186803|877420;1783272|1239|526524|526525|128827|331630;1783272|1239|186801|3085636|186803|297314;1783272|1239|186801|186802|216572|707003,Complete,Lwaldron
bsdb:32690030/3/1,32690030,case-control,32690030,10.1186/s12877-020-01644-2,NA,"Stadlbauer V., Engertsberger L., Komarova I., Feldbacher N., Leber B., Pichler G., Fink N., Scarpatetti M., Schippinger W., Schmidt R. , Horvath A.","Dysbiosis, gut barrier dysfunction and inflammation in dementia: a pilot study",BMC geriatrics,2020,"Butyrate producer, Cognitive function, Diversity, Gut barrier, Inflammation, Microbiome",Experiment 3,Austria,Homo sapiens,Feces,UBERON:0001988,Dementia,MONDO:0001627,"control, mild, and severe dementia",moderate dementia,MMSE 10-19: The Mini-Mental State Examination [19] and the clock drawing test [20] were used to quantify cognitive function. We classified cognitive dysfunction according to the German S3-guideline on Dementia 2016 as MMSE 0–9: severe; MMSE 10–19: moderate; MMSE 20–26: mild; MMSE 27–30: no dementia [21].,NA,NA,1 month,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,"age,sex",NA,NA,NA,unchanged,unchanged,NA,NA,Signature 1,Figure 4A (moderate),28 March 2022,Lwaldron,"Lwaldron,WikiWorks","Moderate vs control, mild, and severe dementia",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus amylovorus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli",1783272|1239|91061|186826|33958|1578|1604;1783272|201174|84998|84999|84107|102106|74426;3379134|976|200643|171549|815|816|29523;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572|1508657;1783272|1239|91061|186826|81850;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061,Complete,Lwaldron
bsdb:32690030/4/1,32690030,case-control,32690030,10.1186/s12877-020-01644-2,NA,"Stadlbauer V., Engertsberger L., Komarova I., Feldbacher N., Leber B., Pichler G., Fink N., Scarpatetti M., Schippinger W., Schmidt R. , Horvath A.","Dysbiosis, gut barrier dysfunction and inflammation in dementia: a pilot study",BMC geriatrics,2020,"Butyrate producer, Cognitive function, Diversity, Gut barrier, Inflammation, Microbiome",Experiment 4,Austria,Homo sapiens,Feces,UBERON:0001988,Dementia,MONDO:0001627,"control, moderate, and severe dementia",mild dementia,MMSE 20-26: The Mini-Mental State Examination [19] and the clock drawing test [20] were used to quantify cognitive function. We classified cognitive dysfunction according to the German S3-guideline on Dementia 2016 as MMSE 0–9: severe; MMSE 10–19: moderate; MMSE 20–26: mild; MMSE 27–30: no dementia [21].,NA,NA,1 month,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,"age,sex",NA,NA,NA,unchanged,unchanged,NA,NA,Signature 1,Figure 4A (mild),28 March 2022,Lwaldron,"Lwaldron,WikiWorks","These are ""biomarkers"" of mild dementia that are lower abundance in controls, moderate, and severe dementia.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens",1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|28050|39485,Complete,Lwaldron
bsdb:32690600/1/1,32690600,prospective cohort,32690600,10.1136/gutjnl-2020-322294,NA,"Zuo T., Liu Q., Zhang F., Lui G.C., Tso E.Y., Yeoh Y.K., Chen Z., Boon S.S., Chan F.K., Chan P.K. , Ng S.C.",Depicting SARS-CoV-2 faecal viral activity in association with gut microbiota composition in patients with COVID-19,Gut,2021,"diagnostic virology, gut inflammation, infectious disease",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Patients with low-to-none SARS CoV-2 infectivity,Patients with high SARS CoV-2 infectivity,"SARS CoV-2 infection confirmed by two consecutive RT-OCR tests. High SARS-CoV2 infectivity defined as higher 3' vs 5', end coverage of SARS CoV-2 genome in fecal viral RNA metagenome.",15,15,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,4 March 2021,Fatima,"Fatima,Claregrieve1,WikiWorks",Differential bacterial species and functional capacities between feces with high severe acute respiratory syndrome coronavirus 2 infectivity and feces with low to-none SARS-CoV-2 infectivity,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii",3379134|976|200643|171549|815|816|46506;1783272|1239|186801|3085636|186803|1898203;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|171550|239759|328813,Complete,Fatima
bsdb:32690600/1/2,32690600,prospective cohort,32690600,10.1136/gutjnl-2020-322294,NA,"Zuo T., Liu Q., Zhang F., Lui G.C., Tso E.Y., Yeoh Y.K., Chen Z., Boon S.S., Chan F.K., Chan P.K. , Ng S.C.",Depicting SARS-CoV-2 faecal viral activity in association with gut microbiota composition in patients with COVID-19,Gut,2021,"diagnostic virology, gut inflammation, infectious disease",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Patients with low-to-none SARS CoV-2 infectivity,Patients with high SARS CoV-2 infectivity,"SARS CoV-2 infection confirmed by two consecutive RT-OCR tests. High SARS-CoV2 infectivity defined as higher 3' vs 5', end coverage of SARS CoV-2 genome in fecal viral RNA metagenome.",15,15,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,4 March 2021,Fatima,"Fatima,Claregrieve1,WikiWorks",Differential bacterial species and functional capacities between feces with high severe acute respiratory syndrome coronavirus 2 infectivity and feces with low to-none SARS-CoV-2 infectivity,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella tanakaei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella|s__Morganella morganii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis",1783272|201174|84998|84999|84107|102106|74426;1783272|201174|84998|84999|84107|102106|626935;3379134|1224|1236|91347|1903414|581|582;1783272|1239|91061|186826|1300|1301|68892,Complete,Fatima
bsdb:32692788/1/NA,32692788,randomized controlled trial,32692788,10.4193/Rhin20.055,NA,"Cherian L.M., Bassiouni A., Cooksley C.M., Vreugde S., Wormald P.J. , Psaltis A.J.","The clinical outcomes of medical therapies in chronic rhinosinusitis are independent of microbiomic outcomes: a double-blinded, randomised placebo-controlled trial",Rhinology,2020,NA,Experiment 1,Finland,Homo sapiens,Middle nasal meatus,UBERON:0015219,Chronic rhinosinusitis,EFO:1000024,Healthy controls-without polyps,Patients with chronic rhinosinusitis,"CRS patients diagnosed as per the criteria outlined in the Euro-
pean Position Paper on Rhinosinusitis and Nasal Polyps (EPOS)
2012",50,50,6 weeks,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:32694705/1/1,32694705,case-control,32694705,10.1038/s41598-020-68952-w,NA,"Willis K.A., Postnikoff C.K., Freeman A., Rezonzew G., Nichols K., Gaggar A. , Lal C.V.",The closed eye harbours a unique microbiome in dry eye disease,Scientific reports,2020,NA,Experiment 1,United States of America,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,Normal Control (NC),Dry Eye,Participants with moderate or severe dry eye disease,36,36,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. S5 and Fig. S6.,14 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","The acquisition of unique taxa separates the dry from the normal eye at baseline. (b) Linear discriminant analysis of effect size (LEfSe). 

Additional unique taxa separate the dry from the normal eye after a month. (b) Linear discriminant analysis of effect size (LEfSe).",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Calotrichaceae|g__Calothrix,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Meiothermus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium",1783272|1239|91061|186826|33958;1783272|1239|91061|186826|1300|1301;1783272|1117|3028117|1161|2661849|1186;1783272|201174|1760|2037|2049|184869;33090|35493|3398|72025|3803|3814|508215;3379134|1224|1236|135625|712|724;3384194|1297|188787|68933|188786|65551;1783272|1239|909932|1843489|31977|39948;1783272|201174|1760|85006|145357|57495;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|216851;3379134|1224|28211|356|82115|357,Complete,Peace Sandy
bsdb:32694705/1/2,32694705,case-control,32694705,10.1038/s41598-020-68952-w,NA,"Willis K.A., Postnikoff C.K., Freeman A., Rezonzew G., Nichols K., Gaggar A. , Lal C.V.",The closed eye harbours a unique microbiome in dry eye disease,Scientific reports,2020,NA,Experiment 1,United States of America,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,Normal Control (NC),Dry Eye,Participants with moderate or severe dry eye disease,36,36,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,NA,14 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","The acquisition of unique taxa separates the dry from the normal eye at baseline. (b) Linear discriminant analysis of effect size (LEfSe).

Additional unique taxa separate the dry from the normal eye after a month. (b) Linear discriminant analysis of effect size (LEfSe).",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Acetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Vogesella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Pleomorphomonadaceae|g__Pleomorphomonas,k__Pseudomonadati|p__Bdellovibrionota|c__Bacteriovoracia|o__Bacteriovoracales|f__Bacteriovoracaceae|g__Peredibacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Beijerinckiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Rubellimicrobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae|g__Rheinheimera",3379134|1224|1236|72274|135621|286;3379134|1224|28211|356|119045;3379134|29547|3031852|213849|72293|209;3379134|1224|28211|3120395|433|434;3379134|1224|28211|356|41294|374;3379134|1224|1236|135614|32033|40323;1783272|201174|84998|84999|84107;1783272|201174|1760|85007|85029|37914;3379134|1224|28216|206351|1499392|57739;3379134|1224|28211|204441|2829815|191;3379134|1224|28211|356|2843308|261933;3379134|3018035|3031419|2024979|263369|263370;3379134|1224|28211|356|45404;3379134|1224|28211|204455|2854170|295418;3379134|1224|1236|91347|543|561;3379134|1224|1236|135613|1046|67575,Complete,Peace Sandy
bsdb:32708743/1/1,32708743,randomized controlled trial,32708743,10.3390/nu12072112,NA,"Sainz T., Gosalbes M.J., Talavera-Rodríguez A., Jimenez-Hernandez N., Prieto L., Escosa L., Guillén S., Ramos J.T., Muñoz-Fernández M.Á., Moya A., Navarro M.L., Mellado M.J. , Serrano-Villar S.",Effect of a Nutritional Intervention on the Intestinal Microbiota of Vertically HIV-Infected Children: The Pediabiota Study,Nutrients,2020,"HIV, children and adolescents, microbiota, vertical transmission",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV-uninfected siblings or children born to HIV-infected mothers,Vertically HIV-infected children,Vertically HIV-infected children,10,23,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,"Text (results), Figure 4",10 January 2021,Michael Lutete,"Claregrieve1,WikiWorks",Comparison of basal samples from vertically HIV-infected children vs. healthy controls,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|74201|203494|48461|1647988|239934;1783272|1239|526524|526525|2810280|100883;3379134|1224|1236|91347|543|561;3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:32708743/1/2,32708743,randomized controlled trial,32708743,10.3390/nu12072112,NA,"Sainz T., Gosalbes M.J., Talavera-Rodríguez A., Jimenez-Hernandez N., Prieto L., Escosa L., Guillén S., Ramos J.T., Muñoz-Fernández M.Á., Moya A., Navarro M.L., Mellado M.J. , Serrano-Villar S.",Effect of a Nutritional Intervention on the Intestinal Microbiota of Vertically HIV-Infected Children: The Pediabiota Study,Nutrients,2020,"HIV, children and adolescents, microbiota, vertical transmission",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV-uninfected siblings or children born to HIV-infected mothers,Vertically HIV-infected children,Vertically HIV-infected children,10,23,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,"Text (results), Figure 4",28 December 2022,Claregrieve1,"Claregrieve1,WikiWorks",Comparison of basal samples from vertically HIV-infected children vs. healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|1239|186801|186802|216572|244127;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|186807|51514;1783272|1239|91061|186826|1300|1357;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|186802|216572|216851;1783272|201174|1760|85004|31953|1678,Complete,Claregrieve1
bsdb:32711581/1/1,32711581,laboratory experiment,32711581,10.1186/s40168-020-00886-x,NA,"Zhang P., Liu J., Xiong B., Zhang C., Kang B., Gao Y., Li Z., Ge W., Cheng S., Hao Y., Shen W., Yu S., Chen L., Tang X., Zhao Y. , Zhang H.",Microbiota from alginate oligosaccharide-dosed mice successfully mitigated small intestinal mucositis,Microbiome,2020,"Alginate oligosaccharides, Busulfan, Correlation, Fecal microbiota transplantation, Metabolome, Mucositis, Rescue",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Mucositis,EFO:1001898,BA0,BA10,Treatment group for mice injected with 40 mg/kg BW (body weight) busulfan once then dosed with 10 mg/kg BW (body weight) AOS(alginate oligosaccharide-dosed.,15,15,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 1d,5 November 2024,Tosin,"Tosin,WikiWorks",Significant different taxa between BA0 and BA10.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli",1783272|1239|91061|186826|186827;1783272|1239|91061|186826|186827|1375;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|28116;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|561|562,Complete,Svetlana up
bsdb:32711581/1/2,32711581,laboratory experiment,32711581,10.1186/s40168-020-00886-x,NA,"Zhang P., Liu J., Xiong B., Zhang C., Kang B., Gao Y., Li Z., Ge W., Cheng S., Hao Y., Shen W., Yu S., Chen L., Tang X., Zhao Y. , Zhang H.",Microbiota from alginate oligosaccharide-dosed mice successfully mitigated small intestinal mucositis,Microbiome,2020,"Alginate oligosaccharides, Busulfan, Correlation, Fecal microbiota transplantation, Metabolome, Mucositis, Rescue",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Mucositis,EFO:1001898,BA0,BA10,Treatment group for mice injected with 40 mg/kg BW (body weight) busulfan once then dosed with 10 mg/kg BW (body weight) AOS(alginate oligosaccharide-dosed.,15,15,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 1d,5 November 2024,Tosin,"Tosin,WikiWorks",Significant different taxa between BA0 and BA10.,decreased,"k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum|s__Mucispirillum schaedleri",3379134|200930|68337|191393|191394;3379134|200930|68337|191393;3379134|200930|68337;3379134|200930|68337|191393|2945020|248038;3379134|200930|68337|191393|2945020|248038|248039,Complete,Svetlana up
bsdb:32711581/2/1,32711581,laboratory experiment,32711581,10.1186/s40168-020-00886-x,NA,"Zhang P., Liu J., Xiong B., Zhang C., Kang B., Gao Y., Li Z., Ge W., Cheng S., Hao Y., Shen W., Yu S., Chen L., Tang X., Zhao Y. , Zhang H.",Microbiota from alginate oligosaccharide-dosed mice successfully mitigated small intestinal mucositis,Microbiome,2020,"Alginate oligosaccharides, Busulfan, Correlation, Fecal microbiota transplantation, Metabolome, Mucositis, Rescue",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Mucositis,EFO:1001898,A10-FMT (fecal microbiota transplantation),A100-FMT (fecal microbiota transplantation),Mice treated with busulfan and FMT (fecal mcrobiota transplantation) from the AOS 100 mg/kg group.,15,15,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 4d,5 November 2024,Tosin,"Tosin,WikiWorks",Significant different taxa between A10-FMT and A100-FMT.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",1783272|1239|91061|186826|33958|46255;1783272|1239|91061|186826|33958,Complete,Svetlana up
bsdb:32711581/2/2,32711581,laboratory experiment,32711581,10.1186/s40168-020-00886-x,NA,"Zhang P., Liu J., Xiong B., Zhang C., Kang B., Gao Y., Li Z., Ge W., Cheng S., Hao Y., Shen W., Yu S., Chen L., Tang X., Zhao Y. , Zhang H.",Microbiota from alginate oligosaccharide-dosed mice successfully mitigated small intestinal mucositis,Microbiome,2020,"Alginate oligosaccharides, Busulfan, Correlation, Fecal microbiota transplantation, Metabolome, Mucositis, Rescue",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Mucositis,EFO:1001898,A10-FMT (fecal microbiota transplantation),A100-FMT (fecal microbiota transplantation),Mice treated with busulfan and FMT (fecal mcrobiota transplantation) from the AOS 100 mg/kg group.,15,15,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 4d,5 November 2024,Tosin,"Tosin,WikiWorks",Significant different taxa between A10-FMT and A-100FMT.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae",1783272|1239|186801|186802|31979|1485;1783272|544448|31969|2085|2092|2093;1783272|544448|31969|2085;1783272|544448|31969;1783272|544448;1783272|544448|31969|2085|2092,Complete,Svetlana up
bsdb:32717152/1/1,32717152,prospective cohort,32717152,10.1164/rccm.201912-2441OC,NA,"Kitsios G.D., Yang H., Yang L., Qin S., Fitch A., Wang X.H., Fair K., Evankovich J., Bain W., Shah F., Li K., Methé B., Benos P.V., Morris A. , McVerry B.J.",Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients,American journal of respiratory and critical care medicine,2020,"acute respiratory distress syndrome, bacterial infections, endotypes, inflammation, microbiota",Experiment 1,United States of America,Homo sapiens,Posterior wall of oropharynx,UBERON:0035240,Acute respiratory distress syndrome,EFO:1000637,Hyper-inflammatory subphenotype and ventilation-free days(VFDs),Mortality,"patients stratified on the basis of 30-day mortality [survivors vs. non-survivors], for whom respiratory specimen cultures were reported as negative (no growth or only normal respiratory flora detected, n=152) as well as those for whom no cultures were obtained (n=76)",228,228,NA,16S,34,Illumina,relative abundances,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,chronic obstructive pulmonary disease",NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary figure E8,2 March 2024,Folakunmi,"Folakunmi,WikiWorks",Relative abundance of individual genera in Endotracheal aspirate (ETA) genera is associated with clinical outcomes and host-response subphenotypes in patients without positive respiratory cultures.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,Folakunmi
bsdb:32717152/2/1,32717152,prospective cohort,32717152,10.1164/rccm.201912-2441OC,NA,"Kitsios G.D., Yang H., Yang L., Qin S., Fitch A., Wang X.H., Fair K., Evankovich J., Bain W., Shah F., Li K., Methé B., Benos P.V., Morris A. , McVerry B.J.",Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients,American journal of respiratory and critical care medicine,2020,"acute respiratory distress syndrome, bacterial infections, endotypes, inflammation, microbiota",Experiment 2,United States of America,Homo sapiens,Epithelium of oropharynx,UBERON:0001952,Acute respiratory failure,MONDO:0001208,Hyper-inflammatory subphenotype and mortality,VFD (Ventilator free days),"Clinical outcome stratification by numbers of ventilator-free days (VFDs) at 30 days in patients for whom respiratory specimen cultures were reported as negative (no growth or only normal respiratory flora detected, n=152) as well as those for whom no cultures were obtained (n=76)",228,228,NA,16S,34,Illumina,relative abundances,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,chronic obstructive pulmonary disease",NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary figure E8,20 June 2023,Atrayees,"Atrayees,Folakunmi,WikiWorks",Relative abundance of individual genera in Endotracheal aspirate (ETA) genera is associated with clinical outcomes and host-response subphenotypes in patients without positive respiratory cultures.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712,Complete,Folakunmi
bsdb:32717152/2/2,32717152,prospective cohort,32717152,10.1164/rccm.201912-2441OC,NA,"Kitsios G.D., Yang H., Yang L., Qin S., Fitch A., Wang X.H., Fair K., Evankovich J., Bain W., Shah F., Li K., Methé B., Benos P.V., Morris A. , McVerry B.J.",Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients,American journal of respiratory and critical care medicine,2020,"acute respiratory distress syndrome, bacterial infections, endotypes, inflammation, microbiota",Experiment 2,United States of America,Homo sapiens,Epithelium of oropharynx,UBERON:0001952,Acute respiratory failure,MONDO:0001208,Hyper-inflammatory subphenotype and mortality,VFD (Ventilator free days),"Clinical outcome stratification by numbers of ventilator-free days (VFDs) at 30 days in patients for whom respiratory specimen cultures were reported as negative (no growth or only normal respiratory flora detected, n=152) as well as those for whom no cultures were obtained (n=76)",228,228,NA,16S,34,Illumina,relative abundances,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,chronic obstructive pulmonary disease",NA,decreased,NA,NA,NA,NA,Signature 2,Supplementary figure E8,20 June 2023,Atrayees,"Atrayees,Folakunmi,WikiWorks",Relative abundance of individual genera in Endotracheal aspirate (ETA) genera is associated with clinical outcomes and host-response subphenotypes in patients without positive respiratory cultures.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,Folakunmi
bsdb:32717152/3/1,32717152,prospective cohort,32717152,10.1164/rccm.201912-2441OC,NA,"Kitsios G.D., Yang H., Yang L., Qin S., Fitch A., Wang X.H., Fair K., Evankovich J., Bain W., Shah F., Li K., Methé B., Benos P.V., Morris A. , McVerry B.J.",Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients,American journal of respiratory and critical care medicine,2020,"acute respiratory distress syndrome, bacterial infections, endotypes, inflammation, microbiota",Experiment 3,United States of America,Homo sapiens,Endothelium of trachea,UBERON:0003279,Acute respiratory failure,MONDO:0001208,VFD (Ventilator free days) and mortality,Hyper-inflammatory subphenotype,participants  were classified into a hyperinflammatory subphenotype of host responses associated with worse outcomes in the pathogen-enriched cluster,112,51,NA,16S,34,Illumina,relative abundances,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,chronic obstructive pulmonary disease",NA,increased,NA,NA,NA,NA,Signature 1,Figure 4,1 March 2024,Folakunmi,"Folakunmi,WikiWorks",The relative abundance of individual genera is associated with clinical outcomes and host-response subphenotypes.,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",3384189|32066|203490|203491|203492|848;3379134|1224|1236|91347|543;3379134|1224|1236|72274|135621;1783272|1239|91061|1385|90964|1279,Complete,Folakunmi
bsdb:32717152/4/1,32717152,prospective cohort,32717152,10.1164/rccm.201912-2441OC,NA,"Kitsios G.D., Yang H., Yang L., Qin S., Fitch A., Wang X.H., Fair K., Evankovich J., Bain W., Shah F., Li K., Methé B., Benos P.V., Morris A. , McVerry B.J.",Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients,American journal of respiratory and critical care medicine,2020,"acute respiratory distress syndrome, bacterial infections, endotypes, inflammation, microbiota",Experiment 4,United States of America,Homo sapiens,Posterior wall of oropharynx,UBERON:0035240,Acute respiratory failure,MONDO:0001208,VFD (Ventilator free days) and mortality,Hyper-inflammatory subphenotype,participants  were classified into a hyperinflammatory subphenotype of host responses associated with worse outcomes in the pathogen-enriched cluster,96,51,NA,16S,34,Illumina,relative abundances,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,chronic obstructive pulmonary disease",NA,increased,NA,NA,NA,NA,Signature 1,Figure 4,1 March 2024,Folakunmi,"Folakunmi,WikiWorks",The relative abundance of individual genera is associated with clinical outcomes and host-response subphenotypes.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Folakunmi
bsdb:32717152/5/1,32717152,prospective cohort,32717152,10.1164/rccm.201912-2441OC,NA,"Kitsios G.D., Yang H., Yang L., Qin S., Fitch A., Wang X.H., Fair K., Evankovich J., Bain W., Shah F., Li K., Methé B., Benos P.V., Morris A. , McVerry B.J.",Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients,American journal of respiratory and critical care medicine,2020,"acute respiratory distress syndrome, bacterial infections, endotypes, inflammation, microbiota",Experiment 5,United States of America,Homo sapiens,Posterior wall of oropharynx,UBERON:0035240,Acute respiratory failure,MONDO:0001208,Hyper-inflammatory subphenotype and ventilation-free days(VFDs),Mortality,patients stratified on the basis of 30-day mortality [survivors vs. non-survivors],92,55,NA,16S,34,Illumina,relative abundances,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,chronic obstructive pulmonary disease",NA,increased,NA,NA,NA,NA,Signature 1,Figure 4,1 March 2024,Folakunmi,"Folakunmi,WikiWorks",The relative abundance of individual genera is associated with clinical outcomes and host-response subphenotypes.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;3379134|1224|28216|206351|481|482,Complete,Folakunmi
bsdb:32717152/6/1,32717152,prospective cohort,32717152,10.1164/rccm.201912-2441OC,NA,"Kitsios G.D., Yang H., Yang L., Qin S., Fitch A., Wang X.H., Fair K., Evankovich J., Bain W., Shah F., Li K., Methé B., Benos P.V., Morris A. , McVerry B.J.",Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients,American journal of respiratory and critical care medicine,2020,"acute respiratory distress syndrome, bacterial infections, endotypes, inflammation, microbiota",Experiment 6,United States of America,Homo sapiens,Endothelium of trachea,UBERON:0003279,Acute respiratory failure,MONDO:0001208,Hyper-inflammatory subphenotype and ventilation-free days(VFDs),Mortality,patients stratified on the basis of 30-day mortality [survivors vs. non-survivors],111,52,NA,16S,34,Illumina,relative abundances,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,chronic obstructive pulmonary disease",NA,increased,NA,NA,NA,NA,Signature 1,Figure 4,23 June 2023,Atrayees,"Atrayees,Folakunmi,WikiWorks",The relative abundance of individual genera is associated with clinical outcomes and host-response subphenotypes.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae",1783272|201174|1760|85007|1653|1716;1783272|1239|186801|186802|186806,Complete,Folakunmi
bsdb:32717152/6/2,32717152,prospective cohort,32717152,10.1164/rccm.201912-2441OC,NA,"Kitsios G.D., Yang H., Yang L., Qin S., Fitch A., Wang X.H., Fair K., Evankovich J., Bain W., Shah F., Li K., Methé B., Benos P.V., Morris A. , McVerry B.J.",Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients,American journal of respiratory and critical care medicine,2020,"acute respiratory distress syndrome, bacterial infections, endotypes, inflammation, microbiota",Experiment 6,United States of America,Homo sapiens,Endothelium of trachea,UBERON:0003279,Acute respiratory failure,MONDO:0001208,Hyper-inflammatory subphenotype and ventilation-free days(VFDs),Mortality,patients stratified on the basis of 30-day mortality [survivors vs. non-survivors],111,52,NA,16S,34,Illumina,relative abundances,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,chronic obstructive pulmonary disease",NA,increased,NA,NA,NA,NA,Signature 2,Figure 4,23 June 2023,Atrayees,"Atrayees,Folakunmi,WikiWorks",The relative abundance of individual genera is associated with clinical outcomes and host-response subphenotypes.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",3379134|976|200643|171549|171552|838;3379134|1224|1236|135625|712|724,Complete,Folakunmi
bsdb:32717152/7/1,32717152,prospective cohort,32717152,10.1164/rccm.201912-2441OC,NA,"Kitsios G.D., Yang H., Yang L., Qin S., Fitch A., Wang X.H., Fair K., Evankovich J., Bain W., Shah F., Li K., Methé B., Benos P.V., Morris A. , McVerry B.J.",Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients,American journal of respiratory and critical care medicine,2020,"acute respiratory distress syndrome, bacterial infections, endotypes, inflammation, microbiota",Experiment 7,United States of America,Homo sapiens,Endothelium of trachea,UBERON:0003279,Acute respiratory failure,MONDO:0001208,Hyper-inflammatory subphenotype and mortality,VFD (Ventilator free days),clinical outcome stratifications by the number of days patients were ventilator-free,103,60,NA,16S,34,Illumina,relative abundances,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,chronic obstructive pulmonary disease",NA,decreased,NA,NA,NA,NA,Signature 1,Figure 4,23 June 2023,Atrayees,"Atrayees,Folakunmi,WikiWorks",The relative abundance of individual genera is associated with clinical outcomes and host-response subphenotypes.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,Folakunmi
bsdb:32717152/7/2,32717152,prospective cohort,32717152,10.1164/rccm.201912-2441OC,NA,"Kitsios G.D., Yang H., Yang L., Qin S., Fitch A., Wang X.H., Fair K., Evankovich J., Bain W., Shah F., Li K., Methé B., Benos P.V., Morris A. , McVerry B.J.",Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients,American journal of respiratory and critical care medicine,2020,"acute respiratory distress syndrome, bacterial infections, endotypes, inflammation, microbiota",Experiment 7,United States of America,Homo sapiens,Endothelium of trachea,UBERON:0003279,Acute respiratory failure,MONDO:0001208,Hyper-inflammatory subphenotype and mortality,VFD (Ventilator free days),clinical outcome stratifications by the number of days patients were ventilator-free,103,60,NA,16S,34,Illumina,relative abundances,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,chronic obstructive pulmonary disease",NA,decreased,NA,NA,NA,NA,Signature 2,Figure 4,23 June 2023,Atrayees,"Atrayees,Folakunmi,WikiWorks",The relative abundance of individual genera is associated with clinical outcomes and host-response subphenotypes.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|1224|1236|135625|712|724;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|171552|838,Complete,Folakunmi
bsdb:32717152/8/1,32717152,prospective cohort,32717152,10.1164/rccm.201912-2441OC,NA,"Kitsios G.D., Yang H., Yang L., Qin S., Fitch A., Wang X.H., Fair K., Evankovich J., Bain W., Shah F., Li K., Methé B., Benos P.V., Morris A. , McVerry B.J.",Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients,American journal of respiratory and critical care medicine,2020,"acute respiratory distress syndrome, bacterial infections, endotypes, inflammation, microbiota",Experiment 8,United States of America,Homo sapiens,Posterior wall of oropharynx,UBERON:0035240,Acute respiratory failure,MONDO:0001208,Hyper-inflammatory subphenotype and mortality,VFD (Ventilator free days),clinical outcome stratifications by the number of days patients were ventilator-free,106,41,NA,16S,34,Illumina,relative abundances,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,chronic obstructive pulmonary disease",NA,decreased,NA,NA,NA,NA,Signature 1,Figure 4,1 March 2024,Folakunmi,"Folakunmi,WikiWorks",The relative abundance of individual genera is associated with clinical outcomes and host-response subphenotypes in oral swab samples genera,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",1783272|1239|91061|186826|186828|117563;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|838;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|135625|712,Complete,Folakunmi
bsdb:32717152/9/1,32717152,prospective cohort,32717152,10.1164/rccm.201912-2441OC,NA,"Kitsios G.D., Yang H., Yang L., Qin S., Fitch A., Wang X.H., Fair K., Evankovich J., Bain W., Shah F., Li K., Methé B., Benos P.V., Morris A. , McVerry B.J.",Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients,American journal of respiratory and critical care medicine,2020,"acute respiratory distress syndrome, bacterial infections, endotypes, inflammation, microbiota",Experiment 9,United States of America,Homo sapiens,Endothelium of trachea,UBERON:0003279,Acute respiratory failure,MONDO:0001208,Hyper-inflammatory subphenotype and ventilation-free days(VFDs),Mortality,"patients stratified on the basis of 30-day mortality [survivors vs. non-survivors] , for whom respiratory specimen cultures were reported as negative (no growth or only normal respiratory flora detected, n=152) as well as those for whom no cultures were obtained (n=76)",228,228,1 month,16S,34,Illumina,relative abundances,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,chronic obstructive pulmonary disease",NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary figure E8,2 March 2024,Folakunmi,"Folakunmi,WikiWorks","Relative abundance of individual genera in Endotracheal aspirate (ETA) genera is associated with clinical outcomes and host-response subphenotypes in patients without positive
respiratory cultures.",decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,Folakunmi
bsdb:32717152/10/1,32717152,prospective cohort,32717152,10.1164/rccm.201912-2441OC,NA,"Kitsios G.D., Yang H., Yang L., Qin S., Fitch A., Wang X.H., Fair K., Evankovich J., Bain W., Shah F., Li K., Methé B., Benos P.V., Morris A. , McVerry B.J.",Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients,American journal of respiratory and critical care medicine,2020,"acute respiratory distress syndrome, bacterial infections, endotypes, inflammation, microbiota",Experiment 10,United States of America,Homo sapiens,Endothelium of trachea,UBERON:0003279,Acute respiratory failure,MONDO:0001208,Hyper-inflammatory subphenotype and mortality,VFD (Ventilator free days),"clinical outcome stratifications by the number of days patients were ventilator-free for whom respiratory specimen cultures were reported as negative (no growth or only normal respiratory flora detected, n=152) as well as those for whom no cultures were obtained (n=76)",228,228,NA,16S,34,Illumina,relative abundances,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,chronic obstructive pulmonary disease",NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary figure E8,2 March 2024,Folakunmi,"Folakunmi,WikiWorks",Relative abundance of individual genera in Endotracheal aspirate (ETA) genera is associated with clinical outcomes and host-response subphenotypes in patients without positive respiratory cultures.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|1224|1236|135625|712|724;3379134|976|200643|171549|171552|838,Complete,Folakunmi
bsdb:32717152/11/NA,32717152,prospective cohort,32717152,10.1164/rccm.201912-2441OC,NA,"Kitsios G.D., Yang H., Yang L., Qin S., Fitch A., Wang X.H., Fair K., Evankovich J., Bain W., Shah F., Li K., Methé B., Benos P.V., Morris A. , McVerry B.J.",Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients,American journal of respiratory and critical care medicine,2020,"acute respiratory distress syndrome, bacterial infections, endotypes, inflammation, microbiota",Experiment 11,United States of America,Homo sapiens,Endothelium of trachea,UBERON:0003279,Acute respiratory failure,MONDO:0001208,VFD (Ventilator free days) and mortality,Hyper-inflammatory subphenotype,"participants who were classified into a hyperinflammatory subphenotype of host responses, for whom respiratory specimen cultures were reported as negative (no growth or only normal respiratory flora detected, n=152) as well as those for whom no cultures were obtained (n=76)",228,228,NA,16S,34,Illumina,relative abundances,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,chronic obstructive pulmonary disease",NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:32717152/12/NA,32717152,prospective cohort,32717152,10.1164/rccm.201912-2441OC,NA,"Kitsios G.D., Yang H., Yang L., Qin S., Fitch A., Wang X.H., Fair K., Evankovich J., Bain W., Shah F., Li K., Methé B., Benos P.V., Morris A. , McVerry B.J.",Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients,American journal of respiratory and critical care medicine,2020,"acute respiratory distress syndrome, bacterial infections, endotypes, inflammation, microbiota",Experiment 12,United States of America,Homo sapiens,Epithelium of oropharynx,UBERON:0001952,Acute respiratory failure,MONDO:0001208,VFD (Ventilator free days) and mortality,Hyper-inflammatory subphenotype,"participants who were classified into a hyperinflammatory subphenotype of host responses, for whom respiratory specimen cultures were reported as negative (no growth or only normal respiratory flora detected, n=152) as well as those for whom no cultures were obtained (n=76)",228,228,NA,16S,34,Illumina,relative abundances,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,chronic obstructive pulmonary disease",NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:32719372/1/1,32719372,"cross-sectional observational, not case-control",32719372,10.1038/s41598-020-69111-x,NA,"Vargas-Robles D., Morales N., Rodríguez I., Nieves T., Godoy-Vitorino F., Alcaraz L.D., Pérez M.E., Ravel J., Forney L.J. , Domínguez-Bello M.G.",Changes in the vaginal microbiota across a gradient of urbanization,Scientific reports,2020,NA,Experiment 1,Venezuela,Homo sapiens,Vagina,UBERON:0000996,Lifestyle measurement,EFO:0010724,Amerindians,Mestizos,"Mestizo women that have sexual practices other than vaginal, sexual contact with mestizo men, and use of vaginal douche.",15,27,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2e,31 October 2024,Tosin,"Tosin,WikiWorks",Discriminant taxa analysis between ethnicities; Amerindians and Mestizos (LEfSe).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus mulieris",3379134|976|200643|171549|171552|838;1783272|201174|1760|2037|2049|2050|2052,Complete,Svetlana up
bsdb:32719372/1/2,32719372,"cross-sectional observational, not case-control",32719372,10.1038/s41598-020-69111-x,NA,"Vargas-Robles D., Morales N., Rodríguez I., Nieves T., Godoy-Vitorino F., Alcaraz L.D., Pérez M.E., Ravel J., Forney L.J. , Domínguez-Bello M.G.",Changes in the vaginal microbiota across a gradient of urbanization,Scientific reports,2020,NA,Experiment 1,Venezuela,Homo sapiens,Vagina,UBERON:0000996,Lifestyle measurement,EFO:0010724,Amerindians,Mestizos,"Mestizo women that have sexual practices other than vaginal, sexual contact with mestizo men, and use of vaginal douche.",15,27,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2e,31 October 2024,Tosin,"Tosin,WikiWorks",Discriminant taxa analysis between ethnicities; Amerindians and Mestizos (LEfSe).,decreased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium|s__Brevibacterium linens",1783272|1239|1737404|1737405|1570339|162289|33031;1783272|201174|1760|85006|85019|1696|1703,Complete,Svetlana up
bsdb:32719372/2/1,32719372,"cross-sectional observational, not case-control",32719372,10.1038/s41598-020-69111-x,NA,"Vargas-Robles D., Morales N., Rodríguez I., Nieves T., Godoy-Vitorino F., Alcaraz L.D., Pérez M.E., Ravel J., Forney L.J. , Domínguez-Bello M.G.",Changes in the vaginal microbiota across a gradient of urbanization,Scientific reports,2020,NA,Experiment 2,Venezuela,Homo sapiens,Vagina,UBERON:0000996,Microbiome,EFO:0004982,"Combination of Community State Types(CST-G.vaginalis,  CST-div2  and CST-div1)",Community State Type- Lactobacillus iners(CST-L. Iners),Community State Type- Lactobacillus iners(CST-L. Iners) refers to the community state type that is dominated by Lactobacillus iners and associated with lowest vaginal pH and alpha diversity.,NA,NA,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3c,1 November 2024,Tosin,"Tosin,WikiWorks","Cervicovaginal microbiota composition and community state type (CST) clustering.
Discriminant taxa for CST-L.iners",increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,1783272|1239|91061|186826|33958|1578|147802,Complete,Svetlana up
bsdb:32719372/3/1,32719372,"cross-sectional observational, not case-control",32719372,10.1038/s41598-020-69111-x,NA,"Vargas-Robles D., Morales N., Rodríguez I., Nieves T., Godoy-Vitorino F., Alcaraz L.D., Pérez M.E., Ravel J., Forney L.J. , Domínguez-Bello M.G.",Changes in the vaginal microbiota across a gradient of urbanization,Scientific reports,2020,NA,Experiment 3,Venezuela,Homo sapiens,Vagina,UBERON:0000996,Microbiome,EFO:0004982,"Combination of CST-L.iners, CST-div2  and CST-div1.",Community State Type- Gardnerella vaginalis(CST-G.vaginalis),Community State Type- Gardnerella vaginalis(CST-G.vaginalis) refers to the community state type that is dominated by Gardnerella vaginalis and associated with intermediate alpha diversity; and two highly diverse clusters.,NA,NA,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3c,3 November 2024,Tosin,"Tosin,WikiWorks",Cervicovaginal microbiota composition and community state type (CST) clustering. Discriminant taxa for CST-G.vaginalis.,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,1783272|201174|1760|85004|31953|2701|2702,Complete,Svetlana up
bsdb:32719372/4/1,32719372,"cross-sectional observational, not case-control",32719372,10.1038/s41598-020-69111-x,NA,"Vargas-Robles D., Morales N., Rodríguez I., Nieves T., Godoy-Vitorino F., Alcaraz L.D., Pérez M.E., Ravel J., Forney L.J. , Domínguez-Bello M.G.",Changes in the vaginal microbiota across a gradient of urbanization,Scientific reports,2020,NA,Experiment 4,Venezuela,Homo sapiens,Vagina,UBERON:0000996,Microbiome,EFO:0004982,"Combination of CST-L.iners, CST-div2  and CST-G.vaginalis",Community State Type diverse cluster 1-CST-div1,Community State Type diverse cluster 1-CST-div1 refers to community state type diverse cluster that is associated with highest vaginal pH and alpha diversity,NA,NA,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3c,4 November 2024,Tosin,"Tosin,WikiWorks",Cervicovaginal microbiota composition and community state type (CST) clustering. Discriminant taxa for CST-div1.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Lachnocurva|s__Candidatus Lachnocurva vaginae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus mulieris,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus koenoeneniae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia",1783272|1239|186801|3085636|186803|3397567|699240;3379134|976|200643|171549|171552|2974257|28127;1783272|1239|186801|3085636|186803|28050;1783272|1239|909932|1843489|31977|906|187326;1783272|201174|1760|2037|2049|2050|2052;1783272|1239|1737404|1737405|1570339|162289|507751;1783272|1239|1737404|1737405|1570339|162289|33031;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|419005;3379134|976|200643|171549|171550;1783272|1239|186801|3085636|186803|841;3384189|32066|203490|203491|1129771|168808,Complete,Svetlana up
bsdb:32719372/5/1,32719372,"cross-sectional observational, not case-control",32719372,10.1038/s41598-020-69111-x,NA,"Vargas-Robles D., Morales N., Rodríguez I., Nieves T., Godoy-Vitorino F., Alcaraz L.D., Pérez M.E., Ravel J., Forney L.J. , Domínguez-Bello M.G.",Changes in the vaginal microbiota across a gradient of urbanization,Scientific reports,2020,NA,Experiment 5,Venezuela,Homo sapiens,Vagina,UBERON:0000996,Microbiome,EFO:0004982,"Combination of CST-L.iners, CST-div1  and CST-G.vaginalis",Community State Type diverse cluster 2-CST-div2,Community State Type diverse cluster 2-CST-div2 refers to community state type diverse cluster that is associated with highest vaginal pH and alpha diversity,NA,NA,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3c,4 November 2024,Tosin,"Tosin,WikiWorks",Cervicovaginal microbiota composition and community state type (CST) clustering. Discriminant taxa for CST-div2.,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia vaginalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra",3384189|32066|203490|203491|1129771|168808|40543;3384189|32066|203490|203491|1129771|168808|187101;3379134|976|200643|171549|171552|838|28125;1783272|201174|84998|84999|1643824|2767327|82135;1783272|1239|909932|1843489|31977|906;1783272|201174|84998|84999|84107|1473205;1783272|1239|186801|186802|31979|1485;1783272|1239|1737404|1737405|1570339|543311|33033,Complete,Svetlana up
bsdb:32719372/6/1,32719372,"cross-sectional observational, not case-control",32719372,10.1038/s41598-020-69111-x,NA,"Vargas-Robles D., Morales N., Rodríguez I., Nieves T., Godoy-Vitorino F., Alcaraz L.D., Pérez M.E., Ravel J., Forney L.J. , Domínguez-Bello M.G.",Changes in the vaginal microbiota across a gradient of urbanization,Scientific reports,2020,NA,Experiment 6,Venezuela,Homo sapiens,Vagina,UBERON:0000996,Microbiome,EFO:0004982,CST-L.iners,Community State Type diverse cluster 3-CST-div3,Community State Type diverse cluster 3-CST-div3 refers to community state type diverse cluster that has a high diversity and low pH. It was found in the introital sample.,NA,NA,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure S3b,4 November 2024,Tosin,"Tosin,WikiWorks",Discriminant taxa analysis for initroital CSTs according to LeFSe.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans|s__Saccharofermentans acetigenes,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia vaginalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis",1783272|1239|186801|186802|31979|1485;1783272|1239|909932|1843489|31977|39948|309120;1783272|1239|186801|186802;1783272|201174|84998|84999|1643824|2767327|82135;1783272|201174|1760|85004|31953|2701|2702;1783272|1239|909932|1843489|31977|906;1783272|1239|1737404|1737405|1570339|543311|33033;3379134|976|200643|171549|171551|836|281920;3379134|976|200643|171549|171552|838|28125;1783272|1239|186801|186802|216572|1200657|319644;3384189|32066|203490|203491|1129771|168808;3384189|32066|203490|203491|1129771|168808|40543;3384189|32066|203490|203491|1129771|168808|187101;1783272|1239|91061|186826|1300|1301|1328;3379134|976|200643|171549|171552|2974257|386414,Complete,Svetlana up
bsdb:32719372/6/2,32719372,"cross-sectional observational, not case-control",32719372,10.1038/s41598-020-69111-x,NA,"Vargas-Robles D., Morales N., Rodríguez I., Nieves T., Godoy-Vitorino F., Alcaraz L.D., Pérez M.E., Ravel J., Forney L.J. , Domínguez-Bello M.G.",Changes in the vaginal microbiota across a gradient of urbanization,Scientific reports,2020,NA,Experiment 6,Venezuela,Homo sapiens,Vagina,UBERON:0000996,Microbiome,EFO:0004982,CST-L.iners,Community State Type diverse cluster 3-CST-div3,Community State Type diverse cluster 3-CST-div3 refers to community state type diverse cluster that has a high diversity and low pH. It was found in the introital sample.,NA,NA,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure S3b,4 November 2024,Tosin,"Tosin,WikiWorks",Discriminant taxa analysis for introital CST according to LEFse.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,1783272|1239|91061|186826|33958|1578|147802,Complete,Svetlana up
bsdb:32719372/7/1,32719372,"cross-sectional observational, not case-control",32719372,10.1038/s41598-020-69111-x,NA,"Vargas-Robles D., Morales N., Rodríguez I., Nieves T., Godoy-Vitorino F., Alcaraz L.D., Pérez M.E., Ravel J., Forney L.J. , Domínguez-Bello M.G.",Changes in the vaginal microbiota across a gradient of urbanization,Scientific reports,2020,NA,Experiment 7,Venezuela,Homo sapiens,Vagina,UBERON:0000996,Sampling site,EFO:0000688,Cervicovaginal,Introitus,Introitus as vaginal sites for Amerindians.,95,73,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig S3d,4 November 2024,Tosin,"Tosin,WikiWorks",Discriminant taxa analysis within Amerinidians by body site.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma parvum",1783272|1239|909932|1843489|31977|39948|309120;1783272|544448|2790996|2790998|2129|134821,Complete,Svetlana up
bsdb:32719372/8/1,32719372,"cross-sectional observational, not case-control",32719372,10.1038/s41598-020-69111-x,NA,"Vargas-Robles D., Morales N., Rodríguez I., Nieves T., Godoy-Vitorino F., Alcaraz L.D., Pérez M.E., Ravel J., Forney L.J. , Domínguez-Bello M.G.",Changes in the vaginal microbiota across a gradient of urbanization,Scientific reports,2020,NA,Experiment 8,Venezuela,Homo sapiens,Vagina,UBERON:0000996,Sampling site,EFO:0000688,Cervicovaginal,Introitus,Introitus as vaginal site for Mestizos.,95,73,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure S3d,4 November 2024,Tosin,"Tosin,Svetlana up,WikiWorks",Discriminant taxa analysis within Mestizos by body site.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus christensenii,1783272|1239|91061|186826|186827|1375|87541,Complete,Svetlana up
bsdb:32719372/9/1,32719372,"cross-sectional observational, not case-control",32719372,10.1038/s41598-020-69111-x,NA,"Vargas-Robles D., Morales N., Rodríguez I., Nieves T., Godoy-Vitorino F., Alcaraz L.D., Pérez M.E., Ravel J., Forney L.J. , Domínguez-Bello M.G.",Changes in the vaginal microbiota across a gradient of urbanization,Scientific reports,2020,NA,Experiment 9,Venezuela,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,Negative,Positive,Positive refers to women with Human Papillomavirus infection(HPV infection).,21,74,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure S4b,4 November 2024,Tosin,"Tosin,WikiWorks",Discriminant taxa analysis by HPV status showing significance in only HPV negative women,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus tetradius",1783272|201174|84998|84999|84107;1783272|1239|1737404|1737405|1570339|165779|33036,Complete,Svetlana up
bsdb:32719372/10/1,32719372,"cross-sectional observational, not case-control",32719372,10.1038/s41598-020-69111-x,NA,"Vargas-Robles D., Morales N., Rodríguez I., Nieves T., Godoy-Vitorino F., Alcaraz L.D., Pérez M.E., Ravel J., Forney L.J. , Domínguez-Bello M.G.",Changes in the vaginal microbiota across a gradient of urbanization,Scientific reports,2020,NA,Experiment 10,Venezuela,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,"Combination of Only low-risk, both risk-types and Negative HPV type",Only high risk HPV Type,Women that have high risk of HPV.,NA,NA,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure S4c,4 November 2024,Tosin,"Tosin,WikiWorks",Discriminant taxa analysis by HPV status showing a significance in women infected with high-risk HPV.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,3379134|976|200643|171549|171552|838|419005,Complete,Svetlana up
bsdb:32719372/11/1,32719372,"cross-sectional observational, not case-control",32719372,10.1038/s41598-020-69111-x,NA,"Vargas-Robles D., Morales N., Rodríguez I., Nieves T., Godoy-Vitorino F., Alcaraz L.D., Pérez M.E., Ravel J., Forney L.J. , Domínguez-Bello M.G.",Changes in the vaginal microbiota across a gradient of urbanization,Scientific reports,2020,NA,Experiment 11,Venezuela,Homo sapiens,Vagina,UBERON:0000996,Lifestyle measurement,EFO:0010724,Combination of Low and Medium Amerindian urbanization group,High Amerindian urbanization group,High Amerindian urbanization group refers to Amerindians living in the high urban areas.,35,20,NA,16S,123,Illumina,relative abundances,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table S7,20 November 2024,Tosin,"Tosin,KateRasheed,WikiWorks","Differential abundance taxa between Low, Medium and High Amerindian urbanization groups.",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma urealyticum",1783272|1239|909932|1843489|31977|39948|309120;1783272|1239|1737404|1737405|1570339|543311|33033;3384189|32066|203490|203491|1129771|168808|40543;1783272|544448|2790996|2790998|2129|2130,Complete,Svetlana up
bsdb:32719372/11/2,32719372,"cross-sectional observational, not case-control",32719372,10.1038/s41598-020-69111-x,NA,"Vargas-Robles D., Morales N., Rodríguez I., Nieves T., Godoy-Vitorino F., Alcaraz L.D., Pérez M.E., Ravel J., Forney L.J. , Domínguez-Bello M.G.",Changes in the vaginal microbiota across a gradient of urbanization,Scientific reports,2020,NA,Experiment 11,Venezuela,Homo sapiens,Vagina,UBERON:0000996,Lifestyle measurement,EFO:0010724,Combination of Low and Medium Amerindian urbanization group,High Amerindian urbanization group,High Amerindian urbanization group refers to Amerindians living in the high urban areas.,35,20,NA,16S,123,Illumina,relative abundances,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table S7,20 November 2024,Tosin,"Tosin,KateRasheed,WikiWorks","Differential abundance taxa between Low, Medium and High Amerindian urbanization groups.",decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,1783272|1239|91061|186826|33958|1578|147802,Complete,Svetlana up
bsdb:32719372/13/1,32719372,"cross-sectional observational, not case-control",32719372,10.1038/s41598-020-69111-x,NA,"Vargas-Robles D., Morales N., Rodríguez I., Nieves T., Godoy-Vitorino F., Alcaraz L.D., Pérez M.E., Ravel J., Forney L.J. , Domínguez-Bello M.G.",Changes in the vaginal microbiota across a gradient of urbanization,Scientific reports,2020,NA,Experiment 13,Venezuela,Homo sapiens,Vagina,UBERON:0000996,Lifestyle measurement,EFO:0010724,Low Amerindian urbanization group,Medium Amerindian urbanization group,Medium Amerindian urbanization group refers to Amerindians living in the medium urban areas.,15,20,NA,16S,123,Illumina,relative abundances,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table S7,11 December 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance taxa between Low and Medium Amerindian urbanization groups.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma urealyticum",1783272|1239|91061|186826|33958|1578|147802;1783272|1239|1737404|1737405|1570339|543311|33033;3384189|32066|203490|203491|1129771|168808|40543;1783272|544448|2790996|2790998|2129|2130,Complete,Svetlana up
bsdb:32719372/14/1,32719372,"cross-sectional observational, not case-control",32719372,10.1038/s41598-020-69111-x,NA,"Vargas-Robles D., Morales N., Rodríguez I., Nieves T., Godoy-Vitorino F., Alcaraz L.D., Pérez M.E., Ravel J., Forney L.J. , Domínguez-Bello M.G.",Changes in the vaginal microbiota across a gradient of urbanization,Scientific reports,2020,NA,Experiment 14,Venezuela,Homo sapiens,Vagina,UBERON:0000996,Lifestyle measurement,EFO:0010724,Combination of Low and High Amerindian urbanization group,Mestizos,"Mestizos refers to Mestizo women that have sexual practices other than vaginal, sexual contact with mestizo men, and use of vaginal douche.",35,27,NA,16S,123,Illumina,relative abundances,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S7,11 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance taxa between Low, High Amerindian urbanization groups and Mestizos.",increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus mulieris,1783272|201174|1760|2037|2049|2050|2052,Complete,Svetlana up
bsdb:32719372/14/2,32719372,"cross-sectional observational, not case-control",32719372,10.1038/s41598-020-69111-x,NA,"Vargas-Robles D., Morales N., Rodríguez I., Nieves T., Godoy-Vitorino F., Alcaraz L.D., Pérez M.E., Ravel J., Forney L.J. , Domínguez-Bello M.G.",Changes in the vaginal microbiota across a gradient of urbanization,Scientific reports,2020,NA,Experiment 14,Venezuela,Homo sapiens,Vagina,UBERON:0000996,Lifestyle measurement,EFO:0010724,Combination of Low and High Amerindian urbanization group,Mestizos,"Mestizos refers to Mestizo women that have sexual practices other than vaginal, sexual contact with mestizo men, and use of vaginal douche.",35,27,NA,16S,123,Illumina,relative abundances,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S7,11 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance taxa between Low, High Amerindian urbanization groups and Mestizos.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium|s__Brevibacterium linens,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis",1783272|201174|1760|85006|85019|1696|1703;1783272|1239|1737404|1737405|1570339|162289|33031,Complete,Svetlana up
bsdb:32719372/15/1,32719372,"cross-sectional observational, not case-control",32719372,10.1038/s41598-020-69111-x,NA,"Vargas-Robles D., Morales N., Rodríguez I., Nieves T., Godoy-Vitorino F., Alcaraz L.D., Pérez M.E., Ravel J., Forney L.J. , Domínguez-Bello M.G.",Changes in the vaginal microbiota across a gradient of urbanization,Scientific reports,2020,NA,Experiment 15,Venezuela,Homo sapiens,Vagina,UBERON:0000996,Lifestyle measurement,EFO:0010724,Medium Amerindian urbanization group,Mestizos,"Mestizos refers to Mestizo women that have sexual practices other than vaginal, sexual contact with mestizo men, and use of vaginal douche.",20,27,NA,16S,123,Illumina,relative abundances,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S7,11 December 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance taxa between Medium Amerindian urbanization groups and Mestizos.,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus mulieris",1783272|1239|1737404|1737405|1570339|162289|33031;1783272|201174|1760|2037|2049|2050|2052,Complete,Svetlana up
bsdb:32719372/15/2,32719372,"cross-sectional observational, not case-control",32719372,10.1038/s41598-020-69111-x,NA,"Vargas-Robles D., Morales N., Rodríguez I., Nieves T., Godoy-Vitorino F., Alcaraz L.D., Pérez M.E., Ravel J., Forney L.J. , Domínguez-Bello M.G.",Changes in the vaginal microbiota across a gradient of urbanization,Scientific reports,2020,NA,Experiment 15,Venezuela,Homo sapiens,Vagina,UBERON:0000996,Lifestyle measurement,EFO:0010724,Medium Amerindian urbanization group,Mestizos,"Mestizos refers to Mestizo women that have sexual practices other than vaginal, sexual contact with mestizo men, and use of vaginal douche.",20,27,NA,16S,123,Illumina,relative abundances,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S7,11 December 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance taxa between Medium Amerindian urbanization groups and Mestizos.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium|s__Brevibacterium linens,1783272|201174|1760|85006|85019|1696|1703,Complete,Svetlana up
bsdb:32727366/1/1,32727366,case-control,32727366,https://doi.org/10.1186/s12866-020-01918-0,NA,"Wang J., Xu J., Han Q., Chu W., Lu G., Chan W.Y., Qin Y. , Du Y.",Changes in the vaginal microbiota associated with primary ovarian failure,BMC microbiology,2020,"16S rRNA, Female reproductive tract, Pathogenesis, Primary ovarian failure, Vaginal microbiota",Experiment 1,China,Homo sapiens,Vaginal fluid,UBERON:0036243,Premature ovarian insufficiency,HP:0008209,Healthy controls,Primary ovarian failure (POF),Women of reproductive age with follicular failure,29,22,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,increased,NA,increased,Signature 1,Figure 2a,25 March 2024,Ndruscilla,"Ndruscilla,Scholastica,WikiWorks",Differential genera in vaginal microbiota in patients with primary ovarian failure (POF) compared to control group,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Helcococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Oceanobacillus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Luteimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Caryophanon,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Marinobacteraceae|g__Marinobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Oligella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella",3379134|976|200643|171549|171552|838;1783272|201174|1760|85004|31953|2701;1783272|201174|1760|85004|31953|1678;3384189|32066|203490|203491|1129771|168808;3379134|976|200643|171549|171551|836;3379134|1224|1236|91347|543|1940338;3379134|976|200643|171549|815|816;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|29465;3379134|29547|3031852|213849|72294|194;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|91061|186826|1300|1301;1783272|1239|1737404|1737405|1570339|31983;3379134|1224|1236|91347|1903414|586;1783272|201174|1760|85007|1653|1716;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|186802|31979|1485;3379134|1224|1236|91347|1903411|613;3379134|29547|3031852|213849|2808963|28196;1783272|1239|91061|1385|186817|182709;3379134|976|117743|200644|2762318|59732;1783272|201174|1760|2037|2049|1654;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|186801|186802|404402;1783272|1239|186801|3085636|186803|572511;3379134|1224|1236|135614|32033|83614;1783272|1239|91061|1385|186818|33976;3379134|1224|1236|72274|2887365|2742;3379134|1224|1236|135624|83763|83770;1783272|1239|1737404|1737405|1570339|1161127;3379134|1224|1236|135619|28256|2745;1783272|1239|909932|1843488|909930|904;1783272|1239|91061|1385|539738|1378;1783272|1239|909932|1843489|31977|909928;1783272|1239|186801|186802|204475;1783272|201174|1760|85006|1268|32207;3379134|1224|28216|80840|506|90243;1783272|1239|91061|186826|81852|1350;1783272|201174|1760|2037|2049|28263;3379134|976|200643|171549|171552|1283313,Complete,Svetlana up
bsdb:32727366/1/2,32727366,case-control,32727366,https://doi.org/10.1186/s12866-020-01918-0,NA,"Wang J., Xu J., Han Q., Chu W., Lu G., Chan W.Y., Qin Y. , Du Y.",Changes in the vaginal microbiota associated with primary ovarian failure,BMC microbiology,2020,"16S rRNA, Female reproductive tract, Pathogenesis, Primary ovarian failure, Vaginal microbiota",Experiment 1,China,Homo sapiens,Vaginal fluid,UBERON:0036243,Premature ovarian insufficiency,HP:0008209,Healthy controls,Primary ovarian failure (POF),Women of reproductive age with follicular failure,29,22,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,increased,NA,increased,Signature 2,Figure 2a,25 March 2024,Ndruscilla,"Ndruscilla,Scholastica,WikiWorks",Differential genera in vaginal microbiota in patients with primary ovarian failure (POF) compared to control group,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|91061|186826|33958|1578;3379134|1224|28211|204458|76892|41275;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3085636|186803|841;3379134|1224|28211|356|118882|528;1783272|201174|84998|84999|1643824|1380;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:32728075/1/1,32728075,case-control,32728075,10.1038/s41598-020-69537-3,NA,"Dei-Cas I., Giliberto F., Luce L., Dopazo H. , Penas-Steinhardt A.",Metagenomic analysis of gut microbiota in non-treated plaque psoriasis patients stratified by disease severity: development of a new Psoriasis-Microbiome Index,Scientific reports,2020,NA,Experiment 1,Argentina,Homo sapiens,Feces,UBERON:0001988,Psoriasis,EFO:0000676,Non-psoriasis Controls,Chronic plaque psoriasis patients,Chronic plaque psoriasis patients refers to patients with untreated chronic plaque psoriasis.,27,55,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 3,15 April 2025,Nithya,"Nithya,KateRasheed",Enriched bacterial genus associated with psoriasis patients,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239,Complete,KateRasheed
bsdb:32728075/1/2,32728075,case-control,32728075,10.1038/s41598-020-69537-3,NA,"Dei-Cas I., Giliberto F., Luce L., Dopazo H. , Penas-Steinhardt A.",Metagenomic analysis of gut microbiota in non-treated plaque psoriasis patients stratified by disease severity: development of a new Psoriasis-Microbiome Index,Scientific reports,2020,NA,Experiment 1,Argentina,Homo sapiens,Feces,UBERON:0001988,Psoriasis,EFO:0000676,Non-psoriasis Controls,Chronic plaque psoriasis patients,Chronic plaque psoriasis patients refers to patients with untreated chronic plaque psoriasis.,27,55,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 3,15 April 2025,Nithya,Nithya,Enriched bacterial genus associated  with non-psoriasis controls,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota",3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976|200643|171549|171552|577309;3379134|976,Complete,KateRasheed
bsdb:32728114/1/1,32728114,"cross-sectional observational, not case-control",32728114,10.1038/s41467-020-17541-6,NA,"Sprockett D.D., Martin M., Costello E.K., Burns A.R., Holmes S.P., Gurven M.D. , Relman D.A.","Microbiota assembly, structure, and dynamics among Tsimane horticulturalists of the Bolivian Amazon",Nature communications,2020,NA,Experiment 1,Bolivia,Homo sapiens,Feces,UBERON:0001988,Restricted to specific location,MONDO:0045042,Proximal River Village,Distal River Village,"Tsimane adults (>14 years old) that live in a village along the Maniqui river, that is more than 20 km away from the regional market and have access to the market via 6-12 hour trips by foot or boat.",19,77,NA,16S,4,Illumina,log transformation,treeDA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5C and Sprockett_Tsimane_ps.rds,9 November 2024,YokoC,"YokoC,WikiWorks",Discriminatory ASVs for proximal and distal river villages identified using a tree-based LDA algorithm.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus",3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|2005473;3379134|976|200643|171549|815|909656|821,Complete,Svetlana up
bsdb:32728114/1/2,32728114,"cross-sectional observational, not case-control",32728114,10.1038/s41467-020-17541-6,NA,"Sprockett D.D., Martin M., Costello E.K., Burns A.R., Holmes S.P., Gurven M.D. , Relman D.A.","Microbiota assembly, structure, and dynamics among Tsimane horticulturalists of the Bolivian Amazon",Nature communications,2020,NA,Experiment 1,Bolivia,Homo sapiens,Feces,UBERON:0001988,Restricted to specific location,MONDO:0045042,Proximal River Village,Distal River Village,"Tsimane adults (>14 years old) that live in a village along the Maniqui river, that is more than 20 km away from the regional market and have access to the market via 6-12 hour trips by foot or boat.",19,77,NA,16S,4,Illumina,log transformation,treeDA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5C and Sprockett_Tsimane_ps.rds,9 November 2024,YokoC,"YokoC,WikiWorks",Discriminatory ASVs for proximal and distal river villages identified using a tree-based LDA algorithm.,decreased,NA,NA,Complete,Svetlana up
bsdb:32728114/2/1,32728114,"cross-sectional observational, not case-control",32728114,10.1038/s41467-020-17541-6,NA,"Sprockett D.D., Martin M., Costello E.K., Burns A.R., Holmes S.P., Gurven M.D. , Relman D.A.","Microbiota assembly, structure, and dynamics among Tsimane horticulturalists of the Bolivian Amazon",Nature communications,2020,NA,Experiment 2,Bolivia,Homo sapiens,Feces,UBERON:0001988,Restricted to specific location,MONDO:0045042,River Village,Forest Village,"Tsimane adults that live in a village from the forest ecotype, distant by 40 km or more from the regional market. Samples were collected in the dry season of 2009.",96,73,NA,16S,4,Illumina,log transformation,treeDA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5C and Sprockett_Tsimane_ps.rds,12 November 2024,YokoC,"YokoC,WikiWorks",Discriminatory ASVs for forest or river villages identified using a tree-based LDA algorithm.,increased,"k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas",3366610|28890|183925|2158|2159|2172;1783272|1239|186801|3082720|543314|86331;3379134|976|200643|171549|2005473;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|1392389,Complete,Svetlana up
bsdb:32728114/2/2,32728114,"cross-sectional observational, not case-control",32728114,10.1038/s41467-020-17541-6,NA,"Sprockett D.D., Martin M., Costello E.K., Burns A.R., Holmes S.P., Gurven M.D. , Relman D.A.","Microbiota assembly, structure, and dynamics among Tsimane horticulturalists of the Bolivian Amazon",Nature communications,2020,NA,Experiment 2,Bolivia,Homo sapiens,Feces,UBERON:0001988,Restricted to specific location,MONDO:0045042,River Village,Forest Village,"Tsimane adults that live in a village from the forest ecotype, distant by 40 km or more from the regional market. Samples were collected in the dry season of 2009.",96,73,NA,16S,4,Illumina,log transformation,treeDA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5C and Sprockett_Tsimane_ps.rds,13 November 2024,YokoC,"YokoC,WikiWorks",Discriminatory ASVs for forest or river villages identified using a tree-based LDA algorithm.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister histaminiformans,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",1783272|1239|909932|1843489|31977|39948|209880;1783272|1239|909932|909929|1843491|82373;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|3342669|45851;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;1783272|1239|909932|1843488|909930|33024;1783272|1239|909932|1843488|909930|33024|626940;3379134|976|200643|171549|171552;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|292632,Complete,Svetlana up
bsdb:32733243/1/1,32733243,prospective cohort,32733243,10.3389/fphar.2020.01000,NA,"Wang B., Zhang Y., Zhao Q., Yan Y., Yang T., Xia Y. , Chen H.",Patients With Reflux Esophagitis Possess a Possible Different Oral Microbiota Compared With Healthy Controls,Frontiers in pharmacology,2020,"biomarker, dysbiosis, high-throughput sequencing, oral microbiota, reflux esophagitis",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Peptic esophagitis,EFO:1001095,healthy controls,reflux esophagus patients,symptoms such as heartburn and regurgitation were in accordance with the endoscopic criteria of Los Angeles Grade and taken no drugs as treatment,51,55,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 3,10 January 2021,Rimsha Azhar,"Atrayees,WikiWorks",Bacterial taxa diversities between Reflux Esophigitis (RE) and healthy controls,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Neomegalonemataceae|g__Neomegalonema",1783272|201174|84998|84999|1643824|1380;3379134|976|200643|171549;3379134|976|200643;3379134|976;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803|1164882;1783272|1239|186801|3085636|186803;1783272|1239|909932|1843489|31977|906;3379134|1224|28211|356|119045;1783272|1239|909932;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|909932|909929;1783272|1239|526524|526525|128827|123375;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977;3379134|1224|28211|204455|2814874|356797,Complete,Atrayees
bsdb:32733243/1/2,32733243,prospective cohort,32733243,10.3389/fphar.2020.01000,NA,"Wang B., Zhang Y., Zhao Q., Yan Y., Yang T., Xia Y. , Chen H.",Patients With Reflux Esophagitis Possess a Possible Different Oral Microbiota Compared With Healthy Controls,Frontiers in pharmacology,2020,"biomarker, dysbiosis, high-throughput sequencing, oral microbiota, reflux esophagitis",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Peptic esophagitis,EFO:1001095,healthy controls,reflux esophagus patients,symptoms such as heartburn and regurgitation were in accordance with the endoscopic criteria of Los Angeles Grade and taken no drugs as treatment,51,55,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 3,10 January 2021,Rimsha Azhar,"Lwaldron,WikiWorks,Merit",Bacterial taxa diversities between Reflux Esophigitis (RE) and healthy controls,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillales Family X. Incertae Sedis,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Acidobacteriota|c__Terriglobia|o__Terriglobales|f__Acidobacteriaceae|g__Granulicella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Lactivibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia,k__Pseudomonadati|p__Spirochaetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales,k__Thermotogati|p__Synergistota|c__Synergistia,k__Thermotogati|p__Synergistota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Syntrophomonadaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Wolinella,k__Viridiplantae|p__Streptophyta,k__Bacillati|p__Cyanobacteriota",1783272|201174|1760|2037;3379134|1224|1236|135625|712|416916;1783272|1239|91061|1385;1783272|1239|91061|1385|539003;1783272|1239|91061;3379134|1224|28216;3379134|1224|28216|80840;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294;3379134|29547|3031852|213849;3379134|29547;1783272|1239|91061|186826|186828;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;3379134|1224|28216|206351|481|538;1783272|1239|186801|3082720|3118655|44259;1783272|201174|1760|85004|31953|2701;1783272|1239|91061|1385|539738|1378;3379134|57723|204432|204433|204434|940557;3379134|976|200643|171549|171552|52228;1783272|1239|186801|3085636|186803|43994;3384194|508458|649775|649776|3029087|1508421;1783272|1239|91061|186826;1783272|201174|1760|85006|1268;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481;3379134|1224|28216|206351;3379134|1224;1783272|1239|186801|186802|186806|113286;1783272|201174|1760|85006|1268|32207;3379134|203691|203692|136|137;3379134|203691|203692|136;3379134|203691|203692;3379134|203691;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;3384194|508458|649775|649776|649777;3384194|508458|649775|649776;3384194|508458|649775;3384194|508458;1783272|1239|186801|186802|68298;3379134|203691|203692|136|2845253|157;3379134|29547|3031852|213849|72293|843;33090|35493;1783272|1117,Complete,Atrayees
bsdb:32747678/1/1,32747678,case-control,32747678,10.1038/s41598-020-69845-8,https://pubmed.ncbi.nlm.nih.gov/32747678/,"Zeng Q., Shen J., Chen K., Zhou J., Liao Q., Lu K., Yuan J. , Bi F.",The alteration of gut microbiome and metabolism in amyotrophic lateral sclerosis patients,Scientific reports,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Amyotrophic lateral sclerosis,MONDO:0004976,Healthy controls,Amyotrophic lateral sclerosis - ALS patients,Patients clinically diagnosed with probably or definite ALS according to the revised El Escorial criteria in the neurology department.,20,20,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,4,age,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2F,14 January 2021,Fatima,"Fatima,Peace Sandy,WikiWorks","The bar chart shows the biomarkers with diferential abundance between the groups and larger than the preset value (LDA score >4, p<0.05). The LDA score indicates the extent to which the corresponding group is affected by the diferential microbes.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|976|200643|171549|171551,Complete,Peace Sandy
bsdb:32747678/1/2,32747678,case-control,32747678,10.1038/s41598-020-69845-8,https://pubmed.ncbi.nlm.nih.gov/32747678/,"Zeng Q., Shen J., Chen K., Zhou J., Liao Q., Lu K., Yuan J. , Bi F.",The alteration of gut microbiome and metabolism in amyotrophic lateral sclerosis patients,Scientific reports,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Amyotrophic lateral sclerosis,MONDO:0004976,Healthy controls,Amyotrophic lateral sclerosis - ALS patients,Patients clinically diagnosed with probably or definite ALS according to the revised El Escorial criteria in the neurology department.,20,20,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,4,age,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2F,14 January 2021,Fatima,"Fatima,Peace Sandy,WikiWorks","The bar chart shows the biomarkers with diferential abundance between the groups and larger than the preset value (LDA score >4, p<0.05). The LDA score indicates the extent to which the corresponding group is affected by the diferential microbes.",decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",1783272|1239|909932|909929|1843491|158846;1783272|1239|909932;1783272|1239|909932|909929;1783272|1239|909932|1843489|31977;1783272|1239|909932|909929|1843491|158846,Complete,Peace Sandy
bsdb:32753953/1/1,32753953,"cross-sectional observational, not case-control",32753953,10.2147/CMAR.S251021,NA,"Zhou J., Wang L., Yuan R., Yu X., Chen Z., Yang F., Sun G. , Dong Q.",Signatures of Mucosal Microbiome in Oral Squamous Cell Carcinoma Identified Using a Random Forest Model,Cancer management and research,2020,"microbiome, oral squamous cell carcinoma, predicted functions, random forest machine learning",Experiment 1,China,Homo sapiens,Mucosa of oral region,UBERON:0003343,Oral squamous cell carcinoma,EFO:0000199,paracancerous tissues,cancerous  lesions,patients at different stages of OSCC were enrolled in the study,24,24,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2A,10 January 2021,Rimsha Azhar,"WikiWorks,ChiomaBlessing",Relative abundance of genera enriched in cancerous tissues VS paracancerous tissues,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",1783272|1239|91061|186826|186828|2747;1783272|1239|186801|3082720|3118655|44259;3384189|32066|203490|203491|203492|848;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|2005525|195950;3379134|203691|203692|136|2845253|157,Complete,ChiomaBlessing
bsdb:32753953/1/2,32753953,"cross-sectional observational, not case-control",32753953,10.2147/CMAR.S251021,NA,"Zhou J., Wang L., Yuan R., Yu X., Chen Z., Yang F., Sun G. , Dong Q.",Signatures of Mucosal Microbiome in Oral Squamous Cell Carcinoma Identified Using a Random Forest Model,Cancer management and research,2020,"microbiome, oral squamous cell carcinoma, predicted functions, random forest machine learning",Experiment 1,China,Homo sapiens,Mucosa of oral region,UBERON:0003343,Oral squamous cell carcinoma,EFO:0000199,paracancerous tissues,cancerous  lesions,patients at different stages of OSCC were enrolled in the study,24,24,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2A,10 January 2021,Rimsha Azhar,"Atrayees,WikiWorks,ChiomaBlessing",Relative abundance of genera enriched in cancerous tissues VS paracancerous tissues,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Viridiplantae|p__Streptophyta",1783272|201174|1760|85006|1268|1663;3379134|1224|28211|204458|76892|41275;3379134|200940|3031449|213115|194924|872;1783272|201174|1760|85006|85023|33882;3379134|200930|68337|191393|2945020|248038;1783272|1239|91061|1385|186822|44249;33090|35493,Complete,ChiomaBlessing
bsdb:32763534/1/1,32763534,case-control,32763534,10.1016/j.psychres.2020.113260,NA,"Pan R., Zhang X., Gao J., Yi W., Wei Q. , Su H.",Analysis of the diversity of intestinal microbiome and its potential value as a biomarker in patients with schizophrenia: A cohort study,Psychiatry research,2020,"16S function prediction, 16S rRNA sequencing, Gut microbiome, Random forest, Schizophrenia",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy controls,acute schizphrenia,"patients who complied with diagnostic criteria for SCZ in the Diagnostic and Statistical Manual of Mental DIsorders Fourth Edition, Positive and negative syndrome scale, PANSS<60; No change in antipsychotic regimen (within two weeks)",29,29,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 2A,10 January 2021,Fatima Zohra,"WikiWorks,Atrayees,Folakunmi",Characterization of fecal microbiota to to distinguish toxigenic types by lineear discriminant anlysis method,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",1783272|1239|186801|186802|216572|258514;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;1783272|1239|186801|186802|216572|244127;3379134|200940|3031449|213115|194924|35832;28221;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3082720|186804|1505657;1783272|1239|186801|186802|216572|1508657;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|216572|707003,Complete,Folakunmi
bsdb:32763534/1/2,32763534,case-control,32763534,10.1016/j.psychres.2020.113260,NA,"Pan R., Zhang X., Gao J., Yi W., Wei Q. , Su H.",Analysis of the diversity of intestinal microbiome and its potential value as a biomarker in patients with schizophrenia: A cohort study,Psychiatry research,2020,"16S function prediction, 16S rRNA sequencing, Gut microbiome, Random forest, Schizophrenia",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy controls,acute schizphrenia,"patients who complied with diagnostic criteria for SCZ in the Diagnostic and Statistical Manual of Mental DIsorders Fourth Edition, Positive and negative syndrome scale, PANSS<60; No change in antipsychotic regimen (within two weeks)",29,29,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 2A,10 January 2021,Fatima Zohra,"WikiWorks,Folakunmi",Characterization of fecal microbiota to to distinguish toxigenic types by lineear discriminant anlysis method,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Catenisphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",1783272|1239|526524|526525|128827|1774107;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|186802|1392389;1783272|1239|186801|186802|216572|707003,Complete,Folakunmi
bsdb:32763534/2/1,32763534,case-control,32763534,10.1016/j.psychres.2020.113260,NA,"Pan R., Zhang X., Gao J., Yi W., Wei Q. , Su H.",Analysis of the diversity of intestinal microbiome and its potential value as a biomarker in patients with schizophrenia: A cohort study,Psychiatry research,2020,"16S function prediction, 16S rRNA sequencing, Gut microbiome, Random forest, Schizophrenia",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy controls,scizophrenia during remission,"patients who complied with diagnostic criteria for SCZ in the Diagnostic and Statistical Manual of Mental DIsorders Fourth Edition, Positive and negative syndrome scale, PANSS<60; No change in antipsychotic regimen (within two weeks)",29,29,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 2B,10 January 2021,Fatima Zohra,"WikiWorks,Folakunmi,Welile",Characterization of fecal microbiota to distinguish toxigenic types by linear discriminant analysis method,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Lactonifactor,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",1783272|201174|1760|2037|2049|1654;1783272|1239|186801|186802|186806|264995;1783272|1239|186801|186802|216572|244127;1783272|201174|84998|84999|1643824|1380;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|2383;1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|31979|1485;3379134|1224|28216|80840|80864|283;1783272|1239|186801|186802|216572|946234;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|3082720|186804|1505657;1783272|1239|186801|186802|31979|420345;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|838;1783272|1239|526524|526525|128827|123375;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|216572|707003,Complete,Folakunmi
bsdb:32763534/2/2,32763534,case-control,32763534,10.1016/j.psychres.2020.113260,NA,"Pan R., Zhang X., Gao J., Yi W., Wei Q. , Su H.",Analysis of the diversity of intestinal microbiome and its potential value as a biomarker in patients with schizophrenia: A cohort study,Psychiatry research,2020,"16S function prediction, 16S rRNA sequencing, Gut microbiome, Random forest, Schizophrenia",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy controls,scizophrenia during remission,"patients who complied with diagnostic criteria for SCZ in the Diagnostic and Statistical Manual of Mental DIsorders Fourth Edition, Positive and negative syndrome scale, PANSS<60; No change in antipsychotic regimen (within two weeks)",29,29,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 2B,10 January 2021,WikiWorks,"WikiWorks,Folakunmi",Characterization of fecal microbiota to distinguish toxigenic types by lineear discriminant analysis method,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Catenisphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",1783272|1239|186801|186802|3085642|580596;1783272|1239|526524|526525|128827|1774107;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|186802|1392389;3379134|976|200643|171549|171552|577309;1783272|1239|526524|526525|2810280|3025755,Complete,Folakunmi
bsdb:32763534/3/1,32763534,case-control,32763534,10.1016/j.psychres.2020.113260,NA,"Pan R., Zhang X., Gao J., Yi W., Wei Q. , Su H.",Analysis of the diversity of intestinal microbiome and its potential value as a biomarker in patients with schizophrenia: A cohort study,Psychiatry research,2020,"16S function prediction, 16S rRNA sequencing, Gut microbiome, Random forest, Schizophrenia",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,symptomatic remission,acute schizphrenia,"patients who complied with diagnostic criteria for SCZ in the Diagnostic and Statistical Manual of Mental DIsorders Fourth Edition, Positive and negative syndrome scale, PANSS<60; No change in antipsychotic regimen (within two weeks)",29,29,4 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3,10 January 2021,Fatima Zohra,"WikiWorks,Folakunmi,MyleeeA",Characterization of fecal microbiota to to distinguish toxigenic types by lineear discriminant anlysis method,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239|186801|186802|31979;1783272|1239|186801|3082720|186804;1783272|1239|186801|186802|31979|1485,Complete,Folakunmi
bsdb:32770859/1/1,32770859,randomized controlled trial,32770859,10.1111/apt.16013,NA,"Church TR, Demmer RT, Knights D, Meyer KA, Onyeaghala GC, Prizment AE, Sadowsky MJ, Shaukat A, Staley C, Straka RJ, Thyagarajan B, Vivek S",Randomised clinical study: oral aspirin 325 mg daily vs placebo alters gut microbial composition and bacterial taxa associated with colorectal cancer risk,Ailmentary Pharmacology and Theraputics,2020,"colorectal cancer, aspirin",Experiment 1,United States of America,Homo sapiens,Colon,UBERON:0001155,Colorectal cancer,EFO:0005842,Placebo,Aspirin,"Experimental group took 325 mg daily aspirin over six weeks, with additional six weeks of washout",20,30,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 3,27 May 2022,Jeshudy,"Jeshudy,WikiWorks",Linear discriminant analysis (LDA) effect size (LEfSe) in samples collected after treatment (week 6),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira sp.",3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|28050|2049031,Complete,Fatima
bsdb:32770859/1/2,32770859,randomized controlled trial,32770859,10.1111/apt.16013,NA,"Church TR, Demmer RT, Knights D, Meyer KA, Onyeaghala GC, Prizment AE, Sadowsky MJ, Shaukat A, Staley C, Straka RJ, Thyagarajan B, Vivek S",Randomised clinical study: oral aspirin 325 mg daily vs placebo alters gut microbial composition and bacterial taxa associated with colorectal cancer risk,Ailmentary Pharmacology and Theraputics,2020,"colorectal cancer, aspirin",Experiment 1,United States of America,Homo sapiens,Colon,UBERON:0001155,Colorectal cancer,EFO:0005842,Placebo,Aspirin,"Experimental group took 325 mg daily aspirin over six weeks, with additional six weeks of washout",20,30,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 3,2 June 2022,Jeshudy,"Jeshudy,Peace Sandy,WikiWorks",Linear discriminant analysis (LDA) effect size (LEfSe) in samples collected after treatment (week 6),decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. DL-VIII",1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|186802|31979|1485|641107,Complete,Fatima
bsdb:32770859/2/1,32770859,randomized controlled trial,32770859,10.1111/apt.16013,NA,"Church TR, Demmer RT, Knights D, Meyer KA, Onyeaghala GC, Prizment AE, Sadowsky MJ, Shaukat A, Staley C, Straka RJ, Thyagarajan B, Vivek S",Randomised clinical study: oral aspirin 325 mg daily vs placebo alters gut microbial composition and bacterial taxa associated with colorectal cancer risk,Ailmentary Pharmacology and Theraputics,2020,"colorectal cancer, aspirin",Experiment 2,United States of America,Homo sapiens,Colon,UBERON:0001155,Colorectal cancer,EFO:0005842,Placebo,Aspirin,"Experimental group took 325 mg daily aspirin over six weeks, with additional six weeks of washout",20,30,3 months,16S,4,Illumina,NA,Mixed-Effects Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 4, text",27 May 2022,Jeshudy,"Jeshudy,Fatima,WikiWorks","Regression coefficients (β) and P-values for the interaction term comparing the abundance of pre-specified faecal bacterial taxa in aspirin to placebo arm after 3 weeks (upper row) and 6 weeks (lower row) of treatment vs baseline, the ASMIC study",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|186803|28050|2049031;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|216851,Complete,Fatima
bsdb:32770859/2/2,32770859,randomized controlled trial,32770859,10.1111/apt.16013,NA,"Church TR, Demmer RT, Knights D, Meyer KA, Onyeaghala GC, Prizment AE, Sadowsky MJ, Shaukat A, Staley C, Straka RJ, Thyagarajan B, Vivek S",Randomised clinical study: oral aspirin 325 mg daily vs placebo alters gut microbial composition and bacterial taxa associated with colorectal cancer risk,Ailmentary Pharmacology and Theraputics,2020,"colorectal cancer, aspirin",Experiment 2,United States of America,Homo sapiens,Colon,UBERON:0001155,Colorectal cancer,EFO:0005842,Placebo,Aspirin,"Experimental group took 325 mg daily aspirin over six weeks, with additional six weeks of washout",20,30,3 months,16S,4,Illumina,NA,Mixed-Effects Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Table 4, text",27 May 2022,Jeshudy,"Jeshudy,Fatima,WikiWorks","Regression coefficients (β) and P-values for the interaction term comparing the abundance of pre-specified faecal bacterial taxa in aspirin to placebo arm after 3 weeks (upper row) and 6 weeks (lower row) of treatment vs baseline, the ASMIC study",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|189330;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|216572|1263,Complete,Fatima
bsdb:32775594/1/1,32775594,"cross-sectional observational, not case-control",32775594,10.1002/dad2.12000,NA,"Bathini P., Foucras S., Dupanloup I., Imeri H., Perna A., Berruex J.L., Doucey M.A., Annoni J.M. , Auber Alberi L.",Classifying dementia progression using microbial profiling of saliva,"Alzheimer's & dementia (Amsterdam, Netherlands)",2020,"Alzheimer's disease, cytokines, olfaction, oral microbiome",Experiment 1,Switzerland,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,Cognitively Normal Healthy (CNh),Cognitively Normal at risk (CNr),Cognitively normal people with hyposmia,27,15,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1C,16 December 2024,AaishahM,"AaishahM,WikiWorks",Significantly different bacterial taxa in CNr and CNh,increased,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia wadei,3384189|32066|203490|203491|1129771|32067|157687,Complete,NA
bsdb:32775594/1/2,32775594,"cross-sectional observational, not case-control",32775594,10.1002/dad2.12000,NA,"Bathini P., Foucras S., Dupanloup I., Imeri H., Perna A., Berruex J.L., Doucey M.A., Annoni J.M. , Auber Alberi L.",Classifying dementia progression using microbial profiling of saliva,"Alzheimer's & dementia (Amsterdam, Netherlands)",2020,"Alzheimer's disease, cytokines, olfaction, oral microbiome",Experiment 1,Switzerland,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,Cognitively Normal Healthy (CNh),Cognitively Normal at risk (CNr),Cognitively normal people with hyposmia,27,15,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2,16 December 2024,AaishahM,"AaishahM,WikiWorks",Significantly different bacterial taxa in CNr and CNh,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor villosus,1783272|1239|186801|3082720|3118655|44259|29374,Complete,NA
bsdb:32775594/2/1,32775594,"cross-sectional observational, not case-control",32775594,10.1002/dad2.12000,NA,"Bathini P., Foucras S., Dupanloup I., Imeri H., Perna A., Berruex J.L., Doucey M.A., Annoni J.M. , Auber Alberi L.",Classifying dementia progression using microbial profiling of saliva,"Alzheimer's & dementia (Amsterdam, Netherlands)",2020,"Alzheimer's disease, cytokines, olfaction, oral microbiome",Experiment 2,Switzerland,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,Cognitively Normal Healthy (CNh),Mild Cognitive Impairment (MCI),Patients with Mild Cognitive Impairment (MCI),27,21,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1C,16 December 2024,AaishahM,"AaishahM,WikiWorks",Significantly different bacterial taxa in MCI and CNh,increased,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia wadei,3384189|32066|203490|203491|1129771|32067|157687,Complete,NA
bsdb:32775594/2/2,32775594,"cross-sectional observational, not case-control",32775594,10.1002/dad2.12000,NA,"Bathini P., Foucras S., Dupanloup I., Imeri H., Perna A., Berruex J.L., Doucey M.A., Annoni J.M. , Auber Alberi L.",Classifying dementia progression using microbial profiling of saliva,"Alzheimer's & dementia (Amsterdam, Netherlands)",2020,"Alzheimer's disease, cytokines, olfaction, oral microbiome",Experiment 2,Switzerland,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,Cognitively Normal Healthy (CNh),Mild Cognitive Impairment (MCI),Patients with Mild Cognitive Impairment (MCI),27,21,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1C,16 December 2024,AaishahM,"AaishahM,WikiWorks",Significantly different bacterial taxa in MCI and CNh,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor villosus,1783272|1239|186801|3082720|3118655|44259|29374,Complete,NA
bsdb:32775594/3/1,32775594,"cross-sectional observational, not case-control",32775594,10.1002/dad2.12000,NA,"Bathini P., Foucras S., Dupanloup I., Imeri H., Perna A., Berruex J.L., Doucey M.A., Annoni J.M. , Auber Alberi L.",Classifying dementia progression using microbial profiling of saliva,"Alzheimer's & dementia (Amsterdam, Netherlands)",2020,"Alzheimer's disease, cytokines, olfaction, oral microbiome",Experiment 3,Switzerland,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,Cognitively Normal Healthy (CNh),Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,27,17,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1C,16 December 2024,AaishahM,"AaishahM,WikiWorks",Significantly different bacterial taxa in CAD patients and CNh,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor villosus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia wadei",1783272|1239|186801|3082720|3118655|44259|29374;3384189|32066|203490|203491|1129771|32067|157687,Complete,NA
bsdb:32775594/4/1,32775594,"cross-sectional observational, not case-control",32775594,10.1002/dad2.12000,NA,"Bathini P., Foucras S., Dupanloup I., Imeri H., Perna A., Berruex J.L., Doucey M.A., Annoni J.M. , Auber Alberi L.",Classifying dementia progression using microbial profiling of saliva,"Alzheimer's & dementia (Amsterdam, Netherlands)",2020,"Alzheimer's disease, cytokines, olfaction, oral microbiome",Experiment 4,Switzerland,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,Cognitively Normal Healthy (CNh),Cognitively Normal at risk (CNr),Cognitively normal people with hyposmia,27,15,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1D + Figure 1E,16 December 2024,AaishahM,"AaishahM,WikiWorks",Significantly different bacterial taxa in CNr and CNh,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium valvarum",3379134|976|200643|171549|171552|1283313|76122;3379134|976|200643|171549|171551|836|837;1783272|1239|186801|3082720|3118655|44259|143361;3379134|1224|1236|135615|868|2717|194702,Complete,NA
bsdb:32775594/5/1,32775594,"cross-sectional observational, not case-control",32775594,10.1002/dad2.12000,NA,"Bathini P., Foucras S., Dupanloup I., Imeri H., Perna A., Berruex J.L., Doucey M.A., Annoni J.M. , Auber Alberi L.",Classifying dementia progression using microbial profiling of saliva,"Alzheimer's & dementia (Amsterdam, Netherlands)",2020,"Alzheimer's disease, cytokines, olfaction, oral microbiome",Experiment 5,Switzerland,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,Cognitively Normal Healthy (CNh),Mild Cognitive Impairment (MCI),Patients with Mild Cognitive Impairment (MCI),27,21,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1D + Figure 1E,16 December 2024,AaishahM,"AaishahM,WikiWorks",Significantly different bacterial taxa in MCI and CNh,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium valvarum,3379134|1224|1236|135615|868|2717|194702,Complete,NA
bsdb:32775594/5/2,32775594,"cross-sectional observational, not case-control",32775594,10.1002/dad2.12000,NA,"Bathini P., Foucras S., Dupanloup I., Imeri H., Perna A., Berruex J.L., Doucey M.A., Annoni J.M. , Auber Alberi L.",Classifying dementia progression using microbial profiling of saliva,"Alzheimer's & dementia (Amsterdam, Netherlands)",2020,"Alzheimer's disease, cytokines, olfaction, oral microbiome",Experiment 5,Switzerland,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,Cognitively Normal Healthy (CNh),Mild Cognitive Impairment (MCI),Patients with Mild Cognitive Impairment (MCI),27,21,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1D + Figure 1E,16 December 2024,AaishahM,"AaishahM,WikiWorks",Significantly different bacterial taxa in MCI and CNh,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis",3379134|976|200643|171549|171551|836|837;3379134|976|200643|171549|171552|1283313|76122;1783272|1239|186801|3082720|3118655|44259|143361,Complete,NA
bsdb:32775594/6/1,32775594,"cross-sectional observational, not case-control",32775594,10.1002/dad2.12000,NA,"Bathini P., Foucras S., Dupanloup I., Imeri H., Perna A., Berruex J.L., Doucey M.A., Annoni J.M. , Auber Alberi L.",Classifying dementia progression using microbial profiling of saliva,"Alzheimer's & dementia (Amsterdam, Netherlands)",2020,"Alzheimer's disease, cytokines, olfaction, oral microbiome",Experiment 6,Switzerland,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,Cognitively Normal Healthy (CNh),Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,27,17,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1D + Figure 1E,16 December 2024,AaishahM,"AaishahM,WikiWorks",Significantly different bacterial taxa in AD patients and CNh,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium valvarum,3379134|1224|1236|135615|868|2717|194702,Complete,NA
bsdb:32775594/6/2,32775594,"cross-sectional observational, not case-control",32775594,10.1002/dad2.12000,NA,"Bathini P., Foucras S., Dupanloup I., Imeri H., Perna A., Berruex J.L., Doucey M.A., Annoni J.M. , Auber Alberi L.",Classifying dementia progression using microbial profiling of saliva,"Alzheimer's & dementia (Amsterdam, Netherlands)",2020,"Alzheimer's disease, cytokines, olfaction, oral microbiome",Experiment 6,Switzerland,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,Cognitively Normal Healthy (CNh),Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,27,17,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1D + Figure 1E,16 December 2024,AaishahM,"AaishahM,WikiWorks",Significantly different bacterial taxa in AD patients and CNh,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis",3379134|976|200643|171549|171551|836|837;3379134|976|200643|171549|171552|1283313|76122;1783272|1239|186801|3082720|3118655|44259|143361,Complete,NA
bsdb:32775594/7/1,32775594,"cross-sectional observational, not case-control",32775594,10.1002/dad2.12000,NA,"Bathini P., Foucras S., Dupanloup I., Imeri H., Perna A., Berruex J.L., Doucey M.A., Annoni J.M. , Auber Alberi L.",Classifying dementia progression using microbial profiling of saliva,"Alzheimer's & dementia (Amsterdam, Netherlands)",2020,"Alzheimer's disease, cytokines, olfaction, oral microbiome",Experiment 7,Switzerland,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,Cognitively Normal Healthy (CNh),Cognitively Normal at risk (CNr),Cognitively normal people with hyposmia,27,15,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S2A + Figure S2B,16 December 2024,AaishahM,"AaishahM,WikiWorks",Significantly different bacterial taxa in CNr and CNh,increased,"k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Calotrichaceae|g__Calothrix,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa",1783272|1117|3028117|1161|2661849|1186;3384189|32066|203490|203491|1129771|32067|157688;1783272|1117|3028117;1783272|201174|1760|85006|1268|32207|43675,Complete,NA
bsdb:32775594/7/2,32775594,"cross-sectional observational, not case-control",32775594,10.1002/dad2.12000,NA,"Bathini P., Foucras S., Dupanloup I., Imeri H., Perna A., Berruex J.L., Doucey M.A., Annoni J.M. , Auber Alberi L.",Classifying dementia progression using microbial profiling of saliva,"Alzheimer's & dementia (Amsterdam, Netherlands)",2020,"Alzheimer's disease, cytokines, olfaction, oral microbiome",Experiment 7,Switzerland,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,Cognitively Normal Healthy (CNh),Cognitively Normal at risk (CNr),Cognitively normal people with hyposmia,27,15,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S2A + Figure S2B,16 December 2024,AaishahM,"AaishahM,WikiWorks",Significantly different bacterial taxa in CNr and CNh,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Pseudomonadati|p__Rhodothermota|c__Rhodothermia|o__Rhodothermales|f__Rhodothermaceae|g__Rhodothermus,k__Pseudomonadati|p__Rhodothermota|c__Rhodothermia|o__Rhodothermales|f__Rhodothermaceae|g__Rhodothermus|s__Rhodothermus clarus",1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|3118655|44259;3379134|1853220|1853222|1853224|563843|29548;3379134|1853220|1853222|1853224|563843|29548|374811,Complete,NA
bsdb:32775594/8/1,32775594,"cross-sectional observational, not case-control",32775594,10.1002/dad2.12000,NA,"Bathini P., Foucras S., Dupanloup I., Imeri H., Perna A., Berruex J.L., Doucey M.A., Annoni J.M. , Auber Alberi L.",Classifying dementia progression using microbial profiling of saliva,"Alzheimer's & dementia (Amsterdam, Netherlands)",2020,"Alzheimer's disease, cytokines, olfaction, oral microbiome",Experiment 8,Switzerland,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,Cognitively Normal Healthy (CNh),Mild Cognitive Impairment (MCI),Patients with Mild Cognitive Impairment (MCI),27,21,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S2C + Figure S2D,16 December 2024,AaishahM,"AaishahM,WikiWorks",Significantly different bacterial taxa in MCI and CNh,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus troglodytae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia wadei,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia",3384189|32066|203490|203491|1129771|32067;3384189|32066|203490|203491|1129771;3384189|32066|203490|203491;1783272|1239|91061|186826|1300|1301|1309;1783272|1239|91061|186826|1300|1301|1111760;3384189|32066|203490|203491|1129771|32067|157687;3384189|32066|203490,Complete,NA
bsdb:32775594/8/2,32775594,"cross-sectional observational, not case-control",32775594,10.1002/dad2.12000,NA,"Bathini P., Foucras S., Dupanloup I., Imeri H., Perna A., Berruex J.L., Doucey M.A., Annoni J.M. , Auber Alberi L.",Classifying dementia progression using microbial profiling of saliva,"Alzheimer's & dementia (Amsterdam, Netherlands)",2020,"Alzheimer's disease, cytokines, olfaction, oral microbiome",Experiment 8,Switzerland,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,Cognitively Normal Healthy (CNh),Mild Cognitive Impairment (MCI),Patients with Mild Cognitive Impairment (MCI),27,21,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S2C + Figure S2D,16 December 2024,AaishahM,"AaishahM,WikiWorks",Significantly different bacterial taxa in MCI and CNh,decreased,"k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema lecithinolyticum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Thermotogati|p__Synergistota|c__Synergistia,k__Thermotogati|p__Synergistota,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Synechococcales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus intermedius,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor villosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum",3384194|508458|649775|649776;3384194|508458|649775|649776|649777;3379134|203691|203692|136|137;3379134|203691|203692|136|2845253|157;3379134|203691|203692|136|2845253|157|53418;1783272|1239|909932|1843489|31977|39948;1783272|1239|526524|526525|128827|1647;1783272|1239|186801|3082720|3118655|44259;3379134|203691|203692;3379134|203691|203692|136;3379134|976|200643|171549|171552|1283313|76122;3379134|976|200643|171549|171552|838|28131;1783272|1239|909932|1843489|31977|39948|218538;3379134|976|200643|171549|171552|838|28133;3384194|508458|649775;3384194|508458;1783272|1117|3028117|1890424;3379134|976|200643|171549|815|816|371601;1783272|1239|91061|186826|1300|1301|1338;1783272|1239|186801|3082720|3118655|44259|29374;1783272|1239|91061|186826|33958|2742598|1613,Complete,NA
bsdb:32775594/9/1,32775594,"cross-sectional observational, not case-control",32775594,10.1002/dad2.12000,NA,"Bathini P., Foucras S., Dupanloup I., Imeri H., Perna A., Berruex J.L., Doucey M.A., Annoni J.M. , Auber Alberi L.",Classifying dementia progression using microbial profiling of saliva,"Alzheimer's & dementia (Amsterdam, Netherlands)",2020,"Alzheimer's disease, cytokines, olfaction, oral microbiome",Experiment 9,Switzerland,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,Cognitively Normal Healthy (CNh),Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,27,17,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S2E + Figure S2F,16 December 2024,AaishahM,"AaishahM,WikiWorks",Significantly different bacterial taxa in AD patients and CNh,increased,"k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminiphilaceae|g__Aminiphilus,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Calotrichaceae|g__Calothrix,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminiphilaceae|g__Aminiphilus|s__Aminiphilus circumscriptus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria|s__Kocuria rosea,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sobrinus",3384194|508458|649775|649776|3029090|290731;1783272|1117|3028117|1161|2661849|1186;1783272|201174|1760|85006|1268|57493;1783272|1117|3028117;3384194|508458|649775|649776|3029090|290731|290732;1783272|201174|1760|85006|1268|57493|1275;1783272|1239|91061|186826|1300|1301|1310,Complete,NA
bsdb:32775594/9/2,32775594,"cross-sectional observational, not case-control",32775594,10.1002/dad2.12000,NA,"Bathini P., Foucras S., Dupanloup I., Imeri H., Perna A., Berruex J.L., Doucey M.A., Annoni J.M. , Auber Alberi L.",Classifying dementia progression using microbial profiling of saliva,"Alzheimer's & dementia (Amsterdam, Netherlands)",2020,"Alzheimer's disease, cytokines, olfaction, oral microbiome",Experiment 9,Switzerland,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,Cognitively Normal Healthy (CNh),Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,27,17,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S2E + Figure S2F,16 December 2024,AaishahM,"AaishahM,WikiWorks",Significantly different bacterial taxa in AD patients and CNh,decreased,"k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus methioninivorax,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor villosus",3379134|203691|203692|136|137;3379134|203691|203692|136|2845253|157;1783272|1239|1737404|1737405|1570339|162289|907224;3379134|203691|203692;3379134|203691|203692|136;3379134|976|200643|171549|171552|1283313|76122;1783272|1239|186801|3082720|3118655|44259|29374,Complete,NA
bsdb:32777190/1/1,32777190,"cross-sectional observational, not case-control",32777190,10.1177/2380084420948779,NA,"Balan P., Brandt B.W., Chong Y.S., Crielaard W., Wong M.L., Lopez V., He H.G. , Seneviratne C.J.",Subgingival Microbiota during Healthy Pregnancy and Pregnancy Gingivitis,JDR clinical and translational research,2021,"Singapore, illumina sequencing, oral health, oral microbiota, pregnant women, prenatal care",Experiment 1,Singapore,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Pregnancy,EFO:0002950,non pregnant women without gingivitis,pregnant women without gingivitis,Pregnant women sampled between 21 to 24 wk of gestation without gingivitis,10,10,6 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,decreased,increased,Signature 1,"Appendix Figure 1, 2, text",16 June 2021,Tislam,"Tislam,Fatima,WikiWorks",Phylum and Genera showing significant differential abundance in subgingival samples.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Spirochaetota,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,p__Candidatus Saccharimonadota",3379134|976|200643|171549|815|816;3384189|32066|203490;3384189|32066|203490|203491|203492|848;3379134|203691;3379134|203691|203692|136|2845253|157;95818,Complete,Fatima
bsdb:32777190/1/2,32777190,"cross-sectional observational, not case-control",32777190,10.1177/2380084420948779,NA,"Balan P., Brandt B.W., Chong Y.S., Crielaard W., Wong M.L., Lopez V., He H.G. , Seneviratne C.J.",Subgingival Microbiota during Healthy Pregnancy and Pregnancy Gingivitis,JDR clinical and translational research,2021,"Singapore, illumina sequencing, oral health, oral microbiota, pregnant women, prenatal care",Experiment 1,Singapore,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Pregnancy,EFO:0002950,non pregnant women without gingivitis,pregnant women without gingivitis,Pregnant women sampled between 21 to 24 wk of gestation without gingivitis,10,10,6 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,decreased,increased,Signature 2,"Appendix Figure 2, text",16 June 2021,Tislam,"Tislam,Fatima,WikiWorks",Phylum and Genera showing significant differential abundance in subgingival samples.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Terrahaemophilus",3379134|976|117743|200644|2762318|59735;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|1300|1301;3379134|1224|1236|135625|712|217201,Complete,Fatima
bsdb:32777190/2/1,32777190,"cross-sectional observational, not case-control",32777190,10.1177/2380084420948779,NA,"Balan P., Brandt B.W., Chong Y.S., Crielaard W., Wong M.L., Lopez V., He H.G. , Seneviratne C.J.",Subgingival Microbiota during Healthy Pregnancy and Pregnancy Gingivitis,JDR clinical and translational research,2021,"Singapore, illumina sequencing, oral health, oral microbiota, pregnant women, prenatal care",Experiment 2,Singapore,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Gingivitis,MONDO:0002508,pregnant women without gingivitis,pregnant women with gingivitis,NA,10,10,6 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 1,"Appendix Figure 1, 2, text",24 June 2021,Tislam,"Tislam,Fatima,WikiWorks",Genera showing significant differential abundance in subgingival samples.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,p__Candidatus Saccharimonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Pseudomonadati|p__Spirochaetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",3379134|976|200643|171549|815|816;3379134|29547|3031852|213849|72294|194;95818;1783272|1239|186801|3082720|3118655|44259;3384194|508458|649775|649776|3029087|1434006;3379134|203691;3379134|976|200643|171549|2005525|195950;3379134|203691|203692|136|2845253|157,Complete,Fatima
bsdb:32777190/3/1,32777190,"cross-sectional observational, not case-control",32777190,10.1177/2380084420948779,NA,"Balan P., Brandt B.W., Chong Y.S., Crielaard W., Wong M.L., Lopez V., He H.G. , Seneviratne C.J.",Subgingival Microbiota during Healthy Pregnancy and Pregnancy Gingivitis,JDR clinical and translational research,2021,"Singapore, illumina sequencing, oral health, oral microbiota, pregnant women, prenatal care",Experiment 3,Singapore,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Gingivitis,MONDO:0002508,pregnant women without gingivitis,pregnant women with gingivitis,NA,10,10,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 1,"Figure 3, text",24 June 2021,Tislam,"Tislam,WikiWorks",Linear discriminant analysis effect size. Differentially abundant taxonomic profile of subgingival plaque (SGP) microbiota in pregnant women with gingivitis versus pregnant women without gingivitis,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 349,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma faucium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium oral taxon 500,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 346,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp. oral taxon 258,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] saphenum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella morbi,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema maltophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema lecithinolyticum,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp. oral taxon 238,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 304,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter actinomycetemcomitans,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp. oral taxon 270,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium sp.",1783272|1239|909932|1843489|31977;3384189|32066|203490|203491|1129771|32067;95818|713051;1783272|544448|2790996|2895623|2895509|56142;1783272|1239|186801|3085636|186803|712991;95818|713049;3379134|203691|203692|136|2845253|157|712739;1783272|1239|186801|3082720|543314|51123;1783272|1239|186801|3085636|186803|43996|43997;3379134|203691|203692|136|2845253|157|51160;1783272|1239|186801|3082720|3118655|44259|143361;3384194|508458|649775|649776|3029087|1434006|651822;3379134|976|200643|171549|2005525|195950|28112;3379134|203691|203692|136|2845253|157|53418;3379134|203691|203692|136|2845253|157|712725;3379134|976|200643|171549|171552|838|712459;3379134|1224|1236|135625|712|416916|714;3379134|203691|203692|136|2845253|157|671227;3379134|203691|203692|136|2845253|157|158;3384194|508458|649775|649776|3029087|1434006|2699746,Complete,NA
bsdb:32777190/3/2,32777190,"cross-sectional observational, not case-control",32777190,10.1177/2380084420948779,NA,"Balan P., Brandt B.W., Chong Y.S., Crielaard W., Wong M.L., Lopez V., He H.G. , Seneviratne C.J.",Subgingival Microbiota during Healthy Pregnancy and Pregnancy Gingivitis,JDR clinical and translational research,2021,"Singapore, illumina sequencing, oral health, oral microbiota, pregnant women, prenatal care",Experiment 3,Singapore,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Gingivitis,MONDO:0002508,pregnant women without gingivitis,pregnant women with gingivitis,NA,10,10,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 2,"Figure 3, text",24 June 2021,Tislam,"Tislam,WikiWorks",Linear discriminant analysis effect size. Differentially abundant taxonomic profile of subgingival plaque (SGP) microbiota in pregnant women with gingivitis versus pregnant women without gingivitis,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,p__Candidatus Absconditibacteriota|s__SR1 bacterium oral taxon 875,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 448,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 172,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp. oral taxon 108,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 221,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. oral taxon 478,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium sp. oral taxon 194,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula",1783272|1239|909932|1843489|31977|29465|29466;1783272|201174|1760|2037|2049|1654|1655;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|186828|117563|46124;1783272|201174|1760|85006|1268|32207|2047;221235|1226342;1783272|201174|1760|2037|2049|1654|712124;1783272|201174|1760|2037|2049|1654|712118;3379134|1224|28216|206351|481|32257|505;1783272|1239|186801|3085636|186803|265975|712414;3384189|32066|203490|203491|1129771|32067|712362;1783272|1239|909932|909929|1843491|970|712538;1783272|201174|1760|85009|31957|1743|712503;1783272|201174|1760|2037|2049|1654|55565;1783272|201174|84998|84999|1643824|2767353|1382,Complete,NA
bsdb:32777190/4/1,32777190,"cross-sectional observational, not case-control",32777190,10.1177/2380084420948779,NA,"Balan P., Brandt B.W., Chong Y.S., Crielaard W., Wong M.L., Lopez V., He H.G. , Seneviratne C.J.",Subgingival Microbiota during Healthy Pregnancy and Pregnancy Gingivitis,JDR clinical and translational research,2021,"Singapore, illumina sequencing, oral health, oral microbiota, pregnant women, prenatal care",Experiment 4,Singapore,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Pregnancy,EFO:0002950,non pregnant women,pregnant women,pregnant women,10,10,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,increased,NA,decreased,NA,Signature 1,"Figure 3, text",7 July 2021,Tislam,"Tislam,WikiWorks",Linear discriminant analysis effect size. pregnant women without gingivitis versus nonpregnant women without gingivitis,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga haemolytica,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium sp.,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Pseudoleptotrichia|s__Pseudoleptotrichia goodfellowii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia shahii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma faucium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella baroniae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella dentalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella micans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] saphenum",1783272|201174|1760|2037|2049|1654|55565;3379134|976|200643|171549|171552|1283313|1872471;3379134|976|200643|171549|171552|1283313|76122;3379134|976|117743|200644|2762318|59735;3379134|29547|3031852|213849|72294|194;3379134|976|117743|200644|49546|1016|45243;3384194|508458|649775|649776|3029087|1434006|651822;3384194|508458|649775|649776|3029087|1434006|2699746;3384189|32066|203490|203491|203492|848|860;3384189|32066|203490|203491|1129771|2755140|157692;3384189|32066|203490|203491|1129771|32067|157691;3384189|32066|203490|203491|1129771|32067|104608;1783272|1239|909932|1843489|31977|906|187326;1783272|544448|2790996|2895623|2895509|56142;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836|837;3379134|976|200643|171549|171552|2974251|305719;3379134|976|200643|171549|171552|838|52227;3379134|976|200643|171549|171552|838|28129;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552|838|189723;3379134|976|200643|171549|171552|838|59823;1783272|201174|1760|85004|31953|196081|230143;1783272|1239|909932|909929|1843491|970|2053611;1783272|1239|909932|909929|1843491|970|69823;3379134|976|200643|171549|2005525|195950|28112;3379134|203691|203692|136|2845253|157|158;3379134|203691|203692|136|2845253|157|166;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|909932|1843489|31977|29465|1926307;1783272|1239|186801|3082720|543314|51123,Complete,NA
bsdb:32777190/4/2,32777190,"cross-sectional observational, not case-control",32777190,10.1177/2380084420948779,NA,"Balan P., Brandt B.W., Chong Y.S., Crielaard W., Wong M.L., Lopez V., He H.G. , Seneviratne C.J.",Subgingival Microbiota during Healthy Pregnancy and Pregnancy Gingivitis,JDR clinical and translational research,2021,"Singapore, illumina sequencing, oral health, oral microbiota, pregnant women, prenatal care",Experiment 4,Singapore,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Pregnancy,EFO:0002950,non pregnant women,pregnant women,pregnant women,10,10,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,increased,NA,decreased,NA,Signature 2,"Figure 3, text",7 July 2021,Tislam,"Tislam,WikiWorks",pregnant women without gingivitis versus nonpregnant women without gingivitis,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella|s__Bergeyella sp. oral taxon 322,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria bacilliformis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Terrahaemophilus|s__Terrahaemophilus aromaticivorans",3379134|976|117743|200644|2762318|59735|712187;1783272|1239|91061|1385|539738|1378|29391;3379134|1224|1236|135625|712|724|740;3379134|1224|28216|206351|481|482|267212;1783272|201174|1760|85006|1268|32207|172042;1783272|1239|91061|186826|1300|1301|1306;3379134|1224|1236|135625|712|217201|217202,Complete,NA
bsdb:32801476/1/1,32801476,"cross-sectional observational, not case-control",32801476,http://doi.org/10.3164/jcbn.20-53,NA,"Komiya S., Naito Y., Okada H., Matsuo Y., Hirota K., Takagi T., Mizushima K., Inoue R., Abe A. , Morimoto Y.",Characterizing the gut microbiota in females with infertility and preliminary results of a water-soluble dietary fiber intervention study,Journal of clinical biochemistry and nutrition,2020,"Bifidobacterium, dietary fiber, gut microbiota, infertility",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Female infertility,EFO:0008560,Control group,Infertile group,Female patients with infertility,18,18,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,age,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 4,25 June 2025,Aleru Divine,Aleru Divine,Comparative analysis of the taxonomic composition of the microbial community at the genus level between control subjects and patients with infertility.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Vulcanimicrobiota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus",3379134|1224|1236|2887326|468|469;3379134|1224|28211;1783272|1154676;3379134|976|200643|171549|2005520|156973;1783272|544448|31969|186332|186333|2086;3379134|976|200643|171549|171550|28138;3379134|976|200643|171549|171550|239759;1783272|1239|91061|1385|186817|1386;1783272|201174|84998|1643822|1643826|84111;3379134|976|200643|171549|2005519;1783272|1239|186801|186802|216572|244127;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3082720|543314;3379134|200940|3031449|213115|194924|872;1783272|1239|526524|526525|2810280|100883,Complete,NA
bsdb:32801476/1/2,32801476,"cross-sectional observational, not case-control",32801476,http://doi.org/10.3164/jcbn.20-53,NA,"Komiya S., Naito Y., Okada H., Matsuo Y., Hirota K., Takagi T., Mizushima K., Inoue R., Abe A. , Morimoto Y.",Characterizing the gut microbiota in females with infertility and preliminary results of a water-soluble dietary fiber intervention study,Journal of clinical biochemistry and nutrition,2020,"Bifidobacterium, dietary fiber, gut microbiota, infertility",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Female infertility,EFO:0008560,Control group,Infertile group,Female patients with infertility,18,18,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,age,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 4,25 June 2025,Aleru Divine,Aleru Divine,Comparative analysis of the taxonomic composition of the microbial community at the genus level between control subjects and patients with infertility.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hydrogenophaga,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leucobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella",3379134|1224|1236|135624|84642;3379134|1224|28216|80840|75682;1783272|201174|1760|2037|2049|76833;3379134|1224|28216|80840|80864|47420;1783272|201174|1760|85006|85023|55968;3379134|1224|1236|135614|32033|40323;3379134|1224|28216|80840|506|222;3379134|1224|28211|356|118882|528;1783272|201174|1760|85006|85023;1783272|1239|91061|1385|539738;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|186828|117563;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|2383;3379134|1224|1236|91347|1903414|581,Complete,NA
bsdb:32801476/2/1,32801476,"cross-sectional observational, not case-control",32801476,http://doi.org/10.3164/jcbn.20-53,NA,"Komiya S., Naito Y., Okada H., Matsuo Y., Hirota K., Takagi T., Mizushima K., Inoue R., Abe A. , Morimoto Y.",Characterizing the gut microbiota in females with infertility and preliminary results of a water-soluble dietary fiber intervention study,Journal of clinical biochemistry and nutrition,2020,"Bifidobacterium, dietary fiber, gut microbiota, infertility",Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Female infertility,EFO:0008560,Non-pregnant group,Pregnant group,Female patients who were pregnant after combined therapy,5,7,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,25 June 2025,Aleru Divine,Aleru Divine,Comparative analysis of the taxonomic composition of the microbial community at the genus level between the pregnant and the non-pregnant groups after treatment with partially hydrolyzed guar gum,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",1783272|1239|186801|3085636|186803|2383;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|171552|577309,Complete,NA
bsdb:32804973/1/1,32804973,case-control,32804973,https://doi.org/10.1371/journal.pone.0237874,https://pubmed.ncbi.nlm.nih.gov/32804973/,"Scarsella E., Stefanon B., Cintio M., Licastro D., Sgorlon S., Dal Monego S. , Sandri M.",Learning machine approach reveals microbial signatures of diet and sex in dog,PloS one,2020,NA,Experiment 1,Italy,Canis lupus familiaris,Feces,UBERON:0001988,Diet,EFO:0002755,Home Made Diet - H,Base Diet - B,"A raw meat diet with the addition of a complementary food, from here on called Base",30,56,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,"diet,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Fig 2 , S5 Table.",26 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","Relative Abundances (RA) for the factor diets of the three represented phyla in the fecal microbiota. RA were compared with the Kruskal-Wallis non-parametric test: (A) Firmicutes; (B) Bacteroidetes; (C) Fusobacteria. Data are reported as mean and standard error. W = Commercial moist complete diet; K = Commercial extruded complete diet; H = Home-made diet; B = Base diet.

Comparison of the mean relative abundances (RA) through a non-parametric Kruskal-Wallis test of the three groups of diets.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Anaerobiospirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia",3379134|976|200643|171549|815|816;3384189|32066|203490|203491|203492|848;1783272|1239|186801|186802|216572|1263;1783272|1239|526524|526525|128827|174708;3379134|1224|1236|135624|83763|13334;1783272|1239|186801|3085636|186803|572511;1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;1783272|1239|526524|526525|2810280|100883;3379134|1224|1236|91347|543|561;3379134|29547|3031852|213849|72293|209;1783272|1239|186801|3085636|186803|28050;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3085636|186803|841;1783272|201174|84998|1643822|1643826|84108,Complete,Peace Sandy
bsdb:32804973/1/2,32804973,case-control,32804973,https://doi.org/10.1371/journal.pone.0237874,https://pubmed.ncbi.nlm.nih.gov/32804973/,"Scarsella E., Stefanon B., Cintio M., Licastro D., Sgorlon S., Dal Monego S. , Sandri M.",Learning machine approach reveals microbial signatures of diet and sex in dog,PloS one,2020,NA,Experiment 1,Italy,Canis lupus familiaris,Feces,UBERON:0001988,Diet,EFO:0002755,Home Made Diet - H,Base Diet - B,"A raw meat diet with the addition of a complementary food, from here on called Base",30,56,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,"diet,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,"Fig 2 , S5 Table.",26 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","Relative Abundances (RA) for the factor diets of the three represented phyla in the fecal microbiota. RA were compared with the Kruskal-Wallis non-parametric test: (A) Firmicutes; (B) Bacteroidetes; (C) Fusobacteria. Data are reported as mean and standard error. W = Commercial moist complete diet; K = Commercial extruded complete diet; H = Home-made diet; B = Base diet.

Comparison of the mean relative abundances (RA) through a non-parametric Kruskal-Wallis test of the three groups of diets.",decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",1783272|1239;3379134|976|200643|171549;1783272|1239|186801|186802|186806|1730;3379134|976|200643|171549|171552|577309;1783272|201174|84998|1643822|1643826|447020;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|1239|526524|526525|2810280|100883;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|189330;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|3085636|186803|2383;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|2005525|375288;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301;3379134|1224|28216|80840|995019|40544;1783272|1239|526524|526525|2810281|191303,Complete,Peace Sandy
bsdb:32804973/2/1,32804973,case-control,32804973,https://doi.org/10.1371/journal.pone.0237874,https://pubmed.ncbi.nlm.nih.gov/32804973/,"Scarsella E., Stefanon B., Cintio M., Licastro D., Sgorlon S., Dal Monego S. , Sandri M.",Learning machine approach reveals microbial signatures of diet and sex in dog,PloS one,2020,NA,Experiment 2,Italy,Canis lupus familiaris,Feces,UBERON:0001988,Diet,EFO:0002755,Commercial moist complete diet - W,Complete diet - K,Commercial extruded complete diet (K),83,171,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,"diet,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Fig 2 , S5 Table.",26 February 2024,Peace Sandy,"Peace Sandy,WikiWorks",Relative Abundances (RA) for the factor diets of the three represented phyla in the fecal microbiota. RA were compared with the Kruskal-Wallis non-parametric test: (A) Firmicutes; (B) Bacteroidetes; (C) Fusobacteria. Data are reported as mean and standard error. W = Commercial moist complete diet; K = Commercial extruded complete diet; H = Home-made diet; B = Base diet.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|84998|1643822|1643826|447020;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|189330;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301,Complete,Peace Sandy
bsdb:32804973/2/2,32804973,case-control,32804973,https://doi.org/10.1371/journal.pone.0237874,https://pubmed.ncbi.nlm.nih.gov/32804973/,"Scarsella E., Stefanon B., Cintio M., Licastro D., Sgorlon S., Dal Monego S. , Sandri M.",Learning machine approach reveals microbial signatures of diet and sex in dog,PloS one,2020,NA,Experiment 2,Italy,Canis lupus familiaris,Feces,UBERON:0001988,Diet,EFO:0002755,Commercial moist complete diet - W,Complete diet - K,Commercial extruded complete diet (K),83,171,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,"diet,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,"Fig 2 , S5 Table.",26 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","Relative Abundances (RA) for the factor diets of the three represented phyla in the fecal microbiota. RA were compared with the Kruskal-Wallis non-parametric test: (A) Firmicutes; (B) Bacteroidetes; (C) Fusobacteria. Data are reported as mean and standard error. W = Commercial moist complete diet; K = Commercial extruded complete diet; H = Home-made diet; B = Base diet.

Comparison of the mean relative abundances (RA) through a non-parametric Kruskal-Wallis test of the three groups of diets.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Anaerobiospirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",3379134|976|200643|171549|815|816;3384189|32066|203490;1783272|1239|186801|186802|186806|1730;3379134|976|200643|171549|171552|577309;1783272|1239|186801|186802|216572|1263;1783272|1239|526524|526525|128827|174708;3379134|1224|1236|135624|83763|13334;1783272|1239|186801|3085636|186803|572511;1783272|1239|526524|526525|2810280|135858;1783272|201174|84998|84999|84107|102106;1783272|1239|526524|526525|2810280|100883;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|2383;3379134|1224|1236|91347|543|561;1783272|1239|186801|186802|216572|216851;3384189|32066|203490|203491|203492|848;3379134|29547|3031852|213849|72293|209;1783272|1239|186801|3085636|186803|28050;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|186807|2740;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3085636|186803|841;1783272|201174|84998|1643822|1643826|84108;3379134|1224|28216|80840|995019|40544;1783272|1239|526524|526525|2810281|191303,Complete,Peace Sandy
bsdb:32804973/3/1,32804973,case-control,32804973,https://doi.org/10.1371/journal.pone.0237874,https://pubmed.ncbi.nlm.nih.gov/32804973/,"Scarsella E., Stefanon B., Cintio M., Licastro D., Sgorlon S., Dal Monego S. , Sandri M.",Learning machine approach reveals microbial signatures of diet and sex in dog,PloS one,2020,NA,Experiment 3,Italy,Canis lupus familiaris,Feces,UBERON:0001988,Diet,EFO:0002755,Spayed Female - FC,Whole Female - F,Whole Female,28,145,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 5,26 February 2024,Peace Sandy,"Peace Sandy,WikiWorks",Relative Abundances (RA) for the category sex of the three represented phyla in the fecal microbiota. RA were compared with the Kruskal-Wallis non-parametric test: (A) Firmicutes; (B) Bacteroidetes; (C) Fusobacteria. Data are reported as mean and standard error. F = whole females subjects; M = whole males subjects; FC = spayed females subjects; MC = neutered males subjects.,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Pseudomonadati|p__Bacteroidota",3384189|32066|203490;3379134|976,Complete,Peace Sandy
bsdb:32804973/3/2,32804973,case-control,32804973,https://doi.org/10.1371/journal.pone.0237874,https://pubmed.ncbi.nlm.nih.gov/32804973/,"Scarsella E., Stefanon B., Cintio M., Licastro D., Sgorlon S., Dal Monego S. , Sandri M.",Learning machine approach reveals microbial signatures of diet and sex in dog,PloS one,2020,NA,Experiment 3,Italy,Canis lupus familiaris,Feces,UBERON:0001988,Diet,EFO:0002755,Spayed Female - FC,Whole Female - F,Whole Female,28,145,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 5,26 February 2024,Peace Sandy,"Peace Sandy,WikiWorks",Relative Abundances (RA) for the category sex of the three represented phyla in the fecal microbiota. RA were compared with the Kruskal-Wallis non-parametric test: (A) Firmicutes; (B) Bacteroidetes; (C) Fusobacteria. Data are reported as mean and standard error. F = whole females subjects; M = whole males subjects; FC = spayed females subjects; MC = neutered males subjects.,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Peace Sandy
bsdb:32804973/4/1,32804973,case-control,32804973,https://doi.org/10.1371/journal.pone.0237874,https://pubmed.ncbi.nlm.nih.gov/32804973/,"Scarsella E., Stefanon B., Cintio M., Licastro D., Sgorlon S., Dal Monego S. , Sandri M.",Learning machine approach reveals microbial signatures of diet and sex in dog,PloS one,2020,NA,Experiment 4,Italy,Canis lupus familiaris,Feces,UBERON:0001988,Diet,EFO:0002755,Castrated Male - MC,Whole Male - M,Whole Male,89,78,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,"age,diet",NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 5,26 February 2024,Peace Sandy,"Peace Sandy,WikiWorks",Relative Abundances (RA) for the category sex of the three represented phyla in the fecal microbiota. RA were compared with the Kruskal-Wallis non-parametric test: (A) Firmicutes; (B) Bacteroidetes; (C) Fusobacteria. Data are reported as mean and standard error. F = whole females subjects; M = whole males subjects; FC = spayed females subjects; MC = neutered males subjects.,increased,"k__Pseudomonadati|p__Bacteroidota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia",3379134|976;3384189|32066|203490,Complete,Peace Sandy
bsdb:32804973/4/2,32804973,case-control,32804973,https://doi.org/10.1371/journal.pone.0237874,https://pubmed.ncbi.nlm.nih.gov/32804973/,"Scarsella E., Stefanon B., Cintio M., Licastro D., Sgorlon S., Dal Monego S. , Sandri M.",Learning machine approach reveals microbial signatures of diet and sex in dog,PloS one,2020,NA,Experiment 4,Italy,Canis lupus familiaris,Feces,UBERON:0001988,Diet,EFO:0002755,Castrated Male - MC,Whole Male - M,Whole Male,89,78,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,"age,diet",NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 5,26 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","Relative Abundances (RA) for the category sex of the three represented phyla in the 
fecal microbiota. RA were compared with the Kruskal-Wallis non-parametric test: (A) Firmicutes; (B) Bacteroidetes; (C) Fusobacteria. Data are reported as mean and standard error. F = whole females subjects; M = whole males subjects; FC = spayed females subjects; MC = neutered males subjects.",decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Peace Sandy
bsdb:32807798/1/1,32807798,case-control,32807798,https://doi.org/10.1038/s41467-020-17916-9,NA,"Zhang X., Ning Z., Mayne J., Yang Y., Deeke S.A., Walker K., Farnsworth C.L., Stokes M.P., Couture J.F., Mack D., Stintzi A. , Figeys D.",Widespread protein lysine acetylation in gut microbiome and its alterations in patients with Crohn's disease,Nature communications,2020,NA,Experiment 1,Canada,Homo sapiens,"Feces,Mucosa of descending colon","UBERON:0004992,UBERON:0001988",Crohn's disease,EFO:0000384,healthy adults,pediatric crohn's disease,"children (<18 years old) diagnosed with crohn’s disease. 
The exclusion criteria implemented to further refine the cohort in this study include: presence of diabetes mellitus, presence of infectious gastroenteritis within the past 2 months, and irritable bowel syndrome.",8,10,1 month,NA,NA,Mass spectrometry,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5a,11 March 2023,Sophy,"Sophy,Chloe,WikiWorks",Taxonomic alterations of protein acetylation in the pediatric CD microbiome. LEfSe analysis of lysine acetylome-based taxonomic compositions.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens",1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|909929|1843491|158846|437897;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|909932|909929|1843491;1783272|1239|909932|909929;1783272|1239|186801|3085636|186803|28050|39485,Complete,Claregrieve1
bsdb:32807798/1/2,32807798,case-control,32807798,https://doi.org/10.1038/s41467-020-17916-9,NA,"Zhang X., Ning Z., Mayne J., Yang Y., Deeke S.A., Walker K., Farnsworth C.L., Stokes M.P., Couture J.F., Mack D., Stintzi A. , Figeys D.",Widespread protein lysine acetylation in gut microbiome and its alterations in patients with Crohn's disease,Nature communications,2020,NA,Experiment 1,Canada,Homo sapiens,"Feces,Mucosa of descending colon","UBERON:0004992,UBERON:0001988",Crohn's disease,EFO:0000384,healthy adults,pediatric crohn's disease,"children (<18 years old) diagnosed with crohn’s disease. 
The exclusion criteria implemented to further refine the cohort in this study include: presence of diabetes mellitus, presence of infectious gastroenteritis within the past 2 months, and irritable bowel syndrome.",8,10,1 month,NA,NA,Mass spectrometry,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5a,11 March 2023,Sophy,"Sophy,WikiWorks",Taxonomic alterations of protein acetylation in the pediatric CD microbiome. acetylome-based. LEfSe analysis of lysine acetylome-based taxonomic compositions.,increased,k__Bacillati|p__Bacillota|c__Bacilli,1783272|1239|91061,Complete,Chloe
bsdb:32807798/2/1,32807798,case-control,32807798,https://doi.org/10.1038/s41467-020-17916-9,NA,"Zhang X., Ning Z., Mayne J., Yang Y., Deeke S.A., Walker K., Farnsworth C.L., Stokes M.P., Couture J.F., Mack D., Stintzi A. , Figeys D.",Widespread protein lysine acetylation in gut microbiome and its alterations in patients with Crohn's disease,Nature communications,2020,NA,Experiment 2,Canada,Homo sapiens,"Feces,Mucosa of descending colon","UBERON:0004992,UBERON:0001988",Crohn's disease,EFO:0000384,healthy adults,pediatric crohn's disease,"children (<18 years old) diagnosed with crohn’s disease. 
The exclusion criteria implemented to further refine the cohort in this study include: presence of diabetes mellitus, presence of infectious gastroenteritis within the past 2 months, and irritable bowel syndrome.",8,10,1 month,NA,NA,Mass spectrometry,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,figure 5b,23 November 2023,Folakunmi,"Folakunmi,WikiWorks",Taxonomic alterations of protein acetylation in the pediatric CD microbiome. LEfSe analysis of metaproteome-based taxonomic compositions.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Fungi,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia,k__Fungi|p__Ascomycota|c__Saccharomycetes,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales,,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta,k__Fungi|p__Ascomycota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes",3379134|1224|1236;4751;3379134|203691|203692;4751|4890|4891;4751|4890|4891|4892;;3379134|203691|203692|136|137|146;4751|4890;1783272|1239|186801|186802|216572|244127;2731360|2731618|2731619,Complete,Folakunmi
bsdb:32807798/2/2,32807798,case-control,32807798,https://doi.org/10.1038/s41467-020-17916-9,NA,"Zhang X., Ning Z., Mayne J., Yang Y., Deeke S.A., Walker K., Farnsworth C.L., Stokes M.P., Couture J.F., Mack D., Stintzi A. , Figeys D.",Widespread protein lysine acetylation in gut microbiome and its alterations in patients with Crohn's disease,Nature communications,2020,NA,Experiment 2,Canada,Homo sapiens,"Feces,Mucosa of descending colon","UBERON:0004992,UBERON:0001988",Crohn's disease,EFO:0000384,healthy adults,pediatric crohn's disease,"children (<18 years old) diagnosed with crohn’s disease. 
The exclusion criteria implemented to further refine the cohort in this study include: presence of diabetes mellitus, presence of infectious gastroenteritis within the past 2 months, and irritable bowel syndrome.",8,10,1 month,NA,NA,Mass spectrometry,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,figure 5b,23 November 2023,Folakunmi,"Folakunmi,WikiWorks",Taxonomic alterations of protein acetylation in the pediatric CD microbiome. LEfSe analysis of metaproteome-based taxonomic compositions.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella micans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",3379134|976|200643|171549|815|816|820;1783272|1239|186801|3085636|186803|189330;3379134|976|200643|171549|171552|838|189723;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810280|3025755|29348;1783272|1239|186801|3085636|186803|572511|1322;1783272|1239|91061|186826|1300;1783272|1239|91061;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|91061|186826;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|526524|526525|2810280|3025755,Complete,Folakunmi
bsdb:32807798/3/1,32807798,case-control,32807798,https://doi.org/10.1038/s41467-020-17916-9,NA,"Zhang X., Ning Z., Mayne J., Yang Y., Deeke S.A., Walker K., Farnsworth C.L., Stokes M.P., Couture J.F., Mack D., Stintzi A. , Figeys D.",Widespread protein lysine acetylation in gut microbiome and its alterations in patients with Crohn's disease,Nature communications,2020,NA,Experiment 3,Canada,Homo sapiens,"Feces,Mucosa of descending colon","UBERON:0004992,UBERON:0001988",Crohn's disease,EFO:0000384,healthy adults,pediatric crohn's disease,"children (<18 years old) diagnosed with crohn’s disease. 
The exclusion criteria implemented to further refine the cohort in this study include: presence of diabetes mellitus, presence of infectious gastroenteritis within the past 2 months, and irritable bowel syndrome.",8,10,1 month,NA,NA,Mass spectrometry,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,figure 5e,23 November 2023,Folakunmi,"Folakunmi,WikiWorks",Taxonomic alterations of protein acetylation in the pediatric CD microbiome. LEfSe analysis of the acetylome-to-metaproteome ratios of all quantified taxa in the lysine acetylome data set.,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239|91061;1783272|1239|186801|186802|216572|1263,Complete,Folakunmi
bsdb:32807798/4/1,32807798,case-control,32807798,https://doi.org/10.1038/s41467-020-17916-9,NA,"Zhang X., Ning Z., Mayne J., Yang Y., Deeke S.A., Walker K., Farnsworth C.L., Stokes M.P., Couture J.F., Mack D., Stintzi A. , Figeys D.",Widespread protein lysine acetylation in gut microbiome and its alterations in patients with Crohn's disease,Nature communications,2020,NA,Experiment 4,Canada,Homo sapiens,Feces,UBERON:0001988,Protein modification process,GO:0036211,Metaproteome aliquot of human gut,Lysine acetylome aliquot of human gut,relative abundance of kac levels (for each taxon listed in supplementary data 3) in human fecal microbiome samples lysine acetylome aliquot,209,209,1 month,NA,NA,Mass spectrometry,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,figure 2b,24 November 2023,Folakunmi,"Folakunmi,WikiWorks","Lysine acetylome-to-metaproteome ratios of quantified phyla and genera in
human gut microbiome. Comparisons of the percentage of acetylation in lysine acetylomic aliquot with that in metaproteomic aliquot.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota",1783272|1239|186801|3085636|186803|1407607;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|186802|3085642|580596;1783272|1239,Complete,Folakunmi
bsdb:32807798/4/2,32807798,case-control,32807798,https://doi.org/10.1038/s41467-020-17916-9,NA,"Zhang X., Ning Z., Mayne J., Yang Y., Deeke S.A., Walker K., Farnsworth C.L., Stokes M.P., Couture J.F., Mack D., Stintzi A. , Figeys D.",Widespread protein lysine acetylation in gut microbiome and its alterations in patients with Crohn's disease,Nature communications,2020,NA,Experiment 4,Canada,Homo sapiens,Feces,UBERON:0001988,Protein modification process,GO:0036211,Metaproteome aliquot of human gut,Lysine acetylome aliquot of human gut,relative abundance of kac levels (for each taxon listed in supplementary data 3) in human fecal microbiome samples lysine acetylome aliquot,209,209,1 month,NA,NA,Mass spectrometry,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,figure 2b,24 November 2023,Folakunmi,"Folakunmi,WikiWorks",Lysine acetylome-to-metaproteome ratios of quantified phyla and genera in human gut microbiome. Comparisons of the percentage of acetylation in lysine acetylomic aliquot with that in metaproteomic aliquot.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Metazoa|p__Chordata,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Metazoa|p__Chordata|c__Mammalia|o__Primates|f__Hominidae|s__Homininae|g__Homo",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|830;1783272|201174;3379134|1224;3379134|1224|28216|80840|995019|577310;1783272|201174|84998|84999|84107|102106;33208|7711;1783272|1239|186801|186802|204475;33208|7711|40674|9443|9604|207598|9605,Complete,Folakunmi
bsdb:32820337/1/1,32820337,"cross-sectional observational, not case-control",32820337,https://doi.org/10.1042/BSR20191242,NA,"Yan H.X., An W.C., Chen F., An B., Pan Y., Jin J., Xia X.P., Cui Z.J., Jiang L., Zhou S.J., Jin H.X., Ou X.H., Huang W., Hong T.P. , Lyu Z.H.",Intestinal microbiota changes in Graves' disease: a prospective clinical study,Bioscience reports,2020,"Case-control, Grave's disease (GD), Hyperthyroidism, Intestinal microbiota, Prospective, Thyroid-stimulating antibodies (TSAb)",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Healthy Controls (HCs),Graves’ disease (GD),Patients diagnosed with Graves’ disease (GD),17,39,3 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,"age,body mass index,sex",NA,NA,decreased,unchanged,unchanged,NA,unchanged,Signature 1,Table 2,24 July 2025,Aleru Divine,Aleru Divine,LEfSe results of significant features,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales",1783272|1239|91061;3379134|976|200643|171549|171552|838;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826,Complete,NA
bsdb:32827699/1/1,32827699,laboratory experiment,32827699,10.1016/j.bbi.2020.08.015,https://pubmed.ncbi.nlm.nih.gov/32827699/,"Jang J.H., Yeom M.J., Ahn S., Oh J.Y., Ji S., Kim T.H. , Park H.J.",Acupuncture inhibits neuroinflammation and gut microbial dysbiosis in a mouse model of Parkinson's disease,"Brain, behavior, and immunity",2020,"Acupuncture, Gut microbial dysbiosis, Microbiome-gut-brain axis, Neuroinflammation, Parkinson’s disease",Experiment 1,South Korea,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control Group,MPTP Group,"Mice were treated with MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine).",6,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,decreased,NA,NA,unchanged,Signature 1,Figure 4G,16 March 2024,Mariposa,"Mariposa,WikiWorks",Differences in bacterial taxa abundance in the MPTP Group (Mice treated with MPTP) VS Control group.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum|s__Faecalibaculum rodentium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia|s__Harryflintia acetispora,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus champanellensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae",3379134|1224|28216;3379134|1224|28216|80840;1783272|1239|526524|526525|128827|1729679;1783272|1239|526524|526525|128827|1729679|1702221;1783272|1239|186801|186802|216572|1892380;1783272|1239|186801|186802|216572|1892380|1849041;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|577310;3379134|1224|28216|80840|995019|577310|487175;1783272|1239|186801|186802|216572|1263|1161942;3379134|1224|28216|80840|995019;3379134|976|200643|171549|2005525,Complete,ChiomaBlessing
bsdb:32827699/1/2,32827699,laboratory experiment,32827699,10.1016/j.bbi.2020.08.015,https://pubmed.ncbi.nlm.nih.gov/32827699/,"Jang J.H., Yeom M.J., Ahn S., Oh J.Y., Ji S., Kim T.H. , Park H.J.",Acupuncture inhibits neuroinflammation and gut microbial dysbiosis in a mouse model of Parkinson's disease,"Brain, behavior, and immunity",2020,"Acupuncture, Gut microbial dysbiosis, Microbiome-gut-brain axis, Neuroinflammation, Parkinson’s disease",Experiment 1,South Korea,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control Group,MPTP Group,"Mice were treated with MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine).",6,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,decreased,NA,NA,unchanged,Signature 2,Figure 4G and 4F,16 March 2024,Mariposa,"Mariposa,WikiWorks",Differences in bacterial taxa abundance in the MPTP group (mice treated with MPTP) vs. the control group.,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacterium",1783272|1239|526524|526525|128827|2749846|31971;1783272|1239|526524|526525|128827|2749267,Complete,ChiomaBlessing
bsdb:32827699/3/1,32827699,laboratory experiment,32827699,10.1016/j.bbi.2020.08.015,https://pubmed.ncbi.nlm.nih.gov/32827699/,"Jang J.H., Yeom M.J., Ahn S., Oh J.Y., Ji S., Kim T.H. , Park H.J.",Acupuncture inhibits neuroinflammation and gut microbial dysbiosis in a mouse model of Parkinson's disease,"Brain, behavior, and immunity",2020,"Acupuncture, Gut microbial dysbiosis, Microbiome-gut-brain axis, Neuroinflammation, Parkinson’s disease",Experiment 3,South Korea,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control Group,MPTP + Acu Group,Mice treated with MPTP received acupuncture.,6,9,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 1,Figure 4G and 4F,23 March 2024,Mariposa,"Mariposa,WikiWorks",Differences in bacterial taxa abundance in the MPTP + Acu (Mice treated with MPTP that received Acupuncture) vs. Control group,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium thermosuccinogenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora xylanisolvens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora aerotolerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoclostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Vallitaleaceae|g__Vallitalea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Vallitaleaceae|g__Vallitalea|s__Vallitalea pronyensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Vallitaleaceae",3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|31979|1485|84032;1783272|1239|186801|3085636|186803|2719231|384636;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|2719231|36832;1783272|1239|186801|186802|216572|2304693;3379134|976|200643|171549|171550;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|186801|3085636|2603322|1348611;1783272|1239|186801|3085636|2603322|1348611|1348613;1783272|1239|186801|3085636|2603322,Complete,ChiomaBlessing
bsdb:32827699/3/2,32827699,laboratory experiment,32827699,10.1016/j.bbi.2020.08.015,https://pubmed.ncbi.nlm.nih.gov/32827699/,"Jang J.H., Yeom M.J., Ahn S., Oh J.Y., Ji S., Kim T.H. , Park H.J.",Acupuncture inhibits neuroinflammation and gut microbial dysbiosis in a mouse model of Parkinson's disease,"Brain, behavior, and immunity",2020,"Acupuncture, Gut microbial dysbiosis, Microbiome-gut-brain axis, Neuroinflammation, Parkinson’s disease",Experiment 3,South Korea,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control Group,MPTP + Acu Group,Mice treated with MPTP received acupuncture.,6,9,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 2,Figure 4G and 4F,23 March 2024,Mariposa,"Mariposa,WikiWorks",Differences in bacterial taxa abundance in the MPTP + Acu (Mice treated with MPTP that received Acupuncture) vs. Control group,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus",1783272|1239|526524|526525|128827|2749846;1783272|1239|526524|526525|128827|2749846|31971,Complete,ChiomaBlessing
bsdb:32827699/4/NA,32827699,laboratory experiment,32827699,10.1016/j.bbi.2020.08.015,https://pubmed.ncbi.nlm.nih.gov/32827699/,"Jang J.H., Yeom M.J., Ahn S., Oh J.Y., Ji S., Kim T.H. , Park H.J.",Acupuncture inhibits neuroinflammation and gut microbial dysbiosis in a mouse model of Parkinson's disease,"Brain, behavior, and immunity",2020,"Acupuncture, Gut microbial dysbiosis, Microbiome-gut-brain axis, Neuroinflammation, Parkinson’s disease",Experiment 4,South Korea,Mus musculus,Feces,UBERON:0001988,Treatment,EFO:0000727,MPTP + Acu Group,MPTP + Non Acu Group,Mice treated with MPTP did not receive acupuncture,9,5,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,decreased,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:32827699/5/1,32827699,laboratory experiment,32827699,10.1016/j.bbi.2020.08.015,https://pubmed.ncbi.nlm.nih.gov/32827699/,"Jang J.H., Yeom M.J., Ahn S., Oh J.Y., Ji S., Kim T.H. , Park H.J.",Acupuncture inhibits neuroinflammation and gut microbial dysbiosis in a mouse model of Parkinson's disease,"Brain, behavior, and immunity",2020,"Acupuncture, Gut microbial dysbiosis, Microbiome-gut-brain axis, Neuroinflammation, Parkinson’s disease",Experiment 5,South Korea,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control group,MPTP group,"Mice that were treated with MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine).",6,10,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,unchanged,Signature 1,Fig 5 and Supplementary Table S1,9 April 2024,MyleeeA,"MyleeeA,Mariposa,ChiomaBlessing,WikiWorks",Bacterial genera with significant differences in the gut microbiota of MPTP group VS Control group.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Aestuariispiraceae|g__Aestuariispira,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Frisingicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae|g__Rhodospirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",3379134|1224|28211|204441|3466454|1647175;1783272|201174|1760|85004|31953|1678;3379134|200940|3031449|213115|194924|872;1783272|1239|526524|526525|128827|1729679;1783272|1239|186801|3085636|186803|1918511;1783272|1239|186801|186802|216572|1892380;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|3085636|186803|248744;3379134|976|200643|171549|171552|577309;3379134|1224|28216|80840|995019|577310;1783272|1239|909932|1843488|909930|33024;3379134|1224|28211|204441|41295|1081;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|44748;1783272|1239|526524|526525|2810280|3025755;1783272|1239|526524|526525|2810281|191303,Complete,ChiomaBlessing
bsdb:32827699/5/2,32827699,laboratory experiment,32827699,10.1016/j.bbi.2020.08.015,https://pubmed.ncbi.nlm.nih.gov/32827699/,"Jang J.H., Yeom M.J., Ahn S., Oh J.Y., Ji S., Kim T.H. , Park H.J.",Acupuncture inhibits neuroinflammation and gut microbial dysbiosis in a mouse model of Parkinson's disease,"Brain, behavior, and immunity",2020,"Acupuncture, Gut microbial dysbiosis, Microbiome-gut-brain axis, Neuroinflammation, Parkinson’s disease",Experiment 5,South Korea,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control group,MPTP group,"Mice that were treated with MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine).",6,10,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,unchanged,Signature 2,Figure 5 and Supplementary Table S1,9 April 2024,MyleeeA,"MyleeeA,Mariposa,ChiomaBlessing,WikiWorks",Bacterial genera with significant differences in the gut microbiota of MPTP group VS Control group.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Acutalibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfitobacteriaceae|g__Desulfitobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Flintibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Gracilibacteraceae|g__Gracilibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans",1783272|1239|186801|186802|3082771|1918385;1783272|1239|186801|186802|216572|244127;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802|2937909|36853;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|1918454;1783272|1239|186801|186802|541019|342658;1783272|1239|186801|186802|216572|3028852;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|1200657,Complete,ChiomaBlessing
bsdb:32827699/6/1,32827699,laboratory experiment,32827699,10.1016/j.bbi.2020.08.015,https://pubmed.ncbi.nlm.nih.gov/32827699/,"Jang J.H., Yeom M.J., Ahn S., Oh J.Y., Ji S., Kim T.H. , Park H.J.",Acupuncture inhibits neuroinflammation and gut microbial dysbiosis in a mouse model of Parkinson's disease,"Brain, behavior, and immunity",2020,"Acupuncture, Gut microbial dysbiosis, Microbiome-gut-brain axis, Neuroinflammation, Parkinson’s disease",Experiment 6,South Korea,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control group,MPTP+Acu group,"Mice treated with MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine) that received Acupuncture",6,9,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 1,Figure 5 and Supplementary Table S1,9 April 2024,MyleeeA,"MyleeeA,ChiomaBlessing,WikiWorks",Bacterial genera with significant differences in the gut microbiota of MPTP + Acu group VS Control group.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Vallitaleaceae|g__Vallitalea,k__Bacillati|p__Candidatus Melainabacteria|c__Vampirovibriophyceae|o__Vampirovibrionales|g__Vampirovibrio",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|2304693;1783272|1239|186801|3085636|2603322|1348611;1783272|1798710|3118680|2211217|213484,Complete,ChiomaBlessing
bsdb:32827699/6/2,32827699,laboratory experiment,32827699,10.1016/j.bbi.2020.08.015,https://pubmed.ncbi.nlm.nih.gov/32827699/,"Jang J.H., Yeom M.J., Ahn S., Oh J.Y., Ji S., Kim T.H. , Park H.J.",Acupuncture inhibits neuroinflammation and gut microbial dysbiosis in a mouse model of Parkinson's disease,"Brain, behavior, and immunity",2020,"Acupuncture, Gut microbial dysbiosis, Microbiome-gut-brain axis, Neuroinflammation, Parkinson’s disease",Experiment 6,South Korea,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control group,MPTP+Acu group,"Mice treated with MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine) that received Acupuncture",6,9,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 2,Figure 5 and Supplementary Table S1,9 April 2024,MyleeeA,"MyleeeA,ChiomaBlessing,WikiWorks",Bacterial genera with significant differences in the gut microbiota of MPTP + Acu group VS Control group.,decreased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacterium,1783272|1239|526524|526525|128827|2749267,Complete,ChiomaBlessing
bsdb:32827699/7/1,32827699,laboratory experiment,32827699,10.1016/j.bbi.2020.08.015,https://pubmed.ncbi.nlm.nih.gov/32827699/,"Jang J.H., Yeom M.J., Ahn S., Oh J.Y., Ji S., Kim T.H. , Park H.J.",Acupuncture inhibits neuroinflammation and gut microbial dysbiosis in a mouse model of Parkinson's disease,"Brain, behavior, and immunity",2020,"Acupuncture, Gut microbial dysbiosis, Microbiome-gut-brain axis, Neuroinflammation, Parkinson’s disease",Experiment 7,South Korea,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,MPTP group,MPTP+Acu group,"Mice treated with MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine) that received Acupuncture",10,9,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 1,Figure 5 and Supplementary Table S1,9 April 2024,MyleeeA,"MyleeeA,Mariposa,ChiomaBlessing,WikiWorks",Bacterial genera with significant differences in the gut microbiota of MPTP + Acu group VS MPTP group.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Acutalibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Alkalibacter,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfitobacteriaceae|g__Desulfitobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Flintibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Gracilibacteraceae|g__Gracilibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Kineothrix,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor",1783272|1239|186801|3085636|186803|1427378;1783272|1239|186801|186802|3082771|1918385;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|186806|274470;1783272|544448|31969|186332|186333|2086;1783272|1239|186801|3085636|186803|653683;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|186802|2937909|36853;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|1918454;1783272|1239|186801|186802|541019|342658;1783272|1239|186801|3085636|186803|2163168;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|186802|216572|3028852;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|1017280,Complete,ChiomaBlessing
bsdb:32827699/7/2,32827699,laboratory experiment,32827699,10.1016/j.bbi.2020.08.015,https://pubmed.ncbi.nlm.nih.gov/32827699/,"Jang J.H., Yeom M.J., Ahn S., Oh J.Y., Ji S., Kim T.H. , Park H.J.",Acupuncture inhibits neuroinflammation and gut microbial dysbiosis in a mouse model of Parkinson's disease,"Brain, behavior, and immunity",2020,"Acupuncture, Gut microbial dysbiosis, Microbiome-gut-brain axis, Neuroinflammation, Parkinson’s disease",Experiment 7,South Korea,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,MPTP group,MPTP+Acu group,"Mice treated with MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine) that received Acupuncture",10,9,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 2,Figure 5 and Supplementary Table S1,9 April 2024,MyleeeA,"MyleeeA,ChiomaBlessing,WikiWorks",Bacterial genera with significant differences in the gut microbiota of MPTP + Acu group VS MPTP group.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Aestuariispiraceae|g__Aestuariispira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Frisingicoccus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae|g__Rhodospirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",3379134|1224|28211|204441|3466454|1647175;3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|3085636|186803|1918511;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|3085636|186803|248744;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|577310;1783272|1239|909932|1843488|909930|33024;3379134|1224|28211|204441|41295|1081;1783272|1239|186801|186802|216572|44748;1783272|1239|526524|526525|2810280|3025755;1783272|1239|526524|526525|2810281|191303,Complete,ChiomaBlessing
bsdb:32830918/1/1,32830918,case-control,32830918,10.1002/aur.2358,NA,"Zou R., Xu F., Wang Y., Duan M., Guo M., Zhang Q., Zhao H. , Zheng H.",Changes in the Gut Microbiota of Children with Autism Spectrum Disorder,Autism research : official journal of the International Society for Autism Research,2020,"Akkermansia, Bacteroides, Prevotella, autism spectrum disorders, children, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Healthy controls,Autistic,Diagnosis of autistic disorder defined by the Diagnostic and Statistical Manual of Mental Disorders - Fourth Edition (DSM IV - TR) and confirmed using the Autism Diagnostic Interview-Revised (ADI-R),48,48,NA,16S,34,Illumina,raw counts,T-Test,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,"Figure 3, Table 3, Table 4",19 September 2024,AlishaM,"AlishaM,WikiWorks","Species, Families and Genera with significantly different abundances between ASD and control groups",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|909932|909929|1843491|158846;3379134|976|200643|171549|815|909656|310298;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|186801|3085636|186803|841|301302;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|186801|3085636|186803,Complete,NA
bsdb:32830918/1/2,32830918,case-control,32830918,10.1002/aur.2358,NA,"Zou R., Xu F., Wang Y., Duan M., Guo M., Zhang Q., Zhao H. , Zheng H.",Changes in the Gut Microbiota of Children with Autism Spectrum Disorder,Autism research : official journal of the International Society for Autism Research,2020,"Akkermansia, Bacteroides, Prevotella, autism spectrum disorders, children, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Healthy controls,Autistic,Diagnosis of autistic disorder defined by the Diagnostic and Statistical Manual of Mental Disorders - Fourth Edition (DSM IV - TR) and confirmed using the Autism Diagnostic Interview-Revised (ADI-R),48,48,NA,16S,34,Illumina,raw counts,T-Test,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,"Figure 3, Table 3, Table 4",19 September 2024,AlishaM,"AlishaM,WikiWorks","Species, Families and Genera with significantly different abundances between ASD and control groups",decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|815|816|817;1783272|1239|186801|3085636|186803|572511|1532;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|186801|3085636|186803|1432051;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|216572|946234|292800;3379134|1224|1236|135625|712|724|729;1783272|1239|186801|186802|216572;3379134|1224|1236|135625|712;3379134|74201|203494|48461|203557;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|186802|216572|946234;3379134|1224|1236|91347|543|1940338;3379134|1224|1236|135625|712|724;3379134|74201|203494|48461|1647988|239934;1783272|1239|909932|1843489|31977|39948,Complete,NA
bsdb:32830918/2/NA,32830918,case-control,32830918,10.1002/aur.2358,NA,"Zou R., Xu F., Wang Y., Duan M., Guo M., Zhang Q., Zhao H. , Zheng H.",Changes in the Gut Microbiota of Children with Autism Spectrum Disorder,Autism research : official journal of the International Society for Autism Research,2020,"Akkermansia, Bacteroides, Prevotella, autism spectrum disorders, children, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Healthy controls,Autistic,Diagnosis of autistic disorder defined by the Diagnostic and Statistical Manual of Mental Disorders - Fourth Edition (DSM IV-TR) and confirmed using the Autism Diagnostic Interview-Revised (ADI-R),48,48,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,increased,increased,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:32839514/1/1,32839514,case-control,32839514,10.1038/s41598-020-71102-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7445256/,"Thyagarajan S., Zhang Y., Thapa S., Allen M.S., Phillips N., Chaudhary P., Kashyap M.V. , Vishwanatha J.K.",Comparative analysis of racial differences in breast tumor microbiome,Scientific reports,2020,NA,Experiment 1,United States of America,Homo sapiens,Breast,UBERON:0000310,Neoplasm,EFO:0000616,BNH with TNBC normal tissue,BNH with TNBC tumor tissue,Tumor tissue from black non-hispanic patients with triple negative breast cancer,7,7,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 6a,26 July 2021,Itslanapark,"Itslanapark,Chloe,WikiWorks","Microbiota relative abundance at phylum (a, b, d) and genus (c,e) levels showed differences between tumor and normal tissue in both triple negative breast cancer and triple positive breast cancer patients using Wilcoxon Signed Rank Test.",decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae",1783272|201174;3379134|1224|28211|356|41294,Complete,Chloe
bsdb:32839514/2/1,32839514,case-control,32839514,10.1038/s41598-020-71102-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7445256/,"Thyagarajan S., Zhang Y., Thapa S., Allen M.S., Phillips N., Chaudhary P., Kashyap M.V. , Vishwanatha J.K.",Comparative analysis of racial differences in breast tumor microbiome,Scientific reports,2020,NA,Experiment 2,United States of America,Homo sapiens,Breast,UBERON:0000310,Neoplasm,EFO:0000616,WNH with TNBC normal tissue,WNH with TNBC normal tissue,Tumor tissue from white non-hispanic patients with triple negative breast cancer,6,6,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 6,26 July 2021,Itslanapark,"Itslanapark,WikiWorks","Microbiota relative abundance at phylum (a, b, d) and genus (c,e) levels showed differences between tumor and normal tissue in both triple negative breast cancer and triple positive breast cancer patients using Wilcoxon Signed Rank Test.",increased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Chloe
bsdb:32839514/3/NA,32839514,case-control,32839514,10.1038/s41598-020-71102-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7445256/,"Thyagarajan S., Zhang Y., Thapa S., Allen M.S., Phillips N., Chaudhary P., Kashyap M.V. , Vishwanatha J.K.",Comparative analysis of racial differences in breast tumor microbiome,Scientific reports,2020,NA,Experiment 3,United States of America,Homo sapiens,Breast,UBERON:0000310,Neoplasm,EFO:0000616,WNH with TNBC normal tissue (second set),WNH with TNBC normal tissue (second set),Tumor tissue from white non-hispanic patients with triple negative breast cancer,10,10,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:32839514/4/1,32839514,case-control,32839514,10.1038/s41598-020-71102-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7445256/,"Thyagarajan S., Zhang Y., Thapa S., Allen M.S., Phillips N., Chaudhary P., Kashyap M.V. , Vishwanatha J.K.",Comparative analysis of racial differences in breast tumor microbiome,Scientific reports,2020,NA,Experiment 4,United States of America,Homo sapiens,Breast,UBERON:0000310,Neoplasm,EFO:0000616,TPBC normal tissue,TPBC tumor tissue,Tumor tissue from patients with triple positive breast cancer,10,10,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,increased,NA,NA,NA,Signature 1,Table 6,26 July 2021,Itslanapark,"Itslanapark,WikiWorks","Microbiota relative abundance at phylum (a, b, d) and genus (c,e) levels showed differences between tumor and normal tissue in both triple negative breast cancer and triple positive breast cancer patients using Wilcoxon Signed Rank Test.",increased,"k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3384189|32066;1783272|1239|91061|186826|1300|1301,Complete,Chloe
bsdb:32839514/5/1,32839514,case-control,32839514,10.1038/s41598-020-71102-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7445256/,"Thyagarajan S., Zhang Y., Thapa S., Allen M.S., Phillips N., Chaudhary P., Kashyap M.V. , Vishwanatha J.K.",Comparative analysis of racial differences in breast tumor microbiome,Scientific reports,2020,NA,Experiment 5,United States of America,Homo sapiens,Breast,UBERON:0000310,Ethnic group,EFO:0001799,WNH,BNH,Normal tissue from black non-hispanic patients with breast cancer,6,7,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 1,Figure 8,26 July 2021,Itslanapark,"Itslanapark,WikiWorks","Relative abundance of taxa showed differences between BNH and WNH at the genus (a, b) and phylum (c) levels in TNBC (a, c) and TPBC (b) patients, significance analyzed using a Wilcoxon Rank Sum Test.",increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,1783272|1239|91061|1385|186818,Complete,Chloe
bsdb:32839514/5/2,32839514,case-control,32839514,10.1038/s41598-020-71102-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7445256/,"Thyagarajan S., Zhang Y., Thapa S., Allen M.S., Phillips N., Chaudhary P., Kashyap M.V. , Vishwanatha J.K.",Comparative analysis of racial differences in breast tumor microbiome,Scientific reports,2020,NA,Experiment 5,United States of America,Homo sapiens,Breast,UBERON:0000310,Ethnic group,EFO:0001799,WNH,BNH,Normal tissue from black non-hispanic patients with breast cancer,6,7,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 2,Figure 8,26 July 2021,Itslanapark,"Itslanapark,WikiWorks","Relative abundance of taxa showed differences between BNH and WNH at the genus (a, b) and phylum (c) levels in TNBC (a, c) and TPBC (b) patients, significance analyzed using a Wilcoxon Rank Sum Test.",decreased,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Phenylobacterium,3379134|1224|28211|204458|76892|20,Complete,Chloe
bsdb:32839514/6/1,32839514,case-control,32839514,10.1038/s41598-020-71102-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7445256/,"Thyagarajan S., Zhang Y., Thapa S., Allen M.S., Phillips N., Chaudhary P., Kashyap M.V. , Vishwanatha J.K.",Comparative analysis of racial differences in breast tumor microbiome,Scientific reports,2020,NA,Experiment 6,United States of America,Homo sapiens,Breast,UBERON:0000310,Ethnic group,EFO:0001799,WNH,BNH,Tumor tissue from black non-hispanic patients with breast cancer,6,7,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 8,27 July 2021,Itslanapark,"Itslanapark,WikiWorks","Relative abundance of taxa showed differences between BNH and WNH at the genus (a, b) and phylum (c) levels in TNBC (a, c) and TPBC (b) patients, significance analyzed using a Wilcoxon Rank Sum Test.",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium",1783272|1239|909932|1843489|31977|29465;3379134|1224|28211|356|69277|28100,Complete,Chloe
bsdb:32839514/6/2,32839514,case-control,32839514,10.1038/s41598-020-71102-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7445256/,"Thyagarajan S., Zhang Y., Thapa S., Allen M.S., Phillips N., Chaudhary P., Kashyap M.V. , Vishwanatha J.K.",Comparative analysis of racial differences in breast tumor microbiome,Scientific reports,2020,NA,Experiment 6,United States of America,Homo sapiens,Breast,UBERON:0000310,Ethnic group,EFO:0001799,WNH,BNH,Tumor tissue from black non-hispanic patients with breast cancer,6,7,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 8,27 July 2021,Itslanapark,"Itslanapark,Atrayees,WikiWorks","Relative abundance of taxa showed differences between BNH and WNH at the genus (a, b) and phylum (c) levels in TNBC (a, c) and TPBC (b) patients, significance analyzed using a Wilcoxon Rank Sum Test.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Phenylobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae",1783272|1239|91061|186826|33958|1578;3379134|1224|28211|204458|76892|20;3379134|1224|28211|356|41294;3379134|1224|28211|204458|76892,Complete,Chloe
bsdb:32842982/1/1,32842982,"cross-sectional observational, not case-control",32842982,0.1186/s12879-020-05324-9,NA,"Chen Y., Qiu X., Wang W., Li D., Wu A., Hong Z., Di W. , Qiu L.",Human papillomavirus infection and cervical intraepithelial neoplasia progression are associated with increased vaginal microbiome diversity in a Chinese cohort,BMC infectious diseases,2020,"Cervical cancer, Cervical intraepithelial neoplasia, Human papillomavirus, Vaginal microbiome",Experiment 1,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Human papilloma virus infection,EFO:0001668,healthy control,HPV +,HPV-infected women without CIN confirmed by HPV genotyping test and examination,68,78,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure 5,20 March 2021,Cynthia Anderson,"Cynthia Anderson,WikiWorks",The unique taxa and microbiomarkers for different groups,increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,1783272|1239|909932|1843489|31977|906,Complete,Atrayees
bsdb:32842982/2/1,32842982,"cross-sectional observational, not case-control",32842982,0.1186/s12879-020-05324-9,NA,"Chen Y., Qiu X., Wang W., Li D., Wu A., Hong Z., Di W. , Qiu L.",Human papillomavirus infection and cervical intraepithelial neoplasia progression are associated with increased vaginal microbiome diversity in a Chinese cohort,BMC infectious diseases,2020,"Cervical cancer, Cervical intraepithelial neoplasia, Human papillomavirus, Vaginal microbiome",Experiment 2,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Cervical glandular intraepithelial neoplasia,EFO:1000165,healthy control,LSIL,women with low-grade squamous intraepithelial lesions confirmed by biopsy,78,51,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Figure 5,20 March 2021,Cynthia Anderson,"Cynthia Anderson,WikiWorks",The unique taxa and microbiomarkers for different groups,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,3379134|976|200643|171549|171552|838|419005,Complete,Atrayees
bsdb:32842982/3/1,32842982,"cross-sectional observational, not case-control",32842982,0.1186/s12879-020-05324-9,NA,"Chen Y., Qiu X., Wang W., Li D., Wu A., Hong Z., Di W. , Qiu L.",Human papillomavirus infection and cervical intraepithelial neoplasia progression are associated with increased vaginal microbiome diversity in a Chinese cohort,BMC infectious diseases,2020,"Cervical cancer, Cervical intraepithelial neoplasia, Human papillomavirus, Vaginal microbiome",Experiment 3,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Cervical glandular intraepithelial neoplasia,EFO:1000165,healthy control,HSIL,women with high-grade squamous intraepithelial lesions confirmed by biopsy,68,23,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 5,20 March 2021,Cynthia Anderson,"Cynthia Anderson,WikiWorks",The unique taxa and microbiomarkers for different groups,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis",3379134|976|200643|171549|171552|838;1783272|1239|186801;1783272|1239|186801|186802;3379134|976|200643|171549|171552;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|177971;1783272|1239|91061|186826|1300;3379134|976|200643|171549|171552|2974257|386414,Complete,Atrayees
bsdb:32842982/4/1,32842982,"cross-sectional observational, not case-control",32842982,0.1186/s12879-020-05324-9,NA,"Chen Y., Qiu X., Wang W., Li D., Wu A., Hong Z., Di W. , Qiu L.",Human papillomavirus infection and cervical intraepithelial neoplasia progression are associated with increased vaginal microbiome diversity in a Chinese cohort,BMC infectious diseases,2020,"Cervical cancer, Cervical intraepithelial neoplasia, Human papillomavirus, Vaginal microbiome",Experiment 4,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Cervical cancer,MONDO:0002974,healthy control,cervical cancer,women with cervical cancer confirmed by biopsy,68,9,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 5,20 March 2021,Cynthia Anderson,"Cynthia Anderson,WikiWorks",The unique taxa and microbiomarkers for different groups,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Oceanobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Oceanobacillus|s__Oceanobacillus profundus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis",1783272|1239|91061|1385;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;1783272|1239|91061|1385|186817;3379134|1224;1783272|1239|91061|1385|186817|1386;3379134|976|200643;3379134|976|200643|171549;3379134|976;3379134|1224|28216;3384189|32066|203490|203491|1129771|168808;3384189|32066|203490|203491|1129771;3379134|1224|28216|80840|80864;3379134|1224|28216|80840;3379134|1224|28216|80840|80864|12916;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492;1783272|1239|91061|1385|186817|182709;1783272|1239|91061|1385|186817|182709|372463;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836;1783272|1239|909932|1843489|31977;1783272|1239|909932;1783272|1239|909932|909929;1783272|1239|186801|186802;1783272|1239|1737404|1737405|1570339|165779;3379134|976|200643|171549|171551|836|281920,Complete,Atrayees
bsdb:32842982/5/1,32842982,"cross-sectional observational, not case-control",32842982,0.1186/s12879-020-05324-9,NA,"Chen Y., Qiu X., Wang W., Li D., Wu A., Hong Z., Di W. , Qiu L.",Human papillomavirus infection and cervical intraepithelial neoplasia progression are associated with increased vaginal microbiome diversity in a Chinese cohort,BMC infectious diseases,2020,"Cervical cancer, Cervical intraepithelial neoplasia, Human papillomavirus, Vaginal microbiome",Experiment 5,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Human papilloma virus infection,EFO:0001668,Healthy control,HPV+,HPV-infected women without CIN confirmed by HPV genotyping test and examination,68,78,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,"Fig 3, 4",28 June 2023,Atrayees,"Atrayees,WikiWorks",Relative abundance of taxa across the samples,increased,"k__Pseudomonadati|p__Bacteroidota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus",3379134|976;3384189|32066|203490;3379134|1224;3379134|976|200643|171549|171552|838;1783272|1239|91061|1385|186817|1386;3384189|32066|203490|203491|1129771|168808;1783272|1239|909932|1843489|31977|906;1783272|1239|91061|186826|1300|1301;1783272|1239|1737404|1737405|1570339|165779,Complete,Atrayees
bsdb:32842982/5/2,32842982,"cross-sectional observational, not case-control",32842982,0.1186/s12879-020-05324-9,NA,"Chen Y., Qiu X., Wang W., Li D., Wu A., Hong Z., Di W. , Qiu L.",Human papillomavirus infection and cervical intraepithelial neoplasia progression are associated with increased vaginal microbiome diversity in a Chinese cohort,BMC infectious diseases,2020,"Cervical cancer, Cervical intraepithelial neoplasia, Human papillomavirus, Vaginal microbiome",Experiment 5,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Human papilloma virus infection,EFO:0001668,Healthy control,HPV+,HPV-infected women without CIN confirmed by HPV genotyping test and examination,68,78,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,"Figure 3, 4",28 June 2023,Atrayees,"Atrayees,WikiWorks",Relative abundance of taxa across the samples,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium",1783272|1239;1783272|201174|84998|84999|1643824|1380,Complete,Atrayees
bsdb:32844199/2/1,32844199,case-control,32844199,10.1093/brain/awaa201,NA,"Qian Y., Yang X., Xu S., Huang P., Li B., Du J., He Y., Su B., Xu L.M., Wang L., Huang R., Chen S. , Xiao Q.",Gut metagenomics-derived genes as potential biomarkers of Parkinson's disease,Brain : a journal of neurology,2020,"Parkinson’s disease, biomarker, gut microbiota, metagenome, shotgun",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls without any form of Parkinson's Disease,Participants with idiopathic Parkinson's Disease,All Parkinson’s disease patients eligible for this study were diagnosed with idiopathic Parkinson’s disease according to the UK Brain Bank criteria.,75,78,3 months,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,life style,sex",NA,NA,increased,NA,NA,NA,increased,Signature 1,Figure 2A-D.,18 January 2022,Fcuevas3,"Fcuevas3,Atrayees,WikiWorks",Differences in phylogenetic abundance between Parkinson’s disease patients and healthy control subjects.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella sp.,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania filiformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Thermotogati|p__Synergistota,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum",3379134|976|200643|171549|171550|239759;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|547|550;1783272|1239|186801|3085636|186803|2719313|333367;1783272|201174|84998|1643822|1643826|644652;1783272|201174|84998|1643822|1643826|644652|471189;1783272|1239|91061|186826|186828|117563;1783272|1239|91061|186826|186828|117563|2049028;1783272|1239|526524|526525|128827|61170;1783272|1239|526524|526525|128827|61170|61171;1783272|1239|186801|3085636|186803|1898203;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|2767887|1624;3379134|976|200643|171549|171552|577309|454154;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|1300|1301|1308;3384194|508458;3379134|74201;1783272|1239|91061|186826|186827|46123;1783272|1239|186801|186802|216572|1535,Complete,Atrayees
bsdb:32844256/1/1,32844256,case-control,32844256,10.1007/s10552-020-01338-5,NA,"Klann E., Williamson J.M., Tagliamonte M.S., Ukhanova M., Asirvatham J.R., Chim H., Yaghjyan L. , Mai V.",Microbiota composition in bilateral healthy breast tissue and breast tumors,Cancer causes & control : CCC,2020,"Breast, Cancer, Microbiota, Tumor microenvironment",Experiment 1,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,Bilateral Normal Breast Tissue,Tumor Breast Tissue,"Breast cancer tumor tissue samples from white, non-Hispanic women, obtained through the University of Florida (UF) Clinical and Translational Sciences Institute (CTSI) Biorepository",36,10,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,decreased,NA,NA,Signature 1,Figure 4,18 June 2025,Ecsharp,Ecsharp,Significantly different taxa identified by differential abundance between normal and tumor tissue. All OTUs shown were found to be statistically significant in terms of differential abundance using Wald’s test with Benjamini–Hochberg adjustment in the DESeq2 package (DESeq function).,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|815|816;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802|216572|216851;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|2005525|375288;1783272|201174|1760|85006|1268|32207;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|1385|90964|1279;3379134|1224|28216|80840|995019|40544;1783272|201174|1760|2037|2049|184869,Complete,NA
bsdb:32844256/1/2,32844256,case-control,32844256,10.1007/s10552-020-01338-5,NA,"Klann E., Williamson J.M., Tagliamonte M.S., Ukhanova M., Asirvatham J.R., Chim H., Yaghjyan L. , Mai V.",Microbiota composition in bilateral healthy breast tissue and breast tumors,Cancer causes & control : CCC,2020,"Breast, Cancer, Microbiota, Tumor microenvironment",Experiment 1,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,Bilateral Normal Breast Tissue,Tumor Breast Tissue,"Breast cancer tumor tissue samples from white, non-Hispanic women, obtained through the University of Florida (UF) Clinical and Translational Sciences Institute (CTSI) Biorepository",36,10,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,decreased,NA,NA,Signature 2,Figure 4,18 June 2025,Ecsharp,Ecsharp,Significantly different taxa identified by differential abundance between normal and tumor tissue. All OTUs shown were found to be statistically significant in terms of differential abundance using Wald’s test with Benjamini–Hochberg adjustment in the DESeq2 package (DESeq function).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Brevibacillus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Limnohabitans,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|186801|186802|186806|1730;3379134|976|200643|171549|171552|838;3379134|1224|1236|2887326|468|469;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|91061|1385|186822|55080;1783272|201174|84998|84999|84107|102106;3379134|1224|28216|80840|80864|283;1783272|201174|1760|85007|1653|1716;3379134|976|117743|200644|49546|237;3379134|1224|28216|80840|80864|665874;1783272|1239|909932|1843488|909930|33024;3379134|1224|1236|72274|135621|286;3384194|508458|649775|649776|3029088|638847;3379134|1224|1236|135624|83763|83770;3379134|1224|28216|80840|995019|40544;1783272|1239|91061|1385|90964|1279;3379134|976|200643|171549|815|816,Complete,NA
bsdb:32844256/2/1,32844256,case-control,32844256,10.1007/s10552-020-01338-5,NA,"Klann E., Williamson J.M., Tagliamonte M.S., Ukhanova M., Asirvatham J.R., Chim H., Yaghjyan L. , Mai V.",Microbiota composition in bilateral healthy breast tissue and breast tumors,Cancer causes & control : CCC,2020,"Breast, Cancer, Microbiota, Tumor microenvironment",Experiment 2,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,Bilateral Normal Breast Tissue,Tumor Breast Tissue,"Breast cancer tumor tissue samples from white, non-Hispanic women, obtained through the University of Florida (UF) Clinical and Translational Sciences Institute (CTSI) Biorepository",36,10,NA,16S,12,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,decreased,NA,NA,Signature 1,Online Resource 3,19 June 2025,Ecsharp,Ecsharp,A total of 131 OTUs were identified as significantly associated with tissue group (normal or tumor) through a generalized linear mixed effects model with individual subject as the random effect and disease status as the fixed effect. The most specific level of taxonomic classification is reported for each OTU. A positive coefficient indicates the OTU is more abundant in normal tissue and a negative coefficient indicates the OTU is more abundant in tumor tissue.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Brevibacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Elizabethkingia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Limnohabitans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Rhodoluna,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae",3379134|1224|1236|2887326|468|469;1783272|201174|1760|2037|2049|1654;3379134|74201|203494|48461|1647988|239934;1783272|1239|1737404|1737405|1570339|165779;1783272|544448|31969|186332|186333;1783272|1239;1783272|1239|91061|1385|186817|1386;1783272|1239|186801|3085636|186803|572511;1783272|1239|91061|1385|186822|55080;1783272|1239|526524|526525|128827|118747;;3379134|976|1853228|1853229|563835;1783272|1239|186801|3082768|990719;1783272|201174|84998|84999|84107|102106;3379134|1224|28216|80840|80864;3379134|1224|28216|80840|80864|283;1783272|201174|1760|85007|1653|1716;3379134|976|768503|768507;3379134|200940|3031449|213115|194924|872;3379134|976|117743|200644|2762318|308865;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|216851;3379134|976|117743|200644|49546|237;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958|1578;3379134|1224|28216|80840|80864|665874;1783272|201174|1760|85006|85023;3379134|976|200643|171549|2005473;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|75682;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171552|838;1783272|201174|1760|85009|31957;3384194|508458|649775|649776|3029088|638847;1783272|201174|1760|85007|85025|1827;1783272|201174|1760|85006|85023|529883;3379134|976|200643|171549|171550;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;3379134|1224|1236|135624|83763|83770;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|3082720|543314,Complete,NA
bsdb:32844256/2/2,32844256,case-control,32844256,10.1007/s10552-020-01338-5,NA,"Klann E., Williamson J.M., Tagliamonte M.S., Ukhanova M., Asirvatham J.R., Chim H., Yaghjyan L. , Mai V.",Microbiota composition in bilateral healthy breast tissue and breast tumors,Cancer causes & control : CCC,2020,"Breast, Cancer, Microbiota, Tumor microenvironment",Experiment 2,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,Bilateral Normal Breast Tissue,Tumor Breast Tissue,"Breast cancer tumor tissue samples from white, non-Hispanic women, obtained through the University of Florida (UF) Clinical and Translational Sciences Institute (CTSI) Biorepository",36,10,NA,16S,12,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,decreased,NA,NA,Signature 2,Online Resource 3,19 June 2025,Ecsharp,Ecsharp,A total of 131 OTUs were identified as significantly associated with tissue group (normal or tumor) through a generalized linear mixed effects model with individual subject as the random effect and disease status as the fixed effect. The most specific level of taxonomic classification is reported for each OTU. A positive coefficient indicates the OTU is more abundant in normal tissue and a negative coefficient indicates the OTU is more abundant in tumor tissue.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae",1783272|1239|186801|186802|216572;3379134|976|200643|171549|171550;3379134|976|200643|171549|1853231|574697;3379134|1224|28216|80840|995019|40544;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|815|816;1783272|1239|91061|1385|539738;3379134|976|200643|171549;3379134|1224|1236|72274|135621;3379134|976|200643|171549|2005525|375288;1783272|201174|1760|2037|2049|184869;1783272|1239|186801|186802;33090|35493|3398|72025|3803|3814|508215;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3082720|543314;3379134|1224|28216|80840|75682|846;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572|216851;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|91347|543;3379134|1224|28216|206351|481;1783272|1239|909932|1843488|909930|904;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|186807,Complete,NA
bsdb:32844256/3/1,32844256,case-control,32844256,10.1007/s10552-020-01338-5,NA,"Klann E., Williamson J.M., Tagliamonte M.S., Ukhanova M., Asirvatham J.R., Chim H., Yaghjyan L. , Mai V.",Microbiota composition in bilateral healthy breast tissue and breast tumors,Cancer causes & control : CCC,2020,"Breast, Cancer, Microbiota, Tumor microenvironment",Experiment 3,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,Bilateral Normal Breast Tissue,Tumor Breast Tissue,"Breast cancer tumor tissue samples from white, non-Hispanic women, obtained through the University of Florida (UF) Clinical and Translational Sciences Institute (CTSI) Biorepository",36,10,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,decreased,NA,NA,Signature 1,Online Resources 1a-c,1 July 2025,Ecsharp,Ecsharp,"Relative abundance of phyla, families, and genera in normal and tumor tissue. P-values were generated using a non-parametric Mann-Whitney U test and were adjusted using the Benjamini-Hochberg method.",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|1853231|574697;3379134|976|200643|171549|1853231;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;3379134|74201|203494|48461|203557;3379134|74201,Complete,NA
bsdb:32844256/3/2,32844256,case-control,32844256,10.1007/s10552-020-01338-5,NA,"Klann E., Williamson J.M., Tagliamonte M.S., Ukhanova M., Asirvatham J.R., Chim H., Yaghjyan L. , Mai V.",Microbiota composition in bilateral healthy breast tissue and breast tumors,Cancer causes & control : CCC,2020,"Breast, Cancer, Microbiota, Tumor microenvironment",Experiment 3,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,Bilateral Normal Breast Tissue,Tumor Breast Tissue,"Breast cancer tumor tissue samples from white, non-Hispanic women, obtained through the University of Florida (UF) Clinical and Translational Sciences Institute (CTSI) Biorepository",36,10,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,decreased,NA,NA,Signature 2,Online Resources 1a-c,1 July 2025,Ecsharp,Ecsharp,"Relative abundance of phyla, families, and genera in normal and tumor tissue. P-values were generated using a non-parametric Mann-Whitney U test and were adjusted using the Benjamini-Hochberg method.",decreased,"k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Pseudomonadota,k__Thermotogati|p__Synergistota,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",1783272|1117;3379134|1224;3384194|508458;1783272|544448;3379134|1224|28216|80840|506;3379134|976|117743|200644|49546;3379134|1224|1236|2887326|468;3379134|976|200643|171549|171552;3379134|1224|1236|2887326|468|469;3379134|976|117743|200644|49546|237;3379134|976|200643|171549|171552|838;1783272|1239|91061|1385|90964|1279;3379134|1224|28216|80840|995019|40544,Complete,NA
bsdb:32855157/1/1,32855157,"cross-sectional observational, not case-control",32855157,https://doi.org/10.1158/2326-6066.CIR-19-1014,NA,"Peng Z., Cheng S., Kou Y., Wang Z., Jin R., Hu H., Zhang X., Gong J.F., Li J., Lu M., Wang X., Zhou J., Lu Z., Zhang Q., Tzeng D.T.W., Bi D., Tan Y. , Shen L.",The Gut Microbiome Is Associated with Clinical Response to Anti-PD-1/PD-L1 Immunotherapy in Gastrointestinal Cancer,Cancer immunology research,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Digestive System Carcinoma,EFO:1000218,Non-responders to anti–PD-1/PD-L1 immunotherapy,Responders to anti–PD-1/PD-L1 immunotherapy,Patients with stage 3 or stage 4 gastrointestinal cancer who achieved an objective response (Partial Responders/Stable Disease) lasting at least 3 months upon treatment start with anti–PD-1/PD-L1 immunotherapy.,29,45,NA,16S,34,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 1,"Fig. 3A, Supp. Table S6",15 March 2024,Hamza,"Hamza,Scholastica,WikiWorks,Tosin",Differential abundance between responders and non-responders to  Anti–PD-1/PD-L1 Immunotherapy in all 74 patients with Gastrointestinal Cancer,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:352",1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|28050;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3085636|186803|297314;1783272|1239|186801|186802|216572|707003;1783272|1239|186801|186802|31979|1485|1262798,Complete,Folakunmi
bsdb:32855157/1/2,32855157,"cross-sectional observational, not case-control",32855157,https://doi.org/10.1158/2326-6066.CIR-19-1014,NA,"Peng Z., Cheng S., Kou Y., Wang Z., Jin R., Hu H., Zhang X., Gong J.F., Li J., Lu M., Wang X., Zhou J., Lu Z., Zhang Q., Tzeng D.T.W., Bi D., Tan Y. , Shen L.",The Gut Microbiome Is Associated with Clinical Response to Anti-PD-1/PD-L1 Immunotherapy in Gastrointestinal Cancer,Cancer immunology research,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Digestive System Carcinoma,EFO:1000218,Non-responders to anti–PD-1/PD-L1 immunotherapy,Responders to anti–PD-1/PD-L1 immunotherapy,Patients with stage 3 or stage 4 gastrointestinal cancer who achieved an objective response (Partial Responders/Stable Disease) lasting at least 3 months upon treatment start with anti–PD-1/PD-L1 immunotherapy.,29,45,NA,16S,34,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 2,"Fig. 3A, Supp. Table S6",15 March 2024,Hamza,"Hamza,Scholastica,WikiWorks",Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 Immunotherapy in all 74 patients with Gastrointestinal Cancer,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",3379134|976|200643|171549|815|816;1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|186802|216572|707003,Complete,Folakunmi
bsdb:32855157/2/1,32855157,"cross-sectional observational, not case-control",32855157,https://doi.org/10.1158/2326-6066.CIR-19-1014,NA,"Peng Z., Cheng S., Kou Y., Wang Z., Jin R., Hu H., Zhang X., Gong J.F., Li J., Lu M., Wang X., Zhou J., Lu Z., Zhang Q., Tzeng D.T.W., Bi D., Tan Y. , Shen L.",The Gut Microbiome Is Associated with Clinical Response to Anti-PD-1/PD-L1 Immunotherapy in Gastrointestinal Cancer,Cancer immunology research,2020,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Non-responders (colorectal cancer - CRC),Responders (colorectal cancer - CRC),Patients with colorectal cancer (CRC) who achieved an objective response (Partial Responders/Stable Disease) lasting at least 3 months upon treatment start with anti–PD-1/PD-L1 immunotherapy.,7,12,NA,16S,34,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 1,"Fig. 3B, Supp. Table S7",29 March 2024,Scholastica,"Scholastica,WikiWorks",Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 immunotherapy in patients with Colorectal Cancer (CRC),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",3379134|976|200643|171549|815|816;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|216572|3068309;1783272|1239|186801|3085636|186803|297314,Complete,Folakunmi
bsdb:32855157/2/2,32855157,"cross-sectional observational, not case-control",32855157,https://doi.org/10.1158/2326-6066.CIR-19-1014,NA,"Peng Z., Cheng S., Kou Y., Wang Z., Jin R., Hu H., Zhang X., Gong J.F., Li J., Lu M., Wang X., Zhou J., Lu Z., Zhang Q., Tzeng D.T.W., Bi D., Tan Y. , Shen L.",The Gut Microbiome Is Associated with Clinical Response to Anti-PD-1/PD-L1 Immunotherapy in Gastrointestinal Cancer,Cancer immunology research,2020,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Non-responders (colorectal cancer - CRC),Responders (colorectal cancer - CRC),Patients with colorectal cancer (CRC) who achieved an objective response (Partial Responders/Stable Disease) lasting at least 3 months upon treatment start with anti–PD-1/PD-L1 immunotherapy.,7,12,NA,16S,34,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 2,"Fig. 3B, Supp. Table S7",29 March 2024,Scholastica,"Scholastica,WikiWorks",Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 immunotherapy in patients with Colorectal Cancer (CRC),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|1506553;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|216572|292632,Complete,Folakunmi
bsdb:32855157/3/1,32855157,"cross-sectional observational, not case-control",32855157,https://doi.org/10.1158/2326-6066.CIR-19-1014,NA,"Peng Z., Cheng S., Kou Y., Wang Z., Jin R., Hu H., Zhang X., Gong J.F., Li J., Lu M., Wang X., Zhou J., Lu Z., Zhang Q., Tzeng D.T.W., Bi D., Tan Y. , Shen L.",The Gut Microbiome Is Associated with Clinical Response to Anti-PD-1/PD-L1 Immunotherapy in Gastrointestinal Cancer,Cancer immunology research,2020,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Esophageal carcinoma,EFO:0002916,Non-responders (esophageal carcinoma),Responders (esophageal carcinoma),Patients with esophageal carcinoma who achieved an objective response (Partial Responders/Stable Disease) lasting at least 3 months upon treatment start with anti–PD-1/PD-L1 immunotherapy.,6,8,NA,16S,34,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 1,"Fig. 3C, Supp. Table S8",30 March 2024,Scholastica,"Scholastica,WikiWorks",Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 Immunotherapy in esophageal carcinoma cancer patients,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",3379134|976|200643|171549|815|816;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|877420;3379134|976|200643|171549|171552|577309;3379134|1224|28216|80840|995019|577310;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3085636|186803|297314,Complete,Folakunmi
bsdb:32855157/3/2,32855157,"cross-sectional observational, not case-control",32855157,https://doi.org/10.1158/2326-6066.CIR-19-1014,NA,"Peng Z., Cheng S., Kou Y., Wang Z., Jin R., Hu H., Zhang X., Gong J.F., Li J., Lu M., Wang X., Zhou J., Lu Z., Zhang Q., Tzeng D.T.W., Bi D., Tan Y. , Shen L.",The Gut Microbiome Is Associated with Clinical Response to Anti-PD-1/PD-L1 Immunotherapy in Gastrointestinal Cancer,Cancer immunology research,2020,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Esophageal carcinoma,EFO:0002916,Non-responders (esophageal carcinoma),Responders (esophageal carcinoma),Patients with esophageal carcinoma who achieved an objective response (Partial Responders/Stable Disease) lasting at least 3 months upon treatment start with anti–PD-1/PD-L1 immunotherapy.,6,8,NA,16S,34,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 2,"Fig. 3C, Supp. Table S8",30 March 2024,Scholastica,"Scholastica,WikiWorks",Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 Immunotherapy in esophageal carcinoma cancer patients,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|3085636|186803|28050;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|248744;1783272|1239|186801|186802|216572|707003,Complete,Folakunmi
bsdb:32855157/4/1,32855157,"cross-sectional observational, not case-control",32855157,https://doi.org/10.1158/2326-6066.CIR-19-1014,NA,"Peng Z., Cheng S., Kou Y., Wang Z., Jin R., Hu H., Zhang X., Gong J.F., Li J., Lu M., Wang X., Zhou J., Lu Z., Zhang Q., Tzeng D.T.W., Bi D., Tan Y. , Shen L.",The Gut Microbiome Is Associated with Clinical Response to Anti-PD-1/PD-L1 Immunotherapy in Gastrointestinal Cancer,Cancer immunology research,2020,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,Non-responders (gastric cancer),Responders (gastric cancer),Patients with gastric cancer who achieved an objective response (Partial Responders/Stable Disease) lasting at least 3 months upon treatment start with anti–PD-1/PD-L1 immunotherapy.,8,15,NA,16S,34,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 1,"Fig. 3D, Supp. Table S9",30 March 2024,Scholastica,"Scholastica,WikiWorks",Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 immunotherapy in gastric cancer patients,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter",1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|28050;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|3068309;1783272|1239|186801|3085636|186803|1766253,Complete,Folakunmi
bsdb:32855157/4/2,32855157,"cross-sectional observational, not case-control",32855157,https://doi.org/10.1158/2326-6066.CIR-19-1014,NA,"Peng Z., Cheng S., Kou Y., Wang Z., Jin R., Hu H., Zhang X., Gong J.F., Li J., Lu M., Wang X., Zhou J., Lu Z., Zhang Q., Tzeng D.T.W., Bi D., Tan Y. , Shen L.",The Gut Microbiome Is Associated with Clinical Response to Anti-PD-1/PD-L1 Immunotherapy in Gastrointestinal Cancer,Cancer immunology research,2020,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,Non-responders (gastric cancer),Responders (gastric cancer),Patients with gastric cancer who achieved an objective response (Partial Responders/Stable Disease) lasting at least 3 months upon treatment start with anti–PD-1/PD-L1 immunotherapy.,8,15,NA,16S,34,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 2,"Fig. 3D, Supp. Table S9",30 March 2024,Scholastica,"Scholastica,WikiWorks",Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 immunotherapy in gastric cancer patients,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",1783272|1239|186801|3085636|186803|1766253;3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549|1853231|574697;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|3085636|186803|297314,Complete,Folakunmi
bsdb:32855157/5/1,32855157,"cross-sectional observational, not case-control",32855157,https://doi.org/10.1158/2326-6066.CIR-19-1014,NA,"Peng Z., Cheng S., Kou Y., Wang Z., Jin R., Hu H., Zhang X., Gong J.F., Li J., Lu M., Wang X., Zhou J., Lu Z., Zhang Q., Tzeng D.T.W., Bi D., Tan Y. , Shen L.",The Gut Microbiome Is Associated with Clinical Response to Anti-PD-1/PD-L1 Immunotherapy in Gastrointestinal Cancer,Cancer immunology research,2020,NA,Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Digestive System Carcinoma,EFO:1000218,Responders to anti–PD-1/PD-L1 immunotherapy,Non-responders to anti–PD-1/PD-L1 immunotherapy,Patients with stage 3 or stage 4 gastrointestinal cancer who did not achieved an objective response (Partial Responders/Stable Disease) lasting at least 3 months upon treatment start with anti–PD-1/PD-L1 immunotherapy.,25,15,NA,WMS,NA,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supp. Table S10,30 March 2024,Scholastica,"Scholastica,WikiWorks","Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 immunotherapy in patients with Gastrointestinal Cancer (Responders, n=25; Non-responders, n=15)",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Latilactobacillus|s__Latilactobacillus curvatus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium mitsuokai,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia",1783272|1239|91061|186826|33958|2767885|28038;1783272|1239|526524|526525|2810280|135858|100886;1783272|1239|909932|1843489|31977|39948|487173;3379134|1224|1236|91347|1903411|629,Complete,Folakunmi
bsdb:32855157/5/2,32855157,"cross-sectional observational, not case-control",32855157,https://doi.org/10.1158/2326-6066.CIR-19-1014,NA,"Peng Z., Cheng S., Kou Y., Wang Z., Jin R., Hu H., Zhang X., Gong J.F., Li J., Lu M., Wang X., Zhou J., Lu Z., Zhang Q., Tzeng D.T.W., Bi D., Tan Y. , Shen L.",The Gut Microbiome Is Associated with Clinical Response to Anti-PD-1/PD-L1 Immunotherapy in Gastrointestinal Cancer,Cancer immunology research,2020,NA,Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Digestive System Carcinoma,EFO:1000218,Responders to anti–PD-1/PD-L1 immunotherapy,Non-responders to anti–PD-1/PD-L1 immunotherapy,Patients with stage 3 or stage 4 gastrointestinal cancer who did not achieved an objective response (Partial Responders/Stable Disease) lasting at least 3 months upon treatment start with anti–PD-1/PD-L1 immunotherapy.,25,15,NA,WMS,NA,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supp. Table S10,30 March 2024,Scholastica,"Scholastica,WikiWorks","Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 immunotherapy in patients with Gastrointestinal Cancer (Responders, n=25; Non-responders, n=15)",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 6_1_45,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|186802|31979|1485|1502;1783272|1239|186801|186802|186806|1730|39490;1783272|1239|91061|186826|33958|2742598|97478;3379134|976|200643|171549|2005525|375288|823;1783272|201174|1760|85006|1268|32207|2047;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|91061|186826|1300|1301|1305;1783272|1239|91061|186826|1300|1301|1343;1783272|1239|91061|186826|186828|117563;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|526524|526525|128827|469614;3379134|74201|203494|48461|1647988|239934|239935,Complete,Folakunmi
bsdb:32869063/1/1,32869063,"cross-sectional observational, not case-control",32869063,10.1093/ndt/gfaa122,NA,"Sato N., Kakuta M., Hasegawa T., Yamaguchi R., Uchino E., Murashita K., Nakaji S., Imoto S., Yanagita M. , Okuno Y.",Metagenomic profiling of gut microbiome in early chronic kidney disease,"Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association",2021,"chronic kidney disease, gut microbiome, metagenomics, pathway analysis",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Non Chronic kidney disease (Diabetic population),Chronic Kidney disease (Diabetic Population),Patients who have chronic kidney disease in the diabetic population,14,7,1 month,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,alcohol drinking,body mass index,diet,hypertension,proton-pump inhibitor,sex,smoking status","age,alcohol drinking,body mass index,diet,hypertension,proton-pump inhibitor,sex design,smoking status",NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 4 & Table 3,10 October 2025,Temmie,Temmie,Differentially abundant species in the non-CKD and CKD groups,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,1783272|1239|91061|186826|33958|1578|47770,Complete,Svetlana up
bsdb:32869063/1/2,32869063,"cross-sectional observational, not case-control",32869063,10.1093/ndt/gfaa122,NA,"Sato N., Kakuta M., Hasegawa T., Yamaguchi R., Uchino E., Murashita K., Nakaji S., Imoto S., Yanagita M. , Okuno Y.",Metagenomic profiling of gut microbiome in early chronic kidney disease,"Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association",2021,"chronic kidney disease, gut microbiome, metagenomics, pathway analysis",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Non Chronic kidney disease (Diabetic population),Chronic Kidney disease (Diabetic Population),Patients who have chronic kidney disease in the diabetic population,14,7,1 month,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,alcohol drinking,body mass index,diet,hypertension,proton-pump inhibitor,sex,smoking status","age,alcohol drinking,body mass index,diet,hypertension,proton-pump inhibitor,sex design,smoking status",NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 4 & Table 3,10 October 2025,Temmie,Temmie,Differentially abundant species in the non-CKD and CKD groups,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis",1783272|1239;1783272|1239|186801|3085636|186803|841|301301,Complete,Svetlana up
bsdb:32869063/2/1,32869063,"cross-sectional observational, not case-control",32869063,10.1093/ndt/gfaa122,NA,"Sato N., Kakuta M., Hasegawa T., Yamaguchi R., Uchino E., Murashita K., Nakaji S., Imoto S., Yanagita M. , Okuno Y.",Metagenomic profiling of gut microbiome in early chronic kidney disease,"Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association",2021,"chronic kidney disease, gut microbiome, metagenomics, pathway analysis",Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Non Chronic Kidney disease (Non-diabetic Population),Chronic Kidney disease (Non-diabetic Population),Patients who have chronic kidney disease in the non-diabetic population,60,30,1 month,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,alcohol drinking,body mass index,diet,hypertension,proton-pump inhibitor,sex,smoking status","age,alcohol drinking,body mass index,diet,hypertension,proton-pump inhibitor,sex,smoking status",NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 4 & Table 3,11 October 2025,Temmie,Temmie,Differentially abundant species in the non-CKD and CKD groups,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola",3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|909656|310298,Complete,Svetlana up
bsdb:32869063/2/2,32869063,"cross-sectional observational, not case-control",32869063,10.1093/ndt/gfaa122,NA,"Sato N., Kakuta M., Hasegawa T., Yamaguchi R., Uchino E., Murashita K., Nakaji S., Imoto S., Yanagita M. , Okuno Y.",Metagenomic profiling of gut microbiome in early chronic kidney disease,"Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association",2021,"chronic kidney disease, gut microbiome, metagenomics, pathway analysis",Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Non Chronic Kidney disease (Non-diabetic Population),Chronic Kidney disease (Non-diabetic Population),Patients who have chronic kidney disease in the non-diabetic population,60,30,1 month,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,alcohol drinking,body mass index,diet,hypertension,proton-pump inhibitor,sex,smoking status","age,alcohol drinking,body mass index,diet,hypertension,proton-pump inhibitor,sex,smoking status",NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 4 & Table 3,11 October 2025,Temmie,Temmie,Differentially abundant species in the non-CKD and CKD groups,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|3085636|186803|2316020|46228;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Svetlana up
bsdb:32869063/3/1,32869063,"cross-sectional observational, not case-control",32869063,10.1093/ndt/gfaa122,NA,"Sato N., Kakuta M., Hasegawa T., Yamaguchi R., Uchino E., Murashita K., Nakaji S., Imoto S., Yanagita M. , Okuno Y.",Metagenomic profiling of gut microbiome in early chronic kidney disease,"Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association",2021,"chronic kidney disease, gut microbiome, metagenomics, pathway analysis",Experiment 3,Japan,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Non Chronic kidney disease (Diabetic population with urinary findings),Chronic Kidney disease (Diabetic population with urinary findings),Patients who have chronic kidney disease in the diabetic population with urinary findings,25,9,1 month,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Text S1,17 October 2025,Temmie,Temmie,Taxonomic differential analysis of the diabetic population with Urinary findings,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis",3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712|724|729;1783272|1239|91061|186826;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|976|200643|171549|815|909656|357276;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1318,Complete,Svetlana up
bsdb:32869063/3/2,32869063,"cross-sectional observational, not case-control",32869063,10.1093/ndt/gfaa122,NA,"Sato N., Kakuta M., Hasegawa T., Yamaguchi R., Uchino E., Murashita K., Nakaji S., Imoto S., Yanagita M. , Okuno Y.",Metagenomic profiling of gut microbiome in early chronic kidney disease,"Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association",2021,"chronic kidney disease, gut microbiome, metagenomics, pathway analysis",Experiment 3,Japan,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Non Chronic kidney disease (Diabetic population with urinary findings),Chronic Kidney disease (Diabetic population with urinary findings),Patients who have chronic kidney disease in the diabetic population with urinary findings,25,9,1 month,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Text S1,17 October 2025,Temmie,Temmie,Taxonomic differential analysis in the diabetic population with Urinary findings,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,3379134|976|200643|171549|815|816|820,Complete,Svetlana up
bsdb:32869063/4/1,32869063,"cross-sectional observational, not case-control",32869063,10.1093/ndt/gfaa122,NA,"Sato N., Kakuta M., Hasegawa T., Yamaguchi R., Uchino E., Murashita K., Nakaji S., Imoto S., Yanagita M. , Okuno Y.",Metagenomic profiling of gut microbiome in early chronic kidney disease,"Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association",2021,"chronic kidney disease, gut microbiome, metagenomics, pathway analysis",Experiment 4,Japan,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Non Chronic Kidney disease (Non-diabetic Population with urinary findings),Chronic Kidney disease (Non-diabetic Population with urinary findings),Patients who have chronic kidney disease in the non-diabetic population with urinary findings,48,24,1 month,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,alcohol drinking,body mass index,diet,hypertension,proton-pump inhibitor,sex,smoking status","age,alcohol drinking,body mass index,diet,hypertension,proton-pump inhibitor,sex,smoking status",NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Text S1,17 October 2025,Temmie,Temmie,Taxonomic differential analysis in the non-diabetic population with Urinary findings,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Latilactobacillus|s__Latilactobacillus curvatus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella",1783272|1239|91061|186826|33958|2767885|28038;3379134|1224|1236|91347|543|620,Complete,Svetlana up
bsdb:32869063/4/2,32869063,"cross-sectional observational, not case-control",32869063,10.1093/ndt/gfaa122,NA,"Sato N., Kakuta M., Hasegawa T., Yamaguchi R., Uchino E., Murashita K., Nakaji S., Imoto S., Yanagita M. , Okuno Y.",Metagenomic profiling of gut microbiome in early chronic kidney disease,"Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association",2021,"chronic kidney disease, gut microbiome, metagenomics, pathway analysis",Experiment 4,Japan,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Non Chronic Kidney disease (Non-diabetic Population with urinary findings),Chronic Kidney disease (Non-diabetic Population with urinary findings),Patients who have chronic kidney disease in the non-diabetic population with urinary findings,48,24,1 month,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,alcohol drinking,body mass index,diet,hypertension,proton-pump inhibitor,sex,smoking status","age,alcohol drinking,body mass index,diet,hypertension,proton-pump inhibitor,sex,smoking status",NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Text S1,17 October 2025,Temmie,Temmie,Taxonomic differential analysis in the non-diabetic population with Urinary findings,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris",1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|909932;1783272|1239|909932|909929;1783272|1239|186801|3085636|186803|2316020|46228,Complete,Svetlana up
bsdb:32912596/1/1,32912596,case-control,32912596,10.1016/j.jpsychires.2020.06.032,NA,"Ding X, Duan G, Li Z, Song C, Wang X, Wang Y, Xu Y, Yang Y, Zhang L, Zhu C",Gut microbiota changes in patients with autism spectrum disorders,Journal of psychiatric research,2020,"autism spectrum disorder, diagnosis, gut microbiota, gut-brain axis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Healthy children,Children with Autism Spectrum Disorder (ASD),"Diagnosed with Diagnostic and Statistical Manual of Mental Disorders, 5th Edition (DSM-5)",50,77,1 month,16S,4,Illumina,relative abundances,"ANOVA,LEfSe,Metastats,PERMANOVA,T-Test",0.05,NA,4,"age,sex",NA,NA,increased,increased,NA,NA,NA,Signature 1,"Figure 2, Tables S1-S4",10 October 2024,AlishaM,"AlishaM,WikiWorks","Relative abundances at the phylum, class, order, genus and family level in the ASD and HC groups",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales",1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;1783272|1239|186801|3085636|186803|189330;3379134|1224|1236|91347|543;1783272|1239|186801|3085636|186803|1506553;1783272|1239|526524|526525|128827;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|201174|84998;1783272|201174|84998|84999,Complete,NA
bsdb:32912596/1/2,32912596,case-control,32912596,10.1016/j.jpsychires.2020.06.032,NA,"Ding X, Duan G, Li Z, Song C, Wang X, Wang Y, Xu Y, Yang Y, Zhang L, Zhu C",Gut microbiota changes in patients with autism spectrum disorders,Journal of psychiatric research,2020,"autism spectrum disorder, diagnosis, gut microbiota, gut-brain axis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Healthy children,Children with Autism Spectrum Disorder (ASD),"Diagnosed with Diagnostic and Statistical Manual of Mental Disorders, 5th Edition (DSM-5)",50,77,1 month,16S,4,Illumina,relative abundances,"ANOVA,LEfSe,Metastats,PERMANOVA,T-Test",0.05,NA,4,"age,sex",NA,NA,increased,increased,NA,NA,NA,Signature 2,"Figure 2, Tables S1-S4",24 October 2024,AlishaM,"AlishaM,WikiWorks","Relative abundances at the phylum, class, order, genus and family level in the ASD and HC groups",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria",3379134|976|200643|171549|815;3379134|1224|28216|80840|119060;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|216851;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|171552|577309;3379134|1224|1236,Complete,NA
bsdb:32925716/1/1,32925716,prospective cohort,32925716,10.1097/MD.0000000000021788,https://pubmed.ncbi.nlm.nih.gov/32925716/,"Li L. , Ye J.",Characterization of gut microbiota in patients with primary hepatocellular carcinoma received immune checkpoint inhibitors: A Chinese population-based study,Medicine,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,"Patients in the clinical response group treated by immune checkpoint inhibitors therapy (defined by radiographic evidence of complete response, partial response or stable disease per RECIST 1.1 criteria for at least 6 months)",NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 1b,15 July 2022,Sharmilac,"Sharmilac,Fatima,WikiWorks",Compositional differences in the gut microbiome are associated with responses to anti-PD-1 immunotherapy.,increased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__Ruminiclostridium hungatei,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239|186801;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239;1783272|201174|1760|85006|1268;1783272|544448|31969;1783272|1239|186801|186802|216572;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|909932|1843488|909930|33024;1783272|1239|909932|1843488|909930|33024|33025;3379134|976|200643|171549|171551|836|1583331;1783272|201174|1760|85006|1268|32207;1783272|1239|186801|186802|216572|1508657|48256;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|909932|1843489|31977;1783272|1239|186801|186802,Complete,Fatima
bsdb:32925716/1/2,32925716,prospective cohort,32925716,10.1097/MD.0000000000021788,https://pubmed.ncbi.nlm.nih.gov/32925716/,"Li L. , Ye J.",Characterization of gut microbiota in patients with primary hepatocellular carcinoma received immune checkpoint inhibitors: A Chinese population-based study,Medicine,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,"Patients in the clinical response group treated by immune checkpoint inhibitors therapy (defined by radiographic evidence of complete response, partial response or stable disease per RECIST 1.1 criteria for at least 6 months)",NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 1b,21 July 2022,Sharmilac,"Sharmilac,Fatima,WikiWorks",Compositional differences in the gut microbiome are associated with responses to anti-PD-1 immunotherapy.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides mediterraneensis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Oleidesulfovibrio|s__Oleidesulfovibrio alaskensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella",3379134|976|200643|171549;3379134|976;3379134|976|200643;1783272|201174|84998|84999|84107|102106|147206;3379134|976|200643|171549|815|816|1841856;3379134|200940|3031449|213115|194924|2909705|58180;3379134|976|200643|171549|171552|838|470565;1783272|201174|1760|85004|31953|2701|2702;1783272|201174|1760|85004|31953|2701,Complete,Fatima
bsdb:32925716/2/NA,32925716,prospective cohort,32925716,10.1097/MD.0000000000021788,https://pubmed.ncbi.nlm.nih.gov/32925716/,"Li L. , Ye J.",Characterization of gut microbiota in patients with primary hepatocellular carcinoma received immune checkpoint inhibitors: A Chinese population-based study,Medicine,2020,NA,Experiment 2,China,Homo sapiens,Buccal mucosa,UBERON:0006956,Response to immunochemotherapy,EFO:0007754,Non-responders,Responders,"Patients in the clinical response group treated by immune checkpoint inhibitors therapy (defined by radiographic evidence of complete response, partial response or stable disease per RECIST 1.1 criteria for at least 6 months)",NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:32931909/1/1,32931909,case-control,32931909,10.1016/j.anai.2020.09.007,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8043253/,"Chen R., Wang L., Koch T., Curtis V., Yin-DeClue H., Handley S.A., Shan L., Holtzman M.J., Castro M. , Wang L.",Sex effects in the association between airway microbiome and asthma,"Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology",2020,NA,Experiment 1,United States of America,Homo sapiens,Sputum,UBERON:0007311,Asthma,MONDO:0004979,Female,Male,Male participants,32,15,1 month,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 1, Figure 2",12 December 2021,Joyessa,"Joyessa,Claregrieve1,WikiWorks",Differential microbial abundance between men and women,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius",1783272|201174;1783272|1239;1783272|1239|91061|186826|1300|1301|1304,Complete,Claregrieve1
bsdb:32931909/1/2,32931909,case-control,32931909,10.1016/j.anai.2020.09.007,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8043253/,"Chen R., Wang L., Koch T., Curtis V., Yin-DeClue H., Handley S.A., Shan L., Holtzman M.J., Castro M. , Wang L.",Sex effects in the association between airway microbiome and asthma,"Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology",2020,NA,Experiment 1,United States of America,Homo sapiens,Sputum,UBERON:0007311,Asthma,MONDO:0004979,Female,Male,Male participants,32,15,1 month,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 1,14 December 2021,Joyessa,"Joyessa,Claregrieve1,WikiWorks",Differential microbial abundance between men and women,increased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Claregrieve1
bsdb:32931909/2/1,32931909,case-control,32931909,10.1016/j.anai.2020.09.007,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8043253/,"Chen R., Wang L., Koch T., Curtis V., Yin-DeClue H., Handley S.A., Shan L., Holtzman M.J., Castro M. , Wang L.",Sex effects in the association between airway microbiome and asthma,"Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology",2020,NA,Experiment 2,United States of America,Homo sapiens,Sputum,UBERON:0007311,Asthma,MONDO:0004979,Female normal controls,Female participants with asthma,Females participants with asthma,17,15,1 month,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2b,31 August 2022,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between female participants with asthma and female normal controls,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,1783272|1239|91061|186826|1300|1301|1304,Complete,Lwaldron
bsdb:32931909/2/3,32931909,case-control,32931909,10.1016/j.anai.2020.09.007,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8043253/,"Chen R., Wang L., Koch T., Curtis V., Yin-DeClue H., Handley S.A., Shan L., Holtzman M.J., Castro M. , Wang L.",Sex effects in the association between airway microbiome and asthma,"Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology",2020,NA,Experiment 2,United States of America,Homo sapiens,Sputum,UBERON:0007311,Asthma,MONDO:0004979,Female normal controls,Female participants with asthma,Females participants with asthma,17,15,1 month,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 3,Figure 3b,31 August 2022,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between female participants with asthma and female normal controls,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Claregrieve1
bsdb:32931939/1/1,32931939,case-control,32931939,10.1016/j.jtos.2020.09.003,NA,"Andersson J., Vogt J.K., Dalgaard M.D., Pedersen O., Holmgaard K. , Heegaard S.",Ocular surface microbiota in patients with aqueous tear-deficient dry eye,The ocular surface,2021,"16S rRNA gene amplicon sequencing, ADDE, Bacilli class, Bacterial biomarker, Dry eye, Ocular surface microbiota",Experiment 1,Denmark,Homo sapiens,Conjunctival fornix,UBERON:0010307,Dry eye syndrome,EFO:1000906,control,Dry Eye,Patients with Aqueous Deficient Dry Eye without Ocular Graft vs Host Disease,28,21,3 months,16S,34,Illumina,raw counts,DESeq2,0.05,NA,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"Figure 4a,  within result text (Several genera were less abundant in ADDE, lines 8-15)",4 September 2023,Mary Bearkland,"Mary Bearkland,Folakunmi,WikiWorks",Comparison of the relative abundances of genera with DESeq2 between patients with DryEye and Control,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ottowia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|85007|1653|1716;3379134|976|117743|200644|49546|237;3384189|32066|203490|203491|203492|848;3379134|1224|1236|135625|712|724;3379134|1224|28216|80840|75682|149698;1783272|201174|1760|85006|85023|33882;3379134|1224|28216|80840|80864|219181;1783272|201174|1760|85006|1268|32207;3379134|1224|28211|204457|41297|13687;3384194|1297|188787|68933|188786|270;1783272|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:32931939/2/1,32931939,case-control,32931939,10.1016/j.jtos.2020.09.003,NA,"Andersson J., Vogt J.K., Dalgaard M.D., Pedersen O., Holmgaard K. , Heegaard S.",Ocular surface microbiota in patients with aqueous tear-deficient dry eye,The ocular surface,2021,"16S rRNA gene amplicon sequencing, ADDE, Bacilli class, Bacterial biomarker, Dry eye, Ocular surface microbiota",Experiment 2,Denmark,Homo sapiens,Conjunctival fornix,UBERON:0010307,Dry eye syndrome,EFO:1000906,control,OGVHD,"Patients with Aqueous Deficient Dry Eye and Ocular Graft vs Host Disease as diagnosed using the criteria described by the International Chronic Ocular Graft-vs-Host-Disease (GVHD) Consensus.
Group and the patients included were classified as either probable or definite chronic GVHD",28,18,3 months,16S,34,Illumina,raw counts,DESeq2,0.05,NA,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"Figure 4b,  within result text (Several genera were less abundant in ADDE, line 19)",4 September 2023,Mary Bearkland,"Mary Bearkland,Folakunmi,WikiWorks",Comparison of the relative abundances of genera with DESeq2 between patients with OGVHD and Control,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Listeria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",1783272|1239|91061|186826|186828|2747;3379134|976|117743|200644|2762318|501783;1783272|1239|91061|1385|186820|1637;1783272|201174|1760|85006|85023|33882;3379134|1224|1236|72274|135621|286,Complete,Folakunmi
bsdb:32931939/2/2,32931939,case-control,32931939,10.1016/j.jtos.2020.09.003,NA,"Andersson J., Vogt J.K., Dalgaard M.D., Pedersen O., Holmgaard K. , Heegaard S.",Ocular surface microbiota in patients with aqueous tear-deficient dry eye,The ocular surface,2021,"16S rRNA gene amplicon sequencing, ADDE, Bacilli class, Bacterial biomarker, Dry eye, Ocular surface microbiota",Experiment 2,Denmark,Homo sapiens,Conjunctival fornix,UBERON:0010307,Dry eye syndrome,EFO:1000906,control,OGVHD,"Patients with Aqueous Deficient Dry Eye and Ocular Graft vs Host Disease as diagnosed using the criteria described by the International Chronic Ocular Graft-vs-Host-Disease (GVHD) Consensus.
Group and the patients included were classified as either probable or definite chronic GVHD",28,18,3 months,16S,34,Illumina,raw counts,DESeq2,0.05,NA,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,"Figure 4b, within result text (Several genera were less abundant in ADDE, line 20)",4 September 2023,Mary Bearkland,"Mary Bearkland,Folakunmi,WikiWorks",Comparison of the relative abundances of genera with DESeq2 between patients with OGVHD and Control,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,1783272|1239|91061|1385|186817|1386,Complete,Folakunmi
bsdb:32931939/3/1,32931939,case-control,32931939,10.1016/j.jtos.2020.09.003,NA,"Andersson J., Vogt J.K., Dalgaard M.D., Pedersen O., Holmgaard K. , Heegaard S.",Ocular surface microbiota in patients with aqueous tear-deficient dry eye,The ocular surface,2021,"16S rRNA gene amplicon sequencing, ADDE, Bacilli class, Bacterial biomarker, Dry eye, Ocular surface microbiota",Experiment 3,Denmark,Homo sapiens,Conjunctival fornix,UBERON:0010307,Dry eye syndrome,EFO:1000906,control,ADDE,"Patients with Aqueous Deficient Dry Eye including those with and without Ocular Graft vs Host Disease as diagnosed using the criteria described by the International Chronic Ocular Graft-vs-Host-Disease (GVHD) Consensus.
Group and the patients included were classified as either probable or definite chronic GVHD",28,39,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,4 September 2023,Mary Bearkland,"Mary Bearkland,WikiWorks","Fig. 5. Bacterial biomarkers identified with the LEfSe algorithm. A. Circular cladogram displaying the relation between taxa at different taxonomic levels (i.e.
phylum to genus level). Among the enriched bacteria (biomarkers) in aqueous tear-deficient dry eye (ADDE) (red) was Bacilli and for controls (green) was Pseudomonadaceae.
The size of the nodes represents the taxa abundance. B. Scores for linear discriminant analysis (LDA) with LEfSe tool for taxa with LDA score >3 and p
<0.05 are shown in the histogram. Similarly, as the cladogram demonstrated, among the bacterial biomarkers, Pseudomonas was identified for controls and Bacilli
for ADDE.",increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae",1783272|1239|91061;1783272|1239;1783272|201174|1760|85006|85019|1696;3379134|1224|28211|356|212791;3379134|1224|1236|2887326|468;1783272|201174|1760|85006|85019,Complete,Folakunmi
bsdb:32931939/3/2,32931939,case-control,32931939,10.1016/j.jtos.2020.09.003,NA,"Andersson J., Vogt J.K., Dalgaard M.D., Pedersen O., Holmgaard K. , Heegaard S.",Ocular surface microbiota in patients with aqueous tear-deficient dry eye,The ocular surface,2021,"16S rRNA gene amplicon sequencing, ADDE, Bacilli class, Bacterial biomarker, Dry eye, Ocular surface microbiota",Experiment 3,Denmark,Homo sapiens,Conjunctival fornix,UBERON:0010307,Dry eye syndrome,EFO:1000906,control,ADDE,"Patients with Aqueous Deficient Dry Eye including those with and without Ocular Graft vs Host Disease as diagnosed using the criteria described by the International Chronic Ocular Graft-vs-Host-Disease (GVHD) Consensus.
Group and the patients included were classified as either probable or definite chronic GVHD",28,39,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5,4 September 2023,Mary Bearkland,"Mary Bearkland,WikiWorks","Fig. 5. Bacterial biomarkers identified with the LEfSe algorithm. A. Circular cladogram displaying the relation between taxa at different taxonomic levels (i.e.
phylum to genus level). Among the enriched bacteria (biomarkers) in aqueous tear-deficient dry eye (ADDE) (red) was Bacilli and for controls (green) was Pseudomonadaceae.
The size of the nodes represents the taxa abundance. B. Scores for linear discriminant analysis (LDA) with LEfSe tool for taxa with LDA score >3 and p
<0.05 are shown in the histogram. Similarly, as the cladogram demonstrated, among the bacterial biomarkers, Pseudomonas was identified for controls and Bacilli
for ADDE.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae",1783272|1239|91061|186826|186828;1783272|1239|91061|186826|186828|2747;3379134|976|117743|200644|49546;3379134|1224|1236|72274|135621;3379134|1224;3379134|1224|1236|72274|135621|286;1783272|201174|1760|85007;1783272|201174|1760|85007|1653;1783272|201174|1760|85006|1268,Complete,Folakunmi
bsdb:32934117/1/1,32934117,case-control,32934117,10.1128/mSystems.00561-20,https://pubmed.ncbi.nlm.nih.gov/32934117,"Vascellari S., Palmas V., Melis M., Pisanu S., Cusano R., Uva P., Perra D., Madau V., Sarchioto M., Oppo V., Simola N., Morelli M., Santoru M.L., Atzori L., Melis M., Cossu G. , Manzin A.",Gut Microbiota and Metabolome Alterations Associated with Parkinson's Disease,mSystems,2020,"16S RNA, PD, gut microbiota, metabolome",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control,Patients with Parkinson's disease,Patients who have Parkinson's disease,51,64,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Fig 2a,2 April 2023,Atrayees,"Atrayees,WikiWorks",significantly differential taxa between patients with Parkinson's disease and Healthy controls.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfonauticaceae|g__Desulfonauticus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfohalobiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Prosthecobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Acetobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|o__Caldicellulosiruptorales|f__Caldicellulosiruptoraceae|g__Caldicellulosiruptor,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Hymenochaetales|f__Rickenellaceae",3379134|74201|203494;3379134|74201|203494|48461|203557;3379134|74201|203494|48461|1647988|239934;3379134|1224;3379134|1224|1236|91347|543|561;1783272|201174;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|31979|1485;3379134|1224|1236|91347|1903411|613;3379134|200940|3031449|213115|2956789|206664;3379134|200940|3031449|213115|213117;1783272|201174|1760|85006|85023;1783272|201174|84998|84999|84107;3379134|1224|1236|91347|543|547;1783272|201174|84998|1643822|1643826|84108;3379134|74201|203494|48461|203557|48463;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|186806|33951;1783272|1239|186801|3085636|186803|207244;3379134|200940|3031449|213115|194924|872;1783272|1239|3071001|3071002|44000;4751|5204|155619|139380|1124673,Complete,Claregrieve1
bsdb:32934117/1/2,32934117,case-control,32934117,10.1128/mSystems.00561-20,https://pubmed.ncbi.nlm.nih.gov/32934117,"Vascellari S., Palmas V., Melis M., Pisanu S., Cusano R., Uva P., Perra D., Madau V., Sarchioto M., Oppo V., Simola N., Morelli M., Santoru M.L., Atzori L., Melis M., Cossu G. , Manzin A.",Gut Microbiota and Metabolome Alterations Associated with Parkinson's Disease,mSystems,2020,"16S RNA, PD, gut microbiota, metabolome",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control,Patients with Parkinson's disease,Patients who have Parkinson's disease,51,64,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Fig 2b,2 April 2023,Atrayees,"Atrayees,WikiWorks",significantly differential taxa between patients with Parkinson's disease and Healthy controls.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Aphanizomenonaceae|g__Dolichospermum,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Candidatus Blochmanniella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia",3379134|1224|28216|80840|80864;1783272|201174|1760|85006|85019;1783272|1239|186801|3085636|186803|830;1783272|201174|1760|85006|85019|1696;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|3085636|186803|46205;1783272|1117;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3085636|186803|33042;1783272|1117|3028117|1161|1892259|748770;3379134|976|117747|200666|84566;3379134|1224|28216|80840|995019|40544;3379134|1224|28216|80840|506;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|841;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|543|203804;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815;3379134|976|200643,Complete,Claregrieve1
bsdb:32934117/2/1,32934117,case-control,32934117,10.1128/mSystems.00561-20,https://pubmed.ncbi.nlm.nih.gov/32934117,"Vascellari S., Palmas V., Melis M., Pisanu S., Cusano R., Uva P., Perra D., Madau V., Sarchioto M., Oppo V., Simola N., Morelli M., Santoru M.L., Atzori L., Melis M., Cossu G. , Manzin A.",Gut Microbiota and Metabolome Alterations Associated with Parkinson's Disease,mSystems,2020,"16S RNA, PD, gut microbiota, metabolome",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control,Patients with Parkinson's disease,Patients who have Parkinson's disease,51,64,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 2,30 May 2023,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between HCs and PD patients,increased,"k__Bacillati|p__Bacillota|o__Caldicellulosiruptorales|f__Caldicellulosiruptoraceae|g__Caldicellulosiruptor,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Acetobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes",1783272|1239|3071001|3071002|44000;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|186802|31979|1485|1506;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|186806|33951;1783272|1239|186801|3085636|186803|207244,Complete,Claregrieve1
bsdb:32934117/2/2,32934117,case-control,32934117,10.1128/mSystems.00561-20,https://pubmed.ncbi.nlm.nih.gov/32934117,"Vascellari S., Palmas V., Melis M., Pisanu S., Cusano R., Uva P., Perra D., Madau V., Sarchioto M., Oppo V., Simola N., Morelli M., Santoru M.L., Atzori L., Melis M., Cossu G. , Manzin A.",Gut Microbiota and Metabolome Alterations Associated with Parkinson's Disease,mSystems,2020,"16S RNA, PD, gut microbiota, metabolome",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control,Patients with Parkinson's disease,Patients who have Parkinson's disease,51,64,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table 2,30 May 2023,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between HCs and PD patients,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|830;1783272|1239|186801|3085636|186803|841,Complete,Claregrieve1
bsdb:32937864/1/1,32937864,case-control,32937864,https://doi.org/10.3390/cancers12092619,NA,"Gunathilake M., Lee J., Choi I.J., Kim Y.I., Yoon J., Sul W.J., Kim J.F. , Kim J.",Alterations in Gastric Microbial Communities Are Associated with Risk of Gastric Cancer in a Korean Population: A Case-Control Study,Cancers,2020,"case-control, gastric cancer, gastric microbiome, microbial dysbiosis index, pathways",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,healthy controls,gastric cancer patients,"patients with histologically confirmed early gastric cancer (invasive carcinoma confined to the mucosa, regardless of lymph node metastasis status) within the preceding 3 months",288,268,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,decreased,decreased,NA,NA,NA,increased,Signature 1,Figure 2,29 June 2022,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between gastric cancer patients and healthy controls,increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter jejuni,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|29547|3031852|213849|72294|194|197;1783272|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:32937864/1/2,32937864,case-control,32937864,https://doi.org/10.3390/cancers12092619,NA,"Gunathilake M., Lee J., Choi I.J., Kim Y.I., Yoon J., Sul W.J., Kim J.F. , Kim J.",Alterations in Gastric Microbial Communities Are Associated with Risk of Gastric Cancer in a Korean Population: A Case-Control Study,Cancers,2020,"case-control, gastric cancer, gastric microbiome, microbial dysbiosis index, pathways",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,healthy controls,gastric cancer patients,"patients with histologically confirmed early gastric cancer (invasive carcinoma confined to the mucosa, regardless of lymph node metastasis status) within the preceding 3 months",288,268,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,decreased,decreased,NA,NA,NA,increased,Signature 2,Figure 2,29 June 2022,Claregrieve1,"Claregrieve1,Merit,WikiWorks",Differential microbial abundance between gastric cancer patients and healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella taiwanensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.",1783272|1239|91061|1385|539738|1378|1179787;3379134|976|200643|171549|171552|838|28131;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552|838|28133;1783272|1239|91061|186826|1300|1301|1343;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1306,Complete,Claregrieve1
bsdb:32938282/1/1,32938282,case-control,32938282,10.1177/0300060520936806,https://pubmed.ncbi.nlm.nih.gov/32938282/,"Wang Y., Ye X., Ding D. , Lu Y.",Characteristics of the intestinal flora in patients with peripheral neuropathy associated with type 2 diabetes,The Journal of international medical research,2020,"Diabetic peripheral neuropathy, bile acids, blood chemistry, gastrointestinal microbiota, insulin resistance, microbial diversity, richness, type 2 diabetes",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Diabetic neuropathy,EFO:1000783,Healthy controls,Individuals diagnosed with peripheral neuropathy associated with type 2 diabetes,"Individuals diagnosed with peripheral neuropathy associated with type 2 diabetes; The criteria for DPN were as follows: spontaneous limb pain, symmetrical or unilateral limb numbness, sensation of dullness and body tension, muscle weakness, weakened or absent tendon reflexes, and significant decreases in sensory and motor nerve conduction velocities as revealed via electromyography indicating the positive involvement of two or more nerves and normal arterial pulses in the foot and back.",14,45,3 months,16S,34,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure 5a, 5b",24 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1,WikiWorks",Differential abundance of bacterial communities in individuals with diabetic peripheral neuropathy compared with healthy controls,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",1783272|201174;1783272|1239|186801|3085636|186803|572511;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|1940338;1783272|1239;1783272|1239|186801|3085636|186803|1506553;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Claregrieve1
bsdb:32938282/1/2,32938282,case-control,32938282,10.1177/0300060520936806,https://pubmed.ncbi.nlm.nih.gov/32938282/,"Wang Y., Ye X., Ding D. , Lu Y.",Characteristics of the intestinal flora in patients with peripheral neuropathy associated with type 2 diabetes,The Journal of international medical research,2020,"Diabetic peripheral neuropathy, bile acids, blood chemistry, gastrointestinal microbiota, insulin resistance, microbial diversity, richness, type 2 diabetes",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Diabetic neuropathy,EFO:1000783,Healthy controls,Individuals diagnosed with peripheral neuropathy associated with type 2 diabetes,"Individuals diagnosed with peripheral neuropathy associated with type 2 diabetes; The criteria for DPN were as follows: spontaneous limb pain, symmetrical or unilateral limb numbness, sensation of dullness and body tension, muscle weakness, weakened or absent tendon reflexes, and significant decreases in sensory and motor nerve conduction velocities as revealed via electromyography indicating the positive involvement of two or more nerves and normal arterial pulses in the foot and back.",14,45,3 months,16S,34,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 5a, 5b",24 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1,WikiWorks",Differential abundance of bacterial communities in individuals with diabetic peripheral neuropathy compared with healthy controls,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",3379134|976|200643|171549|815|816;3379134|976;1783272|1239|186801|186802|216572|216851,Complete,Claregrieve1
bsdb:32938282/2/NA,32938282,case-control,32938282,10.1177/0300060520936806,https://pubmed.ncbi.nlm.nih.gov/32938282/,"Wang Y., Ye X., Ding D. , Lu Y.",Characteristics of the intestinal flora in patients with peripheral neuropathy associated with type 2 diabetes,The Journal of international medical research,2020,"Diabetic peripheral neuropathy, bile acids, blood chemistry, gastrointestinal microbiota, insulin resistance, microbial diversity, richness, type 2 diabetes",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Diabetic neuropathy,EFO:1000783,Individuals diagnosed with type 2 diabetes Mellitus,Individuals diagnosed with peripheral neuropathy associated with type 2 diabetes,"Patients with peripheral neuropathy associated with type 2 diabetes; the criteria for DPN were as follows: spontaneous limb pain, symmetrical or unilateral limb numbness, sensation of dullness and body tension, muscle weakness, weakened or absent tendon reflexes, and significant decreases in sensory and motor nerve conduction velocities as revealed via electromyography indicating the positive involvement of two or more nerves and normal arterial pulses in the foot and back.",21,45,3 months,16S,34,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,increased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:32941440/1/1,32941440,"cross-sectional observational, not case-control",32941440,10.1371/journal.pone.0238705,NA,"So K.A., Yang E.J., Kim N.R., Hong S.R., Lee J.H., Hwang C.S., Shim S.H., Lee S.J. , Kim T.J.",Changes of vaginal microbiota during cervical carcinogenesis in women with human papillomavirus infection,PloS one,2020,NA,Experiment 1,South Korea,Homo sapiens,Vaginal fluid,UBERON:0036243,Cervical glandular intraepithelial neoplasia,EFO:1000165,healthy controls,CIN2+/cervical cancer,patients with cervical intraepithelial neoplasia 2+ or cervical cancer confirmed by biopsy,10,20,NA,16S,34,Illumina,NA,Chi-Square,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 2,21 March 2021,Cynthia Anderson,"Cynthia Anderson,Claregrieve1,WikiWorks",Differential microbial abundance between healthy controls and patients with cervical disease with CIN 2 or 3 and cervical cancer,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis",1783272|1239|909932|1843489|31977|39948|218538;1783272|201174|84998|84999|1643824|2767327|82135;1783272|1239|1737404|1737405|1570339|150022|1260;1783272|201174|1760|85004|31953|2701|2702;3379134|976|200643|171549|171552|2974257|28127;3379134|976|200643|171549|171552|2974257|386414,Complete,Claregrieve1
bsdb:32958790/1/1,32958790,"cross-sectional observational, not case-control",32958790,10.1038/s41598-020-72035-1,https://pubmed.ncbi.nlm.nih.gov/32958790/,"Sun X., Li M., Xia L., Fang Z., Yu S., Gao J., Feng Q. , Yang P.",Alteration of salivary microbiome in periodontitis with or without type-2 diabetes mellitus and metformin treatment,Scientific reports,2020,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Periodontitis,EFO:0000649,Healthy controls group,Individuals diagnosed with Periodontitis group,"Individuals with Peridontitis; Periodontal disease was assessed by determining the PD, CAL, BI, GI, and PLI, which were then measured at six sites (i.e., mesiobuccal, buccal, distobuccal, distolingual, lingual, and mesiolingual) according to the Community Periodontal Index by an experienced dentist. Periodontitis patients had a PD of ≥ 5 mm and CAL of ≥ 3 mm.",27,31,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,increased,NA,NA,Signature 1,"Figure 3, text",22 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1,WikiWorks",Increased abundance of bacterial species in individuals with Periodontitis as compared to healthy controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema medium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|171552|2974251|165179;3379134|203691|203692|136|2845253|157|58231;3379134|976|200643|171549|171552|1283313|671218;3379134|1224|28216|80840|995019|40544;3379134|203691|203692|136|2845253|157|59892;1783272|1239|186801|186802|216572|216851|853,Complete,Claregrieve1
bsdb:32958790/2/1,32958790,"cross-sectional observational, not case-control",32958790,10.1038/s41598-020-72035-1,https://pubmed.ncbi.nlm.nih.gov/32958790/,"Sun X., Li M., Xia L., Fang Z., Yu S., Gao J., Feng Q. , Yang P.",Alteration of salivary microbiome in periodontitis with or without type-2 diabetes mellitus and metformin treatment,Scientific reports,2020,NA,Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Periodontitis,EFO:0000649,Healthy controls,Individuals diagnosed with Periodontitis and Type 2 Diabetes Mellitus (DAP),Individuals diagnosed with Periodontitis and Type 2 Diabetes Mellitus (DAP); Patients were classified into the DAP group when both periodontitis and T2DM were present.,27,46,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,increased,NA,NA,Signature 1,Supplementary Fig 3a,27 June 2021,Madhubani Dey,"Madhubani Dey,WikiWorks",Increased abundance of bacterial communities in individuals in DAP group compared to healthy controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia pickettii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella stercoricanis",3379134|976|200643|171549|171552|1283313|671218;3379134|976|200643|171549|171552|2974251|165179;3379134|1224|28216|80840|119060|48736|329;3379134|1224|28216|80840|995019|40544|234908,Complete,Claregrieve1
bsdb:32958790/4/1,32958790,"cross-sectional observational, not case-control",32958790,10.1038/s41598-020-72035-1,https://pubmed.ncbi.nlm.nih.gov/32958790/,"Sun X., Li M., Xia L., Fang Z., Yu S., Gao J., Feng Q. , Yang P.",Alteration of salivary microbiome in periodontitis with or without type-2 diabetes mellitus and metformin treatment,Scientific reports,2020,NA,Experiment 4,China,Homo sapiens,Saliva,UBERON:0001836,Periodontitis,EFO:0000649,Healthy controls,Individuals diagnosed with both Periodontitis and Type 2 Diabetes and treated with metformin (Met group),"Patients with both Periodontitis and Type 2 Diabetes who received metformin for at least 6 months and achieved glycemic control (HbA1c < 6.5%, without any companion diseases), were classified into the Met group",27,20,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Supplementary Fig 3b,27 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1,WikiWorks",Increased abundance of microbial communities in individuals in Met group compared to the controls,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella jejuni,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema medium",1783272|1239|1737404|1737405|1570339|543311|33033;1783272|1239|186801|3082720|186804|1257|341694;3379134|976|200643|171549|171552|838|28129;3379134|976|200643|171549|171552|838|1177574;3379134|976|200643|171549|171552|838|60133;3379134|976|200643|171549|171552|2974251|228604;1783272|1239|526524|526525|128827|123375|102148;3379134|203691|203692|136|2845253|157|59892;3379134|203691|203692|136|2845253|157|58231,Complete,Claregrieve1
bsdb:32958790/5/1,32958790,"cross-sectional observational, not case-control",32958790,10.1038/s41598-020-72035-1,https://pubmed.ncbi.nlm.nih.gov/32958790/,"Sun X., Li M., Xia L., Fang Z., Yu S., Gao J., Feng Q. , Yang P.",Alteration of salivary microbiome in periodontitis with or without type-2 diabetes mellitus and metformin treatment,Scientific reports,2020,NA,Experiment 5,China,Homo sapiens,Saliva,UBERON:0001836,Periodontitis,EFO:0000649,Individuals diagnosed with Periodontitis and Type 2 Diabetes Mellitus (DAP),Individuals diagnosed with both Periodontitis and Type 2 Diabetes and treated with metformin (Met group),"Patients with both Periodontitis and Type 2 Diabetes who received metformin for at least 6 months and achieved glycemic control (HbA1c < 6.5%, without any companion diseases), were classified into the Met group",46,20,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 5c, 5d",27 June 2021,Madhubani Dey,"Madhubani Dey,WikiWorks",Decreased abundance of bacterial communities in Met group compared to DAP group,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium|s__Phyllobacterium myrsinacearum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia pickettii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella stercoricanis",3379134|976|200643|171549|171552|1283313|671218;3379134|1224|28211|356|69277|28100|28101;3379134|976|200643|171549|171552|2974251|165179;3379134|1224|28216|80840|119060|48736|329;3379134|1224|28216|80840|995019|40544|234908,Complete,Claregrieve1
bsdb:32958790/5/2,32958790,"cross-sectional observational, not case-control",32958790,10.1038/s41598-020-72035-1,https://pubmed.ncbi.nlm.nih.gov/32958790/,"Sun X., Li M., Xia L., Fang Z., Yu S., Gao J., Feng Q. , Yang P.",Alteration of salivary microbiome in periodontitis with or without type-2 diabetes mellitus and metformin treatment,Scientific reports,2020,NA,Experiment 5,China,Homo sapiens,Saliva,UBERON:0001836,Periodontitis,EFO:0000649,Individuals diagnosed with Periodontitis and Type 2 Diabetes Mellitus (DAP),Individuals diagnosed with both Periodontitis and Type 2 Diabetes and treated with metformin (Met group),"Patients with both Periodontitis and Type 2 Diabetes who received metformin for at least 6 months and achieved glycemic control (HbA1c < 6.5%, without any companion diseases), were classified into the Met group",46,20,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 5c, 5d",27 June 2021,Madhubani Dey,"Madhubani Dey,WikiWorks",Increased abundance of bacterial communities in individuals of Met group compared to DAP group,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella jejuni,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus|s__Streptobacillus moniliformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans",3379134|976|200643|171549|171552|838|1177574;3384189|32066|203490|203491|1129771|34104|34105;1783272|1239|91061|186826|1300|1301|1309,Complete,Claregrieve1
bsdb:32973805/1/1,32973805,prospective cohort,32973805,10.3389/fimmu.2020.01994,NA,"Xu R., Tan C., He Y., Wu Q., Wang H. , Yin J.",Dysbiosis of Gut Microbiota and Short-Chain Fatty Acids in Encephalitis: A Chinese Pilot Study,Frontiers in immunology,2020,"dysbiosis, encephalitis, gut microbiome, intestinal barrier, short-chain fatty acids",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Encephalitis,MONDO:0019956,healthy controls (CON),Encephalitis (ENC),Patients who suffered from brain inflammation (encephalitis),28,28,12 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,FIG 1 (G),16 October 2024,Rahila,"Rahila,Aleru Divine,WikiWorks",Cladogram based on LEfSe results of the encephalitis patients (ENC) and healthy subjects serving as controls (CON).,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Chroococcales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Pleurocapsales|f__Xenococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales",1783272|1239|91061;1783272|1239|186801|3082768|990719;1783272|1117|3028117|1118;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;3379134|1224|1236;1783272|1239|91061|186826;1783272|1117|3028117;3379134|976|200643|171549|171551;3379134|1224|1236|72274;3379134|976|200643|171549|171550;3379134|74201|203494|48461|203557;3379134|74201|203494|48461;3379134|74201|203494;1783272|1117|3028117|52604|1890499;3379134|1224|1236|91347,Complete,Svetlana up
bsdb:32973805/1/2,32973805,prospective cohort,32973805,10.3389/fimmu.2020.01994,NA,"Xu R., Tan C., He Y., Wu Q., Wang H. , Yin J.",Dysbiosis of Gut Microbiota and Short-Chain Fatty Acids in Encephalitis: A Chinese Pilot Study,Frontiers in immunology,2020,"dysbiosis, encephalitis, gut microbiome, intestinal barrier, short-chain fatty acids",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Encephalitis,MONDO:0019956,healthy controls (CON),Encephalitis (ENC),Patients who suffered from brain inflammation (encephalitis),28,28,12 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,FIG 1 (G),16 October 2024,Rahila,"Rahila,WikiWorks",Cladogram based on LEfSe results of the encephalitis patients (ENC) and healthy subjects serving as controls (CON).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria",3379134|976|200643|171549|171552;1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|186803;1783272|1239|909932|1843489|31977;3379134|1224|28216|80840|506;3379134|1224|28216|80840;3379134|1224|28216,Complete,Svetlana up
bsdb:32973805/2/1,32973805,prospective cohort,32973805,10.3389/fimmu.2020.01994,NA,"Xu R., Tan C., He Y., Wu Q., Wang H. , Yin J.",Dysbiosis of Gut Microbiota and Short-Chain Fatty Acids in Encephalitis: A Chinese Pilot Study,Frontiers in immunology,2020,"dysbiosis, encephalitis, gut microbiome, intestinal barrier, short-chain fatty acids",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Encephalitis,MONDO:0019956,healthy controls (CON),Encephalitis (ENC),Patients who suffered from brain inflammation (encephalitis),28,28,Antibiotics use in the last year prior to sample collection.,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 2.,17 October 2024,Rahila,"Rahila,Aleru Divine,WikiWorks",Significantly discriminative taxa between the twenty-eight Encephalitis patients and healthy subjects determined by Mann-Whitney U tests.,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",1783272|1239|91061;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|526524|526525;3379134|1224|1236;1783272|1239|91061|186826;3379134|976|200643|171549|2005473;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;3379134|1224;3379134|976|200643|171549|171550,Complete,Svetlana up
bsdb:32973805/2/2,32973805,prospective cohort,32973805,10.3389/fimmu.2020.01994,NA,"Xu R., Tan C., He Y., Wu Q., Wang H. , Yin J.",Dysbiosis of Gut Microbiota and Short-Chain Fatty Acids in Encephalitis: A Chinese Pilot Study,Frontiers in immunology,2020,"dysbiosis, encephalitis, gut microbiome, intestinal barrier, short-chain fatty acids",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Encephalitis,MONDO:0019956,healthy controls (CON),Encephalitis (ENC),Patients who suffered from brain inflammation (encephalitis),28,28,Antibiotics use in the last year prior to sample collection.,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table 2.,17 October 2024,Rahila,"Rahila,Aleru Divine,WikiWorks",Significantly discriminative taxa between the twenty-eight Encephalitis patients and healthy subjects determined by Mann-Whitney U tests.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|1224|28216;3379134|1224|28216|80840;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|1263;3379134|1224|28216|80840|995019|40544,Complete,Svetlana up
bsdb:32987006/3/1,32987006,laboratory experiment,32987006,https://doi.org/10.1016/j.envres.2020.110245,NA,"Gust K.A., Indest K.J., Lotufo G., Everman S.J., Jung C.M., Ballentine M.L., Hoke A.V., Sowe B., Gautam A., Hammamieh R., Ji Q. , Barker N.D.",Genomic investigations of acute munitions exposures on the health and skin microbiome composition of leopard frog (Rana pipiens) tadpoles,Environmental research,2021,"Amphibian health, Amphibian skin microbiome, Aquatic ecotoxicology, Munitions constituents, Transcript expression",Experiment 3,United States of America,Rana pipiens,Tadpole,UBERON:0002547,Environmental exposure measurement,EFO:0008360,Control group,Tadpoles exposed to 3560 mg/L Nitroguanidine (NQ),Tadpoles were exposed to the concentration of 3560 mg/L of Nitroguanidine (NQ) for 96 hours.,4,4,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,7 March 2024,Victoria,"Victoria,ChiomaBlessing,WikiWorks",LEfSe-identified significant taxa in the NQ exposed group compared to the control group,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae",3379134|1224|1236|135624|84642;3379134|1224|1236|135624;3379134|1224|28216|80840|80864;3379134|1224|1236;3379134|1224|1236|72274|135621;3379134|1224|1236|135622|267890,Complete,ChiomaBlessing
bsdb:32987006/3/2,32987006,laboratory experiment,32987006,https://doi.org/10.1016/j.envres.2020.110245,NA,"Gust K.A., Indest K.J., Lotufo G., Everman S.J., Jung C.M., Ballentine M.L., Hoke A.V., Sowe B., Gautam A., Hammamieh R., Ji Q. , Barker N.D.",Genomic investigations of acute munitions exposures on the health and skin microbiome composition of leopard frog (Rana pipiens) tadpoles,Environmental research,2021,"Amphibian health, Amphibian skin microbiome, Aquatic ecotoxicology, Munitions constituents, Transcript expression",Experiment 3,United States of America,Rana pipiens,Tadpole,UBERON:0002547,Environmental exposure measurement,EFO:0008360,Control group,Tadpoles exposed to 3560 mg/L Nitroguanidine (NQ),Tadpoles were exposed to the concentration of 3560 mg/L of Nitroguanidine (NQ) for 96 hours.,4,4,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6,7 March 2024,Victoria,"Victoria,ChiomaBlessing,WikiWorks",LEfSe-identified significant taxa in the NQ exposed group compared to the control group,decreased,"k__Pseudomonadati|p__Acidobacteriota,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Acidobacteriota|c__Terriglobia|o__Bryobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Chloroflexota,k__Pseudomonadati|p__Verrucomicrobiota|c__Spartobacteria|o__Chthoniobacterales|f__Chthoniobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Planctomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Pseudomonadati|p__Acidobacteriota|c__Terriglobia|o__Bryobacterales|f__Solibacteraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Spartobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Acidobacteriota|c__Terriglobia|o__Terriglobales,k__Pseudomonadati|p__Acidobacteriota|c__Terriglobia,k__Bacillati|p__Actinomycetota|c__Thermoleophilia,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Verrucomicrobiota|c__Spartobacteria|o__Chthoniobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae",3379134|57723;1783272|201174;3379134|1224|28211;1783272|1239|91061|1385|186817;1783272|1239|91061|1385;1783272|1239|91061;1783272|1239;3379134|57723|204432|332160;3379134|1224|28216|80840;1783272|200795;3379134|74201|134549|1836787|1836792;3379134|1224|28211|356|45401;3379134|1224|28211|356;3379134|1224|28216|80840|75682;3379134|203682;3379134|1224|28211|204441;3379134|57723|204432|332160|332161;3379134|74201|134549;3379134|1224|28211|204457|41297;3379134|1224|28211|204457;3379134|57723|204432|204433;3379134|57723|204432;1783272|201174|1497346;3379134|74201;3379134|74201|134549|1836787;3379134|1224|28216|80840|119060,Complete,ChiomaBlessing
bsdb:33013704/1/1,33013704,case-control,33013704,10.3389/fendo.2020.00628,NA,"Zhou L., Ni Z., Yu J., Cheng W., Cai Z. , Yu C.",Correlation Between Fecal Metabolomics and Gut Microbiota in Obesity and Polycystic Ovary Syndrome,Frontiers in endocrinology,2020,"biomarkers, gut microbiota, obesity, polycystic ovary syndrome, untargeted metabolomics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Obese women without PCOS,Obese women with PCOS,Obese women with PCOS,15,18,3 months,16S,NA,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,"age,body mass index",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3(G),6 July 2023,Atrayees,"Atrayees,Peace Sandy,WikiWorks","LDA chart. The score was obtained by LDA analysis (linear regression analysis). The greater the LDA score, the greater the impact of the representative species abundance on the differences between groups. *p < 0.05; **p < 0.01.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",1783272|1239|186801|3085636|186803|33042;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|1506577,Complete,Peace Sandy
bsdb:33013704/1/2,33013704,case-control,33013704,10.3389/fendo.2020.00628,NA,"Zhou L., Ni Z., Yu J., Cheng W., Cai Z. , Yu C.",Correlation Between Fecal Metabolomics and Gut Microbiota in Obesity and Polycystic Ovary Syndrome,Frontiers in endocrinology,2020,"biomarkers, gut microbiota, obesity, polycystic ovary syndrome, untargeted metabolomics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Obese women without PCOS,Obese women with PCOS,Obese women with PCOS,15,18,3 months,16S,NA,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,"age,body mass index",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3(G),6 July 2023,Atrayees,"Atrayees,Peace Sandy,WikiWorks","LDA chart. The score was obtained by LDA analysis (linear regression analysis). The greater the LDA score, the greater the impact of the representative species abundance on the differences between groups. *p < 0.05; **p < 0.01.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|3082768|990719;3379134|1224|28216|80840|80864|283;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|1185407;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|1892380;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|3085636|186803;1783272|544448|31969;1783272|544448;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|186807;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|186802|216572|3068309;1783272|1239|526524|526525|128827|123375;1783272|1239|186801|186802|216572|292632;3379134|976|200643|171549;3379134|976|200643|171549,Complete,Peace Sandy
bsdb:33046129/1/1,33046129,laboratory experiment,33046129,10.1186/s13073-020-00784-9,NA,"Binyamin D., Werbner N., Nuriel-Ohayon M., Uzan A., Mor H., Abbas A., Ziv O., Teperino R., Gutman R. , Koren O.",The aging mouse microbiome has obesogenic characteristics,Genome medicine,2020,"Aging, Fecal microbiota transplantation, Metabolism, Microbiome",Experiment 1,Israel,Mus musculus,"Feces,Blood vessel","UBERON:0001981,UBERON:0001988",Body weight,EFO:0004338,Adult,Aging,Aging Mice,42,32,NA,16S,4,Illumina,relative abundances,PERMANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,18 October 2023,Greatman,"Greatman,LGeistlinger,Peace Sandy,WikiWorks","Genera that differed significantly between adult and aged mice. Analysis of microbiome composition (ANCOM) revealed 6 genera a Dehalobacterium, b unspecified Peptococcaceae, c Sutterella, d unspecified Desulfovibrionaceae, and e Bilophila, with significantly different relative abundance in adult versus aged mice",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",1783272|1239|186801|186802|186807|51514;1783272|1239|186801|186802|186807;3379134|1224|28216|80840|995019|40544;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115|194924|35832,Complete,LGeistlinger
bsdb:33046129/2/1,33046129,laboratory experiment,33046129,10.1186/s13073-020-00784-9,NA,"Binyamin D., Werbner N., Nuriel-Ohayon M., Uzan A., Mor H., Abbas A., Ziv O., Teperino R., Gutman R. , Koren O.",The aging mouse microbiome has obesogenic characteristics,Genome medicine,2020,"Aging, Fecal microbiota transplantation, Metabolism, Microbiome",Experiment 2,Israel,Mus musculus,"Feces,Blood vessel","UBERON:0001981,UBERON:0001988",Body fat percentage,EFO:0007800,low body fat percentage,high body fat percentage,High body fat adult and aged mice,32,13,NA,16S,4,Illumina,relative abundances,PERMANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5b,11 November 2023,LGeistlinger,"LGeistlinger,WikiWorks",Bacteria that are associated with fat/lean percent mass in both adult and aged mice,increased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,1783272|1239|526524|526525|2810281|191303,Complete,LGeistlinger
bsdb:33046129/3/1,33046129,laboratory experiment,33046129,10.1186/s13073-020-00784-9,NA,"Binyamin D., Werbner N., Nuriel-Ohayon M., Uzan A., Mor H., Abbas A., Ziv O., Teperino R., Gutman R. , Koren O.",The aging mouse microbiome has obesogenic characteristics,Genome medicine,2020,"Aging, Fecal microbiota transplantation, Metabolism, Microbiome",Experiment 3,Israel,Mus musculus,"Feces,Blood vessel","UBERON:0001988,UBERON:0001981",Body weight,EFO:0004338,Less weight,Higher weight,Mice with Higher Body Weight,13,32,NA,16S,4,Illumina,relative abundances,PERMANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 5,20 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","Bacteria that are associated with weight and fat/lean percent mass in both adult and aged mice. Taxa abundance is represented by color scale. a Three genera Bifidobacterium, Clostridium, and Sutterella were significantly correlated with weight.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|31979|1485;3379134|1224|28216|80840|995019|40544,Complete,Peace Sandy
bsdb:33050883/1/1,33050883,case-control,33050883,10.1186/s12866-020-01938-w,NA,"Zhang Q., Zhao H., Wu D., Cao D. , Ma W.",A comprehensive analysis of the microbiota composition and gene expression in colorectal cancer,BMC microbiology,2020,"Colorectal cancer, Gene expression, Gut microflora, Pathways enrichment, Survival analysis",Experiment 1,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,Control,CRC,Tumor specimens taken from patients with colorectal cancer,19,19,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Text,1 August 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between CRC and control samples,increased,"k__Bacillati|p__Actinomycetota,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",1783272|201174;3384189|32066;3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511,Complete,Claregrieve1
bsdb:33050883/1/2,33050883,case-control,33050883,10.1186/s12866-020-01938-w,NA,"Zhang Q., Zhao H., Wu D., Cao D. , Ma W.",A comprehensive analysis of the microbiota composition and gene expression in colorectal cancer,BMC microbiology,2020,"Colorectal cancer, Gene expression, Gut microflora, Pathways enrichment, Survival analysis",Experiment 1,China,Homo sapiens,Intestine,UBERON:0000160,Colorectal cancer,EFO:0005842,Control,CRC,Tumor specimens taken from patients with colorectal cancer,19,19,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Text,1 August 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between CRC and control samples,decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota",1783272|1239;3379134|1224,Complete,Claregrieve1
bsdb:33052235/1/1,33052235,"cross-sectional observational, not case-control",33052235,10.7150/thno.49515,NA,"Zhang S., Kong C., Yang Y., Cai S., Li X., Cai G. , Ma Y.",Human oral microbiome dysbiosis as a novel non-invasive biomarker in detection of colorectal cancer,Theranostics,2020,"16S rRNA, colorectal adenomas, colorectal cancers, oral microbiome",Experiment 1,China,Homo sapiens,Oral cavity,UBERON:0000167,Colorectal cancer,EFO:0005842,Healthy Individuals,CRC,Patients with colorectal cancer,58,161,NA,16S,34,Illumina,NA,Welch's T-Test,0.05,TRUE,NA,NA,"age,alcohol drinking,body mass index,sex,smoking status",NA,increased,unchanged,increased,NA,NA,Signature 1,Table S9 / Figure S1F,22 June 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between CRC cohort and controls,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Spartobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Thermoactinomycetaceae|g__Thermoflavimicrobium",1783272|1239|1737404|1737405|1570339|165779;1783272|1239|186801|3085636|186803|207244;1783272|201174|1760|85006|85020|43668;3379134|1224|28211|356|41294|374;3379134|976|117743|200644|2762318|501783;1783272|1117;1783272|1239|91061|1385|539738|1378;1783272|201174|1760|85006|1268|1269;3379134|1224|28216|206351|481|482;3379134|1224|1236|91347|1903409|53335;3379134|1224|1236|72274|135621|286;3379134|1224|1236|2887326|468|497;3379134|74201|134549;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|1385|186824|292636,Complete,Claregrieve1
bsdb:33052235/1/2,33052235,"cross-sectional observational, not case-control",33052235,10.7150/thno.49515,NA,"Zhang S., Kong C., Yang Y., Cai S., Li X., Cai G. , Ma Y.",Human oral microbiome dysbiosis as a novel non-invasive biomarker in detection of colorectal cancer,Theranostics,2020,"16S rRNA, colorectal adenomas, colorectal cancers, oral microbiome",Experiment 1,China,Homo sapiens,Oral cavity,UBERON:0000167,Colorectal cancer,EFO:0005842,Healthy Individuals,CRC,Patients with colorectal cancer,58,161,NA,16S,34,Illumina,NA,Welch's T-Test,0.05,TRUE,NA,NA,"age,alcohol drinking,body mass index,sex,smoking status",NA,increased,unchanged,increased,NA,NA,Signature 2,Table S9,22 June 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between CRC cohort and controls,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Actinomycetota,p__Candidatus Saccharimonadota,k__Pseudomonadati|p__Spirochaetota,k__Thermotogati|p__Synergistota,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter",3379134|976;3384189|32066;1783272|201174;95818;3379134|203691;3384194|508458;1783272|1117;1783272|1239|909932|1843489|31977|29465;1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549|171552|838;3384189|32066|203490|203491|203492|848;3379134|1224|1236|135614|32033|68,Complete,Claregrieve1
bsdb:33052235/2/1,33052235,"cross-sectional observational, not case-control",33052235,10.7150/thno.49515,NA,"Zhang S., Kong C., Yang Y., Cai S., Li X., Cai G. , Ma Y.",Human oral microbiome dysbiosis as a novel non-invasive biomarker in detection of colorectal cancer,Theranostics,2020,"16S rRNA, colorectal adenomas, colorectal cancers, oral microbiome",Experiment 2,China,Homo sapiens,Oral cavity,UBERON:0000167,Colorectal adenoma,EFO:0005406,Healthy Individuals,CRA,Patients with colorectal adenoma,58,34,NA,16S,34,Illumina,NA,Welch's T-Test,0.05,TRUE,NA,NA,"age,alcohol drinking,body mass index,sex,smoking status",NA,increased,unchanged,increased,NA,NA,Signature 1,Table S6-7,22 June 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between CRA cohort and controls,increased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Acidobacteriota,k__Pseudomonadati|p__Gemmatimonadota|c__Gemmatimonadia,k__Pseudomonadati|p__Nitrospirota|c__Nitrospiria|o__Nitrospirales|f__Nitrospiraceae|g__Nitrospira,k__Bacillati|p__Chloroflexota,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Gemmatimonadota|c__Gemmatimonadia|o__Gemmatimonadales|f__Gemmatimonadaceae|g__Gemmatimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Pseudomonadati|p__Verrucomicrobiota|c__Spartobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas",1783272|1239;3379134|57723;3379134|142182|219685;3379134|40117|203693|189778|189779|1234;1783272|200795;3379134|74201;1783272|1239|91061|186826|1300|1301;1783272|1117;1783272|1239|91061|1385|539738|1378;3379134|142182|219685|219686|219687|173479;1783272|1239|186801|186802|204475;3379134|74201|134549;3379134|1224|28211|356|41294|374;1783272|201174|1760|85006|85020|43668;1783272|201174|1760|85006|85021;3379134|1224|1236|135614|32033|338,Complete,Claregrieve1
bsdb:33052235/2/2,33052235,"cross-sectional observational, not case-control",33052235,10.7150/thno.49515,NA,"Zhang S., Kong C., Yang Y., Cai S., Li X., Cai G. , Ma Y.",Human oral microbiome dysbiosis as a novel non-invasive biomarker in detection of colorectal cancer,Theranostics,2020,"16S rRNA, colorectal adenomas, colorectal cancers, oral microbiome",Experiment 2,China,Homo sapiens,Oral cavity,UBERON:0000167,Colorectal adenoma,EFO:0005406,Healthy Individuals,CRA,Patients with colorectal adenoma,58,34,NA,16S,34,Illumina,NA,Welch's T-Test,0.05,TRUE,NA,NA,"age,alcohol drinking,body mass index,sex,smoking status",NA,increased,unchanged,increased,NA,NA,Signature 2,Table S6-7,22 June 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between CRA cohort and controls,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Aestuariicoccus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Anoxybacillus,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,p__Candidatus Saccharimonadota,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Diaphorobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Viridiplantae|p__Streptophyta,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas,p__Candidatus Saccharimonadota,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter sp.,k__Pseudomonadati|p__Bacteroidota,k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Spirochaetota,k__Bacillati|p__Actinomycetota,k__Thermotogati|p__Synergistota,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Pseudomonadota",1783272|201174|1760|2037|2049|1654;3379134|1224|28211|204455|31989|2054427;3379134|1224|1236|135625|712|416916;3379134|976|200643|171549|171552|1283313;1783272|1239|909932|1843489|31977|156454;1783272|1239|186801|3082720|543314|109326;1783272|1239|91061|1385|3120669|150247;1783272|544448|31969|186332|186333|2152;1783272|201174|84998|84999|1643824|1380;1783272|1239|186801|3085636|186803|830;3379134|29547|3031852|213849|72294|194;95818;3379134|976|117743|200644|49546|1016;1783272|201174|1760|85007|1653|1716;1783272|1239|909932|1843489|31977|39948;3379134|1224|28216|80840|80864|238749;1783272|1239|526524|526525|2810280|1279384;1783272|1239|186801|186802|186806|1730;1783272|1239;3384194|508458|649775|649776|3029087|1434006;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|1164882;3384189|32066|203490|203491|1129771|32067;3379134|1224|1236|135614|32033|68;1783272|544448|31969|2085|2092|2093;3379134|1224|28216|206351|481|482;1783272|1239|186801|3085636|186803|265975;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1257;3379134|1224|28211|356|69277|28100;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|201174|1760|85009|31957;1783272|201174|1760|85009|31957|1743;1783272|1239|526524|526525|128827|123375;1783272|1239|186801|3085636|186803|1213720;33090|35493;3379134|976|200643|171549|2005525|195950;3379134|203691|203692|136|2845253|157;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|135614|32033|338;95818;3379134|29547|3031852|213849|72294|194|205;3379134|976;3384189|32066;1783272|1117;3379134|203691;1783272|201174;3384194|508458;1783272|544448;3379134|1224,Complete,Claregrieve1
bsdb:33052235/3/1,33052235,"cross-sectional observational, not case-control",33052235,10.7150/thno.49515,NA,"Zhang S., Kong C., Yang Y., Cai S., Li X., Cai G. , Ma Y.",Human oral microbiome dysbiosis as a novel non-invasive biomarker in detection of colorectal cancer,Theranostics,2020,"16S rRNA, colorectal adenomas, colorectal cancers, oral microbiome",Experiment 3,China,Homo sapiens,Oral cavity,UBERON:0000167,Colorectal cancer,EFO:0005842,CRA,CRC,Patients with colorectal cancer,34,161,NA,16S,34,Illumina,NA,Welch's T-Test,0.05,TRUE,NA,NA,"age,alcohol drinking,body mass index,sex,smoking status",NA,increased,unchanged,increased,NA,NA,Signature 1,Table S4-5,22 June 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between CRC and CRA groups,decreased,"k__Pseudomonadati|p__Bacteroidota,p__Candidatus Saccharimonadota,k__Pseudomonadati|p__Pseudomonadota,k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Diaphorobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Brachymonas,p__Candidatus Saccharimonadota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Formosa",3379134|976;95818;3379134|1224;3384189|32066;3379134|976|200643|171549|171551|836;3379134|1224|28216|80840|80864|238749;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|838;3379134|1224|28211|356|69277|28100;3379134|1224|28216|80840|80864|283;1783272|1239|526524|526525|128827|123375;1783272|1239|1737404|1737405|1570339|165779;3379134|976|117743|200644|49546|1016;1783272|1239|186801|3082720|186804|1257;3384189|32066|203490|203491|203492|848;3379134|1224|1236|135625|712|416916;3379134|1224|28216|80840|80864|28219;95818;3379134|1224|28211;1783272|1239|1737404|1737405|1570339|543311;3379134|976|117743|200644|2762318|501783;3379134|29547|3031852|213849|72294|194;1783272|1239|186801|186802|186806|1730;3379134|976|117743|200644|49546|225842,Complete,Claregrieve1
bsdb:33052235/3/2,33052235,"cross-sectional observational, not case-control",33052235,10.7150/thno.49515,NA,"Zhang S., Kong C., Yang Y., Cai S., Li X., Cai G. , Ma Y.",Human oral microbiome dysbiosis as a novel non-invasive biomarker in detection of colorectal cancer,Theranostics,2020,"16S rRNA, colorectal adenomas, colorectal cancers, oral microbiome",Experiment 3,China,Homo sapiens,Oral cavity,UBERON:0000167,Colorectal cancer,EFO:0005842,CRA,CRC,Patients with colorectal cancer,34,161,NA,16S,34,Illumina,NA,Welch's T-Test,0.05,TRUE,NA,NA,"age,alcohol drinking,body mass index,sex,smoking status",NA,increased,unchanged,increased,NA,NA,Signature 2,Table S4-5,22 June 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between CRC and CRA groups,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Gemmatimonadota|c__Gemmatimonadia|o__Gemmatimonadales|f__Gemmatimonadaceae|g__Gemmatimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Viridiplantae|p__Streptophyta,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Acidobacteriota,k__Bacillati|p__Chloroflexota,k__Pseudomonadati|p__Gemmatimonadota|c__Gemmatimonadia|o__Gemmatimonadales",1783272|1239|186801|3085636|186803|572511;1783272|1117;3379134|142182|219685|219686|219687|173479;1783272|1239|186801|186802|204475;1783272|1239|909932|909929|1843491|158846;1783272|1239|91061|186826|1300|1301;33090|35493;3379134|1224|1236|135614|32033|338;1783272|1239|186801|186802|216572;1783272|1239;3379134|57723;1783272|200795;3379134|142182|219685|219686,Complete,Claregrieve1
bsdb:33067559/1/1,33067559,case-control,33067559,10.1038/s41598-020-74678-6,NA,"Traversi D., Rabbone I., Scaioli G., Vallini C., Carletto G., Racca I., Ala U., Durazzo M., Collo A., Ferro A., Carrera D., Savastio S., Cadario F., Siliquini R. , Cerutti F.","Risk factors for type 1 diabetes, including environmental, behavioural and gut microbial factors: a case-control study",Scientific reports,2020,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Autoimmune type 1 diabetes,EFO:0009756,healthy control,autoimmune type 1 diabetes,Children with Type 1 Diabetes (T1D),56,40,3 months,16S,34,Illumina,raw counts,DESeq2,0.001,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Results: T1D risk factors,5 October 2024,Ifeanyisam,"Ifeanyisam,Svetlana up,WikiWorks",Difference between the gut microbiodata of Children with TD1 and Health Controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri",3379134|976|200643|171549|2005519;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|1263|40518;3379134|976|200643|171549|171552|2974251|165179,Complete,Svetlana up
bsdb:33067643/1/1,33067643,"cross-sectional observational, not case-control",33067643,10.1007/s00414-020-02439-1,NA,"Chen X., Xu J., Wang H., Luo J., Wang Z., Chen G., Jiang D., Cao R., Huang H., Luo D., Xiao X. , Hu J.",Profiling the differences of gut microbial structure between schizophrenia patients with and without violent behaviors based on 16S rRNA gene sequencing,International journal of legal medicine,2021,"16S rRNA gene sequencing, Forensic psychiatry, Gut microbiota, Schizophrenia, Violence",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Schizophrenia patients without violence (NV.SCV),Schizophrenia patients with violence (V.SCZ),"The Schizophrenia patients with violence (V.SCV) acted violent behavior since they were diagnosed with schizophrenia. The violent behavior was identified according to the serious violence identification of the MacArthur Community Violence Instrument (MCVI): 
(1) batteries that resulted in physical injury or involved the use of a weapon, 
(2) sexual assaults, 
(3) threats made with a weapon in hand. 
If they acted any of the above behaviors since they were diagnosed with schizophrenia, they were classified into the V.SCZ group",16,26,3 months,16S,34,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,4,NA,"age,diet,region",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 3a,11 November 2024,Tino,"Tino,WikiWorks","The key microbial taxonomic compositions responsible for the
differences between the V.SCZ and NV.SCZ groups.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis",3379134|976|200643|171549;3379134|976|200643;3379134|976|200643|171549|171552;3379134|976|200643|171549|815|816|820,Complete,Svetlana up
bsdb:33067643/1/2,33067643,"cross-sectional observational, not case-control",33067643,10.1007/s00414-020-02439-1,NA,"Chen X., Xu J., Wang H., Luo J., Wang Z., Chen G., Jiang D., Cao R., Huang H., Luo D., Xiao X. , Hu J.",Profiling the differences of gut microbial structure between schizophrenia patients with and without violent behaviors based on 16S rRNA gene sequencing,International journal of legal medicine,2021,"16S rRNA gene sequencing, Forensic psychiatry, Gut microbiota, Schizophrenia, Violence",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Schizophrenia patients without violence (NV.SCV),Schizophrenia patients with violence (V.SCZ),"The Schizophrenia patients with violence (V.SCV) acted violent behavior since they were diagnosed with schizophrenia. The violent behavior was identified according to the serious violence identification of the MacArthur Community Violence Instrument (MCVI): 
(1) batteries that resulted in physical injury or involved the use of a weapon, 
(2) sexual assaults, 
(3) threats made with a weapon in hand. 
If they acted any of the above behaviors since they were diagnosed with schizophrenia, they were classified into the V.SCZ group",16,26,3 months,16S,34,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,4,NA,"age,diet,region",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 3a,11 November 2024,Tino,"Tino,KateRasheed,WikiWorks","The key microbial taxonomic compositions responsible for the
differences between the V.SCZ and NV.SCZ groups.",decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes",1783272|201174;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|28026;95818|2093818|2093825|2171986|1331051;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|909932|1843489|31977;1783272|201174|1760,Complete,Svetlana up
bsdb:33067643/2/1,33067643,"cross-sectional observational, not case-control",33067643,10.1007/s00414-020-02439-1,NA,"Chen X., Xu J., Wang H., Luo J., Wang Z., Chen G., Jiang D., Cao R., Huang H., Luo D., Xiao X. , Hu J.",Profiling the differences of gut microbial structure between schizophrenia patients with and without violent behaviors based on 16S rRNA gene sequencing,International journal of legal medicine,2021,"16S rRNA gene sequencing, Forensic psychiatry, Gut microbiota, Schizophrenia, Violence",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Schizophrenia patients without violence (NV.SCV),Schizophrenia patients with violence (V.SCZ),"The Schizophrenia patients with violence (V.SCV) acted violent behavior since they were diagnosed with schizophrenia. The violent behavior was identified according to the serious violence identification of the MacArthur Community Violence Instrument (MCVI): 
(1) batteries that resulted in physical injury or involved the use of a weapon, 
(2) sexual assaults, 
(3) threats made with a weapon in hand. 
If they acted any of the above behaviors since they were diagnosed with schizophrenia, they were classified into the V.SCZ group",16,26,3 months,16S,34,Ion Torrent,relative abundances,Metastats,0.05,TRUE,4,NA,"age,diet,region",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 2a-2d,27 December 2024,Tino,"Tino,KateRasheed,WikiWorks",The differential gut microbial taxonomic composition between the V.SCZ and NV.SCZ groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae",3379134|976|200643|171549|1853231|283168;1783272|1239|909932|1843489|31977;1783272|1239|186801|186802|216572|596767;1783272|1239|91061|1385|90964|227979;1783272|201174|1760|85007|1653,Complete,Svetlana up
bsdb:33067643/2/2,33067643,"cross-sectional observational, not case-control",33067643,10.1007/s00414-020-02439-1,NA,"Chen X., Xu J., Wang H., Luo J., Wang Z., Chen G., Jiang D., Cao R., Huang H., Luo D., Xiao X. , Hu J.",Profiling the differences of gut microbial structure between schizophrenia patients with and without violent behaviors based on 16S rRNA gene sequencing,International journal of legal medicine,2021,"16S rRNA gene sequencing, Forensic psychiatry, Gut microbiota, Schizophrenia, Violence",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Schizophrenia patients without violence (NV.SCV),Schizophrenia patients with violence (V.SCZ),"The Schizophrenia patients with violence (V.SCV) acted violent behavior since they were diagnosed with schizophrenia. The violent behavior was identified according to the serious violence identification of the MacArthur Community Violence Instrument (MCVI): 
(1) batteries that resulted in physical injury or involved the use of a weapon, 
(2) sexual assaults, 
(3) threats made with a weapon in hand. 
If they acted any of the above behaviors since they were diagnosed with schizophrenia, they were classified into the V.SCZ group",16,26,3 months,16S,34,Ion Torrent,relative abundances,Metastats,0.05,TRUE,4,NA,"age,diet,region",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 2a-2d,27 December 2024,Tino,"Tino,KateRasheed,WikiWorks",The differential gut microbial taxonomic composition between the V.SCZ and NV.SCZ groups.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales,k__Bacillati|p__Actinomycetota|c__Rubrobacteria,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Chloroflexota|c__Anaerolineae,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfarculia|o__Desulfarculales,k__Bacillati|p__Chloroflexota|c__Ardenticatenia|o__Ardenticatenales,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfarculia|o__Desulfarculales|f__Desulfarculaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae|g__Hyphomicrobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Rummeliibacillus,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Brochothrix,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium",3379134|1224|28216|80840|80864|80865;1783272|201174|84995|84996|84997|42255;1783272|201174|84995|84996;1783272|201174|84995;1783272|201174|84995|84996;3379134|1224|28211;1783272|200795|292625;3379134|976|117747|200666;3379134|200940|3031646|453227;1783272|200795|1382928|1382929;3379134|976|117747|200666|84566;1783272|1239|91061|1385|186818;3379134|200940|3031646|453227|453228;1783272|1239|91061|1385|186820;3379134|976|117743|200644|49546;3379134|976|117743|200644;1783272|1239|909932|1843489|31977|909928;3379134|976|117747|200666|84566|28453;3379134|1224|28211|356|45401|81;1783272|1239|91061|1385|186817|400634;1783272|1239|526524|526525|128827|1573536;1783272|1239|91061|1385|186818|648802;95818|2093818|2093825|2171986|1331051;1783272|1239|526524|526525|128827|174708;1783272|1239|91061|1385|186820|2755;3379134|1224|28211|356|69277|68287;3379134|1224|1236|91347|1903411|629;3379134|1224|1236|2887326|468|497;3379134|976|117743|200644|49546|237;1783272|201174|1760|85006|1268|1663;3379134|976|117743|200644|2762318|59732,Complete,Svetlana up
bsdb:33071933/1/1,33071933,case-control,33071933,10.3389/fneur.2020.01041,NA,"Cosma-Grigorov A., Meixner H., Mrochen A., Wirtz S., Winkler J. , Marxreiter F.",Changes in Gastrointestinal Microbiome Composition in PD: A Pivotal Role of Covariates,Frontiers in neurology,2020,"Parkinson's disease, biomarker, constipation, covariates, gut, microbiome, non-motor symptoms",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control group,Parkinson's disease (PD) group,Patients with Parkinson's disease,31,70,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,decreased,NA,NA,Signature 1,Figure 2A & Supplementary Figure 3A-D,15 April 2025,EniolaAde,"EniolaAde,Victoria",Heat tree analysis depicting alterations in microbiota composition between PD and controls.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae",3379134|1224|28216|80840|506;3379134|1224|28216;3379134|1224|28216|80840;1783272|1239|186801|186802|216572|119852;3379134|1224|28216|80840|995019|40544;3379134|1224|28216|80840|995019,Complete,KateRasheed
bsdb:33071933/1/2,33071933,case-control,33071933,10.3389/fneur.2020.01041,NA,"Cosma-Grigorov A., Meixner H., Mrochen A., Wirtz S., Winkler J. , Marxreiter F.",Changes in Gastrointestinal Microbiome Composition in PD: A Pivotal Role of Covariates,Frontiers in neurology,2020,"Parkinson's disease, biomarker, constipation, covariates, gut, microbiome, non-motor symptoms",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control group,Parkinson's disease (PD) group,Patients with Parkinson's disease,31,70,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,decreased,NA,NA,Signature 2,Figure 2A & Supplementary Figure 3A-D,15 April 2025,EniolaAde,"EniolaAde,Victoria",Heat tree analysis depicting alterations in microbiota composition between PD and controls.,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|204475;1783272|1239|186801|3085636|186803,Complete,KateRasheed
bsdb:33071933/2/1,33071933,case-control,33071933,10.3389/fneur.2020.01041,NA,"Cosma-Grigorov A., Meixner H., Mrochen A., Wirtz S., Winkler J. , Marxreiter F.",Changes in Gastrointestinal Microbiome Composition in PD: A Pivotal Role of Covariates,Frontiers in neurology,2020,"Parkinson's disease, biomarker, constipation, covariates, gut, microbiome, non-motor symptoms",Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control group,Parkinson's disease (PD) group,Patients with Parkinson's disease,31,70,1 month,16S,34,Illumina,relative abundances,Random Forest Analysis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,decreased,NA,NA,Signature 1,Figure 2B,14 May 2025,Victoria,Victoria,Unsupervised random forests classification using PD and controls as classes and abundances as classifiers along a decision tree.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",3379134|1224|28216|80840|995019|40544;3379134|74201|203494|48461|1647988|239934;3379134|200940|3031449|213115|194924|35832;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802|186807|51514;1783272|1239|909932|1843488|909930|33024,Complete,KateRasheed
bsdb:33071933/2/2,33071933,case-control,33071933,10.3389/fneur.2020.01041,NA,"Cosma-Grigorov A., Meixner H., Mrochen A., Wirtz S., Winkler J. , Marxreiter F.",Changes in Gastrointestinal Microbiome Composition in PD: A Pivotal Role of Covariates,Frontiers in neurology,2020,"Parkinson's disease, biomarker, constipation, covariates, gut, microbiome, non-motor symptoms",Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control group,Parkinson's disease (PD) group,Patients with Parkinson's disease,31,70,1 month,16S,34,Illumina,relative abundances,Random Forest Analysis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,decreased,NA,NA,Signature 2,Figure 2B,14 May 2025,Victoria,Victoria,Unsupervised random forests classification using PD and controls as classes and abundances as classifiers along a decision tree.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|572511,Complete,KateRasheed
bsdb:33071933/3/1,33071933,case-control,33071933,10.3389/fneur.2020.01041,NA,"Cosma-Grigorov A., Meixner H., Mrochen A., Wirtz S., Winkler J. , Marxreiter F.",Changes in Gastrointestinal Microbiome Composition in PD: A Pivotal Role of Covariates,Frontiers in neurology,2020,"Parkinson's disease, biomarker, constipation, covariates, gut, microbiome, non-motor symptoms",Experiment 3,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control group,Parkinson's disease (PD) group,Patients with Parkinson's disease,19,28,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,constipation,NA,NA,unchanged,unchanged,decreased,NA,NA,Signature 1,Figure 4 a&b,14 May 2025,Victoria,Victoria,Differences in microbiota after matching for obstipation and coffee consumption.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,1783272|1239|186801|186802|216572|1263,Complete,KateRasheed
bsdb:33071933/4/1,33071933,case-control,33071933,10.3389/fneur.2020.01041,NA,"Cosma-Grigorov A., Meixner H., Mrochen A., Wirtz S., Winkler J. , Marxreiter F.",Changes in Gastrointestinal Microbiome Composition in PD: A Pivotal Role of Covariates,Frontiers in neurology,2020,"Parkinson's disease, biomarker, constipation, covariates, gut, microbiome, non-motor symptoms",Experiment 4,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control group,Parkinson's disease (PD) group,Patients with Parkinson's disease,19,28,1 month,16S,34,Illumina,relative abundances,Random Forest Analysis,0.05,TRUE,NA,constipation,NA,NA,unchanged,unchanged,decreased,NA,NA,Signature 1,Figure 4c,16 May 2025,Victoria,Victoria,Random forests classification of differences in microbiota after matching for obstipation and coffee consumption.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",3379134|976|200643|171549|171552|838;3379134|1224|28216|80840|995019|40544;3379134|74201|203494|48461|1647988|239934,Complete,KateRasheed
bsdb:33071933/4/2,33071933,case-control,33071933,10.3389/fneur.2020.01041,NA,"Cosma-Grigorov A., Meixner H., Mrochen A., Wirtz S., Winkler J. , Marxreiter F.",Changes in Gastrointestinal Microbiome Composition in PD: A Pivotal Role of Covariates,Frontiers in neurology,2020,"Parkinson's disease, biomarker, constipation, covariates, gut, microbiome, non-motor symptoms",Experiment 4,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control group,Parkinson's disease (PD) group,Patients with Parkinson's disease,19,28,1 month,16S,34,Illumina,relative abundances,Random Forest Analysis,0.05,TRUE,NA,constipation,NA,NA,unchanged,unchanged,decreased,NA,NA,Signature 2,Figure 4C,16 May 2025,Victoria,Victoria,Random forests classification of differences in microbiota after matching for obstipation and coffee consumption.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes",1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|207244,Complete,KateRasheed
bsdb:33071933/5/1,33071933,case-control,33071933,10.3389/fneur.2020.01041,NA,"Cosma-Grigorov A., Meixner H., Mrochen A., Wirtz S., Winkler J. , Marxreiter F.",Changes in Gastrointestinal Microbiome Composition in PD: A Pivotal Role of Covariates,Frontiers in neurology,2020,"Parkinson's disease, biomarker, constipation, covariates, gut, microbiome, non-motor symptoms",Experiment 5,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control group,Parkinson's disease (PD) group,Patients with Parkinson's disease,31,70,1 month,16S,34,Illumina,log transformation,Sparse Correlations for Compositional data (SparCC),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,decreased,NA,NA,Signature 1,"Figure 3A&B, Supplementary figure 4b",16 May 2025,Victoria,Victoria,SparCC distance measure to identify correlations of individual taxa with groups.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|1224|1236;3379134|976|200643|171549|815;1783272|1239|186801|186802|216572;1783272|1239|91061|186826|1300;1783272|1239|909932|1843489|31977;3379134|976|200643|171549|815|816;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,KateRasheed
bsdb:33071933/5/2,33071933,case-control,33071933,10.3389/fneur.2020.01041,NA,"Cosma-Grigorov A., Meixner H., Mrochen A., Wirtz S., Winkler J. , Marxreiter F.",Changes in Gastrointestinal Microbiome Composition in PD: A Pivotal Role of Covariates,Frontiers in neurology,2020,"Parkinson's disease, biomarker, constipation, covariates, gut, microbiome, non-motor symptoms",Experiment 5,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control group,Parkinson's disease (PD) group,Patients with Parkinson's disease,31,70,1 month,16S,34,Illumina,log transformation,Sparse Correlations for Compositional data (SparCC),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,decreased,NA,NA,Signature 2,Figure 3A&B,16 May 2025,Victoria,Victoria,SparCC distance measure to identify correlations of individual taxa with groups.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|31979|1485,Complete,KateRasheed
bsdb:33071933/6/1,33071933,case-control,33071933,10.3389/fneur.2020.01041,NA,"Cosma-Grigorov A., Meixner H., Mrochen A., Wirtz S., Winkler J. , Marxreiter F.",Changes in Gastrointestinal Microbiome Composition in PD: A Pivotal Role of Covariates,Frontiers in neurology,2020,"Parkinson's disease, biomarker, constipation, covariates, gut, microbiome, non-motor symptoms",Experiment 6,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control group,Parkinson's disease (PD) group,Patients with Parkinson's disease,19,28,1 month,16S,34,Illumina,log transformation,Sparse Correlations for Compositional data (SparCC),0.05,TRUE,NA,constipation,NA,NA,unchanged,unchanged,decreased,NA,NA,Signature 1,Figure 4D,16 May 2025,Victoria,Victoria,Differences in microbiota after matching for obstipation and coffee consumption with SparCC.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,KateRasheed
bsdb:33071933/6/2,33071933,case-control,33071933,10.3389/fneur.2020.01041,NA,"Cosma-Grigorov A., Meixner H., Mrochen A., Wirtz S., Winkler J. , Marxreiter F.",Changes in Gastrointestinal Microbiome Composition in PD: A Pivotal Role of Covariates,Frontiers in neurology,2020,"Parkinson's disease, biomarker, constipation, covariates, gut, microbiome, non-motor symptoms",Experiment 6,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control group,Parkinson's disease (PD) group,Patients with Parkinson's disease,19,28,1 month,16S,34,Illumina,log transformation,Sparse Correlations for Compositional data (SparCC),0.05,TRUE,NA,constipation,NA,NA,unchanged,unchanged,decreased,NA,NA,Signature 2,Figure 4D,16 May 2025,Victoria,Victoria,Differences in microbiota after matching for obstipation and coffee consumption with SparCC.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,1783272|1239|186801|186802|216572|216851,Complete,KateRasheed
bsdb:33085540/1/1,33085540,case-control,33085540,10.2217/fmb-2019-0336,https://pubmed.ncbi.nlm.nih.gov/33085540/,"Del Chierico F., Grassini P., Quagliariello A., Torti M., Russo A., Reddel S. , Stocchi F.",The impact of intestinal microbiota on weight loss in Parkinson's disease patients: a pilot study,Future microbiology,2020,"Parkinson's disease, inflammation, metabolism, microbiota, weight loss",Experiment 1,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Idiopathic Parkinson's Disease Patients,"Patients diagnosed with idiopathic PD according to the UK Brain Bank criteria that either referred an unintended weight loss of at least 7% of the usual weight, in the period from the diagnosis to the time of assessment (WL group) or reported stability of body weight from the diagnosis to the time of evaluation (NWL group).",8,20,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 1,9 May 2023,Jacquelynshevin,"Jacquelynshevin,WikiWorks","The most differentially enriched taxa in Parkinson’s disease patients (PARK) and CTRL groups. Computed Linear discriminant analysis (LDA) scores of the taxa relative
abundance difference between the PARK and CTRL groups at phylum (A)
and genus (B) levels. Positive LDA scores (green) are enriched in PARK
group, while negative LDA scores (red) are enriched in CTRL.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|28216|80840|75682;3379134|1224,Complete,Folakunmi
bsdb:33085540/1/2,33085540,case-control,33085540,10.2217/fmb-2019-0336,https://pubmed.ncbi.nlm.nih.gov/33085540/,"Del Chierico F., Grassini P., Quagliariello A., Torti M., Russo A., Reddel S. , Stocchi F.",The impact of intestinal microbiota on weight loss in Parkinson's disease patients: a pilot study,Future microbiology,2020,"Parkinson's disease, inflammation, metabolism, microbiota, weight loss",Experiment 1,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Idiopathic Parkinson's Disease Patients,"Patients diagnosed with idiopathic PD according to the UK Brain Bank criteria that either referred an unintended weight loss of at least 7% of the usual weight, in the period from the diagnosis to the time of assessment (WL group) or reported stability of body weight from the diagnosis to the time of evaluation (NWL group).",8,20,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 1,9 May 2023,Jacquelynshevin,"Jacquelynshevin,Folakunmi,WikiWorks","Figure 1. The most differentially enriched taxa in Parkinson’s disease
patients (PARK) and CTRL groups. Computed Linear discriminant analysis
(LDA) scores of the taxa relative abundance difference between the
PARK and CTRL groups at phylum (A) and genus (B) levels. Positive LDA
scores (green) are enriched in PARK group, while negative LDA scores (red)
are enriched in CTRL.",decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfotomaculaceae|g__Desulfotomaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",1783272|201174|84998|84999|1643824|1380;1783272|201174|1760|85004|31953|1678|1694;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|2937910|1562;1783272|1239|91061|186826|186828|117563;1783272|1239|186801|3085636|186803;1783272|1239|91061|1385|186818;3379134|976|200643|171549|171552;1783272|1239|186801|3085636|186803|841;1783272|1239|91061|1385|90964;1783272|1239|1737404|1737405|1737406;3379134|976|200643|171549|171552|577309,Complete,Folakunmi
bsdb:33085540/2/1,33085540,case-control,33085540,10.2217/fmb-2019-0336,https://pubmed.ncbi.nlm.nih.gov/33085540/,"Del Chierico F., Grassini P., Quagliariello A., Torti M., Russo A., Reddel S. , Stocchi F.",The impact of intestinal microbiota on weight loss in Parkinson's disease patients: a pilot study,Future microbiology,2020,"Parkinson's disease, inflammation, metabolism, microbiota, weight loss",Experiment 2,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls and Idiopathic Parkinson's Disease Patients with Weight Loss,Idiopathic Parkinson's Disease Patients without Weight Loss,Patients diagnosed with idiopathic PD according to the UK Brain Bank criteria that reported stability of body weight from the diagnosis to the time of evaluation (NWL group).,18,10,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3,9 May 2023,Jacquelynshevin,"Jacquelynshevin,WikiWorks","The most differentially enriched taxa in non weight loss, weight loss and CTRL groups. Computed LDA scores of the relative abundance difference between the three groups. Positive LDA scores (red) are enriched in NWL group.",increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,Folakunmi
bsdb:33085540/3/1,33085540,case-control,33085540,10.2217/fmb-2019-0336,https://pubmed.ncbi.nlm.nih.gov/33085540/,"Del Chierico F., Grassini P., Quagliariello A., Torti M., Russo A., Reddel S. , Stocchi F.",The impact of intestinal microbiota on weight loss in Parkinson's disease patients: a pilot study,Future microbiology,2020,"Parkinson's disease, inflammation, metabolism, microbiota, weight loss",Experiment 3,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Idiopathic Parkinson's Disease Patients with Weight Loss,"Patients diagnosed with idiopathic PD according to the UK Brain Bank criteria that referred an unintended weight loss of at least 7% of the usual weight, in the period from the diagnosis to the time of assessment (WL group).",8,10,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4A,9 May 2023,Jacquelynshevin,"Jacquelynshevin,Folakunmi,WikiWorks",The most differentially enriched taxa in the CTRL versus weight loss comparison.,increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",3379134|200940|3031449|213115|194924|35832;3379134|200940|3031449|213115|194924;3379134|976|200643|171549|1853231|283168;3379134|1224|28216|80840|75682;3379134|976|200643|171549|171552|577309,Complete,Folakunmi
bsdb:33085540/3/2,33085540,case-control,33085540,10.2217/fmb-2019-0336,https://pubmed.ncbi.nlm.nih.gov/33085540/,"Del Chierico F., Grassini P., Quagliariello A., Torti M., Russo A., Reddel S. , Stocchi F.",The impact of intestinal microbiota on weight loss in Parkinson's disease patients: a pilot study,Future microbiology,2020,"Parkinson's disease, inflammation, metabolism, microbiota, weight loss",Experiment 3,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Idiopathic Parkinson's Disease Patients with Weight Loss,"Patients diagnosed with idiopathic PD according to the UK Brain Bank criteria that referred an unintended weight loss of at least 7% of the usual weight, in the period from the diagnosis to the time of assessment (WL group).",8,10,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4A,9 May 2023,Jacquelynshevin,"Jacquelynshevin,WikiWorks",The most differentially enriched taxa in the CTRL versus weight loss comparison.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae",1783272|1239|186801|3082720|543314|109326;1783272|201174|1760|85004|31953|1678|1694;1783272|1239|91061|186826|186828|117563;1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549|171552;1783272|201174|84998|84999|1643824|1380;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|91061|1385|186818,Complete,Folakunmi
bsdb:33085540/4/1,33085540,case-control,33085540,10.2217/fmb-2019-0336,https://pubmed.ncbi.nlm.nih.gov/33085540/,"Del Chierico F., Grassini P., Quagliariello A., Torti M., Russo A., Reddel S. , Stocchi F.",The impact of intestinal microbiota on weight loss in Parkinson's disease patients: a pilot study,Future microbiology,2020,"Parkinson's disease, inflammation, metabolism, microbiota, weight loss",Experiment 4,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Idiopathic Parkinson's Disease Patients without Weight Loss,Patients diagnosed with idiopathic PD according to the UK Brain Bank criteria that reported stability of body weight from the diagnosis to the time of evaluation (NWL group).,8,10,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 4B,9 May 2023,Jacquelynshevin,"Jacquelynshevin,WikiWorks",The most differentially enriched taxa in the CTRL versus NWL comparison.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium",3379134|1224|1236|91347|543;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|3085636|186803|2383,Complete,Folakunmi
bsdb:33085540/4/2,33085540,case-control,33085540,10.2217/fmb-2019-0336,https://pubmed.ncbi.nlm.nih.gov/33085540/,"Del Chierico F., Grassini P., Quagliariello A., Torti M., Russo A., Reddel S. , Stocchi F.",The impact of intestinal microbiota on weight loss in Parkinson's disease patients: a pilot study,Future microbiology,2020,"Parkinson's disease, inflammation, metabolism, microbiota, weight loss",Experiment 4,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Idiopathic Parkinson's Disease Patients without Weight Loss,Patients diagnosed with idiopathic PD according to the UK Brain Bank criteria that reported stability of body weight from the diagnosis to the time of evaluation (NWL group).,8,10,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 4B,9 May 2023,Jacquelynshevin,"Jacquelynshevin,Folakunmi,WikiWorks",The most differentially enriched taxa in the CTRL versus NWL comparison.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptacetobacter|s__Peptacetobacter hiranonis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus flavefaciens,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|186807|51514;1783272|1239|186801|3082720|186804|2743582|89152;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|186801|186802|216572|1263|1265;1783272|1239|91061|1385|90964|1279|1280;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171552|577309,Complete,Folakunmi
bsdb:33085540/5/1,33085540,case-control,33085540,10.2217/fmb-2019-0336,https://pubmed.ncbi.nlm.nih.gov/33085540/,"Del Chierico F., Grassini P., Quagliariello A., Torti M., Russo A., Reddel S. , Stocchi F.",The impact of intestinal microbiota on weight loss in Parkinson's disease patients: a pilot study,Future microbiology,2020,"Parkinson's disease, inflammation, metabolism, microbiota, weight loss",Experiment 5,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Idiopathic Parkinson's Disease Patients without Weight Loss,Idiopathic Parkinson's Disease Patients with Weight Loss,"Patients diagnosed with idiopathic PD according to the UK Brain Bank criteria that referred an unintended weight loss of at least 7% of the usual weight, in the period from the diagnosis to the time of assessment (WL group).",10,10,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex,time from diagnosis",NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 4C,9 May 2023,Jacquelynshevin,"Jacquelynshevin,WikiWorks",The most differentially enriched taxa in the NWL versus weight loss comparison.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|3082768|990719;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|186807;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|186802|216572;1783272|201174|84998|84999|84107|102106;3379134|200940|3031449|213115|194924;1783272|1239|186801|3085636|186803|841,Complete,Folakunmi
bsdb:33085540/5/2,33085540,case-control,33085540,10.2217/fmb-2019-0336,https://pubmed.ncbi.nlm.nih.gov/33085540/,"Del Chierico F., Grassini P., Quagliariello A., Torti M., Russo A., Reddel S. , Stocchi F.",The impact of intestinal microbiota on weight loss in Parkinson's disease patients: a pilot study,Future microbiology,2020,"Parkinson's disease, inflammation, metabolism, microbiota, weight loss",Experiment 5,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Idiopathic Parkinson's Disease Patients without Weight Loss,Idiopathic Parkinson's Disease Patients with Weight Loss,"Patients diagnosed with idiopathic PD according to the UK Brain Bank criteria that referred an unintended weight loss of at least 7% of the usual weight, in the period from the diagnosis to the time of assessment (WL group).",10,10,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex,time from diagnosis",NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 4C,9 May 2023,Jacquelynshevin,"Jacquelynshevin,WikiWorks",The most differentially enriched taxa in the NWL versus weight loss comparison.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus cecorum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",1783272|1239|91061|186826|1300;3379134|1224|1236|91347|543|561|562;1783272|1239|91061|186826|81852|1350;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|186802|216572|216851|853;1783272|1239|91061|186826|81852|1350|44008;3379134|1224|1236|91347|543,Complete,Folakunmi
bsdb:33099131/1/1,33099131,case-control,33099131,10.1016/j.parkreldis.2020.10.034,https://pubmed.ncbi.nlm.nih.gov/33099131/,"Zhang F., Yue L., Fang X., Wang G., Li C., Sun X., Jia X., Yang J., Song J., Zhang Y., Guo C., Ma G., Sang M., Chen F. , Wang P.",Altered gut microbiota in Parkinson's disease patients/healthy spouses and its association with clinical features,Parkinsonism & related disorders,2020,"Clinical features/classifications, Gut microbiota dysbiosis, Metagenomics, Neurodegenerative disease, Parkinson's disease (PD)",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease Patients,"The patients were diagnosed with primary Parkinson's disease according to the Movement Disorder Society Clinical Diagnostic Criteria for Parkinson’s disease (MDS-PD Criteria, 2015) of Xiangyang NO.1 People’s Hospital.",137,63,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,NA,NA,NA,NA,increased,Signature 1,Table S2,22 February 2023,Jacquelynshevin,"Jacquelynshevin,WikiWorks",33 significantly differential gut bacterial markers identified by LEfSe analysis.,increased,"c__Deltaproteobacteria,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota|c__Actinomycetes",28221;3379134|74201|203494|48461|1647988|239934;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|186801;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;3379134|1224|1236|91347|543|561;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|2005525|375288;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171551;1783272|1239|909932|1843489|31977;3379134|74201|203494|48461|203557;3379134|74201|203494;3379134|74201|203494|48461;3379134|74201;1783272|1239|186801|186802|216572;1783272|1239|186801|186802;1783272|1239;3379134|1224;1783272|201174|84992;1783272|201174|1760,Complete,Fatima
bsdb:33099131/1/2,33099131,case-control,33099131,10.1016/j.parkreldis.2020.10.034,https://pubmed.ncbi.nlm.nih.gov/33099131/,"Zhang F., Yue L., Fang X., Wang G., Li C., Sun X., Jia X., Yang J., Song J., Zhang Y., Guo C., Ma G., Sang M., Chen F. , Wang P.",Altered gut microbiota in Parkinson's disease patients/healthy spouses and its association with clinical features,Parkinsonism & related disorders,2020,"Clinical features/classifications, Gut microbiota dysbiosis, Metagenomics, Neurodegenerative disease, Parkinson's disease (PD)",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease Patients,"The patients were diagnosed with primary Parkinson's disease according to the Movement Disorder Society Clinical Diagnostic Criteria for Parkinson’s disease (MDS-PD Criteria, 2015) of Xiangyang NO.1 People’s Hospital.",137,63,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,NA,NA,NA,NA,increased,Signature 2,Table S2,22 February 2023,Jacquelynshevin,"Jacquelynshevin,WikiWorks",33 significantly differential gut bacterial markers identified by LEfSe analysis.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Bacteroidota",3379134|976|200643|171549;3379134|976|200643;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066|203490|203491|203492|848;3384189|32066;3379134|976,Complete,Fatima
bsdb:33101877/1/1,33101877,case-control,33101877,10.1002/advs.202001936,NA,"Ren Z., Fan Y., Li A., Shen Q., Wu J., Ren L., Lu H., Ding S., Ren H., Liu C., Liu W., Gao D., Wu Z., Guo S., Wu G., Liu Z., Yu Z. , Li L.",Alterations of the Human Gut Microbiome in Chronic Kidney Disease,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2020,"chronic kidney disease, gut microbiome, microbial markers, non‐invasive diagnostic tools",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Healthy controls (HC),Chronic kidney disease (CKD),Patients with chronic kidney disease (CKD) in the discovery cohort,210,110,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index,sex",NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,"Figure 3B, Figure 3C, Figure S11, Figure S14, Figure S17, Supporting Excel 5 and 7",18 November 2025,Tosin,Tosin,"Significant differential genera between CKD (chronic kidney disease) and HC (healthy controls) at phylum, genus, class, order and family levels",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium,p__Candidatus Saccharimonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria,k__Pseudomonadati|p__Lentisphaerota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Thalassospiraceae|g__Thalassospira,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|s__uncultured Christensenellaceae bacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|s__uncultured Coriobacteriaceae bacterium",1783272|1239|909932|1843488|909930;1783272|201174|84992;3379134|1224|1236|2887326|468|469;1783272|201174;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;3379134|1224|28211;1783272|1239|186801|186802|216572|244127;1783272|1239|91061;3379134|976|200643|171549|2005519|397864;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|830;1783272|1239|186801|3085636|186803|2383;95818;1783272|1239|186801|3082768|990719;3379134|1224|1236|91347|543|544;1783272|201174|84998|84999|84107|102106;3379134|976|200643|171549|2005519|1348911;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;28221;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|526524|526525|128827;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|216572|946234;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;3384189|32066|203490|203491|203492|848;3379134|1224|1236;3379134|1224|1236|135625|712|724;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826;3379134|256845|1313211;3379134|256845;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;3379134|1224|1236|135625|712;3379134|1224|1236|135625;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171551;3379134|1224;3379134|1224|1236|91347|543|160674;3379134|1224|28211|204441|41295;3379134|1224|28211|204441;3379134|976|200643|171549|171550;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|292632;3379134|1224|28211|204441|2844866|168934;1783272|1239|909932|1843489|31977|29465;3379134|256845|1313211|278082|255528;3379134|256845|1313211|278082;3379134|256845|1313211|278082|255528|172900;3379134|1224|1236|91347|543;1783272|1239|186801|186802|216572|707003;1783272|1239|186801|3082768|990719|1229255;1783272|201174|84998|84999|84107|331632,Complete,KateRasheed
bsdb:33101877/1/2,33101877,case-control,33101877,10.1002/advs.202001936,NA,"Ren Z., Fan Y., Li A., Shen Q., Wu J., Ren L., Lu H., Ding S., Ren H., Liu C., Liu W., Gao D., Wu Z., Guo S., Wu G., Liu Z., Yu Z. , Li L.",Alterations of the Human Gut Microbiome in Chronic Kidney Disease,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2020,"chronic kidney disease, gut microbiome, microbial markers, non‐invasive diagnostic tools",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Healthy controls (HC),Chronic kidney disease (CKD),Patients with chronic kidney disease (CKD) in the discovery cohort,210,110,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index,sex",NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,"Figure 3B, Figure 3C, Figure S11, Figure S14, Figure S17, Supporting Excel 5 and 7",18 November 2025,Tosin,Tosin,"Significant differential genera between CKD (chronic kidney disease) and HC (healthy controls) at phylum, genus, class, order and family levels",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium",3379134|1224|28216|80840|506;1783272|1239|186801|3085636|186803|207244;1783272|1239;3379134|1224|28216;1783272|1239|186801|3085636|186803|572511;3379134|1224|28216|80840;1783272|1239|186801;1783272|1117;1783272|1117|3028117;1783272|1239|186801|3085636|1185407;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803;3379134|1224|1236|2887326|468;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|3085636|186803|46205;3379134|1224|1236|72274;1783272|1239|186801|3085636|186803|841;3379134|74201|203494|48461|203557;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201;1783272|1239;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976;1783272|1239|186801|186802|31979;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;1783272|1239|909932|1843489|31977;1783272|1239|186801|3085636|186803|297314;1783272|1239|526524|526525|128827|331630,Complete,KateRasheed
bsdb:33101877/2/1,33101877,case-control,33101877,10.1002/advs.202001936,NA,"Ren Z., Fan Y., Li A., Shen Q., Wu J., Ren L., Lu H., Ding S., Ren H., Liu C., Liu W., Gao D., Wu Z., Guo S., Wu G., Liu Z., Yu Z. , Li L.",Alterations of the Human Gut Microbiome in Chronic Kidney Disease,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2020,"chronic kidney disease, gut microbiome, microbial markers, non‐invasive diagnostic tools",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Healthy control (HC),Chronic kidney disease (CKD),Patients with chronic kidney disease (CKD) in the discovery cohort,210,110,1 month,16S,34,Illumina,relative abundances,LEfSe,0.01,FALSE,2,"age,body mass index,sex",NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,"Figure 4, Supplementary Figure 18, Supporting Excel 8",18 November 2025,Chyono2,"Chyono2,Tosin",The Linear discriminant analysis effect size (LEfSe) analysis of Crucial bacteria of gut microbiome related to chronic kidney disease (CKD),increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia",1783272|1239|909932|1843488|909930;1783272|201174|84992;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;3379134|1224|28211;1783272|1239|186801|186802|216572|244127;1783272|1239|91061;3379134|976|200643|171549|2005519|397864;3379134|200940|3031449|213115|194924|35832;1783272|1239|91061|186826|186828;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|3082768|990719;3379134|1224|1236|91347|543|544;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|1239|186801|3085636|1185407;28221;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|216572|946234;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066|203490|203491|203492|848;3379134|1224|1236;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;1783272|1239|526524|526525|128827|61170;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|2005525|375288;3379134|1224|1236|135625|712;3379134|1224|1236|135625;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171551;3379134|976|200643|171549|171550;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|292632;1783272|1239|909932|1843489|31977|29465;3379134|74201|203494|48461|203557;3379134|74201|203494|48461;3379134|74201|203494,Complete,NA
bsdb:33101877/2/2,33101877,case-control,33101877,10.1002/advs.202001936,NA,"Ren Z., Fan Y., Li A., Shen Q., Wu J., Ren L., Lu H., Ding S., Ren H., Liu C., Liu W., Gao D., Wu Z., Guo S., Wu G., Liu Z., Yu Z. , Li L.",Alterations of the Human Gut Microbiome in Chronic Kidney Disease,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2020,"chronic kidney disease, gut microbiome, microbial markers, non‐invasive diagnostic tools",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Healthy control (HC),Chronic kidney disease (CKD),Patients with chronic kidney disease (CKD) in the discovery cohort,210,110,1 month,16S,34,Illumina,relative abundances,LEfSe,0.01,FALSE,2,"age,body mass index,sex",NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,"Figure 4, Supplementary Figure 18 and Supporting Excel 8",18 November 2025,Chyono2,"Chyono2,Tosin",The Linear discriminant analysis effect size (LEfSe) analysis of Crucial bacteria of gut microbiome related to chronic kidney disease (CKD),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas",3379134|1224|28216|80840|506;1783272|1239|186801|3085636|186803|207244;;3379134|1224|28216;1783272|1239|186801|3085636|186803|572511;3379134|1224|28216|80840;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|3085636|186803|46205;1783272|1239|186801|3085636|186803|841;3379134|1224|28211|204457|41297;3379134|1224|28211|204457;3379134|1224|28211|204457|41297|13687,Complete,NA
bsdb:33101877/3/1,33101877,case-control,33101877,10.1002/advs.202001936,NA,"Ren Z., Fan Y., Li A., Shen Q., Wu J., Ren L., Lu H., Ding S., Ren H., Liu C., Liu W., Gao D., Wu Z., Guo S., Wu G., Liu Z., Yu Z. , Li L.",Alterations of the Human Gut Microbiome in Chronic Kidney Disease,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2020,"chronic kidney disease, gut microbiome, microbial markers, non‐invasive diagnostic tools",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Stage 5 chronic kidney disease,NA,Combination of Chronic kidney disease (CKD) stage 1-2 and chronic kidney disease (CKD) stage 3-4,Chronic kidney disease (CKD) stage 5,Patients with stage 5 chronic kidney disease (CKD),62,48,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 7B, Figure 7C, Supplementary Figure 21",20 November 2025,Tosin,Tosin,"Significant differential abundant analysis between Chronic kidney disease (CKD) stage 1-2, Chronic kidney disease (CKD) stage 3-4 and Chronic kidney disease (CKD) stage 5 using linear discriminant analysis effect size (LEfSe)",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Thalassospiraceae|g__Thalassospira,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|1853231|574697;28221;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;3379134|1224|28211|204441|2844866|168934;3379134|74201|203494|48461|203557;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201;1783272|1798710|1906119;1783272|1239|186801|186802|216572,Complete,NA
bsdb:33101877/4/1,33101877,case-control,33101877,10.1002/advs.202001936,NA,"Ren Z., Fan Y., Li A., Shen Q., Wu J., Ren L., Lu H., Ding S., Ren H., Liu C., Liu W., Gao D., Wu Z., Guo S., Wu G., Liu Z., Yu Z. , Li L.",Alterations of the Human Gut Microbiome in Chronic Kidney Disease,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2020,"chronic kidney disease, gut microbiome, microbial markers, non‐invasive diagnostic tools",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Combination of chronic kidney disease (CKD) stage 3-4 and chronic kidney disease (CKD) stage 5,Chronic kidney disease (CKD) stage 1-2,Patients with chronic kidney disease (CKD) at stage 1-2,84,26,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 7C, Supplementary Figure 21",19 November 2025,Chyono2,"Chyono2,Tosin","Significant differential abundant analysis between Chronic kidney disease (CKD) stage 1-2, Chronic kidney disease (CKD) stage 3-4 and Chronic kidney disease (CKD) stage 5 using linear discriminant analysis effect size (LEfSe)",increased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Mycoplasmatota",1783272|544448|31969;1783272|544448,Complete,NA
bsdb:33102244/1/1,33102244,"cross-sectional observational, not case-control",33102244,10.3389/fcimb.2020.00434,https://pubmed.ncbi.nlm.nih.gov/33102244/,"Zhou J., Zhang Y., Cui P., Luo L., Chen H., Liang B., Jiang J., Ning C., Tian L., Zhong X., Ye L., Liang H. , Huang J.",Gut Microbiome Changes Associated With HIV Infection and Sexual Orientation,Frontiers in cellular and infection microbiology,2020,"16S rRNA gene amplicon sequencing, AIDS, HIV, gut microbiome, sexual orientation",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV– individuals,HIV+ individuals,HIV positive patients,544,744,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,"age,body mass index,sex,sexual preference",NA,decreased,decreased,unchanged,decreased,decreased,Signature 1,Figure 8,3 April 2023,Atrayees,"Atrayees,ChiomaBlessing,WikiWorks",Differential enrichment of genus or species in HIV+ and HIV– individuals.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta",1783272|1239|186801|3085636|186803|572511;1783272|1239|526524|526525|128827|118747;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|3085642|580596|2049021;3379134|1224|1236|91347|543|544;1783272|201174|1760|85007|1653|1716;3379134|200940|3031449|213115|194924|872;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|561;1783272|1239|186801|186802|186806|1730;3384189|32066|203490|203491|203492|848;1783272|1239|91061|186826|186828|117563;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|909929|1843491|52225;1783272|1239|186801|3082720|543314|86331;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|186806|113286;1783272|1239|91061|1385|90964|1279;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803|2719313|358743;1783272|1239|186801|3085636|186803|189330|39486;1783272|201174|84998|1643822|1643826|84111|84112,Complete,ChiomaBlessing
bsdb:33102244/1/2,33102244,"cross-sectional observational, not case-control",33102244,10.3389/fcimb.2020.00434,https://pubmed.ncbi.nlm.nih.gov/33102244/,"Zhou J., Zhang Y., Cui P., Luo L., Chen H., Liang B., Jiang J., Ning C., Tian L., Zhong X., Ye L., Liang H. , Huang J.",Gut Microbiome Changes Associated With HIV Infection and Sexual Orientation,Frontiers in cellular and infection microbiology,2020,"16S rRNA gene amplicon sequencing, AIDS, HIV, gut microbiome, sexual orientation",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV– individuals,HIV+ individuals,HIV positive patients,544,744,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,"age,body mass index,sex,sexual preference",NA,decreased,decreased,unchanged,decreased,decreased,Signature 2,Figure 8,3 April 2023,Atrayees,"Atrayees,ChiomaBlessing,WikiWorks",Differential enrichment of genus or species in HIV+ and HIV– individuals.,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|84998|1643822|1643826|447020;3379134|1224|28211|356|82115|357;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|830;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|216851;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|3085636|186803|140625;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;3384189|32066|203490|203491|1129771|168808;1783272|1239|91061|186826|1300|1301,Complete,ChiomaBlessing
bsdb:33102244/2/1,33102244,"cross-sectional observational, not case-control",33102244,10.3389/fcimb.2020.00434,https://pubmed.ncbi.nlm.nih.gov/33102244/,"Zhou J., Zhang Y., Cui P., Luo L., Chen H., Liang B., Jiang J., Ning C., Tian L., Zhong X., Ye L., Liang H. , Huang J.",Gut Microbiome Changes Associated With HIV Infection and Sexual Orientation,Frontiers in cellular and infection microbiology,2020,"16S rRNA gene amplicon sequencing, AIDS, HIV, gut microbiome, sexual orientation",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,non-MSM,MSM (men who have sex with men),Men who have sex with men,304,328,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,"age,body mass index,sex,sexual preference",NA,unchanged,decreased,decreased,decreased,decreased,Signature 1,Figure 9,23 January 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential enrichment of genus or species in MSM and non-MSM.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans",3379134|1224|1236|135625|712|416916;1783272|544448|31969|186332|186333|2152;1783272|1239|526524|526525|128827|118747;1783272|1239|186801|3085636|186803|830;1783272|1239|526524|526525|2810280|135858;1783272|201174|84998|84999|84107|102106;3379134|200940|3031449|213115|194924|872;1783272|1239|909932|1843489|31977|39948;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|561;1783272|1239|186801|186802|186806|1730;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|909929|1843491|52225;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|186802|186807|2740;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171552|838;1783272|201174|84998|1643822|1643826|84108;3379134|1224|1236|135624|83763|83770;3379134|1224|28216|80840|995019|40544;3379134|256845|1313211|278082|255528|172900;1783272|1239|186801|3085636|186803|33042|33043;1783272|1239|186801|3085636|186803|189330|39486,Complete,ChiomaBlessing
bsdb:33102244/2/2,33102244,"cross-sectional observational, not case-control",33102244,10.3389/fcimb.2020.00434,https://pubmed.ncbi.nlm.nih.gov/33102244/,"Zhou J., Zhang Y., Cui P., Luo L., Chen H., Liang B., Jiang J., Ning C., Tian L., Zhong X., Ye L., Liang H. , Huang J.",Gut Microbiome Changes Associated With HIV Infection and Sexual Orientation,Frontiers in cellular and infection microbiology,2020,"16S rRNA gene amplicon sequencing, AIDS, HIV, gut microbiome, sexual orientation",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,non-MSM,MSM (men who have sex with men),Men who have sex with men,304,328,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,"age,body mass index,sex,sexual preference",NA,unchanged,decreased,decreased,decreased,decreased,Signature 2,Figure 9,23 January 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential enrichment of genus or species in MSM and non-MSM.,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|84998|1643822|1643826|447020;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|216851;1783272|1239|526524|526525|128827|61170;3366610|28890|183925|2158|2159|2172;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|171551|836;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300|1301,Complete,ChiomaBlessing
bsdb:33106549/1/1,33106549,randomized controlled trial,33106549,10.1038/s41598-020-75229-9,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7589489/,"Stan T.L., Soylu-Kucharz R., Burleigh S., Prykhodko O., Cao L., Franke N., Sjögren M., Haikal C., Hållenius F. , Björkqvist M.",Increased intestinal permeability and gut dysbiosis in the R6/2 mouse model of Huntington's disease,Scientific reports,2020,NA,Experiment 1,Sweden,Mus musculus,Feces,UBERON:0001988,Huntington disease,MONDO:0007739,Wild type,R6/2,"The CAG-repeat lengths of the R6/2 mice used in this study ranged between 242 and 257, resulting in a disease progression slower than that of the R6/2 mouse with 150 CAG repeats as described previously.",10,10,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3 Supplemental Text,9 January 2023,Jacquelynshevin,"Jacquelynshevin,WikiWorks",Relative Abundance between wildtype and R6/2,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",1783272|1239|91061;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|526524|526525|2810280|100883;3379134|1224|1236|91347|543;3379134|1224|1236;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|2005525|375288;3379134|1224|1236|91347;1783272|1239|91061|186826|33958,Complete,Fatima
bsdb:33106549/1/2,33106549,randomized controlled trial,33106549,10.1038/s41598-020-75229-9,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7589489/,"Stan T.L., Soylu-Kucharz R., Burleigh S., Prykhodko O., Cao L., Franke N., Sjögren M., Haikal C., Hållenius F. , Björkqvist M.",Increased intestinal permeability and gut dysbiosis in the R6/2 mouse model of Huntington's disease,Scientific reports,2020,NA,Experiment 1,Sweden,Mus musculus,Feces,UBERON:0001988,Huntington disease,MONDO:0007739,Wild type,R6/2,"The CAG-repeat lengths of the R6/2 mice used in this study ranged between 242 and 257, resulting in a disease progression slower than that of the R6/2 mouse with 150 CAG repeats as described previously.",10,10,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3 Supplemental Text,9 January 2023,Jacquelynshevin,"Jacquelynshevin,WikiWorks",Relative abundance between wildtype and R6/2,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae",1783272|201174|84998|1643822|1643826|447020;1783272|201174|84998|84999|84107;1783272|201174|84998;1783272|201174;1783272|201174|84998|84999;3379134|200940|3031449|213115|194924|872;28221;3379134|200940|3031449|213115;3379134|200940|3031449|213115|194924,Complete,Fatima
bsdb:33110490/1/1,33110490,"cross-sectional observational, not case-control",33110490,10.1186/s13601-020-00345-8,https://ctajournal.biomedcentral.com/articles/10.1186/s13601-020-00345-8,"Huang C., Yu Y., Du W., Liu Y., Dai R., Tang W., Wang P., Zhang C. , Shi G.",Fungal and bacterial microbiome dysbiosis and imbalance of trans-kingdom network in asthma,Clinical and translational allergy,2020,"Asthma, Bacteriome, Correlations, Metagenomics, Mycobiome",Experiment 1,China,Homo sapiens,Sputum,UBERON:0007311,Asthma,MONDO:0004979,Healthy Controls (CON) Group (Airway mycobiome),Untreated Asthma Patients Group (Airway mycobiome),Patients in untreated asthma group were defined as patients who did not use inhaled corticosteroid (ICS).,16,22,1 month,ITS / ITS2,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,"Figure 2A, Table S3",4 November 2025,Oladoye,Oladoye,"Relative abundance of top 15 genera in airway mycobiome. 
Significantly differing mycobiome between CON and untreated 
asthma group, statistical significance was determined using 
Kruskal–Wallis rank-sum test, P value less than 0.05.",increased,"k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Polyporales|f__Irpicaceae|g__Irpex,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Clavicipitaceae|g__Metarhizium,k__Fungi|p__Mucoromycota|c__Mortierellomycetes|o__Mortierellales|f__Mortierellaceae|g__Mortierella,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Chaetothyriales|f__Herpotrichiellaceae|g__Phialophora,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Rhodotorula,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Schizophyllaceae|g__Schizophyllum,k__Fungi|p__Basidiomycota|c__Wallemiomycetes|o__Wallemiales|f__Wallemiaceae|g__Wallemia,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Chaetomiaceae,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Sporormiaceae",4751|4890|147550|5125|110618|5506;4751|5204|155619|5303|1931355|5318;4751|4890|147550|5125|34397|5529;4751|1913637|2212732|214503|4854|4855;4751|4890|147545|34395|43219|5600;4751|5204|162481|231213|1799696|5533;4751|5204|155619|5338|5332|5333;4751|5204|431957|431958|431959|148959;4751|4890|147550|5139|35718;4751|4890|147541|92860|55176,Complete,NA
bsdb:33110490/1/2,33110490,"cross-sectional observational, not case-control",33110490,10.1186/s13601-020-00345-8,https://ctajournal.biomedcentral.com/articles/10.1186/s13601-020-00345-8,"Huang C., Yu Y., Du W., Liu Y., Dai R., Tang W., Wang P., Zhang C. , Shi G.",Fungal and bacterial microbiome dysbiosis and imbalance of trans-kingdom network in asthma,Clinical and translational allergy,2020,"Asthma, Bacteriome, Correlations, Metagenomics, Mycobiome",Experiment 1,China,Homo sapiens,Sputum,UBERON:0007311,Asthma,MONDO:0004979,Healthy Controls (CON) Group (Airway mycobiome),Untreated Asthma Patients Group (Airway mycobiome),Patients in untreated asthma group were defined as patients who did not use inhaled corticosteroid (ICS).,16,22,1 month,ITS / ITS2,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,"Figure 2A, Table S3",4 November 2025,Oladoye,Oladoye,"Relative abundance of top 15 genera in airway mycobiome. Significantly differing mycobiome between CON and untreated asthma group, statistical significance was determined using Kruskal–Wallis rank-sum test, P value less than 0.05.",decreased,"k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae|g__Mycosphaerella,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Filobasidiales|f__Filobasidiaceae|g__Naganishia,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Sporobolomyces,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Polyporales|f__Polyporaceae|g__Trametes,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales|f__Sclerotiniaceae",4751|4890|147541|2726947|93133|41254;4751|5204|155616|90886|5408|1851509;4751|5204|162481|231213|1799696|5429;4751|5204|155619|5303|5317|5324;4751|4890|147548|5178|28983,Complete,NA
bsdb:33110490/2/1,33110490,"cross-sectional observational, not case-control",33110490,10.1186/s13601-020-00345-8,https://ctajournal.biomedcentral.com/articles/10.1186/s13601-020-00345-8,"Huang C., Yu Y., Du W., Liu Y., Dai R., Tang W., Wang P., Zhang C. , Shi G.",Fungal and bacterial microbiome dysbiosis and imbalance of trans-kingdom network in asthma,Clinical and translational allergy,2020,"Asthma, Bacteriome, Correlations, Metagenomics, Mycobiome",Experiment 2,China,Homo sapiens,Sputum,UBERON:0007311,Asthma,MONDO:0004979,Inhaled Corticosteroid (ICS) Receiving Patients Group (Airway mycobiome),Untreated Asthma Patients Group (Airway mycobiome),Patients with untreated asthma group were defined as patients did not use inhaled corticosteroid (ICS).,30,22,1 month,ITS / ITS2,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 2B, Additional file 7: Table S4.",4 November 2025,Oladoye,Oladoye,"Relative abundance of top 15 genera in airway mycobiome. Significantly differing mycobiome between untreated asthma group and inhaled corticosteroid (ICS) receiving patients group, statistical significance was determined using Kruskal–Wallis rank-sum test, P value less than 0.05.",increased,"k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium,k__Fungi|p__Mucoromycota|c__Mortierellomycetes|o__Mortierellales|f__Mortierellaceae|g__Mortierella,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Chaetothyriales|f__Herpotrichiellaceae|g__Phialophora,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Corticiales|f__Corticiaceae|g__Sistotrema,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Sporobolomyces,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Chaetomiaceae,k__Fungi,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Sporormiaceae",4751|4890|147550|5125|110618|5506;4751|1913637|2212732|214503|4854|4855;4751|4890|147545|34395|43219|5600;4751|5204|155619|452338|5304|139131;4751|5204|162481|231213|1799696|5429;4751|4890|147550|5139|35718;4751;4751|4890|147541|92860|55176,Complete,NA
bsdb:33110490/2/2,33110490,"cross-sectional observational, not case-control",33110490,10.1186/s13601-020-00345-8,https://ctajournal.biomedcentral.com/articles/10.1186/s13601-020-00345-8,"Huang C., Yu Y., Du W., Liu Y., Dai R., Tang W., Wang P., Zhang C. , Shi G.",Fungal and bacterial microbiome dysbiosis and imbalance of trans-kingdom network in asthma,Clinical and translational allergy,2020,"Asthma, Bacteriome, Correlations, Metagenomics, Mycobiome",Experiment 2,China,Homo sapiens,Sputum,UBERON:0007311,Asthma,MONDO:0004979,Inhaled Corticosteroid (ICS) Receiving Patients Group (Airway mycobiome),Untreated Asthma Patients Group (Airway mycobiome),Patients with untreated asthma group were defined as patients did not use inhaled corticosteroid (ICS).,30,22,1 month,ITS / ITS2,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 2B, Additional file 7: Table S4.",4 November 2025,Oladoye,Oladoye,"Relative abundance of top 15 genera in airway mycobiome. Significantly differing mycobiome between untreated asthma group and inhaled corticosteroid (ICS) receiving patients group, statistical significance was determined using Kruskal–Wallis rank-sum test, P value less than 0.05.",decreased,"k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Pleosporaceae|g__Alternaria,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Psathyrellaceae|g__Coprinellus,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Sporobolomyces,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Tausonia,k__Fungi|p__Basidiomycota|c__Wallemiomycetes|o__Wallemiales|f__Wallemiaceae|g__Wallemia,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales|f__Sclerotiniaceae",4751|4890|147541|92860|28556|5598;4751|4890|147545|5042|1131492|5052;4751|5204|155619|5338|184208|184430;4751|5204|162481|231213|1799696|5429;4751|5204|155616|90883|1851551|415704;4751|5204|431957|431958|431959|148959;4751|4890|147548|5178|28983,Complete,NA
bsdb:33110490/3/1,33110490,"cross-sectional observational, not case-control",33110490,10.1186/s13601-020-00345-8,https://ctajournal.biomedcentral.com/articles/10.1186/s13601-020-00345-8,"Huang C., Yu Y., Du W., Liu Y., Dai R., Tang W., Wang P., Zhang C. , Shi G.",Fungal and bacterial microbiome dysbiosis and imbalance of trans-kingdom network in asthma,Clinical and translational allergy,2020,"Asthma, Bacteriome, Correlations, Metagenomics, Mycobiome",Experiment 3,China,Homo sapiens,Sputum,UBERON:0007311,Asthma,MONDO:0004979,Healthy Controls (CON) Group (Airway bacteriome),Untreated Asthma Patients Group (Airway bacteriome),Patients in untreated asthma group were defined as patients who did not use inhaled corticosteroid (ICS).,26,23,1 month,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,unchanged,NA,decreased,Signature 1,Additional file 11. Figure S4A and Additional 12.Table S7,5 November 2025,Oladoye,Oladoye,"Relative abundance of top 15 genera in airway bacteriome differing significantly between CON and untreated asthma
group, statistical significance was determined using Kruskal–Wallis rank-sum test.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,",1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|1300|1301;,Complete,NA
bsdb:33110490/3/2,33110490,"cross-sectional observational, not case-control",33110490,10.1186/s13601-020-00345-8,https://ctajournal.biomedcentral.com/articles/10.1186/s13601-020-00345-8,"Huang C., Yu Y., Du W., Liu Y., Dai R., Tang W., Wang P., Zhang C. , Shi G.",Fungal and bacterial microbiome dysbiosis and imbalance of trans-kingdom network in asthma,Clinical and translational allergy,2020,"Asthma, Bacteriome, Correlations, Metagenomics, Mycobiome",Experiment 3,China,Homo sapiens,Sputum,UBERON:0007311,Asthma,MONDO:0004979,Healthy Controls (CON) Group (Airway bacteriome),Untreated Asthma Patients Group (Airway bacteriome),Patients in untreated asthma group were defined as patients who did not use inhaled corticosteroid (ICS).,26,23,1 month,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,unchanged,NA,decreased,Signature 2,Additional file 11. Figure S4A and Additional 12.Table S7,6 November 2025,Oladoye,Oladoye,"Relative abundance of top 15 genera in airway bacteriome differing significantly between CON and untreated asthma
group, statistical significance was determined using Kruskal–Wallis rank-sum test.",decreased,"p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Demequinaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Halieaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",95818|2093818|2093825|2171986;95818|2093818|2093825;1783272|1239|186801|3085636|186803|43996;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1357;1783272|1239|186801|3085636|186803|265975;1783272|1239|91061|186826|33958|1253;3379134|1224|28211|204455|31989;1783272|201174|1760|85006|1042322;3379134|1224|1236|1706369|1706372;1783272|1239|91061|186826|33958|46255,Complete,NA
bsdb:33110490/4/1,33110490,"cross-sectional observational, not case-control",33110490,10.1186/s13601-020-00345-8,https://ctajournal.biomedcentral.com/articles/10.1186/s13601-020-00345-8,"Huang C., Yu Y., Du W., Liu Y., Dai R., Tang W., Wang P., Zhang C. , Shi G.",Fungal and bacterial microbiome dysbiosis and imbalance of trans-kingdom network in asthma,Clinical and translational allergy,2020,"Asthma, Bacteriome, Correlations, Metagenomics, Mycobiome",Experiment 4,China,Homo sapiens,Sputum,UBERON:0007311,Asthma,MONDO:0004979,Inhaled Corticosteroid (ICS) Receiving Patients Group (Airway bacteriome),Untreated Asthma Patients Group (Airway bacteriome),Patients with untreated asthma group were defined as patients did not use inhaled corticosteroid (ICS).,23,33,1 month,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Additional file 11. Figure S4B and Additional 12.Table S7,6 November 2025,Oladoye,Oladoye,"Relative abundance of top 15 genera in airway bacteriome differing significantly between untreated asthma group between untreated asthma group and ICS asthma group, statistical significance was determined using Kruskal-Wallis rank-sum test",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium",3379134|976|200643|171549|171550|239759;1783272|201174|1760|85009|31957|2801844;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|43996;1783272|1239|91061|186826|186828|117563;1783272|1239|186801|3085636|186803|1164882;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|909929|1843491|158846;3379134|976|200643|171549|2005473;1783272|1239|186801|3085636|186803|265975;1783272|1239|909932|909929|1843491|970;1783272|201174|84998|1643822|1643826|84108;1783272|1239|526524|526525|128827|123375,Complete,NA
bsdb:33110490/4/2,33110490,"cross-sectional observational, not case-control",33110490,10.1186/s13601-020-00345-8,https://ctajournal.biomedcentral.com/articles/10.1186/s13601-020-00345-8,"Huang C., Yu Y., Du W., Liu Y., Dai R., Tang W., Wang P., Zhang C. , Shi G.",Fungal and bacterial microbiome dysbiosis and imbalance of trans-kingdom network in asthma,Clinical and translational allergy,2020,"Asthma, Bacteriome, Correlations, Metagenomics, Mycobiome",Experiment 4,China,Homo sapiens,Sputum,UBERON:0007311,Asthma,MONDO:0004979,Inhaled Corticosteroid (ICS) Receiving Patients Group (Airway bacteriome),Untreated Asthma Patients Group (Airway bacteriome),Patients with untreated asthma group were defined as patients did not use inhaled corticosteroid (ICS).,23,33,1 month,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Additional file 11. Figure S4B and Additional 12.Table S7,6 November 2025,Oladoye,Oladoye,"Relative abundance of top 15 genera in airway bacteriome differing significantly between untreated asthma group between untreated asthma group and ICS asthma group, statistical significance was determined using Kruskal-Wallis rank-sum test",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,",1783272|201174|1760|85004|31953|419014;,Complete,NA
bsdb:33110490/5/1,33110490,"cross-sectional observational, not case-control",33110490,10.1186/s13601-020-00345-8,https://ctajournal.biomedcentral.com/articles/10.1186/s13601-020-00345-8,"Huang C., Yu Y., Du W., Liu Y., Dai R., Tang W., Wang P., Zhang C. , Shi G.",Fungal and bacterial microbiome dysbiosis and imbalance of trans-kingdom network in asthma,Clinical and translational allergy,2020,"Asthma, Bacteriome, Correlations, Metagenomics, Mycobiome",Experiment 5,China,Homo sapiens,Sputum,UBERON:0007311,Asthma,MONDO:0004979,Healthy Controls (CON) Group (Airway bacteriome),Untreated Asthma Patients Group (Airway bacteriome),Patients in untreated asthma group were defined as patients who did not use inhaled corticosteroid (ICS).,26,23,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,unchanged,NA,decreased,Signature 1,Additional file 14. Fig. S5C,8 November 2025,Oladoye,Oladoye,Relative abundance of the biomarkers (bacteriome) identified by LEfSe in CON group and untreated asthma group.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061|1385|539738|1378;3379134|1224|28216|206351|481|482;1783272|1239|91061|186826|1300|1301,Complete,NA
bsdb:33110490/5/2,33110490,"cross-sectional observational, not case-control",33110490,10.1186/s13601-020-00345-8,https://ctajournal.biomedcentral.com/articles/10.1186/s13601-020-00345-8,"Huang C., Yu Y., Du W., Liu Y., Dai R., Tang W., Wang P., Zhang C. , Shi G.",Fungal and bacterial microbiome dysbiosis and imbalance of trans-kingdom network in asthma,Clinical and translational allergy,2020,"Asthma, Bacteriome, Correlations, Metagenomics, Mycobiome",Experiment 5,China,Homo sapiens,Sputum,UBERON:0007311,Asthma,MONDO:0004979,Healthy Controls (CON) Group (Airway bacteriome),Untreated Asthma Patients Group (Airway bacteriome),Patients in untreated asthma group were defined as patients who did not use inhaled corticosteroid (ICS).,26,23,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,unchanged,NA,decreased,Signature 2,Additional file 14. Fig. S5C,8 November 2025,Oladoye,Oladoye,Relative abundance of the biomarkers (bacteriome) identified by LEfSe in CON group and untreated asthma group.,decreased,"p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium",95818|2093818|2093825|2171986;1783272|1239|186801|3085636|186803|43996;1783272|1239|186801|3085636|186803|1164882;1783272|1239|186801|3085636|186803|265975;1783272|1239|909932|909929|1843491|970;1783272|1239|526524|526525|128827|123375,Complete,NA
bsdb:33110490/6/1,33110490,"cross-sectional observational, not case-control",33110490,10.1186/s13601-020-00345-8,https://ctajournal.biomedcentral.com/articles/10.1186/s13601-020-00345-8,"Huang C., Yu Y., Du W., Liu Y., Dai R., Tang W., Wang P., Zhang C. , Shi G.",Fungal and bacterial microbiome dysbiosis and imbalance of trans-kingdom network in asthma,Clinical and translational allergy,2020,"Asthma, Bacteriome, Correlations, Metagenomics, Mycobiome",Experiment 6,China,Homo sapiens,Sputum,UBERON:0007311,Asthma,MONDO:0004979,Inhaled Corticosteroid (ICS) Receiving Patients Group (Airway bacteriome),Untreated Asthma Patients Group (Airway bacteriome),Patients in untreated asthma group were defined as patients who did not use inhaled corticosteroid (ICS).,33,23,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Additional file 14. Fig. S5D,8 November 2025,Oladoye,Oladoye,Relative abundance of the biomarkers (bacteriome) identified by LEfSe in untreated asthma group and ICS group.,increased,"p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium",95818|2093818|2093825|2171986;1783272|1239|186801|3085636|186803|43996;1783272|1239|186801|3085636|186803|1164882;1783272|1239|186801|3085636|186803|265975;1783272|1239|909932|909929|1843491|970;1783272|1239|526524|526525|128827|123375,Complete,NA
bsdb:33110490/6/2,33110490,"cross-sectional observational, not case-control",33110490,10.1186/s13601-020-00345-8,https://ctajournal.biomedcentral.com/articles/10.1186/s13601-020-00345-8,"Huang C., Yu Y., Du W., Liu Y., Dai R., Tang W., Wang P., Zhang C. , Shi G.",Fungal and bacterial microbiome dysbiosis and imbalance of trans-kingdom network in asthma,Clinical and translational allergy,2020,"Asthma, Bacteriome, Correlations, Metagenomics, Mycobiome",Experiment 6,China,Homo sapiens,Sputum,UBERON:0007311,Asthma,MONDO:0004979,Inhaled Corticosteroid (ICS) Receiving Patients Group (Airway bacteriome),Untreated Asthma Patients Group (Airway bacteriome),Patients in untreated asthma group were defined as patients who did not use inhaled corticosteroid (ICS).,33,23,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Additional file 14. Fig. S5D,8 November 2025,Oladoye,Oladoye,Relative abundance of the biomarkers (bacteriome) identified by LEfSe in untreated asthma group and ICS group.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061|1385|539738|1378;3379134|1224|28216|206351|481|482;1783272|1239|91061|186826|1300|1301,Complete,NA
bsdb:33112882/1/1,33112882,time series / longitudinal observational,33112882,https://doi.org/10.1371/journal.pone.0236460,https://pubmed.ncbi.nlm.nih.gov/33112882/,"Rattanathammethee T., Tuitemwong P., Thiennimitr P., Sarichai P., Na Pombejra S., Piriyakhuntorn P., Hantrakool S., Chai-Adisaksopha C., Rattarittamrong E., Tantiworawit A. , Norasetthada L.",Gut microbiota profiles of treatment-naïve adult acute myeloid leukemia patients with neutropenic fever during intensive chemotherapy,PloS one,2020,NA,Experiment 1,Thailand,Homo sapiens,Feces,UBERON:0001988,Acute myeloid leukemia,EFO:0000222,Pretreatment,Febrile neutropenia,patients with neutropenic fever during intensive chemotherapy,10,10,3 months,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,S1 table.,14 March 2023,Cyberian,"Cyberian,Chloe,Aiyshaaaa,Folakunmi,WikiWorks",The taxa that increased in relative abundance from pretreatment to febrile neutropenia.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,1783272|1239|91061|186826|81852|1350,Complete,Folakunmi
bsdb:33112882/1/2,33112882,time series / longitudinal observational,33112882,https://doi.org/10.1371/journal.pone.0236460,https://pubmed.ncbi.nlm.nih.gov/33112882/,"Rattanathammethee T., Tuitemwong P., Thiennimitr P., Sarichai P., Na Pombejra S., Piriyakhuntorn P., Hantrakool S., Chai-Adisaksopha C., Rattarittamrong E., Tantiworawit A. , Norasetthada L.",Gut microbiota profiles of treatment-naïve adult acute myeloid leukemia patients with neutropenic fever during intensive chemotherapy,PloS one,2020,NA,Experiment 1,Thailand,Homo sapiens,Feces,UBERON:0001988,Acute myeloid leukemia,EFO:0000222,Pretreatment,Febrile neutropenia,patients with neutropenic fever during intensive chemotherapy,10,10,3 months,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,S1 table.,14 March 2023,Cyberian,"Cyberian,Chloe,Folakunmi,WikiWorks",Taxa that decreased in relative abundance from pretreatment to febrile neutropenia,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,3379134|1224|1236|91347|543|561,Complete,Folakunmi
bsdb:33112882/2/NA,33112882,time series / longitudinal observational,33112882,https://doi.org/10.1371/journal.pone.0236460,https://pubmed.ncbi.nlm.nih.gov/33112882/,"Rattanathammethee T., Tuitemwong P., Thiennimitr P., Sarichai P., Na Pombejra S., Piriyakhuntorn P., Hantrakool S., Chai-Adisaksopha C., Rattarittamrong E., Tantiworawit A. , Norasetthada L.",Gut microbiota profiles of treatment-naïve adult acute myeloid leukemia patients with neutropenic fever during intensive chemotherapy,PloS one,2020,NA,Experiment 2,Thailand,Homo sapiens,Feces,UBERON:0001988,Acute myeloid leukemia,EFO:0000222,febrile neutropenia,Bone marrow recovery,After initiation of induction chemotherapy,10,10,3 months,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:33112882/3/1,33112882,time series / longitudinal observational,33112882,https://doi.org/10.1371/journal.pone.0236460,https://pubmed.ncbi.nlm.nih.gov/33112882/,"Rattanathammethee T., Tuitemwong P., Thiennimitr P., Sarichai P., Na Pombejra S., Piriyakhuntorn P., Hantrakool S., Chai-Adisaksopha C., Rattarittamrong E., Tantiworawit A. , Norasetthada L.",Gut microbiota profiles of treatment-naïve adult acute myeloid leukemia patients with neutropenic fever during intensive chemotherapy,PloS one,2020,NA,Experiment 3,Thailand,Homo sapiens,Feces,UBERON:0001988,Acute myeloid leukemia,EFO:0000222,Pre-treatment,Bone marrow recovery,After initiation of  induction chemotherapy treatment,10,10,3 months,16S,345,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,S1 table.,25 March 2023,Cyberian,"Cyberian,Folakunmi,WikiWorks",taxa that increased in relative abundance from pretreatment to bone marrow recovery.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,1783272|1239|91061|186826|81852|1350,Complete,Folakunmi
bsdb:33112882/3/2,33112882,time series / longitudinal observational,33112882,https://doi.org/10.1371/journal.pone.0236460,https://pubmed.ncbi.nlm.nih.gov/33112882/,"Rattanathammethee T., Tuitemwong P., Thiennimitr P., Sarichai P., Na Pombejra S., Piriyakhuntorn P., Hantrakool S., Chai-Adisaksopha C., Rattarittamrong E., Tantiworawit A. , Norasetthada L.",Gut microbiota profiles of treatment-naïve adult acute myeloid leukemia patients with neutropenic fever during intensive chemotherapy,PloS one,2020,NA,Experiment 3,Thailand,Homo sapiens,Feces,UBERON:0001988,Acute myeloid leukemia,EFO:0000222,Pre-treatment,Bone marrow recovery,After initiation of  induction chemotherapy treatment,10,10,3 months,16S,345,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,S1 table.,25 March 2023,Cyberian,"Cyberian,Folakunmi,WikiWorks",The taxa that decreased in relative abundance from pretreatment to bone marrow recovery,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,3379134|1224|1236|91347|543|561,Complete,Folakunmi
bsdb:33129264/1/1,33129264,"cross-sectional observational, not case-control",33129264,https://doi.org/10.1186/s12866-020-02017-w,NA,"Oduaran O.H., Tamburini F.B., Sahibdeen V., Brewster R., Gómez-Olivé F.X., Kahn K., Norris S.A., Tollman S.M., Twine R., Wade A.N., Wagner R.G., Lombard Z., Bhatt A.S. , Hazelhurst S.",Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition,BMC microbiology,2020,"16S, African microbiome, Epidemiological transition, Obesity, South African microbiome, Transitional microbiome",Experiment 1,South Africa,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Female subjects situated in Bushbuckridge,Female subjects situated in Soweto,Female subjects (both obese and lean) living in Soweto whose microbiota was studied to reflect transitional changes in microbiome on account of the adoption of a more Westernized lifestyle (in terms of diet and activity levels). Soweto represented the urban site of the two; the other (Bushbuckridge) being more relatively rural.,119,51,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 5a and Supplementary Table 2A,23 March 2024,Ehi,"Ehi,Deacme,Scholastica,WikiWorks",Phylum and Genus level significant differential abundance of taxa between Bushbuckbridge and Soweto cohorts (site differences).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Bacillota",1783272|1239|186801|186802|216572|258514;1783272|1239,Complete,Svetlana up
bsdb:33129264/1/2,33129264,"cross-sectional observational, not case-control",33129264,https://doi.org/10.1186/s12866-020-02017-w,NA,"Oduaran O.H., Tamburini F.B., Sahibdeen V., Brewster R., Gómez-Olivé F.X., Kahn K., Norris S.A., Tollman S.M., Twine R., Wade A.N., Wagner R.G., Lombard Z., Bhatt A.S. , Hazelhurst S.",Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition,BMC microbiology,2020,"16S, African microbiome, Epidemiological transition, Obesity, South African microbiome, Transitional microbiome",Experiment 1,South Africa,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Female subjects situated in Bushbuckridge,Female subjects situated in Soweto,Female subjects (both obese and lean) living in Soweto whose microbiota was studied to reflect transitional changes in microbiome on account of the adoption of a more Westernized lifestyle (in terms of diet and activity levels). Soweto represented the urban site of the two; the other (Bushbuckridge) being more relatively rural.,119,51,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 5a and Supplementary Table 2A,23 March 2024,Ehi,"Ehi,Deacme,Scholastica,WikiWorks",Phylum and Genus level significant differential abundance of taxa between Bushbuckbridge and Soweto cohorts (site differences).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Candidatus Melainabacteria|c__Vampirovibriophyceae|o__Vampirovibrionales|g__Vampirovibrio",3379134|976|200643|171549|171550|239759;1783272|544448|31969|186332|186333|2086;1783272|1239;3379134|976;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|946234;1783272|544448;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|1263;3379134|1224|28216|80840|995019|40544;1783272|1798710|3118680|2211217|213484,Complete,Svetlana up
bsdb:33129264/2/1,33129264,"cross-sectional observational, not case-control",33129264,https://doi.org/10.1186/s12866-020-02017-w,NA,"Oduaran O.H., Tamburini F.B., Sahibdeen V., Brewster R., Gómez-Olivé F.X., Kahn K., Norris S.A., Tollman S.M., Twine R., Wade A.N., Wagner R.G., Lombard Z., Bhatt A.S. , Hazelhurst S.",Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition,BMC microbiology,2020,"16S, African microbiome, Epidemiological transition, Obesity, South African microbiome, Transitional microbiome",Experiment 2,South Africa,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Lean female subjects in Bushbuckridge,Lean female subjects in Soweto,Lean females subjects living in Soweto whose microbiota was studied to understand transitional microbiome differences between subjects in Bushbuckridge and those in Soweto.,21,9,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 5b and Supplementary Table 2B,24 March 2024,Ehi,"Ehi,Deacme,Scholastica,WikiWorks",Phylum and Genus level significant differences between lean groups in the Bushbuckridge and Soweto cohorts.,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|201174;1783272|1239;3379134|976;1783272|201174|1760|85004|31953|1678;1783272|1239|526524|526525|2810280|135858;1783272|1239|909932|1843488|909930|33024;3379134|1224;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;3379134|1224|28216|80840|995019|40544;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:33129264/2/2,33129264,"cross-sectional observational, not case-control",33129264,https://doi.org/10.1186/s12866-020-02017-w,NA,"Oduaran O.H., Tamburini F.B., Sahibdeen V., Brewster R., Gómez-Olivé F.X., Kahn K., Norris S.A., Tollman S.M., Twine R., Wade A.N., Wagner R.G., Lombard Z., Bhatt A.S. , Hazelhurst S.",Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition,BMC microbiology,2020,"16S, African microbiome, Epidemiological transition, Obesity, South African microbiome, Transitional microbiome",Experiment 2,South Africa,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Lean female subjects in Bushbuckridge,Lean female subjects in Soweto,Lean females subjects living in Soweto whose microbiota was studied to understand transitional microbiome differences between subjects in Bushbuckridge and those in Soweto.,21,9,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 5b and Supplementary Table 2B,24 March 2024,Ehi,"Ehi,Deacme,WikiWorks",Phylum and Genus level significant differences between lean groups in the Bushbuckridge and Soweto cohorts.,decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota",1783272|1239;3379134|976|200643|171549|815|816;3379134|976;1783272|1239|909932|1843489|31977|39948;3379134|1224,Complete,Svetlana up
bsdb:33129264/3/1,33129264,"cross-sectional observational, not case-control",33129264,https://doi.org/10.1186/s12866-020-02017-w,NA,"Oduaran O.H., Tamburini F.B., Sahibdeen V., Brewster R., Gómez-Olivé F.X., Kahn K., Norris S.A., Tollman S.M., Twine R., Wade A.N., Wagner R.G., Lombard Z., Bhatt A.S. , Hazelhurst S.",Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition,BMC microbiology,2020,"16S, African microbiome, Epidemiological transition, Obesity, South African microbiome, Transitional microbiome",Experiment 3,South Africa,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Obese female subjects in Bushbuckridge,Obese female subjects in Soweto,Obese females in Soweto whose microbiota was studied to understand transitional microbiome differences between subjects in Bushbuckridge and those in Soweto.,66,40,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 5c and Supplementary Table 2C,24 March 2024,Ehi,"Ehi,Deacme,WikiWorks",Phylum and Genus level significant differences between obese groups in the Soweto and Bushbuckridge cohorts.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota",1783272|1239|186801|186802|216572|1263;1783272|1239,Complete,Svetlana up
bsdb:33129264/4/1,33129264,"cross-sectional observational, not case-control",33129264,https://doi.org/10.1186/s12866-020-02017-w,NA,"Oduaran O.H., Tamburini F.B., Sahibdeen V., Brewster R., Gómez-Olivé F.X., Kahn K., Norris S.A., Tollman S.M., Twine R., Wade A.N., Wagner R.G., Lombard Z., Bhatt A.S. , Hazelhurst S.",Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition,BMC microbiology,2020,"16S, African microbiome, Epidemiological transition, Obesity, South African microbiome, Transitional microbiome",Experiment 4,South Africa,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Lean female subjects in both cohorts,Obese female subjects in both cohorts,Obese female subjects in both the Bushbuckridge and Soweto cohorts.,30,106,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 5d and Supplementary Table 2D,24 March 2024,Ehi,"Ehi,Deacme,WikiWorks",Phylum and Genus level inter-cohort differential abundance between lean and obese groups (BMI differences).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota",1783272|1239|186801|186802|1392389;3379134|976|200643|171549|171552|838;1783272|1239;3379134|976,Complete,Svetlana up
bsdb:33129264/5/1,33129264,"cross-sectional observational, not case-control",33129264,https://doi.org/10.1186/s12866-020-02017-w,NA,"Oduaran O.H., Tamburini F.B., Sahibdeen V., Brewster R., Gómez-Olivé F.X., Kahn K., Norris S.A., Tollman S.M., Twine R., Wade A.N., Wagner R.G., Lombard Z., Bhatt A.S. , Hazelhurst S.",Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition,BMC microbiology,2020,"16S, African microbiome, Epidemiological transition, Obesity, South African microbiome, Transitional microbiome",Experiment 5,South Africa,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Lean female subjects in Bushbuckridge,Obese female subjects in Bushbuckridge,Obese females in Bushbuckridge whose microbiota is studied for transitional differences between lean and obese subjects in both Cohorts (Bushbuckridge and Soweto).,21,66,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Figure 5e and Supplementary Table 2E,24 March 2024,Ehi,"Ehi,Deacme,Scholastica,WikiWorks",Phylum and Genus level differential abundance between lean and obese groups in the Bushbuckridge cohort (BMI differences).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Candidatus Melainabacteria|c__Vampirovibriophyceae|o__Vampirovibrionales|g__Vampirovibrio,k__Pseudomonadati|p__Verrucomicrobiota",1783272|1239|186801|186802|216572|258514;3379134|74201|203494|48461|1647988|239934;1783272|1239;3379134|976;1783272|1239|526524|526525|2810280|135858;3379134|976|200643|171549|2005525|375288;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171552|838;3379134|1224;3379134|1224|28216|80840|995019|40544;1783272|1798710|3118680|2211217|213484;3379134|74201,Complete,Svetlana up
bsdb:33129264/6/1,33129264,"cross-sectional observational, not case-control",33129264,https://doi.org/10.1186/s12866-020-02017-w,NA,"Oduaran O.H., Tamburini F.B., Sahibdeen V., Brewster R., Gómez-Olivé F.X., Kahn K., Norris S.A., Tollman S.M., Twine R., Wade A.N., Wagner R.G., Lombard Z., Bhatt A.S. , Hazelhurst S.",Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition,BMC microbiology,2020,"16S, African microbiome, Epidemiological transition, Obesity, South African microbiome, Transitional microbiome",Experiment 6,South Africa,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Lean female subjects in Soweto,Obese female subjects in Soweto,Obese females in Soweto whose microbiota is studied to observe transitional changes between lean and obese groups in the Soweto cohort.,9,40,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 5f and Supplementary Table 2F,24 March 2024,Ehi,"Ehi,Deacme,Scholastica,WikiWorks",Phylum and Genus level differential abundance between lean and obese groups in the Soweto cohort (BMI differences).,increased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter",1783272|1239;3379134|976;3379134|1224|1236|91347|543|561;3379134|1224|1236|135625|712|724;1783272|1239|186801|186802|1392389;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|838;3379134|1224;1783272|1239|186801|186802|216572|44748,Complete,Svetlana up
bsdb:33129264/6/2,33129264,"cross-sectional observational, not case-control",33129264,https://doi.org/10.1186/s12866-020-02017-w,NA,"Oduaran O.H., Tamburini F.B., Sahibdeen V., Brewster R., Gómez-Olivé F.X., Kahn K., Norris S.A., Tollman S.M., Twine R., Wade A.N., Wagner R.G., Lombard Z., Bhatt A.S. , Hazelhurst S.",Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition,BMC microbiology,2020,"16S, African microbiome, Epidemiological transition, Obesity, South African microbiome, Transitional microbiome",Experiment 6,South Africa,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Lean female subjects in Soweto,Obese female subjects in Soweto,Obese females in Soweto whose microbiota is studied to observe transitional changes between lean and obese groups in the Soweto cohort.,9,40,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 5f and Supplementary Table 2F,24 March 2024,Ehi,"Ehi,Deacme,Scholastica,WikiWorks",Phylum and Genus level differential abundance between lean and obese groups in the Soweto cohort (BMI differences).,decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Lentisphaerota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",1783272|1239;3379134|976;3379134|256845;3379134|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:33134190/1/1,33134190,case-control,33134190,10.3389/fcimb.2020.567268,NA,"Zhou Y., Chen C., Yu H. , Yang Z.",Fecal Microbiota Changes in Patients With Postpartum Depressive Disorder,Frontiers in cellular and infection microbiology,2020,"16SrRNA gene, gut microbiota, gut-brain, postpartum depressive disorder, sex hormone",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Postpartum depression,EFO:0007453,Healthy Group,Postpartum Depression (PPD) Group,Patients diagnosed with Postpartum Depression (PPD),16,28,Currently on antibiotics,16S,3,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 5,9 June 2025,Aleru Divine,Aleru Divine,Bacterial taxa differences between healthy control (HC) and postpartum depressive disorder (PPD) patient samples.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,s__bacterium FCS020",1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|81852;3379134|1224|1236|91347|543|1940338;1451755,Complete,NA
bsdb:33134190/1/2,33134190,case-control,33134190,10.3389/fcimb.2020.567268,NA,"Zhou Y., Chen C., Yu H. , Yang Z.",Fecal Microbiota Changes in Patients With Postpartum Depressive Disorder,Frontiers in cellular and infection microbiology,2020,"16SrRNA gene, gut microbiota, gut-brain, postpartum depressive disorder, sex hormone",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Postpartum depression,EFO:0007453,Healthy Group,Postpartum Depression (PPD) Group,Patients diagnosed with Postpartum Depression (PPD),16,28,Currently on antibiotics,16S,3,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 5,9 June 2025,Aleru Divine,Aleru Divine,Bacterial taxa differences between healthy control (HC) and postpartum depressive disorder (PPD) patient samples.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania sp. Marseille-P2844,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",3379134|976|200643|171549|815|909656|204516;1783272|1239|526524|526525|128827|61170|1852366;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|909932|1843488|909930|33024;1783272|1239|909932|1843488|909930;1783272|1239|909932|1843488;1783272|1239|186801|186802|216572|216851;1783272|1239|186801;1783272|1239;1783272|1239|186801|186802,Complete,NA
bsdb:33138790/1/1,33138790,laboratory experiment,33138790,10.1186/s12866-020-02001-4,NA,"Feye K.M., Swaggerty C.L., Kogut M.H., Ricke S.C., Piva A. , Grilli E.",The biological effects of microencapsulated organic acids and botanicals induces tissue-specific and dose-dependent changes to the Gallus gallus microbiota,BMC microbiology,2020,"Botanicals, Ileum, Jejunum, Microbiota, Microencapsulated, Organic acids",Experiment 1,United States of America,Gallus gallus,Jejunum,UBERON:0002115,Diet,EFO:0002755,NTC (0 g/MT AviPlus®P) No treatment control group,(300 g/MT AviPlus®P) Supplement group,"Chickens in this group were given free access to a starter diet mixed with 300g/metric ton (MT) of a microencapsulated blend of citric (25%) and sorbic (16.7%) acids, thymol (1.7%), and vanillin (1.0%) (AviPlus®P, Vetagro S.p.A., Reggio Emilia, Italy). The remaining 55.6% of the feed additive comprises hydrogenated vegetable fats.",5,5,NA,16S,NA,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 3 A&B,7 September 2024,Victoria,"Victoria,WikiWorks",Analysis of communities of the microbiota (ANCOM) for jejunum samples. a NTC; b 300 g/MT; c 500 g/MT. The legends for the specific operational taxonomic units (OTU) associated with treatment as defined by ANCOM (Q < 0.05) are listed in the figure.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|33958;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:33138790/1/2,33138790,laboratory experiment,33138790,10.1186/s12866-020-02001-4,NA,"Feye K.M., Swaggerty C.L., Kogut M.H., Ricke S.C., Piva A. , Grilli E.",The biological effects of microencapsulated organic acids and botanicals induces tissue-specific and dose-dependent changes to the Gallus gallus microbiota,BMC microbiology,2020,"Botanicals, Ileum, Jejunum, Microbiota, Microencapsulated, Organic acids",Experiment 1,United States of America,Gallus gallus,Jejunum,UBERON:0002115,Diet,EFO:0002755,NTC (0 g/MT AviPlus®P) No treatment control group,(300 g/MT AviPlus®P) Supplement group,"Chickens in this group were given free access to a starter diet mixed with 300g/metric ton (MT) of a microencapsulated blend of citric (25%) and sorbic (16.7%) acids, thymol (1.7%), and vanillin (1.0%) (AviPlus®P, Vetagro S.p.A., Reggio Emilia, Italy). The remaining 55.6% of the feed additive comprises hydrogenated vegetable fats.",5,5,NA,16S,NA,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 3 A&B,7 September 2024,Victoria,"Victoria,WikiWorks",Analysis of communities of the microbiota (ANCOM) for jejunum samples. a NTC; b 300 g/MT; c 500 g/MT. The legends for the specific operational taxonomic units (OTU) associated with treatment as defined by ANCOM (Q < 0.05) are listed in the figure.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae",1783272|1239|91061|186826|186827;1783272|1239|91061|1385|90964,Complete,Svetlana up
bsdb:33138790/2/1,33138790,laboratory experiment,33138790,10.1186/s12866-020-02001-4,NA,"Feye K.M., Swaggerty C.L., Kogut M.H., Ricke S.C., Piva A. , Grilli E.",The biological effects of microencapsulated organic acids and botanicals induces tissue-specific and dose-dependent changes to the Gallus gallus microbiota,BMC microbiology,2020,"Botanicals, Ileum, Jejunum, Microbiota, Microencapsulated, Organic acids",Experiment 2,United States of America,Gallus gallus,Jejunum,UBERON:0002115,Diet,EFO:0002755,NTC (0 g/MT AviPlus®P) No treatment control group,(500 g/MT AviPlus®P) Supplement group,"Chickens in this group were given free access to a starter diet mixed with 500g/metric ton (MT) of a microencapsulated blend of citric (25%) and sorbic (16.7%) acids, thymol (1.7%), and vanillin (1.0%) (AviPlus®P, Vetagro S.p.A., Reggio Emilia, Italy). The remaining 55.6% of the feed additive comprises hydrogenated vegetable fats.",5,5,NA,16S,NA,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 3. A&C,7 September 2024,Victoria,"Victoria,WikiWorks",Analysis of communities of the microbiota (ANCOM) for jejunum samples. a NTC; b 300 g/MT; c 500 g/MT. The legends for the specific operational taxonomic units (OTU) associated with treatment as defined by ANCOM (Q < 0.05) are listed in the figure.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|91061|186826|33958;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:33138790/2/2,33138790,laboratory experiment,33138790,10.1186/s12866-020-02001-4,NA,"Feye K.M., Swaggerty C.L., Kogut M.H., Ricke S.C., Piva A. , Grilli E.",The biological effects of microencapsulated organic acids and botanicals induces tissue-specific and dose-dependent changes to the Gallus gallus microbiota,BMC microbiology,2020,"Botanicals, Ileum, Jejunum, Microbiota, Microencapsulated, Organic acids",Experiment 2,United States of America,Gallus gallus,Jejunum,UBERON:0002115,Diet,EFO:0002755,NTC (0 g/MT AviPlus®P) No treatment control group,(500 g/MT AviPlus®P) Supplement group,"Chickens in this group were given free access to a starter diet mixed with 500g/metric ton (MT) of a microencapsulated blend of citric (25%) and sorbic (16.7%) acids, thymol (1.7%), and vanillin (1.0%) (AviPlus®P, Vetagro S.p.A., Reggio Emilia, Italy). The remaining 55.6% of the feed additive comprises hydrogenated vegetable fats.",5,5,NA,16S,NA,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 3 A&C,7 September 2024,Victoria,"Victoria,WikiWorks",Analysis of communities of the microbiota (ANCOM) for jejunum samples. a NTC; b 300 g/MT; c 500 g/MT. The legends for the specific operational taxonomic units (OTU) associated with treatment as defined by ANCOM (Q < 0.05) are listed in the figure.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae",1783272|1239|186801|3082720|186804;1783272|1239|91061|186826|186827;3379134|1224|1236|91347|543;1783272|1239|91061|1385|90964,Complete,Svetlana up
bsdb:33138790/3/1,33138790,laboratory experiment,33138790,10.1186/s12866-020-02001-4,NA,"Feye K.M., Swaggerty C.L., Kogut M.H., Ricke S.C., Piva A. , Grilli E.",The biological effects of microencapsulated organic acids and botanicals induces tissue-specific and dose-dependent changes to the Gallus gallus microbiota,BMC microbiology,2020,"Botanicals, Ileum, Jejunum, Microbiota, Microencapsulated, Organic acids",Experiment 3,United States of America,Gallus gallus,"Ileum,Jejunum","UBERON:0002116,UBERON:0002115",Diet,EFO:0002755,NTC (0 g/MT AviPlus®P) No treatment control group,(500 g/MT AviPlus®P) Supplement group,"Chickens in this group were given free access to a starter diet mixed with 500g/metric ton (MT) of a microencapsulated blend of citric (25%) and sorbic (16.7%) acids, thymol (1.7%), and vanillin (1.0%) (AviPlus®P, Vetagro S.p.A., Reggio Emilia, Italy). The remaining 55.6% of the feed additive comprises hydrogenated vegetable fats.",5,5,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 4,7 September 2024,Victoria,"Victoria,WikiWorks","Linear discriminant analysis effect size (LEfSE) analysis. Missing operational taxonomic units (OUT) are not defined within the Family taxonomical designation and are labelled as unclassified. The 500 and NTC groups are relative to 300. An LDA > +/− 2 with a Q < 0.05 is considered significant and is graphically represented. All comparisons are relative to 300 g/MT, which was selected as it is the intermediary dose and describes the potential dose effect.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae",1783272|1239|186801|186802|31979;1783272|201174|1760|85006|1268,Complete,Svetlana up
bsdb:33138790/3/2,33138790,laboratory experiment,33138790,10.1186/s12866-020-02001-4,NA,"Feye K.M., Swaggerty C.L., Kogut M.H., Ricke S.C., Piva A. , Grilli E.",The biological effects of microencapsulated organic acids and botanicals induces tissue-specific and dose-dependent changes to the Gallus gallus microbiota,BMC microbiology,2020,"Botanicals, Ileum, Jejunum, Microbiota, Microencapsulated, Organic acids",Experiment 3,United States of America,Gallus gallus,"Ileum,Jejunum","UBERON:0002116,UBERON:0002115",Diet,EFO:0002755,NTC (0 g/MT AviPlus®P) No treatment control group,(500 g/MT AviPlus®P) Supplement group,"Chickens in this group were given free access to a starter diet mixed with 500g/metric ton (MT) of a microencapsulated blend of citric (25%) and sorbic (16.7%) acids, thymol (1.7%), and vanillin (1.0%) (AviPlus®P, Vetagro S.p.A., Reggio Emilia, Italy). The remaining 55.6% of the feed additive comprises hydrogenated vegetable fats.",5,5,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 4,7 September 2024,Victoria,"Victoria,WikiWorks","Linear discriminant analysis effect size (LEfSE) analysis. Missing operational taxonomic units (OUT) are not defined within the Family taxonomical designation and are labelled as unclassified. The 500 and NTC groups are relative to 300. An LDA > +/− 2 with a Q < 0.05 is considered significant and is graphically represented. All comparisons are relative to 300 g/MT, which was selected as it is the intermediary dose and describes the potential dose effect.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae",3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236;1783272|1239|91061|186826|186827,Complete,Svetlana up
bsdb:33143658/1/1,33143658,"cross-sectional observational, not case-control",33143658,https://doi.org/10.1186/s12866-020-02021-0,NA,"Yuan X., Chen R., Zhang Y., Lin X. , Yang X.",Gut microbiota: effect of pubertal status,BMC microbiology,2020,"16 s rRNA, Adolescent, Children, Gut microbiota, Puberty",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Puberty,EFO:0001382,Non-pubertal,Pubertal,Male children who have undergone puberty.,42,47,NA,16S,34,NA,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 5,28 March 2024,Nityasinghal 14,"Nityasinghal 14,Junie,WikiWorks",Differential biomarkers associated with genders in pubertal subjects and non-pubertal subjects.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales",3379134|1224|28216;3379134|1224|28216|80840,Complete,Svetlana up
bsdb:33143658/1/2,33143658,"cross-sectional observational, not case-control",33143658,https://doi.org/10.1186/s12866-020-02021-0,NA,"Yuan X., Chen R., Zhang Y., Lin X. , Yang X.",Gut microbiota: effect of pubertal status,BMC microbiology,2020,"16 s rRNA, Adolescent, Children, Gut microbiota, Puberty",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Puberty,EFO:0001382,Non-pubertal,Pubertal,Male children who have undergone puberty.,42,47,NA,16S,34,NA,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 5,28 March 2024,Nityasinghal 14,"Nityasinghal 14,Junie,WikiWorks",Differential biomarkers associated with genders in pubertal subjects and non-pubertal subjects.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",3379134|1224|1236|135625;1783272|1239|186801|186802|31979;3379134|1224|1236|135625|712|724;1783272|1239|526524|526525|2810280|100883;1783272|1239|186801|186802,Complete,Svetlana up
bsdb:33149114/1/1,33149114,randomized controlled trial,33149114,10.1038/s41467-020-19382-9,NA,"Balle C., Konstantinus I.N., Jaumdally S.Z., Havyarimana E., Lennard K., Esra R., Barnabas S.L., Happel A.U., Moodie Z., Gill K., Pidwell T., Karaoz U., Brodie E., Maseko V., Gamieldien H., Bosinger S.E., Myer L., Bekker L.G., Passmore J.S. , Jaspan H.B.",Hormonal contraception alters vaginal microbiota and cytokines in South African adolescents in a randomized trial,Nature communications,2020,NA,Experiment 1,South Africa,Homo sapiens,Vagina,UBERON:0000996,Contraception,EFO:0009520,NET-En (norethisterone enanthate ) arm,COC (combined oral contraceptives) arm,Participants (adolescents) who were randomized to combined oral contraceptives.,28,35,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,antibiotic exposure,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 3A,14 November 2024,Tosin,"Tosin,WikiWorks",DESeq2 analysis of taxa differentially abundant between randomized study arms at crossover [COC (combined oral contraceptives) vs Net EN (norethisterone enanthate) arm].,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus jensenii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus taiwanensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella montpellierensis",1783272|1239|91061|186826|33958|1578|1596;1783272|1239|91061|186826|33958|1578|147802;1783272|1239|91061|186826|33958|1578|109790;1783272|1239|91061|186826|33958|1578|33959;1783272|1239|91061|186826|33958|1578|508451;1783272|1239|909932|1843489|31977|29465|187328,Complete,Svetlana up
bsdb:33149114/1/2,33149114,randomized controlled trial,33149114,10.1038/s41467-020-19382-9,NA,"Balle C., Konstantinus I.N., Jaumdally S.Z., Havyarimana E., Lennard K., Esra R., Barnabas S.L., Happel A.U., Moodie Z., Gill K., Pidwell T., Karaoz U., Brodie E., Maseko V., Gamieldien H., Bosinger S.E., Myer L., Bekker L.G., Passmore J.S. , Jaspan H.B.",Hormonal contraception alters vaginal microbiota and cytokines in South African adolescents in a randomized trial,Nature communications,2020,NA,Experiment 1,South Africa,Homo sapiens,Vagina,UBERON:0000996,Contraception,EFO:0009520,NET-En (norethisterone enanthate ) arm,COC (combined oral contraceptives) arm,Participants (adolescents) who were randomized to combined oral contraceptives.,28,35,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,antibiotic exposure,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 3A,15 November 2024,Tosin,"Tosin,WikiWorks",DESeq2 analysis of taxa differentially abundant between randomized study arms at crossover COC (combined oral contraceptives) vs Net EN (norethisterone enanthate  ) arm].,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella shahii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum saburreum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Mageeibacillus|s__Mageeibacillus indolicus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella baroniae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oulorum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema vincentii,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae",3379134|976|200643|171549|171552|2974257|228603;1783272|1239|186801|3085636|186803|1164882|467210;1783272|1239|186801|186802|216572|1637257|884684;1783272|201174|84998|84999|1643824|133925;3379134|976|200643|171549|171552|838|419005;3379134|976|200643|171549|171552|838|28129;3379134|976|200643|171549|171552|2974251|305719;3379134|976|200643|171549|171552|2974251|28136;3379134|976|200643|171549|2005525|195950;3379134|203691|203692|136|2845253|157|69710;3379134|976|117743|200644|2762318,Complete,Svetlana up
bsdb:33149114/2/1,33149114,randomized controlled trial,33149114,10.1038/s41467-020-19382-9,NA,"Balle C., Konstantinus I.N., Jaumdally S.Z., Havyarimana E., Lennard K., Esra R., Barnabas S.L., Happel A.U., Moodie Z., Gill K., Pidwell T., Karaoz U., Brodie E., Maseko V., Gamieldien H., Bosinger S.E., Myer L., Bekker L.G., Passmore J.S. , Jaspan H.B.",Hormonal contraception alters vaginal microbiota and cytokines in South African adolescents in a randomized trial,Nature communications,2020,NA,Experiment 2,South Africa,Homo sapiens,Vagina,UBERON:0000996,Contraception,EFO:0009520,CCVR (combined contraceptive vaginal ring) arm,COC (combined oral contraceptives) arm,Participants (adolescents) who were randomized to combined oral contraceptives.,32,35,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,antibiotic exposure,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 3A,15 November 2024,Tosin,"Tosin,WikiWorks",DESeq2 analysis of taxa differentially abundant between randomized study arms at crossover [COC (combined oral contraceptives) vs CCVR (combined contraceptive vaginal ring) arm].,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus taiwanensis",1783272|1239|91061|186826|33958|1578|1596;1783272|1239|91061|186826|33958|1578|33959;3379134|976|200643|171549|171552|838|28132;1783272|1239|91061|186826|33958|1578|508451,Complete,Svetlana up
bsdb:33149114/2/2,33149114,randomized controlled trial,33149114,10.1038/s41467-020-19382-9,NA,"Balle C., Konstantinus I.N., Jaumdally S.Z., Havyarimana E., Lennard K., Esra R., Barnabas S.L., Happel A.U., Moodie Z., Gill K., Pidwell T., Karaoz U., Brodie E., Maseko V., Gamieldien H., Bosinger S.E., Myer L., Bekker L.G., Passmore J.S. , Jaspan H.B.",Hormonal contraception alters vaginal microbiota and cytokines in South African adolescents in a randomized trial,Nature communications,2020,NA,Experiment 2,South Africa,Homo sapiens,Vagina,UBERON:0000996,Contraception,EFO:0009520,CCVR (combined contraceptive vaginal ring) arm,COC (combined oral contraceptives) arm,Participants (adolescents) who were randomized to combined oral contraceptives.,32,35,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,antibiotic exposure,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 3A,15 November 2024,Tosin,"Tosin,WikiWorks",DESeq2 analysis of taxa differentially abundant between randomized study arms at crossover [COC (combined oral contraceptives) vs CCVR (combined contraceptive vaginal ring) arm].,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii",3379134|1224|1236|91347|543;3379134|976|200643|171549|171552|838|419005,Complete,Svetlana up
bsdb:33149114/3/1,33149114,randomized controlled trial,33149114,10.1038/s41467-020-19382-9,NA,"Balle C., Konstantinus I.N., Jaumdally S.Z., Havyarimana E., Lennard K., Esra R., Barnabas S.L., Happel A.U., Moodie Z., Gill K., Pidwell T., Karaoz U., Brodie E., Maseko V., Gamieldien H., Bosinger S.E., Myer L., Bekker L.G., Passmore J.S. , Jaspan H.B.",Hormonal contraception alters vaginal microbiota and cytokines in South African adolescents in a randomized trial,Nature communications,2020,NA,Experiment 3,South Africa,Homo sapiens,Vagina,UBERON:0000996,Contraception,EFO:0009520,CCVR (combined contraceptive vaginal ring) arm,Net-En (norethisterone enanthate) arm,Participants (adolescents) who were randomized to injectable norethisterone enanthate.,32,28,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,antibiotic exposure,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 3A,15 November 2024,Tosin,"Tosin,WikiWorks",DESeq2 analysis of taxa differentially abundant between randomized study arms at crossover [Net-En (norethisterone enanthate) vs CCVR (combined contraceptive vaginal ring) arm].,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum saburreum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella baroniae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oulorum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas infelix,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema socranskii,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema vincentii,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae",1783272|201174|1760|2037|2049|1654;3379134|976|117743|200644|2762318|59735;1783272|1239|186801|3085636|186803|1164882|467210;3379134|976|200643|171549|171552|838|28133;3379134|976|200643|171549|171552|2974251|305719;3379134|976|200643|171549|171552|2974251|28136;1783272|1239|909932|909929|1843491|970|135082;3379134|976|200643|171549|2005525|195950;3379134|203691|203692|136|2845253|157;3379134|203691|203692|136|2845253|157|53419;3379134|203691|203692|136|2845253|157|69710;3379134|976|117743|200644|2762318,Complete,Svetlana up
bsdb:33149114/3/2,33149114,randomized controlled trial,33149114,10.1038/s41467-020-19382-9,NA,"Balle C., Konstantinus I.N., Jaumdally S.Z., Havyarimana E., Lennard K., Esra R., Barnabas S.L., Happel A.U., Moodie Z., Gill K., Pidwell T., Karaoz U., Brodie E., Maseko V., Gamieldien H., Bosinger S.E., Myer L., Bekker L.G., Passmore J.S. , Jaspan H.B.",Hormonal contraception alters vaginal microbiota and cytokines in South African adolescents in a randomized trial,Nature communications,2020,NA,Experiment 3,South Africa,Homo sapiens,Vagina,UBERON:0000996,Contraception,EFO:0009520,CCVR (combined contraceptive vaginal ring) arm,Net-En (norethisterone enanthate) arm,Participants (adolescents) who were randomized to injectable norethisterone enanthate.,32,28,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,antibiotic exposure,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 3A,15 November 2024,Tosin,"Tosin,WikiWorks",DESeq2 analysis of taxa differentially abundant between randomized study arms at crossover [Net-En (norethisterone enanthate) vs CCVR (combined contraceptive vaginal ring) arm].,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemelliphila|s__Gemelliphila asaccharolytica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus jensenii,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma hominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens",1783272|201174|1760|85004|31953|2701;1783272|1239|91061|1385|539738|3076174|502393;1783272|1239|91061|186826|33958|1578|109790;1783272|544448|2790996|2895623|2895509|2098;3379134|976|200643|171549|171552|838|28130,Complete,Svetlana up
bsdb:33149114/4/2,33149114,randomized controlled trial,33149114,10.1038/s41467-020-19382-9,NA,"Balle C., Konstantinus I.N., Jaumdally S.Z., Havyarimana E., Lennard K., Esra R., Barnabas S.L., Happel A.U., Moodie Z., Gill K., Pidwell T., Karaoz U., Brodie E., Maseko V., Gamieldien H., Bosinger S.E., Myer L., Bekker L.G., Passmore J.S. , Jaspan H.B.",Hormonal contraception alters vaginal microbiota and cytokines in South African adolescents in a randomized trial,Nature communications,2020,NA,Experiment 4,South Africa,Homo sapiens,Vagina,UBERON:0000996,Contraception,EFO:0009520,Baseline [COC (combined oral contraceptives)] arm,Crossover [COC (combined oral contraceptives)] arm,Participants (adolescents) who were randomized to combined oral contraceptives at crossover.,34,34,3 months,16S,4,Illumina,raw counts,DESeq2,0.5,TRUE,NA,NA,antibiotic exposure,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 3B,15 November 2024,Tosin,"Tosin,WikiWorks",DESeq2 analysis of taxa differentially abundant between randomized study arms at Baseline [COC (combined oral contraceptives) vs Crossover [COC (combined oral contraceptives)].,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,1783272|1239|91061|186826|33958|1578|147802,Complete,Svetlana up
bsdb:33149114/4/3,33149114,randomized controlled trial,33149114,10.1038/s41467-020-19382-9,NA,"Balle C., Konstantinus I.N., Jaumdally S.Z., Havyarimana E., Lennard K., Esra R., Barnabas S.L., Happel A.U., Moodie Z., Gill K., Pidwell T., Karaoz U., Brodie E., Maseko V., Gamieldien H., Bosinger S.E., Myer L., Bekker L.G., Passmore J.S. , Jaspan H.B.",Hormonal contraception alters vaginal microbiota and cytokines in South African adolescents in a randomized trial,Nature communications,2020,NA,Experiment 4,South Africa,Homo sapiens,Vagina,UBERON:0000996,Contraception,EFO:0009520,Baseline [COC (combined oral contraceptives)] arm,Crossover [COC (combined oral contraceptives)] arm,Participants (adolescents) who were randomized to combined oral contraceptives at crossover.,34,34,3 months,16S,4,Illumina,raw counts,DESeq2,0.5,TRUE,NA,NA,antibiotic exposure,NA,unchanged,NA,NA,NA,NA,Signature 3,Table 3B,15 November 2024,Tosin,"Tosin,WikiWorks",Deseq2 analysis of taxa differentially abundant between randomized study arms at Baseline [COC (combined oral contraceptives) vs Crossover [COC (combined oral contraceptives)].,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium moniliforme,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens",1783272|1239|186801|186802|31979|1485|39489;1783272|1239|186801|186802|31979|1485|1502,Complete,Svetlana up
bsdb:33149114/5/1,33149114,randomized controlled trial,33149114,10.1038/s41467-020-19382-9,NA,"Balle C., Konstantinus I.N., Jaumdally S.Z., Havyarimana E., Lennard K., Esra R., Barnabas S.L., Happel A.U., Moodie Z., Gill K., Pidwell T., Karaoz U., Brodie E., Maseko V., Gamieldien H., Bosinger S.E., Myer L., Bekker L.G., Passmore J.S. , Jaspan H.B.",Hormonal contraception alters vaginal microbiota and cytokines in South African adolescents in a randomized trial,Nature communications,2020,NA,Experiment 5,South Africa,Homo sapiens,Vagina,UBERON:0000996,Contraception,EFO:0009520,Baseline [Net-En (norethisterone enanthate)] arm,Crossover [Net-En (norethisterone enanthate)] arm,Participants (adolescents) who were randomized to norethisterone enanthate at crossover.,32,32,3 months,16S,4,Illumina,raw counts,DESeq2,0.5,TRUE,NA,NA,antibiotic exposure,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 3B,15 January 2025,Tosin,"Tosin,WikiWorks",Deseq2 analysis of taxa differentially abundant between randomized study arms at Baseline [Net-En (norethisterone enanthate) vs Crossover [Net-En (norethisterone enanthate)].,increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma hominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens",3379134|29547|3031852|213849|72294|194;1783272|544448|2790996|2895623|2895509|2098;3379134|976|200643|171549|171552|838|28130,Complete,Svetlana up
bsdb:33158452/1/1,33158452,laboratory experiment,33158452,10.1186/s40168-020-00928-4,NA,"Jasinska A.J., Dong T.S., Lagishetty V., Katzka W., Jacobs J.P., Schmitt C.A., Cramer J.D., Ma D., Coetzer W.G., Grobler J.P., Turner T.R., Freimer N., Pandrea I. , Apetrei C.","Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys",Microbiome,2020,"Acute infection, Microbiome, Primate, Proteobacteria, SIV, Succinivibrio",Experiment 1,South Africa,Chlorocebus pygerythrus,Feces,UBERON:0001988,Simian immunodeficiency virus infection,NA,Simian Immunodeficiency Virus (SIV) negative,Simian Immunodeficiency Virus (SIV) positive,SIV positive refers to vervet monkeys that are infected with Simian Immunodeficiency Virus (SIV),11,33,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,geographic area,sex",NA,unchanged,increased,NA,NA,NA,Signature 1,Fig. 3C,29 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of microbiota between SIV infected and uninfected in fecal samples.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|2037|2049|1654;1783272|1239|186801|3085636|186803|653683;3379134|976|117743|200644|49546|1016;1783272|1239|186801|186802|186807|51514;3384189|32066|203490|203491|203492|848;3379134|1224|1236|135625|712|724;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|206351|481|482;1783272|1239|186801|3085636|186803|265975;3379134|1224|28216|80840|75682|846;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|171551|836;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;1783272|201174|1760|85006|1268|32207;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:33158452/1/2,33158452,laboratory experiment,33158452,10.1186/s40168-020-00928-4,NA,"Jasinska A.J., Dong T.S., Lagishetty V., Katzka W., Jacobs J.P., Schmitt C.A., Cramer J.D., Ma D., Coetzer W.G., Grobler J.P., Turner T.R., Freimer N., Pandrea I. , Apetrei C.","Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys",Microbiome,2020,"Acute infection, Microbiome, Primate, Proteobacteria, SIV, Succinivibrio",Experiment 1,South Africa,Chlorocebus pygerythrus,Feces,UBERON:0001988,Simian immunodeficiency virus infection,NA,Simian Immunodeficiency Virus (SIV) negative,Simian Immunodeficiency Virus (SIV) positive,SIV positive refers to vervet monkeys that are infected with Simian Immunodeficiency Virus (SIV),11,33,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,geographic area,sex",NA,unchanged,increased,NA,NA,NA,Signature 2,Fig. 3C,30 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of microbiota between SIV infected and uninfected in fecal samples.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,3379134|1224|1236|135624|83763|83770,Complete,Svetlana up
bsdb:33158452/2/1,33158452,laboratory experiment,33158452,10.1186/s40168-020-00928-4,NA,"Jasinska A.J., Dong T.S., Lagishetty V., Katzka W., Jacobs J.P., Schmitt C.A., Cramer J.D., Ma D., Coetzer W.G., Grobler J.P., Turner T.R., Freimer N., Pandrea I. , Apetrei C.","Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys",Microbiome,2020,"Acute infection, Microbiome, Primate, Proteobacteria, SIV, Succinivibrio",Experiment 2,South Africa,Chlorocebus pygerythrus,Rectum,UBERON:0001052,Simian immunodeficiency virus infection,NA,Simian Immunodeficiency Virus (SIV) negative,Simian Immunodeficiency Virus (SIV) positive,SIV positive refers to vervet monkeys that are infected with Simian Immunodeficiency Virus (SIV),41,62,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,geographic area,sex",NA,NA,NA,NA,NA,NA,Signature 1,Fig. 3C,29 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of microbiota between SIV infected and uninfected in rectal samples.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio",1783272|1239|186801|3085636|186803|830;1783272|1239|186801|186802|216572|119852;3379134|1224|1236|135624|83763|83770,Complete,Svetlana up
bsdb:33158452/3/1,33158452,laboratory experiment,33158452,10.1186/s40168-020-00928-4,NA,"Jasinska A.J., Dong T.S., Lagishetty V., Katzka W., Jacobs J.P., Schmitt C.A., Cramer J.D., Ma D., Coetzer W.G., Grobler J.P., Turner T.R., Freimer N., Pandrea I. , Apetrei C.","Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys",Microbiome,2020,"Acute infection, Microbiome, Primate, Proteobacteria, SIV, Succinivibrio",Experiment 3,South Africa,Chlorocebus pygerythrus,Vagina,UBERON:0000996,Simian immunodeficiency virus infection,NA,Simian Immunodeficiency Virus (SIV) negative,Simian Immunodeficiency Virus (SIV) positive,SIV positive refers to vervet monkeys that are infected with Simian Immunodeficiency Virus (SIV),10,41,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,geographic area,sex",NA,NA,NA,NA,NA,NA,Signature 1,Fig. 3C,29 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of microbiota between SIV infected and uninfected in vaginal samples.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:873,3379134|976|200643|171549|171552|838|1262936,Complete,Svetlana up
bsdb:33158452/3/2,33158452,laboratory experiment,33158452,10.1186/s40168-020-00928-4,NA,"Jasinska A.J., Dong T.S., Lagishetty V., Katzka W., Jacobs J.P., Schmitt C.A., Cramer J.D., Ma D., Coetzer W.G., Grobler J.P., Turner T.R., Freimer N., Pandrea I. , Apetrei C.","Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys",Microbiome,2020,"Acute infection, Microbiome, Primate, Proteobacteria, SIV, Succinivibrio",Experiment 3,South Africa,Chlorocebus pygerythrus,Vagina,UBERON:0000996,Simian immunodeficiency virus infection,NA,Simian Immunodeficiency Virus (SIV) negative,Simian Immunodeficiency Virus (SIV) positive,SIV positive refers to vervet monkeys that are infected with Simian Immunodeficiency Virus (SIV),10,41,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,geographic area,sex",NA,NA,NA,NA,NA,NA,Signature 2,Fig. 3C,29 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of microbiota between SIV infected and uninfected in vaginal samples.,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Rodentibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|201174|1760|85007|1653|1716;3379134|1224|1236|135625|712|1960084;1783272|1239|186801|186802|31979|1266;1783272|1239|91061|186826|1300|1301;3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:33158452/4/1,33158452,laboratory experiment,33158452,10.1186/s40168-020-00928-4,NA,"Jasinska A.J., Dong T.S., Lagishetty V., Katzka W., Jacobs J.P., Schmitt C.A., Cramer J.D., Ma D., Coetzer W.G., Grobler J.P., Turner T.R., Freimer N., Pandrea I. , Apetrei C.","Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys",Microbiome,2020,"Acute infection, Microbiome, Primate, Proteobacteria, SIV, Succinivibrio",Experiment 4,South Africa,Chlorocebus pygerythrus,Vagina,UBERON:0000996,Simian immunodeficiency virus infection,NA,Alkaline,Acidic,Acidic refers to the vaginal-PH below 7. It is found in vagitype A of vervets monkeys.,21,16,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Supplementary Figure 4D,29 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant microbial genera in acidic vaginal samples vs. alkaline vaginal samples.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Trichococcus,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma",1783272|201174|1760|2037|2049|1654;1783272|1239|91061|186826|186827|1375;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|91061|186826|186828;1783272|1239|186801|186802|31979|1266;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|186828|82802;1783272|544448|2790996|2790998|2129,Complete,Svetlana up
bsdb:33158452/4/2,33158452,laboratory experiment,33158452,10.1186/s40168-020-00928-4,NA,"Jasinska A.J., Dong T.S., Lagishetty V., Katzka W., Jacobs J.P., Schmitt C.A., Cramer J.D., Ma D., Coetzer W.G., Grobler J.P., Turner T.R., Freimer N., Pandrea I. , Apetrei C.","Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys",Microbiome,2020,"Acute infection, Microbiome, Primate, Proteobacteria, SIV, Succinivibrio",Experiment 4,South Africa,Chlorocebus pygerythrus,Vagina,UBERON:0000996,Simian immunodeficiency virus infection,NA,Alkaline,Acidic,Acidic refers to the vaginal-PH below 7. It is found in vagitype A of vervets monkeys.,21,16,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Supplementary Figure 4D,29 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant microbial genera in acidic vaginal samples vs. alkaline vaginal samples.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Lentisphaerota",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|207244;1783272|1239|909932|909929|1843491|82373;1783272|201174|1760|85004|31953|1678;3379134|29547|3031852|213849|72294|194;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171551|836;1783272|1239|909932|1843489|31977;3379134|256845,Complete,Svetlana up
bsdb:33158452/5/1,33158452,laboratory experiment,33158452,10.1186/s40168-020-00928-4,NA,"Jasinska A.J., Dong T.S., Lagishetty V., Katzka W., Jacobs J.P., Schmitt C.A., Cramer J.D., Ma D., Coetzer W.G., Grobler J.P., Turner T.R., Freimer N., Pandrea I. , Apetrei C.","Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys",Microbiome,2020,"Acute infection, Microbiome, Primate, Proteobacteria, SIV, Succinivibrio",Experiment 5,South Africa,Chlorocebus pygerythrus,Rectum,UBERON:0001052,Simian immunodeficiency virus infection,NA,Free_State,KwaZulu-Natal,KwaZulu-Natal refers to vervet monkeys representing the Indian Ocean Coastal Belt (N = 33) and Savanna (N = 12) biomes from the KwaZulu-Natal Province (KZN),57,45,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 5E,29 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between KZN and FS in rectal microbiome,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:352,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Methanobacteriati|p__Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomethylophilaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Pseudomonadati|p__Spirochaetota|s__Spirochaetes bacterium GWE2_31_10,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Syntrophomonadaceae|g__Syntrophomonas,k__Pseudomonadati|p__Lentisphaerota",3379134|976|200643|171549|171552|1283313;1783272|1239|186801|186802|216572|52784;3379134|1224|28216|80840|119060;1783272|1239|186801|3085636|186803|830;1783272|1239|186801|186802|31979|1485|1262798;1783272|1239|186801|186802|186807|51514;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|946234;1783272|1239|91061|186826|33958|1578;3366610|28890|183925|2158|2159|2172;3366610|2283796|183967|1235850|2517203;1783272|201174|1760|2037|2049|2050;1783272|1239|186801|186802|216572;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|909932|1843488|909930|33024;3379134|1224;1783272|1239|909932|909929|1843491|970;1783272|1239|526524|526525|128827|123375;3379134|203691|1802186;1783272|1239|186801|186802|68298|862;3379134|256845,Complete,Svetlana up
bsdb:33158452/5/2,33158452,laboratory experiment,33158452,10.1186/s40168-020-00928-4,NA,"Jasinska A.J., Dong T.S., Lagishetty V., Katzka W., Jacobs J.P., Schmitt C.A., Cramer J.D., Ma D., Coetzer W.G., Grobler J.P., Turner T.R., Freimer N., Pandrea I. , Apetrei C.","Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys",Microbiome,2020,"Acute infection, Microbiome, Primate, Proteobacteria, SIV, Succinivibrio",Experiment 5,South Africa,Chlorocebus pygerythrus,Rectum,UBERON:0001052,Simian immunodeficiency virus infection,NA,Free_State,KwaZulu-Natal,KwaZulu-Natal refers to vervet monkeys representing the Indian Ocean Coastal Belt (N = 33) and Savanna (N = 12) biomes from the KwaZulu-Natal Province (KZN),57,45,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 5E,29 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between KZN and FS in rectal microbiome,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetitomaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Methanobacteriati|p__Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Candidatus Methanogranum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Fibrobacterota|c__Fibrobacteria|o__Fibrobacterales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 28-4,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:56,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:873",1783272|1239|186801|3085636|186803|31980;3379134|976|200643|171549|815|816;3379134|976|200643|171549|1853231|574697;3366610|2283796|183967|1235850|1577788|1577789;1783272|1239|186801|186802|31979|1485;1783272|1239|91061|186826|81852|1350;3379134|65842|204430|218872;3379134|29547|3031852|213849|72293|209;1783272|1239|186801|3082720|186804|1505657;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|397287;1783272|544448|31969;1783272|1239|186801|3085636|186803|265975;1783272|201174|1760|2037|2049|184869;1783272|1239|1263031;3379134|976|200643|171549|171552|838|1262936,Complete,Svetlana up
bsdb:33158452/6/1,33158452,laboratory experiment,33158452,10.1186/s40168-020-00928-4,NA,"Jasinska A.J., Dong T.S., Lagishetty V., Katzka W., Jacobs J.P., Schmitt C.A., Cramer J.D., Ma D., Coetzer W.G., Grobler J.P., Turner T.R., Freimer N., Pandrea I. , Apetrei C.","Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys",Microbiome,2020,"Acute infection, Microbiome, Primate, Proteobacteria, SIV, Succinivibrio",Experiment 6,South Africa,Chlorocebus pygerythrus,Feces,UBERON:0001988,Simian immunodeficiency virus infection,NA,Free_State,KwaZulu-Natal,KwaZulu-Natal refers to vervet monkeys representing the Indian Ocean Coastal Belt (N = 33) and Savanna (N = 12) biomes from the KwaZulu-Natal Province (KZN),27,16,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 5F,29 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between KZN and FS in fecal microbiome,increased,"k__Pseudomonadati|p__Fibrobacterota|c__Fibrobacteria|o__Fibrobacterales|f__Fibrobacteraceae|g__Fibrobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella",3379134|65842|204430|218872|204431|832;1783272|1239|526524|526525|128827|123375;3379134|976|200643|171549|171552|1283313,Complete,Svetlana up
bsdb:33158452/6/2,33158452,laboratory experiment,33158452,10.1186/s40168-020-00928-4,NA,"Jasinska A.J., Dong T.S., Lagishetty V., Katzka W., Jacobs J.P., Schmitt C.A., Cramer J.D., Ma D., Coetzer W.G., Grobler J.P., Turner T.R., Freimer N., Pandrea I. , Apetrei C.","Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys",Microbiome,2020,"Acute infection, Microbiome, Primate, Proteobacteria, SIV, Succinivibrio",Experiment 6,South Africa,Chlorocebus pygerythrus,Feces,UBERON:0001988,Simian immunodeficiency virus infection,NA,Free_State,KwaZulu-Natal,KwaZulu-Natal refers to vervet monkeys representing the Indian Ocean Coastal Belt (N = 33) and Savanna (N = 12) biomes from the KwaZulu-Natal Province (KZN),27,16,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 5F,29 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between KZN and FS in fecal microbiome,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetitomaculum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 28-4,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:873",1783272|1239|186801|3085636|186803|31980;1783272|1239|526524|526525|128827|1470349;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|3085636|186803|397287;1783272|1239|186801|3085636|186803|1506577;3379134|976|200643|171549|171552|838|1262936,Complete,Svetlana up
bsdb:33158452/8/1,33158452,laboratory experiment,33158452,10.1186/s40168-020-00928-4,NA,"Jasinska A.J., Dong T.S., Lagishetty V., Katzka W., Jacobs J.P., Schmitt C.A., Cramer J.D., Ma D., Coetzer W.G., Grobler J.P., Turner T.R., Freimer N., Pandrea I. , Apetrei C.","Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys",Microbiome,2020,"Acute infection, Microbiome, Primate, Proteobacteria, SIV, Succinivibrio",Experiment 8,South Africa,Chlorocebus pygerythrus,Rectum,UBERON:0001052,Simian immunodeficiency virus infection,NA,Female,Male,Male refers to the masculine gender of the vervet monkeys.,NA,NA,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 10B,29 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in males compared to females in rectum,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Spirochaetota|s__Spirochaetes bacterium GWE2_31_10,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:352",1783272|1239|186801|186802|186807|51514;1783272|1239|909932|909929|1843491|970;3379134|203691|1802186;1783272|1239|186801|186802|31979|1485|1262798,Complete,Svetlana up
bsdb:33158452/8/2,33158452,laboratory experiment,33158452,10.1186/s40168-020-00928-4,NA,"Jasinska A.J., Dong T.S., Lagishetty V., Katzka W., Jacobs J.P., Schmitt C.A., Cramer J.D., Ma D., Coetzer W.G., Grobler J.P., Turner T.R., Freimer N., Pandrea I. , Apetrei C.","Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys",Microbiome,2020,"Acute infection, Microbiome, Primate, Proteobacteria, SIV, Succinivibrio",Experiment 8,South Africa,Chlorocebus pygerythrus,Rectum,UBERON:0001052,Simian immunodeficiency virus infection,NA,Female,Male,Male refers to the masculine gender of the vervet monkeys.,NA,NA,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 10B,29 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in males compared to females in rectum,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Rodentibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus",3379134|976|200643|171549|171552|838;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|91061|186826|186827|1375;3379134|1224|1236|135625|712|1960084;1783272|201174|1760|2037|2049|2050,Complete,Svetlana up
bsdb:33158452/9/1,33158452,laboratory experiment,33158452,10.1186/s40168-020-00928-4,NA,"Jasinska A.J., Dong T.S., Lagishetty V., Katzka W., Jacobs J.P., Schmitt C.A., Cramer J.D., Ma D., Coetzer W.G., Grobler J.P., Turner T.R., Freimer N., Pandrea I. , Apetrei C.","Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys",Microbiome,2020,"Acute infection, Microbiome, Primate, Proteobacteria, SIV, Succinivibrio",Experiment 9,South Africa,Chlorocebus pygerythrus,Rectum,UBERON:0001052,Simian immunodeficiency virus infection,NA,Adult,Infant,Infant refers to vervet monkeys in their early years of life.,76,10,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,sex,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 11B,29 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant genera between the rectal microbiome in infants and adults.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Mannheimia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|815|816;3379134|1224|1236|135625|712|75984;3379134|976|200643|171549|2005525|375288;3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:33158452/9/2,33158452,laboratory experiment,33158452,10.1186/s40168-020-00928-4,NA,"Jasinska A.J., Dong T.S., Lagishetty V., Katzka W., Jacobs J.P., Schmitt C.A., Cramer J.D., Ma D., Coetzer W.G., Grobler J.P., Turner T.R., Freimer N., Pandrea I. , Apetrei C.","Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys",Microbiome,2020,"Acute infection, Microbiome, Primate, Proteobacteria, SIV, Succinivibrio",Experiment 9,South Africa,Chlorocebus pygerythrus,Rectum,UBERON:0001052,Simian immunodeficiency virus infection,NA,Adult,Infant,Infant refers to vervet monkeys in their early years of life.,76,10,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,sex,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 11B,29 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant genera between the rectal microbiome in infants and adults.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Herbinix",1783272|1239|909932|1843489|31977|39948;3379134|1224|28216|80840|995019|40544;1783272|201174|1760|85007|1653|1716;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|3085636|186803|1663717,Complete,Svetlana up
bsdb:33158452/10/1,33158452,laboratory experiment,33158452,10.1186/s40168-020-00928-4,NA,"Jasinska A.J., Dong T.S., Lagishetty V., Katzka W., Jacobs J.P., Schmitt C.A., Cramer J.D., Ma D., Coetzer W.G., Grobler J.P., Turner T.R., Freimer N., Pandrea I. , Apetrei C.","Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys",Microbiome,2020,"Acute infection, Microbiome, Primate, Proteobacteria, SIV, Succinivibrio",Experiment 10,South Africa,Chlorocebus pygerythrus,Feces,UBERON:0001988,Simian immunodeficiency virus infection,NA,Acute,Chronic,Chronic refers to the severity of the SIV infection in vervet monkeys.,4,23,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,geographic area,sex",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Supplementary Figure 14,30 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant fecal microbiome in chronic vs. acute SIV infection,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Herbinix,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae",1783272|1239|186801|3085636|186803|1663717;3379134|1224|28216|80840|119060,Complete,Svetlana up
bsdb:33158452/10/2,33158452,laboratory experiment,33158452,10.1186/s40168-020-00928-4,NA,"Jasinska A.J., Dong T.S., Lagishetty V., Katzka W., Jacobs J.P., Schmitt C.A., Cramer J.D., Ma D., Coetzer W.G., Grobler J.P., Turner T.R., Freimer N., Pandrea I. , Apetrei C.","Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys",Microbiome,2020,"Acute infection, Microbiome, Primate, Proteobacteria, SIV, Succinivibrio",Experiment 10,South Africa,Chlorocebus pygerythrus,Feces,UBERON:0001988,Simian immunodeficiency virus infection,NA,Acute,Chronic,Chronic refers to the severity of the SIV infection in vervet monkeys.,4,23,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,geographic area,sex",NA,unchanged,unchanged,NA,NA,NA,Signature 2,Supplementary Figure 14,30 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant fecal microbiome in chronic vs. acute SIV infection,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetitomaculum,1783272|1239|186801|3085636|186803|31980,Complete,Svetlana up
bsdb:33158452/11/1,33158452,laboratory experiment,33158452,10.1186/s40168-020-00928-4,NA,"Jasinska A.J., Dong T.S., Lagishetty V., Katzka W., Jacobs J.P., Schmitt C.A., Cramer J.D., Ma D., Coetzer W.G., Grobler J.P., Turner T.R., Freimer N., Pandrea I. , Apetrei C.","Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys",Microbiome,2020,"Acute infection, Microbiome, Primate, Proteobacteria, SIV, Succinivibrio",Experiment 11,South Africa,Chlorocebus pygerythrus,Rectum,UBERON:0001052,Simian immunodeficiency virus infection,NA,Acute,Chronic,Chronic refers to the severity of the SIV infection in vervet monkeys.,11,43,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,geographic area,sex",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Supplementary Figure 14,30 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant rectal microbiome in chronic vs. acute SIV infection,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinotignum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus",1783272|201174|1760|2037|2049|1653174;1783272|1239|91061|186826|186827|66831;1783272|1239|186801|186802|3085642|580596,Complete,Svetlana up
bsdb:33158452/12/1,33158452,laboratory experiment,33158452,10.1186/s40168-020-00928-4,NA,"Jasinska A.J., Dong T.S., Lagishetty V., Katzka W., Jacobs J.P., Schmitt C.A., Cramer J.D., Ma D., Coetzer W.G., Grobler J.P., Turner T.R., Freimer N., Pandrea I. , Apetrei C.","Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys",Microbiome,2020,"Acute infection, Microbiome, Primate, Proteobacteria, SIV, Succinivibrio",Experiment 12,South Africa,Chlorocebus pygerythrus,Vagina,UBERON:0000996,Simian immunodeficiency virus infection,NA,Acute,Chronic,Chronic refers to the severity of the SIV infection in vervet monkeys.,6,30,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,geographic area,sex",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Supplementary Figure 14,30 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant vaginal microbiome in chronic vs. acute SIV infection,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Lentisphaerota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium",3379134|976|200643|171549|2005473;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|186802|216572;3379134|256845;1783272|1239|526524|526525|128827|123375,Complete,Svetlana up
bsdb:33178173/2/1,33178173,laboratory experiment,33178173,10.3389/fmicb.2020.591462,NA,"Li Q. , Pan Y.",Differential Responses to Dietary Protein and Carbohydrate Ratio on Gut Microbiome in Obese vs. Lean Cats,Frontiers in microbiology,2020,"carbohydrate, cat, diet, feline, microbiome, obesity, protein",Experiment 2,United States of America,Felis catus,Feces,UBERON:0001988,Diet,EFO:0002755,CON-fed OW cats at T1(end of baseline feeding),CON-fed OW cats at T2 (end of intervention),Overweight domestic felines placed on the control diet at T2 (end of intervention),20,10,NA,16S,34,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 1,Table S4,5 October 2023,Deacme,"Deacme,Folakunmi,WikiWorks",Increased abundance in CON-fed OW cats at T2 (end of intervention),increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",1783272|201174|84998|84999|84107;3379134|976|200643|171549|171551;3379134|976|200643|171549|171550,Complete,Folakunmi
bsdb:33178173/3/1,33178173,laboratory experiment,33178173,10.3389/fmicb.2020.591462,NA,"Li Q. , Pan Y.",Differential Responses to Dietary Protein and Carbohydrate Ratio on Gut Microbiome in Obese vs. Lean Cats,Frontiers in microbiology,2020,"carbohydrate, cat, diet, feline, microbiome, obesity, protein",Experiment 3,United States of America,Felis catus,Feces,UBERON:0001988,Diet,EFO:0002755,CON-fed OW cats at T1(end of baseline feeding),HPLC-fed OW cats at T2 (end of intervention),Overweight domestic felines placed on the HPLC diet at T2 (end of intervention),20,10,NA,16S,34,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,"age,sex",NA,NA,increased,NA,NA,NA,increased,Signature 1,Table S4,5 October 2023,Deacme,"Deacme,Folakunmi,WikiWorks",Increased abundance in HPLC-fed OW cats at T2 (end of intervention),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptacetobacter|s__Peptacetobacter hiranonis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|186802|31979;1783272|201174|84998|84999|84107;1783272|1239|186801|186802|541000;1783272|1239|186801|3082720|186804|2743582|89152;1783272|1239|186801|186802|186807;1783272|1239|186801|3085636|186803,Complete,Folakunmi
bsdb:33178173/3/2,33178173,laboratory experiment,33178173,10.3389/fmicb.2020.591462,NA,"Li Q. , Pan Y.",Differential Responses to Dietary Protein and Carbohydrate Ratio on Gut Microbiome in Obese vs. Lean Cats,Frontiers in microbiology,2020,"carbohydrate, cat, diet, feline, microbiome, obesity, protein",Experiment 3,United States of America,Felis catus,Feces,UBERON:0001988,Diet,EFO:0002755,CON-fed OW cats at T1(end of baseline feeding),HPLC-fed OW cats at T2 (end of intervention),Overweight domestic felines placed on the HPLC diet at T2 (end of intervention),20,10,NA,16S,34,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,"age,sex",NA,NA,increased,NA,NA,NA,increased,Signature 2,Table S4,10 October 2023,Deacme,"Deacme,Folakunmi,WikiWorks",Decreased abundance in HPLC-fed OW cats at T2 (end of intervention),decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius",1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953;3379134|976|200643|171549|815|909656|310297,Complete,Folakunmi
bsdb:33178173/4/1,33178173,laboratory experiment,33178173,10.3389/fmicb.2020.591462,NA,"Li Q. , Pan Y.",Differential Responses to Dietary Protein and Carbohydrate Ratio on Gut Microbiome in Obese vs. Lean Cats,Frontiers in microbiology,2020,"carbohydrate, cat, diet, feline, microbiome, obesity, protein",Experiment 4,United States of America,Felis catus,Feces,UBERON:0001988,Diet,EFO:0002755,CON-fed OW cats at T2 (end of intervention),HPLC-fed OW cats at T2 (end of intervention),HPLC-fed overweight domestic felines at T2 (end of intervention),10,10,NA,16S,34,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,"age,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"Table S4, Table 3, Text results (Dietary Intervention Changes Gut Microbiota in OW Cats)",10 October 2023,Deacme,"Deacme,Folakunmi,WikiWorks",Increased abundance in HPLC-fed OW cats at T2 (end of intervention),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptacetobacter|s__Peptacetobacter hiranonis",1783272|1239|186801|186802|31979;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3082720|186804|2743582|89152,Complete,Folakunmi
bsdb:33178173/4/2,33178173,laboratory experiment,33178173,10.3389/fmicb.2020.591462,NA,"Li Q. , Pan Y.",Differential Responses to Dietary Protein and Carbohydrate Ratio on Gut Microbiome in Obese vs. Lean Cats,Frontiers in microbiology,2020,"carbohydrate, cat, diet, feline, microbiome, obesity, protein",Experiment 4,United States of America,Felis catus,Feces,UBERON:0001988,Diet,EFO:0002755,CON-fed OW cats at T2 (end of intervention),HPLC-fed OW cats at T2 (end of intervention),HPLC-fed overweight domestic felines at T2 (end of intervention),10,10,NA,16S,34,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,"age,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 2,"Table S4, Table 3, Text results (Dietary Intervention Changes Gut Microbiota in OW Cats)",10 October 2023,Deacme,"Deacme,Folakunmi,WikiWorks",Decreased abundance in HPLC-fed OW cats at T2 (end of intervention),decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|1239|909932|1843489|31977|906;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|171551;3379134|976|200643|171549|171550;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977,Complete,Folakunmi
bsdb:33184260/1/1,33184260,prospective cohort,33184260,10.1038/s41522-020-00162-8,NA,"Feehily C., Crosby D., Walsh C.J., Lawton E.M., Higgins S., McAuliffe F.M. , Cotter P.D.",Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth,NPJ biofilms and microbiomes,2020,NA,Experiment 1,Ireland,Homo sapiens,"Posterior fornix of vagina,External cervical os","UBERON:0016486,UBERON:0013760",Spontaneous preterm birth,EFO:0006917,Full-term Birth,Preterm Birth,Pregnant women who delivered before 37 weeks’ gestation.,41,8,Currently on antibiotics,WMS,NA,Illumina,raw counts,"T-Test,Linear Regression",0.25,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 2b + Figure 2C,7 October 2023,Joan Chuks,"Joan Chuks,ChiomaBlessing,WikiWorks",Differentially abundant species for Preterm Birth (PTB) within the delivery outcome group compared to Full-term birth (FTB),increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus christensenii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Umbribacter|s__Umbribacter vaginalis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella greenwoodii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella colorans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera lornae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia vaginalis,k__Bacillati|p__Bacillota|c__Tissierellia|s__Tissierellia bacterium KA00581,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. S7-1-8",1783272|1239|91061|186826|186827|1375|87541;1783272|201174|84998|1643822|1643826|3472368|1588753;1783272|1239|909932|1843489|31977|39948|309120;1783272|201174|84998|84999|1643824|2767327|82135;1783272|201174|1760|85004|31953|2701|2914925;1783272|201174|1760|85004|31953|2701|2702;1783272|201174|1760|85004|31953|2701|2702;3379134|976|200643|171549|171552|52228|1703337;3379134|976|200643|171549|171552|2974257|386414;1783272|1239|186801|3085636|186803|1898203;1783272|1239|909932|1843489|31977|906|699218;3379134|976|200643|171549|171552|838|419005;3379134|976|200643|171549|171552|838|28125;3379134|976|200643|171549|171552|838|470565;1783272|201174|1760|85004|31953|196081|230143;3384189|32066|203490|203491|1129771|168808|40543;3384189|32066|203490|203491|1129771|168808|187101;1783272|1239|1737404|1588751;1783272|1239|186801|3085636|186803|1213720;3379134|976|200643|171549|171552|838|1284775,Complete,ChiomaBlessing
bsdb:33184260/1/2,33184260,prospective cohort,33184260,10.1038/s41522-020-00162-8,NA,"Feehily C., Crosby D., Walsh C.J., Lawton E.M., Higgins S., McAuliffe F.M. , Cotter P.D.",Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth,NPJ biofilms and microbiomes,2020,NA,Experiment 1,Ireland,Homo sapiens,"Posterior fornix of vagina,External cervical os","UBERON:0016486,UBERON:0013760",Spontaneous preterm birth,EFO:0006917,Full-term Birth,Preterm Birth,Pregnant women who delivered before 37 weeks’ gestation.,41,8,Currently on antibiotics,WMS,NA,Illumina,raw counts,"T-Test,Linear Regression",0.25,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 2b + Figure 2C,7 October 2023,Joan Chuks,"Joan Chuks,ChiomaBlessing,WikiWorks",Differentially abundant species for Preterm Birth (PTB) within the delivery outcome group compared to Full-term birth (FTB),decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii",1783272|201174|1760|85004|31953|1678|1685;1783272|1239|91061|186826|33958|1578|47770;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|91061|186826|33958|1578|33959,Complete,ChiomaBlessing
bsdb:33184260/2/1,33184260,prospective cohort,33184260,10.1038/s41522-020-00162-8,NA,"Feehily C., Crosby D., Walsh C.J., Lawton E.M., Higgins S., McAuliffe F.M. , Cotter P.D.",Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth,NPJ biofilms and microbiomes,2020,NA,Experiment 2,Ireland,Homo sapiens,"Posterior fornix of vagina,External cervical os","UBERON:0016486,UBERON:0013760",Spontaneous preterm birth,EFO:0006917,Low-risk controls,Risk Group,Pregnant women with either a history of previous spontaneous preterm birth (risk_PTB) or women with risk factors for preterm birth but who delivered full term (risk_FTB),14,35,Currently on antibiotics,WMS,NA,Illumina,raw counts,Linear Regression,0.25,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2C,27 October 2023,Joan Chuks,"Joan Chuks,WikiWorks",Differentially abundant species within the Risk group.,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,1783272|201174|1760|85004|31953|1678|1685,Complete,ChiomaBlessing
bsdb:33184260/2/2,33184260,prospective cohort,33184260,10.1038/s41522-020-00162-8,NA,"Feehily C., Crosby D., Walsh C.J., Lawton E.M., Higgins S., McAuliffe F.M. , Cotter P.D.",Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth,NPJ biofilms and microbiomes,2020,NA,Experiment 2,Ireland,Homo sapiens,"Posterior fornix of vagina,External cervical os","UBERON:0016486,UBERON:0013760",Spontaneous preterm birth,EFO:0006917,Low-risk controls,Risk Group,Pregnant women with either a history of previous spontaneous preterm birth (risk_PTB) or women with risk factors for preterm birth but who delivered full term (risk_FTB),14,35,Currently on antibiotics,WMS,NA,Illumina,raw counts,Linear Regression,0.25,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2C,27 October 2023,Joan Chuks,"Joan Chuks,WikiWorks",Differentially abundant species within the Risk group,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Caloramator|s__Caloramator mitchellensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium sp. 852013-50091_SCH5140682,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia",1783272|1239|186801|186802|31979|44258|908809;1783272|201174|1760|85007|1762|1763|1834109;3379134|1224|1236|135614|32033|40323|40324,Complete,ChiomaBlessing
bsdb:33184260/3/1,33184260,prospective cohort,33184260,10.1038/s41522-020-00162-8,NA,"Feehily C., Crosby D., Walsh C.J., Lawton E.M., Higgins S., McAuliffe F.M. , Cotter P.D.",Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth,NPJ biofilms and microbiomes,2020,NA,Experiment 3,Ireland,Homo sapiens,"Posterior fornix of vagina,External cervical os","UBERON:0013760,UBERON:0016486",Spontaneous preterm birth,EFO:0006917,No Previous Preterm birth,Previous Preterm birth,Pregnant women with a history of previous spontaneous preterm birth (PTB),20,29,Currently on antibiotics,WMS,NA,Illumina,raw counts,Linear Regression,0.25,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2C,27 October 2023,Joan Chuks,"Joan Chuks,WikiWorks",Differentially abundant species for Previous Preterm birth(PTB) group,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Caloramator|s__Caloramator mitchellensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium sp. 852013-50091_SCH5140682,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus rhamnosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Virgibacillus|s__Virgibacillus profundi,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Desulfuromonadales|f__Trichloromonadaceae|g__Trichloromonas|s__Trichloromonas acetexigens",3379134|976|200643|171549|815|816|246787;1783272|1239|186801|186802|31979|44258|908809;1783272|201174|1760|85007|1762|1763|1834109;3379134|1224|1236|135614|32033|40323|40324;1783272|1239|91061|186826|33958|2759736|47715;1783272|1239|91061|1385|186817|84406|2024555;3379134|200940|3031651|69541|3031663|3031666|38815,Complete,ChiomaBlessing
bsdb:33184260/3/2,33184260,prospective cohort,33184260,10.1038/s41522-020-00162-8,NA,"Feehily C., Crosby D., Walsh C.J., Lawton E.M., Higgins S., McAuliffe F.M. , Cotter P.D.",Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth,NPJ biofilms and microbiomes,2020,NA,Experiment 3,Ireland,Homo sapiens,"Posterior fornix of vagina,External cervical os","UBERON:0013760,UBERON:0016486",Spontaneous preterm birth,EFO:0006917,No Previous Preterm birth,Previous Preterm birth,Pregnant women with a history of previous spontaneous preterm birth (PTB),20,29,Currently on antibiotics,WMS,NA,Illumina,raw counts,Linear Regression,0.25,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2C,27 October 2023,Joan Chuks,"Joan Chuks,WikiWorks",Differentially abundant species for Previous Preterm birth(PTB) group,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. infantis",1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|1678|216816|1682,Complete,ChiomaBlessing
bsdb:33185912/1/1,33185912,"cross-sectional observational, not case-control",33185912,10.1111/ene.14644,NA,"Melis M., Vascellari S., Santoru M.L., Oppo V., Fabbri M., Sarchioto M., Murgia D., Zibetti M., Lopiano L., Serra A., Palmas V., Pisanu S., Perra D., Madau V., Cusano R., Uva P., Mereu A., Contu P., Morelli M., Atzori L., Melis M., Manzin A. , Cossu G.",Gut microbiota and metabolome distinctive features in Parkinson disease: Focus on levodopa and levodopa-carbidopa intrajejunal gel,European journal of neurology,2021,"LCIG, Parkinson, duodopa, levodopa, microbiota",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Naive,Levodopa (LD),Parkinson’s Disease patients treated with Levodopa (LD),23,46,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Figure 3A,12 April 2025,Anne-mariesharp,"Anne-mariesharp,Ese",LEfSE comparison between Levodopa (LD) and Naive groups showing significantly enriched taxa,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix|s__Erysipelothrix muris",1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|526524|526525|128827|1647|380638,Complete,KateRasheed
bsdb:33185912/1/2,33185912,"cross-sectional observational, not case-control",33185912,10.1111/ene.14644,NA,"Melis M., Vascellari S., Santoru M.L., Oppo V., Fabbri M., Sarchioto M., Murgia D., Zibetti M., Lopiano L., Serra A., Palmas V., Pisanu S., Perra D., Madau V., Cusano R., Uva P., Mereu A., Contu P., Morelli M., Atzori L., Melis M., Manzin A. , Cossu G.",Gut microbiota and metabolome distinctive features in Parkinson disease: Focus on levodopa and levodopa-carbidopa intrajejunal gel,European journal of neurology,2021,"LCIG, Parkinson, duodopa, levodopa, microbiota",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Naive,Levodopa (LD),Parkinson’s Disease patients treated with Levodopa (LD),23,46,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,Figure 3A,12 April 2025,Anne-mariesharp,"Anne-mariesharp,Ese",LEfSE comparison between Levodopa (LD) and Naive groups showing significantly enriched taxa,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides rodentium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium scardovii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium thermosuccinogenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfotomaculaceae|g__Desulfotomaculum,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella|s__Johnsonella ignava,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Kitasatospora,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Natronincola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira|s__Oscillospira guilliermondii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides johnsonii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola paurosaccharolyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio|s__Pseudobutyrivibrio xylanivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia naturae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella sanguinus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Thiotrichaceae|g__Thiothrix,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Thiotrichaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Tolumonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Tolumonas|s__Tolumonas auensis",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;3379134|1224|1236|135624|84642;1783272|1239|186801|186802|216572|52784;3379134|976|200643|171549|815|816|691816;3379134|976|200643|171549|815|816|46506;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|158787;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|186802|31979|1485|84032;1783272|1239|186801|186802|2937910|1562;3384194|508458|649775|649776|3029088;1783272|1239|186801|3085636|186803|189330;1783272|1239|526524|526525|128827|1647;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|43994|43995;1783272|201174|1760|85011|2062|2063;1783272|1239|186801|3085636|186803|28050|28052;1783272|1239|186801|3082720|3118656|89958;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|119852|119853;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288|387661;1783272|1239|909932|1843488|909930|33024|33025;3379134|976|200643|171549|815|909656|732242;3379134|976|200643|171549|815|909656|671267;1783272|1239|186801|3085636|186803|46205;1783272|1239|186801|3085636|186803|46205|185007;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263|40518;1783272|201174|1760|2037|2049|2529408|635203;1783272|201174|1760|85011|2062;3379134|1224|28216|80840|995019|40544|282125;3379134|1224|1236|72273|135617|1030;3379134|1224|1236|72273|135617;3379134|1224|1236|135624|84642|43947;3379134|1224|1236|135624|84642|43947|43948,Complete,KateRasheed
bsdb:33185912/2/1,33185912,"cross-sectional observational, not case-control",33185912,10.1111/ene.14644,NA,"Melis M., Vascellari S., Santoru M.L., Oppo V., Fabbri M., Sarchioto M., Murgia D., Zibetti M., Lopiano L., Serra A., Palmas V., Pisanu S., Perra D., Madau V., Cusano R., Uva P., Mereu A., Contu P., Morelli M., Atzori L., Melis M., Manzin A. , Cossu G.",Gut microbiota and metabolome distinctive features in Parkinson disease: Focus on levodopa and levodopa-carbidopa intrajejunal gel,European journal of neurology,2021,"LCIG, Parkinson, duodopa, levodopa, microbiota",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Naive,LD-carbidopa intestinal gel (LCIG),Parkinson’s Disease patients treated with Levodopa-carbidopa intestinal gel (LCIG),23,38,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Figure 3B,12 April 2025,Anne-mariesharp,"Anne-mariesharp,Ese",LEfSE comparison between LD-carbidopa intestinal gel (LCIG) and Naive groups showing significantly enriched taxa,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter soli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix|s__Erysipelothrix muris,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella granulomatis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella variicola,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus taiwanensis,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia entomophila,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Tolumonas",3379134|1224|1236|135624|84642;3379134|976|200643|171549|1853231|574697;1783272|201174|84998|84999|84107|102106;3379134|200940|3031449|213115|194924|872;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|547|885040;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|1903409|551;1783272|1239|526524|526525|128827|1647|380638;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|543|570|39824;3379134|1224|1236|91347|543|570|244366;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|508451;3379134|1224;3379134|1224|1236|91347|1903411|613;3379134|1224|1236|91347|1903411|613|42906;3379134|1224|1236|135624|84642|43947,Complete,KateRasheed
bsdb:33185912/2/2,33185912,"cross-sectional observational, not case-control",33185912,10.1111/ene.14644,NA,"Melis M., Vascellari S., Santoru M.L., Oppo V., Fabbri M., Sarchioto M., Murgia D., Zibetti M., Lopiano L., Serra A., Palmas V., Pisanu S., Perra D., Madau V., Cusano R., Uva P., Mereu A., Contu P., Morelli M., Atzori L., Melis M., Manzin A. , Cossu G.",Gut microbiota and metabolome distinctive features in Parkinson disease: Focus on levodopa and levodopa-carbidopa intrajejunal gel,European journal of neurology,2021,"LCIG, Parkinson, duodopa, levodopa, microbiota",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Naive,LD-carbidopa intestinal gel (LCIG),Parkinson’s Disease patients treated with Levodopa-carbidopa intestinal gel (LCIG),23,38,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,Figure 3B,12 April 2025,Anne-mariesharp,"Anne-mariesharp,Ese",LEfSE comparison between LD-carbidopa intestinal gel (LCIG) and Naive groups showing significantly enriched taxa,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium scardovii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium thermosuccinogenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Kitasatospora,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Natronincola,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira|s__Oscillospira guilliermondii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio|s__Pseudobutyrivibrio xylanivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia naturae,k__Bacillati|p__Bacillota|c__Tissierellia|g__Sedimentibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Thiotrichaceae|g__Thiothrix,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Thiotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Tindalliaceae|g__Tindallia",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|1239;1783272|201174|1760|85004|31953|1678|158787;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|1322;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485|84032;1783272|1239|186801|3085636|186803|33042;3379134|200940|3031449|213115|194924|872|901;1783272|1239|186801|3085636|186803|189330;1783272|1239|526524|526525|128827|1647;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|201174|1760|85011|2062|2063;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|28052;1783272|1239|186801|3085636|186803;1783272|1239|186801|3082720|3118656|89958;1783272|1239|186801|186802|216572|119852|119853;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|186807;1783272|1239|186801|3085636|186803|46205;1783272|1239|186801|3085636|186803|46205|185007;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|186801|186802|216572|1263|40518;1783272|201174|1760|2037|2049|2529408|635203;1783272|1239|1737404|190972;1783272|201174|1760|85011|2062;3379134|1224|1236|72273|135617|1030;3379134|1224|1236|72273|135617;1783272|1239|186801|3082720|3118658|69894,Complete,KateRasheed
bsdb:33185912/3/1,33185912,"cross-sectional observational, not case-control",33185912,10.1111/ene.14644,NA,"Melis M., Vascellari S., Santoru M.L., Oppo V., Fabbri M., Sarchioto M., Murgia D., Zibetti M., Lopiano L., Serra A., Palmas V., Pisanu S., Perra D., Madau V., Cusano R., Uva P., Mereu A., Contu P., Morelli M., Atzori L., Melis M., Manzin A. , Cossu G.",Gut microbiota and metabolome distinctive features in Parkinson disease: Focus on levodopa and levodopa-carbidopa intrajejunal gel,European journal of neurology,2021,"LCIG, Parkinson, duodopa, levodopa, microbiota",Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Levodopa (LD),Levodopa-carbidopa intestinal gel (LCIG),Parkinson’s Disease patients treated with Levodopa-carbidopa intestinal gel (LCIG),46,38,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 3C,12 April 2025,Anne-mariesharp,"Anne-mariesharp,Ese",LEfSE comparison between Levodopa-carbidopa intestinal gel (LCIG) and Levodopa (LD) groups showing significantly enriched taxa,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides rodentium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfotomaculaceae|g__Desulfotomaculum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter soli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella granulomatis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella variicola,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus taiwanensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides johnsonii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola paurosaccharolyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia entomophila,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella sanguinus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Tolumonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Tolumonas|s__Tolumonas auensis",3379134|1224|1236|135624|84642;1783272|1239|186801|186802|216572|52784;1783272|1239|186801|186802|216572|244127;3379134|976|200643|171549|815|816|691816;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802|2937910|1562;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924|872|901;3384194|508458|649775|649776|3029088;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|547|885040;3379134|1224|1236|91347|543;3379134|1224|1236|91347|1903409|551;3379134|1224|1236|91347|1903409;3379134|1224|1236|91347|543|561;1783272|1239|186801|186802|186806|1730;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|543|570|39824;3379134|1224|1236|91347|543|570|244366;1783272|1239|91061|186826|33958|1578|508451;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|1853231;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|387661;1783272|1239|909932|1843488|909930|33024|33025;3379134|976|200643|171549|815|909656|732242;3379134|976|200643|171549|815|909656|671267;3379134|1224;3379134|1224|1236|91347|1903411|613;3379134|1224|1236|91347|1903411|613|42906;3379134|976|117747|200666|84566;3379134|1224|28216|80840|995019|40544|282125;3379134|1224|1236|135624|84642|43947;3379134|1224|1236|135624|84642|43947|43948,Complete,KateRasheed
bsdb:33185912/3/2,33185912,"cross-sectional observational, not case-control",33185912,10.1111/ene.14644,NA,"Melis M., Vascellari S., Santoru M.L., Oppo V., Fabbri M., Sarchioto M., Murgia D., Zibetti M., Lopiano L., Serra A., Palmas V., Pisanu S., Perra D., Madau V., Cusano R., Uva P., Mereu A., Contu P., Morelli M., Atzori L., Melis M., Manzin A. , Cossu G.",Gut microbiota and metabolome distinctive features in Parkinson disease: Focus on levodopa and levodopa-carbidopa intrajejunal gel,European journal of neurology,2021,"LCIG, Parkinson, duodopa, levodopa, microbiota",Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Levodopa (LD),Levodopa-carbidopa intestinal gel (LCIG),Parkinson’s Disease patients treated with Levodopa-carbidopa intestinal gel (LCIG),46,38,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 3C,12 April 2025,Anne-mariesharp,"Anne-mariesharp,Ese",LEfSE comparison between Levodopa-carbidopa intestinal gel (LCIG) and Levodopa (LD) groups showing significantly enriched taxa,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Tissierellia|g__Sedimentibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Tindalliaceae|g__Tindallia",1783272|1239;1783272|1239|186801|3085636|186803|572511|1322;1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|186803|28050;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3082720|186804;1783272|1239|1737404|190972;1783272|1239|186801|3082720|3118658|69894,Complete,KateRasheed
bsdb:33193081/1/1,33193081,"cross-sectional observational, not case-control",33193081,10.3389/fendo.2020.550319,https://pubmed.ncbi.nlm.nih.gov/33193081/,"Tang N., Luo Z.C., Zhang L., Zheng T., Fan P., Tao Y. , Ouyang F.",The Association Between Gestational Diabetes and Microbiota in Placenta and Cord Blood,Frontiers in endocrinology,2020,"China, cord blood, gestational diabetes mellitus (GDM), microbiota, placenta",Experiment 1,China,Homo sapiens,Placenta,UBERON:0001987,Gestational diabetes,EFO:0004593,euglycemic (control) singleton pregnant women,Pregnant women with Gestational Diabetes Mellitus,"Pregnant women with Gestational Diabetes Mellitus (GDM) who had prenatal care at Xinhua Hospital, a tertiary hospital in Shanghai, and were admitted to the hospital for cesarean deliveries",7,8,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Table 3,14 June 2021,Madhubani Dey,"Madhubani Dey,Peace Sandy,WikiWorks",Table 3: Relative abundances (%) of placental microbiota OTUs that differed between eight women with GDM and seven women without GDM (non-GDM).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",1783272|1239|186801|186802|216572|244127;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|1185407;1783272|1239|186801|3085636|186803|189330;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|297314,Complete,Peace Sandy
bsdb:33193081/1/2,33193081,"cross-sectional observational, not case-control",33193081,10.3389/fendo.2020.550319,https://pubmed.ncbi.nlm.nih.gov/33193081/,"Tang N., Luo Z.C., Zhang L., Zheng T., Fan P., Tao Y. , Ouyang F.",The Association Between Gestational Diabetes and Microbiota in Placenta and Cord Blood,Frontiers in endocrinology,2020,"China, cord blood, gestational diabetes mellitus (GDM), microbiota, placenta",Experiment 1,China,Homo sapiens,Placenta,UBERON:0001987,Gestational diabetes,EFO:0004593,euglycemic (control) singleton pregnant women,Pregnant women with Gestational Diabetes Mellitus,"Pregnant women with Gestational Diabetes Mellitus (GDM) who had prenatal care at Xinhua Hospital, a tertiary hospital in Shanghai, and were admitted to the hospital for cesarean deliveries",7,8,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Table 3,14 June 2021,Madhubani Dey,"Madhubani Dey,Peace Sandy,WikiWorks",Table 3: Relative abundances (%) of placental microbiota OTUs that differed between eight women with GDM and seven women without GDM (non-GDM).,decreased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,1783272|1239|909932|1843489|31977|29465,Complete,Peace Sandy
bsdb:33193813/1/1,33193813,time series / longitudinal observational,33193813,https://doi.org/10.1177/1756284820968423,NA,"Tian Y., Zuo L., Guo Q., Li J., Hu Z., Zhao K., Li C., Li X., Zhou J., Zhou Y. , Li X.A.",Potential role of fecal microbiota in patients with constipation,Therapeutic advances in gastroenterology,2020,"chronic functional constipation, fecal microbiota transplantation, gastrointestinal motility, intestinal flora",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,"Before treatment, After 1st treatment, After 2nd treatment, After 3rd treatment, 2 month follow-up and 3 month follow up",Donor,The donors were healthy individuals without diseases or pathologic conditions potentially associated with changes in the gut microbiota.,34,4,1 month,16S,NA,NA,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,4 May 2025,MyleeeA,MyleeeA,"Linear discriminant analysis effect size (LEfSe) analysis of microbial abundance between Donor versus Before treatment, After 1st treatment, After 2nd treatment, After 3rd treatment, 2 month follow-up and 3 month follow up.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Asticcacaulis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|1224|28211|356|335928;3379134|1224|28211|204458|76892|76890;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572,Complete,KateRasheed
bsdb:33193813/2/1,33193813,time series / longitudinal observational,33193813,https://doi.org/10.1177/1756284820968423,NA,"Tian Y., Zuo L., Guo Q., Li J., Hu Z., Zhao K., Li C., Li X., Zhou J., Zhou Y. , Li X.A.",Potential role of fecal microbiota in patients with constipation,Therapeutic advances in gastroenterology,2020,"chronic functional constipation, fecal microbiota transplantation, gastrointestinal motility, intestinal flora",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,"Donor, After 1st treatment, After 2nd treatment, After 3rd treatment, 2 month follow-up and 3 month follow up",Before treatment,Patients with chronic functional constipation before Fecal microbiota transplantation treatment.,NA,NA,1 month,16S,NA,NA,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,4 May 2025,MyleeeA,MyleeeA,"Linear discriminant analysis effect size (LEfSe) analysis of microbial abundance between Before treatment  versus  Donor, After 1st treatment, After 2nd treatment, After 3rd treatment, 2 month follow-up and 3 month follow up.",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|815|816,Complete,KateRasheed
bsdb:33193813/3/1,33193813,time series / longitudinal observational,33193813,https://doi.org/10.1177/1756284820968423,NA,"Tian Y., Zuo L., Guo Q., Li J., Hu Z., Zhao K., Li C., Li X., Zhou J., Zhou Y. , Li X.A.",Potential role of fecal microbiota in patients with constipation,Therapeutic advances in gastroenterology,2020,"chronic functional constipation, fecal microbiota transplantation, gastrointestinal motility, intestinal flora",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,"Donor, Before treatment, After 2nd treatment, After 3rd treatment, 2 month follow-up and 3 month follow up",After 1st treatment,Patients with chronic functional constipation after first treatment with Fecal microbiota transplantation.,NA,NA,1 month,16S,NA,NA,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,4 May 2025,MyleeeA,MyleeeA,"Linear discriminant analysis effect size (LEfSe) analysis of microbial abundance between   After 1st treatment versus Donor, Before treatment, After 2nd treatment, After 3rd treatment, 2 month follow-up and 3 month follow up.",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,3379134|976|200643|171549|1853231|283168,Complete,KateRasheed
bsdb:33193813/4/1,33193813,time series / longitudinal observational,33193813,https://doi.org/10.1177/1756284820968423,NA,"Tian Y., Zuo L., Guo Q., Li J., Hu Z., Zhao K., Li C., Li X., Zhou J., Zhou Y. , Li X.A.",Potential role of fecal microbiota in patients with constipation,Therapeutic advances in gastroenterology,2020,"chronic functional constipation, fecal microbiota transplantation, gastrointestinal motility, intestinal flora",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,"Donor, Before treatment, After 1st treatment, After 3rd treatment, 2 month follow-up and 3 month follow up",After 2nd treatment,Patients with chronic functional constipation after second treatment with Fecal microbiota transplantation.,NA,NA,1 month,16S,NA,NA,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,4 May 2025,MyleeeA,MyleeeA,"Linear discriminant analysis effect size (LEfSe) analysis of microbial abundance between After 2nd treatment versus Donor, Before treatment, After 1st treatment, After 3rd treatment, 2 month follow-up and 3 month follow up.",increased,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,3379134|200940|3031449|213115|194924|35832,Complete,KateRasheed
bsdb:33193813/5/1,33193813,time series / longitudinal observational,33193813,https://doi.org/10.1177/1756284820968423,NA,"Tian Y., Zuo L., Guo Q., Li J., Hu Z., Zhao K., Li C., Li X., Zhou J., Zhou Y. , Li X.A.",Potential role of fecal microbiota in patients with constipation,Therapeutic advances in gastroenterology,2020,"chronic functional constipation, fecal microbiota transplantation, gastrointestinal motility, intestinal flora",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,"Donor, Before treatment, After 1st treatment, After 2nd treatment, 2-month follow up and 3-month follow up",After 3rd treatment,Patients with chronic functional constipation after third treatment with Fecal microbiota transplantation.,NA,NA,1 month,16S,NA,NA,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,9 June 2025,Anne-mariesharp,Anne-mariesharp,"Linear discriminant analysis effect size (LEfSe) analysis of microbial abundance between After 3rd treatment versus Donor, Before treatment, After 1st treatment, After 2nd treatment, 2-month follow up and 3-month follow up.",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|909929|1843491|158846,Complete,KateRasheed
bsdb:33193813/6/1,33193813,time series / longitudinal observational,33193813,https://doi.org/10.1177/1756284820968423,NA,"Tian Y., Zuo L., Guo Q., Li J., Hu Z., Zhao K., Li C., Li X., Zhou J., Zhou Y. , Li X.A.",Potential role of fecal microbiota in patients with constipation,Therapeutic advances in gastroenterology,2020,"chronic functional constipation, fecal microbiota transplantation, gastrointestinal motility, intestinal flora",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,"Donor, Before treatment, After 1st treatment, After 2nd treatment, After 3rd treatment and 3-month follow up",2-month follow up,Patients with chronic functional constipation after treatment with Fecal microbiota transplantation and at 2-months of follow up,NA,NA,1 month,16S,NA,NA,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,9 June 2025,Anne-mariesharp,Anne-mariesharp,"Linear discriminant analysis effect size (LEfSe) analysis of microbial abundance between 2-month follow up versus Donor, Before treatment, After 1st treatment, After 2nd treatment, After 3rd treatment and 3-month follow up.",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas",1783272|1239|909932|1843488|909930|904;3379134|976|200643|171549|1853231|574697,Complete,KateRasheed
bsdb:33193813/7/1,33193813,time series / longitudinal observational,33193813,https://doi.org/10.1177/1756284820968423,NA,"Tian Y., Zuo L., Guo Q., Li J., Hu Z., Zhao K., Li C., Li X., Zhou J., Zhou Y. , Li X.A.",Potential role of fecal microbiota in patients with constipation,Therapeutic advances in gastroenterology,2020,"chronic functional constipation, fecal microbiota transplantation, gastrointestinal motility, intestinal flora",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,"Donor, Before treatment, After 1st treatment, After 2nd treatment, After 3rd treatment and 2-month follow up",3-month follow up,Patients with chronic functional constipation after treatment with Fecal microbiota transplantation and at 3-months of follow up,NA,NA,1 month,16S,NA,NA,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,9 June 2025,Anne-mariesharp,Anne-mariesharp,"Linear discriminant analysis effect size (LEfSe) analysis of microbial abundance between 3-month follow up versus Donor, Before treatment, After 1st treatment, After 2nd treatment, After 3rd treatment and 2-month follow up.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Geodermatophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Luteimonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Pleomorphomonadaceae|g__Pleomorphomonas,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Synechococcales|f__Synechococcaceae|g__Synechococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Thalassospiraceae|g__Thalassospira,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Pleurocapsales|f__Xenococcaceae",3379134|1224|1236|2887326|468|469;3379134|200940|3031451|3024411|213121;1783272|201174|1760|1643682|85030|1860;3379134|1224|28216|206351|481|32257;3379134|1224|1236|135614|32033|83614;3379134|1224|28211|356|2843308|261933;1783272|1117|3028117|1890424|1890426|1129;3379134|1224|28211|204441|2844866|168934;1783272|1117|3028117|52604|1890499,Complete,KateRasheed
bsdb:33194786/1/1,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic group,Gestational diabetes mellitus (GDM) group,Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM).,72,34,2 months,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,decreased,Signature 1,FIGURE 4 (A),8 October 2024,AishatBolarinwa,"AishatBolarinwa,WikiWorks",Taxonomic biomarkers of gestational diabetes in gut microbiota of newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM),increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Isobaculum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",1783272|1239|91061|186826|186828;1783272|1239|91061|186826|186828|142587;1783272|1239|526524|526525|2810281|191303,Complete,Folakunmi
bsdb:33194786/1/2,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic group,Gestational diabetes mellitus (GDM) group,Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM).,72,34,2 months,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,decreased,Signature 2,FIGURE 4 (A),9 October 2024,AishatBolarinwa,"AishatBolarinwa,WikiWorks",Taxonomic biomarkers of gestational diabetes in gut microbiota of newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|186801|186802|216572|253238;1783272|1239|909932|1843489|31977|906;1783272|201174|1760|85006|1268;1783272|1239|909932;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|201174|1760|85006|1268|32207;1783272|1239|909932|909929;1783272|1239|186801|186802|216572|292632;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977,Complete,Folakunmi
bsdb:33194786/2/1,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 2,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic group,Gestational diabetes mellitus (GDM) group,Infants (9 months of age) born to mothers with gestational diabetes mellitus (GDM).,64,32,2 months,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,FIGURE 4 (B),9 October 2024,AishatBolarinwa,"AishatBolarinwa,Aleru Divine,WikiWorks",Taxonomic biomarkers of gestational diabetes in gut microbiota of infants (9 months of life) born to mothers with gestational diabetes mellitus (GDM),increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,Folakunmi
bsdb:33194786/2/2,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 2,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic group,Gestational diabetes mellitus (GDM) group,Infants (9 months of age) born to mothers with gestational diabetes mellitus (GDM).,64,32,2 months,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,FIGURE 4 (B),9 October 2024,AishatBolarinwa,"AishatBolarinwa,Aleru Divine,WikiWorks",Taxonomic biomarkers of gestational diabetes in gut microbiota of infants (9 months of life) born to mothers with gestational diabetes mellitus (GDM),decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",1783272|201174|1760|2037|2049;1783272|201174;3379134|1224|1236|135622;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|189330;1783272|201174|1760|85009|31957;1783272|201174|1760|85009|31957|1743;3379134|1224|1236|135622|267890|22;3379134|1224|1236|135622|267890;1783272|1239|186801|186802|216572|292632,Complete,Folakunmi
bsdb:33194786/3/1,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 3,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic group,Gestational diabetes mellitus (GDM) group,Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM),72,34,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,decreased,Signature 1,Table S3,10 November 2024,Aleru Divine,"Aleru Divine,AishatBolarinwa,WikiWorks",OTUs differentially abundant in Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",3379134|1224|1236|91347|543|1940338;1783272|1239|91061|1385|90964|1279,Complete,Folakunmi
bsdb:33194786/3/2,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 3,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic group,Gestational diabetes mellitus (GDM) group,Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM),72,34,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,decreased,Signature 2,Table S3,10 November 2024,Aleru Divine,"Aleru Divine,AishatBolarinwa,WikiWorks",OTUs differentially abundant in Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|544;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|186802|216572|216851;3379134|1224|1236|135619|28256|2745;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171552|838;1783272|201174|1760|85009|31957|1743;3379134|1224|1236|135622|267890|22;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:33194786/4/1,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 4,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic group,Gestational diabetes mellitus (GDM) group,Infants (9 months of age) born to mothers with gestational diabetes mellitus (GDM),64,32,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Table S3,11 November 2024,Aleru Divine,"Aleru Divine,AishatBolarinwa,WikiWorks",OTUs differentially abundant in Infants (9 months of life) born to mothers with gestational diabetes mellitus (GDM).,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,1783272|1239|186801|186802|216572|216851,Complete,Folakunmi
bsdb:33194786/4/2,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 4,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic group,Gestational diabetes mellitus (GDM) group,Infants (9 months of age) born to mothers with gestational diabetes mellitus (GDM),64,32,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Table S3,11 November 2024,Aleru Divine,"Aleru Divine,AishatBolarinwa,WikiWorks",OTUs differentially abundant in Infants (9 months of life) born to mothers with gestational diabetes mellitus (GDM).,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|526524|526525|128827;3379134|1224|1236|91347|543|1940338;1783272|1239|909932|1843489|31977|906;3379134|976|200643|171549|171552|577309;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171552|838;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:33194786/5/1,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 5,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic group,Gestational diabetes mellitus (GDM) group,Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM).,72,34,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,mode of birth,unchanged,unchanged,NA,NA,NA,decreased,Signature 1,Table S4,11 November 2024,Aleru Divine,"Aleru Divine,AishatBolarinwa,WikiWorks",OTUs differentially abundant in Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM) adjusted for mode of delivery (vaginal vs. cesarean section).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|1224|1236|91347|543|1940338;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:33194786/5/2,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 5,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic group,Gestational diabetes mellitus (GDM) group,Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM).,72,34,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,mode of birth,unchanged,unchanged,NA,NA,NA,decreased,Signature 2,Table S4,11 November 2024,Aleru Divine,"Aleru Divine,AishatBolarinwa,WikiWorks",OTUs differentially abundant in Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM) adjusted for mode of delivery (vaginal vs. cesarean section).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|186802|216572|216851;3379134|1224|1236|135619|28256|2745;1783272|201174|1760|85009|31957|1743;3379134|1224|1236|135622|267890|22;1783272|1239|91061|1385|90964|1279;1783272|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:33194786/6/1,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 6,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic group,Gestational diabetes mellitus (GDM) group,Infants (9 months of age) born to mothers with gestational diabetes mellitus (GDM).,64,32,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,mode of birth,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Table S4,11 November 2024,Aleru Divine,"Aleru Divine,AishatBolarinwa,WikiWorks",OTUs differentially abundant in Infants (9 months of life) born to mothers with gestational diabetes mellitus (GDM) adjusted for mode of delivery (vaginal vs. cesarean section).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|186801|186802|216572|216851;1783272|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:33194786/6/2,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 6,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic group,Gestational diabetes mellitus (GDM) group,Infants (9 months of age) born to mothers with gestational diabetes mellitus (GDM).,64,32,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,mode of birth,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Table S4,11 November 2024,Aleru Divine,"Aleru Divine,AishatBolarinwa,WikiWorks",OTUs differentially abundant in Infants (9 months of life) born to mothers with gestational diabetes mellitus (GDM) adjusted for mode of delivery (vaginal vs. cesarean section).,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|1224|1236|91347|543|1940338;1783272|1239|909932|1843489|31977|906;3379134|976|200643|171549|171552|577309;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|171552|838;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|186826|1300|1301;3379134|1224|28216|80840|995019|40544;1783272|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:33194786/7/1,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 7,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic group,Gestational diabetes mellitus (GDM) group,Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM).,72,34,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,antibiotic therapy,unchanged,unchanged,NA,NA,NA,decreased,Signature 1,Table S5,11 November 2024,Aleru Divine,"Aleru Divine,AishatBolarinwa,WikiWorks",OTUs differentially abundant in Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM) adjusted for perinatal antibiotic treatment (treated vs. untreated).,increased,NA,NA,Complete,Folakunmi
bsdb:33194786/7/2,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 7,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic group,Gestational diabetes mellitus (GDM) group,Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM).,72,34,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,antibiotic therapy,unchanged,unchanged,NA,NA,NA,decreased,Signature 2,Table S5,11 November 2024,Aleru Divine,"Aleru Divine,AishatBolarinwa,WikiWorks",OTUs differentially abundant in Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM) adjusted for perinatal antibiotic treatment (treated vs. untreated).,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|84998|84999|84107|102106;1783272|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:33194786/8/1,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 8,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic group,Gestational diabetes mellitus (GDM) group,Infants (9 months of age) born to mothers with gestational diabetes mellitus (GDM).,64,32,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,antibiotic therapy,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Table S5,11 November 2024,Aleru Divine,"Aleru Divine,AishatBolarinwa,WikiWorks",OTUs differentially abundant in Infants (9 months of life) born to mothers with gestational diabetes mellitus (GDM) adjusted for perinatal antibiotic treatment (treated vs. untreated).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|216851,Complete,Folakunmi
bsdb:33194786/8/2,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 8,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic group,Gestational diabetes mellitus (GDM) group,Infants (9 months of age) born to mothers with gestational diabetes mellitus (GDM).,64,32,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,antibiotic therapy,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Table S5,11 November 2024,Aleru Divine,"Aleru Divine,AishatBolarinwa,WikiWorks",OTUs differentially abundant in Infants (9 months of life) born to mothers with gestational diabetes mellitus (GDM) adjusted for perinatal antibiotic treatment (treated vs. untreated).,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|1224|1236|91347|543|1940338;3379134|976|200643|171549|171552|838;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:33194786/9/1,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 9,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic group,Gestational diabetes mellitus (GDM) group,Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM).,72,34,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,sex,unchanged,unchanged,NA,NA,NA,decreased,Signature 1,Table S6,11 November 2024,Aleru Divine,"Aleru Divine,AishatBolarinwa,WikiWorks",OTUs differentially abundant in Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM) adjusted for sex of the child.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pseudocitrobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|570;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|2005525|375288;3379134|1224|1236|91347|543|1504576;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;3379134|1224|28216|80840|995019|40544,Complete,Folakunmi
bsdb:33194786/9/2,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 9,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic group,Gestational diabetes mellitus (GDM) group,Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM).,72,34,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,sex,unchanged,unchanged,NA,NA,NA,decreased,Signature 2,Table S6,11 November 2024,Aleru Divine,"Aleru Divine,AishatBolarinwa,WikiWorks",OTUs differentially abundant in Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM) adjusted for sex of the child.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium",3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|544;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|186802|216572|216851;3379134|1224|1236|135625|712|724;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|3082720|186804|1505657;1783272|1239|909932|1843488|909930|33024;1783272|201174|1760|85009|31957|1743,Complete,Folakunmi
bsdb:33194786/10/1,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 10,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic group,Gestational diabetes mellitus (GDM) group,Infants (9 months of age) born to mothers with gestational diabetes mellitus (GDM).,64,32,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,sex,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Table S6,11 November 2024,Aleru Divine,"Aleru Divine,AishatBolarinwa,WikiWorks",OTUs differentially abundant in Infants (9 months of life) born to mothers with gestational diabetes mellitus (GDM) adjusted for sex of the child.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|253238;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:33194786/10/2,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 10,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic group,Gestational diabetes mellitus (GDM) group,Infants (9 months of age) born to mothers with gestational diabetes mellitus (GDM).,64,32,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,sex,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Table S6,11 November 2024,Aleru Divine,"Aleru Divine,AishatBolarinwa,WikiWorks",OTUs differentially abundant in Infants (9 months of life) born to mothers with gestational diabetes mellitus (GDM) adjusted for sex of the child.,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",1783272|201174|84998|84999|84107|102106;3379134|1224|1236|91347|543|1940338;1783272|1239|909932|1843489|31977|906;3379134|1224|28216|80840|995019|40544,Complete,Folakunmi
bsdb:33194786/11/1,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 11,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic group,Gestational diabetes mellitus (GDM) group,Infants (9 months of age) born to mothers with gestational diabetes mellitus (GDM).,64,32,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,feeding practices,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Table S7,11 November 2024,Aleru Divine,"Aleru Divine,AishatBolarinwa,WikiWorks",OTUs differentially abundant in infants (9 months of age) born to mothers with gestational diabetes mellitus (GDM) adjusted for feeding.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:33194786/11/2,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 11,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic group,Gestational diabetes mellitus (GDM) group,Infants (9 months of age) born to mothers with gestational diabetes mellitus (GDM).,64,32,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,feeding practices,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Table S7,11 November 2024,Aleru Divine,"Aleru Divine,AishatBolarinwa,WikiWorks",OTUs differentially abundant in infants (9 months of age) born to mothers with gestational diabetes mellitus (GDM) adjusted for feeding.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pluralibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|2037|2049|1654;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|1940338;3379134|976|200643|171549|171552|577309;3379134|1224|1236|91347|543|1330546;3379134|976|200643|171549|171552|838;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:33194786/12/1,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 12,Denmark,Homo sapiens,Feces,UBERON:0001988,Disposition index measurement,EFO:0006832,Lower Tertile (low disposition index),Upper Tertile (high disposition index),Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM) with with higher maternal disposition index.,NA,NA,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S8,13 November 2024,Aleru Divine,"Aleru Divine,AishatBolarinwa,WikiWorks",Operational taxonomic units in newborns (1 week of life) associated with maternal glycaemic traits (disposition index) unadjusted for maternal pre-pregnancy BMI.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3082720|186804|1505657;3379134|976|200643|171549|2005525|375288;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;3379134|1224|28216|80840|995019|40544,Complete,Folakunmi
bsdb:33194786/12/2,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 12,Denmark,Homo sapiens,Feces,UBERON:0001988,Disposition index measurement,EFO:0006832,Lower Tertile (low disposition index),Upper Tertile (high disposition index),Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM) with with higher maternal disposition index.,NA,NA,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S8,13 November 2024,Aleru Divine,"Aleru Divine,AishatBolarinwa,WikiWorks",Operational taxonomic units in newborns (1 week of life) associated with maternal glycaemic traits (disposition index) unadjusted for maternal pre-pregnancy BMI.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|1224|1236|91347|543|1940338;3379134|1224|1236|135625|712|724;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843488|909930|33024;3379134|1224|28216|80840|995019|40544;1783272|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:33194786/13/1,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 13,Denmark,Homo sapiens,Feces,UBERON:0001988,Fasting blood glucose measurement,EFO:0004465,Lower Tertile (low fasting plasma glucose),Upper Tertile (high fasting plasma glucose),Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM) with higher maternal fasting plasma glucose.,NA,NA,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S8,13 November 2024,Aleru Divine,"Aleru Divine,AishatBolarinwa,WikiWorks",Operational taxonomic units in newborns (1 week of life) associated with maternal glycaemic traits  (fasting plasma glucose) unadjusted for maternal pre-pregnancy BMI.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|1224|1236|91347|543|1940338;3379134|1224|28216|80840|995019|40544,Complete,Folakunmi
bsdb:33194786/13/2,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 13,Denmark,Homo sapiens,Feces,UBERON:0001988,Fasting blood glucose measurement,EFO:0004465,Lower Tertile (low fasting plasma glucose),Upper Tertile (high fasting plasma glucose),Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM) with higher maternal fasting plasma glucose.,NA,NA,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S8,13 November 2024,Aleru Divine,"Aleru Divine,AishatBolarinwa,WikiWorks",Operational taxonomic units in newborns (1 week of life) associated with maternal glycaemic traits (fasting plasma glucose) unadjusted for maternal pre-pregnancy BMI.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Folakunmi
bsdb:33194786/14/1,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 14,Denmark,Homo sapiens,Feces,UBERON:0001988,Glucose measurement,EFO:0004468,Lower Tertile (low stimulated 2-h plasma glucose level),Upper Tertile (high stimulated 2-h plasma glucose level),Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM) with higher maternal stimulated 2-h plasma glucose level.,NA,NA,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S8,13 November 2024,Aleru Divine,"Aleru Divine,AishatBolarinwa,WikiWorks",Operational taxonomic units in newborns (1 week of life) associated with maternal glycaemic traits (stimulated 2-h plasma glucose level) unadjusted for maternal pre-pregnancy BMI.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|91061|186826|33958|1578;3379134|1224|28216|80840|995019|40544;1783272|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:33194786/14/2,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 14,Denmark,Homo sapiens,Feces,UBERON:0001988,Glucose measurement,EFO:0004468,Lower Tertile (low stimulated 2-h plasma glucose level),Upper Tertile (high stimulated 2-h plasma glucose level),Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM) with higher maternal stimulated 2-h plasma glucose level.,NA,NA,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S8,13 November 2024,Aleru Divine,"Aleru Divine,AishatBolarinwa,WikiWorks",Operational taxonomic units in newborns (1 week of life) associated with maternal glycaemic traits (stimulated 2-h plasma glucose level) unadjusted for maternal pre-pregnancy BMI.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|976|200643|171549|815|816;3379134|200940|3031449|213115|194924|35832;1783272|201174|84998|84999|84107|102106;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|171552|838;1783272|201174|1760|85009|31957|1743;1783272|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:33194786/15/1,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 15,Denmark,Homo sapiens,Feces,UBERON:0001988,Insulin sensitivity measurement,EFO:0004471,Lower Tertile (low insulin sensitivity index),Upper Tertile (high insulin sensitivity index),Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM) with higher maternal insulin sensitivity index.,NA,NA,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S8,13 November 2024,Aleru Divine,"Aleru Divine,AishatBolarinwa,WikiWorks",Operational taxonomic units in newborns (1 week of life) associated with maternal glycaemic traits (insulin sensitivity index) unadjusted for maternal pre-pregnancy BMI.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|186801|186802|31979|1485;1783272|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:33194786/15/2,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 15,Denmark,Homo sapiens,Feces,UBERON:0001988,Insulin sensitivity measurement,EFO:0004471,Lower Tertile (low insulin sensitivity index),Upper Tertile (high insulin sensitivity index),Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM) with higher maternal insulin sensitivity index.,NA,NA,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S8,13 November 2024,Aleru Divine,"Aleru Divine,AishatBolarinwa,WikiWorks",Operational taxonomic units in newborns (1 week of life) associated with maternal glycaemic traits (insulin sensitivity index) unadjusted for maternal pre-pregnancy BMI.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pseudocitrobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803;3379134|1224|1236|91347|543|1504576;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;3379134|1224|28216|80840|995019|40544;1783272|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:33194786/16/1,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 16,Denmark,Homo sapiens,Feces,UBERON:0001988,Glucose measurement,EFO:0004468,Lower Tertile (low stimulated 2-h plasma glucose level),Upper Tertile (high stimulated 2-h plasma glucose level),Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM) with higher maternal stimulated 2-h plasma glucose level.,NA,NA,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,body mass index,NA,NA,NA,NA,NA,NA,Signature 1,Figure S8,13 November 2024,Aleru Divine,"Aleru Divine,AishatBolarinwa,WikiWorks",Operational taxonomic units in newborns (1 week of life) associated with maternal glycaemic traits (stimulated 2-h plasma glucose level) adjusted for maternal pre-pregnancy BMI.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:33194786/17/1,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 17,Denmark,Homo sapiens,Feces,UBERON:0001988,Disposition index measurement,EFO:0006832,Lower Tertile (low disposition index),Upper Tertile (high disposition index),Infants (9 months of age) born to mothers with gestational diabetes mellitus (GDM) with with higher maternal disposition index.,NA,NA,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S9,14 November 2024,AishatBolarinwa,"AishatBolarinwa,Aleru Divine,WikiWorks","Operational taxonomic units in infants (9 months of age) associated with maternal glycaemic traits (disposition index), unadjusted for pre-pregnancy BMI.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|1224|1236|135625|712|713;1783272|201174|84998|84999|84107|102106;3379134|1224|1236|91347|543|1940338;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|171552|838;1783272|1239|186801|3082720|186804|1501226;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:33194786/17/2,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 17,Denmark,Homo sapiens,Feces,UBERON:0001988,Disposition index measurement,EFO:0006832,Lower Tertile (low disposition index),Upper Tertile (high disposition index),Infants (9 months of age) born to mothers with gestational diabetes mellitus (GDM) with with higher maternal disposition index.,NA,NA,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S9,14 November 2024,AishatBolarinwa,"AishatBolarinwa,Aleru Divine,WikiWorks","Operational taxonomic units in infants (9 months of age) associated with maternal glycaemic traits (disposition index), unadjusted for pre-pregnancy BMI.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Isobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|189330;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|216572|253238;1783272|1239|186801|186802|216572|216851;1783272|1239|91061|186826|186828|142587;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;1783272|1239|526524|526525|2810281|191303,Complete,Folakunmi
bsdb:33194786/18/1,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 18,Denmark,Homo sapiens,Feces,UBERON:0001988,Fasting blood glucose measurement,EFO:0004465,Lower Tertile (low fasting plasma glucose),Upper Tertile (high fasting plasma glucose),Infants (9 months of age) born to mothers with gestational diabetes mellitus (GDM) with higher maternal fasting plasma glucose.,NA,NA,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S9,14 November 2024,AishatBolarinwa,"AishatBolarinwa,Aleru Divine,WikiWorks","Operational taxonomic units in infants (9 months of age) associated with maternal glycaemic traits (fasting plasma glucose), unadjusted for pre-pregnancy BMI.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|216851;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:33194786/18/2,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 18,Denmark,Homo sapiens,Feces,UBERON:0001988,Fasting blood glucose measurement,EFO:0004465,Lower Tertile (low fasting plasma glucose),Upper Tertile (high fasting plasma glucose),Infants (9 months of age) born to mothers with gestational diabetes mellitus (GDM) with higher maternal fasting plasma glucose.,NA,NA,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S9,14 November 2024,AishatBolarinwa,"AishatBolarinwa,Aleru Divine,WikiWorks","Operational taxonomic units in infants (9 months of age) associated with maternal glycaemic traits (fasting plasma glucose), unadjusted for pre-pregnancy BMI.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",1783272|201174|1760|2037|2049|1654;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|216572|244127;1783272|201174|1760|85004|31953|1678;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|33042;1783272|1239|91061|186826|81852|1350;1783272|1239|909932|1843489|31977|906;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|171552|838;3379134|1224|28216|80840|995019|40544,Complete,Folakunmi
bsdb:33194786/19/1,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 19,Denmark,Homo sapiens,Feces,UBERON:0001988,Glucose measurement,EFO:0004468,Lower Tertile (low stimulated 2-h plasma glucose level),Upper Tertile (high stimulated 2-h plasma glucose level),Infants (9 months of age) born to mothers with gestational diabetes mellitus (GDM) with higher maternal stimulated 2-h plasma glucose level.,NA,NA,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S9,14 November 2024,AishatBolarinwa,"AishatBolarinwa,Aleru Divine,WikiWorks","Operational taxonomic units in infants (9 months of age) associated with maternal glycaemic traits (stimulated 2-h plasma glucose level), unadjusted for pre-pregnancy BMI.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",3379134|976|200643|171549|171550|239759;1783272|1239|91061|186826|81852|1350;3379134|976|200643|171549|171551|836,Complete,Folakunmi
bsdb:33194786/19/2,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 19,Denmark,Homo sapiens,Feces,UBERON:0001988,Glucose measurement,EFO:0004468,Lower Tertile (low stimulated 2-h plasma glucose level),Upper Tertile (high stimulated 2-h plasma glucose level),Infants (9 months of age) born to mothers with gestational diabetes mellitus (GDM) with higher maternal stimulated 2-h plasma glucose level.,NA,NA,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S9,14 November 2024,AishatBolarinwa,"AishatBolarinwa,Aleru Divine,Folakunmi,WikiWorks","Operational taxonomic units in infants (9 months of age) associated with maternal glycaemic traits (stimulated 2-h plasma glucose level), unadjusted for pre-pregnancy BMI.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|841;1783272|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:33194786/20/1,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 20,Denmark,Homo sapiens,Feces,UBERON:0001988,Insulin sensitivity measurement,EFO:0004471,Lower Tertile (low insulin sensitivity index),Upper Tertile (high insulin sensitivity index),Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM) with higher maternal insulin sensitivity index.,NA,NA,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S9,14 November 2024,AishatBolarinwa,"AishatBolarinwa,Aleru Divine,WikiWorks","Operational taxonomic units in infants (9 months of age) associated with maternal glycaemic traits (insulin sensitivity index), unadjusted for pre-pregnancy BMI.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|1224|1236|135625|712|724;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:33194786/20/2,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 20,Denmark,Homo sapiens,Feces,UBERON:0001988,Insulin sensitivity measurement,EFO:0004471,Lower Tertile (low insulin sensitivity index),Upper Tertile (high insulin sensitivity index),Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM) with higher maternal insulin sensitivity index.,NA,NA,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S9,14 November 2024,AishatBolarinwa,"AishatBolarinwa,Aleru Divine,Folakunmi,WikiWorks","Operational taxonomic units in infants (9 months of age) associated with maternal glycaemic traits (insulin sensitivity index), unadjusted for pre-pregnancy BMI.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|186801|186802|31979|1485;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|216572|253238;3379134|1224|1236|91347|543|570;1783272|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:33194786/21/1,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 21,Denmark,Homo sapiens,Feces,UBERON:0001988,Disposition index measurement,EFO:0006832,Lower Tertile (low disposition index),Upper Tertile (high disposition index),Infants (9 months of age) born to mothers with gestational diabetes mellitus (GDM) with with higher maternal disposition index.,NA,NA,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,body mass index,NA,NA,NA,NA,NA,NA,Signature 1,Table S9,14 November 2024,AishatBolarinwa,"AishatBolarinwa,Aleru Divine,Folakunmi,WikiWorks","Operational taxonomic units in infants (9 months of age) associated with maternal glycaemic traits (disposition index), adjusted for pre-pregnancy BMI.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976|200643|171549|815|816;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:33194786/21/2,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 21,Denmark,Homo sapiens,Feces,UBERON:0001988,Disposition index measurement,EFO:0006832,Lower Tertile (low disposition index),Upper Tertile (high disposition index),Infants (9 months of age) born to mothers with gestational diabetes mellitus (GDM) with with higher maternal disposition index.,NA,NA,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,body mass index,NA,NA,NA,NA,NA,NA,Signature 2,Table S9,14 November 2024,AishatBolarinwa,"AishatBolarinwa,Aleru Divine,Folakunmi,WikiWorks","Operational taxonomic units in infants (9 months of age) associated with maternal glycaemic traits (disposition index), adjusted for pre-pregnancy BMI.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia",1783272|1239|91061|186826|186828|117563;1783272|1239|186801|3082720|186804|1501226,Complete,Folakunmi
bsdb:33194786/22/1,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 22,Denmark,Homo sapiens,Feces,UBERON:0001988,Fasting blood glucose measurement,EFO:0004465,Lower Tertile (low fasting plasma glucose),Upper Tertile (high fasting plasma glucose),Infants (9 months of age) born to mothers with gestational diabetes mellitus (GDM) with higher maternal fasting plasma glucose.,NA,NA,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,body mass index,NA,NA,NA,NA,NA,NA,Signature 1,Table S9,14 November 2024,AishatBolarinwa,"AishatBolarinwa,Aleru Divine,WikiWorks","Operational taxonomic units in infants (9 months of age) associated with maternal glycaemic traits (fasting plasma glucose), adjusted for pre-pregnancy BMI.",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,1783272|1239|186801|3085636|186803|33042,Complete,Folakunmi
bsdb:33194786/23/1,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 23,Denmark,Homo sapiens,Feces,UBERON:0001988,Glucose measurement,EFO:0004468,Lower Tertile (low stimulated 2-h plasma glucose level),Upper Tertile (high stimulated 2-h plasma glucose level),Infants (9 months of age) born to mothers with gestational diabetes mellitus (GDM) with higher maternal stimulated 2-h plasma glucose level.,NA,NA,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,body mass index,NA,NA,NA,NA,NA,NA,Signature 1,Table S9,14 November 2024,AishatBolarinwa,"AishatBolarinwa,Aleru Divine,WikiWorks","Operational taxonomic units in infants (9 months of age) associated with maternal glycaemic traits (stimulated 2-h plasma glucose level), adjusted for pre-pregnancy BMI.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|201174|1760|2037|2049|1654;1783272|1239|186801|186802|216572|216851,Complete,Folakunmi
bsdb:33194786/24/1,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 24,Denmark,Homo sapiens,Feces,UBERON:0001988,Insulin sensitivity measurement,EFO:0004471,Lower Tertile (low insulin sensitivity index),Upper Tertile (high insulin sensitivity index),Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM) with higher maternal insulin sensitivity index.,NA,NA,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,body mass index,NA,NA,NA,NA,NA,NA,Signature 1,Table S9,14 November 2024,AishatBolarinwa,"AishatBolarinwa,Aleru Divine,WikiWorks","Operational taxonomic units in infants (9 months of age) associated with maternal glycaemic traits (insulin sensitivity index), adjusted for pre-pregnancy BMI.",increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:33194786/25/1,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 25,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational weight gain measurement,EFO:0008435,Lower Tertile (low gestational weight gain),Upper Tertile (high gestational weight gain),Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM) with higher gestational weight gain.,NA,NA,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S12,13 November 2024,AishatBolarinwa,"AishatBolarinwa,Folakunmi,WikiWorks",OTUs in newborns (1 week of life) associated with maternal gestational weight gain unadjusted for pre-pregnancy BMI,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;1783272|1239|909932|1843489|31977|39948;3379134|1224|1236|135625|712|724;1783272|1239|91061|1385|90964|1279;1783272|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:33194786/25/2,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 25,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational weight gain measurement,EFO:0008435,Lower Tertile (low gestational weight gain),Upper Tertile (high gestational weight gain),Newborns (1 week of life) born to mothers with gestational diabetes mellitus (GDM) with higher gestational weight gain.,NA,NA,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S12,13 November 2024,AishatBolarinwa,"AishatBolarinwa,Aleru Divine,Folakunmi,WikiWorks",OTUs in newborns (1 week of life) associated with maternal gestational weight gain unadjusted for pre-pregnancy BMI,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;1783272|1239|526524|526525|128827|1573535;3379134|1224|1236|91347|543|570;3379134|1224|28216|206351|481|482;1783272|1239|186801|3085636|186803|841;3379134|1224|28216|80840|995019|40544,Complete,Folakunmi
bsdb:33194786/26/1,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 26,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational weight gain measurement,EFO:0008435,Lower Tertile (low gestational weight gain),Upper Tertile (high gestational weight gain),Infants (9 months of age) born to mothers with gestational diabetes mellitus (GDM) with higher gestational weight gain.,NA,NA,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S12,13 November 2024,AishatBolarinwa,"AishatBolarinwa,WikiWorks",OTUs in Infants (9 months of age) associated with maternal gestational weight gain unadjusted for pre-pregnancy BMI,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|1224|1236|135625|712|724;3379134|976|200643|171549|171552|838,Complete,Folakunmi
bsdb:33194786/26/2,33194786,"cross-sectional observational, not case-control",33194786,https://doi.org/10.3389/fcimb.2020.536282,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.536282/full,"Crusell M.K.W., Hansen T.H., Nielsen T., Allin K.H., Rühlemann M.C., Damm P., Vestergaard H., Rørbye C., Jørgensen N.R., Christiansen O.B., Heinsen F.A., Franke A., Hansen T., Lauenborg J. , Pedersen O.",Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes,Frontiers in cellular and infection microbiology,2020,"bacterial genera, gestational diabetes, gut microbiota, infancy, maternal glycaemic traits",Experiment 26,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational weight gain measurement,EFO:0008435,Lower Tertile (low gestational weight gain),Upper Tertile (high gestational weight gain),Infants (9 months of age) born to mothers with gestational diabetes mellitus (GDM) with higher gestational weight gain.,NA,NA,2 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S12,13 November 2024,AishatBolarinwa,"AishatBolarinwa,WikiWorks",OTUs in Infants (9 months of age) associated with maternal gestational weight gain unadjusted for pre-pregnancy BMI,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,1783272|1239|186801|186802|216572|216851,Complete,Folakunmi
bsdb:33207260/1/1,33207260,"cross-sectional observational, not case-control",33207260,10.1016/j.micpath.2020.104617,NA,"Qingqing B., Jie Z., Songben Q., Juan C., Lei Z. , Mu X.",Cervicovaginal microbiota dysbiosis correlates with HPV persistent infection,Microbial pathogenesis,2021,"16S rDNA sequencing, Cervicovaginal microbiota, HPV persistent Infection, Host immunosuppression",Experiment 1,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV- controls and HPV+ transient patients,HPV+ persistence,HPV infection of the same type that lasts for more than 12 months,9,6,1 month,16S,4,Ion Torrent,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,increased,increased,NA,increased,Signature 1,Figure 5,20 March 2021,Cynthia Anderson,"Cynthia Anderson,WikiWorks",LEfSe Analysis. A: LDA value distribution histogram,increased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas leidyi,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__Ruminiclostridium papyrosolvens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus",3379134|1224;3379134|1224|28211;1783272|201174;1783272|1239|186801;1783272|1239|186801|186802;3379134|1224|28211|356;3379134|976;3379134|976|200643;3379134|1224|1236;3379134|1224|28211|356|82115;3379134|1224|28211|356|69277|28100;1783272|1239|909932|1843489|31977;3379134|976|200643|171549;3379134|976|200643|171549|171552;3379134|1224|28211|204457;3379134|1224|28211|204457|41297;3379134|1224|28211|204457|41297|13687;1783272|1239|1737404|1737405|1570339|165779;3379134|1224|28211|204457|41297|13687|68569;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|815|909656|310298;3379134|1224|28216|80840|119060;1783272|1239|186801|186802|216572|1508657|29362;1783272|1239|909932|1843489|31977|39948;1783272|1239|1737404|1737405|1570339|162289,Complete,Folakunmi
bsdb:33207260/1/2,33207260,"cross-sectional observational, not case-control",33207260,10.1016/j.micpath.2020.104617,NA,"Qingqing B., Jie Z., Songben Q., Juan C., Lei Z. , Mu X.",Cervicovaginal microbiota dysbiosis correlates with HPV persistent infection,Microbial pathogenesis,2021,"16S rDNA sequencing, Cervicovaginal microbiota, HPV persistent Infection, Host immunosuppression",Experiment 1,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV- controls and HPV+ transient patients,HPV+ persistence,HPV infection of the same type that lasts for more than 12 months,9,6,1 month,16S,4,Ion Torrent,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,increased,increased,NA,increased,Signature 2,Figure 5,20 March 2021,Cynthia Anderson,"Cynthia Anderson,Folakunmi,WikiWorks",LEfSe Analysis. A: LDA value distribution histogram,decreased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners",1783272|1239|91061;1783272|1239;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|147802,Complete,Folakunmi
bsdb:33207260/2/1,33207260,"cross-sectional observational, not case-control",33207260,10.1016/j.micpath.2020.104617,NA,"Qingqing B., Jie Z., Songben Q., Juan C., Lei Z. , Mu X.",Cervicovaginal microbiota dysbiosis correlates with HPV persistent infection,Microbial pathogenesis,2021,"16S rDNA sequencing, Cervicovaginal microbiota, HPV persistent Infection, Host immunosuppression",Experiment 2,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV- controls and HPV+ persistent patients,HPV+ transient,HPV infection cleared within 12 months,11,4,1 month,16S,4,Ion Torrent,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 5,20 March 2021,Cynthia Anderson,"Cynthia Anderson,WikiWorks",LEfSe Analysis. A: LDA value distribution histogram,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,1783272|1239|91061|186826|33958|1578|147802,Complete,Folakunmi
bsdb:33207260/3/1,33207260,"cross-sectional observational, not case-control",33207260,10.1016/j.micpath.2020.104617,NA,"Qingqing B., Jie Z., Songben Q., Juan C., Lei Z. , Mu X.",Cervicovaginal microbiota dysbiosis correlates with HPV persistent infection,Microbial pathogenesis,2021,"16S rDNA sequencing, Cervicovaginal microbiota, HPV persistent Infection, Host immunosuppression",Experiment 3,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV+ transient,HPV+ persistent,patients whose HPV infection persisted for 12 months,6,4,1 month,16S,4,Ion Torrent,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,increased,increased,NA,increased,Signature 1,supplementary figure s1,6 February 2024,Folakunmi,"Folakunmi,WikiWorks",Lefse analysis between  persistent HPV infection group and transient HPV infection group,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas leidyi,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota",3379134|976|200643|171549|171552;3379134|1224|28216|80840|119060;3379134|1224|1236;3379134|1224|28211|204457|41297|13687|68569;3379134|1224|28211|204457|41297|13687;3379134|976|200643|171549|171552;3379134|1224|28211|204457|41297;3379134|1224|28211|204457;3379134|1224|28211|356|69277|28100;3379134|976|200643|171549;3379134|1224|28211|356|82115;1783272|1239|186801;1783272|1239|186801|186802;3379134|976|200643;1783272|201174;3379134|1224|1236;3379134|1224|28211;3379134|1224,Complete,Folakunmi
bsdb:33207260/3/2,33207260,"cross-sectional observational, not case-control",33207260,10.1016/j.micpath.2020.104617,NA,"Qingqing B., Jie Z., Songben Q., Juan C., Lei Z. , Mu X.",Cervicovaginal microbiota dysbiosis correlates with HPV persistent infection,Microbial pathogenesis,2021,"16S rDNA sequencing, Cervicovaginal microbiota, HPV persistent Infection, Host immunosuppression",Experiment 3,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV+ transient,HPV+ persistent,patients whose HPV infection persisted for 12 months,6,4,1 month,16S,4,Ion Torrent,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,increased,increased,NA,increased,Signature 2,supplementary figure s1,6 February 2024,Folakunmi,"Folakunmi,WikiWorks",Lefse analysis between persistent HPV infection group and transient HPV infection group,decreased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,",1783272|1239|91061;1783272|1239;1783272|1239|91061|186826|81850;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|147802;,Complete,Folakunmi
bsdb:33207260/4/1,33207260,"cross-sectional observational, not case-control",33207260,10.1016/j.micpath.2020.104617,NA,"Qingqing B., Jie Z., Songben Q., Juan C., Lei Z. , Mu X.",Cervicovaginal microbiota dysbiosis correlates with HPV persistent infection,Microbial pathogenesis,2021,"16S rDNA sequencing, Cervicovaginal microbiota, HPV persistent Infection, Host immunosuppression",Experiment 4,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV- controls,HPV+ persistence,HPV infection of the same type that lasts for more than 12 months,5,6,1 month,16S,4,Ion Torrent,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,increased,increased,NA,increased,Signature 1,supplementary figure s1,9 February 2024,Folakunmi,"Folakunmi,WikiWorks",Lefse analysis between persistent HPV infection group and transient HPV infection group,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Colwelliaceae|g__Colwellia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Colwelliaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Cryomorphaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas leidyi,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota",3384189|32066|203490|203491|1129771|168808|40543;3379134|1224|1236|135622|267889|28228;3379134|1224|1236|135622|267889;3379134|976|117743|200644|246874;3379134|976|200643|171549|1853231|283168;1783272|1239|909932|1843489|31977|39948;3379134|976|200643|171549|171552;3379134|1224|28216|80840|119060;3379134|1224|1236;3379134|976|200643|171549|171552|838;3384189|32066|203490|203491;3384189|32066|203490;3379134|1224|1236|91347|543;3379134|1224|1236|91347;1783272|1239|1737404|1737405|1570339|165779;1783272|1117;3379134|1224|28211|204457|41297|13687|68569;3379134|1224|28211|204457|41297;3379134|976|117747|200666;3379134|1224|28211|204457|41297|13687;1783272|1239|186801|186802;3379134|976|200643|171549|171552;3379134|1224|28211|356|69277|28100;3379134|1224|28211|356|82115;3379134|1224|28211|356;3379134|976|200643|171549;3379134|1224|1236;3379134|976|200643;1783272|1239|909932|1843489|31977;1783272|1239|909932|909929;1783272|1239|909932;1783272|201174;1783272|201174;3379134|1224|28211;3379134|1224,Complete,Folakunmi
bsdb:33207260/4/2,33207260,"cross-sectional observational, not case-control",33207260,10.1016/j.micpath.2020.104617,NA,"Qingqing B., Jie Z., Songben Q., Juan C., Lei Z. , Mu X.",Cervicovaginal microbiota dysbiosis correlates with HPV persistent infection,Microbial pathogenesis,2021,"16S rDNA sequencing, Cervicovaginal microbiota, HPV persistent Infection, Host immunosuppression",Experiment 4,China,Homo sapiens,Uterine cervix,UBERON:0000002,Human papilloma virus infection,EFO:0001668,HPV- controls,HPV+ persistence,HPV infection of the same type that lasts for more than 12 months,5,6,1 month,16S,4,Ion Torrent,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,increased,increased,NA,increased,Signature 2,supplementary figure s1,9 February 2024,Folakunmi,"Folakunmi,WikiWorks",Lefse analysis between persistent HPV infection group and transient HPV infection group,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners",1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|1385|186817|1386;1783272|1239;1783272|1239|91061|186826|33958|1578|147802,Complete,Folakunmi
bsdb:33208159/1/1,33208159,laboratory experiment,33208159,10.1186/s12934-020-01473-3,NA,"Li S., He Y., Zhang H., Zheng R., Xu R., Liu Q., Tang S., Ke X. , Huang M.",Formulation of traditional Chinese medicine and its application on intestinal flora of constipated rats,Microbial cell factories,2020,"Constipation, Firmicutes, Gut microbiota, Lactobacillus, Traditional Chinese medicine",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,Functional constipation (FC) model (control) group,Low dose group (DI),Rats in this group were treated with a low dose 5.15 g/(kg d) of traditional Chinese medicine,10,10,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 2C,30 April 2025,Tosin,Tosin,Relative abundance of significant taxa between Functional constipation (FC) and Low Dose (DI) groups,increased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,KateRasheed
bsdb:33208159/1/2,33208159,laboratory experiment,33208159,10.1186/s12934-020-01473-3,NA,"Li S., He Y., Zhang H., Zheng R., Xu R., Liu Q., Tang S., Ke X. , Huang M.",Formulation of traditional Chinese medicine and its application on intestinal flora of constipated rats,Microbial cell factories,2020,"Constipation, Firmicutes, Gut microbiota, Lactobacillus, Traditional Chinese medicine",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,Functional constipation (FC) model (control) group,Low dose group (DI),Rats in this group were treated with a low dose 5.15 g/(kg d) of traditional Chinese medicine,10,10,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 2B,30 April 2025,Tosin,Tosin,Relative abundance of significant taxa between Functional constipation (FC) and Low Dose (DI) groups,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,KateRasheed
bsdb:33208159/2/1,33208159,laboratory experiment,33208159,10.1186/s12934-020-01473-3,NA,"Li S., He Y., Zhang H., Zheng R., Xu R., Liu Q., Tang S., Ke X. , Huang M.",Formulation of traditional Chinese medicine and its application on intestinal flora of constipated rats,Microbial cell factories,2020,"Constipation, Firmicutes, Gut microbiota, Lactobacillus, Traditional Chinese medicine",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,Blank control (KO) group,Functional constipation (FC) model group,Rats in this group were given 4 ml normal saline every time and gavage for 2 weeks.,10,10,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 2B,30 April 2025,Tosin,Tosin,Relative abundance between Functional constipation (FC) model group and Blank control (KO) group,increased,k__Bacillati|p__Bacillota,1783272|1239,Complete,KateRasheed
bsdb:33208159/2/2,33208159,laboratory experiment,33208159,10.1186/s12934-020-01473-3,NA,"Li S., He Y., Zhang H., Zheng R., Xu R., Liu Q., Tang S., Ke X. , Huang M.",Formulation of traditional Chinese medicine and its application on intestinal flora of constipated rats,Microbial cell factories,2020,"Constipation, Firmicutes, Gut microbiota, Lactobacillus, Traditional Chinese medicine",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,Blank control (KO) group,Functional constipation (FC) model group,Rats in this group were given 4 ml normal saline every time and gavage for 2 weeks.,10,10,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 2C,30 April 2025,Tosin,Tosin,Relative abundance between Functional constipation (FC) model and Blank control (KO) groups,decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,KateRasheed
bsdb:33208159/3/1,33208159,laboratory experiment,33208159,10.1186/s12934-020-01473-3,NA,"Li S., He Y., Zhang H., Zheng R., Xu R., Liu Q., Tang S., Ke X. , Huang M.",Formulation of traditional Chinese medicine and its application on intestinal flora of constipated rats,Microbial cell factories,2020,"Constipation, Firmicutes, Gut microbiota, Lactobacillus, Traditional Chinese medicine",Experiment 3,China,Rattus norvegicus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,Low dose (DI) group,Medium dose (ZH) group,Rats in this group were treated with a medium dose 10.3 g/(kg d) of traditional Chinese medicine,10,10,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,NA,NA,decreased,Signature 1,"Figure 2B, 2F",30 April 2025,Tosin,Tosin,Relative abundance between Low dose group (DI) and Medium dose group (ZH),increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239;1783272|1239|91061|186826|33958|1578,Complete,KateRasheed
bsdb:33208159/3/2,33208159,laboratory experiment,33208159,10.1186/s12934-020-01473-3,NA,"Li S., He Y., Zhang H., Zheng R., Xu R., Liu Q., Tang S., Ke X. , Huang M.",Formulation of traditional Chinese medicine and its application on intestinal flora of constipated rats,Microbial cell factories,2020,"Constipation, Firmicutes, Gut microbiota, Lactobacillus, Traditional Chinese medicine",Experiment 3,China,Rattus norvegicus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,Low dose (DI) group,Medium dose (ZH) group,Rats in this group were treated with a medium dose 10.3 g/(kg d) of traditional Chinese medicine,10,10,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,NA,NA,decreased,Signature 2,"Figure 2C, 2E",30 April 2025,Tosin,Tosin,Relative abundance between Low dose (DI) group and Medium dose (ZH) group,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota",1783272|1239|186801|3085636|186803;3379134|976,Complete,KateRasheed
bsdb:33208159/4/1,33208159,laboratory experiment,33208159,10.1186/s12934-020-01473-3,NA,"Li S., He Y., Zhang H., Zheng R., Xu R., Liu Q., Tang S., Ke X. , Huang M.",Formulation of traditional Chinese medicine and its application on intestinal flora of constipated rats,Microbial cell factories,2020,"Constipation, Firmicutes, Gut microbiota, Lactobacillus, Traditional Chinese medicine",Experiment 4,China,Rattus norvegicus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,Blank control (KO) group,High dose (GA) group,Rats in this group were treated with a high dose 20.6 g/(kg d) of traditional Chinese medicine,10,10,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,"Figure 2B, 2F",30 April 2025,Tosin,Tosin,Relative abundance between Blank control (KO) group and High dose group (GA),increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota",1783272|1239|91061|186826|33958|1578;1783272|1239,Complete,KateRasheed
bsdb:33208159/6/1,33208159,laboratory experiment,33208159,10.1186/s12934-020-01473-3,NA,"Li S., He Y., Zhang H., Zheng R., Xu R., Liu Q., Tang S., Ke X. , Huang M.",Formulation of traditional Chinese medicine and its application on intestinal flora of constipated rats,Microbial cell factories,2020,"Constipation, Firmicutes, Gut microbiota, Lactobacillus, Traditional Chinese medicine",Experiment 6,China,Rattus norvegicus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,Blank control (KO) group,Mosapride (MO) group,"Rats in this group were given mosapride 2 mg/(kg d) gavage, with a volume of 4ml per animal each time",10,10,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 2E,30 April 2025,Tosin,Tosin,Relative abundance between Blank control (KO) group and Mosapride (MO) group,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,1783272|1239|186801|3085636|186803,Complete,KateRasheed
bsdb:33208159/7/1,33208159,laboratory experiment,33208159,10.1186/s12934-020-01473-3,NA,"Li S., He Y., Zhang H., Zheng R., Xu R., Liu Q., Tang S., Ke X. , Huang M.",Formulation of traditional Chinese medicine and its application on intestinal flora of constipated rats,Microbial cell factories,2020,"Constipation, Firmicutes, Gut microbiota, Lactobacillus, Traditional Chinese medicine",Experiment 7,China,Rattus norvegicus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,Medium dose (ZH) group,High dose (GA) group,Rats in this group were treated with a high dose 20.6 g/(kg d) of traditional Chinese medicine,10,10,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 2F,30 April 2025,Tosin,Tosin,Relative abundance between Medium dose (ZH) group and High dose (GA) group,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,KateRasheed
bsdb:33208159/7/2,33208159,laboratory experiment,33208159,10.1186/s12934-020-01473-3,NA,"Li S., He Y., Zhang H., Zheng R., Xu R., Liu Q., Tang S., Ke X. , Huang M.",Formulation of traditional Chinese medicine and its application on intestinal flora of constipated rats,Microbial cell factories,2020,"Constipation, Firmicutes, Gut microbiota, Lactobacillus, Traditional Chinese medicine",Experiment 7,China,Rattus norvegicus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,Medium dose (ZH) group,High dose (GA) group,Rats in this group were treated with a high dose 20.6 g/(kg d) of traditional Chinese medicine,10,10,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,"Figure 2C, 2E",30 April 2025,Tosin,Tosin,Relative abundance between Medium dose (ZH) group and High dose (GA) group,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|976;1783272|1239|186801|3085636|186803,Complete,KateRasheed
bsdb:33208159/8/1,33208159,laboratory experiment,33208159,10.1186/s12934-020-01473-3,NA,"Li S., He Y., Zhang H., Zheng R., Xu R., Liu Q., Tang S., Ke X. , Huang M.",Formulation of traditional Chinese medicine and its application on intestinal flora of constipated rats,Microbial cell factories,2020,"Constipation, Firmicutes, Gut microbiota, Lactobacillus, Traditional Chinese medicine",Experiment 8,China,Rattus norvegicus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,Functional constipation (FC) model (control) group,High dose (GA) group,Rats in this group were treated with a high dose 20.6 g/(kg d) of traditional Chinese medicine,10,10,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 2F,30 April 2025,Tosin,Tosin,Relative abundance between Functional constipation (FC) model (control) group and High dose (GA) group,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,KateRasheed
bsdb:33208159/9/1,33208159,laboratory experiment,33208159,10.1186/s12934-020-01473-3,NA,"Li S., He Y., Zhang H., Zheng R., Xu R., Liu Q., Tang S., Ke X. , Huang M.",Formulation of traditional Chinese medicine and its application on intestinal flora of constipated rats,Microbial cell factories,2020,"Constipation, Firmicutes, Gut microbiota, Lactobacillus, Traditional Chinese medicine",Experiment 9,China,Rattus norvegicus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,"Combination of Blank control (KO), Functional constipation model (FC), Mosapride (MO), Low dose (DI) and High dose (GA) groups",Medium dose (ZH) group,Rats in this group were treated with a medium dose 10.3 g/(kg d) of traditional Chinese medicine,50,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a,30 April 2025,Tosin,Tosin,Taxonomic cladogram obtained from LEfSe at six groups.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales",1783272|1239|186801|3082768|990719;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;3366610|28890|183925;3366610|28890|183925|2158|2159;3366610|28890|183925|2158,Complete,KateRasheed
bsdb:33208159/10/1,33208159,laboratory experiment,33208159,10.1186/s12934-020-01473-3,NA,"Li S., He Y., Zhang H., Zheng R., Xu R., Liu Q., Tang S., Ke X. , Huang M.",Formulation of traditional Chinese medicine and its application on intestinal flora of constipated rats,Microbial cell factories,2020,"Constipation, Firmicutes, Gut microbiota, Lactobacillus, Traditional Chinese medicine",Experiment 10,China,Rattus norvegicus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,"Combination of Blank control (KO), Functional constipation (FC) , Low dose (DI), Medium dose (ZH) and High dose (GA) groups",Mosapride (MO) group,"Rats in this group were given mosapride 2 mg/(kg d) gavage, with a volume of 4ml per animal each time",50,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a,30 April 2025,Tosin,Tosin,Taxonomic cladogram obtained from LEfSe at six groups.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia",1783272|1239|91061|186826|186827;1783272|1239|186801|3082720|543314;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|1239|186801|186802|31979;3379134|200930|68337|191393|191394;3379134|200930|68337|191393;3379134|200930|68337;1783272|1239|186801|3085636|1185407;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|186807;1783272|201174|84992,Complete,KateRasheed
bsdb:33208159/11/1,33208159,laboratory experiment,33208159,10.1186/s12934-020-01473-3,NA,"Li S., He Y., Zhang H., Zheng R., Xu R., Liu Q., Tang S., Ke X. , Huang M.",Formulation of traditional Chinese medicine and its application on intestinal flora of constipated rats,Microbial cell factories,2020,"Constipation, Firmicutes, Gut microbiota, Lactobacillus, Traditional Chinese medicine",Experiment 11,China,Rattus norvegicus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,"Combination of Blank control (KO), Functional constipation (FC), Mosapride (MO), Medium dose (ZH) and High dose (GA) groups",Low dose group (DI),Rats in this group were treated with a low dose 5.15 g/(kg d) of traditional Chinese medicine,50,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a,30 April 2025,Tosin,Tosin,Taxonomic cladogram obtained from LEfSe at six groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|976|200643|171549|171551;1783272|1239|186801|3085636|186803,Complete,KateRasheed
bsdb:33208159/12/1,33208159,laboratory experiment,33208159,10.1186/s12934-020-01473-3,NA,"Li S., He Y., Zhang H., Zheng R., Xu R., Liu Q., Tang S., Ke X. , Huang M.",Formulation of traditional Chinese medicine and its application on intestinal flora of constipated rats,Microbial cell factories,2020,"Constipation, Firmicutes, Gut microbiota, Lactobacillus, Traditional Chinese medicine",Experiment 12,China,Rattus norvegicus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,"Combination of Blank control (KO), Functional constipation (FC), Mosapride (MO), Low dose (DI), Medium dose (ZH) groups",High dose (GA) group,Rats in this group were treated with a high dose 20.6 g/(kg d) of traditional Chinese medicine,50,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a,30 April 2025,Tosin,Tosin,Taxonomic cladogram obtained from LEfSe at six groups.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061;1783272|1239|186801|3082720|186804,Complete,KateRasheed
bsdb:33208159/13/1,33208159,laboratory experiment,33208159,10.1186/s12934-020-01473-3,NA,"Li S., He Y., Zhang H., Zheng R., Xu R., Liu Q., Tang S., Ke X. , Huang M.",Formulation of traditional Chinese medicine and its application on intestinal flora of constipated rats,Microbial cell factories,2020,"Constipation, Firmicutes, Gut microbiota, Lactobacillus, Traditional Chinese medicine",Experiment 13,China,Rattus norvegicus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,"Combination of Functional constipation (FC), Mosapride (MO), Low dose (DI), Medium dose (ZH) and High dose (GA) groups",Blank control (KO) group,Rats in this group were fed SPF standard diet until the end of the experiment and given 4 ml normal saline every time and gavage for 2 weeks.,50,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a,30 April 2025,Tosin,Tosin,Taxonomic cladogram obtained from LEfSe at six groups.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Candidatus Melainabacteria",3379134|1224|28216|80840|506;1783272|1239|91061|1385;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643;3379134|1224|28216;3379134|1224|28216|80840;1783272|1798710|1906119;3379134|1224|28216|80840|80864;3379134|200940|3031449|213115|194924;3379134|74152|641853;3379134|74152|641853|641854|641876;3379134|74152|641853|641854;1783272|1239|91061|186826|81852;1783272|1239|186801|186802|186806;1783272|201174|1760|85006|1268;1783272|201174|1760|85006;3379134|976|200643|171549|2005473;1783272|1239|909932;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550;1783272|1239|909932|909929;1783272|1239|91061|1385|90964;1783272|1239|91061|186826|1300;1783272|1239|909932|1843489|31977;1783272|1798710,Complete,KateRasheed
bsdb:33208159/14/1,33208159,laboratory experiment,33208159,10.1186/s12934-020-01473-3,NA,"Li S., He Y., Zhang H., Zheng R., Xu R., Liu Q., Tang S., Ke X. , Huang M.",Formulation of traditional Chinese medicine and its application on intestinal flora of constipated rats,Microbial cell factories,2020,"Constipation, Firmicutes, Gut microbiota, Lactobacillus, Traditional Chinese medicine",Experiment 14,China,Rattus norvegicus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,"Combination of Blank control (KO), Mosapride (MO), Low dose (DI), Medium dose (ZH) and High dose (GA) groups",Functional constipation (FC) model (control) group,Rats in this group were given 4 ml normal saline every time and gavage for 2 weeks.,50,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a,1 May 2025,Tosin,Tosin,Taxonomic cladogram obtained from LEfSe at six groups.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239|91061|186826|186828;1783272|1239|186801;1783272|1239|186801|186802,Complete,KateRasheed
bsdb:33219095/1/1,33219095,"cross-sectional observational, not case-control",33219095,10.1128/mBio.01969-20,NA,"Mostafa H.H., Fissel J.A., Fanelli B., Bergman Y., Gniazdowski V., Dadlani M., Carroll K.C., Colwell R.R. , Simner P.J.",Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients,mBio,2020,"COVID-19, SARS-CoV-2, metagenomic next-generation sequencing, metagenomics, nasopharyngeal",Experiment 1,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls,COVID-19 cases,Positive for SaRS-CoV-2 by diagnostic RT-PCR,10,40,NA,WMS,NA,Nanopore,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,Figure 3,5 June 2021,Claregrieve1,"Claregrieve1,Aiyshaaaa,Atrayees,WikiWorks",Relative abundance of bacteria at species level in COVID-19-positive and COVID-19-negative samples,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium accolens,1783272|201174|1760|85007|1653|1716|38284,Complete,Atrayees
bsdb:33219095/1/2,33219095,"cross-sectional observational, not case-control",33219095,10.1128/mBio.01969-20,NA,"Mostafa H.H., Fissel J.A., Fanelli B., Bergman Y., Gniazdowski V., Dadlani M., Carroll K.C., Colwell R.R. , Simner P.J.",Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients,mBio,2020,"COVID-19, SARS-CoV-2, metagenomic next-generation sequencing, metagenomics, nasopharyngeal",Experiment 1,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls,COVID-19 cases,Positive for SaRS-CoV-2 by diagnostic RT-PCR,10,40,NA,WMS,NA,Nanopore,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,Figure 3,5 June 2021,Claregrieve1,"Claregrieve1,Aiyshaaaa,Atrayees,WikiWorks",Relative abundance of bacteria at species level in COVID-19-positive and COVID-19-negative samples,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,1783272|201174|1760|85009|31957,Complete,Atrayees
bsdb:33220709/1/1,33220709,"cross-sectional observational, not case-control",33220709,10.1186/s40168-020-00932-8,NA,"Alisoltani A., Manhanzva M.T., Potgieter M., Balle C., Bell L., Ross E., Iranzadeh A., du Plessis M., Radzey N., McDonald Z., Calder B., Allali I., Mulder N., Dabee S., Barnabas S., Gamieldien H., Godzik A., Blackburn J.M., Tabb D.L., Bekker L.G., Jaspan H.B., Passmore J.S. , Masson L.",Microbial function and genital inflammation in young South African women at high risk of HIV infection,Microbiome,2020,"Cytokine, Female genital tract, Inflammation, Metaproteomics, Microbial function, Microbiome",Experiment 1,South Africa,Homo sapiens,Wall of vagina,UBERON:0036523,Vaginal inflammation,EFO:0005757,Low Genital Inflammation,High Genital Inflammation,"Women with high levels of genital inflammation, defined by elevated inflammatory cytokine levels in their cervicovaginal secretions.",20,20,NA,16S,4,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,"age,contraception,sexually transmitted infection",NA,NA,NA,NA,NA,NA,Signature 1,Additional file 2: Table S3,9 October 2025,Adenike Awotunde,Adenike Awotunde,"Bacterial relative abundances were compared using16S rRNA gene sequencing data across women with low, medium, and high genital inflammation, classified by cytokine profiles. Differentially abundant bacterial genera were identified using a moderated t-test (limma R package), applying an FDR-adjusted p-value < 0.05 and an absolute log₂ fold-change > 1.2 as the significance threshold.",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Umbribacter|s__Umbribacter vaginalis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sp. UPII 135-E,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. S7-1-8,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Cantharellales|f__Ceratobasidiaceae|g__Rhizoctonia|s__Rhizoctonia solani,k__Fungi|p__Basidiomycota|c__Wallemiomycetes|o__Wallemiales|f__Wallemiaceae|g__Wallemia|s__Wallemia ichthyophaga,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__uncultured Ruminococcus sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera genomosp. C1",1783272|201174|84998|1643822|1643826|3472368|1588753;1783272|201174|84998|84999|1643824|2767327|82135;1783272|201174|1760|85004|31953|2701|2702;1783272|1239|909932|1843489|31977|906|1000569;3379134|976|200643|171549|171552|838|419005;3379134|976|200643|171549|171552|838|1284775;4751|5204|155619|36064|5250|1322061|456999;4751|5204|431957|431958|431959|148959|245174;1783272|1239|186801|186802|216572|1263|165186;1783272|1239|909932|1843489|31977|906|230139,Complete,KateRasheed
bsdb:33220709/1/2,33220709,"cross-sectional observational, not case-control",33220709,10.1186/s40168-020-00932-8,NA,"Alisoltani A., Manhanzva M.T., Potgieter M., Balle C., Bell L., Ross E., Iranzadeh A., du Plessis M., Radzey N., McDonald Z., Calder B., Allali I., Mulder N., Dabee S., Barnabas S., Gamieldien H., Godzik A., Blackburn J.M., Tabb D.L., Bekker L.G., Jaspan H.B., Passmore J.S. , Masson L.",Microbial function and genital inflammation in young South African women at high risk of HIV infection,Microbiome,2020,"Cytokine, Female genital tract, Inflammation, Metaproteomics, Microbial function, Microbiome",Experiment 1,South Africa,Homo sapiens,Wall of vagina,UBERON:0036523,Vaginal inflammation,EFO:0005757,Low Genital Inflammation,High Genital Inflammation,"Women with high levels of genital inflammation, defined by elevated inflammatory cytokine levels in their cervicovaginal secretions.",20,20,NA,16S,4,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,"age,contraception,sexually transmitted infection",NA,NA,NA,NA,NA,NA,Signature 2,Additional file 2: Table S3,9 October 2025,Adenike Awotunde,Adenike Awotunde,"Bacterial relative abundances were compared using 16S rRNA gene sequencing data across women with low, medium, and high genital inflammation, classified by cytokine profiles. Differentially abundant bacterial genera were identified using a moderated t-test (limma R package), applying an FDR-adjusted p-value < 0.05 and an absolute log₂ fold-change > 1.2 as the significance threshold.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus hamsteri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus helveticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus jensenii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus kefiranofaciens,k__Fungi|p__Ascomycota|c__Schizosaccharomycetes|o__Schizosaccharomycetales|f__Schizosaccharomycetaceae|g__Schizosaccharomyces|s__Schizosaccharomyces japonicus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus delbrueckii",1783272|1239|91061|186826|33958|1578|47770;1783272|1239|91061|186826|33958|1578|96565;1783272|1239|91061|186826|33958|1578|1587;1783272|1239|91061|186826|33958|1578|109790;1783272|1239|91061|186826|33958|1578|33959;1783272|1239|91061|186826|33958|1578|267818;4751|4890|147554|34346|4894|4895|4897;1783272|1239|91061|186826|33958|1578|1584,Complete,KateRasheed
bsdb:33224990/1/1,33224990,"cross-sectional observational, not case-control",33224990,10.1155/2020/8842651,https://pubmed.ncbi.nlm.nih.gov/33224990/,"Zhao X., Zhang Y., Guo R., Yu W., Zhang F., Wu F. , Shang J.",The Alteration in Composition and Function of Gut Microbiome in Patients with Type 2 Diabetes,Journal of diabetes research,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Diabetes mellitus,EFO:0000400,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,"Patients with Type 2 Diabetes who were admitted to the First Affiliated Hospital of Zhengzhou University from October 2018 to October 2019;  The diagnostic criteria of diabetes mellitus were as follows: (1) twice fasting plasma glucose ðFPGÞ ≥ 7:0 mmol/L, (2) twice oral glucose tolerance test (OGTT ≥ 11:1 mmol/L), and (3) diabetic symptoms (polyuria, thirst, drinking more water, and unexplained weight loss) accompanied with twice random blood glucose ≥ 11:1 mmol/L.",179,137,NA,16S,34,Illumina,relative abundances,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,NA,2,"age,sex",NA,NA,decreased,NA,unchanged,NA,NA,Signature 1,Figure 2,27 June 2021,Madhubani Dey,"Madhubani Dey,Aiyshaaaa,Peace Sandy,WikiWorks","Figure 2: Composition of the gut microbiome in the DM or Con group. (a, b) Distribution of differential flora at the phylum and genus levels between the DM and Con groups.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815|816;3379134|976;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|248744;3379134|976|200643|171549|1853231|283168;3379134|1224|28216|80840|995019|577310;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3085636|186803|46205;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;3379134|1224|28211|204457|41297|13687;3379134|1224|28216|80840|995019|40544,Complete,Peace Sandy
bsdb:33224990/1/2,33224990,"cross-sectional observational, not case-control",33224990,10.1155/2020/8842651,https://pubmed.ncbi.nlm.nih.gov/33224990/,"Zhao X., Zhang Y., Guo R., Yu W., Zhang F., Wu F. , Shang J.",The Alteration in Composition and Function of Gut Microbiome in Patients with Type 2 Diabetes,Journal of diabetes research,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Diabetes mellitus,EFO:0000400,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,"Patients with Type 2 Diabetes who were admitted to the First Affiliated Hospital of Zhengzhou University from October 2018 to October 2019;  The diagnostic criteria of diabetes mellitus were as follows: (1) twice fasting plasma glucose ðFPGÞ ≥ 7:0 mmol/L, (2) twice oral glucose tolerance test (OGTT ≥ 11:1 mmol/L), and (3) diabetic symptoms (polyuria, thirst, drinking more water, and unexplained weight loss) accompanied with twice random blood glucose ≥ 11:1 mmol/L.",179,137,NA,16S,34,Illumina,relative abundances,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,NA,2,"age,sex",NA,NA,decreased,NA,unchanged,NA,NA,Signature 2,Figure 2,27 June 2021,Madhubani Dey,"Madhubani Dey,Lwaldron,Peace Sandy,WikiWorks","Figure 2: Composition of the gut microbiome in the DM or Con group. (a, b) Distribution of differential flora at the phylum and genus levels between the DM and Con groups.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,p__Candidatus Saccharimonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",1783272|201174|1760|2037|2049|1654;1783272|201174;3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|186802|216572|244127;1783272|201174|1760|85004|31953|1678;95818;3379134|1224|1236|91347|543|544;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|1643822|1643826|84111;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|1940338;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|906;3379134|976|200643|171549|2005525|375288;3379134|1224;3379134|1224|1236|91347|543|160674;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|292632;3379134|74201;1783272|1239|91061|186826|33958|46255,Complete,Peace Sandy
bsdb:33234057/1/1,33234057,"cross-sectional observational, not case-control",33234057,https://doi.org/10.1089/thy.2020.0193,NA,"Jiang W., Yu X., Kosik R.O., Song Y., Qiao T., Tong J., Liu S., Fan S., Luo Q., Chai L., Lv Z. , Li D.",Gut Microbiota May Play a Significant Role in the Pathogenesis of Graves' Disease,Thyroid : official journal of the American Thyroid Association,2021,"16S rRNA sequencing, Graves' disease, alpha diversity, gut microbiota, metabolism",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Healthy controls (HC),Graves’ disease (GD),"Graves’ disease (GD) patients (12 males, 33 females, ages 16–65 years, median age 37) recruited from the Department of Nuclear Medicine at the Shanghai Tenth People's Hospital from January to June 2019.",59,45,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,decreased,increased,NA,decreased,Signature 1,Figure 3C and 3D,24 July 2025,Aleru Divine,Aleru Divine,The LEfSe was used to identify the species that significantly differed between GD patients and HC at the phylum and genus levels. Only taxa meeting a significant LDA threshold value of >3 and p < 0.05 are shown.,increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",3379134|976;3379134|976|200643|171549|815|816;1783272|1239|91061|186826|33958|1578,Complete,NA
bsdb:33234057/1/2,33234057,"cross-sectional observational, not case-control",33234057,https://doi.org/10.1089/thy.2020.0193,NA,"Jiang W., Yu X., Kosik R.O., Song Y., Qiao T., Tong J., Liu S., Fan S., Luo Q., Chai L., Lv Z. , Li D.",Gut Microbiota May Play a Significant Role in the Pathogenesis of Graves' Disease,Thyroid : official journal of the American Thyroid Association,2021,"16S rRNA sequencing, Graves' disease, alpha diversity, gut microbiota, metabolism",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Healthy controls (HC),Graves’ disease (GD),"Graves’ disease (GD) patients (12 males, 33 females, ages 16–65 years, median age 37) recruited from the Department of Nuclear Medicine at the Shanghai Tenth People's Hospital from January to June 2019.",59,45,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,decreased,increased,NA,decreased,Signature 2,Figure 3C and 3D,24 July 2025,Aleru Divine,Aleru Divine,The LEfSe was used to identify the species that significantly differed between GD patients and HC at the phylum and genus levels. Only taxa meeting a significant LDA threshold value of >3 and p < 0.05 are shown.,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",1783272|1239;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3082720|186804;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|1263|438033;3379134|976|200643|171549|2005473,Complete,NA
bsdb:33234057/2/1,33234057,"cross-sectional observational, not case-control",33234057,https://doi.org/10.1089/thy.2020.0193,NA,"Jiang W., Yu X., Kosik R.O., Song Y., Qiao T., Tong J., Liu S., Fan S., Luo Q., Chai L., Lv Z. , Li D.",Gut Microbiota May Play a Significant Role in the Pathogenesis of Graves' Disease,Thyroid : official journal of the American Thyroid Association,2021,"16S rRNA sequencing, Graves' disease, alpha diversity, gut microbiota, metabolism",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,"Graves disease,Hashimoto's thyroiditis","EFO:0004237,EFO:0003779",Hashimoto's negative,Hashimoto's positive,Graves’ disease (GD) patients with Hashimoto's thyroiditis,10,35,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3E,24 July 2025,Aleru Divine,Aleru Divine,Comparison across GD subgroups (GD with and without Hashimoto's thyroiditis).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239|186801|3085636|186803|877420;1783272|1239|91061|186826|33958|1578,Complete,NA
bsdb:33234057/2/2,33234057,"cross-sectional observational, not case-control",33234057,https://doi.org/10.1089/thy.2020.0193,NA,"Jiang W., Yu X., Kosik R.O., Song Y., Qiao T., Tong J., Liu S., Fan S., Luo Q., Chai L., Lv Z. , Li D.",Gut Microbiota May Play a Significant Role in the Pathogenesis of Graves' Disease,Thyroid : official journal of the American Thyroid Association,2021,"16S rRNA sequencing, Graves' disease, alpha diversity, gut microbiota, metabolism",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,"Graves disease,Hashimoto's thyroiditis","EFO:0004237,EFO:0003779",Hashimoto's negative,Hashimoto's positive,Graves’ disease (GD) patients with Hashimoto's thyroiditis,10,35,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3E,24 July 2025,Aleru Divine,Aleru Divine,Comparison across GD subgroups (GD with and without Hashimoto's thyroiditis).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|909932|909929|1843491|158846;3379134|976|200643|171549|171550|239759,Complete,NA
bsdb:33241010/1/1,33241010,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,NA,"Liu J., Luo M., Zhang Y., Cao G. , Wang S.",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,"Cervical cancer, human papillomavirus infection (HPV infection), cervical intraepithelial neoplasia pathological classification, cervical microbiota",Experiment 1,China,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,persistent HPV+ with LSIL,persistent HPV+ with HSIL,persistent HPV+ infection ( same HPV subtype has infected for >12 months) with high grade squamus intraepithelial lesion,NA,NA,NA,16S,NA,Illumina,raw counts,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A,18 March 2021,Cynthia Anderson,"Cynthia Anderson,Fatima,WikiWorks",Differential florae types in the comparison of the microbiota between high-risk human papillomavirus (HPV) persistent infection higher-grade squamous intraepithelial lesion (HSIL) and the high-risk HPV persistent infection with lower-grade squamous intraepithelial lesion (LSIL) group,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Commensalibacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Pseudoduganella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Actinomycetota|c__Thermoleophilia|o__Solirubrobacterales|f__Solirubrobacteraceae|g__Solirubrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Stappiaceae|g__Stappia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus",3379134|1224|28216|80840|506|222;3379134|1224|28216|80840|80864|283;3379134|1224|28211|3120395|433|1079922;1783272|1239|1737404|1737405|1570339|162290;3379134|1224|1236|135619|28256|2745;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|33958|1243;3379134|1224|1236|135614|32033|68;3379134|1224|28216|80840|75682|149698;3379134|1224|28211|356|119045|407;1783272|201174|1760|85009|85015|1839;3379134|1224|28211|204455|31989|265;1783272|1239|909932|1843488|909930|33024;3379134|1224|28216|80840|75682|1522432;3379134|1224|1236|72274|135621|286;1783272|201174|1497346|588673|320599|207599;3379134|1224|28211|356|2821832|152161;1783272|1239|186801|3085636|186803|84036;3384194|1297|188787|68933|188786|270,Complete,Fatima
bsdb:33241010/2/1,33241010,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,NA,"Liu J., Luo M., Zhang Y., Cao G. , Wang S.",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,"Cervical cancer, human papillomavirus infection (HPV infection), cervical intraepithelial neoplasia pathological classification, cervical microbiota",Experiment 2,China,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,transient HPV+ with LSIL,transient HPV+ with HSIL,high-risk HPV transient infection (HPV has regressed within 1 year) with high grade squamus intraepithelial lesion,NA,NA,NA,16S,NA,Illumina,NA,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3B,19 March 2021,Cynthia Anderson,"Cynthia Anderson,WikiWorks",comparison of the microbiota between the high-risk HPV persistent infection with LSIL group and high-risk HPV transient infection with HSIL group,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum",3379134|1224|1236|135614|32033;1783272|1239|186801|186802|31979|1485|1522,Complete,Fatima
bsdb:33241010/3/1,33241010,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,NA,"Liu J., Luo M., Zhang Y., Cao G. , Wang S.",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,"Cervical cancer, human papillomavirus infection (HPV infection), cervical intraepithelial neoplasia pathological classification, cervical microbiota",Experiment 3,China,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,transient HPV+ with LSIL,high-risk HPV transient infection (HPV has regressed within 1 year) with low grade squamus intraepithelial lesion,31,NA,NA,16S,NA,Illumina,NA,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3C,19 March 2021,Cynthia Anderson,"Cynthia Anderson,WikiWorks",Comparison of the microbiota between high-risk HPV transient infection with LSIL group and the non-infected HPV group,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Devosia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella",3384189|32066|203490|203491|1129771|168808;1783272|1239|186801|3085636|186803|177971;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|186802|31979|1485|1522;1783272|1239|909932|1843489|31977|906;3379134|1224|28211|356|2831106|46913;3379134|1224|1236|135614|32033;1783272|201174|1760|85004|31953|2701,Complete,Fatima
bsdb:33241010/4/1,33241010,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,NA,"Liu J., Luo M., Zhang Y., Cao G. , Wang S.",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,"Cervical cancer, human papillomavirus infection (HPV infection), cervical intraepithelial neoplasia pathological classification, cervical microbiota",Experiment 4,China,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,persistent HPV+ with HSIL,high-risk HPV persistent infection with high grade squamus intraepithelial lesion,31,NA,NA,16S,NA,Illumina,NA,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3D,19 March 2021,Cynthia Anderson,"Cynthia Anderson,Fatima,WikiWorks",Comparison of the microbiota between high-risk HPV persistent infection with HSIL and the non-infected HPV group,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia",1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3082720|186804|1257;1783272|1239|186801|3085636|186803|177971;3384189|32066|203490|203491|1129771|168808,Complete,Fatima
bsdb:33241010/5/1,33241010,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,NA,"Liu J., Luo M., Zhang Y., Cao G. , Wang S.",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,"Cervical cancer, human papillomavirus infection (HPV infection), cervical intraepithelial neoplasia pathological classification, cervical microbiota",Experiment 5,China,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,persistent HPV+ with LSIL,persistent HPV+ with HSIL,persistent HPV+ infection ( same HPV subtype has infected for >12 months) with high grade squamus intraepithelial lesion,NA,NA,NA,16S,NA,Illumina,NA,LEfSe,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4A,19 March 2021,Cynthia Anderson,"Cynthia Anderson,WikiWorks",Abundance analysis of the microbiota between high-risk human papillomavirus (HPV) persistent infection with higher-grade squamous intraepithelial lesion (HSIL) and the high-risk HPV persistent infection with lower-grade squamous intraepithelial lesion (LSIL) group,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae,1783272|1239|91061|186826|1300|1301|1311,Complete,Fatima
bsdb:33241010/5/2,33241010,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,NA,"Liu J., Luo M., Zhang Y., Cao G. , Wang S.",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,"Cervical cancer, human papillomavirus infection (HPV infection), cervical intraepithelial neoplasia pathological classification, cervical microbiota",Experiment 5,China,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,persistent HPV+ with LSIL,persistent HPV+ with HSIL,persistent HPV+ infection ( same HPV subtype has infected for >12 months) with high grade squamus intraepithelial lesion,NA,NA,NA,16S,NA,Illumina,NA,LEfSe,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4A,19 March 2021,Cynthia Anderson,"Cynthia Anderson,WikiWorks",Abundance analysis of the microbiota between high-risk human papillomavirus (HPV) persistent infection with higher-grade squamous intraepithelial lesion (HSIL) and the high-risk HPV persistent infection with lower-grade squamous intraepithelial lesion (LSIL) group,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium tuberculostearicum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Pseudarthrobacter|s__Pseudarthrobacter oxydans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium aurimucosum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Thermotogati|p__Deinococcota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Thermotogati|p__Deinococcota|c__Deinococci,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Nitrosomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Aedoeadaptatus|s__Aedoeadaptatus coxii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus durans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",1783272|1239|186801|186802|216572|216851;1783272|1239|91061|1385|186818;1783272|201174|1760|85007|1653|1716|38304;1783272|201174|1760|85007|2805586|1847725;1783272|1239|526524|526525;1783272|201174|1760|85006|1268;1783272|201174|1760|85006|1268|1742993|1671;1783272|201174|1760|85007|1653|1716|169292;1783272|1239|1737404|1737405|1570339|162289;1783272|201174|1760|2037|2049;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|186801|3085636|186803|2316020|33039;3379134|976|200643|171549|171552|838|28130;1783272|201174|1760|85007|85025;1783272|1239|909932|1843489|31977|39948;3384194|1297;1783272|201174|1760|2037;3379134|976|200643|171549|171552|838;1783272|201174|1760|85004|31953|2701;3384194|1297|188787;1783272|1239|91061|186826|33958|1243;3379134|1224|28216|32003|206379;3379134|1224|1236|135614;1783272|1239|186801|186802|404402;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|1737404|1737405|1570339|2981628|755172;1783272|201174|1760|85004|31953|1678|1689;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|1385|90964|1279|1280;1783272|1239|91061|1385|90964;1783272|1239|91061|1385;1783272|1239|91061|186826|81852|1350|53345;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|33958|2767887|1624;1783272|1239|909932|1843489|31977|39948|309120;1783272|1239|909932|909929;1783272|1239|909932;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|1239|91061|186826|1300,Complete,Fatima
bsdb:33241010/6/1,33241010,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,NA,"Liu J., Luo M., Zhang Y., Cao G. , Wang S.",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,"Cervical cancer, human papillomavirus infection (HPV infection), cervical intraepithelial neoplasia pathological classification, cervical microbiota",Experiment 6,China,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,transient HPV+ with HSIL,persistent HPV+ with LSIL,high-risk HPV persistent infection with low grade squamus intraepithelial lesion,NA,NA,NA,16S,NA,Illumina,NA,LEfSe,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,19 March 2021,Cynthia Anderson,"Cynthia Anderson,WikiWorks",Abundance analysis of the microbiota between the high-risk HPV persistent infection with LSIL group and high-risk HPV transient infection with HSIL group,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,1783272|1239|186801|3085636|186803|2316020|33039,Complete,Fatima
bsdb:33241010/6/2,33241010,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,NA,"Liu J., Luo M., Zhang Y., Cao G. , Wang S.",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,"Cervical cancer, human papillomavirus infection (HPV infection), cervical intraepithelial neoplasia pathological classification, cervical microbiota",Experiment 6,China,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,transient HPV+ with HSIL,persistent HPV+ with LSIL,high-risk HPV persistent infection with low grade squamus intraepithelial lesion,NA,NA,NA,16S,NA,Illumina,NA,LEfSe,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4B,19 March 2021,Cynthia Anderson,"Cynthia Anderson,WikiWorks",Abundance analysis of the microbiota between the high-risk HPV persistent infection with LSIL group and high-risk HPV transient infection with HSIL group,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Metazoa|p__Nematoda|c__Enoplea|o__Trichinellida|f__Trichinellidae|g__Trichinella|s__Trichinella pseudospiralis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Quinella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium gelidilacus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides faecis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Azonexaceae|g__Dechloromonas",3379134|976|200643|171549|171551|836;33208|6231|119088|6329|6332|6333|6337;1783272|1239|909932|1843489|31977|1567;1783272|1239|186801|3085636|186803|1506577;3379134|976|117743|200644|49546|237|206041;3379134|976|200643|171549|2005525|375288|1217282;3379134|1224|28216|206389|2008795|73029,Complete,Fatima
bsdb:33241010/7/1,33241010,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,NA,"Liu J., Luo M., Zhang Y., Cao G. , Wang S.",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,"Cervical cancer, human papillomavirus infection (HPV infection), cervical intraepithelial neoplasia pathological classification, cervical microbiota",Experiment 7,China,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,transient HPV+ with LSIL,transient HPV+ with HSIL,high-risk HPV transient infection with high grade squamus intraepithelial lesion,NA,NA,NA,16S,NA,Illumina,NA,LEfSe,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4C,19 March 2021,Cynthia Anderson,"Cynthia Anderson,WikiWorks",Abundance analysis of the microbiota between high-risk HPV transient infection with HSIL group and high-risk HPV transient infection with LSIL group,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Dyella|s__Dyella koreensis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium gelidilacus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Dyella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides faecis",3379134|976|117743;3379134|976|117743|200644;3379134|976|117743|200644|2762318|501783;1783272|1239|91061|186826|33958|1578;3379134|1224|1236|135614|1775411|231454|311235;3379134|976|117743|200644|49546|237|206041;3379134|1224|1236|135614|1775411|231454;3379134|976|200643|171549|2005525|375288|1217282,Complete,Fatima
bsdb:33241010/8/1,33241010,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,NA,"Liu J., Luo M., Zhang Y., Cao G. , Wang S.",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,"Cervical cancer, human papillomavirus infection (HPV infection), cervical intraepithelial neoplasia pathological classification, cervical microbiota",Experiment 8,China,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,transient HPV+ with LSIL,high-risk HPV transient infection with low grade squamus intraepithelial lesion,NA,NA,NA,16S,NA,Illumina,NA,LEfSe,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4D,19 March 2021,Cynthia Anderson,"Cynthia Anderson,WikiWorks",Abundance analysis of the microbiota between high-risk HPV transient infection with LSIL group and the non-infected HPV group,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Devosia|s__Devosia riboflavina,p__Candidatus Saccharimonadota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae",3379134|1224|28211|356|2831106|46913|46914;95818;3384189|32066|203490|203491|1129771|168808;1783272|1239|91061|186826|33958|1578;3379134|1224|1236|72274|135621|286;1783272|1239|186801|3085636|186803|177971;3384189|32066|203490|203491|1129771;1783272|1239|186801|186802|541000;3379134|1224|1236|72274|135621,Complete,Fatima
bsdb:33241010/9/1,33241010,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,NA,"Liu J., Luo M., Zhang Y., Cao G. , Wang S.",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,"Cervical cancer, human papillomavirus infection (HPV infection), cervical intraepithelial neoplasia pathological classification, cervical microbiota",Experiment 9,China,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,persistent HPV+ with HSIL,high-risk HPV persistent infection with low grade squamus intraepithelial lesion,NA,NA,NA,16S,NA,Illumina,NA,LEfSe,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4E,19 March 2021,Cynthia Anderson,"Cynthia Anderson,WikiWorks",Abundance analysis of the microbiota between high-risk HPV persistent infection with HSIL and the non-infected HPV group,increased,"k__Bacillati|p__Actinomycetota|c__Thermoleophilia|o__Solirubrobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella",1783272|201174|1497346|588673;3379134|1224|1236|91347|1903414|581,Complete,Fatima
bsdb:33241010/9/2,33241010,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,NA,"Liu J., Luo M., Zhang Y., Cao G. , Wang S.",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,"Cervical cancer, human papillomavirus infection (HPV infection), cervical intraepithelial neoplasia pathological classification, cervical microbiota",Experiment 9,China,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,persistent HPV+ with HSIL,high-risk HPV persistent infection with low grade squamus intraepithelial lesion,NA,NA,NA,16S,NA,Illumina,NA,LEfSe,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4E,19 March 2021,Cynthia Anderson,"Cynthia Anderson,WikiWorks",Abundance analysis of the microbiota between high-risk HPV persistent infection with HSIL and the non-infected HPV group,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus equicursoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|976|200643|171549|171552|838|28132;1783272|1239|909932|1843489|31977|39948;1783272|1239|91061|186826|33958|1578|420645;3379134|976|200643|171549|171552|838;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|3082720|186804|1257;3379134|1224|1236|72274|135621|286;1783272|1239|1737404|1737405|1570339|162289|33031;3379134|976|200643|171549|171552|838|28130;1783272|1239|186801|186802|541000,Complete,Fatima
bsdb:33248623/1/1,33248623,laboratory experiment,33248623,10.1016/j.psj.2020.09.076,NA,"Du W., Deng J., Yang Z., Zeng L. , Yang X.",Metagenomic analysis reveals linkages between cecal microbiota and feed efficiency in Xiayan chickens,Poultry science,2020,"Xiayan chicken, cecal microbiota, feed efficiency, metagenome sequencing",Experiment 1,China,Gallus gallus,Caecum,UBERON:0001153,Growth condition,EFO:0000523,Male Low Feed Efficiency (M-LFE) groups,Male High Feed Efficiency (M-HFE) groups,Male chickens with the lowest Residual Feed Intake(RFI),3,3,NA,WMS,NA,Illumina,relative abundances,LEfSe,NA,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2A,5 November 2024,Tosin,"Tosin,WikiWorks",Significant differences in the cecum between Male Low Feed Efficiency (M-LFE) groups and Male High Feed Efficiency (M-HFE) groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella sp. An22,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus oris",3379134|976|200643|171549|2005519|397864|1965590;1783272|1239|91061|186826|33958|2742598|1632,Complete,Svetlana up
bsdb:33248623/1/2,33248623,laboratory experiment,33248623,10.1016/j.psj.2020.09.076,NA,"Du W., Deng J., Yang Z., Zeng L. , Yang X.",Metagenomic analysis reveals linkages between cecal microbiota and feed efficiency in Xiayan chickens,Poultry science,2020,"Xiayan chicken, cecal microbiota, feed efficiency, metagenome sequencing",Experiment 1,China,Gallus gallus,Caecum,UBERON:0001153,Growth condition,EFO:0000523,Male Low Feed Efficiency (M-LFE) groups,Male High Feed Efficiency (M-HFE) groups,Male chickens with the lowest Residual Feed Intake(RFI),3,3,NA,WMS,NA,Illumina,relative abundances,LEfSe,NA,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2A,5 November 2024,Tosin,"Tosin,WikiWorks",Significant differences in the cecum between Male Low Feed Efficiency (M-LFE) groups and Male High Feed Efficiency (M-HFE) groups.,decreased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter pullorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum variabile,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Lentisphaerales,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Lentisphaerales|f__Lentisphaeraceae",3379134|29547|3031852|213849|72293|209|35818;1783272|1239|186801|186802|216572|292632|214851;3379134|256845|1313211;3379134|256845|1313211|278081;3379134|256845|1313211|278081|566277,Complete,Svetlana up
bsdb:33248623/2/1,33248623,laboratory experiment,33248623,10.1016/j.psj.2020.09.076,NA,"Du W., Deng J., Yang Z., Zeng L. , Yang X.",Metagenomic analysis reveals linkages between cecal microbiota and feed efficiency in Xiayan chickens,Poultry science,2020,"Xiayan chicken, cecal microbiota, feed efficiency, metagenome sequencing",Experiment 2,China,Gallus gallus,Caecum,UBERON:0001153,Growth condition,EFO:0000523,Female Low feed efficiency (F-LFE) groups,Female High Feed efficiency (F-HFE) groups,Female chickens with the lowest Residual Feed Intake (RFI),3,3,NA,WMS,NA,Illumina,relative abundances,LEfSe,NA,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2B,5 November 2024,Tosin,"Tosin,WikiWorks",Significant differences in the cecum between Female Low Feed Efficiency (F-LFE) groups and Female High Feed Efficiency (F-HFE) groups.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|1236|91347|543;3379134|1224,Complete,Svetlana up
bsdb:33248623/2/2,33248623,laboratory experiment,33248623,10.1016/j.psj.2020.09.076,NA,"Du W., Deng J., Yang Z., Zeng L. , Yang X.",Metagenomic analysis reveals linkages between cecal microbiota and feed efficiency in Xiayan chickens,Poultry science,2020,"Xiayan chicken, cecal microbiota, feed efficiency, metagenome sequencing",Experiment 2,China,Gallus gallus,Caecum,UBERON:0001153,Growth condition,EFO:0000523,Female Low feed efficiency (F-LFE) groups,Female High Feed efficiency (F-HFE) groups,Female chickens with the lowest Residual Feed Intake (RFI),3,3,NA,WMS,NA,Illumina,relative abundances,LEfSe,NA,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2B,5 November 2024,Tosin,"Tosin,WikiWorks",Significant differences in the cecum between Female Low Feed Efficiency (F-LFE) groups and Female High Feed Efficiency (F-HFE) groups.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium WCE2004,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:598,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides togonis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. An46,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp. CAG:409,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter avium",3379134|976|200643|171549|1945890;3379134|976|200643|171549|815|816|1262743;3379134|976|200643|171549|815|816|1917883;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|1965636;3379134|976|200643|171549|1853231|574697;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|2005525|375288|1262913;1783272|1239|526524|526525|2810280|3025755;1783272|1239|909932|1843489;3379134|29547|3031852|213849|72294|194|522485,Complete,Svetlana up
bsdb:33248623/3/1,33248623,laboratory experiment,33248623,10.1016/j.psj.2020.09.076,NA,"Du W., Deng J., Yang Z., Zeng L. , Yang X.",Metagenomic analysis reveals linkages between cecal microbiota and feed efficiency in Xiayan chickens,Poultry science,2020,"Xiayan chicken, cecal microbiota, feed efficiency, metagenome sequencing",Experiment 3,China,Gallus gallus,Caecum,UBERON:0001153,Growth condition,EFO:0000523,Male Low Feed Efficiency (M-LFE) groups,Male High Feed Efficiency (M-HFE) groups,Male chickens with the lowest Residual Feed Intake(RFI),3,3,NA,WMS,NA,Illumina,relative abundances,Kruskall-Wallis,NA,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,12 December 2024,Tosin,"Tosin,Aleru Divine,WikiWorks",Relative abundance of the dominant phyla and genera in the cecum of the high and low feed efficiency (FE) groups of male chickens.,increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota,s__unidentified,k__Pseudomonadati|p__Elusimicrobiota",1783272|201174;3379134|976|200643|171549|171550|239759;1783272|1239;1783272|1239|186801|3085636|186803|1506553;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|909929|1843491|158846;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|838;3379134|1224;32644;3379134|74152,Complete,Svetlana up
bsdb:33248623/3/2,33248623,laboratory experiment,33248623,10.1016/j.psj.2020.09.076,NA,"Du W., Deng J., Yang Z., Zeng L. , Yang X.",Metagenomic analysis reveals linkages between cecal microbiota and feed efficiency in Xiayan chickens,Poultry science,2020,"Xiayan chicken, cecal microbiota, feed efficiency, metagenome sequencing",Experiment 3,China,Gallus gallus,Caecum,UBERON:0001153,Growth condition,EFO:0000523,Male Low Feed Efficiency (M-LFE) groups,Male High Feed Efficiency (M-HFE) groups,Male chickens with the lowest Residual Feed Intake(RFI),3,3,NA,WMS,NA,Illumina,relative abundances,Kruskall-Wallis,NA,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,12 December 2024,Tosin,"Tosin,WikiWorks",Relative abundance of the dominant phyla and genera in the cecum of the high and low feed efficiency (FE) groups of male chickens.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Mediterranea,k__Methanobacteriati|p__Methanobacteriota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Pseudomonadati|p__Spirochaetota,k__Thermotogati|p__Synergistota,k__Pseudomonadati|p__Verrucomicrobiota,k__Fusobacteriati|p__Fusobacteriota",3379134|976|200643|171549|815|816;3379134|976;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|815|1926659;3366610|28890;3379134|976|200643|171549|2005473|1918540;3379134|203691;3384194|508458;3379134|74201;3384189|32066,Complete,Svetlana up
bsdb:33248623/4/1,33248623,laboratory experiment,33248623,10.1016/j.psj.2020.09.076,NA,"Du W., Deng J., Yang Z., Zeng L. , Yang X.",Metagenomic analysis reveals linkages between cecal microbiota and feed efficiency in Xiayan chickens,Poultry science,2020,"Xiayan chicken, cecal microbiota, feed efficiency, metagenome sequencing",Experiment 4,China,Gallus gallus,Caecum,UBERON:0001153,Growth condition,EFO:0000523,Female Low Feed Efficiency (F-LFE) groups,Female High Feed Efficiency (F-HFE) groups,Female chickens with the lowest Residual Feed Intake(RFI),3,3,NA,WMS,NA,Illumina,relative abundances,Kruskall-Wallis,NA,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,13 December 2024,Tosin,"Tosin,Aleru Divine,WikiWorks",Relative abundance of the dominant phyla and genera in the cecum of the high and low feed efficiency (FE) groups of female chickens.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Mediterranea,k__Methanobacteriati|p__Methanobacteriota,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Spirochaetota,k__Pseudomonadati|p__Verrucomicrobiota,s__unidentified",3379134|976|200643|171549|171550|239759;3384189|32066;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|815|1926659;3366610|28890;3379134|1224;3379134|203691;3379134|74201;32644,Complete,Svetlana up
bsdb:33248623/4/2,33248623,laboratory experiment,33248623,10.1016/j.psj.2020.09.076,NA,"Du W., Deng J., Yang Z., Zeng L. , Yang X.",Metagenomic analysis reveals linkages between cecal microbiota and feed efficiency in Xiayan chickens,Poultry science,2020,"Xiayan chicken, cecal microbiota, feed efficiency, metagenome sequencing",Experiment 4,China,Gallus gallus,Caecum,UBERON:0001153,Growth condition,EFO:0000523,Female Low Feed Efficiency (F-LFE) groups,Female High Feed Efficiency (F-HFE) groups,Female chickens with the lowest Residual Feed Intake(RFI),3,3,NA,WMS,NA,Illumina,relative abundances,Kruskall-Wallis,NA,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,13 December 2024,Tosin,"Tosin,WikiWorks",Relative abundance of the dominant phyla and genera in the cecum of the high and low feed efficiency (FE) groups of female chickens.,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota,k__Thermotogati|p__Synergistota,k__Pseudomonadati|p__Elusimicrobiota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",1783272|201174;1783272|1239;3379134|976;3384194|508458;3379134|74152;3379134|976|200643|171549|815|816;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|2005473|1918540;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|1506553;3379134|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:33251163/1/1,33251163,"cross-sectional observational, not case-control",33251163,10.3389/fcimb.2020.602239,NA,"Frid P., Baraniya D., Halbig J., Rypdal V., Songstad N.T., Rosèn A., Berstad J.R., Flatø B., Alakwaa F., Gil E.G., Cetrelli L., Chen T., Al-Hebshi N.N., Nordal E. , Al-Haroni M.",Salivary Oral Microbiome of Children With Juvenile Idiopathic Arthritis: A Norwegian Cross-Sectional Study,Frontiers in cellular and infection microbiology,2020,"16S rRNA, juvenile idiopathic arthritis, next generation sequencing (NGS), oral health, salivary microbiome",Experiment 1,Norway,Homo sapiens,Saliva,UBERON:0001836,Juvenile idiopathic arthritis,EFO:0002609,healthy controls,JIA patients,children with juvenile idiopathic arthritis,34,59,NA,16S,123,Illumina,relative abundances,LEfSe,0.1,TRUE,2.5,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 3,28 September 2021,Tislam,"Tislam,Atrayees,WikiWorks",Differentially abundant taxa,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum orale,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum longum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium diversum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sp.,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 352,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 417,p__Candidatus Saccharimonadota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium",3379134|976|200643|171549|171552|1283313|1872471;1783272|1239|186801|3085636|186803|1164882|979627;1783272|201174|1760|85006|1268|32207|172042;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|186801|3085636|186803|1213720|796942;3379134|976|200643|171549|171552|2974257|425941;1783272|1239|186801|3082720|543314|86331|114527;1783272|1239|909932|1843489|31977|29465|39777;3379134|976|117743|200644|49546|1016|44737;95818|713054;3384189|32066|203490|203491|1129771|32067|712365;95818;1783272|1239|526524|526525|128827|123375;1783272|1239|186801|3082720|543314|86331,Complete,Atrayees
bsdb:33251163/1/2,33251163,"cross-sectional observational, not case-control",33251163,10.3389/fcimb.2020.602239,NA,"Frid P., Baraniya D., Halbig J., Rypdal V., Songstad N.T., Rosèn A., Berstad J.R., Flatø B., Alakwaa F., Gil E.G., Cetrelli L., Chen T., Al-Hebshi N.N., Nordal E. , Al-Haroni M.",Salivary Oral Microbiome of Children With Juvenile Idiopathic Arthritis: A Norwegian Cross-Sectional Study,Frontiers in cellular and infection microbiology,2020,"16S rRNA, juvenile idiopathic arthritis, next generation sequencing (NGS), oral health, salivary microbiome",Experiment 1,Norway,Homo sapiens,Saliva,UBERON:0001836,Juvenile idiopathic arthritis,EFO:0002609,healthy controls,JIA patients,children with juvenile idiopathic arthritis,34,59,NA,16S,123,Illumina,relative abundances,LEfSe,0.1,TRUE,2.5,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 3C,28 September 2021,Tislam,"Tislam,Atrayees,WikiWorks",Differentially abundant taxa.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 223,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus pittmaniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus subtilis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella sp. oral taxon 807,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 314,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella|s__Bergeyella sp. oral taxon 322,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella",3379134|1224|1236|135625|712|724|729;3384189|32066|203490|203491|1129771|32067|712363;3379134|976|200643|171549|171552|838|28129;3379134|1224|1236|135625|712|724|249188;1783272|1239|91061|1385|186817|1386|1423;1783272|201174|84998|84999|1643824|133925|712411;3379134|1224|1236|135625|712|724|735;1783272|201174|1760|85006|1268|32207|2047;3379134|976|200643|171549|171552|838|712464;3379134|976|117743|200644|2762318|59735|712187;3379134|1224;3379134|1224|1236|135625|712|724;1783272|1239|91061|1385|186817|1386;1783272|201174|84998|84999|1643824|133925,Complete,Atrayees
bsdb:33251163/2/1,33251163,"cross-sectional observational, not case-control",33251163,10.3389/fcimb.2020.602239,NA,"Frid P., Baraniya D., Halbig J., Rypdal V., Songstad N.T., Rosèn A., Berstad J.R., Flatø B., Alakwaa F., Gil E.G., Cetrelli L., Chen T., Al-Hebshi N.N., Nordal E. , Al-Haroni M.",Salivary Oral Microbiome of Children With Juvenile Idiopathic Arthritis: A Norwegian Cross-Sectional Study,Frontiers in cellular and infection microbiology,2020,"16S rRNA, juvenile idiopathic arthritis, next generation sequencing (NGS), oral health, salivary microbiome",Experiment 2,Norway,Homo sapiens,Saliva,UBERON:0001836,Temporomandibular joint disorder,EFO:0005279,JIA patients without TMJ,JIA patients with TMJ,children with juvenile idiopathic arthritis,15,44,NA,16S,123,Illumina,relative abundances,LEfSe,0.1,TRUE,2.5,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 6C,",28 September 2021,Tislam,"Tislam,Atrayees,WikiWorks","species that showed significant differences in relative abundance between the JIA subjects with and without TMJ involvement, as identified by linear discriminant analysis (LDA) effect size analysis (LEfSe). 2.5 LDA score cutoff. OT, oral taxon. **FDR ≤ 0.1 (Benjamini-Hochberg method).",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Pseudoleptotrichia|s__Pseudoleptotrichia goodfellowii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 070,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus subtilis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Actinomycetota,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia",1783272|201174|1760|85006|1268|32207|43675;1783272|201174|84998|84999|1643824|2767353|1382;1783272|1239|186801|3085636|186803|265975|237576;3384189|32066|203490|203491|1129771|2755140|157692;1783272|1239|91061|186826|1300|1301|671226;1783272|1239|91061|1385|186817|1386|1423;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|265975;1783272|201174|84998|84999|1643824|1380;1783272|1239|91061|1385|186817|1386;1783272|201174;33090|35493|3398|72025|3803|3814|508215,Complete,Atrayees
bsdb:33251163/2/2,33251163,"cross-sectional observational, not case-control",33251163,10.3389/fcimb.2020.602239,NA,"Frid P., Baraniya D., Halbig J., Rypdal V., Songstad N.T., Rosèn A., Berstad J.R., Flatø B., Alakwaa F., Gil E.G., Cetrelli L., Chen T., Al-Hebshi N.N., Nordal E. , Al-Haroni M.",Salivary Oral Microbiome of Children With Juvenile Idiopathic Arthritis: A Norwegian Cross-Sectional Study,Frontiers in cellular and infection microbiology,2020,"16S rRNA, juvenile idiopathic arthritis, next generation sequencing (NGS), oral health, salivary microbiome",Experiment 2,Norway,Homo sapiens,Saliva,UBERON:0001836,Temporomandibular joint disorder,EFO:0005279,JIA patients without TMJ,JIA patients with TMJ,children with juvenile idiopathic arthritis,15,44,NA,16S,123,Illumina,relative abundances,LEfSe,0.1,TRUE,2.5,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 6C, text",28 September 2021,Tislam,"Tislam,Atrayees,WikiWorks","species that showed significant differences in relative abundance between the JIA subjects with and without TMJ involvement, as identified by linear discriminant analysis (LDA) effect size analysis (LEfSe). 2.5 LDA score cutoff. OT, oral taxon. **FDR ≤ 0.1 (Benjamini-Hochberg method).",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 313,p__Candidatus Absconditibacteriota|s__SR1 bacterium oral taxon 875,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella shahii,p__Candidatus Absconditibacteriota|s__SR1 bacterium oral taxon 874,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp.,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter sp. oral taxon 044,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella|s__Bergeyella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella",3379134|976|200643|171549|171551|836|1924944;3379134|976|200643|171549|171552|838|652722;221235|1226342;1783272|1239|186801|3085636|186803|265975|1501329;3379134|1224|28216|206351|481|538|539;3379134|976|200643|171549|171552|2974257|228603;221235|1226341;3379134|976|200643|171549|171552|1283313|1872471;3379134|29547|3031852|213849|72294|194|712200;3379134|1224|28216|206351|481|32257|505;3379134|976|200643|171549|171552|2974257|425941;3379134|976|200643|171549|171551|836|1583331;3379134|1224|28216|206351|481|482|495;3379134|976|200643|171549|171552|838|60133;3379134|976|117743|200644|2762318|59735|1962306;3379134|1224|1236|135625|712|724|729;3379134|1224;3379134|1224|28216|206351|481|538;3379134|1224|1236|135625|712|724;3379134|976|200643|171549|171552|1283313,Complete,Atrayees
bsdb:33293403/1/1,33293403,"case-control,meta-analysis",33293403,10.1128/mSystems.00797-20,NA,"Nishiwaki H., Hamaguchi T., Ito M., Ishida T., Maeda T., Kashihara K., Tsuboi Y., Ueyama J., Shimamura T., Mori H., Kurokawa K., Katsuno M., Hirayama M. , Ohno K.",Short-Chain Fatty Acid-Producing Gut Microbiota Is Decreased in Parkinson's Disease but Not in Rapid-Eye-Movement Sleep Behavior Disorder,mSystems,2020,"Parkinson’s disease, gut microbiota, meta-analysis, rapid-eye-movement behavior disorder, topic model",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Sleep Disorder,EFO:0008568,Healthy Controls,Rapid-eye-movement sleep behavior disorder (iRBD) patients,Patients with idiopathic rapid-eye-movement sleep behavior disorder (iRBD) diagnosed according to the International Classification of Sleep Disorders Criteria-Third Edition,137,26,1 month,16S,34,Illumina,NA,"ANCOM,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table S2,17 March 2024,Aishat,"Aishat,Aleru Divine,WikiWorks,Tosin",Read counts of genera normalized for 1 × 104 reads in controls and iRBD.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|186806|1730|290054;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|3068309,Complete,Svetlana up
bsdb:33293403/2/1,33293403,"case-control,meta-analysis",33293403,10.1128/mSystems.00797-20,NA,"Nishiwaki H., Hamaguchi T., Ito M., Ishida T., Maeda T., Kashihara K., Tsuboi Y., Ueyama J., Shimamura T., Mori H., Kurokawa K., Katsuno M., Hirayama M. , Ohno K.",Short-Chain Fatty Acid-Producing Gut Microbiota Is Decreased in Parkinson's Disease but Not in Rapid-Eye-Movement Sleep Behavior Disorder,mSystems,2020,"Parkinson’s disease, gut microbiota, meta-analysis, rapid-eye-movement behavior disorder, topic model",Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Sleep Disorder,EFO:0008568,Healthy Controls,Rapid-eye-movement sleep behavior disorder (iRBD) patients,Patients with idiopathic rapid-eye-movement sleep behavior disorder (iRBD) diagnosed according to the International Classification of Sleep Disorders Criteria-Third Edition,137,26,1 month,16S,34,Illumina,NA,"ANCOM,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,"age,body mass index,constipation,proton-pump inhibitor,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table S4,21 January 2025,Aleru Divine,"Aleru Divine,WikiWorks",Generalized linear mixed model (GLMM) analysis to evaluate confounding factors of seven genera and two families that were significantly changed in iRBD compared to controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae",3379134|976|200643|171549|171550|239759;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550;3379134|74201|203494|48461|1647988,Complete,Svetlana up
bsdb:33293403/3/1,33293403,"case-control,meta-analysis",33293403,10.1128/mSystems.00797-20,NA,"Nishiwaki H., Hamaguchi T., Ito M., Ishida T., Maeda T., Kashihara K., Tsuboi Y., Ueyama J., Shimamura T., Mori H., Kurokawa K., Katsuno M., Hirayama M. , Ohno K.",Short-Chain Fatty Acid-Producing Gut Microbiota Is Decreased in Parkinson's Disease but Not in Rapid-Eye-Movement Sleep Behavior Disorder,mSystems,2020,"Parkinson’s disease, gut microbiota, meta-analysis, rapid-eye-movement behavior disorder, topic model",Experiment 3,"Japan,Germany",Homo sapiens,Feces,UBERON:0001988,Sleep Disorder,EFO:0008568,Healthy Controls,Rapid-eye-movement sleep behavior disorder (iRBD) patients,Patients with idiopathic rapid-eye-movement sleep behavior disorder (iRBD) diagnosed according to the International Classification of Sleep Disorders Criteria-Third Edition,2,2,1 month,16S,NA,NA,relative abundances,Mixed-Effects Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table S6A and S6B,21 January 2025,Aleru Divine,"Aleru Divine,WikiWorks",Microbial signatures significantly increased in iRBD in two datasets at the genus and family levels (plotted in Fig. 3A),increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550,Complete,Svetlana up
bsdb:33294219/1/1,33294219,case-control,33294219,10.1155/2020/1957843,NA,"Zhu L.L., Ma Z.J., Ren M., Wei Y.M., Liao Y.H., Shen Y.L., Fan S.M., Li L., Wu Q.X., Gao Z.S., Song J.F. , Ma Y.L.",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Hypertension,EFO:0000537,Han Hypertensive at Low Altitude (LHH),Tibetan Hypertensive at High Altitude (HTH),Tibetan participants with hypertension living at high altitudes.,34,38,3 months,16S,34,Illumina,NA,T-Test,0.05,FALSE,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 2c,17 February 2021,Manuela,"Manuela,WikiWorks",NA,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Lwaldron
bsdb:33294219/1/2,33294219,case-control,33294219,10.1155/2020/1957843,NA,"Zhu L.L., Ma Z.J., Ren M., Wei Y.M., Liao Y.H., Shen Y.L., Fan S.M., Li L., Wu Q.X., Gao Z.S., Song J.F. , Ma Y.L.",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Hypertension,EFO:0000537,Han Hypertensive at Low Altitude (LHH),Tibetan Hypertensive at High Altitude (HTH),Tibetan participants with hypertension living at high altitudes.,34,38,3 months,16S,34,Illumina,NA,T-Test,0.05,FALSE,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 2c,17 February 2021,Manuela,"Manuela,WikiWorks",NA,increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Verrucomicrobiota",3379134|976;3379134|74201,Complete,Lwaldron
bsdb:33294219/2/1,33294219,case-control,33294219,10.1155/2020/1957843,NA,"Zhu L.L., Ma Z.J., Ren M., Wei Y.M., Liao Y.H., Shen Y.L., Fan S.M., Li L., Wu Q.X., Gao Z.S., Song J.F. , Ma Y.L.",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Hypertension,EFO:0000537,Han Hypertensive at Middle Altitude (MHH),Tibetan Hypertensive at High Altitude (HTH),Tibetan participants with hypertension living at high altitudes.,49,38,3 months,16S,34,Illumina,NA,T-Test,0.05,NA,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 2g,17 February 2021,Manuela,"Manuela,WikiWorks",NA,decreased,"p__Candidatus Saccharimonadota,k__Pseudomonadati|p__Pseudomonadota",95818;3379134|1224,Complete,Lwaldron
bsdb:33294219/2/2,33294219,case-control,33294219,10.1155/2020/1957843,NA,"Zhu L.L., Ma Z.J., Ren M., Wei Y.M., Liao Y.H., Shen Y.L., Fan S.M., Li L., Wu Q.X., Gao Z.S., Song J.F. , Ma Y.L.",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Hypertension,EFO:0000537,Han Hypertensive at Middle Altitude (MHH),Tibetan Hypertensive at High Altitude (HTH),Tibetan participants with hypertension living at high altitudes.,49,38,3 months,16S,34,Illumina,NA,T-Test,0.05,NA,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 2g,17 February 2021,Manuela,"Manuela,WikiWorks",NA,increased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Lwaldron
bsdb:33294219/3/1,33294219,case-control,33294219,10.1155/2020/1957843,NA,"Zhu L.L., Ma Z.J., Ren M., Wei Y.M., Liao Y.H., Shen Y.L., Fan S.M., Li L., Wu Q.X., Gao Z.S., Song J.F. , Ma Y.L.",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Hypertension,EFO:0000537,Han Healthy at Low Altitude (LHN),Tibetan Healthy at High Altitude (HTN),Tibetan healthy participants living at high altitudes.,35,34,3 months,16S,34,Illumina,NA,T-Test,0.05,NA,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 2d,17 February 2021,Manuela,"Manuela,WikiWorks",NA,decreased,"p__Candidatus Saccharimonadota,k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Pseudomonadota",95818;3384189|32066;3379134|1224,Complete,Lwaldron
bsdb:33294219/3/2,33294219,case-control,33294219,10.1155/2020/1957843,NA,"Zhu L.L., Ma Z.J., Ren M., Wei Y.M., Liao Y.H., Shen Y.L., Fan S.M., Li L., Wu Q.X., Gao Z.S., Song J.F. , Ma Y.L.",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Hypertension,EFO:0000537,Han Healthy at Low Altitude (LHN),Tibetan Healthy at High Altitude (HTN),Tibetan healthy participants living at high altitudes.,35,34,3 months,16S,34,Illumina,NA,T-Test,0.05,NA,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 2d,17 February 2021,Manuela,"Manuela,WikiWorks",NA,increased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Lwaldron
bsdb:33294219/4/1,33294219,case-control,33294219,10.1155/2020/1957843,NA,"Zhu L.L., Ma Z.J., Ren M., Wei Y.M., Liao Y.H., Shen Y.L., Fan S.M., Li L., Wu Q.X., Gao Z.S., Song J.F. , Ma Y.L.",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Hypertension,EFO:0000537,Han Healthy at Middle Altitude (MHN),Tibetan Healthy at High Altitude (HTN),Tibetan healthy participants living at high altitudes.,35,34,3 months,16S,34,Illumina,NA,T-Test,0.05,FALSE,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 2h,17 February 2021,Manuela,"Manuela,WikiWorks",NA,decreased,p__Candidatus Saccharimonadota,95818,Complete,Lwaldron
bsdb:33294219/5/1,33294219,case-control,33294219,10.1155/2020/1957843,NA,"Zhu L.L., Ma Z.J., Ren M., Wei Y.M., Liao Y.H., Shen Y.L., Fan S.M., Li L., Wu Q.X., Gao Z.S., Song J.F. , Ma Y.L.",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,NA,Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Hypertension,EFO:0000537,Han Hypertensive at Low Altitude (LHH),Han Hypertensive at Middle Altitude (MHH),Han hypertensive participants living at middle altitude.,34,49,3 months,16S,34,Illumina,NA,T-Test,0.05,NA,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2e,17 February 2021,Manuela,"Manuela,WikiWorks",NA,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Lwaldron
bsdb:33294219/5/2,33294219,case-control,33294219,10.1155/2020/1957843,NA,"Zhu L.L., Ma Z.J., Ren M., Wei Y.M., Liao Y.H., Shen Y.L., Fan S.M., Li L., Wu Q.X., Gao Z.S., Song J.F. , Ma Y.L.",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,NA,Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Hypertension,EFO:0000537,Han Hypertensive at Low Altitude (LHH),Han Hypertensive at Middle Altitude (MHH),Han hypertensive participants living at middle altitude.,34,49,3 months,16S,34,Illumina,NA,T-Test,0.05,NA,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2e,17 February 2021,Manuela,"Manuela,WikiWorks",NA,increased,"k__Pseudomonadati|p__Acidobacteriota,k__Pseudomonadati|p__Bacteroidota,p__Candidatus Saccharimonadota,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Verrucomicrobiota",3379134|57723;3379134|976;95818;1783272|544448;3379134|74201,Complete,Lwaldron
bsdb:33294219/6/1,33294219,case-control,33294219,10.1155/2020/1957843,NA,"Zhu L.L., Ma Z.J., Ren M., Wei Y.M., Liao Y.H., Shen Y.L., Fan S.M., Li L., Wu Q.X., Gao Z.S., Song J.F. , Ma Y.L.",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,NA,Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Hypertension,EFO:0000537,Han Healthy at Low Altitude (LHN),Han Healthy at Middle Altitude (MHN),Han healthy participants living at middle altitude.,35,35,3 months,16S,34,Illumina,NA,T-Test,0.05,NA,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2f,17 February 2021,Manuela,"Manuela,WikiWorks",NA,increased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Lwaldron
bsdb:33294219/6/2,33294219,case-control,33294219,10.1155/2020/1957843,NA,"Zhu L.L., Ma Z.J., Ren M., Wei Y.M., Liao Y.H., Shen Y.L., Fan S.M., Li L., Wu Q.X., Gao Z.S., Song J.F. , Ma Y.L.",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,NA,Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Hypertension,EFO:0000537,Han Healthy at Low Altitude (LHN),Han Healthy at Middle Altitude (MHN),Han healthy participants living at middle altitude.,35,35,3 months,16S,34,Illumina,NA,T-Test,0.05,NA,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2f,17 February 2021,Manuela,"Manuela,WikiWorks",NA,decreased,"k__Bacillati|p__Bacillota,k__Fusobacteriati|p__Fusobacteriota",1783272|1239;3384189|32066,Complete,Lwaldron
bsdb:33313185/1/1,33313185,case-control,33313185,10.21037/atm-20-1309,NA,"Chen S., Gu Z., Zhang W., Jia S., Wu Y., Zheng P., Dai Y. , Leng J.",Microbiome of the lower genital tract in Chinese women with endometriosis by 16s-rRNA sequencing technique: a pilot study,Annals of translational medicine,2020,"16s-rRNA sequencing, Endometriosis, bioinformatic analysis, microbiome",Experiment 1,China,Homo sapiens,Cervical cavity,UBERON:0013761,"Adenomyosis,Endometriosis","EFO:1001757,EFO:0001065",Endometriosis patients (EM) and Patients without endometriosis(Control-CT),Endometriosis/ adenomyosis patients (AMEM),All participants were diagnosed with adenomyosis accompanied with endometriosis (a condition where endometrial tissue grows into the uterine wall) through laparoscopic surgery,92,14,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"within results text(under ""Microbiota composition of different diseases"" ,paragraph 5, lines 4-7), figure 6",11 August 2021,Samara.Khan,"Samara.Khan,Folakunmi,WikiWorks","The following taxa were increased in patients with endometriosis and adenomyosis compared to those with just endometriosis, as well as those without endometriosis (control).",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|201174|84998|84999|1643824|1380;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294;1783272|201174|84998|84999|84107;3379134|1224|1236|91347|543|1940338;1783272|1239|1737404|1582879;1783272|1239|186801|186802|216572|216851,Complete,Folakunmi
bsdb:33313185/2/1,33313185,case-control,33313185,10.21037/atm-20-1309,NA,"Chen S., Gu Z., Zhang W., Jia S., Wu Y., Zheng P., Dai Y. , Leng J.",Microbiome of the lower genital tract in Chinese women with endometriosis by 16s-rRNA sequencing technique: a pilot study,Annals of translational medicine,2020,"16s-rRNA sequencing, Endometriosis, bioinformatic analysis, microbiome",Experiment 2,China,Homo sapiens,Cervical cavity,UBERON:0013761,"Adenomyosis,Endometriosis","EFO:1001757,EFO:0001065","Patients without endometriosis (CT), patients with only endometriosis(EM)) and patients with only adenomysis(AM)",Endometriosis/ adenomyosis patients (AMEM),All participants were diagnosed with adenomyosis accompanied with endometriosis (a condition where endometrial tissue grows into the uterine wall) through laparoscopic surgery,120,14,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"within results text(under ""Microbiota composition of different diseases"" ,paragraph 5, lines 4-7), figure 6",11 August 2021,Samara.Khan,"Samara.Khan,Folakunmi,WikiWorks","The following taxa had increased abundance in patients with endometriosis and adenomyosis compared to those without endometriosis, patients with only endometriosis and patients with only adenomysis.",increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",3379134|29547|3031852|213849|72294;1783272|201174|84998|84999|84107,Complete,Folakunmi
bsdb:33313185/3/1,33313185,case-control,33313185,10.21037/atm-20-1309,NA,"Chen S., Gu Z., Zhang W., Jia S., Wu Y., Zheng P., Dai Y. , Leng J.",Microbiome of the lower genital tract in Chinese women with endometriosis by 16s-rRNA sequencing technique: a pilot study,Annals of translational medicine,2020,"16s-rRNA sequencing, Endometriosis, bioinformatic analysis, microbiome",Experiment 3,China,Homo sapiens,Cervical cavity,UBERON:0013761,"Adenomyosis,Endometriosis","EFO:1001757,EFO:0001065",Adenomysis patients,Endometriosis/ adenomyosis patients (AMEM),All participants were diagnosed with endometriosis and/or adenomyosis (a condition where endometrial tissue grows into the uterine wall) through laparoscopic surgery,28,14,1 month,16S,34,Illumina,NA,NA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"within results text (under ""Microbiota composition of different diseases"" ,paragraph 5, lines 4-7), figure 6",15 November 2023,Folakunmi,"Folakunmi,WikiWorks",The following taxa had increased abundance in patients with endometriosis and adenomyosis compared to those with only adenomyosis.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|201174|84998|84999|1643824|1380;3379134|29547|3031852|213849|72294|194;1783272|1239|1737404|1582879;1783272|1239|186801|186802|216572|216851,Complete,Folakunmi
bsdb:33324725/1/1,33324725,"case-control,time series / longitudinal observational",33324725,10.1093/ofid/ofz367,https://academic.oup.com/ofid/article/7/12/ofz367/5552739?login=false,"Sortino O., Phanuphak N., Schuetz A., Ortiz A.M., Chomchey N., Belkaid Y., Davis J., Mystakelis H.A., Quiñones M., Deleage C., Ingram B., Rerknimitr R., Pinyakorn S., Rupert A., Robb M.L., Ananworanich J., Brenchley J. , Sereti I.",Impact of Acute HIV Infection and Early Antiretroviral Therapy on the Human Gut Microbiome,Open forum infectious diseases,2020,"ART, HIV, immune activation, inflammation, microbiome",Experiment 1,Thailand,Homo sapiens,Rectum,UBERON:0001052,HIV infection,EFO:0000764,Human immunodeficiency virus negative (HIV-)Uninfected Controls,Human immunodeficiency virus positive(HIV+) pre - antiretroviral therapy(ART),Patients with human immunodeficiency virus  positive (HIV+) before the initiation of antiretroviral therapy (ART),7,37,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,ethnic group,sex",NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Figure 1C,18 November 2025,Chyono2,Chyono2,Most abundant families in human immunodeficiency virus negative (HIV-) and human immunodeficiency virus positive (HIV+) pre-antiretroviral therapy (ART) measured and compared using the Mann-Whitney test.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae",1783272|1239|909932|1843488|909930;1783272|201174|1760|2037|2049;1783272|201174|84998|84999|84107;3379134|1224|1236|91347|543;1783272|1239|186801|3085636|186803;3379134|1224|1236|2887326|468,Complete,KateRasheed
bsdb:33324725/2/1,33324725,"case-control,time series / longitudinal observational",33324725,10.1093/ofid/ofz367,https://academic.oup.com/ofid/article/7/12/ofz367/5552739?login=false,"Sortino O., Phanuphak N., Schuetz A., Ortiz A.M., Chomchey N., Belkaid Y., Davis J., Mystakelis H.A., Quiñones M., Deleage C., Ingram B., Rerknimitr R., Pinyakorn S., Rupert A., Robb M.L., Ananworanich J., Brenchley J. , Sereti I.",Impact of Acute HIV Infection and Early Antiretroviral Therapy on the Human Gut Microbiome,Open forum infectious diseases,2020,"ART, HIV, immune activation, inflammation, microbiome",Experiment 2,Thailand,Homo sapiens,Rectum,UBERON:0001052,Response to antiviral drug,EFO:0010123,Human immunodeficiency virus negative (HIV-)Uninfected Controls,Human immunodeficiency virus positive (HIV+) post - antiretroviral therapy(ART),Patients with human immunodeficiency virus positive (HIV+) after the initiation of antiretroviral therapy (ART),7,31,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,ethnic group,sex",NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 1F,18 November 2025,Chyono2,Chyono2,Most abundant families in human immunodeficiency virus negative (HIV-) and human immunodeficiency virus positive (HIV+) post- antiretroviral therapy (ART) measured and compared using the Mann-Whitney test.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",1783272|1239|909932|1843489|31977;3379134|1224|1236|2887326|468;1783272|201174|84998|84999|84107;3379134|976|200643|171549|171550,Complete,KateRasheed
bsdb:33324725/3/1,33324725,"case-control,time series / longitudinal observational",33324725,10.1093/ofid/ofz367,https://academic.oup.com/ofid/article/7/12/ofz367/5552739?login=false,"Sortino O., Phanuphak N., Schuetz A., Ortiz A.M., Chomchey N., Belkaid Y., Davis J., Mystakelis H.A., Quiñones M., Deleage C., Ingram B., Rerknimitr R., Pinyakorn S., Rupert A., Robb M.L., Ananworanich J., Brenchley J. , Sereti I.",Impact of Acute HIV Infection and Early Antiretroviral Therapy on the Human Gut Microbiome,Open forum infectious diseases,2020,"ART, HIV, immune activation, inflammation, microbiome",Experiment 3,Thailand,Homo sapiens,Rectum,UBERON:0001052,Response to antiviral drug,EFO:0010123,Baseline - Acute human immunodeficiency virus (AHI) pre- antiretroviral therapy (ART),Acute Human immunodeficiency virus(AHI) post- antiretroviral therapy(ART),Patients with acute human immunodeficiency virus(HIV) after the initiation of antiretroviral therapy (ART),37,31,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2A,18 November 2025,Chyono2,Chyono2,"Cladogram of linear discriminant analysis (LDA) effect size highlighting discriminatory taxa, between human immunodeficiency virus (HIV)+ pre-antiretroviral therapy(ART) and human immunodeficiency virus (HIV)+ post-antiretroviral therapy (ART).",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae",3379134|976|200643|171549;1783272|1239|186801|186802|186806|1730|39496;3379134|29547|3031852|213849|72293|209;3379134|29547|3031852|213849|72293,Complete,KateRasheed
bsdb:33324725/3/2,33324725,"case-control,time series / longitudinal observational",33324725,10.1093/ofid/ofz367,https://academic.oup.com/ofid/article/7/12/ofz367/5552739?login=false,"Sortino O., Phanuphak N., Schuetz A., Ortiz A.M., Chomchey N., Belkaid Y., Davis J., Mystakelis H.A., Quiñones M., Deleage C., Ingram B., Rerknimitr R., Pinyakorn S., Rupert A., Robb M.L., Ananworanich J., Brenchley J. , Sereti I.",Impact of Acute HIV Infection and Early Antiretroviral Therapy on the Human Gut Microbiome,Open forum infectious diseases,2020,"ART, HIV, immune activation, inflammation, microbiome",Experiment 3,Thailand,Homo sapiens,Rectum,UBERON:0001052,Response to antiviral drug,EFO:0010123,Baseline - Acute human immunodeficiency virus (AHI) pre- antiretroviral therapy (ART),Acute Human immunodeficiency virus(AHI) post- antiretroviral therapy(ART),Patients with acute human immunodeficiency virus(HIV) after the initiation of antiretroviral therapy (ART),37,31,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2A,18 November 2025,Chyono2,Chyono2,"Cladogram of linear discriminant analysis (LDA) effect size highlighting discriminatory taxa, between human immunodeficiency virus (HIV+) pre-antiretroviral therapy (ART) and human immunodeficiency (HIV)+ post-antiretroviral therapy (ART).",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239|909932|1843488|909930|904;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|1903411|613;1783272|1239|186801|186802|31979|1485,Complete,KateRasheed
bsdb:33324725/4/1,33324725,"case-control,time series / longitudinal observational",33324725,10.1093/ofid/ofz367,https://academic.oup.com/ofid/article/7/12/ofz367/5552739?login=false,"Sortino O., Phanuphak N., Schuetz A., Ortiz A.M., Chomchey N., Belkaid Y., Davis J., Mystakelis H.A., Quiñones M., Deleage C., Ingram B., Rerknimitr R., Pinyakorn S., Rupert A., Robb M.L., Ananworanich J., Brenchley J. , Sereti I.",Impact of Acute HIV Infection and Early Antiretroviral Therapy on the Human Gut Microbiome,Open forum infectious diseases,2020,"ART, HIV, immune activation, inflammation, microbiome",Experiment 4,Thailand,Homo sapiens,Rectum,UBERON:0001052,HIV infection,EFO:0000764,Human immunodeficiency virus positive(HIV+) pre- antiretroviral therapy (ART) in Fiebig stage 1-2(F1-2),Human immunodeficiency virus positive (HIV+) pre- antiretroviral therapy(ART) in Fiebig stage 3(F3),Patients with acute human immunodeficiency virus positive (HIV+) before the initiation of antiretroviral therapy (ART) at the time of diagnosis at Fiebig Stages 3(F3),15,17,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2C,18 November 2025,Chyono2,Chyono2,LDA scores of differentially abundant taxa among human immunodeficiency virus positive(HIV+) pre-antiretroviral therapy (ART) at Fiebig stage (F1-2) and human immunodeficiency virus positive (HIV+) pre- antiretroviral therapy (ART) at Fiebig stage (F3).,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae",1783272|1239|909932|1843488|909930;3379134|1224|1236|135624;3379134|976|200643|171549|2005519|397864;1783272|1239|186801;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|1224|1236|135624|83763|83770;3379134|1224|1236|135624|83763,Complete,KateRasheed
bsdb:33324725/4/2,33324725,"case-control,time series / longitudinal observational",33324725,10.1093/ofid/ofz367,https://academic.oup.com/ofid/article/7/12/ofz367/5552739?login=false,"Sortino O., Phanuphak N., Schuetz A., Ortiz A.M., Chomchey N., Belkaid Y., Davis J., Mystakelis H.A., Quiñones M., Deleage C., Ingram B., Rerknimitr R., Pinyakorn S., Rupert A., Robb M.L., Ananworanich J., Brenchley J. , Sereti I.",Impact of Acute HIV Infection and Early Antiretroviral Therapy on the Human Gut Microbiome,Open forum infectious diseases,2020,"ART, HIV, immune activation, inflammation, microbiome",Experiment 4,Thailand,Homo sapiens,Rectum,UBERON:0001052,HIV infection,EFO:0000764,Human immunodeficiency virus positive(HIV+) pre- antiretroviral therapy (ART) in Fiebig stage 1-2(F1-2),Human immunodeficiency virus positive (HIV+) pre- antiretroviral therapy(ART) in Fiebig stage 3(F3),Patients with acute human immunodeficiency virus positive (HIV+) before the initiation of antiretroviral therapy (ART) at the time of diagnosis at Fiebig Stages 3(F3),15,17,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2C,18 November 2025,Chyono2,Chyono2,LDA scores of differentially abundant taxa among human immunodeficiency virus positive(HIV+) pre-antiretroviral therapy (ART) at Fiebig stage (F1-2) and human immunodeficiency virus positive (HIV+) pre- antiretroviral therapy (ART) at Fiebig stage (F3).,decreased,NA,NA,Complete,KateRasheed
bsdb:33324725/5/1,33324725,"case-control,time series / longitudinal observational",33324725,10.1093/ofid/ofz367,https://academic.oup.com/ofid/article/7/12/ofz367/5552739?login=false,"Sortino O., Phanuphak N., Schuetz A., Ortiz A.M., Chomchey N., Belkaid Y., Davis J., Mystakelis H.A., Quiñones M., Deleage C., Ingram B., Rerknimitr R., Pinyakorn S., Rupert A., Robb M.L., Ananworanich J., Brenchley J. , Sereti I.",Impact of Acute HIV Infection and Early Antiretroviral Therapy on the Human Gut Microbiome,Open forum infectious diseases,2020,"ART, HIV, immune activation, inflammation, microbiome",Experiment 5,Thailand,Homo sapiens,Rectum,UBERON:0001052,Response to antiviral drug,EFO:0010123,Human immunodeficiency virus positive(HIV+) pre- antiretroviral therapy (ART) in Fiebig stage 1-2(F1-2),Human immunodeficiency virus positive (HIV+) post-antiretroviral therapy(ART) in Fiebig stage 1-2(F1-2),Patients with acute human immunodeficiency virus positive (HIV+) after the initiation of antiretroviral therapy (ART) at the time of diagnosis at Fiebig Stages 1-2(F1-2),15,13,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2D,18 November 2025,Deborah-Fabusuyi,"Deborah-Fabusuyi,Tosin",LDA scores of differentially abundant taxa among human immunodeficiency virus positive(HIV+) pre-antiretroviral therapy (ART) at Fiebig stage (F1-2) and human immunodeficiency virus positive (HIV+) post- antiretroviral therapy (ART) at Fiebig stage (F1 - 2).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota",1783272|1239|186801|3085636|186803|189330;3379134|1224|1236;3379134|1224,Complete,KateRasheed
bsdb:33324725/5/2,33324725,"case-control,time series / longitudinal observational",33324725,10.1093/ofid/ofz367,https://academic.oup.com/ofid/article/7/12/ofz367/5552739?login=false,"Sortino O., Phanuphak N., Schuetz A., Ortiz A.M., Chomchey N., Belkaid Y., Davis J., Mystakelis H.A., Quiñones M., Deleage C., Ingram B., Rerknimitr R., Pinyakorn S., Rupert A., Robb M.L., Ananworanich J., Brenchley J. , Sereti I.",Impact of Acute HIV Infection and Early Antiretroviral Therapy on the Human Gut Microbiome,Open forum infectious diseases,2020,"ART, HIV, immune activation, inflammation, microbiome",Experiment 5,Thailand,Homo sapiens,Rectum,UBERON:0001052,Response to antiviral drug,EFO:0010123,Human immunodeficiency virus positive(HIV+) pre- antiretroviral therapy (ART) in Fiebig stage 1-2(F1-2),Human immunodeficiency virus positive (HIV+) post-antiretroviral therapy(ART) in Fiebig stage 1-2(F1-2),Patients with acute human immunodeficiency virus positive (HIV+) after the initiation of antiretroviral therapy (ART) at the time of diagnosis at Fiebig Stages 1-2(F1-2),15,13,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2D,18 November 2025,Deborah-Fabusuyi,Deborah-Fabusuyi,LDA scores of differentially abundant taxa among human immunodeficiency virus positive(HIV+) pre-antiretroviral therapy (ART) at Fiebig stage (F1-2) and human immunodeficiency virus positive (HIV+) post- antiretroviral therapy (ART) at Fiebig stage (F1 - 2).,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,1783272|1239|91061|1385,Complete,KateRasheed
bsdb:33324725/6/1,33324725,"case-control,time series / longitudinal observational",33324725,10.1093/ofid/ofz367,https://academic.oup.com/ofid/article/7/12/ofz367/5552739?login=false,"Sortino O., Phanuphak N., Schuetz A., Ortiz A.M., Chomchey N., Belkaid Y., Davis J., Mystakelis H.A., Quiñones M., Deleage C., Ingram B., Rerknimitr R., Pinyakorn S., Rupert A., Robb M.L., Ananworanich J., Brenchley J. , Sereti I.",Impact of Acute HIV Infection and Early Antiretroviral Therapy on the Human Gut Microbiome,Open forum infectious diseases,2020,"ART, HIV, immune activation, inflammation, microbiome",Experiment 6,Thailand,Homo sapiens,Rectum,UBERON:0001052,Response to antiviral drug,EFO:0010123,Human immunodeficiency virus positive(HIV+) pre- antiretroviral therapy (ART) in Fiebig stage 3(F3),Human immunodeficiency virus positive (HIV+) post-antiretroviral therapy(ART) in Fiebig stage 3 (F3),Patients with acute human immunodeficiency virus positive (HIV+) after the initiation of antiretroviral therapy (ART) at the time of diagnosis at Fiebig Stage 3(F3),17,16,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2E,18 November 2025,Deborah-Fabusuyi,Deborah-Fabusuyi,LDA scores of differentially abundant taxa among human immunodeficiency virus positive(HIV+) pre-antiretroviral therapy (ART) at Fiebig stage 3 (F3) and human immunodeficiency virus positive (HIV+) post- antiretroviral therapy (ART) at Fiebig stage 3 (F3).,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia",1783272|1239|909932|1843488|909930|904;3379134|976|117743|200644|2762318|501783;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|976|117743|200644|49546;3379134|976|117743|200644;3379134|976|117743;3379134|1224|1236|91347|1903411|613,Complete,KateRasheed
bsdb:33324725/6/2,33324725,"case-control,time series / longitudinal observational",33324725,10.1093/ofid/ofz367,https://academic.oup.com/ofid/article/7/12/ofz367/5552739?login=false,"Sortino O., Phanuphak N., Schuetz A., Ortiz A.M., Chomchey N., Belkaid Y., Davis J., Mystakelis H.A., Quiñones M., Deleage C., Ingram B., Rerknimitr R., Pinyakorn S., Rupert A., Robb M.L., Ananworanich J., Brenchley J. , Sereti I.",Impact of Acute HIV Infection and Early Antiretroviral Therapy on the Human Gut Microbiome,Open forum infectious diseases,2020,"ART, HIV, immune activation, inflammation, microbiome",Experiment 6,Thailand,Homo sapiens,Rectum,UBERON:0001052,Response to antiviral drug,EFO:0010123,Human immunodeficiency virus positive(HIV+) pre- antiretroviral therapy (ART) in Fiebig stage 3(F3),Human immunodeficiency virus positive (HIV+) post-antiretroviral therapy(ART) in Fiebig stage 3 (F3),Patients with acute human immunodeficiency virus positive (HIV+) after the initiation of antiretroviral therapy (ART) at the time of diagnosis at Fiebig Stage 3(F3),17,16,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2E,18 November 2025,Deborah-Fabusuyi,"Deborah-Fabusuyi,Chyono2,Tosin",LDA scores of differentially abundant taxa among human immunodeficiency virus positive(HIV+) pre-antiretroviral therapy (ART) at Fiebig stage 3 (F3) and human immunodeficiency virus positive (HIV+) post- antiretroviral therapy (ART) at Fiebig stage 3 (F3).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239|186801;1783272|1239|186801|186802,Complete,KateRasheed
bsdb:33324725/7/1,33324725,"case-control,time series / longitudinal observational",33324725,10.1093/ofid/ofz367,https://academic.oup.com/ofid/article/7/12/ofz367/5552739?login=false,"Sortino O., Phanuphak N., Schuetz A., Ortiz A.M., Chomchey N., Belkaid Y., Davis J., Mystakelis H.A., Quiñones M., Deleage C., Ingram B., Rerknimitr R., Pinyakorn S., Rupert A., Robb M.L., Ananworanich J., Brenchley J. , Sereti I.",Impact of Acute HIV Infection and Early Antiretroviral Therapy on the Human Gut Microbiome,Open forum infectious diseases,2020,"ART, HIV, immune activation, inflammation, microbiome",Experiment 7,Thailand,Homo sapiens,Rectum,UBERON:0001052,Response to antiviral drug,EFO:0010123,Acute Immunodeficiency virus pre- antiretroviral therapy (ART),Acute Immunodeficiency virus post-antiretroviral therapy(ART),Patients with acute human immunodeficiency virus positive (HIV+) after the initiation of antiretroviral therapy (ART) at the time of diagnosis,16,16,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 2B,18 November 2025,Deborah-Fabusuyi,"Deborah-Fabusuyi,Chyono2",Relative abundance of Fusobacteria in human immunodeficiency virus positive (HIV)+ pre-antiretroviral therapy (ART) compared to human immunodeficiency virus positive(HIV )+ post -antiretroviral therapy (ART) in paired analysis,increased,k__Fusobacteriati|p__Fusobacteriota,3384189|32066,Complete,KateRasheed
bsdb:33324725/7/2,33324725,"case-control,time series / longitudinal observational",33324725,10.1093/ofid/ofz367,https://academic.oup.com/ofid/article/7/12/ofz367/5552739?login=false,"Sortino O., Phanuphak N., Schuetz A., Ortiz A.M., Chomchey N., Belkaid Y., Davis J., Mystakelis H.A., Quiñones M., Deleage C., Ingram B., Rerknimitr R., Pinyakorn S., Rupert A., Robb M.L., Ananworanich J., Brenchley J. , Sereti I.",Impact of Acute HIV Infection and Early Antiretroviral Therapy on the Human Gut Microbiome,Open forum infectious diseases,2020,"ART, HIV, immune activation, inflammation, microbiome",Experiment 7,Thailand,Homo sapiens,Rectum,UBERON:0001052,Response to antiviral drug,EFO:0010123,Acute Immunodeficiency virus pre- antiretroviral therapy (ART),Acute Immunodeficiency virus post-antiretroviral therapy(ART),Patients with acute human immunodeficiency virus positive (HIV+) after the initiation of antiretroviral therapy (ART) at the time of diagnosis,16,16,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 2A,19 November 2025,Deborah-Fabusuyi,"Deborah-Fabusuyi,Chyono2",Relative abundance of Bacteroidetes in human immunodeficiency virus positive (HIV) + post-antiretroviral therapy (ART) compared to human immunodeficiency virus positive (HIV) + pre-antiretroviral therapy (ART) in paired analysis,decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,KateRasheed
bsdb:33335116/1/1,33335116,"cross-sectional observational, not case-control",33335116,10.1038/s41598-020-78891-1,NA,"Sugden S., Sanderson D., Ford K., Stein L.Y. , St Clair C.C.",An altered microbiome in urban coyotes mediates relationships between anthropogenic diet and poor health,Scientific reports,2020,NA,Experiment 1,Canada,Canis latrans,Feces,UBERON:0001988,Population,IDOMAL:0001254,Rural,Urban,"Lethally managed coyote carcasses from the urban area of Edmonton, Alberta.",65,30,NA,16S,4,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,age,NA,increased,NA,NA,NA,unchanged,Signature 1,Figure 2d,23 October 2025,YokoC,YokoC,"Differentially abundant bacteria genera between urban and rural coyotes, ranked by the effect-size difference between groups measured using Hedge’s g (Benjamini–Hochberg adjusted p < 0.05).",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia",1783272|1239|186801|3085636|186803|572511;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|186802|216572|216851;1783272|201174|84998|1643822|1643826|84108,Complete,NA
bsdb:33335116/1/2,33335116,"cross-sectional observational, not case-control",33335116,10.1038/s41598-020-78891-1,NA,"Sugden S., Sanderson D., Ford K., Stein L.Y. , St Clair C.C.",An altered microbiome in urban coyotes mediates relationships between anthropogenic diet and poor health,Scientific reports,2020,NA,Experiment 1,Canada,Canis latrans,Feces,UBERON:0001988,Population,IDOMAL:0001254,Rural,Urban,"Lethally managed coyote carcasses from the urban area of Edmonton, Alberta.",65,30,NA,16S,4,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,age,NA,increased,NA,NA,NA,unchanged,Signature 2,Figure 2d,24 October 2025,YokoC,YokoC,"Differentially abundant bacteria genera between urban and rural coyotes, ranked by the effect-size difference between groups measured using Hedge’s g (Benjamini–Hochberg adjusted p < 0.05).",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter",1783272|1239|186801|186802|31979|1485;3379134|29547|3031852|213849|72293|209,Complete,NA
bsdb:33362375/1/1,33362375,case-control,33362375,10.3748/wjg.v26.i45.7173,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7723673/,"Sun X.Z., Zhao D.Y., Zhou Y.C., Wang Q.Q., Qin G. , Yao S.K.",Alteration of fecal tryptophan metabolism correlates with shifted microbiota and may be involved in pathogenesis of colorectal cancer,World journal of gastroenterology,2020,"Colorectal adenoma, Colorectal cancer, Indoles, Kynurenine, Microbiota, Tryptophan metabolism",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Controls (HC),CRC,Patients with colorectal neoplastic lesions where tumors were removed and pathologically diagnosed with adenomatous polyp or colorectal adenocarcinoma; ages of participants ranged from 18-80.,38,79,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 4C,31 January 2022,Itslanapark,"Itslanapark,Chloe,Aiyshaaaa,Merit,WikiWorks",Linear discriminant analysis effect size analysis of fecal bacterial of colorectal cancer patients and HCs was used to represent which taxa were increased in CRC patients and which were enriched in healthy controls. Taxa enriched in HCs are indicated with a negative LDA score and taxa enriched in the CRC group are indicated with a positive LDA score.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|186803|207244;1783272|1239|91061;3379134|976|200643|171549;3379134|976|200643;3379134|976;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;1783272|201174|84998|1643822|1643826|84111;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|1940338;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|906;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|577310;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836;1783272|1239|909932|909929|1843491|970;3379134|1224|28216|80840|995019|40544;3379134|74201|203494|48461|203557;3379134|74201|203494;3379134|74201|203494|48461;3379134|74201;3379134|1224|28211;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|547;1783272|1239|91061|186826|33958|1578|1591,Complete,Chloe
bsdb:33362375/1/2,33362375,case-control,33362375,10.3748/wjg.v26.i45.7173,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7723673/,"Sun X.Z., Zhao D.Y., Zhou Y.C., Wang Q.Q., Qin G. , Yao S.K.",Alteration of fecal tryptophan metabolism correlates with shifted microbiota and may be involved in pathogenesis of colorectal cancer,World journal of gastroenterology,2020,"Colorectal adenoma, Colorectal cancer, Indoles, Kynurenine, Microbiota, Tryptophan metabolism",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Controls (HC),CRC,Patients with colorectal neoplastic lesions where tumors were removed and pathologically diagnosed with adenomatous polyp or colorectal adenocarcinoma; ages of participants ranged from 18-80.,38,79,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 4c,10 February 2022,Itslanapark,"Itslanapark,Fatima,Chloe,Merit,WikiWorks",Linear discriminant analysis effect size analysis of fecal bacterial of colorectal cancer patients and HCs was used to represent which taxa were increased in CRC patients and which were enriched in healthy controls. Taxa enriched in HCs are indicated with a negative LDA score and taxa enriched in the CRC group are indicated with a positive LDA score.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Asaccharobacter,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira sp.",1783272|1239|186801|186802|216572|52784;1783272|201174|84998|1643822|1643826|553372;1783272|1239;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801;1783272|1239|186801|186802|1898207;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;3384189|32066|203490|203491|203492|848;1783272|1239|186801|186802|204475;1783272|1239|186801|3085636|186803;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|1506577;3384189|32066|203490|203491|203492|848|68766;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|2049031,Complete,Chloe
bsdb:33407119/1/1,33407119,prospective cohort,33407119,https://doi.org/10.1186/s12866-020-02056-3,NA,"Lu Z.H., Liu Y.W., Ji Z.H., Fu T., Yan M., Shao Z.J. , Long Y.",Alterations in the intestinal microbiome and mental health status of workers in an underground tunnel environment,BMC microbiology,2021,"16S rRNA, Brain-gut-microbiota axis, Gut microbiome, Mental distress, Underground tunnel environment",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Workers before entry into an underground tunnel (Baseline status (BS)),Workers after entry into an underground tunnel (Exposed status (ES)),Tunnel workers who spent 3 (three) weeks working in the underground tunnel.,48,48,NA,16S,45,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,"Figure 3A, Text (page 3)",22 March 2024,Flo,"Flo,Scholastica,WikiWorks",LEfSe and LDA analysis revealed changes in the taxonomic composition of the gut microbiota in ES (Exposed status) compared to BS (Baseline status) tunnel workers.,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leucobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|201174;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;28221;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;1783272|201174|1760|85006|85023|55968;1783272|201174|1760|85006|85023;1783272|1239|186801|3082720|186804;3379134|1224|1236|72274|135621;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:33407119/1/2,33407119,prospective cohort,33407119,https://doi.org/10.1186/s12866-020-02056-3,NA,"Lu Z.H., Liu Y.W., Ji Z.H., Fu T., Yan M., Shao Z.J. , Long Y.",Alterations in the intestinal microbiome and mental health status of workers in an underground tunnel environment,BMC microbiology,2021,"16S rRNA, Brain-gut-microbiota axis, Gut microbiome, Mental distress, Underground tunnel environment",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Workers before entry into an underground tunnel (Baseline status (BS)),Workers after entry into an underground tunnel (Exposed status (ES)),Tunnel workers who spent 3 (three) weeks working in the underground tunnel.,48,48,NA,16S,45,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 2,"Figure 3A, Text (page 3)",22 March 2024,Flo,"Flo,WikiWorks",LEfSe and LDA analysis revealed changes in the taxonomic composition of the gut microbiota in ES (Exposed status) compared to BS (Baseline status) tunnel workers.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:33407128/1/1,33407128,case-control,33407128,https://doi.org/10.1186/s12866-020-02074-1,NA,"Xie Y., Sun J., Wei L., Jiang H., Hu C., Yang J., Huang Y., Ruan B. , Zhu B.",Altered gut microbiota correlate with different immune responses to HAART in HIV-infected individuals,BMC microbiology,2021,"Gut microbiota, HAART, HIV-1, Immune activation, Immunological non-responders, Immunological responders",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Healthy HIV negative individual,Immunological Responder (IR) HIV infected individual,"Immunological Responder HIV infected individual(IR), were defined as patients whose CD4+ T-cell counts/μl equal or is more than 500 or less than 200 after 2 years of receiving complete viral suppression therapy respectively. All
 HIV-positive subjects were on two nucleoside reverse
 transcriptase inhibitors (NRTIs) + nonnucleoside reverse
 transcriptase inhibitors (NNRTIs) or the protease inhibitor-based therapy: Zidovudine/Tenofovir Disoproxil
 Fumarate (AZT/TDF) + Lamivudine (3TC) + Efavirenz
(EFV) or Lopinavir/ritonavir (LPV/r).",36,28,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,"age,body mass index",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Additional file 4, figure S4b",4 October 2024,Patience Onah,"Patience Onah,WikiWorks","Taxonomic differences of fecal microbiota between the immunological responders (IR), and healthy controls (Control) group.",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|91061|186826|186827|46123;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|1940338;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803;1783272|1239|909932|1843489|31977|906;1783272|201174|1760|85007|85025|1827;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|186803,Complete,Peace Sandy
bsdb:33407128/1/2,33407128,case-control,33407128,https://doi.org/10.1186/s12866-020-02074-1,NA,"Xie Y., Sun J., Wei L., Jiang H., Hu C., Yang J., Huang Y., Ruan B. , Zhu B.",Altered gut microbiota correlate with different immune responses to HAART in HIV-infected individuals,BMC microbiology,2021,"Gut microbiota, HAART, HIV-1, Immune activation, Immunological non-responders, Immunological responders",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Healthy HIV negative individual,Immunological Responder (IR) HIV infected individual,"Immunological Responder HIV infected individual(IR), were defined as patients whose CD4+ T-cell counts/μl equal or is more than 500 or less than 200 after 2 years of receiving complete viral suppression therapy respectively. All
 HIV-positive subjects were on two nucleoside reverse
 transcriptase inhibitors (NRTIs) + nonnucleoside reverse
 transcriptase inhibitors (NNRTIs) or the protease inhibitor-based therapy: Zidovudine/Tenofovir Disoproxil
 Fumarate (AZT/TDF) + Lamivudine (3TC) + Efavirenz
(EFV) or Lopinavir/ritonavir (LPV/r).",36,28,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,"age,body mass index",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Additional file 4, figure S4b",6 October 2024,Patience Onah,"Patience Onah,WikiWorks",Taxonomic differences of fecal microbiota between the immunological non-responders (INR) and healthy controls (Control) group.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005519|397864;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|33042|2049024;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|171552|577309;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|3068309;1783272|1239|186801|186802|216572|1263|41978;1783272|1239|186801|186802|216572|292632;3379134|256845|1313211|278082|255528|172900;1783272|1239|186801|3085636|186803|1766253|39491,Complete,Peace Sandy
bsdb:33407128/2/1,33407128,case-control,33407128,https://doi.org/10.1186/s12866-020-02074-1,NA,"Xie Y., Sun J., Wei L., Jiang H., Hu C., Yang J., Huang Y., Ruan B. , Zhu B.",Altered gut microbiota correlate with different immune responses to HAART in HIV-infected individuals,BMC microbiology,2021,"Gut microbiota, HAART, HIV-1, Immune activation, Immunological non-responders, Immunological responders",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Healthy HIV negative individual,immunological non-responders (INR) HIV infected individual,"immunological non-responders (INR), and INR were defined as patients whose CD4+ T-cell counts/μl equal or is more than 500 or less than 200 after 2 years of receiving complete viral suppression therapy respectively. All
 HIV-positive subjects were on two nucleoside reverse
 transcriptase inhibitors (NRTIs) + nonnucleoside reverse
 transcriptase inhibitors (NNRTIs) or the protease inhibitor-based therapy: Zidovudine/Tenofovir Disoproxil
 Fumarate (AZT/TDF) + Lamivudine (3TC) + Efavirenz
(EFV) or Lopinavir/ritonavir (LPV/r).",36,30,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,"age,body mass index",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Additional file 4, figure S4 d",10 October 2024,Patience Onah,"Patience Onah,WikiWorks","Taxonomic differences of fecal microbiota between the, immunological non-responders (INR) and healthy controls (Control) group.",increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",3384189|32066|203490|203491|203492|848;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|186802|216572|292632;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|171552|1283313;1783272|1239|186801|186802|216572|3068309;1783272|1239|186801|3085636|186803|2316020|33038,Complete,Peace Sandy
bsdb:33407128/2/6,33407128,case-control,33407128,https://doi.org/10.1186/s12866-020-02074-1,NA,"Xie Y., Sun J., Wei L., Jiang H., Hu C., Yang J., Huang Y., Ruan B. , Zhu B.",Altered gut microbiota correlate with different immune responses to HAART in HIV-infected individuals,BMC microbiology,2021,"Gut microbiota, HAART, HIV-1, Immune activation, Immunological non-responders, Immunological responders",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Healthy HIV negative individual,immunological non-responders (INR) HIV infected individual,"immunological non-responders (INR), and INR were defined as patients whose CD4+ T-cell counts/μl equal or is more than 500 or less than 200 after 2 years of receiving complete viral suppression therapy respectively. All
 HIV-positive subjects were on two nucleoside reverse
 transcriptase inhibitors (NRTIs) + nonnucleoside reverse
 transcriptase inhibitors (NNRTIs) or the protease inhibitor-based therapy: Zidovudine/Tenofovir Disoproxil
 Fumarate (AZT/TDF) + Lamivudine (3TC) + Efavirenz
(EFV) or Lopinavir/ritonavir (LPV/r).",36,30,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,"age,body mass index",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 6,"Additional file 4, figure S4 d",11 October 2024,Patience Onah,"Patience Onah,WikiWorks",Taxonomic differences of fecal microbiota between the immunological non-responders (INR) and healthy controls (Control) group.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|s__Christensenellaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 10-1,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus albus",1783272|1239|186801|3085636|186803|1766253|39491;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|2005519|397864;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3082768|990719|2054177;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|189330;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|1235800;1783272|1239|186801|3085636|186803|877420;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|171552|838|28125;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|3068309;1783272|1239|186801|186802|216572|1263|1264,Complete,Peace Sandy
bsdb:33407128/3/1,33407128,case-control,33407128,https://doi.org/10.1186/s12866-020-02074-1,NA,"Xie Y., Sun J., Wei L., Jiang H., Hu C., Yang J., Huang Y., Ruan B. , Zhu B.",Altered gut microbiota correlate with different immune responses to HAART in HIV-infected individuals,BMC microbiology,2021,"Gut microbiota, HAART, HIV-1, Immune activation, Immunological non-responders, Immunological responders",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,immunological non-responders (INR) HIV infected individual,Immunological Responder (IR) HIV infected individual,Immunological Responder HIV infected individual (IR) was defined as patients whose CD4+ T-cell counts/μl equal or is more than 500 or less than 200 after 2 years of receiving complete viral suppression therapy respectively. All HIV-positive subjects were on two nucleoside reverse transcriptase inhibitors (NRTIs) + nonnucleoside reverse transcriptase inhibitors (NNRTIs) or the protease inhibitor-based therapy: Zidovudine/Tenofovir Disoproxil Fumarate (AZT/TDF) + Lamivudine (3TC) + Efavirenz (EFV) or Lopinavir/ritonavir (LPV/r).,30,28,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,"age,body mass index",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Additional file 4, figure S4 f",11 October 2024,Patience Onah,"Patience Onah,WikiWorks",Taxonomic differences of fecal microbiota between the immunological non-responders (INR) and Immunological Responder (IR) HIV infected individual.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",1783272|1239|526524|526525|128827|123375;1783272|1239|526524|526525|128827|1472649;1783272|1239|186801|3085636|186803|572511;3379134|1224|1236|91347|543|1940338,Complete,Peace Sandy
bsdb:33407128/3/2,33407128,case-control,33407128,https://doi.org/10.1186/s12866-020-02074-1,NA,"Xie Y., Sun J., Wei L., Jiang H., Hu C., Yang J., Huang Y., Ruan B. , Zhu B.",Altered gut microbiota correlate with different immune responses to HAART in HIV-infected individuals,BMC microbiology,2021,"Gut microbiota, HAART, HIV-1, Immune activation, Immunological non-responders, Immunological responders",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,immunological non-responders (INR) HIV infected individual,Immunological Responder (IR) HIV infected individual,Immunological Responder HIV infected individual (IR) was defined as patients whose CD4+ T-cell counts/μl equal or is more than 500 or less than 200 after 2 years of receiving complete viral suppression therapy respectively. All HIV-positive subjects were on two nucleoside reverse transcriptase inhibitors (NRTIs) + nonnucleoside reverse transcriptase inhibitors (NNRTIs) or the protease inhibitor-based therapy: Zidovudine/Tenofovir Disoproxil Fumarate (AZT/TDF) + Lamivudine (3TC) + Efavirenz (EFV) or Lopinavir/ritonavir (LPV/r).,30,28,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,"age,body mass index",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Additional file 4, figure S4 f",11 October 2024,Patience Onah,"Patience Onah,WikiWorks",Taxonomic differences of fecal microbiota between the immunological non-responders (INR) and Immunological Responder (IR) HIV infected,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__Ruminiclostridium sp.",1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|186806|1730|42322;3379134|976|200643|171549|171552|1283313;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|1508657|2053608,Complete,Peace Sandy
bsdb:33429936/1/1,33429936,"cross-sectional observational, not case-control",33429936,https://doi.org/10.3390/jpm11010035,NA,"Barandouzi Z.A., Lee J., Maas K., Starkweather A.R. , Cong X.S.",Altered Gut Microbiota in Irritable Bowel Syndrome and Its Association with Food Components,Journal of personalized medicine,2021,"food components, irritable bowel syndrome, microbiome, microbiota, nutrients",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy control,IBS,The patient's who have been diagnosed from irritable bowel syndrome(IBS).,21,80,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,unchanged,NA,NA,Signature 1,Figure 2(b),25 October 2022,Fatima,"Fatima,Aiyshaaaa,WikiWorks",Taxonomic differences of fecal microbiota between IBS and HC groups,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia",3379134|74201|203494|48461|1647988|239934;1783272|1239|91061;1783272|1239|186801|3085636|186803|572511;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;1783272|1239|909932|1843489|31977|29465;3379134|74201|203494|48461;3379134|74201;1783272|1239|186801|3085636|186803;3379134|74201|203494,Complete,Aiyshaaaa
bsdb:33429936/1/2,33429936,"cross-sectional observational, not case-control",33429936,https://doi.org/10.3390/jpm11010035,NA,"Barandouzi Z.A., Lee J., Maas K., Starkweather A.R. , Cong X.S.",Altered Gut Microbiota in Irritable Bowel Syndrome and Its Association with Food Components,Journal of personalized medicine,2021,"food components, irritable bowel syndrome, microbiome, microbiota, nutrients",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy control,IBS,The patient's who have been diagnosed from irritable bowel syndrome(IBS).,21,80,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,unchanged,NA,NA,Signature 2,Figure 2,25 October 2022,Fatima,"Fatima,WikiWorks",Taxonomic differences of fecal microbiota between IBS and HC groups,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552,Complete,Aiyshaaaa
bsdb:33431578/1/1,33431578,case-control,33431578,10.1136/gutjnl-2020-323020,NA,"Yeoh Y.K., Zuo T., Lui G.C., Zhang F., Liu Q., Li A.Y., Chung A.C., Cheung C.P., Tso E.Y., Fung K.S., Chan V., Ling L., Joynt G., Hui D.S., Chow K.M., Ng S.S.S., Li T.C., Ng R.W., Yip T.C., Wong G.L., Chan F.K., Wong C.K., Chan P.K. , Ng S.C.",Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19,Gut,2021,"colonic bacteria, colonic microflora, inflammation",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 cases,Laboratory-confirmed SARS-CoV-2 positive by quantitative reverse transcription PCR performed on nasopharyngeal swabs,78,87,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 2,28 May 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential bacterial species abundance between COVID-19 samples and non-COVID-19 samples,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila",3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|186803|2316020|33039;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|47678;3379134|74201|203494|48461|1647988|239934|239935,Complete,Fatima
bsdb:33431578/1/2,33431578,case-control,33431578,10.1136/gutjnl-2020-323020,NA,"Yeoh Y.K., Zuo T., Lui G.C., Zhang F., Liu Q., Li A.Y., Chung A.C., Cheung C.P., Tso E.Y., Fung K.S., Chan V., Ling L., Joynt G., Hui D.S., Chow K.M., Ng S.S.S., Li T.C., Ng R.W., Yip T.C., Wong G.L., Chan F.K., Wong C.K., Chan P.K. , Ng S.C.",Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19,Gut,2021,"colonic bacteria, colonic microflora, inflammation",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 cases,Laboratory-confirmed SARS-CoV-2 positive by quantitative reverse transcription PCR performed on nasopharyngeal swabs,78,87,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 2,28 May 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential bacterial species abundance between COVID-19 samples and non-COVID-19 samples,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans",1783272|201174|1760|85004|31953|1678|1680;1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|292632;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|186801|186802|216572|216851|853;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|189330|39486,Complete,Fatima
bsdb:33431578/2/1,33431578,case-control,33431578,10.1136/gutjnl-2020-323020,NA,"Yeoh Y.K., Zuo T., Lui G.C., Zhang F., Liu Q., Li A.Y., Chung A.C., Cheung C.P., Tso E.Y., Fung K.S., Chan V., Ling L., Joynt G., Hui D.S., Chow K.M., Ng S.S.S., Li T.C., Ng R.W., Yip T.C., Wong G.L., Chan F.K., Wong C.K., Chan P.K. , Ng S.C.",Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19,Gut,2021,"colonic bacteria, colonic microflora, inflammation",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 cases,Recovered following negative quantitative reverse transcription PCR (RT-qPCR) tests for SARS-CoV-2 RNA in nasopharyngeal swabs,78,13,Patients whose COVID-19 treatment included antibiotics were excluded,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,30 May 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differences in gut microbiome bacterial species between feces samples from healthy controls and samples from non-antibiotic-treated patients with COVID-19 after recovery,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum",1783272|201174|1760|85004|31953|1678|1689;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|91061|186826|33958|2767887|1623;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|2005525|375288|1869337;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|186801|186802|216572|1263|457412;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|186801|3085636|186803|2941495|1512,Complete,Fatima
bsdb:33431578/2/2,33431578,case-control,33431578,10.1136/gutjnl-2020-323020,NA,"Yeoh Y.K., Zuo T., Lui G.C., Zhang F., Liu Q., Li A.Y., Chung A.C., Cheung C.P., Tso E.Y., Fung K.S., Chan V., Ling L., Joynt G., Hui D.S., Chow K.M., Ng S.S.S., Li T.C., Ng R.W., Yip T.C., Wong G.L., Chan F.K., Wong C.K., Chan P.K. , Ng S.C.",Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19,Gut,2021,"colonic bacteria, colonic microflora, inflammation",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 cases,Recovered following negative quantitative reverse transcription PCR (RT-qPCR) tests for SARS-CoV-2 RNA in nasopharyngeal swabs,78,13,Patients whose COVID-19 treatment included antibiotics were excluded,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,30 May 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differences in gut microbiome bacterial species between feces samples from healthy controls and samples from non-antibiotic-treated patients with COVID-19 after recovery,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",3379134|976|200643|171549|171550|239759|28117;1783272|201174|1760|85004|31953|1678|216816|1679;1783272|201174|1760|85004|31953|1678|28026;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|186802|216572|292632,Complete,Fatima
bsdb:33431578/3/1,33431578,case-control,33431578,10.1136/gutjnl-2020-323020,NA,"Yeoh Y.K., Zuo T., Lui G.C., Zhang F., Liu Q., Li A.Y., Chung A.C., Cheung C.P., Tso E.Y., Fung K.S., Chan V., Ling L., Joynt G., Hui D.S., Chow K.M., Ng S.S.S., Li T.C., Ng R.W., Yip T.C., Wong G.L., Chan F.K., Wong C.K., Chan P.K. , Ng S.C.",Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19,Gut,2021,"colonic bacteria, colonic microflora, inflammation",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 cases,"Recovered following negative quantitative reverse transcription PCR (RT-qPCR) tests for SARS-CoV-2 RNA in nasopharyngeal swabs, treated with antibiotics during course of COVID-19",78,14,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,30 May 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differences in gut microbiome bacterial species between feces samples from healthy controls and samples from antibiotic-treated patients with COVID-19 after recovery,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula",1783272|201174|1760|85004|31953|1678|1689;1783272|1239|91061|186826|33958|2767887|1623;3379134|976|200643|171549|2005525|375288|823;1783272|1239|91061|186826|81852|1350|1351;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|2941495|1512;1783272|1239|909932|1843489|31977|29465|29466,Complete,Fatima
bsdb:33431578/3/2,33431578,case-control,33431578,10.1136/gutjnl-2020-323020,NA,"Yeoh Y.K., Zuo T., Lui G.C., Zhang F., Liu Q., Li A.Y., Chung A.C., Cheung C.P., Tso E.Y., Fung K.S., Chan V., Ling L., Joynt G., Hui D.S., Chow K.M., Ng S.S.S., Li T.C., Ng R.W., Yip T.C., Wong G.L., Chan F.K., Wong C.K., Chan P.K. , Ng S.C.",Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19,Gut,2021,"colonic bacteria, colonic microflora, inflammation",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 cases,"Recovered following negative quantitative reverse transcription PCR (RT-qPCR) tests for SARS-CoV-2 RNA in nasopharyngeal swabs, treated with antibiotics during course of COVID-19",78,14,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,30 May 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differences in gut microbiome bacterial species between feces samples from healthy controls and samples from antibiotic-treated patients with COVID-19 after recovery,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|216851|853;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|186801|186802|216572|292632;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|1760|85004|31953|1678|216816|1679;1783272|1239|186801|186802|216572|1263|457412;1783272|1239|186801|3085636|186803|572511|40520;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330|88431;3379134|976|200643|171549|171550|239759|28117;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|186801|3085636|186803|2569097|39488,Complete,Fatima
bsdb:33431578/4/1,33431578,case-control,33431578,10.1136/gutjnl-2020-323020,NA,"Yeoh Y.K., Zuo T., Lui G.C., Zhang F., Liu Q., Li A.Y., Chung A.C., Cheung C.P., Tso E.Y., Fung K.S., Chan V., Ling L., Joynt G., Hui D.S., Chow K.M., Ng S.S.S., Li T.C., Ng R.W., Yip T.C., Wong G.L., Chan F.K., Wong C.K., Chan P.K. , Ng S.C.",Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19,Gut,2021,"colonic bacteria, colonic microflora, inflammation",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients treated with antibiotics,"Laboratory-confirmed SARS-CoV-2 positive by quantitative reverse transcription PCR performed on nasopharyngeal swabs, treated with antibiotics",78,34,NA,WMS,NA,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S3,11 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential bacterial species abundance between COVID-19 samples from patients were treated with antibiotics and non-COVID-19 samples,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp. 4_3_54A2FAA,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus avium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.",1783272|201174|1760|85004|31953|1678|1680;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|186802|216572|292632|2053618;3379134|1224|1236|91347|543|570|573;1783272|201174|84998|1643822|1643826|447020|446660;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|186802|216572|292632|665956;1783272|1239|91061|186826|81852|1350|33945;1783272|1239|186801|186802|186806|1730|39496;3379134|1224|1236|91347|543|544|1896336,Complete,Fatima
bsdb:33431578/4/2,33431578,case-control,33431578,10.1136/gutjnl-2020-323020,NA,"Yeoh Y.K., Zuo T., Lui G.C., Zhang F., Liu Q., Li A.Y., Chung A.C., Cheung C.P., Tso E.Y., Fung K.S., Chan V., Ling L., Joynt G., Hui D.S., Chow K.M., Ng S.S.S., Li T.C., Ng R.W., Yip T.C., Wong G.L., Chan F.K., Wong C.K., Chan P.K. , Ng S.C.",Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19,Gut,2021,"colonic bacteria, colonic microflora, inflammation",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients treated with antibiotics,"Laboratory-confirmed SARS-CoV-2 positive by quantitative reverse transcription PCR performed on nasopharyngeal swabs, treated with antibiotics",78,34,NA,WMS,NA,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S3,11 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential bacterial species abundance between COVID-19 samples from patients were treated with antibiotics and non-COVID-19 samples,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia inopinata,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Cryptobacterium|s__Cryptobacterium curtum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella|s__Shuttleworthella satelles,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Parascardovia|s__Parascardovia denticolens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus gallinarum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum sp. ICM7,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp. oral taxon 078,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 5_1_63FAA,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia sp.,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella profusa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella rimae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum longum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella uli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp.",1783272|1239|186801|3085636|186803|2569097|39488;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|28116;1783272|1239|186801|186802|216572|1263|457412;1783272|201174|1760|85004|31953|196081|78259;1783272|201174|1760|85009|31957|1912216|1747;1783272|201174|84998|1643822|1643826|84162|84163;1783272|1239|186801|3085636|186803|177971|177972;1783272|201174|1760|85004|31953|196082|78258;1783272|1239|91061|186826|81852|1350|1353;1783272|1239|186801|3085636|186803|1164882|936594;1783272|1239|186801|3085636|186803|265975|652706;1783272|1239|186801|3085636|186803|658089;1783272|201174|84998|1643822|1643826|84108|2049041;1783272|201174|84998|84999|1643824|133925|138595;1783272|1239|186801|3085636|186803|3570277|116085;1783272|201174|84998|84999|1643824|2767353|1383;1783272|1239|91061|1385|90964|1279|1280;1783272|201174|1760|85006|1268|32207|172042;1783272|1239|91061|186826|186827|46123|46125;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|3085636|186803|1213720|796942;1783272|1239|91061|1385|90964|1279|1282;1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|186801|186802|186806|1730|39490;1783272|201174|1760|85004|31953|196081|230143;3379134|1224|28216|80840|995019|40544|40545;3379134|976|200643|171549|171550|239759|328813;1783272|1239|526524|526525|2810280|100883;1783272|201174|84998|84999|1643824|133925|133926;3379134|976|200643|171549|2005525|375288|1869337,Complete,Fatima
bsdb:33435800/1/1,33435800,case-control,33435800,10.1080/19490976.2020.1869504,NA,"Harry Cheuk Hay Lau, Joseph Jao-Yiu Sung",Gut microbiota: impacts on gastrointestinal cancer immunotherapy,Gut microbes,2021,"CpG- oligodeoxynucleotide therapy, Gut microbiota, adoptive cell transfer, blockade-induced adverse events, gastrointestinal cancer, immune checkpoint blockade, probiotics",Experiment 1,United States of America,Mus musculus,Wall of small intestine,UBERON:0001168,Gastric cancer,MONDO:0001056,Mice quarantined to a different breeding environment,Mice kept in original breeding environment,Mature mice from a distinct strain,6,6,1 month,16S,NA,RT-qPCR,raw counts,Kruskall-Wallis,NA,NA,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,20 March 2023,Ellajessica,"Ellajessica,WikiWorks",All animals were housed in environment A until 8 weeks of age. Samples obtained during this period are designated by blue symbols. Red symbols represent fecal samples obtained from animals that remained in the original environment (A) (sampled in the animals over 8 weeks of age); open symbols represent animals relocated to environment B. Numbers indentify individual animals; numbers in parenthesis give the age of animal in weeks.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,3379134|976|200643|171549|815,Complete,ChiomaBlessing
bsdb:33435800/1/2,33435800,case-control,33435800,10.1080/19490976.2020.1869504,NA,"Harry Cheuk Hay Lau, Joseph Jao-Yiu Sung",Gut microbiota: impacts on gastrointestinal cancer immunotherapy,Gut microbes,2021,"CpG- oligodeoxynucleotide therapy, Gut microbiota, adoptive cell transfer, blockade-induced adverse events, gastrointestinal cancer, immune checkpoint blockade, probiotics",Experiment 1,United States of America,Mus musculus,Wall of small intestine,UBERON:0001168,Gastric cancer,MONDO:0001056,Mice quarantined to a different breeding environment,Mice kept in original breeding environment,Mature mice from a distinct strain,6,6,1 month,16S,NA,RT-qPCR,raw counts,Kruskall-Wallis,NA,NA,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,23 March 2023,Ellajessica,"Ellajessica,WikiWorks",Samples obtained from mice relocated at 4 weeks of age are represented by open symbols; red symbols represent animals relocated to environment B at over 8 weeks of age. Numbers identify individual animals; numbers in parenthesis give the age of animal in weeks and (b) UPLC-MS PCA results from the analysis of urine samples from these animals showing the effect of relocation on metabolite profiles.,decreased,k__Bacillati|p__Bacillota|s__Firmicutes bacterium AM10-47,1783272|1239|2292890,Complete,NA
bsdb:33440171/1/1,33440171,randomized controlled trial,33440171,10.1016/j.chom.2020.12.012,NA,"Tanes C., Bittinger K., Gao Y., Friedman E.S., Nessel L., Paladhi U.R., Chau L., Panfen E., Fischbach M.A., Braun J., Xavier R.J., Clish C.B., Li H., Bushman F.D., Lewis J.D. , Wu G.D.",Role of dietary fiber in the recovery of the human gut microbiome and its metabolome,Cell host & microbe,2021,"dietary fiber, vegan, omnivore, amino acid, enteral nutrition, metabolome, microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,regular fiber omnivore diet,no fiber liquid omnivore diet,omnivores randomized to an enteral liquid nutrition diet devoid of any fiber (but similar in profile to regular food omnivore group),10,10,6 months,16S,NA,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,"age,body mass index",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2B,11 November 2021,Lorakasselman,"Lorakasselman,Chloe,WikiWorks","The taxa that are significantly different in EEN diet compared with the omnivore diet during the diet phase based on linear mixed effects models (q < 0.05). The taxa that increase during the diet phase with the EEN diet are annotated in black and the taxa
that decrease in abundance are annotated with white squares. Taxa are further annotated with the Clostridia clade to which they belong",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Chloe
bsdb:33440171/1/2,33440171,randomized controlled trial,33440171,10.1016/j.chom.2020.12.012,NA,"Tanes C., Bittinger K., Gao Y., Friedman E.S., Nessel L., Paladhi U.R., Chau L., Panfen E., Fischbach M.A., Braun J., Xavier R.J., Clish C.B., Li H., Bushman F.D., Lewis J.D. , Wu G.D.",Role of dietary fiber in the recovery of the human gut microbiome and its metabolome,Cell host & microbe,2021,"dietary fiber, vegan, omnivore, amino acid, enteral nutrition, metabolome, microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,regular fiber omnivore diet,no fiber liquid omnivore diet,omnivores randomized to an enteral liquid nutrition diet devoid of any fiber (but similar in profile to regular food omnivore group),10,10,6 months,16S,NA,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,"age,body mass index",NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2B,11 November 2021,Lorakasselman,"Lorakasselman,Chloe,WikiWorks","The taxa that are significantly different in EEN diet compared with the omnivore diet during the diet phase based on linear mixed effects models (q < 0.05). The taxa that increase during the diet phase with the EEN diet are annotated in black and the taxa
that decrease in abundance are annotated with white squares. Taxa are further annotated with the Clostridia clade to which they belong.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",3379134|976|200643|171549|815|816|28116;1783272|1239|186801|186802|216572|216851|853;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|186801|3085636|186803|1766253|39491,Complete,Chloe
bsdb:33481211/1/1,33481211,time series / longitudinal observational,33481211,https://doi.org/10.1007/s40618-021-01507-6,NA,"Chen J., Wang W., Guo Z., Huang S., Lei H., Zang P., Lu B., Shao J. , Gu P.",Associations between gut microbiota and thyroidal function status in Chinese patients with Graves' disease,Journal of endocrinological investigation,2021,"Graves’ disease, Gut microbiota, Lactobacillus, Ruminococcus, TRAb",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Control group (CG),Hyperthyroidism group (HG),Patients with primary Graves’ disease (GD) recruited as the hyperthyroidism group (HG).,14,15,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,decreased,unchanged,decreased,NA,decreased,Signature 1,Figure 4A,24 July 2025,Aleru Divine,Aleru Divine,Figure showing the differential flora with LDA score>2.0 between HG and CG.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958,Complete,NA
bsdb:33481211/1/2,33481211,time series / longitudinal observational,33481211,https://doi.org/10.1007/s40618-021-01507-6,NA,"Chen J., Wang W., Guo Z., Huang S., Lei H., Zang P., Lu B., Shao J. , Gu P.",Associations between gut microbiota and thyroidal function status in Chinese patients with Graves' disease,Journal of endocrinological investigation,2021,"Graves’ disease, Gut microbiota, Lactobacillus, Ruminococcus, TRAb",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Control group (CG),Hyperthyroidism group (HG),Patients with primary Graves’ disease (GD) recruited as the hyperthyroidism group (HG).,14,15,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,decreased,unchanged,decreased,NA,decreased,Signature 2,Figure 4A,24 July 2025,Aleru Divine,Aleru Divine,Figure showing the differential flora with LDA score>2.0 between HG and CG.,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|526524|526525|2810281|191303;3384194|508458|649775|649776|649777|2753;3384194|508458|649775|649776|649777|508459;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|31979;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|543314|86331;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803,Complete,NA
bsdb:33481211/2/1,33481211,time series / longitudinal observational,33481211,https://doi.org/10.1007/s40618-021-01507-6,NA,"Chen J., Wang W., Guo Z., Huang S., Lei H., Zang P., Lu B., Shao J. , Gu P.",Associations between gut microbiota and thyroidal function status in Chinese patients with Graves' disease,Journal of endocrinological investigation,2021,"Graves’ disease, Gut microbiota, Lactobacillus, Ruminococcus, TRAb",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Hyperthyroidism group (HG),Treatment group (TG),Patients with primary Graves’ disease (GD)  after 3–5 months of treatment when subjects’ thyroid function is restored to normal.,15,13,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 1,Figure 4B,24 July 2025,Aleru Divine,Aleru Divine,Figure showing the differential flora with LDA score>2.0 between HG and TG.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira",1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3085636|186803|28050,Complete,NA
bsdb:33481211/2/2,33481211,time series / longitudinal observational,33481211,https://doi.org/10.1007/s40618-021-01507-6,NA,"Chen J., Wang W., Guo Z., Huang S., Lei H., Zang P., Lu B., Shao J. , Gu P.",Associations between gut microbiota and thyroidal function status in Chinese patients with Graves' disease,Journal of endocrinological investigation,2021,"Graves’ disease, Gut microbiota, Lactobacillus, Ruminococcus, TRAb",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Hyperthyroidism group (HG),Treatment group (TG),Patients with primary Graves’ disease (GD)  after 3–5 months of treatment when subjects’ thyroid function is restored to normal.,15,13,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 2,Figure 4B,24 July 2025,Aleru Divine,Aleru Divine,Figure showing the differential flora with LDA score>2.0 between HG and TG.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia",1783272|1239|91061|186826|33958;1783272|1239|91061|186826|1300|1357;1783272|201174|84998|84999;1783272|201174|84998;1783272|201174|84998|84999|84107;1783272|1239|526524|526525|128827;1783272|1239|526524;1783272|1239|526524|526525;1783272|201174|1760|2037;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300;1783272|1239|186801|3085636|186803|572511;1783272|1239|91061|186826;1783272|1239|91061;1783272|201174|84992,Complete,NA
bsdb:33481833/1/1,33481833,case-control,33481833,10.1371/journal.pone.0245534,NA,"Khaliq A., Ravindran R., Afzal S., Jena P.K., Akhtar M.W., Ambreen A., Wan Y.Y., Malik K.A., Irfan M. , Khan I.H.",Gut microbiome dysbiosis and correlation with blood biomarkers in active-tuberculosis in endemic setting,PloS one,2021,NA,Experiment 1,Pakistan,Homo sapiens,"Sputum,Blood","UBERON:0007311,UBERON:0000178",Pulmonary tuberculosis,EFO:1000049,Healthy,TB patients,patients are screened by chest x-ray (CXR) and acid-fast bacilli sputum smear microscopy (AFB microscopy) for two consecutive samples (spot and early morning). Patients positive for AFB smear for at least one sample are considered positive (AFB+),40,42,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 3,24 July 2025,Nuerteye,Nuerteye,Linear discriminant analysis effect size (LEfSe) of the top 25 significant families and/or genera in active-TB patients and healthy individuals.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|526524|526525|128827|118747;3379134|1224|28216|80840|119060|32008;1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;1783272|1239|186801|3085636|186803|189330;1783272|201174|84998|1643822|1643826|84111;3379134|1224|1236|91347|543;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|1263;1783272|201174|84998|1643822|1643826|84108;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|1898203,Complete,NA
bsdb:33481833/1/2,33481833,case-control,33481833,10.1371/journal.pone.0245534,NA,"Khaliq A., Ravindran R., Afzal S., Jena P.K., Akhtar M.W., Ambreen A., Wan Y.Y., Malik K.A., Irfan M. , Khan I.H.",Gut microbiome dysbiosis and correlation with blood biomarkers in active-tuberculosis in endemic setting,PloS one,2021,NA,Experiment 1,Pakistan,Homo sapiens,"Sputum,Blood","UBERON:0007311,UBERON:0000178",Pulmonary tuberculosis,EFO:1000049,Healthy,TB patients,patients are screened by chest x-ray (CXR) and acid-fast bacilli sputum smear microscopy (AFB microscopy) for two consecutive samples (spot and early morning). Patients positive for AFB smear for at least one sample are considered positive (AFB+),40,42,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 3,24 July 2025,Nuerteye,Nuerteye,Linear discriminant analysis effect size (LEfSe) of the top 25 significant families and/or genera in active-TB patients and healthy individuals.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|s__Veillonellaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus",3379134|976|200643|171549|171552|838;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|909929|1843491|52225;1783272|1239|909932|1843489|31977;3379134|74152|641853|641854|641876;1783272|1239|526524|526525|128827;3379134|1224|28216|80840|995019|40544;3379134|976|200643|171549|2005519;1783272|1239|909932|1843489|31977|2049049;1783272|1239|186801|3085636|186803|841;1783272|1239|909932|1843488|909930|904,Complete,NA
bsdb:33485388/2/1,33485388,"cross-sectional observational, not case-control",33485388,10.1186/s40168-020-00977-9,NA,"Baniel A., Amato K.R., Beehner J.C., Bergman T.J., Mercer A., Perlman R.F., Petrullo L., Reitsema L., Sams S., Lu A. , Snyder-Mackler N.",Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas,Microbiome,2021,"Graminivory, Gut microbiome, Primates, Seasonality, Thermoregulation, Theropithecus gelada",Experiment 2,Ethiopia,Theropithecus gelada,Feces,UBERON:0001988,Mixed sex population,EFO:0001271,Male samples,Female samples,Female samples refers to the Ethiopian female geladas whose fecal samples were collected for analysis,138,620,NA,16S,4,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Table S7,28 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between male and female geladas,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Elusimicrobiota|s__Elusimicrobia bacterium HGW-Elusimicrobia-4,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Myxococcota|c__Myxococcia|o__Myxococcales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,c__Deltaproteobacteria,c__Deltaproteobacteria|o__Bradymonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales",1783272|1239|186801|3085636|186803|207244;3379134|1224|1236|135624;3379134|1224|1236|135624|83763;3379134|1224|1236|135624|83763|83770;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958;3379134|74152|2013766;1783272|1239|91061;1783272|1239|91061|186826;1783272|1117|3028117;1783272|1239|526524|526525|2810280|3025755;1783272|1239|909932|909929|1843491|82373;3379134|74201|203494;3379134|74201;3379134|1224|1236|135625;3379134|1224|1236;3379134|2818505|32015|29;1783272|1239|526524|526525|128827|123375;28221;28221|1779134;3379134|1224|28211|766;1783272|1239|186801|186802|216572|1200657;3379134|1224;3379134|1224|28216|80840,Complete,Svetlana up
bsdb:33485388/2/2,33485388,"cross-sectional observational, not case-control",33485388,10.1186/s40168-020-00977-9,NA,"Baniel A., Amato K.R., Beehner J.C., Bergman T.J., Mercer A., Perlman R.F., Petrullo L., Reitsema L., Sams S., Lu A. , Snyder-Mackler N.",Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas,Microbiome,2021,"Graminivory, Gut microbiome, Primates, Seasonality, Thermoregulation, Theropithecus gelada",Experiment 2,Ethiopia,Theropithecus gelada,Feces,UBERON:0001988,Mixed sex population,EFO:0001271,Male samples,Female samples,Female samples refers to the Ethiopian female geladas whose fecal samples were collected for analysis,138,620,NA,16S,4,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,Table S7,28 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between male and female geladas,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|s__Alphaproteobacteria bacterium canine oral taxon 081,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Pirellulales,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia",3379134|1224|28211|1151609;3379134|203682|203683|2691354;3379134|203682|203683,Complete,Svetlana up
bsdb:33485388/3/1,33485388,"cross-sectional observational, not case-control",33485388,10.1186/s40168-020-00977-9,NA,"Baniel A., Amato K.R., Beehner J.C., Bergman T.J., Mercer A., Perlman R.F., Petrullo L., Reitsema L., Sams S., Lu A. , Snyder-Mackler N.",Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas,Microbiome,2021,"Graminivory, Gut microbiome, Primates, Seasonality, Thermoregulation, Theropithecus gelada",Experiment 3,Ethiopia,Theropithecus gelada,Feces,UBERON:0001988,Reproductive behaviour measurement,EFO:0007862,Cycling females,Pregnant females,Pregnant females refers to female at their pregnancy reproductive state. It started on the date of conception and ended the day before parturition.,158,61,NA,16S,4,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table S13,28 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between pregnant and cycling female geladas,increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",3379134|29547|3031852|213849;3379134|29547;3379134|29547|3031852;3379134|29547|3031852|213849|72293|209;3379134|29547|3031852|213849|72293;3379134|74201|203494;3379134|74201;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803|1506553,Complete,Svetlana up
bsdb:33485388/4/1,33485388,"cross-sectional observational, not case-control",33485388,10.1186/s40168-020-00977-9,NA,"Baniel A., Amato K.R., Beehner J.C., Bergman T.J., Mercer A., Perlman R.F., Petrullo L., Reitsema L., Sams S., Lu A. , Snyder-Mackler N.",Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas,Microbiome,2021,"Graminivory, Gut microbiome, Primates, Seasonality, Thermoregulation, Theropithecus gelada",Experiment 4,Ethiopia,Theropithecus gelada,Feces,UBERON:0001988,Reproductive behaviour measurement,EFO:0007862,Lactating females,Pregnant females,Pregnant females refers to female at their pregnancy reproductive state. It started on the date of conception and ended the day before parturition.,346,61,NA,16S,4,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Table S13,28 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between pregnant and cycling female geladas,increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",3379134|29547|3031852|213849;3379134|29547;3379134|29547|3031852;3379134|74201|203494;3379134|74201;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803|1506553,Complete,Svetlana up
bsdb:33485388/5/1,33485388,"cross-sectional observational, not case-control",33485388,10.1186/s40168-020-00977-9,NA,"Baniel A., Amato K.R., Beehner J.C., Bergman T.J., Mercer A., Perlman R.F., Petrullo L., Reitsema L., Sams S., Lu A. , Snyder-Mackler N.",Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas,Microbiome,2021,"Graminivory, Gut microbiome, Primates, Seasonality, Thermoregulation, Theropithecus gelada",Experiment 5,Ethiopia,Theropithecus gelada,Feces,UBERON:0001988,Temperature,EFO:0001702,Average minimum temperature(Average Min Temp),Average maximum temperature(Average Max Temp),Average maximum temperature(Average Max Temp) refers to colder temperature (i.e. <8oC in the past month) in Ethiopia,567,191,NA,16S,4,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table S7,28 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between average minimum temperature and average maximum temperature,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Cyanobacteriota",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826;1783272|1239|186801|186802|216572|596767;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|248744;1783272|1239|186801|186802|31979|1485;1783272|1117,Complete,Svetlana up
bsdb:33485388/5/2,33485388,"cross-sectional observational, not case-control",33485388,10.1186/s40168-020-00977-9,NA,"Baniel A., Amato K.R., Beehner J.C., Bergman T.J., Mercer A., Perlman R.F., Petrullo L., Reitsema L., Sams S., Lu A. , Snyder-Mackler N.",Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas,Microbiome,2021,"Graminivory, Gut microbiome, Primates, Seasonality, Thermoregulation, Theropithecus gelada",Experiment 5,Ethiopia,Theropithecus gelada,Feces,UBERON:0001988,Temperature,EFO:0001702,Average minimum temperature(Average Min Temp),Average maximum temperature(Average Max Temp),Average maximum temperature(Average Max Temp) refers to colder temperature (i.e. <8oC in the past month) in Ethiopia,567,191,NA,16S,4,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table S7,28 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between average minimum temperature and average maximum temperature,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:352,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Methanobacteriati|p__Methanobacteriota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Anaerorhabdus|s__Anaerorhabdus furcosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Catenisphaera,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Phoenicibacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NC2004,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales,k__Pseudomonadati|p__Lentisphaerota",1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|707003;1783272|1239|186801|186802|1470353;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3082720|543314|35518;3379134|976|200643|171549|171552|838;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|3082720|543314|109326;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|31979|1485|1262798;3379134|74201;3379134|74201|203494;3366610|28890;1783272|1239|526524|526525|128827|118966|118967;1783272|1239|186801|3085636|186803|46205;1783272|1239|526524|526525|128827|1774107;1783272|201174|84998|1643822|1643826|1981050;1783272|201174|84998|84999|84107;1783272|201174|84998|84999|84107|1473205;1783272|1239|186801|3085636|186803|877420;3366610|28890|183925|2158|2159|2172;3366610|28890|183925;1783272|1239|186801|3085636|186803|1410626;3366610|28890|183925|2158|2159;3366610|28890|183925|2158;3379134|256845,Complete,Svetlana up
bsdb:33490017/1/1,33490017,"cross-sectional observational, not case-control",33490017,10.3389/fpubh.2020.587298,NA,"Wei Z.T., Chen H.L., Wang C.F., Yang G.L., Han S.M. , Zhang S.L.",Depiction of Vaginal Microbiota in Women With High-Risk Human Papillomavirus Infection,Frontiers in public health,2020,"16s rRNA, bacterial vaginosis, human papillomavirus, persistent infection, vaginal microbiota",Experiment 1,China,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ confirmed by Hybrid Capture II assay,30,30,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 2E,19 March 2021,Cynthia Anderson,"Cynthia Anderson,WikiWorks",Bacterial taxa analysis of the HPV-positive and HPV-negative groups.,increased,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,1783272|544448|31969|2085|2092|2093,Complete,Claregrieve1
bsdb:33490017/1/2,33490017,"cross-sectional observational, not case-control",33490017,10.3389/fpubh.2020.587298,NA,"Wei Z.T., Chen H.L., Wang C.F., Yang G.L., Han S.M. , Zhang S.L.",Depiction of Vaginal Microbiota in Women With High-Risk Human Papillomavirus Infection,Frontiers in public health,2020,"16s rRNA, bacterial vaginosis, human papillomavirus, persistent infection, vaginal microbiota",Experiment 1,China,Homo sapiens,Vagina,UBERON:0000996,Human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ confirmed by Hybrid Capture II assay,30,30,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 2E,19 March 2021,Cynthia Anderson,"Cynthia Anderson,Claregrieve1,WikiWorks",Bacterial taxa analysis of the HPV-positive and HPV-negative groups.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Sporolactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Sporolactobacillaceae|g__Sporolactobacillus",1783272|1239|91061;1783272|1239|91061|186826;1783272|1239|91061|1385|186821;1783272|1239|91061|1385|186821|2077,Complete,Claregrieve1
bsdb:33499229/1/1,33499229,case-control,33499229,10.3390/biom11020144,NA,"Vascellari S., Melis M., Palmas V., Pisanu S., Serra A., Perra D., Santoru M.L., Oppo V., Cusano R., Uva P., Atzori L., Morelli M., Cossu G. , Manzin A.",Clinical Phenotypes of Parkinson's Disease Associate with Distinct Gut Microbiota and Metabolome Enterotypes,Biomolecules,2021,"clinical phenotype, gut microbiota, metabolome, parkinson’s disease",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Parkinson's disease patients with Tremor Dominant  - TD,Parkinson's disease patients with Akinetic Rigid - AR,A phenotype category based on motor signs,19,23,3 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,"age,body mass index,sex,smoking status",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure  3a,18 March 2024,Junie,"Junie,Peace Sandy,WikiWorks","Linear discriminant analysis effect size (LEfSE) analysis: The bar plots represent the
significantly different taxa among PD patients with distinct motor phenotypes, based on effect size (Linear discriminant analysis (LDA) score (log 10) > 2). (a) Positive LDA score (green) highlights the enriched taxa in PD patients with Tremor Dominant (TD) and negative LDA score (red) shows the enriched taxa in PD patients with Akinetic Rigid (AR);",increased,"k__Bacillati|p__Bacillota|c__Tissierellia|g__Sedimentibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",1783272|1239|1737404|190972;3379134|1224|1236|91347|1903411|613;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543,Complete,Peace Sandy
bsdb:33499229/1/2,33499229,case-control,33499229,10.3390/biom11020144,NA,"Vascellari S., Melis M., Palmas V., Pisanu S., Serra A., Perra D., Santoru M.L., Oppo V., Cusano R., Uva P., Atzori L., Morelli M., Cossu G. , Manzin A.",Clinical Phenotypes of Parkinson's Disease Associate with Distinct Gut Microbiota and Metabolome Enterotypes,Biomolecules,2021,"clinical phenotype, gut microbiota, metabolome, parkinson’s disease",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Parkinson's disease patients with Tremor Dominant  - TD,Parkinson's disease patients with Akinetic Rigid - AR,A phenotype category based on motor signs,19,23,3 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,"age,body mass index,sex,smoking status",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 3a,18 March 2024,Junie,"Junie,Peace Sandy,WikiWorks","Linear discriminant analysis effect size (LEfSE) analysis: The bar plots represent the significantly different taxa among PD patients with distinct motor phenotypes, based on effect size (Linear discriminant analysis (LDA) score (log 10) > 2). (a) Positive LDA score (green) highlights the enriched taxa in PD patients with Tremor Dominant (TD) and negative LDA score (red) shows the enriched taxa in PD patients with Akinetic Rigid (AR);",decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Tindalliaceae|g__Tindallia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium",1783272|1239;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3082720|3118658|69894;1783272|1239|91061|1385|539738;1783272|1239|91061|1385|539738|1378;1783272|201174|1760|85006|85019;1783272|201174|1760|85006|85019|1696,Complete,Peace Sandy
bsdb:33499229/2/1,33499229,case-control,33499229,10.3390/biom11020144,NA,"Vascellari S., Melis M., Palmas V., Pisanu S., Serra A., Perra D., Santoru M.L., Oppo V., Cusano R., Uva P., Atzori L., Morelli M., Cossu G. , Manzin A.",Clinical Phenotypes of Parkinson's Disease Associate with Distinct Gut Microbiota and Metabolome Enterotypes,Biomolecules,2021,"clinical phenotype, gut microbiota, metabolome, parkinson’s disease",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Parkinson's disease patients with Tremor Dominant - TD,Parkinson's disease patients with Diskinetic - D,A phenotype category based on motor signs,19,14,3 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,"age,body mass index,sex,smoking status",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 3B,19 March 2024,Peace Sandy,"Peace Sandy,WikiWorks","Linear discriminant analysis effect size (LEfSE) analysis: The bar plots represent the
significantly different taxa among PD patients with distinct motor phenotypes, based on effect size(Linear discriminant analysis (LDA) score (log 10) > 2). (b) Positive LDA score (green) highlights enriched taxa in PD patients with Tremor Dominant (TD) and negative LDA score (red) shows enriched taxa in PD with Dyskinetic (D)",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",3379134|1224|1236|91347|1903411|613;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543,Complete,Peace Sandy
bsdb:33499229/2/2,33499229,case-control,33499229,10.3390/biom11020144,NA,"Vascellari S., Melis M., Palmas V., Pisanu S., Serra A., Perra D., Santoru M.L., Oppo V., Cusano R., Uva P., Atzori L., Morelli M., Cossu G. , Manzin A.",Clinical Phenotypes of Parkinson's Disease Associate with Distinct Gut Microbiota and Metabolome Enterotypes,Biomolecules,2021,"clinical phenotype, gut microbiota, metabolome, parkinson’s disease",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Parkinson's disease patients with Tremor Dominant - TD,Parkinson's disease patients with Diskinetic - D,A phenotype category based on motor signs,19,14,3 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,"age,body mass index,sex,smoking status",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 3B,19 March 2024,Peace Sandy,"Peace Sandy,WikiWorks","Linear discriminant analysis effect size (LEfSE) analysis: The bar plots represent the
significantly different taxa among PD patients with distinct motor phenotypes, based on effect size(Linear discriminant analysis (LDA) score (log 10) > 2). (b) Positive LDA score (green) highlights enriched taxa in PD patients with Tremor Dominant (TD) and negative LDA score (red) shows enriched taxa in PD with Dyskinetic (D)",decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Tissierellia|g__Sedimentibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Tindalliaceae|g__Tindallia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella",1783272|1239;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|186802|186807;1783272|1239|1737404|190972;1783272|1239|186801|3082720|3118658|69894;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|216572|258514;1783272|201174|1760|85006|85019|1696;1783272|201174|1760|85006|85019;1783272|1239|91061|1385|539738;1783272|1239|91061|1385|539738|1378,Complete,Peace Sandy
bsdb:33505487/1/1,33505487,case-control,33505487,10.1155/2021/1416236,NA,"Chen H., Tan P.S., Li C.P., Chen B.Z., Xu Y.Q., He Y.Q. , Ke X.",Acupoint Massage Therapy Alters the Composition of Gut Microbiome in Functional Constipation Patients,Evidence-based complementary and alternative medicine : eCAM,2021,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Control group,Experimental group,Experimental group of patients before and after AMT (Acupoint Massage Therapy),51,50,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 4B,13 April 2025,Montana-D,Montana-D,Significantly differential genera between the samples from the experimental and control groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",3379134|976|200643|171549|171552;1783272|1239|186801|3085636|186803|46205;1783272|1239|186801|186802|216572|1508657,Complete,KateRasheed
bsdb:33505487/1/2,33505487,case-control,33505487,10.1155/2021/1416236,NA,"Chen H., Tan P.S., Li C.P., Chen B.Z., Xu Y.Q., He Y.Q. , Ke X.",Acupoint Massage Therapy Alters the Composition of Gut Microbiome in Functional Constipation Patients,Evidence-based complementary and alternative medicine : eCAM,2021,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Control group,Experimental group,Experimental group of patients before and after AMT (Acupoint Massage Therapy),51,50,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 4B,13 April 2025,Abimbola-beep,"Abimbola-beep,Montana-D",Significantly differential genera between the samples from the experimental and control groups,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter",1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|1407607,Complete,KateRasheed
bsdb:33505487/2/1,33505487,case-control,33505487,10.1155/2021/1416236,NA,"Chen H., Tan P.S., Li C.P., Chen B.Z., Xu Y.Q., He Y.Q. , Ke X.",Acupoint Massage Therapy Alters the Composition of Gut Microbiome in Functional Constipation Patients,Evidence-based complementary and alternative medicine : eCAM,2021,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Control group,Experimental group,Experimental group of patients before and after AMT (Acupoint Massage Therapy),51,50,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 4A,23 April 2025,Montana-D,Montana-D,Significantly differential genera between the samples from the experimental and control groups,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",1783272|1239|186801|3085636|186803|46205;1783272|1239|186801|186802|216572|1508657,Complete,KateRasheed
bsdb:33505487/2/2,33505487,case-control,33505487,10.1155/2021/1416236,NA,"Chen H., Tan P.S., Li C.P., Chen B.Z., Xu Y.Q., He Y.Q. , Ke X.",Acupoint Massage Therapy Alters the Composition of Gut Microbiome in Functional Constipation Patients,Evidence-based complementary and alternative medicine : eCAM,2021,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Control group,Experimental group,Experimental group of patients before and after AMT (Acupoint Massage Therapy),51,50,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 4A,23 April 2025,Montana-D,Montana-D,Significantly differential genera between the samples from the experimental and control groups,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,1783272|1239|186801|3085636|186803|1407607,Complete,KateRasheed
bsdb:33514807/1/1,33514807,"cross-sectional observational, not case-control",33514807,10.1038/s41598-021-82311-3,https://pubmed.ncbi.nlm.nih.gov/33514807/,"Dwiyanto J., Hussain M.H., Reidpath D., Ong K.S., Qasim A., Lee S.W.H., Lee S.M., Foo S.C., Chong C.W. , Rahman S.",Ethnicity influences the gut microbiota of individuals sharing a geographical location: a cross-sectional study from a middle-income country,Scientific reports,2021,NA,Experiment 1,Malaysia,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Chinese,Malay,Malay ethnic group living in the  Segamat Malaysian community.,65,46,NA,16S,34,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 1,Figure 4.,12 July 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks","Multi-ethnic comparison of (a) gut enterotype profiles analyzed using Dirichlet Multinomial Model, and (b) Prevotella: Bacteroides ratio analyzed using a linear mixed model (likelihood ratio test p<0.05).",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,Fatima
bsdb:33514807/1/2,33514807,"cross-sectional observational, not case-control",33514807,10.1038/s41598-021-82311-3,https://pubmed.ncbi.nlm.nih.gov/33514807/,"Dwiyanto J., Hussain M.H., Reidpath D., Ong K.S., Qasim A., Lee S.W.H., Lee S.M., Foo S.C., Chong C.W. , Rahman S.",Ethnicity influences the gut microbiota of individuals sharing a geographical location: a cross-sectional study from a middle-income country,Scientific reports,2021,NA,Experiment 1,Malaysia,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Chinese,Malay,Malay ethnic group living in the  Segamat Malaysian community.,65,46,NA,16S,34,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 2,"Figure 4, text",12 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Fatima,WikiWorks","Multi-ethnic comparison of (a) gut enterotype profiles analyzed using Dirichlet Multinomial Model, and (b) Prevotella: Bacteroides ratio analyzed using a linear mixed model (likelihood ratio test p<0.05).",decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,Fatima
bsdb:33514807/2/1,33514807,"cross-sectional observational, not case-control",33514807,10.1038/s41598-021-82311-3,https://pubmed.ncbi.nlm.nih.gov/33514807/,"Dwiyanto J., Hussain M.H., Reidpath D., Ong K.S., Qasim A., Lee S.W.H., Lee S.M., Foo S.C., Chong C.W. , Rahman S.",Ethnicity influences the gut microbiota of individuals sharing a geographical location: a cross-sectional study from a middle-income country,Scientific reports,2021,NA,Experiment 2,Malaysia,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Chinese,India,India ethnic group living in the  Segamat Malaysian community.,65,49,NA,16S,34,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 1,Figure 4,13 July 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks","Multi-ethnic comparison of (a) gut enterotype profiles analyzed using Dirichlet Multinomial Model, and (b) Prevotella: Bacteroides ratio analyzed using a linear mixed model (likelihood ratio test p<0.05).",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,Fatima
bsdb:33514807/2/2,33514807,"cross-sectional observational, not case-control",33514807,10.1038/s41598-021-82311-3,https://pubmed.ncbi.nlm.nih.gov/33514807/,"Dwiyanto J., Hussain M.H., Reidpath D., Ong K.S., Qasim A., Lee S.W.H., Lee S.M., Foo S.C., Chong C.W. , Rahman S.",Ethnicity influences the gut microbiota of individuals sharing a geographical location: a cross-sectional study from a middle-income country,Scientific reports,2021,NA,Experiment 2,Malaysia,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Chinese,India,India ethnic group living in the  Segamat Malaysian community.,65,49,NA,16S,34,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 2,Figure 4,13 July 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks","Multi-ethnic comparison of (a) gut enterotype profiles analyzed using Dirichlet Multinomial Model, and (b) Prevotella: Bacteroides ratio analyzed using a linear mixed model (likelihood ratio test p<0.05).",decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,Fatima
bsdb:33514807/3/1,33514807,"cross-sectional observational, not case-control",33514807,10.1038/s41598-021-82311-3,https://pubmed.ncbi.nlm.nih.gov/33514807/,"Dwiyanto J., Hussain M.H., Reidpath D., Ong K.S., Qasim A., Lee S.W.H., Lee S.M., Foo S.C., Chong C.W. , Rahman S.",Ethnicity influences the gut microbiota of individuals sharing a geographical location: a cross-sectional study from a middle-income country,Scientific reports,2021,NA,Experiment 3,Malaysia,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Chinese,Jakun,Jakun ethnic group living in the  Segamat Malaysian community.,65,54,NA,16S,34,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 1,Figure 4,13 July 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks","Description: Multi-ethnic comparison of (a) gut enterotype profiles analyzed using Dirichlet Multinomial Model, and (b) Prevotella: Bacteroides ratio analyzed using a linear mixed model (likelihood ratio test p<0.05).",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,Fatima
bsdb:33514807/3/2,33514807,"cross-sectional observational, not case-control",33514807,10.1038/s41598-021-82311-3,https://pubmed.ncbi.nlm.nih.gov/33514807/,"Dwiyanto J., Hussain M.H., Reidpath D., Ong K.S., Qasim A., Lee S.W.H., Lee S.M., Foo S.C., Chong C.W. , Rahman S.",Ethnicity influences the gut microbiota of individuals sharing a geographical location: a cross-sectional study from a middle-income country,Scientific reports,2021,NA,Experiment 3,Malaysia,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Chinese,Jakun,Jakun ethnic group living in the  Segamat Malaysian community.,65,54,NA,16S,34,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 2,Figure 4,13 July 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks","Description: Multi-ethnic comparison of (a) gut enterotype profiles analyzed using Dirichlet Multinomial Model, and (b) Prevotella: Bacteroides ratio analyzed using a linear mixed model (likelihood ratio test p<0.05).",decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,Fatima
bsdb:33514807/4/1,33514807,"cross-sectional observational, not case-control",33514807,10.1038/s41598-021-82311-3,https://pubmed.ncbi.nlm.nih.gov/33514807/,"Dwiyanto J., Hussain M.H., Reidpath D., Ong K.S., Qasim A., Lee S.W.H., Lee S.M., Foo S.C., Chong C.W. , Rahman S.",Ethnicity influences the gut microbiota of individuals sharing a geographical location: a cross-sectional study from a middle-income country,Scientific reports,2021,NA,Experiment 4,Malaysia,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,India,Malay,Malay ethnic group living in the  Segamat Malaysian community.,49,46,NA,16S,34,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,"demographics,diet,health,hygiene",unchanged,unchanged,NA,NA,NA,NA,Signature 1,FIGURE 5,13 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Fatima,WikiWorks","Taxa were significantly differentially abundant across ethnicity in Segamat as analyzed using ALDEx2 generalized linear model (FDR<0.1). Description: IM Indian–Malay, JI Jakun–Indian.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239|186801|186802|216572;1783272|1239|186801|186802,Complete,Fatima
bsdb:33514807/5/1,33514807,"cross-sectional observational, not case-control",33514807,10.1038/s41598-021-82311-3,https://pubmed.ncbi.nlm.nih.gov/33514807/,"Dwiyanto J., Hussain M.H., Reidpath D., Ong K.S., Qasim A., Lee S.W.H., Lee S.M., Foo S.C., Chong C.W. , Rahman S.",Ethnicity influences the gut microbiota of individuals sharing a geographical location: a cross-sectional study from a middle-income country,Scientific reports,2021,NA,Experiment 5,Malaysia,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Jakun,India,India ethnic group living in the  Segamat Malaysian community.,54,49,NA,16S,34,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,"demographics,diet,health,hygiene",unchanged,unchanged,NA,NA,NA,NA,Signature 1,FIGURE 5,13 July 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks",Taxa were significantly differentially abundant across ethnicity in Segamat as analyzed using ALDEx2 generalized linear model (FDR<0.1). Description:  JI Jakun–Indian.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum",1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|1686,Complete,Fatima
bsdb:33514807/5/2,33514807,"cross-sectional observational, not case-control",33514807,10.1038/s41598-021-82311-3,https://pubmed.ncbi.nlm.nih.gov/33514807/,"Dwiyanto J., Hussain M.H., Reidpath D., Ong K.S., Qasim A., Lee S.W.H., Lee S.M., Foo S.C., Chong C.W. , Rahman S.",Ethnicity influences the gut microbiota of individuals sharing a geographical location: a cross-sectional study from a middle-income country,Scientific reports,2021,NA,Experiment 5,Malaysia,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Jakun,India,India ethnic group living in the  Segamat Malaysian community.,54,49,NA,16S,34,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,"demographics,diet,health,hygiene",unchanged,unchanged,NA,NA,NA,NA,Signature 2,FIGURE 5,13 July 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks",Taxa were significantly differentially abundant across ethnicity in Segamat as analyzed using ALDEx2 generalized linear model (FDR<0.1). Description: JI Jakun–Indian.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella quasipneumoniae,3379134|1224|1236|91347|543|570|1463165,Complete,Fatima
bsdb:33517890/1/1,33517890,laboratory experiment,33517890,10.1186/s40168-020-00988-6,NA,"Hou Y.F., Shan C., Zhuang S.Y., Zhuang Q.Q., Ghosh A., Zhu K.C., Kong X.K., Wang S.M., Gong Y.L., Yang Y.Y., Tao B., Sun L.H., Zhao H.Y., Guo X.Z., Wang W.Q., Ning G., Gu Y.Y., Li S.T. , Liu J.M.",Gut microbiota-derived propionate mediates the neuroprotective effect of osteocalcin in a mouse model of Parkinson's disease,Microbiome,2021,"Gut microbiota, Osteocalcin, Parkinson’s disease, Propionate",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control group,6-hydroxydopamine (6-OHDA) group,6-OHDA was injected into the right striatum to establish the Parkinson Disease mouse model. 6-OHDA is a hydroxylated analog of the natural dopamine neurotransmitter and used to destroy nigral dopaminergic neurons and deplete the striatum of DA neurotransmitter after the injection,12,8,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 4D and Supplementary Table 5,28 March 2025,MyleeeA,MyleeeA,Different Relative Abundances of gut microbiota in 6-OHDA-induced vs Control,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Hymenochaetales|f__Rickenellaceae",1783272|1239;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;4751|5204|155619|139380|1124673,Complete,Svetlana up
bsdb:33517890/1/2,33517890,laboratory experiment,33517890,10.1186/s40168-020-00988-6,NA,"Hou Y.F., Shan C., Zhuang S.Y., Zhuang Q.Q., Ghosh A., Zhu K.C., Kong X.K., Wang S.M., Gong Y.L., Yang Y.Y., Tao B., Sun L.H., Zhao H.Y., Guo X.Z., Wang W.Q., Ning G., Gu Y.Y., Li S.T. , Liu J.M.",Gut microbiota-derived propionate mediates the neuroprotective effect of osteocalcin in a mouse model of Parkinson's disease,Microbiome,2021,"Gut microbiota, Osteocalcin, Parkinson’s disease, Propionate",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control group,6-hydroxydopamine (6-OHDA) group,6-OHDA was injected into the right striatum to establish the Parkinson Disease mouse model. 6-OHDA is a hydroxylated analog of the natural dopamine neurotransmitter and used to destroy nigral dopaminergic neurons and deplete the striatum of DA neurotransmitter after the injection,12,8,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 4D and Supplementary Table 5,28 March 2025,MyleeeA,MyleeeA,Different Relative Abundances of gut microbiota in 6-OHDA-induced vs Control,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Hymenochaetales|f__Rickenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",3379134|976;1783272|1239|526524|526525|128827;3379134|976|200643|171549|2005473;4751|5204|155619|139380|1124673;3379134|976|200643|171549|2005473,Complete,Svetlana up
bsdb:33517890/2/1,33517890,laboratory experiment,33517890,10.1186/s40168-020-00988-6,NA,"Hou Y.F., Shan C., Zhuang S.Y., Zhuang Q.Q., Ghosh A., Zhu K.C., Kong X.K., Wang S.M., Gong Y.L., Yang Y.Y., Tao B., Sun L.H., Zhao H.Y., Guo X.Z., Wang W.Q., Ning G., Gu Y.Y., Li S.T. , Liu J.M.",Gut microbiota-derived propionate mediates the neuroprotective effect of osteocalcin in a mouse model of Parkinson's disease,Microbiome,2021,"Gut microbiota, Osteocalcin, Parkinson’s disease, Propionate",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,6-OHDA + OCN (Osteocalcin) group,6-hydroxydopamine (6-OHDA) group,6-OHDA was injected into the right striatum to establish the Parkinson Disease mouse model. 6-OHDA is a hydroxylated analog of the natural dopamine neurotransmitter and used to destroy nigral dopaminergic neurons and deplete the striatum of DA neurotransmitter after the injection.,7,8,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 4D and Supplementary Table 5,28 March 2025,MyleeeA,MyleeeA,Different Relative Abundances of gut microbiota in 6-OHDA-induced vs 6-OHDA + OCN (Osteocalcin) group.,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:33517890/2/2,33517890,laboratory experiment,33517890,10.1186/s40168-020-00988-6,NA,"Hou Y.F., Shan C., Zhuang S.Y., Zhuang Q.Q., Ghosh A., Zhu K.C., Kong X.K., Wang S.M., Gong Y.L., Yang Y.Y., Tao B., Sun L.H., Zhao H.Y., Guo X.Z., Wang W.Q., Ning G., Gu Y.Y., Li S.T. , Liu J.M.",Gut microbiota-derived propionate mediates the neuroprotective effect of osteocalcin in a mouse model of Parkinson's disease,Microbiome,2021,"Gut microbiota, Osteocalcin, Parkinson’s disease, Propionate",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,6-OHDA + OCN (Osteocalcin) group,6-hydroxydopamine (6-OHDA) group,6-OHDA was injected into the right striatum to establish the Parkinson Disease mouse model. 6-OHDA is a hydroxylated analog of the natural dopamine neurotransmitter and used to destroy nigral dopaminergic neurons and deplete the striatum of DA neurotransmitter after the injection.,7,8,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 4D and Supplementary Table 5,28 March 2025,MyleeeA,MyleeeA,Different Relative Abundances of gut microbiota in 6-OHDA-induced vs 6-OHDA + OCN (Osteocalcin) group.,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Hymenochaetales|f__Rickenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Hymenochaetales|f__Rickenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",3379134|976;1783272|1239|526524|526525|128827;3379134|976|200643|171549|2005473;4751|5204|155619|139380|1124673;3379134|1224|28216|80840;4751|5204|155619|139380|1124673;3379134|976|200643|171549|2005473,Complete,Svetlana up
bsdb:33523001/1/1,33523001,case-control,33523001,10.3233/JAD-201040,NA,"Guo M., Peng J., Huang X., Xiao L., Huang F. , Zuo Z.",Gut Microbiome Features of Chinese Patients Newly Diagnosed with Alzheimer's Disease or Mild Cognitive Impairment,Journal of Alzheimer's disease : JAD,2021,"Alzheimer’s disease, Chinese, gut microbiome, mild cognitive impairment",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healthy controls (CON),Alzheimer's Disease (AD),Patients newly diagnosed with Alzheimer's Disease,18,18,NA,16S,34,Illumina,relative abundances,LEfSe,0.01,FALSE,2,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3 A + Figure 4,3 November 2024,AaishahM,"AaishahM,WikiWorks",Different abundances in bacterial taxa among AD and control patients,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,s__uncultured bacterium",3379134|1224|1236|135624;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|171552;3379134|1224|1236|135624|83763;77133,Complete,NA
bsdb:33523001/1/2,33523001,case-control,33523001,10.3233/JAD-201040,NA,"Guo M., Peng J., Huang X., Xiao L., Huang F. , Zuo Z.",Gut Microbiome Features of Chinese Patients Newly Diagnosed with Alzheimer's Disease or Mild Cognitive Impairment,Journal of Alzheimer's disease : JAD,2021,"Alzheimer’s disease, Chinese, gut microbiome, mild cognitive impairment",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healthy controls (CON),Alzheimer's Disease (AD),Patients newly diagnosed with Alzheimer's Disease,18,18,NA,16S,34,Illumina,relative abundances,LEfSe,0.01,FALSE,2,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3 A,3 November 2024,AaishahM,"AaishahM,WikiWorks",Different abundances in bacterial taxa among AD and control patients,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales,k__Thermotogati|p__Synergistota|c__Synergistia,k__Thermotogati|p__Synergistota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae",1783272|1239|909932|1843488|909930;1783272|1239|909932|1843488;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|817;1783272|1239|186801|3085636|186803|572511;3379134|1224|28216|80840|119060;3384194|508458|649775|649776|649777|508459;1783272|1239|186801|3085636|186803|189330;3379134|976|117743|200644|49546;3379134|976|117743|200644;3379134|1224|1236;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|2005525|375288;1783272|1239|909932|1843488|909930|33024;3379134|1224;3384194|508458|649775|649776|649777;3384194|508458|649775|649776;3384194|508458|649775;3384194|508458;3379134|976|200643|171549|2005525,Complete,NA
bsdb:33523001/2/1,33523001,case-control,33523001,10.3233/JAD-201040,NA,"Guo M., Peng J., Huang X., Xiao L., Huang F. , Zuo Z.",Gut Microbiome Features of Chinese Patients Newly Diagnosed with Alzheimer's Disease or Mild Cognitive Impairment,Journal of Alzheimer's disease : JAD,2021,"Alzheimer’s disease, Chinese, gut microbiome, mild cognitive impairment",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healthy controls (CON),Mild Cognitive Impairment (MCI),Patients with mild cognitive impairment,18,20,NA,16S,34,Illumina,relative abundances,LEfSe,0.01,FALSE,2,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3 B,4 November 2024,AaishahM,"AaishahM,WikiWorks",Different abundances in bacterial taxa among MCI and control patients,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Bacillota|g__Negativibacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__uncultured Alistipes sp.",3379134|976|200643|171549|171552|838;1783272|544448;1783272|544448|31969;1783272|1239|1980693;3379134|976|200643|171549|171550|239759|538949,Complete,NA
bsdb:33523001/2/2,33523001,case-control,33523001,10.3233/JAD-201040,NA,"Guo M., Peng J., Huang X., Xiao L., Huang F. , Zuo Z.",Gut Microbiome Features of Chinese Patients Newly Diagnosed with Alzheimer's Disease or Mild Cognitive Impairment,Journal of Alzheimer's disease : JAD,2021,"Alzheimer’s disease, Chinese, gut microbiome, mild cognitive impairment",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healthy controls (CON),Mild Cognitive Impairment (MCI),Patients with mild cognitive impairment,18,20,NA,16S,34,Illumina,relative abundances,LEfSe,0.01,FALSE,2,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3 B,4 November 2024,AaishahM,"AaishahM,WikiWorks",Different abundances in bacterial taxa among MCI and control patients,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia massiliensis (ex Durand et al. 2017),k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|186801|3085636|186803|572511|1737424;1783272|1239|186801|3085636|186803|189330;1783272|1239|909932|1843489|31977|29465;3379134|976|200643|171549|815|816|817;1783272|1239|186801|3085636|186803|28050;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816,Complete,NA
bsdb:33523001/3/1,33523001,case-control,33523001,10.3233/JAD-201040,NA,"Guo M., Peng J., Huang X., Xiao L., Huang F. , Zuo Z.",Gut Microbiome Features of Chinese Patients Newly Diagnosed with Alzheimer's Disease or Mild Cognitive Impairment,Journal of Alzheimer's disease : JAD,2021,"Alzheimer’s disease, Chinese, gut microbiome, mild cognitive impairment",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Mild Cognitive Impairment (MCI),Alzheimer's Disease (AD),Patients newly diagnosed with Alzheimer's Disease,20,18,6 months,16S,34,Illumina,relative abundances,LEfSe,0.01,FALSE,2,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3 C,14 November 2024,AaishahM,"AaishahM,WikiWorks",Different abundances in bacterial taxa among AD and MCI patients,decreased,"k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter piscolens,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales,k__Pseudomonadati|p__Lentisphaerota,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Thermotogati|p__Synergistota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis|s__Merdimmobilis hominis,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales,k__Thermotogati|p__Synergistota|c__Synergistia,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__uncultured Roseburia sp.,k__Bacillati|p__Bacillota|g__Negativibacillus,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota",3384194|508458|649775|649776|3029088|638847|638849;3384194|508458|649775|649776|3029088|638847;3379134|976|117743|200644|49546;3379134|256845|1313211|278082;3379134|256845;3379134|256845|1313211;3379134|976|117743|200644;3384194|508458;1783272|1239|186801|186802|216572|3028852|2897707;3384194|508458|649775|649776;3384194|508458|649775;3384194|508458|649775|649776|649777|508459;3384194|508458|649775|649776|649777;1783272|1239|186801|186802|216572|3028852;1783272|1239|186801|3085636|186803|841|512314;1783272|1239|1980693;1783272|544448|31969;1783272|544448;1783272|1239|186801|186802|216572|459786;3379134|1224|28216|80840|995019|40544;3379134|1224|28216|80840|119060;3379134|1224,Complete,NA
bsdb:33531650/1/1,33531650,case-control,33531650,10.1038/s41598-021-82538-0,https://pubmed.ncbi.nlm.nih.gov/33531650/,"Das T., Jayasudha R., Chakravarthy S., Prashanthi G.S., Bhargava A., Tyagi M., Rani P.K., Pappuru R.R., Sharma S. , Shivaji S.",Alterations in the gut bacterial microbiome in people with type 2 diabetes mellitus and diabetic retinopathy,Scientific reports,2021,NA,Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals having Type 2 Diabetes Mellitus without Diabetic Retinopathy,"Individuals having Type 2 Diabetes Mellitus without Diabetic Retinopathy (T2D group); the T2DM cohort included subjects (a) positive for at least one of the three biochemical tests (HbA1c > 7%, fasting blood sugar > 120 mg% and post-prandial blood sugar > 200 mg%); (b) had history of taking anti-diabetic medications (Metformin or combinations of Metformin and / or Insulin) and (c) had no clinical signs of DR",30,24,3 months,16S,34,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,"age,diet,region,sex",NA,NA,increased,increased,unchanged,NA,increased,Signature 1,"Table 2, Table 3",5 July 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1,WikiWorks",Decreased abundance of bacterial communities in individuals with Type 2 Diabetes compared to healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Thermoproteati|p__Thermoproteota,k__Pseudomonadati|p__Elusimicrobiota,k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|572511;3379134|1224|28216|80840|80864|283;1783272|1239|186801|3085636|186803|33042;1783275|28889;3379134|74152;3384189|32066;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|28050;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3085636|186803|841;3379134|1224|28216|80840|995019|40544;1783272|1239|526524|526525|2810281|191303,Complete,Claregrieve1
bsdb:33531650/1/2,33531650,case-control,33531650,10.1038/s41598-021-82538-0,https://pubmed.ncbi.nlm.nih.gov/33531650/,"Das T., Jayasudha R., Chakravarthy S., Prashanthi G.S., Bhargava A., Tyagi M., Rani P.K., Pappuru R.R., Sharma S. , Shivaji S.",Alterations in the gut bacterial microbiome in people with type 2 diabetes mellitus and diabetic retinopathy,Scientific reports,2021,NA,Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals having Type 2 Diabetes Mellitus without Diabetic Retinopathy,"Individuals having Type 2 Diabetes Mellitus without Diabetic Retinopathy (T2D group); the T2DM cohort included subjects (a) positive for at least one of the three biochemical tests (HbA1c > 7%, fasting blood sugar > 120 mg% and post-prandial blood sugar > 200 mg%); (b) had history of taking anti-diabetic medications (Metformin or combinations of Metformin and / or Insulin) and (c) had no clinical signs of DR",30,24,3 months,16S,34,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,"age,diet,region,sex",NA,NA,increased,increased,unchanged,NA,increased,Signature 2,"Table 2, Table 3",5 July 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1,WikiWorks",Increased abundance of microbial communities in individuals with Type 2 Diabetes compared to healthy controls,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Methanobacteriati|p__Methanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Pseudomonadati|p__Lentisphaerota,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Pseudomonadati|p__Spirochaetota,k__Thermotogati|p__Synergistota,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",1783272|1239|909932|1843488|909930|904;3379134|976|200643|171549|1853231|574697;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|561;3366610|28890;1783272|1239|186801|3085636|186803|140625;3379134|256845;3366610|28890|183925|2158|2159|2172;3379134|203691;3384194|508458;3379134|203691|203692|136|2845253|157;1783272|1239|91061|186826|33958|46255,Complete,Claregrieve1
bsdb:33531650/2/1,33531650,case-control,33531650,10.1038/s41598-021-82538-0,https://pubmed.ncbi.nlm.nih.gov/33531650/,"Das T., Jayasudha R., Chakravarthy S., Prashanthi G.S., Bhargava A., Tyagi M., Rani P.K., Pappuru R.R., Sharma S. , Shivaji S.",Alterations in the gut bacterial microbiome in people with type 2 diabetes mellitus and diabetic retinopathy,Scientific reports,2021,NA,Experiment 2,India,Homo sapiens,Feces,UBERON:0001988,Diabetic retinopathy,EFO:0003770,Healthy controls,Individuals diagnosed with Type 2 Diabetes and clinically manifest Diabetic Retinopathy (DR),Individuals diagnosed with Type 2 Diabetes and clinically manifest Diabetic Retinopathy (DR); Subjects confirmed to having DR based on the fundus examination/photograph followed by fundus fluorescein angiography (FFA) and optical coherence tomography (OCT).,30,28,3 months,16S,34,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,"age,diet,region,sex",NA,NA,increased,unchanged,unchanged,NA,unchanged,Signature 1,"Table 2, Table 4",5 July 2021,Madhubani Dey,"Madhubani Dey,Fatima,Claregrieve1,WikiWorks",Differential microbial abundance of bacterial communities in individuals diagnosed with Type 2 Diabetes and Diabetic Retinopathy (DR) compared with healthy controls,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,p__Candidatus Saccharimonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Thermoproteati|p__Thermoproteota,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Spirochaetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",1783272|201174;1783272|1239|909932|909929|1843491|82373;1783272|544448|31969|186332|186333|2152;3379134|976;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|526524|526525|128827|118747;1783272|1239|186801|3085636|186803|830;95818;1783272|1239|186801|186802|31979|1485;3379134|1224|28216|80840|80864|283;1783275|28889;3379134|200940|3031449|213115|194924|872;3379134|1224|1236|91347|1903409|551;1783272|1239|186801|186802|216572|216851;3384189|32066;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|28050;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|909929|1843491|52225;1783272|1239|186801|3085636|186803|841;1783272|201174|1760|85006|1268|32207;3379134|203691;1783272|1239|91061|186826|1300|1301;3379134|1224|28216|80840|995019|40544;1783272|1239|526524|526525|2810281|191303,Complete,Claregrieve1
bsdb:33531650/2/2,33531650,case-control,33531650,10.1038/s41598-021-82538-0,https://pubmed.ncbi.nlm.nih.gov/33531650/,"Das T., Jayasudha R., Chakravarthy S., Prashanthi G.S., Bhargava A., Tyagi M., Rani P.K., Pappuru R.R., Sharma S. , Shivaji S.",Alterations in the gut bacterial microbiome in people with type 2 diabetes mellitus and diabetic retinopathy,Scientific reports,2021,NA,Experiment 2,India,Homo sapiens,Feces,UBERON:0001988,Diabetic retinopathy,EFO:0003770,Healthy controls,Individuals diagnosed with Type 2 Diabetes and clinically manifest Diabetic Retinopathy (DR),Individuals diagnosed with Type 2 Diabetes and clinically manifest Diabetic Retinopathy (DR); Subjects confirmed to having DR based on the fundus examination/photograph followed by fundus fluorescein angiography (FFA) and optical coherence tomography (OCT).,30,28,3 months,16S,34,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,"age,diet,region,sex",NA,NA,increased,unchanged,unchanged,NA,unchanged,Signature 2,"Table 2, Table 4",5 July 2021,Madhubani Dey,"Madhubani Dey,Fatima,Claregrieve1,WikiWorks",Differential microbial abundance of bacterial communities in individuals diagnosed with Type 2 Diabetes and Diabetic Retinopathy (DR) compared with healthy controls,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Methanobacteriati|p__Methanobacteriota,k__Pseudomonadati|p__Lentisphaerota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Thermotogati|p__Synergistota,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Verrucomicrobiota",1783272|1239|909932|1843488|909930|904;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;3384194|508458|649775|649776|649777|508459;3379134|1224|1236|91347|543|547;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|561;3366610|28890;3379134|256845;1783272|1239|909932|909929|1843491|158846;3379134|1224|28216|80840|75682|846;3379134|976|200643|171549|2005525|375288;3379134|1224|1236|91347|543|620;3384194|508458;1783272|544448;3379134|74201,Complete,Claregrieve1
bsdb:33531650/3/1,33531650,case-control,33531650,10.1038/s41598-021-82538-0,https://pubmed.ncbi.nlm.nih.gov/33531650/,"Das T., Jayasudha R., Chakravarthy S., Prashanthi G.S., Bhargava A., Tyagi M., Rani P.K., Pappuru R.R., Sharma S. , Shivaji S.",Alterations in the gut bacterial microbiome in people with type 2 diabetes mellitus and diabetic retinopathy,Scientific reports,2021,NA,Experiment 3,India,Homo sapiens,Feces,UBERON:0001988,Diabetic retinopathy,EFO:0003770,Individuals diagnosed with type 2 diabetes Mellitus,Individuals diagnosed with Type 2 Diabetes and clinically manifest Diabetic Retinopathy (DR),Individuals diagnosed with Type 2 Diabetes and clinically manifest Diabetic Retinopathy (DR); Subjects confirmed to having DR based on the fundus examination/photograph followed by fundus fluorescein angiography (FFA) and optical coherence tomography (OCT).,24,28,3 months,16S,34,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,"age,diet,region,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Table 2, Table 5",5 July 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1,WikiWorks",Differential microbial abundance of bacterial communities in individuals diagnosed with Type 2 Diabetes and Diabetic Retinopathy (DR) compared to individuals with only Type 2 Diabetes,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Methanobacteriati|p__Methanobacteriota,k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Pseudomonadati|p__Lentisphaerota,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Pseudomonadati|p__Spirochaetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",1783272|201174;1783272|1239|909932|909929|1843491|82373;1783272|544448|31969|186332|186333|2152;1783272|201174|1760|85004|31953|1678;3379134|200940|3031449|213115|194924|872;3379134|1224|1236|91347|1903409|551;3366610|28890;3384189|32066;3379134|1224|1236|135625|712|724;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|140625;3379134|256845;3366610|28890|183925|2158|2159|2172;1783272|1239|909932|909929|1843491|52225;3379134|203691;1783272|1239|91061|186826|1300|1301;3379134|203691|203692|136|2845253|157;1783272|1239|91061|186826|33958|46255,Complete,Claregrieve1
bsdb:33531650/3/2,33531650,case-control,33531650,10.1038/s41598-021-82538-0,https://pubmed.ncbi.nlm.nih.gov/33531650/,"Das T., Jayasudha R., Chakravarthy S., Prashanthi G.S., Bhargava A., Tyagi M., Rani P.K., Pappuru R.R., Sharma S. , Shivaji S.",Alterations in the gut bacterial microbiome in people with type 2 diabetes mellitus and diabetic retinopathy,Scientific reports,2021,NA,Experiment 3,India,Homo sapiens,Feces,UBERON:0001988,Diabetic retinopathy,EFO:0003770,Individuals diagnosed with type 2 diabetes Mellitus,Individuals diagnosed with Type 2 Diabetes and clinically manifest Diabetic Retinopathy (DR),Individuals diagnosed with Type 2 Diabetes and clinically manifest Diabetic Retinopathy (DR); Subjects confirmed to having DR based on the fundus examination/photograph followed by fundus fluorescein angiography (FFA) and optical coherence tomography (OCT).,24,28,3 months,16S,34,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,"age,diet,region,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Table 2, Table 5",5 July 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1,WikiWorks",Differential microbial abundance of bacterial communities in individuals diagnosed with Type 2 Diabetes and Diabetic Retinopathy (DR) compared to individuals with only Type 2 Diabetes,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Pseudomonadati|p__Elusimicrobiota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Thermotogati|p__Synergistota,k__Pseudomonadati|p__Verrucomicrobiota",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;3384194|508458|649775|649776|649777|508459;3379134|74152;1783272|1239|91061|186826|81852|1350;1783272|1239|909932|1843488|909930|33024;3379134|1224|1236|91347|543|620;3384194|508458;3379134|74201,Complete,Claregrieve1
bsdb:33536555/1/2,33536555,"cross-sectional observational, not case-control",33536555,10.1038/s41598-021-82709-z,NA,"Wang Q., Chen X., Hu H., Wei X., Wang X., Peng Z., Ma R., Zhao Q., Zhao J., Liu J. , Deng F.",Structural changes in the oral microbiome of the adolescent patients with moderate or severe dental fluorosis,Scientific reports,2021,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Dental fluorosis,EFO:1000892,Healthy,M&S (Moderate/Severe),"This group includes participants diagnosed with dental fluorosis according to the Dean’s Index, specifically those categorized as Code 4 (moderate) and Code 5 (severe).

    Code 4 (Moderate): Characterized by extensive brown or yellow-brown staining with mild enamel wear.
    Code 5 (Severe): Characterized by deep stains, obvious pits, and increased enamel brittleness.",9,19,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 3C, 4A",13 November 2024,LiliGC,"LiliGC,KateRasheed,WikiWorks",Significantly different bacterial species between Healthy and M&S group based on LEfSe analysis.,increased,"k__Bacillati|p__Bacillota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Morococcus|s__Morococcus cerebrosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella parahaemolysans",1783272|1239;3384189|32066|203490|203491|203492|848|851;1783272|1239|91061|186826|186828|117563|137732;1783272|1239|91061|186826|1300|1357|1358;3379134|1224|28216|206351|481|212742|1056807;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|91061|1385|539738|1378|1179782,Complete,Svetlana up
bsdb:33536555/1/3,33536555,"cross-sectional observational, not case-control",33536555,10.1038/s41598-021-82709-z,NA,"Wang Q., Chen X., Hu H., Wei X., Wang X., Peng Z., Ma R., Zhao Q., Zhao J., Liu J. , Deng F.",Structural changes in the oral microbiome of the adolescent patients with moderate or severe dental fluorosis,Scientific reports,2021,NA,Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Dental fluorosis,EFO:1000892,Healthy,M&S (Moderate/Severe),"This group includes participants diagnosed with dental fluorosis according to the Dean’s Index, specifically those categorized as Code 4 (moderate) and Code 5 (severe).

    Code 4 (Moderate): Characterized by extensive brown or yellow-brown staining with mild enamel wear.
    Code 5 (Severe): Characterized by deep stains, obvious pits, and increased enamel brittleness.",9,19,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 3,"Figure 3C, 4A",15 November 2024,LiliGC,"LiliGC,KateRasheed,WikiWorks",Significantly different bacterial species between Healthy and M&S group based on LEfSe analysis.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella shahii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] sulci,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum umeaense",3379134|976|200643|171549|171552|1283313|76122;3379134|976;3379134|976|200643|171549|171552|2974257|228603;1783272|1239|186801|3085636|186803|265975|1501329;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552|838|60133;1783272|201174|1760|2037|2049|2529408|1660;3379134|976|200643|171549|171552|2974251|228604;1783272|1239|186801|3082720|543314|143393;1783272|1239|186801|3085636|186803|1164882|617123,Complete,Svetlana up
bsdb:33536555/3/1,33536555,"cross-sectional observational, not case-control",33536555,10.1038/s41598-021-82709-z,NA,"Wang Q., Chen X., Hu H., Wei X., Wang X., Peng Z., Ma R., Zhao Q., Zhao J., Liu J. , Deng F.",Structural changes in the oral microbiome of the adolescent patients with moderate or severe dental fluorosis,Scientific reports,2021,NA,Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Dental fluorosis,EFO:1000892,Healthy,M&S (Moderate/Severe),"This group includes participants diagnosed with dental fluorosis according to the Dean’s Index, specifically those categorized as Code 4 (moderate) and Code 5 (severe).

Code 4 (Moderate): Characterized by extensive brown or yellow-brown staining with mild enamel wear.
 Code 5 (Severe): Characterized by deep stains, obvious pits, and increased enamel brittleness.",9,19,6 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Fig. 4C, 4E, 4G",20 November 2024,KateRasheed,"KateRasheed,WikiWorks",Significantly different bacterial species between Healthy and M&S group based on Wilcoxon analysis.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella parahaemolysans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis",1783272|1239|91061|186826|1300|1301|28037;1783272|1239|91061|1385|539738|1378|1179782;1783272|1239|91061|186826|1300|1357|1358,Complete,Svetlana up
bsdb:33536555/3/2,33536555,"cross-sectional observational, not case-control",33536555,10.1038/s41598-021-82709-z,NA,"Wang Q., Chen X., Hu H., Wei X., Wang X., Peng Z., Ma R., Zhao Q., Zhao J., Liu J. , Deng F.",Structural changes in the oral microbiome of the adolescent patients with moderate or severe dental fluorosis,Scientific reports,2021,NA,Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Dental fluorosis,EFO:1000892,Healthy,M&S (Moderate/Severe),"This group includes participants diagnosed with dental fluorosis according to the Dean’s Index, specifically those categorized as Code 4 (moderate) and Code 5 (severe).

Code 4 (Moderate): Characterized by extensive brown or yellow-brown staining with mild enamel wear.
 Code 5 (Severe): Characterized by deep stains, obvious pits, and increased enamel brittleness.",9,19,6 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Fig. 4D, 4F",20 November 2024,KateRasheed,"KateRasheed,WikiWorks",Significantly different bacterial species between Healthy and M&S group based on Wilcoxon analysis.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica",3379134|976|200643|171549|171552|838|28132;1783272|201174|1760|2037|2049|2529408|1660,Complete,Svetlana up
bsdb:33536555/4/1,33536555,"cross-sectional observational, not case-control",33536555,10.1038/s41598-021-82709-z,NA,"Wang Q., Chen X., Hu H., Wei X., Wang X., Peng Z., Ma R., Zhao Q., Zhao J., Liu J. , Deng F.",Structural changes in the oral microbiome of the adolescent patients with moderate or severe dental fluorosis,Scientific reports,2021,NA,Experiment 4,China,Homo sapiens,Saliva,UBERON:0001836,Dental fluorosis,EFO:1000892,Mild,M&S (Moderate/Severe),"This group includes participants diagnosed with dental fluorosis according to the Dean’s Index, specifically those categorized as Code 4 (moderate) and Code 5 (severe). Code 4 (Moderate): Characterized by extensive brown or yellow-brown staining with mild enamel wear. Code 5 (Severe): Characterized by deep stains, obvious pits, and increased enamel brittleness.",14,19,6 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Fig. 4C, 4E, 4G-H",20 November 2024,KateRasheed,"KateRasheed,WikiWorks",Significantly different bacterial species between Mild and M&S group based on Wilcoxon analysis.,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella parahaemolysans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis",3384189|32066|203490|203491|203492|848|851;1783272|1239|91061|1385|539738|1378|1179782;1783272|1239|91061|186826|1300|1357|1358;1783272|1239|91061|186826|1300|1301|28037,Complete,Svetlana up
bsdb:33536555/4/2,33536555,"cross-sectional observational, not case-control",33536555,10.1038/s41598-021-82709-z,NA,"Wang Q., Chen X., Hu H., Wei X., Wang X., Peng Z., Ma R., Zhao Q., Zhao J., Liu J. , Deng F.",Structural changes in the oral microbiome of the adolescent patients with moderate or severe dental fluorosis,Scientific reports,2021,NA,Experiment 4,China,Homo sapiens,Saliva,UBERON:0001836,Dental fluorosis,EFO:1000892,Mild,M&S (Moderate/Severe),"This group includes participants diagnosed with dental fluorosis according to the Dean’s Index, specifically those categorized as Code 4 (moderate) and Code 5 (severe). Code 4 (Moderate): Characterized by extensive brown or yellow-brown staining with mild enamel wear. Code 5 (Severe): Characterized by deep stains, obvious pits, and increased enamel brittleness.",14,19,6 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig. 4D,20 November 2024,KateRasheed,"KateRasheed,WikiWorks",Significantly different bacterial species between Mild and M&S group based on Wilcoxon analysis.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,3379134|976|200643|171549|171552|838|28132,Complete,Svetlana up
bsdb:33552996/1/1,33552996,case-control,33552996,10.3389/fcimb.2020.557515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7859112/,"Li H., Chen J., Ren X., Yang C., Liu S., Bai X., Shan S. , Dong X.",Gut Microbiota Composition Changes in Constipated Women of Reproductive Age,Frontiers in cellular and infection microbiology,2020,"16S rRNA gene sequencing, chronic constipation, gut microbiota, influence factors, women of reproductive age",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy women,Constipated women,Female constipated patients of reproductive age.,30,29,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 2 and Figure3f,26 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Significant Differences in the Microbiota of Constipated Women of Reproductive Age and Healthy Controls.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter",3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976;1783272|1239|909932;3379134|976|200643|171549|815|909656|310298;1783272|1239|909932|909929;1783272|1239|186801|3085636|186803|1407607;1783272|1239|91061|186826|33958;3379134|976|200643|171549|2005525;3379134|976|200643|171549|2005525|375288;3379134|1224|1236|91347|543|544,Complete,Svetlana up
bsdb:33552996/1/2,33552996,case-control,33552996,10.3389/fcimb.2020.557515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7859112/,"Li H., Chen J., Ren X., Yang C., Liu S., Bai X., Shan S. , Dong X.",Gut Microbiota Composition Changes in Constipated Women of Reproductive Age,Frontiers in cellular and infection microbiology,2020,"16S rRNA gene sequencing, chronic constipation, gut microbiota, influence factors, women of reproductive age",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy women,Constipated women,Female constipated patients of reproductive age.,30,29,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 2 and Figure3f,26 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Significant Differences in the Microbiota of Constipated Women of Reproductive Age and Healthy Controls.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|561|562;3379134|1224|1236;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|543|570|573;3379134|1224;3379134|1224|1236|91347|543;1783272|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:33557825/1/1,33557825,laboratory experiment,33557825,10.1186/s12936-021-03606-4,NA,"Omoke D., Kipsum M., Otieno S., Esalimba E., Sheth M., Lenhart A., Njeru E.M., Ochomo E. , Dada N.",Western Kenyan Anopheles gambiae showing intense permethrin resistance harbour distinct microbiota,Malaria journal,2021,"16S rRNA gene amplicon sequencing, Anopheles gambiae s.s., Insecticide resistance, Metabarcoding, Mosquito microbiome, Mosquito microbiota, pyrethroid resistance",Experiment 1,Kenya,Anopheles gambiae,Body proper,UBERON:0013702,Insecticide,CHEBI:24852,permethrin susceptible mosquito,permethrin resistant mosquito,Mosquitoes that were alive after the bioassay with permethrin insecticide were categorized as resistant,36,39,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 5,29 April 2024,Idiaru angela,"Idiaru angela,WikiWorks",Differentially abundant bacterial genera between permethrin resistant and susceptible mosquitoes determined by Lefse analysis,increased,"k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,s__uncultured bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacillati|p__Actinomycetota|c__Rubrobacteria,k__Bacillati|p__Actinomycetota",3379134|976|117747|200666|84566|28453;1783272|1239|91061|1385|186817|400634;1783272|1239|91061|186826|1300|1301;3379134|1224|28211|204441;77133;3379134|1224|28211|204441;3379134|1224|28211;1783272|201174|84995|84996|84997;1783272|201174|84995|84996;1783272|201174|84995|84996|84997|42255;1783272|201174|84995;1783272|201174,Complete,Svetlana up
bsdb:33557825/1/2,33557825,laboratory experiment,33557825,10.1186/s12936-021-03606-4,NA,"Omoke D., Kipsum M., Otieno S., Esalimba E., Sheth M., Lenhart A., Njeru E.M., Ochomo E. , Dada N.",Western Kenyan Anopheles gambiae showing intense permethrin resistance harbour distinct microbiota,Malaria journal,2021,"16S rRNA gene amplicon sequencing, Anopheles gambiae s.s., Insecticide resistance, Metabarcoding, Mosquito microbiome, Mosquito microbiota, pyrethroid resistance",Experiment 1,Kenya,Anopheles gambiae,Body proper,UBERON:0013702,Insecticide,CHEBI:24852,permethrin susceptible mosquito,permethrin resistant mosquito,Mosquitoes that were alive after the bioassay with permethrin insecticide were categorized as resistant,36,39,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 5,29 April 2024,Idiaru angela,"Idiaru angela,WikiWorks",Differentially abundant bacterial genera between permethrin resistant and susceptible mosquitoes determined by Lefse analysis,decreased,"k__Pseudomonadati|p__Myxococcota|c__Myxococcia|o__Myxococcales,c__Deltaproteobacteria,k__Pseudomonadati|p__Myxococcota|c__Myxococcia|o__Myxococcales|f__Myxococcaceae|g__Myxococcus,k__Pseudomonadati|p__Myxococcota|c__Myxococcia|o__Myxococcales|f__Myxococcaceae",3379134|2818505|32015|29;28221;3379134|2818505|32015|29|31|32;3379134|2818505|32015|29|31,Complete,Svetlana up
bsdb:33557896/1/NA,33557896,case-control,33557896,https://doi.org/10.1186/s13024-021-00427-6,https://pubmed.ncbi.nlm.nih.gov/33557896/,"Aho V.T.E., Houser M.C., Pereira P.A.B., Chang J., Rudi K., Paulin L., Hertzberg V., Auvinen P., Tansey M.G. , Scheperjans F.","Relationships of gut microbiota, short-chain fatty acids, inflammation, and the gut barrier in Parkinson's disease",Molecular neurodegeneration,2021,"Inflammation, Intestine, Microbiota, Parkinson’s disease, Short-chain fatty acids",Experiment 1,Norway,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control,Parkinson's disease patients,Patients who have Parkinson's disease,56,55,NA,16S,34,Illumina,raw counts,DESeq2,NA,TRUE,NA,"age,body mass index,sex",sex,NA,decreased,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:33565055/1/1,33565055,case-control,33565055,10.1007/s12275-021-0647-1,NA,"Kim J., Park T., Kim H.J., An S. , Sul W.J.",Inferences in microbial structural signatures of acne microbiome and mycobiome,"Journal of microbiology (Seoul, Korea)",2021,"16S rRNA gene sequencing, ITS1 region sequencing, Staphylococcus, acne, microbiome, mycobiome, skin",Experiment 1,South Korea,Homo sapiens,"Cheek,Forehead","UBERON:0001567,UBERON:0008200",Acne,EFO:0003894,Healthy group,Acne group,"Korean women aged 19-28 years with acne, a common skin condition that affects the hair follicles and sebaceous (oil) glands in the skin.",16,17,NA,16S,45,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Within results text(Taxonomic signatures of acne in bacterial and fungal ASVs, paragraph 2), Figure S3A",10 November 2023,Deacme,"Deacme,Folakunmi,WikiWorks",Result of linear discriminant analysis effect size (LEfSe) for bacteria in the cheek between acne and healthy groups,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",3379134|1224|1236|135624|84642;;1783272|201174|1760|85007|1653|1716;3379134|1224|1236|135614|32033|40323,Complete,Folakunmi
bsdb:33565055/1/2,33565055,case-control,33565055,10.1007/s12275-021-0647-1,NA,"Kim J., Park T., Kim H.J., An S. , Sul W.J.",Inferences in microbial structural signatures of acne microbiome and mycobiome,"Journal of microbiology (Seoul, Korea)",2021,"16S rRNA gene sequencing, ITS1 region sequencing, Staphylococcus, acne, microbiome, mycobiome, skin",Experiment 1,South Korea,Homo sapiens,"Cheek,Forehead","UBERON:0001567,UBERON:0008200",Acne,EFO:0003894,Healthy group,Acne group,"Korean women aged 19-28 years with acne, a common skin condition that affects the hair follicles and sebaceous (oil) glands in the skin.",16,17,NA,16S,45,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Within results text(Taxonomic signatures of acne in bacterial and fungal ASVs, paragraph 2), Figure S3A",10 November 2023,Deacme,"Deacme,Davvve,Folakunmi,WikiWorks",Result of linear discriminant analysis effect size (LEfSe)for bacteria in the cheek between acne and healthy groups,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Acidobacteriota|c__Terriglobia|o__Terriglobales|f__Candidatus Korobacteraceae|g__Candidatus Korobacter|s__Candidatus Korobacter versatilis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,",1783272|201174|1760|2037|2049|1654;3379134|57723|204432|204433|3121618|658061|658062;1783272|201174|1760|85007|1653|1716|61592;1783272|201174|1760|85007|85029|37914;3379134|1224|1236|91347|543|561|562;1783272|1239|1737404|1737405|1570339|150022;3384189|32066|203490|203491|1129771|32067;1783272|1239|186801|3085636|186803|437755;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;,Complete,Folakunmi
bsdb:33565055/2/1,33565055,case-control,33565055,10.1007/s12275-021-0647-1,NA,"Kim J., Park T., Kim H.J., An S. , Sul W.J.",Inferences in microbial structural signatures of acne microbiome and mycobiome,"Journal of microbiology (Seoul, Korea)",2021,"16S rRNA gene sequencing, ITS1 region sequencing, Staphylococcus, acne, microbiome, mycobiome, skin",Experiment 2,South Korea,Homo sapiens,"Cheek,Forehead","UBERON:0001567,UBERON:0008200",Acne,EFO:0003894,Healthy group,Acne group,"Korean women aged 19-28 years with acne, a common skin condition that affects the hair follicles and sebaceous (oil) glands in the skin.",16,17,NA,16S,45,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Within results text(Taxonomic signatures of acne in bacterial and fungal ASVs, paragraph 3), Figure S3B",10 November 2023,Deacme,"Deacme,Folakunmi,WikiWorks",Result of linear discriminant analysis effect size (LEfSe) for bacteria in the forehead between acne and healthy groups,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",1783272|201174|1760|85007|1653|1716;3379134|976|200643|171549|171551|836,Complete,Folakunmi
bsdb:33565055/3/1,33565055,case-control,33565055,10.1007/s12275-021-0647-1,NA,"Kim J., Park T., Kim H.J., An S. , Sul W.J.",Inferences in microbial structural signatures of acne microbiome and mycobiome,"Journal of microbiology (Seoul, Korea)",2021,"16S rRNA gene sequencing, ITS1 region sequencing, Staphylococcus, acne, microbiome, mycobiome, skin",Experiment 3,South Korea,Homo sapiens,"Cheek,Forehead","UBERON:0001567,UBERON:0008200",Acne,EFO:0003894,Healthy group,Acne group,"Korean women aged 19-28 years with acne, a common skin condition that affects the hair follicles and sebaceous (oil) glands in the skin.",16,17,NA,16S,45,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,Signature 1,"Within results text(Taxonomic signatures of acne in bacterial and fungal ASVs, paragraph 2),Figure S3C",10 November 2023,Deacme,"Deacme,Folakunmi,WikiWorks",Result of linear discriminant analysis effect size (LEfSe) for fungi in the cheek microbiome between acne and healthy groups.,increased,"k__Fungi|p__Mucoromycota|c__Endogonomycetes|o__Endogonales|f__Densosporaceae|g__Densospora,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia globosa",4751|1913637|2212702|4869|2052797|2570834;4751|5204|1538075|162474|742845|55193|76773,Complete,Folakunmi
bsdb:33565055/3/2,33565055,case-control,33565055,10.1007/s12275-021-0647-1,NA,"Kim J., Park T., Kim H.J., An S. , Sul W.J.",Inferences in microbial structural signatures of acne microbiome and mycobiome,"Journal of microbiology (Seoul, Korea)",2021,"16S rRNA gene sequencing, ITS1 region sequencing, Staphylococcus, acne, microbiome, mycobiome, skin",Experiment 3,South Korea,Homo sapiens,"Cheek,Forehead","UBERON:0001567,UBERON:0008200",Acne,EFO:0003894,Healthy group,Acne group,"Korean women aged 19-28 years with acne, a common skin condition that affects the hair follicles and sebaceous (oil) glands in the skin.",16,17,NA,16S,45,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,Signature 2,"Within results text(Taxonomic signatures of acne in bacterial and fungal ASVs, paragraph 2), Figure S3C",10 November 2023,Deacme,"Deacme,Folakunmi,WikiWorks",Result of linear discriminant analysis effect size (LEfSe) for fungi in the cheek microbiome between acne and healthy groups.,decreased,"k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia slooffiae,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae",4751|5204|1538075|162474|742845|55193|76775;4751|5204|1538075|162474|742845|55193|76776;4751|5204|1538075|162474;4751|4890|4891|4892|4893|4930|4932,Complete,Folakunmi
bsdb:33565055/4/1,33565055,case-control,33565055,10.1007/s12275-021-0647-1,NA,"Kim J., Park T., Kim H.J., An S. , Sul W.J.",Inferences in microbial structural signatures of acne microbiome and mycobiome,"Journal of microbiology (Seoul, Korea)",2021,"16S rRNA gene sequencing, ITS1 region sequencing, Staphylococcus, acne, microbiome, mycobiome, skin",Experiment 4,South Korea,Homo sapiens,"Cheek,Forehead","UBERON:0001567,UBERON:0008200",Acne,EFO:0003894,Healthy group,Acne group,"Korean women aged 19-28 years with acne, a common skin condition that affects the hair follicles and sebaceous (oil) glands in the skin.",16,17,NA,16S,45,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Within results text(Taxonomic signatures of acne in bacterial and fungal ASVs, paragraph 3),Figure S3D",10 November 2023,Deacme,"Deacme,Folakunmi,WikiWorks",Result of linear discriminant analysis effect size (LEfSe)for fungi in the forehead mycobiome between acne and healthy groups,increased,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia globosa,4751|5204|1538075|162474|742845|55193|76773,Complete,Folakunmi
bsdb:33565055/4/2,33565055,case-control,33565055,10.1007/s12275-021-0647-1,NA,"Kim J., Park T., Kim H.J., An S. , Sul W.J.",Inferences in microbial structural signatures of acne microbiome and mycobiome,"Journal of microbiology (Seoul, Korea)",2021,"16S rRNA gene sequencing, ITS1 region sequencing, Staphylococcus, acne, microbiome, mycobiome, skin",Experiment 4,South Korea,Homo sapiens,"Cheek,Forehead","UBERON:0001567,UBERON:0008200",Acne,EFO:0003894,Healthy group,Acne group,"Korean women aged 19-28 years with acne, a common skin condition that affects the hair follicles and sebaceous (oil) glands in the skin.",16,17,NA,16S,45,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Within results text(Taxonomic signatures of acne in bacterial and fungal ASVs, paragraph 3), Figure S3D",10 November 2023,Deacme,"Deacme,Folakunmi,WikiWorks",Result of linear discriminant analysis effect size (LEfSe)for fungi in the forehead mycobiome between acne and healthy groups,decreased,"k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia globosa,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Hymenochaetales|f__Schizoporaceae|g__Xylodon|s__Xylodon flaviporus",4751|5204|1538075|162474|742845|55193|76773;4751|5204|155619|139380|574935|1124675|2173181,Complete,Folakunmi
bsdb:33572693/1/1,33572693,"cross-sectional observational, not case-control",33572693,10.3390/microorganisms9020294,NA,"Kang G.U., Jung D.R., Lee Y.H., Jeon S.Y., Han H.S., Chong G.O. , Shin J.H.",Potential Association between Vaginal Microbiota and Cervical Carcinogenesis in Korean Women: A Cohort Study,Microorganisms,2021,"CIN prediction, CIN severity, vaginal microbiome, vaginosis",Experiment 1,South Korea,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,healthy controls,CIN 2+,Patients with cervical intraepithelial neoplasia 2 or higher,7,8,NA,16S,3,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,7,NA,NA,NA,increased,NA,increased,NA,increased,Signature 1,"Figure 2A, 2B, 2F",19 March 2021,Cynthia Anderson,"Cynthia Anderson,Atrayees,WikiWorks",Comparative analysis of vaginal microbiota profiles,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota",1783272|201174|1760|85004|31953|2701;1783272|201174;3379134|976,Complete,Atrayees
bsdb:33572693/1/2,33572693,"cross-sectional observational, not case-control",33572693,10.3390/microorganisms9020294,NA,"Kang G.U., Jung D.R., Lee Y.H., Jeon S.Y., Han H.S., Chong G.O. , Shin J.H.",Potential Association between Vaginal Microbiota and Cervical Carcinogenesis in Korean Women: A Cohort Study,Microorganisms,2021,"CIN prediction, CIN severity, vaginal microbiome, vaginosis",Experiment 1,South Korea,Homo sapiens,Vagina,UBERON:0000996,Cervical glandular intraepithelial neoplasia,EFO:1000165,healthy controls,CIN 2+,Patients with cervical intraepithelial neoplasia 2 or higher,7,8,NA,16S,3,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,7,NA,NA,NA,increased,NA,increased,NA,increased,Signature 2,"Figure 2A, 2B, 2F",19 March 2021,Cynthia Anderson,"Cynthia Anderson,Atrayees,WikiWorks",Comparative analysis of vaginal microbiota profiles,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales",1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|91061;1783272|1239|91061|186826,Complete,Atrayees
bsdb:33572693/2/1,33572693,"cross-sectional observational, not case-control",33572693,10.3390/microorganisms9020294,NA,"Kang G.U., Jung D.R., Lee Y.H., Jeon S.Y., Han H.S., Chong G.O. , Shin J.H.",Potential Association between Vaginal Microbiota and Cervical Carcinogenesis in Korean Women: A Cohort Study,Microorganisms,2021,"CIN prediction, CIN severity, vaginal microbiome, vaginosis",Experiment 2,South Korea,Homo sapiens,Vagina,UBERON:0000996,Cervical cancer,MONDO:0002974,healthy controls,cervical cancer,Patients with cervical cancer,7,8,NA,16S,3,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,7,NA,NA,NA,unchanged,NA,unchanged,NA,increased,Signature 1,"Figure 2C, 2D, 2F",19 March 2021,Cynthia Anderson,"Cynthia Anderson,Atrayees,WikiWorks",Comparative analysis of vaginal microbiota profiles,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota",1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|186801;1783272|1239|1737404|1737405;3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|838;3379134|976|200643|171549;3379134|976|200643;1783272|1239;3379134|1224,Complete,Atrayees
bsdb:33572693/2/2,33572693,"cross-sectional observational, not case-control",33572693,10.3390/microorganisms9020294,NA,"Kang G.U., Jung D.R., Lee Y.H., Jeon S.Y., Han H.S., Chong G.O. , Shin J.H.",Potential Association between Vaginal Microbiota and Cervical Carcinogenesis in Korean Women: A Cohort Study,Microorganisms,2021,"CIN prediction, CIN severity, vaginal microbiome, vaginosis",Experiment 2,South Korea,Homo sapiens,Vagina,UBERON:0000996,Cervical cancer,MONDO:0002974,healthy controls,cervical cancer,Patients with cervical cancer,7,8,NA,16S,3,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,7,NA,NA,NA,unchanged,NA,unchanged,NA,increased,Signature 2,"Figure 2C, 2D, 2F",19 March 2021,Cynthia Anderson,"Cynthia Anderson,Atrayees,WikiWorks",Comparative analysis of vaginal microbiota profiles,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Actinomycetota",1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|91061;1783272|1239|91061|186826;1783272|201174,Complete,Atrayees
bsdb:33577896/1/1,33577896,case-control,33577896,10.1016/j.jaci.2021.02.001,NA,"Rosas-Salazar C., Kimura K.S., Shilts M.H., Strickland B.A., Freeman M.H., Wessinger B.C., Gupta V., Brown H.M., Rajagopala S.V., Turner J.H. , Das S.R.",SARS-CoV-2 infection and viral load are associated with the upper respiratory tract microbiome,The Journal of allergy and clinical immunology,2021,"16S rRNA sequencing, COVID-19, SARS-CoV-2, coronavirus, microbiome, nasal, nasopharynx, respiratory",Experiment 1,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Asymptomatic uninfected controls,"Symptomatic, mild to moderate COVID-19 patients","Confirmed symptomatic mild to moderate COVID-19 patients > age 18, nonhospitalized",21,38,2 weeks,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,increased,NA,NA,increased,increased,Signature 1,Figure 3B,10 July 2021,Claregrieve1,"Claregrieve1,Peace Sandy,WikiWorks","Differences in the abundance of taxa of the URT microbiome between adults with and without SARS�CoV-2 infection. Differential abundance testing was conducted using DESeq2 models at the ASV level
including age and sex as covariates B, Bar plot depicting the log2 FCs and SEs for ASVs that were significantly
different between groups.",increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas|s__Brevundimonas sp.,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter hominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium imitans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium|s__Sphingobacterium spiritivorum",1783272|1239|1737404|1737405|1570339|165779|1872515;3379134|1224|28211|204458|76892|41275|1871086;3379134|29547|3031852|213849|72294|194|76517;1783272|201174|1760|85007|1653|1716|156978;1783272|201174|1760|85007|1653|1716|1720;1783272|1239|1737404|1582879;1783272|1239|91061|186826|186828|117563|2049028;1783272|1239|1737404|1737405|1570339|162289|33031;1783272|1239|1737404|1737405|1570339|162289|1971214;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|171552|2974251|165179;3379134|976|117747|200666|84566|28453|258,Complete,Peace Sandy
bsdb:33577896/1/2,33577896,case-control,33577896,10.1016/j.jaci.2021.02.001,NA,"Rosas-Salazar C., Kimura K.S., Shilts M.H., Strickland B.A., Freeman M.H., Wessinger B.C., Gupta V., Brown H.M., Rajagopala S.V., Turner J.H. , Das S.R.",SARS-CoV-2 infection and viral load are associated with the upper respiratory tract microbiome,The Journal of allergy and clinical immunology,2021,"16S rRNA sequencing, COVID-19, SARS-CoV-2, coronavirus, microbiome, nasal, nasopharynx, respiratory",Experiment 1,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Asymptomatic uninfected controls,"Symptomatic, mild to moderate COVID-19 patients","Confirmed symptomatic mild to moderate COVID-19 patients > age 18, nonhospitalized",21,38,2 weeks,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,increased,NA,NA,increased,increased,Signature 2,Figure 3B,10 July 2021,Claregrieve1,"Claregrieve1,Peace Sandy,WikiWorks","Differences in the abundance of taxa of the URT microbiome between adults with and without SARS�CoV-2 infection. Differential abundance testing was conducted using DESeq2 models at the ASV level including age and sex as covariates B, Bar plot depicting the log2 FCs and SEs for ASVs that were significantly different between groups.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus haemolyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|3085636|186803|207244|649756;1783272|201174|1760|85007|1653|1716|1720;3379134|1224|28216|206351|481|482|192066;3379134|976|200643|171549|171552|838|28130;1783272|1239|91061|1385|90964|1279|1283;1783272|1239|186801|3085636|186803,Complete,Peace Sandy
bsdb:33577896/2/1,33577896,case-control,33577896,10.1016/j.jaci.2021.02.001,NA,"Rosas-Salazar C., Kimura K.S., Shilts M.H., Strickland B.A., Freeman M.H., Wessinger B.C., Gupta V., Brown H.M., Rajagopala S.V., Turner J.H. , Das S.R.",SARS-CoV-2 infection and viral load are associated with the upper respiratory tract microbiome,The Journal of allergy and clinical immunology,2021,"16S rRNA sequencing, COVID-19, SARS-CoV-2, coronavirus, microbiome, nasal, nasopharynx, respiratory",Experiment 2,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 patients with low viral load,COVID-19 patients with high viral load,"Confirmed symptomatic mild to moderate COVID-19 patients > age 18, nonhospitalized,  with high viral load (quantitative reverse transcription PCR cycle threshold value
below the median for the detection of SARS-CoV-2 nucleocapside gene region 1)",21,38,2 weeks,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,increased,NA,NA,increased,increased,Signature 1,Figure 4b,10 July 2021,Claregrieve1,"Claregrieve1,Peace Sandy,WikiWorks","Differences in the abundance of taxa of the URT microbiome between SARS-CoV-2–infected adults
with and without high viral load (defined as a quantitative reverse transcription PCR cycle threshold value
below the median for the detection of SARS-CoV-2 nucleocapside gene region 1 [N1]). Differential
abundance testing was conducted using DESeq2 models at the ASV level including age and sex as
covariates. B, Bar plot depicting the log2 FCs and SEs for ASVs that were significantly different between
groups. The asterisks indicate ASVs that were significantly different between groups and had a consistent
direction of association in similar DESeq2 analyses that used a definition of high viral load based on a quan�titative reverse transcription PCR cycle threshold value below the median for the detection of SARS-CoV-2 nucleocapside gene region 2 (N2). The striped bars indicate ASVs that were significantly different between groups and had a consistent direction of association in similar DESeq2 analyses comparing adults with andwithout SARS-CoV-2 infection.",increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus sp.,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter hominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae",1783272|1239|1737404|1737405|1570339|165779|1872515;3379134|29547|3031852|213849|72294|194|76517;1783272|201174|1760|85007|1653|1716|1720;1783272|1239|91061|186826|81852|1350|35783;1783272|1239|186801|186802|216572|216851|853;1783272|1239|1737404|1737405|1570339|162289|1971214;3379134|976|200643|171549|171552|2974251|165179;3379134|1224|1236|91347|543;3379134|1224|28216|206351|481,Complete,Peace Sandy
bsdb:33577896/2/2,33577896,case-control,33577896,10.1016/j.jaci.2021.02.001,NA,"Rosas-Salazar C., Kimura K.S., Shilts M.H., Strickland B.A., Freeman M.H., Wessinger B.C., Gupta V., Brown H.M., Rajagopala S.V., Turner J.H. , Das S.R.",SARS-CoV-2 infection and viral load are associated with the upper respiratory tract microbiome,The Journal of allergy and clinical immunology,2021,"16S rRNA sequencing, COVID-19, SARS-CoV-2, coronavirus, microbiome, nasal, nasopharynx, respiratory",Experiment 2,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 patients with low viral load,COVID-19 patients with high viral load,"Confirmed symptomatic mild to moderate COVID-19 patients > age 18, nonhospitalized,  with high viral load (quantitative reverse transcription PCR cycle threshold value
below the median for the detection of SARS-CoV-2 nucleocapside gene region 1)",21,38,2 weeks,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,increased,NA,NA,increased,increased,Signature 2,Figure 4b,10 July 2021,Claregrieve1,"Claregrieve1,Peace Sandy,WikiWorks","Differences in the abundance of taxa of the URT microbiome between SARS-CoV-2–infected adults
with and without high viral load (defined as a quantitative reverse transcription PCR cycle threshold value
below the median for the detection of SARS-CoV-2 nucleocapside gene region 1 [N1]). Differential
abundance testing was conducted using DESeq2 models at the ASV level including age and sex as
covariates. B, Bar plot depicting the log2 FCs and SEs for ASVs that were significantly different between
groups. The asterisks indicate ASVs that were significantly different between groups and had a consistent
direction of association in similar DESeq2 analyses that used a definition of high viral load based on a quan�titative reverse transcription PCR cycle threshold value below the median for the detection of SARS-CoV-2 nucleocapside gene region 2 (N2). The striped bars indicate ASVs that were significantly different between groups and had a consistent direction of association in similar DESeq2 analyses comparing adults with andwithout SARS-CoV-2 infection.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum pigrum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus haemolyticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",1783272|201174|1760|85007|1653|1716|1720;1783272|1239|91061|186826|186828|29393|29394;1783272|1239|91061|186826|186828|117563|137732;3379134|1224|28216|206351|481|482|192066;3379134|976|200643|171549|171552|838|28130;1783272|1239|91061|1385|90964|1279|1283;1783272|1239|91061|186826|1300|1301|1306;3379134|1224|1236|2887326|468|469;3379134|1224|1236|135614|32033|40323,Complete,Peace Sandy
bsdb:33584071/1/1,33584071,"cross-sectional observational, not case-control",33584071,10.3748/wjg.v27.i5.391,https://www.wjgnet.com/1007-9327/full/v27/i5/391.htm,"Li Y.D., Liu B.N., Zhao S.H., Zhou Y.L., Bai L. , Liu E.Q.",Changes in gut microbiota composition and diversity associated with post-cholecystectomy diarrhea,World journal of gastroenterology,2021,"16S rRNA, Bifidobacterium, Cholecystectomy, Diarrhea, Microbiota, Post-cholecystectomy",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Postcholecystectomy syndrome,EFO:1001117,healthy control (HC),post-cholecystectomy (PC),Participants who have post-cholecystectomy (PC) syndrome are difficult to treat.,20,31,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 1D,30 October 2023,Chinelsy,"Chinelsy,WikiWorks",Comparison of gut microbiota structure and abundance between post-cholecystectomy (PC) and healthy control (HC) groups. Logarithmic linear discriminant analysis scores identify the taxa with the greatest differences in abundance between the healthy control and post-cholecystectomy groups.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes",1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174;1783272|1239|909932|1843489|31977;1783272|1239|909932|909929;1783272|1239|909932,Complete,Folakunmi
bsdb:33584071/2/1,33584071,"cross-sectional observational, not case-control",33584071,10.3748/wjg.v27.i5.391,https://www.wjgnet.com/1007-9327/full/v27/i5/391.htm,"Li Y.D., Liu B.N., Zhao S.H., Zhou Y.L., Bai L. , Liu E.Q.",Changes in gut microbiota composition and diversity associated with post-cholecystectomy diarrhea,World journal of gastroenterology,2021,"16S rRNA, Bifidobacterium, Cholecystectomy, Diarrhea, Microbiota, Post-cholecystectomy",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,post-cholecystectomy non-diarrhea (PCND),post-cholecystectomy diarrhea (PCD),This group included patients who experienced post-cholecystectomy diarrhea (PCD). These individuals had diarrhea as a clinical symptom following gallbladder removal.,15,16,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig.2C,30 October 2023,Chinelsy,"Chinelsy,ChiomaBlessing,WikiWorks",Comparison of gut microbiota structure and abundance between the post-cholecystectomy non-diarrhea (PCND) and post-cholecystectomy diarrhea (PCD) groups. Linear discriminant analysis and effect size analysis show the taxa with the greatest differences in abundance between the PCND and PCD groups. Yellow bars: PCND group-enriched taxa; Green bars: PCD group-enriched taxa.,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|201174;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|1300|1357;1783272|1239|186801|186802|31979|1266;3379134|1224|28211|204457|41297;3379134|1224|28211|204457;3379134|1224|1236|91347|543|160674;3379134|1224|1236|91347|543|544;1783272|1239|186801|186802,Complete,Folakunmi
bsdb:33584071/2/2,33584071,"cross-sectional observational, not case-control",33584071,10.3748/wjg.v27.i5.391,https://www.wjgnet.com/1007-9327/full/v27/i5/391.htm,"Li Y.D., Liu B.N., Zhao S.H., Zhou Y.L., Bai L. , Liu E.Q.",Changes in gut microbiota composition and diversity associated with post-cholecystectomy diarrhea,World journal of gastroenterology,2021,"16S rRNA, Bifidobacterium, Cholecystectomy, Diarrhea, Microbiota, Post-cholecystectomy",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,post-cholecystectomy non-diarrhea (PCND),post-cholecystectomy diarrhea (PCD),This group included patients who experienced post-cholecystectomy diarrhea (PCD). These individuals had diarrhea as a clinical symptom following gallbladder removal.,15,16,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig.2C,30 October 2023,Chinelsy,"Chinelsy,MyleeeA,ChiomaBlessing,WikiWorks",Comparison of gut microbiota structure and abundance between the post-cholecystectomy non-diarrhea (PCND) and post-cholecystectomy diarrhea (PCD) groups. Linear discriminant analysis and effect size analysis show the taxa with the greatest differences in abundance between the PCND and PCD groups. Yellow bars: PCND group-enriched taxa; Green bars: PCD group-enriched taxa.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|976|200643|171549;3379134|976|200643;3379134|1224|28216;3379134|1224|28216|80840;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|1224|28216|80840|995019|40544,Complete,Folakunmi
bsdb:33585471/1/1,33585471,case-control,33585471,10.3389/fcell.2020.631460,NA,"Ling Z., Zhu M., Liu X., Shao L., Cheng Y., Yan X., Jiang R. , Wu S.",Fecal Fungal Dysbiosis in Chinese Patients With Alzheimer's Disease,Frontiers in cell and developmental biology,2020,"Alzheimer’s disease, Candida, TNF-α, fungal microbiota, sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healthy controls (Con),Alzheimer’s disease (AD) patients,"Chinese patients with well-controlled alzheimer’s disease (AD), whose diagnoses were based on the criteria of the National Institute of Neurological and Communicative Diseases and Stroke/AD and Related Disorders Association, recruited from Lishui, Zhejiang province (China) from February 2019 to November 2019",65,88,1 month,ITS / ITS2,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 3,25 November 2025,Arnold Pakis,Arnold Pakis,Differential fungal taxa between the stable Alzheimer’s disease (AD) patients and the healthy controls (con) using LEfSe (linear discriminant analysis effect size),increased,"k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida tropicalis,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Corticiales,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Davidiella,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Didymellaceae|g__Epicoccum,k__Fungi|p__Basidiomycota|c__Cystobasidiomycetes|o__Erythrobasidiales|f__Erythrobasidiaceae|g__Erythrobasidium|s__Erythrobasidium hasegawianum,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Chaetothyriales|f__Herpotrichiellaceae,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Polyporales|f__Polyporaceae,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Polyporales,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Schizophyllaceae,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Schizophyllaceae|g__Schizophyllum,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Schizophyllaceae|g__Schizophyllum|s__Schizophyllum commune,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Polyporales|f__Polyporaceae|g__Trametes,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Polyporales|f__Polyporaceae|g__Trametes|s__Trametes versicolor,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Chaetothyriales|f__Herpotrichiellaceae|g__Exophiala|s__Exophiala dermatitidis,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Didymellaceae|g__Epicoccum,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Cladosporium|s__Cladosporium herbarum,k__Fungi|p__Basidiomycota|c__Agaricomycetes",4751|5204|155619|5338;4751|4890|147545|5042|1131492|5052;4751|4890|3239874|2916678|766764|5475|5482;4751|5204|155619|452338;4751|4890|147541|2726946|452563|237557;4751|4890|147541|92860|683158|104397;4751|5204|432005|432006|165790|5413|5414;4751|4890|147545|34395|43219;4751|5204|155619|5303|5317;4751|5204|155619|5303;4751|5204|155619|452342;4751|5204|155619|5338|5332;4751|5204|155619|5338|5332|5333;4751|5204|155619|5338|5332|5333|5334;4751|5204|155619|5303|5317|5324;4751|5204|155619|5303|5317|5324|5325;4751|4890|147545|34395|43219|5583|5970;4751|4890|147541|92860|683158|104397;4751|4890|147541|2726946|452563|5498|29918;4751|5204|155619,Complete,KateRasheed
bsdb:33585471/1/2,33585471,case-control,33585471,10.3389/fcell.2020.631460,NA,"Ling Z., Zhu M., Liu X., Shao L., Cheng Y., Yan X., Jiang R. , Wu S.",Fecal Fungal Dysbiosis in Chinese Patients With Alzheimer's Disease,Frontiers in cell and developmental biology,2020,"Alzheimer’s disease, Candida, TNF-α, fungal microbiota, sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healthy controls (Con),Alzheimer’s disease (AD) patients,"Chinese patients with well-controlled alzheimer’s disease (AD), whose diagnoses were based on the criteria of the National Institute of Neurological and Communicative Diseases and Stroke/AD and Related Disorders Association, recruited from Lishui, Zhejiang province (China) from February 2019 to November 2019",65,88,1 month,ITS / ITS2,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 3,25 November 2025,Arnold Pakis,"Arnold Pakis,Tosin",Differential fungal taxa between the stable Alzheimer’s disease (AD) patients and the healthy controls (con) using LEfSe (linear discriminant analysis effect size),decreased,"k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae|g__Apiotrichum|s__Apiotrichum veenhuisii,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Bulleraceae|g__Bullera,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Bulleraceae|g__Bullera|s__Bullera unica,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida parapsilosis,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Cystofilobasidiaceae|g__Cystofilobasidium|s__Cystofilobasidium capitatum,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Bulleribasidiaceae|g__Hannaella,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Kazachstania,k__Fungi|p__Ascomycota|c__Leotiomycetes,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia globosa,k__Fungi|p__Basidiomycota|c__Microbotryomycetes,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Millerozyma,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Millerozyma|s__Millerozyma farinosa,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Rhodotorula,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Rhodotorula|s__Rhodotorula mucilaginosa,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Sporobolomyces,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Trichomonascaceae|g__Starmerella|s__Starmerella apicola,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Suhomyces|s__Suhomyces xylopsoci,k__Fungi|p__Basidiomycota|c__Exobasidiomycetes|o__Entylomatales|g__Tilletiopsis,k__Fungi|p__Basidiomycota|c__Tremellomycetes,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Kurtzmaniella|s__[Candida] zeylanoides,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Bulleribasidiaceae|g__Hannaella|s__Hannaella sp. CMON52",4751|5204|155616|1851469|1759442|105983|105713;4751|5204|155616|5234|1905116|4970;4751|5204|155616|5234|1905116|4970|57474;4751|4890|3239874|2916678|766764|5475|5480;4751|5204|155616|90883|165808|5410|5412;4751|4890|3239874|2916678|766764;4751|5204|155616|5234|1884640|663591;4751|4890|4891|4892|4893|71245;4751|4890|147548;4751|5204|1538075|162474|742845|55193|76773;4751|5204|162481;4751|4890|3239874|2916678|766764|766502;4751|4890|3239874|2916678|766764|766502|4920;4751|5204|162481|231213|1799696|5533;4751|5204|162481|231213|1799696|5533|5537;4751|5204|162481|231213;4751|5204|162481|231213|1799696|5429;4751|4890|3239873|3243772|410830|75735|29830;4751|4890|3239874|2916678|766764|1539666|147335;4751|5204|452283|62914|1500560;4751|5204|155616;4751|5204|155616|1851469|1759442;4751|5204|155616|1851469;4751|4890|3239874|2916678|766764|549703|5493;4751|5204|155616|5234|1884640|663591|1194595,Complete,KateRasheed
bsdb:33596245/1/1,33596245,"cross-sectional observational, not case-control",33596245,10.1371/journal.pone.0247041,NA,"Mazzarelli A., Giancola M.L., Farina A., Marchioni L., Rueca M., Gruber C.E.M., Bartolini B., Ascoli Bartoli T., Maffongelli G., Capobianchi M.R., Ippolito G., Di Caro A., Nicastri E. , Pazienza V.",16S rRNA gene sequencing of rectal swab in patients affected by COVID-19,PloS one,2021,NA,Experiment 1,Italy,Homo sapiens,Rectum,UBERON:0001052,COVID-19,MONDO:0100096,Pneumonia control patients (COVID-negative),COVID-positive patients admitted to ICU (i-COVID-19),"COVID-19 patients with nasopharyngeal swab positive for SARS-CoV-2, > 18 years of age admitted in ICU",8,6,NA,16S,23456789,Ion Torrent,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,"Table S5, Table S8, Table S11",4 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance of microbial taxa between controls and ICU-admitted COVID-19 patients,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Candidatus Phytoplasma,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Angelakisella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Fonticella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Ihubacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium amycolatum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus octavius,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium imitans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia|s__Facklamia hominis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus hirae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus rivorum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Candidatus Anaerococcus phoceensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium tuscaniense,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus helveticus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. IrT-R5M2-141,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp. S362,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus luteus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus provencensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sundsvallense,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium afermentans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. S4-8,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Angelakisella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus|s__Rhodococcus sp. (in: high G+C Gram-positive bacteria),k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Gorbachella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia|s__Senegalimassilia anaerobia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus casseliflavus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Fonticella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. TM-40,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium fusiformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.",1783272|201174|1760|85006|85020;1783272|201174|1760|85006;1783272|201174|1760|85007|85025;3379134|1224|28211;1783272|201174;1783272|201174|1760|85010|2070;1783272|201174|1760|85011|2062;1783272|1239|526524|526525;1783272|201174|1760|85007|1762;3379134|1224|28211|356;1783272|1239|909932|1843489;1783272|1239|526524;3379134|1224|28211|204441|41295;1783272|201174|1760|85006|85019;1783272|1239|91061|1385|90964;1783272|201174|1760|85006|1268;1783272|1239|526524|526525|128827;3379134|1224|28216|80840;1783272|201174|1760|85006|85023;1783272|201174|1760|85007|1653;1783272|1239|91061|186826|186827;1783272|1239|909932;1783272|1239|91061|1385|186822;1783272|1239|91061;1783272|1239|91061|1385|186817;1783272|1239|91061|186826|81852;1783272|201174|1760|85006|1268|1663;1783272|1239|909932|1843489|31977|909928;1783272|201174|1760|85006|85020;1783272|1239|91061|186826|81852|2737;1783272|201174|84998|1643822|1643826|84108;1783272|201174|1760|85006;1783272|201174|1760|85006|1268|1269;1783272|201174|1760|85007|85025|1827;1783272|201174|1760|85006|1268|57493;3379134|976|117743|200644|49546;1783272|201174|1760|85011|2062|1883;1783272|1239|526524|526525|128827;1783272|544448|31969|186329|2146|33926;1783272|201174|1760|85007|1762|1763;3379134|1224|28216|80840|995019;1783272|1239|186801|3082720|543314|86331;1783272|1239|526524;1783272|1239|186801|186802|216572|1935176;1783272|1239|186801|186802|404402;1783272|1239|186801|186802|31979|1434004;3379134|1224|1236|135625|712|724;1783272|1239|186801|3082720|543314|1926667;1783272|201174|1760|85006|85019|1696;1783272|1239|91061|186826|81852|1350;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|186826|186827|66831;3379134|1224|28216|80840;1783272|201174|1760|85007;1783272|1239|91061|1385|186822|44249;1783272|1239|91061|1385|186817|1386;1783272|1239|91061|186826|81852|1350|1352;1783272|201174|1760|85007|1653|1716|43765;1783272|1239|1737404|1737405|1570339|165779|54007;1783272|201174|1760|85007|1653|1716|156978;1783272|1239|91061|186826|186827|66831|178214;3384189|32066|203490|203491|203492|848|851;1783272|1239|91061|186826|81852|1350|1354;1783272|1239|91061|186826|81852|1350|762845;3379134|976|200643|171549|171552|2974257|28127;1783272|1239|1737404|1737405|1570339|165779|337317;1783272|1239|91061|186826|81852|2737;1783272|201174|1760|85007|1653|1716|302449;1783272|1239|91061|186826|33958|1578|1587;1783272|201174|1760|85007|1653|1716|146482;1783272|1239|1737404|1737405|1570339|162289|1647712;1783272|201174|84998|1643822|1643826|84108|2049041;1783272|201174|1760|85006|1268|1269|1270;1783272|1239|1737404|1737405|1570339|165779|938293;1783272|201174|1760|85007|1653|1716|161902;1783272|201174|1760|85007|1653|1716|38286;3379134|976|200643|171549|171552|838|1219629;1783272|1239|186801|3085636|186803|3342669|45851;1783272|1239|186801|186802|216572|1935176;1783272|201174|1760|85004|31953;1783272|201174|1760|85007|85025|1827|1831;1783272|1239|186801|186802|216572|1935461;3379134|1224|28211|356;1783272|201174|84998|84999|84107|1473205|1473216;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|186801|186802|404402|404403;1783272|1239|91061|186826|81852|1350|37734;3379134|1224|1236|91347|543|570|571;1783272|1239|186801|186802|31979|1434004;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|186802|31979|1485|371143;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|186802|31979|1485|69833;1783272|1239|91061|186826|81852|1350|35783;1783272|201174|1760|85007|1653|1716|1720,Complete,Fatima
bsdb:33596245/1/2,33596245,"cross-sectional observational, not case-control",33596245,10.1371/journal.pone.0247041,NA,"Mazzarelli A., Giancola M.L., Farina A., Marchioni L., Rueca M., Gruber C.E.M., Bartolini B., Ascoli Bartoli T., Maffongelli G., Capobianchi M.R., Ippolito G., Di Caro A., Nicastri E. , Pazienza V.",16S rRNA gene sequencing of rectal swab in patients affected by COVID-19,PloS one,2021,NA,Experiment 1,Italy,Homo sapiens,Rectum,UBERON:0001052,COVID-19,MONDO:0100096,Pneumonia control patients (COVID-negative),COVID-positive patients admitted to ICU (i-COVID-19),"COVID-19 patients with nasopharyngeal swab positive for SARS-CoV-2, > 18 years of age admitted in ICU",8,6,NA,16S,23456789,Ion Torrent,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,"Table S5, S8, S11",4 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance of microbial taxa between controls and ICU-admitted COVID-19 patients,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium|s__Atopobium deltae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster lavalensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria|s__Fenollaria massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Halanaerobiales|f__Halanaerobiaceae|g__Halanaerobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira|s__Oscillospira guilliermondii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter piscolens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinotignum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Metaprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Caproiciproducens,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus gorbachii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. MC_18,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. DJF_RP53,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium pyruviciproducens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. NML96-0085,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Metaprevotella|s__Metaprevotella massiliensis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp. S470,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp. gpac007,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. BI-42,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobium|s__Anaerobium acetethylicum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinotignum|s__Actinotignum schaalii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans|s__Saccharofermentans acetigenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. A9,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes sp. 992a,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. enrichment culture clone 7-14,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum|s__Varibaculum cambriense,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. 14505,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas sp. FSAA-17,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. BPY5,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon G70,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Caproiciproducens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella",1783272|1239|186801|3120394|3120654|35829;3379134|976|200643|171549|171550|239759|28117;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|186802|216572|244127|169435;1783272|201174|84998|84999|1643824|1380|1393034;3379134|976|200643|171549|815|816|626929;3379134|976|200643|171549|815|816|28111;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|291645;3379134|976|200643|171549|815|816|291644;3379134|976|200643|171549|815|816|29523;3379134|976|200643|171549|815|816|46506;1783272|1239|186801|186802|3085642|580596|2049021;1783272|1239|91061|186826|186828;1783272|1239|186801|3082768|990719;3379134|1224|1236|91347|543|544;1783272|1239|186801|3082720|543314;1783272|1239|186801|186802|31979|1485|1506;1783272|201174|84998|84999|84107|102106;3379134|976|200643|171549|2005519|1348911;3379134|976|200643|171549|2005519|1348911|1099853;1783272|201174|84998|84999|84107;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|2719313|1531;1783272|1239|186801|3085636|186803|2719313|460384;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|216851|1971605;1783272|1239|186801|186802|1686313;1783272|1239|186801|186802|1686313|938288;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|1407607;1783272|1239|91061|186826|186828|117563;1783272|1239|186801|53433|972|2330;1783272|1239|91061|186826|33958|1243;1783272|544448|31969|2085|2092|2093;1783272|544448|31969|2085|2092;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|3085636|186803|265975|1969407;1783272|1239|186801|186802|216572|119852|119853;1783272|1239|186801|186802|186807|2740;3379134|976|200643|171549|815|909656|204516;3379134|976|200643|171549|171552|838|28125;1783272|1239|186801|186802|216572|1017280;3384194|508458|649775|649776|3029088|638847;3384194|508458|649775|649776|3029088|638847|638849;1783272|1239|186801|3085636|186803|588605;3379134|1224|1236|91347|543|590;1783272|1239|186801|186802|216572|292632;3379134|1224|1236|135623|641|662;1783272|1239|526524|526525|2810280|3025755|29348;1783272|201174|84998|84999|84107;1783272|1239|186801|186802|216572;1783272|201174|84998;1783272|201174|1760|2037|2049|1653174;3379134|976|200643|171549|171552|1980689;3379134|976|200643|171549|171550;1783272|1239|186801|3085636|186803|2005359;1783272|1239|186801|186802|3082771|1738645;1783272|1239|1737404|1737405|1570339|162289|411567;3379134|976|200643|171549|171552|838|1755609;3379134|976|200643|171549|171552|838|537298;1783272|201174|1760|85007|1653|1716|598660;1783272|201174|1760|85007|1653|1716|702963;3379134|976|200643|171549|171552|1980689|1870999;1783272|1239|1737404|1737405|1570339|162289|1647714;1783272|1239|1737404|1737405|1570339|162289|361492;3379134|976|200643|171549|171552|838|243905;1783272|1239|186801|3085636|186803|1855714|1619234;1783272|201174|1760|2037|2049|1653174|59505;1783272|1239|186801|186802|216572|1200657|319644;1783272|1239|186801|3085636|186803|1649459;1783272|201174|84998|84999|84107|102106;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802|31979|1485|397283;1783272|1239|186801|3085636|186803|207244|1261637;1783272|1239|186801|186802|31979|1485|598552;3379134|200940|3031449|213115|194924|872;1783272|201174|1760|2037|2049|184869|184870;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|186802|31979|1485|169136;1783272|1239|186801|186802|1392389|1640371;1783272|1239|186801|3085636|186803|1506577;3379134|976|200643|171549|815|816|338188;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|31979|1485|1572655;3379134|976|200643|171549|171552|838|712495;1783272|1239|186801|186802|3082771|1738645;3379134|1224|1236|91347|543|570,Complete,Fatima
bsdb:33596245/2/1,33596245,"cross-sectional observational, not case-control",33596245,10.1371/journal.pone.0247041,NA,"Mazzarelli A., Giancola M.L., Farina A., Marchioni L., Rueca M., Gruber C.E.M., Bartolini B., Ascoli Bartoli T., Maffongelli G., Capobianchi M.R., Ippolito G., Di Caro A., Nicastri E. , Pazienza V.",16S rRNA gene sequencing of rectal swab in patients affected by COVID-19,PloS one,2021,NA,Experiment 2,Italy,Homo sapiens,Rectum,UBERON:0001052,COVID-19,MONDO:0100096,COVID-positive patients admitted to infectious disease ward (w-COVID-19),COVID-positive patients admitted to ICU (i-COVID-19),"COVID-19 patients with nasopharyngeal swab positive for SARS-CoV-2, > 18 years of age admitted in ICU",9,6,NA,16S,23456789,Ion Torrent,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,"Table S6, S9, S12",6 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between ICU COVID-19 patients (i-COVID-19) and non-ICU COVID-19 patients (w-COVID-19),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Candidatus Phytoplasma,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Fonticella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Ihubacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium imitans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp. DJF_SLA47,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia sp.,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium fusiformis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp. S362,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium aurimucosum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus provencensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium afermentans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus durans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus|s__Rhodococcus sp. (in: high G+C Gram-positive bacteria),k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium tuscaniense,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. S4-8,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. MANG,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia|s__Senegalimassilia anaerobia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Gorbachella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus casseliflavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Fonticella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. TM-40,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis",3379134|1224|28216|80840;1783272|201174|1760|85007|85025;3379134|1224|28211;1783272|201174|1760|85010|2070;1783272|1239|526524|526525;1783272|201174|1760|85007|1762;3379134|1224|28211|356;1783272|1239|526524;3379134|1224|1236|135624|84642;3379134|1224|28211|204441|41295;1783272|201174|1760|85006|1268;1783272|201174|1760|85006|85019;1783272|201174|1760|85007|1653;1783272|1239|91061|1385|90964;1783272|201174|1760|85006|85023;1783272|1239|91061|1385|186822;1783272|201174|1760|85006|1268|1663;1783272|201174|1760|85006|1268;1783272|201174|84998|1643822|1643826|84108;1783272|1239|526524|526525|128827;1783272|1239|91061|186826|81852|2737;1783272|201174|1760|85006|85023|33882;1783272|1239|91061|1385|186822|44249;1783272|201174|1760|85006|1268|1269;1783272|201174|1760|85007|85025|1827;1783272|201174|1760|85007|1653;1783272|201174|1760|85006|1268|57493;1783272|201174|1760|85011|2062|1883;1783272|544448|31969|186329|2146|33926;3379134|976|117743|200644|49546;1783272|201174|1760|85007|1762|1763;3379134|1224|1236|135624|84642|642;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|186802|404402;1783272|1239|186801|186802|31979|1434004;3379134|1224|1236|135625|712|724;1783272|1239|186801|3082720|543314|1926667;1783272|1239|91061|1385|90964|1279;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85006|85019|1696;1783272|201174|1760|85007|1653|1716|156978;1783272|1239|91061|186826|81852|1350|537280;1783272|201174|84998|1643822|1643826|84108|2049041;3384189|32066|203490|203491|203492|848|68766;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|186801|186802|31979|1485|69833;1783272|1239|1737404|1737405|1570339|162289|1647712;1783272|201174|1760|85007|1653|1716|169292;1783272|1239|1737404|1737405|1570339|165779|938293;1783272|1239|91061|1385|90964|1279|1280;1783272|201174|1760|85007|1653|1716|38286;1783272|1239|91061|186826|81852|1350|53345;1783272|201174|1760|85007|85025|1827|1831;1783272|201174|1760|85007|1653|1716|302449;1783272|1239|186801|3085636|186803|2316020|46228;3379134|976|200643|171549|171552|838|1219629;3379134|976|200643|171549|815|816|298389;1783272|201174|1760|85004|31953;1783272|1239|186801|3085636|186803|3342669|45851;1783272|201174|84998|84999|84107|1473205|1473216;1783272|1239|91061|186826|81852|2737;1783272|1239|186801|186802|216572|1935461;1783272|1239|186801|186802|404402|404403;1783272|1239|91061|186826|81852|1350|37734;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|186802|31979|1434004;1783272|1239|186801|186802|31979|1485|371143;3379134|1224|28216|80840|995019|577310;1783272|1239|91061|1385|90964|1279|29387;1783272|1239|91061|1385|90964|1279|1282,Complete,Fatima
bsdb:33596245/2/2,33596245,"cross-sectional observational, not case-control",33596245,10.1371/journal.pone.0247041,NA,"Mazzarelli A., Giancola M.L., Farina A., Marchioni L., Rueca M., Gruber C.E.M., Bartolini B., Ascoli Bartoli T., Maffongelli G., Capobianchi M.R., Ippolito G., Di Caro A., Nicastri E. , Pazienza V.",16S rRNA gene sequencing of rectal swab in patients affected by COVID-19,PloS one,2021,NA,Experiment 2,Italy,Homo sapiens,Rectum,UBERON:0001052,COVID-19,MONDO:0100096,COVID-positive patients admitted to infectious disease ward (w-COVID-19),COVID-positive patients admitted to ICU (i-COVID-19),"COVID-19 patients with nasopharyngeal swab positive for SARS-CoV-2, > 18 years of age admitted in ICU",9,6,NA,16S,23456789,Ion Torrent,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,"Table S6, S9, S12",6 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between ICU COVID-19 patients (i-COVID-19) and non-ICU COVID-19 patients (w-COVID-19),decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Alcanivoracaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Alcanivoracaceae|g__Alcanivorax,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Alterileibacterium|s__Alterileibacterium massiliense,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus degeneri,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter hominis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria|s__Fenollaria massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Ileibacterium,k__Bacillati|p__Bacillota|c__Tissierellia|g__Kallipyga|s__Kallipyga massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Lagierella|s__Lagierella massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Metaprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Metaprevotella|s__Metaprevotella massiliensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Moritellaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides johnsonii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella colorans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. DJF_RP53,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum|s__Varibaculum anthropi,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,c__Deltaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. DJF_B097,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__[Lactobacillus] rogosae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. 1120,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella bergensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. S8 F8,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp. C71,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes sp. 992a,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. Marseille-P328,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. BPY5,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. enrichment culture clone,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Pantoea agglomerans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella sonnei,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Marseillibacter|s__Marseillibacter massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp.,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Moritellaceae|g__Moritella|s__Moritella abyssi,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. enrichment culture clone 7-14,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. Marseille-P2398,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. Marseille-P3260,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae",1783272|1239|91061|186826|186827|1375;3379134|1224|1236|135619|224372;3379134|1224|1236|135619|224372|59753;1783272|1239|186801|3082720|543314|1980680|1870997;1783272|1239|1737404|1737405|1570339|165779|361500;1783272|1239|186801|3085636|186803|207244|649756;3379134|29547|3031852|213849|72294|194|76517;1783272|1239|91061|186826|186828;3379134|1224|1236|91347|543|544;1783272|1239|186801|3082720|543314;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|526524|526525|2810280|100883;1783272|1239|526524|526525|2810280|100883|100884;3379134|976|200643|171549|2005519|1348911;3379134|976|200643|171549|2005519|1348911|1099853;1783272|201174|84998|84999|84107;1783272|201174|84998;3379134|1224|1236|91347|543|413496;3379134|200940|3031449|213115|194924|872;1783272|1239|909932|1843489|31977|39948|309120;1783272|1239|186801|3085636|186803|2719313|1531;1783272|1239|186801|186802|186806|1730|39490;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|1971605;1783272|1239|186801|186802|1686313;1783272|1239|186801|186802|1686313|938288;1783272|1239|186801|186802|216572|946234;1783272|1239|91061|186826|186828|117563;1783272|1239|526524|526525|128827|1937007;1783272|1239|1737404|1472763|1472764;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|28052;1783272|1239|91061|186826|1300|1357;1783272|1239|1737404|1737405|1570339|1945592|1689303;3379134|976|200643|171549|171552|1980689;3379134|976|200643|171549|171552|1980689|1870999;1783272|201174|1760|85008|28056;3379134|1224|1236|135622|267891;1783272|1239|1737404|1737405|1570339|1161127;1783272|201174|84998|84999|1643824|133925;3379134|976|200643|171549|2005525|375288|387661;3379134|1224|1236|91347|1903410;3379134|976|200643|171549|815|909656|204516;3379134|976|200643|171549|171552|52228|1703337;3379134|976|200643|171549|171552|838|28130;3379134|976|200643|171549|171552|838|537298;1783272|1239|186801|3085636|186803|841|301302;3379134|1224|1236|91347|543|590;1783272|1239|909932|909929|1843491;1783272|1239|909932|909929|1843491|970;1783272|1239|186801|186802|216572|292632;3379134|1224|28216|80840|995019|40544;1783272|201174|1760|2037|2049|184869|1177728;3379134|1224|1236|135623|641|662;1783272|1239|186801|186802|216572|39492;1783272|1239|909932|1843488|909930;1783272|201174|84998|84999|84107;1783272|201174|84998;28221;1783272|1239|186801|186802|1686313;1783272|1239|186801|3082720|186804;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|815|816|537274;1783272|1239|186801|3085636|186803|28050|706562;1783272|1239|186801|186802|216572|216851|853;3379134|976|200643|171549|171552|838|28125;1783272|1239|186801|3085636|186803|841|2049040;3379134|1224|1236|91347|543|570|548;3379134|1224|1236|91347|543|590|28901;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|841|1227508;3379134|976|200643|171549|171552|52228|242750;1783272|1239|91061|186826|1300|1301|1308;3379134|976|200643|171549|1853231|574697;3379134|1224|1236|91347|543|547;1783272|201174|84998|84999|84107|102106;3379134|1224|1236|91347|543|561;3379134|976|200643|171549|171552|838|1330241;3379134|1224|1236|91347|543|561|1299485;1783272|1239|186801|3085636|186803|207244|1261637;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|186802|216572|1263|1816688;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|186802|31979|1485|1572655;3379134|976|200643|171549|171550|239759|1648956;3379134|1224|1236|91347|1903409|53335|549;3379134|1224|1236|91347|543|620|624;1783272|1239|186801|186802|216572|1930587|1852369;1783272|1239|186801|3085636|186803|33042|2049024;3379134|200940|3031449|213115|194924|872;3379134|1224|1236|135622|267891|58050|111292;1783272|1239|186801|186802|31979|1485|598552;1783272|1239|91061|186826|186828|117563|2049028;1783272|1239|186801|3085636|186803|572511|1805476;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|216572|459786|1871036;3379134|1224|1236|91347|543|547|550,Complete,Fatima
bsdb:33596245/3/1,33596245,"cross-sectional observational, not case-control",33596245,10.1371/journal.pone.0247041,NA,"Mazzarelli A., Giancola M.L., Farina A., Marchioni L., Rueca M., Gruber C.E.M., Bartolini B., Ascoli Bartoli T., Maffongelli G., Capobianchi M.R., Ippolito G., Di Caro A., Nicastri E. , Pazienza V.",16S rRNA gene sequencing of rectal swab in patients affected by COVID-19,PloS one,2021,NA,Experiment 3,Italy,Homo sapiens,Rectum,UBERON:0001052,COVID-19,MONDO:0100096,Pneumonia controls (COVID-negative),COVID-positive patients admitted to infectious disease ward (w-COVID-19),"COVID-19 patients with nasopharyngeal swab positive for SARS-CoV-2, > 18 years of age admitted in infectious disease ward",8,9,NA,16S,23456789,Ion Torrent,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Table S1, S4, S7, S10",4 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance of microbial taxa between non-COVID-19 patients and non-ICU COVID-19 patients,increased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Alcanivoracaceae,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,c__Deltaproteobacteria,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Syntrophomonadaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Acidithiobacillia|o__Acidithiobacillales|f__Acidithiobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Alcanivoracaceae|g__Alcanivorax,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfitobacteriaceae|g__Syntrophobotulus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Syntrophomonadaceae|g__Candidatus Syntrophonatronum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Angelakisella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Pacaella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hespellia,k__Pseudomonadati|p__Pseudomonadota|c__Acidithiobacillia|o__Acidithiobacillales|f__Acidithiobacillaceae|g__Acidithiobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella colorans,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus octavius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides johnsonii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella|s__Murdochiella asaccharolytica,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Alterileibacterium|s__Alterileibacterium massiliense,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp. oral taxon 375,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp. S276,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sp. DNF00912,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. DJF_B097,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacillati|p__Bacillota|c__Tissierellia|g__Kallipyga|s__Kallipyga massiliensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium|s__Atopobium sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia|s__Facklamia hominis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus hirae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. S8 F8,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp. C71,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. Marseille-P328,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium amycolatum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella sonnei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Pantoea agglomerans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfitobacteriaceae|g__Syntrophobotulus|s__Syntrophobotulus glycolicus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. Marseille-P2398,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Syntrophomonadaceae|g__Candidatus Syntrophonatronum|s__Candidatus Syntrophonatronum acetioxidans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Angelakisella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera massiliensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia marcescens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister sp. S7D,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Pacaella|s__Pacaella massiliensis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Candidatus Peptoniphilus massiliensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. Marseille-P3260,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas phoceensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. enrichment culture clone,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas ruminantium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. IrT-R5M2-141,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter|s__Cronobacter sakazakii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus sp.",3379134|1224;3379134|1224|1236|135619|224372;1783272|201174;1783272|201174|1760|85006;28221;1783272|1239|909932|1843488|909930;1783272|1239|909932|1843489|31977;3379134|1224|1236|91347|1903410;1783272|1239|186801|186802|68298;1783272|201174|1760|85011|2062;1783272|1239|909932|909929|1843491;1783272|201174|1760|85006|85020;3379134|976|117747;3379134|1224|1807140|225057|225058;1783272|1239|186801|3082720|186804;3379134|1224|1236|91347|543;1783272|1239|909932;1783272|1239|91061|186826|186827;1783272|1239|91061|1385|90964;1783272|201174|84998|84999|1643824;3379134|1224|1236|135623|641;3379134|1224|1236|135619|224372|59753;1783272|1239|91061|186826|186827|1375;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|186802|2937909|51196;1783272|1239|526524|526525|2810280|100883;1783272|1239|186801|3082720|186804;1783272|201174|84998|84999|1643824|133925;1783272|201174;3379134|1224|28216|80840|995019;1783272|1239|909932|1843489|31977|909928;1783272|1239|91061|186826|1300|1357;1783272|1239|186801|186802|68298|1795789;1783272|1239|186801|186802|216572|1935176;1783272|1239|909932|1843488|909930|904;3384194|508458|649775|649776|649777|1931105;1783272|1239|909932|909929|1843491|970;1783272|1239|91061|186826|81852;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|3085636|186803|241189;3379134|1224|1807140|225057|225058|119977;1783272|1239|909932|1843489|31977|906;3379134|200940|3031449|213115|194924|35832;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543;1783272|1239|91061|186826|1300;3379134|1224|1236|135623|641|662;3379134|976|200643|171549|171552|838|28130;3379134|976|200643|171549|171552|52228|1703337;1783272|1239|909932|1843489|31977|39948|309120;1783272|1239|186801|3082720|186804|1257|1261;1783272|1239|1737404|1737405|1570339|165779|54007;3379134|976|200643|171549|2005525|375288|387661;1783272|1239|1737404|1737405|1570339|1161127|507844;1783272|1239|186801|3082720|543314|1980680|1870997;3379134|976|200643|171549|171550|239759|1288121;1783272|1239|1737404|1737405|1570339|162289|712430;1783272|1239|1737404|1737405|1570339|162289|1647711;1783272|1239|909932|1843489|31977|906|1285934;3379134|976|200643|171549|815|816|537274;1783272|1239|526524|526525|2810280|100883|100884;1783272|1239|526524|526525|128827|1573535|1735;1783272|1239|1737404|1737405|1570339|165779|1287640;1783272|1239|1737404|1472763|1472764;1783272|1239|909932|1843489|31977|906|2023260;1783272|1239|91061|186826|81852|1350|1352;1783272|201174|84998|84999|1643824|1380|1872650;3379134|976|200643|171549|171552|2974257|28127;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|91061|186826|186827|66831|178214;1783272|1239|91061|186826|81852|1350|1354;3379134|976|200643|171549|171552|838|1330241;3379134|976|200643|171549|171551|836|28123;3379134|1224|1236|91347|543|561|1299485;1783272|1239|186801|186802|216572|1263|1816688;1783272|201174|1760|85007|1653|1716|43765;3379134|1224|1236|91347|543|620|624;3379134|1224|1236|91347|1903409|53335|549;1783272|1239|91061|186826|186827|66831;1783272|1239|186801|186802|2937909|51196|51197;1783272|1239|186801|3085636|186803|572511|1805476;1783272|1239|91061|1385|90964|1279|1290;1783272|1239|186801|186802|68298|1795789|1795816;1783272|1239|186801|186802|216572|1935176;1783272|1239|909932|1843489|31977|906|1232428;1783272|1239|909932|1843489|31977|39948|487173;3379134|1224|1236|91347|1903411|613|615;1783272|1239|909932|1843488|909930|904|187327;1783272|1239|909932|1843489|31977|39948|1577797;3384194|508458|649775|649776|649777|1931105|1871009;1783272|1239|1737404|1737405|1570339|162289|337315;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|186802|216572|459786|1871036;3379134|1224|1236|91347|543|570|571;3379134|976|200643|171549|1853231|574697|1720203;3379134|976|200643|171549|171550|239759|1648956;3379134|976|200643|171549|171552|577309|454154;1783272|1239|909932|909929|1843491|970|971;1783272|201174|1760|85007|1653|1716|146482;1783272|1239|91061|186826|1300|1301|1328;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|413496|28141;1783272|1239|186801|3085636|186803|841|2049040;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|91061|1385|90964|1279|29387,Complete,Fatima
bsdb:33596245/3/2,33596245,"cross-sectional observational, not case-control",33596245,10.1371/journal.pone.0247041,NA,"Mazzarelli A., Giancola M.L., Farina A., Marchioni L., Rueca M., Gruber C.E.M., Bartolini B., Ascoli Bartoli T., Maffongelli G., Capobianchi M.R., Ippolito G., Di Caro A., Nicastri E. , Pazienza V.",16S rRNA gene sequencing of rectal swab in patients affected by COVID-19,PloS one,2021,NA,Experiment 3,Italy,Homo sapiens,Rectum,UBERON:0001052,COVID-19,MONDO:0100096,Pneumonia controls (COVID-negative),COVID-positive patients admitted to infectious disease ward (w-COVID-19),"COVID-19 patients with nasopharyngeal swab positive for SARS-CoV-2, > 18 years of age admitted in infectious disease ward",8,9,NA,16S,23456789,Ion Torrent,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Table S1, S4, S7, S10",4 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance of microbial taxa between non-COVID-19 patients and non-ICU COVID-19 patients,decreased,"k__Pseudomonadati|p__Spirochaetota,k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinotignum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Caproiciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium pyruviciproducens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp. S470,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus|s__Proteus mirabilis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. NML96-0085,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio|s__Acetivibrio cellulolyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobium|s__Anaerobium acetethylicum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinotignum|s__Actinotignum schaalii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. A9,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. MANG,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas sp. FSAA-17,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. 14505,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Candidatus Dorea massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter glycyrrhizinilyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Caproiciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas sp. S479,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon G70,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster lavalensis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 653,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. enrichment culture,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans|s__Saccharofermentans acetigenes,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas nexilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] viride,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena orotica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. ID5,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron",3379134|203691;3384189|32066;3379134|1224|1236|135624|84642;1783272|544448|31969|2085|2092;1783272|1239|186801|3082720|543314;3379134|1224|28216|80840|119060;3379134|1224|1236|2887326|468;3379134|1224|28216|80840;3379134|1224|28211|204458|76892;1783272|201174|1760|85009|31957;3379134|1224|1236|91347|1903414|583;3379134|1224|1236|91347|1903414;1783272|201174|1760|85009|31957;1783272|201174|1760|2037|2049|1653174;1783272|201174|1760|85007|1653;1783272|1239|186801|3085636|186803|1432051;1783272|201174|1760|85006|85023|33882;1783272|1239|186801|3085636|186803|2005359;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|186802|3082771|1738645;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3085636|186803|1407607;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|216572|1017280;1783272|1239|91061|1385|186822|44249;3379134|1224|1236|135624|84642|642;1783272|1239|186801|3085636|186803|588605;1783272|1239|186801|3120394|3120654|35829;1783272|1239|91061|186826|33958|1243;1783272|1239|186801|186802|216572|1905344;3379134|976|200643|171549|171550;1783272|1239|186801|3082768|990719;1783272|1239|91061|186826|33958;1783272|544448|31969|2085|2092|2093;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|2887326|468|469;3379134|1224|1236|72274|135621;3379134|976|200643|171549|815|816|28111;3379134|976|200643|171549|815|816|291644;1783272|201174|1760|85007|1653|1716|598660;3379134|976|200643|171549|171550|239759|28117;1783272|1239|1737404|1737405|1570339|162289|1647714;3379134|1224|1236|91347|1903414|583|584;3379134|1224|1236|91347|1903414|583;1783272|201174|1760|85007|1653|1716|702963;1783272|1239|186801|186802|216572|1200657;1783272|1239|186801|3120394|3120654|35829|35830;3379134|976|200643|171549|815|816|46506;1783272|1239|186801|3085636|186803|1855714|1619234;1783272|201174|1760|2037|2049|1653174|59505;1783272|1239|186801|186802|216572|1263|438033;3379134|976|200643|171549|815|816|817;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|186801|186802|31979|1485|1506;1783272|1239|186801|186802|31979|1485|397283;3379134|976|200643|171549|815|816|298389;1783272|201174|1760|85006|85023|33882;1783272|1239|186801|186802|1392389|1640371;1783272|1239|186801|186802|31979|1485|169136;1783272|1239|186801|3085636|186803|189330|1470355;1783272|1239|186801|3085636|186803|1506553|29347;3379134|976|200643|171549|171550|239759|328814;1783272|1239|186801|3085636|186803|2316020|342942;1783272|1239|186801|3085636|186803|1506577;3379134|976|200643|171549|815|816|338188;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|3082771|1738645;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|186802|216572|244127|169435;1783272|1239|186801|186802|3085642|580596;3379134|976|200643|171549|1853231|574697|1647678;3379134|976|200643|171549|171552|838|712495;1783272|1239|186801|3085636|186803|2719313|460384;3384189|32066|203490|203491|203492|848|68766;3379134|976|200643|171549|815|816|29523;1783272|1239|186801|186802|216572|1905344|1550024;3379134|976|200643|171549|815|816|291645;1783272|1239|186801|186802|216572|1263|1227507;1783272|1239|186801|186802|31979|1485|1569942;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|186802|216572|1200657|319644;1783272|1239|91061|1385|186822|44249;1783272|1239|186801|3085636|186803|1432051|1924109;1783272|1239|186801|3085636|186803|2005355|29361;1783272|1239|186801|3085636|186803|1432051|1720294;1783272|1239|186801|186802|216572|47246;1783272|1239|186801|3085636|186803|2005359|1544;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|186802|31979|1485|320882;1783272|1239|909932|1843489|31977|39948|39950;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|816|818,Complete,Lwaldron
bsdb:33596768/1/1,33596768,"cross-sectional observational, not case-control",33596768,10.1080/19490976.2021.1882926,NA,"Balakrishnan B., Selvaraju V., Chen J., Ayine P., Yang L., Babu J.R., Geetha T. , Taneja V.",Ethnic variability associating gut and oral microbiome with obesity in children,Gut microbes,2021,"Microbiome, disparity, minorities, obesity, socioeconomic factors",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Gut microbiome of European American children (EA),Gut microbiome of African American children (AA),"Gut microbiome of 30 African American children (18 female, 12 male; age 6 - 10 years)",30,30,NA,16S,345,Illumina,relative abundances,PERMANOVA,0.05,TRUE,NA,NA,"age,body mass index,education level,household income,sex",NA,NA,NA,NA,NA,increased,Signature 1,Figure 1C,29 June 2022,Kaluifeanyi101,"Kaluifeanyi101,Atrayees,Folakunmi,WikiWorks",Differential abundance of taxa in the gut microbiota variability of AA and EA populations at 10% false discovery rate.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales,k__Thermotogati|p__Synergistota|c__Synergistia,k__Thermotogati|p__Synergistota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",1783272|1239|186801|186802|216572|244127;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|3085636|186803|248744;3379134|1224|28216|80840|75682|846;3379134|976|200643|171549|171552|838;1783272|201174|84998|84999|84107|1473205;1783272|201174|84998|1643822|1643826|84108;3384194|508458|649775|649776;3384194|508458|649775;3384194|508458;1783272|1239|186801|186802|216572|707003,Complete,Atrayees
bsdb:33596768/2/1,33596768,"cross-sectional observational, not case-control",33596768,10.1080/19490976.2021.1882926,NA,"Balakrishnan B., Selvaraju V., Chen J., Ayine P., Yang L., Babu J.R., Geetha T. , Taneja V.",Ethnic variability associating gut and oral microbiome with obesity in children,Gut microbes,2021,"Microbiome, disparity, minorities, obesity, socioeconomic factors",Experiment 2,United States of America,Homo sapiens,Oral opening,UBERON:0000166,Ethnic group,EFO:0001799,Oral microbiota of European American children (EA),Oral microbiota of African American children (AA),"Oral microbiota of 30 African American children (18 female, 12 male; age 6 - 10 years)",30,30,NA,16S,345,Illumina,relative abundances,PERMANOVA,0.05,TRUE,NA,NA,"age,body mass index,education level,household income,sex",NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 2C,29 June 2022,Kaluifeanyi101,"Kaluifeanyi101,Folakunmi,WikiWorks",Genus-level differentially abundant taxa in the oral microbiota comparison between AA and EA groups at a 10% false discovery rate,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:33596768/2/2,33596768,"cross-sectional observational, not case-control",33596768,10.1080/19490976.2021.1882926,NA,"Balakrishnan B., Selvaraju V., Chen J., Ayine P., Yang L., Babu J.R., Geetha T. , Taneja V.",Ethnic variability associating gut and oral microbiome with obesity in children,Gut microbes,2021,"Microbiome, disparity, minorities, obesity, socioeconomic factors",Experiment 2,United States of America,Homo sapiens,Oral opening,UBERON:0000166,Ethnic group,EFO:0001799,Oral microbiota of European American children (EA),Oral microbiota of African American children (AA),"Oral microbiota of 30 African American children (18 female, 12 male; age 6 - 10 years)",30,30,NA,16S,345,Illumina,relative abundances,PERMANOVA,0.05,TRUE,NA,NA,"age,body mass index,education level,household income,sex",NA,NA,NA,NA,NA,unchanged,Signature 2,Figure 2C,29 June 2022,Kaluifeanyi101,"Kaluifeanyi101,Folakunmi,WikiWorks",Genus-level differentially abundant taxa in the oral microbiota comparison between AA and EA groups at a 10% false discovery rate,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|186801|3085636|186803|830;3379134|976|117743|200644|49546|1016;3384189|32066|203490|203491|203492|848;3379134|1224|1236|135625|712|724;3379134|976|200643|171549|171552|838,Complete,Folakunmi
bsdb:33596768/3/1,33596768,"cross-sectional observational, not case-control",33596768,10.1080/19490976.2021.1882926,NA,"Balakrishnan B., Selvaraju V., Chen J., Ayine P., Yang L., Babu J.R., Geetha T. , Taneja V.",Ethnic variability associating gut and oral microbiome with obesity in children,Gut microbes,2021,"Microbiome, disparity, minorities, obesity, socioeconomic factors",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,"Household income (EA & AA) =>$50,000.","Household income (EA & AA) < $50,000.","Gut microbiota of children from low-income households (EA & AA) < $50,000.",30,30,NA,16S,345,Illumina,relative abundances,PERMANOVA,0.05,TRUE,NA,NA,"age,body mass index,education level,ethnic group,sex",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Figure 6B,30 June 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks","Both groups had an increased abundance of gut Phascolarcobacteria, with a decrease in Faecalitalea (both belonging to the phylum Firmicutes) in families with low income 
(P ≤ .05).",increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,1783272|1239|909932|1843488|909930|33024,Complete,Folakunmi
bsdb:33596768/3/2,33596768,"cross-sectional observational, not case-control",33596768,10.1080/19490976.2021.1882926,NA,"Balakrishnan B., Selvaraju V., Chen J., Ayine P., Yang L., Babu J.R., Geetha T. , Taneja V.",Ethnic variability associating gut and oral microbiome with obesity in children,Gut microbes,2021,"Microbiome, disparity, minorities, obesity, socioeconomic factors",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,"Household income (EA & AA) =>$50,000.","Household income (EA & AA) < $50,000.","Gut microbiota of children from low-income households (EA & AA) < $50,000.",30,30,NA,16S,345,Illumina,relative abundances,PERMANOVA,0.05,TRUE,NA,NA,"age,body mass index,education level,ethnic group,sex",NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,Figure 6B,30 June 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks","Both groups had an increased abundance of gut Phascolarcobacteria, with a decrease in Faecalitalea (both belonging to the phylum Firmicutes) in families 
with low income (P ≤ .05).",decreased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,1783272|1239|526524|526525|128827|1573534,Complete,Folakunmi
bsdb:33596768/4/1,33596768,"cross-sectional observational, not case-control",33596768,10.1080/19490976.2021.1882926,NA,"Balakrishnan B., Selvaraju V., Chen J., Ayine P., Yang L., Babu J.R., Geetha T. , Taneja V.",Ethnic variability associating gut and oral microbiome with obesity in children,Gut microbes,2021,"Microbiome, disparity, minorities, obesity, socioeconomic factors",Experiment 4,United States of America,Homo sapiens,Oral opening,UBERON:0000166,Household income,EFO:0009695,"High income in European American households =>$50,000.","Low  income in European American households  < $50,000.","Oral microbiota of children from low-income EA households < $50,000.",30,30,NA,16S,345,Illumina,relative abundances,PERMANOVA,0.05,TRUE,NA,NA,"age,body mass index,education level,ethnic group,sex",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,FIGURE 6D,30 June 2022,Kaluifeanyi101,"Kaluifeanyi101,Folakunmi,WikiWorks","Differentially abundant taxa analysis of oral microbiota showed an increased abundance of Streptococcus in EA children from low-income families. 
No differentially abundant taxa were associated with income in AA children (not shown).",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:33596768/5/1,33596768,"cross-sectional observational, not case-control",33596768,10.1080/19490976.2021.1882926,NA,"Balakrishnan B., Selvaraju V., Chen J., Ayine P., Yang L., Babu J.R., Geetha T. , Taneja V.",Ethnic variability associating gut and oral microbiome with obesity in children,Gut microbes,2021,"Microbiome, disparity, minorities, obesity, socioeconomic factors",Experiment 5,United States of America,Homo sapiens,Oral opening,UBERON:0000166,Obesity,EFO:0001073,Non-obese EA children,Obese EA children,Obese children in the European American group,22,8,NA,16S,345,Illumina,relative abundances,PERMANOVA,0.1,TRUE,NA,NA,"age,body mass index,education level,ethnic group,sex",NA,NA,NA,NA,NA,increased,Signature 1,Figures 3E,30 January 2024,Folakunmi,"Folakunmi,WikiWorks",Oral microbial diversity was associated with obesity in EA children. Genera Aggregatibacter and Eikenella abundance was increased in obese compared to non-obese EA children.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella",3379134|1224|1236|135625|712|416916;3379134|1224|28216|206351|481|538,Complete,Folakunmi
bsdb:33596768/6/1,33596768,"cross-sectional observational, not case-control",33596768,10.1080/19490976.2021.1882926,NA,"Balakrishnan B., Selvaraju V., Chen J., Ayine P., Yang L., Babu J.R., Geetha T. , Taneja V.",Ethnic variability associating gut and oral microbiome with obesity in children,Gut microbes,2021,"Microbiome, disparity, minorities, obesity, socioeconomic factors",Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Non-obese African American children,Obese African American  children,NA,21,9,NA,16S,345,Illumina,relative abundances,PERMANOVA,0.1,TRUE,NA,NA,"age,body mass index,education level,ethnic group,sex",NA,unchanged,NA,NA,unchanged,increased,Signature 1,Figures 3C,31 January 2024,Folakunmi,"Folakunmi,WikiWorks",Differentially abundant taxa in obese and non-obese AA children,increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota,k__Thermotogati|p__Synergistota,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli,k__Thermotogati|p__Synergistota|c__Synergistia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera",1783272|201174;3379134|1224;3384194|508458;1783272|1239|909932;1783272|201174|84998;3379134|1224|1236;1783272|1239|91061;3384194|508458|649775;1783272|1239|909932|909929;1783272|201174|84998|84999;3379134|1224|1236|91347;1783272|1239|91061|186826;3384194|508458|649775|649776;3379134|1224|1236|91347|543|570;1783272|1239|909932|1843489|31977|906,Complete,Folakunmi
bsdb:33596997/1/1,33596997,case-control,33596997,10.1186/s13099-021-00403-x,https://pmc.ncbi.nlm.nih.gov/articles/PMC7888145/,"Sarhadi V., Mathew B., Kokkola A., Karla T., Tikkanen M., Rautelin H., Lahti L., Puolakkainen P. , Knuutila S.",Gut microbiota of patients with different subtypes of gastric cancer and gastrointestinal stromal tumors,Gut pathogens,2021,"Diffuse gastric adenocarcinoma, GIST, Gut microbiota, Intestinal gastric adenocarcinoma",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Gastric adenocarcinoma,EFO:0000503,Healthy controls,Gastric  Adenocarcinoma,Patients diagnosed with gastric adenocarcinoma.,13,29,6 months,16S,NA,Ion Torrent,centered log-ratio,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Table 2,22 April 2025,Shulamite,Shulamite,Taxonomic groups with significant differences (p ≤ 0.05) in pair-wise comparison of gastric cancer types,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",3379134|976|200643|171549|2005519|397864;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|186806;3379134|976|200643|171549|2005525|375288;1783272|1239|91061|186826|33958;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|186802|216572|459786,Complete,KateRasheed
bsdb:33596997/1/2,33596997,case-control,33596997,10.1186/s13099-021-00403-x,https://pmc.ncbi.nlm.nih.gov/articles/PMC7888145/,"Sarhadi V., Mathew B., Kokkola A., Karla T., Tikkanen M., Rautelin H., Lahti L., Puolakkainen P. , Knuutila S.",Gut microbiota of patients with different subtypes of gastric cancer and gastrointestinal stromal tumors,Gut pathogens,2021,"Diffuse gastric adenocarcinoma, GIST, Gut microbiota, Intestinal gastric adenocarcinoma",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Gastric adenocarcinoma,EFO:0000503,Healthy controls,Gastric  Adenocarcinoma,Patients diagnosed with gastric adenocarcinoma.,13,29,6 months,16S,NA,Ion Torrent,centered log-ratio,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Table 2,22 April 2025,Shulamite,Shulamite,Taxonomic groups with significant differences (p ≤ 0.05) in pair-wise comparison of gastric cancer types,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,KateRasheed
bsdb:33596997/2/1,33596997,case-control,33596997,10.1186/s13099-021-00403-x,https://pmc.ncbi.nlm.nih.gov/articles/PMC7888145/,"Sarhadi V., Mathew B., Kokkola A., Karla T., Tikkanen M., Rautelin H., Lahti L., Puolakkainen P. , Knuutila S.",Gut microbiota of patients with different subtypes of gastric cancer and gastrointestinal stromal tumors,Gut pathogens,2021,"Diffuse gastric adenocarcinoma, GIST, Gut microbiota, Intestinal gastric adenocarcinoma",Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Colorectal Gastrointestinal Stromal Tumor,EFO:1000192,Healthy control,Gastrointestinal stromal tumors (GIST),Patients diagnosed with gastrointestinal stromal tumors.,13,23,6 months,16S,NA,Ion Torrent,centered log-ratio,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Table 2 and Fig 4,22 April 2025,Shulamite,Shulamite,Taxonomic groups with significant differences (p ≤ 0.05) in pair-wise comparison of gastric cancer types.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,KateRasheed
bsdb:33596997/2/2,33596997,case-control,33596997,10.1186/s13099-021-00403-x,https://pmc.ncbi.nlm.nih.gov/articles/PMC7888145/,"Sarhadi V., Mathew B., Kokkola A., Karla T., Tikkanen M., Rautelin H., Lahti L., Puolakkainen P. , Knuutila S.",Gut microbiota of patients with different subtypes of gastric cancer and gastrointestinal stromal tumors,Gut pathogens,2021,"Diffuse gastric adenocarcinoma, GIST, Gut microbiota, Intestinal gastric adenocarcinoma",Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Colorectal Gastrointestinal Stromal Tumor,EFO:1000192,Healthy control,Gastrointestinal stromal tumors (GIST),Patients diagnosed with gastrointestinal stromal tumors.,13,23,6 months,16S,NA,Ion Torrent,centered log-ratio,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Table 2 and Fig 4,22 April 2025,Shulamite,Shulamite,Taxonomic groups with significant differences (p ≤ 0.05) in pair-wise comparison of gastric cancer types in pair-wise comparison between gastric cancer subgroups and controls.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",1783272|1239|186801|186802|216572|459786;1783272|1239|91061|186826|33958,Complete,KateRasheed
bsdb:33596997/5/1,33596997,case-control,33596997,10.1186/s13099-021-00403-x,https://pmc.ncbi.nlm.nih.gov/articles/PMC7888145/,"Sarhadi V., Mathew B., Kokkola A., Karla T., Tikkanen M., Rautelin H., Lahti L., Puolakkainen P. , Knuutila S.",Gut microbiota of patients with different subtypes of gastric cancer and gastrointestinal stromal tumors,Gut pathogens,2021,"Diffuse gastric adenocarcinoma, GIST, Gut microbiota, Intestinal gastric adenocarcinoma",Experiment 5,Finland,Homo sapiens,Feces,UBERON:0001988,Gastric adenocarcinoma,EFO:0000503,Healthy control,Diffuse adenocarcinoma,Subset of gastric adenocarcinoma patients with diffuse-type tumors.,13,12,6 months,16S,NA,Ion Torrent,centered log-ratio,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Table 3,22 April 2025,Shulamite,Shulamite,Taxa with significant differences (p ≤ 0.05) in pair-wise comparison of gastric cancer subgroup,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,KateRasheed
bsdb:33596997/5/2,33596997,case-control,33596997,10.1186/s13099-021-00403-x,https://pmc.ncbi.nlm.nih.gov/articles/PMC7888145/,"Sarhadi V., Mathew B., Kokkola A., Karla T., Tikkanen M., Rautelin H., Lahti L., Puolakkainen P. , Knuutila S.",Gut microbiota of patients with different subtypes of gastric cancer and gastrointestinal stromal tumors,Gut pathogens,2021,"Diffuse gastric adenocarcinoma, GIST, Gut microbiota, Intestinal gastric adenocarcinoma",Experiment 5,Finland,Homo sapiens,Feces,UBERON:0001988,Gastric adenocarcinoma,EFO:0000503,Healthy control,Diffuse adenocarcinoma,Subset of gastric adenocarcinoma patients with diffuse-type tumors.,13,12,6 months,16S,NA,Ion Torrent,centered log-ratio,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Table 3,22 April 2025,Shulamite,Shulamite,Taxa with significant differences (p ≤ 0.05) in pair-wise comparison of gastric cancer subgroups,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,1783272|201174|1760|85004|31953,Complete,KateRasheed
bsdb:33596997/7/1,33596997,case-control,33596997,10.1186/s13099-021-00403-x,https://pmc.ncbi.nlm.nih.gov/articles/PMC7888145/,"Sarhadi V., Mathew B., Kokkola A., Karla T., Tikkanen M., Rautelin H., Lahti L., Puolakkainen P. , Knuutila S.",Gut microbiota of patients with different subtypes of gastric cancer and gastrointestinal stromal tumors,Gut pathogens,2021,"Diffuse gastric adenocarcinoma, GIST, Gut microbiota, Intestinal gastric adenocarcinoma",Experiment 7,Finland,Homo sapiens,Feces,UBERON:0001988,Gastric adenocarcinoma,EFO:0000503,Healthy control,Intestinal adenocarcinoma,Subset of gastric adenocarcinoma patients with intestinal-type tumors.,13,15,6 months,16S,NA,Ion Torrent,centered log-ratio,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Table 3,22 April 2025,Shulamite,Shulamite,Taxa with significant differences (p ≤ 0.05) in pair-wise comparison of gastric cancer subgroups.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,KateRasheed
bsdb:33596997/7/2,33596997,case-control,33596997,10.1186/s13099-021-00403-x,https://pmc.ncbi.nlm.nih.gov/articles/PMC7888145/,"Sarhadi V., Mathew B., Kokkola A., Karla T., Tikkanen M., Rautelin H., Lahti L., Puolakkainen P. , Knuutila S.",Gut microbiota of patients with different subtypes of gastric cancer and gastrointestinal stromal tumors,Gut pathogens,2021,"Diffuse gastric adenocarcinoma, GIST, Gut microbiota, Intestinal gastric adenocarcinoma",Experiment 7,Finland,Homo sapiens,Feces,UBERON:0001988,Gastric adenocarcinoma,EFO:0000503,Healthy control,Intestinal adenocarcinoma,Subset of gastric adenocarcinoma patients with intestinal-type tumors.,13,15,6 months,16S,NA,Ion Torrent,centered log-ratio,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Table 3,22 April 2025,Shulamite,Shulamite,Taxa with significant differences (p ≤ 0.05) in pair-wise comparison of gastric cancer subgroups,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,1783272|1239|186801|186802|216572|459786,Complete,KateRasheed
bsdb:33596997/8/1,33596997,case-control,33596997,10.1186/s13099-021-00403-x,https://pmc.ncbi.nlm.nih.gov/articles/PMC7888145/,"Sarhadi V., Mathew B., Kokkola A., Karla T., Tikkanen M., Rautelin H., Lahti L., Puolakkainen P. , Knuutila S.",Gut microbiota of patients with different subtypes of gastric cancer and gastrointestinal stromal tumors,Gut pathogens,2021,"Diffuse gastric adenocarcinoma, GIST, Gut microbiota, Intestinal gastric adenocarcinoma",Experiment 8,Finland,Homo sapiens,Feces,UBERON:0001988,Gastric adenocarcinoma,EFO:0000503,Healthy control,Mixed adenocarcinoma,Subset of gastric adenocarcinoma patients with mixed histological features,13,2,6 months,16S,NA,Ion Torrent,centered log-ratio,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Table 3,22 April 2025,Shulamite,Shulamite,Taxa with significant differences (p ≤ 0.05) in pair-wise comparison of gastric cancer subgroups,increased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,1783272|1239|526524|526525|128827|61170,Complete,KateRasheed
bsdb:33596997/9/1,33596997,case-control,33596997,10.1186/s13099-021-00403-x,https://pmc.ncbi.nlm.nih.gov/articles/PMC7888145/,"Sarhadi V., Mathew B., Kokkola A., Karla T., Tikkanen M., Rautelin H., Lahti L., Puolakkainen P. , Knuutila S.",Gut microbiota of patients with different subtypes of gastric cancer and gastrointestinal stromal tumors,Gut pathogens,2021,"Diffuse gastric adenocarcinoma, GIST, Gut microbiota, Intestinal gastric adenocarcinoma",Experiment 9,Finland,Homo sapiens,Feces,UBERON:0001988,Colorectal Gastrointestinal Stromal Tumor,EFO:1000192,Gastrointestinal stromal tumors (GIST),Mixed adenocarcinoma,Subset of gastric adenocarcinoma patients with mixed histological features,23,2,6 months,16S,NA,Ion Torrent,centered log-ratio,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 3,22 April 2025,Shulamite,Shulamite,Taxa with significant differences (p ≤ 0.05) in pair-wise comparison of gastric cancer subgroups.,increased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,1783272|1239|526524|526525|128827|61170,Complete,KateRasheed
bsdb:33596997/10/1,33596997,case-control,33596997,10.1186/s13099-021-00403-x,https://pmc.ncbi.nlm.nih.gov/articles/PMC7888145/,"Sarhadi V., Mathew B., Kokkola A., Karla T., Tikkanen M., Rautelin H., Lahti L., Puolakkainen P. , Knuutila S.",Gut microbiota of patients with different subtypes of gastric cancer and gastrointestinal stromal tumors,Gut pathogens,2021,"Diffuse gastric adenocarcinoma, GIST, Gut microbiota, Intestinal gastric adenocarcinoma",Experiment 10,Finland,Homo sapiens,Feces,UBERON:0001988,Gastric adenocarcinoma,EFO:0000503,Intestinal adenocarcinoma,Mixed adenocarcinoma,Subset of gastric adenocarcinoma patients with mixed histological features.,15,2,6 months,16S,NA,Ion Torrent,centered log-ratio,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 3,22 April 2025,Shulamite,Shulamite,Taxa with significant differences (p ≤ 0.05) in pair-wise comparison of gastric cancer subgroups,increased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,1783272|1239|526524|526525|128827|61170,Complete,KateRasheed
bsdb:33599402/1/1,33599402,case-control,33599402,10.1111/1751-7915.13761,NA,"Wang S., Yang L., Hu H., Lv L., Ji Z., Zhao Y., Zhang H., Xu M., Fang R., Zheng L., Ding C., Yang M., Xu K. , Li L.",Characteristic gut microbiota and metabolic changes in patients with pulmonary tuberculosis,Microbial biotechnology,2022,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,Healthy controls,PTB patients,"Clinically and/or bacteriologically confirmed active PTB, T-SPOT.TB positive, pre-treatment",52,83,1 month,16S,34,Ion Torrent,relative abundances,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,4,"age,sex",HIV infection,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 2D,17 June 2025,Nuerteye,Nuerteye,"LDA, linear discriminant analysis. The circular cladogram was derived from the LEfSe analysis and showed the relationship between the most differentially abundant taxa in the patients with PTB (green) and the HCs (red). HCs, healthy controls; LEfSe, linear discriminant analysis effect size; PTB, pulmonary tuberculosis.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|976|200643|171549;3379134|976|200643|171549|171552,Complete,NA
bsdb:33599402/1/2,33599402,case-control,33599402,10.1111/1751-7915.13761,NA,"Wang S., Yang L., Hu H., Lv L., Ji Z., Zhao Y., Zhang H., Xu M., Fang R., Zheng L., Ding C., Yang M., Xu K. , Li L.",Characteristic gut microbiota and metabolic changes in patients with pulmonary tuberculosis,Microbial biotechnology,2022,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,Healthy controls,PTB patients,"Clinically and/or bacteriologically confirmed active PTB, T-SPOT.TB positive, pre-treatment",52,83,1 month,16S,34,Ion Torrent,relative abundances,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,4,"age,sex",HIV infection,NA,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 2D,17 June 2025,Nuerteye,Nuerteye,"LDA, linear discriminant analysis. The circular cladogram was derived from the LEfSe analysis and showed the relationship between the most differentially abundant taxa in the patients with PTB (green) and the HCs (red). HCs, healthy controls; LEfSe, linear discriminant analysis effect size; PTB, pulmonary tuberculosis.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales",1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|3085636|186803;1783272|201174|1760|85004,Complete,NA
bsdb:33603076/4/NA,33603076,time series / longitudinal observational,33603076,10.1038/s42003-021-01796-w,NA,"Xu R., Lu R., Zhang T., Wu Q., Cai W., Han X., Wan Z., Jin X., Zhang Z. , Zhang C.",Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults,Communications biology,2021,NA,Experiment 4,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls (Group H),Community Type III patients,"10 COVID-19 patients, 1 healthy control",13,11,NA,16S,4,Illumina,NA,ANOSIM,0.05,TRUE,NA,NA,NA,decreased,NA,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:33603076/5/NA,33603076,time series / longitudinal observational,33603076,10.1038/s42003-021-01796-w,NA,"Xu R., Lu R., Zhang T., Wu Q., Cai W., Han X., Wan Z., Jin X., Zhang Z. , Zhang C.",Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults,Communications biology,2021,NA,Experiment 5,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls (Group H),Community Type IV patients,4 COVID-19 patients,13,4,NA,16S,4,Illumina,NA,ANOSIM,0.05,TRUE,NA,NA,NA,decreased,NA,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:33613481/1/1,33613481,case-control,33613481,10.3389/fmicb.2021.610370,https://pubmed.ncbi.nlm.nih.gov/33613481/,"Almeida-Santos A., Martins-Mendes D., Gayà-Vidal M., Pérez-Pardal L. , Beja-Pereira A.",Characterization of the Oral Microbiome of Medicated Type-2 Diabetes Patients,Frontiers in microbiology,2021,"16S rRNA gene sequencing, Portugal, microbiota, next-generation sequencing, oral hygiene, type 2 diabetes mellitus",Experiment 1,Portugal,Homo sapiens,Saliva,UBERON:0001836,Type II diabetes mellitus,MONDO:0005148,Healthy controls,Medicated Type II Diabetes individuals,Medicated Type II Diabetes individuals,24,22,2 months,16S,34,Illumina,relative abundances,"ANCOM,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 6,17 June 2021,Madhubani Dey,"Madhubani Dey,Chloe,Merit,WikiWorks",Decreased abundance of microbes in individuals with medicated Type 2 Diabetes (Mann-Whitney's U results),decreased,"k__Thermotogati|p__Synergistota|c__Synergistia,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae",3384194|508458|649775;3384194|508458|649775|649776|649777;3384194|508458|649775|649776;3384194|508458|649775|649776|649777,Complete,Chloe
bsdb:33613481/1/2,33613481,case-control,33613481,10.3389/fmicb.2021.610370,https://pubmed.ncbi.nlm.nih.gov/33613481/,"Almeida-Santos A., Martins-Mendes D., Gayà-Vidal M., Pérez-Pardal L. , Beja-Pereira A.",Characterization of the Oral Microbiome of Medicated Type-2 Diabetes Patients,Frontiers in microbiology,2021,"16S rRNA gene sequencing, Portugal, microbiota, next-generation sequencing, oral hygiene, type 2 diabetes mellitus",Experiment 1,Portugal,Homo sapiens,Saliva,UBERON:0001836,Type II diabetes mellitus,MONDO:0005148,Healthy controls,Medicated Type II Diabetes individuals,Medicated Type II Diabetes individuals,24,22,2 months,16S,34,Illumina,relative abundances,"ANCOM,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table S6,14 March 2022,Chloe,"Chloe,Merit,WikiWorks",Decreased abundance of microbes in individuals with medicated Type 2 Diabetes (ANCOM results),decreased,"k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales,k__Thermotogati|p__Synergistota|c__Synergistia,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae",3384194|508458|649775|649776|649777;3384194|508458|649775|649776;3384194|508458|649775;3384194|508458|649775|649776|649777,Complete,Chloe
bsdb:33614635/1/1,33614635,case-control,33614635,https://doi.org/10.3389/fcell.2020.634069,https://www.frontiersin.org/articles/10.3389/fcell.2020.634069,"Ling Z., Zhu M., Yan X., Cheng Y., Shao L., Liu X., Jiang R. , Wu S.",Structural and Functional Dysbiosis of Fecal Microbiota in Chinese Patients With Alzheimer's Disease,Frontiers in cell and developmental biology,2020,"Alzheimer's disease, Bifidobacterium, Faecalibacterium, gut-brain axis, sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,healthy controls,Alzheimer’s disease patients,patients with Alzheimer’s disease,71,100,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 2,11 March 2023,Sophy,"Sophy,Mcarlson,Atrayees,Peace Sandy,WikiWorks",Differential bacterial taxa between the Chinese AD patients and the healthy controls,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Verrucomicrobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. MCF-1,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus|s__Alkaliphilus crotonatoxidans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. DL-VIII",1783272|201174|1760|2037;1783272|201174;3379134|74201|203494|48461|1647988|239934;1783272|1239|91061;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|201174|84998|84999;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|526524;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|186806|1730;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572|292632;3379134|74201|203494|48461|203557;3379134|74201|203494;3379134|74201|203494|48461;3379134|74201|203494|48461|203557|2735;1783272|1239|186801|186802|31979|1485|48257;1783272|1239|186801|3082720|3118656|114627|185693;1783272|1239|186801|186802|31979|1485|641107,Complete,Atrayees
bsdb:33614635/1/2,33614635,case-control,33614635,https://doi.org/10.3389/fcell.2020.634069,https://www.frontiersin.org/articles/10.3389/fcell.2020.634069,"Ling Z., Zhu M., Yan X., Cheng Y., Shao L., Liu X., Jiang R. , Wu S.",Structural and Functional Dysbiosis of Fecal Microbiota in Chinese Patients With Alzheimer's Disease,Frontiers in cell and developmental biology,2020,"Alzheimer's disease, Bifidobacterium, Faecalibacterium, gut-brain axis, sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,healthy controls,Alzheimer’s disease patients,patients with Alzheimer’s disease,71,100,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 2,11 March 2023,Sophy,"Sophy,Mcarlson,Atrayees,Peace Sandy,WikiWorks",Differential bacterial taxa between the Chinese AD patients and the healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|186801|3085636|186803|207244;1783272|1239;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|186803|33042;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|204475;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;1783272|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:33619320/1/1,33619320,prospective cohort,33619320,10.1038/s42003-021-01741-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7900251/pdf/42003_2021_Article_1741.pdf,"Sims T.T., El Alam M.B., Karpinets T.V., Dorta-Estremera S., Hegde V.L., Nookala S., Yoshida-Court K., Wu X., Biegert G.W.G., Delgado Medrano A.Y., Solley T., Ahmed-Kaddar M., Chapman B.V., Sastry K.J., Mezzari M.P., Petrosino J.F., Lin L.L., Ramondetta L., Jhingran A., Schmeler K.M., Ajami N.J., Wargo J., Colbert L.E. , Klopp A.H.",Gut microbiome diversity is an independent predictor of survival in cervical cancer patients receiving chemoradiation,Communications biology,2021,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Survival time,EFO:0000714,Long-term survivors,Short-term surviviors,Cervical Cancer patients that had a follow-up of one year or less because of death,48,7,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2a,16 March 2023,BLESSING123,"BLESSING123,Chloe,WikiWorks","The different abundance of bacterial taxa between the two
groups were identified by LEfSe. It was significantly different when alpha value of the factorial Kruskal–Wallis test was <0.05 and the logarithmic LDA score was
>3.5. The left histogram showed the LDA scores of taxa differentially abundant between the two groups. The taxonomy was listed, followed by its core group.
Putative species (Specific OTUs) identified as significantly more enriched/depleted (Fisher/Wilcoxon test p value < 0.05) in patients with short-term vs longterm in baseline samples",increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|91061;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294;3379134|29547|3031852|213849;3379134|29547;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|1940338;3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|81850;1783272|1239|91061|186826|33958|1578;3379134|1224|1236|135625|712;3379134|1224|1236|135625;1783272|1239|186801|3085636|186803|1506577;1783272|1239|909932|1843489|31977|29465,Complete,Chloe
bsdb:33619320/1/2,33619320,prospective cohort,33619320,10.1038/s42003-021-01741-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7900251/pdf/42003_2021_Article_1741.pdf,"Sims T.T., El Alam M.B., Karpinets T.V., Dorta-Estremera S., Hegde V.L., Nookala S., Yoshida-Court K., Wu X., Biegert G.W.G., Delgado Medrano A.Y., Solley T., Ahmed-Kaddar M., Chapman B.V., Sastry K.J., Mezzari M.P., Petrosino J.F., Lin L.L., Ramondetta L., Jhingran A., Schmeler K.M., Ajami N.J., Wargo J., Colbert L.E. , Klopp A.H.",Gut microbiome diversity is an independent predictor of survival in cervical cancer patients receiving chemoradiation,Communications biology,2021,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Survival time,EFO:0000714,Long-term survivors,Short-term surviviors,Cervical Cancer patients that had a follow-up of one year or less because of death,48,7,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2a,16 March 2023,BLESSING123,"BLESSING123,Chloe,WikiWorks","The different abundance of bacterial taxa between the two
groups were identified by LEfSe. It was significantly different when alpha value of the factorial Kruskal–Wallis test was <0.05 and the logarithmic LDA score was
>3.5. The left histogram showed the LDA scores of taxa differentially abundant between the two groups. The taxonomy was listed, followed by its core group.
Putative species (Specific OTUs) identified as significantly more enriched/depleted (Fisher/Wilcoxon test p value < 0.05) in patients with short-term vs longterm in baseline samples",decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",1783272|1239|909932|1843489|31977|39948;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836,Complete,Chloe
bsdb:33628840/1/1,33628840,case-control,33628840,https://doi.org/10.1155/2021/8892849,NA,"Enwu Yuan, Genxia Li, Jie You, Junya Zhang, Manman Yang, Pan Yin, Shihong Cui, Shuhua Guo, Shuhui Chu, Wanli Gao, Yajuan Xu, Texuan Zhu",Correlation Analysis between GDM and Gut Microbial Composition in Late Pregnancy,Journal of diabetes research,2021,"correlation analysis, diabetes mellitus, intestinal flora, metabolism, pathogenesis, third trimester",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycemic Pregnant Women (NOR),Gestational diabetes mellitus (GDM),Gestational diabetes mellitus patients in the third trimester of pregnancy,29,23,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,unchanged,decreased,NA,unchanged,Signature 1,Figure 4A,24 November 2025,Jamesonyebuchi,"Jamesonyebuchi,Temmie","Analysis of the difference in intestinal flora species between the different groups. Linear discriminant analysis (LDA), analysis of the Normoglycemic Pregnant Women (NOR) and Gestational diabetes mellitus (GDM) groups",increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|33042;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802,Complete,Svetlana up
bsdb:33628840/1/2,33628840,case-control,33628840,https://doi.org/10.1155/2021/8892849,NA,"Enwu Yuan, Genxia Li, Jie You, Junya Zhang, Manman Yang, Pan Yin, Shihong Cui, Shuhua Guo, Shuhui Chu, Wanli Gao, Yajuan Xu, Texuan Zhu",Correlation Analysis between GDM and Gut Microbial Composition in Late Pregnancy,Journal of diabetes research,2021,"correlation analysis, diabetes mellitus, intestinal flora, metabolism, pathogenesis, third trimester",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycemic Pregnant Women (NOR),Gestational diabetes mellitus (GDM),Gestational diabetes mellitus patients in the third trimester of pregnancy,29,23,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,unchanged,decreased,NA,unchanged,Signature 2,Figure 4A,24 November 2025,Jamesonyebuchi,Jamesonyebuchi,"Analysis of the difference in intestinal flora species between the different groups. Linear discriminant analysis (LDA), analysis of the Normoglycemic Pregnant Women (NOR) and Gestational diabetes mellitus (GDM) groups",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|1224|28216|80840|506;3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|1224|28216;3379134|1224|28216|80840;3384194|508458|649775|649776|3029088;3384194|508458|649775|649776|3029088|638847;3379134|1224|28216|80840|995019|40544,Complete,Svetlana up
bsdb:33628840/2/1,33628840,case-control,33628840,https://doi.org/10.1155/2021/8892849,NA,"Enwu Yuan, Genxia Li, Jie You, Junya Zhang, Manman Yang, Pan Yin, Shihong Cui, Shuhua Guo, Shuhui Chu, Wanli Gao, Yajuan Xu, Texuan Zhu",Correlation Analysis between GDM and Gut Microbial Composition in Late Pregnancy,Journal of diabetes research,2021,"correlation analysis, diabetes mellitus, intestinal flora, metabolism, pathogenesis, third trimester",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycemic Pregnant Women (NOR),Gestational diabetes mellitus (GDM),Gestational diabetes mellitus patients in the third trimester of pregnancy,29,23,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,unchanged,decreased,NA,unchanged,Signature 1,Figure 4B & Table 2,26 November 2025,Jamesonyebuchi,"Jamesonyebuchi,Temmie","Normoglycemic Pregnant Women (NOR) group VS Gestational diabetes mellitus (GDM) group, difference bacteria analysis at the species level",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas|s__Brevundimonas vesicularis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus pullicaecorum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella stercoris,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus delbrueckii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter|s__Psychrobacter pulmonis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium|s__Sphingobacterium mizutaii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas acidaminiphila,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] methylpentosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|526524|526525|128827|2749846|31971;3379134|976|200643|171549|815|816|85831;3379134|976|200643|171549|815|816|47678;1783272|1239|186801|3085636|186803|572511|1532;3379134|1224|28211|204458|76892|41275|41276;1783272|1239|186801|186802|3085642|580596|501571;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|84998|84999|84107|102106|147206;1783272|1239|526524|526525|2810280|100883|100884;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|189330|39486;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|3085636|186803|2719313|358743;1783272|1239|186801|186802|216572|216851|853;1783272|201174|84998|84999|1643824|2767327|82135;1783272|1239|186801|186802|204475|745368;1783272|1239|186801|3085636|186803|1649459|154046;1783272|1239|91061|186826|33958|1578|1584;1783272|1239|91061|186826|33958|2742598|97478;1783272|1239|186801|3085636|186803|2316020|33038;3379134|1224|28216|206351|481|482|28449;3379134|1224|1236|2887326|468|497|228654;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|526524|526525|128827|123375|102148;3379134|976|117747|200666|84566|28453|1010;3379134|1224|1236|135614|32033|40323|128780;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|526524|526525|2810280|3025755|29348;1783272|1239|186801|186802|216572|84026;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Svetlana up
bsdb:33628840/2/2,33628840,case-control,33628840,https://doi.org/10.1155/2021/8892849,NA,"Enwu Yuan, Genxia Li, Jie You, Junya Zhang, Manman Yang, Pan Yin, Shihong Cui, Shuhua Guo, Shuhui Chu, Wanli Gao, Yajuan Xu, Texuan Zhu",Correlation Analysis between GDM and Gut Microbial Composition in Late Pregnancy,Journal of diabetes research,2021,"correlation analysis, diabetes mellitus, intestinal flora, metabolism, pathogenesis, third trimester",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycemic Pregnant Women (NOR),Gestational diabetes mellitus (GDM),Gestational diabetes mellitus patients in the third trimester of pregnancy,29,23,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,unchanged,decreased,NA,unchanged,Signature 2,Figure 4B & Table 2,26 November 2025,Jamesonyebuchi,"Jamesonyebuchi,Temmie","Normoglycemic Pregnant Women (NOR) group VS Gestational diabetes mellitus (GDM) group, difference bacteria analysis at the species level",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter piscolens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter|s__Oxalobacter formigenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__Ruminiclostridium hungatei",3379134|976|200643|171549|815|909656|310297;3384194|508458|649775|649776|3029088|638847|638849;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|91061|186826|33958|2742598|1598;3379134|1224|28216|80840|75682|846|847;1783272|1239|186801|186802|216572|1508657|48256,Complete,Svetlana up
bsdb:33653942/1/1,33653942,prospective cohort,33653942,https://doi.org/10.1128/mSystems.00984-20,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8546988,NA,Dysbiosis in Metabolic Genes of the Gut Microbiomes of Patients with an Ileo-anal Pouch Resembles That Observed in Crohn's Disease,NA,NA,"pouchitis, UC, CD, mucin, butyrate, bile acids, oxidative stress, classifier, Crohn's disease, microbiome, ulcerative colitis",Experiment 1,Israel,Homo sapiens,Feces,UBERON:0001988,Inflammatory bowel disease,EFO:0003767,Normal pouch,Pouchitis,Patients with a pouch that developed inflammation,35,34,1 month (recent use) or 6 months off antibiotics,WMS,NA,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,age,NA,decreased,NA,NA,NA,NA,Signature 1,FIG 7,17 February 2024,Peace Sandy,"Peace Sandy,WikiWorks",Highest-scoring microbiome features identified by the classification models as the most informative for distinguishing between patients with a normal pouch and pouchitis and thus possibly predictive of pouchitis. The feature importance scores (averaged across 5-fold cross-validation) for (A) species.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hydrogenotrophica,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium 1_1_47,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Cellvibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 21_3,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 6_1_45,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 5_1_63FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|1224|1236|2887326|468|469;3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|3085636|186803|572511|53443;3379134|1224|28216|80840|469610;3379134|1224|1236|1706369|1706371|10;1783272|1239|91061|186826|81852|1350|1352;1783272|1239|526524|526525|128827|658657;1783272|1239|526524|526525|128827|469614;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|3085636|186803|658089;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|909932|1843489|31977|906|187326;3379134|1224|28216|80840|995019|577310|487175;1783272|1239|91061|186826|1300|1301|1311;1783272|1239|909932|1843489|31977|29465|39778;3379134|1224|1236|91347|1903411|629;1783272|1239|186801|186802|31979|1485|1522;1783272|1239|526524|526525|2810280|100883;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|1903414|586;1783272|201174|84998|1643822|1643826|84108;1783272|1239|909932|1843489|31977|29465,Complete,Peace Sandy
bsdb:33653942/1/2,33653942,prospective cohort,33653942,https://doi.org/10.1128/mSystems.00984-20,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8546988,NA,Dysbiosis in Metabolic Genes of the Gut Microbiomes of Patients with an Ileo-anal Pouch Resembles That Observed in Crohn's Disease,NA,NA,"pouchitis, UC, CD, mucin, butyrate, bile acids, oxidative stress, classifier, Crohn's disease, microbiome, ulcerative colitis",Experiment 1,Israel,Homo sapiens,Feces,UBERON:0001988,Inflammatory bowel disease,EFO:0003767,Normal pouch,Pouchitis,Patients with a pouch that developed inflammation,35,34,1 month (recent use) or 6 months off antibiotics,WMS,NA,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,age,NA,decreased,NA,NA,NA,NA,Signature 2,FIG 7,17 February 2024,Peace Sandy,"Peace Sandy,WikiWorks",Highest-scoring microbiome features identified by the classification models as the most informative for distinguishing between patients with a normal pouch and pouchitis and thus possibly predictive of pouchitis. The feature importance scores (averaged across 5-fold cross-validation) for (A) species.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 2_2_44A,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus pittmaniae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum longum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pasteurianus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Bartonellaceae|g__Bartonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",1783272|201174|1760|85004|31953|1678|28026;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|526524|526525|128827|457422;1783272|1239|186801|186802|216572|216851|853;3379134|1224|1236|135625|712|724|249188;3379134|976|200643|171549|815|909656|204516;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|186802|216572|1263|457412;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|186801|3085636|186803|1213720|796942;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|197614;1783272|1239|91061|186826|1300|1301|1343;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|186801|3085636|186803|2316020|46228;1783272|1239|186801|3085636|186803|2316020|33039;3379134|1224|28211|356|772|773;1783272|1239|186801|3085636|186803|189330;3379134|1224|1236|135619|28256|2745;1783272|1239|91061|186826|33958|1253;1783272|1239|186801|3082720|186804,Complete,Peace Sandy
bsdb:33655988/1/1,33655988,"cross-sectional observational, not case-control",33655988,10.1097/MD.0000000000025091,NA,"Su Y.J., Luo S.D., Hsu C.Y. , Kuo H.C.","Differences in gut microbiota between allergic rhinitis, atopic dermatitis, and skin urticaria: A pilot study",Medicine,2021,NA,Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,"Eczema,Urticaria","HP:0000964,EFO:0005531",Chronic urticaria (hives),Atopic dermatitis (eczema),Patients with atopic dermatitis (eczema),9,19,currently on antibiotics,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,NA,NA,unchanged,Signature 1,Figure 5,15 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","Phylum Firmicutes, class Clostridia, order Clostridiales, families Ruminococcaceae and Lachnospiraceae, genera Eubacterium and atopobium were 10,000 times higher than in the allergic rhinitis (rhinitis) subgroup. Species Bacteroids Plebeius DSM 17135 and genus Prevotella were 10,000 times higher than in the urticaria (hives) subgroup. Order Bacteroidales, class Bacteroidia, phylum Bacteroidetes, and genus Romboutsia were 10,000 times higher than in the atopic dermatitis (eczema) subgroup.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia",3379134|976|200643|171549;1783272|1239|186801|3082720|186804|1501226;3379134|1224|28216|80840|995019|40544;3379134|976|200643,Complete,Peace Sandy
bsdb:33655988/1/2,33655988,"cross-sectional observational, not case-control",33655988,10.1097/MD.0000000000025091,NA,"Su Y.J., Luo S.D., Hsu C.Y. , Kuo H.C.","Differences in gut microbiota between allergic rhinitis, atopic dermatitis, and skin urticaria: A pilot study",Medicine,2021,NA,Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,"Eczema,Urticaria","HP:0000964,EFO:0005531",Chronic urticaria (hives),Atopic dermatitis (eczema),Patients with atopic dermatitis (eczema),9,19,currently on antibiotics,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,NA,NA,unchanged,Signature 2,Fig 5,15 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","Phylum Firmicutes, class Clostridia, order Clostridiales, families Ruminococcaceae and Lachnospiraceae, genera Eubacterium and atopobium were 10,000 times higher than in the allergic rhinitis (rhinitis) subgroup. Species Bacteroids Plebeius DSM 17135 and genus Prevotella were 10,000 times higher than in the urticaria (hives) subgroup. Order Bacteroidales, class Bacteroidia, phylum Bacteroidetes, and genus Romboutsia were 10,000 times higher than in the atopic dermatitis (eczema) subgroup.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|171552|838,Complete,Peace Sandy
bsdb:33655988/2/1,33655988,"cross-sectional observational, not case-control",33655988,10.1097/MD.0000000000025091,NA,"Su Y.J., Luo S.D., Hsu C.Y. , Kuo H.C.","Differences in gut microbiota between allergic rhinitis, atopic dermatitis, and skin urticaria: A pilot study",Medicine,2021,NA,Experiment 2,Taiwan,Homo sapiens,Feces,UBERON:0001988,"Eczema,Allergic rhinitis","HP:0000964,EFO:0005854",Allergic rhinitis,Atopic dermatitis (eczema),currently on antibiotics,9,19,Those with a history of antibiotics,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,NA,NA,unchanged,Signature 1,Fig 5,15 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","Phylum Firmicutes, class Clostridia, order Clostridiales, families Ruminococcaceae and Lachnospiraceae, genera Eubacterium and atopobium were 10,000 times higher than in the allergic rhinitis (rhinitis) subgroup. Species Bacteroids Plebeius DSM 17135 and genus Prevotella were 10,000 times higher than in the urticaria (hives) subgroup. Order Bacteroidales, class Bacteroidia, phylum Bacteroidetes, and genus Romboutsia were 10,000 times higher than in the atopic dermatitis (eczema) subgroup.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|976|200643|171549;3379134|976|200643;1783272|1239|186801|3082720|186804|1501226;3379134|1224|28216|80840|995019|40544,Complete,Peace Sandy
bsdb:33655988/2/2,33655988,"cross-sectional observational, not case-control",33655988,10.1097/MD.0000000000025091,NA,"Su Y.J., Luo S.D., Hsu C.Y. , Kuo H.C.","Differences in gut microbiota between allergic rhinitis, atopic dermatitis, and skin urticaria: A pilot study",Medicine,2021,NA,Experiment 2,Taiwan,Homo sapiens,Feces,UBERON:0001988,"Eczema,Allergic rhinitis","HP:0000964,EFO:0005854",Allergic rhinitis,Atopic dermatitis (eczema),currently on antibiotics,9,19,Those with a history of antibiotics,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,NA,NA,unchanged,Signature 2,Figure 5,15 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","Phylum Firmicutes, class Clostridia, order Clostridiales, families Ruminococcaceae and Lachnospiraceae, genera Eubacterium and atopobium were 10,000 times higher than in the allergic rhinitis (rhinitis) subgroup. Species Bacteroids Plebeius DSM 17135 and genus Prevotella were 10,000 times higher than in the urticaria (hives) subgroup. Order Bacteroidales, class Bacteroidia, phylum Bacteroidetes, and genus Romboutsia were 10,000 times higher than in the atopic dermatitis (eczema) subgroup.",decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|201174|84998|84999|1643824|1380;1783272|1239;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|3085636|186803,Complete,Peace Sandy
bsdb:33657381/1/1,33657381,case-control,33657381,https://doi.org/10.1016/j.celrep.2021.108807,NA,"Rosario D., Bidkhori G., Lee S., Bedarf J., Hildebrand F., Le Chatelier E., Uhlen M., Ehrlich S.D., Proctor G., Wüllner U., Mardinoglu A. , Shoaie S.",Systematic analysis of gut microbiome reveals the role of bacterial folate and homocysteine metabolism in Parkinson's disease,Cell reports,2021,"Parkinson’s disease, gut microbiota, gut-brain axis, metabolic modeling, metagenomics",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Patients with Parkinson's Disease,Patient with Early-stage L-DOPA-Naive Parkinson's Disease,11,26,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S1,9 March 2024,Raihanat,"Raihanat,Peace Sandy,WikiWorks",Representation of the most significant (FDR < 0.01) classified taxonomic alterations between Parkinson’s disease (PD) and controls.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|s__Christensenellaceae bacterium,k__Methanobacteriati|p__Methanobacteriota,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;1783272|1239;3379134|976|200643|171549|815|816;1783272|1239|186801|3082768|990719|2054177;3366610|28890;3366610|28890|183925|2158|2159;3366610|28890|183925|2158|2159|2172;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|186802|216572|1905344;3379134|74201|203494;1783272|1239|186801|186802|1392389;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|3082768|990719,Complete,Peace Sandy
bsdb:33657381/1/2,33657381,case-control,33657381,https://doi.org/10.1016/j.celrep.2021.108807,NA,"Rosario D., Bidkhori G., Lee S., Bedarf J., Hildebrand F., Le Chatelier E., Uhlen M., Ehrlich S.D., Proctor G., Wüllner U., Mardinoglu A. , Shoaie S.",Systematic analysis of gut microbiome reveals the role of bacterial folate and homocysteine metabolism in Parkinson's disease,Cell reports,2021,"Parkinson’s disease, gut microbiota, gut-brain axis, metabolic modeling, metagenomics",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Patients with Parkinson's Disease,Patient with Early-stage L-DOPA-Naive Parkinson's Disease,11,26,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S1,12 March 2024,Raihanat,"Raihanat,WikiWorks",Representation of the most significant (FDR < 0.01) classified taxonomic alterations between Parkinson’s disease (PD) and controls.,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae",3379134|976;1783272|1239|186801|186802|216572|216851;3384189|32066|203490|203491|203492;3379134|1224|1236|135625|712|724;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|2005473;1783272|1239|186801|3085636|186803|841;1783272|201174|84998|1643822|1643826|84108;3379134|1224|28216|80840|995019|40544;1783272|1239|909932|1843489|31977|29465;3384189|32066|203490;1783272|1239|526524|526525|128827;3379134|1224|1236|135625|712;3379134|1224|28216|80840|995019,Complete,Peace Sandy
bsdb:33657381/2/1,33657381,case-control,33657381,https://doi.org/10.1016/j.celrep.2021.108807,NA,"Rosario D., Bidkhori G., Lee S., Bedarf J., Hildebrand F., Le Chatelier E., Uhlen M., Ehrlich S.D., Proctor G., Wüllner U., Mardinoglu A. , Shoaie S.",Systematic analysis of gut microbiome reveals the role of bacterial folate and homocysteine metabolism in Parkinson's disease,Cell reports,2021,"Parkinson’s disease, gut microbiota, gut-brain axis, metabolic modeling, metagenomics",Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Diseased Controls,Patients with Parkinson's Disease,Patients with Early-stage L-DOPA-Naive Parkinson's Disease,14,26,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S1,16 March 2024,Raihanat,"Raihanat,Peace Sandy,WikiWorks",Representation of the most significant (FDR < 0.01) classified taxonomic alterations between Parkinson’s disease (PD) and Diseased Controls(DC),increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Hymenochaetales|f__Rickenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__uncultured Ruminiclostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Merdimonas",1783272|201174|84998|1643822|1643826|447020;3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|207244;3379134|1224|28211|204441|2829815|191;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|186801|3082720|186804;3379134|1224|28211|204441|41295;4751|5204|155619|139380|1124673;1783272|1239|186801|3082720|186804|1501226;1783272|1239|526524|526525|2810280|3025755|1547;3379134|74201|203494;3379134|256845|1313211|278082|255528;3379134|256845|1313211|278082|255528|172900;1783272|1239|186801|186802|216572|1508657|1757166;1783272|1239|186801|3085636|186803|2023266,Complete,Peace Sandy
bsdb:33657381/2/2,33657381,case-control,33657381,https://doi.org/10.1016/j.celrep.2021.108807,NA,"Rosario D., Bidkhori G., Lee S., Bedarf J., Hildebrand F., Le Chatelier E., Uhlen M., Ehrlich S.D., Proctor G., Wüllner U., Mardinoglu A. , Shoaie S.",Systematic analysis of gut microbiome reveals the role of bacterial folate and homocysteine metabolism in Parkinson's disease,Cell reports,2021,"Parkinson’s disease, gut microbiota, gut-brain axis, metabolic modeling, metagenomics",Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Diseased Controls,Patients with Parkinson's Disease,Patients with Early-stage L-DOPA-Naive Parkinson's Disease,14,26,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S1,16 March 2024,Raihanat,"Raihanat,Peace Sandy,WikiWorks",Representation of the most significant (FDR < 0.01) classified taxonomic alterations between Parkinson’s disease (PD) and Diseased Controls (DC),decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera geminata,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinatimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|1239|909932|1843489|31977|906|156456;1783272|201174|84998|84999|1643824;1783272|201174|84998|84999|1643824|1380;3379134|976;3379134|203691|203692|1643686|143786|29521;3379134|203691|203692|1643686|143786;3379134|976|200643|171549|1853231|574697;1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|186802|31979;1783272|201174|84998|84999|84107|102106;3379134|976|200643|171549|2005519|1348911;1783272|201174|84998|84999|84107;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|216572|1940255;3379134|1224|1236|135625|712|724;1783272|1239|526524|526525|128827|1573535;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|201174|84998|84999|1643824|133925;3379134|976|200643|171549|171552|577309;3379134|1224|1236|135625|712;3379134|976|200643|171549|171552|838;3379134|203691|203692|136|137|146;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;3379134|1224|1236|135624|83763|674963;3379134|1224|1236|135624|83763;1783272|1239|186801|3085636|186803|1506577;3379134|976|200643|171549|2005473,Complete,Peace Sandy
bsdb:33658058/1/1,33658058,case-control,33658058,10.1186/s13073-021-00856-4,NA,"Alvarez-Silva C., Kashani A., Hansen T.H., Pinna N.K., Anjana R.M., Dutta A., Saxena S., Støy J., Kampmann U., Nielsen T., Jørgensen T., Gnanaprakash V., Gnanavadivel R., Sukumaran A., Rani C.S.S., Færch K., Radha V., Balasubramanyam M., Nair G.B., Das B., Vestergaard H., Hansen T., Mande S.S., Mohan V., Arumugam M. , Pedersen O.",Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India,Genome medicine,2021,"Danes, Gut microbiota, Indians, Metformin, Populations, Trans-ethnic, Type 2 diabetes",Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Response to metformin,GO:1901558,metformin-naive type 2 diabetes (T2D) patients,metformin-treated T2D patients,"T2D patients treated with the anti-hyperglycemic drug, metformin",71,86,NA,16S,12345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,proton-pump inhibitor,sex",NA,NA,NA,NA,NA,decreased,Signature 1,Supplemental Table S11,6 November 2023,ChiomaBlessing,"ChiomaBlessing,Folakunmi,WikiWorks",Differential abundant taxa between metformin-naive T2D and metformin-treated T2D in the Indian substudy,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,1783272|1239|186801|3085636|186803|1506553,Complete,Folakunmi
bsdb:33658058/2/1,33658058,case-control,33658058,10.1186/s13073-021-00856-4,NA,"Alvarez-Silva C., Kashani A., Hansen T.H., Pinna N.K., Anjana R.M., Dutta A., Saxena S., Støy J., Kampmann U., Nielsen T., Jørgensen T., Gnanaprakash V., Gnanavadivel R., Sukumaran A., Rani C.S.S., Færch K., Radha V., Balasubramanyam M., Nair G.B., Das B., Vestergaard H., Hansen T., Mande S.S., Mohan V., Arumugam M. , Pedersen O.",Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India,Genome medicine,2021,"Danes, Gut microbiota, Indians, Metformin, Populations, Trans-ethnic, Type 2 diabetes",Experiment 2,Denmark,Homo sapiens,Feces,UBERON:0001988,Response to metformin,GO:1901558,metformin-naive type 2 diabetes (T2D) patients,metformin-treated T2D patients,"T2D patients treated with the anti-hyperglycemic drug, metformin",61,80,4 months,16S,12345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,proton-pump inhibitor,sex",NA,NA,NA,NA,NA,decreased,Signature 1,Supplemental Table S10b,6 November 2023,ChiomaBlessing,"ChiomaBlessing,Folakunmi,WikiWorks",Differential abundant taxa between metformin-naive T2D and metformin-treated T2D in the Danish substudy,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,3379134|1224|1236|91347|543|1940338,Complete,Folakunmi
bsdb:33658058/3/1,33658058,case-control,33658058,10.1186/s13073-021-00856-4,NA,"Alvarez-Silva C., Kashani A., Hansen T.H., Pinna N.K., Anjana R.M., Dutta A., Saxena S., Støy J., Kampmann U., Nielsen T., Jørgensen T., Gnanaprakash V., Gnanavadivel R., Sukumaran A., Rani C.S.S., Færch K., Radha V., Balasubramanyam M., Nair G.B., Das B., Vestergaard H., Hansen T., Mande S.S., Mohan V., Arumugam M. , Pedersen O.",Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India,Genome medicine,2021,"Danes, Gut microbiota, Indians, Metformin, Populations, Trans-ethnic, Type 2 diabetes",Experiment 3,"Denmark,India",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Indians (normoglycaemic controls and T2D patients),Denmark (normoglycaemic controls and T2D patients),Gut microbiota in Denmark participants,294,279,4 months (Denmark participants),16S,12345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,proton-pump inhibitor,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table S2b,6 November 2023,ChiomaBlessing,"ChiomaBlessing,Joan Chuks,WikiWorks",Differentially abundant taxa in the gut microbiome between Danes and Indians (normoglycaemic controls and T2D patients),increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Angelakisella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Merdibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis,k__Bacillati|p__Bacillota|g__Negativibacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__Ruminiclostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Sanguibacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Massiliimalia",1783272|201174|84998|1643822|1643826|447020;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|52784;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|186802|216572|1935176;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005519|397864;3379134|200940|3031449|213115|194924|35832;3379134|1224|28211|356|41294|374;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|3082768|990719|990721;3379134|976|200643|171549|2005519|1348911;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|946234;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|877420;1783272|1239|526524|526525|128827|1935200;1783272|1239|186801|186802|216572|3028852;1783272|1239|1980693;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|119852;3379134|1224|28216|80840|75682|846;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|577309;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|186802|186807|2740;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|186802|216572|1017280;1783272|201174|1760|85007|85025|1827;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|186802|216572|1508657|2053608;1783272|1239|186801|186802|216572|1263|41978;3379134|976|200643|171549|171551|1635148;1783272|1239|186801|186802|216572|292632;3379134|1224|28216|80840|995019|40544;1783272|1239|526524|526525|128827|331630;1783272|1239|186801|3085636|186803|297314;1783272|1239|186801|186802|216572|707003;1783272|1239|186801|186802|216572|2895461,Complete,Folakunmi
bsdb:33658058/3/2,33658058,case-control,33658058,10.1186/s13073-021-00856-4,NA,"Alvarez-Silva C., Kashani A., Hansen T.H., Pinna N.K., Anjana R.M., Dutta A., Saxena S., Støy J., Kampmann U., Nielsen T., Jørgensen T., Gnanaprakash V., Gnanavadivel R., Sukumaran A., Rani C.S.S., Færch K., Radha V., Balasubramanyam M., Nair G.B., Das B., Vestergaard H., Hansen T., Mande S.S., Mohan V., Arumugam M. , Pedersen O.",Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India,Genome medicine,2021,"Danes, Gut microbiota, Indians, Metformin, Populations, Trans-ethnic, Type 2 diabetes",Experiment 3,"Denmark,India",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Indians (normoglycaemic controls and T2D patients),Denmark (normoglycaemic controls and T2D patients),Gut microbiota in Denmark participants,294,279,4 months (Denmark participants),16S,12345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,proton-pump inhibitor,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table S2b,6 November 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differentially abundant taxa in the gut microbiome between Danes and Indians (normoglycaemic controls and T2D patients),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Kerstersia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia caballeronis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp.",3379134|1224|28216|80840|506|222;1783272|201174|1760|2037|2049|1654;1783272|1239|186801|3085636|186803|1766253;3379134|976|200643|171549|171552|1283313;1783272|1239|909932|1843489|31977|156454;1783272|1239|186801|3085636|186803|207244;1783272|201174|1760|85004|31953|1678;1783272|1239|526524|526525|2810280|135858;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|1407607;1783272|1239|91061|186826|186828|117563;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|186802|404402;3379134|1224|28216|80840|506|257820;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|248744;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|909929|1843491|52225;1783272|201174|84998|84999|1643824|133925;1783272|1239|186801|3085636|186803|265975;3379134|1224|28216|80840|119060|1822464|416943;1783272|201174|84998|84999|1643824|2082587;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841|166486;1783272|201174|84998|84999|84107|1473205;3379134|1224|1236|91347|1903411|613;1783272|1239|526524|526525|128827|123375;1783272|1239|186801|3082720|186804|1505652;1783272|1239|91061|186826|33958|46255;1783272|1239|186801|186802|216572|707003;3379134|976|200643|171549|171552|838|59823;1783272|1239|186801|3085636|186803|33042|2049024,Complete,Folakunmi
bsdb:33658058/4/1,33658058,case-control,33658058,10.1186/s13073-021-00856-4,NA,"Alvarez-Silva C., Kashani A., Hansen T.H., Pinna N.K., Anjana R.M., Dutta A., Saxena S., Støy J., Kampmann U., Nielsen T., Jørgensen T., Gnanaprakash V., Gnanavadivel R., Sukumaran A., Rani C.S.S., Færch K., Radha V., Balasubramanyam M., Nair G.B., Das B., Vestergaard H., Hansen T., Mande S.S., Mohan V., Arumugam M. , Pedersen O.",Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India,Genome medicine,2021,"Danes, Gut microbiota, Indians, Metformin, Populations, Trans-ethnic, Type 2 diabetes",Experiment 4,"Denmark,India",Homo sapiens,Feces,UBERON:0001988,Metformin,CHEBI:6801,metformin-naive type 2 diabetes (T2D) patients,metformin-treated T2D patients,"T2D patients treated with the anti-hyperglycemic drug, metformin",132,166,4 months (Denmark participants),16S,12345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,geographic area,proton-pump inhibitor,sex",NA,NA,NA,NA,NA,decreased,Signature 1,Supplemental. TableS9,4 January 2024,Folakunmi,"Folakunmi,WikiWorks",Differential abundant taxa between metformin-naive T2D and metformin-treated T2D in the combined Danish-Indian group,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,1783272|1239|186801|186802|216572|216851,Complete,Folakunmi
bsdb:33658058/4/2,33658058,case-control,33658058,10.1186/s13073-021-00856-4,NA,"Alvarez-Silva C., Kashani A., Hansen T.H., Pinna N.K., Anjana R.M., Dutta A., Saxena S., Støy J., Kampmann U., Nielsen T., Jørgensen T., Gnanaprakash V., Gnanavadivel R., Sukumaran A., Rani C.S.S., Færch K., Radha V., Balasubramanyam M., Nair G.B., Das B., Vestergaard H., Hansen T., Mande S.S., Mohan V., Arumugam M. , Pedersen O.",Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India,Genome medicine,2021,"Danes, Gut microbiota, Indians, Metformin, Populations, Trans-ethnic, Type 2 diabetes",Experiment 4,"Denmark,India",Homo sapiens,Feces,UBERON:0001988,Metformin,CHEBI:6801,metformin-naive type 2 diabetes (T2D) patients,metformin-treated T2D patients,"T2D patients treated with the anti-hyperglycemic drug, metformin",132,166,4 months (Denmark participants),16S,12345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,geographic area,proton-pump inhibitor,sex",NA,NA,NA,NA,NA,decreased,Signature 2,Supplemental. TableS9,6 November 2023,ChiomaBlessing,"ChiomaBlessing,Folakunmi,WikiWorks",Differential abundant taxa between metformin-naive T2D and metformin-treated T2D in the combined Danish-Indian group,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,3379134|976|200643|171549|815|816|29523,Complete,Folakunmi
bsdb:33658058/5/1,33658058,case-control,33658058,10.1186/s13073-021-00856-4,NA,"Alvarez-Silva C., Kashani A., Hansen T.H., Pinna N.K., Anjana R.M., Dutta A., Saxena S., Støy J., Kampmann U., Nielsen T., Jørgensen T., Gnanaprakash V., Gnanavadivel R., Sukumaran A., Rani C.S.S., Færch K., Radha V., Balasubramanyam M., Nair G.B., Das B., Vestergaard H., Hansen T., Mande S.S., Mohan V., Arumugam M. , Pedersen O.",Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India,Genome medicine,2021,"Danes, Gut microbiota, Indians, Metformin, Populations, Trans-ethnic, Type 2 diabetes",Experiment 5,"Denmark,India",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic (NG) controls,Type 2 diabetes (T2D) patients,Individuals diagnosed with T2D,275,298,4 months (Denmark participants),16S,12345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,geographic area,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplemental. Table S3A,8 November 2023,ChiomaBlessing,"ChiomaBlessing,Folakunmi,WikiWorks",Differential abundant taxa between type 2 diabetes (T2D) VS normoglycemic controls (NG) in the combined Danish-Indian group,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",1783272|1239|186801|3085636|186803|653683;1783272|1239|186801|186802|3085642|580596;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572|216851;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263|41978;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|216572|707003,Complete,Folakunmi
bsdb:33658058/5/2,33658058,case-control,33658058,10.1186/s13073-021-00856-4,NA,"Alvarez-Silva C., Kashani A., Hansen T.H., Pinna N.K., Anjana R.M., Dutta A., Saxena S., Støy J., Kampmann U., Nielsen T., Jørgensen T., Gnanaprakash V., Gnanavadivel R., Sukumaran A., Rani C.S.S., Færch K., Radha V., Balasubramanyam M., Nair G.B., Das B., Vestergaard H., Hansen T., Mande S.S., Mohan V., Arumugam M. , Pedersen O.",Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India,Genome medicine,2021,"Danes, Gut microbiota, Indians, Metformin, Populations, Trans-ethnic, Type 2 diabetes",Experiment 5,"Denmark,India",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic (NG) controls,Type 2 diabetes (T2D) patients,Individuals diagnosed with T2D,275,298,4 months (Denmark participants),16S,12345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,geographic area,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplemental Table S3A & B,8 November 2023,ChiomaBlessing,"ChiomaBlessing,Folakunmi,WikiWorks",Differential abundant taxa between type 2 diabetes (T2D) VS normoglycemic controls (NG) in the combined Danish-Indian group,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:56,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511|1955243;1783272|1239|186801|3085636|186803|33042|2049024;1783272|1239|186801|3085636|186803|189330;1783272|1239|1263031;1783272|1239|186801|3085636|186803|1506553;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|186802|216572|459786,Complete,Folakunmi
bsdb:33658058/6/1,33658058,case-control,33658058,10.1186/s13073-021-00856-4,NA,"Alvarez-Silva C., Kashani A., Hansen T.H., Pinna N.K., Anjana R.M., Dutta A., Saxena S., Støy J., Kampmann U., Nielsen T., Jørgensen T., Gnanaprakash V., Gnanavadivel R., Sukumaran A., Rani C.S.S., Færch K., Radha V., Balasubramanyam M., Nair G.B., Das B., Vestergaard H., Hansen T., Mande S.S., Mohan V., Arumugam M. , Pedersen O.",Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India,Genome medicine,2021,"Danes, Gut microbiota, Indians, Metformin, Populations, Trans-ethnic, Type 2 diabetes",Experiment 6,"Denmark,India",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic (NG) controls,Type 2 diabetes (T2D) patients,Individuals diagnosed with T2D,275,298,4 months (Denmark participants),16S,12345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,geographic area,proton-pump inhibitor,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Supplemental. Table S4A and B,8 November 2023,ChiomaBlessing,"ChiomaBlessing,Folakunmi,WikiWorks",Differential abundant taxa between type 2 diabetes (T2D) VS normoglycemic controls (NG) in the combined Danish-Indian group,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",1783272|1239|186801|3085636|186803|653683;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|216572|292632,Complete,Folakunmi
bsdb:33658058/6/2,33658058,case-control,33658058,10.1186/s13073-021-00856-4,NA,"Alvarez-Silva C., Kashani A., Hansen T.H., Pinna N.K., Anjana R.M., Dutta A., Saxena S., Støy J., Kampmann U., Nielsen T., Jørgensen T., Gnanaprakash V., Gnanavadivel R., Sukumaran A., Rani C.S.S., Færch K., Radha V., Balasubramanyam M., Nair G.B., Das B., Vestergaard H., Hansen T., Mande S.S., Mohan V., Arumugam M. , Pedersen O.",Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India,Genome medicine,2021,"Danes, Gut microbiota, Indians, Metformin, Populations, Trans-ethnic, Type 2 diabetes",Experiment 6,"Denmark,India",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic (NG) controls,Type 2 diabetes (T2D) patients,Individuals diagnosed with T2D,275,298,4 months (Denmark participants),16S,12345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,geographic area,proton-pump inhibitor,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,Supplemental. Table S4A and B,8 November 2023,ChiomaBlessing,"ChiomaBlessing,Folakunmi,WikiWorks",Differential abundant taxa between type 2 diabetes (T2D) VS normoglycemic controls (NG) in the combined Danish-Indian group,increased,"k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:56,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",1783272|1239|1263031;1783272|1239|186801|3085636|186803|1506553,Complete,Folakunmi
bsdb:33658058/7/1,33658058,case-control,33658058,10.1186/s13073-021-00856-4,NA,"Alvarez-Silva C., Kashani A., Hansen T.H., Pinna N.K., Anjana R.M., Dutta A., Saxena S., Støy J., Kampmann U., Nielsen T., Jørgensen T., Gnanaprakash V., Gnanavadivel R., Sukumaran A., Rani C.S.S., Færch K., Radha V., Balasubramanyam M., Nair G.B., Das B., Vestergaard H., Hansen T., Mande S.S., Mohan V., Arumugam M. , Pedersen O.",Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India,Genome medicine,2021,"Danes, Gut microbiota, Indians, Metformin, Populations, Trans-ethnic, Type 2 diabetes",Experiment 7,Denmark,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic (NG) controls,Type 2 diabetes (T2D) patients,Individuals diagnosed with T2D,275,298,4 months,16S,12345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,proton-pump inhibitor,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Supplemental Table S6A,8 November 2023,ChiomaBlessing,"ChiomaBlessing,Folakunmi,WikiWorks",Differentially abundant taxa between type 2 diabetes (T2D) VS normoglycemic controls (NG) in the Danish substudy,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,1783272|1239|186801|3085636|186803|1506553,Complete,Folakunmi
bsdb:33658065/1/1,33658065,"cross-sectional observational, not case-control",33658065,10.1186/s13073-021-00851-9,NA,"Pinna N.K., Anjana R.M., Saxena S., Dutta A., Gnanaprakash V., Rameshkumar G., Aswath S., Raghavan S., Rani C.S.S., Radha V., Balasubramanyam M., Pant A., Nielsen T., Jørgensen T., Færch K., Kashani A., Silva M.C.A., Vestergaard H., Hansen T.H., Hansen T., Arumugam M., Nair G.B., Das B., Pedersen O., Mohan V. , Mande S.S.",Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark,Genome medicine,2021,NA,Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic (NG) controls - Danish Cohort,Prediabetes (PD) - Danish Cohort,Prediabetes (PD) - Danish Cohort refers to patients in their early stage of prediabetes.,138,121,4 months,16S,12345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Additional file 11: Table S9A,5 November 2024,KateRasheed,"KateRasheed,WikiWorks,Tosin","Differentially abundant taxa between NG and PD subjects, belonging to the Danish cohort, identified using a negative binomial Wald test.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,s__bacterium FCS020,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005",3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|329854;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|40520;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|3085636|186803|1432051|1720294;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|186802|216572;1783272|1239|526524|526525|2810280|3025755;1451755;1783272|1239|186801|186802|216572|707003;1783272|1239|186801|186802|216572|3068309,Complete,Svetlana up
bsdb:33658065/1/2,33658065,"cross-sectional observational, not case-control",33658065,10.1186/s13073-021-00851-9,NA,"Pinna N.K., Anjana R.M., Saxena S., Dutta A., Gnanaprakash V., Rameshkumar G., Aswath S., Raghavan S., Rani C.S.S., Radha V., Balasubramanyam M., Pant A., Nielsen T., Jørgensen T., Færch K., Kashani A., Silva M.C.A., Vestergaard H., Hansen T.H., Hansen T., Arumugam M., Nair G.B., Das B., Pedersen O., Mohan V. , Mande S.S.",Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark,Genome medicine,2021,NA,Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic (NG) controls - Danish Cohort,Prediabetes (PD) - Danish Cohort,Prediabetes (PD) - Danish Cohort refers to patients in their early stage of prediabetes.,138,121,4 months,16S,12345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Additional file 11: Table S9A,5 November 2024,KateRasheed,"KateRasheed,WikiWorks,Tosin","Differentially abundant taxa between NG and PD subjects, belonging to the Danish cohort, identified using a negative binomial Wald test.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,s__rumen bacterium NK4A214,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|s__uncultured Mollicutes bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005",1783272|1239|186801|186802|216572|459786;1783272|1239|909932|1843488|909930|33024|33025;877428;1783272|544448|31969|220137;1783272|1239|186801|186802|216572|3068309,Complete,Svetlana up
bsdb:33658065/2/1,33658065,"cross-sectional observational, not case-control",33658065,10.1186/s13073-021-00851-9,NA,"Pinna N.K., Anjana R.M., Saxena S., Dutta A., Gnanaprakash V., Rameshkumar G., Aswath S., Raghavan S., Rani C.S.S., Radha V., Balasubramanyam M., Pant A., Nielsen T., Jørgensen T., Færch K., Kashani A., Silva M.C.A., Vestergaard H., Hansen T.H., Hansen T., Arumugam M., Nair G.B., Das B., Pedersen O., Mohan V. , Mande S.S.",Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark,Genome medicine,2021,NA,Experiment 2,Denmark,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic (NG) controls - Danish Cohort,Prediabetes (PD) - Danish Cohort,Prediabetes (PD) - Danish Cohort refers to patients in their early stage of prediabetes.,138,121,4 months,16S,12345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Additional file 11: Table S9B,5 November 2024,KateRasheed,"KateRasheed,WikiWorks,Tosin","Differentially abundant taxa between NG and PD subjects, belonging to the Danish cohort, identified after correcting for covariates (age, gender, waist-to-hip ratio, Systolic BP, IL6, TNFα, LBP and IAP)  using a negative binomial Wald test.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,s__rumen bacterium NK4A214,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005",3379134|976|200643|171549|815|909656|821;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|301302;877428;1783272|1239|186801|186802|216572|3068309,Complete,Svetlana up
bsdb:33658065/2/2,33658065,"cross-sectional observational, not case-control",33658065,10.1186/s13073-021-00851-9,NA,"Pinna N.K., Anjana R.M., Saxena S., Dutta A., Gnanaprakash V., Rameshkumar G., Aswath S., Raghavan S., Rani C.S.S., Radha V., Balasubramanyam M., Pant A., Nielsen T., Jørgensen T., Færch K., Kashani A., Silva M.C.A., Vestergaard H., Hansen T.H., Hansen T., Arumugam M., Nair G.B., Das B., Pedersen O., Mohan V. , Mande S.S.",Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark,Genome medicine,2021,NA,Experiment 2,Denmark,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic (NG) controls - Danish Cohort,Prediabetes (PD) - Danish Cohort,Prediabetes (PD) - Danish Cohort refers to patients in their early stage of prediabetes.,138,121,4 months,16S,12345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Additional file 11: Table S9B,5 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differentially abundant taxa between NG and PD subjects, belonging to the Danish cohort, identified after correcting for covariates (age, gender, waist-to-hip ratio, Systolic BP, IL6, TNFα, LBP and IAP)  using a negative binomial Wald test.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella bouchesdurhonensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|186802|216572|216851|853;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|707003;1783272|1239|909932|1843489|31977|29465|39777;1783272|201174|84998|84999|84107|102106|1907654;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:33658065/3/1,33658065,"cross-sectional observational, not case-control",33658065,10.1186/s13073-021-00851-9,NA,"Pinna N.K., Anjana R.M., Saxena S., Dutta A., Gnanaprakash V., Rameshkumar G., Aswath S., Raghavan S., Rani C.S.S., Radha V., Balasubramanyam M., Pant A., Nielsen T., Jørgensen T., Færch K., Kashani A., Silva M.C.A., Vestergaard H., Hansen T.H., Hansen T., Arumugam M., Nair G.B., Das B., Pedersen O., Mohan V. , Mande S.S.",Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark,Genome medicine,2021,NA,Experiment 3,"Denmark,India",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Indian Cohort (IN),Danish Cohort (DK),Danish Cohort (DK) refers to the normoglycemic and prediabetic groups in Danish subjects.,278,259,4 months,16S,12345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,"Additional file 7: Table S5B, Table S5A",5 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between Indian (IN) and Danish (DK) gut microbiomes identified using a negative binomial Wald test.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Beijerinckiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales|f__Desulfobacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Puniceicoccaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Lentisphaerota,k__Fusobacteriati|p__Fusobacteriota,k__Thermotogati|p__Synergistota",1783272|1239|909932|1843488|909930;3379134|74201|203494|48461|1647988;1783272|544448|31969|186332|186333;3379134|976|200643|171549|815;3379134|976|200643|171549|2005519;3379134|1224|28211|356|45404;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|3085636|1185407;3379134|200940|3024418|213118|213119;3379134|976|200643|1970189|1573805;3379134|976|200643|171549|2005473;1783272|201174|1760|85007|85025;1783272|1239|186801|186802|216572;3379134|1224|28211|204455|31989;1783272|1239|186801|186802|186807;3379134|1224|1236|72274|135621;3379134|74201|414999|415001|415002;3379134|976|200643|171549|171550;3384194|508458|649775|649776|649777;3379134|976|200643|171549|2005525;3379134|256845|1313211|278082|255528;3379134|1224|28211|356|335928;1783272|1239;3379134|976;1783272|544448;3379134|74201;1783272|1117;3379134|256845;3384189|32066;3384194|508458,Complete,Svetlana up
bsdb:33658065/3/2,33658065,"cross-sectional observational, not case-control",33658065,10.1186/s13073-021-00851-9,NA,"Pinna N.K., Anjana R.M., Saxena S., Dutta A., Gnanaprakash V., Rameshkumar G., Aswath S., Raghavan S., Rani C.S.S., Radha V., Balasubramanyam M., Pant A., Nielsen T., Jørgensen T., Færch K., Kashani A., Silva M.C.A., Vestergaard H., Hansen T.H., Hansen T., Arumugam M., Nair G.B., Das B., Pedersen O., Mohan V. , Mande S.S.",Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark,Genome medicine,2021,NA,Experiment 3,"Denmark,India",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Indian Cohort (IN),Danish Cohort (DK),Danish Cohort (DK) refers to the normoglycemic and prediabetic groups in Danish subjects.,278,259,4 months,16S,12345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,"Additional file 7: Table S5B, Table S5A",5 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between Indian (IN) and Danish (DK) gut microbiomes identified using a negative binomial Wald test.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella sinensis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Spirochaetota,k__Pseudomonadati|p__Elusimicrobiota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae",1783272|201174|1760|2037|2049;1783272|201174|84998|84999|1643824;1783272|1239|91061|1385|186817;1783272|201174|1760|85004|31953;3379134|1224|28216|80840|119060;1783272|1239|91061|186826|186828;3379134|1224|28211|204458|76892;1783272|201174|84998|84999|84107;1783272|201174|84998|1643822|1643826|84111|242230;1783272|201174|84998|1643822|1643826;3379134|74152|641853|641854|641876;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|526524|526525|128827;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171552;3379134|203691|203692|136|137;1783272|1239|91061|186826|1300;3379134|1224|1236|135624|83763;1783272|1239|909932|1843489|31977;3379134|1224|1236|135623|641;3379134|1224;1783272|201174;3379134|203691;3379134|74152;3379134|1224|1236|135614|32033,Complete,Svetlana up
bsdb:33658065/4/1,33658065,"cross-sectional observational, not case-control",33658065,10.1186/s13073-021-00851-9,NA,"Pinna N.K., Anjana R.M., Saxena S., Dutta A., Gnanaprakash V., Rameshkumar G., Aswath S., Raghavan S., Rani C.S.S., Radha V., Balasubramanyam M., Pant A., Nielsen T., Jørgensen T., Færch K., Kashani A., Silva M.C.A., Vestergaard H., Hansen T.H., Hansen T., Arumugam M., Nair G.B., Das B., Pedersen O., Mohan V. , Mande S.S.",Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark,Genome medicine,2021,NA,Experiment 4,"Denmark,India",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic (NG) controls - Indian & Danish Cohorts,Prediabetes (PD) - Indian & Danish Cohorts,Prediabetes (PD) - Indian & Danish Cohorts refers patients in their early stage of prediabetes in both India and Denmark cohorts.,275,262,4 months,16S,12345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,geographic area,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Additional file 9: Table S7,5 November 2024,KateRasheed,"KateRasheed,WikiWorks,Tosin","Differentially abundant taxa between NG and PD subjects, belonging to the Indian and Danish cohorts (pooled together) identified using a negative binomial Wald test (corrected for geography specific cohort effect).",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum desmolans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes inops,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia massiliensis (ex Liu et al. 2021),k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Obscuribacterales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus delbrueckii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|g__Negativibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella tobetsuensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio cholerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005",1783272|201174|84998|1643822|1643826|447020;1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|186802|3085642|2048137|39484;3379134|976|200643|171549|171550|239759|1501391;3379134|976|200643|171549|171552|1283313;1783272|1239|186801|186802|216572|244127|169435;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|329854;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|871665;1783272|1239|186801|3085636|186803|572511|3062492;1783272|1239|186801|3085636|186803|572511|418240;1783272|1798710|1906152;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|1432051;3379134|1224|1236|91347|543|547;1783272|201174|84998|1643822|1643826|580024;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|3082720|186804|1505657|261299;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|28052;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|1584;1783272|1239|91061|186826|33958|2767887|1623;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|909929|1843491|52225;1783272|1239|1980693;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|186807;1783272|201174|1760|85007|85025|1827;1783272|1239|186801|3085636|186803|841;1783272|201174|84998|84999|84107|1473205;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|292632;3379134|1224|28216|80840|995019|40544;1783272|1239|526524|526525|2810280|3025755;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|909932|1843489|31977|29465|1110546;3379134|1224|1236|135623|641|662|666;1783272|1239|186801|186802|216572|707003;1783272|1239|186801|186802|216572|3068309,Complete,Svetlana up
bsdb:33658065/4/2,33658065,"cross-sectional observational, not case-control",33658065,10.1186/s13073-021-00851-9,NA,"Pinna N.K., Anjana R.M., Saxena S., Dutta A., Gnanaprakash V., Rameshkumar G., Aswath S., Raghavan S., Rani C.S.S., Radha V., Balasubramanyam M., Pant A., Nielsen T., Jørgensen T., Færch K., Kashani A., Silva M.C.A., Vestergaard H., Hansen T.H., Hansen T., Arumugam M., Nair G.B., Das B., Pedersen O., Mohan V. , Mande S.S.",Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark,Genome medicine,2021,NA,Experiment 4,"Denmark,India",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic (NG) controls - Indian & Danish Cohorts,Prediabetes (PD) - Indian & Danish Cohorts,Prediabetes (PD) - Indian & Danish Cohorts refers patients in their early stage of prediabetes in both India and Denmark cohorts.,275,262,4 months,16S,12345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,geographic area,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Additional file 9: Table S7,5 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differentially abundant OTUs between NG and PD subjects, belonging to the Indian and Danish cohorts (pooled together) identified using a negative binomial Wald test (corrected for geography specific cohort effect).",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas nexilis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter",3379134|976|200643|171549|815|816|291645;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|2005519|397864|487174;1783272|1239|186801|3085636|186803|2005355|29361;1783272|1239|909932|1843488|909930|33024|33025;3379134|976|200643|171549|2005473;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|1766253,Complete,Svetlana up
bsdb:33658065/5/1,33658065,"cross-sectional observational, not case-control",33658065,10.1186/s13073-021-00851-9,NA,"Pinna N.K., Anjana R.M., Saxena S., Dutta A., Gnanaprakash V., Rameshkumar G., Aswath S., Raghavan S., Rani C.S.S., Radha V., Balasubramanyam M., Pant A., Nielsen T., Jørgensen T., Færch K., Kashani A., Silva M.C.A., Vestergaard H., Hansen T.H., Hansen T., Arumugam M., Nair G.B., Das B., Pedersen O., Mohan V. , Mande S.S.",Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark,Genome medicine,2021,NA,Experiment 5,India,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic (NG) controls - Indian Cohort,Prediabetes (PD) - Indian Cohort,Prediabetes (PD) - Indian Cohort refers to patients in their early stage of prediabetes.,137,141,NA,16S,12345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Additional file 10: Table S8A,5 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differentially abundant taxa between NG and PD subjects, belonging to the Indian cohort, identified using a negative binomial Wald test.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus delbrueckii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio cholerae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|909932|1843489|31977|906|907;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|572511|871665;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3082720|186804|1505657|261299;1783272|201174|84998|84999|84107|102106;1783272|1239|909932|1843489|31977|39948|487173;1783272|1239|909932|1843489|31977|906;3379134|976|200643|171549|815|816;1783272|201174|84998|84999|84107|1473205;1783272|1239|91061|186826|33958|2767887|1623;1783272|201174|84998|84999|1643824|133925;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843489|31977|39948;3379134|976|200643|171549|171552|1283313;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843488|909930|33024|626940;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|91061|186826|33958|1578|1584;3379134|1224|1236|135623|641|662|666;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:33658065/5/2,33658065,"cross-sectional observational, not case-control",33658065,10.1186/s13073-021-00851-9,NA,"Pinna N.K., Anjana R.M., Saxena S., Dutta A., Gnanaprakash V., Rameshkumar G., Aswath S., Raghavan S., Rani C.S.S., Radha V., Balasubramanyam M., Pant A., Nielsen T., Jørgensen T., Færch K., Kashani A., Silva M.C.A., Vestergaard H., Hansen T.H., Hansen T., Arumugam M., Nair G.B., Das B., Pedersen O., Mohan V. , Mande S.S.",Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark,Genome medicine,2021,NA,Experiment 5,India,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic (NG) controls - Indian Cohort,Prediabetes (PD) - Indian Cohort,Prediabetes (PD) - Indian Cohort refers to patients in their early stage of prediabetes.,137,141,NA,16S,12345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Additional file 10: Table S8A,5 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differentially abundant OTUs between NG and PD subjects, belonging to the Indian cohort, identified using a negative binomial Wald test.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|171552|1283313;1783272|1239|186801|3085636|186803|1766253;3379134|976|200643|171549|2005473,Complete,Svetlana up
bsdb:33658065/6/1,33658065,"cross-sectional observational, not case-control",33658065,10.1186/s13073-021-00851-9,NA,"Pinna N.K., Anjana R.M., Saxena S., Dutta A., Gnanaprakash V., Rameshkumar G., Aswath S., Raghavan S., Rani C.S.S., Radha V., Balasubramanyam M., Pant A., Nielsen T., Jørgensen T., Færch K., Kashani A., Silva M.C.A., Vestergaard H., Hansen T.H., Hansen T., Arumugam M., Nair G.B., Das B., Pedersen O., Mohan V. , Mande S.S.",Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark,Genome medicine,2021,NA,Experiment 6,India,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic (NG) controls - Indian Cohort,Prediabetes (PD) - Indian Cohort,Prediabetes (PD) - Indian Cohort refers to patients in their early stage of prediabetes.,137,141,NA,16S,12345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Additional file 10: Table S8B,6 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differentially abundant OTUs between NG and PD subjects , belonging to the Indian cohort, identified after correcting for covariates (age, gender, waist-to-hip ratio, Systolic BP, IL6, TNFα, LBP and IAP)  using a negative binomial Wald test.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella tobetsuensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus delbrueckii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Kerstersia",1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|572511|871665;1783272|1239|186801|3085636|186803|248744;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|1643822|1643826|84108;1783272|1239|186801|3085636|186803|841|301302;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958|2767887|1623;1783272|1239|909932|1843489|31977|29465|1110546;1783272|1239|91061|186826|33958|1578|1584;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|909932|1843488|909930|33024|626940;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843489|31977|29465|39778;3379134|976|200643|171549|171552|1283313;1783272|1239|909932|1843489|31977|29465;3379134|1224|28216|80840|506|257820,Complete,Svetlana up
bsdb:33658065/6/2,33658065,"cross-sectional observational, not case-control",33658065,10.1186/s13073-021-00851-9,NA,"Pinna N.K., Anjana R.M., Saxena S., Dutta A., Gnanaprakash V., Rameshkumar G., Aswath S., Raghavan S., Rani C.S.S., Radha V., Balasubramanyam M., Pant A., Nielsen T., Jørgensen T., Færch K., Kashani A., Silva M.C.A., Vestergaard H., Hansen T.H., Hansen T., Arumugam M., Nair G.B., Das B., Pedersen O., Mohan V. , Mande S.S.",Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark,Genome medicine,2021,NA,Experiment 6,India,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic (NG) controls - Indian Cohort,Prediabetes (PD) - Indian Cohort,Prediabetes (PD) - Indian Cohort refers to patients in their early stage of prediabetes.,137,141,NA,16S,12345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Additional file 10: Table S8B,6 November 2024,KateRasheed,"KateRasheed,WikiWorks,Tosin","Differentially abundant OTUs between NG and PD subjects , belonging to the Indian cohort, identified after correcting for covariates (age, gender, waist-to-hip ratio, Systolic BP, IL6, TNFα, LBP and IAP)  using a negative binomial Wald test.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium tertium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005",1783272|1239|186801|3085636|186803|1766253;3379134|976|200643|171549|171552|1283313;1783272|1239|186801|186802|31979|1485|1559;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|3068309,Complete,Svetlana up
bsdb:33658065/7/1,33658065,"cross-sectional observational, not case-control",33658065,10.1186/s13073-021-00851-9,NA,"Pinna N.K., Anjana R.M., Saxena S., Dutta A., Gnanaprakash V., Rameshkumar G., Aswath S., Raghavan S., Rani C.S.S., Radha V., Balasubramanyam M., Pant A., Nielsen T., Jørgensen T., Færch K., Kashani A., Silva M.C.A., Vestergaard H., Hansen T.H., Hansen T., Arumugam M., Nair G.B., Das B., Pedersen O., Mohan V. , Mande S.S.",Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark,Genome medicine,2021,NA,Experiment 7,"Denmark,India",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic (NG) controls - Indian & Danish Cohorts,Prediabetes (PD) - Indian & Danish Cohorts,Prediabetes (PD) - Indian & Danish Cohorts refers patients in their early stage of prediabetes in both India and Denmark cohorts.,275,262,4 months,16S,12345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,geographic area,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,"Additional file 12: Table S10A, Table S10B, Table S10C",6 November 2024,KateRasheed,"KateRasheed,WikiWorks,Tosin","Differentially abundant taxa between NG and PD subjects, belonging to the Indian and Danish cohorts (pooled together) identified using a negative binomial Wald test (corrected for geography specific cohort-effect).",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Pseudomonadati|p__Elusimicrobiota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|g__Negativibacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|1224|28216|80840|506|222;1783272|201174;1783272|1239|186801|3085636|186803|572511;3379134|1224|28216|80840|119060;1783272|1239|186801|3085636|186803|1432051;3379134|74152;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;3384189|32066;1783272|1239|186801|3082720|186804|1505657;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|1506553;1783272|1239|91061|186826|33958|1578;1783272|1239|1980693;1783272|201174|1760|85007|85025;3379134|1224|1236|135625|712|745;3379134|1224;1783272|201174|1760|85007|85025|1827;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|135623|641|662;3379134|1224|1236|135623|641;3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:33658065/7/2,33658065,"cross-sectional observational, not case-control",33658065,10.1186/s13073-021-00851-9,NA,"Pinna N.K., Anjana R.M., Saxena S., Dutta A., Gnanaprakash V., Rameshkumar G., Aswath S., Raghavan S., Rani C.S.S., Radha V., Balasubramanyam M., Pant A., Nielsen T., Jørgensen T., Færch K., Kashani A., Silva M.C.A., Vestergaard H., Hansen T.H., Hansen T., Arumugam M., Nair G.B., Das B., Pedersen O., Mohan V. , Mande S.S.",Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark,Genome medicine,2021,NA,Experiment 7,"Denmark,India",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic (NG) controls - Indian & Danish Cohorts,Prediabetes (PD) - Indian & Danish Cohorts,Prediabetes (PD) - Indian & Danish Cohorts refers patients in their early stage of prediabetes in both India and Denmark cohorts.,275,262,4 months,16S,12345,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,geographic area,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,"Additional file 12: Table S10A, Table S10B, Table S10C",6 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differentially abundant taxa between NG and PD subjects, belonging to the Indian and Danish cohorts (pooled together) identified using a negative binomial Wald test (corrected for geography specific cohort-effect).",decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Spirochaetota,k__Pseudomonadati|p__Lentisphaerota,k__Thermotogati|p__Synergistota",1783272|1239;3379134|976;1783272|544448;3379134|74201;1783272|1117;3379134|203691;3379134|256845;3384194|508458,Complete,Svetlana up
bsdb:33659220/1/1,33659220,"cross-sectional observational, not case-control",33659220,10.3389/fcimb.2021.625581,NA,"Nardelli C., Gentile I., Setaro M., Di Domenico C., Pinchera B., Buonomo A.R., Zappulo E., Scotto R., Scaglione G.L., Castaldo G. , Capoluongo E.",Nasopharyngeal Microbiome Signature in COVID-19 Positive Patients: Can We Definitively Get a Role to <i>Fusobacterium periodonticum</i>?,Frontiers in cellular and infection microbiology,2021,"Fusobacterium periodonticum, SARS-CoV-2, microbiota, nasopharyngeal swab, next generation sequencing",Experiment 1,Italy,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls,COVID-19 positive patients,Symptomatic COVID-19 positive patients,12,18,NA,16S,123,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3A-F,28 June 2021,Claregrieve1,"Claregrieve1,Peace Sandy,WikiWorks","Nasopaheryngeal microbiome composition in COVID-19 patients and Control group. The graphs show the percentage of relative abundance (%) of the all taxonomic levels from Phylum to Species, obtained by using the MicrobAT Suite - SmartSeq. Each column in the plot represents a group, and each color in the column represents the relative abundance (%) for each taxon. In panel (A) we show the phyla with average relative abundance greater than 1% in all studied groups; we found two phyla significantly less abundant in COVID-19 patients respect to Controls, Proteobacteria, and Fusobacteria. Not statistically significant difference in taxa abundance was observed when T0 and T1 COVID-19 patients were compared. The other panels (B–F) show the taxa abundance from class to up species level significantly different between groups by Kruskal Wallis test. (B) class (C) order, (D) family, (E) genus (F) species. *p < 0.05; **p < 0.001.",decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales",3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066;3384189|32066|203490|203491|203492|848;3379134|1224|1236;3379134|1224|1236|135625|712|724;3384189|32066|203490|203491|1129771|32067;3384189|32066|203490|203491|1129771;3379134|1224|1236|135625|712;3379134|1224|1236|135625,Complete,Peace Sandy
bsdb:33660232/1/1,33660232,case-control,33660232,10.1007/s43032-021-00506-5,NA,"Svensson A., Brunkwall L., Roth B., Orho-Melander M. , Ohlsson B.",Associations Between Endometriosis and Gut Microbiota,"Reproductive sciences (Thousand Oaks, Calif.)",2021,"Endometriosis, Gastrointestinal symptoms, Gut microbiota, Pathophysiology",Experiment 1,Sweden,Homo sapiens,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Healthy controls taken from a larger cohort study,Endometriosis patients,"Patients with a diagnosis of endometriosis, confirmed by laparoscopy or laparotomy.",198,66,NA,16S,123,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex,smoking status",NA,NA,decreased,NA,NA,NA,NA,Signature 1,Table 2,11 August 2021,Samara.Khan,"Samara.Khan,Claregrieve1,Folakunmi,WikiWorks",The following taxa were decreased among those with endometriosis compared to healthy controls.,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Halanaerobiales|f__Halanaerobiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",1783272|201174|84998|1643822|1643826|447020;3379134|976|200643|171549;3379134|976|200643|171549|2005519;1783272|201174|84998|84999|84107;1783272|1239|186801|53433|972;1783272|1239|186801|3085636|186803|28050;3379134|976|200643|171549|171552|577309;1783272|1239|526524|526525|2810281|191303,Complete,Claregrieve1
bsdb:33660232/1/2,33660232,case-control,33660232,10.1007/s43032-021-00506-5,NA,"Svensson A., Brunkwall L., Roth B., Orho-Melander M. , Ohlsson B.",Associations Between Endometriosis and Gut Microbiota,"Reproductive sciences (Thousand Oaks, Calif.)",2021,"Endometriosis, Gastrointestinal symptoms, Gut microbiota, Pathophysiology",Experiment 1,Sweden,Homo sapiens,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Healthy controls taken from a larger cohort study,Endometriosis patients,"Patients with a diagnosis of endometriosis, confirmed by laparoscopy or laparotomy.",198,66,NA,16S,123,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex,smoking status",NA,NA,decreased,NA,NA,NA,NA,Signature 2,Table 2,11 August 2021,Samara.Khan,"Samara.Khan,Claregrieve1,WikiWorks",The following taxa were increased among those with endometriosis compared to healthy controls after a false-discovery rate adjustment,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005525|375288;3379134|1224|1236|91347|543;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803,Complete,Claregrieve1
bsdb:33660232/2/1,33660232,case-control,33660232,10.1007/s43032-021-00506-5,NA,"Svensson A., Brunkwall L., Roth B., Orho-Melander M. , Ohlsson B.",Associations Between Endometriosis and Gut Microbiota,"Reproductive sciences (Thousand Oaks, Calif.)",2021,"Endometriosis, Gastrointestinal symptoms, Gut microbiota, Pathophysiology",Experiment 2,Sweden,Homo sapiens,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Healthy controls taken from a larger cohort study,Endometriosis patients,"Patients with a diagnosis of endometriosis, confirmed by laparoscopy or laparotomy.",198,66,6 months,16S,123,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex,smoking status",NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary Table 2,11 August 2021,Samara.Khan,"Samara.Khan,Claregrieve1,WikiWorks",Differential microbial abundance between endometriosis patients and healthy controls after a sensitivity analysis and adjustment for false-discovery rate.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,3379134|976|200643|171549,Complete,Claregrieve1
bsdb:33660232/2/2,33660232,case-control,33660232,10.1007/s43032-021-00506-5,NA,"Svensson A., Brunkwall L., Roth B., Orho-Melander M. , Ohlsson B.",Associations Between Endometriosis and Gut Microbiota,"Reproductive sciences (Thousand Oaks, Calif.)",2021,"Endometriosis, Gastrointestinal symptoms, Gut microbiota, Pathophysiology",Experiment 2,Sweden,Homo sapiens,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Healthy controls taken from a larger cohort study,Endometriosis patients,"Patients with a diagnosis of endometriosis, confirmed by laparoscopy or laparotomy.",198,66,6 months,16S,123,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex,smoking status",NA,NA,decreased,NA,NA,NA,NA,Signature 2,Supplementary Table 2,11 August 2021,Samara.Khan,"Samara.Khan,Claregrieve1,WikiWorks",Differential microbial abundance between endometriosis patients and healthy controls after a sensitivity analysis and adjustment for false-discovery rate.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|186802|216572|119852,Complete,Claregrieve1
bsdb:33663411/1/1,33663411,case-control,33663411,10.1186/s12876-021-01693-w,NA,"Mei L., Zhou J., Su Y., Mao K., Wu J., Zhu C., He L. , Cui Y.",Gut microbiota composition and functional prediction in diarrhea-predominant irritable bowel syndrome,BMC gastroenterology,2021,"Diarrhea-predominant irritable bowel syndrome, Functional prediction, Gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-D,Individuals aged from 20 to 64 meeting the Rome IV diagnostic criteria [19] for IBS-D,30,30,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 5,4 July 2021,Kwekuamoo,"Kwekuamoo,Claregrieve1,WikiWorks",Differential microbial abundance between IBS-D patients and controls by LefSe,increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotellamassilia|s__Prevotellamassilia timonensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius",1783272|201174;3379134|976|200643|171549|171552|1283313;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|186801;1783272|1239|186801|186802|216572|216851;1783272|1239;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|1898207;3379134|976|200643|171549|171552|1926672|1852370;3379134|976|200643|171549|815|909656|310297,Complete,Claregrieve1
bsdb:33663411/1/2,33663411,case-control,33663411,10.1186/s12876-021-01693-w,NA,"Mei L., Zhou J., Su Y., Mao K., Wu J., Zhu C., He L. , Cui Y.",Gut microbiota composition and functional prediction in diarrhea-predominant irritable bowel syndrome,BMC gastroenterology,2021,"Diarrhea-predominant irritable bowel syndrome, Functional prediction, Gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-D,Individuals aged from 20 to 64 meeting the Rome IV diagnostic criteria [19] for IBS-D,30,30,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 5,4 July 2021,Kwekuamoo,"Kwekuamoo,Claregrieve1,WikiWorks",Differential microbial abundance between IBS-D patients and controls by LefSe,decreased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales",1783272|1239|91061;3379134|976|200643|171549|815|816|817;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|561|562;3379134|1224|1236;1783272|1239|91061|186826;3379134|1224;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;3379134|1224|1236|91347,Complete,Claregrieve1
bsdb:33665172/1/1,33665172,case-control,33665172,https://doi.org/10.3389%2Ffcimb.2020.624504,NA,"Li N., Li Y., Qian C., Liu Q., Cao W., Ma M., He R., Chen R., Geng R. , Liu Y.",Dysbiosis of the Saliva Microbiome in Patients With Polycystic Ovary Syndrome,Frontiers in cellular and infection microbiology,2020,"16S rRNA, diurnal rhythm, fecal microbiota, polycystic ovary syndrome, salivary microbiome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Polycystic ovary syndrome,EFO:0000660,Healthy control at Zeitgeber (ZT) 0,PCOS patients at Zeitgeber (ZT) 0,"Samples collected from patients with Polycystic Ovary Syndrome who were diagnosed according to the Rotterdam Criteria, who met two out of three of the following criteria: clinical/biochemical hyperandrogenism, oligo-/anovulation, and polycystic ovaries at Zeitgeber (ZT) 0",10,10,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"age,body mass index,metabolic syndrome",NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 3A,20 April 2024,Idiaru angela,"Idiaru angela,WikiWorks",Identification of specific bacterial taxa in PCOS patients and controls at different time points. Linear discriminant analysis (LDA) effect size (LEfSe) was used to identify biomarkers with significant differences between the two groups: Control.ZT0 vs. PCOS.ZT0,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,p__Candidatus Altimarinota,p__Candidatus Altimarinota,p__Candidatus Absconditibacteriota|s__SR1 bacterium oral taxon 875,p__Candidatus Absconditibacteriota|s__SR1 bacterium human oral taxon HOT-345",3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492;3384189|32066|203490|203491|203492|848|860;363464;363464;221235|1226342;221235|1540874,Complete,Svetlana up
bsdb:33665172/1/2,33665172,case-control,33665172,https://doi.org/10.3389%2Ffcimb.2020.624504,NA,"Li N., Li Y., Qian C., Liu Q., Cao W., Ma M., He R., Chen R., Geng R. , Liu Y.",Dysbiosis of the Saliva Microbiome in Patients With Polycystic Ovary Syndrome,Frontiers in cellular and infection microbiology,2020,"16S rRNA, diurnal rhythm, fecal microbiota, polycystic ovary syndrome, salivary microbiome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Polycystic ovary syndrome,EFO:0000660,Healthy control at Zeitgeber (ZT) 0,PCOS patients at Zeitgeber (ZT) 0,"Samples collected from patients with Polycystic Ovary Syndrome who were diagnosed according to the Rotterdam Criteria, who met two out of three of the following criteria: clinical/biochemical hyperandrogenism, oligo-/anovulation, and polycystic ovaries at Zeitgeber (ZT) 0",10,10,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"age,body mass index,metabolic syndrome",NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 3A,20 April 2024,Idiaru angela,"Idiaru angela,WikiWorks",Identification of specific bacterial taxa in PCOS patients and controls at different time points. Linear discriminant analysis (LDA) effect size (LEfSe) was used to identify biomarkers with significant differences between the two groups: Control.ZT0 vs. PCOS.ZT0,decreased,"k__Bacillati|p__Actinomycetota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola",1783272|201174;3384189|32066|203490|203491|1129771|32067;3379134|976|200643|171549|171552|838|470565,Complete,Svetlana up
bsdb:33665172/3/1,33665172,case-control,33665172,https://doi.org/10.3389%2Ffcimb.2020.624504,NA,"Li N., Li Y., Qian C., Liu Q., Cao W., Ma M., He R., Chen R., Geng R. , Liu Y.",Dysbiosis of the Saliva Microbiome in Patients With Polycystic Ovary Syndrome,Frontiers in cellular and infection microbiology,2020,"16S rRNA, diurnal rhythm, fecal microbiota, polycystic ovary syndrome, salivary microbiome",Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Polycystic ovary syndrome,EFO:0000660,Healthy control at Zeitgeber (ZT) 12,PCOS patients at Zeitgeber (ZT) 12,"Samples collected from patients with Polycystic Ovary Syndrome who were diagnosed according to the Rotterdam Criteria, who met two out of three of the following criteria: clinical/biochemical hyperandrogenism, oligo-/anovulation, and polycystic ovaries at Zeitgeber (ZT) 12",10,10,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"age,body mass index,metabolic syndrome",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3C,20 April 2024,Idiaru angela,"Idiaru angela,WikiWorks",Identification of specific bacterial taxa in PCOS patients and controls at different time points. Linear discriminant analysis (LDA) effect size (LEfSe) was used to identify biomarkers with significant differences between the two groups: Control.ZT12 vs. PCOS.ZT12,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum",3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492;3384189|32066|203490|203491|203492|848|860,Complete,Svetlana up
bsdb:33665172/3/2,33665172,case-control,33665172,https://doi.org/10.3389%2Ffcimb.2020.624504,NA,"Li N., Li Y., Qian C., Liu Q., Cao W., Ma M., He R., Chen R., Geng R. , Liu Y.",Dysbiosis of the Saliva Microbiome in Patients With Polycystic Ovary Syndrome,Frontiers in cellular and infection microbiology,2020,"16S rRNA, diurnal rhythm, fecal microbiota, polycystic ovary syndrome, salivary microbiome",Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Polycystic ovary syndrome,EFO:0000660,Healthy control at Zeitgeber (ZT) 12,PCOS patients at Zeitgeber (ZT) 12,"Samples collected from patients with Polycystic Ovary Syndrome who were diagnosed according to the Rotterdam Criteria, who met two out of three of the following criteria: clinical/biochemical hyperandrogenism, oligo-/anovulation, and polycystic ovaries at Zeitgeber (ZT) 12",10,10,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"age,body mass index,metabolic syndrome",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 3C,20 April 2024,Idiaru angela,"Idiaru angela,WikiWorks",Identification of specific bacterial taxa in PCOS patients and controls at different time points. Linear discriminant analysis (LDA) effect size (LEfSe) was used to identify biomarkers with significant differences between the two groups: Control.ZT12 vs. PCOS.ZT12,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola",3384189|32066|203490|203491|1129771|32067;3379134|976|200643|171549|171552|838|470565,Complete,Svetlana up
bsdb:33665172/4/1,33665172,case-control,33665172,https://doi.org/10.3389%2Ffcimb.2020.624504,NA,"Li N., Li Y., Qian C., Liu Q., Cao W., Ma M., He R., Chen R., Geng R. , Liu Y.",Dysbiosis of the Saliva Microbiome in Patients With Polycystic Ovary Syndrome,Frontiers in cellular and infection microbiology,2020,"16S rRNA, diurnal rhythm, fecal microbiota, polycystic ovary syndrome, salivary microbiome",Experiment 4,China,Homo sapiens,Saliva,UBERON:0001836,Polycystic ovary syndrome,EFO:0000660,Healthy control at Zeitgeber (ZT) 18,PCOS patients at Zeitgeber (ZT) 18,"Samples collected from patients with Polycystic Ovary Syndrome who were diagnosed according to the Rotterdam Criteria, who met two out of three of the following criteria: clinical/biochemical hyperandrogenism, oligo-/anovulation, and polycystic ovaries at Zeitgeber (ZT) 18",10,10,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"age,body mass index,metabolic syndrome",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3D,20 April 2024,Idiaru angela,"Idiaru angela,WikiWorks",Identification of specific bacterial taxa in PCOS patients and controls at different time points. Linear discriminant analysis (LDA) effect size (LEfSe) was used to identify biomarkers with significant differences between the two groups: Control.ZT18 vs. PCOS.ZT18,increased,"p__Candidatus Absconditibacteriota|s__SR1 bacterium oral taxon 875,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,p__Candidatus Altimarinota,p__Candidatus Altimarinota",221235|1226342;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492;3384189|32066|203490|203491|203492|848|860;1783272|1239|186801|186802;1783272|1239|186801;3379134|976|117743|200644;1783272|1239|186801|186802|216572;363464;363464,Complete,Svetlana up
bsdb:33665172/4/2,33665172,case-control,33665172,https://doi.org/10.3389%2Ffcimb.2020.624504,NA,"Li N., Li Y., Qian C., Liu Q., Cao W., Ma M., He R., Chen R., Geng R. , Liu Y.",Dysbiosis of the Saliva Microbiome in Patients With Polycystic Ovary Syndrome,Frontiers in cellular and infection microbiology,2020,"16S rRNA, diurnal rhythm, fecal microbiota, polycystic ovary syndrome, salivary microbiome",Experiment 4,China,Homo sapiens,Saliva,UBERON:0001836,Polycystic ovary syndrome,EFO:0000660,Healthy control at Zeitgeber (ZT) 18,PCOS patients at Zeitgeber (ZT) 18,"Samples collected from patients with Polycystic Ovary Syndrome who were diagnosed according to the Rotterdam Criteria, who met two out of three of the following criteria: clinical/biochemical hyperandrogenism, oligo-/anovulation, and polycystic ovaries at Zeitgeber (ZT) 18",10,10,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"age,body mass index,metabolic syndrome",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 3D,21 April 2024,Idiaru angela,"Idiaru angela,WikiWorks",Identification of specific bacterial taxa in PCOS patients and controls at different time points. Linear discriminant analysis (LDA) effect size (LEfSe) was used to identify biomarkers with significant differences between the two groups: Control.ZT18 vs. PCOS.ZT18,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flava,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Cyanobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|1224|28216|206351|481|482|34026;1783272|1117;1783272|1117;3384189|32066|203490|203491|1129771;3384189|32066|203490|203491|1129771|32067;3379134|976|200643|171549|171552|838|470565;3379134|976|200643|171549|171552,Complete,Svetlana up
bsdb:33665172/5/1,33665172,case-control,33665172,https://doi.org/10.3389%2Ffcimb.2020.624504,NA,"Li N., Li Y., Qian C., Liu Q., Cao W., Ma M., He R., Chen R., Geng R. , Liu Y.",Dysbiosis of the Saliva Microbiome in Patients With Polycystic Ovary Syndrome,Frontiers in cellular and infection microbiology,2020,"16S rRNA, diurnal rhythm, fecal microbiota, polycystic ovary syndrome, salivary microbiome",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy controls,PCOS Patients,"PCOS patients who were diagnosed according to the Rotterdam Criteria, who met two out of three of the following criteria: clinical/biochemical hyperandrogenism, oligo-/anovulation, and polycystic ovaries",10,10,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"age,body mass index,metabolic syndrome",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplemental Figure 5E,21 April 2024,Idiaru angela,"Idiaru angela,WikiWorks",The microbiota that showed significant differences between the two groups as analysed by LEfSe with an LDA score threshold of 4.0.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis",1783272|1239|186801|3085636|186803|572511;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301|1308;1783272|201174|1760|85004|31953|1678|1680,Complete,Svetlana up
bsdb:33667869/1/1,33667869,laboratory experiment,33667869,10.1016/j.psj.2021.01.019,https://www.sciencedirect.com/science/article/pii/S0032579121000304?via=ihub,"Huang Y., Lv H., Song Y., Sun C., Zhang Z. , Chen S.",Community composition of cecal microbiota in commercial yellow broilers with high and low feed efficiencies,Poultry science,2021,"16S rRNA gene, cecal microbiota, feed conversion ratio, microbial community, yellow broiler",Experiment 1,China,Gallus gallus,Caecum,UBERON:0001153,Growth rate measurement,EFO:0010572,Low feed efficiency (LFE),High feed efficiency (HFE),Yellow broilers with low feed conversion ratio (FCR).,29,30,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 5,31 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe results for cecal microbiota of HFE and LFE groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:33667869/1/2,33667869,laboratory experiment,33667869,10.1016/j.psj.2021.01.019,https://www.sciencedirect.com/science/article/pii/S0032579121000304?via=ihub,"Huang Y., Lv H., Song Y., Sun C., Zhang Z. , Chen S.",Community composition of cecal microbiota in commercial yellow broilers with high and low feed efficiencies,Poultry science,2021,"16S rRNA gene, cecal microbiota, feed conversion ratio, microbial community, yellow broiler",Experiment 1,China,Gallus gallus,Caecum,UBERON:0001153,Growth rate measurement,EFO:0010572,Low feed efficiency (LFE),High feed efficiency (HFE),Yellow broilers with low feed conversion ratio (FCR).,29,30,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 5,31 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe results for cecal microbiota of HFE and LFE groups.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",1783272|1239|186801|186802|216572;3379134|976|200643|171549|171550,Complete,Svetlana up
bsdb:33672177/1/1,33672177,case-control,33672177,10.3390/ijerph18042174,NA,"Rueca M., Fontana A., Bartolini B., Piselli P., Mazzarelli A., Copetti M., Binda E., Perri F., Gruber C.E.M., Nicastri E., Marchioni L., Ippolito G., Capobianchi M.R., Di Caro A. , Pazienza V.",Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing,International journal of environmental research and public health,2021,"Nasal/Oropharyngeal, SARS-CoV2, microbiota",Experiment 1,Italy,Homo sapiens,"Nasopharynx,Oropharynx","UBERON:0001728,UBERON:0001729",COVID-19,MONDO:0100096,Healthy controls,ICU COVID-19 patients,COVID-19 patients admitted to intensive care unit,10,10,NA,16S,23456789,Ion Torrent,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Table S1,30 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between healthy controls and ICU COVID-19 patients,decreased,"p__Candidatus Saccharimonadota,k__Thermotogati|p__Deinococcota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacterales Family III. Incertae Sedis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Gulbenkiania,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Snodgrassella,k__Pseudomonadati|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Tepidiphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae|g__Thermoanaerobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae|g__Thermoanaerobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae|g__Thermosinus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacillati|p__Bacillota|c__Tissierellia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax",95818;3384194|1297;3379134|1224|1236|135624|84642;1783272|1239|91061|1385|186823;3379134|1224|28211|204458|76892;3379134|1224|28216|206351|1499392;3384194|1297|188787|118964|183710;3379134|29547|3031852|213849|72293;3379134|1224|2008785|119069|206349;1783272|201174|1760|85006|85021;3379134|1224|28216|80840|75682;1783272|201174|84995|84996|84997;1783272|1239|909932|909929|1843490;1783272|1239|186801|68295|186814;1783272|1239|186801|68295|543371;3379134|1224|1236|2887326|468|469;3379134|1224|1236|135624|84642|642;1783272|201174|1760|85006|1268|1663;3379134|976|117743|200644|2762318|59735;1783272|201174|1760|85004|31953|1678;3379134|1224|28216|80840|119060|32008;1783272|1239|186801|3085636|186803|830;1783272|1239|186801|186802|31979|1485;3384194|1297|188787|118964|183710|1298;1783272|1239|186801|3082720|3118655|44259;3379134|1224|28216|206351|1499392|397456;1783272|1239|186801|3085636|186803|43994;1783272|201174|1760|85006|85023|33882;3379134|1224|1236|135625|712|745;3379134|1224|28216|80840|2975441|335058;3379134|1224|28216|80840|119060|48736;1783272|201174|84995|84996|84997|42255;3379134|1224|28216|206351|481|1193515;3379134|1224|2008785|119069|206349|203470;1783272|1239|186801|68295|186814|1754;1783272|1239|186801|68295|186814|28895;1783272|1239|909932|909929|1843490|261684;3379134|976|117743|200644|49546;1783272|544448|31969;3379134|1224|28216|206351;3379134|976|200643|171549|171551;1783272|1239|909932|909929|1843491;1783272|1239|1737404;3379134|1224|28216|80840|80864|34072,Complete,Atrayees
bsdb:33672177/1/2,33672177,case-control,33672177,10.3390/ijerph18042174,NA,"Rueca M., Fontana A., Bartolini B., Piselli P., Mazzarelli A., Copetti M., Binda E., Perri F., Gruber C.E.M., Nicastri E., Marchioni L., Ippolito G., Capobianchi M.R., Di Caro A. , Pazienza V.",Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing,International journal of environmental research and public health,2021,"Nasal/Oropharyngeal, SARS-CoV2, microbiota",Experiment 1,Italy,Homo sapiens,"Nasopharynx,Oropharynx","UBERON:0001728,UBERON:0001729",COVID-19,MONDO:0100096,Healthy controls,ICU COVID-19 patients,COVID-19 patients admitted to intensive care unit,10,10,NA,16S,23456789,Ion Torrent,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Table S1,30 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between healthy controls and ICU COVID-19 patients,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae",1783272|201174|1760|85006|85020;3379134|1224|1236|91347|1903409;1783272|201174|1760|85007|85025;3379134|1224|1236|91347|1903410;3379134|29547|3031852|213849;3379134|1224|1236|135614|32033;3379134|1224|1236|91347|1903411;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|1506553;1783272|201174|1760|85007|2805586|1847725;1783272|201174|1760|85006|1268|1269;1783272|201174|84998|84999|1643824|133925;1783272|1239|91061|1385|186822|44249;3379134|1224|1236|91347|1903409|53335;1783272|201174|1760|85007|85025|1827;3379134|1224|1236|91347|543|590;1783272|201174|1760|85004|31953|196081;3379134|1224|1236|91347|1903411|613;3379134|1224|1236|135614|32033|40323;1783272|1239|186801|3082720|543314;1783272|201174|1760|85007;1783272|1239|91061|186826|81852;3379134|1224|1236|72274|135621;1783272|1239|91061|1385|90964,Complete,Atrayees
bsdb:33672177/2/1,33672177,case-control,33672177,10.3390/ijerph18042174,NA,"Rueca M., Fontana A., Bartolini B., Piselli P., Mazzarelli A., Copetti M., Binda E., Perri F., Gruber C.E.M., Nicastri E., Marchioni L., Ippolito G., Capobianchi M.R., Di Caro A. , Pazienza V.",Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing,International journal of environmental research and public health,2021,"Nasal/Oropharyngeal, SARS-CoV2, microbiota",Experiment 2,Italy,Homo sapiens,"Nasopharynx,Oropharynx","UBERON:0001728,UBERON:0001729",COVID-19,MONDO:0100096,Healthy controls,Mild-moderate COVID-19 patients,COVID-19 patients with mild to moderate symptoms that were not admitted to an intensive care unit,10,11,NA,16S,23456789,Ion Torrent,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Table S1,1 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance of microbial taxa between healthy controls and mild-moderate COVID-19 cases,decreased,"k__Thermotogati|p__Deinococcota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacterales Family III. Incertae Sedis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Gulbenkiania,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Snodgrassella,k__Pseudomonadati|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Tepidiphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae|g__Thermoanaerobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae|g__Thermoanaerobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae|g__Thermosinus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Campylobacterota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax",3384194|1297;1783272|1239|91061|1385|186823;3379134|1224|28211|204458|76892;3379134|1224|28216|206351|1499392;3379134|1224|2008785|119069|206349;1783272|201174|1760|85006|85021;1783272|201174|1760|85006|85023;3379134|1224|28216|80840|75682;1783272|201174|84995|84996|84997;1783272|1239|909932|909929|1843490;1783272|1239|186801|68295|186814;1783272|1239|186801|68295|543371;3379134|1224|28216|80840;1783272|201174|1760|85006|1268|1663;1783272|1239|526524|526525|128827|118747;3379134|1224|28216|80840|119060|32008;3384194|1297|188787|118964|183710|1298;3379134|1224|28216|206351|1499392|397456;1783272|1239|186801|3085636|186803|43994;1783272|201174|1760|85006|1268|57493;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|1300|948104;3379134|1224|28216|80840|2975441|335058;3379134|1224|28216|80840|119060|48736;1783272|201174|84995|84996|84997|42255;3379134|1224|28216|206351|481|1193515;3379134|1224|2008785|119069|206349|203470;1783272|1239|186801|68295|186814|1754;1783272|1239|186801|68295|186814|28895;1783272|1239|909932|909929|1843490|261684;3379134|1224|28216|80840|119060;1783272|1239|186801|186802|31979;1783272|201174|1760|85007;3379134|1224|1236|91347|543;3379134|29547;1783272|201174|1760|85009|31957;1783272|1239|909932|909929|1843491;3379134|1224|28216|80840|80864|34072,Complete,Atrayees
bsdb:33672177/2/2,33672177,case-control,33672177,10.3390/ijerph18042174,NA,"Rueca M., Fontana A., Bartolini B., Piselli P., Mazzarelli A., Copetti M., Binda E., Perri F., Gruber C.E.M., Nicastri E., Marchioni L., Ippolito G., Capobianchi M.R., Di Caro A. , Pazienza V.",Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing,International journal of environmental research and public health,2021,"Nasal/Oropharyngeal, SARS-CoV2, microbiota",Experiment 2,Italy,Homo sapiens,"Nasopharynx,Oropharynx","UBERON:0001728,UBERON:0001729",COVID-19,MONDO:0100096,Healthy controls,Mild-moderate COVID-19 patients,COVID-19 patients with mild to moderate symptoms that were not admitted to an intensive care unit,10,11,NA,16S,23456789,Ion Torrent,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Table S1,1 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance of microbial taxa between healthy controls and mild-moderate COVID-19 cases,increased,"k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Bacillota|c__Clostridia|o__Halanaerobiales|f__Halanaerobiaceae|g__Halanaerobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae",3384194|1297|188787|118964|183710;3379134|1224|28211|356|119045;3379134|1224|28211;3379134|29547|3031852|213849;3379134|29547;3379134|976|117743|200644;1783272|544448;1783272|1239|186801|53433|972|2330;3379134|1224|28211|356|119045|407;3384189|32066|203490|203491|1129771|34104;1783272|1239|186801|3082720|543314;1783272|1239|91061|186826|81852;1783272|1239|186801|186802|186806;3379134|1224|1236|2887326|468;1783272|544448|31969|2085|2092;1783272|1239|91061|1385|90964,Complete,Atrayees
bsdb:33672177/3/1,33672177,case-control,33672177,10.3390/ijerph18042174,NA,"Rueca M., Fontana A., Bartolini B., Piselli P., Mazzarelli A., Copetti M., Binda E., Perri F., Gruber C.E.M., Nicastri E., Marchioni L., Ippolito G., Capobianchi M.R., Di Caro A. , Pazienza V.",Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing,International journal of environmental research and public health,2021,"Nasal/Oropharyngeal, SARS-CoV2, microbiota",Experiment 3,Italy,Homo sapiens,"Nasopharynx,Oropharynx","UBERON:0001728,UBERON:0001729",COVID-19,MONDO:0100096,Mild-Moderate COVID-19 patients,ICU COVID-19 patients,COVID-19 patients admitted to intensive care unit,11,10,NA,16S,23456789,Ion Torrent,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Table S1,1 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance of microbial taxa between mild-moderate COVID-19 patients and ICU-admitted COVID-19 patients,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,p__Candidatus Saccharimonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Halanaerobiales|f__Halanaerobiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Halanaerobiales|f__Halanaerobiaceae|g__Halanaerobium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Pseudomonadati|p__Campylobacterota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Bacillota|c__Tissierellia",3379134|1224|1236|2887326|468|469;3379134|1224|1236|135624|84642;3379134|1224|1236|135624|84642|642;3379134|976|117743|200644|2762318|59735;1783272|201174|1760|85004|31953|1678;1783272|1239|526524|526525|128827|118747;1783272|1239|186801|3085636|186803|830;95818;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3082720|3118655|44259;3379134|976|117743|200644;1783272|1239|186801|53433|972;1783272|1239|186801|53433|972|2330;3379134|29547|3031852|213849|72293;3379134|1224|28211|356|119045|407;1783272|544448|31969|2085|2092;3379134|1224|1236|135625|712|745;1783272|544448|31969|2085|2092;1783272|544448|31969;3379134|1224|1236|2887326|468;1783272|201174|1760|85006|1268;3384189|32066|203490|203491;3384189|32066|203490|203491|203492;3379134|976|117743|200644|49546;1783272|1239|186801|186802|186806;3379134|29547;3379134|1224|28211;1783272|201174|1760|85004|31953;3379134|1224|28216|206351;3379134|976|200643|171549|171551;1783272|544448;1783272|1239|1737404,Complete,Atrayees
bsdb:33672177/3/2,33672177,case-control,33672177,10.3390/ijerph18042174,NA,"Rueca M., Fontana A., Bartolini B., Piselli P., Mazzarelli A., Copetti M., Binda E., Perri F., Gruber C.E.M., Nicastri E., Marchioni L., Ippolito G., Capobianchi M.R., Di Caro A. , Pazienza V.",Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing,International journal of environmental research and public health,2021,"Nasal/Oropharyngeal, SARS-CoV2, microbiota",Experiment 3,Italy,Homo sapiens,"Nasopharynx,Oropharynx","UBERON:0001728,UBERON:0001729",COVID-19,MONDO:0100096,Mild-Moderate COVID-19 patients,ICU COVID-19 patients,COVID-19 patients admitted to intensive care unit,11,10,NA,16S,23456789,Ion Torrent,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Table S1,1 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance of microbial taxa between mild-moderate COVID-19 patients and ICU-admitted COVID-19 patients,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae",3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|1903409;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|570;1783272|201174|1760|85006|1268|57493;1783272|1239|186801|3085636|186803|1506553;1783272|1239|91061|186826|1300|1357;1783272|201174|1760|85007|2805586|1847725;1783272|201174|1760|85006|85023;1783272|201174|1760|85006|1268|1269;1783272|201174|1760|85007|85025;1783272|1239|91061|186826|1300|948104;1783272|201174|84998|84999|1643824|133925;1783272|1239|91061|1385|186822|44249;3379134|1224|1236|91347|1903409|53335;3379134|1224|1236|91347|1903410;1783272|201174|1760|85007|85025|1827;3379134|1224|1236|91347|543|590;1783272|201174|1760|85004|31953|196081;3379134|1224|1236|91347|1903411|613;3379134|1224|1236|135614|32033|40323;3379134|1224|1236|135614|32033;3379134|1224|1236|91347|1903411;1783272|201174|1760|85007|1653;1783272|201174|1760|85007;3379134|1224|1236|91347|543;1783272|201174|1760|85009|31957;3379134|1224|1236|72274|135621|286;3379134|1224|1236|135614|32033,Complete,Atrayees
bsdb:33672177/4/1,33672177,case-control,33672177,10.3390/ijerph18042174,NA,"Rueca M., Fontana A., Bartolini B., Piselli P., Mazzarelli A., Copetti M., Binda E., Perri F., Gruber C.E.M., Nicastri E., Marchioni L., Ippolito G., Capobianchi M.R., Di Caro A. , Pazienza V.",Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing,International journal of environmental research and public health,2021,"Nasal/Oropharyngeal, SARS-CoV2, microbiota",Experiment 4,Italy,Homo sapiens,"Nasopharynx,Oropharynx","UBERON:0001728,UBERON:0001729",COVID-19,MONDO:0100096,Patients infected with other human coronaviruses,ICU COVID-19 patients,COVID-19 patients admitted to intensive care unit,8,10,NA,16S,23456789,Ion Torrent,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Table S1,1 July 2021,Claregrieve1,"Claregrieve1,Atrayees,WikiWorks",Differential abundance of microbial taxa between non-COVID coronavirus patients and ICU COVID patients,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Arsenophonus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Blastococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Casaltella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Demequinaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Janibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Saccharopolyspora,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Snodgrassella,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacillati|p__Bacillota|c__Tissierellia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|1224|28211|3120395|433;3379134|1224|1236|2887326|468|469;1783272|201174|1760|2037|2049|1654|29317;3379134|1224|1236|135624|84642;3379134|1224|1236|135624|84642|642;3379134|1224|28216|80840|506;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|207244;3379134|1224|1236|91347|1903414|637;1783272|201174|1760|85006|1268|1663;3379134|976|117743|200644|2762318|59735;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|1643682|85030|38501;1783272|1239|186801|3085636|186803|572511;1783272|201174|1760|85006|85019;1783272|201174|1760|85006|85019|1696;3379134|1224|28211|204458|76892|41275;3379134|1224|28216|80840|119060|32008;1783272|1239|186801|3082720|543314|1715793;3379134|1224|28211|204458|76892|75;3379134|1224|28211|204458|76892;3379134|1224|1236|1706369|1706371;3379134|976|1853228|1853229|563835;1783272|1239|186801|3082768|424536;3379134|976|117743|200644|2762318|59732;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107;3379134|1224|28216|80840|119060|106589;1783272|201174|1760|85006|1042322;3379134|200940|3031449|213115|194924;1783272|1239|186801|3085636|186803|189330;1783272|1239|91061|186826|186827|66831;1783272|1239|186801|3082720|3118655|44259;1783272|201174|1760|1643682|85030;1783272|1239|526524|526525|128827|1573535;1783272|201174|1760|85006|85021;1783272|201174|1760|85006|85021|53457;3379134|1224|28216|80840|75682|149698;3379134|1224|28211|356|119045;3379134|1224|28211|356|119045|407;1783272|201174|1760|85006|85023|33882;3379134|1224|1236|91347|1903414;1783272|201174|1760|85007|1762;1783272|201174|1760|85007|1762|1763;1783272|1239|909932|1843489|31977|909928;1783272|201174|1760|85009|85015;1783272|201174|1760|85009|85015|1839;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|1853231;3379134|1224|28216|80840|75682;3379134|976|200643|171549|2005525|375288;3379134|1224|28211|204455|31989|265;3379134|976|117747|200666|84566|84567;3379134|1224|28216|80840|2975441|335058;1783272|1239|91061|1385|186818;1783272|201174|1760|85010|2070;3379134|1224|28216|80840|119060|48736;3379134|1224|28211|356|82115;3379134|976|200643|171549|171550;1783272|1239|186801|3085636|186803|841;1783272|201174|84995|84996|84997|42255;1783272|201174|84995|84996|84997;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|186802|216572|1263;1783272|201174|1760|85010|2070|1835;3379134|1224|28216|206351|481|1193515;3379134|976|117747|200666|84566;3379134|1224|28211|204457|41297;3379134|1224|28211|204457|41297|13687;1783272|1239|186801|3085636|186803|1506577;3379134|1224|1236|135614|32033|338;1783272|201174|1760|2037;3379134|1224|28211;1783272|1239|91061|1385|186817;3379134|1224|28216|80840|119060;3379134|1224|28216|80840;1783272|1239|186801|186802|31979;1783272|201174|1760|85006|85020;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|186801|186802|186806;3379134|976|117743|200644|49546;1783272|201174|1760|85006|85021;1783272|201174|1760|85006|85023;1783272|201174|1760|85006|1268;3379134|1224|28216|206351;1783272|201174|1760|85007|85025;3379134|1224|28211|204455|31989;1783272|1239|1737404|1737405|1570339;1783272|1239|186801|186802|216572|1263;3379134|1224|28211|204457|41297;1783272|1239|1737404;1783272|1239|186801|186802|216572,Complete,Atrayees
bsdb:33672177/4/2,33672177,case-control,33672177,10.3390/ijerph18042174,NA,"Rueca M., Fontana A., Bartolini B., Piselli P., Mazzarelli A., Copetti M., Binda E., Perri F., Gruber C.E.M., Nicastri E., Marchioni L., Ippolito G., Capobianchi M.R., Di Caro A. , Pazienza V.",Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing,International journal of environmental research and public health,2021,"Nasal/Oropharyngeal, SARS-CoV2, microbiota",Experiment 4,Italy,Homo sapiens,"Nasopharynx,Oropharynx","UBERON:0001728,UBERON:0001729",COVID-19,MONDO:0100096,Patients infected with other human coronaviruses,ICU COVID-19 patients,COVID-19 patients admitted to intensive care unit,8,10,NA,16S,23456789,Ion Torrent,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Table S1,1 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance of microbial taxa between non-COVID coronavirus patients and ICU COVID patients,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__Eubacteriales Family XIII. Incertae Sedis bacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae",1783272|1239|91061|186826|1300|1357;3379134|1224|1236|91347|543|590;1783272|201174|1760|85004|31953|196081;3379134|1224|1236|91347|1903411|613;3379134|29547|3031852|213849;1783272|1239|186801|3082720|543314|2137877;1783272|1239|91061|186826|81852;3379134|1224|1236|72274|135621,Complete,Atrayees
bsdb:33678150/1/1,33678150,case-control,33678150,10.1080/19490976.2021.1887722,NA,"Cao J., Wang C., Zhang Y., Lei G., Xu K., Zhao N., Lu J., Meng F., Yu L., Yan J., Bai C., Zhang S., Zhang N., Gong Y., Bi Y., Shi Y., Chen Z., Dai L., Wang J. , Yang P.",Integrated gut virome and bacteriome dynamics in COVID-19 patients,Gut microbes,2021,"COVID-19, bacteriome, dysbiosis, genetic mutation, virome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Patients with COVID-19,5,13,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3d,2 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance in microbial taxa between healthy controls and COVID-19 patients,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 2_1_58FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 1_4_56FAA",1783272|1239|186801|3085636|186803|2316020|33038;1783272|201174|84998|1643822|1643826|84111;1783272|1239|526524|526525|2810280|100883;1783272|1239|526524|526525|2810280|3025755|1547;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|3085636|186803|658082;1783272|1239|186801|3085636|186803|658655,Complete,Atrayees
bsdb:33678150/1/2,33678150,case-control,33678150,10.1080/19490976.2021.1887722,NA,"Cao J., Wang C., Zhang Y., Lei G., Xu K., Zhao N., Lu J., Meng F., Yu L., Yan J., Bai C., Zhang S., Zhang N., Gong Y., Bi Y., Shi Y., Chen Z., Dai L., Wang J. , Yang P.",Integrated gut virome and bacteriome dynamics in COVID-19 patients,Gut microbes,2021,"COVID-19, bacteriome, dysbiosis, genetic mutation, virome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Patients with COVID-19,5,13,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 3d,2 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance in microbial taxa between healthy controls and COVID-19 patients,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes ihumii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium 1_1_47,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis",3379134|976|200643|171549|171550|239759|1470347;1783272|1239|186801|3085636|186803|841|166486;3379134|1224|28216|80840|469610;1783272|1239|186801|3085636|186803|2569097|39488;3379134|1224|28216|80840|995019|577310|487175;3379134|976|200643|171549|171550|239759|626932;3379134|976|200643|171549|2005519|1348911|1099853;1783272|1239|186801|3085636|186803|28050|39485;3379134|976|200643|171549|2030927;3379134|976|200643|171549|815|816|291644;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|171550|239759|328814;1783272|1239|186801|186802|216572|1263|40518;3379134|976|200643|171549|815|909656|204516,Complete,Atrayees
bsdb:33678150/2/1,33678150,case-control,33678150,10.1080/19490976.2021.1887722,NA,"Cao J., Wang C., Zhang Y., Lei G., Xu K., Zhao N., Lu J., Meng F., Yu L., Yan J., Bai C., Zhang S., Zhang N., Gong Y., Bi Y., Shi Y., Chen Z., Dai L., Wang J. , Yang P.",Integrated gut virome and bacteriome dynamics in COVID-19 patients,Gut microbes,2021,"COVID-19, bacteriome, dysbiosis, genetic mutation, virome",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Antibiotic-naive COVID-19 patients,Antibiotic-treated COVID-19 patients,Patients with COVID-19 treated with antibiotics,8,5,NA,WMS,NA,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3g,2 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance of microbial taxa between antibiotic-naive COVID-19 patients and antibiotic-treated COVID-19 patients,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa",1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|526524|526525|2810280|100883;1783272|1239|526524|526525|2810280|3025755|1547,Complete,Atrayees
bsdb:33678150/2/2,33678150,case-control,33678150,10.1080/19490976.2021.1887722,NA,"Cao J., Wang C., Zhang Y., Lei G., Xu K., Zhao N., Lu J., Meng F., Yu L., Yan J., Bai C., Zhang S., Zhang N., Gong Y., Bi Y., Shi Y., Chen Z., Dai L., Wang J. , Yang P.",Integrated gut virome and bacteriome dynamics in COVID-19 patients,Gut microbes,2021,"COVID-19, bacteriome, dysbiosis, genetic mutation, virome",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Antibiotic-naive COVID-19 patients,Antibiotic-treated COVID-19 patients,Patients with COVID-19 treated with antibiotics,8,5,NA,WMS,NA,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3g,2 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance of microbial taxa between antibiotic-naive COVID-19 patients and antibiotic-treated COVID-19 patients,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 2 1 46FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus",1783272|1239|186801|186802|216572|292632|2053618;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|3085636|186803|841|301301;3379134|1224|28216|80840|995019|577310|487175;1783272|1239|186801|3085636|186803|2683689;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|3570277|116085;1783272|201174|84998|84999|84107|102106|74426;3379134|976|200643|171549|815|909656|821,Complete,Atrayees
bsdb:33678150/3/1,33678150,case-control,33678150,10.1080/19490976.2021.1887722,NA,"Cao J., Wang C., Zhang Y., Lei G., Xu K., Zhao N., Lu J., Meng F., Yu L., Yan J., Bai C., Zhang S., Zhang N., Gong Y., Bi Y., Shi Y., Chen Z., Dai L., Wang J. , Yang P.",Integrated gut virome and bacteriome dynamics in COVID-19 patients,Gut microbes,2021,"COVID-19, bacteriome, dysbiosis, genetic mutation, virome",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Mild COVID-19 patients,Severe COVID-19 patients,Patients with severe COVID-19,3,3,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,2 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance of microbial taxa between mild and severe COVID-19 patients,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium glucuronolyticum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia|s__Alloscardovia omnicolens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus avium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus casseliflavus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc lactis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella confusa,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella glucosivorans,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis",1783272|201174|1760|85007|1653|1716|61592;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|81852|1350|1352;3379134|29547|3031852|213849|72294|194|824;1783272|201174|1760|85007|1653|1716|39791;1783272|201174|1760|85006|1268|32207|172042;1783272|201174|1760|85004|31953|419014|419015;1783272|1239|91061|186826|81852|1350|33945;1783272|1239|91061|186826|81852|1350|37734;1783272|1239|91061|186826|33958|1243|1246;1783272|1239|91061|186826|33958|46255|1583;3379134|1224|28216|80840|80864|80865;3379134|1224|28216|206351|481|538|2766967;3379134|29547|3031852|213849|72294|194|199;3379134|1224|1236|91347|543|544|546;3379134|1224|1236|91347|543|570|548;1783272|1239|91061|186826|1300|1301|68892;1783272|1239|909932|1843489|31977|906|187326,Complete,Atrayees
bsdb:33678150/3/2,33678150,case-control,33678150,10.1080/19490976.2021.1887722,NA,"Cao J., Wang C., Zhang Y., Lei G., Xu K., Zhao N., Lu J., Meng F., Yu L., Yan J., Bai C., Zhang S., Zhang N., Gong Y., Bi Y., Shi Y., Chen Z., Dai L., Wang J. , Yang P.",Integrated gut virome and bacteriome dynamics in COVID-19 patients,Gut microbes,2021,"COVID-19, bacteriome, dysbiosis, genetic mutation, virome",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Mild COVID-19 patients,Severe COVID-19 patients,Patients with severe COVID-19,3,3,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,2 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance of microbial taxa between mild and severe COVID-19 patients,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,1783272|1239|186801|3085636|186803|1766253|39491,Complete,Atrayees
bsdb:33681234/1/1,33681234,case-control,33681234,10.3389/fmed.2020.00538,NA,"Liu Z., Wu Y., Luo Y., Wei S., Lu C., Zhou Y., Wang J., Miao T., Lin H., Zhao Y., Liu Q. , Liu Y.",Self-Balance of Intestinal Flora in Spouses of Patients With Rheumatoid Arthritis,Frontiers in medicine,2020,"16S rRNA sequencing, environment/gene interaction, gut microbiota, rheumatoid arthritis, spouses",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Rheumatoid arthritis,EFO:0000685,Healthy controls,Rheumatoid arthritis patient,Rheumatoid arthritis patient,20,30,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 3B, text",16 October 2021,Tislam,"Tislam,Peace Sandy,WikiWorks","Discriminant analysis of LEfSe multistage species difference.  (B) Indicator bacteria with LDA scores of ≥ 2 in three groups were screened out. Different-colored regions represent different constituents (red, RA; green, HC; blue, SP). Circles indicate phylogenetic levels from domain to genus. Circle diameters are proportional to abundances for each group. It can be seen from the figure that, among the three groups, the abundance peaks of species with significant differences were distributed in RA and HC, respectively, and there was no peak in the SP group.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",1783272|1239|186801|3085636|186803|572511;1783272|201174|84998|1643822|1643826|84111;1783272|1239|526524|526525|128827|1573535;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|201174|1760|85006|1268;3379134|1224|1236|72274;3379134|1224|1236|72274|135621|286;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|201174|1760|85006|1268|32207,Complete,Peace Sandy
bsdb:33681234/1/2,33681234,case-control,33681234,10.3389/fmed.2020.00538,NA,"Liu Z., Wu Y., Luo Y., Wei S., Lu C., Zhou Y., Wang J., Miao T., Lin H., Zhao Y., Liu Q. , Liu Y.",Self-Balance of Intestinal Flora in Spouses of Patients With Rheumatoid Arthritis,Frontiers in medicine,2020,"16S rRNA sequencing, environment/gene interaction, gut microbiota, rheumatoid arthritis, spouses",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Rheumatoid arthritis,EFO:0000685,Healthy controls,Rheumatoid arthritis patient,Rheumatoid arthritis patient,20,30,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 3, text",19 October 2021,Tislam,"Tislam,Peace Sandy,WikiWorks","Discriminant analysis of LEfSe multistage species difference. (B) Indicator bacteria with LDA scores of ≥ 2 in three groups were screened out. Different-colored regions represent different constituents (red, RA; green, HC; blue, SP). Circles indicate phylogenetic levels from domain to genus. Circle diameters are proportional to abundances for each group. It can be seen from the figure that, among the three groups, the abundance peaks of species with significant differences were distributed in RA and HC, respectively, and there was no peak in the SP group.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia|o__Acidimicrobiales,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia|o__Acidimicrobiales|f__Microthrixaceae|g__Candidatus Neomicrothrix,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Thermoactinomycetaceae|g__Kroppenstedtia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|841;3379134|976|200643|171549;1783272|201174|84992|84993;1783272|544448|31969|2085|2092;1783272|1239|526524|526525|128827;1783272|201174|84992|84993|1798913|41949;1783272|544448|31969|2085|2092|2093;1783272|544448|31969|2085;1783272|1239|1737404|1737405|1570339|162290;1783272|1239|91061|1385|186824|1274351;1783272|1239|909932|1843489|31977,Complete,Peace Sandy
bsdb:33692356/1/1,33692356,"case-control,meta-analysis",33692356,10.1038/s41531-021-00156-z,NA,"Romano S., Savva G.M., Bedarf J.R., Charles I.G., Hildebrand F. , Narbad A.",Meta-analysis of the Parkinson's disease gut microbiome suggests alterations linked to intestinal inflammation,NPJ Parkinson's disease,2021,NA,Experiment 1,"United States of America,Germany,Russian Federation,Italy,China,Finland",Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Controls,PD cases,Cases diagnosed with Parkinson's Disease (PD),10,10,NA,16S,NA,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),DESeq2,ANCOM",0.05,TRUE,NA,NA,"age,sex",NA,NA,increased,NA,NA,increased,Signature 1,Figure 5,30 July 2025,Kristin.abraham,Kristin.abraham,Taxa enriched in PD cases,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Frisingicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|186801|186802|216572|244127;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3082768|990719;3384194|508458|649775|649776|649777|508459;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|1686313;1783272|1239|186801|3085636|186803|1918511;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|186802|1392389;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|906;3366610|28890|183925|2158|2159|2172;1783272|1239|186801|186802|216572|459786;1783272|1239|1737404|1737405|1570339|162289;3379134|976|200643|171549|171551|836;1783272|1239|186801|186802|216572|1508657;1783272|201174|1760|2037|2049|184869,Complete,NA
bsdb:33692356/1/2,33692356,"case-control,meta-analysis",33692356,10.1038/s41531-021-00156-z,NA,"Romano S., Savva G.M., Bedarf J.R., Charles I.G., Hildebrand F. , Narbad A.",Meta-analysis of the Parkinson's disease gut microbiome suggests alterations linked to intestinal inflammation,NPJ Parkinson's disease,2021,NA,Experiment 1,"United States of America,Germany,Russian Federation,Italy,China,Finland",Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Controls,PD cases,Cases diagnosed with Parkinson's Disease (PD),10,10,NA,16S,NA,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),DESeq2,ANCOM",0.05,TRUE,NA,NA,"age,sex",NA,NA,increased,NA,NA,increased,Signature 2,Figure 5,30 July 2025,Kristin.abraham,Kristin.abraham,Taxa depleted in PD cases,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|186801|3085636|186803|437755;1783272|1239|186801|3085636|186803|841,Complete,NA
bsdb:33707706/1/1,33707706,case-control,33707706,10.1038/s41598-021-85464-3,NA,"Al Bataineh M.T., Dash N.R., Bel Lassen P., Banimfreg B.H., Nada A.M., Belda E. , Clément K.",Publisher Correction: Revealing links between gut microbiome and its fungal community in Type 2 Diabetes Mellitus among Emirati subjects: A pilot study,Scientific reports,2021,NA,Experiment 1,United Arab Emirates,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Non-T2DM controls (healthy individuals),T2DM individuals (subjects with Type 2 Diabetes),"Native Emirati subjects diagnosed with T2DM, attending the endocrinology clinic.",25,25,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 1G and within result text.,15 October 2024,Sproff,"Sproff,Tosin,WikiWorks",Prokaryotic profiling of gut microbiome - Barplot of log2 fold changes in taxonomic feature abundances between health controls and T2DM.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae",1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3082720|543314|86331;1783272|1239|909932|1843488|909930|904;3379134|256845|1313211|278082|255528,Complete,Folakunmi
bsdb:33707706/1/2,33707706,case-control,33707706,10.1038/s41598-021-85464-3,NA,"Al Bataineh M.T., Dash N.R., Bel Lassen P., Banimfreg B.H., Nada A.M., Belda E. , Clément K.",Publisher Correction: Revealing links between gut microbiome and its fungal community in Type 2 Diabetes Mellitus among Emirati subjects: A pilot study,Scientific reports,2021,NA,Experiment 1,United Arab Emirates,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Non-T2DM controls (healthy individuals),T2DM individuals (subjects with Type 2 Diabetes),"Native Emirati subjects diagnosed with T2DM, attending the endocrinology clinic.",25,25,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure1G and within result text,15 October 2024,Sproff,"Sproff,Tosin,WikiWorks",Prokaryotic profiling of gut microbiome - Barplot of log2 fold changes in taxonomic feature abundances between health controls and T2DM,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus",3379134|976|200643|171549|1853231|283168;1783272|1239|91061|186826|1300|1357,Complete,Folakunmi
bsdb:33707706/2/1,33707706,case-control,33707706,10.1038/s41598-021-85464-3,NA,"Al Bataineh M.T., Dash N.R., Bel Lassen P., Banimfreg B.H., Nada A.M., Belda E. , Clément K.",Publisher Correction: Revealing links between gut microbiome and its fungal community in Type 2 Diabetes Mellitus among Emirati subjects: A pilot study,Scientific reports,2021,NA,Experiment 2,United Arab Emirates,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Non-T2DM controls (healthy individuals),T2DM individuals (subjects with Type 2 Diabetes),"Native Emirati subjects diagnosed with T2DM, attending the endocrinology clinic.",25,25,3 months,ITS / ITS2,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 2F and within result text,21 October 2024,Tosin,"Tosin,WikiWorks",Fungal profiling of gut microbiome - Bar plot of log2 fold changes in taxonomic feature abundance between non-T2DM controls and T2DM,increased,"k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia furfur,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Davidiella",4751|5204|1538075|162474|742845|55193|55194;4751|4890|147541|2726946|452563|237557,Complete,Folakunmi
bsdb:33707706/2/3,33707706,case-control,33707706,10.1038/s41598-021-85464-3,NA,"Al Bataineh M.T., Dash N.R., Bel Lassen P., Banimfreg B.H., Nada A.M., Belda E. , Clément K.",Publisher Correction: Revealing links between gut microbiome and its fungal community in Type 2 Diabetes Mellitus among Emirati subjects: A pilot study,Scientific reports,2021,NA,Experiment 2,United Arab Emirates,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Non-T2DM controls (healthy individuals),T2DM individuals (subjects with Type 2 Diabetes),"Native Emirati subjects diagnosed with T2DM, attending the endocrinology clinic.",25,25,3 months,ITS / ITS2,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,unchanged,Signature 3,Figure 2F and within result text,21 October 2024,Tosin,"Tosin,WikiWorks",Fungal profiling of gut microbiome- Bar plot of log2 fold changes in taxonomic feature abundance between non-T2DM controls and T2DM,decreased,k__Fungi|p__Basidiomycota,4751|5204,Complete,Folakunmi
bsdb:33708251/1/1,33708251,randomized controlled trial,33708251,10.1155/2021/6645970,NA,"Liu L., Yang M., Dong W., Liu T., Song X., Gu Y., Wang S., Liu Y., Abla Z., Qiao X., Liu W., Jiang K., Wang B., Zhang J. , Cao H.",Gut Dysbiosis and Abnormal Bile Acid Metabolism in Colitis-Associated Cancer,Gastroenterology research and practice,2021,NA,Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer cell line,BTO:0001616,control group at week 10 (C10 group),azoxymethane/dextran sodiumsulfate (AOM/DSS) group at week 10 (AD10 group),"C57BL/6mice aged 7 weeks were obtained from Beijing Huafukang Bioscience Co. Inc. and acclimatized 1 week before the experiment. Intraperitoneal injection of 10mg/kg azoxymethane(AOM) was applied to the AOM/DSS group. After seven days, the AOM/DSS group was given1.5% dextran sodium sulfate (DSS) in drinking water on days 8–13, 27–32, and 46–51, and each cycle of DSS treatment was followed by 14-day drinking water. This was to create the colitis-induced colorectal cancer (CAC) model in the mice. Group 1 is the mice that developed CAC and had their fecal sample collected before being euthanized on day 70 (week 10).",5,5,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 4c,29 November 2023,Yjung24,"Yjung24,ChiomaBlessing,WikiWorks",The LefSe analysis listed bacteria with significant differences at different levels in AD10 group vs C10 group,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549;3379134|976|200643;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|171551;3379134|976|200643|171549|171550,Complete,ChiomaBlessing
bsdb:33708251/1/2,33708251,randomized controlled trial,33708251,10.1155/2021/6645970,NA,"Liu L., Yang M., Dong W., Liu T., Song X., Gu Y., Wang S., Liu Y., Abla Z., Qiao X., Liu W., Jiang K., Wang B., Zhang J. , Cao H.",Gut Dysbiosis and Abnormal Bile Acid Metabolism in Colitis-Associated Cancer,Gastroenterology research and practice,2021,NA,Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer cell line,BTO:0001616,control group at week 10 (C10 group),azoxymethane/dextran sodiumsulfate (AOM/DSS) group at week 10 (AD10 group),"C57BL/6mice aged 7 weeks were obtained from Beijing Huafukang Bioscience Co. Inc. and acclimatized 1 week before the experiment. Intraperitoneal injection of 10mg/kg azoxymethane(AOM) was applied to the AOM/DSS group. After seven days, the AOM/DSS group was given1.5% dextran sodium sulfate (DSS) in drinking water on days 8–13, 27–32, and 46–51, and each cycle of DSS treatment was followed by 14-day drinking water. This was to create the colitis-induced colorectal cancer (CAC) model in the mice. Group 1 is the mice that developed CAC and had their fecal sample collected before being euthanized on day 70 (week 10).",5,5,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 4c,29 November 2023,Yjung24,"Yjung24,ChiomaBlessing,WikiWorks",The LefSe analysis listed bacteria with significant differences at different levels in AD10 group vs C10 group,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|29547|3031852|213849;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;3379134|29547|3031852;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|186806|1730;3379134|29547|3031852|213849|72293|209;3379134|29547|3031852|213849|72293;1783272|1239|186801|186802|1392389;3379134|976|200643|171549|2005525|375288;3379134|1224;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301,Complete,ChiomaBlessing
bsdb:33713890/1/1,33713890,"cross-sectional observational, not case-control",33713890,10.1016/j.eplepsyres.2021.106601,NA,"Lee H., Lee S., Lee D.H. , Kim D.W.",A comparison of the gut microbiota among adult patients with drug-responsive and drug-resistant epilepsy: An exploratory study,Epilepsy research,2021,"Bacteroides, Bifidobacterium, Drug-resistant epilepsy, Gamma-aminobutyric acid, Microbiome, Ruminococcus",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Epilepsy,EFO:0000474,Drug-responsive epilepsy patients,Drug-resistant epilepsy patients,Patients in the drug-resistant epilepsy group had continued seizures despite receiving more than two types of appropriately chosen antiepileptic drugs (AEDs),20,20,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 3a, 3b",17 December 2024,Kavyaayala,"Kavyaayala,WikiWorks,Fiddyhamma",The linear discriminant effect size (LEfSe) analysis of gut microbiota of patients in drug-responsive and drug-resistant epilepsy groups.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",3379134|976|200643|171549|815|816|338188;1783272|1239|186801|3085636|186803|2316020|592978;1783272|1239|186801|3085636|186803|2316020|33038,Complete,DeepShah21
bsdb:33713890/1/2,33713890,"cross-sectional observational, not case-control",33713890,10.1016/j.eplepsyres.2021.106601,NA,"Lee H., Lee S., Lee D.H. , Kim D.W.",A comparison of the gut microbiota among adult patients with drug-responsive and drug-resistant epilepsy: An exploratory study,Epilepsy research,2021,"Bacteroides, Bifidobacterium, Drug-resistant epilepsy, Gamma-aminobutyric acid, Microbiome, Ruminococcus",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Epilepsy,EFO:0000474,Drug-responsive epilepsy patients,Drug-resistant epilepsy patients,Patients in the drug-resistant epilepsy group had continued seizures despite receiving more than two types of appropriately chosen antiepileptic drugs (AEDs),20,20,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 3a, 3b",17 December 2024,Kavyaayala,"Kavyaayala,WikiWorks,Fiddyhamma",The linear discriminant effect size (LEfSe) analysis of gut microbiota of patients in drug-responsive and drug-resistant epilepsy groups.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales",1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|909929|1843491|158846|437897;1783272|1239|909932;1783272|1239|909932|909929|1843491;1783272|1239|909932|909929;1783272|1239|909932|1843489|31977;1783272|1239|909932|1843489,Complete,DeepShah21
bsdb:33713890/2/1,33713890,"cross-sectional observational, not case-control",33713890,10.1016/j.eplepsyres.2021.106601,NA,"Lee H., Lee S., Lee D.H. , Kim D.W.",A comparison of the gut microbiota among adult patients with drug-responsive and drug-resistant epilepsy: An exploratory study,Epilepsy research,2021,"Bacteroides, Bifidobacterium, Drug-resistant epilepsy, Gamma-aminobutyric acid, Microbiome, Ruminococcus",Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,Epilepsy,EFO:0000474,Normal magnetic resonance imaging (MRI) patients,Abnormal magnetic resonance imaging (MRI) patients,Patients with abnormal results from magnetic resonance imaging (MRI); any lesions that can cause seizure are defined as abnormal.,14,26,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 4a, 4b",15 January 2025,Kavyaayala,"Kavyaayala,WikiWorks,Fiddyhamma",The linear discriminant effect size (LEfSe) analysis of gut microbiota of patients with normal and abnormal magnetic resonance imaging (MRI).,decreased,",k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii",;3379134|976|200643|171549|815|816|338188,Complete,DeepShah21
bsdb:33713890/2/2,33713890,"cross-sectional observational, not case-control",33713890,10.1016/j.eplepsyres.2021.106601,NA,"Lee H., Lee S., Lee D.H. , Kim D.W.",A comparison of the gut microbiota among adult patients with drug-responsive and drug-resistant epilepsy: An exploratory study,Epilepsy research,2021,"Bacteroides, Bifidobacterium, Drug-resistant epilepsy, Gamma-aminobutyric acid, Microbiome, Ruminococcus",Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,Epilepsy,EFO:0000474,Normal magnetic resonance imaging (MRI) patients,Abnormal magnetic resonance imaging (MRI) patients,Patients with abnormal results from magnetic resonance imaging (MRI); any lesions that can cause seizure are defined as abnormal.,14,26,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 4a, 4b",19 January 2025,Kavyaayala,"Kavyaayala,WikiWorks,Fiddyhamma",The linear discriminant effect size (LEfSe) analysis of gut microbiota of patients with normal and abnormal magnetic resonance imaging (MRI).,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella flexneri,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales",1783272|1239|909932|1843489|31977|39948;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|620|623;1783272|1239|909932|1843489|31977;1783272|1239|909932|1843489,Complete,DeepShah21
bsdb:33713890/3/1,33713890,"cross-sectional observational, not case-control",33713890,10.1016/j.eplepsyres.2021.106601,NA,"Lee H., Lee S., Lee D.H. , Kim D.W.",A comparison of the gut microbiota among adult patients with drug-responsive and drug-resistant epilepsy: An exploratory study,Epilepsy research,2021,"Bacteroides, Bifidobacterium, Drug-resistant epilepsy, Gamma-aminobutyric acid, Microbiome, Ruminococcus",Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,Electroencephalogram measurement,EFO:0004357,Normal electroencephalogram (EEG) patients,Abnormal electroencephalogram (EEG) patients,"Patients with abnormal electroencephalogram (EEG); any epileptiform discharges (spike, spike-wave complex, polyspikes, or sharp wave), subclinical electrographic seizures, or pathognomic rhythmic activities such as temporal intermittent rhythmic delta activity.",19,21,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,increased,increased,NA,NA,NA,unchanged,Signature 1,"Figure 5a, 5b",19 January 2025,Kavyaayala,"Kavyaayala,WikiWorks,Fiddyhamma",The linear discriminant effect size (LEfSe) analyses of gut microbiota of patients with normal and abnormal electroencephalogram (EEG).,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium callitrichos,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",1783272|201174;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|762209;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|3085636|186803|189330|88431;1783272|201174|84998|1643822|1643826|644652|471189;1783272|1239|186801|3085636|186803|2316020|592978;1783272|1239|186801|186802|216572|1263|438033;1783272|201174|84992;1783272|1239|186801|3085636|186803|2316020|33038,Complete,DeepShah21
bsdb:33713890/3/2,33713890,"cross-sectional observational, not case-control",33713890,10.1016/j.eplepsyres.2021.106601,NA,"Lee H., Lee S., Lee D.H. , Kim D.W.",A comparison of the gut microbiota among adult patients with drug-responsive and drug-resistant epilepsy: An exploratory study,Epilepsy research,2021,"Bacteroides, Bifidobacterium, Drug-resistant epilepsy, Gamma-aminobutyric acid, Microbiome, Ruminococcus",Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,Electroencephalogram measurement,EFO:0004357,Normal electroencephalogram (EEG) patients,Abnormal electroencephalogram (EEG) patients,"Patients with abnormal electroencephalogram (EEG); any epileptiform discharges (spike, spike-wave complex, polyspikes, or sharp wave), subclinical electrographic seizures, or pathognomic rhythmic activities such as temporal intermittent rhythmic delta activity.",19,21,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,increased,increased,NA,NA,NA,unchanged,Signature 2,"Figure 5a, 5b",19 January 2025,Kavyaayala,"Kavyaayala,WikiWorks,Fiddyhamma",The linear discriminant effect size (LEfSe) analyses of gut microbiota of patients with normal and abnormal electroencephalogram (EEG).,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium varium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella granulomatis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus",3384189|32066|203490|203491|203492|848|856;3379134|1224|1236;3379134|1224|1236|91347|543|570|39824;3379134|1224|1236|91347|543|570|573;1783272|201174|84998|84999|1643824|133925;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1328,Complete,DeepShah21
bsdb:33718259/1/1,33718259,case-control,33718259,10.3389/fcimb.2021.549678,NA,"Long Y., Liang F., Guo R., Zhu C., Zhao X., Wang X., Liu F., Jiang M., Liang Q., Zeng S., Han M., Qin J., Li S., Li S. , Yang H.",Gut Microbiota Signatures in Gestational Anemia,Frontiers in cellular and infection microbiology,2021,"16S rRNA gene sequencing, gestational anemia, gut microbiota, microbial dysbiosis, pregnant women",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Anemia,MONDO:0002280,healthy controls(HC1 group),gestational anemia (GA1 group),Gestational diseases are associated with altered intestinal microbiota in pregnant women in the first trimester.,54,24,1 month,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,body mass index,gestational age,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,FIGURE 2B.,10 January 2021,Lora Kasselman,"WikiWorks,Chinelsy,ChiomaBlessing",Bacterial genera significantly enriched in the GA1 group compared to the HC1 group (first trimester).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",1783272|1239|186801|186802|216572|244127;1783272|1239|186801|3085636|186803|265975;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|526524|526525|2810281|191303,Complete,Chinelsy
bsdb:33718259/2/1,33718259,case-control,33718259,10.3389/fcimb.2021.549678,NA,"Long Y., Liang F., Guo R., Zhu C., Zhao X., Wang X., Liu F., Jiang M., Liang Q., Zeng S., Han M., Qin J., Li S., Li S. , Yang H.",Gut Microbiota Signatures in Gestational Anemia,Frontiers in cellular and infection microbiology,2021,"16S rRNA gene sequencing, gestational anemia, gut microbiota, microbial dysbiosis, pregnant women",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Anemia,MONDO:0002280,healthy controls (HC3 group),gestational anemia (GA3 group),Gestational diseases are associated with altered intestinal microbiota in pregnant women in the third trimester.,56,30,1 month,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,body mass index,gestational age,sex",NA,unchanged,decreased,NA,NA,NA,decreased,Signature 1,FIGURE 2C.,29 October 2023,Chinelsy,"Chinelsy,ChiomaBlessing,WikiWorks",Bacterial genera significantly enriched in the GA3 group compared to the HC3 group (third trimester).,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella",1783272|201174|84998|84999|1643824|1380;1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|186802|31979;1783272|201174|84998|1643822|1643826|84111,Complete,Chinelsy
bsdb:33718259/2/2,33718259,case-control,33718259,10.3389/fcimb.2021.549678,NA,"Long Y., Liang F., Guo R., Zhu C., Zhao X., Wang X., Liu F., Jiang M., Liang Q., Zeng S., Han M., Qin J., Li S., Li S. , Yang H.",Gut Microbiota Signatures in Gestational Anemia,Frontiers in cellular and infection microbiology,2021,"16S rRNA gene sequencing, gestational anemia, gut microbiota, microbial dysbiosis, pregnant women",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Anemia,MONDO:0002280,healthy controls (HC3 group),gestational anemia (GA3 group),Gestational diseases are associated with altered intestinal microbiota in pregnant women in the third trimester.,56,30,1 month,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,body mass index,gestational age,sex",NA,unchanged,decreased,NA,NA,NA,decreased,Signature 2,FIGURE 2C.,1 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Bacterial genera significantly enriched in the GA3 group compared to the HC3 group (third trimester).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|186802|216572;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|204475;1783272|201174|84998|1643822|1643826|447020,Complete,ChiomaBlessing
bsdb:33718417/1/1,33718417,case-control,33718417,10.3389/fnut.2021.615064,NA,"Zhou Y., He Y., Liu L., Zhou W., Wang P., Hu H., Nie Y. , Chen Y.",Alterations in Gut Microbial Communities Across Anatomical Locations in Inflammatory Bowel Diseases,Frontiers in nutrition,2021,"Crohn's disease, Fusobacterium, Gardnerella, disease location, gut microbiota, ulcerative colitis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Combination of Healthy Controls (HC) and Ulcerative colitis (UC),Crohn’s disease (CD),Patients with Inflammatory Bowel Disease (IBD) specifically Crohn's disease (CD).,124,72,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3A, 3B",25 October 2025,Tosin,Tosin,Discriminative taxa determined by LEfSe (Linear Discriminant analysis effect size) between healthy controls (HC) and IBD (inflammatory bowel disease) groups; Crohn’s disease (CD) and Ulcerative colitis (UC),increased,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,3384189|32066|203490|203491|203492|848,Complete,Svetlana up
bsdb:33718417/2/1,33718417,case-control,33718417,10.3389/fnut.2021.615064,NA,"Zhou Y., He Y., Liu L., Zhou W., Wang P., Hu H., Nie Y. , Chen Y.",Alterations in Gut Microbial Communities Across Anatomical Locations in Inflammatory Bowel Diseases,Frontiers in nutrition,2021,"Crohn's disease, Fusobacterium, Gardnerella, disease location, gut microbiota, ulcerative colitis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Inflammatory bowel disease,EFO:0003767,Combination of Crohn’s disease (CD) and Ulcerative colitis (UC),Healthy Controls (HC),Healthy volunteers free of all the Inflammatory Bowel Disease (IBD),123,73,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3A, 3B",25 October 2025,Tosin,"Tosin,Reddicx",Discriminative taxa determined by LEfSe (Linear Discriminant analysis effect size) between healthy controls (HC) and IBD (inflammatory bowel disease) groups; Crohn’s disease (CD) and Ulcerative colitis (UC),increased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239;3379134|976|200643|171549;3379134|976|200643;3379134|976;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:33718417/3/1,33718417,case-control,33718417,10.3389/fnut.2021.615064,NA,"Zhou Y., He Y., Liu L., Zhou W., Wang P., Hu H., Nie Y. , Chen Y.",Alterations in Gut Microbial Communities Across Anatomical Locations in Inflammatory Bowel Diseases,Frontiers in nutrition,2021,"Crohn's disease, Fusobacterium, Gardnerella, disease location, gut microbiota, ulcerative colitis",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Combination of Crohn’s disease (CD) and Healthy Controls (HC),Ulcerative colitis (UC),Patients with the Inflammatory Bowel Disease (IBD) specifically Ulcerative Colitis (UC),145,51,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3A, 3B",25 October 2025,Tosin,"Tosin,Reddicx",Discriminative taxa determined by LEfSe (Linear Discriminant analysis effect size) between healthy controls (HC) and IBD (inflammatory bowel disease) groups; Crohn’s disease (CD) and Ulcerative colitis (UC),increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|84992;1783272|201174;1783272|1239|91061;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|84998|84999;1783272|201174|84998;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;3379134|1224|1236;1783272|1239|91061|186826;3379134|1224|1236|72274;3379134|1224;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:33718417/4/1,33718417,case-control,33718417,10.3389/fnut.2021.615064,NA,"Zhou Y., He Y., Liu L., Zhou W., Wang P., Hu H., Nie Y. , Chen Y.",Alterations in Gut Microbial Communities Across Anatomical Locations in Inflammatory Bowel Diseases,Frontiers in nutrition,2021,"Crohn's disease, Fusobacterium, Gardnerella, disease location, gut microbiota, ulcerative colitis",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Inflammatory bowel disease,EFO:0003767,Combination of Crohn’s disease ileal (CD_ileal) and Crohn’s disease colonic (CD_colonic),Healthy Controls (HC),Healthy volunteers free of all the Inflammatory Bowel Disease (IBD),72,73,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4A,25 October 2025,Tosin,"Tosin,Reddicx",Gut microbial biomarkers for disease location identified using LEfSe (Linear Discriminant analysis effect size) between (HC) healthy controls and CD (crohn’s disease) classified as ileal or colonic.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|140625;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171552|838;3379134|1224|1236|91347|1903414|586;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263,Complete,Svetlana up
bsdb:33718417/5/1,33718417,case-control,33718417,10.3389/fnut.2021.615064,NA,"Zhou Y., He Y., Liu L., Zhou W., Wang P., Hu H., Nie Y. , Chen Y.",Alterations in Gut Microbial Communities Across Anatomical Locations in Inflammatory Bowel Diseases,Frontiers in nutrition,2021,"Crohn's disease, Fusobacterium, Gardnerella, disease location, gut microbiota, ulcerative colitis",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Crohn ileitis,MONDO:0000709,Combination of Healthy controls (HC) and colonic Crohn's disease (CD_colonic),Crohn's disease ileal (CD_ileal),Patients with Inflammatory bowel disease (IBD) specifically Crohn's disease ileal (CD_ileal),121,24,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4A,25 October 2025,Tosin,"Tosin,Reddicx",Gut microbial biomarkers for disease location identified using LEfSe (Linear Discriminant analysis effect size) between (HC) healthy controls and CD (crohn’s disease) classified as ileal or colonic,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",1783272|1239|91061|1385|539738;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171550|239759,Complete,Svetlana up
bsdb:33718417/6/1,33718417,case-control,33718417,10.3389/fnut.2021.615064,NA,"Zhou Y., He Y., Liu L., Zhou W., Wang P., Hu H., Nie Y. , Chen Y.",Alterations in Gut Microbial Communities Across Anatomical Locations in Inflammatory Bowel Diseases,Frontiers in nutrition,2021,"Crohn's disease, Fusobacterium, Gardnerella, disease location, gut microbiota, ulcerative colitis",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Crohn's colitis,EFO:0005622,Combination of Healthy controls (HC) and Crohn's disease ileal (CD_ileal),Crohn's disease colonic (CD_colonic),Patients with Inflammatory bowel disease (IBD) specifically Crohn's disease colonic (CD_colonic),97,48,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4A,25 October 2025,Tosin,"Tosin,Reddicx",Gut microbial biomarkers for disease location identified using LEfSe (Linear Discriminant analysis effect size) between (HC) healthy controls and CD (crohn’s disease) classified as ileal or colonic,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|1239|526524|526525|128827|118747;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|33958|1243;1783272|201174|1760|85006|1268;3379134|1224|1236|72274|135621;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;1783272|201174|1760|85006|1268|32207,Complete,Svetlana up
bsdb:33718417/8/1,33718417,case-control,33718417,10.3389/fnut.2021.615064,NA,"Zhou Y., He Y., Liu L., Zhou W., Wang P., Hu H., Nie Y. , Chen Y.",Alterations in Gut Microbial Communities Across Anatomical Locations in Inflammatory Bowel Diseases,Frontiers in nutrition,2021,"Crohn's disease, Fusobacterium, Gardnerella, disease location, gut microbiota, ulcerative colitis",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Pancolitis,NA,"Combination of Healthy Controls (HC), Ulcerative proctitis (UC_E1) and Left-sided distal ulcerative colitis (UC_E2)",Extensive ulcerative colitis (pancolitis) (UC_E3),"Patients with Ulcerative colitis extending beyond the splenic flexure, classified as extensive ulcerative colitis (pancolitis, E3)",97,27,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,26 October 2025,Tosin,"Tosin,Reddicx","Gut microbial biomarkers for disease location identified using LEfSe (Linear Discriminant analysis effect size) between (HC) healthy controls, Ulcerative proctitis (UC_E1), Left-sided distal ulcerative colitis (UC_E2) and Extensive ulcerative colitis (pancolitis) (UC_E3)",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales",1783272|201174|1760|2037|2049;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|91061|1385|539738;1783272|1239|91061|186826,Complete,Svetlana up
bsdb:33718417/9/1,33718417,case-control,33718417,10.3389/fnut.2021.615064,NA,"Zhou Y., He Y., Liu L., Zhou W., Wang P., Hu H., Nie Y. , Chen Y.",Alterations in Gut Microbial Communities Across Anatomical Locations in Inflammatory Bowel Diseases,Frontiers in nutrition,2021,"Crohn's disease, Fusobacterium, Gardnerella, disease location, gut microbiota, ulcerative colitis",Experiment 9,China,Homo sapiens,Feces,UBERON:0001988,Distal colitis,NA,"Combination of Healthy controls (HC), Ulcerative proctitis (UC_E1) and Extensive ulcerative colitis (pancolitis) (UC_E3)",Left-sided distal ulcerative colitis (UC_E2),Patients with Inflammatory bowel disease (IBD) specifically left-sided distal ulcerative colitis (UC_E2).,110,14,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,26 October 2025,Tosin,"Tosin,Reddicx","Gut microbial biomarkers for disease location identified using LEfSe (Linear Discriminant analysis effect size) between (HC) healthy controls, Ulcerative proctitis (UC_E1), Left-sided distal ulcerative colitis (UC_E2) and Extensive ulcerative colitis (pancolitis) (UC_E3)",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:33718417/10/1,33718417,case-control,33718417,10.3389/fnut.2021.615064,NA,"Zhou Y., He Y., Liu L., Zhou W., Wang P., Hu H., Nie Y. , Chen Y.",Alterations in Gut Microbial Communities Across Anatomical Locations in Inflammatory Bowel Diseases,Frontiers in nutrition,2021,"Crohn's disease, Fusobacterium, Gardnerella, disease location, gut microbiota, ulcerative colitis",Experiment 10,China,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,"Combination of Healthy controls (HC), Left-sided distal ulcerative colitis (UC_E2) and Extensive ulcerative colitis (pancolitis) (UC_E3)",Ulcerative proctitis (UC_E1),Patients with Inflammatory bowel disease (IBD) specifically Ulcerative proctitis (UC_E1),114,10,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,26 October 2025,Tosin,"Tosin,Reddicx","Gut microbial biomarkers for disease location identified using LEfSe (Linear Discriminant analysis effect size) between (HC) healthy controls, Extensive ulcerative colitis (pancolitis, E3), left-sided (distal) UC (E2), and ulcerative proctitis (E1)",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales",3379134|1224|1236|72274|135621;3379134|1224|1236|72274,Complete,Svetlana up
bsdb:33718417/11/1,33718417,case-control,33718417,10.3389/fnut.2021.615064,NA,"Zhou Y., He Y., Liu L., Zhou W., Wang P., Hu H., Nie Y. , Chen Y.",Alterations in Gut Microbial Communities Across Anatomical Locations in Inflammatory Bowel Diseases,Frontiers in nutrition,2021,"Crohn's disease, Fusobacterium, Gardnerella, disease location, gut microbiota, ulcerative colitis",Experiment 11,China,Homo sapiens,Feces,UBERON:0001988,Crohn's colitis,EFO:0005622,Ulcerative colitis (UC),Colonic Crohn's disease (cCD),Patients with Inflammatory bowel disease (IBD) specifically Colonic Crohn's disease (cCD),20,21,1 month,16S,NA,RT-qPCR,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5B and 5D,28 October 2025,Reddicx,Reddicx,Bacterial quantification targeting Gardnerella and Bifidobacterium quantified by qPCR,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella",1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|2701,Complete,Svetlana up
bsdb:33722860/1/1,33722860,randomized controlled trial,33722860,10.1136/gutjnl-2020-323877,NA,"Asnicar F., Leeming E.R., Dimidi E., Mazidi M., Franks P.W., Al Khatib H., Valdes A.M., Davies R., Bakker E., Francis L., Chan A., Gibson R., Hadjigeorgiou G., Wolf J., Spector T.D., Segata N. , Berry S.E.",Blue poo: impact of gut transit time on the gut microbiome using a novel marker,Gut,2021,"gastrointestinal transit, intestinal bacteria",Experiment 1,"United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Increased intestinal transit time,HP:0410204,C1-Fast Gut Transit Time,C4-Slow Gut Transit Time,"This group consists of participants with the slowest gut transit time, associated with lower microbial diversity and distinct taxonomic composition.",79,174,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,increased,NA,increased,Signature 1,Fig. 3B,25 March 2025,Joiejoie,Joiejoie,Relative abundances for the four gut transit time classes in PREDICT 1,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|2005519|397864|487174;3379134|976|200643|171549|2005525|375288|823,Complete,Svetlana up
bsdb:33722860/1/2,33722860,randomized controlled trial,33722860,10.1136/gutjnl-2020-323877,NA,"Asnicar F., Leeming E.R., Dimidi E., Mazidi M., Franks P.W., Al Khatib H., Valdes A.M., Davies R., Bakker E., Francis L., Chan A., Gibson R., Hadjigeorgiou G., Wolf J., Spector T.D., Segata N. , Berry S.E.",Blue poo: impact of gut transit time on the gut microbiome using a novel marker,Gut,2021,"gastrointestinal transit, intestinal bacteria",Experiment 1,"United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Increased intestinal transit time,HP:0410204,C1-Fast Gut Transit Time,C4-Slow Gut Transit Time,"This group consists of participants with the slowest gut transit time, associated with lower microbial diversity and distinct taxonomic composition.",79,174,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,increased,NA,increased,Signature 2,Fig. 3B,26 March 2025,Joiejoie,Joiejoie,Relative abundances for the four gut transit time classes in PREDICT 1,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,1783272|1239|186801|3085636|186803|1766253|39491,Complete,Svetlana up
bsdb:33722860/2/1,33722860,randomized controlled trial,33722860,10.1136/gutjnl-2020-323877,NA,"Asnicar F., Leeming E.R., Dimidi E., Mazidi M., Franks P.W., Al Khatib H., Valdes A.M., Davies R., Bakker E., Francis L., Chan A., Gibson R., Hadjigeorgiou G., Wolf J., Spector T.D., Segata N. , Berry S.E.",Blue poo: impact of gut transit time on the gut microbiome using a novel marker,Gut,2021,"gastrointestinal transit, intestinal bacteria",Experiment 2,"United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Increased intestinal transit time,HP:0410204,C1-Fast Gut Transit Time,C2-Normal-Fast Gut Transit Time,"This group represents individuals with a gut transit time of 14–38 hours, distinguishing them as the faster segment within the normal range.",79,424,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,increased,NA,increased,Signature 1,Fig. 3B,26 March 2025,Joiejoie,Joiejoie,Relative abundances for the four gut transit time classes in PREDICT 1,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,3379134|976|200643|171549|815|816|820,Complete,NA
bsdb:33722860/3/1,33722860,randomized controlled trial,33722860,10.1136/gutjnl-2020-323877,NA,"Asnicar F., Leeming E.R., Dimidi E., Mazidi M., Franks P.W., Al Khatib H., Valdes A.M., Davies R., Bakker E., Francis L., Chan A., Gibson R., Hadjigeorgiou G., Wolf J., Spector T.D., Segata N. , Berry S.E.",Blue poo: impact of gut transit time on the gut microbiome using a novel marker,Gut,2021,"gastrointestinal transit, intestinal bacteria",Experiment 3,"United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Increased intestinal transit time,HP:0410204,C2-Normal-Fast Gut Transit Time,C4-Slow Gut Transit Time,"This group consists of participants with the slowest gut transit time, associated with lower microbial diversity and distinct taxonomic composition.",424,174,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,increased,NA,increased,Signature 1,Fig. 3B,21 March 2025,Joiejoie,Joiejoie,"The relative abundances of specific gut microbiome species across four gut transit time classes, highlighting species with significant differences and average relative abundances exceeding 1% in the PREDICT 1 study.",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|2005519|397864|487174,Complete,Svetlana up
bsdb:33722860/3/2,33722860,randomized controlled trial,33722860,10.1136/gutjnl-2020-323877,NA,"Asnicar F., Leeming E.R., Dimidi E., Mazidi M., Franks P.W., Al Khatib H., Valdes A.M., Davies R., Bakker E., Francis L., Chan A., Gibson R., Hadjigeorgiou G., Wolf J., Spector T.D., Segata N. , Berry S.E.",Blue poo: impact of gut transit time on the gut microbiome using a novel marker,Gut,2021,"gastrointestinal transit, intestinal bacteria",Experiment 3,"United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Increased intestinal transit time,HP:0410204,C2-Normal-Fast Gut Transit Time,C4-Slow Gut Transit Time,"This group consists of participants with the slowest gut transit time, associated with lower microbial diversity and distinct taxonomic composition.",424,174,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,increased,NA,increased,Signature 2,Fig. 3B,21 March 2025,Joiejoie,Joiejoie,"The relative abundances of specific gut microbiome species across four gut transit time classes, highlighting species with significant differences and average relative abundances exceeding 1% in the PREDICT 1 study.",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,1783272|1239|186801|3085636|186803|1766253|39491,Complete,Svetlana up
bsdb:33722860/4/1,33722860,randomized controlled trial,33722860,10.1136/gutjnl-2020-323877,NA,"Asnicar F., Leeming E.R., Dimidi E., Mazidi M., Franks P.W., Al Khatib H., Valdes A.M., Davies R., Bakker E., Francis L., Chan A., Gibson R., Hadjigeorgiou G., Wolf J., Spector T.D., Segata N. , Berry S.E.",Blue poo: impact of gut transit time on the gut microbiome using a novel marker,Gut,2021,"gastrointestinal transit, intestinal bacteria",Experiment 4,"United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Increased intestinal transit time,HP:0410204,C3 - Normal Gut Transit Time,C4-Slow Gut Transit Time,"This group consists of participants with the slowest gut transit time, associated with lower microbial diversity and distinct taxonomic composition.",186,174,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,increased,NA,increased,Signature 1,Fig. 3B,26 March 2025,Joiejoie,Joiejoie,Relative abundances for the four gut transit time classes in PREDICT 1,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|2005519|397864|487174;3379134|976|200643|171549|2005525|375288|823,Complete,Svetlana up
bsdb:33722860/4/2,33722860,randomized controlled trial,33722860,10.1136/gutjnl-2020-323877,NA,"Asnicar F., Leeming E.R., Dimidi E., Mazidi M., Franks P.W., Al Khatib H., Valdes A.M., Davies R., Bakker E., Francis L., Chan A., Gibson R., Hadjigeorgiou G., Wolf J., Spector T.D., Segata N. , Berry S.E.",Blue poo: impact of gut transit time on the gut microbiome using a novel marker,Gut,2021,"gastrointestinal transit, intestinal bacteria",Experiment 4,"United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Increased intestinal transit time,HP:0410204,C3 - Normal Gut Transit Time,C4-Slow Gut Transit Time,"This group consists of participants with the slowest gut transit time, associated with lower microbial diversity and distinct taxonomic composition.",186,174,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,increased,NA,increased,Signature 2,Fig. 3B,26 March 2025,Joiejoie,Joiejoie,Relative abundances for the four gut transit time classes in PREDICT 1,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,1783272|1239|186801|3085636|186803|1766253|39491,Complete,Svetlana up
bsdb:33722860/5/1,33722860,randomized controlled trial,33722860,10.1136/gutjnl-2020-323877,NA,"Asnicar F., Leeming E.R., Dimidi E., Mazidi M., Franks P.W., Al Khatib H., Valdes A.M., Davies R., Bakker E., Francis L., Chan A., Gibson R., Hadjigeorgiou G., Wolf J., Spector T.D., Segata N. , Berry S.E.",Blue poo: impact of gut transit time on the gut microbiome using a novel marker,Gut,2021,"gastrointestinal transit, intestinal bacteria",Experiment 5,"United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Increased intestinal transit time,HP:0410204,C1-Fast Gut Transit Time,C3 - Normal Gut Transit Time,"This group represents individuals with a gut transit time of 38–58 hours, distinguishing them as the slower segment within the normal range.",79,186,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,increased,NA,increased,Signature 1,Fig. 3B,26 March 2025,Joiejoie,Joiejoie,Relative abundances for the four gut transit time classes in PREDICT 1,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,3379134|976|200643|171549|815|816|820,Complete,Svetlana up
bsdb:33722860/6/1,33722860,randomized controlled trial,33722860,10.1136/gutjnl-2020-323877,NA,"Asnicar F., Leeming E.R., Dimidi E., Mazidi M., Franks P.W., Al Khatib H., Valdes A.M., Davies R., Bakker E., Francis L., Chan A., Gibson R., Hadjigeorgiou G., Wolf J., Spector T.D., Segata N. , Berry S.E.",Blue poo: impact of gut transit time on the gut microbiome using a novel marker,Gut,2021,"gastrointestinal transit, intestinal bacteria",Experiment 6,"United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Increased intestinal transit time,HP:0410204,C2-Normal-Fast Gut Transit Time,C3-Normal Gut Transit Time,"This group represents individuals with a gut transit time of 38–58 hours, distinguishing them as the slower segment within the normal range.",424,186,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,increased,NA,increased,Signature 1,Fig. 3B,26 March 2025,Joiejoie,Joiejoie,Relative abundances for the four gut transit time classes in PREDICT 1,increased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,3379134|74201|203494|48461|1647988|239934|239935,Complete,Svetlana up
bsdb:33732104/1/1,33732104,case-control,33732104,10.3389/fnins.2021.619051,NA,"Hou M., Xu G., Ran M., Luo W. , Wang H.",<i>APOE-ε4</i> Carrier Status and Gut Microbiota Dysbiosis in Patients With Alzheimer Disease,Frontiers in neuroscience,2021,"Alzheimer disease, apolipoprotein E, dysbiosis, genetic variants, gut microbiome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healthy controls,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,47,30,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,6 December 2024,AaishahM,"AaishahM,WikiWorks",Differential abundance between patients with Alzheimer disease and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella",1783272|1239|186801|186802|216572|244127;1783272|1239|186801|186802|216572;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|186801|186802|186806|264995;3379134|1224;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|1903414|581;3379134|1224|1236|91347|543|1940338;3379134|1224|1236|91347|543;28221;3379134|200940|3031449|213115;3379134|200940|3031449|213115|194924;1783272|1239|186801|3085636|186803|177971,Complete,NA
bsdb:33732104/1/2,33732104,case-control,33732104,10.3389/fnins.2021.619051,NA,"Hou M., Xu G., Ran M., Luo W. , Wang H.",<i>APOE-ε4</i> Carrier Status and Gut Microbiota Dysbiosis in Patients With Alzheimer Disease,Frontiers in neuroscience,2021,"Alzheimer disease, apolipoprotein E, dysbiosis, genetic variants, gut microbiome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healthy controls,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,47,30,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,6 December 2024,AaishahM,"AaishahM,WikiWorks",Differential abundance between patients with Alzheimer disease and healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",1783272|1239|186801|3085636|186803|207244;1783272|1239|909932|909929|1843491|158846;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350,Complete,NA
bsdb:33732655/1/1,33732655,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong C.Y.L., Vatanen T., Alexander T., Bloomfield F.H. , O'Sullivan J.M.",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 1,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,Day-10 (D10) (chronological age),4-months corrected age (4M),Faecal samples collected from moderate–late preterm (MLPT) babies enrolled in a randomized controlled trial of nutritional management at 4-months corrected age (4M).,207,118,NA,16S,34,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Text (page 5),18 March 2024,Scholastica,"Scholastica,WikiWorks",Significantly abundant taxa between the two time points; day-10 (D10) (chronological age) and at 4-months corrected age (4M).,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|909932|1843489|31977;1783272|1239|526524|526525|128827;1783272|1239|186801|3082720|186804;1783272|1239|91061|186826|33958;1783272|201174|1760|85004|31953;1783272|201174|84998|1643822|1643826;1783272|201174|84998|84999|84107;1783272|201174|1760|2037|2049;1783272|201174|84998|84999|1643824;3379134|1224|1236|91347|543;3379134|976|200643|171549|815;1783272|1239|186801|186802|216572,Complete,NA
bsdb:33732655/1/2,33732655,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong C.Y.L., Vatanen T., Alexander T., Bloomfield F.H. , O'Sullivan J.M.",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 1,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,Day-10 (D10) (chronological age),4-months corrected age (4M),Faecal samples collected from moderate–late preterm (MLPT) babies enrolled in a randomized controlled trial of nutritional management at 4-months corrected age (4M).,207,118,NA,16S,34,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Text (page 5),18 March 2024,Scholastica,"Scholastica,WikiWorks",Significantly abundant taxa between the two time points; day-10 (D10) (chronological age) and at 4-months corrected age (4M).,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",1783272|1239|91061|1385|90964;1783272|201174|1760|85007|1653;3379134|1224|1236|135625|712,Complete,NA
bsdb:33732655/2/1,33732655,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong C.Y.L., Vatanen T., Alexander T., Bloomfield F.H. , O'Sullivan J.M.",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 2,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,Higher SES (D10),Lower SES (D10),Moderate–late preterm (MLPT) babies at Day-10 (D10) whose families lived in the lower SES (socioeconomic status) areas,59,80,NA,16S,34,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Text (page 5),18 March 2024,Scholastica,"Scholastica,WikiWorks",Significantly abundant taxa in MLPT babies from lower socioeconomic status (SES) group compared to the higher SES group at D10,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,NA
bsdb:33732655/4/NA,33732655,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong C.Y.L., Vatanen T., Alexander T., Bloomfield F.H. , O'Sullivan J.M.",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 4,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,European (D10),Maori (D10),Moderate–Late Preterm (MLPT) Babies at D10 born to mothers self-reporting as Maori,77,24,NA,16S,34,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:33732655/8/NA,33732655,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong C.Y.L., Vatanen T., Alexander T., Bloomfield F.H. , O'Sullivan J.M.",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 8,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,Mix feeding (4M),Breastmilk feeding (4M),Moderate–late preterm (MLPT) babies at 4-months corrected age who were breastmilk fed,95,36,NA,16S,34,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:33732655/9/1,33732655,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong C.Y.L., Vatanen T., Alexander T., Bloomfield F.H. , O'Sullivan J.M.",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 9,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,Only formula (4M),Breastmilk feeding (4M),Moderate–late preterm (MLPT) babies at 4-months corrected age who were breastmilk fed,42,36,NA,16S,34,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Text (page 6),18 March 2024,Scholastica,"Scholastica,WikiWorks",Significantly abundant taxa in MLPT Babies at 4-months corrected age who were breastmilk fed compared to babies that were fed only formula,increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,1783272|1239|909932|1843489|31977|906,Complete,NA
bsdb:33732655/10/NA,33732655,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong C.Y.L., Vatanen T., Alexander T., Bloomfield F.H. , O'Sullivan J.M.",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 10,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,Only formula (4M),Mixed feeding (4M),Moderate–late preterm (MLPT) babies at 4-months corrected age who were mix fed,42,95,NA,16S,34,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:33732655/11/NA,33732655,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong C.Y.L., Vatanen T., Alexander T., Bloomfield F.H. , O'Sullivan J.M.",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 11,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,No maternal antibiotics,Yes maternal antibiotics,Maternal use of antibiotics within the four-week period before the D10 fecal sample collection,69,130,NA,16S,34,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:33732655/12/1,33732655,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong C.Y.L., Vatanen T., Alexander T., Bloomfield F.H. , O'Sullivan J.M.",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 12,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,No maternal probiotics,Yes maternal probiotics,Maternal use of probiotics within the four-week period before the D10 fecal sample collection,147,19,NA,16S,34,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary Table S4,31 March 2024,MyleeeA,"MyleeeA,WikiWorks","Linear modelling results showing taxa associated with different factors at day10, measured by 16S amplicon data. Only results with Q-value < 0.25 are shown.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|1578,Complete,NA
bsdb:33732655/14/1,33732655,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong C.Y.L., Vatanen T., Alexander T., Bloomfield F.H. , O'Sullivan J.M.",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 14,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,No Antibiotics,Yes Antibiotics,Infant who received antibiotic within the month immediately preceding the 4-month follow-up appointment,5,108,NA,16S,34,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S4 and Text (Page 7),31 March 2024,MyleeeA,"MyleeeA,WikiWorks","Linear modelling results showing taxa associated with factors at 4-month corrected age, measured by 16S amplicon data.",increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,1783272|1239|186801|186802|31979|1485,Complete,NA
bsdb:33732655/15/NA,33732655,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong C.Y.L., Vatanen T., Alexander T., Bloomfield F.H. , O'Sullivan J.M.",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 15,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,Only Formula (4M),Breast Milk (4M),Moderate–late preterm (MLPT) babies at 4-months corrected age who were breastmilk fed,42,36,NA,WMS,NA,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:33732655/16/1,33732655,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong C.Y.L., Vatanen T., Alexander T., Bloomfield F.H. , O'Sullivan J.M.",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 16,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,Only Formula (D10),Breast Milk (D10),Moderate–late preterm (MLPT) babies at Day 10 who were breastmilk fed,42,36,NA,16S,34,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplementary Table S4,31 March 2024,MyleeeA,"MyleeeA,WikiWorks","Linear modelling results showing taxa associated with factors at 4-month corrected age, measured by 16S amplicon data.",increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,NA
bsdb:33732655/17/1,33732655,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong C.Y.L., Vatanen T., Alexander T., Bloomfield F.H. , O'Sullivan J.M.",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 17,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,Mixed Feeding (4M),Breast Milk (4M),Moderate–late preterm (MLPT) babies at 4-months corrected age who were breastmilk fed,95,36,NA,WMS,NA,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary Table S4,31 March 2024,MyleeeA,"MyleeeA,WikiWorks","Linear modelling results showing taxa associated with factors at 4-month corrected age, measured by shotgun metagenomics data.",increased,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,3379134|200940|3031449|213115|194924|35832,Complete,NA
bsdb:33732655/18/1,33732655,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong C.Y.L., Vatanen T., Alexander T., Bloomfield F.H. , O'Sullivan J.M.",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 18,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,Mixed Feeding (D10),Only Formula (D10),Moderate–late preterm (MLPT) babies at Day 10 who were fed with only formula,95,42,NA,16S,34,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplementary Table S4,31 March 2024,MyleeeA,"MyleeeA,WikiWorks","Linear modelling results showing taxa associated with different factors at day10, measured by 16S amplicon data.",increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,NA
bsdb:33732655/19/1,33732655,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong C.Y.L., Vatanen T., Alexander T., Bloomfield F.H. , O'Sullivan J.M.",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 19,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,No Antibiotics (4M),Yes Antibiotics (4M),Maternal use of antibiotics within the one month preceding the four-month follow-up period,69,130,NA,16S,34,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary Table S4,31 March 2024,MyleeeA,"MyleeeA,WikiWorks","Linear modelling results showing taxa associated with factors at 4-month corrected age, measured by 16S amplicon data.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter",1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3082720|186804|1505657,Complete,NA
bsdb:33732655/20/NA,33732655,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong C.Y.L., Vatanen T., Alexander T., Bloomfield F.H. , O'Sullivan J.M.",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 20,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,No Infant Antibiotics (4M),Yes Infant Antibiotics (4M),Infant use of antibiotics within the one month preceding the 4-month follow-up appointment,89,4,NA,WMS,NA,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:33732655/21/1,33732655,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong C.Y.L., Vatanen T., Alexander T., Bloomfield F.H. , O'Sullivan J.M.",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 21,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,No Infant Antibiotics (D10),Yes Infant Antibiotics (D10),Infants who themselves use antibiotic during neonatal admission at D10,97,102,NA,16S,34,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S4,1 April 2024,Scholastica,"Scholastica,WikiWorks","Linear modelling results showing taxa associated with different factors at day10, measured by 16S amplicon data. Only results with Q-value < 0.25 are shown.",increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,NA
bsdb:33732655/22/1,33732655,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong C.Y.L., Vatanen T., Alexander T., Bloomfield F.H. , O'Sullivan J.M.",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 22,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,Caesarean section (D10),Vaginal delivery (D10),D10 fecal samples of MLPT babies born vaginally,136,77,NA,16S,34,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text (page 8), Supplementary Table S4",1 April 2024,Scholastica,"Scholastica,WikiWorks","Linear modelling results showing taxa associated with different factors at day10, measured by 16S amplicon data. Only results with Q-value < 0.25 are shown.",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,NA
bsdb:33732655/24/1,33732655,time series / longitudinal observational,33732655,10.3389/fcimb.2021.595323,https://pubmed.ncbi.nlm.nih.gov/33732655/,"Chong C.Y.L., Vatanen T., Alexander T., Bloomfield F.H. , O'Sullivan J.M.",Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial,Frontiers in cellular and infection microbiology,2021,"early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status",Experiment 24,New Zealand,Homo sapiens,Feces,UBERON:0001988,Spontaneous preterm birth,EFO:0006917,Singletons (4M),Twins (4M),Fecal samples of MLPT babies born as twins at 4-month corrected age,63,31,NA,WMS,NA,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text (page 8), Supplementary Table S4",1 April 2024,Scholastica,"Scholastica,WikiWorks","Linear modelling results showing taxa associated with factors at 4-month corrected age, measured by 16S amplicon data. Only results with Q-value<0.25 are shown.",increased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,1783272|201174|84998|1643822|1643826|84111|84112,Complete,NA
bsdb:33748490/1/1,33748490,case-control,33748490,10.1016/j.heliyon.2021.e06432,NA,"Gryaznova M.V., Solodskikh S.A., Panevina A.V., Syromyatnikov M.Y., Dvoretskaya Y.D., Sviridova T.N., Popov E.S. , Popov V.N.",Study of microbiome changes in patients with ulcerative colitis in the Central European part of Russia,Heliyon,2021,"Inflammatory bowel disease, Intestinal microbiota, Russian population, Sequencing, Ulcerative colitis",Experiment 1,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Healthy controls,Ulcerative colitis,Patients with ulcerative colitis,10,10,NA,PCR,NA,Ion Torrent,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2 and Figure 3,12 December 2023,Yjung24,"Yjung24,Peace Sandy,WikiWorks","Quantitative changes in the bacteria generic composition of the intestinal microbiome in patients with ulcerative colitis relative to control group.

Changes in species composition of intestinal microbiome in patients with ulcerative colitis relative to control group (∗Pvalue≤0.05, ∗∗Pvalue≤0.01, ∗∗∗Pvalue≤0.001).",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|g__Negativibacillus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",1783272|1239|186801|3085636|186803|830;3379134|1224|1236|91347|543|158483;1783272|1239|186801|186802|216572|216851;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|877420;1783272|1239|1980693;1783272|201174|84998|84999|1643824|133925;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|815|909656|310298;1783272|1239|909932|1843488|909930|33024|626940;1783272|1239|909932|1843489|31977|39948|487173;3379134|1224|28216|80840|995019|40544|40545;1783272|1239|186801|186802|216572|216851|853,Complete,Peace Sandy
bsdb:33748490/1/2,33748490,case-control,33748490,10.1016/j.heliyon.2021.e06432,NA,"Gryaznova M.V., Solodskikh S.A., Panevina A.V., Syromyatnikov M.Y., Dvoretskaya Y.D., Sviridova T.N., Popov E.S. , Popov V.N.",Study of microbiome changes in patients with ulcerative colitis in the Central European part of Russia,Heliyon,2021,"Inflammatory bowel disease, Intestinal microbiota, Russian population, Sequencing, Ulcerative colitis",Experiment 1,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Healthy controls,Ulcerative colitis,Patients with ulcerative colitis,10,10,NA,PCR,NA,Ion Torrent,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2 and Figure 3,12 December 2023,Yjung24,"Yjung24,Peace Sandy,WikiWorks","Quantitative changes in the bacteria generic composition of the intestinal microbiome in patients with ulcerative colitis relative to control group.

Changes in species composition of intestinal microbiome in patients with ulcerative colitis relative to control group (∗Pvalue≤0.05, ∗∗Pvalue≤0.01, ∗∗∗Pvalue≤0.001).",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Falsochrobactrum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans",3379134|1224|28211|204458|76892|41275;3379134|976|200643|171549|1853231|574697;3379134|976|200643|171549|2005519|1348911;1783272|201174|1760|85009|31957|1912216;1783272|1239|186801|3085636|186803|1432051;3379134|1224|28211|356|118882|1649292;1783272|1239|186801|3085636|186803|1407607;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|33958|1243;3379134|1224|1236|91347|1903411|629;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|1407607|1150298,Complete,Peace Sandy
bsdb:33754037/1/1,33754037,case-control,33754037,10.7150/thno.55209,NA,"Zhong M., Xiong Y., Zhao J., Gao Z., Ma J., Wu Z., Song Y. , Hong X.",<i>Candida albicans</i> disorder is associated with gastric carcinogenesis,Theranostics,2021,"Candida albicans, Gastric cancer, biomarker, fungal imbalance, mycobiome",Experiment 1,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,Control (contain adjacent noncancerous tissues and healthy samples),Gastric cancer patients,Patients with gastric cancer,45,45,NA,ITS / ITS2,NA,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,"Figure 2C, 2D, 2E, 3A, Table S3, Table S4, Table S5",11 November 2025,Blegodwin,"Blegodwin,Temmie",Taxa found to be significantly more abundant in Gastric Cancer (GC) lesions (Group 1) compared to adjacent noncancerous tissues (Group 0) using a Welch's t-test.,increased,"k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Pleosporaceae|g__Alternaria,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Fungi|p__Ascomycota|c__Dothideomycetes,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusicolla|s__Fusicolla acetilerea,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Pleosporaceae,k__Fungi|p__Ascomycota|c__Saccharomycetes,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida",4751|4890|147541|92860|28556|5598;4751|4890|3239874|2916678|766764|5475|5476;4751|4890|147541;4751|4890|147550|5125|110618|5506;4751|4890|147550|5125|110618|1053100|1053101;4751|4890|147550|5125|110618;4751|4890|147541|92860|28556;4751|4890|4891;4751|4890|3239874|2916678|766764|5475,Complete,NA
bsdb:33754037/1/2,33754037,case-control,33754037,10.7150/thno.55209,NA,"Zhong M., Xiong Y., Zhao J., Gao Z., Ma J., Wu Z., Song Y. , Hong X.",<i>Candida albicans</i> disorder is associated with gastric carcinogenesis,Theranostics,2021,"Candida albicans, Gastric cancer, biomarker, fungal imbalance, mycobiome",Experiment 1,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,Control (contain adjacent noncancerous tissues and healthy samples),Gastric cancer patients,Patients with gastric cancer,45,45,NA,ITS / ITS2,NA,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 2,"Figure 2C, 2D, 2E, 3A, Table S3, Table S4, Table S5",11 November 2025,Blegodwin,"Blegodwin,Temmie",Taxa found to be significantly less abundant (depleted) in Gastric Cancer (GC) lesions (Group 1) compared to adjacent noncancerous tissues (Group 0) using a Welch's t-test.,decreased,"k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Acrocalymmaceae|g__Acrocalymma,k__Fungi|p__Basidiomycota|c__Agaricomycetes,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Chaetomiaceae,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|f__Chrysozymaceae,k__Fungi|p__Ascomycota|c__Eurotiomycetes,k__Fungi|p__Basidiomycota|c__Microbotryomycetes,k__Fungi|p__Mucoromycota|c__Mortierellomycetes|o__Mortierellales|f__Mortierellaceae|g__Mortierella,k__Fungi|p__Mucoromycota|c__Mortierellomycetes,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Amphisphaeriales|f__Sporocadaceae|g__Pestalotiopsis,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Phaffomycetales|f__Phaffomycetaceae,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Thelebolales|f__Pseudeurotiaceae,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Thelebolales|f__Thelebolaceae|g__Pseudogymnoascus,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Amphisphaeriales|f__Sporocadaceae,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Trichomonascaceae|g__Starmerella,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Thelephorales|f__Thelephoraceae,k__Fungi|p__Basidiomycota|c__Tremellomycetes,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae|g__Trichosporon",4751|4890|147541|92860|1589760|1319578;4751|5204|155619;4751|4890|147545|5042|1131492;4751|4890|147545|5042|1131492|5052;4751|4890|147550|5139|35718;4751|5204|162481|1799785;4751|4890|147545;4751|5204|162481;4751|1913637|2212732|214503|4854|4855;4751|1913637|2212732;4751|4890|147550|3402561|1812776|37840;4751|4890|4891|3243778|115784;4751|4890|147548|292491|34379;4751|4890|147548|292491|46451|78156;4751|4890|147550|3402561|1812776;4751|4890|3239873|3243772|410830|75735;4751|5204|155619|56487|56488;4751|5204|155616;4751|5204|155616|1851469|1759442|5552,Complete,NA
bsdb:33754037/2/1,33754037,case-control,33754037,10.7150/thno.55209,NA,"Zhong M., Xiong Y., Zhao J., Gao Z., Ma J., Wu Z., Song Y. , Hong X.",<i>Candida albicans</i> disorder is associated with gastric carcinogenesis,Theranostics,2021,"Candida albicans, Gastric cancer, biomarker, fungal imbalance, mycobiome",Experiment 2,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,Control (contain adjacent noncancerous tissues and healthy samples),Gastric cancer patients,Patients with gastric cancer,45,45,NA,ITS / ITS2,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 3B and Table S6,11 November 2025,Blegodwin,"Blegodwin,Temmie",Taxa found to be significantly more abundant in Gastric Cancer (GC) lesions (Group 1) compared to adjacent noncancerous tissues (Group 0) using a Wilcoxon rank sum test.,increased,"k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus terreus,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans",4751|4890|147545|5042|1131492|5052|33178;4751|4890|3239874|2916678|766764|5475|5476,Complete,NA
bsdb:33754037/2/2,33754037,case-control,33754037,10.7150/thno.55209,NA,"Zhong M., Xiong Y., Zhao J., Gao Z., Ma J., Wu Z., Song Y. , Hong X.",<i>Candida albicans</i> disorder is associated with gastric carcinogenesis,Theranostics,2021,"Candida albicans, Gastric cancer, biomarker, fungal imbalance, mycobiome",Experiment 2,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,Control (contain adjacent noncancerous tissues and healthy samples),Gastric cancer patients,Patients with gastric cancer,45,45,NA,ITS / ITS2,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 3B and Table S6,12 November 2025,Blegodwin,"Blegodwin,Temmie",Taxa found to be significantly less abundant (depleted) in Gastric Cancer (GC) lesions (Group 1) compared to adjacent noncancerous tissues (Group 0) using a Wilcoxon rank sum test.,decreased,"k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus montevidensis,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus sydowii,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida tropicalis,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Nakaseomyces|s__Nakaseomyces glabratus,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Pichiales|f__Pichiaceae|g__Pichia|s__Pichia kudriavzevii,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Naviculisporaceae|g__Pseudorhypophila|s__Pseudorhypophila marina,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Trimorphomycetaceae|g__Saitozyma|s__Saitozyma podzolica",4751|4890|147545|5042|1131492|5052|1173306;4751|4890|147545|5042|1131492|5052|75750;4751|4890|3239874|2916678|766764|5475|5482;4751|5204|1538075|162474|742845|55193|76775;4751|4890|4891|4892|4893|374468|5478;4751|4890|3239874|3243775|1156497|4919|4909;4751|4890|147550|5139|2905925|3385929|573856;4751|5204|155616|5234|1890237|1890244|1890683,Complete,NA
bsdb:33754037/3/1,33754037,case-control,33754037,10.7150/thno.55209,NA,"Zhong M., Xiong Y., Zhao J., Gao Z., Ma J., Wu Z., Song Y. , Hong X.",<i>Candida albicans</i> disorder is associated with gastric carcinogenesis,Theranostics,2021,"Candida albicans, Gastric cancer, biomarker, fungal imbalance, mycobiome",Experiment 3,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,Control (contain adjacent noncancerous tissues and healthy samples),Gastric cancer patients,Patients with gastric cancer,55,45,NA,ITS / ITS2,NA,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure S2C and Figure S2D,7 January 2026,Temmie,Temmie,Indicator species analysis at the genus level,increased,"k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Pleosporaceae|g__Alternaria,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusicolla|s__Fusicolla acetilerea",4751|4890|3239874|2916678|766764|5475;4751|4890|147541|92860|28556|5598;4751|4890|3239874|2916678|766764|5475|5476;4751|4890|147550|5125|110618|1053100|1053101,Complete,NA
bsdb:33754037/3/2,33754037,case-control,33754037,10.7150/thno.55209,NA,"Zhong M., Xiong Y., Zhao J., Gao Z., Ma J., Wu Z., Song Y. , Hong X.",<i>Candida albicans</i> disorder is associated with gastric carcinogenesis,Theranostics,2021,"Candida albicans, Gastric cancer, biomarker, fungal imbalance, mycobiome",Experiment 3,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,Control (contain adjacent noncancerous tissues and healthy samples),Gastric cancer patients,Patients with gastric cancer,55,45,NA,ITS / ITS2,NA,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 2,Figure S2C and Figure S2D,7 January 2026,Temmie,Temmie,Indicator species analysis at the genus level,decreased,"k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Trichocomaceae|g__Thermomyces,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Trimorphomycetaceae|g__Saitozyma,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus montevidensis,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Trimorphomycetaceae|g__Saitozyma|s__Saitozyma podzolica",4751|4890|147545|5042|28568|5540;4751|5204|155616|5234|1890237|1890244;4751|4890|147545|5042|1131492|5052|1173306;4751|5204|155616|5234|1890237|1890244|1890683,Complete,NA
bsdb:33754037/4/1,33754037,case-control,33754037,10.7150/thno.55209,NA,"Zhong M., Xiong Y., Zhao J., Gao Z., Ma J., Wu Z., Song Y. , Hong X.",<i>Candida albicans</i> disorder is associated with gastric carcinogenesis,Theranostics,2021,"Candida albicans, Gastric cancer, biomarker, fungal imbalance, mycobiome",Experiment 4,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,Control (contain adjacent noncancerous tissues and healthy samples),Gastric cancer patients,Patients with gastric cancer,55,45,NA,ITS / ITS2,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure S2E,7 January 2026,Temmie,Temmie,Wilcoxon rank sum test at the species level,increased,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,4751|4890|3239874|2916678|766764|5475|5476,Complete,NA
bsdb:33754037/4/2,33754037,case-control,33754037,10.7150/thno.55209,NA,"Zhong M., Xiong Y., Zhao J., Gao Z., Ma J., Wu Z., Song Y. , Hong X.",<i>Candida albicans</i> disorder is associated with gastric carcinogenesis,Theranostics,2021,"Candida albicans, Gastric cancer, biomarker, fungal imbalance, mycobiome",Experiment 4,China,Homo sapiens,Stomach,UBERON:0000945,Gastric cancer,MONDO:0001056,Control (contain adjacent noncancerous tissues and healthy samples),Gastric cancer patients,Patients with gastric cancer,55,45,NA,ITS / ITS2,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 2,Figure S2E,7 January 2026,Temmie,Temmie,Wilcoxon rank sum test at the species level,decreased,"k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus montevidensis,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Trimorphomycetaceae|g__Saitozyma|s__Saitozyma podzolica,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Eremothecium|s__Eremothecium coryli,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus sydowii",4751|4890|147545|5042|1131492|5052|1173306;4751|5204|155616|5234|1890237|1890244|1890683;4751|4890|4891|4892|4893|33170|33173;4751|4890|147545|5042|1131492|5052|75750,Complete,NA
bsdb:33773586/1/1,33773586,"cross-sectional observational, not case-control",33773586,10.1186/s13048-021-00799-9,NA,"He F. , Li Y.",The gut microbial composition in polycystic ovary syndrome with insulin resistance: findings from a normal-weight population,Journal of ovarian research,2021,"Enterococcus, Gut microbiota, Insulin resistance, Polycystic ovary syndrome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,A combination of women with Polycystic Ovary Syndrome with insulin resistant(PCOS-IR) and PCOS with no insulin resistance (PCOS-NIR),Healthy control,Healthy control refers to women without polycystic ovary syndrome (PCOS),26,10,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 5,20 October 2024,Princess Ben,"Princess Ben,WikiWorks",Differential abundance in women without PCOS (HC) compared to women with PCOS-IR and PCOS-NIR.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:33773586/1/2,33773586,"cross-sectional observational, not case-control",33773586,10.1186/s13048-021-00799-9,NA,"He F. , Li Y.",The gut microbial composition in polycystic ovary syndrome with insulin resistance: findings from a normal-weight population,Journal of ovarian research,2021,"Enterococcus, Gut microbiota, Insulin resistance, Polycystic ovary syndrome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,A combination of women with Polycystic Ovary Syndrome with insulin resistant(PCOS-IR) and PCOS with no insulin resistance (PCOS-NIR),Healthy control,Healthy control refers to women without polycystic ovary syndrome (PCOS),26,10,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"In text of the ""Gut microbiota composition among PCOS patients"" section",20 December 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in women without PCOS (HC) compared to women with PCOS-IR and PCOS-NIR.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,1783272|1239|91061|186826|81852|1350,Complete,Svetlana up
bsdb:33773586/2/1,33773586,"cross-sectional observational, not case-control",33773586,10.1186/s13048-021-00799-9,NA,"He F. , Li Y.",The gut microbial composition in polycystic ovary syndrome with insulin resistance: findings from a normal-weight population,Journal of ovarian research,2021,"Enterococcus, Gut microbiota, Insulin resistance, Polycystic ovary syndrome",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,A combination of healthy control (HC) and PCOS with no insulin resistance (PCOS-NIR) women,PCOS-IR,Women Polycystic ovary syndrome with insulin resistance (PCOS-IR).,22,14,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Figure 5, In text of the ""Gut microbiota composition among PCOS patients"" section",21 October 2024,Princess Ben,"Princess Ben,KateRasheed,WikiWorks",Differential abundance in PCOS-IR compared to PCOS-NIR and healthy control (HC) women.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",1783272|201174|1760|2037;1783272|201174|1760|85006|1268|32207;1783272|1239|186801|3082720|186804;1783272|1239|91061|186826|81852;1783272|201174|1760|85006|1268;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|28050;1783272|1239|91061|186826|81852|1350,Complete,Svetlana up
bsdb:33773586/2/2,33773586,"cross-sectional observational, not case-control",33773586,10.1186/s13048-021-00799-9,NA,"He F. , Li Y.",The gut microbial composition in polycystic ovary syndrome with insulin resistance: findings from a normal-weight population,Journal of ovarian research,2021,"Enterococcus, Gut microbiota, Insulin resistance, Polycystic ovary syndrome",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,A combination of healthy control (HC) and PCOS with no insulin resistance (PCOS-NIR) women,PCOS-IR,Women Polycystic ovary syndrome with insulin resistance (PCOS-IR).,22,14,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"In text of the ""Gut microbiota composition among PCOS patients"" section",20 December 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in PCOS-IR compared to PCOS-NIR and healthy control (HC) women.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:33773586/3/1,33773586,"cross-sectional observational, not case-control",33773586,10.1186/s13048-021-00799-9,NA,"He F. , Li Y.",The gut microbial composition in polycystic ovary syndrome with insulin resistance: findings from a normal-weight population,Journal of ovarian research,2021,"Enterococcus, Gut microbiota, Insulin resistance, Polycystic ovary syndrome",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,A combination of PCOS insulin resistant (PCOS-IR) and healthy control (HC) women.,PCOS-NIR,Polycystic ovary syndrome with no insulin resistance.,24,12,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Figure 5, In text of the ""Gut microbiota composition among PCOS patients"" section",21 October 2024,Princess Ben,"Princess Ben,KateRasheed,WikiWorks",Differential abundance in PCOS-NIR compared to PCOS-IR and healthy control (HC) women.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;3379134|74201|203494|48461|1647988|239934,Complete,Svetlana up
bsdb:33789672/1/1,33789672,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A., Yang Y., Qin S., Lv S., Jin T., Li K., Han Z. , Li Y.",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 1,China,Capra hircus,Jejunum,UBERON:0002115,Age,EFO:0000246,B-Group (B15.2),B-Group (B25.2),This group consists of young black goats in the control group (B-Group) whose intestines (Jejunum) were obtained on the 25th day of the experiment.,3,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 6a,21 May 2024,Victoria,"Victoria,Ifeanyisam,WikiWorks",The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.,increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia|o__Acidimicrobiales,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae,k__Bacillati|p__Chloroflexota|c__Anaerolineae,k__Bacillati|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales,k__Bacillati|p__Actinomycetota|c__Thermoleophilia|o__Gaiellales,k__Pseudomonadati|p__Gemmatimonadota|c__Gemmatimonadia|o__Gemmatimonadales|f__Gemmatimonadaceae,k__Pseudomonadati|p__Gemmatimonadota|c__Gemmatimonadia|o__Gemmatimonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Methylophilaceae,k__Pseudomonadati|p__Myxococcota|c__Myxococcia|o__Myxococcales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Nitrosomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales,k__Pseudomonadati|p__Nitrospirota|c__Nitrospiria|o__Nitrospirales|f__Nitrospiraceae|g__Nitrospira,k__Pseudomonadati|p__Nitrospirota|c__Nitrospiria|o__Nitrospirales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Bacillati|p__Actinomycetota|c__Thermoleophilia",1783272|201174|84992|84993;1783272|201174|84992;1783272|200795|292625|292629|292628;1783272|200795|292625;1783272|200795|292625|292629;3379134|1224|28216|80840|119060;3379134|1224|28211|204458|76892;3379134|1224|28211|204458;3379134|976|1853228|1853229|563835;3379134|976|768503|768507|89373;3379134|976|768503|768507;1783272|201174|1497346|1154584;3379134|142182|219685|219686|219687;3379134|142182|219685|219686;3379134|1224|28211|356|45401;3379134|1224|28211|356;3379134|1224|28216|32003|32011;3379134|2818505|32015|29;3379134|1224|28211|356|41294;3379134|1224|28216|32003|206379;3379134|1224|28216|32003;3379134|40117|203693|189778|189779|1234;3379134|40117|203693|189778;3379134|1224|28211|356|69277;3379134|1224|1236|72274|135621;3379134|1224|28211|356|82115;3379134|1224|28211|204441|41295;3379134|1224|28211|204441;3379134|976|117747|200666|84566;1783272|201174|1497346,Complete,Svetlana up
bsdb:33789672/1/2,33789672,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A., Yang Y., Qin S., Lv S., Jin T., Li K., Han Z. , Li Y.",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 1,China,Capra hircus,Jejunum,UBERON:0002115,Age,EFO:0000246,B-Group (B15.2),B-Group (B25.2),This group consists of young black goats in the control group (B-Group) whose intestines (Jejunum) were obtained on the 25th day of the experiment.,3,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 6a,22 May 2024,Victoria,"Victoria,WikiWorks",The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes",3379134|976|200643|171549|171552;3379134|976|200643|171549;3379134|976|200643|171549;3379134|976|200643;1783272|1239|186801|3085636|186803;1783272|1239|909932|1843489|31977;1783272|1239|909932|909929;1783272|1239|909932,Complete,Svetlana up
bsdb:33789672/2/1,33789672,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A., Yang Y., Qin S., Lv S., Jin T., Li K., Han Z. , Li Y.",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 2,China,Capra hircus,Jejunum,UBERON:0002115,Age,EFO:0000246,B-Group (B15.2)),B-Group (B45.2),This group consists of young black goats in the control group (B-Group) whose intestines (Jejunum) were obtained on the 45th day of the experiment.,3,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 6b,22 May 2024,Victoria,"Victoria,WikiWorks",The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.,increased,"k__Bacillati|p__Actinomycetota|c__Thermoleophilia|o__Gaiellales,k__Bacillati|p__Actinomycetota|c__Thermoleophilia,k__Bacillati|p__Cyanobacteriota",1783272|201174|1497346|1154584;1783272|201174|1497346;1783272|1117,Complete,Svetlana up
bsdb:33789672/2/2,33789672,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A., Yang Y., Qin S., Lv S., Jin T., Li K., Han Z. , Li Y.",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 2,China,Capra hircus,Jejunum,UBERON:0002115,Age,EFO:0000246,B-Group (B15.2)),B-Group (B45.2),This group consists of young black goats in the control group (B-Group) whose intestines (Jejunum) were obtained on the 45th day of the experiment.,3,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 6b,22 May 2024,Victoria,"Victoria,WikiWorks",The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli,c__Deltaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|s__unidentified spirochaete",1783272|1239|91061;28221;3379134|1224|1236|135619|28256;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;3379134|1224|1236|135619;3379134|1224|1236|135622|267890;3379134|203691|203692|136|137;3379134|203691|203692|136;1783272|1239|909932|1843489|31977;3379134|203691|203692|136|137|47717,Complete,Svetlana up
bsdb:33789672/3/1,33789672,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A., Yang Y., Qin S., Lv S., Jin T., Li K., Han Z. , Li Y.",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 3,China,Capra hircus,Jejunum,UBERON:0002115,Age,EFO:0000246,B-Group (B15.2),B-Group (B75.2),This group consists of young black goats in the control group (B-Group) whose intestines (Jejunum) were obtained on the 75th day of the experiment.,3,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 6c,24 May 2024,Victoria,"Victoria,WikiWorks",The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacillati|p__Mycoplasmatota|c__Mollicutes",1783272|1239|909932|1843488|909930;3379134|1224|28211|204457|41297;3379134|1224|1236|135624|83763;3379134|1224|1236|135624;3379134|1224|1236|91347|543;3379134|1224|1236|91347;1783272|544448|31969,Complete,Svetlana up
bsdb:33789672/3/2,33789672,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A., Yang Y., Qin S., Lv S., Jin T., Li K., Han Z. , Li Y.",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 3,China,Capra hircus,Jejunum,UBERON:0002115,Age,EFO:0000246,B-Group (B15.2),B-Group (B75.2),This group consists of young black goats in the control group (B-Group) whose intestines (Jejunum) were obtained on the 75th day of the experiment.,3,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 6c,24 May 2024,Victoria,"Victoria,WikiWorks",The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,1783272|1239|91061|1385|186818,Complete,Svetlana up
bsdb:33789672/4/1,33789672,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A., Yang Y., Qin S., Lv S., Jin T., Li K., Han Z. , Li Y.",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 4,China,Capra hircus,Caecum,UBERON:0001153,Age,EFO:0000246,B-Group (B15.4),B-Group (B25.4),This group consists of young black goats in the control group (B-Group) whose intestines (Cecum) were obtained on the 25th day of the experiment.,3,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 6d,24 May 2024,Victoria,"Victoria,WikiWorks",The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.,increased,"k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales",3379134|256845|1313211;3379134|203691|203692|136|137;3379134|203691|203692|136;3379134|256845|1313211|278082|255528;3379134|256845|1313211|278082,Complete,Svetlana up
bsdb:33789672/4/2,33789672,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A., Yang Y., Qin S., Lv S., Jin T., Li K., Han Z. , Li Y.",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 4,China,Capra hircus,Caecum,UBERON:0001153,Age,EFO:0000246,B-Group (B15.4),B-Group (B25.4),This group consists of young black goats in the control group (B-Group) whose intestines (Cecum) were obtained on the 25th day of the experiment.,3,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 6d,24 May 2024,Victoria,"Victoria,WikiWorks",The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:33789672/5/1,33789672,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A., Yang Y., Qin S., Lv S., Jin T., Li K., Han Z. , Li Y.",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 5,China,Capra hircus,Caecum,UBERON:0001153,Age,EFO:0000246,B-Group (B15.4),B-Group (B45.4),This group consists of young black goats in the control group (B-Group) whose intestines (Cecum) were obtained on the 45th day of the experiment.,3,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 6e,27 May 2024,Victoria,"Victoria,WikiWorks",The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacillati|p__Mycoplasmatota|c__Mollicutes",1783272|1239|186801|3085636|186803;1783272|1239|909932|1843488|909930;3379134|1224|28216|80840|506;3379134|1224|28216|80840;3379134|1224|1236|135624|83763;3379134|1224|1236|135624;1783272|544448|31969,Complete,Svetlana up
bsdb:33789672/5/2,33789672,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A., Yang Y., Qin S., Lv S., Jin T., Li K., Han Z. , Li Y.",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 5,China,Capra hircus,Caecum,UBERON:0001153,Age,EFO:0000246,B-Group (B15.4),B-Group (B45.4),This group consists of young black goats in the control group (B-Group) whose intestines (Cecum) were obtained on the 45th day of the experiment.,3,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 6e,27 May 2024,Victoria,"Victoria,WikiWorks",The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.,decreased,"k__Bacillati|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae,k__Bacillati|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales,k__Bacillati|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae|g__Anaerolinea,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales",1783272|200795|292625|292629|292628;1783272|200795|292625|292629;1783272|200795|292625|292629|292628|233189;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|1300;1783272|1239|91061|186826;1783272|1239|91061;1783272|1239|186801|3082720|186804;3379134|1224|28216|206351|481;3379134|1224|28216|206351,Complete,Svetlana up
bsdb:33789672/6/1,33789672,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A., Yang Y., Qin S., Lv S., Jin T., Li K., Han Z. , Li Y.",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 6,China,Capra hircus,Caecum,UBERON:0001153,Age,EFO:0000246,B-Group (B15.4),B-Group (B75.4),This group consists of young black goats in the control group (B-Group) whose intestines (Cecum) were obtained on the 75th day of the experiment.,3,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 6f,27 May 2024,Victoria,"Victoria,WikiWorks",The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae,k__Pseudomonadati|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae",1783272|1239|909932|1843488|909930;3379134|1224|1236|135624;3379134|204428|204429|51291|809;3379134|204428|204429|51291;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;3379134|1224|1236|135619|28256;1783272|1239|186801|3085636|186803;3379134|1224|1236|135619;3379134|203691|203692|136|137;3379134|203691|203692|136;3379134|1224|1236|135624|83763,Complete,Svetlana up
bsdb:33789672/6/2,33789672,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A., Yang Y., Qin S., Lv S., Jin T., Li K., Han Z. , Li Y.",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 6,China,Capra hircus,Caecum,UBERON:0001153,Age,EFO:0000246,B-Group (B15.4),B-Group (B75.4),This group consists of young black goats in the control group (B-Group) whose intestines (Cecum) were obtained on the 75th day of the experiment.,3,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 6f,27 May 2024,Victoria,"Victoria,WikiWorks",The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales",3379134|1224|28216|206351|481;3379134|1224|28216|206351;3379134|1224|1236|135625|712;3379134|1224|1236|135625,Complete,Svetlana up
bsdb:33789672/8/NA,33789672,laboratory experiment,33789672,10.1186/s12934-021-01568-5,NA,"Li A., Yang Y., Qin S., Lv S., Jin T., Li K., Han Z. , Li Y.",Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age,Microbial cell factories,2021,"Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats",Experiment 8,China,Capra hircus,Jejunum,UBERON:0002115,Diet,EFO:0002755,B-Group (B25.2),R-Group (R25.2),This group consists of young black goats in the milk replacer group (R Group) whose intestines (Jejunum) were obtained on the 25th day of the experiment. This group was provided with milk replacer after weaning on the 10th day of the experiment.,3,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:33789966/1/1,33789966,"cross-sectional observational, not case-control",33789966,10.1136/gutjnl-2020-323826,NA,"Ren Z., Wang H., Cui G., Lu H., Wang L., Luo H., Chen X., Ren H., Sun R., Liu W., Liu X., Liu C., Li A., Wang X., Rao B., Yuan C., Zhang H., Sun J., Chen X., Li B., Hu C., Wu Z., Yu Z., Kan Q. , Li L.",Alterations in the human oral and gut microbiomes and lipidomics in COVID-19,Gut,2021,"COVID-19, intestinal microbiology, lipid metabolism",Experiment 1,China,Homo sapiens,Tongue,UBERON:0001723,COVID-19,MONDO:0100096,Healthy controls,Confirmed COVID-19 patients,"Suspected COVID-19 cases with one of the following etiological or serological evidence:
(1) Fluorescence RT-PCR detects the positive of the COVID-19 virus nucleic acid.
(2) Viral gene sequencing finds highly homologous to COVID-19 virus",100,48,2 months,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Supplementary Figures 1E and 1G,21 June 2021,Claregrieve1,"Claregrieve1,Fatima,WikiWorks",Differential microbial abundance in tongue-coating samples from healthy controls compared with confirmed COVID-19 patients,decreased,"k__Pseudomonadati|p__Bacteroidota,p__Candidatus Altimarinota,p__Candidatus Saccharimonadota|s__Candidatus Saccharibacteria genomosp. TM7-H1,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Mycoplasmatota,p__Candidatus Absconditibacteriota|s__candidate division SR1 bacterium,p__Candidatus Saccharimonadota|s__candidate division TM7 genomosp. GTL1",3379134|976;363464;95818|2080739;95818|2093818|2093825|2171986|1331051;3379134|1224|1236|135615|868|2717;1783272|1239|186801|3085636|186803|43996;1783272|201174|1760|85007|1653|1716;1783272|1239|186801|3082720|543314;1783272|1239|186801|3082720|3118655|44259;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135625|712|724;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|3085636|186803|265975;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836;3379134|1224;1783272|1239|526524|526525|128827|123375;1783272|1239|91061|186826|1300|1301;1783272|544448;221235|2044938;95818|443342,Complete,Claregrieve1
bsdb:33789966/1/2,33789966,"cross-sectional observational, not case-control",33789966,10.1136/gutjnl-2020-323826,NA,"Ren Z., Wang H., Cui G., Lu H., Wang L., Luo H., Chen X., Ren H., Sun R., Liu W., Liu X., Liu C., Li A., Wang X., Rao B., Yuan C., Zhang H., Sun J., Chen X., Li B., Hu C., Wu Z., Yu Z., Kan Q. , Li L.",Alterations in the human oral and gut microbiomes and lipidomics in COVID-19,Gut,2021,"COVID-19, intestinal microbiology, lipid metabolism",Experiment 1,China,Homo sapiens,Tongue,UBERON:0001723,COVID-19,MONDO:0100096,Healthy controls,Confirmed COVID-19 patients,"Suspected COVID-19 cases with one of the following etiological or serological evidence:
(1) Fluorescence RT-PCR detects the positive of the COVID-19 virus nucleic acid.
(2) Viral gene sequencing finds highly homologous to COVID-19 virus",100,48,2 months,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Supplementary Figures 1E and 1G,21 June 2021,Claregrieve1,"Claregrieve1,Fatima,WikiWorks",Differential microbial abundance in tongue-coating samples from healthy controls compared with confirmed COVID-19 patients,increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",3379134|29547|3031852|213849|72294|194;1783272|1117;1783272|1239|91061|186826|186828|117563;3384189|32066|203490|203491|1129771|32067;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|186802|216572|1263|41978;1783272|1239|909932|909929|1843491|970;3379134|203691|203692|136|137|146;3379134|976|200643|171549|2005525|195950,Complete,Claregrieve1
bsdb:33789966/2/1,33789966,"cross-sectional observational, not case-control",33789966,10.1136/gutjnl-2020-323826,NA,"Ren Z., Wang H., Cui G., Lu H., Wang L., Luo H., Chen X., Ren H., Sun R., Liu W., Liu X., Liu C., Li A., Wang X., Rao B., Yuan C., Zhang H., Sun J., Chen X., Li B., Hu C., Wu Z., Yu Z., Kan Q. , Li L.",Alterations in the human oral and gut microbiomes and lipidomics in COVID-19,Gut,2021,"COVID-19, intestinal microbiology, lipid metabolism",Experiment 2,China,Homo sapiens,Tongue,UBERON:0001723,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 patients,Confirmed COVID-19 patients who recovered,150,22,2 months,16S,345,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 4c,25 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance in oral microbiome samples between recovered COVID-19 cases and healthy controls,decreased,"p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",95818|2093818|2093825|2171986|1331051;1783272|1239|186801|3082720|543314;3379134|1224|1236|135625|712|724;1783272|1239|1737404|1737405|1570339|543311;3379134|976|200643|171549|171551|836,Complete,Claregrieve1
bsdb:33789966/2/2,33789966,"cross-sectional observational, not case-control",33789966,10.1136/gutjnl-2020-323826,NA,"Ren Z., Wang H., Cui G., Lu H., Wang L., Luo H., Chen X., Ren H., Sun R., Liu W., Liu X., Liu C., Li A., Wang X., Rao B., Yuan C., Zhang H., Sun J., Chen X., Li B., Hu C., Wu Z., Yu Z., Kan Q. , Li L.",Alterations in the human oral and gut microbiomes and lipidomics in COVID-19,Gut,2021,"COVID-19, intestinal microbiology, lipid metabolism",Experiment 2,China,Homo sapiens,Tongue,UBERON:0001723,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 patients,Confirmed COVID-19 patients who recovered,150,22,2 months,16S,345,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 4c,25 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance in oral microbiome samples between recovered COVID-19 cases and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",1783272|1239|909932|909929|1843491|82202;3384189|32066|203490|203491|1129771|32067;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|909929|1843491|970,Complete,Claregrieve1
bsdb:33789966/3/1,33789966,"cross-sectional observational, not case-control",33789966,10.1136/gutjnl-2020-323826,NA,"Ren Z., Wang H., Cui G., Lu H., Wang L., Luo H., Chen X., Ren H., Sun R., Liu W., Liu X., Liu C., Li A., Wang X., Rao B., Yuan C., Zhang H., Sun J., Chen X., Li B., Hu C., Wu Z., Yu Z., Kan Q. , Li L.",Alterations in the human oral and gut microbiomes and lipidomics in COVID-19,Gut,2021,"COVID-19, intestinal microbiology, lipid metabolism",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,"Suspected COVID-19 cases with one of the following etiological or serological evidence:
(1) Fluorescence RT-PCR detects the positive of the COVID-19 virus nucleic acid.
(2) Viral gene sequencing finds highly homologous to COVID-19 virus",48,24,2 months,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,"Figure 5c, S3E, S3G -Supp 05",25 June 2021,Claregrieve1,"Claregrieve1,Lwaldron,WikiWorks",Differential microbial abundance between samples from healthy controls and samples from COVID-19 patients,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,s__bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|33042;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|216851;3379134|1224|1236|135625|712|724;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|186802|1392389;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|28050;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|3085636|186803|46205;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;3379134|1224|28211|204457|41297|13687;3379134|1224|28216|80840|995019|40544;1783272|1239|526524|526525|2810281|191303;1869227;1783272|1239|186801|186802|216572|707003,Complete,Claregrieve1
bsdb:33789966/3/2,33789966,"cross-sectional observational, not case-control",33789966,10.1136/gutjnl-2020-323826,NA,"Ren Z., Wang H., Cui G., Lu H., Wang L., Luo H., Chen X., Ren H., Sun R., Liu W., Liu X., Liu C., Li A., Wang X., Rao B., Yuan C., Zhang H., Sun J., Chen X., Li B., Hu C., Wu Z., Yu Z., Kan Q. , Li L.",Alterations in the human oral and gut microbiomes and lipidomics in COVID-19,Gut,2021,"COVID-19, intestinal microbiology, lipid metabolism",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,"Suspected COVID-19 cases with one of the following etiological or serological evidence:
(1) Fluorescence RT-PCR detects the positive of the COVID-19 virus nucleic acid.
(2) Viral gene sequencing finds highly homologous to COVID-19 virus",48,24,2 months,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Figure 5c,25 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between samples from healthy controls and samples from COVID-19 patients,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Pelagibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella",3379134|74201|203494|48461|1647988|239934;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|1300|1301;1783272|201174|1760|85006|1268|32207;3379134|1224|1236|135619|28256|2745;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|265975;1783272|1239|909932|1843489|31977|29465;1783272|1239|526524|526525|128827|123375;1783272|201174|84998|84999|1643824|1380;1783272|1239|186801|186802|216572|946234;3379134|1224|28211|356|2831106|1082930;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563,Complete,Claregrieve1
bsdb:33804656/1/1,33804656,laboratory experiment,33804656,10.3390/microorganisms9030647,NA,"Laubitz D., Typpo K., Midura-Kiela M., Brown C., Barberán A., Ghishan F.K. , Kiela P.R.",Dynamics of Gut Microbiota Recovery after Antibiotic Exposure in Young and Old Mice (A Pilot Study),Microorganisms,2021,"16S, aging, antibiotics, bacteria, ciprofloxacin, metronidazole",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,7 week old (young) mice before antibiotic treatment,7 week old (young) mice 10 days after antibiotic treatments,7-week old mice (young mice) administered treated with broad-spectrum antibiotics metronidazole (500 mg/L) and ciprofloxacin (200 mg/L) for 10 days.,5,5,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 5,27 September 2021,Gina,"Gina,WikiWorks",Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between young mice after 10 days of antibiotic treatment,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",1783272|1239|91061|186826|81852;1783272|1239|91061|186826;1783272|1239|91061|186826|81852|1350,Complete,Claregrieve1
bsdb:33804656/1/2,33804656,laboratory experiment,33804656,10.3390/microorganisms9030647,NA,"Laubitz D., Typpo K., Midura-Kiela M., Brown C., Barberán A., Ghishan F.K. , Kiela P.R.",Dynamics of Gut Microbiota Recovery after Antibiotic Exposure in Young and Old Mice (A Pilot Study),Microorganisms,2021,"16S, aging, antibiotics, bacteria, ciprofloxacin, metronidazole",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,7 week old (young) mice before antibiotic treatment,7 week old (young) mice 10 days after antibiotic treatments,7-week old mice (young mice) administered treated with broad-spectrum antibiotics metronidazole (500 mg/L) and ciprofloxacin (200 mg/L) for 10 days.,5,5,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,NA,Signature 2,Figure 5,28 September 2021,Gina,"Gina,WikiWorks",Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between young after 10 days of Abx treatment,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__Eubacteriales Family XIII. Incertae Sedis bacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium",1783272|1239|526524|526525|128827|1470349;1783272|1239|186801|3082720|543314|2137877;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524|526525|128827|1729679;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|1898207,Complete,Claregrieve1
bsdb:33804656/2/1,33804656,laboratory experiment,33804656,10.3390/microorganisms9030647,NA,"Laubitz D., Typpo K., Midura-Kiela M., Brown C., Barberán A., Ghishan F.K. , Kiela P.R.",Dynamics of Gut Microbiota Recovery after Antibiotic Exposure in Young and Old Mice (A Pilot Study),Microorganisms,2021,"16S, aging, antibiotics, bacteria, ciprofloxacin, metronidazole",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,7 week old (young) mice before antibiotic treatment,7 week old (young) mice 6 months after antibiotic treatments,7-week old mice (young mice) administered treated with broad-spectrum antibiotics metronidazole (500 mg/L) and ciprofloxacin (200 mg/L) for 10 days.,5,5,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 5,29 September 2021,Gina,"Gina,WikiWorks",Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between young after 6 months of recovery,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella",1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3082720|186804;1783272|1239|526524|526525|128827|1937008,Complete,Claregrieve1
bsdb:33804656/2/2,33804656,laboratory experiment,33804656,10.3390/microorganisms9030647,NA,"Laubitz D., Typpo K., Midura-Kiela M., Brown C., Barberán A., Ghishan F.K. , Kiela P.R.",Dynamics of Gut Microbiota Recovery after Antibiotic Exposure in Young and Old Mice (A Pilot Study),Microorganisms,2021,"16S, aging, antibiotics, bacteria, ciprofloxacin, metronidazole",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,7 week old (young) mice before antibiotic treatment,7 week old (young) mice 6 months after antibiotic treatments,7-week old mice (young mice) administered treated with broad-spectrum antibiotics metronidazole (500 mg/L) and ciprofloxacin (200 mg/L) for 10 days.,5,5,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,NA,Signature 2,Figure 5,29 September 2021,Gina,"Gina,WikiWorks",Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between young after 6 months of recovery (lower panels),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__Eubacteriales Family XIII. Incertae Sedis bacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus",1783272|1239|186801|3082720|543314|2137877;1783272|1239|526524|526525|128827|1470349,Complete,Claregrieve1
bsdb:33804656/3/1,33804656,laboratory experiment,33804656,10.3390/microorganisms9030647,NA,"Laubitz D., Typpo K., Midura-Kiela M., Brown C., Barberán A., Ghishan F.K. , Kiela P.R.",Dynamics of Gut Microbiota Recovery after Antibiotic Exposure in Young and Old Mice (A Pilot Study),Microorganisms,2021,"16S, aging, antibiotics, bacteria, ciprofloxacin, metronidazole",Experiment 3,United States of America,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,40 week old (old) mice before antibiotic treatment,40 week old (old) mice 10 days after antibiotic treatments,40-week old mice (old) administered treated with broad-spectrum antibiotics metronidazole (500 mg/L) and ciprofloxacin (200 mg/L) for 10 days.,5,5,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,sex,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 5,29 September 2021,Gina,"Gina,WikiWorks",Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between older mice (right panels) after 10 days of Abx treatment,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,3379134|976|200643|171549,Complete,Claregrieve1
bsdb:33804656/3/2,33804656,laboratory experiment,33804656,10.3390/microorganisms9030647,NA,"Laubitz D., Typpo K., Midura-Kiela M., Brown C., Barberán A., Ghishan F.K. , Kiela P.R.",Dynamics of Gut Microbiota Recovery after Antibiotic Exposure in Young and Old Mice (A Pilot Study),Microorganisms,2021,"16S, aging, antibiotics, bacteria, ciprofloxacin, metronidazole",Experiment 3,United States of America,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,40 week old (old) mice before antibiotic treatment,40 week old (old) mice 10 days after antibiotic treatments,40-week old mice (old) administered treated with broad-spectrum antibiotics metronidazole (500 mg/L) and ciprofloxacin (200 mg/L) for 10 days.,5,5,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,sex,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 5,29 September 2021,Gina,"Gina,WikiWorks",Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between older mice (right panels) after 10 days of Abx treatment.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales",1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3082720|186804;1783272|1239|526524|526525|128827|1729679;1783272|1239|526524|526525|128827;1783272|1239|526524|526525,Complete,Claregrieve1
bsdb:33804656/4/1,33804656,laboratory experiment,33804656,10.3390/microorganisms9030647,NA,"Laubitz D., Typpo K., Midura-Kiela M., Brown C., Barberán A., Ghishan F.K. , Kiela P.R.",Dynamics of Gut Microbiota Recovery after Antibiotic Exposure in Young and Old Mice (A Pilot Study),Microorganisms,2021,"16S, aging, antibiotics, bacteria, ciprofloxacin, metronidazole",Experiment 4,United States of America,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,40 week old (old) mice before antibiotic treatment,40 week old (old) mice 6 months after antibiotic treatments,40-week old mice (old) administered treated with broad-spectrum antibiotics metronidazole (500 mg/L) and ciprofloxacin (200 mg/L) for 10 days.,5,5,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,sex,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 5,29 September 2021,Gina,"Gina,WikiWorks",Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between older mice (right panels) after 6 months of recovery (lower panels).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium",3379134|976|200643|171549;1783272|1239|526524|526525|128827|1729679;3379134|976|200643|171549|2005473;3379134|976|200643|171549|2005473|1918540;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|1898207,Complete,Claregrieve1
bsdb:33804656/4/2,33804656,laboratory experiment,33804656,10.3390/microorganisms9030647,NA,"Laubitz D., Typpo K., Midura-Kiela M., Brown C., Barberán A., Ghishan F.K. , Kiela P.R.",Dynamics of Gut Microbiota Recovery after Antibiotic Exposure in Young and Old Mice (A Pilot Study),Microorganisms,2021,"16S, aging, antibiotics, bacteria, ciprofloxacin, metronidazole",Experiment 4,United States of America,Mus musculus,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,40 week old (old) mice before antibiotic treatment,40 week old (old) mice 6 months after antibiotic treatments,40-week old mice (old) administered treated with broad-spectrum antibiotics metronidazole (500 mg/L) and ciprofloxacin (200 mg/L) for 10 days.,5,5,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,sex,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 5,29 September 2021,Gina,"Gina,WikiWorks",Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between older mice after 6 months of recovery,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales",1783272|1239|526524|526525|128827|1937008;1783272|1239|526524|526525|128827;1783272|1239|526524|526525,Complete,Claregrieve1
bsdb:33805810/1/1,33805810,case-control,33805810,10.3390/biology10030219,NA,"Kim J.R., Han K., Han Y., Kang N., Shin T.S., Park H.J., Kim H., Kwon W., Lee S., Kim Y.K., Park T. , Jang J.Y.",Microbiome Markers of Pancreatic Cancer Based on Bacteria-Derived Extracellular Vesicles Acquired from Blood Samples: A Retrospective Propensity Score Matching Analysis,Biology,2021,"early diagnosis, microbial extracellular vesicles, microbiome markers, pancreatic cancer, propensity score matching",Experiment 1,China,Homo sapiens,Blood serum,UBERON:0001977,Pancreatic carcinoma,EFO:0002618,Healthy controls,Pancreatic cancer patients,Patients that have pancreatic cancer,52,38,NA,16S,34,Illumina,centered log-ratio,Permutation Test,0.05,FALSE,NA,"age,sex","age,sex",NA,increased,NA,NA,NA,NA,Signature 1,Table 2,20 October 2025,Temmie,Temmie,Significant biomarkers at the phylum and genus level using the CLR (Centred log ratio) Permutation test.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Deferribacterota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Verrucomicrobiota",3379134|74201|203494|48461|1647988|239934;3379134|200930;1783272|1239|186801|186802|216572|1508657;1783272|1239|526524|526525|2810281|191303;3379134|74201,Complete,Svetlana up
bsdb:33805810/1/2,33805810,case-control,33805810,10.3390/biology10030219,NA,"Kim J.R., Han K., Han Y., Kang N., Shin T.S., Park H.J., Kim H., Kwon W., Lee S., Kim Y.K., Park T. , Jang J.Y.",Microbiome Markers of Pancreatic Cancer Based on Bacteria-Derived Extracellular Vesicles Acquired from Blood Samples: A Retrospective Propensity Score Matching Analysis,Biology,2021,"early diagnosis, microbial extracellular vesicles, microbiome markers, pancreatic cancer, propensity score matching",Experiment 1,China,Homo sapiens,Blood serum,UBERON:0001977,Pancreatic carcinoma,EFO:0002618,Healthy controls,Pancreatic cancer patients,Patients that have pancreatic cancer,52,38,NA,16S,34,Illumina,centered log-ratio,Permutation Test,0.05,FALSE,NA,"age,sex","age,sex",NA,increased,NA,NA,NA,NA,Signature 2,Table 2,20 October 2025,Temmie,Temmie,Significant biomarkers at the phylum and genus level using the CLR (Centred log ratio) Permutation test.,decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium",1783272|201174;3379134|1224|1236|135614|32033|40323;3379134|1224|28211|204457|41297|13687;1783272|201174|1760|85009|31957|1743,Complete,Svetlana up
bsdb:33805810/2/1,33805810,case-control,33805810,10.3390/biology10030219,NA,"Kim J.R., Han K., Han Y., Kang N., Shin T.S., Park H.J., Kim H., Kwon W., Lee S., Kim Y.K., Park T. , Jang J.Y.",Microbiome Markers of Pancreatic Cancer Based on Bacteria-Derived Extracellular Vesicles Acquired from Blood Samples: A Retrospective Propensity Score Matching Analysis,Biology,2021,"early diagnosis, microbial extracellular vesicles, microbiome markers, pancreatic cancer, propensity score matching",Experiment 2,China,Homo sapiens,Blood serum,UBERON:0001977,Pancreatic carcinoma,EFO:0002618,Healthy controls,Pancreatic cancer patients,Patients that have pancreatic cancer,52,38,NA,16S,34,Illumina,raw counts,ANCOM,0.05,FALSE,NA,"age,sex","age,sex",NA,increased,NA,NA,NA,NA,Signature 1,Table 2,21 October 2025,Temmie,Temmie,Significant biomarkers at the phylum and genus level using the ANCOM statistical method,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Deferribacterota,k__Pseudomonadati|p__Verrucomicrobiota",3379134|74201|203494|48461|1647988|239934;3379134|976;3379134|200930;3379134|74201,Complete,Svetlana up
bsdb:33805810/2/2,33805810,case-control,33805810,10.3390/biology10030219,NA,"Kim J.R., Han K., Han Y., Kang N., Shin T.S., Park H.J., Kim H., Kwon W., Lee S., Kim Y.K., Park T. , Jang J.Y.",Microbiome Markers of Pancreatic Cancer Based on Bacteria-Derived Extracellular Vesicles Acquired from Blood Samples: A Retrospective Propensity Score Matching Analysis,Biology,2021,"early diagnosis, microbial extracellular vesicles, microbiome markers, pancreatic cancer, propensity score matching",Experiment 2,China,Homo sapiens,Blood serum,UBERON:0001977,Pancreatic carcinoma,EFO:0002618,Healthy controls,Pancreatic cancer patients,Patients that have pancreatic cancer,52,38,NA,16S,34,Illumina,raw counts,ANCOM,0.05,FALSE,NA,"age,sex","age,sex",NA,increased,NA,NA,NA,NA,Signature 2,Table 2,22 December 2025,Temmie,Temmie,Significant biomarkers at the phylum and genus level using the ANCOM statistical method,decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium",1783272|201174;3379134|1224|1236|135614|32033|40323;3379134|1224|28211|204457|41297|13687;1783272|201174|1760|85009|31957|1743,Complete,NA
bsdb:33805810/3/1,33805810,case-control,33805810,10.3390/biology10030219,NA,"Kim J.R., Han K., Han Y., Kang N., Shin T.S., Park H.J., Kim H., Kwon W., Lee S., Kim Y.K., Park T. , Jang J.Y.",Microbiome Markers of Pancreatic Cancer Based on Bacteria-Derived Extracellular Vesicles Acquired from Blood Samples: A Retrospective Propensity Score Matching Analysis,Biology,2021,"early diagnosis, microbial extracellular vesicles, microbiome markers, pancreatic cancer, propensity score matching",Experiment 3,China,Homo sapiens,Blood serum,UBERON:0001977,Pancreatic carcinoma,EFO:0002618,Healthy controls,Pancreatic cancer patients,Patients that have pancreatic cancer,52,38,NA,16S,34,Illumina,raw counts,DESeq2,0.05,FALSE,NA,"age,sex","age,sex",NA,increased,NA,NA,NA,NA,Signature 1,Table 2,31 October 2025,Temmie,Temmie,Significant biomarkers at the phylum and genus level using the DESeq2 likelihood ratio test (LRT) statistical method,increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Deferribacterota,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",3379134|976;3379134|200930;3379134|74201;3379134|74201|203494|48461|1647988|239934;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|216572|1508657,Complete,Svetlana up
bsdb:33805810/3/2,33805810,case-control,33805810,10.3390/biology10030219,NA,"Kim J.R., Han K., Han Y., Kang N., Shin T.S., Park H.J., Kim H., Kwon W., Lee S., Kim Y.K., Park T. , Jang J.Y.",Microbiome Markers of Pancreatic Cancer Based on Bacteria-Derived Extracellular Vesicles Acquired from Blood Samples: A Retrospective Propensity Score Matching Analysis,Biology,2021,"early diagnosis, microbial extracellular vesicles, microbiome markers, pancreatic cancer, propensity score matching",Experiment 3,China,Homo sapiens,Blood serum,UBERON:0001977,Pancreatic carcinoma,EFO:0002618,Healthy controls,Pancreatic cancer patients,Patients that have pancreatic cancer,52,38,NA,16S,34,Illumina,raw counts,DESeq2,0.05,FALSE,NA,"age,sex","age,sex",NA,increased,NA,NA,NA,NA,Signature 2,Table 2,31 October 2025,Temmie,Temmie,Significant biomarkers at the phylum and genus level using the DESeq2 likelihood ratio test (LRT) statistical method,decreased,"k__Pseudomonadati|p__Acidobacteriota,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Armatimonadota,p__Candidatus Absconditibacteriota,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Planctomycetota,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Spirochaetota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium",3379134|57723;1783272|201174;1783272|67819;221235;1783272|1117;3379134|203682;3379134|1224;3379134|203691;3379134|1224|1236|135614|32033|40323;3379134|1224|28211|204457|41297|13687;1783272|201174|1760|85009|31957|1743,Complete,Svetlana up
bsdb:33805810/4/1,33805810,case-control,33805810,10.3390/biology10030219,NA,"Kim J.R., Han K., Han Y., Kang N., Shin T.S., Park H.J., Kim H., Kwon W., Lee S., Kim Y.K., Park T. , Jang J.Y.",Microbiome Markers of Pancreatic Cancer Based on Bacteria-Derived Extracellular Vesicles Acquired from Blood Samples: A Retrospective Propensity Score Matching Analysis,Biology,2021,"early diagnosis, microbial extracellular vesicles, microbiome markers, pancreatic cancer, propensity score matching",Experiment 4,China,Homo sapiens,Blood serum,UBERON:0001977,Pancreatic carcinoma,EFO:0002618,Healthy controls,Pancreatic cancer patients,Patients that have pancreatic cancer,52,38,NA,16S,34,Illumina,raw counts,"Wald Test,DESeq2",0.05,FALSE,NA,"age,sex","age,sex",NA,increased,NA,NA,NA,NA,Signature 1,Table 2,31 October 2025,Temmie,Temmie,Significant biomarkers at the Phylum and genus level using the DESeq2 Wald statistical method,increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Deferribacterota,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",3379134|976;3379134|200930;3379134|74201;3379134|74201|203494|48461|1647988|239934;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|216572|1508657,Complete,Svetlana up
bsdb:33805810/4/2,33805810,case-control,33805810,10.3390/biology10030219,NA,"Kim J.R., Han K., Han Y., Kang N., Shin T.S., Park H.J., Kim H., Kwon W., Lee S., Kim Y.K., Park T. , Jang J.Y.",Microbiome Markers of Pancreatic Cancer Based on Bacteria-Derived Extracellular Vesicles Acquired from Blood Samples: A Retrospective Propensity Score Matching Analysis,Biology,2021,"early diagnosis, microbial extracellular vesicles, microbiome markers, pancreatic cancer, propensity score matching",Experiment 4,China,Homo sapiens,Blood serum,UBERON:0001977,Pancreatic carcinoma,EFO:0002618,Healthy controls,Pancreatic cancer patients,Patients that have pancreatic cancer,52,38,NA,16S,34,Illumina,raw counts,"Wald Test,DESeq2",0.05,FALSE,NA,"age,sex","age,sex",NA,increased,NA,NA,NA,NA,Signature 2,Table 2,31 October 2025,Temmie,Temmie,Significant biomarkers at the Phylum and genus level using DESeq Wald statistical method,decreased,"k__Pseudomonadati|p__Acidobacteriota,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Armatimonadota,p__Candidatus Absconditibacteriota,k__Bacillati|p__Chloroflexota,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Planctomycetota,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Spirochaetota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium",3379134|57723;1783272|201174;1783272|67819;221235;1783272|200795;1783272|1117;3379134|203682;3379134|1224;3379134|203691;3379134|1224|1236|135614|32033|40323;3379134|1224|28211|204457|41297|13687;1783272|201174|1760|85009|31957|1743,Complete,Svetlana up
bsdb:33805810/5/1,33805810,case-control,33805810,10.3390/biology10030219,NA,"Kim J.R., Han K., Han Y., Kang N., Shin T.S., Park H.J., Kim H., Kwon W., Lee S., Kim Y.K., Park T. , Jang J.Y.",Microbiome Markers of Pancreatic Cancer Based on Bacteria-Derived Extracellular Vesicles Acquired from Blood Samples: A Retrospective Propensity Score Matching Analysis,Biology,2021,"early diagnosis, microbial extracellular vesicles, microbiome markers, pancreatic cancer, propensity score matching",Experiment 5,China,Homo sapiens,Blood serum,UBERON:0001977,Pancreatic carcinoma,EFO:0002618,Healthy controls,Pancreatic cancer patients,Patients that have pancreatic cancer,52,38,NA,16S,34,Illumina,raw counts,edgeR,0.05,FALSE,NA,"age,sex","age,sex",NA,increased,NA,NA,NA,NA,Signature 1,Table 2,1 November 2025,Temmie,Temmie,Significant biomarkers at the Phylum level using the edgeR statistical method,increased,k__Pseudomonadati|p__Verrucomicrobiota,3379134|74201,Complete,Svetlana up
bsdb:33805810/6/1,33805810,case-control,33805810,10.3390/biology10030219,NA,"Kim J.R., Han K., Han Y., Kang N., Shin T.S., Park H.J., Kim H., Kwon W., Lee S., Kim Y.K., Park T. , Jang J.Y.",Microbiome Markers of Pancreatic Cancer Based on Bacteria-Derived Extracellular Vesicles Acquired from Blood Samples: A Retrospective Propensity Score Matching Analysis,Biology,2021,"early diagnosis, microbial extracellular vesicles, microbiome markers, pancreatic cancer, propensity score matching",Experiment 6,China,Homo sapiens,Blood serum,UBERON:0001977,Pancreatic carcinoma,EFO:0002618,Healthy controls,Pancreatic cancer patients,Patients that have pancreatic cancer,52,38,NA,16S,34,Illumina,raw counts,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex","age,sex",NA,increased,NA,NA,NA,NA,Signature 1,Table 2,1 November 2025,Temmie,Temmie,Significant biomarkers at the Phylum and genus level using the Wilcoxon statistical method,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Deferribacterota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",3379134|74201|203494|48461|1647988|239934;3379134|976;3379134|200930;1783272|1239|526524|526525|2810281|191303;3379134|74201;1783272|1239|186801|186802|216572|1508657,Complete,Svetlana up
bsdb:33805810/6/2,33805810,case-control,33805810,10.3390/biology10030219,NA,"Kim J.R., Han K., Han Y., Kang N., Shin T.S., Park H.J., Kim H., Kwon W., Lee S., Kim Y.K., Park T. , Jang J.Y.",Microbiome Markers of Pancreatic Cancer Based on Bacteria-Derived Extracellular Vesicles Acquired from Blood Samples: A Retrospective Propensity Score Matching Analysis,Biology,2021,"early diagnosis, microbial extracellular vesicles, microbiome markers, pancreatic cancer, propensity score matching",Experiment 6,China,Homo sapiens,Blood serum,UBERON:0001977,Pancreatic carcinoma,EFO:0002618,Healthy controls,Pancreatic cancer patients,Patients that have pancreatic cancer,52,38,NA,16S,34,Illumina,raw counts,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex","age,sex",NA,increased,NA,NA,NA,NA,Signature 2,Table 2,1 November 2025,Temmie,Temmie,Significant biomarkers at the Phylum and genus level using the Wilcoxon statistical method,decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium",1783272|201174;3379134|1224|1236|135614|32033|40323;3379134|1224|28211|204457|41297|13687;1783272|201174|1760|85009|31957|1743,Complete,Svetlana up
bsdb:33805810/7/1,33805810,case-control,33805810,10.3390/biology10030219,NA,"Kim J.R., Han K., Han Y., Kang N., Shin T.S., Park H.J., Kim H., Kwon W., Lee S., Kim Y.K., Park T. , Jang J.Y.",Microbiome Markers of Pancreatic Cancer Based on Bacteria-Derived Extracellular Vesicles Acquired from Blood Samples: A Retrospective Propensity Score Matching Analysis,Biology,2021,"early diagnosis, microbial extracellular vesicles, microbiome markers, pancreatic cancer, propensity score matching",Experiment 7,China,Homo sapiens,Blood serum,UBERON:0001977,Pancreatic carcinoma,EFO:0002618,Healthy controls,Pancreatic cancer patients,Patients that have pancreatic cancer,52,38,NA,16S,34,Illumina,raw counts,Zero-Inflated Beta Regression,0.05,FALSE,NA,"age,sex","age,sex",NA,increased,NA,NA,NA,NA,Signature 1,Table 2,1 November 2025,Temmie,Temmie,Significant biomarkers at the Phylum and genus level using the ZIBSeq statistical method,increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",3379134|976;3379134|74201;3379134|74201|203494|48461|1647988|239934,Complete,Svetlana up
bsdb:33805810/7/2,33805810,case-control,33805810,10.3390/biology10030219,NA,"Kim J.R., Han K., Han Y., Kang N., Shin T.S., Park H.J., Kim H., Kwon W., Lee S., Kim Y.K., Park T. , Jang J.Y.",Microbiome Markers of Pancreatic Cancer Based on Bacteria-Derived Extracellular Vesicles Acquired from Blood Samples: A Retrospective Propensity Score Matching Analysis,Biology,2021,"early diagnosis, microbial extracellular vesicles, microbiome markers, pancreatic cancer, propensity score matching",Experiment 7,China,Homo sapiens,Blood serum,UBERON:0001977,Pancreatic carcinoma,EFO:0002618,Healthy controls,Pancreatic cancer patients,Patients that have pancreatic cancer,52,38,NA,16S,34,Illumina,raw counts,Zero-Inflated Beta Regression,0.05,FALSE,NA,"age,sex","age,sex",NA,increased,NA,NA,NA,NA,Signature 2,Table 2,1 November 2025,Temmie,Temmie,Significant biomarkers at the Phylum and genus level using the ZIBSeq statistical method,decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium",1783272|201174;3379134|1224;3379134|1224|1236|135614|32033|40323;3379134|1224|28211|204457|41297|13687;1783272|201174|1760|85009|31957|1743,Complete,Svetlana up
bsdb:33805810/8/1,33805810,case-control,33805810,10.3390/biology10030219,NA,"Kim J.R., Han K., Han Y., Kang N., Shin T.S., Park H.J., Kim H., Kwon W., Lee S., Kim Y.K., Park T. , Jang J.Y.",Microbiome Markers of Pancreatic Cancer Based on Bacteria-Derived Extracellular Vesicles Acquired from Blood Samples: A Retrospective Propensity Score Matching Analysis,Biology,2021,"early diagnosis, microbial extracellular vesicles, microbiome markers, pancreatic cancer, propensity score matching",Experiment 8,China,Homo sapiens,Blood serum,UBERON:0001977,Pancreatic carcinoma,EFO:0002618,Healthy controls,Pancreatic cancer patients,Patients that have pancreatic cancer,52,38,NA,16S,34,Illumina,raw counts,metagenomeSeq,0.05,FALSE,NA,"age,sex","age,sex",NA,increased,NA,NA,NA,NA,Signature 1,Table 2,1 November 2025,Temmie,Temmie,Significant biomarkers at the Phylum and genus level using the ZIG Gaussian statistical method,increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Deferribacterota,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",3379134|976;3379134|200930;3379134|74201;3379134|74201|203494|48461|1647988|239934;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|216572|1508657,Complete,Svetlana up
bsdb:33805810/8/2,33805810,case-control,33805810,10.3390/biology10030219,NA,"Kim J.R., Han K., Han Y., Kang N., Shin T.S., Park H.J., Kim H., Kwon W., Lee S., Kim Y.K., Park T. , Jang J.Y.",Microbiome Markers of Pancreatic Cancer Based on Bacteria-Derived Extracellular Vesicles Acquired from Blood Samples: A Retrospective Propensity Score Matching Analysis,Biology,2021,"early diagnosis, microbial extracellular vesicles, microbiome markers, pancreatic cancer, propensity score matching",Experiment 8,China,Homo sapiens,Blood serum,UBERON:0001977,Pancreatic carcinoma,EFO:0002618,Healthy controls,Pancreatic cancer patients,Patients that have pancreatic cancer,52,38,NA,16S,34,Illumina,raw counts,metagenomeSeq,0.05,FALSE,NA,"age,sex","age,sex",NA,increased,NA,NA,NA,NA,Signature 2,Table 2,1 November 2025,Temmie,"Temmie,Anne-mariesharp",Significant biomarkers at the Phylum and genus levels using the ZIG Gaussian statistical method,decreased,"k__Pseudomonadati|p__Acidobacteriota,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Armatimonadota,k__Bacillati|p__Chloroflexota,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Planctomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Spirochaetota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,p__Candidatus Absconditibacteriota",3379134|57723;1783272|201174;1783272|67819;1783272|200795;1783272|1117;3379134|203682;1783272|201174|1760|85009|31957|1743;3379134|1224|28211|204457|41297|13687;3379134|203691;3379134|1224|1236|135614|32033|40323;221235,Complete,Svetlana up
bsdb:33805810/9/1,33805810,case-control,33805810,10.3390/biology10030219,NA,"Kim J.R., Han K., Han Y., Kang N., Shin T.S., Park H.J., Kim H., Kwon W., Lee S., Kim Y.K., Park T. , Jang J.Y.",Microbiome Markers of Pancreatic Cancer Based on Bacteria-Derived Extracellular Vesicles Acquired from Blood Samples: A Retrospective Propensity Score Matching Analysis,Biology,2021,"early diagnosis, microbial extracellular vesicles, microbiome markers, pancreatic cancer, propensity score matching",Experiment 9,China,Homo sapiens,Blood serum,UBERON:0001977,Pancreatic carcinoma,EFO:0002618,Healthy controls,Pancreatic cancer patients,Patients that have pancreatic cancer,52,38,NA,16S,34,Illumina,raw counts,metagenomeSeq,0.05,FALSE,NA,"age,sex","age,sex",NA,increased,NA,NA,NA,NA,Signature 1,Table 2,1 November 2025,Temmie,Temmie,Significant biomarkers at the Phylum and genus levels using ZIG log normal,increased,"k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",3379134|200930|68337;3379134|74201;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|216572|1508657,Complete,Svetlana up
bsdb:33805810/9/2,33805810,case-control,33805810,10.3390/biology10030219,NA,"Kim J.R., Han K., Han Y., Kang N., Shin T.S., Park H.J., Kim H., Kwon W., Lee S., Kim Y.K., Park T. , Jang J.Y.",Microbiome Markers of Pancreatic Cancer Based on Bacteria-Derived Extracellular Vesicles Acquired from Blood Samples: A Retrospective Propensity Score Matching Analysis,Biology,2021,"early diagnosis, microbial extracellular vesicles, microbiome markers, pancreatic cancer, propensity score matching",Experiment 9,China,Homo sapiens,Blood serum,UBERON:0001977,Pancreatic carcinoma,EFO:0002618,Healthy controls,Pancreatic cancer patients,Patients that have pancreatic cancer,52,38,NA,16S,34,Illumina,raw counts,metagenomeSeq,0.05,FALSE,NA,"age,sex","age,sex",NA,increased,NA,NA,NA,NA,Signature 2,Table 2,23 December 2025,Temmie,Temmie,Significant Biomarkers at the phylum and genus levels using the ZIG Log-normal statistical method,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",1783272|201174|1760|85009|31957|1743;3379134|1224|28211|204457|41297|13687;3379134|1224|1236|135614|32033|40323,Complete,NA
bsdb:33806027/1/1,33806027,"cross-sectional observational, not case-control",33806027,10.3390/nu13041066,https://pubmed.ncbi.nlm.nih.gov/33806027/,"Salamon D., Sroka-Oleksiak A., Gurgul A., Arent Z., Szopa M., Bulanda M., Małecki M.T. , Gosiewski T.",Analysis of the Gut Mycobiome in Adult Patients with Type 1 and Type 2 Diabetes Using Next-Generation Sequencing (NGS) with Increased Sensitivity-Pilot Study,Nutrients,2021,"diabetes, gut mycobiome, next-generation sequencing (NGS)",Experiment 1,Poland,Homo sapiens,Feces,UBERON:0001988,Type I diabetes mellitus,MONDO:0005147,Healthy controls,Individuals diagnosed with Type 1 Diabetes Mellitus,"Individuals diagnosed with Type 1 Diabetes Mellitus in 2012–2015 at the Department of Metabolic Diseases, University Hospital, Krakow, Poland",26,24,1 month,16S,NA,Illumina,relative abundances,PERMANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 4,20 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1,WikiWorks",Differential abundance of fungal genus in individuals diagnosed with Type 1 Diabetes compared to healthy controls,decreased,"k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Bulleribasidiaceae|g__Dioszegia,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces",4751|5204|155616|5234|1884640|165440;4751|4890|4891|4892|4893|4930,Complete,Claregrieve1
bsdb:33806027/1/2,33806027,"cross-sectional observational, not case-control",33806027,10.3390/nu13041066,https://pubmed.ncbi.nlm.nih.gov/33806027/,"Salamon D., Sroka-Oleksiak A., Gurgul A., Arent Z., Szopa M., Bulanda M., Małecki M.T. , Gosiewski T.",Analysis of the Gut Mycobiome in Adult Patients with Type 1 and Type 2 Diabetes Using Next-Generation Sequencing (NGS) with Increased Sensitivity-Pilot Study,Nutrients,2021,"diabetes, gut mycobiome, next-generation sequencing (NGS)",Experiment 1,Poland,Homo sapiens,Feces,UBERON:0001988,Type I diabetes mellitus,MONDO:0005147,Healthy controls,Individuals diagnosed with Type 1 Diabetes Mellitus,"Individuals diagnosed with Type 1 Diabetes Mellitus in 2012–2015 at the Department of Metabolic Diseases, University Hospital, Krakow, Poland",26,24,1 month,16S,NA,Illumina,relative abundances,PERMANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 4,20 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1,WikiWorks",Differential abundance of fungal genus in individuals diagnosed with Type 1 Diabetes compared to healthy controls,increased,"k__Fungi|p__Mucoromycota|c__Mortierellomycetes|o__Mortierellales|f__Mortierellaceae|g__Mortierella,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Udeniomyces,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Hymenochaetales|f__Schizoporaceae|g__Xylodon",4751|1913637|2212732|214503|4854|4855;4751|5204|155616|90883|1851551|42658;4751|5204|155619|139380|574935|1124675,Complete,Claregrieve1
bsdb:33806027/2/1,33806027,"cross-sectional observational, not case-control",33806027,10.3390/nu13041066,https://pubmed.ncbi.nlm.nih.gov/33806027/,"Salamon D., Sroka-Oleksiak A., Gurgul A., Arent Z., Szopa M., Bulanda M., Małecki M.T. , Gosiewski T.",Analysis of the Gut Mycobiome in Adult Patients with Type 1 and Type 2 Diabetes Using Next-Generation Sequencing (NGS) with Increased Sensitivity-Pilot Study,Nutrients,2021,"diabetes, gut mycobiome, next-generation sequencing (NGS)",Experiment 2,Poland,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,"Individuals diagnosed with Type 1 Diabetes Mellitus in 2012–2015 at the Department of Metabolic Diseases, University Hospital, Krakow, Poland",26,26,1 month,16S,NA,Illumina,relative abundances,PERMANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 4,20 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1,WikiWorks",Differential abundance of the fungal genus in individuals diagnosed with Type 2 Diabetes compared to the healthy controls,decreased,"k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Bulleraceae|g__Bullera,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Polyporales|f__Polyporaceae|g__Ganoderma,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Filobasidiales|f__Filobasidiaceae|g__Naganishia,k__Fungi|p__Ascomycota|g__Saitoella,k__Fungi|p__Basidiomycota|c__Wallemiomycetes|o__Wallemiales|f__Wallemiaceae|g__Wallemia",4751|5204|155616|5234|1905116|4970;4751|5204|155619|5303|5317|5314;4751|5204|155616|90886|5408|1851509;4751|4890|5605;4751|5204|431957|431958|431959|148959,Complete,Claregrieve1
bsdb:33806027/2/2,33806027,"cross-sectional observational, not case-control",33806027,10.3390/nu13041066,https://pubmed.ncbi.nlm.nih.gov/33806027/,"Salamon D., Sroka-Oleksiak A., Gurgul A., Arent Z., Szopa M., Bulanda M., Małecki M.T. , Gosiewski T.",Analysis of the Gut Mycobiome in Adult Patients with Type 1 and Type 2 Diabetes Using Next-Generation Sequencing (NGS) with Increased Sensitivity-Pilot Study,Nutrients,2021,"diabetes, gut mycobiome, next-generation sequencing (NGS)",Experiment 2,Poland,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,"Individuals diagnosed with Type 1 Diabetes Mellitus in 2012–2015 at the Department of Metabolic Diseases, University Hospital, Krakow, Poland",26,26,1 month,16S,NA,Illumina,relative abundances,PERMANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 4,20 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1,WikiWorks",Differential abundance of the fungal genus in individuals diagnosed with Type 2 Diabetes compared to healthy controls,increased,"k__Fungi|p__Basidiomycota|c__Exobasidiomycetes|o__Entylomatales|g__Tilletiopsis,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Udeniomyces,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Bulleribasidiaceae|g__Vishniacozyma",4751|5204|452283|62914|1500560;4751|5204|155616|90883|1851551|42658;4751|5204|155616|5234|1884640|1891946,Complete,Claregrieve1
bsdb:33806027/3/1,33806027,"cross-sectional observational, not case-control",33806027,10.3390/nu13041066,https://pubmed.ncbi.nlm.nih.gov/33806027/,"Salamon D., Sroka-Oleksiak A., Gurgul A., Arent Z., Szopa M., Bulanda M., Małecki M.T. , Gosiewski T.",Analysis of the Gut Mycobiome in Adult Patients with Type 1 and Type 2 Diabetes Using Next-Generation Sequencing (NGS) with Increased Sensitivity-Pilot Study,Nutrients,2021,"diabetes, gut mycobiome, next-generation sequencing (NGS)",Experiment 3,Poland,Homo sapiens,Feces,UBERON:0001988,Diabetes mellitus,EFO:0000400,Individuals diagnosed with Type 1 Diabetes Mellitus,Individuals diagnosed with Type 2 Diabetes Mellitus,"Individuals diagnosed with Type 2 Diabetes Mellitus in 2012–2015 at the Department of Metabolic Diseases, University Hospital, Krakow, Poland",26,24,1 month,16S,NA,Illumina,relative abundances,PERMANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 4,20 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1,WikiWorks",Differential abundance in the fungal communities in Type 2 Diabetes patients compared to Type 1 Diabetes patients,decreased,"k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Bulleraceae|g__Bullera,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Polyporales|f__Polyporaceae|g__Ganoderma,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Filobasidiales|f__Filobasidiaceae|g__Naganishia,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Udeniomyces",4751|5204|155616|5234|1905116|4970;4751|5204|155619|5303|5317|5314;4751|5204|155616|90886|5408|1851509;4751|5204|155616|90883|1851551|42658,Complete,Claregrieve1
bsdb:33806027/3/2,33806027,"cross-sectional observational, not case-control",33806027,10.3390/nu13041066,https://pubmed.ncbi.nlm.nih.gov/33806027/,"Salamon D., Sroka-Oleksiak A., Gurgul A., Arent Z., Szopa M., Bulanda M., Małecki M.T. , Gosiewski T.",Analysis of the Gut Mycobiome in Adult Patients with Type 1 and Type 2 Diabetes Using Next-Generation Sequencing (NGS) with Increased Sensitivity-Pilot Study,Nutrients,2021,"diabetes, gut mycobiome, next-generation sequencing (NGS)",Experiment 3,Poland,Homo sapiens,Feces,UBERON:0001988,Diabetes mellitus,EFO:0000400,Individuals diagnosed with Type 1 Diabetes Mellitus,Individuals diagnosed with Type 2 Diabetes Mellitus,"Individuals diagnosed with Type 2 Diabetes Mellitus in 2012–2015 at the Department of Metabolic Diseases, University Hospital, Krakow, Poland",26,24,1 month,16S,NA,Illumina,relative abundances,PERMANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 4 and Figure 6,20 June 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1,WikiWorks",Differential abundance in the fungal communities in Type 2 Diabetes patients compared to Type 1 Diabetes patients,increased,"k__Fungi|p__Ascomycota,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces,k__Fungi|p__Basidiomycota|c__Exobasidiomycetes|o__Entylomatales|g__Tilletiopsis",4751|4890;4751|4890|4891|4892|4893|4930;4751|5204|452283|62914|1500560,Complete,Claregrieve1
bsdb:33815323/1/1,33815323,"cross-sectional observational, not case-control",33815323,10.3389/fmicb.2021.637430,NA,"Ventero M.P., Cuadrat R.R.C., Vidal I., Andrade B.G.N., Molina-Pardines C., Haro-Moreno J.M., Coutinho F.H., Merino E., Regitano L.C.A., Silveira C.B., Afli H., López-Pérez M. , Rodríguez J.C.",Nasopharyngeal Microbial Communities of Patients Infected With SARS-CoV-2 That Developed COVID-19,Frontiers in microbiology,2021,"COVID-19, NGS – next generation sequencing, Prevotella, SARS-CoV-2, coronavirus, microbiome",Experiment 1,Spain,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls,Severe COVID-19 patients,Patients with confirmed COVID-19 infection and severe symptoms; required hospital admission,18,18,NA,16S,34,Illumina,raw counts,Linear Regression,0.25,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table S5,29 June 2021,Claregrieve1,"Claregrieve1,Fatima,WikiWorks",Differential abundance of bacterial taxa between healthy controls and severe COVID-19 patients,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",3379134|976|200643|171549|171552|1283313;1783272|1239|186801|3085636|186803|43996;1783272|1239|186801|3085636|186803|1164882;1783272|1239|186801|3085636|186803|265975;3379134|976|200643|171549|171552|838;1783272|1239|526524|526525|128827,Complete,Fatima
bsdb:33815323/2/1,33815323,"cross-sectional observational, not case-control",33815323,10.3389/fmicb.2021.637430,NA,"Ventero M.P., Cuadrat R.R.C., Vidal I., Andrade B.G.N., Molina-Pardines C., Haro-Moreno J.M., Coutinho F.H., Merino E., Regitano L.C.A., Silveira C.B., Afli H., López-Pérez M. , Rodríguez J.C.",Nasopharyngeal Microbial Communities of Patients Infected With SARS-CoV-2 That Developed COVID-19,Frontiers in microbiology,2021,"COVID-19, NGS – next generation sequencing, Prevotella, SARS-CoV-2, coronavirus, microbiome",Experiment 2,Spain,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls,Severe COVID-19 patients requiring ICU,Patients with confirmed COVID-19 infection and severe symptoms who were admitted into the intensive care unit,18,19,NA,16S,34,Illumina,raw counts,Linear Regression,0.25,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table S5,29 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance of bacterial taxa between healthy controls and severe COVID-19 patients requiring ICU care,increased,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,3379134|203691|203692|136|2845253|157,Complete,Fatima
bsdb:33815323/2/2,33815323,"cross-sectional observational, not case-control",33815323,10.3389/fmicb.2021.637430,NA,"Ventero M.P., Cuadrat R.R.C., Vidal I., Andrade B.G.N., Molina-Pardines C., Haro-Moreno J.M., Coutinho F.H., Merino E., Regitano L.C.A., Silveira C.B., Afli H., López-Pérez M. , Rodríguez J.C.",Nasopharyngeal Microbial Communities of Patients Infected With SARS-CoV-2 That Developed COVID-19,Frontiers in microbiology,2021,"COVID-19, NGS – next generation sequencing, Prevotella, SARS-CoV-2, coronavirus, microbiome",Experiment 2,Spain,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls,Severe COVID-19 patients requiring ICU,Patients with confirmed COVID-19 infection and severe symptoms who were admitted into the intensive care unit,18,19,NA,16S,34,Illumina,raw counts,Linear Regression,0.25,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table S5,29 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance of bacterial taxa between healthy controls and severe COVID-19 patients requiring ICU care,decreased,s__uncultured phototrophic eukaryote,172788,Complete,Fatima
bsdb:33815323/3/1,33815323,"cross-sectional observational, not case-control",33815323,10.3389/fmicb.2021.637430,NA,"Ventero M.P., Cuadrat R.R.C., Vidal I., Andrade B.G.N., Molina-Pardines C., Haro-Moreno J.M., Coutinho F.H., Merino E., Regitano L.C.A., Silveira C.B., Afli H., López-Pérez M. , Rodríguez J.C.",Nasopharyngeal Microbial Communities of Patients Infected With SARS-CoV-2 That Developed COVID-19,Frontiers in microbiology,2021,"COVID-19, NGS – next generation sequencing, Prevotella, SARS-CoV-2, coronavirus, microbiome",Experiment 3,Spain,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Mild COVID-19 patients,Severe COVID-19 patients,Patients with confirmed COVID-19 infection and severe symptoms who were hospitalized,19,18,NA,16S,34,Illumina,raw counts,Linear Regression,0.25,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table S5,29 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance of bacterial taxa between mild and severe COVID-19 cases,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,Fatima
bsdb:33816351/1/1,33816351,case-control,33816351,10.3389/fcimb.2021.646348,NA,"Huang Y., Wang Z., Ma H., Ji S., Chen Z., Cui Z., Chen J. , Tang S.",Dysbiosis and Implication of the Gut Microbiota in Diabetic Retinopathy,Frontiers in cellular and infection microbiology,2021,"16S rRNA gene sequence, diabetes mellitus, diabetic retinopathy, gut microbiota, human",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Retinopathy,EFO:0003839,healthy controls (HC),diabetes mellitus (DM),Participants who identify as diabetic patients without retinopathy (DM),25,25,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2.5,"age,body mass index,sex",NA,NA,decreased,decreased,NA,decreased,NA,Signature 1,Fig.4,29 October 2023,Chinelsy,"Chinelsy,ChiomaBlessing,WikiWorks",Relative abundance of the bacterial community in diabetic patients without retinopathy (DM) and healthy controls (HC),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli",3379134|1224|1236|135625|712|724;1783272|1239|909932|1843489|31977|906;3379134|976|200643|171549|2005525|375288;3379134|1224|1236|135625|712;3379134|1224|1236|135625;1783272|1239|91061|186826|1300;3379134|976|200643|171549|2005525;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061,Complete,ChiomaBlessing
bsdb:33816351/2/1,33816351,case-control,33816351,10.3389/fcimb.2021.646348,NA,"Huang Y., Wang Z., Ma H., Ji S., Chen Z., Cui Z., Chen J. , Tang S.",Dysbiosis and Implication of the Gut Microbiota in Diabetic Retinopathy,Frontiers in cellular and infection microbiology,2021,"16S rRNA gene sequence, diabetes mellitus, diabetic retinopathy, gut microbiota, human",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Retinopathy,EFO:0003839,diabetes mellitus (DM),diabetes retinopathy (DR),Participants who identify as diabetic patients with retinopathy (DR),25,25,1 month,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,NA,2.5,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Supplemental. Table S6,18 December 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Relative abundance between diabetes retinopathy and diabetes mellitus based on the biomarker families correlated with fasting blood sugar (FBG) and duration of type 2 diabetes (T2Dyear),decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,3379134|1224|1236|135625|712,Complete,ChiomaBlessing
bsdb:33816351/2/2,33816351,case-control,33816351,10.3389/fcimb.2021.646348,NA,"Huang Y., Wang Z., Ma H., Ji S., Chen Z., Cui Z., Chen J. , Tang S.",Dysbiosis and Implication of the Gut Microbiota in Diabetic Retinopathy,Frontiers in cellular and infection microbiology,2021,"16S rRNA gene sequence, diabetes mellitus, diabetic retinopathy, gut microbiota, human",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Retinopathy,EFO:0003839,diabetes mellitus (DM),diabetes retinopathy (DR),Participants who identify as diabetic patients with retinopathy (DR),25,25,1 month,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,NA,2.5,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Supplemental. Table S6,18 December 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Relative abundance between diabetes retinopathy and diabetes mellitus based on the biomarker families correlated with fasting blood sugar (FBG) and duration of type 2 diabetes (T2Dyear),increased,NA,NA,Complete,ChiomaBlessing
bsdb:33824448/1/1,33824448,prospective cohort,33824448,10.1038/s41390-021-01494-7,NA,"Ainonen S., Tejesvi M.V., Mahmud M.R., Paalanne N., Pokka T., Li W., Nelson K.E., Salo J., Renko M., Vänni P., Pirttilä A.M. , Tapiainen T.",Antibiotics at birth and later antibiotic courses: effects on gut microbiota,Pediatric research,2021,NA,Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Control group,perinatal antibiotics,Participants who received any perinatal antibiotics (all three perinatal groups combined),27,73,NA,16S,NA,Ion Torrent,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,table 2,16 October 2023,OdigiriGreat,"OdigiriGreat,ChiomaBlessing,WikiWorks",Composition of the gut microbiome in vaginally delivered infants (N = 100) exposed to perinatal antibiotics as compared with the control group after the first year of life.,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239;1783272|1239|186801|186802|31979|1485;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|171552|838,Complete,ChiomaBlessing
bsdb:33824448/1/2,33824448,prospective cohort,33824448,10.1038/s41390-021-01494-7,NA,"Ainonen S., Tejesvi M.V., Mahmud M.R., Paalanne N., Pokka T., Li W., Nelson K.E., Salo J., Renko M., Vänni P., Pirttilä A.M. , Tapiainen T.",Antibiotics at birth and later antibiotic courses: effects on gut microbiota,Pediatric research,2021,NA,Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,Control group,perinatal antibiotics,Participants who received any perinatal antibiotics (all three perinatal groups combined),27,73,NA,16S,NA,Ion Torrent,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,table 2,16 October 2023,OdigiriGreat,"OdigiriGreat,ChiomaBlessing,WikiWorks",Composition of the gut microbiome in vaginally delivered infants (N = 100) exposed to perinatal antibiotics as compared with the control group after the first year of life.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia",3379134|976|200643|171549|815|816;3379134|976|200643,Complete,ChiomaBlessing
bsdb:33824448/2/NA,33824448,prospective cohort,33824448,10.1038/s41390-021-01494-7,NA,"Ainonen S., Tejesvi M.V., Mahmud M.R., Paalanne N., Pokka T., Li W., Nelson K.E., Salo J., Renko M., Vänni P., Pirttilä A.M. , Tapiainen T.",Antibiotics at birth and later antibiotic courses: effects on gut microbiota,Pediatric research,2021,NA,Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Antimicrobial agent,CHEBI:33281,control group,Antibiotic courses,All perinatal groups that received any antibiotic courses,71,28,NA,16S,NA,Ion Torrent,relative abundances,ANOVA,0.05,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:33828220/1/1,33828220,"cross-sectional observational, not case-control",33828220,10.1038/s41598-021-87368-8,https://doi.org/10.1038/s41598-021-87368-8,"Abange W.B., Martin C., Nanfack A.J., Yatchou L.G., Nusbacher N., Nguedia C.A., Kamga H.G., Fokam J., Kennedy S.P., Ndjolo A., Lozupone C. , Nkenfou C.N.","Alteration of the gut fecal microbiome in children living with HIV on antiretroviral therapy in Yaounde, Cameroon",Scientific reports,2021,NA,Experiment 1,Cameroon,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Human Immunodeficiency Virus (HIV)-negative children,Human Immunodeficiency Virus (HIV)-positive children,Children diagnosed with HIV and undergoing treatment with either non-nucleoside reverse transcriptase inhibitors (NNRTI) or protease inhibitor (PI/r)-based anti-retroviral therapy (ART).,82,87,1 month,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,decreased,NA,Signature 1,Figure 4A,7 November 2024,ToluwalaseA,"ToluwalaseA,Aleru Divine,WikiWorks","Differential abundance of ASVs in the HIV-infected and HIV-uninfected cohorts identified via paired, Wilcoxon tests.",increased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,3379134|74201|203494|48461|1647988|239934|239935,Complete,Svetlana up
bsdb:33828220/1/2,33828220,"cross-sectional observational, not case-control",33828220,10.1038/s41598-021-87368-8,https://doi.org/10.1038/s41598-021-87368-8,"Abange W.B., Martin C., Nanfack A.J., Yatchou L.G., Nusbacher N., Nguedia C.A., Kamga H.G., Fokam J., Kennedy S.P., Ndjolo A., Lozupone C. , Nkenfou C.N.","Alteration of the gut fecal microbiome in children living with HIV on antiretroviral therapy in Yaounde, Cameroon",Scientific reports,2021,NA,Experiment 1,Cameroon,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Human Immunodeficiency Virus (HIV)-negative children,Human Immunodeficiency Virus (HIV)-positive children,Children diagnosed with HIV and undergoing treatment with either non-nucleoside reverse transcriptase inhibitors (NNRTI) or protease inhibitor (PI/r)-based anti-retroviral therapy (ART).,82,87,1 month,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,decreased,NA,Signature 2,Figure 4A,7 November 2024,ToluwalaseA,"ToluwalaseA,Aleru Divine,WikiWorks","Differential abundance of ASVs in the HIV-infected and HIV-uninfected cohorts identified via paired, Wilcoxon tests.",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,1783272|1239|186801|186802|216572|216851|853,Complete,Svetlana up
bsdb:33828220/2/1,33828220,"cross-sectional observational, not case-control",33828220,10.1038/s41598-021-87368-8,https://doi.org/10.1038/s41598-021-87368-8,"Abange W.B., Martin C., Nanfack A.J., Yatchou L.G., Nusbacher N., Nguedia C.A., Kamga H.G., Fokam J., Kennedy S.P., Ndjolo A., Lozupone C. , Nkenfou C.N.","Alteration of the gut fecal microbiome in children living with HIV on antiretroviral therapy in Yaounde, Cameroon",Scientific reports,2021,NA,Experiment 2,Cameroon,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,Non-nucleoside reverse transcriptase inhibitors (NNRTI) - based ART,Protease inhibitor (PI/r) - based ART,Children diagnosed with HIV and undergoing treatment with protease inhibitor (PI/r)-based anti-retroviral therapy (ART).,74,13,1 month,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,unchanged,NA,Signature 1,Figure 6A,12 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","Differential abundance of ASVs in the HIV-positive NNRTI and PI/r cohorts identified via paired, Wilcoxon tests.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572|216851,Complete,Svetlana up
bsdb:33828910/1/1,33828910,case-control,33828910,10.7717/peerj.10952,https://pubmed.ncbi.nlm.nih.gov/33828910/,"Zhang Z., Tian T., Chen Z., Liu L., Luo T. , Dai J.",Characteristics of the gut microbiome in patients with prediabetes and type 2 diabetes,PeerJ,2021,"Gut microbiome, Prediabetes, Type 2 diabetes mellitus",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,Individuals diagnosed with Type 2 Diabetes Mellitus; Participants with T2DM were required to meet the following inclusion criteria: (i) fasting blood glucose test (FBG) ≥7 mmol/L and/or 2-h fasting oral glucose tolerance test (OGTT) ≥11.1 mmol/L; and (ii) all cases of T2DM were newly diagnosed.,60,60,2 months,16S,45,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table 3,5 July 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1,WikiWorks",Differential microbial abundance in individuals with type 2 diabetes compared to healthy controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|976|200643|171549|171552|1283313;1783272|1239|909932|1843489|31977|906;1783272|1239|909932;3379134|976|200643|171549|171552|838,Complete,Claregrieve1
bsdb:33828910/1/2,33828910,case-control,33828910,10.7717/peerj.10952,https://pubmed.ncbi.nlm.nih.gov/33828910/,"Zhang Z., Tian T., Chen Z., Liu L., Luo T. , Dai J.",Characteristics of the gut microbiome in patients with prediabetes and type 2 diabetes,PeerJ,2021,"Gut microbiome, Prediabetes, Type 2 diabetes mellitus",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,Individuals diagnosed with Type 2 Diabetes Mellitus; Participants with T2DM were required to meet the following inclusion criteria: (i) fasting blood glucose test (FBG) ≥7 mmol/L and/or 2-h fasting oral glucose tolerance test (OGTT) ≥11.1 mmol/L; and (ii) all cases of T2DM were newly diagnosed.,60,60,2 months,16S,45,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Table 3,5 July 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1,WikiWorks",Differential microbial abundance in individuals with type 2 diabetes compared to healthy controls,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",3379134|976|200643|171549|815|816;3379134|976|200643|171549|171552|577309,Complete,Claregrieve1
bsdb:33828910/2/1,33828910,case-control,33828910,10.7717/peerj.10952,https://pubmed.ncbi.nlm.nih.gov/33828910/,"Zhang Z., Tian T., Chen Z., Liu L., Luo T. , Dai J.",Characteristics of the gut microbiome in patients with prediabetes and type 2 diabetes,PeerJ,2021,"Gut microbiome, Prediabetes, Type 2 diabetes mellitus",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Prediabetes syndrome,EFO:1001121,Healthy controls,Individuals with Prediabetes (PreDM),Individuals with Prediabetes (PreDM); PreDM was defined as FBG of 6.1–7.0 mmol/L or HbA1c levels of 6.0%–6.5%.,60,60,2 months,16S,45,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table 3,5 July 2021,Madhubani Dey,"Madhubani Dey,Claregrieve1,WikiWorks",Differential microbial abundance in individuals with prediabetes compared to healthy controls,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",1783272|1239|909932|1843489|31977|906;3379134|1224;3379134|1224|1236|135625|712|724,Complete,Claregrieve1
bsdb:33828910/2/2,33828910,case-control,33828910,10.7717/peerj.10952,https://pubmed.ncbi.nlm.nih.gov/33828910/,"Zhang Z., Tian T., Chen Z., Liu L., Luo T. , Dai J.",Characteristics of the gut microbiome in patients with prediabetes and type 2 diabetes,PeerJ,2021,"Gut microbiome, Prediabetes, Type 2 diabetes mellitus",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Prediabetes syndrome,EFO:1001121,Healthy controls,Individuals with Prediabetes (PreDM),Individuals with Prediabetes (PreDM); PreDM was defined as FBG of 6.1–7.0 mmol/L or HbA1c levels of 6.0%–6.5%.,60,60,2 months,16S,45,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Table 3,22 July 2022,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance in individuals with prediabetes compared to healthy controls,decreased,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,3379134|29547|3031852|213849|72293|209,Complete,Claregrieve1
bsdb:33833065/2/NA,33833065,time series / longitudinal observational,33833065,10.1136/gutjnl-2021-324090,NA,"Chen Y., Gu S., Chen Y., Lu H., Shi D., Guo J., Wu W.R., Yang Y., Li Y., Xu K.J., Ding C., Luo R., Huang C., Yu L., Xu M., Yi P., Liu J., Tao J.J., Zhang H., Lv L., Wang B., Sheng J. , Li L.",Six-month follow-up of gut microbiota richness in patients with COVID-19,Gut,2021,"COVID-19, intestinal microbiology",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients in convalescence,Sample from COVID-19 convalescence period (from viral clearance to 2 weeks after hospital discharge),30,30,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,"age,body mass index,sex",NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:33839907/1/1,33839907,case-control,33839907,10.1007/s00404-021-06057-z,NA,"Shan J., Ni Z., Cheng W., Zhou L., Zhai D., Sun S. , Yu C.",Gut microbiota imbalance and its correlations with hormone and inflammatory factors in patients with stage 3/4 endometriosis,Archives of gynecology and obstetrics,2021,"Dysbiosis, Endometriosis, Estradiol, Gut microbiota, Inflammatory factors",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Healthy controls,Stage 3/4 endometriosis patients,Women were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).,12,12,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 3,9 August 2021,Samara.Khan,"Samara.Khan,Folakunmi,Welile,Idiaru angela,WikiWorks",Patients with endometriosis demonstrated a significantly higher abundance of the following taxa compared to control patients. There were 36 taxa unique to endometriosis patients that were completely absent in control patients. Some taxa were excluded because they had an unidentified genus/ species,increased,"k__Pseudomonadati|p__Acidobacteriota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,p__Candidatus Saccharimonadota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Pseudarthrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] brachy,k__Pseudomonadati|p__Acidobacteriota|c__Blastocatellia|o__Blastocatellales|f__Blastocatellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhodobiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",3379134|57723;1783272|201174|1760|2037|2049|1654;1783272|1239|186801|3085636|186803|2569097|39488;3379134|976|200643|171549;1783272|1239|186801|3085636|186803|572511;95818;3384189|32066|203490|203491|203492|180162;1783272|201174|1760|85007|1653|1716;1783272|1117;1783272|1239|186801|3085636|186803|189330;1783272|201174|84998|1643822|1643826|84111;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|186828|117563;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1357;1783272|1239|186801|3085636|186803|2316020|33038;1783272|201174|1760|85007|1762|1763;1783272|201174|1760|85006|1268|1742993;1783272|1239|186801|186802|216572|1508657;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3082720|543314|35517;3379134|57723|1562566|1748771|1748772;3379134|976|200643|171549|171552;3379134|1224|28211|356|119043;1783272|1239|186801|186802|31979|1485,Complete,Folakunmi
bsdb:33839907/1/2,33839907,case-control,33839907,10.1007/s00404-021-06057-z,NA,"Shan J., Ni Z., Cheng W., Zhou L., Zhai D., Sun S. , Yu C.",Gut microbiota imbalance and its correlations with hormone and inflammatory factors in patients with stage 3/4 endometriosis,Archives of gynecology and obstetrics,2021,"Dysbiosis, Endometriosis, Estradiol, Gut microbiota, Inflammatory factors",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Healthy controls,Stage 3/4 endometriosis patients,Women were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).,12,12,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 3,9 August 2021,Samara.Khan,"Samara.Khan,Folakunmi,WikiWorks",The following taxa were decreased in endometriosis patients and increased in the control group. There were 11 genera unique to the control group. Some taxa were excluded because they had an unidentified genus/ species,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,s__bacterium ND3007,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|877420;3379134|976|200643|171549|1853231|283168;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|186802|216572|1263|41978;1452070;1783272|1239|186801|3085636|1185407;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|186802|216572|707003;1783272|1239|186801|3085636|186803|297314,Complete,Folakunmi
bsdb:33850111/1/1,33850111,"cross-sectional observational, not case-control",33850111,10.1038/s41421-021-00257-2,NA,"Zhong H., Wang Y., Shi Z., Zhang L., Ren H., He W., Zhang Z., Zhu A., Zhao J., Xiao F., Yang F., Liang T., Ye F., Zhong B., Ruan S., Gan M., Zhu J., Li F., Li F., Wang D., Li J., Ren P., Zhu S., Yang H., Wang J., Kristiansen K., Tun H.M., Chen W., Zhong N., Xu X., Li Y.M., Li J. , Zhao J.",Characterization of respiratory microbial dysbiosis in hospitalized COVID-19 patients,Cell discovery,2021,NA,Experiment 1,China,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Mild COVID-19 patients,Severe COVID-19 patients,COVID-19 infected patients admitted to the ICU and requiring mechanical ventilation,8,15,NA,WMS,NA,DNBSEQ-T7,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Figure 2c,2 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance in microbial taxa between mild and severe COVID-19 patients,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|909932|1843489|31977|29465;3379134|1224|28216|206351|481|482;1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|171552|838,Complete,Fatima
bsdb:33850111/1/2,33850111,"cross-sectional observational, not case-control",33850111,10.1038/s41421-021-00257-2,NA,"Zhong H., Wang Y., Shi Z., Zhang L., Ren H., He W., Zhang Z., Zhu A., Zhao J., Xiao F., Yang F., Liang T., Ye F., Zhong B., Ruan S., Gan M., Zhu J., Li F., Li F., Wang D., Li J., Ren P., Zhu S., Yang H., Wang J., Kristiansen K., Tun H.M., Chen W., Zhong N., Xu X., Li Y.M., Li J. , Zhao J.",Characterization of respiratory microbial dysbiosis in hospitalized COVID-19 patients,Cell discovery,2021,NA,Experiment 1,China,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Mild COVID-19 patients,Severe COVID-19 patients,COVID-19 infected patients admitted to the ICU and requiring mechanical ventilation,8,15,NA,WMS,NA,DNBSEQ-T7,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,Figure 2c,2 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance in microbial taxa between mild and severe COVID-19 patients,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",1783272|1239|91061|1385|90964|1279;3379134|1224|1236|91347|543|561,Complete,Fatima
bsdb:33850111/2/1,33850111,"cross-sectional observational, not case-control",33850111,10.1038/s41421-021-00257-2,NA,"Zhong H., Wang Y., Shi Z., Zhang L., Ren H., He W., Zhang Z., Zhu A., Zhao J., Xiao F., Yang F., Liang T., Ye F., Zhong B., Ruan S., Gan M., Zhu J., Li F., Li F., Wang D., Li J., Ren P., Zhu S., Yang H., Wang J., Kristiansen K., Tun H.M., Chen W., Zhong N., Xu X., Li Y.M., Li J. , Zhao J.",Characterization of respiratory microbial dysbiosis in hospitalized COVID-19 patients,Cell discovery,2021,NA,Experiment 2,China,Homo sapiens,Rectum,UBERON:0001052,COVID-19,MONDO:0100096,Mild COVID-19 patients,Severe COVID-19 patients,COVID-19 infected patients admitted to the ICU and requiring mechanical ventilation,7,15,NA,WMS,NA,DNBSEQ-T7,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S6b,2 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance in microbial taxa between mild and severe COVID-19 patients,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,3379134|976|200643|171549|2005525|375288,Complete,Fatima
bsdb:33869074/1/1,33869074,case-control,33869074,10.3389/fcimb.2021.605825,NA,"Xiao S., Zhang G., Jiang C., Liu X., Wang X., Li Y., Cheng M., Lv H., Xian F., Guo X. , Tan Y.",Deciphering Gut Microbiota Dysbiosis and Corresponding Genetic and Metabolic Dysregulation in Psoriasis Patients Using Metagenomics Sequencing,Frontiers in cellular and infection microbiology,2021,"genetic functions, gut microbiota, metabolites, metagenomics sequencing, psoriasis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Psoriasis,EFO:0000676,Healthy donors,Psoriasis patients,Patients with Psoriasis,15,30,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 5A and 5B,1 April 2025,Tosin,Tosin,Differentially abundant bacteria between psoriasis and control groups,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides oleiciplenus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus haemolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus paraphrohaemolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Methanobacteriati|p__Methanobacteriota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter|s__Oxalobacter formigenes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",3379134|1224|1236|135625|712|416916|739;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550|239759|626932;3379134|976|200643|171549|171550|239759|626932;;3379134|976|200643|171549|815|816|626931;1783272|1239|186801|3085636|186803|2719313|208479;3384189|32066|203490|203491|203492|848|850;3384189|32066|203490|203491|203492|848|850;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712|724|726;3379134|1224|1236|135625|712|724|729;3379134|1224|1236|135625|712|724|736;3379134|1224|1236|91347|543|570|548;1783272|1239|91061|186826|33958|2767887|1623;3366610|28890;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|1853231|283168|28118;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|75682|846;3379134|1224|28216|80840|75682|846|847;3379134|1224|28216|80840|75682;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|976|117747|200666|84566|84567;3379134|976|200643|171549|171551;3379134|976|200643|171549|171550;3379134|976|117747|200666|84566;1783272|1239|186801|186802|216572|459786,Complete,Svetlana up
bsdb:33869074/2/1,33869074,case-control,33869074,10.3389/fcimb.2021.605825,NA,"Xiao S., Zhang G., Jiang C., Liu X., Wang X., Li Y., Cheng M., Lv H., Xian F., Guo X. , Tan Y.",Deciphering Gut Microbiota Dysbiosis and Corresponding Genetic and Metabolic Dysregulation in Psoriasis Patients Using Metagenomics Sequencing,Frontiers in cellular and infection microbiology,2021,"genetic functions, gut microbiota, metabolites, metagenomics sequencing, psoriasis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Psoriasis,EFO:0000676,Healthy donors,Psoriasis patients,Patients with Psoriasis,15,30,6 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 2A and 2B,2 April 2025,Tosin,Tosin,Taxonomic differences between the psoriasis patients and controls at the family (A) and genus (B) levels,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas",1783272|1239|186801|186802|216572|244127;3379134|1224|28216|80840|75682|846;3379134|1224|28216|80840|75682;3379134|976|200643|171549|171551;3379134|1224|1236|135625|712;3379134|976|200643|171549|171550;3379134|976|117747|200666|84566;3379134|1224|28216|80840|80864;3379134|976|200643|171549|1853231|574697;3379134|1224|1236|135625|712|713;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|1017280;3379134|976|117747|200666|84566|84567;3379134|1224|28216|80840|80864|283,Complete,Svetlana up
bsdb:33876475/1/1,33876475,case-control,33876475,10.1111/odi.13883,NA,"Wirth R., Maróti G., Lipták L., Mester M., Al Ayoubi A., Pap B., Madléna M., Minárovits J. , Kovács K.L.",Microbiomes in supragingival biofilms and saliva of adolescents with gingivitis and gingival health,Oral diseases,2022,"amplicon sequencing, gingivitis in adolescents, microbiome, saliva, shotgun sequencing, supragingival biofilm",Experiment 1,Hungary,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Gingivitis,MONDO:0002508,Healthy Controls,Induced Gingivitis patients,"Induced adolescents patients with gingivitis wearing fixed metal braces (nine patients, three males and six females, mean age 16.9 years, range: 15–18 years);",9,9,6 months,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3A and 3B, Text “3.2 Pairwise comparison of study groups”, Page 5 - 7",20 January 2026,Tosin,Tosin,Significant differential abundance between induced gingivitis adolescents patients and healthy controls.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Schwartzia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes",3379134|74201|203494|48461|1647988|239934;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294|194|199;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|1164882;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|909929|1843491|55506;3379134|203691|203692|136|2845253|157;1783272|1239|909932|1843489|31977|39948|39950,Complete,NA
bsdb:33876475/1/2,33876475,case-control,33876475,10.1111/odi.13883,NA,"Wirth R., Maróti G., Lipták L., Mester M., Al Ayoubi A., Pap B., Madléna M., Minárovits J. , Kovács K.L.",Microbiomes in supragingival biofilms and saliva of adolescents with gingivitis and gingival health,Oral diseases,2022,"amplicon sequencing, gingivitis in adolescents, microbiome, saliva, shotgun sequencing, supragingival biofilm",Experiment 1,Hungary,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Gingivitis,MONDO:0002508,Healthy Controls,Induced Gingivitis patients,"Induced adolescents patients with gingivitis wearing fixed metal braces (nine patients, three males and six females, mean age 16.9 years, range: 15–18 years);",9,9,6 months,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3A and 3B, Text “3.2 Pairwise comparison of study groups”, Page 5 - 7",20 January 2026,Tosin,Tosin,Significant differential abundance between induced gingivitis adolescents patients and healthy controls.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter curvus,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Nanosynbacterales|f__Candidatus Nanosynbacteraceae|g__Candidatus Nanosynbacter|s__Candidatus Nanosynbacter lyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa",1783272|201174|1760|2037|2049|1654;3379134|1224|1236|135625|712|416916|739;3379134|29547|3031852|213849|72294|194|200;95818|2093818|2093819|2093822|2093823|2093824;1783272|1239|186801|3085636|186803|43996;3384189|32066|203490|203491|203492|848|851;3384189|32066|203490|203491|203492|848|860;3379134|1224|1236|135625|712|724|729;3379134|1224|28216|206351|481|32257;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|80840|119060|47670|47671;3379134|1224|28216|206351|481|482;1783272|1239|1737404|1737405|1570339|543311|33033;3379134|976|200643|171549|171552|838|28131;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|2047;1783272|201174|1760|85006|1268|32207|43675,Complete,NA
bsdb:33876475/2/1,33876475,case-control,33876475,10.1111/odi.13883,NA,"Wirth R., Maróti G., Lipták L., Mester M., Al Ayoubi A., Pap B., Madléna M., Minárovits J. , Kovács K.L.",Microbiomes in supragingival biofilms and saliva of adolescents with gingivitis and gingival health,Oral diseases,2022,"amplicon sequencing, gingivitis in adolescents, microbiome, saliva, shotgun sequencing, supragingival biofilm",Experiment 2,Hungary,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Gingivitis,MONDO:0002508,Induced gingivitis patients,Spontaneous gingivitis patients,"Adolescents diagnosed with plaque-induced gingivitis (10 patients, seven males and three females, mean age 17 years, range: 16–18 years.",9,10,6 months,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3A and 3B, Text “3.2 Pairwise comparison of study groups”, Page 5 - 7",20 January 2026,Tosin,Tosin,Significant differential abundance between induced and spontaneous gingivitis adolescents patients,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter curvus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Schwartzia",3379134|1224|1236|135625|712|416916|739;3379134|29547|3031852|213849|72294|194|199;3379134|29547|3031852|213849|72294|194|200;1783272|1239|909932|1843489|31977|39948|39950;3384189|32066|203490|203491|203492|848|851;1783272|1239|1737404|1737405|1570339|543311|33033;3379134|976|200643|171549|171552|838|28131;3384189|32066|203490|203491|203492|848;3379134|203691|203692|136|2845253|157;3379134|29547|3031852|213849|72294|194;1783272|1239|186801|3085636|186803|43996;1783272|1239|909932|909929|1843491|55506,Complete,NA
bsdb:33876475/2/2,33876475,case-control,33876475,10.1111/odi.13883,NA,"Wirth R., Maróti G., Lipták L., Mester M., Al Ayoubi A., Pap B., Madléna M., Minárovits J. , Kovács K.L.",Microbiomes in supragingival biofilms and saliva of adolescents with gingivitis and gingival health,Oral diseases,2022,"amplicon sequencing, gingivitis in adolescents, microbiome, saliva, shotgun sequencing, supragingival biofilm",Experiment 2,Hungary,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Gingivitis,MONDO:0002508,Induced gingivitis patients,Spontaneous gingivitis patients,"Adolescents diagnosed with plaque-induced gingivitis (10 patients, seven males and three females, mean age 17 years, range: 16–18 years.",9,10,6 months,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3A and 3B, Text “3.2 Pairwise comparison of study groups”, Page 5 - 7",20 January 2026,Tosin,Tosin,Significant differential abundance between induced and spontaneous gingivitis adolescents patients,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Nanosynbacterales|f__Candidatus Nanosynbacteraceae|g__Candidatus Nanosynbacter|s__Candidatus Nanosynbacter lyticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa",1783272|201174|1760|2037|2049|1654;3379134|74201|203494|48461|1647988|239934;95818|2093818|2093819|2093822|2093823|2093824;3379134|1224|1236|135625|712|724|729;3379134|1224|28216|206351|481|32257;1783272|1239|186801|3085636|186803|1164882;3379134|1224|28216|80840|119060|47670;1783272|1239|909932|1843489|31977|906;3379134|1224|28216|206351|481|482;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|2047;1783272|201174|1760|85006|1268|32207|43675,Complete,NA
bsdb:33876475/3/1,33876475,case-control,33876475,10.1111/odi.13883,NA,"Wirth R., Maróti G., Lipták L., Mester M., Al Ayoubi A., Pap B., Madléna M., Minárovits J. , Kovács K.L.",Microbiomes in supragingival biofilms and saliva of adolescents with gingivitis and gingival health,Oral diseases,2022,"amplicon sequencing, gingivitis in adolescents, microbiome, saliva, shotgun sequencing, supragingival biofilm",Experiment 3,Hungary,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Gingivitis,MONDO:0002508,Healthy controls,Spontaneous gingivitis patients,"Adolescents diagnosed with plaque-induced gingivitis (10 patients, seven males and three females, mean age 17 years, range: 16–18 years.",9,10,6 months,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3A and 3B, Text “3.2 Pairwise comparison of study groups”, Page 5 - 7",22 January 2026,Tosin,Tosin,Significant differential abundance between spontaneous gingivitis adolescents patients and healthy controls.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Schwartzia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter curvus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis",3379134|74201|203494|48461|1647988|239934;3379134|29547|3031852|213849|72294|194;1783272|1239|186801|3085636|186803|43996;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|1164882;1783272|1239|909932|909929|1843491|55506;3379134|203691|203692|136|2845253|157;3379134|976|200643|171549|171552|838|28131;3384189|32066|203490|203491|203492|848|851;1783272|1239|909932|1843489|31977|39948|39950;1783272|1239|1737404|1737405|1570339|543311|33033;3379134|29547|3031852|213849|72294|194|199;3379134|29547|3031852|213849|72294|194|200;3379134|1224|1236|135625|712|416916|739,Complete,NA
bsdb:33876475/3/2,33876475,case-control,33876475,10.1111/odi.13883,NA,"Wirth R., Maróti G., Lipták L., Mester M., Al Ayoubi A., Pap B., Madléna M., Minárovits J. , Kovács K.L.",Microbiomes in supragingival biofilms and saliva of adolescents with gingivitis and gingival health,Oral diseases,2022,"amplicon sequencing, gingivitis in adolescents, microbiome, saliva, shotgun sequencing, supragingival biofilm",Experiment 3,Hungary,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Gingivitis,MONDO:0002508,Healthy controls,Spontaneous gingivitis patients,"Adolescents diagnosed with plaque-induced gingivitis (10 patients, seven males and three females, mean age 17 years, range: 16–18 years.",9,10,6 months,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3A and 3B, Text “3.2 Pairwise comparison of study groups”, Page 5 - 7",22 January 2026,Tosin,Tosin,Significant differential abundance between spontaneous gingivitis adolescents patients and healthy controls.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Nanosynbacterales|f__Candidatus Nanosynbacteraceae|g__Candidatus Nanosynbacter|s__Candidatus Nanosynbacter lyticus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae",3379134|1224|28216|80840|119060|47670;3379134|1224|28216|206351|481|32257;3379134|1224|28216|206351|481|482;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85006|1268|32207;1783272|1239|909932|1843489|31977|906;95818|2093818|2093819|2093822|2093823|2093824;3384189|32066|203490|203491|203492|848|860;1783272|201174|1760|85006|1268|32207|2047;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|1737404|1737405|1570339|543311|33033;3379134|1224|28216|80840|119060|47670|47671;3379134|1224|1236|135625|712|724|729,Complete,NA
bsdb:33879267/1/1,33879267,laboratory experiment,33879267,10.1186/s40104-021-00573-3,NA,"Shang Q., Liu S., Liu H., Mahfuz S. , Piao X.","Impact of sugar beet pulp and wheat bran on serum biochemical profile, inflammatory responses and gut microbiota in sows during late gestation and lactation",Journal of animal science and biotechnology,2021,"Dietary fiber source, Gut microbiota, Inflammatory response, Serum biochemical profile, Sow",Experiment 1,China,Sus scrofa domesticus,Feces,UBERON:0001988,Diet,EFO:0002755,SBP (Sugar Beet Pulp) diet during lactation,WB (Wheat Bran) diet during lactation,The Sows in this group were fed a 15% Wheat bran diet during lactation.,5,5,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Fig. 9B, 10B",15 April 2025,Anne-mariesharp,Anne-mariesharp,Relative abundance of significantly different genera & phyla on day21 of lactation between SBP (sugar beet pulp diet) & WB (wheat bran diet),increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239;1783272|1239|91061|186826|33958|1578,Complete,KateRasheed
bsdb:33879267/1/2,33879267,laboratory experiment,33879267,10.1186/s40104-021-00573-3,NA,"Shang Q., Liu S., Liu H., Mahfuz S. , Piao X.","Impact of sugar beet pulp and wheat bran on serum biochemical profile, inflammatory responses and gut microbiota in sows during late gestation and lactation",Journal of animal science and biotechnology,2021,"Dietary fiber source, Gut microbiota, Inflammatory response, Serum biochemical profile, Sow",Experiment 1,China,Sus scrofa domesticus,Feces,UBERON:0001988,Diet,EFO:0002755,SBP (Sugar Beet Pulp) diet during lactation,WB (Wheat Bran) diet during lactation,The Sows in this group were fed a 15% Wheat bran diet during lactation.,5,5,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Fig. 9B, 10B",15 April 2025,Anne-mariesharp,Anne-mariesharp,Relative abundance of significantly different genera & phyla on day21 of lactation between SBP (sugar beet pulp diet) & WB (wheat bran diet),decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,1783272|1239|186801|3085636|186803,Complete,KateRasheed
bsdb:33879267/2/1,33879267,laboratory experiment,33879267,10.1186/s40104-021-00573-3,NA,"Shang Q., Liu S., Liu H., Mahfuz S. , Piao X.","Impact of sugar beet pulp and wheat bran on serum biochemical profile, inflammatory responses and gut microbiota in sows during late gestation and lactation",Journal of animal science and biotechnology,2021,"Dietary fiber source, Gut microbiota, Inflammatory response, Serum biochemical profile, Sow",Experiment 2,China,Sus scrofa domesticus,Feces,UBERON:0001988,Diet,EFO:0002755,CON (Control) diet during lactation,SBP (Sugar Beet Pulp) diet during lactation,The Sows in this group were fed a 10% Sugar beet pulp diet during lactation,5,5,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 10B,15 April 2025,Anne-mariesharp,Anne-mariesharp,Relative abundance of significantly different taxon on day21 of lactation between Control diet (CON) & SBP (sugar beet pulp diet),increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,1783272|1239|186801|3085636|186803,Complete,KateRasheed
bsdb:33879267/2/2,33879267,laboratory experiment,33879267,10.1186/s40104-021-00573-3,NA,"Shang Q., Liu S., Liu H., Mahfuz S. , Piao X.","Impact of sugar beet pulp and wheat bran on serum biochemical profile, inflammatory responses and gut microbiota in sows during late gestation and lactation",Journal of animal science and biotechnology,2021,"Dietary fiber source, Gut microbiota, Inflammatory response, Serum biochemical profile, Sow",Experiment 2,China,Sus scrofa domesticus,Feces,UBERON:0001988,Diet,EFO:0002755,CON (Control) diet during lactation,SBP (Sugar Beet Pulp) diet during lactation,The Sows in this group were fed a 10% Sugar beet pulp diet during lactation,5,5,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Fig. 10B,15 April 2025,Anne-mariesharp,Anne-mariesharp,Relative abundance of significantly different taxon on day21 of lactation between Control diet (CON) & SBP (sugar beet pulp diet),decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,KateRasheed
bsdb:33879267/4/1,33879267,laboratory experiment,33879267,10.1186/s40104-021-00573-3,NA,"Shang Q., Liu S., Liu H., Mahfuz S. , Piao X.","Impact of sugar beet pulp and wheat bran on serum biochemical profile, inflammatory responses and gut microbiota in sows during late gestation and lactation",Journal of animal science and biotechnology,2021,"Dietary fiber source, Gut microbiota, Inflammatory response, Serum biochemical profile, Sow",Experiment 4,China,Sus scrofa domesticus,Feces,UBERON:0001988,Diet,EFO:0002755,Sugar beet pulp diet (SBP) during gestation,Wheat Bran Diet (WB) during gestation,The Sows in this group were fed a 30% Wheat bran diet during gestation.,5,5,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 9A & 10A,17 April 2025,Victoria,Victoria,"Relative abundance of significantly different phyla and genera on day 110 of gestation, between the sugar beet pulp (SBP) and wheat bran (WB) diet groups.",decreased,k__Bacillati|p__Mycoplasmatota,1783272|544448,Complete,KateRasheed
bsdb:33879267/5/1,33879267,laboratory experiment,33879267,10.1186/s40104-021-00573-3,NA,"Shang Q., Liu S., Liu H., Mahfuz S. , Piao X.","Impact of sugar beet pulp and wheat bran on serum biochemical profile, inflammatory responses and gut microbiota in sows during late gestation and lactation",Journal of animal science and biotechnology,2021,"Dietary fiber source, Gut microbiota, Inflammatory response, Serum biochemical profile, Sow",Experiment 5,China,Sus scrofa domesticus,Feces,UBERON:0001988,Diet,EFO:0002755,Control diet (CON) during gestation,Sugar beet pulp diet (SBP) during gestation,The Sows in this group were fed a 20% Sugar beet pulp diet during gestation.,5,5,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 10A,17 April 2025,Victoria,Victoria,"Relative abundance of significantly different phyla and genera on day 110 of gestation, between the Control (CON) and the sugar beet pulp (SBP) diet groups.",increased,NA,NA,Complete,KateRasheed
bsdb:33879267/5/2,33879267,laboratory experiment,33879267,10.1186/s40104-021-00573-3,NA,"Shang Q., Liu S., Liu H., Mahfuz S. , Piao X.","Impact of sugar beet pulp and wheat bran on serum biochemical profile, inflammatory responses and gut microbiota in sows during late gestation and lactation",Journal of animal science and biotechnology,2021,"Dietary fiber source, Gut microbiota, Inflammatory response, Serum biochemical profile, Sow",Experiment 5,China,Sus scrofa domesticus,Feces,UBERON:0001988,Diet,EFO:0002755,Control diet (CON) during gestation,Sugar beet pulp diet (SBP) during gestation,The Sows in this group were fed a 20% Sugar beet pulp diet during gestation.,5,5,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 10A,17 April 2025,Victoria,Victoria,"Relative abundance of significantly different phyla and genera on day 110 of gestation, between the Control (CON) and the sugar beet pulp (SBP) diet groups.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239|186801|3082720|186804|1505652;1783272|1239|186801|186802|31979|1485,Complete,KateRasheed
bsdb:33879267/6/1,33879267,laboratory experiment,33879267,10.1186/s40104-021-00573-3,NA,"Shang Q., Liu S., Liu H., Mahfuz S. , Piao X.","Impact of sugar beet pulp and wheat bran on serum biochemical profile, inflammatory responses and gut microbiota in sows during late gestation and lactation",Journal of animal science and biotechnology,2021,"Dietary fiber source, Gut microbiota, Inflammatory response, Serum biochemical profile, Sow",Experiment 6,China,Sus scrofa domesticus,Feces,UBERON:0001988,Diet,EFO:0002755,Control diet (CON) during gestation,Wheat bran diet (WB) during gestation,The Sows in this group were fed a 30% wheat bran diet during gestation.,5,5,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 10A,17 April 2025,Victoria,Victoria,"Relative abundance of significantly different phyla and genera on day 110 of gestation, between the Control (CON) and the wheat bran (WB) diet groups.",decreased,NA,NA,Complete,KateRasheed
bsdb:33879972/1/1,33879972,case-control,33879972,10.3164/jcbn.20-93,NA,"Sugitani Y., Inoue R., Inatomi O., Nishida A., Morishima S., Imai T., Kawahara M., Naito Y. , Andoh A.",Mucosa-associated gut microbiome in Japanese patients with functional constipation,Journal of clinical biochemistry and nutrition,2021,"butyrate, constipation, microbiota",Experiment 1,Japan,Homo sapiens,Mucus,NA,Chronic constipation,HP:0012450,Healthy controls,Patients with Functional constipation (FC),Male patients diagnosed with functional constipation according to the Rome IV criteria with average age of 71.4 years (37–84),14,15,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,age,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 2,17 March 2025,Tosin,Tosin,Comparative analyses of the taxonomic composition of the microbial community at the phylum level,increased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Svetlana up
bsdb:33879972/2/1,33879972,case-control,33879972,10.3164/jcbn.20-93,NA,"Sugitani Y., Inoue R., Inatomi O., Nishida A., Morishima S., Imai T., Kawahara M., Naito Y. , Andoh A.",Mucosa-associated gut microbiome in Japanese patients with functional constipation,Journal of clinical biochemistry and nutrition,2021,"butyrate, constipation, microbiota",Experiment 2,Japan,Homo sapiens,Mucus,NA,Chronic constipation,HP:0012450,Healthy controls,Patients with Functional constipation (FC),Male patients diagnosed with functional constipation according to the Rome IV criteria with average age of 71.4 years (37–84),14,15,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3,17 March 2025,Tosin,Tosin,Differential abundant taxa between the constipation group and healthy controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,p__Candidatus Saccharimonadota",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|1224|28216;3379134|1224|28216|80840|80864|283;3384189|32066|203490|203491|203492|848;1783272|1239|91061|186826|1300|1301;95818,Complete,Svetlana up
bsdb:33879972/2/2,33879972,case-control,33879972,10.3164/jcbn.20-93,NA,"Sugitani Y., Inoue R., Inatomi O., Nishida A., Morishima S., Imai T., Kawahara M., Naito Y. , Andoh A.",Mucosa-associated gut microbiome in Japanese patients with functional constipation,Journal of clinical biochemistry and nutrition,2021,"butyrate, constipation, microbiota",Experiment 2,Japan,Homo sapiens,Mucus,NA,Chronic constipation,HP:0012450,Healthy controls,Patients with Functional constipation (FC),Male patients diagnosed with functional constipation according to the Rome IV criteria with average age of 71.4 years (37–84),14,15,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3,17 March 2025,Tosin,Tosin,Differential abundant taxa between the constipation group and Healthy controls,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres,k__Pseudomonadati|p__Deferribacterota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",3379134|1224|1236|2887326|468|469;3379134|1224|28211;1783272|1239|186801|186802|216572|244127;1783272|1239|91061|1385;3379134|200930|68337|191393|191394;3379134|200930|68337|191393;3379134|200930|68337;3379134|200930;3379134|1224|1236|2887326|468;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|186802|216572|119852;1783272|201174|1760|85009|31957;1783272|201174|1760|85009|31957|1743;3379134|1224|1236|72274;3379134|1224|28211|766;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;3379134|1224;3379134|976|200643|171549|2005473,Complete,Svetlana up
bsdb:33894293/1/1,33894293,time series / longitudinal observational,33894293,10.1016/j.micpath.2021.104899,NA,"Gong X., Cai Q., Liu X., An D., Zhou D., Luo R., Peng R. , Hong Z.",Gut flora and metabolism are altered in epilepsy and partially restored after ketogenic diets,Microbial pathogenesis,2021,"16S RNA sequence, Epilepsy, Fecal microbiota, Ketogenic diets, Short chain fatty acids",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Epilepsy,EFO:0000474,Healthy Controls,Pre-ketogenic diet (KD1),Children with drug refractory epilepsy (DRE) before ketogenic diet (KD) treatment,12,12,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,age,NA,NA,NA,increased,unchanged,NA,NA,Signature 1,Figure 2,27 November 2024,Kavyaayala,"Kavyaayala,WikiWorks,Tosin",Fecal microbiome of (pre-ketogenic diet) KD1 group compared to Healthy controls,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacillati|p__Actinomycetota|c__Actinomycetes",3379134|74201|203494|48461|1647988;1783272|1239|91061;3379134|976|200643|171549|815;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|91061|186826;3379134|74201|203494|48461;3379134|74201|203494;1783272|201174|1760,Complete,KateRasheed
bsdb:33894293/1/2,33894293,time series / longitudinal observational,33894293,10.1016/j.micpath.2021.104899,NA,"Gong X., Cai Q., Liu X., An D., Zhou D., Luo R., Peng R. , Hong Z.",Gut flora and metabolism are altered in epilepsy and partially restored after ketogenic diets,Microbial pathogenesis,2021,"16S RNA sequence, Epilepsy, Fecal microbiota, Ketogenic diets, Short chain fatty acids",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Epilepsy,EFO:0000474,Healthy Controls,Pre-ketogenic diet (KD1),Children with drug refractory epilepsy (DRE) before ketogenic diet (KD) treatment,12,12,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,age,NA,NA,NA,increased,unchanged,NA,NA,Signature 2,Figure 2,27 November 2024,Kavyaayala,"Kavyaayala,WikiWorks,Tosin",Fecal microbiome of (pre-ketogenic diet) KD1 group compared to Healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|186802|216572,Complete,KateRasheed
bsdb:33894293/2/1,33894293,time series / longitudinal observational,33894293,10.1016/j.micpath.2021.104899,NA,"Gong X., Cai Q., Liu X., An D., Zhou D., Luo R., Peng R. , Hong Z.",Gut flora and metabolism are altered in epilepsy and partially restored after ketogenic diets,Microbial pathogenesis,2021,"16S RNA sequence, Epilepsy, Fecal microbiota, Ketogenic diets, Short chain fatty acids",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,Healthy controls,Post-ketogenic diet (KD2),Children with drug refractory epilepsy (DRE) after ketogenic diet (KD) treatment,12,12,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,NA,increased,unchanged,NA,NA,Signature 1,Figure 4E-H,27 November 2024,Kavyaayala,"Kavyaayala,WikiWorks,Tosin",Fecal microbiome of (Post-ketogenic diet) KD2 group compared to Healthy controls,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",3379134|976|200643|171549|171552|1283313;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|216572|1263,Complete,KateRasheed
bsdb:33894293/2/2,33894293,time series / longitudinal observational,33894293,10.1016/j.micpath.2021.104899,NA,"Gong X., Cai Q., Liu X., An D., Zhou D., Luo R., Peng R. , Hong Z.",Gut flora and metabolism are altered in epilepsy and partially restored after ketogenic diets,Microbial pathogenesis,2021,"16S RNA sequence, Epilepsy, Fecal microbiota, Ketogenic diets, Short chain fatty acids",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,Healthy controls,Post-ketogenic diet (KD2),Children with drug refractory epilepsy (DRE) after ketogenic diet (KD) treatment,12,12,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,NA,increased,unchanged,NA,NA,Signature 2,Figure 4A-D,27 November 2024,Kavyaayala,"Kavyaayala,WikiWorks,Tosin",Fecal microbiome of (Post-ketogenic diet) KD2 group compared to Healthy controls,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",1783272|201174|1760|2037|2049|1654;3379134|74201|203494|48461|1647988|239934;1783272|1239|91061|186826|81852|1350,Complete,KateRasheed
bsdb:33894293/3/1,33894293,time series / longitudinal observational,33894293,10.1016/j.micpath.2021.104899,NA,"Gong X., Cai Q., Liu X., An D., Zhou D., Luo R., Peng R. , Hong Z.",Gut flora and metabolism are altered in epilepsy and partially restored after ketogenic diets,Microbial pathogenesis,2021,"16S RNA sequence, Epilepsy, Fecal microbiota, Ketogenic diets, Short chain fatty acids",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Epilepsy,EFO:0000474,Healthy controls,Pre-ketogenic diet (KD1),Children with (drug refractory epilepsy) DRE before (ketogenic diet) KD treatment,12,12,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,NA,increased,unchanged,NA,NA,Signature 1,Figures 4A-D & 5A-C,6 December 2024,Kavyaayala,"Kavyaayala,WikiWorks,Tosin",Fecal microbiome of (pre-ketogenic diet) KD1 group compared to Healthy controls,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Mycoplasmatota",1783272|201174|1760|2037|2049|1654;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|81852|1350;1783272|544448,Complete,KateRasheed
bsdb:33894293/3/2,33894293,time series / longitudinal observational,33894293,10.1016/j.micpath.2021.104899,NA,"Gong X., Cai Q., Liu X., An D., Zhou D., Luo R., Peng R. , Hong Z.",Gut flora and metabolism are altered in epilepsy and partially restored after ketogenic diets,Microbial pathogenesis,2021,"16S RNA sequence, Epilepsy, Fecal microbiota, Ketogenic diets, Short chain fatty acids",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Epilepsy,EFO:0000474,Healthy controls,Pre-ketogenic diet (KD1),Children with (drug refractory epilepsy) DRE before (ketogenic diet) KD treatment,12,12,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,NA,increased,unchanged,NA,NA,Signature 2,Figures 4E-G & 5E-F,6 December 2024,Kavyaayala,"Kavyaayala,WikiWorks,Tosin",Fecal microbiome of (pre-ketogenic diet) KD1 group compared to Healthy controls,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae",3379134|976|200643|171549|171552|1283313;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|3082768|990719,Complete,KateRasheed
bsdb:33894293/5/1,33894293,time series / longitudinal observational,33894293,10.1016/j.micpath.2021.104899,NA,"Gong X., Cai Q., Liu X., An D., Zhou D., Luo R., Peng R. , Hong Z.",Gut flora and metabolism are altered in epilepsy and partially restored after ketogenic diets,Microbial pathogenesis,2021,"16S RNA sequence, Epilepsy, Fecal microbiota, Ketogenic diets, Short chain fatty acids",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,Healthy Controls,KD2 (post-ketogenic diet) responders,Children with (drug refractory epilepsy) DRE who were classified as having seizure reduction frequency greater than or equal to 50% after (ketogenic diet) KD treatment. Samples analyzed from (post-ketogenic diet) KD2 group.,12,8,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5D-F,7 December 2024,Kavyaayala,"Kavyaayala,WikiWorks,Tosin",Fecal microbiome of (post-ketogenic diet) KD2 responders compared to Healthy controls,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",3379134|976|200643|171549|171552|1283313;1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|216572|1263,Complete,KateRasheed
bsdb:33894293/6/1,33894293,time series / longitudinal observational,33894293,10.1016/j.micpath.2021.104899,NA,"Gong X., Cai Q., Liu X., An D., Zhou D., Luo R., Peng R. , Hong Z.",Gut flora and metabolism are altered in epilepsy and partially restored after ketogenic diets,Microbial pathogenesis,2021,"16S RNA sequence, Epilepsy, Fecal microbiota, Ketogenic diets, Short chain fatty acids",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,KD2 (Post-ketogenic diet) non responders,KD2 (Post-ketogenic diet) responders,Children with (drug refractory epilepsy) DRE who were classified as having seizure reduction frequency greater than or equal to 50% after (ketogenic diet) KD treatment. Samples analyzed from (post-ketogenic diet) KD2 group.,4,8,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Results Section 3.3 (Text),9 December 2024,Kavyaayala,"Kavyaayala,WikiWorks,Tosin",Fecal microbiome of (Post-ketogenic diet) KD2 responders compared to (Post-ketogenic diet) KD2 non responders,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium",1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|186806|1730,Complete,KateRasheed
bsdb:33894293/7/1,33894293,time series / longitudinal observational,33894293,10.1016/j.micpath.2021.104899,NA,"Gong X., Cai Q., Liu X., An D., Zhou D., Luo R., Peng R. , Hong Z.",Gut flora and metabolism are altered in epilepsy and partially restored after ketogenic diets,Microbial pathogenesis,2021,"16S RNA sequence, Epilepsy, Fecal microbiota, Ketogenic diets, Short chain fatty acids",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,KD1 (Pre-ketogenic diet) without gene mutation,KD2 (Post-ketogenic diet) without gene mutation,Children with (drug refractory epilepsy) DRE and without gene mutation after KD (ketogenic diet) treatment,7,7,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Results Section 3.3 (Text),9 December 2024,Kavyaayala,"Kavyaayala,WikiWorks,Tosin",Fecal microbiome of KD2 (Post-ketogenic diet) children without gene mutation compared to KD1 (Pre-ketogenic diet) children without gene mutation,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,1783272|1239|186801|3085636|186803|1649459,Complete,KateRasheed
bsdb:33894293/7/2,33894293,time series / longitudinal observational,33894293,10.1016/j.micpath.2021.104899,NA,"Gong X., Cai Q., Liu X., An D., Zhou D., Luo R., Peng R. , Hong Z.",Gut flora and metabolism are altered in epilepsy and partially restored after ketogenic diets,Microbial pathogenesis,2021,"16S RNA sequence, Epilepsy, Fecal microbiota, Ketogenic diets, Short chain fatty acids",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,KD1 (Pre-ketogenic diet) without gene mutation,KD2 (Post-ketogenic diet) without gene mutation,Children with (drug refractory epilepsy) DRE and without gene mutation after KD (ketogenic diet) treatment,7,7,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Results Section 3.3 (Text),2 May 2025,Tosin,Tosin,Fecal microbiome of KD2 (Post-ketogenic diet) children without gene mutation compared to KD1 (Pre-ketogenic diet) children without gene mutation,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae|g__Dactylosporangium,1783272|201174|1760|85008|28056|35753,Complete,KateRasheed
bsdb:33894293/8/1,33894293,time series / longitudinal observational,33894293,10.1016/j.micpath.2021.104899,NA,"Gong X., Cai Q., Liu X., An D., Zhou D., Luo R., Peng R. , Hong Z.",Gut flora and metabolism are altered in epilepsy and partially restored after ketogenic diets,Microbial pathogenesis,2021,"16S RNA sequence, Epilepsy, Fecal microbiota, Ketogenic diets, Short chain fatty acids",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,KD1 (Pre-ketogenic diet) with gene mutation,KD2 (Post-ketogenic diet) with gene mutation,Children with (drug refractory epilepsy) DRE and gene mutation after KD (ketogenic diet) treatment,5,5,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Results Section 3.3 (Text),9 December 2024,Kavyaayala,"Kavyaayala,WikiWorks,Tosin",Fecal microbiome of (Post-ketogenic diet) KD2 children with gene mutation compared to (Pre-ketogenic diet) KD1 children with gene mutation,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,3379134|976|200643|171549|2005525|375288,Complete,KateRasheed
bsdb:33894293/8/2,33894293,time series / longitudinal observational,33894293,10.1016/j.micpath.2021.104899,NA,"Gong X., Cai Q., Liu X., An D., Zhou D., Luo R., Peng R. , Hong Z.",Gut flora and metabolism are altered in epilepsy and partially restored after ketogenic diets,Microbial pathogenesis,2021,"16S RNA sequence, Epilepsy, Fecal microbiota, Ketogenic diets, Short chain fatty acids",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,KD1 (Pre-ketogenic diet) with gene mutation,KD2 (Post-ketogenic diet) with gene mutation,Children with (drug refractory epilepsy) DRE and gene mutation after KD (ketogenic diet) treatment,5,5,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Results Section 3.3 (Text),2 May 2025,Tosin,Tosin,Fecal microbiome of (Post-ketogenic diet) KD2 children with gene mutation compared to (Pre-ketogenic diet) KD1 children with gene mutation,decreased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Sulfurospirillaceae|g__Sulfurospirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",3379134|29547|3031852|213849|2932623|57665;3379134|976|200643|171549|2005525|195950,Complete,KateRasheed
bsdb:33903709/1/NA,33903709,"cross-sectional observational, not case-control",33903709,10.1038/s41598-021-88536-6,NA,"Braun T., Halevi S., Hadar R., Efroni G., Glick Saar E., Keller N., Amir A., Amit S. , Haberman Y.",SARS-CoV-2 does not have a strong effect on the nasopharyngeal microbial composition,Scientific reports,2021,NA,Experiment 1,Israel,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative patients,COVID-19 positive patients,SARS-CoV-2 presence by RT-PCR,29,26,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:33921182/1/1,33921182,case-control,33921182,10.3390/ijerph18084211,NA,"Wu Y.F., Lee W.F., Salamanca E., Yao W.L., Su J.N., Wang S.Y., Hu C.J. , Chang W.J.","Oral Microbiota Changes in Elderly Patients, an Indicator of Alzheimer's Disease",International journal of environmental research and public health,2021,"Alzheimer’s disease, dental hygiene, neuroscience/neurobiology, oral health, oral microbiota, plaque/plaque biofilms",Experiment 1,Taiwan,Homo sapiens,Dental plaque,UBERON:0016482,Alzheimer's disease,MONDO:0004975,Controls,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,18,17,2 months,16S,NA,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,12 December 2024,AaishahM,"AaishahM,WikiWorks",Comparison of relative abundance at the oral bacteria,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|976|200643;1783272|1239|91061|186826;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301,Complete,NA
bsdb:33921182/1/2,33921182,case-control,33921182,10.3390/ijerph18084211,NA,"Wu Y.F., Lee W.F., Salamanca E., Yao W.L., Su J.N., Wang S.Y., Hu C.J. , Chang W.J.","Oral Microbiota Changes in Elderly Patients, an Indicator of Alzheimer's Disease",International journal of environmental research and public health,2021,"Alzheimer’s disease, dental hygiene, neuroscience/neurobiology, oral health, oral microbiota, plaque/plaque biofilms",Experiment 1,Taiwan,Homo sapiens,Dental plaque,UBERON:0016482,Alzheimer's disease,MONDO:0004975,Controls,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,18,17,2 months,16S,NA,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,12 December 2024,AaishahM,"AaishahM,WikiWorks",Comparison of relative abundance at the oral bacteria,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium",3384189|32066|203490;3384189|32066|203490|203491;3379134|1224|1236|135615;3384189|32066|203490|203491|203492;3379134|976|200643|171549|171551;3379134|1224|1236|135615|868;3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|171551|836;3379134|1224|1236|135615|868|2717,Complete,NA
bsdb:33921182/2/1,33921182,case-control,33921182,10.3390/ijerph18084211,NA,"Wu Y.F., Lee W.F., Salamanca E., Yao W.L., Su J.N., Wang S.Y., Hu C.J. , Chang W.J.","Oral Microbiota Changes in Elderly Patients, an Indicator of Alzheimer's Disease",International journal of environmental research and public health,2021,"Alzheimer’s disease, dental hygiene, neuroscience/neurobiology, oral health, oral microbiota, plaque/plaque biofilms",Experiment 2,Taiwan,Homo sapiens,Dental plaque,UBERON:0016482,Alzheimer's disease,MONDO:0004975,Controls,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,18,17,2 months,16S,NA,NA,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,12 December 2024,AaishahM,"AaishahM,WikiWorks",Differentially abundant taxa in the AD and control groups,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061|186826;1783272|1239|91061|186826|1300;1783272|1239|91061|186826;1783272|1239|91061;1783272|1239|186801|3085636|186803|177971;1783272|1239|91061|186826|1300|1301,Complete,NA
bsdb:33921182/2/2,33921182,case-control,33921182,10.3390/ijerph18084211,NA,"Wu Y.F., Lee W.F., Salamanca E., Yao W.L., Su J.N., Wang S.Y., Hu C.J. , Chang W.J.","Oral Microbiota Changes in Elderly Patients, an Indicator of Alzheimer's Disease",International journal of environmental research and public health,2021,"Alzheimer’s disease, dental hygiene, neuroscience/neurobiology, oral health, oral microbiota, plaque/plaque biofilms",Experiment 2,Taiwan,Homo sapiens,Dental plaque,UBERON:0016482,Alzheimer's disease,MONDO:0004975,Controls,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,18,17,2 months,16S,NA,NA,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5,12 December 2024,AaishahM,"AaishahM,WikiWorks",Differentially abundant taxa in the AD and control groups,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Rhodocyclaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",3379134|976|200643|171549|171551;3384189|32066|203490|203491|203492;3379134|1224|28216|206389|75787;3379134|1224|28216|206389;3379134|1224|1236|135615|868;3379134|1224|1236|135615;3379134|1224|1236|135615|868|2717;3379134|976|200643|171549|2005525|195950;3379134|976|200643|171549|171552|1283313;3384189|32066|203490|203491|203492|848,Complete,NA
bsdb:33924396/1/1,33924396,"cross-sectional observational, not case-control",33924396,10.3390/nu13041272,NA,"Ramasamy B., Magne F., Tripathy S.K., Venugopal G., Mukherjee D. , Balamurugan R.",Association of Gut Microbiome and Vitamin D Deficiency in Knee Osteoarthritis Patients: A Pilot Study,Nutrients,2021,"gut microbiome, knee osteoarthritis, vitamin D",Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,"Osteoarthritis, knee",EFO:0004616,Normal Vitamin D status,Knee osteroarthritis,Knee osteoarthritis,6,4,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2, text",30 November 2021,Tislam,"Tislam,Fatima,WikiWorks",A histogram of the log 10 transformed Linear discriminant analysis (LDA) scores was computed for features that showed differential abundance between healthy subjects and KOA patients.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",1783272|1239|186801|186802|216572|52784;3379134|976|200643|171549|171551,Complete,Fatima
bsdb:33924396/1/2,33924396,"cross-sectional observational, not case-control",33924396,10.3390/nu13041272,NA,"Ramasamy B., Magne F., Tripathy S.K., Venugopal G., Mukherjee D. , Balamurugan R.",Association of Gut Microbiome and Vitamin D Deficiency in Knee Osteoarthritis Patients: A Pilot Study,Nutrients,2021,"gut microbiome, knee osteoarthritis, vitamin D",Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,"Osteoarthritis, knee",EFO:0004616,Normal Vitamin D status,Knee osteroarthritis,Knee osteoarthritis,6,4,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2, text",30 November 2021,Tislam,"Tislam,Fatima,WikiWorks",A histogram of the log 10 transformed Linear discriminant analysis (LDA) scores was computed for features that showed differential abundance between healthy subjects and KOA patients.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shimwellia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",1783272|1239|186801|186802|1392389;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|186802|186807|2740;1783272|201174|1760|85009|31957|1743;3379134|1224|1236|91347|543|1335483;1783272|201174|84998|84999|84107;1783272|1239|526524|526525|128827,Complete,Fatima
bsdb:33924396/2/1,33924396,"cross-sectional observational, not case-control",33924396,10.3390/nu13041272,NA,"Ramasamy B., Magne F., Tripathy S.K., Venugopal G., Mukherjee D. , Balamurugan R.",Association of Gut Microbiome and Vitamin D Deficiency in Knee Osteoarthritis Patients: A Pilot Study,Nutrients,2021,"gut microbiome, knee osteoarthritis, vitamin D",Experiment 2,India,Homo sapiens,Feces,UBERON:0001988,"Osteoarthritis, knee",EFO:0004616,Vitamin D deficiency,Knee osteroarthritis with vit D deficiency,Knee osteoarthritis,7,7,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3,9 March 2022,Fatima,"Fatima,WikiWorks",differential abundance between KOA_VDD and VDD patients.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|3085636|186803|265975;3379134|976|200643|171549|171552|838,Complete,Fatima
bsdb:33924396/2/2,33924396,"cross-sectional observational, not case-control",33924396,10.3390/nu13041272,NA,"Ramasamy B., Magne F., Tripathy S.K., Venugopal G., Mukherjee D. , Balamurugan R.",Association of Gut Microbiome and Vitamin D Deficiency in Knee Osteoarthritis Patients: A Pilot Study,Nutrients,2021,"gut microbiome, knee osteoarthritis, vitamin D",Experiment 2,India,Homo sapiens,Feces,UBERON:0001988,"Osteoarthritis, knee",EFO:0004616,Vitamin D deficiency,Knee osteroarthritis with vit D deficiency,Knee osteoarthritis,7,7,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3,9 March 2022,Fatima,"Fatima,WikiWorks",differential abundance between KOA_VDD and VDD patients.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium",3379134|976|200643|171549|1853231|574697;95818|2093818|2093825|2171986|1331051;3379134|1224|28216|80840|80864|80865;1783272|201174|84998|1643822|1643826|644652;3379134|976|200643|171549|2005525|375288;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171551;1783272|201174|84998|84999|84107;1783272|1239|186801|186802|1898207,Complete,Fatima
bsdb:33925708/1/1,33925708,case-control,33925708,10.3390/ijms22094608,NA,"Lee S.R., Lee J.C., Kim S.H., Oh Y.S., Chae H.D., Seo H., Kang C.S. , Shin T.S.",Altered Composition of Microbiota in Women with Ovarian Endometrioma: Microbiome Analyses of Extracellular Vesicles in the Peritoneal Fluid,International journal of molecular sciences,2021,"16S rDNA, endometriosis, extracellular vesicles, microbiome",Experiment 1,South Korea,Homo sapiens,Uterovesical pouch,UBERON:0011049,Endometriosis,EFO:0001065,Surgical controls,Stage 3/4 endometriosis patients,Stage 3/4 endometriosis patients that were diagnosed with endometriosis via laparoscopic surgery; stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).,45,45,3 months,16S,34,Illumina,NA,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 1 and Results section,9 August 2021,Samara.Khan,"Samara.Khan,Claregrieve1,WikiWorks",Differential microbial abundance between peritoneal fluid samples among women with endometriosis when compared to surgical controls.,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|201174;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;1783272|201174|1760|85009|31957;1783272|201174|1760|85009|31957|1743;1783272|201174|1760|85006|1268|32207;1783272|1239|909932|1843489|31977,Complete,Claregrieve1
bsdb:33925708/1/2,33925708,case-control,33925708,10.3390/ijms22094608,NA,"Lee S.R., Lee J.C., Kim S.H., Oh Y.S., Chae H.D., Seo H., Kang C.S. , Shin T.S.",Altered Composition of Microbiota in Women with Ovarian Endometrioma: Microbiome Analyses of Extracellular Vesicles in the Peritoneal Fluid,International journal of molecular sciences,2021,"16S rDNA, endometriosis, extracellular vesicles, microbiome",Experiment 1,South Korea,Homo sapiens,Uterovesical pouch,UBERON:0011049,Endometriosis,EFO:0001065,Surgical controls,Stage 3/4 endometriosis patients,Stage 3/4 endometriosis patients that were diagnosed with endometriosis via laparoscopic surgery; stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).,45,45,3 months,16S,34,Illumina,NA,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table 1 and Results section,9 August 2021,Samara.Khan,"Samara.Khan,Claregrieve1,WikiWorks",Differential microbial abundance between peritoneal fluid samples among women with endometriosis when compared to surgical controls.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|1224|1236|2887326|468|469;3379134|1224|28211|356|212791;3379134|1224|1236|72274|135621;3379134|1224|1236|72274;3379134|1224|1236|72274|135621|286;1783272|1239|91061|186826|1300|1301,Complete,Claregrieve1
bsdb:33927704/1/1,33927704,case-control,33927704,10.3389/fmicb.2021.646361,https://pubmed.ncbi.nlm.nih.gov/33927704/,"Yuan L., Wang W., Zhang W., Zhang Y., Wei C., Li J. , Zhou D.",Gut Microbiota in Untreated Diffuse Large B Cell Lymphoma Patients,Frontiers in microbiology,2021,"16S rRNA, diffuse large B cell lymphoma, gut microbiota, hematologic malignancies, proteobacteria",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Diffuse large B-cell lymphoma,EFO:0000403,Control group (CG),Experimental Group (EG),Patients who were diagnosed with untreated diffuse large B-cell lymphoma (DLBCL),26,25,1 month,16S,34,Illumina,relative abundances,Linear Discriminant Analysis,NA,TRUE,NA,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 2C, Figure 2D, Figure S1, Figure S2",29 January 2026,Temmie,Temmie,"Floral differences in the phylum, class, order, family, genus, and species between the experimental group of untreated DLBCL patients and healthy controls.",increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium butyricum",1783272|1239;1783272|201174|1760|85004|31953|1678;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|561|562;3379134|1224|1236;3379134|1224;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|186802|31979|1485|1492,Complete,NA
bsdb:33927704/1/2,33927704,case-control,33927704,10.3389/fmicb.2021.646361,https://pubmed.ncbi.nlm.nih.gov/33927704/,"Yuan L., Wang W., Zhang W., Zhang Y., Wei C., Li J. , Zhou D.",Gut Microbiota in Untreated Diffuse Large B Cell Lymphoma Patients,Frontiers in microbiology,2021,"16S rRNA, diffuse large B cell lymphoma, gut microbiota, hematologic malignancies, proteobacteria",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Diffuse large B-cell lymphoma,EFO:0000403,Control group (CG),Experimental Group (EG),Patients who were diagnosed with untreated diffuse large B-cell lymphoma (DLBCL),26,25,1 month,16S,34,Illumina,relative abundances,Linear Discriminant Analysis,NA,TRUE,NA,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 2C, Figure 2D, Figure S1, Figure S2",30 January 2026,Temmie,Temmie,"Floral differences in the phylum, class, order, family, genus, and species between the experimental group of untreated DLBCL patients and healthy controls",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus garvieae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",3379134|976|200643|171549|815|816;3379134|976|200643;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|841;1783272|1239|91061|186826|1300|1357|1363;3379134|976|200643|171549|815|816|817;1783272|1239|909932|1843489|31977|39948,Complete,NA
bsdb:33935458/1/1,33935458,case-control,33935458,10.5021/ad.2021.33.2.163,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8082000/,"Hur M.S., Lee J.S., Jang M., Shin H.J. , Lee Y.W.",Analysis of the Conjunctival Microbiome in Patients with Atopic Keratoconjunctivitis and Healthy Individuals,Annals of dermatology,2021,"Atopic keratoconjunctivitis, Atopy, Dysbiosis, Microbiota",Experiment 1,South Korea,Homo sapiens,Ocular surface region,UBERON:0010409,Keratoconjunctivitis,MONDO:0004768,Healthy controls,Atopic keratoconjunctivitis (AKC),"Patients diagnosed with Atopic keratoconjunctivitis (AKC) by an ophthalmologist, and with no systemic immune-associated diseases.",10,20,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 2,22 June 2023,Andre,"Andre,WikiWorks",Relative abundance of genus composition,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",3379134|1224|1236|72274|135621|286;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|135625|712|724,Complete,Chloe
bsdb:33935458/1/2,33935458,case-control,33935458,10.5021/ad.2021.33.2.163,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8082000/,"Hur M.S., Lee J.S., Jang M., Shin H.J. , Lee Y.W.",Analysis of the Conjunctival Microbiome in Patients with Atopic Keratoconjunctivitis and Healthy Individuals,Annals of dermatology,2021,"Atopic keratoconjunctivitis, Atopy, Dysbiosis, Microbiota",Experiment 1,South Korea,Homo sapiens,Ocular surface region,UBERON:0010409,Keratoconjunctivitis,MONDO:0004768,Healthy controls,Atopic keratoconjunctivitis (AKC),"Patients diagnosed with Atopic keratoconjunctivitis (AKC) by an ophthalmologist, and with no systemic immune-associated diseases.",10,20,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 1+ 2,22 June 2023,Andre,"Andre,Chloe,WikiWorks",Relative abundance of phylum and genus composition,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,",3379134|1224|28216|80840|119060|48736;1783272|201174|1760|85004|31953|1678;3379134|1224|1236|91347|1903414|583;,Complete,Chloe
bsdb:33935458/1/3,33935458,case-control,33935458,10.5021/ad.2021.33.2.163,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8082000/,"Hur M.S., Lee J.S., Jang M., Shin H.J. , Lee Y.W.",Analysis of the Conjunctival Microbiome in Patients with Atopic Keratoconjunctivitis and Healthy Individuals,Annals of dermatology,2021,"Atopic keratoconjunctivitis, Atopy, Dysbiosis, Microbiota",Experiment 1,South Korea,Homo sapiens,Ocular surface region,UBERON:0010409,Keratoconjunctivitis,MONDO:0004768,Healthy controls,Atopic keratoconjunctivitis (AKC),"Patients diagnosed with Atopic keratoconjunctivitis (AKC) by an ophthalmologist, and with no systemic immune-associated diseases.",10,20,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 3,Table 1,23 June 2023,Andre,"Andre,WikiWorks",Relative abundance of phylum composition,decreased,NA,NA,Complete,NA
bsdb:33947803/1/1,33947803,"case-control,meta-analysis",33947803,10.1128/mSystems.00112-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8269207/,"Jiang P., Wu S., Luo Q., Zhao X.M. , Chen W.H.",Metagenomic Analysis of Common Intestinal Diseases Reveals Relationships among Microbial Signatures and Powers Multidisease Diagnostic Models,mSystems,2021,"gut dysbiosis, human microbiome, intestinal disease, machine learning-based disease classification, noninvasive disease diagnosis",Experiment 1,NA,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Non disease controls,CRC patients,Patients diagnosed with colorectal cancer,632,354,NA,16S,NA,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 1,24 January 2022,Itslanapark,"Itslanapark,Peace Sandy,WikiWorks","Disease-specific and shared microbial markers showed distinct prevalence profiles in patients and controls. (A) Microbial markers and their trends (i.e., case- or control-enriched) in common intestinal diseases. Species significantly enriched in cases (or controls) of corresponding disease in meta-analysis are shown (fdr < 0.05 in meta-analysis, Benjamini-Hochberg FDR correction), with their phylum shown on top. Red indicates case-enriched species and blue indicates control-enriched ones.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 5_1_63FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter laneus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__[Bacteroides] pectinophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|658089;1783272|1239|186801|3085636|186803|841|166486;1783272|201174|1760|85004|31953|1678|1680;3379134|976|200643|171549|815|816|291645;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|816|46506;3379134|976|200643|171549|2030927;3379134|976|200643|171549|1853231|283168|626933;3379134|976|200643|171549|2005525|375288|328812;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|171550|239759|1288121;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|815|816|246787;3379134|976|200643|171549|815|816|818;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|186802|384638;1783272|1239|186801|186802|216572|39492;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|3085636|186803|2316020|46228;1783272|1239|186801|3085636|186803|2941495|1512;1783272|1239|186801|3085636|186803|1898203;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|292632;1783272|1239|909932|909929|1843491|158846|158847;1783272|1239|909932|909929|1843491|158846,Complete,Peace Sandy
bsdb:33947803/1/2,33947803,"case-control,meta-analysis",33947803,10.1128/mSystems.00112-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8269207/,"Jiang P., Wu S., Luo Q., Zhao X.M. , Chen W.H.",Metagenomic Analysis of Common Intestinal Diseases Reveals Relationships among Microbial Signatures and Powers Multidisease Diagnostic Models,mSystems,2021,"gut dysbiosis, human microbiome, intestinal disease, machine learning-based disease classification, noninvasive disease diagnosis",Experiment 1,NA,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Non disease controls,CRC patients,Patients diagnosed with colorectal cancer,632,354,NA,16S,NA,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 1,25 January 2022,Itslanapark,"Itslanapark,Aiyshaaaa,Peace Sandy,WikiWorks","Disease-specific and shared microbial markers showed distinct prevalence profiles in patients and controls. (A) Microbial markers and their trends (i.e., case- or control-enriched) in common intestinal diseases. Species significantly enriched in cases (or controls) of corresponding disease in meta-analysis are shown (fdr < 0.05 in meta-analysis, Benjamini-Hochberg FDR correction), with their phylum shown on top. Red indicates case-enriched species and blue indicates control-enriched ones.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes ihumii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium 1_7_47FAA,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio desulfuricans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 2_2_44A,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 3_1_57FAA_CT1,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 7_1_58FAA,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D16,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia sp.,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp. 4_3_54A2FAA,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes|s__Synergistes sp. 3_1_syn1,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes",3379134|976|200643|171549|171550|239759|1470347;3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|171552|1283313|76122;1783272|1239|186801|186802|216572|244127|169435;1783272|1239|186801|186802|216572|244127|1872531;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|291644;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|186802|457421;3379134|200940|3031449|213115|194924|872|876;1783272|1239|186801|3085636|186803|2719313|333367;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|2719313|358743;1783272|1239|526524|526525|128827|457422;3384189|32066|203490|203491|203492|848|851;1783272|1239|91061|1385|539738|1378|29391;1783272|1239|91061|186826|186828|117563|46124;1783272|1239|186801|3085636|186803|1649459|154046;1783272|1239|186801|3085636|186803|658086;1783272|1239|186801|3085636|186803|658087;1783272|1239|909932|1843489|31977|906|2023260;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|1239|1737404|1737405|1570339|543311|1944660;1783272|1239|186801|3082720|186804|1257|1261;1783272|1239|186801|3082720|186804|1257|1262;1783272|1239|186801|3082720|186804|1257|341694;3379134|976|200643|171549|171551|836|28123;3379134|976|200643|171549|171551|836|322095;3379134|976|200643|171549|171551|836|281920;3379134|976|200643|171549|171552|838|28131;1783272|1239|186801|186802|216572|552398;1783272|201174|84998|1643822|1643826|84108|2049041;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|186801|186802|216572|292632|665956;3384194|508458|649775|649776|649777|2753|457415;1783272|1239|186801|186802|31979|1485|1522;1783272|1239|186801|3085636|186803|2941495|1512;1783272|1239|186801|3085636|186803|2316020|33039;3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|171550|239759|1872444;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|186801|186802|1898207;1783272|1239|1737404|1737405|1570339|165779|33037;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|906;3379134|1224|1236|91347|543|544|546;3379134|1224|1236|91347|543|544|1896336;3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|543|570|571;3379134|1224|1236|91347|543|570|576;3384194|508458|649775|649776|649777|2753,Complete,Peace Sandy
bsdb:33949151/1/1,33949151,"cross-sectional observational, not case-control",33949151,10.1002/art.41780,NA,"Kroese J.M., Brandt B.W., Buijs M.J., Crielaard W., Lobbezoo F., Loos B.G., van Boheemen L., van Schaardenburg D., Zaura E. , Volgenant C.M.C.",Differences in the Oral Microbiome in Patients With Early Rheumatoid Arthritis and Individuals at Risk of Rheumatoid Arthritis Compared to Healthy Individuals,"Arthritis & rheumatology (Hoboken, N.J.)",2021,NA,Experiment 1,Netherlands,Homo sapiens,Saliva,UBERON:0001836,Arthritis,EFO:0005856,healthy control,Early Rheumatoid Arthritis,Early Rheumatoid Arthritis patients (diagnosed within the previous year),50,50,3 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary  Table 3,9 November 2022,Tislam,"Tislam,Atrayees,WikiWorks","Saliva: a summary of the most significant zero-radius operational taxonomic units (zOTUs) that differentiated among the early rheumatoid arthritis (RA) group, at-risk group, and control group, sorted on linear discriminant analysis (LDA) score per group. Differences in relative abundance among the groups were tested with a Kruskal-Wallis test (false discovery rate corrected level of significance of 0.02), and post-hoc Mann-Whitney U tests. Results for zOTUs with a median relative abundance ≥0.01 for ≥1 group are marked with an outline.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis|s__Streptococcus oralis subsp. dentisani,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis",3379134|976|200643|171549|171551|836|1583331;3384189|32066|203490|203491|203492|848|860;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|909932|1843489|31977|29465;3379134|976|200643|171549|171552|2974257|425941;3379134|976|200643|171549|171552|1283313;1783272|1239|91061|186826|186828|117563;3379134|1224|28216|206351|481|482|484;3379134|1224|28216|206351|481|482|28449;1783272|1239|91061|186826|1300|1301|1303|1458253;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|91061|186826|1300|1301|68892;1783272|1239|91061|186826|1300|1301|28037,Complete,Atrayees
bsdb:33949151/1/2,33949151,"cross-sectional observational, not case-control",33949151,10.1002/art.41780,NA,"Kroese J.M., Brandt B.W., Buijs M.J., Crielaard W., Lobbezoo F., Loos B.G., van Boheemen L., van Schaardenburg D., Zaura E. , Volgenant C.M.C.",Differences in the Oral Microbiome in Patients With Early Rheumatoid Arthritis and Individuals at Risk of Rheumatoid Arthritis Compared to Healthy Individuals,"Arthritis & rheumatology (Hoboken, N.J.)",2021,NA,Experiment 1,Netherlands,Homo sapiens,Saliva,UBERON:0001836,Arthritis,EFO:0005856,healthy control,Early Rheumatoid Arthritis,Early Rheumatoid Arthritis patients (diagnosed within the previous year),50,50,3 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplementary  Table 3,9 November 2022,Tislam,"Tislam,Atrayees,WikiWorks","Saliva: a summary of the most significant zero-radius operational taxonomic units (zOTUs) that differentiated among the early rheumatoid arthritis (RA) group, at-risk group, and control group, sorted on linear discriminant analysis (LDA) score per group. Differences in relative abundance among the groups were tested with a Kruskal-Wallis test (false discovery rate corrected level of significance of 0.02), and post-hoc Mann-Whitney U tests. Results for zOTUs with a median relative abundance ≥0.01 for ≥1 group are marked with an outline.",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus downei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sobrinus",1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|1300|1301|1343;1783272|1239|91061|186826|1300|1301|1305;3379134|976|200643|171549|171552|2974251|228604;1783272|1239|91061|186826|1300|1301;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|909932|909929|1843491|970;1783272|1239|91061|186826|1300|1301|1317;1783272|1239|91061|186826|1300|1301|1310,Complete,Atrayees
bsdb:33957990/1/1,33957990,laboratory experiment,33957990,10.1186/s40168-021-01046-5,NA,"Han Q., Wang J., Li W., Chen Z.J. , Du Y.",Androgen-induced gut dysbiosis disrupts glucolipid metabolism and endocrinal functions in polycystic ovary syndrome,Microbiome,2021,"16S rRNA gene sequence, Faecal microbiota transplantation, Gut microbiota, Metabolome, Polycystic ovary syndrome",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Phosphate buffer saline (PBS),Dehydroepiandrosterone (DHEA),Rats in this group were injected subcutaneously with DHEA (6 mg/100 g bodyweight) daily for 35 days to induce polycystic ovary syndrome (PCOS).,6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Additional file 1: Figure S1d & e,7 August 2025,Victoria,Victoria,Cladogram and Linear Discriminant Analysis (LDA) score bar plot of differentially abundant taxa enriched in the phosphate buffer saline (PBS) group.,decreased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",1783272|201174|84992;1783272|201174;1783272|1239|186801|186802|186806|264995;1783272|1239|186801|186802|31979|1485;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|526524|526525|2810281|191303,Complete,KateRasheed
bsdb:33957990/2/1,33957990,laboratory experiment,33957990,10.1186/s40168-021-01046-5,NA,"Han Q., Wang J., Li W., Chen Z.J. , Du Y.",Androgen-induced gut dysbiosis disrupts glucolipid metabolism and endocrinal functions in polycystic ovary syndrome,Microbiome,2021,"16S rRNA gene sequence, Faecal microbiota transplantation, Gut microbiota, Metabolome, Polycystic ovary syndrome",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,t-Phosphate buffer saline (t-PBS),t-Dehydroepiandrosterone (t-DHEA),Faecal microbiota transplant (FMT) recipient rats from the Dehydroepiandrosterone (DHEA) group.,6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3d and e,7 August 2025,Victoria,Victoria,Cladogram and bar plot of LEfSe analysis showed taxa contribution to group separation. Taxa with an LDA score > 2 were displayed.,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma",1783272|1239|526524|526525;1783272|1239|526524|526525|128827;1783272|1239|526524;1783272|544448|31969|186332|186333;1783272|544448|31969|186332;1783272|544448|31969;1783272|544448;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|1643824|133925;1783272|544448|31969|186332|186333|2086,Complete,KateRasheed
bsdb:33957990/3/1,33957990,laboratory experiment,33957990,10.1186/s40168-021-01046-5,NA,"Han Q., Wang J., Li W., Chen Z.J. , Du Y.",Androgen-induced gut dysbiosis disrupts glucolipid metabolism and endocrinal functions in polycystic ovary syndrome,Microbiome,2021,"16S rRNA gene sequence, Faecal microbiota transplantation, Gut microbiota, Metabolome, Polycystic ovary syndrome",Experiment 3,China,Rattus norvegicus,Feces,UBERON:0001988,Glucose tolerance test,EFO:0004307,Low glucose tolerance,High glucose tolerance,Rats in this group had high glucose tolerance.,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3h,8 August 2025,Victoria,Victoria,Heat map of the Spearman’s rho correlation test presenting the association between genus-level microbes and clinical parameters.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,1783272|1239|186801|186802|3085642|580596,Complete,KateRasheed
bsdb:33957990/3/2,33957990,laboratory experiment,33957990,10.1186/s40168-021-01046-5,NA,"Han Q., Wang J., Li W., Chen Z.J. , Du Y.",Androgen-induced gut dysbiosis disrupts glucolipid metabolism and endocrinal functions in polycystic ovary syndrome,Microbiome,2021,"16S rRNA gene sequence, Faecal microbiota transplantation, Gut microbiota, Metabolome, Polycystic ovary syndrome",Experiment 3,China,Rattus norvegicus,Feces,UBERON:0001988,Glucose tolerance test,EFO:0004307,Low glucose tolerance,High glucose tolerance,Rats in this group had high glucose tolerance.,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3h,8 August 2025,Victoria,Victoria,Heat map of the Spearman’s rho correlation test presenting the association between genus-level microbes and clinical parameters.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,1783272|1239|186801|186802|31979|1485,Complete,KateRasheed
bsdb:33957990/4/1,33957990,laboratory experiment,33957990,10.1186/s40168-021-01046-5,NA,"Han Q., Wang J., Li W., Chen Z.J. , Du Y.",Androgen-induced gut dysbiosis disrupts glucolipid metabolism and endocrinal functions in polycystic ovary syndrome,Microbiome,2021,"16S rRNA gene sequence, Faecal microbiota transplantation, Gut microbiota, Metabolome, Polycystic ovary syndrome",Experiment 4,China,Rattus norvegicus,Feces,UBERON:0001988,Fasting blood glucose measurement,EFO:0004465,Low fasting blood glucose level,High fasting blood glucose level,Rats in this group had high fasting blood glucose levels.,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3h,8 August 2025,Victoria,Victoria,Heat map of the Spearman’s rho correlation test presenting the association between genus-level microbes and clinical parameters.,increased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum",1783272|544448|31969|186332|186333|2086;1783272|1239|91061|186826|33958|1578;3379134|200930|68337|191393|2945020|248038,Complete,KateRasheed
bsdb:33957990/4/2,33957990,laboratory experiment,33957990,10.1186/s40168-021-01046-5,NA,"Han Q., Wang J., Li W., Chen Z.J. , Du Y.",Androgen-induced gut dysbiosis disrupts glucolipid metabolism and endocrinal functions in polycystic ovary syndrome,Microbiome,2021,"16S rRNA gene sequence, Faecal microbiota transplantation, Gut microbiota, Metabolome, Polycystic ovary syndrome",Experiment 4,China,Rattus norvegicus,Feces,UBERON:0001988,Fasting blood glucose measurement,EFO:0004465,Low fasting blood glucose level,High fasting blood glucose level,Rats in this group had high fasting blood glucose levels.,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3h,8 August 2025,Victoria,Victoria,Heat map of the Spearman’s rho correlation test presenting the association between genus-level microbes and clinical parameters.,decreased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|216572|44748;3379134|1224|28216|80840|995019|40544;3379134|976|200643|171549|815|816;1783272|1239|526524|526525|128827,Complete,KateRasheed
bsdb:33957990/5/1,33957990,laboratory experiment,33957990,10.1186/s40168-021-01046-5,NA,"Han Q., Wang J., Li W., Chen Z.J. , Du Y.",Androgen-induced gut dysbiosis disrupts glucolipid metabolism and endocrinal functions in polycystic ovary syndrome,Microbiome,2021,"16S rRNA gene sequence, Faecal microbiota transplantation, Gut microbiota, Metabolome, Polycystic ovary syndrome",Experiment 5,China,Rattus norvegicus,Feces,UBERON:0001988,Hormone measurement,EFO:0004730,Low Luteinising hormone/ Follicle-stimulating hormone,High Luteinising hormone/ Follicle-stimulating hormone,Rats in this group had high Luteinising hormone/ Follicle-stimulating hormone levels.,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3h,8 August 2025,Victoria,Victoria,Heat map of the Spearman’s rho correlation test presenting the association between genus-level microbes and clinical parameters.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,1783272|1239|186801|3082720|186804|1501226,Complete,KateRasheed
bsdb:33957990/6/1,33957990,laboratory experiment,33957990,10.1186/s40168-021-01046-5,NA,"Han Q., Wang J., Li W., Chen Z.J. , Du Y.",Androgen-induced gut dysbiosis disrupts glucolipid metabolism and endocrinal functions in polycystic ovary syndrome,Microbiome,2021,"16S rRNA gene sequence, Faecal microbiota transplantation, Gut microbiota, Metabolome, Polycystic ovary syndrome",Experiment 6,China,Rattus norvegicus,Feces,UBERON:0001988,Follicle stimulating hormone measurement,EFO:0004768,Low Follicle-stimulating hormone,High Follicle-stimulating hormone,Rats in this group had high Follicle-stimulating hormone levels.,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3h,8 August 2025,Victoria,Victoria,Heat map of the Spearman’s rho correlation test presenting the association between genus-level microbes and clinical parameters.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239|186801|186802|216572|244127;33090|35493|3398|72025|3803|3814|508215;1783272|201174|84998|84999|1643824|133925;1783272|1239|186801|186802|31979|1485,Complete,KateRasheed
bsdb:33957990/7/1,33957990,laboratory experiment,33957990,10.1186/s40168-021-01046-5,NA,"Han Q., Wang J., Li W., Chen Z.J. , Du Y.",Androgen-induced gut dysbiosis disrupts glucolipid metabolism and endocrinal functions in polycystic ovary syndrome,Microbiome,2021,"16S rRNA gene sequence, Faecal microbiota transplantation, Gut microbiota, Metabolome, Polycystic ovary syndrome",Experiment 7,China,Rattus norvegicus,Feces,UBERON:0001988,Luteinizing hormone measurement,EFO:0007002,Low Luteinising hormone,High Luteinising hormone,Rats in this group had high Luteinising hormone levels.,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3h,8 August 2025,Victoria,Victoria,Heat map of the Spearman’s rho correlation test presenting the association between genus-level microbes and clinical parameters.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia",1783272|1239|91061|186826|81852|1350;33090|35493|3398|72025|3803|3814|508215,Complete,KateRasheed
bsdb:33957990/8/1,33957990,laboratory experiment,33957990,10.1186/s40168-021-01046-5,NA,"Han Q., Wang J., Li W., Chen Z.J. , Du Y.",Androgen-induced gut dysbiosis disrupts glucolipid metabolism and endocrinal functions in polycystic ovary syndrome,Microbiome,2021,"16S rRNA gene sequence, Faecal microbiota transplantation, Gut microbiota, Metabolome, Polycystic ovary syndrome",Experiment 8,China,Rattus norvegicus,Feces,UBERON:0001988,Free androgen index,EFO:0007005,Low Free androgen index,High Free androgen index,Rats in this group had high Free androgen index levels.,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3h,8 August 2025,Victoria,Victoria,Heat map of the Spearman’s rho correlation test presenting the association between genus-level microbes and clinical parameters.,decreased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,1783272|201174|84998|84999|1643824|133925,Complete,KateRasheed
bsdb:33957990/9/1,33957990,laboratory experiment,33957990,10.1186/s40168-021-01046-5,NA,"Han Q., Wang J., Li W., Chen Z.J. , Du Y.",Androgen-induced gut dysbiosis disrupts glucolipid metabolism and endocrinal functions in polycystic ovary syndrome,Microbiome,2021,"16S rRNA gene sequence, Faecal microbiota transplantation, Gut microbiota, Metabolome, Polycystic ovary syndrome",Experiment 9,China,Rattus norvegicus,Feces,UBERON:0001988,Sex hormone-binding globulin measurement,EFO:0004696,Low Sex hormone-binding globulin,High Sex hormone-binding globulin,Rats in this group had high Sex hormone-binding globulin.,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3h,8 August 2025,Victoria,Victoria,Heat map of the Spearman’s rho correlation test presenting the association between genus-level microbes and clinical parameters.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",1783272|1239|186801|3085636|186803;3379134|200940|3031449|213115|194924|35832,Complete,KateRasheed
bsdb:33957990/9/2,33957990,laboratory experiment,33957990,10.1186/s40168-021-01046-5,NA,"Han Q., Wang J., Li W., Chen Z.J. , Du Y.",Androgen-induced gut dysbiosis disrupts glucolipid metabolism and endocrinal functions in polycystic ovary syndrome,Microbiome,2021,"16S rRNA gene sequence, Faecal microbiota transplantation, Gut microbiota, Metabolome, Polycystic ovary syndrome",Experiment 9,China,Rattus norvegicus,Feces,UBERON:0001988,Sex hormone-binding globulin measurement,EFO:0004696,Low Sex hormone-binding globulin,High Sex hormone-binding globulin,Rats in this group had high Sex hormone-binding globulin.,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3h,8 August 2025,Victoria,Victoria,Heat map of the Spearman’s rho correlation test presenting the association between genus-level microbes and clinical parameters.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia",1783272|1239|186801|186802|31979|1485;33090|35493|3398|72025|3803|3814|508215,Complete,KateRasheed
bsdb:33957990/10/1,33957990,laboratory experiment,33957990,10.1186/s40168-021-01046-5,NA,"Han Q., Wang J., Li W., Chen Z.J. , Du Y.",Androgen-induced gut dysbiosis disrupts glucolipid metabolism and endocrinal functions in polycystic ovary syndrome,Microbiome,2021,"16S rRNA gene sequence, Faecal microbiota transplantation, Gut microbiota, Metabolome, Polycystic ovary syndrome",Experiment 10,China,Rattus norvegicus,Feces,UBERON:0001988,Testosterone measurement,EFO:0004908,Low Total testosterone,High Total testosterone,Rats in this group had high Total testosterone levels.,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3h,8 August 2025,Victoria,Victoria,Heat map of the Spearman’s rho correlation test presenting the association between genus-level microbes and clinical parameters.,increased,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,3379134|200940|3031449|213115|194924|35832,Complete,KateRasheed
bsdb:33957990/10/2,33957990,laboratory experiment,33957990,10.1186/s40168-021-01046-5,NA,"Han Q., Wang J., Li W., Chen Z.J. , Du Y.",Androgen-induced gut dysbiosis disrupts glucolipid metabolism and endocrinal functions in polycystic ovary syndrome,Microbiome,2021,"16S rRNA gene sequence, Faecal microbiota transplantation, Gut microbiota, Metabolome, Polycystic ovary syndrome",Experiment 10,China,Rattus norvegicus,Feces,UBERON:0001988,Testosterone measurement,EFO:0004908,Low Total testosterone,High Total testosterone,Rats in this group had high Total testosterone levels.,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3h,8 August 2025,Victoria,Victoria,Heat map of the Spearman’s rho correlation test presenting the association between genus-level microbes and clinical parameters.,decreased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|544448|31969|186332|186333|2086;1783272|201174|84998|84999|1643824|133925;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|31979|1485,Complete,KateRasheed
bsdb:33957990/11/1,33957990,laboratory experiment,33957990,10.1186/s40168-021-01046-5,NA,"Han Q., Wang J., Li W., Chen Z.J. , Du Y.",Androgen-induced gut dysbiosis disrupts glucolipid metabolism and endocrinal functions in polycystic ovary syndrome,Microbiome,2021,"16S rRNA gene sequence, Faecal microbiota transplantation, Gut microbiota, Metabolome, Polycystic ovary syndrome",Experiment 11,China,Rattus norvegicus,Feces,UBERON:0001988,Body weight,EFO:0004338,Low body weight,High body weight,Rats in this group had high body weight.,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3h,8 August 2025,Victoria,Victoria,Heat map of the Spearman’s rho correlation test presenting the association between genus-level microbes and clinical parameters.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,1783272|1239|91061|186826|81852|1350,Complete,KateRasheed
bsdb:33958592/1/1,33958592,laboratory experiment,33958592,10.1038/s41522-021-00213-8,NA,"Chen P.J., Nakano T., Lai C.Y., Chang K.C., Chen C.L. , Goto S.",Daily full spectrum light exposure prevents food allergy-like allergic diarrhea by modulating vitamin D<sub>3</sub> and microbiota composition,NPJ biofilms and microbiomes,2021,NA,Experiment 1,Taiwan,Mus musculus,Feces,UBERON:0001988,Sun exposure measurement,NA,Food allergy (FA) group,Phototherapy (PT) group,"Female Bagg Albino Laboratory-bred (BALB/c) mice that were sensitized twice intraperitoneally with ovalbumin (OVA, 60 μg) and aluminum hydroxide (1 mg) at a 2-week interval, followed by 15 repeated oral OVA challenges (15 mg per dose, every 2–3 days) to induce food allergy, while being exposed daily to full-spectrum light (5500 K, 12 hours per day) throughout the 9-week experimental period to evaluate the effect of phototherapy on allergic responses.",14,12,NA,16S,4,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6B,15 October 2025,Tosin,Tosin,Differences between (FA) food allergy and (PT) phototherapy groups (95% confidential interval) at the genus and species levels.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii",3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|328812,Complete,NA
bsdb:33958592/1/2,33958592,laboratory experiment,33958592,10.1038/s41522-021-00213-8,NA,"Chen P.J., Nakano T., Lai C.Y., Chang K.C., Chen C.L. , Goto S.",Daily full spectrum light exposure prevents food allergy-like allergic diarrhea by modulating vitamin D<sub>3</sub> and microbiota composition,NPJ biofilms and microbiomes,2021,NA,Experiment 1,Taiwan,Mus musculus,Feces,UBERON:0001988,Sun exposure measurement,NA,Food allergy (FA) group,Phototherapy (PT) group,"Female Bagg Albino Laboratory-bred (BALB/c) mice that were sensitized twice intraperitoneally with ovalbumin (OVA, 60 μg) and aluminum hydroxide (1 mg) at a 2-week interval, followed by 15 repeated oral OVA challenges (15 mg per dose, every 2–3 days) to induce food allergy, while being exposed daily to full-spectrum light (5500 K, 12 hours per day) throughout the 9-week experimental period to evaluate the effect of phototherapy on allergic responses.",14,12,NA,16S,4,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6B,16 October 2025,Reddicx,"Reddicx,Tosin",Differences between (FA) food allergy and (PT) phototherapy groups (95% confidential interval) at the genus and species levels.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp. G3,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. Culture-54,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|186802|216572|244127;1783272|1239|186801|186802|216572|244127|397284;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485|1003352;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|3085636|186803,Complete,NA
bsdb:33958592/2/1,33958592,laboratory experiment,33958592,10.1038/s41522-021-00213-8,NA,"Chen P.J., Nakano T., Lai C.Y., Chang K.C., Chen C.L. , Goto S.",Daily full spectrum light exposure prevents food allergy-like allergic diarrhea by modulating vitamin D<sub>3</sub> and microbiota composition,NPJ biofilms and microbiomes,2021,NA,Experiment 2,Taiwan,Mus musculus,Feces,UBERON:0001988,Food allergy,EFO:1001890,Combination of Control and Phototherapy (PT) groups,Food allergy (FA) group,"Female Bagg Albino Laboratory-bred (BALB/c) mice sensitized twice intraperitoneally with ovalbumin (OVA, 60 μg) and aluminum hydroxide (1 mg) at a 2-week interval, followed by 15 repeated oral OVA challenges (15 mg per dose, every 2–3 days) to induce food allergy, without exposure to phototherapy.",6,3,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 5B,15 October 2025,Tosin,Tosin,"Linear Discriminant analysis (LDA) effect size (LeFse) among control, Phototherapy (PT) and Food allergy (FA) groups",increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,1783272|1239|186801|186802|186807,Complete,NA
bsdb:33958592/3/1,33958592,laboratory experiment,33958592,10.1038/s41522-021-00213-8,NA,"Chen P.J., Nakano T., Lai C.Y., Chang K.C., Chen C.L. , Goto S.",Daily full spectrum light exposure prevents food allergy-like allergic diarrhea by modulating vitamin D<sub>3</sub> and microbiota composition,NPJ biofilms and microbiomes,2021,NA,Experiment 3,Taiwan,Mus musculus,Feces,UBERON:0001988,Sun exposure measurement,NA,Combination of Food allergy (FA) and Phototherapy (PT) groups,Control group,"Naïve female Bagg Albino Laboratory-bred (BALB/c) mice that were not immunized with ovalbumin and instead received  phosphate-buffered saline (PBS) intragastrically, serving as a healthy non-allergic control.",6,3,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 5B,16 October 2025,Reddicx,"Reddicx,Tosin","Linear discriminant analysis (LDA) effect size (LeFse) among control, Phototherapy (PT) and Food allergy (FA) groups.",increased,NA,NA,Complete,NA
bsdb:33958592/4/1,33958592,laboratory experiment,33958592,10.1038/s41522-021-00213-8,NA,"Chen P.J., Nakano T., Lai C.Y., Chang K.C., Chen C.L. , Goto S.",Daily full spectrum light exposure prevents food allergy-like allergic diarrhea by modulating vitamin D<sub>3</sub> and microbiota composition,NPJ biofilms and microbiomes,2021,NA,Experiment 4,Taiwan,Mus musculus,Feces,UBERON:0001988,Sun exposure measurement,NA,Combination of Control and Food allergy (FA) groups,Phototherapy (PT) group,"Female Bagg Albino Laboratory-bred (BALB/c) mice that were sensitized twice intraperitoneally with ovalbumin (OVA, 60 μg) and aluminum hydroxide (1 mg) at a 2-week interval, followed by 15 repeated oral OVA challenges (15 mg per dose, every 2-3 days) to induce food allergy, while being exposed daily to full-spectrum light (5500 K, 12 hours per day) throughout the 9-week experimental period to evaluate the effect of phototherapy on allergic responses.",6,3,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 5B,16 October 2025,Reddicx,"Reddicx,Tosin","Linear discriminant analysis (LDA) effect size (LeFse) among control, Phototherapy (PT) and Food allergy (FA) groups.",increased,k__Bacillati|p__Bacillota|c__Bacilli,1783272|1239|91061,Complete,NA
bsdb:33958592/5/1,33958592,laboratory experiment,33958592,10.1038/s41522-021-00213-8,NA,"Chen P.J., Nakano T., Lai C.Y., Chang K.C., Chen C.L. , Goto S.",Daily full spectrum light exposure prevents food allergy-like allergic diarrhea by modulating vitamin D<sub>3</sub> and microbiota composition,NPJ biofilms and microbiomes,2021,NA,Experiment 5,Taiwan,Mus musculus,Feces,UBERON:0001988,Sun exposure measurement,NA,Food allergy (FA) group,Phototherapy (PT) group,"Female Bagg Albino Laboratory-bred (BALB/c) mice that were sensitized twice intraperitoneally with ovalbumin (OVA, 60 μg) and aluminum hydroxide (1 mg) at a 2-week interval, followed by 15 repeated oral OVA challenges (15 mg per dose, every 2–3 days) to induce food allergy, while being exposed daily to full-spectrum light (5500 K, 12 hours per day) throughout the 9-week experimental period to evaluate the effect of phototherapy on allergic responses.",14,12,NA,16S,NA,RT-qPCR,relative abundances,T-Test,0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A,24 October 2025,Tosin,Tosin,Altered fecal microbiota composition in food allergy (FA): Quantitative real-time PCR for verification of the phyla Bacteroidetes and Firmicutes,increased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,NA
bsdb:33958592/5/2,33958592,laboratory experiment,33958592,10.1038/s41522-021-00213-8,NA,"Chen P.J., Nakano T., Lai C.Y., Chang K.C., Chen C.L. , Goto S.",Daily full spectrum light exposure prevents food allergy-like allergic diarrhea by modulating vitamin D<sub>3</sub> and microbiota composition,NPJ biofilms and microbiomes,2021,NA,Experiment 5,Taiwan,Mus musculus,Feces,UBERON:0001988,Sun exposure measurement,NA,Food allergy (FA) group,Phototherapy (PT) group,"Female Bagg Albino Laboratory-bred (BALB/c) mice that were sensitized twice intraperitoneally with ovalbumin (OVA, 60 μg) and aluminum hydroxide (1 mg) at a 2-week interval, followed by 15 repeated oral OVA challenges (15 mg per dose, every 2–3 days) to induce food allergy, while being exposed daily to full-spectrum light (5500 K, 12 hours per day) throughout the 9-week experimental period to evaluate the effect of phototherapy on allergic responses.",14,12,NA,16S,NA,RT-qPCR,relative abundances,T-Test,0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6A,24 October 2025,Tosin,Tosin,Altered fecal microbiota composition in food allergy (FA): Quantitative real-time PCR for verification of the phyla Bacteroidetes and Firmicutes,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,NA
bsdb:33961805/1/1,33961805,prospective cohort,33961805,10.1016/S2213-2600(20)30557-9,https://linkinghub.elsevier.com/retrieve/pii/S2213-2600(20)30557-9,"Dicker A.J., Lonergan M., Keir H.R., Smith A.H., Pollock J., Finch S., Cassidy A.J., Huang J.T.J. , Chalmers J.D.",The sputum microbiome and clinical outcomes in patients with bronchiectasis: a prospective observational study,The Lancet. Respiratory medicine,2021,NA,Experiment 1,United Kingdom,Homo sapiens,Sputum,UBERON:0007311,Bronchiectasis,NA,Less severe bronchiectasis,Severe bronchiectasis,Stable sputum samples with more severe bronchiectasis severity index (BSI) score [BSI ≥ 9],281,281,NA,16S,34,Illumina,relative abundances,"PERMANOVA,Random Forest Analysis",0.05,FALSE,NA,NA,"age,smoking status",NA,decreased,NA,NA,NA,NA,Signature 1,Figure 2C,9 March 2024,Scholastica,"Scholastica,WikiWorks",Random forest plot indicating the bacterial taxa associated with a more severe BSI score and a less severe BSI score,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",3379134|1224|1236|91347|543;3379134|1224|1236|72274|135621|286;3379134|1224|1236|135614|32033|40323,Complete,NA
bsdb:33961805/1/2,33961805,prospective cohort,33961805,10.1016/S2213-2600(20)30557-9,https://linkinghub.elsevier.com/retrieve/pii/S2213-2600(20)30557-9,"Dicker A.J., Lonergan M., Keir H.R., Smith A.H., Pollock J., Finch S., Cassidy A.J., Huang J.T.J. , Chalmers J.D.",The sputum microbiome and clinical outcomes in patients with bronchiectasis: a prospective observational study,The Lancet. Respiratory medicine,2021,NA,Experiment 1,United Kingdom,Homo sapiens,Sputum,UBERON:0007311,Bronchiectasis,NA,Less severe bronchiectasis,Severe bronchiectasis,Stable sputum samples with more severe bronchiectasis severity index (BSI) score [BSI ≥ 9],281,281,NA,16S,34,Illumina,relative abundances,"PERMANOVA,Random Forest Analysis",0.05,FALSE,NA,NA,"age,smoking status",NA,decreased,NA,NA,NA,NA,Signature 2,Figure 2C,9 March 2024,Scholastica,"Scholastica,WikiWorks",Random forest plot indicating the bacterial taxa associated with a more severe BSI score and a less severe BSI score,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",1783272|201174|1760|2037|2049|1654;1783272|201174|84998|84999|1643824|1380;;1783272|1239|526524|526525|128827|118747;3379134|29547|3031852|213849|72294|194;3379134|976|117743|200644|49546|1016;3379134|976|117743|200644|49546;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738;1783272|1239|91061|186826|186828|117563;3379134|1224|28216|206351|481|32257;1783272|1239|186801|3085636|186803;3384189|32066|203490|203491|1129771|32067;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3085636|186803|437755;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481;1783272|1239|186801|3085636|186803|265975;3379134|976|200643|171549|2005523|346096;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|1239|909932|909929|1843491|970;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;1783272|201174|1760|85006|1268|32207,Complete,NA
bsdb:33961805/2/1,33961805,prospective cohort,33961805,10.1016/S2213-2600(20)30557-9,https://linkinghub.elsevier.com/retrieve/pii/S2213-2600(20)30557-9,"Dicker A.J., Lonergan M., Keir H.R., Smith A.H., Pollock J., Finch S., Cassidy A.J., Huang J.T.J. , Chalmers J.D.",The sputum microbiome and clinical outcomes in patients with bronchiectasis: a prospective observational study,The Lancet. Respiratory medicine,2021,NA,Experiment 2,United Kingdom,Homo sapiens,Sputum,UBERON:0007311,Bronchiectasis,NA,Non-frequent exacerbating stable patients,Frequent exacerbating stable patients,Frequent exacerbating stable patients (≥ 3 exacerbation),281,281,NA,16S,34,Illumina,relative abundances,"PERMANOVA,Random Forest Analysis",0.05,FALSE,NA,NA,"age,smoking status",NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3C,9 March 2024,Scholastica,"Scholastica,WikiWorks",Random forest plot showing the bacterial taxa associated with three or more exacerbations in the previous year and those associated with fewer exacerbations,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",3379134|1224|1236|91347|543;3379134|1224|1236|72274|135621|286,Complete,NA
bsdb:33961805/2/2,33961805,prospective cohort,33961805,10.1016/S2213-2600(20)30557-9,https://linkinghub.elsevier.com/retrieve/pii/S2213-2600(20)30557-9,"Dicker A.J., Lonergan M., Keir H.R., Smith A.H., Pollock J., Finch S., Cassidy A.J., Huang J.T.J. , Chalmers J.D.",The sputum microbiome and clinical outcomes in patients with bronchiectasis: a prospective observational study,The Lancet. Respiratory medicine,2021,NA,Experiment 2,United Kingdom,Homo sapiens,Sputum,UBERON:0007311,Bronchiectasis,NA,Non-frequent exacerbating stable patients,Frequent exacerbating stable patients,Frequent exacerbating stable patients (≥ 3 exacerbation),281,281,NA,16S,34,Illumina,relative abundances,"PERMANOVA,Random Forest Analysis",0.05,FALSE,NA,NA,"age,smoking status",NA,decreased,NA,NA,NA,NA,Signature 2,Figure 3C,9 March 2024,Scholastica,"Scholastica,WikiWorks",Random forest plot showing the bacterial taxa associated with three or more exacerbations in the previous year and those associated with fewer exacerbations,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",1783272|201174|1760|2037|2049|1654;3379134|1224|1236|135625|712|416916;1783272|201174|84998|84999|1643824|1380;;3379134|29547|3031852|213849|72294|194;3379134|976|117743|200644|49546|1016;3379134|1224|28216|80840|80864;1783272|201174|1760|85007|1653|1716;3379134|976|117743|200644|49546;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738;1783272|1239|91061|186826|186828|117563;3379134|1224|28216|206351|481|32257;1783272|1239|91061|186826|33958|1578;3384189|32066|203490|203491|1129771|32067;1783272|1239|909932|1843489|31977|906;3379134|1224|1236|2887326|468|475;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481;1783272|1239|186801|3085636|186803|265975;3379134|976|200643|171549|2005523|346096;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|1239|909932|909929|1843491|970;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|135614|32033|40323;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977;3379134|976|117743|200644|2762318;1783272|201174|1760|85006|1268|32207,Complete,NA
bsdb:33961805/3/1,33961805,prospective cohort,33961805,10.1016/S2213-2600(20)30557-9,https://linkinghub.elsevier.com/retrieve/pii/S2213-2600(20)30557-9,"Dicker A.J., Lonergan M., Keir H.R., Smith A.H., Pollock J., Finch S., Cassidy A.J., Huang J.T.J. , Chalmers J.D.",The sputum microbiome and clinical outcomes in patients with bronchiectasis: a prospective observational study,The Lancet. Respiratory medicine,2021,NA,Experiment 3,United Kingdom,Homo sapiens,Sputum,UBERON:0007311,Bronchiectasis,NA,Stable samples,Exacerbation samples,Sputum samples at onset of exacerbation,64,64,NA,16S,34,Illumina,relative abundances,"PERMANOVA,Random Forest Analysis",0.05,FALSE,NA,NA,"age,smoking status",NA,decreased,NA,NA,NA,NA,Signature 1,Figure 4C,10 March 2024,Scholastica,"Scholastica,WikiWorks","Random forest plot showing the bacterial taxa associated with exacerbation samples, and those associated with stable samples from 64 pairs of one stable and one exacerbation sample per patient.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella",3379134|1224|28216|206351|481|538;1783272|1239|91061|186826|186828|117563,Complete,NA
bsdb:33961805/3/2,33961805,prospective cohort,33961805,10.1016/S2213-2600(20)30557-9,https://linkinghub.elsevier.com/retrieve/pii/S2213-2600(20)30557-9,"Dicker A.J., Lonergan M., Keir H.R., Smith A.H., Pollock J., Finch S., Cassidy A.J., Huang J.T.J. , Chalmers J.D.",The sputum microbiome and clinical outcomes in patients with bronchiectasis: a prospective observational study,The Lancet. Respiratory medicine,2021,NA,Experiment 3,United Kingdom,Homo sapiens,Sputum,UBERON:0007311,Bronchiectasis,NA,Stable samples,Exacerbation samples,Sputum samples at onset of exacerbation,64,64,NA,16S,34,Illumina,relative abundances,"PERMANOVA,Random Forest Analysis",0.05,FALSE,NA,NA,"age,smoking status",NA,decreased,NA,NA,NA,NA,Signature 2,Figure 4C,10 March 2024,Scholastica,"Scholastica,WikiWorks","Random forest plot showing the bacterial taxa associated with exacerbation samples, and those associated with stable samples from 64 pairs of one stable and one exacerbation sample per patient.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",3379134|1224|28211|356|82115|357;3379134|29547|3031852|213849|72294|194;3379134|976|117743|200644|2762318|59732;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738;3379134|1224|1236|135625|712|724;3384189|32066|203490|203491|1129771|32067;1783272|1239|909932|1843489|31977|906;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|838;3379134|1224|1236|72274|135621|286;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;1783272|201174|1760|85006|1268|32207,Complete,NA
bsdb:33963227/1/1,33963227,case-control,33963227,10.1038/s41598-021-89166-8,NA,"Li S., Song J., Ke P., Kong L., Lei B., Zhou J., Huang Y., Li H., Li G., Chen J., Li X., Xiang Z., Ning Y., Wu F. , Wu K.",The gut microbiome is associated with brain structure and function in schizophrenia,Scientific reports,2021,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Normal control (NC) group,Schizophrenia (SZ) group,Patients with Schizophrenia,38,38,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2B,18 October 2025,Tosin,Tosin,Bacterial genera that were significantly different between the two groups: Normal control (NC) and Schizophrenia (SZ) groups,increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:33963227/1/2,33963227,case-control,33963227,10.1038/s41598-021-89166-8,NA,"Li S., Song J., Ke P., Kong L., Lei B., Zhou J., Huang Y., Li H., Li G., Chen J., Li X., Xiang Z., Ning Y., Wu F. , Wu K.",The gut microbiome is associated with brain structure and function in schizophrenia,Scientific reports,2021,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Normal control (NC) group,Schizophrenia (SZ) group,Patients with Schizophrenia,38,38,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2B,18 October 2025,Tosin,Tosin,Bacterial genera that were significantly different between the two groups: Normal control (NC) and Schizophrenia (SZ) patients,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263,Complete,Svetlana up
bsdb:33963313/1/1,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Tumor stage,EFO:0004925,Pre-CT Stage I,Pre-CT Stage II/III,Breast cancer patients before chemotherapy with TNM Stage II/III,21,35,NA,WMS,NA,Ion Torrent,relative abundances,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 1B,19 April 2024,Scholastica,"Scholastica,WikiWorks",Variable importance plot (VIP) scores obtained within partial least square discriminant analysis describing the most discriminant species in Pre-CT TNM stage I (orange) compared to Pre-CT TNM stage II-III (blue),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas|s__Turicimonas muris,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:83,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma|s__Dielma fastidiosa,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp. HMSC71H05",3379134|976|200643|171549|815|816|820;3379134|1224|28216|80840|995019|1918598|1796652;3379134|1224|28216|80840|995019|577310|487175;1783272|1239|1262992;1783272|1239|91061|186826|1300|1357|1358;1783272|1239|91061|186826|1300|1301|1308;3379134|976|200643|171549|815|816|626929;3379134|976|200643|171549|815|816|291645;1783272|1239|526524|526525|128827|1472649|1034346;1783272|201174|84998|1643822|1643826|84111|84112;3379134|1224|1236|135625|712|724|1608898,Complete,Svetlana up
bsdb:33963313/1/2,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Tumor stage,EFO:0004925,Pre-CT Stage I,Pre-CT Stage II/III,Breast cancer patients before chemotherapy with TNM Stage II/III,21,35,NA,WMS,NA,Ion Torrent,relative abundances,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 1B,19 April 2024,Scholastica,"Scholastica,WikiWorks",Variable importance plot (VIP) scores obtained within partial least square discriminant analysis describing the most discriminant species in Pre-CT TNM stage I (orange) compared to Pre-CT TNM stage II-III (blue),decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Sanguibacteroides|s__Sanguibacteroides justesenii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium 1_7_47FAA,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis|s__Victivallis vadensis,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:110,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. An138,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:488,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Lawsonibacter|s__Lawsonibacter asaccharolyticus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__Desulfovibrionaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor sp. An184,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:443,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma|s__Enorma massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio sp. CAG:318,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:403,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. An250,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger",1783272|1239|909932|909929|1843491|52225|52226;3379134|976|200643|171549|171551|1635148|1547597;1783272|1239|186801|186802|457421;3379134|256845|1313211|278082|255528|172900|172901;1783272|1239|1263000;1783272|1239|186801|3085636|186803|1506553|1965560;1783272|1239|186801|186802|216572|1263|1262959;1783272|1239|186801|186802|216572|2172004|2108523;3379134|200940|3031449|213115|194924|2049043;1783272|1239|186801|3085636|186803|2316020|46228;1783272|1239|186801|3085636|186803|3342669|45851;1783272|1239|186801|186802|216572|1017280|1965576;3379134|976|200643|171549|815|816|1262739;1783272|201174|84998|84999|84107|1472762|1472761;1783272|1239|186801|3085636|186803|830|1262761;1783272|1239|186801|186802|216572|1263|1262958;1783272|1239|186801|186802|216572|1017280|106588;3379134|976|200643|171549|2005519|397864|487174;1783272|1239|186801|186802|3082771|1924093|1965604;3366610|28890|183925|2158|2159|2172|2173;3379134|200940|3031449|213115|194924|872|901,Complete,Svetlana up
bsdb:33963313/2/1,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 2,France,Homo sapiens,Feces,UBERON:0001988,Tumor stage,EFO:0004925,Post-CT Stage I,Post-CT Stage II/III,Breast cancer patients after chemotherapy with TNM Stage II/III,14,20,NA,WMS,NA,Ion Torrent,relative abundances,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 1E,19 April 2024,Scholastica,"Scholastica,WikiWorks",Variable importance plot (VIP) scores obtained within partial least square discriminant analysis describing the most discriminant species in Post-CT TNM stage I (orange) compared to Post-CT TNM stage II-III (blue),increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas intestinalis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum lactatifermentans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia|s__Harryflintia acetispora,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella massiliensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus durans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:167,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. CAG:257,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella tobetsuensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:180,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium 1_7_47FAA",1783272|201174|84998|1643822|1643826|644652|471189;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|3085636|186803|1769710|1653434;1783272|1239|909932|1843488|909930|33024|626940;1783272|1239|186801|3085636|3118652|2039240|160404;3379134|976|200643|171549|815|816|626929;3379134|976|200643|171549|815|816|820;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|186801|3085636|186803|2719313|358743;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|2719313|1531;3379134|976|200643|171549|2005525|375288|46503;1783272|1239|186801|186802|216572|1892380|1849041;1783272|1239|186801|3085636|186803|2719313|358742;1783272|1239|186801|3085636|186803|1432051|1720294;1783272|1239|91061|186826|81852|1350|53345;1783272|1239|186801|3085636|186803|572511|33035;3379134|976|200643|171549|815|816|46506;3379134|976|200643|171549|815|816|291645;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|186801|186802|31979|1485|1262777;1783272|1239|186801|3085636|186803|572511|1262756;1783272|1239|909932|1843489|31977|29465|1110546;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|186802|186806|1730|1262882;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|526524|526525|2810280|100883|100884;1783272|1239|186801|186802|457421,Complete,Svetlana up
bsdb:33963313/2/2,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 2,France,Homo sapiens,Feces,UBERON:0001988,Tumor stage,EFO:0004925,Post-CT Stage I,Post-CT Stage II/III,Breast cancer patients after chemotherapy with TNM Stage II/III,14,20,NA,WMS,NA,Ion Torrent,relative abundances,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 1E,20 April 2024,Scholastica,"Scholastica,WikiWorks",Variable importance plot (VIP) scores obtained within partial least square discriminant analysis describing the most discriminant species in Post-CT TNM stage I (orange) compared to Post-CT TNM stage II-III (blue),decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:110,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. CAG:241,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecis,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:95,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:755,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor sp. An100,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis|s__Victivallis vadensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium disporicum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1185,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. An31A,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia marmotae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:443,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp. HMSC71H05,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus",1783272|1239|909932|909929|1843491|158846|158847;1783272|201174|84998|1643822|1643826|84108|572010;1783272|1239|1263000;1783272|1239|186801|186802|216572|459786|1262911;1783272|1239|186801|3085636|186803|1407607|1150298;3379134|976|200643|171549|815|816|674529;1783272|1239|1262988;1783272|1239|186801|3085636|186803|2316020|33039;3379134|976|200643|171549|815|816|246787;1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|3085636|186803|572511|40520;3379134|976|200643|171549|171552|838|1262935;1783272|1239|186801|186802|216572|946234|1965538;3379134|256845|1313211|278082|255528|172900|172901;1783272|1239|186801|186802|31979|1485|84024;3379134|976|200643|171549|171552|838|1262921;3379134|976|200643|171549|171550|239759|1965631;3379134|1224|1236|91347|543|561|1499973;3379134|976|200643|171549|815|816|1262739;1783272|201174|1760|2037|2049|1654|55565;1783272|1239|186801|186802|204475|745368;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|171552|2974251|165179;3379134|1224|1236|135625|712|724|1608898;3379134|976|200643|171549|1853231|574697|544645;1783272|1239|186801|3085636|186803|28050|39485;3379134|976|200643|171549|1853231|283168|28118;1783272|1239|186801|186802|216572|216851|853;3379134|200940|3031449|213115|194924|872|901;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|3570277|116085,Complete,Svetlana up
bsdb:33963313/3/1,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 3,France,Homo sapiens,Feces,UBERON:0001988,Tumor size,EFO:0004134,Pre-Chemo tumor size <pT1,Pre-Chemo tumor size >pT1,Breast cancer patients before chemotherapy with pathological tumor size greater than pT1,24,32,NA,WMS,NA,Ion Torrent,relative abundances,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Fig. S2B,20 April 2024,Scholastica,"Scholastica,WikiWorks",Metagenomics analyses of stool samples from early breast cancer patients before chemotherapy with tumor size <pT1 versus tumor size >pT1,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecichinchillae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium paraputrificum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:83,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp. HMSC71H05,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella variicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas nexilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",1783272|1239|186801|3085636|186803|207244|649756;3379134|976|200643|171549|815|816|871325;3379134|976|200643|171549|815|816|674529;3379134|976|200643|171549|815|816|371601;1783272|1239|186801|186802|31979|1485|29363;1783272|1239|909932|1843489|31977|39948|487173;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|1262992;3379134|1224|1236|135625|712|724|729;3379134|1224|1236|135625|712|724|1608898;1783272|1239|186801|3082720|186804|1505657|261299;3379134|1224|1236|91347|543|570|573;3379134|1224|1236|91347|543|570|244366;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|186801|3085636|186803|2005355|29361;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Svetlana up
bsdb:33963313/3/2,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 3,France,Homo sapiens,Feces,UBERON:0001988,Tumor size,EFO:0004134,Pre-Chemo tumor size <pT1,Pre-Chemo tumor size >pT1,Breast cancer patients before chemotherapy with pathological tumor size greater than pT1,24,32,NA,WMS,NA,Ion Torrent,relative abundances,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Fig. S2B,20 April 2024,Scholastica,"Scholastica,WikiWorks",Metagenomics analyses of stool samples from early breast cancer patients before chemotherapy with tumor size <pT1 versus tumor size >pT1,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. An250,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:443,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas synergistica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio sp. CAG:318,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__Desulfovibrionaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella massiliensis,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:145,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Lawsonibacter|s__Lawsonibacter asaccharolyticus,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:403,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Sanguibacteroides|s__Sanguibacteroides justesenii",1783272|1239|186801|186802|3082771|1924093|1965604;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|1262739;3379134|976|200643|171549|2005519|397864|487174;3379134|976|200643|171549|1853231|574697|544644;1783272|1239|186801|3085636|186803|830|1262761;3379134|200940|3031449|213115|194924|872|901;3379134|200940|3031449|213115|194924|2049043;1783272|1239|186801|3085636|186803|1432051|1720294;1783272|1239|1263005;3384194|508458|649775|649776|3029087|1434006|651822;1783272|1239|186801|186802|216572|2172004|2108523;3366610|28890|183925|2158|2159|2172|2173;1783272|1239|186801|186802|216572|1263|1262958;3379134|976|200643|171549|171551|1635148|1547597,Complete,Svetlana up
bsdb:33963313/4/1,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 4,France,Homo sapiens,Feces,UBERON:0001988,Tumor size,EFO:0004134,Post-Chemo tumor size <pT1,Post-Chemo tumor size >pT1,Breast cancer patients after chemotherapy with pathological tumor size greater than pT1,13,21,NA,WMS,NA,Ion Torrent,relative abundances,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Fig. S2D,21 April 2024,Scholastica,"Scholastica,WikiWorks",Metagenomics analyses of stool samples from early breast cancer patients after chemotherapy with tumor size <pT1 versus tumor size >pT1,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus pullicaecorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia|s__Harryflintia acetispora,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:279,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella|s__Rikenella microfusus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas intestinalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. A12,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella tobetsuensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum",3379134|976|200643|171549|815|816|46506;3379134|976|200643|171549|815|816|371601;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|186802|3085642|580596|501571;1783272|1239|186801|186802|31979|1485|1502;1783272|1239|526524|526525|2810280|100883|100884;1783272|1239|186801|3085636|186803|2719313|1531;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|216572|1892380|1849041;1783272|1239|186801|3082720|186804|1505657|261299;3379134|976|200643|171549|2005525|375288|46503;1783272|1239|909932|1843488|909930|33024|626940;3379134|976|200643|171549|171552|838|1262924;3379134|976|200643|171549|171550|28138|28139;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|3085636|186803|1769710|1653434;1783272|1239|91061|186826|1300|1301|1759399;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|91061|186826|1300|1301|1343;1783272|1239|526524|526525|2810280|3025755|29348;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|909932|1843489|31977|29465|423477;1783272|1239|909932|1843489|31977|29465|1110546;1783272|1239|186801|186802|31979|1485|1522;1783272|1239|186801|186802|216572|1535,Complete,Svetlana up
bsdb:33963313/4/2,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 4,France,Homo sapiens,Feces,UBERON:0001988,Tumor size,EFO:0004134,Post-Chemo tumor size <pT1,Post-Chemo tumor size >pT1,Breast cancer patients after chemotherapy with pathological tumor size greater than pT1,13,21,NA,WMS,NA,Ion Torrent,relative abundances,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Fig. S2D,21 April 2024,Scholastica,"Scholastica,WikiWorks",Metagenomics analyses of stool samples from early breast cancer patients after chemotherapy with tumor size <pT1 versus tumor size >pT1,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum butyriciproducens,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter secundus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor sp. An10,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor sp. An100,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp. HMSC71H05,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:309,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum",1783272|1239|186801|186802|3085642|2048137|1628085;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759|626932;3379134|976|200643|171549|2005519|1348911|1099853;3379134|976|200643|171549|2005519|1348911|1501392;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|3569723|410072;3379134|200940|3031449|213115|194924|872|901;1783272|1239|186801|186802|216572|946234|1965537;1783272|1239|186801|186802|216572|946234|1965538;3379134|1224|1236|135625|712|724|1608898;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|3085636|186803|841|1262945;1783272|1239|186801|186802|216572|39492,Complete,Svetlana up
bsdb:33963313/5/1,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 5,France,Homo sapiens,Feces,UBERON:0001988,Tumor grading,OBI:0600002,SBR Gr1/2 Post-Chemo,SBR Gr3 Post-Chemo,Breast cancer patients after chemotherapy with Scarff Bloom & Richardson (SBR) grade Gr3,20,24,NA,WMS,NA,Ion Torrent,relative abundances,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Fig. S3C,21 April 2024,Scholastica,"Scholastica,WikiWorks",Metagenomics analyses of stool samples from early breast cancer patients after chemotherapy according to tumor histological grade SBR; Gr1/2 compared to Gr3,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia|s__Harryflintia acetispora,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. An250,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium disporicum,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:94,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:170,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:58,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales|s__Candidatus Gastranaerophilales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor sp. An10,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:95,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:238,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella xylaniphila,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:145,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:443,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__Desulfovibrionaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. An14,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae",1783272|1239|186801|3085636|186803|3570277|116085;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|186801|186802|216572|39492;1783272|1239|186801|186802|216572|1892380|1849041;3379134|976|200643|171549|1853231|574697|544645;3379134|976|200643|171549|171550|239759|28117;3379134|200940|3031449|213115|194924|872|901;1783272|1239|186801|186802|3082771|1924093|1965604;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|186801|186802|31979|1485|84024;1783272|1239|1262989;1783272|1239|1263006;1783272|1239|186801|186802|31979|1485|1262824;1783272|1798710|1906119|2137880;1783272|1239|186801|186802|216572|946234|1965537;1783272|1239|1262988;1783272|1239|1263011;3379134|976|200643|171549|171552|577309|454155;1783272|1239|1263005;3379134|976|200643|171549|815|816|1262739;3379134|200940|3031449|213115|194924|2049043;1783272|1239|186801|3085636|186803|1506553|1965562;1783272|1239|186801|3085636|186803|2719313|208479,Complete,Svetlana up
bsdb:33963313/5/2,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 5,France,Homo sapiens,Feces,UBERON:0001988,Tumor grading,OBI:0600002,SBR Gr1/2 Post-Chemo,SBR Gr3 Post-Chemo,Breast cancer patients after chemotherapy with Scarff Bloom & Richardson (SBR) grade Gr3,20,24,NA,WMS,NA,Ion Torrent,relative abundances,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Fig. S3C,21 April 2024,Scholastica,"Scholastica,WikiWorks",Metagenomics analyses of stool samples from early breast cancer patients after chemotherapy according to tumor histological grade SBR; Gr1/2 compared to Gr3,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:144,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella tayi,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella hongkongensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__[Lactobacillus] rogosae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:182,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides johnsonii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae",3379134|976|200643|171549|815|816|1262736;1783272|1239|186801|3085636|186803|1432051|1432052;1783272|1239|186801|3085636|186803|1649459|154046;1783272|1239|186801|3082768|990719|990721|270498;1783272|1239|186801|3085636|186803|28050|706562;1783272|1239|186801|3085636|186803|2941495|1512;3379134|976|200643|171549|815|816|291645;3379134|976|200643|171549|815|816|371601;3379134|976|200643|171549|815|816|246787;1783272|1239|909932|1843488|909930|33024|33025;1783272|1239|186801|3085636|186803|841|1262942;1783272|1239|186801|3085636|186803|1769710|1653434;3379134|976|200643|171549|2005525|375288|387661;1783272|1239|186801|3085636|186803|28050|28052;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|186801|3085636|186803|33042|33043;1783272|201174|84998|1643822|1643826|644652|471189;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|2719313|358743,Complete,Svetlana up
bsdb:33963313/6/1,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 6,France,Homo sapiens,Feces,UBERON:0001988,Tumor stage,EFO:0004925,pN- pre-Chemo,pN+ pre-Chemo,Breast cancer patients before chemotherapy with positive axillary lymph node involvement,30,26,NA,WMS,NA,Ion Torrent,relative abundances,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Fig. S4B,21 April 2024,Scholastica,"Scholastica,WikiWorks","Metagenomics analyses of stool samples from early breast cancer patients before chemotherapy according to axillary lymph node involvement: positive lymph node (pN+, blue dots) versus negative lymph node (pN-, orange dots)",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 57_20,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter secundus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:83,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas|s__Turicimonas muris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia alvei,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma|s__Dielma fastidiosa",1783272|1239|186801|186802|216572|459786|1897011;3379134|976|200643|171549|2005519|1348911|1501392;3379134|1224|28216|80840|995019|577310|487175;1783272|1239|1262992;3379134|1224|28216|80840|995019|1918598|1796652;1783272|1239|186801|3085636|186803|2316020|33039;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|2005519|1348911|1099853;1783272|1239|909932|1843488|909930|33024|33025;3379134|200940|3031449|213115|194924|35832|35833;3379134|1224|1236|91347|1903412|568|569;1783272|1239|526524|526525|128827|1472649|1034346,Complete,Svetlana up
bsdb:33963313/6/2,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 6,France,Homo sapiens,Feces,UBERON:0001988,Tumor stage,EFO:0004925,pN- pre-Chemo,pN+ pre-Chemo,Breast cancer patients before chemotherapy with positive axillary lymph node involvement,30,26,NA,WMS,NA,Ion Torrent,relative abundances,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Fig. S4B,21 April 2024,Scholastica,"Scholastica,WikiWorks","Metagenomics analyses of stool samples from early breast cancer patients before chemotherapy according to axillary lymph node involvement: positive lymph node (pN+, blue dots) versus negative lymph node (pN-, orange dots)",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:633,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:167,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis|s__Victivallis vadensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor sp. An184,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Liu et al. 2021),k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:755,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter|s__Oxalobacter formigenes,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma|s__Enorma massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:443,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio sp. CAG:318,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella stercoris,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:403,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. An131,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp. T11011-6,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. An138,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:180,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. An250,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger",3379134|976|200643|171549|815|816|1262744;1783272|1239|186801|186802|31979|1485|1262777;1783272|1239|526524|526525|2810280|3025755|29348;3379134|256845|1313211|278082|255528|172900|172901;1783272|1239|186801|3085636|186803|572511|1532;1783272|201174|1760|2037|2049|1654|55565;3379134|1224|1236|91347|543|544|133448;3379134|1224|1236|91347|543|544|546;1783272|1239|186801|186802|216572|1017280|1965576;3379134|1224|1236|91347|543|570|571;1783272|1239|909932|909929|1843491|158846|158847;1783272|1239|186801|186802|216572|1263|3062497;3379134|976|200643|171549|171552|838|1262935;3379134|1224|28216|80840|75682|846|847;1783272|201174|84998|84999|84107|1472762|1472761;3379134|976|200643|171549|815|816|1262739;1783272|1239|186801|3085636|186803|830|1262761;1783272|201174|84998|84999|84107|102106|147206;1783272|1239|186801|186802|216572|1263|1262958;1783272|1239|186801|3085636|186803|3342669|45851;1783272|1239|186801|3085636|186803|1506553|1965555;3379134|976|200643|171549|815|909656|387090;1783272|1239|909932|1843489|31977|29465|2027459;1783272|1239|186801|3085636|186803|572511|33035;1783272|1239|186801|3085636|186803|1506553|1965560;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|186801|186802|186806|1730|1262882;1783272|1239|186801|3085636|186803|1769710|1653434;1783272|1239|186801|186802|3082771|1924093|1965604;3379134|200940|3031449|213115|194924|872|901,Complete,Svetlana up
bsdb:33963313/7/1,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 7,France,Homo sapiens,Feces,UBERON:0001988,Tumor stage,EFO:0004925,pN- post-Chemo,pN+ post-Chemo,Breast cancer patients after chemotherapy with positive axillary lymph node involvement,19,15,NA,WMS,NA,Ion Torrent,relative abundances,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Fig. S4D,22 April 2024,Scholastica,"Scholastica,WikiWorks","Metagenomics analyses of stool samples from early breast cancer patients after chemotherapy according to axillary lymph node involvement: positive lymph node (pN+, blue dots) versus negative lymph node (pN-, orange dots)",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum lactatifermentans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. CAG:257,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus pullicaecorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:678,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp. CAG:317,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus durans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:38,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus|s__Proteus mirabilis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas intestinalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. A12,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella tobetsuensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas nexilis",3379134|976|200643|171549|171550|239759|328813;1783272|1239|186801|3085636|3118652|2039240|160404;1783272|1239|186801|3085636|186803|572511|33035;1783272|1239|186801|3085636|186803|572511|1262756;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|186802|3085642|580596|501571;1783272|1239|186801|186802|31979|1485|1262831;1783272|1239|186801|3085636|186803|189330|1262873;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|3085636|186803|1432051|1720294;1783272|1239|186801|3085636|186803|2719313|358742;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|91061|186826|81852|1350|53345;1783272|1239|186801|186802|186806|1730|1262889;1783272|201174|84998|1643822|1643826|644652|471189;1783272|1239|186801|3082720|186804|1505657|261299;3379134|976|200643|171549|2005525|375288|46503;3379134|1224|1236|91347|1903414|583|584;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|186801|3085636|186803|1769710|1653434;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|91061|186826|1300|1301|1759399;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|91061|186826|1300|1301|1343;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|909932|1843489|31977|29465|423477;1783272|1239|909932|1843489|31977|29465|1110546;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|3085636|186803|2005355|29361,Complete,Svetlana up
bsdb:33963313/7/2,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 7,France,Homo sapiens,Feces,UBERON:0001988,Tumor stage,EFO:0004925,pN- post-Chemo,pN+ post-Chemo,Breast cancer patients after chemotherapy with positive axillary lymph node involvement,19,15,NA,WMS,NA,Ion Torrent,relative abundances,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Fig. S4D,22 April 2024,Scholastica,"Scholastica,WikiWorks","Metagenomics analyses of stool samples from early breast cancer patients after chemotherapy according to axillary lymph node involvement: positive lymph node (pN+, blue dots) versus negative lymph node (pN-, orange dots)",decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__[Lactobacillus] rogosae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp. HMSC71H05,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea|s__Faecalitalea cylindroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:251,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|3085636|186803|28050|706562;3379134|976|200643|171549|171552|2974251|165179;3379134|1224|1236|135625|712|724|1608898;1783272|1239|186801|3085636|186803|572511|40520;1783272|201174|1760|85004|31953|196081|230143;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|526524|526525|128827|1573534|39483;1783272|1239|909932|909929|1843491|158846|158847;1783272|1239|186801|3085636|186803|3569723|410072;1783272|201174|1760|85004|31953|1678|1681;1783272|1239|186801|186802|186806|1730|1262886;1783272|1239|186801|3085636|186803|28050|39485;3379134|200940|3031449|213115|194924|872|901;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|1853231|283168|28118;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|1766253|39491,Complete,Svetlana up
bsdb:33963313/8/1,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 8,"France,Italy",Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,Healthy volunteers,Breast cancer patients,Breast cancer patients enrolled in the CANTO study,336,76,NA,WMS,NA,Ion Torrent,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 2A,22 April 2024,Scholastica,"Scholastica,WikiWorks",Metagenomics analyses of stool samples from breast cancer patients compared with healthy volunteers (HV) using LEfSe method,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium 1_7_47FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. KLE 1755,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|g__Dhillonvirus|s__Dhillonvirus JL1,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|g__Phapecoctavirus|s__Phapecoctavirus phAPEC8,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|g__Skunavirus|s__Skunavirus sv936,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola barnesiae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D16,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|g__Ceduovirus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|g__Dhillonvirus|s__Dhillonvirus SO1,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis",3379134|976|200643|171549|171550|239759|2585118;3379134|976|200643|171549|171550|239759|626932;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|815|816|338188;3379134|976|200643|171549|815|816|291645;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|186802|457421;1783272|1239|186801|186802|31979|1485|1226325;2731360|2731618|2731619|1623289|1245890;1783272|1239|186801|3085636|186803|2719313|333367;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|2719313|1531;2731360|2731618|2731619|2733124|3431623;2731360|2731618|2731619|1623305|2845183;3379134|976|200643|171549|815|909656|376804;1783272|1239|186801|186802|216572|552398;3379134|200940|3031449|213115|194924|35832;2731360|2731618|2731619|186532;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|909929|1843491|52225;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|1853231|283168|28118;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|3085636|186803|841|166486;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|2005525|375288|46503;3379134|1224|1236|91347|543|570|573;1783272|1239|186801|3085636|186803|28050|39485;3379134|976|200643|171549|2005519|397864|487174;1783272|1239|186801|186802|216572|216851|853;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|816|817;2731360|2731618|2731619|1623289|1954380;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|171552|2974251|165179;3379134|976|200643|171549|815|816|820,Complete,Svetlana up
bsdb:33963313/8/2,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 8,"France,Italy",Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,Healthy volunteers,Breast cancer patients,Breast cancer patients enrolled in the CANTO study,336,76,NA,WMS,NA,Ion Torrent,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 2A,22 April 2024,Scholastica,"Scholastica,WikiWorks",Metagenomics analyses of stool samples from breast cancer patients compared with healthy volunteers (HV) using LEfSe method,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas bennonis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. L2-50,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium mitsuokai,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema succinifaciens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium angulatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus champanellensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantarius,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp. TW09276,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. KLE 1745,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus harei,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis",1783272|201174|1760|85004|31953|1678|1680;1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|186802|216572|1263|457412;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|3085636|186803|2569097|39488;3366610|28890|183925|2158|2159|2172|2173;1783272|1239|186801|3085636|186803|3342669|45851;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803|189330|88431;3379134|976|200643|171549|815|816|46506;3379134|976|200643|171549|171552|2974265|363265;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|526524|526525|128827|1573535|1735;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|186802|216572|39492;3379134|976|200643|171549|171551|836|501496;1783272|1239|909932|1843488|909930|33024|626940;1783272|1239|1737404|1737405|1570339|150022|1260;1783272|1239|186801|186802|31979|1485|411489;1783272|1239|526524|526525|2810280|135858|100886;3379134|203691|203692|136|2845253|157|167;1783272|201174|1760|85004|31953|1678|28026;1783272|201174|1760|85004|31953|1678|1686;1783272|1239|186801|3085636|186803|3570277|116085;3379134|976|200643|171549|171552|2974257|28127;1783272|1239|186801|3085636|186803|33042|33043;1783272|201174|1760|85004|31953|1678|1683;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|1737404|1737405|1570339|162289|33031;3379134|976|200643|171549|815|816|329854;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|91061|186826|33958|2767887|1623;1783272|1239|186801|186802|186806|1730|39490;1783272|1239|186801|3082720|186804;1783272|1239|186801|186802|216572|1263|1161942;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|1737404|1737405|1570339|165779|33037;1783272|201174|84998|1643822|1643826|84111;3379134|1224|1236|91347|543|547|550;3366610|28890|183925|2158|2159|2172;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|91061|186826|1300|1301|102684;3379134|1224|1236|91347|543|561|754330;3379134|976|200643|171549|171551|836|322095;1783272|1239|186801|186802|216572|459786|1226323;1783272|1239|1737404|1737405|1570339|162289|54005;1783272|1239|186801|3085636|186803|1649459|154046;1783272|1239|1737404|1737405|1570339|165779|1287640;1783272|201174|84998|1643822|1643826|644652|471189;3379134|976|200643|171549|171551|836|281920,Complete,Svetlana up
bsdb:33963313/9/1,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 9,France,Homo sapiens,Feces,UBERON:0001988,Tumor stage,EFO:0004925,Neoadjuvant_pN-,Neoadjuvant_pN+,Breast cancer patients after neoadjuvant chemotherapy treatment with pathological lymph node involvement,8,2,NA,WMS,NA,Ion Torrent,relative abundances,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 2D,23 April 2024,Scholastica,"Scholastica,WikiWorks","Metagenomics analyses of stool samples from BC patients comparing species abundance according to the pathological lymph node involvement (no pathological lymph node involvement, pN-, orange; versus pathological lymph node involvement, pN+, blue) in stools collected after neoadjuvant CT (n = 10)",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. CAG:257,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. An250,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis",3379134|976|200643|171549|815|816|818;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|1769710|1653434;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|3085636|186803|1432051|1720294;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|572511|1262756;1783272|1239|186801|3085636|186803|2719313|1531;1783272|1239|186801|3085636|186803|2941495|1512;1783272|1239|186801|186802|3082771|1924093|1965604;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|186801|3085636|186803|2719313|358743;1783272|1239|186801|3085636|186803|2719313|358742,Complete,Svetlana up
bsdb:33963313/9/2,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 9,France,Homo sapiens,Feces,UBERON:0001988,Tumor stage,EFO:0004925,Neoadjuvant_pN-,Neoadjuvant_pN+,Breast cancer patients after neoadjuvant chemotherapy treatment with pathological lymph node involvement,8,2,NA,WMS,NA,Ion Torrent,relative abundances,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 2D,23 April 2024,Scholastica,"Scholastica,WikiWorks","Metagenomics analyses of stool samples from BC patients comparing species abundance according to the pathological lymph node involvement (no pathological lymph node involvement, pN-, orange; versus pathological lymph node involvement, pN+, blue) in stools collected after neoadjuvant CT (n = 10)",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus",1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|3085636|186803|841|360807;3379134|976|200643|171549|815|909656|821,Complete,Svetlana up
bsdb:33963313/10/1,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 10,France,Homo sapiens,Feces,UBERON:0001988,Tumor stage,EFO:0004925,Neoadjuvant stage post-Chemo (Stage 0),Neoadjuvant stage post-Chemo (Stage I/II),Breast cancer patients after neoadjuvant chemotherapy treatment who are pathological non-complete responders (stage I–II),5,5,NA,WMS,NA,Ion Torrent,relative abundances,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Fig. S3D,23 April 2024,Scholastica,"Scholastica,WikiWorks",Metagenomics analyses of stool samples from early BC patients treated in a neoadjuvant setting comparing pathological complete responders (stage I) to non-complete responders (stage I–II),increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,1783272|1239|186801|3085636|186803|2719313|358743,Complete,Svetlana up
bsdb:33963313/10/2,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 10,France,Homo sapiens,Feces,UBERON:0001988,Tumor stage,EFO:0004925,Neoadjuvant stage post-Chemo (Stage 0),Neoadjuvant stage post-Chemo (Stage I/II),Breast cancer patients after neoadjuvant chemotherapy treatment who are pathological non-complete responders (stage I–II),5,5,NA,WMS,NA,Ion Torrent,relative abundances,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Fig. S3D,23 April 2024,Scholastica,"Scholastica,WikiWorks",Metagenomics analyses of stool samples from early BC patients treated in a neoadjuvant setting comparing pathological complete responders (stage I) to non-complete responders (stage I–II),decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum",1783272|1239|91061|1385|539738|1378|84135;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|186801|186802|186806|1730|39496,Complete,Svetlana up
bsdb:33963313/11/1,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 11,France,Homo sapiens,Feces,UBERON:0001988,Response to combination chemotherapy,EFO:0007965,Pre-Chemotherapy,Post-Chemotherapy,Breast cancer patients after Chemotherapy,45,45,NA,WMS,NA,Ion Torrent,relative abundances,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Fig. 3C,23 April 2024,Scholastica,"Scholastica,WikiWorks",Differentially significant abundant taxa in breast cancer patients pre-Chemotherapy compared to post-Chemotherapy,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:110,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii",1783272|1239|526524|526525|128827|1573535|1735;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|1263000;3366610|28890|183925|2158|2159|2172|2173,Complete,Svetlana up
bsdb:33963313/11/2,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 11,France,Homo sapiens,Feces,UBERON:0001988,Response to combination chemotherapy,EFO:0007965,Pre-Chemotherapy,Post-Chemotherapy,Breast cancer patients after Chemotherapy,45,45,NA,WMS,NA,Ion Torrent,relative abundances,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 2,Fig. 3C,23 April 2024,Scholastica,"Scholastica,WikiWorks",Differentially significant abundant taxa in breast cancer patients pre-Chemotherapy compared to post-Chemotherapy,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella tayi,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. OM08-24,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum lactatifermentans,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis",1783272|201174|84998|1643822|1643826|84111|84112;3379134|976|200643|171549|2005519|1348911|1099853;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|186801|3085636|186803|1432051|1432052;3379134|976|200643|171549|815|816|820;1783272|1239|186801|3085636|186803|2719313|333367;1783272|1239|909932|1843489|31977|29465|29466;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|186802|186806|1730|2292352;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|3118652|2039240|160404;1783272|201174|84998|1643822|1643826|644652|471189;1783272|1239|186801|186802|216572|244127|169435,Complete,Svetlana up
bsdb:33963313/12/1,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 12,France,Homo sapiens,Feces,UBERON:0001988,Adverse effect,EFO:0009658,No - increased BMI (Pre-Chemo),Yes - increased BMI (Pre-Chemo),Breast cancer patients before Chemotherapy with increased Body Mass Index (BMI),30,34,NA,WMS,NA,Ion Torrent,relative abundances,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Fig. S6B,23 April 2024,Scholastica,"Scholastica,WikiWorks",Differentially significant abundant taxa in breast cancer patients before Chemotherapy with increased BMI compared to those without increased BMI,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. An250,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter secundus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:94,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:403,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium paraputrificum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:180,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:95,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp. CAG:528,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium 1_7_47FAA,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales|s__Candidatus Gastranaerophilales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 57_20,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens|s__Adlercreutzia equolifaciens subsp. celatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium disporicum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. CAG:241,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella jalaludinii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma|s__Dielma fastidiosa,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor sp. An100,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas|s__Turicimonas muris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1185",3379134|976|200643|171549|815|816|46506;3379134|976|200643|171549|2005525|375288|46503;1783272|1239|186801|186802|3082771|1924093|1965604;3379134|976|200643|171549|815|816|338188;3379134|976|200643|171549|815|816|246787;1783272|1239|186801|186802|216572|1905344|1550024;1783272|201174|1760|85004|31953|1678|1686;1783272|1239|526524|526525|2810280|100883|100884;3379134|976|200643|171549|2005519|1348911|1501392;3379134|976|200643|171549|171552|838|28130;3379134|976|200643|171549|815|909656|821;1783272|1239|1262989;3379134|976|200643|171549|171552|2974251|165179;3379134|976|200643|171549|1853231|574697|544645;1783272|1239|186801|3085636|186803|572511|40520;1783272|201174|1760|85004|31953|1678|28025;1783272|1239|186801|186802|216572|1263|1262958;1783272|201174|84998|1643822|1643826|447020|446660;3379134|976|200643|171549|815|816|28111;1783272|1239|186801|186802|31979|1485|29363;1783272|1239|186801|186802|186806|1730|1262882;1783272|1239|1262988;1783272|1239|909932|1843489|31977|39948|487173;1783272|1239|186801|186802|216572|244127|1262700;3379134|976|200643|171549|2005525|375288|823;1783272|1239|186801|186802|457421;1783272|1798710|1906119|2137880;1783272|1239|186801|186802|216572|459786|1897011;1783272|201174|84998|1643822|1643826|447020|446660|394340;1783272|1239|186801|186802|31979|1485|84024;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|186801|186802|216572|459786|1262911;1783272|1239|909932|909929|1843491|52225|187979;1783272|1239|526524|526525|128827|1472649|1034346;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|186801|186802|216572|946234|1965538;3379134|1224|28216|80840|995019|1918598|1796652;3379134|976|200643|171549|1853231|283168|28118;1783272|201174|1760|85004|31953|1678|1681;3379134|976|200643|171549|171552|838|1262921,Complete,Svetlana up
bsdb:33963313/12/2,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 12,France,Homo sapiens,Feces,UBERON:0001988,Adverse effect,EFO:0009658,No - increased BMI (Pre-Chemo),Yes - increased BMI (Pre-Chemo),Breast cancer patients before Chemotherapy with increased Body Mass Index (BMI),30,34,NA,WMS,NA,Ion Torrent,relative abundances,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Fig. S6B,23 April 2024,Scholastica,"Scholastica,WikiWorks",Differentially significant abundant taxa in breast cancer patients before Chemotherapy with increased BMI compared to those without increased BMI,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:443,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus|s__Cloacibacillus porcorum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp. CAG:317,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor sp. An184,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:182,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella parvirubra,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hydrogenotrophica,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus pullicaecorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:303,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:145,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. PC13,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma|s__Enorma massiliensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__Desulfovibrionaceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides johnsonii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D5,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp. T11011-6,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella infantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__[Lactobacillus] rogosae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella tayi,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:251",3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|815|816|626929;3379134|976|200643|171549|815|816|329854;3379134|976|200643|171549|815|816|291645;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|1262739;3384194|508458|649775|649776|649777|508459|1197717;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|84998|84999|84107|102106|147207;1783272|1239|186801|3085636|186803|33042|33043;3379134|200940|3031449|213115|194924|872|901;1783272|1239|186801|3085636|186803|189330|1262873;3379134|1224|1236|91347|543|561|562;1783272|1239|909932|1843488|909930|33024|33025;1783272|1239|909932|1843488|909930|33024|626940;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|310297;1783272|1239|186801|186802|216572|1017280|1965576;1783272|1239|186801|3085636|186803|841|1262942;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|91061|186826|1300|1301|1318;3379134|1224|28216|80840|995019|40544|437898;1783272|1239|91061|186826|1300|1301|68892;1783272|1239|186801|186802|186806|1730|39490;1783272|1239|186801|3085636|186803|572511|53443;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|186801|186802|3085642|580596|501571;1783272|1239|186801|3085636|186803|841|1262944;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|1263005;1783272|1239|186801|186802|216572|459786|1855299;1783272|201174|84998|84999|84107|1472762|1472761;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|186801|3085636|186803|3342669|45851;3379134|200940|3031449|213115|194924|2049043;3379134|976|200643|171549|2005525|375288|387661;1783272|1239|186801|186802|216572|1520815;1783272|1239|909932|1843489|31977|29465|2027459;3379134|976|200643|171549|815|816|820;1783272|1239|909932|1843489|31977|29465|1911679;1783272|1239|186801|3085636|186803|2719313|1531;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|186801|3085636|186803|28050|706562;3379134|976|200643|171549|815|816|817;1783272|1239|186801|3085636|186803|1432051|1432052;1783272|1239|186801|3085636|186803|2316020|46228;1783272|1239|186801|3085636|186803|28050|28052;1783272|1239|91061|1385|539738|1378|84135;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|186806|1730|1262886,Complete,Svetlana up
bsdb:33963313/13/1,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 13,France,Homo sapiens,Feces,UBERON:0001988,Adverse effect,EFO:0009658,No - increased BMI (Post-Chemo),Yes - increased BMI (Post-Chemo),Breast cancer patients 12 months after Chemotherapy with increased Body Mass Index (BMI),15,24,NA,WMS,NA,Ion Torrent,relative abundances,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Fig. S6D,23 April 2024,Scholastica,"Scholastica,WikiWorks",Differentially significant abundant taxa in breast cancer patients 12 months after Chemotherapy with increased BMI compared to those without increased BMI,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes inops,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp. CAG:528,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor sp. An10,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:94,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:471,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus durans,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales|s__Candidatus Gastranaerophilales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:167,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. An138,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium disporicum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. An250,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas|s__Turicimonas muris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella minuta,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Lawsonibacter|s__Lawsonibacter asaccharolyticus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum lactatifermentans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. An131,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Fructilactobacillus|s__Fructilactobacillus sanfranciscensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma|s__Dielma fastidiosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:678,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor sp. An184,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:755,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor sp. An100,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. A12,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides galacturonicus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis",3379134|976|200643|171549|171550|239759|1501391;1783272|1239|186801|186802|216572|244127|1262700;1783272|1239|186801|3085636|186803|2316020|46228;3379134|976|200643|171549|1853231|574697|544645;1783272|1239|186801|186802|216572|946234|1965537;1783272|1239|1262989;1783272|1239|186801|3085636|186803|841|1262948;1783272|1239|91061|186826|81852|1350|53345;1783272|1239|526524|526525|2810280|3025755|29348;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1798710|1906119|2137880;1783272|1239|186801|186802|31979|1485|1262777;3379134|1224|28216|80840|995019|577310|487175;1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|186801|3085636|186803|1506553|1965560;1783272|1239|526524|526525|2810281|191303|154288;1783272|1239|186801|186802|31979|1485|84024;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|186802|3082771|1924093|1965604;3379134|976|200643|171549|171550|239759|626932;1783272|1239|186801|3085636|186803|28050|28052;3379134|976|200643|171549|2005525|375288|46503;3379134|1224|28216|80840|995019|1918598|1796652;3379134|976|200643|171549|2005525|375288|823;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|909932|1843489|31977|39948|218538;3379134|976|200643|171549|815|816|28111;3379134|976|200643|171549|815|816|246787;1783272|1239|186801|3082768|990719|990721|626937;1783272|1239|186801|186802|216572|2172004|2108523;1783272|201174|1760|85004|31953|196081|230143;1783272|1239|186801|3085636|3118652|2039240|160404;3379134|976|200643|171549|815|816|338188;3379134|976|200643|171549|1853231|283168|28118;1783272|1239|186801|3085636|186803|1506553|1965555;3379134|976|200643|171549|2005519|1348911|1099853;3379134|976|200643|171549|815|816|371601;1783272|1239|186801|186802|216572|216851|853;1783272|1239|91061|186826|33958|2767881|1625;1783272|1239|186801|3082720|186804|1505657|261299;1783272|1239|526524|526525|128827|1472649|1034346;1783272|1239|186801|186802|216572|1017280|106588;1783272|1239|186801|186802|31979|1485|1262831;1783272|1239|186801|186802|216572|1535;3379134|976|200643|171549|171552|577309|454154;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|186802|216572|1017280|1965576;3379134|976|200643|171549|171552|838|1262935;1783272|1239|186801|186802|216572|946234|1965538;1783272|1239|91061|186826|1300|1301|1759399;3379134|976|200643|171549|2005519|397864|487174;1783272|201174|84998|1643822|1643826|84108|572010;1783272|1239|186801|3085636|186803|572511|40520;3379134|976|200643|171549|815|816|384639;1783272|1239|909932|1843488|909930|904|187327;3379134|976|200643|171549|171550|239759|328813;1783272|1239|526524|526525|128827|1573535|1735,Complete,Svetlana up
bsdb:33963313/13/2,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 13,France,Homo sapiens,Feces,UBERON:0001988,Adverse effect,EFO:0009658,No - increased BMI (Post-Chemo),Yes - increased BMI (Post-Chemo),Breast cancer patients 12 months after Chemotherapy with increased Body Mass Index (BMI),15,24,NA,WMS,NA,Ion Torrent,relative abundances,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Fig. S6D,23 April 2024,Scholastica,"Scholastica,WikiWorks",Differentially significant abundant taxa in breast cancer patients 12 months after Chemotherapy with increased BMI compared to those without increased BMI,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella jalaludinii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D5,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:5226,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella infantium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:520,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister histaminiformans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella tayi,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:253,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1092,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis",1783272|1239|186801|186802|216572|1263|40518;1783272|1239|909932|909929|1843491|52225|187979;1783272|1239|91061|186826|1300|1301|1303;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|186801|186802|31979|1485|1502;1783272|1239|186801|186802|216572|1520815;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|909932|909929|1843491|52225|52226;1783272|201174|1760|2037|2049|1654|55565;1783272|1239|91061|186826|1300|1301|1343;1783272|1239|186801|186802|204475|745368;1783272|1239|91061|1385|539738|1378|84135;3379134|976|200643|171549|171552|2974265|363265;3379134|976|200643|171549|171552|838|1262930;1783272|1239|91061|186826|1300|1301|1304;1783272|201174|1760|85004|31953|1678|1689;1783272|1239|909932|1843489|31977|29465|1911679;3379134|976|200643|171549|171552|838|1262929;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|909932|1843489|31977|39948|209880;1783272|1239|186801|3085636|186803|1432051|1432052;3379134|976|200643|171549|815|909656|357276;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|186801|186802|31979|1485|1262785;3379134|976|200643|171549|815|816|818;1783272|1239|186801|3085636|186803|841|301301;3379134|976|200643|171549|171552|838|1262919;1783272|1239|186801|3085636|186803|28050|39485;3379134|976|200643|171549|815|816|291644;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|186801|3085636|186803|1649459|154046;1783272|1239|91061|186826|1300|1301|68892;3379134|976|200643|171549|815|816|817;1783272|1239|186801|3085636|186803|1766253|39491;3379134|1224|1236|135625|712|724|729;1783272|1239|186801|3085636|186803|2719313|358742;1783272|1239|186801|3085636|186803|2719313|1531,Complete,Svetlana up
bsdb:33963313/14/NA,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 14,France,Homo sapiens,Feces,UBERON:0001988,Adverse effect,EFO:0009658,No - constipation (Post-Chemo),Yes - constipation (Post-Chemo),Breast cancer patients 12 months after Chemotherapy with constipation,27,15,NA,WMS,NA,Ion Torrent,NA,NA,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:33963313/15/NA,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 15,France,Homo sapiens,Feces,UBERON:0001988,Adverse effect,EFO:0009658,No - diarrhea (Post-Chemo),Yes - diarrhea (Post-Chemo),Breast cancer patients 12 months after Chemotherapy with diarrhea,33,9,NA,WMS,NA,Ion Torrent,NA,NA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:33963313/16/NA,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 16,France,Homo sapiens,Feces,UBERON:0001988,Adverse effect,EFO:0009658,No - hot flashes (Post-Chemo),Yes - hot flashes (Post-Chemo),Breast cancer patients 12 months after Chemotherapy with hot flashes,21,21,NA,WMS,NA,Ion Torrent,NA,NA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:33963313/17/1,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 17,France,Homo sapiens,Feces,UBERON:0001988,Adverse effect,EFO:0009658,Without neurotoxicity (Post-Chemo),With neurotoxicity (Post-Chemo),Breast cancer patients with neurotoxicity evaluated 12 months after Chemotherapy,12,30,NA,WMS,NA,Ion Torrent,relative abundances,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 4B,24 April 2024,Scholastica,"Scholastica,WikiWorks",Differentially abundant taxa in breast cancer patients 12 months after Chemotherapy with neurotoxicity compared to those without neurotoxicity,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma|s__Dielma fastidiosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. An250,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus durans",3379134|976|200643|171549|815|816|820;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|186802|216572|244127|169435;1783272|1239|186801|3085636|186803|2941495|1512;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|526524|526525|2810280|3025755|29348;1783272|1239|186801|3085636|186803|2719313|358743;3379134|976|200643|171549|815|816|818;1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|526524|526525|128827|1472649|1034346;1783272|1239|186801|186802|1392389|1297617;1783272|1239|186801|3085636|186803|2719313|358742;1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|186802|3082771|1924093|1965604;1783272|1239|186801|3085636|186803|2719313|333367;1783272|1239|91061|186826|81852|1350|53345,Complete,Svetlana up
bsdb:33963313/17/2,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 17,France,Homo sapiens,Feces,UBERON:0001988,Adverse effect,EFO:0009658,Without neurotoxicity (Post-Chemo),With neurotoxicity (Post-Chemo),Breast cancer patients with neurotoxicity evaluated 12 months after Chemotherapy,12,30,NA,WMS,NA,Ion Torrent,relative abundances,PLS-DA (Partial least square discriminant analysis),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 4B,24 April 2024,Scholastica,"Scholastica,WikiWorks",Differentially abundant taxa in breast cancer patients 12 months after Chemotherapy with neurotoxicity compared to those without neurotoxicity,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella parvirubra,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:167,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella infantium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:5226,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 57_20,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella xylaniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:520,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:145,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:238,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:110,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__Desulfovibrionaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp. CAG:528,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum butyriciproducens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:443,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. CAG:241,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:95,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",3379134|1224|28216|80840|995019|40544|437898;1783272|1239|186801|186802|31979|1485|1262777;1783272|1239|909932|1843489|31977|29465|1911679;3379134|976|200643|171549|171552|838|1262930;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|91061|186826|1300|1301|1318;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|186801|186802|216572|459786|1897011;3379134|976|200643|171549|171552|577309|454155;3379134|976|200643|171549|171552|838|1262929;1783272|1239|1263005;1783272|1239|1263011;3379134|976|200643|171549|1853231|574697|544645;1783272|1239|186801|186802|216572|1263|40519;3379134|976|200643|171549|171550|239759|28117;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|1263000;3379134|200940|3031449|213115|194924|2049043;1783272|1239|186801|3085636|186803|3342669|45851;3379134|976|200643|171549|2005519|397864|487174;1783272|1239|91061|186826|1300|1301|1343;1783272|1239|186801|186802|216572|244127|1262700;3379134|1224|1236|135625|712|724|729;1783272|1239|186801|186802|3085642|2048137|1628085;3379134|976|200643|171549|171552|2974265|363265;3379134|200940|3031449|213115|194924|872|901;1783272|1239|91061|186826|1300|1301|68892;3379134|976|200643|171549|815|816|1262739;1783272|1239|186801|186802|216572|459786|1262911;3379134|976|200643|171549|815|816|674529;1783272|1239|909932|1843488|909930|33024|33025;1783272|1239|1262988;1783272|1239|186801|186802|216572|216851|853,Complete,Svetlana up
bsdb:33963313/18/1,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 18,France,Mus musculus,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,Heathy mice,Breast cancer mice,Mice “humanized” by fecal microbial transplantation (FMT) from breast cancer patients,7,5,NA,WMS,NA,Ion Torrent,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 5D,24 April 2024,Scholastica,"Scholastica,WikiWorks","LEfSe differentiating breast cancer (BC) and healthy volunteers (HV), describing the 14 most discriminant species in 5 early BC pre-CT versus 7 HV stools used for FMT in AT3 tumor bearing mice",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium JC118,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis",1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|91061|186826|1300|1357|1358;1783272|1239|186801|186802|31979|1070699;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|2719313|333367,Complete,Svetlana up
bsdb:33963313/18/2,33963313,"laboratory experiment,time series / longitudinal observational",33963313,10.1038/s41418-021-00784-1,NA,"Terrisse S., Derosa L., Iebba V., Ghiringhelli F., Vaz-Luis I., Kroemer G., Fidelle M., Christodoulidis S., Segata N., Thomas A.M., Martin A.L., Sirven A., Everhard S., Aprahamian F., Nirmalathasan N., Aarnoutse R., Smidt M., Ziemons J., Caldas C., Loibl S., Denkert C., Durand S., Iglesias C., Pietrantonio F., Routy B., André F., Pasolli E., Delaloge S. , Zitvogel L.",Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment,Cell death and differentiation,2021,NA,Experiment 18,France,Mus musculus,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,Heathy mice,Breast cancer mice,Mice “humanized” by fecal microbial transplantation (FMT) from breast cancer patients,7,5,NA,WMS,NA,Ion Torrent,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 5D,24 April 2024,Scholastica,"Scholastica,WikiWorks","LEfSe differentiating breast cancer (BC) and healthy volunteers (HV), describing the 14 most discriminant species in 5 early BC pre-CT versus 7 HV stools used for FMT in AT3 tumor bearing mice",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes ihumii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella",3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|171550|239759|1470347;1783272|1239|186801|186802|216572|459786;1783272|201174|1760|85004|31953|1678|216816;3379134|976|200643|171549|171550|239759|626932;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|1760|2037|2049|2529408|1660;1783272|201174|84998|84999|1643824|133925,Complete,Svetlana up
bsdb:33964928/1/1,33964928,case-control,33964928,10.1186/s12903-021-01597-x,NA,"Lehenaff R., Tamashiro R., Nascimento M.M., Lee K., Jenkins R., Whitlock J., Li E.C., Sidhu G., Anderson S., Progulske-Fox A., Bubb M.R., Chan E.K.L. , Wang G.P.",Subgingival microbiome of deep and shallow periodontal sites in patients with rheumatoid arthritis: a pilot study,BMC oral health,2021,"16S rRNA sequencing, Microbial dysbiosis, Periodontal disease, Rheumatoid arthritis, Subgingival microbiome",Experiment 1,United States of America,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Arthritis,EFO:0005856,Healthy Non-RA Controls,Rheumatoid Arthritis,Biologic Naive Rheumatoid Arthritis patient,10,8,3 months,16S,123,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 6,2 November 2022,Tislam,"Tislam,Aiyshaaaa,Peace Sandy,WikiWorks","Differentially abundant OTUs in RA and non-RA controls. Differentially abundant OTUs were identified by LEfSe with a minimum LDA threshold of 2. Taxa enriched in non-RA controls are indicated by green bars. Those enriched in RA subjects are indicated by yellow bars. The OTUs associated with RA or non-RA controls shown were observed for both shallow and deep sites. OTU, Operational taxonomic unit",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia meyeri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis",1783272|201174|1760|2037|2049|2529408|52773;1783272|1239|91061|186826|1300|1301|1318,Complete,Peace Sandy
bsdb:33964928/1/2,33964928,case-control,33964928,10.1186/s12903-021-01597-x,NA,"Lehenaff R., Tamashiro R., Nascimento M.M., Lee K., Jenkins R., Whitlock J., Li E.C., Sidhu G., Anderson S., Progulske-Fox A., Bubb M.R., Chan E.K.L. , Wang G.P.",Subgingival microbiome of deep and shallow periodontal sites in patients with rheumatoid arthritis: a pilot study,BMC oral health,2021,"16S rRNA sequencing, Microbial dysbiosis, Periodontal disease, Rheumatoid arthritis, Subgingival microbiome",Experiment 1,United States of America,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Arthritis,EFO:0005856,Healthy Non-RA Controls,Rheumatoid Arthritis,Biologic Naive Rheumatoid Arthritis patient,10,8,3 months,16S,123,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 6,2 November 2022,Tislam,"Tislam,Aiyshaaaa,Peace Sandy,WikiWorks","Differentially abundant OTUs in RA and non-RA controls. Differentially abundant OTUs were identified by LEfSe with a minimum LDA threshold of 2. Taxa enriched in non-RA controls are indicated by green bars. Those enriched in RA subjects are indicated by yellow bars. The OTUs associated with RA or non-RA controls shown were observed for both shallow and deep sites. OTU, Operational taxonomic unit",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella denitrificans,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica",1783272|1239|91061|1385|539738|1378|29391;3379134|1224|28216|206351|481|32257|502;3384189|32066|203490|203491|1129771|32067;3379134|976|200643|171549|171552|838|28132,Complete,Peace Sandy
bsdb:33977168/1/1,33977168,case-control,33977168,10.1016/j.genrep.2021.101200,NA,"Hoque M.N., Rahman M.S., Ahmed R., Hossain M.S., Islam M.S., Islam T., Hossain M.A. , Siddiki A.Z.",Diversity and genomic determinants of the microbiomes associated with COVID-19 and non-COVID respiratory diseases,Gene reports,2021,"COPD, COVID-19, Diversity, Microbiome, Non-COVID, SARS-CoV-2, URTI",Experiment 1,"Bangladesh,China,United Kingdom,United States of America",Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Non-COVID patients with URTI or COPD,COVID-19 patients,Confirmed COVID-19 diagnosis by RT-qPCR,10,11,NA,WMS,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Text/Figure 3,28 June 2021,Claregrieve1,"Claregrieve1,Fatima,WikiWorks",Differential abundance of bacteria between non-COVID-19 patients and COVID-19 patients,increased,"k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Mycoplasmatota,k__Fusobacteriati|p__Fusobacteriota",1783272|1117;3379134|1224;1783272|544448;3384189|32066,Complete,Fatima
bsdb:33977168/1/2,33977168,case-control,33977168,10.1016/j.genrep.2021.101200,NA,"Hoque M.N., Rahman M.S., Ahmed R., Hossain M.S., Islam M.S., Islam T., Hossain M.A. , Siddiki A.Z.",Diversity and genomic determinants of the microbiomes associated with COVID-19 and non-COVID respiratory diseases,Gene reports,2021,"COPD, COVID-19, Diversity, Microbiome, Non-COVID, SARS-CoV-2, URTI",Experiment 1,"Bangladesh,China,United Kingdom,United States of America",Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Non-COVID patients with URTI or COPD,COVID-19 patients,Confirmed COVID-19 diagnosis by RT-qPCR,10,11,NA,WMS,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,Text/Figure 3,28 June 2021,Claregrieve1,"Claregrieve1,Fatima,WikiWorks",Differential bacterial abundance between non-COVID-19 patients and COVID-19 patients,decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota",1783272|201174;3379134|976;1783272|1239,Complete,Fatima
bsdb:33978940/1/1,33978940,case-control,33978940,10.1007/s12250-021-00391-x,NA,"Xiong D., Muema C., Zhang X., Pan X., Xiong J., Yang H., Yu J. , Wei H.",Enriched Opportunistic Pathogens Revealed by Metagenomic Sequencing Hint Potential Linkages between Pharyngeal Microbiota and COVID-19,Virologica Sinica,2021,"ACE2, COVID-19, Campylobacter, Metagenome sequencing, Prevotella, Streptococcus",Experiment 1,China,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative patients with fever and cough,COVID-19 positive patients,COVID-19 positive patients with fever and cough symptoms,11,11,NA,WMS,NA,MGISEQ-2000,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,decreased,unchanged,NA,NA,NA,unchanged,Signature 1,Figure S2,3 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between COVID-19 patients and non-COVID-19 patients,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. A12,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus suis,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter jejuni,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter ruminicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.",1783272|1239|91061|186826|1300|1301|1759399;1783272|1239|91061|186826|1300|1301|1311;1783272|1239|91061|186826|1300|1301|1307;3379134|29547|3031852|213849|72294|194|197;3379134|976|200643|171549|171552|558436|839;3379134|976|200643|171549|171552|838|59823,Complete,Fatima
bsdb:33978940/2/1,33978940,case-control,33978940,10.1007/s12250-021-00391-x,NA,"Xiong D., Muema C., Zhang X., Pan X., Xiong J., Yang H., Yu J. , Wei H.",Enriched Opportunistic Pathogens Revealed by Metagenomic Sequencing Hint Potential Linkages between Pharyngeal Microbiota and COVID-19,Virologica Sinica,2021,"ACE2, COVID-19, Campylobacter, Metagenome sequencing, Prevotella, Streptococcus",Experiment 2,China,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Healthy controls,COVID-19 positive patients,COVID-19 positive patients with fever and cough symptoms,7,11,NA,WMS,NA,MGISEQ-2000,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 1,Figure 3,9 April 2023,Aiyshaaaa,"Aiyshaaaa,WikiWorks",Analysis of species with differential abundance among the COVID-19 and healthy cohorts.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus sanguinicola,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium botulinum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium pseudoperiodonticum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum umeaense,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia wadei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella jejuni,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus koreensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus suis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus uberis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rodentium",1783272|1239|91061|186826|186827|1375|119206;3379134|29547|3031852|213849|72294|194|199;3379134|29547|3031852|213849|72294|194|204;1783272|1239|186801|186802|31979|1485|1491;3384189|32066|203490|203491|203492|848|2663009;3379134|1224|1236|135625|712|724|729;1783272|1239|186801|3085636|186803|1164882|617123;3384189|32066|203490|203491|1129771|32067|157687;3379134|976|200643|171549|171551|836|837;3379134|976|200643|171549|171552|838|28129;3379134|976|200643|171549|171552|838|28131;3379134|976|200643|171549|171552|838|1177574;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552|2974251|28135;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300|1301|113107;1783272|1239|91061|186826|1300|1301|1302;1783272|1239|91061|186826|1300|1301|2382163;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1313;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|1300|1301|1305;1783272|1239|91061|186826|1300|1301|1307;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|91061|186826|1300|1301|1349;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|909932|1843489|31977|29465|248315,Complete,NA
bsdb:33980943/1/1,33980943,case-control,33980943,10.1038/s41598-021-89516-6,NA,"Gaibani P., Viciani E., Bartoletti M., Lewis R.E., Tonetti T., Lombardo D., Castagnetti A., Bovo F., Horna C.S., Ranieri M., Viale P., Re M.C. , Ambretti S.",The lower respiratory tract microbiome of critically ill patients with COVID-19,Scientific reports,2021,NA,Experiment 1,Italy,Homo sapiens,Lung,UBERON:0002048,COVID-19,MONDO:0100096,COVID-19 negative patients with pneumonia,COVID-19 patients,COVID-19 Critically Ill Subjects,24,24,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 1,Figure 3,14 July 2021,Claregrieve1,"Claregrieve1,Peace Sandy,WikiWorks",The figure shows the microbial taxa with significant differences between the COVID-19 positive (red) and negative patients (green) (LDA score>2) with their original identification codes.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter schindleri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptacetobacter|s__Peptacetobacter hiranonis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Aquipseudomonas|s__Aquipseudomonas alcaligenes,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium",3379134|1224|1236|2887326|468|469;3379134|1224|1236|2887326|468|469|108981;3379134|1224|1236|91347|543;1783272|1239|186801|3082720|186804|2743582|89152;3379134|1224|1236|72274|135621|3236652|43263;3379134|976|117747|200666|84566|28453,Complete,Peace Sandy
bsdb:33980943/1/2,33980943,case-control,33980943,10.1038/s41598-021-89516-6,NA,"Gaibani P., Viciani E., Bartoletti M., Lewis R.E., Tonetti T., Lombardo D., Castagnetti A., Bovo F., Horna C.S., Ranieri M., Viale P., Re M.C. , Ambretti S.",The lower respiratory tract microbiome of critically ill patients with COVID-19,Scientific reports,2021,NA,Experiment 1,Italy,Homo sapiens,Lung,UBERON:0002048,COVID-19,MONDO:0100096,COVID-19 negative patients with pneumonia,COVID-19 patients,COVID-19 Critically Ill Subjects,24,24,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 2,Figure 3,14 July 2021,Claregrieve1,"Claregrieve1,Aleru002,Peace Sandy,WikiWorks","The figure shows the microbial taxa with significant differences between the COVID-19-positive (red) and negative patients 
(green) (LDA score>2) with their original identification codes.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Nanosynbacterales|f__Candidatus Nanosynbacteraceae|g__Candidatus Nanosynbacter|s__Candidatus Nanosynbacter lyticus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|s__Streptococcaceae bacterium RF32,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral clone CW040,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,p__Candidatus Absconditibacteriota|s__candidate division SR1 bacterium",1783272|201174|1760|2037|2049|1654;1783272|201174|84998|84999|1643824|1380;3379134|29547|3031852|213849|72294|194;95818|2093818|2093819|2093822|2093823|1476577;3379134|976|117743|200644|49546|1016;1783272|1239|186801|3085636|186803|43996;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724|727;3379134|1224|1236|135625|712|724|729;3379134|976|200643|171549|171552|2974257|425941;1783272|1239|91061|186826|33958|2759736|57037;3384189|32066|203490|203491|1129771|32067;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3085636|186803|437755;3379134|1224|28216|206351|481|482;1783272|1239|186801|3085636|186803|265975;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552|838|60133;3379134|976|200643|171549|171552;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|909932|909929|1843491|970;1783272|1239|91061|186826|1300|423432;1783272|1239|91061|186826|1300|1301;95818|163601;3379134|976|200643|171549|2005525|195950;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|909932|1843489|31977|29465|29466;221235|2044938,Complete,Peace Sandy
bsdb:33985520/1/1,33985520,"case-control,time series / longitudinal observational",33985520,10.1186/s12934-021-01589-0,NA,"Kuai X.Y., Yao X.H., Xu L.J., Zhou Y.Q., Zhang L.P., Liu Y., Pei S.F. , Zhou C.L.",Evaluation of fecal microbiota transplantation in Parkinson's disease patients with constipation,Microbial cell factories,2021,"16s rDNA sequencing, Constipation, FMT, Gut microbiota, Parkinson’s disease",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,"Constipation,Parkinson's disease","HP:0002019,MONDO:0005180",Healthy Control group,Parkinson's disease patients (PD) before Fecal microbiota transplant (FMT),Parkinson's disease patients with constipation before FMT,13,11,NA,16S,NA,NA,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Fig. 2C and 2D,8 March 2024,Ikehdarlington,"Ikehdarlington,ChiomaBlessing,WikiWorks",Differential microorganism communities observed in the intestinal microbiota of PD patients with constipation before FMT compared to the Health Control group (HC),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota",3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976,Complete,ChiomaBlessing
bsdb:33985520/1/2,33985520,"case-control,time series / longitudinal observational",33985520,10.1186/s12934-021-01589-0,NA,"Kuai X.Y., Yao X.H., Xu L.J., Zhou Y.Q., Zhang L.P., Liu Y., Pei S.F. , Zhou C.L.",Evaluation of fecal microbiota transplantation in Parkinson's disease patients with constipation,Microbial cell factories,2021,"16s rDNA sequencing, Constipation, FMT, Gut microbiota, Parkinson’s disease",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,"Constipation,Parkinson's disease","HP:0002019,MONDO:0005180",Healthy Control group,Parkinson's disease patients (PD) before Fecal microbiota transplant (FMT),Parkinson's disease patients with constipation before FMT,13,11,NA,16S,NA,NA,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Fig. 2C and 2D,10 March 2024,Ikehdarlington,"Ikehdarlington,ChiomaBlessing,WikiWorks",Differential microorganism communities observed in the intestinal microbiota of PD patients with constipation before FMT compared to the Health Control group (HC),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota",3379134|1224|28216;3379134|1224|28216|80840|119060;1783272|1239|186801;3379134|1224|1236|91347|543;1783272|1239|186801|3082720|186804;1783272|1239,Complete,ChiomaBlessing
bsdb:33985520/5/1,33985520,"case-control,time series / longitudinal observational",33985520,10.1186/s12934-021-01589-0,NA,"Kuai X.Y., Yao X.H., Xu L.J., Zhou Y.Q., Zhang L.P., Liu Y., Pei S.F. , Zhou C.L.",Evaluation of fecal microbiota transplantation in Parkinson's disease patients with constipation,Microbial cell factories,2021,"16s rDNA sequencing, Constipation, FMT, Gut microbiota, Parkinson’s disease",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Parkinson's disease patients before fecal microbiota transplant (FMT),Parkinson's disease patients after fecal microbiota transplant (FMT),Parkinson's disease patients 4 weeks after FMT,11,11,NA,16S,NA,NA,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 3D,16 March 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential microorganism communities observed in the intestinal microbiota of PD patients with constipation before FMT compared to PD patients with constipation 4 weeks after FMT,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,3379134|1224|1236|91347|543|1940338,Complete,ChiomaBlessing
bsdb:33985520/5/2,33985520,"case-control,time series / longitudinal observational",33985520,10.1186/s12934-021-01589-0,NA,"Kuai X.Y., Yao X.H., Xu L.J., Zhou Y.Q., Zhang L.P., Liu Y., Pei S.F. , Zhou C.L.",Evaluation of fecal microbiota transplantation in Parkinson's disease patients with constipation,Microbial cell factories,2021,"16s rDNA sequencing, Constipation, FMT, Gut microbiota, Parkinson’s disease",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Parkinson's disease patients before fecal microbiota transplant (FMT),Parkinson's disease patients after fecal microbiota transplant (FMT),Parkinson's disease patients 4 weeks after FMT,11,11,NA,16S,NA,NA,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 3C,16 March 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential microorganism communities observed in the intestinal microbiota of PD patients with constipation before FMT compared to PD patients with constipation 4 weeks after FMT,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,1783272|1239|186801|186802|216572|216851,Complete,ChiomaBlessing
bsdb:33986253/1/1,33986253,"cross-sectional observational, not case-control",33986253,10.1038/s41392-021-00614-3,NA,"Ma S., Zhang F., Zhou F., Li H., Ge W., Gan R., Nie H., Li B., Wang Y., Wu M., Li D., Wang D., Wang Z., You Y. , Huang Z.",Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19,Signal transduction and targeted therapy,2021,NA,Experiment 1,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Confirmed COVID-19 cases,28,31,NA,WMS,NA,MGISEQ-2000,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4c,13 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between COVID-19 patients and healthy controls,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp. oral taxon 108,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. HSID18069,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica",1783272|201174|1760|85009|31957|2801844;1783272|201174|1760|2037|2049|2050;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|3085636|186803|265975|712414;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|2419515;1783272|201174|84998|1643822|1643826|84108;1783272|201174|1760|85009|31957|2801844|1750,Complete,Atrayees
bsdb:33986253/1/2,33986253,"cross-sectional observational, not case-control",33986253,10.1038/s41392-021-00614-3,NA,"Ma S., Zhang F., Zhou F., Li H., Ge W., Gan R., Nie H., Li B., Wang Y., Wu M., Li D., Wang D., Wang Z., You Y. , Huang Z.",Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19,Signal transduction and targeted therapy,2021,NA,Experiment 1,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Confirmed COVID-19 cases,28,31,NA,WMS,NA,MGISEQ-2000,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4c,14 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between COVID-19 patients and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Liquorilactobacillus|s__Liquorilactobacillus nagelii",1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|33958|2767888|82688,Complete,Atrayees
bsdb:33986253/2/1,33986253,"cross-sectional observational, not case-control",33986253,10.1038/s41392-021-00614-3,NA,"Ma S., Zhang F., Zhou F., Li H., Ge W., Gan R., Nie H., Li B., Wang Y., Wu M., Li D., Wang D., Wang Z., You Y. , Huang Z.",Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19,Signal transduction and targeted therapy,2021,NA,Experiment 2,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Flu patients,COVID-19 patients,Confirmed COVID-19 cases,29,31,NA,WMS,NA,MGISEQ-2000,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4c,14 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between COVID-19 patients and other flu patients,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp. oral taxon 108,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. HSID18069,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica",1783272|201174|1760|85009|31957|2801844;1783272|1239|91061|186826|33958|2742598|1613;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|3085636|186803|265975|712414;3379134|976|200643|171549|171552|838|419005;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|2419515;1783272|201174|84998|1643822|1643826|84108;1783272|201174|1760|85009|31957|2801844|1750,Complete,Atrayees
bsdb:33986253/3/1,33986253,"cross-sectional observational, not case-control",33986253,10.1038/s41392-021-00614-3,NA,"Ma S., Zhang F., Zhou F., Li H., Ge W., Gan R., Nie H., Li B., Wang Y., Wu M., Li D., Wang D., Wang Z., You Y. , Huang Z.",Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19,Signal transduction and targeted therapy,2021,NA,Experiment 3,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,Flu patients,Patients with influenza B,29,31,NA,WMS,NA,MGISEQ-2000,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 4c,14 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between flu patients and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Liquorilactobacillus|s__Liquorilactobacillus nagelii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii",1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|33958|2767888|82688;1783272|1239|91061|186826|33958|2742598|1613;3379134|976|200643|171549|171552|838|419005,Complete,Atrayees
bsdb:33986253/3/2,33986253,"cross-sectional observational, not case-control",33986253,10.1038/s41392-021-00614-3,NA,"Ma S., Zhang F., Zhou F., Li H., Ge W., Gan R., Nie H., Li B., Wang Y., Wu M., Li D., Wang D., Wang Z., You Y. , Huang Z.",Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19,Signal transduction and targeted therapy,2021,NA,Experiment 3,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,Flu patients,Patients with influenza B,29,31,NA,WMS,NA,MGISEQ-2000,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 4c,14 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between flu patients and healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. HSID18069,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp. oral taxon 108,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica",1783272|1239|186801|3085636|186803|265975;1783272|201174|1760|85009|31957|2801844;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|2037|2049|2050;1783272|201174|1760|85006|1268|32207|2419515;1783272|1239|186801|3085636|186803|265975|712414;1783272|201174|1760|85009|31957|2801844|1750,Complete,Atrayees
bsdb:33986253/4/1,33986253,"cross-sectional observational, not case-control",33986253,10.1038/s41392-021-00614-3,NA,"Ma S., Zhang F., Zhou F., Li H., Ge W., Gan R., Nie H., Li B., Wang Y., Wu M., Li D., Wang D., Wang Z., You Y. , Huang Z.",Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19,Signal transduction and targeted therapy,2021,NA,Experiment 4,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Confirmed COVID-19 cases,28,31,NA,WMS,NA,MGISEQ-2000,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2a-b,14 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between COVID-19 patients and healthy controls by LefSe,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Cellulomonadaceae|g__Cellulomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Cryptobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Kytococcaceae|g__Kytococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae|g__Xylanimonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus",1783272|201174|1760|2037|2049|76833;1783272|201174|1760|85004|31953|1678;1783272|1239|526524|526525|128827|118747;1783272|201174|1760|85006|85016|1707;1783272|201174|1760|85007|1653|1716;1783272|201174|84998|1643822|1643826|84162;1783272|1239|186801|3082720|3118655|44259;1783272|201174|1760|85006|2805426|57499;1783272|1239|186801|3085636|186803|1164882;1783272|1239|186801|3082720|543314|86331;1783272|1239|1737404|1737405|1570339|543311;1783272|201174|1760|85009|31957|1743;1783272|201174|1760|2037|2049|2529408;1783272|1239|909932|909929|1843491|970;1783272|1239|91061|186826|1300|1301;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85006|1268|32207;1783272|1239|186801|3085636|186803|265975;1783272|201174|1760|85006|85017|186188;1783272|201174|1760|85009|31957|2801844;3379134|1224|1236|135615|868|2717;1783272|201174|1760|2037|2049|184869;1783272|201174|1760|2037|2049|2050,Complete,Atrayees
bsdb:33986253/4/2,33986253,"cross-sectional observational, not case-control",33986253,10.1038/s41392-021-00614-3,NA,"Ma S., Zhang F., Zhou F., Li H., Ge W., Gan R., Nie H., Li B., Wang Y., Wu M., Li D., Wang D., Wang Z., You Y. , Huang Z.",Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19,Signal transduction and targeted therapy,2021,NA,Experiment 4,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Confirmed COVID-19 cases,28,31,NA,WMS,NA,MGISEQ-2000,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2a-b,14 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between COVID-19 patients and healthy controls by LefSe,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia",1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|186827|46123,Complete,Atrayees
bsdb:33986253/5/1,33986253,"cross-sectional observational, not case-control",33986253,10.1038/s41392-021-00614-3,NA,"Ma S., Zhang F., Zhou F., Li H., Ge W., Gan R., Nie H., Li B., Wang Y., Wu M., Li D., Wang D., Wang Z., You Y. , Huang Z.",Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19,Signal transduction and targeted therapy,2021,NA,Experiment 5,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,Flu patients,Patients with influenza B,28,29,NA,WMS,NA,MGISEQ-2000,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2a,14 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between flu patients and healthy controls by LefSe,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae|g__Xylanimonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum",1783272|1239|91061|186826|1300|1301;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85006|1268|32207;1783272|1239|186801|3085636|186803|265975;1783272|201174|1760|85006|85017|186188;1783272|201174|1760|85009|31957|2801844;3379134|1224|1236|135615|868|2717;1783272|201174|1760|2037|2049|184869,Complete,Atrayees
bsdb:33986253/5/2,33986253,"cross-sectional observational, not case-control",33986253,10.1038/s41392-021-00614-3,NA,"Ma S., Zhang F., Zhou F., Li H., Ge W., Gan R., Nie H., Li B., Wang Y., Wu M., Li D., Wang D., Wang Z., You Y. , Huang Z.",Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19,Signal transduction and targeted therapy,2021,NA,Experiment 5,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,Flu patients,Patients with influenza B,28,29,NA,WMS,NA,MGISEQ-2000,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2a,14 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between flu patients and healthy controls by LefSe,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:33996618/1/1,33996618,"cross-sectional observational, not case-control",33996618,https://doi.org/10.3389/fcimb.2021.625589,NA,"Han J., Wu S., Fan Y., Tian Y. , Kong J.",Biliary Microbiota in Choledocholithiasis and Correlation With Duodenal Microbiota,Frontiers in cellular and infection microbiology,2021,"antimicrobial resistance, biliary microbiota, choledocholithiasis, duodenal microbiota, duodenal–biliary reflux",Experiment 1,China,Homo sapiens,"Duodenum,Bile duct",UBERON:0002114,Sampling site,EFO:0000688,biliary microbiota,duodenal microbiota,duodenal juice samples from patients with choledocholithiasis,10,10,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,figure 2D,14 December 2023,Folakunmi,"Folakunmi,WikiWorks",microbial taxa characterizing duodenal juice from bile in patients with choledocholithiasis as determined by LEfSe,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota",1783272|201174;1783272|1239|91061;1783272|1239|91061|186826;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|201174,Complete,ChiomaBlessing
bsdb:34026662/1/1,34026662,case-control,34026662,https://doi.org/10.3389/fcimb.2021.663131,NA,"Chang S.C., Lin S.F., Chen S.T., Chang P.Y., Yeh Y.M., Lo F.S. , Lu J.J.",Alterations of Gut Microbiota in Patients With Graves' Disease,Frontiers in cellular and infection microbiology,2021,"16S rRNA, Graves’ disease, clinical parameters, gut microbiota, next-generation sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Healthy Controls,Graves’ disease (GD),Patients diagnosed with Graves’ disease (GD),48,55,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 2B,24 July 2025,Aleru Divine,Aleru Divine,Linear discriminant analysis (LDA) scores show differences among taxa between GD and healthy controls. Only taxa meeting a significant LDA threshold value of >4 are shown,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota",1783272|1239|909932|1843489|31977;1783272|1239|909932|909929;1783272|1239|909932;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|976|200643;3379134|976|200643|171549;3379134|976,Complete,NA
bsdb:34026662/1/2,34026662,case-control,34026662,https://doi.org/10.3389/fcimb.2021.663131,NA,"Chang S.C., Lin S.F., Chen S.T., Chang P.Y., Yeh Y.M., Lo F.S. , Lu J.J.",Alterations of Gut Microbiota in Patients With Graves' Disease,Frontiers in cellular and infection microbiology,2021,"16S rRNA, Graves’ disease, clinical parameters, gut microbiota, next-generation sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Healthy Controls,Graves’ disease (GD),Patients diagnosed with Graves’ disease (GD),48,55,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 2B,24 July 2025,Aleru Divine,Aleru Divine,Linear discriminant analysis (LDA) scores reveal differences among taxa between the GD and healthy control groups. Only taxa meeting a significant LDA threshold value of >4 are shown,decreased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|1239|186801;1783272|1239|186801|186802;1783272|1239;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|186802|216572|216851,Complete,NA
bsdb:34026662/2/1,34026662,case-control,34026662,https://doi.org/10.3389/fcimb.2021.663131,NA,"Chang S.C., Lin S.F., Chen S.T., Chang P.Y., Yeh Y.M., Lo F.S. , Lu J.J.",Alterations of Gut Microbiota in Patients With Graves' Disease,Frontiers in cellular and infection microbiology,2021,"16S rRNA, Graves’ disease, clinical parameters, gut microbiota, next-generation sequencing",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Healthy Controls,Graves’ disease (GD),Patients diagnosed with Graves’ disease (GD),48,55,2 months,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 2C,24 July 2025,Aleru Divine,Aleru Divine,"Differentially abundant taxa from the phylum to genus level were further analyzed by STAMP analysis using Welch’s t-test (p < 0.05, q < 0.05) (C).",increased,"k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica",3379134|976;1783272|201174;3379134|976|200643|171549|2005525;1783272|1239|526524|526525|128827;1783272|201174|84998|84999|84107;3379134|976|200643|171549|171552;1783272|201174|1760|2037|2049;3379134|976|200643|171549|2005525|375288;1783272|201174|84998|84999|84107|102106;3379134|976|200643|171549|171552|838;1783272|201174|1760|2037|2049|2529408|1660,Complete,NA
bsdb:34026662/2/2,34026662,case-control,34026662,https://doi.org/10.3389/fcimb.2021.663131,NA,"Chang S.C., Lin S.F., Chen S.T., Chang P.Y., Yeh Y.M., Lo F.S. , Lu J.J.",Alterations of Gut Microbiota in Patients With Graves' Disease,Frontiers in cellular and infection microbiology,2021,"16S rRNA, Graves’ disease, clinical parameters, gut microbiota, next-generation sequencing",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Healthy Controls,Graves’ disease (GD),Patients diagnosed with Graves’ disease (GD),48,55,2 months,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 2C,24 July 2025,Aleru Divine,Aleru Divine,"Differentially abundant taxa from the phylum to genus level were further analyzed by STAMP analysis using Welch’s t-test (p < 0.05, q < 0.05) (C).",decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239;1783272|1239|186801|3085636|186803,Complete,NA
bsdb:34031657/1/1,34031657,case-control,34031657,https://doi.org/10.1101/2021.05.20.445008,NA,"Rhoades N.S., Pinski A., Monsibais A.N., Jankeel A., Doratt B.M., Cinco I.R., Ibraim I. , Messaoudi I.",Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including <i>Pseudomonas Aeruginosa</i>,bioRxiv : the preprint server for biology,2021,NA,Experiment 1,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls and healthcare workers,COVID-19 positive patients,Patients positive for SARS-CoV-2,66,68,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2a,6 August 2021,Claregrieve1,"Claregrieve1,Iram jamshed,WikiWorks",Differential microbial abundance between COVID-19 patients and non-COVID patients (COVID negative patients and healthcare workers),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",3379134|1224|1236|2887326|468|469;1783272|201174|1760|85006|1268|1269;3379134|1224|1236|2887326|468|475;3379134|1224|1236|72274|135621|286;1783272|201174|1760|85006|1268|32207,Complete,Folakunmi
bsdb:34031657/2/1,34031657,case-control,34031657,https://doi.org/10.1101/2021.05.20.445008,NA,"Rhoades N.S., Pinski A., Monsibais A.N., Jankeel A., Doratt B.M., Cinco I.R., Ibraim I. , Messaoudi I.",Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including <i>Pseudomonas Aeruginosa</i>,bioRxiv : the preprint server for biology,2021,NA,Experiment 2,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls,COVID-19 positive patients,Patients positive for SARS-CoV-2,21,68,NA,16S,4,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figures 2b-h,6 August 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between COVID-19 positive and COVID-19 negative patients,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Anoxybacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa",1783272|1239|91061|1385|3120669|150247;3379134|1224|1236|2887326|468|469;3379134|1224|1236|72274|135621|286;3379134|1224|1236|72274|135621|286|287,Complete,Folakunmi
bsdb:34031657/3/1,34031657,case-control,34031657,https://doi.org/10.1101/2021.05.20.445008,NA,"Rhoades N.S., Pinski A., Monsibais A.N., Jankeel A., Doratt B.M., Cinco I.R., Ibraim I. , Messaoudi I.",Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including <i>Pseudomonas Aeruginosa</i>,bioRxiv : the preprint server for biology,2021,NA,Experiment 3,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative healthcare workers (controls),COVID-19 positive patients,Patients positive for SARS-CoV-2,45,68,NA,16S,4,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 1,Figures 2b-h,6 August 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between COVID-19 positive and COVID-19 negative healthcare workers,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Anoxybacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa",1783272|1239|91061|1385|3120669|150247;3379134|1224|1236|72274|135621|286|287,Complete,Folakunmi
bsdb:34031657/3/2,34031657,case-control,34031657,https://doi.org/10.1101/2021.05.20.445008,NA,"Rhoades N.S., Pinski A., Monsibais A.N., Jankeel A., Doratt B.M., Cinco I.R., Ibraim I. , Messaoudi I.",Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including <i>Pseudomonas Aeruginosa</i>,bioRxiv : the preprint server for biology,2021,NA,Experiment 3,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative healthcare workers (controls),COVID-19 positive patients,Patients positive for SARS-CoV-2,45,68,NA,16S,4,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 2,Figures 2b-h,6 August 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between COVID-19 positive and COVID-19 negative healthcare workers,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia cepacia,3379134|1224|28216|80840|119060|32008|292,Complete,Folakunmi
bsdb:34031657/4/1,34031657,case-control,34031657,https://doi.org/10.1101/2021.05.20.445008,NA,"Rhoades N.S., Pinski A., Monsibais A.N., Jankeel A., Doratt B.M., Cinco I.R., Ibraim I. , Messaoudi I.",Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including <i>Pseudomonas Aeruginosa</i>,bioRxiv : the preprint server for biology,2021,NA,Experiment 4,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,Viral load,EFO:0010125,high Ct CoV+ patients,low Ct CoV+ patients,SARS-CoV-2 positive patients with low cycle threshold value (>23.5),23,22,NA,16S,4,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,figure 3,26 December 2023,Folakunmi,"Folakunmi,WikiWorks",Differentially abundant genera in the nasal microbiome between CoV+ individuals stratified by viral RNA load into High and Low Ct,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa",1783272|201174|1760|85007|1653|1716;3379134|1224|28216|206351|481|482;3379134|1224|1236|72274|135621|286;3379134|1224|1236|72274|135621|286|287,Complete,Folakunmi
bsdb:34031657/5/1,34031657,case-control,34031657,https://doi.org/10.1101/2021.05.20.445008,NA,"Rhoades N.S., Pinski A., Monsibais A.N., Jankeel A., Doratt B.M., Cinco I.R., Ibraim I. , Messaoudi I.",Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including <i>Pseudomonas Aeruginosa</i>,bioRxiv : the preprint server for biology,2021,NA,Experiment 5,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,Viral load,EFO:0010125,high Ct CoV+ patients,mid Ct CoV+ patients,SARS-CoV-2 positive patients with mid cycle threshold value (32.9-25.0),23,23,NA,16S,4,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,figure 3,26 December 2023,Folakunmi,"Folakunmi,WikiWorks",Differentially abundant genera in the nasal microbiome between CoV+ individuals stratified by viral RNA load into High and Mid Ct,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",1783272|201174|1760|85007|1653|1716;3379134|1224|28216|206351|481|482,Complete,Folakunmi
bsdb:34031657/5/2,34031657,case-control,34031657,https://doi.org/10.1101/2021.05.20.445008,NA,"Rhoades N.S., Pinski A., Monsibais A.N., Jankeel A., Doratt B.M., Cinco I.R., Ibraim I. , Messaoudi I.",Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including <i>Pseudomonas Aeruginosa</i>,bioRxiv : the preprint server for biology,2021,NA,Experiment 5,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,Viral load,EFO:0010125,high Ct CoV+ patients,mid Ct CoV+ patients,SARS-CoV-2 positive patients with mid cycle threshold value (32.9-25.0),23,23,NA,16S,4,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,figure 3,26 December 2023,Folakunmi,"Folakunmi,WikiWorks",Differentially abundant genera in the nasal microbiome between CoV+ individuals stratified by viral RNA load into High and Mid Ct,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:34031657/6/1,34031657,case-control,34031657,https://doi.org/10.1101/2021.05.20.445008,NA,"Rhoades N.S., Pinski A., Monsibais A.N., Jankeel A., Doratt B.M., Cinco I.R., Ibraim I. , Messaoudi I.",Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including <i>Pseudomonas Aeruginosa</i>,bioRxiv : the preprint server for biology,2021,NA,Experiment 6,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,Viral load,EFO:0010125,mid Ct CoV+ patients,low Ct CoV+ patients,SARS-CoV-2 positive patients with low cycle threshold value (>23.5),23,22,NA,16S,4,Illumina,NA,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,figure 3,26 December 2023,Folakunmi,"Folakunmi,WikiWorks",Differentially abundant genera in the nasal microbiome between CoV+ individuals stratified by viral RNA load into Mid and Low Ct,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,3379134|1224|1236|72274|135621|286|287,Complete,Folakunmi
bsdb:34031657/7/1,34031657,case-control,34031657,https://doi.org/10.1101/2021.05.20.445008,NA,"Rhoades N.S., Pinski A., Monsibais A.N., Jankeel A., Doratt B.M., Cinco I.R., Ibraim I. , Messaoudi I.",Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including <i>Pseudomonas Aeruginosa</i>,bioRxiv : the preprint server for biology,2021,NA,Experiment 7,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,Viral load,EFO:0010125,low and mid Ct CoV+ patients,high Ct CoV+ patients,SARS-CoV-2 positive patients with high cycle threshold value (>34.6),45,23,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,figure 3A,26 December 2023,Folakunmi,"Folakunmi,WikiWorks","Differentially abundant genera in the nasal microbiome between CoV+ individuals stratified by viral RNA load into High, Low and Mid Ct",increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:34031657/7/2,34031657,case-control,34031657,https://doi.org/10.1101/2021.05.20.445008,NA,"Rhoades N.S., Pinski A., Monsibais A.N., Jankeel A., Doratt B.M., Cinco I.R., Ibraim I. , Messaoudi I.",Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including <i>Pseudomonas Aeruginosa</i>,bioRxiv : the preprint server for biology,2021,NA,Experiment 7,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,Viral load,EFO:0010125,low and mid Ct CoV+ patients,high Ct CoV+ patients,SARS-CoV-2 positive patients with high cycle threshold value (>34.6),45,23,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,figure 3A,26 December 2023,Folakunmi,"Folakunmi,WikiWorks","Differentially abundant genera in the nasal microbiome between CoV+ individuals stratified by viral RNA load into High, Mid and Low Ct",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85009|31957|1912216;3379134|1224|28216|206351|481|482;3379134|1224|1236|72274|135621|286,Complete,Folakunmi
bsdb:34053449/1/1,34053449,case-control,34053449,https://doi.org/10.1186/s12866-021-02221-2,NA,"Zhen J., Sun Y., Zhao P., Li C., Wang H., Li Y., Zhao L., Wang L., Huang G. , Xu A.",Abundance alteration of nondominant species in fecal-associated microbiome of patients with SAPHO syndrome,BMC microbiology,2021,"Biomarkers, Fecal-associated microbiome, SAPHO syndrome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,SAPHO syndrome,NA,Healthy control group,SAPHO syndrome Patients,"SAPHO (synovitis, acne, pustulosis, hyperostosis and osteosis) syndrome, The main features of SAPHO syndrome consist of cutaneous and osteoarticular manifestations, the latter more often affects the anterior chest wall and has a typical radiologic finding called the “bull’s head sign”",14,17,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 3,8 March 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,Peace Sandy,WikiWorks","Distingushing taxa identified in the HC and SAPHO groups using LEfSe analysis. (a) Cladogram and (b) LDA score bar chart constructed using the LEfSe method. HC, healthy control; SAPHO, SAPHO syndrome",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella",1783272|1239|91061|1385;1783272|1239|91061|1385|539738|1378,Complete,Peace Sandy
bsdb:34053449/1/2,34053449,case-control,34053449,https://doi.org/10.1186/s12866-021-02221-2,NA,"Zhen J., Sun Y., Zhao P., Li C., Wang H., Li Y., Zhao L., Wang L., Huang G. , Xu A.",Abundance alteration of nondominant species in fecal-associated microbiome of patients with SAPHO syndrome,BMC microbiology,2021,"Biomarkers, Fecal-associated microbiome, SAPHO syndrome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,SAPHO syndrome,NA,Healthy control group,SAPHO syndrome Patients,"SAPHO (synovitis, acne, pustulosis, hyperostosis and osteosis) syndrome, The main features of SAPHO syndrome consist of cutaneous and osteoarticular manifestations, the latter more often affects the anterior chest wall and has a typical radiologic finding called the “bull’s head sign”",14,17,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 3,9 March 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,Peace Sandy,WikiWorks","Distingushing taxa identified in the HC and SAPHO groups using LEfSe analysis. (a) Cladogram and (b) LDA score bar chart constructed using the LEfSe method. HC, healthy control; SAPHO, SAPHO syndrome",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|1508657,Complete,Peace Sandy
bsdb:34055851/1/1,34055851,case-control,34055851,10.3389/fnut.2021.638825,NA,"Tian Y., Sun K.Y., Meng T.Q., Ye Z., Guo S.M., Li Z.M., Xiong C.L., Yin Y., Li H.G. , Zhou L.Q.",Gut Microbiota May Not Be Fully Restored in Recovered COVID-19 Patients After 3-Month Recovery,Frontiers in nutrition,2021,"16S sequence, SARS-CoV-2, gut microbiota, recovered COVID-19 patient, short chain fatty acids",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 patients,"Patients between 25-45 years of age with documented recovery from COVID-19, detailed medical records during hospitalization and discharge certificate",7,7,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,decreased,decreased,NA,NA,Signature 1,Figure 4b,29 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance of microbial taxa between controls and recovered COVID-19 patients,increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Metazoa|p__Arthropoda|c__Insecta|o__Coleoptera|f__Lycidae|s__Metriorrhynchinae|g__Microtrichalus,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia|o__Acidimicrobiales|f__Microthrixaceae|g__Candidatus Neomicrothrix,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia|o__Acidimicrobiales|f__Microthrixaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae",1783272|201174|84992;33208|6656|50557|7041|71195|2043424|343821;1783272|201174|84992|84993|1798913|41949;1783272|201174|84992|84993|1798913;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006;1783272|1239|526524|526525|2810280|1505663;1783272|201174|1760|85006|1268,Complete,Fatima
bsdb:34055851/1/2,34055851,case-control,34055851,10.3389/fnut.2021.638825,NA,"Tian Y., Sun K.Y., Meng T.Q., Ye Z., Guo S.M., Li Z.M., Xiong C.L., Yin Y., Li H.G. , Zhou L.Q.",Gut Microbiota May Not Be Fully Restored in Recovered COVID-19 Patients After 3-Month Recovery,Frontiers in nutrition,2021,"16S sequence, SARS-CoV-2, gut microbiota, recovered COVID-19 patient, short chain fatty acids",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 patients,"Patients between 25-45 years of age with documented recovery from COVID-19, detailed medical records during hospitalization and discharge certificate",7,7,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,decreased,decreased,NA,NA,Signature 2,Figure 4b,29 June 2021,Claregrieve1,"Claregrieve1,Merit,WikiWorks",Differential abundance of microbial taxa between controls and recovered COVID-19 patients,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239|186801|3085636|186803|2569097|39488;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572|1263|41978;1783272|1239|186801|186802|216572|2485925;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|1263,Complete,Fatima
bsdb:34058978/1/1,34058978,"cross-sectional observational, not case-control",34058978,10.1186/s12575-021-00148-6,NA,"Engen P.A., Naqib A., Jennings C., Green S.J., Landay A., Keshavarzian A. , Voigt R.M.",Nasopharyngeal Microbiota in SARS-CoV-2 Positive and Negative Patients,Biological procedures online,2021,"COVID-19, Dysbiosis, Microbiota, Nasopharyngeal, SARS-CoV-2",Experiment 1,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls,COVID-19 positive patients,Patients who are COVID-19 positive by RT-PCR,10,9,NA,16S,4,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,unchanged,unchanged,NA,unchanged,NA,unchanged,Signature 1,Supplementary Tables 5 & 6,17 June 2021,Claregrieve1,"Claregrieve1,Chloe,WikiWorks,Merit",Differential abundance of nasopharyngeal bacteria between COVID-19-positive and COVID-19-negative samples,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Blastococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacillati|p__Bacillota|c__Bacilli",3379134|976|200643|171549|171552|1283313;1783272|1239|1737404|1737405|1570339|165779;3379134|976;1783272|201174|1760|1643682|85030|38501;1783272|1239|186801|186802|3085642|580596;3379134|29547|3031852|213849|72294|194;3379134|976|117743|200644|49546|1016;3379134|976|117743|200644|2762318|59732;1783272|1239|1737404|1737405|1570339|150022;3379134|976|117743|200644|49546|237;1783272|1239|91061|1385|539738|1378;1783272|201174|1760|85006|1268|57493;1783272|201174|1760|85006|1268|1269;3379134|1224|1236|2887326|468|475;1783272|1239|1737404|1737405|1570339|162289;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|201174|1760|85006|1268|32207;1783272|1239|909932|909929|1843491|970;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|135623|641|662;1783272|1239|91061,Complete,Chloe
bsdb:34058978/1/2,34058978,"cross-sectional observational, not case-control",34058978,10.1186/s12575-021-00148-6,NA,"Engen P.A., Naqib A., Jennings C., Green S.J., Landay A., Keshavarzian A. , Voigt R.M.",Nasopharyngeal Microbiota in SARS-CoV-2 Positive and Negative Patients,Biological procedures online,2021,"COVID-19, Dysbiosis, Microbiota, Nasopharyngeal, SARS-CoV-2",Experiment 1,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls,COVID-19 positive patients,Patients who are COVID-19 positive by RT-PCR,10,9,NA,16S,4,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,unchanged,unchanged,NA,unchanged,NA,unchanged,Signature 2,Supplementary Tables 5 & 6,17 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance of nasopharyngeal bacteria between COVID-19-positive and COVID-19-negative samples,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae|g__Tumebacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Gulbenkiania",1783272|1239|91061|1385|186823|432330;3379134|1224|28216|206351|1499392|397456,Complete,Chloe
bsdb:34063398/1/1,34063398,case-control,34063398,10.3390/nu13051682,NA,"Łoś-Rycharska E., Gołębiewski M., Sikora M., Grzybowski T., Gorzkiewicz M., Popielarz M., Gawryjołek J. , Krogulska A.",A Combined Analysis of Gut and Skin Microbiota in Infants with Food Allergy and Atopic Dermatitis: A Pilot Study,Nutrients,2021,"16S rRNA sequencing, atopic dermatitis, dysbiosis, food allergy, gut, infants, microbiota, skin",Experiment 1,Poland,Homo sapiens,Feces,UBERON:0001988,Food allergy,EFO:1001890,Control group,Food Allergy,Infants with food allergy,28,16,1 month,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 3 and Table 4,2 November 2023,Peace Sandy,"Peace Sandy,WikiWorks","Table 3. Differentially abundant OTUs , Table 4 Differentially represented OTUs—characteristic either for AD or FA.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",3379134|976|200643|171549|815|816;1783272|1239|909932|1843489|31977|29465|39778,Complete,Folakunmi
bsdb:34063398/2/1,34063398,case-control,34063398,10.3390/nu13051682,NA,"Łoś-Rycharska E., Gołębiewski M., Sikora M., Grzybowski T., Gorzkiewicz M., Popielarz M., Gawryjołek J. , Krogulska A.",A Combined Analysis of Gut and Skin Microbiota in Infants with Food Allergy and Atopic Dermatitis: A Pilot Study,Nutrients,2021,"16S rRNA sequencing, atopic dermatitis, dysbiosis, food allergy, gut, infants, microbiota, skin",Experiment 2,Poland,Homo sapiens,Skin of body,UBERON:0002097,Dermatitis,MONDO:0002406,Control group,Atopic dermatitis,Infants with atopic dermatitis,28,5,1 month,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 3 and Table 4,4 November 2023,Peace Sandy,"Peace Sandy,Folakunmi,WikiWorks","Table 3. Differentially abundant OTUs , Table 4 Differentially represented OTUs—characteristic either for AD or FA.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter variabilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei",3379134|1224|1236|2887326|468|469|70346;3379134|976|200643|171549|2005525|375288;3379134|1224|1236|135614|32033|40323|40324;3379134|976|200643|171549|815|909656|357276,Complete,Folakunmi
bsdb:34063398/3/1,34063398,case-control,34063398,10.3390/nu13051682,NA,"Łoś-Rycharska E., Gołębiewski M., Sikora M., Grzybowski T., Gorzkiewicz M., Popielarz M., Gawryjołek J. , Krogulska A.",A Combined Analysis of Gut and Skin Microbiota in Infants with Food Allergy and Atopic Dermatitis: A Pilot Study,Nutrients,2021,"16S rRNA sequencing, atopic dermatitis, dysbiosis, food allergy, gut, infants, microbiota, skin",Experiment 3,Poland,Homo sapiens,Feces,UBERON:0001988,"Food allergy,Dermatitis","EFO:1001890,MONDO:0002406",Control group,Atopic dermatitis and Food Allergy (ADFA),Infants with both Atopic dermatitis and Food Allergy,28,38,1 month,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 3 and Table 4,13 November 2023,Peace Sandy,"Peace Sandy,Folakunmi,WikiWorks","Table 3: Differentially abundant OTUs 
Table 4: Differentially represented OTUs—characteristic either for AD or FA",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter variabilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei",3379134|1224|1236|2887326|468|469|70346;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005525|375288;1783272|1239|909932|1843489|31977|29465|39778;3379134|976|200643|171549|815|909656|357276,Complete,Folakunmi
bsdb:34063398/4/1,34063398,case-control,34063398,10.3390/nu13051682,NA,"Łoś-Rycharska E., Gołębiewski M., Sikora M., Grzybowski T., Gorzkiewicz M., Popielarz M., Gawryjołek J. , Krogulska A.",A Combined Analysis of Gut and Skin Microbiota in Infants with Food Allergy and Atopic Dermatitis: A Pilot Study,Nutrients,2021,"16S rRNA sequencing, atopic dermatitis, dysbiosis, food allergy, gut, infants, microbiota, skin",Experiment 4,Poland,Homo sapiens,Feces,UBERON:0001988,"Food allergy,Dermatitis","EFO:1001890,MONDO:0002406",Control group,Infants with Allergy Symptoms,"All infants with Allergy symptoms including Food Allergy, Atopic dermatitis, and both Atopic dermatitis and Food Allergy",28,59,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 5,26 December 2023,Folakunmi,"Folakunmi,WikiWorks",OTUs whose abundance on skin and in feces is correlated,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium scardovii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri",1783272|1239|91061|186826|1300|1301|1306;1783272|1239|91061|1385|539738|1378;1783272|201174|1760|85004|31953|1678|158787;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|33958|1578|1596,Complete,Folakunmi
bsdb:34063398/4/2,34063398,case-control,34063398,10.3390/nu13051682,NA,"Łoś-Rycharska E., Gołębiewski M., Sikora M., Grzybowski T., Gorzkiewicz M., Popielarz M., Gawryjołek J. , Krogulska A.",A Combined Analysis of Gut and Skin Microbiota in Infants with Food Allergy and Atopic Dermatitis: A Pilot Study,Nutrients,2021,"16S rRNA sequencing, atopic dermatitis, dysbiosis, food allergy, gut, infants, microbiota, skin",Experiment 4,Poland,Homo sapiens,Feces,UBERON:0001988,"Food allergy,Dermatitis","EFO:1001890,MONDO:0002406",Control group,Infants with Allergy Symptoms,"All infants with Allergy symptoms including Food Allergy, Atopic dermatitis, and both Atopic dermatitis and Food Allergy",28,59,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 5,26 December 2023,Folakunmi,"Folakunmi,WikiWorks",OTUs whose abundance on skin and in feces is correlated,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus haemolyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii",3379134|1224|1236|2887326|468|469|472;1783272|1239|91061|186826|1300|1301|1306;1783272|1239|91061|186826|33958|1578|1596;3379134|1224|1236|135625|712|724|726;3379134|976|200643|171549|815|816|28116;1783272|201174|1760|2037|2049|2529408|1660;1783272|201174|1760|2037|2049|1654|55565,Complete,Folakunmi
bsdb:34081625/1/1,34081625,randomized controlled trial,34081625,10.18632/aging.203095,NA,"Yang C., Liu S., Li H., Bai X., Shan S., Gao P. , Dong X.",The effects of psyllium husk on gut microbiota composition and function in chronically constipated women of reproductive age using 16S rRNA gene sequencing analysis,Aging,2021,"16S rRNA gene sequencing, chronic constipation, gut microbiota, metabolism, women of reproductive age",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Placebo group,Psyllium husk group,Women of reproductive age (15–49 years) with chronic constipation who received psyllium husk intervention,29,25,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"age,body mass index",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 4A and 4B,25 March 2025,Vanisha1606,"Vanisha1606,MyleeeA",LEfSe analysis of gut microbiota bacteria differentially abundant between Psyllium husk group and Placebo group,increased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|186802|216572,Complete,KateRasheed
bsdb:34081625/1/2,34081625,randomized controlled trial,34081625,10.18632/aging.203095,NA,"Yang C., Liu S., Li H., Bai X., Shan S., Gao P. , Dong X.",The effects of psyllium husk on gut microbiota composition and function in chronically constipated women of reproductive age using 16S rRNA gene sequencing analysis,Aging,2021,"16S rRNA gene sequencing, chronic constipation, gut microbiota, metabolism, women of reproductive age",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Placebo group,Psyllium husk group,Women of reproductive age (15–49 years) with chronic constipation who received psyllium husk intervention,29,25,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"age,body mass index",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 4A and 4B,25 March 2025,Vanisha1606,"Vanisha1606,MyleeeA",LEfSe analysis of gut microbiota bacteria differentially abundant between Psyllium husk group and Placebo group,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus",3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|976|200643|171549|815|909656|821,Complete,KateRasheed
bsdb:34090383/1/1,34090383,case-control,34090383,https://doi.org/10.1186/s12884-021-03855-w,NA,"Wu J., Zhuo Y., Liu Y., Chen Y., Ning Y. , Yao J.",Association between premature ovarian insufficiency and gut microbiota,BMC pregnancy and childbirth,2021,"16S rRNA sequencing, Gut microbiota, Premature ovarian insufficiency, Sex hormones",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Premature ovarian insufficiency,HP:0008209,Healthy controls,Primary ovarian insufficiency (POI),Thirty-five women with spontaneous Primary ovarian insufficiency (POI).,18,35,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2C,29 July 2025,Aleru Divine,Aleru Divine,Significantly different and important microbes between the POI and the control group.,increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|976;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|140625;3379134|1224|28216|80840|995019|40544,Complete,NA
bsdb:34090383/1/2,34090383,case-control,34090383,https://doi.org/10.1186/s12884-021-03855-w,NA,"Wu J., Zhuo Y., Liu Y., Chen Y., Ning Y. , Yao J.",Association between premature ovarian insufficiency and gut microbiota,BMC pregnancy and childbirth,2021,"16S rRNA sequencing, Gut microbiota, Premature ovarian insufficiency, Sex hormones",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Premature ovarian insufficiency,HP:0008209,Healthy controls,Primary ovarian insufficiency (POI),Thirty-five women with spontaneous Primary ovarian insufficiency (POI).,18,35,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2C,29 July 2025,Aleru Divine,Aleru Divine,Significantly different and important microbes between the POI and the control group.,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|1239;1783272|1239|526524|526525|128827|118747;1783272|1239|186801|186802|216572|216851,Complete,NA
bsdb:34095558/1/1,34095558,case-control,34095558,10.1016/j.synbio.2021.03.003,NA,"Ye F., Gao X., Wang Z., Cao S., Liang G., He D., Lv Z., Wang L., Xu P. , Zhang Q.",Comparison of gut microbiota in autism spectrum disorders and neurotypical boys in China: A case-control study,Synthetic and systems biotechnology,2021,"Autism spectrum disorders, China, Gut microbiome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Neurotypical controls,Boys with Autism Spectrum Disorder (ASD),Diagnosed according to the ABC screening tool and DSM-V criteria,18,71,1 month,16S,12,Illumina,relative abundances,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,increased,NA,increased,NA,increased,Signature 1,Figure 2,10 December 2024,AlishaM,"AlishaM,WikiWorks",LefSe analysis between the 2 groups,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|3085636|186803|572511;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|216851;1783272|1239;1783272|1239|186801;1783272|1239|186801|186802,Complete,NA
bsdb:34095558/1/2,34095558,case-control,34095558,10.1016/j.synbio.2021.03.003,NA,"Ye F., Gao X., Wang Z., Cao S., Liang G., He D., Lv Z., Wang L., Xu P. , Zhang Q.",Comparison of gut microbiota in autism spectrum disorders and neurotypical boys in China: A case-control study,Synthetic and systems biotechnology,2021,"Autism spectrum disorders, China, Gut microbiome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Neurotypical controls,Boys with Autism Spectrum Disorder (ASD),Diagnosed according to the ABC screening tool and DSM-V criteria,18,71,1 month,16S,12,Illumina,relative abundances,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,increased,NA,increased,NA,increased,Signature 2,Figure 2,10 December 2024,AlishaM,"AlishaM,WikiWorks",LefSe analysis between the 2 groups,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter",1783272|1239|909932|909929;1783272|1239|909932;1783272|1239|909932|1843489|31977;3379134|1224|1236;3379134|1224|1236|91347|543;3379134|1224|1236|91347;3379134|1224|1236|91347|543|1940338;1783272|1239|909932|1843489|31977|29465;3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|203557;3379134|74201|203494|48461;3379134|74201;3379134|1224|1236|91347|1903414|586;1783272|201174;1783272|1239|909932|1843489|31977|39948;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|91061;1783272|1239|91061|186826;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300;1783272|1239|909932|1843489|31977|906;3379134|1224|1236|91347|543|544,Complete,NA
bsdb:34100340/1/1,34100340,case-control,34100340,10.1080/19490976.2021.1926840,NA,"Newsome R.C., Gauthier J., Hernandez M.C., Abraham G.E., Robinson T.O., Williams H.B., Sloan M., Owings A., Laird H., Christian T., Pride Y., Wilson K.J., Hasan M., Parker A., Senitko M., Glover S.C., Gharaibeh R.Z. , Jobin C.",The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort,Gut microbes,2021,"16S rRNA sequencing, COVID-19, Human gut microbiota, SARS-CoV-2, clinical study, microbiome, microbiota",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Non-infected patients with unrelated respiratory medical conditions,SARS-CoV-2 infected patients,">age 18, positive nasopharyngeal swab for SARS-CoV-2 by PCR, COVID-19 related symptoms present, weight > 110 pounds",34,50,NA,16S,123,Illumina,NA,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2c,16 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance of microbial genera in COVID-19 infected cases and controls,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas",1783272|201174|1760|85007|1653|1716;3379134|29547|3031852|213849|72294|194;1783272|1239|1737404|1737405|1570339|150022;1783272|201174|1760|2037|2049|2050;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|1737404|1582879;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|1239|1737404|1737405|1570339|1161127;1783272|1239|186801|186802|216572|236752;1783272|1239|91061|186826|186827|66831;1783272|1239|1737404|1737405|1570339|162290;1783272|1239|91061|1385|90964|1279;1783272|201174|84998|84999|1643824|1380;1783272|1239|186801|3082768|990719|990721;1783272|1239|909932|1843489|31977|39948;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|186802|1392389,Complete,Lwaldron
bsdb:34100340/1/2,34100340,case-control,34100340,10.1080/19490976.2021.1926840,NA,"Newsome R.C., Gauthier J., Hernandez M.C., Abraham G.E., Robinson T.O., Williams H.B., Sloan M., Owings A., Laird H., Christian T., Pride Y., Wilson K.J., Hasan M., Parker A., Senitko M., Glover S.C., Gharaibeh R.Z. , Jobin C.",The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort,Gut microbes,2021,"16S rRNA sequencing, COVID-19, Human gut microbiota, SARS-CoV-2, clinical study, microbiome, microbiota",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Non-infected patients with unrelated respiratory medical conditions,SARS-CoV-2 infected patients,">age 18, positive nasopharyngeal swab for SARS-CoV-2 by PCR, COVID-19 related symptoms present, weight > 110 pounds",34,50,NA,16S,123,Illumina,NA,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2c,16 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance of microbial genera in COVID-19 infected cases and controls,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella",1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3082720|186804|1505657;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|572511;1783272|201174|1760|85006|1268|32207;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803;3379134|1224|1236|91347|543|561;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|186801|186802|216572|292632;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|1766253;3379134|1224|1236|91347|543|570,Complete,Lwaldron
bsdb:34100340/2/1,34100340,case-control,34100340,10.1080/19490976.2021.1926840,NA,"Newsome R.C., Gauthier J., Hernandez M.C., Abraham G.E., Robinson T.O., Williams H.B., Sloan M., Owings A., Laird H., Christian T., Pride Y., Wilson K.J., Hasan M., Parker A., Senitko M., Glover S.C., Gharaibeh R.Z. , Jobin C.",The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort,Gut microbes,2021,"16S rRNA sequencing, COVID-19, Human gut microbiota, SARS-CoV-2, clinical study, microbiome, microbiota",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,SARS-CoV-2 infected patients,SARS-CoV-2 recovered individuals,">age 18, more than 2 weeks post-COVID-19 infection that was confirmed by positive PCR for SARS-CoV-2",50,9,NA,16S,123,Illumina,NA,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3c,16 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance in microbial taxa between COVID-19 infected and COVID-19 recovered samples,decreased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Pseudoclavibacter,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Helcococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Dermabacter,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",3379134|29547|3031852|213849|72294|194;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|2037|2049|2050;1783272|1239|186801|186802|1686313;1783272|1239|1737404|1582879;1783272|1239|1737404|1737405|1570339|1161127;1783272|1239|186801|186802|216572|236752;1783272|1239|91061|186826|186827|66831;1783272|1239|91061|1385|90964|1279;1783272|1239|1737404|1737405|1570339|162290;1783272|201174|1760|85007|2805586|1847725;1783272|1239|1737404|1737405|1570339|150022;3379134|1224|28216|80840|995019|40544;1783272|1239|1737404|1737405|1570339|162289;3379134|976|200643|171549|171551|836;1783272|201174|84998|84999|1643824|1380;1783272|201174|1760|85006|85023|255204;3384194|508458|649775|649776|649777|508459;1783272|1239|186801|3085636|186803|1769710;1783272|1239|526524|526525|2810281|191303;1783272|1239|1737404|1737405|1570339|31983;1783272|1239|1737404|1737405|1570339|165779;1783272|201174|1760|85006|85020|36739;3379134|200940|3031449|213115|194924|872,Complete,Lwaldron
bsdb:34100340/2/2,34100340,case-control,34100340,10.1080/19490976.2021.1926840,NA,"Newsome R.C., Gauthier J., Hernandez M.C., Abraham G.E., Robinson T.O., Williams H.B., Sloan M., Owings A., Laird H., Christian T., Pride Y., Wilson K.J., Hasan M., Parker A., Senitko M., Glover S.C., Gharaibeh R.Z. , Jobin C.",The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort,Gut microbes,2021,"16S rRNA sequencing, COVID-19, Human gut microbiota, SARS-CoV-2, clinical study, microbiome, microbiota",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,SARS-CoV-2 infected patients,SARS-CoV-2 recovered individuals,">age 18, more than 2 weeks post-COVID-19 infection that was confirmed by positive PCR for SARS-CoV-2",50,9,NA,16S,123,Illumina,NA,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3c,16 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance in microbial taxa between COVID-19 infected and COVID-19 recovered samples,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter",1783272|1239|91061|186826|1300|1357;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|216572|1926663;1783272|1239|186801|186802|216572|216851;3379134|1224|1236|91347|543|561;1783272|1239|186801|3082720|186804|1505657;1783272|1239|526524|526525|2810280|135858;3379134|1224|1236|91347|543|570;1783272|1239|186801|186802|216572|292632;1783272|1239|91061|186826|186828|117563;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|1766253,Complete,Lwaldron
bsdb:34100340/3/1,34100340,case-control,34100340,10.1080/19490976.2021.1926840,NA,"Newsome R.C., Gauthier J., Hernandez M.C., Abraham G.E., Robinson T.O., Williams H.B., Sloan M., Owings A., Laird H., Christian T., Pride Y., Wilson K.J., Hasan M., Parker A., Senitko M., Glover S.C., Gharaibeh R.Z. , Jobin C.",The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort,Gut microbes,2021,"16S rRNA sequencing, COVID-19, Human gut microbiota, SARS-CoV-2, clinical study, microbiome, microbiota",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Non-infected patients with unrelated respiratory medical conditions,Recovered COVID-19 patients,">age 18, more than 2 weeks post-COVID-19 infection that was confirmed by positive PCR for SARS-CoV-2",38,9,NA,16S,123,Illumina,NA,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4c,16 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance in microbial taxa between recovered COVID-19 patients and non-infected controls,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis,s__rumen bacterium NK4A214",1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|216572|1926663;877428,Complete,Lwaldron
bsdb:34100340/3/2,34100340,case-control,34100340,10.1080/19490976.2021.1926840,NA,"Newsome R.C., Gauthier J., Hernandez M.C., Abraham G.E., Robinson T.O., Williams H.B., Sloan M., Owings A., Laird H., Christian T., Pride Y., Wilson K.J., Hasan M., Parker A., Senitko M., Glover S.C., Gharaibeh R.Z. , Jobin C.",The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort,Gut microbes,2021,"16S rRNA sequencing, COVID-19, Human gut microbiota, SARS-CoV-2, clinical study, microbiome, microbiota",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Non-infected patients with unrelated respiratory medical conditions,Recovered COVID-19 patients,">age 18, more than 2 weeks post-COVID-19 infection that was confirmed by positive PCR for SARS-CoV-2",38,9,NA,16S,123,Illumina,NA,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4c,16 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance in microbial genera between recovered COVID-19 patients and non-infected controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239|186801|3085636|186803|248744;1783272|1239|186801|3085636|186803;1783272|1239|526524|526525|128827|1470349;3379134|200940|3031449|213115|194924|35832;3379134|976|200643|171549|171552|577309;1783272|1239|909932|1843489|31977|39948;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|186802|216572|1263,Complete,Lwaldron
bsdb:34100340/4/1,34100340,case-control,34100340,10.1080/19490976.2021.1926840,NA,"Newsome R.C., Gauthier J., Hernandez M.C., Abraham G.E., Robinson T.O., Williams H.B., Sloan M., Owings A., Laird H., Christian T., Pride Y., Wilson K.J., Hasan M., Parker A., Senitko M., Glover S.C., Gharaibeh R.Z. , Jobin C.",The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort,Gut microbes,2021,"16S rRNA sequencing, COVID-19, Human gut microbiota, SARS-CoV-2, clinical study, microbiome, microbiota",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Negative for COVID-19 viral RNA in feces,Positive for COVID-19 viral RNA in feces,COVID-19 viral RNA present in feces sample,26,24,NA,16S,123,Illumina,NA,PERMANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 5c,16 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance of microbial genera in COVID-19 qPCR positive and qPCR negative fecal samples,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Sphaerochaetaceae|g__Sphaerochaeta,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Dolosicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter",3379134|1224|28216|80840|80864|283;3379134|203691|203692|136|2791015|399320;3384194|508458|649775|649776|649777|2753;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|3085636|186803|588605;1783272|1239|186801|3085636|1185407;1783272|1239|186801|3082720|186804|1505657;3379134|1224|1236|91347|543|570;1783272|1239|186801|186802|31979|1485|1506;3379134|976|200643|171549|171552|577309;1783272|1239|91061|186826|186827|171413;1783272|1239|186801|3082720|186804|1870884;3379134|1224|1236|91347|1903414|583;3384189|32066|203490|203491|203492|848;1783272|1239|526524|526525|2810280|1505663;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|3085636|186803|1769710;1783272|544448|2790996|2790998|2129;1783272|1239|186801|3085636|186803|1766253,Complete,Lwaldron
bsdb:34100340/4/2,34100340,case-control,34100340,10.1080/19490976.2021.1926840,NA,"Newsome R.C., Gauthier J., Hernandez M.C., Abraham G.E., Robinson T.O., Williams H.B., Sloan M., Owings A., Laird H., Christian T., Pride Y., Wilson K.J., Hasan M., Parker A., Senitko M., Glover S.C., Gharaibeh R.Z. , Jobin C.",The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort,Gut microbes,2021,"16S rRNA sequencing, COVID-19, Human gut microbiota, SARS-CoV-2, clinical study, microbiome, microbiota",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Negative for COVID-19 viral RNA in feces,Positive for COVID-19 viral RNA in feces,COVID-19 viral RNA present in feces sample,26,24,NA,16S,123,Illumina,NA,PERMANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 5c,16 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance of microbial genera in COVID-19 qPCR positive and qPCR negative fecal samples,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Eremococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propioniferax,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Tessaracoccus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Soonwooa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Dermabacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerosphaera,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Pseudoclavibacter",1783272|1239|91061|186826|186827|171412;1783272|201174|1760|85009|31957|53456;1783272|201174|84998|1643822|1643826|447020;1783272|201174|1760|85009|31957|72763;1783272|201174|1760|85006|1268|1269;1783272|1239|91061|186826|1300|1357;3379134|976|117743|200644|2762318|944321;1783272|1239|186801|186802|216572|1926663;3379134|976|200643|171549|2005520|156973;3384189|32066|203490|203491|1129771|168808;1783272|201174|1760|85006|85020|36739;1783272|1239|186801|3082720|186804|1501226;3379134|1224|1236|91347|543|547;1783272|1239|186801|3082720|186804|1505652;1783272|1239|186801|3085636|186803|1213720;1783272|1239|1737404|1737405|1570339|1273095;1783272|201174|1760|85006|85019|1696;1783272|201174|1760|85009|31957|1912216;1783272|201174|1760|85006|85023|255204,Complete,Lwaldron
bsdb:34103263/1/1,34103263,"cross-sectional observational, not case-control",34103263,10.1016/j.jmii.2021.03.015,NA,"Miao Q., Ma Y., Ling Y., Jin W., Su Y., Wang Q., Pan J., Zhang Y., Chen H., Yuan J., Wu H. , Hu B.","Evaluation of superinfection, antimicrobial usage, and airway microbiome with metagenomic sequencing in COVID-19 patients: A cohort study in Shanghai","Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi",2021,"Antimicrobials, COVID-19, Escalation, Metagenomic sequencing, Superinfection",Experiment 1,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Non-intubated patients with non-incubation viral pneumonia or non-incubation non-infectious diseases,COVID-19 patients,Intubated patients with critically severe COVID-19 infection,54,50,NA,WMS,NA,BGISEQ-500 Sequencing,relative abundances,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Text,17 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance of airway microbiome between samples from critically ill intubated COVID-19 patients and samples from non-incubated viral pneumonia/non-infectious disease patients,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles|s__Roseateles sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas",3379134|1224|1236|2887326|468|469;3379134|1224|1236|91347|543|570;3379134|1224|28216|80840|2975441|93681|1909303;3379134|1224|28216|80840|119060|48736;3379134|1224|28211|204457|41297|13687,Complete,Fatima
bsdb:34103263/1/2,34103263,"cross-sectional observational, not case-control",34103263,10.1016/j.jmii.2021.03.015,NA,"Miao Q., Ma Y., Ling Y., Jin W., Su Y., Wang Q., Pan J., Zhang Y., Chen H., Yuan J., Wu H. , Hu B.","Evaluation of superinfection, antimicrobial usage, and airway microbiome with metagenomic sequencing in COVID-19 patients: A cohort study in Shanghai","Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi",2021,"Antimicrobials, COVID-19, Escalation, Metagenomic sequencing, Superinfection",Experiment 1,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Non-intubated patients with non-incubation viral pneumonia or non-incubation non-infectious diseases,COVID-19 patients,Intubated patients with critically severe COVID-19 infection,54,50,NA,WMS,NA,BGISEQ-500 Sequencing,relative abundances,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Text,17 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance of airway microbiome between samples from critically ill intubated COVID-19 patients and samples from non-incubated viral pneumonia/non-infectious disease patients,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|2037|2049|1654;3379134|1224|1236|135625|712|724;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Fatima
bsdb:34123872/1/1,34123872,case-control,34123872,https://doi.org/10.3389/fcimb.2021.658203,https://pubmed.ncbi.nlm.nih.gov/34123872/,"Jia Y.J., Liao Y., He Y.Q., Zheng M.Q., Tong X.T., Xue W.Q., Zhang J.B., Yuan L.L., Zhang W.L. , Jia W.H.",Association Between Oral Microbiota and Cigarette Smoking in the Chinese Population,Frontiers in cellular and infection microbiology,2021,"16S rRNA gene sequencing, China, cigarette smoking, oral microbiota, saliva",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Never smokers,Smokers,"Subjects who smoked at least one cigarette every one to three days in the past year, or who smoked at least one cigarette every one to three days but had quit smoking for at least a year (ever smokers + current smokers groups combined)",150,166,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Table 1, text",15 April 2023,Atrayees,"Atrayees,Claregrieve1,WikiWorks",Differentially abundant genera and species between smokers and non-smokers,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",1783272|201174|1760|2037|2049|1654;1783272|201174|84998|84999|1643824|1380;1783272|1239|526524|526525|128827|118747;3379134|29547|3031852|213849|72294|194;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3085636|186803|437755;1783272|1239|186801|3085636|186803|265975;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552|838|60133;1783272|201174|1760|85006|1268|32207|2047;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|39778,Complete,Claregrieve1
bsdb:34123872/1/2,34123872,case-control,34123872,https://doi.org/10.3389/fcimb.2021.658203,https://pubmed.ncbi.nlm.nih.gov/34123872/,"Jia Y.J., Liao Y., He Y.Q., Zheng M.Q., Tong X.T., Xue W.Q., Zhang J.B., Yuan L.L., Zhang W.L. , Jia W.H.",Association Between Oral Microbiota and Cigarette Smoking in the Chinese Population,Frontiers in cellular and infection microbiology,2021,"16S rRNA gene sequencing, China, cigarette smoking, oral microbiota, saliva",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Never smokers,Smokers,"Subjects who smoked at least one cigarette every one to three days in the past year, or who smoked at least one cigarette every one to three days but had quit smoking for at least a year (ever smokers + current smokers groups combined)",150,166,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Table 1, text",15 April 2023,Atrayees,"Atrayees,Claregrieve1,WikiWorks",Differentially abundant genera and species between smokers and non-smokers,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus",3379134|1224|1236|135625|712|416916;3379134|1224|1236|135615|868|2717;3379134|1224|28216|206351|481|538;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712|724|729;3379134|1224|28216|206351|481|32257;3379134|1224|28216|80840|119060|47670;3379134|1224|1236|2887326|468|475;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481|482|1107316;3379134|1224|28216|206351|481|482|28449;1783272|1239|186801|186802|186807|2740;1783272|201174|1760|85006|1268|32207|172042;3379134|1224|1236|135625|712|724|735,Complete,Claregrieve1
bsdb:34130619/1/1,34130619,randomized controlled trial,34130619,https://doi.org/10.1186/s12866-021-02245-8,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02245-8#Abs1,"Nuzzo A., Van Horn S., Traini C., Perry C.R., Dumont E.F., Scangarella-Oman N.E., Gardiner D.F. , Brown J.R.",Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK140944),BMC microbiology,2021,"Antibiotic, Clinical trial, Gepotidacin, Microbiome, Urinary tract infection",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Urinary tract infection,EFO:0003103,Day 1 (pre-dose),Day 5 (end of dosing or post-dose),This represented the condition at the end of the 5-day regimen of gepotidacin treatment in the GIT microbiome,22,22,NA,16S,4,Illumina,raw counts,DESeq2,0.01,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Within results text(under ""Changes in detected abundances of bacterial genera""line 8-14), Figure 3",14 November 2023,Chinelsy,"Chinelsy,Folakunmi,WikiWorks",Relative abundances of assigned bacterial taxa.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|1224|1236|135625|712|713;1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549|171552|1283313;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|216572|1940255;3384194|508458|649775|649776|3029087|1434006;1783272|201174|1760|85004|31953|2701;1783272|1239|186801|3085636|186803|1164882;1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85007|2805586|1847725;3384189|32066|203490|203491|1129771|32067;1783272|1239|909932|1843489|31977|906;1783272|201174|1760|2037|2049|2050;3379134|1224|28216|206351|481|482;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;1783272|1239|909932|1843488|909930|33024;3379134|1224|1236|72274|135621|286;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;33090|35493|3398|72025|3803|3814|508215;1783272|1239|186801|186802|216572|1508657;1783272|1239|909932|909929|1843491|970;1783272|1239|91061|186826|1300|1301;3379134|1224|28216|80840|995019|40544,Complete,Folakunmi
bsdb:34130619/1/2,34130619,randomized controlled trial,34130619,https://doi.org/10.1186/s12866-021-02245-8,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02245-8#Abs1,"Nuzzo A., Van Horn S., Traini C., Perry C.R., Dumont E.F., Scangarella-Oman N.E., Gardiner D.F. , Brown J.R.",Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK140944),BMC microbiology,2021,"Antibiotic, Clinical trial, Gepotidacin, Microbiome, Urinary tract infection",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Urinary tract infection,EFO:0003103,Day 1 (pre-dose),Day 5 (end of dosing or post-dose),This represented the condition at the end of the 5-day regimen of gepotidacin treatment in the GIT microbiome,22,22,NA,16S,4,Illumina,raw counts,DESeq2,0.01,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"Within results text(under ""Changes in detected abundances of bacterial genera""line 8-14), Figure 3",14 November 2023,Chinelsy,"Chinelsy,Folakunmi,WikiWorks",Relative abundances of assigned bacterial taxa.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|909932|1843489|31977|39948;1783272|1239|91061|186826|81852|1350;3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|838|59823;1783272|1239|909932|909929|1843491|970;3379134|203691|203692|136|2845253|157;1783272|1239|186801|3085636|186803|1506577;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|3085636|186803,Complete,Folakunmi
bsdb:34130619/2/1,34130619,randomized controlled trial,34130619,https://doi.org/10.1186/s12866-021-02245-8,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02245-8#Abs1,"Nuzzo A., Van Horn S., Traini C., Perry C.R., Dumont E.F., Scangarella-Oman N.E., Gardiner D.F. , Brown J.R.",Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK140944),BMC microbiology,2021,"Antibiotic, Clinical trial, Gepotidacin, Microbiome, Urinary tract infection",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Urinary tract infection,EFO:0003103,Day 1 (pre-dose),Follow-up (visit around Day 28 ± 3 days).,"This represented the condition approximately one month post-treatment, after the cessation of gepotidacin in the GIT microbiome",22,22,NA,16S,4,Illumina,raw counts,DESeq2,0.01,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Within results text(under ""Changes in detected abundances of bacterial genera""line 8-14), Figure 3",14 November 2023,Chinelsy,"Chinelsy,Folakunmi,WikiWorks",Relative abundances of assigned bacterial taxa.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__Ruminiclostridium sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,s__uncultured bacterium",1783272|201174|1760|2037|2049|1654;1783272|1239|186801|3085636|186803|207244;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;3379134|29547|3031852|213849|72294|194;1783272|1239|186801|186802|186806|1730|290054;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|877420;1783272|201174|1760|85007|2805586|1847725;3384189|32066|203490|203491|1129771|32067;3379134|1224|28216|206351|481|482;1783272|1239|186801|186802|216572;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171552|838|59823;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;33090|35493|3398|72025|3803|3814|508215;1783272|1239|186801|186802|216572|1508657|2053608;1783272|1239|909932|909929|1843491|970;3379134|1224|28216|80840|995019|40544;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|2005473;1783272|1239|186801|186802|216572|707003;77133,Complete,Folakunmi
bsdb:34130619/2/2,34130619,randomized controlled trial,34130619,https://doi.org/10.1186/s12866-021-02245-8,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02245-8#Abs1,"Nuzzo A., Van Horn S., Traini C., Perry C.R., Dumont E.F., Scangarella-Oman N.E., Gardiner D.F. , Brown J.R.",Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK140944),BMC microbiology,2021,"Antibiotic, Clinical trial, Gepotidacin, Microbiome, Urinary tract infection",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Urinary tract infection,EFO:0003103,Day 1 (pre-dose),Follow-up (visit around Day 28 ± 3 days).,"This represented the condition approximately one month post-treatment, after the cessation of gepotidacin in the GIT microbiome",22,22,NA,16S,4,Illumina,raw counts,DESeq2,0.01,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"Within results text(under ""Changes in detected abundances of bacterial genera""line 8-14), Figure 3",14 November 2023,Chinelsy,"Chinelsy,Folakunmi,WikiWorks",Relative abundances of assigned bacterial taxa,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__Ruminiclostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549|815|816;1783272|201174|84998|84999|84107|102106;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|1407607;1783272|201174|1760|85004|31953|2701;1783272|1239|91061|186826|186828|117563;1783272|1239|186801|3085636|186803|877420;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|838|59823;3379134|976|200643|171549|171550;33090|35493|3398|72025|3803|3814|508215;1783272|1239|186801|186802|216572|1508657|2053608;1783272|1239|186801|186802|216572|1263;3379134|203691|203692|136|2845253|157;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|707003,Complete,Folakunmi
bsdb:34130619/3/1,34130619,randomized controlled trial,34130619,https://doi.org/10.1186/s12866-021-02245-8,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02245-8#Abs1,"Nuzzo A., Van Horn S., Traini C., Perry C.R., Dumont E.F., Scangarella-Oman N.E., Gardiner D.F. , Brown J.R.",Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK140944),BMC microbiology,2021,"Antibiotic, Clinical trial, Gepotidacin, Microbiome, Urinary tract infection",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Urinary tract infection,EFO:0003103,Day 1 (pre-dose),Day 5 (end of dosing or post-dose),This represented the condition at the end of the 5-day regimen of gepotidacin treatment in the pharyngeal cavity microbiome.,22,22,NA,16S,4,Illumina,raw counts,DESeq2,0.01,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"within results text under ""changes in detected abundances in bacterial genera"", paragraph 2, Figure 3",14 November 2023,Chinelsy,"Chinelsy,Folakunmi,WikiWorks",Relative abundances of assigned bacterial taxa.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter",1783272|1239|909932|1843488|909930|904;1783272|1239|91061|186826|186827|1375;1783272|1239|186801|186802|216572|216851;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|177971;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572|216851|1946507;1783272|1239|186801|186802|216572|707003;3379134|976|200643|171549|815|816;3379134|29547|3031852|213849|72294|194,Complete,Folakunmi
bsdb:34130619/3/2,34130619,randomized controlled trial,34130619,https://doi.org/10.1186/s12866-021-02245-8,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02245-8#Abs1,"Nuzzo A., Van Horn S., Traini C., Perry C.R., Dumont E.F., Scangarella-Oman N.E., Gardiner D.F. , Brown J.R.",Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK140944),BMC microbiology,2021,"Antibiotic, Clinical trial, Gepotidacin, Microbiome, Urinary tract infection",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Urinary tract infection,EFO:0003103,Day 1 (pre-dose),Day 5 (end of dosing or post-dose),This represented the condition at the end of the 5-day regimen of gepotidacin treatment in the pharyngeal cavity microbiome.,22,22,NA,16S,4,Illumina,raw counts,DESeq2,0.01,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"within results text under ""changes in detected abundances in bacterial genera"", paragraph 2, Figure 3",14 November 2023,Chinelsy,"Chinelsy,Folakunmi,WikiWorks",Relative abundances of assigned bacterial taxa.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",3379134|1224|1236|135625|712|713;3379134|1224|1236|135625|712|416916;3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|815|816;3379134|29547|3031852|213849|72294|194;3379134|976|117743|200644|49546|1016;1783272|1239|186801|3085636|186803|43996;1783272|1239|909932|1843489|31977|39948;1783272|1239|1737404|1737405|1570339|150022;3384189|32066|203490|203491|203492|848;1783272|1239|91061|186826|186828|117563;1783272|1239|186801|3085636|186803|1164882;1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85007|2805586|1847725;3384189|32066|203490|203491|1129771|32067;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|1508657;1783272|1239|909932|909929|1843491|970;1783272|1239|186801|3085636|186803|1213720;1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|2005525|195950;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Folakunmi
bsdb:34130619/4/1,34130619,randomized controlled trial,34130619,https://doi.org/10.1186/s12866-021-02245-8,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02245-8#Abs1,"Nuzzo A., Van Horn S., Traini C., Perry C.R., Dumont E.F., Scangarella-Oman N.E., Gardiner D.F. , Brown J.R.",Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK140944),BMC microbiology,2021,"Antibiotic, Clinical trial, Gepotidacin, Microbiome, Urinary tract infection",Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,Urinary tract infection,EFO:0003103,Day 1 (pre-dose),Follow-up (visit around Day 28 ± 3 days).,"This represented the condition approximately one month post-treatment, after the cessation of gepotidacin in the pharyngeal cavity microbiome.",22,22,NA,16S,4,Illumina,raw counts,DESeq2,0.01,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"within results text under ""changes in detected abundances in bacterial genera"", paragraph 2, Figure 3",14 November 2023,Chinelsy,"Chinelsy,Folakunmi,WikiWorks",Relative abundances of assigned bacterial taxa.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",1783272|1239|909932|1843488|909930|904;1783272|1239|186801|186802|216572|216851;1783272|1239|909932|1843489|31977|906;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|186802|216572|292632;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|186802|216572|707003,Complete,Folakunmi
bsdb:34130619/4/2,34130619,randomized controlled trial,34130619,https://doi.org/10.1186/s12866-021-02245-8,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02245-8#Abs1,"Nuzzo A., Van Horn S., Traini C., Perry C.R., Dumont E.F., Scangarella-Oman N.E., Gardiner D.F. , Brown J.R.",Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK140944),BMC microbiology,2021,"Antibiotic, Clinical trial, Gepotidacin, Microbiome, Urinary tract infection",Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,Urinary tract infection,EFO:0003103,Day 1 (pre-dose),Follow-up (visit around Day 28 ± 3 days).,"This represented the condition approximately one month post-treatment, after the cessation of gepotidacin in the pharyngeal cavity microbiome.",22,22,NA,16S,4,Illumina,raw counts,DESeq2,0.01,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"within results text under ""changes in detected abundances in bacterial genera"", paragraph 2,, Figure 3",14 November 2023,Chinelsy,"Chinelsy,Folakunmi,WikiWorks",Relative abundances of assigned bacterial taxa.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,p__Candidatus Absconditibacteriota|o__Candidatus Absconditabacterales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",1783272|1239|186801|3085636|186803|1766253;1783272|1239|1737404|1737405|1570339|165779;1783272|201174|84998|84999|1643824|1380;3379134|976|200643|171549|815|816;221235|2900568;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572|236752;1783272|1239|186801|186802|216572|946234;3379134|976|200643|171549|2005525|375288;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3379134|1224|1236|72274|135621|286;1783272|1239|186801|186802|216572|1508657;3384189|32066|203490|203491|1129771|168808;1783272|1239|186801|186802|1470353;3379134|1224|1236|91347|543;1783272|1239|186801|3085636|186803;1783272|1239|909932|1843489|31977;1783272|1239|186801|186802|216572|707003,Complete,Folakunmi
bsdb:34130619/5/1,34130619,randomized controlled trial,34130619,https://doi.org/10.1186/s12866-021-02245-8,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02245-8#Abs1,"Nuzzo A., Van Horn S., Traini C., Perry C.R., Dumont E.F., Scangarella-Oman N.E., Gardiner D.F. , Brown J.R.",Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK140944),BMC microbiology,2021,"Antibiotic, Clinical trial, Gepotidacin, Microbiome, Urinary tract infection",Experiment 5,United States of America,Homo sapiens,Vagina,UBERON:0000996,Urinary tract infection,EFO:0003103,Day 1 (pre-dose),Day 5 (end of dosing or post-dose),This represented the condition at the end of the 5-day regimen of gepotidacin treatment in vaginal microbiome.,22,22,NA,16S,4,Illumina,raw counts,DESeq2,0.01,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"within results text under ""changes in detected abundances in bacterial genera"", paragraph 3, Figure 3",14 November 2023,Chinelsy,"Chinelsy,Folakunmi,WikiWorks",Relative abundances of assigned bacterial taxa.,increased,"p__Evosea|o__Mastigamoebida|f__Entamoebidae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter|s__[Eubacterium] yurii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2605435|2682482|33084;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|171552|838;3379134|1224|1236|72274|135621|286;33090|35493|3398|72025|3803|3814|508215;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|3082720|3118655|1913599|39498;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|186802|216572|216851;3379134|29547|3031852|213849|72294|194;1783272|1239|186801|186802|186806|1730|290054;3384189|32066|203490|203491|203492|848;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843488|909930|33024,Complete,Folakunmi
bsdb:34130619/5/2,34130619,randomized controlled trial,34130619,https://doi.org/10.1186/s12866-021-02245-8,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02245-8#Abs1,"Nuzzo A., Van Horn S., Traini C., Perry C.R., Dumont E.F., Scangarella-Oman N.E., Gardiner D.F. , Brown J.R.",Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK140944),BMC microbiology,2021,"Antibiotic, Clinical trial, Gepotidacin, Microbiome, Urinary tract infection",Experiment 5,United States of America,Homo sapiens,Vagina,UBERON:0000996,Urinary tract infection,EFO:0003103,Day 1 (pre-dose),Day 5 (end of dosing or post-dose),This represented the condition at the end of the 5-day regimen of gepotidacin treatment in vaginal microbiome.,22,22,NA,16S,4,Illumina,raw counts,DESeq2,0.01,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"within results text under ""changes in detected abundances in bacterial genera"", paragraph 3, Figure 3",14 November 2023,Chinelsy,"Chinelsy,Folakunmi,WikiWorks",Relative abundances of assigned bacterial taxa.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|g__Negativibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,s__metagenome",3379134|1224|1236|135625|712|713;1783272|201174|1760|2037|2049|1654;1783272|1239|186801|3085636|186803|1766253;3379134|976|200643|171549|171552|1283313;1783272|201174|1760|85004|31953|419014;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|909932|1843489|31977|156454;3379134|976|200643|171549|815|816;3379134|29547|3031852|213849|72294|194;3379134|976|117743|200644|49546|1016;1783272|1239|186801|3082768|990719;1783272|201174|1760|85007|1653|1716;1783272|1239|909932|1843489|31977|39948;1783272|201174|84998|1643822|1643826|84111;3379134|1224|1236|91347|543|1940338;3384194|508458|649775|649776|3029087|1434006;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|28050;1783272|1239|91061|186826|1300|1357;3384189|32066|203490|203491|1129771|32067;1783272|1239|1980693;1783272|1239|186801|3085636|186803|265975;3379134|976|200643|171549|2005525|375288;1783272|1239|1737404|1737405|1570339|543311;3379134|976|200643|171549|171552|838|59823;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|292632;3379134|203691|203692|136|2845253|157;1783272|1239|186801|3085636|186803|2316020|33039;256318,Complete,Folakunmi
bsdb:34130619/6/1,34130619,randomized controlled trial,34130619,https://doi.org/10.1186/s12866-021-02245-8,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02245-8#Abs1,"Nuzzo A., Van Horn S., Traini C., Perry C.R., Dumont E.F., Scangarella-Oman N.E., Gardiner D.F. , Brown J.R.",Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK140944),BMC microbiology,2021,"Antibiotic, Clinical trial, Gepotidacin, Microbiome, Urinary tract infection",Experiment 6,United States of America,Homo sapiens,Vagina,UBERON:0000996,Urinary tract infection,EFO:0003103,Day 1 (pre-dose),Follow-up (visit around Day 28 ± 3 days).,"this represented the condition approximately one month post-treatment, after the cessation of gepotidacin in vaginal microbiome",22,22,NA,16S,4,Illumina,raw counts,DESeq2,0.01,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"within results text under ""changes in detected abundances in bacterial genera"", paragraph 3, Figure 3",14 November 2023,Chinelsy,"Chinelsy,Folakunmi,WikiWorks",Relative abundances of assigned bacterial taxa.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|186806|1730|39496;3384194|508458|649775|649776|3029087|1434006;1783272|1239|186801|3085636|186803|28050;1783272|1239|909932|909929|1843491|52225;1783272|1239|186801|186802|216572|459786;1783272|1239|1737404|1737405|1570339|543311;3379134|1224|1236|72274|135621|286;1783272|1239|186801|186802|216572|1508657;1783272|1239|909932|909929|1843491|970;3379134|203691|203692|136|2845253|157;3384189|32066|203490|203491|1129771|32067;3379134|976|200643|171549|815|816;3384189|32066|203490|203491|203492|848;1783272|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:34130619/6/2,34130619,randomized controlled trial,34130619,https://doi.org/10.1186/s12866-021-02245-8,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02245-8#Abs1,"Nuzzo A., Van Horn S., Traini C., Perry C.R., Dumont E.F., Scangarella-Oman N.E., Gardiner D.F. , Brown J.R.",Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK140944),BMC microbiology,2021,"Antibiotic, Clinical trial, Gepotidacin, Microbiome, Urinary tract infection",Experiment 6,United States of America,Homo sapiens,Vagina,UBERON:0000996,Urinary tract infection,EFO:0003103,Day 1 (pre-dose),Follow-up (visit around Day 28 ± 3 days).,"this represented the condition approximately one month post-treatment, after the cessation of gepotidacin in vaginal microbiome",22,22,NA,16S,4,Illumina,raw counts,DESeq2,0.01,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"within results text under ""changes in detected abundances in bacterial genera"", paragraph 3, Figure 3",14 November 2023,Chinelsy,"Chinelsy,Folakunmi,WikiWorks",Relative abundances of assigned bacterial taxa.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,s__metagenome,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",1783272|1239|909932|1843488|909930|904;1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171552|1283313;3379134|976|117743|200644|49546|1016;1783272|1239|186801|3082768|990719;1783272|201174|1760|85007|1653|1716;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563;1783272|1239|186801|3085636|186803|1164882;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|3085636|186803|2316020|33039;256318;3384189|32066|203490|203491|203492|848,Complete,Folakunmi
bsdb:34151035/1/1,34151035,"cross-sectional observational, not case-control",34151035,10.1016/j.synbio.2021.06.002,NA,"Liu J., Liu S., Zhang Z., Lee X., Wu W., Huang Z., Lei Z., Xu W., Chen D., Wu X., Guo Y., Peng L., Lin B., Chong Y., Mou X., Shi M., Lan P., Chen T., Zhao W. , Gao Z.",Association between the nasopharyngeal microbiome and metabolome in patients with COVID-19,Synthetic and systems biotechnology,2021,"COVID-19, Metabolome, Nasopharyngeal microbiome, SARS-CoV-2, Susceptibility",Experiment 1,China,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Non-COVID-19 controls,COVID-19 patients,Positive for infection with SARS-CoV-2 by nucleic acid testing,3,6,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figures 3c-d,25 June 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance in nasopharyngeal samples between COVID-19 cases and controls,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia",1783272|1239|91061|1385|539738|1378|1379;3379134|29547|3031852|213849|72294|194|824;3384189|32066|203490|203491|1129771|32067|157688;1783272|1239|91061|1385|539738|1378|29391;3379134|1224|1236|135614|32033|40323|40324,Complete,Fatima
bsdb:34152099/1/NA,34152099,randomized controlled trial,34152099,10.1002/brb3.2259,NA,"Bharwani A., Szamosi J.C., Taylor V.H., Lee Y., Bala A., Mansur R., Subramaniapillai M., Surette M. , McIntyre R.S.",Changes in the gut microbiome associated with infliximab in patients with bipolar disorder,Brain and behavior,2021,"16S rRNA sequencing, bipolar disorder, gut microbiota, inflammation, infliximab",Experiment 1,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Bipolar disorder,MONDO:0004985,Placebo,Infliximab,"Participants who received infliximab, an antibody administered intravenously that is used for treating several chronic inflammatory diseases and works by blocking the effects of TNF-α",8,9,NA,16S,NA,Illumina,raw counts,"PERMANOVA,ANCOM",0.05,FALSE,NA,bipolar disorder,NA,NA,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34168484/1/1,34168484,"cross-sectional observational, not case-control",34168484,10.2147/JIR.S311518,NA,"Zhou Y., Shi X., Fu W., Xiang F., He X., Yang B., Wang X. , Ma W.L.",Gut Microbiota Dysbiosis Correlates with Abnormal Immune Response in Moderate COVID-19 Patients with Fever,Journal of inflammation research,2021,"epitopes, fever, gut microbiota, moderate COVID-19, shotgun metagenomic sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,COVID-19 patients without fever,COVID-19 patients with fever,Symptomatic patients with confirmed COVID-19 (positive for COVID-19 nucleic acid by real-time RT-PCR from throat swab specimens) and fever (axillary temperature > 37.3 degrees Celsius),11,20,NA,WMS,NA,MGISEQ-2000,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2,3 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between COVID-19 patients with fever and COVID-19 patients without fever,increased,"k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",4751|4890|4891|4892|4893|4930;1783272|1239|91061|186826|81852|1350,Complete,Fatima
bsdb:34168484/1/2,34168484,"cross-sectional observational, not case-control",34168484,10.2147/JIR.S311518,NA,"Zhou Y., Shi X., Fu W., Xiang F., He X., Yang B., Wang X. , Ma W.L.",Gut Microbiota Dysbiosis Correlates with Abnormal Immune Response in Moderate COVID-19 Patients with Fever,Journal of inflammation research,2021,"epitopes, fever, gut microbiota, moderate COVID-19, shotgun metagenomic sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,COVID-19 patients without fever,COVID-19 patients with fever,Symptomatic patients with confirmed COVID-19 (positive for COVID-19 nucleic acid by real-time RT-PCR from throat swab specimens) and fever (axillary temperature > 37.3 degrees Celsius),11,20,NA,WMS,NA,MGISEQ-2000,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2,3 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between COVID-19 patients with fever and COVID-19 patients without fever,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella",1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|2005525|375288;1783272|1239|909932|1843488|909930|33024;1783272|201174|84998|1643822|1643826|84111,Complete,Fatima
bsdb:34168484/2/1,34168484,"cross-sectional observational, not case-control",34168484,10.2147/JIR.S311518,NA,"Zhou Y., Shi X., Fu W., Xiang F., He X., Yang B., Wang X. , Ma W.L.",Gut Microbiota Dysbiosis Correlates with Abnormal Immune Response in Moderate COVID-19 Patients with Fever,Journal of inflammation research,2021,"epitopes, fever, gut microbiota, moderate COVID-19, shotgun metagenomic sequencing",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,COVID-19 patients without fever,COVID-19 patients with fever,Symptomatic patients with confirmed COVID-19 (positive for COVID-19 nucleic acid by real-time RT-PCR from throat swab specimens) and fever (axillary temperature > 37.3 degrees Celsius),11,20,NA,WMS,NA,MGISEQ-2000,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table S5-7,3 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between COVID-19 patients with fever and COVID-19 patients without fever,increased,"k__Fungi|p__Ascomycota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis",4751|4890;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|544;4751|4890|4891|4892|4893|4930;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|2719313|208479;4751|4890|4891|4892|4893|4930|4932;3379134|1224|1236|135625|712|724|729;3379134|1224|1236|91347|543|544|546;3379134|1224|1236|91347|543|544|1896336;1783272|1239|91061|186826|81852|1350|1351,Complete,Fatima
bsdb:34168484/2/2,34168484,"cross-sectional observational, not case-control",34168484,10.2147/JIR.S311518,NA,"Zhou Y., Shi X., Fu W., Xiang F., He X., Yang B., Wang X. , Ma W.L.",Gut Microbiota Dysbiosis Correlates with Abnormal Immune Response in Moderate COVID-19 Patients with Fever,Journal of inflammation research,2021,"epitopes, fever, gut microbiota, moderate COVID-19, shotgun metagenomic sequencing",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,COVID-19 patients without fever,COVID-19 patients with fever,Symptomatic patients with confirmed COVID-19 (positive for COVID-19 nucleic acid by real-time RT-PCR from throat swab specimens) and fever (axillary temperature > 37.3 degrees Celsius),11,20,NA,WMS,NA,MGISEQ-2000,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Tables S5-7,3 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between COVID-19 patients with fever and COVID-19 patients without fever,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 7_1_58FAA,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 6_1_45,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 3_1_57FAA_CT1,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium 1_1_47,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 5_1_63FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 2_1_58FAA",3379134|1224|28216|80840|995019|577310;1783272|201174|84998|1643822|1643826|644652;3379134|976|200643|171549|171550|239759|328814;1783272|1239|186801|3085636|186803|658087;1783272|1239|526524|526525|128827|469614;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|246787;3379134|976|200643|171549|815|816|371601;1783272|1239|186801|3085636|186803|658086;1783272|1239|186801|186802|186806|1730|39490;3379134|1224|28216|80840|995019|577310|487175;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|3085636|186803|207244|649756;3379134|1224|28216|80840|469610;1783272|1239|186801|3085636|186803|658089;1783272|1239|186801|3085636|186803|658082,Complete,Fatima
bsdb:34173452/1/1,34173452,prospective cohort,34173452,10.1016/j.medmic.2020.100023,NA,"Tao W., Zhang G., Wang X., Guo M., Zeng W., Xu Z., Cao D., Pan A., Wang Y., Zhang K., Ma X., Chen Z., Jin T., Liu L., Weng J. , Zhu S.",Analysis of the intestinal microbiota in COVID-19 patients and its correlation with the inflammatory factor IL-18,Medicine in microecology,2020,"COVID19, Gut microbiota, IL18, SARS2",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Patients with COVID-19,40,62,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Figure 1E,7 July 2021,Claregrieve1,"Claregrieve1,Fatima,LGeistlinger,WikiWorks",Differential microbial abundance between healthy controls and COVID-19 patients (LDA>2),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|2037|2049|1654;1783272|1239|526524|526525|128827|174708;1783272|1239|1737404|1737405|1570339|165779;1783272|201174|84998|84999|1643824|1380;1783272|201174|1760|85004|31953|1678;1783272|1239|526524|526525|128827|118747;1783272|1239|186801|186802|31979|1485;1783272|201174|1760|85007|1653|1716;1783272|201174|84998|1643822|1643826|84111;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|561;3379134|29547|3031852|213849|72293|209;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|437755;1783272|1239|186801|3085636|186803|265975;3379134|1224|1236|91347|1903414|583;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85004|31953|196081;1783272|1239|186801|3085636|186803|177971;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Fatima
bsdb:34173452/1/2,34173452,prospective cohort,34173452,10.1016/j.medmic.2020.100023,NA,"Tao W., Zhang G., Wang X., Guo M., Zeng W., Xu Z., Cao D., Pan A., Wang Y., Zhang K., Ma X., Chen Z., Jin T., Liu L., Weng J. , Zhu S.",Analysis of the intestinal microbiota in COVID-19 patients and its correlation with the inflammatory factor IL-18,Medicine in microecology,2020,"COVID19, Gut microbiota, IL18, SARS2",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Patients with COVID-19,40,62,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Figure 1E,7 July 2021,Claregrieve1,"Claregrieve1,Fatima,WikiWorks",Differential microbial abundance between healthy controls and COVID-19 patients (LDA>2),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia",3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|207244;3379134|1224|28216|80840|119060|32008;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802|31979|1485;3379134|1224|28216|80840|80864|283;1783272|1239|186801|3085636|186803|33042;3379134|1224|28216|80840|119060|106589;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|216851;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|3085636|186803|28050;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|838;3379134|1224|28216|80840|119060|48736;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;3379134|1224|28216|80840|995019|40544;3379134|256845|1313211|278082|255528|172900;3379134|1224|1236|91347|1903411|629,Complete,Fatima
bsdb:34173452/2/1,34173452,prospective cohort,34173452,10.1016/j.medmic.2020.100023,NA,"Tao W., Zhang G., Wang X., Guo M., Zeng W., Xu Z., Cao D., Pan A., Wang Y., Zhang K., Ma X., Chen Z., Jin T., Liu L., Weng J. , Zhu S.",Analysis of the intestinal microbiota in COVID-19 patients and its correlation with the inflammatory factor IL-18,Medicine in microecology,2020,"COVID19, Gut microbiota, IL18, SARS2",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Seasonal flu patients,COVID-19 patients,Patients with COVID-19,33,62,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Figure 1G,7 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between seasonal flu patients and COVID-19 patients (LDA>2),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",3379134|1224|1236|91347|543|561;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|31979|1485;1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|2005525|375288;1783272|1239|909932|1843489|31977|29465;3379134|1224|28216|80840|995019|40544;3384189|32066|203490|203491|203492|848,Complete,Fatima
bsdb:34173452/2/2,34173452,prospective cohort,34173452,10.1016/j.medmic.2020.100023,NA,"Tao W., Zhang G., Wang X., Guo M., Zeng W., Xu Z., Cao D., Pan A., Wang Y., Zhang K., Ma X., Chen Z., Jin T., Liu L., Weng J. , Zhu S.",Analysis of the intestinal microbiota in COVID-19 patients and its correlation with the inflammatory factor IL-18,Medicine in microecology,2020,"COVID19, Gut microbiota, IL18, SARS2",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Seasonal flu patients,COVID-19 patients,Patients with COVID-19,33,62,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Figure 1G,7 July 2021,Claregrieve1,"Claregrieve1,Merit,WikiWorks",Differential microbial abundance between seasonal flu patients and COVID-19 patients (LDA>2),decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",1783272|201174|1760|2037|2049|1654;3379134|1224|1236|135625|712|416916;1783272|1239|186801|3085636|186803|572511;1783272|1239|526524|526525|128827|118747;3379134|1224|28216|80840|119060|32008;1783272|1239|186801|186802|31979|1485;3379134|1224|28216|80840|119060|106589;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|186806|1730;3379134|1224|1236|135625|712|724;3379134|29547|3031852|213849|72293|209;1783272|1239|91061|186826|33958|1243;1783272|1239|186801|3085636|186803|437755;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|186802|216572|119852;1783272|1239|909932|1843488|909930|33024;3384194|508458|649775|649776|3029088|638847;3379134|1224|28216|80840|119060|48736;1783272|1239|186801|3085636|186803|177971;3379134|1224|1236|135614|32033|40323;1783272|1239|186801;1783272|1239|186801|186802|31979,Complete,Fatima
bsdb:34199203/1/1,34199203,"cross-sectional observational, not case-control",34199203,10.3390/microorganisms9061292,NA,"Khan M., Mathew B.J., Gupta P., Garg G., Khadanga S., Vyas A.K. , Singh A.K.",Gut Dysbiosis and IL-21 Response in Patients with Severe COVID-19,Microorganisms,2021,"COVID-19, IL-21, brain–gut interaction, dietary fibre, gut microbiome, mucosal immunity",Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Asymptomatic COVID-19 patients,Asymptomatic COVID-19 patients (positive for SARS-CoV-2 in an RT-PCR diagnostic assay) with no symptoms,10,10,NA,16S,34,NA,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a,3 July 2021,Claregrieve1,"Claregrieve1,Merit,WikiWorks",Differential microbial abundance between healthy volunteers and asymptomatic COVID-19 patients,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Metazoa|p__Arthropoda|c__Insecta|o__Diptera|f__Micropezidae|s__Calobatinae|g__Compsobata|s__Compsobata cibaria,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus helveticus,k__Metazoa|p__Arthropoda|c__Insecta|o__Hemiptera|f__Aphididae|s__Aphidinae|g__Ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella dysenteriae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.",1783272|1239|186801|186802|31979;1783272|201174|84998|84999|84107|102106|74426;33208|6656|50557|7147|115293|115294|286452|1262234;1783272|201174|84998|1643822|1643826|84111;3379134|1224|1236|91347|543|547;1783272|1239|186801|3085636|186803|2719313|358743;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578|1587;33208|6656|50557|7524|27482|133076|666060;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|171551;1783272|1239|186801|186802|216572|1263;3379134|1224|1236|91347|543|620;3379134|1224|1236|91347|543|620|622;1783272|1239|91061|186826|33958|46255;1783272|1239|186801|3085636|186803|2316020|33038;3379134|1224|1236|91347|543;1783272|1239|186801;1783272|1239|186801|186802|1898207;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|31979|1485|1506;1783272|1239|186801|186802|216572|1263|41978;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|81852|1350|35783,Complete,Fatima
bsdb:34199203/1/2,34199203,"cross-sectional observational, not case-control",34199203,10.3390/microorganisms9061292,NA,"Khan M., Mathew B.J., Gupta P., Garg G., Khadanga S., Vyas A.K. , Singh A.K.",Gut Dysbiosis and IL-21 Response in Patients with Severe COVID-19,Microorganisms,2021,"COVID-19, IL-21, brain–gut interaction, dietary fibre, gut microbiome, mucosal immunity",Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Asymptomatic COVID-19 patients,Asymptomatic COVID-19 patients (positive for SARS-CoV-2 in an RT-PCR diagnostic assay) with no symptoms,10,10,NA,16S,34,NA,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3a,3 July 2021,Claregrieve1,"Claregrieve1,Fatima,WikiWorks",Differential microbial abundance between healthy volunteers and asymptomatic COVID-19 patients,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Pseudomonadati|p__Campylobacterota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|909932|1843488|909930|904;3379134|1224|1236|135624;1783272|1239|186801|3085636|186803|207244;1783272|201174|1760|85004|31953|1678|1680;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294;3379134|29547|3031852|213849;1783272|1239|186801|3085636|186803|2719313|1531;3379134|29547;3379134|1224|1236|135625|712|724|729;1783272|1239|186801|3085636|186803|28050;1783272|1239|91061|186826|81850;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|909929|1843491|52225;1783272|1239|909932|909929|1843491|52225|52226;1783272|201174|84998|84999|1643824|133925;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|186802|216572|1263|40519;3379134|1224|1236|135624|83763|83770;3379134|1224|1236|135624|83763;1783272|1239|909932|1843489|31977;1783272|1239|91061|186826|33958;3379134|1224|1236|135625|712;1783272|1239|909932|1843489|31977,Complete,Fatima
bsdb:34199203/3/1,34199203,"cross-sectional observational, not case-control",34199203,10.3390/microorganisms9061292,NA,"Khan M., Mathew B.J., Gupta P., Garg G., Khadanga S., Vyas A.K. , Singh A.K.",Gut Dysbiosis and IL-21 Response in Patients with Severe COVID-19,Microorganisms,2021,"COVID-19, IL-21, brain–gut interaction, dietary fibre, gut microbiome, mucosal immunity",Experiment 3,India,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Severe COVID-19 patients,COVID-19 patients (positive for SARS-CoV-2 in an RT-PCR diagnostic assay) with severe disease and requiring oxygen support/ventilator,10,10,NA,16S,34,NA,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3c,4 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between healthy volunteers and severe COVID-19 patients,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella sonnei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus helveticus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Melissococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella dysenteriae",3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976|200643|171549;3379134|976;3379134|1224|1236|91347|543;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|201174;1783272|201174|1760|85004;1783272|201174|1760|85004|31953;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|81850;;3379134|1224|1236|91347|543|620;3379134|1224|1236|91347|543|620|624;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578|1587;1783272|201174|84998|84999|1643824|1380;1783272|1239|91061|186826|81852|33969;1783272|1239|186801|3085636|186803|2719313|358743;1783272|1239|91061|186826|81852;3379134|1224|1236|91347|543|620|622,Complete,Claregrieve1
bsdb:34199203/3/2,34199203,"cross-sectional observational, not case-control",34199203,10.3390/microorganisms9061292,NA,"Khan M., Mathew B.J., Gupta P., Garg G., Khadanga S., Vyas A.K. , Singh A.K.",Gut Dysbiosis and IL-21 Response in Patients with Severe COVID-19,Microorganisms,2021,"COVID-19, IL-21, brain–gut interaction, dietary fibre, gut microbiome, mucosal immunity",Experiment 3,India,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Severe COVID-19 patients,COVID-19 patients (positive for SARS-CoV-2 in an RT-PCR diagnostic assay) with severe disease and requiring oxygen support/ventilator,10,10,NA,16S,34,NA,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3c,4 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between healthy volunteers and severe COVID-19 patients,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Pseudomonadati|p__Campylobacterota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Verrucomicrobiota,,k__Bacillati|p__Bacillota|c__Clostridia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|909932|1843488|909930|904;3379134|1224|1236|135624;1783272|1239|186801|186802|3085642|580596;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294;3379134|29547|3031852|213849;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;3379134|1224|28216|80840|80864;1783272|1239|186801|3085636|186803|33042;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|189330;3379134|1224|1236|91347|543|547;1783272|1239|186801|3085636|186803|2719313|1531;3379134|29547;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|28052;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|81850;1783272|1239|909932|1843489|31977|906;1783272|544448|31969;1783272|201174|84998|84999|1643824|133925;1783272|1239|186801|186802|541000;3379134|1224|1236|135625|712;3379134|1224|1236|135625;1783272|1239|186801|3085636|186803|841;3379134|1224|1236|135624|83763|83770;3379134|1224|1236|135624|83763;1783272|544448;3379134|74201;;1783272|1239|186801;3379134|1224|28216|80840|80864;1783272|201174|84998|84999|84107;1783272|1239|186801|186802;1783272|1239;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958;1783272|1239|186801|186802|216572;3379134|1224|1236|135625|712;1783272|1239|909932|1843489|31977,Complete,Claregrieve1
bsdb:34200249/1/1,34200249,time series / longitudinal observational,34200249,10.3390/microorganisms9061237,NA,"Kim H.N., Joo E.J., Lee C.W., Ahn K.S., Kim H.L., Park D.I. , Park S.K.",Reversion of Gut Microbiota during the Recovery Phase in Patients with Asymptomatic or Mild COVID-19: Longitudinal Study,Microorganisms,2021,"COVID-19, FB ratio, SARS-CoV2, asymptomatic, gut microbiota, microbiome, mild",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Infected COVID-19 samples (respiratory positive),Recovered COVID-19 samples (respiratory negative),Samples from symptomatic/mild COVID-19 patients collected on or after negative conversion for SARS-CoV-2 RNA from the respiratory tract,12,12,No history of antibiotics or probiotics,16S,34,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,increased,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary Table S1,4 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Comparison of taxonomic compositions of gut microbiota between respiratory positive and respiratory negative COVID-19 samples,increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",3379134|976;3379134|976|200643;3379134|976|200643|171549,Complete,NA
bsdb:34200249/1/2,34200249,time series / longitudinal observational,34200249,10.3390/microorganisms9061237,NA,"Kim H.N., Joo E.J., Lee C.W., Ahn K.S., Kim H.L., Park D.I. , Park S.K.",Reversion of Gut Microbiota during the Recovery Phase in Patients with Asymptomatic or Mild COVID-19: Longitudinal Study,Microorganisms,2021,"COVID-19, FB ratio, SARS-CoV2, asymptomatic, gut microbiota, microbiome, mild",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Infected COVID-19 samples (respiratory positive),Recovered COVID-19 samples (respiratory negative),Samples from symptomatic/mild COVID-19 patients collected on or after negative conversion for SARS-CoV-2 RNA from the respiratory tract,12,12,No history of antibiotics or probiotics,16S,34,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,increased,unchanged,NA,NA,NA,unchanged,Signature 2,Supplementary Table S1,4 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Comparison of taxonomic compositions of gut microbiota between respiratory positive and respiratory negative COVID-19 samples,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,1783272|201174|1760|2037,Complete,NA
bsdb:34200249/2/1,34200249,time series / longitudinal observational,34200249,10.3390/microorganisms9061237,NA,"Kim H.N., Joo E.J., Lee C.W., Ahn K.S., Kim H.L., Park D.I. , Park S.K.",Reversion of Gut Microbiota during the Recovery Phase in Patients with Asymptomatic or Mild COVID-19: Longitudinal Study,Microorganisms,2021,"COVID-19, FB ratio, SARS-CoV2, asymptomatic, gut microbiota, microbiome, mild",Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 samples (respiratory negative),Samples from symptomatic/mild COVID-19 patients collected on or after negative conversion for SARS-CoV-2 RNA from the respiratory tract,36,12,NA,16S,34,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,decreased,unchanged,NA,NA,NA,increased,Signature 1,Supplementary Table S2,4 July 2021,Claregrieve1,"Claregrieve1,Merit,WikiWorks",Comparison of taxonomic composition of gut microbiota in respiratory-negative recovered COVID-19 patients and healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,s__rumen bacterium NK4A214,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|909932;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|541000;1783272|1239|186801|3085636|186803|841;1783272|1239|909932|909929;877428;1783272|1239|186801|186802|216572,Complete,NA
bsdb:34200249/2/2,34200249,time series / longitudinal observational,34200249,10.3390/microorganisms9061237,NA,"Kim H.N., Joo E.J., Lee C.W., Ahn K.S., Kim H.L., Park D.I. , Park S.K.",Reversion of Gut Microbiota during the Recovery Phase in Patients with Asymptomatic or Mild COVID-19: Longitudinal Study,Microorganisms,2021,"COVID-19, FB ratio, SARS-CoV2, asymptomatic, gut microbiota, microbiome, mild",Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 samples (respiratory negative),Samples from symptomatic/mild COVID-19 patients collected on or after negative conversion for SARS-CoV-2 RNA from the respiratory tract,36,12,NA,16S,34,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,decreased,unchanged,NA,NA,NA,increased,Signature 2,Supplementary Table S2,4 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Comparison of taxonomic composition of gut microbiota in respiratory-negative recovered COVID-19 patients and healthy controls,increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter",1783272|201174;3379134|1224;1783272|201174|84998;1783272|1239|91061;3379134|1224|1236;1783272|201174|84998|84999;1783272|1239|91061|186826;3379134|1224|1236|91347;1783272|201174|84998|84999|84107;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81850;1783272|201174|84998|1643822|1643826;1783272|1239|91061|186826|1300;1783272|1239|186801|3082720|186804;1783272|201174|1760|85004|31953;3379134|1224|1236|91347|543;1783272|1239|186801|186802|31979;1783272|201174|84998|84999|84107|102106;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|216572|216851|1946507;1783272|1239|91061|186826|33958|1253;3379134|1224|1236|91347|543|544,Complete,NA
bsdb:34200249/3/1,34200249,time series / longitudinal observational,34200249,10.3390/microorganisms9061237,NA,"Kim H.N., Joo E.J., Lee C.W., Ahn K.S., Kim H.L., Park D.I. , Park S.K.",Reversion of Gut Microbiota during the Recovery Phase in Patients with Asymptomatic or Mild COVID-19: Longitudinal Study,Microorganisms,2021,"COVID-19, FB ratio, SARS-CoV2, asymptomatic, gut microbiota, microbiome, mild",Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Infected COVID-19 samples (respiratory positive),Samples from symptomatic/mild COVID-19 patients collected on or before positive detection of SARS-CoV-2 RNA from the respiratory tract,36,12,No history of antibiotics or probiotics,16S,34,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,decreased,decreased,NA,NA,NA,unchanged,Signature 1,Supplementary Table S2,4 July 2021,Claregrieve1,"Claregrieve1,Merit,WikiWorks",Comparison of taxonomic composition of gut microbiota in respiratory-positive infected COVID-19 patients and healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,s__rumen bacterium NK4A214,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira|s__uncultured Oscillospira sp.",1783272|1239|186801|3085636|186803|1766253;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|2005519;1783272|1239|186801|186802|3085642|580596;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802|1980681;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|877420;3379134|976|200643|1970189|1573805;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|909932;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|541000;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|909932|909929;3379134|1224|28216|80840|995019|40544;3379134|976|200643|171549|2005525;1783272|1239|909932|1843489|31977;877428;1783272|1239|186801|186802|216572|119852|512316,Complete,NA
bsdb:34200249/3/2,34200249,time series / longitudinal observational,34200249,10.3390/microorganisms9061237,NA,"Kim H.N., Joo E.J., Lee C.W., Ahn K.S., Kim H.L., Park D.I. , Park S.K.",Reversion of Gut Microbiota during the Recovery Phase in Patients with Asymptomatic or Mild COVID-19: Longitudinal Study,Microorganisms,2021,"COVID-19, FB ratio, SARS-CoV2, asymptomatic, gut microbiota, microbiome, mild",Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Infected COVID-19 samples (respiratory positive),Samples from symptomatic/mild COVID-19 patients collected on or before positive detection of SARS-CoV-2 RNA from the respiratory tract,36,12,No history of antibiotics or probiotics,16S,34,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,decreased,decreased,NA,NA,NA,unchanged,Signature 2,Supplementary Table S2,4 July 2021,Claregrieve1,"Claregrieve1,WikiWorks",Comparison of taxonomic composition of gut microbiota in respiratory-positive infected COVID-19 patients and healthy controls,increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter",1783272|201174;3379134|1224;1783272|201174|84998;1783272|1239|91061;3379134|1224|1236;1783272|201174|84998|84999;1783272|1239|91061|186826;1783272|1239|1737404|1737405;1783272|201174|1760|85004;3379134|1224|1236|91347;1783272|1239|186801|186802;1783272|201174|84998|84999|84107;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|33958;1783272|201174|84998|1643822|1643826;1783272|1239|91061|186826|1300;1783272|1239|186801|3082720|186804;1783272|201174|1760|85004|31953;3379134|1224|1236|91347|543;1783272|1239|186801|186802|31979;1783272|201174|84998|84999|84107|102106;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3082720|186804|1501226;1783272|1239|91061|186826|33958|1253;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|2569097|39488;3379134|1224|1236|91347|543|620;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3082720|186804|1505657,Complete,NA
bsdb:34220852/1/1,34220852,time series / longitudinal observational,34220852,10.3389/fimmu.2021.692225,NA,"Heidrich V., Bruno J.S., Knebel F.H., de Molla V.C., Miranda-Silva W., Asprino P.F., Tucunduva L., Rocha V., Novis Y., Arrais-Rodrigues C., Fregnani E.R. , Camargo A.A.",Dental Biofilm Microbiota Dysbiosis Is Associated With the Risk of Acute Graft-<i>Versus</i>-Host Disease After Allogeneic Hematopoietic Stem Cell Transplantation,Frontiers in immunology,2021,"acute GVHD, allogeneic HSCT, bone marrow transplant, microbiome dysbiosis, oral microbiota, supragingival plaque",Experiment 1,Brazil,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,Preconditioning (Patients Before Allogeneic Hematopoietic Stem Cell Transplantation),Engraftment (Patients After Allogeneic Hematopoietic Stem Cell Transplantation),"Patients at the final phase of Allogeneic Hematopoietic Stem Cell transplant, when the new transplanted stem cells start to grow and produce new blood cells.",30,27,NA,16S,34,Illumina,centered log-ratio,ANCOM,0.7,FALSE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,Figure 1C,8 March 2024,Joan Chuks,"Joan Chuks,ChiomaBlessing,WikiWorks",Significant genera relative abundance in the engraftment (After transplantation) group compared to the preconditioning (Before transplantation) group according to ANCOM test (W > 0.7).,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1243;1783272|544448|31969|2085|2092|2093;1783272|1239|91061|1385|90964|1279,Complete,ChiomaBlessing
bsdb:34220852/1/2,34220852,time series / longitudinal observational,34220852,10.3389/fimmu.2021.692225,NA,"Heidrich V., Bruno J.S., Knebel F.H., de Molla V.C., Miranda-Silva W., Asprino P.F., Tucunduva L., Rocha V., Novis Y., Arrais-Rodrigues C., Fregnani E.R. , Camargo A.A.",Dental Biofilm Microbiota Dysbiosis Is Associated With the Risk of Acute Graft-<i>Versus</i>-Host Disease After Allogeneic Hematopoietic Stem Cell Transplantation,Frontiers in immunology,2021,"acute GVHD, allogeneic HSCT, bone marrow transplant, microbiome dysbiosis, oral microbiota, supragingival plaque",Experiment 1,Brazil,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,Preconditioning (Patients Before Allogeneic Hematopoietic Stem Cell Transplantation),Engraftment (Patients After Allogeneic Hematopoietic Stem Cell Transplantation),"Patients at the final phase of Allogeneic Hematopoietic Stem Cell transplant, when the new transplanted stem cells start to grow and produce new blood cells.",30,27,NA,16S,34,Illumina,centered log-ratio,ANCOM,0.7,FALSE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Figure 1C,8 March 2024,Joan Chuks,"Joan Chuks,ChiomaBlessing,WikiWorks",Significant genera relative abundance in the engraftment (After transplantation) group compared to the preconditioning (Before transplantation) group according to ANCOM test (W > 0.7).,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|1760|2037|2049|1654;1783272|1239|91061|1385|539738|1378;1783272|1239|186801|3085636|186803|1164882;3384189|32066|203490|203491|1129771|32067;1783272|1239|91061|186826|1300|1301,Complete,ChiomaBlessing
bsdb:34220852/2/NA,34220852,time series / longitudinal observational,34220852,10.3389/fimmu.2021.692225,NA,"Heidrich V., Bruno J.S., Knebel F.H., de Molla V.C., Miranda-Silva W., Asprino P.F., Tucunduva L., Rocha V., Novis Y., Arrais-Rodrigues C., Fregnani E.R. , Camargo A.A.",Dental Biofilm Microbiota Dysbiosis Is Associated With the Risk of Acute Graft-<i>Versus</i>-Host Disease After Allogeneic Hematopoietic Stem Cell Transplantation,Frontiers in immunology,2021,"acute GVHD, allogeneic HSCT, bone marrow transplant, microbiome dysbiosis, oral microbiota, supragingival plaque",Experiment 2,Brazil,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,Preconditioning (Patients Before Allogeneic Hematopoietic Stem Cell Transplantation),Aplasia group,"Patients after the conditioning regimen, when the patient's bone marrow is intentionally depleted of cells, necessary for the success of the transplant",30,30,NA,16S,34,Illumina,centered log-ratio,ANCOM,0.7,FALSE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34220852/3/NA,34220852,time series / longitudinal observational,34220852,10.3389/fimmu.2021.692225,NA,"Heidrich V., Bruno J.S., Knebel F.H., de Molla V.C., Miranda-Silva W., Asprino P.F., Tucunduva L., Rocha V., Novis Y., Arrais-Rodrigues C., Fregnani E.R. , Camargo A.A.",Dental Biofilm Microbiota Dysbiosis Is Associated With the Risk of Acute Graft-<i>Versus</i>-Host Disease After Allogeneic Hematopoietic Stem Cell Transplantation,Frontiers in immunology,2021,"acute GVHD, allogeneic HSCT, bone marrow transplant, microbiome dysbiosis, oral microbiota, supragingival plaque",Experiment 3,Brazil,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,Aplasia group,Engraftment group,"Patients at the final phase of Allogeneic Hematopoietic Stem Cell transplant, when the new transplanted stem cells start to grow and produce new blood cells.",30,27,NA,16S,34,Illumina,centered log-ratio,ANCOM,0.7,FALSE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34222034/1/1,34222034,case-control,34222034,10.3389/fcimb.2021.598093,https://pubmed.ncbi.nlm.nih.gov/34222034/,"Martínez-Cuesta M.C., Del Campo R., Garriga-García M., Peláez C. , Requena T.",Taxonomic Characterization and Short-Chain Fatty Acids Production of the Obese Microbiota,Frontiers in cellular and infection microbiology,2021,"diversity, in vitro incubations, metabolic activity, microbiota, obesity, short-chain fatty acids",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Normal weight volunteers (N),Obese Volunteers (O),Obese adult volunteers with body mass index (BMI) > 30 kg/m^2,13,13,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Figure 5,7 November 2023,Aleru002,"Aleru002,Peace Sandy,WikiWorks",The significant differences in gut microbiota composition in normal weight (N) and obese (O) subjects.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium",1783272|1239|91061|186826|186827|46123;1783272|1239|91061|186826|186827;1783272|1239|526524|526525|2810280|135858;1783272|201174|84998|84999|84107|102106;1783272|1239|526524|526525|2810280|100883;1783272|1239|909932;1783272|1239|909932|909929;1783272|201174|84998|1643822|1643826|84108;1783272|1239|526524|526525|128827|123375,Complete,Peace Sandy
bsdb:34222034/1/2,34222034,case-control,34222034,10.3389/fcimb.2021.598093,https://pubmed.ncbi.nlm.nih.gov/34222034/,"Martínez-Cuesta M.C., Del Campo R., Garriga-García M., Peláez C. , Requena T.",Taxonomic Characterization and Short-Chain Fatty Acids Production of the Obese Microbiota,Frontiers in cellular and infection microbiology,2021,"diversity, in vitro incubations, metabolic activity, microbiota, obesity, short-chain fatty acids",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Normal weight volunteers (N),Obese Volunteers (O),Obese adult volunteers with body mass index (BMI) > 30 kg/m^2,13,13,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Figure 5,7 November 2023,Aleru002,"Aleru002,Peace Sandy,WikiWorks",The significant differences in gut microbiota composition in normal weight (N) and obese (O) subjects.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. (in: firmicutes),,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|s__Peptostreptococcaceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Verrucomicrobiota",3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|244127;1783272|1239;1783272|1239|91061|1385|186817|1386|1409;;3379134|976|200643|171549|2005519|397864;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1898204;1783272|1239|186801|186802|1898207;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107;1783272|1239|1737404|1582879;3379134|976|117743|200644;3379134|976|117743;3384189|32066|203490|203491;3384189|32066|203490;1783272|1239|186801|186802|216572|596767;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|75682;3379134|1224|28216|80840|995019|577310;1783272|1239|1737404|1737405|1570339;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1904861;3379134|976|200643|171549|171551|836;3379134|1224|28211|204441;3379134|976|200643|171549|171550;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|186802|216572|292632;1783272|1239|526524|526525|2810281|191303;3379134|74201,Complete,Peace Sandy
bsdb:34225483/1/1,34225483,laboratory experiment,34225483,10.1128/mBio.01155-21,NA,"Matsui M., Fukunishi S., Nakano T., Ueno T., Higuchi K. , Asai A.",Ileal Bile Acid Transporter Inhibitor Improves Hepatic Steatosis by Ameliorating Gut Microbiota Dysbiosis in NAFLD Model Mice,mBio,2021,"gut microbiome, ileal bile acid transporter inhibitor, nonalcoholic fatty liver disease, nonalcoholic steatohepatitis",Experiment 1,Japan,Mus musculus,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,"Combination of IBATi (ileal bile acid transporter inhibitor), HFD (High fat diet) and HFD + IBATi (High fat diet + ileal bile acid transporter inhibitor) groups",Control diet,Mice in the control diet groups were subjected to the same oral dose of phosphate-buffered saline (PBS).,9,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1D, Figure S3A and Figure S3B",14 April 2025,Tosin,Tosin,"Relative abundance at the family, genus and species level by linear discriminant analysis effect size (LEfSe) in each group",increased,"k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Flammeovirgaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae",3379134|976|768503|768507|89373;3379134|976|768503|768507|200667;3379134|976|117743|200644|49546;1783272|1239|186801|3085636|186803|1506553;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|909656|671267;3379134|976|200643|171549|171551;3379134|976|200643|171549|171552;1783272|1239|91061|1385|90964;3379134|1224|28216|80840|995019,Complete,KateRasheed
bsdb:34225483/2/1,34225483,laboratory experiment,34225483,10.1128/mBio.01155-21,NA,"Matsui M., Fukunishi S., Nakano T., Ueno T., Higuchi K. , Asai A.",Ileal Bile Acid Transporter Inhibitor Improves Hepatic Steatosis by Ameliorating Gut Microbiota Dysbiosis in NAFLD Model Mice,mBio,2021,"gut microbiome, ileal bile acid transporter inhibitor, nonalcoholic fatty liver disease, nonalcoholic steatohepatitis",Experiment 2,Japan,Mus musculus,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,"Combination of Control diet, HFD (High fat diet) and HFD + IBATi (High fat diet + ileal bile acid transporter inhibitor) groups",IBATi (ileal bile acid transporter inhibitor) group,Mice treated with IBATi (ileal bile acid transporter inhibitor),9,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1D, Figure S3A and Figure S3B",14 April 2025,Tosin,Tosin,"Relative abundance at the family, genus and species level by linear discriminant analysis effect size (LEfSe) in each group",increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis",1783272|1239|526524|526525|128827;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|186806|1730;1783272|1239|91061|186826|33958|2742598|1598;1783272|1239|91061|186826|33958|1578|33959;3379134|976|200643|171549|171550|239759|28117,Complete,KateRasheed
bsdb:34225483/3/1,34225483,laboratory experiment,34225483,10.1128/mBio.01155-21,NA,"Matsui M., Fukunishi S., Nakano T., Ueno T., Higuchi K. , Asai A.",Ileal Bile Acid Transporter Inhibitor Improves Hepatic Steatosis by Ameliorating Gut Microbiota Dysbiosis in NAFLD Model Mice,mBio,2021,"gut microbiome, ileal bile acid transporter inhibitor, nonalcoholic fatty liver disease, nonalcoholic steatohepatitis",Experiment 3,Japan,Mus musculus,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,"Combination of Control diet, IBATi (ileal bile acid transporter inhibitor) and HFD + IBATi (High fat diet + ileal bile acid transporter inhibitor) groups",HFD (High fat diet) group,Six weeks Old mice fed with High fat diet for 12 weeks,9,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1D, Figure S3A and Figure S3B",14 April 2025,Tosin,Tosin,"Relative abundance at the family, genus and species level by linear discriminant analysis effect size (LEfSe) in each group",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",1783272|1239|186801|186802|186806;1783272|1239|91061|186826|1300;3379134|976|200643|171549|815|816|29523;1783272|1239|91061|186826|1300|1357|1358;1783272|1239|91061|186826|1300|1357;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|1506577,Complete,KateRasheed
bsdb:34225483/4/1,34225483,laboratory experiment,34225483,10.1128/mBio.01155-21,NA,"Matsui M., Fukunishi S., Nakano T., Ueno T., Higuchi K. , Asai A.",Ileal Bile Acid Transporter Inhibitor Improves Hepatic Steatosis by Ameliorating Gut Microbiota Dysbiosis in NAFLD Model Mice,mBio,2021,"gut microbiome, ileal bile acid transporter inhibitor, nonalcoholic fatty liver disease, nonalcoholic steatohepatitis",Experiment 4,Japan,Mus musculus,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,"Combination of Control diet, IBATi (ileal bile acid transporter inhibitor) and HFD (High fat diet) groups",HFD + IBATi (High fat diet + ileal bile acid transporter inhibitor) group,Mice fed with High fat diet and ileal bile acid transporter inhibitor,9,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1D and Figure S3B,14 April 2025,Tosin,Tosin,Relative abundance at the family and species level by linear discriminant analysis effect size (LEfSe) in each group,increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.",3379134|200940|3031449|213115|194924;1783272|1239|186801|186802|31979|1485|1506,Complete,KateRasheed
bsdb:34225483/5/1,34225483,laboratory experiment,34225483,10.1128/mBio.01155-21,NA,"Matsui M., Fukunishi S., Nakano T., Ueno T., Higuchi K. , Asai A.",Ileal Bile Acid Transporter Inhibitor Improves Hepatic Steatosis by Ameliorating Gut Microbiota Dysbiosis in NAFLD Model Mice,mBio,2021,"gut microbiome, ileal bile acid transporter inhibitor, nonalcoholic fatty liver disease, nonalcoholic steatohepatitis",Experiment 5,Japan,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Mice with FMT (fecal microbiota transplantation) from HFD (high fat diet) mice,Mice with FMT (fecal microbiota transplantation) from HFD + IBATi (High fat diet + ileal bile acid transporter inhibitor) mice,Mice with FMT (fecal microbiota transplantation) from HFD + IBATi (High fat diet + ileal bile acid transporter inhibitor) mice,3,3,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 4C,14 April 2025,Tosin,Tosin,Microbial composition at the family level in each FMT group.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae",3379134|976|200643|171549|171551;1783272|1239|186801|186802|186806,Complete,KateRasheed
bsdb:34225483/5/2,34225483,laboratory experiment,34225483,10.1128/mBio.01155-21,NA,"Matsui M., Fukunishi S., Nakano T., Ueno T., Higuchi K. , Asai A.",Ileal Bile Acid Transporter Inhibitor Improves Hepatic Steatosis by Ameliorating Gut Microbiota Dysbiosis in NAFLD Model Mice,mBio,2021,"gut microbiome, ileal bile acid transporter inhibitor, nonalcoholic fatty liver disease, nonalcoholic steatohepatitis",Experiment 5,Japan,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Mice with FMT (fecal microbiota transplantation) from HFD (high fat diet) mice,Mice with FMT (fecal microbiota transplantation) from HFD + IBATi (High fat diet + ileal bile acid transporter inhibitor) mice,Mice with FMT (fecal microbiota transplantation) from HFD + IBATi (High fat diet + ileal bile acid transporter inhibitor) mice,3,3,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 4C,14 April 2025,Tosin,Tosin,Microbial composition at the family level in each FMT group.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",3379134|976|200643|171549|815;1783272|1239|91061|186826|1300,Complete,KateRasheed
bsdb:34225483/6/1,34225483,laboratory experiment,34225483,10.1128/mBio.01155-21,NA,"Matsui M., Fukunishi S., Nakano T., Ueno T., Higuchi K. , Asai A.",Ileal Bile Acid Transporter Inhibitor Improves Hepatic Steatosis by Ameliorating Gut Microbiota Dysbiosis in NAFLD Model Mice,mBio,2021,"gut microbiome, ileal bile acid transporter inhibitor, nonalcoholic fatty liver disease, nonalcoholic steatohepatitis",Experiment 6,Japan,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Mice with FMT (fecal microbiota transplantation) from HFD (high fat diet) mice,Mice with FMT (fecal microbiota transplantation) from HFD + IBATi (High fat diet + ileal bile acid transporter inhibitor) mice,Mice with FMT (fecal microbiota transplantation) from HFD + IBATi (High fat diet + ileal bile acid transporter inhibitor) mice,3,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Figure 4D, Figure S3C and S3D",14 April 2025,Tosin,Tosin,"Relative abundance at the family, genus and species level by LEfSe in each FMT group.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor|s__Acetatifactor muris,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia caecimuris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kineosporiales|f__Kineosporiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus danieliae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Syntrophomonadaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia cocleata",1783272|1239|186801|3085636|186803|1427378|879566;1783272|201174|84998|1643822|1643826|447020|671266;3379134|976|200643|171549|171550|239759;1783272|1239|91061|1385|186817;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485;3379134|976|768503|768507|89373;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|216572|216851;1783272|201174|1760|622452|83778;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|328812;3379134|976|200643|171549|171551;3379134|1224|1236|91347|1903414|583;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|747656;1783272|201174|1760|85011|2062;1783272|1239|186801|186802|68298;1783272|1239|526524|526525|2810280|3025755;1783272|1239|526524|526525|2810280|3025755|69824,Complete,KateRasheed
bsdb:34225483/6/2,34225483,laboratory experiment,34225483,10.1128/mBio.01155-21,NA,"Matsui M., Fukunishi S., Nakano T., Ueno T., Higuchi K. , Asai A.",Ileal Bile Acid Transporter Inhibitor Improves Hepatic Steatosis by Ameliorating Gut Microbiota Dysbiosis in NAFLD Model Mice,mBio,2021,"gut microbiome, ileal bile acid transporter inhibitor, nonalcoholic fatty liver disease, nonalcoholic steatohepatitis",Experiment 6,Japan,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Mice with FMT (fecal microbiota transplantation) from HFD (high fat diet) mice,Mice with FMT (fecal microbiota transplantation) from HFD + IBATi (High fat diet + ileal bile acid transporter inhibitor) mice,Mice with FMT (fecal microbiota transplantation) from HFD + IBATi (High fat diet + ileal bile acid transporter inhibitor) mice,3,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Figure 4D, Figure S3C and S3D",14 April 2025,Tosin,Tosin,"Relative abundance at the family, genus and species level by LEfSe in each FMT group.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus animalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus murinus,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum|s__Mucispirillum schaedleri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Parvibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae",1783272|1239|186801|186802|216572|244127;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|85831;3379134|976|200643|171549|815|816|29523;3379134|976|200643|171549|815|816|371601;3379134|200930|68337|191393|191394;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|91061|186826|33958|2767887|1605;1783272|1239|91061|186826|33958|2767887|1622;3379134|200930|68337|191393|2945020|248038;3379134|200930|68337|191393|2945020|248038|248039;3379134|976|200643|171549|2005525|375288|823;1783272|201174|84998|84999|84107|1427376;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|68295|186814,Complete,KateRasheed
bsdb:34225483/7/1,34225483,laboratory experiment,34225483,10.1128/mBio.01155-21,NA,"Matsui M., Fukunishi S., Nakano T., Ueno T., Higuchi K. , Asai A.",Ileal Bile Acid Transporter Inhibitor Improves Hepatic Steatosis by Ameliorating Gut Microbiota Dysbiosis in NAFLD Model Mice,mBio,2021,"gut microbiome, ileal bile acid transporter inhibitor, nonalcoholic fatty liver disease, nonalcoholic steatohepatitis",Experiment 7,Japan,Mus musculus,Feces,UBERON:0001988,High fat diet,EFO:0002757,Control diet group,HFD (High fat diet) group,Mice fed with High fat diet,3,3,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 1C,15 April 2025,Tosin,Tosin,Microbial composition at the family level in each group,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae",1783272|1239|91061|186826|1300;3379134|200940|3031449|213115|194924;1783272|1239|186801|186802|186806,Complete,KateRasheed
bsdb:34225483/7/2,34225483,laboratory experiment,34225483,10.1128/mBio.01155-21,NA,"Matsui M., Fukunishi S., Nakano T., Ueno T., Higuchi K. , Asai A.",Ileal Bile Acid Transporter Inhibitor Improves Hepatic Steatosis by Ameliorating Gut Microbiota Dysbiosis in NAFLD Model Mice,mBio,2021,"gut microbiome, ileal bile acid transporter inhibitor, nonalcoholic fatty liver disease, nonalcoholic steatohepatitis",Experiment 7,Japan,Mus musculus,Feces,UBERON:0001988,High fat diet,EFO:0002757,Control diet group,HFD (High fat diet) group,Mice fed with High fat diet,3,3,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 1C,15 April 2025,Tosin,Tosin,Microbial composition at the family level in each group,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae",3379134|976|200643|171549|171551;3379134|976|200643|171549|171552;3379134|976|117743|200644|49546,Complete,KateRasheed
bsdb:34225483/8/1,34225483,laboratory experiment,34225483,10.1128/mBio.01155-21,NA,"Matsui M., Fukunishi S., Nakano T., Ueno T., Higuchi K. , Asai A.",Ileal Bile Acid Transporter Inhibitor Improves Hepatic Steatosis by Ameliorating Gut Microbiota Dysbiosis in NAFLD Model Mice,mBio,2021,"gut microbiome, ileal bile acid transporter inhibitor, nonalcoholic fatty liver disease, nonalcoholic steatohepatitis",Experiment 8,Japan,Mus musculus,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,Control diet group,HFD + IBATi (High fat diet + ileal bile acid transporter inhibitor) group,Mice fed with High fat diet and ileal bile acid transporter inhibitor,3,3,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 1C,15 April 2025,Tosin,"Tosin,KateRasheed",Microbial composition at the family level in each group,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Geobacterales|f__Geobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",1783272|1239|186801|186802|31979;3379134|200940|3031651|3031668|213422;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|1300,Complete,KateRasheed
bsdb:34225483/8/2,34225483,laboratory experiment,34225483,10.1128/mBio.01155-21,NA,"Matsui M., Fukunishi S., Nakano T., Ueno T., Higuchi K. , Asai A.",Ileal Bile Acid Transporter Inhibitor Improves Hepatic Steatosis by Ameliorating Gut Microbiota Dysbiosis in NAFLD Model Mice,mBio,2021,"gut microbiome, ileal bile acid transporter inhibitor, nonalcoholic fatty liver disease, nonalcoholic steatohepatitis",Experiment 8,Japan,Mus musculus,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,Control diet group,HFD + IBATi (High fat diet + ileal bile acid transporter inhibitor) group,Mice fed with High fat diet and ileal bile acid transporter inhibitor,3,3,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 1C,15 April 2025,Tosin,"Tosin,KateRasheed",Microbial composition at the family level in each group,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|976|117743|200644|49546;3379134|976|200643|171549|171551;3379134|976|200643|171549|171552,Complete,KateRasheed
bsdb:34225483/9/1,34225483,laboratory experiment,34225483,10.1128/mBio.01155-21,NA,"Matsui M., Fukunishi S., Nakano T., Ueno T., Higuchi K. , Asai A.",Ileal Bile Acid Transporter Inhibitor Improves Hepatic Steatosis by Ameliorating Gut Microbiota Dysbiosis in NAFLD Model Mice,mBio,2021,"gut microbiome, ileal bile acid transporter inhibitor, nonalcoholic fatty liver disease, nonalcoholic steatohepatitis",Experiment 9,Japan,Mus musculus,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,Control diet group,IBATi (ileal bile acid transporter inhibitor) group,Mice treated with IBATi (ileal bile acid transporter inhibitor),3,3,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 1C,15 April 2025,Tosin,Tosin,Microbial composition at the family level in each group,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,3379134|976|200643|171549|171550,Complete,KateRasheed
bsdb:34225483/9/2,34225483,laboratory experiment,34225483,10.1128/mBio.01155-21,NA,"Matsui M., Fukunishi S., Nakano T., Ueno T., Higuchi K. , Asai A.",Ileal Bile Acid Transporter Inhibitor Improves Hepatic Steatosis by Ameliorating Gut Microbiota Dysbiosis in NAFLD Model Mice,mBio,2021,"gut microbiome, ileal bile acid transporter inhibitor, nonalcoholic fatty liver disease, nonalcoholic steatohepatitis",Experiment 9,Japan,Mus musculus,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,Control diet group,IBATi (ileal bile acid transporter inhibitor) group,Mice treated with IBATi (ileal bile acid transporter inhibitor),3,3,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 1C,15 April 2025,Tosin,Tosin,Microbial composition at the family level in each group,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|976|117743|200644|49546;3379134|976|200643|171549|171552,Complete,KateRasheed
bsdb:34225483/10/1,34225483,laboratory experiment,34225483,10.1128/mBio.01155-21,NA,"Matsui M., Fukunishi S., Nakano T., Ueno T., Higuchi K. , Asai A.",Ileal Bile Acid Transporter Inhibitor Improves Hepatic Steatosis by Ameliorating Gut Microbiota Dysbiosis in NAFLD Model Mice,mBio,2021,"gut microbiome, ileal bile acid transporter inhibitor, nonalcoholic fatty liver disease, nonalcoholic steatohepatitis",Experiment 10,Japan,Mus musculus,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,HFD (High fat diet) groups,HFD + IBATi (High fat diet + ileal bile acid transporter inhibitor) group,Mice fed with High fat diet and ileal bile acid transporter inhibitor,3,3,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1C,15 April 2025,Tosin,Tosin,Microbial composition at the family level in each group,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",3379134|976|200643|171549|171551;1783272|1239|91061|186826|1300,Complete,KateRasheed
bsdb:34225483/11/1,34225483,laboratory experiment,34225483,10.1128/mBio.01155-21,NA,"Matsui M., Fukunishi S., Nakano T., Ueno T., Higuchi K. , Asai A.",Ileal Bile Acid Transporter Inhibitor Improves Hepatic Steatosis by Ameliorating Gut Microbiota Dysbiosis in NAFLD Model Mice,mBio,2021,"gut microbiome, ileal bile acid transporter inhibitor, nonalcoholic fatty liver disease, nonalcoholic steatohepatitis",Experiment 11,Japan,Mus musculus,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,Control,IBATi -Tx (Ileal Bile Acid Transporter inhibitor - Treatment),"Six-week-old mice were fed HFD(High Fat Diet) for 12 weeks and
received IBATi (Ileal Bile Acid Transporter inhibitor) treatment between weeks 6 to 12.",3,3,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Fig. 8C,15 April 2025,Anne-mariesharp,Anne-mariesharp,Microbial composition at the family level in both groups.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,3379134|976|200643|171549|171551,Complete,KateRasheed
bsdb:34225483/11/2,34225483,laboratory experiment,34225483,10.1128/mBio.01155-21,NA,"Matsui M., Fukunishi S., Nakano T., Ueno T., Higuchi K. , Asai A.",Ileal Bile Acid Transporter Inhibitor Improves Hepatic Steatosis by Ameliorating Gut Microbiota Dysbiosis in NAFLD Model Mice,mBio,2021,"gut microbiome, ileal bile acid transporter inhibitor, nonalcoholic fatty liver disease, nonalcoholic steatohepatitis",Experiment 11,Japan,Mus musculus,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,Control,IBATi -Tx (Ileal Bile Acid Transporter inhibitor - Treatment),"Six-week-old mice were fed HFD(High Fat Diet) for 12 weeks and
received IBATi (Ileal Bile Acid Transporter inhibitor) treatment between weeks 6 to 12.",3,3,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Fig. 8C,15 April 2025,Anne-mariesharp,Anne-mariesharp,Microbial composition at the family level in both groups.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|1300,Complete,KateRasheed
bsdb:34225483/12/1,34225483,laboratory experiment,34225483,10.1128/mBio.01155-21,NA,"Matsui M., Fukunishi S., Nakano T., Ueno T., Higuchi K. , Asai A.",Ileal Bile Acid Transporter Inhibitor Improves Hepatic Steatosis by Ameliorating Gut Microbiota Dysbiosis in NAFLD Model Mice,mBio,2021,"gut microbiome, ileal bile acid transporter inhibitor, nonalcoholic fatty liver disease, nonalcoholic steatohepatitis",Experiment 12,Japan,Mus musculus,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,Control,IBATi -Tx (Ileal Bile Acid Transporter inhibitor - Treatment),Six-week-old mice were fed HFD(High Fat Diet) for 12 weeks and received IBATi (Ileal Bile Acid Transporter inhibitor) treatment between weeks 6 to 12.,3,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Fig. 8D, Supplemental figure 3E & 3F",15 April 2025,Anne-mariesharp,Anne-mariesharp,"Microbial composition at the family, genus and species level in both groups.",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cyclobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Flammeovirgaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptacetobacter|s__Peptacetobacter hiranonis",1783272|201174|84998|84999|1643824|1380;3379134|976|200643|171549|815|816|85831;1783272|201174|84998|84999|84107;3379134|976|768503|768507|563798;3379134|976|768503|768507|200667;3379134|976|117743|200644|49546;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|171551;3379134|976|200643|171549|171550;1783272|201174|1760|85011|2062;1783272|1239|186801|186802|31979|1485|1506;1783272|1239|91061|186826|33958|1578|33959;1783272|1239|186801|3082720|186804|2743582|89152,Complete,KateRasheed
bsdb:34225483/12/2,34225483,laboratory experiment,34225483,10.1128/mBio.01155-21,NA,"Matsui M., Fukunishi S., Nakano T., Ueno T., Higuchi K. , Asai A.",Ileal Bile Acid Transporter Inhibitor Improves Hepatic Steatosis by Ameliorating Gut Microbiota Dysbiosis in NAFLD Model Mice,mBio,2021,"gut microbiome, ileal bile acid transporter inhibitor, nonalcoholic fatty liver disease, nonalcoholic steatohepatitis",Experiment 12,Japan,Mus musculus,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,Control,IBATi -Tx (Ileal Bile Acid Transporter inhibitor - Treatment),Six-week-old mice were fed HFD(High Fat Diet) for 12 weeks and received IBATi (Ileal Bile Acid Transporter inhibitor) treatment between weeks 6 to 12.,3,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Fig. 8D, Supplemental figure 3E & 3F",15 April 2025,Anne-mariesharp,Anne-mariesharp,"Microbial composition at the family, genus and species level in both groups.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|186801|186802|216572|244127|169435;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|33035;1783272|1239|186801|3085636|186803|189330;1783272|1239|526524|526525|128827;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|1300|1357|1358;1783272|1239|186801|3085636|186803|248744;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|186802|216572|459786|351091;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977,Complete,KateRasheed
bsdb:34233092/1/1,34233092,"cross-sectional observational, not case-control",34233092,10.1111/aos.14967,NA,"Lee J.W., Lim S.H., Shin J.H., Lee Y. , Seo J.H.",Differences in the eyelid and buccal microbiome between open-angle glaucoma and uveitic glaucoma,Acta ophthalmologica,2022,"eyelid, metagenome, microbiome, open-angle glaucoma, uveitic glaucoma",Experiment 1,Republic of Korea,Homo sapiens,Margin of eyelid,UBERON:0034772,Glaucoma,MONDO:0005041,Open-angle glaucoma (OAG),Uveitic glaucoma (UG),Patients with uveitic glaucoma,62,34,1 month,16S,34,Illumina,raw counts,edgeR,0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 4, Supplementary Table S1",19 September 2025,Anne-mariesharp,Anne-mariesharp,Differentially abundant taxa of the eyelid microbiome in uveitic glaucoma patients compared to that of open-angle glaucoma patients,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales|f__Desulfosalsimonadaceae|g__Desulfonatronobacter,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales|f__Desulfobacteraceae|g__Desulfotignum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Fontibacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Mariniphaga,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Sulfurovaceae|g__Sulfurovum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|g__Tomitella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Deferrisomatia|o__Deferrisomatales|f__Deferrisomataceae|g__Deferrisoma,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Owenweeksiaceae|g__Owenweeksia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Thauera,k__Pseudomonadati|p__Planctomycetota|c__Phycisphaerae|o__Phycisphaerales|f__Phycisphaeraceae|g__Phycisphaera,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Acidicaldus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Desulfuromonadales|f__Desulfuromonadaceae|g__Pelobacter,k__Pseudomonadati|p__Aquificota|c__Aquificia|o__Desulfurobacteriales|f__Desulfurobacteriaceae|g__Balnearium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Thioprofundaceae|g__Thioprofundum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales|f__Desulfosarcinaceae|g__Desulfosarcina,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Natronobacillus,k__Pseudomonadati|p__Ignavibacteriota|c__Ignavibacteria|o__Ignavibacteriales|f__Melioribacteraceae|g__Melioribacter,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Desulfuromonadales|f__Desulfuromonadaceae|g__Desulfuromonas,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Gemmatales|f__Gemmataceae|g__Gemmata,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae|g__Ornatilinea",3379134|1224|1236|91347|543|544;3379134|200940|3024418|213118|2904714|1417297;3379134|200940|3024418|213118|213119|115780;3379134|1224|28211|356|212791;1783272|1239|91061|1385|186822|995014;1783272|201174|1760|85007|85026|2053;3379134|976|200643|1970189|1471398|1573806;1783272|1239|91061|1385|186822|44249;1783272|201174|1760|85007|85025|1827;3379134|29547|3031852|213849|2771472|265570;1783272|201174|1760|85007|741759;3379134|200940|3031652|2814222|3031670|1125862;3379134|976|117743|200644|3024551|267986;3379134|1224|28216|206389|2008794|33057;3379134|203682|666505|666506|666507|666508;3379134|1224|28211|3120395|433|368783;3379134|200940|3031651|69541|213421|18;3379134|200783|187857|1485951|558314|223787;3379134|1224|1236|135613|2034509|665868;3379134|200940|3024418|213118|3031624|2299;1783272|1239|91061|1385|186817|472977;3379134|1134404|795747|795748|1334117|1134403;3379134|200940|3031651|69541|213421|890;3379134|200940|3031451|3024411|213121|893;3379134|203682|203683|2691355|1914233|113;3379134|203691|203692|136|2845253|157;1783272|200795|292625|292629|292628|1434028,Complete,Svetlana up
bsdb:34233092/1/2,34233092,"cross-sectional observational, not case-control",34233092,10.1111/aos.14967,NA,"Lee J.W., Lim S.H., Shin J.H., Lee Y. , Seo J.H.",Differences in the eyelid and buccal microbiome between open-angle glaucoma and uveitic glaucoma,Acta ophthalmologica,2022,"eyelid, metagenome, microbiome, open-angle glaucoma, uveitic glaucoma",Experiment 1,Republic of Korea,Homo sapiens,Margin of eyelid,UBERON:0034772,Glaucoma,MONDO:0005041,Open-angle glaucoma (OAG),Uveitic glaucoma (UG),Patients with uveitic glaucoma,62,34,1 month,16S,34,Illumina,raw counts,edgeR,0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 4, Supplementary Table S1",19 September 2025,Anne-mariesharp,Anne-mariesharp,Differentially abundant taxa of the eyelid microbiome in uveitic glaucoma patients compared to that of open-angle glaucoma patients,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,3379134|1224|1236|91347|1903411|613,Complete,Svetlana up
bsdb:34233092/2/1,34233092,"cross-sectional observational, not case-control",34233092,10.1111/aos.14967,NA,"Lee J.W., Lim S.H., Shin J.H., Lee Y. , Seo J.H.",Differences in the eyelid and buccal microbiome between open-angle glaucoma and uveitic glaucoma,Acta ophthalmologica,2022,"eyelid, metagenome, microbiome, open-angle glaucoma, uveitic glaucoma",Experiment 2,Republic of Korea,Homo sapiens,Buccal mucosa,UBERON:0006956,Glaucoma,MONDO:0005041,Open-angle glaucoma (OAG),Uveitic glaucoma (UG),Patients with uveitic glaucoma,62,34,1 month,16S,34,Illumina,raw counts,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 5, Supplementary Table S2",24 September 2025,Anne-mariesharp,Anne-mariesharp,Differentially abundant taxa of the buccal microbiome in uveitic glaucoma patients compared to that of open-angle glaucoma patients,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Endobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,c__Cryptophyceae|o__Cryptomonadales|f__Cryptomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Tropherymataceae|g__Tropheryma,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella",3379134|1224|28211|3120395|433|1649268;1783272|1239|91061|186826|81852|1350;3027|589350|2896;3379134|1224|28216|80840|75682|29580;1783272|201174|1760|85006|2805591|2038;3379134|1224|1236|91347|543|160674,Complete,Svetlana up
bsdb:34233092/2/2,34233092,"cross-sectional observational, not case-control",34233092,10.1111/aos.14967,NA,"Lee J.W., Lim S.H., Shin J.H., Lee Y. , Seo J.H.",Differences in the eyelid and buccal microbiome between open-angle glaucoma and uveitic glaucoma,Acta ophthalmologica,2022,"eyelid, metagenome, microbiome, open-angle glaucoma, uveitic glaucoma",Experiment 2,Republic of Korea,Homo sapiens,Buccal mucosa,UBERON:0006956,Glaucoma,MONDO:0005041,Open-angle glaucoma (OAG),Uveitic glaucoma (UG),Patients with uveitic glaucoma,62,34,1 month,16S,34,Illumina,raw counts,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 5, Supplementary Table S2",24 September 2025,Anne-mariesharp,Anne-mariesharp,Differentially abundant taxa of the buccal microbiome in uveitic glaucoma patients compared to that of open-angle glaucoma patients,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Aeriscardovia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus",1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85004|31953|240233;3379134|1224|1236|91347|1903414|583,Complete,Svetlana up
bsdb:34238926/1/1,34238926,case-control,34238926,10.1038/s41398-021-01504-6,NA,"Richarte V., Sánchez-Mora C., Corrales M., Fadeuilhe C., Vilar-Ribó L., Arribas L., Garcia E., Rosales-Ortiz S.K., Arias-Vasquez A., Soler-Artigas M., Ribasés M. , Ramos-Quiroga J.A.",Gut microbiota signature in treatment-naïve attention-deficit/hyperactivity disorder,Translational psychiatry,2021,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Attention deficit-hyperactivity disorder,MONDO:0007743,Controls,Attention-deficit/hyperactivity disorder (ADHD),Medication-naïve adults with ADHD (Attention-deficit/hyperactivity disorder (ADHD),100,100,Recent antibiotics use,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"ethnic group,sex",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,"Table 1, Figure 1A, 1B and Supplemenatary Figure 4",28 October 2025,Tosin,Tosin,Differential abundance results according to Deseq2 method between ADHD (attention-deficit/hyperactivity disorder patients) and control,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Leclercia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotellamassilia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|976|200643|171549|171552|1283313;1783272|1239|909932|1843489|31977|39948;3379134|1224|1236|91347|543|83654;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|1926672;1783272|1239|186801|3082720|186804|1501226;1783272|1239|909932|909929|1843491;1783272|1239|909932|1843489|31977,Complete,KateRasheed
bsdb:34238926/1/2,34238926,case-control,34238926,10.1038/s41398-021-01504-6,NA,"Richarte V., Sánchez-Mora C., Corrales M., Fadeuilhe C., Vilar-Ribó L., Arribas L., Garcia E., Rosales-Ortiz S.K., Arias-Vasquez A., Soler-Artigas M., Ribasés M. , Ramos-Quiroga J.A.",Gut microbiota signature in treatment-naïve attention-deficit/hyperactivity disorder,Translational psychiatry,2021,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Attention deficit-hyperactivity disorder,MONDO:0007743,Controls,Attention-deficit/hyperactivity disorder (ADHD),Medication-naïve adults with ADHD (Attention-deficit/hyperactivity disorder (ADHD),100,100,Recent antibiotics use,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"ethnic group,sex",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,"Table 1, Figure 1A, 1B and Supplemenatary Figure 4",28 October 2025,Tosin,Tosin,Differential abundance results according to Deseq2 method between ADHD (attention-deficit/hyperactivity disorder patients) and controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerotaenia,k__Bacillati|p__Candidatus Melainabacteria,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Fucophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Gracilibacteraceae|g__Gracilibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Gracilibacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Herbinix,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Candidatus Melainabacteria|c__Vampirovibriophyceae|o__Vampirovibrionales|g__Vampirovibrio,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",1783272|1239|186801|3120394|3120654|35829;1783272|1239|186801|3085636|186803|1843206;1783272|1798710;3379134|74201|203494|48461|203557|177411;1783272|1239|186801|186802|541019|342658;1783272|1239|186801|186802|541019;1783272|1239|186801|3085636|186803|1663717;3379134|976|200643|171549|1853231|283168;1783272|1798710|3118680|2211217|213484;3379134|74201|203494|48461|203557,Complete,KateRasheed
bsdb:34238926/2/1,34238926,case-control,34238926,10.1038/s41398-021-01504-6,NA,"Richarte V., Sánchez-Mora C., Corrales M., Fadeuilhe C., Vilar-Ribó L., Arribas L., Garcia E., Rosales-Ortiz S.K., Arias-Vasquez A., Soler-Artigas M., Ribasés M. , Ramos-Quiroga J.A.",Gut microbiota signature in treatment-naïve attention-deficit/hyperactivity disorder,Translational psychiatry,2021,NA,Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Attention deficit-hyperactivity disorder,MONDO:0007743,Controls,Attention-deficit/hyperactivity disorder (ADHD),Medication-naïve adults with ADHD (Attention-deficit/hyperactivity disorder (ADHD),100,100,Recent antibiotics use,16S,34,Illumina,relative abundances,Random Forest Analysis,0.05,TRUE,NA,"ethnic group,sex",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,"Table 1, Figure 1A and Figure 1B",29 October 2025,Tosin,Tosin,Differential abundance results according to random forest analysis method between ADHD (attention-deficit/hyperactivity disorder patients) and controls,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Flintibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|1918454;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|909929|1843491;1783272|1239|909932|1843489|31977,Complete,KateRasheed
bsdb:34238926/2/2,34238926,case-control,34238926,10.1038/s41398-021-01504-6,NA,"Richarte V., Sánchez-Mora C., Corrales M., Fadeuilhe C., Vilar-Ribó L., Arribas L., Garcia E., Rosales-Ortiz S.K., Arias-Vasquez A., Soler-Artigas M., Ribasés M. , Ramos-Quiroga J.A.",Gut microbiota signature in treatment-naïve attention-deficit/hyperactivity disorder,Translational psychiatry,2021,NA,Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Attention deficit-hyperactivity disorder,MONDO:0007743,Controls,Attention-deficit/hyperactivity disorder (ADHD),Medication-naïve adults with ADHD (Attention-deficit/hyperactivity disorder (ADHD),100,100,Recent antibiotics use,16S,34,Illumina,relative abundances,Random Forest Analysis,0.05,TRUE,NA,"ethnic group,sex",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,"Table 1, Figure 1A and 1B",29 October 2025,Tosin,Tosin,Differential abundance results according to random forest analysis method between ADHD (attention-deficit/hyperactivity disorder patients) and controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerotaenia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Gracilibacteraceae|g__Gracilibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Gracilibacteraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella",1783272|1239|186801|3085636|186803|1843206;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|541019|342658;1783272|1239|186801|186802|541019;1783272|1239|91061|186826|33958;3379134|1224|28216|80840|995019|577310,Complete,KateRasheed
bsdb:34248903/1/1,34248903,"cross-sectional observational, not case-control",34248903,10.3389/fmicb.2021.683685,NA,"de Jesus V.C., Khan M.W., Mittermuller B.A., Duan K., Hu P., Schroth R.J. , Chelikani P.",Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries,Frontiers in microbiology,2021,"artificial intelligence, bacteria, case-control, dental plaque, fungi, machine learning, microbiota, oral swab",Experiment 1,Canada,Homo sapiens,"Supragingival dental plaque,Saliva","UBERON:0001836,UBERON:0016485",Dental caries,EFO:0003819,Oral swab from severe early childhood caries (S-ECC),Supragingival plaque from severe early childhood caries (S-ECC),Supragingival plaque samples of children < 72 months of age with severe early childhood caries (S-ECC),40,40,Current use of antibiotics,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,FIG. 3B,21 April 2024,Rahila,"Rahila,Scholastica,WikiWorks",Differential abundance analysis of species that were overabundant in supragingival plaque compared to oral swab samples within the S-ECC (severe early childhood caries) group,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella kingae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella maculosa,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas artemidis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius",1783272|1239|91061|186826|186827|46123|46125;3379134|976|117743|200644|49546|1016|1019;1783272|201174|1760|85007|1653|1716|61592;1783272|201174|1760|85007|1653|1716|43768;3379134|1224|28216|206351|481|32257|504;3379134|1224|28216|206351|481|32257|505;3379134|1224|28216|80840|119060|47670|47671;1783272|201174|1760|85006|1268|32207|172042;1783272|201174|1760|85006|1268|32207|2047;3379134|976|200643|171549|171552|2974251|439703;3379134|976|200643|171549|171552|2974251|28135;1783272|1239|909932|909929|1843491|970|671224;1783272|1239|909932|909929|1843491|970|69823;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|91061|186826|1300|1301|1309;1783272|1239|91061|186826|1300|1301|1304,Complete,Svetlana up
bsdb:34248903/1/2,34248903,"cross-sectional observational, not case-control",34248903,10.3389/fmicb.2021.683685,NA,"de Jesus V.C., Khan M.W., Mittermuller B.A., Duan K., Hu P., Schroth R.J. , Chelikani P.",Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries,Frontiers in microbiology,2021,"artificial intelligence, bacteria, case-control, dental plaque, fungi, machine learning, microbiota, oral swab",Experiment 1,Canada,Homo sapiens,"Supragingival dental plaque,Saliva","UBERON:0001836,UBERON:0016485",Dental caries,EFO:0003819,Oral swab from severe early childhood caries (S-ECC),Supragingival plaque from severe early childhood caries (S-ECC),Supragingival plaque samples of children < 72 months of age with severe early childhood caries (S-ECC),40,40,Current use of antibiotics,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,FIG. 3B,21 April 2024,Rahila,"Rahila,Scholastica,WikiWorks",Differential abundance analysis of species that were overabundant in supragingival plaque compared to oral swab samples within the S-ECC (severe early childhood caries) group,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella|s__Simonsiella muelleri,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia vaginalis",1783272|1239|91061|1385|539738|1378|29391;1783272|1239|91061|186826|186828|117563|137732;3379134|1224|1236|135625|712|724|727;3379134|1224|1236|135625|712|724|729;3379134|976|200643|171549|171552|2974257|425941;3379134|1224|28216|206351|481|71|72;3384189|32066|203490|203491|1129771|168808|187101,Complete,Svetlana up
bsdb:34248903/2/1,34248903,"cross-sectional observational, not case-control",34248903,10.3389/fmicb.2021.683685,NA,"de Jesus V.C., Khan M.W., Mittermuller B.A., Duan K., Hu P., Schroth R.J. , Chelikani P.",Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries,Frontiers in microbiology,2021,"artificial intelligence, bacteria, case-control, dental plaque, fungi, machine learning, microbiota, oral swab",Experiment 2,Canada,Homo sapiens,"Saliva,Supragingival dental plaque","UBERON:0001836,UBERON:0016485",Dental caries,EFO:0003819,Oral swab from caries-free,Supragingival plaque from caries-free,"Supragingival plaque samples of children < 72 months of age who are caries-free, confirmed by a dental examination",40,40,Current use of antibiotics,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,FIG. 3C,21 April 2024,Rahila,"Rahila,Scholastica,WikiWorks",Differential abundance analysis of species that were overabundant in supragingival plaque compared to oral swab samples within the caries-free group,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces gerencseriae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter aphrophilus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter rectus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hongkongensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas artemidis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus intermedius",1783272|1239|91061|186826|186827|46123|46125;1783272|201174|1760|2037|2049|1654|52769;3379134|1224|1236|135625|712|416916|732;3379134|29547|3031852|213849|72294|194|824;3379134|29547|3031852|213849|72294|194|203;3379134|976|117743|200644|49546|1016|1017;3379134|976|117743|200644|49546|1016|45242;3379134|976|117743|200644|49546|1016|327575;3379134|976|117743|200644|49546|1016|1019;3379134|1224|1236|135615|868|2717|2718;1783272|201174|1760|85007|1653|1716|61592;1783272|201174|1760|85007|1653|1716|43768;3379134|1224|28216|206351|481|538|539;3379134|1224|28216|206351|481|32257|505;3379134|1224|28216|80840|119060|47670|47671;3384189|32066|203490|203491|1129771|32067|554406;1783272|201174|1760|85006|1268|32207|172042;1783272|201174|1760|85006|1268|32207|2047;1783272|1239|909932|909929|1843491|970|671224;1783272|1239|909932|909929|1843491|970|69823;1783272|1239|91061|186826|1300|1301|1338,Complete,Svetlana up
bsdb:34248903/2/2,34248903,"cross-sectional observational, not case-control",34248903,10.3389/fmicb.2021.683685,NA,"de Jesus V.C., Khan M.W., Mittermuller B.A., Duan K., Hu P., Schroth R.J. , Chelikani P.",Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries,Frontiers in microbiology,2021,"artificial intelligence, bacteria, case-control, dental plaque, fungi, machine learning, microbiota, oral swab",Experiment 2,Canada,Homo sapiens,"Saliva,Supragingival dental plaque","UBERON:0001836,UBERON:0016485",Dental caries,EFO:0003819,Oral swab from caries-free,Supragingival plaque from caries-free,"Supragingival plaque samples of children < 72 months of age who are caries-free, confirmed by a dental examination",40,40,Current use of antibiotics,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,FIG. 3C,21 April 2024,Rahila,"Rahila,Scholastica,WikiWorks",Differential abundance analysis of species that were overabundant in supragingival plaque compared to oral swab samples within the caries-free group,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia vaginalis",1783272|1239|91061|1385|539738|1378|29391;1783272|1239|91061|186826|186828|117563|137732;3379134|1224|1236|135625|712|724|729;3379134|976|200643|171549|171551|836|1583331;3379134|976|200643|171549|171552|838|28132;1783272|201174|1760|85006|1268|32207|43675;3384189|32066|203490|203491|1129771|168808|187101,Complete,Svetlana up
bsdb:34248903/3/1,34248903,"cross-sectional observational, not case-control",34248903,10.3389/fmicb.2021.683685,NA,"de Jesus V.C., Khan M.W., Mittermuller B.A., Duan K., Hu P., Schroth R.J. , Chelikani P.",Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries,Frontiers in microbiology,2021,"artificial intelligence, bacteria, case-control, dental plaque, fungi, machine learning, microbiota, oral swab",Experiment 3,Canada,Homo sapiens,"Supragingival dental plaque,Saliva","UBERON:0001836,UBERON:0016485",Dental caries,EFO:0003819,Oral swab from severe early childhood caries (S-ECC),Supragingival plaque from severe early childhood caries (S-ECC),Supragingival plaque samples of children < 72 months of age with severe early childhood caries (S-ECC),40,40,Use of antibiotics,ITS / ITS2,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 2,5 June 2024,Scholastica,"Scholastica,WikiWorks",Differential abundance analysis of fungal taxa in supragingival plaque compared to oral swab samples within the S-ECC (severe early childhood caries) group,increased,"k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida dubliniensis,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Thelephorales|f__Thelephoraceae,k__Fungi|p__Zoopagomycota|o__Ramicandelaberales|f__Ramicandelaberaceae|g__Ramicandelaber|s__Ramicandelaber taiwanensis,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium|s__Fusarium sp.,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales|f__Stereaceae|g__Stereum|s__Stereum rugosum,k__Fungi|p__Basidiomycota|c__Wallemiomycetes|o__Wallemiales|f__Wallemiaceae|g__Wallemia|s__Wallemia tropicalis",4751|4890|3239874|2916678|766764|5475|42374;4751|4890|3239874|2916678|766764|5475|5476;4751|5204|155619|56487|56488;4751|1913638|2219773|2219775|304330|858342;4751|4890|147550|5125|110618|5506|29916;4751|5204|155619|452342|103376|5644|55358;4751|5204|431957|431958|431959|148959|1708540,Complete,Svetlana up
bsdb:34248903/3/2,34248903,"cross-sectional observational, not case-control",34248903,10.3389/fmicb.2021.683685,NA,"de Jesus V.C., Khan M.W., Mittermuller B.A., Duan K., Hu P., Schroth R.J. , Chelikani P.",Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries,Frontiers in microbiology,2021,"artificial intelligence, bacteria, case-control, dental plaque, fungi, machine learning, microbiota, oral swab",Experiment 3,Canada,Homo sapiens,"Supragingival dental plaque,Saliva","UBERON:0001836,UBERON:0016485",Dental caries,EFO:0003819,Oral swab from severe early childhood caries (S-ECC),Supragingival plaque from severe early childhood caries (S-ECC),Supragingival plaque samples of children < 72 months of age with severe early childhood caries (S-ECC),40,40,Use of antibiotics,ITS / ITS2,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 2,5 June 2024,Scholastica,"Scholastica,WikiWorks",Differential abundance analysis of fungal taxa in supragingival plaque compared to oral swab samples within the S-ECC (severe early childhood caries) group,decreased,"k__Fungi|p__Basidiomycota|c__Agaricomycetes,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae|g__Trichosporon|s__Trichosporon asahii,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia globosa",4751|5204|155619;4751|5204|1538075|162474|742845|55193|76775;4751|5204|155616|1851469|1759442|5552|82508;4751|5204|1538075|162474|742845|55193|76773,Complete,Svetlana up
bsdb:34248903/4/1,34248903,"cross-sectional observational, not case-control",34248903,10.3389/fmicb.2021.683685,NA,"de Jesus V.C., Khan M.W., Mittermuller B.A., Duan K., Hu P., Schroth R.J. , Chelikani P.",Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries,Frontiers in microbiology,2021,"artificial intelligence, bacteria, case-control, dental plaque, fungi, machine learning, microbiota, oral swab",Experiment 4,Canada,Homo sapiens,"Saliva,Supragingival dental plaque","UBERON:0001836,UBERON:0016485",Dental caries,EFO:0003819,Oral swab from caries-free,Supragingival plaque from caries-free,"Supragingival plaque samples of children < 72 months of age who are caries-free, confirmed by a dental examination",40,40,Use of antibiotics,ITS / ITS2,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Table 2,5 June 2024,Scholastica,"Scholastica,WikiWorks",Differential abundance analysis of fungal taxa in supragingival plaque compared to oral swab samples within the caries-free group,increased,"k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Erysiphales|f__Erysiphaceae|g__Blumeria|s__Blumeria sp.,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae|g__Trichosporon|s__Trichosporon asahii,k__Fungi|p__Zoopagomycota|o__Ramicandelaberales|f__Ramicandelaberaceae|g__Ramicandelaber|s__Ramicandelaber taiwanensis,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium|s__Fusarium sp.,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Meyerozyma|s__Meyerozyma guilliermondii,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales,k__Fungi|p__Cryptomycota,k__Fungi|p__Chytridiomycota,k__Fungi|p__Basidiomycota|c__Wallemiomycetes|o__Wallemiales|f__Wallemiaceae|g__Wallemia|s__Wallemia tropicalis",4751|4890|147548|5120|34371|34372|2874738;4751|5204|1538075|162474|742845|55193|76775;4751|5204|155616|1851469|1759442|5552|82508;4751|1913638|2219773|2219775|304330|858342;4751|4890|147550|5125|110618|5506|29916;4751|4890|3239874|2916678|766764|766728|4929;4751|5204|1538075|162474;4751|1031332;4751|4761;4751|5204|431957|431958|431959|148959|1708540,Complete,Svetlana up
bsdb:34248903/4/2,34248903,"cross-sectional observational, not case-control",34248903,10.3389/fmicb.2021.683685,NA,"de Jesus V.C., Khan M.W., Mittermuller B.A., Duan K., Hu P., Schroth R.J. , Chelikani P.",Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries,Frontiers in microbiology,2021,"artificial intelligence, bacteria, case-control, dental plaque, fungi, machine learning, microbiota, oral swab",Experiment 4,Canada,Homo sapiens,"Saliva,Supragingival dental plaque","UBERON:0001836,UBERON:0016485",Dental caries,EFO:0003819,Oral swab from caries-free,Supragingival plaque from caries-free,"Supragingival plaque samples of children < 72 months of age who are caries-free, confirmed by a dental examination",40,40,Use of antibiotics,ITS / ITS2,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Table 2,5 June 2024,Scholastica,"Scholastica,WikiWorks",Differential abundance analysis of fungal taxa in supragingival plaque compared to oral swab samples within the caries-free group,decreased,"k__Fungi|p__Basidiomycota|c__Agaricomycetes,k__Fungi|p__Ascomycota",4751|5204|155619;4751|4890,Complete,Svetlana up
bsdb:34248903/5/1,34248903,"cross-sectional observational, not case-control",34248903,10.3389/fmicb.2021.683685,NA,"de Jesus V.C., Khan M.W., Mittermuller B.A., Duan K., Hu P., Schroth R.J. , Chelikani P.",Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries,Frontiers in microbiology,2021,"artificial intelligence, bacteria, case-control, dental plaque, fungi, machine learning, microbiota, oral swab",Experiment 5,Canada,Homo sapiens,Saliva,UBERON:0001836,Dental caries,EFO:0003819,Oral swab from caries-free,Oral swab from severe early childhood caries (S-ECC),"Oral swap samples of children < 72 months of age who are caries-free, confirmed by a dental examination",40,40,Current use of antibiotics,ITS / ITS2,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,5 June 2024,Scholastica,"Scholastica,WikiWorks",Differential abundance analysis of fungal taxa in oral swab samples within the caries-free group versus oral swab samples within the  S-ECC (severe early childhood caries) group,increased,"k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida dubliniensis,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida tropicalis",4751|4890|3239874|2916678|766764|5475|42374;4751|5204|1538075|162474|742845|55193|76775;4751|4890|3239874|2916678|766764|5475|5482,Complete,Svetlana up
bsdb:34248903/5/2,34248903,"cross-sectional observational, not case-control",34248903,10.3389/fmicb.2021.683685,NA,"de Jesus V.C., Khan M.W., Mittermuller B.A., Duan K., Hu P., Schroth R.J. , Chelikani P.",Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries,Frontiers in microbiology,2021,"artificial intelligence, bacteria, case-control, dental plaque, fungi, machine learning, microbiota, oral swab",Experiment 5,Canada,Homo sapiens,Saliva,UBERON:0001836,Dental caries,EFO:0003819,Oral swab from caries-free,Oral swab from severe early childhood caries (S-ECC),"Oral swap samples of children < 72 months of age who are caries-free, confirmed by a dental examination",40,40,Current use of antibiotics,ITS / ITS2,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,5 June 2024,Scholastica,"Scholastica,WikiWorks",Differential abundance analysis of fungal taxa in oral swab samples within the caries-free group versus oral swab samples within the  S-ECC (severe early childhood caries) group,decreased,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Thelephorales|f__Thelephoraceae,4751|5204|155619|56487|56488,Complete,Svetlana up
bsdb:34264502/1/1,34264502,"cross-sectional observational, not case-control",34264502,https://doi.org/10.1007/s42770-021-00539-7,NA,"de Oliveira Scoaris D., Hughes F.M., Silveira M.A., Evans J.D., Pettis J.S., Bastos E.M.A.F. , Rosa C.A.",Microbial communities associated with honey bees in Brazil and in the United States,Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology],2021,"Apis mellifera, Bacteria, Diversity, Environment, Microorganisms, Yeasts",Experiment 1,"Brazil,United States of America",Not specified,Intestinal mucosa,UBERON:0001242,Restricted to specific location,MONDO:0045042,Brazilian hive microenvironment,North American hive microenvironments,North American samples were collected from four hives of honey bees,5,4,2 weeks,ITS / ITS2,NA,RT-qPCR,raw counts,NA,NA,NA,NA,NA,physical activity,NA,NA,NA,NA,NA,NA,Signature 1,Table 5,7 March 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,Rahila,WikiWorks","Frequency of occurrence (fi) and density (ρ, in log CFU g−1 or CFU individual bee−1) of bacteria associated with honey bee substrates from the United States and Brazil",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus licheniformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. (in: firmicutes),k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Priestia|s__Priestia megaterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Priestia|s__Priestia aryabhattai",1783272|1239|91061|1385|186817|1386|1402;1783272|1239|91061|1385|186817|1386|1409;1783272|1239|91061|1385|186817|2800373|1404;1783272|1239|91061|1385|186817|2800373|412384,Complete,NA
bsdb:34264502/1/2,34264502,"cross-sectional observational, not case-control",34264502,https://doi.org/10.1007/s42770-021-00539-7,NA,"de Oliveira Scoaris D., Hughes F.M., Silveira M.A., Evans J.D., Pettis J.S., Bastos E.M.A.F. , Rosa C.A.",Microbial communities associated with honey bees in Brazil and in the United States,Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology],2021,"Apis mellifera, Bacteria, Diversity, Environment, Microorganisms, Yeasts",Experiment 1,"Brazil,United States of America",Not specified,Intestinal mucosa,UBERON:0001242,Restricted to specific location,MONDO:0045042,Brazilian hive microenvironment,North American hive microenvironments,North American samples were collected from four hives of honey bees,5,4,2 weeks,ITS / ITS2,NA,RT-qPCR,raw counts,NA,NA,NA,NA,NA,physical activity,NA,NA,NA,NA,NA,NA,Signature 2,Table 5,7 March 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,WikiWorks","Frequency of occurrence (fi) and density (ρ, in log CFU g−1 or CFU individual bee−1) of bacteria associated with honey bee substrates from the United States and Brazil",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus subtilis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus|s__Lysinibacillus fusiformis",1783272|1239|91061|1385|186817|1386|1423;1783272|1239|91061|186826|33958|1578|1591;1783272|1239|91061|1385|186817|400634|28031,Complete,NA
bsdb:34264976/1/1,34264976,laboratory experiment,34264976,10.1371/journal.pone.0253728,https://pmc.ncbi.nlm.nih.gov/articles/PMC8282076/,"Xiaobin L., Jinglong X., Fang Z., Chenchen W. , Kailun Y.",Effect of the HXBM408 bacteria on rat intestinal bacterial diversity and the metabolism of soybean isoflavones,PloS one,2021,NA,Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Metabolic process,GO:0008152,Control group,Trial group; 7d (Feces),Fecal samples collected from rats after 7 days of intragastric administration of HXBM408 bacteria.,10,10,NA,NA,NA,NA,relative abundances,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Table 6,23 April 2025,Shulamite,Shulamite,Effects of feeding HXBM408 on the abundance of bacterium in rat feces and intestinal digesta by phylum and genus.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:34264976/2/1,34264976,laboratory experiment,34264976,10.1371/journal.pone.0253728,https://pmc.ncbi.nlm.nih.gov/articles/PMC8282076/,"Xiaobin L., Jinglong X., Fang Z., Chenchen W. , Kailun Y.",Effect of the HXBM408 bacteria on rat intestinal bacterial diversity and the metabolism of soybean isoflavones,PloS one,2021,NA,Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Metabolic process,GO:0008152,Control,Trial group 21d (Feces),Fecal samples collected from rats after 21 days of intragastric administration of HXBM408 bacteria.,10,10,NA,NA,NA,NA,relative abundances,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 6,24 April 2025,Shulamite,Shulamite,Effect of feeding HXBM408 on the abundance of bacterium in rat feces and intestinal digesta and by phylum and by genus.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:34264976/4/1,34264976,laboratory experiment,34264976,10.1371/journal.pone.0253728,https://pmc.ncbi.nlm.nih.gov/articles/PMC8282076/,"Xiaobin L., Jinglong X., Fang Z., Chenchen W. , Kailun Y.",Effect of the HXBM408 bacteria on rat intestinal bacterial diversity and the metabolism of soybean isoflavones,PloS one,2021,NA,Experiment 4,China,Homo sapiens,Intestine,UBERON:0000160,Metabolic process,GO:0008152,Control group,Trial group; 35d (Intestinal),Intestinal content samples collected from rats after 35 days of intrasgastric administration of HXBM408 bacteria,10,10,NA,NA,NA,NA,relative abundances,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 6,24 April 2025,Shulamite,Shulamite,Effect of feeding HXBM408 on the abundance of bacterium in rat feces and intestinal digesta and by phylum and genus.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511,Complete,KateRasheed
bsdb:34264976/4/2,34264976,laboratory experiment,34264976,10.1371/journal.pone.0253728,https://pmc.ncbi.nlm.nih.gov/articles/PMC8282076/,"Xiaobin L., Jinglong X., Fang Z., Chenchen W. , Kailun Y.",Effect of the HXBM408 bacteria on rat intestinal bacterial diversity and the metabolism of soybean isoflavones,PloS one,2021,NA,Experiment 4,China,Homo sapiens,Intestine,UBERON:0000160,Metabolic process,GO:0008152,Control group,Trial group; 35d (Intestinal),Intestinal content samples collected from rats after 35 days of intrasgastric administration of HXBM408 bacteria,10,10,NA,NA,NA,NA,relative abundances,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table 5 and 6,24 April 2025,Shulamite,Shulamite,Effect of feeding HXBM408 on the abundance of bacterium in rat feces and intestinal digesta and by phylum and genus.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Pseudomonadati|p__Pseudomonadota",1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3082720|186804|1501226;3379134|1224,Complete,KateRasheed
bsdb:34264976/5/1,34264976,laboratory experiment,34264976,10.1371/journal.pone.0253728,https://pmc.ncbi.nlm.nih.gov/articles/PMC8282076/,"Xiaobin L., Jinglong X., Fang Z., Chenchen W. , Kailun Y.",Effect of the HXBM408 bacteria on rat intestinal bacterial diversity and the metabolism of soybean isoflavones,PloS one,2021,NA,Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Metabolic process,GO:0008152,Control group,Trial group; 7d (Feces),Fecal samples collected from rats after 7 days of intrasgastric administration of HXBM408 bacteria.,10,10,NA,NA,NA,NA,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Fig. 2A,24 April 2025,Shulamite,Shulamite,The LEfSe profile of bacterial flora in rat feces and intestinal digesta.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|186801|186802|216572|258514;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816,Complete,KateRasheed
bsdb:34264976/6/1,34264976,laboratory experiment,34264976,10.1371/journal.pone.0253728,https://pmc.ncbi.nlm.nih.gov/articles/PMC8282076/,"Xiaobin L., Jinglong X., Fang Z., Chenchen W. , Kailun Y.",Effect of the HXBM408 bacteria on rat intestinal bacterial diversity and the metabolism of soybean isoflavones,PloS one,2021,NA,Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Metabolic process,GO:0008152,Control group; 21d (Feces),Trial group,Fecal samples collected from rats after 21 days of intragastric administration of HXBM408 bacteria,10,10,NA,NA,NA,NA,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Fig 2B,24 April 2025,Shulamite,Shulamite,The LEfSe profile of bacterial flora in rat feces and intestinal digesta.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus murinus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005",1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|2767887|1622;1783272|1239|186801|186802|216572|3068309,Complete,KateRasheed
bsdb:34264976/7/1,34264976,laboratory experiment,34264976,10.1371/journal.pone.0253728,https://pmc.ncbi.nlm.nih.gov/articles/PMC8282076/,"Xiaobin L., Jinglong X., Fang Z., Chenchen W. , Kailun Y.",Effect of the HXBM408 bacteria on rat intestinal bacterial diversity and the metabolism of soybean isoflavones,PloS one,2021,NA,Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Metabolic process,GO:0008152,Control group; 35d(Feces),Trial group,Fecal samples collected from rats after 35 days of intragastric administration of HXBM408 bacteria,10,10,NA,NA,NA,NA,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Fig 2C,24 April 2025,Shulamite,Shulamite,The LEfSe profile of bacterial flora in rat feces and intestinal digesta.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,1783272|1239|186801|186802|216572|3068309,Complete,KateRasheed
bsdb:34264976/8/1,34264976,laboratory experiment,34264976,10.1371/journal.pone.0253728,https://pmc.ncbi.nlm.nih.gov/articles/PMC8282076/,"Xiaobin L., Jinglong X., Fang Z., Chenchen W. , Kailun Y.",Effect of the HXBM408 bacteria on rat intestinal bacterial diversity and the metabolism of soybean isoflavones,PloS one,2021,NA,Experiment 8,China,Homo sapiens,Intestine,UBERON:0000160,Metabolic process,GO:0008152,Control group,Trial group; 35d (Intestinal),Intestinal content samples collected from rats after 35 days of intragastric administration of HXBM408 bacteria.,10,10,NA,NA,NA,NA,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Fig 2D,24 April 2025,Shulamite,Shulamite,The LEfSe profile of bacterial flora in rat feces and intestinal digesta.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511,Complete,KateRasheed
bsdb:34264976/8/2,34264976,laboratory experiment,34264976,10.1371/journal.pone.0253728,https://pmc.ncbi.nlm.nih.gov/articles/PMC8282076/,"Xiaobin L., Jinglong X., Fang Z., Chenchen W. , Kailun Y.",Effect of the HXBM408 bacteria on rat intestinal bacterial diversity and the metabolism of soybean isoflavones,PloS one,2021,NA,Experiment 8,China,Homo sapiens,Intestine,UBERON:0000160,Metabolic process,GO:0008152,Control group,Trial group; 35d (Intestinal),Intestinal content samples collected from rats after 35 days of intragastric administration of HXBM408 bacteria.,10,10,NA,NA,NA,NA,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Fig 2D,24 April 2025,Shulamite,Shulamite,The LEfSe profile of bacterial flora in rat feces and intestinal digesta.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,1783272|1239|186801|3085636|186803|877420,Complete,KateRasheed
bsdb:34268384/1/1,34268384,case-control,34268384,10.21037/atm-20-4586,NA,"Chao X., Liu Y., Fan Q., Shi H., Wang S. , Lang J.",The role of the vaginal microbiome in distinguishing female chronic pelvic pain caused by endometriosis/adenomyosis,Annals of translational medicine,2021,"16S rRNA, Chronic pelvic pain (CPP), endometriosis/adenomyosis (EM/AM), function prediction, vaginal microbiome",Experiment 1,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Endometriosis,EFO:0001065,Women without CPPS presenting for routine examinations,Women with EM-associated CPPS,Thirty-seven women with endometriosis-associated chronic pelvic pain syndrome (CPPS) confirmed  by exploratory laparoscopy or surgical pathology,66,37,2 weeks,16S,4,Illumina,raw counts,T-Test,0.05,FALSE,NA,age,NA,NA,NA,NA,NA,NA,increased,Signature 1,Table 2,11 August 2021,Samara.Khan,"Samara.Khan,Atrayees,WikiWorks",The following taxa were found to be decreased in women with endometriosis associated CPPS.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Atrayees
bsdb:34268384/2/1,34268384,case-control,34268384,10.21037/atm-20-4586,NA,"Chao X., Liu Y., Fan Q., Shi H., Wang S. , Lang J.",The role of the vaginal microbiome in distinguishing female chronic pelvic pain caused by endometriosis/adenomyosis,Annals of translational medicine,2021,"16S rRNA, Chronic pelvic pain (CPP), endometriosis/adenomyosis (EM/AM), function prediction, vaginal microbiome",Experiment 2,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Endometriosis,EFO:0001065,Women without CPPS presenting for routine examinations,Women with EM-associated CPPS,Thirty-seven women with endometriosis-associated chronic pelvic pain syndrome (CPPS) confirmed  by exploratory laparoscopy or surgical pathology,66,37,2 weeks,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,age,NA,NA,NA,NA,NA,NA,increased,Signature 1,Table 2,11 August 2021,Samara.Khan,"Samara.Khan,Atrayees,WikiWorks",The following taxa were increased in women with endometriosis associated CPPS pain,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|85004|31953|419014;3379134|1224|1236|135614|32033|40323;1783272|1239|909932|1843489|31977|29465,Complete,Atrayees
bsdb:34268384/2/2,34268384,case-control,34268384,10.21037/atm-20-4586,NA,"Chao X., Liu Y., Fan Q., Shi H., Wang S. , Lang J.",The role of the vaginal microbiome in distinguishing female chronic pelvic pain caused by endometriosis/adenomyosis,Annals of translational medicine,2021,"16S rRNA, Chronic pelvic pain (CPP), endometriosis/adenomyosis (EM/AM), function prediction, vaginal microbiome",Experiment 2,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Endometriosis,EFO:0001065,Women without CPPS presenting for routine examinations,Women with EM-associated CPPS,Thirty-seven women with endometriosis-associated chronic pelvic pain syndrome (CPPS) confirmed  by exploratory laparoscopy or surgical pathology,66,37,2 weeks,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,age,NA,NA,NA,NA,NA,NA,increased,Signature 2,Table 2,11 August 2021,Samara.Khan,"Samara.Khan,Atrayees,WikiWorks",The following taxa were decreased in women with endometriosis associated CPPS pain,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia",1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3085636|186803|177971;3384189|32066|203490|203491|1129771|168808,Complete,Atrayees
bsdb:34276644/1/1,34276644,case-control,34276644,10.3389/fimmu.2021.632482,NA,"Li Z., Lu G., Li Z., Wu B., Luo E., Qiu X., Guo J., Xia Z., Zheng C., Su Q., Zeng Y., Chan W.Y., Su X., Cai Q., Xu Y., Chen Y., Wang M., Poon W.S. , Luo X.",Altered Actinobacteria and Firmicutes Phylum Associated Epitopes in Patients With Parkinson's Disease,Frontiers in immunology,2021,"Actinobacteria phylum, Firmicutes phylum, Parkinson’s disease, glutamate and propionate metabolism, immunity, metagenome-wide association study, microbiota-associated epitopes",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,In-house control (HC) + Age-matched Normal group (NG),Parkinson disease patients (PD),"Parkinson disease patients (PD) refers to patients with Parkinson’s disease (one of the most common neurodegenerative disorders worldwide, for which there is currently no complete cure).",178,69,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2.5,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S1,25 February 2025,KateRasheed,KateRasheed,Potential bacterial biomarkers with altered abundance,increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp. 4_3_54A2FAA,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",1783272|201174|84992;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|201174|84998|84999|84107;1783272|201174|1760|85004;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999;1783272|201174;1783272|201174|1760|85004|31953|1678|1689;1783272|201174|1760|85004|31953|1678|216816;3379134|976|200643|171549|171550;3379134|976|200643|171549|171550|239759;1783272|1239|91061|186826|33958;1783272|1239|186801|186802|216572;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|292632|665956;28221;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;1783272|1239|186801|3085636|186803|841;3379134|200940|3031449|213115|194924|35832,Complete,Svetlana up
bsdb:34289209/1/1,34289209,laboratory experiment,34289209,10.1111/cas.15078,NA,"Ding G., Gong Q., Ma J., Liu X., Wang Y. , Cheng X.",Immunosuppressive activity is attenuated by Astragalus polysaccharides through remodeling the gut microenvironment in melanoma mice,Cancer science,2021,"Astragalus polysaccharides, gut microenvironment, immunosuppressive activity, melanoma, myeloid-derived suppressor cells",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,Model,APS (Astragalus polysaccharides),"C57BL/6 mice (male, approximately 20 g, 5-6 weeks) injected subcutaneously with approximately 5 × 10^5 cells of a melanoma cell line to establish tumor models, these were administered Astragalus polysaccharides (APS) for 14 days.",NA,NA,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 4e,17 October 2025,YokoC,YokoC,Bar plot of compositional differences at the species level in the gut microbiota of mice in the APS group vs the Model group using Student’s t-test.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum|s__Faecalibaculum rodentium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__uncultured Desulfovibrio sp.",1783272|1239|526524|526525|128827|1729679|1702221;1783272|1239|91061|186826|33958|1578|33959;1783272|1239|91061|186826|33958|1578;3379134|200940|3031449|213115|194924|872|167968,Complete,Svetlana up
bsdb:34289209/1/2,34289209,laboratory experiment,34289209,10.1111/cas.15078,NA,"Ding G., Gong Q., Ma J., Liu X., Wang Y. , Cheng X.",Immunosuppressive activity is attenuated by Astragalus polysaccharides through remodeling the gut microenvironment in melanoma mice,Cancer science,2021,"Astragalus polysaccharides, gut microenvironment, immunosuppressive activity, melanoma, myeloid-derived suppressor cells",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,Model,APS (Astragalus polysaccharides),"C57BL/6 mice (male, approximately 20 g, 5-6 weeks) injected subcutaneously with approximately 5 × 10^5 cells of a melanoma cell line to establish tumor models, these were administered Astragalus polysaccharides (APS) for 14 days.",NA,NA,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 4e,17 October 2025,YokoC,YokoC,Bar plot of compositional differences at the species level in the gut microbiota of mice in the APS (Astragalus polysaccharides) group vs the Model group using Student’s t-test.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|s__Christensenellaceae bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas leidyi,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma|s__uncultured Anaeroplasma sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__uncultured Anaerotruncus sp.",1783272|201174|1760|85004|31953|1678|1694;1783272|1239|186801|3082768|990719|2054177;3379134|1224|28211|204457|41297|13687|68569;1783272|1239|186801|186802|216572|1535;1783272|201174|1760|85006|85020|43668;1783272|1239|186801|3082768|990719;1783272|544448|31969|186332|186333|2086|538969;1783272|1239|186801|186802|216572|244127|905011,Complete,Svetlana up
bsdb:34294722/1/1,34294722,"cross-sectional observational, not case-control",34294722,10.1038/s41522-021-00232-5,NA,"Wu Y., Cheng X., Jiang G., Tang H., Ming S., Tang L., Lu J., Guo C., Shan H. , Huang X.",Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization,NPJ biofilms and microbiomes,2021,NA,Experiment 1,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests,44,140,NA,16S,34,Illumina,relative abundances,"LEfSe,Linear Regression",0.05,TRUE,2,"age,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 1,Figure 2D,2 August 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between healthy controls and COVID-19 patients,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor",3379134|1224|1236|135625|712|724|729;1783272|1239|909932|1843489|31977|29465;3379134|29547|3031852|213849|72294|194;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|186828|117563;3379134|1224|28216|206351|481|482|28449;3379134|1224|28216|206351|481|32257;1783272|1239|186801|3082720|3118655|44259,Complete,Fatima
bsdb:34294722/1/2,34294722,"cross-sectional observational, not case-control",34294722,10.1038/s41522-021-00232-5,NA,"Wu Y., Cheng X., Jiang G., Tang H., Ming S., Tang L., Lu J., Guo C., Shan H. , Huang X.",Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization,NPJ biofilms and microbiomes,2021,NA,Experiment 1,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests,44,140,NA,16S,34,Illumina,relative abundances,"LEfSe,Linear Regression",0.05,TRUE,2,"age,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 2,Figure 2D,2 August 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between healthy controls and COVID-19 patients,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum",3379134|1224|28216|206351|481|482;1783272|201174|1760|85007|1653|1716;3379134|1224|1236|135625|712|713;1783272|1239|186801|3085636|186803|437755;3379134|1224|1236|135625|712|416916;3379134|976|200643|171549|171552|838|28131;3379134|203691|203692|136|2845253|157;3379134|1224|1236|72274|135621|286;3379134|203691|203692|136|2845253|157|59892,Complete,Fatima
bsdb:34294722/2/1,34294722,"cross-sectional observational, not case-control",34294722,10.1038/s41522-021-00232-5,NA,"Wu Y., Cheng X., Jiang G., Tang H., Ming S., Tang L., Lu J., Guo C., Shan H. , Huang X.",Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization,NPJ biofilms and microbiomes,2021,NA,Experiment 2,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,COVID-19 patients (mild/moderate),COVID-19 patients (severe/critical),Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests deemed to have severe/critical disease,30,22,NA,16S,34,Illumina,relative abundances,"LEfSe,Linear Regression",0.05,TRUE,2,"age,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 1,Supplementary Table 3,2 August 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between mild/moderate and severe/critical COVID-19 patients,decreased,"k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus",3379134|203691|203692|136|2845253|157;3379134|1224|1236|135625|712|416916;3379134|1224|1236|135625|712|416916|739;3379134|976|200643|171549|171552|838|28131;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|909932|909929|1843491|970;1783272|1239|186801|3082720|3118655|44259;3379134|203691|203692|136|2845253|157|59892;1783272|1239|186801|186802|186807|2740,Complete,Fatima
bsdb:34294722/3/1,34294722,"cross-sectional observational, not case-control",34294722,10.1038/s41522-021-00232-5,NA,"Wu Y., Cheng X., Jiang G., Tang H., Ming S., Tang L., Lu J., Guo C., Shan H. , Huang X.",Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization,NPJ biofilms and microbiomes,2021,NA,Experiment 3,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients not treated with antibiotics,Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests who were not treated with antibiotics,44,17,NA,16S,34,Illumina,relative abundances,"LEfSe,Linear Regression",0.05,TRUE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 3,2 August 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between COVID-19 patients who were not treated with antibiotics and healthy controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus",3379134|1224|28216|206351|481|482|28449;1783272|1239|91061|186826|186828|117563;1783272|1239|909932|1843489|31977|29465;3379134|29547|3031852|213849|72294|194;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|1737404|1737405|1570339|162289,Complete,Fatima
bsdb:34294722/3/2,34294722,"cross-sectional observational, not case-control",34294722,10.1038/s41522-021-00232-5,NA,"Wu Y., Cheng X., Jiang G., Tang H., Ming S., Tang L., Lu J., Guo C., Shan H. , Huang X.",Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization,NPJ biofilms and microbiomes,2021,NA,Experiment 3,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients not treated with antibiotics,Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests who were not treated with antibiotics,44,17,NA,16S,34,Illumina,relative abundances,"LEfSe,Linear Regression",0.05,TRUE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 3,2 August 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between COVID-19 patients who were not treated with antibiotics and healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia",1783272|1239|186801|3085636|186803|437755;3379134|203691|203692|136|2845253|157;3379134|976|200643|171549|171552|838|28131,Complete,Fatima
bsdb:34294722/4/1,34294722,"cross-sectional observational, not case-control",34294722,10.1038/s41522-021-00232-5,NA,"Wu Y., Cheng X., Jiang G., Tang H., Ming S., Tang L., Lu J., Guo C., Shan H. , Huang X.",Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization,NPJ biofilms and microbiomes,2021,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests,32,81,NA,16S,34,Illumina,relative abundances,"LEfSe,Linear Regression",0.05,TRUE,2,"age,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 1,Supplementary Table 4,2 August 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between healthy controls and COVID-19 patients,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella",1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|33958|46255;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|3085636|186803|2719313|358743;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85006|1268|32207|43675;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|186826|33958|1578;1783272|201174|1760|2037|2049|1654;1783272|1239|91061|186826|186828|117563,Complete,Fatima
bsdb:34294722/4/2,34294722,"cross-sectional observational, not case-control",34294722,10.1038/s41522-021-00232-5,NA,"Wu Y., Cheng X., Jiang G., Tang H., Ming S., Tang L., Lu J., Guo C., Shan H. , Huang X.",Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization,NPJ biofilms and microbiomes,2021,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests,32,81,NA,16S,34,Illumina,relative abundances,"LEfSe,Linear Regression",0.05,TRUE,2,"age,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 2,Supplementary Table 4,2 August 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between healthy controls and COVID-19 patients,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] colinum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|33042;3379134|976|200643|171549|815|816|47678;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|1506577|36835;1783272|201174|84998|84999|84107|102106;3379134|976|200643|171549|815|909656|387090,Complete,Fatima
bsdb:34294722/5/1,34294722,"cross-sectional observational, not case-control",34294722,10.1038/s41522-021-00232-5,NA,"Wu Y., Cheng X., Jiang G., Tang H., Ming S., Tang L., Lu J., Guo C., Shan H. , Huang X.",Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization,NPJ biofilms and microbiomes,2021,NA,Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients not treated with antibiotics,Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests who were not treated with antibiotics,32,13,NA,16S,34,Illumina,relative abundances,"LEfSe,Linear Regression",0.05,TRUE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 5,2 August 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between COVID-19 patients who were not treated with antibiotics and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium",1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|2719313|358743;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|1737404|1737405|1570339|162289;3379134|29547|3031852|213849|72294|194;1783272|201174|84998|84999|1643824|1380,Complete,Fatima
bsdb:34294722/5/2,34294722,"cross-sectional observational, not case-control",34294722,10.1038/s41522-021-00232-5,NA,"Wu Y., Cheng X., Jiang G., Tang H., Ming S., Tang L., Lu J., Guo C., Shan H. , Huang X.",Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization,NPJ biofilms and microbiomes,2021,NA,Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients not treated with antibiotics,Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests who were not treated with antibiotics,32,13,NA,16S,34,Illumina,relative abundances,"LEfSe,Linear Regression",0.05,TRUE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 5,2 August 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between COVID-19 patients who were not treated with antibiotics and healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] colinum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|33042;3379134|976|200643|171549|815|816|28111;3379134|976|200643|171549|815|909656|387090;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|572511|33035;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|1506577|36835;3379134|1224|28216|206351|481|482,Complete,Fatima
bsdb:34302684/1/1,34302684,case-control,34302684,10.1007/s40618-021-01595-4,https://pubmed.ncbi.nlm.nih.gov/34302684/,"Wei J., Qing Y., Zhou H., Liu J., Qi C. , Gao J.",16S rRNA gene amplicon sequencing of gut microbiota in gestational diabetes mellitus and their correlation with disease risk factors,Journal of endocrinological investigation,2021,"16S rRNA gene amplicon sequencing, Gestational diabetes mellitus, Gut microbiota, qPCR",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Pregnant individuals who are normal glucose tolerance (NGT)],Pregnant individuals with gestational diabetes,Pregnant individuals with gestational diabetes,18,15,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 3b, 3c, Table S1",16 August 2021,Madhubani Dey,"Madhubani Dey,WikiWorks",Increased abundance of bacterial communities in GDM individuals as compared to NGT controls,increased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica|s__Salmonella enterica subsp. enterica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] colinum",1783272|1239|186801;1783272|1239|186801|186802|1898207;1783272|1239;1783272|1239|186801|186802|216572|1263|40518;3379134|1224|1236|91347|543|590|28901|59201;1783272|1239|186801|3085636|186803|1506577|36835,Complete,Claregrieve1
bsdb:34302684/1/2,34302684,case-control,34302684,10.1007/s40618-021-01595-4,https://pubmed.ncbi.nlm.nih.gov/34302684/,"Wei J., Qing Y., Zhou H., Liu J., Qi C. , Gao J.",16S rRNA gene amplicon sequencing of gut microbiota in gestational diabetes mellitus and their correlation with disease risk factors,Journal of endocrinological investigation,2021,"16S rRNA gene amplicon sequencing, Gestational diabetes mellitus, Gut microbiota, qPCR",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Pregnant individuals who are normal glucose tolerance (NGT)],Pregnant individuals with gestational diabetes,Pregnant individuals with gestational diabetes,18,15,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 3b, 3c, Table S1",16 August 2021,Madhubani Dey,"Madhubani Dey,WikiWorks",Decreased abundance of bacterial communities in GDM individuals as compared to NGT controls,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium",3379134|976|200643|171549;3379134|976;3379134|976|200643;1783272|1239|186801|3085636|186803|140625,Complete,Claregrieve1
bsdb:34315772/1/1,34315772,"cross-sectional observational, not case-control",34315772,https://doi.org/10.1136/gutjnl-2021-325168,NA,"Tarallo S., Ferrero G., De Filippis F., Francavilla A., Pasolli E., Panero V., Cordero F., Segata N., Grioni S., Pensa R.G., Pardini B., Ercolini D. , Naccarati A.",Stool microRNA profiles reflect different dietary and gut microbiome patterns in healthy individuals,Gut,2022,"colonic microflora, diet, molecular genetics",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Omnivores (O),Vegans(VN),Healthy individuals following a vegan diet (excludes all animal-derived foods) for at least 1 year,40,40,3 months,16S,345,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A,4 May 2025,Ese,Ese,Differentially abundant bacterial taxa in Vegans(VN) compared to Omnivores(O),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:182,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri",1783272|1239|186801|3085636|186803|841|1262942;3379134|976|200643|171549|171552|2974251|165179,Complete,KateRasheed
bsdb:34315772/1/2,34315772,"cross-sectional observational, not case-control",34315772,https://doi.org/10.1136/gutjnl-2021-325168,NA,"Tarallo S., Ferrero G., De Filippis F., Francavilla A., Pasolli E., Panero V., Cordero F., Segata N., Grioni S., Pensa R.G., Pardini B., Ercolini D. , Naccarati A.",Stool microRNA profiles reflect different dietary and gut microbiome patterns in healthy individuals,Gut,2022,"colonic microflora, diet, molecular genetics",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Omnivores (O),Vegans(VN),Healthy individuals following a vegan diet (excludes all animal-derived foods) for at least 1 year,40,40,3 months,16S,345,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3A,6 May 2025,Ese,Ese,Differentially abundant bacterial taxa in Vegans(VN) compared to Omnivores(O),decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,3379134|976|200643|171549|815|909656|357276,Complete,KateRasheed
bsdb:34315772/2/1,34315772,"cross-sectional observational, not case-control",34315772,https://doi.org/10.1136/gutjnl-2021-325168,NA,"Tarallo S., Ferrero G., De Filippis F., Francavilla A., Pasolli E., Panero V., Cordero F., Segata N., Grioni S., Pensa R.G., Pardini B., Ercolini D. , Naccarati A.",Stool microRNA profiles reflect different dietary and gut microbiome patterns in healthy individuals,Gut,2022,"colonic microflora, diet, molecular genetics",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Omnivores(O),Vegetarians(VT),"Healthy individuals following a vegetarian diet (excludes all meat and fish, but may include dairy and eggs) for at least 1 year",40,40,3 months,16S,345,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A,4 May 2025,Ese,Ese,Differentially abundant bacterial taxa in Vegetarians(VT) compared to Omnivores(O),increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,3379134|976|200643|171549|171552|2974251|165179,Complete,KateRasheed
bsdb:34315772/3/1,34315772,"cross-sectional observational, not case-control",34315772,https://doi.org/10.1136/gutjnl-2021-325168,NA,"Tarallo S., Ferrero G., De Filippis F., Francavilla A., Pasolli E., Panero V., Cordero F., Segata N., Grioni S., Pensa R.G., Pardini B., Ercolini D. , Naccarati A.",Stool microRNA profiles reflect different dietary and gut microbiome patterns in healthy individuals,Gut,2022,"colonic microflora, diet, molecular genetics",Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Gene expression protocol,EFO:0003788,Low miR-425-3p,High miR-425-3p,Healthy individuals with high stool expression levels of microRNA-425-3p,NA,NA,3 months,16S,345,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3F, Figure S4, Result Text",4 May 2025,Ese,Ese,Taxonomy of bacterial taxa among individuals with high stool expression levels of microRNA-425-3p,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 57_20,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. CAG:241,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D5,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:182",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|186802|216572|459786|1897011;1783272|1239|186801|186802|216572|459786|1262911;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|186802|216572|1520815;1783272|1239|186801|3085636|186803|841|1262942,Complete,KateRasheed
bsdb:34315772/3/2,34315772,"cross-sectional observational, not case-control",34315772,https://doi.org/10.1136/gutjnl-2021-325168,NA,"Tarallo S., Ferrero G., De Filippis F., Francavilla A., Pasolli E., Panero V., Cordero F., Segata N., Grioni S., Pensa R.G., Pardini B., Ercolini D. , Naccarati A.",Stool microRNA profiles reflect different dietary and gut microbiome patterns in healthy individuals,Gut,2022,"colonic microflora, diet, molecular genetics",Experiment 3,Italy,Homo sapiens,Feces,UBERON:0001988,Gene expression protocol,EFO:0003788,Low miR-425-3p,High miR-425-3p,Healthy individuals with high stool expression levels of microRNA-425-3p,NA,NA,3 months,16S,345,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3F, Figure S4, Result Text",4 May 2025,Ese,Ese,Taxonomy of bacterial taxa among individuals with high stool expression levels of microRNA-425-3p,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii",1783272|1239|186801|186802|216572|244127|169435;1783272|1239|186801|186802|216572|946234|292800,Complete,KateRasheed
bsdb:34315772/4/1,34315772,"cross-sectional observational, not case-control",34315772,https://doi.org/10.1136/gutjnl-2021-325168,NA,"Tarallo S., Ferrero G., De Filippis F., Francavilla A., Pasolli E., Panero V., Cordero F., Segata N., Grioni S., Pensa R.G., Pardini B., Ercolini D. , Naccarati A.",Stool microRNA profiles reflect different dietary and gut microbiome patterns in healthy individuals,Gut,2022,"colonic microflora, diet, molecular genetics",Experiment 4,Italy,Homo sapiens,Feces,UBERON:0001988,Gene expression protocol,EFO:0003788,Low miR-638,High miR-638,Healthy individuals with high stool expression levels of microRNA-638,NA,NA,3 months,16S,345,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3F, Figure S4, Result Text",11 May 2025,Ese,Ese,Taxonomy of bacterial taxa among individuals with high stool expression levels of microRNA-638,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:182,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D5,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:95",1783272|1239|186801|3085636|186803|841|1262942;1783272|1239|186801|186802|216572|1520815;1783272|1239|1262988,Complete,KateRasheed
bsdb:34315772/4/2,34315772,"cross-sectional observational, not case-control",34315772,https://doi.org/10.1136/gutjnl-2021-325168,NA,"Tarallo S., Ferrero G., De Filippis F., Francavilla A., Pasolli E., Panero V., Cordero F., Segata N., Grioni S., Pensa R.G., Pardini B., Ercolini D. , Naccarati A.",Stool microRNA profiles reflect different dietary and gut microbiome patterns in healthy individuals,Gut,2022,"colonic microflora, diet, molecular genetics",Experiment 4,Italy,Homo sapiens,Feces,UBERON:0001988,Gene expression protocol,EFO:0003788,Low miR-638,High miR-638,Healthy individuals with high stool expression levels of microRNA-638,NA,NA,3 months,16S,345,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3F, Figure S4, Result Text",11 May 2025,Ese,Ese,Taxonomy of bacterial taxa among individuals with high stool expression levels of microRNA-638,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:83,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii",1783272|1239|186801|186802|216572|244127|169435;1783272|1239|1262992;1783272|1239|186801|186802|216572|946234|292800,Complete,KateRasheed
bsdb:34322135/1/1,34322135,laboratory experiment,34322135,https://doi.org/10.3389/fimmu.2021.704621,https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2021.704621/full,"Mateos-Hernández L., Obregón D., Wu-Chuang A., Maye J., Bornères J., Versillé N., de la Fuente J., Díaz-Sánchez S., Bermúdez-Humarán L.G., Torres-Maravilla E., Estrada-Peña A., Hodžić A., Šimo L. , Cabezas-Cruz A.",Anti-Microbiota Vaccines Modulate the Tick Microbiome in a Taxon-Specific Manner,Frontiers in immunology,2021,"anti-microbiota vaccines, keystone bacteria, microbiome modulation, networks analysis, tick",Experiment 1,France,Ixodes ricinus,Entire surface of organism,UBERON:0035159,Response to vaccine,EFO:0004645,Ticks fed on mock-immunized mice,Ticks fed on Leuconostoc mesenteroides-immunized mice,Ticks fed on mice immunized with Leuconostoc mesenteroides,7,5,NA,16S,4,Illumina,centered log-ratio,Wald Test,0.001,FALSE,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,Signature 1,Figure 4D,17 October 2025,Tumi,"Tumi,Fiddyhamma","Relative abundance (calculated as clr transformed values) of the 20 top bacterial taxa with the highest significant differences on ticks fed on mock-immunized vs. Leuconostoc mesenteroides-immunized mice (D) as detected by the DeSeq2 algorithm (Wald test, p < 0.001).",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Anoxybacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter",1783272|1239|91061|1385|3120669|150247;1783272|1239|526524|526525|2810280|3025755;3379134|29547|3031852|213849|72293|209,Complete,Svetlana up
bsdb:34322135/1/2,34322135,laboratory experiment,34322135,https://doi.org/10.3389/fimmu.2021.704621,https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2021.704621/full,"Mateos-Hernández L., Obregón D., Wu-Chuang A., Maye J., Bornères J., Versillé N., de la Fuente J., Díaz-Sánchez S., Bermúdez-Humarán L.G., Torres-Maravilla E., Estrada-Peña A., Hodžić A., Šimo L. , Cabezas-Cruz A.",Anti-Microbiota Vaccines Modulate the Tick Microbiome in a Taxon-Specific Manner,Frontiers in immunology,2021,"anti-microbiota vaccines, keystone bacteria, microbiome modulation, networks analysis, tick",Experiment 1,France,Ixodes ricinus,Entire surface of organism,UBERON:0035159,Response to vaccine,EFO:0004645,Ticks fed on mock-immunized mice,Ticks fed on Leuconostoc mesenteroides-immunized mice,Ticks fed on mice immunized with Leuconostoc mesenteroides,7,5,NA,16S,4,Illumina,centered log-ratio,Wald Test,0.001,FALSE,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,Signature 2,Figure 4D,17 October 2025,Tumi,"Tumi,Fiddyhamma,Anne-mariesharp","Relative abundance (calculated as clr transformed values) of the 20 top bacterial taxa with the highest significant differences on ticks fed on mock-immunized vs. Leuconostoc mesenteroides-immunized mice (D) as detected by the DeSeq2 algorithm (Wald test, p < 0.001).",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Aminobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Tissierellia|g__Sedimentibacter,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Syntrophomonadaceae|g__Syntrophomonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae|g__Tissierella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium",1783272|201174|1760|2037|2049|1654;3384194|508458|649775|649776|3029087|81466;1783272|1239|91061|1385|186817|1386;3379134|976|117743|200644|2762318|59732;1783272|1239|186801|186802|216572|236752;1783272|1239|186801|3085636|186803|248744;1783272|1239|186801|186802|216572|1508657;1783272|1239|1737404|190972;3379134|976|117747|200666|84566|28453;1783272|1239|186801|186802|68298|862;1783272|1239|1737404|1737405|1737406|41273;1783272|1239|526524|526525|128827|331630,Complete,Svetlana up
bsdb:34322135/2/1,34322135,laboratory experiment,34322135,https://doi.org/10.3389/fimmu.2021.704621,https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2021.704621/full,"Mateos-Hernández L., Obregón D., Wu-Chuang A., Maye J., Bornères J., Versillé N., de la Fuente J., Díaz-Sánchez S., Bermúdez-Humarán L.G., Torres-Maravilla E., Estrada-Peña A., Hodžić A., Šimo L. , Cabezas-Cruz A.",Anti-Microbiota Vaccines Modulate the Tick Microbiome in a Taxon-Specific Manner,Frontiers in immunology,2021,"anti-microbiota vaccines, keystone bacteria, microbiome modulation, networks analysis, tick",Experiment 2,France,Ixodes ricinus,Entire surface of organism,UBERON:0035159,Response to vaccine,EFO:0004645,Ticks fed on mock-immunized mice,Ticks fed on Escherichia coli-immunized mice,Ticks fed on mice immunized with Escherichia coli,7,9,NA,16S,4,Illumina,centered log-ratio,Wald Test,0.001,FALSE,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,Signature 1,Figure 4E,17 October 2025,Tumi,"Tumi,Fiddyhamma","Relative abundance (calculated as clr transformed values) of the 20 top bacterial taxa with the highest significant differences on ticks fed on mock-immunized vs. Escherichia coli-immunized mice (E), as detected by the DeSeq2 algorithm (Wald test, p < 0.001).",increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Dermabacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae",3379134|200940|3031449|213115|194924|35832;1783272|201174|1760|85006|85020|36739;1783272|201174|1760|85007|2805586|1847725;1783272|1239|186801|3085636|186803|248744;3379134|976|117743|200644|2762318,Complete,Svetlana up
bsdb:34322135/2/2,34322135,laboratory experiment,34322135,https://doi.org/10.3389/fimmu.2021.704621,https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2021.704621/full,"Mateos-Hernández L., Obregón D., Wu-Chuang A., Maye J., Bornères J., Versillé N., de la Fuente J., Díaz-Sánchez S., Bermúdez-Humarán L.G., Torres-Maravilla E., Estrada-Peña A., Hodžić A., Šimo L. , Cabezas-Cruz A.",Anti-Microbiota Vaccines Modulate the Tick Microbiome in a Taxon-Specific Manner,Frontiers in immunology,2021,"anti-microbiota vaccines, keystone bacteria, microbiome modulation, networks analysis, tick",Experiment 2,France,Ixodes ricinus,Entire surface of organism,UBERON:0035159,Response to vaccine,EFO:0004645,Ticks fed on mock-immunized mice,Ticks fed on Escherichia coli-immunized mice,Ticks fed on mice immunized with Escherichia coli,7,9,NA,16S,4,Illumina,centered log-ratio,Wald Test,0.001,FALSE,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,Signature 2,Figure 4E,20 October 2025,Fiddyhamma,Fiddyhamma,"Relative abundance (calculated as clr transformed values) of the 20 top bacterial taxa with the highest significant differences on ticks fed on mock-immunized vs. Escherichia coli-immunized mice (E), as detected by the DeSeq2 algorithm (Wald test, p < 0.001).",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Hydrogenophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Roseomonadaceae|g__Roseomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",3379134|976|200643|171549|815|816;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|1940338;3379134|1224|2008785|119069|206349|70774;1783272|201174|1760|85006|1268|1269;1783272|1239|186801|3085656|3085657|2039302;3379134|200930|68337|191393|2945020|248038;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|577310;3379134|1224|1236|135625|712|745;3379134|1224|28211|3120395|3385906|125216;3379134|1224|28211|204457|3423717|165695;1783272|1239|526524|526525|2810280|1505663,Complete,Svetlana up
bsdb:34329692/1/1,34329692,time series / longitudinal observational,34329692,10.1016/j.diabres.2021.108985,NA,"Lee Y., Kim A.H., Kim E., Lee S., Yu K.S., Jang I.J., Chung J.Y. , Cho J.Y.",Changes in the gut microbiome influence the hypoglycemic effect of metformin through the altered metabolism of branched-chain and nonessential amino acids,Diabetes research and clinical practice,2021,"Gut microbiome, Hypoglycemic effect, Metabolomics, Metformin",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Response to metformin,GO:1901558,Baseline,Postmetformin,Samples collected from participants on day 4 after the last metformin dose.,20,20,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 1D and Supplementary Table 2,30 January 2025,Aleru Divine,"Aleru Divine,WikiWorks",Bacteria differentially represented between baseline and postmetformin identified by linear discriminant analysis coupled with effect size (LEfSe).,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,3379134|1224|1236|91347|543|561,Complete,Svetlana up
bsdb:34329692/1/2,34329692,time series / longitudinal observational,34329692,10.1016/j.diabres.2021.108985,NA,"Lee Y., Kim A.H., Kim E., Lee S., Yu K.S., Jang I.J., Chung J.Y. , Cho J.Y.",Changes in the gut microbiome influence the hypoglycemic effect of metformin through the altered metabolism of branched-chain and nonessential amino acids,Diabetes research and clinical practice,2021,"Gut microbiome, Hypoglycemic effect, Metabolomics, Metformin",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Response to metformin,GO:1901558,Baseline,Postmetformin,Samples collected from participants on day 4 after the last metformin dose.,20,20,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 1D and Supplementary Table 2,30 January 2025,Aleru Divine,"Aleru Divine,WikiWorks",Bacteria differentially represented between baseline and postmetformin identified by linear discriminant analysis coupled with effect size (LEfSe).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia",1783272|1239|186801|3082720|186804|1505657;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3082720|186804|1501226,Complete,Svetlana up
bsdb:34336719/1/1,34336719,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S., Zhu J., Su B., Wei H., Chen F., Liu H., Wei J., Yang X., Zhang Q., Xia W., Wu H., He Q. , Zhang T.",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,HIV-uninfected MSM -  controls (D),Acute HIV-infected participants at baseline (A0),Men who have sex with men (MSM) with acute HIV infection at baseline (A0).,15,15,1 month,16S,45,Illumina,raw counts,T-Test,0.05,NA,NA,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 2a,30 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differences in the composition of oral microbiome between controls and people living with HIV (PLWH).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:34336719/1/2,34336719,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S., Zhu J., Su B., Wei H., Chen F., Liu H., Wei J., Yang X., Zhang Q., Xia W., Wu H., He Q. , Zhang T.",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,HIV-uninfected MSM -  controls (D),Acute HIV-infected participants at baseline (A0),Men who have sex with men (MSM) with acute HIV infection at baseline (A0).,15,15,1 month,16S,45,Illumina,raw counts,T-Test,0.05,NA,NA,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 2a,30 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differences in the composition of oral microbiome between controls and people living with HIV (PLWH).,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella",3384189|32066|203490|203491|1129771|32067;1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85006|1268|32207;3379134|1224|28216|80840|119060|47670;3379134|976|200643|171549|2005525|195950;3379134|203691|203692|136|137;1783272|1239|186801|186802|216572;1783272|201174|1760|85007|1653|1716;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802;1783272|1239|186801|3082720|186804|1501226;3379134|976|200643|171549|815|816;3384189|32066|203490|203491|1129771;1783272|1239|909932|909929|1843491|82202;1783272|1239|186801|186802|216572|459786;3379134|1224|1236|2887326|468|475;1783272|1239|186801|3085636|186803|43996,Complete,Svetlana up
bsdb:34336719/2/1,34336719,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S., Zhu J., Su B., Wei H., Chen F., Liu H., Wei J., Yang X., Zhang Q., Xia W., Wu H., He Q. , Zhang T.",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 2,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,HIV-uninfected MSM -  controls (D),Chronic HIV-infected participants at baseline (B0),Men who have sex with men (MSM) with Chronic HIV infection at baseline (B0).,15,15,1 month,16S,45,Illumina,raw counts,T-Test,0.05,NA,NA,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 2b,30 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differences in the composition of oral microbiome between controls and people living with HIV (PLWH).,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|171552,Complete,Svetlana up
bsdb:34336719/2/2,34336719,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S., Zhu J., Su B., Wei H., Chen F., Liu H., Wei J., Yang X., Zhang Q., Xia W., Wu H., He Q. , Zhang T.",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 2,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,HIV-uninfected MSM -  controls (D),Chronic HIV-infected participants at baseline (B0),Men who have sex with men (MSM) with Chronic HIV infection at baseline (B0).,15,15,1 month,16S,45,Illumina,raw counts,T-Test,0.05,NA,NA,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 2b,30 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differences in the composition of oral microbiome between controls and people living with HIV (PLWH).,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium",1783272|201174|1760|2037|2049|1654;1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85006|1268|32207;3379134|1224|28216|80840|119060|47670;3379134|976|200643|171549|2005525|195950;3379134|203691|203692|136|137;1783272|1239|186801|186802|216572;1783272|201174|1760|85007|1653|1716;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802;1783272|1239|186801|3082720|186804|1501226;3379134|976|200643|171549|815|816;1783272|1239|909932|909929|1843491|82202;1783272|1239|186801|186802|216572|459786;3379134|1224|1236|2887326|468|475;1783272|1239|186801|3085636|186803|1213720;1783272|1239|186801|3085636|186803|43996;1783272|1239|186801|3085636|186803|265975,Complete,Svetlana up
bsdb:34336719/3/1,34336719,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S., Zhu J., Su B., Wei H., Chen F., Liu H., Wei J., Yang X., Zhang Q., Xia W., Wu H., He Q. , Zhang T.",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 3,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,HIV-uninfected MSM -  controls (D),Acute HIV-infected participants (A12),Men who have sex with men (MSM) with Acute HIV infection after 12 weeks of Antiretroviral Therapy (ART).,15,15,1 month,16S,45,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 3a,30 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Linear discriminative analysis (LDA) effect size (LefSe) at the genus level shown between Acute HIV-infected participants (A12) and control (D) groups.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium elkanii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",3379134|1224|28211|356|41294|374|29448;3379134|1224|28211|356|41294|374;3379134|1224|28211|356|335928;3379134|1224|28211|356;3379134|1224|28211;3379134|1224|1236|135625|712|724,Complete,Svetlana up
bsdb:34336719/3/2,34336719,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S., Zhu J., Su B., Wei H., Chen F., Liu H., Wei J., Yang X., Zhang Q., Xia W., Wu H., He Q. , Zhang T.",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 3,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,HIV-uninfected MSM -  controls (D),Acute HIV-infected participants (A12),Men who have sex with men (MSM) with Acute HIV infection after 12 weeks of Antiretroviral Therapy (ART).,15,15,1 month,16S,45,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 3a,30 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Linear discriminative analysis (LDA) effect size (LefSe) at the genus level shown between Acute HIV-infected participants (A12) and control (D) groups.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae",1783272|1239|186801;1783272|1239|186801|186802;1783272|201174;1783272|201174;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958;1783272|1239|186801|186802|216572;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;1783272|201174|1760|2037|2049|1654;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|80840|119060;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268,Complete,Svetlana up
bsdb:34336719/4/1,34336719,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S., Zhu J., Su B., Wei H., Chen F., Liu H., Wei J., Yang X., Zhang Q., Xia W., Wu H., He Q. , Zhang T.",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 4,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,HIV-uninfected MSM -  controls (D),Chronic HIV-infected participants (B12),Men who have sex with men (MSM) with Chronic HIV infection after 12 weeks of Antiretroviral Therapy (ART).,15,15,1 month,16S,45,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 3c,30 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Linear discriminative analysis (LDA) effect size (LefSe) at the genus level shown between Chronic HIV-infected participants (B12) and control (D) groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Ihuprevotella|s__Ihuprevotella massiliensis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium elkanii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria",3379134|976|200643|171549|171552|3151711|1852368;3379134|1224|28211|356|41294|374|29448;3379134|1224|28211|356|41294|374;3379134|1224|28211|356|335928;3379134|1224|28211|356;3379134|1224|28211,Complete,Svetlana up
bsdb:34336719/4/2,34336719,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S., Zhu J., Su B., Wei H., Chen F., Liu H., Wei J., Yang X., Zhang Q., Xia W., Wu H., He Q. , Zhang T.",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 4,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,HIV-uninfected MSM -  controls (D),Chronic HIV-infected participants (B12),Men who have sex with men (MSM) with Chronic HIV infection after 12 weeks of Antiretroviral Therapy (ART).,15,15,1 month,16S,45,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 3c,30 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Linear discriminative analysis (LDA) effect size (LefSe) at the genus level shown between Chronic HIV-infected participants (B12) and control (D) groups.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus",1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958;1783272|201174;1783272|201174;1783272|1239|186801|186802|216572;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;1783272|201174|1760|2037|2049|1654;3379134|1224|1236|135625|712|724|735;3379134|1224|1236|135625|712|713,Complete,Svetlana up
bsdb:34336719/5/1,34336719,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S., Zhu J., Su B., Wei H., Chen F., Liu H., Wei J., Yang X., Zhang Q., Xia W., Wu H., He Q. , Zhang T.",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 5,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,Acute HIV-infected participants at baseline (A0),Acute HIV-infected participants on Antiretroviral Therapy (A12),Men who have sex with men (MSM) with Acute HIV infection after 12 weeks of Antiretroviral Therapy (ART).,15,15,1 month,16S,45,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 4a,30 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Linear discriminative analysis (LDA) effect size (LefSe) at the genus level shown between Acute HIV-infected participants on Antiretroviral Therapy(A12) and Acute HIV-infected participants (A0).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium elkanii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae",3379134|1224|28211;3379134|1224|28211|356|41294|374;3379134|1224|28211|356|41294|374|29448;3379134|1224|28211|356;3379134|1224|28211|356|335928,Complete,Svetlana up
bsdb:34336719/5/2,34336719,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S., Zhu J., Su B., Wei H., Chen F., Liu H., Wei J., Yang X., Zhang Q., Xia W., Wu H., He Q. , Zhang T.",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 5,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,Acute HIV-infected participants at baseline (A0),Acute HIV-infected participants on Antiretroviral Therapy (A12),Men who have sex with men (MSM) with Acute HIV infection after 12 weeks of Antiretroviral Therapy (ART).,15,15,1 month,16S,45,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 4a,30 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Linear discriminative analysis (LDA) effect size (LefSe) at the genus level shown between Acute HIV-infected participants on Antiretroviral Therapy(A12) and Acute HIV-infected participants (A0).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|976|200643|171549|171552|838|470565;3379134|976|200643|171549|171552|838|28132;3379134|976|200643;3379134|976;3379134|976|200643|171549|171552;3379134|976|200643|171549;3379134|976|200643|171549|171552,Complete,Svetlana up
bsdb:34336719/6/1,34336719,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S., Zhu J., Su B., Wei H., Chen F., Liu H., Wei J., Yang X., Zhang Q., Xia W., Wu H., He Q. , Zhang T.",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 6,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,Chronic HIV-infected participants at baseline (B0),Chronic HIV-infected participants on Antiretroviral Therapy(B12),Men who have sex with men (MSM) with Chronic HIV infection after 12 weeks of Antiretroviral Therapy (ART).,15,15,1 month,16S,45,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 1,Figure 4c,30 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Linear discriminative analysis (LDA) effect size (LefSe) at the genus level shown between Chronic HIV-infected participants on Antiretroviral Therapy(B12) and Chronic HIV-infected participants (B0).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium elkanii",3379134|1224|28211;3379134|1224|28211|356;3379134|1224|28211|356|335928;3379134|1224|28211|356|41294|374;3379134|1224|28211|356|41294|374|29448,Complete,Svetlana up
bsdb:34336719/6/2,34336719,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S., Zhu J., Su B., Wei H., Chen F., Liu H., Wei J., Yang X., Zhang Q., Xia W., Wu H., He Q. , Zhang T.",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 6,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,Chronic HIV-infected participants at baseline (B0),Chronic HIV-infected participants on Antiretroviral Therapy(B12),Men who have sex with men (MSM) with Chronic HIV infection after 12 weeks of Antiretroviral Therapy (ART).,15,15,1 month,16S,45,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 2,Figure 4c,30 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Linear discriminative analysis (LDA) effect size (LefSe) at the genus level shown between Chronic HIV-infected participants on Antiretroviral Therapy(B12) and Chronic HIV-infected participants (B0).,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|909932;3379134|976|200643|171549|171552|838|470565;1783272|1239|909932|909929;1783272|1239|909932|1843489|31977;3379134|976|200643|171549|171552;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:34336719/7/1,34336719,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S., Zhu J., Su B., Wei H., Chen F., Liu H., Wei J., Yang X., Zhang Q., Xia W., Wu H., He Q. , Zhang T.",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 7,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,Acute HIV-infected participants at baseline (A0),Chronic HIV-infected participants at baseline (B0),Men who have sex with men (MSM) with Chronic HIV infection.,15,15,1 month,16S,45,Illumina,raw counts,T-Test,0.05,NA,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Figure 4e,30 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Comparisons of the relative abundance in oral microbiota at the genus level between people living with acute HIV infection at baseline (A0) and people living with chronic HIV infection at baseline (B0).,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,1783272|1239|186801|3085636|186803|265975,Complete,Svetlana up
bsdb:34336719/8/1,34336719,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S., Zhu J., Su B., Wei H., Chen F., Liu H., Wei J., Yang X., Zhang Q., Xia W., Wu H., He Q. , Zhang T.",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 8,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,Acute HIV-infected participants on Antiretroviral Therapy(A12),Chronic HIV-infected participants on Antiretroviral Therapy(B12),Men who have sex with men (MSM) with Chronic HIV infection after 12 weeks of Antiretroviral Therapy (ART).,15,15,1 month,16S,45,Illumina,raw counts,T-Test,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 4f,30 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Comparisons of the relative abundance in oral microbiota at the genus level between people living with acute HIV infection after 12 weeks of ART (A12) and people living with chronic HIV infection after 12 weeks of ART (B12).,increased,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,3379134|29547|3031852|213849|72294|194,Complete,Svetlana up
bsdb:34336719/9/1,34336719,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S., Zhu J., Su B., Wei H., Chen F., Liu H., Wei J., Yang X., Zhang Q., Xia W., Wu H., He Q. , Zhang T.",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 9,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,Uninfected Controls,CD4+ T cells < 200 cells/mm3,Subjects whose CD4+ T cells were defined as < 200 cells/mm3.,15,NA,1 month,16S,45,Illumina,raw counts,T-Test,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,1 May 2024,Aleru Divine,"Aleru Divine,WikiWorks",The relationship between the alteration observed in the oral microbiome and the CD4+ T-cell count of patients.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|1224|1236|135625|712|724;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85006|1268|32207;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:34336719/10/2,34336719,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S., Zhu J., Su B., Wei H., Chen F., Liu H., Wei J., Yang X., Zhang Q., Xia W., Wu H., He Q. , Zhang T.",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 10,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,Uninfected Controls,CD4+ T cells > 200 cells/mm3,Subjects whose CD4+ T cells were defined as > 200 cells/mm3.,15,NA,1 month,16S,45,Illumina,raw counts,T-Test,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5,1 May 2024,Aleru Divine,"Aleru Divine,WikiWorks",The relationship between the alteration observed in the oral microbiome and the CD4+ T-cell count of patients.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",1783272|201174|1760|2037|2049|1654;1783272|1239|186801|186802|216572;1783272|201174|1760|85006|1268|32207,Complete,Svetlana up
bsdb:34336719/11/1,34336719,time series / longitudinal observational,34336719,10.3389/fcimb.2021.695515,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317457/,"Li S., Zhu J., Su B., Wei H., Chen F., Liu H., Wei J., Yang X., Zhang Q., Xia W., Wu H., He Q. , Zhang T.",Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy,Frontiers in cellular and infection microbiology,2021,"16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome",Experiment 11,China,Homo sapiens,Throat,UBERON:0000341,Human immunodeficiency virus,NCBITAXON:12721,CD4+ T cells < 200 cells/mm3,CD4+ T cells > 200 cells/mm3,Subjects whose CD4+ T cells were defined as > 200 cells/mm3.,NA,NA,1 month,16S,45,Illumina,raw counts,T-Test,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,1 May 2024,Aleru Divine,"Aleru Divine,WikiWorks",The relationship between the alteration observed in the oral microbiome and the CD4+ T-cell count of patients.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",3379134|1224|1236|135625|712|724;1783272|201174|1760|2037|2049|1654;1783272|1239|186801|186802|216572;1783272|201174|1760|85006|1268|32207,Complete,Svetlana up
bsdb:34336726/1/1,34336726,time series / longitudinal observational,34336726,10.2147/JHC.S315696,NA,"Shen Y.C., Lee P.C., Kuo Y.L., Wu W.K., Chen C.C., Lei C.H., Yeh C.P., Hsu C., Hsu C.H., Lin Z.Z., Shao Y.Y., Lu L.C., Liu T.H., Chen C.H., Wu M.S., Huang Y.H. , Cheng A.L.",An Exploratory Study for the Association of Gut Microbiome with Efficacy of Immune Checkpoint Inhibitor in Patients with Hepatocellular Carcinoma,Journal of hepatocellular carcinoma,2021,"biomarkers, gut microbiome, hepatocellular carcinoma, immune checkpoint inhibitor",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Hepatocellular carcinoma,EFO:0000182,Non-responders to Immune checkpoint inhibitors,Responders to Immune checkpoint inhibitors,"Patients who responded to ICI therapy, defined as complete or partial response per Response
Evaluation Criteria in Solid Tumors (RECIST) v.1.1.",26,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3a,12 October 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1,WikiWorks",Differential microbial abundance in baseline gut microbiome between responders and nonresponders,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",3379134|1224|1236|135624|83763|83770;1783272|1239|186801|3085636|186803|1506577,Complete,Claregrieve1
bsdb:34336726/1/2,34336726,time series / longitudinal observational,34336726,10.2147/JHC.S315696,NA,"Shen Y.C., Lee P.C., Kuo Y.L., Wu W.K., Chen C.C., Lei C.H., Yeh C.P., Hsu C., Hsu C.H., Lin Z.Z., Shao Y.Y., Lu L.C., Liu T.H., Chen C.H., Wu M.S., Huang Y.H. , Cheng A.L.",An Exploratory Study for the Association of Gut Microbiome with Efficacy of Immune Checkpoint Inhibitor in Patients with Hepatocellular Carcinoma,Journal of hepatocellular carcinoma,2021,"biomarkers, gut microbiome, hepatocellular carcinoma, immune checkpoint inhibitor",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Hepatocellular carcinoma,EFO:0000182,Non-responders to Immune checkpoint inhibitors,Responders to Immune checkpoint inhibitors,"Patients who responded to ICI therapy, defined as complete or partial response per Response
Evaluation Criteria in Solid Tumors (RECIST) v.1.1.",26,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 3a,12 October 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1,WikiWorks",Differential microbial abundance in baseline gut microbiome between responders and nonresponders,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;1783272|1239|186801|3082720|186804;3379134|74201|203494;3379134|74201|203494|48461;3379134|74201,Complete,Claregrieve1
bsdb:34336726/2/1,34336726,time series / longitudinal observational,34336726,10.2147/JHC.S315696,NA,"Shen Y.C., Lee P.C., Kuo Y.L., Wu W.K., Chen C.C., Lei C.H., Yeh C.P., Hsu C., Hsu C.H., Lin Z.Z., Shao Y.Y., Lu L.C., Liu T.H., Chen C.H., Wu M.S., Huang Y.H. , Cheng A.L.",An Exploratory Study for the Association of Gut Microbiome with Efficacy of Immune Checkpoint Inhibitor in Patients with Hepatocellular Carcinoma,Journal of hepatocellular carcinoma,2021,"biomarkers, gut microbiome, hepatocellular carcinoma, immune checkpoint inhibitor",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Hepatocellular carcinoma,EFO:0000182,Non-Disease control with Immune checkpoint inhibitors,Disease control with Immune checkpoint inhibitors,“disease control” was defined as objective response or stable disease lasting =16 weeks.” Objective response was defined as complete or partial response per Response Evaluation Criteria in Solid Tumors (RECIST) v.1.1.,17,19,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3b,12 October 2022,Mary Bearkland,"Mary Bearkland,Aiyshaaaa,Claregrieve1,WikiWorks",Differential microbial abundance in baseline gut microbiome between patients whose disease was not controlled and patients whose disease was controlled,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinatimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens",1783272|1239|909932|1843488|909930|904;1783272|201174;3379134|1224|1236|135624;3379134|976|200643|171549|171552|1283313;1783272|201174|84998|84999|1643824;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|33042;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|186801|3085636|186803|28050;1783272|1239|909932|1843489|31977|906;3379134|1224|1236|135624|83763|674963;3379134|1224|1236|135624|83763;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|3085636|186803|1506553|29347,Complete,Claregrieve1
bsdb:34336726/2/2,34336726,time series / longitudinal observational,34336726,10.2147/JHC.S315696,NA,"Shen Y.C., Lee P.C., Kuo Y.L., Wu W.K., Chen C.C., Lei C.H., Yeh C.P., Hsu C., Hsu C.H., Lin Z.Z., Shao Y.Y., Lu L.C., Liu T.H., Chen C.H., Wu M.S., Huang Y.H. , Cheng A.L.",An Exploratory Study for the Association of Gut Microbiome with Efficacy of Immune Checkpoint Inhibitor in Patients with Hepatocellular Carcinoma,Journal of hepatocellular carcinoma,2021,"biomarkers, gut microbiome, hepatocellular carcinoma, immune checkpoint inhibitor",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Hepatocellular carcinoma,EFO:0000182,Non-Disease control with Immune checkpoint inhibitors,Disease control with Immune checkpoint inhibitors,“disease control” was defined as objective response or stable disease lasting =16 weeks.” Objective response was defined as complete or partial response per Response Evaluation Criteria in Solid Tumors (RECIST) v.1.1.,17,19,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 3b,12 October 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1,WikiWorks",Differential microbial abundance in baseline gut microbiome between patients whose disease was not controlled and patients whose disease was controlled,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,1783272|1239|186801|186802|216572|216851,Complete,Claregrieve1
bsdb:34336726/3/1,34336726,time series / longitudinal observational,34336726,10.2147/JHC.S315696,NA,"Shen Y.C., Lee P.C., Kuo Y.L., Wu W.K., Chen C.C., Lei C.H., Yeh C.P., Hsu C., Hsu C.H., Lin Z.Z., Shao Y.Y., Lu L.C., Liu T.H., Chen C.H., Wu M.S., Huang Y.H. , Cheng A.L.",An Exploratory Study for the Association of Gut Microbiome with Efficacy of Immune Checkpoint Inhibitor in Patients with Hepatocellular Carcinoma,Journal of hepatocellular carcinoma,2021,"biomarkers, gut microbiome, hepatocellular carcinoma, immune checkpoint inhibitor",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Hepatocellular carcinoma,EFO:0000182,Non-responders to Immune checkpoint inhibitors,Responders to Immune checkpoint inhibitors,"“Objective response” was defined as complete or partial response per Response
Evaluation Criteria in Solid Tumors (RECIST) v.1.1.",12,6,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3a,12 October 2022,Mary Bearkland,"Mary Bearkland,Claregrieve1,WikiWorks",Differential microbial abundance in baseline gut microbiome between responders and nonresponders,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp.",3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|171552|1283313|1872471,Complete,Claregrieve1
bsdb:34341764/1/1,34341764,"cross-sectional observational, not case-control",34341764,https://doi.org/10.1155%2F2021%2F5579608,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8325587/,"Wen M., Liu T., Zhao M., Dang X., Feng S., Ding X., Xu Z., Huang X., Lin Q., Xiang W., Li X., He X. , He Q.",Correlation Analysis between Gut Microbiota and Metabolites in Children with Systemic Lupus Erythematosus,Journal of immunology research,2021,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Systemic lupus erythematosus,MONDO:0007915,HC,SLE,Individuals who have been diagnosed with systemic lupus erythematosus (SLE). Systemic lupus erythematosus (SLE) is an autoimmune-mediated diffuse connective tissue disease characterized by immune inflammation with an unclear aetiology and pathogenesis.,28,33,3 months,16S,45,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table 2,20 March 2023,Aiyshaaaa,"Aiyshaaaa,WikiWorks","The differently abundant species at genus, class, phylum, order and family level in both the groups are listed.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kluyvera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Rudaea,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",3379134|1224|28211;1783272|1239|91061;3379134|1224|28211|204458|76892;3379134|1224|28211|204458;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|1940338;3379134|1224|1236;1783272|1239|186801|3085636|186803|1649459;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|543|579;1783272|1239|186801|3085636|186803|1506553;1783272|1239|91061|186826;3379134|1224;3379134|1224|1236|135614|1775411;3379134|1224|1236|135614|1775411|886360;3379134|1224|28211|204457|41297;3379134|1224|28211|204457;3379134|1224|28211|204457|41297|13687;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810280|3025755;3379134|1224|1236|135614;1783272|1239|186801|186802|31979|1485|1522;1783272|1239|186801|3085636|186803|2316020|33038,Complete,Claregrieve1
bsdb:34341764/1/2,34341764,"cross-sectional observational, not case-control",34341764,https://doi.org/10.1155%2F2021%2F5579608,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8325587/,"Wen M., Liu T., Zhao M., Dang X., Feng S., Ding X., Xu Z., Huang X., Lin Q., Xiang W., Li X., He X. , He Q.",Correlation Analysis between Gut Microbiota and Metabolites in Children with Systemic Lupus Erythematosus,Journal of immunology research,2021,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Systemic lupus erythematosus,MONDO:0007915,HC,SLE,Individuals who have been diagnosed with systemic lupus erythematosus (SLE). Systemic lupus erythematosus (SLE) is an autoimmune-mediated diffuse connective tissue disease characterized by immune inflammation with an unclear aetiology and pathogenesis.,28,33,3 months,16S,45,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Table 2,20 March 2023,Aiyshaaaa,"Aiyshaaaa,WikiWorks","The differently abundant species at genus, class, phylum, order and family level in both the groups are listed in this table.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NC2004,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens",1783272|1239|186801|3085636|186803|1766253;3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;1783272|1239|186801|3082768|990719;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|1410626;1783272|1239|186801|3085636|186803|877420;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|3085636|186803|28050|39485,Complete,Claregrieve1
bsdb:34354176/1/1,34354176,"cross-sectional observational, not case-control",34354176,10.1038/s41598-021-95409-5,NA,"Nel Van Zyl K., Whitelaw A.C., Hesseling A.C., Seddon J.A., Demers A.M. , Newton-Foot M.",Association between clinical and environmental factors and the gut microbiota profiles in young South African children,Scientific reports,2021,NA,Experiment 1,South Africa,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Group C (> 2 to 5 age),Group A (0-1 age),Children within 0-1 year of age.,66,24,12 months,16S,4,Illumina,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,15 October 2024,ToluwalaseA,"ToluwalaseA,Tosin,WikiWorks",Statistically significant taxa identified by ANCOM  labelled in the Comparison between groups A (0-1 age) & C (>2 to <5 age).,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85004|31953|1678;1783272|201174|84998|1643822|1643826|84111;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|3085636|186803|1506577;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|186802|31979|1485|1522;3379134|1224|1236|91347|543,Complete,Svetlana up
bsdb:34354176/1/2,34354176,"cross-sectional observational, not case-control",34354176,10.1038/s41598-021-95409-5,NA,"Nel Van Zyl K., Whitelaw A.C., Hesseling A.C., Seddon J.A., Demers A.M. , Newton-Foot M.",Association between clinical and environmental factors and the gut microbiota profiles in young South African children,Scientific reports,2021,NA,Experiment 1,South Africa,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Group C (> 2 to 5 age),Group A (0-1 age),Children within 0-1 year of age.,66,24,12 months,16S,4,Illumina,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5A,15 October 2024,ToluwalaseA,"ToluwalaseA,Tosin,WikiWorks",Statistically significant taxa identified by ANCOM labelled in the Comparison between groups A (0-1 age) & C (>2 to <5 age).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|877420,Complete,Svetlana up
bsdb:34354176/2/1,34354176,"cross-sectional observational, not case-control",34354176,10.1038/s41598-021-95409-5,NA,"Nel Van Zyl K., Whitelaw A.C., Hesseling A.C., Seddon J.A., Demers A.M. , Newton-Foot M.",Association between clinical and environmental factors and the gut microbiota profiles in young South African children,Scientific reports,2021,NA,Experiment 2,South Africa,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Group A (0-1 age),Group B (>1 to 2 age),Children with age group between > 1 to 2.,24,25,12 months,16S,4,Illumina,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 5B,6 November 2024,Tosin,"Tosin,WikiWorks",Statistically significant taxa identified by ANCOM labelled in the Comparison between groups A (0-1 age) & B (>1 to 2 age).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|216851;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:34354176/2/2,34354176,"cross-sectional observational, not case-control",34354176,10.1038/s41598-021-95409-5,NA,"Nel Van Zyl K., Whitelaw A.C., Hesseling A.C., Seddon J.A., Demers A.M. , Newton-Foot M.",Association between clinical and environmental factors and the gut microbiota profiles in young South African children,Scientific reports,2021,NA,Experiment 2,South Africa,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Group A (0-1 age),Group B (>1 to 2 age),Children with age group between > 1 to 2.,24,25,12 months,16S,4,Illumina,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 5B,6 November 2024,Tosin,"Tosin,WikiWorks",Statistically significant taxa identified by ANCOM labelled in the Comparison between groups A (0-1 age) & B (>1 to 2 age).,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,1783272|1239|186801|186802|31979|1485|1522,Complete,Svetlana up
bsdb:34354176/3/1,34354176,"cross-sectional observational, not case-control",34354176,10.1038/s41598-021-95409-5,NA,"Nel Van Zyl K., Whitelaw A.C., Hesseling A.C., Seddon J.A., Demers A.M. , Newton-Foot M.",Association between clinical and environmental factors and the gut microbiota profiles in young South African children,Scientific reports,2021,NA,Experiment 3,South Africa,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Group B (> 1 to 2 age),Group C (> 2 to < 5 age),Children with age group between > 2 to 5.,25,66,12 months,16S,4,Illumina,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5C,6 November 2024,Tosin,"Tosin,WikiWorks",Statistically significant taxa identified by ANCOM labelled in the Comparison between groups B (>1 to 2 age) and C (>2 to <5 age).,increased,NA,NA,Complete,Svetlana up
bsdb:34354176/3/2,34354176,"cross-sectional observational, not case-control",34354176,10.1038/s41598-021-95409-5,NA,"Nel Van Zyl K., Whitelaw A.C., Hesseling A.C., Seddon J.A., Demers A.M. , Newton-Foot M.",Association between clinical and environmental factors and the gut microbiota profiles in young South African children,Scientific reports,2021,NA,Experiment 3,South Africa,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Group B (> 1 to 2 age),Group C (> 2 to < 5 age),Children with age group between > 2 to 5.,25,66,12 months,16S,4,Illumina,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5C,6 November 2024,Tosin,"Tosin,WikiWorks",Statistically significant taxa identified by ANCOM labelled in the Comparison between groups B (>1 to 2 age) and C (>2 to <5 age).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:34375351/1/1,34375351,case-control,34375351,10.1371/journal.pone.0255446,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0255446,"Duan M., Wang Y., Zhang Q., Zou R., Guo M. , Zheng H.",Characteristics of gut microbiota in people with obesity,PloS one,2021,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Control group,Obesity group,"Adults with obesity recruited from a gym of Jinan, Shandong Province (mean body mass index 35.3, ranging from 31.4 to 49.5, 16 males, 5 females, with an average age of 35 years), who also were not under dietary or medication control to lose weight",21,21,1 month,16S,34,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),Welch's T-Test",0.05,FALSE,NA,NA,NA,decreased,decreased,decreased,NA,NA,decreased,Signature 1,"Figures 3, 4, 6 and Tables 1,2",2 November 2025,Fiddyhamma,Fiddyhamma,Gut microbiota comparison between obesity and control across several taxonomic ranks.,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota,k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri",3384189|32066|203490|203491|203492;1783272|1239|909932|1843489|31977;3379134|976|200643|171549|171552;1783272|1239|186801|3085636|186803|572511;3384189|32066|203490|203491|203492|848;1783272|1239|909932|909929|1843491|158846;3379134|976|200643|171549|171552|838;3379134|976;3384189|32066;1783272|1239|909932|909929|1843491|158846|437897;3384189|32066|203490|203491|203492|848|850;3379134|976|200643|171549|171552|2974251|165179,Complete,NA
bsdb:34375351/1/2,34375351,case-control,34375351,10.1371/journal.pone.0255446,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0255446,"Duan M., Wang Y., Zhang Q., Zou R., Guo M. , Zheng H.",Characteristics of gut microbiota in people with obesity,PloS one,2021,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Control group,Obesity group,"Adults with obesity recruited from a gym of Jinan, Shandong Province (mean body mass index 35.3, ranging from 31.4 to 49.5, 16 males, 5 females, with an average age of 35 years), who also were not under dietary or medication control to lose weight",21,21,1 month,16S,34,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),Welch's T-Test",0.05,FALSE,NA,NA,NA,decreased,decreased,decreased,NA,NA,decreased,Signature 2,"Figures 3, 4, 6 and Tables 1,2",2 November 2025,Tosin,Tosin,Gut microbiota comparison between obesity and control across several taxonomic ranks,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|2005519|397864;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|204475;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|216851;1783272|1239;1783272|201174;1783272|1239|186801|186802|216572|216851|853;3379134|976|200643|171549|2005519|397864|487174;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|2005525|375288|823;1783272|1239|186801|3085636|186803|1407607|1150298,Complete,NA
bsdb:34376634/1/1,34376634,time series / longitudinal observational,34376634,10.1038/s41398-021-01531-3,NA,"Yuan X., Wang Y., Li X., Jiang J., Kang Y., Pang L., Zhang P., Li A., Lv L., Andreassen O.A., Fan X., Hu S. , Song X.","Gut microbial biomarkers for the treatment response in first-episode, drug-naïve schizophrenia: a 24-week follow-up study",Translational psychiatry,2021,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Response to risperidone,GO:0097336,Healthy controls (C),Schizophrenia (SCH) patients at Baseline (S0),"Schizophrenia drug-naïve patients who were newly admitted, and no treatment had begun. Patients had not yet received risperidone.",107,107,1 month,16S,34,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,education level,sex,smoking behavior","age,body mass index,education level,sex,smoking behavior",NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,Figure 4c and Supplementary Table 3,29 July 2024,JoyceQ,"JoyceQ,MyleeeA,WikiWorks",Taxa enriched in the gut microbiota of Schizophrenia (SCH) patients at Baseline (S0) and Healthy controls (C).,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,1783272|1239|186801|3085636|186803|1506553,Complete,Svetlana up
bsdb:34376634/1/2,34376634,time series / longitudinal observational,34376634,10.1038/s41398-021-01531-3,NA,"Yuan X., Wang Y., Li X., Jiang J., Kang Y., Pang L., Zhang P., Li A., Lv L., Andreassen O.A., Fan X., Hu S. , Song X.","Gut microbial biomarkers for the treatment response in first-episode, drug-naïve schizophrenia: a 24-week follow-up study",Translational psychiatry,2021,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Response to risperidone,GO:0097336,Healthy controls (C),Schizophrenia (SCH) patients at Baseline (S0),"Schizophrenia drug-naïve patients who were newly admitted, and no treatment had begun. Patients had not yet received risperidone.",107,107,1 month,16S,34,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,education level,sex,smoking behavior","age,body mass index,education level,sex,smoking behavior",NA,decreased,unchanged,decreased,NA,unchanged,Signature 2,Figure 4d and Supplementary Table 3,3 August 2024,JoyceQ,"JoyceQ,MyleeeA,WikiWorks",Taxa enriched in the gut microbiota of Schizophrenia (SCH) patients at Baseline (S0) and Healthy controls (C).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter",1783272|1239|186801|186802;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3082720|186804|1501226;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|189330;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|1407607;1783272|1239|526524|526525|128827;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|33958|46255;1783272|1239|186801|3082720|186804|1505652;3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|544,Complete,Svetlana up
bsdb:34376634/2/1,34376634,time series / longitudinal observational,34376634,10.1038/s41398-021-01531-3,NA,"Yuan X., Wang Y., Li X., Jiang J., Kang Y., Pang L., Zhang P., Li A., Lv L., Andreassen O.A., Fan X., Hu S. , Song X.","Gut microbial biomarkers for the treatment response in first-episode, drug-naïve schizophrenia: a 24-week follow-up study",Translational psychiatry,2021,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Response to risperidone,GO:0097336,Healthy controls (C),Schizophrenia (SCH) patients at Week 6 (S1),Schizophrenia drug-naïve patients who had received 6 weeks of risperidone treatment and were accessed during the treatment.,107,96,1 month,16S,34,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,education level,sex,smoking behavior","age,body mass index,education level,sex,smoking behavior",NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 4C,14 October 2024,MyleeeA,"MyleeeA,WikiWorks",Taxa enriched in the gut microbiota of Schizophrenia (SCH) patients at Week 6 (S1) and Healthy controls (C).,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,1783272|1239|186801|3082720|186804|1501226,Complete,Svetlana up
bsdb:34376634/3/1,34376634,time series / longitudinal observational,34376634,10.1038/s41398-021-01531-3,NA,"Yuan X., Wang Y., Li X., Jiang J., Kang Y., Pang L., Zhang P., Li A., Lv L., Andreassen O.A., Fan X., Hu S. , Song X.","Gut microbial biomarkers for the treatment response in first-episode, drug-naïve schizophrenia: a 24-week follow-up study",Translational psychiatry,2021,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Response to risperidone,GO:0097336,Healthy controls (C),Schizophrenia (SCH) patients at Week 12 (S2),Schizophrenia drug-naïve patients who had received 12 weeks of risperidone treatment and were accessed during the treatment.,107,74,1 month,16S,34,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,education level,sex,smoking behavior","age,body mass index,education level,sex,smoking behavior",NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 4C,14 October 2024,MyleeeA,"MyleeeA,WikiWorks",Taxa enriched in the gut microbiota of SCH patients at Week 12 (S2) and Healthy controls (C).,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,1783272|1239|186801|3082720|186804|1501226,Complete,Svetlana up
bsdb:34376634/4/1,34376634,time series / longitudinal observational,34376634,10.1038/s41398-021-01531-3,NA,"Yuan X., Wang Y., Li X., Jiang J., Kang Y., Pang L., Zhang P., Li A., Lv L., Andreassen O.A., Fan X., Hu S. , Song X.","Gut microbial biomarkers for the treatment response in first-episode, drug-naïve schizophrenia: a 24-week follow-up study",Translational psychiatry,2021,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Response to risperidone,GO:0097336,Healthy controls (C),Schizophrenia (SCH) patients at Week 24 (S3),Schizophrenia drug-naïve patients who had received 24 weeks of risperidone treatment and were accessed after the treatment.,107,60,1 month,16S,34,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,education level,sex,smoking behavior","age,body mass index,education level,sex,smoking behavior",NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 4d,18 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Taxa enriched in the gut microbiota of SCH patients at Week 24 (S3) and Healthy controls (C).,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,1783272|1239|186801|3082720|186804|1501226,Complete,Svetlana up
bsdb:34376634/6/1,34376634,time series / longitudinal observational,34376634,10.1038/s41398-021-01531-3,NA,"Yuan X., Wang Y., Li X., Jiang J., Kang Y., Pang L., Zhang P., Li A., Lv L., Andreassen O.A., Fan X., Hu S. , Song X.","Gut microbial biomarkers for the treatment response in first-episode, drug-naïve schizophrenia: a 24-week follow-up study",Translational psychiatry,2021,NA,Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Response to risperidone,GO:0097336,Schizophrenia (SCH) patients at Baseline (S0),Schizophrenia (SCH) patients at Week 24 (S3),Schizophrenia drug-naïve patients who had received 24 weeks of risperidone treatment and were accessed after the treatment.,107,60,1 month,16S,34,Ion Torrent,relative abundances,LEfSe,0.05,TRUE,3,"age,body mass index,education level,sex,smoking behavior","age,body mass index,education level,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S5,16 October 2024,MyleeeA,"MyleeeA,WikiWorks,Ese",Taxa enriched in the gut microbiota of Schizophrenia (SCH) patients at Baseline(S0) and After treatment at Week 24 (S3),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetitomaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. MC 40,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG_194_44_15,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. ER4,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Hymenochaetales|f__Rickenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria",1783272|1239|186801|3085636|186803|31980;3379134|976|200643|171549|171550|239759;1783272|1239|91061;3379134|1224|28216|80840|119060;1783272|1239|186801|186802|31979|1485|2683682;1783272|1239|1897037;3379134|1224|1236;1783272|1239|186801|3085636|186803|28050;1783272|1239|91061|186826;1783272|1239|186801|186802|216572|459786|1519439;4751|5204|155619|139380|1124673;3379134|1224|28216|80840|995019|40544;3379134|1224|1236,Complete,Svetlana up
bsdb:34376634/6/2,34376634,time series / longitudinal observational,34376634,10.1038/s41398-021-01531-3,NA,"Yuan X., Wang Y., Li X., Jiang J., Kang Y., Pang L., Zhang P., Li A., Lv L., Andreassen O.A., Fan X., Hu S. , Song X.","Gut microbial biomarkers for the treatment response in first-episode, drug-naïve schizophrenia: a 24-week follow-up study",Translational psychiatry,2021,NA,Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Response to risperidone,GO:0097336,Schizophrenia (SCH) patients at Baseline (S0),Schizophrenia (SCH) patients at Week 24 (S3),Schizophrenia drug-naïve patients who had received 24 weeks of risperidone treatment and were accessed after the treatment.,107,60,1 month,16S,34,Ion Torrent,relative abundances,LEfSe,0.05,TRUE,3,"age,body mass index,education level,sex,smoking behavior","age,body mass index,education level,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 5 and Figure 4c,18 October 2024,Aleru Divine,"Aleru Divine,MyleeeA,WikiWorks",Taxa enriched in the gut microbiota of Schizophrenia patients at Baseline(S0) and After treatment at Week 24 (S3),decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,1783272|1239|186801|3085636|186803|1506553,Complete,Svetlana up
bsdb:34378948/1/1,34378948,"cross-sectional observational, not case-control",34378948,10.1128/Spectrum.00708-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8552706/pdf/spectrum.00708-21.pdf,"Ishizaka A., Koga M., Mizutani T., Parbie P.K., Prawisuda D., Yusa N., Sedohara A., Kikuchi T., Ikeuchi K., Adachi E., Koibuchi T., Furukawa Y., Tojo A., Imoto S., Suzuki Y., Tsutsumi T., Kiyono H., Matano T. , Yotsuyanagi H.",Unique Gut Microbiome in HIV Patients on Antiretroviral Therapy (ART) Suggests Association with Chronic Inflammation,Microbiology spectrum,2021,"HIV, dysbiosis, human immunodeficiency virus, inflammation, microbiome, microbiota",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Healthy controls,HIV Patients,Patients with HIV infection,61,71,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,body mass index,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2, Figure 3",9 January 2022,Joyessa,"Joyessa,Claregrieve1,WikiWorks",Differential microbial abundance between healthy controls and HIV-infected patients with CD4 counts > 500 cells/uL,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes",1783272|201174;1783272|1239|186801|3085636|186803|265975;1783272|1239|526524|526525|128827|123375;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958;1783272|1239|186801|186802|216572|1926663;1783272|201174|84998|84999|1643824|133925;1783272|201174|84998|1643822|1643826|580024;1783272|1239|186801|3082720|543314|86331;3379134|1224|1236|135624;1783272|201174|84998|84999|1643824|2082587;3379134|1224|1236|135624|83763;3379134|1224|1236|135624|83763|83770;1783272|1239|909932|1843489|31977|906;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;1783272|201174|84998|84999|84107|1473205;1783272|201174|84998|1643822|1643826|84108;1783272|201174|84998|84999|1643824;1783272|1239|526524|526525|128827|1573535;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;1783272|1239|526524|526525|128827;1783272|1239|909932|1843488|909930;1783272|1239|909932|1843488;1783272|1239|526524|526525|2810280|135858;1783272|201174|84998|1643822|1643826;3379134|976|200643|171549|171552|838;1783272|1239|526524|526525;3379134|976|200643|171549|171552;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|909929|1843491;1783272|1239|909932|1843489|31977|39948;1783272|1239|91061;1783272|201174|84998;1783272|201174|84998|84999;1783272|1239|909932|1843489|31977;1783272|1239|909932|1843489;1783272|1239|909932|909929;1783272|1239|909932,Complete,Claregrieve1
bsdb:34378948/1/2,34378948,"cross-sectional observational, not case-control",34378948,10.1128/Spectrum.00708-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8552706/pdf/spectrum.00708-21.pdf,"Ishizaka A., Koga M., Mizutani T., Parbie P.K., Prawisuda D., Yusa N., Sedohara A., Kikuchi T., Ikeuchi K., Adachi E., Koibuchi T., Furukawa Y., Tojo A., Imoto S., Suzuki Y., Tsutsumi T., Kiyono H., Matano T. , Yotsuyanagi H.",Unique Gut Microbiome in HIV Patients on Antiretroviral Therapy (ART) Suggests Association with Chronic Inflammation,Microbiology spectrum,2021,"HIV, dysbiosis, human immunodeficiency virus, inflammation, microbiome, microbiota",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Healthy controls,HIV Patients,Patients with HIV infection,61,71,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,body mass index,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3,9 January 2022,Joyessa,"Joyessa,Claregrieve1,WikiWorks",Differential microbial abundance between healthy controls and HIV-infected patients with CD4 counts > 500 cells/uL,decreased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815;3379134|1224|1236|91347|543;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085656|3085657|2039302;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|1407607;3379134|976|200643|171549|171550;3379134|1224|1236|91347|543|547;1783272|1239|91061|186826|186828;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712;3379134|1224|1236|135625|712|724;1783272|1239|186801|186802|216572,Complete,Claregrieve1
bsdb:34382150/1/1,34382150,case-control,34382150,10.1007/s12275-021-1206-5,NA,"Zhou Y., Zhang J., Zhang D., Ma W.L. , Wang X.",Linking the gut microbiota to persistent symptoms in survivors of COVID-19 after discharge,"Journal of microbiology (Seoul, Korea)",2021,"COVID-19, gut microbiota, recovered healthcare workers, symptoms after discharge",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 patients,Health-care workers who recovered from COVID-19 and were discharged from the hospital between May and July 2020,14,15,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 4,27 September 2021,Claregrieve1,"Claregrieve1,Peace Sandy,WikiWorks","Taxonomic differences of gut microbiota between recovered HCWs and HCs. Comparison of relative abundance at the bacterial phylum (A), family
(B), genus (C), and species (D) between the two groups. p-value < 0.05 is considered to be statistically significant, *p < 0.05, **p < 0.01.",increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus pullicaecorum",1783272|201174;1783272|1239|186801|3085636|186803|2719313|358742;1783272|1239|186801|3085636|186803|2719313|208479;3379134|1224|1236|91347|543|561;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3082720|186804|1505657;1783272|1239|186801|3082720|186804|1505657|261299;1783272|1239|526524|526525|2810280|3025755|1547;3379134|1224|1236|91347|543|561;1783272|1239|186801|186802|216572|946234|292800;1783272|201174|1760|85004|31953|1678|1686;1783272|1239|186801|186802|3085642|580596|501571,Complete,Peace Sandy
bsdb:34382150/1/2,34382150,case-control,34382150,10.1007/s12275-021-1206-5,NA,"Zhou Y., Zhang J., Zhang D., Ma W.L. , Wang X.",Linking the gut microbiota to persistent symptoms in survivors of COVID-19 after discharge,"Journal of microbiology (Seoul, Korea)",2021,"COVID-19, gut microbiota, recovered healthcare workers, symptoms after discharge",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 patients,Health-care workers who recovered from COVID-19 and were discharged from the hospital between May and July 2020,14,15,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 4,27 September 2021,Claregrieve1,"Claregrieve1,Peace Sandy,WikiWorks","Taxonomic differences of gut microbiota between recovered HCWs and HCs. Comparison of relative abundance at the bacterial phylum (A), family
(B), genus (C), and species (D) between the two groups. p-value < 0.05 is considered to be statistically significant, *p < 0.05, **p < 0.01.",decreased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia sedimentorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii",3379134|200940|3031449|213115|194924|35832;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|3085636|186803|572511|871665;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|186802|3085642|580596;3379134|200940|3031449|213115|194924;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|186802|1392389;1783272|1239|186801|186802|1392389|1297617;1783272|1239|186801|3085636|186803;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3082720|186804|1501226|1368474;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|40518,Complete,Peace Sandy
bsdb:34394853/1/1,34394853,case-control,34394853,10.1080/20002297.2021.1962125,NA,"Yoon B.W., Lim S.H., Shin J.H., Lee J.W., Lee Y. , Seo J.H.",Analysis of oral microbiome in glaucoma patients using machine learning prediction models,Journal of oral microbiology,2021,"Neurodegenerative, biomarker, dysbiosis, glaucoma, oral microbiome",Experiment 1,Republic of Korea,Homo sapiens,Buccal mucosa,UBERON:0006956,Glaucoma,MONDO:0005041,Control subjects,Glaucoma,Patients diagnosed with glaucoma,25,96,1 month,16S,34,Illumina,raw counts,edgeR,1e-5,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"Figure 5b, Supplementary Table S1",10 September 2025,Anne-mariesharp,Anne-mariesharp,Differentially abundant taxa between glaucoma patients and control subjects,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Candidatus Carsonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Methanobacteriati|p__Methanobacteriota|c__Halobacteria|o__Halobacteriales|f__Halobacteriaceae|g__Salarchaeum,k__Thermoproteati|p__Thermoproteota|c__Thermoprotei|o__Desulfurococcales|f__Desulfurococcaceae|g__Sulfophobococcus,k__Bacillati|p__Candidatus Melainabacteria|c__Vampirovibriophyceae|o__Vampirovibrionales|g__Vampirovibrio,k__Nanobdellati|p__Candidatus Aenigmatarchaeota|c__Candidatus Aenigmatarchaeia|o__Candidatus Aenigmatarchaeales|f__Candidatus Aenigmatarchaeaceae|g__Candidatus Aenigmatarchaeum",1783272|1239|186801|3085636|186803|572511;3379134|1224|1236|135619|28256|114185;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803;3366610|28890|183963|2235|2236|1075398;1783275|28889|183924|114380|2272|53425;1783272|1798710|3118680|2211217|213484;1783276|743724|3444699|3444700|3444701|1462427,Complete,Svetlana up
bsdb:34394853/1/2,34394853,case-control,34394853,10.1080/20002297.2021.1962125,NA,"Yoon B.W., Lim S.H., Shin J.H., Lee J.W., Lee Y. , Seo J.H.",Analysis of oral microbiome in glaucoma patients using machine learning prediction models,Journal of oral microbiology,2021,"Neurodegenerative, biomarker, dysbiosis, glaucoma, oral microbiome",Experiment 1,Republic of Korea,Homo sapiens,Buccal mucosa,UBERON:0006956,Glaucoma,MONDO:0005041,Control subjects,Glaucoma,Patients diagnosed with glaucoma,25,96,1 month,16S,34,Illumina,raw counts,edgeR,1e-5,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,"Figure 5b, Supplementary Table S1",10 September 2025,Anne-mariesharp,Anne-mariesharp,Differentially abundant taxa between glaucoma patients and control subjects,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinilabiliaceae|g__Alkaliflexus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae|g__Anaerosinus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Anoxybacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Atopobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermatophilaceae|g__Austwickia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Bavariicoccus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Beutenbergiaceae|g__Beutenbergia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Candidatus Pelagibacterales|f__Candidatus Pelagibacteraceae|g__Candidatus Pelagibacter,k__Pseudomonadati|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Dermabacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Desemzia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Kordiimonadales|f__Kordiimonadaceae|g__Eilatimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Geobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinilabiliaceae|g__Geofilum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Haloechinothrix,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Humibacillus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Hydrogenimonadaceae|g__Hydrogenimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Isobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Jeotgalibaca,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Lacticigenium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Luteipulveratus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Marihabitans,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Melissococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Methylococcales|f__Methylococcaceae|g__Methylomarinum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Beutenbergiaceae|g__Miniimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Ornithinicoccus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermatophilaceae|g__Piscicoccus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae|g__Pelosinus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Beutenbergiaceae|g__Salana,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Sedimenticolaceae|g__Sedimenticola,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Tetragenococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae|g__Anaeroarcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae|g__Anaeromusa",3379134|976|200643|1970189|558415|286729;1783272|1239|909932|909929|1843490|151037;1783272|1239|186801|3085636|186803|653683;1783272|1239|91061|1385|3120669|150247;1783272|1239|91061|186826|186828|136491;1783272|201174|84998|84999|1643824|1380;1783272|201174|1760|85006|85018|1184606;1783272|1239|91061|186826|81852|697279;1783272|201174|1760|85006|125316|84756;3379134|1224|28211|54526|1655514|198251;3379134|204428|204429|51291|809|810;1783272|201174|1760|85006|85020|36739;1783272|1239|91061|186826|186828|82800;3379134|1224|28211|362534|1331809|1434000;1783272|1239|91061|1385|3120669|129337;3379134|976|200643|1970189|558415|1236988;1783272|1239|91061|186826|186828|117563;1783272|201174|1760|85010|2070|1425377;1783272|201174|1760|85006|85021|556178;3379134|29547|3031852|213849|292630|223785;1783272|1239|91061|186826|186828|142587;1783272|1239|91061|186826|186828|1470540;1783272|1239|186801|3085636|186803|1164882;1783272|1239|91061|186826|186828|633405;1783272|1239|91061|186826|1300|1357;1783272|201174|1760|85006|145357|745364;1783272|201174|1760|85006|85021|568214;1783272|1239|909932|1843489|31977|906;1783272|1239|91061|186826|81852|33969;3379134|1224|1236|135618|403|1221209;1783272|201174|1760|85006|125316|947525;3379134|1224|1236|91347|1903414|581;1783272|1239|909932|1843489|31977|909928;1783272|1239|186801|3085636|186803|265975;1783272|201174|1760|85006|85021|82345;1783272|201174|1760|85006|85018|985001;3379134|976|200643|171549|171552|838;3379134|1224|1236|2887326|468|497;1783272|1239|909932|909929|1843490|552808;1783272|201174|1760|85006|125316|120376;3379134|1224|1236|135613|3067276|349742;1783272|1239|526524|526525|128827|123375;1783272|1239|186801|3085636|186803|1213720;1783272|1239|91061|186826|81852|51668;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|909929|1843490|151038;1783272|1239|909932|909929|1843490|81463,Complete,Svetlana up
bsdb:34394853/2/1,34394853,case-control,34394853,10.1080/20002297.2021.1962125,NA,"Yoon B.W., Lim S.H., Shin J.H., Lee J.W., Lee Y. , Seo J.H.",Analysis of oral microbiome in glaucoma patients using machine learning prediction models,Journal of oral microbiology,2021,"Neurodegenerative, biomarker, dysbiosis, glaucoma, oral microbiome",Experiment 2,Republic of Korea,Homo sapiens,Buccal mucosa,UBERON:0006956,Open-angle glaucoma,EFO:0004190,Control subjects,POAG (Primary open-angle glaucoma),Patients diagnosed with primary open-angle glaucoma,25,62,1 month,16S,34,Illumina,raw counts,edgeR,1e-5,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"Figure 6b, Supplementary Table S2",15 September 2025,Anne-mariesharp,Anne-mariesharp,Differentially abundant taxa between primary open-angle glaucoma patients and control subjects,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Thermoproteati|p__Thermoproteota|c__Thermoprotei|o__Desulfurococcales|f__Desulfurococcaceae|g__Sulfophobococcus",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|2005525|375288;1783275|28889|183924|114380|2272|53425,Complete,Svetlana up
bsdb:34394853/2/2,34394853,case-control,34394853,10.1080/20002297.2021.1962125,NA,"Yoon B.W., Lim S.H., Shin J.H., Lee J.W., Lee Y. , Seo J.H.",Analysis of oral microbiome in glaucoma patients using machine learning prediction models,Journal of oral microbiology,2021,"Neurodegenerative, biomarker, dysbiosis, glaucoma, oral microbiome",Experiment 2,Republic of Korea,Homo sapiens,Buccal mucosa,UBERON:0006956,Open-angle glaucoma,EFO:0004190,Control subjects,POAG (Primary open-angle glaucoma),Patients diagnosed with primary open-angle glaucoma,25,62,1 month,16S,34,Illumina,raw counts,edgeR,1e-5,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,"Figure 6b, Supplementary Table S2",15 September 2025,Anne-mariesharp,Anne-mariesharp,Differentially abundant taxa between primary open-angle glaucoma patients and control subjects,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae|g__Anaerosinus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermatophilaceae|g__Austwickia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Bavariicoccus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Candidatus Pelagibacterales|f__Candidatus Pelagibacteraceae|g__Candidatus Pelagibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Dermabacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Kordiimonadales|f__Kordiimonadaceae|g__Eilatimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Haloechinothrix,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Humibacillus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Hydrogenimonadaceae|g__Hydrogenimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Isobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Luteipulveratus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Marihabitans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Melissococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Beutenbergiaceae|g__Miniimonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Ornithinicoccus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae|g__Pelosinus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Beutenbergiaceae|g__Salana,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae|g__Anaeromusa,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae|g__Anaeroarcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermatophilaceae|g__Piscicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Lacticigenium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinilabiliaceae|g__Geofilum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Tetragenococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Endobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Pseudomonadati|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Demetria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Beutenbergiaceae|g__Beutenbergia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Atopobacter",1783272|1239|909932|909929|1843490|151037;1783272|1239|186801|3085636|186803|653683;1783272|201174|84998|84999|1643824|1380;1783272|201174|1760|85006|85018|1184606;1783272|1239|91061|186826|81852|697279;3379134|1224|28211|54526|1655514|198251;1783272|201174|1760|85006|85020|36739;3379134|1224|28211|362534|1331809|1434000;1783272|1239|91061|186826|186828|117563;1783272|201174|1760|85010|2070|1425377;1783272|201174|1760|85006|85021|556178;3379134|29547|3031852|213849|292630|223785;1783272|1239|91061|186826|186828|142587;1783272|1239|91061|186826|1300|1357;1783272|201174|1760|85006|145357|745364;1783272|201174|1760|85006|85021|568214;1783272|1239|91061|186826|81852|33969;1783272|201174|1760|85006|125316|947525;1783272|1239|909932|1843489|31977|909928;1783272|201174|1760|85006|85021|82345;1783272|1239|909932|909929|1843490|552808;1783272|201174|1760|85006|125316|120376;1783272|1239|186801|3085636|186803|1213720;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|3085636|186803|1164882;1783272|1239|909932|909929|1843490|81463;1783272|1239|909932|909929|1843490|151038;1783272|201174|1760|85006|85018|985001;1783272|1239|91061|186826|186828|633405;3379134|976|200643|1970189|558415|1236988;3379134|1224|1236|2887326|468|497;1783272|1239|91061|186826|81852|51668;3379134|1224|1236|91347|1903414|581;3379134|1224|28211|3120395|433|1649268;1783272|1239|91061|186826|81852|2737;3379134|204428|204429|51291|809|810;1783272|201174|1760|85006|145357|63958;1783272|201174|1760|85006|125316|84756;1783272|1239|91061|186826|186828|136491,Complete,Svetlana up
bsdb:34401412/1/1,34401412,laboratory experiment,34401412,10.1016/j.ynstr.2021.100376,NA,"LaGamma E.F., Hu F., Pena Cruz F., Bouchev P. , Nankova B.B.",Bacteria - derived short chain fatty acids restore sympathoadrenal responsiveness to hypoglycemia after antibiotic-induced gut microbiota depletion,Neurobiology of stress,2021,"Acute hypoglycemia, Epinephrine, Fecal whole genome sequencing, Microbiome, Oral antibiotics, Short chain fatty acids supplement",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Antibiotics (Abx) mice and Recolonized mice (Abx + R),Control mice,Group of male mice given regular water.,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,31 January 2025,Aleru Divine,"Aleru Divine,WikiWorks","Differentially abundant taxa (species level) that showed significant differences in relative abundance of bacterial communities in control (blue), Abx (red) and Abx + R (green) cohorts as identified by linear discriminant analysis (LDA) assessed by effect size analysis (LefSe) algorithm.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium A4,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 28-4,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp. G3(2012),k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 1-3,k__Bacillati|p__Bacillota|s__Firmicutes bacterium ASF500,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 10-1,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium plexicaudatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis",1783272|1239|186801|3085636|186803|397291;1783272|1239|186801|186802;1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|186801|3085636|186803|397287;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|186801|186802|216572|244127|1235835;1783272|1239|186801|186802|216572|459786|1235797;1783272|1239|1378168;1783272|1239|186801|3085636|186803|1235800;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|186802|186806|1730|97253;1783272|1239|186801|3085636|186803|2719313|1531,Complete,Svetlana up
bsdb:34401412/2/1,34401412,laboratory experiment,34401412,10.1016/j.ynstr.2021.100376,NA,"LaGamma E.F., Hu F., Pena Cruz F., Bouchev P. , Nankova B.B.",Bacteria - derived short chain fatty acids restore sympathoadrenal responsiveness to hypoglycemia after antibiotic-induced gut microbiota depletion,Neurobiology of stress,2021,"Acute hypoglycemia, Epinephrine, Fecal whole genome sequencing, Microbiome, Oral antibiotics, Short chain fatty acids supplement",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Control mice and Antibiotics (Abx) mice,Recolonized mice (Abx + R),Group of male mice with antibiotics treatment followed by two weeks recolonization with co-housed age matched controls.,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,31 January 2025,Aleru Divine,"Aleru Divine,WikiWorks","Differentially abundant taxa (species level) that showed significant differences in relative abundance of bacterial communities in control (blue), Abx (red) and Abx + R (green) cohorts as identified by linear discriminant analysis (LDA) assessed by effect size analysis (LefSe) algorithm.",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia caecimuris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus|s__Cupriavidus metallidurans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus|s__Lactiplantibacillus plantarum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|201174|84998|1643822|1643826|447020|671266;1783272|1239|186801|3085636|186803|1766253|39491;3379134|1224|28216|80840|119060|106589|119219;1783272|1239|91061|186826|33958|2767842|1590;1783272|1239|91061|186826|33958|2742598|1598;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|909656|387090;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:34401412/3/1,34401412,laboratory experiment,34401412,10.1016/j.ynstr.2021.100376,NA,"LaGamma E.F., Hu F., Pena Cruz F., Bouchev P. , Nankova B.B.",Bacteria - derived short chain fatty acids restore sympathoadrenal responsiveness to hypoglycemia after antibiotic-induced gut microbiota depletion,Neurobiology of stress,2021,"Acute hypoglycemia, Epinephrine, Fecal whole genome sequencing, Microbiome, Oral antibiotics, Short chain fatty acids supplement",Experiment 3,United States of America,Mus musculus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Control mice and Recolonized mice (Abx + R),Antibiotics (Abx) mice,Group of male mice given a cocktail of non-absorbable broad-spectrum antibiotics (Abx) in the drinking water for two weeks before injection with insulin or saline.,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,31 January 2025,Aleru Divine,"Aleru Divine,WikiWorks","Differentially abundant taxa (species level) that showed significant differences in relative abundance of bacterial communities in control (blue), Abx (red) and Abx + R (green) cohorts as identified by linear discriminant analysis (LDA) assessed by effect size analysis (LefSe) algorithm.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella boydii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella flexneri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella dysenteriae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella sonnei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",3379134|1224|1236|91347|543|620|621;3379134|1224|1236|91347|543|620|623;3379134|1224|1236|91347|543|620|622;3379134|1224|1236|91347|543|620|624;3379134|1224|1236|91347|543|561,Complete,Svetlana up
bsdb:34401412/4/1,34401412,laboratory experiment,34401412,10.1016/j.ynstr.2021.100376,NA,"LaGamma E.F., Hu F., Pena Cruz F., Bouchev P. , Nankova B.B.",Bacteria - derived short chain fatty acids restore sympathoadrenal responsiveness to hypoglycemia after antibiotic-induced gut microbiota depletion,Neurobiology of stress,2021,"Acute hypoglycemia, Epinephrine, Fecal whole genome sequencing, Microbiome, Oral antibiotics, Short chain fatty acids supplement",Experiment 4,United States of America,Mus musculus,Feces,UBERON:0001988,Response to stress,GO:0006950,Control mice,Recolonized mice (Abx + R),Group of male mice with antibiotics treatment followed by two weeks recolonization with co-housed age matched controls.,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 5A,31 January 2025,Aleru Divine,"Aleru Divine,WikiWorks","Differentially abundant taxa associated with stress response (species level) that showed significance in relative abundance between control  and Abx + R cohorts, as identified by LefSe.",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia caecimuris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus|s__Cupriavidus metallidurans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus|s__Lactiplantibacillus plantarum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|201174|84998|1643822|1643826|447020|671266;1783272|1239|186801|3085636|186803|1766253|39491;3379134|976|200643|171549|815|816|85831;3379134|1224|28216|80840|119060|106589|119219;1783272|1239|91061|186826|33958|2767842|1590;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|909656|387090;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:34401412/4/2,34401412,laboratory experiment,34401412,10.1016/j.ynstr.2021.100376,NA,"LaGamma E.F., Hu F., Pena Cruz F., Bouchev P. , Nankova B.B.",Bacteria - derived short chain fatty acids restore sympathoadrenal responsiveness to hypoglycemia after antibiotic-induced gut microbiota depletion,Neurobiology of stress,2021,"Acute hypoglycemia, Epinephrine, Fecal whole genome sequencing, Microbiome, Oral antibiotics, Short chain fatty acids supplement",Experiment 4,United States of America,Mus musculus,Feces,UBERON:0001988,Response to stress,GO:0006950,Control mice,Recolonized mice (Abx + R),Group of male mice with antibiotics treatment followed by two weeks recolonization with co-housed age matched controls.,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 5A,31 January 2025,Aleru Divine,"Aleru Divine,WikiWorks","Differentially abundant taxa associated with stress response (species level) that showed significance in relative abundance between control  and Abx + R cohorts, as identified by LefSe.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium A4,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 28-4,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp. G3(2012),k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacillati|p__Bacillota|s__Firmicutes bacterium ASF500,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 10-1,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis",1783272|1239|186801|3085636|186803|397291;1783272|1239|186801|3085636|186803|397287;1783272|1239|186801|186802|216572|244127|1235835;3379134|976|200643|171549|815|816|371601;1783272|1239|1378168;1783272|1239|186801|3085636|186803|1235800;1783272|1239|186801|3082768|990719|990721;3379134|976|200643|171549|815|816|817;1783272|1239|186801|3085636|186803|2719313|1531,Complete,Svetlana up
bsdb:34401412/5/1,34401412,laboratory experiment,34401412,10.1016/j.ynstr.2021.100376,NA,"LaGamma E.F., Hu F., Pena Cruz F., Bouchev P. , Nankova B.B.",Bacteria - derived short chain fatty acids restore sympathoadrenal responsiveness to hypoglycemia after antibiotic-induced gut microbiota depletion,Neurobiology of stress,2021,"Acute hypoglycemia, Epinephrine, Fecal whole genome sequencing, Microbiome, Oral antibiotics, Short chain fatty acids supplement",Experiment 5,United States of America,Mus musculus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Control mice,Antibiotics (Abx) mice,Group of male mice given a cocktail of non-absorbable broad-spectrum antibiotics (Abx) in the drinking water for two weeks before injection with insulin or saline.,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S1,31 January 2025,Aleru Divine,"Aleru Divine,WikiWorks","Relative abundances of dominant species identified in the control, Abx and Abx+R cohorts",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella boydii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella dysenteriae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella flexneri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella sonnei,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus",3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|543|620|621;3379134|1224|1236|91347|543|620|622;3379134|1224|1236|91347|543|620|623;3379134|1224|1236|91347|543|620|624;1783272|1239|91061|1385|90964|1279|1280,Complete,Svetlana up
bsdb:34401412/5/2,34401412,laboratory experiment,34401412,10.1016/j.ynstr.2021.100376,NA,"LaGamma E.F., Hu F., Pena Cruz F., Bouchev P. , Nankova B.B.",Bacteria - derived short chain fatty acids restore sympathoadrenal responsiveness to hypoglycemia after antibiotic-induced gut microbiota depletion,Neurobiology of stress,2021,"Acute hypoglycemia, Epinephrine, Fecal whole genome sequencing, Microbiome, Oral antibiotics, Short chain fatty acids supplement",Experiment 5,United States of America,Mus musculus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Control mice,Antibiotics (Abx) mice,Group of male mice given a cocktail of non-absorbable broad-spectrum antibiotics (Abx) in the drinking water for two weeks before injection with insulin or saline.,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table S1,31 January 2025,Aleru Divine,"Aleru Divine,WikiWorks","Relative abundances of dominant species identified in the control, Abx and Abx+R cohorts",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp. G3(2012),k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp. 5-2,k__Bacillati|p__Bacillota|s__Firmicutes bacterium ASF500,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 1-3,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus murinus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium A4,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 10-1,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 3-1,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Schaedlerella|s__Schaedlerella arabinosiphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium plexicaudatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium A2,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. 14-2",1783272|1239|186801|186802|216572|244127|1235835;1783272|1239|186801|3085636|186803|189330|1235798;1783272|1239|1378168;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|186802|216572|459786|1235797;1783272|1239|91061|186826|33958|2767887|1622;1783272|1239|186801|3085636|186803|2719313|1531;1783272|1239|186801|3085636|186803|397291;1783272|1239|186801|3085636|186803|1235800;1783272|1239|186801|3085636|186803|397288;1783272|1239|186801|186802;1783272|1239|91061|186826|33958|2742598|1598;1783272|1239|186801|3085636|186803|2676048|97139;1783272|1239|186801|186802|186806|1730|97253;1783272|1239|186801|3085636|186803|397290;1783272|1239|186801|186802|186806|1730|1235790,Complete,Svetlana up
bsdb:34401412/6/1,34401412,laboratory experiment,34401412,10.1016/j.ynstr.2021.100376,NA,"LaGamma E.F., Hu F., Pena Cruz F., Bouchev P. , Nankova B.B.",Bacteria - derived short chain fatty acids restore sympathoadrenal responsiveness to hypoglycemia after antibiotic-induced gut microbiota depletion,Neurobiology of stress,2021,"Acute hypoglycemia, Epinephrine, Fecal whole genome sequencing, Microbiome, Oral antibiotics, Short chain fatty acids supplement",Experiment 6,United States of America,Mus musculus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Control mice,Recolonized mice (Abx + R),Group of male mice with antibiotics treatment followed by two weeks recolonization with co-housed age matched controls.,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S1,31 January 2025,Aleru Divine,"Aleru Divine,WikiWorks","Relative abundances of dominant species identified in the control, Abx and Abx+R cohorts",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus|s__Cupriavidus metallidurans,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia caecimuris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",3379134|1224|28216|80840|119060|106589|119219;1783272|201174|84998|1643822|1643826|447020|671266;1783272|1239|186801|3085636|186803|1766253|39491,Complete,Svetlana up
bsdb:34401412/6/2,34401412,laboratory experiment,34401412,10.1016/j.ynstr.2021.100376,NA,"LaGamma E.F., Hu F., Pena Cruz F., Bouchev P. , Nankova B.B.",Bacteria - derived short chain fatty acids restore sympathoadrenal responsiveness to hypoglycemia after antibiotic-induced gut microbiota depletion,Neurobiology of stress,2021,"Acute hypoglycemia, Epinephrine, Fecal whole genome sequencing, Microbiome, Oral antibiotics, Short chain fatty acids supplement",Experiment 6,United States of America,Mus musculus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Control mice,Recolonized mice (Abx + R),Group of male mice with antibiotics treatment followed by two weeks recolonization with co-housed age matched controls.,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table S1,31 January 2025,Aleru Divine,"Aleru Divine,WikiWorks","Relative abundances of dominant species identified in the control, Abx and Abx+R cohorts",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp. G3(2012),k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium A4,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 10-1,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens",1783272|1239|186801|186802|216572|244127|1235835;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|3085636|186803|2719313|1531;1783272|1239|186801|3085636|186803|397291;1783272|1239|186801|3085636|186803|1235800;3379134|976|200643|171549|815|816|371601,Complete,Svetlana up
bsdb:34401412/7/1,34401412,laboratory experiment,34401412,10.1016/j.ynstr.2021.100376,NA,"LaGamma E.F., Hu F., Pena Cruz F., Bouchev P. , Nankova B.B.",Bacteria - derived short chain fatty acids restore sympathoadrenal responsiveness to hypoglycemia after antibiotic-induced gut microbiota depletion,Neurobiology of stress,2021,"Acute hypoglycemia, Epinephrine, Fecal whole genome sequencing, Microbiome, Oral antibiotics, Short chain fatty acids supplement",Experiment 7,United States of America,Mus musculus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Antibiotics (Abx) mice,Recolonized mice (Abx + R),Group of male mice with antibiotics treatment followed by two weeks recolonization with co-housed age matched controls.,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S1,31 January 2025,Aleru Divine,"Aleru Divine,WikiWorks","Relative abundances of dominant species identified in the control, Abx and Abx+R cohorts",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus|s__Cupriavidus metallidurans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus animalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium MD335,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia caecimuris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 10-1,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium plexicaudatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 28-4,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",3379134|1224|28216|80840|119060|106589|119219;1783272|1239|91061|186826|33958|2767887|1605;3379134|976|200643|171549|815|909656|387090;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|3085636|186803|1235793;1783272|201174|84998|1643822|1643826|447020|671266;1783272|1239|186801|3085636|186803|1235800;3379134|976|200643|171549|815|816|820;1783272|1239|91061|186826|33958|2742598|1598;1783272|1239|186801|186802|186806|1730|97253;1783272|1239|186801|3085636|186803|397287;3379134|976|200643|171549|2005525|375288|328812;3379134|976|200643|171549|2005525|375288|823;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|3085636|186803|1766253|39491,Complete,Svetlana up
bsdb:34401412/7/2,34401412,laboratory experiment,34401412,10.1016/j.ynstr.2021.100376,NA,"LaGamma E.F., Hu F., Pena Cruz F., Bouchev P. , Nankova B.B.",Bacteria - derived short chain fatty acids restore sympathoadrenal responsiveness to hypoglycemia after antibiotic-induced gut microbiota depletion,Neurobiology of stress,2021,"Acute hypoglycemia, Epinephrine, Fecal whole genome sequencing, Microbiome, Oral antibiotics, Short chain fatty acids supplement",Experiment 7,United States of America,Mus musculus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Antibiotics (Abx) mice,Recolonized mice (Abx + R),Group of male mice with antibiotics treatment followed by two weeks recolonization with co-housed age matched controls.,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table S1,31 January 2025,Aleru Divine,"Aleru Divine,WikiWorks","Relative abundances of dominant species identified in the control, Abx and Abx+R cohorts",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella flexneri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella sonnei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella boydii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella dysenteriae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli",3379134|1224|1236|91347|543|620|623;3379134|1224|1236|91347|543|620|624;3379134|1224|1236|91347|543|620|621;3379134|1224|1236|91347|543|620|622;3379134|1224|1236|91347|543|561|562,Complete,Svetlana up
bsdb:34407769/1/1,34407769,"cross-sectional observational, not case-control",34407769,10.1186/s12866-021-02288-x,NA,"Goolam Mahomed T., Peters R., Pretorius G., Goolam Mahomed A., Ueckermann V., Kock M.M. , Ehlers M.M.",Comparison of targeted metagenomics and IS-Pro methods for analysing the lung microbiome,BMC microbiology,2021,NA,Experiment 1,South Africa,Homo sapiens,Sputum,UBERON:0007311,Chronic obstructive pulmonary disease,EFO:0000341,Samples sequenced by IS-pro method,Samples sequenced by targeted metagenomics,"Targeted metagenomics is a method that focuses on analyzing specific regions of the microbial genome, typically V1-V3 regions of the 16s rRNA gene, to study the composition and diversity of microbial communities. While the IS-Pro method targets the intergenic spacer (IS) region between the 16 S rRNA and 23 S rRNA.",23,23,1 month,16S,123,Illumina,raw counts,DESeq2,0.01,TRUE,NA,NA,NA,NA,increased,NA,unchanged,NA,NA,Signature 1,Fig. 3,26 October 2024,KateRasheed,"KateRasheed,Svetlana up,WikiWorks",Differential abundance in the sputum microbiota of Chronic obstructive pulmonary disease (COPD) patients between IS Pro and targeted metagenomics methods.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Oleomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|2037|2049|1654;1783272|1239|91061|186826|186828|117563;3384189|32066|203490|203491|1129771|32067;3379134|1224|28211|3120395|433|217063;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:34407769/1/2,34407769,"cross-sectional observational, not case-control",34407769,10.1186/s12866-021-02288-x,NA,"Goolam Mahomed T., Peters R., Pretorius G., Goolam Mahomed A., Ueckermann V., Kock M.M. , Ehlers M.M.",Comparison of targeted metagenomics and IS-Pro methods for analysing the lung microbiome,BMC microbiology,2021,NA,Experiment 1,South Africa,Homo sapiens,Sputum,UBERON:0007311,Chronic obstructive pulmonary disease,EFO:0000341,Samples sequenced by IS-pro method,Samples sequenced by targeted metagenomics,"Targeted metagenomics is a method that focuses on analyzing specific regions of the microbial genome, typically V1-V3 regions of the 16s rRNA gene, to study the composition and diversity of microbial communities. While the IS-Pro method targets the intergenic spacer (IS) region between the 16 S rRNA and 23 S rRNA.",23,23,1 month,16S,123,Illumina,raw counts,DESeq2,0.01,TRUE,NA,NA,NA,NA,increased,NA,unchanged,NA,NA,Signature 2,Figure 3,27 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differential abundance in the sputum microbiota of COPD patients between IS Pro and targeted metagenomics methods.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia",1783272|201174|1760|85007|1653|1716;1783272|1239|1737404|1737405|1570339|543311;3379134|1224|1236|91347|1903411|613;3379134|1224|1236|72274|135621|286;1783272|1239|91061|186826|33958|1578;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3082720|186804|1257;3379134|1224|28216|206351|481|538;3379134|1224|1236|91347|543|561;1783272|201174|1760|85006|1268|1269;3379134|1224|1236|91347|1903414|583;3379134|1224|28216|206351|481|482;3379134|1224|28216|80840|119060|32008,Complete,Svetlana up
bsdb:34414134/1/1,34414134,prospective cohort,34414134,10.3389/fcimb.2021.715475,NA,"Xia G.H., Zhang M.S., Wu Q.H., Wang H.D., Zhou H.W., He Y. , Yin J.",Dysbiosis of Gut Microbiota Is an Independent Risk Factor of Stroke-Associated Pneumonia: A Chinese Pilot Study,Frontiers in cellular and infection microbiology,2021,"gut microbiota, risk, short-chain fatty acids, stroke, stroke-associated pneumonia",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Non-Stroke Associated Pneumonia (non-SAP) Training cohort,Stroke Associated Pneumonia (SAP) Training cohort,Patients with acute ischemic stroke (AIS) as the Training cohort .,136,52,3 months,16S,4,Illumina,relative abundances,LEfSe,0.1,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 2 (B),14 October 2024,Rahila,"Rahila,WikiWorks",Comparison of the microbial communities of the SAP and non-SAP groups in the training cohort using LEfSe to identified the 13 most differentially abundant taxa.,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae",1783272|1239|91061;3379134|200940|3031449|213115|194924|35832;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|1903409|551;3379134|1224|1236;1783272|1239|91061|186826;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;3379134|1224;1783272|1239|91061|186826|81852,Complete,Svetlana up
bsdb:34414134/1/2,34414134,prospective cohort,34414134,10.3389/fcimb.2021.715475,NA,"Xia G.H., Zhang M.S., Wu Q.H., Wang H.D., Zhou H.W., He Y. , Yin J.",Dysbiosis of Gut Microbiota Is an Independent Risk Factor of Stroke-Associated Pneumonia: A Chinese Pilot Study,Frontiers in cellular and infection microbiology,2021,"gut microbiota, risk, short-chain fatty acids, stroke, stroke-associated pneumonia",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Non-Stroke Associated Pneumonia (non-SAP) Training cohort,Stroke Associated Pneumonia (SAP) Training cohort,Patients with acute ischemic stroke (AIS) as the Training cohort .,136,52,3 months,16S,4,Illumina,relative abundances,LEfSe,0.1,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,FIG 2 (B),14 October 2024,Rahila,"Rahila,WikiWorks",Comparison of the microbial communities of the SAP and non-SAP groups in the training cohort using LEfSe to identified the 13 most differentially abundant taxa.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,1783272|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:34414134/2/1,34414134,prospective cohort,34414134,10.3389/fcimb.2021.715475,NA,"Xia G.H., Zhang M.S., Wu Q.H., Wang H.D., Zhou H.W., He Y. , Yin J.",Dysbiosis of Gut Microbiota Is an Independent Risk Factor of Stroke-Associated Pneumonia: A Chinese Pilot Study,Frontiers in cellular and infection microbiology,2021,"gut microbiota, risk, short-chain fatty acids, stroke, stroke-associated pneumonia",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Non-Stroke Associated Pneumonia (non-SAP) independent cohort,Stroke Associated Pneumonia (SAP) independent cohort,Patients with acute ischemic stroke (AIS) as the independent cohort .,116,28,3 months,16S,4,Illumina,relative abundances,LEfSe,0.1,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure (S2B),14 October 2024,Rahila,"Rahila,WikiWorks",Comparison of the microbial communities of the SAP and non-SAP groups in the  validation cohort using  LEfSe to identified the most differentially abundant taxon between the two groups.,increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",3379134|200940|3031449|213115|194924|872;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236;1783272|1239|91061|186826;3379134|1224;3379134|976|200643|171549|171550;3379134|1224|1236|91347|543|547;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958,Complete,Svetlana up
bsdb:34414134/2/2,34414134,prospective cohort,34414134,10.3389/fcimb.2021.715475,NA,"Xia G.H., Zhang M.S., Wu Q.H., Wang H.D., Zhou H.W., He Y. , Yin J.",Dysbiosis of Gut Microbiota Is an Independent Risk Factor of Stroke-Associated Pneumonia: A Chinese Pilot Study,Frontiers in cellular and infection microbiology,2021,"gut microbiota, risk, short-chain fatty acids, stroke, stroke-associated pneumonia",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Non-Stroke Associated Pneumonia (non-SAP) independent cohort,Stroke Associated Pneumonia (SAP) independent cohort,Patients with acute ischemic stroke (AIS) as the independent cohort .,116,28,3 months,16S,4,Illumina,relative abundances,LEfSe,0.1,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure (S2B),14 October 2024,Rahila,"Rahila,WikiWorks",Comparison of the microbial communities of the SAP and non-SAP groups in the  validation cohort using  LEfSe to identified the most differentially abundant taxon between the two groups.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976|200643|171549;3379134|1224|1236|135625;3379134|1224|1236|135625|712;3379134|1224|1236|135625|712|724;3379134|1224|28216|80840;3379134|1224|28216;3379134|1224|28216|80840|995019|40544;3379134|1224|28216|80840|506;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|33042,Complete,Svetlana up
bsdb:34414134/3/1,34414134,prospective cohort,34414134,10.3389/fcimb.2021.715475,NA,"Xia G.H., Zhang M.S., Wu Q.H., Wang H.D., Zhou H.W., He Y. , Yin J.",Dysbiosis of Gut Microbiota Is an Independent Risk Factor of Stroke-Associated Pneumonia: A Chinese Pilot Study,Frontiers in cellular and infection microbiology,2021,"gut microbiota, risk, short-chain fatty acids, stroke, stroke-associated pneumonia",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Non-Stroke Associated Pneumonia (non-SAP) subgroup in the training cohort,Stroke Associated Pneumonia (SAP) subgroup in the training cohort,Patients with acute ischemic stroke (AIS) as the subgroup in the training cohort.,25,25,3 months,16S,4,Illumina,relative abundances,LEfSe,0.1,FALSE,2,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S4B,15 October 2024,Rahila,"Rahila,KateRasheed,WikiWorks",Comparison of the microbial communities of the SAP and non-SAP groups in the  subset of the training cohort using LEfSe to identified the most differentially abundant taxon between the two groups.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio",3379134|1224|1236|135624;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|1903409|551;3379134|1224|1236|135624|83763|83770,Complete,Svetlana up
bsdb:34414134/3/2,34414134,prospective cohort,34414134,10.3389/fcimb.2021.715475,NA,"Xia G.H., Zhang M.S., Wu Q.H., Wang H.D., Zhou H.W., He Y. , Yin J.",Dysbiosis of Gut Microbiota Is an Independent Risk Factor of Stroke-Associated Pneumonia: A Chinese Pilot Study,Frontiers in cellular and infection microbiology,2021,"gut microbiota, risk, short-chain fatty acids, stroke, stroke-associated pneumonia",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Non-Stroke Associated Pneumonia (non-SAP) subgroup in the training cohort,Stroke Associated Pneumonia (SAP) subgroup in the training cohort,Patients with acute ischemic stroke (AIS) as the subgroup in the training cohort.,25,25,3 months,16S,4,Illumina,relative abundances,LEfSe,0.1,FALSE,2,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S4B,15 October 2024,Rahila,"Rahila,KateRasheed,WikiWorks",Comparison of the microbial communities of the SAP and non-SAP groups in the  subset of the training cohort using LEfSe to identified the most differentially abundant taxon between the two groups.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|186802|186807|51514;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:34414134/4/1,34414134,prospective cohort,34414134,10.3389/fcimb.2021.715475,NA,"Xia G.H., Zhang M.S., Wu Q.H., Wang H.D., Zhou H.W., He Y. , Yin J.",Dysbiosis of Gut Microbiota Is an Independent Risk Factor of Stroke-Associated Pneumonia: A Chinese Pilot Study,Frontiers in cellular and infection microbiology,2021,"gut microbiota, risk, short-chain fatty acids, stroke, stroke-associated pneumonia",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Non-Stroke Associated Pneumonia (non-SAP) Training cohort,Stroke Associated Pneumonia (SAP) Training cohort,Patients with acute ischemic stroke (AIS) as the Training cohort .,136,52,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 2C,8 January 2025,KateRasheed,"KateRasheed,WikiWorks",Comparison of the microbial communities of the SAP and non-SAP groups in the training cohort using Mann-Whitney,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,1783272|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:34414134/4/2,34414134,prospective cohort,34414134,10.3389/fcimb.2021.715475,NA,"Xia G.H., Zhang M.S., Wu Q.H., Wang H.D., Zhou H.W., He Y. , Yin J.",Dysbiosis of Gut Microbiota Is an Independent Risk Factor of Stroke-Associated Pneumonia: A Chinese Pilot Study,Frontiers in cellular and infection microbiology,2021,"gut microbiota, risk, short-chain fatty acids, stroke, stroke-associated pneumonia",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Non-Stroke Associated Pneumonia (non-SAP) Training cohort,Stroke Associated Pneumonia (SAP) Training cohort,Patients with acute ischemic stroke (AIS) as the Training cohort .,136,52,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 2C,8 January 2025,KateRasheed,"KateRasheed,WikiWorks",Comparison of the microbial communities of the SAP and non-SAP groups in the training cohort using Mann-Whitney,increased,"k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|1224;1783272|1239|91061;3379134|1224|1236;1783272|1239|91061|186826;1783272|1239|91061|186826|81852;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|976|200643|171549|171551;3379134|1224|1236|91347|1903409|551;1783272|1239|91061|186826|81852|1350;3379134|200940|3031449|213115|194924|35832;3379134|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:34414134/5/1,34414134,prospective cohort,34414134,10.3389/fcimb.2021.715475,NA,"Xia G.H., Zhang M.S., Wu Q.H., Wang H.D., Zhou H.W., He Y. , Yin J.",Dysbiosis of Gut Microbiota Is an Independent Risk Factor of Stroke-Associated Pneumonia: A Chinese Pilot Study,Frontiers in cellular and infection microbiology,2021,"gut microbiota, risk, short-chain fatty acids, stroke, stroke-associated pneumonia",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Non-Stroke Associated Pneumonia (non-SAP) subgroup in the training cohort,Stroke Associated Pneumonia (SAP) subgroup in the training cohort,Patients with acute ischemic stroke (AIS) as the subgroup in the training cohort.,25,25,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,FALSE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. S4C,8 January 2025,KateRasheed,"KateRasheed,WikiWorks",Comparison of the microbial communities of the subset of SAP and non-SAP groups in the training cohort using Mann-Whitney,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia",1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|1903409|551,Complete,Svetlana up
bsdb:34414134/5/2,34414134,prospective cohort,34414134,10.3389/fcimb.2021.715475,NA,"Xia G.H., Zhang M.S., Wu Q.H., Wang H.D., Zhou H.W., He Y. , Yin J.",Dysbiosis of Gut Microbiota Is an Independent Risk Factor of Stroke-Associated Pneumonia: A Chinese Pilot Study,Frontiers in cellular and infection microbiology,2021,"gut microbiota, risk, short-chain fatty acids, stroke, stroke-associated pneumonia",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Non-Stroke Associated Pneumonia (non-SAP) subgroup in the training cohort,Stroke Associated Pneumonia (SAP) subgroup in the training cohort,Patients with acute ischemic stroke (AIS) as the subgroup in the training cohort.,25,25,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,FALSE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. S4C,8 January 2025,KateRasheed,"KateRasheed,WikiWorks",Comparison of the microbial communities of the subset of SAP and non-SAP groups in the training cohort using Mann-Whitney,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,1783272|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:34414134/6/1,34414134,prospective cohort,34414134,10.3389/fcimb.2021.715475,NA,"Xia G.H., Zhang M.S., Wu Q.H., Wang H.D., Zhou H.W., He Y. , Yin J.",Dysbiosis of Gut Microbiota Is an Independent Risk Factor of Stroke-Associated Pneumonia: A Chinese Pilot Study,Frontiers in cellular and infection microbiology,2021,"gut microbiota, risk, short-chain fatty acids, stroke, stroke-associated pneumonia",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Non-Stroke Associated Pneumonia (non-SAP),Stroke Associated Pneumonia (non-SAP),Stroke Associated Pneumonia (non-SAP) refers to patients with stroke associated pneumonia (SAP),NA,NA,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. S6A,8 January 2025,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa in stroke patients.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:34414134/7/1,34414134,prospective cohort,34414134,10.3389/fcimb.2021.715475,NA,"Xia G.H., Zhang M.S., Wu Q.H., Wang H.D., Zhou H.W., He Y. , Yin J.",Dysbiosis of Gut Microbiota Is an Independent Risk Factor of Stroke-Associated Pneumonia: A Chinese Pilot Study,Frontiers in cellular and infection microbiology,2021,"gut microbiota, risk, short-chain fatty acids, stroke, stroke-associated pneumonia",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Pneumonia severity measurement,EFO:0010966,Low Pneumonia Severity Index (Low-PSI),High Pneumonia Severity Index (High-PSI),High Pneumonia Severity Index (High-PSI) refers to patients with severe pneumonia,NA,NA,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. S6B,8 January 2025,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between low pneumonia severity index and high pneumonia severity index.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:34414134/8/1,34414134,prospective cohort,34414134,10.3389/fcimb.2021.715475,NA,"Xia G.H., Zhang M.S., Wu Q.H., Wang H.D., Zhou H.W., He Y. , Yin J.",Dysbiosis of Gut Microbiota Is an Independent Risk Factor of Stroke-Associated Pneumonia: A Chinese Pilot Study,Frontiers in cellular and infection microbiology,2021,"gut microbiota, risk, short-chain fatty acids, stroke, stroke-associated pneumonia",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Non-Stroke Associated Pneumonia (non-SAP) Training cohort,Stroke Associated Pneumonia (SAP) Training cohort,Patients with acute ischemic stroke (AIS) as the Training cohort .,136,52,3 months,16S,4,Illumina,log transformation,Logistic Regression,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,8 January 2025,KateRasheed,"KateRasheed,WikiWorks",Relative abundance of selected microbial taxa in patients with and without SAP in the training cohort.,increased,"k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|1224;1783272|1239|91061;3379134|1224|1236;1783272|1239|91061|186826;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;3379134|976|200643|171549|171551;3379134|1224|1236|91347|1903409|551;1783272|1239|91061|186826|81852|1350;3379134|200940|3031449|213115|194924|35832;3379134|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:34414134/8/2,34414134,prospective cohort,34414134,10.3389/fcimb.2021.715475,NA,"Xia G.H., Zhang M.S., Wu Q.H., Wang H.D., Zhou H.W., He Y. , Yin J.",Dysbiosis of Gut Microbiota Is an Independent Risk Factor of Stroke-Associated Pneumonia: A Chinese Pilot Study,Frontiers in cellular and infection microbiology,2021,"gut microbiota, risk, short-chain fatty acids, stroke, stroke-associated pneumonia",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Non-Stroke Associated Pneumonia (non-SAP) Training cohort,Stroke Associated Pneumonia (SAP) Training cohort,Patients with acute ischemic stroke (AIS) as the Training cohort .,136,52,3 months,16S,4,Illumina,log transformation,Logistic Regression,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,8 January 2025,KateRasheed,"KateRasheed,WikiWorks",Relative abundance of selected microbial taxa in patients with and without SAP in the training cohort.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,1783272|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:34414134/9/1,34414134,prospective cohort,34414134,10.3389/fcimb.2021.715475,NA,"Xia G.H., Zhang M.S., Wu Q.H., Wang H.D., Zhou H.W., He Y. , Yin J.",Dysbiosis of Gut Microbiota Is an Independent Risk Factor of Stroke-Associated Pneumonia: A Chinese Pilot Study,Frontiers in cellular and infection microbiology,2021,"gut microbiota, risk, short-chain fatty acids, stroke, stroke-associated pneumonia",Experiment 9,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Non-Stroke Associated Pneumonia (non-SAP) validation cohort,Stroke Associated Pneumonia (SAP) validation cohort,Patients with acute ischemic stroke (AIS) as the validation cohort .,116,28,3 months,16S,4,Illumina,log transformation,Logistic Regression,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S2,8 January 2025,KateRasheed,"KateRasheed,WikiWorks",Relative abundance of selected microbial taxa in patients with and without SAP in the validation cohort.,increased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",3379134|1224;3379134|1224|1236;1783272|1239|91061;1783272|1239|91061|186826;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852|1350,Complete,Svetlana up
bsdb:34414134/9/2,34414134,prospective cohort,34414134,10.3389/fcimb.2021.715475,NA,"Xia G.H., Zhang M.S., Wu Q.H., Wang H.D., Zhou H.W., He Y. , Yin J.",Dysbiosis of Gut Microbiota Is an Independent Risk Factor of Stroke-Associated Pneumonia: A Chinese Pilot Study,Frontiers in cellular and infection microbiology,2021,"gut microbiota, risk, short-chain fatty acids, stroke, stroke-associated pneumonia",Experiment 9,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Non-Stroke Associated Pneumonia (non-SAP) validation cohort,Stroke Associated Pneumonia (SAP) validation cohort,Patients with acute ischemic stroke (AIS) as the validation cohort .,116,28,3 months,16S,4,Illumina,log transformation,Logistic Regression,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S2,8 January 2025,KateRasheed,"KateRasheed,WikiWorks",Relative abundance of selected microbial taxa in patients with and without SAP in the validation cohort.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,1783272|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:34423593/1/1,34423593,prospective cohort,34423593,10.1002/advs.202102785,NA,"Gao M., Wang H., Luo H., Sun Y., Wang L., Ding S., Ren H., Gang J., Rao B., Liu S., Wang X., Gao X., Li M., Zou Y., Liu C., Yuan C., Sun J., Cui G. , Ren Z.",Characterization of the Human Oropharyngeal Microbiomes in SARS-CoV-2 Infection and Recovery Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2021,"COVID-19, SARS-CoV-2, noninvasive biomarkers, oropharyngeal microbiome",Experiment 1,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,COVID-19 cases,Confirmed COVID-19 cases by RT-PCR,48,94,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,"age,body mass index,sex",NA,NA,decreased,NA,decreased,NA,NA,Signature 1,"Figure 3b, 3d",28 September 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between COVID-19 cases and healthy controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,,k__Bacillati|p__Bacillota",3379134|1224|1236|135619|28256|2745;1783272|1239|91061|186826|186828|117563;3384189|32066|203490|203491|1129771|32067;1783272|1239|91061|186826|1300|1301;;1783272|1239,Complete,Claregrieve1
bsdb:34423593/1/2,34423593,prospective cohort,34423593,10.1002/advs.202102785,NA,"Gao M., Wang H., Luo H., Sun Y., Wang L., Ding S., Ren H., Gang J., Rao B., Liu S., Wang X., Gao X., Li M., Zou Y., Liu C., Yuan C., Sun J., Cui G. , Ren Z.",Characterization of the Human Oropharyngeal Microbiomes in SARS-CoV-2 Infection and Recovery Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2021,"COVID-19, SARS-CoV-2, noninvasive biomarkers, oropharyngeal microbiome",Experiment 1,China,Homo sapiens,Oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,COVID-19 cases,Confirmed COVID-19 cases by RT-PCR,48,94,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,"age,body mass index,sex",NA,NA,decreased,NA,decreased,NA,NA,Signature 2,"Figure 3b, 3d",28 September 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between COVID-19 cases and healthy controls,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota,,k__Pseudomonadati|p__Campylobacterota,k__Pseudomonadati|p__Spirochaetota,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales,k__Thermotogati|p__Synergistota,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",3379134|976;3379134|1224;;3379134|29547;3379134|203691;3379134|200940|3024418|213118;3384194|508458;3379134|200930|68337;3379134|74201;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|1283313;3384189|32066|203490|203491|203492|848;3379134|1224|1236|135625|712|724,Complete,Claregrieve1
bsdb:34425246/1/1,34425246,"cross-sectional observational, not case-control",34425246,10.1016/j.micinf.2021.104880,NA,"Gupta A., Karyakarte R., Joshi S., Das R., Jani K., Shouche Y. , Sharma A.",Nasopharyngeal microbiome reveals the prevalence of opportunistic pathogens in SARS-CoV-2 infected individuals and their association with host types,Microbes and infection,2021,"SARS-CoV-2, asymptomatic, host types, nasopharyngeal microbiome, symptomatic",Experiment 1,India,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Non-infected controls,COVID-19 cases,COVID-19 infected individuals,26,63,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Supplementary Info - Figure 1,27 September 2021,Claregrieve1,"Claregrieve1,WikiWorks",Differential abundance of microbial taxa between infected and non-infected individuals,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,Peace Sandy
bsdb:34425246/1/2,34425246,"cross-sectional observational, not case-control",34425246,10.1016/j.micinf.2021.104880,NA,"Gupta A., Karyakarte R., Joshi S., Das R., Jani K., Shouche Y. , Sharma A.",Nasopharyngeal microbiome reveals the prevalence of opportunistic pathogens in SARS-CoV-2 infected individuals and their association with host types,Microbes and infection,2021,"SARS-CoV-2, asymptomatic, host types, nasopharyngeal microbiome, symptomatic",Experiment 1,India,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Non-infected controls,COVID-19 cases,COVID-19 infected individuals,26,63,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,"Supplementary Info - Figure 1, Figure 2a-b",27 September 2021,Claregrieve1,"Claregrieve1,Peace Sandy,WikiWorks",Differential abundance of microbial taxa between infected and non-infected individuals,decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",1783272|1239;3379134|976;3384189|32066|203490|203491|203492;3384189|32066|203490|203491|203492|848;3379134|1224|1236|135625|712|724;3384189|32066|203490|203491|1129771;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481;3379134|976|200643|171549|171552;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171551,Complete,Peace Sandy
bsdb:34436669/1/1,34436669,case-control,34436669,10.1007/s00784-021-04137-7,NA,"Gopinath D., Wie C.C., Banerjee M., Thangavelu L., Kumar R P., Nallaswamy D., Botelho M.G. , Johnson N.W.",Compositional profile of mucosal bacteriome of smokers and smokeless tobacco users,Clinical oral investigations,2022,"Microbiome, Microbiota, Oral microbiome, Smokeless tobacco, Smoking, Tobacco",Experiment 1,India,Homo sapiens,Buccal mucosa,UBERON:0006956,Chewing tobacco behavior,EFO:0004774,age-matched controls,smokeless tobacco users,Smokeless tobacco users with or without areca nut.,13,14,NA,16S,34,Illumina,raw counts,DESeq2,0.01,NA,NA,"age,sex",NA,increased,increased,NA,increased,NA,NA,Signature 1,Figure 5,13 June 2023,Atrayees,"Atrayees,Lwaldron,WikiWorks",Differentially abundant taxa identified in smokeless tobacco users and controls using DESeq2.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces plicatus",1783272|1239|186801|3085636|186803|43996;3384194|508458|649775|649776|3029087|1434006;1783272|201174|1760|85011|2062|1883|1922,Complete,Lwaldron
bsdb:34436669/2/1,34436669,case-control,34436669,10.1007/s00784-021-04137-7,NA,"Gopinath D., Wie C.C., Banerjee M., Thangavelu L., Kumar R P., Nallaswamy D., Botelho M.G. , Johnson N.W.",Compositional profile of mucosal bacteriome of smokers and smokeless tobacco users,Clinical oral investigations,2022,"Microbiome, Microbiota, Oral microbiome, Smokeless tobacco, Smoking, Tobacco",Experiment 2,India,Homo sapiens,Buccal mucosa,UBERON:0006956,Smoking behavior,EFO:0004318,age-matched controls,Smokers who were using either bidis or cigarettes,"Smokers who were using either bidis (thin, hand-rolled cigarettes composed of tobacco wrapped in a “tendu” or “temburni” leaf) or cigarettes",13,17,NA,16S,34,Illumina,raw counts,DESeq2,0.01,NA,NA,"age,sex",NA,increased,increased,NA,increased,NA,NA,Signature 1,Figure 5,13 June 2023,Atrayees,"Atrayees,Lwaldron,WikiWorks",Differentially abundant taxa identified in smokers and controls using DESeq2.,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,p__Candidatus Saccharimonadota",3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|177971;95818,Complete,Lwaldron
bsdb:34436669/3/1,34436669,case-control,34436669,10.1007/s00784-021-04137-7,NA,"Gopinath D., Wie C.C., Banerjee M., Thangavelu L., Kumar R P., Nallaswamy D., Botelho M.G. , Johnson N.W.",Compositional profile of mucosal bacteriome of smokers and smokeless tobacco users,Clinical oral investigations,2022,"Microbiome, Microbiota, Oral microbiome, Smokeless tobacco, Smoking, Tobacco",Experiment 3,India,Homo sapiens,Buccal mucosa,UBERON:0006956,Smoking behavior,EFO:0004318,Smokeless tobacco users,Smokers,Smokers who were using either bidis or cigarettes,14,17,NA,16S,34,Illumina,raw counts,DESeq2,0.01,NA,NA,"age,sex",NA,increased,increased,NA,increased,NA,NA,Signature 1,Figure 5,13 June 2023,Atrayees,"Atrayees,WikiWorks",Differentially abundant taxa identified in smokeless tobacco users and smokers using DESeq2.,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter",3384189|32066|203490|203491|203492|848;3379134|29547|3031852|213849|72294|194,Complete,Lwaldron
bsdb:34442626/1/1,34442626,case-control,34442626,10.3390/microorganisms9081548,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8401100/,"Fang C.Y., Chen J.S., Hsu B.M., Hussain B., Rathod J. , Lee K.H.",Colorectal Cancer Stage-Specific Fecal Bacterial Community Fingerprinting of the Taiwanese Population and Underpinning of Potential Taxonomic Biomarkers,Microorganisms,2021,"biomarker, colorectal cancer, functional predictions, gut microbial dysbiosis, gut microbiota, metagenomics, prognosis",Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy subjects,colorectal cancer patients,persons aged 25–95 years old with cancerous large intestine tumor symptoms,17,21,1 month,16S,34,Illumina,relative abundances,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 4,5 January 2022,Itslanapark,"Itslanapark,Chloe,WikiWorks",differential abundance of bacteria in patients with colorectal cancer and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Coriobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Coxiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Limnobacter,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sporobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinatimonas,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Haloferula",1783272|1239|91061|186826|186827|46123;3379134|1224|1236|2887326|468|469;1783272|201174|84998|84999|84107|33870;3379134|1224|1236|118969|118968|776;1783272|1239|91061|186826|33958|1243;3379134|1224|28216|80840|119060|131079;3366610|28890|183925|2158|2159|2172;1783272|201174|1760|85006|1268|32207;1783272|1239|186801|3085636|186803|100132;3379134|1224|1236|135624|83763|674963;3379134|74201|203494|48461|203557|574899,Complete,Chloe
bsdb:34442626/1/2,34442626,case-control,34442626,10.3390/microorganisms9081548,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8401100/,"Fang C.Y., Chen J.S., Hsu B.M., Hussain B., Rathod J. , Lee K.H.",Colorectal Cancer Stage-Specific Fecal Bacterial Community Fingerprinting of the Taiwanese Population and Underpinning of Potential Taxonomic Biomarkers,Microorganisms,2021,"biomarker, colorectal cancer, functional predictions, gut microbial dysbiosis, gut microbiota, metagenomics, prognosis",Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,healthy subjects,colorectal cancer patients,persons aged 25–95 years old with cancerous large intestine tumor symptoms,17,21,1 month,16S,34,Illumina,relative abundances,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 4,5 January 2022,Itslanapark,"Itslanapark,Chloe,WikiWorks",differential abundance of bacteria in patients with colorectal cancer and healthy controls,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,1783272|1239|186801|186802|216572|119852,Complete,Chloe
bsdb:34442626/2/1,34442626,case-control,34442626,10.3390/microorganisms9081548,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8401100/,"Fang C.Y., Chen J.S., Hsu B.M., Hussain B., Rathod J. , Lee K.H.",Colorectal Cancer Stage-Specific Fecal Bacterial Community Fingerprinting of the Taiwanese Population and Underpinning of Potential Taxonomic Biomarkers,Microorganisms,2021,"biomarker, colorectal cancer, functional predictions, gut microbial dysbiosis, gut microbiota, metagenomics, prognosis",Experiment 2,Taiwan,Homo sapiens,Feces,UBERON:0001988,Intestinal polyp,EFO:0003855,healthy subjects,polyps patients,persons aged 25–95 years old with polyps,17,21,1 month,16S,NA,Illumina,NA,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 4,8 March 2023,Chloe,"Chloe,WikiWorks","The post hoc plots of enriched bacterial genera among three health conditions (healthy, polyps, and cancer). The left side of these figures shows the abundance ratio of differentially enriched bacterial genera. The right side represents the significant difference at p < 0.05, whereas the middle one indicates the mean proportion of differentially enriched bacterial genera in the 95% confidence interval.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella",1783272|1239|186801|186802|216572|244127;1783272|1239|909932|909929|1843491|52225,Complete,Chloe
bsdb:34442626/2/2,34442626,case-control,34442626,10.3390/microorganisms9081548,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8401100/,"Fang C.Y., Chen J.S., Hsu B.M., Hussain B., Rathod J. , Lee K.H.",Colorectal Cancer Stage-Specific Fecal Bacterial Community Fingerprinting of the Taiwanese Population and Underpinning of Potential Taxonomic Biomarkers,Microorganisms,2021,"biomarker, colorectal cancer, functional predictions, gut microbial dysbiosis, gut microbiota, metagenomics, prognosis",Experiment 2,Taiwan,Homo sapiens,Feces,UBERON:0001988,Intestinal polyp,EFO:0003855,healthy subjects,polyps patients,persons aged 25–95 years old with polyps,17,21,1 month,16S,NA,Illumina,NA,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 4,8 March 2023,Chloe,"Chloe,WikiWorks","The post hoc plots of enriched bacterial genera among three health conditions (healthy, polyps, and cancer). The left side of these figures shows the abundance ratio of differentially enriched bacterial genera. The right side represents the significant difference at p < 0.05, whereas the middle one indicates the mean proportion of differentially enriched bacterial genera in the 95% confidence interval.",decreased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae|g__Cytophaga",3379134|29547|3031852|213849|72294|194;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|72274|135621|286;3379134|976|768503|768507|89373|978,Complete,Chloe
bsdb:34442626/3/1,34442626,case-control,34442626,10.3390/microorganisms9081548,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8401100/,"Fang C.Y., Chen J.S., Hsu B.M., Hussain B., Rathod J. , Lee K.H.",Colorectal Cancer Stage-Specific Fecal Bacterial Community Fingerprinting of the Taiwanese Population and Underpinning of Potential Taxonomic Biomarkers,Microorganisms,2021,"biomarker, colorectal cancer, functional predictions, gut microbial dysbiosis, gut microbiota, metagenomics, prognosis",Experiment 3,Taiwan,Homo sapiens,Feces,UBERON:0001988,Intestinal polyp,EFO:0003855,polyps patients,cancer patients,persons aged 25–95 years old with cancerous large intestine tumor symptoms,21,21,1 month,16S,NA,Illumina,NA,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 4,8 March 2023,Chloe,"Chloe,WikiWorks","The post hoc plots of enriched bacterial genera among three health conditions (healthy, polyps, and cancer). The left side of these figures shows the abundance ratio of differentially enriched bacterial genera. The right side represents the significant difference at p < 0.05, whereas the middle one indicates the mean proportion of differentially enriched bacterial genera in the 95% confidence interval.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Coriobacterium,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Coxiella,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Haloferula,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",1783272|201174|1760|2037|2049|1654;3379134|29547|3031852|213849|72294|194;1783272|1239|91061|186826|81852|1350;1783272|201174|84998|1643822|1643826|84108;3384194|508458|649775|649776|3029088|638847;1783272|201174|84998|84999|84107|33870;3366610|28890|183925|2158|2159|2172;1783272|1239|186801|3082720|186804|1257;1783272|1239|91061|186826|186827|46123;3379134|1224|1236|118969|118968|776;3379134|74201|203494|48461|203557|574899;1783272|1239|91061|186826|33958|1243;1783272|1239|91061|186826|33958|46255,Complete,Chloe
bsdb:34442626/3/2,34442626,case-control,34442626,10.3390/microorganisms9081548,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8401100/,"Fang C.Y., Chen J.S., Hsu B.M., Hussain B., Rathod J. , Lee K.H.",Colorectal Cancer Stage-Specific Fecal Bacterial Community Fingerprinting of the Taiwanese Population and Underpinning of Potential Taxonomic Biomarkers,Microorganisms,2021,"biomarker, colorectal cancer, functional predictions, gut microbial dysbiosis, gut microbiota, metagenomics, prognosis",Experiment 3,Taiwan,Homo sapiens,Feces,UBERON:0001988,Intestinal polyp,EFO:0003855,polyps patients,cancer patients,persons aged 25–95 years old with cancerous large intestine tumor symptoms,21,21,1 month,16S,NA,Illumina,NA,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 4,8 March 2023,Chloe,"Chloe,WikiWorks",NA,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sporobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus",3379134|1224|1236|135624|84642|642;1783272|1239|186801|3085636|186803|100132;1783272|1239|186801|186802|216572|119852;1783272|1239|909932|909929|1843491|52225;3384189|32066|203490|203491|1129771|34104,Complete,Chloe
bsdb:34442687/1/1,34442687,"cross-sectional observational, not case-control",34442687,10.3390/microorganisms9081608,https://pubmed.ncbi.nlm.nih.gov/34442687/,"Lewis C.R., Bonham K.S., McCann S.H., Volpe A.R., D'Sa V., Naymik M., De Both M.D., Huentelman M.J., Lemery-Chalfant K., Highlander S.K., Deoni S.C.L. , Klepac-Ceraj V.",Family SES Is Associated with the Gut Microbiome in Infants and Children,Microorganisms,2021,"childhood, infant, microbiome, socioeconomic status, stress",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,lower socioeconomic status,Increasing socioeconomic status,588 Metagenomics from infants and children of high and low socioeconomic families as continuous variables.,NA,NA,2 weeks,WMS,NA,Illumina,relative abundances,NA,0.05,NA,NA,NA,"age,delivery procedure,race,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,FIGURE 2; FIGURE 3,6 June 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks","Figure 2. Model Taxonomic Summaries. Stacked bar plots showing the average relative abundance of the genera assessed with socioeconomic status (SES).


Variables are continuous measures. Each of the gut microbiomes increases for a 1 unit increase in SES.

Figure 3. Parents with higher SES(higher years of education) had children who scored higher in the latent microbiome factor. That is, they were higher on Faecalibacterium, Eubacterium, Anaerostipes, and Lachnospiraceae compared with the scores of infants and children from low SES families.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803,Complete,Chloe
bsdb:34442687/1/2,34442687,"cross-sectional observational, not case-control",34442687,10.3390/microorganisms9081608,https://pubmed.ncbi.nlm.nih.gov/34442687/,"Lewis C.R., Bonham K.S., McCann S.H., Volpe A.R., D'Sa V., Naymik M., De Both M.D., Huentelman M.J., Lemery-Chalfant K., Highlander S.K., Deoni S.C.L. , Klepac-Ceraj V.",Family SES Is Associated with the Gut Microbiome in Infants and Children,Microorganisms,2021,"childhood, infant, microbiome, socioeconomic status, stress",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,lower socioeconomic status,Increasing socioeconomic status,588 Metagenomics from infants and children of high and low socioeconomic families as continuous variables.,NA,NA,2 weeks,WMS,NA,Illumina,relative abundances,NA,0.05,NA,NA,NA,"age,delivery procedure,race,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,FIGURE 3,6 June 2022,Kaluifeanyi101,"Kaluifeanyi101,WikiWorks","Parents with higher SES (higher years of education) had children who scored lower 
in Bacteroides relative abundance compared with infants and children from families of low SES.

 Variables are continuous measures. The gut microbiome decreases for a 1 unit increase in SES.",decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,Chloe
bsdb:34442739/1/1,34442739,case-control,34442739,10.3390/microorganisms9081657,NA,"Esberg A., Johansson L., Johansson I. , Dahlqvist S.R.",Oral Microbiota Identifies Patients in Early Onset Rheumatoid Arthritis,Microorganisms,2021,"16S rDNA sequencing, oral microbiota, periodontitis, rheumatoid arthritis",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,Healthy Controls,Early Rheumatoid Arthritis,Patients with Early Rheumatoid Arthritis,59,61,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,increased,NA,NA,NA,increased,Signature 1,Figure 3 (B),2 November 2022,Tislam,"Tislam,Peace Sandy,WikiWorks",(b) Bar graph showing species and genera with an LDA score > 2.0. A star (*) by the species indicates that it was detected as influential in the OPLS-DA model too,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium polymorphum,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 314,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium vincentii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella pleuritidis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella veroralis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter sp.,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 349,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella saccharolytica,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella maculosa,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella dentalis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia|s__Bulleidia extructa,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium sp.,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Pseudomonadati|p__Bacteroidota",3379134|976|200643|171549|171552|1283313|76122;3384189|32066|203490|203491|203492|848|76857;3379134|976|117743|200644|49546|1016|327575;3379134|976|200643|171549|171552|838|712464;3379134|976|200643|171549|171551|836|28124;3384189|32066|203490|203491|203492|848|155615;3379134|1224|28216|206351|481|482|495;3379134|976|200643|171549|171552|838|28131;3379134|976|200643|171549|171552|2974257|407975;3379134|976|200643|171549|171552|838|28137;3379134|1224|1236|135625|712|416916|1872413;3379134|203691|203692|136|2845253|157|158;3379134|29547|3031852|213849|72294|194|824;1783272|1239|186801|3082720|3118655|44259|143361;1783272|1239|1737404|1737405|1570339|543311|33033;95818|713051;3379134|976|200643|171549|171552|2974257|633701;3379134|203691|203692|136|2845253|157|166;3379134|976|200643|171549|171552|2974251|439703;3379134|976|200643|171549|171552|838|52227;1783272|1239|526524|526525|128827|118747|118748;3384194|508458|649775|649776|3029087|1434006|2699746;3379134|976|117743|200644|49546|1016;3379134|203691|203692|136|2845253|157;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3082720|3118655|44259;3384194|508458|649775|649776|3029087|1434006;1783272|1239|526524|526525|128827|118747;3379134|976,Complete,Peace Sandy
bsdb:34442739/1/2,34442739,case-control,34442739,10.3390/microorganisms9081657,NA,"Esberg A., Johansson L., Johansson I. , Dahlqvist S.R.",Oral Microbiota Identifies Patients in Early Onset Rheumatoid Arthritis,Microorganisms,2021,"16S rDNA sequencing, oral microbiota, periodontitis, rheumatoid arthritis",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Rheumatoid arthritis,EFO:0000685,Healthy Controls,Early Rheumatoid Arthritis,Patients with Early Rheumatoid Arthritis,59,61,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,increased,NA,NA,NA,increased,Signature 2,Figure 3 (B),2 November 2022,Tislam,"Tislam,Peace Sandy,WikiWorks",(b) Bar graph showing species and genera with an LDA score > 2.0. A star (*) by the species indicates that it was detected as influential in the OPLS-DA model too,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella morbi,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__uncultured Stomatobaculum sp.",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049|1654|29317;3379134|29547|3031852|213849|72294|194|199;1783272|1239|186801|3085636|186803|43996;1783272|1239|186801|3085636|186803|43996|43997;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|80840|119060|47670|47671;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|3085636|186803|265975|237576;1783272|1239|186801|3085636|186803|1213720;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|423477;1783272|1239|186801|3085636|186803|1213720|1662277,Complete,Peace Sandy
bsdb:34444813/1/1,34444813,"cross-sectional observational, not case-control",34444813,10.3390/nu13082645,https://pubmed.ncbi.nlm.nih.gov/34444813/,"Lapidot Y., Reshef L., Goldsmith R., Na'amnih W., Kassem E., Ornoy A., Gophna U. , Muhsen K.",The Associations between Diet and Socioeconomic Disparities and the Intestinal Microbiome in Preadolescence,Nutrients,2021,"dietary intake, microbiome, obesity, school age, socioeconomic status",Experiment 1,Israel,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,Low SES,High SES,"Children from the higher SES village (A)
SES scores below the median score of 6.4 based on (a) residential SES rank; (b) the number of paternal schooling years; and (c) household crowding index.",69,70,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,"age,body mass index,diet,sex",NA,unchanged,NA,unchanged,NA,decreased,Signature 1,Figure 2D;,21 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Peace Sandy,WikiWorks","Figure 2D. A heatmap of the multivariable model describing
the top 50 associations between the independent variables and bacterial features. Positive associations are colored in red, while inverse associations are colored in blue. The color gradient represents the strength of the association (the effect
size), with darker colors representing the stronger associations. The effect size was calculated by the following formula: (−log(qval)*SIGN (coeff)).",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",3379134|1224|28216|80840|80864|80865;3379134|976|200643|171549|171550;3379134|976|200643|171549|2005519;1783272|1239|186801|186802|31979|1485;1783272|1239|526524|526525|128827;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|1263,Complete,Peace Sandy
bsdb:34444813/1/2,34444813,"cross-sectional observational, not case-control",34444813,10.3390/nu13082645,https://pubmed.ncbi.nlm.nih.gov/34444813/,"Lapidot Y., Reshef L., Goldsmith R., Na'amnih W., Kassem E., Ornoy A., Gophna U. , Muhsen K.",The Associations between Diet and Socioeconomic Disparities and the Intestinal Microbiome in Preadolescence,Nutrients,2021,"dietary intake, microbiome, obesity, school age, socioeconomic status",Experiment 1,Israel,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,Low SES,High SES,"Children from the higher SES village (A)
SES scores below the median score of 6.4 based on (a) residential SES rank; (b) the number of paternal schooling years; and (c) household crowding index.",69,70,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,"age,body mass index,diet,sex",NA,unchanged,NA,unchanged,NA,decreased,Signature 2,Figure 2D,21 July 2022,Kaluifeanyi101,"Kaluifeanyi101,Peace Sandy,WikiWorks","Figure 2D. A heatmap of the multivariable model describing the top 50 associations between the independent variables and bacterial features. Positive associations are colored in red, while inverse associations are colored in blue. The color gradient represents the strength of the association (the effect size), with darker colors representing the stronger associations. The effect size was calculated by the following formula: (−log(qval)*SIGN (coeff)).",decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia",1783272|1239|526524|526525|2810280|135858;1783272|201174|84998|84999|84107;1783272|1239|526524|526525|128827|118747;1783272|1239|186801|3082720|543314|86331;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803|189330;1783272|201174|84998|1643822|1643826|447020,Complete,Peace Sandy
bsdb:34444865/1/1,34444865,case-control,34444865,10.3390/nu13082705,NA,"Bobin-Dubigeon C., Luu H.T., Leuillet S., Lavergne S.N., Carton T., Le Vacon F., Michel C., Nazih H. , Bard J.M.",Faecal Microbiota Composition Varies between Patients with Breast Cancer and Healthy Women: A Comparative Case-Control Study,Nutrients,2021,"16S rRNA, abundance, breast cancer, healthy women, metabarcoding analyses, microbiota, qPCR",Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,healthy controls,BC patients,"Early-stage breast cancer (BC) patients, with samples taken before any anticancer therapy was started.",29,25,NA,PCR,NA,RT-qPCR,log transformation,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,15 July 2025,Ecsharp,Ecsharp,Relative abundance of specific bacterial groups in stools of BC patients and control group by specific primers per bacteria group /species (qPCR for specific bacterial copy numbers results using wilcoxon test).,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.",1783272|1239;1783272|1239|186801|3085636|186803|572511|1955243,Complete,NA
bsdb:34444865/1/2,34444865,case-control,34444865,10.3390/nu13082705,NA,"Bobin-Dubigeon C., Luu H.T., Leuillet S., Lavergne S.N., Carton T., Le Vacon F., Michel C., Nazih H. , Bard J.M.",Faecal Microbiota Composition Varies between Patients with Breast Cancer and Healthy Women: A Comparative Case-Control Study,Nutrients,2021,"16S rRNA, abundance, breast cancer, healthy women, metabarcoding analyses, microbiota, qPCR",Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,healthy controls,BC patients,"Early-stage breast cancer (BC) patients, with samples taken before any anticancer therapy was started.",29,25,NA,PCR,NA,RT-qPCR,log transformation,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,15 July 2025,Ecsharp,Ecsharp,Relative abundance of specific bacterial groups in stools of BC patients and control group by specific primers per bacteria group /species (qPCR for specific bacterial copy numbers results using wilcoxon test).,decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,NA
bsdb:34444865/2/1,34444865,case-control,34444865,10.3390/nu13082705,NA,"Bobin-Dubigeon C., Luu H.T., Leuillet S., Lavergne S.N., Carton T., Le Vacon F., Michel C., Nazih H. , Bard J.M.",Faecal Microbiota Composition Varies between Patients with Breast Cancer and Healthy Women: A Comparative Case-Control Study,Nutrients,2021,"16S rRNA, abundance, breast cancer, healthy women, metabarcoding analyses, microbiota, qPCR",Experiment 2,France,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,healthy controls,BC patients,"Early-stage breast cancer (BC) patients, with samples taken before any anticancer therapy was started.",30,25,NA,16S,34,Illumina,NA,ANOVA,0.05,FALSE,NA,NA,age,NA,decreased,unchanged,NA,NA,NA,Signature 1,Figure 3b & 3.2.2. V3–V4 16S r RNA Gene Sequencing bullet #2,15 July 2025,Ecsharp,Ecsharp,Barplots of relative abundances at the phylum level for individual data from Figure 3b and text excerpt with MHT adjusted p-values from text.,increased,k__Bacillati|p__Bacillota,1783272|1239,Complete,NA
bsdb:34444865/2/2,34444865,case-control,34444865,10.3390/nu13082705,NA,"Bobin-Dubigeon C., Luu H.T., Leuillet S., Lavergne S.N., Carton T., Le Vacon F., Michel C., Nazih H. , Bard J.M.",Faecal Microbiota Composition Varies between Patients with Breast Cancer and Healthy Women: A Comparative Case-Control Study,Nutrients,2021,"16S rRNA, abundance, breast cancer, healthy women, metabarcoding analyses, microbiota, qPCR",Experiment 2,France,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,healthy controls,BC patients,"Early-stage breast cancer (BC) patients, with samples taken before any anticancer therapy was started.",30,25,NA,16S,34,Illumina,NA,ANOVA,0.05,FALSE,NA,NA,age,NA,decreased,unchanged,NA,NA,NA,Signature 2,Figure 3b & 3.2.2. V3–V4 16S r RNA Gene Sequencing bullet #2,15 July 2025,Ecsharp,Ecsharp,Barplots of relative abundances at the phylum level for individual data from Figure 3b and text excerpt with MHT adjusted p-values from text.,decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,NA
bsdb:34445764/1/1,34445764,case-control,34445764,10.3390/ijms22169058,NA,"Hadzega D., Minarik G., Karaba M., Kalavska K., Benca J., Ciernikova S., Sedlackova T., Nemcova P., Bohac M., Pindak D., Klucar L. , Mego M.",Uncovering Microbial Composition in Human Breast Cancer Primary Tumour Tissue Using Transcriptomic RNA-seq,International journal of molecular sciences,2021,"Kraken2, RNA-seq, breast cancer, circulating tumour cells, metatranscriptomics, microbiome, microbiota, primary tumour",Experiment 1,Slovakia,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,normal breast tissue,breast cancer tumor tissue,Slovakia breast cancer patients (stage I–III) treated with surgery from April 2012 to February 2015,5,18,NA,NA,NA,Illumina,relative abundances,"LEfSe,Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3 (A),22 June 2025,Ecsharp,Ecsharp,"Differentially represented taxa between normal breast tissue samples (from cancer-free donors) and breast tumour tissue. (A) Comparison of the microbiome in primary tumours of Slovak patients and normal breast tissue of Slovak cancer-free donors. Since standard conditions identified too many results, to visualise data, LEfSe was run with parameters (LDA > 3, Kruskal Wallis testp-value < 0.05, Wilcoxon testp-value < 0.05)",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|g__Rhodobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Priestia|s__Priestia megaterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Priestia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|g__Gorganvirus|s__Gorganvirus isfahan,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|g__Gorganvirus,k__Heunggongvirae|p__Uroviricota,",3379134|1224|28211|204455|1060;1783272|201174|1760|85006|1268|1269;1783272|1239|91061|1385|186817|2800373|1404;1783272|1239|91061|1385|186817|2800373;1783272|201174|1760|85007;3379134|1224|1236|2887326|468|469;2731360|2731618|2731619;2731360|2731618|2731619|2560142|2560650;2731360|2731618|2731619|2560142;2731360|2731618;,Complete,NA
bsdb:34445764/1/2,34445764,case-control,34445764,10.3390/ijms22169058,NA,"Hadzega D., Minarik G., Karaba M., Kalavska K., Benca J., Ciernikova S., Sedlackova T., Nemcova P., Bohac M., Pindak D., Klucar L. , Mego M.",Uncovering Microbial Composition in Human Breast Cancer Primary Tumour Tissue Using Transcriptomic RNA-seq,International journal of molecular sciences,2021,"Kraken2, RNA-seq, breast cancer, circulating tumour cells, metatranscriptomics, microbiome, microbiota, primary tumour",Experiment 1,Slovakia,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,normal breast tissue,breast cancer tumor tissue,Slovakia breast cancer patients (stage I–III) treated with surgery from April 2012 to February 2015,5,18,NA,NA,NA,Illumina,relative abundances,"LEfSe,Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3 (A),22 June 2025,Ecsharp,Ecsharp,"Differentially represented taxa between normal breast tissue samples (from cancer-free donors) and breast tumour tissue. (A) Comparison of the microbiome in primary tumours of Slovak patients and normal breast tissue of Slovak cancer-free donors. Since standard conditions identified too many results, to visualise data, LEfSe was run with parameters (LDA > 3, Kruskal Wallis testp-value < 0.05, Wilcoxon testp-value < 0.05)",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter|s__Hymenobacter psoromatis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter|s__Hymenobacter sp. BRD128,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter|s__Hymenobacter sedentarius,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Microlunatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus bovis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Microlunatus|s__Microlunatus sagamiharensis,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",3379134|976|200643;3379134|976|768503;3379134|976|768503|768507;3379134|976|768503|768507|1853232;3379134|976|768503|768507|1853232|89966;1783272|1239|91061|1385|186822;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|91061|1385|186822|44249;1783272|201174|84998;1783272|201174|1760|85004|31953|1678;3379134|976|768503|768507|1853232|89966|1484116;1783272|201174|84998|84999;1783272|201174|84998|84999|84107;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107|102106|74426;3379134|976|768503|768507|1853232|89966|2675878;3379134|976|768503|768507|1853232|89966|1411621;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85009|31957|29404;1783272|1239|186801|186802|216572;1783272|1239|91061|1385|186822|44249|1616788;1783272|201174|1760|85009|31957|29404|546874;3379134|976|117747|200666|84566;3379134|976|117747;3379134|976|117747|200666;1783272|1239|186801|186802|216572|459786,Complete,NA
bsdb:34445764/2/1,34445764,case-control,34445764,10.3390/ijms22169058,NA,"Hadzega D., Minarik G., Karaba M., Kalavska K., Benca J., Ciernikova S., Sedlackova T., Nemcova P., Bohac M., Pindak D., Klucar L. , Mego M.",Uncovering Microbial Composition in Human Breast Cancer Primary Tumour Tissue Using Transcriptomic RNA-seq,International journal of molecular sciences,2021,"Kraken2, RNA-seq, breast cancer, circulating tumour cells, metatranscriptomics, microbiome, microbiota, primary tumour",Experiment 2,China,Homo sapiens,Breast,UBERON:0000310,Triple-negative breast cancer,NA,normal breast tissue,triple-negative breast cancer tumor tissue,RNA-seq transcriptomic data obtained from triple-negative breast cancer patients in China (Data taken from study PRJNA553096),18,72,NA,NA,NA,Illumina,relative abundances,"LEfSe,Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,FALSE,5.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3 (B),24 June 2025,Ecsharp,Ecsharp,"Differentially represented taxa between normal breast tissue samples and breast tumour tissue. (B) Comparison of microbiome in primary tumours of 72 patients from China and 18 normal breast tissues of cancer-free donors from China. For visualisation, LEfSe was run with parameters (LDA > 5.5, Kruskal Wallis test p-value < 0.05, Wilcoxon test p-value < 0.05), for the purpose of visualising the best hits.",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae",1783272|1239|91061|1385|186817|1386;1783272|1239|91061|1385;1783272|1239|91061|1385|186817;3379134|1224|28216|80840|506|222;1783272|1239|186801|3082720|186804;3379134|1224|28216|80840|506,Complete,NA
bsdb:34445764/2/2,34445764,case-control,34445764,10.3390/ijms22169058,NA,"Hadzega D., Minarik G., Karaba M., Kalavska K., Benca J., Ciernikova S., Sedlackova T., Nemcova P., Bohac M., Pindak D., Klucar L. , Mego M.",Uncovering Microbial Composition in Human Breast Cancer Primary Tumour Tissue Using Transcriptomic RNA-seq,International journal of molecular sciences,2021,"Kraken2, RNA-seq, breast cancer, circulating tumour cells, metatranscriptomics, microbiome, microbiota, primary tumour",Experiment 2,China,Homo sapiens,Breast,UBERON:0000310,Triple-negative breast cancer,NA,normal breast tissue,triple-negative breast cancer tumor tissue,RNA-seq transcriptomic data obtained from triple-negative breast cancer patients in China (Data taken from study PRJNA553096),18,72,NA,NA,NA,Illumina,relative abundances,"LEfSe,Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,FALSE,5.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3 (B),24 June 2025,Ecsharp,Ecsharp,"Differentially represented taxa between normal breast tissue samples and breast tumour tissue. (B) Comparison of microbiome in primary tumours of 72 patients from China and 18 normal breast tissues of cancer-free donors from China. For visualisation, LEfSe was run with parameters (LDA > 5.5, Kruskal Wallis test p-value < 0.05, Wilcoxon test p-value < 0.05), for the purpose of visualising the best hits.",decreased,"k__Bacillati,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus rhamnosus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella|s__Pasteurella multocida,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas|s__Xanthomonas oryzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Faucicola|s__Faucicola osloensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Nitratireductor,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium botulinum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus|s__Lactiplantibacillus plantarum",1783272;1783272|1239|91061;1783272|1239|91061|186826;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|2759736;3379134|1224;3379134|1224|1236;1783272|1239|91061|186826|33958|2759736|47715;3379134|1224|1236|135614;3379134|1224|1236|135614|32033;3379134|1224|28211;3379134|1224|1236|135614|32033|338;3379134|1224|28211|356;3379134|1224|1236|72274;3379134|1224|1236|135625;3379134|1224|1236|135625|712;3379134|1224|1236|135625|712|745;3379134|1224|1236|135625|712|745|747;3379134|1224|1236|2887326|468;1783272|201174;1783272|201174|1760;1783272|1117;3379134|1224|28211|356|69277;3379134|1224|1236|135614|32033|338|347;3379134|1224|1236|2887326|468|469;3379134|1224|28211|356|69277|68287;3379134|1224|1236|2887326|468|475;1783272|1239|186801|186802|31979;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|186802|31979|1485;3379134|1224|1236|2887326|468|1604696|34062;3379134|1224|1236|72274|135621;3379134|1224|1236|72274|135621|286;1783272|201174|1760|85007;3379134|976;3379134|1224|28211|356|69277|245876;3379134|1224|28211|204455;3379134|1224|28211|204455|31989;1783272|201174|1760|85010;1783272|201174|1760|85010|2070;1783272|1239|186801|186802|31979|1485|1491;1783272|201174|1760|85009;1783272|1239|91061|186826|33958|2767842;1783272|1239|91061|186826|33958|2767842|1590,Complete,NA
bsdb:34445764/3/1,34445764,case-control,34445764,10.3390/ijms22169058,NA,"Hadzega D., Minarik G., Karaba M., Kalavska K., Benca J., Ciernikova S., Sedlackova T., Nemcova P., Bohac M., Pindak D., Klucar L. , Mego M.",Uncovering Microbial Composition in Human Breast Cancer Primary Tumour Tissue Using Transcriptomic RNA-seq,International journal of molecular sciences,2021,"Kraken2, RNA-seq, breast cancer, circulating tumour cells, metatranscriptomics, microbiome, microbiota, primary tumour",Experiment 3,Slovakia,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,BC patients without CTC,BC patients with CTC,Slovakia breast cancer patients with circulating tumour cells (CTC) in their blood,9,9,NA,NA,NA,Illumina,relative abundances,"Kruskall-Wallis,LEfSe,Mann-Whitney (Wilcoxon)",0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4 (A),24 June 2025,Ecsharp,Ecsharp,Differentially represented taxa in primary tumour tissues of Slovak patients between multiple markers statuses. (A) Comparison of the microbiome in primary tumours of patients with CTC in their blood and primary tumours of patients without CTC detected in their blood (LDA threshold = 3).,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Phycicoccus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae|g__Actinoplanes,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Blastomonadaceae|g__Blastomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Nakamurellales|f__Nakamurellaceae|g__Nakamurella|s__Nakamurella antarctica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Faucicola|s__Faucicola osloensis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,",1783272|201174|1760|85006|85021|367298;1783272|201174|1760|85008|28056|1865;3379134|1224|28211|356|45401;3379134|1224|28211|204457|3423720|150203;1783272|201174|1760|1643684|85031|53460|1902245;3379134|1224|1236|2887326|468|1604696|34062;3379134|1224|28211|204455;3379134|1224|28211|204455|31989;3379134|1224|1236|2887326|468|475;1783272|201174|1760|85007|85025|1827;1783272|201174|1760|85007|85025;1783272|201174|1760|85006;,Complete,NA
bsdb:34445764/3/2,34445764,case-control,34445764,10.3390/ijms22169058,NA,"Hadzega D., Minarik G., Karaba M., Kalavska K., Benca J., Ciernikova S., Sedlackova T., Nemcova P., Bohac M., Pindak D., Klucar L. , Mego M.",Uncovering Microbial Composition in Human Breast Cancer Primary Tumour Tissue Using Transcriptomic RNA-seq,International journal of molecular sciences,2021,"Kraken2, RNA-seq, breast cancer, circulating tumour cells, metatranscriptomics, microbiome, microbiota, primary tumour",Experiment 3,Slovakia,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,BC patients without CTC,BC patients with CTC,Slovakia breast cancer patients with circulating tumour cells (CTC) in their blood,9,9,NA,NA,NA,Illumina,relative abundances,"Kruskall-Wallis,LEfSe,Mann-Whitney (Wilcoxon)",0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4 (A),24 June 2025,Ecsharp,Ecsharp,Differentially represented taxa in primary tumour tissues of Slovak patients between multiple markers statuses. (A) Comparison of the microbiome in primary tumours of patients with CTC in their blood and primary tumours of patients without CTC detected in their blood (LDA threshold = 3).,decreased,",k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes,k__Heunggongvirae|p__Uroviricota,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|g__Gorganvirus|s__Gorganvirus isfahan,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|g__Gorganvirus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella|s__Pasteurella multocida,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Asticcacaulis|s__Asticcacaulis excentricus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Asticcacaulis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter johnsonii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia",;2731360|2731618|2731619;2731360|2731618;2731360|2731618|2731619|2560142|2560650;2731360|2731618|2731619|2560142;3379134|1224|1236|135625;3379134|1224|1236|135625|712|745|747;3379134|1224|1236|135625|712|745;3379134|1224|28216|80840|80864|80865;3379134|1224|28211|204458|76892|76890|78587;3379134|1224|28211|204458|76892|76890;3379134|1224|1236|2887326|468|469|40214;3379134|1224|28216|80840|119060|32008,Complete,NA
bsdb:34445764/4/1,34445764,case-control,34445764,10.3390/ijms22169058,NA,"Hadzega D., Minarik G., Karaba M., Kalavska K., Benca J., Ciernikova S., Sedlackova T., Nemcova P., Bohac M., Pindak D., Klucar L. , Mego M.",Uncovering Microbial Composition in Human Breast Cancer Primary Tumour Tissue Using Transcriptomic RNA-seq,International journal of molecular sciences,2021,"Kraken2, RNA-seq, breast cancer, circulating tumour cells, metatranscriptomics, microbiome, microbiota, primary tumour",Experiment 4,Slovakia,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,HR- BC patients,HR+ BC patients,"Slovakia breast cancer patients with hormone receptor status (HR+ vs HR-) was defined as positive for either oestrogen receptor or progesterone receptor vs negative for both, 1% of cells positive for hormone receptor was used as the cut-off to define hormone receptor positivity.",5,13,NA,NA,NA,Illumina,relative abundances,"Kruskall-Wallis,LEfSe,Mann-Whitney (Wilcoxon)",0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4 (B),24 June 2025,Ecsharp,Ecsharp,"Differentially represented taxa in primary tumour tissues of Slovak patients between multiple markers statuses. For all comparisons, LEfSe was run with parameters: LDA > 3 (stricter than default LDA > 2 just for purpose of visualisation), Kruskal Wallis test p-value < 0.05, Wilcoxon test p-value < 0.05. (B) Comparison of the microbiome in primary tumours of patients positive on HR marker and negative on HR marker.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella|s__Lawsonella clevelandensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacillati|p__Actinomycetota|c__Nitriliruptoria,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae|g__Spirosoma,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae|g__Spirosoma|s__Spirosoma pollinicola,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium tetani,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium botulinum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus cereus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hydrogenophaga|s__Hydrogenophaga sp. NH-16,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hydrogenophaga,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas|s__Halomonas sp. JS92-SW72,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales",1783272|201174|1760|85007|2805586|1847725|1528099;1783272|201174|1760|85007|2805586;1783272|201174|1760|85007|2805586|1847725;1783272|201174|908620;3379134|976|768503|768507|89373|107;3379134|976|768503|768507|89373|107|2057025;3379134|1224|28211|204455|31989|265;1783272|1239|186801|186802|31979|1485|1513;1783272|1239|186801|186802|31979|1485|1491;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049|1654|544580;1783272|1239|91061|1385|90964|1279|1280;1783272|1239|91061|1385|186817|1386|1396;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|31979;1783272|1239|91061|1385|186817|1386;3379134|1224|28216|80840|80864|47420|2184519;3379134|1224|28216|80840|80864|47420;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|1385|90964;3379134|1224|1236|135619|28256;3379134|1224|1236|135619|28256|2745|2306583;3379134|1224|1236|135619|28256|2745;3379134|1224|1236|135619,Complete,NA
bsdb:34445764/4/2,34445764,case-control,34445764,10.3390/ijms22169058,NA,"Hadzega D., Minarik G., Karaba M., Kalavska K., Benca J., Ciernikova S., Sedlackova T., Nemcova P., Bohac M., Pindak D., Klucar L. , Mego M.",Uncovering Microbial Composition in Human Breast Cancer Primary Tumour Tissue Using Transcriptomic RNA-seq,International journal of molecular sciences,2021,"Kraken2, RNA-seq, breast cancer, circulating tumour cells, metatranscriptomics, microbiome, microbiota, primary tumour",Experiment 4,Slovakia,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,HR- BC patients,HR+ BC patients,"Slovakia breast cancer patients with hormone receptor status (HR+ vs HR-) was defined as positive for either oestrogen receptor or progesterone receptor vs negative for both, 1% of cells positive for hormone receptor was used as the cut-off to define hormone receptor positivity.",5,13,NA,NA,NA,Illumina,relative abundances,"Kruskall-Wallis,LEfSe,Mann-Whitney (Wilcoxon)",0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4 (B),24 June 2025,Ecsharp,Ecsharp,"Differentially represented taxa in primary tumour tissues of Slovak patients between multiple markers statuses. For all comparisons, LEfSe was run with parameters: LDA > 3 (stricter than default LDA > 2 just for purpose of visualisation), Kruskal Wallis test p-value < 0.05, Wilcoxon test p-value < 0.05. (B) Comparison of the microbiome in primary tumours of patients positive on HR marker and negative on HR marker.",decreased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Priestia|s__Priestia megaterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Priestia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|g__Rhodobacter|s__Rhodobacter xanthinilyticus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|g__Rhodobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Pseudolysobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Pseudolysobacter|s__Pseudolysobacter antarcticus,k__Pararnavirae|p__Artverviricota|c__Revtraviricetes|o__Ortervirales|f__Retroviridae|s__Orthoretrovirinae|g__Gammaretrovirus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus|s__Rhodococcus ruber,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium|s__Janthinobacterium sp. LM6",3379134|1224;3379134|1224|1236|2887326|468;3379134|1224|1236|2887326|468|469;3379134|1224|28216;1783272|1239|91061|1385|186817|2800373|1404;1783272|1239|91061|1385|186817|2800373;3379134|1224|28216|80840;3379134|1224|28216|80840|119060;3379134|1224|28211|204458;3379134|1224|28211|356;1783272|201174|1760|85011|2062|1883;3379134|1224|28211|356|41294;3379134|1224|28211|204455|1060|1850250;3379134|1224|28211|204455|1060;3379134|1224|28211|356|41294|374;3379134|1224|1236|135614|1775411|2709666;3379134|1224|1236|135614|1775411|2709666|2511995;2732397|2732409|2732514|2169561|11632|327045|153135;3379134|1224|28216|80840|80864|12916;1783272|201174|1760|85007|85025|1827|1830;3379134|1224|28216|80840|75682|29580|1938606,Complete,NA
bsdb:34445764/5/1,34445764,case-control,34445764,10.3390/ijms22169058,NA,"Hadzega D., Minarik G., Karaba M., Kalavska K., Benca J., Ciernikova S., Sedlackova T., Nemcova P., Bohac M., Pindak D., Klucar L. , Mego M.",Uncovering Microbial Composition in Human Breast Cancer Primary Tumour Tissue Using Transcriptomic RNA-seq,International journal of molecular sciences,2021,"Kraken2, RNA-seq, breast cancer, circulating tumour cells, metatranscriptomics, microbiome, microbiota, primary tumour",Experiment 5,Slovakia,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,HER2- BC patients,HER2+ BC patients,Slovakia breast cancer patients with HER2 status (HER+ vs HER-). 1% of cells positive for hormone receptor was used as the cut-off to define hormone receptor positivity and HER2 status.,14,4,NA,NA,NA,Illumina,relative abundances,"Kruskall-Wallis,LEfSe,Mann-Whitney (Wilcoxon)",0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4 (C),25 June 2025,Ecsharp,Ecsharp,"Differentially represented taxa in primary tumour tissues of Slovak patients between multiple markers statuses. For all comparisons, LEfSe was run with parameters: LDA > 3 (stricter than default LDA > 2 just for purpose of visualisation), Kruskal Wallis test p-value < 0.05, Wilcoxon test p-value < 0.05. (C) Comparison of the microbiome in primary tumours of patients positive on HER2 marker and negative on HER2 marker status.",increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter pylori,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Musicola|s__Musicola paradisiaca,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Cellulomonadaceae|g__Pseudactinotalea|s__Pseudactinotalea sp. HY158,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia fungorum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia|s__Massilia oculi,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria",3379134|29547|3031852|213849|72293|209|210;3379134|1224|1236|91347|1903410|2884243|69223;1783272|201174|1760|85006|85016|1926259|2654547;3379134|1224|28216|80840|119060|1822464|134537;3379134|1224|28216|80840|75682|149698|945844;3379134|1224|28216|80840;3379134|1224|28216,Complete,NA
bsdb:34445764/5/2,34445764,case-control,34445764,10.3390/ijms22169058,NA,"Hadzega D., Minarik G., Karaba M., Kalavska K., Benca J., Ciernikova S., Sedlackova T., Nemcova P., Bohac M., Pindak D., Klucar L. , Mego M.",Uncovering Microbial Composition in Human Breast Cancer Primary Tumour Tissue Using Transcriptomic RNA-seq,International journal of molecular sciences,2021,"Kraken2, RNA-seq, breast cancer, circulating tumour cells, metatranscriptomics, microbiome, microbiota, primary tumour",Experiment 5,Slovakia,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,HER2- BC patients,HER2+ BC patients,Slovakia breast cancer patients with HER2 status (HER+ vs HER-). 1% of cells positive for hormone receptor was used as the cut-off to define hormone receptor positivity and HER2 status.,14,4,NA,NA,NA,Illumina,relative abundances,"Kruskall-Wallis,LEfSe,Mann-Whitney (Wilcoxon)",0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4 (C),25 June 2025,Ecsharp,Ecsharp,"Differentially represented taxa in primary tumour tissues of Slovak patients between multiple markers statuses. For all comparisons, LEfSe was run with parameters: LDA > 3 (stricter than default LDA > 2 just for purpose of visualisation), Kruskal Wallis test p-value < 0.05, Wilcoxon test p-value < 0.05. (C) Comparison of the microbiome in primary tumours of patients positive on HER2 marker and negative on HER2 marker status.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Thermotogati|p__Deinococcota|c__Deinococci,k__Thermotogati|p__Deinococcota",3379134|976|117743;3379134|976|117743|200644;3379134|976|117743|200644|2762318;1783272|201174|1760|85009|85015|1839;3384194|1297|188787;3384194|1297,Complete,NA
bsdb:34445764/6/1,34445764,case-control,34445764,10.3390/ijms22169058,NA,"Hadzega D., Minarik G., Karaba M., Kalavska K., Benca J., Ciernikova S., Sedlackova T., Nemcova P., Bohac M., Pindak D., Klucar L. , Mego M.",Uncovering Microbial Composition in Human Breast Cancer Primary Tumour Tissue Using Transcriptomic RNA-seq,International journal of molecular sciences,2021,"Kraken2, RNA-seq, breast cancer, circulating tumour cells, metatranscriptomics, microbiome, microbiota, primary tumour",Experiment 6,Slovakia,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,Ki67 < 20% BC patients,Ki67 > 20% BC patients,Slovakia breast cancer patients were labeled Ki67 > 20% or Ki67 < 20%. Ki-67 labelling index was reported as a percentage of cells with Ki-67 positive nuclear immunostaining.,7,11,NA,NA,NA,Illumina,relative abundances,"Kruskall-Wallis,LEfSe,Mann-Whitney (Wilcoxon)",0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4 (E),25 June 2025,Ecsharp,Ecsharp,"Differentially represented taxa in primary tumour tissues of Slovak patients between multiple markers statuses. For all comparisons, LEfSe was run with parameters: LDA > 3 (stricter than default LDA > 2 just for purpose of visualisation), Kruskal Wallis test p-value < 0.05, Wilcoxon test p-value < 0.05. (E) Comparison of the microbiome in primary tumours of Ki67 > 20% and Ki67 < 20%.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Mycetohabitans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Mycetohabitans|s__Mycetohabitans rhizoxinica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|g__Rhodobacter|s__Rhodobacter xanthinilyticus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Asticcacaulis|s__Asticcacaulis excentricus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Asticcacaulis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|28216|80840|119060|2571159;3379134|1224|28216|80840|119060|2571159|412963;1783272|1239|186801|3085636|186803;3379134|1224|28211|204455|1060|1850250;3379134|1224|28211|356|41294;3379134|1224|28211|204458|76892|76890|78587;3379134|1224|28211|204458|76892|76890;3379134|1224|1236|91347;3379134|1224|28216|80840|119060;3379134|1224|28211|204458|76892;3379134|1224|28211|204458;3379134|1224|28211|204457|41297|13687;3379134|1224|28216|80840;3379134|1224|28211|204457|41297;3379134|1224|28211|204457;3379134|1224|28216;3379134|1224,Complete,NA
bsdb:34445764/6/2,34445764,case-control,34445764,10.3390/ijms22169058,NA,"Hadzega D., Minarik G., Karaba M., Kalavska K., Benca J., Ciernikova S., Sedlackova T., Nemcova P., Bohac M., Pindak D., Klucar L. , Mego M.",Uncovering Microbial Composition in Human Breast Cancer Primary Tumour Tissue Using Transcriptomic RNA-seq,International journal of molecular sciences,2021,"Kraken2, RNA-seq, breast cancer, circulating tumour cells, metatranscriptomics, microbiome, microbiota, primary tumour",Experiment 6,Slovakia,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,Ki67 < 20% BC patients,Ki67 > 20% BC patients,Slovakia breast cancer patients were labeled Ki67 > 20% or Ki67 < 20%. Ki-67 labelling index was reported as a percentage of cells with Ki-67 positive nuclear immunostaining.,7,11,NA,NA,NA,Illumina,relative abundances,"Kruskall-Wallis,LEfSe,Mann-Whitney (Wilcoxon)",0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4 (E),25 June 2025,Ecsharp,Ecsharp,"Differentially represented taxa  in primary tumour tissues of Slovak patients between multiple markers statuses. For all comparisons, LEfSe was run with parameters: LDA > 3 (stricter than default LDA > 2 just for purpose of visualisation), Kruskal Wallis test p-value < 0.05, Wilcoxon test p-value < 0.05. (E) Comparison of the microbiome in primary tumours of Ki67 > 20% and Ki67 < 20%.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas|s__Halomonas sp. JS92-SW72,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Faucicola|s__Faucicola osloensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus cereus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cyclobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium tetani,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cyclobacteriaceae|g__Algoriphagus",3379134|1224|1236|135619;3379134|1224|1236|135619|28256|2745|2306583;3379134|1224|1236|135619|28256|2745;3379134|1224|1236|135619|28256;1783272|1239|91061|1385|90964;3379134|1224|1236|2887326|468|475;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|2887326|468|1604696|34062;1783272|1239|91061|1385|186817|1386|1396;1783272|1239|91061|1385|90964|1279|1280;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|31979;1783272|201174|1760|85004|31953|2701|2702;3379134|976|768503|768507|563798;1783272|201174|1760|2037|2049|1654;1783272|1239|186801|186802|31979|1485|1513;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;1783272|201174|1760|2037|2049|1654|544580;1783272|1239|91061|186826|33958|1578|147802;3379134|976|768503|768507|563798|246875,Complete,NA
bsdb:34495955/1/1,34495955,"cross-sectional observational, not case-control",34495955,https://doi.org/10.1371/journal.pone.0255323,NA,"Fei N., Choo-Kang C., Reutrakul S., Crowley S.J., Rae D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Riesen W., Korte W., Luke A., Layden B.T., Gilbert J.A. , Dugas L.R.",Gut microbiota alterations in response to sleep length among African-origin adults,PloS one,2021,NA,Experiment 1,"Ghana,South Africa,Jamaica,United States of America",Homo sapiens,Feces,UBERON:0001988,Sleep duration,EFO:0005271,Normal Sleepers,Short Sleepers,Participants of African descent aged 22 to 45 years who sleep for less than 7 hours daily,250,154,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,NA,NA,NA,NA,Signature 1,FIGURE 1(D),14 October 2024,AishatBolarinwa,"AishatBolarinwa,WikiWorks","Differential ESV abundance among short, normal and long sleepers adjusted for BMI, age, gender and countries. ESV with relative abundance ≥ 1% in at least one group shown.",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|909932|1843489|31977|39948;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:34495955/1/2,34495955,"cross-sectional observational, not case-control",34495955,https://doi.org/10.1371/journal.pone.0255323,NA,"Fei N., Choo-Kang C., Reutrakul S., Crowley S.J., Rae D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Riesen W., Korte W., Luke A., Layden B.T., Gilbert J.A. , Dugas L.R.",Gut microbiota alterations in response to sleep length among African-origin adults,PloS one,2021,NA,Experiment 1,"Ghana,South Africa,Jamaica,United States of America",Homo sapiens,Feces,UBERON:0001988,Sleep duration,EFO:0005271,Normal Sleepers,Short Sleepers,Participants of African descent aged 22 to 45 years who sleep for less than 7 hours daily,250,154,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,NA,NA,NA,NA,Signature 2,FIGURE 1(D),14 October 2024,AishatBolarinwa,"AishatBolarinwa,KateRasheed,WikiWorks","Differential ESV abundance among short, normal and long sleepers adjusted for BMI, age, gender and countries. ESV with relative abundance ≥ 1% in at least one group shown.",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,1783272|1239|186801|186802|216572|119852,Complete,Svetlana up
bsdb:34495955/2/1,34495955,"cross-sectional observational, not case-control",34495955,https://doi.org/10.1371/journal.pone.0255323,NA,"Fei N., Choo-Kang C., Reutrakul S., Crowley S.J., Rae D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Riesen W., Korte W., Luke A., Layden B.T., Gilbert J.A. , Dugas L.R.",Gut microbiota alterations in response to sleep length among African-origin adults,PloS one,2021,NA,Experiment 2,"Ghana,South Africa,Jamaica,United States of America",Homo sapiens,Feces,UBERON:0001988,Sleep duration,EFO:0005271,Normal Sleepers,Long Sleepers,Participants of African descent aged 22 to 45 years who sleep for longer than 9 hours daily,250,248,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,increased,NA,NA,NA,NA,Signature 1,FIGURE 1(D),18 October 2024,AishatBolarinwa,"AishatBolarinwa,KateRasheed,WikiWorks","Differential ESV abundance among short, normal and long sleepers adjusted for BMI, age, gender and countries. ESV with relative abundance ≥ 1% in at least one group shown.",increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|526524|526525|2810280|135858;1783272|1239|909932|1843489|31977|39948;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:34495955/3/1,34495955,"cross-sectional observational, not case-control",34495955,https://doi.org/10.1371/journal.pone.0255323,NA,"Fei N., Choo-Kang C., Reutrakul S., Crowley S.J., Rae D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Riesen W., Korte W., Luke A., Layden B.T., Gilbert J.A. , Dugas L.R.",Gut microbiota alterations in response to sleep length among African-origin adults,PloS one,2021,NA,Experiment 3,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Sleep duration,EFO:0005271,Short sleepers,Long Sleepers,Participants of African descent aged 22 to 45 years who sleep for longer than 9 hours daily,154,248,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,increased,NA,NA,NA,NA,Signature 1,FIGURE 1(D),18 October 2024,AishatBolarinwa,"AishatBolarinwa,KateRasheed,WikiWorks","Differential ESV abundance among short, normal and long sleepers adjusted for BMI, age, gender and countries. ESV with relative abundance ≥ 1% in at least one group shown.",increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|526524|526525|128827;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572;1783272|1239|909932|1843489|31977|39948;3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:34495955/3/2,34495955,"cross-sectional observational, not case-control",34495955,https://doi.org/10.1371/journal.pone.0255323,NA,"Fei N., Choo-Kang C., Reutrakul S., Crowley S.J., Rae D., Bedu-Addo K., Plange-Rhule J., Forrester T.E., Lambert E.V., Bovet P., Riesen W., Korte W., Luke A., Layden B.T., Gilbert J.A. , Dugas L.R.",Gut microbiota alterations in response to sleep length among African-origin adults,PloS one,2021,NA,Experiment 3,"Ghana,Jamaica,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Sleep duration,EFO:0005271,Short sleepers,Long Sleepers,Participants of African descent aged 22 to 45 years who sleep for longer than 9 hours daily,154,248,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,increased,NA,NA,NA,NA,Signature 2,FIGURE 1(D),18 October 2024,AishatBolarinwa,"AishatBolarinwa,KateRasheed,WikiWorks","Differential ESV abundance among short, normal and long sleepers adjusted for BMI, age, gender and countries. ESV with relative abundance ≥ 1% in at least one group shown.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",3379134|976|200643|171549|815|816;1783272|1239|909932|1843489|31977|39948,Complete,Svetlana up
bsdb:34505401/1/1,34505401,"cross-sectional observational, not case-control",34505401,https://doi.org/10.1002/cre2.489,https://pubmed.ncbi.nlm.nih.gov/34505401/,"Masahiro Yoneda, Nao Suzuki, Takao Hirofuji, Takashi Hanioka, Yoshio Nakano",The effects of cigarette smoking on the salivary and tongue microbiome,Clinical and experimental dental research,2022,"saliva, 16S rRNA gene sequencing, cigarette smoking, oral microbiome, tongue",Experiment 1,Japan,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Nonsmokers,Smokers,Smokers who have smoked 100 or more cigarettes since they started smoking.,32,18,3 months,16S,34,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,figure 3a,13 March 2023,Chioma,"Chioma,WikiWorks",Bacteria genera in saliva that differed significantly between smokers and nonsmokers.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",1783272|1239|909932|909929|1843491|970;3379134|203691|203692|136|2845253|157,Complete,Fatima
bsdb:34505401/1/2,34505401,"cross-sectional observational, not case-control",34505401,https://doi.org/10.1002/cre2.489,https://pubmed.ncbi.nlm.nih.gov/34505401/,"Masahiro Yoneda, Nao Suzuki, Takao Hirofuji, Takashi Hanioka, Yoshio Nakano",The effects of cigarette smoking on the salivary and tongue microbiome,Clinical and experimental dental research,2022,"saliva, 16S rRNA gene sequencing, cigarette smoking, oral microbiome, tongue",Experiment 1,Japan,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Nonsmokers,Smokers,Smokers who have smoked 100 or more cigarettes since they started smoking.,32,18,3 months,16S,34,Roche454,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,figure 3a,13 March 2023,Chioma,"Chioma,WikiWorks",Bacteria genera in saliva that differed significantly between smokers and nonsmokers.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium",3379134|976|117743|200644|49546|1016;3379134|1224|1236|135615|868|2717,Complete,Fatima
bsdb:34505401/2/1,34505401,"cross-sectional observational, not case-control",34505401,https://doi.org/10.1002/cre2.489,https://pubmed.ncbi.nlm.nih.gov/34505401/,"Masahiro Yoneda, Nao Suzuki, Takao Hirofuji, Takashi Hanioka, Yoshio Nakano",The effects of cigarette smoking on the salivary and tongue microbiome,Clinical and experimental dental research,2022,"saliva, 16S rRNA gene sequencing, cigarette smoking, oral microbiome, tongue",Experiment 2,Japan,Homo sapiens,Tongue,UBERON:0001723,Smoking behavior,EFO:0004318,Nonsmokers,Smokers,Smokers who have smoked 100 or more cigarettes since they started smoking.,32,18,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,figure 3b,23 March 2023,Chioma,"Chioma,WikiWorks",Bacteria genera in tongue that differed significantly between smokers and nonsmokers,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",1783272|201174|84998|84999|1643824|1380;1783272|1239|909932|1843489|31977|39948,Complete,Fatima
bsdb:34505401/2/2,34505401,"cross-sectional observational, not case-control",34505401,https://doi.org/10.1002/cre2.489,https://pubmed.ncbi.nlm.nih.gov/34505401/,"Masahiro Yoneda, Nao Suzuki, Takao Hirofuji, Takashi Hanioka, Yoshio Nakano",The effects of cigarette smoking on the salivary and tongue microbiome,Clinical and experimental dental research,2022,"saliva, 16S rRNA gene sequencing, cigarette smoking, oral microbiome, tongue",Experiment 2,Japan,Homo sapiens,Tongue,UBERON:0001723,Smoking behavior,EFO:0004318,Nonsmokers,Smokers,Smokers who have smoked 100 or more cigarettes since they started smoking.,32,18,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,figure 3b,23 March 2023,Chioma,"Chioma,WikiWorks",Bacteria genera in tongue that differed significantly between smokers and nonsmokers,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus",1783272|1239|186801|3085636|186803|43996;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1257,Complete,Fatima
bsdb:34556654/1/1,34556654,case-control,34556654,10.1038/s41522-021-00247-y,NA,"Belstrøm D., Constancias F., Drautz-Moses D.I., Schuster S.C., Veleba M., Mahé F. , Givskov M.",Periodontitis associates with species-specific gene expression of the oral microbiota,NPJ biofilms and microbiomes,2021,NA,Experiment 1,Denmark,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Chronic periodontitis,EFO:0006343,Orally healthy controls,Chronic periodontitis patients,Patients with chronic periodontitis,11,11,3 months,WMS,NA,Illumina,centered log-ratio,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary Figure 1A,4 February 2026,NA,NA,Differentially abundant species between Healthy controls and Periodontitis patients.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia|s__Bulleidia extructa,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter rectus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus|s__Desulfobulbus oralis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] brachy,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] saphenum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola",1783272|1239|526524|526525|128827|118747|118748;3379134|29547|3031852|213849|72294|194|203;3379134|200940|3031451|3024411|213121|893|1986146;1783272|1239|909932|1843489|31977|39948|39950;1783272|1239|186801|3082720|543314|35517;1783272|1239|186801|3082720|543314|35518;1783272|1239|186801|3082720|543314|51123;1783272|1239|186801|3082720|3118655|44259|143361;3384194|508458|649775|649776|3029087|1434006|651822;3384189|32066|203490|203491|203492|848|851;3379134|1224|28216|80840|119060|47670|47671;1783272|1239|1737404|1737405|1570339|543311|33033;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|171552|838|28131;1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|2005525|195950|28112;3379134|203691|203692|136|2845253|157|158,Complete,NA
bsdb:34556654/1/2,34556654,case-control,34556654,10.1038/s41522-021-00247-y,NA,"Belstrøm D., Constancias F., Drautz-Moses D.I., Schuster S.C., Veleba M., Mahé F. , Givskov M.",Periodontitis associates with species-specific gene expression of the oral microbiota,NPJ biofilms and microbiomes,2021,NA,Experiment 1,Denmark,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Chronic periodontitis,EFO:0006343,Orally healthy controls,Chronic periodontitis patients,Patients with chronic periodontitis,11,11,3 months,WMS,NA,Illumina,centered log-ratio,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Supplementary Figure 1A,4 February 2026,NA,NA,Differentially abundant species between Healthy controls and Periodontitis patients.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces johnsonii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 448,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter sp. oral taxon 458,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. oral taxon 014,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella serpentiformis",1783272|201174|1760|2037|2049|1654|544581;1783272|201174|1760|2037|2049|1654|1655;1783272|201174|1760|2037|2049|1654|712124;3379134|1224|1236|135625|712|416916|712148;3384189|32066|203490|203491|1129771|32067|157688;3379134|1224|28216|206351|481|482|495;3379134|1224|28216|206351|481|482|641148;3379134|976|200643|171549|2005525|195950|712710,Complete,NA
bsdb:34568329/1/1,34568329,laboratory experiment,34568329,10.3389/fcell.2021.716760,NA,"Wang Q., Yi S., Su G., Du Z., Pan S., Huang X., Cao Q., Yuan G., Kijlstra A. , Yang P.",Changes in the Gut Microbiome Contribute to the Development of Behcet's Disease <i>via</i> Adjuvant Effects,Frontiers in cell and developmental biology,2021,"Behcet’s disease, T cells, autoimmune disease, fecal transplantation, gut microbiome, neutrophils",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Behcet's syndrome,EFO:0003780,Healthy controls-recipient mice,Behcet's disease-recipient mice,Mice colonized by fecal microbial transplantation (FMT) from Behcet's disease patients,5,5,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 1C,24 April 2024,Scholastica,"Scholastica,Peace Sandy,WikiWorks",Differentially abundant taxa in Behcet's disease-recipient mice versus healthy controls-recipient mice,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",1783272|1239|91061|186826|1300|1357;3379134|200940|3031449|213115|194924|35832;3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|543;3379134|1224|1236|91347;3379134|1224|1236;1783272|1239|186801|3085636|186803|33042;3379134|1224|28216|80840|80864|283;3379134|976|200643|171549|1853231|283168;1783272|201174|84998|1643822|1643826|580024;1783272|201174|84995|84996|84997;1783272|201174|84995|84996;1783272|1239|909932|1843488|909930|33024;1783272|1239|909932|1843488|909930;1783272|201174|84995|84996|84997|42255;1783272|1239|186801|3085636|186803|1432051;1783272|1239|909932|909929;1783272|1239|909932;1783272|544448|2790996|2790998|2129;3379134|1224|28216|80840|75682;3379134|1224|28216|80840|75682|149698;1783272|1239|909932|1843489|31977|209879,Complete,Peace Sandy
bsdb:34568329/1/2,34568329,laboratory experiment,34568329,10.3389/fcell.2021.716760,NA,"Wang Q., Yi S., Su G., Du Z., Pan S., Huang X., Cao Q., Yuan G., Kijlstra A. , Yang P.",Changes in the Gut Microbiome Contribute to the Development of Behcet's Disease <i>via</i> Adjuvant Effects,Frontiers in cell and developmental biology,2021,"Behcet’s disease, T cells, autoimmune disease, fecal transplantation, gut microbiome, neutrophils",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Behcet's syndrome,EFO:0003780,Healthy controls-recipient mice,Behcet's disease-recipient mice,Mice colonized by fecal microbial transplantation (FMT) from Behcet's disease patients,5,5,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig. 1C,24 April 2024,Scholastica,"Scholastica,Peace Sandy,WikiWorks",Differentially abundant taxa in Behcet's disease-recipient mice versus healthy controls-recipient mice,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella",1783272|201174|84998|84999;1783272|201174;1783272|201174|84998|84999|1643824|133925;1783272|201174|84998|84999|84107;1783272|1239|91061|1385|186817;1783272|1239|91061|1385|186817|1386;3379134|976|200643|171549|171552;3379134|74201|203494|48461|203557;3379134|74201|203494;3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461;3379134|976|200643|171549|171552|1283313,Complete,Peace Sandy
bsdb:34584098/2/1,34584098,case-control,34584098,10.1038/s41467-021-25965-x,NA,"Okumura S., Konishi Y., Narukawa M., Sugiura Y., Yoshimoto S., Arai Y., Sato S., Yoshida Y., Tsuji S., Uemura K., Wakita M., Matsudaira T., Matsumoto T., Kawamoto S., Takahashi A., Itatani Y., Miki H., Takamatsu M., Obama K., Takeuchi K., Suematsu M., Ohtani N., Fukunaga Y., Ueno M., Sakai Y., Nagayama S. , Hara E.",Gut bacteria identified in colorectal cancer patients promote tumourigenesis via butyrate secretion,Nature communications,2021,NA,Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Individuals,Patients with early CRC,Patients with early colorectal cancer,129,136,1 month,16S,12,Illumina,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1B,5 June 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between early CRC patients and healthy controls,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis",3384189|32066|203490|203491|203492|848|851;1783272|1239|91061|1385|539738|1378|29391;1783272|1239|186801|3082720|186804|1257|341694,Complete,Claregrieve1
bsdb:34584098/3/1,34584098,case-control,34584098,10.1038/s41467-021-25965-x,NA,"Okumura S., Konishi Y., Narukawa M., Sugiura Y., Yoshimoto S., Arai Y., Sato S., Yoshida Y., Tsuji S., Uemura K., Wakita M., Matsudaira T., Matsumoto T., Kawamoto S., Takahashi A., Itatani Y., Miki H., Takamatsu M., Obama K., Takeuchi K., Suematsu M., Ohtani N., Fukunaga Y., Ueno M., Sakai Y., Nagayama S. , Hara E.",Gut bacteria identified in colorectal cancer patients promote tumourigenesis via butyrate secretion,Nature communications,2021,NA,Experiment 3,Japan,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Individuals,Patients with advanced CRC,Patients with early colorectal cancer,129,153,1 month,16S,12,Illumina,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1B,5 June 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between advanced CRC patients and healthy controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei",3379134|976|200643|171549|171552|1283313|76122;1783272|1239|909932|1843489|31977|39948|39950;3384189|32066|203490|203491|203492|848|851;1783272|1239|91061|1385|539738|1378|29391;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|1239|186801|3082720|186804|1257|1261;1783272|1239|186801|3082720|186804|1257|341694;3379134|976|200643|171549|171551|836|28123;3379134|976|200643|171549|171551|836|837;3379134|976|200643|171549|171552|838|28131;1783272|1239|526524|526525|128827|123375|102148,Complete,Claregrieve1
bsdb:34584098/4/NA,34584098,case-control,34584098,10.1038/s41467-021-25965-x,NA,"Okumura S., Konishi Y., Narukawa M., Sugiura Y., Yoshimoto S., Arai Y., Sato S., Yoshida Y., Tsuji S., Uemura K., Wakita M., Matsudaira T., Matsumoto T., Kawamoto S., Takahashi A., Itatani Y., Miki H., Takamatsu M., Obama K., Takeuchi K., Suematsu M., Ohtani N., Fukunaga Y., Ueno M., Sakai Y., Nagayama S. , Hara E.",Gut bacteria identified in colorectal cancer patients promote tumourigenesis via butyrate secretion,Nature communications,2021,NA,Experiment 4,Japan,Homo sapiens,Feces,UBERON:0001988,Surgical resection,EFO:0009744,Before resection,After resection,Patients post surgical resection of Cohort-1 CRC specimens,380,380,1 month,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34584529/1/1,34584529,case-control,34584529,https://doi.org/10.33073/pjm-2021-033,NA,"Kim S., Seo H., Rahim M.A., Tajdozian H., Kim Y.S. , Song H.Y.",Characteristics of Vaginal Microbiome in Women with Pelvic Inflammatory Disease in Korea,Polish journal of microbiology,2021,"16S rRNA amplicon sequencing, Korean, pelvic inflammatory disease, premenopausal, vaginal microflora",Experiment 1,South Korea,Homo sapiens,Vagina,UBERON:0000996,Pelvic Inflammatory Disease,EFO:1001388,Control group,Pelvic Inflammatory Disease (PID) group,Vaginal samples from premenopausal women with Pelvic Inflammatory Disease (PID).,33,41,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,unchanged,decreased,NA,unchanged,Signature 1,Table 4,24 June 2025,Aleru Divine,Aleru Divine,The Kruskal-Wallis H tests and LEfSe analysis of the associations between normal control women and PID patients.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia",3379134|1224|1236|72274|135621;3379134|1224|1236|91347|1903411;1783272|201174|1760|85004|31953|2701;3379134|1224|1236|72274|135621|286;1783272|1239|1737404|1737405|1570339|543311;3379134|1224|1236|91347|543;1783272|1239|909932|1843489|31977|906;3379134|1224|1236|91347|1903411|629,Complete,NA
bsdb:34584529/1/2,34584529,case-control,34584529,https://doi.org/10.33073/pjm-2021-033,NA,"Kim S., Seo H., Rahim M.A., Tajdozian H., Kim Y.S. , Song H.Y.",Characteristics of Vaginal Microbiome in Women with Pelvic Inflammatory Disease in Korea,Polish journal of microbiology,2021,"16S rRNA amplicon sequencing, Korean, pelvic inflammatory disease, premenopausal, vaginal microflora",Experiment 1,South Korea,Homo sapiens,Vagina,UBERON:0000996,Pelvic Inflammatory Disease,EFO:1001388,Control group,Pelvic Inflammatory Disease (PID) group,Vaginal samples from premenopausal women with Pelvic Inflammatory Disease (PID).,33,41,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,unchanged,decreased,NA,unchanged,Signature 2,Table 4,24 June 2025,Aleru Divine,Aleru Divine,The Kruskal-Wallis H tests and LEfSe analysis of the associations between normal control women and PID patients.,decreased,"k__Bacillati|p__Bacillota,p__Candidatus Saccharimonadota,k__Bacillati|p__Bacillota|c__Bacilli,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinotignum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales",1783272|1239;95818;1783272|1239|91061;95818|2093818;95818|2093818|2093825;95818|2093818|2093825|2171986;1783272|201174|1760|85009;1783272|1239|91061|186826|33958;3379134|1224|1236|2887326|468;1783272|201174|1760|85009|31957;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958;1783272|201174|1760|85009|31957|1912216;1783272|201174|1760|2037|2049|1653174;1783272|1239|91061|186826,Complete,NA
bsdb:34592155/1/1,34592155,prospective cohort,34592155,10.1016/j.celrep.2021.109765,https://pubmed.ncbi.nlm.nih.gov/34592155/,"Leite G., Pimentel M., Barlow G.M., Chang C., Hosseini A., Wang J., Parodi G., Sedighi R., Rezaie A. , Mathur R.",Age and the aging process significantly alter the small bowel microbiome,Cell reports,2021,"Escherichia, Lactobacillus, Proteobacteria, age, aging, coliforms, concomitant diseases, duodenal microbiome, medication use, small intestinal microbiome",Experiment 1,Switzerland,Homo sapiens,Duodenum,UBERON:0002114,Aging,GO:0007568,Group 1 (18–35 years old),Group 2,36-50 years old,32,41,NA,16S,34,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Table S2,1 June 2023,Atrayees,"Atrayees,Folakunmi,WikiWorks","Genera solely associated with age after multivariate analysis controlling for the number of
medications used and the number of concomitant diseases.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",3379134|1224|1236|135625|712|713;3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|561;1783272|1239|91061|186826|33958|1578,Complete,Folakunmi
bsdb:34592155/1/2,34592155,prospective cohort,34592155,10.1016/j.celrep.2021.109765,https://pubmed.ncbi.nlm.nih.gov/34592155/,"Leite G., Pimentel M., Barlow G.M., Chang C., Hosseini A., Wang J., Parodi G., Sedighi R., Rezaie A. , Mathur R.",Age and the aging process significantly alter the small bowel microbiome,Cell reports,2021,"Escherichia, Lactobacillus, Proteobacteria, age, aging, coliforms, concomitant diseases, duodenal microbiome, medication use, small intestinal microbiome",Experiment 1,Switzerland,Homo sapiens,Duodenum,UBERON:0002114,Aging,GO:0007568,Group 1 (18–35 years old),Group 2,36-50 years old,32,41,NA,16S,34,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Table S2,2 January 2024,Folakunmi,"Folakunmi,WikiWorks","Genera solely associated with age after multivariate analysis controlling for the number of
medications used and the number of concomitant diseases.",decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,3379134|1224|1236|135614|32033,Complete,Folakunmi
bsdb:34592155/2/1,34592155,prospective cohort,34592155,10.1016/j.celrep.2021.109765,https://pubmed.ncbi.nlm.nih.gov/34592155/,"Leite G., Pimentel M., Barlow G.M., Chang C., Hosseini A., Wang J., Parodi G., Sedighi R., Rezaie A. , Mathur R.",Age and the aging process significantly alter the small bowel microbiome,Cell reports,2021,"Escherichia, Lactobacillus, Proteobacteria, age, aging, coliforms, concomitant diseases, duodenal microbiome, medication use, small intestinal microbiome",Experiment 2,Switzerland,Homo sapiens,Duodenum,UBERON:0002114,Aging,GO:0007568,Group 1 (18–35 years old),Group 3,participants aged 51 to 65 years old,32,96,NA,16S,34,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Table S2,1 June 2023,Atrayees,"Atrayees,Folakunmi,WikiWorks","Genera solely associated with age after multivariate analysis controlling for the number of
medications used and the number of concomitant diseases.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",3379134|1224|1236|135625|712|713;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|561,Complete,Folakunmi
bsdb:34592155/2/2,34592155,prospective cohort,34592155,10.1016/j.celrep.2021.109765,https://pubmed.ncbi.nlm.nih.gov/34592155/,"Leite G., Pimentel M., Barlow G.M., Chang C., Hosseini A., Wang J., Parodi G., Sedighi R., Rezaie A. , Mathur R.",Age and the aging process significantly alter the small bowel microbiome,Cell reports,2021,"Escherichia, Lactobacillus, Proteobacteria, age, aging, coliforms, concomitant diseases, duodenal microbiome, medication use, small intestinal microbiome",Experiment 2,Switzerland,Homo sapiens,Duodenum,UBERON:0002114,Aging,GO:0007568,Group 1 (18–35 years old),Group 3,participants aged 51 to 65 years old,32,96,NA,16S,34,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Table S2,1 June 2023,Atrayees,"Atrayees,Folakunmi,WikiWorks","Genera solely associated with age after multivariate analysis controlling for the number of
medications used and the number of concomitant diseases.",decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,3379134|1224|1236|135614|32033,Complete,Folakunmi
bsdb:34592155/3/1,34592155,prospective cohort,34592155,10.1016/j.celrep.2021.109765,https://pubmed.ncbi.nlm.nih.gov/34592155/,"Leite G., Pimentel M., Barlow G.M., Chang C., Hosseini A., Wang J., Parodi G., Sedighi R., Rezaie A. , Mathur R.",Age and the aging process significantly alter the small bowel microbiome,Cell reports,2021,"Escherichia, Lactobacillus, Proteobacteria, age, aging, coliforms, concomitant diseases, duodenal microbiome, medication use, small intestinal microbiome",Experiment 3,Switzerland,Homo sapiens,Duodenum,UBERON:0002114,Aging,GO:0007568,Group 1 (18–35 years old),Group 4,66 to 80 years old,32,82,NA,16S,34,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Table S2,1 June 2023,Atrayees,"Atrayees,Folakunmi,WikiWorks","Genera solely associated with age after multivariate analysis controlling for the number of
medications used and the number of concomitant diseases.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",3379134|1224|1236|135625|712|713;3379134|976|200643|171549|815|816;1783272|1239|91061|186826|33958|1578;3379134|1224|1236|91347|543|561,Complete,Folakunmi
bsdb:34592155/3/2,34592155,prospective cohort,34592155,10.1016/j.celrep.2021.109765,https://pubmed.ncbi.nlm.nih.gov/34592155/,"Leite G., Pimentel M., Barlow G.M., Chang C., Hosseini A., Wang J., Parodi G., Sedighi R., Rezaie A. , Mathur R.",Age and the aging process significantly alter the small bowel microbiome,Cell reports,2021,"Escherichia, Lactobacillus, Proteobacteria, age, aging, coliforms, concomitant diseases, duodenal microbiome, medication use, small intestinal microbiome",Experiment 3,Switzerland,Homo sapiens,Duodenum,UBERON:0002114,Aging,GO:0007568,Group 1 (18–35 years old),Group 4,66 to 80 years old,32,82,NA,16S,34,Illumina,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Table S2,1 June 2023,Atrayees,"Atrayees,Folakunmi,WikiWorks","Genera solely associated with age after multivariate analysis controlling for the number of
medications used and the number of concomitant diseases.",decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,3379134|1224|1236|135614|32033,Complete,Folakunmi
bsdb:34609073/1/1,34609073,case-control,34609073,10.1002/jcsm.12804,NA,"Ubachs J., Ziemons J., Soons Z., Aarnoutse R., van Dijk D.P.J., Penders J., van Helvoort A., Smidt M.L., Kruitwagen R.F.P.M., Baade-Corpelijn L., Olde Damink S.W.M. , Rensen S.S.",Gut microbiota and short-chain fatty acid alterations in cachectic cancer patients,"Journal of cachexia, sarcopenia and muscle",2021,"Breast cancer, Cachexia, Inflammation, Lung cancer, Pancreatic cancer, Weight loss",Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Cancer,MONDO:0004992,Healthy Controls,Cachectic Cancer,These are cancer patients who lost >5% body weight in the last 6 months.,76,33,3 months,16S,4,Illumina,relative abundances,Wald Test,0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2B& 3,2 May 2025,Mautin,Mautin,Distinct gut microbiota composition in cachectic cancer patients,increased,"k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",3379134|1224;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|91347|543,Complete,KateRasheed
bsdb:34609073/1/2,34609073,case-control,34609073,10.1002/jcsm.12804,NA,"Ubachs J., Ziemons J., Soons Z., Aarnoutse R., van Dijk D.P.J., Penders J., van Helvoort A., Smidt M.L., Kruitwagen R.F.P.M., Baade-Corpelijn L., Olde Damink S.W.M. , Rensen S.S.",Gut microbiota and short-chain fatty acid alterations in cachectic cancer patients,"Journal of cachexia, sarcopenia and muscle",2021,"Breast cancer, Cachexia, Inflammation, Lung cancer, Pancreatic cancer, Weight loss",Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Cancer,MONDO:0004992,Healthy Controls,Cachectic Cancer,These are cancer patients who lost >5% body weight in the last 6 months.,76,33,3 months,16S,4,Illumina,relative abundances,Wald Test,0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2B &3,2 May 2025,Mautin,Mautin,Distinct gut microbiota composition in cachectic cancer patients,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,1783272|1239|186801|186802|186807|2740,Complete,KateRasheed
bsdb:34609073/2/1,34609073,case-control,34609073,10.1002/jcsm.12804,NA,"Ubachs J., Ziemons J., Soons Z., Aarnoutse R., van Dijk D.P.J., Penders J., van Helvoort A., Smidt M.L., Kruitwagen R.F.P.M., Baade-Corpelijn L., Olde Damink S.W.M. , Rensen S.S.",Gut microbiota and short-chain fatty acid alterations in cachectic cancer patients,"Journal of cachexia, sarcopenia and muscle",2021,"Breast cancer, Cachexia, Inflammation, Lung cancer, Pancreatic cancer, Weight loss",Experiment 2,Netherlands,Homo sapiens,Feces,UBERON:0001988,Cancer,MONDO:0004992,Non-Cachectic Cancer,Cachetic Cancer,These are cancer patients who lost >5% body weight in the last 6 months.,74,33,3 months,16S,4,Illumina,relative abundances,Wald Test,0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2B,3",2 May 2025,Mautin,Mautin,Distinct gut microbiota composition in cachectic cancer patients,increased,"k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",3379134|1224;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|91347|543,Complete,KateRasheed
bsdb:34609073/2/2,34609073,case-control,34609073,10.1002/jcsm.12804,NA,"Ubachs J., Ziemons J., Soons Z., Aarnoutse R., van Dijk D.P.J., Penders J., van Helvoort A., Smidt M.L., Kruitwagen R.F.P.M., Baade-Corpelijn L., Olde Damink S.W.M. , Rensen S.S.",Gut microbiota and short-chain fatty acid alterations in cachectic cancer patients,"Journal of cachexia, sarcopenia and muscle",2021,"Breast cancer, Cachexia, Inflammation, Lung cancer, Pancreatic cancer, Weight loss",Experiment 2,Netherlands,Homo sapiens,Feces,UBERON:0001988,Cancer,MONDO:0004992,Non-Cachectic Cancer,Cachetic Cancer,These are cancer patients who lost >5% body weight in the last 6 months.,74,33,3 months,16S,4,Illumina,relative abundances,Wald Test,0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2B,3",2 May 2025,Mautin,Mautin,Distinct gut microbiota composition in cachectic cancer patients,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus",1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|186802|186807|2740,Complete,KateRasheed
bsdb:34609073/3/1,34609073,case-control,34609073,10.1002/jcsm.12804,NA,"Ubachs J., Ziemons J., Soons Z., Aarnoutse R., van Dijk D.P.J., Penders J., van Helvoort A., Smidt M.L., Kruitwagen R.F.P.M., Baade-Corpelijn L., Olde Damink S.W.M. , Rensen S.S.",Gut microbiota and short-chain fatty acid alterations in cachectic cancer patients,"Journal of cachexia, sarcopenia and muscle",2021,"Breast cancer, Cachexia, Inflammation, Lung cancer, Pancreatic cancer, Weight loss",Experiment 3,Netherlands,Homo sapiens,Feces,UBERON:0001988,Pancreatic carcinoma,EFO:0002618,Healthy Controls,Cachectic Cancer,These are Pancreatic cancer patients who lost >5% body weight in the last 6 months analyzed for pancreatic Cancer,NA,18,3 months,16S,4,Illumina,relative abundances,Wald Test,0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure S3A,2 May 2025,Mautin,Mautin,Distinct gut microbiota composition in cachectic cancer patients,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|91347|543,Complete,KateRasheed
bsdb:34609073/4/1,34609073,case-control,34609073,10.1002/jcsm.12804,NA,"Ubachs J., Ziemons J., Soons Z., Aarnoutse R., van Dijk D.P.J., Penders J., van Helvoort A., Smidt M.L., Kruitwagen R.F.P.M., Baade-Corpelijn L., Olde Damink S.W.M. , Rensen S.S.",Gut microbiota and short-chain fatty acid alterations in cachectic cancer patients,"Journal of cachexia, sarcopenia and muscle",2021,"Breast cancer, Cachexia, Inflammation, Lung cancer, Pancreatic cancer, Weight loss",Experiment 4,Netherlands,Homo sapiens,Feces,UBERON:0001988,Pancreatic carcinoma,EFO:0002618,Healthy Controls,Non-Cachectic Cancer,These are Pancreatic cancer patients who did not lost >5% body weight in the last 6 months.,NA,9,3 months,16S,4,Illumina,relative abundances,Wald Test,0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure S3A,3 May 2025,Mautin,Mautin,Distinct gut microbiota composition in Non-cachectic cancer patients,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,1783272|1239|91061|186826|81852|1350,Complete,KateRasheed
bsdb:34609073/5/1,34609073,case-control,34609073,10.1002/jcsm.12804,NA,"Ubachs J., Ziemons J., Soons Z., Aarnoutse R., van Dijk D.P.J., Penders J., van Helvoort A., Smidt M.L., Kruitwagen R.F.P.M., Baade-Corpelijn L., Olde Damink S.W.M. , Rensen S.S.",Gut microbiota and short-chain fatty acid alterations in cachectic cancer patients,"Journal of cachexia, sarcopenia and muscle",2021,"Breast cancer, Cachexia, Inflammation, Lung cancer, Pancreatic cancer, Weight loss",Experiment 5,Netherlands,Homo sapiens,Feces,UBERON:0001988,Lung cancer,MONDO:0008903,Healthy Controls,Cachectic Cancer,These are Lung Cancer patients who lost >5% body weight in the last 6 months.,NA,5,3 months,16S,4,Illumina,relative abundances,Wald Test,0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure S3B,3 May 2025,Mautin,Mautin,Distinct gut microbiota composition in cachectic cancer patients,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,1783272|1239|91061|186826|81852|1350,Complete,KateRasheed
bsdb:34609073/6/1,34609073,case-control,34609073,10.1002/jcsm.12804,NA,"Ubachs J., Ziemons J., Soons Z., Aarnoutse R., van Dijk D.P.J., Penders J., van Helvoort A., Smidt M.L., Kruitwagen R.F.P.M., Baade-Corpelijn L., Olde Damink S.W.M. , Rensen S.S.",Gut microbiota and short-chain fatty acid alterations in cachectic cancer patients,"Journal of cachexia, sarcopenia and muscle",2021,"Breast cancer, Cachexia, Inflammation, Lung cancer, Pancreatic cancer, Weight loss",Experiment 6,Netherlands,Homo sapiens,Feces,UBERON:0001988,Lung cancer,MONDO:0008903,Non-Cachectic Cancer,Cachectic Cancer,These are Lung Cancer patients who lost >5% body weight in the last 6 months.,19,5,3 months,16S,4,Illumina,relative abundances,Wald Test,0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure S3B,3 May 2025,Mautin,Mautin,Distinct gut microbiota composition in cachectic cancer patients,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,KateRasheed
bsdb:34611216/1/1,34611216,"cross-sectional observational, not case-control",34611216,https://doi.org/10.1038/s41598-021-99127-w,https://www.nature.com/articles/s41598-021-99127-w,"Goolam Mahomed T., Peters R.P.H., Allam M., Ismail A., Mtshali S., Goolam Mahomed A., Ueckermann V., Kock M.M. , Ehlers M.M.","Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa",Scientific reports,2021,NA,Experiment 1,South Africa,Homo sapiens,Sputum,UBERON:0007311,Chronic obstructive pulmonary disease,EFO:0000341,Stable state chronic obstructive pulmonary disease (COPD) patients,Exacerbated state chronic obstructive pulmonary disease (COPD) patients,Patients in the exacerbated state of chronic obstructive pulmonary disease (COPD).,18,6,"Group 0: past month
Group 1: past 24 hours",16S,123,Illumina,raw counts,DESeq2,0.2,TRUE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,Signature 1,Figure 2,10 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Graph of the DESeq2 analysis showing the log2fold differential abundance of the different genera between the exacerbated state and stable state of disease (n=24) in the sputum microbiome of chronic obstructive pulmonary disease (COPD) participants.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella",1783272|201174|1760|2037|2049|1654;3379134|1224|28216|206351|481|482;1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|186828|117563,Complete,Svetlana up
bsdb:34617511/1/1,34617511,"cross-sectional observational, not case-control",34617511,10.7554/eLife.70349,https://pubmed.ncbi.nlm.nih.gov/34617511,"Ang Q.Y., Alba D.L., Upadhyay V., Bisanz J.E., Cai J., Lee H.L., Barajas E., Wei G., Noecker C., Patterson A.D., Koliwad S.K. , Turnbaugh P.J.",The East Asian gut microbiome is distinct from colocalized White subjects and connected to metabolic health,eLife,2021,"biogeography, ethnicity, human, human gut microbiome, infectious disease, metabolic syndrome, microbiology, mouse, multi-omics, obesity",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,White (W),East Asian (EA),A balanced distribution of both lean and obese adults who identified as East Asians residing within the Bay area of San Fransisco.,24,22,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 1,8 June 2022,Kaluifeanyi101,"Kaluifeanyi101,Aiyshaaaa,Peace Sandy,WikiWorks","The gut microbiota is distinct between East Asian (EA) and White (W) subjects living in the Bay Area.
(C) CLR abundances of all bacterial phyla between EA and W subjects. p-values determined using Wilcoxon rank-sum tests.",increased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Peace Sandy
bsdb:34617511/1/2,34617511,"cross-sectional observational, not case-control",34617511,10.7554/eLife.70349,https://pubmed.ncbi.nlm.nih.gov/34617511,"Ang Q.Y., Alba D.L., Upadhyay V., Bisanz J.E., Cai J., Lee H.L., Barajas E., Wei G., Noecker C., Patterson A.D., Koliwad S.K. , Turnbaugh P.J.",The East Asian gut microbiome is distinct from colocalized White subjects and connected to metabolic health,eLife,2021,"biogeography, ethnicity, human, human gut microbiome, infectious disease, metabolic syndrome, microbiology, mouse, multi-omics, obesity",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,White (W),East Asian (EA),A balanced distribution of both lean and obese adults who identified as East Asians residing within the Bay area of San Fransisco.,24,22,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Figure 1,8 June 2022,Kaluifeanyi101,"Kaluifeanyi101,Aiyshaaaa,Peace Sandy,WikiWorks",The gut microbiota is distinct between East Asian (EA) and White (W) subjects living in the Bay Area. (C) CLR abundances of all bacterial phyla between EA and W subjects. p-values determined using Wilcoxon rank-sum tests.,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|s__Actinomycetes bacterium,k__Pseudomonadati|p__Verrucomicrobiota,k__Fusobacteriati|p__Fusobacteriota,k__Thermotogati|p__Synergistota,k__Pseudomonadati|p__Campylobacterota",1783272|1239;1783272|201174|1760|1883427;3379134|74201;3384189|32066;3384194|508458;3379134|29547,Complete,Peace Sandy
bsdb:34620922/1/1,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 1,Japan,Apodemus speciosus,Ileum,UBERON:0002116,Species design,EFO:0001753,Colon of Large Japanese field mouse,Small intestine of Large Japanese field mouse,Gut content was collected from the ileum within the small intestine of the large Japanese field mouse following removal of the digestive tract.,41,42,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 1,Supplementary Table 25,26 November 2025,Firdaws,Firdaws,Relative abundance of bacterial genera compared between the upper (Small intestine) and lower (Colon) Gastrointestinal tract (GIT) in Apodemus speciosus based on pairwise LEfSe analysis.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Pseudomonadati|p__Verrucomicrobiota|c__Spartobacteria|o__Chthoniobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|g__Exiguobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Rodentibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|1224|1236|2887326|468|469;3379134|976|117743|200644|2762318|59735;1783272|1239|91061|186826|186828|2747;3379134|74201|134549|1836787;3379134|1224|28216|80840|80864|80865;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|1385|33986;3384189|32066|203490|203491|203492|848;1783272|1239|91061|186826|33958|1578;3384189|32066|203490|203491|1129771|32067;3379134|1224|1236|91347|1903414|586;3379134|1224|1236|72274|135621|286;3379134|1224|1236|135625|712|1960084;3379134|1224|1236|91347|1903411|613;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|135614|32033|40323;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810281|191303;1783272|544448|2790996|2790998|2129;1783272|1239|909932|1843489|31977|29465,Complete,NA
bsdb:34620922/1/2,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 1,Japan,Apodemus speciosus,Ileum,UBERON:0002116,Species design,EFO:0001753,Colon of Large Japanese field mouse,Small intestine of Large Japanese field mouse,Gut content was collected from the ileum within the small intestine of the large Japanese field mouse following removal of the digestive tract.,41,42,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 2,Supplementary Table 25,26 November 2025,Firdaws,Firdaws,"Relative abundance of bacterial order, genera and species compared between the upper (Small intestine) and lower (Colon) Gastrointestinal tract (GIT) in Apodemus speciosus based on pairwise LEfSe analysis.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Cerasicoccaceae|g__Cerasicoccus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium oxidoreducens,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] brachy,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum",1783272|1239|186801|3085636|186803|1427378;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|830;1783272|1798710|1906119;95818|2093818|2093825|2171986|1331051;3379134|74201|414999|415001|3056374|468938;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|1732;3379134|29547|3031852|213849|72293|209;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803|1506553;3379134|976|200643|171549|2005473|1918540;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;3379134|1224|28216|80840|75682|846;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|186807|2740;3379134|976|200643|171549|171550|28138;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|3082720|543314|35517;1783272|1239|186801|3082720|543314|35518,Complete,NA
bsdb:34620922/3/1,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 3,Japan,Apodemus speciosus,Ileum,UBERON:0002116,Species design,EFO:0001753,Rectum of Large Japanese field mouse,Small intestine of Large Japanese field mouse,Gut content was collected from the ileum within the small intestine of the large Japanese field mouse following removal of the digestive tract.,25,42,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 1,Supplementary Table 25,27 November 2025,Firdaws,Firdaws,Relative abundance of bacterial genera compared between the upper (Small intestine) and lower (Rectum) Gastrointestinal tract (GIT) in Apodemus speciosus based on pairwise LEfSe analysis.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Rodentibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|1224|1236|2887326|468|469;3379134|976|117743|200644|2762318|59735;1783272|1239|91061|186826|186828|2747;3379134|1224|28216|80840|80864|80865;1783272|1239|91061|186826|81852|1350;3384189|32066|203490|203491|203492|848;1783272|1239|91061|186826|33958|1578;3384189|32066|203490|203491|1129771|32067;3379134|1224|1236|91347|1903414|586;3379134|1224|1236|72274|135621|286;3379134|1224|1236|135625|712|1960084;3379134|1224|1236|91347|1903411|613;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|135614|32033|40323;1783272|1239|526524|526525|2810281|191303;1783272|544448|2790996|2790998|2129;1783272|1239|909932|1843489|31977|29465,Complete,NA
bsdb:34620922/3/2,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 3,Japan,Apodemus speciosus,Ileum,UBERON:0002116,Species design,EFO:0001753,Rectum of Large Japanese field mouse,Small intestine of Large Japanese field mouse,Gut content was collected from the ileum within the small intestine of the large Japanese field mouse following removal of the digestive tract.,25,42,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 2,Supplementary Table 24 and Supplementary Table 25,27 November 2025,Firdaws,Firdaws,Relative abundance of bacterial genera and species compared between the upper (Small intestine) and lower (Rectum) Gastrointestinal tract (GIT) in Apodemus speciosus based on pairwise LEfSe analysis.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum",1783272|1239|186801|3085636|186803|1427378;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|830;95818|2093818|2093825|2171986|1331051;1783272|1239|186801|186802|1470353;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|186806|1730|290054;3379134|29547|3031852|213849|72293|209;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803|1506553;3379134|200930|68337|191393|2945020|248038;3379134|976|200643|171549|2005473|1918540;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;3379134|1224|28216|80840|75682|846;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|186807|2740;3379134|976|200643|171549|171550|28138;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|3082720|543314|35518,Complete,NA
bsdb:34620922/4/1,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 4,Japan,Apodemus speciosus,Cecum mucosa,UBERON:0000314,Species design,EFO:0001753,Rectum of Large Japanese field mouse,Cecum of Large Japanese field mouse,Gut content was collected from the central part of the cecum of the large Japanese field mouse following removal of the digestive tract.,25,27,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary Table 26,27 November 2025,Firdaws,Firdaws,"Relative abundance of bacteria genera compared between the lower regions (Cecum & Rectum) of the Gastrointestinal tract (GIT) in Apodemus speciosus based on pairwise LEfSe
analysis.",increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",3379134|29547|3031852|213849|72293|209;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3085636|186803|1506553,Complete,NA
bsdb:34620922/4/2,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 4,Japan,Apodemus speciosus,Cecum mucosa,UBERON:0000314,Species design,EFO:0001753,Rectum of Large Japanese field mouse,Cecum of Large Japanese field mouse,Gut content was collected from the central part of the cecum of the large Japanese field mouse following removal of the digestive tract.,25,27,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Supplementary Table 24 and Supplementary Table 26,27 November 2025,Firdaws,Firdaws,Relative abundance of bacteria genera compared between the lower regions (Cecum & Rectum) of the Gastrointestinal tract (GIT) in Apodemus speciosus based on pairwise LEfSe analysis.,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|84998|1643822|1643826|580024;1783272|1239|91061|1385|539738|1378;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300|1301,Complete,NA
bsdb:34620922/5/1,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 5,Japan,Apodemus speciosus,Ascending colon,NA,Species design,EFO:0001753,Cecum of Large Japanese field mouse,Colon of Large Japanese field mouse,Gut content was collected from the ascending colon of the large Japanese field mouse following removal of the digestive tract.,27,41,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary Table 26,27 November 2025,Firdaws,Firdaws,Relative abundance of bacteria genera compared between the lower regions (Colon & Cecum) of the Gastrointestinal tract (GIT) in Apodemus speciosus based on pairwise LEfSe analysis.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|1385|539738|1378,Complete,NA
bsdb:34620922/5/2,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 5,Japan,Apodemus speciosus,Ascending colon,NA,Species design,EFO:0001753,Cecum of Large Japanese field mouse,Colon of Large Japanese field mouse,Gut content was collected from the ascending colon of the large Japanese field mouse following removal of the digestive tract.,27,41,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Supplementary Table 26,27 November 2025,Firdaws,Firdaws,Relative abundance of bacteria genera compared between the lower regions (Colon & Cecum) of the Gastrointestinal tract (GIT) in Apodemus speciosus based on pairwise LEfSe analysis.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,1783272|1239|186801|186802|216572|459786,Complete,NA
bsdb:34620922/6/1,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 6,Japan,Apodemus speciosus,Ascending colon,NA,Species design,EFO:0001753,Rectum of Large Japanese field mouse,Colon of Large Japanese field mouse,Gut content was collected from the ascending colon of the large Japanese field mouse following removal of the digestive tract.,25,41,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary Table 26,27 November 2025,Firdaws,Firdaws,Relative abundance of bacteria genera compared between the lower regions (Colon & Rectum) of the Gastrointestinal tract (GIT) in Apodemus speciosus based on pairwise LEfSe analysis.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Cerasicoccaceae|g__Cerasicoccus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter",1783272|1239|186801|3085636|186803|1427378;3379134|74201|414999|415001|3056374|468938;3379134|29547|3031852|213849|72293|209,Complete,NA
bsdb:34620922/6/2,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 6,Japan,Apodemus speciosus,Ascending colon,NA,Species design,EFO:0001753,Rectum of Large Japanese field mouse,Colon of Large Japanese field mouse,Gut content was collected from the ascending colon of the large Japanese field mouse following removal of the digestive tract.,25,41,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Supplementary Table 24 and Supplementary Table 26,27 November 2025,Firdaws,Firdaws,Relative abundance of bacteria genera compared between the lower regions (Colon & Rectum) of the Gastrointestinal tract (GIT) in Apodemus speciosus based on pairwise LEfSe analysis.,decreased,"p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella",95818|2093818|2093825|2171986|1331051;3379134|976|200643|171549|2005473|1918540;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|171550|28138,Complete,NA
bsdb:34620922/7/1,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 7,Japan,Apodemus argenteus,Ileum,UBERON:0002116,Species design,EFO:0001753,Colon of Small Japanese field mouse,Small intestine of Small Japanese field mouse,Gut content was collected from the ileum within the small intestine of the small Japanese field mouse following removal of the digestive tract.,7,9,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 1,Supplementary Table 27,28 November 2025,Firdaws,Firdaws,Relative abundance of bacterial genera and species compared between the upper (Small intestine) and lower (Colon) Gastrointestinal tract (GIT) in Apodemus argenteus based on pairwise LEfSe analysis.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum",1783272|1239|186801|3085636|186803|1427378;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|3085642|580596;3379134|29547|3031852|213849|72294|194;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|1392389;3379134|976|200643|171549|2005473|1918540;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;3379134|1224|28216|80840|75682|846;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|171550|28138;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|3082720|543314|35518,Complete,NA
bsdb:34620922/7/2,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 7,Japan,Apodemus argenteus,Ileum,UBERON:0002116,Species design,EFO:0001753,Colon of Small Japanese field mouse,Small intestine of Small Japanese field mouse,Gut content was collected from the ileum within the small intestine of the small Japanese field mouse following removal of the digestive tract.,7,9,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 2,Supplementary Table 27,28 November 2025,Firdaws,Firdaws,Relative abundance of bacterial genera compared between the upper (Small intestine) and lower (Colon) Gastrointestinal tract (GIT) in Apodemus argenteus based on pairwise LEfSe analysis.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Rodentibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Coxiella",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1301;3379134|1224|1236|135625|712|1960084;3379134|1224|1236|72274|135621|286;1783272|1239|91061|1385|539738|1378;1783272|1239|909932|1843489|31977|29465;3384189|32066|203490|203491|1129771|32067;3379134|1224|1236|118969|118968|776,Complete,NA
bsdb:34620922/8/1,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 8,Japan,Apodemus argenteus,Ileum,UBERON:0002116,Species design,EFO:0001753,Cecum of Small Japanese field mouse,Small intestine of Small Japanese field mouse,Gut content was collected from the ileum within the small intestine of the small Japanese field mouse following removal of the digestive tract.,9,9,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 1,Supplementary Table 24 and Supplementary Table 27,28 November 2025,Firdaws,Firdaws,Relative abundance of bacterial genera compared between the upper (Small intestine) and lower (Cecum) Gastrointestinal tract (GIT) in Apodemus argenteus based on pairwise LEfSe analysis.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Coxiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Rodentibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|85004|31953|1678;3379134|1224|1236|118969|118968|776;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|33958|1578;3384189|32066|203490|203491|1129771|32067;1783272|544448|31969|2085|2092|2093;3379134|1224|1236|72274|135621|286;3379134|1224|1236|135625|712|1960084;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,NA
bsdb:34620922/8/2,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 8,Japan,Apodemus argenteus,Ileum,UBERON:0002116,Species design,EFO:0001753,Cecum of Small Japanese field mouse,Small intestine of Small Japanese field mouse,Gut content was collected from the ileum within the small intestine of the small Japanese field mouse following removal of the digestive tract.,9,9,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 2,Supplementary Table 24 and Supplementary Table 27,28 November 2025,Firdaws,Firdaws,Relative abundance of bacterial genera and species compared between the upper (Small intestine) and lower (Cecum) Gastrointestinal tract (GIT) in Apodemus argenteus based on pairwise LEfSe analysis.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum",1783272|1239|186801|3085636|186803|1427378;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;3379134|29547|3031852|213849|72294|194;95818|2093818|2093825|2171986|1331051;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803|1506553;3379134|976|200643|171549|2005473|1918540;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;3379134|1224|28216|80840|75682|846;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|171550|28138;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|3082720|543314|35518,Complete,NA
bsdb:34620922/9/1,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 9,Japan,Apodemus argenteus,Ileum,UBERON:0002116,Species design,EFO:0001753,Rectum of Small Japanese field mouse,Small intestine of Small Japanese field mouse,Gut content was collected from the ileum within the small intestine of the small Japanese field mouse following removal of the digestive tract.,9,9,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 1,Supplementary Table 24 and Supplementary Table 27,28 November 2025,Firdaws,Firdaws,Relative abundance of bacterial genera compared between the upper (Small intestine) and lower (Rectum) Gastrointestinal tract (GIT) in Apodemus argenteus based on pairwise LEfSe analysis.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Coxiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Rodentibacter",3379134|1224|1236|118969|118968|776;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|33958|1578;3384189|32066|203490|203491|1129771|32067;3379134|1224|1236|72274|135621|286;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|135625|712|1960084,Complete,NA
bsdb:34620922/9/2,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 9,Japan,Apodemus argenteus,Ileum,UBERON:0002116,Species design,EFO:0001753,Rectum of Small Japanese field mouse,Small intestine of Small Japanese field mouse,Gut content was collected from the ileum within the small intestine of the small Japanese field mouse following removal of the digestive tract.,9,9,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 2,Supplementary Table 24 and Supplementary Table 27,28 November 2025,Firdaws,Firdaws,Relative abundance of bacterial genera and species compared between the upper (Small intestine) and lower (Rectum) Gastrointestinal tract (GIT) in Apodemus argenteus based on pairwise LEfSe analysis.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum",1783272|1239|186801|3085636|186803|1427378;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|3085642|580596;3379134|29547|3031852|213849|72294|194;95818|2093818|2093825|2171986|1331051;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|1392389;3379134|976|200643|171549|2005473|1918540;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;3379134|1224|28216|80840|75682|846;3379134|976|200643|171549|171550|28138;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|3082720|543314|35518,Complete,NA
bsdb:34620922/10/1,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 10,Japan,Apodemus argenteus,Cecum mucosa,UBERON:0000314,Species design,EFO:0001753,Rectum of Small Japanese field mouse,Cecum of Small Japanese field mouse,Gut content was collected from the central part of the cecum of the small Japanese field mouse following removal of the digestive tract.,9,9,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary Table 24 and Supplementary Table 28,28 November 2025,Firdaws,Firdaws,Relative abundance of bacteria genera compared between the lower regions (Cecum & Rectum) of the Gastrointestinal tract (GIT) in Apodemus argenteus based on pairwise LEfSe analysis.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",1783272|1239|186801|3085636|186803|1427378;3379134|29547|3031852|213849|72294|194;3379134|200940|3031449|213115|194924|872;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|1506577,Complete,NA
bsdb:34620922/10/2,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 10,Japan,Apodemus argenteus,Cecum mucosa,UBERON:0000314,Species design,EFO:0001753,Rectum of Small Japanese field mouse,Cecum of Small Japanese field mouse,Gut content was collected from the central part of the cecum of the small Japanese field mouse following removal of the digestive tract.,9,9,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Supplementary Table 24 and Supplementary Table 28,28 November 2025,Firdaws,Firdaws,Relative abundance of bacteria genera and species compared between the lower regions (Cecum & Rectum) of the Gastrointestinal tract (GIT) in Apodemus argenteus based on pairwise LEfSe analysis.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Rodentibacter",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|186806|1730|290054;3379134|976|200643|171549|2005473|1918540;3379134|976|200643|171549|171550|28138;3379134|1224|1236|135625|712|1960084,Complete,NA
bsdb:34620922/11/1,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 11,Japan,Apodemus argenteus,Ascending colon,NA,Species design,EFO:0001753,Cecum of Small Japanese field mouse,Colon of Small Japanese field mouse,Gut content was collected from the ascending colon of the small Japanese field mouse following removal of the digestive tract.,9,7,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary Table 24 and Supplementary Table 28,28 November 2025,Firdaws,Firdaws,Relative abundance of bacteria genera compared between the lower regions (Colon & Cecum) of the Gastrointestinal tract (GIT) in Apodemus argenteus based on pairwise LEfSe analysis.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter",1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|186802|1392389;3379134|1224|28216|80840|75682|846,Complete,NA
bsdb:34620922/11/2,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 11,Japan,Apodemus argenteus,Ascending colon,NA,Species design,EFO:0001753,Cecum of Small Japanese field mouse,Colon of Small Japanese field mouse,Gut content was collected from the ascending colon of the small Japanese field mouse following removal of the digestive tract.,9,7,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Supplementary Table 24 and Supplementary Table 28,1 December 2025,Firdaws,Firdaws,Relative abundance of bacteria genera compared between the lower regions (Colon & Cecum) of the Gastrointestinal tract (GIT) in Apodemus argenteus based on pairwise LEfSe analysis.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",1783272|1239|186801|3085636|186803|1427378;3379134|29547|3031852|213849|72294|194;3379134|200940|3031449|213115|194924|872;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|1506577,Complete,NA
bsdb:34620922/12/1,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 12,Japan,Myodes rufocanus,Ileum,UBERON:0002116,Species design,EFO:0001753,Colon of Grey red-backed vole,Small intestine of Grey red-backed vole,Gut content was collected from the ileum within the small intestine of  the Grey red-backed vole following removal of the digestive tract.,38,43,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 1,Supplementary Table 29,26 November 2025,Chyono2,Chyono2,Relative abundance of bacterial genera compared between the upper (small intestine) and lower (colon) Gastrointestinal tract (GIT) in Myodes rufocanus based on pairwise LEfSe analysis.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Coxiella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Anaplasmataceae|g__Ehrlichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|g__Exiguobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Rickettsiaceae|g__Rickettsia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Rodentibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|1224|1236|2887326|468|469;95818|2093818|2093825|2171986|1331051;1783272|1239|91061|186826|186828|2747;3379134|1224|1236|118969|118968|776;3379134|200940|3031449|213115|194924|872;3379134|1224|28211|766|942|943;1783272|1239|91061|186826|81852|1350;1783272|201174|84998|1643822|1643826|580024;1783272|1239|91061|1385|33986;3384189|32066|203490|203491|203492|848;3379134|29547|3031852|213849|72293|209;1783272|1239|91061|186826|33958|1578;3379134|1224|28211|766|775|780;3379134|1224|1236|135625|712|1960084;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;1783272|544448|2790996|2790998|2129;1783272|1239|909932|1843489|31977|29465,Complete,NA
bsdb:34620922/12/2,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 12,Japan,Myodes rufocanus,Ileum,UBERON:0002116,Species design,EFO:0001753,Colon of Grey red-backed vole,Small intestine of Grey red-backed vole,Gut content was collected from the ileum within the small intestine of  the Grey red-backed vole following removal of the digestive tract.,38,43,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 2,Supplementary Table 29,27 November 2025,Chyono2,Chyono2,Relative abundance of bacterial genera and species compared between the upper (small intestine) and lower (colon) Gastrointestinal tract (GIT) in Myodes rufocanus based on pairwise LEfSe analysis,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Cerasicoccaceae|g__Cerasicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium oxidoreducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Millionella,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pygmaiobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",1783272|1239|186801|3085636|186803|1427378;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|1940255;1783272|1239|186801|3082720|543314|109326;3379134|200940|3031449|213115|194924|35832;3379134|203691|203692|1643686|143786|29521;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|830;1783272|1239|186801|186802|1470353;3379134|74201|414999|415001|3056374|468938;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|1732;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|186801|186802|216572|1892380;1783272|1239|186801|186802|1392389;3379134|976|200643|171549|171550|1980038;3379134|200930|68337|191393|2945020|248038;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;3379134|1224|28216|80840|75682|846;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|186802|216572|1929305;3379134|976|200643|171549|171550|28138;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3085636|186803|1506577,Complete,NA
bsdb:34620922/13/1,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 13,Japan,Myodes rufocanus,Ileum,UBERON:0002116,Species design,EFO:0001753,Cecum of Grey red-backed vole,Small intestine of Grey red- backed vole,Gut content was collected from the ileum within the small intestine of the Grey red-backed vole following removal of the digestive tract.,14,43,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,decreased,unchanged,NA,NA,NA,decreased,Signature 1,Supplementary Table 29,27 November 2025,Chyono2,Chyono2,Relative abundance of bacterial genera compared between the upper (small intestine) and lower (cecum) Gastrointestinal tract (GIT) in Myodes rufocanus based on pairwise LEfSe analysis,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Coxiella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|91061|186826|186828|2747;3379134|1224|1236|118969|118968|776;3379134|200940|3031449|213115|194924|872;3379134|29547|3031852|213849|72293|209;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1301;1783272|544448|2790996|2790998|2129;1783272|1239|909932|1843489|31977|29465,Complete,NA
bsdb:34620922/13/2,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 13,Japan,Myodes rufocanus,Ileum,UBERON:0002116,Species design,EFO:0001753,Cecum of Grey red-backed vole,Small intestine of Grey red- backed vole,Gut content was collected from the ileum within the small intestine of the Grey red-backed vole following removal of the digestive tract.,14,43,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,decreased,unchanged,NA,NA,NA,decreased,Signature 2,Supplementary Table 29 and Supplementary Table 24,27 November 2025,Chyono2,Chyono2,Relative abundance of bacterial genera and species compared between the upper (small intestine) and lower (cecum) Gastrointestinal tract (GIT) in Myodes rufocanus based on pairwise LEfSe analysis,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Angelakisella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium oxidoreducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Millionella,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pygmaiobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] brachy",1783272|1239|186801|3085636|186803|1427378;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|1940255;1783272|1239|186801|186802|216572|1935176;3379134|200940|3031449|213115|194924|35832;3379134|203691|203692|1643686|143786|29521;1783272|1239|186801|3085636|186803|830;95818|2093818|2093825|2171986|1331051;1783272|1239|186801|186802|1470353;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|1732;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|186801|186802|216572|1892380;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803|1506553;3379134|976|200643|171549|171550|1980038;3379134|200930|68337|191393|2945020|248038;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;3379134|1224|28216|80840|75682|846;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|186802|216572|1929305;3379134|976|200643|171549|171550|28138;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|3082720|543314|35517,Complete,NA
bsdb:34620922/14/1,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 14,Japan,Myodes rufocanus,Ileum,UBERON:0002116,Species design,EFO:0001753,Rectum of Grey red-backed vole,Small intestine of Grey red- backed vole,Gut content was collected from the ileum within the small intestine of the Grey red-backed vole following removal of the digestive tract.,16,43,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 1,Supplementary Table 29,27 November 2025,Chyono2,Chyono2,Relative abundance of bacterial genera compared between the upper (small intestine) and lower (Rectum) Gastrointestinal tract (GIT) in Myodes rufocanus based on pairwise LEfSe analysis,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Coxiella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Rodentibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|91061|186826|186828|2747;3379134|1224|1236|118969|118968|776;3384189|32066|203490|203491|203492|848;3379134|29547|3031852|213849|72293|209;1783272|1239|91061|186826|33958|1578;3379134|1224|1236|135625|712|1960084;1783272|1239|91061|186826|1300|1301;1783272|544448|2790996|2790998|2129;1783272|1239|909932|1843489|31977|29465,Complete,NA
bsdb:34620922/14/2,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 14,Japan,Myodes rufocanus,Ileum,UBERON:0002116,Species design,EFO:0001753,Rectum of Grey red-backed vole,Small intestine of Grey red- backed vole,Gut content was collected from the ileum within the small intestine of the Grey red-backed vole following removal of the digestive tract.,16,43,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 2,Supplementary Table 29,27 November 2025,Chyono2,Chyono2,Relative abundance of bacteria genera and species compared between the upper (small intestine) and lower (rectum) Gastrointestinal tract (GIT) in Myodes rufocanus based on pairwise LEfSe analysis.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Millionella,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pygmaiobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Quinella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium oxidoreducens",1783272|1239|186801|3085636|186803|1427378;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|1940255;1783272|1239|186801|186802|216572|52784;3379134|200940|3031449|213115|194924|35832;3379134|203691|203692|1643686|143786|29521;1783272|1239|186801|3085636|186803|830;95818|2093818|2093825|2171986|1331051;1783272|1239|186801|186802|1470353;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|186801|186802|216572|1892380;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803|1506553;3379134|976|200643|171549|171550|1980038;3379134|200930|68337|191393|2945020|248038;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;3379134|1224|28216|80840|75682|846;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|186802|216572|1929305;1783272|1239|909932|1843489|31977|1567;3379134|976|200643|171549|171550|28138;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|186802|186806|1730|1732,Complete,NA
bsdb:34620922/15/1,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 15,Japan,Myodes rufocanus,Cecum mucosa,UBERON:0000314,Species design,EFO:0001753,Rectum of Grey red-backed vole,Cecum of Grey red-backed vole,Gut content was collected from the central part of the cecum of the Grey red-backed vole following removal of the digestive tract.,16,14,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary Table 30 and Supplementary Table 24,27 November 2025,Chyono2,Chyono2,Relative abundance of bacteria genera compared between the lower regions (Cecum & Rectum) of Gastrointestinal tract (GIT) in Myodes rufocanus based on pairwise comparison,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,1783272|1239|186801|186802|216572|459786,Complete,NA
bsdb:34620922/15/2,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 15,Japan,Myodes rufocanus,Cecum mucosa,UBERON:0000314,Species design,EFO:0001753,Rectum of Grey red-backed vole,Cecum of Grey red-backed vole,Gut content was collected from the central part of the cecum of the Grey red-backed vole following removal of the digestive tract.,16,14,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Supplementary Table 30,27 November 2025,Chyono2,Chyono2,Relative abundance of bacteria genera compared between the lower regions (Cecum & Rectum) of Gastrointestinal tract (GIT) in Myodes rufocanus based on pairwise comparison,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pygmaiobacter",1783272|1239|186801|186802|186806|1730|39497;1783272|1239|186801|186802|216572|1929305,Complete,NA
bsdb:34620922/18/1,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 18,Japan,Apodemus speciosus,Ileum,UBERON:0002116,Species design,EFO:0001753,Small Japanese field mouse (Apodemus argenteus) : Small intestine,Large Japanese field mouse(Apodemus speciosus): Small intestine,Gut content was collected from the small intestine of the large Japanese field mouse following the removal of the digestive tract.,9,25,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,increased,increased,NA,NA,NA,unchanged,Signature 1,Supplementary Table 34 and Supplementary Table 33,27 November 2025,Chyono2,Chyono2,Relative abundance of bacterial genera within the small intestine of each host species based on pairwise  LEfSe analysis between Apodemus speciosus and Apodemus argenteus.,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella",3384189|32066|203490|203491|203492|848;3379134|200930|68337|191393|2945020|248038;1783272|544448|2790996|2790998|2129;3379134|976|117743|200644|2762318|59735;1783272|1239|526524|526525|2810281|191303;3379134|1224|1236|91347|1903411|613;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005473|1918540;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|171550|28138,Complete,NA
bsdb:34620922/18/2,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 18,Japan,Apodemus speciosus,Ileum,UBERON:0002116,Species design,EFO:0001753,Small Japanese field mouse (Apodemus argenteus) : Small intestine,Large Japanese field mouse(Apodemus speciosus): Small intestine,Gut content was collected from the small intestine of the large Japanese field mouse following the removal of the digestive tract.,9,25,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,increased,increased,NA,NA,NA,unchanged,Signature 2,Supplementary Table 34 and Supplementary Table 33,28 November 2025,Chyono2,Chyono2,Relative abundance of bacterial genera within the small intestine of each host species based on pairwise  LEfSe analysis between Apodemus speciosus and Apodemus argenteus.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Aquicella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Coxiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Gemmatimonadota|c__Gemmatimonadia|o__Gemmatimonadales|f__Gemmatimonadaceae|g__Gemmatimonas,k__Pseudomonadati|p__Myxococcota|o__Haliangiales|f__Kofleriaceae|g__Haliangium,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia|o__Acidimicrobiales|f__Ilumatobacteraceae|g__Ilumatobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Pseudomonadati|p__Myxococcota|o__Polyangiales|f__Polyangiaceae|g__Minicystis,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae|g__Pelosinus,k__Pseudomonadati|p__Myxococcota|o__Polyangiales|f__Phaselicystidaceae|g__Phaselicystis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Rodentibacter,k__Pseudomonadati|p__Myxococcota|o__Polyangiales|f__Sandaracinaceae|g__Sandaracinus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax",3379134|1224|1236|118969|118968|254245;1783272|201174|1760|85004|31953|1678;3379134|203691|203692|1643686|143786|29521;3379134|1224|28211|356|41294|374;3379134|29547|3031852|213849|72294|194;3379134|976|117743|200644|2762318|59732;3379134|1224|1236|118969|118968|776;1783272|1239|91061|1385|539738|1378;3379134|142182|219685|219686|219687|173479;3379134|2818505|3031714|224464|162027;1783272|201174|84992|84993|2448023|682522;1783272|1239|91061|186826|33958|1578;3384189|32066|203490|203491|1129771|32067;3379134|1224|28211|356|119045|407;3379134|2818505|3031712|49|1649470;1783272|544448|31969|2085|2092|2093;3379134|976|200643|171549|2005523|346096;1783272|1239|909932|909929|1843490|365348;3379134|2818505|3031712|651809|651810;3379134|1224|28211|356|69277|28100;3379134|1224|1236|91347|1903414|586;3379134|1224|1236|135625|712|1960084;3379134|2818505|3031712|1055686|1055688;3379134|1224|28211|204457|41297|13687;1783272|1239|91061|186826|1300|1301;1783272|201174|1760|85011|2062|1883;3379134|1224|28216|80840|80864|34072,Complete,NA
bsdb:34620922/19/1,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 19,Japan,Myodes rufocanus,Ileum,UBERON:0002116,Species design,EFO:0001753,Large Japanese field mouse (Apodemus speciosus) : Small intestine,Grey red-backed vole (Myodes rufocanus) : Small intestine,Gut content was collected from the ileum within the small intestine of the Grey red-backed vole following the removal of the digestive tract.,42,43,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,increased,increased,NA,NA,NA,increased,Signature 1,Supplementary Table 34 and Supplementary Table 33,28 November 2025,Chyono2,Chyono2,Relative abundance of bacterial genera and species within the small intestine of each host species based on pairwise LEfSe analysis between Apodemus speciosus and Myodes rufocanus,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Amoebophilaceae|g__Candidatus Cardinium,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Coxiella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Millionella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Rickettsiaceae|g__Rickettsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma",1783272|1239|186801|186802|216572|1940255;3379134|976|768503|768507|1501348|273135;95818|2093818|2093825|2171986|1331051;3379134|1224|1236|118969|118968|776;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|171550|1980038;1783272|1239|186801|186802|186807|2740;3379134|1224|28211|766|775|780;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1508657;1783272|544448|2790996|2790998|2129,Complete,NA
bsdb:34620922/19/2,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 19,Japan,Myodes rufocanus,Ileum,UBERON:0002116,Species design,EFO:0001753,Large Japanese field mouse (Apodemus speciosus) : Small intestine,Grey red-backed vole (Myodes rufocanus) : Small intestine,Gut content was collected from the ileum within the small intestine of the Grey red-backed vole following the removal of the digestive tract.,42,43,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,increased,increased,NA,NA,NA,increased,Signature 2,Supplementary Table 34 and Supplementary Table 33,28 November 2025,Chyono2,Chyono2,Relative abundance of bacterial genera within the small intestine of each host species based on pairwise LEfSe analysis between Apodemus speciosus and Myodes rufocanus,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Anaerobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",3379134|1224|1236|2887326|468|469;1783272|1239|91061|1385|186817|704093;3379134|976|200643|171549|815|816;3379134|976|117743|200644|2762318|59735;3379134|1224|28216|80840|80864|80865;1783272|1239|526524|526525|128827|1729679;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378;3384189|32066|203490|203491|1129771|32067;3379134|200930|68337|191393|2945020|248038;3379134|976|200643|171549|2005473|1918540;3379134|976|200643|171549|1853231|283168;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171550|28138;3379134|1224|1236|91347|1903411|613;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810281|191303,Complete,NA
bsdb:34620922/21/1,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 21,Japan,Apodemus speciosus,Cecum mucosa,UBERON:0000314,Species design,EFO:0001753,Small Japanese field mouse (Apodemus argenteus) : Cecum,Large Japanese field mouse (Apodemus speciosus) : Cecum,Gut content was collected from the central part of the cecum of the large Japanese field mouse following the removal of the digestive tract.,9,27,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,increased,increased,NA,NA,NA,unchanged,Signature 1,Supplementary Table 35 and Supplementary Table 33,28 November 2025,Chyono2,Chyono2,Relative abundance of bacterial genera and species within the cecum of each host species based on pairwise LEfSe analysis between Apodemus speciosus and Apodemus argenteus.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum",3379134|976|200643|171549|815|816;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|3085642|580596;3379134|29547|3031852|213849|72293|209;3379134|200930|68337|191393|2945020|248038;3379134|976|200643|171549|2005473|1918540;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|1508657;1783272|544448|2790996|2790998|2129;1783272|1239|186801|3082720|543314|35518,Complete,NA
bsdb:34620922/21/2,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 21,Japan,Apodemus speciosus,Cecum mucosa,UBERON:0000314,Species design,EFO:0001753,Small Japanese field mouse (Apodemus argenteus) : Cecum,Large Japanese field mouse (Apodemus speciosus) : Cecum,Gut content was collected from the central part of the cecum of the large Japanese field mouse following the removal of the digestive tract.,9,27,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,increased,increased,NA,NA,NA,unchanged,Signature 2,Supplementary Table 35 and Supplementary Table 33,28 November 2025,Chyono2,Chyono2,Relative abundance of bacterial genera within the cecum of each host species based on pairwise LEfSe analysis between Apodemus speciosus and Apodemus argenteus.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Rickettsiaceae|g__Rickettsia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",3379134|976|200643|171549|171550|239759;3379134|203691|203692|1643686|143786|29521;3379134|29547|3031852|213849|72294|194;3379134|1224|28216|80840|75682|846;3379134|1224|28216|80840|995019|577310;3379134|1224|28211|766|775|780;3379134|976|200643|171549|171550|28138;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810281|191303,Complete,NA
bsdb:34620922/22/1,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 22,Japan,Myodes rufocanus,Cecum mucosa,UBERON:0000314,Species design,EFO:0001753,Large Japanese field mouse (Apodemus speciosus) : Cecum,Grey red-backed vole (Myodes rufocanus) : Cecum,Gut content was collected from the central part of cecum of Grey red-backed vole following the removal of the digestive tract.,27,14,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,increased,increased,NA,NA,NA,increased,Signature 1,Supplementary Table 35 and Supplementary Table 33,30 November 2025,Chyono2,Chyono2,Relative abundance of bacterial genera and species within the cecum of each host species based on pairwise LEfSe analysis between Apodemus speciosus and Myodes rufocanus,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium oxidoreducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Millionella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pygmaiobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Quinella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",1783272|1239|186801|186802|216572|1940255;1783272|1239|186801|3085636|186803|207244;3379134|203691|203692|1643686|143786|29521;95818|2093818|2093825|2171986|1331051;1783272|1239|186801|186802|1470353;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|186806|1730|1732;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|186801|186802|216572|1892380;3379134|976|200643|171549|171550|1980038;3379134|1224|28216|80840|75682|846;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|186802|216572|1929305;1783272|1239|909932|1843489|31977|1567;1783272|1239|186801|186802|216572|1508657,Complete,NA
bsdb:34620922/22/2,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 22,Japan,Myodes rufocanus,Cecum mucosa,UBERON:0000314,Species design,EFO:0001753,Large Japanese field mouse (Apodemus speciosus) : Cecum,Grey red-backed vole (Myodes rufocanus) : Cecum,Gut content was collected from the central part of cecum of Grey red-backed vole following the removal of the digestive tract.,27,14,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,increased,increased,NA,NA,NA,increased,Signature 2,Supplementary Table 35 and Supplementary Table 33,30 November 2025,Chyono2,Chyono2,Relative abundance of bacterial genera and species within the cecum of each host species based on pairwise LEfSe analysis between Apodemus speciosus and Myodes rofocanus,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|3085642|580596;3379134|29547|3031852|213849|72293|209;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803|1506553;3379134|200930|68337|191393|2945020|248038;3379134|976|200643|171549|2005473|1918540;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|577310;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3082720|543314|35518,Complete,NA
bsdb:34620922/23/1,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 23,Japan,Apodemus argenteus,Ascending colon,NA,Species design,EFO:0001753,Rectum of Small Japanese field mouse,Colon of Small Japanese field mouse,Gut content was collected from the ascending colon of the small Japanese field mouse following removal of the digestive tract.,9,7,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary Table 24 and Supplementary Table 28,28 November 2025,Firdaws,Firdaws,Relative abundance of bacteria genera compared between the lower regions (Colon & Rectum) of the Gastrointestinal tract (GIT) in Apodemus argenteus based on pairwise LEfSe analysis.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter",1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|186802|1392389;3379134|1224|28216|80840|75682|846,Complete,NA
bsdb:34620922/23/2,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 23,Japan,Apodemus argenteus,Ascending colon,NA,Species design,EFO:0001753,Rectum of Small Japanese field mouse,Colon of Small Japanese field mouse,Gut content was collected from the ascending colon of the small Japanese field mouse following removal of the digestive tract.,9,7,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Supplementary Table 24 and Supplementary Table 28,1 December 2025,Firdaws,Firdaws,Relative abundance of bacteria genera and species compared between the lower regions (Colon & Rectum) of the Gastrointestinal tract (GIT) in Apodemus argenteus based on pairwise LEfSe analysis.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Rodentibacter",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|186806|1730|290054;3379134|976|200643|171549|2005473|1918540;3379134|976|200643|171549|171550|28138;3379134|1224|1236|135625|712|1960084,Complete,NA
bsdb:34620922/24/1,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 24,Japan,Apodemus speciosus,Rectum,UBERON:0001052,Species design,EFO:0001753,Small Japanese field mouse (Apodemus argenteus) : Rectum,Large Japanese field mouse (Apodemus speciosus) : Rectum,Fecal sample was collected from the rectum of the large Japanese field mouse following removal of the digestive tract.,9,25,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary Table 33 and Supplementary Table 37,29 November 2025,Firdaws,Firdaws,Relative abundance of bacterial genera and species within the rectum of each host species based on pairwise LEfSe analysis between Apodemus speciosus and Apodemus argenteus.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum",3379134|976|200643|171549|815|816;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|3085642|580596;1783272|201174|84998|1643822|1643826|580024;3379134|29547|3031852|213849|72293|209;3379134|200930|68337|191393|2945020|248038;3379134|976|200643|171549|2005473|1918540;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|577310;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810281|191303;1783272|544448|2790996|2790998|2129;1783272|1239|186801|3082720|543314|35518,Complete,NA
bsdb:34620922/24/2,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 24,Japan,Apodemus speciosus,Rectum,UBERON:0001052,Species design,EFO:0001753,Small Japanese field mouse (Apodemus argenteus) : Rectum,Large Japanese field mouse (Apodemus speciosus) : Rectum,Fecal sample was collected from the rectum of the large Japanese field mouse following removal of the digestive tract.,9,25,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Supplementary Table 33 and Supplementary Table 37,29 November 2025,Firdaws,Firdaws,Relative abundance of bacterial genera within the rectum of each host species based on pairwise LEfSe analysis between Apodemus speciosus and Apodemus argenteus.,decreased,"k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",3379134|203691|203692|1643686|143786|29521;3379134|29547|3031852|213849|72294|194;3379134|976|200643|171549|171550|28138;1783272|544448|31969|2085|2092|2093;3379134|976|200643|171549|171550|239759,Complete,NA
bsdb:34620922/25/1,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 25,Japan,Myodes rufocanus,Rectum,UBERON:0001052,Species design,EFO:0001753,Large Japanese field mouse (Apodemus speciosus) : Rectum,Grey red-backed vole (Myodes rufocanus) : Rectum,Fecal sample was collected from the rectum of the Grey red-backed vole following removal of the digestive tract.,25,16,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,increased,increased,NA,NA,NA,increased,Signature 1,Supplementary Table 33 and Supplementary Table 37,29 November 2025,Firdaws,Firdaws,Relative abundance of bacterial genera and species within the rectum of each host species based on pairwise LEfSe analysis between Myodes rufocanus and Apodemus speciosus.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Millionella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pygmaiobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Quinella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes",1783272|1239|186801|3085636|186803|1427378;1783272|1239|186801|186802|216572|1940255;1783272|1239|186801|186802|216572|52784;1783272|544448|31969|186332|186333|2086;3379134|203691|203692|1643686|143786|29521;95818|2093818|2093825|2171986|1331051;1783272|1239|186801|186802|1470353;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|186801|186802|216572|1892380;3379134|976|200643|171549|171550|1980038;3379134|1224|28216|80840|75682|846;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|186802|216572|1929305;1783272|1239|909932|1843489|31977|1567;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3085636|186803|207244,Complete,NA
bsdb:34620922/25/2,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 25,Japan,Myodes rufocanus,Rectum,UBERON:0001052,Species design,EFO:0001753,Large Japanese field mouse (Apodemus speciosus) : Rectum,Grey red-backed vole (Myodes rufocanus) : Rectum,Fecal sample was collected from the rectum of the Grey red-backed vole following removal of the digestive tract.,25,16,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,increased,increased,NA,NA,NA,increased,Signature 2,Supplementary Table 33 and Supplementary Table 37,29 November 2025,Firdaws,Firdaws,Relative abundance of bacterial genera and species within the rectum of each host species based on pairwise LEfSe analysis between Myodes rufocanus and Apodemus speciosus.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|3085642|580596;3379134|29547|3031852|213849|72293|209;3379134|200930|68337|191393|2945020|248038;3379134|976|200643|171549|2005473|1918540;1783272|544448|31969|2085|2092|2093;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|171550|28138;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3082720|543314|35518,Complete,NA
bsdb:34620922/26/1,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 26,Japan,Myodes rufocanus,Rectum,UBERON:0001052,Species design,EFO:0001753,Small Japanese field mouse (Apodemus argenteus) : Rectum,Grey red-backed vole (Myodes rufocanus) : Rectum,Fecal sample was collected from the rectum of the Grey red-backed vole following removal of the digestive tract.,9,16,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,increased,increased,NA,NA,NA,increased,Signature 1,Supplementary Table 33 and Supplementary Table 37,29 November 2025,Firdaws,Firdaws,Relative abundance of bacterial genera and species within the rectum of each host species based on pairwise LEfSe analysis between Myodes rufocanus and Apodemus argenteus.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Millionella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pygmaiobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter",1783272|1239|186801|3085636|186803|1427378;1783272|1239|186801|186802|216572|1940255;1783272|544448|31969|186332|186333|2086;95818|2093818|2093825|2171986|1331051;1783272|1239|186801|186802|1470353;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|186806|1730|39497;3379134|976|200643|171549|171550|1980038;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|186802|216572|1929305;1783272|1239|186801|186802|216572|1508657;1783272|544448|2790996|2790998|2129;3379134|1224|28216|80840|75682|846,Complete,NA
bsdb:34620922/26/2,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 26,Japan,Myodes rufocanus,Rectum,UBERON:0001052,Species design,EFO:0001753,Small Japanese field mouse (Apodemus argenteus) : Rectum,Grey red-backed vole (Myodes rufocanus) : Rectum,Fecal sample was collected from the rectum of the Grey red-backed vole following removal of the digestive tract.,9,16,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,increased,increased,NA,NA,NA,increased,Signature 2,Supplementary Table 33 and Supplementary Table 37,29 November 2025,Firdaws,Firdaws,Relative abundance of bacterial genera and species within the rectum of each host species based on pairwise LEfSe analysis between Myodes rufocanus and Apodemus argenteus.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|3085642|580596;3379134|29547|3031852|213849|72294|194;3379134|976|200643|171549|2005473|1918540;1783272|544448|31969|2085|2092|2093;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|171550|28138;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3082720|543314|35518;3379134|203691|203692|1643686|143786|29521,Complete,NA
bsdb:34620922/27/1,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 27,Japan,Myodes rufocanus,Cecum mucosa,UBERON:0000314,Species design,EFO:0001753,Small Japanese field mouse (Apodemus argenteus) : Cecum,Grey red-backed vole (Myodes rufocanus) : Cecum,Gut content was collected from the central part of the cecum of Grey red-backed vole following the removal of the digestive tract.,9,14,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,increased,increased,NA,NA,NA,increased,Signature 1,Supplementary Table 35 and Supplementary Table 33,30 November 2025,Chyono2,Chyono2,Relative abundance of bacterial genera and species within the Cecum of each host species based on pairwise LEfSe analysis between Myodes rufocanus and Apodemus argenteus,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Millionella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pygmaiobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma",1783272|1239|186801|186802|216572|1940255;1783272|544448|31969|186332|186333|2086;95818|2093818|2093825|2171986|1331051;1783272|1239|186801|186802|1470353;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|186801|186802|216572|1892380;3379134|976|200643|171549|171550|1980038;3379134|1224|28216|80840|75682|846;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|186802|216572|1929305;1783272|1239|186801|186802|216572|1508657;1783272|544448|2790996|2790998|2129,Complete,NA
bsdb:34620922/27/2,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 27,Japan,Myodes rufocanus,Cecum mucosa,UBERON:0000314,Species design,EFO:0001753,Small Japanese field mouse (Apodemus argenteus) : Cecum,Grey red-backed vole (Myodes rufocanus) : Cecum,Gut content was collected from the central part of the cecum of Grey red-backed vole following the removal of the digestive tract.,9,14,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,increased,increased,NA,NA,NA,increased,Signature 2,Supplementary Table 35 and Supplementary Table 33,30 November 2025,Chyono2,Chyono2,Relative abundance of bacterial genera and species within the cecum of each host species based on pairwise LEfSe analysis between Myodes rufocanus and Apodemus argenteus.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;3379134|203691|203692|1643686|143786|29521;1783272|1239|186801|186802|3085642|580596;3379134|976|200643|171549|2005473|1918540;1783272|544448|31969|2085|2092|2093;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|171550|28138;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3082720|543314|35518,Complete,NA
bsdb:34620922/28/1,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 28,Japan,Apodemus speciosus,Ascending colon,NA,Species design,EFO:0001753,Small Japanese field mouse (Apodemus argenteus) : Colon,Large Japanese field mouse (Apodemus speciosus) : Colon,Gut content was collected from the ascending colon of the large Japanese field mouse following the removal of the digestive tract.,7,41,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,unchanged,increased,NA,NA,NA,increased,Signature 1,Supplementary Table 36 and Supplemetary Table 33,30 November 2025,Chyono2,Chyono2,Relative abundance of bacterial genera and species within the colon of each host species based on pairwise LEfSe analysis between  Apodemus speciosus and Apodemus argenteus,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Cerasicoccaceae|g__Cerasicoccus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;3379134|74201|414999|415001|3056374|468938;1783272|201174|84998|1643822|1643826|580024;1783272|1239|186801|186802|186806|1730|290054;3379134|29547|3031852|213849|72293|209;1783272|1239|186801|3085636|186803|1506553;3379134|200930|68337|191393|2945020|248038;3379134|976|200643|171549|2005473|1918540;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3085636|186803|1506577;1783272|544448|2790996|2790998|2129;1783272|1239|186801|3082720|543314|35518,Complete,NA
bsdb:34620922/28/2,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 28,Japan,Apodemus speciosus,Ascending colon,NA,Species design,EFO:0001753,Small Japanese field mouse (Apodemus argenteus) : Colon,Large Japanese field mouse (Apodemus speciosus) : Colon,Gut content was collected from the ascending colon of the large Japanese field mouse following the removal of the digestive tract.,7,41,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,unchanged,increased,NA,NA,NA,increased,Signature 2,Supplementary  Table 36 and Supplementary Table 33,30 November 2025,Chyono2,Chyono2,Relative abundance of bacterial genera and species within the colon of each host species based on pairwise LEfSe analysis between Apodemus speciosus and Apodemus argenteus,decreased,"k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella",3379134|203691|203692|1643686|143786|29521;3379134|29547|3031852|213849|72294|194;3379134|1224|28216|80840|80864|80865;1783272|1239|186801|186802|186806|1730|39497;3379134|1224|28216|80840|75682|846;1783272|544448|31969|2085|2092|2093;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550|28138;3379134|1224|28216|80840|995019|577310,Complete,NA
bsdb:34620922/29/1,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 29,Japan,Myodes rufocanus,Ascending colon,NA,Species design,EFO:0001753,Large Japanese field mouse (Apodemus speciosus) : Colon,Grey red-backed vole (Myodes rufocanus) : Colon,Gut content was collected from the ascending colon of the Grey red-backed vole following the removal of the digestive tract.,41,38,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,increased,increased,NA,NA,NA,increased,Signature 1,Supplementary Table 36 and Supplemetary Table 33,30 November 2025,Chyono2,Chyono2,Relative abundance of bacterial genera and species within the colon of each host species based on pairwise LEfSe analysis between Myodes rufocanus and Apodemus speciosus.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Millionella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pygmaiobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Quinella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira",1783272|1239|186801|186802|216572|1508657;95818|2093818|2093825|2171986|1331051;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|186806|1730|39497;3379134|976|200643|171549|171550|1980038;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3082720|543314|109326;1783272|544448|31969|186332|186333|2086;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|186802|216572|1940255;1783272|1239|186801|186802|216572|1929305;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|909932|1843489|31977|1567;3379134|1224|28216|80840|75682|846;1783272|1239|186801|186802|216572|1892380;1783272|1239|186801|186802|1470353;3379134|203691|203692|1643686|143786|29521,Complete,NA
bsdb:34620922/29/2,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 29,Japan,Myodes rufocanus,Ascending colon,NA,Species design,EFO:0001753,Large Japanese field mouse (Apodemus speciosus) : Colon,Grey red-backed vole (Myodes rufocanus) : Colon,Gut content was collected from the ascending colon of the Grey red-backed vole following the removal of the digestive tract.,41,38,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,increased,increased,NA,NA,NA,increased,Signature 2,Supplementary Table 36 and Supplemetary Table 33,30 November 2025,Chyono2,Chyono2,Relative abundance of bacterial genera and species within the colon of each host species based on pairwise LEfSe analysis between Myodes rufocanus and Apodemus speciosus,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Cerasicoccaceae|g__Cerasicoccus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] brachy,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;3379134|74201|414999|415001|3056374|468938;1783272|201174|84998|1643822|1643826|580024;1783272|1239|186801|186802|186806|1730|290054;3379134|29547|3031852|213849|72293|209;1783272|1239|186801|3085636|186803|1506553;3379134|200930|68337|191393|2945020|248038;3379134|976|200643|171549|2005473|1918540;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|171550|28138;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3085636|186803|1506577;1783272|544448|2790996|2790998|2129;1783272|1239|186801|3082720|543314|35518;3379134|976|200643|171549|171550|239759;1783272|544448|31969|2085|2092|2093;3384189|32066|203490|203491|1129771|32067;1783272|1239|91061|1385|539738|1378;1783272|1239|186801|3082720|543314|35517;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|577310,Complete,NA
bsdb:34620922/30/1,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 30,Japan,Myodes rufocanus,Ascending colon,NA,Species design,EFO:0001753,Small Japanese field mouse (Apodemus argenteus) : Colon,Grey red-backed vole (Myodes rufocanus) : Colon,Gut content was collected from the ascending colon of the Grey red-backed vole following the removal of the digestive tract.,7,38,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,increased,increased,NA,NA,NA,increased,Signature 1,Supplementary Table 36 and Supplemetary Table 33,30 November 2025,Chyono2,Chyono2,Relative abundance of bacterial genera and species within the colon of each host species based on pairwise LEfSe analysis between Myodes rufocanus and Apodemus argenteus,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Millionella,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pygmaiobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma",1783272|1239|186801|186802|216572|1940255;1783272|544448|31969|186332|186333|2086;95818|2093818|2093825|2171986|1331051;1783272|1239|186801|186802|1470353;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|39497;3379134|976|200643|171549|171550|1980038;3379134|200930|68337|191393|2945020|248038;3379134|1224|28216|80840|75682|846;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|186802|216572|1929305;1783272|1239|186801|186802|216572|1508657;1783272|544448|2790996|2790998|2129,Complete,NA
bsdb:34620922/30/2,34620922,"cross-sectional observational, not case-control",34620922,10.1038/s41598-021-99379-6,NA,"Anders J.L., Moustafa M.A.M., Mohamed W.M.A., Hayakawa T., Nakao R. , Koizumi I.",Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents,Scientific reports,2021,NA,Experiment 30,Japan,Myodes rufocanus,Ascending colon,NA,Species design,EFO:0001753,Small Japanese field mouse (Apodemus argenteus) : Colon,Grey red-backed vole (Myodes rufocanus) : Colon,Gut content was collected from the ascending colon of the Grey red-backed vole following the removal of the digestive tract.,7,38,NA,16S,34,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,increased,increased,NA,NA,NA,increased,Signature 2,Supplementary Table 36 and Supplemetary Table 33,30 November 2025,Chyono2,Chyono2,Relative abundance of bacterial genera and species within the colon of each host species based on pairwise LEfSe analysis between Myodes rufocanus and Apodemus argenteus,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;3379134|203691|203692|1643686|143786|29521;3379134|29547|3031852|213849|72294|194;3384189|32066|203490|203491|1129771|32067;3379134|976|200643|171549|2005473|1918540;1783272|544448|31969|2085|2092|2093;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|171550|28138;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3082720|543314|35518,Complete,NA
bsdb:34622226/1/1,34622226,randomized controlled trial,34622226,https://doi.org/10.1016/j.xcrm.2021.100383,https://www.cell.com/cell-reports-medicine/fulltext/S2666-3791(21)00237-8,"Wang F., He M.M., Yao Y.C., Zhao X., Wang Z.Q., Jin Y., Luo H.Y., Li J.B., Wang F.H., Qiu M.Z., Lv Z.D., Wang D.S., Li Y.H., Zhang D.S. , Xu R.H.",Regorafenib plus toripalimab in patients with metastatic colorectal cancer: a phase Ib/II clinical trial and gut microbiome analysis,Cell reports. Medicine,2021,"colorectal cancer, immunotherapy, microbiome, programmed cell death protein 1, regorafenib, toripalimab",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Non-responders (Progressive Disease),Responders (Partial Response or Stable Disease),"Patients with histologically confirmed metastatic or unresectable MSS/MSI-L/pMMR colorectal cancer treated with 80 mg, or 120 mg regorafenib, plus toripalimab resulting in stable disease or partial response.",21,11,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supp table S3,9 October 2022,Mary Bearkland,"Mary Bearkland,Aiyshaaaa,Peace Sandy,WikiWorks","Linear discriminant analysis effect size (LDA) from phylum to species level shows 
differentially enriched taxa in NR and R groups. Related to Figure 4. R, response; NR, non-response.",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister massiliensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",1783272|1239|909932|1843489|31977|39948|2161821;1783272|1239|909932|909929;1783272|1239|909932|1843489;3379134|976|200643|171549|171552|577309,Complete,Peace Sandy
bsdb:34622226/1/2,34622226,randomized controlled trial,34622226,https://doi.org/10.1016/j.xcrm.2021.100383,https://www.cell.com/cell-reports-medicine/fulltext/S2666-3791(21)00237-8,"Wang F., He M.M., Yao Y.C., Zhao X., Wang Z.Q., Jin Y., Luo H.Y., Li J.B., Wang F.H., Qiu M.Z., Lv Z.D., Wang D.S., Li Y.H., Zhang D.S. , Xu R.H.",Regorafenib plus toripalimab in patients with metastatic colorectal cancer: a phase Ib/II clinical trial and gut microbiome analysis,Cell reports. Medicine,2021,"colorectal cancer, immunotherapy, microbiome, programmed cell death protein 1, regorafenib, toripalimab",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Non-responders (Progressive Disease),Responders (Partial Response or Stable Disease),"Patients with histologically confirmed metastatic or unresectable MSS/MSI-L/pMMR colorectal cancer treated with 80 mg, or 120 mg regorafenib, plus toripalimab resulting in stable disease or partial response.",21,11,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Supp table S3,9 October 2022,Mary Bearkland,"Mary Bearkland,Aiyshaaaa,Peace Sandy,WikiWorks","Linear discriminant analysis effect size (LDA) from phylum to species level shows differentially enriched taxa in NR and R groups. Related to Figure 4. R, response; NR, non-response.",decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Thermodesulfobacteriota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__uncultured Bilophila sp.",1783272|1239|909932|1843488|909930;1783272|1239|909932|1843488;1783272|1239|909932|1843488|909930|904;3379134|976|200643|171549|171550|239759;3379134|200940|3031449|213115|194924|35832;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;3379134|200940|3031449;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492|848|68766;1783272|1239|186801|3085636|186803|1506553;3379134|976|200643|1970189|1573805;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171550;3379134|2904303;1783272|1239|909932|1843488|909930|904;3379134|976|200643|171549|171550|239759;3379134|200940|3031449|213115|194924|35832|529385,Complete,Peace Sandy
bsdb:34631595/1/1,34631595,case-control,34631595,10.3389/fcimb.2021.654202,NA,"Hao X., Li P., Wu S. , Tan J.",Association of the Cervical Microbiota With Pregnancy Outcome in a Subfertile Population Undergoing <i>In Vitro</i> Fertilization: A Case-Control Study,Frontiers in cellular and infection microbiology,2021,"16S r RNA, IVF (in vitro fertilization), cervical microbiota, infertility, pregnancy",Experiment 1,China,Homo sapiens,Cervical mucus,UBERON:0000316,Pregnancy,EFO:0002950,Non-pregnant (FN),Clinical pregnancy (FP),Female IVF patients undergoing fresh embryo transfer (ET) who achieved clinical pregnancy,26,25,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,increased,NA,NA,Signature 1,FIG 4 (A),9 April 2024,Rahila,"Rahila,Scholastica,WikiWorks",Differential abundance and association analysis among the cervical microbiota of the fresh pregnancy group (FP) compared to the non-pregnancy group (FN),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Acetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Prosthecobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",3379134|1224|28211|3120395|433|434;3379134|1224|28211|3120395|433;1783272|1239|909932|1843488|909930;1783272|1239|91061;1783272|1239;1783272|1239|186801|186802|216572|216851;3384189|32066|203490|203491|203492;3384189|32066|203490|203491|203492|848;1783272|1239|186801|186802|204475;3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843488|909930|33024;3379134|74201|203494|48461|203557|48463;1783272|1239|186801|3085636|186803|841;1783272|1239|91061|186826|33958|46255,Complete,Svetlana up
bsdb:34631595/1/2,34631595,case-control,34631595,10.3389/fcimb.2021.654202,NA,"Hao X., Li P., Wu S. , Tan J.",Association of the Cervical Microbiota With Pregnancy Outcome in a Subfertile Population Undergoing <i>In Vitro</i> Fertilization: A Case-Control Study,Frontiers in cellular and infection microbiology,2021,"16S r RNA, IVF (in vitro fertilization), cervical microbiota, infertility, pregnancy",Experiment 1,China,Homo sapiens,Cervical mucus,UBERON:0000316,Pregnancy,EFO:0002950,Non-pregnant (FN),Clinical pregnancy (FP),Female IVF patients undergoing fresh embryo transfer (ET) who achieved clinical pregnancy,26,25,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,increased,NA,NA,Signature 2,FIG 4 (A),9 April 2024,Rahila,"Rahila,Scholastica,WikiWorks",Differential abundance and association analysis among the cervical microbiota of the fresh pregnancy group (FP) compared to the non-pregnancy group (FN),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Pseudomonadati|p__Acidobacteriota,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,p__Candidatus Parcubacteria,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Polynucleobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Rhodocyclaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Rickettsiaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae,k__Pseudomonadati|p__Bacteroidota",1783272|1239|186801|3085636|186803|1427378;3379134|57723;1783272|201174;1783272|1239|91061|186826|186827;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171552|1283313;1783272|544448|31969|186332|186333|2086;1783272|544448|31969|186332;1783272|1239|186801|186802|216572|244127;3379134|29547|3031852|213849|2808963|28196;1783272|201174|84998|84999|1643824|1380;3379134|976|200643|171549;3379134|976|200643;3379134|200940|3031449|213115|194924|35832;3379134|1224|28216|80840|119060;3379134|976|200643|171549|1853231|574697;3379134|29547|3031852|213849;221216;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;28221;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;1783272|1239|909932|1843489|31977|39948;3379134|29547|3031852;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|201174|1760|85004|31953|2701;3379134|29547|3031852|213849|72293|209;3379134|29547|3031852|213849|72293;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481;3379134|1224|28216|206351;1783272|201174|1760|85009|85015;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|577309;3379134|1224|28216|80840|995019|577310;3379134|1224|28216|80840|119060|44013;3379134|976|200643|171549|171551;1783272|201174|1760|85007|85025|1827;3379134|1224|28216|206389|75787;3379134|1224|28216|206389;3379134|1224|28211|766;1783272|1239|186801|186802|216572|1263;1783272|1239|526524|526525|2810281|191303;3379134|74201|203494|48461|203557;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201;3379134|1224|28211|356|212791;3379134|1224|28211|766|775;1783272|544448|31969|186332|186333;3379134|976,Complete,Svetlana up
bsdb:34643448/1/1,34643448,case-control,34643448,10.1128/Spectrum.00055-21,NA,"Miller E.H., Annavajhala M.K., Chong A.M., Park H., Nobel Y.R., Soroush A., Blackett J.W., Krigel A., Phipps M.M., Freedberg D.E., Zucker J., Sano E.D., Uhlemann A.C. , Abrams J.A.",Oral Microbiome Alterations and SARS-CoV-2 Saliva Viral Load in Patients with COVID-19,Microbiology spectrum,2021,"COVID-19, SARS-CoV-2, saliva microbiome, viral load",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,SARS coronavirus,NCBITAXON:694009,Controls,Covid-19,Patients who tested positive for SARS-CoV-2 based on nasopharyngeal swabs and who did not require intensive care at admission.,54,46,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Results text (Page 3),4 May 2024,MyleeeA,"MyleeeA,Scholastica,WikiWorks",Differentially abundant taxa between COVID-19 positive patients versus controls,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,3379134|976|200643|171549|171552|838|60133,Complete,Svetlana up
bsdb:34643448/1/2,34643448,case-control,34643448,10.1128/Spectrum.00055-21,NA,"Miller E.H., Annavajhala M.K., Chong A.M., Park H., Nobel Y.R., Soroush A., Blackett J.W., Krigel A., Phipps M.M., Freedberg D.E., Zucker J., Sano E.D., Uhlemann A.C. , Abrams J.A.",Oral Microbiome Alterations and SARS-CoV-2 Saliva Viral Load in Patients with COVID-19,Microbiology spectrum,2021,"COVID-19, SARS-CoV-2, saliva microbiome, viral load",Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,SARS coronavirus,NCBITAXON:694009,Controls,Covid-19,Patients who tested positive for SARS-CoV-2 based on nasopharyngeal swabs and who did not require intensive care at admission.,54,46,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Results text (Page 3),4 May 2024,MyleeeA,"MyleeeA,Scholastica,WikiWorks",Differentially abundant taxa between COVID-19 positive patients versus controls,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.",1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300|1301|1306,Complete,Svetlana up
bsdb:34643448/2/1,34643448,case-control,34643448,10.1128/Spectrum.00055-21,NA,"Miller E.H., Annavajhala M.K., Chong A.M., Park H., Nobel Y.R., Soroush A., Blackett J.W., Krigel A., Phipps M.M., Freedberg D.E., Zucker J., Sano E.D., Uhlemann A.C. , Abrams J.A.",Oral Microbiome Alterations and SARS-CoV-2 Saliva Viral Load in Patients with COVID-19,Microbiology spectrum,2021,"COVID-19, SARS-CoV-2, saliva microbiome, viral load",Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,SARS coronavirus,NCBITAXON:694009,SARS Cov-2 Saliva Negative,SARS Cov-2 Saliva Positive,COVID-19 patients with positive SARS-CoV-2 viral load in saliva,15,28,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 3,22 April 2024,MyleeeA,"MyleeeA,Scholastica,WikiWorks",Differentially abundant taxa based on SARS-CoV-2 viral load in SARS-CoV-2-positive (pink) versus -negative (blue) saliva,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp. oral taxon 473,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 172,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 180,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum sp.",3379134|976|200643|171549|171552|838|60133;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|91061|186826|1300|1301|68892;1783272|1239|91061|186826|1300|1301|1305;3379134|203691|203692|136|2845253|157|166;3379134|976|200643|171549|171552|1283313|712469;1783272|201174|1760|2037|2049|1654|712118;1783272|201174|1760|2037|2049|1654|651609;1783272|1239|186801|3085636|186803|1213720|1984869,Complete,Svetlana up
bsdb:34643448/2/2,34643448,case-control,34643448,10.1128/Spectrum.00055-21,NA,"Miller E.H., Annavajhala M.K., Chong A.M., Park H., Nobel Y.R., Soroush A., Blackett J.W., Krigel A., Phipps M.M., Freedberg D.E., Zucker J., Sano E.D., Uhlemann A.C. , Abrams J.A.",Oral Microbiome Alterations and SARS-CoV-2 Saliva Viral Load in Patients with COVID-19,Microbiology spectrum,2021,"COVID-19, SARS-CoV-2, saliva microbiome, viral load",Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,SARS coronavirus,NCBITAXON:694009,SARS Cov-2 Saliva Negative,SARS Cov-2 Saliva Positive,COVID-19 patients with positive SARS-CoV-2 viral load in saliva,15,28,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 3,22 April 2024,MyleeeA,"MyleeeA,Scholastica,WikiWorks",Differentially abundant taxa based on SARS-CoV-2 viral load in SARS-CoV-2-positive (pink) versus -negative (blue) saliva,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus peroris,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 356",3379134|976|200643|171549|171552|838|28129;3379134|976|200643|171549|171552|2974251|28135;1783272|1239|91061|186826|1300|1301|68891;1783272|1239|91061|186826|1300|1301|1306;95818|713057,Complete,Svetlana up
bsdb:34643448/3/1,34643448,case-control,34643448,10.1128/Spectrum.00055-21,NA,"Miller E.H., Annavajhala M.K., Chong A.M., Park H., Nobel Y.R., Soroush A., Blackett J.W., Krigel A., Phipps M.M., Freedberg D.E., Zucker J., Sano E.D., Uhlemann A.C. , Abrams J.A.",Oral Microbiome Alterations and SARS-CoV-2 Saliva Viral Load in Patients with COVID-19,Microbiology spectrum,2021,"COVID-19, SARS-CoV-2, saliva microbiome, viral load",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,SARS coronavirus,NCBITAXON:694009,SARS Cov-2 Negative,SARS Cov-2 Low Viral Load,Patients who tested positive to SARS Cov-2 with low viral load (CT>30) in saliva,15,14,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3,28 April 2024,MyleeeA,"MyleeeA,Scholastica,WikiWorks",Differentially abundant taxa based on SARS-CoV-2 viral load in SARS-CoV-2-positive with low viral load (pink) versus negative (blue) saliva,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 180,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 172,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp. oral taxon 473,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 074,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum sp.",3384189|32066|203490|203491|203492|848|860;3379134|976|200643|171549|171552|838|60133;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|91061|186826|1300|1301|68892;1783272|1239|91061|186826|1300|1301|1305;1783272|201174|1760|2037|2049|1654|651609;1783272|201174|1760|2037|2049|1654|712118;3379134|976|200643|171549|171552|1283313|712469;1783272|1239|91061|186826|1300|1301|712631;1783272|1239|186801|3085636|186803|1213720|1984869,Complete,Svetlana up
bsdb:34643448/3/2,34643448,case-control,34643448,10.1128/Spectrum.00055-21,NA,"Miller E.H., Annavajhala M.K., Chong A.M., Park H., Nobel Y.R., Soroush A., Blackett J.W., Krigel A., Phipps M.M., Freedberg D.E., Zucker J., Sano E.D., Uhlemann A.C. , Abrams J.A.",Oral Microbiome Alterations and SARS-CoV-2 Saliva Viral Load in Patients with COVID-19,Microbiology spectrum,2021,"COVID-19, SARS-CoV-2, saliva microbiome, viral load",Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,SARS coronavirus,NCBITAXON:694009,SARS Cov-2 Negative,SARS Cov-2 Low Viral Load,Patients who tested positive to SARS Cov-2 with low viral load (CT>30) in saliva,15,14,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 3,28 April 2024,MyleeeA,"MyleeeA,Scholastica,WikiWorks",Differentially abundant taxa based on SARS-CoV-2 viral load in SARS-CoV-2-positive with low viral load (pink) versus negative (blue) saliva,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces lingnae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium vincentii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 306,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 351,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 356",1783272|201174|1760|2037|2049|1654|114702;3384189|32066|203490|203491|203492|848|155615;3379134|976|200643|171549|171552|838|470565;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552|838|60133;3379134|976|200643|171549|171552|2974251|28135;3379134|976|200643|171549|171552|2974251|228604;3379134|976|200643|171549|171552|838|712461;1783272|1239|91061|186826|1300|1301|1306;95818|713053;95818|713057,Complete,Svetlana up
bsdb:34643448/4/1,34643448,case-control,34643448,10.1128/Spectrum.00055-21,NA,"Miller E.H., Annavajhala M.K., Chong A.M., Park H., Nobel Y.R., Soroush A., Blackett J.W., Krigel A., Phipps M.M., Freedberg D.E., Zucker J., Sano E.D., Uhlemann A.C. , Abrams J.A.",Oral Microbiome Alterations and SARS-CoV-2 Saliva Viral Load in Patients with COVID-19,Microbiology spectrum,2021,"COVID-19, SARS-CoV-2, saliva microbiome, viral load",Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,SARS coronavirus,NCBITAXON:694009,SARS-CoV-2 Negative,SARS-CoV-2 High Viral load,Patients who tested positive to SARS-CoV-2 with high (CT<30) viral load in saliva,15,14,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3,28 April 2024,MyleeeA,"MyleeeA,Scholastica,WikiWorks",Differentially abundant taxa based on SARS-CoV-2 viral load in SARS-CoV-2-positive with high viral load (pink) versus negative (blue) saliva,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp. oral taxon 473,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 074,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 172,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.",3379134|976|200643|171549|171552|838|60133;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|91061|186826|1300|1301|68892;1783272|1239|91061|186826|1300|1301|1305;3379134|976|200643|171549|171552|1283313|712469;1783272|1239|91061|186826|1300|1301|712631;1783272|1239|186801|3085636|186803|1213720|1984869;1783272|201174|1760|2037|2049|1654|712118;1783272|201174|1760|2037|2049|1654|29317,Complete,Svetlana up
bsdb:34643448/4/2,34643448,case-control,34643448,10.1128/Spectrum.00055-21,NA,"Miller E.H., Annavajhala M.K., Chong A.M., Park H., Nobel Y.R., Soroush A., Blackett J.W., Krigel A., Phipps M.M., Freedberg D.E., Zucker J., Sano E.D., Uhlemann A.C. , Abrams J.A.",Oral Microbiome Alterations and SARS-CoV-2 Saliva Viral Load in Patients with COVID-19,Microbiology spectrum,2021,"COVID-19, SARS-CoV-2, saliva microbiome, viral load",Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,SARS coronavirus,NCBITAXON:694009,SARS-CoV-2 Negative,SARS-CoV-2 High Viral load,Patients who tested positive to SARS-CoV-2 with high (CT<30) viral load in saliva,15,14,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 3,28 April 2024,MyleeeA,"MyleeeA,Scholastica,WikiWorks",Differentially abundant taxa based on SARS-CoV-2 viral load in SARS-CoV-2-positive with high viral load (pink) versus negative (blue) saliva,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium vincentii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus peroris,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 356,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 304,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 066",3384189|32066|203490|203491|203492|848|155615;3379134|976|200643|171549|171552|838|28129;3379134|976|200643|171549|171552|838|470565;3379134|976|200643|171549|171552|2974251|28135;3379134|976|200643|171549|171552|2974251|228604;1783272|1239|91061|186826|1300|1301|1302;1783272|1239|91061|186826|1300|1301|68891;1783272|1239|91061|186826|1300|1301|1306;95818|713057;3379134|976|200643|171549|171552|838|712459;1783272|1239|91061|186826|1300|1301|712626,Complete,Svetlana up
bsdb:34650532/1/1,34650532,"cross-sectional observational, not case-control",34650532,10.3389/fmicb.2021.728479,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8506127/,"Mao L., Zhang Y., Tian J., Sang M., Zhang G., Zhou Y. , Wang P.",Cross-Sectional Study on the Gut Microbiome of Parkinson's Disease Patients in Central China,Frontiers in microbiology,2021,"Parkinson’s disease, gastrointestinal dysbiosis, gut-brain-axis, short-chain fatty acids, shotgun metagenomic sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy spouses,Parkinson's Disease Patients,Partcipants with Parkinson's Disease,39,39,3 months,WMS,NA,BGISEQ-500 Sequencing,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2A and 2B,31 May 2023,Jacquelynshevin,"Jacquelynshevin,Peace Sandy,WikiWorks",The stool microbiota profile in PD and SP groups. Differential abundance of genera (A) and species (B) between PD and SP groups identified by LEfSe,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes ihumii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hydrogenotrophica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas synergistica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium 1_7_47FAA,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 21_3,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 2_2_44A,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 3_1_57FAA_CT1,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc pseudomesenteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. KLE 1728,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter|s__Oxalobacter formigenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia inopinata,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp. 4_3_54A2FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum variabile,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] hylemonae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550|239759|1470347;3379134|976|200643|171549|171550|239759|626932;3379134|976|200643|171549|171550|239759|28117;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|186802|216572|244127|169435;1783272|201174|1760|85004|31953|1678|1689;3379134|200940|3031449|213115|194924|35832;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|3085636|186803|572511|53443;3379134|976|200643|171549|1853231|574697;3379134|976|200643|171549|1853231|574697|544644;1783272|1239|186801|3085636|186803|830;1783272|1239|186801|186802|457421;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|3085636|186803|2719313|333367;1783272|1239|186801|3085636|186803|2719313|358743;1783272|1239|526524|526525|128827|658657;1783272|1239|526524|526525|128827|457422;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803|1649459|154046;1783272|1239|186801|3085636|186803|658086;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|91061|186826|33958|1243|33968;1783272|1239|91061|186826|33958|2767887|1624;1783272|1239|186801|186802|216572|459786|1226322;3379134|1224|28216|80840|75682|846;3379134|1224|28216|80840|75682|846|847;3379134|976|200643|171549|2005525|375288|328812;1783272|201174|1760|85006|1268|32207|2047;1783272|201174|1760|85004|31953|196081;1783272|201174|1760|85004|31953|196081|78259;1783272|201174|1760|85004|31953|196081|230143;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|216572|292632|665956;1783272|1239|186801|186802|216572|292632|214851;1783272|1239|186801|3085636|186803|1506553|89153;3379134|200940|3031449|213115|194924|35832;1783272|201174|84998|84999|1643824|133925;1783272|201174|1760|85004|31953|196081;1783272|1239|186801|186802|216572|292632,Complete,Peace Sandy
bsdb:34650532/1/2,34650532,"cross-sectional observational, not case-control",34650532,10.3389/fmicb.2021.728479,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8506127/,"Mao L., Zhang Y., Tian J., Sang M., Zhang G., Zhou Y. , Wang P.",Cross-Sectional Study on the Gut Microbiome of Parkinson's Disease Patients in Central China,Frontiers in microbiology,2021,"Parkinson’s disease, gastrointestinal dysbiosis, gut-brain-axis, short-chain fatty acids, shotgun metagenomic sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy spouses,Parkinson's Disease Patients,Partcipants with Parkinson's Disease,39,39,3 months,WMS,NA,BGISEQ-500 Sequencing,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2A and 2B,31 May 2023,Jacquelynshevin,"Jacquelynshevin,Peace Sandy,WikiWorks",The stool microbiota profile in PD and SP groups. Differential abundance of genera (A) and species (B) between PD and SP groups identified by LEfSe,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 3_1_19,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. L2-50,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia|s__Eggerthia catenaformis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium varium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 9_1_43BFAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D16,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pasteurianus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,p__Candidatus Saccharimonadota|s__candidate division TM7 single-cell isolate TM7b,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae",3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|469592;1783272|1239|186801|186802|31979|1485|411489;1783272|1239|526524|526525|2810280|1279384;1783272|1239|526524|526525|2810280|1279384|31973;3384189|32066|203490|203491|203492|848|856;1783272|1239|91061|1385|539738|1378|1379;1783272|1239|186801|3085636|186803|658088;1783272|1239|186801|186802|216572;3379134|976|200643|171549|815|909656|310298;1783272|1239|186801|186802|216572|552398;1783272|1239|91061|186826|1300|1301|197614;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|3085636|186803|2941495|1512;95818|447455;1783272|1239|186801|3082720|186804;3379134|1224|28216|80840|995019,Complete,Peace Sandy
bsdb:34650681/1/1,34650681,case-control,34650681,NA,NA,"Wu R., Ruan X.L., Ruan D.D., Zhang J.H., Wang H.L., Zeng Q.Z., Lu T., Gan Y.M., Luo J.W. , Wu J.B.",Differences in gut microbiota structure in patients with stages 4-5 chronic kidney disease,American journal of translational research,2021,"16S rDNA sequencing, Chronic kidney disease stages 4-5, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Healthy Controls,Chronic kidney disease,Diagnosed with stage 4-5 Chronic Kidney Disease (CKD) based on established medical criteria and diagnostic assessments conducted by nephrology experts.,40,39,1 month,16S,34,MGISEQ-2000,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 4,26 March 2024,Sneha6003,"Sneha6003,Peace Sandy,WikiWorks","LEfSe analysis was used to statistically resolve the microbiota with 
significant effects in the different groups. The LDA threshold was set as 2. (A) 
The stage 4-5 CKD group and (B) the control group.",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,p__Candidatus Saccharimonadota,p__Candidatus Saccharimonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061|186826|186827|46123;3379134|1224|1236|2887326|468|469;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;1783272|201174;1783272|1239|91061|186826|186827;1783272|201174|84998|84999|1643824|1380;1783272|1239|91061|1385;1783272|1239|91061;3379134|1224|28216;3379134|1224|28216|80840;95818;95818;1783272|1239|91061|186826|186828;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;1783272|1239|526524|526525|2810280|100883;3379134|976|200643|171549|2005519|1348911;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;1783272|201174|84998|1643822|1643826|84111;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|526524|526525|128827;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|186806|1730;3379134|1224|1236;1783272|1239|186801|186802|204475;1783272|1239|91061|186826|186828|117563;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;3384189|32066|203490|203491|1129771|32067;1783272|201174|1760|85006|1268;3379134|1224|1236|2887326|468;3379134|1224|1236|91347|1903414|581;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481;3379134|1224|28216|206351;1783272|201174|84998|84999|1643824|133925;3379134|976|200643|171549|171552|577309;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1257;3379134|1224|1236|72274|135621;3379134|1224|1236|72274;3379134|1224;3379134|1224|1236|72274|135621|286;3384194|508458|649775|649776|3029088|638847;1783272|201174|1760|85006|1268|32207;1783272|1239|186801|186802|216572|1263;1783272|201174|1760|85004|31953|196081;1783272|1239|186801|3085636|186803|177971;1783272|1239|526524|526525|128827|123375;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301,Complete,Peace Sandy
bsdb:34650681/1/2,34650681,case-control,34650681,NA,NA,"Wu R., Ruan X.L., Ruan D.D., Zhang J.H., Wang H.L., Zeng Q.Z., Lu T., Gan Y.M., Luo J.W. , Wu J.B.",Differences in gut microbiota structure in patients with stages 4-5 chronic kidney disease,American journal of translational research,2021,"16S rDNA sequencing, Chronic kidney disease stages 4-5, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Healthy Controls,Chronic kidney disease,Diagnosed with stage 4-5 Chronic Kidney Disease (CKD) based on established medical criteria and diagnostic assessments conducted by nephrology experts.,40,39,1 month,16S,34,MGISEQ-2000,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 4,27 March 2024,Peace Sandy,"Peace Sandy,WikiWorks",LEfSe analysis was used to statistically resolve the microbiota with significant effects in the different groups. The LDA threshold was set as 2. (A) The stage 4-5 CKD group and (B) the control group.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Asaccharobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",1783272|1239|186801;1783272|1239|186801|186802;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|841;1783272|1239|909932|909929;1783272|1239|909932;1783272|1239|186801|3085636|186803;1783272|1239|909932|1843488|909930;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3085636|186803;1783272|1239|909932|1843489|31977;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|33042;1783272|1239|909932|1843489|31977|39948;3379134|976|200643|171549|171550;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|459786;3379134|1224|28216|80840|995019;3379134|1224|28216|80840|995019|577310;3379134|1224|28211|204441|41295;3379134|1224|28211|204441;1783272|201174|84998|1643822|1643826|553372;3379134|1224|1236|135625|712|724;3379134|1224|28216|80840|75682;1783272|1239|186801|186802|3085642|580596;3379134|1224|28216|80840|75682|846;1783272|201174|84998|1643822|1643826|84108;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|1407607;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|186802|31979|1485;3379134|976|200643|171549|2005519|397864;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|1853231|574697;3379134|976|200643|171549|1853231|283168;1783272|1239|909932|1843488|909930|904;1783272|1239|909932|1843489|31977|209879,Complete,Peace Sandy
bsdb:34668745/1/1,34668745,laboratory experiment,34668745,10.1128/Spectrum.00157-21,NA,"Pelloquin B., Kristan M., Edi C., Meiwald A., Clark E., Jeffries C.L., Walker T., Dada N. , Messenger L.A.","Overabundance of <i>Asaia</i> and <i>Serratia</i> Bacteria Is Associated with Deltamethrin Insecticide Susceptibility in <i>Anopheles coluzzii</i> from Agboville, Côte d'Ivoire",Microbiology spectrum,2021,"Anopheles coluzzii, Asaia, Côte d’Ivoire, Serratia, deltamethrin, insecticide resistance, malaria, microbiota",Experiment 1,Côte d'Ivoire,Anopheles coluzzii,Body proper,UBERON:0013702,Insecticide,CHEBI:24852,Resistant + Control mosquitoes (2 to 3 days old),Susceptible mosquitoes (2 to 3 days old),Susceptible mosquitoes refers to the mosquitoes knocked down after exposure to 1× deltamethrin,93,87,NA,16S,34,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,"In text of the ""Serratia and Asaia dominated in older and younger susceptible An. coluzzii."" section and Fig. S5",24 February 2025,KateRasheed,KateRasheed,"Differential abundance of taxa between susceptible, resistant and control mosquitoes using ANCOM",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Asaia",3379134|1224|1236|91347|1903411|613;3379134|1224|28211|3120395|433|91914,Complete,KateRasheed
bsdb:34668745/2/1,34668745,laboratory experiment,34668745,10.1128/Spectrum.00157-21,NA,"Pelloquin B., Kristan M., Edi C., Meiwald A., Clark E., Jeffries C.L., Walker T., Dada N. , Messenger L.A.","Overabundance of <i>Asaia</i> and <i>Serratia</i> Bacteria Is Associated with Deltamethrin Insecticide Susceptibility in <i>Anopheles coluzzii</i> from Agboville, Côte d'Ivoire",Microbiology spectrum,2021,"Anopheles coluzzii, Asaia, Côte d’Ivoire, Serratia, deltamethrin, insecticide resistance, malaria, microbiota",Experiment 2,Côte d'Ivoire,Anopheles coluzzii,Body proper,UBERON:0013702,Insecticide,CHEBI:24852,Susceptible + Control mosquitoes (2 to 3 days old),Resistant mosquitoes (2 to 3 days old),"Resistant mosquitoes refers to mosquitoes that survived 60 min (2 to 3 days old) postexposure to 5×, or 10× deltamethrin.",129,51,NA,16S,34,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,"In text of the ""Serratia and Asaia dominated in older and younger susceptible An. coluzzii."" section and Fig. S5",24 February 2025,KateRasheed,KateRasheed,"Differential abundance of taxa between susceptible, resistant and control mosquitoes using ANCOM",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus",3379134|1224|1236|91347|543;3379134|1224|28211|356|118882|528;1783272|1239|91061|1385|186817|400634,Complete,KateRasheed
bsdb:34668745/3/1,34668745,laboratory experiment,34668745,10.1128/Spectrum.00157-21,NA,"Pelloquin B., Kristan M., Edi C., Meiwald A., Clark E., Jeffries C.L., Walker T., Dada N. , Messenger L.A.","Overabundance of <i>Asaia</i> and <i>Serratia</i> Bacteria Is Associated with Deltamethrin Insecticide Susceptibility in <i>Anopheles coluzzii</i> from Agboville, Côte d'Ivoire",Microbiology spectrum,2021,"Anopheles coluzzii, Asaia, Côte d’Ivoire, Serratia, deltamethrin, insecticide resistance, malaria, microbiota",Experiment 3,Côte d'Ivoire,Anopheles coluzzii,Body proper,UBERON:0013702,Insecticide,CHEBI:24852,Susceptible + Resistant mosquitoes (2 to 3 days old),Control mosquitoes (2 to 3 days old),Control mosquitoes refers to mosquitoes that were unexposed to insecticide (comprising a mix of age-matched individuals of unknown phenotype). They are mosquitoes from control bottle which were alive 60 minutes after the initiation of bioassay,138,42,NA,16S,34,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,"In text of the ""Serratia and Asaia dominated in older and younger susceptible An. coluzzii."" section and Fig. S5",24 February 2025,KateRasheed,KateRasheed,"Differential abundance of taxa between susceptible, resistant and control mosquitoes using ANCOM",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus",3379134|1224|1236|91347|543;3379134|1224|28211|356|118882|528;1783272|1239|91061|1385|186817|400634,Complete,KateRasheed
bsdb:34668745/4/1,34668745,laboratory experiment,34668745,10.1128/Spectrum.00157-21,NA,"Pelloquin B., Kristan M., Edi C., Meiwald A., Clark E., Jeffries C.L., Walker T., Dada N. , Messenger L.A.","Overabundance of <i>Asaia</i> and <i>Serratia</i> Bacteria Is Associated with Deltamethrin Insecticide Susceptibility in <i>Anopheles coluzzii</i> from Agboville, Côte d'Ivoire",Microbiology spectrum,2021,"Anopheles coluzzii, Asaia, Côte d’Ivoire, Serratia, deltamethrin, insecticide resistance, malaria, microbiota",Experiment 4,Côte d'Ivoire,Anopheles coluzzii,Body proper,UBERON:0013702,Insecticide,CHEBI:24852,Control mosquitoes (2 to 3 days old),Susceptible mosquitoes (2 to 3 days old),Susceptible mosquitoes refers to the mosquitoes knocked down after exposure to 1× deltamethrin,42,87,NA,16S,34,Illumina,raw counts,Songbird,0.05,TRUE,NA,age,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Table S5,25 February 2025,KateRasheed,KateRasheed,"Differential abundance of taxa present in 2-3 day old Anopheles coluzzii (susceptible and control mosquitoes), as computed by Songbird.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium afermentans|s__Corynebacterium afermentans subsp. afermentans,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria|s__Kocuria marina,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|201174|1760|85007|85025|1827;3379134|1224|1236|135625|712|724;3379134|1224|28211|204457|41297|13687;3379134|1224|1236|91347|543|1940338;3379134|1224|28211|356|118882|528;1783272|201174|1760|85006|1268|1269;3379134|1224|28211|356|41294|374;1783272|201174|1760|85007|1653|1716|38286|144183;1783272|1239|91061|1385|186817|1386;1783272|1239|91061|186826|1300|1301;3379134|1224|1236|135624|84642|642;1783272|1239|91061|1385|90964|1279;1783272|1239|1737404|1737405|1570339|150022;3379134|1224|28211|356|212791;3379134|1224|28211;3379134|1224|1236|2887326|468|469;3379134|1224|28216|80840|80864|80865;3379134|1224|1236|135614|32033|40323;3379134|1224|1236|91347|543;1783272|1239|91061|1385|186817|400634;1783272|201174|1760|85006|1268|57493|223184;3379134|976|117743|200644|2762318|59732;1783272|201174|1760|85009|31957|1912216;1783272|201174|1760|85006|1268;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|186826|33958|1578,Complete,KateRasheed
bsdb:34668745/4/2,34668745,laboratory experiment,34668745,10.1128/Spectrum.00157-21,NA,"Pelloquin B., Kristan M., Edi C., Meiwald A., Clark E., Jeffries C.L., Walker T., Dada N. , Messenger L.A.","Overabundance of <i>Asaia</i> and <i>Serratia</i> Bacteria Is Associated with Deltamethrin Insecticide Susceptibility in <i>Anopheles coluzzii</i> from Agboville, Côte d'Ivoire",Microbiology spectrum,2021,"Anopheles coluzzii, Asaia, Côte d’Ivoire, Serratia, deltamethrin, insecticide resistance, malaria, microbiota",Experiment 4,Côte d'Ivoire,Anopheles coluzzii,Body proper,UBERON:0013702,Insecticide,CHEBI:24852,Control mosquitoes (2 to 3 days old),Susceptible mosquitoes (2 to 3 days old),Susceptible mosquitoes refers to the mosquitoes knocked down after exposure to 1× deltamethrin,42,87,NA,16S,34,Illumina,raw counts,Songbird,0.05,TRUE,NA,age,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Table S5,25 February 2025,KateRasheed,KateRasheed,"Differential abundance of taxa present in 2-3 day old Anopheles coluzzii (susceptible and control mosquitoes), as computed by Songbird.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Chroococcidiopsidales|f__Chroococcidiopsidaceae|g__Chroococcidiopsis|s__uncultured Chroococcidiopsis sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Asaia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia",3379134|976|117743|200644|2762318|501783;3379134|1224|1236|2887326|468|469;1783272|201174|84992;1783272|1239|91061|186826|186828|2747;1783272|201174|1760|85006|1268|57493;1783272|1239|91061|186826|186827|1375;3379134|1224|1236|91347|543;1783272|1117|3028117|1890505|1890528|54298|259957;3379134|1224|28211|3120395|433|91914;3379134|1224|1236|91347|1903411|613,Complete,KateRasheed
bsdb:34668745/5/1,34668745,laboratory experiment,34668745,10.1128/Spectrum.00157-21,NA,"Pelloquin B., Kristan M., Edi C., Meiwald A., Clark E., Jeffries C.L., Walker T., Dada N. , Messenger L.A.","Overabundance of <i>Asaia</i> and <i>Serratia</i> Bacteria Is Associated with Deltamethrin Insecticide Susceptibility in <i>Anopheles coluzzii</i> from Agboville, Côte d'Ivoire",Microbiology spectrum,2021,"Anopheles coluzzii, Asaia, Côte d’Ivoire, Serratia, deltamethrin, insecticide resistance, malaria, microbiota",Experiment 5,Côte d'Ivoire,Anopheles coluzzii,Body proper,UBERON:0013702,Insecticide,CHEBI:24852,Resistant mosquitoes (2 to 3 days old),Susceptible mosquitoes (2 to 3 days old),Susceptible mosquitoes refers to the mosquitoes knocked down after exposure to 1× deltamethrin,51,87,NA,16S,34,Illumina,raw counts,Songbird,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Table S5,25 February 2025,KateRasheed,KateRasheed,"Differential abundance of taxa present in 2-3 day old Anopheles coluzzii (susceptible and resistant mosquitoes), as computed by Songbird.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria|s__Kocuria marina,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium afermentans|s__Corynebacterium afermentans subsp. afermentans,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Chroococcidiopsidales|f__Chroococcidiopsidaceae|g__Chroococcidiopsis|s__uncultured Chroococcidiopsis sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas",3379134|1224|1236|135614|32033|40323;3379134|1224|28211|356|118882|528;1783272|1239|91061|1385|186817|400634;3379134|1224|28211;1783272|201174|1760|85006|1268|57493|223184;1783272|201174|1760|85007|1653|1716|38286|144183;1783272|1117|3028117|1890505|1890528|54298|259957;1783272|201174|1760|85006|1268|32207;1783272|201174|84992;3379134|1224|1236|2887326|468|469;3379134|1224|28216|80840|80864|80865;1783272|1239|91061|186826|186828|2747;3379134|1224|1236|91347|543;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|33958|1578;1783272|1239|1737404|1737405|1570339|150022;1783272|201174|1760|85007|85025|1827;1783272|201174|1760|85009|31957|1912216;3379134|1224|28211|356|41294|374;3379134|1224|28211|356|212791;3379134|1224|28211|204457|41297|13687,Complete,KateRasheed
bsdb:34668745/5/2,34668745,laboratory experiment,34668745,10.1128/Spectrum.00157-21,NA,"Pelloquin B., Kristan M., Edi C., Meiwald A., Clark E., Jeffries C.L., Walker T., Dada N. , Messenger L.A.","Overabundance of <i>Asaia</i> and <i>Serratia</i> Bacteria Is Associated with Deltamethrin Insecticide Susceptibility in <i>Anopheles coluzzii</i> from Agboville, Côte d'Ivoire",Microbiology spectrum,2021,"Anopheles coluzzii, Asaia, Côte d’Ivoire, Serratia, deltamethrin, insecticide resistance, malaria, microbiota",Experiment 5,Côte d'Ivoire,Anopheles coluzzii,Body proper,UBERON:0013702,Insecticide,CHEBI:24852,Resistant mosquitoes (2 to 3 days old),Susceptible mosquitoes (2 to 3 days old),Susceptible mosquitoes refers to the mosquitoes knocked down after exposure to 1× deltamethrin,51,87,NA,16S,34,Illumina,raw counts,Songbird,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Table S5,25 February 2025,KateRasheed,KateRasheed,"Differential abundance of taxa present in 2-3 day old Anopheles coluzzii (susceptible and resistant mosquitoes), as computed by Songbird.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Asaia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus",1783272|1239|91061|1385|186817|1386;3379134|1224|1236|91347|1903411|613;1783272|201174|1760|85006|1268;3379134|976|117743|200644|2762318|501783;3379134|1224|1236|135624|84642|642;3379134|1224|28211|3120395|433|91914;3379134|976|117743|200644|2762318|59732;1783272|201174|1760|85006|1268|1269;3379134|1224|1236|2887326|468|469;3379134|1224|1236|91347|543|1940338;3379134|1224|1236|135625|712|724;3379134|1224|1236|91347|543;1783272|201174|1760|85006|1268|57493;1783272|1239|91061|186826|186827|1375,Complete,KateRasheed
bsdb:34683436/1/1,34683436,"cross-sectional observational, not case-control",34683436,10.3390/microorganisms9102115,NA,"Vu Thi Ngoc B., Ho Bich H., Galazzo G., Vu Tien Viet D., Oomen M., Nghiem Nguyen Minh T., Tran Huy H., van Doorn H.R., Wertheim H.F.L. , Penders J.",Cross-Sectional Analysis of the Microbiota of Human Gut and Its Direct Environment in a Household Cohort with High Background of Antibiotic Use,Microorganisms,2021,"One Health, Vietnam, antibiotic resistance, environmental microbiota, metagenomics, microbiota",Experiment 1,Viet Nam,Homo sapiens,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Individuals with no antibiotic use past four months,Individuals with antibiotic use past four months,Individuals who used antibiotics in the last four months prior to fees sampling.,63,44,4 months,16S,4,Illumina,relative abundances,ANCOM,NA,TRUE,NA,NA,"age,geographic area,sex",NA,unchanged,decreased,NA,NA,decreased,Signature 1,Supplementary Table S4,16 January 2026,Olanma.o,Olanma.o,Differential abundance of microbial taxa across stool samples from humans of different age groups and geographical clusters.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,1783272|1239|186801|3085636|186803|2316020|33038,Complete,NA
bsdb:34683469/1/1,34683469,meta-analysis,34683469,https://doi.org/10.3390/microorganisms9102149,NA,"Chen Y., Wu T., Lu W., Yuan W., Pan M., Lee Y.K., Zhao J., Zhang H., Chen W., Zhu J. , Wang H.",Predicting the Role of the Human Gut Microbiome in Constipation Using Machine-Learning Methods: A Meta-Analysis,Microorganisms,2021,"classification model, constipation, feature selection, gut microbiome, machine learning",Experiment 1,"Australia,China,Poland,United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,Healthy controls,Constipation patients,"Patients clinically diagnosed of constipation by evaluating the stool form and the associated persistent bowel symptoms, such as the Bristol Stool Form Scale and the Rome IV criteria",2138,918,NA,16S,NA,NA,relative abundances,NA,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,unchanged,Signature 1,Figure 4D,2 April 2025,Nithya,"Nithya,Anne-mariesharp,KateRasheed",The balance selected genera that significantly differed between the two groups,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Eremococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rahnella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|3085636|186803|1766253;1783272|201174|1760|85004|31953|419014;1783272|201174|1760|85006|85020|43668;3379134|1224|28211|204458|76892|75;1783272|1239|91061|186826|186827|171412;1783272|201174|84998|84999|1643824|2082587;3379134|1224|1236|91347|1903411|34037;1783272|1239|186801|186802|216572|707003;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:34683469/1/2,34683469,meta-analysis,34683469,https://doi.org/10.3390/microorganisms9102149,NA,"Chen Y., Wu T., Lu W., Yuan W., Pan M., Lee Y.K., Zhao J., Zhang H., Chen W., Zhu J. , Wang H.",Predicting the Role of the Human Gut Microbiome in Constipation Using Machine-Learning Methods: A Meta-Analysis,Microorganisms,2021,"classification model, constipation, feature selection, gut microbiome, machine learning",Experiment 1,"Australia,China,Poland,United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,Healthy controls,Constipation patients,"Patients clinically diagnosed of constipation by evaluating the stool form and the associated persistent bowel symptoms, such as the Bristol Stool Form Scale and the Rome IV criteria",2138,918,NA,16S,NA,NA,relative abundances,NA,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,unchanged,Signature 2,Figure 4D,2 April 2025,Nithya,"Nithya,Anne-mariesharp",The balance selected genera that significantly differed between the two groups,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Caproiciproducens,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Puniceicoccaceae",1783272|1239|186801|3085636|186803|653683;1783272|1239;1783272|1239|186801|186802|3082771|1738645;3379134|200940|3031449|213115|194924;1783272|1239|186801|3085636|186803|189330;1783272|201174|84998|1643822|1643826;1783272|1239|186801|186802|216572|946234;3379134|1224|1236;3379134|74201|414999|415001|415002,Complete,Svetlana up
bsdb:34690948/1/1,34690948,"cross-sectional observational, not case-control",34690948,10.3389/fmicb.2021.700718,NA,"Zhang X., Li N., Chen Q. , Qin H.",Fecal Microbiota Transplantation Modulates the Gut Flora Favoring Patients With Functional Constipation,Frontiers in microbiology,2021,"16S rDNA gene sequencing, fecal microbiota transplantation, functional constipation, gut microbiome, serum inflammatory factor, short chain fatty acid",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Health-related quality of life measurement,EFO:0011014,Low PAC-SYM (Patient Assessment of Constipation-Symptoms),High PAC-SYM (Patient Assessment of Constipation-Symptoms),"Patients with high Patient Assessment of Constipation-Symptoms (PAC-SYM) scores, indicating more severe constipation symptoms.",NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3B,8 July 2025,Anne-mariesharp,Anne-mariesharp,Spearman correlation analysis revealed a correlation between patients’ clinical symptoms and the significantly altered bacteria from the LEfSe analysis.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",1783272|1239|186801|3085636|186803|1407607;3379134|976|200643|171549|171552|577309,Complete,KateRasheed
bsdb:34690948/2/1,34690948,"cross-sectional observational, not case-control",34690948,10.3389/fmicb.2021.700718,NA,"Zhang X., Li N., Chen Q. , Qin H.",Fecal Microbiota Transplantation Modulates the Gut Flora Favoring Patients With Functional Constipation,Frontiers in microbiology,2021,"16S rDNA gene sequencing, fecal microbiota transplantation, functional constipation, gut microbiome, serum inflammatory factor, short chain fatty acid",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,bef (pre-Fecal microbiota transplantation),aft (post-Fecal microbiota transplantation),post-FMT samples from patients who were not cured by fecal microbiota transplantation(FMT),18,18,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,unchanged,Signature 1,Figure 3A,30 March 2025,Inisimeon,"Inisimeon,Anne-mariesharp",LEfSe analysis revealed significant changes in the fecal microbiota compositions before and after FMT.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",1783272|1239|909932|1843488|909930;1783272|1239|909932|1843489|31977|209879;1783272|1239|186801;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803|1407607;1783272|1239|91061|186826|33958;3379134|976|200643|171549|171552|577309;1783272|1239|909932|1843488|909930|33024;1783272|1239|91061|186826|33958|46255,Complete,KateRasheed
bsdb:34690948/2/2,34690948,"cross-sectional observational, not case-control",34690948,10.3389/fmicb.2021.700718,NA,"Zhang X., Li N., Chen Q. , Qin H.",Fecal Microbiota Transplantation Modulates the Gut Flora Favoring Patients With Functional Constipation,Frontiers in microbiology,2021,"16S rDNA gene sequencing, fecal microbiota transplantation, functional constipation, gut microbiome, serum inflammatory factor, short chain fatty acid",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,bef (pre-Fecal microbiota transplantation),aft (post-Fecal microbiota transplantation),post-FMT samples from patients who were not cured by fecal microbiota transplantation(FMT),18,18,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,unchanged,Signature 2,Figure 3A,30 March 2025,Inisimeon,"Inisimeon,Anne-mariesharp",LEfSe analysis revealed significant changes in the fecal microbiota compositions before and after FMT.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",1783272|1239|186801|186802|216572|52784;1783272|1239|186801|3085636|186803|1164882;3379134|1224|28216|206351|481|482,Complete,KateRasheed
bsdb:34690948/3/1,34690948,"cross-sectional observational, not case-control",34690948,10.3389/fmicb.2021.700718,NA,"Zhang X., Li N., Chen Q. , Qin H.",Fecal Microbiota Transplantation Modulates the Gut Flora Favoring Patients With Functional Constipation,Frontiers in microbiology,2021,"16S rDNA gene sequencing, fecal microbiota transplantation, functional constipation, gut microbiome, serum inflammatory factor, short chain fatty acid",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Health-related quality of life measurement,EFO:0011014,Low PAC_QOL (Patient-Assessment of Constipation Quality of Life),High PAC_QOL (Patient-Assessment of Constipation Quality of Life),"Patients with high Patient-Assessment of Constipation Quality of Life (PAC_QOL) score, indicating more severe constipation symptoms.",NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3B,8 July 2025,Anne-mariesharp,Anne-mariesharp,Spearman correlation analysis revealed a correlation between patients’ clinical symptoms and the significantly altered bacteria from the LEfSe analysis.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus",1783272|1239|186801|3085636|186803|1407607;3379134|976|200643|171549|171552|577309;1783272|1239|186801|3085636|186803|33042,Complete,KateRasheed
bsdb:34690948/4/1,34690948,"cross-sectional observational, not case-control",34690948,10.3389/fmicb.2021.700718,NA,"Zhang X., Li N., Chen Q. , Qin H.",Fecal Microbiota Transplantation Modulates the Gut Flora Favoring Patients With Functional Constipation,Frontiers in microbiology,2021,"16S rDNA gene sequencing, fecal microbiota transplantation, functional constipation, gut microbiome, serum inflammatory factor, short chain fatty acid",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Bowel dysfunction,MONDO:0004880,Low CSBM (Complete spontaneous bowel movement),High CSBM (Complete spontaneous bowel movement),Patients with a high frequency of complete spontaneous bowel movements per week,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3B,8 July 2025,Anne-mariesharp,Anne-mariesharp,Spearman correlation analysis revealed a correlation between patients’ clinical symptoms and the significantly altered bacteria from the LEfSe analysis.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239|186801|3085636|186803|1407607;3379134|976|200643|171549|171552|577309;1783272|1239|909932|1843488|909930|33024;1783272|1239|909932|1843488|909930;1783272|1239|186801;1783272|1239|186801|186802,Complete,KateRasheed
bsdb:34690948/4/2,34690948,"cross-sectional observational, not case-control",34690948,10.3389/fmicb.2021.700718,NA,"Zhang X., Li N., Chen Q. , Qin H.",Fecal Microbiota Transplantation Modulates the Gut Flora Favoring Patients With Functional Constipation,Frontiers in microbiology,2021,"16S rDNA gene sequencing, fecal microbiota transplantation, functional constipation, gut microbiome, serum inflammatory factor, short chain fatty acid",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Bowel dysfunction,MONDO:0004880,Low CSBM (Complete spontaneous bowel movement),High CSBM (Complete spontaneous bowel movement),Patients with a high frequency of complete spontaneous bowel movements per week,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3B,8 July 2025,Anne-mariesharp,Anne-mariesharp,Spearman correlation analysis revealed a correlation between patients’ clinical symptoms and the significantly altered bacteria from the LEfSe analysis.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,1783272|1239|186801|3085636|186803|1164882,Complete,KateRasheed
bsdb:34690948/5/1,34690948,"cross-sectional observational, not case-control",34690948,10.3389/fmicb.2021.700718,NA,"Zhang X., Li N., Chen Q. , Qin H.",Fecal Microbiota Transplantation Modulates the Gut Flora Favoring Patients With Functional Constipation,Frontiers in microbiology,2021,"16S rDNA gene sequencing, fecal microbiota transplantation, functional constipation, gut microbiome, serum inflammatory factor, short chain fatty acid",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,Low BSFS (Bristol stool form scale) score,High BSFS (Bristol stool form scale) score,Patients with high bristol stool form scale score,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3B,8 July 2025,Anne-mariesharp,Anne-mariesharp,Spearman correlation analysis revealed a correlation between patients’ clinical symptoms and the significantly altered bacteria from the LEfSe analysis.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239|186801|3085636|186803|1407607;3379134|976|200643|171549|171552|577309;1783272|1239|909932|1843489|31977|209879;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801;1783272|1239|186801|186802,Complete,KateRasheed
bsdb:34698096/1/1,34698096,case-control,34698096,10.3390/cimb43030103,https://www.mdpi.com/1467-3045/43/3/103,"de Jesus V.C., Singh M., Schroth R.J., Chelikani P. , Hitchon C.A.","Association of Bitter Taste Receptor T2R38 Polymorphisms, Oral Microbiota, and Rheumatoid Arthritis",Current issues in molecular biology,2021,"G protein-coupled receptor, autoimmune disease, oral microbiome, oral–systemic disease, rheumatoid arthritis, taste genetics",Experiment 1,Canada,Homo sapiens,Internal cheek pouch,UBERON:0013640,Rheumatoid arthritis,EFO:0000685,Non Rheumatoid Arthritis,Rheumatoid Arthritis,Individual who have been diagnosed with Rheumatoid Arthritis(RA).,64,35,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3(a&b),1 April 2023,Aiyshaaaa,"Aiyshaaaa,WikiWorks",Linear discriminant analysis (LDA) effect size (LEfSe) analysis demonstrated differences in the relative abundance of some taxa between RA and non-RA controls at genus and  species level.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas flueggei",1783272|1239|91061|186826|1300|1301;1783272|201174|1760|85006|1268|32207;3384189|32066|203490|203491|1129771|32067;1783272|1239|91061|186826|1300|1301|1304;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|909932|909929|1843491|970|135080,Complete,Atrayees
bsdb:34698096/1/2,34698096,case-control,34698096,10.3390/cimb43030103,https://www.mdpi.com/1467-3045/43/3/103,"de Jesus V.C., Singh M., Schroth R.J., Chelikani P. , Hitchon C.A.","Association of Bitter Taste Receptor T2R38 Polymorphisms, Oral Microbiota, and Rheumatoid Arthritis",Current issues in molecular biology,2021,"G protein-coupled receptor, autoimmune disease, oral microbiome, oral–systemic disease, rheumatoid arthritis, taste genetics",Experiment 1,Canada,Homo sapiens,Internal cheek pouch,UBERON:0013640,Rheumatoid arthritis,EFO:0000685,Non Rheumatoid Arthritis,Rheumatoid Arthritis,Individual who have been diagnosed with Rheumatoid Arthritis(RA).,64,35,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3(a&b),1 April 2023,Aiyshaaaa,"Aiyshaaaa,Atrayees,WikiWorks",Linear discriminant analysis (LDA) effect size (LEfSe) analysis demonstrated differences in the relative abundance of some taxa between RA and non-RA controls at genus and species level.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|s__Bacteroidota bacterium",3379134|976|117743|200644|49546|1016;3379134|1224|1236|135625|712|416916;3379134|976|200643|171549|171551|836;3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|171551|836|28124;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|91061|186826|186828|117563|137732;3384189|32066|203490|203491|203492|848|860;3379134|976|200643|171549|171552|838|28132;3379134|976|1898104,Complete,Atrayees
bsdb:34698096/2/1,34698096,case-control,34698096,10.3390/cimb43030103,https://www.mdpi.com/1467-3045/43/3/103,"de Jesus V.C., Singh M., Schroth R.J., Chelikani P. , Hitchon C.A.","Association of Bitter Taste Receptor T2R38 Polymorphisms, Oral Microbiota, and Rheumatoid Arthritis",Current issues in molecular biology,2021,"G protein-coupled receptor, autoimmune disease, oral microbiome, oral–systemic disease, rheumatoid arthritis, taste genetics",Experiment 2,Canada,Homo sapiens,Internal cheek pouch,UBERON:0013640,Sensory perception of bitter taste,GO:0050913,rheumatoid arthritis patients carrying the AVI/AVI genotype (“non-tasters”),rheumatoid arthritis patients with the homozygous PAV/PAV (“supertasters”),rheumatoid arthritis patients with the homozygous PAV/PAV (“supertasters”),16,35,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4(a),26 July 2023,Atrayees,"Atrayees,WikiWorks",Most highly differentially abundant bacteria in RA patients in buccal swab samples from participants with the homozygous AVI/AVI and PAV/PAV TAS2R38 genotypes by the LEfSE,decreased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter rectus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas artemidis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,p__Candidatus Absconditibacteriota|s__Candidatus Absconditabacteria bacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.",3379134|29547|3031852|213849|72294|194|203;1783272|1239|909932|909929|1843491|970|671224;1783272|201174|1760|85007|1653|1716|61592;3379134|976|117743|200644|49546|1016|1019;221235|3018262;3384189|32066|203490|203491|1129771|32067|104608,Complete,Folakunmi
bsdb:34698096/2/2,34698096,case-control,34698096,10.3390/cimb43030103,https://www.mdpi.com/1467-3045/43/3/103,"de Jesus V.C., Singh M., Schroth R.J., Chelikani P. , Hitchon C.A.","Association of Bitter Taste Receptor T2R38 Polymorphisms, Oral Microbiota, and Rheumatoid Arthritis",Current issues in molecular biology,2021,"G protein-coupled receptor, autoimmune disease, oral microbiome, oral–systemic disease, rheumatoid arthritis, taste genetics",Experiment 2,Canada,Homo sapiens,Internal cheek pouch,UBERON:0013640,Sensory perception of bitter taste,GO:0050913,rheumatoid arthritis patients carrying the AVI/AVI genotype (“non-tasters”),rheumatoid arthritis patients with the homozygous PAV/PAV (“supertasters”),rheumatoid arthritis patients with the homozygous PAV/PAV (“supertasters”),16,35,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4(b),26 July 2023,Atrayees,"Atrayees,WikiWorks",Most highly differentially abundant bacteria in RA patients in buccal swab samples from participants with the homozygous AVI/AVI and PAV/PAV TAS2R38 genotypes by the LEfSE,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,1783272|1239|91061|186826|1300|1301|1304,Complete,Folakunmi
bsdb:34698096/3/1,34698096,case-control,34698096,10.3390/cimb43030103,https://www.mdpi.com/1467-3045/43/3/103,"de Jesus V.C., Singh M., Schroth R.J., Chelikani P. , Hitchon C.A.","Association of Bitter Taste Receptor T2R38 Polymorphisms, Oral Microbiota, and Rheumatoid Arthritis",Current issues in molecular biology,2021,"G protein-coupled receptor, autoimmune disease, oral microbiome, oral–systemic disease, rheumatoid arthritis, taste genetics",Experiment 3,Canada,Homo sapiens,Internal cheek pouch,UBERON:0013640,Sensory perception of bitter taste,GO:0050913,Non-rheumatoid arthritis patients carrying the AVI/AVI genotype (“non-tasters”),Non-rheumatoid arthritis patients with the homozygous PAV/PAV (“supertasters”),Non-rheumatoid arthritis patients with the homozygous PAV/PAV (“supertasters”),64,64,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4(b),26 July 2023,Atrayees,"Atrayees,WikiWorks",Most highly differentially abundant bacteria in non-RA patients in buccal swab samples from participants with the homozygous AVI/AVI and PAV/PAV TAS2R38 genotypes by the LEfSE,decreased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,1783272|201174|84998|84999|1643824|2767353|1382,Complete,Folakunmi
bsdb:34698096/3/2,34698096,case-control,34698096,10.3390/cimb43030103,https://www.mdpi.com/1467-3045/43/3/103,"de Jesus V.C., Singh M., Schroth R.J., Chelikani P. , Hitchon C.A.","Association of Bitter Taste Receptor T2R38 Polymorphisms, Oral Microbiota, and Rheumatoid Arthritis",Current issues in molecular biology,2021,"G protein-coupled receptor, autoimmune disease, oral microbiome, oral–systemic disease, rheumatoid arthritis, taste genetics",Experiment 3,Canada,Homo sapiens,Internal cheek pouch,UBERON:0013640,Sensory perception of bitter taste,GO:0050913,Non-rheumatoid arthritis patients carrying the AVI/AVI genotype (“non-tasters”),Non-rheumatoid arthritis patients with the homozygous PAV/PAV (“supertasters”),Non-rheumatoid arthritis patients with the homozygous PAV/PAV (“supertasters”),64,64,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4(b),26 July 2023,Atrayees,"Atrayees,WikiWorks",Most highly differentially abundant bacteria in non-RA patients in buccal swab samples from participants with the homozygous AVI/AVI and PAV/PAV TAS2R38 genotypes by the LEfSE,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,p__Candidatus Saccharimonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella morbi,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium asaccharolyticum",3379134|976|200643|171549|171552|838|470565;1783272|1239|909932|1843489|31977|906|187326;3379134|976|200643|171549|171552|2974251|228604;95818;1783272|1239|186801|3085636|186803|43996|43997;1783272|1239|909932|1843489|31977|29465|423477;1783272|1239|186801|3085636|186803|265975|1501332,Complete,Folakunmi
bsdb:34698096/4/1,34698096,case-control,34698096,10.3390/cimb43030103,https://www.mdpi.com/1467-3045/43/3/103,"de Jesus V.C., Singh M., Schroth R.J., Chelikani P. , Hitchon C.A.","Association of Bitter Taste Receptor T2R38 Polymorphisms, Oral Microbiota, and Rheumatoid Arthritis",Current issues in molecular biology,2021,"G protein-coupled receptor, autoimmune disease, oral microbiome, oral–systemic disease, rheumatoid arthritis, taste genetics",Experiment 4,Canada,Homo sapiens,Internal cheek pouch,UBERON:0013640,Sensory perception of bitter taste,GO:0050913,All participants carrying the AVI/AVI genotype (“non-tasters”),All participants with the homozygous PAV/PAV (“supertasters”),All participants with the homozygous PAV/PAV (“supertasters”),99,99,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4(c),26 July 2023,Atrayees,"Atrayees,WikiWorks",Most highly differentially abundant bacteria in all patients in buccal swab samples from participants with the homozygous AVI/AVI and PAV/PAV TAS2R38 genotypes by the LEfSE,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,1783272|1239|91061|186826|186827|46123|46125,Complete,Folakunmi
bsdb:34698096/4/2,34698096,case-control,34698096,10.3390/cimb43030103,https://www.mdpi.com/1467-3045/43/3/103,"de Jesus V.C., Singh M., Schroth R.J., Chelikani P. , Hitchon C.A.","Association of Bitter Taste Receptor T2R38 Polymorphisms, Oral Microbiota, and Rheumatoid Arthritis",Current issues in molecular biology,2021,"G protein-coupled receptor, autoimmune disease, oral microbiome, oral–systemic disease, rheumatoid arthritis, taste genetics",Experiment 4,Canada,Homo sapiens,Internal cheek pouch,UBERON:0013640,Sensory perception of bitter taste,GO:0050913,All participants carrying the AVI/AVI genotype (“non-tasters”),All participants with the homozygous PAV/PAV (“supertasters”),All participants with the homozygous PAV/PAV (“supertasters”),99,99,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4(c),26 July 2023,Atrayees,"Atrayees,WikiWorks",Most highly differentially abundant bacteria in all patients in buccal swab samples from participants with the homozygous AVI/AVI and PAV/PAV TAS2R38 genotypes by the LEfSE,increased,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,3379134|29547|3031852|213849|72294|194|824,Complete,Folakunmi
bsdb:34707191/1/1,34707191,case-control,34707191,10.1038/s12276-021-00686-9,NA,"Hou M.F., Ou-Yang F., Li C.L., Chen F.M., Chuang C.H., Kan J.Y., Wu C.C., Shih S.L., Shiau J.P., Kao L.C., Kao C.N., Lee Y.C., Moi S.H., Yeh Y.T., Cheng C.J. , Chiang C.P.",Comprehensive profiles and diagnostic value of menopausal-specific gut microbiota in premenopausal breast cancer,Experimental & molecular medicine,2021,NA,Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,Breast carcinoma,EFO:0000305,Premenopausal female controls (Pre-C),premenopausal breast cancer patients (Pre-BC),Premenopausal breast cancer patients diagnosed with stage I–II disease by pathological examination.,50,100,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,decreased,NA,NA,NA,NA,Signature 1,FIG 2 (B),8 April 2024,Rahila,"Rahila,Scholastica,WikiWorks",Significantly differential gut microbiota in premenopausal breast cancer (Pre-BC) patients compared to premenopausal female controls (Pre-C),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales",3379134|976|200643|171549|815|816;3384189|32066|203490|203491|203492|848;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712|724|729;3379134|976|200643|171549|171552|2974265|363265;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|1263|40519;3379134|1224|28216|80840|995019|40544;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3379134|1224|28211;3379134|1224|28216|80840|506;3379134|1224|28216|80840;3379134|1224|28216;3379134|1224|1236|135625|712;3379134|1224|1236|135625,Complete,Svetlana up
bsdb:34707191/1/2,34707191,case-control,34707191,10.1038/s12276-021-00686-9,NA,"Hou M.F., Ou-Yang F., Li C.L., Chen F.M., Chuang C.H., Kan J.Y., Wu C.C., Shih S.L., Shiau J.P., Kao L.C., Kao C.N., Lee Y.C., Moi S.H., Yeh Y.T., Cheng C.J. , Chiang C.P.",Comprehensive profiles and diagnostic value of menopausal-specific gut microbiota in premenopausal breast cancer,Experimental & molecular medicine,2021,NA,Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,Breast carcinoma,EFO:0000305,Premenopausal female controls (Pre-C),premenopausal breast cancer patients (Pre-BC),Premenopausal breast cancer patients diagnosed with stage I–II disease by pathological examination.,50,100,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,decreased,NA,NA,NA,NA,Signature 2,FIG 2 (B),8 April 2024,Rahila,"Rahila,Scholastica,WikiWorks",Significantly differential gut microbiota in premenopausal breast cancer (Pre-BC) patients compared to premenopausal female controls (Pre-C),decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes massiliensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550|239759|626932;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|1681;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|3085636|186803|33042;1783272|1239|909932|1843489|31977|39948;3379134|1224|1236|91347|543|547;1783272|1239|91061|186826|81852|1350;1783272|1239|526524|526525|128827|1573535|1735;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|909929|1843491|52225;3379134|1224|28216|80840|75682|846;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|823;33090|35493|3398|72025|3803|3814|508215;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|171550|239759|265312;1783272|201174|1760|85006|1268;1783272|201174|1760|2037;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;3379134|976|200643|171549|171551;3379134|976|200643|171549|171550;3379134|976|200643|171549|2005519;1783272|1239|91061|1385|539738;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|1300;1783272|1239|91061|186826;1783272|1239|91061;1783272|1239|186801|186802|216572;1783272|1239|909932|1843489|31977;1783272|1239|186801|186802;1783272|1239|186801;3379134|1224|28216|80840|75682;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201|203494|48461|203557,Complete,Svetlana up
bsdb:34707191/3/1,34707191,case-control,34707191,10.1038/s12276-021-00686-9,NA,"Hou M.F., Ou-Yang F., Li C.L., Chen F.M., Chuang C.H., Kan J.Y., Wu C.C., Shih S.L., Shiau J.P., Kao L.C., Kao C.N., Lee Y.C., Moi S.H., Yeh Y.T., Cheng C.J. , Chiang C.P.",Comprehensive profiles and diagnostic value of menopausal-specific gut microbiota in premenopausal breast cancer,Experimental & molecular medicine,2021,NA,Experiment 3,Taiwan,Homo sapiens,Feces,UBERON:0001988,Menopause,EFO:0003922,Premenopausal female controls (Pre-C),Postmenopausal female controls (Post-C),Postmenopausal female controls (Post-C) participants,50,17,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,FIG 2 (A),10 June 2024,Scholastica,"Scholastica,WikiWorks",Significantly differential gut microbiota in premenopausal female controls (Pre-C) compared to postmenopausal female controls (Post-C),increased,"k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales,k__Thermotogati|p__Synergistota|c__Synergistia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus",3384194|508458|649775|649776;3384194|508458|649775;1783272|1239|526524|526525|128827|2749846|31971,Complete,Svetlana up
bsdb:34707191/3/2,34707191,case-control,34707191,10.1038/s12276-021-00686-9,NA,"Hou M.F., Ou-Yang F., Li C.L., Chen F.M., Chuang C.H., Kan J.Y., Wu C.C., Shih S.L., Shiau J.P., Kao L.C., Kao C.N., Lee Y.C., Moi S.H., Yeh Y.T., Cheng C.J. , Chiang C.P.",Comprehensive profiles and diagnostic value of menopausal-specific gut microbiota in premenopausal breast cancer,Experimental & molecular medicine,2021,NA,Experiment 3,Taiwan,Homo sapiens,Feces,UBERON:0001988,Menopause,EFO:0003922,Premenopausal female controls (Pre-C),Postmenopausal female controls (Post-C),Postmenopausal female controls (Post-C) participants,50,17,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,FIG 2 (A),10 June 2024,Scholastica,"Scholastica,WikiWorks",Significantly differential gut microbiota in premenopausal female controls (Pre-C) compared to postmenopausal female controls (Post-C),decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum",1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174;1783272|1239|186801|186802|216572|216851;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|216572|216851|853;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|216816,Complete,Svetlana up
bsdb:34707191/4/1,34707191,case-control,34707191,10.1038/s12276-021-00686-9,NA,"Hou M.F., Ou-Yang F., Li C.L., Chen F.M., Chuang C.H., Kan J.Y., Wu C.C., Shih S.L., Shiau J.P., Kao L.C., Kao C.N., Lee Y.C., Moi S.H., Yeh Y.T., Cheng C.J. , Chiang C.P.",Comprehensive profiles and diagnostic value of menopausal-specific gut microbiota in premenopausal breast cancer,Experimental & molecular medicine,2021,NA,Experiment 4,Taiwan,Homo sapiens,Feces,UBERON:0001988,Menopause,EFO:0003922,Premenopausal breast cancer patients (Pre-BC),Postmenopausal breast cancer patients (Post-BC),Postmenopausal breast cancer patients diagnosed with stage I–II disease by pathological examination.,100,100,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,FIG 3 (C),10 June 2024,Scholastica,"Scholastica,WikiWorks",Significantly differential gut microbiota in premenopausal (Pre-BC) compared to postmenopausal breast cancer (Post-BC) patients,increased,"k__Viridiplantae|p__Streptophyta,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Pseudomonadati|p__Candidatus Electryoneota|c__Candidatus Tariuqbacteria|o__Candidatus Tariuqbacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",33090|35493;1783272|1239|526524|526525|2810281;3379134|3031806|3075765|3075766;3379134|1224|1236;3379134|200940|3031449|213115|194924|872;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|909932|1843489|31977|29465|39778,Complete,Svetlana up
bsdb:34707191/4/2,34707191,case-control,34707191,10.1038/s12276-021-00686-9,NA,"Hou M.F., Ou-Yang F., Li C.L., Chen F.M., Chuang C.H., Kan J.Y., Wu C.C., Shih S.L., Shiau J.P., Kao L.C., Kao C.N., Lee Y.C., Moi S.H., Yeh Y.T., Cheng C.J. , Chiang C.P.",Comprehensive profiles and diagnostic value of menopausal-specific gut microbiota in premenopausal breast cancer,Experimental & molecular medicine,2021,NA,Experiment 4,Taiwan,Homo sapiens,Feces,UBERON:0001988,Menopause,EFO:0003922,Premenopausal breast cancer patients (Pre-BC),Postmenopausal breast cancer patients (Post-BC),Postmenopausal breast cancer patients diagnosed with stage I–II disease by pathological examination.,100,100,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,FIG 3 (C),10 June 2024,Scholastica,"Scholastica,WikiWorks",Significantly differential gut microbiota in premenopausal (Pre-BC) compared to postmenopausal breast cancer (Post-BC) patients,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum",1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|216572|119852;3379134|200940|3031449|213115|194924|35832;1783272|201174|84998|1643822|1643826|447020;1783272|1239|186801|3085636|186803|841|301302;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|216816,Complete,Svetlana up
bsdb:34710620/1/1,34710620,case-control,34710620,10.1016/j.micinf.2021.104893,NA,"Ding X., Zhou J., Chai Y., Yan Z., Liu X., Dong Y., Mei X., Jiang Y. , Lei H.",A metagenomic study of the gut microbiome in PTB'S disease,Microbes and infection,2022,"16SrDNA, Gut microbiota, Immune, Tuberculosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,Healthy controls,PTB patients,"Newly diagnosed pulmonary TB, no antibiotics in prior month.",20,10,1 month,16S,34,Illumina,relative abundances,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,4,"age,sex",NA,NA,decreased,unchanged,decreased,decreased,NA,Signature 1,Fig. 3A and B,24 June 2025,Nuerteye,Nuerteye,Different genus as biomarkers in relative abundance identified by LEfSe analysis between the two groups of tuberculosis patients and the healthy control.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",1783272|1239|526524|526525|128827|123375;1783272|201174|1760|2037|2049|1654,Complete,NA
bsdb:34710620/1/2,34710620,case-control,34710620,10.1016/j.micinf.2021.104893,NA,"Ding X., Zhou J., Chai Y., Yan Z., Liu X., Dong Y., Mei X., Jiang Y. , Lei H.",A metagenomic study of the gut microbiome in PTB'S disease,Microbes and infection,2022,"16SrDNA, Gut microbiota, Immune, Tuberculosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,Healthy controls,PTB patients,"Newly diagnosed pulmonary TB, no antibiotics in prior month.",20,10,1 month,16S,34,Illumina,relative abundances,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,4,"age,sex",NA,NA,decreased,unchanged,decreased,decreased,NA,Signature 2,Figure 3A  and B,25 June 2025,Nuerteye,Nuerteye,Different genus as biomarkers in relative abundance identified by LEfSe analysis between the two groups of tuberculosis patients and the healthy control.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,NA
bsdb:34726487/1/1,34726487,case-control,34726487,10.1128/mSystems.01215-21,NA,"Phan J., Nair D., Jain S., Montagne T., Flores D.V., Nguyen A., Dietsche S., Gombar S. , Cotter P.",Alterations in Gut Microbiome Composition and Function in Irritable Bowel Syndrome and Increased Probiotic Abundance with Daily Supplementation,mSystems,2021,"gut microbiome, irritable bowel syndrome, metagenomics, prebiotics, probiotics, synbiotics",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS,"Self-reported IBS based on symptoms including constipation, diarrhea, alternating, or unspecified subtypes",122,490,"No, authors state there was no significant beta-diversity difference between subjects who had or had not taken antibiotics in the last 3 months",WMS,NA,Illumina,relative abundances,"T-Test,Random Forest Analysis",0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Reduced microbial diversity and microbial signatures associated with IBS, Figure 2.",15 January 2026,Aqc576444,Aqc576444,Species of Shigella were significantly elevated in IBS compared with healthy controls based on whole-metagenome shotgun sequencing and unpaired t-tests with FDR correction.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,3379134|1224|1236|91347|543|620,Complete,NA
bsdb:34726487/1/2,34726487,case-control,34726487,10.1128/mSystems.01215-21,NA,"Phan J., Nair D., Jain S., Montagne T., Flores D.V., Nguyen A., Dietsche S., Gombar S. , Cotter P.",Alterations in Gut Microbiome Composition and Function in Irritable Bowel Syndrome and Increased Probiotic Abundance with Daily Supplementation,mSystems,2021,"gut microbiome, irritable bowel syndrome, metagenomics, prebiotics, probiotics, synbiotics",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS,"Self-reported IBS based on symptoms including constipation, diarrhea, alternating, or unspecified subtypes",122,490,"No, authors state there was no significant beta-diversity difference between subjects who had or had not taken antibiotics in the last 3 months",WMS,NA,Illumina,relative abundances,"T-Test,Random Forest Analysis",0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,"Reduced microbial diversity and microbial signatures associated with IBS, Figure 2",15 January 2026,Aqc576444,Aqc576444,Eubacterium rectale and Faecalibacterium prausnitzii were significantly increased in healthy controls relative to IBS subjects based on whole-metagenome shotgun sequencing and unpaired t-tests with FDR correction.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,1783272|1239|186801|186802|216572|216851|853,Complete,NA
bsdb:34745091/1/1,34745091,laboratory experiment,34745091,10.3389/fimmu.2021.710513,NA,"Wu J., Zhu Y., Zhou L., Lu Y., Feng T., Dai M., Liu J., Xu W., Cheng W., Sun F., Liu H., Pan W. , Yang X.",Parasite-Derived Excretory-Secretory Products Alleviate Gut Microbiota Dysbiosis and Improve Cognitive Impairment Induced by a High-Fat Diet,Frontiers in immunology,2021,"Echinococcus granulosus, cognition, excretory-secretory products, gut microbiota, microbiota-gut-brain axis, neuroinflammation, obesity",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Low-Fat Diet (LF) group,High-Fat Diet (HF) group,This group includes mice receiving the High Fat diet (60% fat by weight) and intraperitoneally injected with 200 ml vehicle control twice a week in the Shannon Index.,12,12,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3,body weight,"antibiotic,body weight,diet",NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 5I,4 November 2024,Joiejoie,"Joiejoie,MyleeeA,KateRasheed,WikiWorks",Relative abundance of taxa in the LF vs HF groups,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",1783272|1239;1783272|1239|186801;28221;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;1783272|1239|186801|186802;1783272|1239|526524|526525|128827|1729679;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;3379134|1224;1783272|1239|186801|186802|216572|1508657;1783272|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:34745091/1/2,34745091,laboratory experiment,34745091,10.3389/fimmu.2021.710513,NA,"Wu J., Zhu Y., Zhou L., Lu Y., Feng T., Dai M., Liu J., Xu W., Cheng W., Sun F., Liu H., Pan W. , Yang X.",Parasite-Derived Excretory-Secretory Products Alleviate Gut Microbiota Dysbiosis and Improve Cognitive Impairment Induced by a High-Fat Diet,Frontiers in immunology,2021,"Echinococcus granulosus, cognition, excretory-secretory products, gut microbiota, microbiota-gut-brain axis, neuroinflammation, obesity",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Low-Fat Diet (LF) group,High-Fat Diet (HF) group,This group includes mice receiving the High Fat diet (60% fat by weight) and intraperitoneally injected with 200 ml vehicle control twice a week in the Shannon Index.,12,12,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3,body weight,"antibiotic,body weight,diet",NA,decreased,NA,decreased,NA,NA,Signature 2,Figure 5I,4 November 2024,Joiejoie,"Joiejoie,MyleeeA,KateRasheed,WikiWorks",Relative abundance of taxa between the LF and HF groups,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella",3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|976|200643|171549|2005473;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|577310,Complete,Svetlana up
bsdb:34745091/2/1,34745091,laboratory experiment,34745091,10.3389/fimmu.2021.710513,NA,"Wu J., Zhu Y., Zhou L., Lu Y., Feng T., Dai M., Liu J., Xu W., Cheng W., Sun F., Liu H., Pan W. , Yang X.",Parasite-Derived Excretory-Secretory Products Alleviate Gut Microbiota Dysbiosis and Improve Cognitive Impairment Induced by a High-Fat Diet,Frontiers in immunology,2021,"Echinococcus granulosus, cognition, excretory-secretory products, gut microbiota, microbiota-gut-brain axis, neuroinflammation, obesity",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,High-Fat Diet with Excretory-secretory products (HFE) group,High-Fat Diet (HF) group,This group includes mice receiving the High Fat diet (60% fat by weight) and intraperitoneally injected with 200 ml vehicle control twice a week for the Shannon Index.,12,12,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3,body weight,"antibiotic,body weight,diet",NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 5J,13 November 2024,MyleeeA,"Joiejoie,MyleeeA,KateRasheed,WikiWorks",Relative abundance of taxa in the HF and HFE groups,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239|91061|186826|33958|1578|151781;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802,Complete,Svetlana up
bsdb:34745091/2/2,34745091,laboratory experiment,34745091,10.3389/fimmu.2021.710513,NA,"Wu J., Zhu Y., Zhou L., Lu Y., Feng T., Dai M., Liu J., Xu W., Cheng W., Sun F., Liu H., Pan W. , Yang X.",Parasite-Derived Excretory-Secretory Products Alleviate Gut Microbiota Dysbiosis and Improve Cognitive Impairment Induced by a High-Fat Diet,Frontiers in immunology,2021,"Echinococcus granulosus, cognition, excretory-secretory products, gut microbiota, microbiota-gut-brain axis, neuroinflammation, obesity",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,High-Fat Diet with Excretory-secretory products (HFE) group,High-Fat Diet (HF) group,This group includes mice receiving the High Fat diet (60% fat by weight) and intraperitoneally injected with 200 ml vehicle control twice a week for the Shannon Index.,12,12,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3,body weight,"antibiotic,body weight,diet",NA,decreased,NA,decreased,NA,NA,Signature 2,Figure 5J,13 November 2024,MyleeeA,"Joiejoie,MyleeeA,KateRasheed,WikiWorks",Relative abundance of taxa between the HF and HFE groups,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Hungateiclostridiaceae bacterium KB18,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Ileibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Ileibacterium|s__Ileibacterium valens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum",1783272|1239|186801|3082720|543314|109326;28221;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|186802|216572|1834198;1783272|1239|526524|526525|128827|1937007;1783272|1239|526524|526525|128827|1937007|1862668;1783272|1239|186801|3085636|186803;3379134|1224;1783272|1239|186801|186802|216572|1535,Complete,Svetlana up
bsdb:34745091/3/1,34745091,laboratory experiment,34745091,10.3389/fimmu.2021.710513,NA,"Wu J., Zhu Y., Zhou L., Lu Y., Feng T., Dai M., Liu J., Xu W., Cheng W., Sun F., Liu H., Pan W. , Yang X.",Parasite-Derived Excretory-Secretory Products Alleviate Gut Microbiota Dysbiosis and Improve Cognitive Impairment Induced by a High-Fat Diet,Frontiers in immunology,2021,"Echinococcus granulosus, cognition, excretory-secretory products, gut microbiota, microbiota-gut-brain axis, neuroinflammation, obesity",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Low-Fat Diet (LF) group,High-Fat Diet (HF) group,This group includes mice receiving the High Fat diet (60% fat by weight) and intraperitoneally injected with 200 ml vehicle control twice a week in the Simpson Index.,12,12,NA,16S,4,Illumina,log transformation,ANOVA,0.05,FALSE,NA,body weight,"antibiotic,body weight,diet",NA,decreased,NA,decreased,NA,NA,Signature 1,Fig. 5E,5 February 2025,KateRasheed,"KateRasheed,WikiWorks",Relative abundance of taxa in the HF and LF groups using ANOVA,decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Svetlana up
bsdb:34745091/3/2,34745091,laboratory experiment,34745091,10.3389/fimmu.2021.710513,NA,"Wu J., Zhu Y., Zhou L., Lu Y., Feng T., Dai M., Liu J., Xu W., Cheng W., Sun F., Liu H., Pan W. , Yang X.",Parasite-Derived Excretory-Secretory Products Alleviate Gut Microbiota Dysbiosis and Improve Cognitive Impairment Induced by a High-Fat Diet,Frontiers in immunology,2021,"Echinococcus granulosus, cognition, excretory-secretory products, gut microbiota, microbiota-gut-brain axis, neuroinflammation, obesity",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Low-Fat Diet (LF) group,High-Fat Diet (HF) group,This group includes mice receiving the High Fat diet (60% fat by weight) and intraperitoneally injected with 200 ml vehicle control twice a week in the Simpson Index.,12,12,NA,16S,4,Illumina,log transformation,ANOVA,0.05,FALSE,NA,body weight,"antibiotic,body weight,diet",NA,decreased,NA,decreased,NA,NA,Signature 2,"Fig. 5D, 5G, 5K",5 February 2025,KateRasheed,"KateRasheed,WikiWorks",Relative abundance of taxa in the HF and LF groups using ANOVA,increased,"k__Bacillati|p__Bacillota,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Pseudomonadota",1783272|1239;28221;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;3379134|1224,Complete,Svetlana up
bsdb:34745091/4/1,34745091,laboratory experiment,34745091,10.3389/fimmu.2021.710513,NA,"Wu J., Zhu Y., Zhou L., Lu Y., Feng T., Dai M., Liu J., Xu W., Cheng W., Sun F., Liu H., Pan W. , Yang X.",Parasite-Derived Excretory-Secretory Products Alleviate Gut Microbiota Dysbiosis and Improve Cognitive Impairment Induced by a High-Fat Diet,Frontiers in immunology,2021,"Echinococcus granulosus, cognition, excretory-secretory products, gut microbiota, microbiota-gut-brain axis, neuroinflammation, obesity",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,High-Fat Diet with Excretory-secretory products (HFE) group,High-Fat Diet (HF) group,This group includes mice receiving the High Fat diet (60% fat by weight) and intraperitoneally injected with 200 ml vehicle control twice a week for the Simpson Index.,12,12,NA,16S,4,Illumina,log transformation,ANOVA,0.05,FALSE,NA,body weight,"antibiotic,body weight,diet",NA,increased,NA,increased,NA,NA,Signature 1,Fig. 5L,5 February 2025,KateRasheed,"KateRasheed,WikiWorks",Relative abundance of taxa in the HF and HFE groups using ANOVA,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,3379134|976|200643|171549|1853231|283168,Complete,Svetlana up
bsdb:34745091/4/2,34745091,laboratory experiment,34745091,10.3389/fimmu.2021.710513,NA,"Wu J., Zhu Y., Zhou L., Lu Y., Feng T., Dai M., Liu J., Xu W., Cheng W., Sun F., Liu H., Pan W. , Yang X.",Parasite-Derived Excretory-Secretory Products Alleviate Gut Microbiota Dysbiosis and Improve Cognitive Impairment Induced by a High-Fat Diet,Frontiers in immunology,2021,"Echinococcus granulosus, cognition, excretory-secretory products, gut microbiota, microbiota-gut-brain axis, neuroinflammation, obesity",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,High-Fat Diet with Excretory-secretory products (HFE) group,High-Fat Diet (HF) group,This group includes mice receiving the High Fat diet (60% fat by weight) and intraperitoneally injected with 200 ml vehicle control twice a week for the Simpson Index.,12,12,NA,16S,4,Illumina,log transformation,ANOVA,0.05,FALSE,NA,body weight,"antibiotic,body weight,diet",NA,increased,NA,increased,NA,NA,Signature 2,"Fig. 5D, 5G, 5K",5 February 2025,KateRasheed,"KateRasheed,WikiWorks",Relative abundance of taxa in the HF and HFE groups using ANOVA,decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,c__Deltaproteobacteria",1783272|1239;3379134|1224;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;28221,Complete,Svetlana up
bsdb:34745091/21/1,34745091,laboratory experiment,34745091,10.3389/fimmu.2021.710513,NA,"Wu J., Zhu Y., Zhou L., Lu Y., Feng T., Dai M., Liu J., Xu W., Cheng W., Sun F., Liu H., Pan W. , Yang X.",Parasite-Derived Excretory-Secretory Products Alleviate Gut Microbiota Dysbiosis and Improve Cognitive Impairment Induced by a High-Fat Diet,Frontiers in immunology,2021,"Echinococcus granulosus, cognition, excretory-secretory products, gut microbiota, microbiota-gut-brain axis, neuroinflammation, obesity",Experiment 21,China,Mus musculus,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,High-Fat Diet with Excretory-secretory products (HFE) group,High-Fat ESPs supplement with antibiotics (HFE+AB) group,This group includes the HFE group given a cocktail of antibiotics ( HFE+Ab) in the drinking water to investigate the role of gut microbiota in ESPs intervention.,6,6,NA,16S,4,Illumina,log transformation,ANOVA,0.05,FALSE,NA,body weight,"antibiotic,body weight,diet",NA,NA,NA,NA,NA,NA,Signature 1,Fig. S6,2 February 2025,Joiejoie,"Joiejoie,WikiWorks",Antibiotics significantly decreased bacterial DNA of faces in HFE mice supplemented with ESPs.,decreased,NA,NA,Complete,Svetlana up
bsdb:34766210/1/1,34766210,time series / longitudinal observational,34766210,10.1007/s00248-021-01914-5,NA,"Sanseverino I., Pretto P., António D.C., Lahm A., Facca C., Loos R., Skejo H., Beghi A., Pandolfi F., Genoni P. , Lettieri T.",Metagenomics Analysis to Investigate the Microbial Communities and Their Functional Profile During Cyanobacterial Blooms in Lake Varese,Microbial ecology,2022,"Algal bloom, Freshwater, Lyngbya, Metagenomics, Microbial populations, Water quality",Experiment 1,Italy,Not specified,Space surrounding organism,UBERON:0013514,Environmental factor,EFO:0000469,No healthy samples,2017 samples,"2017 samples are samples obtained from the three river depths(Meso, Secchi, and surface depth) during the cyanobacterial bloom in 2017.",NA,3,NA,16S,34,Illumina,relative abundances,NA,0.05,NA,NA,NA,NA,decreased,decreased,unchanged,decreased,NA,decreased,Signature 1,Figure 3,7 March 2024,Imaspecial,"Imaspecial,WikiWorks","Taxonomic analysis at the phylum level showed that, in most of the samples, Proteobacteria was the predominant taxonomic group followed by Actinobacteriota, Cyanobacteria and Bacteroidota .",increased,NA,NA,Complete,NA
bsdb:34790583/1/1,34790583,case-control,34790583,10.3389/fcimb.2021.572752,NA,"Ding H, Yi X, Zhang X, Wang H, Liu H, Mou W",Imbalance in the Gut Microbiota of Children With Autism Spectrum Disorders,Frontiers in cellular and infection microbiology,2021,"gut microbiota, autism spectrum disorders, children, high-throughput sequencing, firmicutes, actinobacteria",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Healthy children,Children with Autism Spectrum Disorder (ASD),Diagnosed with the Diagnostic and Statistical Manual for Mental Disorders (Fifth Edition (DSM-5)),20,25,6 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Figure 4, Figure 5",10 October 2024,AlishaM,"AlishaM,WikiWorks",The difference of gut microbiota between ASD and control group on genus and phylum level,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",1783272|1239|186801|3085636|186803|1766253;1783272|1239;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|292632,Complete,NA
bsdb:34790583/1/2,34790583,case-control,34790583,10.3389/fcimb.2021.572752,NA,"Ding H, Yi X, Zhang X, Wang H, Liu H, Mou W",Imbalance in the Gut Microbiota of Children With Autism Spectrum Disorders,Frontiers in cellular and infection microbiology,2021,"gut microbiota, autism spectrum disorders, children, high-throughput sequencing, firmicutes, actinobacteria",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Healthy children,Children with Autism Spectrum Disorder (ASD),Diagnosed with the Diagnostic and Statistical Manual for Mental Disorders (Fifth Edition (DSM-5)),20,25,6 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Figure 4, Figure 5",10 October 2024,AlishaM,"AlishaM,WikiWorks",The difference of gut microbiota between ASD and control group on genus and phylum level,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii",1783272|201174;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|186806|1730;3384189|32066|203490;1783272|544448;1783272|1239|186801|3085636|186803|2569097|39488,Complete,NA
bsdb:34790583/2/1,34790583,case-control,34790583,10.3389/fcimb.2021.572752,NA,"Ding H, Yi X, Zhang X, Wang H, Liu H, Mou W",Imbalance in the Gut Microbiota of Children With Autism Spectrum Disorders,Frontiers in cellular and infection microbiology,2021,"gut microbiota, autism spectrum disorders, children, high-throughput sequencing, firmicutes, actinobacteria",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Healthy children,Children with Autism Spectrum Disorder (ASD),Diagnosed with the Diagnostic and Statistical Manual for Mental Disorders (Fifth Edition (DSM-5)),20,25,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 6,12 December 2024,AlishaM,"AlishaM,WikiWorks",Differentially abundant taxon between ASD and healthy controls,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Raoultibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens",1783272|1239|186801|186802|216572;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|292632;1783272|201174|84998|1643822|1643826|1926677;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|1766253;1783272|1239|909932|1843489|31977|209879;1783272|1239|186801|3082768|990719;1783272|1239|186801|3085636|186803|28050|39485,Complete,NA
bsdb:34790583/2/2,34790583,case-control,34790583,10.3389/fcimb.2021.572752,NA,"Ding H, Yi X, Zhang X, Wang H, Liu H, Mou W",Imbalance in the Gut Microbiota of Children With Autism Spectrum Disorders,Frontiers in cellular and infection microbiology,2021,"gut microbiota, autism spectrum disorders, children, high-throughput sequencing, firmicutes, actinobacteria",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Healthy children,Children with Autism Spectrum Disorder (ASD),Diagnosed with the Diagnostic and Statistical Manual for Mental Disorders (Fifth Edition (DSM-5)),20,25,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 6,13 December 2024,AlishaM,"AlishaM,WikiWorks",Differentially abundant taxon between ASD and healthy controls,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Frankiales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales",1783272|201174;1783272|201174|1760|85004;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;3384189|32066|203490|203491|203492|180162;1783272|1239|186801|3085636|186803|2569097|39488;3379134|1224|1236|135624;3379134|1224|1236|135624|84642;3379134|1224|1236|135624|84642|642;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|81852;1783272|1239|186801|3085636|186803|2316020|33038;1783272|201174|1760|85013;1783272|1239|526524|526525|2810280|3025755;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826,Complete,NA
bsdb:34795317/1/1,34795317,case-control,34795317,10.1038/s41531-021-00244-0,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8602383/,"Weis S., Meisner A., Schwiertz A., Unger M.M., Becker A., Faßbender K., Schnell S., Schäfer K.H. , Egert M.",Association between Parkinson's disease and the faecal eukaryotic microbiota,NPJ Parkinson's disease,2021,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls (HC),Parkinson's disease patients (PD),Patients suffering from Parkinson's disease,25,34,3 months,18S,NA,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,age,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,Table 1,29 March 2024,Samreen-19,"Samreen-19,WikiWorks",Taxa differing significantly between PD samples and controls.,increased,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Dipodascaceae|g__Geotrichum|s__Geotrichum candidum,4751|4890|3239873|3243772|34353|43987|1173061,Complete,Svetlana up
bsdb:34795317/1/2,34795317,case-control,34795317,10.1038/s41531-021-00244-0,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8602383/,"Weis S., Meisner A., Schwiertz A., Unger M.M., Becker A., Faßbender K., Schnell S., Schäfer K.H. , Egert M.",Association between Parkinson's disease and the faecal eukaryotic microbiota,NPJ Parkinson's disease,2021,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls (HC),Parkinson's disease patients (PD),Patients suffering from Parkinson's disease,25,34,3 months,18S,NA,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,age,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Table 1,29 March 2024,Samreen-19,"Samreen-19,WikiWorks",Taxa differing significantly between PD samples and controls.,decreased,"p__Cercozoa|o__Glissomonadida|f__Sandonidae|g__Sandona|s__Sandona heptamutans,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Malpighiales|f__Linaceae|g__Linum|s__Linum usitatissimum,p__Cercozoa|o__Cercomonadida|f__Cercomonadidae|g__Paracercomonas|s__Paracercomonas sp.,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Penicillium|s__Penicillium roqueforti,c__Synurophyceae|o__Ochromonadales|f__Ochromonadaceae|g__Poterioochromonas|s__Poterioochromonas malhamensis",136419|1238681|2586441|1239209|983299;33090|35493|3398|3646|4004|4005|4006;136419|188941|45108|372085|1979800;4751|4890|147545|5042|1131492|5073|5082;33859|98652|88165|88166|88167,Complete,Svetlana up
bsdb:34799562/1/1,34799562,"cross-sectional observational, not case-control",34799562,10.1038/s41467-021-27112-y,NA,"Yang Y., Du L., Shi D., Kong C., Liu J., Liu G., Li X. , Ma Y.",Dysbiosis of human gut microbiome in young-onset colorectal cancer,Nature communications,2021,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,yControl,yCRC,young-onset CRC patients (<50 years old),148,144,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,"age,sex",NA,unchanged,NA,NA,NA,decreased,Signature 1,Figure 3B,24 June 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between yCRC and yControl groups,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|2037|2049|1654;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|216572|946234|292800;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|1853231|283168;1783272|1239|909932|1843489|31977|29465,Complete,Claregrieve1
bsdb:34799562/1/2,34799562,"cross-sectional observational, not case-control",34799562,10.1038/s41467-021-27112-y,NA,"Yang Y., Du L., Shi D., Kong C., Liu J., Liu G., Li X. , Ma Y.",Dysbiosis of human gut microbiome in young-onset colorectal cancer,Nature communications,2021,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,yControl,yCRC,young-onset CRC patients (<50 years old),148,144,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,"age,sex",NA,unchanged,NA,NA,NA,decreased,Signature 2,Figure 3B,24 June 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between yCRC and yControl groups,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|31979|1485;1783272|1239|909932|1843489|31977|39948;1783272|1239|526524|526525|128827;3379134|1224|1236|91347|543|561;1783272|1239|186801|186802|186806|1730|39496;3379134|1224|1236|135625|712|724;3379134|1224|1236|91347|543|570;1783272|1239|909932|909929|1843491|158846;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|3082720|186804|1501226;3379134|1224|1236|91347|543|620;1783272|1239|186801|3085636|186803|1766253|39491,Complete,Claregrieve1
bsdb:34799562/2/1,34799562,"cross-sectional observational, not case-control",34799562,10.1038/s41467-021-27112-y,NA,"Yang Y., Du L., Shi D., Kong C., Liu J., Liu G., Li X. , Ma Y.",Dysbiosis of human gut microbiome in young-onset colorectal cancer,Nature communications,2021,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,oControls,oCRC,old-onset CRC patients (50 years old or older),203,233,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,"age,sex",NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 3A,24 June 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between oCRC and oControl groups,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium butyricum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Wegman et al. 2014),k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus champanellensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|207244;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|1955243;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|31979|1485|1492;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|33042;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085656|3085657|2039302;3379134|1224|28216|80840|995019|577310;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|1160721;1783272|1239|186801|186802|216572|1263|1161942;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|3085636|186803|1766253|39491,Complete,Claregrieve1
bsdb:34799562/2/2,34799562,"cross-sectional observational, not case-control",34799562,10.1038/s41467-021-27112-y,NA,"Yang Y., Du L., Shi D., Kong C., Liu J., Liu G., Li X. , Ma Y.",Dysbiosis of human gut microbiome in young-onset colorectal cancer,Nature communications,2021,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,oControls,oCRC,old-onset CRC patients (50 years old or older),203,233,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,"age,sex",NA,decreased,NA,NA,NA,decreased,Signature 2,Figure 3A,24 June 2022,Jeshudy,"Jeshudy,Claregrieve1,WikiWorks",Differential microbial abundance between oCRC and oControl groups,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Massilistercora|s__Massilistercora timonensis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens",3379134|1224|28211|204458|76892|41275;1783272|201174|84998|1643822|1643826|84111;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|526524|526525|2810280|1505663;3379134|1224|1236|91347|543|561;1783272|1239|186801|186802|216572|216851|1946507;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|186802|2717089|2086584;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;3379134|1224|1236|91347|543|620;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|1506553|29347,Complete,Claregrieve1
bsdb:34809575/2/1,34809575,prospective cohort,34809575,https://doi.org/10.1186/s12866-021-02387-9,NA,"Wu Z., Hullings A.G., Ghanbari R., Etemadi A., Wan Y., Zhu B., Poustchi H., Fahraji B.B., Sakhvidi M.J.Z., Shi J., Knight R., Malekzadeh R., Sinha R. , Vogtmann E.",Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts,BMC microbiology,2021,"Comparability, Feces, Iran, Microbiome, Saliva, Stability",Experiment 2,Iran,Homo sapiens,Feces,UBERON:0001988,Sample treatment protocol,EFO:0003809,RNAlater - Day 0,Fecal occult blood test [FOBT] cards - Day 0,"Fecal occult blood test [FOBT] cards fecal samples frozen immediately (day-0) from Gonbad and Yazd, Iran",69,70,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Additional files 2 Table S4,26 March 2024,EGO,"EGO,Scholastica,WikiWorks","Differential abundance analysis of phylum and genus level changes comparing RNAlater to FOBT card fecal samples frozen immediately (day-0) from Gonbad and Yazd, Iran",increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|s__Eggerthellaceae bacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__Eubacteriales Family XIII. Incertae Sedis bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|g__Negativibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella",1783272|201174;1783272|1239;1783272|201174|1760|85004|31953|1678;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|1643822|1643826|84111;1783272|201174|84998|1643822|1643826|580024;1783272|201174|84998|84999|84107|1473205;1783272|201174|84998|1643822|1643826|1972561;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|3082720|543314|2137877;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|248744;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|186801|186802|216572|1263|438033;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803;1783272|1239|186801|3082720|186804|1505657;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3082720|186804|1505652;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|216572|216851;1783272|1239|1980693;1783272|1239|186801|186802|216572|707003;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|526524|526525|128827|1573535;1783272|1239|526524|526525|128827|123375;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|909929|1843491|52225,Complete,Svetlana up
bsdb:34809575/2/2,34809575,prospective cohort,34809575,https://doi.org/10.1186/s12866-021-02387-9,NA,"Wu Z., Hullings A.G., Ghanbari R., Etemadi A., Wan Y., Zhu B., Poustchi H., Fahraji B.B., Sakhvidi M.J.Z., Shi J., Knight R., Malekzadeh R., Sinha R. , Vogtmann E.",Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts,BMC microbiology,2021,"Comparability, Feces, Iran, Microbiome, Saliva, Stability",Experiment 2,Iran,Homo sapiens,Feces,UBERON:0001988,Sample treatment protocol,EFO:0003809,RNAlater - Day 0,Fecal occult blood test [FOBT] cards - Day 0,"Fecal occult blood test [FOBT] cards fecal samples frozen immediately (day-0) from Gonbad and Yazd, Iran",69,70,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Additional files 2 Table S8,26 March 2024,EGO,"EGO,Scholastica,WikiWorks","Differential abundance analysis of phylum level changes comparing OMNIgene ORAL kit samples to Scope mouthwash oral samples from Gonbad and Yazd, Iran",decreased,"k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Lentisphaerota,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,s__metagenome,s__gut metagenome,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|s__uncultured Prevotellaceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Candidatus Izemoplasmatales,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Puniceicoccaceae",3379134|976;1783272|1117;3379134|256845;3379134|1224;1783272|544448;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|1853231|574697;3379134|976|200643|171549|1853231|283168;256318;749906;3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|171552|370804;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|2005525|375288;1783272|1798710|1906119;1783272|1239|186801|3085636|186803|830;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|297314;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|186802|1470353;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|707003;1783272|1239|186801|186802;1783272|544448|31969|186332|186333|2152;3379134|256845|1313211|278082|255528|172900;3379134|1224|28211|204441;3379134|200940|3031449|213115|194924|35832;3379134|200940|3031449|213115|194924|872;3379134|1224|1236|135624|83763|83770;3379134|1224|28216|80840|995019|577310;3379134|1224|28216|80840|995019|40544;3379134|1224|28216|80840|119060;1783272|544448|31969|2975519;1783272|544448|31969;3379134|74201|414999|415001|415002,Complete,Svetlana up
bsdb:34809575/3/1,34809575,prospective cohort,34809575,https://doi.org/10.1186/s12866-021-02387-9,NA,"Wu Z., Hullings A.G., Ghanbari R., Etemadi A., Wan Y., Zhu B., Poustchi H., Fahraji B.B., Sakhvidi M.J.Z., Shi J., Knight R., Malekzadeh R., Sinha R. , Vogtmann E.",Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts,BMC microbiology,2021,"Comparability, Feces, Iran, Microbiome, Saliva, Stability",Experiment 3,Iran,Homo sapiens,Saliva,UBERON:0001836,Sample treatment protocol,EFO:0003809,Scope mouthwash - Day 0,Scope mouthwash - Day 4,"Scope mouthwash samples after incubation at room temperature for four days (day-4) from Gonbad and Yazd, Iran",70,55,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Additional files 2 Table S6,23 July 2024,Scholastica,"Scholastica,WikiWorks","Differential abundance analysis of phylum and genus level changes comparing Scope mouthwash samples after incubation at room temperature for four days (day-4) to frozen immediately (day-0) from Gonbad and Yazd, Iran",increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",1783272|1239;1783272|201174|1760|2037|2049;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|186802|216572|707003;1783272|1239|526524|526525|128827|123375;1783272|1239|909932|1843489|31977;3379134|1224|28216|80840|119060|47670;3379134|1224|1236|72274|135621|286,Complete,Svetlana up
bsdb:34809575/3/2,34809575,prospective cohort,34809575,https://doi.org/10.1186/s12866-021-02387-9,NA,"Wu Z., Hullings A.G., Ghanbari R., Etemadi A., Wan Y., Zhu B., Poustchi H., Fahraji B.B., Sakhvidi M.J.Z., Shi J., Knight R., Malekzadeh R., Sinha R. , Vogtmann E.",Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts,BMC microbiology,2021,"Comparability, Feces, Iran, Microbiome, Saliva, Stability",Experiment 3,Iran,Homo sapiens,Saliva,UBERON:0001836,Sample treatment protocol,EFO:0003809,Scope mouthwash - Day 0,Scope mouthwash - Day 4,"Scope mouthwash samples after incubation at room temperature for four days (day-4) from Gonbad and Yazd, Iran",70,55,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Additional files 2 Table S6,23 July 2024,Scholastica,"Scholastica,WikiWorks","Differential abundance analysis of phylum and genus level changes comparing Scope mouthwash samples after incubation at room temperature for four days (day-4) to frozen immediately (day-0) from Gonbad and Yazd, Iran",decreased,"k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",3379134|1224;1783272|201174|1760|85006|1268|32207;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|1283313;1783272|1239|91061|1385|539738|1378;3379134|1224|28216|206351|481|482;3379134|1224|1236|135625|712|416916;3379134|1224|1236|135625|712|724,Complete,Svetlana up
bsdb:34809575/4/1,34809575,prospective cohort,34809575,https://doi.org/10.1186/s12866-021-02387-9,NA,"Wu Z., Hullings A.G., Ghanbari R., Etemadi A., Wan Y., Zhu B., Poustchi H., Fahraji B.B., Sakhvidi M.J.Z., Shi J., Knight R., Malekzadeh R., Sinha R. , Vogtmann E.",Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts,BMC microbiology,2021,"Comparability, Feces, Iran, Microbiome, Saliva, Stability",Experiment 4,Iran,Homo sapiens,Saliva,UBERON:0001836,Sample treatment protocol,EFO:0003809,OMNIgene ORAL kit,Scope mouthwash,"Scope mouthwash oral samples from Gonbad and Yazd, Iran",77,125,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Additional files 2 Table S8,23 July 2024,Scholastica,"Scholastica,WikiWorks","Differential abundance analysis of phylum and genus level changes comparing OMNIgene ORAL kit samples to Scope mouthwash oral samples from Gonbad and Yazd, Iran",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Geobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Spirochaetota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,p__Candidatus Absconditibacteriota|s__candidate division SR1 bacterium MGEHA",1783272|1239|91061|186826|186827|46123;1783272|201174|1760|85004|31953|419014;3379134|976;3379134|29547|3031852|213849|72294|194;3379134|29547;3379134|976|117743|200644|49546|1016;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|1385|3120669|129337;1783272|1239|91061|186826|33958|1578;3379134|1224|28216|80840|119060|47670;;3379134|976|200643|171549|815|909656;3379134|1224|1236|72274|135621|286;1783272|201174|1760|85004|31953|196081;1783272|1239|909932|909929|1843491|970;3379134|203691;1783272|1239|909932|1843489|31977;1783272|1239|186801|186802|216572|707003;221235|1293577,Complete,Svetlana up
bsdb:34809575/4/2,34809575,prospective cohort,34809575,https://doi.org/10.1186/s12866-021-02387-9,NA,"Wu Z., Hullings A.G., Ghanbari R., Etemadi A., Wan Y., Zhu B., Poustchi H., Fahraji B.B., Sakhvidi M.J.Z., Shi J., Knight R., Malekzadeh R., Sinha R. , Vogtmann E.",Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts,BMC microbiology,2021,"Comparability, Feces, Iran, Microbiome, Saliva, Stability",Experiment 4,Iran,Homo sapiens,Saliva,UBERON:0001836,Sample treatment protocol,EFO:0003809,OMNIgene ORAL kit,Scope mouthwash,"Scope mouthwash oral samples from Gonbad and Yazd, Iran",77,125,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Additional files 2 Table S8,23 July 2024,Scholastica,"Scholastica,WikiWorks","Differential abundance analysis of phylum and genus level changes comparing OMNIgene ORAL kit samples to Scope mouthwash oral samples from Gonbad and Yazd, Iran",decreased,"k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] brachy,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",3379134|1224;1783272|201174|1760|85006|1268|32207;3379134|976|200643|171549|171552|1283313;1783272|1239|186801|3082720|543314|35517;1783272|1239|186801|3082720|543314|35518;1783272|1239|186801|3085636|186803|43996;1783272|1239|186801|3085636|186803|1164882;1783272|1239|186801|3085636|186803|265975;1783272|1239|526524|526525|128827|123375;3384189|32066|203490|203491|203492|848;3379134|1224|28216|206351|481|482;3379134|1224|1236|135625|712|713;3379134|1224|1236|135625|712|416916;3379134|1224|1236|135625|712|724,Complete,Svetlana up
bsdb:34852831/1/1,34852831,time series / longitudinal observational,34852831,10.1186/s12967-021-03152-2,NA,"Xie L., Xu C., Fan Y., Li Y., Wang Y., Zhang X., Yu S., Wang J., Chai R., Zhao Z., Jin Y., Xu Z., Zhao S. , Bian Y.",Effect of fecal microbiota transplantation in patients with slow transit constipation and the relative mechanisms based on the protein digestion and absorption pathway,Journal of translational medicine,2021,"Fecal microbiota transplantation (FMT), Slow transit constipation (STC), The protein digestion and absorption pathway",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Fecal microbiota transplant patients at baseline (B1),Post-fecal microbiota transplant patients (B2),This group consists of post-FMT patients after the first fecal microbiota transplant.,8,8,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4A,17 May 2025,Victoria,"Victoria,Amaanarif",LEfSe analysis with an LDA value of > 2 displayed the dominant microbiomes in each group (B1 & B2).,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Sharpea",1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|526524|526525|2810280|519427,Complete,KateRasheed
bsdb:34852831/1/2,34852831,time series / longitudinal observational,34852831,10.1186/s12967-021-03152-2,NA,"Xie L., Xu C., Fan Y., Li Y., Wang Y., Zhang X., Yu S., Wang J., Chai R., Zhao Z., Jin Y., Xu Z., Zhao S. , Bian Y.",Effect of fecal microbiota transplantation in patients with slow transit constipation and the relative mechanisms based on the protein digestion and absorption pathway,Journal of translational medicine,2021,"Fecal microbiota transplantation (FMT), Slow transit constipation (STC), The protein digestion and absorption pathway",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Fecal microbiota transplant patients at baseline (B1),Post-fecal microbiota transplant patients (B2),This group consists of post-FMT patients after the first fecal microbiota transplant.,8,8,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4A,17 May 2025,Victoria,"Victoria,Amaanarif",LEfSe analysis with an LDA value of > 2 displayed the dominant microbiomes in each group (B1 & B2),decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,1783272|1239|186801|186802|216572|1263,Complete,KateRasheed
bsdb:34852831/2/1,34852831,time series / longitudinal observational,34852831,10.1186/s12967-021-03152-2,NA,"Xie L., Xu C., Fan Y., Li Y., Wang Y., Zhang X., Yu S., Wang J., Chai R., Zhao Z., Jin Y., Xu Z., Zhao S. , Bian Y.",Effect of fecal microbiota transplantation in patients with slow transit constipation and the relative mechanisms based on the protein digestion and absorption pathway,Journal of translational medicine,2021,"Fecal microbiota transplantation (FMT), Slow transit constipation (STC), The protein digestion and absorption pathway",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Fecal microbiota transplant patients at baseline (B1),Post-fecal microbiota transplant patients (B3),This group consists of post-FMT patients after the second fecal microbiota transplant.,8,8,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,17 May 2025,Victoria,Victoria,LEfSe analysis with an LDA value of > 2 displayed the dominant microbiomes in each group (B1 & B3).,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Azonexaceae|g__Dechloromonas,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfarculia|o__Desulfarculales|f__Desulfarculaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Rhodocyclaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfarculia|o__Desulfarculales,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Succiniclasticum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826;3379134|1224|1236;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|561;3379134|1224|28211|3120395|433;3379134|1224|28216|206389;3379134|1224|28216|206389|2008795|73029;3379134|200940|3031646|453227|453228;1783272|201174|1760|85006|85023|33882;3379134|1224|28216|206389|75787;3379134|1224|1236|135614|32033|68;3379134|976|1853228|1853229|563835|504481;3379134|200940|3031646|453227;3379134|976|117747|200666;3379134|976|117747;1783272|1239|909932|1843488|909930|40840;1783272|201174|1760|85011|2062,Complete,KateRasheed
bsdb:34852831/2/2,34852831,time series / longitudinal observational,34852831,10.1186/s12967-021-03152-2,NA,"Xie L., Xu C., Fan Y., Li Y., Wang Y., Zhang X., Yu S., Wang J., Chai R., Zhao Z., Jin Y., Xu Z., Zhao S. , Bian Y.",Effect of fecal microbiota transplantation in patients with slow transit constipation and the relative mechanisms based on the protein digestion and absorption pathway,Journal of translational medicine,2021,"Fecal microbiota transplantation (FMT), Slow transit constipation (STC), The protein digestion and absorption pathway",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Fecal microbiota transplant patients at baseline (B1),Post-fecal microbiota transplant patients (B3),This group consists of post-FMT patients after the second fecal microbiota transplant.,8,8,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4B,17 May 2025,Victoria,Victoria,LEfSe analysis with an LDA value of > 2 displayed the dominant microbiomes in each group (B1 & B3).,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Mycoplana,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|1224|28211|356|82115|13159;3379134|976|200643|171549|171552;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803,Complete,KateRasheed
bsdb:34852831/3/1,34852831,time series / longitudinal observational,34852831,10.1186/s12967-021-03152-2,NA,"Xie L., Xu C., Fan Y., Li Y., Wang Y., Zhang X., Yu S., Wang J., Chai R., Zhao Z., Jin Y., Xu Z., Zhao S. , Bian Y.",Effect of fecal microbiota transplantation in patients with slow transit constipation and the relative mechanisms based on the protein digestion and absorption pathway,Journal of translational medicine,2021,"Fecal microbiota transplantation (FMT), Slow transit constipation (STC), The protein digestion and absorption pathway",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Fecal microbiota transplant patients at baseline (B1),Post-fecal microbiota transplant patients (B4),This group consists of post-FMT patients after the third fecal microbiota transplant.,8,8,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4C,17 May 2025,Victoria,Victoria,LEfSe analysis with an LDA value of > 2 displayed the dominant microbiomes in each group (B1 & B4).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Cellvibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,s__bacterium F16,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae",3379134|1224|28216|80840|80864|12916;3379134|1224|1236|135622;1783272|1239|186801|186802|186806|264995;1783272|1239|909932|909929|1843491|82373;3379134|1224|1236|1706369|1706371|10;1783272|1239|186801|3082768|990719;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572;1932694;3379134|1224|1236|135622|72275,Complete,KateRasheed
bsdb:34852831/3/2,34852831,time series / longitudinal observational,34852831,10.1186/s12967-021-03152-2,NA,"Xie L., Xu C., Fan Y., Li Y., Wang Y., Zhang X., Yu S., Wang J., Chai R., Zhao Z., Jin Y., Xu Z., Zhao S. , Bian Y.",Effect of fecal microbiota transplantation in patients with slow transit constipation and the relative mechanisms based on the protein digestion and absorption pathway,Journal of translational medicine,2021,"Fecal microbiota transplantation (FMT), Slow transit constipation (STC), The protein digestion and absorption pathway",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Fecal microbiota transplant patients at baseline (B1),Post-fecal microbiota transplant patients (B4),This group consists of post-FMT patients after the third fecal microbiota transplant.,8,8,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4C,17 May 2025,Victoria,Victoria,LEfSe analysis with an LDA value of > 2 displayed the dominant microbiomes in each group (B1 & B4).,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia|o__Acidimicrobiales,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Pseudomonadati|p__Verrucomicrobiota|c__Spartobacteria|g__Candidatus Xiphinematobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Mycoplana,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",3379134|1224|28216|80840|119060|48736;1783272|201174|84992|84993;1783272|201174|84992;3379134|1224|28211|204458|76892;3379134|1224|28211|204458;3379134|74201|134549|134550;3379134|1224|28211|356|82115|13159;3379134|1224|28211|204457|41297|13687;1783272|1239|909932|1843488|909930|33024,Complete,KateRasheed
bsdb:34879874/1/1,34879874,case-control,34879874,https://doi.org/10.1186/s13048-021-00923-9,NA,"Wu J., Ning Y., Tan L., Chen Y., Huang X. , Zhuo Y.",Characteristics of the vaginal microbiome in women with premature ovarian insufficiency,Journal of ovarian research,2021,"16S rRNA sequencing, Gonadal steroid hormones, Premature ovarian insufficiency, Vaginal microbiota",Experiment 1,China,Homo sapiens,Vagina,UBERON:0000996,Premature ovarian insufficiency,HP:0008209,Healthy subjects,Primary ovarian insufficiency (POI),Twenty-eight women with spontaneous Primary ovarian insufficiency (POI).,12,28,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2C,29 July 2025,Aleru Divine,Aleru Divine,Microbes that significantly differed between the POI and control groups.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,NA
bsdb:34879874/1/2,34879874,case-control,34879874,https://doi.org/10.1186/s13048-021-00923-9,NA,"Wu J., Ning Y., Tan L., Chen Y., Huang X. , Zhuo Y.",Characteristics of the vaginal microbiome in women with premature ovarian insufficiency,Journal of ovarian research,2021,"16S rRNA sequencing, Gonadal steroid hormones, Premature ovarian insufficiency, Vaginal microbiota",Experiment 1,China,Homo sapiens,Vagina,UBERON:0000996,Premature ovarian insufficiency,HP:0008209,Healthy subjects,Primary ovarian insufficiency (POI),Twenty-eight women with spontaneous Primary ovarian insufficiency (POI).,12,28,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2C,29 July 2025,Aleru Divine,Aleru Divine,Microbes that significantly differed between the POI and control groups.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter",1783272|1239|91061|186826|33958|1578;3379134|1224|28211|204458|76892|41275;3379134|976|200643|171549|1853231|283168,Complete,NA
bsdb:34880258/1/1,34880258,case-control,34880258,10.1038/s41531-021-00254-y,NA,"Pal G., Ramirez V., Engen P.A., Naqib A., Forsyth C.B., Green S.J., Mahdavinia M., Batra P.S., Tajudeen B.A. , Keshavarzian A.",Deep nasal sinus cavity microbiota dysbiosis in Parkinson's disease,NPJ Parkinson's disease,2021,NA,Experiment 1,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Parkinson's disease,MONDO:0005180,rHC (Random non-household healthy controls),PD (Parkinson's Disease),This group consists of 30 Parkinson's disease subjects.,17,30,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,race,sex",NA,NA,unchanged,NA,unchanged,NA,decreased,Signature 1,Supplementary figure 2 and Supplementary table 10 & 11.,18 March 2024,Idiat,"Idiat,Victoria,WikiWorks",Nasal microbial differences between rHC and PD subjects. Differential abundance differences were measured using DESeq2 within PD (n=30) subjects compared to rHC (n=17) subjects. At the genus and species taxonomic level.,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus hydrogenalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium propinquum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia|s__Delftia tsuruhatensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus yunnanensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella catarrhalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas brenneri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas mandelii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia insidiosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Piscirickettsiaceae|g__Methylophaga,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Dermabacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Desulfuromonadales|f__Geopsychrobacteraceae|g__Desulfuromusa,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter",1783272|1239|1737404|1737405|1570339|165779|33029;1783272|201174|1760|85007|1653|1716|43769;3379134|1224|28216|80840|80864|80865|180282;1783272|201174|1760|85006|1268|1269|566027;3379134|1224|1236|2887326|468|475|480;3379134|1224|1236|72274|135621|286|129817;3379134|1224|1236|72274|135621|286|75612;3379134|1224|28216|80840|119060|48736|190721;1783272|1239|91061|1385|90964|1279|1282;3379134|1224|1236|2887326|468|475;3379134|1224|1236|72273|135616|40222;1783272|201174|1760|85006|85020|36739;3379134|1224|28216|80840|80864|80865;3379134|1224|28216|80840|119060|48736;3379134|200940|3031651|69541|3031659|37817;3379134|1224|1236|2887326|468|469,Complete,Svetlana up
bsdb:34880258/1/2,34880258,case-control,34880258,10.1038/s41531-021-00254-y,NA,"Pal G., Ramirez V., Engen P.A., Naqib A., Forsyth C.B., Green S.J., Mahdavinia M., Batra P.S., Tajudeen B.A. , Keshavarzian A.",Deep nasal sinus cavity microbiota dysbiosis in Parkinson's disease,NPJ Parkinson's disease,2021,NA,Experiment 1,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Parkinson's disease,MONDO:0005180,rHC (Random non-household healthy controls),PD (Parkinson's Disease),This group consists of 30 Parkinson's disease subjects.,17,30,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,race,sex",NA,NA,unchanged,NA,unchanged,NA,decreased,Signature 2,Supplementary figure 2 and Supplementary table 10 & 11.,19 March 2024,Idiat,"Idiat,Ayibatari,Victoria,WikiWorks","Nasal microbial differences between rHC and PD subjects. Differential abundance
differences were measured using DESeq2 within PD (n=30) subjects compared to rHC (n=17) subjects. At the genus and species taxonomic level.",decreased,"k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminiphilaceae|g__Aminiphilus|s__Aminiphilus circumscriptus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum|s__Azospirillum palatum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides denticanium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia mallei,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia multivorans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia ubonensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia vietnamiensis,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter canadensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium acetoacidophilum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium atypicum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium doosanense,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium massiliense,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium pyruviciproducens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium ulceribovis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Curvibacter|s__Curvibacter gracilis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Curvibacter|s__Curvibacter lanceolatus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium modestum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia|s__Dietzia kunjamensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia albertii,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Alismatales|f__Araceae|s__Gymnostachydoideae|g__Gymnostachys|s__Gymnostachys anceps,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella|s__Johnsonella ignava,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria|s__Kocuria rosea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Mannheimia|s__Mannheimia caviae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium|s__Microbacterium paludicola,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycolicibacterium|s__Mycolicibacterium chitae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Myroides|s__Myroides odoratus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia bryophila,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia kururiensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia phenoliruptrix,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus methioninivorax,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus olsenii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus tyrrelliae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus|s__Proteus hauseri,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Qipengyuania|s__Qipengyuania aquimaris,k__Pseudomonadati|p__Rhodothermota|c__Rhodothermia|o__Rhodothermales|f__Rhodothermaceae|g__Rhodothermus|s__Rhodothermus clarus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles|s__Roseateles saccharophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia meyeri,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia naturae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas flueggei,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hyicus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas pavanii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces danangensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Tolumonas|s__Tolumonas auensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia|s__Yersinia massiliensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia|s__Yersinia pestis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|s__[Actinobacillus] rossii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Listeria,k__Metazoa|p__Arthropoda|c__Insecta|o__Coleoptera|f__Lampyridae|s__Luciolinae|g__Serratia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Erythrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Rhodothermota|c__Rhodothermia|o__Rhodothermales|f__Rhodothermaceae|g__Rhodothermus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Trabulsiella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Azonexaceae|g__Dechloromonas,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminiphilaceae|g__Aminiphilus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Thalassospiraceae|g__Thalassospira,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Limnohabitans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Edwardsiella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Gemmatimonadota|c__Gemmatimonadia|o__Gemmatimonadales|f__Gemmatimonadaceae|g__Gemmatimonas,k__Pseudomonadati|p__Acidobacteriota|c__Holophagae|o__Holophagales|f__Holophagaceae|g__Geothrix,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Curvibacter",3384194|508458|649775|649776|3029090|290731|290732;3379134|1224|28211|204441|2829815|191|561521;3379134|976|200643|171549|815|816|266833;1783272|1239|186801|3085636|186803|572511|418240;3379134|1224|28216|80840|119060|32008|13373;3379134|1224|28216|80840|119060|32008|87883;3379134|1224|28216|80840|119060|32008|101571;3379134|1224|28216|80840|119060|32008|60552;3379134|29547|3031852|213849|72294|194|449520;1783272|201174|1760|85007|1653|1716|38285;1783272|201174|1760|85007|1653|1716|191610;1783272|201174|1760|85007|1653|1716|1121358;1783272|201174|1760|85007|1653|1716|441501;1783272|201174|1760|85007|1653|1716|598660;1783272|201174|1760|85007|1653|1716|487732;3379134|1224|28216|80840|80864|281915|230310;3379134|1224|28216|80840|80864|281915|86182;1783272|201174|1760|85009|31957|1912216|2559073;1783272|201174|1760|85007|85029|37914|322509;3379134|1224|1236|91347|543|561|208962;33090|35493|3398|16360|4454|284549|4466|4467;3379134|1224|1236|135625|712|724|729;1783272|1239|186801|3085636|186803|43994|43995;1783272|201174|1760|85006|1268|57493|1275;1783272|1239|186801|3085636|186803|28050|28052;3379134|1224|1236|135625|712|75984|879276;1783272|201174|1760|85006|85023|33882|300019;1783272|201174|1760|85007|1762|1866885|1792;3379134|976|117743|200644|49546|76831|256;3379134|976|200643|171549|2005525|375288|328812;3379134|1224|28216|80840|119060|1822464|420952;3379134|1224|28216|80840|119060|1822464|984307;3379134|1224|28216|80840|119060|1822464|252970;1783272|1239|1737404|1737405|1570339|162289|907224;1783272|1239|1737404|1737405|1570339|162289|411570;1783272|1239|1737404|1737405|1570339|162289|755171;3379134|1224|1236|91347|1903414|583|183417;3379134|1224|28211|204457|335929|1855416|255984;3379134|1853220|1853222|1853224|563843|29548|374811;3379134|1224|28216|80840|2975441|93681|304;1783272|201174|1760|2037|2049|2529408|52773;1783272|201174|1760|2037|2049|2529408|635203;1783272|1239|909932|909929|1843491|970|135080;1783272|1239|91061|1385|90964|1279|1284;3379134|1224|1236|135614|32033|40323|487698;1783272|201174|1760|85011|2062|1883|248040;3379134|1224|1236|135624|84642|43947|43948;3379134|1224|1236|91347|1903411|629|419257;3379134|1224|1236|91347|1903411|629|632;3379134|1224|1236|135625|712|123820;1783272|201174|1760|85007|85029|37914;3379134|1224|28216|80840|119060|32008;3379134|1224|28216|80840|2975441|93681;1783272|1239|91061|1385|186820|1637;33208|6656|50557|7041|7049|433515|2985502;1783272|1239|91061|1385|186817|1386;3379134|1224|28211|204457|335929|1041;3379134|1224|1236|91347|1903411|629;1783272|1239|186801|3082720|3118656|114627;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|28050;3379134|1853220|1853222|1853224|563843|29548;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|43994;3379134|1224|1236|91347|543|158851;3379134|1224|28216|206389|2008795|73029;3384194|508458|649775|649776|3029090|290731;3379134|1224|28211|204441|2844866|168934;3379134|1224|28216|80840|80864|665874;3379134|1224|1236|91347|1903412|635;1783272|1239|526524|526525|2810281|191303;3379134|142182|219685|219686|219687|173479;3379134|57723|533205|574975|574976|44675;3379134|1224|28216|80840|80864|281915,Complete,Svetlana up
bsdb:34880258/2/1,34880258,case-control,34880258,10.1038/s41531-021-00254-y,NA,"Pal G., Ramirez V., Engen P.A., Naqib A., Forsyth C.B., Green S.J., Mahdavinia M., Batra P.S., Tajudeen B.A. , Keshavarzian A.",Deep nasal sinus cavity microbiota dysbiosis in Parkinson's disease,NPJ Parkinson's disease,2021,NA,Experiment 2,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Parkinson's disease,MONDO:0005180,rHC (Random non-household healthy controls),PD (Parkinson's Disease),This group consists of 30 Parkinson's disease subjects.,17,30,3 months,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,"age,race,sex",NA,NA,unchanged,NA,unchanged,NA,decreased,Signature 1,Supplementary table 10 & 11.,20 August 2024,Victoria,"Victoria,WikiWorks",Nasal microbial differences between rHC and PD subjects. The differential abundance differences were measured using ANCOM within PD (n=30) subjects compared to rHC (n=17) subjects. At the genus and species taxonomic level.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter guillouiae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Desulfuromonadales|f__Geopsychrobacteraceae|g__Desulfuromusa",3379134|1224|1236|2887326|468|469;3379134|1224|1236|2887326|468|469|106649;3379134|200940|3031651|69541|3031659|37817,Complete,Svetlana up
bsdb:34880258/3/1,34880258,case-control,34880258,10.1038/s41531-021-00254-y,NA,"Pal G., Ramirez V., Engen P.A., Naqib A., Forsyth C.B., Green S.J., Mahdavinia M., Batra P.S., Tajudeen B.A. , Keshavarzian A.",Deep nasal sinus cavity microbiota dysbiosis in Parkinson's disease,NPJ Parkinson's disease,2021,NA,Experiment 3,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Parkinson's disease,MONDO:0005180,rHC (Random non-household healthy controls),SpHC (Spousal household healthy controls),This group consists of 11 spousal healthy controls of Parkinson's disease subjects.,17,11,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,race,sex",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Supplementary Figure 1 and Supplementary table 6 & 7.,20 August 2024,Victoria,"Victoria,WikiWorks",Nasal microbial differences between rHC and SpHC subjects. The differential abundance differences were measured using DESeq2 within SpHC (n=11) compared to rHC (n=17) subjects. At the genus and species taxonomic level.,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus hydrogenalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium|s__Brevibacterium paucivorans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium imitans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia|s__Delftia tsuruhatensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Dermabacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus yunnanensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas brenneri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas mandelii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces nanchangensis",1783272|1239|1737404|1737405|1570339|165779|33029;1783272|201174|1760|85006|85019|1696|170994;1783272|201174|1760|85007|1653|1716|156978;3379134|1224|28216|80840|80864|80865;3379134|1224|28216|80840|80864|80865|180282;1783272|201174|1760|85006|85020|36739;1783272|201174|1760|85006|1268|1269|566027;3379134|1224|1236|72274|135621|286|129817;3379134|1224|1236|72274|135621|286|75612;1783272|1239|91061|1385|90964|1279|1282;1783272|201174|1760|85011|2062|1883|204925,Complete,Svetlana up
bsdb:34880258/3/2,34880258,case-control,34880258,10.1038/s41531-021-00254-y,NA,"Pal G., Ramirez V., Engen P.A., Naqib A., Forsyth C.B., Green S.J., Mahdavinia M., Batra P.S., Tajudeen B.A. , Keshavarzian A.",Deep nasal sinus cavity microbiota dysbiosis in Parkinson's disease,NPJ Parkinson's disease,2021,NA,Experiment 3,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Parkinson's disease,MONDO:0005180,rHC (Random non-household healthy controls),SpHC (Spousal household healthy controls),This group consists of 11 spousal healthy controls of Parkinson's disease subjects.,17,11,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,race,sex",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Supplementary Figure 1 and Supplementary table 6 & 7.,20 August 2024,Victoria,"Victoria,WikiWorks",Nasal microbial differences between rHC and SpHC subjects. Differential abundance differences were measured using DESeq2 within SpHC (n=11) compared to rHC (n=17) subjects. At the genus and species taxonomic level.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas|s__Brevundimonas terrae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia ubonensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia vietnamiensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium acetoacidophilum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Curvibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Curvibacter|s__Curvibacter lanceolatus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Dyella|s__Dyella ginsengisoli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia albertii,k__Pseudomonadati|p__Acidobacteriota|c__Holophagae|o__Holophagales|f__Holophagaceae|g__Geothrix,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lentibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lentibacillus|s__Lentibacillus kapialis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Limnohabitans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium|s__Microbacterium paludicola,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Myroides,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Myroides|s__Myroides odoratus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia bryophila,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia kururiensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia phenoliruptrix,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia phytofirmans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia sabiae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia terrae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia tuberum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia xenovorans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus|s__Proteus hauseri,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Qipengyuania|s__Qipengyuania aquimaris,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia detusculanense,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia insidiosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus|s__Rhodococcus opacus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles|s__Roseateles saccharophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae|g__Salinispora,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Segetibacter|s__Segetibacter aerophilus,k__Metazoa|p__Arthropoda|c__Insecta|o__Coleoptera|f__Lampyridae|s__Luciolinae|g__Serratia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia entomophila,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces danangensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia|s__Yersinia massiliensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Trabulsiella|s__Trabulsiella odontotermitis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae|g__Salinispora|s__Salinispora tropica",1783272|1239|91061|1385|186817|1386;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|418240;3379134|1224|28211|204458|76892|41275|363631;3379134|1224|28216|80840|119060|32008;3379134|1224|28216|80840|119060|32008|101571;3379134|1224|28216|80840|119060|32008|60552;1783272|201174|1760|85007|1653|1716|38285;3379134|1224|28216|80840|80864|281915;3379134|1224|28216|80840|80864|281915|86182;3379134|1224|1236|135614|1775411|231454|363848;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|561|208962;3379134|57723|533205|574975|574976|44675;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|1385|186817|175304;1783272|1239|91061|1385|186817|175304|340214;3379134|1224|28216|80840|80864|665874;1783272|201174|1760|85006|85023|33882|300019;3379134|976|117743|200644|49546|76831;3379134|976|117743|200644|49546|76831|256;1783272|1239|186801|186802|216572|119852;3379134|1224|28216|80840|119060|1822464|420952;3379134|1224|28216|80840|119060|1822464|984307;3379134|1224|28216|80840|119060|1822464|252970;3379134|1224|28216|80840|119060|1822464|261302;3379134|1224|28216|80840|119060|1822464|273251;3379134|1224|28216|80840|119060|1822464|311230;3379134|1224|28216|80840|119060|1822464|157910;3379134|1224|28216|80840|119060|1822464|36873;3379134|1224|1236|91347|1903414|583|183417;3379134|1224|28211|204457|335929|1855416|255984;3379134|1224|28216|80840|119060|48736;3379134|1224|28216|80840|119060|48736|148618;3379134|1224|28216|80840|119060|48736|190721;1783272|201174|1760|85007|85025|1827|37919;3379134|1224|28216|80840|2975441|93681;3379134|1224|28216|80840|2975441|93681|304;1783272|201174|1760|85008|28056|168694;3379134|976|1853228|1853229|563835|460073|670293;33208|6656|50557|7041|7049|433515|2985502;3379134|1224|1236|91347|1903411|613|42906;1783272|201174|1760|85011|2062|1883|248040;3379134|1224|1236|91347|1903411|629|419257;3379134|1224|1236|91347|543|158851|379893;1783272|201174|1760|85008|28056|168694|168695,Complete,Svetlana up
bsdb:34880258/4/1,34880258,case-control,34880258,10.1038/s41531-021-00254-y,NA,"Pal G., Ramirez V., Engen P.A., Naqib A., Forsyth C.B., Green S.J., Mahdavinia M., Batra P.S., Tajudeen B.A. , Keshavarzian A.",Deep nasal sinus cavity microbiota dysbiosis in Parkinson's disease,NPJ Parkinson's disease,2021,NA,Experiment 4,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Parkinson's disease,MONDO:0005180,rHC (Random non-household healthy controls),SpHC (Spousal household healthy controls),This group consists of 11 spousal healthy controls of Parkinson's disease subjects.,17,11,3 months,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,"age,race,sex",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Supplementary table 6 & 7.,21 August 2024,Victoria,"Victoria,WikiWorks",Nasal microbial differences between rHC and SpHC subjects. Differential abundance differences were measured using ANCOM within SpHC (n=11) compared to rHC (n=17) subjects. At the genus and species taxonomic level.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter guillouiae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter",3379134|1224|1236|2887326|468|469|106649;3379134|1224|1236|2887326|468|469,Complete,Svetlana up
bsdb:34880258/4/2,34880258,case-control,34880258,10.1038/s41531-021-00254-y,NA,"Pal G., Ramirez V., Engen P.A., Naqib A., Forsyth C.B., Green S.J., Mahdavinia M., Batra P.S., Tajudeen B.A. , Keshavarzian A.",Deep nasal sinus cavity microbiota dysbiosis in Parkinson's disease,NPJ Parkinson's disease,2021,NA,Experiment 4,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Parkinson's disease,MONDO:0005180,rHC (Random non-household healthy controls),SpHC (Spousal household healthy controls),This group consists of 11 spousal healthy controls of Parkinson's disease subjects.,17,11,3 months,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,"age,race,sex",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Supplementary table 6 & 7.,21 August 2024,Victoria,"Victoria,WikiWorks",Nasal microbial differences between rHC and SpHC subjects. Differential abundance differences were measured using ANCOM within SpHC (n=11) compared to rHC (n=17) subjects. At the genus and species taxonomic level.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia xenovorans,3379134|1224|28216|80840|119060|1822464|36873,Complete,Svetlana up
bsdb:34880258/5/1,34880258,case-control,34880258,10.1038/s41531-021-00254-y,NA,"Pal G., Ramirez V., Engen P.A., Naqib A., Forsyth C.B., Green S.J., Mahdavinia M., Batra P.S., Tajudeen B.A. , Keshavarzian A.",Deep nasal sinus cavity microbiota dysbiosis in Parkinson's disease,NPJ Parkinson's disease,2021,NA,Experiment 5,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Parkinson's disease,MONDO:0005180,SpHC (Spousal household Healthy Control),SpPD (Spousal household Parkinson's Disease),This group consists of Parkinson's Disease subjects living in the same household as their healthy control spouses.,11,11,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,race,sex",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Supplementary table 13 and Fig. 2b,21 August 2024,Victoria,"Victoria,WikiWorks",Significant differential abundance analysis values of the microbial profiles between spousal household (SpHC) healthy control subjects and their corresponding household PD (SpPD) subjects. At the genus and species taxonomic level.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Chromobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium bovis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella catarrhalis",3379134|1224|28216|206351|1499392|535;3379134|1224|1236|2887326|468|475;1783272|201174|1760|85007|1653|1716|36808;3379134|1224|1236|2887326|468|475|480,Complete,Svetlana up
bsdb:34880258/5/2,34880258,case-control,34880258,10.1038/s41531-021-00254-y,NA,"Pal G., Ramirez V., Engen P.A., Naqib A., Forsyth C.B., Green S.J., Mahdavinia M., Batra P.S., Tajudeen B.A. , Keshavarzian A.",Deep nasal sinus cavity microbiota dysbiosis in Parkinson's disease,NPJ Parkinson's disease,2021,NA,Experiment 5,United States of America,Homo sapiens,Nasal cavity,UBERON:0001707,Parkinson's disease,MONDO:0005180,SpHC (Spousal household Healthy Control),SpPD (Spousal household Parkinson's Disease),This group consists of Parkinson's Disease subjects living in the same household as their healthy control spouses.,11,11,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,race,sex",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Supplementary table 13 and Fig. 2b,21 August 2024,Victoria,"Victoria,WikiWorks",Significant differential abundance analysis values of the microbial profiles between spousal household (SpHC) healthy control subjects and their corresponding household PD (SpPD) subjects. At the genus and species taxonomic level.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Nitrospirota|c__Thermodesulfovibrionia|o__Thermodesulfovibrionales|f__Thermodesulfovibrionaceae|g__Thermodesulfovibrio,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus prevotii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus chromogenes,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus cohnii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus fryi,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia|s__Yersinia frederiksenii",1783272|201174|1760|85006|145357|57495;1783272|1239|91061|1385|90964|1279;3379134|40117|2811502|2811503|2811504|28261;1783272|1239|1737404|1737405|1570339|165779|33034;1783272|1239|91061|1385|90964|1279|1280;1783272|1239|91061|1385|90964|1279|46126;1783272|1239|91061|1385|90964|1279|29382;1783272|1239|91061|1385|90964|1279|1282;1783272|1239|91061|186826|1300|1301|661498;1783272|1239|91061|186826|1300|1301|68892;3379134|1224|1236|91347|1903411|629|29484,Complete,Svetlana up
bsdb:34884399/1/1,34884399,case-control,34884399,https://doi.org/10.3390/jcm10235698,NA,"Zapała B., Stefura T., Wójcik-Pędziwiatr M., Kabut R., Bałajewicz-Nowak M., Milewicz T., Dudek A., Stój A. , Rudzińska-Bar M.",Differences in the Composition of Gut Microbiota between Patients with Parkinson's Disease and Healthy Controls: A Cohort Study,Journal of clinical medicine,2021,"Parkinson’s disease, gut microbiome, microbiota",Experiment 1,Poland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease Patients,Hospitalized Patients diagnosed with Parkinson's disease with well-controlled symptoms.,44,27,3 weeks,16S,34,"Illumina,MGISEQ-2000",relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,increased,increased,increased,NA,increased,Signature 1,"Figure 6 , Figure 7",7 March 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,Peace Sandy,WikiWorks","Bacterial species are more abundant in the PD than in the control group, according to the LefSE analysis.

Cladogram generated by LEfSe shows the taxa differences between PD patients (2) and healthy controls (1).",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Acidaminobacteraceae|g__Acidaminobacter|s__Acidaminobacter hydrogenoformans,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella timonensis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,c__Deltaproteobacteria,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium thermosuccinogenes,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella|s__Robinsoniella peoriensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Thermotogati|p__Synergistota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] viride,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",1783272|1239|186801|3082720|3118653|65402|65403;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|815|816|47678;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|3082768|990719|990721|1816678;1783272|201174|84998;28221;1783272|1239|526524;3379134|976|117743;1783272|1239|186801|186802|216572|946234|292800;3379134|1224|1236;1783272|1239|526524|526525|128827|1573535|1735;1783272|1239|186801|3085636|186803|1649459|154046;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|815|909656|204516;1783272|1239|186801|186802|31979|1485|84032;3379134|1224;1783272|1239|186801|3085636|186803|588605|180332;1783272|1239|186801|186802|216572|1263|438033;1783272|1239|91061|186826|1300|1301|1309;3384194|508458;3379134|74201|203494;3379134|74201;1783272|1239|186801|186802|216572|47246;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Peace Sandy
bsdb:34884399/1/2,34884399,case-control,34884399,https://doi.org/10.3390/jcm10235698,NA,"Zapała B., Stefura T., Wójcik-Pędziwiatr M., Kabut R., Bałajewicz-Nowak M., Milewicz T., Dudek A., Stój A. , Rudzińska-Bar M.",Differences in the Composition of Gut Microbiota between Patients with Parkinson's Disease and Healthy Controls: A Cohort Study,Journal of clinical medicine,2021,"Parkinson’s disease, gut microbiome, microbiota",Experiment 1,Poland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease Patients,Hospitalized Patients diagnosed with Parkinson's disease with well-controlled symptoms.,44,27,3 weeks,16S,34,"Illumina,MGISEQ-2000",relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,increased,increased,increased,NA,increased,Signature 2,"Figure 6 , Figure 7",8 March 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,Peace Sandy,WikiWorks","Bacterial species are more abundant in the PD than in the control group, according to the LefSE analysis.

Cladogram generated by LEfSe shows the taxa differences between PD patients (2) and
healthy controls (1).",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes butyraticus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Intestinibacillus|s__Intestinibacillus massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus albus,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia",1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|207244|645466;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|3085636|186803|572511|871665;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|186801|186802|186806|1730|39490;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|3085642|1928820|1871029;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|909932|909929|1843491|158846|437897;1783272|1239|186801|186802|216572|1263|1264;1783272|1239|186801;1783272|1239;3384189|32066|203490,Complete,Peace Sandy
bsdb:34897759/1/1,34897759,case-control,34897759,10.1111/lam.13630,https://academic.oup.com/lambio/article-abstract/74/4/498/6989204?redirectedFrom=fulltext&login=false,"Schade L., Mesa D., Faria A.R., Santamaria J.R., Xavier C.A., Ribeiro D., Hajar F.N. , Azevedo V.F.",The gut microbiota profile in psoriasis: a Brazilian case-control study,Letters in applied microbiology,2022,"Akkermansia muciniphila, dysbiosis, gut microbiome, inflammatory bowel disease, psoriasis, psoriatic arthritis, skin disease",Experiment 1,Brazil,Homo sapiens,Feces,UBERON:0001988,Psoriasis,EFO:0000676,Healthy controls,Psoriasis patients,Psoriasis has been diagnosed by a dermatologist,24,21,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,body mass index,comorbidity,sex,smoking status",NA,NA,NA,NA,NA,NA,decreased,Signature 1,"Figure 2, within results text (Taxonomic composition, paragraph 4, lines 7-12)",28 November 2023,Andre,"Andre,Folakunmi,WikiWorks",Taxa that showed a significant difference between the groups,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula",1783272|1239|526524|526525|2810280|135858;1783272|1239|909932|1843489|31977|39948;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|909932|1843489|31977|29465|29466,Complete,Folakunmi
bsdb:34897759/1/2,34897759,case-control,34897759,10.1111/lam.13630,https://academic.oup.com/lambio/article-abstract/74/4/498/6989204?redirectedFrom=fulltext&login=false,"Schade L., Mesa D., Faria A.R., Santamaria J.R., Xavier C.A., Ribeiro D., Hajar F.N. , Azevedo V.F.",The gut microbiota profile in psoriasis: a Brazilian case-control study,Letters in applied microbiology,2022,"Akkermansia muciniphila, dysbiosis, gut microbiome, inflammatory bowel disease, psoriasis, psoriatic arthritis, skin disease",Experiment 1,Brazil,Homo sapiens,Feces,UBERON:0001988,Psoriasis,EFO:0000676,Healthy controls,Psoriasis patients,Psoriasis has been diagnosed by a dermatologist,24,21,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,body mass index,comorbidity,sex,smoking status",NA,NA,NA,NA,NA,NA,decreased,Signature 2,"Figure 2,  within results text (Taxonomic composition, paragraph 4, lines 7-12)",28 November 2023,Andre,"Andre,Folakunmi,WikiWorks",Taxa that showed a significant difference between the groups,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|186802|186806|264995;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|186802|216572|1263,Complete,Folakunmi
bsdb:34900990/1/2,34900990,case-control,34900990,10.3389/fcell.2021.731867,NA,"Liang Q., Li J., Zou Y., Hu X., Deng X., Zou B., Liu Y., Wei L., Liang L. , Wen X.",Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease,Frontiers in cell and developmental biology,2021,"aqueous tear deficiency, conjunctival microbiota, dry eye disease, meibomian gland dysfunction, metagenomic shotgun sequencing",Experiment 1,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Biological sex,PATO:0000047,female patients with dry eye disease,male patients with dry eye disease,male patients with dry eye disease,22,25,3 months,WMS,NA,Illumina,relative abundances,Linear Regression,0.05,NA,NA,NA,age,NA,decreased,NA,NA,NA,NA,Signature 2,Supp fig 2c and 2d,14 October 2023,Mary Bearkland,"Mary Bearkland,ChiomaBlessing,WikiWorks",Sex-related differences of the conjunctival microbiota in patients with dry eye.,decreased,"k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus sp. NW-56,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa",3384194|1297|188787|118964|183710|1298|2080419;3379134|1224|1236|72274|135621|286|287,Complete,ChiomaBlessing
bsdb:34900990/2/1,34900990,case-control,34900990,10.3389/fcell.2021.731867,NA,"Liang Q., Li J., Zou Y., Hu X., Deng X., Zou B., Liu Y., Wei L., Liang L. , Wen X.",Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease,Frontiers in cell and developmental biology,2021,"aqueous tear deficiency, conjunctival microbiota, dry eye disease, meibomian gland dysfunction, metagenomic shotgun sequencing",Experiment 2,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Biological sex,PATO:0000047,Healthy female,Healthy male,Healthy male without dry eye disease,22,25,3 months,WMS,NA,Illumina,relative abundances,Linear Regression,0.05,NA,NA,NA,age,NA,increased,NA,NA,NA,NA,Signature 1,"Supp fig 2c and 2d, Figure 3D",14 October 2023,Mary Bearkland,"Mary Bearkland,ChiomaBlessing,WikiWorks",Sex-related differences of the conjunctival microbiota in healthy individuals.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia globosa",3379134|1224|1236|72274|135621|286|287;4751|5204|1538075|162474|742845|55193|76773,Complete,ChiomaBlessing
bsdb:34900990/3/1,34900990,case-control,34900990,10.3389/fcell.2021.731867,NA,"Liang Q., Li J., Zou Y., Hu X., Deng X., Zou B., Liu Y., Wei L., Liang L. , Wen X.",Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease,Frontiers in cell and developmental biology,2021,"aqueous tear deficiency, conjunctival microbiota, dry eye disease, meibomian gland dysfunction, metagenomic shotgun sequencing",Experiment 3,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Dry eye syndrome,EFO:1000906,Aqueous tear deficient (ATD) DED,Meibomian Gland Dysfunction (MGD) DED,Patients with MGD DED,14,19,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.15,NA,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Supp. fig 5,14 October 2023,Mary Bearkland,"Mary Bearkland,ChiomaBlessing,WikiWorks",Differentially abundant Staphylococcus species between patients with aqueous tear deficiency (ATD) and meibomian gland dysfunction (MGD),increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus capitis",1783272|1239|91061|1385|90964|1279|1280;1783272|1239|91061|1385|90964|1279|29388,Complete,ChiomaBlessing
bsdb:34900990/3/2,34900990,case-control,34900990,10.3389/fcell.2021.731867,NA,"Liang Q., Li J., Zou Y., Hu X., Deng X., Zou B., Liu Y., Wei L., Liang L. , Wen X.",Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease,Frontiers in cell and developmental biology,2021,"aqueous tear deficiency, conjunctival microbiota, dry eye disease, meibomian gland dysfunction, metagenomic shotgun sequencing",Experiment 3,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Dry eye syndrome,EFO:1000906,Aqueous tear deficient (ATD) DED,Meibomian Gland Dysfunction (MGD) DED,Patients with MGD DED,14,19,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.15,NA,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,Supp. fig 5,14 October 2023,Mary Bearkland,"Mary Bearkland,ChiomaBlessing,WikiWorks",Differentially abundant Staphylococcus species between patients with aqueous tear deficiency (ATD) and meibomian gland dysfunction (MGD),decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,1783272|1239|91061|1385|90964|1279|1290,Complete,ChiomaBlessing
bsdb:34900990/4/1,34900990,case-control,34900990,10.3389/fcell.2021.731867,NA,"Liang Q., Li J., Zou Y., Hu X., Deng X., Zou B., Liu Y., Wei L., Liang L. , Wen X.",Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease,Frontiers in cell and developmental biology,2021,"aqueous tear deficiency, conjunctival microbiota, dry eye disease, meibomian gland dysfunction, metagenomic shotgun sequencing",Experiment 4,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Dry eye syndrome,EFO:1000906,Aqueous tear deficient (ATD) DED,Mixed DED,Patients with mixed type diagnosis of DED (more closely related to MGD than ATD),14,35,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.15,NA,NA,NA,"age,sex",NA,increased,NA,NA,NA,NA,Signature 1,Supp fig 5,15 October 2023,Mary Bearkland,"Mary Bearkland,ChiomaBlessing,WikiWorks",Differentially abundant Staphylococcus species between patients with aqueous tear deficiency (ATD) and mixed dry eye,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus capitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus cohnii",1783272|1239|91061|1385|90964|1279|1280;1783272|1239|91061|1385|90964|1279|29388;1783272|1239|91061|1385|90964|1279|29382,Complete,ChiomaBlessing
bsdb:34900990/6/1,34900990,case-control,34900990,10.3389/fcell.2021.731867,NA,"Liang Q., Li J., Zou Y., Hu X., Deng X., Zou B., Liu Y., Wei L., Liang L. , Wen X.",Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease,Frontiers in cell and developmental biology,2021,"aqueous tear deficiency, conjunctival microbiota, dry eye disease, meibomian gland dysfunction, metagenomic shotgun sequencing",Experiment 6,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Dry eye syndrome,EFO:1000906,healthy controls,Dry Eye,Patients with Dry eye disease,48,47,3 months,WMS,NA,Illumina,relative abundances,MaAsLin2,0.05,NA,NA,NA,"age,sex",NA,decreased,NA,NA,NA,NA,Signature 1,Supp table 4,3 December 2023,Mary Bearkland,"Mary Bearkland,ChiomaBlessing,WikiWorks",Comparison between dry eye group and healthy group showing species with polarized abundance (decreased abundance) in dry eye samples,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter radioresistens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter sp. WCHA45,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium sp.,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium taklimakanense,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus ficus,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus sp. NW-56,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Janibacter|s__Janibacter melonis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia globosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Micropruina|s__Micropruina glycogenica,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus|s__Paracoccus yeei,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 431,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium",3379134|1224|1236|2887326|468|469|40216;3379134|1224|1236|2887326|468|469|2004644;3379134|1224|1236|135625|712|416916|739;3379134|976|117743|200644|2762318|59732|1871047;3379134|976|117743|200644|2762318|59732|536441;1783272|201174|1760|85007|1653|1716|43768;3384194|1297|188787|118964|183710|1298|317577;3384194|1297|188787|118964|183710|1298|2080419;3384189|32066|203490|203491|203492|848|851;1783272|201174|1760|85006|85021|53457|262209;1783272|1239|91061|186826|33958|1578|147802;4751|5204|1538075|162474|742845|55193|76773;1783272|201174|1760|85009|85015|116071|75385;3379134|1224|28216|206351|481|482|28449;3379134|1224|28211|204455|31989|265|147645;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|1385|90964|1279|1280;1783272|1239|91061|1385|90964|1279|1290;1783272|1239|91061|186826|1300|1301|1305;1783272|1239|91061|186826|1300|1301|712633;1783272|1239|909932|1843489|31977|29465|29466;1783272|201174|1760|85007|1653|1716,Complete,ChiomaBlessing
bsdb:34900990/7/1,34900990,case-control,34900990,10.3389/fcell.2021.731867,NA,"Liang Q., Li J., Zou Y., Hu X., Deng X., Zou B., Liu Y., Wei L., Liang L. , Wen X.",Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease,Frontiers in cell and developmental biology,2021,"aqueous tear deficiency, conjunctival microbiota, dry eye disease, meibomian gland dysfunction, metagenomic shotgun sequencing",Experiment 7,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Dry eye syndrome,EFO:1000906,Dry Eye -nonATD,Dry Eye- ATD,Patients with Dry eye disease characterized as aqueous tear deficient,54,14,3 months,WMS,NA,Illumina,relative abundances,MaAsLin2,0.1,NA,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4b,29 December 2023,Mary Bearkland,"Mary Bearkland,WikiWorks","B) Model coefficients of top-ranked species associated with either ATD or non-ATD dry eye (p < 0.1, coefficient >0.2)",increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Janibacter|s__Janibacter melonis,1783272|201174|1760|85006|85021|53457|262209,Complete,Folakunmi
bsdb:34900990/7/2,34900990,case-control,34900990,10.3389/fcell.2021.731867,NA,"Liang Q., Li J., Zou Y., Hu X., Deng X., Zou B., Liu Y., Wei L., Liang L. , Wen X.",Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease,Frontiers in cell and developmental biology,2021,"aqueous tear deficiency, conjunctival microbiota, dry eye disease, meibomian gland dysfunction, metagenomic shotgun sequencing",Experiment 7,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Dry eye syndrome,EFO:1000906,Dry Eye -nonATD,Dry Eye- ATD,Patients with Dry eye disease characterized as aqueous tear deficient,54,14,3 months,WMS,NA,Illumina,relative abundances,MaAsLin2,0.1,NA,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 4b,29 December 2023,Mary Bearkland,"Mary Bearkland,WikiWorks","Figure 4b) Model coefficients of top-ranked species associated with either ATD or non-ATD dry eye (p < 0.1, coefficient >0.2) (",decreased,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,3379134|976|117743|200644|49546|1016|1017,Complete,Folakunmi
bsdb:34900990/8/1,34900990,case-control,34900990,10.3389/fcell.2021.731867,NA,"Liang Q., Li J., Zou Y., Hu X., Deng X., Zou B., Liu Y., Wei L., Liang L. , Wen X.",Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease,Frontiers in cell and developmental biology,2021,"aqueous tear deficiency, conjunctival microbiota, dry eye disease, meibomian gland dysfunction, metagenomic shotgun sequencing",Experiment 8,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Dry eye syndrome,EFO:1000906,Dry Eye -nonMGD,Dry Eye- MGD,Patients with Dry eye disease characterized as meibomian gland disorder,49,19,3 months,WMS,NA,Illumina,relative abundances,MaAsLin2,0.1,NA,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4c,29 December 2023,Mary Bearkland,"Mary Bearkland,WikiWorks","Model coefficients of
top-ranked species associated with either MGD or non-MGD dry eye (p < 0.1, coefficient >0.2)",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter sp. WCHA45,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus sp. NW-56,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus capitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus cohnii",3379134|1224|1236|2887326|468|469|2004644;3384194|1297|188787|118964|183710|1298|2080419;1783272|1239|91061|1385|90964|1279|1280;1783272|1239|91061|1385|90964|1279|29388;1783272|1239|91061|1385|90964|1279|29382,Complete,Folakunmi
bsdb:34900990/8/2,34900990,case-control,34900990,10.3389/fcell.2021.731867,NA,"Liang Q., Li J., Zou Y., Hu X., Deng X., Zou B., Liu Y., Wei L., Liang L. , Wen X.",Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease,Frontiers in cell and developmental biology,2021,"aqueous tear deficiency, conjunctival microbiota, dry eye disease, meibomian gland dysfunction, metagenomic shotgun sequencing",Experiment 8,China,Homo sapiens,Bulbar conjunctiva,UBERON:0010306,Dry eye syndrome,EFO:1000906,Dry Eye -nonMGD,Dry Eye- MGD,Patients with Dry eye disease characterized as meibomian gland disorder,49,19,3 months,WMS,NA,Illumina,relative abundances,MaAsLin2,0.1,NA,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 4c,29 December 2023,Mary Bearkland,"Mary Bearkland,WikiWorks","Model coefficients of
top-ranked species associated with either MGD or non-MGD dry eye (p < 0.1, coefficient >0.2)",decreased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,1783272|201174|84998|84999|84107|102106|74426,Complete,Folakunmi
bsdb:34908436/1/1,34908436,case-control,34908436,10.1128/spectrum.00615-21,NA,"Cao D., Liu W., Lyu N., Li B., Song W., Yang Y., Zhu J., Zhang Z. , Zhu B.",Gut Mycobiota Dysbiosis in Pulmonary Tuberculosis Patients Undergoing Anti-Tuberculosis Treatment,Microbiology spectrum,2021,"anti-tuberculosis treatment, gut mycobiota, pulmonary tuberculosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,Healthy controls,Untreated PTB patients,Active PTB confirmed by sputum culture or GeneXpert prior to any treatment,31,27,NA,ITS / ITS2,NA,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),LEfSe",0.05,TRUE,2,"age,sex",NA,decreased,decreased,decreased,decreased,NA,NA,Signature 1,Figure 3A and 3B,17 June 2025,Nuerteye,Nuerteye,"LEfSe plots, Characteristics of the bacterial and fungal taxa in the four study groups.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Ophiocordycipitaceae|g__Purpureocillium,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Rhodotorula,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Rhodotorula|s__Rhodotorula mucilaginosa,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Nakaseomyces|s__Nakaseomyces glabratus",1783272|1239|186801|3085636|186803|207244;3379134|1224|1236|91347|543|570;4751|4890|147550|5125|474942|1052105;4751|5204|162481|231213|1799696|5533;4751|5204|162481|231213|1799696|5533|5537;4751|4890|4891|4892|4893|374468|5478,Complete,NA
bsdb:34908436/1/2,34908436,case-control,34908436,10.1128/spectrum.00615-21,NA,"Cao D., Liu W., Lyu N., Li B., Song W., Yang Y., Zhu J., Zhang Z. , Zhu B.",Gut Mycobiota Dysbiosis in Pulmonary Tuberculosis Patients Undergoing Anti-Tuberculosis Treatment,Microbiology spectrum,2021,"anti-tuberculosis treatment, gut mycobiota, pulmonary tuberculosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,Healthy controls,Untreated PTB patients,Active PTB confirmed by sputum culture or GeneXpert prior to any treatment,31,27,NA,ITS / ITS2,NA,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),LEfSe",0.05,TRUE,2,"age,sex",NA,decreased,decreased,decreased,decreased,NA,NA,Signature 2,Figure 3A and 3B,17 June 2025,Nuerteye,Nuerteye,"LEfSe plots, Characteristics of the bacterial and fungal taxa in the four study groups.",decreased,"k__Fungi|p__Basidiomycota,k__Fungi|p__Ascomycota",4751|5204;4751|4890,Complete,NA
bsdb:34917142/1/1,34917142,prospective cohort,34917142,10.1155/2021/1469339,NA,"Dang Y., Zhang X., Zheng Y., Yu B., Pan D., Jiang X., Yan C., Yu Q. , Lu X.",Distinctive Gut Microbiota Alteration Is Associated with Poststroke Functional Recovery: Results from a Prospective Cohort Study,Neural plasticity,2021,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,healthy controls,stroke patients,"A number of 38 subjects with clinical diagnosis of poststroke patients (aged 59.18 ± 15.34; male/female 25/13) were recruited, including 18 subacute and 20 chronic patients.",35,38,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,"age,sex",NA,NA,increased,NA,NA,NA,increased,Signature 1,Figure 3b,22 October 2024,Tino,"Tino,Rahila,WikiWorks",Identification of microbiota-based biomarkers for stroke.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus massiliensis,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium necrogenes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",1783272|1239|909932|1843488|909930|904|1852375;1783272|1239|91061;3379134|976|200643|171549|815|816|46506;1783272|201174|1760|85004|31953|1678|1680;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|561;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492|848|858;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|909929|1843491|158846|437897;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|91061|186826|33958,Complete,Peace Sandy
bsdb:34917142/1/2,34917142,prospective cohort,34917142,10.1155/2021/1469339,NA,"Dang Y., Zhang X., Zheng Y., Yu B., Pan D., Jiang X., Yan C., Yu Q. , Lu X.",Distinctive Gut Microbiota Alteration Is Associated with Poststroke Functional Recovery: Results from a Prospective Cohort Study,Neural plasticity,2021,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,healthy controls,stroke patients,"A number of 38 subjects with clinical diagnosis of poststroke patients (aged 59.18 ± 15.34; male/female 25/13) were recruited, including 18 subacute and 20 chronic patients.",35,38,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,"age,sex",NA,NA,increased,NA,NA,NA,increased,Signature 2,Figure 3b,22 October 2024,Tino,"Tino,Rahila,WikiWorks",identification of microbiota-based biomarkers for stroke.,decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia luti,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia massiliensis (ex Durand et al. 2017),k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria meningitidis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia cecicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239;3379134|1224|28216;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|89014;1783272|1239|186801|3085636|186803|572511|1737424;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801;1783272|1239|186801|186802|1898207;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|84998|84999|84107;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|186802|204475|745368;1783272|1239|186801|3085636|186803;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481|482|487;3379134|1224|28216|206351|481;3379134|1224|28216|206351;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|815|909656|310298;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|842;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|40518;3379134|976|200643|171549|171552|2974251|165179;3379134|976|200643|171549|171552|2974251|28135;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|216572,Complete,Peace Sandy
bsdb:34917142/2/1,34917142,prospective cohort,34917142,10.1155/2021/1469339,NA,"Dang Y., Zhang X., Zheng Y., Yu B., Pan D., Jiang X., Yan C., Yu Q. , Lu X.",Distinctive Gut Microbiota Alteration Is Associated with Poststroke Functional Recovery: Results from a Prospective Cohort Study,Neural plasticity,2021,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,subacute,chronic patients,The chronic stroke is defined as duration of stroke for more than 30 days.,18,20,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4f,23 October 2024,Tino,"Tino,WikiWorks",Subgroup analysis of gut microbiota in stroke.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum|s__Bifidobacterium catenulatum subsp. kashiwanohense,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio proteoclasticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus garvieae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus|s__Proteus mirabilis",3379134|976|200643|171549|2005519|397864|487174;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|2005519;3379134|976|200643|171549|815|816|291644;1783272|201174|1760|85004|31953|1678|1686|630129;1783272|1239|186801|3085636|186803|830|43305;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|1300|1357|1363;3379134|1224|1236|91347|1903414|583;3379134|1224|1236|91347|1903414|583|584,Complete,Peace Sandy
bsdb:34917142/2/2,34917142,prospective cohort,34917142,10.1155/2021/1469339,NA,"Dang Y., Zhang X., Zheng Y., Yu B., Pan D., Jiang X., Yan C., Yu Q. , Lu X.",Distinctive Gut Microbiota Alteration Is Associated with Poststroke Functional Recovery: Results from a Prospective Cohort Study,Neural plasticity,2021,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,subacute,chronic patients,The chronic stroke is defined as duration of stroke for more than 30 days.,18,20,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4f,23 October 2024,Tino,"Tino,WikiWorks",Subgroup analysis of gut microbiota in stroke.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides johnsonii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus|s__Peptococcus niger,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus troglodytidis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|201174|1760|2037|2049|1654|544580;3379134|976|200643|171549|815|816|818;1783272|1239|186801|186802|31979|1485|1502;1783272|1239|186801|186802|404402;1783272|1239|186801|186802|404402|404403;1783272|1239|91061|186826|33958|2742598|97478;1783272|1239|909932|1843489|31977|906;3379134|976|200643|171549|2005525|375288|387661;3379134|976|200643|171549|171552|577309|454154;3379134|976|200643|171549|171552|577309;1783272|1239|186801|186802|186807|2740|2741;1783272|1239|91061|186826|1300|1301|1071886;1783272|1239|909932|1843489|31977,Complete,Peace Sandy
bsdb:34923209/1/NA,34923209,case-control,34923209,10.1016/j.euroneuro.2021.11.009,NA,"Malan-Muller S., Valles-Colomer M., Foxx C.L., Vieira-Silva S., van den Heuvel L.L., Raes J., Seedat S., Lowry C.A. , Hemmings S.M.J.",Exploring the relationship between the gut microbiome and mental health outcomes in a posttraumatic stress disorder cohort relative to trauma-exposed controls,European neuropsychopharmacology : the journal of the European College of Neuropsychopharmacology,2022,"Depression, Gut microbiome, Microbiome-gut-brain axis, Oral microbiome, Posttraumatic stress disorder, Psychotropics",Experiment 1,South Africa,Homo sapiens,Feces,UBERON:0001988,Post-traumatic stress disorder,EFO:0001358,Trauma exposed controls (TECs),Post Traumatic Stress Disorder (PTSD),"Individuals with Post Traumatic Stress Disorder (PTSD). 
Post traumatic stress disorder (PTSD) cases met the DSM-5 criteria of PTSD, in accordance with diagnostic evaluation using the Clinician Administered Post Traumatic Stress Disorder Scale for DSM–5 (CAPS-5) and had a CAPS 5 severity score greater than 23.",58,79,1 month,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34923209/2/1,34923209,case-control,34923209,10.1016/j.euroneuro.2021.11.009,NA,"Malan-Muller S., Valles-Colomer M., Foxx C.L., Vieira-Silva S., van den Heuvel L.L., Raes J., Seedat S., Lowry C.A. , Hemmings S.M.J.",Exploring the relationship between the gut microbiome and mental health outcomes in a posttraumatic stress disorder cohort relative to trauma-exposed controls,European neuropsychopharmacology : the journal of the European College of Neuropsychopharmacology,2022,"Depression, Gut microbiome, Microbiome-gut-brain axis, Oral microbiome, Posttraumatic stress disorder, Psychotropics",Experiment 2,South Africa,Homo sapiens,Feces,UBERON:0001988,Clinical treatment,EFO:0007056,Individuals not using psychotropic medication,Individuals using psychotropic medication,Individuals using psychotropic medication that may associate with the gut microbiome of the sample.,6,21,1 month,16S,4,Illumina,relative abundances,Linear Regression,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4A, C and D",7 March 2024,Keamy,"Keamy,ChiomaBlessing,WikiWorks",Relative abundance (clr-transformed and filtered) of specific taxa at the genus and phylum level in individuals who were using psychotropic medication at the time of sample collection compared to individuals not using psychotropic medication,increased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239;3379134|976;1783272|1239|186801|186802|216572|1263,Complete,ChiomaBlessing
bsdb:34923209/2/2,34923209,case-control,34923209,10.1016/j.euroneuro.2021.11.009,NA,"Malan-Muller S., Valles-Colomer M., Foxx C.L., Vieira-Silva S., van den Heuvel L.L., Raes J., Seedat S., Lowry C.A. , Hemmings S.M.J.",Exploring the relationship between the gut microbiome and mental health outcomes in a posttraumatic stress disorder cohort relative to trauma-exposed controls,European neuropsychopharmacology : the journal of the European College of Neuropsychopharmacology,2022,"Depression, Gut microbiome, Microbiome-gut-brain axis, Oral microbiome, Posttraumatic stress disorder, Psychotropics",Experiment 2,South Africa,Homo sapiens,Feces,UBERON:0001988,Clinical treatment,EFO:0007056,Individuals not using psychotropic medication,Individuals using psychotropic medication,Individuals using psychotropic medication that may associate with the gut microbiome of the sample.,6,21,1 month,16S,4,Illumina,relative abundances,Linear Regression,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 4B and 4E,7 March 2024,Keamy,"Keamy,ChiomaBlessing,WikiWorks",Relative abundance (clr-transformed and filtered) of specific taxa at the genus and phylum level in individuals who were using psychotropic medication at the time of sample collection compared to individuals not using psychotropic medication,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota",3379134|74201|203494|48461|1647988|239934;3379134|74201,Complete,ChiomaBlessing
bsdb:34923209/3/1,34923209,case-control,34923209,10.1016/j.euroneuro.2021.11.009,NA,"Malan-Muller S., Valles-Colomer M., Foxx C.L., Vieira-Silva S., van den Heuvel L.L., Raes J., Seedat S., Lowry C.A. , Hemmings S.M.J.",Exploring the relationship between the gut microbiome and mental health outcomes in a posttraumatic stress disorder cohort relative to trauma-exposed controls,European neuropsychopharmacology : the journal of the European College of Neuropsychopharmacology,2022,"Depression, Gut microbiome, Microbiome-gut-brain axis, Oral microbiome, Posttraumatic stress disorder, Psychotropics",Experiment 3,South Africa,Homo sapiens,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Individuals without MDD diagnoses,Individuals with MDD diagnoses,Individuals diagnosed with Major Depressive Disorder (MDD). The MINI was used to diagnose MDD.,2,20,1 month,16S,4,Illumina,relative abundances,Linear Regression,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,7 March 2024,Keamy,"Keamy,ChiomaBlessing,WikiWorks",GLM box plot showing relative abundance levels (clr-transformed and filtered) of the phylum Bacteroidetes in individuals who have MDD compared to those who did not have MDD,increased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,ChiomaBlessing
bsdb:34930922/1/1,34930922,"cross-sectional observational, not case-control",34930922,10.1038/s41522-021-00261-0,NA,"Ng S., Chen M., Kundu S., Wang X., Zhou Z., Zheng Z., Qing W., Sheng H., Wang Y., He Y., Bennett P.R., MacIntyre D.A. , Zhou H.",Large-scale characterisation of the pregnancy vaginal microbiome and sialidase activity in a low-risk Chinese population,NPJ biofilms and microbiomes,2021,NA,Experiment 1,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Birth measurement,EFO:0006921,Low vaginal sialidase activity,High vaginal sialidase activity,"Women with high vaginal sialidase activity, which is often associated with bacterial vaginosis (BV)",783,36,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,FIG 2 (C),23 April 2024,Rahila,"Rahila,Scholastica,WikiWorks",LDA analysis in vaginal microbiota of women with low (green) versus high (red) vaginal sialidase activity,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus sp.,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|201174;1783272|1239|91061|186826|186827;1783272|1239|91061|186826|186827|1375;1783272|1239|91061|186826|186827|1375|1872398;1783272|201174|84998|84999|1643824|1380;3379134|976|200643|171549;3379134|976|200643;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|31979|1485|1506;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|39948|1955814;1783272|1239|186801|186802;1783272|201174|84998|84999|1643824|2767327|82135;1783272|201174|1760|85004|31953|2701;1783272|201174|1760|85004|31953|2701|2049026;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|1385|539738|1378|1966354;1783272|1239|91061|1385|539738;1783272|1239|91061|186826|33958|2742598|1613;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843489|31977|906|2023260;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|1737404|1737405|1570339|543311|1944660;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|59823;3379134|976|200643|171549|171552;1783272|1239|1737404|1737405|1737406;1783272|1239|909932|1843489|31977,Complete,Svetlana up
bsdb:34930922/1/2,34930922,"cross-sectional observational, not case-control",34930922,10.1038/s41522-021-00261-0,NA,"Ng S., Chen M., Kundu S., Wang X., Zhou Z., Zheng Z., Qing W., Sheng H., Wang Y., He Y., Bennett P.R., MacIntyre D.A. , Zhou H.",Large-scale characterisation of the pregnancy vaginal microbiome and sialidase activity in a low-risk Chinese population,NPJ biofilms and microbiomes,2021,NA,Experiment 1,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Birth measurement,EFO:0006921,Low vaginal sialidase activity,High vaginal sialidase activity,"Women with high vaginal sialidase activity, which is often associated with bacterial vaginosis (BV)",783,36,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,FIG 2 (C),23 April 2024,Rahila,"Rahila,Scholastica,WikiWorks",LDA analysis in vaginal microbiota of women with low (green) versus high (red) vaginal sialidase activity,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia|s__Delftia sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum|s__Herbaspirillum sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus jensenii,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Saprospiria|o__Saprospirales|f__Saprospiraceae|g__Saprospira,k__Pseudomonadati|p__Bacteroidota|c__Saprospiria|o__Saprospirales,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium|s__Sediminibacterium sp.",3379134|1224|28211;1783272|1239|91061;1783272|1239;3379134|1224|28216;3379134|1224|28216|80840|119060|32008;3379134|1224|28216|80840|119060|32008|36773;3379134|1224|28216|80840|119060;3379134|1224|28216|80840;3379134|976|1853228|1853229|563835;3379134|1224|28216|80840|80864;3379134|1224|28216|80840|80864|80865;3379134|1224|28216|80840|80864|80865|1886637;3379134|1224|28216|80840|75682|963;3379134|1224|28216|80840|75682|963|1890675;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|47770;1783272|1239|91061|186826|33958|1578|109790;3379134|1224;3379134|976|1937959|1936988|89374|1007;3379134|976|1937959|1936988;3379134|976|1853228|1853229|563835|504481;3379134|976|1853228|1853229|563835|504481|1917865,Complete,Svetlana up
bsdb:34930922/2/1,34930922,"cross-sectional observational, not case-control",34930922,10.1038/s41522-021-00261-0,NA,"Ng S., Chen M., Kundu S., Wang X., Zhou Z., Zheng Z., Qing W., Sheng H., Wang Y., He Y., Bennett P.R., MacIntyre D.A. , Zhou H.",Large-scale characterisation of the pregnancy vaginal microbiome and sialidase activity in a low-risk Chinese population,NPJ biofilms and microbiomes,2021,NA,Experiment 2,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Birth measurement,EFO:0006921,Leukocyte low (grades I-II),Leukocyte high (grades III-IV),Vaginal microbiota of women  with Leukocyte high (grades III-IV),783,36,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 3 (C),23 April 2024,Rahila,"Rahila,Scholastica,WikiWorks","LDA analysis in vaginal microbiota of women with leukocyte low (grades I-II, green) versus leukocyte high (grades III-IV, red)",increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia|s__Delftia sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp.",1783272|1239|91061;1783272|1239;3379134|1224|28216;3379134|1224|28216|80840|119060|32008;3379134|1224|28216|80840|119060|32008|36773;3379134|1224|28216|80840|119060;3379134|1224|28216|80840;3379134|1224|28216|80840|80864|80865;3379134|1224|28216|80840|80864|80865|1886637;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|147802;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|1737404|1737405|1570339|162289|1971214,Complete,Svetlana up
bsdb:34930922/2/2,34930922,"cross-sectional observational, not case-control",34930922,10.1038/s41522-021-00261-0,NA,"Ng S., Chen M., Kundu S., Wang X., Zhou Z., Zheng Z., Qing W., Sheng H., Wang Y., He Y., Bennett P.R., MacIntyre D.A. , Zhou H.",Large-scale characterisation of the pregnancy vaginal microbiome and sialidase activity in a low-risk Chinese population,NPJ biofilms and microbiomes,2021,NA,Experiment 2,China,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Birth measurement,EFO:0006921,Leukocyte low (grades I-II),Leukocyte high (grades III-IV),Vaginal microbiota of women  with Leukocyte high (grades III-IV),783,36,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,FIG 3 (C),23 April 2024,Rahila,"Rahila,Scholastica,WikiWorks","LDA analysis in vaginal microbiota of women with leukocyte low (grades I-II, green) versus leukocyte high (grades III-IV, red)",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Bacillota|c__Clostridia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus lutetiensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae",3379134|1224|28216|80840|506;3379134|1224|28211;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|1737404|1737405|1570339|165779|1872515;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|1239|186801;3379134|1224|28216|80840|80864;1783272|1239|186801|186802;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|91061|186826|1300|1301|150055;3379134|1224|28216|80840|995019|40544;3379134|1224|28216|80840|995019|40544|1981025;1783272|1239|1737404|1737405|1737406;1783272|1239|1737404|1737405|1737406,Complete,Svetlana up
bsdb:34931394/1/1,34931394,case-control,34931394,10.1111/odi.14110,NA,"Guo H., Li B., Yao H., Liu D., Chen R., Zhou S., Ji Y., Zeng L. , Du M.",Profiling the oral microbiomes in patients with Alzheimer's disease,Oral diseases,2023,"Alzheimer's disease, oral microbiomes, periodontal bacteria, periodontal disease",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,Cognitive intact subjects,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,26,26,3 months,16S,NA,NA,relative abundances,Metastats,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a,13 December 2024,AaishahM,"AaishahM,WikiWorks",Differential salivary microbes in AD patients and cognitive-intact subjects,increased,k__Thermotogati|p__Deinococcota,3384194|1297,Complete,NA
bsdb:34931394/1/2,34931394,case-control,34931394,10.1111/odi.14110,NA,"Guo H., Li B., Yao H., Liu D., Chen R., Zhou S., Ji Y., Zeng L. , Du M.",Profiling the oral microbiomes in patients with Alzheimer's disease,Oral diseases,2023,"Alzheimer's disease, oral microbiomes, periodontal bacteria, periodontal disease",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,Cognitive intact subjects,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,26,26,3 months,16S,NA,NA,relative abundances,Metastats,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3a,13 December 2024,AaishahM,"AaishahM,WikiWorks",Differential salivary microbes in AD patients and cognitive-intact subjects,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Pseudomonadati|p__Pseudomonadota",3384189|32066|203490;3379134|1224,Complete,NA
bsdb:34931394/2/1,34931394,case-control,34931394,10.1111/odi.14110,NA,"Guo H., Li B., Yao H., Liu D., Chen R., Zhou S., Ji Y., Zeng L. , Du M.",Profiling the oral microbiomes in patients with Alzheimer's disease,Oral diseases,2023,"Alzheimer's disease, oral microbiomes, periodontal bacteria, periodontal disease",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,Cognitive intact subjects,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,26,26,3 months,16S,NA,NA,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3b,13 December 2024,AaishahM,"AaishahM,WikiWorks",Differential salivary microbes in AD patients and cognitive-intact subjects,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Bacillati|p__Bacillota|c__Negativicutes",3379134|976|200643|171549|171552|838|28129;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|91061|186826|33958|2767887|1624;1783272|1239|91061|186826|1300|1301|1302;1783272|1239|91061|186826;1783272|1239|91061;1783272|1239|186801|3085636|186803|1213720|796942;1783272|1239|186801|3085636|186803|1213720;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802;1783272|1239|186801;1783272|1239|909932|1843489|31977|906|187326;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977;1783272|1239|909932|1843489;1783272|1239|909932,Complete,NA
bsdb:34931394/2/2,34931394,case-control,34931394,10.1111/odi.14110,NA,"Guo H., Li B., Yao H., Liu D., Chen R., Zhou S., Ji Y., Zeng L. , Du M.",Profiling the oral microbiomes in patients with Alzheimer's disease,Oral diseases,2023,"Alzheimer's disease, oral microbiomes, periodontal bacteria, periodontal disease",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,Cognitive intact subjects,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,26,26,3 months,16S,NA,NA,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3b,13 December 2024,AaishahM,"AaishahM,WikiWorks",Differential salivary microbes in AD patients and cognitive-intact subjects,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Metaprevotella|s__Metaprevotella massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Metaprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus helveticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Pseudoleptotrichia|s__Pseudoleptotrichia goodfellowii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia wadei,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium valvarum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter aphrophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus haemolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Acholeplasma,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae",1783272|201174|1760|85009|31957|2801844;1783272|201174|1760|85009|31957;1783272|201174|1760|85009;3379134|976|200643|171549|171552|1980689|1870999;3379134|976|200643|171549|171552|1980689;3379134|976|200643|171549|2005525|195950|28112;3379134|976|200643|171549|2005525|195950;1783272|1239|91061|186826|33958|1578|1587;1783272|1239|91061|186826|33958|46255;1783272|1239|91061|186826|33958;3384189|32066|203490|203491|203492|848|860;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492;3384189|32066|203490|203491|1129771|32067|40542;3384189|32066|203490|203491|1129771|2755140|157692;3384189|32066|203490|203491|1129771|32067|157687;3384189|32066|203490|203491|1129771|32067;3384189|32066|203490|203491|1129771;3384189|32066|203490|203491;3384189|32066|203490;3379134|1224|28216|80840|119060|47670|47671;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|80840|119060;3379134|1224|28216|206351|481|482|1107316;3379134|1224|1236|135615|868|2717|2718;3379134|1224|1236|135615|868|2717|194702;3379134|1224|1236|135615|868|2717;3379134|1224|1236|135615|868;3379134|1224|1236|135615;3379134|1224|1236|135625|712|416916|732;3379134|1224|1236|135625|712|416916;3379134|1224|1236|135625|712|724|726;3379134|1224|1236|135625|712|724|735;3379134|1224|1236|135625|712|724|729;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|1224|1236;1783272|544448|31969|186329|2146|2147;1783272|544448|31969|186329|2146,Complete,NA
bsdb:34931394/3/1,34931394,case-control,34931394,10.1111/odi.14110,NA,"Guo H., Li B., Yao H., Liu D., Chen R., Zhou S., Ji Y., Zeng L. , Du M.",Profiling the oral microbiomes in patients with Alzheimer's disease,Oral diseases,2023,"Alzheimer's disease, oral microbiomes, periodontal bacteria, periodontal disease",Experiment 3,China,Homo sapiens,Gingival groove,UBERON:0008805,Alzheimer's disease,MONDO:0004975,Cognitive intact subjects,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,26,26,3 months,16S,NA,NA,relative abundances,Metastats,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4a,14 December 2024,AaishahM,"AaishahM,WikiWorks",Differential gingival crevicular fluid (GCF) microbes in AD patients and cognitive-intact subjects,increased,k__Bacillati|p__Actinomycetota,1783272|201174,Complete,NA
bsdb:34931394/3/2,34931394,case-control,34931394,10.1111/odi.14110,NA,"Guo H., Li B., Yao H., Liu D., Chen R., Zhou S., Ji Y., Zeng L. , Du M.",Profiling the oral microbiomes in patients with Alzheimer's disease,Oral diseases,2023,"Alzheimer's disease, oral microbiomes, periodontal bacteria, periodontal disease",Experiment 3,China,Homo sapiens,Gingival groove,UBERON:0008805,Alzheimer's disease,MONDO:0004975,Cognitive intact subjects,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,26,26,3 months,16S,NA,NA,relative abundances,Metastats,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4a,14 December 2024,AaishahM,"AaishahM,WikiWorks",Differential gingival crevicular fluid (GCF) microbes in AD patients and cognitive-intact subjects,decreased,"k__Pseudomonadati|p__Pseudomonadota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Chloroflexota|c__Chloroflexia",3379134|1224;3384189|32066|203490;1783272|544448;1783272|200795|32061,Complete,NA
bsdb:34931394/4/1,34931394,case-control,34931394,10.1111/odi.14110,NA,"Guo H., Li B., Yao H., Liu D., Chen R., Zhou S., Ji Y., Zeng L. , Du M.",Profiling the oral microbiomes in patients with Alzheimer's disease,Oral diseases,2023,"Alzheimer's disease, oral microbiomes, periodontal bacteria, periodontal disease",Experiment 4,China,Homo sapiens,Gingival groove,UBERON:0008805,Alzheimer's disease,MONDO:0004975,Cognitive intact subjects,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,26,26,3 months,16S,NA,NA,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4b,14 December 2024,AaishahM,"AaishahM,WikiWorks",Differential gingival crevicular fluid (GCF) microbes in AD patients and cognitive-intact subjects,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella rimae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella uli,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas flueggei,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Bacillati|p__Bacillota|c__Negativicutes",1783272|201174|1760|85004|31953|1678|1689;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|84998|84999|1643824|2767353|1382;1783272|201174|84998|84999|1643824|2767353|1383;1783272|201174|84998|84999|1643824|1380;1783272|201174|84998|84999|1643824|133925|133926;1783272|201174|84998|84999|1643824|133925;1783272|201174|84998|84999|1643824;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|91061|186826|1300|1301|1305;1783272|1239|91061|186826;1783272|1239|91061;1783272|1239|186801|3085636|186803|265975|1501329;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|3085636|186803|1213720|796942;1783272|1239|186801|3085636|186803|1213720;1783272|1239|186801|3085636|186803;1783272|1239|909932|909929|1843491|970|135080;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977;1783272|1239|909932|1843489;1783272|1239|909932,Complete,NA
bsdb:34931394/4/2,34931394,case-control,34931394,10.1111/odi.14110,NA,"Guo H., Li B., Yao H., Liu D., Chen R., Zhou S., Ji Y., Zeng L. , Du M.",Profiling the oral microbiomes in patients with Alzheimer's disease,Oral diseases,2023,"Alzheimer's disease, oral microbiomes, periodontal bacteria, periodontal disease",Experiment 4,China,Homo sapiens,Gingival groove,UBERON:0008805,Alzheimer's disease,MONDO:0004975,Cognitive intact subjects,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,26,26,3 months,16S,NA,NA,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4b,14 December 2024,AaishahM,"AaishahM,WikiWorks",Differential gingival crevicular fluid (GCF) microbes in AD patients and cognitive-intact subjects,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter|s__Paludibacter propionicigenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus helveticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Syntrophomonadaceae|g__Syntrophomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Syntrophomonadaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda|s__Centipeda periodontii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Myxococcota|o__Polyangiales|f__Polyangiaceae,k__Pseudomonadati|p__Myxococcota|c__Myxococcia|o__Myxococcales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter rectus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium valvarum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter aphrophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus haemolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria",3379134|976|200643|171549|2005523|346096|185300;3379134|976|200643|171549|2005523|346096;3379134|976|200643|171549|2005523;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|1970189;1783272|1239|91061|186826|33958|1578|1587;1783272|1239|186801|186802|68298|862;1783272|1239|186801|186802|68298;1783272|1239|909932|909929|1843491|82202|82203;1783272|1239|909932|909929|1843491|82202;3384189|32066|203490|203491|203492|848|851;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492;3384189|32066|203490|203491|1129771|32067|40542;3384189|32066|203490|203491|1129771|32067|157688;3384189|32066|203490|203491|1129771|32067;3384189|32066|203490|203491|1129771;3384189|32066|203490|203491;3384189|32066|203490;3379134|1224|28216|80840|119060|47670|47671;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|80840|119060;3379134|1224|28216|80840;3379134|2818505|3031712|49;3379134|2818505|32015|29;3379134|29547|3031852|213849|72294|194|203;3379134|29547|3031852|213849|72294|194|204;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294;3379134|29547|3031852|213849;3379134|29547|3031852;3379134|1224|1236|135615|868|2717|2718;3379134|1224|1236|135615|868|2717|194702;3379134|1224|1236|135615|868|2717;3379134|1224|1236|135615|868;3379134|1224|1236|135615;3379134|1224|1236|135625|712|416916|732;3379134|1224|1236|135625|712|416916|739;3379134|1224|1236|135625|712|416916;3379134|1224|1236|135625|712|724|726;3379134|1224|1236|135625|712|724|729;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|1224|1236,Complete,NA
bsdb:34931394/5/1,34931394,case-control,34931394,10.1111/odi.14110,NA,"Guo H., Li B., Yao H., Liu D., Chen R., Zhou S., Ji Y., Zeng L. , Du M.",Profiling the oral microbiomes in patients with Alzheimer's disease,Oral diseases,2023,"Alzheimer's disease, oral microbiomes, periodontal bacteria, periodontal disease",Experiment 5,China,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,Early-onset Alzheimer's Disease patients (EAS),Late-onset Alzheimer's Disease patients (NAS),Patients with late-onset Alzheimer's Disease,10,16,3 months,16S,NA,NA,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5a,14 December 2024,AaishahM,"AaishahM,WikiWorks",Differential bacteria in AD patients with different clinical types,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella veroralis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius",1783272|1239|1737404|1737405|1570339|543311|33033;3379134|976|200643|171549|171552|838|28137;3379134|976|200643|171549|171552|2974251|28135;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|91061|186826|33958|2767887|1624,Complete,NA
bsdb:34931394/5/2,34931394,case-control,34931394,10.1111/odi.14110,NA,"Guo H., Li B., Yao H., Liu D., Chen R., Zhou S., Ji Y., Zeng L. , Du M.",Profiling the oral microbiomes in patients with Alzheimer's disease,Oral diseases,2023,"Alzheimer's disease, oral microbiomes, periodontal bacteria, periodontal disease",Experiment 5,China,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,Early-onset Alzheimer's Disease patients (EAS),Late-onset Alzheimer's Disease patients (NAS),Patients with late-onset Alzheimer's Disease,10,16,3 months,16S,NA,NA,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5a,14 December 2024,AaishahM,"AaishahM,WikiWorks",Differential bacteria in AD patients with different clinical types,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum longum",3379134|976|117743|200644|49546|1016|327575;1783272|1239|91061|186826|1300|1301|45634;3379134|976|117743|200644|49546|1016|45242;3379134|1224|28216|206351|481|482|495;1783272|1239|186801|3085636|186803|1213720|796942,Complete,NA
bsdb:34931394/6/1,34931394,case-control,34931394,10.1111/odi.14110,NA,"Guo H., Li B., Yao H., Liu D., Chen R., Zhou S., Ji Y., Zeng L. , Du M.",Profiling the oral microbiomes in patients with Alzheimer's disease,Oral diseases,2023,"Alzheimer's disease, oral microbiomes, periodontal bacteria, periodontal disease",Experiment 6,China,Homo sapiens,Gingival groove,UBERON:0008805,Alzheimer's disease,MONDO:0004975,Early-onset Alzheimer's Disease patients (EAG),Late-onset Alzheimer's Disease patients (NAG),Patients with late-onset Alzheimer's Disease,10,16,3 months,16S,NA,NA,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5b,14 December 2024,AaishahM,"AaishahM,WikiWorks",Differential bacteria in AD patients with different clinical types,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium timidum",1783272|1239|91061|186826|1300|1301|76860;3379134|976|200643|171549|171551|836|837;1783272|1239|186801|3082720|543314|86331|35519,Complete,NA
bsdb:34931394/7/1,34931394,case-control,34931394,10.1111/odi.14110,NA,"Guo H., Li B., Yao H., Liu D., Chen R., Zhou S., Ji Y., Zeng L. , Du M.",Profiling the oral microbiomes in patients with Alzheimer's disease,Oral diseases,2023,"Alzheimer's disease, oral microbiomes, periodontal bacteria, periodontal disease",Experiment 7,China,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,Cognitive intact subjects,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,26,26,3 months,16S,NA,NA,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S2a,14 December 2024,AaishahM,"AaishahM,WikiWorks",Differential microbes in the saliva from AD patients and cognitive intact subjects,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum longum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis",1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|186801|3085636|186803|1213720|796942;1783272|1239|909932|1843489|31977|29465|39778;3379134|976|200643|171549|171552|838|28129;1783272|1239|91061|186826|33958|2767887|1624;1783272|1239|91061|186826|186828|117563|46124;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|91061|1385|539738|1378|84135,Complete,NA
bsdb:34931394/7/2,34931394,case-control,34931394,10.1111/odi.14110,NA,"Guo H., Li B., Yao H., Liu D., Chen R., Zhou S., Ji Y., Zeng L. , Du M.",Profiling the oral microbiomes in patients with Alzheimer's disease,Oral diseases,2023,"Alzheimer's disease, oral microbiomes, periodontal bacteria, periodontal disease",Experiment 7,China,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,Cognitive intact subjects,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,26,26,3 months,16S,NA,NA,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S2a,14 December 2024,AaishahM,"AaishahM,WikiWorks",Differential microbes in the saliva from AD patients and cognitive intact subjects,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus haemolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus helveticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter aphrophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium valvarum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum",3379134|1224|1236|135625|712|724|729;3379134|1224|1236|135625|712|724|726;3379134|1224|28216|80840|119060|47670|47671;1783272|1239|91061|186826|33958|1578|1587;3379134|1224|1236|135625|712|416916|732;3379134|1224|1236|135615|868|2717|194702;3384189|32066|203490|203491|203492|848|860;3379134|29547|3031852|213849|72294|194|824;3384189|32066|203490|203491|203492|848|851,Complete,NA
bsdb:34931394/8/1,34931394,case-control,34931394,10.1111/odi.14110,NA,"Guo H., Li B., Yao H., Liu D., Chen R., Zhou S., Ji Y., Zeng L. , Du M.",Profiling the oral microbiomes in patients with Alzheimer's disease,Oral diseases,2023,"Alzheimer's disease, oral microbiomes, periodontal bacteria, periodontal disease",Experiment 8,China,Homo sapiens,Gingival groove,UBERON:0008805,Alzheimer's disease,MONDO:0004975,Cognitive intact subjects,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,26,26,3 months,16S,NA,NA,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S2b,14 December 2024,AaishahM,"AaishahM,WikiWorks",Differential microbes in the gingival crevicular fluid (GCF) from AD patients and cognitive intact subjects,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella uli,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella rimae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum longum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas artemidis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii",1783272|201174|84998|84999|1643824|133925|133926;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|186801|3085636|186803|265975|1501329;1783272|201174|84998|84999|1643824|2767353|1383;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|186801|3085636|186803|1213720|796942;1783272|1239|909932|909929|1843491|970|671224;1783272|1239|909932|909929|1843491|970|69823;1783272|1239|91061|186826|1300|1301|1302,Complete,NA
bsdb:34931394/8/2,34931394,case-control,34931394,10.1111/odi.14110,NA,"Guo H., Li B., Yao H., Liu D., Chen R., Zhou S., Ji Y., Zeng L. , Du M.",Profiling the oral microbiomes in patients with Alzheimer's disease,Oral diseases,2023,"Alzheimer's disease, oral microbiomes, periodontal bacteria, periodontal disease",Experiment 8,China,Homo sapiens,Gingival groove,UBERON:0008805,Alzheimer's disease,MONDO:0004975,Cognitive intact subjects,Alzheimer's Disease (AD) patients,Patients with Alzheimer's Disease,26,26,3 months,16S,NA,NA,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S2b,14 December 2024,AaishahM,"AaishahM,WikiWorks",Differential microbes in the gingival crevicular fluid (GCF) from AD patients and cognitive intact subjects,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium valvarum,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter rectus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotellamassilia|s__Prevotellamassilia timonensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter aphrophilus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter|s__Paludibacter propionicigenes,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfomicrobiaceae|g__Desulfomicrobium|s__Desulfomicrobium orale,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus haemolyticus",3384189|32066|203490|203491|203492|848|851;3379134|29547|3031852|213849|72294|194|204;3379134|1224|1236|135625|712|724|729;3379134|1224|1236|135615|868|2717|194702;3379134|29547|3031852|213849|72294|194|203;3379134|976|200643|171549|171552|1926672|1852370;3379134|1224|1236|135625|712|416916|732;3384189|32066|203490|203491|1129771|32067|40542;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|2005523|346096|185300;3379134|200940|3031449|213115|213116|898|132132;3379134|1224|1236|135625|712|724|726,Complete,NA
bsdb:34931394/9/1,34931394,case-control,34931394,10.1111/odi.14110,NA,"Guo H., Li B., Yao H., Liu D., Chen R., Zhou S., Ji Y., Zeng L. , Du M.",Profiling the oral microbiomes in patients with Alzheimer's disease,Oral diseases,2023,"Alzheimer's disease, oral microbiomes, periodontal bacteria, periodontal disease",Experiment 9,China,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,Early-onset Alzheimer's Disease patients (EAS),Late-onset Alzheimer's Disease patients (NAS),Patients with late-onset Alzheimer's Disease,10,16,3 months,16S,NA,NA,relative abundances,Metastats,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S3d,14 December 2024,AaishahM,"AaishahM,WikiWorks",Differential abundance of bacteria in AD patients with different clinical types,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris",1783272|1239|909932|1843489|31977|29465|29466;3379134|976|200643|171549|171552|2974251|28135,Complete,NA
bsdb:34931394/9/2,34931394,case-control,34931394,10.1111/odi.14110,NA,"Guo H., Li B., Yao H., Liu D., Chen R., Zhou S., Ji Y., Zeng L. , Du M.",Profiling the oral microbiomes in patients with Alzheimer's disease,Oral diseases,2023,"Alzheimer's disease, oral microbiomes, periodontal bacteria, periodontal disease",Experiment 9,China,Homo sapiens,Saliva,UBERON:0001836,Alzheimer's disease,MONDO:0004975,Early-onset Alzheimer's Disease patients (EAS),Late-onset Alzheimer's Disease patients (NAS),Patients with late-onset Alzheimer's Disease,10,16,3 months,16S,NA,NA,relative abundances,Metastats,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S3d,14 December 2024,AaishahM,"AaishahM,WikiWorks",Differential abundance of bacteria in AD patients with different clinical types,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas catoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum longum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter aphrophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea",3379134|976|117743|200644|49546|1016|45242;3379134|976|117743|200644|49546|1016|327575;3379134|1224|28216|206351|481|482|495;1783272|1239|91061|186826|1300|1301|45634;3379134|976|200643|171549|171551|836|41976;3379134|1224|1236|135625|712|416916|739;1783272|1239|186801|3085636|186803|1213720|796942;3379134|1224|1236|135625|712|416916|732;1783272|201174|1760|85007|1653|1716|43768;1783272|201174|1760|85007|1653|1716|61592;3384189|32066|203490|203491|1129771|32067|157688;3379134|1224|1236|135615|868|2717|2718;3379134|976|117743|200644|49546|1016|1018,Complete,NA
bsdb:34931394/10/1,34931394,case-control,34931394,10.1111/odi.14110,NA,"Guo H., Li B., Yao H., Liu D., Chen R., Zhou S., Ji Y., Zeng L. , Du M.",Profiling the oral microbiomes in patients with Alzheimer's disease,Oral diseases,2023,"Alzheimer's disease, oral microbiomes, periodontal bacteria, periodontal disease",Experiment 10,China,Homo sapiens,Gingival groove,UBERON:0008805,Alzheimer's disease,MONDO:0004975,Early-onset Alzheimer's Disease patients (EAG),Late-onset Alzheimer's Disease patients (NAG),Patients with late-onset Alzheimer's Disease,10,16,3 months,16S,NA,NA,relative abundances,Metastats,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S3e,14 December 2024,AaishahM,"AaishahM,WikiWorks",Differential abundance of bacteria in AD patients with different clinical types,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus",3379134|976|200643|171549|171551|836|837;1783272|1239|91061|186826|1300|1301|76860,Complete,NA
bsdb:34931394/10/2,34931394,case-control,34931394,10.1111/odi.14110,NA,"Guo H., Li B., Yao H., Liu D., Chen R., Zhou S., Ji Y., Zeng L. , Du M.",Profiling the oral microbiomes in patients with Alzheimer's disease,Oral diseases,2023,"Alzheimer's disease, oral microbiomes, periodontal bacteria, periodontal disease",Experiment 10,China,Homo sapiens,Gingival groove,UBERON:0008805,Alzheimer's disease,MONDO:0004975,Early-onset Alzheimer's Disease patients (EAG),Late-onset Alzheimer's Disease patients (NAG),Patients with late-onset Alzheimer's Disease,10,16,3 months,16S,NA,NA,relative abundances,Metastats,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S3e,14 December 2024,AaishahM,"AaishahM,WikiWorks",Differential abundance of bacteria in AD patients with different clinical types,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,1783272|201174|1760|85006|1268|32207|2047,Complete,NA
bsdb:34937163/1/1,34937163,case-control,34937163,10.1128/Spectrum.01255-21,https://journals.asm.org/doi/10.1128/spectrum.01255-21,"Zhu X., Hong G., Li Y., Yang P., Cheng M., Zhang L., Li Y., Ji L., Li G., Chen C., Zhong C., Jin Y., Yang M., Xiong H., Qian W., Ding Z., Ning K. , Hou X.",Understanding of the Site-Specific Microbial Patterns towards Accurate Identification for Patients with Diarrhea-Predominant Irritable Bowel Syndrome,Microbiology spectrum,2021,"IBS-D, microbial biomarkers, multiple intestinal sites, site-specific microbial patterns",Experiment 1,China,Homo sapiens,Duodenal mucosa,UBERON:0000320,Irritable bowel syndrome,EFO:0000555,Healthy controls (Duodenal mucosa samples),IBS-D patients (Duodenal mucosa samples),Patients with diarrhea-dominant irritable bowel syndrome (IBS-D),20,37,1 month,16S,123,Roche454,relative abundances,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 5A,17 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",Site-specific biomarkers detected by LEfSe.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium",1783272|1239|91061|1385|186817|1386;1783272|1239|91061|186826|186828|2747;3379134|1224|28211|356|118882|528;1783272|1239|91061|186826|1300|1357;1783272|201174|1760|85006|1268|1269;1783272|201174|1760|85009|31957|1743;3379134|1224|28211|356|119045|407;1783272|201174|1760|85006|85023|33882;1783272|1239|91061|1385|186822|44249;1783272|201174|1760|85007|1653|1716;3379134|1224|28216|80840|80864|80865;3379134|1224|28211|204458|76892|41275;1783272|201174|1760|85007|1762|1763,Complete,Svetlana up
bsdb:34937163/1/2,34937163,case-control,34937163,10.1128/Spectrum.01255-21,https://journals.asm.org/doi/10.1128/spectrum.01255-21,"Zhu X., Hong G., Li Y., Yang P., Cheng M., Zhang L., Li Y., Ji L., Li G., Chen C., Zhong C., Jin Y., Yang M., Xiong H., Qian W., Ding Z., Ning K. , Hou X.",Understanding of the Site-Specific Microbial Patterns towards Accurate Identification for Patients with Diarrhea-Predominant Irritable Bowel Syndrome,Microbiology spectrum,2021,"IBS-D, microbial biomarkers, multiple intestinal sites, site-specific microbial patterns",Experiment 1,China,Homo sapiens,Duodenal mucosa,UBERON:0000320,Irritable bowel syndrome,EFO:0000555,Healthy controls (Duodenal mucosa samples),IBS-D patients (Duodenal mucosa samples),Patients with diarrhea-dominant irritable bowel syndrome (IBS-D),20,37,1 month,16S,123,Roche454,relative abundances,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 5A,17 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",Site-specific biomarkers detected by LEfSe.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter",3379134|1224|1236|2887326|468|469;3379134|1224|28216|80840|506|222,Complete,Svetlana up
bsdb:34937163/2/1,34937163,case-control,34937163,10.1128/Spectrum.01255-21,https://journals.asm.org/doi/10.1128/spectrum.01255-21,"Zhu X., Hong G., Li Y., Yang P., Cheng M., Zhang L., Li Y., Ji L., Li G., Chen C., Zhong C., Jin Y., Yang M., Xiong H., Qian W., Ding Z., Ning K. , Hou X.",Understanding of the Site-Specific Microbial Patterns towards Accurate Identification for Patients with Diarrhea-Predominant Irritable Bowel Syndrome,Microbiology spectrum,2021,"IBS-D, microbial biomarkers, multiple intestinal sites, site-specific microbial patterns",Experiment 2,China,Homo sapiens,Lumen of duodenum,UBERON:0016512,Irritable bowel syndrome,EFO:0000555,Healthy controls (Duodenal lumen samples),IBS-D patients (Duodenal lumen samples),Patients with diarrhea-dominant irritable bowel syndrome (IBS-D),19,43,1 month,16S,123,Roche454,relative abundances,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 5A,17 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",Site-specific biomarkers detected by LEfSe.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",1783272|1239|526524|526525|128827|118747;3384189|32066|203490|203491|1129771|32067;1783272|1239|909932|1843489|31977|29465;1783272|201174|1760|85006|1268|32207,Complete,Svetlana up
bsdb:34937163/2/2,34937163,case-control,34937163,10.1128/Spectrum.01255-21,https://journals.asm.org/doi/10.1128/spectrum.01255-21,"Zhu X., Hong G., Li Y., Yang P., Cheng M., Zhang L., Li Y., Ji L., Li G., Chen C., Zhong C., Jin Y., Yang M., Xiong H., Qian W., Ding Z., Ning K. , Hou X.",Understanding of the Site-Specific Microbial Patterns towards Accurate Identification for Patients with Diarrhea-Predominant Irritable Bowel Syndrome,Microbiology spectrum,2021,"IBS-D, microbial biomarkers, multiple intestinal sites, site-specific microbial patterns",Experiment 2,China,Homo sapiens,Lumen of duodenum,UBERON:0016512,Irritable bowel syndrome,EFO:0000555,Healthy controls (Duodenal lumen samples),IBS-D patients (Duodenal lumen samples),Patients with diarrhea-dominant irritable bowel syndrome (IBS-D),19,43,1 month,16S,123,Roche454,relative abundances,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 5A,17 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",Site-specific biomarkers detected by LEfSe.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium",3379134|976|200643|171549|171551|836;3379134|1224|28211|204457|41297|13687;3379134|1224|28211|204457|3423717|165695;3379134|976|117743|200644|49546|237,Complete,Svetlana up
bsdb:34937163/3/1,34937163,case-control,34937163,10.1128/Spectrum.01255-21,https://journals.asm.org/doi/10.1128/spectrum.01255-21,"Zhu X., Hong G., Li Y., Yang P., Cheng M., Zhang L., Li Y., Ji L., Li G., Chen C., Zhong C., Jin Y., Yang M., Xiong H., Qian W., Ding Z., Ning K. , Hou X.",Understanding of the Site-Specific Microbial Patterns towards Accurate Identification for Patients with Diarrhea-Predominant Irritable Bowel Syndrome,Microbiology spectrum,2021,"IBS-D, microbial biomarkers, multiple intestinal sites, site-specific microbial patterns",Experiment 3,China,Homo sapiens,Mucosa of rectum,UBERON:0003346,Irritable bowel syndrome,EFO:0000555,Healthy controls (Rectal mucosa samples),IBS-D patients (Rectal mucosa samples),Patients with diarrhea-dominant irritable bowel syndrome (IBS-D),20,53,1 month,16S,123,Roche454,relative abundances,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 5A,17 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",Site-specific biomarkers detected by LEfSe.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus",3379134|976|200643|171549|815|816;3379134|1224|28211|356|212791;3384194|1297|188787|68933|188786|270,Complete,Svetlana up
bsdb:34937163/3/2,34937163,case-control,34937163,10.1128/Spectrum.01255-21,https://journals.asm.org/doi/10.1128/spectrum.01255-21,"Zhu X., Hong G., Li Y., Yang P., Cheng M., Zhang L., Li Y., Ji L., Li G., Chen C., Zhong C., Jin Y., Yang M., Xiong H., Qian W., Ding Z., Ning K. , Hou X.",Understanding of the Site-Specific Microbial Patterns towards Accurate Identification for Patients with Diarrhea-Predominant Irritable Bowel Syndrome,Microbiology spectrum,2021,"IBS-D, microbial biomarkers, multiple intestinal sites, site-specific microbial patterns",Experiment 3,China,Homo sapiens,Mucosa of rectum,UBERON:0003346,Irritable bowel syndrome,EFO:0000555,Healthy controls (Rectal mucosa samples),IBS-D patients (Rectal mucosa samples),Patients with diarrhea-dominant irritable bowel syndrome (IBS-D),20,53,1 month,16S,123,Roche454,relative abundances,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 5A,17 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",Site-specific biomarkers detected by LEfSe.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",3379134|976|200643|171549|171552|838;3379134|1224|28211|204455|31989|265;1783272|1239|186801|186802|216572|119852,Complete,Svetlana up
bsdb:34937163/4/1,34937163,case-control,34937163,10.1128/Spectrum.01255-21,https://journals.asm.org/doi/10.1128/spectrum.01255-21,"Zhu X., Hong G., Li Y., Yang P., Cheng M., Zhang L., Li Y., Ji L., Li G., Chen C., Zhong C., Jin Y., Yang M., Xiong H., Qian W., Ding Z., Ning K. , Hou X.",Understanding of the Site-Specific Microbial Patterns towards Accurate Identification for Patients with Diarrhea-Predominant Irritable Bowel Syndrome,Microbiology spectrum,2021,"IBS-D, microbial biomarkers, multiple intestinal sites, site-specific microbial patterns",Experiment 4,China,Homo sapiens,Rectal lumen,UBERON:0009670,Irritable bowel syndrome,EFO:0000555,Healthy controls (Rectal lumen samples),IBS-D patients (Rectal lumen samples),Patients with diarrhea-dominant irritable bowel syndrome (IBS-D),17,74,1 month,16S,123,Roche454,relative abundances,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 5A,17 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",Site-specific biomarkers detected by LEfSe.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,3379134|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:34937163/4/2,34937163,case-control,34937163,10.1128/Spectrum.01255-21,https://journals.asm.org/doi/10.1128/spectrum.01255-21,"Zhu X., Hong G., Li Y., Yang P., Cheng M., Zhang L., Li Y., Ji L., Li G., Chen C., Zhong C., Jin Y., Yang M., Xiong H., Qian W., Ding Z., Ning K. , Hou X.",Understanding of the Site-Specific Microbial Patterns towards Accurate Identification for Patients with Diarrhea-Predominant Irritable Bowel Syndrome,Microbiology spectrum,2021,"IBS-D, microbial biomarkers, multiple intestinal sites, site-specific microbial patterns",Experiment 4,China,Homo sapiens,Rectal lumen,UBERON:0009670,Irritable bowel syndrome,EFO:0000555,Healthy controls (Rectal lumen samples),IBS-D patients (Rectal lumen samples),Patients with diarrhea-dominant irritable bowel syndrome (IBS-D),17,74,1 month,16S,123,Roche454,relative abundances,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 5A,17 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",Site-specific biomarkers detected by LEfSe.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus",1783272|1239|186801|186802|216572|216851;3384194|1297|188787|118964|183710|1298,Complete,Svetlana up
bsdb:34954497/1/1,34954497,"cross-sectional observational, not case-control",34954497,10.1016/j.parkreldis.2021.12.012,https://doi.org/10.1016/j.parkreldis.2021.12.012,"Takahashi K., Nishiwaki H., Ito M., Iwaoka K., Takahashi K., Suzuki Y., Taguchi K., Yamahara K., Tsuboi Y., Kashihara K., Hirayama M., Ohno K. , Maeda T.",Altered gut microbiota in Parkinson's disease patients with motor complications,Parkinsonism & related disorders,2022,"Dyskinesia, Gut microbiota, Motor complications, Parkinson's disease, Wearing-off",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,PD patients with dyskinesia,PD patients with  wearing-off,Parkinson's disease patients with wearing-off,106,49,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,18 March 2024,PraiseAgbetuyi,"PraiseAgbetuyi,Peace Sandy,WikiWorks","Relationships between Lachnospiraceae Blautia or Lactobacillaceae Lactobacillus and motor complications  In patients with wearing-off, the relative abundance of Lachnospiraceae Blautia (A) and Lactobacillaceae Lactobacillus (C) significantly decreased and increased, respectively. Patients with dyskinesia (B and D) showed no change in relative abundance.",increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Peace Sandy
bsdb:34954497/1/2,34954497,"cross-sectional observational, not case-control",34954497,10.1016/j.parkreldis.2021.12.012,https://doi.org/10.1016/j.parkreldis.2021.12.012,"Takahashi K., Nishiwaki H., Ito M., Iwaoka K., Takahashi K., Suzuki Y., Taguchi K., Yamahara K., Tsuboi Y., Kashihara K., Hirayama M., Ohno K. , Maeda T.",Altered gut microbiota in Parkinson's disease patients with motor complications,Parkinsonism & related disorders,2022,"Dyskinesia, Gut microbiota, Motor complications, Parkinson's disease, Wearing-off",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,PD patients with dyskinesia,PD patients with  wearing-off,Parkinson's disease patients with wearing-off,106,49,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1,18 March 2024,PraiseAgbetuyi,"PraiseAgbetuyi,Peace Sandy,WikiWorks",". Relationships between Lachnospiraceae Blautia or Lactobacillaceae Lactobacillus and motor complications In patients with wearing-off, the relative abundance of Lachnospiraceae Blautia (A) and Lactobacillaceae Lactobacillus (C) significantly decreased and increased, respectively. Patients with dyskinesia (B and D) showed no change in relative abundance.",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,1783272|1239|186801|3085636|186803|572511,Complete,Peace Sandy
bsdb:34963452/1/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/2/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/3/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/4/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/5/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/6/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/7/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/8/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/9/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 9,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/10/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 10,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/11/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 11,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/12/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 12,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/13/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 13,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/14/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 14,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/15/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 15,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/16/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 16,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/17/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 17,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/18/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 18,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/19/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 19,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/20/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 20,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/21/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 21,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/22/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 22,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/23/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 23,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/24/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 24,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/25/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 25,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/26/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 26,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/27/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 27,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/28/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 28,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/29/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 29,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/30/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 30,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/31/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 31,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/32/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 32,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/33/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 33,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/34/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 34,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/35/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 35,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/36/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 36,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/37/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 37,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/38/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 38,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/39/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 39,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/40/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 40,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/41/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 41,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/42/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 42,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/43/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 43,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/44/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 44,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/45/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 45,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/46/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 46,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/47/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 47,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/48/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 48,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/49/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 49,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/50/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 50,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/51/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 51,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/52/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 52,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/53/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 53,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/54/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 54,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/55/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 55,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/56/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 56,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/57/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 57,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/58/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 58,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/59/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 59,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/60/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 60,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/61/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 61,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/62/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 62,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/63/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 63,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/64/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 64,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/65/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 65,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/66/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 66,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/67/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 67,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/68/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 68,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/69/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 69,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/70/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 70,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/71/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 71,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/72/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 72,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/73/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 73,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/74/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 74,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/75/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 75,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/76/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 76,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/77/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 77,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/78/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 78,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/79/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 79,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/80/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 80,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/81/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 81,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/82/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 82,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/83/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 83,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/84/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 84,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/85/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 85,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/86/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 86,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/87/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 87,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/88/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 88,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/89/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 89,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/90/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 90,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/91/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 91,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/92/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 92,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/93/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 93,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/94/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 94,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/95/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 95,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/96/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 96,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/97/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 97,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/98/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 98,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/99/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 99,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/100/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 100,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/101/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 101,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/102/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 102,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/103/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 103,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/104/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 104,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/105/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 105,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/106/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 106,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/107/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 107,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/108/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 108,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/109/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 109,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/110/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 110,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/111/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 111,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/112/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 112,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/113/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 113,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/114/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 114,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/115/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 115,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/116/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 116,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/117/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 117,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/118/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 118,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/119/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 119,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/120/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 120,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/121/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 121,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/122/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 122,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/123/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 123,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/124/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 124,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/125/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 125,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/126/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 126,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/127/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 127,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/128/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 128,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/129/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 129,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/130/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 130,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/131/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 131,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/132/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 132,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/133/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 133,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/134/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 134,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/135/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 135,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/136/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 136,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/137/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 137,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/138/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 138,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/139/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 139,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/140/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 140,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/141/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 141,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/142/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 142,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/143/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 143,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/144/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 144,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/145/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 145,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/146/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 146,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/147/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 147,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/148/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 148,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/149/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 149,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/150/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 150,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/151/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 151,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/152/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 152,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/153/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 153,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/154/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 154,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/155/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 155,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/156/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 156,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/157/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 157,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/158/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 158,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/159/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 159,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/160/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 160,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/161/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 161,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/162/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 162,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/163/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 163,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/164/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 164,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/165/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 165,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/166/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 166,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/167/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 167,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/168/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 168,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/169/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 169,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/170/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 170,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/171/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 171,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/172/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 172,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/173/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 173,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/174/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 174,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/175/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 175,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/176/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 176,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/177/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 177,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/178/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 178,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/179/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 179,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/180/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 180,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/181/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 181,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/182/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 182,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/183/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 183,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/184/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 184,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/185/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 185,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/186/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 186,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/187/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 187,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/188/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 188,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/189/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 189,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/190/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 190,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/191/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 191,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/192/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 192,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/193/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 193,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/194/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 194,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/195/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 195,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/196/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 196,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/197/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 197,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/198/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 198,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/199/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 199,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34963452/200/NA,34963452,case-control,34963452,10.1186/s12934-021-01720-1,NA,"Lin H., Guo Q., Wen Z., Tan S., Chen J., Lin L., Chen P., He J., Wen J. , Chen Y.",The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors,Microbial cell factories,2021,"Anxiety and depression, Fecal microbiota transplantation, Irritable bowel syndrome, Metagenome, Short-chain fatty acids",Experiment 200,China,Homo sapiens,Feces,UBERON:0001988,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34966183/1/1,34966183,prospective cohort,34966183,10.1038/s41598-021-04271-y,NA,"Kateete D.P., Mbabazi M.M., Nakazzi F., Katabazi F.A., Kigozi E., Ssengooba W., Nakiyingi L., Namiiro S., Okwera A., Joloba M.L. , Muwonge A.",Sputum microbiota profiles of treatment-naïve TB patients in Uganda before and during first-line therapy,Scientific reports,2021,NA,Experiment 1,Uganda,Homo sapiens,Sputum,UBERON:0007311,Pulmonary tuberculosis,EFO:1000049,Baseline (pre-treatment),Month 2 and Month 5 follow-up,Sputum collected at 2 months (end of intensive phase) and 5 months (end of therapy) of first-line anti-TB regimen.,106,44,NA,16S,34,Illumina,relative abundances,"ANOVA,Kruskall-Wallis,Mixed-Effects Regression,PERMANOVA,T-Test",0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,Figure 2,11 June 2025,Nuerteye,Nuerteye,"Fig. 2 shows relative-abundance shifts of major genera across baseline, Month 2 and Month 5.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus|s__Peptococcus niger,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava",1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|186807|2740|2741;3379134|1224|28216|206351|481|482|28449,Complete,NA
bsdb:34966183/1/2,34966183,prospective cohort,34966183,10.1038/s41598-021-04271-y,NA,"Kateete D.P., Mbabazi M.M., Nakazzi F., Katabazi F.A., Kigozi E., Ssengooba W., Nakiyingi L., Namiiro S., Okwera A., Joloba M.L. , Muwonge A.",Sputum microbiota profiles of treatment-naïve TB patients in Uganda before and during first-line therapy,Scientific reports,2021,NA,Experiment 1,Uganda,Homo sapiens,Sputum,UBERON:0007311,Pulmonary tuberculosis,EFO:1000049,Baseline (pre-treatment),Month 2 and Month 5 follow-up,Sputum collected at 2 months (end of intensive phase) and 5 months (end of therapy) of first-line anti-TB regimen.,106,44,NA,16S,34,Illumina,relative abundances,"ANOVA,Kruskall-Wallis,Mixed-Effects Regression,PERMANOVA,T-Test",0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Figure 2,11 June 2025,Nuerteye,Nuerteye,"Fig. 2 shows relative-abundance shifts of major genera across baseline, Month 2 and Month 5.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium tuberculosis,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum",1783272|201174|1760|85007|1762|1763|1773;3384194|508458|649775|649776|3029087|1434006|651822;3379134|976|200643|171549|2005525|195950|28112;3384189|32066|203490|203491|203492|848|851,Complete,NA
bsdb:34966183/2/NA,34966183,prospective cohort,34966183,10.1038/s41598-021-04271-y,NA,"Kateete D.P., Mbabazi M.M., Nakazzi F., Katabazi F.A., Kigozi E., Ssengooba W., Nakiyingi L., Namiiro S., Okwera A., Joloba M.L. , Muwonge A.",Sputum microbiota profiles of treatment-naïve TB patients in Uganda before and during first-line therapy,Scientific reports,2021,NA,Experiment 2,Uganda,Homo sapiens,Sputum,UBERON:0007311,Pulmonary tuberculosis,EFO:1000049,Baseline (pre-treatment),Month 2 and Month 5 follow-up,Sputum collected at 2 months (end of intensive phase) and 5 months (end of therapy) of first-line anti-TB regimen,106,44,NA,16S,34,Illumina,relative abundances,"ANOVA,Kruskall-Wallis,Mixed-Effects Regression,PERMANOVA,T-Test",0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:34980006/1/1,34980006,case-control,34980006,10.1186/s12885-021-09074-y,NA,"Esposito M.V., Fosso B., Nunziato M., Casaburi G., D'Argenio V., Calabrese A., D'Aiuto M., Botti G., Pesole G. , Salvatore F.","Microbiome composition indicate dysbiosis and lower richness in tumor breast tissues compared to healthy adjacent paired tissue, within the same women",BMC cancer,2022,"16S rRNA, Breast cancer microbiome, Breast cancer tissues, Breast healthy tissues, Microbial dysbiosis, Microbiome composition, Next generation sequencing, cancer/healthy paired samples",Experiment 1,Italy,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,healthy adjacent paired tissue (H),tumor breast tissue (T),Tumor breast tissue sample from women with unilateral breast cancer,34,34,NA,16S,456,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 3,10 June 2025,Ecsharp,Ecsharp,Taxa that differ significantly between healthy adjacent paired tissue and tumor breast tissue samples,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas brenneri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella sp. S2",3379134|1224|28211;3379134|1224|1236|72274|135621|286|129817;3379134|1224|1236|2887326|468|475|985266,Complete,NA
bsdb:34980006/1/2,34980006,case-control,34980006,10.1186/s12885-021-09074-y,NA,"Esposito M.V., Fosso B., Nunziato M., Casaburi G., D'Argenio V., Calabrese A., D'Aiuto M., Botti G., Pesole G. , Salvatore F.","Microbiome composition indicate dysbiosis and lower richness in tumor breast tissues compared to healthy adjacent paired tissue, within the same women",BMC cancer,2022,"16S rRNA, Breast cancer microbiome, Breast cancer tissues, Breast healthy tissues, Microbial dysbiosis, Microbiome composition, Next generation sequencing, cancer/healthy paired samples",Experiment 1,Italy,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,healthy adjacent paired tissue (H),tumor breast tissue (T),Tumor breast tissue sample from women with unilateral breast cancer,34,34,NA,16S,456,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 3,10 June 2025,Ecsharp,Ecsharp,Taxa that differ significantly between healthy adjacent paired tissue and tumor breast tissue samples,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax|s__Variovorax sp. WO3,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. PS9(2007),k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium sp. enrichment culture clone MRHull-FeSM-11E,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. IMER-A2-21,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata",1783272|201174|1760|85009;3379134|1224|1236|135624;1783272|1239|909932|909929;1783272|201174|1760|85009|31957;3379134|1224|1236|135624|84642;1783272|201174|1760|85009|31957|1743;3379134|1224|1236|135624|84642|642;3379134|1224|28216|80840|80864|34072|507807;3379134|1224|1236|72274|135621|286|469558;1783272|201174|1760|85009|31957|1743|1344436;3379134|1224|1236|72274|135621|286|575311;3379134|1224|28216|206351|481|482|495,Complete,NA
bsdb:34996812/1/1,34996812,case-control,34996812,https://doi.org/10.1136/jitc-2021-003069,https://jitc.bmj.com/content/10/1/e003069,"Liu B., Zhou Z., Jin Y., Lu J., Feng D., Peng R., Sun H., Mu X., Li C. , Chen Y.",Hepatic stellate cell activation and senescence induced by intrahepatic microbiota disturbances drive progression of liver cirrhosis toward hepatocellular carcinoma,Journal for immunotherapy of cancer,2022,"biomarkers, inflammation, tumor, tumor microenvironment",Experiment 1,China,Homo sapiens,Liver,UBERON:0002107,Hepatocellular carcinoma,EFO:0000182,Normal liver tissue; control (N),Hepatocellular carcinoma tumor tissue (T),Intrahepatic liver tissue samples obtained directly from the malignant hepatocellular carcinoma (HCC) tumor lesion in patients with HCC.,33,46,Recent antibiotics use,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"age,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 3A and B,1 November 2025,Adiba Patel,Adiba Patel,Linear discriminant analysis of Effect Size (Lefse) analysis identified differentially abundant taxa between Hepatocellular carcinoma tumor tissue (T) and Normal liver tissue (N) (T vs N),increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae",1783272|1239|91061|186826|81852|1350;3379134|1224|28211|356|69277|28100;1783272|1239;1783272|1239|91061;1783272|1239|91061|186826;1783272|1239|91061|186826|81852,Complete,NA
bsdb:34996812/1/2,34996812,case-control,34996812,https://doi.org/10.1136/jitc-2021-003069,https://jitc.bmj.com/content/10/1/e003069,"Liu B., Zhou Z., Jin Y., Lu J., Feng D., Peng R., Sun H., Mu X., Li C. , Chen Y.",Hepatic stellate cell activation and senescence induced by intrahepatic microbiota disturbances drive progression of liver cirrhosis toward hepatocellular carcinoma,Journal for immunotherapy of cancer,2022,"biomarkers, inflammation, tumor, tumor microenvironment",Experiment 1,China,Homo sapiens,Liver,UBERON:0002107,Hepatocellular carcinoma,EFO:0000182,Normal liver tissue; control (N),Hepatocellular carcinoma tumor tissue (T),Intrahepatic liver tissue samples obtained directly from the malignant hepatocellular carcinoma (HCC) tumor lesion in patients with HCC.,33,46,Recent antibiotics use,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"age,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Figure 3A and B,1 November 2025,Adiba Patel,Adiba Patel,Linear discriminant analysis of Effect Size (Lefse) analysis identified differentially abundant taxa between Hepatocellular carcinoma tumor tissue (T) and Normal liver tissue (N) (T vs N),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|1236;3379134|1224|1236|72274;3379134|1224|28211|204455;3379134|976|117743|200644;3379134|1224|28211;3379134|1224|28211|204455|31989;3379134|1224,Complete,NA
bsdb:34996812/2/1,34996812,case-control,34996812,https://doi.org/10.1136/jitc-2021-003069,https://jitc.bmj.com/content/10/1/e003069,"Liu B., Zhou Z., Jin Y., Lu J., Feng D., Peng R., Sun H., Mu X., Li C. , Chen Y.",Hepatic stellate cell activation and senescence induced by intrahepatic microbiota disturbances drive progression of liver cirrhosis toward hepatocellular carcinoma,Journal for immunotherapy of cancer,2022,"biomarkers, inflammation, tumor, tumor microenvironment",Experiment 2,China,Homo sapiens,Liver,UBERON:0002107,Hepatocellular carcinoma,EFO:0000182,Normal adjacent tissue (NA),Hepatocellular carcinoma tumor tissue (T),Intrahepatic liver tissue samples obtained directly from the malignant hepatocellular carcinoma (HCC) tumor lesion in patients with HCC,28,46,Recent antibiotics use,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Figure 3A and B,1 November 2025,Adiba Patel,Adiba Patel,Linear discriminant analysis of Effect Size (Lefse) analysis identified differentially abundant taxa between Hepatocellular carcinoma tumor tissue (T) and Normal adjacent tissue (NA) (T vs NA),increased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801;1783272|1239|186801|186802;3379134|976;3379134|976|200643;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958;1783272|1239|186801|186802|216572,Complete,NA
bsdb:34996812/2/2,34996812,case-control,34996812,https://doi.org/10.1136/jitc-2021-003069,https://jitc.bmj.com/content/10/1/e003069,"Liu B., Zhou Z., Jin Y., Lu J., Feng D., Peng R., Sun H., Mu X., Li C. , Chen Y.",Hepatic stellate cell activation and senescence induced by intrahepatic microbiota disturbances drive progression of liver cirrhosis toward hepatocellular carcinoma,Journal for immunotherapy of cancer,2022,"biomarkers, inflammation, tumor, tumor microenvironment",Experiment 2,China,Homo sapiens,Liver,UBERON:0002107,Hepatocellular carcinoma,EFO:0000182,Normal adjacent tissue (NA),Hepatocellular carcinoma tumor tissue (T),Intrahepatic liver tissue samples obtained directly from the malignant hepatocellular carcinoma (HCC) tumor lesion in patients with HCC,28,46,Recent antibiotics use,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,Figure 3A and B,1 November 2025,Adiba Patel,Adiba Patel,Linear discriminant analysis of Effect Size (Lefse) analysis identified differentially abundant taxa between Hepatocellular carcinoma tumor tissue (T) and Normal adjacent tissue (NA) (T vs NA),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kosakonia|s__Kosakonia oryzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kosakonia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus durans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales",3379134|1224|1236|91347|543|1330547|497725;3379134|1224|1236|91347|543|1330547;1783272|1239|91061|186826|81852|1350|53345;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|81852;3379134|1224|28211|356|69277|28100;3379134|1224|1236;3379134|1224;3379134|1224|28211|356,Complete,NA
bsdb:34996812/3/1,34996812,case-control,34996812,https://doi.org/10.1136/jitc-2021-003069,https://jitc.bmj.com/content/10/1/e003069,"Liu B., Zhou Z., Jin Y., Lu J., Feng D., Peng R., Sun H., Mu X., Li C. , Chen Y.",Hepatic stellate cell activation and senescence induced by intrahepatic microbiota disturbances drive progression of liver cirrhosis toward hepatocellular carcinoma,Journal for immunotherapy of cancer,2022,"biomarkers, inflammation, tumor, tumor microenvironment",Experiment 3,China,Homo sapiens,Liver,UBERON:0002107,Hepatocellular carcinoma,EFO:0000182,Normal liver tissue; control (N),Hepatocellular carcinoma tumor tissue (T),Intrahepatic liver tissue samples obtained directly from the malignant hepatocellular carcinoma (HCC) tumor lesion in patients with HCC.,33,46,Recent antibiotics use,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"Figure 3D, Figure S4A-D, Table S4",1 November 2025,Adiba Patel,"Adiba Patel,Firdaws","Mann–Whitney U (Wilcoxon) test of different bacteria between Hepatocellular carcinoma tumor tissue (T) and Normal liver tissue (N) in the phylum, class, order, family, genus and species levels (T vs N)",increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus durans,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas leidyi,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",1783272|1239|91061;1783272|1117;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|81852|1350|53345;3379134|1224|28211|356;1783272|1239|91061|186826;3379134|1224|1236|135614|32033;3379134|1224|1236|135614;1783272|1239|91061|1385|186822;3379134|1224|28211|356|69277|28100;3379134|1224|28211|356|82115;3379134|1224|28211|204457|41297|13687|68569;3379134|1224|1236|135614|32033|40323,Complete,NA
bsdb:34996812/3/2,34996812,case-control,34996812,https://doi.org/10.1136/jitc-2021-003069,https://jitc.bmj.com/content/10/1/e003069,"Liu B., Zhou Z., Jin Y., Lu J., Feng D., Peng R., Sun H., Mu X., Li C. , Chen Y.",Hepatic stellate cell activation and senescence induced by intrahepatic microbiota disturbances drive progression of liver cirrhosis toward hepatocellular carcinoma,Journal for immunotherapy of cancer,2022,"biomarkers, inflammation, tumor, tumor microenvironment",Experiment 3,China,Homo sapiens,Liver,UBERON:0002107,Hepatocellular carcinoma,EFO:0000182,Normal liver tissue; control (N),Hepatocellular carcinoma tumor tissue (T),Intrahepatic liver tissue samples obtained directly from the malignant hepatocellular carcinoma (HCC) tumor lesion in patients with HCC.,33,46,Recent antibiotics use,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 2,"Figure 3D, Figure S4A-D, Table S4",1 November 2025,Adiba Patel,Adiba Patel,"Mann–Whitney U (Wilcoxon) test of different bacteria between Hepatocellular carcinoma tumor tissue (T) and Normal liver tissue (N) in the order, family and genus levels (T vs N)",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",3379134|1224|1236|2887326|468|469;3379134|1224|1236|2887326|468;3379134|1224|1236|72274;1783272|1239|186801|186802,Complete,NA
bsdb:34996812/4/1,34996812,case-control,34996812,https://doi.org/10.1136/jitc-2021-003069,https://jitc.bmj.com/content/10/1/e003069,"Liu B., Zhou Z., Jin Y., Lu J., Feng D., Peng R., Sun H., Mu X., Li C. , Chen Y.",Hepatic stellate cell activation and senescence induced by intrahepatic microbiota disturbances drive progression of liver cirrhosis toward hepatocellular carcinoma,Journal for immunotherapy of cancer,2022,"biomarkers, inflammation, tumor, tumor microenvironment",Experiment 4,China,Homo sapiens,Liver,UBERON:0002107,Hepatocellular carcinoma,EFO:0000182,Normal adjacent tissue (NA),Hepatocellular carcinoma tumor tissue (T),Intrahepatic liver tissue samples obtained directly from the malignant hepatocellular carcinoma (HCC) tumor lesion in patients with HCC,28,46,Recent antibiotics use,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,"Figure 3E, Supplementary Figure S4A-D and Supplementary Table 4",27 January 2026,Firdaws,Firdaws,"Mann–Whitney U (Wilcoxon) test of different bacteria between Hepatocellular carcinoma tumor tissue (T) and Normal adjacent tissue (NA) in the phylum, class, order, family and genus levels (T vs NA)",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia",3379134|976|200643;3379134|976;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572;1783272|1239|186801|3082720|186804|1501226,Complete,NA
bsdb:34996812/4/2,34996812,case-control,34996812,https://doi.org/10.1136/jitc-2021-003069,https://jitc.bmj.com/content/10/1/e003069,"Liu B., Zhou Z., Jin Y., Lu J., Feng D., Peng R., Sun H., Mu X., Li C. , Chen Y.",Hepatic stellate cell activation and senescence induced by intrahepatic microbiota disturbances drive progression of liver cirrhosis toward hepatocellular carcinoma,Journal for immunotherapy of cancer,2022,"biomarkers, inflammation, tumor, tumor microenvironment",Experiment 4,China,Homo sapiens,Liver,UBERON:0002107,Hepatocellular carcinoma,EFO:0000182,Normal adjacent tissue (NA),Hepatocellular carcinoma tumor tissue (T),Intrahepatic liver tissue samples obtained directly from the malignant hepatocellular carcinoma (HCC) tumor lesion in patients with HCC,28,46,Recent antibiotics use,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,"Figure 3E, Supplementary Figure S4A-D and Supplementary Table 4",27 January 2026,Firdaws,Firdaws,"Mann–Whitney U (Wilcoxon) test of different bacteria between Hepatocellular carcinoma tumor tissue (T) and Normal adjacent tissue (NA) in the phylum, class, family and genus levels (T vs NA)",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota",1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;3379134|1224|1236;3379134|1224,Complete,NA
bsdb:34996812/5/1,34996812,case-control,34996812,https://doi.org/10.1136/jitc-2021-003069,https://jitc.bmj.com/content/10/1/e003069,"Liu B., Zhou Z., Jin Y., Lu J., Feng D., Peng R., Sun H., Mu X., Li C. , Chen Y.",Hepatic stellate cell activation and senescence induced by intrahepatic microbiota disturbances drive progression of liver cirrhosis toward hepatocellular carcinoma,Journal for immunotherapy of cancer,2022,"biomarkers, inflammation, tumor, tumor microenvironment",Experiment 5,China,Homo sapiens,Liver,UBERON:0002107,Cirrhosis of liver,EFO:0001422,Non-cirrhosis in Hepatocellular carcinoma (HCC) patients,Cirrhosis in Hepatocellular carcinoma (HCC) patients,Hepatocellular carcinoma (HCC) patients with cirrhosis.,26,20,Recent antibiotics use,16S,4,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4G and 4H,27 January 2026,Firdaws,Firdaws,Unpaired Student’s t-test was performed to assess differences between patients with liver cirrhosis and those without cirrhosis.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",1783272|1239|91061|186826|33958|1578;3379134|1224|1236|135614|32033|40323,Complete,NA
bsdb:34996812/6/1,34996812,case-control,34996812,https://doi.org/10.1136/jitc-2021-003069,https://jitc.bmj.com/content/10/1/e003069,"Liu B., Zhou Z., Jin Y., Lu J., Feng D., Peng R., Sun H., Mu X., Li C. , Chen Y.",Hepatic stellate cell activation and senescence induced by intrahepatic microbiota disturbances drive progression of liver cirrhosis toward hepatocellular carcinoma,Journal for immunotherapy of cancer,2022,"biomarkers, inflammation, tumor, tumor microenvironment",Experiment 6,China,Homo sapiens,Liver,UBERON:0002107,Hepatocellular carcinoma,EFO:0000182,Normal liver tissue; control (N),Hepatocellular carcinoma tumor tissue (T),Intrahepatic liver tissue samples obtained directly from the malignant hepatocellular carcinoma (HCC) tumor lesion in patients with HCC in the independent cohort.,14,33,Recent antibiotics use,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Supplementary Figure 4E,27 January 2026,Firdaws,Firdaws,Mann–Whitney U-test of different bacteria between Hepatocellular carcinoma tumor tissue (T) and Normal liver tissue (N) in independent cohort (T vs N),increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia",1783272|1239|91061|186826|81852|1350;3379134|1224|28211|356|69277|28100;3379134|1224|1236|135614|32033|40323|40324,Complete,NA
bsdb:34996812/7/1,34996812,case-control,34996812,https://doi.org/10.1136/jitc-2021-003069,https://jitc.bmj.com/content/10/1/e003069,"Liu B., Zhou Z., Jin Y., Lu J., Feng D., Peng R., Sun H., Mu X., Li C. , Chen Y.",Hepatic stellate cell activation and senescence induced by intrahepatic microbiota disturbances drive progression of liver cirrhosis toward hepatocellular carcinoma,Journal for immunotherapy of cancer,2022,"biomarkers, inflammation, tumor, tumor microenvironment",Experiment 7,China,Homo sapiens,Liver,UBERON:0002107,Hepatocellular carcinoma,EFO:0000182,Normal adjacent tissue (NA),Hepatocellular carcinoma tumor tissue (T),Intrahepatic liver tissue samples obtained directly from the malignant hepatocellular carcinoma (HCC) tumor lesion in patients with HCC in the independent cohort.,27,33,Recent antibiotics use,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Supplementary Figure 4E,27 January 2026,Firdaws,Firdaws,Mann–Whitney U-test of different bacteria between Hepatocellular carcinoma tumor tissue (T) and Normal adjacent tissue (NA) in independent cohort (T vs NA).,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia",1783272|1239|91061|186826|81852|1350;1783272|1239|186801|3082720|186804|1501226,Complete,NA
bsdb:35003794/1/1,35003794,case-control,35003794,https://doi.org/10.1016/j.jare.2021.04.001,https://pmc.ncbi.nlm.nih.gov/articles/PMC8721249/,"Yu X., Jiang W., Kosik R.O., Song Y., Luo Q., Qiao T., Tong J., Liu S., Deng C., Qin S., Lv Z. , Li D.",Gut microbiota changes and its potential relations with thyroid carcinoma,Journal of advanced research,2022,"16S rRNA gene sequencing, Gut microbiota, Stool biomarkers, Thyroid carcinoma",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Thyroid carcinoma,EFO:0002892,Healthy controls (HCs),Thyroid carcinoma patients (TCs),Patients clinically diagnosed with thyroid cancer within six months and were planning to undergo total thyroidectomy.,60,60,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,"age,body mass index,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 2k,8 December 2025,Shiber256,"Shiber256,Firdaws","Linear discriminant analysis Effect Size (LEfSe) analysis identified the microbes at the phylum, family and genus level whose abundances significantly differed between the Thyroid Carcinoma (TC) and Healthy Control (HC) groups.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803;3379134|1224,Complete,KateRasheed
bsdb:35003794/1/2,35003794,case-control,35003794,https://doi.org/10.1016/j.jare.2021.04.001,https://pmc.ncbi.nlm.nih.gov/articles/PMC8721249/,"Yu X., Jiang W., Kosik R.O., Song Y., Luo Q., Qiao T., Tong J., Liu S., Deng C., Qin S., Lv Z. , Li D.",Gut microbiota changes and its potential relations with thyroid carcinoma,Journal of advanced research,2022,"16S rRNA gene sequencing, Gut microbiota, Stool biomarkers, Thyroid carcinoma",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Thyroid carcinoma,EFO:0002892,Healthy controls (HCs),Thyroid carcinoma patients (TCs),Patients clinically diagnosed with thyroid cancer within six months and were planning to undergo total thyroidectomy.,60,60,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,"age,body mass index,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Figure 2k,8 December 2025,Shiber256,"Shiber256,Firdaws","Linear discriminant analysis Effect Size (LEfSe) analysis identified the microbes at the phylum, family and genus level whose abundances significantly differed between the Thyroid Carcinoma (TC) and Healthy Control (HC) groups.",decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",1783272|201174;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171552;1783272|1239|186801|186802|216572|292632,Complete,KateRasheed
bsdb:35003794/2/1,35003794,case-control,35003794,https://doi.org/10.1016/j.jare.2021.04.001,https://pmc.ncbi.nlm.nih.gov/articles/PMC8721249/,"Yu X., Jiang W., Kosik R.O., Song Y., Luo Q., Qiao T., Tong J., Liu S., Deng C., Qin S., Lv Z. , Li D.",Gut microbiota changes and its potential relations with thyroid carcinoma,Journal of advanced research,2022,"16S rRNA gene sequencing, Gut microbiota, Stool biomarkers, Thyroid carcinoma",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Lymph node metastatic carcinoma,EFO:0004906,N0 (without lymph node metastasis group),N1 (local lymph node metastasis group),Thyroid carcinoma patients with the presence of local lymph node metastasis.,34,56,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,body mass index,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4a,10 December 2025,Shiber256,Shiber256,Linear discriminant analysis Effect Size (LEfSe) analysis identified the genera whose abundances significantly differed between the Thyroid Carcinoma patients (TC) N0 and Thyroid Carcinoma patients (TC) N1 subgroups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",3379134|976|200643|171549|171550|239759;3384189|32066|203490|203491|203492|848;1783272|1239|909932|909929|1843491|158846,Complete,KateRasheed
bsdb:35003794/2/2,35003794,case-control,35003794,https://doi.org/10.1016/j.jare.2021.04.001,https://pmc.ncbi.nlm.nih.gov/articles/PMC8721249/,"Yu X., Jiang W., Kosik R.O., Song Y., Luo Q., Qiao T., Tong J., Liu S., Deng C., Qin S., Lv Z. , Li D.",Gut microbiota changes and its potential relations with thyroid carcinoma,Journal of advanced research,2022,"16S rRNA gene sequencing, Gut microbiota, Stool biomarkers, Thyroid carcinoma",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Lymph node metastatic carcinoma,EFO:0004906,N0 (without lymph node metastasis group),N1 (local lymph node metastasis group),Thyroid carcinoma patients with the presence of local lymph node metastasis.,34,56,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,body mass index,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4a,10 December 2025,Shiber256,Shiber256,Linear discriminant analysis Effect Size (LEfSe) analysis identified the genera whose abundances significantly differed between the Thyroid Carcinoma patients (TC) N0 and Thyroid Carcinoma patients (TC) N1 subgroups.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|3085636|186803|1506553;1783272|1239|909932|1843488|909930|33024;3379134|1224|1236|91347|543|1940338,Complete,KateRasheed
bsdb:35003794/3/1,35003794,case-control,35003794,https://doi.org/10.1016/j.jare.2021.04.001,https://pmc.ncbi.nlm.nih.gov/articles/PMC8721249/,"Yu X., Jiang W., Kosik R.O., Song Y., Luo Q., Qiao T., Tong J., Liu S., Deng C., Qin S., Lv Z. , Li D.",Gut microbiota changes and its potential relations with thyroid carcinoma,Journal of advanced research,2022,"16S rRNA gene sequencing, Gut microbiota, Stool biomarkers, Thyroid carcinoma",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Thyroid carcinoma,EFO:0002892,Type 2 and Type 3,Type 1,The cluster with the greater number amongst the three types in the healthy control (HC) group after analysis on the unweighted UniFrac distance.,NA,NA,2 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.001,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2j,12 December 2025,Shiber256,"Shiber256,Firdaws","The Kruskal-Wallis H test comparing the microbial differences on the phylum level across the three types (Type 1, 2 and 3)",decreased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,KateRasheed
bsdb:35017199/1/1,35017199,"laboratory experiment,time series / longitudinal observational",35017199,10.1136/gutjnl-2021-326269,NA,"Chen C., Liao J., Xia Y., Liu X., Jones R., Haran J., McCormick B., Sampson T.R., Alam A. , Ye K.",Gut microbiota regulate Alzheimer's disease pathologies and cognitive disorders via PUFA-associated neuroinflammation,Gut,2022,brain/gut interaction,Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healthy control FMT mice,Alzheimer's disease FMT mice,ex germ-free mice inoculated with fecal samples from human Alzheimer's disease donors,3,3,1 month,16S,4,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,9 March 2024,Graycepaul,"Graycepaul,Welile,Folakunmi,WikiWorks","Microbiome analysis in humanised ex-germ-free 3xTg mouse stool, revealing the significant abundance in the faeces from human AD fecal inoculated germ-free mice and faeces from healthy human inoculated germ-free mice",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens",3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|329854;3379134|976|200643|171549|815|816|371601,Complete,Folakunmi
bsdb:35017199/1/2,35017199,"laboratory experiment,time series / longitudinal observational",35017199,10.1136/gutjnl-2021-326269,NA,"Chen C., Liao J., Xia Y., Liu X., Jones R., Haran J., McCormick B., Sampson T.R., Alam A. , Ye K.",Gut microbiota regulate Alzheimer's disease pathologies and cognitive disorders via PUFA-associated neuroinflammation,Gut,2022,brain/gut interaction,Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healthy control FMT mice,Alzheimer's disease FMT mice,ex germ-free mice inoculated with fecal samples from human Alzheimer's disease donors,3,3,1 month,16S,4,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5,9 March 2024,Graycepaul,"Graycepaul,Welile,Muqtadirat,Folakunmi,WikiWorks","Microbiome analysis in humanised ex-germ-free 3xTg mouse stool, revealing the significant abundance in the faeces from human AD fecal inoculated germ-free mice and faeces from healthy human inoculated germ-free mice",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii",1783272|1239|186801|3085636|186803|2719313|208479;3379134|976|200643|171549|2005525|375288|328812,Complete,Folakunmi
bsdb:35019769/1/1,35019769,randomized controlled trial,35019769,10.1128/spectrum.01757-21,https://pubmed.ncbi.nlm.nih.gov/35019769/,"Plummer E.L., Maddaford K., Murray G.L., Fairley C.K., Pasricha S., Mu A., Bradshaw C.S., Williamson D.A. , Chow E.P.F.",The Impact of Mouthwash on the Oropharyngeal Microbiota of Men Who Have Sex with Men: a Substudy of the OMEGA Trial,Microbiology spectrum,2022,"Neisseria gonorrhoeae, men who have sex with men, mouthwash, oral microbiome, oropharyngeal gonorrhea",Experiment 1,Australia,Homo sapiens,Tonsillar fossa,UBERON:0035228,Gonorrhea,DOID:7551,Men who have sex with men using Biotène - 0 weeks,Men who have sex with men using Biotène - 12 weeks,"Men who have sex with men using Biotène - 12 weeks refers to those using Biotène mouthwash at 12 weeks, as a treatment for Gonorrhea",75,75,NA,16S,4,Illumina,centered log-ratio,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Fig. 3b,18 March 2024,Uhabiba14,"Uhabiba14,KateRasheed,WikiWorks",Boxplots showing the center-log ratio (CLR) transformed relative abundance of bacteria that were differentially abundant following 12 weeks of mouthwash use with Biotène using ALDEx2 (Wilcoxon),decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3384189|32066|203490|203491|1129771|32067;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:35019769/2/1,35019769,randomized controlled trial,35019769,10.1128/spectrum.01757-21,https://pubmed.ncbi.nlm.nih.gov/35019769/,"Plummer E.L., Maddaford K., Murray G.L., Fairley C.K., Pasricha S., Mu A., Bradshaw C.S., Williamson D.A. , Chow E.P.F.",The Impact of Mouthwash on the Oropharyngeal Microbiota of Men Who Have Sex with Men: a Substudy of the OMEGA Trial,Microbiology spectrum,2022,"Neisseria gonorrhoeae, men who have sex with men, mouthwash, oral microbiome, oropharyngeal gonorrhea",Experiment 2,Australia,Homo sapiens,Tonsillar fossa,UBERON:0035228,Gonorrhea,DOID:7551,Men who have sex with men using Biotène - 0 weeks,Men who have sex with men using Biotène - 12 weeks,"Men who have sex with men using Biotène - 12 weeks refers to those using Biotène mouthwash at 12 weeks, as a treatment for Gonorrhea",75,75,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"In-text of ""Effect of mouthwash on the composition of the oropharyngeal microbiota""",3 February 2025,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant following 12 weeks of mouthwash use with Biotène using ANCOM,decreased,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,3384189|32066|203490|203491|1129771|34104,Complete,Svetlana up
bsdb:35035709/1/1,35035709,case-control,35035709,NA,https://pubmed.ncbi.nlm.nih.gov/35035709/,"Chen W., Bi Z., Zhu Q., Gao H., Fan Y., Zhang C., Liu X. , Ye M.",An analysis of the characteristics of the intestinal flora in patients with Parkinson's disease complicated with constipation,American journal of translational research,2021,"16S rRNA sequencing, Parkinson’s disease (PD), constipation, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls and Parkinson's Disease patients with constipation,Parkinson's Disease patients without constipation,The PD patients were all screened from the outpatients and inpatients in the Department of Neurology and their Wexner scores (evaluation of constipation severity) were collected. Patients diagnosed with idiopathic PD by a neurologist according to the revised PD diagnostic criteria published by the International Movement Disorders Association in 2015.,30,14,3 months,16S,45,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 1G,21 May 2023,Jacquelynshevin,"Jacquelynshevin,WikiWorks",Difference contribution analysis chart,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella parvirubra,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Kiloniellaceae|g__Candidatus Kopriimonas|s__uncultured Kopriimonas sp.",3379134|1224|28216|80840|995019|40544|437898;3379134|1224|28211|204441|597359|343331|1221381,Complete,Atrayees
bsdb:35035709/2/1,35035709,case-control,35035709,NA,https://pubmed.ncbi.nlm.nih.gov/35035709/,"Chen W., Bi Z., Zhu Q., Gao H., Fan Y., Zhang C., Liu X. , Ye M.",An analysis of the characteristics of the intestinal flora in patients with Parkinson's disease complicated with constipation,American journal of translational research,2021,"16S rRNA sequencing, Parkinson’s disease (PD), constipation, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson's Disease patients without constipation and Parkinson's Disease patients with constipation,The PD patients were all screened from the outpatients and inpatients in the Department of Neurology and their Wexner scores (evaluation of constipation severity) were collected. Patients diagnosed with idiopathic PD by a neurologist according to the revised PD diagnostic criteria published by the International Movement Disorders Association in 2015.,15,29,3 months,16S,45,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 1G,21 May 2023,Jacquelynshevin,"Jacquelynshevin,WikiWorks",Difference contribution analysis chart,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter",3379134|976|200643|171549|815|909656|204516;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|1407607,Complete,Atrayees
bsdb:35035709/3/1,35035709,case-control,35035709,NA,https://pubmed.ncbi.nlm.nih.gov/35035709/,"Chen W., Bi Z., Zhu Q., Gao H., Fan Y., Zhang C., Liu X. , Ye M.",An analysis of the characteristics of the intestinal flora in patients with Parkinson's disease complicated with constipation,American journal of translational research,2021,"16S rRNA sequencing, Parkinson’s disease (PD), constipation, gut microbiota",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls and Parkinson's Disease patients without constipation,Parkinson's Disease patients with constipation,The PD patients were all screened from the outpatients and inpatients in the Department of Neurology and their Wexner scores (evaluation of constipation severity) were collected. Patients diagnosed with idiopathic PD by a neurologist according to the revised PD diagnostic criteria published by the International Movement Disorders Association in 2015.,29,15,3 months,16S,45,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 1G,21 May 2023,Jacquelynshevin,"Jacquelynshevin,WikiWorks",Difference contribution analysis chart,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp. 4_3_54A2FAA,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",1783272|201174;1783272|1239|186801|186802|216572|2485925;1783272|1239|186801|186802|216572|292632|665956;1783272|201174|84998;1783272|201174|84998|84999;1783272|201174|84998|84999|84107;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|1649459;1783272|1239|91061|186826;1783272|1239|91061;1783272|1239|91061|186826|1300,Complete,Atrayees
bsdb:35035709/4/1,35035709,case-control,35035709,NA,https://pubmed.ncbi.nlm.nih.gov/35035709/,"Chen W., Bi Z., Zhu Q., Gao H., Fan Y., Zhang C., Liu X. , Ye M.",An analysis of the characteristics of the intestinal flora in patients with Parkinson's disease complicated with constipation,American journal of translational research,2021,"16S rRNA sequencing, Parkinson’s disease (PD), constipation, gut microbiota",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Parkinson's Disease patients without constipation,Parkinson's Disease patients with constipation,The PD patients were all screened from the outpatients and inpatients in the Department of Neurology and their Wexner scores (evaluation of constipation severity) were collected. Patients diagnosed with idiopathic PD by a neurologist according to the revised PD diagnostic criteria published by the International Movement Disorders Association in 2015.,14,15,3 months,16S,45,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 2H,21 May 2023,Jacquelynshevin,"Jacquelynshevin,WikiWorks",Difference contribution analysis chart.,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales",1783272|1239|526524|526525|128827|1573535;1783272|1239|909932|909929|1843491|158846;3379134|976|200643|171549|171552|2974265|363265;3379134|1224|28211|204441|41295;3379134|1224|28211|204441,Complete,Atrayees
bsdb:35035709/4/2,35035709,case-control,35035709,NA,https://pubmed.ncbi.nlm.nih.gov/35035709/,"Chen W., Bi Z., Zhu Q., Gao H., Fan Y., Zhang C., Liu X. , Ye M.",An analysis of the characteristics of the intestinal flora in patients with Parkinson's disease complicated with constipation,American journal of translational research,2021,"16S rRNA sequencing, Parkinson’s disease (PD), constipation, gut microbiota",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Parkinson's Disease patients without constipation,Parkinson's Disease patients with constipation,The PD patients were all screened from the outpatients and inpatients in the Department of Neurology and their Wexner scores (evaluation of constipation severity) were collected. Patients diagnosed with idiopathic PD by a neurologist according to the revised PD diagnostic criteria published by the International Movement Disorders Association in 2015.,14,15,3 months,16S,45,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 2H,21 May 2023,Jacquelynshevin,"Jacquelynshevin,WikiWorks",Difference contribution analysis chart.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp. 4_3_54A2FAA,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius",1783272|1239|186801|186802|216572|244127;1783272|1239|91061;1783272|1239|186801|3085636|186803|1649459;1783272|1239|91061|186826;1783272|1239|186801|186802|216572|2485925;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|292632|665956;1783272|1239|91061|186826|1300|1301|1304,Complete,Atrayees
bsdb:35039079/1/1,35039079,"cross-sectional observational, not case-control",35039079,10.1186/s40168-021-01204-9,NA,"Adu-Oppong B., Thänert R., Wallace M.A., Burnham C.D. , Dantas G.",Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states,Microbiome,2022,"Clinical diagnostics, Dysbiosis, Genitourinary microbiome, Urinary tract infections",Experiment 1,United States of America,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,No Growth,Culture Positive,Patients with urine specimen with significant growth of 1–2 uropathogenic species at ≥10^5 colony forming units (CFU)/mL,51,48,2 weeks,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Fig 3 and Result Text (under ""Diagnostic categories reflect different states of urobiome health, paragraph 2"")",6 March 2024,MyleeeA,"MyleeeA,Folakunmi,WikiWorks",Significantly enriched microbiota in suspected Urinary Tract Infection specimens from different clinical categories.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae",3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|543|570|571;3379134|1224|1236|91347|543|570|573,Complete,Folakunmi
bsdb:35039079/1/2,35039079,"cross-sectional observational, not case-control",35039079,10.1186/s40168-021-01204-9,NA,"Adu-Oppong B., Thänert R., Wallace M.A., Burnham C.D. , Dantas G.",Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states,Microbiome,2022,"Clinical diagnostics, Dysbiosis, Genitourinary microbiome, Urinary tract infections",Experiment 1,United States of America,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,No Growth,Culture Positive,Patients with urine specimen with significant growth of 1–2 uropathogenic species at ≥10^5 colony forming units (CFU)/mL,51,48,2 weeks,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Fig 3 and Result Text (under ""Diagnostic categories reflect different states of urobiome health, paragraph 2"")",6 March 2024,MyleeeA,"MyleeeA,Folakunmi,WikiWorks",Significantly enriched microbiota in suspected Urinary Tract Infection specimens from different clinical categories.,decreased,"k__Fungi|p__Ascomycota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes",4751|4890;1783272|201174|1760|85009|31957|1912216|1747,Complete,Folakunmi
bsdb:35039079/2/1,35039079,"cross-sectional observational, not case-control",35039079,10.1186/s40168-021-01204-9,NA,"Adu-Oppong B., Thänert R., Wallace M.A., Burnham C.D. , Dantas G.",Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states,Microbiome,2022,"Clinical diagnostics, Dysbiosis, Genitourinary microbiome, Urinary tract infections",Experiment 2,United States of America,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,Insignificant Samples,Culture Positive Samples,Patients with urine specimen with significant growth of 1–2 uropathogenic species at ≥10^5 colony forming units (CFU)/mL,17,48,2 weeks,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Fig 3 and Result Text (under ""Diagnostic categories reflect different states of urobiome health, paragraph 2"")",6 March 2024,MyleeeA,"MyleeeA,Folakunmi,WikiWorks",Significantly enriched microbiota in suspected Urinary Tract Infection specimens from different clinical categories.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,3379134|1224|1236|91347|543|570|573,Complete,Folakunmi
bsdb:35039079/2/2,35039079,"cross-sectional observational, not case-control",35039079,10.1186/s40168-021-01204-9,NA,"Adu-Oppong B., Thänert R., Wallace M.A., Burnham C.D. , Dantas G.",Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states,Microbiome,2022,"Clinical diagnostics, Dysbiosis, Genitourinary microbiome, Urinary tract infections",Experiment 2,United States of America,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,Insignificant Samples,Culture Positive Samples,Patients with urine specimen with significant growth of 1–2 uropathogenic species at ≥10^5 colony forming units (CFU)/mL,17,48,2 weeks,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Fig 3 and Result Text (under ""Diagnostic categories reflect different states of urobiome health, paragraph 2"")",6 March 2024,MyleeeA,"MyleeeA,Folakunmi,WikiWorks",Significantly enriched microbiota in suspected Urinary Tract Infection specimens from different clinical categories.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",3379134|976|200643|171549|815|816|28116;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Folakunmi
bsdb:35039079/3/1,35039079,"cross-sectional observational, not case-control",35039079,10.1186/s40168-021-01204-9,NA,"Adu-Oppong B., Thänert R., Wallace M.A., Burnham C.D. , Dantas G.",Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states,Microbiome,2022,"Clinical diagnostics, Dysbiosis, Genitourinary microbiome, Urinary tract infections",Experiment 3,United States of America,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,Asymptomatic,Insignificant Samples,Patients with specimen with bacterial growth <10^5 CFU/mL present during culturing but below the threshold for significance,10,17,2 weeks,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig 3,6 March 2024,MyleeeA,"MyleeeA,WikiWorks",Significantly enriched microbiota in suspected Urinary Tract Infections specimens from different clinical categories.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,1783272|1239|91061|1385|90964|1279|1280,Complete,Folakunmi
bsdb:35039079/4/1,35039079,"cross-sectional observational, not case-control",35039079,10.1186/s40168-021-01204-9,NA,"Adu-Oppong B., Thänert R., Wallace M.A., Burnham C.D. , Dantas G.",Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states,Microbiome,2022,"Clinical diagnostics, Dysbiosis, Genitourinary microbiome, Urinary tract infections",Experiment 4,United States of America,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,Asymptomatic,No Growth,Patients with urine samples with no visible Microorganism growth (Bacterial/Fungal),10,51,2 weeks,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig 3 and Table S3,6 March 2024,MyleeeA,"MyleeeA,WikiWorks",LefSe enrichment results; Significantly enriched microbiota in suspected Urinary Tract Infection specimens from different clinical categories.,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,1783272|201174|1760|85009|31957|1912216|1747,Complete,Folakunmi
bsdb:35039079/4/2,35039079,"cross-sectional observational, not case-control",35039079,10.1186/s40168-021-01204-9,NA,"Adu-Oppong B., Thänert R., Wallace M.A., Burnham C.D. , Dantas G.",Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states,Microbiome,2022,"Clinical diagnostics, Dysbiosis, Genitourinary microbiome, Urinary tract infections",Experiment 4,United States of America,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,Asymptomatic,No Growth,Patients with urine samples with no visible Microorganism growth (Bacterial/Fungal),10,51,2 weeks,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig 3 and Table S3,6 March 2024,MyleeeA,"MyleeeA,WikiWorks",LefSe enrichment results; Significantly enriched microbiota in suspected Urinary Tract Infection specimens from different clinical categories.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp.,1783272|1239|186801|186802|216572|292632|2053618,Complete,Folakunmi
bsdb:35069544/1/1,35069544,case-control,35069544,10.3389/fimmu.2021.771136,NA,"Yuan Y., Wang C., Wang G., Guo X., Jiang S., Zuo X., Wang X., Hsu A.C., Qi M. , Wang F.",Airway Microbiome and Serum Metabolomics Analysis Identify Differential Candidate Biomarkers in Allergic Rhinitis,Frontiers in immunology,2021,"allergic rhinitis, biomarkers, metabolomics, microbiome, multiomics",Experiment 1,China,Homo sapiens,Inferior nasal concha,UBERON:0005922,Allergic rhinitis,EFO:0005854,healthy controls (HC),Allergic rhinitis (AR),Patients with allergic rhinitis (AR),15,28,NA,16S,34,Ion Torrent,relative abundances,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,NA,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 3. C, D.",30 March 2024,Ayibatari,"Omojokunoluwatomisin,Ayibatari,WikiWorks",The distribution of taxa in phylum and genus levels of AR and HC groups. (C) the statistical results of top 10 phyla. (D) the statistical results of top 35 genera.,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacillati|p__Cyanobacteriota|s__uncultured cyanobacterium",1783272|201174;1783272|1239;3379134|976|200643;3379134|1224|28216|80840|80864|80865;1783272|1239|1737404|1737405|1570339|150022;3379134|1224|1236|91347|543|570;3379134|976|200643|171549|171552|838;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|135623|641|662;1783272|1117|1211,Complete,Svetlana up
bsdb:35069544/1/2,35069544,case-control,35069544,10.3389/fimmu.2021.771136,NA,"Yuan Y., Wang C., Wang G., Guo X., Jiang S., Zuo X., Wang X., Hsu A.C., Qi M. , Wang F.",Airway Microbiome and Serum Metabolomics Analysis Identify Differential Candidate Biomarkers in Allergic Rhinitis,Frontiers in immunology,2021,"allergic rhinitis, biomarkers, metabolomics, microbiome, multiomics",Experiment 1,China,Homo sapiens,Inferior nasal concha,UBERON:0005922,Allergic rhinitis,EFO:0005854,healthy controls (HC),Allergic rhinitis (AR),Patients with allergic rhinitis (AR),15,28,NA,16S,34,Ion Torrent,relative abundances,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,NA,unchanged,unchanged,NA,unchanged,Signature 2,Figure 3 D.,30 March 2024,Ayibatari,"Ayibatari,Svetlana up,WikiWorks",The distribution of taxa in phylum and genus levels of AR and HC groups. (D) the statistical results of top 35 genera.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles,3379134|1224|28216|80840|2975441|93681,Complete,Svetlana up
bsdb:35071858/1/1,35071858,"cross-sectional observational, not case-control",35071858,10.1021/acsomega.1c02120,NA,"Yang H.T., Xiu W.J., Liu J.K., Yang Y., Zhang Y.J., Zheng Y.Y., Wu T.T., Hou X.G., Wu C.X., Ma Y.T. , Xie X.",Characteristics of the Intestinal Microorganisms in Middle-Aged and Elderly Patients: Effects of Smoking,ACS omega,2022,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Smoking status measurement,EFO:0006527,Non- smokers,Current Smokers,Patients who smoke,114,74,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,Figure 6B,3 April 2025,Montana-D,"Montana-D,Joiejoie",Comparison of intestinal microbiota composition between smokers and non-smokers.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella",3379134|976|200643|171549|171552|577309;1783272|1239|909932|909929|1843491|158846;3379134|1224|28216|80840|995019|40544;3379134|1224|28216|80840|506;3379134|1224|28216|80840|119060|32008;3379134|1224|28216|80840|119060;3379134|1224|1236|91347|543|620,Complete,Svetlana up
bsdb:35071858/1/2,35071858,"cross-sectional observational, not case-control",35071858,10.1021/acsomega.1c02120,NA,"Yang H.T., Xiu W.J., Liu J.K., Yang Y., Zhang Y.J., Zheng Y.Y., Wu T.T., Hou X.G., Wu C.X., Ma Y.T. , Xie X.",Characteristics of the Intestinal Microorganisms in Middle-Aged and Elderly Patients: Effects of Smoking,ACS omega,2022,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Smoking status measurement,EFO:0006527,Non- smokers,Current Smokers,Patients who smoke,114,74,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 2,Figure 6B,3 April 2025,Montana-D,"Montana-D,Joiejoie",Comparison of intestinal microbiota composition between smokers and non-smokers.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales",1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|526524|526525|2810280|100883;1783272|201174|1760|85006|85023;3379134|29547|3031852|213849,Complete,Svetlana up
bsdb:35071858/2/1,35071858,"cross-sectional observational, not case-control",35071858,10.1021/acsomega.1c02120,NA,"Yang H.T., Xiu W.J., Liu J.K., Yang Y., Zhang Y.J., Zheng Y.Y., Wu T.T., Hou X.G., Wu C.X., Ma Y.T. , Xie X.",Characteristics of the Intestinal Microorganisms in Middle-Aged and Elderly Patients: Effects of Smoking,ACS omega,2022,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Fasting blood glucose measurement,EFO:0004465,Low FBG (Low Fasting blood glucose),High FBG (High Fasting blood glucose),"This group includes patients with elevated FBG levels, prediabetes ( 100 to 125 mg/dL ) and  diabetes (5.6 to 6.9 mmol/L)",NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7,3 April 2025,Montana-D,"Montana-D,Joiejoie",Differential abundant bacteria in the high FBG( High Fasting blood glucose),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|1224|1236|91347|543|620;3379134|1224|28216|80840|995019|40544,Complete,Svetlana up
bsdb:35071858/2/2,35071858,"cross-sectional observational, not case-control",35071858,10.1021/acsomega.1c02120,NA,"Yang H.T., Xiu W.J., Liu J.K., Yang Y., Zhang Y.J., Zheng Y.Y., Wu T.T., Hou X.G., Wu C.X., Ma Y.T. , Xie X.",Characteristics of the Intestinal Microorganisms in Middle-Aged and Elderly Patients: Effects of Smoking,ACS omega,2022,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Fasting blood glucose measurement,EFO:0004465,Low FBG (Low Fasting blood glucose),High FBG (High Fasting blood glucose),"This group includes patients with elevated FBG levels, prediabetes ( 100 to 125 mg/dL ) and  diabetes (5.6 to 6.9 mmol/L)",NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 7,3 April 2025,Montana-D,"Montana-D,Joiejoie",Differential abundant bacteria in the high FBG( High Fasting blood glucose),decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Svetlana up
bsdb:35071858/3/1,35071858,"cross-sectional observational, not case-control",35071858,10.1021/acsomega.1c02120,NA,"Yang H.T., Xiu W.J., Liu J.K., Yang Y., Zhang Y.J., Zheng Y.Y., Wu T.T., Hou X.G., Wu C.X., Ma Y.T. , Xie X.",Characteristics of the Intestinal Microorganisms in Middle-Aged and Elderly Patients: Effects of Smoking,ACS omega,2022,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Creatinine,CHEBI:16737,Low Cr(Creatinine),High Cr(Creatinine),This group includes patients with Creatinine levels > 1.4 mg/dL,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 7,4 April 2025,Joiejoie,Joiejoie,The representative differential bacteria for the clinical indicator Creatinine,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,3379134|1224|28216|80840|995019|40544,Complete,Svetlana up
bsdb:35071858/4/1,35071858,"cross-sectional observational, not case-control",35071858,10.1021/acsomega.1c02120,NA,"Yang H.T., Xiu W.J., Liu J.K., Yang Y., Zhang Y.J., Zheng Y.Y., Wu T.T., Hou X.G., Wu C.X., Ma Y.T. , Xie X.",Characteristics of the Intestinal Microorganisms in Middle-Aged and Elderly Patients: Effects of Smoking,ACS omega,2022,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Body mass index,EFO:0004340,Low BMI(Body Mass Index),High- BMI(Body Mass Index),This group includes Individuals who presented with a high Body Mass Index threshold.,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 7,4 April 2025,Joiejoie,Joiejoie,The representative differential bacteria for the clinical indicator body mass indicator (BMI),decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,3379134|976|200643|171549|171552|577309,Complete,Svetlana up
bsdb:35071858/5/1,35071858,"cross-sectional observational, not case-control",35071858,10.1021/acsomega.1c02120,NA,"Yang H.T., Xiu W.J., Liu J.K., Yang Y., Zhang Y.J., Zheng Y.Y., Wu T.T., Hou X.G., Wu C.X., Ma Y.T. , Xie X.",Characteristics of the Intestinal Microorganisms in Middle-Aged and Elderly Patients: Effects of Smoking,ACS omega,2022,NA,Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Gamma-glutamyl transpeptidase deficiency,NA,Low GGT(Gamma Glutamyl Transpeptidase),High- GGT(Gamma Glutamyl Transpeptidase),Individuals who presented with a high Gamma Glutamyl Transpeptidase,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7,4 April 2025,Montana-D,Montana-D,Differential abundance of bacteria between Low and High GGT(Gamma Glutamyl Transpeptidase) patients,increased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,3379134|1224|28216|80840|119060|32008,Complete,Svetlana up
bsdb:35071858/6/1,35071858,"cross-sectional observational, not case-control",35071858,10.1021/acsomega.1c02120,NA,"Yang H.T., Xiu W.J., Liu J.K., Yang Y., Zhang Y.J., Zheng Y.Y., Wu T.T., Hou X.G., Wu C.X., Ma Y.T. , Xie X.",Characteristics of the Intestinal Microorganisms in Middle-Aged and Elderly Patients: Effects of Smoking,ACS omega,2022,NA,Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Uric acid,NA,Low UA(Uric Acid),High- UA(Uric Acid),Individuals who presented with a high levels of Uric Acid,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7,4 April 2025,Montana-D,Montana-D,Differential abundance of bacteria between Low and High UA(Uric Acid) patients,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella",1783272|201174|1760|85004|31953|1678;3379134|1224|1236|91347|543|620,Complete,Svetlana up
bsdb:35071858/7/1,35071858,"cross-sectional observational, not case-control",35071858,10.1021/acsomega.1c02120,NA,"Yang H.T., Xiu W.J., Liu J.K., Yang Y., Zhang Y.J., Zheng Y.Y., Wu T.T., Hou X.G., Wu C.X., Ma Y.T. , Xie X.",Characteristics of the Intestinal Microorganisms in Middle-Aged and Elderly Patients: Effects of Smoking,ACS omega,2022,NA,Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Bilirubin,CHEBI:16990,Low TBIL(Total Bilirubin),High- TBIL(Total Bilirubin),Individuals who presented with a high levels of Total Bilirubin,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7,4 April 2025,Montana-D,"Montana-D,Joiejoie",Differential abundance of bacteria between Low and High TBIL(Total Bilirubin) patients,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Svetlana up
bsdb:35073343/1/1,35073343,case-control,35073343,https://doi.org/10.1371/journal.pone.0262806,NA,"Burton M., Krumbeck J.A., Wu G., Tang S., Prem A., Gupta A.K. , Dawson T.L.",The adult microbiome of healthy and otitis patients: Definition of the core healthy and diseased ear microbiomes,PloS one,2022,NA,Experiment 1,United States of America,Homo sapiens,Ear,UBERON:0001690,"Otitis media,Otitis externa","EFO:0004992,EFO:0009560",Healthy group,Otitis media and otitis externa,Adults patients affected by otitis externa (OE) and otitis media (OM),92,70,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 3A,30 May 2024,Scholastica,"Scholastica,WikiWorks",Taxa significantly different in healthy versus otitis externa (OE) and otitis media (OM) groups at the phylum to genus level for bacteria.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli",1783272|201174|1760|85009|31957;1783272|201174|1760|85009;1783272|201174;1783272|1239|91061|1385|90964;1783272|1239|91061|1385;1783272|1239|91061|186826|186828;1783272|1239|91061,Complete,Svetlana up
bsdb:35073343/2/1,35073343,case-control,35073343,https://doi.org/10.1371/journal.pone.0262806,NA,"Burton M., Krumbeck J.A., Wu G., Tang S., Prem A., Gupta A.K. , Dawson T.L.",The adult microbiome of healthy and otitis patients: Definition of the core healthy and diseased ear microbiomes,PloS one,2022,NA,Experiment 2,United States of America,Homo sapiens,Ear,UBERON:0001690,"Otitis externa,Otitis media","EFO:0009560,EFO:0004992",Healthy and Otitis media,Otitis externa,Adults patients affected by otitis externa (OE),140,22,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 3A,30 May 2024,Scholastica,"Scholastica,WikiWorks",Taxa significantly different in healthy and otitis media (OM) versus otitis externa (OE) groups at the phylum to genus level for bacteria.,increased,"k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Chroococcidiopsidales|f__Chroococcidiopsidaceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Chroococcidiopsidales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria",1783272|1117|3028117|1890505|1890528;1783272|1117|3028117|1890505;3379134|1224|1236|91347|543;3379134|1224|1236|91347;3379134|1224|1236|72274|135621;3379134|1224|1236|72274;3379134|1224|1236,Complete,Svetlana up
bsdb:35073343/3/1,35073343,case-control,35073343,https://doi.org/10.1371/journal.pone.0262806,NA,"Burton M., Krumbeck J.A., Wu G., Tang S., Prem A., Gupta A.K. , Dawson T.L.",The adult microbiome of healthy and otitis patients: Definition of the core healthy and diseased ear microbiomes,PloS one,2022,NA,Experiment 3,United States of America,Homo sapiens,Ear,UBERON:0001690,"Otitis externa,Otitis media","EFO:0009560,EFO:0004992",Healthy and Otitis externa,Otitis media,Adults patients affected by otitis media (OM),114,48,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 3A,30 May 2024,Scholastica,"Scholastica,WikiWorks",Taxa significantly different in healthy and otitis externa (OE) versus otitis media (OM) groups at the phylum to genus level for bacteria.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales,k__Bacillati|p__Bacillota|c__Tissierellia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae",1783272|1239|91061|186826|81852;1783272|1239|1737404|1737405|1570339;1783272|1239|1737404|1737405;1783272|1239|1737404;3379134|1224|28216|80840|506;3379134|29547|3031852|213849|72294;3379134|29547|3031852|213849;3379134|29547|3031852;3379134|1224|1236|91347|1903411,Complete,Svetlana up
bsdb:35073343/4/1,35073343,case-control,35073343,https://doi.org/10.1371/journal.pone.0262806,NA,"Burton M., Krumbeck J.A., Wu G., Tang S., Prem A., Gupta A.K. , Dawson T.L.",The adult microbiome of healthy and otitis patients: Definition of the core healthy and diseased ear microbiomes,PloS one,2022,NA,Experiment 4,United States of America,Homo sapiens,Ear,UBERON:0001690,"Otitis media,Otitis externa","EFO:0004992,EFO:0009560",Healthy group,Otitis media and otitis externa,Adults patients affected by otitis externa (OE) and otitis media (OM),92,70,NA,ITS / ITS2,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Fig. 3B,30 May 2024,Scholastica,"Scholastica,WikiWorks",Taxa significantly different in healthy versus otitis externa (OE) and otitis media (OM) groups at the phylum to genus level for fungi.,decreased,"k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales,k__Fungi|p__Basidiomycota|c__Malasseziomycetes,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae",4751|5204|1538075|162474;4751|5204|1538075;4751|5204|1538075|162474|742845,Complete,Svetlana up
bsdb:35073343/5/1,35073343,case-control,35073343,https://doi.org/10.1371/journal.pone.0262806,NA,"Burton M., Krumbeck J.A., Wu G., Tang S., Prem A., Gupta A.K. , Dawson T.L.",The adult microbiome of healthy and otitis patients: Definition of the core healthy and diseased ear microbiomes,PloS one,2022,NA,Experiment 5,United States of America,Homo sapiens,Ear,UBERON:0001690,"Otitis externa,Otitis media","EFO:0009560,EFO:0004992",Healthy and Otitis media,Otitis externa,Adults patients affected by otitis externa (OE),140,22,NA,ITS / ITS2,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 3B,30 May 2024,Scholastica,"Scholastica,WikiWorks",Taxa significantly different in healthy and otitis media (OM) versus otitis externa (OE) groups at the phylum to genus level for fungi.,increased,"k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales,k__Fungi|p__Ascomycota|c__Eurotiomycetes,k__Fungi|p__Ascomycota|c__Sordariomycetes,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Hymenochaetales,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Polyporales,k__Fungi|p__Basidiomycota|c__Agaricomycetes,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales,k__Fungi|p__Basidiomycota|c__Tremellomycetes",4751|4890|147545|5042|1131492;4751|4890|147545|5042;4751|4890|147545;4751|4890|147550;4751|5204|155619|139380;4751|5204|155619|5303;4751|5204|155619;4751|5204|155616|5234;4751|5204|155616,Complete,Svetlana up
bsdb:35073343/6/1,35073343,case-control,35073343,https://doi.org/10.1371/journal.pone.0262806,NA,"Burton M., Krumbeck J.A., Wu G., Tang S., Prem A., Gupta A.K. , Dawson T.L.",The adult microbiome of healthy and otitis patients: Definition of the core healthy and diseased ear microbiomes,PloS one,2022,NA,Experiment 6,United States of America,Homo sapiens,Ear,UBERON:0001690,"Otitis externa,Otitis media","EFO:0009560,EFO:0004992",Healthy and Otitis externa,Otitis media,Adults patients affected by otitis media (OM),114,48,NA,ITS / ITS2,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Fig. 3B,30 May 2024,Scholastica,"Scholastica,WikiWorks",Taxa significantly different in healthy and otitis externa (OE) versus otitis media (OM) groups at the phylum to genus level for fungi.,increased,"k__Fungi|p__Ascomycota|c__Dothideomycetes,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales,k__Fungi|p__Ascomycota|c__Saccharomycetes,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales|f__Stereaceae,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Filobasidiales|f__Filobasidiaceae",4751|4890|147541;4751|4890|3239874|2916678|766764;4751|4890|4891|4892;4751|4890|4891;4751|5204|155619|452342|103376;4751|5204|155619|452342;4751|5204|155616|90883;4751|5204|155616|90886|5408,Complete,Svetlana up
bsdb:35076270/1/1,35076270,laboratory experiment,35076270,https://doi.org/10.1128/msystems.01191-21,NA,"van Kessel S.P., Bullock A., van Dijk G. , El Aidy S.",Parkinson's Disease Medication Alters Small Intestinal Motility and Microbiota Composition in Healthy Rats,mSystems,2022,"Parkinson’s disease treatment, dopamine, drug side effects, gut motility, levodopa, microbiota, pramipexole, ropinirole, small intestinal bacterial overgrowth",Experiment 1,Netherlands,Rattus norvegicus,Jejunum,UBERON:0002115,Treatment,EFO:0000727,Vehicle group (VH),Dopamine treatment group (D),Jejunal samples from rats treated for 14 sequential days with dopamine (D),6,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.01,TRUE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Supplementary Table S1,9 March 2024,Adeitan,"Adeitan,Scholastica,WikiWorks",Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant taxa in the vehicle group (VH) versus dopamine treatment group (D),increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Pantoea agglomerans",1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|1903409|53335|549,Complete,Svetlana up
bsdb:35076270/1/2,35076270,laboratory experiment,35076270,https://doi.org/10.1128/msystems.01191-21,NA,"van Kessel S.P., Bullock A., van Dijk G. , El Aidy S.",Parkinson's Disease Medication Alters Small Intestinal Motility and Microbiota Composition in Healthy Rats,mSystems,2022,"Parkinson’s disease treatment, dopamine, drug side effects, gut motility, levodopa, microbiota, pramipexole, ropinirole, small intestinal bacterial overgrowth",Experiment 1,Netherlands,Rattus norvegicus,Jejunum,UBERON:0002115,Treatment,EFO:0000727,Vehicle group (VH),Dopamine treatment group (D),Jejunal samples from rats treated for 14 sequential days with dopamine (D),6,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.01,TRUE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Supplementary Table S1,9 March 2024,Adeitan,"Adeitan,Welile,Scholastica,WikiWorks",Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant taxa in the vehicle group (VH) versus dopamine treatment group (D),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter cholecystus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Ileibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__uncultured Bacteroidales bacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|s__uncultured Coriobacteriales bacterium",1783272|1239|186801|3085636|186803|572511;1783272|1239|526524|526525|128827;3379134|29547|3031852|213849|72293|209;3379134|29547|3031852|213849|72293|209|45498;1783272|1239|526524|526525|128827|1937007;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|877420;3379134|976|200643|171549|2005473;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|171552;3379134|976|200643|171549|194843;1783272|201174|84998|84999|349920,Complete,Svetlana up
bsdb:35076270/2/1,35076270,laboratory experiment,35076270,https://doi.org/10.1128/msystems.01191-21,NA,"van Kessel S.P., Bullock A., van Dijk G. , El Aidy S.",Parkinson's Disease Medication Alters Small Intestinal Motility and Microbiota Composition in Healthy Rats,mSystems,2022,"Parkinson’s disease treatment, dopamine, drug side effects, gut motility, levodopa, microbiota, pramipexole, ropinirole, small intestinal bacterial overgrowth",Experiment 2,Netherlands,Rattus norvegicus,Jejunum,UBERON:0002115,Treatment,EFO:0000727,Vehicle group (VH),Pramipexole treatment group (P),"Jejunal samples from rats treated for 14 sequential days with pramipexole (P, in combination with levodopa-carbidopa)",6,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.01,TRUE,2,NA,NA,NA,NA,increased,NA,NA,NA,Signature 1,Supplementary Table S1,7 April 2024,Scholastica,"Scholastica,WikiWorks","Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant taxa in the vehicle group (VH) versus pramipexole (P, in combination with levodopa-carbidopa) treatment group",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium elkanii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Ectobacillus|s__Ectobacillus funiculus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Intrasporangium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Neobacillus|s__Neobacillus drentensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Pantoea agglomerans,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Priestia|s__Priestia aryabhattai,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Pseudoduganella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Rummeliibacillus,k__Bacillati|p__Actinomycetota|c__Thermoleophilia|o__Solirubrobacterales|f__Solirubrobacteraceae|g__Solirubrobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae|g__Tumebacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|s__uncultured Alphaproteobacteria bacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Frankiales|s__uncultured Frankiales bacterium",3379134|1224|28211|356|41294|374|29448;1783272|1239|91061|1385|186817|2837502|137993;1783272|201174|1760|85006|85021|53357;1783272|1239|91061|1385|186817|400634;1783272|201174|1760|85006|85023|33882;1783272|201174|1760|85006|1268;1783272|201174|1760|85007|1762|1763;1783272|1239|91061|1385|186817|2675232|220684;3379134|1224|1236|91347|1903409|53335|549;1783272|1239|91061|1385|186817|2800373|412384;3379134|1224|28216|80840|75682|1522432;1783272|1239|91061|1385|186818|648802;1783272|201174|1497346|588673|320599|207599;1783272|201174|1760|85011|2062|1883;1783272|1239|91061|1385|186823|432330;3379134|1224|28211|91750;1783272|201174|1760|85013|2735681,Complete,Svetlana up
bsdb:35076270/2/2,35076270,laboratory experiment,35076270,https://doi.org/10.1128/msystems.01191-21,NA,"van Kessel S.P., Bullock A., van Dijk G. , El Aidy S.",Parkinson's Disease Medication Alters Small Intestinal Motility and Microbiota Composition in Healthy Rats,mSystems,2022,"Parkinson’s disease treatment, dopamine, drug side effects, gut motility, levodopa, microbiota, pramipexole, ropinirole, small intestinal bacterial overgrowth",Experiment 2,Netherlands,Rattus norvegicus,Jejunum,UBERON:0002115,Treatment,EFO:0000727,Vehicle group (VH),Pramipexole treatment group (P),"Jejunal samples from rats treated for 14 sequential days with pramipexole (P, in combination with levodopa-carbidopa)",6,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.01,TRUE,2,NA,NA,NA,NA,increased,NA,NA,NA,Signature 2,Supplementary Table S1,8 April 2024,Scholastica,"Scholastica,WikiWorks","Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant taxa in the vehicle group (VH) versus pramipexole (P, in combination with levodopa-carbidopa) treatment group",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter cholecystus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas paucimobilis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sp. LA61,s__gut metagenome,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__uncultured Bacteroidales bacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__uncultured Desulfovibrionaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|s__uncultured Rhizobiaceae bacterium",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171552|1283313;1783272|1239|526524|526525|128827|1472649;1783272|1239|526524|526525|128827;3379134|29547|3031852|213849|72293|209;3379134|29547|3031852|213849|72293|209|45498;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|877420;1783272|1239|91061|186826;3379134|976|200643|171549|2005473;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|171552;1783272|1239|186801|3082720|186804|1501226;3379134|1224|28211|204457|41297|13687|13689;1783272|1239|526524|526525|2810281|191303|1197429;749906;3379134|976|200643|171549|194843;3379134|200940|3031449|213115|194924|194926;1783272|1239|186801|3085636|186803|297314;1783272|1239|186801|186802|216572|707003;3379134|1224|28211|356|82115|271151,Complete,Svetlana up
bsdb:35076270/3/1,35076270,laboratory experiment,35076270,https://doi.org/10.1128/msystems.01191-21,NA,"van Kessel S.P., Bullock A., van Dijk G. , El Aidy S.",Parkinson's Disease Medication Alters Small Intestinal Motility and Microbiota Composition in Healthy Rats,mSystems,2022,"Parkinson’s disease treatment, dopamine, drug side effects, gut motility, levodopa, microbiota, pramipexole, ropinirole, small intestinal bacterial overgrowth",Experiment 3,Netherlands,Rattus norvegicus,Jejunum,UBERON:0002115,Treatment,EFO:0000727,Vehicle group (VH),Ropinirole treatment group (R),"Jejunal samples from rats treated for 14 sequential days with ropinirole (R, in combination with levodopa-carbidopa)",6,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.01,TRUE,2,NA,NA,NA,NA,increased,NA,NA,NA,Signature 1,Supplementary Table S1,8 April 2024,Scholastica,"Scholastica,WikiWorks","Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant taxa in the vehicle group (VH) versus ropinirole (R, in combination with levodopa-carbidopa) treatment group",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__uncultured Bacteroidales bacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816|85831;1783272|201174|84998|1643822|1643826|580024;1783272|1239|526524|526525|128827;3379134|29547|3031852|213849|72293|209;3379134|976|200643|171549|2005473;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|194843;1783272|1239|526524|526525|128827|331630,Complete,Svetlana up
bsdb:35076270/4/1,35076270,laboratory experiment,35076270,https://doi.org/10.1128/msystems.01191-21,NA,"van Kessel S.P., Bullock A., van Dijk G. , El Aidy S.",Parkinson's Disease Medication Alters Small Intestinal Motility and Microbiota Composition in Healthy Rats,mSystems,2022,"Parkinson’s disease treatment, dopamine, drug side effects, gut motility, levodopa, microbiota, pramipexole, ropinirole, small intestinal bacterial overgrowth",Experiment 4,Netherlands,Rattus norvegicus,Ileum,UBERON:0002116,Treatment,EFO:0000727,Vehicle group (VH),Dopamine treatment group (D),Ileal samples from rats treated for 14 sequential days with dopamine (D),6,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.01,TRUE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Supplementary Table S1,8 April 2024,Scholastica,"Scholastica,WikiWorks",Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant taxa in the vehicle group (VH) versus dopamine treatment group (D),increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG_194_44_15,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,s__uncultured prokaryote",1783272|1239|526524|526525|128827|174708;1783272|1239|1897037;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|877420;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;198431,Complete,Svetlana up
bsdb:35076270/4/2,35076270,laboratory experiment,35076270,https://doi.org/10.1128/msystems.01191-21,NA,"van Kessel S.P., Bullock A., van Dijk G. , El Aidy S.",Parkinson's Disease Medication Alters Small Intestinal Motility and Microbiota Composition in Healthy Rats,mSystems,2022,"Parkinson’s disease treatment, dopamine, drug side effects, gut motility, levodopa, microbiota, pramipexole, ropinirole, small intestinal bacterial overgrowth",Experiment 4,Netherlands,Rattus norvegicus,Ileum,UBERON:0002116,Treatment,EFO:0000727,Vehicle group (VH),Dopamine treatment group (D),Ileal samples from rats treated for 14 sequential days with dopamine (D),6,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.01,TRUE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Supplementary Table S1,8 April 2024,Scholastica,"Scholastica,WikiWorks",Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant taxa in the vehicle group (VH) versus dopamine treatment group (D),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetitomaculum,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella|s__Dubosiella newyorkensis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 615,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium A2,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium MD335,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__uncultured Bacteroidales bacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|s__uncultured Desulfovibrionales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",1783272|1239|186801|3085636|186803|31980;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;3379134|200940|3031449|213115|194924|872;1783272|1239|526524|526525|128827|1937008|1862672;1783272|201174|84998|1643822|1643826|580024;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|1156038;1783272|1239|186801|3085636|186803|397290;1783272|1239|186801|3085636|186803|1235793;1783272|1239|186801|3085636|186803|877420;3379134|976|200643|171549|2005473;3379134|976|200643|171549|2005473|1918540;1783272|1239|186801|186802|216572|459786;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|815|909656|671267;3379134|976|200643|171549|171550;1783272|1239|186801|3085636|186803|841;3379134|976|200643|171549|194843;3379134|200940|3031449|213115|345727;1783272|1239|186801|3085636|186803|297314;1783272|1239|186801|186802|216572|707003,Complete,Svetlana up
bsdb:35076270/5/1,35076270,laboratory experiment,35076270,https://doi.org/10.1128/msystems.01191-21,NA,"van Kessel S.P., Bullock A., van Dijk G. , El Aidy S.",Parkinson's Disease Medication Alters Small Intestinal Motility and Microbiota Composition in Healthy Rats,mSystems,2022,"Parkinson’s disease treatment, dopamine, drug side effects, gut motility, levodopa, microbiota, pramipexole, ropinirole, small intestinal bacterial overgrowth",Experiment 5,Netherlands,Rattus norvegicus,Ileum,UBERON:0002116,Treatment,EFO:0000727,Vehicle group (VH),Pramipexole treatment group (P),"Ileal samples from rats treated for 14 sequential days with pramipexole (P, in combination with levodopa-carbidopa)",6,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.01,TRUE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Supplementary Table S1,9 April 2024,Scholastica,"Scholastica,WikiWorks","Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant taxa in the vehicle group (VH) versus pramipexole (P, in combination with levodopa-carbidopa) treatment group",increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG_194_44_15,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Ileibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,s__gut metagenome,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__uncultured Desulfovibrionaceae bacterium",1783272|1239|526524|526525|128827|174708;1783272|201174|1760|85004|31953|1678;1783272|1239|1897037;1783272|1239|526524|526525|128827|1937007;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|3068309;1783272|1239|186801|3085636|186803|1506577;749906;3379134|200940|3031449|213115|194924|194926,Complete,Svetlana up
bsdb:35076270/5/2,35076270,laboratory experiment,35076270,https://doi.org/10.1128/msystems.01191-21,NA,"van Kessel S.P., Bullock A., van Dijk G. , El Aidy S.",Parkinson's Disease Medication Alters Small Intestinal Motility and Microbiota Composition in Healthy Rats,mSystems,2022,"Parkinson’s disease treatment, dopamine, drug side effects, gut motility, levodopa, microbiota, pramipexole, ropinirole, small intestinal bacterial overgrowth",Experiment 5,Netherlands,Rattus norvegicus,Ileum,UBERON:0002116,Treatment,EFO:0000727,Vehicle group (VH),Pramipexole treatment group (P),"Ileal samples from rats treated for 14 sequential days with pramipexole (P, in combination with levodopa-carbidopa)",6,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.01,TRUE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Supplementary Table S1,9 April 2024,Scholastica,"Scholastica,WikiWorks","Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant taxa in the vehicle group (VH) versus pramipexole (P, in combination with levodopa-carbidopa) treatment group",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetitomaculum,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium sp. canine oral taxon 238,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella|s__Dubosiella newyorkensis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 615,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium A2,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium MD335,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__uncultured Bacteroidales bacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|s__uncultured Desulfovibrionales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|s__uncultured Peptococcaceae bacterium",1783272|1239|186801|3085636|186803|31980;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;3379134|1224|1236|135615|868|2717|1151525;3379134|200940|3031449|213115|194924|872;1783272|1239|526524|526525|128827|1937008|1862672;1783272|201174|84998|1643822|1643826|580024;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|1156038;1783272|1239|186801|3085636|186803|397290;1783272|1239|186801|3085636|186803|1235793;1783272|1239|186801|3085636|186803|877420;3379134|976|200643|171549|2005473;1783272|1239|186801|186802|216572|459786;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|815|909656|671267;3379134|976|200643|171549|171550|28138;3379134|976|200643|171549|171550;3379134|976|200643|171549|194843;3379134|200940|3031449|213115|345727;1783272|1239|186801|3085636|186803|297314;1783272|1239|186801|186802|186807|329911,Complete,Svetlana up
bsdb:35076270/6/1,35076270,laboratory experiment,35076270,https://doi.org/10.1128/msystems.01191-21,NA,"van Kessel S.P., Bullock A., van Dijk G. , El Aidy S.",Parkinson's Disease Medication Alters Small Intestinal Motility and Microbiota Composition in Healthy Rats,mSystems,2022,"Parkinson’s disease treatment, dopamine, drug side effects, gut motility, levodopa, microbiota, pramipexole, ropinirole, small intestinal bacterial overgrowth",Experiment 6,Netherlands,Rattus norvegicus,Ileum,UBERON:0002116,Treatment,EFO:0000727,Vehicle group (VH),Ropinirole treatment group (R),"Ileal samples from rats treated for 14 sequential days with ropinirole (R, in combination with levodopa-carbidopa)",6,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.01,TRUE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Supplementary Table S1,8 April 2024,Scholastica,"Scholastica,WikiWorks","Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant taxa in the vehicle group (VH) versus ropinirole (R, in combination with levodopa-carbidopa) treatment group",increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Ileibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|s__uncultured Erysipelotrichia bacterium",1783272|1239|526524|526525|128827|174708;1783272|1239|526524|526525|128827|1937007;1783272|1239|91061|186826|33958|1578;1783272|1239|526524|666559,Complete,Svetlana up
bsdb:35076270/6/2,35076270,laboratory experiment,35076270,https://doi.org/10.1128/msystems.01191-21,NA,"van Kessel S.P., Bullock A., van Dijk G. , El Aidy S.",Parkinson's Disease Medication Alters Small Intestinal Motility and Microbiota Composition in Healthy Rats,mSystems,2022,"Parkinson’s disease treatment, dopamine, drug side effects, gut motility, levodopa, microbiota, pramipexole, ropinirole, small intestinal bacterial overgrowth",Experiment 6,Netherlands,Rattus norvegicus,Ileum,UBERON:0002116,Treatment,EFO:0000727,Vehicle group (VH),Ropinirole treatment group (R),"Ileal samples from rats treated for 14 sequential days with ropinirole (R, in combination with levodopa-carbidopa)",6,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.01,TRUE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Supplementary Table S1,8 April 2024,Scholastica,"Scholastica,WikiWorks","Differential abundance analysis performed with LDA effect size (LEfSe) showing only significant taxa in the vehicle group (VH) versus ropinirole (R, in combination with levodopa-carbidopa) treatment group",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",1783272|1239|186801|3085636|186803|877420;3379134|976|200643|171549|2005473;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|297314,Complete,Svetlana up
bsdb:35083314/1/1,35083314,"cross-sectional observational, not case-control",35083314,10.1016/j.celrep.2021.109765,https://www.sciencedirect.com/science/article/pii/S2211124721012195,"Leite G., Pimentel M., Barlow G.M. , Mathur R.",The small bowel microbiome changes significantly with age and aspects of the ageing process,"Microbial cell (Graz, Austria)",2022,"age, aging, coliforms, concomitant diseases, medication use, proteobacteria, small intestinal microbiome",Experiment 1,United States of America,Homo sapiens,Small intestine,UBERON:0002108,Aging,GO:0007568,Group 1- youngest age group (18 to 35 years old),Group 4- oldest age group (66 to 80 years old. elderly people),This is the oldest age advanced group from the study,32,82,NA,16S,34,Illumina,relative abundances,PLS-DA (Partial least square discriminant analysis),1e-4,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,"Figure S6 + Results (text): Page 6, under sub-heading ""Microbiome differences are most pronounced between younger (group 1) and elderly (group 4) adults.""",19 October 2023,Davvve,"Davvve,ChiomaBlessing,WikiWorks",Variable importance in projection (VIP) selected during PLS-DA analysis of families in the duodenal microbiome of subjects in Groups 4 compared to Group 1.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",1783272|1239|186801|186802|31979;3379134|200940|3031449|213115|194924;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958;3379134|1224|1236|91347|543|561,Complete,ChiomaBlessing
bsdb:35083314/1/2,35083314,"cross-sectional observational, not case-control",35083314,10.1016/j.celrep.2021.109765,https://www.sciencedirect.com/science/article/pii/S2211124721012195,"Leite G., Pimentel M., Barlow G.M. , Mathur R.",The small bowel microbiome changes significantly with age and aspects of the ageing process,"Microbial cell (Graz, Austria)",2022,"age, aging, coliforms, concomitant diseases, medication use, proteobacteria, small intestinal microbiome",Experiment 1,United States of America,Homo sapiens,Small intestine,UBERON:0002108,Aging,GO:0007568,Group 1- youngest age group (18 to 35 years old),Group 4- oldest age group (66 to 80 years old. elderly people),This is the oldest age advanced group from the study,32,82,NA,16S,34,Illumina,relative abundances,PLS-DA (Partial least square discriminant analysis),1e-4,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Figure S6,30 January 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Variable importance in projection (VIP) selected during PLS-DA analysis of families in the duodenal microbiome of subjects in Groups 4 compared to Group 1.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",1783272|201174|1760|2037|2049;1783272|1239|91061|186826|186828;1783272|1239|526524|526525|128827;1783272|1239|186801|3085636|186803;3384189|32066|203490|203491|1129771;3379134|1224|1236|2887326|468;3379134|976|200643|171549|171552|577309;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171551;3379134|976|200643|171549|171552;3379134|1224|1236|72274|135621;3379134|203691|203692|136|137;1783272|1239|1737404|1737405|1737406;1783272|1239|186801|3082720|543314|86331;3379134|976|200643|171549|171552|577309,Complete,ChiomaBlessing
bsdb:35083314/2/1,35083314,"cross-sectional observational, not case-control",35083314,10.1016/j.celrep.2021.109765,https://www.sciencedirect.com/science/article/pii/S2211124721012195,"Leite G., Pimentel M., Barlow G.M. , Mathur R.",The small bowel microbiome changes significantly with age and aspects of the ageing process,"Microbial cell (Graz, Austria)",2022,"age, aging, coliforms, concomitant diseases, medication use, proteobacteria, small intestinal microbiome",Experiment 2,United States of America,Homo sapiens,Small intestine,UBERON:0002108,Aging,GO:0007568,Group 1- youngest age group (18 to 35 years old),"Group 2, 3 and 4 - older age groups (36 to 50 years old; 51 to 65 years old and 66 to 80 years old.)","These are the remaining 3 groups of subjects grouped according to advancing chronological age (N= 41, 36 to 50 years old; N= 96, 51 to 65 years old and N= 82, 66 to 80 years old).",32,219,NA,16S,34,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,Table S2,30 January 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks","Facultative and strict anaerobic genera in the duodenal microbiome of older subjects from groups 2, 3, and 4, when compared to group 1",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",3379134|1224|1236|135625|712|713;3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|561;1783272|1239|91061|186826|33958|1578,Complete,ChiomaBlessing
bsdb:35083314/2/2,35083314,"cross-sectional observational, not case-control",35083314,10.1016/j.celrep.2021.109765,https://www.sciencedirect.com/science/article/pii/S2211124721012195,"Leite G., Pimentel M., Barlow G.M. , Mathur R.",The small bowel microbiome changes significantly with age and aspects of the ageing process,"Microbial cell (Graz, Austria)",2022,"age, aging, coliforms, concomitant diseases, medication use, proteobacteria, small intestinal microbiome",Experiment 2,United States of America,Homo sapiens,Small intestine,UBERON:0002108,Aging,GO:0007568,Group 1- youngest age group (18 to 35 years old),"Group 2, 3 and 4 - older age groups (36 to 50 years old; 51 to 65 years old and 66 to 80 years old.)","These are the remaining 3 groups of subjects grouped according to advancing chronological age (N= 41, 36 to 50 years old; N= 96, 51 to 65 years old and N= 82, 66 to 80 years old).",32,219,NA,16S,34,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Table S2,30 January 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks","Facultative and strict anaerobic genera in the duodenal microbiome of older subjects from groups 2, 3, and 4, when compared to group 1",decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,3379134|1224|1236|135614|32033,Complete,ChiomaBlessing
bsdb:35087123/1/1,35087123,case-control,35087123,10.1038/s41598-022-05480-9,https://pubmed.ncbi.nlm.nih.gov/35087123/,"Domènech L., Willis J., Alemany-Navarro M., Morell M., Real E., Escaramís G., Bertolín S., Sánchez Chinchilla D., Balcells S., Segalàs C., Estivill X., Menchón J.M., Gabaldón T., Alonso P. , Rabionet R.",Changes in the stool and oropharyngeal microbiome in obsessive-compulsive disorder,Scientific reports,2022,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Obsessive-compulsive disorder,EFO:0004242,Control (healthy group),OCD T0 (Baseline),"Patients with Obsessive-compulsive disorder (OCD), which is a neuropsychiatric condition characterized by intrusive and unwanted thoughts (termed obsessions) and repetitive behaviors or mental acts (termed compulsions), which are carried out to at least partially alleviate the anxiety or distress brought on by the obsessions. Timepoint 0 was the baseline timepoint prior to three months of pharmacological treatment and cognitive behavioral therapy (referred to as T0).",33,32,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,unchanged,decreased,unchanged,unchanged,decreased,Signature 1,Figure 3A,24 March 2023,Kahvecirem,"Kahvecirem,Aiyshaaaa,Merit,Claregrieve1,WikiWorks",Differential microbial abundance in stool samples between controls and OCD patients at the T0 timepoint,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium",3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|2005519;3379134|976|200643|171549|2005519|1348911;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|171550;1783272|544448|31969;1783272|1239|186801|186802|216572|2485925,Complete,Claregrieve1
bsdb:35087123/1/2,35087123,case-control,35087123,10.1038/s41598-022-05480-9,https://pubmed.ncbi.nlm.nih.gov/35087123/,"Domènech L., Willis J., Alemany-Navarro M., Morell M., Real E., Escaramís G., Bertolín S., Sánchez Chinchilla D., Balcells S., Segalàs C., Estivill X., Menchón J.M., Gabaldón T., Alonso P. , Rabionet R.",Changes in the stool and oropharyngeal microbiome in obsessive-compulsive disorder,Scientific reports,2022,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Obsessive-compulsive disorder,EFO:0004242,Control (healthy group),OCD T0 (Baseline),"Patients with Obsessive-compulsive disorder (OCD), which is a neuropsychiatric condition characterized by intrusive and unwanted thoughts (termed obsessions) and repetitive behaviors or mental acts (termed compulsions), which are carried out to at least partially alleviate the anxiety or distress brought on by the obsessions. Timepoint 0 was the baseline timepoint prior to three months of pharmacological treatment and cognitive behavioral therapy (referred to as T0).",33,32,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,unchanged,decreased,unchanged,unchanged,decreased,Signature 2,Figure 3A,24 March 2023,Kahvecirem,"Kahvecirem,Merit,Claregrieve1,WikiWorks",Differential microbial abundance in stool samples between controls and OCD patients at the T0 timepoint,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|186802|3085642|580596;1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|33042;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|404402;1783272|1239|186801|3085636|186803|28050;1783272|1239|909932;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|171552;1783272|1239|186801|3082720|186804|1501226;1783272|1239|909932|909929;1783272|1239|909932|1843489|31977,Complete,Claregrieve1
bsdb:35087123/2/1,35087123,case-control,35087123,10.1038/s41598-022-05480-9,https://pubmed.ncbi.nlm.nih.gov/35087123/,"Domènech L., Willis J., Alemany-Navarro M., Morell M., Real E., Escaramís G., Bertolín S., Sánchez Chinchilla D., Balcells S., Segalàs C., Estivill X., Menchón J.M., Gabaldón T., Alonso P. , Rabionet R.",Changes in the stool and oropharyngeal microbiome in obsessive-compulsive disorder,Scientific reports,2022,NA,Experiment 2,Spain,Homo sapiens,Oropharynx,UBERON:0001729,Obsessive-compulsive disorder,EFO:0004242,Control (healthy group),OCD T0,"Patients with Obsessive-compulsive disorder (OCD), which is a neuropsychiatric condition characterized by intrusive and unwanted thoughts (termed obsessions) and repetitive behaviors or mental acts (termed compulsions), which are carried out to at least partially alleviate the anxiety or distress brought on by the obsessions. Timepoint 0 was the baseline timepoint prior to three months of pharmacological treatment and cognitive behavioral therapy (referred to as T0).",32,32,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 1,Figure 4A,24 March 2023,Kahvecirem,"Kahvecirem,Aiyshaaaa,Merit,Claregrieve1,WikiWorks",Differential microbial abundance in oropharyngeal samples between controls and T0 OCD patients,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp.",1783272|1239|186801|3085636|186803|265975;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037;1783272|201174|84998|84999|1643824;1783272|201174|84998|84999|1643824|1380;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|186801|3085636|186803|1164882;1783272|1239|186801|3085636|186803;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|3085636|186803|265975|1969407,Complete,Claregrieve1
bsdb:35087123/2/2,35087123,case-control,35087123,10.1038/s41598-022-05480-9,https://pubmed.ncbi.nlm.nih.gov/35087123/,"Domènech L., Willis J., Alemany-Navarro M., Morell M., Real E., Escaramís G., Bertolín S., Sánchez Chinchilla D., Balcells S., Segalàs C., Estivill X., Menchón J.M., Gabaldón T., Alonso P. , Rabionet R.",Changes in the stool and oropharyngeal microbiome in obsessive-compulsive disorder,Scientific reports,2022,NA,Experiment 2,Spain,Homo sapiens,Oropharynx,UBERON:0001729,Obsessive-compulsive disorder,EFO:0004242,Control (healthy group),OCD T0,"Patients with Obsessive-compulsive disorder (OCD), which is a neuropsychiatric condition characterized by intrusive and unwanted thoughts (termed obsessions) and repetitive behaviors or mental acts (termed compulsions), which are carried out to at least partially alleviate the anxiety or distress brought on by the obsessions. Timepoint 0 was the baseline timepoint prior to three months of pharmacological treatment and cognitive behavioral therapy (referred to as T0).",32,32,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 2,Figure 4A,24 March 2023,Kahvecirem,"Kahvecirem,Aiyshaaaa,Merit,Claregrieve1,WikiWorks",Differential microbial abundance in oropharyngeal samples between controls and T0 OCD patients,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|s__Peptostreptococcaceae bacterium",3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;1783272|1239|186801|3082720|186804|1904861,Complete,Claregrieve1
bsdb:35087123/3/1,35087123,case-control,35087123,10.1038/s41598-022-05480-9,https://pubmed.ncbi.nlm.nih.gov/35087123/,"Domènech L., Willis J., Alemany-Navarro M., Morell M., Real E., Escaramís G., Bertolín S., Sánchez Chinchilla D., Balcells S., Segalàs C., Estivill X., Menchón J.M., Gabaldón T., Alonso P. , Rabionet R.",Changes in the stool and oropharyngeal microbiome in obsessive-compulsive disorder,Scientific reports,2022,NA,Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Obsessive-compulsive disorder,EFO:0004242,Control (healthy group),OCD T3,"Patients with obsessive-compulsive disorder (OCD) which is a neuropsychiatric condition characterized by intrusive and unwanted thoughts (termed obsessions) and repetitive behaviors or mental acts (termed compulsions), which are carried out to at least partially alleviate the anxiety or distress brought on by the obsessions. Timepoint 3 is following three months of pharmacological treatment and cognitive behavioral therapy (referred to as T3).",33,31,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 1,Figure S4,29 March 2023,Kahvecirem,"Kahvecirem,Atrayees,Merit,Claregrieve1,WikiWorks",Differential microbial abundance in stool samples between controls and OCD patients at the T3 timepoint,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pygmaiobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|216572|244127;3379134|976|200643|171549|2005519;3379134|200940|3031449|213115|194924|35832;3379134|976|200643|171549|2005519|1348911;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|186802|216572|946234;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|1929305;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|1508657,Complete,Claregrieve1
bsdb:35087123/3/2,35087123,case-control,35087123,10.1038/s41598-022-05480-9,https://pubmed.ncbi.nlm.nih.gov/35087123/,"Domènech L., Willis J., Alemany-Navarro M., Morell M., Real E., Escaramís G., Bertolín S., Sánchez Chinchilla D., Balcells S., Segalàs C., Estivill X., Menchón J.M., Gabaldón T., Alonso P. , Rabionet R.",Changes in the stool and oropharyngeal microbiome in obsessive-compulsive disorder,Scientific reports,2022,NA,Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Obsessive-compulsive disorder,EFO:0004242,Control (healthy group),OCD T3,"Patients with obsessive-compulsive disorder (OCD) which is a neuropsychiatric condition characterized by intrusive and unwanted thoughts (termed obsessions) and repetitive behaviors or mental acts (termed compulsions), which are carried out to at least partially alleviate the anxiety or distress brought on by the obsessions. Timepoint 3 is following three months of pharmacological treatment and cognitive behavioral therapy (referred to as T3).",33,31,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 2,Figure S4,29 March 2023,Kahvecirem,"Kahvecirem,Merit,Claregrieve1,WikiWorks",Differential microbial abundance in stool samples between controls and OCD patients at the T3 timepoint,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3082720|186804|1505657;1783272|1239|186801|3085636|186803|28050|2049031;3379134|976|200643|171549|171552|577309;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171552;1783272|1239|186801|3082720|186804|1501226;1783272|1239|909932|1843489|31977,Complete,Claregrieve1
bsdb:35087123/4/1,35087123,case-control,35087123,10.1038/s41598-022-05480-9,https://pubmed.ncbi.nlm.nih.gov/35087123/,"Domènech L., Willis J., Alemany-Navarro M., Morell M., Real E., Escaramís G., Bertolín S., Sánchez Chinchilla D., Balcells S., Segalàs C., Estivill X., Menchón J.M., Gabaldón T., Alonso P. , Rabionet R.",Changes in the stool and oropharyngeal microbiome in obsessive-compulsive disorder,Scientific reports,2022,NA,Experiment 4,Spain,Homo sapiens,Oropharynx,UBERON:0001729,Obsessive-compulsive disorder,EFO:0004242,Control (healthy group),OCD T3,"Patients with obsessive-compulsive disorder (OCD) which is a neuropsychiatric condition characterized by intrusive and unwanted thoughts (termed obsessions) and repetitive behaviors or mental acts (termed compulsions), which are carried out to at least partially alleviate the anxiety or distress brought on by the obsessions. Timepoint 3 is following three months of pharmacological treatment and cognitive behavioral therapy (referred to as T3).",32,31,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 1,Figure S6,29 March 2023,Kahvecirem,"Kahvecirem,Aiyshaaaa,Claregrieve1,WikiWorks",Differential microbial abundance in oropharyngeal samples between controls and T3 OCD patients,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;1783272|201174|84998|84999|1643824;1783272|201174|84998|84999|1643824|1380;1783272|1239|186801|3085636|186803|43996;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|186801|3085636|186803;1783272|1239|186801|3082720|543314|86331,Complete,Claregrieve1
bsdb:35087123/4/2,35087123,case-control,35087123,10.1038/s41598-022-05480-9,https://pubmed.ncbi.nlm.nih.gov/35087123/,"Domènech L., Willis J., Alemany-Navarro M., Morell M., Real E., Escaramís G., Bertolín S., Sánchez Chinchilla D., Balcells S., Segalàs C., Estivill X., Menchón J.M., Gabaldón T., Alonso P. , Rabionet R.",Changes in the stool and oropharyngeal microbiome in obsessive-compulsive disorder,Scientific reports,2022,NA,Experiment 4,Spain,Homo sapiens,Oropharynx,UBERON:0001729,Obsessive-compulsive disorder,EFO:0004242,Control (healthy group),OCD T3,"Patients with obsessive-compulsive disorder (OCD) which is a neuropsychiatric condition characterized by intrusive and unwanted thoughts (termed obsessions) and repetitive behaviors or mental acts (termed compulsions), which are carried out to at least partially alleviate the anxiety or distress brought on by the obsessions. Timepoint 3 is following three months of pharmacological treatment and cognitive behavioral therapy (referred to as T3).",32,31,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 2,Figure S6,29 March 2023,Kahvecirem,"Kahvecirem,Aiyshaaaa,Claregrieve1,WikiWorks",Differential microbial abundance in oropharyngeal samples between controls and T3 OCD patients,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella",1783272|1239|186801|3085636|186803|830;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;1783272|1239|186801|3085636|186803|43994,Complete,Claregrieve1
bsdb:35096637/1/1,35096637,case-control,35096637,10.3389/fcimb.2021.770913,https://www.frontiersin.org/articles/10.3389/fcimb.2021.770913/full,"Wang S., Wei Y., Liu L. , Li Z.",Association Between Breastmilk Microbiota and Food Allergy in Infants,Frontiers in cellular and infection microbiology,2021,"breastfeeding, breastmilk microbiome, butyrate, food allergies, infant",Experiment 1,China,Homo sapiens,Milk,UBERON:0001913,Food allergy,EFO:1001890,non-allergy (NA) group,food allergy (FA) group,Group with food allergy.,22,11,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,"gestational age,maternal age,race",NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Figure 4A,6 November 2023,Davvve,"Davvve,WikiWorks","LEfSe analysis between the food allergy (FA) and non-allergy (NA) groups, showing genera with absolute values of linear discriminant analysis (LDA)
score.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium",3379134|1224|1236|2887326|468|469;3379134|1224|1236|72274|135621|286;1783272|201174|1760|85006|85019|1696,Complete,Folakunmi
bsdb:35096637/1/2,35096637,case-control,35096637,10.3389/fcimb.2021.770913,https://www.frontiersin.org/articles/10.3389/fcimb.2021.770913/full,"Wang S., Wei Y., Liu L. , Li Z.",Association Between Breastmilk Microbiota and Food Allergy in Infants,Frontiers in cellular and infection microbiology,2021,"breastfeeding, breastmilk microbiome, butyrate, food allergies, infant",Experiment 1,China,Homo sapiens,Milk,UBERON:0001913,Food allergy,EFO:1001890,non-allergy (NA) group,food allergy (FA) group,Group with food allergy.,22,11,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,"gestational age,maternal age,race",NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,fig 4,6 November 2023,Davvve,"Davvve,WikiWorks","LEfSe analysis between the food allergy (FA) and non-allergy (NA) groups, showing genera with absolute values of linear discriminant analysis (LDA)
score",decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Methanobacteriati|p__Methanobacteriota|c__Methanomicrobia|o__Methanomicrobiales|f__Methanoregulaceae|g__Methanolinea,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Thermovirgaceae|g__Thermovirga,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Syntrophia|o__Syntrophales|f__Syntrophaceae|g__Syntrophus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Janibacter,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae|g__Elusimicrobium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Thermotogati|p__Thermotogota|c__Thermotogae|o__Kosmotogales|f__Kosmotogaceae|g__Mesotoga,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Geodermatophilus",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171552|1283313;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|31979|1485;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|3085636|186803;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171552|838;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|186802|204475;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|459786;1783272|201174|84998|84999|1643824|1380;3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|171552|577309;1783272|1239|526524|526525|2810281|191303;1783272|1239|91061|186826|186827|66831;3366610|28890|224756|2191|1198451|499551;3384194|508458|649775|649776|3029089|336260;1783272|1239|186801|186802|216572|1017280;1783272|1239|186801|186802|3085642|580596;3379134|200940|3031648|2914038|213468|43773;1783272|201174|1760|85006|85021|53457;3379134|74152|641853|641854|641876|423604;1783272|1239|909932|1843489|31977|906;1783272|201174|84998|1643822|1643826|580024;3384194|200918|188708|1643946|1643948|1184396;3379134|976|200643|171549|1853231|283168;3366610|28890|183925|2158|2159|2172;1783272|1239|186801|186802|186807|2740;1783272|201174|1760|1643682|85030|1860,Complete,Folakunmi
bsdb:35114943/1/1,35114943,prospective cohort,35114943,https://doi.org/10.1186/s12866-021-02364-2,NA,"Le Roy C.I., Kurilshikov A., Leeming E.R., Visconti A., Bowyer R.C.E., Menni C., Falchi M., Koutnikova H., Veiga P., Zhernakova A., Derrien M. , Spector T.D.",Yoghurt consumption is associated with changes in the composition of the human gut microbiome and metabolome,BMC microbiology,2022,"16S rRNA and whole shotgun metagenomic sequencing, Bifidobacterium animalis, Streptococcus thermophilus, Yoghurt, diet, gut microbiome, healthy eating, metabolomics",Experiment 1,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Beverage consumption measurement,EFO:0010088,Non yoghurt eaters,Yoghurt eaters,Individual who have consumed yoghurt for at least once in a week.,400,1057,NA,16S,4,NA,relative abundances,Mixed-Effects Regression,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,increased,NA,unchanged,NA,increased,Signature 1,Additional file 4: Supplementary Table 3,3 November 2024,Agatha,"Agatha,KateRasheed,Aleru Divine,WikiWorks,Tosin",Differential abundance of taxa between yoghurt eaters and non-yoghurt eaters using 16S rRNA sequencing,increased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:352,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005",1783272|544448|31969|186332|186333|2086;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|31979|1485|1262798;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|248744;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|707003;1783272|1239|186801|186802|216572|3068309,Complete,Svetlana up
bsdb:35114943/1/2,35114943,prospective cohort,35114943,https://doi.org/10.1186/s12866-021-02364-2,NA,"Le Roy C.I., Kurilshikov A., Leeming E.R., Visconti A., Bowyer R.C.E., Menni C., Falchi M., Koutnikova H., Veiga P., Zhernakova A., Derrien M. , Spector T.D.",Yoghurt consumption is associated with changes in the composition of the human gut microbiome and metabolome,BMC microbiology,2022,"16S rRNA and whole shotgun metagenomic sequencing, Bifidobacterium animalis, Streptococcus thermophilus, Yoghurt, diet, gut microbiome, healthy eating, metabolomics",Experiment 1,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Beverage consumption measurement,EFO:0010088,Non yoghurt eaters,Yoghurt eaters,Individual who have consumed yoghurt for at least once in a week.,400,1057,NA,16S,4,NA,relative abundances,Mixed-Effects Regression,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,increased,NA,unchanged,NA,increased,Signature 2,Additional file 4: Supplementary Table 3,13 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between yoghurt eaters and non-yoghurt eaters using 16S rRNA sequencing,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|1506553;1783272|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:35114943/2/1,35114943,prospective cohort,35114943,https://doi.org/10.1186/s12866-021-02364-2,NA,"Le Roy C.I., Kurilshikov A., Leeming E.R., Visconti A., Bowyer R.C.E., Menni C., Falchi M., Koutnikova H., Veiga P., Zhernakova A., Derrien M. , Spector T.D.",Yoghurt consumption is associated with changes in the composition of the human gut microbiome and metabolome,BMC microbiology,2022,"16S rRNA and whole shotgun metagenomic sequencing, Bifidobacterium animalis, Streptococcus thermophilus, Yoghurt, diet, gut microbiome, healthy eating, metabolomics",Experiment 2,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Beverage consumption measurement,EFO:0010088,Non yoghurt eaters,Yoghurt eaters,Individual who have consumed yoghurt for at least once in a week.,144,400,NA,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Additional file 5: Supplementary Table 4,15 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between yoghurt eaters and non-yoghurt eaters using shotgun metabolomic sequencing,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium kroppenstedtii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|g__Ceduovirus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Fructilactobacillus|s__Fructilactobacillus sanfranciscensis",1783272|1239|91061|186826|1300|1301|1308;1783272|201174|1760|85004|31953|1678|28025;1783272|201174|1760|85007|1653|1716|161879;1783272|1239|909932|1843489|31977|29465;3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|815|909656|204516;1783272|1239|91061|186826|33958|1578|1579;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|91061|186826|1300|1357|1358;3379134|976|200643|171549|171550|239759|2585118;2731360|2731618|2731619|186532;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|91061|186826|33958|2767881|1625,Complete,Svetlana up
bsdb:35114943/2/2,35114943,prospective cohort,35114943,https://doi.org/10.1186/s12866-021-02364-2,NA,"Le Roy C.I., Kurilshikov A., Leeming E.R., Visconti A., Bowyer R.C.E., Menni C., Falchi M., Koutnikova H., Veiga P., Zhernakova A., Derrien M. , Spector T.D.",Yoghurt consumption is associated with changes in the composition of the human gut microbiome and metabolome,BMC microbiology,2022,"16S rRNA and whole shotgun metagenomic sequencing, Bifidobacterium animalis, Streptococcus thermophilus, Yoghurt, diet, gut microbiome, healthy eating, metabolomics",Experiment 2,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Beverage consumption measurement,EFO:0010088,Non yoghurt eaters,Yoghurt eaters,Individual who have consumed yoghurt for at least once in a week.,144,400,NA,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Additional file 5: Supplementary Table 4,15 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between yoghurt eaters and non-yoghurt eaters using shotgun metabolomic sequencing,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 1_4_56FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 3_1_57FAA_CT1,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 7_1_58FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia|s__Marvinbryantia formatexigens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas nexilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",1783272|1239|186801|186802|216572|244127|169435;1783272|201174|84998|84999|84107|102106|147207;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|658655;1783272|1239|186801|3085636|186803|658086;1783272|1239|186801|3085636|186803|658087;1783272|1239|186801|3085636|186803|248744|168384;3379134|976|200643|171549|171551|836|281920;1783272|1239|186801|3085636|186803|1213720|796942;1783272|1239|186801|3085636|186803|2005355|29361;1783272|1239|186801|186802|216572|459786;3379134|1224|1236|72274|135621|286,Complete,Svetlana up
bsdb:35114943/3/1,35114943,prospective cohort,35114943,https://doi.org/10.1186/s12866-021-02364-2,NA,"Le Roy C.I., Kurilshikov A., Leeming E.R., Visconti A., Bowyer R.C.E., Menni C., Falchi M., Koutnikova H., Veiga P., Zhernakova A., Derrien M. , Spector T.D.",Yoghurt consumption is associated with changes in the composition of the human gut microbiome and metabolome,BMC microbiology,2022,"16S rRNA and whole shotgun metagenomic sequencing, Bifidobacterium animalis, Streptococcus thermophilus, Yoghurt, diet, gut microbiome, healthy eating, metabolomics",Experiment 3,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Beverage consumption measurement,EFO:0010088,Non-Yoghurt consumers,Low Yoghurt consumers,Low Yoghurt consumers refers to those that consumed yoghurt 1-5 times in a week,144,183,NA,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Fig. 1C-D,15 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between low yoghurt consumers and non-yoghurt consumers using linear regression,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis",1783272|1239|91061|186826|1300|1301|1308;1783272|201174|1760|85004|31953|1678|28025,Complete,Svetlana up
bsdb:35114943/4/1,35114943,prospective cohort,35114943,https://doi.org/10.1186/s12866-021-02364-2,NA,"Le Roy C.I., Kurilshikov A., Leeming E.R., Visconti A., Bowyer R.C.E., Menni C., Falchi M., Koutnikova H., Veiga P., Zhernakova A., Derrien M. , Spector T.D.",Yoghurt consumption is associated with changes in the composition of the human gut microbiome and metabolome,BMC microbiology,2022,"16S rRNA and whole shotgun metagenomic sequencing, Bifidobacterium animalis, Streptococcus thermophilus, Yoghurt, diet, gut microbiome, healthy eating, metabolomics",Experiment 4,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Beverage consumption measurement,EFO:0010088,Non-Yoghurt consumers,High Yoghurt consumers,High Yoghurt consumers refers to individuals that consume yoghurt more than 5times in a week.,144,217,NA,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Fig. 1C-D,15 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between high yoghurt eaters and non-yoghurt eaters using linear regression.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis",1783272|1239|91061|186826|1300|1301|1308;1783272|201174|1760|85004|31953|1678|28025,Complete,Svetlana up
bsdb:35114943/5/1,35114943,prospective cohort,35114943,https://doi.org/10.1186/s12866-021-02364-2,NA,"Le Roy C.I., Kurilshikov A., Leeming E.R., Visconti A., Bowyer R.C.E., Menni C., Falchi M., Koutnikova H., Veiga P., Zhernakova A., Derrien M. , Spector T.D.",Yoghurt consumption is associated with changes in the composition of the human gut microbiome and metabolome,BMC microbiology,2022,"16S rRNA and whole shotgun metagenomic sequencing, Bifidobacterium animalis, Streptococcus thermophilus, Yoghurt, diet, gut microbiome, healthy eating, metabolomics",Experiment 5,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Beverage consumption measurement,EFO:0010088,Low Yoghurt consumers,High Yoghurt consumers,High Yoghurt consumers refers to individuals that consume yoghurt more than 5times in a week.,183,217,NA,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Fig. 1C-D,15 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between high yoghurt eaters and low yoghurt eaters using linear regression.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis",1783272|1239|91061|186826|1300|1301|1308;1783272|201174|1760|85004|31953|1678|28025,Complete,Svetlana up
bsdb:35114943/6/1,35114943,prospective cohort,35114943,https://doi.org/10.1186/s12866-021-02364-2,NA,"Le Roy C.I., Kurilshikov A., Leeming E.R., Visconti A., Bowyer R.C.E., Menni C., Falchi M., Koutnikova H., Veiga P., Zhernakova A., Derrien M. , Spector T.D.",Yoghurt consumption is associated with changes in the composition of the human gut microbiome and metabolome,BMC microbiology,2022,"16S rRNA and whole shotgun metagenomic sequencing, Bifidobacterium animalis, Streptococcus thermophilus, Yoghurt, diet, gut microbiome, healthy eating, metabolomics",Experiment 6,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Beverage consumption measurement,EFO:0010088,Non-Yoghurt consumers(didn't consume yoghurt 24hrs before sampling),High Yoghurt consumers(consumed yoghurt 24hrs before sampling),High Yoghurt consumers(consumed yoghurt 24hrs before sampling) refers to those who ate yoghurt a day before sampling (24hours before sampling).,43,27,NA,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Fig. 2A-B,15 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between non-yoghurt consumers (didn't consume yoghurt 24hrs before sampling) and high yoghurt eaters(consumed yoghurt 24hrs before sampling).,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis|s__Bifidobacterium animalis subsp. lactis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus",1783272|201174|1760|85004|31953|1678|28025|302911;1783272|1239|91061|186826|1300|1301|1308,Complete,Svetlana up
bsdb:35114943/7/1,35114943,prospective cohort,35114943,https://doi.org/10.1186/s12866-021-02364-2,NA,"Le Roy C.I., Kurilshikov A., Leeming E.R., Visconti A., Bowyer R.C.E., Menni C., Falchi M., Koutnikova H., Veiga P., Zhernakova A., Derrien M. , Spector T.D.",Yoghurt consumption is associated with changes in the composition of the human gut microbiome and metabolome,BMC microbiology,2022,"16S rRNA and whole shotgun metagenomic sequencing, Bifidobacterium animalis, Streptococcus thermophilus, Yoghurt, diet, gut microbiome, healthy eating, metabolomics",Experiment 7,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Beverage consumption measurement,EFO:0010088,Low Yoghurt consumers(didn't consume yoghurt 24hrs before sampling),High Yoghurt consumers(consume yoghurt 24hrs before sampling),High Yoghurt consumers refers to those who ate yoghurt a day before sampling (24hours before sampling),29,27,NA,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Fig. 2A-B,15 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between low-yoghurt consumers (didn't consume yoghurt 24hrs before sampling) and high yoghurt eaters(consumed yoghurt 24hrs before sampling).,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis|s__Bifidobacterium animalis subsp. lactis",1783272|1239|91061|186826|1300|1301|1308;1783272|201174|1760|85004|31953|1678|28025|302911,Complete,Svetlana up
bsdb:35114943/8/1,35114943,prospective cohort,35114943,https://doi.org/10.1186/s12866-021-02364-2,NA,"Le Roy C.I., Kurilshikov A., Leeming E.R., Visconti A., Bowyer R.C.E., Menni C., Falchi M., Koutnikova H., Veiga P., Zhernakova A., Derrien M. , Spector T.D.",Yoghurt consumption is associated with changes in the composition of the human gut microbiome and metabolome,BMC microbiology,2022,"16S rRNA and whole shotgun metagenomic sequencing, Bifidobacterium animalis, Streptococcus thermophilus, Yoghurt, diet, gut microbiome, healthy eating, metabolomics",Experiment 8,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Beverage consumption measurement,EFO:0010088,Low Yoghurt consumers (consume yoghurt 24hrs before sampling),High Yoghurt consumers(consume yoghurt 24hrs before sampling),High Yoghurt consumers(consume yoghurt 24hrs before sampling) refers to those who ate yoghurt a day before sampling (24hours before sampling),18,27,NA,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Fig. 2A,15 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between low-yoghurt consumers (consumed yoghurt 24hrs before sampling) and high yoghurt eaters(consumed yoghurt 24hrs before sampling).,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis|s__Bifidobacterium animalis subsp. lactis,1783272|201174|1760|85004|31953|1678|28025|302911,Complete,Svetlana up
bsdb:35114943/9/2,35114943,prospective cohort,35114943,https://doi.org/10.1186/s12866-021-02364-2,NA,"Le Roy C.I., Kurilshikov A., Leeming E.R., Visconti A., Bowyer R.C.E., Menni C., Falchi M., Koutnikova H., Veiga P., Zhernakova A., Derrien M. , Spector T.D.",Yoghurt consumption is associated with changes in the composition of the human gut microbiome and metabolome,BMC microbiology,2022,"16S rRNA and whole shotgun metagenomic sequencing, Bifidobacterium animalis, Streptococcus thermophilus, Yoghurt, diet, gut microbiome, healthy eating, metabolomics",Experiment 9,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Beverage consumption measurement,EFO:0010088,High Yoghurt Consumers(didn't consume yoghurt 24hrs before sampling),High Yoghurt consumers(consume yoghurt 24hrs before sampling),High Yoghurt consumers(consume yoghurt 24hrs before sampling) refers to those who ate yoghurt a day before sampling (24hours before sampling).,34,27,NA,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Fig. 2A,15 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between high-yoghurt consumers (didn't consume yoghurt 24hrs before sampling) and high yoghurt eaters(consumed yoghurt 24hrs before sampling).,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis|s__Bifidobacterium animalis subsp. lactis,1783272|201174|1760|85004|31953|1678|28025|302911,Complete,Svetlana up
bsdb:35114943/10/1,35114943,prospective cohort,35114943,https://doi.org/10.1186/s12866-021-02364-2,NA,"Le Roy C.I., Kurilshikov A., Leeming E.R., Visconti A., Bowyer R.C.E., Menni C., Falchi M., Koutnikova H., Veiga P., Zhernakova A., Derrien M. , Spector T.D.",Yoghurt consumption is associated with changes in the composition of the human gut microbiome and metabolome,BMC microbiology,2022,"16S rRNA and whole shotgun metagenomic sequencing, Bifidobacterium animalis, Streptococcus thermophilus, Yoghurt, diet, gut microbiome, healthy eating, metabolomics",Experiment 10,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Beverage consumption measurement,EFO:0010088,Non-Yoghurt consumers(didn't consume yoghurt 24hrs before sampling),High Yoghurt consumers(didn't consume yoghurt 24hrs before sampling),High Yoghurt consumers(didn't consume yoghurt 24hrs before sampling) refers to high intake yoghurt consumers who did not consume yoghurt 24hrs before fecal sampling,43,34,NA,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Fig. 2B,15 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between non-yoghurt consumers (didn't consume yoghurt 24hrs before sampling) and high yoghurt eaters(didn't consume yoghurt 24hrs before sampling).,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,1783272|1239|91061|186826|1300|1301|1308,Complete,Svetlana up
bsdb:35114943/11/1,35114943,prospective cohort,35114943,https://doi.org/10.1186/s12866-021-02364-2,NA,"Le Roy C.I., Kurilshikov A., Leeming E.R., Visconti A., Bowyer R.C.E., Menni C., Falchi M., Koutnikova H., Veiga P., Zhernakova A., Derrien M. , Spector T.D.",Yoghurt consumption is associated with changes in the composition of the human gut microbiome and metabolome,BMC microbiology,2022,"16S rRNA and whole shotgun metagenomic sequencing, Bifidobacterium animalis, Streptococcus thermophilus, Yoghurt, diet, gut microbiome, healthy eating, metabolomics",Experiment 11,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Beverage consumption measurement,EFO:0010088,Low Yoghurt consumers(didn't consume yoghurt 24hrs before sampling),High Yoghurt consumers(didn't consume yoghurt 24hrs before sampling),High Yoghurt consumers(didn't consume yoghurt 24hrs before sampling) refers to those who did not take yoghurt a day before sampling (24hours before sampling).,29,34,NA,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Fig. 2B,15 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between low-yoghurt consumers (didn't consume yoghurt 24hrs before sampling) and high yoghurt eaters(didn't consume yoghurt 24hrs before sampling).,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,1783272|1239|91061|186826|1300|1301|1308,Complete,Svetlana up
bsdb:35114943/12/1,35114943,prospective cohort,35114943,https://doi.org/10.1186/s12866-021-02364-2,NA,"Le Roy C.I., Kurilshikov A., Leeming E.R., Visconti A., Bowyer R.C.E., Menni C., Falchi M., Koutnikova H., Veiga P., Zhernakova A., Derrien M. , Spector T.D.",Yoghurt consumption is associated with changes in the composition of the human gut microbiome and metabolome,BMC microbiology,2022,"16S rRNA and whole shotgun metagenomic sequencing, Bifidobacterium animalis, Streptococcus thermophilus, Yoghurt, diet, gut microbiome, healthy eating, metabolomics",Experiment 12,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Beverage consumption measurement,EFO:0010088,Low Yoghurt consumers(didn't consume yoghurt 24hrs before sampling),Low Yoghurt consumers(consumed yoghurt 24hrs before sampling),Low Yoghurt consumers(consume yoghurt 24hrs before sampling) refers to those who ate yoghurt a day before sampling (24hours before sampling).,29,18,NA,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Fig. 2B,15 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between low-yoghurt consumers (didn't consume yoghurt 24hrs before sampling) and low yoghurt eaters(consumed yoghurt 24hrs before sampling).,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,1783272|1239|91061|186826|1300|1301|1308,Complete,Svetlana up
bsdb:35114943/13/1,35114943,prospective cohort,35114943,https://doi.org/10.1186/s12866-021-02364-2,NA,"Le Roy C.I., Kurilshikov A., Leeming E.R., Visconti A., Bowyer R.C.E., Menni C., Falchi M., Koutnikova H., Veiga P., Zhernakova A., Derrien M. , Spector T.D.",Yoghurt consumption is associated with changes in the composition of the human gut microbiome and metabolome,BMC microbiology,2022,"16S rRNA and whole shotgun metagenomic sequencing, Bifidobacterium animalis, Streptococcus thermophilus, Yoghurt, diet, gut microbiome, healthy eating, metabolomics",Experiment 13,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Beverage consumption measurement,EFO:0010088,Non-Yoghurt consumers(didn't consume yoghurt 24hrs before sampling),Low Yoghurt consumers(consumed yoghurt 24hrs before sampling),Low Yoghurt consumers(consumed yoghurt 24hrs before sampling) refers to those who ate yoghurt a day before sampling (24hours before sampling).,43,18,NA,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Fig. 2B,15 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between non-yoghurt consumers (didn't consume yoghurt 24hrs before sampling) and low yoghurt eaters(consumed yoghurt 24hrs before sampling).,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,1783272|1239|91061|186826|1300|1301|1308,Complete,Svetlana up
bsdb:35133187/1/1,35133187,case-control,35133187,10.1128/msystems.00004-22,NA,"Yıldırım S., Nalbantoğlu Ö.U., Bayraktar A., Ercan F.B., Gündoğdu A., Velioğlu H.A., Göl M.F., Soylu A.E., Koç F., Gülpınar E.A., Kadak K.S., Arıkan M., Mardinoğlu A., Koçak M., Köseoğlu E. , Hanoğlu L.",Stratification of the Gut Microbiota Composition Landscape across the Alzheimer's Disease Continuum in a Turkish Cohort,mSystems,2022,"16S rRNA, Alzheimer’s disease, brain-gut axis, gut microbiome, gut microbiota, precision medicine, precision nutrition, stratification",Experiment 1,Turkey,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Non-demented Controls,Alzheimer's disease patients,"Patients with Alzheimer's disease, mostly exhibiting mild to very mild dementia",51,47,1 month,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,diet,"age,sex",NA,increased,increased,unchanged,unchanged,NA,Signature 1,Supplementary Table S2A and Supplementary Table S2CC,24 October 2023,Joan Chuks,"Joan Chuks,Peace Sandy,WikiWorks",Differentially Abundant Genus level Taxa Between Alzheimer's disease Patients and Non-demented control groups Detected by Limma-Voom Model (Age and Sex Adjusted),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",3379134|976|200643|171549|815|816;1783272|201174|84998|84999|84107|102106;3379134|1224|1236|91347|543|1940338;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|1869337;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|171552|838;1783272|1239|526524|526525|128827,Complete,Peace Sandy
bsdb:35133187/1/2,35133187,case-control,35133187,10.1128/msystems.00004-22,NA,"Yıldırım S., Nalbantoğlu Ö.U., Bayraktar A., Ercan F.B., Gündoğdu A., Velioğlu H.A., Göl M.F., Soylu A.E., Koç F., Gülpınar E.A., Kadak K.S., Arıkan M., Mardinoğlu A., Koçak M., Köseoğlu E. , Hanoğlu L.",Stratification of the Gut Microbiota Composition Landscape across the Alzheimer's Disease Continuum in a Turkish Cohort,mSystems,2022,"16S rRNA, Alzheimer’s disease, brain-gut axis, gut microbiome, gut microbiota, precision medicine, precision nutrition, stratification",Experiment 1,Turkey,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Non-demented Controls,Alzheimer's disease patients,"Patients with Alzheimer's disease, mostly exhibiting mild to very mild dementia",51,47,1 month,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,diet,"age,sex",NA,increased,increased,unchanged,unchanged,NA,Signature 2,Supplementary Table S2A and Supplementary Table S2CC,24 October 2023,Joan Chuks,"Joan Chuks,Iram jamshed,Peace Sandy,WikiWorks",Differentially Abundant Genus level Taxa Between Alzheimer's disease Patients and Non-demented control groups Detected by Limma-Voom Model (Age and Sex Adjusted),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Mycoplasmatota|c__Mollicutes",1783272|1239|186801|186802|3085642|580596;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|841;1783272|544448|31969,Complete,Peace Sandy
bsdb:35133187/2/1,35133187,case-control,35133187,10.1128/msystems.00004-22,NA,"Yıldırım S., Nalbantoğlu Ö.U., Bayraktar A., Ercan F.B., Gündoğdu A., Velioğlu H.A., Göl M.F., Soylu A.E., Koç F., Gülpınar E.A., Kadak K.S., Arıkan M., Mardinoğlu A., Koçak M., Köseoğlu E. , Hanoğlu L.",Stratification of the Gut Microbiota Composition Landscape across the Alzheimer's Disease Continuum in a Turkish Cohort,mSystems,2022,"16S rRNA, Alzheimer’s disease, brain-gut axis, gut microbiome, gut microbiota, precision medicine, precision nutrition, stratification",Experiment 2,Turkey,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Non-demented Controls,Mild Cognitive Impairment group,Amnestic patients with mild cognitive impairment (MCI),51,27,1 month,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,"age,sex",NA,increased,decreased,NA,increased,increased,Signature 1,Supplementary Table S2D and Supplementary Table S2B,24 October 2023,Joan Chuks,"Joan Chuks,Peace Sandy,Welile,WikiWorks","Differentially Abundant Genus level Taxa Between mild cognitive impairment (MCI)
and Non-demented Control (C) groups Detected by Limma-Voom Model (Age and Sex Adjusted)",increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Catenisphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239|526524|526525|128827|1774107;1783272|1239|909932|1843489|31977|39948;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|2005473;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171550;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|186802|31979|1485,Complete,Peace Sandy
bsdb:35133187/2/2,35133187,case-control,35133187,10.1128/msystems.00004-22,NA,"Yıldırım S., Nalbantoğlu Ö.U., Bayraktar A., Ercan F.B., Gündoğdu A., Velioğlu H.A., Göl M.F., Soylu A.E., Koç F., Gülpınar E.A., Kadak K.S., Arıkan M., Mardinoğlu A., Koçak M., Köseoğlu E. , Hanoğlu L.",Stratification of the Gut Microbiota Composition Landscape across the Alzheimer's Disease Continuum in a Turkish Cohort,mSystems,2022,"16S rRNA, Alzheimer’s disease, brain-gut axis, gut microbiome, gut microbiota, precision medicine, precision nutrition, stratification",Experiment 2,Turkey,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Non-demented Controls,Mild Cognitive Impairment group,Amnestic patients with mild cognitive impairment (MCI),51,27,1 month,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,"age,sex",NA,increased,decreased,NA,increased,increased,Signature 2,Supplementary Table S2D,24 October 2023,Joan Chuks,"Joan Chuks,ChiomaBlessing,Peace Sandy,WikiWorks",Differentially Abundant Genus level Taxa Between mild cognitive impairment (MCI) and Non-demented Control (C) groups Detected by Limma-Voom Model (Age and Sex Adjusted),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella sp.",1783272|1239|186801|186802|3085642|580596;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|186802|216572|3068309;1783272|544448|31969;1783272|1239|186801|186802|31979|1485|59620;1783272|1239|526524|526525|128827|331630;1783272|1239|186801|3085636|186803|297314;1783272|1239|186801|3085636|186803|841;1783272|1239|909932|1843489|31977|39948;1783272|1239|526524|526525|128827;1783272|1239|186801|3085636|186803;3379134|1224|28216|80840|995019|577310|2049037,Complete,Peace Sandy
bsdb:35140064/1/1,35140064,prospective cohort,35140064,10.1136/gutjnl-2021-326563,NA,"Ng S.C., Peng Y., Zhang L., Mok C.K., Zhao S., Li A., Ching J.Y., Liu Y., Yan S., Chan D.L.S., Zhu J., Chen C., Fung A.C., Wong K.K., Hui D.S., Chan F.K. , Tun H.M.",Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events,Gut,2022,"COVID-19, enteric bacterial microflora, immune response",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Low responders (sVNT </= 60%),High responders (sVNT > 60%),Participants in the CoronaVac group with surrogate virus neutralisation test (sVNT) inhibition > 60% at 1 month after the second vaccine dose.,21,16,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2A,19 November 2025,Blegodwin,Blegodwin,Bacterial species enriched in the baseline gut microbiome of CoronaVac High responders (Group 1)(sVNT of 10-fold diluted plasma >60%).,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens|s__Adlercreutzia equolifaciens subsp. celatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus petauri,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 57_20",1783272|201174|84998|1643822|1643826|447020|446660;1783272|201174|84998|1643822|1643826|447020|446660|394340;3379134|976|200643|171549|171550|239759|28117;1783272|201174|1760|85004|31953|1678|1680;3379134|976|200643|171549|1853231|574697|544645;1783272|1239|186801|3082720|186804|1505657|261299;1783272|1239|91061|186826|1300|1357|1940789;1783272|1239|909932|909929|1843491|52225|52226;1783272|1239|186801|186802|216572|459786|1897011,Complete,NA
bsdb:35140064/1/2,35140064,prospective cohort,35140064,10.1136/gutjnl-2021-326563,NA,"Ng S.C., Peng Y., Zhang L., Mok C.K., Zhao S., Li A., Ching J.Y., Liu Y., Yan S., Chan D.L.S., Zhu J., Chen C., Fung A.C., Wong K.K., Hui D.S., Chan F.K. , Tun H.M.",Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events,Gut,2022,"COVID-19, enteric bacterial microflora, immune response",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Low responders (sVNT </= 60%),High responders (sVNT > 60%),Participants in the CoronaVac group with surrogate virus neutralisation test (sVNT) inhibition > 60% at 1 month after the second vaccine dose.,21,16,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2A,19 November 2025,Blegodwin,Blegodwin,Bacterial species enriched in the baseline gut microbiome of CoronaVac Low responders (Group 0).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hydrogenotrophica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella xylaniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus",3379134|976|200643|171549|815|816|818;1783272|1239|186801|3085636|186803|572511|53443;1783272|1239|186801|3085636|186803|2316020|33038;3379134|976|200643|171549|171552|577309|454155;3379134|976|200643|171549|815|909656|821,Complete,NA
bsdb:35140064/2/1,35140064,prospective cohort,35140064,10.1136/gutjnl-2021-326563,NA,"Ng S.C., Peng Y., Zhang L., Mok C.K., Zhao S., Li A., Ching J.Y., Liu Y., Yan S., Chan D.L.S., Zhu J., Chen C., Fung A.C., Wong K.K., Hui D.S., Chan F.K. , Tun H.M.",Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events,Gut,2022,"COVID-19, enteric bacterial microflora, immune response",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Response to vaccine,EFO:0004645,Others,Highest-tier responders,BNT162b2 vaccinees in the first quartile (Q1) of sVNT of 200-fold diluted plasma (top 25% of responders).,76,25,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2B,19 November 2025,Blegodwin,Blegodwin,Bacterial species enriched in the baseline gut microbiome of BNT162b2 Highest-tier responders (Group 1).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis",1783272|1239|186801|3085636|186803|1766253|39491;3379134|976|200643|171549|815|816|818;1783272|1239|186801|3085636|186803|841|301302,Complete,NA
bsdb:35140064/2/2,35140064,prospective cohort,35140064,10.1136/gutjnl-2021-326563,NA,"Ng S.C., Peng Y., Zhang L., Mok C.K., Zhao S., Li A., Ching J.Y., Liu Y., Yan S., Chan D.L.S., Zhu J., Chen C., Fung A.C., Wong K.K., Hui D.S., Chan F.K. , Tun H.M.",Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events,Gut,2022,"COVID-19, enteric bacterial microflora, immune response",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Response to vaccine,EFO:0004645,Others,Highest-tier responders,BNT162b2 vaccinees in the first quartile (Q1) of sVNT of 200-fold diluted plasma (top 25% of responders).,76,25,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2B,19 November 2025,Blegodwin,Blegodwin,Bacterial species enriched in the baseline gut microbiome of BNT162b2 Others (Group 0).,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora saccharolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae",3384189|32066|203490|203491|203492|848|850;1783272|1239|186801|3085636|186803|2719231|84030;3379134|976|200643|171549|2005525|375288|46503,Complete,NA
bsdb:35140064/3/1,35140064,prospective cohort,35140064,10.1136/gutjnl-2021-326563,NA,"Ng S.C., Peng Y., Zhang L., Mok C.K., Zhao S., Li A., Ching J.Y., Liu Y., Yan S., Chan D.L.S., Zhu J., Chen C., Fung A.C., Wong K.K., Hui D.S., Chan F.K. , Tun H.M.",Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events,Gut,2022,"COVID-19, enteric bacterial microflora, immune response",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Response to vaccine,EFO:0004645,High responders (Normal Weight),Low responders (Normal Weight),CoronaVac vaccinees at 1 month after second dose of vaccination with Normal Weight (BMI < 23) and sVNT > 60%.,11,11,NA,WMS,NA,Illumina,relative abundances,Dunn's test,0.05,TRUE,NA,NA,body mass index,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4A, 4C, 4D",20 November 2025,Blegodwin,Blegodwin,Bacterial species significantly lower in Normal Weight Low Responders compared to the reference group (Normal Weight High Responders).,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens|s__Adlercreutzia equolifaciens subsp. celatus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis",1783272|201174|84998|1643822|1643826|447020|446660;1783272|201174|84998|1643822|1643826|447020|446660|394340;1783272|201174|1760|85004|31953|1678|1680,Complete,NA
bsdb:35140064/4/1,35140064,prospective cohort,35140064,10.1136/gutjnl-2021-326563,NA,"Ng S.C., Peng Y., Zhang L., Mok C.K., Zhao S., Li A., Ching J.Y., Liu Y., Yan S., Chan D.L.S., Zhu J., Chen C., Fung A.C., Wong K.K., Hui D.S., Chan F.K. , Tun H.M.",Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events,Gut,2022,"COVID-19, enteric bacterial microflora, immune response",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Response to vaccine,EFO:0004645,High responders (Normal Weight),High responders (Overweight/Obese),CoronaVac vaccinees with BMI >/= (Overweight/Obese) and sVNT > 60%. Also referred to as OWOB-High.,13,7,NA,WMS,NA,Illumina,relative abundances,Dunn's test,0.05,TRUE,NA,NA,body mass index,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4A, 4D",20 November 2025,Blegodwin,Blegodwin,Bacterial species significantly lower in Overweight/Obese High Responders compared to Normal Weight High Responders.,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens|s__Adlercreutzia equolifaciens subsp. celatus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis",1783272|201174|84998|1643822|1643826|447020|446660|394340;1783272|201174|1760|85004|31953|1678|1680,Complete,NA
bsdb:35140064/5/1,35140064,prospective cohort,35140064,10.1136/gutjnl-2021-326563,NA,"Ng S.C., Peng Y., Zhang L., Mok C.K., Zhao S., Li A., Ching J.Y., Liu Y., Yan S., Chan D.L.S., Zhu J., Chen C., Fung A.C., Wong K.K., Hui D.S., Chan F.K. , Tun H.M.",Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events,Gut,2022,"COVID-19, enteric bacterial microflora, immune response",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Response to vaccine,EFO:0004645,High responders (Normal Weight),Low responders (Overweight/Obese),CoronaVac vaccinees with BMI >/= (Overweight/Obese) and sVNT </= 60%. Also referred to as OWOB-Low.,11,8,NA,WMS,NA,Illumina,relative abundances,Dunn's test,0.05,TRUE,NA,NA,body mass index,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4A, 4D",20 November 2025,Blegodwin,Blegodwin,Bacterial species significantly lower in Overweight/Obese Low Responders compared to Normal Weight High Responders.,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens|s__Adlercreutzia equolifaciens subsp. celatus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis",1783272|201174|84998|1643822|1643826|447020|446660|394340;1783272|201174|1760|85004|31953|1678|1680,Complete,NA
bsdb:35140064/6/1,35140064,prospective cohort,35140064,10.1136/gutjnl-2021-326563,NA,"Ng S.C., Peng Y., Zhang L., Mok C.K., Zhao S., Li A., Ching J.Y., Liu Y., Yan S., Chan D.L.S., Zhu J., Chen C., Fung A.C., Wong K.K., Hui D.S., Chan F.K. , Tun H.M.",Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events,Gut,2022,"COVID-19, enteric bacterial microflora, immune response",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Response to vaccine,EFO:0004645,Cluster 1 (Low Adverse Events),Cluster 2 (High Adverse Events),"BNT162b2 vaccinees belonging to baseline gut microbiota Cluster 2, associated with a significantly higher risk of adverse events after both vaccine doses 1 and 2.",20,80,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 9H,29 November 2025,Blegodwin,Blegodwin,Bacterial species enriched in Cluster 2 (High Adverse Events) associated with baseline gut microbiota BNT162b2 vaccine.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. CAG:257,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:274,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:5226,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas intestinalis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa",3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|815|816|338188;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|820;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|186801|3085636|186803|572511|1262756;1783272|1239|186801|3085636|186803|572511|418240;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|186802|186806|1730|1262888;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|909932|1843488|909930|33024|33025;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|171552|838|1262930;1783272|1239|186801|3085636|186803|1769710|1653434;1783272|1239|526524|526525|2810280|3025755|1547,Complete,NA
bsdb:35140064/6/2,35140064,prospective cohort,35140064,10.1136/gutjnl-2021-326563,NA,"Ng S.C., Peng Y., Zhang L., Mok C.K., Zhao S., Li A., Ching J.Y., Liu Y., Yan S., Chan D.L.S., Zhu J., Chen C., Fung A.C., Wong K.K., Hui D.S., Chan F.K. , Tun H.M.",Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events,Gut,2022,"COVID-19, enteric bacterial microflora, immune response",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Response to vaccine,EFO:0004645,Cluster 1 (Low Adverse Events),Cluster 2 (High Adverse Events),"BNT162b2 vaccinees belonging to baseline gut microbiota Cluster 2, associated with a significantly higher risk of adverse events after both vaccine doses 1 and 2.",20,80,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 9H,29 November 2025,Blegodwin,Blegodwin,"Bacterial species enriched in Cluster 1 (Low Adverse Events), meaning they are decreased in the high-risk Group 1.",decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus fermentans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium mitsuokai,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter secundus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister sp. CAG:357,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus hirae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:251,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:110,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:170,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:238,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. CAG:241,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella xylaniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. 885,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:520,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella|s__Raoultella ornithinolytica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:488,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Tractidigestivibacter|s__Tractidigestivibacter scatoligenes",1783272|1239|909932|1843488|909930|904|905;3379134|976|200643|171549|2005519|397864|487174;1783272|1239|526524|526525|2810280|135858|100886;1783272|201174|84998|84999|84107|102106|74426;3379134|976|200643|171549|2005519|1348911|1501392;1783272|1239|186801|3085636|186803|33042|33043;3379134|200940|3031449|213115|194924|872|901;1783272|1239|909932|1843489|31977|39948|1262869;1783272|1239|909932|1843489|31977|39948|487173;1783272|1239|91061|186826|81852|1350|1354;1783272|1239|186801|186802|186806|1730|1262886;1783272|1239|1263000;1783272|1239|1263006;1783272|1239|1263011;1783272|1239|526524|526525|128827|1573535|1735;1783272|1239|909932|909929|1843491|158846|437897;1783272|1239|909932|909929|1843491|158846|437897;1783272|1239|909932|909929|1843491|158846|158847;1783272|1239|186801|186802|216572|459786|1262911;3379134|976|200643|171549|171552|577309|454155;3379134|976|200643|171549|815|909656|387090;3379134|976|200643|171549|171552|838|2022527;3379134|976|200643|171549|171552|838|1262929;3379134|1224|1236|91347|543|160674|54291;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|186802|216572|1263|1262959;1783272|1239|91061|186826|1300|1301|1318;1783272|201174|84998|84999|1643824|2847313|1299998,Complete,NA
bsdb:35140064/7/1,35140064,prospective cohort,35140064,10.1136/gutjnl-2021-326563,NA,"Ng S.C., Peng Y., Zhang L., Mok C.K., Zhao S., Li A., Ching J.Y., Liu Y., Yan S., Chan D.L.S., Zhu J., Chen C., Fung A.C., Wong K.K., Hui D.S., Chan F.K. , Tun H.M.",Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events,Gut,2022,"COVID-19, enteric bacterial microflora, immune response",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Response to vaccine,EFO:0004645,Cluster 1 (Low Adverse Events) for CoronaVac,Cluster 2 (High Adverse Events) for CoronaVac,"CoronaVac vaccinees belonging to baseline gut microbiota Cluster 2, associated with a significantly higher risk of adverse events after the first vaccine dose.",10,27,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 9D,29 November 2025,Blegodwin,Blegodwin,Bacterial species enriched in Cluster 2 (High Adverse Events),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella tayi,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Pseudomonadati|p__Pseudomonadota|s__Proteobacteria bacterium CAG:139,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas intestinalis",1783272|1239|186801|186802|216572|244127|169435;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|820;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|3085636|186803|1432051|1432052;1783272|1239|186801|3085636|186803|2719313|208479;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|216572|946234|292800;1783272|201174|84998|1643822|1643826|644652|471189;1783272|1239|186801|3085636|186803|1649459|154046;3379134|976|200643|171549|2005525|375288|328812;3379134|1224|1262986;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|186801|3085636|186803|1769710|1653434,Complete,NA
bsdb:35140064/7/2,35140064,prospective cohort,35140064,10.1136/gutjnl-2021-326563,NA,"Ng S.C., Peng Y., Zhang L., Mok C.K., Zhao S., Li A., Ching J.Y., Liu Y., Yan S., Chan D.L.S., Zhu J., Chen C., Fung A.C., Wong K.K., Hui D.S., Chan F.K. , Tun H.M.",Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events,Gut,2022,"COVID-19, enteric bacterial microflora, immune response",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Response to vaccine,EFO:0004645,Cluster 1 (Low Adverse Events) for CoronaVac,Cluster 2 (High Adverse Events) for CoronaVac,"CoronaVac vaccinees belonging to baseline gut microbiota Cluster 2, associated with a significantly higher risk of adverse events after the first vaccine dose.",10,27,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 9D,29 November 2025,Blegodwin,Blegodwin,Bacterial species enriched in Cluster 1 (Low Adverse Events),decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis",1783272|201174|84998|84999|84107|102106|74426;1783272|1239|909932|909929|1843491|158846|437897;1783272|1239|909932|909929|1843491|158846|437897;1783272|1239|909932|909929|1843491|158846|158847;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|91061|186826|1300|1301|1343,Complete,NA
bsdb:35140064/8/1,35140064,prospective cohort,35140064,10.1136/gutjnl-2021-326563,NA,"Ng S.C., Peng Y., Zhang L., Mok C.K., Zhao S., Li A., Ching J.Y., Liu Y., Yan S., Chan D.L.S., Zhu J., Chen C., Fung A.C., Wong K.K., Hui D.S., Chan F.K. , Tun H.M.",Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events,Gut,2022,"COVID-19, enteric bacterial microflora, immune response",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,CoronaVac baseline,CoronaVac 1 month,CoronaVac vaccinees sampled 1 month after completion of vaccine.,37,36,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,unchanged,Signature 1,Figure 1D,29 November 2025,Blegodwin,Blegodwin,Bacterial species enriched at One Month compared to Baseline for CoronaVac.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,3379134|976|200643|171549|815|816|47678,Complete,NA
bsdb:35140064/8/2,35140064,prospective cohort,35140064,10.1136/gutjnl-2021-326563,NA,"Ng S.C., Peng Y., Zhang L., Mok C.K., Zhao S., Li A., Ching J.Y., Liu Y., Yan S., Chan D.L.S., Zhu J., Chen C., Fung A.C., Wong K.K., Hui D.S., Chan F.K. , Tun H.M.",Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events,Gut,2022,"COVID-19, enteric bacterial microflora, immune response",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,CoronaVac baseline,CoronaVac 1 month,CoronaVac vaccinees sampled 1 month after completion of vaccine.,37,36,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,unchanged,Signature 2,Figure 1D,30 November 2025,Blegodwin,Blegodwin,Bacterial species enriched at One Month compared to Baseline.,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens|s__Adlercreutzia equolifaciens subsp. celatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis",1783272|201174|84998|1643822|1643826|447020|446660;1783272|201174|84998|1643822|1643826|447020|446660|394340;1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|572511|418240;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|91061|186826|1300|1301|1343,Complete,NA
bsdb:35140064/9/1,35140064,prospective cohort,35140064,10.1136/gutjnl-2021-326563,NA,"Ng S.C., Peng Y., Zhang L., Mok C.K., Zhao S., Li A., Ching J.Y., Liu Y., Yan S., Chan D.L.S., Zhu J., Chen C., Fung A.C., Wong K.K., Hui D.S., Chan F.K. , Tun H.M.",Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events,Gut,2022,"COVID-19, enteric bacterial microflora, immune response",Experiment 9,China,Homo sapiens,Feces,UBERON:0001988,Response to vaccine,EFO:0004645,BNT162b2 baseline,BNT162b2 1 month,BNT162b2 vaccinees sampled 1 month after completion of vaccine.,101,98,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,unchanged,Signature 1,Figure 1D,30 November 2025,Blegodwin,Blegodwin,Bacterial species enriched at One Month compared to Baseline for BNT162b2.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae",3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|815|816|47678,Complete,NA
bsdb:35140064/9/2,35140064,prospective cohort,35140064,10.1136/gutjnl-2021-326563,NA,"Ng S.C., Peng Y., Zhang L., Mok C.K., Zhao S., Li A., Ching J.Y., Liu Y., Yan S., Chan D.L.S., Zhu J., Chen C., Fung A.C., Wong K.K., Hui D.S., Chan F.K. , Tun H.M.",Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events,Gut,2022,"COVID-19, enteric bacterial microflora, immune response",Experiment 9,China,Homo sapiens,Feces,UBERON:0001988,Response to vaccine,EFO:0004645,BNT162b2 baseline,BNT162b2 1 month,BNT162b2 vaccinees sampled 1 month after completion of vaccine.,101,98,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,unchanged,Signature 2,Figure 1D,30 November 2025,Blegodwin,Blegodwin,Bacterial species enriched at Baseline compared to One Month for BNT162b2 vaccine.,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens|s__Adlercreutzia equolifaciens subsp. celatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum butyriciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hydrogenotrophica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Lactonifactor|s__Lactonifactor longoviformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas intestinalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis",1783272|201174|84998|1643822|1643826|447020|446660;1783272|201174|84998|1643822|1643826|447020|446660|394340;1783272|1239|186801|186802|3085642|2048137|1628085;1783272|1239|186801|3085636|186803|2569097|39488;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|186801|3085636|186803|572511|53443;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|572511|418240;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330|88431;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|91061|1385|539738|1378|84135;1783272|1239|186801|186802|31979|420345|341220;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|186803|1769710|1653434;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|68892;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|1300|1301|1305;1783272|1239|91061|186826|1300|1301|1343,Complete,NA
bsdb:35140064/10/1,35140064,prospective cohort,35140064,10.1136/gutjnl-2021-326563,NA,"Ng S.C., Peng Y., Zhang L., Mok C.K., Zhao S., Li A., Ching J.Y., Liu Y., Yan S., Chan D.L.S., Zhu J., Chen C., Fung A.C., Wong K.K., Hui D.S., Chan F.K. , Tun H.M.",Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events,Gut,2022,"COVID-19, enteric bacterial microflora, immune response",Experiment 10,China,Homo sapiens,Feces,UBERON:0001988,Response to vaccine,EFO:0004645,CoronaVac Low responders,CoronaVac High responders,CoronaVac vaccinees with sVNT > 60% at 1 month after second dose.,36,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 2A,1 December 2025,Blegodwin,Blegodwin,Bacterial species enriched in High Responders (Group 1) at one month post-vaccination.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:58,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Tractidigestivibacter|s__Tractidigestivibacter scatoligenes,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens|s__Adlercreutzia equolifaciens subsp. celatus",1783272|201174|84998|1643822|1643826|447020|446660;1783272|201174|1760|85004|31953|1678|1680;1783272|1239|186801|186802|31979|1485|1262824;1783272|1239|909932|909929|1843491|52225|52226;1783272|201174|84998|84999|1643824|2847313|1299998;1783272|201174|84998|1643822|1643826|447020|446660|394340,Complete,NA
bsdb:35140064/10/2,35140064,prospective cohort,35140064,10.1136/gutjnl-2021-326563,NA,"Ng S.C., Peng Y., Zhang L., Mok C.K., Zhao S., Li A., Ching J.Y., Liu Y., Yan S., Chan D.L.S., Zhu J., Chen C., Fung A.C., Wong K.K., Hui D.S., Chan F.K. , Tun H.M.",Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events,Gut,2022,"COVID-19, enteric bacterial microflora, immune response",Experiment 10,China,Homo sapiens,Feces,UBERON:0001988,Response to vaccine,EFO:0004645,CoronaVac Low responders,CoronaVac High responders,CoronaVac vaccinees with sVNT > 60% at 1 month after second dose.,36,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 2A,1 December 2025,Blegodwin,Blegodwin,Bacterial species enriched in Low Responders (Group 0) at one month post-vaccination.,decreased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus",3379134|200940|3031449|213115|194924|35832|35833;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|815|909656|821,Complete,NA
bsdb:35140064/11/1,35140064,prospective cohort,35140064,10.1136/gutjnl-2021-326563,NA,"Ng S.C., Peng Y., Zhang L., Mok C.K., Zhao S., Li A., Ching J.Y., Liu Y., Yan S., Chan D.L.S., Zhu J., Chen C., Fung A.C., Wong K.K., Hui D.S., Chan F.K. , Tun H.M.",Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events,Gut,2022,"COVID-19, enteric bacterial microflora, immune response",Experiment 11,China,Homo sapiens,Feces,UBERON:0001988,Response to vaccine,EFO:0004645,Others,Highest-tier responders,BNT162b2 vaccinees in the first quartile (Q1) of sVNT levels at 1 month after second dose.,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 2B,1 December 2025,Blegodwin,Blegodwin,Description: Bacterial species enriched in Highest-tier Responders (Group 1) at one month post-vaccination.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum",3379134|976|200643|171549|815|816|818;3379134|1224|1236|91347|543|544|1639133;1783272|1239|91061|186826|33958|2742598|1613,Complete,NA
bsdb:35140064/11/2,35140064,prospective cohort,35140064,10.1136/gutjnl-2021-326563,NA,"Ng S.C., Peng Y., Zhang L., Mok C.K., Zhao S., Li A., Ching J.Y., Liu Y., Yan S., Chan D.L.S., Zhu J., Chen C., Fung A.C., Wong K.K., Hui D.S., Chan F.K. , Tun H.M.",Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events,Gut,2022,"COVID-19, enteric bacterial microflora, immune response",Experiment 11,China,Homo sapiens,Feces,UBERON:0001988,Response to vaccine,EFO:0004645,Others,Highest-tier responders,BNT162b2 vaccinees in the first quartile (Q1) of sVNT levels at 1 month after second dose.,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 2B,1 December 2025,Blegodwin,Blegodwin,"Bacterial species enriched in Others (Group 0), meaning they are decreased in the Highest-tier group.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:299,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella parvirubra,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius",1783272|1239|186801|186802|31979|1485|1262792;3379134|1224|28216|80840|995019|40544|437898;3384189|32066|203490|203491|203492|848|850;3379134|976|200643|171549|815|909656|310297,Complete,NA
bsdb:35140064/12/1,35140064,prospective cohort,35140064,10.1136/gutjnl-2021-326563,NA,"Ng S.C., Peng Y., Zhang L., Mok C.K., Zhao S., Li A., Ching J.Y., Liu Y., Yan S., Chan D.L.S., Zhu J., Chen C., Fung A.C., Wong K.K., Hui D.S., Chan F.K. , Tun H.M.",Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events,Gut,2022,"COVID-19, enteric bacterial microflora, immune response",Experiment 12,China,Homo sapiens,Feces,UBERON:0001988,Response to vaccine,EFO:0004645,Low responders (Persistent),High responders (Persistent),CoronaVac vaccinees who were consistently identified as high responders across baseline and one-month timepoints in a mixed-effect model.,21,16,NA,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.05,FALSE,NA,NA,"age,time",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 7,1 December 2025,Blegodwin,Blegodwin,"Bacterial species with a significant positive effect size in High Responders (Model 2, P < 0.05).",increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,1783272|201174|1760|85004|31953|1678|1680,Complete,NA
bsdb:35140064/12/2,35140064,prospective cohort,35140064,10.1136/gutjnl-2021-326563,NA,"Ng S.C., Peng Y., Zhang L., Mok C.K., Zhao S., Li A., Ching J.Y., Liu Y., Yan S., Chan D.L.S., Zhu J., Chen C., Fung A.C., Wong K.K., Hui D.S., Chan F.K. , Tun H.M.",Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events,Gut,2022,"COVID-19, enteric bacterial microflora, immune response",Experiment 12,China,Homo sapiens,Feces,UBERON:0001988,Response to vaccine,EFO:0004645,Low responders (Persistent),High responders (Persistent),CoronaVac vaccinees who were consistently identified as high responders across baseline and one-month timepoints in a mixed-effect model.,21,16,NA,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.05,FALSE,NA,NA,"age,time",NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 7,1 December 2025,Blegodwin,Blegodwin,"Bacterial species with a significant negative effect size in High Responders (Model 2, P < 0.05), indicating persistent depletion compared to Low Responders.",decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,3379134|976|200643|171549|815|909656|821,Complete,NA
bsdb:35140064/14/1,35140064,prospective cohort,35140064,10.1136/gutjnl-2021-326563,NA,"Ng S.C., Peng Y., Zhang L., Mok C.K., Zhao S., Li A., Ching J.Y., Liu Y., Yan S., Chan D.L.S., Zhu J., Chen C., Fung A.C., Wong K.K., Hui D.S., Chan F.K. , Tun H.M.",Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events,Gut,2022,"COVID-19, enteric bacterial microflora, immune response",Experiment 14,China,Homo sapiens,Feces,UBERON:0001988,Response to vaccine,EFO:0004645,Low sVNT levels,High sVNT levels,CoronaVac vaccinees with higher levels of sVNT%.,37,37,NA,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,1 December 2025,Blegodwin,Blegodwin,Bacterial species with a significant negative correlation to sVNT levels (Model 2 Adjusted).,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,3379134|976|200643|171549|1853231|574697|544645,Complete,NA
bsdb:35140064/15/1,35140064,prospective cohort,35140064,10.1136/gutjnl-2021-326563,NA,"Ng S.C., Peng Y., Zhang L., Mok C.K., Zhao S., Li A., Ching J.Y., Liu Y., Yan S., Chan D.L.S., Zhu J., Chen C., Fung A.C., Wong K.K., Hui D.S., Chan F.K. , Tun H.M.",Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events,Gut,2022,"COVID-19, enteric bacterial microflora, immune response",Experiment 15,China,Homo sapiens,Feces,UBERON:0001988,Response to vaccine,EFO:0004645,BNT162b2 Low sVNT levels,BNT162b2 High sVNT levels,BNT162b2 vaccinees with higher levels of sVNT% (analyzed as a continuous variable).,101,101,NA,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,1 December 2025,Blegodwin,Blegodwin,Bacterial species with a significant positive correlation to sVNT levels (Model 2 Adjusted).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron",1783272|1239|186801|3085636|186803|841|301302;1783272|1239|186801|3085636|186803|1766253|39491;3379134|976|200643|171549|815|816|818,Complete,NA
bsdb:35140064/15/2,35140064,prospective cohort,35140064,10.1136/gutjnl-2021-326563,NA,"Ng S.C., Peng Y., Zhang L., Mok C.K., Zhao S., Li A., Ching J.Y., Liu Y., Yan S., Chan D.L.S., Zhu J., Chen C., Fung A.C., Wong K.K., Hui D.S., Chan F.K. , Tun H.M.",Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events,Gut,2022,"COVID-19, enteric bacterial microflora, immune response",Experiment 15,China,Homo sapiens,Feces,UBERON:0001988,Response to vaccine,EFO:0004645,BNT162b2 Low sVNT levels,BNT162b2 High sVNT levels,BNT162b2 vaccinees with higher levels of sVNT% (analyzed as a continuous variable).,101,101,NA,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,1 December 2025,Blegodwin,Blegodwin,Bacterial species with a significant negative correlation to sVNT levels (Model 2 Adjusted).,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,3379134|976|200643|171549|2005525|375288|46503,Complete,NA
bsdb:35171931/1/1,35171931,case-control,35171931,10.1371/journal.pone.0263283,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0263283,"Kunaseth J., Waiyaput W., Chanchaem P., Sawaswong V., Permpech R., Payungporn S. , Sophonsritsuk A.",Vaginal microbiome of women with adenomyosis: A case-control study,PloS one,2022,NA,Experiment 1,Thailand,Homo sapiens,Upper part of vagina,UBERON:0003974,Adenomyosis,EFO:1001757,Healthy controls,adenomyosis patients,"Patients with adenomoysis diagnosed using at least three diagnostic ultrasound-based criteria: globular shape uterus, asymmetric myometrial wall, thickening of the endometrial myometrial junction, hyperechoic striae along the sub-endometrial region, and presence of sub-endometrial microcyst",38,40,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,age,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Fig 4,24 September 2023,Andre,"Andre,Peace Sandy,Folakunmi,WikiWorks",Linear discriminant analysis effect size (LEfSe) analysis of microbial abundance in the vaginal sample between adenomyosis and normal uterus.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,s__uncultured bacterium",1783272|201174|1760|85004|31953|419014;1783272|201174|84998|84999|84107;3379134|1224|28211|356|212791;1783272|1239|186801|186802|216572|216851;1783272|1239|909932|909929|1843491|158846;3379134|1224|1236|2887326|468;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572;1783272|1239|909932|909929|1843491;1783272|1239|186801|186802|216572|292632;77133,Complete,Folakunmi
bsdb:35171931/1/2,35171931,case-control,35171931,10.1371/journal.pone.0263283,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0263283,"Kunaseth J., Waiyaput W., Chanchaem P., Sawaswong V., Permpech R., Payungporn S. , Sophonsritsuk A.",Vaginal microbiome of women with adenomyosis: A case-control study,PloS one,2022,NA,Experiment 1,Thailand,Homo sapiens,Upper part of vagina,UBERON:0003974,Adenomyosis,EFO:1001757,Healthy controls,adenomyosis patients,"Patients with adenomoysis diagnosed using at least three diagnostic ultrasound-based criteria: globular shape uterus, asymmetric myometrial wall, thickening of the endometrial myometrial junction, hyperechoic striae along the sub-endometrial region, and presence of sub-endometrial microcyst",38,40,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,age,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Fig 4,24 September 2023,Andre,"Andre,Peace Sandy,Folakunmi,WikiWorks",Linear discriminant analysis effect size (LEfSe) analysis of microbial abundance in the vaginal sample between adenomyosis and normal uterus.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,s__uncultured bacterium",1783272|1239|186801;1783272|1239|186801|186802|216572|236752;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|186802|216572;77133,Complete,Folakunmi
bsdb:35188868/1/1,35188868,case-control,35188868,10.1080/19490976.2022.2038863,NA,"Bosch S., Acharjee A., Quraishi M.N., Rojas P., Bakkali A., Jansen E.E., Brizzio Brentar M., Kuijvenhoven J., Stokkers P., Struys E., Beggs A.D., Gkoutos G.V., de Meij T.G. , de Boer N.K.",The potential of fecal microbiota and amino acids to detect and monitor patients with adenoma,Gut microbes,2022,"Omics, adenoma, biomarker, colorectal cancer, surveillance",Experiment 1,Netherlands,Homo sapiens,Intestine,UBERON:0000160,Colorectal adenoma,EFO:0005406,non-adenoma group,adenoma group,"Patients with a successful polypectomy. A total of 9 patients had advanced adenomas and 10 patients had non-advanced adenoma (NA), with a median size of the largest adenoma being 0.7 cm [IQR 0.5–0.8].
PRIOR to polypectomy.",32,32,3 months,16S,4,Illumina,relative abundances,LEfSe,2,NA,2,"age,body mass index,smoking behavior",NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 2,31 July 2022,Jeshudy,"Jeshudy,WikiWorks",Distribution of selected taxa for adenomas versus controls at baseline,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|976|200643|171549|1853231|574697;1783272|1239|526524|526525|2810280|135858;3379134|1224|28216|80840|995019|40544,Complete,Atrayees
bsdb:35188868/1/2,35188868,case-control,35188868,10.1080/19490976.2022.2038863,NA,"Bosch S., Acharjee A., Quraishi M.N., Rojas P., Bakkali A., Jansen E.E., Brizzio Brentar M., Kuijvenhoven J., Stokkers P., Struys E., Beggs A.D., Gkoutos G.V., de Meij T.G. , de Boer N.K.",The potential of fecal microbiota and amino acids to detect and monitor patients with adenoma,Gut microbes,2022,"Omics, adenoma, biomarker, colorectal cancer, surveillance",Experiment 1,Netherlands,Homo sapiens,Intestine,UBERON:0000160,Colorectal adenoma,EFO:0005406,non-adenoma group,adenoma group,"Patients with a successful polypectomy. A total of 9 patients had advanced adenomas and 10 patients had non-advanced adenoma (NA), with a median size of the largest adenoma being 0.7 cm [IQR 0.5–0.8].
PRIOR to polypectomy.",32,32,3 months,16S,4,Illumina,relative abundances,LEfSe,2,NA,2,"age,body mass index,smoking behavior",NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Figure 2,31 July 2022,Jeshudy,"Jeshudy,WikiWorks",Distribution of selected taxa for adenomas versus controls at baseline,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales",1783272|1239|186801|3085636|186803|207244;1783272|201174|1760|85004|31953|1678;1783272|1239|526524|526525|128827|1573534;1783272|1798710|1906119,Complete,Atrayees
bsdb:35188868/2/NA,35188868,case-control,35188868,10.1080/19490976.2022.2038863,NA,"Bosch S., Acharjee A., Quraishi M.N., Rojas P., Bakkali A., Jansen E.E., Brizzio Brentar M., Kuijvenhoven J., Stokkers P., Struys E., Beggs A.D., Gkoutos G.V., de Meij T.G. , de Boer N.K.",The potential of fecal microbiota and amino acids to detect and monitor patients with adenoma,Gut microbes,2022,"Omics, adenoma, biomarker, colorectal cancer, surveillance",Experiment 2,Netherlands,Homo sapiens,Intestine,UBERON:0000160,Colorectal adenoma,EFO:0005406,non-adenoma group,adenoma group,"Patients with a successful polypectomy. A total of 9 patients had advanced adenomas and 10 patients had non-advanced adenoma (NA), with a median size of the largest adenoma being 0.7 cm [IQR 0.5–0.8].",19,19,3 months,16S,4,Illumina,NA,LEfSe,0.05,NA,2,"age,body mass index,smoking status",NA,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:35188868/3/1,35188868,case-control,35188868,10.1080/19490976.2022.2038863,NA,"Bosch S., Acharjee A., Quraishi M.N., Rojas P., Bakkali A., Jansen E.E., Brizzio Brentar M., Kuijvenhoven J., Stokkers P., Struys E., Beggs A.D., Gkoutos G.V., de Meij T.G. , de Boer N.K.",The potential of fecal microbiota and amino acids to detect and monitor patients with adenoma,Gut microbes,2022,"Omics, adenoma, biomarker, colorectal cancer, surveillance",Experiment 3,Netherlands,Homo sapiens,Intestine,UBERON:0000160,Colorectal adenoma,EFO:0005406,non-adenoma group,adenoma group,"Patients with a successful polypectomy. A total of 9 patients had advanced adenomas and 10 patients had non-advanced adenoma (NA), with a median size of the largest adenoma being 0.7 cm [IQR 0.5–0.8].
POST polypectomy.",32,32,3 months,16S,4,Illumina,NA,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 2,31 July 2022,Jeshudy,"Jeshudy,WikiWorks",Distribution of selected taxa for adenomas versus controls at follow-up.,decreased,"k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|1798710|1906119;1783272|201174|1760|85004|31953|1678,Complete,Atrayees
bsdb:35188868/3/2,35188868,case-control,35188868,10.1080/19490976.2022.2038863,NA,"Bosch S., Acharjee A., Quraishi M.N., Rojas P., Bakkali A., Jansen E.E., Brizzio Brentar M., Kuijvenhoven J., Stokkers P., Struys E., Beggs A.D., Gkoutos G.V., de Meij T.G. , de Boer N.K.",The potential of fecal microbiota and amino acids to detect and monitor patients with adenoma,Gut microbes,2022,"Omics, adenoma, biomarker, colorectal cancer, surveillance",Experiment 3,Netherlands,Homo sapiens,Intestine,UBERON:0000160,Colorectal adenoma,EFO:0005406,non-adenoma group,adenoma group,"Patients with a successful polypectomy. A total of 9 patients had advanced adenomas and 10 patients had non-advanced adenoma (NA), with a median size of the largest adenoma being 0.7 cm [IQR 0.5–0.8].
POST polypectomy.",32,32,3 months,16S,4,Illumina,NA,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Figure 2,31 July 2022,Jeshudy,"Jeshudy,WikiWorks",Distribution of selected taxa for adenomas versus controls at follow-up.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,3379134|1224|28216|80840|995019|40544,Complete,Atrayees
bsdb:35188868/4/1,35188868,case-control,35188868,10.1080/19490976.2022.2038863,NA,"Bosch S., Acharjee A., Quraishi M.N., Rojas P., Bakkali A., Jansen E.E., Brizzio Brentar M., Kuijvenhoven J., Stokkers P., Struys E., Beggs A.D., Gkoutos G.V., de Meij T.G. , de Boer N.K.",The potential of fecal microbiota and amino acids to detect and monitor patients with adenoma,Gut microbes,2022,"Omics, adenoma, biomarker, colorectal cancer, surveillance",Experiment 4,Netherlands,Homo sapiens,Intestine,UBERON:0000160,Colorectal adenoma,EFO:0005406,adenoma group pre-polypectomy,adenoma group post-polypectomy,"Patients with a successful polypectomy. A total of 9 patients had advanced adenomas and 10 patients had non-advanced adenoma (NA), with a median size of the largest adenoma being 0.7 cm [IQR 0.5–0.8].",32,32,3 months,16S,4,Illumina,NA,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,31 July 2022,Jeshudy,"Jeshudy,WikiWorks",Distribution of selected taxa for baseline versus follow-up.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Puniceicoccaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239|186801|3085636|186803|2569097|39488;1783272|544448|31969;3379134|1224|1236|91347|543;3379134|74201|414999|415001|415002;1783272|1239|186801|186802|31979|1485,Complete,Atrayees
bsdb:35188868/4/2,35188868,case-control,35188868,10.1080/19490976.2022.2038863,NA,"Bosch S., Acharjee A., Quraishi M.N., Rojas P., Bakkali A., Jansen E.E., Brizzio Brentar M., Kuijvenhoven J., Stokkers P., Struys E., Beggs A.D., Gkoutos G.V., de Meij T.G. , de Boer N.K.",The potential of fecal microbiota and amino acids to detect and monitor patients with adenoma,Gut microbes,2022,"Omics, adenoma, biomarker, colorectal cancer, surveillance",Experiment 4,Netherlands,Homo sapiens,Intestine,UBERON:0000160,Colorectal adenoma,EFO:0005406,adenoma group pre-polypectomy,adenoma group post-polypectomy,"Patients with a successful polypectomy. A total of 9 patients had advanced adenomas and 10 patients had non-advanced adenoma (NA), with a median size of the largest adenoma being 0.7 cm [IQR 0.5–0.8].",32,32,3 months,16S,4,Illumina,NA,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2,31 July 2022,Jeshudy,"Jeshudy,WikiWorks",Distribution of selected taxa for adenomas at baseline and follow-up.,increased,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,1783272|1798710|1906119,Complete,Atrayees
bsdb:35188868/5/1,35188868,case-control,35188868,10.1080/19490976.2022.2038863,NA,"Bosch S., Acharjee A., Quraishi M.N., Rojas P., Bakkali A., Jansen E.E., Brizzio Brentar M., Kuijvenhoven J., Stokkers P., Struys E., Beggs A.D., Gkoutos G.V., de Meij T.G. , de Boer N.K.",The potential of fecal microbiota and amino acids to detect and monitor patients with adenoma,Gut microbes,2022,"Omics, adenoma, biomarker, colorectal cancer, surveillance",Experiment 5,Netherlands,Homo sapiens,Intestine,UBERON:0000160,Colorectal adenoma,EFO:0005406,control group pre-endoscopy,control group post-endoscopy,Patients with a successful endoscopy.,32,32,3 months,16S,4,Illumina,NA,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2, 3",31 July 2022,Jeshudy,"Jeshudy,Atrayees,WikiWorks",Distribution of selected taxa for baseline versus follow-up,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Puniceicoccaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales",1783272|1239|186801|3085636|186803|2569097|39488;3379134|200940|3031449|213115|194924|872;1783272|1239|909932|1843489|31977|39948;1783272|1239|91061|186826|1300|1301;3379134|256845|1313211|278082|255528|172900;1783272|544448|31969;3379134|74201|414999|415001|415002;1783272|1239|186801|186802|31979|1485;1783272|1798710|1906119,Complete,Atrayees
bsdb:35188868/5/2,35188868,case-control,35188868,10.1080/19490976.2022.2038863,NA,"Bosch S., Acharjee A., Quraishi M.N., Rojas P., Bakkali A., Jansen E.E., Brizzio Brentar M., Kuijvenhoven J., Stokkers P., Struys E., Beggs A.D., Gkoutos G.V., de Meij T.G. , de Boer N.K.",The potential of fecal microbiota and amino acids to detect and monitor patients with adenoma,Gut microbes,2022,"Omics, adenoma, biomarker, colorectal cancer, surveillance",Experiment 5,Netherlands,Homo sapiens,Intestine,UBERON:0000160,Colorectal adenoma,EFO:0005406,control group pre-endoscopy,control group post-endoscopy,Patients with a successful endoscopy.,32,32,3 months,16S,4,Illumina,NA,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,31 July 2022,Jeshudy,"Jeshudy,WikiWorks",Distribution of selected taxa for baseline versus follow-up,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,1783272|1239|186801|3085636|186803,Complete,Atrayees
bsdb:35196800/1/1,35196800,case-control,35196800,https://doi.org/10.1128/spectrum.01901-21,NA,"Guohui Xiao, Guoliang Zhang, Juanjuan Zhang, Lei Liu, Liang Yang yangl@sustech.edu.cn, Lili Ren, Min Ou, Minfei Yu, Peikun Guan, Qinglong Guo, Taosheng Ye, Xiangdong Fu, Yimin Tang, Zhao Cai, Zhaoqin Wang",Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing,Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing,2022,"tuberculosis, Mycobacterium tuberculosis, anti-TB treatment, antibiotic resistance genes, lung microbiota, metagenomics",Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,"Mycobacterium tuberculosis,Lung cancer","NCBITAXON:1773,MONDO:0008903",Healthy Control Group (HCG),Untreated TB Group (UTG) and lung cancer patient group (LCG),"This group consists of patients who have untreated pulmonary tuberculosis group (UTG; 5 males, 7 females) and lung cancer patient group (LCG; 5 males, 2 females)",8,19,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 3C,17 March 2024,BSpac126,"BSpac126,Victoria,Scholastica,WikiWorks",Differentially enriched taxa identified by linear discriminant analysis effect size (LEfSe) among the three groups.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia pickettii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus haemolyticus",3379134|1224|28216|80840|119060|48736|329;1783272|1239|91061|1385|90964|1279|1283,Complete,Svetlana up
bsdb:35196800/2/1,35196800,case-control,35196800,https://doi.org/10.1128/spectrum.01901-21,NA,"Guohui Xiao, Guoliang Zhang, Juanjuan Zhang, Lei Liu, Liang Yang yangl@sustech.edu.cn, Lili Ren, Min Ou, Minfei Yu, Peikun Guan, Qinglong Guo, Taosheng Ye, Xiangdong Fu, Yimin Tang, Zhao Cai, Zhaoqin Wang",Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing,Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing,2022,"tuberculosis, Mycobacterium tuberculosis, anti-TB treatment, antibiotic resistance genes, lung microbiota, metagenomics",Experiment 2,China,Homo sapiens,Throat,UBERON:0000341,Mycobacterium tuberculosis,NCBITAXON:1773,Healthy Control Group (HCG) and Lung Cancer Group (LCG),Untreated TB Group (UTG),This group consists of patients who have Untreated Pulmonary Tuberculosis and are not taking any antibiotics.,15,12,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 3C,20 March 2024,BSpac126,"BSpac126,Victoria,WikiWorks",Differentially enriched taxa identified by linear discriminant analysis effect size (LEfSe) among the three groups.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella|s__Pasteurella multocida,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia solanacearum",3379134|1224|1236|135625|712|745|747;1783272|1239|91061|1385|90964|1279|1280;3379134|1224|28216|80840|119060|48736|305,Complete,Svetlana up
bsdb:35196800/3/1,35196800,case-control,35196800,https://doi.org/10.1128/spectrum.01901-21,NA,"Guohui Xiao, Guoliang Zhang, Juanjuan Zhang, Lei Liu, Liang Yang yangl@sustech.edu.cn, Lili Ren, Min Ou, Minfei Yu, Peikun Guan, Qinglong Guo, Taosheng Ye, Xiangdong Fu, Yimin Tang, Zhao Cai, Zhaoqin Wang",Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing,Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing,2022,"tuberculosis, Mycobacterium tuberculosis, anti-TB treatment, antibiotic resistance genes, lung microbiota, metagenomics",Experiment 3,China,Homo sapiens,Throat,UBERON:0000341,Lung cancer,MONDO:0008903,Healthy Control Group (HCG) and Untreated TB Group (UTG),Lung cancer patient group (LCG),Patients with lung cancer,20,7,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 4D,22 March 2024,BSpac126,"BSpac126,Victoria,Scholastica,WikiWorks",Differentially enriched taxa identified by linear discriminant analysis effect size (LEfSe) among the three groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces sp. ICC4",3379134|976|200643|171549|171552|838|28131;1783272|201174|1760|85011|2062|1883|2099584,Complete,Svetlana up
bsdb:35196800/4/1,35196800,case-control,35196800,https://doi.org/10.1128/spectrum.01901-21,NA,"Guohui Xiao, Guoliang Zhang, Juanjuan Zhang, Lei Liu, Liang Yang yangl@sustech.edu.cn, Lili Ren, Min Ou, Minfei Yu, Peikun Guan, Qinglong Guo, Taosheng Ye, Xiangdong Fu, Yimin Tang, Zhao Cai, Zhaoqin Wang",Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing,Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing,2022,"tuberculosis, Mycobacterium tuberculosis, anti-TB treatment, antibiotic resistance genes, lung microbiota, metagenomics",Experiment 4,China,Homo sapiens,Throat,UBERON:0000341,Mycobacterium tuberculosis,NCBITAXON:1773,Treated pulmonary TB group (TTG) and cured pulmonary TB group (CTG),Untreated pulmonary TB group (UTG),This group consists of patients who have Untreated Pulmonary Tuberculosis and are not taking any antibiotics.,26,12,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 4D,31 July 2024,Scholastica,"Scholastica,WikiWorks",Differentially enriched taxa identified by linear discriminant analysis effect size (LEfSe) among the three groups.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella|s__Pasteurella multocida,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus",3379134|1224|1236|135625|712|745|747;1783272|1239|91061|1385|90964|1279|1280,Complete,Svetlana up
bsdb:35211481/1/1,35211481,case-control,35211481,10.3389/fmed.2021.777961,NA,"Tian H., Ye C., Yang B., Cui J., Zheng Z., Wu C., Zhou S., Lv X., Qin N., Qin H., Li N. , Chen Q.",Gut Metagenome as a Potential Diagnostic and Predictive Biomarker in Slow Transit Constipation,Frontiers in medicine,2021,"biomarker, diagnostic, gut microbiome, metagenomic analysis, pathogenesis, slow transit constipation",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy controls,Slow transit constipation (STC) group,Patients with slow transit constipation (STC),52,66,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1, Table S2, Table S3, Table S4, Table 3",22 March 2025,Tosin,Tosin,Differentially abundant taxa between slow transit constipation (STC) patients and healthy controls,increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium 1_7_47FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 21_3,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 2_2_44A,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 3_1_57FAA_CT1,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 7_1_58FAA,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",1783272|201174;3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|244127;1783272|1239;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|457421;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|1643822|1643826|84111;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|3085636|186803|2719313|333367;1783272|1239|186801|3085636|186803|2719313|358743;1783272|1239|526524|526525|128827|658657;1783272|1239|526524|526525|128827|457422;1783272|1239|186801|186802|216572|946234;1783272|201174|84998|1643822|1643826|644652;1783272|201174|84998|1643822|1643826|644652|471189;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|3085636|186803|1649459|154046;1783272|1239|186801|3085636|186803|658086;1783272|1239|186801|3085636|186803|658087;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|328812;3379134|976|200643|171549|2005525|375288|46503;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|292632;3379134|74201;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|3085636|186803|2941495|1512;1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|292632,Complete,Svetlana up
bsdb:35211481/1/2,35211481,case-control,35211481,10.3389/fmed.2021.777961,NA,"Tian H., Ye C., Yang B., Cui J., Zheng Z., Wu C., Zhou S., Lv X., Qin N., Qin H., Li N. , Chen Q.",Gut Metagenome as a Potential Diagnostic and Predictive Biomarker in Slow Transit Constipation,Frontiers in medicine,2021,"biomarker, diagnostic, gut microbiome, metagenomic analysis, pathogenesis, slow transit constipation",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy controls,Slow transit constipation (STC) group,Patients with slow transit constipation (STC),52,66,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 1, Table S2, Table S3, Table S4, Table 3",22 March 2025,Tosin,"Tosin,Ese",Differentially abundant taxa between slow transit constipation (STC) patients and healthy controls,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 5_1_57FAA,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Methanobacteriati|p__Methanobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp. 4_3_54A2FAA,k__Thermotogati|p__Synergistota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis",3379134|976;3379134|1224|1236|91347|543|547;3384189|32066;1783272|1239|186801|3085636|186803|658085;1783272|1239|909932|909929|1843491|158846;3366610|28890;3379134|1224|28216|80840|75682|846;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|186802|216572|292632|665956;3384194|508458;1783272|1239|186801|3085636|186803|1506553|29347;1783272|1239|186801|186802|216572;1783272|1239|526524|526525|2810280|100883|100884,Complete,Svetlana up
bsdb:35216552/1/1,35216552,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C., Skalnikova H.K., Cizkova J., Cizkova V., Palanova A., Horak V. , Mrazek J.",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 1,Czechia,Sus scrofa domesticus,Skin of body,UBERON:0002097,Disease staging,EFO:0000410,Melanoma surface of pigs with with melanoma regression,Melanoma surface of pigs with Melanoma progression,Melanoma surface samples collected from piglets with melanoma progression,14,10,NA,16S,45,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 1,Figure 4A,1 April 2024,Snehhumann,"Snehhumann,Idiaru angela,WikiWorks",Differential abundance calculated using Linear discriminant analysis (LDA) effect size (LEfSe) at genera level in skin microbiome between melanoma surface in melanoma progression and melanoma regression,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Globicatella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Helcococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Trueperella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium canine oral taxon 260",1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549|815|816;3379134|29547|3031852|213849|72294|194;1783272|1239|186801|3082720|3118655|44259;3384189|32066|203490|203491|203492|848;1783272|1239|91061|186826|186827|13075;1783272|1239|1737404|1737405|1570339|31983;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836;1783272|201174|1760|2037|2049|1069494;1783272|1239|186801|186802|1151637,Complete,Svetlana up
bsdb:35216552/1/2,35216552,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C., Skalnikova H.K., Cizkova J., Cizkova V., Palanova A., Horak V. , Mrazek J.",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 1,Czechia,Sus scrofa domesticus,Skin of body,UBERON:0002097,Disease staging,EFO:0000410,Melanoma surface of pigs with with melanoma regression,Melanoma surface of pigs with Melanoma progression,Melanoma surface samples collected from piglets with melanoma progression,14,10,NA,16S,45,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 2,Figure 4A,1 April 2024,Snehhumann,"Snehhumann,Idiaru angela,MyleeeA,WikiWorks",Differential abundance calculated using Linear discriminant analysis (LDA) effect size (LEfSe) at genera level in skin microbiome between melanoma surface in melanoma progression and melanoma regression,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|g__Aerosphaera,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Atopostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Ignavigranum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Jeotgalibaca,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Oligella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239|91061|186826|137460;1783272|1239|91061|186826|186828|292480;1783272|1239|186801|3085636|186803|572511;1783272|201174|1760|85006|85020|43668;3379134|200940|3031449|213115|194924|872;1783272|201174|1760|85007|85029|37914;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|186827|66831;1783272|1239|186801|186802|216572|216851;1783272|1239|91061|186826|186827|89092;1783272|1239|91061|186826|186828|1470540;1783272|1239|91061|1385|90964|227979;1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85006|1268|1269;3379134|1224|28216|80840|506|90243;3379134|1224|1236|2887326|468|497;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|3068309;1783272|1239|186801|186802|216572|1263|438033;1783272|1239|186801|3082720|186804|1505652;1783272|1239|526524|526525|2810281|191303;1783272|1239|91061|186826|33958|46255;1783272|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:35216552/2/1,35216552,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C., Skalnikova H.K., Cizkova J., Cizkova V., Palanova A., Horak V. , Mrazek J.",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 2,Czechia,Sus scrofa domesticus,Skin of body,UBERON:0002097,Disease staging,EFO:0000410,Melanoma tissue of pigs with with melanoma regression,Melanoma tissue of pigs with Melanoma progression,Melanoma tissue samples collected from piglets with melanoma progression,14,10,NA,16S,45,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 1,Figure 4B,8 April 2024,Idiaru angela,"Idiaru angela,WikiWorks",Differential abundance calculated using Linear discriminant analysis (LDA) effect size (LEfSe) at genera level in skin microbiome between melanoma tissue in melanoma progression and melanoma regression,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Helcococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Trueperella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Umbribacter|s__Umbribacter vaginalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__Clostridiales bacterium S5-A14a",1783272|201174|1760|85007|1653|1716;3384189|32066|203490|203491|203492|848;1783272|1239|1737404|1737405|1570339|31983;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836;33090|35493|3398|72025|3803|3814|508215;1783272|201174|1760|2037|2049|1069494;1783272|201174|84998|1643822|1643826|3472368|1588753;1783272|1239|186801|3082720|543314|1230734,Complete,Svetlana up
bsdb:35216552/2/2,35216552,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C., Skalnikova H.K., Cizkova J., Cizkova V., Palanova A., Horak V. , Mrazek J.",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 2,Czechia,Sus scrofa domesticus,Skin of body,UBERON:0002097,Disease staging,EFO:0000410,Melanoma tissue of pigs with with melanoma regression,Melanoma tissue of pigs with Melanoma progression,Melanoma tissue samples collected from piglets with melanoma progression,14,10,NA,16S,45,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 2,Figure 4B,8 April 2024,Idiaru angela,"Idiaru angela,WikiWorks",Differential abundance calculated using Linear discriminant analysis (LDA) effect size (LEfSe) at genera level in skin microbiome between melanoma tissue in melanoma progression and melanoma regression,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Metazoa|p__Mollusca|c__Gastropoda|o__Neogastropoda|f__Buccinidae|g__Colubraria|s__Colubraria reticulata,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",3379134|1224|1236|2887326|468|469;3379134|1224|1236|135625|712|713;1783272|1239|91061|1385|186817|1386;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|49082;1783272|201174|84998|84999|84107|102106;33208|6447|6448|6479|37796|604271|604273;1783272|201174|1760|85009|31957|1912216;1783272|1239|186801|3085636|186803|189330;3379134|1224|1236|91347|543|547;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|216572|216851;1783272|1239|91061|186826|33958|1578;3379134|1224|28211|356|69277|68287;3379134|1224|28211|356|119045|407;3379134|1224|1236|135614|32033|40323,Complete,Svetlana up
bsdb:35216552/3/1,35216552,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C., Skalnikova H.K., Cizkova J., Cizkova V., Palanova A., Horak V. , Mrazek J.",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 3,Czechia,Sus scrofa domesticus,Skin of body,UBERON:0002097,Cutaneous melanoma,EFO:0000389,healthy skin,melanoma surface from black pigs,cutaneous melanoma surface samples collected from the skin of black pigs,10,24,NA,16S,45,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,decreased,decreased,decreased,Signature 1,Supplementary figure 5,8 April 2024,Idiaru angela,"Idiaru angela,WikiWorks,Tosin","Differential abundance calculated using linear discriminant analysis (LDA) effect size
(LEfSe) results at genus level in skin microbiome between Healthy skin and melanoma surface",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|g__Aerosphaera,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Atopostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Ignavigranum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Jeotgalibaca,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Kurthia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Oligella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii",3379134|1224|1236|2887326|468|469;1783272|1239|91061|186826|137460;1783272|1239|91061|186826|186828|292480;1783272|1239|186801|3085636|186803|572511;1783272|201174|1760|85006|85020|43668;1783272|201174|1760|85006|85019|1696;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85007|85029|37914;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|186827|66831;1783272|1239|186801|186802|216572|216851;1783272|1239|91061|186826|186827|89092;1783272|1239|91061|186826|186828|1470540;1783272|1239|91061|1385|90964|227979;1783272|201174|1760|85006|1268|57493;1783272|1239|91061|1385|186818|1649;1783272|1239|91061|186826|33958|1578;3379134|1224|28216|80840|75682|149698;3379134|1224|28216|80840|506|90243;3379134|1224|1236|72274|135621|286;3379134|1224|1236|2887326|468|497;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|3068309;3379134|1224|28211|204457|41297|13687;1783272|1239|186801|3082720|186804|1505652;1783272|1239|526524|526525|2810281|191303;1783272|1239|91061|186826|33958|46255;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|216572|1263|438033,Complete,Svetlana up
bsdb:35216552/3/2,35216552,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C., Skalnikova H.K., Cizkova J., Cizkova V., Palanova A., Horak V. , Mrazek J.",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 3,Czechia,Sus scrofa domesticus,Skin of body,UBERON:0002097,Cutaneous melanoma,EFO:0000389,healthy skin,melanoma surface from black pigs,cutaneous melanoma surface samples collected from the skin of black pigs,10,24,NA,16S,45,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,decreased,decreased,decreased,Signature 2,Supplementary figure 5,8 April 2024,Idiaru angela,"Idiaru angela,WikiWorks",Differential abundance calculated using linear discriminant analysis (LDA) effect size (LEfSe) results at genus level in skin microbiome between Healthy skin and melanoma surface.,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Helcococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3384189|32066|203490|203491|203492|848;1783272|1239|1737404|1737405|1570339|31983;3379134|1224|1236|2887326|468|475;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|3082720|186804|1257;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:35216552/4/1,35216552,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C., Skalnikova H.K., Cizkova J., Cizkova V., Palanova A., Horak V. , Mrazek J.",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 4,Czechia,Sus scrofa domesticus,Skin of body,UBERON:0002097,Cutaneous melanoma,EFO:0000389,healthy skin,melanoma tissue from black pigs,cutaneous melanoma tissue samples collected from the skin of black pigs,10,24,NA,16S,45,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,decreased,decreased,decreased,Signature 1,Supplementary figure 6,9 April 2024,Idiaru angela,"Idiaru angela,WikiWorks,Tosin",Differential abundance calculated using linear discriminant analysis (LDA) effect size (LEfSe) results at genus level in skin microbiome between Healthy skin and melanoma tissue.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|g__Aerosphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Atopostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Frigoribacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Ignavigranum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Janibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Jeotgalibaca,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Kurthia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Oligella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",3379134|1224|1236|2887326|468|469;1783272|1239|91061|186826|137460;1783272|1239|909932|909929|1843491|82373;1783272|1239|91061|186826|186828|292480;1783272|1239|186801|3085636|186803|572511;1783272|201174|1760|85006|85020|43668;1783272|201174|1760|85006|85019|1696;1783272|1239|186801|186802|31979|1485;1783272|201174|1760|85007|85029|37914;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|186827|66831;1783272|1239|186801|186802|216572|216851;3379134|976|117743|200644|49546|237;1783272|201174|1760|85006|85023|96492;1783272|1239|91061|186826|186827|89092;1783272|201174|1760|85006|85021|53457;1783272|1239|91061|186826|186828|1470540;1783272|1239|91061|1385|90964|227979;1783272|201174|1760|85006|1268|57493;1783272|1239|91061|1385|186818|1649;1783272|1239|91061|186826|33958|1578;3379134|1224|28216|80840|75682|149698;1783272|201174|1760|85006|1268|1269;3379134|1224|1236|2887326|468|475;3379134|1224|28216|80840|506|90243;3379134|1224|1236|72274|135621|286;3379134|1224|1236|2887326|468|497;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;1783272|201174|1760|85006|1268|32207;1783272|1239|186801|186802|216572|3068309;1783272|1239|186801|186802|216572|1263|438033;3379134|1224|28211|204457|41297|13687;1783272|1239|186801|3082720|186804|1505652;1783272|1239|526524|526525|2810281|191303;1783272|1239|91061|186826|33958|46255,Complete,Svetlana up
bsdb:35216552/4/2,35216552,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C., Skalnikova H.K., Cizkova J., Cizkova V., Palanova A., Horak V. , Mrazek J.",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 4,Czechia,Sus scrofa domesticus,Skin of body,UBERON:0002097,Cutaneous melanoma,EFO:0000389,healthy skin,melanoma tissue from black pigs,cutaneous melanoma tissue samples collected from the skin of black pigs,10,24,NA,16S,45,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,decreased,decreased,decreased,Signature 2,Supplementary figure 6,9 April 2024,Idiaru angela,"Idiaru angela,WikiWorks",Differential abundance calculated using linear discriminant analysis (LDA) effect size (LEfSe) results at genus level in skin microbiome between Healthy skin and melanoma tissue.,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Trueperella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium",3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|90964|1279;1783272|201174|1760|2037|2049|1069494;1783272|1239|186801|3082720|186804|1257;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|1737404|1737405|1570339|543311;1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549|815|816;1783272|201174|1760|85009|31957|1912216,Complete,Svetlana up
bsdb:35216552/5/1,35216552,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C., Skalnikova H.K., Cizkova J., Cizkova V., Palanova A., Horak V. , Mrazek J.",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 5,Czechia,Sus scrofa domesticus,Feces,UBERON:0001988,Cutaneous melanoma,EFO:0000389,controls without melanoma and melanoma regression,Melanoma progression,samples collected from piglets undergoing melanoma progression.,24,10,NA,16S,45,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary figure 7,9 April 2024,Idiaru angela,"Idiaru angela,WikiWorks",Differential abundance calculated using linear discriminant analysis (LDA) effect size (LEfSe) results at genus level in fecal microbiome between control and melanoma progression and regression samples,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Helcococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819",3379134|976|200643|171549|815|816;1783272|1239|186801|3082720|3118655|44259;3384189|32066|203490|203491|203492|848;1783272|1239|1737404|1737405|1570339|31983;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|216851|1946507,Complete,Svetlana up
bsdb:35216552/6/1,35216552,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C., Skalnikova H.K., Cizkova J., Cizkova V., Palanova A., Horak V. , Mrazek J.",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 6,Czechia,Sus scrofa domesticus,Feces,UBERON:0001988,Cutaneous melanoma,EFO:0000389,controls without melanoma and melanoma progression,melanoma regression,samples collected from piglets undergoing melanoma regression,20,14,NA,16S,45,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary figure 7,10 April 2024,Idiaru angela,"Idiaru angela,WikiWorks",Differential abundance calculated using linear discriminant analysis (LDA) effect size (LEfSe) results at genus level in fecal microbiome between control and melanoma progression and regression samples,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:35216552/7/1,35216552,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C., Skalnikova H.K., Cizkova J., Cizkova V., Palanova A., Horak V. , Mrazek J.",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 7,Czechia,Sus scrofa domesticus,Feces,UBERON:0001988,Cutaneous melanoma,EFO:0000389,Controls without melanoma,Melanoma progression and regression,samples collected from piglets undergoing melanoma regression and progression,10,24,NA,16S,45,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary figure 7,10 April 2024,Idiaru angela,"Idiaru angela,WikiWorks",Differential abundance calculated using linear discriminant analysis (LDA) effect size (LEfSe) results at genus level in fecal microbiome between control and melanoma progression and regression samples,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136",3379134|976|200643|171549|171552|1283313;1783272|1239|909932|909929|1843491|82373;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|248744;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|3085636|186803|877420,Complete,Svetlana up
bsdb:35216552/9/NA,35216552,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C., Skalnikova H.K., Cizkova J., Cizkova V., Palanova A., Horak V. , Mrazek J.",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 9,Czechia,Sus scrofa domesticus,Skin of body,UBERON:0002097,Sample splitting,EFO:0030016,melanoma surface,melanoma tissue,melanoma inner tissue samples collected from piglets with melanoma,24,24,NA,16S,45,Ion Torrent,relative abundances,NA,NA,NA,NA,NA,NA,NA,decreased,decreased,decreased,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:35216552/10/NA,35216552,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C., Skalnikova H.K., Cizkova J., Cizkova V., Palanova A., Horak V. , Mrazek J.",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 10,Czechia,Sus scrofa domesticus,Skin of body,UBERON:0002097,Cutaneous melanoma,EFO:0000389,skin samples from white piglets,skin samples from crossbred piglets,skin samples from Black crossbred piglets.,10,4,NA,16S,45,Ion Torrent,relative abundances,NA,NA,NA,NA,NA,NA,NA,decreased,decreased,unchanged,unchanged,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:35216552/11/NA,35216552,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C., Skalnikova H.K., Cizkova J., Cizkova V., Palanova A., Horak V. , Mrazek J.",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 11,Czechia,Sus scrofa domesticus,Skin of body,UBERON:0002097,Cutaneous melanoma,EFO:0000389,samples from white piglets,samples from MeLiM piglets,samples from piglets gotten through Homogenous breeding of two Black MeLiM pigs.,10,20,NA,16S,45,Ion Torrent,relative abundances,NA,NA,NA,NA,NA,NA,NA,decreased,decreased,decreased,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:35216552/12/NA,35216552,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C., Skalnikova H.K., Cizkova J., Cizkova V., Palanova A., Horak V. , Mrazek J.",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 12,Czechia,Sus scrofa domesticus,Skin of body,UBERON:0002097,Breed,EFO:0005238,Black crossbred between white and MeLiM piglets,Homogenous breed Black MeLiM piglets,samples from piglets gotten through Homogenous breeding of two Black MeLiM pigs.,4,20,NA,16S,45,Ion Torrent,relative abundances,NA,NA,NA,NA,NA,NA,NA,decreased,decreased,decreased,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:35216552/13/NA,35216552,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C., Skalnikova H.K., Cizkova J., Cizkova V., Palanova A., Horak V. , Mrazek J.",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 13,Czechia,Sus scrofa domesticus,Skin of body,UBERON:0002097,Age at assessment,EFO:0008007,melanoma regression at age 8 weeks,melanoma regression at age 12 weeks,samples gotten from piglets undergoing melanoma regression at age 12 weeks,14,14,NA,16S,45,Ion Torrent,relative abundances,NA,NA,NA,NA,NA,NA,NA,increased,increased,unchanged,unchanged,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:35216552/14/NA,35216552,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C., Skalnikova H.K., Cizkova J., Cizkova V., Palanova A., Horak V. , Mrazek J.",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 14,Czechia,Sus scrofa domesticus,Skin of body,UBERON:0002097,Age at assessment,EFO:0008007,melanoma regression at age 10 weeks,melanoma regression at age 12 weeks,samples gotten from piglets undergoing melanoma regression at age 12 weeks,14,14,NA,16S,45,Ion Torrent,relative abundances,NA,NA,NA,NA,NA,NA,NA,decreased,decreased,decreased,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:35216552/15/NA,35216552,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C., Skalnikova H.K., Cizkova J., Cizkova V., Palanova A., Horak V. , Mrazek J.",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 15,Czechia,Sus scrofa domesticus,Skin of body,UBERON:0002097,Age at assessment,EFO:0008007,melanoma regression at age 8 weeks,melanoma regression at age 10 weeks,samples gotten from piglets undergoing melanoma regression at age 10 weeks,14,14,NA,16S,45,Ion Torrent,relative abundances,NA,NA,NA,NA,NA,NA,NA,increased,increased,increased,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:35216552/16/NA,35216552,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C., Skalnikova H.K., Cizkova J., Cizkova V., Palanova A., Horak V. , Mrazek J.",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 16,Czechia,Sus scrofa domesticus,Feces,UBERON:0001988,Age at assessment,EFO:0008007,melanoma regression at age 8 weeks,melanoma regression at age 10 weeks,samples gotten from piglets undergoing melanoma regression at age 10 weeks,14,14,NA,16S,45,Ion Torrent,relative abundances,NA,NA,NA,NA,NA,NA,NA,increased,increased,unchanged,unchanged,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:35216552/17/NA,35216552,laboratory experiment,35216552,https://doi.org/10.1186/s12866-022-02458-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5,"Mekadim C., Skalnikova H.K., Cizkova J., Cizkova V., Palanova A., Horak V. , Mrazek J.",Dysbiosis of skin microbiome and gut microbiome in melanoma progression,BMC microbiology,2022,"Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment",Experiment 17,Czechia,Sus scrofa domesticus,Feces,UBERON:0001988,Breed,EFO:0005238,crossbred piglets undergoing regression,MeLiM piglets undergoing regression,samples gotten from Black MeLiM piglets undergoing regression,4,10,NA,16S,45,Ion Torrent,relative abundances,NA,NA,NA,NA,NA,NA,NA,decreased,decreased,decreased,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:35229279/1/1,35229279,"cross-sectional observational, not case-control",35229279,https://doi.org/10.1007%2Fs42770-022-00721-5,NA,"Wang X., Mi Q., Yang J., Guan Y., Zeng W., Xiang H., Liu X., Yang W., Yang G., Li X., Cui Y. , Gao Q.",Effect of electronic cigarette and tobacco smoking on the human saliva microbial community,Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology],2022,"Community profiles, E-cigarettes, Oral microbial flora, Smoking",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Non Smokers,Tobacco smokers,The volunteers who smoked tobacco,6,14,6 months,16S,45,Ion Torrent,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,increased,unchanged,NA,NA,Signature 1,Figure 4 (C-F),14 March 2023,Annabelcute,"Annabelcute,Aiyshaaaa,Atrayees,WikiWorks","The relative abundances of Neisseria, Prevotellaceae, Corynebacterium, and Porphyromonas in the two groups.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",3379134|976|200643|171549|171552;3379134|976|200643|171549|171551|836,Complete,Atrayees
bsdb:35229279/2/2,35229279,"cross-sectional observational, not case-control",35229279,https://doi.org/10.1007%2Fs42770-022-00721-5,NA,"Wang X., Mi Q., Yang J., Guan Y., Zeng W., Xiang H., Liu X., Yang W., Yang G., Li X., Cui Y. , Gao Q.",Effect of electronic cigarette and tobacco smoking on the human saliva microbial community,Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology],2022,"Community profiles, E-cigarettes, Oral microbial flora, Smoking",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Non Smokers,E-cigarette smokers,The volunteers who smoked electronic cigarettes.,6,5,6 months,16S,45,Ion Torrent,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,NA,Signature 2,Figure 4 (C-F),6 June 2023,Aiyshaaaa,"Aiyshaaaa,WikiWorks","The relative abundances of Neisseria, Prevotellaceae, Corynebacterium, and Porphyromonas in the two groups.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium",3379134|1224|28216|206351|481|482;1783272|201174|1760|85007|1653|1716,Complete,Atrayees
bsdb:35229279/3/1,35229279,"cross-sectional observational, not case-control",35229279,https://doi.org/10.1007%2Fs42770-022-00721-5,NA,"Wang X., Mi Q., Yang J., Guan Y., Zeng W., Xiang H., Liu X., Yang W., Yang G., Li X., Cui Y. , Gao Q.",Effect of electronic cigarette and tobacco smoking on the human saliva microbial community,Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology],2022,"Community profiles, E-cigarettes, Oral microbial flora, Smoking",Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Tobacco smokers,E-cigarette smokers,The volunteers who smoked electronic cigarettes.,14,5,6 months,16S,45,Ion Torrent,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 4 (C-F),6 June 2023,Aiyshaaaa,"Atrayees,Aiyshaaaa,WikiWorks","The relative abundances of Neisseria, Prevotellaceae, Corynebacterium, and Porphyromonas in the two groups.",decreased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,3379134|1224|28216|206351|481|482,Complete,Atrayees
bsdb:35229279/3/2,35229279,"cross-sectional observational, not case-control",35229279,https://doi.org/10.1007%2Fs42770-022-00721-5,NA,"Wang X., Mi Q., Yang J., Guan Y., Zeng W., Xiang H., Liu X., Yang W., Yang G., Li X., Cui Y. , Gao Q.",Effect of electronic cigarette and tobacco smoking on the human saliva microbial community,Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology],2022,"Community profiles, E-cigarettes, Oral microbial flora, Smoking",Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Tobacco smokers,E-cigarette smokers,The volunteers who smoked electronic cigarettes.,14,5,6 months,16S,45,Ion Torrent,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 4 (C-F),6 June 2023,Aiyshaaaa,"Aiyshaaaa,Atrayees,WikiWorks","The relative abundances of Neisseria, Prevotellaceae, Corynebacterium, and Porphyromonas in the two groups.",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,3379134|976|200643|171549|171552,Complete,Atrayees
bsdb:35229279/5/1,35229279,"cross-sectional observational, not case-control",35229279,https://doi.org/10.1007%2Fs42770-022-00721-5,NA,"Wang X., Mi Q., Yang J., Guan Y., Zeng W., Xiang H., Liu X., Yang W., Yang G., Li X., Cui Y. , Gao Q.",Effect of electronic cigarette and tobacco smoking on the human saliva microbial community,Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology],2022,"Community profiles, E-cigarettes, Oral microbial flora, Smoking",Experiment 5,China,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Quitting smokers,Tobacco smokers,Volunteers who are tobacco smokers,8,14,6 months,16S,45,Ion Torrent,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,NA,Signature 1,Figure 4(C-F),20 June 2023,Atrayees,"Atrayees,WikiWorks","The relative abundances of Neisseria, Prevotellaceae, Corynebacterium, and Porphyromonas in the two groups.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",3379134|976|200643|171549|171552;3379134|976|200643|171549|171551|836,Complete,Atrayees
bsdb:35229279/5/2,35229279,"cross-sectional observational, not case-control",35229279,https://doi.org/10.1007%2Fs42770-022-00721-5,NA,"Wang X., Mi Q., Yang J., Guan Y., Zeng W., Xiang H., Liu X., Yang W., Yang G., Li X., Cui Y. , Gao Q.",Effect of electronic cigarette and tobacco smoking on the human saliva microbial community,Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology],2022,"Community profiles, E-cigarettes, Oral microbial flora, Smoking",Experiment 5,China,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Quitting smokers,Tobacco smokers,Volunteers who are tobacco smokers,8,14,6 months,16S,45,Ion Torrent,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,NA,Signature 2,Figure 4(C-F),21 June 2023,Atrayees,"Atrayees,WikiWorks","The relative abundances of Neisseria, Prevotellaceae, Corynebacterium, and Porphyromonas in the two groups.",decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,1783272|201174|1760|85007|1653|1716,Complete,Atrayees
bsdb:35229279/6/2,35229279,"cross-sectional observational, not case-control",35229279,https://doi.org/10.1007%2Fs42770-022-00721-5,NA,"Wang X., Mi Q., Yang J., Guan Y., Zeng W., Xiang H., Liu X., Yang W., Yang G., Li X., Cui Y. , Gao Q.",Effect of electronic cigarette and tobacco smoking on the human saliva microbial community,Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology],2022,"Community profiles, E-cigarettes, Oral microbial flora, Smoking",Experiment 6,China,Homo sapiens,Saliva,UBERON:0001836,Smoking behavior,EFO:0004318,Quitting smokers,E-cigarette smokers,Volunteers who smoke E-cigarettes,8,5,6 months,16S,45,Ion Torrent,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 4(C-F),20 June 2023,Atrayees,"Atrayees,WikiWorks","The relative abundances of Neisseria, Prevotellaceae, Corynebacterium, and Porphyromonas in the two groups.",decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,1783272|201174|1760|85007|1653|1716,Complete,Atrayees
bsdb:35233023/1/1,35233023,time series / longitudinal observational,35233023,10.1038/s41598-022-07086-7,NA,"Amaruddin A.I., Koopman J.P.R., Muhammad M., Lenaerts K., van Eijk H.M.H., Brienen E.A.T., Geelen A.R., van Lieshout L., Wahyuni S., Kuijper E.J., Zwittink R.D., Hamid F., Sartono E. , Yazdanbakhsh M.","Intestinal permeability before and after albendazole treatment in low and high socioeconomic status schoolchildren in Makassar, Indonesia",Scientific reports,2022,NA,Experiment 1,Indonesia,Homo sapiens,Feces,UBERON:0001988,Intestinal helminthiasis,MONDO:0024271,Low-SES helminth-uninfected group (before treatment),Low-SES helminth-uninfected group (after treatment),Stool samples collected four (4) weeks after albendazole treatment from children of low socioeconomic status (SES) who were uninfected with helminths.,29,29,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3B,25 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differential abundance analysis by DESeq2 indicating increased relative abundance and decreased relative abundance after treatment with albendazole in Low-SES helminth-uninfected children.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|292632,Complete,Svetlana up
bsdb:35233023/1/2,35233023,time series / longitudinal observational,35233023,10.1038/s41598-022-07086-7,NA,"Amaruddin A.I., Koopman J.P.R., Muhammad M., Lenaerts K., van Eijk H.M.H., Brienen E.A.T., Geelen A.R., van Lieshout L., Wahyuni S., Kuijper E.J., Zwittink R.D., Hamid F., Sartono E. , Yazdanbakhsh M.","Intestinal permeability before and after albendazole treatment in low and high socioeconomic status schoolchildren in Makassar, Indonesia",Scientific reports,2022,NA,Experiment 1,Indonesia,Homo sapiens,Feces,UBERON:0001988,Intestinal helminthiasis,MONDO:0024271,Low-SES helminth-uninfected group (before treatment),Low-SES helminth-uninfected group (after treatment),Stool samples collected four (4) weeks after albendazole treatment from children of low socioeconomic status (SES) who were uninfected with helminths.,29,29,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3B,25 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differential abundance analysis by DESeq2 indicating increased relative abundance and decreased relative abundance after treatment with albendazole in Low-SES helminth-uninfected children.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio",1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572|216851;3379134|1224|1236|135624|83763|83770,Complete,Svetlana up
bsdb:35233023/2/1,35233023,time series / longitudinal observational,35233023,10.1038/s41598-022-07086-7,NA,"Amaruddin A.I., Koopman J.P.R., Muhammad M., Lenaerts K., van Eijk H.M.H., Brienen E.A.T., Geelen A.R., van Lieshout L., Wahyuni S., Kuijper E.J., Zwittink R.D., Hamid F., Sartono E. , Yazdanbakhsh M.","Intestinal permeability before and after albendazole treatment in low and high socioeconomic status schoolchildren in Makassar, Indonesia",Scientific reports,2022,NA,Experiment 2,Indonesia,Homo sapiens,Feces,UBERON:0001988,Intestinal helminthiasis,MONDO:0024271,High-SES group (before treatment),High-SES group (after treatment),Stool samples collected four (4) weeks after albendazole treatment from children of high socioeconomic status (SES).,66,66,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3B,25 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differential abundance analysis by DESeq2 indicating increased relative abundance and decreased relative abundance after treatment with albendazole in High-SES children.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:35233023/2/2,35233023,time series / longitudinal observational,35233023,10.1038/s41598-022-07086-7,NA,"Amaruddin A.I., Koopman J.P.R., Muhammad M., Lenaerts K., van Eijk H.M.H., Brienen E.A.T., Geelen A.R., van Lieshout L., Wahyuni S., Kuijper E.J., Zwittink R.D., Hamid F., Sartono E. , Yazdanbakhsh M.","Intestinal permeability before and after albendazole treatment in low and high socioeconomic status schoolchildren in Makassar, Indonesia",Scientific reports,2022,NA,Experiment 2,Indonesia,Homo sapiens,Feces,UBERON:0001988,Intestinal helminthiasis,MONDO:0024271,High-SES group (before treatment),High-SES group (after treatment),Stool samples collected four (4) weeks after albendazole treatment from children of high socioeconomic status (SES).,66,66,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3B,25 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differential abundance analysis by DESeq2 indicating increased relative abundance and decreased relative abundance after treatment with albendazole in High-SES children.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,1783272|1239|186801|186802|216572|216851,Complete,Svetlana up
bsdb:35250962/1/1,35250962,case-control,35250962,10.3389/fmicb.2022.851670,NA,"Kim M.J., Lee S., Kwon M.Y. , Kim M.",Clinical Significance of Composition and Functional Diversity of the Vaginal Microbiome in Recurrent Vaginitis,Frontiers in microbiology,2022,"Lactobacillus spp., microbiome, recurrent vaginitis, taxonomy, vagina",Experiment 1,South Korea,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Vaginitis,MONDO:0002234,Healthy women (control),Recurrent vaginitis (RV),Women of reproductive age diagnosed with Recurrent vaginitis (RV).,100,40,3 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,decreased,decreased,NA,decreased,Signature 1,Figure 1,9 April 2024,Rahila,"Rahila,Scholastica,WikiWorks",Statistically significant taxa (y-axis) between 40 cases with recurrent vaginitis (RV) and 100 healthy individuals (x-axis).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemelliphila|s__Gemelliphila asaccharolytica,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia vaginalis,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma urealyticum",3379134|1224|1236|91347|543|561|562;1783272|201174|84998|84999|1643824|2767327|82135;1783272|201174|1760|85004|31953|2701|2702;1783272|1239|91061|1385|539738|3076174|502393;3384189|32066|203490|203491|1129771|168808|187101;1783272|544448|2790996|2790998|2129|2130,Complete,Svetlana up
bsdb:35250962/1/2,35250962,case-control,35250962,10.3389/fmicb.2022.851670,NA,"Kim M.J., Lee S., Kwon M.Y. , Kim M.",Clinical Significance of Composition and Functional Diversity of the Vaginal Microbiome in Recurrent Vaginitis,Frontiers in microbiology,2022,"Lactobacillus spp., microbiome, recurrent vaginitis, taxonomy, vagina",Experiment 1,South Korea,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Vaginitis,MONDO:0002234,Healthy women (control),Recurrent vaginitis (RV),Women of reproductive age diagnosed with Recurrent vaginitis (RV).,100,40,3 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,decreased,decreased,NA,decreased,Signature 2,Figure 1,20 June 2024,Scholastica,"Scholastica,WikiWorks",Statistically significant taxa (y-axis) between 40 cases with recurrent vaginitis (RV) and 100 healthy individuals (x-axis).,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus jensenii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|47770;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|91061|186826|33958|1578|109790;1783272|1239|91061|186826|33958|2742598|1598,Complete,Svetlana up
bsdb:35250962/2/1,35250962,case-control,35250962,10.3389/fmicb.2022.851670,NA,"Kim M.J., Lee S., Kwon M.Y. , Kim M.",Clinical Significance of Composition and Functional Diversity of the Vaginal Microbiome in Recurrent Vaginitis,Frontiers in microbiology,2022,"Lactobacillus spp., microbiome, recurrent vaginitis, taxonomy, vagina",Experiment 2,South Korea,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Microbiome,EFO:0004982,Community state type (CST) I,Community state type (CST) III and IV,Women of reproductive age diagnosed with Recurrent vaginitis (RV) categorized as community state type (CST) III and IV,5,29,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,20 June 2024,Scholastica,"Scholastica,WikiWorks","Differential abundance of the bacterial taxa in three CST (I, III, and IV) groups of vaginal samples of patients with recurrent vaginitis (RV)",decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,1783272|1239|91061|186826|33958|1578|47770,Complete,Svetlana up
bsdb:35250962/3/1,35250962,case-control,35250962,10.3389/fmicb.2022.851670,NA,"Kim M.J., Lee S., Kwon M.Y. , Kim M.",Clinical Significance of Composition and Functional Diversity of the Vaginal Microbiome in Recurrent Vaginitis,Frontiers in microbiology,2022,"Lactobacillus spp., microbiome, recurrent vaginitis, taxonomy, vagina",Experiment 3,South Korea,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Microbiome,EFO:0004982,Community state type (CST) I and IV,Community state type (CST) III,Women of reproductive age diagnosed with Recurrent vaginitis (RV) categorized as community state type (CST) III,26,8,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,20 June 2024,Scholastica,"Scholastica,WikiWorks","Differential abundance of the bacterial taxa in three CST (I, III, and IV) groups of vaginal samples of patients with recurrent vaginitis (RV)",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri",1783272|1239|91061|186826|33958|1578|147802;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061;1783272|1239|91061|186826|33958|1578;1783272|1239;1783272|1239|91061|186826|33958|2742598|1598,Complete,Svetlana up
bsdb:35250962/4/1,35250962,case-control,35250962,10.3389/fmicb.2022.851670,NA,"Kim M.J., Lee S., Kwon M.Y. , Kim M.",Clinical Significance of Composition and Functional Diversity of the Vaginal Microbiome in Recurrent Vaginitis,Frontiers in microbiology,2022,"Lactobacillus spp., microbiome, recurrent vaginitis, taxonomy, vagina",Experiment 4,South Korea,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Microbiome,EFO:0004982,Community state type (CST) I and III,Community state type (CST) IV,Women of reproductive age diagnosed with Recurrent vaginitis (RV) categorized as community state type (CST) III and IV,13,21,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,20 June 2024,Scholastica,"Scholastica,WikiWorks","Differential abundance of the bacterial taxa in three CST (I, III, and IV) groups of vaginal samples of patients with recurrent vaginitis (RV)",increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales,k__Bacillati|p__Bacillota|c__Tissierellia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|201174;3379134|976|200643|171549;3379134|976|200643;3379134|976;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;1783272|201174|84998|84999|1643824|2767327|82135;1783272|201174|1760|85004|31953|2701;1783272|201174|1760|85004|31953|2701|2702;1783272|1239|1737404|1737405|1570339;1783272|1239|1737404|1737405;1783272|1239|1737404;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:35276770/1/1,35276770,laboratory experiment,35276770,10.3390/nu14030412,NA,"McMillen S., Thomas S., Liang E., Nonnecke E.B., Slupsky C. , Lönnerdal B.",Gut Microbiome Alterations following Postnatal Iron Supplementation Depend on Iron Form and Persist into Adulthood,Nutrients,2022,"ferrous bis-glycinate chelate, ferrous sulfate, gut microbiome, infant nutrition, iron supplement, metabolomics, rat model",Experiment 1,United States of America,Rattus norvegicus,Cecum mucosa,UBERON:0000314,Iron biomarker measurement,EFO:0004461,Vehicle control-supplemented (CON) pups,Ferrous sulfate (FS) treated pups (PD 15),Pre-weaning Sprague-Dawley rat pups given oral supplements of ferrous sulfate (FS) on postnatal day (PD) 2–14 and samples collected from 4–6 hours fasted animals on postnatal day (PD) 15.,28,27,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 1,Supplementary Table S3 + Table S4,19 March 2024,Keamy,"Keamy,Joan Chuks,MyleeeA,Victoria,WikiWorks",Taxa Differing in Abundance Between Ferrous sulfate (FS) treated pups (PD 15) and Vehicle control-supplemented (CON) pups as determined by DESeq2,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|s__uncultured Clostridia bacterium",1783272|1239|186801|3085636|186803|1427378;1783272|1239|91061|186826|186827|1375;1783272|544448|31969|186332|186333|2086;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|216851|1946507;1783272|1239|526524|526525|128827|1729679;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|216572|1892380;1783272|544448;1783272|1239|186801|186802|216572|100175;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|244328,Complete,Svetlana up
bsdb:35276770/1/2,35276770,laboratory experiment,35276770,10.3390/nu14030412,NA,"McMillen S., Thomas S., Liang E., Nonnecke E.B., Slupsky C. , Lönnerdal B.",Gut Microbiome Alterations following Postnatal Iron Supplementation Depend on Iron Form and Persist into Adulthood,Nutrients,2022,"ferrous bis-glycinate chelate, ferrous sulfate, gut microbiome, infant nutrition, iron supplement, metabolomics, rat model",Experiment 1,United States of America,Rattus norvegicus,Cecum mucosa,UBERON:0000314,Iron biomarker measurement,EFO:0004461,Vehicle control-supplemented (CON) pups,Ferrous sulfate (FS) treated pups (PD 15),Pre-weaning Sprague-Dawley rat pups given oral supplements of ferrous sulfate (FS) on postnatal day (PD) 2–14 and samples collected from 4–6 hours fasted animals on postnatal day (PD) 15.,28,27,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 2,Supplementary Table S3 + Table S4,19 March 2024,Keamy,"Keamy,Joan Chuks,Victoria,WikiWorks",Taxa Differing in Abundance Between Ferrous sulfate (FS) treated pups (PD 15) and Vehicle control-supplemented (CON) pups as determined by DESeq2,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Yaniella,s__uncultured bacterium,s__uncultured organism",1783272|201174|84998|1643822|1643826|447020;3379134|976|200643|171549|171550|239759;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85006|85020|43668;1783272|201174|1760|85006|85019|1696;1783272|1239|186801|3085636|186803|830;1783272|1239|186801|186802|1470353;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|186827|66831;1783272|1239|91061|1385|90964|227979;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|248744;3379134|1224|28216|80840|995019|577310;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810281|191303;1783272|201174|1760|85006|1268|225447;77133;155900,Complete,Svetlana up
bsdb:35276770/2/1,35276770,laboratory experiment,35276770,10.3390/nu14030412,NA,"McMillen S., Thomas S., Liang E., Nonnecke E.B., Slupsky C. , Lönnerdal B.",Gut Microbiome Alterations following Postnatal Iron Supplementation Depend on Iron Form and Persist into Adulthood,Nutrients,2022,"ferrous bis-glycinate chelate, ferrous sulfate, gut microbiome, infant nutrition, iron supplement, metabolomics, rat model",Experiment 2,United States of America,Rattus norvegicus,Cecum mucosa,UBERON:0000314,Iron biomarker measurement,EFO:0004461,Vehicle control-supplemented (CON) pups,Ferrous bis-glycinate chelate (FC) treated pups (PD 15),"Pre-weaning Sprague-Dawley rat pups given oral supplements of ferrous bis-glycinate chelate (Ferrochel, FC) on postnatal day (PD) and samples collected from 4–6 hours fasted animals on postnatal day (PD) 15.",28,29,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Supplementary Table S3 + Table S4,19 March 2024,Keamy,"Keamy,Glorious,Victoria,WikiWorks",Taxa Differing in Abundance Between ferrous bis-glycinate chelate (FC) treated pups (PD 15) and Vehicle control-supplemented (CON) pups as determined by DESeq2,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Pseudomonadati|p__Verrucomicrobiota",3379134|74201|203494|48461|1647988|239934;1783272|1239|526524|526525|128827|174708;1783272|1239|526524|526525|128827|1937008;1783272|1239|186801|186802|216572|100175;1783272|1239|186801|186802|216572|1263|438033;1783272|1239|186801|3085636|186803|1506577;3379134|74201,Complete,Svetlana up
bsdb:35276770/2/2,35276770,laboratory experiment,35276770,10.3390/nu14030412,NA,"McMillen S., Thomas S., Liang E., Nonnecke E.B., Slupsky C. , Lönnerdal B.",Gut Microbiome Alterations following Postnatal Iron Supplementation Depend on Iron Form and Persist into Adulthood,Nutrients,2022,"ferrous bis-glycinate chelate, ferrous sulfate, gut microbiome, infant nutrition, iron supplement, metabolomics, rat model",Experiment 2,United States of America,Rattus norvegicus,Cecum mucosa,UBERON:0000314,Iron biomarker measurement,EFO:0004461,Vehicle control-supplemented (CON) pups,Ferrous bis-glycinate chelate (FC) treated pups (PD 15),"Pre-weaning Sprague-Dawley rat pups given oral supplements of ferrous bis-glycinate chelate (Ferrochel, FC) on postnatal day (PD) and samples collected from 4–6 hours fasted animals on postnatal day (PD) 15.",28,29,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Supplementary Table S3 + Table S4,19 March 2024,Keamy,"Keamy,Glorious,Victoria,WikiWorks",Taxa Differing in Abundance Between ferrous bis-glycinate chelate (FC) treated pups (PD 15) and Vehicle control-supplemented (CON) pups as determined by DESeq2,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Yaniella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__uncultured Bacteroidales bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__uncultured Barnesiella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.,s__uncultured bacterium,s__uncultured organism,s__unidentified,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella",1783272|1239|186801|3085636|186803|1427378;1783272|201174|84998|1643822|1643826|447020;3379134|976|200643|171549|171550|239759;1783272|1239;3379134|976;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|201174|1760|85006|85020|43668;1783272|201174|1760|85006|85019|1696;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|830;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|1432051;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|91061|186826|186827|66831;1783272|1239|91061|1385|90964|227979;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|877420;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|248744;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|3085636|186803|841;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810281|191303;1783272|201174|1760|85006|1268|225447;3379134|976|200643|171549|194843;3379134|976|200643|171549|2005519|397864|584861;1783272|1239|186801|186802|31979|1485|59620;77133;155900;32644;3379134|976|200643|171549|815|816;1783272|1239|526524|526525|128827|1937008,Complete,Svetlana up
bsdb:35276770/3/1,35276770,laboratory experiment,35276770,10.3390/nu14030412,NA,"McMillen S., Thomas S., Liang E., Nonnecke E.B., Slupsky C. , Lönnerdal B.",Gut Microbiome Alterations following Postnatal Iron Supplementation Depend on Iron Form and Persist into Adulthood,Nutrients,2022,"ferrous bis-glycinate chelate, ferrous sulfate, gut microbiome, infant nutrition, iron supplement, metabolomics, rat model",Experiment 3,United States of America,Rattus norvegicus,Cecum mucosa,UBERON:0000314,Iron biomarker measurement,EFO:0004461,Ferrous sulfate (FS) treated pups (PD 15),Ferrous bis-glycinate chelate (FC) treated pups (PD 15),"Pre-weaning Sprague-Dawley rat pups given oral supplements of ferrous bis-glycinate chelate (Ferrochel, FC) on postnatal day (PD) 2-14 and samples collected from 4–6 hours-fasted animals on postnatal day (PD) 15",27,29,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Figure S3 + Table S3 + Table S4,19 March 2024,Keamy,"Keamy,Joan Chuks,Victoria,WikiWorks",Taxa Differing in Abundance Between Ferrous sulfate (FS) treated pups (PD 15) and Ferrous bis-glycinate chelate (FC) treated pups (PD 15) as determined by DESeq2,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Verrucomicrobiota,",1783272|1239|526524|526525|128827|174708;1783272|1239|186801|186802|1470353;1783272|1117;1783272|1239|526524|526525|128827|1937008;3379134|1224;1783272|1239|91061|186826|1300|1301;3379134|74201;,Complete,Svetlana up
bsdb:35276770/3/2,35276770,laboratory experiment,35276770,10.3390/nu14030412,NA,"McMillen S., Thomas S., Liang E., Nonnecke E.B., Slupsky C. , Lönnerdal B.",Gut Microbiome Alterations following Postnatal Iron Supplementation Depend on Iron Form and Persist into Adulthood,Nutrients,2022,"ferrous bis-glycinate chelate, ferrous sulfate, gut microbiome, infant nutrition, iron supplement, metabolomics, rat model",Experiment 3,United States of America,Rattus norvegicus,Cecum mucosa,UBERON:0000314,Iron biomarker measurement,EFO:0004461,Ferrous sulfate (FS) treated pups (PD 15),Ferrous bis-glycinate chelate (FC) treated pups (PD 15),"Pre-weaning Sprague-Dawley rat pups given oral supplements of ferrous bis-glycinate chelate (Ferrochel, FC) on postnatal day (PD) 2-14 and samples collected from 4–6 hours-fasted animals on postnatal day (PD) 15",27,29,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Figure S3 + Table S3 + Table S4,19 March 2024,Keamy,"Keamy,Joan Chuks,MyleeeA,Victoria,WikiWorks",Taxa Differing in Abundance Between Ferrous sulfate (FS) treated pups (PD 15) and Ferrous bis-glycinate chelate (FC) treated pups (PD 15) as determined by DESeq2,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__uncultured Bacteroidales bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__uncultured Barnesiella sp.,k__Bacillati|p__Bacillota|c__Clostridia|s__uncultured Clostridia bacterium,s__uncultured bacterium,s__uncultured organism,s__unidentified,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Deferribacterota,k__Bacillati|p__Bacillota",1783272|1239|186801|3085636|186803|1427378;1783272|1239|91061|186826|186827|1375;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;3379134|976;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|186801|186802|216572|216851|1946507;3379134|1224|1236|135625|712|724;1783272|1239|186801|186802|216572|1892380;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|877420;1783272|544448;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3085636|186803|841;3379134|976|200643|171549|194843;3379134|976|200643|171549|2005519|397864|584861;1783272|1239|186801|244328;77133;155900;32644;1783272|201174;3379134|200930;1783272|1239,Complete,Svetlana up
bsdb:35276770/4/1,35276770,laboratory experiment,35276770,10.3390/nu14030412,NA,"McMillen S., Thomas S., Liang E., Nonnecke E.B., Slupsky C. , Lönnerdal B.",Gut Microbiome Alterations following Postnatal Iron Supplementation Depend on Iron Form and Persist into Adulthood,Nutrients,2022,"ferrous bis-glycinate chelate, ferrous sulfate, gut microbiome, infant nutrition, iron supplement, metabolomics, rat model",Experiment 4,United States of America,Rattus norvegicus,Cecum mucosa,UBERON:0000314,Iron biomarker measurement,EFO:0004461,Vehicle control-supplemented (CON) young Adult (YA) rats,Ferrous sulfate (FS) treated young Adult  (YA) rats (PD 58 +/- 4),"Young Adult (YA) Sprague-Dawley rats given oral supplements of ferrous sulfate (FS) on postnatal day (PD) 2-20, weaned on postnatal day (PD) 21 and samples collected from 4–6 hours fasted animals on postnatal day (PD) 58 +/- 4.",23,23,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Figure 5d and 6  +Figure S6 + Table S7 and S8,19 March 2024,Keamy,"Keamy,Glorious,KateRasheed,WikiWorks",Taxa Differing in Abundance Between Young Adult (YA) Sprague-Dawley rats given oral supplements of ferrous sulfate (FS) and Vehicle control-supplemented (CON) as determined by DESeq2,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|s__uncultured Bacillota bacterium,s__uncultured bacterium,s__unidentified,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.",1783272|1239|186801|3085636|186803|1427378;1783272|1239|186801|186802|216572|1940255;1783272|201174|84998|1643822|1643826|580024;3379134|976|200643|171549|2005525|375288;1783272|201174|1760|85006|1268|32207;1783272|1239|344338;77133;32644;1783272|1239|186801|186802|31979|1485|59620,Complete,Svetlana up
bsdb:35276770/4/2,35276770,laboratory experiment,35276770,10.3390/nu14030412,NA,"McMillen S., Thomas S., Liang E., Nonnecke E.B., Slupsky C. , Lönnerdal B.",Gut Microbiome Alterations following Postnatal Iron Supplementation Depend on Iron Form and Persist into Adulthood,Nutrients,2022,"ferrous bis-glycinate chelate, ferrous sulfate, gut microbiome, infant nutrition, iron supplement, metabolomics, rat model",Experiment 4,United States of America,Rattus norvegicus,Cecum mucosa,UBERON:0000314,Iron biomarker measurement,EFO:0004461,Vehicle control-supplemented (CON) young Adult (YA) rats,Ferrous sulfate (FS) treated young Adult  (YA) rats (PD 58 +/- 4),"Young Adult (YA) Sprague-Dawley rats given oral supplements of ferrous sulfate (FS) on postnatal day (PD) 2-20, weaned on postnatal day (PD) 21 and samples collected from 4–6 hours fasted animals on postnatal day (PD) 58 +/- 4.",23,23,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,"Figure 5d,6 and S6 + Table S7and S8",19 March 2024,Keamy,"Keamy,Glorious,Victoria,WikiWorks",Taxa Differing in Abundance Between fYoung Adult (YA) Sprague-Dawley rats given oral supplements of ferrous sulfate (FS). and Vehicle control-supplemented (CON),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena fissicatena,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,s__uncultured bacterium,s__unidentified",3379134|1224|1236|2887326|468|469;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|3085636|186803|2005359|290055;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572|3028852;3379134|1224;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810281|191303;77133;32644,Complete,Svetlana up
bsdb:35276770/5/1,35276770,laboratory experiment,35276770,10.3390/nu14030412,NA,"McMillen S., Thomas S., Liang E., Nonnecke E.B., Slupsky C. , Lönnerdal B.",Gut Microbiome Alterations following Postnatal Iron Supplementation Depend on Iron Form and Persist into Adulthood,Nutrients,2022,"ferrous bis-glycinate chelate, ferrous sulfate, gut microbiome, infant nutrition, iron supplement, metabolomics, rat model",Experiment 5,United States of America,Rattus norvegicus,Cecum mucosa,UBERON:0000314,Iron biomarker measurement,EFO:0004461,Vehicle control-supplemented (CON) young Adult rats,Ferrous bis-glycinate chelate (FC) treated young Adult  (YA) rats (PD 58 +/- 4),"Young Adult (YA) Sprague-Dawley rats given oral supplements of ferrous bis-glycinate chelate (FC) on postnatal day (PD) 2-20, weaned on postnatal day (PD) 21 and samples collected from 4–6 h-fasted animals on postnatal day (PD) 58 +/- 4.",23,19,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 5d +  Figure 6 + Figure S6 + Table s7 +Table s8,19 March 2024,Keamy,"Keamy,Joan Chuks,WikiWorks",Taxa Differing in Abundance Between Ferrous bis-glycinate chelate (FC) treated young Adult  (YA) rats (PD 58 +/- 4) and Vehicle control-supplemented (CON) young Adult rats as determined by DESeq2.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Caldicoprobacterales|f__Caldicoprobacteraceae|g__Caldicoprobacter,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__Ruminiclostridium sufflavum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Yaniella,s__uncultured organism,s__uncultured rumen bacterium,s__unidentified rumen bacterium RF32",1783272|201174|1760|85006|85020|43668;1783272|201174|1760|85006|85019|1696;1783272|1239|186801|3120405|715221|715222;1783272|1117;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|100175;;1783272|201174|1760|85006|1268|32207;1783272|1239|186801|186802|216572|1508657|396504;1783272|1239|186801|3085636|186803|1506577;3379134|74201;1783272|201174|1760|85006|1268|225447;155900;136703;60675,Complete,Svetlana up
bsdb:35276770/5/2,35276770,laboratory experiment,35276770,10.3390/nu14030412,NA,"McMillen S., Thomas S., Liang E., Nonnecke E.B., Slupsky C. , Lönnerdal B.",Gut Microbiome Alterations following Postnatal Iron Supplementation Depend on Iron Form and Persist into Adulthood,Nutrients,2022,"ferrous bis-glycinate chelate, ferrous sulfate, gut microbiome, infant nutrition, iron supplement, metabolomics, rat model",Experiment 5,United States of America,Rattus norvegicus,Cecum mucosa,UBERON:0000314,Iron biomarker measurement,EFO:0004461,Vehicle control-supplemented (CON) young Adult rats,Ferrous bis-glycinate chelate (FC) treated young Adult  (YA) rats (PD 58 +/- 4),"Young Adult (YA) Sprague-Dawley rats given oral supplements of ferrous bis-glycinate chelate (FC) on postnatal day (PD) 2-20, weaned on postnatal day (PD) 21 and samples collected from 4–6 h-fasted animals on postnatal day (PD) 58 +/- 4.",23,19,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Figure 5d +  Figure 6 + Figure S6 + Table s7 +Table s8,20 March 2024,Keamy,"Keamy,Joan Chuks,Victoria,WikiWorks",Taxa Differing in Abundance Between Ferrous bis-glycinate chelate (FC) treated young Adult  (YA) rats (PD 58 +/- 4) and Vehicle control-supplemented (CON) young Adult rats as determined by DESeq2.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetitomaculum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__uncultured Bacteroidales bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__uncultured Barnesiella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,s__uncultured bacterium,s__unidentified",1783272|1239|186801|3085636|186803|1427378;1783272|1239|186801|3085636|186803|31980;3379134|1224|1236|2887326|468|469;1783272|201174;1783272|201174|84998|1643822|1643826|447020;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|216572|244127;3379134|976|200643|171549|815|816;3379134|976;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|189330;1783272|201174|84998|1643822|1643826|580024;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803|1506553;1783272|1239|91061|186826|33958|1578;1783272|544448;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|577310;3379134|1224;1783272|1239|186801|3085636|186803|841;1783272|1239|526524|526525|2810281|191303;3379134|976|200643|171549|194843;3379134|976|200643|171549|2005519|397864|584861;1783272|1239|186801|186802|31979|1485|59620;1783272|1239|186801|3085636|186803|297314;77133;32644,Complete,Svetlana up
bsdb:35276770/6/1,35276770,laboratory experiment,35276770,10.3390/nu14030412,NA,"McMillen S., Thomas S., Liang E., Nonnecke E.B., Slupsky C. , Lönnerdal B.",Gut Microbiome Alterations following Postnatal Iron Supplementation Depend on Iron Form and Persist into Adulthood,Nutrients,2022,"ferrous bis-glycinate chelate, ferrous sulfate, gut microbiome, infant nutrition, iron supplement, metabolomics, rat model",Experiment 6,United States of America,Rattus norvegicus,Cecum mucosa,UBERON:0000314,Iron biomarker measurement,EFO:0004461,Ferrous sulfate (FS) treated young Adult  (YA) rats (PD 58 +/- 4),Ferrous bis-glycinate chelate (FC) treated young Adult  (YA) rats (PD 58 +/- 4),"Young Adult (YA) Sprague-Dawley rats given oral supplements of ferrous bis-glycinate chelate (FC) on postnatal day (PD) 2-20, weaned on postnatal day (PD) 21 and samples collected from 4–6 h-fasted animals on postnatal day (PD) 58 +/- 4.",23,19,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 5d +  Figure 6 + Figure S6 + Table S7 and S8,19 March 2024,Keamy,"Keamy,Glorious,Victoria,WikiWorks",Taxa Differing in Abundance Between Ferrous bis-glycinate chelate (FC) treated young Adult (YA) rats (PD 58 +/- 4) and Ferrous Sulfate (FS) young Adult rats as determined by DESeq2.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Caldicoprobacterales|f__Caldicoprobacteraceae|g__Caldicoprobacter,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Deferribacterota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena fissicatena,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NC2004,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__Ruminiclostridium sufflavum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Yaniella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum,s__uncultured organism,s__uncultured rumen bacterium,s__unidentified,s__unidentified rumen bacterium RF32,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota",1783272|1239|186801|186802|216572|52784;1783272|1239|186801|186802|186806|264995;1783272|1239|91061|1385|186817|1386;1783272|201174|1760|85006|85020|43668;1783272|201174|1760|85006|85019|1696;1783272|1239|186801|3120405|715221|715222;95818|2093818|2093825|2171986|1331051;1783272|1239|186801|186802|1470353;1783272|1117;3379134|200930;1783272|201174|1760|85007|85029|37914;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|91061|186826|186827|66831;1783272|1239|526524|526525|128827|1729679;1783272|1239|186801|3085636|186803|2005359|290055;3379134|1224|1236|135625|712|724;1783272|1239|186801|186802|216572|596767;1783272|1239|186801|3085636|186803|1410626;1783272|1239|186801|3085636|186803|437755;1783272|1239|186801|186802|216572|100175;;1783272|1239|186801|186802|216572|1508657|396504;1783272|1239|186801|186802|216572|3068309;1783272|1239|186801|186802|216572|1263|438033;1783272|1239|186801|3085636|186803|1769710;1783272|1239|91061|1385|90964|1279;3379134|74201;1783272|201174|1760|85006|1268|225447;1783272|1239|186801|3082720|543314|35518;155900;136703;32644;60675;1783272|1239;3379134|1224,Complete,Svetlana up
bsdb:35276770/6/2,35276770,laboratory experiment,35276770,10.3390/nu14030412,NA,"McMillen S., Thomas S., Liang E., Nonnecke E.B., Slupsky C. , Lönnerdal B.",Gut Microbiome Alterations following Postnatal Iron Supplementation Depend on Iron Form and Persist into Adulthood,Nutrients,2022,"ferrous bis-glycinate chelate, ferrous sulfate, gut microbiome, infant nutrition, iron supplement, metabolomics, rat model",Experiment 6,United States of America,Rattus norvegicus,Cecum mucosa,UBERON:0000314,Iron biomarker measurement,EFO:0004461,Ferrous sulfate (FS) treated young Adult  (YA) rats (PD 58 +/- 4),Ferrous bis-glycinate chelate (FC) treated young Adult  (YA) rats (PD 58 +/- 4),"Young Adult (YA) Sprague-Dawley rats given oral supplements of ferrous bis-glycinate chelate (FC) on postnatal day (PD) 2-20, weaned on postnatal day (PD) 21 and samples collected from 4–6 h-fasted animals on postnatal day (PD) 58 +/- 4.",23,19,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 5d +  Figure 6 + Figure S6 + Table S7 andS8,20 March 2024,Keamy,"Keamy,Glorious,Victoria,WikiWorks",Taxa Differing in Abundance Between Ferrous bis-glycinate chelate (FC) treated young Adult (YA) rats (PD 58 +/- 4) and Ferrous Sulfate (FS) young Adult rats as determined by DESeq2.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetitomaculum,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium enrichment culture clone 06-1235251-67,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|s__uncultured Bacillota bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__uncultured Bacteroidales bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__uncultured Barnesiella sp.,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|s__uncultured Mollicutes bacterium,s__uncultured bacterium,s__uncultured rumen bacterium,s__unidentified,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",1783272|1239|186801|3085636|186803|1427378;1783272|1239|186801|3085636|186803|31980;1783272|201174;1783272|201174|84998|1643822|1643826|447020;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815|816;3379134|976;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|1141839;1783272|1239|186801|3085636|186803|189330;1783272|201174|84998|1643822|1643826|580024;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803|1506553;1783272|544448;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|3085636|186803|841;1783272|1239|344338;3379134|976|200643|171549|194843;3379134|976|200643|171549|2005519|397864|584861;1783272|544448|31969|220137;77133;136703;32644;1783272|1239|186801|3085636|186803|297314,Complete,Svetlana up
bsdb:35277280/1/1,35277280,"cross-sectional observational, not case-control",35277280,10.1016/j.ygyno.2022.02.021,NA,"Hawkins G.M., Burkett W.C., McCoy A.N., Nichols H.B., Olshan A.F., Broaddus R., Merker J.D., Weissman B., Brewster W.R., Roach J., Keku T.O. , Bae-Jump V.",Differences in the microbial profiles of early stage endometrial cancers between Black and White women,Gynecologic oncology,2022,"Endometrial cancer, Race disparities, Uterine microbiome",Experiment 1,United States of America,Homo sapiens,Uterus,UBERON:0000995,Endometrial cancer,MONDO:0011962,Benign endometrium,Endometrioid endometrial cancers,Endometrioid endometrial cancers refers to the early stage endometrial tumors which was majorly found in obese Black women.,16,95,3 months,16S,123,Ion Torrent,relative abundances,Metastats,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Fig. 1,12 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between Benign (non-cancerous) and Endometrial cancer(malignant).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae|g__Hyphomicrobium",3379134|976|117743|200644|49546|237;3379134|1224|28211|356|45401|81,Complete,Svetlana up
bsdb:35277280/2/1,35277280,"cross-sectional observational, not case-control",35277280,10.1016/j.ygyno.2022.02.021,NA,"Hawkins G.M., Burkett W.C., McCoy A.N., Nichols H.B., Olshan A.F., Broaddus R., Merker J.D., Weissman B., Brewster W.R., Roach J., Keku T.O. , Bae-Jump V.",Differences in the microbial profiles of early stage endometrial cancers between Black and White women,Gynecologic oncology,2022,"Endometrial cancer, Race disparities, Uterine microbiome",Experiment 2,United States of America,Homo sapiens,Uterus,UBERON:0000995,Endometrial cancer,MONDO:0011962,Non-Obese White Women,Obese White Women,Obese White Women refers to the early stage endometrial tumors in white women with obesity.,26,38,3 months,16S,123,Ion Torrent,relative abundances,Metastats,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Fig. 2,12 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between Non-obese white women and obese white women.,increased,p__Candidatus Parcubacteria,221216,Complete,Svetlana up
bsdb:35277280/2/2,35277280,"cross-sectional observational, not case-control",35277280,10.1016/j.ygyno.2022.02.021,NA,"Hawkins G.M., Burkett W.C., McCoy A.N., Nichols H.B., Olshan A.F., Broaddus R., Merker J.D., Weissman B., Brewster W.R., Roach J., Keku T.O. , Bae-Jump V.",Differences in the microbial profiles of early stage endometrial cancers between Black and White women,Gynecologic oncology,2022,"Endometrial cancer, Race disparities, Uterine microbiome",Experiment 2,United States of America,Homo sapiens,Uterus,UBERON:0000995,Endometrial cancer,MONDO:0011962,Non-Obese White Women,Obese White Women,Obese White Women refers to the early stage endometrial tumors in white women with obesity.,26,38,3 months,16S,123,Ion Torrent,relative abundances,Metastats,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Fig. 2,12 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between Non-obese white women and obese white women.,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Svetlana up
bsdb:35277280/3/1,35277280,"cross-sectional observational, not case-control",35277280,10.1016/j.ygyno.2022.02.021,NA,"Hawkins G.M., Burkett W.C., McCoy A.N., Nichols H.B., Olshan A.F., Broaddus R., Merker J.D., Weissman B., Brewster W.R., Roach J., Keku T.O. , Bae-Jump V.",Differences in the microbial profiles of early stage endometrial cancers between Black and White women,Gynecologic oncology,2022,"Endometrial cancer, Race disparities, Uterine microbiome",Experiment 3,United States of America,Homo sapiens,Uterus,UBERON:0000995,Endometrial cancer,MONDO:0011962,Obese White Women,Obese Black Women,Obese Black Women refers to the early stage endometrial tumors in black women with obesity.,62,19,3 months,16S,123,Ion Torrent,relative abundances,Metastats,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Fig. 3A,12 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between Obese white women and obese black women.,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Cyanobacteriota,p__Candidatus Parcubacteria",1783272|1239;1783272|1117;221216,Complete,Svetlana up
bsdb:35277280/3/2,35277280,"cross-sectional observational, not case-control",35277280,10.1016/j.ygyno.2022.02.021,NA,"Hawkins G.M., Burkett W.C., McCoy A.N., Nichols H.B., Olshan A.F., Broaddus R., Merker J.D., Weissman B., Brewster W.R., Roach J., Keku T.O. , Bae-Jump V.",Differences in the microbial profiles of early stage endometrial cancers between Black and White women,Gynecologic oncology,2022,"Endometrial cancer, Race disparities, Uterine microbiome",Experiment 3,United States of America,Homo sapiens,Uterus,UBERON:0000995,Endometrial cancer,MONDO:0011962,Obese White Women,Obese Black Women,Obese Black Women refers to the early stage endometrial tumors in black women with obesity.,62,19,3 months,16S,123,Ion Torrent,relative abundances,Metastats,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Fig. 3B,12 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between Obese white women and obese black women.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Geobacillus",1783272|201174|1760|85007|85029|37914;1783272|1239|91061|1385|3120669|129337,Complete,Svetlana up
bsdb:35291914/1/1,35291914,case-control,35291914,https://doi.org/10.1080/21655979.2022.2049959,https://www.tandfonline.com/doi/full/10.1080/21655979.2022.2049959#d1e282,"Jiang H., Zeng W., Zhang X., Pei Y., Zhang H. , Li Y.",The role of gut microbiota in patients with benign and malignant brain tumors: a pilot study,Bioengineered,2022,"Gut microbiota, biomarker, brain-gut axis, glioma, meningioma, tumors",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Brain growth measurement,EFO:0009326,Benign meningioma group(M) + malignant glioma group(G),Healthy group (H),Healthy individuals without benign or malignant brain tumors,59,41,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A & 3B,8 January 2026,Chyono2,Chyono2,Linear discriminant analysis (LDA) coupled with effect size (LEfSe) showing enriched taxa in intestinal flora of the healthy subjects(H) and patients with meningioma(M) and glioma(G).,increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales|f__Candidatus Gastranaerophilaceae,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales,k__Bacillati|p__Bacillota|c__Clostridia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,c__Peptococcia|o__Peptococcales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae",1783272|201174|84992;1783272|201174;1783272|1239|186801|3085636|186803|1766253;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3082720|543314;1783272|1239|91061;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1798710|1906119|3022868;1783272|1798710|1906119;1783272|1239|186801|3082768;1783272|1239|186801;3379134|976|200643|171549|2005519|1348911;1783272|1239|186801|3085636|186803|33042;1783272|201174|84998|1643822|1643826;1783272|1239|186801|186802;1783272|1239|1737404|1582879;1783272|1239|1737404|1737405|1570339|150022;3379134|976|117743|200644|49546;3379134|976|117743|200644;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636;1783272|1239|186801|3085656|3085657;1783272|1239|186801|3085656;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|186801|3085636|186803|437755;1783272|544448|31969|2085|2092;1783272|544448|31969|2085;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|186802|186807;3118672|3120435;1783272|1239|186801|186802|186807|2740;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|3082768|990719,Complete,KateRasheed
bsdb:35291914/2/1,35291914,case-control,35291914,https://doi.org/10.1080/21655979.2022.2049959,https://www.tandfonline.com/doi/full/10.1080/21655979.2022.2049959#d1e282,"Jiang H., Zeng W., Zhang X., Pei Y., Zhang H. , Li Y.",The role of gut microbiota in patients with benign and malignant brain tumors: a pilot study,Bioengineered,2022,"Gut microbiota, biomarker, brain-gut axis, glioma, meningioma, tumors",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Meningioma,MONDO:0016642,Healthy group (H) + malignant glioma group(G),Benign meningioma group(M),Patients with benign meningioma,68,32,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A & 3B,8 January 2026,Chyono2,Chyono2,Linear discriminant analysis (LDA) coupled with effect size (LEfSe) showing enriched taxa in intestinal flora of the healthy subjects(H) and patients with meningioma(M) and glioma(G).,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",1783272|1239|526524|526525|2810280|100883;3379134|1224|1236|91347|543;1783272|1239|186801|186802|216572|946234;3379134|1224|1236;1783272|1239|186801|3085636|186803|1649459;3379134|1224|1236|91347|543|1940338,Complete,KateRasheed
bsdb:35291914/3/1,35291914,case-control,35291914,https://doi.org/10.1080/21655979.2022.2049959,https://www.tandfonline.com/doi/full/10.1080/21655979.2022.2049959#d1e282,"Jiang H., Zeng W., Zhang X., Pei Y., Zhang H. , Li Y.",The role of gut microbiota in patients with benign and malignant brain tumors: a pilot study,Bioengineered,2022,"Gut microbiota, biomarker, brain-gut axis, glioma, meningioma, tumors",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Malignant glioma,MONDO:0100342,Healthy group (H) + Benign meningioma group(M),Malignant glioma group(G),Patients with malignant glioma,73,27,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A & 3B,8 January 2026,Chyono2,Chyono2,Linear discriminant analysis (LDA) coupled with effect size (LEfSe) showing enriched taxa in intestinal flora of the healthy subjects(H) and patients with meningioma(M) and glioma(G).,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;3379134|976|200643|171549;3379134|976|200643;3379134|976;1783272|1239|526524|526525|128827|1573534;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;3384189|32066|203490|203491|203492|848;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201,Complete,KateRasheed
bsdb:35305613/1/1,35305613,"cross-sectional observational, not case-control",35305613,10.1186/s12894-022-00990-0,NA,"Li K., Chen C., Zeng J., Wen Y., Chen W., Zhao J. , Wu P.",Interplay between bladder microbiota and overactive bladder symptom severity: a cross-sectional study,BMC urology,2022,"Bladder microbiota, Overactive bladder, Severity of OAB symptom, Urinary microbiome",Experiment 1,China,Homo sapiens,Urinary bladder,UBERON:0001255,Overactive bladder,NA,Mild Overactive Bladder,Moderate/Severe Overactive Bladder,Adult patients with Overactive Bladder Symptom Score greater than five (OABSS > 5).,17,53,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,"age,body mass index,hypertension,race",NA,unchanged,increased,increased,increased,NA,increased,Signature 1,Table 2,23 October 2023,Deacme,"Deacme,Chinelsy,WikiWorks",Increased abundance of bacteria in moderate/severe overactive bladder patients.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae",1783272|201174|1760|85004|31953;3379134|1224|28211|356|119045;3379134|976|200643|171549|171552;1783272|1239|91061|1385|90964,Complete,Chinelsy
bsdb:35305613/1/2,35305613,"cross-sectional observational, not case-control",35305613,10.1186/s12894-022-00990-0,NA,"Li K., Chen C., Zeng J., Wen Y., Chen W., Zhao J. , Wu P.",Interplay between bladder microbiota and overactive bladder symptom severity: a cross-sectional study,BMC urology,2022,"Bladder microbiota, Overactive bladder, Severity of OAB symptom, Urinary microbiome",Experiment 1,China,Homo sapiens,Urinary bladder,UBERON:0001255,Overactive bladder,NA,Mild Overactive Bladder,Moderate/Severe Overactive Bladder,Adult patients with Overactive Bladder Symptom Score greater than five (OABSS > 5).,17,53,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,"age,body mass index,hypertension,race",NA,unchanged,increased,increased,increased,NA,increased,Signature 2,Table 2,23 October 2023,Deacme,"Deacme,WikiWorks",Decreased abundance of bacteria in moderate/severe overactive bladder patients.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae",1783272|1239|91061|186826|33958;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|1300;3379134|1224|1236|2887326|468;3379134|1224|28211|204457|41297,Complete,Chinelsy
bsdb:35310158/1/2,35310158,laboratory experiment,35310158,10.7717/peerj.13095,NA,"Bensch H.M., Tolf C., Waldenström J., Lundin D. , Zöttl M.",Freeze-drying can replace cold-chains for transport and storage of fecal microbiome samples,PeerJ,2022,"16S, Amplicon, DNA metabarcoding, Damaraland mole-rat, Fecal samples, Freeze-drying, Fukomys damarensis, Microbiome",Experiment 1,South Africa,Fukomys damarensis,Feces,UBERON:0001988,Freeze dried specimen,EFO:0005121,Frozen samples,Freeze dried samples.,Freeze dried samples are samples preservation treatment stored and transported at ambient temperature until DNA extraction.,20,20,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 4, Table S1",21 November 2024,Tosin,"Tosin,WikiWorks",Log-transformed relative abundances of families with > 1% mean relative abundance between Frozen and Freeze-dried sample preservation treatments.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|3082768|990719;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:35350577/1/1,35350577,case-control,35350577,10.3389/fmed.2022.841112,NA,"Song H., Xiao K., Chen Z. , Long Q.",Analysis of Conjunctival Sac Microbiome in Dry Eye Patients With and Without Sjögren's Syndrome,Frontiers in medicine,2022,"Sjögren's syndrome, dry eyes, microbial composition, microbial diversity, ocular surface",Experiment 1,China,Homo sapiens,Conjunctival sac,UBERON:0005908,Dry eye syndrome,EFO:1000906,Normal Control (NC),Sjogrens Syndrome Dry Eye (SSDE),Patients with Sjogrens Syndrome Dry Eye,39,23,1 month,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Tables 3 and 4,10 November 2023,Mary Bearkland,"Mary Bearkland,Peace Sandy,WikiWorks","TABLE 3 Percentage of the top five phyla in each group.
TABLE 4 Percentage of the top five genus in each group.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota",3379134|1224|1236|2887326|468|469;1783272|1239|186801|186802|31979|1485;1783272|201174|1760|85007|1653|1716;1783272|1239,Complete,Peace Sandy
bsdb:35350577/1/2,35350577,case-control,35350577,10.3389/fmed.2022.841112,NA,"Song H., Xiao K., Chen Z. , Long Q.",Analysis of Conjunctival Sac Microbiome in Dry Eye Patients With and Without Sjögren's Syndrome,Frontiers in medicine,2022,"Sjögren's syndrome, dry eyes, microbial composition, microbial diversity, ocular surface",Experiment 1,China,Homo sapiens,Conjunctival sac,UBERON:0005908,Dry eye syndrome,EFO:1000906,Normal Control (NC),Sjogrens Syndrome Dry Eye (SSDE),Patients with Sjogrens Syndrome Dry Eye,39,23,1 month,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Tables 3 and 4,10 November 2023,Mary Bearkland,"Mary Bearkland,Peace Sandy,WikiWorks","TABLE 3 Percentage of the top five phyla in each group.
TABLE 4 Percentage of the top five genus in each group.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Pseudomonadota",1783272|1239|91061|1385|186817|1386;3379134|976;1783272|1117;3379134|1224,Complete,Peace Sandy
bsdb:35350577/2/1,35350577,case-control,35350577,10.3389/fmed.2022.841112,NA,"Song H., Xiao K., Chen Z. , Long Q.",Analysis of Conjunctival Sac Microbiome in Dry Eye Patients With and Without Sjögren's Syndrome,Frontiers in medicine,2022,"Sjögren's syndrome, dry eyes, microbial composition, microbial diversity, ocular surface",Experiment 2,China,Homo sapiens,Conjunctival sac,UBERON:0005908,Dry eye syndrome,EFO:1000906,Normal Control (NC),Non Sjogrens Syndrome Dry Eye (NSSDE),Patients with Non-Sjogrens Syndrome Dry Eye,39,36,1 month,16S,34,Illumina,NA,ANOVA,0.05,NA,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Tables 3 and 4,10 November 2023,Mary Bearkland,"Mary Bearkland,WikiWorks","TABLE 3 Percentage of the top five phyla in each group.
TABLE 4 Percentage of the top five genus in each group.",increased,"k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",3379134|1224;1783272|201174;3379134|1224|1236|2887326|468|469;1783272|1239|186801|186802|31979|1485,Complete,Peace Sandy
bsdb:35350577/2/2,35350577,case-control,35350577,10.3389/fmed.2022.841112,NA,"Song H., Xiao K., Chen Z. , Long Q.",Analysis of Conjunctival Sac Microbiome in Dry Eye Patients With and Without Sjögren's Syndrome,Frontiers in medicine,2022,"Sjögren's syndrome, dry eyes, microbial composition, microbial diversity, ocular surface",Experiment 2,China,Homo sapiens,Conjunctival sac,UBERON:0005908,Dry eye syndrome,EFO:1000906,Normal Control (NC),Non Sjogrens Syndrome Dry Eye (NSSDE),Patients with Non-Sjogrens Syndrome Dry Eye,39,36,1 month,16S,34,Illumina,NA,ANOVA,0.05,NA,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Tables 3 and 4,10 November 2023,Mary Bearkland,"Mary Bearkland,WikiWorks","TABLE 3 Percentage of the top five phyla in each group.
TABLE 4 Percentage of the top five genus in each group.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Cyanobacteriota",1783272|1239|91061|1385|186817|1386;1783272|1117,Complete,Peace Sandy
bsdb:35350577/3/1,35350577,case-control,35350577,10.3389/fmed.2022.841112,NA,"Song H., Xiao K., Chen Z. , Long Q.",Analysis of Conjunctival Sac Microbiome in Dry Eye Patients With and Without Sjögren's Syndrome,Frontiers in medicine,2022,"Sjögren's syndrome, dry eyes, microbial composition, microbial diversity, ocular surface",Experiment 3,China,Homo sapiens,Conjunctival sac,UBERON:0005908,Dry eye syndrome,EFO:1000906,Non Sjogrens Syndrome Dry Eye (NSSDE),Sjogrens Syndrome Dry Eye (SSDE),Patients with Sjogrens Syndrome Dry Eye,36,23,1 month,16S,34,Illumina,NA,ANOVA,0.05,NA,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Tables 3 and 4,10 November 2023,Mary Bearkland,"Mary Bearkland,WikiWorks","TABLE 3 Percentage of the top five phyla in each group.
TABLE 4 Percentage of the top five genus in each group.",increased,k__Bacillati|p__Actinomycetota,1783272|201174,Complete,Peace Sandy
bsdb:35350577/3/2,35350577,case-control,35350577,10.3389/fmed.2022.841112,NA,"Song H., Xiao K., Chen Z. , Long Q.",Analysis of Conjunctival Sac Microbiome in Dry Eye Patients With and Without Sjögren's Syndrome,Frontiers in medicine,2022,"Sjögren's syndrome, dry eyes, microbial composition, microbial diversity, ocular surface",Experiment 3,China,Homo sapiens,Conjunctival sac,UBERON:0005908,Dry eye syndrome,EFO:1000906,Non Sjogrens Syndrome Dry Eye (NSSDE),Sjogrens Syndrome Dry Eye (SSDE),Patients with Sjogrens Syndrome Dry Eye,36,23,1 month,16S,34,Illumina,NA,ANOVA,0.05,NA,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Tables 3 and 4,10 November 2023,Mary Bearkland,"Mary Bearkland,WikiWorks","TABLE 3 Percentage of the top five phyla in each group.
TABLE 4 Percentage of the top five genus in each group.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota",1783272|1239|186801|186802|31979|1485;3379134|1224,Complete,Peace Sandy
bsdb:35386429/1/1,35386429,laboratory experiment,35386429,10.7717/peerj.12826,NA,"Li M., Wang Z., Wang L., Xue B., Hu R., Zou H., Liu S., Shah A.M. , Peng Q.",Comparison of changes in fecal microbiota of calves with and without dam,PeerJ,2022,"Calf, Cultivation method, Dynamics, Microbial community",Experiment 1,China,Bos grunniens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,Calves with dam on day 35,Calves without dam on day 35,Calves without dam on day 35 of the whole 95 days formal experimental period.,8,8,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figures 5&6,3 November 2023,Folakunmi,"Folakunmi,WikiWorks","Differentially abundant taxa between calves with dam at day 35 of experiment, and calves without dam at day 35 of experiment.",increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Myroides,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Paraeggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus",1783272|201174;3379134|976|117743|200644|49546|76831;1783272|201174|84998|1643822|1643826|651554;1783272|1239|186801|3082720|186804|1257,Complete,ChiomaBlessing
bsdb:35386429/1/2,35386429,laboratory experiment,35386429,10.7717/peerj.12826,NA,"Li M., Wang Z., Wang L., Xue B., Hu R., Zou H., Liu S., Shah A.M. , Peng Q.",Comparison of changes in fecal microbiota of calves with and without dam,PeerJ,2022,"Calf, Cultivation method, Dynamics, Microbial community",Experiment 1,China,Bos grunniens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,Calves with dam on day 35,Calves without dam on day 35,Calves without dam on day 35 of the whole 95 days formal experimental period.,8,8,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figures 5&6,4 November 2023,Folakunmi,"Folakunmi,WikiWorks","Differentially abundant taxa between calves with dam at day 35 of experiment, and calves without dam at day 35 of experiment.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|1940338;3379134|976|200643|171549|2005525|375288,Complete,ChiomaBlessing
bsdb:35386429/2/1,35386429,laboratory experiment,35386429,10.7717/peerj.12826,NA,"Li M., Wang Z., Wang L., Xue B., Hu R., Zou H., Liu S., Shah A.M. , Peng Q.",Comparison of changes in fecal microbiota of calves with and without dam,PeerJ,2022,"Calf, Cultivation method, Dynamics, Microbial community",Experiment 2,China,Bos grunniens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,Calves with dam on day 65,Calves without dam on day 65,Calves without dam on day 65 of the whole 95 days formal experimental period.,8,8,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,Figures 5&6,4 November 2023,Folakunmi,"Folakunmi,WikiWorks","Differentially abundant taxa between calves with dam at day 65 of experiment, and calves without dam at day 65 of experiment.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|976|200643|171549|815|816;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572,Complete,ChiomaBlessing
bsdb:35386429/2/2,35386429,laboratory experiment,35386429,10.7717/peerj.12826,NA,"Li M., Wang Z., Wang L., Xue B., Hu R., Zou H., Liu S., Shah A.M. , Peng Q.",Comparison of changes in fecal microbiota of calves with and without dam,PeerJ,2022,"Calf, Cultivation method, Dynamics, Microbial community",Experiment 2,China,Bos grunniens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,Calves with dam on day 65,Calves without dam on day 65,Calves without dam on day 65 of the whole 95 days formal experimental period.,8,8,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,Figures 5&6,4 November 2023,Folakunmi,"Folakunmi,WikiWorks","Differentially abundant taxa between calves with dam at day 65 of experiment, and calves without dam at day 65 of experiment.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|186802|216572|3068309;3379134|203691|203692|136|2845253|157;1783272|1239|186801|186802|216572,Complete,ChiomaBlessing
bsdb:35386429/3/1,35386429,laboratory experiment,35386429,10.7717/peerj.12826,NA,"Li M., Wang Z., Wang L., Xue B., Hu R., Zou H., Liu S., Shah A.M. , Peng Q.",Comparison of changes in fecal microbiota of calves with and without dam,PeerJ,2022,"Calf, Cultivation method, Dynamics, Microbial community",Experiment 3,China,Bos grunniens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,Calves with dam on day 95,Calves without dam on day 95,Calves without dam on day 95 of the whole 95 days formal experimental period.,8,8,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,NA,decreased,decreased,increased,NA,NA,Signature 1,Figures 5&6,4 November 2023,Folakunmi,"Folakunmi,WikiWorks","Differentially abundant taxa between calves with dam at day 95 of experiment, and calves without dam at day 95 of experiment.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",1783272|1239|186801|186802|186806|1730|290054;3379134|203691|203692|136|2845253|157,Complete,ChiomaBlessing
bsdb:35386429/3/2,35386429,laboratory experiment,35386429,10.7717/peerj.12826,NA,"Li M., Wang Z., Wang L., Xue B., Hu R., Zou H., Liu S., Shah A.M. , Peng Q.",Comparison of changes in fecal microbiota of calves with and without dam,PeerJ,2022,"Calf, Cultivation method, Dynamics, Microbial community",Experiment 3,China,Bos grunniens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,Calves with dam on day 95,Calves without dam on day 95,Calves without dam on day 95 of the whole 95 days formal experimental period.,8,8,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,NA,decreased,decreased,increased,NA,NA,Signature 2,Figures 5&6,4 November 2023,Folakunmi,"Folakunmi,WikiWorks","Differentially abundant taxa between calves with dam at day 95 of experiment, and calves without dam at day 95 of experiment.",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,1783272|1239|186801|186802|216572|3068309,Complete,ChiomaBlessing
bsdb:35387878/2/1,35387878,laboratory experiment,35387878,http://dx.doi.org/10.1136/gutjnl-2021-325021,https://gut.bmj.com/content/71/12/2439,"Bai X., Wei H., Liu W., Coker O.O., Gou H., Liu C., Zhao L., Li C., Zhou Y., Wang G., Kang W., Ng E.K. , Yu J.",Cigarette smoke promotes colorectal cancer through modulation of gut microbiota and related metabolites,Gut,2022,"BACTERIAL PATHOGENESIS, BILE ACID METABOLISM, COLORECTAL CANCER",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Smoking behavior,EFO:0004318,Smoke-free control group intraperitoneally injected with carcinogen azoxymethane (AOM) (10 mg/kg),"Smoke-exposed group intraperitoneally injected with carcinogen, AOM (AOM + Smoking)",Mice exposed to cigarette smoke directly (4% of 2000 mL/ min airflow) 2 hours per day for 28 weeks (at end time point),15,15,NA,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 2c,8 March 2023,Busayo,"Busayo,Mcarlson,ChiomaBlessing,WikiWorks",Differentially abundant bacteria in smoke-free and smoke-exposed mice (AOM vs AOM + Smoking),increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus thuringiensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus velezensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium choerinum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter massiliensis (ex Traore et al. 2017),k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter urolithinfaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum|s__Muribaculum gordoncarteri,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella|s__Parolsenella massiliensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus capitis",1783272|1239|91061|1385|186817|1386|1428;1783272|1239|91061|1385|186817|1386|492670;1783272|201174|1760|85004|31953|1678|35760;1783272|201174|84998|1643822|1643826|84111|84112;3379134|1224|1236|91347|543|561|562;1783272|201174|84998|1643822|1643826|644652|1841863;1783272|201174|84998|1643822|1643826|644652|471189;1783272|201174|84998|1643822|1643826|644652|1335613;3379134|976|200643|171549|2005473|1918540|2530390;1783272|201174|84998|84999|1643824|2082587|1871022;1783272|1239|91061|1385|90964|1279|29388,Complete,ChiomaBlessing
bsdb:35387878/2/2,35387878,laboratory experiment,35387878,http://dx.doi.org/10.1136/gutjnl-2021-325021,https://gut.bmj.com/content/71/12/2439,"Bai X., Wei H., Liu W., Coker O.O., Gou H., Liu C., Zhao L., Li C., Zhou Y., Wang G., Kang W., Ng E.K. , Yu J.",Cigarette smoke promotes colorectal cancer through modulation of gut microbiota and related metabolites,Gut,2022,"BACTERIAL PATHOGENESIS, BILE ACID METABOLISM, COLORECTAL CANCER",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Smoking behavior,EFO:0004318,Smoke-free control group intraperitoneally injected with carcinogen azoxymethane (AOM) (10 mg/kg),"Smoke-exposed group intraperitoneally injected with carcinogen, AOM (AOM + Smoking)",Mice exposed to cigarette smoke directly (4% of 2000 mL/ min airflow) 2 hours per day for 28 weeks (at end time point),15,15,NA,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 2c,8 March 2023,Busayo,"Busayo,Mcarlson,ChiomaBlessing,WikiWorks",Differentially abundant bacteria in smoke-free and smoke-exposed mice (AOM vs AOM + Smoking),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium CCNA10,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium GAM147,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp. CT06,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus suis",3379134|976|200643|171549|815|816|246787;1783272|1239|186801|186802|2109688;1783272|1239|526524|526525|128827|2109692;1783272|1239|91061|186826|33958|2742598|1598;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|2005525|375288|2025876;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|821;1783272|1239|91061|186826|1300|1301|1307,Complete,ChiomaBlessing
bsdb:35410125/1/1,35410125,"cross-sectional observational, not case-control",35410125,10.1186/s12866-022-02502-4,NA,"Showering A., Martinez J., Benavente E.D., Gezan S.A., Jones R.T., Oke C., Tytheridge S., Pretorius E., Scott D., Allen R.L., D'Alessandro U., Lindsay S.W., Armour J.A.L., Pickett J. , Logan J.G.",Skin microbiome alters attractiveness to Anopheles mosquitoes,BMC microbiology,2022,"Anopheles coluzzii, Body odour, Diversity, Human attractiveness, Malaria, Mosquitoes, Repellents, Skin microbiome",Experiment 1,United Kingdom,Homo sapiens,Skin of sole of pes,UBERON:0013778,Perceived unattractiveness to mosquitos measurement,EFO:0008380,Poorly-attractive group,Highly-attractive group,"Post-menopausal females, aged between 50 and 90 years, whose skin/body odour were highly attractive to Anopheles mosquitoes.",28,27,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,18 May 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differential abundance of bacterial genera between attractiveness groups tested using DESEQ2,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Methylococcales|f__Methylococcaceae|g__Methylocaldum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",3379134|1224|1236|135618|403|73778;3379134|1224|28211|204457|41297|13687;1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:35410125/1/2,35410125,"cross-sectional observational, not case-control",35410125,10.1186/s12866-022-02502-4,NA,"Showering A., Martinez J., Benavente E.D., Gezan S.A., Jones R.T., Oke C., Tytheridge S., Pretorius E., Scott D., Allen R.L., D'Alessandro U., Lindsay S.W., Armour J.A.L., Pickett J. , Logan J.G.",Skin microbiome alters attractiveness to Anopheles mosquitoes,BMC microbiology,2022,"Anopheles coluzzii, Body odour, Diversity, Human attractiveness, Malaria, Mosquitoes, Repellents, Skin microbiome",Experiment 1,United Kingdom,Homo sapiens,Skin of sole of pes,UBERON:0013778,Perceived unattractiveness to mosquitos measurement,EFO:0008380,Poorly-attractive group,Highly-attractive group,"Post-menopausal females, aged between 50 and 90 years, whose skin/body odour were highly attractive to Anopheles mosquitoes.",28,27,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,18 May 2024,Aleru Divine,"Aleru Divine,WikiWorks",The differential abundance of bacterial genera between attractiveness groups tested using DESEQ2,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Limnohabitans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae",3379134|1224|28211|204458|76892|41275;1783272|201174|1760|85007|1653|1716;3379134|1224|28216|80840|80864|665874;1783272|201174|1760|2037;1783272|201174|1760|85006|85021,Complete,Svetlana up
bsdb:35411293/1/1,35411293,"cross-sectional observational, not case-control",35411293,10.34172/bi.2021.23378,NA,"Han Y., Jia Z., Shi J., Wang W. , He K.",The active lung microbiota landscape of COVID-19 patients through the metatranscriptome data analysis,BioImpacts : BI,2022,"COVID-19, Faecalibacterium prausnitzii, Lactic acid bacteria, Microbiota, SARS-CoV-2",Experiment 1,China,Homo sapiens,Lung,UBERON:0002048,COVID-19,MONDO:0100096,Healthy controls,COVID-19 cases,COVID-19 infected patients,23,19,NA,WMS,NA,NA,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplementary Table 2,12 June 2021,Claregrieve1,"Claregrieve1,Davvve,WikiWorks",Differential microbial abundance between the COVID-19 patients and the healthy controls,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces pacaensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerocolumna|s__Anaerocolumna sedimenticola,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum propionicum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus cereus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium cucumeris,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter braakii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii complex sp. CFNIH3,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium CCNA10,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium beijerinckii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium carboxidivorans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas terrigena,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas testosteroni,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter asburiae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter bugandensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cancerogenus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae complex sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter kobei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter oligotrophicus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter roggenkampii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter soli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. 638,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. E76,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. ODB01,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. T2,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Filimonas|s__Filimonas lacunae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella michiganensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium phytofermentans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora saccharolytica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora sphenoides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus|s__Lactiplantibacillus plantarum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus delbrueckii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Latilactobacillus|s__Latilactobacillus curvatus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Leclercia|s__Leclercia adecarboxylata,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Leclercia|s__Leclercia sp. 29361,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Leclercia|s__Leclercia sp. J807,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Leclercia|s__Leclercia sp. LSNIH1,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Leclercia|s__Leclercia sp. W17,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Lelliottia|s__Lelliottia amnigena,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Lelliottia|s__Lelliottia jeotgali,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Lelliottia|s__Lelliottia sp. WB101,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus|s__Lysinibacillus sp. B2A1,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus|s__Lysinibacillus sphaericus,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mesomycoplasma|s__Mesomycoplasma hyorhinis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium|s__Methylobacterium sp. DM1,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus graminis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus guangzhouensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Pantoea sp. SO10,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Peribacillus|s__Peribacillus frigoritolerans,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium|s__Phyllobacterium myrsinacearum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pluralibacter|s__Pluralibacter gergoviae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas alkylphenolica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas oryzihabitans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas rhodesiae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. JY-Q,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. MRSN 12121,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. PONIH3,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. XWY-1,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rahnella|s__Rahnella aquatilis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia pickettii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Ruminobacter|s__Ruminobacter amylophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia meyeri,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium|s__Sphingobacterium sp. B29,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium|s__Sphingobacterium sp. G1-14,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas sp. FARSPH,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas sp. LM091,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 064,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio|s__Succinivibrio dextrinosolvens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Suicoccus|s__Suicoccus acidiformans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax|s__Variovorax boronicumulans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax|s__Variovorax paradoxus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax|s__Variovorax sp. PBL-H6,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax|s__Variovorax sp. PMC12,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio anguillarum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax|s__uncultured Variovorax sp.",1783272|201174|1760|2037|2049|1654|1852377;1783272|1239|186801|3085636|186803|1843210|2696063;1783272|1239|186801|3085636|3118652|2039240|28446;1783272|1239|91061|1385|186817|1386|1396;3379134|976|117743|200644|2762318|59732|1813611;3379134|1224|1236|91347|543|544|57706;3379134|1224|1236|91347|543|544|546;3379134|1224|1236|91347|543|544|2077147;1783272|1239|186801|186802|1898207;1783272|1239|186801|186802|2109688;1783272|1239|186801|186802|31979|1485|1520;1783272|1239|186801|186802|31979|1485|217159;3379134|1224|28216|80840|80864|283|32013;3379134|1224|28216|80840|80864|283|285;3379134|1224|1236|91347|543|547|61645;3379134|1224|1236|91347|543|547|881260;3379134|1224|1236|91347|543|547|69218;3379134|1224|1236|91347|543|547|550;3379134|1224|1236|91347|543|547|2027919;3379134|1224|1236|91347|543|547|158836;3379134|1224|1236|91347|543|547|208224;3379134|1224|1236|91347|543|547|2478464;3379134|1224|1236|91347|543|547|1812935;3379134|1224|1236|91347|543|547|885040;3379134|1224|1236|91347|543|547|399742;3379134|1224|1236|91347|543|547|2596949;3379134|1224|1236|91347|543|547|1827481;3379134|1224|1236|91347|543|547|2707174;1783272|1239|186801|186802|216572|216851|853;3379134|976|1853228|1853229|563835|649460|477680;1783272|1239|186801|186802|216572|946234|292800;3379134|1224|1236|91347|543|570|1134687;3379134|1224|1236|91347|543|570|571;1783272|1239|186801|3085636|186803|1506553|66219;1783272|1239|186801|3085636|186803|2719231|84030;1783272|1239|186801|3085636|186803|2719231|29370;1783272|1239|91061|186826|33958|2767842|1590;1783272|1239|91061|186826|33958|1578|1584;1783272|1239|91061|186826|33958|1578|33959;1783272|1239|91061|186826|33958|2767885|28038;3379134|1224|1236|91347|543|83654|83655;3379134|1224|1236|91347|543|83654|2714951;3379134|1224|1236|91347|543|83654|2681307;3379134|1224|1236|91347|543|83654|1920114;3379134|1224|1236|91347|543|83654|2282309;3379134|1224|1236|91347|543|1330545|61646;3379134|1224|1236|91347|543|1330545|1907578;3379134|1224|1236|91347|543|1330545|2153385;1783272|1239|91061|186826|33958|2767887|1624;1783272|1239|91061|186826|33958|2742598|1613;1783272|1239|91061|186826|33958|2742598|1598;1783272|1239|91061|1385|186817|400634|2081964;1783272|1239|91061|1385|186817|400634|1421;1783272|544448|2790996|2895623|2923352|2100;3379134|1224|28211|356|119045|407|2067957;1783272|1239|91061|1385|186822|44249|189425;1783272|1239|91061|1385|186822|44249|1473112;3379134|1224|1236|91347|1903409|53335|2575375;1783272|1239|91061|1385|186817|2675229|450367;3379134|1224|28211|356|69277|28100|28101;3379134|1224|1236|91347|543|1330546|61647;3379134|1224|1236|72274|135621|286|237609;3379134|1224|1236|72274|135621|286|47885;3379134|1224|1236|72274|135621|286|76760;3379134|1224|1236|72274|135621|286|306;3379134|1224|1236|72274|135621|286|1338689;3379134|1224|1236|72274|135621|286|1611770;3379134|1224|1236|72274|135621|286|1636610;3379134|1224|1236|72274|135621|286|2069256;3379134|1224|1236|91347|1903411|34037|34038;3379134|1224|28216|80840|119060|48736|329;1783272|201174|1760|85006|1268|32207|172042;1783272|201174|1760|85006|1268|32207|43675;3379134|1224|1236|135624|83763|866|867;1783272|201174|1760|2037|2049|2529408|52773;3379134|976|117747|200666|84566|28453|1933220;3379134|976|117747|200666|84566|28453|2003121;3379134|1224|28211|204457|41297|13687|2219696;3379134|1224|1236|135614|32033|40323|1904944;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|1300|1301|1305;1783272|1239|91061|186826|1300|1301|712624;3379134|1224|1236|135624|83763|83770|83771;1783272|1239|91061|186826|186827|2689587|2036206;3379134|1224|28216|80840|80864|34072|436515;3379134|1224|28216|80840|80864|34072|34073;3379134|1224|28216|80840|80864|34072|434009;3379134|1224|28216|80840|80864|34072|2126319;3379134|1224|1236|135623|641|662|55601;1783272|1239|186801|3085636|186803|2316020|33038;3379134|1224|28216|80840|80864|34072|114708,Complete,Peace Sandy
bsdb:35411293/1/2,35411293,"cross-sectional observational, not case-control",35411293,10.34172/bi.2021.23378,NA,"Han Y., Jia Z., Shi J., Wang W. , He K.",The active lung microbiota landscape of COVID-19 patients through the metatranscriptome data analysis,BioImpacts : BI,2022,"COVID-19, Faecalibacterium prausnitzii, Lactic acid bacteria, Microbiota, SARS-CoV-2",Experiment 1,China,Homo sapiens,Lung,UBERON:0002048,COVID-19,MONDO:0100096,Healthy controls,COVID-19 cases,COVID-19 infected patients,23,19,NA,WMS,NA,NA,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Supplementary Table 2,12 June 2021,Claregrieve1,"Claregrieve1,Davvve,Peace Sandy,WikiWorks",Differential microbial abundance between the COVID-19 patients and the healthy controls,decreased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter rectus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema putidum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium phytofermentans",3379134|29547|3031852|213849|72294|194|203;3379134|29547|3031852|213849|72294|194|204;3379134|203691|203692|136|2845253|157|221027;1783272|1239|186801|3085636|186803|1506553|66219,Complete,Peace Sandy
bsdb:35416686/1/NA,35416686,"cross-sectional observational, not case-control",35416686,https://doi.org/10.1128/spectrum.00344-21,NA,"Su J., Li C.X., Liu H.Y., Lian Q.Y., Chen A., You Z.X., Li K., Cai Y.H., Lin Y.X., Pan J.B., Zhang G.X., Ju C.R., You C.X. , He J.X.",The Airway Microbiota Signatures of Infection and Rejection in Lung Transplant Recipients,Microbiology spectrum,2022,"16S rRNA, airway microbiota, infection, lung transplant, rejection",Experiment 1,China,Homo sapiens,Sputum,UBERON:0007311,Lung transplantation,EFO:0010721,Clinically stable (or event-free) recipients,Recipients with infection,Lung transplant recipients (LTRs) with infection,47,103,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:35416686/2/1,35416686,"cross-sectional observational, not case-control",35416686,https://doi.org/10.1128/spectrum.00344-21,NA,"Su J., Li C.X., Liu H.Y., Lian Q.Y., Chen A., You Z.X., Li K., Cai Y.H., Lin Y.X., Pan J.B., Zhang G.X., Ju C.R., You C.X. , He J.X.",The Airway Microbiota Signatures of Infection and Rejection in Lung Transplant Recipients,Microbiology spectrum,2022,"16S rRNA, airway microbiota, infection, lung transplant, rejection",Experiment 2,China,Homo sapiens,Sputum,UBERON:0007311,Lung transplantation,EFO:0010721,Clinically stable (or event-free) recipients,Recipients with rejection,Lung transplant recipients (LTRs) with rejection,47,31,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Fig. 4C,26 March 2024,Scholastica,"Scholastica,WikiWorks",LEfSe analysis identifying the airway microbiota that were differentially altered among the transplant groups. Only those taxa with LDA scores 4.0 were ultimately considered.,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae",1783272|201174;1783272|201174|1760|85006|1268;1783272|201174|1760|85006;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|186826|186827;1783272|1239|91061|186826|186827|46123;3379134|1224|28216|206351|481;3379134|1224|28216|206351|481|482;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037;1783272|201174|1760|2037|2049;3384189|32066|203490|203491;3384189|32066|203490|203491|1129771|32067;3384189|32066|203490;3384189|32066|203490|203491|1129771,Complete,Peace Sandy
bsdb:35421938/1/1,35421938,case-control,35421938,10.1186/s12886-022-02395-x,NA,"Shin J.H., Lee J.W., Lim S.H., Yoon B.W., Lee Y. , Seo J.H.",The microbiomes of the eyelid and buccal area of patients with uveitic glaucoma,BMC ophthalmology,2022,"Buccal, Dysbiosis, Eyelid, Lactococcus, Microbiome, Uveitic glaucoma",Experiment 1,Republic of Korea,Homo sapiens,Eyelid,UBERON:0001711,Glaucoma,MONDO:0005041,Controls,UG (Uveitic Glaucoma),Patients with Uveitic Glaucoma,25,20,1 month,16S,34,Illumina,raw counts,edgeR,0.01,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 1,"Figure 5A, Supplementary Table S1",29 August 2025,Anne-mariesharp,Anne-mariesharp,Differentially abundant taxa between uveitic glaucoma patients and control participants,increased,"p__Bacillariophyta,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Buttiauxella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Calidifontibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Candidatus Carsonella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Fontibacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Kandleria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Planctomycetales|f__Planctomycetaceae|g__Planctopirus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Soonwooa,k__Thermoproteati|p__Thermoproteota|c__Thermoprotei|o__Desulfurococcales|f__Desulfurococcaceae|g__Sulfophobococcus,k__Thermoproteati|p__Thermoproteota|c__Thermoprotei|o__Sulfolobales|f__Sulfolobaceae|g__Sulfurisphaera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Tepidimonas,k__Bacillati|p__Candidatus Melainabacteria|c__Vampirovibriophyceae|o__Vampirovibrionales|g__Vampirovibrio,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Vibrionimonas",2836;3379134|976|200643|171549|815|816;3379134|1224|28211|204458|76892|41275;3379134|1224|1236|91347|543|82976;1783272|201174|1760|85006|145357|1158982;3379134|1224|1236|135619|28256|114185;3379134|976|117743|200644|2762318|59732;3379134|1224|1236|91347|543|544;1783272|201174|1760|85006|145357|57495;1783272|1239|526524|526525|2810280|1279384;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|216572|216851;1783272|1239|91061|1385|186822|995014;1783272|1239|526524|526525|2810280|1279388;1783272|201174|1760|85006|1268|57493;1783272|1239|91061|1385|186822|44249;3379134|203682|203683|112|126|1649480;1783272|1239|186801|3085636|186803|841;3379134|976|117743|200644|2762318|944321;1783275|28889|183924|114380|2272|53425;1783275|28889|183924|2281|118883|69655;3379134|1224|28216|80840|114248;1783272|1798710|3118680|2211217|213484;3379134|976|1853228|1853229|563835|1649511,Complete,Svetlana up
bsdb:35421938/1/2,35421938,case-control,35421938,10.1186/s12886-022-02395-x,NA,"Shin J.H., Lee J.W., Lim S.H., Yoon B.W., Lee Y. , Seo J.H.",The microbiomes of the eyelid and buccal area of patients with uveitic glaucoma,BMC ophthalmology,2022,"Buccal, Dysbiosis, Eyelid, Lactococcus, Microbiome, Uveitic glaucoma",Experiment 1,Republic of Korea,Homo sapiens,Eyelid,UBERON:0001711,Glaucoma,MONDO:0005041,Controls,UG (Uveitic Glaucoma),Patients with Uveitic Glaucoma,25,20,1 month,16S,34,Illumina,raw counts,edgeR,0.01,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 2,"Figure 5A, Supplementary Table S1",29 August 2025,Anne-mariesharp,Anne-mariesharp,Differentially abundant taxa between uveitic glaucoma patients and control participants,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Dermabacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Halalkalibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Moellerella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pluralibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pseudocitrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xylella",1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85006|85020|36739;1783272|1239|91061|186826|186828|29393;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|91061|1385|186817|392825;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1357;3379134|1224|1236|91347|1903414|158848;3379134|1224|1236|91347|1903414|581;3379134|1224|1236|91347|543|1330546;3379134|1224|1236|91347|543|1504576;3379134|1224|1236|2887326|468|497;3379134|1224|1236|91347|1903411|613;3379134|1224|1236|135614|32033|40323;3379134|1224|28216|80840|80864|34072;1783272|1239|91061|186826|33958|46255;3379134|1224|1236|135614|32033|2370,Complete,Svetlana up
bsdb:35421938/2/1,35421938,case-control,35421938,10.1186/s12886-022-02395-x,NA,"Shin J.H., Lee J.W., Lim S.H., Yoon B.W., Lee Y. , Seo J.H.",The microbiomes of the eyelid and buccal area of patients with uveitic glaucoma,BMC ophthalmology,2022,"Buccal, Dysbiosis, Eyelid, Lactococcus, Microbiome, Uveitic glaucoma",Experiment 2,Republic of Korea,Homo sapiens,Buccal mucosa,UBERON:0006956,Glaucoma,MONDO:0005041,Controls,UG (Uveitic Glaucoma),Patients with Uveitic Glaucoma,25,34,1 month,16S,34,Illumina,raw counts,edgeR,0.01,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 1,"Figure 5B, Supplementary Table S2",3 September 2025,Anne-mariesharp,Anne-mariesharp,Differentially abundant taxa between uveitic glaucoma patients and control participants,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Acetobacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Alkalibaculum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerosphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Thermoproteati|p__Thermoproteota|c__Thermoprotei|o__Thermoproteales|f__Thermoproteaceae|g__Caldivirga,k__Nanobdellati|p__Candidatus Aenigmatarchaeota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Candidatus Carsonella,k__Nanobdellati|p__Candidatus Parvarchaeota|g__Candidatus Parvarchaeum,k__Pseudomonadati|p__Planctomycetota|c__Candidatus Brocadiia|o__Candidatus Brocadiales|f__Candidatus Scalinduaceae|g__Candidatus Scalindua,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Dichelobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Kandleria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Methanobacteriati|p__Methanobacteriota|c__Methanomicrobia|o__Methanosarcinales|f__Methermicoccaceae|g__Methermicoccus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Rhodocytophagaceae|g__Rhodocytophaga,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Methanobacteriati|p__Methanobacteriota|c__Halobacteria|o__Halobacteriales|f__Halobacteriaceae|g__Salarchaeum,k__Thermoproteati|p__Thermoproteota|c__Thermoprotei|o__Desulfurococcales|f__Desulfurococcaceae|g__Sulfophobococcus,k__Thermoproteati|p__Thermoproteota|c__Thermoprotei|o__Sulfolobales|f__Sulfolobaceae|g__Sulfurisphaera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Thermoproteati|p__Thermoproteota|c__Thermoprotei|o__Thermoproteales|f__Thermoproteaceae|g__Thermocladium,k__Methanobacteriati|p__Thermoplasmatota|c__Thermoplasmata|o__Thermoplasmatales|g__Thermogymnomonas,k__Bacillati|p__Candidatus Melainabacteria|c__Vampirovibriophyceae|o__Vampirovibrionales|g__Vampirovibrio",3379134|976|200643|171549|171550|1647173;1783272|201174|1760|2037|2049|76833;3379134|74201|203494|48461|1647988|239934;3379134|1224|28216|80840|506|507;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|186806|696745;1783272|1239|1737404|1737405|1570339|1273095;1783272|1239|186801|3085636|186803|572511;1783275|28889|183924|2266|2267|76886;1783276|743724;3379134|1224|1236|135619|28256|114185;1783276|1462422|662758;3379134|203682|2517206|1127829|2897346|236756;1783272|201174|84998|84999|84107|102106;1783272|1239|526524|526525|2810280|100883;3379134|1224|1236|135615|868|869;1783272|1239|186801|3085636|186803|189330;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|204475;1783272|1239|526524|526525|2810280|1279388;1783272|201174|1760|85006|1268|57493;1783272|1239|186801|3085636|186803;1783272|1239|909932|909929|1843491|158846;3366610|28890|224756|94695|660062|660063;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3082720|186804;1783272|1239|909932|1843488|909930|33024;3379134|1224|1236|72274|135621|286;3379134|976|768503|768507|3078917|455076;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;3366610|28890|183963|2235|2236|1075398;1783275|28889|183924|114380|2272|53425;1783275|28889|183924|2281|118883|69655;3379134|1224|28216|80840|995019|40544;1783275|28889|183924|2266|2267|62608;3366610|2283796|183967|2301|482135;1783272|1798710|3118680|2211217|213484,Complete,Svetlana up
bsdb:35421938/2/2,35421938,case-control,35421938,10.1186/s12886-022-02395-x,NA,"Shin J.H., Lee J.W., Lim S.H., Yoon B.W., Lee Y. , Seo J.H.",The microbiomes of the eyelid and buccal area of patients with uveitic glaucoma,BMC ophthalmology,2022,"Buccal, Dysbiosis, Eyelid, Lactococcus, Microbiome, Uveitic glaucoma",Experiment 2,Republic of Korea,Homo sapiens,Buccal mucosa,UBERON:0006956,Glaucoma,MONDO:0005041,Controls,UG (Uveitic Glaucoma),Patients with Uveitic Glaucoma,25,34,1 month,16S,34,Illumina,raw counts,edgeR,0.01,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 2,"Figure 5B, Supplementary Table S2",3 September 2025,Anne-mariesharp,Anne-mariesharp,Differentially abundant taxa between uveitic glaucoma patients and control participants,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinilabiliaceae|g__Alkaliflexus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Allobogoriellales|f__Allobogoriellaceae|g__Allobogoriella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae|g__Anaeroarcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae|g__Anaeromusa,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae|g__Anaerosinus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Anoxybacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Atopobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Atopococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermatophilaceae|g__Austwickia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Bavariicoccus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Beutenbergiaceae|g__Beutenbergia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Calidifontibacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Candidatus Pelagibacterales|f__Candidatus Pelagibacteraceae|g__Candidatus Pelagibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Catellicoccus,k__Pseudomonadati|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Dermabacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Desemzia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Kordiimonadales|f__Kordiimonadaceae|g__Eilatimonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Garicola,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Geobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinilabiliaceae|g__Geofilum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Allobogoriellales|f__Allobogoriellaceae|g__Georgenia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Halalkalibacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Haloechinothrix,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Humibacillus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Hydrogenimonadaceae|g__Hydrogenimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Isobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Jeotgalibaca,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermatophilaceae|g__Kineosphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Lacticigenium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactovum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Luteipulveratus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Marihabitans,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Melissococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Beutenbergiaceae|g__Miniimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Ornithinicoccus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Owenweeksiaceae|g__Owenweeksia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Parascardovia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Pilibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermatophilaceae|g__Piscicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Pisciglobus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Psychrilyobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae|g__Pelosinus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Beutenbergiaceae|g__Salana,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Salirhabdus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Sciscionella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Sedimenticolaceae|g__Sedimenticola,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Cellulomonadaceae|g__Sediminihabitans,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Tetragenococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976|200643|1970189|558415|286729;1783272|201174|1760|3467296|145358|56054;1783272|1239|909932|909929|1843490|151038;1783272|1239|909932|909929|1843490|81463;1783272|1239|909932|909929|1843490|151037;1783272|1239|186801|3085636|186803|653683;1783272|1239|91061|1385|3120669|150247;1783272|1239|91061|186826|186828|136491;1783272|201174|84998|84999|1643824|1380;1783272|1239|91061|186826|186828|269773;1783272|201174|1760|85006|85018|1184606;1783272|1239|91061|186826|81852|697279;1783272|201174|1760|85006|125316|84756;1783272|201174|1760|85006|145357|1158982;3379134|1224|28211|54526|1655514|198251;1783272|1239|91061|186826|81852|300418;3379134|204428|204429|51291|809|810;1783272|201174|1760|85006|85020|36739;1783272|1239|91061|186826|186828|82800;1783272|1239|91061|186826|186828|29393;3379134|1224|28211|362534|1331809|1434000;1783272|1239|1737404|1737405|1570339|150022;1783272|201174|1760|85006|1268|1774136;1783272|1239|91061|1385|3120669|129337;3379134|976|200643|1970189|558415|1236988;1783272|201174|1760|3467296|145358|154116;1783272|1239|91061|186826|186828|117563;1783272|1239|91061|1385|186817|392825;1783272|201174|1760|85010|2070|1425377;1783272|201174|1760|85006|85021|556178;3379134|29547|3031852|213849|292630|223785;1783272|1239|91061|186826|186828|142587;1783272|1239|91061|186826|186828|1470540;1783272|201174|1760|85006|85018|211469;1783272|1239|186801|3085636|186803|1164882;1783272|1239|91061|186826|186828|633405;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|1300|303226;1783272|1239|91061|186826|33958|1243;1783272|201174|1760|85006|145357|745364;1783272|201174|1760|85006|85021|568214;1783272|1239|909932|1843489|31977|906;1783272|1239|91061|186826|81852|33969;1783272|201174|1760|85006|125316|947525;3379134|1224|1236|91347|1903414|581;1783272|1239|186801|3085636|186803|437755;1783272|1239|909932|1843489|31977|909928;1783272|1239|186801|3085636|186803|265975;1783272|201174|1760|85006|85021|82345;3379134|976|117743|200644|3024551|267986;1783272|201174|1760|85004|31953|196082;1783272|1239|91061|186826|81852|337670;1783272|201174|1760|85006|85018|985001;1783272|1239|91061|186826|186828|1384499;3379134|976|200643|171549|171552|838;3384189|32066|203490|203491|203492|623282;3379134|1224|1236|2887326|468|497;1783272|1239|909932|909929|1843490|552808;1783272|201174|1760|85006|125316|120376;1783272|1239|91061|1385|186817|394505;1783272|201174|1760|85010|2070|596495;3379134|1224|1236|135613|3067276|349742;1783272|201174|1760|85006|85016|1217414;1783272|1239|526524|526525|128827|123375;3379134|1224|1236|135614|32033|40323;1783272|1239|186801|3085636|186803|1213720;1783272|1239|91061|186826|81852|51668;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:35427393/1/1,35427393,case-control,35427393,10.1371/journal.pone.0267045,NA,"Chen J., Yang Y., Yu N., Sun W., Yang Y. , Zhao M.",Relationship between gut microbiome characteristics and the effect of nutritional therapy on glycemic control in pregnant women with gestational diabetes mellitus,PloS one,2022,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Ineffective group before the therapy (N1),Effective group before the therapy (Y1),The Y1 group consisted of pregnant women with Gestational Diabetes Mellitus (GDM) whose glycemic control effect was on target before medical nutrition therapy  (MNT).,12,62,5 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index",NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 2B,4 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Bacterial signatures that are statistically different between the effective and ineffective groups before medical nutrition therapy  (MNT).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus",1783272|1239|186801|3085636|186803|841;1783272|201174|1760|85004;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|1239|526524|526525|128827|61170;3379134|1224|1236|91347|1903414|583,Complete,Svetlana up
bsdb:35427393/1/2,35427393,case-control,35427393,10.1371/journal.pone.0267045,NA,"Chen J., Yang Y., Yu N., Sun W., Yang Y. , Zhao M.",Relationship between gut microbiome characteristics and the effect of nutritional therapy on glycemic control in pregnant women with gestational diabetes mellitus,PloS one,2022,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Ineffective group before the therapy (N1),Effective group before the therapy (Y1),The Y1 group consisted of pregnant women with Gestational Diabetes Mellitus (GDM) whose glycemic control effect was on target before medical nutrition therapy  (MNT).,12,62,5 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index",NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 2B,4 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Bacterial signatures that are statistically different between the effective and ineffective groups before medical nutrition therapy  (MNT).,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae",3379134|1224|1236|135624;3379134|976|200643|171549|171552|1283313;1783272|1239|91061|1385;3379134|200940|3031449|213115|194924|872;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|46255;1783272|1239|91061|1385|539738,Complete,Svetlana up
bsdb:35427393/2/1,35427393,case-control,35427393,10.1371/journal.pone.0267045,NA,"Chen J., Yang Y., Yu N., Sun W., Yang Y. , Zhao M.",Relationship between gut microbiome characteristics and the effect of nutritional therapy on glycemic control in pregnant women with gestational diabetes mellitus,PloS one,2022,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Ineffective group after the therapy (N2),Effective group after the therapy (Y2),The Y2 group consisted of pregnant women with Gestational Diabetes Mellitus (GDM)  whose glycemic control effect was on target after medical nutrition therapy  (MNT).,12,62,5 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index",NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 5C,4 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Bacterial signatures that are statistically different between the effective and ineffective groups after medical nutrition therapy  (MNT).,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia",1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174;1783272|201174|84992,Complete,Svetlana up
bsdb:35427393/2/2,35427393,case-control,35427393,10.1371/journal.pone.0267045,NA,"Chen J., Yang Y., Yu N., Sun W., Yang Y. , Zhao M.",Relationship between gut microbiome characteristics and the effect of nutritional therapy on glycemic control in pregnant women with gestational diabetes mellitus,PloS one,2022,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Ineffective group after the therapy (N2),Effective group after the therapy (Y2),The Y2 group consisted of pregnant women with Gestational Diabetes Mellitus (GDM)  whose glycemic control effect was on target after medical nutrition therapy  (MNT).,12,62,5 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index",NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 5C,4 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Bacterial signatures that are statistically different between the effective and ineffective groups after medical nutrition therapy  (MNT).,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella",1783272|1239|526524|526525|128827|61170;3379134|1224|1236|91347|1903414|583;1783272|1239|91061|186826|186828;1783272|1239|91061|186826|186828|117563,Complete,Svetlana up
bsdb:35427393/3/1,35427393,case-control,35427393,10.1371/journal.pone.0267045,NA,"Chen J., Yang Y., Yu N., Sun W., Yang Y. , Zhao M.",Relationship between gut microbiome characteristics and the effect of nutritional therapy on glycemic control in pregnant women with gestational diabetes mellitus,PloS one,2022,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Effective group before the therapy (Y1),Effective group after the therapy (Y2),The Y2 group consisted of pregnant women with Gestational Diabetes Mellitus (GDM)  whose glycemic control effect was on target after medical nutrition therapy  (MNT).,62,62,5 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 4C,4 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Results of linear discriminant analysis of gut microbiome before and after therapy outcome between effective group.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,1783272|1239|186801|186802|216572|459786,Complete,Svetlana up
bsdb:35440670/1/1,35440670,case-control,35440670,https://doi.org/10.1038/s41598-022-07995-7,NA,"Zuo W., Wang B., Bai X., Luan Y., Fan Y., Michail S. , Sun F.",16S rRNA and metagenomic shotgun sequencing data revealed consistent patterns of gut microbiome signature in pediatric ulcerative colitis,Scientific reports,2022,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Healthy controls,Patients with ulcerative colitis,Children aged 7-21 with mild to moderate ulcerative colitis,23,19,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Table S4,20 October 2022,Claregrieve1,"Claregrieve1,Lwaldron,Suwaiba,WikiWorks",Differential microbial abundance between controls and UC subjects,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira|s__uncultured Oscillospira sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|s__Enterococcaceae bacterium RF39",1783272|201174|84998|1643822|1643826|447020;3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|186802|216572|244127;1783272|1239;3379134|976|200643|171549|2005519|397864;1783272|1239|186801|3082720|186804|1870884;1783272|201174|84998|84999;1783272|1239|186801|186802|186806|1730|290054;3366610|28890|183925|2158|2159|2172;1783272|1239|186801|186802|216572;1783272|201174|84998|1643822|1643826|84108;3379134|976|200643|171549|2005525|195950;3379134|74201|203494|48461;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|186802|216572|39492;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|186802|216572|119852|512316;1783272|1239|91061|186826|81852|423410,Complete,Claregrieve1
bsdb:35440670/1/2,35440670,case-control,35440670,https://doi.org/10.1038/s41598-022-07995-7,NA,"Zuo W., Wang B., Bai X., Luan Y., Fan Y., Michail S. , Sun F.",16S rRNA and metagenomic shotgun sequencing data revealed consistent patterns of gut microbiome signature in pediatric ulcerative colitis,Scientific reports,2022,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Healthy controls,Patients with ulcerative colitis,Children aged 7-21 with mild to moderate ulcerative colitis,23,19,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Table S4,20 October 2022,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between controls and UC subjects,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171551|836|28123;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|31979|1485|1502;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3082720|186804|1870884;1783272|1239|186801|3082720|186804|1257;1783272|1239|1737404|1737405;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|909932|1843489|31977|29465;3384189|32066;3384189|32066|203490|203491;3384189|32066|203490|203491|203492;3384189|32066|203490|203491|203492|848;3379134|1224;3379134|1224|1236;3379134|1224|28216|206351|481;3379134|1224|28216|206351|481|538;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|1940338;3379134|1224|1236|135625;3379134|1224|1236|135625|712;3379134|1224|1236|135625|712|724,Complete,Claregrieve1
bsdb:35459771/1/1,35459771,"cross-sectional observational, not case-control",35459771,10.1038/s41598-022-10532-1,NA,"Xu X., Zhang Y., Yu L., Shi X., Min M., Xiong L., Pan J., Liu P., Wu G. , Gao G.","A cross-sectional analysis about bacterial vaginosis, high-risk human papillomavirus infection, and cervical intraepithelial neoplasia in Chinese women",Scientific reports,2022,NA,Experiment 1,China,Homo sapiens,"Uterine cervix,Vaginal fluid","UBERON:0036243,UBERON:0000002",Bacterial vaginosis,EFO:0003932,Normal Healthy Women & High‑risk human papillomavirus(HR-HPV) Infected Women (HPV),Bacterial Vaginosis (BV) Infected Women,"Women attending the Aviation General hospital, located in Beijing, China, who were diagnosed with Bacterial Vaginosis (BV) Infection.",136,52,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,22 April 2024,Joan Chuks,"Joan Chuks,WikiWorks",Bacterial Taxa differentially abundant in the vaginal microbiome of Bacterial Vaginosis (BV) Infected women compared to Normal healthy women & High‑risk human papillomavirus(HR-HPV) Infected Women as determined by LEfSe Analysis.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|976|200643|171549|171552|2974257|386414;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552,Complete,Svetlana up
bsdb:35459771/3/1,35459771,"cross-sectional observational, not case-control",35459771,10.1038/s41598-022-10532-1,NA,"Xu X., Zhang Y., Yu L., Shi X., Min M., Xiong L., Pan J., Liu P., Wu G. , Gao G.","A cross-sectional analysis about bacterial vaginosis, high-risk human papillomavirus infection, and cervical intraepithelial neoplasia in Chinese women",Scientific reports,2022,NA,Experiment 3,China,Homo sapiens,"Uterine cervix,Vaginal fluid","UBERON:0036243,UBERON:0000002","Bacterial vaginosis,Human papilloma virus infection","EFO:0003932,EFO:0001668",Normal Healthy Women,Bacterial vaginosis (BV) infected women & High‑risk human papillomavirus (HR-HPV) (HPV) infected Women,"Women attending the Aviation General hospital, located in Beijing, China, who were diagnosed with Bacterial vaginosis (BV) infection and those diagnosed with High‑risk human papillomavirus (HR-HPV) infection.",65,123,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,22 April 2024,Joan Chuks,"Joan Chuks,WikiWorks",Bacterial Taxa differentially abundant in the vaginal microbiome of  Bacterial Vaginosis (BV) infected women and High‑risk human papillomavirus (HR-HPV) infected women compared to Normal healthy women as determined by LEfSe Analysis.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239|91061;1783272|1239;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:35459771/4/NA,35459771,"cross-sectional observational, not case-control",35459771,10.1038/s41598-022-10532-1,NA,"Xu X., Zhang Y., Yu L., Shi X., Min M., Xiong L., Pan J., Liu P., Wu G. , Gao G.","A cross-sectional analysis about bacterial vaginosis, high-risk human papillomavirus infection, and cervical intraepithelial neoplasia in Chinese women",Scientific reports,2022,NA,Experiment 4,China,Homo sapiens,"Uterine cervix,Vaginal fluid","UBERON:0000002,UBERON:0036243","Human papilloma virus infection,Cervical intraepithelial neoplasia","MONDO:0022394,EFO:0001668",Normal Healthy Women,High‑risk human papillomavirus(HR-HPV) & Cervical Intraepithelial Neoplasia(CIN) co-infected women (HC),"Women attending the Aviation General hospital, located in Beijing, China, who were diagnosed with infection of High‑risk human papillomavirus (HR-HPV) combined with Cervical Intraepithelial Neoplasia (CIN).",65,48,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,increased,unchanged,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:35459771/5/NA,35459771,"cross-sectional observational, not case-control",35459771,10.1038/s41598-022-10532-1,NA,"Xu X., Zhang Y., Yu L., Shi X., Min M., Xiong L., Pan J., Liu P., Wu G. , Gao G.","A cross-sectional analysis about bacterial vaginosis, high-risk human papillomavirus infection, and cervical intraepithelial neoplasia in Chinese women",Scientific reports,2022,NA,Experiment 5,China,Homo sapiens,"Uterine cervix,Vaginal fluid","UBERON:0036243,UBERON:0000002","Bacterial vaginosis,Cervical intraepithelial neoplasia,Human papilloma virus infection","EFO:0003932,MONDO:0022394,EFO:0001668",Normal Healthy Women,Bacteial Vaginosis (BV) & High‑risk human papillomavirus(HR-HPV) with Cervical Intraepithelial Neoplasia(CIN) co-infected women (BHC),"Women attending the Aviation General hospital, located in Beijing, China, who were diagnosed with co-infection of Bacteial Vaginosis (BV) & High‑risk human papillomavirus (HR-HPV) in combination with Cervical Intraepithelial Neoplasia (CIN).",65,46,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,increased,increased,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:35459771/6/NA,35459771,"cross-sectional observational, not case-control",35459771,10.1038/s41598-022-10532-1,NA,"Xu X., Zhang Y., Yu L., Shi X., Min M., Xiong L., Pan J., Liu P., Wu G. , Gao G.","A cross-sectional analysis about bacterial vaginosis, high-risk human papillomavirus infection, and cervical intraepithelial neoplasia in Chinese women",Scientific reports,2022,NA,Experiment 6,China,Homo sapiens,"Uterine cervix,Vaginal fluid","UBERON:0000002,UBERON:0036243","Human papilloma virus infection,Cervical intraepithelial neoplasia","MONDO:0022394,EFO:0001668",Bacterial Vaginosis (BV) Infected Women,High‑risk human papillomavirus(HR-HPV) & Cervical Intraepithelial Neoplasia(CIN) co-infected women (HC),"Women attending the Aviation General hospital, located in Beijing, China, who were diagnosed with infection of High‑risk human papillomavirus (HR-HPV) combined with Cervical Intraepithelial Neoplasia (CIN).",52,48,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,decreased,decreased,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:35459771/7/NA,35459771,"cross-sectional observational, not case-control",35459771,10.1038/s41598-022-10532-1,NA,"Xu X., Zhang Y., Yu L., Shi X., Min M., Xiong L., Pan J., Liu P., Wu G. , Gao G.","A cross-sectional analysis about bacterial vaginosis, high-risk human papillomavirus infection, and cervical intraepithelial neoplasia in Chinese women",Scientific reports,2022,NA,Experiment 7,China,Homo sapiens,"Uterine cervix,Vaginal fluid","UBERON:0000002,UBERON:0036243","Cervical intraepithelial neoplasia,Human papilloma virus infection","MONDO:0022394,EFO:0001668",High‑risk human papillomavirus (HR-HPV) Infected Women (HPV),High‑risk human papillomavirus(HR-HPV) & Cervical Intraepithelial Neoplasia(CIN) co-infected women (HC),"Women attending the Aviation General hospital, located in Beijing, China, who were diagnosed with infection of High‑risk human papillomavirus (HR-HPV) combined with Cervical Intraepithelial Neoplasia (CIN).",71,48,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,increased,decreased,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:35459771/8/NA,35459771,"cross-sectional observational, not case-control",35459771,10.1038/s41598-022-10532-1,NA,"Xu X., Zhang Y., Yu L., Shi X., Min M., Xiong L., Pan J., Liu P., Wu G. , Gao G.","A cross-sectional analysis about bacterial vaginosis, high-risk human papillomavirus infection, and cervical intraepithelial neoplasia in Chinese women",Scientific reports,2022,NA,Experiment 8,China,Homo sapiens,"Uterine cervix,Vaginal fluid","UBERON:0036243,UBERON:0000002","Bacterial vaginosis,Human papilloma virus infection","EFO:0003932,EFO:0001668",Bacterial vaginosis (BV) and High‑risk human papillomavirus (HR-HPV) (HPV) co-infected Women (BH),High‑risk human papillomavirus(HR-HPV) & Cervical Intraepithelial Neoplasia(CIN) co-infected women (HC),"Women attending the Aviation General hospital, located in Beijing, China, who were diagnosed with infection of High‑risk human papillomavirus (HR-HPV) combined with Cervical Intraepithelial Neoplasia (CIN).",60,48,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,increased,increased,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:35459771/9/NA,35459771,"cross-sectional observational, not case-control",35459771,10.1038/s41598-022-10532-1,NA,"Xu X., Zhang Y., Yu L., Shi X., Min M., Xiong L., Pan J., Liu P., Wu G. , Gao G.","A cross-sectional analysis about bacterial vaginosis, high-risk human papillomavirus infection, and cervical intraepithelial neoplasia in Chinese women",Scientific reports,2022,NA,Experiment 9,China,Homo sapiens,"Uterine cervix,Vaginal fluid","UBERON:0036243,UBERON:0000002","Bacterial vaginosis,Cervical intraepithelial neoplasia,Human papilloma virus infection","EFO:0003932,MONDO:0022394,EFO:0001668",High‑risk human papillomavirus(HR-HPV) Infected Women (HPV),Bacteial Vaginosis (BV) & High‑risk human papillomavirus(HR-HPV) with Cervical Intraepithelial Neoplasia(CIN) co-infected women (BHC),"Women attending the Aviation General hospital, located in Beijing, China, who were diagnosed with with co-infection of Bacteial Vaginosis (BV) & High‑risk human papillomavirus (HR-HPV) in combination with Cervical Intraepithelial Neoplasia (CIN).",71,46,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,increased,increased,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:35459771/10/NA,35459771,"cross-sectional observational, not case-control",35459771,10.1038/s41598-022-10532-1,NA,"Xu X., Zhang Y., Yu L., Shi X., Min M., Xiong L., Pan J., Liu P., Wu G. , Gao G.","A cross-sectional analysis about bacterial vaginosis, high-risk human papillomavirus infection, and cervical intraepithelial neoplasia in Chinese women",Scientific reports,2022,NA,Experiment 10,China,Homo sapiens,"Uterine cervix,Vaginal fluid","UBERON:0036243,UBERON:0000002","Bacterial vaginosis,Cervical intraepithelial neoplasia,Human papilloma virus infection","EFO:0003932,MONDO:0022394,EFO:0001668",High‑risk human papillomavirus(HR-HPV) & Cervical Intraepithelial Neoplasia(CIN) co-infected women (HC),Bacteial Vaginosis (BV) & High‑risk human papillomavirus(HR-HPV) with Cervical Intraepithelial Neoplasia(CIN) co-infected women (BHC),"Women attending the Aviation General hospital, located in Beijing, China, who were diagnosed with with co-infection of Bacteial Vaginosis (BV) & High‑risk human papillomavirus (HR-HPV) in combination with Cervical Intraepithelial Neoplasia (CIN).",48,46,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,increased,increased,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:35459771/11/NA,35459771,"cross-sectional observational, not case-control",35459771,10.1038/s41598-022-10532-1,NA,"Xu X., Zhang Y., Yu L., Shi X., Min M., Xiong L., Pan J., Liu P., Wu G. , Gao G.","A cross-sectional analysis about bacterial vaginosis, high-risk human papillomavirus infection, and cervical intraepithelial neoplasia in Chinese women",Scientific reports,2022,NA,Experiment 11,China,Homo sapiens,"Uterine cervix,Vaginal fluid","UBERON:0036243,UBERON:0000002",Bacterial vaginosis,EFO:0003932,Normal Healthy Women,Bacterial Vaginosis (BV) Infected Women,"Women attending the Aviation General hospital, located in Beijing, China, who were diagnosed with Bacterial Vaginosis (BV) Infection.",65,52,1 month,16S,34,Illumina,NA,LEfSe,0.05,NA,4,NA,NA,NA,increased,increased,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:35459771/12/NA,35459771,"cross-sectional observational, not case-control",35459771,10.1038/s41598-022-10532-1,NA,"Xu X., Zhang Y., Yu L., Shi X., Min M., Xiong L., Pan J., Liu P., Wu G. , Gao G.","A cross-sectional analysis about bacterial vaginosis, high-risk human papillomavirus infection, and cervical intraepithelial neoplasia in Chinese women",Scientific reports,2022,NA,Experiment 12,China,Homo sapiens,"Uterine cervix,Vaginal fluid","UBERON:0000002,UBERON:0036243",Human papilloma virus infection,EFO:0001668,Normal Healthy Women,High‑risk human papillomavirus(HR-HPV) Infected Women (HPV),"Women attending the Aviation General hospital, located in Beijing, China, who were diagnosed with High‑risk human papillomavirus (HR-HPV) infection.",65,71,1 month,16S,34,Illumina,NA,LEfSe,0.05,NA,4,NA,NA,NA,increased,increased,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:35459771/13/NA,35459771,"cross-sectional observational, not case-control",35459771,10.1038/s41598-022-10532-1,NA,"Xu X., Zhang Y., Yu L., Shi X., Min M., Xiong L., Pan J., Liu P., Wu G. , Gao G.","A cross-sectional analysis about bacterial vaginosis, high-risk human papillomavirus infection, and cervical intraepithelial neoplasia in Chinese women",Scientific reports,2022,NA,Experiment 13,China,Homo sapiens,"Uterine cervix,Vaginal fluid","UBERON:0036243,UBERON:0000002","Bacterial vaginosis,Human papilloma virus infection","EFO:0003932,EFO:0001668",Normal Healthy Women,Bacterial vaginosis (BV) and High‑risk human papillomavirus (HR-HPV) (HPV) co-infected Women (BH),"Women attending the Aviation General hospital, located in Beijing, China, who were diagnosed with co-infection of Bacterial vaginosis (BV) and High‑risk human papillomavirus (HR-HPV).",65,71,1 month,16S,34,Illumina,NA,LEfSe,0.05,NA,4,NA,NA,NA,increased,increased,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:35463646/1/1,35463646,"cross-sectional observational, not case-control",35463646,10.3389/fcimb.2022.837019,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9022099/,"Fu S.C., Lee C.H., Hsieh Y.C., Wu P.H., Lin S.H. , Wang H.","A Pilot Study Exploring the Association of Entacapone, Gut Microbiota, and the Subsequent Side Effects in Patients With Parkinson's Disease",Frontiers in cellular and infection microbiology,2022,"Parkinson’s disease, constipation, drowsiness, entacapone, levodopa, microbiome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Clinical treatment,EFO:0007056,Parkinson's disease (PD) patients treated with levodopa only (PD_L),Parkinson's disease (PD) patients treated with both levodopa and Entacapone (PD_LE),"Parkinson's disease (PD) patients treated with both levodopa and Entacapone, a peripherally acting catechol-O-methyltransferase (COMT) inhibitor that is used in addition to levodopa to control symptoms.",13,11,NA,16S,45,Ion Torrent,relative abundances,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 3, text",9 April 2024,Fiddyhamma,"Fiddyhamma,Scholastica,WikiWorks",Genera significantly different in abundance in Parkinson's disease patients treated with levodopa only (PD_L) versus Parkinson's disease (PD) patients treated with both levodopa and Entacapone (PD_LE).,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium",1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|186806|1730,Complete,Svetlana up
bsdb:35463646/1/2,35463646,"cross-sectional observational, not case-control",35463646,10.3389/fcimb.2022.837019,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9022099/,"Fu S.C., Lee C.H., Hsieh Y.C., Wu P.H., Lin S.H. , Wang H.","A Pilot Study Exploring the Association of Entacapone, Gut Microbiota, and the Subsequent Side Effects in Patients With Parkinson's Disease",Frontiers in cellular and infection microbiology,2022,"Parkinson’s disease, constipation, drowsiness, entacapone, levodopa, microbiome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Clinical treatment,EFO:0007056,Parkinson's disease (PD) patients treated with levodopa only (PD_L),Parkinson's disease (PD) patients treated with both levodopa and Entacapone (PD_LE),"Parkinson's disease (PD) patients treated with both levodopa and Entacapone, a peripherally acting catechol-O-methyltransferase (COMT) inhibitor that is used in addition to levodopa to control symptoms.",13,11,NA,16S,45,Ion Torrent,relative abundances,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 3, text",9 April 2024,Fiddyhamma,"Fiddyhamma,Scholastica,WikiWorks",Genera significantly different in abundance in Parkinson's disease patients treated with levodopa only (PD_L) versus Parkinson's disease (PD) patients treated with both levodopa and Entacapone (PD_LE).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3082720|186804|1505657;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|1769710,Complete,Svetlana up
bsdb:35467373/1/1,35467373,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M., Shao D., Zhou J., Gu J., Qin J., Li X., Hao C. , Wei W.","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 1,China,Homo sapiens,"Saliva,Gastric juice,Stomach,Feces,Esophagus","UBERON:0001971,UBERON:0001988,UBERON:0001836,UBERON:0001043,UBERON:0000945",Upper digestive tract disease,MONDO:0044991,"Esophageal swab, cardia biopsy, noncardia biopsy, gastric juice, and fecal samples",Saliva samples,Saliva samples from participants undergoing upper gastrointestinal endoscopy.,200,40,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2B,12 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe results showing differentially abundant genera in different GI sites.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:35467373/2/1,35467373,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M., Shao D., Zhou J., Gu J., Qin J., Li X., Hao C. , Wei W.","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 2,China,Homo sapiens,"Saliva,Gastric juice,Stomach,Feces,Esophagus","UBERON:0001836,UBERON:0001971,UBERON:0001988,UBERON:0001043,UBERON:0000945",Upper digestive tract disease,MONDO:0044991,"Saliva, cardia biopsy, noncardia biopsy, gastric juice, and fecal samples",Esophageal swab samples,Esophageal swab samples from participants undergoing upper gastrointestinal endoscopy.,200,40,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2B,12 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe results showing differentially abundant genera in different GI sites.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",1783272|1239|91061|186826|1300|1301;3379134|1224|1236|135625|712|724,Complete,Svetlana up
bsdb:35467373/3/1,35467373,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M., Shao D., Zhou J., Gu J., Qin J., Li X., Hao C. , Wei W.","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 3,China,Homo sapiens,"Saliva,Gastric juice,Stomach,Feces,Esophagus","UBERON:0001836,UBERON:0001971,UBERON:0001988,UBERON:0001043,UBERON:0000945",Upper digestive tract disease,MONDO:0044991,"Saliva, esophageal swab, noncardia biopsy, gastric juice, and fecal samples",Cardia biopsy samples,Cardia biopsy samples from participants undergoing upper gastrointestinal endoscopy.,200,40,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2B,12 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe results showing differentially abundant genera in different GI sites.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,1783272|1239|91061|186826|33958|46255,Complete,Svetlana up
bsdb:35467373/4/1,35467373,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M., Shao D., Zhou J., Gu J., Qin J., Li X., Hao C. , Wei W.","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 4,China,Homo sapiens,"Saliva,Stomach,Gastric juice,Feces,Esophagus","UBERON:0001971,UBERON:0001988,UBERON:0001836,UBERON:0001043,UBERON:0000945",Upper digestive tract disease,MONDO:0044991,"Saliva, esophageal swab, cardia biopsy, gastric juice, and fecal samples",Noncardia biopsy samples,Noncardia biopsy samples from participants undergoing upper gastrointestinal endoscopy.,200,40,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2B,12 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe results showing differentially abundant genera in different GI sites.,increased,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,3379134|29547|3031852|213849|72293|209,Complete,Svetlana up
bsdb:35467373/5/1,35467373,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M., Shao D., Zhou J., Gu J., Qin J., Li X., Hao C. , Wei W.","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 5,China,Homo sapiens,"Saliva,Stomach,Gastric juice,Feces,Esophagus","UBERON:0001971,UBERON:0001988,UBERON:0001836,UBERON:0001043,UBERON:0000945",Upper digestive tract disease,MONDO:0044991,"Saliva, esophageal swab, cardia biopsy, noncardia biopsy, and fecal samples",Gastric juice samples,Gastric juice samples from participants undergoing upper gastrointestinal endoscopy.,200,40,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2B,12 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe results showing differentially abundant genera in different GI sites.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,3379134|1224|1236|72274|135621|286,Complete,Svetlana up
bsdb:35467373/6/1,35467373,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M., Shao D., Zhou J., Gu J., Qin J., Li X., Hao C. , Wei W.","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 6,China,Homo sapiens,"Saliva,Stomach,Gastric juice,Feces,Esophagus","UBERON:0001836,UBERON:0001971,UBERON:0001988,UBERON:0001043,UBERON:0000945",Upper digestive tract disease,MONDO:0044991,"Saliva, esophageal swab, cardia biopsy, noncardia biopsy, and gastric juice samples",Fecal samples,Fecal samples from participants undergoing upper gastrointestinal endoscopy.,200,40,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2B,12 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe results showing differentially abundant genera in different GI sites.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|572511,Complete,Svetlana up
bsdb:35467373/7/1,35467373,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M., Shao D., Zhou J., Gu J., Qin J., Li X., Hao C. , Wei W.","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 7,China,Homo sapiens,Cardia of stomach,UBERON:0001162,Helicobacter pylori,NCBITAXON:210,H. pylori-negative cardia group (NC),H. pylori-positive cardia group (PC),Biopsy samples from the cardia of patients with H. pylori infection.,20,20,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Table 2,14 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",Comparison of dominant phyla and genera in cardia and noncardia biopsy specimens,increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Pseudomonadota",3379134|29547|3031852|213849|72293|209;3379134|1224,Complete,Svetlana up
bsdb:35467373/7/2,35467373,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M., Shao D., Zhou J., Gu J., Qin J., Li X., Hao C. , Wei W.","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 7,China,Homo sapiens,Cardia of stomach,UBERON:0001162,Helicobacter pylori,NCBITAXON:210,H. pylori-negative cardia group (NC),H. pylori-positive cardia group (PC),Biopsy samples from the cardia of patients with H. pylori infection.,20,20,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Table 2,15 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",Comparison of dominant phyla and genera in cardia and noncardia biopsy specimens,decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",1783272|201174;3379134|976|200643|171549|171552|1283313;3379134|976;3379134|976|200643|171549|171552|838;3379134|1224|1236|72274|135621|286;1783272|1239|909932|909929|1843491|970,Complete,Svetlana up
bsdb:35467373/8/1,35467373,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M., Shao D., Zhou J., Gu J., Qin J., Li X., Hao C. , Wei W.","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 8,China,Homo sapiens,Stomach,UBERON:0000945,Helicobacter pylori,NCBITAXON:210,H. pylori-negative noncardia group (NN),H. pylori-positive noncardia group (PN),Biopsy samples from the noncardia of patients with H. pylori infection.,20,20,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Table 2,15 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",Comparison of dominant phyla and genera in cardia and noncardia biopsy specimens,increased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter",3379134|1224;3379134|29547|3031852|213849|72293|209,Complete,Svetlana up
bsdb:35467373/8/2,35467373,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M., Shao D., Zhou J., Gu J., Qin J., Li X., Hao C. , Wei W.","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 8,China,Homo sapiens,Stomach,UBERON:0000945,Helicobacter pylori,NCBITAXON:210,H. pylori-negative noncardia group (NN),H. pylori-positive noncardia group (PN),Biopsy samples from the noncardia of patients with H. pylori infection.,20,20,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Table 2,15 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",Comparison of dominant phyla and genera in cardia and noncardia biopsy specimens,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota,k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia",3379134|976;1783272|1239;1783272|201174;3384189|32066;3379134|976|200643|171549|171552|838;1783272|1239|909932|1843489|31977|29465;3379134|1224|28216|206351|481|482;3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|1300|1301;3379134|1224|1236|72274|135621|286;3379134|1224|28211|204458|76892|41275;3379134|976|200643|171549|171552|1283313;3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|815|816;1783272|1239|909932|909929|1843491|970;3379134|1224|28216|80840|80864|80865,Complete,Svetlana up
bsdb:35467373/9/1,35467373,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M., Shao D., Zhou J., Gu J., Qin J., Li X., Hao C. , Wei W.","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 9,China,Homo sapiens,Stomach,UBERON:0000945,Helicobacter pylori,NCBITAXON:210,H. pylori-positive noncardia group (PN),H. pylori-positive cardia group (PC),Biopsy samples from the cardia of patients with H. pylori infection.,20,20,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,15 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",Comparison of dominant phyla and genera in cardia and noncardia biopsy specimens,increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174;3379134|976|200643|171549|171552|1283313;1783272|1239;3379134|976|200643|171549|815|816;3379134|976;3384189|32066;3384189|32066|203490|203491|203492|848;3379134|1224|1236|135625|712|724;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:35467373/9/2,35467373,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M., Shao D., Zhou J., Gu J., Qin J., Li X., Hao C. , Wei W.","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 9,China,Homo sapiens,Stomach,UBERON:0000945,Helicobacter pylori,NCBITAXON:210,H. pylori-positive noncardia group (PN),H. pylori-positive cardia group (PC),Biopsy samples from the cardia of patients with H. pylori infection.,20,20,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,15 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",Comparison of dominant phyla and genera in cardia and noncardia biopsy specimens,decreased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter",3379134|1224;3379134|29547|3031852|213849|72293|209,Complete,Svetlana up
bsdb:35467373/10/1,35467373,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M., Shao D., Zhou J., Gu J., Qin J., Li X., Hao C. , Wei W.","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 10,China,Homo sapiens,Gastric juice,UBERON:0001971,Helicobacter pylori,NCBITAXON:210,Lower-pH (L) group,Higher-pH (H) group,Gastric juice samples from patients with a gastric pH level higher than 2.,28,12,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Table S4,15 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe results showing the microbial composition in gastric juice,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301;3379134|1224|28216|206351|481|482;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|135625|712|724;1783272|201174|1760|85006|1268|32207,Complete,Svetlana up
bsdb:35467373/10/2,35467373,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M., Shao D., Zhou J., Gu J., Qin J., Li X., Hao C. , Wei W.","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 10,China,Homo sapiens,Gastric juice,UBERON:0001971,Helicobacter pylori,NCBITAXON:210,Lower-pH (L) group,Higher-pH (H) group,Gastric juice samples from patients with a gastric pH level higher than 2.,28,12,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,Table S4,15 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe results showing the microbial composition in gastric juice,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Amycolatopsis",3379134|1224|1236|72274|135621|286;3379134|1224|1236|2887326|468|469;3379134|1224|28216|80840|75682|963;1783272|201174|1760|85010|2070|1813,Complete,Svetlana up
bsdb:35467373/11/1,35467373,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M., Shao D., Zhou J., Gu J., Qin J., Li X., Hao C. , Wei W.","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 11,China,Homo sapiens,Gastric juice,UBERON:0001971,Helicobacter pylori,NCBITAXON:210,H. pylori-negative (N) group,H. pylori-positive (P) group,Gastric juice samples from patients with H. pylori infection.,20,20,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table S4,15 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe results showing the microbial composition in gastric juice,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,1783272|201174|1760|85006|1268|32207,Complete,Svetlana up
bsdb:35467373/11/2,35467373,"cross-sectional observational, not case-control",35467373,10.1128/spectrum.00645-21,https://journals.asm.org/doi/10.1128/spectrum.00645-21#tab1,"Li M., Shao D., Zhou J., Gu J., Qin J., Li X., Hao C. , Wei W.","Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China",Microbiology spectrum,2022,"Helicobacter pylori, gastric cardia, gastric juice, gastric pH, gastrointestinal tract, microbiota",Experiment 11,China,Homo sapiens,Gastric juice,UBERON:0001971,Helicobacter pylori,NCBITAXON:210,H. pylori-negative (N) group,H. pylori-positive (P) group,Gastric juice samples from patients with H. pylori infection.,20,20,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table S4,15 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe results showing the microbial composition in gastric juice,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter",3379134|1224|1236|72274|135621|286;3379134|1224|1236|2887326|468|469,Complete,Svetlana up
bsdb:35476894/1/1,35476894,laboratory experiment,35476894,10.15252/embr.202052316,https://www.embopress.org/doi/full/10.15252/embr.202052316,"Lee C.C., Liang F., Lee I.C., Lu T.H., Shan Y.Y., Jeng C.F., Zou Y.F., Yu H.T. , Chen Alen S.K.",External light-dark cycle shapes gut microbiota through intrinsically photosensitive retinal ganglion cells,EMBO reports,2022,"dim light at night, gut microbiota, ipRGC, melanopsin",Experiment 1,Taiwan,Mus musculus,Feces,UBERON:0001988,Light,EFO:0000568,Normal light‐dark cycle (LD) - Control group,Dim light at night (dLAN) - Control group,Exposure to aberrant light conditions such as dim light at night (dLAN) in the control group,NA,NA,NA,16S,45,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 4B,20 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",Figure 4B represents a cladogram that shows the difference in the relative abundance of microbes from control mice housed under conditions of LD and dLAN.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|s__Enterococcaceae bacterium RF39",3379134|976|200643|171549|2005473;3379134|976|200643|171549|171552|577309;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|81852|423410,Complete,Svetlana up
bsdb:35476894/1/2,35476894,laboratory experiment,35476894,10.15252/embr.202052316,https://www.embopress.org/doi/full/10.15252/embr.202052316,"Lee C.C., Liang F., Lee I.C., Lu T.H., Shan Y.Y., Jeng C.F., Zou Y.F., Yu H.T. , Chen Alen S.K.",External light-dark cycle shapes gut microbiota through intrinsically photosensitive retinal ganglion cells,EMBO reports,2022,"dim light at night, gut microbiota, ipRGC, melanopsin",Experiment 1,Taiwan,Mus musculus,Feces,UBERON:0001988,Light,EFO:0000568,Normal light‐dark cycle (LD) - Control group,Dim light at night (dLAN) - Control group,Exposure to aberrant light conditions such as dim light at night (dLAN) in the control group,NA,NA,NA,16S,45,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 4B,20 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",Figure 4B represents a cladogram that shows the difference in the relative abundance of microbes from control mice housed under conditions of LD and dLAN.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae",3379134|976|200643|171549|171550|28138;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|1853231,Complete,Svetlana up
bsdb:35476894/2/NA,35476894,laboratory experiment,35476894,10.15252/embr.202052316,https://www.embopress.org/doi/full/10.15252/embr.202052316,"Lee C.C., Liang F., Lee I.C., Lu T.H., Shan Y.Y., Jeng C.F., Zou Y.F., Yu H.T. , Chen Alen S.K.",External light-dark cycle shapes gut microbiota through intrinsically photosensitive retinal ganglion cells,EMBO reports,2022,"dim light at night, gut microbiota, ipRGC, melanopsin",Experiment 2,Taiwan,Mus musculus,Feces,UBERON:0001988,Light,EFO:0000568,Normal light‐dark cycle (LD) - MKO group,Dim light at night (dLAN) - MKO group,Exposure to aberrant light conditions such as dim light at night (dLAN) in the group with knockout of the photopigment melanopsin (MKO).,NA,NA,NA,16S,45,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:35476894/3/1,35476894,laboratory experiment,35476894,10.15252/embr.202052316,https://www.embopress.org/doi/full/10.15252/embr.202052316,"Lee C.C., Liang F., Lee I.C., Lu T.H., Shan Y.Y., Jeng C.F., Zou Y.F., Yu H.T. , Chen Alen S.K.",External light-dark cycle shapes gut microbiota through intrinsically photosensitive retinal ganglion cells,EMBO reports,2022,"dim light at night, gut microbiota, ipRGC, melanopsin",Experiment 3,Taiwan,Mus musculus,Feces,UBERON:0001988,Light,EFO:0000568,Normal light‐dark cycle (LD) - DTA group,Dim light at night (dLAN) - DTA group,Exposure to aberrant light conditions such as dim light at night (dLAN) in the group that underwent the genetic elimination of ipRGCs using the Opn4‐DTA or Opn4‐Cre (DTA).,NA,NA,NA,16S,45,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4D,20 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",The cladogram shows the difference in relative abundance of microbes from Opn4DTA/DTA mice under LD and dLAN conditions.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales",1783272|1239|186801|186802|31979;1783272|1239|526524|526525|128827|174708;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|203557;3379134|74201|203494|48461,Complete,Svetlana up
bsdb:35476894/3/2,35476894,laboratory experiment,35476894,10.15252/embr.202052316,https://www.embopress.org/doi/full/10.15252/embr.202052316,"Lee C.C., Liang F., Lee I.C., Lu T.H., Shan Y.Y., Jeng C.F., Zou Y.F., Yu H.T. , Chen Alen S.K.",External light-dark cycle shapes gut microbiota through intrinsically photosensitive retinal ganglion cells,EMBO reports,2022,"dim light at night, gut microbiota, ipRGC, melanopsin",Experiment 3,Taiwan,Mus musculus,Feces,UBERON:0001988,Light,EFO:0000568,Normal light‐dark cycle (LD) - DTA group,Dim light at night (dLAN) - DTA group,Exposure to aberrant light conditions such as dim light at night (dLAN) in the group that underwent the genetic elimination of ipRGCs using the Opn4‐DTA or Opn4‐Cre (DTA).,NA,NA,NA,16S,45,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4D,20 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",The cladogram shows the difference in relative abundance of microbes from Opn4DTA/DTA mice under LD and dLAN conditions.,decreased,"s__rumen bacterium YS2,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,s__bacterium AF12,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|s__Enterococcaceae bacterium RF39,s__bacterium F16,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral clone CW040",209265;3379134|976|200643|171549|171550;1729795;1783272|1239|91061|186826|81852|423410;1932694;95818|163601,Complete,Svetlana up
bsdb:35532243/1/1,35532243,"cross-sectional observational, not case-control",35532243,https://doi.org/10.1128/spectrum.00616-22,NA,"Pisani A., Rausch P., Bang C., Ellul S., Tabone T., Marantidis Cordina C., Zahra G., Franke A. , Ellul P.",Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission,Microbiology spectrum,2022,"Enterobacteriaceae, dysbiosis, flavonoid-degrading bacteria, inflammatory bowel disease, microbiota, remission",Experiment 1,Malta,Homo sapiens,Feces,UBERON:0001988,Inflammatory bowel disease,EFO:0003767,Healthy controls (HC),Ulcerative colitis (UC),Patients with Ulcerative colitis (UC) in a state of remission,97,66,3 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,decreased,increased,NA,decreased,Signature 1,Appendix Table 5,24 March 2024,Samreen-19,"Samreen-19,WikiWorks",Analyses of differential abundances at lower taxonomic levels with respect to IBD status/health condition,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|909932|1843488|909930|904;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|186802|216572|459786,Complete,Svetlana up
bsdb:35532243/1/2,35532243,"cross-sectional observational, not case-control",35532243,https://doi.org/10.1128/spectrum.00616-22,NA,"Pisani A., Rausch P., Bang C., Ellul S., Tabone T., Marantidis Cordina C., Zahra G., Franke A. , Ellul P.",Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission,Microbiology spectrum,2022,"Enterobacteriaceae, dysbiosis, flavonoid-degrading bacteria, inflammatory bowel disease, microbiota, remission",Experiment 1,Malta,Homo sapiens,Feces,UBERON:0001988,Inflammatory bowel disease,EFO:0003767,Healthy controls (HC),Ulcerative colitis (UC),Patients with Ulcerative colitis (UC) in a state of remission,97,66,3 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,decreased,increased,NA,decreased,Signature 2,Appendix Table 5,24 March 2024,Samreen-19,"Samreen-19,WikiWorks",Analyses of differential abundances at lower taxonomic levels with respect to IBD status/health condition,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|33042;3379134|1224|28216|80840|75682|846;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|216572|216851;3379134|1224|1236|135625|712|724|729;3379134|1224|28216|80840|995019|40544,Complete,Svetlana up
bsdb:35532243/2/1,35532243,"cross-sectional observational, not case-control",35532243,https://doi.org/10.1128/spectrum.00616-22,NA,"Pisani A., Rausch P., Bang C., Ellul S., Tabone T., Marantidis Cordina C., Zahra G., Franke A. , Ellul P.",Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission,Microbiology spectrum,2022,"Enterobacteriaceae, dysbiosis, flavonoid-degrading bacteria, inflammatory bowel disease, microbiota, remission",Experiment 2,Malta,Homo sapiens,Feces,UBERON:0001988,Inflammatory bowel disease,EFO:0003767,Healthy controls (HC),Crohn’s disease (CD),Patients with Crohn’s disease (CD) in a state of remission,97,32,3 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,decreased,unchanged,NA,decreased,Signature 1,Appendix Table 5,24 March 2024,Samreen-19,"Samreen-19,WikiWorks",Analyses of differential abundances at lower taxonomic levels with respect to IBD status/health condition,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus",1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|292632;3379134|1224|1236|91347|543|561;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|815|816;1783272|1239|909932|1843488|909930|904,Complete,Svetlana up
bsdb:35532243/2/2,35532243,"cross-sectional observational, not case-control",35532243,https://doi.org/10.1128/spectrum.00616-22,NA,"Pisani A., Rausch P., Bang C., Ellul S., Tabone T., Marantidis Cordina C., Zahra G., Franke A. , Ellul P.",Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission,Microbiology spectrum,2022,"Enterobacteriaceae, dysbiosis, flavonoid-degrading bacteria, inflammatory bowel disease, microbiota, remission",Experiment 2,Malta,Homo sapiens,Feces,UBERON:0001988,Inflammatory bowel disease,EFO:0003767,Healthy controls (HC),Crohn’s disease (CD),Patients with Crohn’s disease (CD) in a state of remission,97,32,3 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,decreased,unchanged,NA,decreased,Signature 2,Appendix Table 5,24 March 2024,Samreen-19,"Samreen-19,WikiWorks",Analyses of differential abundances at lower taxonomic levels with respect to IBD status/health condition,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|33042;3379134|1224|28216|80840|75682|846;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|216572|216851;3379134|1224|1236|135625|712|724|729;3379134|1224|28216|80840|995019|40544,Complete,Svetlana up
bsdb:35532243/3/1,35532243,"cross-sectional observational, not case-control",35532243,https://doi.org/10.1128/spectrum.00616-22,NA,"Pisani A., Rausch P., Bang C., Ellul S., Tabone T., Marantidis Cordina C., Zahra G., Franke A. , Ellul P.",Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission,Microbiology spectrum,2022,"Enterobacteriaceae, dysbiosis, flavonoid-degrading bacteria, inflammatory bowel disease, microbiota, remission",Experiment 3,Malta,Homo sapiens,Feces,UBERON:0001988,Inflammatory bowel disease,EFO:0003767,Crohn's disease (CD),Ulcerative colitis (UC),Patients with Ulcerative colitis (UC) in a state of remission,32,66,3 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,decreased,increased,NA,decreased,Signature 1,Appendix Table 5,24 March 2024,Samreen-19,"Samreen-19,WikiWorks",Analyses of differential abundances at lower taxonomic levels with respect to IBD status/health condition,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella",3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|216572|216851;3379134|1224|28216|80840|995019|577310,Complete,Svetlana up
bsdb:35532243/3/2,35532243,"cross-sectional observational, not case-control",35532243,https://doi.org/10.1128/spectrum.00616-22,NA,"Pisani A., Rausch P., Bang C., Ellul S., Tabone T., Marantidis Cordina C., Zahra G., Franke A. , Ellul P.",Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission,Microbiology spectrum,2022,"Enterobacteriaceae, dysbiosis, flavonoid-degrading bacteria, inflammatory bowel disease, microbiota, remission",Experiment 3,Malta,Homo sapiens,Feces,UBERON:0001988,Inflammatory bowel disease,EFO:0003767,Crohn's disease (CD),Ulcerative colitis (UC),Patients with Ulcerative colitis (UC) in a state of remission,32,66,3 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,decreased,increased,NA,decreased,Signature 2,Appendix Table 5,24 March 2024,Samreen-19,"Samreen-19,WikiWorks",Analyses of differential abundances at lower taxonomic levels with respect to IBD status/health condition,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|292632;3379134|1224|1236|91347|543|561,Complete,Svetlana up
bsdb:35532243/4/1,35532243,"cross-sectional observational, not case-control",35532243,https://doi.org/10.1128/spectrum.00616-22,NA,"Pisani A., Rausch P., Bang C., Ellul S., Tabone T., Marantidis Cordina C., Zahra G., Franke A. , Ellul P.",Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission,Microbiology spectrum,2022,"Enterobacteriaceae, dysbiosis, flavonoid-degrading bacteria, inflammatory bowel disease, microbiota, remission",Experiment 4,Malta,Homo sapiens,Feces,UBERON:0001988,Smoking behavior,EFO:0004318,Non Smokers (No),Smokers (Yes),Patients with Inflammatory Bowel Disease (IBD) who are smokers,63,10,3 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,decreased,increased,NA,decreased,Signature 1,Appendix Table 9,24 March 2024,Samreen-19,"Samreen-19,WikiWorks",Differential abundance analysis for smoking behaviour,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",1783272|1239|186801|3085636|186803;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|216851;3379134|1224|28216|80840|995019|40544,Complete,Svetlana up
bsdb:35532243/4/2,35532243,"cross-sectional observational, not case-control",35532243,https://doi.org/10.1128/spectrum.00616-22,NA,"Pisani A., Rausch P., Bang C., Ellul S., Tabone T., Marantidis Cordina C., Zahra G., Franke A. , Ellul P.",Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission,Microbiology spectrum,2022,"Enterobacteriaceae, dysbiosis, flavonoid-degrading bacteria, inflammatory bowel disease, microbiota, remission",Experiment 4,Malta,Homo sapiens,Feces,UBERON:0001988,Smoking behavior,EFO:0004318,Non Smokers (No),Smokers (Yes),Patients with Inflammatory Bowel Disease (IBD) who are smokers,63,10,3 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,decreased,increased,NA,decreased,Signature 2,Appendix Table 9,24 March 2024,Samreen-19,"Samreen-19,WikiWorks",Differential abundance analysis for smoking behaviour,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter",3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|909656|357276;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815|816;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|995019|577310;3379134|1224|1236|91347|543|544,Complete,Svetlana up
bsdb:35532243/5/1,35532243,"cross-sectional observational, not case-control",35532243,https://doi.org/10.1128/spectrum.00616-22,NA,"Pisani A., Rausch P., Bang C., Ellul S., Tabone T., Marantidis Cordina C., Zahra G., Franke A. , Ellul P.",Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission,Microbiology spectrum,2022,"Enterobacteriaceae, dysbiosis, flavonoid-degrading bacteria, inflammatory bowel disease, microbiota, remission",Experiment 5,Malta,Homo sapiens,Feces,UBERON:0001988,Smoking behavior,EFO:0004318,Non Smokers (No),Ex-smokers (Ex),"Patients with Inflammatory Bowel Disease (IBD) who were ex-smokers (had
stopped smoking for at least 6 months).",63,15,3 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,decreased,increased,NA,decreased,Signature 1,Appendix Table 9,24 March 2024,Samreen-19,"Samreen-19,WikiWorks",Differential abundance analysis for smoking behaviour,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",3379134|976|200643|171549|815|909656|357276;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|815|816;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|186802|216572|216851,Complete,Svetlana up
bsdb:35532243/5/2,35532243,"cross-sectional observational, not case-control",35532243,https://doi.org/10.1128/spectrum.00616-22,NA,"Pisani A., Rausch P., Bang C., Ellul S., Tabone T., Marantidis Cordina C., Zahra G., Franke A. , Ellul P.",Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission,Microbiology spectrum,2022,"Enterobacteriaceae, dysbiosis, flavonoid-degrading bacteria, inflammatory bowel disease, microbiota, remission",Experiment 5,Malta,Homo sapiens,Feces,UBERON:0001988,Smoking behavior,EFO:0004318,Non Smokers (No),Ex-smokers (Ex),"Patients with Inflammatory Bowel Disease (IBD) who were ex-smokers (had
stopped smoking for at least 6 months).",63,15,3 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,decreased,increased,NA,decreased,Signature 2,Appendix Table 9,24 March 2024,Samreen-19,"Samreen-19,WikiWorks",Differential abundance analysis for smoking behaviour,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter",3379134|976|200643|171549|815|816|28116;1783272|1239|186801|3085636|186803|207244;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|995019|40544;3379134|1224|1236|91347|543|544,Complete,Svetlana up
bsdb:35532243/6/1,35532243,"cross-sectional observational, not case-control",35532243,https://doi.org/10.1128/spectrum.00616-22,NA,"Pisani A., Rausch P., Bang C., Ellul S., Tabone T., Marantidis Cordina C., Zahra G., Franke A. , Ellul P.",Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission,Microbiology spectrum,2022,"Enterobacteriaceae, dysbiosis, flavonoid-degrading bacteria, inflammatory bowel disease, microbiota, remission",Experiment 6,Malta,Homo sapiens,Feces,UBERON:0001988,Smoking behavior,EFO:0004318,Ex-smokers (Ex),Smokers (Yes),Patients with Inflammatory Bowel Disease (IBD) who are smokers,25,10,3 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,decreased,increased,NA,decreased,Signature 1,Appendix Table 9,25 March 2024,Samreen-19,"Samreen-19,WikiWorks",Differential abundance analysis for smoking behaviour,increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|815|816;3379134|1224|28216|80840|995019|40544,Complete,Svetlana up
bsdb:35532243/6/2,35532243,"cross-sectional observational, not case-control",35532243,https://doi.org/10.1128/spectrum.00616-22,NA,"Pisani A., Rausch P., Bang C., Ellul S., Tabone T., Marantidis Cordina C., Zahra G., Franke A. , Ellul P.",Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission,Microbiology spectrum,2022,"Enterobacteriaceae, dysbiosis, flavonoid-degrading bacteria, inflammatory bowel disease, microbiota, remission",Experiment 6,Malta,Homo sapiens,Feces,UBERON:0001988,Smoking behavior,EFO:0004318,Ex-smokers (Ex),Smokers (Yes),Patients with Inflammatory Bowel Disease (IBD) who are smokers,25,10,3 months,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,decreased,increased,NA,decreased,Signature 2,Appendix Table 9,25 March 2024,Samreen-19,"Samreen-19,WikiWorks",Differential abundance analysis for smoking behavior,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter",3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|909656|357276;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|995019|577310;3379134|1224|1236|91347|543|544,Complete,Svetlana up
bsdb:35533832/1/1,35533832,case-control,35533832,10.1016/j.ijid.2022.05.006,NA,"Lu S., Zhang W., Li X., Xian J., Hu Y. , Zhou Y.",Skin bacterial richness and diversity in intensive care unit patients with severe pneumonia,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2022,"16S rRNA sequencing, Intensive care unit, Microbiome diversity, Severe pneumonia, Skin bacteria",Experiment 1,China,Homo sapiens,Skin of cheek,UBERON:0008803,Pneumonia,EFO:0003106,Control group (CG),Patient group (PG),Patients with severe pneumonia admitted to the intensive care unit (ICU),30,30,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 4B,4 November 2025,Tosin,Tosin,The relative abundance of the six genera enriched in the patient group (PG) compared with that of the control group (CG),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Brevibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",3379134|1224|1236|2887326|468|469;1783272|1239|91061|1385|186822|55080;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|135619|28256|2745;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|135614|32033|40323,Complete,KateRasheed
bsdb:35533832/2/1,35533832,case-control,35533832,10.1016/j.ijid.2022.05.006,NA,"Lu S., Zhang W., Li X., Xian J., Hu Y. , Zhou Y.",Skin bacterial richness and diversity in intensive care unit patients with severe pneumonia,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2022,"16S rRNA sequencing, Intensive care unit, Microbiome diversity, Severe pneumonia, Skin bacteria",Experiment 2,China,Homo sapiens,Skin of cheek,UBERON:0008803,Pneumonia,EFO:0003106,Control group (CG),Patient group (PG),Patients with severe pneumonia admitted to the intensive care unit (ICU),30,30,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 4A,5 November 2025,Deborah-Fabusuyi,"Deborah-Fabusuyi,Tosin",Differentially abundant skin microbiota between the patient group (PG) and control group (CG) using Lefse (Linear discriminant analysis effect size),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Brevibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",3379134|1224|1236|2887326|468|469;1783272|1239|91061|1385|186822|55080;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|135619|28256|2745;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|135614|32033|40323,Complete,KateRasheed
bsdb:35533832/2/2,35533832,case-control,35533832,10.1016/j.ijid.2022.05.006,NA,"Lu S., Zhang W., Li X., Xian J., Hu Y. , Zhou Y.",Skin bacterial richness and diversity in intensive care unit patients with severe pneumonia,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2022,"16S rRNA sequencing, Intensive care unit, Microbiome diversity, Severe pneumonia, Skin bacteria",Experiment 2,China,Homo sapiens,Skin of cheek,UBERON:0008803,Pneumonia,EFO:0003106,Control group (CG),Patient group (PG),Patients with severe pneumonia admitted to the intensive care unit (ICU),30,30,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 4A,5 November 2025,Deborah-Fabusuyi,"Deborah-Fabusuyi,Tosin",Differentially abundant skin microbiota between the patient group (PG) and control group (CG) using Lefse (Linear discriminant analysis effect size),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Phenylobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|976|200643|171549|815|816;3379134|1224|28211|204458|76892|20;3379134|976|200643|171549|171552|838;1783272|201174|1760|85009|31957|1743;1783272|201174|1760|85007|85025|1827;1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:35547149/1/1,35547149,time series / longitudinal observational,35547149,10.3389/fmicb.2022.780568,NA,"Hanachi M., Maghrebi O., Bichiou H., Trabelsi F., Bouyahia N.M., Zhioua F., Belghith M., Harigua-Souiai E., Baouendi M., Guizani-Tabbane L., Benkahla A. , Souiai O.",Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode,Frontiers in microbiology,2022,"ESKAPE bacteria, Tunisia, elective cesarean deliveries, microbiome, newborns, shotgun metagenome sequencing",Experiment 1,Tunisia,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,Vaginally Delivered(VD),Elective Cesarean Section (ECS),Participants whose delivery mode (DM) was through elective cesarean section (ECS),5,5,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Supplementary Figure 2 c.,11 March 2024,Ayibatari,"Ayibatari,WikiWorks",Differentially abundant taxa between elective cesarean section (ECS) versus vaginally delivered (VD) newborns detected by linear discriminant analysis effect size (LEfSe) analysis.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter braakii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii complex sp. CFNIH9,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. E20,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 414,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 897",1783272|201174|1760|2037|2049|1654|544580;1783272|201174|1760|85004|31953|1678|1689;3379134|1224|1236|91347|543|544|57706;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|31979|1485|1502;3379134|1224|1236|135614|32033|40323|40324;3379134|1224|1236|91347|543|544|2077149;3379134|1224|1236|91347|543|547|1560339;1783272|201174|1760|2037|2049|1654|712122;1783272|201174|1760|2037|2049|1654|2081702,Complete,Folakunmi
bsdb:35547149/1/2,35547149,time series / longitudinal observational,35547149,10.3389/fmicb.2022.780568,NA,"Hanachi M., Maghrebi O., Bichiou H., Trabelsi F., Bouyahia N.M., Zhioua F., Belghith M., Harigua-Souiai E., Baouendi M., Guizani-Tabbane L., Benkahla A. , Souiai O.",Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode,Frontiers in microbiology,2022,"ESKAPE bacteria, Tunisia, elective cesarean deliveries, microbiome, newborns, shotgun metagenome sequencing",Experiment 1,Tunisia,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,Vaginally Delivered(VD),Elective Cesarean Section (ECS),Participants whose delivery mode (DM) was through elective cesarean section (ECS),5,5,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Supplementary Figure 2 c.,17 March 2024,Ayibatari,"Ayibatari,WikiWorks",Differentially abundant taxa between elective cesarean section (ECS) versus vaginally delivered (VD) newborns detected by linear discriminant analysis effect size (LEfSe) analysis.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides helcogenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Prevotella heparinolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister massiliensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis",3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549;3379134|976|200643|171549|815|816|290053;3379134|976|200643|171549|815|816|28113;3379134|976|200643|171549|815|816|28116;3379134|976|200643;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|39948|2161821;1783272|201174|1760|85004|31953|2701;1783272|201174|1760|85004|31953|2701|2702;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|823,Complete,Folakunmi
bsdb:35547149/2/1,35547149,time series / longitudinal observational,35547149,10.3389/fmicb.2022.780568,NA,"Hanachi M., Maghrebi O., Bichiou H., Trabelsi F., Bouyahia N.M., Zhioua F., Belghith M., Harigua-Souiai E., Baouendi M., Guizani-Tabbane L., Benkahla A. , Souiai O.",Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode,Frontiers in microbiology,2022,"ESKAPE bacteria, Tunisia, elective cesarean deliveries, microbiome, newborns, shotgun metagenome sequencing",Experiment 2,Tunisia,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,Vaginally Delivered(VD) at Day 0,Elective Cesarean Section (ECS) at Day 0,Participants whose delivery mode (DM) was through elective cesarean section (ECS),5,5,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4 A.,11 March 2024,Ayibatari,"Ayibatari,WikiWorks",Differentially abundant taxa between ECS and VD newborns at each collection data. Linear discriminant analysis effect size (LEfSe) analysis of metagenomic sequences from ECS and VD newborn stool samples at Day 0 (A). Relative abundance of ESKAPE members in ECS newborns at each collection time point.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543|544|546;1783272|1239|186801;1783272|1239|186801|186802,Complete,Folakunmi
bsdb:35547149/2/2,35547149,time series / longitudinal observational,35547149,10.3389/fmicb.2022.780568,NA,"Hanachi M., Maghrebi O., Bichiou H., Trabelsi F., Bouyahia N.M., Zhioua F., Belghith M., Harigua-Souiai E., Baouendi M., Guizani-Tabbane L., Benkahla A. , Souiai O.",Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode,Frontiers in microbiology,2022,"ESKAPE bacteria, Tunisia, elective cesarean deliveries, microbiome, newborns, shotgun metagenome sequencing",Experiment 2,Tunisia,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,Vaginally Delivered(VD) at Day 0,Elective Cesarean Section (ECS) at Day 0,Participants whose delivery mode (DM) was through elective cesarean section (ECS),5,5,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4 A.,17 March 2024,Ayibatari,"Ayibatari,WikiWorks",Differentially abundant taxa between ECS and VD newborns at each collection data. Linear discriminant analysis effect size (LEfSe) analysis of metagenomic sequences from ECS and VD newborn stool samples at Day 0 (A). Relative abundance of ESKAPE members in ECS newborns at each collection time point.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylorubrum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylorubrum|s__Methylorubrum populi",3379134|1224|28211|356|119045|2282523;3379134|1224|28211|356|119045|2282523|223967,Complete,Folakunmi
bsdb:35547149/3/1,35547149,time series / longitudinal observational,35547149,10.3389/fmicb.2022.780568,NA,"Hanachi M., Maghrebi O., Bichiou H., Trabelsi F., Bouyahia N.M., Zhioua F., Belghith M., Harigua-Souiai E., Baouendi M., Guizani-Tabbane L., Benkahla A. , Souiai O.",Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode,Frontiers in microbiology,2022,"ESKAPE bacteria, Tunisia, elective cesarean deliveries, microbiome, newborns, shotgun metagenome sequencing",Experiment 3,Tunisia,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,Vaginally Delivered(VD) at Day 15,Elective Cesarean Section (ECS) at Day 15,Participants whose delivery mode (DM) was through elective cesarean section (ECS),5,5,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4 B.,11 March 2024,Ayibatari,"Ayibatari,WikiWorks",Differentially abundant taxa between ECS and VD newborns at each collection data. Linear discriminant analysis effect size (LEfSe) analysis of metagenomic sequences from ECS and VD newborn stool samples at Day 15 (B). Relative abundance of ESKAPE members in ECS newborns at each collection time point.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 897,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium actinocoloniiforme",1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|201174|1760|85004|31953|1678|1689;1783272|201174|1760|2037|2049|1654|544580;1783272|201174|1760|2037|2049|1654|2081702;1783272|201174|1760|85004|31953|1678|638619,Complete,Folakunmi
bsdb:35547149/3/2,35547149,time series / longitudinal observational,35547149,10.3389/fmicb.2022.780568,NA,"Hanachi M., Maghrebi O., Bichiou H., Trabelsi F., Bouyahia N.M., Zhioua F., Belghith M., Harigua-Souiai E., Baouendi M., Guizani-Tabbane L., Benkahla A. , Souiai O.",Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode,Frontiers in microbiology,2022,"ESKAPE bacteria, Tunisia, elective cesarean deliveries, microbiome, newborns, shotgun metagenome sequencing",Experiment 3,Tunisia,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,Vaginally Delivered(VD) at Day 15,Elective Cesarean Section (ECS) at Day 15,Participants whose delivery mode (DM) was through elective cesarean section (ECS),5,5,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4 B.,17 March 2024,Ayibatari,"Ayibatari,WikiWorks",Differentially abundant taxa between ECS and VD newborns at each collection data. Linear discriminant analysis effect size (LEfSe) analysis of metagenomic sequences from ECS and VD newborn stool samples at Day 15 (B). Relative abundance of ESKAPE members in ECS newborns at each collection time point.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum|s__Bifidobacterium catenulatum subsp. kashiwanohense,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella dysenteriae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Prevotella heparinolytica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia marmotae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae",3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224;3379134|1224|1236;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|561|562;3379134|976|200643;3379134|976|200643|171549;3379134|1224|1236|91347|543|620;1783272|201174|1760|85004|31953|1678|28026;1783272|201174|1760|85004|31953|1678|1686|630129;3379134|1224|1236|91347|543|620|622;3379134|976|200643|171549|815|816|28113;3379134|1224|1236|91347|543|544|545;1783272|1239|909932|1843489|31977|906;3379134|1224|1236|91347|543|561|1499973;3379134|1224|1236|91347|1903410,Complete,Folakunmi
bsdb:35547149/4/1,35547149,time series / longitudinal observational,35547149,10.3389/fmicb.2022.780568,NA,"Hanachi M., Maghrebi O., Bichiou H., Trabelsi F., Bouyahia N.M., Zhioua F., Belghith M., Harigua-Souiai E., Baouendi M., Guizani-Tabbane L., Benkahla A. , Souiai O.",Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode,Frontiers in microbiology,2022,"ESKAPE bacteria, Tunisia, elective cesarean deliveries, microbiome, newborns, shotgun metagenome sequencing",Experiment 4,Tunisia,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,Vaginally Delivered(VD) at Day 30,Elective Cesarean Section (ECS) at Day 30,Participants whose delivery mode (DM) was through elective cesarean section (ECS),5,5,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4 C.,11 March 2024,Ayibatari,"Ayibatari,WikiWorks",Differentially abundant taxa between ECS and VD newborns at each collection data. Linear discriminant analysis effect size (LEfSe) analysis of metagenomic sequences from ECS and VD newborn stool samples at Day 30 (C). Relative abundance of ESKAPE members in ECS newborns at each collection time point.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae complex sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. Crenshaw,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp. M5al,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter braakii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter bugandensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Lelliottia|s__Lelliottia nimipressuralis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Candidatus Williamhamiltonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Candidatus Williamhamiltonella|s__Candidatus Williamhamiltonella defendens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum umeaense,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales",3379134|1224|1236|91347|543|547|550;3379134|1224|1236|91347|543|570|571;3379134|1224|1236|91347|543|547|2027919;3379134|1224|1236|91347|543|547|1977566;3379134|1224|1236|91347|543|570|1934254;3379134|1224|1236|91347|543|544|57706;3379134|1224|1236|91347|543|547|881260;3379134|1224|1236|91347|543|1330545|69220;3379134|1224|1236|91347|543|568987;3379134|1224|1236|91347|543|568987|138072;1783272|1239|186801|3085636|186803|1164882|617123;1783272|1239|186801|3085636|186803|1164882;1783272|1239|91061|1385,Complete,Folakunmi
bsdb:35547149/4/2,35547149,time series / longitudinal observational,35547149,10.3389/fmicb.2022.780568,NA,"Hanachi M., Maghrebi O., Bichiou H., Trabelsi F., Bouyahia N.M., Zhioua F., Belghith M., Harigua-Souiai E., Baouendi M., Guizani-Tabbane L., Benkahla A. , Souiai O.",Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode,Frontiers in microbiology,2022,"ESKAPE bacteria, Tunisia, elective cesarean deliveries, microbiome, newborns, shotgun metagenome sequencing",Experiment 4,Tunisia,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,Vaginally Delivered(VD) at Day 30,Elective Cesarean Section (ECS) at Day 30,Participants whose delivery mode (DM) was through elective cesarean section (ECS),5,5,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4 C.,17 March 2024,Ayibatari,"Ayibatari,WikiWorks",Differentially abundant taxa between ECS and VD newborns at each collection data. Linear discriminant analysis effect size (LEfSe) analysis of metagenomic sequences from ECS and VD newborn stool samples at Day 30 (C). Relative abundance of ESKAPE members in ECS newborns at each collection time point.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium diphtheriae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales,k__Thermotogati|p__Synergistota|c__Synergistia,k__Thermotogati|p__Synergistota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister massiliensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella",1783272|201174|1760|85004|31953|1678|28026;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|2005525;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|823;3379134|976|117743|200644;3379134|976|117743;3379134|976|117743|200644|49546;3379134|976|200643|171549|171551;1783272|201174|1760|85007|1653|1716|1717;3384194|508458|649775|649776|649777;3384194|508458|649775|649776;3384194|508458|649775;3384194|508458;1783272|1239|909932|1843489|31977|39948|2161821;1783272|201174|1760|85004|31953|2701|2702;1783272|201174|1760|85004|31953|2701,Complete,Folakunmi
bsdb:35547149/5/1,35547149,time series / longitudinal observational,35547149,10.3389/fmicb.2022.780568,NA,"Hanachi M., Maghrebi O., Bichiou H., Trabelsi F., Bouyahia N.M., Zhioua F., Belghith M., Harigua-Souiai E., Baouendi M., Guizani-Tabbane L., Benkahla A. , Souiai O.",Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode,Frontiers in microbiology,2022,"ESKAPE bacteria, Tunisia, elective cesarean deliveries, microbiome, newborns, shotgun metagenome sequencing",Experiment 5,Tunisia,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,NA,An experiment for group 1 (day 0) vs. group 0 (days 15 and 30),Tunisian newborns' at day 0 sampling time points.,5,5,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,decreased,NA,decreased,NA,increased,Signature 1,Supplementary Table_3.,17 March 2024,Ayibatari,"Ayibatari,WikiWorks",Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns at Day 0 with Day 15 and Day 30 .,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylorubrum",3379134|1224|28216|80840|80864;3379134|1224|1236|135614|32033;3379134|1224|1236|135614;3379134|1224|1236|135614|32033|40323;3379134|1224|1236|72274|135621;3379134|1224|1236|72274|135621|286;3379134|1224|28211|356|119045|2282523,Complete,Svetlana up
bsdb:35547149/6/1,35547149,time series / longitudinal observational,35547149,10.3389/fmicb.2022.780568,NA,"Hanachi M., Maghrebi O., Bichiou H., Trabelsi F., Bouyahia N.M., Zhioua F., Belghith M., Harigua-Souiai E., Baouendi M., Guizani-Tabbane L., Benkahla A. , Souiai O.",Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode,Frontiers in microbiology,2022,"ESKAPE bacteria, Tunisia, elective cesarean deliveries, microbiome, newborns, shotgun metagenome sequencing",Experiment 6,Tunisia,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,NA,An experiment for group 1 (day 15) vs. group 0 (days 0 and 30),Tunisian newborns' at day 15 sampling time points.,5,5,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,decreased,NA,decreased,NA,increased,Signature 1,Supplementary Table_3.,17 March 2024,Ayibatari,"Ayibatari,WikiWorks",Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns at Day 15 with Day 0 and Day 30 .,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum|s__Bifidobacterium catenulatum subsp. kashiwanohense,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium atypicum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus|s__Negativicoccus massiliensis,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella dysenteriae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella flexneri,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pasteurianus",1783272|1239|909932|1843488|909930|904;1783272|201174;1783272|1239|91061|1385;1783272|1239|91061;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|1681;1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|1678|1686;1783272|201174|1760|85004|31953|1678|1686|630129;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85007|1653|1716|191610;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|561|562;3379134|1224|1236;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|543|570|548;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|47770;1783272|1239|91061|186826|33958|2742598|1613;1783272|201174|1760|85007;1783272|1239|909932|1843489|31977|909928;1783272|1239|909932|1843489|31977|909928|1702287;3379134|1224;3379134|1224|1236|91347|543|590;3379134|1224|1236|91347|543|590|28901;3379134|1224|1236|91347|543|620;3379134|1224|1236|91347|543|620|622;3379134|1224|1236|91347|543|620|623;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|1385|90964|1279|1282;1783272|1239|91061|1385|90964|1279|1290;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|197614,Complete,NA
bsdb:35547149/6/2,35547149,time series / longitudinal observational,35547149,10.3389/fmicb.2022.780568,NA,"Hanachi M., Maghrebi O., Bichiou H., Trabelsi F., Bouyahia N.M., Zhioua F., Belghith M., Harigua-Souiai E., Baouendi M., Guizani-Tabbane L., Benkahla A. , Souiai O.",Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode,Frontiers in microbiology,2022,"ESKAPE bacteria, Tunisia, elective cesarean deliveries, microbiome, newborns, shotgun metagenome sequencing",Experiment 6,Tunisia,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,NA,An experiment for group 1 (day 15) vs. group 0 (days 0 and 30),Tunisian newborns' at day 15 sampling time points.,5,5,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,decreased,NA,decreased,NA,increased,Signature 2,Supplementary Table_3.,8 April 2024,Folakunmi,"Folakunmi,WikiWorks",Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns at Day 15 with Day 0 and Day 30 .,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus|s__Negativicoccus massiliensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella flexneri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pasteurianus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum|s__Bifidobacterium catenulatum subsp. kashiwanohense,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella dysenteriae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter bugandensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium atypicum",1783272|201174;1783272|201174|1760|85004;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236;1783272|201174|1760|85004|31953|1678|1685;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|561|562;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|1681;1783272|1239|91061;1783272|1239|91061|186826|81850;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;3379134|1224|1236|91347|543|590;3379134|1224|1236|91347|543|590|28901;1783272|1239|91061|1385;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|91347|543|570|548;1783272|1239|909932|1843489|31977|909928|1702287;1783272|1239|909932|1843489|31977|909928;1783272|1239|91061|1385|90964|1279|1282;3379134|1224|1236|91347|543|620;3379134|1224|1236|91347|543|620|623;1783272|1239|91061|186826|33958|2742598|1613;1783272|1239|91061|1385|90964|1279|1290;1783272|1239|91061|186826|1300|1301|197614;1783272|201174|1760|85004|31953|1678|1686|630129;3379134|1224|1236|91347|543|620|622;1783272|201174|1760|85004|31953|1678|1686;1783272|1239|909932|1843488|909930|904|187327;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85007;3379134|1224|1236|91347|543|547|881260;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|33958|1578|47770;1783272|201174|1760|85007|1653|1716|191610,Complete,Svetlana up
bsdb:35547149/7/1,35547149,time series / longitudinal observational,35547149,10.3389/fmicb.2022.780568,NA,"Hanachi M., Maghrebi O., Bichiou H., Trabelsi F., Bouyahia N.M., Zhioua F., Belghith M., Harigua-Souiai E., Baouendi M., Guizani-Tabbane L., Benkahla A. , Souiai O.",Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode,Frontiers in microbiology,2022,"ESKAPE bacteria, Tunisia, elective cesarean deliveries, microbiome, newborns, shotgun metagenome sequencing",Experiment 7,Tunisia,Homo sapiens,Feces,UBERON:0001988,Delivery method,EFO:0000395,NA,An experiment for group 1 (day 30) vs. group 0 (days 0 and 15),Tunisian newborns' at day 30 sampling time points.,5,5,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,decreased,NA,decreased,NA,increased,Signature 1,Supplementary Table_3.,17 March 2024,Ayibatari,"Ayibatari,WikiWorks",Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns at Day 30 with Day 0 and Day 15.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium avidum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter asburiae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae complex sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. Crenshaw,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium limosum,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella michiganensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella quasipneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella variicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella|s__Raoultella ornithinolytica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus equinus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. FDAARGOS_192,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rodentium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella|s__Raoultella planticola,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus rhamnosus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella quasivariicola",3379134|976|200643|171549|815|816|818;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|1322;3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543|544|546;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|31979|1485|1502;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;1783272|201174|1760|85009|31957|1912216|33010;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|547|61645;3379134|1224|1236|91347|543|547|550;3379134|1224|1236|91347|543|547|2027919;3379134|1224|1236|91347|543|547|158836;3379134|1224|1236|91347|543|547|1977566;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|186806|1730|1736;3379134|976|117743|200644|49546;3379134|976|117743|200644;3379134|976|117743;3379134|1224|1236|135625|712|724;3379134|1224|1236|91347|543|570|1134687;3379134|1224|1236|91347|543|570|571;3379134|1224|1236|91347|543|570|1463165;3379134|1224|1236|91347|543|570|244366;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803;1783272|1239|909932;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|1224|1236|91347|1903410;3379134|1224|1236|91347|543|160674;3379134|1224|1236|91347|543|160674|54291;3379134|1224|1236|91347|1903411|613;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1335;1783272|1239|91061|186826|1300|1301|1302;1783272|1239|91061|186826|1300|1301|102684;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|1300|1301|1839799;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|909932|1843489|31977|29465|248315;1783272|1239|909932|1843489|31977;1783272|1239|909932|1843489;3379134|1224|1236|91347|1903411;1783272|1239;1783272|1239|186801|186802;3379134|1224|1236|91347|543|160674|575;1783272|1239|91061|186826|33958|2759736|47715;3379134|1224|1236|91347|543|570|2026240,Complete,Svetlana up
bsdb:35558553/1/1,35558553,laboratory experiment,35558553,10.3389/fmolb.2022.786492,NA,"Hu K., Liao X.X., Wu X.Y., Wang R., Hu Z.W., Liu S.Y., He W.F. , Zhou J.J.",Effects of the Lipid Metabolites and the Gut Microbiota in ApoE<sup>-/-</sup> Mice on Atherosclerosis Co-Depression From the Microbiota-Gut-Brain Axis,Frontiers in molecular biosciences,2022,"ApoE−/−, atherosclerosis, depression, gut microbiota, lipid metabolites, microbiota-gut-brain axis",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,NC (Normal Control),HFB (Hyperlipid feeding combined with binding),ApoE−/− male mice fed a high-fat diet for 16 weeks with 1hour/day restraint (“binding”) to induce both atherosclerosis and depression‐like behavior,6,6,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 5D & F,29 April 2025,Amaanarif,"Amaanarif,Anne-mariesharp",Statistical plots showing differential taxa at phylum and genus levels between NC and HFB groups,increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Deferribacterota",3379134|200940|3031449|213115|194924|872;3379134|29547|3031852|213849|72293|209;1783272|1239|186801|186802|216572|1017280;3379134|1224;3379134|200930,Complete,KateRasheed
bsdb:35558553/1/3,35558553,laboratory experiment,35558553,10.3389/fmolb.2022.786492,NA,"Hu K., Liao X.X., Wu X.Y., Wang R., Hu Z.W., Liu S.Y., He W.F. , Zhou J.J.",Effects of the Lipid Metabolites and the Gut Microbiota in ApoE<sup>-/-</sup> Mice on Atherosclerosis Co-Depression From the Microbiota-Gut-Brain Axis,Frontiers in molecular biosciences,2022,"ApoE−/−, atherosclerosis, depression, gut microbiota, lipid metabolites, microbiota-gut-brain axis",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,NC (Normal Control),HFB (Hyperlipid feeding combined with binding),ApoE−/− male mice fed a high-fat diet for 16 weeks with 1hour/day restraint (“binding”) to induce both atherosclerosis and depression‐like behavior,6,6,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 3,Figures 5D & 5F,29 April 2025,Amaanarif,"Amaanarif,Anne-mariesharp",Statistical plots showing differential taxa at phylum and genus levels between NC and HFB groups,decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota",1783272|201174;3379134|74201|203494|48461|1647988|239934;3379134|74201,Complete,KateRasheed
bsdb:35558553/2/1,35558553,laboratory experiment,35558553,10.3389/fmolb.2022.786492,NA,"Hu K., Liao X.X., Wu X.Y., Wang R., Hu Z.W., Liu S.Y., He W.F. , Zhou J.J.",Effects of the Lipid Metabolites and the Gut Microbiota in ApoE<sup>-/-</sup> Mice on Atherosclerosis Co-Depression From the Microbiota-Gut-Brain Axis,Frontiers in molecular biosciences,2022,"ApoE−/−, atherosclerosis, depression, gut microbiota, lipid metabolites, microbiota-gut-brain axis",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,NC (Normal Control),HFB (Hyperlipid feeding combined with binding),ApoE−/− male mice fed a high-fat diet for 16 weeks with 1hour/day restraint (“binding”) to induce both atherosclerosis and depression‐like behavior,6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 5G, H",4 May 2025,Amaanarif,"Amaanarif,Anne-mariesharp",LEfSe analyses showing differential microbial taxa in NC and HFB groups,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales,k__Pseudomonadati|p__Deferribacterota,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres",1783272|1239|186801|3085636|186803|1427378;1783272|1239|91061|186826|186827;1783272|1239|91061|186826|186827|1375;1783272|1239|186801|186802|216572|244127;1783272|1239|91061|1385;3379134|29547|3031852|213849;3379134|200930|68337|191393|191394;3379134|200930|68337|191393;3379134|200930;28221;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;3379134|29547|3031852;3379134|29547|3031852|213849|72293|209;3379134|29547|3031852|213849|72293;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171552|577309;1783272|1239|186801|186802|216572|1017280;3379134|1224;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;3379134|200930|68337,Complete,KateRasheed
bsdb:35558553/2/2,35558553,laboratory experiment,35558553,10.3389/fmolb.2022.786492,NA,"Hu K., Liao X.X., Wu X.Y., Wang R., Hu Z.W., Liu S.Y., He W.F. , Zhou J.J.",Effects of the Lipid Metabolites and the Gut Microbiota in ApoE<sup>-/-</sup> Mice on Atherosclerosis Co-Depression From the Microbiota-Gut-Brain Axis,Frontiers in molecular biosciences,2022,"ApoE−/−, atherosclerosis, depression, gut microbiota, lipid metabolites, microbiota-gut-brain axis",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,NC (Normal Control),HFB (Hyperlipid feeding combined with binding),ApoE−/− male mice fed a high-fat diet for 16 weeks with 1hour/day restraint (“binding”) to induce both atherosclerosis and depression‐like behavior,6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 5G, H",4 May 2025,Amaanarif,"Amaanarif,Anne-mariesharp",LEfSe analyses showing differential microbial taxa in NC and HFB groups,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Parvibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota",3379134|74201|203494|48461|1647988|239934;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|204475;1783272|201174|84998|84999|84107|1427376;1783272|1239|186801|186802|216572|1263;3379134|74201|203494|48461|203557;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201,Complete,KateRasheed
bsdb:35573767/1/1,35573767,laboratory experiment,35573767,10.3389/fcimb.2022.894216,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.894216/full,"Jiang T., Lu W., Fang Z., Wang H., Zhu J., Zhang H. , Zhao J.",<i>Bifidobacterium</i> Treated by Electrostatic Spray Drying Relieved Constipation by Changing the Relative Abundance of Bacteria Associated With Gastrointestinal Regulatory Peptides,Frontiers in cellular and infection microbiology,2022,"Bifidobacterium, aquaporin, constipation, electrostatic spray drying, gastrointestinal regulatory peptide, intestinal microbiota, microencapsulation",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,BL03-1(B. animalis subsp. lactis)+BI63-2(B. longum subsp. infantis)+BAL005-3(B. animalis subsp. lactis)+BI63-3(B. longum subsp. infantis)+BLL-2-1(B. longum)+BLL2-2(B. longum)+BL03-3(B. animalis subsp. lactis)+BI20-3(B. longum subsp. infantis)+model group(positive control)+BI63-1(B. longum subsp. infantis)+BLL11-2(B. longum),Control group,Normal healthy mice without constipation induction or probiotic treatment.,66,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 9,5 November 2025,Chyono2,Chyono2,The LEfSe (linear discriminant effect size) analysis of gut microbiota in mice treated with different embedding methods.,increased,NA,NA,Complete,NA
bsdb:35573767/2/1,35573767,laboratory experiment,35573767,10.3389/fcimb.2022.894216,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.894216/full,"Jiang T., Lu W., Fang Z., Wang H., Zhu J., Zhang H. , Zhao J.",<i>Bifidobacterium</i> Treated by Electrostatic Spray Drying Relieved Constipation by Changing the Relative Abundance of Bacteria Associated With Gastrointestinal Regulatory Peptides,Frontiers in cellular and infection microbiology,2022,"Bifidobacterium, aquaporin, constipation, electrostatic spray drying, gastrointestinal regulatory peptide, intestinal microbiota, microencapsulation",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,control group+BI63-2(B. longum subsp. infantis)+BAL005-3(B. animalis subsp. lactis)+BI63-3(B. longum subsp. infantis)+BLL-2-1(B. longum)+BLL2-2(B. longum)+BL03-3(B. animalis subsp. lactis)+BI20-3(B. longum subsp. infantis)+model group(positive control)+BI63-1(B. longum subsp. infantis)+BLL11-2(B. longum),BL03-1(B. animalis subsp. lactis BL03 group)),BL03-1 (Bifidobacterium animalis subsp.lactis BL03 group) treated with the conventional spray drying method.,66,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 9,5 November 2025,Chyono2,Chyono2,The LEfSe (linear discriminant analysis effect size) analysis of gut microbiota in mice treated with different embedding methods.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella",1783272|1239|186801|3085636|186803|1432051;1783272|1239|526524|526525|128827|1729679;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|3082720|186804|1505652;1783272|1239|186801|186802|216572|1940255,Complete,NA
bsdb:35573767/3/1,35573767,laboratory experiment,35573767,10.3389/fcimb.2022.894216,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.894216/full,"Jiang T., Lu W., Fang Z., Wang H., Zhu J., Zhang H. , Zhao J.",<i>Bifidobacterium</i> Treated by Electrostatic Spray Drying Relieved Constipation by Changing the Relative Abundance of Bacteria Associated With Gastrointestinal Regulatory Peptides,Frontiers in cellular and infection microbiology,2022,"Bifidobacterium, aquaporin, constipation, electrostatic spray drying, gastrointestinal regulatory peptide, intestinal microbiota, microencapsulation",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,control group+BL03-1(B. animalis subsp. lactis)+BAL005-3(B. animalis subsp. lactis)+BI63-3(B. longum subsp. infantis)+BLL-2-1(B. longum)+BLL2-2(B. longum)+BL03-3(B. animalis subsp. lactis)+BI20-3(B. longum subsp. infantis)+model group(positive control)+BI63-1(B. longum subsp. infantis)+BLL11-2(B. longum),BI63-2(B. infantis BI63-2 group ),Bifidobacteria infantis BI63 group treated with the emulsification freeze-drying method,66,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 9,5 November 2025,Chyono2,Chyono2,The LEfSe (linear discriminant analysis effect size) analysis of gut microbiota in mice treated with different embedding methods.,increased,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,95818|2093818|2093825|2171986|1331051,Complete,NA
bsdb:35573767/4/1,35573767,laboratory experiment,35573767,10.3389/fcimb.2022.894216,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.894216/full,"Jiang T., Lu W., Fang Z., Wang H., Zhu J., Zhang H. , Zhao J.",<i>Bifidobacterium</i> Treated by Electrostatic Spray Drying Relieved Constipation by Changing the Relative Abundance of Bacteria Associated With Gastrointestinal Regulatory Peptides,Frontiers in cellular and infection microbiology,2022,"Bifidobacterium, aquaporin, constipation, electrostatic spray drying, gastrointestinal regulatory peptide, intestinal microbiota, microencapsulation",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,control group+BL03-1(B. animalis subsp. lactis)+BI63-2(B. longum subsp. infantis)+BI63-3(B. longum subsp. infantis)+BLL-2-1(B. longum)+BLL2-2(B. longum)+BL03-3(B. animalis subsp. lactis)+BI20-3(B. longum subsp. infantis)+model group(positive control)+BI63-1(B. longum subsp. infantis)+BLL11-2(B. longum),BAL005-3(B. animalis subsp. lactis),BAL005-3(Bifidobacterium animalis subsp. lactis BAL005) group treated with electrostatic spray drying method,66,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 9,5 November 2025,Chyono2,Chyono2,The LEfSe (linear discriminant analysis effect size) analysis of gut microbiota in mice treated with different embedding methods.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Gemmobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|526524|526525|128827|174708;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005519|397864;1783272|201174|84998|1643822|1643826|84111;3379134|1224|28211|204455|31989|204456;1783272|1239|909932|1843489|31977|29465,Complete,NA
bsdb:35573767/5/1,35573767,laboratory experiment,35573767,10.3389/fcimb.2022.894216,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.894216/full,"Jiang T., Lu W., Fang Z., Wang H., Zhu J., Zhang H. , Zhao J.",<i>Bifidobacterium</i> Treated by Electrostatic Spray Drying Relieved Constipation by Changing the Relative Abundance of Bacteria Associated With Gastrointestinal Regulatory Peptides,Frontiers in cellular and infection microbiology,2022,"Bifidobacterium, aquaporin, constipation, electrostatic spray drying, gastrointestinal regulatory peptide, intestinal microbiota, microencapsulation",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Control + Constipation model + BL03-1 (B. animalis subsp. lactis BL03 group) + BL03-3 (B. animalis subsp. lactis BL03 group) + BI63-1 (B. infantis BI63 group) + BI63-2 (B. infantis BI63 group) + BLL2-1 (B. longum BLL2 group) + BLL2-2 (B. longum BLL2 group) + BLL11-2 (B. longum BLL2 group) + BAL005-3 (Bifidobacteria-treated group) + BI20-3 (B. infantis BI20 group),BI63-3 (B. infantis BI63 group),Bifidobacterium longum subsp. infantis BI63 group treated with the conventional spray drying method,66,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 9,6 November 2025,Tosin,Tosin,The LEfSe (Linear discriminant analysis effect size) analysis of gut microbiota in mice treated with different embedding methods,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,1783272|1239|186801|186802|216572|459786,Complete,NA
bsdb:35573767/6/1,35573767,laboratory experiment,35573767,10.3389/fcimb.2022.894216,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.894216/full,"Jiang T., Lu W., Fang Z., Wang H., Zhu J., Zhang H. , Zhao J.",<i>Bifidobacterium</i> Treated by Electrostatic Spray Drying Relieved Constipation by Changing the Relative Abundance of Bacteria Associated With Gastrointestinal Regulatory Peptides,Frontiers in cellular and infection microbiology,2022,"Bifidobacterium, aquaporin, constipation, electrostatic spray drying, gastrointestinal regulatory peptide, intestinal microbiota, microencapsulation",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Control + Constipation model + BL03-1 (B. animalis subsp. lactis BL03 group) + BL03-3 (B. animalis subsp. lactis BL03 group) + BI63-1 (B. infantis BI63 group) + BI63-2 (B. infantis BI63 group) + BI63-3 (B. infantis BI63 group) + BLL2-2 (B. longum BLL2 group) + BLL11-2 (B. longum BLL2 group) + BAL005-3 (Bifidobacteria-treated group) + BI20-3 (B. infantis BI20 group),BLL2-1 (B. longum BLL2 group),BLL2-1 (Bifidobacterium longum BLL2) group treated with the conventional spray drying method,66,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 9,6 November 2025,Tosin,Tosin,The LEfSe (Linear discriminant analysis effect size) analysis of gut microbiota in mice treated with different embedding methods,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,NA
bsdb:35573767/7/1,35573767,laboratory experiment,35573767,10.3389/fcimb.2022.894216,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.894216/full,"Jiang T., Lu W., Fang Z., Wang H., Zhu J., Zhang H. , Zhao J.",<i>Bifidobacterium</i> Treated by Electrostatic Spray Drying Relieved Constipation by Changing the Relative Abundance of Bacteria Associated With Gastrointestinal Regulatory Peptides,Frontiers in cellular and infection microbiology,2022,"Bifidobacterium, aquaporin, constipation, electrostatic spray drying, gastrointestinal regulatory peptide, intestinal microbiota, microencapsulation",Experiment 7,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Control + Constipation model + BL03-1 (B. animalis subsp. lactis BL03 group) + BL03-3 (B. animalis subsp. lactis BL03 group) + BI63-1 (B. infantis BI63 group) + BI63-2 (B. infantis BI63 group) + BI63-3 (B. infantis BI63 group) + BLL2-1 (B. longum BLL2 group)  + BLL11-2 (B. longum BLL2 group) + BAL005-3 (Bifidobacteria-treated group) + BI20-3 (B. infantis BI20 group),BLL2-2 (B. longum BLL2 group),BLL2-2 (Bifidobacterium longum BLL2) group treated with the emulsification freeze drying method,66,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 9,6 November 2025,Tosin,Tosin,The LEfSe (Linear discriminant analysis effect size) analysis of gut microbiota in mice treated with different embedding methods,increased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,1783272|201174|84998|1643822|1643826|447020,Complete,NA
bsdb:35573767/9/1,35573767,laboratory experiment,35573767,10.3389/fcimb.2022.894216,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.894216/full,"Jiang T., Lu W., Fang Z., Wang H., Zhu J., Zhang H. , Zhao J.",<i>Bifidobacterium</i> Treated by Electrostatic Spray Drying Relieved Constipation by Changing the Relative Abundance of Bacteria Associated With Gastrointestinal Regulatory Peptides,Frontiers in cellular and infection microbiology,2022,"Bifidobacterium, aquaporin, constipation, electrostatic spray drying, gastrointestinal regulatory peptide, intestinal microbiota, microencapsulation",Experiment 9,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Control + Constipation model + BL03-1 (B. animalis subsp. lactis BL03 group) + BL03-3 (B. animalis subsp. lactis BL03 group) + BI63-1 (B. infantis BI63 group) + BI63-2 (B. infantis BI63 group) + BI63-3 (B. infantis BI63 group) + BLL2-1 (B. longum BLL2 group) + BLL2-2 (B. longum BLL2 group) + BLL11-2 (B. longum BLL2 group) + BAL005-3 (Bifidobacteria-treated group),BI20-3 (B. infantis BI20 group),Bifidobacteria infantis BI20 group treated with an electrostatic spray drying method,66,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 9,6 November 2025,Fiddyhamma,Fiddyhamma,The LEfSe analysis of gut microbiota in mice treated with different embedding methods.,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",3384189|32066|203490|203491|203492|848;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843488|909930|33024,Complete,NA
bsdb:35573767/10/1,35573767,laboratory experiment,35573767,10.3389/fcimb.2022.894216,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.894216/full,"Jiang T., Lu W., Fang Z., Wang H., Zhu J., Zhang H. , Zhao J.",<i>Bifidobacterium</i> Treated by Electrostatic Spray Drying Relieved Constipation by Changing the Relative Abundance of Bacteria Associated With Gastrointestinal Regulatory Peptides,Frontiers in cellular and infection microbiology,2022,"Bifidobacterium, aquaporin, constipation, electrostatic spray drying, gastrointestinal regulatory peptide, intestinal microbiota, microencapsulation",Experiment 10,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Control + BL03-1 (B. animalis subsp. lactis BL03 group) + BL03-3 (B. animalis subsp. lactis BL03 group) + BI20-3 (B. infantis BI20 group) + BI63-1 (B. infantis BI63 group) + BI63-2 (B. infantis BI63 group) + BI63-3 (B. infantis BI63 group) + BLL2-1 (B. longum BLL2 group) + BLL2-2 (B. longum BLL2 group) + BLL11-2 (B. longum BLL2 group) + BAL005-3 (Bifidobacteria-treated group),Constipation model,These are constipated mice,66,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 9,6 November 2025,Fiddyhamma,Fiddyhamma,The LEfSe analysis of gut microbiota in mice treated with different embedding methods.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus",1783272|1239|91061|186826|1300|1301;3379134|1224|28211|356|69277|68287;1783272|1239|186801|186802|31979|49082,Complete,NA
bsdb:35573767/11/1,35573767,laboratory experiment,35573767,10.3389/fcimb.2022.894216,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.894216/full,"Jiang T., Lu W., Fang Z., Wang H., Zhu J., Zhang H. , Zhao J.",<i>Bifidobacterium</i> Treated by Electrostatic Spray Drying Relieved Constipation by Changing the Relative Abundance of Bacteria Associated With Gastrointestinal Regulatory Peptides,Frontiers in cellular and infection microbiology,2022,"Bifidobacterium, aquaporin, constipation, electrostatic spray drying, gastrointestinal regulatory peptide, intestinal microbiota, microencapsulation",Experiment 11,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Control + Constipation model + BL03-1 (B. animalis subsp. lactis BL03 group) + BL03-3 (B. animalis subsp. lactis BL03 group) + BI20-3 (B. infantis BI20 group) + BI63-2 (B. infantis BI63 group) + BI63-3 (B. infantis BI63 group) + BLL2-1 (B. longum BLL2 group) + BLL2-2 (B. longum BLL2 group) + BLL11-2 (B. longum BLL2 group) + BAL005-3 (Bifidobacteria-treated group),BI63-1 (B. infantis BI63 group),Bifidobacteria infantis BI63 group treated with a conventional spray drying method,66,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 9,6 November 2025,Fiddyhamma,Fiddyhamma,The LEfSe analysis of gut microbiota in mice treated with different embedding methods.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Perlucidibacaceae|g__Perlucidibaca,3379134|1224|1236|72274|2887331|661182,Complete,NA
bsdb:35573767/12/1,35573767,laboratory experiment,35573767,10.3389/fcimb.2022.894216,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.894216/full,"Jiang T., Lu W., Fang Z., Wang H., Zhu J., Zhang H. , Zhao J.",<i>Bifidobacterium</i> Treated by Electrostatic Spray Drying Relieved Constipation by Changing the Relative Abundance of Bacteria Associated With Gastrointestinal Regulatory Peptides,Frontiers in cellular and infection microbiology,2022,"Bifidobacterium, aquaporin, constipation, electrostatic spray drying, gastrointestinal regulatory peptide, intestinal microbiota, microencapsulation",Experiment 12,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Control + Constipation model + BL03-1 (B. animalis subsp. lactis BL03 group) + BL03-3 (B. animalis subsp. lactis BL03 group) + BI20-3 (B. infantis BI20 group) + BI63-1 (B. infantis BI63 group) + BI63-2 (B. infantis BI63 group) + BI63-3 (B. infantis BI63 group) + BLL2-1 (B. longum BLL2 group) + BLL2-2 (B. longum BLL2 group) + BAL005-3 (Bifidobacteria-treated group),BLL11-2 (B. longum BLL2 group),Bifidobacterium longum BLL2 group treated with an emulsification freeze-drying method,66,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 9,6 November 2025,Fiddyhamma,Fiddyhamma,The LEfSe analysis of gut microbiota in mice treated with different embedding methods.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Paenarthrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Nitratireductor,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|2005525|375288;1783272|201174|1760|85006|1268|1742992;3379134|1224|28216|80840|506|222;1783272|1239|186801|3085636|186803|1766253;3379134|1224|28211|356|69277|245876;3379134|1224|28211|356|118882|528;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|2005473|1918540;3379134|29547|3031852|213849|72293|209;3379134|976|200643|171549|171550|28138,Complete,NA
bsdb:35573767/13/1,35573767,laboratory experiment,35573767,10.3389/fcimb.2022.894216,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.894216/full,"Jiang T., Lu W., Fang Z., Wang H., Zhu J., Zhang H. , Zhao J.",<i>Bifidobacterium</i> Treated by Electrostatic Spray Drying Relieved Constipation by Changing the Relative Abundance of Bacteria Associated With Gastrointestinal Regulatory Peptides,Frontiers in cellular and infection microbiology,2022,"Bifidobacterium, aquaporin, constipation, electrostatic spray drying, gastrointestinal regulatory peptide, intestinal microbiota, microencapsulation",Experiment 13,China,Mus musculus,Feces,UBERON:0001988,Positive regulation of defecation,GO:2000294,Decreased fecal water content,Increased fecal water content,Increased levels of fecal water content,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 10,7 November 2025,Tosin,Tosin,Spearman’s correlation analysis between changed bacterial genera and constipation-related indicators,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",3379134|976|200643|171549|2005473|1918540;1783272|1239|186801|3085636|186803|572511,Complete,NA
bsdb:35573767/14/1,35573767,laboratory experiment,35573767,10.3389/fcimb.2022.894216,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.894216/full,"Jiang T., Lu W., Fang Z., Wang H., Zhu J., Zhang H. , Zhao J.",<i>Bifidobacterium</i> Treated by Electrostatic Spray Drying Relieved Constipation by Changing the Relative Abundance of Bacteria Associated With Gastrointestinal Regulatory Peptides,Frontiers in cellular and infection microbiology,2022,"Bifidobacterium, aquaporin, constipation, electrostatic spray drying, gastrointestinal regulatory peptide, intestinal microbiota, microencapsulation",Experiment 14,China,Mus musculus,Feces,UBERON:0001988,Peptide measurement,EFO:0010520,Decreased substance P (SP),Increased substance P (SP),Increased levels of substance P (SP),NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 10,7 November 2025,Tosin,Tosin,Spearman’s correlation analysis between changed bacterial genera and constipation-related indicators,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",3379134|976|200643|171549|2005473|1918540;1783272|1239|186801|3085636|186803|572511,Complete,NA
bsdb:35573767/15/1,35573767,laboratory experiment,35573767,10.3389/fcimb.2022.894216,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.894216/full,"Jiang T., Lu W., Fang Z., Wang H., Zhu J., Zhang H. , Zhao J.",<i>Bifidobacterium</i> Treated by Electrostatic Spray Drying Relieved Constipation by Changing the Relative Abundance of Bacteria Associated With Gastrointestinal Regulatory Peptides,Frontiers in cellular and infection microbiology,2022,"Bifidobacterium, aquaporin, constipation, electrostatic spray drying, gastrointestinal regulatory peptide, intestinal microbiota, microencapsulation",Experiment 15,China,Mus musculus,Feces,UBERON:0001988,Fatty acid measurement,EFO:0005110,Decreased butyric acid,Increased butyric acid,Increased levels of butyric acid,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 10,7 November 2025,Tosin,Tosin,Spearman’s correlation analysis between changed bacterial genera and constipation-related indicators,increased,NA,NA,Complete,NA
bsdb:35573767/15/2,35573767,laboratory experiment,35573767,10.3389/fcimb.2022.894216,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.894216/full,"Jiang T., Lu W., Fang Z., Wang H., Zhu J., Zhang H. , Zhao J.",<i>Bifidobacterium</i> Treated by Electrostatic Spray Drying Relieved Constipation by Changing the Relative Abundance of Bacteria Associated With Gastrointestinal Regulatory Peptides,Frontiers in cellular and infection microbiology,2022,"Bifidobacterium, aquaporin, constipation, electrostatic spray drying, gastrointestinal regulatory peptide, intestinal microbiota, microencapsulation",Experiment 15,China,Mus musculus,Feces,UBERON:0001988,Fatty acid measurement,EFO:0005110,Decreased butyric acid,Increased butyric acid,Increased levels of butyric acid,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 10,7 November 2025,Tosin,Tosin,Spearman’s correlation analysis between changed bacterial genera and constipation-related indicators,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,NA
bsdb:35573767/16/1,35573767,laboratory experiment,35573767,10.3389/fcimb.2022.894216,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.894216/full,"Jiang T., Lu W., Fang Z., Wang H., Zhu J., Zhang H. , Zhao J.",<i>Bifidobacterium</i> Treated by Electrostatic Spray Drying Relieved Constipation by Changing the Relative Abundance of Bacteria Associated With Gastrointestinal Regulatory Peptides,Frontiers in cellular and infection microbiology,2022,"Bifidobacterium, aquaporin, constipation, electrostatic spray drying, gastrointestinal regulatory peptide, intestinal microbiota, microencapsulation",Experiment 16,China,Mus musculus,Feces,UBERON:0001988,Gastrin secretion abnormality,MONDO:0001770,Decreased Gastrin level (GAS),Increased Gastrin level (GAS),Increased levels of Gastrin,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 10,7 November 2025,Tosin,Tosin,Spearman’s correlation analysis between changed bacterial genera and constipation-related indicators,increased,NA,NA,Complete,NA
bsdb:35573767/17/1,35573767,laboratory experiment,35573767,10.3389/fcimb.2022.894216,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.894216/full,"Jiang T., Lu W., Fang Z., Wang H., Zhu J., Zhang H. , Zhao J.",<i>Bifidobacterium</i> Treated by Electrostatic Spray Drying Relieved Constipation by Changing the Relative Abundance of Bacteria Associated With Gastrointestinal Regulatory Peptides,Frontiers in cellular and infection microbiology,2022,"Bifidobacterium, aquaporin, constipation, electrostatic spray drying, gastrointestinal regulatory peptide, intestinal microbiota, microencapsulation",Experiment 17,China,Mus musculus,Feces,UBERON:0001988,Acetic acid,CHEBI:15366,Decreased Acetic acid,Increased Acetic acid,Increased levels of acetic acid,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 10,7 November 2025,Tosin,Tosin,Spearman’s correlation analysis between changed bacterial genera and constipation-related indicators,increased,NA,NA,Complete,NA
bsdb:35573767/17/2,35573767,laboratory experiment,35573767,10.3389/fcimb.2022.894216,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.894216/full,"Jiang T., Lu W., Fang Z., Wang H., Zhu J., Zhang H. , Zhao J.",<i>Bifidobacterium</i> Treated by Electrostatic Spray Drying Relieved Constipation by Changing the Relative Abundance of Bacteria Associated With Gastrointestinal Regulatory Peptides,Frontiers in cellular and infection microbiology,2022,"Bifidobacterium, aquaporin, constipation, electrostatic spray drying, gastrointestinal regulatory peptide, intestinal microbiota, microencapsulation",Experiment 17,China,Mus musculus,Feces,UBERON:0001988,Acetic acid,CHEBI:15366,Decreased Acetic acid,Increased Acetic acid,Increased levels of acetic acid,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 10,7 November 2025,Tosin,Tosin,Spearman’s correlation analysis between changed bacterial genera and constipation-related indicators,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia",1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|248744,Complete,NA
bsdb:35573767/18/1,35573767,laboratory experiment,35573767,10.3389/fcimb.2022.894216,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.894216/full,"Jiang T., Lu W., Fang Z., Wang H., Zhu J., Zhang H. , Zhao J.",<i>Bifidobacterium</i> Treated by Electrostatic Spray Drying Relieved Constipation by Changing the Relative Abundance of Bacteria Associated With Gastrointestinal Regulatory Peptides,Frontiers in cellular and infection microbiology,2022,"Bifidobacterium, aquaporin, constipation, electrostatic spray drying, gastrointestinal regulatory peptide, intestinal microbiota, microencapsulation",Experiment 18,China,Mus musculus,Feces,UBERON:0001988,Peptide measurement,EFO:0010520,Decreased motilin (MTL),Increased motilin (MTL),Increased levels of motilin (MTL),NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 10,7 November 2025,Tosin,Tosin,Spearman’s correlation analysis between changed bacterial genera and constipation-related indicators,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia",1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|248744,Complete,NA
bsdb:35573767/19/1,35573767,laboratory experiment,35573767,10.3389/fcimb.2022.894216,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.894216/full,"Jiang T., Lu W., Fang Z., Wang H., Zhu J., Zhang H. , Zhao J.",<i>Bifidobacterium</i> Treated by Electrostatic Spray Drying Relieved Constipation by Changing the Relative Abundance of Bacteria Associated With Gastrointestinal Regulatory Peptides,Frontiers in cellular and infection microbiology,2022,"Bifidobacterium, aquaporin, constipation, electrostatic spray drying, gastrointestinal regulatory peptide, intestinal microbiota, microencapsulation",Experiment 19,China,Mus musculus,Feces,UBERON:0001988,Cellular protein metabolic process,GO:0019538,Decreased aquaporin 3 (APQ3),Increased aquaporin 3 (APQ3),Increased levels of aquaporin 3 (APQ3),NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 10,8 November 2025,Tosin,Tosin,Spearman's correlation analysis between changed bacterial genera and constipation- related indicators,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",3379134|976|200643|171549|171550|239759;1783272|544448|31969|186332|186333|2086;3379134|976|200643|171549|2005473|1918540;1783272|1239|186801|3085636|186803|572511,Complete,NA
bsdb:35573767/19/2,35573767,laboratory experiment,35573767,10.3389/fcimb.2022.894216,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.894216/full,"Jiang T., Lu W., Fang Z., Wang H., Zhu J., Zhang H. , Zhao J.",<i>Bifidobacterium</i> Treated by Electrostatic Spray Drying Relieved Constipation by Changing the Relative Abundance of Bacteria Associated With Gastrointestinal Regulatory Peptides,Frontiers in cellular and infection microbiology,2022,"Bifidobacterium, aquaporin, constipation, electrostatic spray drying, gastrointestinal regulatory peptide, intestinal microbiota, microencapsulation",Experiment 19,China,Mus musculus,Feces,UBERON:0001988,Cellular protein metabolic process,GO:0019538,Decreased aquaporin 3 (APQ3),Increased aquaporin 3 (APQ3),Increased levels of aquaporin 3 (APQ3),NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 10,8 November 2025,Tosin,Tosin,Spearman's correlation analysis between changed bacterial genera and constipation- related indicators,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,NA
bsdb:35573767/20/1,35573767,laboratory experiment,35573767,10.3389/fcimb.2022.894216,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.894216/full,"Jiang T., Lu W., Fang Z., Wang H., Zhu J., Zhang H. , Zhao J.",<i>Bifidobacterium</i> Treated by Electrostatic Spray Drying Relieved Constipation by Changing the Relative Abundance of Bacteria Associated With Gastrointestinal Regulatory Peptides,Frontiers in cellular and infection microbiology,2022,"Bifidobacterium, aquaporin, constipation, electrostatic spray drying, gastrointestinal regulatory peptide, intestinal microbiota, microencapsulation",Experiment 20,China,Mus musculus,Feces,UBERON:0001988,Increased intestinal transit time,HP:0410204,Decreased small intestine propulsion rate,Increased small intestine propulsion rate,Increased levels of small intestine propulsion rate,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,fig 10,7 November 2025,Chyono2,Chyono2,Spearman's correlation analysis between changed bacterial genera and constipation- related indicators.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",3379134|976|200643|171549|171550|239759;1783272|544448|31969|186332|186333|2086;1783272|1239|186801|3085636|186803|572511,Complete,NA
bsdb:35573767/20/2,35573767,laboratory experiment,35573767,10.3389/fcimb.2022.894216,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.894216/full,"Jiang T., Lu W., Fang Z., Wang H., Zhu J., Zhang H. , Zhao J.",<i>Bifidobacterium</i> Treated by Electrostatic Spray Drying Relieved Constipation by Changing the Relative Abundance of Bacteria Associated With Gastrointestinal Regulatory Peptides,Frontiers in cellular and infection microbiology,2022,"Bifidobacterium, aquaporin, constipation, electrostatic spray drying, gastrointestinal regulatory peptide, intestinal microbiota, microencapsulation",Experiment 20,China,Mus musculus,Feces,UBERON:0001988,Increased intestinal transit time,HP:0410204,Decreased small intestine propulsion rate,Increased small intestine propulsion rate,Increased levels of small intestine propulsion rate,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,fig 10,7 November 2025,Chyono2,Chyono2,Spearman's correlation analysis between changed bacterial genera and constipation-related indicators.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,NA
bsdb:35573767/21/1,35573767,laboratory experiment,35573767,10.3389/fcimb.2022.894216,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.894216/full,"Jiang T., Lu W., Fang Z., Wang H., Zhu J., Zhang H. , Zhao J.",<i>Bifidobacterium</i> Treated by Electrostatic Spray Drying Relieved Constipation by Changing the Relative Abundance of Bacteria Associated With Gastrointestinal Regulatory Peptides,Frontiers in cellular and infection microbiology,2022,"Bifidobacterium, aquaporin, constipation, electrostatic spray drying, gastrointestinal regulatory peptide, intestinal microbiota, microencapsulation",Experiment 21,China,Mus musculus,Feces,UBERON:0001988,Interleukin-1 beta measurement,EFO:0004812,Decreased (IL-1B) Interleukin-1 beta,Increased (IL-1B) Interleukin- 1 beta,Increased levels of (IL-1B) Interleukin-1 beta,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,fig 10,7 November 2025,Chyono2,Chyono2,Spearman's correlation analysis between changed bacterial genera and constipation-related indicators,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,3379134|976|200643|171549|171550|239759,Complete,NA
bsdb:35573767/22/1,35573767,laboratory experiment,35573767,10.3389/fcimb.2022.894216,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.894216/full,"Jiang T., Lu W., Fang Z., Wang H., Zhu J., Zhang H. , Zhao J.",<i>Bifidobacterium</i> Treated by Electrostatic Spray Drying Relieved Constipation by Changing the Relative Abundance of Bacteria Associated With Gastrointestinal Regulatory Peptides,Frontiers in cellular and infection microbiology,2022,"Bifidobacterium, aquaporin, constipation, electrostatic spray drying, gastrointestinal regulatory peptide, intestinal microbiota, microencapsulation",Experiment 22,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Decreased time of first black stool,Increased time of first black stool,Increased levels of time of first black stool,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,fig 10,7 November 2025,Chyono2,Chyono2,Spearman's correlation analysis between changed bacterial genera and constipation-related indicators,decreased,NA,NA,Complete,NA
bsdb:35573767/23/1,35573767,laboratory experiment,35573767,10.3389/fcimb.2022.894216,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.894216/full,"Jiang T., Lu W., Fang Z., Wang H., Zhu J., Zhang H. , Zhao J.",<i>Bifidobacterium</i> Treated by Electrostatic Spray Drying Relieved Constipation by Changing the Relative Abundance of Bacteria Associated With Gastrointestinal Regulatory Peptides,Frontiers in cellular and infection microbiology,2022,"Bifidobacterium, aquaporin, constipation, electrostatic spray drying, gastrointestinal regulatory peptide, intestinal microbiota, microencapsulation",Experiment 23,China,Mus musculus,Feces,UBERON:0001988,Peptide measurement,EFO:0010520,Decreased Vasoactive Intestinal peptide (VIP),Increased Vasoactive Intestinal peptide (VIP),Increased levels of vasoactive Intestinal peptide,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,fig 10,7 November 2025,Chyono2,Chyono2,Spearman's correlation analysis between changed bacterial genera and constipation-related indicators,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,1783272|1239|186801|3085636|186803|248744,Complete,NA
bsdb:35573767/24/1,35573767,laboratory experiment,35573767,10.3389/fcimb.2022.894216,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.894216/full,"Jiang T., Lu W., Fang Z., Wang H., Zhu J., Zhang H. , Zhao J.",<i>Bifidobacterium</i> Treated by Electrostatic Spray Drying Relieved Constipation by Changing the Relative Abundance of Bacteria Associated With Gastrointestinal Regulatory Peptides,Frontiers in cellular and infection microbiology,2022,"Bifidobacterium, aquaporin, constipation, electrostatic spray drying, gastrointestinal regulatory peptide, intestinal microbiota, microencapsulation",Experiment 24,China,Mus musculus,Feces,UBERON:0001988,Peptide measurement,EFO:0010520,Decreased Somatostatin (SS),Increased Somatostatin (SS),Increased levels of Somatostatin,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,fig 10,7 November 2025,Chyono2,Chyono2,Spearman's correlation analysis between changed bacterial genera and constipation-related indicators.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1301,Complete,NA
bsdb:35573767/24/2,35573767,laboratory experiment,35573767,10.3389/fcimb.2022.894216,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.894216/full,"Jiang T., Lu W., Fang Z., Wang H., Zhu J., Zhang H. , Zhao J.",<i>Bifidobacterium</i> Treated by Electrostatic Spray Drying Relieved Constipation by Changing the Relative Abundance of Bacteria Associated With Gastrointestinal Regulatory Peptides,Frontiers in cellular and infection microbiology,2022,"Bifidobacterium, aquaporin, constipation, electrostatic spray drying, gastrointestinal regulatory peptide, intestinal microbiota, microencapsulation",Experiment 24,China,Mus musculus,Feces,UBERON:0001988,Peptide measurement,EFO:0010520,Decreased Somatostatin (SS),Increased Somatostatin (SS),Increased levels of Somatostatin,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,fig 10,7 November 2025,Chyono2,Chyono2,Spearman's correlation analysis between changed bacterial genera and constipation-related indicators,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum",3379134|976|200643|171549|171550|239759;1783272|544448|31969|186332|186333|2086;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|2005473|1918540,Complete,NA
bsdb:35573767/25/1,35573767,laboratory experiment,35573767,10.3389/fcimb.2022.894216,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.894216/full,"Jiang T., Lu W., Fang Z., Wang H., Zhu J., Zhang H. , Zhao J.",<i>Bifidobacterium</i> Treated by Electrostatic Spray Drying Relieved Constipation by Changing the Relative Abundance of Bacteria Associated With Gastrointestinal Regulatory Peptides,Frontiers in cellular and infection microbiology,2022,"Bifidobacterium, aquaporin, constipation, electrostatic spray drying, gastrointestinal regulatory peptide, intestinal microbiota, microencapsulation",Experiment 25,China,Mus musculus,Feces,UBERON:0001988,Endothelin-1,CHEBI:153671,Decreased Endothelin-1 (ET-1),Increased Endothelin-1 (ET-1),Increased levels of Endothelin-1 (ET-1),NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,fig 10,7 November 2025,Chyono2,Chyono2,Spearman's correlation analysis between changed bacterial genera and constipation-related indicators,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1301,Complete,NA
bsdb:35573767/25/2,35573767,laboratory experiment,35573767,10.3389/fcimb.2022.894216,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.894216/full,"Jiang T., Lu W., Fang Z., Wang H., Zhu J., Zhang H. , Zhao J.",<i>Bifidobacterium</i> Treated by Electrostatic Spray Drying Relieved Constipation by Changing the Relative Abundance of Bacteria Associated With Gastrointestinal Regulatory Peptides,Frontiers in cellular and infection microbiology,2022,"Bifidobacterium, aquaporin, constipation, electrostatic spray drying, gastrointestinal regulatory peptide, intestinal microbiota, microencapsulation",Experiment 25,China,Mus musculus,Feces,UBERON:0001988,Endothelin-1,CHEBI:153671,Decreased Endothelin-1 (ET-1),Increased Endothelin-1 (ET-1),Increased levels of Endothelin-1 (ET-1),NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,fig 10,7 November 2025,Chyono2,Chyono2,Spearman's correlation analysis between changed bacterial genera and constipation-related indicators,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum",3379134|976|200643|171549|171550|239759;1783272|544448|31969|186332|186333|2086;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|2005473|1918540,Complete,NA
bsdb:35579429/2/1,35579429,"cross-sectional observational, not case-control",35579429,10.1128/spectrum.02311-21,NA,"Devi P., Maurya R., Mehta P., Shamim U., Yadav A., Chattopadhyay P., Kanakan A., Khare K., Vasudevan J.S., Sahni S., Mishra P., Tyagi A., Jha S., Budhiraja S., Tarai B. , Pandey R.",Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome,Microbiology spectrum,2022,"COVID-19, Holo-Seq, co-infection, disease outcome, disease sub-phenotype, host-pathogen interactions, metabolic pathways, nasopharyngeal RNA, pathogen genomics, respiratory virus oligo panel (RVOP), transcriptionally active microbial isolates",Experiment 2,India,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19 symptoms measurement,EFO:0600019,mild,mortality,patients who succumbed to COVID-19 during hospital stay,24,12,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3e,10 March 2024,Leenaa,"Leenaa,WikiWorks",Differentially abundant bacterial species between mild group and mortality group,increased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter|s__Achromobacter xylosoxidans,3379134|1224|28216|80840|506|222|85698,Complete,Folakunmi
bsdb:35579429/3/1,35579429,"cross-sectional observational, not case-control",35579429,10.1128/spectrum.02311-21,NA,"Devi P., Maurya R., Mehta P., Shamim U., Yadav A., Chattopadhyay P., Kanakan A., Khare K., Vasudevan J.S., Sahni S., Mishra P., Tyagi A., Jha S., Budhiraja S., Tarai B. , Pandey R.",Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome,Microbiology spectrum,2022,"COVID-19, Holo-Seq, co-infection, disease outcome, disease sub-phenotype, host-pathogen interactions, metabolic pathways, nasopharyngeal RNA, pathogen genomics, respiratory virus oligo panel (RVOP), transcriptionally active microbial isolates",Experiment 3,India,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19 symptoms measurement,EFO:0600019,moderate,severe,patients showing respiratory distress with respiratory support requirement and SpO2 levels < 90%,36,14,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3g,10 March 2024,Leenaa,"Leenaa,WikiWorks",Differentially abundant bacterial species between moderate group and severe group,increased,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,3384189|32066|203490|203491|1129771|32067|40542,Complete,Folakunmi
bsdb:35579429/4/1,35579429,"cross-sectional observational, not case-control",35579429,10.1128/spectrum.02311-21,NA,"Devi P., Maurya R., Mehta P., Shamim U., Yadav A., Chattopadhyay P., Kanakan A., Khare K., Vasudevan J.S., Sahni S., Mishra P., Tyagi A., Jha S., Budhiraja S., Tarai B. , Pandey R.",Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome,Microbiology spectrum,2022,"COVID-19, Holo-Seq, co-infection, disease outcome, disease sub-phenotype, host-pathogen interactions, metabolic pathways, nasopharyngeal RNA, pathogen genomics, respiratory virus oligo panel (RVOP), transcriptionally active microbial isolates",Experiment 4,India,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19 symptoms measurement,EFO:0600019,moderate,mortality,patients who succumbed to COVID-19 during hospital stay,36,12,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3f,10 March 2024,Leenaa,"Leenaa,WikiWorks",Differentially abundant bacterial species between moderate group and mortality group,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus cereus,1783272|1239|91061|1385|186817|1386|1396,Complete,Folakunmi
bsdb:35579429/4/2,35579429,"cross-sectional observational, not case-control",35579429,10.1128/spectrum.02311-21,NA,"Devi P., Maurya R., Mehta P., Shamim U., Yadav A., Chattopadhyay P., Kanakan A., Khare K., Vasudevan J.S., Sahni S., Mishra P., Tyagi A., Jha S., Budhiraja S., Tarai B. , Pandey R.",Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome,Microbiology spectrum,2022,"COVID-19, Holo-Seq, co-infection, disease outcome, disease sub-phenotype, host-pathogen interactions, metabolic pathways, nasopharyngeal RNA, pathogen genomics, respiratory virus oligo panel (RVOP), transcriptionally active microbial isolates",Experiment 4,India,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19 symptoms measurement,EFO:0600019,moderate,mortality,patients who succumbed to COVID-19 during hospital stay,36,12,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3h,10 March 2024,Leenaa,"Leenaa,WikiWorks",Differentially abundant bacterial species between moderate group and mortality group,decreased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,1783272|1239|909932|1843489|31977|29465|29466,Complete,Folakunmi
bsdb:35579429/5/1,35579429,"cross-sectional observational, not case-control",35579429,10.1128/spectrum.02311-21,NA,"Devi P., Maurya R., Mehta P., Shamim U., Yadav A., Chattopadhyay P., Kanakan A., Khare K., Vasudevan J.S., Sahni S., Mishra P., Tyagi A., Jha S., Budhiraja S., Tarai B. , Pandey R.",Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome,Microbiology spectrum,2022,"COVID-19, Holo-Seq, co-infection, disease outcome, disease sub-phenotype, host-pathogen interactions, metabolic pathways, nasopharyngeal RNA, pathogen genomics, respiratory virus oligo panel (RVOP), transcriptionally active microbial isolates",Experiment 5,India,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19 symptoms measurement,EFO:0600019,severe,mortality,patients who succumbed to COVID-19 during hospital stay,14,12,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3g,10 March 2024,Leenaa,"Leenaa,WikiWorks",Differentially abundant bacterial species between severe group and mortality group,decreased,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,3384189|32066|203490|203491|1129771|32067|40542,Complete,Folakunmi
bsdb:35598439/1/1,35598439,prospective cohort,35598439,10.1016/j.ebiom.2022.104061,NA,"Dahlin M., Singleton S.S., David J.A., Basuchoudhary A., Wickström R., Mazumder R. , Prast-Nielsen S.",Higher levels of Bifidobacteria and tumor necrosis factor in children with drug-resistant epilepsy are associated with anti-seizure response to the ketogenic diet,EBioMedicine,2022,"Bifidobacterium, Bioinformatics, Epilepsy, Gut microbiota, Inflammation, Ketogenic diet, Machine learning, Omics, TNF",Experiment 1,Sweden,Homo sapiens,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,Responders before ketogenic diet (R_Ep1),Responders during ketogenic diet (R_Ep2),This group consists of children with ≥50% seizure reduction during ketogenic diet treatment.,27,27,3 months,WMS,NA,Illumina,centered log-ratio,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4C,17 December 2024,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of R_Ep2 group compared to R_Ep1 group,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. infantis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. infantis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum",1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|1678|216816|1682;1783272|201174|1760|85004|31953|1678|216816|1682;1783272|201174|1760|85004|31953|1678|216816|1679,Complete,KateRasheed
bsdb:35598439/2/1,35598439,prospective cohort,35598439,10.1016/j.ebiom.2022.104061,NA,"Dahlin M., Singleton S.S., David J.A., Basuchoudhary A., Wickström R., Mazumder R. , Prast-Nielsen S.",Higher levels of Bifidobacteria and tumor necrosis factor in children with drug-resistant epilepsy are associated with anti-seizure response to the ketogenic diet,EBioMedicine,2022,"Bifidobacterium, Bioinformatics, Epilepsy, Gut microbiota, Inflammation, Ketogenic diet, Machine learning, Omics, TNF",Experiment 2,Sweden,Homo sapiens,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,Decreasing correlation in non-responders before ketogenic diet (NR_Ep1),Increasing correlation in non-responders before ketogenic diet (NR_Ep1),This group consists of children with a < 50% reduction before ketogenic diet treatment.,NA,NA,3 months,WMS,NA,Illumina,centered log-ratio,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,21 May 2025,Victoria,Victoria,Spearman's correlation of members of the B. longum cluster.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. infantis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. infantis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum",1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|216816|1682;1783272|201174|1760|85004|31953|1678|216816|1682;1783272|201174|1760|85004|31953|1678|216816|1679,Complete,KateRasheed
bsdb:35598439/3/1,35598439,prospective cohort,35598439,10.1016/j.ebiom.2022.104061,NA,"Dahlin M., Singleton S.S., David J.A., Basuchoudhary A., Wickström R., Mazumder R. , Prast-Nielsen S.",Higher levels of Bifidobacteria and tumor necrosis factor in children with drug-resistant epilepsy are associated with anti-seizure response to the ketogenic diet,EBioMedicine,2022,"Bifidobacterium, Bioinformatics, Epilepsy, Gut microbiota, Inflammation, Ketogenic diet, Machine learning, Omics, TNF",Experiment 3,Sweden,Homo sapiens,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,Decreasing correlation in non-responders during ketogenic diet (NR_Ep2),Increasing correlation in non-responders during ketogenic diet (NR_Ep2),This group consists of children with a <50% seizure reduction during ketogenic diet treatment.,NA,NA,3 months,WMS,NA,Illumina,centered log-ratio,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,21 May 2025,Victoria,Victoria,Spearman's correlation of members of the B. longum cluster.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. infantis,1783272|201174|1760|85004|31953|1678|216816|1682,Complete,KateRasheed
bsdb:35598439/4/1,35598439,prospective cohort,35598439,10.1016/j.ebiom.2022.104061,NA,"Dahlin M., Singleton S.S., David J.A., Basuchoudhary A., Wickström R., Mazumder R. , Prast-Nielsen S.",Higher levels of Bifidobacteria and tumor necrosis factor in children with drug-resistant epilepsy are associated with anti-seizure response to the ketogenic diet,EBioMedicine,2022,"Bifidobacterium, Bioinformatics, Epilepsy, Gut microbiota, Inflammation, Ketogenic diet, Machine learning, Omics, TNF",Experiment 4,Sweden,Homo sapiens,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,Non-responders before ketogenic diet (NR_Ep1),Responders before ketogenic diet (R_Ep1),This group consists of children with ≥50% seizure reduction before ketogenic diet treatment.,27,27,3 months,WMS,NA,Illumina,centered log-ratio,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4C,15 January 2025,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of R_Ep1 group compared to NR_Ep1 group,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. infantis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. infantis",1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|216816|1682;1783272|201174|1760|85004|31953|1678|216816|1682,Complete,KateRasheed
bsdb:35598439/5/1,35598439,prospective cohort,35598439,10.1016/j.ebiom.2022.104061,NA,"Dahlin M., Singleton S.S., David J.A., Basuchoudhary A., Wickström R., Mazumder R. , Prast-Nielsen S.",Higher levels of Bifidobacteria and tumor necrosis factor in children with drug-resistant epilepsy are associated with anti-seizure response to the ketogenic diet,EBioMedicine,2022,"Bifidobacterium, Bioinformatics, Epilepsy, Gut microbiota, Inflammation, Ketogenic diet, Machine learning, Omics, TNF",Experiment 5,Sweden,Homo sapiens,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,Decreasing correlation in responders during ketogenic diet (R_Ep2),Increasing correlation in responders during ketogenic diet (R_Ep2),This group consists of children with a ≥50% seizure reduction during ketogenic diet treatment.,NA,NA,3 months,WMS,NA,Illumina,centered log-ratio,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,21 May 2025,Victoria,Victoria,Spearman's correlation of members of the B. longum cluster.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. infantis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum",1783272|201174|1760|85004|31953|1678|216816|1682;1783272|201174|1760|85004|31953|1678|216816|1679,Complete,KateRasheed
bsdb:35615912/1/1,35615912,"cross-sectional observational, not case-control",35615912,10.1002/acr2.11436,https://onlinelibrary.wiley.com/doi/pdf/10.1002/acr2.11436,"Bae S.S., Dong T.S., Wang J., Lagishetty V., Katzka W., Jacobs J.P. , Charles-Schoeman C.",Altered Gut Microbiome in Patients With Dermatomyositis,ACR open rheumatology,2022,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Dermatomyositis,EFO:0000398,healthy controls,dermatomyositis - ILD-MSA,Patients with dermatomyositis - ILD-associated myositis antibodies subgroup,26,12,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Text,12 March 2023,Merit,"Merit,Claregrieve1,WikiWorks",Differential microbial abundance between healthy controls and ILD-MSA dermatomyositis patients,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,3379134|976|200643|171549|815,Complete,Claregrieve1
bsdb:35615912/2/1,35615912,"cross-sectional observational, not case-control",35615912,10.1002/acr2.11436,https://onlinelibrary.wiley.com/doi/pdf/10.1002/acr2.11436,"Bae S.S., Dong T.S., Wang J., Lagishetty V., Katzka W., Jacobs J.P. , Charles-Schoeman C.",Altered Gut Microbiome in Patients With Dermatomyositis,ACR open rheumatology,2022,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Dermatomyositis,EFO:0000398,healthy controls,dermatomyositis - Cancer-MSA,Patients with dermatomyositis - cancer-associated myositis antibodies subgroup,26,13,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Text,23 May 2023,Claregrieve1,"Claregrieve1,WikiWorks",Differential microbial abundance between healthy controls and cancer-MSA dermatomyositis patients,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,1783272|1239|186801|3085636|186803,Complete,Claregrieve1
bsdb:35615912/3/1,35615912,"cross-sectional observational, not case-control",35615912,10.1002/acr2.11436,https://onlinelibrary.wiley.com/doi/pdf/10.1002/acr2.11436,"Bae S.S., Dong T.S., Wang J., Lagishetty V., Katzka W., Jacobs J.P. , Charles-Schoeman C.",Altered Gut Microbiome in Patients With Dermatomyositis,ACR open rheumatology,2022,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Dermatomyositis,EFO:0000398,dermatomyositis - Cancer-MSA,dermatomyositis - ILD-MSA,Patients with dermatomyositis - ILD associated myositis antibodies,13,12,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Text , Figure 2F-H",15 December 2023,Peace Sandy,"Peace Sandy,Atrayees,WikiWorks","Patients with DM with ILD�MSA also had significant depletion of the Christensenellaceae R-7
group (within the Christensenellaceae family), and multiple ASVs
within the Ruminococcaceae family (Ruminococcus 1, Ruminococ�caceae UCG-002, and Subdoligranulum) compared with controls
and the cancer-MSA group.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|216572,Complete,Lwaldron
bsdb:35619714/1/1,35619714,laboratory experiment,35619714,10.3389/fimmu.2022.900132,NA,"Zhang B., Chen T., Cao M., Yuan C., Reiter R.J., Zhao Z., Zhao Y., Chen L., Fan W., Wang X., Zhou X. , Li C.",Gut Microbiota Dysbiosis Induced by Decreasing Endogenous Melatonin Mediates the Pathogenesis of Alzheimer's Disease and Obesity,Frontiers in immunology,2022,"alzheimer's disease, fecal microbiota transplantation, gut- brain axis, melatonin, microbiota dysbiosis, obesity, systemic inflammation",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease biomarker measurement,EFO:0006514,Wild type (WT) mice,Endogenous melatonin reduction (EMR) mice,"Mice that exhibited a pan-metabolic disorder, with significant transcriptome changes in 11 organs, serum metabolome alterations as well as microbiota dysbiosis.",NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 4C,24 March 2024,Shulamite,"Shulamite,Deacme,Scholastica,WikiWorks",Distinct gut microbiota identified by LEfSe in endogenous melatonin reduction (EMR) versus  wild type (WT) mice with biomarkers at all levels,increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacterium,k__Bacillati|p__Bacillota|c__Bacilli,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Paenarthrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",1783272|201174;3379134|1224|28211;1783272|1239|526524|526525|128827|2749267;1783272|1239|91061;95818|2093818|2093825|2171986;95818|2093818|2093825;95818|2093818;95818|2093818|2093825|2171986|1331051;1783272|201174|84998|84999;1783272|201174|84998;1783272|201174|84998|1643822|1643826;1783272|201174|84998|1643822|1643826|580024;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85006|1268;1783272|201174|1760|85006;1783272|201174|1760|85006|1268|1742992;1783272|1239|186801|186802|216572|100175;;1783272|1239|186801|186802|216572|1508657,Complete,Svetlana up
bsdb:35619714/1/2,35619714,laboratory experiment,35619714,10.3389/fimmu.2022.900132,NA,"Zhang B., Chen T., Cao M., Yuan C., Reiter R.J., Zhao Z., Zhao Y., Chen L., Fan W., Wang X., Zhou X. , Li C.",Gut Microbiota Dysbiosis Induced by Decreasing Endogenous Melatonin Mediates the Pathogenesis of Alzheimer's Disease and Obesity,Frontiers in immunology,2022,"alzheimer's disease, fecal microbiota transplantation, gut- brain axis, melatonin, microbiota dysbiosis, obesity, systemic inflammation",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease biomarker measurement,EFO:0006514,Wild type (WT) mice,Endogenous melatonin reduction (EMR) mice,"Mice that exhibited a pan-metabolic disorder, with significant transcriptome changes in 11 organs, serum metabolome alterations as well as microbiota dysbiosis.",NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 4C,25 March 2024,Shulamite,"Shulamite,Deacme,Scholastica,WikiWorks",Distinct gut microbiota identified by LEfSe in endogenous melatonin reduction (EMR) versus  wild type (WT) mice with biomarkers at all levels,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota",3379134|976|200643|171549;3379134|976|200643;3379134|976|200643|171549|2005473;1783272|1239|186801|186802|216572|3068309;3379134|976|200643|171549;3379134|976|200643|171549|2005473;3379134|976,Complete,Svetlana up
bsdb:35622782/1/1,35622782,"cross-sectional observational, not case-control",35622782,https://doi.org/10.1371/journal.pone.0268466,NA,"Takeda T., Yoshimi K., Kai S., Ozawa G., Yamada K. , Hiramatsu K.",Characteristics of the gut microbiota in women with premenstrual symptoms: A cross-sectional study,PloS one,2022,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Menstrual disorder,EFO:0010270,Control group,Premenstrual Disorder (PMD),Participants who suffered PMDs defined by the International Society of Premenstrual Disorder.,22,21,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 4,19 May 2025,Aleru Divine,Aleru Divine,The most differentially abundant taxa between the PMD group (P) and the control group (C).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerotaenia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239|186801|3085636|186803|1843206;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|216572;1783272|1239|186801|186802,Complete,NA
bsdb:35622782/1/2,35622782,"cross-sectional observational, not case-control",35622782,https://doi.org/10.1371/journal.pone.0268466,NA,"Takeda T., Yoshimi K., Kai S., Ozawa G., Yamada K. , Hiramatsu K.",Characteristics of the gut microbiota in women with premenstrual symptoms: A cross-sectional study,PloS one,2022,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Menstrual disorder,EFO:0010270,Control group,Premenstrual Disorder (PMD),Participants who suffered PMDs defined by the International Society of Premenstrual Disorder.,22,21,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 4,19 May 2025,Aleru Divine,Aleru Divine,The most differentially abundant taxa between the PMD group (P) and the control group (C),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Extibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",1783272|1239|186801|3085636|186803|1918452;1783272|1239|186801|186802|3085642|580596;1783272|1239|909932|1843489|31977|906;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549,Complete,NA
bsdb:35624429/1/1,35624429,"cross-sectional observational, not case-control",35624429,10.1186/s12866-022-02557-3,NA,"Kirishima M., Yokoyama S., Matsuo K., Hamada T., Shimokawa M., Akahane T., Sugimoto T., Tsurumaru H., Ishibashi M., Mataki Y., Ootsuka T., Nomoto M., Hayashi C., Horiguchi A., Higashi M. , Tanimoto A.",Gallbladder microbiota composition is associated with pancreaticobiliary and gallbladder cancer prognosis,BMC microbiology,2022,"Alpha diversity, Beta diversity, Bile, Biomarker, Cancer, Gallbladder, Microbiota, Overall survival, Pancreaticobiliary tract, Prognosis",Experiment 1,Japan,Homo sapiens,Bile,UBERON:0001970,Disease progression measurement,EFO:0008336,Early cholangiocarcinoma,Advanced cholangiocarcinoma,"Patients with lymph node metastasis in cholangiocarcinoma, where lymph node metastasis denotes advanced stage and the absence of lymph node metastasis denotes early stage.",NA,NA,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,Table 2,30 October 2023,Folakunmi,"Folakunmi,WikiWorks","Patients with lymph node metastasis in cholangiocarcinoma, where lymph node metastasis denotes advanced stage and the absence of lymph node metastasis denotes early stage.",increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",3379134|29547|3031852|213849|72294|194;3379134|1224|1236|91347|543|544;3384189|32066|203490|203491|1129771|32067,Complete,ChiomaBlessing
bsdb:35624429/2/1,35624429,"cross-sectional observational, not case-control",35624429,10.1186/s12866-022-02557-3,NA,"Kirishima M., Yokoyama S., Matsuo K., Hamada T., Shimokawa M., Akahane T., Sugimoto T., Tsurumaru H., Ishibashi M., Mataki Y., Ootsuka T., Nomoto M., Hayashi C., Horiguchi A., Higashi M. , Tanimoto A.",Gallbladder microbiota composition is associated with pancreaticobiliary and gallbladder cancer prognosis,BMC microbiology,2022,"Alpha diversity, Beta diversity, Bile, Biomarker, Cancer, Gallbladder, Microbiota, Overall survival, Pancreaticobiliary tract, Prognosis",Experiment 2,Japan,Homo sapiens,Bile,UBERON:0001970,Disease progression measurement,EFO:0008336,Early pancreatic ductal adenocarcinoma,Advanced pancreatic ductal adenocarcinoma,"Patients with lymph node metastasis in pancreatic ductal adenocarcinoma (PDAC), where lymph node metastasis denotes advanced stage and the absence of lymph node metastasis denotes early stage.",NA,NA,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,Table 2,30 October 2023,Folakunmi,"Folakunmi,WikiWorks","Patients with lymph node metastasis in pancreatic ductal adenocarcinoma (PDAC), where lymph node metastasis denotes advanced stage and the absence of lymph node metastasis denotes early stage.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas",3379134|1224|28211|356|69277|28100;3379134|1224|28211|204457|41297|13687,Complete,ChiomaBlessing
bsdb:35624429/2/2,35624429,"cross-sectional observational, not case-control",35624429,10.1186/s12866-022-02557-3,NA,"Kirishima M., Yokoyama S., Matsuo K., Hamada T., Shimokawa M., Akahane T., Sugimoto T., Tsurumaru H., Ishibashi M., Mataki Y., Ootsuka T., Nomoto M., Hayashi C., Horiguchi A., Higashi M. , Tanimoto A.",Gallbladder microbiota composition is associated with pancreaticobiliary and gallbladder cancer prognosis,BMC microbiology,2022,"Alpha diversity, Beta diversity, Bile, Biomarker, Cancer, Gallbladder, Microbiota, Overall survival, Pancreaticobiliary tract, Prognosis",Experiment 2,Japan,Homo sapiens,Bile,UBERON:0001970,Disease progression measurement,EFO:0008336,Early pancreatic ductal adenocarcinoma,Advanced pancreatic ductal adenocarcinoma,"Patients with lymph node metastasis in pancreatic ductal adenocarcinoma (PDAC), where lymph node metastasis denotes advanced stage and the absence of lymph node metastasis denotes early stage.",NA,NA,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 2,Table 2,30 October 2023,Folakunmi,"Folakunmi,WikiWorks","Patients with lymph node metastasis in pancreatic ductal adenocarcinoma (PDAC), where lymph node metastasis denotes advanced stage and the absence of lymph node metastasis denotes early stage.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium",3379134|1224|1236|91347|543|547;1783272|1239|186801|3085636|186803|1649459;1783272|201174|1760|85007|1762|1763,Complete,ChiomaBlessing
bsdb:35624429/3/1,35624429,"cross-sectional observational, not case-control",35624429,10.1186/s12866-022-02557-3,NA,"Kirishima M., Yokoyama S., Matsuo K., Hamada T., Shimokawa M., Akahane T., Sugimoto T., Tsurumaru H., Ishibashi M., Mataki Y., Ootsuka T., Nomoto M., Hayashi C., Horiguchi A., Higashi M. , Tanimoto A.",Gallbladder microbiota composition is associated with pancreaticobiliary and gallbladder cancer prognosis,BMC microbiology,2022,"Alpha diversity, Beta diversity, Bile, Biomarker, Cancer, Gallbladder, Microbiota, Overall survival, Pancreaticobiliary tract, Prognosis",Experiment 3,Japan,Homo sapiens,Bile,UBERON:0001970,Disease progression measurement,EFO:0008336,intraductal papillary mucinous neoplasm (IPMN),Intraductal papillary mucinous carcinoma (IPMC),Patients with Intraductal papillary mucinous carcinoma (IPMC) in pancreas cystic lesions.,20,10,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,Table 2,30 October 2023,Folakunmi,"Folakunmi,WikiWorks",Abundant taxa in Intraductal papillary mucinous carcinoma (IPMC) when compared to intraductal papillary mucinous neoplasm.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549|171552|1283313;3379134|200940|3031449|213115|194924|35832;1783272|1239|909932|1843489|31977|39948;1783272|201174|84998|1643822|1643826|84111;1783272|1239|909932|909929|1843491|970;1783272|1239|91061|186826|1300|1301,Complete,ChiomaBlessing
bsdb:35624429/4/1,35624429,"cross-sectional observational, not case-control",35624429,10.1186/s12866-022-02557-3,NA,"Kirishima M., Yokoyama S., Matsuo K., Hamada T., Shimokawa M., Akahane T., Sugimoto T., Tsurumaru H., Ishibashi M., Mataki Y., Ootsuka T., Nomoto M., Hayashi C., Horiguchi A., Higashi M. , Tanimoto A.",Gallbladder microbiota composition is associated with pancreaticobiliary and gallbladder cancer prognosis,BMC microbiology,2022,"Alpha diversity, Beta diversity, Bile, Biomarker, Cancer, Gallbladder, Microbiota, Overall survival, Pancreaticobiliary tract, Prognosis",Experiment 4,Japan,Homo sapiens,Bile,UBERON:0001970,Disease prognosis measurement,EFO:0007936,Poor prognosis in bile duct lesion cases,Good prognosis in bile duct lesion cases,"The group with good prognostic factors after adjustment for clinicopathologic variables ( sex, age, ASA score, stages, and the administration of preoperative chemotherapy) in bile duct lesion cases. These clinical conditions were found to be non-confounding.",101,101,NA,16S,34,Illumina,raw counts,Cox Proportional-Hazards Regression,0.05,NA,NA,NA,NA,unchanged,increased,unchanged,NA,NA,NA,Signature 1,"Table 4 + Results within text (Page 4, under subheading - ""Evaluation of threshold value of individual microbiota relative abundance for prognosis"")",6 November 2023,Folakunmi,"Folakunmi,ChiomaBlessing,WikiWorks",Differentially abundant taxa between poor prognosis and good prognosis in bile duct lesion cases using Cox proportional hazards model analysis.,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3384189|32066|203490|203491|203492|848;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,ChiomaBlessing
bsdb:35624429/4/2,35624429,"cross-sectional observational, not case-control",35624429,10.1186/s12866-022-02557-3,NA,"Kirishima M., Yokoyama S., Matsuo K., Hamada T., Shimokawa M., Akahane T., Sugimoto T., Tsurumaru H., Ishibashi M., Mataki Y., Ootsuka T., Nomoto M., Hayashi C., Horiguchi A., Higashi M. , Tanimoto A.",Gallbladder microbiota composition is associated with pancreaticobiliary and gallbladder cancer prognosis,BMC microbiology,2022,"Alpha diversity, Beta diversity, Bile, Biomarker, Cancer, Gallbladder, Microbiota, Overall survival, Pancreaticobiliary tract, Prognosis",Experiment 4,Japan,Homo sapiens,Bile,UBERON:0001970,Disease prognosis measurement,EFO:0007936,Poor prognosis in bile duct lesion cases,Good prognosis in bile duct lesion cases,"The group with good prognostic factors after adjustment for clinicopathologic variables ( sex, age, ASA score, stages, and the administration of preoperative chemotherapy) in bile duct lesion cases. These clinical conditions were found to be non-confounding.",101,101,NA,16S,34,Illumina,raw counts,Cox Proportional-Hazards Regression,0.05,NA,NA,NA,NA,unchanged,increased,unchanged,NA,NA,NA,Signature 2,"Table 4 + Results within text (Page 4, under subheading - ""Evaluation of threshold value of individual microbiota relative abundance for prognosis"")",6 November 2023,Folakunmi,"Folakunmi,ChiomaBlessing,WikiWorks",Differentially abundant taxa between poor prognosis and good prognosis in bile duct lesion cases using Cox proportional hazards model analysis.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",3379134|976|200643|171549|815|816;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|1649459;1783272|201174|1760|85007|2805586|1847725;3379134|1224|1236|2887326|468|475;1783272|1239|91061|1385|90964|1279,Complete,ChiomaBlessing
bsdb:35624429/5/1,35624429,"cross-sectional observational, not case-control",35624429,10.1186/s12866-022-02557-3,NA,"Kirishima M., Yokoyama S., Matsuo K., Hamada T., Shimokawa M., Akahane T., Sugimoto T., Tsurumaru H., Ishibashi M., Mataki Y., Ootsuka T., Nomoto M., Hayashi C., Horiguchi A., Higashi M. , Tanimoto A.",Gallbladder microbiota composition is associated with pancreaticobiliary and gallbladder cancer prognosis,BMC microbiology,2022,"Alpha diversity, Beta diversity, Bile, Biomarker, Cancer, Gallbladder, Microbiota, Overall survival, Pancreaticobiliary tract, Prognosis",Experiment 5,Japan,Homo sapiens,Bile,UBERON:0001970,Disease prognosis measurement,EFO:0007936,Poor prognosis in pancreatic lesion cases,Good prognosis in pancreatic lesion cases,"The group with good prognostic factors after adjustment for clinicopathologic variables ( sex, age, ASA score, stages, and the administration of preoperative chemotherapy) in pancreatic lesion cases. These clinicopathologic variables were found to be non-confounding.",112,112,NA,16S,34,Illumina,raw counts,Cox Proportional-Hazards Regression,0.05,NA,NA,NA,NA,unchanged,increased,unchanged,NA,NA,NA,Signature 1,"Table 4 + Results within text (Page 5, under subheading - ""Evaluation of threshold value of individual microbiota relative abundance for prognosis"")",6 November 2023,Folakunmi,"Folakunmi,ChiomaBlessing,WikiWorks",Differentially abundant taxa between poor prognosis and good prognosis in pancreatic lesion cases using Cox proportional hazards model analysis.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|976|200643|171549|815|816;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|160674;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301,Complete,ChiomaBlessing
bsdb:35624429/5/2,35624429,"cross-sectional observational, not case-control",35624429,10.1186/s12866-022-02557-3,NA,"Kirishima M., Yokoyama S., Matsuo K., Hamada T., Shimokawa M., Akahane T., Sugimoto T., Tsurumaru H., Ishibashi M., Mataki Y., Ootsuka T., Nomoto M., Hayashi C., Horiguchi A., Higashi M. , Tanimoto A.",Gallbladder microbiota composition is associated with pancreaticobiliary and gallbladder cancer prognosis,BMC microbiology,2022,"Alpha diversity, Beta diversity, Bile, Biomarker, Cancer, Gallbladder, Microbiota, Overall survival, Pancreaticobiliary tract, Prognosis",Experiment 5,Japan,Homo sapiens,Bile,UBERON:0001970,Disease prognosis measurement,EFO:0007936,Poor prognosis in pancreatic lesion cases,Good prognosis in pancreatic lesion cases,"The group with good prognostic factors after adjustment for clinicopathologic variables ( sex, age, ASA score, stages, and the administration of preoperative chemotherapy) in pancreatic lesion cases. These clinicopathologic variables were found to be non-confounding.",112,112,NA,16S,34,Illumina,raw counts,Cox Proportional-Hazards Regression,0.05,NA,NA,NA,NA,unchanged,increased,unchanged,NA,NA,NA,Signature 2,"Table 4 + Results within text (Page 5, under subheading - ""Evaluation of threshold value of individual microbiota relative abundance for prognosis"")",6 November 2023,Folakunmi,"Folakunmi,ChiomaBlessing,WikiWorks",Differentially abundant taxa between poor prognosis and good prognosis in pancreatic lesion cases using Cox proportional hazards model analysis.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|1224|1236|2887326|468|469;3379134|1224|1236|91347|543|570;3379134|1224|28211|204455|31989|265;1783272|1239|909932|909929|1843491|970;1783272|1239|909932|1843489|31977|29465,Complete,ChiomaBlessing
bsdb:35630486/1/1,35630486,case-control,35630486,10.3390/microorganisms10051044,NA,"Kitae H., Takagi T., Naito Y., Inoue R., Azuma Y., Torii T., Mizushima K., Doi T., Inoue K., Dohi O., Yoshida N., Kamada K., Uchiyama K., Ishikawa T., Konishi H. , Itoh Y.",Gut Microbiota Associated with Clinical Relapse in Patients with Quiescent Ulcerative Colitis,Microorganisms,2022,"LEfSe, fecal microbiota, quiescent ulcerative colitis, ulcerative colitis relapse",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Healthy controls,Quiescent ulcerative colitis patients,Consecutive recruitment of patients with quiescent UC in our outpatient clinic from November 2016 to September 2017. Clinical remission was defined as a Lichtiger index score of ≤4.,59,59,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,"age,sex",NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 1f,12 December 2023,Yjung24,"Yjung24,Peace Sandy,WikiWorks","linear discriminant analysis effect size (LEfSe) analysis identified taxa that characterized each group. Cladogram of LEfSe analysis results. Yellow-shaded areas indicate taxa that characterize UC, and green-shaded areas indicate taxa that characterize HCs. Linear discriminant analysis (LDA) scores for identified taxa of patient of UCs (7 taxa) and HC (6 taxa) was shown. ** p < 0.01.",increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales",1783272|201174|84992;1783272|201174;1783272|1239|91061;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826,Complete,Peace Sandy
bsdb:35630486/1/2,35630486,case-control,35630486,10.3390/microorganisms10051044,NA,"Kitae H., Takagi T., Naito Y., Inoue R., Azuma Y., Torii T., Mizushima K., Doi T., Inoue K., Dohi O., Yoshida N., Kamada K., Uchiyama K., Ishikawa T., Konishi H. , Itoh Y.",Gut Microbiota Associated with Clinical Relapse in Patients with Quiescent Ulcerative Colitis,Microorganisms,2022,"LEfSe, fecal microbiota, quiescent ulcerative colitis, ulcerative colitis relapse",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Healthy controls,Quiescent ulcerative colitis patients,Consecutive recruitment of patients with quiescent UC in our outpatient clinic from November 2016 to September 2017. Clinical remission was defined as a Lichtiger index score of ≤4.,59,59,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,"age,sex",NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 1f,12 December 2023,Yjung24,"Yjung24,Peace Sandy,WikiWorks","linear discriminant analysis effect size (LEfSe) analysis identified taxa that characterized each group. Cladogram of LEfSe analysis results. Yellow-shaded areas indicate taxa that characterize UC, and green-shaded areas indicate taxa that characterize HCs. Linear discriminant analysis (LDA) scores for identified taxa of patient of UCs (7 taxa) and HC (6 taxa) was shown. ** p < 0.01.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",3379134|976|200643|171549;3379134|976|200643;3379134|976;1783272|1239|186801;1783272|1239|186801|186802,Complete,Peace Sandy
bsdb:35630486/2/1,35630486,case-control,35630486,10.3390/microorganisms10051044,NA,"Kitae H., Takagi T., Naito Y., Inoue R., Azuma Y., Torii T., Mizushima K., Doi T., Inoue K., Dohi O., Yoshida N., Kamada K., Uchiyama K., Ishikawa T., Konishi H. , Itoh Y.",Gut Microbiota Associated with Clinical Relapse in Patients with Quiescent Ulcerative Colitis,Microorganisms,2022,"LEfSe, fecal microbiota, quiescent ulcerative colitis, ulcerative colitis relapse",Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Disease progression measurement,EFO:0008336,Sustained remission of ulcerative colitis group,Relapsed ulcerative colitis group,Patients who had clinically relapsed during the 3.5 year-long follow-up period. Clinical relapse was defined as clinical or endoscopic deterioration requiring therapeutic modification.,40,19,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 2g,12 December 2023,Yjung24,"Yjung24,Peace Sandy,WikiWorks","linear discriminant analysis effect size (LEfSe) analysis identified taxa that characterized each group. Cladogram of LEfSe analysis results. Red-shaded areas indicate taxathat characterize relapse group, and blue-shaded areas indicate taxa that characterize SusRem group. Linear discriminant analysis (LDA) scores for identified taxa of SusRem (2 taxa) and Relapse (6 taxa)",increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|201174|84992;1783272|201174;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|216572|216851,Complete,Peace Sandy
bsdb:35630486/2/2,35630486,case-control,35630486,10.3390/microorganisms10051044,NA,"Kitae H., Takagi T., Naito Y., Inoue R., Azuma Y., Torii T., Mizushima K., Doi T., Inoue K., Dohi O., Yoshida N., Kamada K., Uchiyama K., Ishikawa T., Konishi H. , Itoh Y.",Gut Microbiota Associated with Clinical Relapse in Patients with Quiescent Ulcerative Colitis,Microorganisms,2022,"LEfSe, fecal microbiota, quiescent ulcerative colitis, ulcerative colitis relapse",Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Disease progression measurement,EFO:0008336,Sustained remission of ulcerative colitis group,Relapsed ulcerative colitis group,Patients who had clinically relapsed during the 3.5 year-long follow-up period. Clinical relapse was defined as clinical or endoscopic deterioration requiring therapeutic modification.,40,19,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 2g,12 December 2023,Yjung24,"Yjung24,Peace Sandy,WikiWorks","linear discriminant analysis effect size (LEfSe) analysis identified taxa that characterized each group. Cladogram of LEfSe analysis results. Red-shaded areas indicate taxa that characterize relapse group, and blue-shaded areas indicate taxa that characterize SusRem group. Linear discriminant analysis (LDA) scores for identified taxa of SusRem (2 taxa) and Relapse (6 taxa)",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552,Complete,Peace Sandy
bsdb:35642922/1/1,35642922,"cross-sectional observational, not case-control",35642922,10.1128/msystems.01489-21,NA,"Hoskinson C., Zheng K., Gabel J., Kump A., German R., Podicheti R., Marino N. , Stiemsma L.T.",Composition and Functional Potential of the Human Mammary Microbiota Prior to and Following Breast Tumor Diagnosis,mSystems,2022,"16S, breast cancer, breast tissue, functional metagenome, microbiome, transcriptome",Experiment 1,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,Healthy (H),Prediagnostic (PD),Samples donated prior to breast cancer diagnosis,49,15,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3b,29 October 2023,OdigiriGreat,"OdigiriGreat,ChiomaBlessing,WikiWorks",Differentially abundant taxa in Prediagnostic group versus Healthy group,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Caldimonas,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.",3379134|1224|28216|80840|2975441|196013;3384189|32066|203490|203491|203492|848;3379134|1224|1236|91347|1903409|53335;1783272|1239|186801|3082720|186804|1501226;3379134|1224|28211|204457|41297|13687;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301|1306,Complete,ChiomaBlessing
bsdb:35642922/1/2,35642922,"cross-sectional observational, not case-control",35642922,10.1128/msystems.01489-21,NA,"Hoskinson C., Zheng K., Gabel J., Kump A., German R., Podicheti R., Marino N. , Stiemsma L.T.",Composition and Functional Potential of the Human Mammary Microbiota Prior to and Following Breast Tumor Diagnosis,mSystems,2022,"16S, breast cancer, breast tissue, functional metagenome, microbiome, transcriptome",Experiment 1,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,Healthy (H),Prediagnostic (PD),Samples donated prior to breast cancer diagnosis,49,15,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3b,29 October 2023,OdigiriGreat,"OdigiriGreat,ChiomaBlessing,WikiWorks",Differentially abundant taxa in Prediagnostic group versus Healthy group,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,1783272|201174|1760|85007|1653|1716,Complete,ChiomaBlessing
bsdb:35642922/2/1,35642922,"cross-sectional observational, not case-control",35642922,10.1128/msystems.01489-21,NA,"Hoskinson C., Zheng K., Gabel J., Kump A., German R., Podicheti R., Marino N. , Stiemsma L.T.",Composition and Functional Potential of the Human Mammary Microbiota Prior to and Following Breast Tumor Diagnosis,mSystems,2022,"16S, breast cancer, breast tissue, functional metagenome, microbiome, transcriptome",Experiment 2,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,Healthy (H),Adjacent normal (AN),samples donated after breast cancer diagnosis (AN),49,49,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3c,29 October 2023,OdigiriGreat,"OdigiriGreat,ChiomaBlessing,WikiWorks",Differentially abundant taxa in Adjacent normal group versus Healthy group,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes|s__Alcaligenes sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Atopostipes|s__Atopostipes sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Duganella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum|s__Herbaspirillum sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Oceanobacillus|s__Oceanobacillus sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Pseudogracilibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae|g__Tissierella|s__Tissierella sp.",3379134|1224|28216|80840|506|507|512;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|91061|186826|186828|292480|1872652;1783272|201174|1760|85007|1653|1716;3379134|1224|28216|80840|75682|75654;1783272|1239|91061|186826|81852|1350|35783;3379134|1224|28216|80840|75682|963|1890675;3379134|1224|1236|91347|543|570;1783272|1239|91061|1385|186817|182709|1871622;3379134|1224|1236|91347|1903414|583;1783272|1239|91061|1385|186817|1494958;3379134|1224|1236|72274|135621|286|306;1783272|1239|1737404|1737405|1737406|41273|41274,Complete,ChiomaBlessing
bsdb:35642922/2/2,35642922,"cross-sectional observational, not case-control",35642922,10.1128/msystems.01489-21,NA,"Hoskinson C., Zheng K., Gabel J., Kump A., German R., Podicheti R., Marino N. , Stiemsma L.T.",Composition and Functional Potential of the Human Mammary Microbiota Prior to and Following Breast Tumor Diagnosis,mSystems,2022,"16S, breast cancer, breast tissue, functional metagenome, microbiome, transcriptome",Experiment 2,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,Healthy (H),Adjacent normal (AN),samples donated after breast cancer diagnosis (AN),49,49,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3c,29 October 2023,OdigiriGreat,"OdigiriGreat,ChiomaBlessing,WikiWorks",Differentially abundant taxa in Adjacent normal group versus Healthy group,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Brochothrix,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium|s__Carnobacterium sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chitinibacteraceae|g__Iodobacter|s__Iodobacter sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus",3379134|1224|1236|2887326|468|469|472;1783272|201174|1760|85006|1268|1663;3379134|976|200643|171549|815|816;3379134|1224|28211|356|41294|374;1783272|1239|91061|1385|186820|2755;1783272|1239|91061|186826|186828|2747|48221;1783272|201174|1760|85007|1653|1716|1720;1783272|201174|1760|85009|31957|1912216;3379134|1224|28216|206351|2897177|32014|1915058;1783272|1239|91061|186826|1300|1357;3379134|1224|1236|135623|641|657;3379134|1224|1236|72274|135621|286|306;1783272|201174|84995|84996|84997|42255;1783272|1239|186801|186802|216572|1263;3379134|1224|1236|91347|1903411|613;1783272|1239|91061|1385|90964|1279|29387;1783272|1239|91061|186826|81852|2737,Complete,ChiomaBlessing
bsdb:35642922/3/1,35642922,"cross-sectional observational, not case-control",35642922,10.1128/msystems.01489-21,NA,"Hoskinson C., Zheng K., Gabel J., Kump A., German R., Podicheti R., Marino N. , Stiemsma L.T.",Composition and Functional Potential of the Human Mammary Microbiota Prior to and Following Breast Tumor Diagnosis,mSystems,2022,"16S, breast cancer, breast tissue, functional metagenome, microbiome, transcriptome",Experiment 3,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,Healthy (H),Tumor (T),Samples donated after breast cancer diagnosis (tumor),49,46,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3d,29 October 2023,OdigiriGreat,"OdigiriGreat,ChiomaBlessing,WikiWorks",Differentially abundant taxa in Tumor group versus Healthy group,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum|s__Herbaspirillum sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Pseudogracilibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus sp.",1783272|1239|1737404|1737405|1570339|165779;1783272|1239|91061|186826|81852|1350|35783;3379134|1224|28216|80840|75682|963|1890675;1783272|1239|91061|1385|186817|1494958;3379134|1224|1236|72274|135621|286|306;1783272|201174|1760|85007|85025|1827;1783272|1239|91061|1385|90964|1279|29387,Complete,ChiomaBlessing
bsdb:35642922/3/2,35642922,"cross-sectional observational, not case-control",35642922,10.1128/msystems.01489-21,NA,"Hoskinson C., Zheng K., Gabel J., Kump A., German R., Podicheti R., Marino N. , Stiemsma L.T.",Composition and Functional Potential of the Human Mammary Microbiota Prior to and Following Breast Tumor Diagnosis,mSystems,2022,"16S, breast cancer, breast tissue, functional metagenome, microbiome, transcriptome",Experiment 3,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,Healthy (H),Tumor (T),Samples donated after breast cancer diagnosis (tumor),49,46,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3d,29 October 2023,OdigiriGreat,"OdigiriGreat,ChiomaBlessing,WikiWorks",Differentially abundant taxa in Tumor group versus Healthy group,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Brochothrix|s__Brochothrix sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium|s__Carnobacterium sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chitinibacteraceae|g__Iodobacter|s__Iodobacter sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Rubellimicrobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus sp.,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus",3379134|1224|1236|2887326|468|469;1783272|201174|1760|85006|1268|1663;3379134|976|200643|171549|815|816;3379134|200940|3031449|213115|194924|35832;3379134|1224|28211|356|41294|374|376;1783272|1239|91061|1385|186820|2755|1993875;1783272|1239|91061|186826|186828|2747|48221;1783272|201174|1760|85007|1653|1716|1720;3379134|1224|28216|206351|2897177|32014|1915058;1783272|1239|91061|186826|1300|1357;1783272|201174|1760|85007|2805586|1847725;3379134|976|200643|171549|2005473;3379134|1224|1236|135623|641|657;3379134|1224|1236|72274|135621|286|306;3379134|1224|28211|204455|2854170|295418;3379134|1224|1236|91347|1903411|613;1783272|1239|91061|1385|90964|1279|29387;3384194|1297|188787|68933|188786|270;1783272|1239|91061|186826|81852|2737,Complete,ChiomaBlessing
bsdb:35642922/4/NA,35642922,"cross-sectional observational, not case-control",35642922,10.1128/msystems.01489-21,NA,"Hoskinson C., Zheng K., Gabel J., Kump A., German R., Podicheti R., Marino N. , Stiemsma L.T.",Composition and Functional Potential of the Human Mammary Microbiota Prior to and Following Breast Tumor Diagnosis,mSystems,2022,"16S, breast cancer, breast tissue, functional metagenome, microbiome, transcriptome",Experiment 4,United States of America,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,Prediagnostic (PD),Tumor (T),Samples donated after breast cancer diagnosis (tumor),15,46,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,unchanged,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:35643931/1/1,35643931,"cross-sectional observational, not case-control",35643931,https://doi.org/10.1038/s41598-022-12970-3,NA,"Ueckermann V., Lebre P., Geldenhuys J., Hoosien E., Cowan D., van Rensburg L.J. , Ehlers M.",The lung microbiome in HIV-positive patients with active pulmonary tuberculosis,Scientific reports,2022,NA,Experiment 1,South Africa,Homo sapiens,Sputum,UBERON:0007311,Pulmonary tuberculosis,EFO:1000049,Human Immunodeficiency Virus (HIV) positive control cohort,Human Immunodeficiency Virus (HIV) positive (Tuberculosis cohort),HIV-positive with pneumonia and Tuberculosis (TB) cultures positive.,20,20,6 weeks,16S,34,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 1,Supplementary File 3,4 November 2024,AishatBolarinwa,"AishatBolarinwa,MyleeeA,WikiWorks",Differential abundance analysis of the genera in HIV positive (Tuberculosis cohort) and HIV-positive control cohort (sputum (SPU).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",3379134|1224|28216|80840|506|222;3379134|1224|1236|2887326|468|469;1783272|201174|1760|85007|1762|1763;3379134|1224|1236|72274|135621|286;3379134|1224|1236|135614|32033|40323,Complete,Svetlana up
bsdb:35643931/1/2,35643931,"cross-sectional observational, not case-control",35643931,https://doi.org/10.1038/s41598-022-12970-3,NA,"Ueckermann V., Lebre P., Geldenhuys J., Hoosien E., Cowan D., van Rensburg L.J. , Ehlers M.",The lung microbiome in HIV-positive patients with active pulmonary tuberculosis,Scientific reports,2022,NA,Experiment 1,South Africa,Homo sapiens,Sputum,UBERON:0007311,Pulmonary tuberculosis,EFO:1000049,Human Immunodeficiency Virus (HIV) positive control cohort,Human Immunodeficiency Virus (HIV) positive (Tuberculosis cohort),HIV-positive with pneumonia and Tuberculosis (TB) cultures positive.,20,20,6 weeks,16S,34,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 2,Supplementary File 3,4 November 2024,AishatBolarinwa,"AishatBolarinwa,MyleeeA,WikiWorks",Differential abundance analysis of the genera in HIV positive (Tuberculosis cohort) and HIV-positive control cohort (sputum (SPU).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",1783272|1239|186801|3082720|3118655|44259;3379134|1224|1236|135625|712|724;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|206351|481|482,Complete,Svetlana up
bsdb:35643931/2/1,35643931,"cross-sectional observational, not case-control",35643931,https://doi.org/10.1038/s41598-022-12970-3,NA,"Ueckermann V., Lebre P., Geldenhuys J., Hoosien E., Cowan D., van Rensburg L.J. , Ehlers M.",The lung microbiome in HIV-positive patients with active pulmonary tuberculosis,Scientific reports,2022,NA,Experiment 2,South Africa,Homo sapiens,Sputum,UBERON:0007311,Pulmonary tuberculosis,EFO:1000049,HIV positive Control cohort,HIV positive with Pneumonia,Patients who were HIV-positive with pneumonia but TB cultures negative (“Pneumonia” cohort),20,31,6 weeks,16S,34,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 1,Supplementary File 3,5 November 2024,AishatBolarinwa,"AishatBolarinwa,MyleeeA,WikiWorks",Differential abundance analysis of the genera in HIV positive (Pneumonia cohort) and HIV-positive control cohort (sputum (SPU).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",3379134|1224|28216|80840|506|222;3379134|1224|1236|2887326|468|469;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85007|1762|1763;3379134|1224|1236|72274|135621|286;3379134|1224|1236|135614|32033|40323,Complete,Svetlana up
bsdb:35643931/3/1,35643931,"cross-sectional observational, not case-control",35643931,https://doi.org/10.1038/s41598-022-12970-3,NA,"Ueckermann V., Lebre P., Geldenhuys J., Hoosien E., Cowan D., van Rensburg L.J. , Ehlers M.",The lung microbiome in HIV-positive patients with active pulmonary tuberculosis,Scientific reports,2022,NA,Experiment 3,South Africa,Homo sapiens,Bronchoalveolar duct junction,UBERON:0004903,Pulmonary tuberculosis,EFO:1000049,HIV positive with Pneumonia,HIV positive (Tuberculosis cohort),Patients who were HIV-positive with pneumonia and Tuberculosis (TB) cultures positive. Broncho-alveolar lavage fluid (BALF) were gotten.,31,20,6 weeks,16S,34,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 1,Supplementary File 4,5 November 2024,AishatBolarinwa,"AishatBolarinwa,MyleeeA,KateRasheed,WikiWorks",Differential abundance analysis of the genera in HIV positive (Pneumonia cohort) and HIV-positive TB cohort (BALF).,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,3379134|1224|1236|135614|32033|40323,Complete,Svetlana up
bsdb:35643931/3/2,35643931,"cross-sectional observational, not case-control",35643931,https://doi.org/10.1038/s41598-022-12970-3,NA,"Ueckermann V., Lebre P., Geldenhuys J., Hoosien E., Cowan D., van Rensburg L.J. , Ehlers M.",The lung microbiome in HIV-positive patients with active pulmonary tuberculosis,Scientific reports,2022,NA,Experiment 3,South Africa,Homo sapiens,Bronchoalveolar duct junction,UBERON:0004903,Pulmonary tuberculosis,EFO:1000049,HIV positive with Pneumonia,HIV positive (Tuberculosis cohort),Patients who were HIV-positive with pneumonia and Tuberculosis (TB) cultures positive. Broncho-alveolar lavage fluid (BALF) were gotten.,31,20,6 weeks,16S,34,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 2,Supplementary File 4,13 November 2024,MyleeeA,"MyleeeA,KateRasheed,WikiWorks",Differential abundance analysis of the genera in HIV positive (Pneumonia cohort) and HIV-positive TB cohort (BALF).,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|201174|1760|85007|1653|1716;1783272|1239|909932|1843489|31977|39948;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:35645785/1/1,35645785,case-control,35645785,10.3389/fnagi.2022.881872,NA,"Lubomski M., Xu X., Holmes A.J., Muller S., Yang J.Y.H., Davis R.L. , Sue C.M.",Nutritional Intake and Gut Microbiome Composition Predict Parkinson's Disease,Frontiers in aging neuroscience,2022,"Parkinson’s disease, biomarker, dysbiosis, gastrointestinal microbiome, gut microbiota, medication, prediction model",Experiment 1,Australia,Homo sapiens,"Feces,Blood","UBERON:0001988,UBERON:0000178",Parkinson's disease,MONDO:0005180,Healthy controls,Participants with Parkinson's Disease,Patients with a clinical diagnosis of idiopathic PD according to the UK Parkinson’s Disease Society Brain Bank Diagnostic Criteria,81,103,1 month,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,unchanged,NA,NA,Signature 1,Table 3,15 March 2024,Assel,"Assel,WikiWorks",Gastrointestinal microbiota compositional differences between Parkinson’s Disease patients and Household Controls.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea|s__Candidatus Soleaferrea sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.",1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802|1470353|2856521;1783272|1239|186801|186802|216572|216851|1946507;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|216572|1263|41978,Complete,Peace Sandy
bsdb:35645785/1/2,35645785,case-control,35645785,10.3389/fnagi.2022.881872,NA,"Lubomski M., Xu X., Holmes A.J., Muller S., Yang J.Y.H., Davis R.L. , Sue C.M.",Nutritional Intake and Gut Microbiome Composition Predict Parkinson's Disease,Frontiers in aging neuroscience,2022,"Parkinson’s disease, biomarker, dysbiosis, gastrointestinal microbiome, gut microbiota, medication, prediction model",Experiment 1,Australia,Homo sapiens,"Feces,Blood","UBERON:0001988,UBERON:0000178",Parkinson's disease,MONDO:0005180,Healthy controls,Participants with Parkinson's Disease,Patients with a clinical diagnosis of idiopathic PD according to the UK Parkinson’s Disease Society Brain Bank Diagnostic Criteria,81,103,1 month,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,unchanged,NA,NA,Signature 2,Table 3,15 March 2024,Assel,"Assel,Ayibatari,WikiWorks",Gastrointestinal microbiota compositional differences between Parkinson’s Disease patients and Household Controls.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium ND3006,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|186802|3085642|580596;1783272|1239|526524|526525|128827|2049044;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|1410629;1783272|1239|186801|186802|216572|1263|438033;1783272|1239|186801|186802|186806|1730|39497,Complete,Peace Sandy
bsdb:35656540/1/1,35656540,time series / longitudinal observational,35656540,10.3389/fnagi.2022.875261,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/,"Lubomski M., Xu X., Holmes A.J., Muller S., Yang J.Y.H., Davis R.L. , Sue C.M.",The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies,Frontiers in aging neuroscience,2022,"Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression",Experiment 1,Australia,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Household Control (HC) at t=0 to t=12,Parkinson's disease (PD) patients at t=0 to t=12,Parkinson disease patients on existing therapy regimes at t=0 to t=12,74,74,1 month,16S,34,Illumina,centered log-ratio,T-Test,0.01,TRUE,NA,region of residence,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 2B,13 March 2024,Bolanle,"Bolanle,Fiddyhamma,WikiWorks","Volcano plots representing abundance differences (fold change) of different taxa between HC and PD patients at t = 0, t = 6, and t = 12 months. Statistically significant [–log(p) > 3; fold change > ± 1.3] compositional differences at the family levels (represented by red dots) were apparent and indicative of a PD-related GM composition.",increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,1783272|1239|91061|186826|33958,Complete,Svetlana up
bsdb:35656540/1/2,35656540,time series / longitudinal observational,35656540,10.3389/fnagi.2022.875261,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/,"Lubomski M., Xu X., Holmes A.J., Muller S., Yang J.Y.H., Davis R.L. , Sue C.M.",The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies,Frontiers in aging neuroscience,2022,"Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression",Experiment 1,Australia,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Household Control (HC) at t=0 to t=12,Parkinson's disease (PD) patients at t=0 to t=12,Parkinson disease patients on existing therapy regimes at t=0 to t=12,74,74,1 month,16S,34,Illumina,centered log-ratio,T-Test,0.01,TRUE,NA,region of residence,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Figure 2B,23 January 2025,Fiddyhamma,"Fiddyhamma,WikiWorks","Volcano plots representing abundance differences (fold change) of different taxa between HC and PD patients at t = 0, t = 6, and t = 12 months. Statistically significant [–log(p) > 3; fold change > ± 1.3] compositional differences at the family levels (represented by red dots) were apparent and indicative of a PD-related GM composition.",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,1783272|1239|186801|186802|3085642,Complete,Svetlana up
bsdb:35656540/3/1,35656540,time series / longitudinal observational,35656540,10.3389/fnagi.2022.875261,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/,"Lubomski M., Xu X., Holmes A.J., Muller S., Yang J.Y.H., Davis R.L. , Sue C.M.",The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies,Frontiers in aging neuroscience,2022,"Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression",Experiment 3,Australia,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Patients with Slow progressing Parkinson's disease  at t=0,Patients with Faster progressing Parkinson's disease  at t=0,Patients with faster progressing parkinson's disease over a 12 month period  at t=0,40,34,1 month,16S,34,Illumina,centered log-ratio,T-Test,0.01,TRUE,NA,region of residence,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,27 January 2025,Fiddyhamma,"Fiddyhamma,WikiWorks",Differential abundance of taxa between faster progressing and slower progressing PD patients within 12 months at t=0 to t=12 (genus taxonomic level),decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,3379134|976|200643|171549|2005519|397864,Complete,Svetlana up
bsdb:35656540/4/1,35656540,time series / longitudinal observational,35656540,10.3389/fnagi.2022.875261,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/,"Lubomski M., Xu X., Holmes A.J., Muller S., Yang J.Y.H., Davis R.L. , Sue C.M.",The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies,Frontiers in aging neuroscience,2022,"Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression",Experiment 4,Australia,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Levodopa-Carbidopa Intestinal Gel (LCIG) DAT patients (t = 0 to t = 6),Deep Brain Stimulation DAT patients (t = 0 to t = 6),Deep Brain Stimulation DAT patients after initiation of DBS therapy,10,9,1 month,16S,34,Illumina,centered log-ratio,T-Test,0.01,TRUE,NA,region of residence,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 7,30 January 2025,Fiddyhamma,"Fiddyhamma,WikiWorks",Results across genus taxonomic rank for DBS and LCIG participants shows the most differentially abundant taxa after the initiation of DBS therapy (t = 0 to t = 6),increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:35656540/5/3,35656540,time series / longitudinal observational,35656540,10.3389/fnagi.2022.875261,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/,"Lubomski M., Xu X., Holmes A.J., Muller S., Yang J.Y.H., Davis R.L. , Sue C.M.",The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies,Frontiers in aging neuroscience,2022,"Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression",Experiment 5,Australia,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Levodopa-Carbidopa Intestinal Gel (LCIG) DAT patients,Deep Brain Stimulation DAT patients,Deep Brain Stimulation DAT patients after initiation of DBS therapy,10,9,1 month,16S,34,Illumina,centered log-ratio,T-Test,0.01,TRUE,NA,region of residence,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 3,Figure 7,30 January 2025,Fiddyhamma,"Fiddyhamma,WikiWorks",Results across family taxonomic rank for DBS and LCIG participants shows the most differentially abundant taxa after the initiation of DBS therapy (t = 0 to t = 12).,increased,"k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae",3366610|28890|183925|2158|2159;1783272|1239|91061|1385|186817;3379134|203691|203692|136|137,Complete,Svetlana up
bsdb:35656540/6/1,35656540,time series / longitudinal observational,35656540,10.3389/fnagi.2022.875261,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/,"Lubomski M., Xu X., Holmes A.J., Muller S., Yang J.Y.H., Davis R.L. , Sue C.M.",The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies,Frontiers in aging neuroscience,2022,"Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression",Experiment 6,Australia,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Levodopa-Carbidopa Intestinal Gel (LCIG) DAT patients  (t = 0 to t = 12).,Deep Brain Stimulation DAT patients (t = 0 to t = 12).,Deep Brain Stimulation DAT patients after initiation of DBS therapy,10,9,1 month,16S,34,Illumina,centered log-ratio,T-Test,0.01,TRUE,NA,region of residence,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 7,18 March 2024,Bolanle,"Bolanle,Fiddyhamma,WikiWorks",Results across genus taxonomic rank for DBS and LCIG participants shows the most differentially abundant taxa after the initiation of DBS therapy (t = 0 to t = 12).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalicoccus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella",3379134|976|200643|171549|171552|838;3366610|28890|183925|2158|2159|2172;3379134|203691|203692|136|2845253|157;1783272|1239|91061|1385|186817|1386;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|91347|543|544;1783272|1239|526524|526525|128827|1573536;3379134|1224|1236|91347|1903414|581,Complete,Svetlana up
bsdb:35656540/6/3,35656540,time series / longitudinal observational,35656540,10.3389/fnagi.2022.875261,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/,"Lubomski M., Xu X., Holmes A.J., Muller S., Yang J.Y.H., Davis R.L. , Sue C.M.",The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies,Frontiers in aging neuroscience,2022,"Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression",Experiment 6,Australia,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Levodopa-Carbidopa Intestinal Gel (LCIG) DAT patients  (t = 0 to t = 12).,Deep Brain Stimulation DAT patients (t = 0 to t = 12).,Deep Brain Stimulation DAT patients after initiation of DBS therapy,10,9,1 month,16S,34,Illumina,centered log-ratio,T-Test,0.01,TRUE,NA,region of residence,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 3,Figure 7,18 March 2024,Bolanle,"Bolanle,Fiddyhamma,WikiWorks",Results across genus taxonomic rank for DBS and LCIG participants shows the most differentially abundant taxa after the initiation of DBS therapy (t = 0 to t = 12).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hespellia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor",1783272|1239|186801|3085636|186803|241189;1783272|1239|186801|186802|216572|258514;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|186802|404402;1783272|1239|186801|186802|216572|946234,Complete,Svetlana up
bsdb:35656540/7/1,35656540,time series / longitudinal observational,35656540,10.3389/fnagi.2022.875261,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/,"Lubomski M., Xu X., Holmes A.J., Muller S., Yang J.Y.H., Davis R.L. , Sue C.M.",The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies,Frontiers in aging neuroscience,2022,"Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression",Experiment 7,Australia,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Levodopa-Carbidopa Intestinal Gel (LCIG) DAT patients (t = 0 to t = 6),Deep Brain Stimulation DAT patients (t = 0 to t = 6),Deep Brain Stimulation DAT patients in response to LCIG therapy initiation and continuation (t=0 to t=6),10,9,1 month,16S,34,Illumina,centered log-ratio,T-Test,0.01,TRUE,NA,region of residence,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,figure 7,16 March 2024,Bolanle,"Bolanle,Fiddyhamma,WikiWorks",The most differentially abundant taxa after the initiation of LCIG therapy at the genus level over the (t = 0 to t = 6) interval.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,1783272|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:35656540/9/1,35656540,time series / longitudinal observational,35656540,10.3389/fnagi.2022.875261,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/,"Lubomski M., Xu X., Holmes A.J., Muller S., Yang J.Y.H., Davis R.L. , Sue C.M.",The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies,Frontiers in aging neuroscience,2022,"Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression",Experiment 9,Australia,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Levodopa-Carbidopa Intestinal Gel (LCIG) DAT patients (t = 0 to t = 6),Deep Brain Stimulation DAT patients (t = 0 to t = 6),Deep Brain Stimulation DAT patients in response to LCIG therapy initiation and continuation (t=0 to t=6),10,9,1 month,16S,34,Illumina,centered log-ratio,T-Test,0.01,TRUE,NA,region of residence,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 7,16 March 2024,Bolanle,"Bolanle,Fiddyhamma,WikiWorks",The most differentially abundant taxa after the initiation of LCIG therapy at the family level over the (t = 0 to t = 6) interval.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,3379134|976|200643|171549|171552,Complete,Svetlana up
bsdb:35656540/9/2,35656540,time series / longitudinal observational,35656540,10.3389/fnagi.2022.875261,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/,"Lubomski M., Xu X., Holmes A.J., Muller S., Yang J.Y.H., Davis R.L. , Sue C.M.",The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies,Frontiers in aging neuroscience,2022,"Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression",Experiment 9,Australia,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Levodopa-Carbidopa Intestinal Gel (LCIG) DAT patients (t = 0 to t = 6),Deep Brain Stimulation DAT patients (t = 0 to t = 6),Deep Brain Stimulation DAT patients in response to LCIG therapy initiation and continuation (t=0 to t=6),10,9,1 month,16S,34,Illumina,centered log-ratio,T-Test,0.01,TRUE,NA,region of residence,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 7,16 March 2024,Bolanle,"Bolanle,Fiddyhamma,WikiWorks",The most differentially abundant taxa after the initiation of LCIG therapy at the family level over the (t = 0 to t = 6) interval.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hespellia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania",1783272|1239|186801|186802|216572|258514;1783272|201174|84998|1643822|1643826|84111;1783272|201174|84998|1643822|1643826|644652;1783272|1239|186801|3085636|186803|241189;1783272|1239|526524|526525|128827|61170,Complete,Svetlana up
bsdb:35656540/10/1,35656540,time series / longitudinal observational,35656540,10.3389/fnagi.2022.875261,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/,"Lubomski M., Xu X., Holmes A.J., Muller S., Yang J.Y.H., Davis R.L. , Sue C.M.",The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies,Frontiers in aging neuroscience,2022,"Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression",Experiment 10,Australia,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Levodopa-Carbidopa Intestinal Gel (LCIG) DAT patients (t = 0 to t = 12),Deep Brain Stimulation DAT patients (t = 0 to t = 12),Deep Brain Stimulation DAT patients in response to LCIG therapy initiation and continuation (t=0 to t=12),10,9,1 month,16S,34,Illumina,centered log-ratio,T-Test,0.01,TRUE,NA,region of residence,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 7,16 March 2024,Bolanle,"Bolanle,Fiddyhamma,WikiWorks",The most differentially abundant taxa after the initiation of LCIG therapy at the family level over the (t = 0 to t = 12) interval.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|91061|1385|186817|1386;3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:35656540/11/1,35656540,time series / longitudinal observational,35656540,10.3389/fnagi.2022.875261,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/,"Lubomski M., Xu X., Holmes A.J., Muller S., Yang J.Y.H., Davis R.L. , Sue C.M.",The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies,Frontiers in aging neuroscience,2022,"Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression",Experiment 11,Australia,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Household Control (HC) at (t=0),Parkinson's disease (PD) patients at (t=0),Parkinson disease patients on existing therapy regimes at (t=0),74,74,1 month,16S,34,Illumina,centered log-ratio,T-Test,0.01,TRUE,NA,region of residence,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 2B,23 January 2025,Fiddyhamma,"Fiddyhamma,Svetlana up,WikiWorks","Volcano plots representing abundance differences (fold change) of different taxa between HC and PD patients at t = 0, t = 6, and t = 12 months. Statistically significant [–log(p) > 3; fold change > ± 1.3] compositional differences at the genus and family levels (represented by red dots) were apparent and indicative of a PD-related GM composition. Genus taxonomic level, at the t = 0",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:56,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter",1783272|1239|186801|186802|3085642|580596;1783272|1239|1263031;1783272|1239|186801|3085636|186803|1407607,Complete,Svetlana up
bsdb:35656540/12/1,35656540,time series / longitudinal observational,35656540,10.3389/fnagi.2022.875261,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/,"Lubomski M., Xu X., Holmes A.J., Muller S., Yang J.Y.H., Davis R.L. , Sue C.M.",The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies,Frontiers in aging neuroscience,2022,"Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression",Experiment 12,Australia,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Household Control (HC) at (t=6),Parkinson's disease (PD) patients at (t=6),Parkinson disease patients on existing therapy regimes at (t=6),74,74,1 month,16S,34,Illumina,centered log-ratio,T-Test,0.01,TRUE,NA,region of residence,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 2B,27 January 2025,Fiddyhamma,"Fiddyhamma,Svetlana up,WikiWorks","Volcano plots representing abundance differences (fold change) of different taxa between HC and PD patients at t = 0, t = 6, and t = 12 months. Statistically significant [–log(p) > 3; fold change > ± 1.3] compositional differences at the genus and family levels (represented by red dots) were apparent and indicative of a PD-related GM composition. Genus taxonomic level, at the t = 6",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:56,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|216572|216851;1783272|1239|1263031;1783272|1239|186801|3085636|186803|1407607,Complete,Svetlana up
bsdb:35656540/13/1,35656540,time series / longitudinal observational,35656540,10.3389/fnagi.2022.875261,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/,"Lubomski M., Xu X., Holmes A.J., Muller S., Yang J.Y.H., Davis R.L. , Sue C.M.",The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies,Frontiers in aging neuroscience,2022,"Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression",Experiment 13,Australia,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Household Control (HC) at (t=6),Parkinson's disease (PD) patients at (t=6),Parkinson disease patients on existing therapy regimes at (t=6),74,74,1 month,16S,34,Illumina,centered log-ratio,T-Test,0.01,TRUE,NA,region of residence,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 2B,27 January 2025,Fiddyhamma,"Fiddyhamma,WikiWorks","Volcano plots representing abundance differences (fold change) of different taxa between HC and PD patients at t = 0, t = 6, and t = 12 months. Statistically significant [–log(p) > 3; fold change > ± 1.3] compositional differences at the genus and family levels (represented by red dots) were apparent and indicative of a PD-related GM composition. Family taxonomic level, at the t = 6",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",1783272|1239|91061|186826|33958;3379134|1224|1236|91347|543,Complete,Svetlana up
bsdb:35656540/13/2,35656540,time series / longitudinal observational,35656540,10.3389/fnagi.2022.875261,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/,"Lubomski M., Xu X., Holmes A.J., Muller S., Yang J.Y.H., Davis R.L. , Sue C.M.",The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies,Frontiers in aging neuroscience,2022,"Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression",Experiment 13,Australia,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Household Control (HC) at (t=6),Parkinson's disease (PD) patients at (t=6),Parkinson disease patients on existing therapy regimes at (t=6),74,74,1 month,16S,34,Illumina,centered log-ratio,T-Test,0.01,TRUE,NA,region of residence,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Figure 2B,27 January 2025,Fiddyhamma,"Fiddyhamma,WikiWorks","Volcano plots representing abundance differences (fold change) of different taxa between HC and PD patients at t = 0, t = 6, and t = 12 months. Statistically significant [–log(p) > 3; fold change > ± 1.3] compositional differences at the genus and family levels (represented by red dots) were apparent and indicative of a PD-related GM composition. Family taxonomic level, at the t = 6",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,1783272|1239|186801|186802|3085642,Complete,Svetlana up
bsdb:35656540/14/1,35656540,time series / longitudinal observational,35656540,10.3389/fnagi.2022.875261,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/,"Lubomski M., Xu X., Holmes A.J., Muller S., Yang J.Y.H., Davis R.L. , Sue C.M.",The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies,Frontiers in aging neuroscience,2022,"Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression",Experiment 14,Australia,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Household Control (HC) at (t=12),Parkinson's disease (PD) patients at (t=12),Parkinson disease patients on existing therapy regimes at (t=12),74,74,1 month,16S,34,Illumina,centered log-ratio,T-Test,0.01,TRUE,NA,region of residence,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 2B,27 January 2025,Fiddyhamma,"Fiddyhamma,Svetlana up,WikiWorks","Volcano plots representing abundance differences (fold change) of different taxa between HC and PD patients at t = 0, t = 6, and t = 12 months. Statistically significant [–log(p) > 3; fold change > ± 1.3] compositional differences at the genus and family levels (represented by red dots) were apparent and indicative of a PD-related GM composition. Genus taxonomic level, at the t = 12",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter",1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|1407607,Complete,Svetlana up
bsdb:35657343/1/1,35657343,case-control,35657343,10.1002/ijc.34145,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9420782/,"Wu Z., Byrd D.A., Wan Y., Ansong D., Clegg-Lamptey J.N., Wiafe-Addai B., Edusei L., Adjei E., Titiloye N., Dedey F., Aitpillah F., Oppong J., Vanderpuye V., Osei-Bonsu E., Dagnall C.L., Jones K., Hutchinson A., Hicks B.D., Ahearn T.U., Shi J., Knight R., Biritwum R., Yarney J., Wiafe S., Awuah B., Nyarko K., Figueroa J.D., Sinha R., Garcia-Closas M., Brinton L.A. , Vogtmann E.","The oral microbiome and breast cancer and nonmalignant breast disease, and its relationship with the fecal microbiome in the Ghana Breast Health Study",International journal of cancer,2022,"Ghana, breast cancer, fecal microbiome, nonmalignant breast diseases, oral microbiome",Experiment 1,Ghana,Homo sapiens,Saliva,UBERON:0001836,Breast cancer,MONDO:0007254,Control,Breast Health Condition,Women with breast cancer cases,419,369,1 month,16S,4,Illumina,relative abundances,Logistic Regression,0.05,TRUE,NA,"age,geographic area","age,alcohol drinking,antibiotic exposure,body mass index,contraception,education level,family history of cancer,geographic area,smoking status",NA,increased,NA,NA,NA,increased,Signature 1,Suppl. Table S1,9 March 2024,Muqtadirat,"Muqtadirat,MyleeeA,WikiWorks",Genera with higher odds ratio in breast cancer cases in comparison with control,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. 1-8",1783272|1239|1737404|1737405|1570339|1161127;1783272|1239|1737404|1737405|1570339|543311;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|201174|1760|85004|31953|196081;3379134|976|200643|171549|2005525|195950;3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|838|1486937,Complete,NA
bsdb:35657343/2/1,35657343,case-control,35657343,10.1002/ijc.34145,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9420782/,"Wu Z., Byrd D.A., Wan Y., Ansong D., Clegg-Lamptey J.N., Wiafe-Addai B., Edusei L., Adjei E., Titiloye N., Dedey F., Aitpillah F., Oppong J., Vanderpuye V., Osei-Bonsu E., Dagnall C.L., Jones K., Hutchinson A., Hicks B.D., Ahearn T.U., Shi J., Knight R., Biritwum R., Yarney J., Wiafe S., Awuah B., Nyarko K., Figueroa J.D., Sinha R., Garcia-Closas M., Brinton L.A. , Vogtmann E.","The oral microbiome and breast cancer and nonmalignant breast disease, and its relationship with the fecal microbiome in the Ghana Breast Health Study",International journal of cancer,2022,"Ghana, breast cancer, fecal microbiome, nonmalignant breast diseases, oral microbiome",Experiment 2,Ghana,Homo sapiens,Saliva,UBERON:0001836,Breast cancer,MONDO:0007254,Control,Breast Health Condition,Women with non malignant cases,419,93,1 month,16S,4,Illumina,relative abundances,Logistic Regression,0.05,TRUE,NA,"age,geographic area","age,alcohol drinking,antibiotic exposure,body mass index,contraception,education level,family history of cancer,geographic area,smoking status",NA,increased,NA,NA,NA,increased,Signature 1,Suppl. Table S1,10 March 2024,Muqtadirat,"Muqtadirat,MyleeeA,WikiWorks",Genera with higher odds ratio in non malignant cases in comparison with control,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. 1-8",3379134|976|117743|200644|2762318|59735;1783272|1239|186801|3082720|543314|86331;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|201174|1760|85004|31953|196081;3379134|976|200643|171549|2005525|195950;3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|838|1486937,Complete,NA
bsdb:35657343/3/1,35657343,case-control,35657343,10.1002/ijc.34145,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9420782/,"Wu Z., Byrd D.A., Wan Y., Ansong D., Clegg-Lamptey J.N., Wiafe-Addai B., Edusei L., Adjei E., Titiloye N., Dedey F., Aitpillah F., Oppong J., Vanderpuye V., Osei-Bonsu E., Dagnall C.L., Jones K., Hutchinson A., Hicks B.D., Ahearn T.U., Shi J., Knight R., Biritwum R., Yarney J., Wiafe S., Awuah B., Nyarko K., Figueroa J.D., Sinha R., Garcia-Closas M., Brinton L.A. , Vogtmann E.","The oral microbiome and breast cancer and nonmalignant breast disease, and its relationship with the fecal microbiome in the Ghana Breast Health Study",International journal of cancer,2022,"Ghana, breast cancer, fecal microbiome, nonmalignant breast diseases, oral microbiome",Experiment 3,Ghana,Homo sapiens,Saliva,UBERON:0001836,Breast cancer,MONDO:0007254,Non malignant,Breast cancer,Women with breast cancer cases,93,369,1 month,16S,4,Illumina,relative abundances,Logistic Regression,0.05,TRUE,NA,"age,geographic area","age,alcohol drinking,antibiotic exposure,body mass index,contraception,education level,family history of cancer,geographic area,smoking status",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Suppl. Table S1,10 March 2024,Muqtadirat,"Muqtadirat,WikiWorks",Genera with higher odds ratio in breast cancer cases in comparison with non malignant cases,increased,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,1783272|1239|1737404|1737405|1570339|1161127,Complete,NA
bsdb:35675824/1/1,35675824,"cross-sectional observational, not case-control",35675824,https://doi.org/10.33073/pjm-2022-016,NA,"Zhao H., Yuan L., Zhu D., Sun B., Du J. , Wang J.",Alterations and Mechanism of Gut Microbiota in Graves' Disease and Hashimoto's Thyroiditis,Polish journal of microbiology,2022,"Graves’ disease, Hashimoto’s thyroiditis, autoimmune thyroid disease, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Hypothyroidism group (HT) + Normal,Graves’ disease/Hyperthyroidism (GD),Patients diagnosed with Graves’ disease(GD) also known as the Hyperthyroidism group,43,27,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2A,24 July 2025,Aleru Divine,Aleru Divine,LEfSe shows the greatest difference in abundance (taxa) between the three groups (LDA threshold > 3).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|1263;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;3379134|976|200643|171549|171552|838;3379134|1224|28216|80840|995019|577310,Complete,NA
bsdb:35675824/2/1,35675824,"cross-sectional observational, not case-control",35675824,https://doi.org/10.33073/pjm-2022-016,NA,"Zhao H., Yuan L., Zhu D., Sun B., Du J. , Wang J.",Alterations and Mechanism of Gut Microbiota in Graves' Disease and Hashimoto's Thyroiditis,Polish journal of microbiology,2022,"Graves’ disease, Hashimoto’s thyroiditis, autoimmune thyroid disease, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Hashimoto's thyroiditis,EFO:0003779,Graves’ disease/Hyperthyroidism (GD)+ Normal,Hypothyroidism group (HT),"Patients diagnosed with Hashimoto’s Thyroiditis, also known as the Hypothyroidism group (HT).",43,27,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2A,24 July 2025,Aleru Divine,Aleru Divine,LEfSe shows the greatest difference in abundance (taxa) between the three groups (LDA threshold > 3).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales",1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|186802|216572|258514;1783272|1239|91061|186826,Complete,NA
bsdb:35675824/3/1,35675824,"cross-sectional observational, not case-control",35675824,https://doi.org/10.33073/pjm-2022-016,NA,"Zhao H., Yuan L., Zhu D., Sun B., Du J. , Wang J.",Alterations and Mechanism of Gut Microbiota in Graves' Disease and Hashimoto's Thyroiditis,Polish journal of microbiology,2022,"Graves’ disease, Hashimoto’s thyroiditis, autoimmune thyroid disease, gut microbiota",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,"Graves disease,Hashimoto's thyroiditis","EFO:0004237,EFO:0003779",Normal,Graves’ disease/Hyperthyroidism (GD) + Hypothyroidism group (HT),"Patients diagnosed with Graves’ disease(GD), also known as the Hyperthyroidism group and patients with Hashimoto’s Thyroiditis, also known as the Hypothyroidism group (HT).",16,54,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2A,24 July 2025,Aleru Divine,Aleru Divine,LEfSe shows the greatest difference in abundance (taxa) between the three groups (LDA threshold > 3).,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",1783272|1239|909932;1783272|1239|909932|909929;1783272|1239|909932|909929|1843491|158846,Complete,NA
bsdb:35675824/4/1,35675824,"cross-sectional observational, not case-control",35675824,https://doi.org/10.33073/pjm-2022-016,NA,"Zhao H., Yuan L., Zhu D., Sun B., Du J. , Wang J.",Alterations and Mechanism of Gut Microbiota in Graves' Disease and Hashimoto's Thyroiditis,Polish journal of microbiology,2022,"Graves’ disease, Hashimoto’s thyroiditis, autoimmune thyroid disease, gut microbiota",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Normal,Graves’ disease/Hyperthyroidism (GD),Patients diagnosed with Graves’ disease(GD) also known as the Hyperthyroidism group,16,27,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2B,  2D, and 2F",24 July 2025,Aleru Divine,Aleru Divine,"The difference in microbiota between the GD group or HT groups and the healthy control group at the phylum level (B, C), at the family level (D, E), and at the genus level (F, G). *p < 0.05; ** p < 0.01; ***p < 0.001.",decreased,"k__Thermotogati|p__Deinococcota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",3384194|1297;1783272|1239|91061|1385|186817;1783272|201174|1760|85009|85015;3379134|976|117743|200644|49546;1783272|201174|1760|85006|85020;1783272|201174|1760|85007|1653;1783272|201174|1760|85006|85021;1783272|1239|909932|909929|1843491;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|3082720|186804,Complete,NA
bsdb:35675824/4/2,35675824,"cross-sectional observational, not case-control",35675824,https://doi.org/10.33073/pjm-2022-016,NA,"Zhao H., Yuan L., Zhu D., Sun B., Du J. , Wang J.",Alterations and Mechanism of Gut Microbiota in Graves' Disease and Hashimoto's Thyroiditis,Polish journal of microbiology,2022,"Graves’ disease, Hashimoto’s thyroiditis, autoimmune thyroid disease, gut microbiota",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Normal,Graves’ disease/Hyperthyroidism (GD),Patients diagnosed with Graves’ disease(GD) also known as the Hyperthyroidism group,16,27,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2B, 2D, and 2F",24 July 2025,Aleru Divine,Aleru Divine,"The difference in microbiota between the GD group or HT groups and the healthy control group at the phylum level (B, C), at the family level (D, E), and at the genus level (F, G). *p < 0.05; ** p < 0.01; ***p < 0.001.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Chloroflexota,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__Eubacteriales Family XIII. Incertae Sedis bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae",3379134|1224|28216|80840|506;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|200795;1783272|1239|186801|3082768|990719;1783272|1117;1783272|1239|526524|526525|128827;1783272|1239|186801|3082720|543314|2137877;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|3085636|186803|2316020|33038;1783272|201174|1760|85007|85025;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|186802|186807;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803;1783272|1117|3028117,Complete,NA
bsdb:35675824/5/1,35675824,"cross-sectional observational, not case-control",35675824,https://doi.org/10.33073/pjm-2022-016,NA,"Zhao H., Yuan L., Zhu D., Sun B., Du J. , Wang J.",Alterations and Mechanism of Gut Microbiota in Graves' Disease and Hashimoto's Thyroiditis,Polish journal of microbiology,2022,"Graves’ disease, Hashimoto’s thyroiditis, autoimmune thyroid disease, gut microbiota",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Hashimoto's thyroiditis,EFO:0003779,Normal,Hashimoto's thyroiditis/Hypothyroidism (GD),Patients diagnosed with Hashimoto's thyroiditis also known as the Hypothyroidism group (HT).,16,27,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2C, 2E, and 2G",24 July 2025,Aleru Divine,Aleru Divine,"The difference in microbiota between the GD group or HT groups and the healthy control group at the phylum level (B, C), at the family level (D, E), and at the genus level (F, G). *p < 0.05; ** p < 0.01; ***p < 0.001.",increased,"k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__Eubacteriales Family XIII. Incertae Sedis bacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",1783272|1117;1783272|1239|91061|186826|81852;1783272|1239|526524|526525|128827;1783272|201174|84998|84999|84107;1783272|1239|186801|3082720|543314|2137877;1783272|201174|1760|2037|2049;1783272|201174|1760|85006|1268;1783272|1117|3028117;1783272|1239|186801|3085636|1185407;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|186802|216572|1508657;1783272|201174|1760|2037|2049|1654;1783272|1239|526524|526525|2810280|3025755;1783272|201174|1760|85006|1268|32207,Complete,NA
bsdb:35675824/5/2,35675824,"cross-sectional observational, not case-control",35675824,https://doi.org/10.33073/pjm-2022-016,NA,"Zhao H., Yuan L., Zhu D., Sun B., Du J. , Wang J.",Alterations and Mechanism of Gut Microbiota in Graves' Disease and Hashimoto's Thyroiditis,Polish journal of microbiology,2022,"Graves’ disease, Hashimoto’s thyroiditis, autoimmune thyroid disease, gut microbiota",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Hashimoto's thyroiditis,EFO:0003779,Normal,Hashimoto's thyroiditis/Hypothyroidism (GD),Patients diagnosed with Hashimoto's thyroiditis also known as the Hypothyroidism group (HT).,16,27,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2C, 2E, and 2G",24 July 2025,Aleru Divine,Aleru Divine,"The difference in microbiota between the GD group or HT groups and the healthy control group at the phylum level (B, C), at the family level (D, E), and at the genus level (F, G). *p < 0.05; ** p < 0.01; ***p < 0.001.",decreased,"k__Bacillati|p__Chloroflexota,k__Thermotogati|p__Deinococcota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NC2004,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter",1783272|200795;3384194|1297;1783272|1239|186801|3082720|186804;1783272|1239|91061|1385|186817;1783272|1239|186801|186802;1783272|1239|909932|909929;1783272|201174|1760|85006|85021;1783272|201174|1760|85007|1653;1783272|201174|1760|85006|85020;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|3085636|186803|1410626;1783272|1239|186801|3082720|186804;1783272|1239|91061|1385|186817|1386;3379134|976|200643|171549|2005519|1348911,Complete,NA
bsdb:35681554/1/1,35681554,"case-control,laboratory experiment",35681554,10.3390/cancers14112573,NA,"Yu Y., Cai Y., Yang B., Xie S., Shen W., Wu Y., Sui Z., Cai J., Ni C. , Ye J.",High-Fat Diet Enhances the Liver Metastasis Potential of Colorectal Cancer through Microbiota Dysbiosis,Cancers,2022,"Desulfovibrio, colorectal cancer, high-fat diet, liver metastasis, microbiota dysbiosis, tumour microenvironment",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,High fat diet,EFO:0002757,Healthy controls,High fat diet,This refers to adult male Wistar rats and adult male BALB/c mice; who were fed with high fat diet.,7,7,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4C, 4D, 4E, 5G",23 March 2025,ShadeAkinremi,"ShadeAkinremi,KateRasheed",Comparison of fecal bacterial composition at the phylum and genus levels between rats subjected to eight weeks of high-fat diet treatment and healthy controls.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales",1783272|1239|186801|3085636|186803|1427378;3379134|976;1783272|1239|186801|3082768|990719|990721;3379134|200940|3031449|213115|194924|872;1783272|201174|84998|1643822|1643826|580024;3379134|29547|3031852|213849|72293|209;1783272|201174|84998|84999|1643824|133925;1783272|1239|186801|186802|216572|459786;3379134|1224;1783272|1239|186801|186802|216572|1263;1783272|1239;3379134|1224|1236|72274|135621|286;3379134|200940|3031449|213115,Complete,Svetlana up
bsdb:35681554/1/2,35681554,"case-control,laboratory experiment",35681554,10.3390/cancers14112573,NA,"Yu Y., Cai Y., Yang B., Xie S., Shen W., Wu Y., Sui Z., Cai J., Ni C. , Ye J.",High-Fat Diet Enhances the Liver Metastasis Potential of Colorectal Cancer through Microbiota Dysbiosis,Cancers,2022,"Desulfovibrio, colorectal cancer, high-fat diet, liver metastasis, microbiota dysbiosis, tumour microenvironment",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,High fat diet,EFO:0002757,Healthy controls,High fat diet,This refers to adult male Wistar rats and adult male BALB/c mice; who were fed with high fat diet.,7,7,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4E,24 March 2025,ShadeAkinremi,ShadeAkinremi,Comparison of fecal bacterial composition at the phylum and genus levels between rats subjected to eight weeks of high-fat diet treatment and healthy controls.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus",3379134|976|200643|171549|171552|838;1783272|1239|909932|1843489|31977;1783272|1239|186801|186802|216572|244127,Complete,Svetlana up
bsdb:35681554/2/1,35681554,"case-control,laboratory experiment",35681554,10.3390/cancers14112573,NA,"Yu Y., Cai Y., Yang B., Xie S., Shen W., Wu Y., Sui Z., Cai J., Ni C. , Ye J.",High-Fat Diet Enhances the Liver Metastasis Potential of Colorectal Cancer through Microbiota Dysbiosis,Cancers,2022,"Desulfovibrio, colorectal cancer, high-fat diet, liver metastasis, microbiota dysbiosis, tumour microenvironment",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Metastatic colorectal cancer,EFO:1001480,non-metastatic group of colorectal cancer,metastatic group of colorectal cancer,Colorectal cancer patients with liver metastases.,10,13,1 month,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5C,24 March 2025,ShadeAkinremi,ShadeAkinremi,Comparison of fecal bacterial composition at the phylum and genus levels between colorectal cancer patients with and without liver metastases.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",3379134|976|200643|171549|2005519|397864;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|204475;1783272|1239|186801|186802|216572|1263,Complete,Svetlana up
bsdb:35692191/1/1,35692191,"cross-sectional observational, not case-control",35692191,10.5217/ir.2021.00168,NA,"Shin S.Y., Kim Y., Kim W.S., Moon J.M., Lee K.M., Jung S.A., Park H., Huh E.Y., Kim B.C., Lee S.C. , Choi C.H.",Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease,Intestinal research,2023,"Biomarkers, Inflammatory bowel disease, Microbiota, Phenotype, Prognosis",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Healthy control individual,Ulcerative colitis patient,Patients diagnosed with ulcerative colitis from 3 different academic hospitals in Korea.,100,70,1 month,16S,4,Illumina,relative abundances,LEfSe,NA,FALSE,3,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 4a,24 November 2023,Yjung24,"Yjung24,Atrayees,WikiWorks","Taxa list according to linear discriminate analysis values determined from comparisons between HC and UC patients. HC, healthy control individuals; UC, ulcerative colitis.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus|s__Proteus vulgaris,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",1783272|201174|1760|85004|31953|1678|1689;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|2719313|1531;1783272|1239|186801|186802|216572|946234|292800;3379134|1224|1236|135625|712|724|729;1783272|1239|186801|3085636|186803|28050|39485;3379134|1224|1236|91347|1903414|583|585;1783272|1239|909932|1843489|31977|29465|39778;3379134|976|200643|171549|2005525|375288,Complete,Peace Sandy
bsdb:35692191/1/2,35692191,"cross-sectional observational, not case-control",35692191,10.5217/ir.2021.00168,NA,"Shin S.Y., Kim Y., Kim W.S., Moon J.M., Lee K.M., Jung S.A., Park H., Huh E.Y., Kim B.C., Lee S.C. , Choi C.H.",Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease,Intestinal research,2023,"Biomarkers, Inflammatory bowel disease, Microbiota, Phenotype, Prognosis",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Healthy control individual,Ulcerative colitis patient,Patients diagnosed with ulcerative colitis from 3 different academic hospitals in Korea.,100,70,1 month,16S,4,Illumina,relative abundances,LEfSe,NA,FALSE,3,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 4a,24 November 2023,Yjung24,"Yjung24,WikiWorks","Taxa list according to linear discriminate analysis values determined from comparisons between HC and UC patients. HC, healthy control individuals; UC, ulcerative colitis.",decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas rupellensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pullorum|s__Bifidobacterium pullorum subsp. gallinarum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum variabile,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter faecis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia|s__Senegalimassilia anaerobia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila",1783272|1239|909932|909929|1843491|158846|491921;3379134|976|200643|171549|171550|239759|28117;1783272|201174|1760|85004|31953|1678|1694;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|3085636|186803|189330|88431;3379134|976|200643|171549|2005525|375288|46503;1783272|201174|1760|85004|31953|1678|78448|78344;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|526524|526525|128827|1573535|1735;1783272|1239|186801|186802|216572|292632|214851;1783272|1239|186801|3085636|186803|2316020|592978;1783272|1239|91061|186826|33958|2767887|1623;1783272|201174|84998|84999|84107|1473205|1473216;3379134|74201|203494|48461|1647988|239934|239935,Complete,Peace Sandy
bsdb:35692191/2/1,35692191,"cross-sectional observational, not case-control",35692191,10.5217/ir.2021.00168,NA,"Shin S.Y., Kim Y., Kim W.S., Moon J.M., Lee K.M., Jung S.A., Park H., Huh E.Y., Kim B.C., Lee S.C. , Choi C.H.",Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease,Intestinal research,2023,"Biomarkers, Inflammatory bowel disease, Microbiota, Phenotype, Prognosis",Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Healthy control individual,Crohn's disease patient,Patients diagnosed with Crohn's disease from 3 different academic hospitals in Korea.,100,39,1 month,16S,4,Illumina,relative abundances,LEfSe,NA,FALSE,3,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 4b,24 November 2023,Yjung24,"Yjung24,Peace Sandy,WikiWorks","Taxa list according to linear discriminate analysis values determined from comparisons between HC and CD patients. HC, healthy control individuals; CD, Crohn’s disease.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas umbilicata,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc lactis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas fragi,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gallolyticus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",1783272|201174|1760|85004|31953|1678|1689;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|3085636|186803|2719313|1531;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|3085636|186803|2005355|1912855;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|91061|186826|33958|1243|1246;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|909932|1843489|31977|906|907;3379134|1224|1236|72274|135621|286|296;1783272|1239|91061|186826|1300|1301|315405;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|909932|1843489|31977|29465|39778,Complete,Peace Sandy
bsdb:35692191/2/2,35692191,"cross-sectional observational, not case-control",35692191,10.5217/ir.2021.00168,NA,"Shin S.Y., Kim Y., Kim W.S., Moon J.M., Lee K.M., Jung S.A., Park H., Huh E.Y., Kim B.C., Lee S.C. , Choi C.H.",Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease,Intestinal research,2023,"Biomarkers, Inflammatory bowel disease, Microbiota, Phenotype, Prognosis",Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Healthy control individual,Crohn's disease patient,Patients diagnosed with Crohn's disease from 3 different academic hospitals in Korea.,100,39,1 month,16S,4,Illumina,relative abundances,LEfSe,NA,FALSE,3,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 4b,24 November 2023,Yjung24,"Yjung24,Peace Sandy,WikiWorks","Taxa list according to linear discriminate analysis values determined from comparisons between HC and CD patients. HC, healthy control individuals; CD, Crohn’s disease.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pullorum|s__Bifidobacterium pullorum subsp. gallinarum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter faecis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia cecicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum variabile,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum",3379134|976|200643|171549|171550|239759|28117;1783272|201174|1760|85004|31953|1678|1694;1783272|201174|1760|85004|31953|1678|78448|78344;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|186802|216572|216851|853;1783272|1239|526524|526525|128827|1573535|1735;1783272|1239|186801|3085636|186803|2316020|592978;3379134|976|200643|171549|2005525|375288|46503;1783272|1239|186801|3082720|186804|1501226|1776391;1783272|1239|186801|3085636|186803|841|842;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|292632|214851;1783272|1239|186801|186802|216572|39492,Complete,Peace Sandy
bsdb:35692191/3/1,35692191,"cross-sectional observational, not case-control",35692191,10.5217/ir.2021.00168,NA,"Shin S.Y., Kim Y., Kim W.S., Moon J.M., Lee K.M., Jung S.A., Park H., Huh E.Y., Kim B.C., Lee S.C. , Choi C.H.",Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease,Intestinal research,2023,"Biomarkers, Inflammatory bowel disease, Microbiota, Phenotype, Prognosis",Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Patients with mild ulcerative colitis,Patients with moderate to severe ulcerative colitis,"patients diagnosed with ulcerative colitis (UC) from 3 different academic hospitals in Korea categorized as moderate to severe forms of UC. The severity of disease was assessed by the Mayo score for UC. Severity was estimated at the time of fecal sampling, and the average follow-up period was 8.0 ± 1.3 years.",37,18,1 month,16S,4,Illumina,relative abundances,LEfSe,NA,FALSE,3,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 5a,24 November 2023,Yjung24,"Yjung24,WikiWorks",Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in ulcerative colitis (UC) patients. Comparisons between moderate to severe and mild UC (A).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius",1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|91061|186826|33958|2767887|1624,Complete,Peace Sandy
bsdb:35692191/3/2,35692191,"cross-sectional observational, not case-control",35692191,10.5217/ir.2021.00168,NA,"Shin S.Y., Kim Y., Kim W.S., Moon J.M., Lee K.M., Jung S.A., Park H., Huh E.Y., Kim B.C., Lee S.C. , Choi C.H.",Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease,Intestinal research,2023,"Biomarkers, Inflammatory bowel disease, Microbiota, Phenotype, Prognosis",Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Patients with mild ulcerative colitis,Patients with moderate to severe ulcerative colitis,"patients diagnosed with ulcerative colitis (UC) from 3 different academic hospitals in Korea categorized as moderate to severe forms of UC. The severity of disease was assessed by the Mayo score for UC. Severity was estimated at the time of fecal sampling, and the average follow-up period was 8.0 ± 1.3 years.",37,18,1 month,16S,4,Illumina,relative abundances,LEfSe,NA,FALSE,3,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 5a,24 November 2023,Yjung24,"Yjung24,Atrayees,WikiWorks",Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in ulcerative colitis (UC) patients. Comparisons between moderate to severe and mild UC (A).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",3379134|976|200643|171549|815|816|85831;3379134|976|200643|171549|815|816|47678;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|186802|404402|404403;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|91061|186826|1300|1301|1313;1783272|1239|186801|186802|31979|1485|1522;3379134|976|200643|171549|171550|239759,Complete,Peace Sandy
bsdb:35692191/4/1,35692191,"cross-sectional observational, not case-control",35692191,10.5217/ir.2021.00168,NA,"Shin S.Y., Kim Y., Kim W.S., Moon J.M., Lee K.M., Jung S.A., Park H., Huh E.Y., Kim B.C., Lee S.C. , Choi C.H.",Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease,Intestinal research,2023,"Biomarkers, Inflammatory bowel disease, Microbiota, Phenotype, Prognosis",Experiment 4,South Korea,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Patients with remission ulcerative colitis (symptoms of UC are reduced or inapparent),Patients with moderate to severe ulcerative colitis,"Patients diagnosed with ulcerative colitis (UC) from 3 different academic hospitals in Korea categorized as moderate to severe forms of UC. The severity of disease was assessed by the Mayo score for UC. Severity was estimated at the time of fecal sampling, and the average follow-up period was 8.0 ± 1.3 years.",15,18,1 month,16S,4,Illumina,relative abundances,LEfSe,NA,FALSE,3,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 5b,24 November 2023,Yjung24,"Yjung24,WikiWorks",Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in ulcerative colitis (UC) patients. Comparisons between moderate to severe UC and remission (B).,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella confusa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc lactis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Pseudolactococcus|s__Pseudolactococcus plantarum",1783272|1239|91061|186826|1300|1357|1358;1783272|1239|186801|3082720|186804|1505657|261299;1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|91061|186826|33958|46255|1583;1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|526524|526525|2810280|3025755|29348;1783272|1239|91061|186826|33958|1243|1246;1783272|1239|91061|186826|1300|3436058|1365,Complete,Peace Sandy
bsdb:35692191/4/2,35692191,"cross-sectional observational, not case-control",35692191,10.5217/ir.2021.00168,NA,"Shin S.Y., Kim Y., Kim W.S., Moon J.M., Lee K.M., Jung S.A., Park H., Huh E.Y., Kim B.C., Lee S.C. , Choi C.H.",Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease,Intestinal research,2023,"Biomarkers, Inflammatory bowel disease, Microbiota, Phenotype, Prognosis",Experiment 4,South Korea,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Patients with remission ulcerative colitis (symptoms of UC are reduced or inapparent),Patients with moderate to severe ulcerative colitis,"Patients diagnosed with ulcerative colitis (UC) from 3 different academic hospitals in Korea categorized as moderate to severe forms of UC. The severity of disease was assessed by the Mayo score for UC. Severity was estimated at the time of fecal sampling, and the average follow-up period was 8.0 ± 1.3 years.",15,18,1 month,16S,4,Illumina,relative abundances,LEfSe,NA,FALSE,3,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 5b,24 November 2023,Yjung24,"Yjung24,Atrayees,WikiWorks",Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in ulcerative colitis (UC) patients. Comparisons between moderate to severe UC and remission (B).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas paravirosa,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|815|816|85831;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|246787;3379134|200940|3031449|213115|194924|35832|35833;3379134|976|200643|171549|1853231|574697|1472417;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|2005525|375288|823;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|91061|186826|1300|1301|1305;3379134|976|200643|171549|171550|239759;3379134|1224|28216|80840|995019|40544,Complete,Peace Sandy
bsdb:35692191/5/1,35692191,"cross-sectional observational, not case-control",35692191,10.5217/ir.2021.00168,NA,"Shin S.Y., Kim Y., Kim W.S., Moon J.M., Lee K.M., Jung S.A., Park H., Huh E.Y., Kim B.C., Lee S.C. , Choi C.H.",Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease,Intestinal research,2023,"Biomarkers, Inflammatory bowel disease, Microbiota, Phenotype, Prognosis",Experiment 5,South Korea,Homo sapiens,Feces,UBERON:0001988,"Distal colitis,Pancolitis",NA,patients with proctitis ulcerative colitis,patients with left sided or extensive ulcerative colitis,patients diagnosed with ulcerative colitis (UC) from 3 different academic hospitals in Korea defined as left sided (distal colitis) or extensive (pancolitis).,21,28,1 month,16S,4,Illumina,relative abundances,LEfSe,NA,FALSE,3,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,Figure 5c,25 November 2023,Yjung24,"Yjung24,WikiWorks",Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in ulcerative colitis (UC) patients. Comparisons between left sided or extensive UC and proctitis.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus paracasei,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",1783272|201174|1760|85004|31953|1678|1681;1783272|1239|186801|3082720|186804|1505657|261299;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|91061|186826|33958|2759736|1597;1783272|1239|186801|3085636|186803|2316020|33038,Complete,Peace Sandy
bsdb:35692191/5/2,35692191,"cross-sectional observational, not case-control",35692191,10.5217/ir.2021.00168,NA,"Shin S.Y., Kim Y., Kim W.S., Moon J.M., Lee K.M., Jung S.A., Park H., Huh E.Y., Kim B.C., Lee S.C. , Choi C.H.",Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease,Intestinal research,2023,"Biomarkers, Inflammatory bowel disease, Microbiota, Phenotype, Prognosis",Experiment 5,South Korea,Homo sapiens,Feces,UBERON:0001988,"Distal colitis,Pancolitis",NA,patients with proctitis ulcerative colitis,patients with left sided or extensive ulcerative colitis,patients diagnosed with ulcerative colitis (UC) from 3 different academic hospitals in Korea defined as left sided (distal colitis) or extensive (pancolitis).,21,28,1 month,16S,4,Illumina,relative abundances,LEfSe,NA,FALSE,3,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,Figure 5c,25 November 2023,Yjung24,"Yjung24,Atrayees,WikiWorks",Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in ulcerative colitis (UC) patients. Comparisons between left sided or extensive UC and proctitis.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia|s__Senegalimassilia anaerobia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Tractidigestivibacter|s__Tractidigestivibacter scatoligenes",3379134|976|200643|171549|171550|239759|2585118;3379134|976|200643|171549|171550|239759|1288121;1783272|1239|186801|186802|404402|404403;3379134|976|200643|171549|171552|2974265|363265;1783272|1239|91061|186826|33958|2767887|1623;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|171552|577309|454154;3379134|1224|28216|80840|995019|577310|487175;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|2974251|165179;1783272|201174|84998|84999|84107|1473205|1473216;1783272|201174|84998|1643822|1643826|84108|572010;1783272|1239|186801|186802|216572|44748;1783272|201174|84998|84999|1643824|2847313|1299998,Complete,Peace Sandy
bsdb:35692191/6/1,35692191,"cross-sectional observational, not case-control",35692191,10.5217/ir.2021.00168,NA,"Shin S.Y., Kim Y., Kim W.S., Moon J.M., Lee K.M., Jung S.A., Park H., Huh E.Y., Kim B.C., Lee S.C. , Choi C.H.",Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease,Intestinal research,2023,"Biomarkers, Inflammatory bowel disease, Microbiota, Phenotype, Prognosis",Experiment 6,South Korea,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,patients with remission Crohn's disease,patients with active Crohn's disease,"Patients diagnosed with Crohn's disease (CD) from 3 different academic hospitals in Korea. The severity of disease was assessed by the Crohn’s Disease Activity Index CD. Active status including mild, moderate, severe forms of CD. Severity was estimated at the time of fecal sampling, and the average follow-up period was 8.0 ± 1.3 years.",24,15,1 month,16S,4,Illumina,relative abundances,LEfSe,NA,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6a,25 November 2023,Yjung24,"Yjung24,WikiWorks",Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in Crohn’s disease (CD) patients. Comparisons between remission and active CD (A).,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus",1783272|1239|909932|1843488|909930|33024|626940;1783272|1239|91061|186826|33958|2767887|1624;1783272|1239|91061|186826|33958|2742598|97478;3379134|976|200643|171549|171551|836|28123;1783272|1239|186801|3085636|186803|3570277|116085,Complete,Peace Sandy
bsdb:35692191/6/2,35692191,"cross-sectional observational, not case-control",35692191,10.5217/ir.2021.00168,NA,"Shin S.Y., Kim Y., Kim W.S., Moon J.M., Lee K.M., Jung S.A., Park H., Huh E.Y., Kim B.C., Lee S.C. , Choi C.H.",Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease,Intestinal research,2023,"Biomarkers, Inflammatory bowel disease, Microbiota, Phenotype, Prognosis",Experiment 6,South Korea,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,patients with remission Crohn's disease,patients with active Crohn's disease,"Patients diagnosed with Crohn's disease (CD) from 3 different academic hospitals in Korea. The severity of disease was assessed by the Crohn’s Disease Activity Index CD. Active status including mild, moderate, severe forms of CD. Severity was estimated at the time of fecal sampling, and the average follow-up period was 8.0 ± 1.3 years.",24,15,1 month,16S,4,Illumina,relative abundances,LEfSe,NA,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6a,25 November 2023,Yjung24,"Yjung24,WikiWorks",Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in Crohn’s disease (CD) patients. Comparisons between remission and active CD (A).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter glycyrrhizinilyticus",3379134|976|200643|171549|815|816|820;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|186802|31979|1485|1522;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|186801|3085636|186803|572511|1532;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|2316020|33038;3379134|976|200643|171549|815|909656|310297;1783272|1239|186801|3085636|186803|207244|649756;3379134|976|200643|171549|2005525|375288|823;1783272|1239|186801|3085636|186803|2719313|1531;1783272|1239|186801|3085636|186803|2316020|342942,Complete,Peace Sandy
bsdb:35692191/7/1,35692191,"cross-sectional observational, not case-control",35692191,10.5217/ir.2021.00168,NA,"Shin S.Y., Kim Y., Kim W.S., Moon J.M., Lee K.M., Jung S.A., Park H., Huh E.Y., Kim B.C., Lee S.C. , Choi C.H.",Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease,Intestinal research,2023,"Biomarkers, Inflammatory bowel disease, Microbiota, Phenotype, Prognosis",Experiment 7,South Korea,Homo sapiens,Feces,UBERON:0001988,Ileocolitis,EFO:0005624,patients with small bowel Crohn's disease,patients with ileocolonic Crohn's disease,Patients diagnosed with ileocolonic Crohn's disease (CD) from 3 different academic hospitals in Korea.,17,17,1 month,16S,4,Illumina,relative abundances,LEfSe,NA,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6b,25 November 2023,Yjung24,"Yjung24,WikiWorks",Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in Crohn’s disease (CD) patients. Comparisons between ileocolonic and small bowel CD (B).,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella confusa",1783272|1239|91061|186826|33958|1578|1596;3379134|976|200643|171549|815|816|28116;1783272|1239|91061|186826|33958|46255|1583,Complete,Peace Sandy
bsdb:35692191/7/2,35692191,"cross-sectional observational, not case-control",35692191,10.5217/ir.2021.00168,NA,"Shin S.Y., Kim Y., Kim W.S., Moon J.M., Lee K.M., Jung S.A., Park H., Huh E.Y., Kim B.C., Lee S.C. , Choi C.H.",Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease,Intestinal research,2023,"Biomarkers, Inflammatory bowel disease, Microbiota, Phenotype, Prognosis",Experiment 7,South Korea,Homo sapiens,Feces,UBERON:0001988,Ileocolitis,EFO:0005624,patients with small bowel Crohn's disease,patients with ileocolonic Crohn's disease,Patients diagnosed with ileocolonic Crohn's disease (CD) from 3 different academic hospitals in Korea.,17,17,1 month,16S,4,Illumina,relative abundances,LEfSe,NA,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6b,25 November 2023,Yjung24,"Yjung24,WikiWorks",Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in Crohn’s disease (CD) patients. Comparisons between ileocolonic and small bowel CD (B).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis",1783272|1239|186801|3085636|186803|572511|1532;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|3085636|186803|2719313|1531,Complete,Peace Sandy
bsdb:35719348/1/1,35719348,case-control,35719348,https://doi.org/10.3389/fcimb.2022.886872,https://www.frontiersin.org/articles/10.3389/fcimb.2022.886872/full,"Ling Z., Jin G., Yan X., Cheng Y., Shao L., Song Q., Liu X. , Zhao L.",Fecal Dysbiosis and Immune Dysfunction in Chinese Elderly Patients With Schizophrenia: An Observational Study,Frontiers in cellular and infection microbiology,2022,"Faecalibacterium, LEfSe, Schizophrenia, dysbiosis, non-invasive diagnosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy control,Elderly Schizophrenia Patients,Elderly Schizophrenia Patients,71,90,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 2A,10 March 2023,Dupe,"Dupe,Aiyshaaaa,Atrayees,WikiWorks",Differential LEfSe- associated bacterial taxa between the elderly SZ patients and the healthy controls,increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Thermotogati|p__Synergistota,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",1783272|201174;3379134|1224|1236|135624;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171552|1283313;3379134|976|200643;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;3379134|200940|3031449|213115|194924|35832;1783272|1239|526524|526525|2810280|135858;1783272|201174|84998|84999|84107;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;3384189|32066|203490|203491|203492;3384189|32066|203490|203491|203492|848;1783272|1239|526524|526525|128827|1573535;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|909929|1843491|52225;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171552;1783272|1239|186801|3082720|186804|1501226;1783272|201174|84998|84999|84107|1473205;1783272|201174|84998|1643822|1643826|84108;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;3379134|1224|1236|135624|83763|83770;3379134|1224|28216|80840|995019|40544;3384194|508458;3379134|74201;3379134|976|200643|171549;1783272|201174|84998|84999|84107;3379134|976|200643|171549|171551,Complete,Atrayees
bsdb:35719348/1/2,35719348,case-control,35719348,https://doi.org/10.3389/fcimb.2022.886872,https://www.frontiersin.org/articles/10.3389/fcimb.2022.886872/full,"Ling Z., Jin G., Yan X., Cheng Y., Shao L., Song Q., Liu X. , Zhao L.",Fecal Dysbiosis and Immune Dysfunction in Chinese Elderly Patients With Schizophrenia: An Observational Study,Frontiers in cellular and infection microbiology,2022,"Faecalibacterium, LEfSe, Schizophrenia, dysbiosis, non-invasive diagnosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy control,Elderly Schizophrenia Patients,Elderly Schizophrenia Patients,71,90,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 2A,10 March 2023,Dupe,"Dupe,Atrayees,WikiWorks",Differential LEfSe- associated bacterial taxa between the elderly SZ patients and the healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|3085636|186803|207244;1783272|1239|91061;1783272|1239;1783272|1239|186801|186802|3085642|580596;3379134|1224|1236|91347|543|544;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|186802|204475;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572,Complete,Atrayees
bsdb:35719348/2/1,35719348,case-control,35719348,https://doi.org/10.3389/fcimb.2022.886872,https://www.frontiersin.org/articles/10.3389/fcimb.2022.886872/full,"Ling Z., Jin G., Yan X., Cheng Y., Shao L., Song Q., Liu X. , Zhao L.",Fecal Dysbiosis and Immune Dysfunction in Chinese Elderly Patients With Schizophrenia: An Observational Study,Frontiers in cellular and infection microbiology,2022,"Faecalibacterium, LEfSe, Schizophrenia, dysbiosis, non-invasive diagnosis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy control,Schizophrenia,Elderly Schizophrenia Patients,71,90,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,3,"age,sex",NA,NA,decreased,increased,decreased,NA,NA,Signature 1,Figure 2B,11 March 2023,Dupe,"Dupe,WikiWorks",the mean relative abundances of bacterial taxa in SZ patients and healthy control from phylum to genus level,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomonadales|f__Hyphomonadaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Pelagibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Thermotogati|p__Synergistota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae",1783272|1239|909932|1843488|909930;1783272|1239|909932|1843488|909930|904;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|201174;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171552|1283313;1783272|201174|84998|84999|1643824|1380;3379134|976|200643;3379134|200940|3031449|213115|194924|35832;1783272|1239|526524|526525|2810280|135858;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;1783272|1239|186801|3085636|186803|189330;1783272|1239|526524|526525|128827;3384189|32066|203490;3379134|1224|1236|135625|712|724;3379134|1224|1236|135619|28256;3379134|1224|1236|135619|28256|2745;1783272|1239|526524|526525|128827|1573535;3379134|1224|28211|356|45401;3379134|1224|28211|2800060|69657;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843489|31977|906;1783272|201174|1760|85006|1268;1783272|201174|84998|84999|1643824|133925;3379134|1224|28211|204455|31989;1783272|1239|1737404|1737405|1570339|543311;3379134|1224|1236|135625|712;3379134|1224|28211|356|2831106|1082930;1783272|1239|186801|3082720|186804;1783272|1239|909932|1843488|909930|33024;3379134|1224|28211|356|69277;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|186801|3082720|186804|1501226;1783272|201174|84998|84999|84107|1473205;1783272|1239|91061|1385|90964;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;3379134|1224|1236|135624|83763|83770;3379134|1224|1236|135624|83763;3379134|1224|28216|80840|995019|40544;3384194|508458|649775|649776|649777;3384194|508458;3379134|74201|203494|48461|203557;3379134|74201;3379134|1224|1236|135614|32033,Complete,Atrayees
bsdb:35719348/2/2,35719348,case-control,35719348,https://doi.org/10.3389/fcimb.2022.886872,https://www.frontiersin.org/articles/10.3389/fcimb.2022.886872/full,"Ling Z., Jin G., Yan X., Cheng Y., Shao L., Song Q., Liu X. , Zhao L.",Fecal Dysbiosis and Immune Dysfunction in Chinese Elderly Patients With Schizophrenia: An Observational Study,Frontiers in cellular and infection microbiology,2022,"Faecalibacterium, LEfSe, Schizophrenia, dysbiosis, non-invasive diagnosis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,healthy control,Schizophrenia,Elderly Schizophrenia Patients,71,90,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,3,"age,sex",NA,NA,decreased,increased,decreased,NA,NA,Signature 2,Figure 2B,11 March 2023,Dupe,"Dupe,Atrayees,WikiWorks",the mean relative abundances of bacterial taxa in SZ patients and healthy control from phylum to genus level,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|204475;1783272|1239|186801|3085636|186803;3379134|1224;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572,Complete,Atrayees
bsdb:35722294/1/1,35722294,meta-analysis,35722294,https://doi.org/10.3389%2Ffmicb.2022.875101,NA,"Guo X., Tang P., Hou C., Chong L., Zhang X., Liu P., Chen L., Liu Y., Zhang L. , Li R.","Integrated Microbiome and Host Transcriptome Profiles Link Parkinson's Disease to <i>Blautia</i> Genus: Evidence From Feces, Blood, and Brain",Frontiers in microbiology,2022,"16S, Blautia, Parkinson’s disease, feces, microbiome",Experiment 1,"China,Denmark,Finland,Germany,Italy,Japan,United States of America",Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Controls,PD patients,Patients with Parkinson's disease,10,10,NA,16S,NA,"Illumina,Roche454",relative abundances,DESeq2,0.05,FALSE,NA,NA,NA,NA,increased,increased,increased,NA,NA,Signature 1,Supplementary Table 4,27 March 2024,Leenaa,"Leenaa,Fiddyhamma,WikiWorks",Significantly changed fecal genera classified by Greengenes between PD patients and controls,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Methanobacteriati|p__Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter|s__Pseudoramibacter alactolyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sporobacterium|s__Sporobacterium sp. WAL 1855D,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum",1783272|1239|909932|1843488|909930|904;1783272|1239|186801|186802|186806|264995;1783272|1239|186801|186802|216572|244127;3379134|29547|3031852|213849|72294|194;3379134|1224|1236|91347|543|544;1783272|1239|526524|526525|2810280|100883;1783272|1239|186801|186802|186807|51514;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|186806|1730;1783272|1239|1737404|1737405|1570339|150022;3379134|1224|1236|135619|28256|2745;3366610|28890|183925|2158|2159|2172;3366610|2283796|183967|1235850|1577788|1080709;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|186802|186806|113286|113287;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|100132|507843;3384194|508458|649775|649776|649777|2753;1783272|1239|526524|526525|2810281|191303;1783272|201174|1760|2037|2049|184869,Complete,Svetlana up
bsdb:35722294/1/2,35722294,meta-analysis,35722294,https://doi.org/10.3389%2Ffmicb.2022.875101,NA,"Guo X., Tang P., Hou C., Chong L., Zhang X., Liu P., Chen L., Liu Y., Zhang L. , Li R.","Integrated Microbiome and Host Transcriptome Profiles Link Parkinson's Disease to <i>Blautia</i> Genus: Evidence From Feces, Blood, and Brain",Frontiers in microbiology,2022,"16S, Blautia, Parkinson’s disease, feces, microbiome",Experiment 1,"China,Denmark,Finland,Germany,Italy,Japan,United States of America",Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Controls,PD patients,Patients with Parkinson's disease,10,10,NA,16S,NA,"Illumina,Roche454",relative abundances,DESeq2,0.05,FALSE,NA,NA,NA,NA,increased,increased,increased,NA,NA,Signature 2,Supplementary Table 4,27 March 2024,Leenaa,"Leenaa,Fiddyhamma,WikiWorks",Significantly changed fecal genera classified by Greengenes between PD patients and controls,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|28050;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|841;3379134|1224|28216|80840|995019|40544,Complete,Svetlana up
bsdb:35722294/2/1,35722294,meta-analysis,35722294,https://doi.org/10.3389%2Ffmicb.2022.875101,NA,"Guo X., Tang P., Hou C., Chong L., Zhang X., Liu P., Chen L., Liu Y., Zhang L. , Li R.","Integrated Microbiome and Host Transcriptome Profiles Link Parkinson's Disease to <i>Blautia</i> Genus: Evidence From Feces, Blood, and Brain",Frontiers in microbiology,2022,"16S, Blautia, Parkinson’s disease, feces, microbiome",Experiment 2,China,Homo sapiens,Blood,UBERON:0000178,Parkinson's disease,MONDO:0005180,Controls,PD patients,Patients with Parkinson's disease,1,1,NA,16S,34,Illumina,relative abundances,DESeq2,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Supplementary Table 6,27 March 2024,Leenaa,"Leenaa,WikiWorks",Significantly changed genera in the blood samples between PD patients and controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Meiothermus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Nesterenkonia",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|189330;3384194|1297|188787|68933|188786|65551;1783272|201174|1760|85006|1268|57494,Complete,Svetlana up
bsdb:35722294/3/1,35722294,meta-analysis,35722294,https://doi.org/10.3389%2Ffmicb.2022.875101,NA,"Guo X., Tang P., Hou C., Chong L., Zhang X., Liu P., Chen L., Liu Y., Zhang L. , Li R.","Integrated Microbiome and Host Transcriptome Profiles Link Parkinson's Disease to <i>Blautia</i> Genus: Evidence From Feces, Blood, and Brain",Frontiers in microbiology,2022,"16S, Blautia, Parkinson’s disease, feces, microbiome",Experiment 3,"Israel,Netherlands,United States of America",Homo sapiens,Brain,UBERON:0000955,Parkinson's disease,MONDO:0005180,Controls,PD patients,Patients with Parkinson's disease,5,5,NA,WMS,NA,Illumina,relative abundances,DESeq2,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Supplementary Table 7,27 March 2024,Leenaa,"Leenaa,Fiddyhamma,WikiWorks",Significantly changed genera in the brain between PD patients and controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Planctomycetales|f__Planctomycetaceae|g__Planctomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Rathayibacter,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Syntrophobacteria|o__Syntrophobacterales|f__Syntrophobacteraceae|g__Syntrophobacter",3379134|1224|1236|91347|543|413496;1783272|201174|1760|85009|85015|1839;3379134|203682|203683|112|126|118;1783272|201174|1760|85006|85023|33886;3379134|200940|3024408|213462|213465|29526,Complete,Svetlana up
bsdb:35722294/3/2,35722294,meta-analysis,35722294,https://doi.org/10.3389%2Ffmicb.2022.875101,NA,"Guo X., Tang P., Hou C., Chong L., Zhang X., Liu P., Chen L., Liu Y., Zhang L. , Li R.","Integrated Microbiome and Host Transcriptome Profiles Link Parkinson's Disease to <i>Blautia</i> Genus: Evidence From Feces, Blood, and Brain",Frontiers in microbiology,2022,"16S, Blautia, Parkinson’s disease, feces, microbiome",Experiment 3,"Israel,Netherlands,United States of America",Homo sapiens,Brain,UBERON:0000955,Parkinson's disease,MONDO:0005180,Controls,PD patients,Patients with Parkinson's disease,5,5,NA,WMS,NA,Illumina,relative abundances,DESeq2,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Supplementary table 7,27 March 2024,Leenaa,"Leenaa,Fiddyhamma,WikiWorks",Significantly changed genera in the brain between PD patients and controls,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Elizabethkingia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Erythrobacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Pseudonocardia,k__Bacillati|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae|g__Thermoanaerobacterium",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;3379134|976|117743|200644|2762318|308865;3379134|1224|28211|204457|335929|1041;1783272|1239|1737404|1737405|1570339|150022;3379134|1224|1236|135619|28256|2745;1783272|201174|1760|85010|2070|1847;1783272|1239|186801|68295|186814|28895,Complete,Svetlana up
bsdb:35722294/4/1,35722294,meta-analysis,35722294,https://doi.org/10.3389%2Ffmicb.2022.875101,NA,"Guo X., Tang P., Hou C., Chong L., Zhang X., Liu P., Chen L., Liu Y., Zhang L. , Li R.","Integrated Microbiome and Host Transcriptome Profiles Link Parkinson's Disease to <i>Blautia</i> Genus: Evidence From Feces, Blood, and Brain",Frontiers in microbiology,2022,"16S, Blautia, Parkinson’s disease, feces, microbiome",Experiment 4,"China,Denmark,Finland,Germany,Italy,Japan,United States of America",Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Controls,PD patients,Patients with Parkinson's disease,16,16,NA,16S,NA,"Illumina,Roche454",relative abundances,DESeq2,0.05,FALSE,NA,NA,NA,NA,increased,increased,increased,NA,NA,Signature 1,Supplementary table 5,20 December 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",Significantly changed fecal genera classified by SILVA between PD patients and controls,increased,"k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus",3366610|28890|183925|2158|2159|2172;1783272|1239|909932|1843488|909930|904;3379134|29547|3031852|213849|72294|194;3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|1903414|583;1783272|201174|1760|2037|2049|184869;1783272|1239|1737404|1737405|1570339|162290;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|3082720|543314|86331;1783272|1239|526524|526525|2810281|191303;1783272|1239|91061|186826|33958|1253;1783272|1239|186801|186802|186806|264995;1783272|1239|186801|186802|216572|244127,Complete,Svetlana up
bsdb:35722294/4/2,35722294,meta-analysis,35722294,https://doi.org/10.3389%2Ffmicb.2022.875101,NA,"Guo X., Tang P., Hou C., Chong L., Zhang X., Liu P., Chen L., Liu Y., Zhang L. , Li R.","Integrated Microbiome and Host Transcriptome Profiles Link Parkinson's Disease to <i>Blautia</i> Genus: Evidence From Feces, Blood, and Brain",Frontiers in microbiology,2022,"16S, Blautia, Parkinson’s disease, feces, microbiome",Experiment 4,"China,Denmark,Finland,Germany,Italy,Japan,United States of America",Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Controls,PD patients,Patients with Parkinson's disease,16,16,NA,16S,NA,"Illumina,Roche454",relative abundances,DESeq2,0.05,FALSE,NA,NA,NA,NA,increased,increased,increased,NA,NA,Signature 2,Supplementary table 5,20 December 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",Significantly changed fecal genera classified by SILVA between PD patients and controls,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea",1783272|1239|909932|1843488|909930|33024;3379134|1224|28216|80840|995019|40544;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|189330,Complete,Svetlana up
bsdb:35722326/1/1,35722326,case-control,35722326,10.3389/fmicb.2022.888681,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9200618/,"Huang L., Li X., Zheng B., Li P., Wei D., Huang C., Sun L. , Li H.",Differential Urinary Microbiota Composition Between Women With and Without Recurrent Urinary Tract Infection,Frontiers in microbiology,2022,"16S rRNA, next generation sequencing (NGS), recurrent urinary tract infection (RUTI), standard urine culture, urinary microbiota",Experiment 1,China,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,Asymptomatic controls,Recurrent Urinary Tract Infection (RUTI) patients,Women with clinically diagnosed RUTI with negative Standard Urine Cultures (SUCs),44,67,2 days,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,age,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 1,Figure 5,7 October 2023,Aleru002,"Aleru002,WikiWorks","Differentially abundant bacteria between RUTI and controls, revealed by linear discriminant analysis effect size (LEfSe) analysis.",increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinotignum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae",1783272|1239|1737404|1737405|1570339|165779;3379134|1224|28216;3379134|1224|28216|80840|119060;3379134|1224|28216|80840;1783272|201174|1760|85007|1653|1716;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|906;1783272|201174|1760|85007;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|28125;3379134|976|200643|171549|171552;3379134|1224;3379134|1224|28216|80840|119060|48736;1783272|201174|1760|2037|2049|1653174;1783272|1239|1737404|1737405|1570339|162289;1783272|201174|1760|2037;1783272|201174|1760|2037|2049;3379134|29547|3031852;3379134|29547|3031852|213849;3379134|29547|3031852|213849|72294;3379134|29547|3031852|213849|72294|194;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492;3379134|1224|28211|356|212791;1783272|201174|1760|85007|1653,Complete,Svetlana up
bsdb:35722326/1/2,35722326,case-control,35722326,10.3389/fmicb.2022.888681,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9200618/,"Huang L., Li X., Zheng B., Li P., Wei D., Huang C., Sun L. , Li H.",Differential Urinary Microbiota Composition Between Women With and Without Recurrent Urinary Tract Infection,Frontiers in microbiology,2022,"16S rRNA, next generation sequencing (NGS), recurrent urinary tract infection (RUTI), standard urine culture, urinary microbiota",Experiment 1,China,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,Asymptomatic controls,Recurrent Urinary Tract Infection (RUTI) patients,Women with clinically diagnosed RUTI with negative Standard Urine Cultures (SUCs),44,67,2 days,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,age,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 2,Figure 5,7 October 2023,Aleru002,"Aleru002,WikiWorks","Differentially abundant bacteria between RUTI and controls, revealed by linear discriminant analysis effect size (LEfSe) analysis.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Phaseolus|s__Phaseolus acutifolius,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacillati|p__Bacillota",3379134|1224|1236|2887326|468|469;3379134|976|200643|171549|171550|239759;1783272|1239|91061;1783272|1239|1737404|1582879;1783272|201174|1760|85004|31953|2701;1783272|1239|186801|3085636|186803|877420;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|1596;3384189|32066|203490|203491|1129771;33090|35493|3398|72025|3803|3814|3883|33129;3384189|32066|203490|203491|1129771|168808;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1313;1783272|1239,Complete,Svetlana up
bsdb:35727391/1/1,35727391,case-control,35727391,10.1007/s10637-022-01263-1,NA,"Yuan D., Tao Y., Wang H., Wang J., Cao Y., Cao W., Pan S. , Yu Z.",A comprehensive analysis of the microbiota composition and host driver gene mutations in colorectal cancer,Investigational new drugs,2022,"16S, Colorectal cancer, Driver gene mutation, Microbiota, Target therapy",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal adenocarcinoma,EFO:0000365,healthy controls,colorectal cancer patients,diagnosed of colorectal cancer by colonoscopy and histopathology,20,44,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Figures 4b,29 August 2022,Mary Bearkland,"Mary Bearkland,WikiWorks","Fig. 4 Difference of fecal microbiota in CRC patients and HC. b. LDA score computed
from features differentially abundant in CRC and HC fecal samples.
The criteria for feature selection were LDA score > 4, p < 0.05,
Green and red represent the HC group and CRC group, respectively.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;3379134|1224|1236|91347|543|620;3379134|1224|1236|91347|543|561,Complete,Fatima
bsdb:35727391/1/2,35727391,case-control,35727391,10.1007/s10637-022-01263-1,NA,"Yuan D., Tao Y., Wang H., Wang J., Cao Y., Cao W., Pan S. , Yu Z.",A comprehensive analysis of the microbiota composition and host driver gene mutations in colorectal cancer,Investigational new drugs,2022,"16S, Colorectal cancer, Driver gene mutation, Microbiota, Target therapy",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal adenocarcinoma,EFO:0000365,healthy controls,colorectal cancer patients,diagnosed of colorectal cancer by colonoscopy and histopathology,20,44,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Figures 4b,29 August 2022,Mary Bearkland,"Mary Bearkland,Fatima,WikiWorks","Fig. 4 Difference of fecal microbiota in CRC patients and HC. b. LDA score computed
from features differentially abundant in CRC and HC fecal samples.
The criteria for feature selection were LDA score > 4, p < 0.05,
Green and red represent the HC group and CRC group, respectively.",decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter",1783272|201174|84998|84999|84107|102106;1783272|1239|526524|526525|2810280|100883;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3082720|186804|1501226;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|1766253,Complete,Fatima
bsdb:35727391/2/1,35727391,case-control,35727391,10.1007/s10637-022-01263-1,NA,"Yuan D., Tao Y., Wang H., Wang J., Cao Y., Cao W., Pan S. , Yu Z.",A comprehensive analysis of the microbiota composition and host driver gene mutations in colorectal cancer,Investigational new drugs,2022,"16S, Colorectal cancer, Driver gene mutation, Microbiota, Target therapy",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Colorectal adenocarcinoma,EFO:0000365,colorectal cancer patients without KRAS mutation,colorectal cancer patients with KRAS mutation,diagnosed of colorectal cancer by colonoscopy and histopathology,21,18,No antibiotics for one month prior to surgery (fecal sample was taken the night before surgery),16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5a,31 August 2022,Mary Bearkland,"Mary Bearkland,Fatima,Merit,WikiWorks",LEfSe was used to compare the microbial variation of the KRAS,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Caproiciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Gracilibacteraceae|g__Gracilibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia|s__Harryflintia acetispora,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania filiformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium edouardi,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. 11SE38,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Caproiciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__uncultured Eubacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Gracilibacteraceae|g__Gracilibacter|s__uncultured Gracilibacter sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__uncultured Prevotella sp.",1783272|1239|909932|1843488|909930;3379134|976|200643|171549|171550|239759|1872444;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|3082771|1738645;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|541019|342658;1783272|1239|186801|186802|216572|1892380;1783272|1239|186801|186802|216572|1892380|1849041;1783272|1239|526524|526525|128827|61170|61171;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|1506553|1926283;1783272|1239|186801|3085636|186803;1783272|1239|909932|909929|1843491|158846;3379134|1224|28211|204457|41297|165696;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|583272;3379134|1224|28211|204457|41297;3379134|1224|28211|204457;1783272|1239|186801|3085636|186803|2569097;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|3082771|1738645;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|216851;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|186802|186806|1730|165185;1783272|1239|186801|186802|541019|342658|517604;3379134|976|200643|171549|171552|838|159272,Complete,Fatima
bsdb:35727391/2/2,35727391,case-control,35727391,10.1007/s10637-022-01263-1,NA,"Yuan D., Tao Y., Wang H., Wang J., Cao Y., Cao W., Pan S. , Yu Z.",A comprehensive analysis of the microbiota composition and host driver gene mutations in colorectal cancer,Investigational new drugs,2022,"16S, Colorectal cancer, Driver gene mutation, Microbiota, Target therapy",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Colorectal adenocarcinoma,EFO:0000365,colorectal cancer patients without KRAS mutation,colorectal cancer patients with KRAS mutation,diagnosed of colorectal cancer by colonoscopy and histopathology,21,18,No antibiotics for one month prior to surgery (fecal sample was taken the night before surgery),16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5a,31 August 2022,Mary Bearkland,"Mary Bearkland,Fatima,WikiWorks",LEfSe was used to compare the microbial variation of the KRAS,decreased,"k__Bacillati|p__Actinomycetota,,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp. T17/4F,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__uncultured Bifidobacterium sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum|s__Bifidobacterium catenulatum subsp. kashiwanohense",1783272|201174;;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|1689;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|28026;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|91061|186826|33958|1578|765944;1783272|201174|1760|85004|31953|1678|165187;1783272|201174|1760|85004|31953|1678|1686|630129,Complete,Fatima
bsdb:35727391/3/1,35727391,case-control,35727391,10.1007/s10637-022-01263-1,NA,"Yuan D., Tao Y., Wang H., Wang J., Cao Y., Cao W., Pan S. , Yu Z.",A comprehensive analysis of the microbiota composition and host driver gene mutations in colorectal cancer,Investigational new drugs,2022,"16S, Colorectal cancer, Driver gene mutation, Microbiota, Target therapy",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Colorectal adenocarcinoma,EFO:0000365,colorectal cancer patients without TP53 mutation,colorectal cancer patients with TP53 mutation,diagnosed of colorectal cancer by colonoscopy and histopathology,11,28,No antibiotics for one month prior to surgery (fecal sample was taken the night before surgery),16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5b,2 September 2022,Mary Bearkland,"Mary Bearkland,WikiWorks",LEfSe was used to compare the microbial variation of the TP53,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,1783272|1239|186801|186802|186806|1730|290054,Complete,Atrayees
bsdb:35727391/3/2,35727391,case-control,35727391,10.1007/s10637-022-01263-1,NA,"Yuan D., Tao Y., Wang H., Wang J., Cao Y., Cao W., Pan S. , Yu Z.",A comprehensive analysis of the microbiota composition and host driver gene mutations in colorectal cancer,Investigational new drugs,2022,"16S, Colorectal cancer, Driver gene mutation, Microbiota, Target therapy",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Colorectal adenocarcinoma,EFO:0000365,colorectal cancer patients without TP53 mutation,colorectal cancer patients with TP53 mutation,diagnosed of colorectal cancer by colonoscopy and histopathology,11,28,No antibiotics for one month prior to surgery (fecal sample was taken the night before surgery),16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5b,2 September 2022,Mary Bearkland,"Mary Bearkland,Merit,Atrayees,WikiWorks",LEfSe was used to compare the microbial variation of the TP53,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572,Complete,Atrayees
bsdb:35727391/4/1,35727391,case-control,35727391,10.1007/s10637-022-01263-1,NA,"Yuan D., Tao Y., Wang H., Wang J., Cao Y., Cao W., Pan S. , Yu Z.",A comprehensive analysis of the microbiota composition and host driver gene mutations in colorectal cancer,Investigational new drugs,2022,"16S, Colorectal cancer, Driver gene mutation, Microbiota, Target therapy",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Colorectal adenocarcinoma,EFO:0000365,colorectal cancer patients without APC mutation,colorectal cancer patients with APC mutation,diagnosed with colorectal cancer by colonoscopy and histopathology,9,30,No antibiotics for one month prior to surgery (fecal sample was taken the night before surgery),16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5c,3 September 2022,Mary Bearkland,"Mary Bearkland,WikiWorks",LEfSe was used to compare the microbial variation of the  APC groups.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|201174|1760|2037,Complete,Atrayees
bsdb:35727391/5/1,35727391,case-control,35727391,10.1007/s10637-022-01263-1,NA,"Yuan D., Tao Y., Wang H., Wang J., Cao Y., Cao W., Pan S. , Yu Z.",A comprehensive analysis of the microbiota composition and host driver gene mutations in colorectal cancer,Investigational new drugs,2022,"16S, Colorectal cancer, Driver gene mutation, Microbiota, Target therapy",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Colorectal adenocarcinoma,EFO:0000365,colorectal cancer patients without PIK3CA mutation,colorectal cancer patients with PIK3CA mutation,diagnosed with colorectal cancer by colonoscopy and histopathology,33,6,No antibiotics for one month prior to surgery (fecal sample was taken the night before surgery),16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5d,3 September 2022,Mary Bearkland,"Mary Bearkland,WikiWorks",LEfSe was used to compare the microbial variation of the PIK3CA groups.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",1783272|201174|1760|2037;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|201174|1760|2037|2049|1654,Complete,Atrayees
bsdb:35727391/5/2,35727391,case-control,35727391,10.1007/s10637-022-01263-1,NA,"Yuan D., Tao Y., Wang H., Wang J., Cao Y., Cao W., Pan S. , Yu Z.",A comprehensive analysis of the microbiota composition and host driver gene mutations in colorectal cancer,Investigational new drugs,2022,"16S, Colorectal cancer, Driver gene mutation, Microbiota, Target therapy",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Colorectal adenocarcinoma,EFO:0000365,colorectal cancer patients without PIK3CA mutation,colorectal cancer patients with PIK3CA mutation,diagnosed with colorectal cancer by colonoscopy and histopathology,33,6,No antibiotics for one month prior to surgery (fecal sample was taken the night before surgery),16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5d,3 September 2022,Mary Bearkland,"Mary Bearkland,Fatima,WikiWorks",LEfSe was used to compare the microbial variation of the PIK3CA groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio sp. LNB2,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. enrichment culture clone HSL70,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella|s__Moryella indoligenes,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__uncultured Selenomonas sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",3379134|976|200643|171549|171550|239759;1783272|201174|1760|85004|31953|1678|1686;3379134|200940|3031449|213115|194924|872|281992;3379134|1224|1236|91347|543|547|887631;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3085636|186803|437755|371674;1783272|1239|909932;3379134|1224|28216|80840|119060|48736;1783272|1239|909932|909929;1783272|1239|909932|1843489|31977;1783272|1239|909932|1843489|31977|906;3379134|1224|28216|80840|119060|48736;1783272|1239|909932|909929|1843491|970|159275;1783272|1239|91061|186826|33958,Complete,Atrayees
bsdb:35744659/1/1,35744659,"cross-sectional observational, not case-control",35744659,10.3390/microorganisms10061141,NA,"Tsakeng C.U.B., Tanekou T.T.M., Soffack S.F., Tirados I., Noutchih C., Njiokou F., Bigoga J.D. , Wondji C.S.",Assessing the Tsetse Fly Microbiome Composition and the Potential Association of Some Bacteria Taxa with Trypanosome Establishment,Microorganisms,2022,"microbiome, trypanosomes, tsetse flies, vector competence, vector control",Experiment 1,Cameroon,Glossina palpalis palpalis,"Insect head,Body proper","UBERON:6000004,UBERON:0013702",Human african trypanosomiasis,EFO:0005225,Non-infected,Infected,Tsetse flies with midguts infected with trypanosomes.,NA,NA,NA,16S,34,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 2,8 May 2025,Anne-mariesharp,Anne-mariesharp,Operational Taxonomic Units (at the genus level) displaying a significant difference in abundance between tsetse flies with midguts non-infected vs. infected with trypanosomes.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Wigglesworthia",3379134|1224|1236|91347|1903411|613;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|91347|1903409|51228,Complete,KateRasheed
bsdb:35744659/1/2,35744659,"cross-sectional observational, not case-control",35744659,10.3390/microorganisms10061141,NA,"Tsakeng C.U.B., Tanekou T.T.M., Soffack S.F., Tirados I., Noutchih C., Njiokou F., Bigoga J.D. , Wondji C.S.",Assessing the Tsetse Fly Microbiome Composition and the Potential Association of Some Bacteria Taxa with Trypanosome Establishment,Microorganisms,2022,"microbiome, trypanosomes, tsetse flies, vector competence, vector control",Experiment 1,Cameroon,Glossina palpalis palpalis,"Insect head,Body proper","UBERON:6000004,UBERON:0013702",Human african trypanosomiasis,EFO:0005225,Non-infected,Infected,Tsetse flies with midguts infected with trypanosomes.,NA,NA,NA,16S,34,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 2,8 May 2025,Anne-mariesharp,Anne-mariesharp,Operational Taxonomic Units (at the genus level) displaying a significant difference in abundance between tsetse flies with midguts non-infected vs. infected with trypanosomes.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Aquabacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Azonexaceae|g__Dechloromonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Listeria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Methylophilaceae|g__Methylophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles",3379134|1224|28216|80840|92793;1783272|1239|91061|1385|186817|1386;3379134|1224|28216|80840|119060|106589;3379134|1224|28216|206389|2008795|73029;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|1385|186820|1637;3379134|1224|28216|32003|32011|16;3379134|1224|1236|72274|135621|286;3379134|1224|28216|80840|119060|48736;3379134|1224|28216|80840|2975441|93681,Complete,KateRasheed
bsdb:35744659/2/1,35744659,"cross-sectional observational, not case-control",35744659,10.3390/microorganisms10061141,NA,"Tsakeng C.U.B., Tanekou T.T.M., Soffack S.F., Tirados I., Noutchih C., Njiokou F., Bigoga J.D. , Wondji C.S.",Assessing the Tsetse Fly Microbiome Composition and the Potential Association of Some Bacteria Taxa with Trypanosome Establishment,Microorganisms,2022,"microbiome, trypanosomes, tsetse flies, vector competence, vector control",Experiment 2,Cameroon,Glossina palpalis palpalis,"Insect head,Body proper","UBERON:6000004,UBERON:0013702",Disease staging,EFO:0000410,Non-mature infection,Mature infection,Tsetse flies with mature infection with trypanosomes.,NA,NA,NA,16S,34,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Table 3,11 May 2025,Montana-D,Montana-D,Operational Taxonomic Units (in the genus level) displaying a significant difference in abundance between tsetse flies with non-mature vs. mature infection with trypanosomes.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter",1783272|1239|91061|1385|186817|1386;3379134|1224|28211|356|212791,Complete,KateRasheed
bsdb:35744659/2/2,35744659,"cross-sectional observational, not case-control",35744659,10.3390/microorganisms10061141,NA,"Tsakeng C.U.B., Tanekou T.T.M., Soffack S.F., Tirados I., Noutchih C., Njiokou F., Bigoga J.D. , Wondji C.S.",Assessing the Tsetse Fly Microbiome Composition and the Potential Association of Some Bacteria Taxa with Trypanosome Establishment,Microorganisms,2022,"microbiome, trypanosomes, tsetse flies, vector competence, vector control",Experiment 2,Cameroon,Glossina palpalis palpalis,"Insect head,Body proper","UBERON:6000004,UBERON:0013702",Disease staging,EFO:0000410,Non-mature infection,Mature infection,Tsetse flies with mature infection with trypanosomes.,NA,NA,NA,16S,34,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Table 3,11 May 2025,Montana-D,Montana-D,Operational Taxonomic Units (at the genus level) displaying a significant difference in abundance between tsetse flies with non-mature vs. mature infection with trypanosomes.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",3379134|1224|28216|80840|119060|48736;3379134|1224|1236|91347|1903411|613;1783272|1239|91061|1385|90964|1279,Complete,KateRasheed
bsdb:35757783/1/1,35757783,"cross-sectional observational, not case-control",35757783,10.1016/j.xjidi.2022.100115,NA,"Chang H.W., Yan D., Singh R., Bui A., Lee K., Truong A., Milush J.M., Somsouk M. , Liao W.",Multiomic Analysis of the Gut Microbiome in Psoriasis Reveals Distinct Host‒Microbe Associations,JID innovations : skin science from molecules to population health,2022,"IBD, inflammatory bowel disease, RNA-seq, RNA sequencing",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Psoriasis,EFO:0000676,Healthy controls,Psoriasis patients (PSO),Patients with Psoriasis had a diagnosis of psoriasis from a physician for at least 6 months before study enrollment and had a normal-appearing lower gastrointestinal endoscopic examination.,15,33,1 month,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,sex","age,sex",NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 2B and Supplementary Table 1,29 April 2025,MyleeeA,"MyleeeA,Anne-mariesharp",Differentially abundant microbial species between Psoriasis patients and Healthy controls.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides oleiciplenus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium 1_1_47,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. KLE 1755,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella stercoris,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 5_2_54FAA,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus pittmaniae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 9_1_43BFAA,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella buccae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] hylemonae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",1783272|1239|526524|526525|128827|2749846|31971;3379134|976|200643|171549|815|816|626931;3379134|1224|28216|80840|469610;1783272|1239|186801|186802|31979|1485|1226325;1783272|201174|84998|84999|84107|102106|147206;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|91061|186826|81852|1350|1352;1783272|1239|526524|526525|128827|552396;1783272|1239|91061|1385|539738|1378|84135;3379134|1224|1236|135625|712|724|249188;1783272|1239|186801|3085636|186803|658088;3379134|976|200643|171549|2005525|375288|328812;3379134|1224|28216|80840|995019|577310|487175;3379134|976|200643|171549|815|909656|310298;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|171552|838|28130;3379134|976|200643|171549|171552|2974251|28126;3379134|1224|28216|80840|995019|40544|40545;1783272|1239|186801|3085636|186803|1506553|89153;1783272|1239|186801|186802|216572|244127;3379134|203691|203692|1643686|143786|29521;1783272|1239|186801|3085636|186803|189330;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3085636|186803|841;1783272|1239|91061|186826|33958|46255,Complete,KateRasheed
bsdb:35757783/1/2,35757783,"cross-sectional observational, not case-control",35757783,10.1016/j.xjidi.2022.100115,NA,"Chang H.W., Yan D., Singh R., Bui A., Lee K., Truong A., Milush J.M., Somsouk M. , Liao W.",Multiomic Analysis of the Gut Microbiome in Psoriasis Reveals Distinct Host‒Microbe Associations,JID innovations : skin science from molecules to population health,2022,"IBD, inflammatory bowel disease, RNA-seq, RNA sequencing",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Psoriasis,EFO:0000676,Healthy controls,Psoriasis patients (PSO),Patients with Psoriasis had a diagnosis of psoriasis from a physician for at least 6 months before study enrollment and had a normal-appearing lower gastrointestinal endoscopic examination.,15,33,1 month,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,sex","age,sex",NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 2B and Supplementary Table 1,29 April 2025,MyleeeA,"MyleeeA,Anne-mariesharp",Differentially abundant microbial species between Psoriasis patients and Healthy controls.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia|s__Alloscardovia omnicolens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides gallinarum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 2_1_22,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus pullicaecorum,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter hominis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium|s__Carnobacterium maltaromaticum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium JC118,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp. ART55_1,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium glutamicum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio desulfuricans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus avium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium ulcerans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus delbrueckii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Latilactobacillus|s__Latilactobacillus curvatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Latilactobacillus|s__Latilactobacillus sakei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc gelidum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc lactis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus|s__Proteus penneri,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus champanellensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. BS35b,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum variabile,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella cibaria,p__Candidatus Saccharimonadota|s__candidate division TM7 single-cell isolate TM7c,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus",1783272|201174|1760|85004|31953|419014|419015;3379134|976|200643|171549|815|816|376806;3379134|976|200643|171549|815|816|469588;3379134|976|200643|171549|815|816|818;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|186801|186802|3085642|580596|501571;3379134|29547|3031852|213849|72294|194|76517;1783272|1239|91061|186826|186828|2747|2751;3379134|1224|1236|91347|543|544|546;1783272|1239|186801|186802|31979|1070699;1783272|1239|186801|3085636|186803|33042|2710826;1783272|201174|1760|85007|1653|1716|1718;3379134|200940|3031449|213115|194924|872|876;1783272|1239|91061|186826|81852|1350|33945;3384189|32066|203490|203491|203492|848|861;1783272|1239|91061|186826|33958|1578|1584;1783272|201174|84998|84999|1643824|2767353|1382;1783272|1239|91061|186826|33958|2767885|28038;1783272|1239|91061|186826|33958|2767885|1599;1783272|1239|91061|186826|33958|1243|1244;1783272|1239|91061|186826|33958|1243|1246;1783272|1239|909932|909929|1843491|52225|52226;1783272|1239|909932|1843488|909930|33024|626940;3379134|976|200643|171549|171551|836|322095;3379134|1224|1236|91347|1903414|583|102862;1783272|1239|186801|186802|216572|1263|1161942;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|91061|186826|1300|1301|1105032;1783272|1239|186801|186802|216572|292632|214851;1783272|1239|91061|186826|33958|46255|137591;95818|447456;3379134|1224|1236|91347|543|544;1783272|1239|91061|1385|539738|1378;1783272|1239|909932|909929|1843491|52225;1783272|1239|186801|3082720|186804;3379134|1224|1236|91347|1903414|583,Complete,KateRasheed
bsdb:35757783/3/1,35757783,"cross-sectional observational, not case-control",35757783,10.1016/j.xjidi.2022.100115,NA,"Chang H.W., Yan D., Singh R., Bui A., Lee K., Truong A., Milush J.M., Somsouk M. , Liao W.",Multiomic Analysis of the Gut Microbiome in Psoriasis Reveals Distinct Host‒Microbe Associations,JID innovations : skin science from molecules to population health,2022,"IBD, inflammatory bowel disease, RNA-seq, RNA sequencing",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Psoriasis,EFO:0000676,Psoriasis patients (PSO 1/C1),Psoriasis patients (PSO 2/C2),Psoriasis patients in subgroup 2,29,9,1 month,WMS,NA,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Supplementary Table 5,29 April 2025,MyleeeA,MyleeeA,"Differentially abundant microbial species between subgroups, Psoriasis (PSO 2/C2) vs Psoriasis (PSO 1/C1) in the cohort.",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,3379134|976|200643|171549|815|816|371601,Complete,KateRasheed
bsdb:35757783/3/2,35757783,"cross-sectional observational, not case-control",35757783,10.1016/j.xjidi.2022.100115,NA,"Chang H.W., Yan D., Singh R., Bui A., Lee K., Truong A., Milush J.M., Somsouk M. , Liao W.",Multiomic Analysis of the Gut Microbiome in Psoriasis Reveals Distinct Host‒Microbe Associations,JID innovations : skin science from molecules to population health,2022,"IBD, inflammatory bowel disease, RNA-seq, RNA sequencing",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Psoriasis,EFO:0000676,Psoriasis patients (PSO 1/C1),Psoriasis patients (PSO 2/C2),Psoriasis patients in subgroup 2,29,9,1 month,WMS,NA,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Supplementary Table 5,29 April 2025,MyleeeA,"MyleeeA,Anne-mariesharp","Differentially abundant microbial species between subgroups, Psoriasis (PSO 2/C2) vs Psoriasis (PSO 1/C1) in the cohort.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp. ART55_1,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",1783272|1239|186801|3085636|186803|33042|2710826;1783272|1239|909932|1843488|909930|33024|626940;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|526524|526525|2810281|191303|154288;1783272|1239|909932|909929|1843491|158846;1783272|1239|526524|526525|2810281|191303,Complete,KateRasheed
bsdb:35757783/4/1,35757783,"cross-sectional observational, not case-control",35757783,10.1016/j.xjidi.2022.100115,NA,"Chang H.W., Yan D., Singh R., Bui A., Lee K., Truong A., Milush J.M., Somsouk M. , Liao W.",Multiomic Analysis of the Gut Microbiome in Psoriasis Reveals Distinct Host‒Microbe Associations,JID innovations : skin science from molecules to population health,2022,"IBD, inflammatory bowel disease, RNA-seq, RNA sequencing",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Psoriasis,EFO:0000676,Psoriasis patients (PSO 3/C3),Psoriasis patients (PSO 2/C2),Psoriasis patients in subgroup 2,10,9,1 month,WMS,NA,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Supplementary Table 5,29 April 2025,MyleeeA,"MyleeeA,Anne-mariesharp","Differentially abundant microbial species between subgroups, Psoriasis (PSO 2/C2) vs Psoriasis (PSO 3/C3) in the cohort.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp. ART55_1,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",1783272|1239|186801|3085636|186803|33042|2710826;1783272|1239|909932|1843488|909930|33024|626940;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|526524|526525|2810281|191303|154288;1783272|1239|909932|909929|1843491|158846;1783272|1239|526524|526525|2810281|191303,Complete,KateRasheed
bsdb:35757783/5/1,35757783,"cross-sectional observational, not case-control",35757783,10.1016/j.xjidi.2022.100115,NA,"Chang H.W., Yan D., Singh R., Bui A., Lee K., Truong A., Milush J.M., Somsouk M. , Liao W.",Multiomic Analysis of the Gut Microbiome in Psoriasis Reveals Distinct Host‒Microbe Associations,JID innovations : skin science from molecules to population health,2022,"IBD, inflammatory bowel disease, RNA-seq, RNA sequencing",Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Psoriasis,EFO:0000676,Psoriasis patients (PSO 1/C1),Psoriasis patients (PSO 3/C3),Psoriasis patients in subgroup 3,29,10,1 month,WMS,NA,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Supplementary Table 5,29 April 2025,MyleeeA,"MyleeeA,Anne-mariesharp","Differentially abundant microbial species between subgroups, Psoriasis (PSO 3/C3) vs Psoriasis (PSO 1/C1) in the cohort.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 1_1_57FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D16,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis",1783272|1239|186801|3085636|186803|658081;1783272|1239|186801|186802|216572|552398;1783272|1239|526524|526525|2810281|191303|154288,Complete,KateRasheed
bsdb:35783418/1/1,35783418,time series / longitudinal observational,35783418,https://doi.org/10.3389/fmicb.2022.909729,NA,"Xiang M., Zheng L., Pu D., Lin F., Ma X., Ye H., Pu D., Zhang Y., Wang D., Wang X., Zou K., Chen L., Zhang Y., Sun Z., Zhang T. , Wu G.",Intestinal Microbes in Patients With Schizophrenia Undergoing Short-Term Treatment: Core Species Identification Based on Co-Occurrence Networks and Regression Analysis,Frontiers in microbiology,2022,"16S rRNA sequencing, fecal microbiota transplantation, gut microbiota, gut-brain axis, schizophrenia",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Schizophrenia patients before treatment (BT),Schizophrenia patients after treatment (AT),Schizophrenia patients after antipsychotic treatment,25,25,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2A,10 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,Scholastica,WikiWorks",Bacterial taxa differentially abundant in patients before treatment (BT) compared to after treatment (AT),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Acidobacteriota|c__Blastocatellia|o__Chloracidobacteriales|f__Chloracidobacteriaceae|g__Chloracidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|976|200643|171549;3379134|976|200643;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|186801|3085636|186803|841;3379134|976;3379134|57723|1562566|3681502|3681503|458032;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:35783418/1/2,35783418,time series / longitudinal observational,35783418,https://doi.org/10.3389/fmicb.2022.909729,NA,"Xiang M., Zheng L., Pu D., Lin F., Ma X., Ye H., Pu D., Zhang Y., Wang D., Wang X., Zou K., Chen L., Zhang Y., Sun Z., Zhang T. , Wu G.",Intestinal Microbes in Patients With Schizophrenia Undergoing Short-Term Treatment: Core Species Identification Based on Co-Occurrence Networks and Regression Analysis,Frontiers in microbiology,2022,"16S rRNA sequencing, fecal microbiota transplantation, gut microbiota, gut-brain axis, schizophrenia",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Schizophrenia patients before treatment (BT),Schizophrenia patients after treatment (AT),Schizophrenia patients after antipsychotic treatment,25,25,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2A,10 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,Scholastica,WikiWorks",Bacterial taxa differentially abundant in patients before treatment (BT) compared to after treatment (AT),decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",1783272|201174|1760|85006|1268;1783272|201174|1760|85006|1268|32207,Complete,Svetlana up
bsdb:35787106/1/1,35787106,laboratory experiment,35787106,10.1080/19490976.2022.2085961,NA,"Rodriguez Paris V., Wong X.Y.D., Solon-Biet S.M., Edwards M.C., Aflatounian A., Gilchrist R.B., Simpson S.J., Handelsman D.J., Kaakoush N.O. , Walters K.A.",The interplay between PCOS pathology and diet on gut microbiota in a mouse model,Gut microbes,2022,"Microbiome, PCOS, animal model, diet, hyperandrogenism, polycystic ovary syndrome",Experiment 1,Australia,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Controls,polycystic ovary syndrome (PCOS)-like mice,"Dihydrotestosterone (DHT)-induced PCOS- like mice exposed to diets that varied in protein (P), carbohydrate (C) and fat (F) content.",NA,NA,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 3b,14 May 2024,Scholastica,"Scholastica,WikiWorks",Abundant OTU’s identified as being significantly different in control compared to polycystic ovary syndrome (PCOS)-like mice,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",1783272|1239|186801|186802;3379134|1224;1783272|1239|526524|526525|128827,Complete,Svetlana up
bsdb:35787106/1/2,35787106,laboratory experiment,35787106,10.1080/19490976.2022.2085961,NA,"Rodriguez Paris V., Wong X.Y.D., Solon-Biet S.M., Edwards M.C., Aflatounian A., Gilchrist R.B., Simpson S.J., Handelsman D.J., Kaakoush N.O. , Walters K.A.",The interplay between PCOS pathology and diet on gut microbiota in a mouse model,Gut microbes,2022,"Microbiome, PCOS, animal model, diet, hyperandrogenism, polycystic ovary syndrome",Experiment 1,Australia,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Controls,polycystic ovary syndrome (PCOS)-like mice,"Dihydrotestosterone (DHT)-induced PCOS- like mice exposed to diets that varied in protein (P), carbohydrate (C) and fat (F) content.",NA,NA,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 3b,14 May 2024,Scholastica,"Scholastica,WikiWorks",Abundant OTU’s identified as being significantly different in control compared to polycystic ovary syndrome (PCOS)-like mice,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Aestuariispiraceae|g__Aestuariispira",3379134|976|200643|171549|171551;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005525|375288;3379134|1224|28211|204441|3466454|1647175,Complete,Svetlana up
bsdb:35798742/2/1,35798742,case-control,35798742,https://doi.org/10.1038/s41531-022-00351-6,NA,"Jo S., Kang W., Hwang Y.S., Lee S.H., Park K.W., Kim M.S., Lee H., Yoon H.J., Park Y.K., Chalita M., Lee J.H., Sung H., Lee J.Y., Bae J.W. , Chung S.J.",Oral and gut dysbiosis leads to functional alterations in Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 2,South Korea,Homo sapiens,Buccal mucosa,UBERON:0006956,Parkinson's disease symptom measurement,EFO:0600011,Patients with mild Parkinson's disease  (mild PD),Patients with severe Parkinson's disease (severe PD),Patients with Parkinson's disease whose H&Y stage was 3 or greater,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary figure 3d,30 March 2024,Idiaru angela,"Idiaru angela,WikiWorks",Comparison of oral microbiome between mild PD and severe PD using LEfSe analysis,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia",1783272|1239|909932|1843489|31977|906;1783272|201174|1760|85004|31953|1678;3379134|976|117743|200644|49546|1016;3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|33958|1578;1783272|201174|84998|84999|1643824|133925;1783272|1239|186801|186802|186806|113286;1783272|201174|1760|85004|31953|196081,Complete,Svetlana up
bsdb:35798742/2/2,35798742,case-control,35798742,https://doi.org/10.1038/s41531-022-00351-6,NA,"Jo S., Kang W., Hwang Y.S., Lee S.H., Park K.W., Kim M.S., Lee H., Yoon H.J., Park Y.K., Chalita M., Lee J.H., Sung H., Lee J.Y., Bae J.W. , Chung S.J.",Oral and gut dysbiosis leads to functional alterations in Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 2,South Korea,Homo sapiens,Buccal mucosa,UBERON:0006956,Parkinson's disease symptom measurement,EFO:0600011,Patients with mild Parkinson's disease  (mild PD),Patients with severe Parkinson's disease (severe PD),Patients with Parkinson's disease whose H&Y stage was 3 or greater,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary figure 3d,30 March 2024,Idiaru angela,"Idiaru angela,WikiWorks",Comparison of oral microbiome between mild PD and severe PD using LEfSe analysis,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,3379134|1224|28216|80840|119060|47670,Complete,Svetlana up
bsdb:35798742/3/1,35798742,case-control,35798742,https://doi.org/10.1038/s41531-022-00351-6,NA,"Jo S., Kang W., Hwang Y.S., Lee S.H., Park K.W., Kim M.S., Lee H., Yoon H.J., Park Y.K., Chalita M., Lee J.H., Sung H., Lee J.Y., Bae J.W. , Chung S.J.",Oral and gut dysbiosis leads to functional alterations in Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease symptom measurement,EFO:0600011,Patients with mild Parkinson's disease  (mild PD),Patients with severe Parkinson's disease (severe PD),Parkinson's disease patients whose H&Y scale stage was 3 or greater.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary figure 3b,30 March 2024,Idiaru angela,"Idiaru angela,WikiWorks",Comparison of gut microbiome between mild PD and severe PD using LEfSe analysis.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Cellulosilyticaceae|g__Cellulosilyticum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus",1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|3018741|698776;1783272|1239|186801|3085636|186803|33042;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|33958|1578;1783272|201174|84998|84999|1643824|133925;3379134|1224|1236|91347|1903414|583,Complete,Svetlana up
bsdb:35798742/3/2,35798742,case-control,35798742,https://doi.org/10.1038/s41531-022-00351-6,NA,"Jo S., Kang W., Hwang Y.S., Lee S.H., Park K.W., Kim M.S., Lee H., Yoon H.J., Park Y.K., Chalita M., Lee J.H., Sung H., Lee J.Y., Bae J.W. , Chung S.J.",Oral and gut dysbiosis leads to functional alterations in Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease symptom measurement,EFO:0600011,Patients with mild Parkinson's disease  (mild PD),Patients with severe Parkinson's disease (severe PD),Parkinson's disease patients whose H&Y scale stage was 3 or greater.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary figure 3b,30 March 2024,Idiaru angela,"Idiaru angela,WikiWorks",Comparison of gut microbiome between mild PD and severe PD using LEfSe analysis,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira",1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|3118652|2039240;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803|28050,Complete,Svetlana up
bsdb:35798742/4/1,35798742,case-control,35798742,https://doi.org/10.1038/s41531-022-00351-6,NA,"Jo S., Kang W., Hwang Y.S., Lee S.H., Park K.W., Kim M.S., Lee H., Yoon H.J., Park Y.K., Chalita M., Lee J.H., Sung H., Lee J.Y., Bae J.W. , Chung S.J.",Oral and gut dysbiosis leads to functional alterations in Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 4,South Korea,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls (HC),Patients with Parkinson's Disease (PD),Patients with Parkinson's disease enrolled using the UK PD Society brain bank clinical diagnostic criteria.,84,88,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 1,"figure 1e & text in paragraph 4, page 4",30 March 2024,Idiaru angela,"Idiaru angela,WikiWorks",Comparison of the gut microbiome between PD and HCs using genus level LEfSe analysis.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter",3379134|976|200643|171549|171550|239759;1783272|201174|1760|85004|31953|1678;1783272|201174|84998|84999|84107|102106;3379134|1224|1236|91347|543|561;1783272|1239|186801|3085636|186803|1649459;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3082720|543314|86331;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|216572|44748,Complete,Svetlana up
bsdb:35798742/4/2,35798742,case-control,35798742,https://doi.org/10.1038/s41531-022-00351-6,NA,"Jo S., Kang W., Hwang Y.S., Lee S.H., Park K.W., Kim M.S., Lee H., Yoon H.J., Park Y.K., Chalita M., Lee J.H., Sung H., Lee J.Y., Bae J.W. , Chung S.J.",Oral and gut dysbiosis leads to functional alterations in Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 4,South Korea,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls (HC),Patients with Parkinson's Disease (PD),Patients with Parkinson's disease enrolled using the UK PD Society brain bank clinical diagnostic criteria.,84,88,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 2,figure 1e,30 March 2024,Idiaru angela,"Idiaru angela,WikiWorks",Comparison of gut microbiome between PD and HCs using genus level LEfSe analysis.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|33042;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|135625|712|724;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263,Complete,Svetlana up
bsdb:35798742/5/1,35798742,case-control,35798742,https://doi.org/10.1038/s41531-022-00351-6,NA,"Jo S., Kang W., Hwang Y.S., Lee S.H., Park K.W., Kim M.S., Lee H., Yoon H.J., Park Y.K., Chalita M., Lee J.H., Sung H., Lee J.Y., Bae J.W. , Chung S.J.",Oral and gut dysbiosis leads to functional alterations in Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 5,South Korea,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls (HC),Patients with Parkinson's Disease (PD),Patients with Parkinson's disease enrolled using the UK PD Society brain bank clinical diagnostic criteria.,84,88,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,"Figure 3c & paragraph 2, page 5",30 March 2024,Idiaru angela,"Idiaru angela,WikiWorks",Gut microbial species-level community structures based on whole-genome shotgun sequencing between HC and PD.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter|s__Dysosmobacter welbionis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei",3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|815|816|246787;3379134|976|200643|171549|815|816|28111;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|2005519|397864|487174;3379134|200940|3031449|213115|194924|35832|35833;3379134|976|200643|171549|1853231|574697|544645;1783272|1239|186801|3085636|186803|3342669|45851;1783272|1239|186801|186802|216572|2591381|2093857;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|2005525|375288|46503;1783272|1239|909932|1843488|909930|33024|33025;3379134|976|200643|171549|815|909656|357276,Complete,Svetlana up
bsdb:35798742/5/2,35798742,case-control,35798742,https://doi.org/10.1038/s41531-022-00351-6,NA,"Jo S., Kang W., Hwang Y.S., Lee S.H., Park K.W., Kim M.S., Lee H., Yoon H.J., Park Y.K., Chalita M., Lee J.H., Sung H., Lee J.Y., Bae J.W. , Chung S.J.",Oral and gut dysbiosis leads to functional alterations in Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 5,South Korea,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls (HC),Patients with Parkinson's Disease (PD),Patients with Parkinson's disease enrolled using the UK PD Society brain bank clinical diagnostic criteria.,84,88,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 3c,30 March 2024,Idiaru angela,"Idiaru angela,WikiWorks",Gut microbial species-level community structures based on whole-genome shotgun sequencing between HC and PD.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri",1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|186802|204475|745368;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|186801|186802|216572|1263|40519;3379134|976|200643|171549|171552|2974251|165179,Complete,Svetlana up
bsdb:35847083/1/1,35847083,case-control,35847083,10.3389/fmicb.2022.911992,NA,"Li G., Liu Z., Ren F., Shi H., Zhao Q., Song Y., Fan X., Ma X. , Qin G.",Alterations of Gut Microbiome and Fecal Fatty Acids in Patients With Polycystic Ovary Syndrome in Central China,Frontiers in microbiology,2022,"16S rRNA gene sequencing, fecal fatty acids, gut microbiome, polycystic ovary syndrome, untargeted metabolomics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy Control,PCOS (Polycystic Ovary Syndrome),Women diagnosed with Polycystic Ovary Syndrome (PCOS) according to the Rotterdam criteria,27,31,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 5A & 5B,18 May 2025,Ese,"Ese,Tosin",Results of LefSe analysis showing differentially abundant taxa between Healthy control and Women with Polycystic Ovary Syndrome (PCOS),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",3379134|1224|1236|91347|543|544;1783272|1239|186801|3085636|186803|189330;3379134|1224|1236;1783272|1239|186801|3082720|186804|1505657;3379134|1224|1236|91347|543|570;3379134|976|200643|171549|2005473;1783272|1239|186801|3082720|186804;1783272|1239|91061|186826|33958|46255;3379134|1224|1236|91347|543;3379134|976|200643|171549|2005473;1783272|1239|186801|3082720|186804,Complete,Svetlana up
bsdb:35847083/1/2,35847083,case-control,35847083,10.3389/fmicb.2022.911992,NA,"Li G., Liu Z., Ren F., Shi H., Zhao Q., Song Y., Fan X., Ma X. , Qin G.",Alterations of Gut Microbiome and Fecal Fatty Acids in Patients With Polycystic Ovary Syndrome in Central China,Frontiers in microbiology,2022,"16S rRNA gene sequencing, fecal fatty acids, gut microbiome, polycystic ovary syndrome, untargeted metabolomics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy Control,PCOS (Polycystic Ovary Syndrome),Women diagnosed with Polycystic Ovary Syndrome (PCOS) according to the Rotterdam criteria,27,31,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 5A & 5B,19 May 2025,Ese,"Ese,Chloe",Results of LefSe analysis showing differentially abundant taxa between Healthy control and Women with Polycystic Ovary Syndrome (PCOS),decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,1783272|1239|186801|186802|404402,Complete,Svetlana up
bsdb:35847083/2/1,35847083,case-control,35847083,10.3389/fmicb.2022.911992,NA,"Li G., Liu Z., Ren F., Shi H., Zhao Q., Song Y., Fan X., Ma X. , Qin G.",Alterations of Gut Microbiome and Fecal Fatty Acids in Patients With Polycystic Ovary Syndrome in Central China,Frontiers in microbiology,2022,"16S rRNA gene sequencing, fecal fatty acids, gut microbiome, polycystic ovary syndrome, untargeted metabolomics",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,PCOST (PCOS patients with BMI<24 kg/m²),PCOSF (PCOS patients with BMI≥24kg/m²),Participants were categorized into this subgroup based on a body mass index(BMI) greater than or equal to 24kg/m²,19,12,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Supplementary Figure 4A & 4B,3 June 2025,Ese,Ese,Results of Lesfe analysis showing significantly abundant bacterial groups and dominant flora between PCOSF and PCOST,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|91061|186826|186827|46123;1783272|1239|91061|186826|186827;1783272|1239|91061;1783272|1239|91061|186826|186828;1783272|1239|186801|186802|31979|1485;1783272|1239|91061|186826|186828|117563;1783272|1239|91061|186826;1783272|1239|186801|3082720|186804;1783272|201174|84998|1643822|1643826|84108;3379134|1224|28216|80840|995019|40544;1783272|1239|909932|1843489|31977,Complete,Svetlana up
bsdb:35847083/2/2,35847083,case-control,35847083,10.3389/fmicb.2022.911992,NA,"Li G., Liu Z., Ren F., Shi H., Zhao Q., Song Y., Fan X., Ma X. , Qin G.",Alterations of Gut Microbiome and Fecal Fatty Acids in Patients With Polycystic Ovary Syndrome in Central China,Frontiers in microbiology,2022,"16S rRNA gene sequencing, fecal fatty acids, gut microbiome, polycystic ovary syndrome, untargeted metabolomics",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,PCOST (PCOS patients with BMI<24 kg/m²),PCOSF (PCOS patients with BMI≥24kg/m²),Participants were categorized into this subgroup based on a body mass index(BMI) greater than or equal to 24kg/m²,19,12,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Supplementary Figure 4A & 4B,4 June 2025,Ese,"Ese,Tosin",Results of Lesfe analysis showing significantly abundant bacterial groups and dominant flora between PCOSF and PCOST,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",1783272|1239|186801|186802|1470353;1783272|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:35847083/3/1,35847083,case-control,35847083,10.3389/fmicb.2022.911992,NA,"Li G., Liu Z., Ren F., Shi H., Zhao Q., Song Y., Fan X., Ma X. , Qin G.",Alterations of Gut Microbiome and Fecal Fatty Acids in Patients With Polycystic Ovary Syndrome in Central China,Frontiers in microbiology,2022,"16S rRNA gene sequencing, fecal fatty acids, gut microbiome, polycystic ovary syndrome, untargeted metabolomics",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy Control,PCOS (Polycystic Ovary Syndrome),Women diagnosed with Polycystic Ovary Syndrome (PCOS) according to the Rotterdam criteria,27,31,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 4B & D,10 November 2025,Ese,"Ese,Tosin",The composition and differences of gut microbiota between PCOS (Polycystic Ovary Syndrome) and healthy controls at family and genus level,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",3379134|1224|1236|91347|543|544;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3082720|186804|1505657;3379134|1224|1236|91347|543|570;3379134|976|200643|171549|2005473;1783272|1239|186801|3082720|186804;1783272|1239|91061|186826|33958|46255;3379134|1224|1236|91347|543;3379134|976|200643|171549|2005473;1783272|1239|186801|3082720|186804,Complete,Svetlana up
bsdb:35847083/3/2,35847083,case-control,35847083,10.3389/fmicb.2022.911992,NA,"Li G., Liu Z., Ren F., Shi H., Zhao Q., Song Y., Fan X., Ma X. , Qin G.",Alterations of Gut Microbiome and Fecal Fatty Acids in Patients With Polycystic Ovary Syndrome in Central China,Frontiers in microbiology,2022,"16S rRNA gene sequencing, fecal fatty acids, gut microbiome, polycystic ovary syndrome, untargeted metabolomics",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy Control,PCOS (Polycystic Ovary Syndrome),Women diagnosed with Polycystic Ovary Syndrome (PCOS) according to the Rotterdam criteria,27,31,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 4B & D,10 November 2025,Ese,Ese,The composition and differences of gut microbiota between PCOS (Polycystic Ovary Syndrome) and healthy controls at family and genus level,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,1783272|1239|186801|186802|404402,Complete,Svetlana up
bsdb:35847083/4/1,35847083,case-control,35847083,10.3389/fmicb.2022.911992,NA,"Li G., Liu Z., Ren F., Shi H., Zhao Q., Song Y., Fan X., Ma X. , Qin G.",Alterations of Gut Microbiome and Fecal Fatty Acids in Patients With Polycystic Ovary Syndrome in Central China,Frontiers in microbiology,2022,"16S rRNA gene sequencing, fecal fatty acids, gut microbiome, polycystic ovary syndrome, untargeted metabolomics",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,PCOST (PCOS patients with BMI <24 kg/m²),PCOSF (PCOS patients with BMI≥24kg/m²),Participants were categorized into this subgroup based on a body mass index(BMI) greater than or equal to 24kg/m²,19,12,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Supplementary Figure 3B & 3D,11 November 2025,Ese,"Ese,Tosin",Composition and differences of the gut microbiome of PCOSF and PCOST at family and genus level,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|91061|186826|186827|46123;1783272|1239|91061|186826|186827;1783272|1239|91061|186826|186828;1783272|1239|186801|186802|31979|1485;1783272|1239|91061|186826|186828|117563;1783272|1239|186801|3082720|186804;1783272|201174|84998|1643822|1643826|84108;3379134|1224|28216|80840|995019|40544;1783272|1239|909932|1843489|31977,Complete,Svetlana up
bsdb:35847083/4/2,35847083,case-control,35847083,10.3389/fmicb.2022.911992,NA,"Li G., Liu Z., Ren F., Shi H., Zhao Q., Song Y., Fan X., Ma X. , Qin G.",Alterations of Gut Microbiome and Fecal Fatty Acids in Patients With Polycystic Ovary Syndrome in Central China,Frontiers in microbiology,2022,"16S rRNA gene sequencing, fecal fatty acids, gut microbiome, polycystic ovary syndrome, untargeted metabolomics",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,PCOST (PCOS patients with BMI <24 kg/m²),PCOSF (PCOS patients with BMI≥24kg/m²),Participants were categorized into this subgroup based on a body mass index(BMI) greater than or equal to 24kg/m²,19,12,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Supplementary Figure 3B & 3D,11 November 2025,Ese,"Ese,Tosin",Composition and differences of the gut microbiome of PCOSF and PCOST at family and genus level,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",1783272|1239|186801|186802|1470353;1783272|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:35847083/5/1,35847083,case-control,35847083,10.3389/fmicb.2022.911992,NA,"Li G., Liu Z., Ren F., Shi H., Zhao Q., Song Y., Fan X., Ma X. , Qin G.",Alterations of Gut Microbiome and Fecal Fatty Acids in Patients With Polycystic Ovary Syndrome in Central China,Frontiers in microbiology,2022,"16S rRNA gene sequencing, fecal fatty acids, gut microbiome, polycystic ovary syndrome, untargeted metabolomics",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Fasting blood glucose measurement,EFO:0004465,Low FBG (Low Fasting blood glucose),High FBG (High Fasting blood glucose),Participants in this group had high fasting blood glucose levels,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A,27 November 2025,Ese,Ese,Heatmap of correlation analysis between gut microflora and clinical indexes of PCOS,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,1783272|1239|186801|3082720|186804,Complete,Svetlana up
bsdb:35847083/5/2,35847083,case-control,35847083,10.3389/fmicb.2022.911992,NA,"Li G., Liu Z., Ren F., Shi H., Zhao Q., Song Y., Fan X., Ma X. , Qin G.",Alterations of Gut Microbiome and Fecal Fatty Acids in Patients With Polycystic Ovary Syndrome in Central China,Frontiers in microbiology,2022,"16S rRNA gene sequencing, fecal fatty acids, gut microbiome, polycystic ovary syndrome, untargeted metabolomics",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Fasting blood glucose measurement,EFO:0004465,Low FBG (Low Fasting blood glucose),High FBG (High Fasting blood glucose),Participants in this group had high fasting blood glucose levels,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6A,27 November 2025,Ese,Ese,Heatmap of correlation analysis between gut microflora and clinical indexes of PCOS,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:35847083/6/1,35847083,case-control,35847083,10.3389/fmicb.2022.911992,NA,"Li G., Liu Z., Ren F., Shi H., Zhao Q., Song Y., Fan X., Ma X. , Qin G.",Alterations of Gut Microbiome and Fecal Fatty Acids in Patients With Polycystic Ovary Syndrome in Central China,Frontiers in microbiology,2022,"16S rRNA gene sequencing, fecal fatty acids, gut microbiome, polycystic ovary syndrome, untargeted metabolomics",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Metabolite measurement,EFO:0004725,Low D-LA (Low D-Lactic acid),High D-LA (High D-Lactic acid),Participants in this group had high D-Lactic acid levels,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A,27 November 2025,Ese,Ese,Heatmap of correlation analysis between gut microflora and clinical indexes of PCOS,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,1783272|1239|186801|3082720|186804,Complete,Svetlana up
bsdb:35847083/8/1,35847083,case-control,35847083,10.3389/fmicb.2022.911992,NA,"Li G., Liu Z., Ren F., Shi H., Zhao Q., Song Y., Fan X., Ma X. , Qin G.",Alterations of Gut Microbiome and Fecal Fatty Acids in Patients With Polycystic Ovary Syndrome in Central China,Frontiers in microbiology,2022,"16S rRNA gene sequencing, fecal fatty acids, gut microbiome, polycystic ovary syndrome, untargeted metabolomics",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Insulin measurement,EFO:0004467,Low INS (Low insulin levels),High INS (High insulin levels),Participants in this group had high insulin levels,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A,27 November 2025,Ese,Ese,Heatmap of correlation analysis between gut microflora and clinical indexes of PCOS,increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,1783272|1239|909932|909929|1843491|158846,Complete,Svetlana up
bsdb:35847083/8/2,35847083,case-control,35847083,10.3389/fmicb.2022.911992,NA,"Li G., Liu Z., Ren F., Shi H., Zhao Q., Song Y., Fan X., Ma X. , Qin G.",Alterations of Gut Microbiome and Fecal Fatty Acids in Patients With Polycystic Ovary Syndrome in Central China,Frontiers in microbiology,2022,"16S rRNA gene sequencing, fecal fatty acids, gut microbiome, polycystic ovary syndrome, untargeted metabolomics",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Insulin measurement,EFO:0004467,Low INS (Low insulin levels),High INS (High insulin levels),Participants in this group had high insulin levels,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6A,27 November 2025,Ese,Ese,Heatmap of correlation analysis between gut microflora and clinical indexes of PCOS,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:35847083/9/1,35847083,case-control,35847083,10.3389/fmicb.2022.911992,NA,"Li G., Liu Z., Ren F., Shi H., Zhao Q., Song Y., Fan X., Ma X. , Qin G.",Alterations of Gut Microbiome and Fecal Fatty Acids in Patients With Polycystic Ovary Syndrome in Central China,Frontiers in microbiology,2022,"16S rRNA gene sequencing, fecal fatty acids, gut microbiome, polycystic ovary syndrome, untargeted metabolomics",Experiment 9,China,Homo sapiens,Feces,UBERON:0001988,Body mass index,EFO:0004340,Low BMI (Low Body mass index),High BMI (High Body mass index),Participants in this group had high body mass index,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A,27 November 2025,Ese,Ese,Heatmap of correlation analysis between gut microflora and clinical indexes of PCOS,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,1783272|1239|186801|3085636|186803|572511,Complete,Svetlana up
bsdb:35847083/10/1,35847083,case-control,35847083,10.3389/fmicb.2022.911992,NA,"Li G., Liu Z., Ren F., Shi H., Zhao Q., Song Y., Fan X., Ma X. , Qin G.",Alterations of Gut Microbiome and Fecal Fatty Acids in Patients With Polycystic Ovary Syndrome in Central China,Frontiers in microbiology,2022,"16S rRNA gene sequencing, fecal fatty acids, gut microbiome, polycystic ovary syndrome, untargeted metabolomics",Experiment 10,China,Homo sapiens,Feces,UBERON:0001988,Waist-hip ratio,EFO:0004343,Low WHR (Low Waist-hip ratio),High WHR (High Waist-hip ratio),Participants in this group had high waist-hip ratio,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A,27 November 2025,Ese,Ese,Heatmap of correlation analysis between gut microflora and clinical indexes of PCOS,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,1783272|1239|186801|186802|216572|216851,Complete,Svetlana up
bsdb:35847083/11/1,35847083,case-control,35847083,10.3389/fmicb.2022.911992,NA,"Li G., Liu Z., Ren F., Shi H., Zhao Q., Song Y., Fan X., Ma X. , Qin G.",Alterations of Gut Microbiome and Fecal Fatty Acids in Patients With Polycystic Ovary Syndrome in Central China,Frontiers in microbiology,2022,"16S rRNA gene sequencing, fecal fatty acids, gut microbiome, polycystic ovary syndrome, untargeted metabolomics",Experiment 11,China,Homo sapiens,Feces,UBERON:0001988,Testosterone measurement,EFO:0004908,Low FT (Low Free testosterone levels),High FT (High Free testosterone levels),Participants in this group had high free testosterone levels,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A,27 November 2025,Ese,Ese,Heatmap of correlation analysis between gut microflora and clinical indexes of PCOS,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843489|31977|39948,Complete,Svetlana up
bsdb:35847083/11/2,35847083,case-control,35847083,10.3389/fmicb.2022.911992,NA,"Li G., Liu Z., Ren F., Shi H., Zhao Q., Song Y., Fan X., Ma X. , Qin G.",Alterations of Gut Microbiome and Fecal Fatty Acids in Patients With Polycystic Ovary Syndrome in Central China,Frontiers in microbiology,2022,"16S rRNA gene sequencing, fecal fatty acids, gut microbiome, polycystic ovary syndrome, untargeted metabolomics",Experiment 11,China,Homo sapiens,Feces,UBERON:0001988,Testosterone measurement,EFO:0004908,Low FT (Low Free testosterone levels),High FT (High Free testosterone levels),Participants in this group had high free testosterone levels,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6A,14 December 2025,Ese,Ese,Heatmap of correlation analysis between gut microflora and clinical indexes of PCOS,decreased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,1783272|1239|909932|1843488|909930|33024,Complete,Svetlana up
bsdb:35847083/12/1,35847083,case-control,35847083,10.3389/fmicb.2022.911992,NA,"Li G., Liu Z., Ren F., Shi H., Zhao Q., Song Y., Fan X., Ma X. , Qin G.",Alterations of Gut Microbiome and Fecal Fatty Acids in Patients With Polycystic Ovary Syndrome in Central China,Frontiers in microbiology,2022,"16S rRNA gene sequencing, fecal fatty acids, gut microbiome, polycystic ovary syndrome, untargeted metabolomics",Experiment 12,China,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Age (Decreasing),Age (Increasing),Participants with increased age,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A,27 November 2025,Ese,"Ese,Tosin",Heatmap of correlation analysis between gut microflora and clinical indexes of PCOS,increased,NA,NA,Complete,Svetlana up
bsdb:35847083/13/1,35847083,case-control,35847083,10.3389/fmicb.2022.911992,NA,"Li G., Liu Z., Ren F., Shi H., Zhao Q., Song Y., Fan X., Ma X. , Qin G.",Alterations of Gut Microbiome and Fecal Fatty Acids in Patients With Polycystic Ovary Syndrome in Central China,Frontiers in microbiology,2022,"16S rRNA gene sequencing, fecal fatty acids, gut microbiome, polycystic ovary syndrome, untargeted metabolomics",Experiment 13,China,Homo sapiens,Feces,UBERON:0001988,Testosterone measurement,EFO:0004908,Low TT(Low Total testosterone levels),High TT (High Total testosterone levels),Participants in this group had high total testosterone levels,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A,27 November 2025,Ese,Ese,Heatmap of correlation analysis between gut microflora and clinical indexes of PCOS,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella",3379134|976|200643|171549|171550|239759;3379134|1224|28216|80840|995019|577310,Complete,Svetlana up
bsdb:35847083/14/1,35847083,case-control,35847083,10.3389/fmicb.2022.911992,NA,"Li G., Liu Z., Ren F., Shi H., Zhao Q., Song Y., Fan X., Ma X. , Qin G.",Alterations of Gut Microbiome and Fecal Fatty Acids in Patients With Polycystic Ovary Syndrome in Central China,Frontiers in microbiology,2022,"16S rRNA gene sequencing, fecal fatty acids, gut microbiome, polycystic ovary syndrome, untargeted metabolomics",Experiment 14,China,Homo sapiens,Feces,UBERON:0001988,Androstenedione measurement,NA,Low AD (Low Androstenedione levels),High AD (High Androstenedione levels),Participants in this group had high Androstenedione levels,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A,14 December 2025,Ese,Ese,Heatmap of correlation analysis between gut microflora and clinical indexes of PCOS,increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,1783272|1239|909932|909929|1843491|158846,Complete,Svetlana up
bsdb:35847083/15/1,35847083,case-control,35847083,10.3389/fmicb.2022.911992,NA,"Li G., Liu Z., Ren F., Shi H., Zhao Q., Song Y., Fan X., Ma X. , Qin G.",Alterations of Gut Microbiome and Fecal Fatty Acids in Patients With Polycystic Ovary Syndrome in Central China,Frontiers in microbiology,2022,"16S rRNA gene sequencing, fecal fatty acids, gut microbiome, polycystic ovary syndrome, untargeted metabolomics",Experiment 15,China,Homo sapiens,Feces,UBERON:0001988,Dehydroepiandrosterone sulphate measurement,EFO:0007001,Low DHEA-S (Low Dehydroepiandrosterone sulphate levels),High DHEA-S (High Dehydroepiandrosterone sulphate levels),Participants in this group had high Dehydroepiandrosterone sulphate levels,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A,14 December 2025,Ese,"Ese,Tosin",Heatmap of correlation analysis between gut microflora and clinical indexes of PCOS,decreased,NA,NA,Complete,Svetlana up
bsdb:35852145/1/1,35852145,case-control,35852145,10.1002/ana.26454,NA,"Bolliri C., Fontana A., Cereda E., Barichella M., Cilia R., Ferri V., Caronni S., Calandrella D., Morelli L. , Pezzoli G.",Gut Microbiota in Monozygotic Twins Discordant for Parkinson's Disease,Annals of neurology,2022,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls - co-twins,Parkinson’s disease patients (PD patients),Parkinson’s disease patients (PD patients) refers to monozygotic twin patients diagnosed with Parkinson’s disease.,20,20,2 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"In text of the ""Results"" section.",3 March 2025,KateRasheed,KateRasheed,Significant differences in bacterial taxa abundance at species level between Control co-twins and PD patients; after adjusting for the duration of disease.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__[Bacteroides] pectinophilus",1783272|201174|1760|85004|31953|1678|1686;1783272|1239|186801|186802|384638,Complete,Svetlana up
bsdb:35852145/2/1,35852145,case-control,35852145,10.1002/ana.26454,NA,"Bolliri C., Fontana A., Cereda E., Barichella M., Cilia R., Ferri V., Caronni S., Calandrella D., Morelli L. , Pezzoli G.",Gut Microbiota in Monozygotic Twins Discordant for Parkinson's Disease,Annals of neurology,2022,NA,Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls - co-twins,Parkinson’s disease patients (PD patients),Parkinson’s disease patients (PD patients) refers to monozygotic twin patients diagnosed with PD.,20,20,2 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 1,3 March 2025,KateRasheed,KateRasheed,Significant differences in bacterial taxa abundance at species level between Control co-twins and PD patients,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__[Bacteroides] pectinophilus",1783272|201174|1760|85004|31953|1678|28026;1783272|201174|1760|85004|31953|1678|1686;1783272|1239|186801|186802|384638,Complete,Svetlana up
bsdb:35863004/1/1,35863004,case-control,35863004,10.1128/spectrum.00324-22,NA,"Zhang L., Wang Z., Zhang X., Zhao L., Chu J., Li H., Sun W., Yang C., Wang H., Dai W., Yan S., Chen X. , Xu D.",Alterations of the Gut Microbiota in Patients with Diabetic Nephropathy,Microbiology spectrum,2022,"composition, diabetic nephropathy, function, gut microbiota, metagenomics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Diabetic nephropathy,EFO:0000401,healthy controls (CON),Diabetic nephropathy (DN),"Patients with diabetic nephropathy (DN). DN is a chronic kidney disease (CKD), which is one of the most common complications of diabetic microangiopathy and the primary cause of end-stage renal disease (ESRD).",14,12,1 month,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,FIG 3 (B),12 March 2024,Rahila,"Rahila,ChiomaBlessing,WikiWorks",Differentially abundant taxa identified in the diabetic nephropathy (DN) group compared to the healthy control (CON) group,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes ihumii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp. 20_3,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. MSX73,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella sp. CAG:51",3379134|976|200643|171549|171550|239759|1470347;3379134|976|200643|171549|815|816|46506;3379134|976|200643|171549|815|816|46506;3379134|976|200643|171549|2005519|397864|2033407;3379134|976|200643|171549|2005525|375288|469591;3379134|976|200643|171549|171552|838|1032506;3379134|976|200643|171549|2005525|195950|1262979,Complete,ChiomaBlessing
bsdb:35863004/2/1,35863004,case-control,35863004,10.1128/spectrum.00324-22,NA,"Zhang L., Wang Z., Zhang X., Zhao L., Chu J., Li H., Sun W., Yang C., Wang H., Dai W., Yan S., Chen X. , Xu D.",Alterations of the Gut Microbiota in Patients with Diabetic Nephropathy,Microbiology spectrum,2022,"composition, diabetic nephropathy, function, gut microbiota, metagenomics",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,healthy controls (CON),type 2 diabetes mellitus (T2DM),Patients with type 2 diabetes mellitus (T2DM) without DN,14,12,1 month,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,FIG 3 (B),12 March 2024,Rahila,"Rahila,ChiomaBlessing,WikiWorks",Differentially abundant taxa identified in the Type 2 diabetes mellitus (T2DM) group compared to the healthy control (CON) group,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides hominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. PHL 2737,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:715,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp. AF19-14,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:873,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",3379134|976|200643|171549|815|816|2763023;3379134|976|200643|171549|815|816|2162637;1783272|1239|186801|186802|31979|1485|1262834;1783272|1239|91061|186826|33958|2742598|97478;3379134|976|200643|171549|2005525|375288|2293114;3379134|976|200643|171549|171552|838|1262936;1783272|1239|909932|1843489|31977|29465|39778,Complete,ChiomaBlessing
bsdb:35865814/1/1,35865814,"cross-sectional observational, not case-control",35865814,10.3389/fcimb.2022.894777,NA,"Sarkar P., Malik S., Banerjee A., Datta C., Pal D.K., Ghosh A. , Saha A.",Differential Microbial Signature Associated With Benign Prostatic Hyperplasia and Prostate Cancer,Frontiers in cellular and infection microbiology,2022,"EBV, HPV, benign prostate hyperplasia, microbiome, prostate cancer",Experiment 1,India,Homo sapiens,Prostate gland,UBERON:0002367,Prostate carcinoma,EFO:0001663,"Benign prostatic hyperplasia (BPH),  Cohort-1 (Discovery Cohort)","Prostate Cancer (PCa),  Cohort-1 (Discovery Cohort)",Patients who are diagnosed with Prostate Cancer (PCa),13,33,NA,16S,23456789,Ion Torrent,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,"Fig 2D, Supp. Fig 1E",6 April 2024,Ayibatari,"Ayibatari,Scholastica,WikiWorks",Differential Microbial Signature Associated With Benign Prostatic Hyperplasia versus Prostate Cancer.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Leclercia|s__Leclercia adecarboxylata,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter|s__Caulobacter segnis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus|s__Cupriavidus basilensis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium cytisi,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter junii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas|s__Brevundimonas vancanneytii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium|s__Methylobacterium organophilum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus|s__Cupriavidus taiwanensis",3379134|1224|28211|356|41294|374;3379134|1224|28216|206351|481|482|495;3379134|1224|1236|91347|543|83654|83655;3379134|1224|28211|204458|76892|75|88688;3379134|1224|28216|80840|119060|106589|68895;3379134|1224|28211|356|41294|374|515489;3379134|1224|1236|2887326|468|469|40215;3379134|1224|28216|206351|481|482|484;3379134|1224|28211|204458|76892|41275|1325724;3379134|1224|28211|356|119045|407|410;3379134|1224|28216|80840|119060|106589|164546,Complete,Svetlana up
bsdb:35865814/1/2,35865814,"cross-sectional observational, not case-control",35865814,10.3389/fcimb.2022.894777,NA,"Sarkar P., Malik S., Banerjee A., Datta C., Pal D.K., Ghosh A. , Saha A.",Differential Microbial Signature Associated With Benign Prostatic Hyperplasia and Prostate Cancer,Frontiers in cellular and infection microbiology,2022,"EBV, HPV, benign prostate hyperplasia, microbiome, prostate cancer",Experiment 1,India,Homo sapiens,Prostate gland,UBERON:0002367,Prostate carcinoma,EFO:0001663,"Benign prostatic hyperplasia (BPH),  Cohort-1 (Discovery Cohort)","Prostate Cancer (PCa),  Cohort-1 (Discovery Cohort)",Patients who are diagnosed with Prostate Cancer (PCa),13,33,NA,16S,23456789,Ion Torrent,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,"Fig 2D, Supp. Fig 1E",6 April 2024,Ayibatari,"Ayibatari,Scholastica,WikiWorks",Differential Microbial Signature Associated With Benign Prostatic Hyperplasia versus Prostate Cancer.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Aeromicrobium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Cellvibrio,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Empedobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Microvirga,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Pseudoxanthomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|g__Rhodobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Ornithinimicrobiaceae|g__Serinicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria|s__Kocuria palustris,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Cellvibrio|s__Cellvibrio mixtus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Stutzerimonas|s__Stutzerimonas stutzeri,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium tuberculostearicum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium|s__Brachybacterium paraconglomeratum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus arlettae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus cohnii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus octavius",1783272|201174|1760|85009|85015|2040;1783272|1239|1737404|1737405|1570339|165779;1783272|201174|1760|85006|85020|43668;1783272|201174|1760|85006|85019|1696;3379134|1224|1236|1706369|1706371|10;3379134|976|117743|200644|2762318|59732;3379134|1224|28216|80840|80864|283;1783272|201174|1760|85007|1653|1716;3379134|976|117743|200644|2762318|59734;1783272|201174|1760|85006|1268|57493;3379134|1224|1236|135614|32033|68;3379134|1224|28211|356|119045|186650;3379134|1224|28211|204455|31989|265;3379134|1224|1236|72274|135621|286;3379134|1224|1236|135614|32033|83618;3379134|1224|28211|204455|1060;1783272|201174|1760|85006|2805590|265976;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|135614|32033|40323;1783272|201174|1760|85006|1268|57493|71999;3379134|1224|1236|1706369|1706371|10|39650;3379134|1224|1236|72274|135621|2901164|316;1783272|1239|91061|1385|90964|1279|1290;1783272|201174|1760|85007|1653|1716|38304;1783272|201174|1760|85006|85020|43668|173362;1783272|1239|91061|1385|90964|1279|29378;1783272|1239|91061|1385|90964|1279|29382;1783272|1239|1737404|1737405|1570339|165779|54007,Complete,Svetlana up
bsdb:35888992/1/1,35888992,case-control,35888992,10.3390/microorganisms10071273,NA,"Olbjørn C., Småstuen M.C. , Moen A.E.F.","Targeted Analysis of the Gut Microbiome for Diagnosis, Prognosis and Treatment Individualization in Pediatric Inflammatory Bowel Disease",Microorganisms,2022,"IBD, biologic therapy, biomarker, microbiota, pediatric, prognosis",Experiment 1,Norway,Homo sapiens,Feces,UBERON:0001988,Inflammatory bowel disease,EFO:0003767,Healthy controls,Inflammatory bowel disease patients,Patients under 18 years old diagnosed with inflammatory bowel disease (Crohn's Disease or ulcerative colitis) from the catchment areas of two university hospitals in three population-based prospective epidemiological studies of treatment-naïve pediatric IBD in South-Eastern Norway between 2005-2015.,75,107,6 months,PCR,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 December 2023,Yjung24,"Yjung24,WikiWorks",Bacterial species exhibiting deviating abundances between patient and control groups. IBD vs Healthy.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium angulatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella minuta,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus paracasei,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila",1783272|201174|1760|85004|31953|1678|1683;1783272|201174|1760|85004|31953|1678|1681;1783272|201174|1760|85004|31953|1678|1686;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|186801|3082768|990719|990721|626937;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|3085636|186803|1506553|29347;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|91061|186826|33958|1578|1579;1783272|1239|91061|186826|33958|2759736|1597;3366610|28890|183925|2158|2159|2172|2173;3379134|976|200643|171549|171552|577309|454154;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|91061|186826|1300|1301|1305;1783272|1239|91061|186826|1300|1301|1308;3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|171550|239759|328813;1783272|1239|186801|3085636|186803|207244|649756;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|2005519|397864|487174;1783272|1239|186801|3082720|186804|1505657|261299;3379134|74201|203494|48461|1647988|239934|239935,Complete,Chloe
bsdb:35888992/2/1,35888992,case-control,35888992,10.3390/microorganisms10071273,NA,"Olbjørn C., Småstuen M.C. , Moen A.E.F.","Targeted Analysis of the Gut Microbiome for Diagnosis, Prognosis and Treatment Individualization in Pediatric Inflammatory Bowel Disease",Microorganisms,2022,"IBD, biologic therapy, biomarker, microbiota, pediatric, prognosis",Experiment 2,Norway,Homo sapiens,Feces,UBERON:0001988,Inflammatory bowel disease,EFO:0003767,Healthy children,Non-inflammatory bowel disease symptomatic controls,patients under 18 years presented with symptoms of inflammatory bowel disease (Crohn's Disease or ulcerative colitis) but did not meet the criteria for IBD and who had a  macroscopically and histologically normal mucosa and normal MRI examination from the catchment areas of two university hospitals in three population-based prospective epidemiological studies of treatment-naïve pediatric IBD in South-Eastern Norway between 2005-2015.,75,50,6 months,PCR,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 December 2023,Yjung24,"Yjung24,WikiWorks",Bacterial species exhibiting deviating abundances between patient and control groups. Non-IBD vs. Healthy.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium angulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei",1783272|201174|1760|85004|31953|1678|1683;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|186802|216572|39492;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|91061|186826|1300|1301|1308;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|909656|357276,Complete,Chloe
bsdb:35888992/2/2,35888992,case-control,35888992,10.3390/microorganisms10071273,NA,"Olbjørn C., Småstuen M.C. , Moen A.E.F.","Targeted Analysis of the Gut Microbiome for Diagnosis, Prognosis and Treatment Individualization in Pediatric Inflammatory Bowel Disease",Microorganisms,2022,"IBD, biologic therapy, biomarker, microbiota, pediatric, prognosis",Experiment 2,Norway,Homo sapiens,Feces,UBERON:0001988,Inflammatory bowel disease,EFO:0003767,Healthy children,Non-inflammatory bowel disease symptomatic controls,patients under 18 years presented with symptoms of inflammatory bowel disease (Crohn's Disease or ulcerative colitis) but did not meet the criteria for IBD and who had a  macroscopically and histologically normal mucosa and normal MRI examination from the catchment areas of two university hospitals in three population-based prospective epidemiological studies of treatment-naïve pediatric IBD in South-Eastern Norway between 2005-2015.,75,50,6 months,PCR,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,10 December 2023,Yjung24,"Yjung24,WikiWorks",Bacterial species exhibiting deviating abundances between patient and control groups. Non-IBD vs. Healthy.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri",1783272|1239|91061|186826|81852|1350|1352;3379134|1224|1236|91347|543|544|545,Complete,Chloe
bsdb:35888992/3/1,35888992,case-control,35888992,10.3390/microorganisms10071273,NA,"Olbjørn C., Småstuen M.C. , Moen A.E.F.","Targeted Analysis of the Gut Microbiome for Diagnosis, Prognosis and Treatment Individualization in Pediatric Inflammatory Bowel Disease",Microorganisms,2022,"IBD, biologic therapy, biomarker, microbiota, pediatric, prognosis",Experiment 3,Norway,Homo sapiens,Feces,UBERON:0001988,Inflammatory bowel disease,EFO:0003767,non-inflammatory bowel disease symptomatic controls,inflammatory bowel disease patients,patients under 18 diagnosed with inflammatory bowel disease (Crohn's Disease or ulcerative colitis) from the catchment areas of two university hospitals in three population-based prospective epidemiological studies of treatment-naïve pediatric IBD in South-Eastern Norway between 2005-2015.,50,110,6 months,PCR,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 December 2023,Yjung24,"Yjung24,WikiWorks",Bacterial species exhibiting deviating abundances between patient and control groups.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium angulatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella minuta,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus paracasei,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila",3379134|976|200643|171549|171552|577309|454154;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|1683;1783272|201174|1760|85004|31953|1678|1681;1783272|1239|186801|3082768|990719|990721|626937;1783272|1239|186801|186802|216572|1535;3379134|200940|3031449|213115|194924|872|901;1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|186802|216572|39492;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|91061|186826|33958|1578|1579;1783272|1239|91061|186826|33958|2759736|1597;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|186802|216572|1263|40518;3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|816|46506;3379134|74201|203494|48461|1647988|239934|239935,Complete,Chloe
bsdb:35888992/3/2,35888992,case-control,35888992,10.3390/microorganisms10071273,NA,"Olbjørn C., Småstuen M.C. , Moen A.E.F.","Targeted Analysis of the Gut Microbiome for Diagnosis, Prognosis and Treatment Individualization in Pediatric Inflammatory Bowel Disease",Microorganisms,2022,"IBD, biologic therapy, biomarker, microbiota, pediatric, prognosis",Experiment 3,Norway,Homo sapiens,Feces,UBERON:0001988,Inflammatory bowel disease,EFO:0003767,non-inflammatory bowel disease symptomatic controls,inflammatory bowel disease patients,patients under 18 diagnosed with inflammatory bowel disease (Crohn's Disease or ulcerative colitis) from the catchment areas of two university hospitals in three population-based prospective epidemiological studies of treatment-naïve pediatric IBD in South-Eastern Norway between 2005-2015.,50,110,6 months,PCR,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,10 December 2023,Yjung24,"Yjung24,WikiWorks",Bacterial species exhibiting deviating abundances between patient and control groups. IBD vs. Non-IBD.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,3379134|1224|1236|135625|712|724|729,Complete,Chloe
bsdb:35888992/4/1,35888992,case-control,35888992,10.3390/microorganisms10071273,NA,"Olbjørn C., Småstuen M.C. , Moen A.E.F.","Targeted Analysis of the Gut Microbiome for Diagnosis, Prognosis and Treatment Individualization in Pediatric Inflammatory Bowel Disease",Microorganisms,2022,"IBD, biologic therapy, biomarker, microbiota, pediatric, prognosis",Experiment 4,Norway,Homo sapiens,Feces,UBERON:0001988,Phenotype,EFO:0000651,Crohn's Disease patients with inflammatory phenotypes,Crohn's Disease patients with stricturing and/or penetrating phenotypes,patients under 18 diagnosed with Crohn's Disease with stricturing and/or penetrating phenotypes,53,27,6 months,PCR,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Section 3.4 (text),10 December 2023,Yjung24,"Yjung24,WikiWorks","The CD patients had a significantly lower abundance for five bacterial species and a
higher abundance for five bacterial species. The CD patients with stricturing and/or penetrating phenotypes had a lower abundance of four species and a higher abundance of Escherichia coli (p = 0.010) compared to the CD patients
with an inflammatory phenotype.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella minuta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis",1783272|1239|186801|3082768|990719|990721|626937;1783272|1239|186801|3085636|186803|1506553|29347;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|841|301301,Complete,Chloe
bsdb:35888992/4/2,35888992,case-control,35888992,10.3390/microorganisms10071273,NA,"Olbjørn C., Småstuen M.C. , Moen A.E.F.","Targeted Analysis of the Gut Microbiome for Diagnosis, Prognosis and Treatment Individualization in Pediatric Inflammatory Bowel Disease",Microorganisms,2022,"IBD, biologic therapy, biomarker, microbiota, pediatric, prognosis",Experiment 4,Norway,Homo sapiens,Feces,UBERON:0001988,Phenotype,EFO:0000651,Crohn's Disease patients with inflammatory phenotypes,Crohn's Disease patients with stricturing and/or penetrating phenotypes,patients under 18 diagnosed with Crohn's Disease with stricturing and/or penetrating phenotypes,53,27,6 months,PCR,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Section 3.4 (text),10 December 2023,Yjung24,"Yjung24,WikiWorks",The CD patients had a significantly lower abundance for five bacterial species and a higher abundance for five bacterial species. The CD patients with stricturing and/or penetrating phenotypes had a lower abundance of four species and a higher abundance of Escherichia coli (p = 0.010) compared to the CD patients with an inflammatory phenotype.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,3379134|1224|1236|91347|543|561|562,Complete,Chloe
bsdb:35888992/5/1,35888992,case-control,35888992,10.3390/microorganisms10071273,NA,"Olbjørn C., Småstuen M.C. , Moen A.E.F.","Targeted Analysis of the Gut Microbiome for Diagnosis, Prognosis and Treatment Individualization in Pediatric Inflammatory Bowel Disease",Microorganisms,2022,"IBD, biologic therapy, biomarker, microbiota, pediatric, prognosis",Experiment 5,Norway,Homo sapiens,Feces,UBERON:0001988,Treatment,EFO:0000727,Inflammatory bowel disease patients treated with conventional therapy,Inflammatory bowel disease patients treated with biological therapy,58% of inflammatory bowel disease patients were later treated with biologic therapy due to failure to induce remission with conventional treatments or relapse after primary induction.,46,64,6 months,PCR,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 December 2023,Yjung24,"Yjung24,WikiWorks","Bacterial species exhibiting deviating abundances between medical therapy groups and
between groups with high and low calprotectin levels.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara",1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|1681;1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|186802|216572|1263|40518;3379134|976|200643|171549|815|816|338188;3379134|976|200643|171549|815|816|329854;3379134|976|200643|171549|815|816|246787;3379134|976|200643|171549|171552|577309|454154,Complete,Chloe
bsdb:35888992/5/2,35888992,case-control,35888992,10.3390/microorganisms10071273,NA,"Olbjørn C., Småstuen M.C. , Moen A.E.F.","Targeted Analysis of the Gut Microbiome for Diagnosis, Prognosis and Treatment Individualization in Pediatric Inflammatory Bowel Disease",Microorganisms,2022,"IBD, biologic therapy, biomarker, microbiota, pediatric, prognosis",Experiment 5,Norway,Homo sapiens,Feces,UBERON:0001988,Treatment,EFO:0000727,Inflammatory bowel disease patients treated with conventional therapy,Inflammatory bowel disease patients treated with biological therapy,58% of inflammatory bowel disease patients were later treated with biologic therapy due to failure to induce remission with conventional treatments or relapse after primary induction.,46,64,6 months,PCR,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,10 December 2023,Yjung24,"Yjung24,WikiWorks","Bacterial species exhibiting deviating abundances between medical therapy groups and
between groups with high and low calprotectin levels.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus",1783272|1239|186801|3085636|186803|2316020|33038;3379134|976|200643|171549|815|909656|821,Complete,Chloe
bsdb:35888992/6/1,35888992,case-control,35888992,10.3390/microorganisms10071273,NA,"Olbjørn C., Småstuen M.C. , Moen A.E.F.","Targeted Analysis of the Gut Microbiome for Diagnosis, Prognosis and Treatment Individualization in Pediatric Inflammatory Bowel Disease",Microorganisms,2022,"IBD, biologic therapy, biomarker, microbiota, pediatric, prognosis",Experiment 6,Norway,Homo sapiens,Feces,UBERON:0001988,Increased inflammatory response,HP:0012649,Inflammatory bowel disease patients with fecal calprotectin levels < 1000 mg/kg,Inflammatory bowel disease patients with fecal calprotectin levels > 1000 mg/kg,Inflammatory bowel disease patients with higher fecal protectin levels (31 with CD and 12 with UC had above 1000 mg/kg).,67,43,6 months,PCR,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 December 2023,Yjung24,"Yjung24,WikiWorks","Bacterial species exhibiting deviating abundances between medical therapy groups and
between groups with high and low calprotectin levels.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis",1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|3085636|186803|841|166486;3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|2005519|397864|487174,Complete,Chloe
bsdb:35888992/7/1,35888992,case-control,35888992,10.3390/microorganisms10071273,NA,"Olbjørn C., Småstuen M.C. , Moen A.E.F.","Targeted Analysis of the Gut Microbiome for Diagnosis, Prognosis and Treatment Individualization in Pediatric Inflammatory Bowel Disease",Microorganisms,2022,"IBD, biologic therapy, biomarker, microbiota, pediatric, prognosis",Experiment 7,Norway,Homo sapiens,Feces,UBERON:0001988,Increased inflammatory response,HP:0012649,Inflammatory bowel disease patients receiving one biologic or conventional therapy,Inflammatory bowel disease patients receiving second class of biologic drug,A subset of the IBD patients receiving biologic therapy needed further treatment escalation to a second class of biologics.,88,22,6 months,PCR,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text: Page 6 Paragraph 2,21 January 2024,Yjung24,"Yjung24,WikiWorks","A subset of the IBD patients receiving biologic therapy needed further treatment escalation to a second class of biologics. These patients had a significantly lower abundance of Bifidobacterium bifidum, Roseburia hominis and Bacteroides xylanisolvens compared to the IBD patients who received one biologic or conventional therapy.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens",1783272|201174|1760|85004|31953|1678|1681;1783272|1239|186801|3085636|186803|841|301301;3379134|976|200643|171549|815|816|371601,Complete,NA
bsdb:35900092/1/1,35900092,case-control,35900092,https://doi.org/10.1128/spectrum.01676-22,NA,"Yang X., Pan X., Li M., Zeng Z., Guo Y., Chen P., Liang X., Chen P. , Liu G.",Interaction between Cervical Microbiota and Host Gene Regulation in Caesarean Section Scar Diverticulum,Microbiology spectrum,2022,"cesarean section scar diverticulum, gene regulation, host-microbiota interaction, microbiome",Experiment 1,China,Homo sapiens,"Uterine cervix,Endometrium","UBERON:0000002,UBERON:0001295",Cesarean section,EFO:0009636,Control,Cesarean section scar diverticulum (CSD),"Women with cesarean section scar diverticulum (CSD), a complication that can occur following a cesarean section (C-section) delivery.",24,28,1 month,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,figure 2,17 March 2024,Eve10111,"Eve10111,Scholastica,WikiWorks",Differential genera between cesarean section scar diverticulum (CSD) and control group based on linear discriminant analysis (LDA),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|976|200643|171549|815|816;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|1940338;1783272|201174|1760|85004|31953|2701;3379134|976|200643|171549|2005473;3379134|976|200643|171549|171552|838;3379134|1224|28216|80840|119060|48736;3379134|1224|28211|204457|41297|13687;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:35900092/1/2,35900092,case-control,35900092,https://doi.org/10.1128/spectrum.01676-22,NA,"Yang X., Pan X., Li M., Zeng Z., Guo Y., Chen P., Liang X., Chen P. , Liu G.",Interaction between Cervical Microbiota and Host Gene Regulation in Caesarean Section Scar Diverticulum,Microbiology spectrum,2022,"cesarean section scar diverticulum, gene regulation, host-microbiota interaction, microbiome",Experiment 1,China,Homo sapiens,"Uterine cervix,Endometrium","UBERON:0000002,UBERON:0001295",Cesarean section,EFO:0009636,Control,Cesarean section scar diverticulum (CSD),"Women with cesarean section scar diverticulum (CSD), a complication that can occur following a cesarean section (C-section) delivery.",24,28,1 month,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,figure 2,17 March 2024,Eve10111,"Eve10111,Scholastica,WikiWorks",Differential genera between cesarean section scar diverticulum (CSD) and control group based on linear discriminant analysis (LDA),decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239|526524|526525|128827|1729679;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:35928983/1/1,35928983,"cross-sectional observational, not case-control",35928983,https://doi.org/10.1158/2767-9764.CRC-22-0075,NA,"Hakimjavadi H., George S.H., Taub M., Dodds L.V., Sanchez-Covarrubias A.P., Huang M., Pearson J.M., Slomovitz B.M., Kobetz E.N., Gharaibeh R., Sowamber R., Pinto A., Chamala S. , Schlumbrecht M.P.",The vaginal microbiome is associated with endometrial cancer grade and histology,Cancer research communications,2022,"Endometrial cancer, high-grade, low-grade, metagenomics, microbiome",Experiment 1,United States of America,Homo sapiens,Vagina,UBERON:0000996,Endometrial cancer,MONDO:0011962,Benign,Tumor (Low Grade + High Grade),Tumor represents patients with low grade and high grade endometrial cancer.,11,50,2 weeks,WMS,NA,BGISEQ-500 Sequencing,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 3A,21 November 2024,Prolific,"Prolific,KateRasheed,WikiWorks",Differential abundance of taxa between Tumor and Benign patients,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis",1783272|1239|186801|186802|31979|1485|1506;3379134|976|200643|171549|171551|836|281920,Complete,Svetlana up
bsdb:35928983/1/2,35928983,"cross-sectional observational, not case-control",35928983,https://doi.org/10.1158/2767-9764.CRC-22-0075,NA,"Hakimjavadi H., George S.H., Taub M., Dodds L.V., Sanchez-Covarrubias A.P., Huang M., Pearson J.M., Slomovitz B.M., Kobetz E.N., Gharaibeh R., Sowamber R., Pinto A., Chamala S. , Schlumbrecht M.P.",The vaginal microbiome is associated with endometrial cancer grade and histology,Cancer research communications,2022,"Endometrial cancer, high-grade, low-grade, metagenomics, microbiome",Experiment 1,United States of America,Homo sapiens,Vagina,UBERON:0000996,Endometrial cancer,MONDO:0011962,Benign,Tumor (Low Grade + High Grade),Tumor represents patients with low grade and high grade endometrial cancer.,11,50,2 weeks,WMS,NA,BGISEQ-500 Sequencing,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 3A,25 December 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between Tumor and Benign patients,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Winkia|s__Winkia neuii",1783272|1239|91061|1385|90964|1279|1282;1783272|1239|91061|186826|1300|1301|1311;1783272|201174|1760|2037|2049|2692118|33007,Complete,Svetlana up
bsdb:35928983/2/1,35928983,"cross-sectional observational, not case-control",35928983,https://doi.org/10.1158/2767-9764.CRC-22-0075,NA,"Hakimjavadi H., George S.H., Taub M., Dodds L.V., Sanchez-Covarrubias A.P., Huang M., Pearson J.M., Slomovitz B.M., Kobetz E.N., Gharaibeh R., Sowamber R., Pinto A., Chamala S. , Schlumbrecht M.P.",The vaginal microbiome is associated with endometrial cancer grade and histology,Cancer research communications,2022,"Endometrial cancer, high-grade, low-grade, metagenomics, microbiome",Experiment 2,United States of America,Homo sapiens,Vagina,UBERON:0000996,Endometrial cancer,MONDO:0011962,Benign,High Grade,High Grade refers to patients with high grade endometrial cancer,11,20,2 weeks,WMS,NA,BGISEQ-500 Sequencing,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Fig. 3B,25 December 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between High grade and Benign patients,increased,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium ulcerans,3384189|32066|203490|203491|203492|848|861,Complete,Svetlana up
bsdb:35928983/2/2,35928983,"cross-sectional observational, not case-control",35928983,https://doi.org/10.1158/2767-9764.CRC-22-0075,NA,"Hakimjavadi H., George S.H., Taub M., Dodds L.V., Sanchez-Covarrubias A.P., Huang M., Pearson J.M., Slomovitz B.M., Kobetz E.N., Gharaibeh R., Sowamber R., Pinto A., Chamala S. , Schlumbrecht M.P.",The vaginal microbiome is associated with endometrial cancer grade and histology,Cancer research communications,2022,"Endometrial cancer, high-grade, low-grade, metagenomics, microbiome",Experiment 2,United States of America,Homo sapiens,Vagina,UBERON:0000996,Endometrial cancer,MONDO:0011962,Benign,High Grade,High Grade refers to patients with high grade endometrial cancer,11,20,2 weeks,WMS,NA,BGISEQ-500 Sequencing,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,Fig. 3B,25 December 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between High grade and Benign patients,decreased,"k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma parvum,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma urealyticum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus jensenii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia vaginalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus tetradius,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Winkia|s__Winkia neuii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum|s__Actinobaculum massiliense",1783272|544448|2790996|2790998|2129|134821;1783272|544448|2790996|2790998|2129|2130;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|91061|186826|1300|1301|1311;1783272|1239|91061|1385|90964|1279|1282;3379134|976|200643|171549|171552|838|419005;1783272|1239|91061|186826|33958|1578|109790;3384189|32066|203490|203491|1129771|168808|187101;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|91061|186826|33958|1578|47770;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|1685;1783272|201174|84998|84999|1643824|2767327|82135;1783272|1239|1737404|1737405|1570339|165779|33036;1783272|201174|1760|2037|2049|2692118|33007;1783272|201174|1760|2037|2049|76833|202789,Complete,Svetlana up
bsdb:35928983/3/1,35928983,"cross-sectional observational, not case-control",35928983,https://doi.org/10.1158/2767-9764.CRC-22-0075,NA,"Hakimjavadi H., George S.H., Taub M., Dodds L.V., Sanchez-Covarrubias A.P., Huang M., Pearson J.M., Slomovitz B.M., Kobetz E.N., Gharaibeh R., Sowamber R., Pinto A., Chamala S. , Schlumbrecht M.P.",The vaginal microbiome is associated with endometrial cancer grade and histology,Cancer research communications,2022,"Endometrial cancer, high-grade, low-grade, metagenomics, microbiome",Experiment 3,United States of America,Homo sapiens,Vagina,UBERON:0000996,Endometrial cancer,MONDO:0011962,Benign,Low Grade,Low Grade refers to patients with low grade endometrial cancer,11,30,2 weeks,WMS,NA,BGISEQ-500 Sequencing,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 3D,25 December 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between Low grade and Benign patients,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium amycolatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus duerdenii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis",1783272|1239|186801|186802|31979|1485|1506;1783272|201174|1760|85007|1653|1716|43765;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|1737404|1737405|1570339|162289|507750;3379134|976|200643|171549|171551|836|281920,Complete,Svetlana up
bsdb:35928983/3/2,35928983,"cross-sectional observational, not case-control",35928983,https://doi.org/10.1158/2767-9764.CRC-22-0075,NA,"Hakimjavadi H., George S.H., Taub M., Dodds L.V., Sanchez-Covarrubias A.P., Huang M., Pearson J.M., Slomovitz B.M., Kobetz E.N., Gharaibeh R., Sowamber R., Pinto A., Chamala S. , Schlumbrecht M.P.",The vaginal microbiome is associated with endometrial cancer grade and histology,Cancer research communications,2022,"Endometrial cancer, high-grade, low-grade, metagenomics, microbiome",Experiment 3,United States of America,Homo sapiens,Vagina,UBERON:0000996,Endometrial cancer,MONDO:0011962,Benign,Low Grade,Low Grade refers to patients with low grade endometrial cancer,11,30,2 weeks,WMS,NA,BGISEQ-500 Sequencing,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig. 3D,25 December 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between Low grade and Benign patients,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,1783272|1239|91061|1385|90964|1279|1282,Complete,Svetlana up
bsdb:35928983/4/1,35928983,"cross-sectional observational, not case-control",35928983,https://doi.org/10.1158/2767-9764.CRC-22-0075,NA,"Hakimjavadi H., George S.H., Taub M., Dodds L.V., Sanchez-Covarrubias A.P., Huang M., Pearson J.M., Slomovitz B.M., Kobetz E.N., Gharaibeh R., Sowamber R., Pinto A., Chamala S. , Schlumbrecht M.P.",The vaginal microbiome is associated with endometrial cancer grade and histology,Cancer research communications,2022,"Endometrial cancer, high-grade, low-grade, metagenomics, microbiome",Experiment 4,United States of America,Homo sapiens,Vagina,UBERON:0000996,Endometrial cancer,MONDO:0011962,Low Grade,High Grade,High Grade refers to patients with high grade endometrial cancer,30,20,2 weeks,WMS,NA,BGISEQ-500 Sequencing,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 3C,26 December 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between High grade and low grade patients,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium ulcerans",3379134|976|200643|171549|171552|838|28125;3384189|32066|203490|203491|203492|848|861,Complete,Svetlana up
bsdb:35928983/4/2,35928983,"cross-sectional observational, not case-control",35928983,https://doi.org/10.1158/2767-9764.CRC-22-0075,NA,"Hakimjavadi H., George S.H., Taub M., Dodds L.V., Sanchez-Covarrubias A.P., Huang M., Pearson J.M., Slomovitz B.M., Kobetz E.N., Gharaibeh R., Sowamber R., Pinto A., Chamala S. , Schlumbrecht M.P.",The vaginal microbiome is associated with endometrial cancer grade and histology,Cancer research communications,2022,"Endometrial cancer, high-grade, low-grade, metagenomics, microbiome",Experiment 4,United States of America,Homo sapiens,Vagina,UBERON:0000996,Endometrial cancer,MONDO:0011962,Low Grade,High Grade,High Grade refers to patients with high grade endometrial cancer,30,20,2 weeks,WMS,NA,BGISEQ-500 Sequencing,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig. 3C,26 December 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between High grade and low grade patients,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum|s__Actinobaculum massiliense,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia turicensis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus hydrogenalis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus lactolyticus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus prevotii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus tetradius,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma parvum,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma urealyticum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium amycolatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus jensenii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus helveticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus oris,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Mageeibacillus|s__Mageeibacillus indolicus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus curtisii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera genomosp. C1,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus mulieris,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus duerdenii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionimicrobium|s__Propionimicrobium lymphophilum",1783272|201174|1760|2037|2049|76833|202789;1783272|201174|1760|2037|2049|1654|29317;1783272|201174|1760|2037|2049|2529408|131111;1783272|1239|1737404|1737405|1570339|165779|33029;1783272|1239|1737404|1737405|1570339|165779|33032;1783272|1239|1737404|1737405|1570339|165779|33034;1783272|1239|1737404|1737405|1570339|165779|33036;1783272|201174|84998|84999|1643824|2767327|82135;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|186802|31979|1485|1506;1783272|544448|2790996|2790998|2129|134821;1783272|544448|2790996|2790998|2129|2130;1783272|201174|1760|85007|1653|1716|43765;1783272|1239|91061|186826|33958|1578|47770;1783272|1239|91061|186826|33958|1578|109790;1783272|1239|91061|186826|33958|1578|33959;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|91061|186826|33958|1578|1587;1783272|1239|91061|186826|33958|2742598|1632;1783272|1239|186801|186802|216572|1637257|884684;1783272|1239|909932|1843489|31977|906|2023260;1783272|201174|1760|2037|2049|2050|2051;1783272|1239|909932|1843489|31977|906|230139;1783272|201174|1760|2037|2049|2050|2052;1783272|1239|1737404|1737405|1570339|162289|507750;3384189|32066|203490|203491|1129771|168808|40543;1783272|1239|91061|186826|1300|1301|1311;1783272|201174|1760|85009|31957|203133|33012,Complete,Svetlana up
bsdb:35928983/5/1,35928983,"cross-sectional observational, not case-control",35928983,https://doi.org/10.1158/2767-9764.CRC-22-0075,NA,"Hakimjavadi H., George S.H., Taub M., Dodds L.V., Sanchez-Covarrubias A.P., Huang M., Pearson J.M., Slomovitz B.M., Kobetz E.N., Gharaibeh R., Sowamber R., Pinto A., Chamala S. , Schlumbrecht M.P.",The vaginal microbiome is associated with endometrial cancer grade and histology,Cancer research communications,2022,"Endometrial cancer, high-grade, low-grade, metagenomics, microbiome",Experiment 5,United States of America,Homo sapiens,Vagina,UBERON:0000996,Endometrial cancer,MONDO:0011962,Benign,Serous,"Serous histology is a term used to describe the histology of tumors, carcinomas, and other tissues that are associated with serum, the clear liquid part of blood.",11,NA,2 weeks,WMS,NA,BGISEQ-500 Sequencing,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 5A,26 December 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between Benign and Serous,increased,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium ulcerans,3384189|32066|203490|203491|203492|848|861,Complete,Svetlana up
bsdb:35928983/5/2,35928983,"cross-sectional observational, not case-control",35928983,https://doi.org/10.1158/2767-9764.CRC-22-0075,NA,"Hakimjavadi H., George S.H., Taub M., Dodds L.V., Sanchez-Covarrubias A.P., Huang M., Pearson J.M., Slomovitz B.M., Kobetz E.N., Gharaibeh R., Sowamber R., Pinto A., Chamala S. , Schlumbrecht M.P.",The vaginal microbiome is associated with endometrial cancer grade and histology,Cancer research communications,2022,"Endometrial cancer, high-grade, low-grade, metagenomics, microbiome",Experiment 5,United States of America,Homo sapiens,Vagina,UBERON:0000996,Endometrial cancer,MONDO:0011962,Benign,Serous,"Serous histology is a term used to describe the histology of tumors, carcinomas, and other tissues that are associated with serum, the clear liquid part of blood.",11,NA,2 weeks,WMS,NA,BGISEQ-500 Sequencing,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 5A,26 December 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between Benign and Serous,decreased,"k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma urealyticum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oulorum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella bergensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus mulieris,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus curtisii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus oris,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia|s__Facklamia hominis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter hominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium|s__Arcanobacterium sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus tetradius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus urinae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia turicensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Winkia|s__Winkia neuii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Gleimia|s__Gleimia europaea,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinotignum|s__Actinotignum schaalii",1783272|544448|2790996|2790998|2129|2130;3379134|976|200643|171549|2005525|195950|28112;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|91061|186826|1300|1301|1343;1783272|1239|91061|1385|90964|1279|1280;1783272|1239|91061|1385|90964|1279|1282;3379134|976|200643|171549|171552|838|28129;3379134|976|200643|171549|171552|2974251|28136;3379134|976|200643|171549|171552|838|419005;3379134|976|200643|171549|171552|52228|242750;3379134|976|200643|171549|171552|838|59823;1783272|1239|1737404|1737405|1570339|162289|33031;1783272|201174|1760|2037|2049|2050|2052;1783272|201174|1760|2037|2049|2050|2051;3384189|32066|203490|203491|1129771|32067|157688;1783272|1239|91061|186826|33958|2742598|1632;1783272|1239|91061|186826|33958|1578|147802;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|91061|186826|33958|2742598|1613;1783272|1239|186801|3082720|3118655|44259|143361;1783272|1239|91061|186826|186827|66831|178214;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|186801|3085636|186803|189330|39486;3379134|29547|3031852|213849|72294|194|76517;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|2037|2049|28263|72409;1783272|1239|1737404|1737405|1570339|165779|33036;1783272|1239|91061|186826|186827|1375|1376;1783272|201174|1760|2037|2049|2529408|131111;1783272|201174|1760|2037|2049|2692118|33007;1783272|201174|1760|2037|2049|1654|55565;1783272|201174|1760|2037|2049|2692113|66228;1783272|201174|1760|2037|2049|1653174|59505,Complete,Svetlana up
bsdb:35928983/6/1,35928983,"cross-sectional observational, not case-control",35928983,https://doi.org/10.1158/2767-9764.CRC-22-0075,NA,"Hakimjavadi H., George S.H., Taub M., Dodds L.V., Sanchez-Covarrubias A.P., Huang M., Pearson J.M., Slomovitz B.M., Kobetz E.N., Gharaibeh R., Sowamber R., Pinto A., Chamala S. , Schlumbrecht M.P.",The vaginal microbiome is associated with endometrial cancer grade and histology,Cancer research communications,2022,"Endometrial cancer, high-grade, low-grade, metagenomics, microbiome",Experiment 6,United States of America,Homo sapiens,Vagina,UBERON:0000996,Endometrial cancer,MONDO:0011962,Benign,Endometroid,Endometrioid histology is a type of endometrial carcinoma that is the most common histological type of uterine body cancer.,11,NA,2 weeks,WMS,NA,BGISEQ-500 Sequencing,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 5B,26 December 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between Benign and Endometroid,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,1783272|1239|91061|186826|33958|1578|1596,Complete,Svetlana up
bsdb:35928983/7/1,35928983,"cross-sectional observational, not case-control",35928983,https://doi.org/10.1158/2767-9764.CRC-22-0075,NA,"Hakimjavadi H., George S.H., Taub M., Dodds L.V., Sanchez-Covarrubias A.P., Huang M., Pearson J.M., Slomovitz B.M., Kobetz E.N., Gharaibeh R., Sowamber R., Pinto A., Chamala S. , Schlumbrecht M.P.",The vaginal microbiome is associated with endometrial cancer grade and histology,Cancer research communications,2022,"Endometrial cancer, high-grade, low-grade, metagenomics, microbiome",Experiment 7,United States of America,Homo sapiens,Vagina,UBERON:0000996,Endometrial cancer,MONDO:0011962,Endometroid,Serous,"Serous histology is a term used to describe the histology of tumors, carcinomas, and other tissues that are associated with serum, the clear liquid part of blood.",NA,NA,2 weeks,WMS,NA,BGISEQ-500 Sequencing,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 5C,26 December 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between Endometroid and Serous,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Gleimia|s__Gleimia europaea,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia turicensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus urinae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus hydrogenalis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus lactolyticus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus prevotii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus tetradius,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter hominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium amycolatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium aurimucosum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium glucuronolyticum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium jeikeium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium pseudogenitalium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium striatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia|s__Facklamia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Eremococcus|s__Eremococcus coleocola,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus helveticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus oris,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Pseudoleptotrichia|s__Pseudoleptotrichia goodfellowii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus curtisii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus mulieris,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus duerdenii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus harei,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella bergensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oulorum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionimicrobium|s__Propionimicrobium lymphophilum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus dysgalactiae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus equinus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudoporcinus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema phagedenis,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma urealyticum,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma parvum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella ratti",1783272|201174|1760|2037|2049|2692113|66228;1783272|201174|1760|2037|2049|1654|55565;1783272|201174|1760|2037|2049|2529408|131111;1783272|1239|91061|186826|186827|1375|1376;1783272|1239|1737404|1737405|1570339|165779|33029;1783272|1239|1737404|1737405|1570339|165779|33032;1783272|1239|1737404|1737405|1570339|165779|33034;1783272|1239|1737404|1737405|1570339|165779|33036;1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|1678|216816;3379134|29547|3031852|213849|72294|194|76517;1783272|201174|1760|85007|1653|1716|43765;1783272|201174|1760|85007|1653|1716|169292;1783272|201174|1760|85007|1653|1716|39791;1783272|201174|1760|85007|1653|1716|38289;1783272|201174|1760|85007|1653|1716|38303;1783272|201174|1760|85007|1653|1716|43770;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|91061|186826|81852|1350|1352;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|91061|186826|186827|66831|178214;1783272|1239|186801|3082720|3118655|44259|143361;1783272|1239|91061|186826|186827|171412|88132;1783272|1239|1737404|1737405|1570339|150022|1260;1783272|1239|91061|186826|33958|2742598|1613;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|91061|186826|33958|1578|1587;1783272|1239|91061|186826|33958|2742598|1632;1783272|1239|91061|186826|33958|1578|147802;3384189|32066|203490|203491|1129771|2755140|157692;3384189|32066|203490|203491|1129771|32067|157688;1783272|1239|186801|3085636|186803|265975|1969407;1783272|201174|1760|2037|2049|2050|2051;1783272|201174|1760|2037|2049|2050|2052;1783272|1239|1737404|1737405|1570339|162289|507750;1783272|1239|1737404|1737405|1570339|162289|54005;1783272|1239|1737404|1737405|1570339|162289|33031;3379134|976|200643|171549|171551|836|322095;3379134|976|200643|171549|171552|52228|242750;3379134|976|200643|171549|171552|2974251|28136;3379134|976|200643|171549|171552|838|28129;3379134|976|200643|171549|171552|838|59823;1783272|201174|1760|85009|31957|203133|33012;1783272|1239|91061|1385|90964|1279|1280;1783272|1239|91061|186826|1300|1301|1334;1783272|1239|91061|186826|1300|1301|1335;1783272|1239|91061|186826|1300|1301|361101;3379134|976|200643|171549|2005525|195950|28112;3379134|203691|203692|136|2845253|157|162;1783272|544448|2790996|2790998|2129|2130;1783272|544448|2790996|2790998|2129|134821;1783272|1239|909932|1843489|31977|29465|103892,Complete,Svetlana up
bsdb:35985814/1/1,35985814,"cross-sectional observational, not case-control",35985814,10.1681/ASN.2022030378,NA,"Holle J., Bartolomaeus H., Löber U., Behrens F., Bartolomaeus T.U.P., Anandakumar H., Wimmer M.I., Vu D.L., Kuhring M., Brüning U., Maifeld A., Geisberger S., Kempa S., Schumacher F., Kleuser B., Bufler P., Querfeld U., Kitschke S., Engler D., Kuhrt L.D., Drechsel O., Eckardt K.U., Forslund S.K., Thürmer A., McParland V., Kirwan J.A., Wilck N. , Müller D.",Inflammation in Children with CKD Linked to Gut Dysbiosis and Metabolite Imbalance,Journal of the American Society of Nephrology : JASN,2022,"cardiovascular disease, children, chronic inflammation, chronic kidney disease, dysbiosis, hypertension, immunology, pediatric nephrology, vascular disease",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Healthy controls (HC),Chronic Kidney Disease (CKD G3-G4),Patients with Chronic Kidney Disease (CKD) stage G3–G4 and an eGFR of 15–60 ml/min per 1.73 m2.,9,7,1 month,16S,34,Illumina,raw counts,DESeq2,0.1,TRUE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2D and Supplementary Figure 2,22 April 2025,MyleeeA,MyleeeA,"Taxonomic changes in the abundance of taxa on the genus, family, and phylum level. The heatmap shows significant changes in abundance using the DESeq2.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Cyanobacteriota",3379134|976|200643|171549|815|816;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|186802|216572|1263;1783272|1239|526524|526525|2810280|3025755;1783272|1117,Complete,KateRasheed
bsdb:35985814/1/2,35985814,"cross-sectional observational, not case-control",35985814,10.1681/ASN.2022030378,NA,"Holle J., Bartolomaeus H., Löber U., Behrens F., Bartolomaeus T.U.P., Anandakumar H., Wimmer M.I., Vu D.L., Kuhring M., Brüning U., Maifeld A., Geisberger S., Kempa S., Schumacher F., Kleuser B., Bufler P., Querfeld U., Kitschke S., Engler D., Kuhrt L.D., Drechsel O., Eckardt K.U., Forslund S.K., Thürmer A., McParland V., Kirwan J.A., Wilck N. , Müller D.",Inflammation in Children with CKD Linked to Gut Dysbiosis and Metabolite Imbalance,Journal of the American Society of Nephrology : JASN,2022,"cardiovascular disease, children, chronic inflammation, chronic kidney disease, dysbiosis, hypertension, immunology, pediatric nephrology, vascular disease",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Healthy controls (HC),Chronic Kidney Disease (CKD G3-G4),Patients with Chronic Kidney Disease (CKD) stage G3–G4 and an eGFR of 15–60 ml/min per 1.73 m2.,9,7,1 month,16S,34,Illumina,raw counts,DESeq2,0.1,TRUE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2D,22 April 2025,MyleeeA,MyleeeA,"Taxonomic changes in the abundance of taxa on the genus, family, and phylum level. The heatmap shows significant changes in abundance using the DESeq2.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3085636|186803|2316020|33039,Complete,KateRasheed
bsdb:35985814/2/1,35985814,"cross-sectional observational, not case-control",35985814,10.1681/ASN.2022030378,NA,"Holle J., Bartolomaeus H., Löber U., Behrens F., Bartolomaeus T.U.P., Anandakumar H., Wimmer M.I., Vu D.L., Kuhring M., Brüning U., Maifeld A., Geisberger S., Kempa S., Schumacher F., Kleuser B., Bufler P., Querfeld U., Kitschke S., Engler D., Kuhrt L.D., Drechsel O., Eckardt K.U., Forslund S.K., Thürmer A., McParland V., Kirwan J.A., Wilck N. , Müller D.",Inflammation in Children with CKD Linked to Gut Dysbiosis and Metabolite Imbalance,Journal of the American Society of Nephrology : JASN,2022,"cardiovascular disease, children, chronic inflammation, chronic kidney disease, dysbiosis, hypertension, immunology, pediatric nephrology, vascular disease",Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Clinical treatment,EFO:0007056,Healthy controls (HC),Hemodialysis (HD),"Patients with Chronic Kidney Disease stage G5D, receiving maintenance Hemodialysis (HD), and enrolled at an earliest of 4 weeks after initiation of Hemodialysis (HD).",9,8,1 month,16S,34,Illumina,raw counts,DESeq2,0.1,TRUE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2D,23 April 2025,MyleeeA,MyleeeA,"Taxonomic changes in the abundance of taxa on the genus, family, and phylum level. The heatmap shows significant changes in abundance using the DESeq2.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",1783272|1239|186801|186802|216572|258514;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005519|397864;3379134|1224|1236|91347|543|544;1783272|1239|526524|526525|128827|1472649;1783272|1239|526524|526525|2810280|3025755,Complete,KateRasheed
bsdb:35985814/2/2,35985814,"cross-sectional observational, not case-control",35985814,10.1681/ASN.2022030378,NA,"Holle J., Bartolomaeus H., Löber U., Behrens F., Bartolomaeus T.U.P., Anandakumar H., Wimmer M.I., Vu D.L., Kuhring M., Brüning U., Maifeld A., Geisberger S., Kempa S., Schumacher F., Kleuser B., Bufler P., Querfeld U., Kitschke S., Engler D., Kuhrt L.D., Drechsel O., Eckardt K.U., Forslund S.K., Thürmer A., McParland V., Kirwan J.A., Wilck N. , Müller D.",Inflammation in Children with CKD Linked to Gut Dysbiosis and Metabolite Imbalance,Journal of the American Society of Nephrology : JASN,2022,"cardiovascular disease, children, chronic inflammation, chronic kidney disease, dysbiosis, hypertension, immunology, pediatric nephrology, vascular disease",Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Clinical treatment,EFO:0007056,Healthy controls (HC),Hemodialysis (HD),"Patients with Chronic Kidney Disease stage G5D, receiving maintenance Hemodialysis (HD), and enrolled at an earliest of 4 weeks after initiation of Hemodialysis (HD).",9,8,1 month,16S,34,Illumina,raw counts,DESeq2,0.1,TRUE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2D and Supplementary Figure 2,23 April 2025,MyleeeA,MyleeeA,"Taxonomic changes in the abundance of taxa on the genus, family, and phylum level. The heatmap shows significant changes in abundance using the DESeq2.",decreased,"k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|1117;1783272|201174;1783272|544448;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|3085636|186803|1407607;1783272|201174|1760|85004|31953|1678,Complete,KateRasheed
bsdb:35985814/3/1,35985814,"cross-sectional observational, not case-control",35985814,10.1681/ASN.2022030378,NA,"Holle J., Bartolomaeus H., Löber U., Behrens F., Bartolomaeus T.U.P., Anandakumar H., Wimmer M.I., Vu D.L., Kuhring M., Brüning U., Maifeld A., Geisberger S., Kempa S., Schumacher F., Kleuser B., Bufler P., Querfeld U., Kitschke S., Engler D., Kuhrt L.D., Drechsel O., Eckardt K.U., Forslund S.K., Thürmer A., McParland V., Kirwan J.A., Wilck N. , Müller D.",Inflammation in Children with CKD Linked to Gut Dysbiosis and Metabolite Imbalance,Journal of the American Society of Nephrology : JASN,2022,"cardiovascular disease, children, chronic inflammation, chronic kidney disease, dysbiosis, hypertension, immunology, pediatric nephrology, vascular disease",Experiment 3,Germany,Homo sapiens,Feces,UBERON:0001988,Kidney transplant,EFO:0010134,Healthy controls (HC),Kidney transplantation (KT),"Patients after successful KT, at an earliest of 4 weeks after KT, without a history of rejection or chronic graft failure, and an eGFR of >60 ml/min per 1.73 m2",9,8,1 month,16S,34,Illumina,raw counts,DESeq2,0.1,TRUE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2D and Supplementary Figure 2,23 April 2025,MyleeeA,MyleeeA,"Taxonomic changes in the abundance of taxa on the genus, family, and phylum level. The heatmap shows significant changes in abundance using the DESeq2.",increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella",1783272|201174;1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005519|397864,Complete,KateRasheed
bsdb:35985814/3/2,35985814,"cross-sectional observational, not case-control",35985814,10.1681/ASN.2022030378,NA,"Holle J., Bartolomaeus H., Löber U., Behrens F., Bartolomaeus T.U.P., Anandakumar H., Wimmer M.I., Vu D.L., Kuhring M., Brüning U., Maifeld A., Geisberger S., Kempa S., Schumacher F., Kleuser B., Bufler P., Querfeld U., Kitschke S., Engler D., Kuhrt L.D., Drechsel O., Eckardt K.U., Forslund S.K., Thürmer A., McParland V., Kirwan J.A., Wilck N. , Müller D.",Inflammation in Children with CKD Linked to Gut Dysbiosis and Metabolite Imbalance,Journal of the American Society of Nephrology : JASN,2022,"cardiovascular disease, children, chronic inflammation, chronic kidney disease, dysbiosis, hypertension, immunology, pediatric nephrology, vascular disease",Experiment 3,Germany,Homo sapiens,Feces,UBERON:0001988,Kidney transplant,EFO:0010134,Healthy controls (HC),Kidney transplantation (KT),"Patients after successful KT, at an earliest of 4 weeks after KT, without a history of rejection or chronic graft failure, and an eGFR of >60 ml/min per 1.73 m2",9,8,1 month,16S,34,Illumina,raw counts,DESeq2,0.1,TRUE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2D,23 April 2025,MyleeeA,MyleeeA,"Taxonomic changes in the abundance of taxa on the genus, family, and phylum level. The heatmap shows significant changes in abundance using the DESeq2.",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,1783272|1239|186801|186802|216572|1263,Complete,KateRasheed
bsdb:35985814/4/1,35985814,"cross-sectional observational, not case-control",35985814,10.1681/ASN.2022030378,NA,"Holle J., Bartolomaeus H., Löber U., Behrens F., Bartolomaeus T.U.P., Anandakumar H., Wimmer M.I., Vu D.L., Kuhring M., Brüning U., Maifeld A., Geisberger S., Kempa S., Schumacher F., Kleuser B., Bufler P., Querfeld U., Kitschke S., Engler D., Kuhrt L.D., Drechsel O., Eckardt K.U., Forslund S.K., Thürmer A., McParland V., Kirwan J.A., Wilck N. , Müller D.",Inflammation in Children with CKD Linked to Gut Dysbiosis and Metabolite Imbalance,Journal of the American Society of Nephrology : JASN,2022,"cardiovascular disease, children, chronic inflammation, chronic kidney disease, dysbiosis, hypertension, immunology, pediatric nephrology, vascular disease",Experiment 4,Germany,Homo sapiens,Feces,UBERON:0001988,Clinical treatment,EFO:0007056,Chronic Kidney Disease (CKD),Hemodialysis (HD),"Patients with Chronic Kidney Disease stage G5D, receiving maintenance Hemodialysis (HD), and enrolled at an earliest of 4 weeks after initiation of Hemodialysis (HD).",7,8,1 month,16S,34,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2D,23 April 2025,MyleeeA,MyleeeA,"Taxonomic changes in the abundance of taxa on the genus, family, and phylum level. The heatmap shows significant changes in abundance using the DESeq2.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|976|200643|171549|2005519|397864;3379134|1224|1236|91347|543|1940338,Complete,KateRasheed
bsdb:35985814/4/2,35985814,"cross-sectional observational, not case-control",35985814,10.1681/ASN.2022030378,NA,"Holle J., Bartolomaeus H., Löber U., Behrens F., Bartolomaeus T.U.P., Anandakumar H., Wimmer M.I., Vu D.L., Kuhring M., Brüning U., Maifeld A., Geisberger S., Kempa S., Schumacher F., Kleuser B., Bufler P., Querfeld U., Kitschke S., Engler D., Kuhrt L.D., Drechsel O., Eckardt K.U., Forslund S.K., Thürmer A., McParland V., Kirwan J.A., Wilck N. , Müller D.",Inflammation in Children with CKD Linked to Gut Dysbiosis and Metabolite Imbalance,Journal of the American Society of Nephrology : JASN,2022,"cardiovascular disease, children, chronic inflammation, chronic kidney disease, dysbiosis, hypertension, immunology, pediatric nephrology, vascular disease",Experiment 4,Germany,Homo sapiens,Feces,UBERON:0001988,Clinical treatment,EFO:0007056,Chronic Kidney Disease (CKD),Hemodialysis (HD),"Patients with Chronic Kidney Disease stage G5D, receiving maintenance Hemodialysis (HD), and enrolled at an earliest of 4 weeks after initiation of Hemodialysis (HD).",7,8,1 month,16S,34,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2D and Supplementary Figure 2,23 April 2025,MyleeeA,MyleeeA,"Taxonomic changes in the abundance of taxa on the genus, family, and phylum level. The heatmap shows significant changes in abundance using the DESeq2.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Mycoplasmatota",1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3085636|186803|1506577;1783272|544448,Complete,KateRasheed
bsdb:35985814/5/1,35985814,"cross-sectional observational, not case-control",35985814,10.1681/ASN.2022030378,NA,"Holle J., Bartolomaeus H., Löber U., Behrens F., Bartolomaeus T.U.P., Anandakumar H., Wimmer M.I., Vu D.L., Kuhring M., Brüning U., Maifeld A., Geisberger S., Kempa S., Schumacher F., Kleuser B., Bufler P., Querfeld U., Kitschke S., Engler D., Kuhrt L.D., Drechsel O., Eckardt K.U., Forslund S.K., Thürmer A., McParland V., Kirwan J.A., Wilck N. , Müller D.",Inflammation in Children with CKD Linked to Gut Dysbiosis and Metabolite Imbalance,Journal of the American Society of Nephrology : JASN,2022,"cardiovascular disease, children, chronic inflammation, chronic kidney disease, dysbiosis, hypertension, immunology, pediatric nephrology, vascular disease",Experiment 5,Germany,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Kidney transplantation (KT),Chronic Kidney Disease (CKD),Patients with Chronic Kidney Disease (CKD) stage G3–G4 and an eGFR of 15–60 ml/min per 1.73 m2.,8,7,1 month,16S,34,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2D,23 April 2025,MyleeeA,MyleeeA,"Taxonomic changes in the abundance of taxa on the genus, family, and phylum level. The heatmap shows significant changes in abundance using the DESeq2.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|526524|526525|128827|1573535;3379134|1224|28216|80840|995019|577310,Complete,KateRasheed
bsdb:35985814/5/2,35985814,"cross-sectional observational, not case-control",35985814,10.1681/ASN.2022030378,NA,"Holle J., Bartolomaeus H., Löber U., Behrens F., Bartolomaeus T.U.P., Anandakumar H., Wimmer M.I., Vu D.L., Kuhring M., Brüning U., Maifeld A., Geisberger S., Kempa S., Schumacher F., Kleuser B., Bufler P., Querfeld U., Kitschke S., Engler D., Kuhrt L.D., Drechsel O., Eckardt K.U., Forslund S.K., Thürmer A., McParland V., Kirwan J.A., Wilck N. , Müller D.",Inflammation in Children with CKD Linked to Gut Dysbiosis and Metabolite Imbalance,Journal of the American Society of Nephrology : JASN,2022,"cardiovascular disease, children, chronic inflammation, chronic kidney disease, dysbiosis, hypertension, immunology, pediatric nephrology, vascular disease",Experiment 5,Germany,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Kidney transplantation (KT),Chronic Kidney Disease (CKD),Patients with Chronic Kidney Disease (CKD) stage G3–G4 and an eGFR of 15–60 ml/min per 1.73 m2.,8,7,1 month,16S,34,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2D,23 April 2025,MyleeeA,MyleeeA,"Taxonomic changes in the abundance of taxa on the genus, family, and phylum level. The heatmap shows significant changes in abundance using the DESeq2.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|1940338,Complete,KateRasheed
bsdb:35985814/6/1,35985814,"cross-sectional observational, not case-control",35985814,10.1681/ASN.2022030378,NA,"Holle J., Bartolomaeus H., Löber U., Behrens F., Bartolomaeus T.U.P., Anandakumar H., Wimmer M.I., Vu D.L., Kuhring M., Brüning U., Maifeld A., Geisberger S., Kempa S., Schumacher F., Kleuser B., Bufler P., Querfeld U., Kitschke S., Engler D., Kuhrt L.D., Drechsel O., Eckardt K.U., Forslund S.K., Thürmer A., McParland V., Kirwan J.A., Wilck N. , Müller D.",Inflammation in Children with CKD Linked to Gut Dysbiosis and Metabolite Imbalance,Journal of the American Society of Nephrology : JASN,2022,"cardiovascular disease, children, chronic inflammation, chronic kidney disease, dysbiosis, hypertension, immunology, pediatric nephrology, vascular disease",Experiment 6,Germany,Homo sapiens,Feces,UBERON:0001988,Clinical treatment,EFO:0007056,Kidney transplantation (KT),Hemodialysis (HD),"Patients with Chronic Kidney Disease stage G5D, receiving maintenance Hemodialysis (HD), and enrolled at an earliest of 4 weeks after initiation of Hemodialysis (HD).",8,8,1 month,16S,34,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2D,23 April 2025,MyleeeA,MyleeeA,"Taxonomic changes in the abundance of taxa on the genus, family, and phylum level. The heatmap shows significant changes in abundance using the DESeq2.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|1853231|574697;1783272|1239|526524|526525|128827|1573534;3379134|976|200643|171549|171552|838,Complete,KateRasheed
bsdb:35985814/6/2,35985814,"cross-sectional observational, not case-control",35985814,10.1681/ASN.2022030378,NA,"Holle J., Bartolomaeus H., Löber U., Behrens F., Bartolomaeus T.U.P., Anandakumar H., Wimmer M.I., Vu D.L., Kuhring M., Brüning U., Maifeld A., Geisberger S., Kempa S., Schumacher F., Kleuser B., Bufler P., Querfeld U., Kitschke S., Engler D., Kuhrt L.D., Drechsel O., Eckardt K.U., Forslund S.K., Thürmer A., McParland V., Kirwan J.A., Wilck N. , Müller D.",Inflammation in Children with CKD Linked to Gut Dysbiosis and Metabolite Imbalance,Journal of the American Society of Nephrology : JASN,2022,"cardiovascular disease, children, chronic inflammation, chronic kidney disease, dysbiosis, hypertension, immunology, pediatric nephrology, vascular disease",Experiment 6,Germany,Homo sapiens,Feces,UBERON:0001988,Clinical treatment,EFO:0007056,Kidney transplantation (KT),Hemodialysis (HD),"Patients with Chronic Kidney Disease stage G5D, receiving maintenance Hemodialysis (HD), and enrolled at an earliest of 4 weeks after initiation of Hemodialysis (HD).",8,8,1 month,16S,34,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2D and Supplementary Figure 2,23 April 2025,MyleeeA,MyleeeA,"Taxonomic changes in the abundance of taxa on the genus, family, and phylum level. The heatmap shows significant changes in abundance using the DESeq2.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|216572|1263;1783272|1117;1783272|1239|186801|186802|216572|1508657,Complete,KateRasheed
bsdb:35987213/1/1,35987213,randomized controlled trial,35987213,10.1016/j.cell.2022.07.016,https://pubmed.ncbi.nlm.nih.gov/35987213/,"Suez J., Cohen Y., Valdés-Mas R., Mor U., Dori-Bachash M., Federici S., Zmora N., Leshem A., Heinemann M., Linevsky R., Zur M., Ben-Zeev Brik R., Bukimer A., Eliyahu-Miller S., Metz A., Fischbein R., Sharov O., Malitsky S., Itkin M., Stettner N., Harmelin A., Shapiro H., Stein-Thoeringer C.K., Segal E. , Elinav E.",Personalized microbiome-driven effects of non-nutritive sweeteners on human glucose tolerance,Cell,2022,"artificial sweeteners, hyperglycemia, metabolic syndrome, metabolomics, metagenomics, microbiome, non-nutritive sweeteners",Experiment 1,Israel,Mus musculus,Feces,UBERON:0001988,Glucose tolerance test,EFO:0004307,Top Responder at Day 21,Bottom Responder at Day 21,The mice were recipients of the bottom sucralose responder human donors at 21 days.,3,3,NA,WMS,NA,Illumina,log transformation,Mixed-Effects Regression,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S7,28 March 2025,Shulamite,Shulamite,Linear mixed model test results of top and bottom responders bacteria at day 21 mice (Bottom vs. top day 21 bacteria).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. 56_sp_Nov_56_25,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides neonati,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. N54.MGS-20,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. UBA7116,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium 1_7_47FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium VE202-26,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. DSM 4029,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus sp. 8_2_54BFAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola paurosaccharolyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__uncultured Anaerotruncus sp.",3379134|976|200643|171549|171550|239759|1896969;3379134|976|200643|171549|815|816|1347393;3379134|976|200643|171549|815|816|1637511;3379134|976|200643|171549|815|816|1946088;1783272|1239|186801|186802|457421;1783272|1239|186801|186802|1232454;1783272|1239|186801|186802|31979|1485|1502;1783272|1239|186801|186802|31979|1485|1882754;1783272|1239|526524|526525|2810280|100883|469597;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|186802|1392389|1297617;3379134|976|200643|171549|815|909656|732242;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|186802|216572|244127|905011,Complete,Svetlana up
bsdb:35987213/1/2,35987213,randomized controlled trial,35987213,10.1016/j.cell.2022.07.016,https://pubmed.ncbi.nlm.nih.gov/35987213/,"Suez J., Cohen Y., Valdés-Mas R., Mor U., Dori-Bachash M., Federici S., Zmora N., Leshem A., Heinemann M., Linevsky R., Zur M., Ben-Zeev Brik R., Bukimer A., Eliyahu-Miller S., Metz A., Fischbein R., Sharov O., Malitsky S., Itkin M., Stettner N., Harmelin A., Shapiro H., Stein-Thoeringer C.K., Segal E. , Elinav E.",Personalized microbiome-driven effects of non-nutritive sweeteners on human glucose tolerance,Cell,2022,"artificial sweeteners, hyperglycemia, metabolic syndrome, metabolomics, metagenomics, microbiome, non-nutritive sweeteners",Experiment 1,Israel,Mus musculus,Feces,UBERON:0001988,Glucose tolerance test,EFO:0004307,Top Responder at Day 21,Bottom Responder at Day 21,The mice were recipients of the bottom sucralose responder human donors at 21 days.,3,3,NA,WMS,NA,Illumina,log transformation,Mixed-Effects Regression,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S7,28 March 2025,Shulamite,Shulamite,Linear mixed model test results of top and bottom responders bacteria at day 21 mice (Bottom vs. top day 21 bacteria).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Africanella|s__Africanella massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. HGB5,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cutis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Culturomica|s__Culturomica massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii",1783272|1239|186801|3085636|186803|3151706|1816694;3379134|976|200643|171549|171550|239759|908612;3379134|976|200643|171549|815|816|2024197;3379134|976|200643|171549|1853231|1926651|1841857;3379134|976|200643|171549|171552|577309|454154;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|671267;3379134|976|200643|171549|171550|239759|214856,Complete,Svetlana up
bsdb:35987213/2/1,35987213,randomized controlled trial,35987213,10.1016/j.cell.2022.07.016,https://pubmed.ncbi.nlm.nih.gov/35987213/,"Suez J., Cohen Y., Valdés-Mas R., Mor U., Dori-Bachash M., Federici S., Zmora N., Leshem A., Heinemann M., Linevsky R., Zur M., Ben-Zeev Brik R., Bukimer A., Eliyahu-Miller S., Metz A., Fischbein R., Sharov O., Malitsky S., Itkin M., Stettner N., Harmelin A., Shapiro H., Stein-Thoeringer C.K., Segal E. , Elinav E.",Personalized microbiome-driven effects of non-nutritive sweeteners on human glucose tolerance,Cell,2022,"artificial sweeteners, hyperglycemia, metabolic syndrome, metabolomics, metagenomics, microbiome, non-nutritive sweeteners",Experiment 2,Israel,Mus musculus,Feces,UBERON:0001988,Glucose tolerance test,EFO:0004307,Top Responder at Baseline,Bottom Responder at Baseline,The mice were recipients of the bottom sucralose responder human donors at Baseline.,3,3,NA,WMS,NA,Illumina,log transformation,Mixed-Effects Regression,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S7,29 March 2025,Shulamite,Shulamite,Linear mixed model test results of top and bottom responders bacteria at baseline mice (Bottom vs. Top Baseline Bacteria),increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp. UBA7090,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecichinchillae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fluxus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides togonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia schinkii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. An249,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. CAG:237,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. CAG:257,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 1_4_56FAA,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides massiliensis",3379134|74201|203494|48461|1647988|239934|1945966;3379134|976|200643|171549|815|816|626929;3379134|976|200643|171549|815|816|871325;3379134|976|200643|171549|815|816|626930;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|329854;3379134|976|200643|171549|815|816|1917883;3379134|976|200643|171549|815|816|371601;1783272|1239|186801|3085636|186803|572511|180164;1783272|1239|186801|3085636|186803|572511|1965603;1783272|1239|186801|3085636|186803|572511|1262755;1783272|1239|186801|3085636|186803|572511|1262756;1783272|1239|186801|3085636|186803|658655;3379134|976|200643|171549|2005525|375288|1750560,Complete,Svetlana up
bsdb:35987213/2/2,35987213,randomized controlled trial,35987213,10.1016/j.cell.2022.07.016,https://pubmed.ncbi.nlm.nih.gov/35987213/,"Suez J., Cohen Y., Valdés-Mas R., Mor U., Dori-Bachash M., Federici S., Zmora N., Leshem A., Heinemann M., Linevsky R., Zur M., Ben-Zeev Brik R., Bukimer A., Eliyahu-Miller S., Metz A., Fischbein R., Sharov O., Malitsky S., Itkin M., Stettner N., Harmelin A., Shapiro H., Stein-Thoeringer C.K., Segal E. , Elinav E.",Personalized microbiome-driven effects of non-nutritive sweeteners on human glucose tolerance,Cell,2022,"artificial sweeteners, hyperglycemia, metabolic syndrome, metabolomics, metagenomics, microbiome, non-nutritive sweeteners",Experiment 2,Israel,Mus musculus,Feces,UBERON:0001988,Glucose tolerance test,EFO:0004307,Top Responder at Baseline,Bottom Responder at Baseline,The mice were recipients of the bottom sucralose responder human donors at Baseline.,3,3,NA,WMS,NA,Illumina,log transformation,Mixed-Effects Regression,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S7,29 March 2025,Shulamite,Shulamite,Linear mixed model test results of top and bottom responders bacteria at baseline mice (Bottom vs. Top Baseline Bacteria),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. D1,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola salanitronis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__uncultured Flavonifractor sp.",3379134|976|200643|171549|171550|239759|1288121;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|556258;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|1853231|574697|544645;3379134|976|200643|171549|2005519|1348911|1099853;3379134|976|200643|171549|171552|2974257|386414;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|171552|577309|454154;3379134|976|200643|171549|815|909656|376805;1783272|1239|186801|186802|216572|946234|1193534,Complete,Svetlana up
bsdb:35990344/1/1,35990344,randomized controlled trial,35990344,10.3389/fnut.2022.971666,NA,"Baldi S., Dinu M., Pagliai G., Colombini B., Di Gloria L., Curini L., Pallecchi M., Ramazzotti M., Bartolucci G., Benedettelli S., Amedei A. , Sofi F.",Effect of ancient wheat pasta on gut microbiota composition and bacteria-derived metabolites: A randomized controlled trial,Frontiers in nutrition,2022,"MCFAs, SCFAs, ancient wheat, gut microbiota, modern wheat, pasta",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Pre-ancient-wheat diet (AD),Post-ancient-wheat diet (AD),"Post–ancient-wheat diet (post-AD) refers to samples collected from participants who consumed pasta made from ancient wheat during the second intervention period, following the washout phase comprising of (5F; 5M)",10,10,6 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 4B, Within Results text “GM composition”, Page 5",29 November 2025,Tosin,Tosin,Significant differential abundant bacteria between pre and post ancient wheat diet samples,increased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,1783272|1239|526524|526525|2810280|3025755,Complete,KateRasheed
bsdb:35990344/1/2,35990344,randomized controlled trial,35990344,10.3389/fnut.2022.971666,NA,"Baldi S., Dinu M., Pagliai G., Colombini B., Di Gloria L., Curini L., Pallecchi M., Ramazzotti M., Bartolucci G., Benedettelli S., Amedei A. , Sofi F.",Effect of ancient wheat pasta on gut microbiota composition and bacteria-derived metabolites: A randomized controlled trial,Frontiers in nutrition,2022,"MCFAs, SCFAs, ancient wheat, gut microbiota, modern wheat, pasta",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Pre-ancient-wheat diet (AD),Post-ancient-wheat diet (AD),"Post–ancient-wheat diet (post-AD) refers to samples collected from participants who consumed pasta made from ancient wheat during the second intervention period, following the washout phase comprising of (5F; 5M)",10,10,6 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 4B, Within Results text “GM composition”, Page 5",29 November 2025,Tosin,Tosin,Significant differential abundant bacteria between pre and post ancient wheat diet samples,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:873",1783272|1239|526524|526525|128827|1573535;3379134|976|200643|171549|171552|838|1262936,Complete,KateRasheed
bsdb:35990344/2/1,35990344,randomized controlled trial,35990344,10.3389/fnut.2022.971666,NA,"Baldi S., Dinu M., Pagliai G., Colombini B., Di Gloria L., Curini L., Pallecchi M., Ramazzotti M., Bartolucci G., Benedettelli S., Amedei A. , Sofi F.",Effect of ancient wheat pasta on gut microbiota composition and bacteria-derived metabolites: A randomized controlled trial,Frontiers in nutrition,2022,"MCFAs, SCFAs, ancient wheat, gut microbiota, modern wheat, pasta",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Pre-Modern Wheat Diet (Pre-CD),Post-Modern Wheat Diet (Post-CD),"Post–modern-wheat diet (post-CD) refers to samples collected from participants who consumed pasta made from modern wheat during the second intervention period following the washout phase. Due to the withdrawal of two participants prior to crossover, the post-CD group comprised 8 participants (5F; 3M)",10,8,6 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 4A, Within Results text “GM composition”, Page 5",29 November 2025,YokoC,"YokoC,Tosin",Box plots showing significant differentially abundant bacteria between pre- and post-CD (modern-wheat diet).,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:873",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|186803|1649459;3379134|976|200643|171549|171552|838|1262936,Complete,KateRasheed
bsdb:35990344/2/2,35990344,randomized controlled trial,35990344,10.3389/fnut.2022.971666,NA,"Baldi S., Dinu M., Pagliai G., Colombini B., Di Gloria L., Curini L., Pallecchi M., Ramazzotti M., Bartolucci G., Benedettelli S., Amedei A. , Sofi F.",Effect of ancient wheat pasta on gut microbiota composition and bacteria-derived metabolites: A randomized controlled trial,Frontiers in nutrition,2022,"MCFAs, SCFAs, ancient wheat, gut microbiota, modern wheat, pasta",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Pre-Modern Wheat Diet (Pre-CD),Post-Modern Wheat Diet (Post-CD),"Post–modern-wheat diet (post-CD) refers to samples collected from participants who consumed pasta made from modern wheat during the second intervention period following the washout phase. Due to the withdrawal of two participants prior to crossover, the post-CD group comprised 8 participants (5F; 3M)",10,8,6 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 4A, Within Results text “GM composition”, Page 5",29 November 2025,YokoC,"YokoC,Tosin",Box plots showing significant differentially abundant genera between pre- and post-CD (modern-wheat diet).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Frisingicoccus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",1783272|1239|186801|3085636|186803|1918511;1783272|1239|909932|1843489|31977|906;3384194|508458|649775|649776|649777|2753;1783272|1239|186801|3085636|186803|1506577,Complete,KateRasheed
bsdb:36002642/1/1,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 1,China,Homo sapiens,Thyroid gland,UBERON:0002046,Papillary thyroid carcinoma,EFO:0000641,PTC patients with mild lesions (T1_2),PTC patients with advanced lesions (T3_4),Papillary thyroid cancer (PTC) patients with advanced lesions.,64,16,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.2,NA,NA,NA,increased,NA,decreased,NA,unchanged,Signature 1,Figure 2g and 2h,24 April 2024,Aleru Divine,"Aleru Divine,WikiWorks","Taxonomic cladogram from LEfSe, depicting taxonomic associations between microbiome communities from patients with T1_2 and T3_4 PTC and LDA score computed from differentially abundant features between T1_2 and T3_4.",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales",1783272|201174|84998|84999;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;1783272|1239|91061|186826;3379134|1224|1236|135625|712;3379134|1224|1236|135625;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;3379134|1224|28211|356,Complete,Svetlana up
bsdb:36002642/1/2,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 1,China,Homo sapiens,Thyroid gland,UBERON:0002046,Papillary thyroid carcinoma,EFO:0000641,PTC patients with mild lesions (T1_2),PTC patients with advanced lesions (T3_4),Papillary thyroid cancer (PTC) patients with advanced lesions.,64,16,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.2,NA,NA,NA,increased,NA,decreased,NA,unchanged,Signature 2,Figure 2g and 2h,24 April 2024,Aleru Divine,"Aleru Divine,WikiWorks","Taxonomic cladogram from LEfSe, depicting taxonomic associations between microbiome communities from patients with T1_2 and T3_4 PTC and LDA score computed from differentially abundant features between T1_2 and T3_4.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas",3379134|1224|1236|72274|135621;3379134|1224|1236|72274|135621|286;3379134|1224|1236|72274;1783272|201174|1760|85007;1783272|201174|1760|85007|85025;1783272|201174|1760|85007|85025|1827;3379134|1224|28211|204457;3379134|1224|28211|204457|41297;3379134|1224|28211|204457|41297|13687,Complete,Svetlana up
bsdb:36002642/2/1,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 2,China,Homo sapiens,Thyroid gland,UBERON:0002046,Papillary thyroid carcinoma,EFO:0000641,Patients with PTC at clinical stage T1,Patients with PTC at clinical stage T2,Patients with Papillary thyroid cancer (PTC) at clinical stage T2.,35,29,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Supplementary Data 4 (Sheet 2),9 January 2025,Aleru Divine,"Aleru Divine,WikiWorks",Microbiome alterations at the genus level in patients with PTC of clinical stages T1–T4.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Aliicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Chloroflexota|c__Ardenticatenia|o__Ardenticatenales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Asticcacaulis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Candidatus Izemoplasmatales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Crossiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Ruegeria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingosinicellaceae|g__Sandaracinobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacillati|p__Actinomycetota|c__Thermoleophilia|o__Solirubrobacterales|f__Solirubrobacteraceae|g__Solirubrobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Sterolibacteriaceae|g__Sulfurisoma,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Sterolibacteriaceae|g__Sulfuritalea,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae",1783272|1239|91061|1385|90964|1647178;1783272|1239|186801|186802|216572|1940255;3379134|976|200643|171549|171552|1283313;1783272|200795|1382928|1382929;3379134|1224|28211|204458|76892|76890;1783272|201174|84998|84999|1643824|1380;3379134|976|117743|200644|2762318|59735;3379134|1224|28211|356|41294|374;1783272|544448|31969|2975519;1783272|1239|186801|186802|1470353;1783272|1239|186801|3085636|186803|43996;3379134|976|1853228|1853229|563835;1783272|201174|1760|85010|2070|130795;1783272|1239|186801|186802|186806|1730;1783272|1239|91061|186826|186827|66831;3379134|1224|1236|135625|712|724;3379134|1224|1236|135619|28256|2745;1783272|1239|186801|3085636|186803|43994;1783272|1239|186801|3085636|186803|1164882;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|186802|186807;3379134|1224|1236|91347|1903414|583;3379134|1224|1236|72274|135621|286;3384194|508458|649775|649776|3029088|638847;1783272|201174|1760|85007|85025|1827;3379134|1224|28211|204455|2854170|97050;3379134|1224|28211|204457|2820280|56358;3379134|1224|1236|135622|267890|22;1783272|201174|1497346|588673|320599|207599;1783272|1239|526524|526525|128827|123375;3379134|203691|203692|136|137|146;1783272|1239|186801|3085636|186803|1213720;3384189|32066|203490|203491|1129771|34104;1783272|1239|91061|186826|1300|1301;3379134|1224|28216|32003|2008793|1499082;3379134|1224|28216|32003|2008793|1054211;3379134|1224|28216|80840;3379134|1224|28216|80840|80864;3379134|1224|1236;3379134|1224|1236|135614|1775411,Complete,Svetlana up
bsdb:36002642/2/2,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 2,China,Homo sapiens,Thyroid gland,UBERON:0002046,Papillary thyroid carcinoma,EFO:0000641,Patients with PTC at clinical stage T1,Patients with PTC at clinical stage T2,Patients with Papillary thyroid cancer (PTC) at clinical stage T2.,35,29,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Supplementary Data 4 (Sheet 2),9 January 2025,Aleru Divine,"Aleru Divine,WikiWorks",Microbiome alterations at the genus level in patients with PTC of clinical stages T1–T4.,increased,"k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Novispirillaceae|g__Insolitispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Trueperales|f__Trueperaceae|g__Truepera",1783272|1798710|1906119;3379134|976|117743|200644|49546|1016;1783272|1239|186801|186802|216572|946234;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563;1783272|1239|526524|526525|128827|1573535;3379134|1224|28211|204441|3031145|660628;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|186802|216572|459786;3379134|1224|28211|204457|41297|13687;3379134|1224|28216|80840|995019|40544;3384194|1297|188787|2762275|332247|332248,Complete,Svetlana up
bsdb:36002642/3/1,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 3,China,Homo sapiens,Thyroid gland,UBERON:0002046,Papillary thyroid carcinoma,EFO:0000641,Patients with PTC at clinical stage T1,Patients with PTC at clinical stage T3,Patients with Papillary thyroid cancer (PTC) at clinical stage T3.,35,10,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,decreased,NA,unchanged,Signature 1,Figure 2f,24 April 2024,Aleru Divine,"Aleru Divine,WikiWorks","Microbiome alterations at the genus level in patients with PTC of clinical stages T1–T4. Intragroup differences were analyzed using the Kruskal–Wallis test, and differences between groups were analyzed based on the post-hoc test using Welch’s uncorrected test, adjusted by false discovery rate. The top three differential bacteria (genus) identified were tested individually.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas",3379134|1224|1236|72274|135621|286;1783272|201174|1760|85007|85025|1827;3379134|1224|28211|204457|41297|13687,Complete,Svetlana up
bsdb:36002642/4/1,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 4,China,Homo sapiens,Thyroid gland,UBERON:0002046,Papillary thyroid carcinoma,EFO:0000641,Patients with PTC at clinical stage T1,Patients with PTC at clinical stage T4,Patients with Papillary thyroid cancer (PTC) at clinical stage T4.,35,6,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 2f,24 April 2024,Aleru Divine,"Aleru Divine,WikiWorks","Microbiome alterations at the genus level in patients with PTC of clinical stages T1–T4. Intragroup differences were analyzed using the Kruskal–Wallis test, and differences between groups were analyzed based on the post-hoc test using Welch’s uncorrected test, adjusted by false discovery rate. The top three differential bacteria (genus) identified were tested individually.",decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,3379134|1224|1236|72274|135621|286,Complete,Svetlana up
bsdb:36002642/5/1,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 5,China,Homo sapiens,Thyroid gland,UBERON:0002046,Papillary thyroid carcinoma,EFO:0000641,Patients with PTC at clinical stage T2,Patients with PTC at clinical stage T3,Patients with Papillary thyroid cancer (PTC) at clinical stage T3.,29,10,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,decreased,NA,unchanged,Signature 1,Figure 2f,24 April 2024,Aleru Divine,"Aleru Divine,WikiWorks","Microbiome alterations at the genus level in patients with PTC of clinical stages T1–T4. Intragroup differences were analyzed using the Kruskal–Wallis test, and differences between groups were analyzed based on the post-hoc test using Welch’s uncorrected test, adjusted by false discovery rate. The top three differential bacteria (genus) identified were tested individually.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas",3379134|1224|1236|72274|135621|286;3379134|1224|28211|204457|41297|13687,Complete,Svetlana up
bsdb:36002642/6/1,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 6,China,Homo sapiens,Thyroid gland,UBERON:0002046,Papillary thyroid carcinoma,EFO:0000641,Patients with PTC at clinical stage T2,Patients with PTC at clinical stage T4,Patients with Papillary thyroid cancer (PTC) at clinical stage T4.,29,6,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 2f,24 April 2024,Aleru Divine,"Aleru Divine,WikiWorks","Microbiome alterations at the genus level in patients with PTC of clinical stages T1–T4. Intragroup differences were analyzed using the Kruskal–Wallis test, and differences between groups were analyzed based on the post-hoc test using Welch’s uncorrected test, adjusted by false discovery rate. The top three differential bacteria (genus) identified were tested individually.",decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,3379134|1224|1236|72274|135621|286,Complete,Svetlana up
bsdb:36002642/7/1,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 7,China,Homo sapiens,Thyroid gland,UBERON:0002046,Papillary thyroid carcinoma,EFO:0000641,Patients with PTC at clinical stage T1,Patients with PTC at clinical stage T3,Patients with Papillary thyroid cancer (PTC) at clinical stage T3.,35,10,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,decreased,NA,unchanged,Signature 1,Supplementary Data 4 (Sheet 2),9 January 2025,Aleru Divine,"Aleru Divine,WikiWorks",Microbiome alterations at the genus level in patients with PTC of clinical stages T1–T4.,decreased,"k__Bacillati|p__Chloroflexota|c__Ardenticatenia|o__Ardenticatenales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Novispirillaceae|g__Insolitispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacillati|p__Actinomycetota|c__Thermoleophilia|o__Solirubrobacterales|f__Solirubrobacteraceae|g__Solirubrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Sterolibacteriaceae|g__Sulfurisoma,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Sterolibacteriaceae|g__Sulfuritalea,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Trueperales|f__Trueperaceae|g__Truepera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Crossiella",1783272|200795|1382928|1382929;1783272|201174|84998|84999|1643824|1380;3379134|1224|28211|356|41294|374;3379134|976|117743|200644|49546|1016;1783272|1239|186801|3085636|186803|43996;3379134|976|1853228|1853229|563835;1783272|1239|91061|186826|186827|66831;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135619|28256|2745;3379134|1224|28211|204441|3031145|660628;1783272|1239|186801|3085636|186803|43994;1783272|1239|186801|3085636|186803|1164882;3379134|1224|1236|72274|135621|286;1783272|201174|1760|85007|85025|1827;3379134|1224|1236|135622|267890|22;1783272|201174|1497346|588673|320599|207599;3379134|1224|28211|204457|41297|13687;3379134|203691|203692|136|137|146;1783272|1239|186801|3085636|186803|1213720;1783272|1239|91061|186826|1300|1301;3379134|1224|28216|32003|2008793|1499082;3379134|1224|28216|32003|2008793|1054211;3384194|1297|188787|2762275|332247|332248;3379134|1224|28216|80840;3379134|1224|28216|80840|80864;3379134|1224|1236;3379134|1224|1236|135614|1775411;1783272|201174|1760|85010|2070|130795,Complete,Svetlana up
bsdb:36002642/7/2,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 7,China,Homo sapiens,Thyroid gland,UBERON:0002046,Papillary thyroid carcinoma,EFO:0000641,Patients with PTC at clinical stage T1,Patients with PTC at clinical stage T3,Patients with Papillary thyroid cancer (PTC) at clinical stage T3.,35,10,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,decreased,NA,unchanged,Signature 2,Supplementary Data 4 (Sheet 2),9 January 2025,Aleru Divine,"Aleru Divine,WikiWorks",Microbiome alterations at the genus level in patients with PTC of clinical stages T1–T4.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Aliicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Asticcacaulis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Candidatus Izemoplasmatales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Ruegeria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingosinicellaceae|g__Sandaracinobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",1783272|1239|91061|1385|90964|1647178;1783272|1239|186801|186802|216572|1940255;3379134|976|200643|171549|171552|1283313;3379134|1224|28211|204458|76892|76890;3379134|976|117743|200644|2762318|59735;1783272|1798710|1906119;1783272|544448|31969|2975519;1783272|1239|186801|186802|1470353;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|946234;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|186807;3379134|1224|1236|91347|1903414|583;3384194|508458|649775|649776|3029088|638847;3379134|1224|28211|204455|2854170|97050;3379134|1224|28211|204457|2820280|56358;1783272|1239|526524|526525|128827|123375;3384189|32066|203490|203491|1129771|34104;3379134|1224|28216|80840|995019|40544,Complete,Svetlana up
bsdb:36002642/8/1,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 8,China,Homo sapiens,Thyroid gland,UBERON:0002046,Papillary thyroid carcinoma,EFO:0000641,Male Patients with PTC (G1),Female Patients with PTC (G2),Female Patients with Papillary thyroid cancer (PTC),19,61,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,decreased,NA,unchanged,Signature 1,Figure 4c,24 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Microbiome alterations at the genus level in patients of different sexes with PTC. Differences between groups were analyzed using the Wilcoxon rank-sum test,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Caballeronia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia",1783272|201174|1760|85007|85025|1827;3379134|1224|28216|80840|119060|48736;3379134|976|117743|200644|2762318|59732;3379134|1224|28216|80840|119060|32008;3379134|1224|28216|80840|119060|1827195;3379134|1224|28216|80840|119060|1822464,Complete,Svetlana up
bsdb:36002642/9/1,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 9,China,Homo sapiens,Thyroid gland,UBERON:0002046,Hormone,CHEBI:24621,Thyroid-Stimulating Hormone (TSH) - Low levels,Thyroid-Stimulating Hormone (TSH) - High levels,The association between Thyroid-Stimulating Hormone (TSH) and different microbial genera in Papillary Thyroid Cancer (PTC) patients.,NA,NA,NA,16S,34,Illumina,arcsine square-root,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a,25 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap of Spearman’s correlation analysis showing the relationship between the specific bacterial and thyroid-related hormones.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|91061|186826|186828|2747;3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:36002642/10/1,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 10,China,Homo sapiens,Thyroid gland,UBERON:0002046,Hormone,CHEBI:24621,Triiodothyronine (T3) - Low Levels,Triiodothyronine (T3) - High Levels,The association between Triiodothyronine (T3) and different microbial genera in Papillary Thyroid Cancer (PTC) patients.,NA,NA,NA,16S,34,Illumina,arcsine square-root,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a,25 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap of Spearman’s correlation analysis showing the relationship between the specific bacterial and thyroid-related hormones.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,1783272|1239|91061|186826|186828|117563,Complete,Svetlana up
bsdb:36002642/11/1,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 11,China,Homo sapiens,Thyroid gland,UBERON:0002046,Hormone,CHEBI:24621,Thyroxine (T4) -  Low levels,Thyroxine (T4) -  High levels,The association between Thyroxine (T4) and different microbial genera in Papillary Thyroid Cancer (PTC) patients.,NA,NA,NA,16S,34,Illumina,arcsine square-root,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a,25 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap of Spearman’s correlation analysis showing the relationship between the specific bacterial and thyroid-related hormones.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella",3379134|1224|1236|91347|543|1940338;3379134|1224|1236|91347|543|570,Complete,Svetlana up
bsdb:36002642/12/1,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 12,China,Homo sapiens,Thyroid gland,UBERON:0002046,Hormone,CHEBI:24621,Free Triiodothyronine (FT3) -  Low levels,Free Triiodothyronine (FT3) -  High levels,The association between Free Triiodothyronine (FT3) and different microbial genera in Papillary Thyroid Cancer (PTC) patients.,NA,NA,NA,16S,34,Illumina,arcsine square-root,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a,25 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap of Spearman’s correlation analysis showing the relationship between the specific bacterial and thyroid-related hormones.,increased,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,3379134|203691|203692|136|2845253|157,Complete,Svetlana up
bsdb:36002642/13/1,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 13,China,Homo sapiens,Thyroid gland,UBERON:0002046,Hormone,CHEBI:24621,Free Thyroxine (FT4) - Low levels,Free Thyroxine (FT4) - High levels,The association between Free Thyroxine (FT4) and different microbial genera in Papillary Thyroid Cancer (PTC) patients.,NA,NA,NA,16S,34,Illumina,arcsine square-root,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a,25 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap of Spearman’s correlation analysis showing the relationship between the specific bacterial and thyroid-related hormones.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Cyanobacteriota",3379134|1224|28216|206351|481|482;1783272|1117,Complete,Svetlana up
bsdb:36002642/13/2,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 13,China,Homo sapiens,Thyroid gland,UBERON:0002046,Hormone,CHEBI:24621,Free Thyroxine (FT4) - Low levels,Free Thyroxine (FT4) - High levels,The association between Free Thyroxine (FT4) and different microbial genera in Papillary Thyroid Cancer (PTC) patients.,NA,NA,NA,16S,34,Illumina,arcsine square-root,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3a,25 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap of Spearman’s correlation analysis showing the relationship between the specific bacterial and thyroid-related hormones.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,3379134|1224|1236|91347|543|570,Complete,Svetlana up
bsdb:36002642/14/1,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 14,China,Homo sapiens,Thyroid gland,UBERON:0002046,Antibody,EFO:0000264,Anti-thyroid-stimulating receptors (Anti-TSHR) - Low levels,Anti-thyroid-stimulating receptors (Anti-TSHR) - High levels,The association between Anti-thyroid-stimulating receptors (Anti-TSHR) and microbial abundance in Papillary Thyroid Cancer (PTC) patients.,NA,NA,NA,16S,34,Illumina,arcsine square-root,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3b,25 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap of Spearman’s correlation analysis between the specific bacterial and thyroid diseases (AITD)-related antibodies.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,3379134|1224|1236|91347|543|570,Complete,Svetlana up
bsdb:36002642/15/1,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 15,China,Homo sapiens,Thyroid gland,UBERON:0002046,Antibody,EFO:0000264,Anti-thyroid peroxidase (Anti-TPO) - Low levels,Anti-thyroid peroxidase (Anti-TPO) - High levels,The association between Anti-thyroid peroxidase (Anti-TPO) and microbial abundance in Papillary Thyroid Cancer (PTC) patients.,NA,NA,NA,16S,34,Illumina,arcsine square-root,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3b,25 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap of Spearman’s correlation analysis between the specific bacterial and thyroid diseases (AITD)-related antibodies.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",1783272|201174|1760|85004|31953|1678;1783272|1239|909932|909929|1843491|970;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301;1783272|1239|1737404|1737405|1570339|543311;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|815|816;3379134|1224|1236|135625|712|724,Complete,Svetlana up
bsdb:36002642/16/1,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 16,China,Homo sapiens,Thyroid gland,UBERON:0002046,Antibody,EFO:0000264,Anti-thyroglobulin (Anti-TG) - Low levels,Anti-thyroglobulin (Anti-TG) - High levels,The association between Anti-thyroglobulin (Anti-TG) and microbial abundance in Papillary Thyroid Cancer (PTC) patients.,NA,NA,NA,16S,34,Illumina,arcsine square-root,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3b,26 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap of Spearman’s correlation analysis between the specific bacterial and thyroid diseases (AITD)-related antibodies.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas",3379134|1224|28211|204457|41297|13687;1783272|201174|1760|85007|85025|1827;3379134|1224|28216|80840|119060|48736;3379134|1224|28211|204458|76892|41275,Complete,Svetlana up
bsdb:36002642/16/2,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 16,China,Homo sapiens,Thyroid gland,UBERON:0002046,Antibody,EFO:0000264,Anti-thyroglobulin (Anti-TG) - Low levels,Anti-thyroglobulin (Anti-TG) - High levels,The association between Anti-thyroglobulin (Anti-TG) and microbial abundance in Papillary Thyroid Cancer (PTC) patients.,NA,NA,NA,16S,34,Illumina,arcsine square-root,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3b,26 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap of Spearman’s correlation analysis between the specific bacterial and thyroid diseases (AITD)-related antibodies.,decreased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",1783272|1239|1737404|1737405|1570339|165779;3379134|74201|203494|48461|1647988|239934,Complete,Svetlana up
bsdb:36002642/17/1,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 17,China,Homo sapiens,Thyroid gland,UBERON:0002046,Hormone,CHEBI:24621,Triiodothyronine (T3) - Low Levels,Triiodothyronine (T3) - High Levels,The association between Triiodothyronine (T3) and different microbial genera in Papillary Thyroid Cancer (PTC) patients in the validation set.,NA,NA,NA,16S,34,Illumina,arcsine square-root,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S5c,26 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap of Spearman’s correlation analysis between the specific bacterial and thyroid-related hormones in the validation set.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,1783272|1239|91061|186826|186828|117563,Complete,Svetlana up
bsdb:36002642/18/1,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 18,China,Homo sapiens,Thyroid gland,UBERON:0002046,Hormone,CHEBI:24621,Free Triiodothyronine (FT3) -  Low levels,Free Triiodothyronine (FT3) -  High levels,The association between Free Triiodothyronine (FT3) and different microbial genera in Papillary Thyroid Cancer (PTC) patients in the validation set.,NA,NA,NA,16S,34,Illumina,arcsine square-root,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S5c,26 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap of Spearman’s correlation analysis between the specific bacterial and thyroid-related hormones in the validation set.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,1783272|1239|91061|186826|186828|117563,Complete,Svetlana up
bsdb:36002642/19/1,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 19,China,Homo sapiens,Thyroid gland,UBERON:0002046,Hormone,CHEBI:24621,Free Thyroxine (FT4) - Low levels,Free Thyroxine (FT4) - High levels,The association between Free Thyroxine (FT4) and different microbial genera in Papillary Thyroid Cancer (PTC) patients in the validation set.,NA,NA,NA,16S,34,Illumina,arcsine square-root,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S5c,26 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap of Spearman’s correlation analysis between the specific bacterial and thyroid-related hormones in the validation set.,increased,NA,NA,Complete,Svetlana up
bsdb:36002642/20/1,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 20,China,Homo sapiens,Thyroid gland,UBERON:0002046,Antibody,EFO:0000264,Anti-thyroid-stimulating receptors (Anti-TSHR) - Low levels,Anti-thyroid-stimulating receptors (Anti-TSHR) - High levels,The association between Anti-thyroid-stimulating receptors (Anti-TSHR) and microbial abundance in Papillary Thyroid Cancer (PTC) patients in the validation set.,NA,NA,NA,16S,34,Illumina,arcsine square-root,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S5d,26 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap of Spearman’s correlation analysis between the specific bacterial and thyroid diseases (AITD)-related antibodies in the validation set.,increased,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,3384189|32066|203490|203491|1129771|32067,Complete,Svetlana up
bsdb:36002642/21/1,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 21,China,Homo sapiens,Thyroid gland,UBERON:0002046,Antibody,EFO:0000264,Anti-thyroid peroxidase (Anti-TPO) - Low levels,Anti-thyroid peroxidase (Anti-TPO) - High levels,The association between Anti-thyroid peroxidase (Anti-TPO) and microbial abundance in Papillary Thyroid Cancer (PTC) patients in the validation set.,NA,NA,NA,16S,34,Illumina,arcsine square-root,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S5d,26 April 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap of Spearman’s correlation analysis between the specific bacterial and thyroid diseases (AITD)-related antibodies in the validation set.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",1783272|201174|1760|85004|31953|1678;3379134|1224|1236|135625|712|724,Complete,Svetlana up
bsdb:36002642/22/1,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 22,China,Homo sapiens,Thyroid gland,UBERON:0002046,Papillary thyroid carcinoma,EFO:0000641,Patients with PTC at clinical stage T3,Patients with PTC at clinical stage T4,Patients with Papillary thyroid cancer (PTC) at clinical stage T4.,10,6,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Supplementary Data 4 (Sheet 2),9 January 2025,Aleru Divine,"Aleru Divine,WikiWorks",Microbiome alterations at the genus level in patients with PTC of clinical stages T1–T4.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Aliicoccus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Candidatus Izemoplasmatales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Ruegeria,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria",1783272|1239|91061|1385|90964|1647178;3379134|976|200643|171549|171552|1283313;3379134|976|117743|200644|2762318|59735;1783272|1798710|1906119;1783272|544448|31969|2975519;1783272|1239|186801|186802|1470353;3379134|976|1853228|1853229|563835;1783272|1239|186801|186802|216572|946234;1783272|1239|91061|186826|186828|117563;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|186807;3379134|1224|1236|91347|1903414|583;3379134|1224|28211|204455|2854170|97050;1783272|1239|526524|526525|128827|123375;3379134|1224|28216|80840|995019|40544;3379134|1224|28216|80840|80864;3379134|1224|1236,Complete,Svetlana up
bsdb:36002642/22/2,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 22,China,Homo sapiens,Thyroid gland,UBERON:0002046,Papillary thyroid carcinoma,EFO:0000641,Patients with PTC at clinical stage T3,Patients with PTC at clinical stage T4,Patients with Papillary thyroid cancer (PTC) at clinical stage T4.,10,6,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Supplementary Data 4 (Sheet 2),9 January 2025,Aleru Divine,"Aleru Divine,WikiWorks",Microbiome alterations at the genus level in patients with PTC of clinical stages T1–T4.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella,k__Bacillati|p__Chloroflexota|c__Ardenticatenia|o__Ardenticatenales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Asticcacaulis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Crossiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Novispirillaceae|g__Insolitispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingosinicellaceae|g__Sandaracinobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacillati|p__Actinomycetota|c__Thermoleophilia|o__Solirubrobacterales|f__Solirubrobacteraceae|g__Solirubrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Sterolibacteriaceae|g__Sulfurisoma,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Sterolibacteriaceae|g__Sulfuritalea,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Trueperales|f__Trueperaceae|g__Truepera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae",1783272|1239|186801|186802|216572|1940255;1783272|200795|1382928|1382929;3379134|1224|28211|204458|76892|76890;1783272|201174|84998|84999|1643824|1380;3379134|1224|28211|356|41294|374;1783272|1798710|1906119;3379134|976|117743|200644|49546|1016;1783272|1239|186801|3085636|186803|43996;1783272|201174|1760|85010|2070|130795;1783272|1239|186801|186802|186806|1730;1783272|1239|91061|186826|186827|66831;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135625|712|724;3379134|1224|1236|135619|28256|2745;1783272|1239|526524|526525|128827|1573535;3379134|1224|28211|204441|3031145|660628;1783272|1239|186801|3085636|186803|43994;1783272|1239|186801|3085636|186803|1164882;3379134|1224|1236|72274|135621|286;3384194|508458|649775|649776|3029088|638847;1783272|201174|1760|85007|85025|1827;3379134|1224|28211|204457|2820280|56358;3379134|1224|1236|135622|267890|22;1783272|201174|1497346|588673|320599|207599;3379134|1224|28211|204457|41297|13687;3379134|203691|203692|136|137|146;1783272|1239|186801|3085636|186803|1213720;3384189|32066|203490|203491|1129771|34104;1783272|1239|91061|186826|1300|1301;3379134|1224|28216|32003|2008793|1499082;3379134|1224|28216|32003|2008793|1054211;3384194|1297|188787|2762275|332247|332248;3379134|1224|28216|80840;3379134|1224|1236|135614|1775411,Complete,Svetlana up
bsdb:36002642/23/1,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 23,China,Homo sapiens,Thyroid gland,UBERON:0002046,Papillary thyroid carcinoma,EFO:0000641,Patients with PTC at clinical stage T2,Patients with PTC at clinical stage T3,Patients with Papillary thyroid cancer (PTC) at clinical stage T3.,29,10,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,decreased,NA,unchanged,Signature 1,Supplementary Data 4 (Sheet 2),9 January 2025,Aleru Divine,"Aleru Divine,WikiWorks",Microbiome alterations at the genus level in patients with PTC of clinical stages T1–T4.,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Novispirillaceae|g__Insolitispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacillati|p__Actinomycetota|c__Thermoleophilia|o__Solirubrobacterales|f__Solirubrobacteraceae|g__Solirubrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Sterolibacteriaceae|g__Sulfuritalea,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Trueperales|f__Trueperaceae|g__Truepera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Crossiella,k__Bacillati|p__Chloroflexota|c__Ardenticatenia|o__Ardenticatenales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Sterolibacteriaceae|g__Sulfurisoma,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia",1783272|201174|84998|84999|1643824|1380;3379134|1224|28211|356|41294|374;3379134|976|117743|200644|49546|1016;1783272|1239|186801|3085636|186803|43996;3379134|976|1853228|1853229|563835;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135619|28256|2745;1783272|1239|526524|526525|128827|1573535;3379134|1224|28211|204441|3031145|660628;1783272|1239|186801|3085636|186803|43994;3379134|1224|1236|72274|135621|286;1783272|201174|1760|85007|85025|1827;1783272|201174|1497346|588673|320599|207599;3379134|1224|28211|204457|41297|13687;1783272|1239|186801|3085636|186803|1213720;3379134|1224|28216|32003|2008793|1054211;3379134|1224|28216|80840|995019|40544;3384194|1297|188787|2762275|332247|332248;3379134|1224|28216|80840;3379134|1224|1236|135614|1775411;3379134|203691|203692|136|137|146;1783272|201174|1760|85010|2070|130795;1783272|200795|1382928|1382929;3379134|1224|28216|32003|2008793|1499082;1783272|1239|91061|186826|186827|66831,Complete,Svetlana up
bsdb:36002642/23/2,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 23,China,Homo sapiens,Thyroid gland,UBERON:0002046,Papillary thyroid carcinoma,EFO:0000641,Patients with PTC at clinical stage T2,Patients with PTC at clinical stage T3,Patients with Papillary thyroid cancer (PTC) at clinical stage T3.,29,10,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,decreased,NA,unchanged,Signature 2,Supplementary Data 4 (Sheet 2),9 January 2025,Aleru Divine,"Aleru Divine,WikiWorks",Microbiome alterations at the genus level in patients with PTC of clinical stages T1–T4.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Aliicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Asticcacaulis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Candidatus Izemoplasmatales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Ruegeria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingosinicellaceae|g__Sandaracinobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria",1783272|1239|91061|1385|90964|1647178;1783272|1239|186801|186802|216572|1940255;3379134|976|200643|171549|171552|1283313;3379134|1224|28211|204458|76892|76890;3379134|976|117743|200644|2762318|59735;1783272|1798710|1906119;1783272|544448|31969|2975519;1783272|1239|186801|186802|1470353;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|946234;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|1164882;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|186807;3379134|1224|1236|91347|1903414|583;3384194|508458|649775|649776|3029088|638847;3379134|1224|28211|204455|2854170|97050;3379134|1224|28211|204457|2820280|56358;3379134|1224|1236|135622|267890|22;1783272|1239|526524|526525|128827|123375;3384189|32066|203490|203491|1129771|34104;1783272|1239|91061|186826|1300|1301;3379134|1224|28216|80840|995019|40544;3379134|1224|28216|80840|80864;3379134|1224|1236,Complete,Svetlana up
bsdb:36002642/24/1,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 24,China,Homo sapiens,Thyroid gland,UBERON:0002046,Papillary thyroid carcinoma,EFO:0000641,Patients with PTC at clinical stage T1,Patients with PTC at clinical stage T4,Patients with Papillary thyroid cancer (PTC) at clinical stage T4.,35,6,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Supplementary Data 4 (Sheet 2),9 January 2025,Aleru Divine,"Aleru Divine,WikiWorks",Microbiome alterations at the genus level in patients with PTC of clinical stages T1–T4.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Aliicoccus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Candidatus Izemoplasmatales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacillati|p__Actinomycetota|c__Thermoleophilia|o__Solirubrobacterales|f__Solirubrobacteraceae|g__Solirubrobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Sterolibacteriaceae|g__Sulfuritalea,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Ruegeria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus",1783272|1239|91061|1385|90964|1647178;3379134|1224|28211|356|41294|374;1783272|544448|31969|2975519;1783272|1239|186801|186802|1470353;1783272|1239|186801|3085636|186803|43996;3379134|976|1853228|1853229|563835;1783272|1239|186801|3085636|186803|43994;1783272|1239|186801|3085636|186803|1164882;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|186807;3379134|1224|1236|72274|135621|286;1783272|201174|1760|85007|85025|1827;3379134|1224|1236|135622|267890|22;1783272|201174|1497346|588673|320599|207599;1783272|1239|526524|526525|128827|123375;3379134|1224|28211|204457|41297|13687;1783272|1239|186801|3085636|186803|1213720;3379134|1224|28216|32003|2008793|1054211;3379134|1224|28216|80840;3379134|1224|28216|80840|80864;3379134|1224|1236;3379134|1224|1236|135614|1775411;3379134|1224|28216|80840|995019|40544;3379134|1224|28211|204455|2854170|97050;3379134|1224|1236|91347|1903414|583,Complete,Svetlana up
bsdb:36002642/24/2,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 24,China,Homo sapiens,Thyroid gland,UBERON:0002046,Papillary thyroid carcinoma,EFO:0000641,Patients with PTC at clinical stage T1,Patients with PTC at clinical stage T4,Patients with Papillary thyroid cancer (PTC) at clinical stage T4.,35,6,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Supplementary Data 4 (Sheet 2),9 January 2025,Aleru Divine,"Aleru Divine,WikiWorks",Microbiome alterations at the genus level in patients with PTC of clinical stages T1–T4.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Chloroflexota|c__Ardenticatenia|o__Ardenticatenales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Asticcacaulis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Crossiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Novispirillaceae|g__Insolitispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingosinicellaceae|g__Sandaracinobacter,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Sterolibacteriaceae|g__Sulfurisoma,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Trueperales|f__Trueperaceae|g__Truepera",1783272|1239|186801|186802|216572|1940255;3379134|976|200643|171549|171552|1283313;1783272|200795|1382928|1382929;3379134|1224|28211|204458|76892|76890;1783272|201174|84998|84999|1643824|1380;3379134|976|117743|200644|2762318|59735;1783272|1798710|1906119;3379134|976|117743|200644|49546|1016;1783272|201174|1760|85010|2070|130795;1783272|1239|186801|186802|186806|1730;1783272|1239|91061|186826|186827|66831;1783272|1239|186801|186802|216572|946234;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;3379134|1224|1236|135619|28256|2745;1783272|1239|526524|526525|128827|1573535;3379134|1224|28211|204441|3031145|660628;1783272|1239|186801|3085656|3085657|2039302;3384194|508458|649775|649776|3029088|638847;3379134|1224|28211|204457|2820280|56358;3379134|203691|203692|136|137|146;3384189|32066|203490|203491|1129771|34104;1783272|1239|91061|186826|1300|1301;3379134|1224|28216|32003|2008793|1499082;3384194|1297|188787|2762275|332247|332248,Complete,Svetlana up
bsdb:36002642/25/1,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 25,China,Homo sapiens,Thyroid gland,UBERON:0002046,Papillary thyroid carcinoma,EFO:0000641,Patients with PTC at clinical stage T2,Patients with PTC at clinical stage T4,Patients with Papillary thyroid cancer (PTC) at clinical stage T4.,29,6,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Supplementary Data 4 (Sheet 2),9 January 2025,Aleru Divine,"Aleru Divine,WikiWorks",Microbiome alterations at the genus level in patients with PTC of clinical stages T1–T4.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Aliicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Ruegeria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Sterolibacteriaceae|g__Sulfuritalea,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Candidatus Izemoplasmatales",1783272|1239|91061|1385|90964|1647178;1783272|1239|186801|3085636|186803|43996;1783272|1239|186801|186802|216572|946234;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|186807;3379134|1224|1236|91347|1903414|583;3379134|1224|1236|72274|135621|286;1783272|201174|1760|85007|85025|1827;3379134|1224|28211|204455|2854170|97050;3379134|1224|28211|204457|41297|13687;3379134|1224|28216|32003|2008793|1054211;3379134|1224|28216|80840|995019|40544;3379134|1224|28216|80840;3379134|976|1853228|1853229|563835;3379134|1224|28216|80840|80864;3379134|1224|1236|135614|1775411;1783272|1239|186801|186802|1470353;1783272|544448|31969|2975519,Complete,Svetlana up
bsdb:36002642/25/2,36002642,prospective cohort,36002642,10.1038/s42003-022-03814-x,NA,"Yuan L., Yang P., Wei G., Hu X., Chen S., Lu J., Yang L., He X. , Bao G.",Tumor microbiome diversity influences papillary thyroid cancer invasion,Communications biology,2022,NA,Experiment 25,China,Homo sapiens,Thyroid gland,UBERON:0002046,Papillary thyroid carcinoma,EFO:0000641,Patients with PTC at clinical stage T2,Patients with PTC at clinical stage T4,Patients with Papillary thyroid cancer (PTC) at clinical stage T4.,29,6,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Supplementary Data 4 (Sheet 2),9 January 2025,Aleru Divine,"Aleru Divine,WikiWorks",Microbiome alterations at the genus level in patients with PTC of clinical stages T1–T4.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Chloroflexota|c__Ardenticatenia|o__Ardenticatenales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Asticcacaulis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Crossiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Novispirillaceae|g__Insolitispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingosinicellaceae|g__Sandaracinobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacillati|p__Actinomycetota|c__Thermoleophilia|o__Solirubrobacterales|f__Solirubrobacteraceae|g__Solirubrobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Sterolibacteriaceae|g__Sulfurisoma,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Trueperales|f__Trueperaceae|g__Truepera,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria",1783272|1239|186801|186802|216572|1940255;3379134|976|200643|171549|171552|1283313;1783272|200795|1382928|1382929;3379134|1224|28211|204458|76892|76890;1783272|201174|84998|84999|1643824|1380;3379134|976|117743|200644|2762318|59735;3379134|1224|28211|356|41294|374;1783272|1798710|1906119;3379134|976|117743|200644|49546|1016;1783272|201174|1760|85010|2070|130795;1783272|1239|186801|186802|186806|1730;1783272|1239|91061|186826|186827|66831;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;3379134|1224|1236|135619|28256|2745;3379134|1224|28211|204441|3031145|660628;1783272|1239|186801|3085636|186803|43994;1783272|1239|186801|3085636|186803|1164882;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|186801|3085636|186803|265975;3384194|508458|649775|649776|3029088|638847;3379134|1224|28211|204457|2820280|56358;3379134|1224|1236|135622|267890|22;1783272|201174|1497346|588673|320599|207599;1783272|1239|526524|526525|128827|123375;3379134|203691|203692|136|137|146;1783272|1239|186801|3085636|186803|1213720;3384189|32066|203490|203491|1129771|34104;1783272|1239|91061|186826|1300|1301;3379134|1224|28216|32003|2008793|1499082;3384194|1297|188787|2762275|332247|332248;3379134|1224|1236,Complete,Svetlana up
bsdb:36002814/1/1,36002814,time series / longitudinal observational,36002814,10.1186/s12887-022-03570-1,NA,"Sun X., Cai Y., Dai W., Jiang W. , Tang W.",The difference of gut microbiome in different biliary diseases in infant before operation and the changes after operation,BMC pediatrics,2022,"16S rDNA, Biliary atresia, Cholestatic, Gut microbiome, Intestinal flora",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Biliary atresia,MONDO:0008867,Cholestasis disease (CD_1) group,Biliary atresia (BA_1) group,Infants diagnosed with biliary atresia (BA) 1 day before surgery,8,17,NA,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 4,17 November 2025,Tosin,Tosin,LEfSe (Linear Discriminant analysis Effect Size) analysis of BA (biliary atresia) group and CD (Cholestasis disease) group,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Actinomycetota|c__Nitriliruptoria|o__Nitriliruptorales|f__Nitriliruptoraceae,k__Bacillati|p__Actinomycetota|c__Nitriliruptoria|o__Nitriliruptorales,k__Bacillati|p__Actinomycetota|c__Nitriliruptoria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacillati|p__Actinomycetota|c__Nitriliruptoria|o__Nitriliruptorales|f__Nitriliruptoraceae,k__Bacillati|p__Actinomycetota",3379134|1224|28211;3379134|1224|28216|80840|119060;3379134|1224|28216|80840|119060|106589;3379134|1224|28216|80840|80864|80865;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|201174|908620|596497|596498;1783272|201174|908620|596497;1783272|201174|908620;1783272|201174|1760|85007|85025;3379134|1224|28216|80840|119060|48736;1783272|201174|1760|85007|85025|1827;1783272|201174|908620|596497|596498;1783272|201174,Complete,KateRasheed
bsdb:36002814/1/2,36002814,time series / longitudinal observational,36002814,10.1186/s12887-022-03570-1,NA,"Sun X., Cai Y., Dai W., Jiang W. , Tang W.",The difference of gut microbiome in different biliary diseases in infant before operation and the changes after operation,BMC pediatrics,2022,"16S rDNA, Biliary atresia, Cholestatic, Gut microbiome, Intestinal flora",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Biliary atresia,MONDO:0008867,Cholestasis disease (CD_1) group,Biliary atresia (BA_1) group,Infants diagnosed with biliary atresia (BA) 1 day before surgery,8,17,NA,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 4,17 November 2025,Deborah-Fabusuyi,"Deborah-Fabusuyi,Tosin",LEfSe (Linear Discriminant analysis Effect Size) analysis of BA (biliary atresia) group and CD (Cholestasis disease) group,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kluyvera,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;1783272|1239|186801;1783272|1239|186801|186802;3384189|32066|203490|203491|203492;3384189|32066|203490|203491|203492|848;3379134|1224|1236|91347|543|579;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|909932;3379134|1224|1236|91347|543|160674;1783272|1239|909932|909929;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201;1783272|1239|186801|186802|31979|1485,Complete,KateRasheed
bsdb:36004326/1/1,36004326,case-control,36004326,10.3389/fcimb.2022.858732,NA,"Yan C., Hong F., Xin G., Duan S., Deng X. , Xu Y.",Alterations in the vaginal microbiota of patients with preterm premature rupture of membranes,Frontiers in cellular and infection microbiology,2022,"PPROM, PROM, PTB, preterm birth, vaginal microbiota",Experiment 1,China,Homo sapiens,"Anterior fornix of vagina,Lateral fornix of vagina,Uterine cervix","UBERON:0016487,UBERON:0034963,UBERON:0000002",Preterm premature rupture of the membranes,MONDO:0012511,Control(term delivery),Preterm premature rupture of membranes (PPROM),PPROM is characterized by vaginal microbial dysbiosis.,54,48,2 months,16S,34,Illumina,NA,LEfSe,0.05,NA,3.5,"age,gestational age",NA,increased,increased,increased,increased,NA,NA,Signature 1,Fig.2C,21 October 2023,Chinelsy,"Chinelsy,WikiWorks",Differences in bacterial abundance in patients with PPROM versus controls.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum|s__Ochrobactrum sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma parvum",1783272|201174|1760|85004|31953|2701|2702;3379134|976|200643|171549|171552|2974257|386414;1783272|1239|91061|186826|33958|1578|147802;3379134|1224|28211|356|118882|528|42190;3379134|976|200643|171549|171552|838|28125;1783272|544448|2790996|2790998|2129|134821,Complete,Folakunmi
bsdb:36004326/1/2,36004326,case-control,36004326,10.3389/fcimb.2022.858732,NA,"Yan C., Hong F., Xin G., Duan S., Deng X. , Xu Y.",Alterations in the vaginal microbiota of patients with preterm premature rupture of membranes,Frontiers in cellular and infection microbiology,2022,"PPROM, PROM, PTB, preterm birth, vaginal microbiota",Experiment 1,China,Homo sapiens,"Anterior fornix of vagina,Lateral fornix of vagina,Uterine cervix","UBERON:0016487,UBERON:0034963,UBERON:0000002",Preterm premature rupture of the membranes,MONDO:0012511,Control(term delivery),Preterm premature rupture of membranes (PPROM),PPROM is characterized by vaginal microbial dysbiosis.,54,48,2 months,16S,34,Illumina,NA,LEfSe,0.05,NA,3.5,"age,gestational age",NA,increased,increased,increased,increased,NA,NA,Signature 2,Fig.2C,11 February 2024,Folakunmi,"Folakunmi,WikiWorks",Differences in bacterial abundance in patients with PPROM versus controls.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri",1783272|1239|91061|186826|33958|1578|47770;1783272|1239|91061|186826|33958|1578|1596,Complete,Folakunmi
bsdb:36016793/1/1,36016793,laboratory experiment,36016793,https://doi.org/10.3389/fmicb.2022.956438,NA,"Zhao Y., Liu Q., Hou Y. , Zhao Y.",Alleviating effects of gut micro-ecologically regulatory treatments on mice with constipation,Frontiers in microbiology,2022,"constipation, gut microbial regulation, postbiotics, probiotics, short-chain fatty acids, synbiotics",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Control group,Model group,Mice in Model group was orally treated only with saline per day during the experimental period.,8,8,NA,16S,4,Illumina,relative abundances,NA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"""Within-text result of ""The synbiotics changed gut microbial composition in mice"" section""",15 April 2025,PreciousChijioke,PreciousChijioke,Heatmap of the top 20 fecal microbial genera among groups.,increased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,3379134|74201|203494|48461|1647988|239934,Complete,Svetlana up
bsdb:36016793/4/1,36016793,laboratory experiment,36016793,https://doi.org/10.3389/fmicb.2022.956438,NA,"Zhao Y., Liu Q., Hou Y. , Zhao Y.",Alleviating effects of gut micro-ecologically regulatory treatments on mice with constipation,Frontiers in microbiology,2022,"constipation, gut microbial regulation, postbiotics, probiotics, short-chain fatty acids, synbiotics",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Model group,Mice in MP (mixed probiotics) group,"Mice in MP (mixed probiotics) group was treated every day with loperamide (10 mg/kg body weight), and with corresponding products (Mixed probiotics) 1 h after loperamide administration.",8,8,NA,16S,4,Illumina,relative abundances,NA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"""Within-text result of ""The synbiotics changed gut microbial composition in mice"" section""",11 April 2025,PreciousChijioke,PreciousChijioke,Heatmap of the top 20 fecal microbial genera among groups.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,1783272|1239|186801|186802|186806|1730|39497,Complete,Svetlana up
bsdb:36016793/4/2,36016793,laboratory experiment,36016793,https://doi.org/10.3389/fmicb.2022.956438,NA,"Zhao Y., Liu Q., Hou Y. , Zhao Y.",Alleviating effects of gut micro-ecologically regulatory treatments on mice with constipation,Frontiers in microbiology,2022,"constipation, gut microbial regulation, postbiotics, probiotics, short-chain fatty acids, synbiotics",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Model group,Mice in MP (mixed probiotics) group,"Mice in MP (mixed probiotics) group was treated every day with loperamide (10 mg/kg body weight), and with corresponding products (Mixed probiotics) 1 h after loperamide administration.",8,8,NA,16S,4,Illumina,relative abundances,NA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"""Within-text result of ""The synbiotics changed gut microbial composition in mice"" section""",11 April 2025,PreciousChijioke,PreciousChijioke,Heatmap of the top 20 fecal microbial genera among groups.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,3379134|976|200643|171549|171550|239759,Complete,Svetlana up
bsdb:36016793/5/1,36016793,laboratory experiment,36016793,https://doi.org/10.3389/fmicb.2022.956438,NA,"Zhao Y., Liu Q., Hou Y. , Zhao Y.",Alleviating effects of gut micro-ecologically regulatory treatments on mice with constipation,Frontiers in microbiology,2022,"constipation, gut microbial regulation, postbiotics, probiotics, short-chain fatty acids, synbiotics",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Model group,Mice in MPP (mixed probiotics plus postbiotics) group,"Mice in MPP (mixed probiotics plus postbiotics) group was treated every day with loperamide (10 mg/kg body weight), and with corresponding products (Mixed probiotics plus postbiotics) 1 h after loperamide administration.",8,8,NA,16S,4,Illumina,relative abundances,NA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"""Within-text result of ""The synbiotics changed gut microbial composition in mice"" section""",11 April 2025,PreciousChijioke,PreciousChijioke,Heatmap of the top 20 fecal microbial genera among groups.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,1783272|1239|186801|186802|186806|1730|39497,Complete,Svetlana up
bsdb:36016793/5/2,36016793,laboratory experiment,36016793,https://doi.org/10.3389/fmicb.2022.956438,NA,"Zhao Y., Liu Q., Hou Y. , Zhao Y.",Alleviating effects of gut micro-ecologically regulatory treatments on mice with constipation,Frontiers in microbiology,2022,"constipation, gut microbial regulation, postbiotics, probiotics, short-chain fatty acids, synbiotics",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Model group,Mice in MPP (mixed probiotics plus postbiotics) group,"Mice in MPP (mixed probiotics plus postbiotics) group was treated every day with loperamide (10 mg/kg body weight), and with corresponding products (Mixed probiotics plus postbiotics) 1 h after loperamide administration.",8,8,NA,16S,4,Illumina,relative abundances,NA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"""Within-text result of ""The synbiotics changed gut microbial composition in mice"" section""",11 April 2025,PreciousChijioke,PreciousChijioke,Heatmap of the top 20 fecal microbial genera among groups.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,3379134|976|200643|171549|171550|239759,Complete,Svetlana up
bsdb:36016793/6/1,36016793,laboratory experiment,36016793,https://doi.org/10.3389/fmicb.2022.956438,NA,"Zhao Y., Liu Q., Hou Y. , Zhao Y.",Alleviating effects of gut micro-ecologically regulatory treatments on mice with constipation,Frontiers in microbiology,2022,"constipation, gut microbial regulation, postbiotics, probiotics, short-chain fatty acids, synbiotics",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Model group,Mice in P (postbiotics) group,"Mice in P (postbiotics) group was treated every day with loperamide (10 mg/kg body weight), and with corresponding products (Postbiotics) 1 h after loperamide administration.",8,8,NA,16S,4,Illumina,relative abundances,NA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"""Within-text result of ""The synbiotics changed gut microbial composition in mice"" section""",11 April 2025,PreciousChijioke,PreciousChijioke,Heatmap of the top 20 fecal microbial genera among groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|1508657,Complete,Svetlana up
bsdb:36016793/6/2,36016793,laboratory experiment,36016793,https://doi.org/10.3389/fmicb.2022.956438,NA,"Zhao Y., Liu Q., Hou Y. , Zhao Y.",Alleviating effects of gut micro-ecologically regulatory treatments on mice with constipation,Frontiers in microbiology,2022,"constipation, gut microbial regulation, postbiotics, probiotics, short-chain fatty acids, synbiotics",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Model group,Mice in P (postbiotics) group,"Mice in P (postbiotics) group was treated every day with loperamide (10 mg/kg body weight), and with corresponding products (Postbiotics) 1 h after loperamide administration.",8,8,NA,16S,4,Illumina,relative abundances,NA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"""Within-text result of ""The synbiotics changed gut microbial composition in mice"" section""",11 April 2025,PreciousChijioke,PreciousChijioke,Heatmap of the top 20 fecal microbial genera among groups.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,3379134|976|200643|171549|171550|239759,Complete,Svetlana up
bsdb:36016793/7/1,36016793,laboratory experiment,36016793,https://doi.org/10.3389/fmicb.2022.956438,NA,"Zhao Y., Liu Q., Hou Y. , Zhao Y.",Alleviating effects of gut micro-ecologically regulatory treatments on mice with constipation,Frontiers in microbiology,2022,"constipation, gut microbial regulation, postbiotics, probiotics, short-chain fatty acids, synbiotics",Experiment 7,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Model group,Mice in P5 (5-fold dose of postbiotics) group,"Mice in P5 (5-fold dose of postbiotics) group was treated every day with loperamide (10 mg/kg body weight), and with corresponding products (Postbiotics) 1 h after loperamide administration.",8,8,NA,16S,4,Illumina,relative abundances,NA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"""Within-text result of ""The synbiotics changed gut microbial composition in mice"" section""",11 April 2025,PreciousChijioke,PreciousChijioke,Heatmap of the top 20 fecal microbial genera among groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|1508657,Complete,Svetlana up
bsdb:36016793/7/2,36016793,laboratory experiment,36016793,https://doi.org/10.3389/fmicb.2022.956438,NA,"Zhao Y., Liu Q., Hou Y. , Zhao Y.",Alleviating effects of gut micro-ecologically regulatory treatments on mice with constipation,Frontiers in microbiology,2022,"constipation, gut microbial regulation, postbiotics, probiotics, short-chain fatty acids, synbiotics",Experiment 7,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Model group,Mice in P5 (5-fold dose of postbiotics) group,"Mice in P5 (5-fold dose of postbiotics) group was treated every day with loperamide (10 mg/kg body weight), and with corresponding products (Postbiotics) 1 h after loperamide administration.",8,8,NA,16S,4,Illumina,relative abundances,NA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"""Within-text result of ""The synbiotics changed gut microbial composition in mice"" section""",11 April 2025,PreciousChijioke,PreciousChijioke,Heatmap of the top 20 fecal microbial genera among groups.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,3379134|976|200643|171549|171550|239759,Complete,Svetlana up
bsdb:36016793/8/1,36016793,laboratory experiment,36016793,https://doi.org/10.3389/fmicb.2022.956438,NA,"Zhao Y., Liu Q., Hou Y. , Zhao Y.",Alleviating effects of gut micro-ecologically regulatory treatments on mice with constipation,Frontiers in microbiology,2022,"constipation, gut microbial regulation, postbiotics, probiotics, short-chain fatty acids, synbiotics",Experiment 8,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Model group,S (synbiotics) group,"S (synbiotics) group was treated every day with loperamide (10 mg/kg body weight), and with corresponding products (Synbiotics) 1 h after loperamide administration.",8,8,NA,16S,4,Illumina,relative abundances,NA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"""Within-text result of ""The synbiotics changed gut microbial composition in mice"" section""",11 April 2025,PreciousChijioke,PreciousChijioke,Heatmap of the top 20 fecal microbial genera among groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|1508657,Complete,Svetlana up
bsdb:36016793/8/2,36016793,laboratory experiment,36016793,https://doi.org/10.3389/fmicb.2022.956438,NA,"Zhao Y., Liu Q., Hou Y. , Zhao Y.",Alleviating effects of gut micro-ecologically regulatory treatments on mice with constipation,Frontiers in microbiology,2022,"constipation, gut microbial regulation, postbiotics, probiotics, short-chain fatty acids, synbiotics",Experiment 8,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Model group,S (synbiotics) group,"S (synbiotics) group was treated every day with loperamide (10 mg/kg body weight), and with corresponding products (Synbiotics) 1 h after loperamide administration.",8,8,NA,16S,4,Illumina,relative abundances,NA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"""Within-text result of ""The synbiotics changed gut microbial composition in mice"" section""",11 April 2025,PreciousChijioke,PreciousChijioke,Heatmap of the top 20 fecal microbial genera among groups.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,3379134|976|200643|171549|171550|239759,Complete,Svetlana up
bsdb:36016793/9/1,36016793,laboratory experiment,36016793,https://doi.org/10.3389/fmicb.2022.956438,NA,"Zhao Y., Liu Q., Hou Y. , Zhao Y.",Alleviating effects of gut micro-ecologically regulatory treatments on mice with constipation,Frontiers in microbiology,2022,"constipation, gut microbial regulation, postbiotics, probiotics, short-chain fatty acids, synbiotics",Experiment 9,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Model group,S2 (synbiotics) group,"S2 (synbiotics) group was treated every day with loperamide (10 mg/kg body weight), and with corresponding products (Synbiotics) 1 h after loperamide administration.",8,8,NA,16S,4,Illumina,relative abundances,NA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"""Within-text result of ""The synbiotics changed gut microbial composition in mice"" section""",11 April 2025,PreciousChijioke,PreciousChijioke,Heatmap of the top 20 fecal microbial genera among groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|1508657,Complete,Svetlana up
bsdb:36016793/9/2,36016793,laboratory experiment,36016793,https://doi.org/10.3389/fmicb.2022.956438,NA,"Zhao Y., Liu Q., Hou Y. , Zhao Y.",Alleviating effects of gut micro-ecologically regulatory treatments on mice with constipation,Frontiers in microbiology,2022,"constipation, gut microbial regulation, postbiotics, probiotics, short-chain fatty acids, synbiotics",Experiment 9,China,Mus musculus,Feces,UBERON:0001988,Constipation,HP:0002019,Model group,S2 (synbiotics) group,"S2 (synbiotics) group was treated every day with loperamide (10 mg/kg body weight), and with corresponding products (Synbiotics) 1 h after loperamide administration.",8,8,NA,16S,4,Illumina,relative abundances,NA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"""Within-text result of ""The synbiotics changed gut microbial composition in mice"" section""",11 April 2025,PreciousChijioke,PreciousChijioke,Heatmap of the top 20 fecal microbial genera among groups.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,3379134|976|200643|171549|171550|239759,Complete,Svetlana up
bsdb:36026526/1/1,36026526,meta-analysis,36026526,10.1093/ajcn/nqac217,NA,"Palmnäs-Bédard M.S.A., Costabile G., Vetrani C., Åberg S., Hjalmarsson Y., Dicksved J., Riccardi G. , Landberg R.",The human gut microbiota and glucose metabolism: a scoping review of key bacteria and the potential role of SCFAs,The American journal of clinical nutrition,2022,"diet–gut microbiota interactions, glucose metabolism, gut microbiota, humans, insulin resistance, microbial metabolites, precision nutrition, prediabetes, short-chain fatty acids, type 2 diabetes prevention",Experiment 1,"India,Denmark,Ghana,South Africa,Jamaica,United States of America,Sweden,France,United Kingdom,Taiwan,Mexico,Japan,China,Spain,Brazil,Greece,Australia,Finland,Poland,Iran,South Korea,Israel,Ireland",Homo sapiens,Feces,UBERON:0001988,Glucose,CHEBI:17234,Bacteria associated with glucose metabolism outcomes,Bacteria associated with glucose metabolism outcomes,Relationship between the human gut microbiota and glucose metabolism,45,45,NA,NA,NA,NA,NA,NA,NA,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,3 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Summary of reported associations between bacteria on different taxonomic levels and glucose-related outcomes,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Thermotogati|p__Synergistota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",1783272|1239|186801|3085636|186803|207244;1783272|1239;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|2719313|208479;3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|216572|216851|853;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|186802|216572;1783272|201174|84998|1643822|1643826|84108;1783272|1239|91061|186826|1300|1301|1304;3384194|508458;1783272|1239|909932|1843489|31977;1783272|1239|186801|186802|216572|1535;3379134|1224|1236|91347|543,Complete,Svetlana up
bsdb:36026526/1/2,36026526,meta-analysis,36026526,10.1093/ajcn/nqac217,NA,"Palmnäs-Bédard M.S.A., Costabile G., Vetrani C., Åberg S., Hjalmarsson Y., Dicksved J., Riccardi G. , Landberg R.",The human gut microbiota and glucose metabolism: a scoping review of key bacteria and the potential role of SCFAs,The American journal of clinical nutrition,2022,"diet–gut microbiota interactions, glucose metabolism, gut microbiota, humans, insulin resistance, microbial metabolites, precision nutrition, prediabetes, short-chain fatty acids, type 2 diabetes prevention",Experiment 1,"India,Denmark,Ghana,South Africa,Jamaica,United States of America,Sweden,France,United Kingdom,Taiwan,Mexico,Japan,China,Spain,Brazil,Greece,Australia,Finland,Poland,Iran,South Korea,Israel,Ireland",Homo sapiens,Feces,UBERON:0001988,Glucose,CHEBI:17234,Bacteria associated with glucose metabolism outcomes,Bacteria associated with glucose metabolism outcomes,Relationship between the human gut microbiota and glucose metabolism,45,45,NA,NA,NA,NA,NA,NA,NA,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,3 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Summary of reported associations between bacteria on different taxonomic levels and glucose-related outcomes,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii",3379134|976;1783272|1239;1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|216572;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|216851;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|1263;3379134|74201|203494|48461|1647988|239934|239935;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|3085636|186803|572511|1532;1783272|1239|186801|186802|216572|1535;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|186801|186802|216572|216851|853;3379134|1224|1236|135625|712|724|729;1783272|1239|186801|3082720|186804|1505657|261299,Complete,Svetlana up
bsdb:36026526/2/1,36026526,meta-analysis,36026526,10.1093/ajcn/nqac217,NA,"Palmnäs-Bédard M.S.A., Costabile G., Vetrani C., Åberg S., Hjalmarsson Y., Dicksved J., Riccardi G. , Landberg R.",The human gut microbiota and glucose metabolism: a scoping review of key bacteria and the potential role of SCFAs,The American journal of clinical nutrition,2022,"diet–gut microbiota interactions, glucose metabolism, gut microbiota, humans, insulin resistance, microbial metabolites, precision nutrition, prediabetes, short-chain fatty acids, type 2 diabetes prevention",Experiment 2,"Australia,Brazil,China,Denmark,Finland,France,Ghana,Greece,India,Iran,Ireland,Israel,Jamaica,Japan,Mexico,Poland,South Africa,South Korea,Spain,Sweden,United Kingdom,United States of America,Taiwan",Homo sapiens,Feces,UBERON:0001988,Glucose,CHEBI:17234,Bacteria associated with glucose metabolism outcomes,Bacteria associated with glucose metabolism outcomes,"Relationship between the human gut microbiota and glucose metabolism, adjusted for body measures.",45,45,NA,NA,NA,NA,NA,NA,NA,TRUE,NA,NA,"body mass index,body weight,waist circumference",NA,NA,NA,NA,NA,NA,Signature 1,Table 1,3 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Summary of reported associations between bacteria on different taxonomic levels and glucose-related outcomes adjusted for body measures.,increased,"k__Thermotogati|p__Synergistota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius",3384194|508458;3379134|1224|1236|91347|543;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;1783272|1239|909932|1843489|31977;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|216851;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|906;3379134|976|200643|171549|171552|838;1783272|201174|84998|1643822|1643826|84108;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|572511|418240;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|186802|216572|216851|853;1783272|1239|909932|1843489|31977|906|907;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|91061|186826|1300|1301|1304,Complete,Svetlana up
bsdb:36026526/2/2,36026526,meta-analysis,36026526,10.1093/ajcn/nqac217,NA,"Palmnäs-Bédard M.S.A., Costabile G., Vetrani C., Åberg S., Hjalmarsson Y., Dicksved J., Riccardi G. , Landberg R.",The human gut microbiota and glucose metabolism: a scoping review of key bacteria and the potential role of SCFAs,The American journal of clinical nutrition,2022,"diet–gut microbiota interactions, glucose metabolism, gut microbiota, humans, insulin resistance, microbial metabolites, precision nutrition, prediabetes, short-chain fatty acids, type 2 diabetes prevention",Experiment 2,"Australia,Brazil,China,Denmark,Finland,France,Ghana,Greece,India,Iran,Ireland,Israel,Jamaica,Japan,Mexico,Poland,South Africa,South Korea,Spain,Sweden,United Kingdom,United States of America,Taiwan",Homo sapiens,Feces,UBERON:0001988,Glucose,CHEBI:17234,Bacteria associated with glucose metabolism outcomes,Bacteria associated with glucose metabolism outcomes,"Relationship between the human gut microbiota and glucose metabolism, adjusted for body measures.",45,45,NA,NA,NA,NA,NA,NA,NA,TRUE,NA,NA,"body mass index,body weight,waist circumference",NA,NA,NA,NA,NA,NA,Signature 2,Table 1,3 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Summary of reported associations between bacteria on different taxonomic levels and glucose-related outcomes adjusted for body measures.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii",1783272|1239|186801|186802;1783272|1239|186801|3082768|990719;1783272|1239|909932|1843489|31977;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|1263;3379134|74201|203494|48461|1647988|239934|239935;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|186802|216572|1535;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|186801|186802|216572|216851|853;3379134|1224|1236|135625|712|724|729;1783272|1239|186801|3082720|186804|1505657|261299,Complete,Svetlana up
bsdb:36026526/3/1,36026526,meta-analysis,36026526,10.1093/ajcn/nqac217,NA,"Palmnäs-Bédard M.S.A., Costabile G., Vetrani C., Åberg S., Hjalmarsson Y., Dicksved J., Riccardi G. , Landberg R.",The human gut microbiota and glucose metabolism: a scoping review of key bacteria and the potential role of SCFAs,The American journal of clinical nutrition,2022,"diet–gut microbiota interactions, glucose metabolism, gut microbiota, humans, insulin resistance, microbial metabolites, precision nutrition, prediabetes, short-chain fatty acids, type 2 diabetes prevention",Experiment 3,"Australia,Brazil,China,Denmark,Finland,France,Ghana,Greece,India,Iran,Ireland,Israel,Jamaica,Japan,Mexico,Poland,South Africa,South Korea,Spain,Sweden,United Kingdom,United States of America,Taiwan",Homo sapiens,Feces,UBERON:0001988,Glucose,CHEBI:17234,Bacteria associated with glucose metabolism outcomes,Bacteria associated with glucose metabolism outcomes,"Relationship between the human gut microbiota and glucose metabolism, adjusted for metabolic drugs.",45,45,NA,NA,NA,NA,NA,NA,NA,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,3 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Summary of reported associations between bacteria on different taxonomic levels and glucose-related outcomes adjusted for metabolic drugs.,increased,"k__Bacillati|p__Bacillota,k__Thermotogati|p__Synergistota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",1783272|1239;3384194|508458;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|216851;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|906;3379134|976|200643|171549|171552|838;1783272|201174|84998|1643822|1643826|84108;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|572511|418240;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|186802|216572|216851|853;1783272|1239|909932|1843489|31977|906|907;1783272|1239|186801|3085636|186803|2316020|33038,Complete,Svetlana up
bsdb:36026526/3/2,36026526,meta-analysis,36026526,10.1093/ajcn/nqac217,NA,"Palmnäs-Bédard M.S.A., Costabile G., Vetrani C., Åberg S., Hjalmarsson Y., Dicksved J., Riccardi G. , Landberg R.",The human gut microbiota and glucose metabolism: a scoping review of key bacteria and the potential role of SCFAs,The American journal of clinical nutrition,2022,"diet–gut microbiota interactions, glucose metabolism, gut microbiota, humans, insulin resistance, microbial metabolites, precision nutrition, prediabetes, short-chain fatty acids, type 2 diabetes prevention",Experiment 3,"Australia,Brazil,China,Denmark,Finland,France,Ghana,Greece,India,Iran,Ireland,Israel,Jamaica,Japan,Mexico,Poland,South Africa,South Korea,Spain,Sweden,United Kingdom,United States of America,Taiwan",Homo sapiens,Feces,UBERON:0001988,Glucose,CHEBI:17234,Bacteria associated with glucose metabolism outcomes,Bacteria associated with glucose metabolism outcomes,"Relationship between the human gut microbiota and glucose metabolism, adjusted for metabolic drugs.",45,45,NA,NA,NA,NA,NA,NA,NA,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,3 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Summary of reported associations between bacteria on different taxonomic levels and glucose-related outcomes adjusted for metabolic drugs.,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii",1783272|1239;1783272|1239|186801|186802;1783272|1239|186801|3082768|990719;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|1263;3379134|74201|203494|48461|1647988|239934|239935;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|3085636|186803|572511|1532;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|186802|216572|1535;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3082720|186804|1505657|261299,Complete,Svetlana up
bsdb:36026526/4/1,36026526,meta-analysis,36026526,10.1093/ajcn/nqac217,NA,"Palmnäs-Bédard M.S.A., Costabile G., Vetrani C., Åberg S., Hjalmarsson Y., Dicksved J., Riccardi G. , Landberg R.",The human gut microbiota and glucose metabolism: a scoping review of key bacteria and the potential role of SCFAs,The American journal of clinical nutrition,2022,"diet–gut microbiota interactions, glucose metabolism, gut microbiota, humans, insulin resistance, microbial metabolites, precision nutrition, prediabetes, short-chain fatty acids, type 2 diabetes prevention",Experiment 4,"Australia,Brazil,China,Denmark,Finland,France,Ghana,Greece,India,Iran,Ireland,Israel,Jamaica,Japan,Mexico,Poland,South Africa,South Korea,Spain,Sweden,United Kingdom,United States of America,Taiwan",Homo sapiens,Feces,UBERON:0001988,Glucose,CHEBI:17234,Bacteria associated with postprandial glucose,Bacteria associated with postprandial glucose,Relationship between the human gut microbiota and postprandial glucose.,45,45,NA,NA,NA,NA,NA,NA,NA,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,3 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Summary of reported associations between bacteria on different taxonomic levels and postprandial glucose.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",3379134|1224|1236|91347|543;1783272|1239|186801|3085636|186803|2316020|33038,Complete,Svetlana up
bsdb:36026526/4/2,36026526,meta-analysis,36026526,10.1093/ajcn/nqac217,NA,"Palmnäs-Bédard M.S.A., Costabile G., Vetrani C., Åberg S., Hjalmarsson Y., Dicksved J., Riccardi G. , Landberg R.",The human gut microbiota and glucose metabolism: a scoping review of key bacteria and the potential role of SCFAs,The American journal of clinical nutrition,2022,"diet–gut microbiota interactions, glucose metabolism, gut microbiota, humans, insulin resistance, microbial metabolites, precision nutrition, prediabetes, short-chain fatty acids, type 2 diabetes prevention",Experiment 4,"Australia,Brazil,China,Denmark,Finland,France,Ghana,Greece,India,Iran,Ireland,Israel,Jamaica,Japan,Mexico,Poland,South Africa,South Korea,Spain,Sweden,United Kingdom,United States of America,Taiwan",Homo sapiens,Feces,UBERON:0001988,Glucose,CHEBI:17234,Bacteria associated with postprandial glucose,Bacteria associated with postprandial glucose,Relationship between the human gut microbiota and postprandial glucose.,45,45,NA,NA,NA,NA,NA,NA,NA,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,3 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Summary of reported associations between bacteria on different taxonomic levels and postprandial glucose.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,3379134|1224|1236|135625|712|724|729,Complete,Svetlana up
bsdb:36026526/5/1,36026526,meta-analysis,36026526,10.1093/ajcn/nqac217,NA,"Palmnäs-Bédard M.S.A., Costabile G., Vetrani C., Åberg S., Hjalmarsson Y., Dicksved J., Riccardi G. , Landberg R.",The human gut microbiota and glucose metabolism: a scoping review of key bacteria and the potential role of SCFAs,The American journal of clinical nutrition,2022,"diet–gut microbiota interactions, glucose metabolism, gut microbiota, humans, insulin resistance, microbial metabolites, precision nutrition, prediabetes, short-chain fatty acids, type 2 diabetes prevention",Experiment 5,"Australia,Brazil,China,Denmark,Finland,France,Ghana,Greece,India,Iran,Ireland,Israel,Jamaica,Japan,Mexico,Poland,South Africa,South Korea,Spain,Sweden,United Kingdom,United States of America,Taiwan",Homo sapiens,Feces,UBERON:0001988,Insulin,CHEBI:5931,Bacteria associated with insulin-related outcomes,Bacteria associated with insulin-related outcomes,Relationship between the human gut microbiota and insulin-related outcomes.,45,45,NA,NA,NA,NA,NA,NA,NA,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,3 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Summary of reported associations between bacteria on different taxonomic levels and insulin-related outcomes.,increased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|1224;3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:36026526/5/2,36026526,meta-analysis,36026526,10.1093/ajcn/nqac217,NA,"Palmnäs-Bédard M.S.A., Costabile G., Vetrani C., Åberg S., Hjalmarsson Y., Dicksved J., Riccardi G. , Landberg R.",The human gut microbiota and glucose metabolism: a scoping review of key bacteria and the potential role of SCFAs,The American journal of clinical nutrition,2022,"diet–gut microbiota interactions, glucose metabolism, gut microbiota, humans, insulin resistance, microbial metabolites, precision nutrition, prediabetes, short-chain fatty acids, type 2 diabetes prevention",Experiment 5,"Australia,Brazil,China,Denmark,Finland,France,Ghana,Greece,India,Iran,Ireland,Israel,Jamaica,Japan,Mexico,Poland,South Africa,South Korea,Spain,Sweden,United Kingdom,United States of America,Taiwan",Homo sapiens,Feces,UBERON:0001988,Insulin,CHEBI:5931,Bacteria associated with insulin-related outcomes,Bacteria associated with insulin-related outcomes,Relationship between the human gut microbiota and insulin-related outcomes.,45,45,NA,NA,NA,NA,NA,NA,NA,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,3 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Summary of reported associations between bacteria on different taxonomic levels and insulin-related outcomes.,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",3379134|976;1783272|1239;1783272|1239|186801|186802|216572;1783272|201174|1760|85004|31953|1678;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|815|816|329854;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|186802|216572|216851|853,Complete,Svetlana up
bsdb:36026526/6/1,36026526,meta-analysis,36026526,10.1093/ajcn/nqac217,NA,"Palmnäs-Bédard M.S.A., Costabile G., Vetrani C., Åberg S., Hjalmarsson Y., Dicksved J., Riccardi G. , Landberg R.",The human gut microbiota and glucose metabolism: a scoping review of key bacteria and the potential role of SCFAs,The American journal of clinical nutrition,2022,"diet–gut microbiota interactions, glucose metabolism, gut microbiota, humans, insulin resistance, microbial metabolites, precision nutrition, prediabetes, short-chain fatty acids, type 2 diabetes prevention",Experiment 6,"Australia,Brazil,China,Denmark,Finland,France,Ghana,Greece,India,Iran,Ireland,Israel,Jamaica,Japan,Mexico,Poland,South Africa,South Korea,Spain,Sweden,United Kingdom,United States of America,Taiwan",Homo sapiens,Feces,UBERON:0001988,Insulin,CHEBI:5931,Bacteria associated with insulin-related outcomes,Bacteria associated with insulin-related outcomes,"Relationship between the human gut microbiota and insulin-related outcomes, adjusted for body measures.",45,45,NA,NA,NA,NA,NA,NA,NA,TRUE,NA,NA,"body mass index,body weight,waist circumference",NA,NA,NA,NA,NA,NA,Signature 1,Table 2,3 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Summary of reported associations between bacteria on different taxonomic levels and insulin-related outcomes adjusted for body measures.,increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota",3379134|976;3379134|1224,Complete,Svetlana up
bsdb:36026526/6/2,36026526,meta-analysis,36026526,10.1093/ajcn/nqac217,NA,"Palmnäs-Bédard M.S.A., Costabile G., Vetrani C., Åberg S., Hjalmarsson Y., Dicksved J., Riccardi G. , Landberg R.",The human gut microbiota and glucose metabolism: a scoping review of key bacteria and the potential role of SCFAs,The American journal of clinical nutrition,2022,"diet–gut microbiota interactions, glucose metabolism, gut microbiota, humans, insulin resistance, microbial metabolites, precision nutrition, prediabetes, short-chain fatty acids, type 2 diabetes prevention",Experiment 6,"Australia,Brazil,China,Denmark,Finland,France,Ghana,Greece,India,Iran,Ireland,Israel,Jamaica,Japan,Mexico,Poland,South Africa,South Korea,Spain,Sweden,United Kingdom,United States of America,Taiwan",Homo sapiens,Feces,UBERON:0001988,Insulin,CHEBI:5931,Bacteria associated with insulin-related outcomes,Bacteria associated with insulin-related outcomes,"Relationship between the human gut microbiota and insulin-related outcomes, adjusted for body measures.",45,45,NA,NA,NA,NA,NA,NA,NA,TRUE,NA,NA,"body mass index,body weight,waist circumference",NA,NA,NA,NA,NA,NA,Signature 2,Table 2,3 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Summary of reported associations between bacteria on different taxonomic levels and insulin-related outcomes adjusted for body measures.,decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",1783272|1239;3379134|1224;1783272|1239|186801|186802|31979;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|31979|1485;3379134|74201|203494|48461|1647988|239934|239935;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|3085636|186803|572511|1532;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|186802|216572|216851|853,Complete,Svetlana up
bsdb:36026526/7/1,36026526,meta-analysis,36026526,10.1093/ajcn/nqac217,NA,"Palmnäs-Bédard M.S.A., Costabile G., Vetrani C., Åberg S., Hjalmarsson Y., Dicksved J., Riccardi G. , Landberg R.",The human gut microbiota and glucose metabolism: a scoping review of key bacteria and the potential role of SCFAs,The American journal of clinical nutrition,2022,"diet–gut microbiota interactions, glucose metabolism, gut microbiota, humans, insulin resistance, microbial metabolites, precision nutrition, prediabetes, short-chain fatty acids, type 2 diabetes prevention",Experiment 7,"Australia,Brazil,China,Denmark,Finland,France,Ghana,Greece,India,Iran,Ireland,Israel,Jamaica,Japan,Mexico,Poland,South Africa,South Korea,Spain,Sweden,United Kingdom,United States of America,Taiwan",Homo sapiens,Feces,UBERON:0001988,Insulin,CHEBI:5931,Bacteria associated with insulin-related outcomes,Bacteria associated with insulin-related outcomes,"Relationship between the human gut microbiota and insulin-related outcomes, adjusted for metabolic drugs.",45,45,NA,NA,NA,NA,NA,NA,NA,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,3 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Summary of reported associations between bacteria on different taxonomic levels and insulin-related outcomes adjusted for metabolic drugs.,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:36026526/7/2,36026526,meta-analysis,36026526,10.1093/ajcn/nqac217,NA,"Palmnäs-Bédard M.S.A., Costabile G., Vetrani C., Åberg S., Hjalmarsson Y., Dicksved J., Riccardi G. , Landberg R.",The human gut microbiota and glucose metabolism: a scoping review of key bacteria and the potential role of SCFAs,The American journal of clinical nutrition,2022,"diet–gut microbiota interactions, glucose metabolism, gut microbiota, humans, insulin resistance, microbial metabolites, precision nutrition, prediabetes, short-chain fatty acids, type 2 diabetes prevention",Experiment 7,"Australia,Brazil,China,Denmark,Finland,France,Ghana,Greece,India,Iran,Ireland,Israel,Jamaica,Japan,Mexico,Poland,South Africa,South Korea,Spain,Sweden,United Kingdom,United States of America,Taiwan",Homo sapiens,Feces,UBERON:0001988,Insulin,CHEBI:5931,Bacteria associated with insulin-related outcomes,Bacteria associated with insulin-related outcomes,"Relationship between the human gut microbiota and insulin-related outcomes, adjusted for metabolic drugs.",45,45,NA,NA,NA,NA,NA,NA,NA,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,3 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Summary of reported associations between bacteria on different taxonomic levels and insulin-related outcomes adjusted for metabolic drugs.,decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",1783272|1239;3379134|1224;1783272|1239|186801|186802;1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|31979|1485;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|815|816|329854;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|3085636|186803|572511|1532;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|186802|216572|216851|853,Complete,Svetlana up
bsdb:36026526/8/1,36026526,meta-analysis,36026526,10.1093/ajcn/nqac217,NA,"Palmnäs-Bédard M.S.A., Costabile G., Vetrani C., Åberg S., Hjalmarsson Y., Dicksved J., Riccardi G. , Landberg R.",The human gut microbiota and glucose metabolism: a scoping review of key bacteria and the potential role of SCFAs,The American journal of clinical nutrition,2022,"diet–gut microbiota interactions, glucose metabolism, gut microbiota, humans, insulin resistance, microbial metabolites, precision nutrition, prediabetes, short-chain fatty acids, type 2 diabetes prevention",Experiment 8,"Australia,Brazil,China,Denmark,Finland,France,Ghana,Greece,India,Iran,Ireland,Israel,Jamaica,Japan,Mexico,Poland,South Africa,South Korea,Spain,Sweden,United Kingdom,United States of America,Taiwan",Homo sapiens,Feces,UBERON:0001988,Insulin,CHEBI:5931,Bacteria associated with postprandial insulin,Bacteria associated with postprandial insulin,Relationship between the human gut microbiota and postprandial insulin.,45,45,NA,NA,NA,NA,NA,NA,NA,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,3 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Summary of reported associations between bacteria on different taxonomic levels and insulin-related outcomes.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,1783272|1239|186801|186802|216572|216851|853,Complete,Svetlana up
bsdb:36034713/1/1,36034713,laboratory experiment,36034713,10.3389/fcimb.2022.968992,NA,"Zhang Y., Zhou X. , Lu Y.",Gut microbiota and derived metabolomic profiling in glaucoma with progressive neurodegeneration,Frontiers in cellular and infection microbiology,2022,"Glaucoma, glutathione, gut microbiota, microbial metabolite, retinal ganglion cell (RGC)",Experiment 1,China,Rattus norvegicus,Caecum,UBERON:0001153,Glaucoma,MONDO:0005041,Control,Glaucoma,Male wistar rats in the glaucomatous group,NA,NA,NA,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,"Figure 3A, B",31 July 2025,Anne-mariesharp,Anne-mariesharp,Significant differentially abundant bacterial taxa between glaucoma and control rats using LEfSe analysis,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter ganmani,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;3379134|976|200643|171549|171550|239759|328814;3379134|1224|28211;1783272|1239|186801|186802|186806|264995;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|186806;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1501226;1783272|1239|526524|526525|2810281|191303;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201;3379134|29547|3031852|213849|72293|209|60246;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816|329854;3379134|976|200643|171549|171550;3379134|976|200643|171549|2005473|1918540;3379134|29547|3031852|213849;3379134|29547|3031852|213849|72293;3379134|29547|3031852|213849|72293|209,Complete,KateRasheed
bsdb:36034713/1/2,36034713,laboratory experiment,36034713,10.3389/fcimb.2022.968992,NA,"Zhang Y., Zhou X. , Lu Y.",Gut microbiota and derived metabolomic profiling in glaucoma with progressive neurodegeneration,Frontiers in cellular and infection microbiology,2022,"Glaucoma, glutathione, gut microbiota, microbial metabolite, retinal ganglion cell (RGC)",Experiment 1,China,Rattus norvegicus,Caecum,UBERON:0001153,Glaucoma,MONDO:0005041,Control,Glaucoma,Male wistar rats in the glaucomatous group,NA,NA,NA,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,"Figure 3A, B",31 July 2025,Anne-mariesharp,Anne-mariesharp,Significant differentially abundant bacterial taxa between glaucoma and control rats using LEfSe analysis,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales,k__Bacillati|p__Candidatus Melainabacteria,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium UC5.1-1D1,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,s__bacterium enrichment culture clone LA92,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus animalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|976|200643|171549|171552|1283313;1783272|544448|31969|186332|186333|2086;1783272|544448|31969|186332|186333;1783272|544448|31969|186332;1783272|1798710;1783272|1239|186801|1697794;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|2005525;630815;1783272|1239|91061|186826|33958|2742598|1598;1783272|1239|91061|186826|33958|2767887|1605;1783272|1239|91061|186826|33958|1578|33959;1783272|1239|186801|3085636|186803,Complete,KateRasheed
bsdb:36034713/2/1,36034713,laboratory experiment,36034713,10.3389/fcimb.2022.968992,NA,"Zhang Y., Zhou X. , Lu Y.",Gut microbiota and derived metabolomic profiling in glaucoma with progressive neurodegeneration,Frontiers in cellular and infection microbiology,2022,"Glaucoma, glutathione, gut microbiota, microbial metabolite, retinal ganglion cell (RGC)",Experiment 2,China,Rattus norvegicus,Caecum,UBERON:0001153,Glaucoma,MONDO:0005041,Control,Glaucoma,Male wistar rats in the glaucomatous group,NA,NA,NA,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,"Figure 3D, E",31 July 2025,Anne-mariesharp,Anne-mariesharp,Significant differentially abundant bacterial taxa between glaucoma and control groups,increased,"k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|74201;1783272|1239|186801|3082720|186804|1501226;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|815|816,Complete,KateRasheed
bsdb:36034713/2/2,36034713,laboratory experiment,36034713,10.3389/fcimb.2022.968992,NA,"Zhang Y., Zhou X. , Lu Y.",Gut microbiota and derived metabolomic profiling in glaucoma with progressive neurodegeneration,Frontiers in cellular and infection microbiology,2022,"Glaucoma, glutathione, gut microbiota, microbial metabolite, retinal ganglion cell (RGC)",Experiment 2,China,Rattus norvegicus,Caecum,UBERON:0001153,Glaucoma,MONDO:0005041,Control,Glaucoma,Male wistar rats in the glaucomatous group,NA,NA,NA,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,"Figure 3D, E",31 July 2025,Anne-mariesharp,Anne-mariesharp,Significant differentially abundant bacterial taxa between glaucoma and control groups,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,KateRasheed
bsdb:36036910/1/1,36036910,case-control,36036910,10.1167/iovs.63.9.32,NA,"Chang C.J., Somohano K., Zemsky C., Uhlemann A.C., Liebmann J., Cioffi G.A., Al-Aswad L.A., Lynch S.V. , Winn B.J.",Topical Glaucoma Therapy Is Associated With Alterations of the Ocular Surface Microbiome,Investigative ophthalmology & visual science,2022,NA,Experiment 1,United States of America,Homo sapiens,"Margin of eyelid,Conjunctiva","UBERON:0001811,UBERON:0034772",Glaucoma,MONDO:0005041,Control subject samples,Patients samples with eyedrops,Samples from glaucoma patients that were treated with eyedrops,28,20,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Figure 4A, B",24 July 2025,Anne-mariesharp,Anne-mariesharp,Linear discriminant analysis (LDA) effect size (LEfSe) plot of taxonomic biomarkers identified in the ocular surface microbiome of patients and controls,increased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Gluconobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Komagataeibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",1783272|1239;3379134|976|200643|171549|815|816;1783272|1798710|1906119;1783272|1239|186801|186802|1392389;1783272|201174|1760|85007|2805586|1847725;1783272|1239|186801|3085636|186803|265975;3379134|1224;3379134|74201;1783272|1239|186801|3082720|543314;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|186801|186802|216572|39492;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|1737404|1737405|1570339|162289;3379134|1224|28211|3120395|433|441;1783272|1239|186801|3085636|186803|877420;3379134|1224|28211|3120395|433|1434011;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|216851;3379134|74201|203494|48461|1647988|239934,Complete,KateRasheed
bsdb:36036910/1/2,36036910,case-control,36036910,10.1167/iovs.63.9.32,NA,"Chang C.J., Somohano K., Zemsky C., Uhlemann A.C., Liebmann J., Cioffi G.A., Al-Aswad L.A., Lynch S.V. , Winn B.J.",Topical Glaucoma Therapy Is Associated With Alterations of the Ocular Surface Microbiome,Investigative ophthalmology & visual science,2022,NA,Experiment 1,United States of America,Homo sapiens,"Margin of eyelid,Conjunctiva","UBERON:0001811,UBERON:0034772",Glaucoma,MONDO:0005041,Control subject samples,Patients samples with eyedrops,Samples from glaucoma patients that were treated with eyedrops,28,20,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Figure 4A, B",24 July 2025,Anne-mariesharp,Anne-mariesharp,Linear discriminant analysis (LDA) effect size (LEfSe) plot of taxonomic biomarkers identified in the ocular surface microbiome of patients and controls,decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Thermotogati|p__Deinococcota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium",1783272|201174;3379134|1224|28211|356|41294|374;3384194|1297;1783272|201174|1760|85006|145357;1783272|1239|186801|186802|186806|1730|42322;1783272|201174|1760|85006|1268|57493;1783272|201174|1760|85006|1268|1269;3379134|1224|28211|204457|41297|165696;1783272|201174|1760|85006|85019|1696;3384194|1297|188787|118964|183710|1298;1783272|201174|1760|85007|85026|2053;1783272|1239|186801|3085636|186803|572511;1783272|201174|1760|85009|31957|1912216;1783272|201174|1760|85007|1653|1716,Complete,KateRasheed
bsdb:36036910/2/1,36036910,case-control,36036910,10.1167/iovs.63.9.32,NA,"Chang C.J., Somohano K., Zemsky C., Uhlemann A.C., Liebmann J., Cioffi G.A., Al-Aswad L.A., Lynch S.V. , Winn B.J.",Topical Glaucoma Therapy Is Associated With Alterations of the Ocular Surface Microbiome,Investigative ophthalmology & visual science,2022,NA,Experiment 2,United States of America,Homo sapiens,"Margin of eyelid,Conjunctiva","UBERON:0001811,UBERON:0034772",Glaucoma,MONDO:0005041,Control subject samples,Patients samples with no eyedrops,Samples from glaucoma patients that were not treated with eyedrops,28,20,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Figure 4C, D",24 July 2025,Anne-mariesharp,Anne-mariesharp,Linear discriminant analysis (LDA) effect size (LEfSe) plot of taxonomic biomarkers identified in the ocular surface microbiome of patients and controls,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Gluconobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Komagataeibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,",1783272|201174|1760|2037|2049|1654;3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|186803|207244;1783272|1239;1783272|1239|186801|186802|31979|49082;1783272|1798710|1906119;1783272|1239|186801|186802|1980681;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|186801|186802|216572|216851;3379134|1224|28211|3120395|433|441;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|186802|1392389;3379134|1224|28211|3120395|433|1434011;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|877420;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;3379134|1224;1783272|1239|186801|3082720|186804|1501226;3379134|74201;1783272|1239|186801|3085636|186803|2316020|33039;,Complete,KateRasheed
bsdb:36036910/2/2,36036910,case-control,36036910,10.1167/iovs.63.9.32,NA,"Chang C.J., Somohano K., Zemsky C., Uhlemann A.C., Liebmann J., Cioffi G.A., Al-Aswad L.A., Lynch S.V. , Winn B.J.",Topical Glaucoma Therapy Is Associated With Alterations of the Ocular Surface Microbiome,Investigative ophthalmology & visual science,2022,NA,Experiment 2,United States of America,Homo sapiens,"Margin of eyelid,Conjunctiva","UBERON:0001811,UBERON:0034772",Glaucoma,MONDO:0005041,Control subject samples,Patients samples with no eyedrops,Samples from glaucoma patients that were not treated with eyedrops,28,20,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Figure 4C, D",24 July 2025,Anne-mariesharp,Anne-mariesharp,Linear discriminant analysis (LDA) effect size (LEfSe) plot of taxonomic biomarkers identified in the ocular surface microbiome of patients and controls,decreased,"k__Bacillati|p__Actinomycetota,k__Thermotogati|p__Deinococcota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium",1783272|201174;3384194|1297;1783272|201174|1760|85007|2805586|1847725;3379134|1224|28211|356|41294|374;1783272|201174|1760|85006|1268|57493;3384194|1297|188787|118964|183710|1298;1783272|1239|186801|186802|186806|1730|42322;3379134|1224|28211|204457|41297|165696;1783272|201174|1760|85006|145357|57495;3379134|1224|28211|356|119045|407;1783272|201174|1760|85006|1268|1269;1783272|1239|186801|3085636|186803|572511;1783272|201174|1760|85009|31957|1912216;1783272|201174|1760|85006|85019|1696;1783272|201174|1760|85007|85026|2053;1783272|201174|1760|85007|1653|1716,Complete,KateRasheed
bsdb:36036910/3/1,36036910,case-control,36036910,10.1167/iovs.63.9.32,NA,"Chang C.J., Somohano K., Zemsky C., Uhlemann A.C., Liebmann J., Cioffi G.A., Al-Aswad L.A., Lynch S.V. , Winn B.J.",Topical Glaucoma Therapy Is Associated With Alterations of the Ocular Surface Microbiome,Investigative ophthalmology & visual science,2022,NA,Experiment 3,United States of America,Homo sapiens,"Margin of eyelid,Conjunctiva","UBERON:0001811,UBERON:0034772",Glaucoma,MONDO:0005041,Control subject samples,Patients samples with eyedrops,Samples from glaucoma patients that were treated with eyedrops,28,20,3 months,16S,34,Illumina,relative abundances,Wald Test,0.05,TRUE,NA,age,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Table 4, Supplemental Table 1",4 August 2025,Anne-mariesharp,Anne-mariesharp,Significant differentially abundant taxa between patient samples with eyedrops and control subject samples,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Aedoeadaptatus|s__Aedoeadaptatus coxii,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Gluconobacter|s__Gluconobacter oxydans,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|g__Negativibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",1783272|1239|1737404|1737405|1570339|2981628|755172;3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|1737404|1737405|1570339|165779|33037;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|207244|649756;1783272|201174|1760|85004|31953|1678|1681;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|201174|84998|1643822|1643826|580024;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|1737404|1582879;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|946234|292800;3379134|1224|28211|3120395|433|441|442;1783272|1239|186801|3082720|186804|1505657|261299;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|1980693;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|841|360807;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|186801|186802|216572|39492;1783272|1239|186801|3085636|186803|2316020|33039,Complete,KateRasheed
bsdb:36036910/3/2,36036910,case-control,36036910,10.1167/iovs.63.9.32,NA,"Chang C.J., Somohano K., Zemsky C., Uhlemann A.C., Liebmann J., Cioffi G.A., Al-Aswad L.A., Lynch S.V. , Winn B.J.",Topical Glaucoma Therapy Is Associated With Alterations of the Ocular Surface Microbiome,Investigative ophthalmology & visual science,2022,NA,Experiment 3,United States of America,Homo sapiens,"Margin of eyelid,Conjunctiva","UBERON:0001811,UBERON:0034772",Glaucoma,MONDO:0005041,Control subject samples,Patients samples with eyedrops,Samples from glaucoma patients that were treated with eyedrops,28,20,3 months,16S,34,Illumina,relative abundances,Wald Test,0.05,TRUE,NA,age,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Table 4, Supplemental Table 1",4 August 2025,Anne-mariesharp,Anne-mariesharp,Significant differentially abundant taxa between patient samples with eyedrops and control subject samples,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium bovis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium kroppenstedtii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium macginleyi,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium|s__Sphingobium yanoikuyae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium granulosum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium",1783272|201174|1760|85007|1653|1716|36808;1783272|201174|1760|85007|1653|1716|161879;1783272|201174|1760|85007|1653|1716|38290;3379134|1224|28211|356|41294|374;1783272|201174|1760|85006|1268|32207|2047;3379134|1224|28211|204457|3423717|165695|13690;1783272|1239|186801|3085636|186803;1783272|201174|1760|85007|2805586|1847725;3379134|1224|28211|204457|41297|165696;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|1737404|1737405|1570339|165779;1783272|201174|1760|85009|31957|1912216|33011;1783272|201174|1760|85009|31957|1912216,Complete,KateRasheed
bsdb:36036910/4/1,36036910,case-control,36036910,10.1167/iovs.63.9.32,NA,"Chang C.J., Somohano K., Zemsky C., Uhlemann A.C., Liebmann J., Cioffi G.A., Al-Aswad L.A., Lynch S.V. , Winn B.J.",Topical Glaucoma Therapy Is Associated With Alterations of the Ocular Surface Microbiome,Investigative ophthalmology & visual science,2022,NA,Experiment 4,United States of America,Homo sapiens,"Margin of eyelid,Conjunctiva","UBERON:0001811,UBERON:0034772",Glaucoma,MONDO:0005041,Control subject samples,Patients samples without eyedrops,Samples from glaucoma patients that were not treated with eyedrops,28,20,3 months,16S,34,Illumina,relative abundances,Wald Test,0.05,TRUE,NA,age,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Table 4, Supplemental Table 2",4 August 2025,Anne-mariesharp,Anne-mariesharp,Significant differentially abundant taxa between patient samples without eyedrops and control subject samples,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Gluconobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Liu et al. 2021),k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|g__Negativibacillus,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae",1783272|1239|186801|3085636|186803|1766253;3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|3085636|186803|207244|649756;;1783272|201174|1760|85004|31953|1678|1681;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|49082;1783272|1239|186801|186802|1980681;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|186801|186802|216572|216851|853;3379134|1224|28211|3120395|433|441;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|877420;1783272|1239|91061|186826|33958|1578;3366610|28890|183925|2158|2159|2172;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|186802|216572|1263|3062497;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|216572|39492;1783272|1239|186801|3085636|186803|2316020|33039;1783272|201174|1760|85004|31953|1678;95818|2093818|2093825|2171986|1331051;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|186801|186802|216572|1263;1783272|1239|1980693;3384194|508458|649775|649776|649777|508459;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050|28052;1783272|201174|84998|1643822|1643826|580024;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|216572|459786;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|909932|909929;1783272|1239|186801|3082720|543314|35518;3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|186803|841;3379134|976|200643|171549|2005473;1783272|1239|186801|3082768|990719,Complete,KateRasheed
bsdb:36036910/4/2,36036910,case-control,36036910,10.1167/iovs.63.9.32,NA,"Chang C.J., Somohano K., Zemsky C., Uhlemann A.C., Liebmann J., Cioffi G.A., Al-Aswad L.A., Lynch S.V. , Winn B.J.",Topical Glaucoma Therapy Is Associated With Alterations of the Ocular Surface Microbiome,Investigative ophthalmology & visual science,2022,NA,Experiment 4,United States of America,Homo sapiens,"Margin of eyelid,Conjunctiva","UBERON:0001811,UBERON:0034772",Glaucoma,MONDO:0005041,Control subject samples,Patients samples without eyedrops,Samples from glaucoma patients that were not treated with eyedrops,28,20,3 months,16S,34,Illumina,relative abundances,Wald Test,0.05,TRUE,NA,age,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Table 4, Supplemental Table 2",4 August 2025,Anne-mariesharp,Anne-mariesharp,Significant differentially abundant taxa between patient samples without eyedrops and control subject samples,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium bovis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium kroppenstedtii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium macginleyi,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Endobacter|s__Endobacter medicaginis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium|s__Methylobacterium jeotgali,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium|s__Sphingobium yanoikuyae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium granulosum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|572511;1783272|201174|1760|85007|1653|1716|36808;1783272|201174|1760|85007|1653|1716|161879;1783272|201174|1760|85007|1653|1716|38290;1783272|201174|84998|1643822|1643826|84111|84112;3379134|1224|28211|3120395|433|1649268|1181271;1783272|201174|84998|1643822|1643826|580024;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|3085636|186803|877420;1783272|201174|84998|84999|1643824|2767353|1382;3379134|1224|28211|356|119045|407|381630;3379134|976|200643|171549|2005473;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|301301;1783272|201174|1760|85006|1268|32207;1783272|201174|84998|1643822|1643826|84108|572010;1783272|1239|186801|3085636|186803|1506577;1783272|201174|1760|85007|2805586|1847725;1783272|201174|1760|85006|1268|32207|2047;3379134|1224|28211|204457|3423717|165695|13690;3384189|32066|203490|203491|203492|848|860;3379134|1224|28211|204457|41297|165696;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|1737404|1737405|1570339|165779;1783272|201174|1760|85009|31957|1912216|33011;3379134|1224|28211|356|41294|374;1783272|201174|1760|85009|31957|1912216,Complete,KateRasheed
bsdb:36064620/1/1,36064620,case-control,36064620,10.1186/s13071-022-05435-z,https://parasitesandvectors.biomedcentral.com/articles/10.1186/s13071-022-05435-z,"Deng L., Lee J.W.J. , Tan K.S.W.",Infection with pathogenic Blastocystis ST7 is associated with decreased bacterial diversity and altered gut microbiome profiles in diarrheal patients,Parasites & vectors,2022,"Bacterial diversity, Blastocystis, Gut microbiome, Pathogenic, ST7",Experiment 1,Singapore,Homo sapiens,Feces,UBERON:0001988,Blastocystis hominis infectious disease,EFO:0007173,Blastocystis-negative diarrheal controls,Blastocystis ST7 (Subtype 7)-infected diarrheal patients,Diarrheal patients infected with Blastocystis subtype 7,14,14,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,Figure 3A and 3B,20 November 2025,Deborah-Fabusuyi,Deborah-Fabusuyi,LEfSe (linear discriminant analysis effect size) analysis and Cladogram of bacterial taxa with significant differences between Controls and ST7(Subtype 7) infected patients.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|543|1940338;3379134|1224|1236;3379134|1224,Complete,KateRasheed
bsdb:36064620/1/2,36064620,case-control,36064620,10.1186/s13071-022-05435-z,https://parasitesandvectors.biomedcentral.com/articles/10.1186/s13071-022-05435-z,"Deng L., Lee J.W.J. , Tan K.S.W.",Infection with pathogenic Blastocystis ST7 is associated with decreased bacterial diversity and altered gut microbiome profiles in diarrheal patients,Parasites & vectors,2022,"Bacterial diversity, Blastocystis, Gut microbiome, Pathogenic, ST7",Experiment 1,Singapore,Homo sapiens,Feces,UBERON:0001988,Blastocystis hominis infectious disease,EFO:0007173,Blastocystis-negative diarrheal controls,Blastocystis ST7 (Subtype 7)-infected diarrheal patients,Diarrheal patients infected with Blastocystis subtype 7,14,14,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 2,Figure 3A and 3B,20 November 2025,Deborah-Fabusuyi,Deborah-Fabusuyi,LEfSe (linear discriminant analysis effect size) analysis and Cladogram of bacterial taxa with significant differences between Controls and ST7(Subtype 7) infected patients.,decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,s__uncultured bacterium",1783272|1239;3379134|976|200643|171549;3379134|976|200643;3379134|976;1783272|1239|186801;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;1783272|1239|186801|3085636;3379134|976|200643|171549|171550;3379134|976|200643|171549|2005525;77133,Complete,KateRasheed
bsdb:36064620/2/1,36064620,case-control,36064620,10.1186/s13071-022-05435-z,https://parasitesandvectors.biomedcentral.com/articles/10.1186/s13071-022-05435-z,"Deng L., Lee J.W.J. , Tan K.S.W.",Infection with pathogenic Blastocystis ST7 is associated with decreased bacterial diversity and altered gut microbiome profiles in diarrheal patients,Parasites & vectors,2022,"Bacterial diversity, Blastocystis, Gut microbiome, Pathogenic, ST7",Experiment 2,Singapore,Homo sapiens,Feces,UBERON:0001988,Blastocystis hominis infectious disease,EFO:0007173,Blastocystis-negative diarrheal controls,Blastocystis ST7 (Subtype 7)-infected diarrheal patients,Diarrheal patients infected with Blastocystis subtype 7,14,14,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,"Figure 4A, Figure 4B, Figure S4",20 November 2025,Deborah-Fabusuyi,Deborah-Fabusuyi,Relative abundances of taxas between Blastocystis ST7(Subtype 7)-infected patients and non-Blastocystis controls.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236;3379134|1224,Complete,KateRasheed
bsdb:36064620/2/2,36064620,case-control,36064620,10.1186/s13071-022-05435-z,https://parasitesandvectors.biomedcentral.com/articles/10.1186/s13071-022-05435-z,"Deng L., Lee J.W.J. , Tan K.S.W.",Infection with pathogenic Blastocystis ST7 is associated with decreased bacterial diversity and altered gut microbiome profiles in diarrheal patients,Parasites & vectors,2022,"Bacterial diversity, Blastocystis, Gut microbiome, Pathogenic, ST7",Experiment 2,Singapore,Homo sapiens,Feces,UBERON:0001988,Blastocystis hominis infectious disease,EFO:0007173,Blastocystis-negative diarrheal controls,Blastocystis ST7 (Subtype 7)-infected diarrheal patients,Diarrheal patients infected with Blastocystis subtype 7,14,14,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 2,"Figure 4A, Figure 4B, Figure S4",20 November 2025,Deborah-Fabusuyi,Deborah-Fabusuyi,Relative abundances of the taxas between Blastocystis ST7(subtype 7)-infected patients and non-Blastocystis controls,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota",3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643;3379134|976,Complete,KateRasheed
bsdb:36068280/1/1,36068280,case-control,36068280,10.1038/s41598-022-19393-0,NA,"Kaiyrlykyzy A., Kozhakhmetov S., Babenko D., Zholdasbekova G., Alzhanova D., Olzhayev F., Baibulatova A., Kushugulova A.R. , Askarova S.",Study of gut microbiota alterations in Alzheimer's dementia patients from Kazakhstan,Scientific reports,2022,NA,Experiment 1,Kazakhstan,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healthy senior group,Alzheimer's group,Patients with Alzheimer's disease,43,41,NA,16S,NA,Illumina,relative abundances,MaAsLin2,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 1,"Supplementary Table 1a,b,c",13 March 2024,EniolaAde,"EniolaAde,Scholastica,WikiWorks",Differentially abundant taxa in healthy control versus Alzheimer's disease group determined using MaAsLin2,increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Pseudomonadati|p__Acidobacteriota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Acidobacteriota|c__Blastocatellia,k__Pseudomonadati|p__Candidatus Latescibacterota,k__Pseudomonadati|p__Verrucomicrobiota|c__Spartobacteria|o__Chthoniobacterales|f__Chthoniobacteraceae|g__Candidatus Udaeobacter,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Dinghuibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Pseudomonadati|p__Gemmatimonadota|c__Longimicrobiia|o__Longimicrobiales|f__Longimicrobiaceae|g__Longimicrobium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Methylophilaceae|g__Methylotenera,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Niastella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Parasegetibacter,k__Pseudomonadati|p__Planctomycetota|c__Phycisphaerae,k__Pseudomonadati|p__Planctomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Polaromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Solitalea,k__Thermotogati|p__Synergistota|c__Synergistia,k__Thermotogati|p__Synergistota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Ectothiorhodospiraceae|g__Thioalkalivibrio,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Acidobacteriota|c__Vicinamibacteria|o__Vicinamibacterales|f__Vicinamibacteraceae|g__Vicinamibacter,s__metagenome,s__uncultured organism,s__uncultured soil bacterium,k__Bacillati|p__Bacillota",1783272|201174|84992;3379134|57723;3379134|74201|203494|48461|1647988|239934;3379134|57723|1562566;3379134|74015;3379134|74201|134549|1836787|1836792|1921511;3384194|508458|649775|649776|649777|508459;1783272|201174|1760|85007|1653|1716;3379134|976|1853228|1853229|563835|1795363;1783272|1239|186801|186802|186806|1730;3379134|976|117743|200644|49546|237;3379134|142182|1804991|1804992|1804993|1804994;3379134|1224|28216|32003|32011|359407;3379134|976|1853228|1853229|563835|354354;3379134|1224|28216|80840|75682|846;3379134|976|1853228|1853229|563835|1004302;3379134|203682|666505;3379134|203682;3379134|1224|28216|80840|80864|52972;3379134|976|200643|171549|171552|838;3379134|976|117747|200666|84566|929509;3384194|508458|649775;3384194|508458;3379134|1224|1236|135613|72276|106633;3379134|74201|203494;3379134|74201;3379134|57723|1813735|2910145|2211325|1847386;256318;155900;164851;1783272|1239,Complete,Svetlana up
bsdb:36068280/1/2,36068280,case-control,36068280,10.1038/s41598-022-19393-0,NA,"Kaiyrlykyzy A., Kozhakhmetov S., Babenko D., Zholdasbekova G., Alzhanova D., Olzhayev F., Baibulatova A., Kushugulova A.R. , Askarova S.",Study of gut microbiota alterations in Alzheimer's dementia patients from Kazakhstan,Scientific reports,2022,NA,Experiment 1,Kazakhstan,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healthy senior group,Alzheimer's group,Patients with Alzheimer's disease,43,41,NA,16S,NA,Illumina,relative abundances,MaAsLin2,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 2,"Supplementary Table 1a,b,c",13 March 2024,EniolaAde,"EniolaAde,Scholastica,WikiWorks",Differentially abundant taxa in healthy control versus Alzheimer's disease group determined using MaAsLin2,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Castellaniella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Latilactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Levilactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae|g__Nitrosococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,s__gut metagenome,k__Bacillati|p__Bacillota|c__Clostridia|s__uncultured Clostridia bacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium",1783272|201174;1783272|201174|1760|85004|31953|1678;3379134|1224|28216|80840|506|359336;3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|33958|2767842;1783272|1239|91061|186826|33958|2767885;1783272|1239|91061|186826|33958|2767886;1783272|1239|186801|3085656|3085657|2039302;3379134|1224|1236|135613|1046|1227;3379134|1224|28211|356|69277|28100;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|1506577;1783272|1239|909932|1843489|31977|29465;749906;1783272|1239|186801|244328;1783272|1239|526524|526525|128827|331630,Complete,Svetlana up
bsdb:36073815/1/1,36073815,prospective cohort,36073815,10.1128/mbio.01229-22,NA,"Jackson C.L., Frank D.N., Robertson C.E., Ir D., Kofonow J.M., Montlha M.P., Mutsaerts E.A.M.L., Nunes M.C., Madhi S.A., Ghosh D. , Weinberg A.",Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life,mBio,2022,"HIV, HIV-exposed uninfected infants, breast milk microbiome, gut microbiome, human immunodeficiency virus, pregnant women with HIV",Experiment 1,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV mother to child transmission,EFO:0004595,HIV-unexposed infants (HUU) at 6 weeks,HIV-exposed uninfected infants (HEU) at 6 weeks,6 weeks,78,76,6 weeks,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 2d,9 March 2023,BLESSING123,"BLESSING123,WikiWorks",Genera with significantly different relative abundances between HEU and HUU at 6-weeks.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|976|200643|171549|2005519|397864;1783272|1239|186801|3085636|186803|572511;1783272|201174|84998|1643822|1643826|84111;3379134|976|200643|171549|1853231|283168;3384189|32066|203490|203491|1129771|168808;1783272|1239;1783272|1239|186801|186802|216572,Complete,Atrayees
bsdb:36073815/1/2,36073815,prospective cohort,36073815,10.1128/mbio.01229-22,NA,"Jackson C.L., Frank D.N., Robertson C.E., Ir D., Kofonow J.M., Montlha M.P., Mutsaerts E.A.M.L., Nunes M.C., Madhi S.A., Ghosh D. , Weinberg A.",Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life,mBio,2022,"HIV, HIV-exposed uninfected infants, breast milk microbiome, gut microbiome, human immunodeficiency virus, pregnant women with HIV",Experiment 1,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV mother to child transmission,EFO:0004595,HIV-unexposed infants (HUU) at 6 weeks,HIV-exposed uninfected infants (HEU) at 6 weeks,6 weeks,78,76,6 weeks,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 2d,9 March 2023,BLESSING123,"BLESSING123,WikiWorks",Genera with significantly different relative abundances between HEU and HUU at 6-weeks.,decreased,"p__Candidatus Saccharimonadota|s__Candidatus Saccharibacteria genomosp. TM7-H1,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Bacteroidota",95818|2080739;1783272|1239|526524|526525|2810280|135858;3379134|1224|1236|91347|543|547;1783272|1239|909932|909929|1843491|158846;3379134|976,Complete,Atrayees
bsdb:36073815/2/1,36073815,prospective cohort,36073815,10.1128/mbio.01229-22,NA,"Jackson C.L., Frank D.N., Robertson C.E., Ir D., Kofonow J.M., Montlha M.P., Mutsaerts E.A.M.L., Nunes M.C., Madhi S.A., Ghosh D. , Weinberg A.",Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life,mBio,2022,"HIV, HIV-exposed uninfected infants, breast milk microbiome, gut microbiome, human immunodeficiency virus, pregnant women with HIV",Experiment 2,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV mother to child transmission,EFO:0004595,HIV-unexposed infants (HUU) at 28 weeks,HIV-exposed uninfected infants (HEU) at 28 weeks,In utero-HIV exposed uninfected infants (HEU),74,71,7 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,antibiotic exposure,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 2d,9 March 2023,BLESSING123,"BLESSING123,WikiWorks",Genera with significantly different relative abundances between HEU and HUU at 28-weeks.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium|s__Candidatus Epulonipiscium sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239|186801|3085636|186803|2383|2384;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|1300|1357;1783272|1239|909932|909929|1843491|158846;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|186802,Complete,Atrayees
bsdb:36073815/2/2,36073815,prospective cohort,36073815,10.1128/mbio.01229-22,NA,"Jackson C.L., Frank D.N., Robertson C.E., Ir D., Kofonow J.M., Montlha M.P., Mutsaerts E.A.M.L., Nunes M.C., Madhi S.A., Ghosh D. , Weinberg A.",Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life,mBio,2022,"HIV, HIV-exposed uninfected infants, breast milk microbiome, gut microbiome, human immunodeficiency virus, pregnant women with HIV",Experiment 2,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV mother to child transmission,EFO:0004595,HIV-unexposed infants (HUU) at 28 weeks,HIV-exposed uninfected infants (HEU) at 28 weeks,In utero-HIV exposed uninfected infants (HEU),74,71,7 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,antibiotic exposure,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 2d,9 March 2023,BLESSING123,"BLESSING123,WikiWorks",Genera with significantly different relative abundances between HEU and HUU at 28-weeks.,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia",1783272|201174|84998|84999|1643824|1380;1783272|201174|1760|85004|31953|2701;1783272|1239|91061|1385|539738|1378;1783272|201174|1760|2037|2049|2050;1783272|1239|1737404|1737405|1570339|543311;3384189|32066|203490|203491|1129771|168808,Complete,Atrayees
bsdb:36073815/3/1,36073815,prospective cohort,36073815,10.1128/mbio.01229-22,NA,"Jackson C.L., Frank D.N., Robertson C.E., Ir D., Kofonow J.M., Montlha M.P., Mutsaerts E.A.M.L., Nunes M.C., Madhi S.A., Ghosh D. , Weinberg A.",Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life,mBio,2022,"HIV, HIV-exposed uninfected infants, breast milk microbiome, gut microbiome, human immunodeficiency virus, pregnant women with HIV",Experiment 3,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV mother to child transmission,EFO:0004595,HIV-unexposed infants (HUU) at 62 weeks,HIV-exposed uninfected infants (HEU) at 62 weeks,HIV-exposed uninfected infants (HEU) at 6 weeks,70,61,15 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,antibiotic exposure,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 2d,9 March 2023,BLESSING123,"BLESSING123,WikiWorks",Genera with significantly different relative abundances between HEU and HUU at the indicated time points (FDR P < 0.05). 62 weeks,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",3379134|1224|1236|91347|1903414|583;1783272|201174|84998|84999|84107,Complete,Atrayees
bsdb:36073815/4/1,36073815,prospective cohort,36073815,10.1128/mbio.01229-22,NA,"Jackson C.L., Frank D.N., Robertson C.E., Ir D., Kofonow J.M., Montlha M.P., Mutsaerts E.A.M.L., Nunes M.C., Madhi S.A., Ghosh D. , Weinberg A.",Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life,mBio,2022,"HIV, HIV-exposed uninfected infants, breast milk microbiome, gut microbiome, human immunodeficiency virus, pregnant women with HIV",Experiment 4,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV mother to child transmission,EFO:0004595,Healthy controls at delivery,HIV-infected mothers at delivery,Mothers infected with HIV at delivery time point,110,119,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,sex,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3F,10 March 2023,BLESSING123,"BLESSING123,Folakunmi,WikiWorks",Genera with significantly different relative abundances between mothers with and without HIV at the indicated time points (FDR P < 0.05). Delivery,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",1783272|1239|909932|1843488|909930|904;1783272|1239|1737404|1737405|1570339|165779;3379134|976|200643|171549|815|816;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|572511;1783272|201174|1760|85007|1653|1716;1783272|1239|186801|186802|216572|946234;3384189|32066|203490|203491|203492|848;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|91347|543|570;1783272|544448|31969|2085|2092|2093;1783272|1239|91061|1385|90964|1279;3379134|1224|28216|80840|995019|40544;1783272|1239|91061;3379134|1224|28216|80840;1783272|201174|1760|85007|1653;1783272|1239|526524|526525|128827;3384189|32066|203490|203491;1783272|1239|186801|3085636|186803;1783272|1239|909932|909929|1843491|158846;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804,Complete,Atrayees
bsdb:36073815/4/2,36073815,prospective cohort,36073815,10.1128/mbio.01229-22,NA,"Jackson C.L., Frank D.N., Robertson C.E., Ir D., Kofonow J.M., Montlha M.P., Mutsaerts E.A.M.L., Nunes M.C., Madhi S.A., Ghosh D. , Weinberg A.",Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life,mBio,2022,"HIV, HIV-exposed uninfected infants, breast milk microbiome, gut microbiome, human immunodeficiency virus, pregnant women with HIV",Experiment 4,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV mother to child transmission,EFO:0004595,Healthy controls at delivery,HIV-infected mothers at delivery,Mothers infected with HIV at delivery time point,110,119,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,sex,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3F,13 March 2023,BLESSING123,"BLESSING123,WikiWorks",Genera with significantly different relative abundances between mothers with and without HIV at the indicated time points (FDR P < 0.05). Delivery,decreased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae|g__Elusimicrobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiales Family XVII. Incertae Sedis",1783272|544448|31969|186332|186333|2152;3379134|74152|641853|641854|641876|423604;1783272|1239|186801|186802|216572|216851;3379134|1224|1236|135625|712|724;1783272|1239|186801|186802|539000,Complete,Atrayees
bsdb:36073815/5/1,36073815,prospective cohort,36073815,10.1128/mbio.01229-22,NA,"Jackson C.L., Frank D.N., Robertson C.E., Ir D., Kofonow J.M., Montlha M.P., Mutsaerts E.A.M.L., Nunes M.C., Madhi S.A., Ghosh D. , Weinberg A.",Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life,mBio,2022,"HIV, HIV-exposed uninfected infants, breast milk microbiome, gut microbiome, human immunodeficiency virus, pregnant women with HIV",Experiment 5,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV mother to child transmission,EFO:0004595,Healthy controls at 62 weeks,HIV-infected  mothers at 62 weeks,Mothers infected with HIV at 62 weeks time point,65,71,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,sex,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3F,13 March 2023,BLESSING123,"BLESSING123,Folakunmi,WikiWorks",Genera with significantly different relative abundances between mothers with and without HIV at the indicated time points (FDR P < 0.05). 62 weeks,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Thalassospiraceae|g__Thalassospira,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania",1783272|1239|909932|1843488|909930|904;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|572511;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|946234;1783272|1239|909932|909929|1843491|158846;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|216572|292632;3379134|1224|28211|204441|2844866|168934;3384194|508458|649775|649776|649777;1783272|1239|526524|526525|128827|61170,Complete,Folakunmi
bsdb:36073815/5/2,36073815,prospective cohort,36073815,10.1128/mbio.01229-22,NA,"Jackson C.L., Frank D.N., Robertson C.E., Ir D., Kofonow J.M., Montlha M.P., Mutsaerts E.A.M.L., Nunes M.C., Madhi S.A., Ghosh D. , Weinberg A.",Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life,mBio,2022,"HIV, HIV-exposed uninfected infants, breast milk microbiome, gut microbiome, human immunodeficiency virus, pregnant women with HIV",Experiment 5,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV mother to child transmission,EFO:0004595,Healthy controls at 62 weeks,HIV-infected  mothers at 62 weeks,Mothers infected with HIV at 62 weeks time point,65,71,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,sex,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3F,13 March 2023,BLESSING123,"BLESSING123,WikiWorks",Genera with significantly different relative abundances between mothers with and without HIV at the indicated time points (FDR P < 0.05). 62 weeks,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae|g__Elusimicrobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|1224|1236|2887326|468|469;3379134|74152|641853|641854|641876|423604;1783272|1239|91061|1385|539738|1378;3379134|976|200643|171549|171552|838;1783272|1239|91061|1385|90964|1279;1783272|1239|909932|1843489|31977|29465;1783272|201174|1760|85007|1653;1783272|1239|909932|1843489|31977,Complete,Folakunmi
bsdb:36073815/6/1,36073815,prospective cohort,36073815,10.1128/mbio.01229-22,NA,"Jackson C.L., Frank D.N., Robertson C.E., Ir D., Kofonow J.M., Montlha M.P., Mutsaerts E.A.M.L., Nunes M.C., Madhi S.A., Ghosh D. , Weinberg A.",Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life,mBio,2022,"HIV, HIV-exposed uninfected infants, breast milk microbiome, gut microbiome, human immunodeficiency virus, pregnant women with HIV",Experiment 6,South Africa,Homo sapiens,Milk,UBERON:0001913,HIV mother to child transmission,EFO:0004595,Healthy controls,HIV-infected mothers,Mothers infected with HIV,76,88,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,sex,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 4F,13 March 2023,BLESSING123,"BLESSING123,WikiWorks",Genera with significantly different abundances in mothers with and without HIV (FDR P < 0.05).,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,1783272|1239|186801|3082720|186804,Complete,Folakunmi
bsdb:36073815/6/2,36073815,prospective cohort,36073815,10.1128/mbio.01229-22,NA,"Jackson C.L., Frank D.N., Robertson C.E., Ir D., Kofonow J.M., Montlha M.P., Mutsaerts E.A.M.L., Nunes M.C., Madhi S.A., Ghosh D. , Weinberg A.",Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life,mBio,2022,"HIV, HIV-exposed uninfected infants, breast milk microbiome, gut microbiome, human immunodeficiency virus, pregnant women with HIV",Experiment 6,South Africa,Homo sapiens,Milk,UBERON:0001913,HIV mother to child transmission,EFO:0004595,Healthy controls,HIV-infected mothers,Mothers infected with HIV,76,88,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,sex,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 4F,13 March 2023,BLESSING123,"BLESSING123,WikiWorks",Genera with significantly different abundances in mothers with and without HIV (FDR P < 0.05).,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Blastococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|g__Exiguobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Microvirga,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Pseudonocardia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Rubellimicrobium,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia|o__Acidimicrobiales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae",1783272|1239|1737404|1737405|1570339|165779;1783272|201174|1760|85006|1268|1663;1783272|201174|84998|84999|1643824|1380;1783272|1239|91061|1385|186817|1386;1783272|201174|1760|1643682|85030|38501;1783272|201174|1760|85006|85019|1696;3379134|976|117743|200644|2762318|59732;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|1385|33986;1783272|1239|186801|186802|216572|216851;1783272|1239|1737404|1737405|1570339|150022;1783272|201174|1760|85004|31953|2701;3379134|1224|28216|80840|75682|963;3379134|976|768503|768507|1853232|89966;1783272|1239|91061|186826|1300|1357;3379134|1224|28216|80840|75682|149698;3379134|1224|28211|356|119045|407;1783272|201174|1760|85006|1268|1269;3379134|1224|28211|356|119045|186650;3379134|1224|1236|2887326|468|475;3379134|1224|28216|206351|481|482;1783272|201174|1760|85009|85015|1839;1783272|1239|1737404|1737405|1570339|162289;3379134|976|200643|171549|171552|838;1783272|201174|1760|85009|31957|1743;1783272|1239|186801|3085636|186803|46205;1783272|201174|1760|85010|2070|1847;3379134|1224|28211|204455|2854170|295418;1783272|201174|84995|84996|84997|42255;1783272|1239|91061|1385|90964|1279;1783272|201174|84992|84993;1783272|1239|91061|1385;1783272|1239|91061|186826|186828;3379134|976|1853228|1853229|563835;1783272|201174|1760|85007;3379134|1224|1236|91347|543;1783272|201174|1760|1643682|85030;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826;1783272|201174|1760|85006|85023;1783272|201174|1760|85008|28056;3379134|1224|28216|206351|481;1783272|201174|1760|85007|85025;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|75682;3379134|1224|28211|204457;3379134|1224|1236|135614|32033,Complete,Folakunmi
bsdb:36073815/7/1,36073815,prospective cohort,36073815,10.1128/mbio.01229-22,NA,"Jackson C.L., Frank D.N., Robertson C.E., Ir D., Kofonow J.M., Montlha M.P., Mutsaerts E.A.M.L., Nunes M.C., Madhi S.A., Ghosh D. , Weinberg A.",Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life,mBio,2022,"HIV, HIV-exposed uninfected infants, breast milk microbiome, gut microbiome, human immunodeficiency virus, pregnant women with HIV",Experiment 7,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV mother to child transmission,EFO:0004595,Exclusively breastfed HIV-unexposed infants (HUU) at 28 weeks,Exclusively breastfed HIV-exposed uninfected infants (HEU) at 28 weeks,Exclusively breastfed In utero-HIV exposed uninfected infants (HEU) at 28 weeks,40,52,7 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,antibiotic exposure,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 2e,9 February 2024,Folakunmi,"Folakunmi,WikiWorks",Genera with significantly different relative abundances between HEU and HUU exclusively (Excl.) breastfed at 28 weeks of life,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium,1783272|1239|186801|3085636|186803|2383,Complete,Folakunmi
bsdb:36073815/7/2,36073815,prospective cohort,36073815,10.1128/mbio.01229-22,NA,"Jackson C.L., Frank D.N., Robertson C.E., Ir D., Kofonow J.M., Montlha M.P., Mutsaerts E.A.M.L., Nunes M.C., Madhi S.A., Ghosh D. , Weinberg A.",Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life,mBio,2022,"HIV, HIV-exposed uninfected infants, breast milk microbiome, gut microbiome, human immunodeficiency virus, pregnant women with HIV",Experiment 7,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV mother to child transmission,EFO:0004595,Exclusively breastfed HIV-unexposed infants (HUU) at 28 weeks,Exclusively breastfed HIV-exposed uninfected infants (HEU) at 28 weeks,Exclusively breastfed In utero-HIV exposed uninfected infants (HEU) at 28 weeks,40,52,7 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,antibiotic exposure,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 2e,9 February 2024,Folakunmi,"Folakunmi,WikiWorks",Genera with significantly different relative abundances between HEU and HUU exclusively (Excl.) breastfed at 28 weeks of life,decreased,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,3384189|32066|203490|203491|1129771|168808,Complete,Folakunmi
bsdb:36073815/8/1,36073815,prospective cohort,36073815,10.1128/mbio.01229-22,NA,"Jackson C.L., Frank D.N., Robertson C.E., Ir D., Kofonow J.M., Montlha M.P., Mutsaerts E.A.M.L., Nunes M.C., Madhi S.A., Ghosh D. , Weinberg A.",Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life,mBio,2022,"HIV, HIV-exposed uninfected infants, breast milk microbiome, gut microbiome, human immunodeficiency virus, pregnant women with HIV",Experiment 8,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV mother to child transmission,EFO:0004595,Not exclusively breastfed HIV-unexposed infants (HUU) at 28 weeks,Not exclusively breastfed HIV-exposed uninfected infants (HEU) at 28 weeks,Not exclusively breastfed (formula feeding) In utero-HIV exposed uninfected infants (HEU) at 28 weeks,9,19,7 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,antibiotic exposure,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 2e,9 February 2024,Folakunmi,"Folakunmi,WikiWorks",Genera with significantly different relative abundances between HEU and HUU not exclusively (Excl.) breastfed at 28 weeks of lif,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella",1783272|1239|186801|3085636|186803|2383;3379134|1224|1236|91347|543|570;3379134|1224|1236|135625|712|745,Complete,Folakunmi
bsdb:36073815/8/2,36073815,prospective cohort,36073815,10.1128/mbio.01229-22,NA,"Jackson C.L., Frank D.N., Robertson C.E., Ir D., Kofonow J.M., Montlha M.P., Mutsaerts E.A.M.L., Nunes M.C., Madhi S.A., Ghosh D. , Weinberg A.",Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life,mBio,2022,"HIV, HIV-exposed uninfected infants, breast milk microbiome, gut microbiome, human immunodeficiency virus, pregnant women with HIV",Experiment 8,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV mother to child transmission,EFO:0004595,Not exclusively breastfed HIV-unexposed infants (HUU) at 28 weeks,Not exclusively breastfed HIV-exposed uninfected infants (HEU) at 28 weeks,Not exclusively breastfed (formula feeding) In utero-HIV exposed uninfected infants (HEU) at 28 weeks,9,19,7 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,antibiotic exposure,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,figure 2e,9 February 2024,Folakunmi,"Folakunmi,WikiWorks",Genera with significantly different relative abundances between HEU and HUU not exclusively (Excl.) breastfed at 28 weeks of life,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia",1783272|201174|1760|85004|31953|2701;1783272|201174|1760|2037|2049|2050;3379134|976|200643|171549|171550|239759;1783272|1239|526524|526525|2810280|135858;1783272|1239|909932|1843489|31977|39948;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|91061|1385|539738|1378;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3082720|186804|1257;1783272|1239|526524|526525|128827|123375;3384189|32066|203490|203491|1129771|168808,Complete,Folakunmi
bsdb:36077282/1/1,36077282,case-control,36077282,10.3390/ijms23179883,NA,"Chen Y.J., Hung W.C., Chou Y.H., Lai C.H., Peng P., Jhou P.S., Tsai M.R., Sheu J.J. , Yen J.H.",Subgingival Microbiome in Rheumatoid Arthritis Patients with Periodontitis,International journal of molecular sciences,2022,"anti-citrullinated protein antibody (ACPA), microbial dysbiosis, periodontitis, rheumatoid arthritis, subgingival microbiome",Experiment 1,Taiwan,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,Healthy Controls,All Matched (AM) Rheumatoid Arthritis,All Matched (AM) Rheumatoid Arthritis Patients,21,21,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"age,diabetes mellitus,sex",NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,"Text , Supplementary Figure S1A",2 November 2022,Tislam,"Tislam,Peace Sandy,WikiWorks","he composition of subgingival microbiota between the RA 
patients and controls in groups AM and PD were estimated by LEfSe with the parameter 
of the logarithmic LDA score > 2. In group AM, 176 discriminative taxa in total were found 
(Supplementary Figure S1A). Of the species level with the logarithmic LDA score > 4, 
Streptococcus",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",1783272|1239|91061|186826|1300|1301|1328;3379134|203691|203692|136|2845253|157|158;3384189|32066|203490|203491|203492|848,Complete,Peace Sandy
bsdb:36077282/1/2,36077282,case-control,36077282,10.3390/ijms23179883,NA,"Chen Y.J., Hung W.C., Chou Y.H., Lai C.H., Peng P., Jhou P.S., Tsai M.R., Sheu J.J. , Yen J.H.",Subgingival Microbiome in Rheumatoid Arthritis Patients with Periodontitis,International journal of molecular sciences,2022,"anti-citrullinated protein antibody (ACPA), microbial dysbiosis, periodontitis, rheumatoid arthritis, subgingival microbiome",Experiment 1,Taiwan,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,Healthy Controls,All Matched (AM) Rheumatoid Arthritis,All Matched (AM) Rheumatoid Arthritis Patients,21,21,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"age,diabetes mellitus,sex",NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,"Text , Supplementary Figure S1A",2 November 2022,Tislam,"Tislam,Peace Sandy,WikiWorks","he composition of subgingival microbiota between the RA 
patients and controls in groups AM and PD were estimated by LEfSe with the parameter 
of the logarithmic LDA score > 2. In group AM, 176 discriminative taxa in total were found 
(Supplementary Figure S1A). Of the species level with the logarithmic LDA score > 4, 
Streptococcus",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis",3379134|1224|1236|135625|712|724|729;1783272|1239|91061|186826|1300|1301|1305,Complete,Peace Sandy
bsdb:36077282/2/1,36077282,case-control,36077282,10.3390/ijms23179883,NA,"Chen Y.J., Hung W.C., Chou Y.H., Lai C.H., Peng P., Jhou P.S., Tsai M.R., Sheu J.J. , Yen J.H.",Subgingival Microbiome in Rheumatoid Arthritis Patients with Periodontitis,International journal of molecular sciences,2022,"anti-citrullinated protein antibody (ACPA), microbial dysbiosis, periodontitis, rheumatoid arthritis, subgingival microbiome",Experiment 2,Taiwan,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,Healthy Controls,Periodontally diseased (PD) Rheumatoid Arthritis,"Patients with periodontally
diseased) Rheumatoid Arthritis",12,12,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"age,diabetes mellitus,sex",NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,"Text , Supplementary Figure S1B",28 December 2023,Peace Sandy,"Peace Sandy,WikiWorks","In group PD, a total of 129 taxa showed differential abundances between the
RA patients and controls (Supplementary Figure S1B). Of the species level with the loga�rithmic LDA score > 4, S. anginosus and three unidentified species of genera Actinomyces,
Fusobacterium, and Parvimonas demonstrated a significant increase in the RA patients, while
Pseudomonas batumici (P. batumici) was the only enriched species found in the controls (the
logarithmic LDA score = 5.42).",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas",1783272|1239|91061|186826|1300|1301|1328;1783272|201174|1760|2037|2049|1654;3384189|32066|203490|203491|203492|848;1783272|1239|1737404|1737405|1570339|543311,Complete,Peace Sandy
bsdb:36077282/2/2,36077282,case-control,36077282,10.3390/ijms23179883,NA,"Chen Y.J., Hung W.C., Chou Y.H., Lai C.H., Peng P., Jhou P.S., Tsai M.R., Sheu J.J. , Yen J.H.",Subgingival Microbiome in Rheumatoid Arthritis Patients with Periodontitis,International journal of molecular sciences,2022,"anti-citrullinated protein antibody (ACPA), microbial dysbiosis, periodontitis, rheumatoid arthritis, subgingival microbiome",Experiment 2,Taiwan,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Rheumatoid arthritis,EFO:0000685,Healthy Controls,Periodontally diseased (PD) Rheumatoid Arthritis,"Patients with periodontally
diseased) Rheumatoid Arthritis",12,12,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"age,diabetes mellitus,sex",NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,"Text , Supplementary Figure S1B",28 December 2023,Peace Sandy,"Peace Sandy,WikiWorks","In group PD, a total of 129 taxa showed differential abundances between the
RA patients and controls (Supplementary Figure S1B). Of the species level with the loga�rithmic LDA score > 4, S. anginosus and three unidentified species of genera Actinomyces,
Fusobacterium, and Parvimonas demonstrated a significant increase in the RA patients, while
Pseudomonas batumici (P. batumici) was the only enriched species found in the controls (the
logarithmic LDA score = 5.42)",decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas batumici,3379134|1224|1236|72274|135621|286|226910,Complete,Peace Sandy
bsdb:36138438/1/1,36138438,time series / longitudinal observational,36138438,https://doi.org/10.1186/s40168-022-01322-y,https://pubmed.ncbi.nlm.nih.gov/36138438/,"Martin V.M., Virkud Y.V., Dahan E., Seay H.L., Itzkovits D., Vlamakis H., Xavier R., Shreffler W.G., Yuan Q. , Yassour M.",Longitudinal disease-associated gut microbiome differences in infants with food protein-induced allergic proctocolitis,Microbiome,2022,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Ulcerative proctosigmoiditis,EFO:1001223,Infants diagnosed without food protein-induced allergic proctocolitis (FPIAP),Infants diagnosed with food protein-induced allergic proctocolitis (FPIAP),Infants diagnosed with food protein-induced allergic proctocolitis (FPIAP) who had a minimum of 4 longitudinal stool samples in the first year.  FPIAP was diagnosed by the treating physician and confirmed by comprehensive study staff chart review.,81,79,NA,16S,4,Illumina,arcsine square-root,MaAsLin2,0.2,TRUE,NA,age,"age,diet,mode of birth",NA,NA,NA,NA,NA,unchanged,Signature 1,Fig 3 (A) and 3 (B),10 October 2023,Tolulopeo,"Tolulopeo,Peace Sandy,WikiWorks","Summary of key differential taxa between infants with FPIAP and healthy controls. A Significantly different taxa comparing infants with FPIAP to healthy controls (q < 0.20; absolute coefficient > = 0.05) when looking at sample subsets: 0–2 months, last pre-symptomatic, first symptomatic, and first resolved. Bars to the right are enriched in infants with FPIAP, while bars to the left are enriched in the controls. Number of samples in each group is shown under the name of the subset analyzed in that model (FPIAP, control). B Significantly different taxa (q < 0.20) when comparing infants with FPIAP to matched controls before their symptom onset (top section) and then during the symptomatic period (lower section) over the first 2 months of age. Association directionality and numbers are as in (A).",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802,Complete,Peace Sandy
bsdb:36138438/1/2,36138438,time series / longitudinal observational,36138438,https://doi.org/10.1186/s40168-022-01322-y,https://pubmed.ncbi.nlm.nih.gov/36138438/,"Martin V.M., Virkud Y.V., Dahan E., Seay H.L., Itzkovits D., Vlamakis H., Xavier R., Shreffler W.G., Yuan Q. , Yassour M.",Longitudinal disease-associated gut microbiome differences in infants with food protein-induced allergic proctocolitis,Microbiome,2022,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Ulcerative proctosigmoiditis,EFO:1001223,Infants diagnosed without food protein-induced allergic proctocolitis (FPIAP),Infants diagnosed with food protein-induced allergic proctocolitis (FPIAP),Infants diagnosed with food protein-induced allergic proctocolitis (FPIAP) who had a minimum of 4 longitudinal stool samples in the first year.  FPIAP was diagnosed by the treating physician and confirmed by comprehensive study staff chart review.,81,79,NA,16S,4,Illumina,arcsine square-root,MaAsLin2,0.2,TRUE,NA,age,"age,diet,mode of birth",NA,NA,NA,NA,NA,unchanged,Signature 2,Figure 3 (A) and (B),22 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","Summary of key differential taxa between infants with FPIAP and healthy controls. A Significantly different taxa comparing infants with FPIAP to healthy controls (q < 0.20; absolute coefficient > = 0.05) when looking at sample subsets: 0–2 months, last pre-symptomatic, first symptomatic, and first resolved. Bars to the right are enriched in infants with FPIAP, while bars to the left are enriched in the controls. Number of samples in each group is shown under the name of the subset analyzed in that model (FPIAP, control). B Significantly different taxa (q < 0.20) when comparing infants with FPIAP to matched controls before their symptom onset (top section) and then during the symptomatic period (lower section) over the first 2 months of age. Association directionality and numbers are as in (A).",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",3379134|1224|1236|91347|543;1783272|1239|91061|186826|33958|1578,Complete,Peace Sandy
bsdb:36154141/1/1,36154141,case-control,36154141,10.1128/msystems.00465-22,NA,"Zhu Q., Yang X., Zhang Y., Shan C. , Shi Z.",Role of the Gut Microbiota in the Increased Infant Body Mass Index Induced by Gestational Diabetes Mellitus,mSystems,2022,"16S rRNA, BMI, gestational diabetes mellitus, microbiota",Experiment 1,China,Homo sapiens,Meconium,UBERON:0007109,Gestational diabetes,EFO:0004593,Healthy controls,Gestational diabetes mellitus (GDM),Infants born to women who had gestational diabetes mellitus (GDM),60,60,3 months,16S,3,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,FIG 2 (D),3 October 2024,Rahila,"Rahila,WikiWorks",Linear discriminant analysis (LDA) scores for crucial bacteria classification with different abundances in  Gestational diabetes mellitus (GDM) versus healthy controls,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae|g__Cytophaga,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae|g__Xanthobacter,k__Metazoa|p__Arthropoda|c__Insecta|o__Coleoptera|f__Lampyridae|s__Luciolinae|g__Serratia",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;3379134|976|768503|768507|89373|978;3379134|976|768503|768507|89373;3379134|1224|28211|356|335928;3379134|1224|1236|91347|1903411;3379134|1224|28211|356|335928|279;33208|6656|50557|7041|7049|433515|2985502,Complete,Svetlana up
bsdb:36154141/1/2,36154141,case-control,36154141,10.1128/msystems.00465-22,NA,"Zhu Q., Yang X., Zhang Y., Shan C. , Shi Z.",Role of the Gut Microbiota in the Increased Infant Body Mass Index Induced by Gestational Diabetes Mellitus,mSystems,2022,"16S rRNA, BMI, gestational diabetes mellitus, microbiota",Experiment 1,China,Homo sapiens,Meconium,UBERON:0007109,Gestational diabetes,EFO:0004593,Healthy controls,Gestational diabetes mellitus (GDM),Infants born to women who had gestational diabetes mellitus (GDM),60,60,3 months,16S,3,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,FIG 2 (D),3 October 2024,Rahila,"Rahila,WikiWorks",Linear discriminant analysis (LDA) scores for crucial bacteria classification with different abundances in  Gestational diabetes mellitus (GDM) versus healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles",1783272|1239|91061|186826|186827;1783272|1239|91061|186826|186827|1375;3379134|1224|28216|80840|506;3379134|1224|28211|356|212791;3379134|1224|1236|91347|543;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;3379134|1224|28216|80840|75682|963;1783272|1239|186801|186802|216572;3379134|1224|1236|2887326|468|497;3379134|1224|28216|80840|2975441|93681,Complete,Svetlana up
bsdb:36168945/1/1,36168945,"cross-sectional observational, not case-control",36168945,https://doi.org/10.1111/jcmm.17402,https://onlinelibrary.wiley.com/doi/10.1111/jcmm.17402,"Delgadinho M., Ginete C., Santos B., Mendes J., Miranda A., Vasconcelos J. , Brito M.",Microbial gut evaluation in an angolan paediatric population with sickle cell disease,Journal of cellular and molecular medicine,2022,"16S rRNA, foetal haemoglobin, microbiome, sickle cell disease",Experiment 1,Angola,Homo sapiens,Feces,UBERON:0001988,Sickle cell anemia,MONDO:0011382,Healthy Siblings,Sickle Cell Anaemia Children,Angolan children between 3 and 14 years with Sickle Cell Anemia,36,36,3 months,16S,NA,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4,23 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differential abundance in the microbiota of sickle cell anaemia (SCA) children compared to their siblings(controls).,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bohemicum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella bouchesdurhonensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella massiliensis",1783272|201174;1783272|201174|84998|84999;1783272|1239|186801|3082720|186804;1783272|201174|84992;1783272|201174|84998|84999|84107;3379134|976|200643|171549|815|816|626929;1783272|201174|1760|85004|31953|1678|638617;1783272|201174|84998|84999|84107|102106|1907654;3379134|1224|28216|80840|995019|40544|1816689,Complete,Svetlana up
bsdb:36168945/1/2,36168945,"cross-sectional observational, not case-control",36168945,https://doi.org/10.1111/jcmm.17402,https://onlinelibrary.wiley.com/doi/10.1111/jcmm.17402,"Delgadinho M., Ginete C., Santos B., Mendes J., Miranda A., Vasconcelos J. , Brito M.",Microbial gut evaluation in an angolan paediatric population with sickle cell disease,Journal of cellular and molecular medicine,2022,"16S rRNA, foetal haemoglobin, microbiome, sickle cell disease",Experiment 1,Angola,Homo sapiens,Feces,UBERON:0001988,Sickle cell anemia,MONDO:0011382,Healthy Siblings,Sickle Cell Anaemia Children,Angolan children between 3 and 14 years with Sickle Cell Anemia,36,36,3 months,16S,NA,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4,23 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differential abundance in the microbiota of sickle cell anaemia (SCA) children compared to their siblings(controls).,decreased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Polaribacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Aestuariispiraceae|g__Aestuariispira,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Anaerorhabdus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Anaerorhabdus|s__Anaerorhabdus furcosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Caproiciproducens|s__Caproiciproducens galactitolivorans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oulorum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella veroralis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae|s__Rhodospirillaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus flavefaciens,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae",3379134|29547|3031852|213849;3379134|1224|28211|204441;3379134|976|117743|200644|49546|52959;3379134|1224|28211|204441|3466454|1647175;3379134|29547|3031852|213849|72293|209;1783272|1239|526524|526525|128827|118966;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852;3379134|1224|28211|204441|41295;3379134|976|200643|171549|171552|1283313|671218;1783272|1239|526524|526525|128827|118966|118967;1783272|1239|186801|186802|3082771|1738645|642589;3379134|976|200643|171549|171552|838|470565;3379134|976|200643|171549|171552|2974251|28135;3379134|976|200643|171549|171552|2974251|28136;3379134|976|200643|171549|171552|2974265|363265;3379134|976|200643|171549|171552|838|28137;3379134|1224|28211|204441|41295|1898112;1783272|1239|186801|186802|216572|1263|1265;3379134|29547|3031852|213849|72294,Complete,Svetlana up
bsdb:36168945/2/1,36168945,"cross-sectional observational, not case-control",36168945,https://doi.org/10.1111/jcmm.17402,https://onlinelibrary.wiley.com/doi/10.1111/jcmm.17402,"Delgadinho M., Ginete C., Santos B., Mendes J., Miranda A., Vasconcelos J. , Brito M.",Microbial gut evaluation in an angolan paediatric population with sickle cell disease,Journal of cellular and molecular medicine,2022,"16S rRNA, foetal haemoglobin, microbiome, sickle cell disease",Experiment 2,Angola,Homo sapiens,Feces,UBERON:0001988,Sickle cell disease associated with an other hemoglobin anomaly,MONDO:0016667,Foetal haemoglobin level < 5%,Foetal haemoglobin level > 5%,Sickle Cell Anemia(SCA) children with Foetal haemoglobin level > 5%,27,9,3 months,16S,NA,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 7B,23 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differential abundance in the microbiota of sickle cell anaemia (SCA) children with < 5% of HbF compared SCA children with < 5% of HbF.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,1783272|1239|186801|186802|216572|1263,Complete,Svetlana up
bsdb:36168945/2/2,36168945,"cross-sectional observational, not case-control",36168945,https://doi.org/10.1111/jcmm.17402,https://onlinelibrary.wiley.com/doi/10.1111/jcmm.17402,"Delgadinho M., Ginete C., Santos B., Mendes J., Miranda A., Vasconcelos J. , Brito M.",Microbial gut evaluation in an angolan paediatric population with sickle cell disease,Journal of cellular and molecular medicine,2022,"16S rRNA, foetal haemoglobin, microbiome, sickle cell disease",Experiment 2,Angola,Homo sapiens,Feces,UBERON:0001988,Sickle cell disease associated with an other hemoglobin anomaly,MONDO:0016667,Foetal haemoglobin level < 5%,Foetal haemoglobin level > 5%,Sickle Cell Anemia(SCA) children with Foetal haemoglobin level > 5%,27,9,3 months,16S,NA,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 7B,23 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differential abundance in the microbiota of sickle cell anaemia (SCA) children with < 5% of HbF compared SCA children with < 5% of HbF.,decreased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Kandleria,1783272|1239|526524|526525|2810280|1279388,Complete,Svetlana up
bsdb:36171620/3/1,36171620,laboratory experiment,36171620,10.1186/s12974-022-02599-4,NA,"Qian X.H., Liu X.L., Chen G., Chen S.D. , Tang H.D.",Injection of amyloid-β to lateral ventricle induces gut microbiota dysbiosis in association with inhibition of cholinergic anti-inflammatory pathways in Alzheimer's disease,Journal of neuroinflammation,2022,"Alzheimer’s disease, Aβ, Cholinergic anti-inflammatory pathway, Gut microbiota",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Sham-operated group,Alzheimer’s disease (4 weeks after surgery),Alzheimer's disease (AD) model mice injected in the lateral ventricle with Aβ1–42 intracerebroventricular injection 4 weeks after surgery,10,10,NA,16S,34,Illumina,NA,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,increased,Signature 1,Figure 3 (I - N),15 March 2024,Flo,"Flo,Scholastica,WikiWorks",Bacterial genera significantly different at the genus level in the Aβ1–42 treatment group compared to the phosphate-buffered saline (PBS) sham-operated group,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella",1783272|201174|84998|1643822|1643826|447020;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|28138,Complete,Svetlana up
bsdb:36171620/3/2,36171620,laboratory experiment,36171620,10.1186/s12974-022-02599-4,NA,"Qian X.H., Liu X.L., Chen G., Chen S.D. , Tang H.D.",Injection of amyloid-β to lateral ventricle induces gut microbiota dysbiosis in association with inhibition of cholinergic anti-inflammatory pathways in Alzheimer's disease,Journal of neuroinflammation,2022,"Alzheimer’s disease, Aβ, Cholinergic anti-inflammatory pathway, Gut microbiota",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Sham-operated group,Alzheimer’s disease (4 weeks after surgery),Alzheimer's disease (AD) model mice injected in the lateral ventricle with Aβ1–42 intracerebroventricular injection 4 weeks after surgery,10,10,NA,16S,34,Illumina,NA,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,increased,Signature 2,Figure 3 (I - N),15 March 2024,Flo,"Flo,Scholastica,WikiWorks",Bacterial genera significantly different at the genus level in the Aβ1–42 treatment group compared to the phosphate-buffered saline (PBS) sham-operated group,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|976|200643|171549|171552|1283313;1783272|1239|186801|186802|216572|1508657;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:36171620/6/1,36171620,laboratory experiment,36171620,10.1186/s12974-022-02599-4,NA,"Qian X.H., Liu X.L., Chen G., Chen S.D. , Tang H.D.",Injection of amyloid-β to lateral ventricle induces gut microbiota dysbiosis in association with inhibition of cholinergic anti-inflammatory pathways in Alzheimer's disease,Journal of neuroinflammation,2022,"Alzheimer’s disease, Aβ, Cholinergic anti-inflammatory pathway, Gut microbiota",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Control group,Alzheimer’s disease (4 weeks after surgery),Alzheimer's disease (AD) model mice injected in the lateral ventricle with Aβ1–42 intracerebroventricular injection 4 weeks after surgery,10,10,NA,16S,34,Illumina,NA,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,increased,Signature 1,Figure 3 (I - N),13 March 2024,Flo,"Flo,Scholastica,WikiWorks",Bacterial genera significantly different at the genus level in the Aβ1–42 treatment group compared to the control group,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella",1783272|201174|84998|1643822|1643826|447020;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|28138,Complete,Svetlana up
bsdb:36171620/6/2,36171620,laboratory experiment,36171620,10.1186/s12974-022-02599-4,NA,"Qian X.H., Liu X.L., Chen G., Chen S.D. , Tang H.D.",Injection of amyloid-β to lateral ventricle induces gut microbiota dysbiosis in association with inhibition of cholinergic anti-inflammatory pathways in Alzheimer's disease,Journal of neuroinflammation,2022,"Alzheimer’s disease, Aβ, Cholinergic anti-inflammatory pathway, Gut microbiota",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Control group,Alzheimer’s disease (4 weeks after surgery),Alzheimer's disease (AD) model mice injected in the lateral ventricle with Aβ1–42 intracerebroventricular injection 4 weeks after surgery,10,10,NA,16S,34,Illumina,NA,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,increased,Signature 2,Figure 3 (I - N),13 March 2024,Flo,"Flo,Scholastica,WikiWorks",Bacterial genera significantly different at the genus level in the Aβ1–42 treatment group compared to the control group,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|976|200643|171549|171552|1283313;1783272|1239|186801|186802|216572|1508657;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:36171758/1/1,36171758,meta-analysis,36171758,10.3389/fcimb.2022.961644,NA,"Chai J., Liu X., Usdrowski H., Deng F., Li Y. , Zhao J.","Geography, niches, and transportation influence bovine respiratory microbiome and health",Frontiers in cellular and infection microbiology,2022,"bovine, bovine respiratory disease, geography, lung, metagenomics, nasopharynx, respiratory microbiota, transportation",Experiment 1,"Canada,China",Bos taurus,"Nasopharynx,Lung","UBERON:0001728,UBERON:0002048",Population,IDOMAL:0001254,Nasopharyngeal swabs from Canada and bronchoalveolar lavage from Canada,Nasopharyngeal swabs from China,Nasopharyngeal swabs from two cities (Qiqihaer and Guangan) in China from the study of Cui et al (2021).,127,18,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,figure 2,12 November 2023,Folakunmi,"Folakunmi,ChiomaBlessing,WikiWorks",Differentially abundant taxa in the nasopharyngeal samples (NPS) of China (Qiqihaer and Guangan) when compared with the nasopharyngeal samples of Saskatoon in Canada and bronchoalveolar lavage samples (BAL) of Alberta in Canada.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium efficiens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium glutamicum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter|s__Enhydrobacter aerosaccus,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mesomycoplasma|s__Mesomycoplasma conjunctivae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella catarrhalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter|s__Psychrobacter arcticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter|s__Psychrobacter sp. PRwf-1,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae",1783272|201174|1760|85007|1653|1716|152794;1783272|201174|1760|85007|1653|1716|1718;3379134|1224|28211|356|212791|225324;1783272|544448|2790996|2895623|2923352|45361;3379134|1224|1236|2887326|468|475|480;3379134|1224|1236|2887326|468|497|334543;3379134|1224|1236|2887326|468|497|349106;3379134|1224|1236|2887326|468|469|470;3379134|1224|1236|91347|543|570|573,Complete,ChiomaBlessing
bsdb:36171758/2/1,36171758,meta-analysis,36171758,10.3389/fcimb.2022.961644,NA,"Chai J., Liu X., Usdrowski H., Deng F., Li Y. , Zhao J.","Geography, niches, and transportation influence bovine respiratory microbiome and health",Frontiers in cellular and infection microbiology,2022,"bovine, bovine respiratory disease, geography, lung, metagenomics, nasopharynx, respiratory microbiota, transportation",Experiment 2,"Canada,China",Bos taurus,"Nasopharynx,Lung","UBERON:0001728,UBERON:0002048",Population,IDOMAL:0001254,Nasopharyngeal swabs from China and bronchoalveolar lavage from Canada,"Nasopharyngeal swabs from Saskatoon, Canada.",Nasopharyngeal swabs from Saskatoon in Canada from the study of Malmuthuge et al. (2021).,33,112,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,figure 2,12 November 2023,Folakunmi,"Folakunmi,ChiomaBlessing,WikiWorks","Differentially abundant taxa in the nasopharyngeal samples (NPS) of Saskatoon, Canada when compared with the NPS of China and bronchoalveolar lavage samples (BAL) of Alberta in Canada.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia ambifaria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia cenocepacia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia dolosa,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia lata,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia multivorans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia ubonensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia vietnamiensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia phymatum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia xenovorans",3379134|1224|28216|80840|119060|32008|152480;3379134|1224|28216|80840|119060|32008|95486;3379134|1224|28216|80840|119060|32008|152500;3379134|1224|28216|80840|119060|32008|482957;3379134|1224|28216|80840|119060|32008|87883;3379134|1224|28216|80840|119060|32008|101571;3379134|1224|28216|80840|119060|32008|60552;3379134|1224|28216|80840|119060|1822464|148447;3379134|1224|28216|80840|119060|1822464|36873,Complete,ChiomaBlessing
bsdb:36171758/3/1,36171758,meta-analysis,36171758,10.3389/fcimb.2022.961644,NA,"Chai J., Liu X., Usdrowski H., Deng F., Li Y. , Zhao J.","Geography, niches, and transportation influence bovine respiratory microbiome and health",Frontiers in cellular and infection microbiology,2022,"bovine, bovine respiratory disease, geography, lung, metagenomics, nasopharynx, respiratory microbiota, transportation",Experiment 3,"Canada,China",Bos taurus,"Nasopharynx,Lung","UBERON:0001728,UBERON:0002048",Sampling site,EFO:0000688,Nasopharyngeal swabs from Canada and Nasopharyngeal swabs from China,"Bronchoalveolar lavage from Alberta, Canada","Bronchoalveolar lavage collected from feedlot calves which died from bovine respiratory disease in Alberta, Canada from the study of Klima et al. (2019).",130,15,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 2,12 November 2023,Folakunmi,"Folakunmi,ChiomaBlessing,WikiWorks","Differentially abundant taxa in the bronchoalveolar lavage samples (BAL) of Alberta in Canada when compared with the nasopharyngeal samples (NPS) of China and NPS of Saskatoon, Canada .",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus|s__Actinobacillus pleuropneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus|s__Actinobacillus succinogenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Glaesserella|s__Glaesserella parasuis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Histophilus|s__Histophilus somni,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Mannheimia|s__Mannheimia haemolytica,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma arthritidis,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma hominis,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma|s__Mycoplasma mycoides,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mycoplasmopsis|s__Mycoplasmopsis agalactiae,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mycoplasmopsis|s__Mycoplasmopsis bovis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella bryantii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella buccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter ruminicola,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__[Haemophilus] ducreyi,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Basfia|s__[Mannheimia] succiniciproducens",3379134|1224|1236|135625|712|713|715;3379134|1224|1236|135625|712|713|67854;1783272|1239|186801|186802|31979|1485|1502;3379134|1224|1236|135625|712|2094023|738;3379134|1224|1236|135625|712|724|727;3379134|1224|1236|135625|712|214906|731;3379134|1224|1236|135625|712|75984|75985;1783272|544448|2790996|2895623|2895509|2111;1783272|544448|2790996|2895623|2895509|2098;1783272|544448|31969|2085|2092|2093|2102;1783272|544448|2790996|2895623|2767358|2110;1783272|544448|2790996|2895623|2767358|28903;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552|2974251|77095;3379134|976|200643|171549|171552|2974251|28126;3379134|976|200643|171549|171552|2974251|165179;3379134|976|200643|171549|171552|2974251|28135;3379134|976|200643|171549|171552|558436|839;3379134|1224|1236|135625|712|724|730;3379134|1224|1236|135625|712|697331|157673,Complete,ChiomaBlessing
bsdb:36171758/4/1,36171758,meta-analysis,36171758,10.3389/fcimb.2022.961644,NA,"Chai J., Liu X., Usdrowski H., Deng F., Li Y. , Zhao J.","Geography, niches, and transportation influence bovine respiratory microbiome and health",Frontiers in cellular and infection microbiology,2022,"bovine, bovine respiratory disease, geography, lung, metagenomics, nasopharynx, respiratory microbiota, transportation",Experiment 4,"Canada,China",Bos taurus,Nasopharynx,UBERON:0001728,Transport,GO:0006810,Non-transportation (control),Before loading for short distance transportation,"calves before loading to truck for transportation at short distance. LefSe was used to identify the longitudinal changes of microbiota from the studies of Cui et al. (2021) and Malmuthuge et al. (2021), following transportation",10,10,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,supplementary figure S4,13 November 2023,Folakunmi,"Folakunmi,WikiWorks",Signature microbiota in calves before loading into trucks for transportation at a short distance,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Nocardia|s__Nocardia farcinica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Idiomarinaceae|g__Idiomarina|s__Idiomarina loihiensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces sp. e14,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Bruguierivoracaceae|g__Sodalis|s__Sodalis glossinidius",1783272|201174|1760|85007|85025|1817|37329;3379134|1224|1236|135622|267893|135575|135577;1783272|201174|1760|85011|2062|1883|645465;3379134|1224|1236|91347|2812006|84565|63612,Complete,ChiomaBlessing
bsdb:36171758/5/1,36171758,meta-analysis,36171758,10.3389/fcimb.2022.961644,NA,"Chai J., Liu X., Usdrowski H., Deng F., Li Y. , Zhao J.","Geography, niches, and transportation influence bovine respiratory microbiome and health",Frontiers in cellular and infection microbiology,2022,"bovine, bovine respiratory disease, geography, lung, metagenomics, nasopharynx, respiratory microbiota, transportation",Experiment 5,"Canada,China",Bos taurus,Nasopharynx,UBERON:0001728,Transport,GO:0006810,Non-transportation (control),unloading after short distance transportation,"calves at the time of unloading from truck after transportation at short distance. LefSe was used to identify the longitudinal changes of microbiota from the studies of Cui et al. (2021) and Malmuthuge et al. (2021), following transportation",10,10,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,supplementary figure S4,13 November 2023,Folakunmi,"Folakunmi,WikiWorks",Signature microbiota in calves at the time of unloading from trucks after transportation at a short distance.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium|s__Rhizobium etli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae|g__Marinomonas|s__Marinomonas sp. MED121,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Yoonia|s__Yoonia vestfoldensis",3379134|1224|28211|356|82115|379|29449;3379134|1224|1236|135619|135620|28253|314277;3379134|1224|28211|204455|31989|2211641|245188,Complete,ChiomaBlessing
bsdb:36171758/6/1,36171758,meta-analysis,36171758,10.3389/fcimb.2022.961644,NA,"Chai J., Liu X., Usdrowski H., Deng F., Li Y. , Zhao J.","Geography, niches, and transportation influence bovine respiratory microbiome and health",Frontiers in cellular and infection microbiology,2022,"bovine, bovine respiratory disease, geography, lung, metagenomics, nasopharynx, respiratory microbiota, transportation",Experiment 6,"Canada,China",Bos taurus,Nasopharynx,UBERON:0001728,Transport,GO:0006810,Non-transportation (control),7 days after placement and adaptive feeding (short distance),"calves 7 days after placement and adaptive feeding following transportation at short distance. LefSe was used to identify the longitudinal changes of microbiota from the studies of Cui et al. (2021) and Malmuthuge et al. (2021), following transportation.",10,10,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,supplementary figure S4,14 November 2023,Folakunmi,"Folakunmi,ChiomaBlessing,WikiWorks",calves 7 days after placement and adaptive feeding following transportation at short distance.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus|s__Dermacoccus sp. Ellin185,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Geobacterales|f__Geobacteraceae|g__Geotalea|s__Geotalea uraniireducens,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Microscillaceae|g__Microscilla|s__Microscilla marina,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Streptosporangiales|f__Nocardiopsidaceae|g__Nocardiopsis|s__Nocardiopsis dassonvillei,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae|g__Spirosoma|s__Spirosoma linguale,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces avermitilis",1783272|201174|1760|85006|145357|57495|188626;3379134|200940|3031651|3031668|213422|2910589|351604;3379134|976|768503|768507|1937962|1023|1027;1783272|201174|1760|85012|83676|2013|2014;3379134|976|768503|768507|89373|107|108;1783272|201174|1760|85011|2062|1883|33903,Complete,ChiomaBlessing
bsdb:36171758/7/1,36171758,meta-analysis,36171758,10.3389/fcimb.2022.961644,NA,"Chai J., Liu X., Usdrowski H., Deng F., Li Y. , Zhao J.","Geography, niches, and transportation influence bovine respiratory microbiome and health",Frontiers in cellular and infection microbiology,2022,"bovine, bovine respiratory disease, geography, lung, metagenomics, nasopharynx, respiratory microbiota, transportation",Experiment 7,"Canada,China",Bos taurus,Nasopharynx,UBERON:0001728,Transport,GO:0006810,Non-transportation (control),before loading for long distance transportation,"calves before loading into truck for long distance transportation. LefSe was used to identify the longitudinal changes of microbiota from the studies of Cui et al. (2021) and Malmuthuge et al. (2021), following transportation.",10,18,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,supplementary figure S4,14 November 2023,Folakunmi,"Folakunmi,WikiWorks","calves before loading for long distance transportation. LefSe was used to identify the longitudinal changes of microbiota from the studies of Cui et al. (2021) and Malmuthuge et al. (2021), following transportation.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella|s__Simonsiella muelleri,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium|s__Methylobacterium radiotolerans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas fluorescens,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Rhizorhabdaceae|g__Rhizorhabdus|s__Rhizorhabdus wittichii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylorubrum|s__Methylorubrum extorquens",3379134|1224|28216|206351|481|71|72;3379134|1224|28211|356|119045|407|31998;3379134|1224|1236|72274|135621|286|294;3379134|1224|28211|204457|3423714|1649486|160791;3379134|1224|28211|356|119045|2282523|408,Complete,ChiomaBlessing
bsdb:36171758/8/1,36171758,meta-analysis,36171758,10.3389/fcimb.2022.961644,NA,"Chai J., Liu X., Usdrowski H., Deng F., Li Y. , Zhao J.","Geography, niches, and transportation influence bovine respiratory microbiome and health",Frontiers in cellular and infection microbiology,2022,"bovine, bovine respiratory disease, geography, lung, metagenomics, nasopharynx, respiratory microbiota, transportation",Experiment 8,"Canada,China",Bos taurus,Nasopharynx,UBERON:0001728,Transport,GO:0006810,Non-transportation (control),unloading from long distance transportation,"calves at the time of unloading from truck after long distance transportation. LefSe was used to identify the longitudinal changes of microbiota from the studies of Cui et al. (2021) and Malmuthuge et al. (2021), following transportation.",10,18,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,supplementary figure S4,14 November 2023,Folakunmi,"Folakunmi,WikiWorks","abundant taxa in calves at the time of unloading from truck after long distance transportation. LefSe was used to identify the longitudinal changes of microbiota from the studies of Cui et al. (2021) and Malmuthuge et al. (2021), following transportation.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baylyi,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus|s__Actinobacillus minor,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus|s__Actinobacillus pleuropneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus|s__Actinobacillus succinogenes,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter|s__Enhydrobacter aerosaccus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Glaesserella|s__Glaesserella parasuis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Histophilus|s__Histophilus somni,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Mannheimia|s__Mannheimia haemolytica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella catarrhalis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria gonorrhoeae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria lactamica,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria meningitidis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella|s__Pasteurella dagmatis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella|s__Pasteurella multocida,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter|s__Psychrobacter arcticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter|s__Psychrobacter cryohalolentis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter|s__Psychrobacter sp. PRwf-1,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__[Haemophilus] ducreyi,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Basfia|s__[Mannheimia] succiniciproducens,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Riemerella|s__Riemerella anatipestifer",3379134|1224|1236|2887326|468|469|202950;3379134|1224|1236|135625|712|713|51047;3379134|1224|1236|135625|712|713|715;3379134|1224|1236|135625|712|713|67854;3379134|1224|28211|356|212791|225324;3379134|1224|1236|135625|712|2094023|738;3379134|1224|1236|135625|712|724|727;3379134|1224|1236|135625|712|214906|731;3379134|1224|28216|206351|481|32257|505;3379134|1224|1236|135625|712|75984|75985;3379134|1224|1236|2887326|468|475|480;3379134|1224|28216|206351|481|482|485;3379134|1224|28216|206351|481|482|486;3379134|1224|28216|206351|481|482|487;3379134|1224|1236|135625|712|745|754;3379134|1224|1236|135625|712|745|747;3379134|1224|1236|2887326|468|497|334543;3379134|1224|1236|2887326|468|497|330922;3379134|1224|1236|2887326|468|497|349106;3379134|1224|1236|135625|712|724|730;3379134|1224|1236|135625|712|697331|157673;3379134|976|117743|200644|2762318|34084|34085,Complete,ChiomaBlessing
bsdb:36171758/9/1,36171758,meta-analysis,36171758,10.3389/fcimb.2022.961644,NA,"Chai J., Liu X., Usdrowski H., Deng F., Li Y. , Zhao J.","Geography, niches, and transportation influence bovine respiratory microbiome and health",Frontiers in cellular and infection microbiology,2022,"bovine, bovine respiratory disease, geography, lung, metagenomics, nasopharynx, respiratory microbiota, transportation",Experiment 9,"Canada,China",Bos taurus,Nasopharynx,UBERON:0001728,Transport,GO:0006810,Non-transportation (control),7 days after placement and adaptive feeding(long distance),"calves at  7 days after placement and adaptive feeding after long distance transportation. LefSe was used to identify the longitudinal changes of microbiota from the studies of Cui et al. (2021) and Malmuthuge et al. (2021), following transportation.",10,18,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,supplementary figure S4,15 November 2023,Folakunmi,"Folakunmi,Davvve,ChiomaBlessing,WikiWorks","abundant taxa in calves at 7 days after placement and adaptive feeding after long distance transportation. LefSe was used to identify the longitudinal changes of microbiota from the studies of Cui et al. (2021) and Malmuthuge et al. (2021), following transportation.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio|s__Acetivibrio thermocellus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus viridans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium|s__Agrobacterium tumefaciens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter|s__Arthrobacter sp. FB24,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas|s__Brevundimonas subvibrioides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium|s__Carnobacterium sp. AT7,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter|s__Caulobacter vibrioides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium botulinum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium ammoniagenes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium amycolatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium aurimucosum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium diphtheriae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium efficiens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium jeikeium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria|s__Kocuria rhizophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium phytofermentans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora saccharolytica,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Macrococcoides|s__Macrococcoides caseolyticum,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mesomycoplasma|s__Mesomycoplasma conjunctivae,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mesomycoplasma|s__Mesomycoplasma hyopneumoniae,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mesomycoplasma|s__Mesomycoplasma hyorhinis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides|s__Nocardioides sp. JS614,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Ectopseudomonas|s__Ectopseudomonas mendocina,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium|s__Rhizobium leguminosarum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Rhodopseudomonas|s__Rhodopseudomonas palustris,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D16,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus albus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Saccharopolyspora|s__Saccharopolyspora erythraea,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus saprophyticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Stutzerimonas|s__Stutzerimonas stutzeri,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio proteoclasticus",1783272|1239|186801|3120394|3120654|35829|1515;1783272|1239|91061|186826|186827|1375|1377;1783272|1239|186801|3085636|186803|1766253|39491;3379134|1224|28211|356|82115|357|358;1783272|201174|1760|85006|1268|1663|290399;3379134|1224|28211|204458|76892|41275|74313;1783272|1239|91061|186826|186828|2747|333990;3379134|1224|28211|204458|76892|75|155892;1783272|1239|186801|186802|31979|1485|1491;1783272|201174|1760|85007|1653|1716|1697;1783272|201174|1760|85007|1653|1716|43765;1783272|201174|1760|85007|1653|1716|169292;1783272|201174|1760|85007|1653|1716|1717;1783272|201174|1760|85007|1653|1716|152794;1783272|201174|1760|85007|1653|1716|38289;1783272|1239|91061|186826|81852|1350|1352;3379134|1224|1236|91347|543|561|562;1783272|201174|1760|85006|1268|57493|72000;1783272|1239|186801|3085636|186803|1506553|66219;1783272|1239|186801|3085636|186803|2719231|84030;1783272|1239|91061|1385|90964|3076173|69966;1783272|544448|2790996|2895623|2923352|45361;1783272|544448|2790996|2895623|2923352|2099;1783272|544448|2790996|2895623|2923352|2100;1783272|201174|1760|85009|85015|1839|196162;1783272|1239|186801|186802|216572|1017280|106588;3379134|1224|1236|72274|135621|3236654|300;3379134|1224|28211|356|82115|379|384;3379134|1224|28211|356|41294|1073|1076;1783272|1239|186801|186802|216572|552398;1783272|1239|186801|186802|216572|1263|1264;1783272|201174|1760|85010|2070|1835|1836;1783272|1239|91061|1385|90964|1279|1280;1783272|1239|91061|1385|90964|1279|1282;1783272|1239|91061|1385|90964|1279|29385;3379134|1224|1236|72274|135621|2901164|316;1783272|1239|186801|3085636|186803|830|43305,Complete,ChiomaBlessing
bsdb:36171758/10/1,36171758,meta-analysis,36171758,10.3389/fcimb.2022.961644,NA,"Chai J., Liu X., Usdrowski H., Deng F., Li Y. , Zhao J.","Geography, niches, and transportation influence bovine respiratory microbiome and health",Frontiers in cellular and infection microbiology,2022,"bovine, bovine respiratory disease, geography, lung, metagenomics, nasopharynx, respiratory microbiota, transportation",Experiment 10,Canada,Bos taurus,Nasopharynx,UBERON:0001728,"Breastfeeding duration,Transport","EFO:0006864,GO:0006810",suckling calves (control),weaning+short transportation,"These were the calves in the treatment group that got weaned and transported at short distance. Metagenomics of the bovine respiratory microbiome in treatment groups on days 0 (prior to weaning and short-distance transportation), 2, 4, 8, 14, and 28 was used to compare with the control group that stayed with their dams (suckling).",10,10,NA,WMS,NA,Illumina,raw counts,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 1,figure 7,16 November 2023,Folakunmi,"Folakunmi,WikiWorks",Significantly abundant taxa in the weaning+short-transport group on day 14 when compared to the suckling group on day 14.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Mannheimia,3379134|1224|1236|135625|712|75984,Complete,ChiomaBlessing
bsdb:36171758/10/2,36171758,meta-analysis,36171758,10.3389/fcimb.2022.961644,NA,"Chai J., Liu X., Usdrowski H., Deng F., Li Y. , Zhao J.","Geography, niches, and transportation influence bovine respiratory microbiome and health",Frontiers in cellular and infection microbiology,2022,"bovine, bovine respiratory disease, geography, lung, metagenomics, nasopharynx, respiratory microbiota, transportation",Experiment 10,Canada,Bos taurus,Nasopharynx,UBERON:0001728,"Breastfeeding duration,Transport","EFO:0006864,GO:0006810",suckling calves (control),weaning+short transportation,"These were the calves in the treatment group that got weaned and transported at short distance. Metagenomics of the bovine respiratory microbiome in treatment groups on days 0 (prior to weaning and short-distance transportation), 2, 4, 8, 14, and 28 was used to compare with the control group that stayed with their dams (suckling).",10,10,NA,WMS,NA,Illumina,raw counts,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 2,figure 7,16 November 2023,Folakunmi,"Folakunmi,WikiWorks",Significantly abundant taxa in the weaning+short-transport group on day 14 when compared to the suckling group on day 14.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,3379134|1224|1236|2887326|468|475,Complete,ChiomaBlessing
bsdb:36182683/1/1,36182683,"cross-sectional observational, not case-control",36182683,10.1016/j.xcrm.2022.100753,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9588997/,"Neugent M.L., Kumar A., Hulyalkar N.V., Lutz K.C., Nguyen V.H., Fuentes J.L., Zhang C., Nguyen A., Sharon B.M., Kuprasertkul A., Arute A.P., Ebrahimzadeh T., Natesan N., Xing C., Shulaev V., Li Q., Zimmern P.E., Palmer K.L. , De Nisco N.J.",Recurrent urinary tract infection and estrogen shape the taxonomic ecology and function of the postmenopausal urogenital microbiome,Cell reports. Medicine,2022,"Escherichia coli, Lactobacillus crispatus, antibiotic resistance, bladder, dysbiosis, estrogen, metagenomics, postmenopausal women, urinary tract infection, urogenital microbiome",Experiment 1,United States of America,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,No UTI History,"rUTI History, UTI (-)","Consists of post menopausal (PM) women with a recent history of recurring urinary tract infection ( rUTI) but no active UTI at the time of urine donation (rUTI History, UTI(−))",25,25,1 month,WMS,NA,Sanger,relative abundances,Negative Binomial Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Fig 3D + 3E,25 October 2023,Tolulopeo,"Tolulopeo,ChiomaBlessing,WikiWorks","Differentially abundant taxa in the rUTI History, UTI(−) group compared to the No UTI History group",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus lactolyticus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus vaginalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus urinae",1783272|1239|91061|186826|186827|1375;1783272|1239|1737404|1737405|1570339|165779|33032;1783272|1239|1737404|1737405|1570339|165779|33037;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|47770;1783272|1239|91061|186826|33958|2742598|1633;1783272|1239|91061|186826|186827|1375|1376,Complete,ChiomaBlessing
bsdb:36182683/1/2,36182683,"cross-sectional observational, not case-control",36182683,10.1016/j.xcrm.2022.100753,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9588997/,"Neugent M.L., Kumar A., Hulyalkar N.V., Lutz K.C., Nguyen V.H., Fuentes J.L., Zhang C., Nguyen A., Sharon B.M., Kuprasertkul A., Arute A.P., Ebrahimzadeh T., Natesan N., Xing C., Shulaev V., Li Q., Zimmern P.E., Palmer K.L. , De Nisco N.J.",Recurrent urinary tract infection and estrogen shape the taxonomic ecology and function of the postmenopausal urogenital microbiome,Cell reports. Medicine,2022,"Escherichia coli, Lactobacillus crispatus, antibiotic resistance, bladder, dysbiosis, estrogen, metagenomics, postmenopausal women, urinary tract infection, urogenital microbiome",Experiment 1,United States of America,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,No UTI History,"rUTI History, UTI (-)","Consists of post menopausal (PM) women with a recent history of recurring urinary tract infection ( rUTI) but no active UTI at the time of urine donation (rUTI History, UTI(−))",25,25,1 month,WMS,NA,Sanger,relative abundances,Negative Binomial Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Fig 3D + 3E,25 October 2023,Tolulopeo,"Tolulopeo,Chinelsy,Chloe,ChiomaBlessing,WikiWorks","Differentially abundant taxa in the rUTI History, UTI(−) group compared to the No UTI History group",increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus hydrogenalis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus prevotii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium|s__Brevibacterium ravenspurgense,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__Eubacteriales Family XIII. Incertae Sedis bacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium pseudogenitalium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia|s__Facklamia hominis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Gleimia|s__Gleimia europaea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia turicensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma parvum",1783272|1239|1737404|1737405|1570339|165779|33029;1783272|1239|1737404|1737405|1570339|165779|33034;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|820;1783272|201174|1760|85006|85019|1696|479117;1783272|1239|186801|3082720|543314|2137877;1783272|201174|1760|85007|1653|1716|38303;1783272|201174|84998|1643822|1643826|84111;1783272|1239|91061|186826|81852|1350|1351;3379134|1224|1236|91347|543|561;1783272|1239|91061|186826|186827|66831|178214;1783272|1239|1737404|1737405|1570339|150022|1260;1783272|1239|91061|1385|539738|1378;1783272|201174|1760|2037|2049|2692113|66228;3379134|976|200643|171549|171552|2974257|386414;3379134|1224|1236|91347|543|570;1783272|1239|1737404|1737405|1570339|162289|33031;1783272|201174|1760|2037|2049|2529408|131111;1783272|1239|91061|1385|90964|1279|1282;1783272|1239|91061|1385|90964|1279|1290;1783272|1239|91061|186826|1300|1301;1783272|544448|2790996|2790998|2129;1783272|544448|2790996|2790998|2129|134821,Complete,ChiomaBlessing
bsdb:36182683/2/1,36182683,"cross-sectional observational, not case-control",36182683,10.1016/j.xcrm.2022.100753,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9588997/,"Neugent M.L., Kumar A., Hulyalkar N.V., Lutz K.C., Nguyen V.H., Fuentes J.L., Zhang C., Nguyen A., Sharon B.M., Kuprasertkul A., Arute A.P., Ebrahimzadeh T., Natesan N., Xing C., Shulaev V., Li Q., Zimmern P.E., Palmer K.L. , De Nisco N.J.",Recurrent urinary tract infection and estrogen shape the taxonomic ecology and function of the postmenopausal urogenital microbiome,Cell reports. Medicine,2022,"Escherichia coli, Lactobacillus crispatus, antibiotic resistance, bladder, dysbiosis, estrogen, metagenomics, postmenopausal women, urinary tract infection, urogenital microbiome",Experiment 2,United States of America,Homo sapiens,Urine,UBERON:0001088,Hormone replacement therapy,EFO:0003961,EHT- Group (Premenopausal women in the 'No UTI History and rUTI History( UTI(−) cohorts' who did not use estrogen hormone therapy (EHT)),EHT+ Group (Premenopausal women in the 'No UTI History and rUTI History( UTI(−) cohorts' who used estrogen hormone therapy (EHT)),Premenopausal women in the 'No UTI History and rUTI History( UTI(−) cohorts' with systemic and vaginal estrogen hormone therapy (EHT) who did not have UTI at the time of urine donation.,21,29,1 month,WMS,NA,Sanger,relative abundances,LEfSe,0.05,TRUE,4.5,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,Fig 4C + 4H,25 October 2023,Tolulopeo,"Tolulopeo,Chinelsy,ChiomaBlessing,WikiWorks",Urogenital microbiomes of EHT(+) (aggregated systemic and vaginal) women compared to those of EHT(−) women,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus vaginalis",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|47770;1783272|1239|91061|186826|33958|2742598|1633,Complete,ChiomaBlessing
bsdb:36182683/2/2,36182683,"cross-sectional observational, not case-control",36182683,10.1016/j.xcrm.2022.100753,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9588997/,"Neugent M.L., Kumar A., Hulyalkar N.V., Lutz K.C., Nguyen V.H., Fuentes J.L., Zhang C., Nguyen A., Sharon B.M., Kuprasertkul A., Arute A.P., Ebrahimzadeh T., Natesan N., Xing C., Shulaev V., Li Q., Zimmern P.E., Palmer K.L. , De Nisco N.J.",Recurrent urinary tract infection and estrogen shape the taxonomic ecology and function of the postmenopausal urogenital microbiome,Cell reports. Medicine,2022,"Escherichia coli, Lactobacillus crispatus, antibiotic resistance, bladder, dysbiosis, estrogen, metagenomics, postmenopausal women, urinary tract infection, urogenital microbiome",Experiment 2,United States of America,Homo sapiens,Urine,UBERON:0001088,Hormone replacement therapy,EFO:0003961,EHT- Group (Premenopausal women in the 'No UTI History and rUTI History( UTI(−) cohorts' who did not use estrogen hormone therapy (EHT)),EHT+ Group (Premenopausal women in the 'No UTI History and rUTI History( UTI(−) cohorts' who used estrogen hormone therapy (EHT)),Premenopausal women in the 'No UTI History and rUTI History( UTI(−) cohorts' with systemic and vaginal estrogen hormone therapy (EHT) who did not have UTI at the time of urine donation.,21,29,1 month,WMS,NA,Sanger,relative abundances,LEfSe,0.05,TRUE,4.5,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Fig 4H,25 October 2023,Tolulopeo,"Tolulopeo,OdigiriGreat,ChiomaBlessing,WikiWorks",Urogenital microbiomes of  EHT(+) women compared to those of EHT(-) women,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae",1783272|201174|84998|84999|1643824|2767327|82135;1783272|1239|91061|186826|1300|1301|68892;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|91061|186826|1300|1301|1313,Complete,ChiomaBlessing
bsdb:36182683/3/NA,36182683,"cross-sectional observational, not case-control",36182683,10.1016/j.xcrm.2022.100753,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9588997/,"Neugent M.L., Kumar A., Hulyalkar N.V., Lutz K.C., Nguyen V.H., Fuentes J.L., Zhang C., Nguyen A., Sharon B.M., Kuprasertkul A., Arute A.P., Ebrahimzadeh T., Natesan N., Xing C., Shulaev V., Li Q., Zimmern P.E., Palmer K.L. , De Nisco N.J.",Recurrent urinary tract infection and estrogen shape the taxonomic ecology and function of the postmenopausal urogenital microbiome,Cell reports. Medicine,2022,"Escherichia coli, Lactobacillus crispatus, antibiotic resistance, bladder, dysbiosis, estrogen, metagenomics, postmenopausal women, urinary tract infection, urogenital microbiome",Experiment 3,United States of America,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,No UTI History,"rUTI History, UTI (+)","Consists of post menopausal (PM) women with a recent history of recurring urinary tract infection ( rUTI) and an active, symptomatic UTI at the time of urine donation",25,25,1 month,WMS,NA,Sanger,relative abundances,Negative Binomial Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:36197290/1/1,36197290,time series / longitudinal observational,36197290,10.1128/spectrum.01899-22,NA,"Jiang C.H., Fang X., Huang W., Guo J.Y., Chen J.Y., Wu H.Y., Li Z.S., Zou W.B. , Liao Z.",Alterations in the Gut Microbiota and Metabolomics of Seafarers after a Six-Month Sea Voyage,Microbiology spectrum,2022,"16S rRNA gene sequencing, gut microbiota, metabolic pathways, sea voyage, seafarers’ health care, untargeted metabolomics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Sampling time,EFO:0000689,Day 0,Day 180,Seafarers at the end (day 180) of the 6-month voyage,30,30,NA,16S,34,Illumina,relative abundances,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Fig. 1c, Fig. 1d",31 March 2024,Scholastica,"Scholastica,Welile,WikiWorks","Differential relative abundances of bacterial genera between day 0 and day 180 of the voyage. *, P , 0.05; **, P , 0.01. (Wilcoxon rank sum test and LeFse)",increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Plesiomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ramlibacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|s__Rhodobacteraceae bacterium HIMB11,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",1783272|1239|526524|526525|128827|174708;1783272|1239|186801|3085636|186803|43996;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|526524|526525|128827|1573535;3379134|1224|1236|91347|543|702;3379134|1224|28216|80840|80864|174951;3379134|1224|28211|204455|31989|1366046;1783272|1239|91061|186826|33958|46255;1783272|1239|91061|186826|33958,Complete,Svetlana up
bsdb:36197290/1/2,36197290,time series / longitudinal observational,36197290,10.1128/spectrum.01899-22,NA,"Jiang C.H., Fang X., Huang W., Guo J.Y., Chen J.Y., Wu H.Y., Li Z.S., Zou W.B. , Liao Z.",Alterations in the Gut Microbiota and Metabolomics of Seafarers after a Six-Month Sea Voyage,Microbiology spectrum,2022,"16S rRNA gene sequencing, gut microbiota, metabolic pathways, sea voyage, seafarers’ health care, untargeted metabolomics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Sampling time,EFO:0000689,Day 0,Day 180,Seafarers at the end (day 180) of the 6-month voyage,30,30,NA,16S,34,Illumina,relative abundances,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Fig. 1c, Fig. 1d",31 March 2024,Scholastica,"Scholastica,Welile,WikiWorks","Differential relative abundances of bacterial genera between day 0 and day 180 of the voyage. *, P , 0.05; **, P , 0.01. (Wilcoxon rank sum test and LeFse)",decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,c__Deltaproteobacteria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales",1783272|1239|526524|526525|2810280|3025755;3379134|200940|3031449|213115|194924|35832;1783272|1239|526524|526525|128827|1573534;1783272|1239|186801|3085636|186803|1506553;1783272|1239|909932|1843488|909930|33024;1783272|1239|909932|1843488|909930;28221;1783272|201174|1760|85007;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115,Complete,Svetlana up
bsdb:36198385/1/1,36198385,randomized controlled trial,36198385,10.1016/j.anaerobe.2022.102652,NA,"Bamola V.D., Dubey D., Samanta P., Kedia S., Ahuja V., Madempudi R.S., Neelamraju J. , Chaudhry R.",Role of a probiotic strain in the modulation of gut microbiota and cytokines in inflammatory bowel disease,Anaerobe,2022,"Bacillus clausii UBBC-07, Cytokines, Gut microbiome, IBD, Probiotic",Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Treatment,EFO:0000727,Placebo group before intervention/treatment,Bacillus clausii UBBC-07 group after intervention/treatment,"Patients who were treated with Bacillus clausii UBBC-07 and evaluated after treatment/intervention for the effect of the probiotic on gut microbiota. Patients were of either sex, clinically diagnosed with Ulcerative Colitis or Crohn's Disease, and between 18 and 60 years.",54,54,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Results within text: Page 4, under subheading ""Metagenomic analysis""",17 October 2023,Folakunmi,"Folakunmi,ChiomaBlessing,WikiWorks",Differentially abundant taxa in the UC patients of the Bacillus clausii UBBC-07 group post intervention/ treatment compared to placebo groups post intervention/ treatment,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|1239|91061;1783272|1239;1783272|1239|526524|526525;1783272|1239|186801|186802|216572|216851;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85004|31953|1678,Complete,ChiomaBlessing
bsdb:36198385/1/2,36198385,randomized controlled trial,36198385,10.1016/j.anaerobe.2022.102652,NA,"Bamola V.D., Dubey D., Samanta P., Kedia S., Ahuja V., Madempudi R.S., Neelamraju J. , Chaudhry R.",Role of a probiotic strain in the modulation of gut microbiota and cytokines in inflammatory bowel disease,Anaerobe,2022,"Bacillus clausii UBBC-07, Cytokines, Gut microbiome, IBD, Probiotic",Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Treatment,EFO:0000727,Placebo group before intervention/treatment,Bacillus clausii UBBC-07 group after intervention/treatment,"Patients who were treated with Bacillus clausii UBBC-07 and evaluated after treatment/intervention for the effect of the probiotic on gut microbiota. Patients were of either sex, clinically diagnosed with Ulcerative Colitis or Crohn's Disease, and between 18 and 60 years.",54,54,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Results within text: Page 4, under subheading ""Metagenomic analysis.""",18 October 2023,Folakunmi,"Folakunmi,ChiomaBlessing,WikiWorks",Differentially abundant taxa in the UC patients of the Bacillus clausii UBBC-07 group post intervention/ treatment compared to placebo groups post intervention/ treatment,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales",3379134|976|200643;1783272|1239|909932|909929,Complete,ChiomaBlessing
bsdb:36199913/1/1,36199913,case-control,36199913,https://doi.org/10.2147/IJWH.S377066,NA,"Okuma K., Kono K., Otaka M., Ebara A., Odachi A., Tokuno H. , Masuyama H.",Characteristics of the Gut Microbiota in Japanese Patients with Premenstrual Syndrome,International journal of women's health,2022,"16S rRNA, Collinsella, gut microbiota, premenstrual syndrome",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Menstrual disorder,EFO:0010270,Control group,Premenstrual syndrome (PMS) group,"Participants who passed the criteria for premenstrual syndrome (PMS),",144,24,1 week,16S,123,Illumina,centered log-ratio,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,age,unchanged,NA,NA,increased,NA,increased,Signature 1,Figure 4,13 May 2025,Aleru Divine,Aleru Divine,Significant differences in the gut microbial abundance at the genus level between the PMS and control groups.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Massilimicrobiota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|572511;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|2719313;1783272|1239|186801|3085636|186803|1769710;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|186802|216572|946234;1783272|201174|84998|1643822|1643826|84111;3379134|976|200643|171549|815|909656;1783272|1239|186801|186802|216572|2591381;1783272|1239|186801|3085636|186803|2005355;1783272|1239|186801|186802|216572|1263;1783272|1239|526524|526525|128827|1924110;1783272|1239|526524|526525|128827|61170;1783272|1239|91061|186826|1300|1301,Complete,NA
bsdb:36199913/1/2,36199913,case-control,36199913,https://doi.org/10.2147/IJWH.S377066,NA,"Okuma K., Kono K., Otaka M., Ebara A., Odachi A., Tokuno H. , Masuyama H.",Characteristics of the Gut Microbiota in Japanese Patients with Premenstrual Syndrome,International journal of women's health,2022,"16S rRNA, Collinsella, gut microbiota, premenstrual syndrome",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Menstrual disorder,EFO:0010270,Control group,Premenstrual syndrome (PMS) group,"Participants who passed the criteria for premenstrual syndrome (PMS),",144,24,1 week,16S,123,Illumina,centered log-ratio,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,age,unchanged,NA,NA,increased,NA,increased,Signature 2,Figure 4,13 May 2025,Aleru Divine,Aleru Divine,Significant differences in the gut microbial abundance at the genus level between the PMS and control groups.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572|459786,Complete,NA
bsdb:36203175/1/1,36203175,case-control,36203175,10.1186/s12903-022-02480-z,https://bmcoralhealth.biomedcentral.com/articles/10.1186/s12903-022-02480-z,"Morishima S., Takeda K., Greenan S. , Maki Y.",Salivary microbiome in children with Down syndrome: a case-control study,BMC oral health,2022,"Children, Down syndrome, Microbiota, Saliva",Experiment 1,Japan,Homo sapiens,Oral cavity,UBERON:0000167,Down syndrome,EFO:0001064,Controls children with primary dentition (PD),Down Syndrome children with primary dentition (PD),Children with Down Syndrome and in the primary dentition stage (from 0.5 years to around 6 years old),12,12,1 week,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4,16 August 2023,Andre,"Andre,WikiWorks",Species-level of salivary microbiomes between children with DS and ND (PD stage),increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sicca",1783272|1239|91061|1385|539738|1378|1379;3379134|1224|28216|206351|481|482|495;1783272|201174|1760|85006|1268|32207|172042;1783272|201174|1760|85006|1268|32207|2047;3379134|1224|28216|206351|481|482|490,Complete,Folakunmi
bsdb:36203175/1/2,36203175,case-control,36203175,10.1186/s12903-022-02480-z,https://bmcoralhealth.biomedcentral.com/articles/10.1186/s12903-022-02480-z,"Morishima S., Takeda K., Greenan S. , Maki Y.",Salivary microbiome in children with Down syndrome: a case-control study,BMC oral health,2022,"Children, Down syndrome, Microbiota, Saliva",Experiment 1,Japan,Homo sapiens,Oral cavity,UBERON:0000167,Down syndrome,EFO:0001064,Controls children with primary dentition (PD),Down Syndrome children with primary dentition (PD),Children with Down Syndrome and in the primary dentition stage (from 0.5 years to around 6 years old),12,12,1 week,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4,16 August 2023,Andre,"Andre,WikiWorks",Species-level of salivary microbiomes between children with DS and ND (PD stage),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sputorum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral strain T1-E5,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus genomosp. C5,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum",3379134|1224|1236|135625|712|724|1078480;1783272|201174|1760|2037|2049|1654|29317;1783272|1239|91061|186826|1300|1301|113107;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|91061|186826|1300|1301|68892;1783272|1239|91061|186826|1300|1301|163599;1783272|1239|91061|186826|1300|1301|230122;3384189|32066|203490|203491|203492|848|860,Complete,Folakunmi
bsdb:36203175/2/1,36203175,case-control,36203175,10.1186/s12903-022-02480-z,https://bmcoralhealth.biomedcentral.com/articles/10.1186/s12903-022-02480-z,"Morishima S., Takeda K., Greenan S. , Maki Y.",Salivary microbiome in children with Down syndrome: a case-control study,BMC oral health,2022,"Children, Down syndrome, Microbiota, Saliva",Experiment 2,Japan,Homo sapiens,Oral cavity,UBERON:0000167,Down syndrome,EFO:0001064,Controls children with mixed dentition (PD),Down Syndrome children with mixed dentition (PD),Children with Down Syndrome and in the mixed dentition stage (from 6 years to around 12 years old),15,15,1 week,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 5,16 August 2023,Andre,"Andre,WikiWorks",Species level of salivary microbiomes between children with DS and ND (MD stage),increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces viscosus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis",1783272|1239|91061|1385|539738|1378|1379;1783272|1239|91061|186826|186827|46123|46125;1783272|1239|91061|186826|1300|1301|1305;1783272|1239|91061|186826|1300|1301|1313;1783272|1239|91061|186826|1300|1301|45634;1783272|201174|1760|85006|1268|32207|172042;3379134|1224|28216|80840|119060|47670|47671;1783272|201174|1760|85007|1653|1716|61592;1783272|201174|1760|85006|1268|32207|2047;1783272|201174|1760|2037|2049|1654|1655;3379134|1224|28216|206351|481|482|495;1783272|201174|1760|2037|2049|1654|544580;3384189|32066|203490|203491|1129771|32067|104608;1783272|201174|1760|2037|2049|1654|1656;3379134|1224|1236|135625|712|416916|739,Complete,Folakunmi
bsdb:36203175/2/2,36203175,case-control,36203175,10.1186/s12903-022-02480-z,https://bmcoralhealth.biomedcentral.com/articles/10.1186/s12903-022-02480-z,"Morishima S., Takeda K., Greenan S. , Maki Y.",Salivary microbiome in children with Down syndrome: a case-control study,BMC oral health,2022,"Children, Down syndrome, Microbiota, Saliva",Experiment 2,Japan,Homo sapiens,Oral cavity,UBERON:0000167,Down syndrome,EFO:0001064,Controls children with mixed dentition (PD),Down Syndrome children with mixed dentition (PD),Children with Down Syndrome and in the mixed dentition stage (from 6 years to around 12 years old),15,15,1 week,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 5,16 August 2023,Andre,"Andre,WikiWorks",Species-level of salivary microbiomes between children with DS and ND (MD stage),decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral strain Hal-1065,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 306,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 352,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral clone IK062,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. ICM47,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia meyeri,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. ICM39,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp. oral taxon 158,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CD3:34,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius",1783272|201174|1760|2037|2049|1654|163586;3379134|976|200643|171549|171552|838|712461;95818|713054;1783272|1239|526524|526525|128827|123375|102148;3379134|976|200643|171549|171552|838|242672;3379134|976|200643|171549|171552|838|60133;1783272|201174|1760|2037|2049|1654|936548;3379134|976|200643|171549|171552|838|470565;3379134|976|200643|171549|171552|2974257|425941;1783272|201174|1760|2037|2049|1654|29317;1783272|201174|1760|2037|2049|2529408|52773;1783272|201174|1760|2037|2049|1654|1105029;1783272|201174|1760|2037|2049|1654|55565;1783272|1239|909932|1843489|31977|29465|671228;1783272|1239|91061|1385|539738|1378|84135;3379134|976|200643|171549|171552|838|1177577;1783272|1239|91061|186826|1300|1301|1304,Complete,Folakunmi
bsdb:36209079/1/1,36209079,case-control,36209079,doi: 10.1186/s12967-022-03669-0.,https://pubmed.ncbi.nlm.nih.gov/36209079/,"Zhao L., Wang C., Peng S., Zhu X., Zhang Z., Zhao Y., Zhang J., Zhao G., Zhang T., Heng X. , Zhang L.",Pivotal interplays between fecal metabolome and gut microbiome reveal functional signatures in cerebral ischemic stroke,Journal of translational medicine,2022,"Gut microbiota, Integrative analysis, Ischemic stroke, Metabolomics, Microbiome",Experiment 1,China,Homo sapiens,"Feces,Urine,Blood plasma","UBERON:0001988,UBERON:0001088,UBERON:0001969",Stroke,EFO:0000712,Healthy individuals,Cerebral ischemic stroke patients,Patients diagnosed with ischemic stroke by skull computed tomography examination who have not experienced any pre-existing metabolic or gut diseases.,30,60,1 month,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure. 6,15 March 2024,Adeoyo Olajumoke,"Adeoyo Olajumoke,WikiWorks",Significantly different abundant taxa with LDA score (log10) > 2.0 and P < 0.05,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Acetobacter|s__Acetobacter sp. CAG:267,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum|s__Azospirillum sp. CAG:239,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides oleiciplenus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:1024,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:226,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:715,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Coraliomargaritaceae|g__Coraliomargarita|s__Coraliomargarita sp. CAG:312,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp. CAG:105,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium limosum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. CAG:241,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. ER4,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:488,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Acetobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Puniceicoccaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Coraliomargaritaceae|g__Coraliomargarita,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales",3379134|1224|28211|3120395|433|434|1262684;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759|1288121;3379134|976|200643|171549|171550|239759|328814;3379134|1224|28211|204441|2829815|191|1262705;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|626931;1783272|1239|186801|186802|31979|1485|1262770;1783272|1239|186801|186802|31979|1485|1262781;1783272|1239|186801|186802|31979|1485|1262834;3379134|74201|414999|415001|3056371|442430|1262865;3379134|200940|3031449|213115|194924|872|901;1783272|1239|186801|3085636|186803|189330|1262872;1783272|1239|186801|186802|186806|1730|1736;3379134|976|200643|171549|171552|2974265|363265;3379134|976|200643|171549|1853231|283168|28118;1783272|1239|186801|186802|216572|459786|1262911;1783272|1239|186801|186802|216572|459786|1519439;3379134|976|200643|171549|171552|838|419005;1783272|1239|186801|186802|216572|1263|1262959;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|2485925;3379134|1224|28211;3379134|1224|28211|3120395|433|434;1783272|201174|84998|84999|84107;3379134|976|200643|171549|1853231|283168;1783272|201174|84998|84999|84107|102106;3379134|200940|3031449|213115|194924|872;3379134|74201|414999;3379134|74201|414999|415001|415002;3379134|74201|414999|415001;3379134|74201|414999|415001|3056371|442430;3379134|1224|1236|135625|712;3379134|1224|1236|135625,Complete,Peace Sandy
bsdb:36209079/1/2,36209079,case-control,36209079,doi: 10.1186/s12967-022-03669-0.,https://pubmed.ncbi.nlm.nih.gov/36209079/,"Zhao L., Wang C., Peng S., Zhu X., Zhang Z., Zhao Y., Zhang J., Zhao G., Zhang T., Heng X. , Zhang L.",Pivotal interplays between fecal metabolome and gut microbiome reveal functional signatures in cerebral ischemic stroke,Journal of translational medicine,2022,"Gut microbiota, Integrative analysis, Ischemic stroke, Metabolomics, Microbiome",Experiment 1,China,Homo sapiens,"Feces,Urine,Blood plasma","UBERON:0001988,UBERON:0001088,UBERON:0001969",Stroke,EFO:0000712,Healthy individuals,Cerebral ischemic stroke patients,Patients diagnosed with ischemic stroke by skull computed tomography examination who have not experienced any pre-existing metabolic or gut diseases.,30,60,1 month,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Figure. 6,15 March 2024,Adeoyo Olajumoke,"Adeoyo Olajumoke,WikiWorks",Significantly different abundant taxa with LDA score (log10) > 2.0 and P < 0.05,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Acetobacter|s__Acetobacter sp. CAG:977,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum|s__Azospirillum sp. CAG:260,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caecimuris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:841,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae",3379134|1224|28211|3120395|433|434|1262685;3379134|1224|28211|204441|2829815|191;3379134|1224|28211|204441|2829815|191|1262706;3379134|976|200643|171549|815|816|1796613;3379134|976|200643|171549|2005519|397864|487174;1783272|1239|186801|186802|186806|1730|1262894;3379134|1224|28211|204441|41295,Complete,Peace Sandy
bsdb:36212420/1/1,36212420,"cross-sectional observational, not case-control",36212420,https://doi.org/10.3389/fonc.2022.955313,https://www.frontiersin.org/journals/oncology/articles/10.3389/fonc.2022.955313/full,"Chen Y.C., Chuang C.H., Miao Z.F., Yip K.L., Liu C.J., Li L.H., Wu D.C., Cheng T.L., Lin C.Y. , Wang J.Y.",Gut microbiota composition in chemotherapy and targeted therapy of patients with metastatic colorectal cancer,Frontiers in oncology,2022,"Bifidobacterium species, Fusobacterium nucleatum, Klebsiella quasipneumoniae, Lactobacillus species, metastatic colorectal cancer, targeted therapy",Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,Metastatic colorectal cancer,EFO:1001480,Partial response group- PR,Progressive disease group- PD,Patients who had a progressive disease (PD) for at least 12 cycles of therapy,31,24,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 4A,24 March 2025,Miss Lulu,Miss Lulu,Results of the log2 fold change in the disease progression and partial response groups,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella orientalis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella nakazawae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HSISS3,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus vaginalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus paracasei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella quasipneumoniae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum",1783272|1239|909932|1843489|31977|29465|2682455;1783272|1239|909932|1843489|31977|29465|2682456;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|91061|186826|1300|1301|1316412;1783272|1239|91061|186826|33958|2742598|1633;1783272|1239|91061|186826|33958|2742598|97478;1783272|1239|91061|186826|33958|2767887|1624;1783272|1239|91061|186826|33958|1578|47770;1783272|1239|91061|186826|33958|2759736|1597;3379134|1224|1236|91347|543|570|1463165;3384189|32066|203490|203491|203492|848|851;1783272|201174|1760|85004|31953|1678|1689;1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|1678|1681,Complete,Svetlana up
bsdb:36212420/1/2,36212420,"cross-sectional observational, not case-control",36212420,https://doi.org/10.3389/fonc.2022.955313,https://www.frontiersin.org/journals/oncology/articles/10.3389/fonc.2022.955313/full,"Chen Y.C., Chuang C.H., Miao Z.F., Yip K.L., Liu C.J., Li L.H., Wu D.C., Cheng T.L., Lin C.Y. , Wang J.Y.",Gut microbiota composition in chemotherapy and targeted therapy of patients with metastatic colorectal cancer,Frontiers in oncology,2022,"Bifidobacterium species, Fusobacterium nucleatum, Klebsiella quasipneumoniae, Lactobacillus species, metastatic colorectal cancer, targeted therapy",Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,Metastatic colorectal cancer,EFO:1001480,Partial response group- PR,Progressive disease group- PD,Patients who had a progressive disease (PD) for at least 12 cycles of therapy,31,24,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 4A,24 March 2025,Miss Lulu,Miss Lulu,Results of the log2 fold change in the disease progression and partial response groups,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella dentalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium sp. Marseille-Q4147,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio fairfieldensis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens",3379134|976|200643|171549|171552|838|52227;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|909932|1843488|909930|33024|2823317;3379134|1224|1236|91347|543|570|548;3384189|32066|203490|203491|203492|848|850;3379134|200940|3031449|213115|194924|872|44742;1783272|201174|84998|1643822|1643826|447020|446660,Complete,Svetlana up
bsdb:36212420/2/1,36212420,"cross-sectional observational, not case-control",36212420,https://doi.org/10.3389/fonc.2022.955313,https://www.frontiersin.org/journals/oncology/articles/10.3389/fonc.2022.955313/full,"Chen Y.C., Chuang C.H., Miao Z.F., Yip K.L., Liu C.J., Li L.H., Wu D.C., Cheng T.L., Lin C.Y. , Wang J.Y.",Gut microbiota composition in chemotherapy and targeted therapy of patients with metastatic colorectal cancer,Frontiers in oncology,2022,"Bifidobacterium species, Fusobacterium nucleatum, Klebsiella quasipneumoniae, Lactobacillus species, metastatic colorectal cancer, targeted therapy",Experiment 2,Taiwan,Homo sapiens,Feces,UBERON:0001988,Metastatic colorectal cancer,EFO:1001480,Bevacizumab-PR subgroup,Bevacizumab-PD subgroup,Patients with progressive disease (PD) who had anti-vascular endothelial growth factor (bevacizumab) subgroups.,17,18,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 4B,24 March 2025,Miss Lulu,Miss Lulu,Results of the log2 fold change in the subgroups of bevacizumab,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus avium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp. FDAARGOS_553,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus paracasei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus delbrueckii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella|s__Morganella morganii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus vaginalis",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|3085636|186803|207244|105841;1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|1678|1689;1783272|1239|91061|186826|81852|1350|33945;1783272|1239|91061|186826|81852|1350|2420313;3384189|32066|203490|203491|203492|848|851;3379134|1224|1236|135625|712|724|727;1783272|1239|91061|186826|33958|2759736|1597;1783272|1239|91061|186826|33958|1578|1584;1783272|1239|91061|186826|33958|2742598|1613;3379134|1224|1236|91347|1903414|581|582;3379134|1224|28216|80840|995019|40544|40545;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|91061|186826|33958|2742598|1633,Complete,Svetlana up
bsdb:36212420/2/2,36212420,"cross-sectional observational, not case-control",36212420,https://doi.org/10.3389/fonc.2022.955313,https://www.frontiersin.org/journals/oncology/articles/10.3389/fonc.2022.955313/full,"Chen Y.C., Chuang C.H., Miao Z.F., Yip K.L., Liu C.J., Li L.H., Wu D.C., Cheng T.L., Lin C.Y. , Wang J.Y.",Gut microbiota composition in chemotherapy and targeted therapy of patients with metastatic colorectal cancer,Frontiers in oncology,2022,"Bifidobacterium species, Fusobacterium nucleatum, Klebsiella quasipneumoniae, Lactobacillus species, metastatic colorectal cancer, targeted therapy",Experiment 2,Taiwan,Homo sapiens,Feces,UBERON:0001988,Metastatic colorectal cancer,EFO:1001480,Bevacizumab-PR subgroup,Bevacizumab-PD subgroup,Patients with progressive disease (PD) who had anti-vascular endothelial growth factor (bevacizumab) subgroups.,17,18,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 4B,24 March 2025,Miss Lulu,Miss Lulu,Results of the log2 fold change in the subgroups of bevacizumab,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella dentalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus",3379134|976|200643|171549|171552|2974251|165179;3379134|976|200643|171549|171552|838|52227;3379134|976|200643|171549|815|909656|387090,Complete,Svetlana up
bsdb:36212420/3/1,36212420,"cross-sectional observational, not case-control",36212420,https://doi.org/10.3389/fonc.2022.955313,https://www.frontiersin.org/journals/oncology/articles/10.3389/fonc.2022.955313/full,"Chen Y.C., Chuang C.H., Miao Z.F., Yip K.L., Liu C.J., Li L.H., Wu D.C., Cheng T.L., Lin C.Y. , Wang J.Y.",Gut microbiota composition in chemotherapy and targeted therapy of patients with metastatic colorectal cancer,Frontiers in oncology,2022,"Bifidobacterium species, Fusobacterium nucleatum, Klebsiella quasipneumoniae, Lactobacillus species, metastatic colorectal cancer, targeted therapy",Experiment 3,Taiwan,Homo sapiens,Feces,UBERON:0001988,Metastatic colorectal cancer,EFO:1001480,Cetuximab-PR subgroup,Cetuximab-PD subgroup,Patients with progressive disease (PD) who had anti-epidermal growth factor receptor (cetuximab) subgroups.,14,6,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4C,24 March 2025,Miss Lulu,Miss Lulu,Results of the log2 fold change in the subgroups of cetuximab,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens",1783272|1239|186801|3085636|186803|207244|105841;1783272|201174|84998|1643822|1643826|447020|446660,Complete,Svetlana up
bsdb:36216843/1/1,36216843,case-control,36216843,10.1038/s41531-022-00395-8,NA,"Boertien J.M., Murtomäki K., Pereira P.A.B., van der Zee S., Mertsalmi T.H., Levo R., Nojonen T., Mäkinen E., Jaakkola E., Laine P., Paulin L., Pekkonen E., Kaasinen V., Auvinen P., Scheperjans F. , van Laar T.",Fecal microbiome alterations in treatment-naive de novo Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's Disease subjects,"Dutch(NL) Cohort: Parkinson's disease diagnosis by a movement disorder specialist according to the Movement Disorders Society (MDS) clinical diagnostic criteria1, confirmed by a dopaminergic deficit quantified by FDOPA-PET or one-year follow-up if no FDOPA-PET was performed.",85,136,1 month,16S,4,Illumina,centered log-ratio,ANCOM,0.1,NA,NA,NA,"age,body mass index",NA,NA,increased,NA,NA,increased,Signature 1,Table 3. Differentially abundant taxa between PD and HC in NL cohort..,3 June 2023,Fcuevas3,"Fcuevas3,Atrayees,WikiWorks","Differentially abundant taxa between PD and HC detected using ANCOM.



*(A negative change indicates lower abundance in PD compared to HC)",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,3379134|976|200643|171549|171550,Complete,Atrayees
bsdb:36216843/1/2,36216843,case-control,36216843,10.1038/s41531-022-00395-8,NA,"Boertien J.M., Murtomäki K., Pereira P.A.B., van der Zee S., Mertsalmi T.H., Levo R., Nojonen T., Mäkinen E., Jaakkola E., Laine P., Paulin L., Pekkonen E., Kaasinen V., Auvinen P., Scheperjans F. , van Laar T.",Fecal microbiome alterations in treatment-naive de novo Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's Disease subjects,"Dutch(NL) Cohort: Parkinson's disease diagnosis by a movement disorder specialist according to the Movement Disorders Society (MDS) clinical diagnostic criteria1, confirmed by a dopaminergic deficit quantified by FDOPA-PET or one-year follow-up if no FDOPA-PET was performed.",85,136,1 month,16S,4,Illumina,centered log-ratio,ANCOM,0.1,NA,NA,NA,"age,body mass index",NA,NA,increased,NA,NA,increased,Signature 2,Table 3.,3 June 2023,Fcuevas3,"Fcuevas3,Atrayees,WikiWorks",Differentially abundant taxa between PD and HC detected using ANCOM.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|841;1783272|1239|909932|1843489|31977,Complete,Atrayees
bsdb:36216843/2/1,36216843,case-control,36216843,10.1038/s41531-022-00395-8,NA,"Boertien J.M., Murtomäki K., Pereira P.A.B., van der Zee S., Mertsalmi T.H., Levo R., Nojonen T., Mäkinen E., Jaakkola E., Laine P., Paulin L., Pekkonen E., Kaasinen V., Auvinen P., Scheperjans F. , van Laar T.",Fecal microbiome alterations in treatment-naive de novo Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's Disease subjects,"Finnish(FIN) Cohort: Parkinson's disease diagnosis by a movement disorder specialist according to the MDS clinical diagnostic criteria1, confirmed by a dopaminergic deficit quantified by [I-123]FP-CIT SPECT. [I-123]FP-CIT SPECT were analyzed with BRASS software (Hermes Medical Solutions AB, Stockholm, Sweden), in which a dopaminergic deficit was defined as more than two standard deviations below the reference mean in any of the six analyzed regions.",87,56,1 month,16S,4,Illumina,centered log-ratio,ANCOM,0.1,NA,NA,NA,NA,NA,decreased,decreased,NA,decreased,decreased,Signature 1,Table 3.,3 June 2023,Fcuevas3,"Fcuevas3,Atrayees,WikiWorks",Differentially abundant taxa between PD and HC detected using ANCOM,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,1783272|1239|186801|3082768|990719,Complete,Atrayees
bsdb:36216843/2/2,36216843,case-control,36216843,10.1038/s41531-022-00395-8,NA,"Boertien J.M., Murtomäki K., Pereira P.A.B., van der Zee S., Mertsalmi T.H., Levo R., Nojonen T., Mäkinen E., Jaakkola E., Laine P., Paulin L., Pekkonen E., Kaasinen V., Auvinen P., Scheperjans F. , van Laar T.",Fecal microbiome alterations in treatment-naive de novo Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's Disease subjects,"Finnish(FIN) Cohort: Parkinson's disease diagnosis by a movement disorder specialist according to the MDS clinical diagnostic criteria1, confirmed by a dopaminergic deficit quantified by [I-123]FP-CIT SPECT. [I-123]FP-CIT SPECT were analyzed with BRASS software (Hermes Medical Solutions AB, Stockholm, Sweden), in which a dopaminergic deficit was defined as more than two standard deviations below the reference mean in any of the six analyzed regions.",87,56,1 month,16S,4,Illumina,centered log-ratio,ANCOM,0.1,NA,NA,NA,NA,NA,decreased,decreased,NA,decreased,decreased,Signature 2,Table 3.,3 June 2023,Fcuevas3,"Fcuevas3,Atrayees,WikiWorks",Differentially abundant taxa between PD and HC detected using ANCOM,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium edouardi,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|3085636|186803|1506553|1926283;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|1980681;1783272|1239|186801|3085636|186803|841,Complete,Atrayees
bsdb:36216843/3/1,36216843,case-control,36216843,10.1038/s41531-022-00395-8,NA,"Boertien J.M., Murtomäki K., Pereira P.A.B., van der Zee S., Mertsalmi T.H., Levo R., Nojonen T., Mäkinen E., Jaakkola E., Laine P., Paulin L., Pekkonen E., Kaasinen V., Auvinen P., Scheperjans F. , van Laar T.",Fecal microbiome alterations in treatment-naive de novo Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 3,Netherlands,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's Disease subjects,"Dutch(NL) Cohort: Parkinson's disease diagnosis by a movement disorder specialist according to the Movement Disorders Society (MDS) clinical diagnostic criteria1, confirmed by a dopaminergic deficit quantified by FDOPA-PET or one-year follow-up if no FDOPA-PET was performed.",85,136,1 month,16S,4,Illumina,raw counts,DESeq2,0.1,NA,NA,NA,"age,body mass index",NA,NA,increased,NA,NA,increased,Signature 1,Table 3.,3 June 2023,Fcuevas3,"Fcuevas3,Atrayees,WikiWorks",Differentially abundant taxa between PD and HC detected using DESeq2.,decreased,k__Bacillati|p__Bacillota|c__Clostridia,1783272|1239|186801,Complete,Atrayees
bsdb:36216843/4/1,36216843,case-control,36216843,10.1038/s41531-022-00395-8,NA,"Boertien J.M., Murtomäki K., Pereira P.A.B., van der Zee S., Mertsalmi T.H., Levo R., Nojonen T., Mäkinen E., Jaakkola E., Laine P., Paulin L., Pekkonen E., Kaasinen V., Auvinen P., Scheperjans F. , van Laar T.",Fecal microbiome alterations in treatment-naive de novo Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 4,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's Disease subjects,"Finnish(FIN) Cohort: Parkinson's disease diagnosis by a movement disorder specialist according to the MDS clinical diagnostic criteria1, confirmed by a dopaminergic deficit quantified by [I-123]FP-CIT SPECT. [I-123]FP-CIT SPECT were analyzed with BRASS software (Hermes Medical Solutions AB, Stockholm, Sweden), in which a dopaminergic deficit was defined as more than two standard deviations below the reference mean in any of the six analyzed regions.",87,56,1 month,16S,4,Illumina,raw counts,DESeq2,0.1,NA,NA,NA,NA,NA,decreased,decreased,NA,decreased,decreased,Signature 1,Table 3.,3 June 2023,Fcuevas3,"Fcuevas3,Atrayees,WikiWorks",Differentially abundant taxa between PD and HC detected using DESeq2.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae",3379134|74201|203494|48461|1647988;1783272|201174|84998|1643822|1643826,Complete,Atrayees
bsdb:36216843/4/2,36216843,case-control,36216843,10.1038/s41531-022-00395-8,NA,"Boertien J.M., Murtomäki K., Pereira P.A.B., van der Zee S., Mertsalmi T.H., Levo R., Nojonen T., Mäkinen E., Jaakkola E., Laine P., Paulin L., Pekkonen E., Kaasinen V., Auvinen P., Scheperjans F. , van Laar T.",Fecal microbiome alterations in treatment-naive de novo Parkinson's disease,NPJ Parkinson's disease,2022,NA,Experiment 4,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's Disease subjects,"Finnish(FIN) Cohort: Parkinson's disease diagnosis by a movement disorder specialist according to the MDS clinical diagnostic criteria1, confirmed by a dopaminergic deficit quantified by [I-123]FP-CIT SPECT. [I-123]FP-CIT SPECT were analyzed with BRASS software (Hermes Medical Solutions AB, Stockholm, Sweden), in which a dopaminergic deficit was defined as more than two standard deviations below the reference mean in any of the six analyzed regions.",87,56,1 month,16S,4,Illumina,raw counts,DESeq2,0.1,NA,NA,NA,NA,NA,decreased,decreased,NA,decreased,decreased,Signature 2,Table 3.,3 June 2023,Fcuevas3,"Fcuevas3,Atrayees,WikiWorks",Differentially abundant taxa between PD and HC detected using DESeq2.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae",1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|3085642|580596;1783272|544448|31969|186329|2146,Complete,Atrayees
bsdb:36220843/1/1,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 1,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Neurotypical (NT) children,Autism Spectrum Disorder (ASD) children,"Children diagnosed with Autism spectrum disorder (ASD) (all datasets pooled, no adjustment for bowel function, age, or sex).",13,13,NA,WMS,NA,Illumina,raw counts,Mixed-Effects Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,24 March 2025,ChiomaBlessing,"ChiomaBlessing,Ese","Results of effect sizes and q-values from random-effects models (meta-analysis) comparing Autism Spectrum Disorder (ASD) children (negative direction) with Neurotypical (NT) children (positive direction) at different taxonomic levels (all datasets pooled, no adjustment for bowel function, age, or sex).",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter towneri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Roseomonadaceae|g__Roseomonas",3379134|1224|1236|2887326|468|469|202956;3379134|1224|1236|135625|712|416916|739;3379134|1224|28216|80840|80864|80865;3379134|1224|28211|3120395|3385906|125216,Complete,NA
bsdb:36220843/1/2,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 1,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Neurotypical (NT) children,Autism Spectrum Disorder (ASD) children,"Children diagnosed with Autism spectrum disorder (ASD) (all datasets pooled, no adjustment for bowel function, age, or sex).",13,13,NA,WMS,NA,Illumina,raw counts,Mixed-Effects Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,6 September 2025,Ese,Ese,"Results of effect sizes and q-values from random-effects models (meta-analysis) comparing Autism Spectrum Disorder (ASD) children (negative direction) with Neurotypical (NT) children (positive direction) at different taxonomic levels (all datasets pooled, no adjustment for bowel function, age, or sex).",decreased,NA,NA,Complete,NA
bsdb:36220843/2/1,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 2,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Neurotypical (NT) children,Autism Spectrum Disorder (ASD) children,"Children diagnosed with Autism spectrum disorder (ASD) (all datasets pooled, no adjustment for bowel function, age, or sex).",13,13,NA,16S,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S4,6 September 2025,Ese,Ese,"Result of strain level meta-analysis comparing Neurotypical (NT) children and Autism Spectrum Disorder (ASD) children (all datasets pooled, no adjustment for bowel function, age, or sex).",increased,NA,NA,Complete,NA
bsdb:36220843/2/2,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 2,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Neurotypical (NT) children,Autism Spectrum Disorder (ASD) children,"Children diagnosed with Autism spectrum disorder (ASD) (all datasets pooled, no adjustment for bowel function, age, or sex).",13,13,NA,16S,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S4,11 September 2025,Ese,Ese,"Result of strain level meta-analysis comparing Neurotypical (NT) children and Autism Spectrum Disorder (ASD) children (all datasets pooled, no adjustment for bowel function, age, or sex).",decreased,NA,NA,Complete,NA
bsdb:36220843/3/1,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 3,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Neurotypical (NT) children with normal bowel function,Autism Spectrum Disorder (ASD) children with normal bowel function,"Children diagnosed with Autism Spectrum Disorder (ASD), excluding those experiencing gastrointestinal symptoms such as constipation or diarrhea.",6,6,NA,WMS,NA,Illumina,raw counts,Mixed-Effects Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4 (right panel) & Figure S7,16 September 2025,Ese,Ese,Bacterial taxa significantly associated with Neurotypical (NT) children with normal bowel function and Autism Spectrum Disorder (ASD) children with normal bowel function by meta-analysis,increased,NA,NA,Complete,NA
bsdb:36220843/3/2,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 3,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Neurotypical (NT) children with normal bowel function,Autism Spectrum Disorder (ASD) children with normal bowel function,"Children diagnosed with Autism Spectrum Disorder (ASD), excluding those experiencing gastrointestinal symptoms such as constipation or diarrhea.",6,6,NA,WMS,NA,Illumina,raw counts,Mixed-Effects Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4 (right panel) & Figure S7,16 September 2025,Ese,Ese,Bacterial taxa significantly associated with Neurotypical (NT) children with normal bowel function and Autism Spectrum Disorder (ASD) children with normal bowel function by meta-analysis,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Massilioclostridium|s__Massilioclostridium coli",1783272|1239|91061|186826|186828|117563|137732;1783272|1239|186801|186802|31979|1935927|1870991,Complete,NA
bsdb:36220843/4/1,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 4,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Neurotypical (NT) children with bowel dysfunction,Autism Spectrum Disorder (ASD) children with bowel dysfunction,"Children diagnosed with Autism Spectrum Disorder (ASD), including those experiencing gastrointestinal symptoms such as constipation or diarrhea",6,4,NA,WMS,NA,Illumina,raw counts,Mixed-Effects Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4 (left panel),16 September 2025,Ese,Ese,Bacterial taxa significantly associated with Neurotypical (NT) children with bowel dysfunction and Autism Spectrum Disorder (ASD) children with bowel dysfunction by meta-analysis,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter towneri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Roseomonadaceae|g__Roseomonas",3379134|1224|1236|2887326|468|469|202956;3379134|1224|1236|135625|712|416916;1783272|201174|1760|85006|85020|43668;3379134|1224|28216|80840|80864|80865;1783272|201174|1760|85006|85020;3379134|1224|28211|3120395|3385906|125216,Complete,NA
bsdb:36220843/4/2,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 4,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Neurotypical (NT) children with bowel dysfunction,Autism Spectrum Disorder (ASD) children with bowel dysfunction,"Children diagnosed with Autism Spectrum Disorder (ASD), including those experiencing gastrointestinal symptoms such as constipation or diarrhea",6,4,NA,WMS,NA,Illumina,raw counts,Mixed-Effects Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4 (left panel),16 September 2025,Ese,Ese,Bacterial taxa significantly associated with Neurotypical (NT) children with bowel dysfunction and Autism Spectrum Disorder (ASD) children with bowel dysfunction by meta-analysis,decreased,NA,NA,Complete,NA
bsdb:36220843/5/1,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 5,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Autism Spectrum Disorder (ASD) children with constipation,Autism Spectrum Disorder (ASD) children with diarrhea,"Children diagnosed with Autism Spectrum Disorder (ASD), including those experiencing diarrhea",4,4,NA,16S,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,17 September 2025,Ese,Ese,Result of strain level meta-analysis comparing Autism Spectrum Disorder (ASD) children with constipation (positive direction) and Autism Spectrum Disorder (ASD) children with diarrhea (negative direction),increased,NA,NA,Complete,NA
bsdb:36220843/5/2,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 5,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Autism Spectrum Disorder (ASD) children with constipation,Autism Spectrum Disorder (ASD) children with diarrhea,"Children diagnosed with Autism Spectrum Disorder (ASD), including those experiencing diarrhea",4,4,NA,16S,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S5,27 September 2025,Ese,Ese,"Result of strain level meta-analysis comparing Autism Spectrum Disorder (ASD) children with constipation and Autism Spectrum Disorder (ASD) children with diarrhea (ASD constipation-positive direction, ASD diarrhea-negative direction)",decreased,NA,NA,Complete,NA
bsdb:36220843/6/1,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 6,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Autism Spectrum Disorder (ASD) children with constipation,Autism Spectrum Disorder (ASD) children with diarrhea,"Children diagnosed with Autism Spectrum Disorder (ASD), including those experiencing diarrhea",4,4,NA,WMS,NA,Illumina,raw counts,Mixed-Effects Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S6,29 September 2025,Ese,Ese,Results of Effect sizes and q-values from random-effects models testing associations between different taxa and Autism Spectrum Disorder (ASD) children with constipation (positive direction) or Autism Spectrum Disorder (ASD) children with diarrhea (negative direction),increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales",1783272|1239|909932|909929|1843491;1783272|1239|909932|909929,Complete,NA
bsdb:36220843/6/2,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 6,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Autism Spectrum Disorder (ASD) children with constipation,Autism Spectrum Disorder (ASD) children with diarrhea,"Children diagnosed with Autism Spectrum Disorder (ASD), including those experiencing diarrhea",4,4,NA,WMS,NA,Illumina,raw counts,Mixed-Effects Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S6,29 September 2025,Ese,Ese,Results of Effect sizes and q-values from random-effects models testing associations between different taxa and Autism Spectrum Disorder (ASD) children with constipation (positive direction) or Autism Spectrum Disorder (ASD) children with diarrhea (negative direction),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota",3379134|976|200643|171549|815|816|329854;3379134|200940|3031449|213115|194924|35832;3379134|200940|3031449|213115|194924|35832|35833;3379134|29547|3031852|213849;3379134|29547,Complete,NA
bsdb:36220843/7/1,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 7,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Childhood Neurotypical (NT),Childhood Autism Spectrum Disorder (ASD),Children aged 2–9 years diagnosed with Autism Spectrum Disorder (ASD),10,10,NA,WMS,NA,Illumina,raw counts,Mixed-Effects Regression,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5 (left panel),29 September 2025,Ese,Ese,Bacterial taxa significantly associated with childhood Neurotypical (NT) and childhood Autism Spectrum Disorder (ASD) by meta-analysis,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Verrucomicrobiota",3379134|1224|1236|135625|712;3379134|74201,Complete,NA
bsdb:36220843/7/2,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 7,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Childhood Neurotypical (NT),Childhood Autism Spectrum Disorder (ASD),Children aged 2–9 years diagnosed with Autism Spectrum Disorder (ASD),10,10,NA,WMS,NA,Illumina,raw counts,Mixed-Effects Regression,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5 (left panel),29 September 2025,Ese,Ese,Bacterial taxa significantly associated with childhood Neurotypical (NT) and childhood Autism Spectrum Disorder (ASD) by meta-analysis,decreased,NA,NA,Complete,NA
bsdb:36220843/8/1,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 8,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Childhood Neurotypical (NT),Childhood Autism Spectrum Disorder (ASD),Children aged 2–9 years diagnosed with Autism Spectrum Disorder (ASD),10,10,NA,16S,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,age,age,NA,NA,NA,NA,NA,NA,Signature 1,Table S6,30 September 2025,Ese,Ese,Result of strain level meta- analysis comparing Neurotypical (NT) children (2-9 years old) and Autism Spectrum Disorder (ASD) children (2-9 years old),increased,NA,NA,Complete,NA
bsdb:36220843/8/2,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 8,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Childhood Neurotypical (NT),Childhood Autism Spectrum Disorder (ASD),Children aged 2–9 years diagnosed with Autism Spectrum Disorder (ASD),10,10,NA,16S,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,age,age,NA,NA,NA,NA,NA,NA,Signature 2,Table S6,30 September 2025,Ese,Ese,Result of strain level meta- analysis comparing Neurotypical (NT) children (2-9 years old) and Autism Spectrum Disorder (ASD) children (2-9 years old),decreased,NA,NA,Complete,NA
bsdb:36220843/9/1,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 9,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Adolescence Neurotypical (NT),Adolescence Autism Spectrum disorder (ASD),Adolescents aged 10-17 years diagnosed with Autism Spectrum Disorder (ASD),10,10,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5 (right panel),2 October 2025,Ese,Ese,Bacterial taxa significantly associated with adolescence Neurotypical (NT) and adolescence Autism Spectrum Disorder (ASD) by meta- analysis,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella hongkongensis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae",3379134|976|200643|171549|815|816|329854;1783272|201174|1760|85004|31953|1678|1685;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|3082768|990719|990721|270498;1783272|1239|526524|526525|128827|61170;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|2005525,Complete,NA
bsdb:36220843/9/2,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 9,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Adolescence Neurotypical (NT),Adolescence Autism Spectrum disorder (ASD),Adolescents aged 10-17 years diagnosed with Autism Spectrum Disorder (ASD),10,10,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5 (right panel),2 October 2025,Ese,Ese,Bacterial taxa significantly associated with adolescence Neurotypical (NT) and adolescence Autism Spectrum Disorder (ASD) by meta-analysis,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Massiliimalia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Massilioclostridium|s__Massilioclostridium coli",1783272|1239|186801|3085636|186803|1766253;1783272|1239|91061|186826|186828|117563|137732;1783272|1239|186801|186802|216572|2895461;1783272|1239|186801|186802|31979|1935927|1870991,Complete,NA
bsdb:36220843/10/1,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 10,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Autism Spectrum Disorder (ASD) female,Autism Spectrum Disorder (ASD) male,Males diagnosed with Autism Spectrum Disorder (ASD),10,10,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,sex,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6a(left panel),3 October 2025,Ese,Ese,"Result of effect sizes and q-values from random-effects models investigating the associations between different taxa and sex (female: positive direction, male: negative direction)",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977,Complete,NA
bsdb:36220843/11/1,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 11,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Autism Spectrum Disorder (ASD) female,Autism Spectrum Disorder (ASD) male,Males diagnosed with Autism Spectrum Disorder (ASD),10,10,NA,16S,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,sex,sex,NA,NA,NA,NA,NA,NA,Signature 1,Table S7,3 October 2025,Ese,Ese,"Result of strain level meta-analysis comparing Autism Spectrum Disorder (ASD) female and Autism Spectrum Disorder (ASD) male (ASD female: positive direction, ASD male: negative direction)",increased,NA,NA,Complete,NA
bsdb:36220843/11/2,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 11,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Autism Spectrum Disorder (ASD) female,Autism Spectrum Disorder (ASD) male,Males diagnosed with Autism Spectrum Disorder (ASD),10,10,NA,16S,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,sex,sex,NA,NA,NA,NA,NA,NA,Signature 2,Table S7,3 October 2025,Ese,Ese,"Result of strain level meta-analysis comparing Autism Spectrum Disorder (ASD) female and Autism Spectrum Disorder (ASD) male (ASD female: positive direction, ASD male: negative direction)",decreased,NA,NA,Complete,NA
bsdb:36220843/12/1,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 12,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Neurotypical (NT) female,Neurotypical (NT) male,Males whose brains develop and function in ways considered typical or average for their age without specific neurological conditions like Autism Spectrum Disorder (ASD),10,10,NA,WMS,NA,Illumina,raw counts,Mixed-Effects Regression,0.05,TRUE,NA,sex,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6a (right panel),5 October 2025,Ese,Ese,"Results of effect sizes and q-values from random-effects models investigating the associations between different taxa and sex (female NT: positive direction, male NT: negative direction)",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae",3379134|976|200643|171549|2005519|1348911;3379134|976|200643|171549|2005519|1348911|1099853;1783272|201174|84998|1643822|1643826|84111;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|3085636|186803|1769710;1783272|1239|186801|3085636|186803|1769710|1653434;3379134|976|200643|171549|2005519,Complete,NA
bsdb:36220843/12/2,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 12,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Neurotypical (NT) female,Neurotypical (NT) male,Males whose brains develop and function in ways considered typical or average for their age without specific neurological conditions like Autism Spectrum Disorder (ASD),10,10,NA,WMS,NA,Illumina,raw counts,Mixed-Effects Regression,0.05,TRUE,NA,sex,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6a (right panel),5 October 2025,Ese,Ese,"Results of effect sizes and q-values from random-effects models investigating the associations between different taxa and sex (female NT: positive direction, male NT: negative direction)",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum lactatifermentans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae",1783272|1239|186801|3085636|3118652|2039240|160404;1783272|1239|186801|3085636|186803|1432051;1783272|201174|84998|84999|1643824,Complete,NA
bsdb:36220843/13/1,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 13,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Neurotypical (NT) female,Neurotypical (NT) male,Males whose brains develop and function in ways considered typical or average for their age without specific neurological conditions like Autism Spectrum Disorder (ASD),10,10,NA,16S,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,sex,sex,NA,NA,NA,NA,NA,NA,Signature 1,Table S7,5 October 2025,Ese,Ese,"Results of strain level meta-analysis comparing Neurotypical (NT) female and Neurotypical (NT) male (NT female: positive direction, NT male: negative direction)",increased,NA,NA,Complete,NA
bsdb:36220843/13/2,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 13,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Neurotypical (NT) female,Neurotypical (NT) male,Males whose brains develop and function in ways considered typical or average for their age without specific neurological conditions like Autism Spectrum Disorder (ASD),10,10,NA,16S,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,sex,sex,NA,NA,NA,NA,NA,NA,Signature 2,Table S7,27 October 2025,Ese,Ese,"Results of strain level meta-analysis comparing Neurotypical (NT) female and Neurotypical (NT) male (NT female: positive direction, NT male: negative direction)",decreased,NA,NA,Complete,NA
bsdb:36220843/14/1,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 14,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,female Neurotypical (NT),female Autism Spectrum Disorder (ASD),Females diagnosed with Autism Spectrum Disorder (ASD),10,10,NA,WMS,NA,Illumina,raw counts,Mixed-Effects Regression,0.05,TRUE,NA,sex,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6b (left panel),29 October 2025,Ese,Ese,"Results of models investigating ASD-associated taxa between female neurotypical (NT) and female Autism Spectrum Disorder (ASD) (Female NT: positive direction, Female ASD: negative direction)",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",1783272|1239|91061|186826|1300|1357;3379134|976|200643|171549|2005473,Complete,NA
bsdb:36220843/15/1,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 15,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,female Neurotypical (NT),female Autism Spectrum Disorder (ASD),Females diagnosed with Autism Spectrum Disorder (ASD),10,10,NA,16S,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,sex,sex,NA,NA,NA,NA,NA,NA,Signature 1,Table S7,29 October 2025,Ese,Ese,Results of strain level meta-analysis comparing female neurotypical (NT) and female Autism Spectrum Disorder (ASD) (female NT: positive direction; female ASD: negative direction),increased,NA,NA,Complete,NA
bsdb:36220843/15/2,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 15,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,female Neurotypical (NT),female Autism Spectrum Disorder (ASD),Females diagnosed with Autism Spectrum Disorder (ASD),10,10,NA,16S,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,sex,sex,NA,NA,NA,NA,NA,NA,Signature 2,Table S7,31 October 2025,Ese,Ese,Results of strain level meta-analysis comparing female neurotypical (NT) and female Autism Spectrum Disorder (ASD) (female NT: positive direction; female ASD: negative direction),decreased,NA,NA,Complete,NA
bsdb:36220843/16/1,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 16,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,male Neurotypical (NT),male Autism Spectrum Disorder (ASD),Males diagnosed with Autism Spectrum Disorder (ASD),10,10,NA,WMS,NA,Illumina,raw counts,Mixed-Effects Regression,0.05,TRUE,NA,sex,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6b (right panel),1 November 2025,Ese,Ese,"Results of models investigating ASD-associated taxa between male neurotypical (NT) and male Autism Spectrum Disorder (ASD) (male NT: positive direction, male ASD: negative direction)",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Lawsonibacter",1783272|1239|186801|186802|216572|1940255;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|1432051;1783272|201174|1760|85004|31953|1678|1680;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|186802|216572|2172004,Complete,NA
bsdb:36220843/16/2,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 16,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,male Neurotypical (NT),male Autism Spectrum Disorder (ASD),Males diagnosed with Autism Spectrum Disorder (ASD),10,10,NA,WMS,NA,Illumina,raw counts,Mixed-Effects Regression,0.05,TRUE,NA,sex,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6b (right panel),1 November 2025,Ese,Ese,"Results of models investigating ASD-associated taxa between male neurotypical (NT) and male Autism Spectrum Disorder (ASD) (male NT: positive direction, male ASD: negative direction)",decreased,NA,NA,Complete,NA
bsdb:36220843/17/1,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 17,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,male Neurotypical (NT),male Autism Spectrum Disorder (ASD),Males diagnosed with Autism Spectrum Disorder (ASD),10,10,NA,16S,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,sex,sex,NA,NA,NA,NA,NA,NA,Signature 1,Table S7,1 November 2025,Ese,Ese,Results of strain level meta-analysis comparing male neurotypical (NT) and male Autism Spectrum Disorder (ASD) (male NT: positive direction; male ASD: negative direction),increased,NA,NA,Complete,NA
bsdb:36220843/17/2,36220843,meta-analysis,36220843,10.1038/s41598-022-21327-9,NA,"West K.A., Yin X., Rutherford E.M., Wee B., Choi J., Chrisman B.S., Dunlap K.L., Hannibal R.L., Hartono W., Lin M., Raack E., Sabino K., Wu Y., Wall D.P., David M.M., Dabbagh K., DeSantis T.Z. , Iwai S.",Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups,Scientific reports,2022,NA,Experiment 17,"Canada,China,India,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,male Neurotypical (NT),male Autism Spectrum Disorder (ASD),Males diagnosed with Autism Spectrum Disorder (ASD),10,10,NA,16S,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,sex,sex,NA,NA,NA,NA,NA,NA,Signature 2,Table S7,1 November 2025,Ese,Ese,Results of strain level meta-analysis comparing male neurotypical (NT) and male Autism Spectrum Disorder (ASD) (male NT: positive direction; male ASD: negative direction),decreased,NA,NA,Complete,NA
bsdb:36228569/1/1,36228569,randomized controlled trial,36228569,10.1016/j.clnu.2022.09.012,NA,"Aljumaah M.R., Bhatia U., Roach J., Gunstad J. , Azcarate Peril M.A.","The gut microbiome, mild cognitive impairment, and probiotics: A randomized clinical trial in middle-aged and older adults","Clinical nutrition (Edinburgh, Scotland)",2022,"Cogitative aging, Gut microbiome, Lactobacillus rhamnosus GG, Prevotella, Psychobiotics",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Cognitively Intact Group,Cognitively Impaired Group,This group consists of 23 patients with cognitive impairment.,60,23,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 2C,1 August 2024,JoyceQ,"JoyceQ,Victoria,WikiWorks","Cladogram and linear discriminant analysis of effect size (Lefse) showing
biomarker taxa associated with cognitively intact and impaired individuals. The Lefse analysis included non-probiotic groups only.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,s__uncultured organism",3379134|976|200643|171549|815|909656|310298;3379134|976|200643|171549|815|909656|204516;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|74201;3379134|976|200643|171549|171552|838;155900,Complete,Svetlana up
bsdb:36228569/1/2,36228569,randomized controlled trial,36228569,10.1016/j.clnu.2022.09.012,NA,"Aljumaah M.R., Bhatia U., Roach J., Gunstad J. , Azcarate Peril M.A.","The gut microbiome, mild cognitive impairment, and probiotics: A randomized clinical trial in middle-aged and older adults","Clinical nutrition (Edinburgh, Scotland)",2022,"Cogitative aging, Gut microbiome, Lactobacillus rhamnosus GG, Prevotella, Psychobiotics",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Cognitively Intact Group,Cognitively Impaired Group,This group consists of 23 patients with cognitive impairment.,60,23,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 2C,2 August 2024,JoyceQ,"JoyceQ,Rahila,Victoria,WikiWorks",Cladogram and linear discriminant analysis of effect size (Lefse) showing biomarker taxa associated with cognitively intact and impaired individuals. The Lefse analysis included non-probiotic groups only.,decreased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus",3379134|1224;3379134|976|200643|171549|815|909656|821,Complete,Svetlana up
bsdb:36228569/2/1,36228569,randomized controlled trial,36228569,10.1016/j.clnu.2022.09.012,NA,"Aljumaah M.R., Bhatia U., Roach J., Gunstad J. , Azcarate Peril M.A.","The gut microbiome, mild cognitive impairment, and probiotics: A randomized clinical trial in middle-aged and older adults","Clinical nutrition (Edinburgh, Scotland)",2022,"Cogitative aging, Gut microbiome, Lactobacillus rhamnosus GG, Prevotella, Psychobiotics",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Baseline Group,Placebo Group,"Patients in this group received two Culturelle Placebo Veggie capsules containing microcrystalline cellulose, which the gut microbiota cannot ferment.",169,83,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 5D,23 October 2024,Victoria,"Victoria,WikiWorks,Tosin",Cladogram and Linear Discriminant Analysis of effect size (Lefse) showing biomarker taxa for each group.,increased,"s__uncultured organism,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",155900;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Svetlana up
bsdb:36228569/2/2,36228569,randomized controlled trial,36228569,10.1016/j.clnu.2022.09.012,NA,"Aljumaah M.R., Bhatia U., Roach J., Gunstad J. , Azcarate Peril M.A.","The gut microbiome, mild cognitive impairment, and probiotics: A randomized clinical trial in middle-aged and older adults","Clinical nutrition (Edinburgh, Scotland)",2022,"Cogitative aging, Gut microbiome, Lactobacillus rhamnosus GG, Prevotella, Psychobiotics",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Baseline Group,Placebo Group,"Patients in this group received two Culturelle Placebo Veggie capsules containing microcrystalline cellulose, which the gut microbiota cannot ferment.",169,83,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 5D,23 October 2024,Victoria,"Victoria,WikiWorks",Cladogram and Linear Discriminant Analysis of effect size (Lefse) showing biomarker taxa for each group.,decreased,NA,NA,Complete,Svetlana up
bsdb:36228569/3/1,36228569,randomized controlled trial,36228569,10.1016/j.clnu.2022.09.012,NA,"Aljumaah M.R., Bhatia U., Roach J., Gunstad J. , Azcarate Peril M.A.","The gut microbiome, mild cognitive impairment, and probiotics: A randomized clinical trial in middle-aged and older adults","Clinical nutrition (Edinburgh, Scotland)",2022,"Cogitative aging, Gut microbiome, Lactobacillus rhamnosus GG, Prevotella, Psychobiotics",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Baseline Group,Probiotic Group,Patients in this group received an LGG supplement in the form of two Culturelle Vegetarian Capsules containing a 10 billion CFU blend of L. rhamnosus GG and 200mg prebiotic inulin from chicory root extract.,169,86,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 5D,23 October 2024,Victoria,"Victoria,WikiWorks",Cladogram and Linear Discriminant Analysis of effect size (Lefse) showing biomarker taxa for each group.,increased,"s__uncultured bacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,s__unidentified,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium",77133;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958;32644;1783272|1239|186801|3082720|543314|86331,Complete,Svetlana up
bsdb:36228569/3/2,36228569,randomized controlled trial,36228569,10.1016/j.clnu.2022.09.012,NA,"Aljumaah M.R., Bhatia U., Roach J., Gunstad J. , Azcarate Peril M.A.","The gut microbiome, mild cognitive impairment, and probiotics: A randomized clinical trial in middle-aged and older adults","Clinical nutrition (Edinburgh, Scotland)",2022,"Cogitative aging, Gut microbiome, Lactobacillus rhamnosus GG, Prevotella, Psychobiotics",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Baseline Group,Probiotic Group,Patients in this group received an LGG supplement in the form of two Culturelle Vegetarian Capsules containing a 10 billion CFU blend of L. rhamnosus GG and 200mg prebiotic inulin from chicory root extract.,169,86,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 5D,23 October 2024,Victoria,"Victoria,WikiWorks",Cladogram and Linear Discriminant Analysis of effect size (Lefse) showing biomarker taxa for each group.,decreased,NA,NA,Complete,Svetlana up
bsdb:36228569/4/1,36228569,randomized controlled trial,36228569,10.1016/j.clnu.2022.09.012,NA,"Aljumaah M.R., Bhatia U., Roach J., Gunstad J. , Azcarate Peril M.A.","The gut microbiome, mild cognitive impairment, and probiotics: A randomized clinical trial in middle-aged and older adults","Clinical nutrition (Edinburgh, Scotland)",2022,"Cogitative aging, Gut microbiome, Lactobacillus rhamnosus GG, Prevotella, Psychobiotics",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Placebo Group,Probiotic Group,Patients in this group received an LGG supplement in the form of two Culturelle Vegetarian Capsules containing a 10 billion CFU blend of L. rhamnosus GG and 200mg prebiotic inulin from chicory root extract.,83,86,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 5D,23 October 2024,Victoria,"Victoria,WikiWorks",Cladogram and Linear Discriminant Analysis of effect size (Lefse) showing biomarker taxa for each group.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,s__uncultured bacterium,s__unidentified,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3082720|543314|86331;77133;32644;1783272|1239|91061|186826|33958,Complete,Svetlana up
bsdb:36228569/4/2,36228569,randomized controlled trial,36228569,10.1016/j.clnu.2022.09.012,NA,"Aljumaah M.R., Bhatia U., Roach J., Gunstad J. , Azcarate Peril M.A.","The gut microbiome, mild cognitive impairment, and probiotics: A randomized clinical trial in middle-aged and older adults","Clinical nutrition (Edinburgh, Scotland)",2022,"Cogitative aging, Gut microbiome, Lactobacillus rhamnosus GG, Prevotella, Psychobiotics",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Placebo Group,Probiotic Group,Patients in this group received an LGG supplement in the form of two Culturelle Vegetarian Capsules containing a 10 billion CFU blend of L. rhamnosus GG and 200mg prebiotic inulin from chicory root extract.,83,86,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 5D,23 October 2024,Victoria,"Victoria,WikiWorks,Tosin",Cladogram and Linear Discriminant Analysis of effect size (Lefse) showing biomarker taxa for each group.,decreased,"s__uncultured organism,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",155900;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Svetlana up
bsdb:36235735/1/1,36235735,laboratory experiment,36235735,10.3390/nu14194083,NA,"Qiu B., Zhu L., Zhang S., Han S., Fei Y., Ba F., Berglund B., Li L. , Yao M.",Prevention of Loperamide-Induced Constipation in Mice and Alteration of 5-Hydroxytryotamine Signaling by <i>Ligilactobacillus salivarius</i> Li01,Nutrients,2022,"5-hydroxytryotamine, Ligilactobacillus salivarius Li01, constipation, gut microbiota",Experiment 1,China,Mus musculus,Intestine secretion,UBERON:0002466,Constipation,HP:0002019,NC (Normal Control),LOP (Loperamide-induced constipation),Mice that received a daily gavage of 0.4 mL saline buffer for 15 days and 0.2 mL loperamide hydrochloride (10 mg/kg body weight) from the 8th to 15th day to induce constipation.,6,6,NA,16S,34,Illumina,relative abundances,"ANOVA,Kruskall-Wallis",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5D,30 April 2025,Anne-mariesharp,Anne-mariesharp,Differentially abundant taxon between the NC (Normal Control) group and LOP (Loperamide-induced constipation) group.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,3379134|976|200643|171549|2005473,Complete,KateRasheed
bsdb:36235735/1/2,36235735,laboratory experiment,36235735,10.3390/nu14194083,NA,"Qiu B., Zhu L., Zhang S., Han S., Fei Y., Ba F., Berglund B., Li L. , Yao M.",Prevention of Loperamide-Induced Constipation in Mice and Alteration of 5-Hydroxytryotamine Signaling by <i>Ligilactobacillus salivarius</i> Li01,Nutrients,2022,"5-hydroxytryotamine, Ligilactobacillus salivarius Li01, constipation, gut microbiota",Experiment 1,China,Mus musculus,Intestine secretion,UBERON:0002466,Constipation,HP:0002019,NC (Normal Control),LOP (Loperamide-induced constipation),Mice that received a daily gavage of 0.4 mL saline buffer for 15 days and 0.2 mL loperamide hydrochloride (10 mg/kg body weight) from the 8th to 15th day to induce constipation.,6,6,NA,16S,34,Illumina,relative abundances,"ANOVA,Kruskall-Wallis",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5E,30 April 2025,Anne-mariesharp,Anne-mariesharp,Differentially abundant taxa between the NC (Normal Control) group and LOP (Loperamide-induced constipation) group.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|186802|216572|1263,Complete,KateRasheed
bsdb:36235735/3/1,36235735,laboratory experiment,36235735,10.3390/nu14194083,NA,"Qiu B., Zhu L., Zhang S., Han S., Fei Y., Ba F., Berglund B., Li L. , Yao M.",Prevention of Loperamide-Induced Constipation in Mice and Alteration of 5-Hydroxytryotamine Signaling by <i>Ligilactobacillus salivarius</i> Li01,Nutrients,2022,"5-hydroxytryotamine, Ligilactobacillus salivarius Li01, constipation, gut microbiota",Experiment 3,China,Mus musculus,Intestine secretion,UBERON:0002466,Constipation,HP:0002019,LOP (Loperamide-induced constipation),Li01 (Ligilactobacillus salivarius treatment),Mice that received a daily gavage of 0.4 mL Li01 solution (~10^10 CFU/mL) for 15 days and 0.2 mL loperamide hydrochloride (10 mg/kg body weight) from the 8th to 15th day to induce constipation.,6,6,NA,16S,34,Illumina,relative abundances,"ANOVA,Kruskall-Wallis",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5E,2 May 2025,Montana-D,Montana-D,Differentially abundant taxon between the LOP (Loperamide-induced) group and Li01 (Ligilactobacillus salivarius) group.,increased,NA,NA,Complete,KateRasheed
bsdb:36246928/1/1,36246928,"cross-sectional observational, not case-control",36246928,10.3389/fendo.2022.942383,NA,"Nizigiyimana P., Xu B., Liu L., Luo L., Liu T., Jiang M., Liu Z., Li C., Luo X. , Lei M.",Gut microbiota is associated with differential metabolic characteristics: A study on a defined cohort of Africans and Chinese,Frontiers in endocrinology,2022,"16S rRNA gene sequencing, Africans, Chinese, bacterial communities, gut microbiota, healthy",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Glucose metabolism measurement,EFO:0009367,Han-Chinese citizens,African citizens,African citizens born in Africa with no known recent non-African ancestry.,27,29,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.8,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure 3C,3 October 2024,Balogun adekemi,"Balogun adekemi,Folakunmi,WikiWorks",Lefse cladogram generated to depict the key and most differentially abundant taxa associated with ethnicity in Chinese and Africans.,increased,k__Pseudomonadati|p__Verrucomicrobiota,3379134|74201,Complete,Folakunmi
bsdb:36246928/1/2,36246928,"cross-sectional observational, not case-control",36246928,10.3389/fendo.2022.942383,NA,"Nizigiyimana P., Xu B., Liu L., Luo L., Liu T., Jiang M., Liu Z., Li C., Luo X. , Lei M.",Gut microbiota is associated with differential metabolic characteristics: A study on a defined cohort of Africans and Chinese,Frontiers in endocrinology,2022,"16S rRNA gene sequencing, Africans, Chinese, bacterial communities, gut microbiota, healthy",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Glucose metabolism measurement,EFO:0009367,Han-Chinese citizens,African citizens,African citizens born in Africa with no known recent non-African ancestry.,27,29,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.8,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Figure 3C,3 October 2024,Balogun adekemi,"Balogun adekemi,Folakunmi,WikiWorks",Lefse cladogram generated to depict the key and most differentially abundant taxa associated with ethnicity in Chinese and Africans.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia",3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643,Complete,Folakunmi
bsdb:36246928/2/1,36246928,"cross-sectional observational, not case-control",36246928,10.3389/fendo.2022.942383,NA,"Nizigiyimana P., Xu B., Liu L., Luo L., Liu T., Jiang M., Liu Z., Li C., Luo X. , Lei M.",Gut microbiota is associated with differential metabolic characteristics: A study on a defined cohort of Africans and Chinese,Frontiers in endocrinology,2022,"16S rRNA gene sequencing, Africans, Chinese, bacterial communities, gut microbiota, healthy",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Glucose metabolism measurement,EFO:0009367,Han-Chinese citizens,African citizens,African citizens born in Africa with no known recent non-African ancestry.,27,29,NA,16S,34,Illumina,relative abundances,Metastats,0.05,FALSE,3.8,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure 3A,21 October 2024,Balogun adekemi,"Balogun adekemi,Folakunmi,WikiWorks",Metastats analysis showing the significantly different taxa in the gut microbiota of  Chinese and African citizens,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AT4,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis",3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|46506;1783272|1239|186801|186802|31979|1485|1720194;3379134|1224|28216|80840|995019|577310|487175;1783272|1239|909932|1843488|909930|33024|33025;3379134|976|200643|171549|815|909656|310298;3379134|976|200643|171549|815|909656|387090;3379134|976|200643|171549|815|909656|204516,Complete,Folakunmi
bsdb:36246928/2/2,36246928,"cross-sectional observational, not case-control",36246928,10.3389/fendo.2022.942383,NA,"Nizigiyimana P., Xu B., Liu L., Luo L., Liu T., Jiang M., Liu Z., Li C., Luo X. , Lei M.",Gut microbiota is associated with differential metabolic characteristics: A study on a defined cohort of Africans and Chinese,Frontiers in endocrinology,2022,"16S rRNA gene sequencing, Africans, Chinese, bacterial communities, gut microbiota, healthy",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Glucose metabolism measurement,EFO:0009367,Han-Chinese citizens,African citizens,African citizens born in Africa with no known recent non-African ancestry.,27,29,NA,16S,34,Illumina,relative abundances,Metastats,0.05,FALSE,3.8,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Figure 3A,21 October 2024,Balogun adekemi,"Balogun adekemi,Folakunmi,WikiWorks",Metastats analysis showing the significantly different taxa in the gut microbiota of Chinese and African citizens,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus sp. K4410.MGS-46,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Duodenibacillus|s__Duodenibacillus massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella colorans,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Marseillibacter|s__Marseillibacter massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Massiliprevotella|s__Massiliprevotella massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. ER4,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio|s__Succinivibrio dextrinosolvens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",3379134|74201|203494|48461|1647988|239934|239935;1783272|201174|1760|85004|31953|1678|1680;1783272|1239|186801|186802|3085642|580596|1828554;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|189330|88431;3379134|1224|28216|80840|995019|1980697|1852381;1783272|1239|186801|3085636|186803|3342669|45851;1783272|1239|186801|186802|186806|1730|290054;3379134|976|200643|171549|171552|52228|1703337;1783272|1239|526524|526525|128827|1573535|1735;3379134|976|200643|171549|171552|2974265|363265;1783272|1239|186801|186802|216572|1930587|1852369;3379134|976|200643|171549|171552|1981037|1816687;1783272|1239|186801|186802|216572|459786|1519439;1783272|1239|909932|1843488|909930|33024|626940;3379134|1224|1236|135624|83763|83770|83771;1783272|1239|909932|1843489|31977|29465|39778,Complete,Folakunmi
bsdb:36249017/1/1,36249017,time series / longitudinal observational,36249017,10.3389/fonc.2022.1005537,NA,"Zeber-Lubecka N., Kulecka M., Lindner B., Krynicki R., Paziewska A., Nowakowski A., Bidzinski M. , Ostrowski J.",Increased diversity of a cervical microbiome associates with cervical cancer,Frontiers in oncology,2022,"16S rRNA gene sequencing, cervical microbiome, chemoradiation therapy, lactobacillus, postmenopause",Experiment 1,Poland,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical squamous cell carcinoma,EFO:1000172,Premenopausal healthy controls (HPV Negative women),Premenopausal Pre-treatment group,"Women, aged 25–54 years, with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected a day before starting external beam radiation therapy (EBRT).",15,6,2 months,16S,23456789,Ion Torrent,NA,ANCOM,0.05,TRUE,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 1,Table 2,27 April 2024,Joan Chuks,"Joan Chuks,WikiWorks","Differential bacterial abundance in the cervical microbiome between premenopausal healthy controls (HPV Negative women) and premenopausal women with squamous cell carcinoma of the cervix, before starting external beam radiation therapy (EBRT), as determined by ANCOM-BC Analysis.",increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum",1783272|1239|1737404|1737405|1570339|165779;1783272|201174|84998|84999|1643824|1380;1783272|1239|526524|526525|128827|118747;3379134|29547|3031852|213849|72294|194;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572|236752;1783272|1239|186801|186802|1686313;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378;1783272|201174|1760|2037|2049|2050;1783272|1239|186801|3085636|186803|437755;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|186802|186807|2740;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|1239|526524|526525|128827|123375;1783272|1239|186801|3085636|186803|1213720,Complete,Svetlana up
bsdb:36249017/1/2,36249017,time series / longitudinal observational,36249017,10.3389/fonc.2022.1005537,NA,"Zeber-Lubecka N., Kulecka M., Lindner B., Krynicki R., Paziewska A., Nowakowski A., Bidzinski M. , Ostrowski J.",Increased diversity of a cervical microbiome associates with cervical cancer,Frontiers in oncology,2022,"16S rRNA gene sequencing, cervical microbiome, chemoradiation therapy, lactobacillus, postmenopause",Experiment 1,Poland,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical squamous cell carcinoma,EFO:1000172,Premenopausal healthy controls (HPV Negative women),Premenopausal Pre-treatment group,"Women, aged 25–54 years, with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected a day before starting external beam radiation therapy (EBRT).",15,6,2 months,16S,23456789,Ion Torrent,NA,ANCOM,0.05,TRUE,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 2,Table 2,27 April 2024,Joan Chuks,"Joan Chuks,WikiWorks","Differential bacterial abundance in the cervical microbiome between premenopausal healthy controls (HPV Negative women) and premenopausal women with squamous cell carcinoma of the cervix, before starting external beam radiation therapy (EBRT), as determined by ANCOM-BC Analysis.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Aminobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae|g__Rheinheimera,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",3379134|1224|1236|2887326|468|469;3379134|1224|28211|356|69277|31988;1783272|201174|1760|85009|31957|1912216;3379134|1224|1236|91347|543|1940338;1783272|1239|91061|186826|33958|1578;3379134|1224|1236|72274|135621|286;3379134|1224|1236|135613|1046|67575;1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:36249017/2/1,36249017,time series / longitudinal observational,36249017,10.3389/fonc.2022.1005537,NA,"Zeber-Lubecka N., Kulecka M., Lindner B., Krynicki R., Paziewska A., Nowakowski A., Bidzinski M. , Ostrowski J.",Increased diversity of a cervical microbiome associates with cervical cancer,Frontiers in oncology,2022,"16S rRNA gene sequencing, cervical microbiome, chemoradiation therapy, lactobacillus, postmenopause",Experiment 2,Poland,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical squamous cell carcinoma,EFO:1000172,Postmenopausal healthy controls (HPV Negative women),Postmenopausal Pre-treatment group,"Women, aged 54–62 years, with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected a day before starting external beam radiation therapy (EBRT).",15,10,2 months,16S,23456789,Ion Torrent,NA,ANCOM,0.05,TRUE,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 1,Table 2,28 April 2024,Joan Chuks,"Joan Chuks,WikiWorks","Differential bacterial abundance in the cervical microbiome between postmenopausal healthy controls (HPV Negative women) and postmenopausal women with squamous cell carcinoma of the cervix, before starting external beam radiation therapy (EBRT), as determined by ANCOM-BC Analysis.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum",1783272|201174|1760|2037|2049|28263;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|437755;1783272|1239|186801|186802|186807|2740;1783272|1239|1737404|1737405|1570339|162289;3379134|976|200643|171549|171551|836;1783272|1239|186801|3085636|186803|1213720,Complete,Svetlana up
bsdb:36249017/2/2,36249017,time series / longitudinal observational,36249017,10.3389/fonc.2022.1005537,NA,"Zeber-Lubecka N., Kulecka M., Lindner B., Krynicki R., Paziewska A., Nowakowski A., Bidzinski M. , Ostrowski J.",Increased diversity of a cervical microbiome associates with cervical cancer,Frontiers in oncology,2022,"16S rRNA gene sequencing, cervical microbiome, chemoradiation therapy, lactobacillus, postmenopause",Experiment 2,Poland,Homo sapiens,Uterine cervix,UBERON:0000002,Cervical squamous cell carcinoma,EFO:1000172,Postmenopausal healthy controls (HPV Negative women),Postmenopausal Pre-treatment group,"Women, aged 54–62 years, with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected a day before starting external beam radiation therapy (EBRT).",15,10,2 months,16S,23456789,Ion Torrent,NA,ANCOM,0.05,TRUE,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 2,Table 2,28 April 2024,Joan Chuks,"Joan Chuks,WikiWorks","Differential bacterial abundance in the cervical microbiome between postmenopausal healthy controls (HPV Negative women) and postmenopausal women with squamous cell carcinoma of the cervix, before starting external beam radiation therapy (EBRT), as determined by ANCOM-BC Analysis.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Lentilitoribacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium",1783272|201174|1760|85004|31953|2701;1783272|1239|91061|1385|539738|1378;3379134|1224|28211|356|82115|1649463;3379134|1224|28211|356|69277|68287,Complete,Svetlana up
bsdb:36249017/3/1,36249017,time series / longitudinal observational,36249017,10.3389/fonc.2022.1005537,NA,"Zeber-Lubecka N., Kulecka M., Lindner B., Krynicki R., Paziewska A., Nowakowski A., Bidzinski M. , Ostrowski J.",Increased diversity of a cervical microbiome associates with cervical cancer,Frontiers in oncology,2022,"16S rRNA gene sequencing, cervical microbiome, chemoradiation therapy, lactobacillus, postmenopause",Experiment 3,Poland,Homo sapiens,Uterine cervix,UBERON:0000002,Response to radiation,GO:0009314,Premenopausal healthy controls (HPV Negative women),Premenopausal Post-treatment group,"Women, aged 25–54 years, with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected immediately after the last fraction of brachytherapy (ICBT) was given.",15,6,2 months,16S,23456789,Ion Torrent,NA,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table S2,28 April 2024,Joan Chuks,"Joan Chuks,WikiWorks","Differential bacterial abundance in the cervical microbiome between premenopausal healthy controls (HPV Negative women) and premenopausal women with squamous cell carcinoma of the cervix, immediately after the last fraction of brachytherapy (ICBT) was given, as determined by ANCOM-BC Analysis.",increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__Clostridiales bacterium S5-A14a,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|1737404|1737405|1570339|165779;3379134|29547|3031852|213849|72294|194;1783272|1239|186801|3082720|543314|1230734;1783272|201174|1760|85007|1653|1716;1783272|1239|909932|1843489|31977|39948;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:36249017/3/2,36249017,time series / longitudinal observational,36249017,10.3389/fonc.2022.1005537,NA,"Zeber-Lubecka N., Kulecka M., Lindner B., Krynicki R., Paziewska A., Nowakowski A., Bidzinski M. , Ostrowski J.",Increased diversity of a cervical microbiome associates with cervical cancer,Frontiers in oncology,2022,"16S rRNA gene sequencing, cervical microbiome, chemoradiation therapy, lactobacillus, postmenopause",Experiment 3,Poland,Homo sapiens,Uterine cervix,UBERON:0000002,Response to radiation,GO:0009314,Premenopausal healthy controls (HPV Negative women),Premenopausal Post-treatment group,"Women, aged 25–54 years, with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected immediately after the last fraction of brachytherapy (ICBT) was given.",15,6,2 months,16S,23456789,Ion Torrent,NA,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table S2,28 April 2024,Joan Chuks,"Joan Chuks,WikiWorks","Differential bacterial abundance in the cervical microbiome between premenopausal healthy controls (HPV Negative women) and premenopausal women with squamous cell carcinoma of the cervix, immediately after the last fraction of brachytherapy (ICBT) was given, as determined by ANCOM-BC Analysis.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Aminobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Hoeflea,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ottowia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pluralibacter",3379134|1224|28211|356|69277|31988;1783272|201174|1760|85004|31953|1678;3379134|1224|28211|356|118882|234;1783272|1239|91061|186826|186828|117563;3379134|1224|28211|356|82115|274591;3379134|1224|28216|80840|80864|219181;3379134|976|200643|171549|2005525|375288;3379134|1224|1236|91347|543|1330546,Complete,Svetlana up
bsdb:36249017/4/1,36249017,time series / longitudinal observational,36249017,10.3389/fonc.2022.1005537,NA,"Zeber-Lubecka N., Kulecka M., Lindner B., Krynicki R., Paziewska A., Nowakowski A., Bidzinski M. , Ostrowski J.",Increased diversity of a cervical microbiome associates with cervical cancer,Frontiers in oncology,2022,"16S rRNA gene sequencing, cervical microbiome, chemoradiation therapy, lactobacillus, postmenopause",Experiment 4,Poland,Homo sapiens,Uterine cervix,UBERON:0000002,Response to radiation,GO:0009314,Postmenopausal healthy controls (HPV Negative women),Postmenopausal Post-treatment group,"Women, aged 54–62 years, with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected immediately after the last fraction of brachytherapy (ICBT) was given.",15,10,2 months,16S,23456789,Ion Torrent,NA,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table S2,29 April 2024,Joan Chuks,"Joan Chuks,WikiWorks","Differential bacterial abundance in the cervical microbiome between postmenopausal healthy controls (HPV Negative women) and postmenopausal women with squamous cell carcinoma of the cervix, immediately after the last fraction of brachytherapy (ICBT) was given, as determined by ANCOM-BC Analysis.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Diaphorobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Renibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas",3379134|1224|28211|204458|76892|75;3379134|1224|28216|80840|80864|238749;3379134|976|200643|171549|171551|836;1783272|201174|1760|85006|1268|1645;3379134|1224|28211|204457|41297|13687,Complete,Svetlana up
bsdb:36249017/4/2,36249017,time series / longitudinal observational,36249017,10.3389/fonc.2022.1005537,NA,"Zeber-Lubecka N., Kulecka M., Lindner B., Krynicki R., Paziewska A., Nowakowski A., Bidzinski M. , Ostrowski J.",Increased diversity of a cervical microbiome associates with cervical cancer,Frontiers in oncology,2022,"16S rRNA gene sequencing, cervical microbiome, chemoradiation therapy, lactobacillus, postmenopause",Experiment 4,Poland,Homo sapiens,Uterine cervix,UBERON:0000002,Response to radiation,GO:0009314,Postmenopausal healthy controls (HPV Negative women),Postmenopausal Post-treatment group,"Women, aged 54–62 years, with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected immediately after the last fraction of brachytherapy (ICBT) was given.",15,10,2 months,16S,23456789,Ion Torrent,NA,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table S2,29 April 2024,Joan Chuks,"Joan Chuks,WikiWorks","Differential bacterial abundance in the cervical microbiome between postmenopausal healthy controls (HPV Negative women) and postmenopausal women with squamous cell carcinoma of the cervix, immediately after the last fraction of brachytherapy (ICBT) was given, as determined by ANCOM-BC Analysis.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Lentilitoribacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium",1783272|201174|1760|85004|31953|2701;3379134|1224|28211|356|82115|1649463;3379134|1224|28211|356|69277|68287,Complete,Svetlana up
bsdb:36249017/5/1,36249017,time series / longitudinal observational,36249017,10.3389/fonc.2022.1005537,NA,"Zeber-Lubecka N., Kulecka M., Lindner B., Krynicki R., Paziewska A., Nowakowski A., Bidzinski M. , Ostrowski J.",Increased diversity of a cervical microbiome associates with cervical cancer,Frontiers in oncology,2022,"16S rRNA gene sequencing, cervical microbiome, chemoradiation therapy, lactobacillus, postmenopause",Experiment 5,Poland,Homo sapiens,Uterine cervix,UBERON:0000002,Response to radiation,GO:0009314,Pre-treatment group,Post-treatment and 3-month post-treatment group,"Women with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected immediately after the last fraction of brachytherapy (ICBT) was given and 3 months after the last fraction of brachytherapy (ICBT) was given (n=9).",15,15,2 months,16S,23456789,Ion Torrent,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 3,29 April 2024,Joan Chuks,"Joan Chuks,WikiWorks","Differential bacterial abundance in the cervical microbiome of women with squamous cell carcinoma of the cervix, before starting the external beam radiation therapy (EBRT) compared to immediately after the last fraction of brachytherapy (ICBT) was given, as determined by ANCOM-BC Analysis",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Diaphorobacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Renibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae|g__Rheinheimera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|1224|1236|2887326|468|469;1783272|1239|186801|3085636|186803|572511;3379134|1224|28211|204458|76892|75;3379134|976|117743|200644|2762318|501783;1783272|201174|1760|85007|1653|1716;3379134|1224|28216|80840|119060|106589;1783272|201174|1760|85009|31957|1912216;3379134|1224|28216|80840|80864|238749;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|91061|186826|1300|1357;3379134|1224|28216|80840|75682|149698;3379134|976|200643|171549|2005473|1918540;3379134|1224|28216|206351|481|482;3379134|976|117747|200666|84566|84567;3379134|1224|1236|72274|135621|286;3379134|1224|28216|80840|119060|48736;1783272|201174|1760|85006|1268|1645;3379134|1224|1236|135613|1046|67575;3379134|1224|28216|80840|2975441|93681;3379134|1224|28211|204457|41297|13687;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:36249017/5/2,36249017,time series / longitudinal observational,36249017,10.3389/fonc.2022.1005537,NA,"Zeber-Lubecka N., Kulecka M., Lindner B., Krynicki R., Paziewska A., Nowakowski A., Bidzinski M. , Ostrowski J.",Increased diversity of a cervical microbiome associates with cervical cancer,Frontiers in oncology,2022,"16S rRNA gene sequencing, cervical microbiome, chemoradiation therapy, lactobacillus, postmenopause",Experiment 5,Poland,Homo sapiens,Uterine cervix,UBERON:0000002,Response to radiation,GO:0009314,Pre-treatment group,Post-treatment and 3-month post-treatment group,"Women with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected immediately after the last fraction of brachytherapy (ICBT) was given and 3 months after the last fraction of brachytherapy (ICBT) was given (n=9).",15,15,2 months,16S,23456789,Ion Torrent,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 3,29 April 2024,Joan Chuks,"Joan Chuks,WikiWorks","Differential bacterial abundance in the cervical microbiome of women with squamous cell carcinoma of the cervix, before starting the external beam radiation therapy (EBRT) compared to immediately after the last fraction of brachytherapy (ICBT) was given, as determined by ANCOM-BC Analysis",decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum",1783272|1239|526524|526525|128827|118747;3384189|32066|203490|203491|203492|848;1783272|201174|84998|84999|1643824|133925;1783272|1239|186801|186802|186807|2740;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|1239|526524|526525|128827|123375;1783272|1239|186801|3085636|186803|1213720,Complete,Svetlana up
bsdb:36250371/1/1,36250371,randomized controlled trial,36250371,10.5056/jnm21202,NA,"Shin S.Y., Park S., Moon J.M., Kim K., Kim J.W., Chun J., Lee T.H. , Choi C.H.",Compositional Changes in the Gut Microbiota of Responders and Non-responders to Probiotic Treatment Among Patients With Diarrhea-predominant Irritable Bowel Syndrome: A Post Hoc Analysis of a Randomized Clinical Trial,Journal of neurogastroenterology and motility,2022,"Biomarkers, Irritable bowel syndrome, Microbiota, Prediction, Probiotics",Experiment 1,Republic of Korea,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Pre-treatment (probiotics),Post-treatment (probiotics),Samples collected after completing the 8-week probiotic therapy in patients with diarrhea-predominant IBS (IBS-D) who received the probiotic mixture,24,22,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,Signature 1,Figure 2,1 November 2025,Tosin,Tosin,Relative abundance of the taxa related to irritable bowel syndrome (IBS) between pre and post treatment samples in probiotics,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota",3379134|976|200643|171549|815|816;3379134|1224,Complete,KateRasheed
bsdb:36250371/2/1,36250371,randomized controlled trial,36250371,10.5056/jnm21202,NA,"Shin S.Y., Park S., Moon J.M., Kim K., Kim J.W., Chun J., Lee T.H. , Choi C.H.",Compositional Changes in the Gut Microbiota of Responders and Non-responders to Probiotic Treatment Among Patients With Diarrhea-predominant Irritable Bowel Syndrome: A Post Hoc Analysis of a Randomized Clinical Trial,Journal of neurogastroenterology and motility,2022,"Biomarkers, Irritable bowel syndrome, Microbiota, Prediction, Probiotics",Experiment 2,Republic of Korea,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Non-responder (Pre-treatment samples),Responder (Pre-treatment samples),Patients who experienced adequate relief of overall irritable bowel syndrome symptoms before probiotic therapy,12,12,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 5A,1 November 2025,Tosin,Tosin,Linear discriminant analysis (LDA) effect size biomarker identification of responders and non-responders to probiotic treatment in the pre-treatment samples,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus",3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|815|909656|387090;3379134|976|200643|171549|815|909656|821,Complete,KateRasheed
bsdb:36250371/2/2,36250371,randomized controlled trial,36250371,10.5056/jnm21202,NA,"Shin S.Y., Park S., Moon J.M., Kim K., Kim J.W., Chun J., Lee T.H. , Choi C.H.",Compositional Changes in the Gut Microbiota of Responders and Non-responders to Probiotic Treatment Among Patients With Diarrhea-predominant Irritable Bowel Syndrome: A Post Hoc Analysis of a Randomized Clinical Trial,Journal of neurogastroenterology and motility,2022,"Biomarkers, Irritable bowel syndrome, Microbiota, Prediction, Probiotics",Experiment 2,Republic of Korea,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Non-responder (Pre-treatment samples),Responder (Pre-treatment samples),Patients who experienced adequate relief of overall irritable bowel syndrome symptoms before probiotic therapy,12,12,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 5A,1 November 2025,Tosin,Tosin,Linear discriminant analysis (LDA) effect size biomarker identification of responders and non-responders to probiotic treatment in the pre-treatment samples,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,1783272|1239|91061|186826|81852|1350|1351,Complete,KateRasheed
bsdb:36250371/3/1,36250371,randomized controlled trial,36250371,10.5056/jnm21202,NA,"Shin S.Y., Park S., Moon J.M., Kim K., Kim J.W., Chun J., Lee T.H. , Choi C.H.",Compositional Changes in the Gut Microbiota of Responders and Non-responders to Probiotic Treatment Among Patients With Diarrhea-predominant Irritable Bowel Syndrome: A Post Hoc Analysis of a Randomized Clinical Trial,Journal of neurogastroenterology and motility,2022,"Biomarkers, Irritable bowel syndrome, Microbiota, Prediction, Probiotics",Experiment 3,Republic of Korea,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Non-responder (Post-treatment samples),Responder (Post-treatment samples),Patients who experienced adequate relief of overall irritable bowel syndrome symptoms after probiotic therapy,10,12,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 5B,1 November 2025,Tosin,Tosin,Linear discriminant analysis (LDA) effect size biomarker identification of responders and non-responders to probiotic treatment in the post-treatment samples,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae",1783272|1239|186801|3085636|186803|1769710;1783272|1239|909932|1843489|31977|29465|423477,Complete,KateRasheed
bsdb:36250371/3/2,36250371,randomized controlled trial,36250371,10.5056/jnm21202,NA,"Shin S.Y., Park S., Moon J.M., Kim K., Kim J.W., Chun J., Lee T.H. , Choi C.H.",Compositional Changes in the Gut Microbiota of Responders and Non-responders to Probiotic Treatment Among Patients With Diarrhea-predominant Irritable Bowel Syndrome: A Post Hoc Analysis of a Randomized Clinical Trial,Journal of neurogastroenterology and motility,2022,"Biomarkers, Irritable bowel syndrome, Microbiota, Prediction, Probiotics",Experiment 3,Republic of Korea,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Non-responder (Post-treatment samples),Responder (Post-treatment samples),Patients who experienced adequate relief of overall irritable bowel syndrome symptoms after probiotic therapy,10,12,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 5B,1 November 2025,Tosin,Tosin,Linear discriminant analysis (LDA) effect size biomarker identification of responders and non-responders to probiotic treatment in the post-treatment samples,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium",1783272|201174|1760|2037|2049|1654;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3082720|543314|86331,Complete,KateRasheed
bsdb:36250371/4/1,36250371,randomized controlled trial,36250371,10.5056/jnm21202,NA,"Shin S.Y., Park S., Moon J.M., Kim K., Kim J.W., Chun J., Lee T.H. , Choi C.H.",Compositional Changes in the Gut Microbiota of Responders and Non-responders to Probiotic Treatment Among Patients With Diarrhea-predominant Irritable Bowel Syndrome: A Post Hoc Analysis of a Randomized Clinical Trial,Journal of neurogastroenterology and motility,2022,"Biomarkers, Irritable bowel syndrome, Microbiota, Prediction, Probiotics",Experiment 4,Republic of Korea,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Pre-treatment samples (responder group),Post-treatment samples (responder group),Post-treatment fecal samples from irritable bowel syndrome with diarrhea (IBS-D) responders after eight weeks of probiotic therapy,12,12,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5C,2 November 2025,Tosin,Tosin,Linear discriminant analysis (LDA) effect size biomarkers of the pre- and post-treatment samples in the responder group.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,1783272|1239|186801|3085636|186803|1407607|1150298,Complete,KateRasheed
bsdb:36250371/4/2,36250371,randomized controlled trial,36250371,10.5056/jnm21202,NA,"Shin S.Y., Park S., Moon J.M., Kim K., Kim J.W., Chun J., Lee T.H. , Choi C.H.",Compositional Changes in the Gut Microbiota of Responders and Non-responders to Probiotic Treatment Among Patients With Diarrhea-predominant Irritable Bowel Syndrome: A Post Hoc Analysis of a Randomized Clinical Trial,Journal of neurogastroenterology and motility,2022,"Biomarkers, Irritable bowel syndrome, Microbiota, Prediction, Probiotics",Experiment 4,Republic of Korea,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Pre-treatment samples (responder group),Post-treatment samples (responder group),Post-treatment fecal samples from irritable bowel syndrome with diarrhea (IBS-D) responders after eight weeks of probiotic therapy,12,12,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5C,2 November 2025,Tosin,Tosin,Linear discriminant analysis (LDA) effect size biomarkers of the pre- and post-treatment samples in the responder group,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae",3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|1224|28216;1783272|1239|526524|526525|2810280|100883|100884;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|1853231;3379134|976|200643|171549|815|909656|821;3379134|1224|28216|80840|995019,Complete,KateRasheed
bsdb:36250371/5/1,36250371,randomized controlled trial,36250371,10.5056/jnm21202,NA,"Shin S.Y., Park S., Moon J.M., Kim K., Kim J.W., Chun J., Lee T.H. , Choi C.H.",Compositional Changes in the Gut Microbiota of Responders and Non-responders to Probiotic Treatment Among Patients With Diarrhea-predominant Irritable Bowel Syndrome: A Post Hoc Analysis of a Randomized Clinical Trial,Journal of neurogastroenterology and motility,2022,"Biomarkers, Irritable bowel syndrome, Microbiota, Prediction, Probiotics",Experiment 5,Republic of Korea,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Placebo (Baseline),Probiotics (Baseline),"Patients with irritable bowel syndrome with diarrhea (IBS-D) in the probiotic group pre-treatment, before starting probiotic supplementation",21,24,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3A,2 November 2025,Tosin,Tosin,Differentially abundant taxa in the probiotic and placebo groups by Deseq2 at the baseline (pre-treatment),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales,k__Bacillati|p__Bacillota|c__Tissierellia",3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|561;1783272|1239|186801|186802|216572|946234|292800;3379134|1224|1236;1783272|1239|91061|186826|33958|2767887|1623;1783272|1239|1737404|1737405|1570339;3379134|1224;1783272|1239|186801|186802|216572|1905344;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|1737404|1737405;1783272|1239|1737404,Complete,KateRasheed
bsdb:36250371/5/2,36250371,randomized controlled trial,36250371,10.5056/jnm21202,NA,"Shin S.Y., Park S., Moon J.M., Kim K., Kim J.W., Chun J., Lee T.H. , Choi C.H.",Compositional Changes in the Gut Microbiota of Responders and Non-responders to Probiotic Treatment Among Patients With Diarrhea-predominant Irritable Bowel Syndrome: A Post Hoc Analysis of a Randomized Clinical Trial,Journal of neurogastroenterology and motility,2022,"Biomarkers, Irritable bowel syndrome, Microbiota, Prediction, Probiotics",Experiment 5,Republic of Korea,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Placebo (Baseline),Probiotics (Baseline),"Patients with irritable bowel syndrome with diarrhea (IBS-D) in the probiotic group pre-treatment, before starting probiotic supplementation",21,24,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 3A,2 November 2025,Tosin,Tosin,Differentially abundant taxa in the probiotic and placebo groups by Deseq2 at the baseline (pre-treatment),decreased,NA,NA,Complete,KateRasheed
bsdb:36250371/6/1,36250371,randomized controlled trial,36250371,10.5056/jnm21202,NA,"Shin S.Y., Park S., Moon J.M., Kim K., Kim J.W., Chun J., Lee T.H. , Choi C.H.",Compositional Changes in the Gut Microbiota of Responders and Non-responders to Probiotic Treatment Among Patients With Diarrhea-predominant Irritable Bowel Syndrome: A Post Hoc Analysis of a Randomized Clinical Trial,Journal of neurogastroenterology and motility,2022,"Biomarkers, Irritable bowel syndrome, Microbiota, Prediction, Probiotics",Experiment 6,Republic of Korea,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Placebo (post-treatment),Probiotics (post-treatment),"Patients in the probiotic group post-treatment, after completing 8 weeks of probiotic supplementation",18,22,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3B,2 November 2025,Tosin,Tosin,Differentially abundant taxa in the probiotic and placebo groups by Deseq2 after probiotics treatment (post-treatment),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas umbilicata,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales,k__Bacillati|p__Bacillota|c__Tissierellia",1783272|201174|1760|85004|31953|1678|1681;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|3085636|186803|2005355;1783272|1239|186801|3085636|186803|2005355|1912855;1783272|1239|91061|186826|33958|2767887|1623;1783272|1239|91061|186826|33958|1253;1783272|1239|1737404|1737405|1570339;1783272|1239|1737404|1737405;1783272|1239|1737404,Complete,KateRasheed
bsdb:36250371/6/2,36250371,randomized controlled trial,36250371,10.5056/jnm21202,NA,"Shin S.Y., Park S., Moon J.M., Kim K., Kim J.W., Chun J., Lee T.H. , Choi C.H.",Compositional Changes in the Gut Microbiota of Responders and Non-responders to Probiotic Treatment Among Patients With Diarrhea-predominant Irritable Bowel Syndrome: A Post Hoc Analysis of a Randomized Clinical Trial,Journal of neurogastroenterology and motility,2022,"Biomarkers, Irritable bowel syndrome, Microbiota, Prediction, Probiotics",Experiment 6,Republic of Korea,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Placebo (post-treatment),Probiotics (post-treatment),"Patients in the probiotic group post-treatment, after completing 8 weeks of probiotic supplementation",18,22,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3B,2 November 2025,Tosin,Tosin,Differentially abundant taxa in the probiotic and placebo groups by Deseq2 after probiotics treatment (post-treatment),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus",3379134|976|200643|171549|815|816;3379134|976|200643|171549|815;1783272|1239|909932|1843489|31977|39948|487173,Complete,KateRasheed
bsdb:36253847/1/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Pre-Experimental Autoimmune Encephalomyelitis induction(pre-EAE induction/Day 0): 0 day post immunization(0 DPI),Post-Experimental Autoimmune Encephalomyelitis induction-latent period(post-EAE induction): 3 days post immunization(3 DPI),"Post-Experimental Autoimmune Encephalomyelitis induction-latent period(post-EAE induction): 3 days post immunization(3 DPI), refers to fecal samples collected three days after immunization. Mice were immunized with Myelin oligodendrocyte glycoprotein(MOG) for EAE induction. EAE was induced by injecting 8- to 10-week-old female C57BL/6J mice with 150 mg MOG35–55 peptide (Genemed Synthesis) emulsified in complete Freund’s adjuvant (CFA) (BD Difco) per mouse subcutaneously in the flanks, followed by intraperitoneal administration of 150 ng pertussis toxin (List Biological Laboratories, Inc.) per mouse on days 0 and 2.",11,11,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 1F,23 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between 3 days post immunization(3 DPI) and 0 day post immunization(0 DPI),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus flavefaciens,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia cocleata,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium chauvoei",1783272|1239|186801|186802|31979|1485|1960653;1783272|1239|186801|186802|216572|1263|1265;1783272|1239|526524|526525|2810280|3025755|69824;1783272|1239|186801|186802|31979|1485|46867,Complete,Svetlana up
bsdb:36253847/1/2,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Pre-Experimental Autoimmune Encephalomyelitis induction(pre-EAE induction/Day 0): 0 day post immunization(0 DPI),Post-Experimental Autoimmune Encephalomyelitis induction-latent period(post-EAE induction): 3 days post immunization(3 DPI),"Post-Experimental Autoimmune Encephalomyelitis induction-latent period(post-EAE induction): 3 days post immunization(3 DPI), refers to fecal samples collected three days after immunization. Mice were immunized with Myelin oligodendrocyte glycoprotein(MOG) for EAE induction. EAE was induced by injecting 8- to 10-week-old female C57BL/6J mice with 150 mg MOG35–55 peptide (Genemed Synthesis) emulsified in complete Freund’s adjuvant (CFA) (BD Difco) per mouse subcutaneously in the flanks, followed by intraperitoneal administration of 150 ng pertussis toxin (List Biological Laboratories, Inc.) per mouse on days 0 and 2.",11,11,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig. 1F,23 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between 3 days post immunization(3 DPI) and 0 day post immunization(0 DPI),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora indolis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] viride",1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|2719231|69825;1783272|1239|186801|186802|216572|47246,Complete,Svetlana up
bsdb:36253847/2/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Pre-Experimental Autoimmune Encephalomyelitis induction(pre-EAE induction/Day 0): 0 day post immunization(0 DPI),Post-Experimental Autoimmune Encephalomyelitis induction-latent period(post-EAE induction): 8 days post immunization(8 DPI),"Post-Experimental Autoimmune Encephalomyelitis induction-latent period(post-EAE induction): 8 days post immunization(8 DPI), refers to the timepoint for fecal sample collection(eight days after immunization). EAE was induced by injecting 8- to 10-week-old female C57BL/6J mice with 150 mg MOG35–55 peptide (Genemed Synthesis) emulsified in complete Freund’s adjuvant (CFA) (BD Difco) per mouse subcutaneously in the flanks, followed by intraperitoneal administration of 150 ng pertussis toxin (List Biological Laboratories, Inc.) per mouse on days 0 and 2.",11,11,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 1F,23 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between 8 days post immunization(8 DPI) and 0 day post immunization(0 DPI),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium celatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium quinii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter|s__Papillibacter cinnamivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus flavefaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium chauvoei",1783272|1239|186801|186802|31979|1485|36834;1783272|1239|186801|186802|31979|1485|36850;1783272|1239|186801|186802|31979|1485|1960653;1783272|1239|186801|186802|1392389|1297617;1783272|1239|186801|186802|216572|100175|100176;1783272|1239|186801|186802|216572|1263|1265;1783272|1239|186801|3085636|186803|1506553|29347;1783272|1239|186801|186802|31979|1485|46867,Complete,Svetlana up
bsdb:36253847/2/2,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Pre-Experimental Autoimmune Encephalomyelitis induction(pre-EAE induction/Day 0): 0 day post immunization(0 DPI),Post-Experimental Autoimmune Encephalomyelitis induction-latent period(post-EAE induction): 8 days post immunization(8 DPI),"Post-Experimental Autoimmune Encephalomyelitis induction-latent period(post-EAE induction): 8 days post immunization(8 DPI), refers to the timepoint for fecal sample collection(eight days after immunization). EAE was induced by injecting 8- to 10-week-old female C57BL/6J mice with 150 mg MOG35–55 peptide (Genemed Synthesis) emulsified in complete Freund’s adjuvant (CFA) (BD Difco) per mouse subcutaneously in the flanks, followed by intraperitoneal administration of 150 ng pertussis toxin (List Biological Laboratories, Inc.) per mouse on days 0 and 2.",11,11,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig. 1F,23 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between 8 days post immunization(8 DPI) and 0 day post immunization(0 DPI),decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira|s__Oscillospira guilliermondii,1783272|1239|186801|186802|216572|119852|119853,Complete,Svetlana up
bsdb:36253847/3/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 3,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Pre-Experimental Autoimmune Encephalomyelitis induction(pre-EAE induction/Day 0): 0 day post immunization(0 DPI),Post-Experimental Autoimmune Encephalomyelitis induction-peak disease(post-EAE induction): 15 days post immunization(15 DPI),"Post-Experimental Autoimmune Encephalomyelitis induction-peak disease(post-EAE induction): 15 days post immunization(15 DPI), refers to the timepoint for fecal sample collection(fifteen days after immunization). This was also the peak of multiple sclerosis disease.",11,11,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 1F,23 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between 15 days post immunization(15 DPI) and 0 day post immunization(0 DPI),increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus flavefaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|186802|216572|1263|1265;1783272|1239|186801|186802|31979|1485|1960653;1783272|1239|186801|3085636|186803|1506553|29347,Complete,Svetlana up
bsdb:36253847/3/2,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 3,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Pre-Experimental Autoimmune Encephalomyelitis induction(pre-EAE induction/Day 0): 0 day post immunization(0 DPI),Post-Experimental Autoimmune Encephalomyelitis induction-peak disease(post-EAE induction): 15 days post immunization(15 DPI),"Post-Experimental Autoimmune Encephalomyelitis induction-peak disease(post-EAE induction): 15 days post immunization(15 DPI), refers to the timepoint for fecal sample collection(fifteen days after immunization). This was also the peak of multiple sclerosis disease.",11,11,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig. 1F,23 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between 15 days post immunization(15 DPI) and 0 day post immunization(0 DPI),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia luti,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena orotica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora indolis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella profusa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira|s__Oscillospira guilliermondii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] hylemonae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] polysaccharolyticum",1783272|1239|186801|3085636|186803|572511|871665;1783272|1239|186801|3085636|186803|572511|89014;1783272|1239|186801|3085636|186803|2719313|358742;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|2719313|1531;1783272|1239|186801|3085636|186803|2005359|1544;1783272|1239|186801|3085636|186803|2719231|69825;1783272|201174|84998|84999|1643824|133925|138595;1783272|1239|186801|186802|216572|119852|119853;1783272|1239|526524|526525|2810281|191303|154288;1783272|1239|186801|3085636|186803|1506553|89153;1783272|1239|186801|3085636|186803|1506553|29364,Complete,Svetlana up
bsdb:36253847/4/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 4,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed control mice - 0 DPI,Single-treatment housed vancomycin mice - 0 DPI,"Single-treatment housed vancomycin mice - 0 DPI refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 0 day post immunization(0 DPI).",NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Fig. S4A,24 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 0 day post immunization(0 DPI) using LEfSe,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium celatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium chauvoei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|186802|31979|1485|36834;1783272|1239|186801|186802|31979|1485|46867;1783272|1239|91061|186826|81852|1350;1783272|1239|526524|526525|2810281|191303|154288,Complete,Svetlana up
bsdb:36253847/4/2,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 4,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed control mice - 0 DPI,Single-treatment housed vancomycin mice - 0 DPI,"Single-treatment housed vancomycin mice - 0 DPI refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 0 day post immunization(0 DPI).",NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Fig. S4A,24 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 0 day post immunization(0 DPI) using LEfSe,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor|s__Acetatifactor muris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerocolumna|s__Anaerocolumna jejuensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia luti,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora indolis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella profusa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Parasporobacterium|s__Parasporobacterium paucivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] hylemonae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] polysaccharolyticum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] viride",1783272|1239|186801|3085636|186803|1427378|879566;1783272|1239|186801|3085636|186803|1843210|259063;1783272|1239|186801|186802|216572|244127|169435;1783272|1239|186801|3085636|186803|572511|871665;1783272|1239|186801|3085636|186803|572511|89014;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|2719231|69825;1783272|201174|84998|84999|1643824|133925|138595;1783272|1239|186801|3085636|186803|115543|115544;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|1506553|89153;1783272|1239|186801|3085636|186803|1506553|29364;1783272|1239|186801|3085636|186803|1506553|29347;1783272|1239|186801|186802|216572|47246,Complete,Svetlana up
bsdb:36253847/5/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 5,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed control mice - 3 DPI,Single-treatment housed vancomycin mice - 3 DPI,"Single-treatment housed vancomycin mice - 3 DPI refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 3 days post immunization(3 DPI).",NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Fig. S4A,24 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 3 days post immunization(3 DPI) using LEfSe,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor|s__Acetatifactor muris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerocolumna|s__Anaerocolumna jejuensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] viride",1783272|1239|186801|3085636|186803|1427378|879566;1783272|1239|186801|3085636|186803|1843210|259063;1783272|1239|186801|186802|216572|244127|169435;1783272|1239|186801|3085636|186803|572511|871665;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|186802|216572|47246,Complete,Svetlana up
bsdb:36253847/5/2,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 5,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed control mice - 3 DPI,Single-treatment housed vancomycin mice - 3 DPI,"Single-treatment housed vancomycin mice - 3 DPI refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 3 days post immunization(3 DPI).",NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Fig. S4A,24 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 3 days post immunization(3 DPI) using LEfSe,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium celatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena orotica,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia cocleata,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|186802|31979|1485|36834;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|3085636|186803|2005359|1544;1783272|1239|526524|526525|2810280|3025755|69824;1783272|1239|526524|526525|2810281|191303|154288;1783272|1239|186801|3085636|186803|1506553|29347,Complete,Svetlana up
bsdb:36253847/6/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 6,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed control mice - 8 DPI,Single-treatment housed vancomycin mice - 8 DPI,"Single-treatment housed vancomycin mice refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 8 days post immunization(8 DPI).",NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Fig. S4A,24 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 8 day post immunization(8 DPI) using LEfSe,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor|s__Acetatifactor muris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerocolumna|s__Anaerocolumna jejuensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora indolis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] viride",1783272|1239|186801|3085636|186803|1427378|879566;1783272|1239|186801|3085636|186803|1843210|259063;1783272|1239|186801|186802|216572|244127|169435;1783272|1239|186801|3085636|186803|572511|871665;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|186802|1392389|1297617;1783272|1239|186801|3085636|186803|2719231|69825;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|186802|216572|47246,Complete,Svetlana up
bsdb:36253847/6/2,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 6,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed control mice - 8 DPI,Single-treatment housed vancomycin mice - 8 DPI,"Single-treatment housed vancomycin mice refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 8 days post immunization(8 DPI).",NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Fig. S4A,24 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 8 days post immunization(8 DPI) using LEfSe,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia cocleata,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|91061|186826|33958|1578;1783272|1239|526524|526525|2810280|3025755|69824;1783272|1239|186801|3085636|186803|1506553|29347,Complete,Svetlana up
bsdb:36253847/7/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 7,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed control mice - 15 DPI,Single-treatment housed vancomycin mice - 15 DPI,"Single-treatment housed vancomycin mice refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 15 days post immunization(15 DPI).",NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 1,Fig. S4A,24 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 15 days post immunization(15 DPI) using LEfSe,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerocolumna|s__Anaerocolumna jejuensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium celatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora indolis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella profusa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia cocleata,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens",1783272|1239|186801|3085636|186803|1843210|259063;1783272|1239|186801|3085636|186803|572511|871665;1783272|1239|186801|186802|31979|1485|36834;1783272|1239|186801|3085636|186803|2719231|69825;1783272|1239|91061|186826|33958|1578;1783272|201174|84998|84999|1643824|133925|138595;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|526524|526525|2810280|3025755|69824;1783272|1239|526524|526525|2810281|191303|154288;1783272|1239|186801|3085636|186803|1506553|29347,Complete,Svetlana up
bsdb:36253847/7/2,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 7,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed control mice - 15 DPI,Single-treatment housed vancomycin mice - 15 DPI,"Single-treatment housed vancomycin mice refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 15 days post immunization(15 DPI).",NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 2,Fig. S4A,25 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 15 days post immunization(15 DPI) using LEfSe,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor|s__Acetatifactor muris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] viride",1783272|1239|186801|3085636|186803|1427378|879566;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|186802|216572|47246,Complete,Svetlana up
bsdb:36253847/8/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 8,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed vancomycin mice (vancomycin) - 0 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 0 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 0 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 0 day post immunization(0 DPI).,NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Fig. S4B,24 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 0 day post immunization(0 DPI) using LEfSe,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerocolumna|s__Anaerocolumna jejuensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena orotica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora indolis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia cocleata,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] polysaccharolyticum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] viride",1783272|1239|186801|3085636|186803|1843210|259063;1783272|1239|186801|3085636|186803|2005359|1544;1783272|1239|186801|3085636|186803|2719231|69825;1783272|1239|91061|186826|33958|1578;1783272|1239|526524|526525|2810280|3025755|69824;1783272|1239|186801|3085636|186803|1506553|29364;1783272|1239|186801|3085636|186803|1506553|29347;1783272|1239|186801|186802|216572|47246,Complete,Svetlana up
bsdb:36253847/8/2,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 8,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed vancomycin mice (vancomycin) - 0 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 0 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 0 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 0 day post immunization(0 DPI).,NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,Fig. S4B,24 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 0 day post immunization(0 DPI) using LEfSe,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium chauvoei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|186802|31979|1485|46867;1783272|1239|91061|186826|81852|1350;1783272|1239|526524|526525|2810281|191303|154288,Complete,Svetlana up
bsdb:36253847/9/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 9,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed vancomycin mice (vancomycin) - 3 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 3 days post immunization(3 DPI).,NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. S4B,24 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 3 days post immunization(3 DPI) using LEfSe,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerocolumna|s__Anaerocolumna jejuensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora indolis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] polysaccharolyticum",1783272|1239|186801|3085636|186803|1843210|259063;1783272|1239|186801|186802|216572|244127|169435;1783272|1239|186801|3085636|186803|2719231|69825;1783272|1239|186801|3085636|186803|1506553|29364,Complete,Svetlana up
bsdb:36253847/9/2,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 9,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed vancomycin mice (vancomycin) - 3 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 3 days post immunization(3 DPI).,NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig. S4B,24 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 3 days post immunization(3 DPI) using LEfSe,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia cocleata,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|91061|186826|81852|1350;1783272|1239|526524|526525|2810280|3025755|69824;1783272|1239|526524|526525|2810281|191303|154288,Complete,Svetlana up
bsdb:36253847/10/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 10,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed vancomycin mice (vancomycin) - 8 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 8 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 8 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 8 days post immunization(8 DPI).,NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. S4B,24 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 8 days post immunization(8 DPI) using LEfSe,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora indolis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] polysaccharolyticum",1783272|1239|186801|186802|216572|244127|169435;1783272|1239|186801|3085636|186803|2719313|358742;1783272|1239|186801|3085636|186803|2719231|69825;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|1506553|29364,Complete,Svetlana up
bsdb:36253847/10/2,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 10,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed vancomycin mice (vancomycin) - 8 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 8 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 8 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 8 days post immunization(8 DPI).,NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig. S4B,24 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 8 days post immunization(8 DPI) using LEfSe,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella profusa,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia cocleata,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|91061|186826|33958|1578;1783272|201174|84998|84999|1643824|133925|138595;1783272|1239|526524|526525|2810280|3025755|69824;1783272|1239|526524|526525|2810281|191303|154288,Complete,Svetlana up
bsdb:36253847/11/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 11,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed vancomycin mice (vancomycin) - 15 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 15 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 15 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 15 days post immunization(15 DPI).,NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. S4B,24 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 15 days post immunization(15 DPI) using LEfSe,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor|s__Acetatifactor muris,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora indolis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis",1783272|1239|186801|3085636|186803|1427378|879566;1783272|1239|186801|186802|216572|244127|169435;1783272|1239|186801|3085636|186803|2719313|358742;1783272|1239|186801|186802|1392389|1297617;1783272|1239|186801|3085636|186803|2719231|69825;1783272|1239|186801|3085636|186803|841|166486,Complete,Svetlana up
bsdb:36253847/11/2,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 11,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed vancomycin mice (vancomycin) - 15 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 15 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 15 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 15 days post immunization(15 DPI).,NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig. S4B,24 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 15 days post immunization(15 DPI) using LEfSe,decreased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella profusa,1783272|201174|84998|84999|1643824|133925|138595,Complete,Svetlana up
bsdb:36253847/12/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 12,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Untreated mice cohoused with vancomycin-treated mice (ControlCoho) - 0 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 0 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 0 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 0 day post immunization(0 DPI),NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Fig. S4C,24 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between untreated mice cohoused with vancomycin-treated mice (ControlCoho) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 0 day post immunization(0 DPI) using LEfSe,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia cocleata,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Tindalliaceae|g__Tindallia|s__Tindallia texcoconensis",1783272|1239|526524|526525|2810280|100883|100884;1783272|1239|526524|526525|2810280|3025755|69824;1783272|1239|186801|3082720|3118658|69894|361365,Complete,Svetlana up
bsdb:36253847/12/2,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 12,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Untreated mice cohoused with vancomycin-treated mice (ControlCoho) - 0 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 0 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 0 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 0 day post immunization(0 DPI),NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Fig. S4C,25 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between untreated mice cohoused with vancomycin-treated mice (ControlCoho) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 0 day post immunization(0 DPI) using LEfSe,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora indolis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Parasporobacterium|s__Parasporobacterium paucivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis",1783272|1239|186801|186802|216572|244127|169435;1783272|1239|186801|3085636|186803|2719313|358742;1783272|1239|186801|3085636|186803|2719231|69825;1783272|1239|186801|186802|216572|459786|351091;1783272|1239|186801|3085636|186803|115543|115544;1783272|1239|186801|3085636|186803|841|166486,Complete,Svetlana up
bsdb:36253847/13/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 13,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Untreated mice cohoused with vancomycin-treated mice (ControlCoho) - 3 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 3 days post immunization(3 DPI).,NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. S4C,24 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between untreated mice cohoused with vancomycin-treated mice (ControlCoho) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 3 days post immunization(3 DPI) using LEfSe,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena orotica,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira|s__Oscillospira guilliermondii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia cocleata",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|526524|526525|2810280|100883|100884;1783272|1239|186801|3085636|186803|2005359|1544;1783272|1239|186801|186802|216572|459786|351091;1783272|1239|186801|186802|216572|119852|119853;1783272|1239|526524|526525|2810280|3025755|69824,Complete,Svetlana up
bsdb:36253847/13/2,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 13,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Untreated mice cohoused with vancomycin-treated mice (ControlCoho) - 3 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 3 days post immunization(3 DPI).,NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig. S4C,25 November 2024,KateRasheed,KateRasheed,Differentially abundant taxa between untreated mice cohoused with vancomycin-treated mice (ControlCoho) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 3 days post immunization(3 DPI) using LEfSe,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,1783272|1239|186801|3085636|186803|841|166486,Complete,NA
bsdb:36253847/13/3,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 13,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Untreated mice cohoused with vancomycin-treated mice (ControlCoho) - 3 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 3 days post immunization(3 DPI).,NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 3,Fig. S4C,16 January 2025,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between untreated mice cohoused with vancomycin-treated mice (ControlCoho) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 3 days post immunization(3 DPI) using LEfSe,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,1783272|1239|186801|3085636|186803|841|166486,Complete,Svetlana up
bsdb:36253847/14/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 14,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Untreated mice cohoused with vancomycin-treated mice (ControlCoho) - 8 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 8 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 8 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 8 days post immunization(8 DPI),NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. S4C,24 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between untreated mice cohoused with vancomycin-treated mice (ControlCoho) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 8 days post immunization(8 DPI) using LEfSe,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Gracilibacteraceae|g__Gracilibacter|s__Gracilibacter thermotolerans",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|186802|541019|342658|342666,Complete,Svetlana up
bsdb:36253847/14/2,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 14,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Untreated mice cohoused with vancomycin-treated mice (ControlCoho) - 8 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 8 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 8 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 8 days post immunization(8 DPI),NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig. S4C,25 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between untreated mice cohoused with vancomycin-treated mice (ControlCoho) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 8 days post immunization(8 DPI) using LEfSe,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena orotica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella|s__Robinsoniella peoriensis",1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|2719313|1531;1783272|1239|186801|3085636|186803|2005359|1544;1783272|1239|186801|3085636|186803|588605|180332,Complete,Svetlana up
bsdb:36253847/15/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 15,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Untreated mice cohoused with vancomycin-treated mice (ControlCoho) - 15 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 15 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 15 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 15 days post immunization(15 DPI),NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. S4C,24 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between untreated mice cohoused with vancomycin-treated mice (ControlCoho) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 15 days post immunization(15 DPI) using LEfSe,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerocolumna|s__Anaerocolumna jejuensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora indolis",1783272|1239|186801|3085636|186803|1843210|259063;1783272|1239|186801|3085636|186803|2719231|69825,Complete,Svetlana up
bsdb:36253847/15/2,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 15,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Untreated mice cohoused with vancomycin-treated mice (ControlCoho) - 15 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 15 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 15 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 15 days post immunization(15 DPI),NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig. S4C,25 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between untreated mice cohoused with vancomycin-treated mice (ControlCoho) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 15 days post immunization(15 DPI),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena orotica,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes",1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|2719313|1531;1783272|1239|186801|3085636|186803|2005359|1544;1783272|1239|186801|186802|216572|459786|351091,Complete,Svetlana up
bsdb:36253847/16/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 16,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed control mice - 0 DPI,Single-treatment housed vancomycin mice - 0 DPI,"Single-treatment housed vancomycin mice refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin.",NA,NA,NA,16S,4,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Fig. 5A,25 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed untreated mice (control) and single-treatment housed vancomycin mice (vancomycin) at 0 day post immunization(3 DPI) using spearman correlation matrix.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",1783272|1239|91061|186826|81852|1350;1783272|1239|526524|526525|2810281|191303;3379134|74201|203494|48461|1647988|239934,Complete,Svetlana up
bsdb:36253847/16/2,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 16,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed control mice - 0 DPI,Single-treatment housed vancomycin mice - 0 DPI,"Single-treatment housed vancomycin mice refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin.",NA,NA,NA,16S,4,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Fig. 5A,25 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed untreated mice (control) and single-treatment housed vancomycin mice (vancomycin) at 0 day post immunization(0 DPI) using spearman correlation matrix.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora indolis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Parasporobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Parasporobacterium|s__Parasporobacterium paucivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|653683;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|2719231|69825;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|248744;1783272|1239|186801|3085636|186803|437755;1783272|1239|186801|3085636|186803|115543;1783272|1239|186801|3085636|186803|115543|115544;1783272|1239|186801|3085636|186803|588605;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3082720|3118655|44259;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|100175;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|44748;1783272|544448|31969|186332|186333|2086,Complete,Svetlana up
bsdb:36253847/17/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 17,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed control mice - 3 DPI,Single-treatment housed vancomycin mice - 3 DPI,"Single-treatment housed vancomycin mice refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 3 days post immunization(3 DPI).",NA,NA,NA,16S,4,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Fig. 5A,25 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed untreated mice (control) and single-treatment housed vancomycin mice (vancomycin) at 3 days post immunization(3 DPI) using spearman correlation matrix.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",1783272|1239|91061|186826|81852|1350;1783272|1239|526524|526525|2810281|191303;3379134|74201|203494|48461|1647988|239934,Complete,Svetlana up
bsdb:36253847/17/2,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 17,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed control mice - 3 DPI,Single-treatment housed vancomycin mice - 3 DPI,"Single-treatment housed vancomycin mice refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 3 days post immunization(3 DPI).",NA,NA,NA,16S,4,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Fig. 5A,25 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed untreated mice (control) and single-treatment housed vancomycin mice (vancomycin) at 3 days post immunization(3 DPI) using spearman correlation matrix.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma",1783272|1239|186801|3085636|186803|653683;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|526524|526525|128827|61170;1783272|544448|31969|186332|186333|2086,Complete,Svetlana up
bsdb:36253847/18/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 18,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed control mice - 8 DPI,Single-treatment housed vancomycin mice - 8 DPI,"Single-treatment housed vancomycin mice refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 8 days post immunization(8 DPI).",NA,NA,NA,16S,4,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Fig. 5A,25 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed untreated mice (control) and single-treatment housed vancomycin mice (vancomycin) at 8 day post immunization(8 DPI) using spearman correlation matrix.,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerocolumna|s__Anaerocolumna jejuensis",1783272|1239|526524|526525|128827|61170;1783272|1239|186801|186802|216572|244127|169435;1783272|1239|186801|186802|216572|596767;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|1843210|259063,Complete,Svetlana up
bsdb:36253847/19/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 19,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed control mice - 15 DPI,Single-treatment housed vancomycin mice - 15 DPI,"Single-treatment housed vancomycin mice - 15 DPI refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 15 days post immunization(15 DPI).",NA,NA,NA,16S,4,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 1,Fig. 5A,25 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed untreated mice (control) and single-treatment housed vancomycin mice (vancomycin) at 15 days post immunization(15 DPI) using spearman correlation matrix.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor|s__Acetatifactor muris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium",1783272|1239|186801|3082720|3118656|114627;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|46205;1783272|1239|186801|3085636|186803|1427378|879566;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|186802|216572|596767,Complete,Svetlana up
bsdb:36253847/19/2,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 19,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed control mice - 15 DPI,Single-treatment housed vancomycin mice - 15 DPI,"Single-treatment housed vancomycin mice - 15 DPI refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 15 days post immunization(15 DPI).",NA,NA,NA,16S,4,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 2,Fig. 5A,25 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed untreated mice (control) and single-treatment housed vancomycin mice (vancomycin) at 15 days post immunization(15 DPI) using spearman correlation matrix.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium celatum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella profusa,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis",3379134|976|200643|171549|2005519|397864;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|31979|1485|36834;1783272|201174|84998|84999|1643824|133925|138595;1783272|1239|526524|526525|2810281|191303;1783272|1239|526524|526525|2810281|191303|154288,Complete,Svetlana up
bsdb:36253847/20/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 20,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Pre-Experimental Autoimmune Encephalomyelitis induction(pre-EAE induction/Day 0): 0 day post immunization(0 DPI),Post-Experimental Autoimmune Encephalomyelitis induction-latent period(post-EAE induction): 3 days post immunization(3 DPI),"Post-Experimental Autoimmune Encephalomyelitis induction-latent period(post-EAE induction): 3 days post immunization(3 DPI), refers to fecal samples collected three days after immunization. Mice were immunized with Myelin oligodendrocyte glycoprotein(MOG) for EAE induction. EAE was induced by injecting 8- to 10-week-old female C57BL/6J mice with 150 mg MOG35–55 peptide (Genemed Synthesis) emulsified in complete Freund’s adjuvant (CFA) (BD Difco) per mouse subcutaneously in the flanks, followed by intraperitoneal administration of 150 ng pertussis toxin (List Biological Laboratories, Inc.) per mouse on days 0 and 2.",11,11,NA,16S,4,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 1G,26 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between 3 days post immunization(3 DPI) and 0 day post immunization(0 DPI) using Mann-Whitney,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora indolis,1783272|1239|186801|3085636|186803|2719231|69825,Complete,Svetlana up
bsdb:36253847/21/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 21,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Pre-Experimental Autoimmune Encephalomyelitis induction(pre-EAE induction/Day 0): 0 day post immunization(0 DPI),Post-Experimental Autoimmune Encephalomyelitis induction-latent period(post-EAE induction): 8 days post immunization(8 DPI),"Post-Experimental Autoimmune Encephalomyelitis induction-latent period(post-EAE induction): 8 days post immunization(8 DPI), refers to the timepoint for fecal sample collection(eight days after immunization). EAE was induced by injecting 8- to 10-week-old female C57BL/6J mice with 150 mg MOG35–55 peptide (Genemed Synthesis) emulsified in complete Freund’s adjuvant (CFA) (BD Difco) per mouse subcutaneously in the flanks, followed by intraperitoneal administration of 150 ng pertussis toxin (List Biological Laboratories, Inc.) per mouse on days 0 and 2.",11,11,NA,16S,4,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 1G,26 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between 8 days post immunization(8 DPI) and 0 day post immunization(0 DPI) using Mann-Whitney,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,1783272|1239|186801|3085636|186803|1506553|29347,Complete,Svetlana up
bsdb:36253847/22/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 22,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Pre-Experimental Autoimmune Encephalomyelitis induction(pre-EAE induction/Day 0): 0 day post immunization(0 DPI),Post-Experimental Autoimmune Encephalomyelitis induction-peak disease(post-EAE induction): 15 days post immunization(15 DPI),"Post-Experimental Autoimmune Encephalomyelitis induction-peak disease(post-EAE induction): 15 days post immunization(15 DPI), refers to the timepoint for fecal sample collection(fifteen days after immunization). This was also the peak of multiple sclerosis disease.",11,11,NA,16S,4,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 1G,26 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between 15 days post immunization(15 DPI) and 0 day post immunization(0 DPI) using Mann-Whitney,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|3085636|186803|1506553|29347,Complete,Svetlana up
bsdb:36253847/22/2,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 22,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Pre-Experimental Autoimmune Encephalomyelitis induction(pre-EAE induction/Day 0): 0 day post immunization(0 DPI),Post-Experimental Autoimmune Encephalomyelitis induction-peak disease(post-EAE induction): 15 days post immunization(15 DPI),"Post-Experimental Autoimmune Encephalomyelitis induction-peak disease(post-EAE induction): 15 days post immunization(15 DPI), refers to the timepoint for fecal sample collection(fifteen days after immunization). This was also the peak of multiple sclerosis disease.",11,11,NA,16S,4,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig. 1G,26 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between 15 days post immunization(15 DPI) and 0 day post immunization(0 DPI) using Mann-Whitney,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora indolis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis",1783272|1239|186801|3085636|186803|2719231|69825;1783272|1239|526524|526525|2810281|191303|154288,Complete,Svetlana up
bsdb:36253847/23/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 23,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed control mice - 0 DPI,Single-treatment housed vancomycin mice - 0 DPI,"Single-treatment housed vancomycin mice - 0 DPI refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 0 day post immunization(0 DPI).",NA,NA,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Fig. 4A,26 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 0 day post immunization(0 DPI) using Mann-Whitney,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|526524|526525|2810281|191303|154288,Complete,Svetlana up
bsdb:36253847/23/2,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 23,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed control mice - 0 DPI,Single-treatment housed vancomycin mice - 0 DPI,"Single-treatment housed vancomycin mice - 0 DPI refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 0 day post immunization(0 DPI).",NA,NA,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Fig. 4A,26 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 0 day post immunization(0 DPI) using Mann-Whitney,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerocolumna|s__Anaerocolumna jejuensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora indolis",1783272|1239|186801|3085636|186803|1843210|259063;1783272|1239|186801|186802|216572|244127|169435;1783272|1239|186801|3085636|186803|2719231|69825,Complete,Svetlana up
bsdb:36253847/24/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 24,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed control mice - 3 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI,"Single-treatment housed vancomycin mice - 3 DPI refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 3 days post immunization(3 DPI).",NA,NA,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Fig. 4A,26 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 3 days post immunization(3 DPI) using Mann-Whitney,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,1783272|1239|186801|186802|216572|244127|169435,Complete,Svetlana up
bsdb:36253847/24/2,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 24,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed control mice - 3 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI,"Single-treatment housed vancomycin mice - 3 DPI refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 3 days post immunization(3 DPI).",NA,NA,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Fig. 4A,26 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 3 days post immunization(3 DPI) using Mann-Whitney,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia cocleata,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|526524|526525|2810280|3025755|69824;1783272|1239|526524|526525|2810281|191303|154288;1783272|1239|186801|3085636|186803|1506553|29347,Complete,Svetlana up
bsdb:36253847/25/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 25,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed control mice - 8 DPI,Single-treatment housed vancomycin mice - 8 DPI,"Single-treatment housed vancomycin mice refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 8 days post immunization(8 DPI).",NA,NA,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Fig. 4A,26 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 8 day post immunization(8 DPI) using Mann-Whitney,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,1783272|1239|186801|186802|216572|244127|169435,Complete,Svetlana up
bsdb:36253847/25/2,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 25,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed control mice - 8 DPI,Single-treatment housed vancomycin mice - 8 DPI,"Single-treatment housed vancomycin mice refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 8 days post immunization(8 DPI).",NA,NA,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Fig. 4A,26 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 8 day post immunization(8 DPI) using Mann-Whitney,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia cocleata,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|526524|526525|2810280|3025755|69824;1783272|1239|186801|3085636|186803|1506553|29347,Complete,Svetlana up
bsdb:36253847/26/2,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 26,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed control mice - 15 DPI,Single-treatment housed vancomycin mice - 15 DPI,"Single-treatment housed vancomycin mice refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 15 days post immunization(15 DPI).",NA,NA,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 2,Fig. 4A,26 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 15 days post immunization(15 DPI) using Mann-Whitney,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerocolumna|s__Anaerocolumna jejuensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora indolis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens",1783272|1239|186801|3085636|186803|1843210|259063;1783272|1239|186801|3085636|186803|2719231|69825;1783272|1239|526524|526525|2810281|191303|154288;1783272|1239|186801|3085636|186803|1506553|29347,Complete,Svetlana up
bsdb:36253847/27/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 27,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed vancomycin mice (vancomycin) - 0 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 0 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 0 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 0 day post immunization(0 DPI).,NA,NA,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Fig. 4B,26 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 0 day post immunization(0 DPI) using Mann-Whitney,decreased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,3379134|74201|203494|48461|1647988|239934|239935,Complete,Svetlana up
bsdb:36253847/27/2,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 27,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed vancomycin mice (vancomycin) - 0 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 0 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 0 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 0 day post immunization(0 DPI).,NA,NA,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,Fig. 4B,26 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 0 day post immunization(0 DPI) using Mann-Whitney,increased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia cocleata,1783272|1239|526524|526525|2810280|3025755|69824,Complete,Svetlana up
bsdb:36253847/28/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 28,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed vancomycin mice (vancomycin) - 3 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 3 days post immunization(3 DPI).,NA,NA,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 4B,26 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 3 days post immunization(3 DPI) using Mann-Whitney,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,1783272|1239|186801|186802|216572|244127|169435,Complete,Svetlana up
bsdb:36253847/28/2,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 28,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed vancomycin mice (vancomycin) - 3 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 3 days post immunization(3 DPI).,NA,NA,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig. 4B,26 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 3 days post immunization(3 DPI) using Mann-Whitney,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia cocleata",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|526524|526525|2810280|3025755|69824,Complete,Svetlana up
bsdb:36253847/29/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 29,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed vancomycin mice (vancomycin) - 8 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 8 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 8 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 8 days post immunization(8 DPI).,NA,NA,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 4B,26 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 8 days post immunization(8 DPI) using Mann-Whitney,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,1783272|1239|186801|186802|216572|244127|169435,Complete,Svetlana up
bsdb:36253847/29/2,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 29,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed vancomycin mice (vancomycin) - 8 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 8 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 8 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 8 days post immunization(8 DPI).,NA,NA,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig. 4B,26 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 8 days post immunization(8 DPI) using Mann-Whitney,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia cocleata",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|526524|526525|2810280|3025755|69824,Complete,Svetlana up
bsdb:36253847/30/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 30,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed vancomycin mice (vancomycin) - 15 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 15 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 15 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 15 days post immunization(15 DPI).,NA,NA,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 4B,26 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 15 days post immunization(15 DPI) using Mann-Whitney,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,1783272|1239|186801|186802|216572|244127|169435,Complete,Svetlana up
bsdb:36253847/30/2,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 30,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Single-treatment housed vancomycin mice (vancomycin) - 15 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 15 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 15 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 15 days post immunization(15 DPI).,NA,NA,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig. 4B,26 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 15 days post immunization(15 DPI) using Mann-Whitney,decreased,NA,NA,Complete,Svetlana up
bsdb:36253847/31/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 31,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Untreated mice cohoused with vancomycin-treated mice (ControlCoho) - 0 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 0 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 0 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 0 day post immunization(0 DPI),NA,NA,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Fig. 4C,26 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between untreated mice cohoused with vancomycin-treated mice (ControlCoho) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 0 day post immunization(0 DPI),increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia cocleata",1783272|1239|526524|526525|2810280|100883|100884;1783272|1239|526524|526525|2810280|3025755|69824,Complete,Svetlana up
bsdb:36253847/32/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 32,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Untreated mice cohoused with vancomycin-treated mice (ControlCoho) - 3 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 3 days post immunization(3 DPI).,NA,NA,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 4C,26 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between untreated mice cohoused with vancomycin-treated mice (ControlCoho) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 3 days post immunization(3 DPI) using Mann-Whitney,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena orotica,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia cocleata",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|526524|526525|2810280|100883|100884;1783272|1239|186801|3085636|186803|2005359|1544;1783272|1239|526524|526525|2810280|3025755|69824,Complete,Svetlana up
bsdb:36253847/33/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 33,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Untreated mice cohoused with vancomycin-treated mice (ControlCoho) - 8 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 8 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 8 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 8 days post immunization(8 DPI),NA,NA,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 4C,26 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between untreated mice cohoused with vancomycin-treated mice (ControlCoho) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 8 days post immunization(8 DPI) using Mann-Whitney,increased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,3379134|74201|203494|48461|1647988|239934|239935,Complete,Svetlana up
bsdb:36253847/34/1,36253847,laboratory experiment,36253847,10.1186/s40168-022-01364-2,NA,"Bianchimano P., Britton G.J., Wallach D.S., Smith E.M., Cox L.M., Liu S., Iwanowski K., Weiner H.L., Faith J.J., Clemente J.C. , Tankou S.K.",Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis,Microbiome,2022,NA,Experiment 34,United States of America,Mus musculus,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Untreated mice cohoused with vancomycin-treated mice (ControlCoho) - 15 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 15 DPI,Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 15 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 15 days post immunization(15 DPI),NA,NA,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 4C,26 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between untreated mice cohoused with vancomycin-treated mice (ControlCoho) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 15 days post immunization(15 DPI) using Mann-Whitney,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora indolis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerocolumna|s__Anaerocolumna jejuensis",1783272|1239|186801|3085636|186803|2719231|69825;1783272|1239|186801|3085636|186803|1843210|259063,Complete,Svetlana up
bsdb:36303234/1/1,36303234,"cross-sectional observational, not case-control",36303234,10.1186/s13048-022-01051-8,NA,"Yin G., Chen F., Chen G., Yang X., Huang Q., Chen L., Chen M., Zhang W., Ou M., Cao M., Lin H., Chen M., Xu H., Ren J., Chen Y. , Chen Z.","Alterations of bacteriome, mycobiome and metabolome characteristics in PCOS patients with normal/overweight individuals",Journal of ovarian research,2022,"Diagnostic model, Metabolome, Mycobiome, Obesity, PCOS",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy Controls,PCOS (Polycystic ovary syndrome) Patients,This group comprises women diagnosed with Polycystic Ovary Syndrome (PCOS),41,47,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Fig. 2D,5 May 2025,Nithya,"Nithya,Joiejoie",Characteristic bacterial taxa based on LDA effect size (LEfSe) analysis between PCOS patients and healthy individuals.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira",3379134|1224|1236|91347|543|1940338;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|3085636|186803|28050,Complete,KateRasheed
bsdb:36303234/1/2,36303234,"cross-sectional observational, not case-control",36303234,10.1186/s13048-022-01051-8,NA,"Yin G., Chen F., Chen G., Yang X., Huang Q., Chen L., Chen M., Zhang W., Ou M., Cao M., Lin H., Chen M., Xu H., Ren J., Chen Y. , Chen Z.","Alterations of bacteriome, mycobiome and metabolome characteristics in PCOS patients with normal/overweight individuals",Journal of ovarian research,2022,"Diagnostic model, Metabolome, Mycobiome, Obesity, PCOS",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy Controls,PCOS (Polycystic ovary syndrome) Patients,This group comprises women diagnosed with Polycystic Ovary Syndrome (PCOS),41,47,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Fig. 2D,5 May 2025,Nithya,"Nithya,Joiejoie,Anne-mariesharp",Characteristic bacterial taxa based on LDA effect size (LEfSe) analysis between PCOS patients and healthy individuals.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|2005519|397864;1783272|201174|84998|84999|84107|102106;1783272|1239|526524|526525|2810280|100883;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|3085636|186803|28050|39485;1783272|201174|84998|1643822|1643826|84108;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|1508657,Complete,KateRasheed
bsdb:36303234/4/1,36303234,"cross-sectional observational, not case-control",36303234,10.1186/s13048-022-01051-8,NA,"Yin G., Chen F., Chen G., Yang X., Huang Q., Chen L., Chen M., Zhang W., Ou M., Cao M., Lin H., Chen M., Xu H., Ren J., Chen Y. , Chen Z.","Alterations of bacteriome, mycobiome and metabolome characteristics in PCOS patients with normal/overweight individuals",Journal of ovarian research,2022,"Diagnostic model, Metabolome, Mycobiome, Obesity, PCOS",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy-HB (High Body mass index) Subjects,PCOS-HB (Polycystic ovary syndrome - High Body mass index) Patients,This group refers to Polycystic ovary syndrome (PCOS) patients with a high body mass index (BMI ≥ 24),20,25,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Additional file 2: Figure S2b,6 May 2025,Nithya,"Nithya,Joiejoie,Anne-mariesharp",Reveal of characteristic bacterial taxa based on LDA Effect Size (LEfSe) analysis between Healthy-HB and PCOS-HB,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|186802|31979|1485|1522,Complete,KateRasheed
bsdb:36303234/4/2,36303234,"cross-sectional observational, not case-control",36303234,10.1186/s13048-022-01051-8,NA,"Yin G., Chen F., Chen G., Yang X., Huang Q., Chen L., Chen M., Zhang W., Ou M., Cao M., Lin H., Chen M., Xu H., Ren J., Chen Y. , Chen Z.","Alterations of bacteriome, mycobiome and metabolome characteristics in PCOS patients with normal/overweight individuals",Journal of ovarian research,2022,"Diagnostic model, Metabolome, Mycobiome, Obesity, PCOS",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy-HB (High Body mass index) Subjects,PCOS-HB (Polycystic ovary syndrome - High Body mass index) Patients,This group refers to Polycystic ovary syndrome (PCOS) patients with a high body mass index (BMI ≥ 24),20,25,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Additional file 2: Figure S2b,6 May 2025,Nithya,"Nithya,Joiejoie,Anne-mariesharp",Reveal of characteristic bacterial taxa based on LDA Effect Size (LEfSe) analysis between Healthy-HB and PCOS-HB,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter",3379134|1224|28216|80840|75682|846;1783272|201174|84998|1643822|1643826|84108;1783272|1239|186801|186802|186807|2740;1783272|201174|84998|1643822|1643826|447020;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|186801|186802|216572|1508657;3379134|200940|3031449|213115|194924|872;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|186806|1730|39496;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|171552|577309;1783272|1239|186801|186802|216572|3068309;1783272|1239|186801|3085636|186803|33042;1783272|201174|84998|84999|84107|102106;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|216572|1263;1783272|1239|909932|1843489|31977|39948;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|1766253,Complete,KateRasheed
bsdb:36303234/6/1,36303234,"cross-sectional observational, not case-control",36303234,10.1186/s13048-022-01051-8,NA,"Yin G., Chen F., Chen G., Yang X., Huang Q., Chen L., Chen M., Zhang W., Ou M., Cao M., Lin H., Chen M., Xu H., Ren J., Chen Y. , Chen Z.","Alterations of bacteriome, mycobiome and metabolome characteristics in PCOS patients with normal/overweight individuals",Journal of ovarian research,2022,"Diagnostic model, Metabolome, Mycobiome, Obesity, PCOS",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy-HB (High Body mass index) Subjects,PCOS-HB (Polycystic ovary syndrome - High Body mass index) Patients,This group refers to Polycystic ovary syndrome (PCOS) patients with a high body mass index (BMI ≥ 24),20,25,NA,ITS / ITS2,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Additional file 2: Figure S5,7 May 2025,Joiejoie,"Joiejoie,Nithya,Anne-mariesharp",Reveal of characteristic fungal taxa based on LDA Effect Size (LEfSe) analysis. Comparison between Healthy-HB and PCOS-HB.,increased,"k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Bolbitiaceae|g__Bolbitius,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Cladosporium,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Coniochaetales|f__Coniochaetaceae|g__Coniochaeta,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Kazachstania,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Meyerozyma,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Sordariaceae|g__Neurospora,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Thyridiales|f__Thyridiaceae|g__Thyridium,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Hypocreaceae|g__Trichoderma,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Xeromyces",4751|5204|155619|5338|5398|34438;4751|4890|3239874|2916678|766764|5475;4751|4890|147541|2726946|452563|5498;4751|4890|147550|292576|79807|79808;4751|4890|4891|4892|4893|71245;4751|5204|1538075|162474|742845|55193;4751|4890|3239874|2916678|766764|766728;4751|4890|147550|5139|5148|5140;4751|4890|147550|3402571|265081|265082;4751|4890|147550|5125|5129|5543;4751|4890|147545|5042|1131492|89490,Complete,KateRasheed
bsdb:36303234/6/2,36303234,"cross-sectional observational, not case-control",36303234,10.1186/s13048-022-01051-8,NA,"Yin G., Chen F., Chen G., Yang X., Huang Q., Chen L., Chen M., Zhang W., Ou M., Cao M., Lin H., Chen M., Xu H., Ren J., Chen Y. , Chen Z.","Alterations of bacteriome, mycobiome and metabolome characteristics in PCOS patients with normal/overweight individuals",Journal of ovarian research,2022,"Diagnostic model, Metabolome, Mycobiome, Obesity, PCOS",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy-HB (High Body mass index) Subjects,PCOS-HB (Polycystic ovary syndrome - High Body mass index) Patients,This group refers to Polycystic ovary syndrome (PCOS) patients with a high body mass index (BMI ≥ 24),20,25,NA,ITS / ITS2,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Additional file 2: Figure S5,7 May 2025,Joiejoie,"Joiejoie,Nithya,Anne-mariesharp",Reveal of characteristic fungal taxa based on LDA Effect Size (LEfSe) analysis. Comparison between Healthy-HB and PCOS-HB.,decreased,"k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Microascales|f__Microascaceae|g__Acaulium,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Acrocalymmaceae|g__Acrocalymma,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Chaetomiaceae|g__Acrophialophora,k__Fungi|p__Ascomycota|c__Archaeorhizomycetes|o__Archaeorhizomycetales|f__Archaeorhizomycetaceae|g__Archaeorhizomyces|s__Archaeorhizomyces sp.,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales|f__Ploettnerulaceae|g__Cadophora,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Calonectria,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Microascales|f__Microascaceae|g__Cephalotrichum,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Lasiosphaeriaceae|g__Cercophora,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Chaetomiaceae|g__Chaetomium,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Onygenales|f__Onygenaceae|g__Chrysosporium,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Chaetothyriales|f__Herpotrichiellaceae|g__Cladophialophora,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Clavariaceae|g__Clavulinopsis,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Glomerellaceae|g__Colletotrichum,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Cordycipitaceae|g__Cordyceps,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Hygrophoraceae|g__Cuphophyllus,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Dactylonectria,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Chaetomiaceae|g__Dichotomopilus,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Didymellaceae|g__Didymella,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Didymellaceae|g__Endophoma,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Didymellaceae|g__Epicoccum,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Chaetothyriales|f__Herpotrichiellaceae|g__Exophiala,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Onygenales|f__Gymnoascaceae|g__Gymnoascus,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Melanommataceae|g__Herpotrichia,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Hypocreaceae|g__Hypomyces,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Xylariales|f__Microdochiaceae|g__Idriella,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Ilyonectria,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Chaetothyriales|f__Trichomeriaceae|g__Knufia,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales|f__Lachnaceae|g__Lachnum,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Plectosphaerellaceae|g__Lectera,k__Fungi|p__Ascomycota|c__Leotiomycetes|g__Leohumicola,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Clavicipitaceae|g__Metarhizium,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Microascales|f__Microascaceae|g__Microascus,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Cantharellales|f__Hydnaceae|g__Minimedusa,k__Fungi|p__Mucoromycota|c__Mortierellomycetes|o__Mortierellales|f__Mortierellaceae|g__Mortierella,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Phaeosphaeriaceae|g__Ophiosphaerella,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales|f__Pezizellaceae|g__Pezizella,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Leptosphaeriaceae|g__Plenodomus,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Thelebolales|f__Thelebolaceae|g__Pseudogymnoascus,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Ophiocordycipitaceae|g__Purpureocillium,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Pyrenochaetopsidaceae|g__Pyrenochaetopsis,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Rachicladosporium,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|g__Remersonia,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Trichocomaceae|g__Sagenomella,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Schizotheciaceae|g__Schizothecium,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Venturiales|f__Sympoventuriaceae|g__Scolecobasidium,k__Fungi|p__Ascomycota|c__Leotiomycetes|g__Scytalidium,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Sebacinales|f__Serendipitaceae|g__Serendipita,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Filobasidiales|f__Piskurozymaceae|g__Solicoccozyma,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Chaetomiaceae|g__Staphylotrichum,k__Fungi|p__Zoopagomycota|c__Zoopagomycetes|o__Zoopagales|f__Piptocephalidaceae|g__Syncephalis,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales|g__Tetracladium,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Thelonectria,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Chaetomiaceae|g__Trichocladium",4751|4890|147550|5592|5593|1960041;4751|4890|147541|92860|1589760|1319578;4751|4890|147550|5139|35718|389487;4751|4890|1075807|1075813|1075814|1075815|1903959;4751|4890|147548|5178|2316155|210567;4751|4890|147550|5125|110618|57138;4751|4890|147550|5592|5593|1658452;4751|4890|147550|5139|42302|42303;4751|4890|147550|5139|35718|5149;4751|4890|147545|33183|33184|40411;4751|4890|147545|34395|43219|82105;4751|5204|155619|5338|40105|104211;4751|4890|147550|1028384|681950|5455;4751|4890|147550|5125|474943|45234;4751|5204|155619|5338|51005|596302;4751|4890|147550|5125|110618|1620264;4751|4890|147550|5139|35718|1934375;4751|4890|147541|92860|683158|55170;4751|4890|147541|92860|683158|1069085;4751|4890|147541|92860|683158|104397;4751|4890|147545|34395|43219|5583;4751|4890|147550|5125|110618|5506;4751|4890|147545|33183|37243|69889;4751|4890|147541|92860|45307|45144;4751|4890|147550|5125|5129|5130;4751|4890|147550|37989|1682405|412494;4751|4890|147550|5125|110618|1079112;4751|4890|147545|34395|1233474|430999;4751|4890|147548|5178|2589077|47817;4751|4890|147550|1028384|1033978|1208924;4751|4890|147548|290614;4751|4890|147550|5125|34397|5529;4751|4890|147550|5592|5593|5594;4751|5204|155619|36064|68758|411563;4751|1913637|2212732|214503|4854|4855;4751|4890|147541|92860|5020|33174;4751|4890|147548|5178|2488219|1033671;4751|4890|147541|92860|34374|118259;4751|4890|147548|292491|46451|78156;4751|4890|147550|5125|474942|1052105;4751|4890|147541|92860|2078572|798144;4751|4890|147541|2726946|452563|470018;4751|4890|147550|5139|72143;4751|4890|147545|5042|28568|89791;4751|4890|147550|5139|2891592|252155;4751|4890|147541|1111111|1111112|37940;4751|4890|147548|5538;4751|5204|155619|297313|1506295|358905;4751|5204|155616|90886|1851565|1851575;4751|4890|147550|5139|35718|370954;4751|1913638|2233521|78899|78903|78910;4751|4890|147548|5178|164535;4751|4890|147550|5125|110618|1053258;4751|4890|147550|5139|35718|290625,Complete,KateRasheed
bsdb:36303234/7/1,36303234,"cross-sectional observational, not case-control",36303234,10.1186/s13048-022-01051-8,NA,"Yin G., Chen F., Chen G., Yang X., Huang Q., Chen L., Chen M., Zhang W., Ou M., Cao M., Lin H., Chen M., Xu H., Ren J., Chen Y. , Chen Z.","Alterations of bacteriome, mycobiome and metabolome characteristics in PCOS patients with normal/overweight individuals",Journal of ovarian research,2022,"Diagnostic model, Metabolome, Mycobiome, Obesity, PCOS",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy subjects,PCOS (Polycystic ovary syndrome) patients,This group comprises polycystic ovary syndrome (PCOS) patients,41,47,NA,ITS / ITS2,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Fig. 3F,7 May 2025,Nithya,"Nithya,Joiejoie",Characteristic fungal taxa based on LDA effect size (LEfSe) analysis between PCOS patients and healthy individuals,increased,"k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus,k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Ascodesmidaceae|g__Cephaliophora,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Coniochaetales|f__Coniochaetaceae|g__Coniochaeta,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycodales|f__Saccharomycodaceae|g__Hanseniaspora,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Kazachstania,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Microascales|f__Microascaceae|g__Microascus,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Phaeosphaeriaceae|g__Paraphoma,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Schizophyllaceae|g__Schizophyllum",4751|4890|147545|5042|1131492|5052;4751|4890|147549|5185|47181|77526;4751|4890|147550|292576|79807|79808;4751|4890|4891|3243779|34365|29832;4751|4890|4891|4892|4893|71245;4751|5204|1538075|162474|742845|55193;4751|4890|147550|5592|5593|5594;4751|4890|147541|92860|5020|798070;4751|5204|155619|5338|5332|5333,Complete,KateRasheed
bsdb:36303234/7/2,36303234,"cross-sectional observational, not case-control",36303234,10.1186/s13048-022-01051-8,NA,"Yin G., Chen F., Chen G., Yang X., Huang Q., Chen L., Chen M., Zhang W., Ou M., Cao M., Lin H., Chen M., Xu H., Ren J., Chen Y. , Chen Z.","Alterations of bacteriome, mycobiome and metabolome characteristics in PCOS patients with normal/overweight individuals",Journal of ovarian research,2022,"Diagnostic model, Metabolome, Mycobiome, Obesity, PCOS",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy subjects,PCOS (Polycystic ovary syndrome) patients,This group comprises polycystic ovary syndrome (PCOS) patients,41,47,NA,ITS / ITS2,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Fig. 3F,7 May 2025,Nithya,"Nithya,Joiejoie",Characteristic fungal taxa based on LDA effect size (LEfSe) analysis between PCOS patients and healthy individuals.,decreased,"k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Acrocalymmaceae|g__Acrocalymma,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Chaetomiaceae|g__Acrophialophora,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales|f__Ploettnerulaceae|g__Cadophora,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Calonectria,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Microascales|f__Microascaceae|g__Cephalotrichum,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Lasiosphaeriaceae|g__Cercophora,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Chaetomiaceae|g__Chaetomidium,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Chaetomiaceae|g__Chaetomium,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Onygenales|f__Onygenaceae|g__Chrysosporium,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Chaetothyriales|f__Herpotrichiellaceae|g__Cladophialophora,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Clavariaceae|g__Clavulinopsis,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Bionectriaceae|g__Clonostachys,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Cordycipitaceae|g__Cordyceps,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Hygrophoraceae|g__Cuphophyllus,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Dactylonectria,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Chaetomiaceae|g__Dichotomopilus,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Didymellaceae|g__Didymella,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Entolomataceae|g__Entoloma,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Didymellaceae|g__Epicoccum,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Chaetothyriales|f__Herpotrichiellaceae|g__Exophiala,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Onygenales|f__Gymnoascaceae|g__Gymnoascus,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Melanommataceae|g__Herpotrichia,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Xylariales|f__Microdochiaceae|g__Idriella,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Ilyonectria,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Chaetothyriales|f__Trichomeriaceae|g__Knufia,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Plectosphaerellaceae|g__Lectera,k__Fungi|p__Ascomycota|c__Leotiomycetes|g__Leohumicola,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Clavicipitaceae|g__Metarhizium,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Cantharellales|f__Hydnaceae|g__Minimedusa,k__Fungi|p__Mucoromycota|c__Mortierellomycetes|o__Mortierellales|f__Mortierellaceae|g__Mortierella,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Nectria,k__Fungi|p__Ascomycota|c__Leotiomycetes|f__Myxotrichaceae|g__Oidiodendron,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Phaeosphaeriaceae|g__Ophiosphaerella,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Thelebolales|f__Thelebolaceae|g__Pseudogymnoascus,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Ophiocordycipitaceae|g__Purpureocillium,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|g__Remersonia,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Trichocomaceae|g__Sagenomella,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Sarocladiaceae|g__Sarocladium,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Schizotheciaceae|g__Schizothecium,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Sebacinales|f__Serendipitaceae|g__Serendipita,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Phaeosphaeriaceae|g__Setophoma,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Filobasidiales|f__Piskurozymaceae|g__Solicoccozyma,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Chaetomiaceae|g__Staphylotrichum,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Strophariaceae|g__Stropharia,k__Fungi|p__Zoopagomycota|c__Zoopagomycetes|o__Zoopagales|f__Piptocephalidaceae|g__Syncephalis,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Tausonia,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales|g__Tetracladium",4751|4890|147541|92860|1589760|1319578;4751|4890|147550|5139|35718|389487;4751|4890|147548|5178|2316155|210567;4751|4890|147550|5125|110618|57138;4751|4890|147550|5592|5593|1658452;4751|4890|147550|5139|42302|42303;4751|4890|147550|5139|35718|223383;4751|4890|147550|5139|35718|5149;4751|4890|147545|33183|33184|40411;4751|4890|147545|34395|43219|82105;4751|5204|155619|5338|40105|104211;4751|4890|147550|5125|103887|110564;4751|4890|147550|5125|474943|45234;4751|5204|155619|5338|51005|596302;4751|4890|147550|5125|110618|1620264;4751|4890|147550|5139|35718|1934375;4751|4890|147541|92860|683158|55170;4751|5204|155619|5338|71934|71937;4751|4890|147541|92860|683158|104397;4751|4890|147545|34395|43219|5583;4751|4890|147550|5125|110618|5506;4751|4890|147545|33183|37243|69889;4751|4890|147541|92860|45307|45144;4751|4890|147550|37989|1682405|412494;4751|4890|147550|5125|110618|1079112;4751|4890|147545|34395|1233474|430999;4751|4890|147550|1028384|1033978|1208924;4751|4890|147548|290614;4751|4890|147550|5125|34397|5529;4751|5204|155619|36064|68758|411563;4751|1913637|2212732|214503|4854|4855;4751|4890|147550|5125|110618|5133;4751|4890|147548|37240|78141;4751|4890|147541|92860|5020|33174;4751|4890|147548|292491|46451|78156;4751|4890|147550|5125|474942|1052105;4751|4890|147550|5139|72143;4751|4890|147545|5042|28568|89791;4751|4890|147550|5125|2502719|284134;4751|4890|147550|5139|2891592|252155;4751|5204|155619|297313|1506295|358905;4751|4890|147541|92860|5020|798159;4751|5204|155616|90886|1851565|1851575;4751|4890|147550|5139|35718|370954;4751|5204|155619|5338|40562|68745;4751|1913638|2233521|78899|78903|78910;4751|5204|155616|90883|1851551|415704;4751|4890|147548|5178|164535,Complete,KateRasheed
bsdb:36303234/8/1,36303234,"cross-sectional observational, not case-control",36303234,10.1186/s13048-022-01051-8,NA,"Yin G., Chen F., Chen G., Yang X., Huang Q., Chen L., Chen M., Zhang W., Ou M., Cao M., Lin H., Chen M., Xu H., Ren J., Chen Y. , Chen Z.","Alterations of bacteriome, mycobiome and metabolome characteristics in PCOS patients with normal/overweight individuals",Journal of ovarian research,2022,"Diagnostic model, Metabolome, Mycobiome, Obesity, PCOS",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy-LB (Normal Body mass index) subjects,PCOS-LB (Polycystic ovary syndrome - Normal Body mass index) patients,This group comprises Polycystic ovary syndrome (PCOS) patients with a body mass index (BMI < 24),21,22,NA,ITS / ITS2,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Additional file 2: Figure S4,9 May 2025,Nithya,"Nithya,Anne-mariesharp",Reveal of characteristic fungal taxa based on LDA Effect Size (LEfSe) analysis. Comparison between Healthy-LB and PCOS-LB.,increased,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Thyridiales|f__Thyridiaceae|g__Thyridium,4751|4890|147550|3402571|265081|265082,Complete,KateRasheed
bsdb:36303234/8/2,36303234,"cross-sectional observational, not case-control",36303234,10.1186/s13048-022-01051-8,NA,"Yin G., Chen F., Chen G., Yang X., Huang Q., Chen L., Chen M., Zhang W., Ou M., Cao M., Lin H., Chen M., Xu H., Ren J., Chen Y. , Chen Z.","Alterations of bacteriome, mycobiome and metabolome characteristics in PCOS patients with normal/overweight individuals",Journal of ovarian research,2022,"Diagnostic model, Metabolome, Mycobiome, Obesity, PCOS",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy-LB (Normal Body mass index) subjects,PCOS-LB (Polycystic ovary syndrome - Normal Body mass index) patients,This group comprises Polycystic ovary syndrome (PCOS) patients with a body mass index (BMI < 24),21,22,NA,ITS / ITS2,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Additional file 2: Figure S4,9 May 2025,Nithya,"Nithya,Anne-mariesharp",Reveal of characteristic fungal taxa based on LDA Effect Size (LEfSe) analysis. Comparison between Healthy-LB and PCOS-LB.,decreased,"k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Onygenales|f__Ascosphaeraceae|g__Ascosphaera,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Bolbitiaceae|g__Bolbitius,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Chaetomiaceae|g__Botryotrichum,k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Ascodesmidaceae|g__Cephaliophora,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Cylindrocarpon,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Meyerozyma,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Nectria,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Sordariaceae|g__Neurospora,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Sarocladiaceae|g__Sarocladium,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Phaeosphaeriaceae|g__Setophoma,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Filobasidiales|f__Piskurozymaceae|g__Solicoccozyma,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Didymellaceae|g__Stagonosporopsis,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales|g__Tetracladium,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Sporormiaceae|g__Westerdykella",4751|4890|147545|33183|5103|5104;4751|5204|155619|5338|5398|34438;4751|4890|147550|5139|35718|1934360;4751|4890|147549|5185|47181|77526;4751|4890|147550|5125|110618|13474;4751|4890|3239874|2916678|766764|766728;4751|4890|147550|5125|110618|5133;4751|4890|147550|5139|5148|5140;4751|4890|147550|5125|2502719|284134;4751|4890|147541|92860|5020|798159;4751|5204|155616|90886|1851565|1851575;4751|4890|147541|92860|683158|749880;4751|4890|147548|5178|164535;4751|4890|147541|92860|55176|45153,Complete,KateRasheed
bsdb:36303234/11/1,36303234,"cross-sectional observational, not case-control",36303234,10.1186/s13048-022-01051-8,NA,"Yin G., Chen F., Chen G., Yang X., Huang Q., Chen L., Chen M., Zhang W., Ou M., Cao M., Lin H., Chen M., Xu H., Ren J., Chen Y. , Chen Z.","Alterations of bacteriome, mycobiome and metabolome characteristics in PCOS patients with normal/overweight individuals",Journal of ovarian research,2022,"Diagnostic model, Metabolome, Mycobiome, Obesity, PCOS",Experiment 11,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy-LB (Normal Body mass index) subjects,PCOS-LB (Polycystic ovary syndrome - Normal Body mass index) patients,This group comprises Polycystic ovary syndrome (PCOS) patients with a body mass index (BMI < 24),21,22,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Additional file 2: Figure S2a,8 May 2025,Nithya,"Nithya,Anne-mariesharp",Reveal of characteristic bacterial taxa based on LDA Effect Size (LEfSe) analysis between Healthy-LB and PCOS-LB,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572|459786,Complete,KateRasheed
bsdb:36303234/11/2,36303234,"cross-sectional observational, not case-control",36303234,10.1186/s13048-022-01051-8,NA,"Yin G., Chen F., Chen G., Yang X., Huang Q., Chen L., Chen M., Zhang W., Ou M., Cao M., Lin H., Chen M., Xu H., Ren J., Chen Y. , Chen Z.","Alterations of bacteriome, mycobiome and metabolome characteristics in PCOS patients with normal/overweight individuals",Journal of ovarian research,2022,"Diagnostic model, Metabolome, Mycobiome, Obesity, PCOS",Experiment 11,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy-LB (Normal Body mass index) subjects,PCOS-LB (Polycystic ovary syndrome - Normal Body mass index) patients,This group comprises Polycystic ovary syndrome (PCOS) patients with a body mass index (BMI < 24),21,22,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Additional file 2: Figure S2a,8 May 2025,Nithya,"Nithya,Anne-mariesharp",Reveal of characteristic bacterial taxa based on LDA Effect Size (LEfSe) analysis between Healthy-LB and PCOS-LB,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus",1783272|1239|526524|526525|2810280|135858;1783272|1239|526524|526525|2810280|100883;1783272|1239|186801|3085636|186803|33042,Complete,KateRasheed
bsdb:36316382/1/1,36316382,"cross-sectional observational, not case-control",36316382,10.1038/s41598-022-23124-w,NA,"Hazarika P., Chattopadhyay I., Umpo M., Choudhury Y. , Sharma I.",Elucidating the gut microbiome alterations of tribal community of Arunachal Pradesh: perspectives on their lifestyle or food habits,Scientific reports,2022,NA,Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Combination of Adi Tribe + Apatani Tribe,Nyshi Tribe,"The Nyshi tribe, which is Group 3, consisted of individuals whose diet mainly included rice, with differences in the consumption of cereals, millets, leaves, fish, meat and they had a mean age ± SD of (41.9 ± 4.7,range 20–60)",20,10,6 months,16S,34,Illumina,raw counts,G-test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,26 October 2025,Mukesh,Mukesh,"Statistically significant different bacterial species in the Adi tribe(Group 1), Apatani tribe(Group 2) and Nyshi tribe(Group 3).",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter johnsonii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri",3379134|1224|1236|2887326|468|469|40214;1783272|201174|84998|84999|84107|102106|74426;3379134|976|200643|171549|171552|2974251|165179,Complete,NA
bsdb:36316382/2/1,36316382,"cross-sectional observational, not case-control",36316382,10.1038/s41598-022-23124-w,NA,"Hazarika P., Chattopadhyay I., Umpo M., Choudhury Y. , Sharma I.",Elucidating the gut microbiome alterations of tribal community of Arunachal Pradesh: perspectives on their lifestyle or food habits,Scientific reports,2022,NA,Experiment 2,India,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Combination of Adi Tribe + Nyshi Tribe,Apatani Tribe,"The Apatani tribe, which is Group 2, consisted of individuals whose diet primarily included boiled rice, boiled vegetables, boiled fish, meat, dairy products in each serving and they had a mean age ± SD of (42.5 ± 4.1, range 21–60)",20,10,6 months,16S,34,Illumina,raw counts,G-test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,26 October 2025,Tosin,Tosin,"Statistically significant different bacterial species in the Adi tribe(Group 1), Apatani tribe(Group 2) and Nyshi tribe(Group 3)",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans",1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|3085636|186803|189330|39486,Complete,NA
bsdb:36316382/2/2,36316382,"cross-sectional observational, not case-control",36316382,10.1038/s41598-022-23124-w,NA,"Hazarika P., Chattopadhyay I., Umpo M., Choudhury Y. , Sharma I.",Elucidating the gut microbiome alterations of tribal community of Arunachal Pradesh: perspectives on their lifestyle or food habits,Scientific reports,2022,NA,Experiment 2,India,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Combination of Adi Tribe + Nyshi Tribe,Apatani Tribe,"The Apatani tribe, which is Group 2, consisted of individuals whose diet primarily included boiled rice, boiled vegetables, boiled fish, meat, dairy products in each serving and they had a mean age ± SD of (42.5 ± 4.1, range 21–60)",20,10,6 months,16S,34,Illumina,raw counts,G-test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,30 October 2025,Tosin,Tosin,"Statistically significant different bacterial species in the Adi tribe(Group 1), Apatani tribe(Group 2) and Nyshi tribe(Group 3)",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|171552|2974257|425941;3379134|976|200643|171549|171552|2974265|363265;1783272|1239|91061|186826|33958|2767887|1623;1783272|1239|909932|1843489|31977|29465|39778,Complete,NA
bsdb:36316382/3/1,36316382,"cross-sectional observational, not case-control",36316382,10.1038/s41598-022-23124-w,NA,"Hazarika P., Chattopadhyay I., Umpo M., Choudhury Y. , Sharma I.",Elucidating the gut microbiome alterations of tribal community of Arunachal Pradesh: perspectives on their lifestyle or food habits,Scientific reports,2022,NA,Experiment 3,India,Homo sapiens,Feces,UBERON:0001988,Ethnic group,EFO:0001799,Combination of Apatani Tribe + Nyshi Tribe,Adi Tribe,"The Adi tribe, which is Group 1, consisted of individuals whose common diet mainly included rice, with variations in the consumption of cereals, millets, leaves, fish, meat and they had a mean age ± SD of (39.5 ± 4.3; range 20–60).",20,10,6 months,16S,34,Illumina,raw counts,G-test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,28 October 2025,Mukesh,Mukesh,"Statistically significant different bacterial species in the Adi tribe(Group 1), Apatani tribe(Group 2) and Nyshi tribe(Group 3)",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus flavefaciens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus",3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|820;1783272|201174|1760|85004|31953|1678|1680;1783272|1239|186801|3085636|186803|33042|33043;1783272|1239|526524|526525|128827|1573535|1735;1783272|1239|186801|186802|216572|1263|1265;1783272|1239|91061|186826|1300|1301|1328,Complete,NA
bsdb:36318010/1/1,36318010,laboratory experiment,36318010,https://doi.org/10.1128/spectrum.00157-22,https://journals.asm.org/doi/10.1128/spectrum.00157-22,"Zhao J., Lu W., Huang S., Le Maho Y., Habold C. , Zhang Z.","Impacts of Dietary Protein and Niacin Deficiency on Reproduction Performance, Body Growth, and Gut Microbiota of Female Hamsters (Tscherskia triton) and Their Offspring",Microbiology spectrum,2022,"cropland monoculture, greater long-tailed hamster, gut microbiota, low-protein diet, niacin deficiency",Experiment 1,China,Tscherskia triton,Feces,UBERON:0001988,Response to diet,EFO:0010757,Female hamsters Normal-protein diet (NPD) group,Female hamsters Low-protein diet (LPD) group,Female hamsters under low-protein diet LPD,NA,NA,NA,16S,34,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S5 and Figure 5A,24 March 2024,Aleru Divine,"Aleru Divine,KateRasheed,WikiWorks",Significant differential abundance in fecal microbiota of female hamster in Normal-protein diet (NPD) versus low-protein diet (LPD).,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Sterolibacteriaceae|g__Georgfuchsia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae",1783272|1239|526524|526525|128827|174708;3379134|976|200643|171549|815|816;1783272|1239|91061|1385|186817;1783272|1239|909932|1843489|31977;3379134|976|200643|171549|2005520|156973;3379134|1224|28216|32003|2008793|690621;3379134|976|200643|171549|171552;1783272|544448|31969|186332|186333|2086;3384189|32066|203490|203491|203492,Complete,Peace Sandy
bsdb:36318010/1/2,36318010,laboratory experiment,36318010,https://doi.org/10.1128/spectrum.00157-22,https://journals.asm.org/doi/10.1128/spectrum.00157-22,"Zhao J., Lu W., Huang S., Le Maho Y., Habold C. , Zhang Z.","Impacts of Dietary Protein and Niacin Deficiency on Reproduction Performance, Body Growth, and Gut Microbiota of Female Hamsters (Tscherskia triton) and Their Offspring",Microbiology spectrum,2022,"cropland monoculture, greater long-tailed hamster, gut microbiota, low-protein diet, niacin deficiency",Experiment 1,China,Tscherskia triton,Feces,UBERON:0001988,Response to diet,EFO:0010757,Female hamsters Normal-protein diet (NPD) group,Female hamsters Low-protein diet (LPD) group,Female hamsters under low-protein diet LPD,NA,NA,NA,16S,34,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S5 and Figure 5A,24 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",Significant differential abundance in fecal microbiota of female hamster in Normal-protein diet (NPD) versus low-protein diet (LPD).,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium afermentans,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Elizabethkingia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Macellibacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Millisia,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Oleomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae",3379134|1224|1236|2887326|468|469;1783272|1239|526524|526525|128827|174708;1783272|201174|1760|85007|1653|1716|38286;3379134|976|117743|200644|2762318|308865;1783272|1239|186801|186802|204475;3379134|976|200643|171549|171551|1159323;1783272|201174|1760|85007|85026|264147;3379134|200930|68337|191393|2945020|248038;1783272|544448|31969|2085|2092|2093;3379134|1224|28211|3120395|433|217063;1783272|1239|186801|186802|216572|119852;3379134|203691|203692|136|137|146;1783272|1239;3379134|976;3379134|1224|1236;3379134|976|200643|171549|171552|577309;1783272|1239|186801|3082720|186804;3379134|976|117743|200644|2762318,Complete,Peace Sandy
bsdb:36318010/4/1,36318010,laboratory experiment,36318010,https://doi.org/10.1128/spectrum.00157-22,https://journals.asm.org/doi/10.1128/spectrum.00157-22,"Zhao J., Lu W., Huang S., Le Maho Y., Habold C. , Zhang Z.","Impacts of Dietary Protein and Niacin Deficiency on Reproduction Performance, Body Growth, and Gut Microbiota of Female Hamsters (Tscherskia triton) and Their Offspring",Microbiology spectrum,2022,"cropland monoculture, greater long-tailed hamster, gut microbiota, low-protein diet, niacin deficiency",Experiment 4,China,Tscherskia triton,Feces,UBERON:0001988,Response to diet,EFO:0010757,Offspring hamsters naicin+ group,Offspring hamsters niacin- group,Offspring hamsters under niacin-deficient (niacin-) diet.,NA,NA,NA,16S,34,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Table S7 and Figure 5B,24 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",Significant differential abundance in fecal microbiota of offspring hamster in niacin-supplemented diet (Niacin+) versus niacin-deficient diet (Niacin−).,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Proteiniborus",1783272|201174|1760|2037;3379134|203691|203692|136|137|146;1783272|1239|186801|186802|415014,Complete,Svetlana up
bsdb:36318010/4/2,36318010,laboratory experiment,36318010,https://doi.org/10.1128/spectrum.00157-22,https://journals.asm.org/doi/10.1128/spectrum.00157-22,"Zhao J., Lu W., Huang S., Le Maho Y., Habold C. , Zhang Z.","Impacts of Dietary Protein and Niacin Deficiency on Reproduction Performance, Body Growth, and Gut Microbiota of Female Hamsters (Tscherskia triton) and Their Offspring",Microbiology spectrum,2022,"cropland monoculture, greater long-tailed hamster, gut microbiota, low-protein diet, niacin deficiency",Experiment 4,China,Tscherskia triton,Feces,UBERON:0001988,Response to diet,EFO:0010757,Offspring hamsters naicin+ group,Offspring hamsters niacin- group,Offspring hamsters under niacin-deficient (niacin-) diet.,NA,NA,NA,16S,34,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Table S7 and Figure 5B,24 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",Significant differential abundance in fecal microbiota of offspring hamster in niacin-supplemented diet (Niacin+) versus niacin-deficient diet (Niacin−).,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Alkanindiges,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hespellia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Macrococcus,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",3379134|1224|1236|2887326|468|222991;1783272|201174|1760|85006|1268|1663;1783272|1239|186801|3085636|186803|241189;1783272|1239|91061|1385|90964|69965;3379134|200930|68337|191393|2945020|248038;3379134|1224|28216|80840|80864;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|171551;1783272|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:36329122/3/1,36329122,"cross-sectional observational, not case-control",36329122,https://doi.org/10.1038/s41598-022-21779-z,NA,"Clarke T., Brinkac L., Greco C., Alleyne A.T., Carrasco P., Inostroza C., Tau T., Wisitrasameewong W., Torralba M.G., Nelson K. , Singh H.",Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes,Scientific reports,2022,NA,Experiment 3,"Barbados,Chile,South Africa,Thailand",Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,"Barbados, Chile, South Africa",Thailand,"Thailand refers to the samples from healthy females aged between 18 and 26 years, based in Thailand.",138,68,currently on antibiotics,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S8,12 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in stool samples for Thailand location.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae",3379134|1224|1236|91347|543|561|562;3384189|32066|203490|203491|203492|848|850;3379134|976|200643|171549|815|909656|310298;3379134|976|200643|171549|815|909656|204516;3379134|976|200643|171549|815|909656|310297;1783272|1239|186801|186802|216572|1263|457412;3379134|976|200643|171549|171550|239759;3379134|1224|28216|80840|995019|40544;3379134|976|200643|171549|2005525|375288|46503,Complete,Svetlana up
bsdb:36329122/3/2,36329122,"cross-sectional observational, not case-control",36329122,https://doi.org/10.1038/s41598-022-21779-z,NA,"Clarke T., Brinkac L., Greco C., Alleyne A.T., Carrasco P., Inostroza C., Tau T., Wisitrasameewong W., Torralba M.G., Nelson K. , Singh H.",Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes,Scientific reports,2022,NA,Experiment 3,"Barbados,Chile,South Africa,Thailand",Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,"Barbados, Chile, South Africa",Thailand,"Thailand refers to the samples from healthy females aged between 18 and 26 years, based in Thailand.",138,68,currently on antibiotics,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S8,12 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in stool samples for Thailand location.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio|s__uncultured Pseudobutyrivibrio sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|s__uncultured Prevotellaceae bacterium,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Liu et al. 2021),k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__uncultured Bacteroides sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|s__uncultured Christensenellaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__uncultured Dorea sp.",1783272|1239|186801|3085636|186803|46205|557192;3379134|976|200643|171549|171552|370804;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|815|816|28116;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|1263|3062497;3379134|976|200643|171549|815|816|162156;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3082768|990719|1229255;1783272|1239|186801|3085636|186803|189330|286138,Complete,Svetlana up
bsdb:36329122/4/1,36329122,"cross-sectional observational, not case-control",36329122,https://doi.org/10.1038/s41598-022-21779-z,NA,"Clarke T., Brinkac L., Greco C., Alleyne A.T., Carrasco P., Inostroza C., Tau T., Wisitrasameewong W., Torralba M.G., Nelson K. , Singh H.",Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes,Scientific reports,2022,NA,Experiment 4,"Barbados,Chile,South Africa,Thailand",Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,"Chile, South Africa, Thailand",Barbados,"Barbados refers to the samples from healthy females aged between 18 and 26 years, based in Barbados.",174,32,currently on antibiotics,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S9,12 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in stool samples for Barbados location.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio|s__uncultured Pseudobutyrivibrio sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__uncultured Bacteroides sp.",1783272|1239|186801|3085636|186803|46205|557192;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|162156,Complete,Svetlana up
bsdb:36329122/4/2,36329122,"cross-sectional observational, not case-control",36329122,https://doi.org/10.1038/s41598-022-21779-z,NA,"Clarke T., Brinkac L., Greco C., Alleyne A.T., Carrasco P., Inostroza C., Tau T., Wisitrasameewong W., Torralba M.G., Nelson K. , Singh H.",Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes,Scientific reports,2022,NA,Experiment 4,"Barbados,Chile,South Africa,Thailand",Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,"Chile, South Africa, Thailand",Barbados,"Barbados refers to the samples from healthy females aged between 18 and 26 years, based in Barbados.",174,32,currently on antibiotics,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S9,12 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in stool samples for Barbados location.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum",3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|909656|310298;3379134|1224|1236|91347|543|561|562;3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|186802|186806|1730|290054;3384189|32066|203490|203491|203492|848|850,Complete,Svetlana up
bsdb:36329122/5/1,36329122,"cross-sectional observational, not case-control",36329122,https://doi.org/10.1038/s41598-022-21779-z,NA,"Clarke T., Brinkac L., Greco C., Alleyne A.T., Carrasco P., Inostroza C., Tau T., Wisitrasameewong W., Torralba M.G., Nelson K. , Singh H.",Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes,Scientific reports,2022,NA,Experiment 5,"Barbados,Chile,South Africa,Thailand",Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,"Barbados, South Africa, and Thailand",Chile,"Chile refers to the samples from healthy females aged between 18 and 26 years, based in Chile.",137,69,currently on antibiotics,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S10,12 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in stool samples for Chile location.,increased,NA,NA,Complete,Svetlana up
bsdb:36329122/5/2,36329122,"cross-sectional observational, not case-control",36329122,https://doi.org/10.1038/s41598-022-21779-z,NA,"Clarke T., Brinkac L., Greco C., Alleyne A.T., Carrasco P., Inostroza C., Tau T., Wisitrasameewong W., Torralba M.G., Nelson K. , Singh H.",Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes,Scientific reports,2022,NA,Experiment 5,"Barbados,Chile,South Africa,Thailand",Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,"Barbados, South Africa, and Thailand",Chile,"Chile refers to the samples from healthy females aged between 18 and 26 years, based in Chile.",137,69,currently on antibiotics,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S10,12 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in stool samples for Chile location.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__uncultured Faecalibacterium sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|s__uncultured Prevotellaceae bacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|816|46506;3379134|976|200643|171549|815|909656|204516;1783272|1239|186801|186802|216572|216851|259315;3379134|976|200643|171549|815|909656|310298;3379134|976|200643|171549|171552|370804;1783272|201174|1760|85004|31953|1678;3384189|32066|203490|203491|203492|848|850;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:36329122/6/1,36329122,"cross-sectional observational, not case-control",36329122,https://doi.org/10.1038/s41598-022-21779-z,NA,"Clarke T., Brinkac L., Greco C., Alleyne A.T., Carrasco P., Inostroza C., Tau T., Wisitrasameewong W., Torralba M.G., Nelson K. , Singh H.",Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes,Scientific reports,2022,NA,Experiment 6,"Barbados,Chile,South Africa,Thailand",Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,"Barbados, Chile, and Thailand",South Africa,"South Africa refers to the samples from healthy females aged between 18 and 26 years, based in South Africa.",169,37,currently on antibiotics,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S11,12 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in stool samples between South Africa and other location.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__uncultured Faecalibacterium sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|1239|186801|186802|216572|216851|259315;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|216572|216851,Complete,Svetlana up
bsdb:36329122/6/2,36329122,"cross-sectional observational, not case-control",36329122,https://doi.org/10.1038/s41598-022-21779-z,NA,"Clarke T., Brinkac L., Greco C., Alleyne A.T., Carrasco P., Inostroza C., Tau T., Wisitrasameewong W., Torralba M.G., Nelson K. , Singh H.",Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes,Scientific reports,2022,NA,Experiment 6,"Barbados,Chile,South Africa,Thailand",Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,"Barbados, Chile, and Thailand",South Africa,"South Africa refers to the samples from healthy females aged between 18 and 26 years, based in South Africa.",169,37,currently on antibiotics,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S11,12 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in stool samples between South Africa and other location.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|976|200643|171549|815|816|28116;3384189|32066|203490|203491|203492|848|850;3379134|976|200643|171549|815|909656|310298;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|1407607;3379134|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:36329122/7/1,36329122,"cross-sectional observational, not case-control",36329122,https://doi.org/10.1038/s41598-022-21779-z,NA,"Clarke T., Brinkac L., Greco C., Alleyne A.T., Carrasco P., Inostroza C., Tau T., Wisitrasameewong W., Torralba M.G., Nelson K. , Singh H.",Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes,Scientific reports,2022,NA,Experiment 7,"Barbados,Chile,South Africa,Thailand",Homo sapiens,Cheek,UBERON:0001567,Lifestyle measurement,EFO:0010724,"Barbados, Chile, and South Africa",Thailand,"Thailand refers to the oral samples from healthy females aged between 18 and 26 years, based in Thailand.",138,68,currently on antibiotics,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S12,12 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in oral samples between Thailand and other location.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__uncultured Aggregatibacter sp.,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella|s__uncultured Bergeyella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__uncultured Neisseria sp.",1783272|1239|91061|186826|1300|1301|1305;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712|416916|470564;3379134|976|117743|200644|2762318|59735|417617;3379134|1224|28216|206351|481|482|237778,Complete,Svetlana up
bsdb:36329122/7/2,36329122,"cross-sectional observational, not case-control",36329122,https://doi.org/10.1038/s41598-022-21779-z,NA,"Clarke T., Brinkac L., Greco C., Alleyne A.T., Carrasco P., Inostroza C., Tau T., Wisitrasameewong W., Torralba M.G., Nelson K. , Singh H.",Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes,Scientific reports,2022,NA,Experiment 7,"Barbados,Chile,South Africa,Thailand",Homo sapiens,Cheek,UBERON:0001567,Lifestyle measurement,EFO:0010724,"Barbados, Chile, and South Africa",Thailand,"Thailand refers to the oral samples from healthy females aged between 18 and 26 years, based in Thailand.",138,68,currently on antibiotics,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S12,12 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in oral samples between Thailand and other location.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__uncultured Granulicatella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp. oral taxon 780,k__Pseudomonadati|p__Bacteroidota|s__uncultured Bacteroidota bacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__uncultured Rothia sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella",1783272|1239|909932|1843489|31977|29465;3379134|976|200643|171549|171552|838|28132;1783272|1239|91061|186826|186828|117563|316089;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|909932|1843489|31977|29465|671229;3379134|976|152509;1783272|201174|1760|85006|1268|32207|316088;3379134|976|200643|171549|171552|838|60133;3379134|976|200643|171549|171552|2974251|28135;3379134|976|200643|171549|171552|1283313,Complete,Svetlana up
bsdb:36329122/8/1,36329122,"cross-sectional observational, not case-control",36329122,https://doi.org/10.1038/s41598-022-21779-z,NA,"Clarke T., Brinkac L., Greco C., Alleyne A.T., Carrasco P., Inostroza C., Tau T., Wisitrasameewong W., Torralba M.G., Nelson K. , Singh H.",Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes,Scientific reports,2022,NA,Experiment 8,"Barbados,Chile,South Africa,Thailand",Homo sapiens,Cheek,UBERON:0001567,Lifestyle measurement,EFO:0010724,"Chile, South Africa, Thailand",Barbados,"Barbados refers to the samples from healthy females aged between 18 and 26 years, based in Barbados",174,32,currently on antibiotics,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S13,12 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in oral samples between Barbados and other locations.,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral clone DR002,1783272|201174|1760|2037|2049|1654|163588,Complete,Svetlana up
bsdb:36329122/8/2,36329122,"cross-sectional observational, not case-control",36329122,https://doi.org/10.1038/s41598-022-21779-z,NA,"Clarke T., Brinkac L., Greco C., Alleyne A.T., Carrasco P., Inostroza C., Tau T., Wisitrasameewong W., Torralba M.G., Nelson K. , Singh H.",Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes,Scientific reports,2022,NA,Experiment 8,"Barbados,Chile,South Africa,Thailand",Homo sapiens,Cheek,UBERON:0001567,Lifestyle measurement,EFO:0010724,"Chile, South Africa, Thailand",Barbados,"Barbados refers to the samples from healthy females aged between 18 and 26 years, based in Barbados",174,32,currently on antibiotics,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S13,12 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in oral samples between Barbados and other locations.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__uncultured Dialister sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__uncultured Prevotella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter|s__Cronobacter muytjensii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola",1783272|1239|909932|1843489|31977|39948|278064;3379134|976|200643|171549|171552|838|159272;3379134|1224|1236|91347|543|413496|413501;3379134|976|200643|171549|815|909656|310297;3379134|1224|1236|135624|83763|83770;1783272|201174|1760|2037|2049|1654;1783272|201174|84998|84999|1643824|1380;1783272|201174|1760|2037|2049|2529408|1660;3379134|976|200643|171549|815|909656|310298,Complete,Svetlana up
bsdb:36329122/9/1,36329122,"cross-sectional observational, not case-control",36329122,https://doi.org/10.1038/s41598-022-21779-z,NA,"Clarke T., Brinkac L., Greco C., Alleyne A.T., Carrasco P., Inostroza C., Tau T., Wisitrasameewong W., Torralba M.G., Nelson K. , Singh H.",Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes,Scientific reports,2022,NA,Experiment 9,"Barbados,Chile,South Africa,Thailand",Homo sapiens,Cheek,UBERON:0001567,Lifestyle measurement,EFO:0010724,"Barbados, South Africa, Thailand",Chile,"Chile refers to the samples from healthy females aged between 18 and 26 years, based in Chile.",137,69,currently on antibiotics,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S14,12 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in oral samples between Chile and other locations.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:36329122/9/2,36329122,"cross-sectional observational, not case-control",36329122,https://doi.org/10.1038/s41598-022-21779-z,NA,"Clarke T., Brinkac L., Greco C., Alleyne A.T., Carrasco P., Inostroza C., Tau T., Wisitrasameewong W., Torralba M.G., Nelson K. , Singh H.",Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes,Scientific reports,2022,NA,Experiment 9,"Barbados,Chile,South Africa,Thailand",Homo sapiens,Cheek,UBERON:0001567,Lifestyle measurement,EFO:0010724,"Barbados, South Africa, Thailand",Chile,"Chile refers to the samples from healthy females aged between 18 and 26 years, based in Chile.",137,69,currently on antibiotics,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S14,12 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in oral samples between Chile and other locations.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota|s__uncultured Bacteroidota bacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus",3379134|1224|28216|206351|481|482|1107316;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552|838|60133;1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549|171552|838;1783272|1239|909932|1843489|31977|29465;3379134|976|152509;1783272|1239|91061|186826|1300|1301|1308,Complete,Svetlana up
bsdb:36329122/10/1,36329122,"cross-sectional observational, not case-control",36329122,https://doi.org/10.1038/s41598-022-21779-z,NA,"Clarke T., Brinkac L., Greco C., Alleyne A.T., Carrasco P., Inostroza C., Tau T., Wisitrasameewong W., Torralba M.G., Nelson K. , Singh H.",Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes,Scientific reports,2022,NA,Experiment 10,"Barbados,Chile,South Africa,Thailand",Homo sapiens,Cheek,UBERON:0001567,Lifestyle measurement,EFO:0010724,"Barbados, Chile, Thailand",South Africa,"South Africa refers to the samples from healthy females aged between 18 and 26 years, based in South Africa.",169,37,currently on antibiotics,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S15,12 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in oral samples between South Africa and other locations.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__uncultured Granulicatella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__uncultured Porphyromonas sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp. oral taxon 780,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Pseudomonadati|p__Bacteroidota|s__uncultured Bacteroidota bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella",1783272|1239|909932|1843489|31977|29465;3379134|976|200643|171549|171552|838|28132;1783272|1239|91061|186826|186828|117563|316089;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171551|836|159274;1783272|1239|909932|1843489|31977|29465|671229;1783272|1239|91061|186826|1300|1301|1308;3379134|976|152509;3379134|976|200643|171549|171552|1283313,Complete,Svetlana up
bsdb:36329122/10/2,36329122,"cross-sectional observational, not case-control",36329122,https://doi.org/10.1038/s41598-022-21779-z,NA,"Clarke T., Brinkac L., Greco C., Alleyne A.T., Carrasco P., Inostroza C., Tau T., Wisitrasameewong W., Torralba M.G., Nelson K. , Singh H.",Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes,Scientific reports,2022,NA,Experiment 10,"Barbados,Chile,South Africa,Thailand",Homo sapiens,Cheek,UBERON:0001567,Lifestyle measurement,EFO:0010724,"Barbados, Chile, Thailand",South Africa,"South Africa refers to the samples from healthy females aged between 18 and 26 years, based in South Africa.",169,37,currently on antibiotics,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S15,12 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in oral samples between South Africa and other locations.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|s__uncultured Neisseriales bacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__uncultured Aggregatibacter sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__uncultured Lautropia sp.,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella|s__uncultured Bergeyella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",3379134|1224|28216|206351|376761;1783272|201174|1760|85006|1268|32207;3379134|1224|1236|135625|712|416916|470564;3379134|1224|28216|80840|119060|47670|200449;3379134|976|117743|200644|2762318|59735|417617;3379134|1224|1236|135625|712|724,Complete,Svetlana up
bsdb:36338055/1/1,36338055,case-control,36338055,10.3389/fmicb.2022.1017147,https://pmc.ncbi.nlm.nih.gov/articles/PMC9627625/,"Yang Z., Fu H., Su H., Cai X., Wang Y., Hong Y., Hu J., Xie Z. , Wang X.",Multi-omics analyses reveal the specific changes in gut metagenome and serum metabolome of patients with polycystic ovary syndrome,Frontiers in microbiology,2022,"fecal microbiota transplantation, gut microbiota, polycystic ovary syndrome, serum metabolome, shotgun metagenomics, untargeted metabolomics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy individuals (Control),Polycystic ovary syndrome (PCOS),"Patients diagnosed with polycystic ovary syndrome (PCOS) according to the Rotterdam criteria, which include at least two of the following: oligo- or anovulation, clinical/biochemical signs of hyperandrogenism, and polycystic ovaries detected by ultrasound.",18,32,1 month,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Figure S2B and S3B,19 May 2025,Shulamite,Shulamite,"Different microbial genera with abundance of over 0.05% between PCOS and healthy controls. The comparison between two groups is performed by the two-tailed Mann-Whitney U-test, and P value is adjusted by Benjamini-Hochberg method.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter",1783272|1239|186801|3085636|186803|572511;1783272|201174;1783272|201174|1760|2037|2049|1654;1783272|1239|91061|186826|81852|1350;1783272|1239|526524|526525|2810280|100883;3379134|1224|1236|72274|135621|286;1783272|1239|526524|526525|2810280|3025755;1783272|201174|84998|1643822|1643826|644652,Complete,KateRasheed
bsdb:36338055/1/2,36338055,case-control,36338055,10.3389/fmicb.2022.1017147,https://pmc.ncbi.nlm.nih.gov/articles/PMC9627625/,"Yang Z., Fu H., Su H., Cai X., Wang Y., Hong Y., Hu J., Xie Z. , Wang X.",Multi-omics analyses reveal the specific changes in gut metagenome and serum metabolome of patients with polycystic ovary syndrome,Frontiers in microbiology,2022,"fecal microbiota transplantation, gut microbiota, polycystic ovary syndrome, serum metabolome, shotgun metagenomics, untargeted metabolomics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy individuals (Control),Polycystic ovary syndrome (PCOS),"Patients diagnosed with polycystic ovary syndrome (PCOS) according to the Rotterdam criteria, which include at least two of the following: oligo- or anovulation, clinical/biochemical signs of hyperandrogenism, and polycystic ovaries detected by ultrasound.",18,32,1 month,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Figure S2B and S3B,20 May 2025,Shulamite,Shulamite,"Different microbial genera with abundance of over 0.05% between PCOS and healthy controls. The comparison between two groups is performed by the two-tailed Mann-Whitney U-test, and P value is adjusted by Benjamini-Hochberg method.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|577309;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3085636|186803|841,Complete,KateRasheed
bsdb:36338055/2/1,36338055,case-control,36338055,10.3389/fmicb.2022.1017147,https://pmc.ncbi.nlm.nih.gov/articles/PMC9627625/,"Yang Z., Fu H., Su H., Cai X., Wang Y., Hong Y., Hu J., Xie Z. , Wang X.",Multi-omics analyses reveal the specific changes in gut metagenome and serum metabolome of patients with polycystic ovary syndrome,Frontiers in microbiology,2022,"fecal microbiota transplantation, gut microbiota, polycystic ovary syndrome, serum metabolome, shotgun metagenomics, untargeted metabolomics",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy individuals (Control),Polycystic ovary syndrome (PCOS),"Patients diagnosed with polycystic ovary syndrome (PCOS) according to the Rotterdam criteria, which include at least two of the following: oligo- or anovulation, clinical/biochemical signs of hyperandrogenism, and polycystic ovaries detected by ultrasound.",18,32,1 month,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 1A,19 May 2025,Shulamite,"Shulamite,Victoria",Linear discrimination analysis (LDA) effect size (LEfSe) approach was used to identify the discriminatory microbial species with the LDA score (log10) ≥ 2.0 and the adjusted p < 0.05.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter|s__Achromobacter xylosoxidans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Aquitalea|s__Aquitalea pelogenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 3_1_19,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium biavatii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium VE202-06,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp. HPP0074,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|s__Coriobacteriaceae bacterium CHKCI002,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp. 5-2,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella sp. 1_3_56FAA,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella sp. HGA1,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Faecalimicrobium|s__Faecalimicrobium dakarense,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:227,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 6_1_37FAA,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Leisingera|s__Leisingera sp. ANG-Vp,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp. D13,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Porphyrobacter|s__Porphyrobacter sp. HL-46,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. M1,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Sinorhizobium|s__Sinorhizobium meliloti,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio fortis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,s__bacterium OL-1,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia massiliensis (ex Durand et al. 2017)",3379134|1224|28216|80840|506|222|85698;1783272|1239|186801|3085636|186803|207244|105841;3379134|1224|28216|206351|1499392|407217|1293573;3379134|976|200643|171549|815|816|469592;1783272|201174|1760|85004|31953|1678|762212;1783272|1239|186801|186802|1232442;1783272|1239|186801|3085636|186803|33042|1078090;1783272|201174|84998|84999|84107|1780377;1783272|1239|186801|3085636|186803|189330|1235798;1783272|201174|84998|1643822|1643826|84111|84112;1783272|201174|84998|1643822|1643826|84111|665943;1783272|201174|84998|1643822|1643826|84111|910311;1783272|1239|91061|186826|81852|1350|1352;1783272|1239|186801|3082720|186804|3120164|1301100;1783272|1239|1263010;1783272|201174|84998|1643822|1643826|644652|471189;1783272|1239|186801|3085636|186803|658656;3379134|1224|28211|204455|2854170|191028|1577896;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|2005525|375288|563193;3379134|1224|28211|204457|335929|1111|1479239;3379134|1224|1236|72274|135621|286|95619;1783272|1239|186801|186802|216572|1263|438033;1783272|201174|1760|2037|2049|2529408|1660;3379134|1224|28211|356|82115|28105|382;1783272|1239|91061|1385|90964|1279|1280;1783272|1239|526524|526525|2810280|3025755|29348;3379134|1224|1236|135623|641|662|212667;1783272|1239|186801|3085636|186803|1506553|29347;1504822;1783272|1239|186801|3085636|186803|572511|1737424,Complete,KateRasheed
bsdb:36338055/2/2,36338055,case-control,36338055,10.3389/fmicb.2022.1017147,https://pmc.ncbi.nlm.nih.gov/articles/PMC9627625/,"Yang Z., Fu H., Su H., Cai X., Wang Y., Hong Y., Hu J., Xie Z. , Wang X.",Multi-omics analyses reveal the specific changes in gut metagenome and serum metabolome of patients with polycystic ovary syndrome,Frontiers in microbiology,2022,"fecal microbiota transplantation, gut microbiota, polycystic ovary syndrome, serum metabolome, shotgun metagenomics, untargeted metabolomics",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy individuals (Control),Polycystic ovary syndrome (PCOS),"Patients diagnosed with polycystic ovary syndrome (PCOS) according to the Rotterdam criteria, which include at least two of the following: oligo- or anovulation, clinical/biochemical signs of hyperandrogenism, and polycystic ovaries detected by ultrasound.",18,32,1 month,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Figure 1A,19 May 2025,Shulamite,Shulamite,Linear discrimination analysis (LDA) effect size (LEfSe) approach was used to identify the discriminatory microbial species with the LDA score (log10) ≥ 2.0 and the adjusted p < 0.05.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:1076,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:443,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:530,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:875,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:343,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:470,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella sp. CAG:1427,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. CAG:82,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:882,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides gordonii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides johnsonii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp. HGS0025,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella xylaniphila,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium sp. CAG:266,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola barnesiae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola salanitronis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella confusa,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae",3379134|976|200643|171549|815|816|1262735;3379134|976|200643|171549|815|816|1262739;3379134|976|200643|171549|815|816|1262741;3379134|976|200643|171549|815|816|1262752;1783272|1239|186801|186802|31979|1485|1262796;1783272|1239|186801|186802|31979|1485|1262812;1783272|201174|84998|1643822|1643826|84111|1262874;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|216851|1262898;1783272|1239|1262991;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|2005525|375288|574930;3379134|976|200643|171549|2005525|375288|387661;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|2005525|375288|1078087;3379134|976|200643|171549|171552|577309|454154;3379134|976|200643|171549|171552|577309|454155;1783272|1239|909932|1843488|909930|33024|1262915;1783272|1239|909932|1843488|909930|33024|626940;3379134|976|200643|171549|815|909656|376804;3379134|976|200643|171549|815|909656|310298;3379134|976|200643|171549|815|909656|310298;3379134|976|200643|171549|815|909656|387090;3379134|976|200643|171549|815|909656|204516;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|909656|376805;3379134|976|200643|171549|815|909656|671267;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|91061|186826|33958|46255|1583;3379134|976|200643|171549|2005525|375288|46503,Complete,KateRasheed
bsdb:36348390/1/1,36348390,case-control,36348390,10.1186/s12905-022-02029-w,NA,"Liu Y., Zhou Y., Mao T., Huang Y., Liang J., Zhu M., Yao P., Zong Y., Lang J. , Zhang Y.",The relationship between menopausal syndrome and gut microbes,BMC women's health,2022,"16S ribosomal RNA gene sequencing, Functional prediction, Gut microbes, Gut microbiota dysbiosis, Menopausal syndrome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Menopausal or post-menopausal disease,EFO:0010685,Healthy women,Menopausal Syndrome (MPS),Patients with Menopausal Syndrome (MPS),24,77,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2D,23 July 2025,Aleru Divine,Aleru Divine,Taxa enriched in the case group indicated with a positive LDA score (red) and negative LDA score (green).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis",3379134|976|200643|171549|815|816|28116;1783272|201174|1760|85004|31953;1783272|1239|909932|1843489|31977|29465|39778;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|201174|84992;1783272|201174|1760|85004|31953|1678|1680;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|186802|186806|1730;1783272|1239|526524|526525|128827|1573535|1735;1783272|1239|91061|186826|33958|2767887|1623,Complete,NA
bsdb:36348390/1/2,36348390,case-control,36348390,10.1186/s12905-022-02029-w,NA,"Liu Y., Zhou Y., Mao T., Huang Y., Liang J., Zhu M., Yao P., Zong Y., Lang J. , Zhang Y.",The relationship between menopausal syndrome and gut microbes,BMC women's health,2022,"16S ribosomal RNA gene sequencing, Functional prediction, Gut microbes, Gut microbiota dysbiosis, Menopausal syndrome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Menopausal or post-menopausal disease,EFO:0010685,Healthy women,Menopausal Syndrome (MPS),Patients with Menopausal Syndrome (MPS),24,77,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2D,23 July 2025,Aleru Divine,Aleru Divine,Taxa enriched in the case group indicated with a positive LDA score (red) and negative LDA score (green).,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium stationis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium celatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus albus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter rodentium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter guillouiae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,k__Pseudomonadati|p__Pseudomonadota",1783272|201174|1760|85007|1653|1716|1705;1783272|201174|1760|85004|31953|1678|28025;3379134|976|200643|171549|815|909656|387090;1783272|1239|186801|186802|31979|1485|36834;1783272|1239|186801|186802|216572|1263|1264;3379134|29547|3031852|213849|72293|209|59617;3379134|1224|1236|135625|712|416916|739;3379134|1224|1236|2887326|468|469|106649;3379134|1224|1236|72274;3379134|1224|1236|2887326|468|469;3379134|1224|1236|2887326|468;3379134|1224|1236|135625|712|416916;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85007|1653;3379134|29547|3031852|213849|72293;3379134|29547|3031852|213849;3379134|29547|3031852|213849|72293|209;3379134|29547|3031852;3379134|1224,Complete,NA
bsdb:36350127/1/1,36350127,case-control,36350127,10.1128/spectrum.02196-22,https://journals.asm.org/doi/10.1128/spectrum.02196-22#fig1,"Lai C.K.C., Cheung M.K., Lui G.C.Y., Ling L., Chan J.Y.K., Ng R.W.Y., Chan H.C., Yeung A.C.M., Ho W.C.S., Boon S.S., Chan P.K.S. , Chen Z.",Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients,Microbiology spectrum,2022,"16S rRNA, COVID-19, SARS-CoV-2, hospitalized, naso-oropharyngeal microbiome",Experiment 1,China,Homo sapiens,"Nasopharynx,Throat","UBERON:0001728,UBERON:0000341",COVID-19,MONDO:0100096,local controls,COVID-19 patients,Hospitalized COVID-19 patients,76,76,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 1,Fig 2A,14 March 2024,Abiola-Salako,"Abiola-Salako,Scholastica,WikiWorks",Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized COVID-19 patients versus local controls.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549|171552|1283313;1783272|201174|84998|84999|1643824|1380;1783272|1239|909932|1843489|31977|906;3379134|976|200643|171549|171552|838;1783272|1239|526524|526525|128827|123375;3379134|1224|28211|204457|41297|13687;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:36350127/1/2,36350127,case-control,36350127,10.1128/spectrum.02196-22,https://journals.asm.org/doi/10.1128/spectrum.02196-22#fig1,"Lai C.K.C., Cheung M.K., Lui G.C.Y., Ling L., Chan J.Y.K., Ng R.W.Y., Chan H.C., Yeung A.C.M., Ho W.C.S., Boon S.S., Chan P.K.S. , Chen Z.",Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients,Microbiology spectrum,2022,"16S rRNA, COVID-19, SARS-CoV-2, hospitalized, naso-oropharyngeal microbiome",Experiment 1,China,Homo sapiens,"Nasopharynx,Throat","UBERON:0001728,UBERON:0000341",COVID-19,MONDO:0100096,local controls,COVID-19 patients,Hospitalized COVID-19 patients,76,76,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 2,Fig 2A,18 March 2024,Abiola-Salako,"Abiola-Salako,Scholastica,WikiWorks",Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized COVID-19 patients versus local controls.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Alysiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Lentimicrobiaceae|g__Lentimicrobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",3379134|1224|1236|135625|712|713;3379134|1224|28216|206351|481|194195;3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;3379134|976|117743|200644|49546|1016;1783272|1239|186801|3085636|186803|43996;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3082720|3118655|44259;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|1300|1357;3379134|1224|28216|80840|119060|47670;1783272|201174|1760|85007|2805586|1847725;3379134|976|200643|171549|1840213|1840214;1783272|1239|186801|3082720|543314|86331;3379134|1224|28216|206351|481|482;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|2005525|195950;3379134|203691|203692|136|2845253|157,Complete,Svetlana up
bsdb:36350127/2/1,36350127,case-control,36350127,10.1128/spectrum.02196-22,https://journals.asm.org/doi/10.1128/spectrum.02196-22#fig1,"Lai C.K.C., Cheung M.K., Lui G.C.Y., Ling L., Chan J.Y.K., Ng R.W.Y., Chan H.C., Yeung A.C.M., Ho W.C.S., Boon S.S., Chan P.K.S. , Chen Z.",Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients,Microbiology spectrum,2022,"16S rRNA, COVID-19, SARS-CoV-2, hospitalized, naso-oropharyngeal microbiome",Experiment 2,China,Homo sapiens,"Nasopharynx,Throat","UBERON:0001728,UBERON:0000341",Abnormality of the respiratory system,HP:0002086,local controls,Non-Covid-19 Patients,Hospitalized non-COVID-19 patients with respiratory symptoms or related illnesses.,76,69,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Fig 2B,18 March 2024,Abiola-Salako,"Abiola-Salako,Scholastica,WikiWorks",Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized non-COVID-19 patients versus local controls.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|2037|2049|1654;1783272|201174|84998|84999|1643824|1380;1783272|1239|91061|186826|186828|29393;1783272|1239|91061|186826|33958|2759736;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|2767887;1783272|1239|91061|186826|33958|2742598;1783272|1239|909932|1843489|31977|906;3379134|976|200643|171549|171552|838;33090|35493|3398|72025|3803|3814|508215;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:36350127/2/2,36350127,case-control,36350127,10.1128/spectrum.02196-22,https://journals.asm.org/doi/10.1128/spectrum.02196-22#fig1,"Lai C.K.C., Cheung M.K., Lui G.C.Y., Ling L., Chan J.Y.K., Ng R.W.Y., Chan H.C., Yeung A.C.M., Ho W.C.S., Boon S.S., Chan P.K.S. , Chen Z.",Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients,Microbiology spectrum,2022,"16S rRNA, COVID-19, SARS-CoV-2, hospitalized, naso-oropharyngeal microbiome",Experiment 2,China,Homo sapiens,"Nasopharynx,Throat","UBERON:0001728,UBERON:0000341",Abnormality of the respiratory system,HP:0002086,local controls,Non-Covid-19 Patients,Hospitalized non-COVID-19 patients with respiratory symptoms or related illnesses.,76,69,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Fig 2B,18 March 2024,Abiola-Salako,"Abiola-Salako,Scholastica,WikiWorks",Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized non-COVID-19 patients versus local controls.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Alysiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Aminipila,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Lentimicrobiaceae|g__Lentimicrobium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",3379134|1224|1236|135625|712|713;3379134|1224|28216|206351|481|194195;1783272|1239|186801|3082720|543314|2060094;1783272|1239|91061|1385|186817|1386;3379134|976|117743|200644|2762318|59735;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;95818|2093818|2093825|2171986|1331051;1783272|1239|186801|3085636|186803|43996;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|216572|216851;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135625|712|724;3379134|1224|28216|80840|119060|47670;1783272|201174|1760|85007|2805586|1847725;3379134|976|200643|171549|1840213|1840214;3379134|1224|28216|206351|481|482;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|3082720|186804|1257;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|1385|90964|1279;1783272|1239|186801|3085636|186803|1213720;3379134|203691|203692|136|2845253|157,Complete,Svetlana up
bsdb:36350127/3/1,36350127,case-control,36350127,10.1128/spectrum.02196-22,https://journals.asm.org/doi/10.1128/spectrum.02196-22#fig1,"Lai C.K.C., Cheung M.K., Lui G.C.Y., Ling L., Chan J.Y.K., Ng R.W.Y., Chan H.C., Yeung A.C.M., Ho W.C.S., Boon S.S., Chan P.K.S. , Chen Z.",Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients,Microbiology spectrum,2022,"16S rRNA, COVID-19, SARS-CoV-2, hospitalized, naso-oropharyngeal microbiome",Experiment 3,China,Homo sapiens,"Nasopharynx,Throat","UBERON:0001728,UBERON:0000341",COVID-19,MONDO:0100096,non-Covid-19 patients,Covid-19 patients,Hospitalised Covid-19 patients.,69,76,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig 2C,18 March 2024,Abiola-Salako,"Abiola-Salako,Scholastica,WikiWorks",Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized COVID-19 versus non-COVID-19 patients.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Nanosynbacterales|f__Candidatus Nanosynbacteraceae|g__Candidatus Nanosynbacter|s__Candidatus Nanosynbacter lyticus",3379134|976|200643|171549|171552|1283313;3379134|976|117743|200644|2762318|59735;3379134|29547|3031852|213849|72294|194;95818|2093818|2093825|2171986|1331051;1783272|1239|186801|3085636|186803|43996;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;1783272|201174|1760|85007|2805586|1847725;3379134|1224|1236|2887326|468|475;1783272|1239|186801|3082720|186804|1257;1783272|1239|526524|526525|128827|123375;95818|2093818|2093819|2093822|2093823|2093824,Complete,Svetlana up
bsdb:36350127/3/2,36350127,case-control,36350127,10.1128/spectrum.02196-22,https://journals.asm.org/doi/10.1128/spectrum.02196-22#fig1,"Lai C.K.C., Cheung M.K., Lui G.C.Y., Ling L., Chan J.Y.K., Ng R.W.Y., Chan H.C., Yeung A.C.M., Ho W.C.S., Boon S.S., Chan P.K.S. , Chen Z.",Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients,Microbiology spectrum,2022,"16S rRNA, COVID-19, SARS-CoV-2, hospitalized, naso-oropharyngeal microbiome",Experiment 3,China,Homo sapiens,"Nasopharynx,Throat","UBERON:0001728,UBERON:0000341",COVID-19,MONDO:0100096,non-Covid-19 patients,Covid-19 patients,Hospitalised Covid-19 patients.,69,76,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig 2C,18 March 2024,Abiola-Salako,"Abiola-Salako,Scholastica,WikiWorks",Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized COVID-19 versus non-COVID-19 patients.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia",1783272|1239|909932|1843489|31977|156454;1783272|1239|91061|186826|33958|2759736;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|2767887;1783272|1239|91061|186826|33958|2742598;1783272|1239|186801|3082720|543314|86331;33090|35493|3398|72025|3803|3814|508215,Complete,Svetlana up
bsdb:36350127/4/1,36350127,case-control,36350127,10.1128/spectrum.02196-22,https://journals.asm.org/doi/10.1128/spectrum.02196-22#fig1,"Lai C.K.C., Cheung M.K., Lui G.C.Y., Ling L., Chan J.Y.K., Ng R.W.Y., Chan H.C., Yeung A.C.M., Ho W.C.S., Boon S.S., Chan P.K.S. , Chen Z.",Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients,Microbiology spectrum,2022,"16S rRNA, COVID-19, SARS-CoV-2, hospitalized, naso-oropharyngeal microbiome",Experiment 4,China,Homo sapiens,"Nasopharynx,Throat","UBERON:0001728,UBERON:0000341",Pneumonia,EFO:0003106,Covid-19 with no Pneumonia,Covid-19 with Pneumonia,Hospitalized COVID-19 patients with Pneumonia,38,38,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A,21 March 2024,Abiola-Salako,"Abiola-Salako,Scholastica,WikiWorks",Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized COVID-19 patients with pneumonia compared to those with no pneumonia.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:36350127/4/2,36350127,case-control,36350127,10.1128/spectrum.02196-22,https://journals.asm.org/doi/10.1128/spectrum.02196-22#fig1,"Lai C.K.C., Cheung M.K., Lui G.C.Y., Ling L., Chan J.Y.K., Ng R.W.Y., Chan H.C., Yeung A.C.M., Ho W.C.S., Boon S.S., Chan P.K.S. , Chen Z.",Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients,Microbiology spectrum,2022,"16S rRNA, COVID-19, SARS-CoV-2, hospitalized, naso-oropharyngeal microbiome",Experiment 4,China,Homo sapiens,"Nasopharynx,Throat","UBERON:0001728,UBERON:0000341",Pneumonia,EFO:0003106,Covid-19 with no Pneumonia,Covid-19 with Pneumonia,Hospitalized COVID-19 patients with Pneumonia,38,38,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6A,21 March 2024,Abiola-Salako,"Abiola-Salako,Scholastica,WikiWorks",Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized COVID-19 patients with pneumonia compared to those with no pneumonia.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus",3379134|1224|1236|2887326|468|475;1783272|1239|1737404|1737405|1570339|162289,Complete,Svetlana up
bsdb:36350127/5/1,36350127,case-control,36350127,10.1128/spectrum.02196-22,https://journals.asm.org/doi/10.1128/spectrum.02196-22#fig1,"Lai C.K.C., Cheung M.K., Lui G.C.Y., Ling L., Chan J.Y.K., Ng R.W.Y., Chan H.C., Yeung A.C.M., Ho W.C.S., Boon S.S., Chan P.K.S. , Chen Z.",Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients,Microbiology spectrum,2022,"16S rRNA, COVID-19, SARS-CoV-2, hospitalized, naso-oropharyngeal microbiome",Experiment 5,China,Homo sapiens,"Nasopharynx,Throat","UBERON:0001728,UBERON:0000341",Viral load,EFO:0010125,viral load (≤7.5),viral load (>7.5),COVID-19 patients with viral load greater than 7.5,33,35,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6B,22 March 2024,Abiola-Salako,"Abiola-Salako,Scholastica,WikiWorks",Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized COVID-19 patients with viral load ≤7.5 versus viral load >7.5.,increased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Acholeplasma,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum",1783272|544448|31969|186329|2146|2147;3379134|976|200643|171549|815|816;3379134|976|200643|171549|171551|836;1783272|1239|186801|3082720|543314|35518,Complete,Svetlana up
bsdb:36350127/5/2,36350127,case-control,36350127,10.1128/spectrum.02196-22,https://journals.asm.org/doi/10.1128/spectrum.02196-22#fig1,"Lai C.K.C., Cheung M.K., Lui G.C.Y., Ling L., Chan J.Y.K., Ng R.W.Y., Chan H.C., Yeung A.C.M., Ho W.C.S., Boon S.S., Chan P.K.S. , Chen Z.",Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients,Microbiology spectrum,2022,"16S rRNA, COVID-19, SARS-CoV-2, hospitalized, naso-oropharyngeal microbiome",Experiment 5,China,Homo sapiens,"Nasopharynx,Throat","UBERON:0001728,UBERON:0000341",Viral load,EFO:0010125,viral load (≤7.5),viral load (>7.5),COVID-19 patients with viral load greater than 7.5,33,35,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6B,22 March 2024,Abiola-Salako,"Abiola-Salako,Scholastica,WikiWorks",Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized COVID-19 patients with viral load ≤7.5 versus viral load >7.5.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia caballeronis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",1783272|1239|91061|186826|81852|1350;1783272|1239|91061|1385|539738|1378;3379134|1224|28216|80840|119060|1822464|416943;3379134|1224|1236|72274|135621|286,Complete,Svetlana up
bsdb:36350127/6/1,36350127,case-control,36350127,10.1128/spectrum.02196-22,https://journals.asm.org/doi/10.1128/spectrum.02196-22#fig1,"Lai C.K.C., Cheung M.K., Lui G.C.Y., Ling L., Chan J.Y.K., Ng R.W.Y., Chan H.C., Yeung A.C.M., Ho W.C.S., Boon S.S., Chan P.K.S. , Chen Z.",Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients,Microbiology spectrum,2022,"16S rRNA, COVID-19, SARS-CoV-2, hospitalized, naso-oropharyngeal microbiome",Experiment 6,China,Homo sapiens,"Nasopharynx,Throat","UBERON:0001728,UBERON:0000341",COVID-19,MONDO:0100096,local controls,Hospitalized patients,"Hospitalized COVID and non-COVID patients,",76,145,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4A,22 March 2024,Abiola-Salako,"Abiola-Salako,Scholastica,WikiWorks",Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized (COVID-19 and non-COVID-19) patients versus local controls.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549|171552|1283313;1783272|201174|84998|84999|1643824|1380;1783272|1239|909932|909929|1843491|82202;1783272|1239|91061|186826|33958|2767887;1783272|1239|91061|186826|33958|2742598;1783272|1239|909932|1843489|31977|906;3379134|976|200643|171549|171552|838;1783272|1239|526524|526525|128827|123375;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:36350127/6/2,36350127,case-control,36350127,10.1128/spectrum.02196-22,https://journals.asm.org/doi/10.1128/spectrum.02196-22#fig1,"Lai C.K.C., Cheung M.K., Lui G.C.Y., Ling L., Chan J.Y.K., Ng R.W.Y., Chan H.C., Yeung A.C.M., Ho W.C.S., Boon S.S., Chan P.K.S. , Chen Z.",Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients,Microbiology spectrum,2022,"16S rRNA, COVID-19, SARS-CoV-2, hospitalized, naso-oropharyngeal microbiome",Experiment 6,China,Homo sapiens,"Nasopharynx,Throat","UBERON:0001728,UBERON:0000341",COVID-19,MONDO:0100096,local controls,Hospitalized patients,"Hospitalized COVID and non-COVID patients,",76,145,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4A,22 March 2024,Abiola-Salako,"Abiola-Salako,Scholastica,WikiWorks",Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized (COVID-19 and non-COVID-19) patients versus local controls.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Alysiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Aminipila,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Lentimicrobiaceae|g__Lentimicrobium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",3379134|1224|1236|135625|712|713;3379134|1224|28216|206351|481|194195;1783272|1239|186801|3082720|543314|2060094;1783272|1239|91061|1385|186817|1386;3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|43996;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|216572|216851;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135625|712|724;3379134|1224|28216|80840|119060|47670;1783272|201174|1760|85007|2805586|1847725;3379134|976|200643|171549|1840213|1840214;3379134|1224|28216|206351|481|482;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|1385|90964|1279;1783272|1239|186801|3085636|186803|1213720;3379134|976|200643|171549|2005525|195950;3379134|203691|203692|136|2845253|157,Complete,Svetlana up
bsdb:36350161/1/1,36350161,"cross-sectional observational, not case-control",36350161,https://doi.org/10.1128/spectrum.01926-22,NA,"Li S., Guo J., Liu R., Zhang F., Wen S., Liu Y., Ren W., Zhang X., Shang Y., Gao M., Lu J. , Pang Y.",Predominance of Escherichia-Shigella in Gut Microbiome and Its Potential Correlation with Elevated Level of Plasma Tumor Necrosis Factor Alpha in Patients with Tuberculous Meningitis,Microbiology spectrum,2022,"Escherichia-Shigella, TNF-α, claudin-5, gut microbiota, tuberculous meningitis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Meningeal tuberculosis,EFO:1000039,Healthy Control (HC),Tuberculosis Meningitis (TBM),The patients who have been diagnosed from Tuberculosis Meningitis (TBM).,9,9,6 months,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Supplementary Figure. 1 and 2(A),8 June 2023,Aiyshaaaa,"Aiyshaaaa,WikiWorks",The Welch’s t-test was used to analyze phylum and genus level differences in microbiota compositions between pairs of groups: HC and TBM,increased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|1224;3379134|1224|1236|91347|543|1940338,Complete,Aiyshaaaa
bsdb:36350161/1/2,36350161,"cross-sectional observational, not case-control",36350161,https://doi.org/10.1128/spectrum.01926-22,NA,"Li S., Guo J., Liu R., Zhang F., Wen S., Liu Y., Ren W., Zhang X., Shang Y., Gao M., Lu J. , Pang Y.",Predominance of Escherichia-Shigella in Gut Microbiome and Its Potential Correlation with Elevated Level of Plasma Tumor Necrosis Factor Alpha in Patients with Tuberculous Meningitis,Microbiology spectrum,2022,"Escherichia-Shigella, TNF-α, claudin-5, gut microbiota, tuberculous meningitis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Meningeal tuberculosis,EFO:1000039,Healthy Control (HC),Tuberculosis Meningitis (TBM),The patients who have been diagnosed from Tuberculosis Meningitis (TBM).,9,9,6 months,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Supplementary Figure. 1 and 2(A),8 June 2023,Aiyshaaaa,"Aiyshaaaa,Atrayees,WikiWorks",The Welch’s t-test was used to analyze phylum and genus level differences in microbiota compositions between pairs of groups: HC and TBM,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia",1783272|201174;1783272|1239;1783272|1239|186801|3085636|186803|572511;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|1407607;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3082720|186804|1501226,Complete,Aiyshaaaa
bsdb:36350161/2/1,36350161,"cross-sectional observational, not case-control",36350161,https://doi.org/10.1128/spectrum.01926-22,NA,"Li S., Guo J., Liu R., Zhang F., Wen S., Liu Y., Ren W., Zhang X., Shang Y., Gao M., Lu J. , Pang Y.",Predominance of Escherichia-Shigella in Gut Microbiome and Its Potential Correlation with Elevated Level of Plasma Tumor Necrosis Factor Alpha in Patients with Tuberculous Meningitis,Microbiology spectrum,2022,"Escherichia-Shigella, TNF-α, claudin-5, gut microbiota, tuberculous meningitis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Meningeal tuberculosis,EFO:1000039,Healthy Control (HC),Pulmonary tuberculosis (PTB),The  patients who have been diagnosed from Pulmonary tuberculosis (PTB).,9,13,6 months,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Supplementary Figure. 1 and 2(B),8 June 2023,Aiyshaaaa,"Aiyshaaaa,WikiWorks","Welch’s t-test was used to analyze phylum-level differences in microbiota compositions
between pairs of groups: HC and PTB",increased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|1224;3379134|976|200643;3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|1940338,Complete,Aiyshaaaa
bsdb:36350161/2/2,36350161,"cross-sectional observational, not case-control",36350161,https://doi.org/10.1128/spectrum.01926-22,NA,"Li S., Guo J., Liu R., Zhang F., Wen S., Liu Y., Ren W., Zhang X., Shang Y., Gao M., Lu J. , Pang Y.",Predominance of Escherichia-Shigella in Gut Microbiome and Its Potential Correlation with Elevated Level of Plasma Tumor Necrosis Factor Alpha in Patients with Tuberculous Meningitis,Microbiology spectrum,2022,"Escherichia-Shigella, TNF-α, claudin-5, gut microbiota, tuberculous meningitis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Meningeal tuberculosis,EFO:1000039,Healthy Control (HC),Pulmonary tuberculosis (PTB),The  patients who have been diagnosed from Pulmonary tuberculosis (PTB).,9,13,6 months,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Supplementary Figure. 1 and 2(B),8 June 2023,Aiyshaaaa,"Aiyshaaaa,Atrayees,WikiWorks",Welch’s t-test was used to analyze phylum-level differences in microbiota compositions between pairs of groups: HC and PTB,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus",1783272|1239;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|33042,Complete,Aiyshaaaa
bsdb:36350161/3/1,36350161,"cross-sectional observational, not case-control",36350161,https://doi.org/10.1128/spectrum.01926-22,NA,"Li S., Guo J., Liu R., Zhang F., Wen S., Liu Y., Ren W., Zhang X., Shang Y., Gao M., Lu J. , Pang Y.",Predominance of Escherichia-Shigella in Gut Microbiome and Its Potential Correlation with Elevated Level of Plasma Tumor Necrosis Factor Alpha in Patients with Tuberculous Meningitis,Microbiology spectrum,2022,"Escherichia-Shigella, TNF-α, claudin-5, gut microbiota, tuberculous meningitis",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Meningeal tuberculosis,EFO:1000039,Pulmonary tuberculosis (PTB),Tuberculosis Meningitis (TBM),The patients who have been diagnosed from Tuberculosis Meningitis (TBM),13,9,6 months,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Supplementary Figure. 1 and 2(C),8 June 2023,Aiyshaaaa,"Aiyshaaaa,WikiWorks","Welch’s t-test was used to analyze phylum-level differences in microbiota compositions
between pairs of groups: TBM and PTB",increased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|1224;3379134|1224|1236|91347|543|1940338,Complete,Aiyshaaaa
bsdb:36350161/3/2,36350161,"cross-sectional observational, not case-control",36350161,https://doi.org/10.1128/spectrum.01926-22,NA,"Li S., Guo J., Liu R., Zhang F., Wen S., Liu Y., Ren W., Zhang X., Shang Y., Gao M., Lu J. , Pang Y.",Predominance of Escherichia-Shigella in Gut Microbiome and Its Potential Correlation with Elevated Level of Plasma Tumor Necrosis Factor Alpha in Patients with Tuberculous Meningitis,Microbiology spectrum,2022,"Escherichia-Shigella, TNF-α, claudin-5, gut microbiota, tuberculous meningitis",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Meningeal tuberculosis,EFO:1000039,Pulmonary tuberculosis (PTB),Tuberculosis Meningitis (TBM),The patients who have been diagnosed from Tuberculosis Meningitis (TBM),13,9,6 months,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Supplementary Figure. 1 and 2(C),8 June 2023,Aiyshaaaa,"Aiyshaaaa,WikiWorks",Welch’s t-test was used to analyze phylum-level differences in microbiota compositions between pairs of groups: TBM and PTB,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota",1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|815|816;1783272|201174;3379134|976|200643;1783272|1239,Complete,Aiyshaaaa
bsdb:36362360/3/1,36362360,"laboratory experiment,meta-analysis",36362360,10.3390/ijms232113574,NA,"Park S. , Wu X.",Modulation of the Gut Microbiota in Memory Impairment and Alzheimer's Disease via the Inhibition of the Parasympathetic Nervous System,International journal of molecular sciences,2022,"Alzheimer’s disease, gut dysbiosis, mild memory impairment, parasympathetic nervous system, scopolamine",Experiment 3,"China,Singapore,Turkey",Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Healthy group and Alzheimer's Disease (AD),Mild Cognitive Impairment (MCI),Patients with mild cognitive impairment (MCI),228,141,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A,16 March 2024,Samreen-19,"Samreen-19,Scholastica,WikiWorks",Linear discriminant analysis (LDA) scores of the bacteria at the genus level significantly different in healthy group and mild cognitive impairment (MCI) versus Alzheimer’s disease (AD),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",1783272|1239|186801|3085636|186803|572511;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|28050;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:36362360/4/1,36362360,"laboratory experiment,meta-analysis",36362360,10.3390/ijms232113574,NA,"Park S. , Wu X.",Modulation of the Gut Microbiota in Memory Impairment and Alzheimer's Disease via the Inhibition of the Parasympathetic Nervous System,International journal of molecular sciences,2022,"Alzheimer’s disease, gut dysbiosis, mild memory impairment, parasympathetic nervous system, scopolamine",Experiment 4,South Korea,Rattus norvegicus,Feces,UBERON:0001988,Memory impairment,EFO:0001072,Normal health group,Positive and memory deficit (MD) group,Rats divided into the positive group (n = 10) given intraperitoneal scopolamine plus donepezil injection and those belonging to the memory deficit (MD) group (n = 10) given intraperitoneal scopolamine injection,10,20,NA,16S,34,"Illumina,Roche454",relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6F,16 March 2024,Samreen-19,"Samreen-19,Scholastica,WikiWorks",LDA scores of the bacteria at the species level significantly different in normal health group versus positive and memory deficit (MD) group,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster lavalensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus casseliflavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus vaginalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides gordonii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",3379134|976|200643|171549|171550|239759|626932;3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|815|816|820;1783272|1239|186801|3085636|186803|2719313|358742;1783272|1239|186801|3085636|186803|2719313|460384;1783272|1239|91061|186826|81852|1350|37734;1783272|1239|186801|186802|216572|216851|853;1783272|1239|91061|186826|33958|2742598|1633;3379134|976|200643|171549|2005525|375288|574930;1783272|1239|186801|186802|216572|1263|438033;1783272|1239|91061|1385|90964|1279|1280;1783272|1239|186801|3085636|186803|2941495|1512;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Svetlana up
bsdb:36362360/5/1,36362360,"laboratory experiment,meta-analysis",36362360,10.3390/ijms232113574,NA,"Park S. , Wu X.",Modulation of the Gut Microbiota in Memory Impairment and Alzheimer's Disease via the Inhibition of the Parasympathetic Nervous System,International journal of molecular sciences,2022,"Alzheimer’s disease, gut dysbiosis, mild memory impairment, parasympathetic nervous system, scopolamine",Experiment 5,South Korea,Rattus norvegicus,Feces,UBERON:0001988,Memory impairment,EFO:0001072,Normal health group and memory deficit (MD) group,Positive group,Rats in the positive group (n = 10) given intraperitoneal scopolamine plus donepezil injection,20,10,NA,16S,34,"Illumina,Roche454",relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6F,16 March 2024,Samreen-19,"Samreen-19,Scholastica,WikiWorks",LDA scores of the bacteria at the species level significantly different in positive group  versus normal health and memory deficit (MD) group,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum variabile",3379134|976|200643|171549|815|816|338188;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|1694;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|91061|186826|33958|2742598|1598;1783272|1239|186801|186802|216572|292632|214851,Complete,Svetlana up
bsdb:36362360/6/1,36362360,"laboratory experiment,meta-analysis",36362360,10.3390/ijms232113574,NA,"Park S. , Wu X.",Modulation of the Gut Microbiota in Memory Impairment and Alzheimer's Disease via the Inhibition of the Parasympathetic Nervous System,International journal of molecular sciences,2022,"Alzheimer’s disease, gut dysbiosis, mild memory impairment, parasympathetic nervous system, scopolamine",Experiment 6,South Korea,Rattus norvegicus,Feces,UBERON:0001988,Memory impairment,EFO:0001072,Normal health group and positive group,Memory deficit (MD) group,Rats in the memory deficit (MD) group (n = 10) given intraperitoneal scopolamine injection,20,10,NA,16S,34,"Illumina,Roche454",relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6F,30 June 2024,Scholastica,"Scholastica,WikiWorks",LDA scores of the bacteria at the species level significantly different in memory deficit (MD) group versus normal health and positive group,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Anaerorhabdus|s__Anaerorhabdus furcosa,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium celatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Lactonifactor|s__Lactonifactor longoviformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter ruminantium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa",1783272|1239|526524|526525|128827|118966|118967;3379134|976|200643|171549|815|816|674529;3379134|976|200643|171549|815|816|28116;1783272|1239|186801|186802|31979|1485|36834;1783272|1239|186801|186802|31979|1485|1502;1783272|1239|186801|3085636|186803|2719313|358743;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|31979|420345|341220;1783272|1239|91061|186826|33958|2742598|97478;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|186802|216572|459786|1263547;3379134|976|200643|171549|2005525|375288|823;1783272|1239|526524|526525|2810280|3025755|1547,Complete,Svetlana up
bsdb:36368924/1/1,36368924,laboratory experiment,36368924,10.1186/s12866-022-02687-8,NA,"Du C., Zhou X., Zhang K., Huang S., Wang X., Zhou S. , Chen Y.",Inactivation of the MSTN gene expression changes the composition and function of the gut microbiome in sheep,BMC microbiology,2022,"Gut microbiome, Microbiota function, Myostatin edited, Sheep",Experiment 1,China,Ovis aries,Feces,UBERON:0001988,Myostatin-related muscle hypertrophy,MONDO:0013598,WTF(Wild-type female),GEF(Gene-edited female),GEF refers to the Myostatin edited female sheep(MSTN-edited female sheep).,8,8,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,increased,NA,NA,Signature 1,"Figure 2C, 2E and 2F",22 October 2024,KateRasheed,"KateRasheed,MyleeeA,WikiWorks",Differential abundance of gut microbiota taxa between Gene-edited female (GEF) and Wild-type Female (WTF).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Aminipila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Beduinellaceae|g__Beduinella|s__Beduinella massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|s__Eubacteriaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Evtepia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Evtepia|s__Evtepia gabavorous,k__Bacillati|p__Bacillota|s__Firmicutes bacterium ADurb.Bin467,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:124,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:170,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota,k__Thermotogati|p__Synergistota,k__Bacillati|p__Chloroflexota,k__Thermoproteati|p__Nitrososphaerota",1783272|1239|186801|186802|3085642|2048137;1783272|1239|186801|3082720|543314|2060094;1783272|1239|186801|3085636|3118652|2039240;1783272|1239|186801|186802|3151707|3151708|1852363;1783272|1239|186801|186802|1898207;1783272|1239|186801|186802|1980681;1783272|1239|186801|186802|186806|2049045;1783272|1239|186801|186802|2211178;1783272|1239|186801|186802|2211178|2211183;1783272|1239|1852894;1783272|1239|1263002;1783272|1239|1263006;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|3085636|186803|1649459|154046;1783272|1239|186801|186802|1392389;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|186802|216572|459786|1945593;1783272|1239|186801|186802|216572|1017280;1783272|1239|186801|186802|216572|1905344;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|292632;1783272|1239;3384194|508458;1783272|200795;1783275|651137,Complete,Svetlana up
bsdb:36368924/1/2,36368924,laboratory experiment,36368924,10.1186/s12866-022-02687-8,NA,"Du C., Zhou X., Zhang K., Huang S., Wang X., Zhou S. , Chen Y.",Inactivation of the MSTN gene expression changes the composition and function of the gut microbiome in sheep,BMC microbiology,2022,"Gut microbiome, Microbiota function, Myostatin edited, Sheep",Experiment 1,China,Ovis aries,Feces,UBERON:0001988,Myostatin-related muscle hypertrophy,MONDO:0013598,WTF(Wild-type female),GEF(Gene-edited female),GEF refers to the Myostatin edited female sheep(MSTN-edited female sheep).,8,8,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,increased,NA,NA,Signature 2,"Figure 2C, 2E and 2F",22 October 2024,KateRasheed,"KateRasheed,MyleeeA,WikiWorks",Differential abundance of gut microbiota taxa between Gene-edited female (GEF) and Wild-type Female (WTF).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|s__Bacteroidia bacterium,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus",3379134|976|200643|171549|171552|1283313;3379134|976|200643|2044936;3379134|976;3379134|976|200643|171549|815|909656|821,Complete,Svetlana up
bsdb:36368924/2/1,36368924,laboratory experiment,36368924,10.1186/s12866-022-02687-8,NA,"Du C., Zhou X., Zhang K., Huang S., Wang X., Zhou S. , Chen Y.",Inactivation of the MSTN gene expression changes the composition and function of the gut microbiome in sheep,BMC microbiology,2022,"Gut microbiome, Microbiota function, Myostatin edited, Sheep",Experiment 2,China,Ovis aries,Feces,UBERON:0001988,Myostatin-related muscle hypertrophy,MONDO:0013598,WTF(Wild-type female),GEF(Gene-edited female),GEF refers to the Myostatin edited female sheep(MSTN-edited female sheep).,8,8,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,increased,NA,NA,Signature 1,Figure 2G,22 October 2024,KateRasheed,"KateRasheed,MyleeeA,WikiWorks",Differential abundance of gut microbiota taxa between Gene-edited female (GEF) and Wild-type Female (WTF) using LEfSe.,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239;1783272|1239|186801;1783272|1239|186801|186802|1898207;1783272|1239|186801|186802,Complete,Svetlana up
bsdb:36368924/2/2,36368924,laboratory experiment,36368924,10.1186/s12866-022-02687-8,NA,"Du C., Zhou X., Zhang K., Huang S., Wang X., Zhou S. , Chen Y.",Inactivation of the MSTN gene expression changes the composition and function of the gut microbiome in sheep,BMC microbiology,2022,"Gut microbiome, Microbiota function, Myostatin edited, Sheep",Experiment 2,China,Ovis aries,Feces,UBERON:0001988,Myostatin-related muscle hypertrophy,MONDO:0013598,WTF(Wild-type female),GEF(Gene-edited female),GEF refers to the Myostatin edited female sheep(MSTN-edited female sheep).,8,8,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,increased,NA,NA,Signature 2,Figure 2G,22 October 2024,KateRasheed,"KateRasheed,MyleeeA,WikiWorks",Differential abundance of gut microbiota taxa between Gene-edited female (GEF) and Wild-type Female (WTF) using LEfSe.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|976|200643|171549|171552,Complete,Svetlana up
bsdb:36368924/3/1,36368924,laboratory experiment,36368924,10.1186/s12866-022-02687-8,NA,"Du C., Zhou X., Zhang K., Huang S., Wang X., Zhou S. , Chen Y.",Inactivation of the MSTN gene expression changes the composition and function of the gut microbiome in sheep,BMC microbiology,2022,"Gut microbiome, Microbiota function, Myostatin edited, Sheep",Experiment 3,China,Ovis aries,Feces,UBERON:0001988,Myostatin-related muscle hypertrophy,MONDO:0013598,WTM(Wild-type male),GEM(Gene-edited male),GEM refers to the Myostatin edited male sheep(MSTN-edited male sheep).,8,8,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,unchanged,increased,NA,NA,Signature 1,"Supplementary Figure 2C, Supplementary Figure 2D and Supplementary Figure 2F",22 October 2024,KateRasheed,"KateRasheed,MyleeeA,WikiWorks",Differential abundance of gut microbiota taxa between Gene-edited Male (GEM) and Wild-type Male (WTM).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Aminipila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Beduinellaceae|g__Beduinella|s__Beduinella massiliensis,k__Bacillati|p__Chloroflexota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|s__Eubacteriaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Evtepia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Evtepia|s__Evtepia gabavorous,k__Bacillati|p__Bacillota|s__Firmicutes bacterium ADurb.Bin467,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:124,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:170,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Thermoproteati|p__Nitrososphaerota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Thermotogati|p__Synergistota",1783272|1239|186801|186802|3085642|2048137;1783272|1239|186801|3082720|543314|2060094;1783272|1239|186801|3085636|3118652|2039240;1783272|1239;1783272|1239|186801|186802|3151707|3151708|1852363;1783272|200795;1783272|1239|186801|186802|1898207;1783272|1239|186801|186802|1980681;1783272|1239|186801|186802|186806|2049045;1783272|1239|186801|186802|2211178;1783272|1239|186801|186802|2211178|2211183;1783272|1239|1852894;1783272|1239|1263002;1783272|1239|1263006;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|3085636|186803|1649459|154046;1783272|1239|186801|186802|1392389;1783272|1239|91061|186826|33958|1578;1783275|651137;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|186802|216572|459786|1945593;1783272|1239|186801|186802|216572|1017280;1783272|1239|186801|186802|216572|1905344;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|292632;3384194|508458,Complete,Svetlana up
bsdb:36368924/3/2,36368924,laboratory experiment,36368924,10.1186/s12866-022-02687-8,NA,"Du C., Zhou X., Zhang K., Huang S., Wang X., Zhou S. , Chen Y.",Inactivation of the MSTN gene expression changes the composition and function of the gut microbiome in sheep,BMC microbiology,2022,"Gut microbiome, Microbiota function, Myostatin edited, Sheep",Experiment 3,China,Ovis aries,Feces,UBERON:0001988,Myostatin-related muscle hypertrophy,MONDO:0013598,WTM(Wild-type male),GEM(Gene-edited male),GEM refers to the Myostatin edited male sheep(MSTN-edited male sheep).,8,8,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,unchanged,increased,NA,NA,Signature 2,"Supplementary Figure 2C, Supplementary Figure 2D and Supplementary Figure 2F",22 October 2024,KateRasheed,"KateRasheed,MyleeeA,WikiWorks",Differential abundance of gut microbiota taxa between Gene-edited Male (GEM) and Wild-type Male (WTM).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|s__Bacteroidia bacterium,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus",3379134|976|200643|171549|171552|1283313;3379134|976|200643|2044936;3379134|976;3379134|976|200643|171549|815|909656|821,Complete,Svetlana up
bsdb:36368924/4/1,36368924,laboratory experiment,36368924,10.1186/s12866-022-02687-8,NA,"Du C., Zhou X., Zhang K., Huang S., Wang X., Zhou S. , Chen Y.",Inactivation of the MSTN gene expression changes the composition and function of the gut microbiome in sheep,BMC microbiology,2022,"Gut microbiome, Microbiota function, Myostatin edited, Sheep",Experiment 4,China,Ovis aries,Feces,UBERON:0001988,Myostatin-related muscle hypertrophy,MONDO:0013598,WTM(Wild-type male),GEM(Gene-edited male),GEM refers to the Myostatin edited male sheep(MSTN-edited male sheep).,8,8,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,unchanged,increased,NA,NA,Signature 1,Supplementary Figure 2G,22 October 2024,KateRasheed,"KateRasheed,MyleeeA,WikiWorks",Differential abundance of gut microbiota taxa between Gene-edited Male (GEM) and Wild-type Male (WTM) using LEfSe.,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239;1783272|1239|186801;1783272|1239|186801|186802|1898207;1783272|1239|186801|186802,Complete,Svetlana up
bsdb:36368924/4/2,36368924,laboratory experiment,36368924,10.1186/s12866-022-02687-8,NA,"Du C., Zhou X., Zhang K., Huang S., Wang X., Zhou S. , Chen Y.",Inactivation of the MSTN gene expression changes the composition and function of the gut microbiome in sheep,BMC microbiology,2022,"Gut microbiome, Microbiota function, Myostatin edited, Sheep",Experiment 4,China,Ovis aries,Feces,UBERON:0001988,Myostatin-related muscle hypertrophy,MONDO:0013598,WTM(Wild-type male),GEM(Gene-edited male),GEM refers to the Myostatin edited male sheep(MSTN-edited male sheep).,8,8,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,unchanged,increased,NA,NA,Signature 2,Supplementary Figure 2G,22 October 2024,KateRasheed,"KateRasheed,MyleeeA,WikiWorks",Differential abundance of gut microbiota taxa between Gene-edited Male (GEM) and Wild-type Male (WTM) using LEfSe.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|976|200643|171549|171552,Complete,Svetlana up
bsdb:36376318/1/1,36376318,case-control,36376318,10.1038/s41467-022-34667-x,NA,"Wallen Z.D., Demirkan A., Twa G., Cohen G., Dean M.N., Standaert D.G., Sampson T.R. , Payami H.",Metagenomics of Parkinson's disease implicates the gut microbiome in multiple disease mechanisms,Nature communications,2022,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls.,Parkinson's Disease subjects.,Potential PD cases for enrollment were identified via systematic pre-screening of electronic medical records (EMR) of patients with an upcoming appointment in the Movement Disorder Clinic at UAB. Subjects were invited to enroll in the study after their clinic visit if the attending specialist confirmed PD diagnosis and the patient was willing to hear about the study.,234,490,3 months,WMS,NA,Illumina,centered log-ratio,"ANCOM,MaAsLin2",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 3,3 June 2023,Fcuevas3,"Fcuevas3,Peace Sandy,WikiWorks","Differential abundances and effect sizes of PD-associated species.
Analysis included N = 724 biologically independent samples from 490 PD and 234 neurologically healthy control (NHC) subjects. Forty-six species that had at least 75% (and up to 750%) change in abundance in PD are shown here; for all 84 PD-associated species see Supplementary Fig. 3. a Distribution of relative abundances. Log2 transformed relative abundance values, as used in MaAsLin2, were used to generate the boxplots. Untransformed relative abundances, shown in parenthesis, are provided on the X-axis for easier interpretation of data. Boxplots show distribution of the data for PD (blue green) and NHC (orange). Each sample was plotted according to its abundance of the species. The left, middle, and right vertical boundaries of each box represents the first, second (median), and third quartiles of the data; that is, 25% of samples have abundance lower than the left border of the box, 25% of samples have abundances that are higher than the right border of the box. Absence of a box indicates 75% of samples had zero abundance. The lines extending from the two ends of each box represent 1.5x outside the interquartile range (range = (abundance value at 75% minus abundance value at 25%) x 1.5). Points beyond the lines are outlier samples.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella tayi,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D16,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum",1783272|201174|1760|85004|31953|1678|1689;1783272|201174|1760|2037|2049|1654|544580;1783272|1239|91061|186826|1300|1301|1309;1783272|1239|186801|186802|216572|1535;1783272|1239|909932|1843488|909930|904|187327;1783272|1239|186801|3085636|186803|1432051|1432052;3366610|28890|183925|2158|2159|2172|2173;3379134|976|200643|171549|171550|239759|626932;1783272|201174|1760|85004|31953|1678|1681;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|216572|552398;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|3085636|186803|1649459|154046;1783272|1239|186801|186802|216572|1905344|1550024;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|171550|239759|214856;3379134|1224|1236|91347|543|570|573;1783272|201174|1760|2037|2049|1654;1783272|1239|186801|186802|31979|1485|1522,Complete,Peace Sandy
bsdb:36376318/1/2,36376318,case-control,36376318,10.1038/s41467-022-34667-x,NA,"Wallen Z.D., Demirkan A., Twa G., Cohen G., Dean M.N., Standaert D.G., Sampson T.R. , Payami H.",Metagenomics of Parkinson's disease implicates the gut microbiome in multiple disease mechanisms,Nature communications,2022,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls.,Parkinson's Disease subjects.,Potential PD cases for enrollment were identified via systematic pre-screening of electronic medical records (EMR) of patients with an upcoming appointment in the Movement Disorder Clinic at UAB. Subjects were invited to enroll in the study after their clinic visit if the attending specialist confirmed PD diagnosis and the patient was willing to hear about the study.,234,490,3 months,WMS,NA,Illumina,centered log-ratio,"ANCOM,MaAsLin2",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 3,3 June 2023,Fcuevas3,"Fcuevas3,Peace Sandy,WikiWorks","Differential abundances and effect sizes of PD-associated species. Analysis included N = 724 biologically independent samples from 490 PD and 234 neurologically healthy control (NHC) subjects. Forty-six species that had at least 75% (and up to 750%) change in abundance in PD are shown here; for all 84 PD-associated species see Supplementary Fig. 3. a Distribution of relative abundances. Log2 transformed relative abundance values, as used in MaAsLin2, were used to generate the boxplots. Untransformed relative abundances, shown in parenthesis, are provided on the X-axis for easier interpretation of data. Boxplots show distribution of the data for PD (blue green) and NHC (orange). Each sample was plotted according to its abundance of the species. The left, middle, and right vertical boundaries of each box represents the first, second (median), and third quartiles of the data; that is, 25% of samples have abundance lower than the left border of the box, 25% of samples have abundances that are higher than the right border of the box. Absence of a box indicates 75% of samples had zero abundance. The lines extending from the two ends of each box represent 1.5x outside the interquartile range (range = (abundance value at 75% minus abundance value at 25%) x 1.5). Points beyond the lines are outlier samples.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Wegman et al. 2014),k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella corporis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus|s__Monoglobus pectinilyticus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens",1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|1263|1160721;1783272|1239|186801|3085636|186803|2316020|46228;1783272|1239|186801|3085636|186803|841|360807;3379134|976|200643|171549|171552|838|28128;1783272|1239|186801|3085636|186803|572511|1322;1783272|1239|186801|186802|186806|1730|39490;1783272|1239|186801|186802|31979|1485|1506;1783272|1239|186801|3085656|3085657|2039302|1981510;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|186801|3085636|186803|28050|39485,Complete,Peace Sandy
bsdb:36381318/1/1,36381318,prospective cohort,36381318,NA,NA,"Himbert C., Stephens W.Z., Gigic B., Hardikar S., Holowatyj A.N., Lin T., Ose J., Swanson E., Ashworth A., Warby C.A., Peoples A.R., Nix D., Jedrzkiewicz J., Bronner M., Pickron B., Scaife C., Cohan J.N., Schrotz-King P., Habermann N., Boehm J., Hullar M., Figueiredo J.C., Toriola A.T., Siegel E.M., Li C.I., Ulrich A.B., Shibata D., Boucher K., Huang L.C., Schneider M., Round J.L. , Ulrich C.M.",Differences in the gut microbiome by physical activity and BMI among colorectal cancer patients,American journal of cancer research,2022,"Colorectal cancer, energy balance, microbiome, obesity, physical activity",Experiment 1,"Germany,United States of America",Homo sapiens,Feces,UBERON:0001988,Physical activity,EFO:0003940,Active patients,Inactive patients,Patients that are not engaged in any regular physical activity or exercise.,72,107,1 month,16S,34,Illumina,relative abundances,Wald Test,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,decreased,Signature 1,Supplementary Table 2,14 March 2023,Deacme,"Deacme,Atrayees,ChiomaBlessing,WikiWorks",Differential abundance (mean normalized counts) at phylum level inactive group VS active group,increased,k__Bacillati|p__Actinomycetota,1783272|201174,Complete,Atrayees
bsdb:36381318/1/2,36381318,prospective cohort,36381318,NA,NA,"Himbert C., Stephens W.Z., Gigic B., Hardikar S., Holowatyj A.N., Lin T., Ose J., Swanson E., Ashworth A., Warby C.A., Peoples A.R., Nix D., Jedrzkiewicz J., Bronner M., Pickron B., Scaife C., Cohan J.N., Schrotz-King P., Habermann N., Boehm J., Hullar M., Figueiredo J.C., Toriola A.T., Siegel E.M., Li C.I., Ulrich A.B., Shibata D., Boucher K., Huang L.C., Schneider M., Round J.L. , Ulrich C.M.",Differences in the gut microbiome by physical activity and BMI among colorectal cancer patients,American journal of cancer research,2022,"Colorectal cancer, energy balance, microbiome, obesity, physical activity",Experiment 1,"Germany,United States of America",Homo sapiens,Feces,UBERON:0001988,Physical activity,EFO:0003940,Active patients,Inactive patients,Patients that are not engaged in any regular physical activity or exercise.,72,107,1 month,16S,34,Illumina,relative abundances,Wald Test,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,decreased,Signature 2,Table 2,14 March 2023,Deacme,"Deacme,Atrayees,ChiomaBlessing,WikiWorks",Differential abundance (mean normalized counts) at genus level in inactive group VS active group,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Succiniclasticum",3379134|1224|1236|135624|83763|83770;1783272|1239|909932|1843488|909930|40840,Complete,Atrayees
bsdb:36381318/2/2,36381318,prospective cohort,36381318,NA,NA,"Himbert C., Stephens W.Z., Gigic B., Hardikar S., Holowatyj A.N., Lin T., Ose J., Swanson E., Ashworth A., Warby C.A., Peoples A.R., Nix D., Jedrzkiewicz J., Bronner M., Pickron B., Scaife C., Cohan J.N., Schrotz-King P., Habermann N., Boehm J., Hullar M., Figueiredo J.C., Toriola A.T., Siegel E.M., Li C.I., Ulrich A.B., Shibata D., Boucher K., Huang L.C., Schneider M., Round J.L. , Ulrich C.M.",Differences in the gut microbiome by physical activity and BMI among colorectal cancer patients,American journal of cancer research,2022,"Colorectal cancer, energy balance, microbiome, obesity, physical activity",Experiment 2,"Germany,United States of America",Homo sapiens,Feces,UBERON:0001988,Body mass index,EFO:0004340,Normal weight patients,Overweight patients,Patient with a BMI greater than or equal to 25 kg/m2 but not greater than 30 kg/m2.,59,76,1 month,16S,34,Illumina,relative abundances,Wald Test,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,decreased,Signature 2,Table 2,16 March 2023,Deacme,"Deacme,Aiyshaaaa,Atrayees,ChiomaBlessing,WikiWorks",Differential abundance (mean normalized counts) at genus level in overweight group VS normal weight group,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Succiniclasticum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio",1783272|201174|84998|84999|1643824|133925;1783272|1239|186801|3082720|543314|86331;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|31979|1485;1783272|1239|909932|1843488|909930|40840;3379134|1224|1236|135624|83763|83770,Complete,Atrayees
bsdb:36381318/3/1,36381318,prospective cohort,36381318,NA,NA,"Himbert C., Stephens W.Z., Gigic B., Hardikar S., Holowatyj A.N., Lin T., Ose J., Swanson E., Ashworth A., Warby C.A., Peoples A.R., Nix D., Jedrzkiewicz J., Bronner M., Pickron B., Scaife C., Cohan J.N., Schrotz-King P., Habermann N., Boehm J., Hullar M., Figueiredo J.C., Toriola A.T., Siegel E.M., Li C.I., Ulrich A.B., Shibata D., Boucher K., Huang L.C., Schneider M., Round J.L. , Ulrich C.M.",Differences in the gut microbiome by physical activity and BMI among colorectal cancer patients,American journal of cancer research,2022,"Colorectal cancer, energy balance, microbiome, obesity, physical activity",Experiment 3,"Germany,United States of America",Homo sapiens,Feces,UBERON:0001988,Body mass index,EFO:0004340,Normal weight patients,Obese patients,Patients with a BMI greater than 30 kg/m2,59,44,1 month,16S,34,Illumina,relative abundances,Wald Test,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,decreased,Signature 1,Table 2,16 March 2023,Deacme,"Deacme,Atrayees,ChiomaBlessing,WikiWorks",Differential abundance (mean normalized counts) at genus level in obese group VS normal weight group,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,1783272|1239|186801|186802|216572|1263,Complete,Atrayees
bsdb:36381318/3/2,36381318,prospective cohort,36381318,NA,NA,"Himbert C., Stephens W.Z., Gigic B., Hardikar S., Holowatyj A.N., Lin T., Ose J., Swanson E., Ashworth A., Warby C.A., Peoples A.R., Nix D., Jedrzkiewicz J., Bronner M., Pickron B., Scaife C., Cohan J.N., Schrotz-King P., Habermann N., Boehm J., Hullar M., Figueiredo J.C., Toriola A.T., Siegel E.M., Li C.I., Ulrich A.B., Shibata D., Boucher K., Huang L.C., Schneider M., Round J.L. , Ulrich C.M.",Differences in the gut microbiome by physical activity and BMI among colorectal cancer patients,American journal of cancer research,2022,"Colorectal cancer, energy balance, microbiome, obesity, physical activity",Experiment 3,"Germany,United States of America",Homo sapiens,Feces,UBERON:0001988,Body mass index,EFO:0004340,Normal weight patients,Obese patients,Patients with a BMI greater than 30 kg/m2,59,44,1 month,16S,34,Illumina,relative abundances,Wald Test,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,decreased,Signature 2,Table 2,16 March 2023,Deacme,"Deacme,Atrayees,ChiomaBlessing,WikiWorks",Differential abundance (mean normalized counts) at genus level in obese group VS normal weight group,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio",1783272|201174|84998|1643822|1643826|447020;1783272|1239|186801|186802|31979|1485;3379134|1224|1236|135624|83763|83770,Complete,Atrayees
bsdb:36381318/4/1,36381318,prospective cohort,36381318,NA,NA,"Himbert C., Stephens W.Z., Gigic B., Hardikar S., Holowatyj A.N., Lin T., Ose J., Swanson E., Ashworth A., Warby C.A., Peoples A.R., Nix D., Jedrzkiewicz J., Bronner M., Pickron B., Scaife C., Cohan J.N., Schrotz-King P., Habermann N., Boehm J., Hullar M., Figueiredo J.C., Toriola A.T., Siegel E.M., Li C.I., Ulrich A.B., Shibata D., Boucher K., Huang L.C., Schneider M., Round J.L. , Ulrich C.M.",Differences in the gut microbiome by physical activity and BMI among colorectal cancer patients,American journal of cancer research,2022,"Colorectal cancer, energy balance, microbiome, obesity, physical activity",Experiment 4,"Germany,United States of America",Homo sapiens,Feces,UBERON:0001988,"Body mass index,Physical activity","EFO:0004340,EFO:0003940",Normal weight/active patients,Normal weight/inactive patients,Patient that has a BMI greater than 18.5 kg/m2 but less than 25 kg/m2 and engaged in little to no physical activity on a regular basis.,26,33,1 month,16S,34,Illumina,relative abundances,Wald Test,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,decreased,Signature 1,Table 3,4 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential abundance (mean normalized counts) at genus level (by individual BMI and physical activity groups) in normal weight/ inactive group compared to normal weight/ active group,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Succiniclasticum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio",1783272|1239|909932|1843488|909930|40840;3379134|1224|1236|135624|83763|83770,Complete,ChiomaBlessing
bsdb:36381318/4/2,36381318,prospective cohort,36381318,NA,NA,"Himbert C., Stephens W.Z., Gigic B., Hardikar S., Holowatyj A.N., Lin T., Ose J., Swanson E., Ashworth A., Warby C.A., Peoples A.R., Nix D., Jedrzkiewicz J., Bronner M., Pickron B., Scaife C., Cohan J.N., Schrotz-King P., Habermann N., Boehm J., Hullar M., Figueiredo J.C., Toriola A.T., Siegel E.M., Li C.I., Ulrich A.B., Shibata D., Boucher K., Huang L.C., Schneider M., Round J.L. , Ulrich C.M.",Differences in the gut microbiome by physical activity and BMI among colorectal cancer patients,American journal of cancer research,2022,"Colorectal cancer, energy balance, microbiome, obesity, physical activity",Experiment 4,"Germany,United States of America",Homo sapiens,Feces,UBERON:0001988,"Body mass index,Physical activity","EFO:0004340,EFO:0003940",Normal weight/active patients,Normal weight/inactive patients,Patient that has a BMI greater than 18.5 kg/m2 but less than 25 kg/m2 and engaged in little to no physical activity on a regular basis.,26,33,1 month,16S,34,Illumina,relative abundances,Wald Test,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,decreased,Signature 2,Table 3,4 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential abundance (mean normalized counts) at genus level (by individual BMI and physical activity groups) in normal weight/ inactive group compared to normal weight/ active group,increased,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,3384194|508458|649775|649776|3029088|638847,Complete,NA
bsdb:36381318/6/1,36381318,prospective cohort,36381318,NA,NA,"Himbert C., Stephens W.Z., Gigic B., Hardikar S., Holowatyj A.N., Lin T., Ose J., Swanson E., Ashworth A., Warby C.A., Peoples A.R., Nix D., Jedrzkiewicz J., Bronner M., Pickron B., Scaife C., Cohan J.N., Schrotz-King P., Habermann N., Boehm J., Hullar M., Figueiredo J.C., Toriola A.T., Siegel E.M., Li C.I., Ulrich A.B., Shibata D., Boucher K., Huang L.C., Schneider M., Round J.L. , Ulrich C.M.",Differences in the gut microbiome by physical activity and BMI among colorectal cancer patients,American journal of cancer research,2022,"Colorectal cancer, energy balance, microbiome, obesity, physical activity",Experiment 6,"Germany,United States of America",Homo sapiens,Feces,UBERON:0001988,"Body mass index,Physical activity","EFO:0004340,EFO:0003940",Normal weight/active patients,Overweight/Obese/inactive patients,Patient with a BMI equal to or greater than 25 kg/m2 and is physically inactive.,26,74,1 month,16S,34,Illumina,relative abundances,Wald Test,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,decreased,Signature 1,Supplementary Table 3,16 March 2023,Deacme,"Deacme,Aiyshaaaa,Atrayees,ChiomaBlessing,WikiWorks",Differential abundances (mean normalized counts) at phylum level (by combined BMI and physical activity groups) in overweight/ obese/ inactive group VS normal weight/ active group,increased,k__Bacillati|p__Actinomycetota,1783272|201174,Complete,ChiomaBlessing
bsdb:36381318/6/2,36381318,prospective cohort,36381318,NA,NA,"Himbert C., Stephens W.Z., Gigic B., Hardikar S., Holowatyj A.N., Lin T., Ose J., Swanson E., Ashworth A., Warby C.A., Peoples A.R., Nix D., Jedrzkiewicz J., Bronner M., Pickron B., Scaife C., Cohan J.N., Schrotz-King P., Habermann N., Boehm J., Hullar M., Figueiredo J.C., Toriola A.T., Siegel E.M., Li C.I., Ulrich A.B., Shibata D., Boucher K., Huang L.C., Schneider M., Round J.L. , Ulrich C.M.",Differences in the gut microbiome by physical activity and BMI among colorectal cancer patients,American journal of cancer research,2022,"Colorectal cancer, energy balance, microbiome, obesity, physical activity",Experiment 6,"Germany,United States of America",Homo sapiens,Feces,UBERON:0001988,"Body mass index,Physical activity","EFO:0004340,EFO:0003940",Normal weight/active patients,Overweight/Obese/inactive patients,Patient with a BMI equal to or greater than 25 kg/m2 and is physically inactive.,26,74,1 month,16S,34,Illumina,relative abundances,Wald Test,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,decreased,Signature 2,Table 3,4 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential abundances (mean normalized counts) at genus level (by combined BMI and physical activity groups) in overweight/ obese/ inactive group VS normal weight/ active group,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,3379134|1224|1236|135624|83763|83770,Complete,ChiomaBlessing
bsdb:36381318/7/1,36381318,prospective cohort,36381318,NA,NA,"Himbert C., Stephens W.Z., Gigic B., Hardikar S., Holowatyj A.N., Lin T., Ose J., Swanson E., Ashworth A., Warby C.A., Peoples A.R., Nix D., Jedrzkiewicz J., Bronner M., Pickron B., Scaife C., Cohan J.N., Schrotz-King P., Habermann N., Boehm J., Hullar M., Figueiredo J.C., Toriola A.T., Siegel E.M., Li C.I., Ulrich A.B., Shibata D., Boucher K., Huang L.C., Schneider M., Round J.L. , Ulrich C.M.",Differences in the gut microbiome by physical activity and BMI among colorectal cancer patients,American journal of cancer research,2022,"Colorectal cancer, energy balance, microbiome, obesity, physical activity",Experiment 7,"Germany,United States of America",Homo sapiens,Feces,UBERON:0001988,"Body mass index,Physical activity","EFO:0004340,EFO:0003940",Overweight/Obese/active patients,Overweight/Obese/inactive patients,Patients with BMI greater than or equal to 25 kg/m2 and are not physically active.,46,74,1 month,16S,34,Illumina,relative abundances,Wald Test,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,decreased,Signature 1,Table 3,4 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential abundances (mean normalized counts) at genus level by combined BMI and physical activity groups in overweight/ obese inactive group VS overweight/ obese active group,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Succiniclasticum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio",1783272|1239|909932|1843488|909930|40840;3379134|1224|1236|135624|83763|83770,Complete,ChiomaBlessing
bsdb:36388691/1/1,36388691,"cross-sectional observational, not case-control",36388691,10.21037/jgo-22-116,NA,"Obuya S., Elkholy A., Avuthu N., Behring M., Bajpai P., Agarwal S., Kim H.G., El-Nikhely N., Akinyi P., Orwa J., Afaq F., Abdalla M., Michael A., Farouk M., Bateman L.B., Fouad M., Saleh M., Guda C., Manne U. , Arafat W.","A signature of <i>Prevotella copri</i> and <i>Faecalibacterium prausnitzii</i> depletion, and a link with bacterial glutamate degradation in the Kenyan colorectal cancer patients",Journal of gastrointestinal oncology,2022,"Colorectal cancer (CRC), Faecalibacterium prausnitzii, Kenya, Prevotella copri, microbiome",Experiment 1,Kenya,Homo sapiens,Colon,UBERON:0001155,Colorectal cancer,EFO:0005842,Healthy Control,CRC Patients,patients with Colorectal Cancer,18,18,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 2,29 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",Bar graph of LEfSe analysis CRC vs. healthy controls,increased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter ureolyticus,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Flexispira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella|s__Moryella indoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Schwartzia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sporobacterium|s__Sporobacterium sp. WAL 1855D,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis",1783272|544448|31969|2085|2092|2093;1783272|544448|31969|2085;3379134|29547|3031852|213849|72294|194|827;1783272|544448|31969|2085|2092;1783272|1239|186801|3082720|186804|1257|1261;3379134|1224|28211|204441;1783272|1239|186801|3082720|543314|86331;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|91061|186826|33958|1578|147802;1783272|201174|1760|2037|2049|2050;1783272|1239|526524|526525|128827|123375|102148;3379134|29547|3031852|213849|72293;3379134|29547|3031852|213849|72293|2353;1783272|1239|186801|3085636|186803|437755|371674;1783272|1239|186801|3085636|186803|437755;1783272|1239|186801|186802|31979|1485;1783272|1239|909932|909929|1843491|55506;1783272|1239|186801|3085636|186803|100132|507843;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|186801|3082720|186804|1257;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|91061|1385;1783272|1239|1737404|1737405|1737406;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838|28133;3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|815|816|817,Complete,Svetlana up
bsdb:36388691/1/2,36388691,"cross-sectional observational, not case-control",36388691,10.21037/jgo-22-116,NA,"Obuya S., Elkholy A., Avuthu N., Behring M., Bajpai P., Agarwal S., Kim H.G., El-Nikhely N., Akinyi P., Orwa J., Afaq F., Abdalla M., Michael A., Farouk M., Bateman L.B., Fouad M., Saleh M., Guda C., Manne U. , Arafat W.","A signature of <i>Prevotella copri</i> and <i>Faecalibacterium prausnitzii</i> depletion, and a link with bacterial glutamate degradation in the Kenyan colorectal cancer patients",Journal of gastrointestinal oncology,2022,"Colorectal cancer (CRC), Faecalibacterium prausnitzii, Kenya, Prevotella copri, microbiome",Experiment 1,Kenya,Homo sapiens,Colon,UBERON:0001155,Colorectal cancer,EFO:0005842,Healthy Control,CRC Patients,patients with Colorectal Cancer,18,18,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 2,29 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",Bar graph of LEfSe analysis CRC vs. healthy controls.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,s__rumen bacterium YS2",1783272|201174|1760|2037;3379134|1224|28216|80840|506;3379134|1224|28211;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|28111;3379134|1224|28216|80840;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|84998|84999;1783272|201174|84998;1783272|1117;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;3379134|1224|1236|135625|712|724|729;1783272|1239|526524|526525|128827|1573535|1735;3379134|976|200643|171549|2005525|375288;3379134|1224|1236|135625|712;3379134|1224|1236|135625;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|301302;3379134|976|200643|171549|171552|2974251|165179;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|3085636|186803|2316020|46228;209265,Complete,Svetlana up
bsdb:36388691/2/1,36388691,"cross-sectional observational, not case-control",36388691,10.21037/jgo-22-116,NA,"Obuya S., Elkholy A., Avuthu N., Behring M., Bajpai P., Agarwal S., Kim H.G., El-Nikhely N., Akinyi P., Orwa J., Afaq F., Abdalla M., Michael A., Farouk M., Bateman L.B., Fouad M., Saleh M., Guda C., Manne U. , Arafat W.","A signature of <i>Prevotella copri</i> and <i>Faecalibacterium prausnitzii</i> depletion, and a link with bacterial glutamate degradation in the Kenyan colorectal cancer patients",Journal of gastrointestinal oncology,2022,"Colorectal cancer (CRC), Faecalibacterium prausnitzii, Kenya, Prevotella copri, microbiome",Experiment 2,Kenya,Homo sapiens,Colon,UBERON:0001155,Colorectal cancer,EFO:0005842,CRC patients under 40 years of age,CRC Patients over 40 years of age,Patients with Colorectal Cancer over 40 years of age,8,10,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,29 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",Bar graph of LEfSe analysis for CRC patients under 40 years of age vs. over 40 years of age.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum",3379134|976|200643|171549|815|816|28116;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|186801|3085636|186803|2941495|1512,Complete,Svetlana up
bsdb:36388691/2/2,36388691,"cross-sectional observational, not case-control",36388691,10.21037/jgo-22-116,NA,"Obuya S., Elkholy A., Avuthu N., Behring M., Bajpai P., Agarwal S., Kim H.G., El-Nikhely N., Akinyi P., Orwa J., Afaq F., Abdalla M., Michael A., Farouk M., Bateman L.B., Fouad M., Saleh M., Guda C., Manne U. , Arafat W.","A signature of <i>Prevotella copri</i> and <i>Faecalibacterium prausnitzii</i> depletion, and a link with bacterial glutamate degradation in the Kenyan colorectal cancer patients",Journal of gastrointestinal oncology,2022,"Colorectal cancer (CRC), Faecalibacterium prausnitzii, Kenya, Prevotella copri, microbiome",Experiment 2,Kenya,Homo sapiens,Colon,UBERON:0001155,Colorectal cancer,EFO:0005842,CRC patients under 40 years of age,CRC Patients over 40 years of age,Patients with Colorectal Cancer over 40 years of age,8,10,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,29 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",Bar graph of LEfSe analysis for CRC patients under 40 years of age vs. over 40 years of age.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales",3379134|976|200643|171549|171552|2974251|165179;;3379134|1224|28216|80840|75682;1783272|1239|91061|186826|33958|2767887|1624;3379134|1224|28216|80840|75682|963;3379134|1224|28211|356|212791;3379134|1224|1236|135614|32033;3379134|1224|1236|135614,Complete,Svetlana up
bsdb:36389135/1/1,36389135,case-control,36389135,10.3389/fcimb.2022.1024867,NA,"Xia X., Chen J., Cheng Y., Chen F., Lu H., Liu J., Wang L., Pu F., Wang Y., Liu H., Cao D., Zhang Z., Xia Z., Fan M., Ling Z. , Zhao L.","Comparative analysis of the lung microbiota in patients with respiratory infections, tuberculosis, and lung cancer: A preliminary study",Frontiers in cellular and infection microbiology,2022,"community-acquired pneumonia, inflammation, lung cancer, lung microbiota, pulmonary tuberculosis",Experiment 1,China,Homo sapiens,Lung,UBERON:0002048,"Lung cancer,Pulmonary tuberculosis","MONDO:0008903,EFO:1000049",Lung cancer,Tuberculosis patients (PTB),Confirmed pulmonary tuberculosis,8,21,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,decreased,decreased,unchanged,NA,NA,Signature 1,Figure 3,8 July 2025,Nuerteye,Nuerteye,"Taxonomic differences of the lung microbiota among patients with primary pulmonary tuberculosis (PTB), newly diagnosed lung cancer (LC),
and community-acquired pneumonia (CAP). LEfSe identified the most differentially abundant taxa between the two groups",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium",1783272|1239|909932|909929|1843491|970;1783272|201174|1760|85007|1762;1783272|201174|1760|85007|1762|1763,Complete,NA
bsdb:36389135/1/2,36389135,case-control,36389135,10.3389/fcimb.2022.1024867,NA,"Xia X., Chen J., Cheng Y., Chen F., Lu H., Liu J., Wang L., Pu F., Wang Y., Liu H., Cao D., Zhang Z., Xia Z., Fan M., Ling Z. , Zhao L.","Comparative analysis of the lung microbiota in patients with respiratory infections, tuberculosis, and lung cancer: A preliminary study",Frontiers in cellular and infection microbiology,2022,"community-acquired pneumonia, inflammation, lung cancer, lung microbiota, pulmonary tuberculosis",Experiment 1,China,Homo sapiens,Lung,UBERON:0002048,"Lung cancer,Pulmonary tuberculosis","MONDO:0008903,EFO:1000049",Lung cancer,Tuberculosis patients (PTB),Confirmed pulmonary tuberculosis,8,21,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,decreased,decreased,unchanged,NA,NA,Signature 2,Figure 3,8 July 2025,Nuerteye,Nuerteye,"Taxonomic differences of the lung microbiota among patients with primary pulmonary tuberculosis (PTB), newly diagnosed lung cancer (LC), and community-acquired pneumonia (CAP). LEfSe identified the most differentially abundant taxa between the two groups",decreased,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium,3379134|1224|28211|204457|3423717|165695,Complete,NA
bsdb:36389135/2/1,36389135,case-control,36389135,10.3389/fcimb.2022.1024867,NA,"Xia X., Chen J., Cheng Y., Chen F., Lu H., Liu J., Wang L., Pu F., Wang Y., Liu H., Cao D., Zhang Z., Xia Z., Fan M., Ling Z. , Zhao L.","Comparative analysis of the lung microbiota in patients with respiratory infections, tuberculosis, and lung cancer: A preliminary study",Frontiers in cellular and infection microbiology,2022,"community-acquired pneumonia, inflammation, lung cancer, lung microbiota, pulmonary tuberculosis",Experiment 2,China,Homo sapiens,Lung,UBERON:0002048,"Pulmonary tuberculosis,Pneumonia","EFO:1000049,EFO:0003106",community-acquired pneumonia (CAP),Pulmonary tuberculosis,Confirmed pulmonary tuberculosis,49,21,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,increased,increased,unchanged,NA,NA,Signature 1,Figure 3,9 July 2025,Nuerteye,Nuerteye,"Taxonomic differences of the lung microbiota among patients with primary pulmonary tuberculosis (PTB), newly diagnosed lung cancer (LC), and community-acquired pneumonia (CAP). LEfSe identified the most differentially abundant taxa between the two groups.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Roseomonadaceae|g__Roseomonas,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Janibacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales",3379134|976|117743|200644;3379134|1224|1236|135625|712;1783272|1239|186801|3082720|186804|1501226;3379134|1224|28211|204457|41297|13687;3379134|1224|28216|80840|80864;1783272|1239|91061|186826|33958|2767887;3379134|1224|28216|206351|481|32257;1783272|1239|91061|186826|33958|1578;3379134|1224|28216|206351|481|538;1783272|201174|1760|85006|1268|1269;1783272|1239|186801|3085636|186803|2316020;1783272|1239|909932|909929|1843491|970;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;1783272|1239|186801|3085636|186803|1407607;1783272|201174|1760|85009;1783272|1239|91061|186826|33958|2742598;1783272|201174|1760|85009|85015;1783272|201174|1760|85007|85029|37914;1783272|201174|1760|85007|85029;3379134|1224|28211|3120395|3385906|125216;3379134|976|117743|200644|2762318|59732;3379134|976|117743|200644|2762318;1783272|201174|1760|85006|85021;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|186802|186807;1783272|201174|1760|85006|85021|53457;1783272|201174|84998|1643822|1643826;1783272|201174|84998|1643822;3379134|1224|28211|356|212791;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294;3379134|29547|3031852|213849;3379134|976|117743|200644|49546|1016;3379134|976|117743;3379134|1224|1236|2887326|468;3379134|1224|1236|72274;3384189|32066|203490|203491|1129771|32067;1783272|201174|1760|85007|1762;1783272|201174|1760|85007|1762|1763;3384189|32066|203490;3384189|32066|203490|203491;3379134|1224|28216;3379134|1224|28216|206351;1783272|201174|1760|85007,Complete,NA
bsdb:36389135/2/2,36389135,case-control,36389135,10.3389/fcimb.2022.1024867,NA,"Xia X., Chen J., Cheng Y., Chen F., Lu H., Liu J., Wang L., Pu F., Wang Y., Liu H., Cao D., Zhang Z., Xia Z., Fan M., Ling Z. , Zhao L.","Comparative analysis of the lung microbiota in patients with respiratory infections, tuberculosis, and lung cancer: A preliminary study",Frontiers in cellular and infection microbiology,2022,"community-acquired pneumonia, inflammation, lung cancer, lung microbiota, pulmonary tuberculosis",Experiment 2,China,Homo sapiens,Lung,UBERON:0002048,"Pulmonary tuberculosis,Pneumonia","EFO:1000049,EFO:0003106",community-acquired pneumonia (CAP),Pulmonary tuberculosis,Confirmed pulmonary tuberculosis,49,21,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,increased,increased,unchanged,NA,NA,Signature 2,Figure 3,9 July 2025,Nuerteye,Nuerteye,"Taxonomic differences of the lung microbiota among patients with primary pulmonary tuberculosis (PTB), newly diagnosed lung cancer (LC), and community-acquired pneumonia (CAP). LEfSe identified the most differentially abundant taxa between the two groups.",decreased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Thermotogati|p__Deinococcota|c__Deinococci,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Mediterranea,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae",1783272|1239|1737404|1737405|1570339|543311;1783272|1239|1737404|1737405|1570339;3384194|1297|188787|118964|183710;3384194|1297|188787|118964;3384194|1297|188787|118964|183710|1298;3384194|1297|188787;3379134|976|200643|171549|815|1926659;1783272|1239|909932|909929|1843491,Complete,NA
bsdb:36389135/3/1,36389135,case-control,36389135,10.3389/fcimb.2022.1024867,NA,"Xia X., Chen J., Cheng Y., Chen F., Lu H., Liu J., Wang L., Pu F., Wang Y., Liu H., Cao D., Zhang Z., Xia Z., Fan M., Ling Z. , Zhao L.","Comparative analysis of the lung microbiota in patients with respiratory infections, tuberculosis, and lung cancer: A preliminary study",Frontiers in cellular and infection microbiology,2022,"community-acquired pneumonia, inflammation, lung cancer, lung microbiota, pulmonary tuberculosis",Experiment 3,China,Homo sapiens,Lung,UBERON:0002048,"Lung cancer,Pneumonia","MONDO:0008903,EFO:0003106",community-acquired pneumonia (CAP),Lung cancer,patients with newly diagnosed lung cancer.,49,8,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 3,9 July 2025,Nuerteye,Nuerteye,"Taxonomic differences of the lung microbiota among patients with primary pulmonary tuberculosis (PTB), newly diagnosed lung cancer (LC), and community-acquired pneumonia (CAP). LEfSe identified the most differentially abundant taxa between the two groups.",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Anaerobiospirillum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Cellulomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Janibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Mailhella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Marmoricola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Mediterranea,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Tropherymataceae|g__Tropheryma",1783272|1239|909932|1843488|909930;1783272|1239|909932|1843488;1783272|201174|1760|2037|2049|1654;3379134|1224|1236|135624;3379134|976|200643|171549|171550|239759;3379134|1224|1236|135624|83763|13334;1783272|201174|84998|84999|1643824;3379134|1224|28216;1783272|1239|91061|186826|186828;1783272|201174|1760|85006|85016;3379134|1224|28216|80840|80864;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|909932|1843489|31977|39948;3379134|1224|28216|206351|481|538;3379134|1224|28211|356|212791;3379134|976|117743|200644;3384189|32066|203490|203491|203492;3384189|32066|203490|203491|203492|848;1783272|201174|1760|85006|85021;1783272|201174|1760|85006|85021|53457;1783272|201174|1760|85007|2805586|1847725;1783272|201174|1760|85007|2805586;3379134|200940|3031449|213115|194924|1981028;1783272|201174|1760|85009|85015|86795;3379134|976|200643|171549|815|1926659;1783272|1239|909932|909929|1843491|158846;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481;3379134|1224|28216|206351;1783272|201174|1760|85009|85015;1783272|201174|84998|84999|1643824|133925;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171550;1783272|1239|186801|3082720|186804|1501226;3379134|1224|1236|135624|83763;1783272|201174|1760|85006|2805591|2038,Complete,NA
bsdb:36389135/3/2,36389135,case-control,36389135,10.3389/fcimb.2022.1024867,NA,"Xia X., Chen J., Cheng Y., Chen F., Lu H., Liu J., Wang L., Pu F., Wang Y., Liu H., Cao D., Zhang Z., Xia Z., Fan M., Ling Z. , Zhao L.","Comparative analysis of the lung microbiota in patients with respiratory infections, tuberculosis, and lung cancer: A preliminary study",Frontiers in cellular and infection microbiology,2022,"community-acquired pneumonia, inflammation, lung cancer, lung microbiota, pulmonary tuberculosis",Experiment 3,China,Homo sapiens,Lung,UBERON:0002048,"Lung cancer,Pneumonia","MONDO:0008903,EFO:0003106",community-acquired pneumonia (CAP),Lung cancer,patients with newly diagnosed lung cancer.,49,8,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 3,9 July 2025,Nuerteye,Nuerteye,"Taxonomic differences of the lung microbiota among patients with primary pulmonary tuberculosis (PTB), newly diagnosed lung cancer (LC), and community-acquired pneumonia (CAP). LEfSe identified the most differentially abundant taxa between the two groups.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Phenylobacterium",3379134|1224|28216|80840|119060|47670;3379134|1224|28211|204458|76892|20,Complete,NA
bsdb:36389150/1/1,36389150,case-control,36389150,10.3389/fcimb.2022.1036946,NA,"Xiong H., Wang J., Chang Z., Hu H., Yuan Z., Zhu Y., Hu Z., Wang C., Liu Y., Wang Y., Wang G. , Tang Q.",Gut microbiota display alternative profiles in patients with early-onset colorectal cancer,Frontiers in cellular and infection microbiology,2022,"16S rRNA, colorectal cancer, early onset, functional annotation, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls,EOCRC (Early-onset Colorectal cancer) patients,Colorectal cancer diagnosed before the age of 50 years.,31,24,3 months,16S,34,Illumina,relative abundances,"Kruskall-Wallis,LEfSe",0.05,NA,3.5,"age,alcohol drinking,body mass index,sex",NA,NA,decreased,NA,increased,NA,NA,Signature 1,Figure 3,17 October 2023,Deacme,"Deacme,Yjung24,Davvve,Folakunmi,WikiWorks",Differentially abundant taxa in Early onset colorectal cancer (EOCR) when compared to healthy controls as obtained by LEfSe analysis. Kruskal-wallis test was also performed on the abundance of bacteria in the three groups at different levels to verify the results of LEfSe analysis.,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Lentimicrobiaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Tissierellia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|1840213;1783272|1239|909932|909929|1843491|158846;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836;1783272|1239|1737404;1783272|1239|186801|3085636|186803|2316020|33038,Complete,Folakunmi
bsdb:36389150/3/1,36389150,case-control,36389150,10.3389/fcimb.2022.1036946,NA,"Xiong H., Wang J., Chang Z., Hu H., Yuan Z., Zhu Y., Hu Z., Wang C., Liu Y., Wang Y., Wang G. , Tang Q.",Gut microbiota display alternative profiles in patients with early-onset colorectal cancer,Frontiers in cellular and infection microbiology,2022,"16S rRNA, colorectal cancer, early onset, functional annotation, gut microbiota",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls,LOCRC (Late onset colorectal cancer),Late onset colorectal cancer (diagnosed >=50 years of age),31,43,3 months,16S,34,Illumina,relative abundances,"Kruskall-Wallis,LEfSe",0.05,NA,3.5,"age,alcohol drinking,body mass index,sex",NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 3,19 October 2023,Yjung24,"Yjung24,ChiomaBlessing,Folakunmi,WikiWorks",Differentially abundant taxa in Late onset colorectal cancer (LOCR) when compared to healthy controls as obtained by LEfSe analysis. Kruskal-wallis test was also performed on the abundance of bacteria in the three groups at different levels to verify the results of LEfSe analysis.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",1783272|1239|909932|1843488|909930;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|976|200643|171549|2005525|375288;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550;3379134|976|200643|171549|2005525;3379134|1224|1236|91347|543;1783272|1239|186801|186802|216572|707003,Complete,Folakunmi
bsdb:36405958/1/3,36405958,time series / longitudinal observational,36405958,10.3389/fcimb.2022.965471,NA,"Zhou C., Gong S., Xiang S., Liang L., Hu X., Huang R., Liao Z., Ma Y., Xiao Z. , Qiu J.",Changes and significance of gut microbiota in children with focal epilepsy before and after treatment,Frontiers in cellular and infection microbiology,2022,"16S rDNA gene sequencing, children, epilepsy, focal onset, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Epilepsy,EFO:0000474,healthy control (HC),pre-treatment (focal epilepsy),These are individuals with newly diagnosed focal epilepsy before they started receiving treatment.,14,10,2 weeks,16S,45,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,increased,increased,decreased,NA,increased,Signature 3,Figure 2D,1 November 2023,Deacme,"Deacme,Chinelsy,WikiWorks",Diversity and relative abundance of gut microbiota between the group before treatment and the control group,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. cv1,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|976|200643|171549|171550|239759|1622071;1783272|1239|91061|1385;1783272|1239|91061;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826;3379134|1224|1236|91347|543|1940338,Complete,Folakunmi
bsdb:36405958/2/1,36405958,time series / longitudinal observational,36405958,10.3389/fcimb.2022.965471,NA,"Zhou C., Gong S., Xiang S., Liang L., Hu X., Huang R., Liao Z., Ma Y., Xiao Z. , Qiu J.",Changes and significance of gut microbiota in children with focal epilepsy before and after treatment,Frontiers in cellular and infection microbiology,2022,"16S rDNA gene sequencing, children, epilepsy, focal onset, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Epilepsy,EFO:0000474,healthy control (HC),post-treatment (focal epilepsy),"This subgroup comprises individuals from the case group who have undergone a specific treatment, in this case, three months of treatment with oxcarbazepine (OXC).",14,10,2 weeks,16S,45,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,increased,increased,unchanged,NA,increased,Signature 1,Fig.4D,15 November 2023,Chinelsy,"Chinelsy,WikiWorks",Diversity and relative abundance of gut microbiota between the group after treatment and the control group,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,s__uncultured organism",3379134|976|200643|171549|1853231|574697;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|171550|239759|626932;155900,Complete,Folakunmi
bsdb:36405958/3/1,36405958,time series / longitudinal observational,36405958,10.3389/fcimb.2022.965471,NA,"Zhou C., Gong S., Xiang S., Liang L., Hu X., Huang R., Liao Z., Ma Y., Xiao Z. , Qiu J.",Changes and significance of gut microbiota in children with focal epilepsy before and after treatment,Frontiers in cellular and infection microbiology,2022,"16S rDNA gene sequencing, children, epilepsy, focal onset, gut microbiota",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Response to oxcarbazepine,EFO:0009893,pre-treatment (focal epilepsy),post-treatment (focal epilepsy),"This subgroup comprises individuals from the case group who have undergone a specific treatment, in this case, three months of treatment with oxcarbazepine (OXC).",14,10,2 weeks,16S,45,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Fig.3D,15 November 2023,Chinelsy,"Chinelsy,WikiWorks",Diversity and relative abundance of gut microbiota between the groups before and after treatment,increased,"k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. G2,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|s__Victivallaceae bacterium NML 080035,s__uncultured rumen bacterium",3379134|256845|1313211;1783272|1239|186801|186802|216572|459786;3379134|1224|28216|80840|995019;3379134|256845|1313211|278082|255528;3379134|256845|1313211|278082;3379134|256845|1313211|278082|255528|172900;1783272|1239|186801|186802|216572|459786|871666;3379134|256845|1313211|278082|255528|573638;136703,Complete,Folakunmi
bsdb:36405958/3/2,36405958,time series / longitudinal observational,36405958,10.3389/fcimb.2022.965471,NA,"Zhou C., Gong S., Xiang S., Liang L., Hu X., Huang R., Liao Z., Ma Y., Xiao Z. , Qiu J.",Changes and significance of gut microbiota in children with focal epilepsy before and after treatment,Frontiers in cellular and infection microbiology,2022,"16S rDNA gene sequencing, children, epilepsy, focal onset, gut microbiota",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Response to oxcarbazepine,EFO:0009893,pre-treatment (focal epilepsy),post-treatment (focal epilepsy),"This subgroup comprises individuals from the case group who have undergone a specific treatment, in this case, three months of treatment with oxcarbazepine (OXC).",14,10,2 weeks,16S,45,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Fig.3D,15 November 2023,Chinelsy,"Chinelsy,WikiWorks",Diversity and relative abundance of gut microbiota between the groups before and after treatment,decreased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",1783272|1239|91061;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826;1783272|1239|186801|3082720|186804|1501226;1783272|1239|909932|909929;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;3379134|1224|1236|91347|543|1940338;1783272|1239|91061|186826|33958,Complete,Folakunmi
bsdb:36405958/4/1,36405958,time series / longitudinal observational,36405958,10.3389/fcimb.2022.965471,NA,"Zhou C., Gong S., Xiang S., Liang L., Hu X., Huang R., Liao Z., Ma Y., Xiao Z. , Qiu J.",Changes and significance of gut microbiota in children with focal epilepsy before and after treatment,Frontiers in cellular and infection microbiology,2022,"16S rDNA gene sequencing, children, epilepsy, focal onset, gut microbiota",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Epilepsy,EFO:0000474,healthy control (HC),pre-treatment (focal epilepsy),These are individuals with newly diagnosed focal epilepsy before they started receiving treatment.,14,10,2 weeks,16S,45,Illumina,relative abundances,Metastats,0.05,TRUE,NA,NA,NA,NA,increased,increased,decreased,NA,increased,Signature 1,Supplementary Figure 1,17 January 2024,Folakunmi,"Folakunmi,WikiWorks",Significant results of Metastats analysis at the phyla and genus level,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",1783272|201174;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|2005525|375288;3379134|1224|1236|91347|543|1940338;1783272|1239|909932|909929|1843491|158846;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3082720|186804|1501226;1783272|201174|84998|84999|84107|102106,Complete,Folakunmi
bsdb:36405958/6/1,36405958,time series / longitudinal observational,36405958,10.3389/fcimb.2022.965471,NA,"Zhou C., Gong S., Xiang S., Liang L., Hu X., Huang R., Liao Z., Ma Y., Xiao Z. , Qiu J.",Changes and significance of gut microbiota in children with focal epilepsy before and after treatment,Frontiers in cellular and infection microbiology,2022,"16S rDNA gene sequencing, children, epilepsy, focal onset, gut microbiota",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Response to oxcarbazepine,EFO:0009893,pre-treatment (focal epilepsy),post-treatment (focal epilepsy),"This subgroup comprises individuals from the case group who have undergone a specific treatment, in this case, three months of treatment with oxcarbazepine (OXC).",14,10,2 weeks,16S,45,Illumina,relative abundances,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,supplementary figure 3,17 January 2024,Folakunmi,"Folakunmi,WikiWorks",Significant results of Metastats analysis at the phyla and genus levels,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes",1783272|201174;1783272|1239|186801|3085636|186803|572511;3379134|1224|1236|91347|543|1940338;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|186802|216572|459786;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3082720|186804|1501226;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|207244,Complete,Folakunmi
bsdb:36442206/1/1,36442206,case-control,36442206,10.3233/JPD-223500,NA,"Zhang K., Paul K.C., Jacobs J.P., Chou H.L., Duarte Folle A., Del Rosario I., Yu Y., Bronstein J.M., Keener A.M. , Ritz B.",Parkinson's Disease and the Gut Microbiome in Rural California,Journal of Parkinson's disease,2022,"Parkinson’s disease, Unified Parkinson’s Disease Rating Scale, brain-gut axis, gut microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls.,Parkinson's Disease Patients,Participants newly diagnosed with Parkinson's Disease (within 3–5 years).,74,96,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,race,sex",NA,decreased,NA,NA,NA,NA,Signature 1,Table 2.,3 June 2023,Fcuevas3,"Fcuevas3,Peace Sandy,WikiWorks",Differential taxa abundance associated with PD compared to controls (N=170).,increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Verrucomicrobiota",1783272|201174;3379134|74201|203494|48461|1647988|239934;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|3085636|186803|1649459;3379134|1224;3379134|74201,Complete,Peace Sandy
bsdb:36453905/1/1,36453905,case-control,36453905,https://doi.org/10.1128/spectrum.01593-22,https://journals.asm.org/doi/10.1128/spectrum.01593-22,"Han S., Zhuang J., Pan Y., Wu W. , Ding K.",Different Characteristics in Gut Microbiome between Advanced Adenoma Patients and Colorectal Cancer Patients by Metagenomic Analysis,Microbiology spectrum,2022,"SNP, artificial intelligence, colorectal cancer, gut microbiome, metagenomic sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Advanced Adenoma Patients,Colorectal Cancer Patients,Patients with fully  developed Colorectal cancer,26,26,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 2 G and H,7 March 2024,Imaspecial,"Imaspecial,Peace Sandy,WikiWorks",LEfSe analysis filtered out the biomarkers of the microbial community between AA and CRC patients. and cladogram plot of LEfSe analysis (G) and histogram of LDA analysis (H) of bacteria.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Ectothiorhodospiraceae|g__Acidihalobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Kushneria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Lelliottia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas",3379134|1224|1236|135613|72276|1765964;3379134|1224|1236|135619|28256|504090;3379134|1224|1236|91347|543|1330545;1783272|1239|1737404|1737405|1570339|543311,Complete,Peace Sandy
bsdb:36453905/1/2,36453905,case-control,36453905,https://doi.org/10.1128/spectrum.01593-22,https://journals.asm.org/doi/10.1128/spectrum.01593-22,"Han S., Zhuang J., Pan Y., Wu W. , Ding K.",Different Characteristics in Gut Microbiome between Advanced Adenoma Patients and Colorectal Cancer Patients by Metagenomic Analysis,Microbiology spectrum,2022,"SNP, artificial intelligence, colorectal cancer, gut microbiome, metagenomic sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Advanced Adenoma Patients,Colorectal Cancer Patients,Patients with fully  developed Colorectal cancer,26,26,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 2 G and H,7 March 2024,Imaspecial,"Imaspecial,Peace Sandy,WikiWorks",LEfSe analysis filtered out the biomarkers of the microbial community between AA and CRC patients. and cladogram plot of LEfSe analysis (G) and histogram of LDA analysis (H) of bacteria.,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|g__Negativibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Angelakisella,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Merdimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Massilioclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Merdibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Levyella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum",1783272|1239;1783272|1239|186801|186802;1783272|1239|186801;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|841;1783272|1239|526524|526525|128827;1783272|1239|526524;1783272|1239|526524|526525;1783272|1239|186801|3085636|186803|1407607;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|459786;1783272|1239|1980693;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|1935176;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|3082768|990719;1783272|1239|186801|3085636|186803|2005359;1783272|1239|186801|3085636|186803|2023266;1783272|1239|186801|186802|1392389;1783272|1239|186801|186802|31979|1935927;1783272|1239|186801|3085636|186803|207244;1783272|1239|526524|526525|128827|1935200;1783272|1239|526524|526525|128827|61170;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3120394|3120654|35829;1783272|1239|186801|186802|1715798;1783272|1239|186801|3085636|186803|1164882;3379134|1224|28216|80840|995019;1783272|1239|186801|186802|216572|1940255;1783272|1239|186801|186802|216572|244127;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3085636|186803|588605;1783272|1239|186801|3085636|186803|1213720,Complete,Peace Sandy
bsdb:36467550/1/1,36467550,laboratory experiment,36467550,10.1155/2022/9110560,NA,"Zhu H., Zhang H., Hou B., Xu B., Ji L. , Wu Y.",Curcumin Regulates Gut Microbiota and Exerts a Neuroprotective Effect in the MPTP Model of Parkinson's Disease,Evidence-based complementary and alternative medicine : eCAM,2022,NA,Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Curcumin,CHEBI:3962,MPTP,CUR-L,"Curcumin low-dose (CUR-L) group received a combination of both treatments in
which curcumin (40 mg/kg)",12,12,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,unchanged,unchanged,NA,NA,Signature 1,Fig 5 and Text,13 March 2024,MyleeeA,"MyleeeA,WikiWorks",Differential distribution of Specie in the gut Microbiota between MPTP and CUR-L.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes inops,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. S457,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacillati|p__Cyanobacteriota,k__Bacillati,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp. L-YJ,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Paramuribaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Paramuribaculum|s__Paramuribaculum intestinale,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] brachy,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.",1783272|201174|84998|1643822|1643826|447020;1783272|201174|84998|1643822|1643826|447020|446660;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550|239759|1501391;3379134|976|200643|171549|171550|239759|1647659;3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|171552|1283313|76122;1783272|544448|31969|186332|186333|2086;1783272|544448|31969|186332|186333;1783272|544448|31969|186332;1783272|1239|186801|3085636|3118652|2039240;1783272|1239|186801|3085636|3118652|2039240|2039241;3379134|976|200643|171549;3379134|976|200643;1783272|1798710|1906119;1783272|1117;1783272;1783272|201174|84998|1643822|1643826;1783272|201174|84998|1643822;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|1506553|2028282;1783272|1239|91061|186826|33958|1578|215530;3379134|976|200643|171549|2005473|2518497;3379134|976|200643|171549|2005473|2518497|2094151;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550;1783272|1239|186801|3082720|543314|35517;1783272|544448|31969|186332|186333|2086;1783272|1798710|1906119;;1783272|1239|186801|186802|31979|1485|59620,Complete,Svetlana up
bsdb:36467550/1/2,36467550,laboratory experiment,36467550,10.1155/2022/9110560,NA,"Zhu H., Zhang H., Hou B., Xu B., Ji L. , Wu Y.",Curcumin Regulates Gut Microbiota and Exerts a Neuroprotective Effect in the MPTP Model of Parkinson's Disease,Evidence-based complementary and alternative medicine : eCAM,2022,NA,Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Curcumin,CHEBI:3962,MPTP,CUR-L,"Curcumin low-dose (CUR-L) group received a combination of both treatments in
which curcumin (40 mg/kg)",12,12,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,unchanged,unchanged,NA,NA,Signature 2,Fig 5 and Text,14 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential distribution of Specie in the gut Microbiota between MPTP and CUR-L
.",decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lentilactobacillus|s__Lentilactobacillus hilgardii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum|s__Muribaculum intestinale,,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__uncultured Bifidobacterium sp.",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988|239934|239935;3379134|74201|203494|48461|1647988;1783272|201174|84998|84999|1643824;;95818|2093818|2093825|2171986;95818|2093818|2093825;95818|2093818;95818|2093818|2093825|2171986|1331051;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|1392389;1783272|1239|91061|186826|33958|2767893|1588;1783272|1239|91061|186826|33958|2742598|1598;3379134|976|200643|171549|2005473|1918540|1796646;;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201;95818|2093818|2093825|2171986|1331051;1783272|1239|186801|186802|1392389;1783272|201174|1760|85004|31953|1678|165187,Complete,Svetlana up
bsdb:36467550/3/1,36467550,laboratory experiment,36467550,10.1155/2022/9110560,NA,"Zhu H., Zhang H., Hou B., Xu B., Ji L. , Wu Y.",Curcumin Regulates Gut Microbiota and Exerts a Neuroprotective Effect in the MPTP Model of Parkinson's Disease,Evidence-based complementary and alternative medicine : eCAM,2022,NA,Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Curcumin,CHEBI:3962,MPTP,CUR-H,Curcumin High-dose (CUR-H) group received a combination of both treatments in which curcumin (160 mg/kg),12,12,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,unchanged,unchanged,NA,NA,Signature 1,Fig 5 and Text,14 March 2024,MyleeeA,"MyleeeA,WikiWorks",Differential distribution of Specie in the gut Microbiota between MPTP and CUR-H.,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp. L-YJ,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Paramuribaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Paramuribaculum|s__Paramuribaculum intestinale,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. DENB20,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum|s__uncultured Allobaculum sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__uncultured Ruminiclostridium sp.",1783272|201174;1783272|1239|526524|526525|128827|174708;1783272|1239;1783272|201174|84998|84999;1783272|201174|84998;1783272|201174|84998|1643822|1643826;1783272|201174|84998|1643822|1643826|580024;1783272|1239|186801|186802|1392389;1783272|1239|91061|186826|33958|1578|215530;1783272|544448|31969;1783272|544448;3379134|976|200643|171549|2005473|2518497;3379134|976|200643|171549|2005473|2518497|2094151;3379134|1224|1236|72274|135621;3379134|1224|1236|72274;3379134|1224|1236|72274|135621|286;3379134|1224|1236|72274|135621|286|1231603;1783272|201174|84998|1643822|1643826|580024;1783272|1239|186801|186802|1392389;1783272|1239|526524|526525|128827|174708|1187017;1783272|1239|186801|186802|216572|1508657|1757166,Complete,Svetlana up
bsdb:36467550/3/2,36467550,laboratory experiment,36467550,10.1155/2022/9110560,NA,"Zhu H., Zhang H., Hou B., Xu B., Ji L. , Wu Y.",Curcumin Regulates Gut Microbiota and Exerts a Neuroprotective Effect in the MPTP Model of Parkinson's Disease,Evidence-based complementary and alternative medicine : eCAM,2022,NA,Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Curcumin,CHEBI:3962,MPTP,CUR-H,Curcumin High-dose (CUR-H) group received a combination of both treatments in which curcumin (160 mg/kg),12,12,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,unchanged,unchanged,NA,NA,Signature 2,Fig 5 and Text,15 March 2024,MyleeeA,"MyleeeA,WikiWorks,Tosin",Differential distribution of Specie in the gut Microbiota between MPTP and CUR-H.,decreased,"p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania massiliensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lentilactobacillus|s__Lentilactobacillus hilgardii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__uncultured Bacteroides sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__uncultured Eubacterium sp.",95818|2093818|2093825;95818|2093818;95818|2093818|2093825|2171986|1331051;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|526524|526525|128827|61170;1783272|1239|526524|526525|128827|61170|1468449;1783272|1239|91061|186826|33958|2767893|1588;1783272|1239|91061|186826|33958|2742598|1598;;1783272|1239|186801|3082720|543314|35518;95818|2093818|2093825|2171986|1331051;3379134|976|200643|171549|815|816|162156;1783272|1239|186801|186802|186806|1730|165185,Complete,Svetlana up
bsdb:36475759/1/NA,36475759,case-control,36475759,10.1128/spectrum.01956-22,NA,"Chen B.Y., Lin W.Z., Li Y.L., Bi C., Du L.J., Liu Y., Zhou L.J., Liu T., Xu S., Shi C.J., Zhu H., Wang Y.L., Sun J.Y., Liu Y., Zhang W.C., Zhang Z., Zhang H.L., Zhu Y.Q. , Duan S.Z.",Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension,Microbiology spectrum,2023,"gut fungal microbiome, hypertension, oral fungal microbiome, oral-gut fungal correlations",Experiment 1,China,Homo sapiens,"Saliva,Subgingival dental plaque","UBERON:0001836,UBERON:0016484",Hypertension,EFO:0000537,Saliva samples,Subgingival plague samples,"Subgingival plague samples from participants with Hypertension (HTN); n = 36
and without Hypertension (No HTN); n = 24...i.e samples from the entire study population",60,60,2 months,WMS,NA,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,increased,increased,unchanged,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:36475759/2/NA,36475759,case-control,36475759,10.1128/spectrum.01956-22,NA,"Chen B.Y., Lin W.Z., Li Y.L., Bi C., Du L.J., Liu Y., Zhou L.J., Liu T., Xu S., Shi C.J., Zhu H., Wang Y.L., Sun J.Y., Liu Y., Zhang W.C., Zhang Z., Zhang H.L., Zhu Y.Q. , Duan S.Z.",Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension,Microbiology spectrum,2023,"gut fungal microbiome, hypertension, oral fungal microbiome, oral-gut fungal correlations",Experiment 2,China,Homo sapiens,"Saliva,Feces","UBERON:0001836,UBERON:0001988",Hypertension,EFO:0000537,Saliva samples,Fecal samples,Fecal samples from participants with Hypertension (HTN); n = 36 and without Hypertension (No HTN); n = 24.....i.e samples from the entire study population,60,60,2 months,WMS,NA,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:36475759/3/NA,36475759,case-control,36475759,10.1128/spectrum.01956-22,NA,"Chen B.Y., Lin W.Z., Li Y.L., Bi C., Du L.J., Liu Y., Zhou L.J., Liu T., Xu S., Shi C.J., Zhu H., Wang Y.L., Sun J.Y., Liu Y., Zhang W.C., Zhang Z., Zhang H.L., Zhu Y.Q. , Duan S.Z.",Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension,Microbiology spectrum,2023,"gut fungal microbiome, hypertension, oral fungal microbiome, oral-gut fungal correlations",Experiment 3,China,Homo sapiens,"Subgingival dental plaque,Feces","UBERON:0016484,UBERON:0001988",Hypertension,EFO:0000537,Subgingival plague samples,Fecal samples,Fecal samples from participants with Hypertension (HTN); n = 36 and without Hypertension (No HTN); n = 24.....i.e samples from the entire study population,60,60,2 months,WMS,NA,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,unchanged,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:36475759/4/1,36475759,case-control,36475759,10.1128/spectrum.01956-22,NA,"Chen B.Y., Lin W.Z., Li Y.L., Bi C., Du L.J., Liu Y., Zhou L.J., Liu T., Xu S., Shi C.J., Zhu H., Wang Y.L., Sun J.Y., Liu Y., Zhang W.C., Zhang Z., Zhang H.L., Zhu Y.Q. , Duan S.Z.",Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension,Microbiology spectrum,2023,"gut fungal microbiome, hypertension, oral fungal microbiome, oral-gut fungal correlations",Experiment 4,China,Homo sapiens,Saliva,UBERON:0001836,Hypertension,EFO:0000537,no-Hypertension (no-HTN),Hypertension (HTN),Participants with Hypertension (HTN),24,36,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,FIG 3 (A),12 April 2024,Rahila,"Rahila,Folakunmi,WikiWorks",Different fungal enrichments between the HTN and no-HTN groups in saliva samples,increased,"k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Agaricaceae,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Agaricaceae|g__Agaricus,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Agaricaceae|g__Agaricus|s__Agaricus bisporus,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Glomerellaceae|g__Colletotrichum|s__Colletotrichum orchidophilum,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Chaetothyriales|f__Herpotrichiellaceae|g__Exophiala|s__Exophiala spinifera,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Kluyveromyces,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Ascoideales|f__Saccharomycopsidaceae|g__Saccharomycopsis|s__Saccharomycopsis fibuligera,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Tetrapisispora,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Chaetomiaceae|g__Thermochaetoides|s__Thermochaetoides thermophila",4751|5204|155619|5338|5339;4751|5204|155619|5338|5339|5340;4751|5204|155619|5338|5339|5340|5341;4751|4890|147550|1028384|681950|5455|1209926;4751|4890|147545|34395|43219|5583|91928;4751|4890|4891|4892|4893|4910;4751|4890|4891|2926619|34366|4943|4944;4751|4890|4891|4892|4893|113604;4751|4890|147550|5139|35718|2944547|209285,Complete,Folakunmi
bsdb:36475759/4/2,36475759,case-control,36475759,10.1128/spectrum.01956-22,NA,"Chen B.Y., Lin W.Z., Li Y.L., Bi C., Du L.J., Liu Y., Zhou L.J., Liu T., Xu S., Shi C.J., Zhu H., Wang Y.L., Sun J.Y., Liu Y., Zhang W.C., Zhang Z., Zhang H.L., Zhu Y.Q. , Duan S.Z.",Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension,Microbiology spectrum,2023,"gut fungal microbiome, hypertension, oral fungal microbiome, oral-gut fungal correlations",Experiment 4,China,Homo sapiens,Saliva,UBERON:0001836,Hypertension,EFO:0000537,no-Hypertension (no-HTN),Hypertension (HTN),Participants with Hypertension (HTN),24,36,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,FIG 3 (A),12 April 2024,Rahila,"Rahila,Folakunmi,WikiWorks",Different fungal enrichments between the HTN and no-HTN groups in saliva samples,decreased,"k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus bombycis,k__Fungi|p__Basidiomycota|c__Pucciniomycetes|o__Pucciniales|f__Melampsoraceae|g__Melampsora,k__Fungi|p__Basidiomycota|c__Pucciniomycetes|o__Pucciniales|f__Melampsoraceae|g__Melampsora|s__Melampsora laricis-populina,k__Fungi|p__Basidiomycota|c__Pucciniomycetes|o__Pucciniales|f__Melampsoraceae,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Clavicipitaceae|g__Metarhizium,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Trichomonascaceae|g__Sugiyamaella,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Trichomonascaceae|g__Sugiyamaella|s__Sugiyamaella lignohabitans,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Trichomonascaceae,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae|g__Zymoseptoria,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae|g__Zymoseptoria|s__Zymoseptoria tritici,k__Fungi|p__Ascomycota|c__Sordariomycetes,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Magnaporthales|f__Magnaporthaceae|g__Magnaporthe",4751|4890|147545|5042|1131492|5052|109264;4751|5204|162484|5258|5259|5260;4751|5204|162484|5258|5259|5260|203908;4751|5204|162484|5258|5259;4751|4890|147550|5125|34397|5529;4751|4890|3239873|3243772|410830|410829;4751|4890|3239873|3243772|410830|410829|796027;4751|4890|3239873|3243772|410830;4751|4890|147541|2726947|93133|1047167;4751|4890|147541|2726947|93133|1047167|1047171;4751|4890|147550;4751|4890|147550|639021|81093|148303,Complete,Folakunmi
bsdb:36475759/5/1,36475759,case-control,36475759,10.1128/spectrum.01956-22,NA,"Chen B.Y., Lin W.Z., Li Y.L., Bi C., Du L.J., Liu Y., Zhou L.J., Liu T., Xu S., Shi C.J., Zhu H., Wang Y.L., Sun J.Y., Liu Y., Zhang W.C., Zhang Z., Zhang H.L., Zhu Y.Q. , Duan S.Z.",Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension,Microbiology spectrum,2023,"gut fungal microbiome, hypertension, oral fungal microbiome, oral-gut fungal correlations",Experiment 5,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Hypertension,EFO:0000537,no-Hypertension (no-HTN),Hypertension (HTN),Participants with Hypertension (HTN),24,36,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,FIG 3 (B),12 April 2024,Rahila,"Rahila,Folakunmi,WikiWorks",Different fungal enrichments in the subgingival plaque samples between the HTN and no-HTN groups.,increased,"k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Onygenales|f__Arthrodermataceae,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Onygenales|f__Ajellomycetaceae|g__Blastomyces,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Onygenales|f__Ajellomycetaceae|g__Blastomyces|s__Blastomyces gilchristii,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Cryptococcaceae|g__Kwoniella|s__Kwoniella pini,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Onygenales|f__Arthrodermataceae|g__Nannizzia,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Onygenales|f__Arthrodermataceae|g__Nannizzia|s__Nannizzia gypsea,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Onygenales,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Hypocreaceae|g__Trichoderma|s__Trichoderma gamsii,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Plectosphaerellaceae|g__Verticillium|s__Verticillium dahliae,k__Fungi|p__Basidiomycota|c__Wallemiomycetes|o__Wallemiales|f__Wallemiaceae|g__Wallemia,k__Fungi|p__Basidiomycota|c__Wallemiomycetes|o__Wallemiales|f__Wallemiaceae|g__Wallemia|s__Wallemia mellicola,k__Fungi|p__Basidiomycota|c__Wallemiomycetes|o__Wallemiales|f__Wallemiaceae,k__Fungi|p__Basidiomycota|c__Wallemiomycetes|o__Wallemiales,k__Fungi|p__Basidiomycota|c__Wallemiomycetes",4751|4890|147545|33183|34384;4751|4890|147545|33183|299071|229219;4751|4890|147545|33183|299071|229219|1681229;4751|5204|155616|5234|1884633|490731|453459;4751|4890|147545|33183|34384|1915381;4751|4890|147545|33183|34384|1915381|63402;4751|4890|147545|33183;4751|5204|155619|452342;4751|4890|147550|5125|5129|5543|398673;4751|4890|147550|1028384|1033978|1036719|27337;4751|5204|431957|431958|431959|148959;4751|5204|431957|431958|431959|148959|1708541;4751|5204|431957|431958|431959;4751|5204|431957|431958;4751|5204|431957,Complete,Folakunmi
bsdb:36475759/5/2,36475759,case-control,36475759,10.1128/spectrum.01956-22,NA,"Chen B.Y., Lin W.Z., Li Y.L., Bi C., Du L.J., Liu Y., Zhou L.J., Liu T., Xu S., Shi C.J., Zhu H., Wang Y.L., Sun J.Y., Liu Y., Zhang W.C., Zhang Z., Zhang H.L., Zhu Y.Q. , Duan S.Z.",Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension,Microbiology spectrum,2023,"gut fungal microbiome, hypertension, oral fungal microbiome, oral-gut fungal correlations",Experiment 5,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Hypertension,EFO:0000537,no-Hypertension (no-HTN),Hypertension (HTN),Participants with Hypertension (HTN),24,36,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,FIG 3 (B),12 April 2024,Rahila,"Rahila,Folakunmi,WikiWorks",Different fungal enrichments in the subgingival plaque samples between the HTN and no-HTN groups.,decreased,"k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Pleosporaceae|g__Alternaria|s__Alternaria alternata,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Chaetomiaceae|g__Chaetomium|s__Chaetomium globosum,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Cryptococcaceae|g__Cryptococcus|s__Cryptococcus neoformans,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Magnaporthales|f__Magnaporthaceae|g__Gaeumannomyces|s__Gaeumannomyces tritici,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Leptosphaeriaceae|g__Leptosphaeria,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Leptosphaeriaceae,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Magnaporthales|f__Magnaporthaceae,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Magnaporthales,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Amphisphaeriales|f__Sporocadaceae|g__Pestalotiopsis,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Amphisphaeriales|f__Sporocadaceae|g__Pestalotiopsis|s__Pestalotiopsis fici,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Leptosphaeriaceae|g__Plenodomus|s__Plenodomus biglobosus,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Ascoideales|f__Saccharomycopsidaceae,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Ascoideales|f__Saccharomycopsidaceae|g__Saccharomycopsis|s__Saccharomycopsis fibuligera,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Scheffersomyces,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Scheffersomyces|s__Scheffersomyces stipitis,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Amphisphaeriales|f__Sporocadaceae,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Torulaspora,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Torulaspora|s__Torulaspora delbrueckii,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Xylariales,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Ascoideales|f__Saccharomycopsidaceae|g__Saccharomycopsis,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Ascoideales|f__Saccharomycopsidaceae|g__Saccharomycopsis,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Magnaporthales|f__Magnaporthaceae|g__Gaeumannomyces",4751|4890|147541|92860|28556|5598|5599;4751|4890|147550|5139|35718|5149|38033;4751|5204|155616|5234|1884633|5206|5207;4751|4890|147550|639021|81093|29849|36779;4751|4890|147541|92860|34374|5021;4751|4890|147541|92860|34374;4751|4890|147550|639021|81093;4751|4890|147550|639021;4751|4890|147550|3402561|1812776|37840;4751|4890|147550|3402561|1812776|37840|393283;4751|4890|147541|92860|34374|118259|220672;4751|4890|4891|2926619|34366;4751|4890|4891|2926619|34366|4943|4944;4751|4890|3239874|2916678|766764|766733;4751|4890|3239874|2916678|766764|766733|4924;4751|4890|147550|5139;4751|4890|147550|3402561|1812776;4751|4890|4891|4892|4893|4948;4751|4890|4891|4892|4893|4948|4950;4751|4890|147550|37989;4751|4890|147550|5125;4751|4890|4891|2926619|34366|4943;4751|4890|4891|2926619|34366|4943;4751|4890|147550|639021|81093|29849,Complete,Folakunmi
bsdb:36475759/6/1,36475759,case-control,36475759,10.1128/spectrum.01956-22,NA,"Chen B.Y., Lin W.Z., Li Y.L., Bi C., Du L.J., Liu Y., Zhou L.J., Liu T., Xu S., Shi C.J., Zhu H., Wang Y.L., Sun J.Y., Liu Y., Zhang W.C., Zhang Z., Zhang H.L., Zhu Y.Q. , Duan S.Z.",Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension,Microbiology spectrum,2023,"gut fungal microbiome, hypertension, oral fungal microbiome, oral-gut fungal correlations",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Hypertension,EFO:0000537,no-Hypertension (no-HTN),Hypertension (HTN),Participants with Hypertension (HTN),24,36,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,increased,unchanged,NA,unchanged,Signature 1,FIG 3 (C),12 April 2024,Rahila,"Rahila,Folakunmi,WikiWorks",Different fungal enrichments in the faecal samples between the HTN and no-HTN groups.,increased,"k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus fumigatus,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus nomiae,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus terreus,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Glomerellaceae|g__Colletotrichum,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Glomerellaceae|g__Colletotrichum|s__Colletotrichum higginsianum,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Cryptococcaceae,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Cryptococcaceae|g__Cryptococcus,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Glomerellaceae,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Pichiales|f__Pichiaceae|g__Komagataella,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Pichiales|f__Pichiaceae|g__Komagataella|s__Komagataella phaffii,k__Fungi|p__Chytridiomycota|c__Chytridiomycetes|o__Spizellomycetales|f__Spizellomycetaceae|g__Spizellomyces,k__Fungi|p__Chytridiomycota|c__Chytridiomycetes|o__Spizellomycetales|f__Spizellomycetaceae|g__Spizellomyces|s__Spizellomyces punctatus,k__Fungi|p__Chytridiomycota|c__Chytridiomycetes|o__Spizellomycetales|f__Spizellomycetaceae,k__Fungi|p__Chytridiomycota|c__Chytridiomycetes|o__Spizellomycetales,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Torulaspora,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Torulaspora|s__Torulaspora delbrueckii,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales,k__Fungi|p__Basidiomycota|c__Tremellomycetes,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Hypocreaceae|g__Trichoderma|s__Trichoderma reesei,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Hypocreaceae|g__Trichoderma|s__Trichoderma virens,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Cryptococcaceae|g__Cryptococcus,k__Fungi|p__Ascomycota|c__Dothideomycetes",4751|4890|147545|5042|1131492|5052|746128;4751|4890|147545|5042|1131492|5052|41061;4751|4890|147545|5042|1131492|5052|33178;4751|4890|147550|1028384|681950|5455;4751|4890|147550|1028384|681950|5455|80884;4751|5204|155616|5234|1884633;4751|5204|155616|5234|1884633|5206;4751|4890|147550|1028384|681950;4751|4890|3239874|3243775|1156497|460517;4751|4890|3239874|3243775|1156497|460517|460519;4751|4761|451435|34478|34479|4815;4751|4761|451435|34478|34479|4815|109760;4751|4761|451435|34478|34479;4751|4761|451435|34478;4751|4890|4891|4892|4893|4948;4751|4890|4891|4892|4893|4948|4950;4751|5204|155616|5234;4751|5204|155616;4751|4890|147550|5125|5129|5543|51453;4751|4890|147550|5125|5129|5543|29875;4751|5204|155616|5234|1884633|5206;4751|4890|147541,Complete,Folakunmi
bsdb:36475759/6/2,36475759,case-control,36475759,10.1128/spectrum.01956-22,NA,"Chen B.Y., Lin W.Z., Li Y.L., Bi C., Du L.J., Liu Y., Zhou L.J., Liu T., Xu S., Shi C.J., Zhu H., Wang Y.L., Sun J.Y., Liu Y., Zhang W.C., Zhang Z., Zhang H.L., Zhu Y.Q. , Duan S.Z.",Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension,Microbiology spectrum,2023,"gut fungal microbiome, hypertension, oral fungal microbiome, oral-gut fungal correlations",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Hypertension,EFO:0000537,no-Hypertension (no-HTN),Hypertension (HTN),Participants with Hypertension (HTN),24,36,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,increased,unchanged,NA,unchanged,Signature 2,FIG 3 (C),12 April 2024,Rahila,"Rahila,Folakunmi,WikiWorks",Different fungal enrichments in the faecal samples between the HTN and no-HTN groups.,decreased,"k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Chaetothyriales,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Boletales|f__Coniophoraceae|g__Coniophora,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Boletales|f__Coniophoraceae|g__Coniophora|s__Coniophora puteana,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Boletales|f__Coniophoraceae,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Chaetothyriales|f__Herpotrichiellaceae,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Trichocomaceae|g__Talaromyces|s__Talaromyces pinophilus",4751|4890|147545|34395;4751|5204|155619|68889|80634|80635;4751|5204|155619|68889|80634|80635|80637;4751|5204|155619|68889|80634;4751|4890|147545|34395|43219;4751|4890|147550|5139;4751|4890|147545|5042|28568|5094|128442,Complete,Folakunmi
bsdb:36475759/7/NA,36475759,case-control,36475759,10.1128/spectrum.01956-22,NA,"Chen B.Y., Lin W.Z., Li Y.L., Bi C., Du L.J., Liu Y., Zhou L.J., Liu T., Xu S., Shi C.J., Zhu H., Wang Y.L., Sun J.Y., Liu Y., Zhang W.C., Zhang Z., Zhang H.L., Zhu Y.Q. , Duan S.Z.",Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension,Microbiology spectrum,2023,"gut fungal microbiome, hypertension, oral fungal microbiome, oral-gut fungal correlations",Experiment 7,China,Homo sapiens,"Saliva,Subgingival dental plaque","UBERON:0001836,UBERON:0016484",Hypertension,EFO:0000537,Saliva samples (No HTN),Subgingival plague samples (No HTN),Subgingival plague samples from participants without Hypertension (No HTN),24,24,2 months,WMS,NA,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,increased,increased,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:36475759/8/NA,36475759,case-control,36475759,10.1128/spectrum.01956-22,NA,"Chen B.Y., Lin W.Z., Li Y.L., Bi C., Du L.J., Liu Y., Zhou L.J., Liu T., Xu S., Shi C.J., Zhu H., Wang Y.L., Sun J.Y., Liu Y., Zhang W.C., Zhang Z., Zhang H.L., Zhu Y.Q. , Duan S.Z.",Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension,Microbiology spectrum,2023,"gut fungal microbiome, hypertension, oral fungal microbiome, oral-gut fungal correlations",Experiment 8,China,Homo sapiens,"Saliva,Subgingival dental plaque","UBERON:0001836,UBERON:0016484",Hypertension,EFO:0000537,Saliva samples (HTN),Subgingival plague samples (HTN),Subgingival plague samples from participants with Hypertension (HTN),36,36,2 months,WMS,NA,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,increased,increased,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:36475759/9/NA,36475759,case-control,36475759,10.1128/spectrum.01956-22,NA,"Chen B.Y., Lin W.Z., Li Y.L., Bi C., Du L.J., Liu Y., Zhou L.J., Liu T., Xu S., Shi C.J., Zhu H., Wang Y.L., Sun J.Y., Liu Y., Zhang W.C., Zhang Z., Zhang H.L., Zhu Y.Q. , Duan S.Z.",Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension,Microbiology spectrum,2023,"gut fungal microbiome, hypertension, oral fungal microbiome, oral-gut fungal correlations",Experiment 9,China,Homo sapiens,"Subgingival dental plaque,Feces","UBERON:0016484,UBERON:0001988",Hypertension,EFO:0000537,Subgingival plague samples (No HTN),Fecal samples (No HTN),Fecal samples from participants without Hypertension (No HTN),24,24,2 months,WMS,NA,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,unchanged,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:36475759/10/NA,36475759,case-control,36475759,10.1128/spectrum.01956-22,NA,"Chen B.Y., Lin W.Z., Li Y.L., Bi C., Du L.J., Liu Y., Zhou L.J., Liu T., Xu S., Shi C.J., Zhu H., Wang Y.L., Sun J.Y., Liu Y., Zhang W.C., Zhang Z., Zhang H.L., Zhu Y.Q. , Duan S.Z.",Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension,Microbiology spectrum,2023,"gut fungal microbiome, hypertension, oral fungal microbiome, oral-gut fungal correlations",Experiment 10,China,Homo sapiens,"Subgingival dental plaque,Feces","UBERON:0016484,UBERON:0001988",Hypertension,EFO:0000537,Subgingival plague samples (HTN),Fecal samples (HTN),Fecal samples from participants with Hypertension (HTN),36,36,2 months,WMS,NA,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,unchanged,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:36475922/1/1,36475922,case-control,36475922,10.1128/spectrum.02805-22,NA,"Chen T.H., Cheng C.Y., Huang C.K., Ho Y.H. , Lin J.C.",Exploring the Relevance between Gut Microbiota-Metabolites Profile and Chronic Kidney Disease with Distinct Pathogenic Factor,Microbiology spectrum,2023,"chronic kidney disease, diabetes mellitus, fecal metabolite, gut microbiota, hypertension",Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Healthy Controls,Chronic Kidney Disease,Chronic kidney disease patients,60,105,NA,16S,NA,Nanopore,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 3,21 March 2024,PreciousMike,"PreciousMike,Ayibatari,WikiWorks",Classification of operational taxonomy unit (OTU) with long-read sequencing in healthy participants and enrolled CKD patients.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia marmotae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pasteurianus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum variabile,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Culturomica|s__Culturomica massiliensis",3379134|976|200643|171549|815|816|46506;3379134|1224|1236|91347|543|561|1499973;3384189|32066|203490|203491|203492|848|850;1783272|1239|91061|186826|33958|2742598|97478;1783272|1239|91061|186826|1300|1301|197614;1783272|1239|186801|186802|216572|292632|214851;3379134|976|200643|171549|1853231|1926651|1841857,Complete,Svetlana up
bsdb:36475922/1/2,36475922,case-control,36475922,10.1128/spectrum.02805-22,NA,"Chen T.H., Cheng C.Y., Huang C.K., Ho Y.H. , Lin J.C.",Exploring the Relevance between Gut Microbiota-Metabolites Profile and Chronic Kidney Disease with Distinct Pathogenic Factor,Microbiology spectrum,2023,"chronic kidney disease, diabetes mellitus, fecal metabolite, gut microbiota, hypertension",Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Healthy Controls,Chronic Kidney Disease,Chronic kidney disease patients,60,105,NA,16S,NA,Nanopore,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 3,21 March 2024,PreciousMike,"PreciousMike,Ayibatari,WikiWorks",Classification of operational taxonomy unit (OTU) with long-read sequencing in healthy participants and enrolled CKD patients.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas ruminantium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella jalaludinii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera indica",1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|909932|909929|1843491|970|971;1783272|1239|909932|909929|1843491|52225|187979;1783272|1239|909932|1843489|31977|906|879612,Complete,Svetlana up
bsdb:36475922/2/NA,36475922,case-control,36475922,10.1128/spectrum.02805-22,NA,"Chen T.H., Cheng C.Y., Huang C.K., Ho Y.H. , Lin J.C.",Exploring the Relevance between Gut Microbiota-Metabolites Profile and Chronic Kidney Disease with Distinct Pathogenic Factor,Microbiology spectrum,2023,"chronic kidney disease, diabetes mellitus, fecal metabolite, gut microbiota, hypertension",Experiment 2,Taiwan,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Healthy Controls,NC-CKD,Chronic kidney disease patients without comorbidities,60,40,NA,16S,NA,Nanopore,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:36475922/3/NA,36475922,case-control,36475922,10.1128/spectrum.02805-22,NA,"Chen T.H., Cheng C.Y., Huang C.K., Ho Y.H. , Lin J.C.",Exploring the Relevance between Gut Microbiota-Metabolites Profile and Chronic Kidney Disease with Distinct Pathogenic Factor,Microbiology spectrum,2023,"chronic kidney disease, diabetes mellitus, fecal metabolite, gut microbiota, hypertension",Experiment 3,Taiwan,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Healthy Controls,H-CKD,Hypertensive chronic kidney disease patients,60,26,NA,16S,NA,Nanopore,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:36475922/4/NA,36475922,case-control,36475922,10.1128/spectrum.02805-22,NA,"Chen T.H., Cheng C.Y., Huang C.K., Ho Y.H. , Lin J.C.",Exploring the Relevance between Gut Microbiota-Metabolites Profile and Chronic Kidney Disease with Distinct Pathogenic Factor,Microbiology spectrum,2023,"chronic kidney disease, diabetes mellitus, fecal metabolite, gut microbiota, hypertension",Experiment 4,Taiwan,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Healthy Controls,D-CKD,Diabetic chronic kidney disease patients,60,39,NA,16S,NA,Nanopore,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:36494405/1/1,36494405,case-control,36494405,10.1038/s41531-022-00428-2,https://www.nature.com/articles/s41531-022-00428-2,"Nishiwaki H., Ueyama J., Kashihara K., Ito M., Hamaguchi T., Maeda T., Tsuboi Y., Katsuno M., Hirayama M. , Ohno K.",Gut microbiota in dementia with Lewy bodies,NPJ Parkinson's disease,2022,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Lewy body dementia,EFO:0006792,Healthy controls,Dementia with Lewy bodies (DLB) patients,"Patients diagnosed with Dementia with Lewy bodies (DLB) a type of dementia characterized by changes in sleep, behavior, cognition, movement, and regulation of automatic bodily functions",147,28,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1, Supplementary Tables 2A and 2B",26 July 2025,Kristin.abraham,"Kristin.abraham,Fiddyhamma","Comparison of genera, family between Controls and Dementia with Lewy Body (DLB)",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|3082720|543314;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;3379134|200940|3031449|213115|194924;1783272|201174|84998|1643822|1643826|84111;1783272|201174|84998|1643822|1643826;3379134|74201|203494|48461|1647988|239934;1783272|1239|91061|186826|33958|1578;3379134|74201|203494|48461|1647988;1783272|1239|186801|3082768|990719;1783272|1239|91061|186826|33958;3379134|1224|1236|91347|543;1783272|1239|186801|186802|216572,Complete,NA
bsdb:36494405/1/2,36494405,case-control,36494405,10.1038/s41531-022-00428-2,https://www.nature.com/articles/s41531-022-00428-2,"Nishiwaki H., Ueyama J., Kashihara K., Ito M., Hamaguchi T., Maeda T., Tsuboi Y., Katsuno M., Hirayama M. , Ohno K.",Gut microbiota in dementia with Lewy bodies,NPJ Parkinson's disease,2022,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Lewy body dementia,EFO:0006792,Healthy controls,Dementia with Lewy bodies (DLB) patients,"Patients diagnosed with Dementia with Lewy bodies (DLB) a type of dementia characterized by changes in sleep, behavior, cognition, movement, and regulation of automatic bodily functions",147,28,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 1, Supplementary Tables 2A and 2B",26 July 2025,Kristin.abraham,"Kristin.abraham,Fiddyhamma","Comparison of genera, family between Controls and Dementia with Lewy Body (DLB)",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;3379134|1224|1236|135625|712|724;1783272|1239|186801|186802|216572;3379134|1224|1236|135625|712;3379134|1224|28216|80840|995019;1783272|1239|909932|1843489|31977;3379134|976|200643|171549|815;1783272|1239|186801|186802|3085642;1783272|1239|186801|3085636|186803|28050,Complete,NA
bsdb:36494405/2/1,36494405,case-control,36494405,10.1038/s41531-022-00428-2,https://www.nature.com/articles/s41531-022-00428-2,"Nishiwaki H., Ueyama J., Kashihara K., Ito M., Hamaguchi T., Maeda T., Tsuboi Y., Katsuno M., Hirayama M. , Ohno K.",Gut microbiota in dementia with Lewy bodies,NPJ Parkinson's disease,2022,NA,Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's Disease (PD) patients,Patients diagnosed with Parkinson's Disease (PD) a progressive brain disorder that affects movement due to the loss of dopamine-producing cells,147,224,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Tables 3A and 3B,26 July 2025,Kristin.abraham,"Kristin.abraham,Fiddyhamma,Tosin","Comparison of genera, family between Controls and Parkinson’s Disease (PD)",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3082720|543314;;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|2005519;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|1980681;3379134|200940|3031449|213115|194924;1783272|1239|526524|526525|128827|1573534;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;3379134|976|200643|1970189|1573805;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171550;1783272|1239|186801|3085636|186803|1769710;3379134|976|200643|171549|2005525;1783272|1239|526524|526525|2810280|3025755,Complete,NA
bsdb:36494405/2/2,36494405,case-control,36494405,10.1038/s41531-022-00428-2,https://www.nature.com/articles/s41531-022-00428-2,"Nishiwaki H., Ueyama J., Kashihara K., Ito M., Hamaguchi T., Maeda T., Tsuboi Y., Katsuno M., Hirayama M. , Ohno K.",Gut microbiota in dementia with Lewy bodies,NPJ Parkinson's disease,2022,NA,Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's Disease (PD) patients,Patients diagnosed with Parkinson's Disease (PD) a progressive brain disorder that affects movement due to the loss of dopamine-producing cells,147,224,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Tables 3A and 3B,26 July 2025,Kristin.abraham,"Kristin.abraham,Fiddyhamma","Comparison of genera, family between Controls and Parkinson’s Disease (PD)",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|33042;1783272|201174|84998|1643822|1643826;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|1407607;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085656|3085657;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|186801|3085636|186803|841;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977,Complete,NA
bsdb:36494405/3/1,36494405,case-control,36494405,10.1038/s41531-022-00428-2,https://www.nature.com/articles/s41531-022-00428-2,"Nishiwaki H., Ueyama J., Kashihara K., Ito M., Hamaguchi T., Maeda T., Tsuboi Y., Katsuno M., Hirayama M. , Ohno K.",Gut microbiota in dementia with Lewy bodies,NPJ Parkinson's disease,2022,NA,Experiment 3,Japan,Homo sapiens,Feces,UBERON:0001988,Lewy body dementia,EFO:0006792,Parkinson’s disease dementia negative (PDD-),Dementia with Lewy Bodies (DLB) patients,"Patients diagnosed with Dementia with Lewy bodies (DLB) a type of dementia characterized by changes in sleep, behavior, cognition, movement, and regulation of automatic bodily functions",71,28,1 month,16S,34,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3D,26 July 2025,Kristin.abraham,"Kristin.abraham,Fiddyhamma",Relative abundances of genera between Parkinson’s disease dementia negative (PDD-) and Dementia with Lewy Bodies (DLB),increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,1783272|1239|186801|3085636|186803|2316020|33039,Complete,Svetlana up
bsdb:36494405/3/2,36494405,case-control,36494405,10.1038/s41531-022-00428-2,https://www.nature.com/articles/s41531-022-00428-2,"Nishiwaki H., Ueyama J., Kashihara K., Ito M., Hamaguchi T., Maeda T., Tsuboi Y., Katsuno M., Hirayama M. , Ohno K.",Gut microbiota in dementia with Lewy bodies,NPJ Parkinson's disease,2022,NA,Experiment 3,Japan,Homo sapiens,Feces,UBERON:0001988,Lewy body dementia,EFO:0006792,Parkinson’s disease dementia negative (PDD-),Dementia with Lewy Bodies (DLB) patients,"Patients diagnosed with Dementia with Lewy bodies (DLB) a type of dementia characterized by changes in sleep, behavior, cognition, movement, and regulation of automatic bodily functions",71,28,1 month,16S,34,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3E,26 July 2025,Kristin.abraham,"Kristin.abraham,Fiddyhamma",Relative abundances of genera between Parkinson’s disease dementia negative (PDD-) and Dementia with Lewy Bodies (DLB),decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Svetlana up
bsdb:36494405/4/1,36494405,case-control,36494405,10.1038/s41531-022-00428-2,https://www.nature.com/articles/s41531-022-00428-2,"Nishiwaki H., Ueyama J., Kashihara K., Ito M., Hamaguchi T., Maeda T., Tsuboi Y., Katsuno M., Hirayama M. , Ohno K.",Gut microbiota in dementia with Lewy bodies,NPJ Parkinson's disease,2022,NA,Experiment 4,Japan,Homo sapiens,Feces,UBERON:0001988,Lewy body dementia,EFO:0006792,Healthy Controls,Dementia with Lewy Bodies (DLB) patients,"Patients diagnosed with Dementia with Lewy bodies (DLB) a type of dementia characterized by changes in sleep, behavior, cognition, movement, and regulation of automatic bodily functions",147,28,1 month,16S,34,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3D, 3F and Supplementary Figure 3",15 August 2025,Kristin.abraham,"Kristin.abraham,Fiddyhamma",Relative abundances of genera between Control and Dementia with Lewy Bodies (DLB),increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803|2316020|33038,Complete,Svetlana up
bsdb:36494405/5/1,36494405,case-control,36494405,10.1038/s41531-022-00428-2,https://www.nature.com/articles/s41531-022-00428-2,"Nishiwaki H., Ueyama J., Kashihara K., Ito M., Hamaguchi T., Maeda T., Tsuboi Y., Katsuno M., Hirayama M. , Ohno K.",Gut microbiota in dementia with Lewy bodies,NPJ Parkinson's disease,2022,NA,Experiment 5,Japan,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson’s disease dementia negative (PDD-) patients,Patients diagnosed with Parkinson’s disease dementia negative (PDD-),147,71,NA,16S,34,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3E,22 November 2025,Fiddyhamma,Fiddyhamma,Relative abundances of genera between Controls and Parkinson’s disease dementia positive (PDD+),increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Svetlana up
bsdb:36494405/6/1,36494405,case-control,36494405,10.1038/s41531-022-00428-2,https://www.nature.com/articles/s41531-022-00428-2,"Nishiwaki H., Ueyama J., Kashihara K., Ito M., Hamaguchi T., Maeda T., Tsuboi Y., Katsuno M., Hirayama M. , Ohno K.",Gut microbiota in dementia with Lewy bodies,NPJ Parkinson's disease,2022,NA,Experiment 6,Japan,Homo sapiens,Feces,UBERON:0001988,Lewy body dementia,EFO:0006792,Parkinson’s disease dementia positive (PDD+) patients,Dementia with Lewy Bodies (DLB) patients,"Patients diagnosed with Dementia with Lewy bodies (DLB) a type of dementia characterized by changes in sleep, behavior, cognition, movement, and regulation of automatic bodily functions",31,28,1 month,16S,34,Illumina,relative abundances,ANCOM-BC,0.05,TRUE,NA,NA,"age,body mass index,constipation,proton-pump inhibitor,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 7B,22 November 2025,Fiddyhamma,Fiddyhamma,Comparison of genera between Dementia with Lewy Bodies (DLB) and Parkinson’s disease dementia positive (PDD+) patients at any Hoehn & Yahr (HY) stages,increased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,1783272|201174|84998|84999|84107|102106,Complete,Svetlana up
bsdb:36494405/7/1,36494405,case-control,36494405,10.1038/s41531-022-00428-2,https://www.nature.com/articles/s41531-022-00428-2,"Nishiwaki H., Ueyama J., Kashihara K., Ito M., Hamaguchi T., Maeda T., Tsuboi Y., Katsuno M., Hirayama M. , Ohno K.",Gut microbiota in dementia with Lewy bodies,NPJ Parkinson's disease,2022,NA,Experiment 7,Japan,Homo sapiens,Feces,UBERON:0001988,Lewy body dementia,EFO:0006792,Mini–Mental State Examination (MMSE) in Healthy Controls,Mini–Mental State Examination (MMSE) in Dementia with Lewy Bodies (DLB) patients,"Mini–Mental State Examination (MMSE) of patients diagnosed with Dementia with Lewy bodies (DLB) a type of dementia characterized by changes in sleep, behavior, cognition, movement, and regulation of automatic bodily functions",147,28,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 8,22 November 2025,Fiddyhamma,Fiddyhamma,Correlation analysis between five clinical features and ten genera that were significantly changed in DLB compared to controls.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,1783272|1239|186801|3085636|186803|2316020|33039,Complete,Svetlana up
bsdb:36494405/8/1,36494405,case-control,36494405,10.1038/s41531-022-00428-2,https://www.nature.com/articles/s41531-022-00428-2,"Nishiwaki H., Ueyama J., Kashihara K., Ito M., Hamaguchi T., Maeda T., Tsuboi Y., Katsuno M., Hirayama M. , Ohno K.",Gut microbiota in dementia with Lewy bodies,NPJ Parkinson's disease,2022,NA,Experiment 8,Japan,Homo sapiens,Feces,UBERON:0001988,Lewy body dementia,EFO:0006792,Total Movement Disorder Society’s (MDS) version of the Unified Parkinson’s Disease Rating Scale (UPDRS) in Healthy Controls,Total Movement Disorder Society’s (MDS) version of the Unified Parkinson’s Disease Rating Scale (UPDRS) in Dementia with Lewy Bodies (DLB) patients,"Total Movement Disorder Society’s (MDS) version of the Unified Parkinson’s Disease Rating Scale (UPDRS) of patients diagnosed with Dementia with Lewy bodies (DLB) a type of dementia characterized by changes in sleep, behavior, cognition, movement, and regulation of automatic bodily functions",147,28,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 8,22 November 2025,Fiddyhamma,Fiddyhamma,Correlation analysis between five clinical features and ten genera that were significantly changed in DLB compared to controls.,increased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,1783272|201174|84998|1643822|1643826|84111,Complete,Svetlana up
bsdb:36494405/8/2,36494405,case-control,36494405,10.1038/s41531-022-00428-2,https://www.nature.com/articles/s41531-022-00428-2,"Nishiwaki H., Ueyama J., Kashihara K., Ito M., Hamaguchi T., Maeda T., Tsuboi Y., Katsuno M., Hirayama M. , Ohno K.",Gut microbiota in dementia with Lewy bodies,NPJ Parkinson's disease,2022,NA,Experiment 8,Japan,Homo sapiens,Feces,UBERON:0001988,Lewy body dementia,EFO:0006792,Total Movement Disorder Society’s (MDS) version of the Unified Parkinson’s Disease Rating Scale (UPDRS) in Healthy Controls,Total Movement Disorder Society’s (MDS) version of the Unified Parkinson’s Disease Rating Scale (UPDRS) in Dementia with Lewy Bodies (DLB) patients,"Total Movement Disorder Society’s (MDS) version of the Unified Parkinson’s Disease Rating Scale (UPDRS) of patients diagnosed with Dementia with Lewy bodies (DLB) a type of dementia characterized by changes in sleep, behavior, cognition, movement, and regulation of automatic bodily functions",147,28,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 8,22 November 2025,Fiddyhamma,Fiddyhamma,Correlation analysis between five clinical features and ten genera that were significantly changed in DLB compared to controls.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,1783272|1239|186801|3085636|186803|33042,Complete,Svetlana up
bsdb:36494405/10/1,36494405,case-control,36494405,10.1038/s41531-022-00428-2,https://www.nature.com/articles/s41531-022-00428-2,"Nishiwaki H., Ueyama J., Kashihara K., Ito M., Hamaguchi T., Maeda T., Tsuboi Y., Katsuno M., Hirayama M. , Ohno K.",Gut microbiota in dementia with Lewy bodies,NPJ Parkinson's disease,2022,NA,Experiment 10,Japan,Homo sapiens,Feces,UBERON:0001988,Lewy body dementia,EFO:0006792,Parkinson's Disease (PD) patients,Dementia with Lewy bodies (DLB) patients,"Patients diagnosed with Dementia with Lewy bodies (DLB) a type of dementia characterized by changes in sleep, behavior, cognition, movement, and regulation of automatic bodily functions",224,28,1 month,16S,34,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 3,22 November 2025,Fiddyhamma,Fiddyhamma,Plots of relative abundances of genera (Ruminococcus torques and Collinsella) in Parkinson’s disease (PD) and Dementia with Lewy Bodies (DLB),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",1783272|1239|186801|3085636|186803|2316020|33039;1783272|201174|84998|84999|84107|102106,Complete,Svetlana up
bsdb:36494405/11/1,36494405,case-control,36494405,10.1038/s41531-022-00428-2,https://www.nature.com/articles/s41531-022-00428-2,"Nishiwaki H., Ueyama J., Kashihara K., Ito M., Hamaguchi T., Maeda T., Tsuboi Y., Katsuno M., Hirayama M. , Ohno K.",Gut microbiota in dementia with Lewy bodies,NPJ Parkinson's disease,2022,NA,Experiment 11,Japan,Homo sapiens,Feces,UBERON:0001988,Lewy body dementia,EFO:0006792,Idiopathic rapid eye movement sleep behavior disorder (iRBD) patients,Dementia with Lewy bodies (DLB) patients,"Patients diagnosed with Dementia with Lewy bodies (DLB) a type of dementia characterized by changes in sleep, behavior, cognition, movement, and regulation of automatic bodily functions",26,28,1 month,16S,34,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 3,22 November 2025,Fiddyhamma,Fiddyhamma,Plots of relative abundances of genera (Ruminococcus gnavus) in idiopathic rapid eye movement sleep behavior disorder (iRBD) and Dementia with Lewy bodies (DLB),increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,1783272|1239|186801|3085636|186803|2316020|33038,Complete,Svetlana up
bsdb:36494405/12/1,36494405,case-control,36494405,10.1038/s41531-022-00428-2,https://www.nature.com/articles/s41531-022-00428-2,"Nishiwaki H., Ueyama J., Kashihara K., Ito M., Hamaguchi T., Maeda T., Tsuboi Y., Katsuno M., Hirayama M. , Ohno K.",Gut microbiota in dementia with Lewy bodies,NPJ Parkinson's disease,2022,NA,Experiment 12,Japan,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Idiopathic rapid eye movement sleep behavior disorder (iRBD) patients,Parkinson’s disease (PD) patients,Patients diagnosed with Parkinson's Disease (PD) a progressive brain disorder that affects movement due to the loss of dopamine-producing cells,26,224,NA,16S,34,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 3,22 November 2025,Fiddyhamma,Fiddyhamma,Plots of relative abundances of genera (Bifidobacterium) in idiopathic rapid eye movement sleep behavior disorder (iRBD) and Parkinson’s disease (PD),increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Svetlana up
bsdb:36494405/13/1,36494405,case-control,36494405,10.1038/s41531-022-00428-2,https://www.nature.com/articles/s41531-022-00428-2,"Nishiwaki H., Ueyama J., Kashihara K., Ito M., Hamaguchi T., Maeda T., Tsuboi Y., Katsuno M., Hirayama M. , Ohno K.",Gut microbiota in dementia with Lewy bodies,NPJ Parkinson's disease,2022,NA,Experiment 13,Japan,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson’s disease (PD) with Catechol‑O‑methyltransferase (COMT) inhibitor,Patients diagnosed with Parkinson's Disease (PD) using Catechol‑O‑methyltransferase (COMT) inhibitor,147,71,NA,16S,34,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 4A,22 November 2025,Fiddyhamma,Fiddyhamma,Relative abundances of Bifidobacterium in controls and Parkinson’s disease (PD) with Catechol‑O‑methyltransferase (COMT) inhibitor,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Svetlana up
bsdb:36494405/14/1,36494405,case-control,36494405,10.1038/s41531-022-00428-2,https://www.nature.com/articles/s41531-022-00428-2,"Nishiwaki H., Ueyama J., Kashihara K., Ito M., Hamaguchi T., Maeda T., Tsuboi Y., Katsuno M., Hirayama M. , Ohno K.",Gut microbiota in dementia with Lewy bodies,NPJ Parkinson's disease,2022,NA,Experiment 14,Japan,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Parkinson’s disease (PD) without Catechol‑O‑methyltransferase (COMT) inhibitor,Parkinson’s disease (PD) with Catechol‑O‑methyltransferase (COMT) inhibitor,Patients diagnosed with Parkinson's Disease (PD) using Catechol‑O‑methyltransferase (COMT) inhibitor,153,71,NA,16S,34,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 4A,22 November 2025,Fiddyhamma,Fiddyhamma,Relative abundances of Bifidobacterium in Parkinson’s disease (PD) without Catechol‑O‑methyltransferase (COMT) inhibitor and Parkinson’s disease (PD) with Catechol‑O‑methyltransferase (COMT) inhibitor,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Svetlana up
bsdb:36494405/15/1,36494405,case-control,36494405,10.1038/s41531-022-00428-2,https://www.nature.com/articles/s41531-022-00428-2,"Nishiwaki H., Ueyama J., Kashihara K., Ito M., Hamaguchi T., Maeda T., Tsuboi Y., Katsuno M., Hirayama M. , Ohno K.",Gut microbiota in dementia with Lewy bodies,NPJ Parkinson's disease,2022,NA,Experiment 15,Japan,Homo sapiens,Feces,UBERON:0001988,Lewy body dementia,EFO:0006792,Healthy controls,Dementia with Lewy bodies (DLB) patients,"Patients diagnosed with Dementia with Lewy bodies (DLB) a type of dementia characterized by changes in sleep, behavior, cognition, movement, and regulation of automatic bodily functions",147,28,1 month,16S,34,Illumina,relative abundances,ANCOM-BC,0.05,TRUE,NA,NA,"age,body mass index,constipation,proton-pump inhibitor,sex",NA,NA,NA,NA,NA,NA,Signature 1,"Supplementary Tables 2A, 2B",11 January 2026,Fiddyhamma,Fiddyhamma,"Comparison of genera, family between Controls and Dementia with Lewy Body (DLB)",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae",1783272|201174|84998|84999|84107|102106;1783272|201174|84998|1643822|1643826|84111;1783272|201174|84998|1643822|1643826;3379134|200940|3031449|213115|194924;1783272|201174|84998|84999|84107;1783272|1239|186801|3082720|543314,Complete,NA
bsdb:36494405/15/2,36494405,case-control,36494405,10.1038/s41531-022-00428-2,https://www.nature.com/articles/s41531-022-00428-2,"Nishiwaki H., Ueyama J., Kashihara K., Ito M., Hamaguchi T., Maeda T., Tsuboi Y., Katsuno M., Hirayama M. , Ohno K.",Gut microbiota in dementia with Lewy bodies,NPJ Parkinson's disease,2022,NA,Experiment 15,Japan,Homo sapiens,Feces,UBERON:0001988,Lewy body dementia,EFO:0006792,Healthy controls,Dementia with Lewy bodies (DLB) patients,"Patients diagnosed with Dementia with Lewy bodies (DLB) a type of dementia characterized by changes in sleep, behavior, cognition, movement, and regulation of automatic bodily functions",147,28,1 month,16S,34,Illumina,relative abundances,ANCOM-BC,0.05,TRUE,NA,NA,"age,body mass index,constipation,proton-pump inhibitor,sex",NA,NA,NA,NA,NA,NA,Signature 2,"Supplementary Tables 2A, 2B",11 January 2026,Fiddyhamma,Fiddyhamma,"Comparison of genera, family between Controls and Dementia with Lewy Body (DLB)",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|216572,Complete,NA
bsdb:36511710/1/1,36511710,case-control,36511710,https://doi.org/10.1128/spectrum.02472-22,NA,"Meng J., Tao J., Abu Y., Sussman D.A., Girotra M., Franceschi D. , Roy S.",HIV-Positive Patients on Antiretroviral Therapy Have an Altered Mucosal Intestinal but Not Oral Microbiome,Microbiology spectrum,2023,"16S RNA, HIV, antiretroviral therapy, human microbiome, intestinal microbiome, oral microbiome",Experiment 1,United States of America,Homo sapiens,"Ileum,Colon","UBERON:0001155,UBERON:0002116",Response to antiviral drug,EFO:0010123,Intestinal samples of Healthy Control,Intestinal samples of HIV Positive Patients,"All intestinal samples (colon brush, colon wash, terminal ileum brush, and terminal ileum wash) of HIV-positive individuals on antiretroviral therapy",12,5,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Fig. 1C,14 March 2024,Eve10111,"Eve10111,Scholastica,WikiWorks",Linear discriminant analysis effect size (LEfSe) analysis of top discriminative bacteria genera between gut samples from HIV-positive compared to HIV-negative patients.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter",3379134|74201|203494|48461|1647988|239934;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|186802|186806|1730;3384189|32066|203490|203491|203492|848;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|909929|1843491|52225;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|3082720|186804|1257;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171552|838;3379134|1224|1236|135624|83763|83770;3366610|28890|183925|2158|2159|2172,Complete,Svetlana up
bsdb:36511710/1/2,36511710,case-control,36511710,https://doi.org/10.1128/spectrum.02472-22,NA,"Meng J., Tao J., Abu Y., Sussman D.A., Girotra M., Franceschi D. , Roy S.",HIV-Positive Patients on Antiretroviral Therapy Have an Altered Mucosal Intestinal but Not Oral Microbiome,Microbiology spectrum,2023,"16S RNA, HIV, antiretroviral therapy, human microbiome, intestinal microbiome, oral microbiome",Experiment 1,United States of America,Homo sapiens,"Ileum,Colon","UBERON:0001155,UBERON:0002116",Response to antiviral drug,EFO:0010123,Intestinal samples of Healthy Control,Intestinal samples of HIV Positive Patients,"All intestinal samples (colon brush, colon wash, terminal ileum brush, and terminal ileum wash) of HIV-positive individuals on antiretroviral therapy",12,5,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Fig. 1C,14 March 2024,Eve10111,"Eve10111,Scholastica,WikiWorks",Linear discriminant analysis effect size (LEfSe) analysis of top discriminative bacteria genera between gut samples from HIV-positive compared to HIV-negative patients.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|216572|1263,Complete,Svetlana up
bsdb:36511710/2/1,36511710,case-control,36511710,https://doi.org/10.1128/spectrum.02472-22,NA,"Meng J., Tao J., Abu Y., Sussman D.A., Girotra M., Franceschi D. , Roy S.",HIV-Positive Patients on Antiretroviral Therapy Have an Altered Mucosal Intestinal but Not Oral Microbiome,Microbiology spectrum,2023,"16S RNA, HIV, antiretroviral therapy, human microbiome, intestinal microbiome, oral microbiome",Experiment 2,United States of America,Homo sapiens,Colon,UBERON:0001155,Response to antiviral drug,EFO:0010123,Colon wash samples of Healthy Control,Colon wash samples of HIV Positive Patients,Colon wash samples of HIV-positive individuals on antiretroviral therapy,12,5,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 3C,27 May 2024,Scholastica,"Scholastica,WikiWorks",Linear discriminant analysis effect size (LEfSe) analysis of top discriminative bacteria genera between colon wash samples from HIV-positive compared to HIV-negative patients.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter",3379134|1224|1236|135624|83763|83770;3379134|1224|1236|135625|712|416916,Complete,Svetlana up
bsdb:36511710/3/1,36511710,case-control,36511710,https://doi.org/10.1128/spectrum.02472-22,NA,"Meng J., Tao J., Abu Y., Sussman D.A., Girotra M., Franceschi D. , Roy S.",HIV-Positive Patients on Antiretroviral Therapy Have an Altered Mucosal Intestinal but Not Oral Microbiome,Microbiology spectrum,2023,"16S RNA, HIV, antiretroviral therapy, human microbiome, intestinal microbiome, oral microbiome",Experiment 3,United States of America,Homo sapiens,Colon,UBERON:0001155,Response to antiviral drug,EFO:0010123,Colon brush samples of Healthy Control,Colon brush samples of HIV Positive Patients,Colon brush samples of HIV-positive individuals on antiretroviral therapy,12,5,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 4C,27 May 2024,Scholastica,"Scholastica,WikiWorks",Linear discriminant analysis effect size (LEfSe) analysis of top discriminative bacteria genera between colon brush samples from HIV-positive compared to HIV-negative patients.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia",1783272|1239|909932|1843489|31977|906;1783272|201174|84998|1643822|1643826|84108,Complete,Svetlana up
bsdb:36511710/4/1,36511710,case-control,36511710,https://doi.org/10.1128/spectrum.02472-22,NA,"Meng J., Tao J., Abu Y., Sussman D.A., Girotra M., Franceschi D. , Roy S.",HIV-Positive Patients on Antiretroviral Therapy Have an Altered Mucosal Intestinal but Not Oral Microbiome,Microbiology spectrum,2023,"16S RNA, HIV, antiretroviral therapy, human microbiome, intestinal microbiome, oral microbiome",Experiment 4,United States of America,Homo sapiens,Ileum,UBERON:0002116,Response to antiviral drug,EFO:0010123,Terminal ileum wash samples of Healthy Control,Terminal ileum wash samples of HIV Positive Patients,Terminal ileum (TI) wash samples of HIV-positive individuals on antiretroviral therapy,12,5,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Fig. 5C,27 May 2024,Scholastica,"Scholastica,WikiWorks",Linear discriminant analysis effect size (LEfSe) analysis of top discriminative bacteria genera between terminal ileum (TI) samples from HIV-positive compared to HIV-negative patients.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter",3379134|976|200643|171549|171552|838;1783272|1239|186801|3082720|543314|86331;1783272|1239|909932|909929|1843491|52225;3379134|1224|1236|135625|712|416916,Complete,Svetlana up
bsdb:36517824/1/1,36517824,case-control,36517824,https://doi.org/10.1186/s12931-022-02230-3,https://respiratory-research.biomedcentral.com/articles/10.1186/s12931-022-02230-3,"Miao Q., Liang T., Pei N., Liu C., Pan J., Li N., Wang Q., Chen Y., Chen Y., Ma Y., Jin W., Zhang Y., Su Y., Yao Y., Huang Y., Zhou C., Bao R., Xu X., Chen W., Hu B. , Li J.",Evaluation of respiratory samples in etiology diagnosis and microbiome characterization by metagenomic sequencing,Respiratory research,2022,"Bronchoalveolar lavage fluid, Clinical metagenomic, Microbiome characterization",Experiment 1,China,Homo sapiens,Bronchoalveolar duct junction,UBERON:0004903,Respiratory tract infectious disease,MONDO:0024355,Mycobacterium (Bronchoalveolar lavage fluid - Respiratory tract infection - Mycobacterium) + Fungi (Bronchoalveolar lavage fluid - Respiratory tract infection - Fungi) + Control,Non-mycobacterium (Bronchoalveolar lavage fluid - Respiratory tract infection - Non-mycobacterium),Patients with Respiratory tract infections (RTIs) caused by non-mycobacterium,151,19,NA,WMS,NA,NA,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,13 November 2025,Fiddyhamma,Fiddyhamma,LEfSe analysis to rank the discriminating species in three infection types and the control group,increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter rectus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus aegyptius,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus haemolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus quentini,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella denitrificans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Nocardia|s__Nocardia brasiliensis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia",3379134|29547|3031852|213849|72294|194|203;3379134|1224|1236|135625|712|724|197575;3379134|1224|1236|135625|712|724|726;3379134|1224|1236|135625|712|724|123834;3379134|1224|28216|206351|481|32257|502;1783272|201174|1760|85007|85025|1817|37326;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|1239|186801|3082720|186804|1257|341694;3379134|1224|1236|135614|32033|40323|40324,Complete,KateRasheed
bsdb:36517824/2/1,36517824,case-control,36517824,https://doi.org/10.1186/s12931-022-02230-3,https://respiratory-research.biomedcentral.com/articles/10.1186/s12931-022-02230-3,"Miao Q., Liang T., Pei N., Liu C., Pan J., Li N., Wang Q., Chen Y., Chen Y., Ma Y., Jin W., Zhang Y., Su Y., Yao Y., Huang Y., Zhou C., Bao R., Xu X., Chen W., Hu B. , Li J.",Evaluation of respiratory samples in etiology diagnosis and microbiome characterization by metagenomic sequencing,Respiratory research,2022,"Bronchoalveolar lavage fluid, Clinical metagenomic, Microbiome characterization",Experiment 2,China,Homo sapiens,Bronchoalveolar duct junction,UBERON:0004903,Respiratory tract infectious disease,MONDO:0024355,Non-mycobacterium (Bronchoalveolar lavage fluid - Respiratory tract infection - Non-mycobacterium) + Fungi (Bronchoalveolar lavage fluid - Respiratory tract infection - Fungi) + Control,Mycobacterium (Bronchoalveolar lavage fluid - Respiratory tract infection - Mycobacterium),Patients with Respiratory tract infections (RTIs) caused by mycobacterium,118,52,NA,WMS,NA,NA,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,13 November 2025,Fiddyhamma,Fiddyhamma,LEfSe analysis to rank the discriminating species in three infection types and the control group,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium orygis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium tuberculosis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium tuberculosis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae",1783272|201174|1760|2037|2049|1654|55565;3379134|1224|28216|80840|119060|47670|47671;1783272|201174|1760|85007|1762|1763|1305738;1783272|201174|1760|85007|1762|1763|1773;1783272|201174|1760|85007|1762|1763|1773;3379134|976|200643|171549|171552|838|28133;1783272|201174|1760|85006|1268|32207|2047;3379134|976|200643|171549|171552|2974251|28135;1783272|1239|91061|186826|1300|1301|45634;1783272|1239|91061|186826|1300|1301|1313,Complete,KateRasheed
bsdb:36517824/3/1,36517824,case-control,36517824,https://doi.org/10.1186/s12931-022-02230-3,https://respiratory-research.biomedcentral.com/articles/10.1186/s12931-022-02230-3,"Miao Q., Liang T., Pei N., Liu C., Pan J., Li N., Wang Q., Chen Y., Chen Y., Ma Y., Jin W., Zhang Y., Su Y., Yao Y., Huang Y., Zhou C., Bao R., Xu X., Chen W., Hu B. , Li J.",Evaluation of respiratory samples in etiology diagnosis and microbiome characterization by metagenomic sequencing,Respiratory research,2022,"Bronchoalveolar lavage fluid, Clinical metagenomic, Microbiome characterization",Experiment 3,China,Homo sapiens,Bronchoalveolar duct junction,UBERON:0004903,Respiratory tract infectious disease,MONDO:0024355,Mycobacterium (Bronchoalveolar lavage fluid-Respiratory tract infection - Mycobacterium) + Non - mycobacterium (Bronchoalveolar lavage fluid - Respiratory tract infection - Non-mycobacterium) + Control,Fungi (Bronchoalveolar lavage fluid - Respiratory tract infection - Fungi),Patients with Respiratory tract infections (RTIs) caused by fungi,150,20,NA,WMS,NA,NA,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,13 November 2025,Fiddyhamma,Fiddyhamma,LEfSe analysis to rank the discriminating species in three infection types and the control group,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia ambifaria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella oralis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria gonorrhoeae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria lactamica,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria meningitidis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas echinoides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudopneumoniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis",3379134|1224|28216|80840|119060|32008|152480;1783272|1239|91061|1385|539738|1378|84135;1783272|1239|91061|186826|1300|1301|1318;3379134|976|200643|171549|171552|2974257|28134;3379134|1224|28216|206351|481|482|485;3379134|1224|28216|206351|481|482|486;3379134|1224|28216|206351|481|482|487;3379134|1224|28211|204457|41297|13687|59803;1783272|1239|91061|186826|1300|1301|68892;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|91061|186826|1300|1301|257758;1783272|1239|91061|186826|1300|1301|1305,Complete,KateRasheed
bsdb:36517824/4/1,36517824,case-control,36517824,https://doi.org/10.1186/s12931-022-02230-3,https://respiratory-research.biomedcentral.com/articles/10.1186/s12931-022-02230-3,"Miao Q., Liang T., Pei N., Liu C., Pan J., Li N., Wang Q., Chen Y., Chen Y., Ma Y., Jin W., Zhang Y., Su Y., Yao Y., Huang Y., Zhou C., Bao R., Xu X., Chen W., Hu B. , Li J.",Evaluation of respiratory samples in etiology diagnosis and microbiome characterization by metagenomic sequencing,Respiratory research,2022,"Bronchoalveolar lavage fluid, Clinical metagenomic, Microbiome characterization",Experiment 4,China,Homo sapiens,Bronchoalveolar duct junction,UBERON:0004903,Respiratory tract infectious disease,MONDO:0024355,Mycobacterium (Bronchoalveolar lavage fluid-Respiratory tract infection - Mycobacterium) + Non - mycobacterium (Bronchoalveolar lavage fluid - Respiratory tract infection - Non-mycobacterium) + Fungi (Bronchoalveolar lavage fluid - Respiratory tract infection - Fungi),Control,Patients without Respiratory tract infection (RTI) nor immune disorder,91,79,NA,WMS,NA,NA,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,13 November 2025,Fiddyhamma,Fiddyhamma,LEfSe analysis to rank the discriminating species in three infection types and the control group,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter johnsonii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter parvus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia dolosa,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia ubonensis,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium accolens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia|s__Delftia acidovorans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia|s__Delftia tsuruhatensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Faucicola|s__Faucicola osloensis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium hwasookii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria macacae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria mucosa,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sicca,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas veronii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia insidiosa,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia mannitolilytica,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia pickettii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas parapaucimobilis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus peroris,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus ilei",3379134|1224|1236|2887326|468|469|40214;3379134|1224|1236|2887326|468|469|134533;3379134|976|200643|171549|171552|1283313|76122;3379134|1224|28216|80840|119060|32008|152500;3379134|1224|28216|80840|119060|32008|101571;3379134|29547|3031852|213849|72294|194|199;3379134|976|117743|200644|49546|1016|1017;1783272|201174|1760|85007|1653|1716|38284;3379134|1224|28216|80840|80864|80865|80866;3379134|1224|28216|80840|80864|80865|180282;3379134|1224|28216|206351|481|538|539;3379134|1224|1236|2887326|468|1604696|34062;3384189|32066|203490|203491|203492|848|1583098;1783272|1239|91061|186826|186828|117563|46124;3379134|976|200643|171549|171552|2974257|425941;3379134|1224|28216|206351|481|482|495;3379134|1224|28216|206351|481|482|484;3379134|1224|28216|206351|481|482|496;3379134|1224|28216|206351|481|482|488;3379134|1224|28216|206351|481|482|490;3379134|1224|28216|206351|481|482|28449;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|171552|838|60133;3379134|1224|1236|72274|135621|286|76761;3379134|1224|28216|80840|119060|48736|190721;3379134|1224|28216|80840|119060|48736|105219;3379134|1224|28216|80840|119060|48736|329;1783272|201174|1760|85006|1268|32207|172042;3379134|1224|28211|204457|41297|13687|28213;1783272|1239|91061|1385|90964|1279|1290;1783272|1239|91061|186826|1300|1301|68891;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|91061|186826|1300|1301|1156431,Complete,KateRasheed
bsdb:36517824/5/1,36517824,case-control,36517824,https://doi.org/10.1186/s12931-022-02230-3,https://respiratory-research.biomedcentral.com/articles/10.1186/s12931-022-02230-3,"Miao Q., Liang T., Pei N., Liu C., Pan J., Li N., Wang Q., Chen Y., Chen Y., Ma Y., Jin W., Zhang Y., Su Y., Yao Y., Huang Y., Zhou C., Bao R., Xu X., Chen W., Hu B. , Li J.",Evaluation of respiratory samples in etiology diagnosis and microbiome characterization by metagenomic sequencing,Respiratory research,2022,"Bronchoalveolar lavage fluid, Clinical metagenomic, Microbiome characterization",Experiment 5,China,Homo sapiens,Bronchoalveolar duct junction,UBERON:0004903,Mycobacterium tuberculosis,NCBITAXON:1773,Non tuberculous mycobacteria (NTM),Mycobacterium tuberculosis (MTB),This is a type of bacteria that causes tuberculosis (TB) in humans,NA,NA,NA,WMS,NA,NA,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4C,13 November 2025,Tosin,Tosin,LEfSe (linear discriminant analysis effect size) analysis to rank the discriminating microbes in NTM (non tuberculous mycobacteria) and MTB (mycobacterium tuberculosis) infections,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium oligotrophicum,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium canetti,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium orygis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium tuberculosis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium tuberculosis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium tuberculosis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia solanacearum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis",3379134|1224|28211|356|41294|374|44255;3379134|976|117743|200644|49546|1016|1018;1783272|201174|1760|85009|31957|1912216|1747;3379134|1224|1236|135625|712|724|729;1783272|201174|1760|85007|1762|1763|78331;1783272|201174|1760|85007|1762|1763|1305738;1783272|201174|1760|85007|1762|1763|1773;1783272|201174|1760|85007|1762|1763|1773;1783272|201174|1760|85007|1762|1763|1773;3379134|976|200643|171549|171551|836|837;3379134|976|200643|171549|171552|838|28129;3379134|1224|28216|80840|119060|48736|305;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|91061|186826|1300|1301|1318;3379134|976|200643|171549|2005525|195950|28112;1783272|1239|91061|186826|1300|1301|1305,Complete,KateRasheed
bsdb:36517824/5/2,36517824,case-control,36517824,https://doi.org/10.1186/s12931-022-02230-3,https://respiratory-research.biomedcentral.com/articles/10.1186/s12931-022-02230-3,"Miao Q., Liang T., Pei N., Liu C., Pan J., Li N., Wang Q., Chen Y., Chen Y., Ma Y., Jin W., Zhang Y., Su Y., Yao Y., Huang Y., Zhou C., Bao R., Xu X., Chen W., Hu B. , Li J.",Evaluation of respiratory samples in etiology diagnosis and microbiome characterization by metagenomic sequencing,Respiratory research,2022,"Bronchoalveolar lavage fluid, Clinical metagenomic, Microbiome characterization",Experiment 5,China,Homo sapiens,Bronchoalveolar duct junction,UBERON:0004903,Mycobacterium tuberculosis,NCBITAXON:1773,Non tuberculous mycobacteria (NTM),Mycobacterium tuberculosis (MTB),This is a type of bacteria that causes tuberculosis (TB) in humans,NA,NA,NA,WMS,NA,NA,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4C,13 November 2025,Tosin,Tosin,LEfSe (linear discriminant analysis effect size) analysis to rank the discriminating microbes in NTM (non tuberculous mycobacteria) and MTB (mycobacterium tuberculosis) infections,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacteroides|s__Mycobacteroides abscessus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria gonorrhoeae",1783272|201174|1760|85007|1762|670516|36809;1783272|1239|91061|186826|81852|1350|1352;1783272|1239|91061|186826|1300|1301|45634;3379134|1224|28216|206351|481|482|485,Complete,KateRasheed
bsdb:36517824/6/1,36517824,case-control,36517824,https://doi.org/10.1186/s12931-022-02230-3,https://respiratory-research.biomedcentral.com/articles/10.1186/s12931-022-02230-3,"Miao Q., Liang T., Pei N., Liu C., Pan J., Li N., Wang Q., Chen Y., Chen Y., Ma Y., Jin W., Zhang Y., Su Y., Yao Y., Huang Y., Zhou C., Bao R., Xu X., Chen W., Hu B. , Li J.",Evaluation of respiratory samples in etiology diagnosis and microbiome characterization by metagenomic sequencing,Respiratory research,2022,"Bronchoalveolar lavage fluid, Clinical metagenomic, Microbiome characterization",Experiment 6,China,Homo sapiens,Bronchoalveolar duct junction,UBERON:0004903,Immune system disease,EFO:0000540,Control group,Bronchoalveolar lavage fluid - Immune disorder - Tumor,Immune disorder patients with tumor,24,37,NA,WMS,NA,NA,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5B,13 November 2025,Fiddyhamma,Fiddyhamma,"LEfSe analysis to rank the discriminating specimen-specific microbes in patients with tumors (Bronchoalveolar lavage fluid - Immune disorder - Tumor), and the control group",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium aurimucosum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium hwasookii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sputorum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria gonorrhoeae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria lactamica,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria macacae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudopneumoniae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia lata",1783272|201174|1760|85007|1653|1716|169292;3384189|32066|203490|203491|203492|848|1583098;3379134|1224|1236|135625|712|724|1078480;3379134|1224|28216|206351|481|482|485;3379134|1224|28216|206351|481|482|486;3379134|1224|28216|206351|481|482|496;3379134|976|200643|171549|171552|838|28133;1783272|1239|91061|186826|1300|1301|45634;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|91061|186826|1300|1301|257758;3379134|976|200643|171549|2005525|195950|28112;1783272|1239|909932|1843489|31977|29465|29466;3379134|1224|28216|80840|119060|32008|482957,Complete,KateRasheed
bsdb:36517824/6/2,36517824,case-control,36517824,https://doi.org/10.1186/s12931-022-02230-3,https://respiratory-research.biomedcentral.com/articles/10.1186/s12931-022-02230-3,"Miao Q., Liang T., Pei N., Liu C., Pan J., Li N., Wang Q., Chen Y., Chen Y., Ma Y., Jin W., Zhang Y., Su Y., Yao Y., Huang Y., Zhou C., Bao R., Xu X., Chen W., Hu B. , Li J.",Evaluation of respiratory samples in etiology diagnosis and microbiome characterization by metagenomic sequencing,Respiratory research,2022,"Bronchoalveolar lavage fluid, Clinical metagenomic, Microbiome characterization",Experiment 6,China,Homo sapiens,Bronchoalveolar duct junction,UBERON:0004903,Immune system disease,EFO:0000540,Control group,Bronchoalveolar lavage fluid - Immune disorder - Tumor,Immune disorder patients with tumor,24,37,NA,WMS,NA,NA,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5B,13 November 2025,Fiddyhamma,Fiddyhamma,"LEfSe analysis to rank the discriminating specimen-specific microbes in patients with tumors (Bronchoalveolar lavage fluid - Immune disorder - Tumor), and the control group",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia dolosa,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia multivorans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia ubonensis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas testosteroni,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium accolens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia|s__Delftia acidovorans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia|s__Delftia tsuruhatensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Faucicola|s__Faucicola osloensis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria mucosa,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella multiformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella scopos,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella veroralis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas veronii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia insidiosa,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia mannitolilytica,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia pickettii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia solanacearum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella flexneri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella sonnei,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas parapaucimobilis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus ilei",3379134|976|200643|171549|171552|1283313|76122;3379134|1224|28216|80840|119060|32008|152500;3379134|1224|28216|80840|119060|32008|87883;3379134|1224|28216|80840|119060|32008|101571;3379134|976|117743|200644|49546|1016|1017;3379134|976|117743|200644|49546|1016|1019;3379134|1224|28216|80840|80864|283|285;1783272|201174|1760|85007|1653|1716|38284;3379134|1224|28216|80840|80864|80865|80866;3379134|1224|28216|80840|80864|80865|180282;3379134|1224|28216|206351|481|538|539;3379134|1224|1236|91347|543|561|562;3379134|1224|1236|2887326|468|1604696|34062;3384189|32066|203490|203491|203492|848|860;1783272|1239|91061|186826|186828|117563|46124;3379134|976|200643|171549|171552|2974257|425941;3379134|1224|28216|80840|119060|47670|47671;3379134|1224|28216|206351|481|482|484;3379134|1224|28216|206351|481|482|488;3379134|1224|28216|206351|481|482|28449;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|171551|836|322095;3379134|976|200643|171549|171552|838|282402;3379134|976|200643|171549|171552|838|60133;3379134|976|200643|171549|171552|838|589437;3379134|976|200643|171549|171552|838|28137;3379134|1224|1236|72274|135621|286|76761;3379134|1224|28216|80840|119060|48736|190721;3379134|1224|28216|80840|119060|48736|105219;3379134|1224|28216|80840|119060|48736|329;3379134|1224|28216|80840|119060|48736|305;1783272|201174|1760|85006|1268|32207|172042;3379134|1224|1236|91347|543|620|623;3379134|1224|1236|91347|543|620|624;3379134|1224|28211|204457|41297|13687|28213;1783272|1239|91061|1385|90964|1279|1290;1783272|1239|91061|186826|1300|1301|113107;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|91061|186826|1300|1301|1156431,Complete,KateRasheed
bsdb:36517824/7/1,36517824,case-control,36517824,https://doi.org/10.1186/s12931-022-02230-3,https://respiratory-research.biomedcentral.com/articles/10.1186/s12931-022-02230-3,"Miao Q., Liang T., Pei N., Liu C., Pan J., Li N., Wang Q., Chen Y., Chen Y., Ma Y., Jin W., Zhang Y., Su Y., Yao Y., Huang Y., Zhou C., Bao R., Xu X., Chen W., Hu B. , Li J.",Evaluation of respiratory samples in etiology diagnosis and microbiome characterization by metagenomic sequencing,Respiratory research,2022,"Bronchoalveolar lavage fluid, Clinical metagenomic, Microbiome characterization",Experiment 7,China,Homo sapiens,Sputum,UBERON:0007311,Specimen,OBI:0100051,BALF (Bronchoalveolar lavage fluid) + Lung tissue + Pleural fluid,Sputum,"Sputum, a respiratory specimen type collected from patients across the three groups (RTI-C+M: clinically diagnosed RTI with microbiology evidence; RTI-C: clinically diagnosed RTI without microbiology evidence; non-RTI: non-infectious respiratory disease), used for comparative analysis of diagnostic performance and microbiome features.",775,486,NA,WMS,NA,NA,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3C,14 November 2025,Tosin,Tosin,Heatmap of the bacteria abundance and LEfSe analysis to rank the discriminating specimen-specific species,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus aegyptius,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia wadei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc lactis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria gonorrhoeae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria lactamica,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria meningitidis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella veroralis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus peroris,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudopneumoniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus ilei",1783272|201174|1760|2037|2049|1654|55565;3379134|29547|3031852|213849|72294|194|199;1783272|1239|91061|186826|186828|117563|46124;3379134|1224|1236|135625|712|724|197575;3384189|32066|203490|203491|1129771|32067|40542;3384189|32066|203490|203491|1129771|32067|157687;1783272|1239|91061|186826|33958|1243|1246;3379134|1224|28216|206351|481|482|485;3379134|1224|28216|206351|481|482|486;3379134|1224|28216|206351|481|482|487;3379134|976|200643|171549|171552|838|28137;1783272|201174|1760|85006|1268|32207|2047;1783272|201174|1760|85006|1268|32207|43675;3379134|976|200643|171549|171552|2974251|28135;3379134|976|200643|171549|171552|2974251|228604;1783272|1239|91061|186826|1300|1301|113107;1783272|1239|91061|186826|1300|1301|1302;1783272|1239|91061|186826|1300|1301|68892;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|68891;1783272|1239|91061|186826|1300|1301|257758;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|1300|1301|1305;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|91061|186826|1300|1301|1343;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|91061|186826|1300|1301|1156431,Complete,KateRasheed
bsdb:36517824/8/1,36517824,case-control,36517824,https://doi.org/10.1186/s12931-022-02230-3,https://respiratory-research.biomedcentral.com/articles/10.1186/s12931-022-02230-3,"Miao Q., Liang T., Pei N., Liu C., Pan J., Li N., Wang Q., Chen Y., Chen Y., Ma Y., Jin W., Zhang Y., Su Y., Yao Y., Huang Y., Zhou C., Bao R., Xu X., Chen W., Hu B. , Li J.",Evaluation of respiratory samples in etiology diagnosis and microbiome characterization by metagenomic sequencing,Respiratory research,2022,"Bronchoalveolar lavage fluid, Clinical metagenomic, Microbiome characterization",Experiment 8,China,Homo sapiens,Bronchoalveolar duct junction,UBERON:0004903,Specimen,OBI:0100051,Sputum + Lung tissue + Pleural fluid,BALF (Bronchoalveolar lavage fluid),"BALF (Bronchoalveolar Lavage Fluid), a respiratory specimen type from the three patient groups (RTI-C+M: clinically diagnosed RTI with microbiology evidence; RTI-C: clinically diagnosed RTI without microbiology evidence; non-RTI: non-infectious respiratory disease), included in the comparison of diagnostic performance and microbiome characterization",874,387,NA,WMS,NA,NA,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3C,14 November 2025,Tosin,Tosin,Heatmap of the bacteria abundance and LEfSe analysis to rank the discriminating specimen-specific species,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium striatum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Umbribacter|s__Umbribacter vaginalis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium sp. BTAi1,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium accolens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas fluorescens,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis",1783272|1239|91061|186826|1300|1301|1313;1783272|201174|1760|85007|1653|1716|43770;1783272|201174|84998|1643822|1643826|3472368|1588753;3379134|1224|28211|356|41294|374|288000;1783272|201174|1760|85007|1653|1716|38284;3379134|1224|1236|72274|135621|286|294;1783272|1239|91061|1385|539738|1378|84135,Complete,KateRasheed
bsdb:36517824/9/1,36517824,case-control,36517824,https://doi.org/10.1186/s12931-022-02230-3,https://respiratory-research.biomedcentral.com/articles/10.1186/s12931-022-02230-3,"Miao Q., Liang T., Pei N., Liu C., Pan J., Li N., Wang Q., Chen Y., Chen Y., Ma Y., Jin W., Zhang Y., Su Y., Yao Y., Huang Y., Zhou C., Bao R., Xu X., Chen W., Hu B. , Li J.",Evaluation of respiratory samples in etiology diagnosis and microbiome characterization by metagenomic sequencing,Respiratory research,2022,"Bronchoalveolar lavage fluid, Clinical metagenomic, Microbiome characterization",Experiment 9,China,Homo sapiens,Lung,UBERON:0002048,Specimen,OBI:0100051,Sputum + BALF (Bronchoalveolar lavage fluid) + Pleural fluid,Lung tissue,"Lung tissue, one of the respiratory specimen types obtained from relevant patients in the three groups (RTI-C+M: clinically diagnosed RTI with microbiology evidence; RTI-C: clinically diagnosed RTI without microbiology evidence; non-RTI: non-infectious respiratory disease), used for the comparative evaluation.",1023,238,NA,WMS,NA,NA,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3C,14 November 2025,Tosin,Tosin,Heatmap of the bacteria abundance and LEfSe analysis to rank the discriminating specimen-specific species,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia insidiosa,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter|s__Enhydrobacter aerosaccus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella flexneri,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia ubonensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia multivorans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium|s__Microbacterium trichothecenolyticum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia dolosa,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia vietnamiensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia latens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia anthina,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia metallica,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia lata",3379134|1224|28216|80840|119060|48736|190721;3379134|1224|28211|356|212791|225324;3379134|1224|1236|91347|543|620|623;3379134|1224|28216|80840|119060|32008|101571;3379134|1224|28216|80840|119060|32008|87883;1783272|201174|1760|85006|85023|33882|69370;3379134|1224|28216|80840|119060|32008|152500;3379134|1224|28216|80840|119060|32008|60552;3379134|1224|28216|80840|119060|32008|488446;3379134|1224|28216|80840|119060|32008|179879;3379134|1224|28216|80840|119060|32008|488729;3379134|1224|28216|80840|119060|32008|482957,Complete,KateRasheed
bsdb:36517824/10/1,36517824,case-control,36517824,https://doi.org/10.1186/s12931-022-02230-3,https://respiratory-research.biomedcentral.com/articles/10.1186/s12931-022-02230-3,"Miao Q., Liang T., Pei N., Liu C., Pan J., Li N., Wang Q., Chen Y., Chen Y., Ma Y., Jin W., Zhang Y., Su Y., Yao Y., Huang Y., Zhou C., Bao R., Xu X., Chen W., Hu B. , Li J.",Evaluation of respiratory samples in etiology diagnosis and microbiome characterization by metagenomic sequencing,Respiratory research,2022,"Bronchoalveolar lavage fluid, Clinical metagenomic, Microbiome characterization",Experiment 10,China,Homo sapiens,Pleural fluid,UBERON:0001087,Specimen,OBI:0100051,Sputum + BALF (Bronchoalveolar lavage fluid) + Lung tissue,Pleural fluid,"Pleural fluid, a respiratory specimen type from selected patients within the three groups (RTI-C+M: clinically diagnosed RTI with microbiology evidence; RTI-C: clinically diagnosed RTI without microbiology evidence; non-RTI: non-infectious respiratory disease), assessed alongside other specimen types in the study.",1111,150,NA,WMS,NA,NA,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3C,14 November 2025,Tosin,Tosin,Heatmap of the bacteria abundance and LEfSe analysis to rank the discriminating specimen-specific species,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella boydii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella sonnei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella dysenteriae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella oralis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax|s__Acidovorax sp. KKS102,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus intermedius,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia ambifaria",1783272|201174|1760|85009|31957|1912216|1747;3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|543|620|621;3379134|1224|1236|91347|543|620|624;3379134|1224|1236|91347|543|620|622;1783272|1239|91061|186826|1300|1301|76860;3379134|976|200643|171549|171552|2974257|28134;3379134|1224|28216|80840|80864|12916|358220;1783272|1239|91061|186826|1300|1301|1338;3379134|976|117743|200644|49546|1016|1018;3379134|1224|28216|80840|119060|32008|152480,Complete,KateRasheed
bsdb:36518275/1/1,36518275,"cross-sectional observational, not case-control",36518275,https://doi.org/10.7717/peerj.14449,NA,"Roachford O.S.E., Alleyne A.T. , Nelson K.E.","Insights into the vaginal microbiome in a diverse group of women of African, Asian and European ancestries",PeerJ,2022,"Ancestries, CST subtypes, Community state types, Ethnicity, Gardnerella, Lactobacillus, Mycoplasma, Pathobionts, Prevotella, Vaginal microbiome",Experiment 1,"Germany,Indonesia,Kenya,United States of America",Homo sapiens,Mucosa of vagina,UBERON:0004983,Ethnic group,EFO:0001799,"Combination of groups - African American (AA), Afro-Caribbean (AC), Asian Indonesian (AI) and African Kenyan (AK) women",Main group - Caucasian German (CG) women,Caucasian German women with varying vaginal microbiome compositions.,113,38,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,3 October 2024,Chrisawoke,"Chrisawoke,WikiWorks","Linear discriminant analysis plot showing differentiating bacterial taxa of the vaginal microbiomes of the five ethnic groups (AA, African American; AC, Afro-Caribbean; AI, Asian Indonesian; AK, African Kenyan and CG, Caucasian German).",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemelliphila|s__Gemelliphila asaccharolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella montpellierensis",1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|2701|2702;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|1385|539738|3076174|502393;3379134|976|200643|171549|171552|838|419005;1783272|1239|909932|1843489|31977|29465|187328,Complete,ChiomaBlessing
bsdb:36518275/2/1,36518275,"cross-sectional observational, not case-control",36518275,https://doi.org/10.7717/peerj.14449,NA,"Roachford O.S.E., Alleyne A.T. , Nelson K.E.","Insights into the vaginal microbiome in a diverse group of women of African, Asian and European ancestries",PeerJ,2022,"Ancestries, CST subtypes, Community state types, Ethnicity, Gardnerella, Lactobacillus, Mycoplasma, Pathobionts, Prevotella, Vaginal microbiome",Experiment 2,"Germany,Indonesia,Kenya,United States of America",Homo sapiens,Mucosa of vagina,NA,Ethnic group,EFO:0001799,"Combination of groups - African American (AA), Afro-Caribbean (AC), Asian Indonesian (AI) and Caucasian German (CG) women",African Kenyan (AK) women,The vaginal microbiome compositions of African Kenyan women descent.,120,31,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,17 October 2024,Chrisawoke,"Chrisawoke,WikiWorks","Linear discriminant analysis plot showing differentiating bacterial taxa of the vaginal microbiomes of the five ethnic groups (AA, African American; AC, Afro-Caribbean; AI, Asian Indonesian; AK, African Kenyan and CG, Caucasian German).",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium pyruviciproducens",3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836;1783272|201174|1760|85007|1653|1716|598660,Complete,ChiomaBlessing
bsdb:36518275/3/1,36518275,"cross-sectional observational, not case-control",36518275,https://doi.org/10.7717/peerj.14449,NA,"Roachford O.S.E., Alleyne A.T. , Nelson K.E.","Insights into the vaginal microbiome in a diverse group of women of African, Asian and European ancestries",PeerJ,2022,"Ancestries, CST subtypes, Community state types, Ethnicity, Gardnerella, Lactobacillus, Mycoplasma, Pathobionts, Prevotella, Vaginal microbiome",Experiment 3,"Germany,Indonesia,Kenya,United States of America",Homo sapiens,Mucosa of vagina,NA,Ethnic group,EFO:0001799,"Combination of groups - African American (AA), Afro-Caribbean (AC), Caucasian German (CG) and African Kenyan (AK) women",Asian Indonesian (AI) women,Asian Indonesian women with different vaginal microbiome compositions.,115,36,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,17 October 2024,Chrisawoke,"Chrisawoke,WikiWorks","Linear discriminant analysis plot showing differentiating bacterial taxa of the vaginal microbiomes of the five ethnic groups (AA, African American; AC, Afro-Caribbean; AI, Asian Indonesian; AK, African Kenyan and CG, Caucasian German).",increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli,,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria|s__Fenollaria timonensis",1783272|1239|1737404|1737405|1570339|165779;1783272|1239|91061|1385;1783272|1239|91061;;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801;1783272|1239|1737404|1582879;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1257;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|91061|186826|1300|1301|1304;1783272|1239;1783272|1239|186801|186802;1783272|1239|186801|186802|1686313|1723384,Complete,ChiomaBlessing
bsdb:36518275/4/1,36518275,"cross-sectional observational, not case-control",36518275,https://doi.org/10.7717/peerj.14449,NA,"Roachford O.S.E., Alleyne A.T. , Nelson K.E.","Insights into the vaginal microbiome in a diverse group of women of African, Asian and European ancestries",PeerJ,2022,"Ancestries, CST subtypes, Community state types, Ethnicity, Gardnerella, Lactobacillus, Mycoplasma, Pathobionts, Prevotella, Vaginal microbiome",Experiment 4,"Germany,Kenya,Indonesia,United States of America",Homo sapiens,Mucosa of vagina,NA,Ethnic group,EFO:0001799,"Combination of groups - African American (AA), Caucasian German (CG), Asian Indonesian (AI) and African Kenyan (AK) women",Afro-Caribbean (AC) women,Vaginal microbiome compositions of Afro-Caribbean women descent.,133,18,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,17 October 2024,Chrisawoke,"Chrisawoke,WikiWorks","Linear discriminant analysis plot showing differentiating bacterial taxa of the vaginal microbiomes of the five ethnic groups (AA, African American; AC, Afro-Caribbean; AI, Asian Indonesian; AK, African Kenyan and CG, Caucasian German).",increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",1783272|1239|1737404|1737405|1570339|165779|33037;3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|976|200643|171549|171552|2974257|28127;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|1737404|1737405|1570339|162289|33031;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|28125;3379134|976|200643|171549|171552,Complete,ChiomaBlessing
bsdb:36518275/5/1,36518275,"cross-sectional observational, not case-control",36518275,https://doi.org/10.7717/peerj.14449,NA,"Roachford O.S.E., Alleyne A.T. , Nelson K.E.","Insights into the vaginal microbiome in a diverse group of women of African, Asian and European ancestries",PeerJ,2022,"Ancestries, CST subtypes, Community state types, Ethnicity, Gardnerella, Lactobacillus, Mycoplasma, Pathobionts, Prevotella, Vaginal microbiome",Experiment 5,"Germany,Indonesia,Kenya,United States of America",Homo sapiens,Mucosa of vagina,NA,Ethnic group,EFO:0001799,"Combination of groups - Caucasian German (CG), Afro-Caribbean (AC), Asian Indonesian (AI) and African Kenyan (AK) women",African American (AA) women,African American women with different vaginal microbiome compositions.,123,28,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,17 October 2024,Chrisawoke,"Chrisawoke,WikiWorks","Linear discriminant analysis plot showing differentiating bacterial taxa of the vaginal microbiomes of the five ethnic groups (AA, African American; AC, Afro-Caribbean; AI, Asian Indonesian; AK, African Kenyan and CG, Caucasian German).",increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,1783272|1239|91061|186826|33958|1578|47770,Complete,ChiomaBlessing
bsdb:36523636/1/1,36523636,case-control,36523636,https://doi.org/10.3389/fcimb.2022.943609,https://www.frontiersin.org/articles/10.3389/fcimb.2022.943609/full,"Morales C., Rojas G., Rebolledo C., Rojas-Herrera M., Arias-Carrasco R., Cuadros-Orellana S., Maracaja-Coutinho V., Saavedra K., Leal P., Lanas F., Salazar L.A. , Saavedra N.",Characterization of microbial communities from gut microbiota of hypercholesterolemic and control subjects,Frontiers in cellular and infection microbiology,2022,"16S rRNA sequencing, LDL cholesterol, LEfSe analysis, gut microbiota, microbial signature",Experiment 1,Chile,Homo sapiens,Feces,UBERON:0001988,Hypercholesterolemia,HP:0003124,normocholesterolemic individuals (controls),hypercholesterolemic (cases),Patients with hypercholesterolemia (concentration of LDL-C greater than 4.16mmol/L),30,27,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,8 March 2024,Abiola-Salako,"Abiola-Salako,Folakunmi,WikiWorks",Microbial taxa with Linear discriminant analysis (LDA) score greater than 2 present in hypercholesterolemic individuals (red) and controls (green). P-value <0.05,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis",1783272|1239|186801|186802|216572|216851;1783272|1239|909932|909929|1843491|970;3379134|256845|1313211|278082|255528|172900,Complete,Folakunmi
bsdb:36523636/1/2,36523636,case-control,36523636,https://doi.org/10.3389/fcimb.2022.943609,https://www.frontiersin.org/articles/10.3389/fcimb.2022.943609/full,"Morales C., Rojas G., Rebolledo C., Rojas-Herrera M., Arias-Carrasco R., Cuadros-Orellana S., Maracaja-Coutinho V., Saavedra K., Leal P., Lanas F., Salazar L.A. , Saavedra N.",Characterization of microbial communities from gut microbiota of hypercholesterolemic and control subjects,Frontiers in cellular and infection microbiology,2022,"16S rRNA sequencing, LDL cholesterol, LEfSe analysis, gut microbiota, microbial signature",Experiment 1,Chile,Homo sapiens,Feces,UBERON:0001988,Hypercholesterolemia,HP:0003124,normocholesterolemic individuals (controls),hypercholesterolemic (cases),Patients with hypercholesterolemia (concentration of LDL-C greater than 4.16mmol/L),30,27,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,8 March 2024,Abiola-Salako,"Abiola-Salako,Folakunmi,WikiWorks",Microbial taxa with Linear discriminant analysis (LDA) score greater than 2 present in hypercholesterolemic individuals (red) and controls (green). P-value <0.05.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanosphaera,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia",1783272|1239|91061|1385|186817;3379134|1224|1236|135613;1783272|201174|84998|84999|84107;1783272|1239|186801|186802;3366610|28890|183925|2158|2159|2316;33090|35493|3398|72025|3803|3814|508215,Complete,Folakunmi
bsdb:36527132/8/1,36527132,laboratory experiment,36527132,https://doi.org/10.1186/s40168-022-01399-5,NA,"Midha A., Jarquín-Díaz V.H., Ebner F., Löber U., Hayani R., Kundik A., Cardilli A., Heitlinger E., Forslund S.K. , Hartmann S.",Guts within guts: the microbiome of the intestinal helminth parasite Ascaris suum is derived but distinct from its host,Microbiome,2022,NA,Experiment 8,Germany,Sus scrofa domesticus,Jejunum,UBERON:0002115,Biological sex,PATO:0000047,Ascaris summ (Males),Ascaris suum (Females),Microbiome of intestines harvested from female adult Ascaris worms that were harvested from host's (pig) gut,NA,NA,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,"Figure 4D, Table S7",12 April 2024,Barrakat,"Barrakat,Scholastica,WikiWorks",Differentially abundant bacterial taxa in male versus female worms (Ascaris suum) present in German Landrace pig gut.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella jalaludinii,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|186801|186802|31979|1485;1783272|1239|909932|909929|1843491|52225|187979;1783272|1239|186801|3082720|186804|1505652;3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:36527132/8/2,36527132,laboratory experiment,36527132,https://doi.org/10.1186/s40168-022-01399-5,NA,"Midha A., Jarquín-Díaz V.H., Ebner F., Löber U., Hayani R., Kundik A., Cardilli A., Heitlinger E., Forslund S.K. , Hartmann S.",Guts within guts: the microbiome of the intestinal helminth parasite Ascaris suum is derived but distinct from its host,Microbiome,2022,NA,Experiment 8,Germany,Sus scrofa domesticus,Jejunum,UBERON:0002115,Biological sex,PATO:0000047,Ascaris summ (Males),Ascaris suum (Females),Microbiome of intestines harvested from female adult Ascaris worms that were harvested from host's (pig) gut,NA,NA,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,"Figure 4D, Table S7",12 April 2024,Barrakat,"Barrakat,Scholastica,WikiWorks",Differentially abundant bacterial taxa in male versus female worms (Ascaris suum) present in German Landrace pig gut.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Fibrobacterota|c__Fibrobacteria|o__Fibrobacterales|f__Fibrobacteraceae|g__Fibrobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus porcorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",3379134|976|200643|171549|171552|1283313;1783272|1239|909932|1843489|31977|39948;3379134|65842|204430|218872|204431|832;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300|1301|701526;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:36527132/9/1,36527132,laboratory experiment,36527132,https://doi.org/10.1186/s40168-022-01399-5,NA,"Midha A., Jarquín-Díaz V.H., Ebner F., Löber U., Hayani R., Kundik A., Cardilli A., Heitlinger E., Forslund S.K. , Hartmann S.",Guts within guts: the microbiome of the intestinal helminth parasite Ascaris suum is derived but distinct from its host,Microbiome,2022,NA,Experiment 9,Germany,Sus scrofa domesticus,Jejunum,UBERON:0002115,Interaction with host,GO:0051701,Host (Ascaris suum infected Pigs) Microbiome,Parasite (Ascaris suum) Microbiome,Microbiome of intestines harvested from female adult Ascaris worms that were harvested from host's (pig) gut,10,NA,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,"Figure 5A, Table S8",12 April 2024,Barrakat,"Barrakat,Scholastica,WikiWorks",Differentially abundant bacteria taxa in Host (Pig) versus Parasite (Ascaris suum) Microbiome,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239|186801|3085636|186803|1766253;3379134|976|200643|171549|171552|1283313;1783272|1239|186801|3085636|186803|653683;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|3085636|186803|28050;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|171552|838;3379134|1224|1236|72274|135621|286;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:36527132/9/2,36527132,laboratory experiment,36527132,https://doi.org/10.1186/s40168-022-01399-5,NA,"Midha A., Jarquín-Díaz V.H., Ebner F., Löber U., Hayani R., Kundik A., Cardilli A., Heitlinger E., Forslund S.K. , Hartmann S.",Guts within guts: the microbiome of the intestinal helminth parasite Ascaris suum is derived but distinct from its host,Microbiome,2022,NA,Experiment 9,Germany,Sus scrofa domesticus,Jejunum,UBERON:0002115,Interaction with host,GO:0051701,Host (Ascaris suum infected Pigs) Microbiome,Parasite (Ascaris suum) Microbiome,Microbiome of intestines harvested from female adult Ascaris worms that were harvested from host's (pig) gut,10,NA,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,"Figure 5A, Table S8",12 April 2024,Barrakat,"Barrakat,Scholastica,WikiWorks",Differentially abundant bacteria taxa in Host (Pig) versus Parasite (Ascaris suum) Microbiome,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Asaccharospora,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Pseudoscardovia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|s__uncultured Prevotellaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239|186801|3082720|186804|1505660;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|186802|186807|2740;3379134|976|200643|171549|171552|838;1783272|201174|1760|85004|31953|1302778;3379134|976|200643|171549|171552|370804;1783272|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:36532422/1/1,36532422,laboratory experiment,36532422,10.3389/fmicb.2022.1037257,NA,"Liu X., Zhang M., Wang X., Liu P., Wang L., Li Y., Wang X. , Ren F.",Fecal microbiota transplantation restores normal fecal composition and delays malignant development of mild chronic kidney disease in rats,Frontiers in microbiology,2022,"chronic kidney disease, fecal microbiota transplantation, lysine production, metagenomics, protein-bound uremic toxins",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Donor Sham rats,CKD/CKD (Donor chronic kidney disease) rats,The 5/6 nephrectomy rats which developed severe chronic kidney disease (CKD) after 10 months used as fecal donors for Fecal microbiota transplantation (FMT),5,5,NA,WMS,NA,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3C,7 May 2025,Tosin,Tosin,"Differential microbial species (Wilcoxon rank sum test). The vertical coordinates indicate the species names at different taxonomic levels, and the horizontal coordinates indicate the percentage value of the abundance of a species for that sample, with different colors indicating different groupings.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp. 1XD22-93,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron",3379134|976|200643|171549|815|816|820;3379134|1224|1236|91347|543|561|562;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|186802|216572|244127|2320082;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|818,Complete,KateRasheed
bsdb:36532422/1/2,36532422,laboratory experiment,36532422,10.3389/fmicb.2022.1037257,NA,"Liu X., Zhang M., Wang X., Liu P., Wang L., Li Y., Wang X. , Ren F.",Fecal microbiota transplantation restores normal fecal composition and delays malignant development of mild chronic kidney disease in rats,Frontiers in microbiology,2022,"chronic kidney disease, fecal microbiota transplantation, lysine production, metagenomics, protein-bound uremic toxins",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Donor Sham rats,CKD/CKD (Donor chronic kidney disease) rats,The 5/6 nephrectomy rats which developed severe chronic kidney disease (CKD) after 10 months used as fecal donors for Fecal microbiota transplantation (FMT),5,5,NA,WMS,NA,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3C,12 June 2025,Tosin,Tosin,"Differential microbial species (Wilcoxon rank sum test). The vertical coordinates indicate the species names at different taxonomic levels, and the horizontal coordinates indicate the percentage value of the abundance of a species for that sample, with different colors indicating different groupings.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus intestinalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,s__bacterium 1xD42-87",1783272|1239|91061|186826|33958|1578|151781;1783272|1239|91061|186826|33958|1578|33959;2320113,Complete,KateRasheed
bsdb:36532422/2/1,36532422,laboratory experiment,36532422,10.3389/fmicb.2022.1037257,NA,"Liu X., Zhang M., Wang X., Liu P., Wang L., Li Y., Wang X. , Ren F.",Fecal microbiota transplantation restores normal fecal composition and delays malignant development of mild chronic kidney disease in rats,Frontiers in microbiology,2022,"chronic kidney disease, fecal microbiota transplantation, lysine production, metagenomics, protein-bound uremic toxins",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,CKD/Sham (Donor sham) rats,CKD/CKD (Donor Chronic kidney disease) rats,"The 1/2 nephrectomy rats treated with a 3 week course of mixed antibiotics treatment (ampicillin, metronidazole, neomycin, and vancomycin according to the ratio 2:2:2:1) randomly assigned into the fecal microbiota transplantation (FMT) recipient group which received intestinal flora from Donor Chronic Kidney disease (CKD).",5,5,NA,WMS,NA,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6B,12 June 2025,Tosin,Tosin,Differentially expressed species abundance among rats (B) CKD/CKD (Donor Chronic kidney disease) VS CKD/Sham (Donor Sham),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp. 1XD22-93,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis",1783272|1239|186801|186802|216572|244127|2320082;3379134|976|200643|171549|815|816|820,Complete,KateRasheed
bsdb:36532422/2/2,36532422,laboratory experiment,36532422,10.3389/fmicb.2022.1037257,NA,"Liu X., Zhang M., Wang X., Liu P., Wang L., Li Y., Wang X. , Ren F.",Fecal microbiota transplantation restores normal fecal composition and delays malignant development of mild chronic kidney disease in rats,Frontiers in microbiology,2022,"chronic kidney disease, fecal microbiota transplantation, lysine production, metagenomics, protein-bound uremic toxins",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,CKD/Sham (Donor sham) rats,CKD/CKD (Donor Chronic kidney disease) rats,"The 1/2 nephrectomy rats treated with a 3 week course of mixed antibiotics treatment (ampicillin, metronidazole, neomycin, and vancomycin according to the ratio 2:2:2:1) randomly assigned into the fecal microbiota transplantation (FMT) recipient group which received intestinal flora from Donor Chronic Kidney disease (CKD).",5,5,NA,WMS,NA,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6B,12 June 2025,Tosin,Tosin,Differentially expressed species abundance among rats (B) CKD/CKD (Donor Chronic kidney disease) VS CKD/Sham (Donor Sham),decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus intestinalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii",1783272|1239|91061|186826|33958|1578|151781;1783272|1239|91061|186826|33958|1578|33959,Complete,KateRasheed
bsdb:36532422/4/1,36532422,laboratory experiment,36532422,10.3389/fmicb.2022.1037257,NA,"Liu X., Zhang M., Wang X., Liu P., Wang L., Li Y., Wang X. , Ren F.",Fecal microbiota transplantation restores normal fecal composition and delays malignant development of mild chronic kidney disease in rats,Frontiers in microbiology,2022,"chronic kidney disease, fecal microbiota transplantation, lysine production, metagenomics, protein-bound uremic toxins",Experiment 4,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Sham (no nephrectomy) rats,CKD/CKD (Donor Chronic kidney disease) rats,"The 1/2 nephrectomy rats treated with a 3 week course of mixed antibiotics treatment (ampicillin, metronidazole, neomycin, and vancomycin according to the ratio 2:2:2:1) randomly assigned into the fecal microbiota transplantation (FMT) recipient group which received intestinal flora from Donor Chronic Kidney disease (CKD).",5,5,NA,WMS,NA,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6D,13 June 2025,Tosin,Tosin,Differentially expressed species abundance among rats (D) Sham (no nephrectomy rats) VS CKD/CKD (Donor Chronic kidney disease) rats,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp. 1XD22-93",3379134|976|200643|171549|815|816|820;1783272|1239|186801|186802|216572|244127|2320082,Complete,KateRasheed
bsdb:36532422/4/2,36532422,laboratory experiment,36532422,10.3389/fmicb.2022.1037257,NA,"Liu X., Zhang M., Wang X., Liu P., Wang L., Li Y., Wang X. , Ren F.",Fecal microbiota transplantation restores normal fecal composition and delays malignant development of mild chronic kidney disease in rats,Frontiers in microbiology,2022,"chronic kidney disease, fecal microbiota transplantation, lysine production, metagenomics, protein-bound uremic toxins",Experiment 4,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Sham (no nephrectomy) rats,CKD/CKD (Donor Chronic kidney disease) rats,"The 1/2 nephrectomy rats treated with a 3 week course of mixed antibiotics treatment (ampicillin, metronidazole, neomycin, and vancomycin according to the ratio 2:2:2:1) randomly assigned into the fecal microbiota transplantation (FMT) recipient group which received intestinal flora from Donor Chronic Kidney disease (CKD).",5,5,NA,WMS,NA,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6D,13 June 2025,Tosin,Tosin,Differentially expressed species abundance among rats (D) Sham (no nephrectomy rats) VS CKD/CKD (Donor Chronic kidney disease) rats,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus intestinalis",1783272|1239|91061|186826|33958|1578|33959;1783272|1239|91061|186826|33958|1578|151781,Complete,KateRasheed
bsdb:36532422/5/1,36532422,laboratory experiment,36532422,10.3389/fmicb.2022.1037257,NA,"Liu X., Zhang M., Wang X., Liu P., Wang L., Li Y., Wang X. , Ren F.",Fecal microbiota transplantation restores normal fecal composition and delays malignant development of mild chronic kidney disease in rats,Frontiers in microbiology,2022,"chronic kidney disease, fecal microbiota transplantation, lysine production, metagenomics, protein-bound uremic toxins",Experiment 5,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,CKD (Chronic kidney disease- 1/2 nephrectomy rats),CKD/Sham (Donor Sham) rats,"The 1/2 nephrectomy rats treated with a 3 week course of mixed antibiotics treatment (ampicillin, metronidazole, neomycin, and vancomycin according to the ratio 2:2:2:1) randomly assigned into the fecal microbiota transplantation (FMT) recipient group which received intestinal flora from Donor Sham.",5,5,NA,WMS,NA,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6F,13 June 2025,Tosin,Tosin,Differentially expressed species abundance among rats (F) CKD (Chronic kidney disease- 1/2 nephrectomy rats without FMT) VS CKD/Sham (Donor Sham) rats,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,1783272|1239|91061|186826|33958|1578|33959,Complete,KateRasheed
bsdb:36532422/5/2,36532422,laboratory experiment,36532422,10.3389/fmicb.2022.1037257,NA,"Liu X., Zhang M., Wang X., Liu P., Wang L., Li Y., Wang X. , Ren F.",Fecal microbiota transplantation restores normal fecal composition and delays malignant development of mild chronic kidney disease in rats,Frontiers in microbiology,2022,"chronic kidney disease, fecal microbiota transplantation, lysine production, metagenomics, protein-bound uremic toxins",Experiment 5,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,CKD (Chronic kidney disease- 1/2 nephrectomy rats),CKD/Sham (Donor Sham) rats,"The 1/2 nephrectomy rats treated with a 3 week course of mixed antibiotics treatment (ampicillin, metronidazole, neomycin, and vancomycin according to the ratio 2:2:2:1) randomly assigned into the fecal microbiota transplantation (FMT) recipient group which received intestinal flora from Donor Sham.",5,5,NA,WMS,NA,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6F,13 June 2025,Tosin,Tosin,Differentially expressed species abundance among rats (F) CKD (Chronic kidney disease- 1/2 nephrectomy rats without FMT) VS CKD/Sham (Donor Sham) rats,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,3379134|976|200643|171549|815|816|820,Complete,KateRasheed
bsdb:36532754/1/1,36532754,laboratory experiment,36532754,10.3389/fphar.2022.1033069,NA,"Li R., Li M., Li B., Chen W.H. , Liu Z.",<i>Cannabis sativa</i> L. alleviates loperamide-induced constipation by modulating the composition of gut microbiota in mice,Frontiers in pharmacology,2022,"Butyricicoccus, Cannabis sativa L., Parasutterella, constipation, gut microbiota",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,Combination of Con (blank) and Lop + WECSL (Loperamide hydrochloride-induced constipation model + water extract of Cannabis sativa L.),Lop (Loperamide hydrochloride-induced constipation model),Mice injected with loperamide (10.0 mg/kg) twice a day for 2 weeks,16,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A and 6B,7 April 2025,Tosin,Tosin,Identification of most characteristic taxa among experimental groups by linear discriminant analysis (LDA) effect size (LEfSe).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] brachy",3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|3085636|186803|572511;1783272|201174|84998|1643822|1643826|644652;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3082720|543314|35517,Complete,KateRasheed
bsdb:36532754/2/1,36532754,laboratory experiment,36532754,10.3389/fphar.2022.1033069,NA,"Li R., Li M., Li B., Chen W.H. , Liu Z.",<i>Cannabis sativa</i> L. alleviates loperamide-induced constipation by modulating the composition of gut microbiota in mice,Frontiers in pharmacology,2022,"Butyricicoccus, Cannabis sativa L., Parasutterella, constipation, gut microbiota",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,Combination of Con (blank) and Lop (Loperamide hydrochloride-induced constipation model),Lop + WESCL (Loperamide hydrochloride-induced constipation model + water extract of Cannabis sativa L. ),Constipation mice pretreated with the water extract of Cannabis sativa L. (WECSL),16,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A and 6B,7 April 2025,Tosin,Tosin,Identification of most characteristic taxa among experimental groups by linear discriminant analysis (LDA) effect size (LEfSe).,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",1783272|1239|526524|526525|128827|174708;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085656|3085657|2039302;3379134|976|200643|171549|2005473|1918540;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|1506577,Complete,KateRasheed
bsdb:36532754/3/1,36532754,laboratory experiment,36532754,10.3389/fphar.2022.1033069,NA,"Li R., Li M., Li B., Chen W.H. , Liu Z.",<i>Cannabis sativa</i> L. alleviates loperamide-induced constipation by modulating the composition of gut microbiota in mice,Frontiers in pharmacology,2022,"Butyricicoccus, Cannabis sativa L., Parasutterella, constipation, gut microbiota",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,Combination of Lop (Loperamide hydrochloride-induced constipation model) and Lop +WESCL (Loperamide hydrochloride-induced constipation model + water extract of Cannabis sativa L.),Con (blank),Mice in the Con group were injected with the same volume of saline,16,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A and 6B,7 April 2025,Tosin,Tosin,Identification of most characteristic taxa among experimental groups by linear discriminant analysis (LDA) effect size (LEfSe).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",3379134|976|200643|171549|171550|239759;1783272|544448|31969|186332|186333|2086;3379134|976|200643|171549|815|816;3379134|200940|3031449|213115|194924|35832;95818|2093818|2093825|2171986|1331051;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803|1506553;3379134|976|200643|171549|2005473,Complete,KateRasheed
bsdb:36544085/1/1,36544085,case-control,36544085,10.1186/s12866-022-02730-8,NA,"Shabayek S., Abdellah A.M., Salah M., Ramadan M. , Fahmy N.",Alterations of the vaginal microbiome in healthy pregnant women positive for group B Streptococcus colonization during the third trimester,BMC microbiology,2022,"Group B Streptococcus, Healthy, Microbiome, Pregnant, Streptococcus agalactiae, Third trimester, Vagina",Experiment 1,Egypt,Homo sapiens,Vagina,UBERON:0000996,Streptococcal infection,EFO:1001476,GBS culture-negative pregnant women,GBS culture-positive pregnant women,Pregnant women who tested positive for Group B Streptococcus (GBS) by culture during the third trimester,22,22,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,"age,parity",NA,NA,increased,unchanged,increased,NA,NA,Signature 1,Figs. 3 and 4,21 March 2024,Ayibatari,"Ayibatari,Scholastica,WikiWorks",Linear discriminant analysis (LDA) effect size (LEfSe) biomarker analysis showing taxa with significant differential abundance in GBS culture-negative versus GBS culture-positive pregnant Egyptian women,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus coleohominis",1783272|1239;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|147802;1783272|1239|91061|186826|33958|1578|147802;1783272|1239|91061|186826|33958|2742598|181675,Complete,Svetlana up
bsdb:36544085/1/2,36544085,case-control,36544085,10.1186/s12866-022-02730-8,NA,"Shabayek S., Abdellah A.M., Salah M., Ramadan M. , Fahmy N.",Alterations of the vaginal microbiome in healthy pregnant women positive for group B Streptococcus colonization during the third trimester,BMC microbiology,2022,"Group B Streptococcus, Healthy, Microbiome, Pregnant, Streptococcus agalactiae, Third trimester, Vagina",Experiment 1,Egypt,Homo sapiens,Vagina,UBERON:0000996,Streptococcal infection,EFO:1001476,GBS culture-negative pregnant women,GBS culture-positive pregnant women,Pregnant women who tested positive for Group B Streptococcus (GBS) by culture during the third trimester,22,22,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,"age,parity",NA,NA,increased,unchanged,increased,NA,NA,Signature 2,Figs. 3 and 4,21 March 2024,Ayibatari,"Ayibatari,Scholastica,WikiWorks",Linear discriminant analysis (LDA) effect size (LEfSe) biomarker analysis showing taxa with significant differential abundance in GBS culture-negative versus GBS culture-positive pregnant Egyptian women,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Campylobacterota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella pickettii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma parvum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium urealyticum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius",1783272|201174;1783272|201174|1760|85004|31953;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294;3379134|29547;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;3384189|32066|203490;1783272|201174|1760|85004|31953|2701;1783272|201174|1760|85004|31953|2701|2914924;3384189|32066|203490|203491|1129771;1783272|544448|31969|2085|2092;1783272|544448;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1257;3379134|1224;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|544448|2790996|2790998|2129;1783272|544448|2790996|2790998|2129|134821;1783272|201174|1760|85007|1653|1716|43771;1783272|1239|186801|3082720|186804|1257|1261,Complete,Svetlana up
bsdb:36563663/1/1,36563663,time series / longitudinal observational,36563663,https://doi.org/10.1016/j.cell.2022.11.023,NA,"Vatanen T., Jabbar K.S., Ruohtula T., Honkanen J., Avila-Pacheco J., Siljander H., Stražar M., Oikarinen S., Hyöty H., Ilonen J., Mitchell C.M., Yassour M., Virtanen S.M., Clish C.B., Plichta D.R., Vlamakis H., Knip M. , Xavier R.J.",Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism,Cell,2022,"gut metabolome, horizontal gene transfer, infant gut microbiome, mother-to-infant microbiome transmission",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Postpartum,EFO:0008562,Gestational week 27,Mothers at delivery,Women at the time of childbirth,69,63,NA,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.25,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2A,22 January 2025,Miss Lulu,"Miss Lulu,WikiWorks",Differences in species at delivery compared to gestational week 27,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula",1783272|1239|91061|186826|33958|1578|1579;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|909932|1843489|31977|29465|29466,Complete,Svetlana up
bsdb:36563663/1/2,36563663,time series / longitudinal observational,36563663,https://doi.org/10.1016/j.cell.2022.11.023,NA,"Vatanen T., Jabbar K.S., Ruohtula T., Honkanen J., Avila-Pacheco J., Siljander H., Stražar M., Oikarinen S., Hyöty H., Ilonen J., Mitchell C.M., Yassour M., Virtanen S.M., Clish C.B., Plichta D.R., Vlamakis H., Knip M. , Xavier R.J.",Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism,Cell,2022,"gut metabolome, horizontal gene transfer, infant gut microbiome, mother-to-infant microbiome transmission",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Postpartum,EFO:0008562,Gestational week 27,Mothers at delivery,Women at the time of childbirth,69,63,NA,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.25,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2A,22 January 2025,Miss Lulu,"Miss Lulu,WikiWorks",Differences in species at delivery compared to gestational week 27,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:145,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:299,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:274,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella minuta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus|s__Monoglobus pectinilyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia ilealis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii",1783272|1239|186801|186802|216572|244127|169435;1783272|1239|1263005;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|526524|526525|2810281|191303|154288;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|186802|31979|1485|1262792;1783272|1239|186801|186802|186806|1730|1262888;1783272|1239|186801|3082768|990719|990721|626937;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085656|3085657|2039302|1981510;1783272|1239|186801|3082720|186804|1501226|1115758;3379134|976|200643|171549|171550|239759|328814,Complete,Svetlana up
bsdb:36563663/2/1,36563663,time series / longitudinal observational,36563663,https://doi.org/10.1016/j.cell.2022.11.023,NA,"Vatanen T., Jabbar K.S., Ruohtula T., Honkanen J., Avila-Pacheco J., Siljander H., Stražar M., Oikarinen S., Hyöty H., Ilonen J., Mitchell C.M., Yassour M., Virtanen S.M., Clish C.B., Plichta D.R., Vlamakis H., Knip M. , Xavier R.J.",Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism,Cell,2022,"gut metabolome, horizontal gene transfer, infant gut microbiome, mother-to-infant microbiome transmission",Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Postpartum,EFO:0008562,Women at gestational week 27,Women at 3 months postpartum,Mothers at their third month after childbirth.,69,64,NA,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.25,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2A,23 January 2025,Miss Lulu,"Miss Lulu,WikiWorks",Differences in species at 3 months postpartum compared to gestational week 27,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus",3379134|976|200643|171549|815|816|338188;1783272|1239|909932|1843489|31977|39948|218538,Complete,Svetlana up
bsdb:36563663/2/2,36563663,time series / longitudinal observational,36563663,https://doi.org/10.1016/j.cell.2022.11.023,NA,"Vatanen T., Jabbar K.S., Ruohtula T., Honkanen J., Avila-Pacheco J., Siljander H., Stražar M., Oikarinen S., Hyöty H., Ilonen J., Mitchell C.M., Yassour M., Virtanen S.M., Clish C.B., Plichta D.R., Vlamakis H., Knip M. , Xavier R.J.",Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism,Cell,2022,"gut metabolome, horizontal gene transfer, infant gut microbiome, mother-to-infant microbiome transmission",Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Postpartum,EFO:0008562,Women at gestational week 27,Women at 3 months postpartum,Mothers at their third month after childbirth.,69,64,NA,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.25,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2A,23 January 2025,Miss Lulu,"Miss Lulu,WikiWorks",Differences in species at 3months postpartum compared to gestational week 27,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas synergistica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium CHKCI006,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Pseudomonadati|p__Pseudomonadota|s__Proteobacteria bacterium CAG:139,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis",3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|817;3379134|200940|3031449|213115|194924|35832|35833;3379134|976|200643|171549|1853231|574697|544644;3379134|976|200643|171549|1853231|574697|544645;1783272|1239|186801|186802|1780379;1783272|1239|186801|3085636|186803|2719313|358743;3379134|976|200643|171549|1853231|283168|28118;3379134|1224|28216|80840|995019|577310|487175;3379134|1224|1262986;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|526524|526525|2810281|191303|154288;1783272|1239|186801|3085636|186803|2719313|333367;3379134|976|200643|171549|2005519|397864|487174,Complete,Svetlana up
bsdb:36563663/3/1,36563663,time series / longitudinal observational,36563663,https://doi.org/10.1016/j.cell.2022.11.023,NA,"Vatanen T., Jabbar K.S., Ruohtula T., Honkanen J., Avila-Pacheco J., Siljander H., Stražar M., Oikarinen S., Hyöty H., Ilonen J., Mitchell C.M., Yassour M., Virtanen S.M., Clish C.B., Plichta D.R., Vlamakis H., Knip M. , Xavier R.J.",Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism,Cell,2022,"gut metabolome, horizontal gene transfer, infant gut microbiome, mother-to-infant microbiome transmission",Experiment 3,Finland,Homo sapiens,Feces,UBERON:0001988,Postpartum,EFO:0008562,Women at 3 months postpartum,Infants,Samples collected from infants up to 3 months old,64,74,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S3C,6 February 2025,Miss Lulu,"Miss Lulu,Aleru Divine,WikiWorks",Association of maternal B. cellulosilyticus with infant abundances of microbial glycoside hydrolases,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus",3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|674529;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|46506;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|820;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|1681;1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|1678|1689;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|28026;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|821,Complete,Svetlana up
bsdb:36563663/3/2,36563663,time series / longitudinal observational,36563663,https://doi.org/10.1016/j.cell.2022.11.023,NA,"Vatanen T., Jabbar K.S., Ruohtula T., Honkanen J., Avila-Pacheco J., Siljander H., Stražar M., Oikarinen S., Hyöty H., Ilonen J., Mitchell C.M., Yassour M., Virtanen S.M., Clish C.B., Plichta D.R., Vlamakis H., Knip M. , Xavier R.J.",Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism,Cell,2022,"gut metabolome, horizontal gene transfer, infant gut microbiome, mother-to-infant microbiome transmission",Experiment 3,Finland,Homo sapiens,Feces,UBERON:0001988,Postpartum,EFO:0008562,Women at 3 months postpartum,Infants,Samples collected from infants up to 3 months old,64,74,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S3C,13 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Association of maternal B. cellulosilyticus with infant abundances of microbial glycoside hydrolases,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,3379134|976|200643|171549|815|816|246787,Complete,Svetlana up
bsdb:36563663/4/1,36563663,time series / longitudinal observational,36563663,https://doi.org/10.1016/j.cell.2022.11.023,NA,"Vatanen T., Jabbar K.S., Ruohtula T., Honkanen J., Avila-Pacheco J., Siljander H., Stražar M., Oikarinen S., Hyöty H., Ilonen J., Mitchell C.M., Yassour M., Virtanen S.M., Clish C.B., Plichta D.R., Vlamakis H., Knip M. , Xavier R.J.",Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism,Cell,2022,"gut metabolome, horizontal gene transfer, infant gut microbiome, mother-to-infant microbiome transmission",Experiment 4,Finland,Homo sapiens,Feces,UBERON:0001988,Postpartum,EFO:0008562,Women at 3 months postpartum,Infants,Samples collected from infants up to 3 months old,64,74,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S3E,6 February 2025,Miss Lulu,"Miss Lulu,Aleru Divine,WikiWorks",Associations of maternal B. cellulosilyticus with species in infants up to 3 months old.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. HMSC035G02,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella intestinalis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella stercoris,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma|s__Enorma massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus rhamnosus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Tractidigestivibacter|s__Tractidigestivibacter scatoligenes,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma|s__[Collinsella] massiliensis",1783272|201174|1760|2037|2049|1654|1739406;1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|1678|28026;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|84998|84999|84107|102106|147207;1783272|201174|84998|84999|84107|102106|147206;1783272|201174|84998|84999|84107|1472762|1472761;3379134|976|200643|171549|171552|2974257|386414;1783272|1239|91061|186826|33958|2759736|47715;1783272|201174|84998|84999|1643824|2847313|1299998;1783272|201174|84998|84999|84107|1472762|1232426,Complete,Svetlana up
bsdb:36563663/4/2,36563663,time series / longitudinal observational,36563663,https://doi.org/10.1016/j.cell.2022.11.023,NA,"Vatanen T., Jabbar K.S., Ruohtula T., Honkanen J., Avila-Pacheco J., Siljander H., Stražar M., Oikarinen S., Hyöty H., Ilonen J., Mitchell C.M., Yassour M., Virtanen S.M., Clish C.B., Plichta D.R., Vlamakis H., Knip M. , Xavier R.J.",Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism,Cell,2022,"gut metabolome, horizontal gene transfer, infant gut microbiome, mother-to-infant microbiome transmission",Experiment 4,Finland,Homo sapiens,Feces,UBERON:0001988,Postpartum,EFO:0008562,Women at 3 months postpartum,Infants,Samples collected from infants up to 3 months old,64,74,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S3E,6 February 2025,Miss Lulu,"Miss Lulu,WikiWorks",Associations of maternal B. cellulosilyticus with species in infants up to 3 months old.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,1783272|1239|91061|186826|81852|1350|1351,Complete,Svetlana up
bsdb:36563663/5/1,36563663,time series / longitudinal observational,36563663,https://doi.org/10.1016/j.cell.2022.11.023,NA,"Vatanen T., Jabbar K.S., Ruohtula T., Honkanen J., Avila-Pacheco J., Siljander H., Stražar M., Oikarinen S., Hyöty H., Ilonen J., Mitchell C.M., Yassour M., Virtanen S.M., Clish C.B., Plichta D.R., Vlamakis H., Knip M. , Xavier R.J.",Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism,Cell,2022,"gut metabolome, horizontal gene transfer, infant gut microbiome, mother-to-infant microbiome transmission",Experiment 5,Finland,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Hydrolyzed Formula,Regular Formula,Standard infant formula (with the intention to treat).,107,111,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,"age,antibiotic exposure,breast feeding,delivery procedure,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,7 February 2025,Miss Lulu,"Miss Lulu,Aleru Divine,WikiWorks",Species difference between infants who received regular versus hydrolyzed formula (with intention to treat).,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinotignum|s__Actinotignum timonense,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium avidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia radingae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum|s__Varibaculum cambriense",1783272|201174|1760|2037|2049|1653174|1870995;1783272|201174|1760|85009|31957|1912216|33010;1783272|201174|1760|2037|2049|2529408|131110;1783272|1239|91061|186826|1300|1301|1308;1783272|201174|1760|2037|2049|184869|184870,Complete,Svetlana up
bsdb:36563663/5/2,36563663,time series / longitudinal observational,36563663,https://doi.org/10.1016/j.cell.2022.11.023,NA,"Vatanen T., Jabbar K.S., Ruohtula T., Honkanen J., Avila-Pacheco J., Siljander H., Stražar M., Oikarinen S., Hyöty H., Ilonen J., Mitchell C.M., Yassour M., Virtanen S.M., Clish C.B., Plichta D.R., Vlamakis H., Knip M. , Xavier R.J.",Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism,Cell,2022,"gut metabolome, horizontal gene transfer, infant gut microbiome, mother-to-infant microbiome transmission",Experiment 5,Finland,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Hydrolyzed Formula,Regular Formula,Standard infant formula (with the intention to treat).,107,111,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,"age,antibiotic exposure,breast feeding,delivery procedure,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5A,7 February 2025,Miss Lulu,"Miss Lulu,Aleru Divine,WikiWorks",Species difference between infants who received regular versus hydrolyzed formula (with intention to treat).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum",1783272|1239|186801|3085636|186803|2316020|33038;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|1385|90964|1279|1290;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|186801|186802|31979|1485|1522,Complete,Svetlana up
bsdb:36563663/6/1,36563663,time series / longitudinal observational,36563663,https://doi.org/10.1016/j.cell.2022.11.023,NA,"Vatanen T., Jabbar K.S., Ruohtula T., Honkanen J., Avila-Pacheco J., Siljander H., Stražar M., Oikarinen S., Hyöty H., Ilonen J., Mitchell C.M., Yassour M., Virtanen S.M., Clish C.B., Plichta D.R., Vlamakis H., Knip M. , Xavier R.J.",Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism,Cell,2022,"gut metabolome, horizontal gene transfer, infant gut microbiome, mother-to-infant microbiome transmission",Experiment 6,Finland,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Hydrolyzed Formula,Regular Formula,Standard infant formula (Real use),107,111,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,"age,antibiotic exposure,breast feeding,delivery procedure,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,7 February 2025,Miss Lulu,"Miss Lulu,Aleru Divine,WikiWorks",Species difference between infants who received regular versus hydrolyzed formula.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium|s__Atopobium deltae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia radingae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum|s__Varibaculum cambriense",1783272|201174|84998|84999|1643824|1380|1393034;1783272|1239|91061|186826|81852|1350|1351;1783272|201174|1760|2037|2049|2529408|131110;1783272|1239|91061|186826|1300|1301|1308;1783272|201174|1760|2037|2049|184869|184870,Complete,Svetlana up
bsdb:36563663/6/2,36563663,time series / longitudinal observational,36563663,https://doi.org/10.1016/j.cell.2022.11.023,NA,"Vatanen T., Jabbar K.S., Ruohtula T., Honkanen J., Avila-Pacheco J., Siljander H., Stražar M., Oikarinen S., Hyöty H., Ilonen J., Mitchell C.M., Yassour M., Virtanen S.M., Clish C.B., Plichta D.R., Vlamakis H., Knip M. , Xavier R.J.",Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism,Cell,2022,"gut metabolome, horizontal gene transfer, infant gut microbiome, mother-to-infant microbiome transmission",Experiment 6,Finland,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Hydrolyzed Formula,Regular Formula,Standard infant formula (Real use),107,111,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.25,TRUE,NA,"age,antibiotic exposure,breast feeding,delivery procedure,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5A,7 February 2025,Miss Lulu,"Miss Lulu,Aleru Divine,WikiWorks",Species difference between infants who received regular versus hydrolyzed formula.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica",1783272|201174|1760|2037|2049|1654|55565;3379134|976|200643|171549|815|816|47678;1783272|1239|186801|3085636|186803|2719313|358742;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|2316020|33038;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|909932|1843489|31977|29465|39777,Complete,Svetlana up
bsdb:36564416/1/1,36564416,"cross-sectional observational, not case-control",36564416,10.1038/s41598-022-25041-4,NA,"Yu Z., Qin E., Cheng S., Yang H., Liu R., Xu T., Liu Y., Yuan J., Yu S., Yang J. , Liang F.",Gut microbiome in PCOS associates to serum metabolomics: a cross-sectional study,Scientific reports,2022,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,healthy controls (HC),Polycystic Ovary Syndrome (PCOS),"This group consists of women diagnosed with Polycystic Ovary Syndrome (PCOS), based on the Rotterdam criteria, requiring at least two of the following: clinical and/or biochemical hyperandrogenism, oligo- and/or anovulation, and polycystic ovaries.",20,20,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,3.5,NA,geographic area,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 3D,27 January 2025,Joiejoie,"Joiejoie,WikiWorks",Differential abundance of microbial taxa in relation to PCOS (Polycystic Ovary Syndrome).,increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",1783272|201174|84992;3379134|976|200643|171549|171550|239759;3379134|1224|28211;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|1940338;3379134|1224|1236;3379134|1224;3379134|976|200643|171549|171550,Complete,Svetlana up
bsdb:36564416/1/2,36564416,"cross-sectional observational, not case-control",36564416,10.1038/s41598-022-25041-4,NA,"Yu Z., Qin E., Cheng S., Yang H., Liu R., Xu T., Liu Y., Yuan J., Yu S., Yang J. , Liang F.",Gut microbiome in PCOS associates to serum metabolomics: a cross-sectional study,Scientific reports,2022,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,healthy controls (HC),Polycystic Ovary Syndrome (PCOS),"This group consists of women diagnosed with Polycystic Ovary Syndrome (PCOS), based on the Rotterdam criteria, requiring at least two of the following: clinical and/or biochemical hyperandrogenism, oligo- and/or anovulation, and polycystic ovaries.",20,20,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,3.5,NA,geographic area,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 3D,29 January 2025,Joiejoie,"Joiejoie,Taofeecoh,Svetlana up,WikiWorks,Tosin",Differential abundance of microbial taxa in relation to PCOS (Polycystic Ovary Syndrome).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:352",1783272|1239|186801|3082768|990719;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|31979|1266;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|31979|1485|1262798,Complete,Svetlana up
bsdb:36566290/1/1,36566290,prospective cohort,36566290,10.1038/s41598-022-26058-5,NA,"You Y.A., Park S., Kim K., Kwon E.J., Hur Y.M., Kim S.M., Lee G., Ansari A., Park J. , Kim Y.J.",Transition in vaginal Lactobacillus species during pregnancy and prediction of preterm birth in Korean women,Scientific reports,2022,NA,Experiment 1,Republic of Korea,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Birth measurement,EFO:0006921,Full Term or Term Birth (FTB or TB) by Gestational Age at Sampling < 24weeks (GAS < 24weeks) - Timepoint A,Preterm birth (PTB)  by Gestational Age at Sampling < 24weeks (GAS < 24weeks) - Timepoint A,Preterm birth (PTB) is defined as delivery at less than 37 weeks of gestation and accounts for 8% of childbirths in South Korea,42,14,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 2A,12 February 2025,KateRasheed,"KateRasheed,WikiWorks",FTB- or PTB-associated microbiome using linear discriminant analysis effect size,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus simulans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis",1783272|1239|91061|1385|90964|1279|1286;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|459786|1263547;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|204475|745368,Complete,KateRasheed
bsdb:36566290/2/1,36566290,prospective cohort,36566290,10.1038/s41598-022-26058-5,NA,"You Y.A., Park S., Kim K., Kwon E.J., Hur Y.M., Kim S.M., Lee G., Ansari A., Park J. , Kim Y.J.",Transition in vaginal Lactobacillus species during pregnancy and prediction of preterm birth in Korean women,Scientific reports,2022,NA,Experiment 2,Republic of Korea,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Birth measurement,EFO:0006921,Full Term or Term Birth (FTB or TB) by Gestational Age at Sampling 24 - < 32weeks (GAS 24 - < 32weeks) - Timepoint B,Preterm birth (PTB)  by Gestational Age at Sampling 24 - < 32weeks (GAS 24 - < 32weeks) - Timepoint B,Preterm birth (PTB) is defined as delivery at less than 37 weeks of gestation and accounts for 8% of childbirths in South Korea,26,23,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Fig. 2A,12 February 2025,KateRasheed,"KateRasheed,WikiWorks",FTB- or PTB-associated microbiome using linear discriminant analysis effect size,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Faucicola|s__Faucicola osloensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma parvum",3379134|1224|1236|2887326|468|1604696|34062;1783272|201174|1760|85009|31957|1912216|1747;1783272|544448|2790996|2790998|2129|134821,Complete,KateRasheed
bsdb:36566290/3/1,36566290,prospective cohort,36566290,10.1038/s41598-022-26058-5,NA,"You Y.A., Park S., Kim K., Kwon E.J., Hur Y.M., Kim S.M., Lee G., Ansari A., Park J. , Kim Y.J.",Transition in vaginal Lactobacillus species during pregnancy and prediction of preterm birth in Korean women,Scientific reports,2022,NA,Experiment 3,Republic of Korea,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Birth measurement,EFO:0006921,Full Term or Term Birth (FTB or TB) by Gestational Age at Sampling 32 - < 37weeks (GAS 32 - < 37weeks) - Timepoint C,Preterm birth (PTB)  by Gestational Age at Sampling 32 - < 37weeks (GAS 32 - < 37weeks) - Timepoint C,Preterm birth (PTB) is defined as delivery at less than 37 weeks of gestation and accounts for 8% of childbirths in South Korea,17,37,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 2A,12 February 2025,KateRasheed,"KateRasheed,WikiWorks",FTB- or PTB-associated microbiome using linear discriminant analysis effect size,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pseudescherichia|s__Pseudescherichia vulneris",1783272|1239|1737404|1737405|1570339|150022|1260;1783272|1239|91061|1385|90964|1279|1282;3379134|1224|1236|91347|543|2055880|566,Complete,KateRasheed
bsdb:36566290/4/1,36566290,prospective cohort,36566290,10.1038/s41598-022-26058-5,NA,"You Y.A., Park S., Kim K., Kwon E.J., Hur Y.M., Kim S.M., Lee G., Ansari A., Park J. , Kim Y.J.",Transition in vaginal Lactobacillus species during pregnancy and prediction of preterm birth in Korean women,Scientific reports,2022,NA,Experiment 4,Republic of Korea,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Birth measurement,EFO:0006921,Full Term or Term Birth (FTB or TB) by Gestational Age at Sampling < 24weeks (GAS < 24weeks) - Timepoint A,Preterm birth (PTB)  by Gestational Age at Sampling < 24weeks (GAS < 24weeks) - Timepoint A,Preterm birth (PTB) is defined as delivery at less than 37 weeks of gestation and accounts for 8% of childbirths in South Korea,42,14,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 2B,14 February 2025,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of the vaginal microbiome in women with FTB and PTB at each sampling time point using STAMP,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|186802|216572|459786|351091,Complete,KateRasheed
bsdb:36566290/5/1,36566290,prospective cohort,36566290,10.1038/s41598-022-26058-5,NA,"You Y.A., Park S., Kim K., Kwon E.J., Hur Y.M., Kim S.M., Lee G., Ansari A., Park J. , Kim Y.J.",Transition in vaginal Lactobacillus species during pregnancy and prediction of preterm birth in Korean women,Scientific reports,2022,NA,Experiment 5,Republic of Korea,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Birth measurement,EFO:0006921,Full Term or Term Birth (FTB or TB) by Gestational Age at Sampling 24 - < 32weeks (GAS 24 - < 32weeks) - Timepoint B,Preterm birth (PTB)  by Gestational Age at Sampling 24 - < 32weeks (GAS 24 - < 32weeks) - Timepoint B,Preterm birth (PTB) is defined as delivery at less than 37 weeks of gestation and accounts for 8% of childbirths in South Korea,26,23,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Fig. 2B,14 February 2025,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of the vaginal microbiome in women with FTB and PTB at each sampling time point using STAMP,increased,NA,NA,Complete,KateRasheed
bsdb:36566290/5/2,36566290,prospective cohort,36566290,10.1038/s41598-022-26058-5,NA,"You Y.A., Park S., Kim K., Kwon E.J., Hur Y.M., Kim S.M., Lee G., Ansari A., Park J. , Kim Y.J.",Transition in vaginal Lactobacillus species during pregnancy and prediction of preterm birth in Korean women,Scientific reports,2022,NA,Experiment 5,Republic of Korea,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Birth measurement,EFO:0006921,Full Term or Term Birth (FTB or TB) by Gestational Age at Sampling 24 - < 32weeks (GAS 24 - < 32weeks) - Timepoint B,Preterm birth (PTB)  by Gestational Age at Sampling 24 - < 32weeks (GAS 24 - < 32weeks) - Timepoint B,Preterm birth (PTB) is defined as delivery at less than 37 weeks of gestation and accounts for 8% of childbirths in South Korea,26,23,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Fig. 2B,14 February 2025,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of the vaginal microbiome in women with FTB and PTB at each sampling time point using STAMP,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,1783272|1239|91061|186826|33958|1578|147802,Complete,KateRasheed
bsdb:36566290/6/1,36566290,prospective cohort,36566290,10.1038/s41598-022-26058-5,NA,"You Y.A., Park S., Kim K., Kwon E.J., Hur Y.M., Kim S.M., Lee G., Ansari A., Park J. , Kim Y.J.",Transition in vaginal Lactobacillus species during pregnancy and prediction of preterm birth in Korean women,Scientific reports,2022,NA,Experiment 6,Republic of Korea,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,Birth measurement,EFO:0006921,Full Term or Term Birth (FTB or TB) by Gestational Age at Sampling 32 - < 37weeks (GAS 32 - < 37weeks) - Timepoint C,Preterm birth (PTB)  by Gestational Age at Sampling 32 - < 37weeks (GAS 32 - < 37weeks) - Timepoint C,Preterm birth (PTB) is defined as delivery at less than 37 weeks of gestation and accounts for 8% of childbirths in South Korea,17,37,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 2B,14 February 2025,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of the vaginal microbiome in women with FTB and PTB at each sampling time point using STAMP,increased,NA,NA,Complete,KateRasheed
bsdb:36573834/1/1,36573834,case-control,36573834,10.1080/19490976.2022.2157697,NA,"Su Q., Tun H.M., Liu Q., Yeoh Y.K., Mak J.W.Y., Chan F.K. , Ng S.C.",Gut microbiome signatures reflect different subtypes of irritable bowel syndrome,Gut microbes,2023,"Irritable bowel syndrome, depression, diet, gut microbiome, subtype",Experiment 1,"United Kingdom,United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Non-IBS1 (Non-irritable bowel syndrome 1),IBS-C (IBS-Constipation),"Patients diagnosed with IBS-C, a subtype of IBS characterized by constipation (difficulty passing stool)",180,180,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,alcohol drinking,body mass index,diet,geographic area,sex","age,alcohol drinking,diet,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2a, b and c and Supplemental. Table 3",25 October 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential microbial abundance between IBS-C and Non-IBS1,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,s__bacterium FCS020,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,s__bacterium ND3007",1783272|201174;1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|653683;1783272|1239|186801|3085636|186803|207244;1783272|1239;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|33042;1783272|201174|1760|85007|1653|1716;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|3085656|3085657|2039302;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|438033;1783272|1239|186801|186802|216572|292632;3379134|1224|1236|135624|83763|83770;3379134|1224|28216|80840|995019|40544;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|186802|216572|39492;1451755;1783272|1239|526524|526525|128827|331630;1783272|1239|186801|3085636|186803|297314;1783272|1239|186801|186802|216572|707003;1452070,Complete,Folakunmi
bsdb:36573834/1/2,36573834,case-control,36573834,10.1080/19490976.2022.2157697,NA,"Su Q., Tun H.M., Liu Q., Yeoh Y.K., Mak J.W.Y., Chan F.K. , Ng S.C.",Gut microbiome signatures reflect different subtypes of irritable bowel syndrome,Gut microbes,2023,"Irritable bowel syndrome, depression, diet, gut microbiome, subtype",Experiment 1,"United Kingdom,United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Non-IBS1 (Non-irritable bowel syndrome 1),IBS-C (IBS-Constipation),"Patients diagnosed with IBS-C, a subtype of IBS characterized by constipation (difficulty passing stool)",180,180,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,alcohol drinking,body mass index,diet,geographic area,sex","age,alcohol drinking,diet,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2a, b and c and Supplemental Table 3",26 October 2023,ChiomaBlessing,"ChiomaBlessing,Folakunmi,Joan Chuks,WikiWorks",Differential microbial abundance between IBS-C and Non-IBS1,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__Eubacteriales Family XIII. Incertae Sedis bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Frisingicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|g__Negativibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Pseudomonadati|p__Thermodesulfobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Diplocloster",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|2005519|397864;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801;1783272|1239|186801|3082720|543314|2137877;3379134|1224|28216|80840|80864|80865;3379134|200940|3031449|213115|194924|872;1783272|1239|526524|526525|128827|1472649;1783272|1239|186801|3085636|186803|1432051;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|186806|1730;1783272|1239|526524|526525|128827|1573534;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|1918511;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|186802|216572|596767;1783272|1239|186801|186802|1392389;1783272|1239|1980693;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|216572|1508657;3379134|200940;1783272|1239|186801|186802|31979|1485|1522;1783272|1239|186801|3085636|186803|2918511,Complete,Folakunmi
bsdb:36573834/2/1,36573834,case-control,36573834,10.1080/19490976.2022.2157697,NA,"Su Q., Tun H.M., Liu Q., Yeoh Y.K., Mak J.W.Y., Chan F.K. , Ng S.C.",Gut microbiome signatures reflect different subtypes of irritable bowel syndrome,Gut microbes,2023,"Irritable bowel syndrome, depression, diet, gut microbiome, subtype",Experiment 2,"United Kingdom,United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Non-IBS2 (Non-irritable bowel syndrome 2),IBS-D (IBS-Diarrhea),"Patients diagnosed with IBS-D, a subtype of IBS characterized by diarrhea (watery stool)",302,302,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,alcohol drinking,body mass index,diet,geographic area,sex","age,alcohol drinking,diet,sex",NA,decreased,NA,NA,NA,decreased,Signature 1,"Figure 2a, b and c and Supplemental. Table 4",26 October 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential microbial abundance between IBS-D and Non-IBS2,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Candidatus Izemoplasmatales,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__Eubacteriales Family XIII. Incertae Sedis bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Azonexaceae|g__Dechloromonas,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Pseudomonadati|p__Lentisphaerota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,s__bacterium ND3007,k__Pseudomonadati|p__Lentisphaerota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|s__uncultured Clostridia bacterium",3379134|1224|28216|80840|506|222;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|2005519|397864;1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|3085636|186803|830;3379134|29547|3031852|213849|72294|194;1783272|544448|31969|2975519;1783272|1239|186801|3082768|990719;1783272|1239|186801|3082720|543314|2137877;1783272|1239|186801|3085636|186803|33042;1783272|1117;3379134|1224|28216|206389|2008795|73029;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|1686313;1783272|1239|186801|186802|216572|596767;3379134|256845;3379134|976|200643|171549|2005473;3379134|976|200643|171549|1853231|283168;3379134|1224|28216|80840|75682|846;3379134|1224|28216|80840|995019|577310;1783272|1239|1737404|1737405|1570339|162289;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|1263;3379134|1224|28216|80840|995019|40544;1783272|201174|1760|2037|2049|184869;1783272|1239|909932|1843489|31977|29465;3379134|256845|1313211|278082|255528|172900;1783272|1239|186801|186802|216572|39492;1452070;3379134|256845;1783272|1239|526524|526525|128827|331630;1783272|1239|186801|3085636|186803|297314;1783272|1239|186801|186802|216572|707003;1783272|1239|186801|244328,Complete,Folakunmi
bsdb:36573834/2/2,36573834,case-control,36573834,10.1080/19490976.2022.2157697,NA,"Su Q., Tun H.M., Liu Q., Yeoh Y.K., Mak J.W.Y., Chan F.K. , Ng S.C.",Gut microbiome signatures reflect different subtypes of irritable bowel syndrome,Gut microbes,2023,"Irritable bowel syndrome, depression, diet, gut microbiome, subtype",Experiment 2,"United Kingdom,United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Non-IBS2 (Non-irritable bowel syndrome 2),IBS-D (IBS-Diarrhea),"Patients diagnosed with IBS-D, a subtype of IBS characterized by diarrhea (watery stool)",302,302,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,alcohol drinking,body mass index,diet,geographic area,sex","age,alcohol drinking,diet,sex",NA,decreased,NA,NA,NA,decreased,Signature 2,"Figure 2a, b and c and Supplemental Table 4",26 October 2023,ChiomaBlessing,"ChiomaBlessing,Iram jamshed,Folakunmi,WikiWorks",Differential microbial abundance between IBS-D and Non-IBS2,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae",1783272|1239|91061|186826|186827|46123;1783272|1239|186801|3085636|186803|189330;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|216572|946234;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|3085636|186803|2569097|39488;3379134|1224|28211|204458|76892|41275;1783272|1239|186801|3085636|1185407,Complete,Folakunmi
bsdb:36573834/3/1,36573834,case-control,36573834,10.1080/19490976.2022.2157697,NA,"Su Q., Tun H.M., Liu Q., Yeoh Y.K., Mak J.W.Y., Chan F.K. , Ng S.C.",Gut microbiome signatures reflect different subtypes of irritable bowel syndrome,Gut microbes,2023,"Irritable bowel syndrome, depression, diet, gut microbiome, subtype",Experiment 3,"United Kingdom,United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Non-IBS3 (Non-irritable bowel syndrome 3),IBS-U (IBS-Unclassified),"Patients diagnosed with IBS-U, a distinct category characterized by normal formed stool",460,460,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,alcohol drinking,body mass index,diet,geographic area,sex","age,alcohol drinking,diet,sex",NA,decreased,NA,NA,NA,unchanged,Signature 1,"Figure 2a, b and c and Supplemental. Table 5",26 October 2023,ChiomaBlessing,"ChiomaBlessing,Folakunmi,WikiWorks",Differential microbial abundance between IBS-U and Non-IBS3,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Pseudomonadati|p__Lentisphaerota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|s__uncultured Erysipelotrichia bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|207244;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;3379134|29547|3031852|213849|72294|194;1783272|1239|526524|526525|2810280|135858;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|1686313;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|186801|3085636|186803|1407607;1783272|1239|91061|1385|539738|1378;1783272|1239|526524|526525|128827|1573535;1783272|1239|1737404|1737405|1570339|162289;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|292632;3379134|1224|28216|80840|995019|40544;1783272|1239|526524|526525|2810281|191303;1783272|201174|1760|2037|2049|184869;3379134|256845;1783272|1239|526524|666559;1783272|1239|186801|3085636|186803|297314;1783272|1239|91061|186826|81852|1350,Complete,Folakunmi
bsdb:36573834/3/2,36573834,case-control,36573834,10.1080/19490976.2022.2157697,NA,"Su Q., Tun H.M., Liu Q., Yeoh Y.K., Mak J.W.Y., Chan F.K. , Ng S.C.",Gut microbiome signatures reflect different subtypes of irritable bowel syndrome,Gut microbes,2023,"Irritable bowel syndrome, depression, diet, gut microbiome, subtype",Experiment 3,"United Kingdom,United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Non-IBS3 (Non-irritable bowel syndrome 3),IBS-U (IBS-Unclassified),"Patients diagnosed with IBS-U, a distinct category characterized by normal formed stool",460,460,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,alcohol drinking,body mass index,diet,geographic area,sex","age,alcohol drinking,diet,sex",NA,decreased,NA,NA,NA,unchanged,Signature 2,IBS-U (IBS-Unclassified),26 October 2023,ChiomaBlessing,"ChiomaBlessing,Folakunmi,WikiWorks",Differential microbial abundance between IBS-U and Non-IBS3,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Succiniclasticum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|1236|91347|543|1940338;3379134|1224|1236|72274|135621|286;1783272|1239|909932|1843488|909930|40840;1783272|1239|186801|3085636|186803|2316020|33039;3379134|1224,Complete,Folakunmi
bsdb:36573834/4/1,36573834,case-control,36573834,10.1080/19490976.2022.2157697,NA,"Su Q., Tun H.M., Liu Q., Yeoh Y.K., Mak J.W.Y., Chan F.K. , Ng S.C.",Gut microbiome signatures reflect different subtypes of irritable bowel syndrome,Gut microbes,2023,"Irritable bowel syndrome, depression, diet, gut microbiome, subtype",Experiment 4,"Canada,United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Depressive disorder,MONDO:0002050,IBS patients without depression,"IBS patients with depression in all three subtypes (IBS-D, IBS-C and IBS-U)","IBS patients with depression in all three subtypes (IBS-D, IBS-C and IBS-U)",134,134,6 months,16S,4,Illumina,relative abundances,MaAsLin2,0.05,FALSE,NA,"age,alcohol drinking,body mass index,diet,geographic area,sex","age,alcohol drinking,diet,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 3C, Results (text)",26 October 2023,ChiomaBlessing,"ChiomaBlessing,Atrayees,WikiWorks","Differential microbial abundance between IBS patients with depression in all three subtypes (IBS-D, IBS-C and IBS-U) and IBS patients without depression",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae",1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549|1853231|574697;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|186802|3085642,Complete,Folakunmi
bsdb:36573834/4/2,36573834,case-control,36573834,10.1080/19490976.2022.2157697,NA,"Su Q., Tun H.M., Liu Q., Yeoh Y.K., Mak J.W.Y., Chan F.K. , Ng S.C.",Gut microbiome signatures reflect different subtypes of irritable bowel syndrome,Gut microbes,2023,"Irritable bowel syndrome, depression, diet, gut microbiome, subtype",Experiment 4,"Canada,United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Depressive disorder,MONDO:0002050,IBS patients without depression,"IBS patients with depression in all three subtypes (IBS-D, IBS-C and IBS-U)","IBS patients with depression in all three subtypes (IBS-D, IBS-C and IBS-U)",134,134,6 months,16S,4,Illumina,relative abundances,MaAsLin2,0.05,FALSE,NA,"age,alcohol drinking,body mass index,diet,geographic area,sex","age,alcohol drinking,diet,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 3C, Results (text)",27 October 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks","Differential microbial abundance between IBS patients with depression in all three subtypes (IBS-D, IBS-C and IBS-U) and IBS patients without depression",increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,3379134|1224|1236|91347|1903414|583,Complete,Folakunmi
bsdb:36573834/5/1,36573834,case-control,36573834,10.1080/19490976.2022.2157697,NA,"Su Q., Tun H.M., Liu Q., Yeoh Y.K., Mak J.W.Y., Chan F.K. , Ng S.C.",Gut microbiome signatures reflect different subtypes of irritable bowel syndrome,Gut microbes,2023,"Irritable bowel syndrome, depression, diet, gut microbiome, subtype",Experiment 5,"United Kingdom,United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Non-IBS (Non-irritable bowel syndrome),IBS-C (IBS-Constipation) Validation Cohort,"Patients diagnosed with IBS-C, a subtype of IBS characterized by constipation (difficulty passing stool) in the Validation Cohort",44,44,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,alcohol drinking,body mass index,diet,geographic area,sex","age,alcohol drinking,diet,sex",NA,decreased,NA,NA,NA,decreased,Signature 1,Supplemental. Figure 5C,27 October 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential microbial abundance between IBS-C and Non-IBS (Validation cohort),decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota",1783272|1239;1783272|201174,Complete,Folakunmi
bsdb:36573834/5/2,36573834,case-control,36573834,10.1080/19490976.2022.2157697,NA,"Su Q., Tun H.M., Liu Q., Yeoh Y.K., Mak J.W.Y., Chan F.K. , Ng S.C.",Gut microbiome signatures reflect different subtypes of irritable bowel syndrome,Gut microbes,2023,"Irritable bowel syndrome, depression, diet, gut microbiome, subtype",Experiment 5,"United Kingdom,United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Non-IBS (Non-irritable bowel syndrome),IBS-C (IBS-Constipation) Validation Cohort,"Patients diagnosed with IBS-C, a subtype of IBS characterized by constipation (difficulty passing stool) in the Validation Cohort",44,44,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,alcohol drinking,body mass index,diet,geographic area,sex","age,alcohol drinking,diet,sex",NA,decreased,NA,NA,NA,decreased,Signature 2,Supplemental Figure 5C,27 October 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential microbial abundance between IBS-C and Non-IBS (Validation cohort),increased,k__Pseudomonadati|p__Verrucomicrobiota,3379134|74201,Complete,Folakunmi
bsdb:36573834/6/1,36573834,case-control,36573834,10.1080/19490976.2022.2157697,NA,"Su Q., Tun H.M., Liu Q., Yeoh Y.K., Mak J.W.Y., Chan F.K. , Ng S.C.",Gut microbiome signatures reflect different subtypes of irritable bowel syndrome,Gut microbes,2023,"Irritable bowel syndrome, depression, diet, gut microbiome, subtype",Experiment 6,"United Kingdom,United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Non-IBS (Non-irritable bowel syndrome),IBS-D (IBS-Diarrhea) Validation Cohort,"Patients diagnosed with IBS-D, a subtype of IBS characterized by diarrhea (watery stool) in the Validation Cohort",48,48,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,alcohol drinking,body mass index,diet,geographic area,sex","age,alcohol drinking,diet,sex",NA,decreased,NA,NA,NA,decreased,Signature 1,Supplemental Figure 5C,27 October 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential microbial abundance between IBS-D and Non-IBS (Validation cohort),decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Campylobacterota",1783272|201174;1783272|1239;3379134|29547,Complete,Folakunmi
bsdb:36573834/6/2,36573834,case-control,36573834,10.1080/19490976.2022.2157697,NA,"Su Q., Tun H.M., Liu Q., Yeoh Y.K., Mak J.W.Y., Chan F.K. , Ng S.C.",Gut microbiome signatures reflect different subtypes of irritable bowel syndrome,Gut microbes,2023,"Irritable bowel syndrome, depression, diet, gut microbiome, subtype",Experiment 6,"United Kingdom,United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Non-IBS (Non-irritable bowel syndrome),IBS-D (IBS-Diarrhea) Validation Cohort,"Patients diagnosed with IBS-D, a subtype of IBS characterized by diarrhea (watery stool) in the Validation Cohort",48,48,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,alcohol drinking,body mass index,diet,geographic area,sex","age,alcohol drinking,diet,sex",NA,decreased,NA,NA,NA,decreased,Signature 2,Supplemental Figure 5C,27 October 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential microbial abundance between IBS-D and Non-IBS (Validation cohort),increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,Folakunmi
bsdb:36573834/7/1,36573834,case-control,36573834,10.1080/19490976.2022.2157697,NA,"Su Q., Tun H.M., Liu Q., Yeoh Y.K., Mak J.W.Y., Chan F.K. , Ng S.C.",Gut microbiome signatures reflect different subtypes of irritable bowel syndrome,Gut microbes,2023,"Irritable bowel syndrome, depression, diet, gut microbiome, subtype",Experiment 7,"United Kingdom,United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Non-IBS (Non-irritable bowel syndrome),IBS-U (IBS-Unclassified) Validation Cohort,"Patients diagnosed with IBS-U, a distinct category characterized by normal formed stool in the Validation Cohort",61,61,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,alcohol drinking,body mass index,diet,geographic area,sex","age,alcohol drinking,diet,sex",NA,decreased,NA,NA,NA,decreased,Signature 1,Supplemental Figure 5C,27 October 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential microbial abundance between IBS-U and Non-IBS (Validation cohort),decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota",1783272|1239;1783272|201174,Complete,Folakunmi
bsdb:36573834/7/2,36573834,case-control,36573834,10.1080/19490976.2022.2157697,NA,"Su Q., Tun H.M., Liu Q., Yeoh Y.K., Mak J.W.Y., Chan F.K. , Ng S.C.",Gut microbiome signatures reflect different subtypes of irritable bowel syndrome,Gut microbes,2023,"Irritable bowel syndrome, depression, diet, gut microbiome, subtype",Experiment 7,"United Kingdom,United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Non-IBS (Non-irritable bowel syndrome),IBS-U (IBS-Unclassified) Validation Cohort,"Patients diagnosed with IBS-U, a distinct category characterized by normal formed stool in the Validation Cohort",61,61,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,alcohol drinking,body mass index,diet,geographic area,sex","age,alcohol drinking,diet,sex",NA,decreased,NA,NA,NA,decreased,Signature 2,Supplemental Figure 5C,27 October 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential microbial abundance between IBS-U and Non-IBS (Validation cohort),increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,Folakunmi
bsdb:36593694/1/1,36593694,meta-analysis,36593694,https://doi.org/10.1111/ene.15671,NA,"Kleine Bardenhorst S., Cereda E., Severgnini M., Barichella M., Pezzoli G., Keshavarzian A., Desideri A., Pietrucci D., Aho V.T.E., Scheperjans F., Hildebrand F., Weis S., Egert M., Karch A., Vital M. , Rübsamen N.",Gut microbiota dysbiosis in Parkinson disease: A systematic review and pooled analysis,European journal of neurology,2023,"Parkinson disease, brain-gut axis, dysbiosis, gastrointestinal microbiome, systematic review",Experiment 1,"Germany,Italy,Finland,United States of America,China",Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Control,Parkinson's Disease (PD) patients,Participants were classified as Parkinson's Disease (PD) patients after the use of UK Brain Bank criteria for the diagnosis of Parkinson's Disease (PD),751,1092,NA,16S,4,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 4,25 April 2025,Ese,"Ese,Victoria",Differentially abundant bacterial taxa in Parkinson's Disease patients,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|201174;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678,Complete,KateRasheed
bsdb:36593694/1/2,36593694,meta-analysis,36593694,https://doi.org/10.1111/ene.15671,NA,"Kleine Bardenhorst S., Cereda E., Severgnini M., Barichella M., Pezzoli G., Keshavarzian A., Desideri A., Pietrucci D., Aho V.T.E., Scheperjans F., Hildebrand F., Weis S., Egert M., Karch A., Vital M. , Rübsamen N.",Gut microbiota dysbiosis in Parkinson disease: A systematic review and pooled analysis,European journal of neurology,2023,"Parkinson disease, brain-gut axis, dysbiosis, gastrointestinal microbiome, systematic review",Experiment 1,"Germany,Italy,Finland,United States of America,China",Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Control,Parkinson's Disease (PD) patients,Participants were classified as Parkinson's Disease (PD) patients after the use of UK Brain Bank criteria for the diagnosis of Parkinson's Disease (PD),751,1092,NA,16S,4,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 4,28 April 2025,Ese,"Ese,Victoria",Differentially abundant bacterial taxa in Parkinson's Disease patients,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803,Complete,KateRasheed
bsdb:36593694/2/1,36593694,meta-analysis,36593694,https://doi.org/10.1111/ene.15671,NA,"Kleine Bardenhorst S., Cereda E., Severgnini M., Barichella M., Pezzoli G., Keshavarzian A., Desideri A., Pietrucci D., Aho V.T.E., Scheperjans F., Hildebrand F., Weis S., Egert M., Karch A., Vital M. , Rübsamen N.",Gut microbiota dysbiosis in Parkinson disease: A systematic review and pooled analysis,European journal of neurology,2023,"Parkinson disease, brain-gut axis, dysbiosis, gastrointestinal microbiome, systematic review",Experiment 2,"China,Finland,Germany,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Control,Parkinson's Disease (PD) patients,Participants were classified as Parkinson's Disease (PD) patients after the use of UK Brain Bank criteria for the diagnosis of Parkinson's Disease (PD),751,1092,NA,16S,4,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table 2,2 July 2025,Ese,"Ese,Victoria",Significant bacterial taxa identified while comparing individuals with Parkinson’s Disease (PD) to healthy controls (Results from a pooled analysis).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Acidaminobacteraceae|g__Acidaminobacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfurisporaceae|g__Desulfurispora,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XII. Incertae Sedis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Thermotogati|p__Synergistota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota",1783272|1239|186801|3082720|3118653|65402;3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|186802|3064153|510701;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|186802|543313;3379134|976|200643|171549|171551;3384194|508458|649775|649776|649777;3384194|508458;3379134|74201|203494|48461|203557;3379134|74201,Complete,KateRasheed
bsdb:36593694/2/2,36593694,meta-analysis,36593694,https://doi.org/10.1111/ene.15671,NA,"Kleine Bardenhorst S., Cereda E., Severgnini M., Barichella M., Pezzoli G., Keshavarzian A., Desideri A., Pietrucci D., Aho V.T.E., Scheperjans F., Hildebrand F., Weis S., Egert M., Karch A., Vital M. , Rübsamen N.",Gut microbiota dysbiosis in Parkinson disease: A systematic review and pooled analysis,European journal of neurology,2023,"Parkinson disease, brain-gut axis, dysbiosis, gastrointestinal microbiome, systematic review",Experiment 2,"China,Finland,Germany,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Control,Parkinson's Disease (PD) patients,Participants were classified as Parkinson's Disease (PD) patients after the use of UK Brain Bank criteria for the diagnosis of Parkinson's Disease (PD),751,1092,NA,16S,4,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Table 2,3 July 2025,Ese,"Ese,Victoria",Significant bacterial taxa identified while comparing individuals with Parkinson’s Disease (PD) to healthy controls (Results from a pooled analysis).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|841,Complete,KateRasheed
bsdb:36593694/3/1,36593694,meta-analysis,36593694,https://doi.org/10.1111/ene.15671,NA,"Kleine Bardenhorst S., Cereda E., Severgnini M., Barichella M., Pezzoli G., Keshavarzian A., Desideri A., Pietrucci D., Aho V.T.E., Scheperjans F., Hildebrand F., Weis S., Egert M., Karch A., Vital M. , Rübsamen N.",Gut microbiota dysbiosis in Parkinson disease: A systematic review and pooled analysis,European journal of neurology,2023,"Parkinson disease, brain-gut axis, dysbiosis, gastrointestinal microbiome, systematic review",Experiment 3,"China,Finland,Germany,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Control,Parkinson's Disease (PD) patients,Participants were classified as Parkinson's Disease (PD) patients after the use of UK Brain Bank criteria for the diagnosis of Parkinson's Disease (PD),751,1092,NA,16S,4,Illumina,centered log-ratio,ANCOM-BC,0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table SE1,5 July 2025,Ese,"Ese,Victoria",Differentially abundant bacterial taxa identified in a sub group meta analysis with confounders controlled for age and sex,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Acidaminobacteraceae|g__Acidaminobacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfurisporaceae|g__Desulfurispora,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XII. Incertae Sedis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota,k__Thermotogati|p__Synergistota",1783272|1239|186801|3082720|3118653|65402;3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|186802|216572|244127;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|3064153|510701;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|186802|543313;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836;3384194|508458|649775|649776|649777;3379134|74201|203494|48461|203557;3379134|74201;3384194|508458,Complete,KateRasheed
bsdb:36593694/3/2,36593694,meta-analysis,36593694,https://doi.org/10.1111/ene.15671,NA,"Kleine Bardenhorst S., Cereda E., Severgnini M., Barichella M., Pezzoli G., Keshavarzian A., Desideri A., Pietrucci D., Aho V.T.E., Scheperjans F., Hildebrand F., Weis S., Egert M., Karch A., Vital M. , Rübsamen N.",Gut microbiota dysbiosis in Parkinson disease: A systematic review and pooled analysis,European journal of neurology,2023,"Parkinson disease, brain-gut axis, dysbiosis, gastrointestinal microbiome, systematic review",Experiment 3,"China,Finland,Germany,Italy,United States of America",Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Control,Parkinson's Disease (PD) patients,Participants were classified as Parkinson's Disease (PD) patients after the use of UK Brain Bank criteria for the diagnosis of Parkinson's Disease (PD),751,1092,NA,16S,4,Illumina,centered log-ratio,ANCOM-BC,0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Table SE1,6 July 2025,Ese,Ese,Differentially abundant bacterial taxa identified in a sub group meta analysis with confounders controlled for age and sex,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;3379134|1224|1236|91347|543;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171552|838;3379134|1224;1783272|1239|186801|3085636|186803|841,Complete,KateRasheed
bsdb:36604616/1/1,36604616,"cross-sectional observational, not case-control",36604616,10.1186/s12866-022-02747-z,NA,"Chandiwana P., Munjoma P.T., Mazhandu A.J., Li J., Baertschi I., Wyss J., Jordi S.B.U., Mazengera L.R., Yilmaz B., Misselwitz B. , Duri K.",Antenatal gut microbiome profiles and effect on pregnancy outcome in HIV infected and HIV uninfected women in a resource limited setting,BMC microbiology,2023,"Birth weight, HIV infection, Microbiome, Microbiota, Pregnancy",Experiment 1,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Human immunodeficiency virus (HIV) - uninfected Pregnant women,Human immunodeficiency virus (HIV) - infected Pregnant women,Human immunodeficiency virus (HIV) - infected pregnant women who were recruited in Harare from 4 polyclinics serving populations with relatively poor socioeconomic status.,59,35,NA,16S,56,Ion Torrent,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 3a,17 October 2024,Tosin,"Tosin,WikiWorks",Taxonomic differences between the gut microbiota of HIV-infected women and healthy controls.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85006|1268;3379134|1224|1236|135624|83763|83770;3379134|1224|1236|135624|83763,Complete,Svetlana up
bsdb:36604616/1/2,36604616,"cross-sectional observational, not case-control",36604616,10.1186/s12866-022-02747-z,NA,"Chandiwana P., Munjoma P.T., Mazhandu A.J., Li J., Baertschi I., Wyss J., Jordi S.B.U., Mazengera L.R., Yilmaz B., Misselwitz B. , Duri K.",Antenatal gut microbiome profiles and effect on pregnancy outcome in HIV infected and HIV uninfected women in a resource limited setting,BMC microbiology,2023,"Birth weight, HIV infection, Microbiome, Microbiota, Pregnancy",Experiment 1,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Human immunodeficiency virus (HIV) - uninfected Pregnant women,Human immunodeficiency virus (HIV) - infected Pregnant women,Human immunodeficiency virus (HIV) - infected pregnant women who were recruited in Harare from 4 polyclinics serving populations with relatively poor socioeconomic status.,59,35,NA,16S,56,Ion Torrent,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Figure 3a,17 October 2024,Tosin,"Tosin,WikiWorks",Taxonomic differences between the gut microbiota of HIV-infected women and healthy controls.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|1853231;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;1783272|1239|186801|186802|216572|1263;3379134|203691|203692|136|137;3379134|203691|203692|136|2845253|157;1783272|1239|526524|526525|2810281|191303;1783272|1239|526524|526525|2810281,Complete,Svetlana up
bsdb:36604616/2/1,36604616,"cross-sectional observational, not case-control",36604616,10.1186/s12866-022-02747-z,NA,"Chandiwana P., Munjoma P.T., Mazhandu A.J., Li J., Baertschi I., Wyss J., Jordi S.B.U., Mazengera L.R., Yilmaz B., Misselwitz B. , Duri K.",Antenatal gut microbiome profiles and effect on pregnancy outcome in HIV infected and HIV uninfected women in a resource limited setting,BMC microbiology,2023,"Birth weight, HIV infection, Microbiome, Microbiota, Pregnancy",Experiment 2,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,Birth weight,EFO:0004344,Infants with High birthweight >2500g,Infants with Low birthweight <2500g,infants weighing less than 2500g at birth.,81,12,NA,16S,56,Ion Torrent,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,17 October 2024,Tosin,"Tosin,WikiWorks",Microbiota abundance and birth outcome. Taxonomic differences between the gut microbiota of groups stratified by baby birth weight,increased,"k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Spirochaetota",3379134|203691|203692|136|137;3379134|203691|203692|136|2845253|157;1783272|1239|909932|1843489|31977;3379134|203691,Complete,Svetlana up
bsdb:36604616/3/1,36604616,"cross-sectional observational, not case-control",36604616,10.1186/s12866-022-02747-z,NA,"Chandiwana P., Munjoma P.T., Mazhandu A.J., Li J., Baertschi I., Wyss J., Jordi S.B.U., Mazengera L.R., Yilmaz B., Misselwitz B. , Duri K.",Antenatal gut microbiome profiles and effect on pregnancy outcome in HIV infected and HIV uninfected women in a resource limited setting,BMC microbiology,2023,"Birth weight, HIV infection, Microbiome, Microbiota, Pregnancy",Experiment 3,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,Viral load,EFO:0010125,Human immunodeficiency virus (HIV) virally suppressed pregnant women (Viral Load ≤ 1000 copies/ml),Human immunodeficiency virus (HIV) virally un-suppressed pregnant women (Viral Load > 1000 copies/ml),HIV Un-suppressed pregnant women with viral load greater than 1000 cps/ml.,29,5,NA,16S,56,Ion Torrent,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 3b,18 October 2024,Tosin,"Tosin,WikiWorks",Taxonomic differences between the gut microbiota of groups stratified by viral load.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|577309,Complete,Svetlana up
bsdb:36604616/3/2,36604616,"cross-sectional observational, not case-control",36604616,10.1186/s12866-022-02747-z,NA,"Chandiwana P., Munjoma P.T., Mazhandu A.J., Li J., Baertschi I., Wyss J., Jordi S.B.U., Mazengera L.R., Yilmaz B., Misselwitz B. , Duri K.",Antenatal gut microbiome profiles and effect on pregnancy outcome in HIV infected and HIV uninfected women in a resource limited setting,BMC microbiology,2023,"Birth weight, HIV infection, Microbiome, Microbiota, Pregnancy",Experiment 3,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,Viral load,EFO:0010125,Human immunodeficiency virus (HIV) virally suppressed pregnant women (Viral Load ≤ 1000 copies/ml),Human immunodeficiency virus (HIV) virally un-suppressed pregnant women (Viral Load > 1000 copies/ml),HIV Un-suppressed pregnant women with viral load greater than 1000 cps/ml.,29,5,NA,16S,56,Ion Torrent,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 3b,18 October 2024,Tosin,"Tosin,WikiWorks",Taxonomic differences between the gut microbiota of groups stratified by viral load.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,1783272|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:36621696/1/1,36621696,"cross-sectional observational, not case-control",36621696,10.1016/j.micpath.2023.105970,NA,"Wen C., Pan Y., Gao M., Wang J., Huang K. , Tu P.",Altered gut microbiome composition in nontreated plaque psoriasis patients,Microbial pathogenesis,2023,"Disease severity, Gut microbiome, Healthy couples, Metagenomics sequencing, Psoriasis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Psoriasis vulgaris,EFO:1001494,Healthy controls,Psoriasis vulgaris,Patients diagnosed with Psoriasis vulgaris by two attending dermatologists.,15,32,6 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,race,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figures 2d, 2f",1 April 2025,Anne-mariesharp,Anne-mariesharp,Boxplot showing the difference of the relative abundance at the phylum and species level between psoriatic and healthy control samples,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota",3379134|976|200643|171549|815|816|820;3379134|976,Complete,Svetlana up
bsdb:36621696/1/2,36621696,"cross-sectional observational, not case-control",36621696,10.1016/j.micpath.2023.105970,NA,"Wen C., Pan Y., Gao M., Wang J., Huang K. , Tu P.",Altered gut microbiome composition in nontreated plaque psoriasis patients,Microbial pathogenesis,2023,"Disease severity, Gut microbiome, Healthy couples, Metagenomics sequencing, Psoriasis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Psoriasis vulgaris,EFO:1001494,Healthy controls,Psoriasis vulgaris,Patients diagnosed with Psoriasis vulgaris by two attending dermatologists.,15,32,6 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,race,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig 2d - f,1 April 2025,Anne-mariesharp,Anne-mariesharp,"Boxplot showing the difference of the relative abundance at the phylum, genus and species level between psoriatic and healthy control samples",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803|841|301301;1783272|1239;1783272|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:36621696/2/1,36621696,"cross-sectional observational, not case-control",36621696,10.1016/j.micpath.2023.105970,NA,"Wen C., Pan Y., Gao M., Wang J., Huang K. , Tu P.",Altered gut microbiome composition in nontreated plaque psoriasis patients,Microbial pathogenesis,2023,"Disease severity, Gut microbiome, Healthy couples, Metagenomics sequencing, Psoriasis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Psoriasis vulgaris,EFO:1001494,Healthy controls,Psoriasis vulgaris,Patients diagnosed with Psoriasis vulgaris by two attending dermatologists.,15,32,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,race,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig 2g,1 April 2025,Anne-mariesharp,Anne-mariesharp,Plot from LEfSe examination revealing enriched bacterial taxa related to either psoriasis individuals (green) or healthy controls (red),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",3379134|976|200643|171549|815|816|820;3379134|1224|1236|91347|543|561,Complete,Svetlana up
bsdb:36621696/2/2,36621696,"cross-sectional observational, not case-control",36621696,10.1016/j.micpath.2023.105970,NA,"Wen C., Pan Y., Gao M., Wang J., Huang K. , Tu P.",Altered gut microbiome composition in nontreated plaque psoriasis patients,Microbial pathogenesis,2023,"Disease severity, Gut microbiome, Healthy couples, Metagenomics sequencing, Psoriasis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Psoriasis vulgaris,EFO:1001494,Healthy controls,Psoriasis vulgaris,Patients diagnosed with Psoriasis vulgaris by two attending dermatologists.,15,32,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,race,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig 2g,1 April 2025,Anne-mariesharp,Anne-mariesharp,Plot from LEfSe examination revealing enriched bacterial taxa related to either psoriasis individuals (green) or healthy controls (red),decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,1783272|1239|186801|3085636|186803|841|301301,Complete,Svetlana up
bsdb:36621696/3/1,36621696,"cross-sectional observational, not case-control",36621696,10.1016/j.micpath.2023.105970,NA,"Wen C., Pan Y., Gao M., Wang J., Huang K. , Tu P.",Altered gut microbiome composition in nontreated plaque psoriasis patients,Microbial pathogenesis,2023,"Disease severity, Gut microbiome, Healthy couples, Metagenomics sequencing, Psoriasis",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Psoriasis vulgaris,EFO:1001494,Healthy partners(couples or spouses),Psoriasis vulgaris,Sub group of patients diagnosed with Psoriasis vulgaris by two attending dermatologists.,17,17,6 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig 3f,1 April 2025,Anne-mariesharp,Anne-mariesharp,Boxplot showing the difference of the relative abundance at the species level between psoriatic and healthy partners' samples,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,3379134|976|200643|171549|171550|239759|214856,Complete,Svetlana up
bsdb:36621696/3/2,36621696,"cross-sectional observational, not case-control",36621696,10.1016/j.micpath.2023.105970,NA,"Wen C., Pan Y., Gao M., Wang J., Huang K. , Tu P.",Altered gut microbiome composition in nontreated plaque psoriasis patients,Microbial pathogenesis,2023,"Disease severity, Gut microbiome, Healthy couples, Metagenomics sequencing, Psoriasis",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Psoriasis vulgaris,EFO:1001494,Healthy partners(couples or spouses),Psoriasis vulgaris,Sub group of patients diagnosed with Psoriasis vulgaris by two attending dermatologists.,17,17,6 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig 3f,1 April 2025,Anne-mariesharp,Anne-mariesharp,Boxplot showing the difference of the relative abundance at the species level between psoriatic and healthy partners' samples,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,3379134|976|200643|171549|815|816|28111,Complete,Svetlana up
bsdb:36621696/4/1,36621696,"cross-sectional observational, not case-control",36621696,10.1016/j.micpath.2023.105970,NA,"Wen C., Pan Y., Gao M., Wang J., Huang K. , Tu P.",Altered gut microbiome composition in nontreated plaque psoriasis patients,Microbial pathogenesis,2023,"Disease severity, Gut microbiome, Healthy couples, Metagenomics sequencing, Psoriasis",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Psoriasis vulgaris,EFO:1001494,Healthy partners(couples or spouses),Psoriasis vulgaris,Sub group of patients diagnosed with Psoriasis vulgaris by two attending dermatologists.,17,17,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig 3g,1 April 2025,Anne-mariesharp,Anne-mariesharp,Plot from LEfSe examination revealing enriched bacterial taxa related to either psoriasis individuals (green) or healthy partners (red).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii",3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|171550|239759|328813,Complete,Svetlana up
bsdb:36621696/4/2,36621696,"cross-sectional observational, not case-control",36621696,10.1016/j.micpath.2023.105970,NA,"Wen C., Pan Y., Gao M., Wang J., Huang K. , Tu P.",Altered gut microbiome composition in nontreated plaque psoriasis patients,Microbial pathogenesis,2023,"Disease severity, Gut microbiome, Healthy couples, Metagenomics sequencing, Psoriasis",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Psoriasis vulgaris,EFO:1001494,Healthy partners(couples or spouses),Psoriasis vulgaris,Sub group of patients diagnosed with Psoriasis vulgaris by two attending dermatologists.,17,17,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig 3g,1 April 2025,Anne-mariesharp,Anne-mariesharp,Plot from LEfSe examination revealing enriched bacterial taxa related to either psoriasis individuals (green) or healthy partners (red).,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,3379134|976|200643|171549|815|816|28111,Complete,Svetlana up
bsdb:36621696/5/1,36621696,"cross-sectional observational, not case-control",36621696,10.1016/j.micpath.2023.105970,NA,"Wen C., Pan Y., Gao M., Wang J., Huang K. , Tu P.",Altered gut microbiome composition in nontreated plaque psoriasis patients,Microbial pathogenesis,2023,"Disease severity, Gut microbiome, Healthy couples, Metagenomics sequencing, Psoriasis",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Psoriasis vulgaris,EFO:1001494,Healthy controls,Psoriasis vulgaris,Patients diagnosed with Psoriasis vulgaris by two attending dermatologists.,15,32,6 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,race,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig 4d,1 April 2025,Anne-mariesharp,Anne-mariesharp,Boxplot showing the difference of the relative abundance at the phylum level between psoriatic and healthy controls samples,increased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Svetlana up
bsdb:36621696/5/2,36621696,"cross-sectional observational, not case-control",36621696,10.1016/j.micpath.2023.105970,NA,"Wen C., Pan Y., Gao M., Wang J., Huang K. , Tu P.",Altered gut microbiome composition in nontreated plaque psoriasis patients,Microbial pathogenesis,2023,"Disease severity, Gut microbiome, Healthy couples, Metagenomics sequencing, Psoriasis",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Psoriasis vulgaris,EFO:1001494,Healthy controls,Psoriasis vulgaris,Patients diagnosed with Psoriasis vulgaris by two attending dermatologists.,15,32,6 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,race,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig 4d - f,1 April 2025,Anne-mariesharp,Anne-mariesharp,"Boxplot showing the difference of the relative abundance at the phylum, genus and species level between psoriatic and healthy controls samples",decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 8_1_57FAA,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis",1783272|1239;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|665951;3379134|976|200643|171549|815|909656|387090;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|166486,Complete,Svetlana up
bsdb:36621696/6/1,36621696,"cross-sectional observational, not case-control",36621696,10.1016/j.micpath.2023.105970,NA,"Wen C., Pan Y., Gao M., Wang J., Huang K. , Tu P.",Altered gut microbiome composition in nontreated plaque psoriasis patients,Microbial pathogenesis,2023,"Disease severity, Gut microbiome, Healthy couples, Metagenomics sequencing, Psoriasis",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Psoriasis vulgaris,EFO:1001494,Healthy partners(couples or spouses) & Healthy controls,Psoriasis vulgaris,Patients diagnosed with Psoriasis vulgaris by two attending dermatologists.,32,32,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,race,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig 4g,1 April 2025,Anne-mariesharp,Anne-mariesharp,Plot from LEfSe examination revealing enriched bacterial taxa related to either psoriasis individuals (pink) or healthy partners (green) or healthy controls (red),increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,3379134|1224|1236|91347|543|561|562,Complete,Svetlana up
bsdb:36621696/7/1,36621696,"cross-sectional observational, not case-control",36621696,10.1016/j.micpath.2023.105970,NA,"Wen C., Pan Y., Gao M., Wang J., Huang K. , Tu P.",Altered gut microbiome composition in nontreated plaque psoriasis patients,Microbial pathogenesis,2023,"Disease severity, Gut microbiome, Healthy couples, Metagenomics sequencing, Psoriasis",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Psoriasis vulgaris,EFO:1001494,Healthy controls & Psoriasis,Healthy partners(couples or spouses),Healthy partners of Psoriasis patients,47,17,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,race,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig 4g,1 April 2025,Anne-mariesharp,Anne-mariesharp,Plot from LEfSe examination revealing enriched bacterial taxa related to either psoriasis individuals (pink) or healthy partners (green) or healthy controls (red),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 3_1_19,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei",3379134|976|200643|171549|815|816|28111;3379134|976|200643|171549|815|816|469592;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|1649459|154046;1783272|1239|526524|526525|128827|123375|102148,Complete,Svetlana up
bsdb:36621696/8/1,36621696,"cross-sectional observational, not case-control",36621696,10.1016/j.micpath.2023.105970,NA,"Wen C., Pan Y., Gao M., Wang J., Huang K. , Tu P.",Altered gut microbiome composition in nontreated plaque psoriasis patients,Microbial pathogenesis,2023,"Disease severity, Gut microbiome, Healthy couples, Metagenomics sequencing, Psoriasis",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Psoriasis vulgaris,EFO:1001494,Healthy partners(couples or spouses) & Psoriasis,Healthy controls,Healthy controls(participants) with no Psoriasis,49,15,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,race,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig 4g,2 April 2025,Anne-mariesharp,Anne-mariesharp,Plot from LEfSe examination revealing enriched bacterial taxa related to either psoriasis individuals (pink) or healthy partners (green) or healthy controls (red).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 8_1_57FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis",1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|665951;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|91061|186826|33958|2767887|1623,Complete,Svetlana up
bsdb:36621696/10/1,36621696,"cross-sectional observational, not case-control",36621696,10.1016/j.micpath.2023.105970,NA,"Wen C., Pan Y., Gao M., Wang J., Huang K. , Tu P.",Altered gut microbiome composition in nontreated plaque psoriasis patients,Microbial pathogenesis,2023,"Disease severity, Gut microbiome, Healthy couples, Metagenomics sequencing, Psoriasis",Experiment 10,China,Homo sapiens,Feces,UBERON:0001988,Psoriasis vulgaris,EFO:1001494,Healthy controls,Healthy partners(couples or spouses),Healthy partners(couples or spouses) with no psoriasis,15,17,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig 5g,2 April 2025,Anne-mariesharp,Anne-mariesharp,Plot from LEfSe examination revealing enriched bacterial taxa related to either healthy partners (green) or healthy controls(red),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 3_1_19,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum",3379134|976|200643|171549|815|816|28111;3379134|976|200643|171549|815|816|469592;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|1649459|154046;3379134|1224|28216|80840|995019|577310|487175;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|186801|3085636|186803|2941495|1512,Complete,Svetlana up
bsdb:36621696/10/2,36621696,"cross-sectional observational, not case-control",36621696,10.1016/j.micpath.2023.105970,NA,"Wen C., Pan Y., Gao M., Wang J., Huang K. , Tu P.",Altered gut microbiome composition in nontreated plaque psoriasis patients,Microbial pathogenesis,2023,"Disease severity, Gut microbiome, Healthy couples, Metagenomics sequencing, Psoriasis",Experiment 10,China,Homo sapiens,Feces,UBERON:0001988,Psoriasis vulgaris,EFO:1001494,Healthy controls,Healthy partners(couples or spouses),Healthy partners(couples or spouses) with no psoriasis,15,17,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig 5g,2 April 2025,Anne-mariesharp,Anne-mariesharp,Plot from LEfSe examination revealing enriched bacterial taxa related to either healthy partners (green) or healthy controls(red),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Orthornavirae|p__Pisuviricota|c__Stelpaviricetes|o__Patatavirales|f__Potyviridae|g__Potyvirus|s__Potyvirus dasheenis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 8_1_57FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",1783272|1239|186801|3085636|186803|2569097|39488;4751|4890|3239874|2916678|766764|5475|5476;2732396|2732408|2732507|2732550|39729|12195|3240520;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|665951;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3082720|186804,Complete,Svetlana up
bsdb:36621696/11/1,36621696,"cross-sectional observational, not case-control",36621696,10.1016/j.micpath.2023.105970,NA,"Wen C., Pan Y., Gao M., Wang J., Huang K. , Tu P.",Altered gut microbiome composition in nontreated plaque psoriasis patients,Microbial pathogenesis,2023,"Disease severity, Gut microbiome, Healthy couples, Metagenomics sequencing, Psoriasis",Experiment 11,China,Homo sapiens,Feces,UBERON:0001988,Psoriasis vulgaris,EFO:1001494,Mild psoriasis,Moderate to severe psoriasis,Patients identified as having moderate to severe psoriasis based on a Psoriasis Area and Severity Index PASI score ≥10.,21,11,6 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Fig 6e, 6f",2 April 2025,Anne-mariesharp,Anne-mariesharp,Boxplot showing the difference of the relative abundance at the genus and species level between mild psoriasis and moderate-to-severe psoriasis,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella sp.",3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|547|550;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|171552|577309|2049036,Complete,Svetlana up
bsdb:36621696/11/2,36621696,"cross-sectional observational, not case-control",36621696,10.1016/j.micpath.2023.105970,NA,"Wen C., Pan Y., Gao M., Wang J., Huang K. , Tu P.",Altered gut microbiome composition in nontreated plaque psoriasis patients,Microbial pathogenesis,2023,"Disease severity, Gut microbiome, Healthy couples, Metagenomics sequencing, Psoriasis",Experiment 11,China,Homo sapiens,Feces,UBERON:0001988,Psoriasis vulgaris,EFO:1001494,Mild psoriasis,Moderate to severe psoriasis,Patients identified as having moderate to severe psoriasis based on a Psoriasis Area and Severity Index PASI score ≥10.,21,11,6 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Fig 6e, 6f",2 April 2025,Anne-mariesharp,Anne-mariesharp,Boxplot showing the difference of the relative abundance at the genus and species level between mild psoriasis and moderate-to-severe psoriasis,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis",1783272|1239|91061|1385|539738|1378;3379134|976|200643|171549|2005525|375288|328812;1783272|1239|186801|3085636|186803|841|166486,Complete,Svetlana up
bsdb:36621696/12/1,36621696,"cross-sectional observational, not case-control",36621696,10.1016/j.micpath.2023.105970,NA,"Wen C., Pan Y., Gao M., Wang J., Huang K. , Tu P.",Altered gut microbiome composition in nontreated plaque psoriasis patients,Microbial pathogenesis,2023,"Disease severity, Gut microbiome, Healthy couples, Metagenomics sequencing, Psoriasis",Experiment 12,China,Homo sapiens,Feces,UBERON:0001988,Psoriasis vulgaris,EFO:1001494,Mild psoriasis,Moderate to severe psoriasis,Patients identified as having moderate to severe psoriasis based on a Psoriasis Area and Severity Index PASI score ≥10.,21,11,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig 6g,2 April 2025,Anne-mariesharp,Anne-mariesharp,Plot from LEfSe examination revealing enriched bacterial taxa related to either mild psoriasis (red) or moderate-to-severe psoriasis(green).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella sp.",3379134|1224|1236|91347|543|547|550;3379134|976|200643|171549|171552|577309|2049036,Complete,Svetlana up
bsdb:36621696/12/2,36621696,"cross-sectional observational, not case-control",36621696,10.1016/j.micpath.2023.105970,NA,"Wen C., Pan Y., Gao M., Wang J., Huang K. , Tu P.",Altered gut microbiome composition in nontreated plaque psoriasis patients,Microbial pathogenesis,2023,"Disease severity, Gut microbiome, Healthy couples, Metagenomics sequencing, Psoriasis",Experiment 12,China,Homo sapiens,Feces,UBERON:0001988,Psoriasis vulgaris,EFO:1001494,Mild psoriasis,Moderate to severe psoriasis,Patients identified as having moderate to severe psoriasis based on a Psoriasis Area and Severity Index PASI score ≥10.,21,11,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig 6g,2 April 2025,Anne-mariesharp,Anne-mariesharp,Plot from LEfSe examination revealing enriched bacterial genera related to either mild psoriasis (red) or moderate-to-severe individuals(green).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis",3379134|976|200643|171549|2005525|375288|328812;1783272|1239|186801|3085636|186803|841|166486,Complete,Svetlana up
bsdb:36621696/13/1,36621696,"cross-sectional observational, not case-control",36621696,10.1016/j.micpath.2023.105970,NA,"Wen C., Pan Y., Gao M., Wang J., Huang K. , Tu P.",Altered gut microbiome composition in nontreated plaque psoriasis patients,Microbial pathogenesis,2023,"Disease severity, Gut microbiome, Healthy couples, Metagenomics sequencing, Psoriasis",Experiment 13,China,Homo sapiens,Feces,UBERON:0001988,Psoriasis vulgaris,EFO:1001494,Healthy controls,Healthy partners(couples or spouses),Healthy partners of psoriasis patients,15,17,6 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig 4d,5 April 2025,Anne-mariesharp,"Anne-mariesharp,Aleru Divine",Boxplot showing the difference of the relative abundance at the phylum level between healthy partners and healthy controls samples,increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii",3379134|976;3379134|976|200643|171549|815|816|28111,Complete,Svetlana up
bsdb:36621696/13/2,36621696,"cross-sectional observational, not case-control",36621696,10.1016/j.micpath.2023.105970,NA,"Wen C., Pan Y., Gao M., Wang J., Huang K. , Tu P.",Altered gut microbiome composition in nontreated plaque psoriasis patients,Microbial pathogenesis,2023,"Disease severity, Gut microbiome, Healthy couples, Metagenomics sequencing, Psoriasis",Experiment 13,China,Homo sapiens,Feces,UBERON:0001988,Psoriasis vulgaris,EFO:1001494,Healthy controls,Healthy partners(couples or spouses),Healthy partners of psoriasis patients,15,17,6 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig 4d - f,5 April 2025,Anne-mariesharp,Anne-mariesharp,"Boxplot showing the difference of the relative abundance at the phylum, genus and species level between healthy partners and healthy controls samples",decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 8_1_57FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus",1783272|1239;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|665951;1783272|1239|186801|3085636|186803|28050|39485;3379134|976|200643|171549|815|909656|387090,Complete,Svetlana up
bsdb:36621696/14/1,36621696,"cross-sectional observational, not case-control",36621696,10.1016/j.micpath.2023.105970,NA,"Wen C., Pan Y., Gao M., Wang J., Huang K. , Tu P.",Altered gut microbiome composition in nontreated plaque psoriasis patients,Microbial pathogenesis,2023,"Disease severity, Gut microbiome, Healthy couples, Metagenomics sequencing, Psoriasis",Experiment 14,China,Homo sapiens,Feces,UBERON:0001988,Psoriasis vulgaris,EFO:1001494,Healthy partners(couples or spouses),Psoriasis vulgaris,Patients diagnosed with Psoriasis vulgaris by two attending dermatologists.,17,32,6 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Fig 4d, 4f",5 April 2025,Anne-mariesharp,"Anne-mariesharp,Aleru Divine",Boxplot showing the difference of the relative abundance at the phylum and species level between psoriatic and healthy partners samples,increased,"k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis",3379134|976;1783272|1239|186801|3085636|186803|841|166486,Complete,Svetlana up
bsdb:36621696/14/2,36621696,"cross-sectional observational, not case-control",36621696,10.1016/j.micpath.2023.105970,NA,"Wen C., Pan Y., Gao M., Wang J., Huang K. , Tu P.",Altered gut microbiome composition in nontreated plaque psoriasis patients,Microbial pathogenesis,2023,"Disease severity, Gut microbiome, Healthy couples, Metagenomics sequencing, Psoriasis",Experiment 14,China,Homo sapiens,Feces,UBERON:0001988,Psoriasis vulgaris,EFO:1001494,Healthy partners(couples or spouses),Psoriasis vulgaris,Patients diagnosed with Psoriasis vulgaris by two attending dermatologists.,17,32,6 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig 4d - f,5 April 2025,Anne-mariesharp,"Anne-mariesharp,Aleru Divine","Boxplot showing the difference of the relative abundance at the phylum, genus and species level between psoriatic and healthy partners samples",decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens",1783272|1239;3379134|976|200643|171549|815|816|28111;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|28050|39485,Complete,Svetlana up
bsdb:36624530/1/1,36624530,case-control,36624530,10.1186/s40168-022-01450-5,NA,"Jacobs J.P., Lagishetty V., Hauer M.C., Labus J.S., Dong T.S., Toma R., Vuyisich M., Naliboff B.D., Lackner J.M., Gupta A., Tillisch K. , Mayer E.A.",Multi-omics profiles of the intestinal microbiome in irritable bowel syndrome and its bowel habit subtypes,Microbiome,2023,"Biomarkers, Bowel habit subtypes, Irritable bowel syndrome, Metabolomics, Metatranscriptomics, Microbiome, Multi-omics",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,Irritable Bowel Syndrome,Patients diagnosed with Irritable Bowel Syndrome via Rome III criteria,177,318,3 months,16S,4,Illumina,relative abundances,Random Forest Analysis,0.05,TRUE,NA,NA,"age,anxiety disorder,body mass index,diet,race,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2B,15 October 2023,Chisom,"Chisom,WikiWorks","Differentially abundant bacterial taxa (q < 0.25) between IBS subjects and HC were identified in multivariate models adjusting for batch, age, sex, race/ethnicity, BMI, dietary category, and HAD-A. The result of assessing the taxonomic profiles of the metatranscriptome.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fluxus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hydrogenotrophica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella morbi,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] hylemonae",1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549|815|816|626930;1783272|1239|186801|3085636|186803|572511|53443;1783272|1239|186801|3085636|186803|43996|43997;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|909932|1843488|909930|33024|626940;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|171552|2974257|386414;1783272|1239|186801|3085636|186803|1506553|89153,Complete,Peace Sandy
bsdb:36624530/1/2,36624530,case-control,36624530,10.1186/s40168-022-01450-5,NA,"Jacobs J.P., Lagishetty V., Hauer M.C., Labus J.S., Dong T.S., Toma R., Vuyisich M., Naliboff B.D., Lackner J.M., Gupta A., Tillisch K. , Mayer E.A.",Multi-omics profiles of the intestinal microbiome in irritable bowel syndrome and its bowel habit subtypes,Microbiome,2023,"Biomarkers, Bowel habit subtypes, Irritable bowel syndrome, Metabolomics, Metatranscriptomics, Microbiome, Multi-omics",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,Irritable Bowel Syndrome,Patients diagnosed with Irritable Bowel Syndrome via Rome III criteria,177,318,3 months,16S,4,Illumina,relative abundances,Random Forest Analysis,0.05,TRUE,NA,NA,"age,anxiety disorder,body mass index,diet,race,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2B,15 October 2023,Chisom,"Chisom,WikiWorks","Differentially abundant bacterial taxa (q < 0.25) between IBS subjects and HC were identified in multivariate models adjusting for batch, age, sex, race/ethnicity, BMI, dietary category, and HAD-A. The result of assessing the taxonomic profiles of the metatranscriptome.",decreased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola barnesiae",3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|3085636|186803|841|360807;1783272|201174|1760|85004|31953|1678|28025;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|909656|376804,Complete,Peace Sandy
bsdb:36625596/1/1,36625596,case-control,36625596,10.1128/spectrum.03796-22,NA,"Li Y., Qian F., Cheng X., Wang D., Wang Y., Pan Y., Chen L., Wang W. , Tian Y.",Dysbiosis of Oral Microbiota and Metabolite Profiles Associated with Type 2 Diabetes Mellitus,Microbiology spectrum,2023,"metabolomic, metagenomic, oral diseases, oral microbiome, type 2 diabetes mellitus",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Type II diabetes mellitus,MONDO:0005148,Healthy Control,Type 2 Diabetes Mellitus Patients,"Saliva samples of patients with Type 2 Diabetes Mellitus ( fasting plasma glucose (FPG)≥7.0 mmol/L, HbA1C ≥6.5%, and 2-h postprandial blood glucose (2-hPBG)≥11.1 mmol/L)",10,10,6 months,WMS,NA,MGISEQ-2000,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 1E,12 March 2024,Aishat,"Aishat,Folakunmi,WikiWorks",LEfSe analysis of salivary microorganisms in the T2DM (Type 2 Diabetes Mellitus) group and healthy control group,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella morbi,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__Eubacteriales Family XIII. Incertae Sedis bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Morococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema vincentii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Morococcus|s__Morococcus cerebrosus",3379134|1224|1236|135625|712|416916|739;1783272|1239|186801|3085636|186803|43996;1783272|1239|186801|3085636|186803|43996|43997;1783272|1239|186801;1783272|1239|186801|3082720|543314|2137877;1783272|1239|186801|186802|1898207;3384189|32066|203490|203491|203492|848|851;1783272|1239|186801|3085636|186803;3379134|1224|28216|206351|481|212742;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|1239|1737404|1737405|1570339;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836|837;3379134|976|200643|171549|171552|838|28129;1783272|201174|1760|85006|1268|32207|43675;3379134|203691|203692|136|137;3379134|203691|203692|136;3379134|203691|203692;3379134|203691|203692|136|2845253|157;3379134|203691|203692|136|2845253|157|69710;3379134|1224|28216|206351|481|212742|1056807,Complete,Folakunmi
bsdb:36625596/1/2,36625596,case-control,36625596,10.1128/spectrum.03796-22,NA,"Li Y., Qian F., Cheng X., Wang D., Wang Y., Pan Y., Chen L., Wang W. , Tian Y.",Dysbiosis of Oral Microbiota and Metabolite Profiles Associated with Type 2 Diabetes Mellitus,Microbiology spectrum,2023,"metabolomic, metagenomic, oral diseases, oral microbiome, type 2 diabetes mellitus",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Type II diabetes mellitus,MONDO:0005148,Healthy Control,Type 2 Diabetes Mellitus Patients,"Saliva samples of patients with Type 2 Diabetes Mellitus ( fasting plasma glucose (FPG)≥7.0 mmol/L, HbA1C ≥6.5%, and 2-h postprandial blood glucose (2-hPBG)≥11.1 mmol/L)",10,10,6 months,WMS,NA,MGISEQ-2000,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 1E,12 March 2024,Aishat,"Aishat,Folakunmi,WikiWorks",LEfSe analysis of salivary microorganisms in the T2DM (Type 2 Diabetes Mellitus) group and healthy control group,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,p__Candidatus Saccharimonadota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella aurantiaca",3379134|976|200643|171549|171552|1283313;3379134|1224|28216|80840|119060;3379134|1224|28216|80840;95818;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|80840|119060|47670|47671;3379134|976|200643|171549|171552|838|596085,Complete,Folakunmi
bsdb:36625596/2/1,36625596,case-control,36625596,10.1128/spectrum.03796-22,NA,"Li Y., Qian F., Cheng X., Wang D., Wang Y., Pan Y., Chen L., Wang W. , Tian Y.",Dysbiosis of Oral Microbiota and Metabolite Profiles Associated with Type 2 Diabetes Mellitus,Microbiology spectrum,2023,"metabolomic, metagenomic, oral diseases, oral microbiome, type 2 diabetes mellitus",Experiment 2,China,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Type II diabetes mellitus,MONDO:0005148,Healthy Control,Type 2 Diabetes Mellitus Patients,"Supragingival dental plaque samples of patients with Type 2 Diabetes Mellitus ( fasting plasma glucose (FPG)≥7.0 mmol/L, HbA1C ≥6.5%, and 2-h postprandial blood glucose (2-hPBG)≥11.1 mmol/L)",10,10,"6 months, 1 week",WMS,NA,MGISEQ-2000,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 1F,20 March 2024,Folakunmi,"Folakunmi,WikiWorks",LEfSe analysis of supragingival plaque samples between patients with type II diabetes and healthy controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sp. CM59,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sp. oral taxon 329",3379134|976|200643;3379134|976|117743|200644|49546|1016;3379134|976|117743|200644|49546|1016|45242;3379134|976|117743|200644|49546;3379134|976|117743|200644;3379134|976|117743|200644|49546|237;3379134|1224|28216|206351|481|482|484;3379134|976|200643|171549|171552|838|28132;3379134|976|117743|200644|49546|1016|936370;3379134|976|117743|200644|49546|1016|706435,Complete,Folakunmi
bsdb:36625596/2/2,36625596,case-control,36625596,10.1128/spectrum.03796-22,NA,"Li Y., Qian F., Cheng X., Wang D., Wang Y., Pan Y., Chen L., Wang W. , Tian Y.",Dysbiosis of Oral Microbiota and Metabolite Profiles Associated with Type 2 Diabetes Mellitus,Microbiology spectrum,2023,"metabolomic, metagenomic, oral diseases, oral microbiome, type 2 diabetes mellitus",Experiment 2,China,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Type II diabetes mellitus,MONDO:0005148,Healthy Control,Type 2 Diabetes Mellitus Patients,"Supragingival dental plaque samples of patients with Type 2 Diabetes Mellitus ( fasting plasma glucose (FPG)≥7.0 mmol/L, HbA1C ≥6.5%, and 2-h postprandial blood glucose (2-hPBG)≥11.1 mmol/L)",10,10,"6 months, 1 week",WMS,NA,MGISEQ-2000,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 1F,20 March 2024,Folakunmi,"Folakunmi,WikiWorks",LEfSe analysis of supragingival plaque samples between patients with type II diabetes and healthy controls,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces johnsonii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces massiliensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 170,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. oral taxon 014,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049|1654|544581;1783272|201174|1760|2037|2049|1654|461393;1783272|201174|1760|2037|2049|1654|1655;1783272|201174|1760|2037|2049|1654|712117;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;1783272|201174;3379134|1224|28216|80840|506;1783272|201174|1760|85009|31957|2801844|1750;3379134|1224|28216|80840|119060;3379134|1224|28216|80840;3379134|1224|1236|135615|868;3379134|1224|1236|135615|868|2717;3379134|1224|1236|135615|868|2717|2718;1783272|201174|1760|85007|1653|1716|61592;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|80840|119060|47670|47671;1783272|201174|1760|85006|1268;3379134|1224|1236|2887326|468;3379134|1224|28216|206351|481|482|641148;1783272|201174|1760|85009|31957;1783272|201174|1760|85009|31957|1743;3379134|1224|1236|72274|135621;3379134|1224|1236|72274;3379134|1224|1236|72274|135621|286;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|172042;1783272|1239|91061|186826|1300|1301|1305;3379134|1224|1236|135615,Complete,Folakunmi
bsdb:36627678/1/1,36627678,"cross-sectional observational, not case-control,laboratory experiment",36627678,10.1186/s13578-023-00956-1,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9832664,"Fu J., Shan J., Cui Y., Yan C., Wang Q., Han J. , Cao G.",Metabolic disorder and intestinal microflora dysbiosis in chronic inflammatory demyelinating polyradiculoneuropathy,Cell & bioscience,2023,"Arachidonic acid, Bile acids, Chronic inflammatory demyelinating polyradiculoneuropathy, Gut microbial dysbiosis, Metabolic disorder",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic inflammatory demyelinating polyradiculoneuropathy,EFO:1000868,Healthy controls (non-CIDP),Chronic inflammatory demyelinating polyradiculoneuropathy (CIDP),"Patients with chronic inflammatory demyelinating polyradiculoneuropathy (CIDP), a rare acquired immune-mediated neuropathy",33,31,NA,WMS,NA,DNBSEQ-T7,relative abundances,T-Test,0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 6A,12 March 2024,Zheeburg,"Zheeburg,Scholastica,WikiWorks",Bacterial species abundance in the stools of the chronic inflammatory demyelinating polyradiculoneuropathy (CIDP) group versus non-CIDP group.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus amylovorus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella variicola,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella quasipneumoniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis",1783272|1239|91061|186826|1300|1301|1304;1783272|1239|909932|1843489|31977|906|907;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|909932|1843488|909930|33024|33025;1783272|1239|91061|186826|33958|1578|1604;1783272|1239|909932|909929|1843491|158846|437897;3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|543|570|548;3379134|1224|1236|91347|543|570|244366;1783272|1239|91061|186826|33958|1578|47770;1783272|1239|91061|186826|33958|2767887|1624;3379134|1224|1236|91347|543|570|573;3379134|1224|1236|91347|543|547|158836;3379134|1224|1236|91347|543|570|1463165;1783272|1239|91061|186826|1300|1301|1343,Complete,Svetlana up
bsdb:36627678/1/2,36627678,"cross-sectional observational, not case-control,laboratory experiment",36627678,10.1186/s13578-023-00956-1,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9832664,"Fu J., Shan J., Cui Y., Yan C., Wang Q., Han J. , Cao G.",Metabolic disorder and intestinal microflora dysbiosis in chronic inflammatory demyelinating polyradiculoneuropathy,Cell & bioscience,2023,"Arachidonic acid, Bile acids, Chronic inflammatory demyelinating polyradiculoneuropathy, Gut microbial dysbiosis, Metabolic disorder",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic inflammatory demyelinating polyradiculoneuropathy,EFO:1000868,Healthy controls (non-CIDP),Chronic inflammatory demyelinating polyradiculoneuropathy (CIDP),"Patients with chronic inflammatory demyelinating polyradiculoneuropathy (CIDP), a rare acquired immune-mediated neuropathy",33,31,NA,WMS,NA,DNBSEQ-T7,relative abundances,T-Test,0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 6A,12 March 2024,Zheeburg,"Zheeburg,Scholastica,WikiWorks",Bacterial species abundance in the stools of the chronic inflammatory demyelinating polyradiculoneuropathy (CIDP) group versus non-CIDP group.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella xylaniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides coprosuis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola salanitronis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides zoogleoformans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. PHL 2737,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp. CT06,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. M10,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes dispar,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae",3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|171552|577309|454155;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|815|816|151276;3379134|976|200643|171549|815|909656|376805;3379134|976|200643|171549|815|816|28119;3379134|976|200643|171549|815|816|2162637;3379134|976|200643|171549|2005525|375288|2025876;3379134|976|200643|171549|815|816|2763022;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|171550|239759|2585119;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|816|47678,Complete,Svetlana up
bsdb:36631533/1/1,36631533,case-control,36631533,10.1038/s41598-023-27436-3,NA,"Shrode R.L., Knobbe J.E., Cady N., Yadav M., Hoang J., Cherwin C., Curry M., Garje R., Vikas P., Sugg S., Phadke S., Filardo E. , Mangalam A.K.",Breast cancer patients from the Midwest region of the United States have reduced levels of short-chain fatty acid-producing gut bacteria,Scientific reports,2023,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,Healthy controls (HC),Breast cancer (BC),"All BC patients eligible for this study were diagnosed with invasive BC of any stage, and recruited from the Breast Molecular Epidemiology Resource (BMER) of the Holden Comprehensive Cancer Center (HCCC)",19,22,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"body mass index,race,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3,3 October 2023,ChiomaBlessing,"ChiomaBlessing,Peace Sandy,WikiWorks","Bacteria significantly increased in patients with breast cancer compared to healthy controls. (a–f) Based on the Wilcoxon test and the Benjamini–Hochberg procedure, 6 features were significantly higher in abundance in the breast cancer cohort compared to the healthy controls (p ≤ 0.05, q ≤ .15). Significance: * < 0.05 and ** < 0.01.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|201174|1760|2037|2049|1654;1783272|1239|186801|3085636|186803|572511;1783272|201174|84998|1643822|1643826|84111;1783272|1239|526524|526525|128827|1573534;1783272|1239|186801|3082720|186804|1505657|261299;1783272|1239|186801|186802|216572,Complete,Peace Sandy
bsdb:36631533/1/2,36631533,case-control,36631533,10.1038/s41598-023-27436-3,NA,"Shrode R.L., Knobbe J.E., Cady N., Yadav M., Hoang J., Cherwin C., Curry M., Garje R., Vikas P., Sugg S., Phadke S., Filardo E. , Mangalam A.K.",Breast cancer patients from the Midwest region of the United States have reduced levels of short-chain fatty acid-producing gut bacteria,Scientific reports,2023,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,Healthy controls (HC),Breast cancer (BC),"All BC patients eligible for this study were diagnosed with invasive BC of any stage, and recruited from the Breast Molecular Epidemiology Resource (BMER) of the Holden Comprehensive Cancer Center (HCCC)",19,22,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"body mass index,race,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 4,3 October 2023,ChiomaBlessing,"ChiomaBlessing,Peace Sandy,WikiWorks","Bacteria significantly decreased in patients with breast cancer compared to healthy controls. (a–h) Based on the Wilcoxon test and the Benjamini–Hochberg procedure, 8 features weresignificantly lower in abundance in the breast cancer cohort compared to the healthy controls (p ≤ 0.05, q ≤ 0.15). Significance: * < 0.05, ** < 0.01, and *** < 0.001.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium edouardi,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",3379134|976|200643|171549|171550|239759|1872444;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|1506553|1926283;1783272|1239|186801|3085636|186803|28050|28052;1783272|1239|186801|186802|216572|459786|1945593;3379134|976|200643|171549|2005525|375288|46503;1783272|1239|526524|526525|128827|331630;1783272|1239|186801|3085636|186803|297314,Complete,Peace Sandy
bsdb:36631533/2/1,36631533,case-control,36631533,10.1038/s41598-023-27436-3,NA,"Shrode R.L., Knobbe J.E., Cady N., Yadav M., Hoang J., Cherwin C., Curry M., Garje R., Vikas P., Sugg S., Phadke S., Filardo E. , Mangalam A.K.",Breast cancer patients from the Midwest region of the United States have reduced levels of short-chain fatty acid-producing gut bacteria,Scientific reports,2023,NA,Experiment 2,United States of America,Macaca mulatta,Breast,UBERON:0000310,Clinical laboratory measurement,EFO:0004297,health-control,Breast cancer,"gut bacterial
dysbiosis in breast cancer could lead to refned prevention and treatment",24,23,1 month,16S,34,Illumina,relative abundances,LEfSe,1e-4,FALSE,3,"age,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3,14 October 2024,Som252,"Som252,WikiWorks","Bacteria signifcantly increased in patients with breast cancer compared to healthy controls. (a–f)
Based on the Wilcoxon test and the Benjamini–Hochberg procedure, 6 features were signifcantly higher in abundance in the breast cancer cohort compared to the healthy controls (p≤0.05, q≤.15). Signifcance: *<0.05 and **<0.01.",increased,",k__Pseudomonadati|p__Acidobacteriota,k__Pseudomonadati|p__Acidobacteriota|c__Blastocatellia",;3379134|57723;3379134|57723|1562566,Complete,NA
bsdb:36631533/2/2,36631533,case-control,36631533,10.1038/s41598-023-27436-3,NA,"Shrode R.L., Knobbe J.E., Cady N., Yadav M., Hoang J., Cherwin C., Curry M., Garje R., Vikas P., Sugg S., Phadke S., Filardo E. , Mangalam A.K.",Breast cancer patients from the Midwest region of the United States have reduced levels of short-chain fatty acid-producing gut bacteria,Scientific reports,2023,NA,Experiment 2,United States of America,Macaca mulatta,Breast,UBERON:0000310,Clinical laboratory measurement,EFO:0004297,health-control,Breast cancer,"gut bacterial
dysbiosis in breast cancer could lead to refned prevention and treatment",24,23,1 month,16S,34,Illumina,relative abundances,LEfSe,1e-4,FALSE,3,"age,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3,14 October 2024,Som252,"Som252,WikiWorks","Bacteria significantly increased in patients with breast cancer compared to healthy controls. (a–f) Based on the Wilcoxon test and the Benjamini–Hochberg procedure, 6 features were significantly higher in abundance in the breast cancer cohort compared to the healthy controls (p≤0.05, q≤.15). Significance: *<0.05 and **<0.01.",decreased,",k__Pseudomonadati|p__Acidobacteriota,k__Pseudomonadati|p__Acidobacteriota|c__Blastocatellia",;3379134|57723;3379134|57723|1562566,Complete,NA
bsdb:36631857/1/1,36631857,case-control,36631857,10.1186/s12931-023-02312-w,NA,"Huang H.L., Luo Y.C., Lu P.L., Huang C.H., Lin K.D., Lee M.R., Cheng M.H., Yeh Y.T., Kao C.Y., Wang J.Y., Yang J.M. , Chong I.W.",Gut microbiota composition can reflect immune responses of latent tuberculosis infection in patients with poorly controlled diabetes,Respiratory research,2023,"Diabetic mellitus, Gut microbiota, Immunity, Latent tuberculosis infection",Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,"Tuberculosis,Diabetes mellitus",EFO:0000400,poorly-controlled diabetes mellitus (pDM) without latent tuberculosis infection (LTBI),poorly-controlled diabetes mellitus with latent tuberculosis infection (pDM + LTBI),poorly-controlled diabetes mellitus with latent tuberculosis infection (pDM + LTBI),87,43,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 3A and B,23 July 2025,Nuerteye,Nuerteye,"Differential abundance analysis and identification of representative genera as predictive signatures through linear discriminant analysis (LDA) with effect size measurements (LEfSe) analysis and a random forest model to discriminate between patients with poorly controlled diabetes with and without latent tuberculosis infection (LTBI). (A) Significantly different taxa in the cladogram according to a LDA score of ≥ 2 (each
circle represents phylogenetic levels from phylum to genus [inside to outside], and each diameter is proportional to the taxon’s abundance). (B) Significantly different genera in terms of relative abundance (LDA score of ≥ 2) between LTBI and non-LTBI groups.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,s__Candidatus Soleaferrea sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__uncultured Muribaculaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__Ruminiclostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|186801|3085636|186803|830;1783272|1239|186801|186802|216572|596767;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|216572|946234;2856521;3379134|976|200643|171549|2005473|2301481;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|186802|216572|1508657|2053608;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816,Complete,NA
bsdb:36631857/1/2,36631857,case-control,36631857,10.1186/s12931-023-02312-w,NA,"Huang H.L., Luo Y.C., Lu P.L., Huang C.H., Lin K.D., Lee M.R., Cheng M.H., Yeh Y.T., Kao C.Y., Wang J.Y., Yang J.M. , Chong I.W.",Gut microbiota composition can reflect immune responses of latent tuberculosis infection in patients with poorly controlled diabetes,Respiratory research,2023,"Diabetic mellitus, Gut microbiota, Immunity, Latent tuberculosis infection",Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,"Tuberculosis,Diabetes mellitus",EFO:0000400,poorly-controlled diabetes mellitus (pDM) without latent tuberculosis infection (LTBI),poorly-controlled diabetes mellitus with latent tuberculosis infection (pDM + LTBI),poorly-controlled diabetes mellitus with latent tuberculosis infection (pDM + LTBI),87,43,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3A and B,23 July 2025,Nuerteye,Nuerteye,"Differential abundance analysis and identification of representative genera as predictive signatures through linear discriminant analysis (LDA) with effect size measurements (LEfSe) analysis and a random forest model to discriminate between patients with poorly controlled diabetes with and without latent tuberculosis infection (LTBI). A) Significantly different taxa in the cladogram according to a LDA score of ≥ 2 (each circle represents phylogenetic levels from phylum to genus [inside to outside], and each diameter is proportional to the taxon’s abundance). B) Significantly different genera in terms of relative abundance (LDA score of ≥ 2) between LTBI and non-LTBI groups.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus",1783272|1239|91061|186826|1300|1301;1783272|201174|1760|2037|2049|1654;3379134|1224|1236|135625|712|724;1783272|1239|186801|186802|1392389;1783272|1239|909932|1843488|909930|904,Complete,NA
bsdb:36639731/1/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 1,United States of America,Homo sapiens,"Vagina,Uterine cervix","UBERON:0000996,UBERON:0000002",Ovarian cancer,MONDO:0008170,Benign,Ovarian cancer,Ovarian cancer refers to women with Ovarian cancer who are currently undergoing hysterectomy,30,34,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,unchanged,increased,Signature 1,"Fig. 2M, Supplementary Table 1, Supplementary Table 3",16 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between Benign and Ovarian cancer patients, gotten from Lower reproductive tract (vaginal and cervical samples)",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium tuberculostearicum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia|s__Facklamia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia",1783272|201174|1760|85007|1653|1716|38304;1783272|1239|91061|186826|186827|66831|178214;1783272|1239|186801|3085636|186803|2316020|592978;1783272|1239|186801|3085636|186803|2316020|33039;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|186826|186827|66831,Complete,Svetlana up
bsdb:36639731/2/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 2,United States of America,Homo sapiens,Ovary,UBERON:0000992,Ovarian cancer,MONDO:0008170,Benign,Ovarian cancer,Ovarian cancer refers to women with Ovarian cancer who are currently undergoing hysterectomy,30,34,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Fig. 2N, Supplementary Table 1, Supplementary Table 3",16 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between Benign and Ovarian cancer patients, gotten from the ovaries",decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium|s__Microbacterium lacus",1783272|201174;1783272|201174|1760|85006|85023|33882|415217,Complete,Svetlana up
bsdb:36639731/3/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 3,United States of America,Homo sapiens,Peritoneal fluid,UBERON:0001268,Ovarian cancer,MONDO:0008170,Benign,Ovarian cancer,Ovarian cancer refers to women with Ovarian cancer who are currently undergoing hysterectomy,30,34,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Fig. 2O, Supplementary Table 1, Supplementary Table 3",16 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between Benign and Ovarian cancer patients, gotten from Ascites/Peritoneal fluid",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylorubrum|s__Methylorubrum extorquens,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium",3379134|1224|28211|356|119045|2282523|408;3379134|1224|28211|356|119045|407,Complete,Svetlana up
bsdb:36639731/4/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 4,United States of America,Homo sapiens,"Vagina,Uterine cervix","UBERON:0000996,UBERON:0000002",Ovarian cancer,MONDO:0008170,Benign,Early Stage Ovarian Cancer (Early Stage OC),Early Stage Ovarian Cancer (Early Stage OC) refers to patients at their early stage of ovarian cancer.,30,5,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,increased,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 4",16 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between Benign and Early Stage Ovarian cancer patients, gotten from Lower reproductive tract (vaginal and cervical samples)",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium singulare,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium tuberculostearicum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia|s__Facklamia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria|s__Fenollaria massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter faecis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus koenoeneniae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__uncultured Dialister sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",1783272|201174|1760|85007|1653|1716|161899;1783272|201174|1760|85007|1653|1716|1720;1783272|201174|1760|85007|1653|1716|38304;1783272|1239|91061|186826|186827|66831|178214;1783272|1239|186801|186802|1686313|938288;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|3085636|186803|2316020|592978;1783272|1239|1737404|1737405|1570339|162289|507751;1783272|1239|909932|1843489|31977|39948|278064;1783272|1239|909932|1843489|31977|39948;1783272|1239|91061|186826|186827|66831;1783272|1239|1737404|1582879;1783272|201174;1783272|201174|1760|85007|1653|1716;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Svetlana up
bsdb:36639731/5/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 5,United States of America,Homo sapiens,Urine,UBERON:0001088,Ovarian cancer,MONDO:0008170,Benign,Early Stage Ovarian Cancer (Early Stage OC),Early Stage Ovarian Cancer (Early Stage OC) refers to patients at their early stage of ovarian cancer.,30,5,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 4",16 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between Benign and Early Stage Ovarian cancer patients, gotten from urine",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera geminata,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister propionicifaciens",1783272|1239|909932|1843489|31977|156454;1783272|1239|909932|1843489|31977|906|156456;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|39948|308994,Complete,Svetlana up
bsdb:36639731/6/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 6,United States of America,Homo sapiens,"Vagina,Uterine cervix","UBERON:0000996,UBERON:0000002",Ovarian cancer,MONDO:0008170,Benign,Advanced Stage Ovarian Cancer,Advanced Stage Ovarian Cancer refers to patients at the advanced stage of ovarian cancer.,30,29,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,decreased,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 5",16 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between Benign and Advanced Stage Ovarian cancer patients, gotten from Lower reproductive tract (vaginal and cervical samples)",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium tuberculostearicum",1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85007|1653|1716|38304,Complete,Svetlana up
bsdb:36639731/7/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 7,United States of America,Homo sapiens,Peritoneal fluid,UBERON:0001268,Ovarian cancer,MONDO:0008170,Benign,Advanced Stage Ovarian Cancer,Advanced Stage Ovarian Cancer refers to patients at the advanced stage of ovarian cancer.,30,29,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,decreased,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 5",16 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between Benign and Advanced Stage Ovarian cancer patients, gotten from Ascites/Peritoneal fluid",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylorubrum|s__Methylorubrum extorquens,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium",3379134|1224|28211|356|119045|2282523|408;3379134|1224|28211|356|119045|407,Complete,Svetlana up
bsdb:36639731/9/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 9,United States of America,Homo sapiens,"Vagina,Uterine cervix","UBERON:0000996,UBERON:0000002",Ovarian cancer,MONDO:0008170,Early Stage Ovarian cancer,Advanced Stage Ovarian Cancer,Advanced Stage Ovarian Cancer refers to patients at the advanced stage of ovarian cancer.,5,29,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,decreased,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 6",16 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between Advanced and Early Stage Ovarian cancer patients, gotten from Lower reproductive tract (vaginal and cervical samples)",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__uncultured Dialister sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",1783272|201174|1760|85007|1653|1716|1720;1783272|1239|909932|1843489|31977|39948|278064;1783272|201174|1760|85007|1653|1716;1783272|1239|909932|1843489|31977|39948,Complete,Svetlana up
bsdb:36639731/10/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 10,United States of America,Homo sapiens,Urine,UBERON:0001088,Ovarian cancer,MONDO:0008170,Early Stage Ovarian cancer,Advanced Stage Ovarian Cancer,Advanced Stage Ovarian Cancer refers to patients at the advanced stage of ovarian cancer.,5,29,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 6",16 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between Advanced and Early Stage Ovarian cancer patients, gotten from urine.",decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera geminata,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister propionicifaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella bergensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__uncultured Prevotella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera",1783272|1239|909932|1843489|31977|906|156456;1783272|1239|909932|1843489|31977|39948|308994;3379134|976|200643|171549|171552|52228|242750;3379134|976|200643|171549|171552|838|159272;3379134|976|200643|171549|171552|838;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|156454,Complete,Svetlana up
bsdb:36639731/11/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 11,United States of America,Homo sapiens,Uterus,UBERON:0000995,Ovarian cancer,MONDO:0008170,Early Stage Ovarian cancer,Advanced Stage Ovarian Cancer,Advanced Stage Ovarian Cancer refers to patients at the advanced stage of ovarian cancer.,5,29,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 6",16 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between Advanced and Early Stage Ovarian cancer patients, gotten from uterus",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium tuberculostearicum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles|s__Roseateles depolymerans",1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85007|1653|1716|38304;3379134|1224|28216|80840|2975441|93681;3379134|1224|28216|80840|2975441|93681|76731,Complete,Svetlana up
bsdb:36639731/12/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 12,United States of America,Homo sapiens,Feces,UBERON:0001988,Ovarian cancer,MONDO:0008170,Early Stage Ovarian cancer,Advanced Stage Ovarian Cancer,Advanced Stage Ovarian Cancer refers to patients at the advanced stage of ovarian cancer.,5,29,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 6",16 December 2024,KateRasheed,"KateRasheed,WikiWorks,Tosin","Differential abundance of taxa between Advanced and Early Stage Ovarian cancer patients, gotten from stool",decreased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Aedoeadaptatus|s__Aedoeadaptatus nemausensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium|s__Arcanobacterium urinimassiliense,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:352,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Umbribacter|s__Umbribacter vaginalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium avidum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila|s__Fastidiosipila sanguinis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Metaprevotella|s__Metaprevotella massiliensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus curtisii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella|s__Murdochiella sp. Marseille-P8839,k__Bacillati|p__Bacillota|g__Ndongobacter|s__Ndongobacter massiliensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus|s__Negativicoccus succinicivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|s__Peptoniphilaceae bacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus duerdenii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas bennonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,s__rumen bacterium NK4A214,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum|s__uncultured Anaerofilum sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__uncultured Eubacteriales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus|s__uncultured Peptococcus sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Succiniclasticum|s__uncultured Succiniclasticum sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|s__uncultured Thermoanaerobacterales bacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__uncultured Veillonella sp.,s__uncultured bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005",1783272|1239|1737404|1737405|1570339|2981628|2582829;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|171550|239759|328814;1783272|1239|186801|186802|216572|52784;1783272|1239|186801|186802|3082771|1924093|1924094;1783272|1239|186801|186802|216572|244127|1872531;1783272|201174|1760|2037|2049|28263;1783272|201174|1760|2037|2049|28263|1871014;1783272|1239;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|47678;1783272|1239|186801|186802|31979|1485|1262798;1783272|201174|84998|1643822|1643826|3472368|1588753;1783272|201174|1760|85009|31957|1912216;1783272|201174|1760|85009|31957|1912216|33010;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|216572|236752;1783272|1239|186801|186802|216572|236752|236753;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492|848|851;3379134|976|200643|171549|171552|2974257|28127;1783272|1239|186801|186802|216572|596767;3379134|976|200643|171549|171552|1980689|1870999;1783272|201174|1760|2037|2049|2050;1783272|201174|1760|2037|2049|2050|2051;1783272|1239|1737404|1737405|1570339|1161127;1783272|1239|1737404|1737405|1570339|1161127|2717291;1783272|1239|1930845|1871025;1783272|1239|909932|1843489|31977|909928;1783272|1239|909932|1843489|31977|909928|620903;1783272|1239|186801|186802|186807|2740;1783272|1239|1737404|1737405|1570339|1891242;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|1737404|1737405|1570339|162289|507750;1783272|1239|909932|1843488|909930|33024;1783272|1239|909932|1843488|909930|33024|626940;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171551|836|501496;3379134|976|200643|171549|171552|838;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|1385|90964|1279|1282;877428;1783272|1239|186801|186802|216572|52784|269679;1783272|1239|186801|186802|172733;1783272|1239|186801|186802|216572|707003;1783272|1239|186801|186802|186807|2740|335458;1783272|1239|909932|1843488|909930|40840|1500547;1783272|1239|186801|68295|157468;1783272|1239|909932|1843489|31977|29465|159268;77133;1783272|1239|186801|186802|216572|3068309,Complete,Svetlana up
bsdb:36639731/13/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 13,United States of America,Homo sapiens,Ovary,UBERON:0000992,Ovarian cancer,MONDO:0008170,Benign,Low Grade Tumor,Low Grade Tumor refers to patients with low-grade tumor,30,5,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 7",17 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between Benign and Low grade tumor patients, gotten from ovaries",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter|s__Achromobacter spanius,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter",3379134|1224|28216|80840|506|222|217203;3379134|1224|28216|80840|506|222,Complete,Svetlana up
bsdb:36639731/14/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 14,United States of America,Homo sapiens,"Vagina,Uterine cervix","UBERON:0000996,UBERON:0000002",Ovarian cancer,MONDO:0008170,Benign,Low Grade Tumor,Low Grade Tumor refers to patients with low-grade tumor,30,5,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 7",17 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between Benign and Low grade tumor patients, gotten from Lower reproductive tract (vaginal and cervical samples)",increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Aedoeadaptatus|s__Aedoeadaptatus urinae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum soehngenii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginimassiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium amycolatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium singulare,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium tuberculostearicum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Dermabacter|s__Dermabacter jinjuensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister propionicifaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila|s__Fastidiosipila sanguinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella bergensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter faecis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus curtisii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella|s__Murdochiella asaccharolytica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus|s__Negativicoccus succinicivorans,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Olegusella|s__Olegusella massiliensis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus harei,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus koenoeneniae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas bennonis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia radingae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia turicensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum|s__Varibaculum cambriense,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|s__uncultured Actinomycetales bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__uncultured Bacteroides sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__uncultured Eubacteriales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__uncultured Lachnoclostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus|s__uncultured Peptococcus sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__uncultured Peptoniphilus sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|s__Peptostreptococcaceae bacterium oral taxon 113,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Dermabacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus",1783272|1239|1737404|1737405|1570339|2981628|1871017;1783272|1239|186801|3085636|186803|1766253|39491;3379134|976|200643|171549|171550|239759|28117;1783272|1239|186801|3085636|186803|2569097|105843;1783272|1239|1737404|1737405|1570339|165779|2042308;1783272|1239|186801|3085636|186803|207244|649756;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|820;1783272|1239|186801|3085636|186803|572511|871665;1783272|1239|186801|3085636|186803|572511|1955243;1783272|1239|186801|3085636|186803|572511|418240;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|1760|85007|1653|1716|43765;1783272|201174|1760|85007|1653|1716|161899;1783272|201174|1760|85007|1653|1716|1720;1783272|201174|1760|85007|1653|1716|38304;1783272|201174|1760|85006|85020|36739|1667168;1783272|1239|909932|1843489|31977|39948|308994;1783272|1239|186801|3085636|186803|189330|88431;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|236752|236753;1783272|1239|186801|3085636|186803|1407607|1150298;3384189|32066|203490|203491|203492|848|851;3379134|976|200643|171549|171552|52228|242750;3379134|976|200643|171549|171552|2974257|386414;1783272|1239|186801|3085636|186803|2316020|592978;1783272|201174|1760|2037|2049|2050|2051;1783272|1239|1737404|1737405|1570339|1161127|507844;1783272|1239|909932|1843489|31977|909928|620903;1783272|201174|84998|84999|84107|1979843|1776381;1783272|1239|1737404|1737405|1570339|162289|54005;1783272|1239|1737404|1737405|1570339|162289|507751;1783272|1239|186801|3082720|186804|1257|1261;3379134|976|200643|171549|171551|836|501496;1783272|201174|1760|2037|2049|2529408|131110;1783272|201174|1760|2037|2049|2529408|131111;1783272|1239|91061|1385|90964|1279|1280;1783272|1239|91061|1385|90964|1279|1282;1783272|1239|91061|186826|1300|1301|68892;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1306;3379134|1224|28216|80840|995019|40544|1981025;1783272|201174|1760|2037|2049|184869|184870;1783272|1239|186801|3085636|186803|2316020|33039;1783272|201174|1760|2037|239730;3379134|976|200643|171549|815|816|162156;1783272|1239|186801|186802|172733;1783272|1239|186801|3085636|186803|1506553|1586779;1783272|1239|186801|3085636|186803|297314;1783272|1239|186801|186802|186807|2740|335458;1783272|1239|1737404|1737405|1570339|162289|254354;1783272|201174|1760|2037|2049|184869;3379134|1224|1236|91347|543|1940338;1783272|201174|84998|84999|84107|102106;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|186801|3082720|186804|1257;1783272|1239|1737404|1737405|1570339|1161127;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|186802|186807|2740;3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;3379134|976|200643|171549|171552|838;1783272|201174|1760|2037|2049|2050;3379134|976|200643|171549|171551|836;1783272|1239|186801|186802|216572|236752;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|292632;3379134|1224|28216|80840|995019|40544;1783272|201174|1760|2037|2049|1654;1783272|1239|186801|3082720|186804|1321783;1783272|201174|1760|85007|1653|1716;1783272|201174;1783272|201174|1760|85006|85020|36739;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|1385|90964|1279;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|909928,Complete,Svetlana up
bsdb:36639731/15/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 15,United States of America,Homo sapiens,"Vagina,Uterine cervix","UBERON:0000996,UBERON:0000002",Ovarian cancer,MONDO:0008170,Benign,High Grade Tumor,High Grade Tumor refers to patients with high-grade tumor,30,29,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 8",17 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between Benign and High grade tumor patients, gotten from Lower reproductive tract (vaginal and cervical samples)",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium tuberculostearicum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia|s__Facklamia hominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia",1783272|201174|1760|85007|1653|1716|38304;1783272|1239|91061|186826|186827|66831|178214;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|186826|186827|66831,Complete,Svetlana up
bsdb:36639731/16/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 16,United States of America,Homo sapiens,Ovary,UBERON:0000992,Ovarian cancer,MONDO:0008170,Benign,High Grade Tumor,High Grade Tumor refers to patients with high-grade tumor,30,29,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 8",17 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between Benign and High-grade tumor patients, gotten from ovaries",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium|s__Microbacterium lacus,k__Bacillati|p__Actinomycetota",1783272|201174|1760|85006|85023|33882|415217;1783272|201174,Complete,Svetlana up
bsdb:36639731/17/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 17,United States of America,Homo sapiens,Peritoneal fluid,UBERON:0001268,Ovarian cancer,MONDO:0008170,Benign,High Grade Tumor,High Grade Tumor refers to patients with high-grade tumor,30,29,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 8",17 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between Benign and High grade tumor patients, gotten from Ascites/Peritoneal Fluid.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylorubrum|s__Methylorubrum extorquens,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium",3379134|1224|28211|356|119045|2282523|408;3379134|1224|28211|356|119045|407,Complete,Svetlana up
bsdb:36639731/18/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 18,United States of America,Homo sapiens,Ovary,UBERON:0000992,Ovarian cancer,MONDO:0008170,Low Grade Tumor,High Grade Tumor,High Grade Tumor refers to patients with high-grade tumor,5,29,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 9",17 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between Low and High grade tumor patients, gotten from ovaries.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter|s__Achromobacter spanius,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter",3379134|1224|28216|80840|506|222|217203;3379134|1224|28216|80840|506|222,Complete,Svetlana up
bsdb:36639731/19/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 19,United States of America,Homo sapiens,Uterus,UBERON:0000995,Ovarian cancer,MONDO:0008170,Low Grade Tumor,High Grade Tumor,High Grade Tumor refers to patients with high-grade tumor,5,29,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 9",17 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between Low and High grade tumor patients, gotten from uterus.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles|s__Roseateles depolymerans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles",3379134|1224|28216|80840|2975441|93681|76731;3379134|1224|28216|80840|2975441|93681,Complete,Svetlana up
bsdb:36639731/20/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 20,United States of America,Homo sapiens,Urine,UBERON:0001088,Ovarian cancer,MONDO:0008170,Low Grade Tumor,High Grade Tumor,High Grade Tumor refers to patients with high-grade tumor,5,29,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 9",17 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between Low and High grade tumor patients, gotten from urine.",decreased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus murdochii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus sp. Marseille-P3915,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium|s__Atopobium deltae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister propionicifaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria|s__Fenollaria massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella bergensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus curtisii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus duerdenii,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas bennonis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum|s__Varibaculum cambriense,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__uncultured Dialister sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella|s__uncultured Howardella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__uncultured Prevotella sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacillati|p__Bacillota",1783272|1239|1737404|1737405|1570339|165779|411577;1783272|1239|1737404|1737405|1570339|165779|2057799;1783272|201174|84998|84999|1643824|1380|1393034;1783272|1239|909932|1843489|31977|39948|309120;1783272|1239|909932|1843489|31977|39948|308994;1783272|1239|186801|186802|1686313|938288;3379134|976|200643|171549|171552|52228|242750;3379134|976|200643|171549|171552|2974257|386414;1783272|201174|1760|2037|2049|2050|2051;1783272|1239|1737404|1737405|1570339|162289|507750;1783272|1239|186801|3082720|186804|1257|1261;3379134|976|200643|171549|171551|836|501496;1783272|201174|1760|2037|2049|184869|184870;1783272|1239|909932|1843489|31977|39948|278064;1783272|1239|186801|186802|404402|768570;3379134|976|200643|171549|171552|838|159272;1783272|201174|1760|2037|2049|184869;1783272|201174|84998|84999|1643824|1380;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|186801|3082720|186804|1257;1783272|1239|1737404|1737405|1570339|162289;3379134|976|200643|171549|171552|838;1783272|201174|1760|2037|2049|2050;3379134|976|200643|171549|171551|836;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|404402;1783272|1239|1737404|1582879;1783272|1239,Complete,Svetlana up
bsdb:36639731/21/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 21,United States of America,Homo sapiens,"Vagina,Uterine cervix","UBERON:0000996,UBERON:0000002",Ovarian cancer,MONDO:0008170,Low Grade Tumor,High Grade Tumor,High Grade Tumor refers to patients with high-grade tumor,5,29,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 9",17 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between Low and High grade tumor patients, gotten from Lower reproductive tract (vaginal and cervical samples)",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum soehngenii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister propionicifaciens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella bergensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter faecis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus curtisii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella|s__Murdochiella asaccharolytica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus|s__Negativicoccus succinicivorans,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Olegusella|s__Olegusella massiliensis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus koenoeneniae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum|s__Varibaculum cambriense,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|s__uncultured Actinomycetales bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__uncultured Bacteroides sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__uncultured Eubacteriales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus|s__uncultured Peptococcus sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__uncultured Peptoniphilus sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|s__Peptostreptococcaceae bacterium oral taxon 113,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus",1783272|1239|186801|3085636|186803|1766253|39491;3379134|976|200643|171549|171550|239759|28117;1783272|1239|186801|3085636|186803|2569097|105843;1783272|1239|186801|3085636|186803|207244|649756;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|820;1783272|1239|186801|3085636|186803|572511|871665;1783272|1239|186801|3085636|186803|572511|1955243;1783272|1239|186801|3085636|186803|572511|418240;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|1760|85007|1653|1716|1720;1783272|1239|909932|1843489|31977|39948|308994;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|1407607|1150298;3384189|32066|203490|203491|203492|848|851;3379134|976|200643|171549|171552|52228|242750;3379134|976|200643|171549|171552|2974257|386414;1783272|1239|186801|3085636|186803|2316020|592978;1783272|201174|1760|2037|2049|2050|2051;1783272|1239|1737404|1737405|1570339|1161127|507844;1783272|1239|909932|1843489|31977|909928|620903;1783272|201174|84998|84999|84107|1979843|1776381;1783272|1239|1737404|1737405|1570339|162289|507751;1783272|1239|186801|3082720|186804|1257|1261;1783272|1239|91061|1385|90964|1279|1282;1783272|1239|91061|186826|1300|1301|68892;1783272|1239|91061|186826|1300|1301|1318;1783272|201174|1760|2037|2049|184869|184870;1783272|1239|186801|3085636|186803|2316020|33039;1783272|201174|1760|2037|239730;3379134|976|200643|171549|815|816|162156;1783272|1239|186801|186802|172733;1783272|1239|186801|3085636|186803|297314;1783272|1239|186801|186802|186807|2740|335458;1783272|1239|1737404|1737405|1570339|162289|254354;3379134|1224|1236|91347|543|1940338;1783272|201174|1760|2037|2049|184869;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3082720|186804|1257;1783272|1239|1737404|1737405|1570339|1161127;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|186802|186807|2740;3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;3379134|976|200643|171549|171552|838;1783272|201174|1760|2037|2049|2050;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|216572|216851;1783272|201174|1760|85007|1653|1716;1783272|201174;1783272|1239;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|1385|90964|1279;1783272|1239|186801|3082720|186804|1321783;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|909928,Complete,Svetlana up
bsdb:36639731/22/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 22,United States of America,Homo sapiens,"Vagina,Uterine cervix","UBERON:0000996,UBERON:0000002",Ovarian cancer,MONDO:0008170,Benign,Serous ovarian cancer,Serous ovarian cancer is a type of ovarian cancer that forms in the tissue that lines the ovaries.,30,29,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,increased,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 10",17 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between Benign and Serous ovarian cancer patients, gotten from Lower reproductive tract (vaginal and cervical samples)",increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus senegalensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium tuberculostearicum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia|s__Facklamia hominis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium",1783272|1239|1737404|1737405|1570339|165779|1288120;1783272|201174|1760|85007|1653|1716|38304;1783272|1239|91061|186826|186827|66831|178214;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|91061|186826|186827|66831;1783272|201174|1760|85007|1653|1716,Complete,Svetlana up
bsdb:36639731/23/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 23,United States of America,Homo sapiens,Ovary,UBERON:0000992,Ovarian cancer,MONDO:0008170,Benign,Serous ovarian cancer,Serous ovarian cancer is a type of ovarian cancer that forms in the tissue that lines the ovaries.,30,29,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 10",17 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between Benign and Serous ovarian cancer patients, gotten from ovaries",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium|s__Microbacterium lacus,k__Bacillati|p__Actinomycetota",1783272|201174|1760|85006|85023|33882|415217;1783272|201174,Complete,Svetlana up
bsdb:36639731/24/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 24,United States of America,Homo sapiens,Peritoneal fluid,UBERON:0001268,Ovarian cancer,MONDO:0008170,Benign,Serous ovarian cancer,Serous ovarian cancer is a type of ovarian cancer that forms in the tissue that lines the ovaries.,30,29,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 10",17 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between Benign and Serous ovarian cancer patients, gotten from Ascites/Peritoneal Fluid",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylorubrum|s__Methylorubrum extorquens,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium",3379134|1224|28211|356|119045|2282523|408;3379134|1224|28211|356|119045|407,Complete,Svetlana up
bsdb:36639731/25/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 25,United States of America,Homo sapiens,Urine,UBERON:0001088,Ovarian cancer,MONDO:0008170,Benign,Other histologies,"Other histologies refers to patients with mucinous, endometroid and clear cell.",30,5,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 11",17 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between Benign and patients with other histologies, gotten from urine.",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera geminata,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister propionicifaciens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera",1783272|1239|909932|1843489|31977|906|156456;1783272|1239|909932|1843489|31977|39948|308994;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|156454,Complete,Svetlana up
bsdb:36639731/26/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 26,United States of America,Homo sapiens,Fallopian tube,UBERON:0003889,Ovarian cancer,MONDO:0008170,Benign,Other histologies,"Other histologies refers to patients with mucinous, endometroid and clear cell.",30,5,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 11",17 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between Benign and patients with other histologies, gotten from the fallopian tubes.",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239|91061|186826|33958|1578|147802;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:36639731/27/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 27,United States of America,Homo sapiens,"Vagina,Uterine cervix","UBERON:0000996,UBERON:0000002",Ovarian cancer,MONDO:0008170,Benign,Other histologies,"Other histologies refers to patients with mucinous, endometroid and clear cell.",30,5,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,increased,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 11",17 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between Benign and patients with other histologies, gotten from Lower reproductive tract (vaginal and cervical samples)",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium singulare,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter faecis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus curtisii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia turicensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__uncultured Dialister sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|3085636|186803|572511|1955243;1783272|201174|1760|85007|1653|1716|161899;1783272|201174|1760|85007|1653|1716|1720;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|3085636|186803|2316020|592978;1783272|201174|1760|2037|2049|2050|2051;1783272|201174|1760|2037|2049|2529408|131111;1783272|1239|909932|1843489|31977|39948|278064;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|572511;1783272|201174|1760|2037|2049|2050;1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|186802|216572|216851;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85007|1653|1716;1783272|201174,Complete,Svetlana up
bsdb:36639731/29/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 29,United States of America,Homo sapiens,Omentum,NA,Ovarian cancer,MONDO:0008170,Serous ovarian cancer,Other histologies,"Other histologies refers to patients with mucinous, endometroid and clear cell.",29,5,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 12",17 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between Serous and patients with other histologies, gotten from omentum.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Angelakisella|s__Angelakisella massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|s__uncultured Bacillota bacterium",1783272|1239|186801|186802|216572|1935176|1871018;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|344338,Complete,Svetlana up
bsdb:36639731/30/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 30,United States of America,Homo sapiens,Urine,UBERON:0001088,Ovarian cancer,MONDO:0008170,Serous ovarian cancer,Other histologies,"Other histologies refers to patients with mucinous, endometroid and clear cell.",29,5,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 12",17 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between Benign and patients with other histologies, gotten from urine.",increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus murdochii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus sp. Marseille-P3915,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera geminata,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister propionicifaciens,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella bergensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__uncultured Prevotella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera",1783272|1239|1737404|1737405|1570339|165779|411577;1783272|1239|1737404|1737405|1570339|165779|2057799;1783272|1239|909932|1843489|31977|906|156456;1783272|1239|909932|1843489|31977|39948|308994;3384189|32066|203490|203491|203492|848|851;3379134|976|200643|171549|171552|52228|242750;3379134|976|200643|171549|171552|2974257|28127;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|171552|838|159272;3379134|976|200643|171549|171552|838;1783272|1239|1737404|1737405|1570339|165779;3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|171551|836;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|156454,Complete,Svetlana up
bsdb:36639731/31/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 31,United States of America,Homo sapiens,Peritoneal fluid,UBERON:0001268,Ovarian cancer,MONDO:0008170,Sensitive (chemotherapy sensitive OCs),Other tumor responses (refractory/resistant),Other tumor responses refers to other responses (refractory/resistant) to tumor treatment that was gotten from patients. Refractory means recurrence while receiving the chemotherapy or within four weeks of the last dose of therapy; while resistant means recurrence from 4 weeks to 6 months after the last dose of chemotherapy,21,4,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 13",17 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between Sensitive and other tumor responses, gotten from Ascites/peritoneal fluid",increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus tetradius,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus",1783272|1239|1737404|1737405|1570339|165779|33036;1783272|1239|1737404|1737405|1570339|165779,Complete,Svetlana up
bsdb:36639731/32/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 32,United States of America,Homo sapiens,Peritoneal fluid,UBERON:0001268,Ovarian cancer,MONDO:0008170,No event - 2 years post-diagnosis,Patient status (Alive) - 2 years post-diagnosis,Patient status (Alive) refers to patients that are alive after two years of diagnosis,17,11,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 14",18 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between no event vs alive, gotten from Ascites/peritoneal fluid",increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus tetradius,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter ureolyticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium|s__Methylobacterium radiotolerans,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus harei,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium",1783272|1239|1737404|1737405|1570339|165779|33036;3379134|29547|3031852|213849|72294|194|827;1783272|1239|91061|186826|33958|1578|1596;3379134|1224|28211|356|119045|407|31998;1783272|1239|1737404|1737405|1570339|162289|54005;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|1737404|1737405|1570339|162289;3379134|29547|3031852|213849|72294|194;1783272|1239|91061|186826|33958|1578;3379134|1224|28211|356|119045|407,Complete,Svetlana up
bsdb:36639731/33/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 33,United States of America,Homo sapiens,Feces,UBERON:0001988,Ovarian cancer,MONDO:0008170,No event - 2 years post-diagnosis,Patient status (Alive) - 2 years post-diagnosis,Patient status (Alive) refers to patients that are alive after two years of diagnosis,17,11,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 14",18 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between no event vs alive, gotten from stool.",increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacterium|s__Amedibacterium intestinale,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia pseudococcoides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella nakazawae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Pseudomonadati|p__Bacteroidota|s__uncultured Bacteroidota bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__uncultured Dorea sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",1783272|1239|526524|526525|128827|2749267|2583452;3379134|976|200643|171549|815|816|28116;1783272|1239|186801|3085636|186803|572511|1796616;1783272|1239|186801|186802|31979|1485;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|186801|186802|1392389|1965293;1783272|1239|186801|3085636|186803|1506553|2028282;1783272|1239|186801|3085636|186803|2316020|33038;3379134|1224|28216|80840|995019|577310|487175;1783272|1239|909932|1843489|31977|29465|2682456;1783272|1239|909932|1843489|31977|29465|29466;3379134|976|152509;1783272|1239|186801|3085636|186803|189330|286138;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|1392389;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|572511;1783272|1239;3379134|1224|28216|80840|995019|577310;1783272|1239|526524|526525|128827|1573534;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|186802|216572|1508657,Complete,Svetlana up
bsdb:36639731/34/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 34,United States of America,Homo sapiens,Urine,UBERON:0001088,Ovarian cancer,MONDO:0008170,No event - 2 years post-diagnosis,Patient status (Dead) - 2 years post-diagnosis,Patient status (Dead) refers to patients that are dead after two years of diagnosis,17,5,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,increased,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 15",18 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between no event vs dead, gotten from urine.",increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia radingae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",1783272|1239|1737404|1737405|1570339|165779|33037;1783272|201174|1760|2037|2049|2529408|131110;1783272|1239|1737404|1737405|1570339|165779;1783272|201174|1760|2037|2049|1654,Complete,Svetlana up
bsdb:36639731/35/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 35,United States of America,Homo sapiens,Feces,UBERON:0001988,Ovarian cancer,MONDO:0008170,No event - 2 years post-diagnosis,Patient status (Dead) - 2 years post-diagnosis,Patient status (Dead) refers to patients that are dead after two years of diagnosis,17,5,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 15",18 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between no event vs dead, gotten from stool.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus faecihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella tayi,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus paracasei,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum|s__Varibaculum cambriense,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__uncultured Coprococcus sp.,s__uncultured bacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus",1783272|1239|186801|186802|3085642|580596|1712515;1783272|1239|186801|3085636|186803|1432051|1432052;1783272|1239|91061|186826|33958|2759736|1597;3379134|1224|28216|80840|995019|40544|40545;1783272|201174|1760|2037|2049|184869|184870;1783272|1239|186801|3085636|186803|33042|458253;77133;1783272|201174|1760|2037|2049|184869;1783272|1239|186801|3085636|186803|33042;1783272|1239;1783272|1239|186801|3085636|186803|1432051;3379134|1224|28216|80840|995019|40544;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|3085642|580596,Complete,Svetlana up
bsdb:36639731/36/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 36,United States of America,Homo sapiens,Feces,UBERON:0001988,Ovarian cancer,MONDO:0008170,Event - 2 years,Patient status (Dead) - 2 years post-diagnosis,Patient status (Dead) refers to patients that are dead after two years of diagnosis,11,5,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 16",18 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between event vs dead, gotten from stool after two years post-diagnosis.",decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|909932|1843489|31977|39948,Complete,Svetlana up
bsdb:36639731/37/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 37,United States of America,Homo sapiens,"Vagina,Uterine cervix","UBERON:0000996,UBERON:0000002",Ovarian cancer,MONDO:0008170,No event - 4 years post-diagnosis,Patient status (Alive) - 4 years post-diagnosis,Patient status (Alive) refers to patients that are alive after four years of diagnosis,4,6,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 17",18 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between no event vs alive after four years post-diagnosis, gotten from the Lower reproductive tract (vagina and cervix).",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces urogenitalis,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum butyriciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum soehngenii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus octavius,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera geminata,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter ureolyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__Clostridiales bacterium S5-A14a,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister propionicifaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium difficile,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella|s__Ezakiella coagulans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria|s__Fenollaria massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Olegusella|s__Olegusella massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus|s__Peptococcus niger,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus|s__Peptococcus sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus koenoeneniae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacydonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas bennonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles|s__Roseateles depolymerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum|s__Varibaculum cambriense,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|s__uncultured Actinomycetales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax|s__uncultured Anaerovorax sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__uncultured Dialister sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__uncultured Eubacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__uncultured Mogibacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus|s__uncultured Peptococcus sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__uncultured Peptoniphilus sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__uncultured Prevotella sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|s__Veillonellaceae bacterium DNF00626,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Rarimicrobium|s__Rarimicrobium hominis",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049|1654|103621;1783272|201174;1783272|201174|84998|1643822|1643826|447020;1783272|201174|84998|1643822|1643826|447020|446660;1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|186802|3085642|2048137|1628085;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|2569097|105843;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|1737404|1737405|1570339|165779|54007;1783272|1239|909932|1843489|31977|156454;1783272|1239|909932|1843489|31977|906|156456;1783272|1239;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|820;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|2509240;1783272|1239|186801|3085636|186803|572511|1955243;1783272|1239|186801|186802|3085642|580596;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294|194|827;1783272|1239|186801|3082720|543314|1230734;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85007|1653|1716|1720;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|909932|1843489|31977|39948|308994;1783272|1239|186801|186802|186806|1730|2763044;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|1737404|1582879;1783272|1239|1737404|1582879|46507;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|1686313|938288;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|1407607|1150298;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492|848|851;3379134|976|200643|171549|171552|2974257|28127;3379134|976|200643|171549|171552|2974257|386414;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|1506553|2028282;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|147802;1783272|1239|186801|3082720|543314|86331;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|1853231|283168|28118;1783272|201174|84998|84999|84107|1979843|1776381;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|823;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|186802|186807|2740|2741;1783272|1239|186801|186802|186807|2740|2049038;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|1737404|1737405|1570339|162289|507751;1783272|1239|1737404|1737405|1570339|162289|1673725;1783272|1239|186801|3082720|186804|1257;1783272|1239|186801|3082720|186804|1257|1261;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171551|836|501496;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|171552|838;3384194|508458|649775|649776|3029088|638847;3379134|1224|28216|80840|2975441|93681;3379134|1224|28216|80840|2975441|93681|76731;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|186802|216572|1263|438033;1783272|201174|1760|2037|2049|184869;1783272|201174|1760|2037|2049|184869|184870;1783272|1239|186801|186802|216572|1535;1783272|201174|1760|2037|239730;1783272|1239|186801|3082720|543314|109326|427146;1783272|1239|909932|1843489|31977|39948|278064;1783272|1239|186801|186802|186806|1730|165185;1783272|1239|186801|3082720|543314|86331|278065;1783272|1239|186801|186802|186807|2740|335458;1783272|1239|1737404|1737405|1570339|162289|254354;3379134|976|200643|171549|171552|838|159272;1783272|1239|909932|1843489|31977|1588754;3384194|508458|649775|649776|3029088|1931212|434126,Complete,Svetlana up
bsdb:36639731/38/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 38,United States of America,Homo sapiens,"Vagina,Uterine cervix","UBERON:0000996,UBERON:0000002",Ovarian cancer,MONDO:0008170,No event - 4 years post-diagnosis,Patient status (Dead) - 4 years post-diagnosis,Patient status (Dead) refers to patients that are dead after four years of diagnosis,4,11,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 18",18 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between no event vs dead after four years post-diagnosis, gotten from the Lower reproductive tract (vagina and cervix).",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|976|200643|171549|171552|2974257|28127;3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:36639731/39/1,36639731,time series / longitudinal observational,36639731,10.1038/s41598-023-27555-x,NA,"Asangba A.E., Chen J., Goergen K.M., Larson M.C., Oberg A.L., Casarin J., Multinu F., Kaufmann S.H., Mariani A., Chia N. , Walther-Antonio M.R.S.",Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response,Scientific reports,2023,NA,Experiment 39,United States of America,Homo sapiens,"Vagina,Uterine cervix","UBERON:0000996,UBERON:0000002",Ovarian cancer,MONDO:0008170,Event - 4 years post-diagnosis,Patient status (Dead) - 4 years post-diagnosis,Patient status (Dead) refers to patients that are dead after four years of diagnosis,6,11,2 weeks,16S,345,Illumina,centered log-ratio,Linear Regression,0.1,TRUE,NA,NA,"body mass index,menopause",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,"Supplementary Table 1, Supplementary Table 19",18 December 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between event vs dead after four years post-diagnosis, gotten from the Lower reproductive tract (vagina and cervix).",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|976|200643|171549|171552|2974257|28127;3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:36651357/1/1,36651357,case-control,36651357,https://doi.org/10.1111/ene.15679,NA,"Svačina M.K.R., Sprenger-Svačina A., Tsakmaklis A., Rüb A.M., Klein I., Wüstenberg H., Fink G.R., Lehmann H.C., Vehreschild M.J.G.T. , Farowski F.",The gut microbiome in intravenous immunoglobulin-treated chronic inflammatory demyelinating polyneuropathy,European journal of neurology,2023,"autoimmunity, firmicutes, immune neuropathies, intestinal barrier, short-chain fatty acids (SCFA)",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Chronic inflammatory demyelinating polyneuropathy,EFO:0009538,Healthy Controls (HC),CIDP patients (Chronic inflammatory demyelinating polyneuropathy),Patients who have been diagnosed with Chronic inflammatory demyelinating polyneuropathy,15,16,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,increased,NA,NA,NA,NA,Signature 1,Fig-1a and c,15 April 2025,Aiyshaaaa,"Aiyshaaaa,Svetlana up","Linear discriminant analysis (LDA) effect size of the gut microbiota of healthy subjects (HC) and chronic inflammatory demyelinating polyneuropathy (CIDP) patients of bacterial at phylum, order and family level",increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales,k__Methanobacteriati|p__Methanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",1783272|201174;1783272|1239;1783272|1239|186801|186802|3085642;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|526524|526525|2810280;1783272|201174|84998|84999;1783272|201174|84998;1783272|201174|84998|1643822|1643826;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;3366610|28890|183925;3366610|28890|183925|2158|2159;3366610|28890|183925|2158;3366610|28890;1783272|1239|186801|3085656|3085657;1783272|1239|186801|3085656;3379134|976|200643|171549|2005473;1783272|1239|909932;1783272|1239|186801|186802|216572;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720;3379134|976|200643|171549|171552,Complete,Svetlana up
bsdb:36651357/1/2,36651357,case-control,36651357,https://doi.org/10.1111/ene.15679,NA,"Svačina M.K.R., Sprenger-Svačina A., Tsakmaklis A., Rüb A.M., Klein I., Wüstenberg H., Fink G.R., Lehmann H.C., Vehreschild M.J.G.T. , Farowski F.",The gut microbiome in intravenous immunoglobulin-treated chronic inflammatory demyelinating polyneuropathy,European journal of neurology,2023,"autoimmunity, firmicutes, immune neuropathies, intestinal barrier, short-chain fatty acids (SCFA)",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Chronic inflammatory demyelinating polyneuropathy,EFO:0009538,Healthy Controls (HC),CIDP patients (Chronic inflammatory demyelinating polyneuropathy),Patients who have been diagnosed with Chronic inflammatory demyelinating polyneuropathy,15,16,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,increased,NA,NA,NA,NA,Signature 2,Fig-1a and c,15 April 2025,Aiyshaaaa,Aiyshaaaa,"Linear discriminant analysis (LDA) effect size of the gut microbiota of healthy subjects (HC) and chronic inflammatory demyelinating polyneuropathy (CIDP) patients of bacterial at phylum, order and family level",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Pseudomonadota",3379134|976|200643|171549|815;3379134|976|200643|171549|2005519;3379134|976|200643|1970189|1573805;3379134|976|200643|171549|171550;3379134|1224,Complete,Svetlana up
bsdb:36651357/2/1,36651357,case-control,36651357,https://doi.org/10.1111/ene.15679,NA,"Svačina M.K.R., Sprenger-Svačina A., Tsakmaklis A., Rüb A.M., Klein I., Wüstenberg H., Fink G.R., Lehmann H.C., Vehreschild M.J.G.T. , Farowski F.",The gut microbiome in intravenous immunoglobulin-treated chronic inflammatory demyelinating polyneuropathy,European journal of neurology,2023,"autoimmunity, firmicutes, immune neuropathies, intestinal barrier, short-chain fatty acids (SCFA)",Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Chronic inflammatory demyelinating polyneuropathy,EFO:0009538,Healthy Controls (HC),CIDP patients (Chronic inflammatory demyelinating polyneuropathy),Patients who have been diagnosed with Chronic inflammatory demyelinating polyneuropathy,15,16,6 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,increased,NA,NA,NA,NA,Signature 1,Table-S1,15 April 2025,Aiyshaaaa,Aiyshaaaa,Relative abundances of the gut microbiota of healthy subjects (HC) and chronic inflammatory demyelinating polyneuropathy (CIDP) patients of bacterial at family and genus level,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|g__Negativibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",1783272|1239|186801|3085636|186803|572511;1783272|1239|526524|526525|2810280;1783272|201174|84998|1643822|1643826;1783272|1239|526524|526525|128827;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085656|3085657;1783272|1239|186801|3085656|3085657|2039302;3379134|976|200643|171549|2005473;1783272|1239|1980693;1783272|1239|186801|186802|216572;1783272|1239|186801|3082720|186804;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Svetlana up
bsdb:36651663/1/1,36651663,"cross-sectional observational, not case-control",36651663,10.1080/19490976.2022.2162306,NA,"Malan-Müller S., Valles-Colomer M., Palomo T. , Leza J.C.","The gut-microbiota-brain axis in a Spanish population in the aftermath of the COVID-19 pandemic: microbiota composition linked to anxiety, trauma, and depression profiles",Gut microbes,2023,"COVID-19, Microbiome, anxiety, depression, gut-microbiota-brain axis, mental health, posttraumatic stress disorder, trauma",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Psychiatric disorder,MONDO:0002025,Individuals without the comorbid state,Individuals with comorbid PTSD + depression + state + trait anxiety symptoms (Comorbidity with Psychiatric Symptoms),"This group included individuals with comorbid PTSD, depression, state and trait anxiety symptoms",190,8,6 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,inflammatory bowel disease,irritable bowel syndrome,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4A,20 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Relative abundance of taxa in individuals with comorbid PTSD + depression + state and trait anxiety symptoms compared to those without the comorbid state,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,1783272|1239|186801|3085636|186803|1407607|1150298,Complete,ChiomaBlessing
bsdb:36651663/2/1,36651663,"cross-sectional observational, not case-control",36651663,10.1080/19490976.2022.2162306,NA,"Malan-Müller S., Valles-Colomer M., Palomo T. , Leza J.C.","The gut-microbiota-brain axis in a Spanish population in the aftermath of the COVID-19 pandemic: microbiota composition linked to anxiety, trauma, and depression profiles",Gut microbes,2023,"COVID-19, Microbiome, anxiety, depression, gut-microbiota-brain axis, mental health, posttraumatic stress disorder, trauma",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Psychiatric disorder,MONDO:0002025,Healthy controls (good mental health),PTSD + depression + state + trait anxiety symptoms (Comorbidity with Psychiatric Symptoms),"This group included individuals with comorbid PTSD, depression, state and trait anxiety symptoms",106,8,6 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,20 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Relative abundance of taxa in individuals with comorbid PTSD + depression + state and trait anxiety symptoms compared to healthy controls (good mental health),decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,1783272|1239|186801|3085636|186803|1407607|1150298,Complete,ChiomaBlessing
bsdb:36651663/3/1,36651663,"cross-sectional observational, not case-control",36651663,10.1080/19490976.2022.2162306,NA,"Malan-Müller S., Valles-Colomer M., Palomo T. , Leza J.C.","The gut-microbiota-brain axis in a Spanish population in the aftermath of the COVID-19 pandemic: microbiota composition linked to anxiety, trauma, and depression profiles",Gut microbes,2023,"COVID-19, Microbiome, anxiety, depression, gut-microbiota-brain axis, mental health, posttraumatic stress disorder, trauma",Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Depressive disorder,MONDO:0002050,Individuals without depressive symptoms,Individuals with depressive symptoms,This group included individuals with depressive symptoms,166,32,6 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4C,20 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Relative abundance of taxa in individuals with depressive symptoms compared to those without depressive symptoms,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,ChiomaBlessing
bsdb:36651663/3/2,36651663,"cross-sectional observational, not case-control",36651663,10.1080/19490976.2022.2162306,NA,"Malan-Müller S., Valles-Colomer M., Palomo T. , Leza J.C.","The gut-microbiota-brain axis in a Spanish population in the aftermath of the COVID-19 pandemic: microbiota composition linked to anxiety, trauma, and depression profiles",Gut microbes,2023,"COVID-19, Microbiome, anxiety, depression, gut-microbiota-brain axis, mental health, posttraumatic stress disorder, trauma",Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Depressive disorder,MONDO:0002050,Individuals without depressive symptoms,Individuals with depressive symptoms,This group included individuals with depressive symptoms,166,32,6 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4D,20 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Relative abundance of taxa in individuals with depressive symptoms compared to those without depressive symptoms,decreased,k__Thermotogati|p__Synergistota,3384194|508458,Complete,ChiomaBlessing
bsdb:36651663/4/1,36651663,"cross-sectional observational, not case-control",36651663,10.1080/19490976.2022.2162306,NA,"Malan-Müller S., Valles-Colomer M., Palomo T. , Leza J.C.","The gut-microbiota-brain axis in a Spanish population in the aftermath of the COVID-19 pandemic: microbiota composition linked to anxiety, trauma, and depression profiles",Gut microbes,2023,"COVID-19, Microbiome, anxiety, depression, gut-microbiota-brain axis, mental health, posttraumatic stress disorder, trauma",Experiment 4,Spain,Homo sapiens,Feces,UBERON:0001988,Childhood trauma measurement,EFO:0007979,Individuals who did not experience life-threatening childhood trauma,Individuals who experienced life-threatening childhood trauma,This group included individuals who experienced life-threatening childhood trauma,162,36,6 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5B,20 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Relative abundance of taxa in individuals who experienced life-threatening childhood trauma compared to those who did not experience life-threatening childhood trauma,increased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis,1783272|1239|526524|526525|2810281|191303|154288,Complete,ChiomaBlessing
bsdb:36651663/4/2,36651663,"cross-sectional observational, not case-control",36651663,10.1080/19490976.2022.2162306,NA,"Malan-Müller S., Valles-Colomer M., Palomo T. , Leza J.C.","The gut-microbiota-brain axis in a Spanish population in the aftermath of the COVID-19 pandemic: microbiota composition linked to anxiety, trauma, and depression profiles",Gut microbes,2023,"COVID-19, Microbiome, anxiety, depression, gut-microbiota-brain axis, mental health, posttraumatic stress disorder, trauma",Experiment 4,Spain,Homo sapiens,Feces,UBERON:0001988,Childhood trauma measurement,EFO:0007979,Individuals who did not experience life-threatening childhood trauma,Individuals who experienced life-threatening childhood trauma,This group included individuals who experienced life-threatening childhood trauma,162,36,6 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5C,20 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Relative abundance of taxa in individuals who experienced life-threatening childhood trauma compared to those who did not experience life-threatening childhood trauma,decreased,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Lentisphaerales|f__Lentisphaeraceae|g__Lentisphaera,3379134|256845|1313211|278081|566277|256846,Complete,ChiomaBlessing
bsdb:36652592/1/1,36652592,case-control,36652592,10.1128/spectrum.02125-22,NA,"Kim G.H., Lee K. , Shim J.O.",Gut Bacterial Dysbiosis in Irritable Bowel Syndrome: a Case-Control Study and a Cross-Cohort Analysis Using Publicly Available Data Sets,Microbiology spectrum,2023,"16S rRNA, diversity, dysbiosis, gastrointestinal, microbiota, microbiota-gut-brain axis",Experiment 1,"South Korea,Russian Federation,Serbia,United States of America,Italy,Spain,Japan,Netherlands",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS,Individuals diagnosed with Irritable Bowel Syndrome according to the Rome IV criteria (for the case-control study) or Rome III criteria (for various shared data sets included in the cross-cohort analysis).,567,487,NA,16S,34,Illumina,centered log-ratio,Meta-Analysis,0.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 10 (mega-cohort IBS vs healthy controls analysis),22 January 2026,Aqc576444,Aqc576444,This signature represents bacterial species that were significantly enriched in IBS compared with healthy controls based on a combined mega-cohort ALDEx2 analysis.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron",3379134|976|200643|171549|815|816|291645;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|815|816|818,Complete,NA
bsdb:36652592/1/2,36652592,case-control,36652592,10.1128/spectrum.02125-22,NA,"Kim G.H., Lee K. , Shim J.O.",Gut Bacterial Dysbiosis in Irritable Bowel Syndrome: a Case-Control Study and a Cross-Cohort Analysis Using Publicly Available Data Sets,Microbiology spectrum,2023,"16S rRNA, diversity, dysbiosis, gastrointestinal, microbiota, microbiota-gut-brain axis",Experiment 1,"South Korea,Russian Federation,Serbia,United States of America,Italy,Spain,Japan,Netherlands",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS,Individuals diagnosed with Irritable Bowel Syndrome according to the Rome IV criteria (for the case-control study) or Rome III criteria (for various shared data sets included in the cross-cohort analysis).,567,487,NA,16S,34,Illumina,centered log-ratio,Meta-Analysis,0.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 10 (mega-cohort IBS vs healthy controls analysis),22 January 2026,Aqc576444,Aqc576444,This signature represents bacterial species that were significantly depleted in IBS compared with healthy controls based on a combined mega-cohort ALDEx2 analysis.,decreased,NA,NA,Complete,NA
bsdb:36652592/1/3,36652592,case-control,36652592,10.1128/spectrum.02125-22,NA,"Kim G.H., Lee K. , Shim J.O.",Gut Bacterial Dysbiosis in Irritable Bowel Syndrome: a Case-Control Study and a Cross-Cohort Analysis Using Publicly Available Data Sets,Microbiology spectrum,2023,"16S rRNA, diversity, dysbiosis, gastrointestinal, microbiota, microbiota-gut-brain axis",Experiment 1,"South Korea,Russian Federation,Serbia,United States of America,Italy,Spain,Japan,Netherlands",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS,Individuals diagnosed with Irritable Bowel Syndrome according to the Rome IV criteria (for the case-control study) or Rome III criteria (for various shared data sets included in the cross-cohort analysis).,567,487,NA,16S,34,Illumina,centered log-ratio,Meta-Analysis,0.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 3,Figure 4,22 January 2026,Aqc576444,Aqc576444,IBS-D vs Healthy Controls (increased),increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,1783272|201174|1760|85007|1653|1716,Complete,NA
bsdb:36652592/1/4,36652592,case-control,36652592,10.1128/spectrum.02125-22,NA,"Kim G.H., Lee K. , Shim J.O.",Gut Bacterial Dysbiosis in Irritable Bowel Syndrome: a Case-Control Study and a Cross-Cohort Analysis Using Publicly Available Data Sets,Microbiology spectrum,2023,"16S rRNA, diversity, dysbiosis, gastrointestinal, microbiota, microbiota-gut-brain axis",Experiment 1,"South Korea,Russian Federation,Serbia,United States of America,Italy,Spain,Japan,Netherlands",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS,Individuals diagnosed with Irritable Bowel Syndrome according to the Rome IV criteria (for the case-control study) or Rome III criteria (for various shared data sets included in the cross-cohort analysis).,567,487,NA,16S,34,Illumina,centered log-ratio,Meta-Analysis,0.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 4,Figure 4,22 January 2026,Aqc576444,Aqc576444,IBS-D vs Healthy Controls (Decreased),decreased,NA,NA,Complete,NA
bsdb:36652592/1/5,36652592,case-control,36652592,10.1128/spectrum.02125-22,NA,"Kim G.H., Lee K. , Shim J.O.",Gut Bacterial Dysbiosis in Irritable Bowel Syndrome: a Case-Control Study and a Cross-Cohort Analysis Using Publicly Available Data Sets,Microbiology spectrum,2023,"16S rRNA, diversity, dysbiosis, gastrointestinal, microbiota, microbiota-gut-brain axis",Experiment 1,"South Korea,Russian Federation,Serbia,United States of America,Italy,Spain,Japan,Netherlands",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS,Individuals diagnosed with Irritable Bowel Syndrome according to the Rome IV criteria (for the case-control study) or Rome III criteria (for various shared data sets included in the cross-cohort analysis).,567,487,NA,16S,34,Illumina,centered log-ratio,Meta-Analysis,0.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 5,Figure 4,22 January 2026,Aqc576444,Aqc576444,IBS-ND vs Healthy Controls (Increased),increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,1783272|1239|186801|3085636|186803|1649459,Complete,NA
bsdb:36652592/1/6,36652592,case-control,36652592,10.1128/spectrum.02125-22,NA,"Kim G.H., Lee K. , Shim J.O.",Gut Bacterial Dysbiosis in Irritable Bowel Syndrome: a Case-Control Study and a Cross-Cohort Analysis Using Publicly Available Data Sets,Microbiology spectrum,2023,"16S rRNA, diversity, dysbiosis, gastrointestinal, microbiota, microbiota-gut-brain axis",Experiment 1,"South Korea,Russian Federation,Serbia,United States of America,Italy,Spain,Japan,Netherlands",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS,Individuals diagnosed with Irritable Bowel Syndrome according to the Rome IV criteria (for the case-control study) or Rome III criteria (for various shared data sets included in the cross-cohort analysis).,567,487,NA,16S,34,Illumina,centered log-ratio,Meta-Analysis,0.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 6,Figure 4,22 January 2026,Aqc576444,Aqc576444,IBS-ND vs Healthy Controls (Decreased),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",3379134|976|200643|171549|2005519;1783272|201174|1760|85009|31957;3379134|976|200643|171549|171550|239759,Complete,NA
bsdb:36678227/1/1,36678227,randomized controlled trial,36678227,10.3390/nu15020356,NA,"Huang F., Li S., Chen W., Han Y., Yao Y., Yang L., Li Q., Xiao Q., Wei J., Liu Z., Chen T. , Deng X.",Postoperative Probiotics Administration Attenuates Gastrointestinal Complications and Gut Microbiota Dysbiosis Caused by Chemotherapy in Colorectal Cancer Patients,Nutrients,2023,"CRC, chemotherapy, gastrointestinal complications, gut microbiota, probiotics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Placebo control group,Probio group,Patients in the Probio group were instructed to take probiotic tablets orally,50,50,2 weeks,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,increased,increased,increased,NA,NA,NA,Signature 1,Figure 4,14 September 2023,Yjung24,"Yjung24,Atrayees,Peace Sandy,WikiWorks","LEfSe cladogram showing differently abundant gut microbiota taxa among CRC patients at
different levels. The current LDA threshold score is over 2; p, phylum; c, class; o, order; f, family; g, genus. The blue, red, and green color refers to different bacterial taxa in CRC group, Placebo, and Probio group, respectively.",increased,"k__Bacillati|p__Actinomycetota|c__Rubrobacteria,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Lactonifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",1783272|201174|84995;1783272|201174|84995|84996;1783272|201174|1760|85006|1268;1783272|201174|84995|84996|84997;3379134|976|200643|171549|171550;1783272|1239|526524|526525|2810281;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|186807;1783272|201174|1760|85006|1268|32207;1783272|201174|84995|84996|84997|42255;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|171550|239759;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|420345;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|186802|216572|244127;3379134|1224|1236|135625|712|724,Complete,Peace Sandy
bsdb:36678227/1/2,36678227,randomized controlled trial,36678227,10.3390/nu15020356,NA,"Huang F., Li S., Chen W., Han Y., Yao Y., Yang L., Li Q., Xiao Q., Wei J., Liu Z., Chen T. , Deng X.",Postoperative Probiotics Administration Attenuates Gastrointestinal Complications and Gut Microbiota Dysbiosis Caused by Chemotherapy in Colorectal Cancer Patients,Nutrients,2023,"CRC, chemotherapy, gastrointestinal complications, gut microbiota, probiotics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Placebo control group,Probio group,Patients in the Probio group were instructed to take probiotic tablets orally,50,50,2 weeks,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,increased,increased,increased,NA,NA,NA,Signature 2,Figure 4,14 September 2023,Yjung24,"Yjung24,Peace Sandy,WikiWorks","LEfSe cladogram showing differently abundant gut microbiota taxa among CRC patients at different levels. The current LDA threshold score is over 2; p, phylum; c, class; o, order; f, family; g, genus. The blue, red, and green color refers to different bacterial taxa in CRC group, Placebo, and Probio group, respectively.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Paraeggerthella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota",1783272|1239|91061|186826|186827|46123;3379134|1224|1236|135625|712|713;1783272|1239|91061|186826|186827;3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3082768|990719|990721|1935934;1783272|1239|91061|186826|81852;1783272|1239|526524|526525|128827;1783272|1239|91061|1385|90964|227979;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;3379134|1224|1236|91347|1903414|581;3379134|976|200643|171549|2005525|375288;1783272|201174|84998|1643822|1643826|651554;3379134|976|200643|171549|171552|577309;3379134|1224|1236|72274|135621;3379134|1224|1236|2887326|468|497;1783272|1239|186801|186802|216572|1263;3379134|74201|203494|48461|203557;3379134|74201|203494;3379134|74201|203494|48461;3379134|74201,Complete,Peace Sandy
bsdb:36678227/2/1,36678227,randomized controlled trial,36678227,10.3390/nu15020356,NA,"Huang F., Li S., Chen W., Han Y., Yao Y., Yang L., Li Q., Xiao Q., Wei J., Liu Z., Chen T. , Deng X.",Postoperative Probiotics Administration Attenuates Gastrointestinal Complications and Gut Microbiota Dysbiosis Caused by Chemotherapy in Colorectal Cancer Patients,Nutrients,2023,"CRC, chemotherapy, gastrointestinal complications, gut microbiota, probiotics",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,CRC [colorectal cancer]  Patients Pre-treatment group,Probio group,Patients in the Probio group were instructed to take probiotic tablets orally,50,50,2 weeks,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,Fig 4,1 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","LEfSe cladogram showing differently abundant gut microbiota taxa among CRC patients at different levels. The current LDA threshold score is over 2; p, phylum; c, class; o, order; f, family; g, genus. The blue, red, and green color refers to different bacterial taxa in CRC group, Placebo, and Probio group, respectively.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Anaerorhabdus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Lactonifactor,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales,k__Bacillati|p__Actinomycetota|c__Rubrobacteria,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae",3379134|976|200643|171549|171550|239759;1783272|1239|526524|526525|128827|118966;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1898204;1783272|1239|186801|186802|204475;3379134|1224|1236|135625|712|724;1783272|1239|186801|186802|31979|420345;1783272|201174|1760|85006|1268;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|186807;1783272|1239|186801|186802|186807|2740;3379134|976|200643|171549|171550;1783272|201174|1760|85006|1268|32207;1783272|201174|84995|84996|84997|42255;1783272|201174|84995|84996|84997;1783272|201174|84995|84996;1783272|201174|84995;1783272|1239|526524|526525|2810281|191303;1783272|1239|526524|526525|2810281,Complete,Peace Sandy
bsdb:36678227/2/2,36678227,randomized controlled trial,36678227,10.3390/nu15020356,NA,"Huang F., Li S., Chen W., Han Y., Yao Y., Yang L., Li Q., Xiao Q., Wei J., Liu Z., Chen T. , Deng X.",Postoperative Probiotics Administration Attenuates Gastrointestinal Complications and Gut Microbiota Dysbiosis Caused by Chemotherapy in Colorectal Cancer Patients,Nutrients,2023,"CRC, chemotherapy, gastrointestinal complications, gut microbiota, probiotics",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,CRC [colorectal cancer]  Patients Pre-treatment group,Probio group,Patients in the Probio group were instructed to take probiotic tablets orally,50,50,2 weeks,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 2,Fig 4,1 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","LEfSe cladogram showing differently abundant gut microbiota taxa among CRC patients at different levels. The current LDA threshold score is over 2; p, phylum; c, class; o, order; f, family; g, genus. The blue, red, and green color refers to different bacterial taxa in CRC group, Placebo, and Probio group, respectively.",decreased,"k__Pseudomonadati|p__Lentisphaerota,k__Pseudomonadati|p__Gemmatimonadota|c__Gemmatimonadia,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae|s__Opitutaceae bacterium TAV5,k__Bacillati|p__Bacillota|c__Clostridia,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Rhodocyclaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",3379134|256845;3379134|142182|219685;3379134|74201|414999|415000|134623|794903;1783272|1239|186801;3379134|256845|1313211;1783272|1239|186801|186802;3379134|256845|1313211|278082;3379134|1224|28216|206389;3379134|1224|28216|80840|80864;3379134|1224|28216|206389|75787;1783272|1239|91061|186826|33958;3379134|256845|1313211|278082|255528;1783272|201174|84998|1643822|1643826|447020;1783272|1239|91061|186826|33958|1578;1783272|1239|1737404|1737405|1570339|162290;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|830;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|841;1783272|1239|909932|1843488|909930|33024;3379134|256845|1313211|278082|255528|172900;3379134|200940|3031449|213115|194924|872,Complete,Peace Sandy
bsdb:36678227/3/1,36678227,randomized controlled trial,36678227,10.3390/nu15020356,NA,"Huang F., Li S., Chen W., Han Y., Yao Y., Yang L., Li Q., Xiao Q., Wei J., Liu Z., Chen T. , Deng X.",Postoperative Probiotics Administration Attenuates Gastrointestinal Complications and Gut Microbiota Dysbiosis Caused by Chemotherapy in Colorectal Cancer Patients,Nutrients,2023,"CRC, chemotherapy, gastrointestinal complications, gut microbiota, probiotics",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,CRC [colorectal cancer] Patients Pre-treatment group,Placebo group,"Patients in the Placebo group routinely treated with placebo tablets instead of
probiotics",50,50,2 weeks,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,decreased,decreased,decreased,NA,NA,NA,Signature 1,Figure 4,14 September 2023,Yjung24,"Yjung24,Peace Sandy,WikiWorks","LEfSe cladogram showing differently abundant gut microbiota taxa among CRC patients at different levels. The current LDA threshold score is over 2; p, phylum; c, class; o, order; f, family; g, genus. The blue, red, and green color refers to different bacterial taxa in CRC group, Placebo, and Probio group, respectively.",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Paraeggerthella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota",1783272|1239|91061|186826|186827|46123;3379134|1224|1236|135625|712|713;1783272|1239|91061|186826|186827;3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3082768|990719|990721|1935934;1783272|1239|91061|186826|81852;1783272|1239|526524|526525|128827;1783272|1239|91061|1385|90964|227979;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;3379134|1224|1236|91347|1903414|581;3379134|976|200643|171549|2005525|375288;1783272|201174|84998|1643822|1643826|651554;3379134|1224|1236|72274|135621;3379134|1224|1236|2887326|468|497;3379134|74201|203494|48461|203557;3379134|74201|203494;3379134|74201|203494|48461;3379134|74201,Complete,Peace Sandy
bsdb:36678227/3/2,36678227,randomized controlled trial,36678227,10.3390/nu15020356,NA,"Huang F., Li S., Chen W., Han Y., Yao Y., Yang L., Li Q., Xiao Q., Wei J., Liu Z., Chen T. , Deng X.",Postoperative Probiotics Administration Attenuates Gastrointestinal Complications and Gut Microbiota Dysbiosis Caused by Chemotherapy in Colorectal Cancer Patients,Nutrients,2023,"CRC, chemotherapy, gastrointestinal complications, gut microbiota, probiotics",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,CRC [colorectal cancer] Patients Pre-treatment group,Placebo group,"Patients in the Placebo group routinely treated with placebo tablets instead of
probiotics",50,50,2 weeks,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,decreased,decreased,decreased,NA,NA,NA,Signature 2,Fig 4,2 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","LEfSe cladogram showing differently abundant gut microbiota taxa among CRC patients at different levels. The current LDA threshold score is over 2; p, phylum; c, class; o, order; f, family; g, genus. The blue, red, and green color refers to different bacterial taxa in CRC group, Placebo, and Probio group, respectively.",decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Pseudomonadati|p__Gemmatimonadota|c__Gemmatimonadia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria,k__Pseudomonadati|p__Lentisphaerota,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Rhodocyclaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis",1783272|201174|84998|1643822|1643826|447020;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|830;1783272|1239|186801;3379134|1224|28216|80840|80864;1783272|1239|186801|3085636|186803|33042;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802;1783272|1239|1737404|1737405|1570339|162290;3379134|142182|219685;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;3379134|256845|1313211;3379134|256845;3379134|74201|414999;1783272|1239|909932|1843488|909930|33024;3379134|1224|28216|206389|75787;3379134|1224|28216|206389;3379134|256845|1313211|278082|255528;3379134|256845|1313211|278082;3379134|256845|1313211|278082|255528|172900,Complete,Peace Sandy
bsdb:36683389/1/1,36683389,"cross-sectional observational, not case-control",36683389,https://doi.org/10.1210/clinem/dgad596,NA,"Biscarini F., Masetti G., Muller I., Verhasselt H.L., Covelli D., Colucci G., Zhang L., Draman M.S., Okosieme O., Taylor P., Daumerie C., Burlacu M.C., Marinò M., Ezra D.G., Perros P., Plummer S., Eckstein A., Salvi M., Marchesi J.R. , Ludgate M.",Gut Microbiome Associated With Graves Disease and Graves Orbitopathy: The INDIGO Multicenter European Study,The Journal of clinical endocrinology and metabolism,2023,"Firmicutes:Bacteroidetes ratio, Graves disease, Graves orbitopathy, autoimmunity, gut microbiota, hyperthyroidism",Experiment 1,"Belgium,Germany,Italy,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Controls,Graves’ disease (GD),Patients with Graves’ disease (GD),41,59,3 months,16S,12,Illumina,relative abundances,T-Test,0.05,TRUE,NA,"age,sex","age,geographic area,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,Figure 1A and 2,24 July 2025,Aleru Divine,Aleru Divine,"Significantly different genera across eye-disease severity (distributed as control, no sign/Graves disease [GD] only, mild, moderate-severe according to the EUGOGO guidelines).",increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter sp.",1783272|201174;1783272|201174|1760|85004|31953|1678|41200;1783272|1239|186801|3085636|186803|1407607|2773922,Complete,NA
bsdb:36683389/1/2,36683389,"cross-sectional observational, not case-control",36683389,https://doi.org/10.1210/clinem/dgad596,NA,"Biscarini F., Masetti G., Muller I., Verhasselt H.L., Covelli D., Colucci G., Zhang L., Draman M.S., Okosieme O., Taylor P., Daumerie C., Burlacu M.C., Marinò M., Ezra D.G., Perros P., Plummer S., Eckstein A., Salvi M., Marchesi J.R. , Ludgate M.",Gut Microbiome Associated With Graves Disease and Graves Orbitopathy: The INDIGO Multicenter European Study,The Journal of clinical endocrinology and metabolism,2023,"Firmicutes:Bacteroidetes ratio, Graves disease, Graves orbitopathy, autoimmunity, gut microbiota, hyperthyroidism",Experiment 1,"Belgium,Germany,Italy,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Controls,Graves’ disease (GD),Patients with Graves’ disease (GD),41,59,3 months,16S,12,Illumina,relative abundances,T-Test,0.05,TRUE,NA,"age,sex","age,geographic area,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 2,Figure 1A and 2,24 July 2025,Aleru Divine,Aleru Divine,"Significantly different genera across eye-disease severity (distributed as control, no sign/Graves disease [GD] only, mild, moderate-severe according to the EUGOGO guidelines).",decreased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.",3379134|976;3379134|976|200643|171549|815|816|29523,Complete,NA
bsdb:36683389/2/1,36683389,"cross-sectional observational, not case-control",36683389,https://doi.org/10.1210/clinem/dgad596,NA,"Biscarini F., Masetti G., Muller I., Verhasselt H.L., Covelli D., Colucci G., Zhang L., Draman M.S., Okosieme O., Taylor P., Daumerie C., Burlacu M.C., Marinò M., Ezra D.G., Perros P., Plummer S., Eckstein A., Salvi M., Marchesi J.R. , Ludgate M.",Gut Microbiome Associated With Graves Disease and Graves Orbitopathy: The INDIGO Multicenter European Study,The Journal of clinical endocrinology and metabolism,2023,"Firmicutes:Bacteroidetes ratio, Graves disease, Graves orbitopathy, autoimmunity, gut microbiota, hyperthyroidism",Experiment 2,"Belgium,Germany,Italy,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Graves ophthalmopathy,EFO:1001466,Controls,Graves’ ophthalmopathy (GO),Patients with Graves’ ophthalmopathy (GD),41,46,3 months,16S,12,Illumina,relative abundances,T-Test,0.05,TRUE,NA,"age,sex","age,geographic area,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,Figure 1A,24 July 2025,Aleru Divine,Aleru Divine,"Distributions of the main phyla Bacteroidetes, Firmicutes, and Actinobacteria in controls (HCs), GD, and Graves orbitopathy (GO) patients.",increased,k__Bacillati|p__Actinomycetota,1783272|201174,Complete,NA
bsdb:36683389/2/2,36683389,"cross-sectional observational, not case-control",36683389,https://doi.org/10.1210/clinem/dgad596,NA,"Biscarini F., Masetti G., Muller I., Verhasselt H.L., Covelli D., Colucci G., Zhang L., Draman M.S., Okosieme O., Taylor P., Daumerie C., Burlacu M.C., Marinò M., Ezra D.G., Perros P., Plummer S., Eckstein A., Salvi M., Marchesi J.R. , Ludgate M.",Gut Microbiome Associated With Graves Disease and Graves Orbitopathy: The INDIGO Multicenter European Study,The Journal of clinical endocrinology and metabolism,2023,"Firmicutes:Bacteroidetes ratio, Graves disease, Graves orbitopathy, autoimmunity, gut microbiota, hyperthyroidism",Experiment 2,"Belgium,Germany,Italy,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Graves ophthalmopathy,EFO:1001466,Controls,Graves’ ophthalmopathy (GO),Patients with Graves’ ophthalmopathy (GD),41,46,3 months,16S,12,Illumina,relative abundances,T-Test,0.05,TRUE,NA,"age,sex","age,geographic area,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 2,Figure 1A,24 July 2025,Aleru Divine,Aleru Divine,"Distributions of the main phyla Bacteroidetes, Firmicutes, and Actinobacteria in controls (HCs), GD, and Graves orbitopathy (GO) patients.",decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,NA
bsdb:36683389/3/1,36683389,"cross-sectional observational, not case-control",36683389,https://doi.org/10.1210/clinem/dgad596,NA,"Biscarini F., Masetti G., Muller I., Verhasselt H.L., Covelli D., Colucci G., Zhang L., Draman M.S., Okosieme O., Taylor P., Daumerie C., Burlacu M.C., Marinò M., Ezra D.G., Perros P., Plummer S., Eckstein A., Salvi M., Marchesi J.R. , Ludgate M.",Gut Microbiome Associated With Graves Disease and Graves Orbitopathy: The INDIGO Multicenter European Study,The Journal of clinical endocrinology and metabolism,2023,"Firmicutes:Bacteroidetes ratio, Graves disease, Graves orbitopathy, autoimmunity, gut microbiota, hyperthyroidism",Experiment 3,"Belgium,Germany,Italy,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Graves ophthalmopathy,EFO:1001466,Controls,Mild Graves’ ophthalmopathy (GO),Patients with mild Graves’ ophthalmopathy (GD),41,36,3 months,16S,12,Illumina,relative abundances,T-Test,0.05,TRUE,NA,"age,sex","age,geographic area,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,24 July 2025,Aleru Divine,Aleru Divine,"Significantly different genera across eye-disease severity (distributed as control, no sign/Graves disease [GD] only, mild, moderate-severe according to the EUGOGO guidelines).",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter sp.",1783272|201174|1760|85004|31953|1678|41200;1783272|1239|186801|3085636|186803|1407607|2773922,Complete,NA
bsdb:36683389/3/2,36683389,"cross-sectional observational, not case-control",36683389,https://doi.org/10.1210/clinem/dgad596,NA,"Biscarini F., Masetti G., Muller I., Verhasselt H.L., Covelli D., Colucci G., Zhang L., Draman M.S., Okosieme O., Taylor P., Daumerie C., Burlacu M.C., Marinò M., Ezra D.G., Perros P., Plummer S., Eckstein A., Salvi M., Marchesi J.R. , Ludgate M.",Gut Microbiome Associated With Graves Disease and Graves Orbitopathy: The INDIGO Multicenter European Study,The Journal of clinical endocrinology and metabolism,2023,"Firmicutes:Bacteroidetes ratio, Graves disease, Graves orbitopathy, autoimmunity, gut microbiota, hyperthyroidism",Experiment 3,"Belgium,Germany,Italy,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Graves ophthalmopathy,EFO:1001466,Controls,Mild Graves’ ophthalmopathy (GO),Patients with mild Graves’ ophthalmopathy (GD),41,36,3 months,16S,12,Illumina,relative abundances,T-Test,0.05,TRUE,NA,"age,sex","age,geographic area,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 2,Figure 2,24 July 2025,Aleru Divine,Aleru Divine,"Significantly different genera across eye-disease severity (distributed as control, no sign/Graves disease [GD] only, mild, moderate-severe according to the EUGOGO guidelines).",decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,3379134|976|200643|171549|815|816|29523,Complete,NA
bsdb:36683389/4/1,36683389,"cross-sectional observational, not case-control",36683389,https://doi.org/10.1210/clinem/dgad596,NA,"Biscarini F., Masetti G., Muller I., Verhasselt H.L., Covelli D., Colucci G., Zhang L., Draman M.S., Okosieme O., Taylor P., Daumerie C., Burlacu M.C., Marinò M., Ezra D.G., Perros P., Plummer S., Eckstein A., Salvi M., Marchesi J.R. , Ludgate M.",Gut Microbiome Associated With Graves Disease and Graves Orbitopathy: The INDIGO Multicenter European Study,The Journal of clinical endocrinology and metabolism,2023,"Firmicutes:Bacteroidetes ratio, Graves disease, Graves orbitopathy, autoimmunity, gut microbiota, hyperthyroidism",Experiment 4,"Belgium,Germany,Italy,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Graves ophthalmopathy,EFO:1001466,Controls,Severe Graves’ ophthalmopathy (GO),Patients with severe Graves’ ophthalmopathy (GD),41,10,3 months,16S,12,Illumina,relative abundances,T-Test,0.05,TRUE,NA,"age,sex","age,geographic area,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,24 July 2025,Aleru Divine,Aleru Divine,"Significantly different genera across eye-disease severity (distributed as control, no sign/Graves disease [GD] only, mild, moderate-severe according to the EUGOGO guidelines).",increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp.,1783272|1239|186801|3085636|186803|841|2049040,Complete,NA
bsdb:36683389/5/1,36683389,"cross-sectional observational, not case-control",36683389,https://doi.org/10.1210/clinem/dgad596,NA,"Biscarini F., Masetti G., Muller I., Verhasselt H.L., Covelli D., Colucci G., Zhang L., Draman M.S., Okosieme O., Taylor P., Daumerie C., Burlacu M.C., Marinò M., Ezra D.G., Perros P., Plummer S., Eckstein A., Salvi M., Marchesi J.R. , Ludgate M.",Gut Microbiome Associated With Graves Disease and Graves Orbitopathy: The INDIGO Multicenter European Study,The Journal of clinical endocrinology and metabolism,2023,"Firmicutes:Bacteroidetes ratio, Graves disease, Graves orbitopathy, autoimmunity, gut microbiota, hyperthyroidism",Experiment 5,"Belgium,Germany,Italy,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Graves ophthalmopathy,EFO:1001466,Graves’ disease (GD),Severe Graves’ ophthalmopathy (GO),Patients with severe Graves’ ophthalmopathy (GD),59,10,3 months,16S,12,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,"age,geographic area,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,24 July 2025,Aleru Divine,Aleru Divine,"Significantly different genera across eye-disease severity (distributed as control, no sign/Graves disease [GD] only, mild, moderate-severe according to the EUGOGO guidelines).",increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp.,1783272|1239|186801|3085636|186803|841|2049040,Complete,NA
bsdb:36683389/6/1,36683389,"cross-sectional observational, not case-control",36683389,https://doi.org/10.1210/clinem/dgad596,NA,"Biscarini F., Masetti G., Muller I., Verhasselt H.L., Covelli D., Colucci G., Zhang L., Draman M.S., Okosieme O., Taylor P., Daumerie C., Burlacu M.C., Marinò M., Ezra D.G., Perros P., Plummer S., Eckstein A., Salvi M., Marchesi J.R. , Ludgate M.",Gut Microbiome Associated With Graves Disease and Graves Orbitopathy: The INDIGO Multicenter European Study,The Journal of clinical endocrinology and metabolism,2023,"Firmicutes:Bacteroidetes ratio, Graves disease, Graves orbitopathy, autoimmunity, gut microbiota, hyperthyroidism",Experiment 6,"Belgium,Germany,Italy,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Graves ophthalmopathy,EFO:1001466,Mild Graves’ ophthalmopathy (GO),Severe Graves’ ophthalmopathy (GO),Patients with severe Graves’ ophthalmopathy (GD),36,10,3 months,16S,12,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,"age,geographic area,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,24 July 2025,Aleru Divine,Aleru Divine,"Significantly different genera across eye-disease severity (distributed as control, no sign/Graves disease [GD] only, mild, moderate-severe according to the EUGOGO guidelines).",increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp.,1783272|1239|186801|3085636|186803|841|2049040,Complete,NA
bsdb:36683389/6/2,36683389,"cross-sectional observational, not case-control",36683389,https://doi.org/10.1210/clinem/dgad596,NA,"Biscarini F., Masetti G., Muller I., Verhasselt H.L., Covelli D., Colucci G., Zhang L., Draman M.S., Okosieme O., Taylor P., Daumerie C., Burlacu M.C., Marinò M., Ezra D.G., Perros P., Plummer S., Eckstein A., Salvi M., Marchesi J.R. , Ludgate M.",Gut Microbiome Associated With Graves Disease and Graves Orbitopathy: The INDIGO Multicenter European Study,The Journal of clinical endocrinology and metabolism,2023,"Firmicutes:Bacteroidetes ratio, Graves disease, Graves orbitopathy, autoimmunity, gut microbiota, hyperthyroidism",Experiment 6,"Belgium,Germany,Italy,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Graves ophthalmopathy,EFO:1001466,Mild Graves’ ophthalmopathy (GO),Severe Graves’ ophthalmopathy (GO),Patients with severe Graves’ ophthalmopathy (GD),36,10,3 months,16S,12,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,"age,geographic area,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 2,Figure 2,24 July 2025,Aleru Divine,Aleru Divine,"Significantly different genera across eye-disease severity (distributed as control, no sign/Graves disease [GD] only, mild, moderate-severe according to the EUGOGO guidelines).",decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,1783272|201174|1760|85004|31953|1678|41200,Complete,NA
bsdb:36687728/1/1,36687728,"cross-sectional observational, not case-control",36687728,10.3389/fnut.2022.1059163,NA,"Moser B., Moore D., Khadka B., Lyons C., Foxall T., Andam C.P., Parker C.J., Ochin C., Garelnabi M., Sevigny J., Thomas W.K., Bigornia S. , Dao M.C.","Association between inflammation, lipopolysaccharide binding protein, and gut microbiota composition in a New Hampshire Bhutanese refugee population with a high burden of type 2 diabetes",Frontiers in nutrition,2022,"Bhutanese refugee adults, gastrointestinal microbiome, inflammation, metabolic endotoxemia, type 2 diabetes",Experiment 1,United States of America,Homo sapiens,"Blood,Feces","UBERON:0000178,UBERON:0001988",Age,EFO:0000246,Non-T2D(prediabetes),type 2 diabetes (T2D),"Participants with chronic metabolic condition characterized by high levels of blood sugar (glucose), insulin resistance, and relative insulin deficiency.",29,21,6 months,WMS,NA,Illumina,raw counts,Spearman Correlation,0.05,TRUE,NA,NA,"age,sex",NA,decreased,NA,unchanged,unchanged,decreased,Signature 1,"Within result text under ""Association between gut microbiota composition and glycemic status"", paragraph 2, line 3-6, figure 3",12 November 2023,Chinelsy,"Chinelsy,MyleeeA,Folakunmi,WikiWorks","Spearman correlation matrix heatmap of inflammatory associated taxonomic groups with clinical biomarkers and dietary data, showing fecal pro-inflammatory bacteria and anti-inflammatory/SCFA-producing bacteria correlated with age.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976|200643|171549|815|816;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|29465,Complete,Folakunmi
bsdb:36687728/1/2,36687728,"cross-sectional observational, not case-control",36687728,10.3389/fnut.2022.1059163,NA,"Moser B., Moore D., Khadka B., Lyons C., Foxall T., Andam C.P., Parker C.J., Ochin C., Garelnabi M., Sevigny J., Thomas W.K., Bigornia S. , Dao M.C.","Association between inflammation, lipopolysaccharide binding protein, and gut microbiota composition in a New Hampshire Bhutanese refugee population with a high burden of type 2 diabetes",Frontiers in nutrition,2022,"Bhutanese refugee adults, gastrointestinal microbiome, inflammation, metabolic endotoxemia, type 2 diabetes",Experiment 1,United States of America,Homo sapiens,"Blood,Feces","UBERON:0000178,UBERON:0001988",Age,EFO:0000246,Non-T2D(prediabetes),type 2 diabetes (T2D),"Participants with chronic metabolic condition characterized by high levels of blood sugar (glucose), insulin resistance, and relative insulin deficiency.",29,21,6 months,WMS,NA,Illumina,raw counts,Spearman Correlation,0.05,TRUE,NA,NA,"age,sex",NA,decreased,NA,unchanged,unchanged,decreased,Signature 2,"Within result text under ""Association between gut microbiota composition and glycemic status"", paragraph 2, line 3-6, figure 3",17 December 2023,Folakunmi,"Folakunmi,WikiWorks","Spearman correlation matrix heatmap of inflammatory associated taxonomic groups with clinical biomarkers and dietary data, showing fecal pro-inflammatory bacteria and anti-inflammatory/SCFA-producing bacteria correlated with age.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853,Complete,Folakunmi
bsdb:36687728/2/1,36687728,"cross-sectional observational, not case-control",36687728,10.3389/fnut.2022.1059163,NA,"Moser B., Moore D., Khadka B., Lyons C., Foxall T., Andam C.P., Parker C.J., Ochin C., Garelnabi M., Sevigny J., Thomas W.K., Bigornia S. , Dao M.C.","Association between inflammation, lipopolysaccharide binding protein, and gut microbiota composition in a New Hampshire Bhutanese refugee population with a high burden of type 2 diabetes",Frontiers in nutrition,2022,"Bhutanese refugee adults, gastrointestinal microbiome, inflammation, metabolic endotoxemia, type 2 diabetes",Experiment 2,United States of America,Homo sapiens,"Feces,Blood","UBERON:0001988,UBERON:0000178",Cytokine,EFO:0003786,Non-Type 2 Diabetes (Prediabetes),Type 2 Diabetes,"Participants with chronic metabolic condition characterized by high levels of blood sugar (glucose), insulin resistance, and relative insulin deficiency, after adjusting for age (used as a covariate).",29,21,6 Months,WMS,NA,Illumina,raw counts,Spearman Correlation,0.05,TRUE,NA,NA,"age,sex",NA,decreased,NA,unchanged,unchanged,decreased,Signature 1,"Within result text under ""Association between gut microbiota composition and glycemic status"", paragraph 3, Figure 3",13 November 2023,MyleeeA,"MyleeeA,Folakunmi,WikiWorks","Spearman correlation matrix heatmap of inflammatory associated taxonomic groups with clinical biomarkers and dietary data, showing fecal pro-inflammatory
bacteria and  anti-inflammatory/SCFA-producing bacteria correlated with the inflammatory cytokine TNF-a",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005525|375288,Complete,Folakunmi
bsdb:36687728/2/2,36687728,"cross-sectional observational, not case-control",36687728,10.3389/fnut.2022.1059163,NA,"Moser B., Moore D., Khadka B., Lyons C., Foxall T., Andam C.P., Parker C.J., Ochin C., Garelnabi M., Sevigny J., Thomas W.K., Bigornia S. , Dao M.C.","Association between inflammation, lipopolysaccharide binding protein, and gut microbiota composition in a New Hampshire Bhutanese refugee population with a high burden of type 2 diabetes",Frontiers in nutrition,2022,"Bhutanese refugee adults, gastrointestinal microbiome, inflammation, metabolic endotoxemia, type 2 diabetes",Experiment 2,United States of America,Homo sapiens,"Feces,Blood","UBERON:0001988,UBERON:0000178",Cytokine,EFO:0003786,Non-Type 2 Diabetes (Prediabetes),Type 2 Diabetes,"Participants with chronic metabolic condition characterized by high levels of blood sugar (glucose), insulin resistance, and relative insulin deficiency, after adjusting for age (used as a covariate).",29,21,6 Months,WMS,NA,Illumina,raw counts,Spearman Correlation,0.05,TRUE,NA,NA,"age,sex",NA,decreased,NA,unchanged,unchanged,decreased,Signature 2,"Within result text under ""Association between gut microbiota composition and glycemic status"", paragraph 3, Figure 3",13 November 2023,MyleeeA,"MyleeeA,Folakunmi,WikiWorks","Spearman correlation matrix heatmap of inflammatory associated taxonomic groups with clinical biomarkers and dietary data, showing fecal pro-inflammatory bacteria and anti-inflammatory/SCFA-producing bacteria correlated with the inflammatory cytokine TNF-a",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens",3379134|976|200643|171549|171552|838;1783272|201174|84998|84999|84107|102106|74426,Complete,Folakunmi
bsdb:36687728/4/1,36687728,"cross-sectional observational, not case-control",36687728,10.3389/fnut.2022.1059163,NA,"Moser B., Moore D., Khadka B., Lyons C., Foxall T., Andam C.P., Parker C.J., Ochin C., Garelnabi M., Sevigny J., Thomas W.K., Bigornia S. , Dao M.C.","Association between inflammation, lipopolysaccharide binding protein, and gut microbiota composition in a New Hampshire Bhutanese refugee population with a high burden of type 2 diabetes",Frontiers in nutrition,2022,"Bhutanese refugee adults, gastrointestinal microbiome, inflammation, metabolic endotoxemia, type 2 diabetes",Experiment 4,United States of America,Homo sapiens,"Feces,Blood","UBERON:0000178,UBERON:0001988",HbA1c measurement,EFO:0004541,Non-Type 2 Diabetes (Prediabetes),Type 2 Diabetes,"Participants with chronic metabolic condition characterized by high levels of blood sugar (glucose), insulin resistance, and relative insulin deficiency, after adjusting for age (used as a covariate).",29,21,6 Months,WMS,NA,Illumina,raw counts,Spearman Correlation,0.05,TRUE,NA,NA,"age,sex",NA,decreased,NA,unchanged,unchanged,decreased,Signature 1,"Within result text under ""Association between gut microbiota composition and glycemic status"", paragraphs 3 and 4, Figure 3",17 December 2023,Folakunmi,"Folakunmi,WikiWorks","Spearman correlation matrix heatmap of inflammatory associated taxonomic groups with clinical biomarkers and dietary data, showing fecal pro-inflammatory bacteria and anti-inflammatory/SCFA-producing bacteria correlated with HbA1c",increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,1783272|1239|909932|1843488|909930|33024,Complete,Folakunmi
bsdb:36687728/4/2,36687728,"cross-sectional observational, not case-control",36687728,10.3389/fnut.2022.1059163,NA,"Moser B., Moore D., Khadka B., Lyons C., Foxall T., Andam C.P., Parker C.J., Ochin C., Garelnabi M., Sevigny J., Thomas W.K., Bigornia S. , Dao M.C.","Association between inflammation, lipopolysaccharide binding protein, and gut microbiota composition in a New Hampshire Bhutanese refugee population with a high burden of type 2 diabetes",Frontiers in nutrition,2022,"Bhutanese refugee adults, gastrointestinal microbiome, inflammation, metabolic endotoxemia, type 2 diabetes",Experiment 4,United States of America,Homo sapiens,"Feces,Blood","UBERON:0000178,UBERON:0001988",HbA1c measurement,EFO:0004541,Non-Type 2 Diabetes (Prediabetes),Type 2 Diabetes,"Participants with chronic metabolic condition characterized by high levels of blood sugar (glucose), insulin resistance, and relative insulin deficiency, after adjusting for age (used as a covariate).",29,21,6 Months,WMS,NA,Illumina,raw counts,Spearman Correlation,0.05,TRUE,NA,NA,"age,sex",NA,decreased,NA,unchanged,unchanged,decreased,Signature 2,"Within result text under ""Association between gut microbiota composition and glycemic status"", paragraphs 3 and 4, Figure 3",17 December 2023,Folakunmi,"Folakunmi,WikiWorks","Spearman correlation matrix heatmap of inflammatory associated taxonomic groups with clinical biomarkers and dietary data, showing fecal pro-inflammatory bacteria and anti-inflammatory/SCFA-producing bacteria correlated with HbA1c",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,1783272|1239|186801|186802|31979|1485,Complete,Folakunmi
bsdb:36691982/1/1,36691982,meta-analysis,36691982,10.1002/mds.29300,NA,"Boktor J.C., Sharon G., Verhagen Metman L.A., Hall D.A., Engen P.A., Zreloff Z., Hakim D.J., Bostick J.W., Ousey J., Lange D., Humphrey G., Ackermann G., Carlin M., Knight R., Keshavarzian A. , Mazmanian S.K.",Integrated Multi-Cohort Analysis of the Parkinson's Disease Gut Metagenome,Movement disorders : official journal of the Movement Disorder Society,2023,"Parkinson's disease, dysbiosis, gut microbiome, microbial metabolism, shotgun metagenomics",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,HC: household controls,PD: individuals with Parkinson's disease,"cohort 1: movement disorder specialists examined and confirmed the diagnosis of all PD participants at a baseline screening. Parkinsonian symptoms were assessed using the Unified Parkinson's Disease Rating Scale (UPDRS) and Hoehn and Yahr (H&Y) staging scale.
cohort 2: PD participants were self-identified, verifying that they had received a PD diagnosis from a qualified physician.",56,88,3 months,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure S2,10 March 2024,Idiaru angela,"Idiaru angela,WikiWorks",Summary of differential abundance results contrasting household controls and PD patients.,increased,k__Pseudomonadati|p__Verrucomicrobiota,3379134|74201,Complete,Folakunmi
bsdb:36691982/1/2,36691982,meta-analysis,36691982,10.1002/mds.29300,NA,"Boktor J.C., Sharon G., Verhagen Metman L.A., Hall D.A., Engen P.A., Zreloff Z., Hakim D.J., Bostick J.W., Ousey J., Lange D., Humphrey G., Ackermann G., Carlin M., Knight R., Keshavarzian A. , Mazmanian S.K.",Integrated Multi-Cohort Analysis of the Parkinson's Disease Gut Metagenome,Movement disorders : official journal of the Movement Disorder Society,2023,"Parkinson's disease, dysbiosis, gut microbiome, microbial metabolism, shotgun metagenomics",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,HC: household controls,PD: individuals with Parkinson's disease,"cohort 1: movement disorder specialists examined and confirmed the diagnosis of all PD participants at a baseline screening. Parkinsonian symptoms were assessed using the Unified Parkinson's Disease Rating Scale (UPDRS) and Hoehn and Yahr (H&Y) staging scale.
cohort 2: PD participants were self-identified, verifying that they had received a PD diagnosis from a qualified physician.",56,88,3 months,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure S2,11 March 2024,Idiaru angela,"Idiaru angela,WikiWorks",Summary of differential abundance results contrasting household controls and PD patients.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,1783272|1239|186801|3085636|186803|841,Complete,Folakunmi
bsdb:36691982/2/1,36691982,meta-analysis,36691982,10.1002/mds.29300,NA,"Boktor J.C., Sharon G., Verhagen Metman L.A., Hall D.A., Engen P.A., Zreloff Z., Hakim D.J., Bostick J.W., Ousey J., Lange D., Humphrey G., Ackermann G., Carlin M., Knight R., Keshavarzian A. , Mazmanian S.K.",Integrated Multi-Cohort Analysis of the Parkinson's Disease Gut Metagenome,Movement disorders : official journal of the Movement Disorder Society,2023,"Parkinson's disease, dysbiosis, gut microbiome, microbial metabolism, shotgun metagenomics",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,PC: healthy population controls without Parkinson's Disease,PD: Individuals with Parkinson's disease,"cohort 1: movement disorder specialists examined and confirmed the diagnosis of all PD participants at a baseline screening. Parkinsonian symptoms were assessed using the Unified Parkinson's Disease Rating Scale (UPDRS) and Hoehn and Yahr (H&Y) staging scale. 
cohort 2: PD participants were self-identified, verifying that they had received a PD diagnosis from a qualified physician.",83,88,3 months,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.1,TRUE,NA,"age,body mass index,race,sex",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 2 & figure S2,11 March 2024,Idiaru angela,"Idiaru angela,Folakunmi,WikiWorks",Summary of differential abundance results contrasting healthy population controls and PD patients.,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella tayi,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans",1783272|201174;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|3085636|186803|1432051|1432052;1783272|1239|186801|186802|216572|1905344;1783272|1239|186801|186802|216572|1905344|1550024,Complete,Folakunmi
bsdb:36691982/2/2,36691982,meta-analysis,36691982,10.1002/mds.29300,NA,"Boktor J.C., Sharon G., Verhagen Metman L.A., Hall D.A., Engen P.A., Zreloff Z., Hakim D.J., Bostick J.W., Ousey J., Lange D., Humphrey G., Ackermann G., Carlin M., Knight R., Keshavarzian A. , Mazmanian S.K.",Integrated Multi-Cohort Analysis of the Parkinson's Disease Gut Metagenome,Movement disorders : official journal of the Movement Disorder Society,2023,"Parkinson's disease, dysbiosis, gut microbiome, microbial metabolism, shotgun metagenomics",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,PC: healthy population controls without Parkinson's Disease,PD: Individuals with Parkinson's disease,"cohort 1: movement disorder specialists examined and confirmed the diagnosis of all PD participants at a baseline screening. Parkinsonian symptoms were assessed using the Unified Parkinson's Disease Rating Scale (UPDRS) and Hoehn and Yahr (H&Y) staging scale. 
cohort 2: PD participants were self-identified, verifying that they had received a PD diagnosis from a qualified physician.",83,88,3 months,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.1,TRUE,NA,"age,body mass index,race,sex",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 2 & figure S2,11 March 2024,Idiaru angela,"Idiaru angela,Folakunmi,WikiWorks",Summary of differential abundance results contrasting healthy population controls and PD patients.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:95,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio",1783272|1239|186801|186802|216572|216851|853;1783272|1239|1262988;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|830,Complete,Folakunmi
bsdb:36719190/1/1,36719190,case-control,36719190,10.1128/spectrum.02819-22,NA,"Wang Z., Liang L., Liu L., Wang Z., Wang Y., Yu Z., Wu B. , Chen Y.",Changes in the Gut Microbiome Associated with Intussusception in Patients with Peutz-Jeghers Syndrome,Microbiology spectrum,2023,"Peutz-Jeghers syndrome, biomarkers, functional analysis, gut microbiota, intussusception",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Peutz-Jeghers Polyp,EFO:1000470,healthy control (family members),Peutz-Jeghers syndrome (PJS),Patients who has Peutz-Jeghers syndrome (PJS),68,168,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,NA,NA,unchanged,NA,NA,Signature 1,FIG 1 (F),19 March 2024,Rahila,"Rahila,Scholastica,WikiWorks",LEfSe analysis identified the differentially abundant taxa between Peutz-Jeghers syndrome (PJS) patients and healthy controls (LDA > 3.0),increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|1940338;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066|203490|203491|203492|848;3379134|1224|1236;3379134|1224|1236|91347|543|570;3379134|1224;1783272|1239|909932|1843489|31977|29465;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201,Complete,Svetlana up
bsdb:36719190/1/2,36719190,case-control,36719190,10.1128/spectrum.02819-22,NA,"Wang Z., Liang L., Liu L., Wang Z., Wang Y., Yu Z., Wu B. , Chen Y.",Changes in the Gut Microbiome Associated with Intussusception in Patients with Peutz-Jeghers Syndrome,Microbiology spectrum,2023,"Peutz-Jeghers syndrome, biomarkers, functional analysis, gut microbiota, intussusception",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Peutz-Jeghers Polyp,EFO:1000470,healthy control (family members),Peutz-Jeghers syndrome (PJS),Patients who has Peutz-Jeghers syndrome (PJS),68,168,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,NA,NA,unchanged,NA,NA,Signature 2,FIG 1 (F),25 June 2024,Scholastica,"Scholastica,WikiWorks",LEfSe analysis identified the differentially abundant taxa between Peutz-Jeghers syndrome (PJS) patients and healthy controls (LDA > 3.0),decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",1783272|1239;3379134|1224|28216|80840|119060;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3082720|186804|1505657;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|909929|1843491|52225;1783272|1239|186801|186802|216572;1783272|1239|186801|3082720|186804;1783272|1239|186801|186802|216572|292632;3379134|1224|28216|80840|995019|40544,Complete,Svetlana up
bsdb:36719190/2/1,36719190,case-control,36719190,10.1128/spectrum.02819-22,NA,"Wang Z., Liang L., Liu L., Wang Z., Wang Y., Yu Z., Wu B. , Chen Y.",Changes in the Gut Microbiome Associated with Intussusception in Patients with Peutz-Jeghers Syndrome,Microbiology spectrum,2023,"Peutz-Jeghers syndrome, biomarkers, functional analysis, gut microbiota, intussusception",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Peutz-Jeghers Polyp,EFO:1000470,Without Intussusception (NI-PJS),With Intussusception (I-PJS),Patients who had undergone at least one intussusception (I-PJS),57,106,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,NA,NA,unchanged,NA,NA,Signature 1,FIG 2 (D),19 March 2024,Rahila,"Rahila,WikiWorks",LEfSe analysis identified the differences in abundance between I-PJS and NI-PJS patients (LDA > 3.0).,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia",1783272|201174;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;3379134|1224|28216|80840|119060;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1501226,Complete,Svetlana up
bsdb:36719190/2/2,36719190,case-control,36719190,10.1128/spectrum.02819-22,NA,"Wang Z., Liang L., Liu L., Wang Z., Wang Y., Yu Z., Wu B. , Chen Y.",Changes in the Gut Microbiome Associated with Intussusception in Patients with Peutz-Jeghers Syndrome,Microbiology spectrum,2023,"Peutz-Jeghers syndrome, biomarkers, functional analysis, gut microbiota, intussusception",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Peutz-Jeghers Polyp,EFO:1000470,Without Intussusception (NI-PJS),With Intussusception (I-PJS),Patients who had undergone at least one intussusception (I-PJS),57,106,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,NA,NA,unchanged,NA,NA,Signature 2,FIG 2 (D),19 March 2024,Rahila,"Rahila,WikiWorks",LEfSe analysis identified the differences in abundance between I-PJS and NI-PJS patients (LDA > 3.0).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota",1783272|1239|186801|3085636|186803|572511;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|1940338;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066|203490|203491|203492|848;3379134|1224|1236;3379134|1224|1236|91347|543|570;3379134|1224,Complete,Svetlana up
bsdb:36719190/3/1,36719190,case-control,36719190,10.1128/spectrum.02819-22,NA,"Wang Z., Liang L., Liu L., Wang Z., Wang Y., Yu Z., Wu B. , Chen Y.",Changes in the Gut Microbiome Associated with Intussusception in Patients with Peutz-Jeghers Syndrome,Microbiology spectrum,2023,"Peutz-Jeghers syndrome, biomarkers, functional analysis, gut microbiota, intussusception",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Peutz-Jeghers Polyp,EFO:1000470,healthy control (family members),Peutz-Jeghers syndrome (PJS),Patients who has Peutz-Jeghers syndrome (PJS),27,61,3 months,WMS,NA,Illumina,relative abundances,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 3 (D),19 March 2024,Rahila,"Rahila,Scholastica,WikiWorks",LEfSe analysis identified the differential species between Peutz-Jeghers syndrome (PJS) patients and healthy controls (LDA > 2.0),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella quasipneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella variicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Plesiomonas|s__Plesiomonas shigelloides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella boydii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella dysenteriae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella flexneri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella sonnei,,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|1236|2887326|468|469|470;3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|543|570|573;3379134|1224|1236|91347|543|570|1463165;3379134|1224|1236|91347|543|570|244366;3379134|976|200643|171549|171552|2974265|363265;3379134|976|200643|171549|171552|2974265|363265;3379134|1224|1236|91347|543|702|703;3379134|1224|1236|91347|543|590|28901;3379134|1224|1236|91347|543|620|621;3379134|1224|1236|91347|543|620|622;3379134|1224|1236|91347|543|620|623;3379134|1224|1236|91347|543|620|624;;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|561;3379134|1224|1236;3379134|1224|1236|91347|543|570;3379134|1224,Complete,Svetlana up
bsdb:36719190/3/2,36719190,case-control,36719190,10.1128/spectrum.02819-22,NA,"Wang Z., Liang L., Liu L., Wang Z., Wang Y., Yu Z., Wu B. , Chen Y.",Changes in the Gut Microbiome Associated with Intussusception in Patients with Peutz-Jeghers Syndrome,Microbiology spectrum,2023,"Peutz-Jeghers syndrome, biomarkers, functional analysis, gut microbiota, intussusception",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Peutz-Jeghers Polyp,EFO:1000470,healthy control (family members),Peutz-Jeghers syndrome (PJS),Patients who has Peutz-Jeghers syndrome (PJS),27,61,3 months,WMS,NA,Illumina,relative abundances,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,FIG 3 (D),25 June 2024,Scholastica,"Scholastica,WikiWorks",LEfSe analysis identified the differential species between Peutz-Jeghers syndrome (PJS) patients and healthy controls (LDA > 2.0),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum|s__Azospirillum sp. 51_20,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__uncultured Faecalibacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium disporicum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF27-2AA,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AM33-3,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. ICM47,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:227,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. SS2/1,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:248,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia",1783272|1239|186801|186802|216572|216851|853;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803|207244|649756;3379134|1224|28211|204441|2829815|191|1896972;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3082720|186804|1501226|1776391;1783272|1239|186801|186802|216572|216851|1971605;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3082720|186804|1505657|261299;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|2316020|46228;1783272|1239|526524|526525|128827;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|186802|216572|216851|259315;1783272|1239|186801|186802|31979|1485|84024;1783272|1239|186801|186802|31979|1485|2292206;1783272|1239|186801|186802|31979|1485|2292304;1783272|1239|186801|3085636|186803|189330;1783272|201174|1760|2037|2049|1654|936548;1783272|1239|1263010;1783272|1239|186801|186802|31979|1485|411484;1783272|1239|186801|186802|186806|1730|1262885;3379134|1224|28216|80840|80864|80865,Complete,Svetlana up
bsdb:36719190/4/1,36719190,case-control,36719190,10.1128/spectrum.02819-22,NA,"Wang Z., Liang L., Liu L., Wang Z., Wang Y., Yu Z., Wu B. , Chen Y.",Changes in the Gut Microbiome Associated with Intussusception in Patients with Peutz-Jeghers Syndrome,Microbiology spectrum,2023,"Peutz-Jeghers syndrome, biomarkers, functional analysis, gut microbiota, intussusception",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Peutz-Jeghers Polyp,EFO:1000470,Without Intussusception (NI-PJS),With Intussusception (I-PJS),Patients who had undergone at least one intussusception (I-PJS),26,35,3 months,WMS,NA,Illumina,relative abundances,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 4 (D),19 March 2024,Rahila,"Rahila,WikiWorks",LEfSe analysis showed the differential species between I-PJS and NI-PJS patients (LDA > 2.0).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas|s__Aeromonas veronii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella sp. AF08-23,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium necrogenes,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,s__bacterium 1xD8-27",3379134|1224|1236|135624|84642|642|654;1783272|201174|84998|84999|84107|102106|2292211;1783272|1239|909932|1843489|31977|39948|218538;3384189|32066|203490|203491|203492|848|858;3384189|32066|203490|203491|203492|848|68766;3379134|1224|1236|135624|84642|642;2320108,Complete,Svetlana up
bsdb:36719190/4/2,36719190,case-control,36719190,10.1128/spectrum.02819-22,NA,"Wang Z., Liang L., Liu L., Wang Z., Wang Y., Yu Z., Wu B. , Chen Y.",Changes in the Gut Microbiome Associated with Intussusception in Patients with Peutz-Jeghers Syndrome,Microbiology spectrum,2023,"Peutz-Jeghers syndrome, biomarkers, functional analysis, gut microbiota, intussusception",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Peutz-Jeghers Polyp,EFO:1000470,Without Intussusception (NI-PJS),With Intussusception (I-PJS),Patients who had undergone at least one intussusception (I-PJS),26,35,3 months,WMS,NA,Illumina,relative abundances,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,FIG 4 (D),19 March 2024,Rahila,"Rahila,WikiWorks",LEfSe analysis showed the differential species between I-PJS and NI-PJS patients (LDA > 2.0).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. CAG:74_58_120,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. AM42-24,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. AF10-46,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae",1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|1971605;1783272|1239|186801|186802|216572|216851|1897005;3379134|976|200643|171549|171552|838|2293125;3379134|976|200643|171549|171550|239759|1288121;3379134|976|117743|200644|49546;3379134|976|200643|171549|2005519|1348911|1099853;1783272|1239|186801|186802|216572|216851|2302955;3379134|1224|1236|135625|712|724|729,Complete,Svetlana up
bsdb:36719617/1/1,36719617,case-control,36719617,https://doi.org/10.1007/s13760-023-02195-0,NA,"Babacan Yildiz G., Kayacan Z.C., Karacan I., Sumbul B., Elibol B., Gelisin O. , Akgul O.",Altered gut microbiota in patients with idiopathic Parkinson's disease: an age-sex matched case-control study,Acta neurologica Belgica,2023,"16S rRNA sequencing, Gut microbiota, Non-motor symptoms, Parkinson’s disease",Experiment 1,Turkey,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy spouses,Patients with Parkinson's disease,Patients were diagnosed with idiopathic Parkinson's disease (PD),42,42,3 months,16S,34,Illumina,arcsine square-root,MaAsLin2,0.25,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 2,19 December 2024,Karima,"Karima,WikiWorks",Significantly Increased different taxa in relative abundances between PD patients and healthy control,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales",1783272|1239|909932|1843488;3379134|74201|203494|48461|1647988;1783272|1239|91061;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;3379134|256845|1313211;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201;3379134|256845|1313211|278082,Complete,Svetlana up
bsdb:36719617/1/2,36719617,case-control,36719617,https://doi.org/10.1007/s13760-023-02195-0,NA,"Babacan Yildiz G., Kayacan Z.C., Karacan I., Sumbul B., Elibol B., Gelisin O. , Akgul O.",Altered gut microbiota in patients with idiopathic Parkinson's disease: an age-sex matched case-control study,Acta neurologica Belgica,2023,"16S rRNA sequencing, Gut microbiota, Non-motor symptoms, Parkinson’s disease",Experiment 1,Turkey,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy spouses,Patients with Parkinson's disease,Patients were diagnosed with idiopathic Parkinson's disease (PD),42,42,3 months,16S,34,Illumina,arcsine square-root,MaAsLin2,0.25,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 2,19 December 2024,Karima,"Karima,WikiWorks",Significantly decreased different taxa in relative abundances between PD patients and healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239;1783272|201174|84998|84999|84107;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636;1783272|1239|186801|186802|216572|1263|438033;1783272|1239|186801|3085636|186803|1506577,Complete,Svetlana up
bsdb:36719617/2/1,36719617,case-control,36719617,https://doi.org/10.1007/s13760-023-02195-0,NA,"Babacan Yildiz G., Kayacan Z.C., Karacan I., Sumbul B., Elibol B., Gelisin O. , Akgul O.",Altered gut microbiota in patients with idiopathic Parkinson's disease: an age-sex matched case-control study,Acta neurologica Belgica,2023,"16S rRNA sequencing, Gut microbiota, Non-motor symptoms, Parkinson’s disease",Experiment 2,Turkey,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy spouses,more than 5 years PD patients,"Patients were diagnosed with idiopathic PD according to the UK Brain Bank criteria by a movement disorder specialist, and the original Hoehn + Yahr scale was followed for disease staging",42,42,3 months,16S,34,Illumina,arcsine square-root,MaAsLin2,0.25,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 3,20 December 2024,Karima,"Karima,WikiWorks",Comparison of Taxa Relative Abundances Among PD Patients Based on Disease Duration (≥5 Years),decreased,k__Bacillati|p__Cyanobacteriota,1783272|1117,Complete,Svetlana up
bsdb:36719617/3/1,36719617,case-control,36719617,https://doi.org/10.1007/s13760-023-02195-0,NA,"Babacan Yildiz G., Kayacan Z.C., Karacan I., Sumbul B., Elibol B., Gelisin O. , Akgul O.",Altered gut microbiota in patients with idiopathic Parkinson's disease: an age-sex matched case-control study,Acta neurologica Belgica,2023,"16S rRNA sequencing, Gut microbiota, Non-motor symptoms, Parkinson’s disease",Experiment 3,Turkey,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy spouses,PD patients with REM sleep behavior disorder,"Patients who has Parkinson's disease and REM sleep behavior disorder(RBD), a sleep disorder in which they physically act out your dreams unknowingly while they’re asleep",42,42,3 months,16S,34,Illumina,arcsine square-root,MaAsLin2,0.25,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 2,27 December 2024,Karima,"Karima,WikiWorks","Genus found to be significantly increased in
PD patients with RBD",increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:36719617/3/2,36719617,case-control,36719617,https://doi.org/10.1007/s13760-023-02195-0,NA,"Babacan Yildiz G., Kayacan Z.C., Karacan I., Sumbul B., Elibol B., Gelisin O. , Akgul O.",Altered gut microbiota in patients with idiopathic Parkinson's disease: an age-sex matched case-control study,Acta neurologica Belgica,2023,"16S rRNA sequencing, Gut microbiota, Non-motor symptoms, Parkinson’s disease",Experiment 3,Turkey,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy spouses,PD patients with REM sleep behavior disorder,"Patients who has Parkinson's disease and REM sleep behavior disorder(RBD), a sleep disorder in which they physically act out your dreams unknowingly while they’re asleep",42,42,3 months,16S,34,Illumina,arcsine square-root,MaAsLin2,0.25,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 2,27 December 2024,Karima,"Karima,WikiWorks","Genus found to be significantly changed in 
PD patients with RBD",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,1783272|1239|186801|3085636|186803|1407607,Complete,Svetlana up
bsdb:36719617/4/1,36719617,case-control,36719617,https://doi.org/10.1007/s13760-023-02195-0,NA,"Babacan Yildiz G., Kayacan Z.C., Karacan I., Sumbul B., Elibol B., Gelisin O. , Akgul O.",Altered gut microbiota in patients with idiopathic Parkinson's disease: an age-sex matched case-control study,Acta neurologica Belgica,2023,"16S rRNA sequencing, Gut microbiota, Non-motor symptoms, Parkinson’s disease",Experiment 4,Turkey,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy spouses,PD patients without RBD,"Patients who has Parkinson's disease without REM sleep behavior disorder(RBD), a sleep disorder in which they physically act out your dreams unknowingly while they’re asleep",42,42,3 months,16S,34,Illumina,arcsine square-root,MaAsLin2,0.25,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 2,27 December 2024,Karima,"Karima,KateRasheed,WikiWorks","Genus found to be significantly changed in
PD patient without RBD",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239|186801|3085636|186803|1407607;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:36719617/6/1,36719617,case-control,36719617,https://doi.org/10.1007/s13760-023-02195-0,NA,"Babacan Yildiz G., Kayacan Z.C., Karacan I., Sumbul B., Elibol B., Gelisin O. , Akgul O.",Altered gut microbiota in patients with idiopathic Parkinson's disease: an age-sex matched case-control study,Acta neurologica Belgica,2023,"16S rRNA sequencing, Gut microbiota, Non-motor symptoms, Parkinson’s disease",Experiment 6,Turkey,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,PD patients without constipation,PD patients with constipation,Parkinson's disease patients who has constipation,42,42,3 months,16S,34,Illumina,arcsine square-root,MaAsLin2,0.25,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,27 December 2024,Karima,"Karima,WikiWorks",Comparison of taxa relative abundances among PD patients with and without constipation,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,1783272|1239|186801|3085636|186803|2316020|33038,Complete,Svetlana up
bsdb:36719617/7/1,36719617,case-control,36719617,https://doi.org/10.1007/s13760-023-02195-0,NA,"Babacan Yildiz G., Kayacan Z.C., Karacan I., Sumbul B., Elibol B., Gelisin O. , Akgul O.",Altered gut microbiota in patients with idiopathic Parkinson's disease: an age-sex matched case-control study,Acta neurologica Belgica,2023,"16S rRNA sequencing, Gut microbiota, Non-motor symptoms, Parkinson’s disease",Experiment 7,Turkey,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,PD patients without RBD,PD patients with RBD,"Patients who has Parkinson's disease and REM sleep behavior disorder(RBD), a sleep disorder in which they physically act out your dreams unknowingly while they’re asleep",42,42,3 months,16S,34,Illumina,arcsine square-root,MaAsLin2,0.25,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,28 December 2024,Karima,"Karima,WikiWorks",Comparison of taxa relative abundances among PD patients with and without RBD,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:56,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|186802|216572|1263|438033;1783272|1239|1263031;1783272|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:36719617/7/2,36719617,case-control,36719617,https://doi.org/10.1007/s13760-023-02195-0,NA,"Babacan Yildiz G., Kayacan Z.C., Karacan I., Sumbul B., Elibol B., Gelisin O. , Akgul O.",Altered gut microbiota in patients with idiopathic Parkinson's disease: an age-sex matched case-control study,Acta neurologica Belgica,2023,"16S rRNA sequencing, Gut microbiota, Non-motor symptoms, Parkinson’s disease",Experiment 7,Turkey,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,PD patients without RBD,PD patients with RBD,"Patients who has Parkinson's disease and REM sleep behavior disorder(RBD), a sleep disorder in which they physically act out your dreams unknowingly while they’re asleep",42,42,3 months,16S,34,Illumina,arcsine square-root,MaAsLin2,0.25,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,28 December 2024,Karima,"Karima,WikiWorks",Comparison of taxa relative abundances among PD patients with and without RBD,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus",1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843488|909930|904,Complete,Svetlana up
bsdb:36719617/8/1,36719617,case-control,36719617,https://doi.org/10.1007/s13760-023-02195-0,NA,"Babacan Yildiz G., Kayacan Z.C., Karacan I., Sumbul B., Elibol B., Gelisin O. , Akgul O.",Altered gut microbiota in patients with idiopathic Parkinson's disease: an age-sex matched case-control study,Acta neurologica Belgica,2023,"16S rRNA sequencing, Gut microbiota, Non-motor symptoms, Parkinson’s disease",Experiment 8,Turkey,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,PD patients without anosmia,PD patients with anosmia,Parkinson's Disease patient who has lost of the ability to detect one or more smells,42,42,3 months,16S,34,Illumina,arcsine square-root,MaAsLin2,0.25,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,28 December 2024,Karima,"Karima,WikiWorks",Comparison of taxa relative abundances among PD patients with and without anosmia,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota",1783272|201174|84998|84999|1643824;1783272|1239|91061;3379134|1224|1236;3379134|1224,Complete,Svetlana up
bsdb:36721179/1/1,36721179,laboratory experiment,36721179,https://doi.org/10.1186/s40168-022-01452-3,NA,"Wang X., Wang Z., Cao J., Dong Y. , Chen Y.",Gut microbiota-derived metabolites mediate the neuroprotective effect of melatonin in cognitive impairment induced by sleep deprivation,Microbiome,2023,"Cognitive impairment, Hippocampus, Melatonin, Microbial–gut–brain axis, Sleep deprivation",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,SD-FMT AND SD+MEL-FMT,CON-FMT: receiving control microbiota FMT mice,FMT administered mice without sleep deprivation.,7,7,NA,16S,123456789,NA,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,fig 4,13 October 2023,Davvve,"Davvve,Chinelsy,Peace Sandy,Folakunmi,WikiWorks",Difference between the gut microbiome of the CON- FNT and the SD-FMT groups by LEFse,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres,k__Pseudomonadati|p__Deferribacterota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum|s__Mucispirillum schaedleri,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,s__uncultured bacterium A2_10",1783272|1239|186801|186802|31979|1485|1506;3379134|200930|68337|191393|191394;3379134|200930|68337|191393;3379134|200930|68337;3379134|200930;1783272|1239|186801|3085636|186803|877420;3379134|200930|68337|191393|2945020|248038;3379134|200930|68337|191393|2945020|248038|248039;1783272|1239|186801|186802|216572|1508657;3379134|1224|28216|80840|995019|1918598;1783272|1239|186801|3085636|186803|297314;1112285,Complete,Folakunmi
bsdb:36721179/2/1,36721179,laboratory experiment,36721179,https://doi.org/10.1186/s40168-022-01452-3,NA,"Wang X., Wang Z., Cao J., Dong Y. , Chen Y.",Gut microbiota-derived metabolites mediate the neuroprotective effect of melatonin in cognitive impairment induced by sleep deprivation,Microbiome,2023,"Cognitive impairment, Hippocampus, Melatonin, Microbial–gut–brain axis, Sleep deprivation",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,CON-FMT:( receiving control microbiota FMT mice) and SD+Mel-FMT:( receiving SD+Mel (20 mg/kg) microbiota  FMT mice),SD-FMT: receiving Sleep deprivation  FMT mice,This are sleep deprived mice that are also subjected to FMT .,7,7,NA,16S,123456789,NA,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Fig 4C, 4F, 4D",6 November 2023,Davvve,"Davvve,Folakunmi,WikiWorks","C Linear discriminant analysis efect 
size (LEfSe) was performed to identify the bacteria that are differentially represented between the different groups",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Methylophilaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas|s__Turicimonas muris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__uncultured Alloprevotella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__uncultured Parasutterella sp.",3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549;3379134|976;3379134|1224|28216;3379134|1224|28216|80840|119060;3379134|1224|28216|80840;1783272|1239|526524|526525;3379134|1224|1236;3379134|1224|28216|32003|32011;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|171552;3379134|1224;3379134|1224|28216|80840|995019;3379134|1224|28216|80840|995019|1918598;3379134|1224|28216|80840|995019|1918598|1796652;3379134|976|200643;3379134|976|200643|171549|171552|1283313|1283315;3379134|1224|28216|80840|995019|577310|1263098,Complete,Folakunmi
bsdb:36721179/2/2,36721179,laboratory experiment,36721179,https://doi.org/10.1186/s40168-022-01452-3,NA,"Wang X., Wang Z., Cao J., Dong Y. , Chen Y.",Gut microbiota-derived metabolites mediate the neuroprotective effect of melatonin in cognitive impairment induced by sleep deprivation,Microbiome,2023,"Cognitive impairment, Hippocampus, Melatonin, Microbial–gut–brain axis, Sleep deprivation",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,CON-FMT:( receiving control microbiota FMT mice) and SD+Mel-FMT:( receiving SD+Mel (20 mg/kg) microbiota  FMT mice),SD-FMT: receiving Sleep deprivation  FMT mice,This are sleep deprived mice that are also subjected to FMT .,7,7,NA,16S,123456789,NA,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Fig 4G-J,12 February 2024,Folakunmi,"Folakunmi,WikiWorks",Linear discriminant analysis effect size (LEfSe) performed to identify the bacteria that are differentially represented between the different groups,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium A2",1783272|1239|186801|186802|186806|1730|39497;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|397290,Complete,Folakunmi
bsdb:36721179/3/1,36721179,laboratory experiment,36721179,https://doi.org/10.1186/s40168-022-01452-3,NA,"Wang X., Wang Z., Cao J., Dong Y. , Chen Y.",Gut microbiota-derived metabolites mediate the neuroprotective effect of melatonin in cognitive impairment induced by sleep deprivation,Microbiome,2023,"Cognitive impairment, Hippocampus, Melatonin, Microbial–gut–brain axis, Sleep deprivation",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,CON-FMT and SD-FMT,SD+Mel-FMT:( receiving SD+Mel (20 mg/kg) microbiota FMT mice),Sleep deprived mice receiving Mel and FMT,7,7,NA,16S,123456789,NA,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,fig 4c,6 November 2023,Davvve,"Davvve,WikiWorks","Linear discriminant analysis efect 
size (LEfSe) was performed to identify the bacteria that are differentially represented between the different groups",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium CIEAF 020,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__uncultured Alistipes sp.,,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas|s__uncultured Candidatus Saccharimonas sp.,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__uncultured Ruminococcus sp.,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma|s__uncultured Anaeroplasma sp.,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales|s__uncultured Gastranaerophilales bacterium,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Candidatus Melainabacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|s__uncultured Mollicutes bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes ihumii",1783272|1239|186801|186802|1159215;1783272|544448|31969;1783272|544448;3379134|976|200643|171549|171550;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550|239759|538949;;95818|2093818|2093825;95818|2093818|2093825|2171986;95818|2093818|2093825|2171986|1331051|1983405;95818|2093818|2093825|2171986|1331051;95818|2093818;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|165186;1783272|544448|31969|186332|186333|2086;1783272|544448|31969|186332;1783272|544448|31969|186332|186333|2086|538969;1783272|544448|31969|186332|186333;1783272|1798710|1906119;1783272|1798710|1906119|3076055;1783272|1117;1783272|1798710;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|186806|1730|39497;1783272|544448|31969|220137;3379134|976|200643|171549|171550|239759|1470347,Complete,Folakunmi
bsdb:36744910/1/1,36744910,"cross-sectional observational, not case-control",36744910,https://doi.org/10.1128/mbio.03519-22,https://journals.asm.org/doi/10.1128/mbio.03519-22,"Guo M., Wu G., Tan Y., Li Y., Jin X., Qi W., Guo X., Zhang C., Zhu Z. , Zhao L.",Guild-Level Microbiome Signature Associated with COVID-19 Severity and Prognosis,mBio,2023,"COVID-19, guild, gut microbiome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Mild severity,Moderate severity,COVID-19 Patients with moderate severity symptoms.,88,196,NA,WMS,NA,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Fig. 2A,9 March 2024,Zheeburg,"Zheeburg,Aleru Divine,WikiWorks",Heatmap of 33 high-quality metagenome-assembled genomes (HQMAGs) identified by redundancy analysis (RDA) and showing differential abundance between the 3 severity groups.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|3085636|3118652|2039240;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3082720|186804|1505657|261299;1783272|1239|91061|186826|33958|2767887|1624;1783272|1239|91061|186826|33958|2742598|1613;1783272|1239|909932|1843488|909930|33024|33025;1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|186801|3085636|186803|189330,Complete,Svetlana up
bsdb:36744910/1/2,36744910,"cross-sectional observational, not case-control",36744910,https://doi.org/10.1128/mbio.03519-22,https://journals.asm.org/doi/10.1128/mbio.03519-22,"Guo M., Wu G., Tan Y., Li Y., Jin X., Qi W., Guo X., Zhang C., Zhu Z. , Zhao L.",Guild-Level Microbiome Signature Associated with COVID-19 Severity and Prognosis,mBio,2023,"COVID-19, guild, gut microbiome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Mild severity,Moderate severity,COVID-19 Patients with moderate severity symptoms.,88,196,NA,WMS,NA,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 2A,22 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap of 33 high-quality metagenome-assembled genomes (HQMAGs) identified by redundancy analysis (RDA) and showing differential abundance between the 3 severity groups.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister histaminiformans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae,k__Bacillati|p__Bacillota|g__Negativibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus avium",1783272|1239|186801|186802|216572|216851|853;1783272|1239|909932|1843489|31977|39948|209880;1783272|1239|186801|186802|3082771;1783272|1239|1980693;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3082720|186804|1501226|1776391;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|81852|1350|1352;1783272|1239|91061|186826|81852|1350|33945,Complete,Svetlana up
bsdb:36744910/2/1,36744910,"cross-sectional observational, not case-control",36744910,https://doi.org/10.1128/mbio.03519-22,https://journals.asm.org/doi/10.1128/mbio.03519-22,"Guo M., Wu G., Tan Y., Li Y., Jin X., Qi W., Guo X., Zhang C., Zhu Z. , Zhao L.",Guild-Level Microbiome Signature Associated with COVID-19 Severity and Prognosis,mBio,2023,"COVID-19, guild, gut microbiome",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Mild severity,Severe/Critical severity,COVID-19 Patients with severe/critical severity symptoms.,88,12,NA,WMS,NA,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Fig. 2A,9 March 2024,Zheeburg,"Zheeburg,Aleru Divine,WikiWorks",Heatmap of 33 high-quality metagenome-assembled genomes (HQMAGs) identified by redundancy analysis (RDA) and showing differential abundance between the 3 severity groups.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus avium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|3085636|3118652|2039240;3379134|976|200643|171549|2005519|397864|487174;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|91061|186826|81852|1350|33945;1783272|1239|91061|186826|81852|1350|1352;1783272|1239|186801|3082720|186804|1505657|261299;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958|2767887|1624;1783272|1239|91061|186826|33958|2742598|1613;1783272|1239|909932|1843488|909930|33024|33025;1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|186801|186802|3082771,Complete,Svetlana up
bsdb:36744910/2/2,36744910,"cross-sectional observational, not case-control",36744910,https://doi.org/10.1128/mbio.03519-22,https://journals.asm.org/doi/10.1128/mbio.03519-22,"Guo M., Wu G., Tan Y., Li Y., Jin X., Qi W., Guo X., Zhang C., Zhu Z. , Zhao L.",Guild-Level Microbiome Signature Associated with COVID-19 Severity and Prognosis,mBio,2023,"COVID-19, guild, gut microbiome",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Mild severity,Severe/Critical severity,COVID-19 Patients with severe/critical severity symptoms.,88,12,NA,WMS,NA,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 2A,22 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap of 33 high-quality metagenome-assembled genomes (HQMAGs) identified by redundancy analysis (RDA) and showing differential abundance between the 3 severity groups.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister histaminiformans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae,k__Bacillati|p__Bacillota|g__Negativibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|186802|216572|216851|853;1783272|1239|909932|1843489|31977|39948|209880;1783272|1239|186801|186802|3082771;1783272|1239|1980693;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3082720|186804|1501226|1776391;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:36744910/3/1,36744910,"cross-sectional observational, not case-control",36744910,https://doi.org/10.1128/mbio.03519-22,https://journals.asm.org/doi/10.1128/mbio.03519-22,"Guo M., Wu G., Tan Y., Li Y., Jin X., Qi W., Guo X., Zhang C., Zhu Z. , Zhao L.",Guild-Level Microbiome Signature Associated with COVID-19 Severity and Prognosis,mBio,2023,"COVID-19, guild, gut microbiome",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Moderate severity,Severe/Critical severity,COVID-19 Patients with severe/critical severity symptoms.,196,12,NA,WMS,NA,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 2A,22 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap of 33 high-quality metagenome-assembled genomes (HQMAGs) identified by redundancy analysis (RDA) and showing differential abundance between the 3 severity groups.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus avium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis",1783272|1239|186801|186802|3082771;3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|3085636|3118652|2039240;3379134|976|200643|171549|2005519|397864|487174;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|91061|186826|81852|1350|33945;1783272|1239|91061|186826|81852|1350|1352;1783272|1239|186801|3082720|186804|1505657|261299;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958|2767887|1624;1783272|1239|91061|186826|33958|2742598|1613;1783272|1239|909932|1843488|909930|33024|33025;1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|186801|3082720|186804|1501226|1776391,Complete,Svetlana up
bsdb:36744910/3/2,36744910,"cross-sectional observational, not case-control",36744910,https://doi.org/10.1128/mbio.03519-22,https://journals.asm.org/doi/10.1128/mbio.03519-22,"Guo M., Wu G., Tan Y., Li Y., Jin X., Qi W., Guo X., Zhang C., Zhu Z. , Zhao L.",Guild-Level Microbiome Signature Associated with COVID-19 Severity and Prognosis,mBio,2023,"COVID-19, guild, gut microbiome",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Moderate severity,Severe/Critical severity,COVID-19 Patients with severe/critical severity symptoms.,196,12,NA,WMS,NA,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 2A,22 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap of 33 high-quality metagenome-assembled genomes (HQMAGs) identified by redundancy analysis (RDA) and showing differential abundance between the 3 severity groups.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister histaminiformans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae,k__Bacillati|p__Bacillota|g__Negativibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|186802|216572|216851|853;1783272|1239|909932|1843489|31977|39948|209880;1783272|1239|186801|186802|3082771;1783272|1239|1980693;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3082720|186804|1501226|1776391;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:36760344/1/1,36760344,"cross-sectional observational, not case-control",36760344,10.1136/gpsych-2022-100893,NA,"Sun Y., Ju P., Xue T., Ali U., Cui D. , Chen J.",Alteration of faecal microbiota balance related to long-term deep meditation,General psychiatry,2023,"Healthy Lifestyle, Mental Health, Psychosomatic Medicine",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Exercise,EFO:0000483,Control group,Meditation group,Tibetan Buddhist monks that performed meditation practices of Samatha and Vipassana for at least 2 hours a day for 3 to 30 years.,19,37,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.6,"age,alcohol drinking,diet,sex,smoking status",NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 4,5 October 2023,Nwajei Edgar,"Nwajei Edgar,Deacme,WikiWorks",Relative abundances of gut microbiota and linear discriminant analysis (LDA) effect size (LEfSe) in the meditation and control groups.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria",1783272|1239|186801|186802|216572|216851;1783272|1239|909932|909929|1843491|158846;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|815|816;3379134|976|200643|171549;3379134|1224|28216|80840|995019;3379134|1224|28216|80840;3379134|1224|28216,Complete,Folakunmi
bsdb:36760344/1/2,36760344,"cross-sectional observational, not case-control",36760344,10.1136/gpsych-2022-100893,NA,"Sun Y., Ju P., Xue T., Ali U., Cui D. , Chen J.",Alteration of faecal microbiota balance related to long-term deep meditation,General psychiatry,2023,"Healthy Lifestyle, Mental Health, Psychosomatic Medicine",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Exercise,EFO:0000483,Control group,Meditation group,Tibetan Buddhist monks that performed meditation practices of Samatha and Vipassana for at least 2 hours a day for 3 to 30 years.,19,37,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.6,"age,alcohol drinking,diet,sex,smoking status",NA,NA,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 4,5 October 2023,Nwajei Edgar,"Nwajei Edgar,Deacme,Folakunmi,WikiWorks",Relative abundances of gut microbiota and linear discriminant analysis (LDA) effect size (LEfSe) in the meditation and control groups.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,p__Candidatus Saccharimonadota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Viridiplantae|p__Streptophyta,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria",1783272|201174|1760|85004|31953|1678;95818;1783272|201174|84998|84999|84107|102106;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3085636|186803|841;33090|35493;1783272|1239|909932|1843489|31977;1783272|201174;3379134|1224|1236,Complete,Folakunmi
bsdb:36765550/1/1,36765550,case-control,36765550,10.3390/cancers15030594,NA,"Caleça T., Ribeiro P., Vitorino M., Menezes M., Sampaio-Alves M., Mendes A.D., Vicente R., Negreiros I., Faria A. , Costa D.A.","Breast Cancer Survivors and Healthy Women: Could Gut Microbiota Make a Difference?-""BiotaCancerSurvivors"": A Case-Control Study",Cancers,2023,"breast cancer, cancer, case-control study, microbiome, microbiota, survivors, survivorship",Experiment 1,"Portugal,United States of America",Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,Healthy female controls,BC survivors,"Women aged over 18 with a breast cancer (BC) diagnosis who had completed their core treatments (surgery, chemotherapy, and/or radiotherapy).",291,23,NA,16S,34,"Illumina,Ion Torrent",relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Table 2 & Section 3.3: Microbiota Analysis,11 July 2025,Ecsharp,Ecsharp,"Table 2 consists of relative abundance of specific bacterial groups in stools of BC survivors and control group by specific primers and Section 3.3. Microbiota Analysis discusses further significant relative abundance results in text. (p value of ≤ 0.05, Mann-Whitney U test)",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Acetobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Acidaminobacteraceae|g__Acidaminobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacillati|p__Armatimonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Brachymonas,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter rectus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,k__Pseudomonadati|p__Candidatus Latescibacterota,p__Candidatus Saccharimonadota,k__Bacillati|p__Chloroflexota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfurisporaceae|g__Desulfurispora,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter kobei,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Pseudomonadati|p__Fibrobacterota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Franconibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Frigoribacterium,k__Pseudomonadati|p__Gemmatimonadota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Gluconobacter|s__Gluconobacter oxydans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Idiomarinaceae|g__Idiomarina,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Kitasatospora,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora aerotolerans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Legionellaceae|g__Legionella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Macrococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae|g__Marinomonas,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Oscillatoriales|f__Microcoleaceae|g__Microcoleus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Natronincola,k__Pseudomonadati|p__Nitrospirota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Pandoraea,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Paraclostridium|s__Paraclostridium sordellii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Photorhabdus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Renibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles|s__Roseateles depolymerans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Sharpea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella flexneri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella sonnei,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Sphaerochaetaceae|g__Sphaerochaeta,k__Pseudomonadati|p__Spirochaetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus lutetiensis,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Sulfurimonadaceae|g__Sulfurimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae|g__Thermoanaerobacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae|g__Tissierella,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Fidelibacterota,k__Bacillati|p__Bacillota|c__Clostridia|o__Neomoorellales|f__Neomoorellaceae|g__Neomoorella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Maricaulales|f__Maricaulaceae|g__Oceanicaulis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae|g__Soehngenia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium acetobutylicum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Desulforamulus|s__Desulforamulus aeronauticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora algidixylanolytica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Litchfieldella|s__Litchfieldella anticariensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio atlanticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Paraclostridium|s__Paraclostridium bifermentans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Liquorilactobacillus|s__Liquorilactobacillus capillatus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Franconibacter|s__Franconibacter daqui,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Brachymonas|s__Brachymonas denitrificans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium intestinale,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Virgibacillus|s__Virgibacillus marismortui,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Edwardsiella|s__Edwardsiella piscicida,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Kitasatospora|s__Kitasatospora pitsanulaokmensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas psychrophila,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kosakonia|s__Kosakonia radicincitans,k__Bacillati|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae|g__Thermoanaerobacterium|s__Thermoanaerobacterium saccharolyticum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sartagoforme,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Pseudarthrobacter|s__Pseudarthrobacter scleromae",1783272|1239|186801|186802|186806|33951;1783272|1239|186801|3082720|3118653|65402;1783272|1239|909932|1843488|909930|904;3379134|976|200643|171549|171552|1283313|76122;1783272|1239|186801|186802|216572|52784;3379134|29547|3031852|213849|2808963|28196;1783272|67819;3379134|976|200643|171549|815|816|291645;3379134|1224|28216|80840|80864|28219;3379134|29547|3031852|213849|72294|194|203;1783272|1239|186801|186802|31979|49082;3379134|74015;95818;1783272|200795;3379134|1224|1236|91347|543|544|546;1783272|1239|526524|526525|2810280|100883|100884;1783272|1239|186801|186802|3064153|510701;3379134|1224|1236|91347|543|547|208224;1783272|1239|186801|3085636|186803|2719313|1531;3379134|65842;3379134|1224|1236|91347|543|1649295;1783272|201174|1760|85006|85023|96492;3379134|142182;3379134|1224|28211|3120395|433|441|442;1783272|1239|186801|3085636|186803|1649459|154046;3379134|1224|1236|135622|267893|135575;1783272|201174|1760|85011|2062|2063;1783272|1239|186801|3085636|186803|2719231|36832;3379134|1224|1236|118969|444|445;1783272|1239|91061|1385|90964|69965;3379134|1224|1236|135619|135620|28253;1783272|1117|3028117|1150|1892252|44471;1783272|1239|909932|909929|1843491|52225|52226;1783272|1239|186801|3082720|3118656|89958;3379134|40117;3379134|976|200643|171549|2005523|346096;3379134|1224|28216|80840|119060|93217;1783272|1239|186801|3082720|186804|1849822|1505;3379134|1224|1236|91347|1903414|29487;3379134|976|200643|171549|171552|838|28131;3379134|976|200643|171549|171552|838|28133;3379134|976|200643|171549|171552|838|60133;1783272|201174|1760|85006|1268|1645;3379134|1224|28216|80840|2975441|93681;3379134|1224|28216|80840|2975441|93681|76731;1783272|201174|1760|85004|31953|196081;1783272|1239|526524|526525|2810280|519427;3379134|1224|1236|91347|543|620;3379134|1224|1236|91347|543|620|623;3379134|1224|1236|91347|543|620|624;3379134|203691|203692|136|2791015|399320;3379134|203691;1783272|1239|91061|186826|1300|1301|150055;3379134|29547|3031852|213849|2771471|202746;1783272|1239|186801|68295|186814|28895;1783272|1239|1737404|1737405|1737406|41273;3379134|74201;3379134|62680;1783272|1239|186801|3039167|3039168|44260;3379134|1224|28211|2800059|2800061|153232;1783272|1239|1737404|1737405|1737406|253255;1783272|1239|186801|186802|31979|1485|1488;1783272|1239|186801|186802|186807|2916693|53343;1783272|1239|186801|3085636|186803|2719231|94868;3379134|1224|1236|135619|28256|3137764|258591;3379134|1224|1236|135623|641|662|693153;1783272|1239|186801|3082720|186804|1849822|1490;1783272|1239|91061|186826|33958|2767888|480931;3379134|1224|1236|91347|543|1649295|2047724;3379134|1224|28216|80840|80864|28219|28220;1783272|1239|186801|186802|31979|1485|36845;1783272|1239|91061|1385|186817|84406|79660;3379134|1224|1236|91347|1903412|635|1263550;1783272|201174|1760|85011|2062|2063|340469;3379134|1224|1236|72274|135621|286|122355;3379134|1224|1236|91347|543|1330547|283686;1783272|1239|186801|68295|186814|28895|28896;1783272|1239|186801|186802|31979|1485|84031;1783272|201174|1760|85006|1268|1742993|158897,Complete,NA
bsdb:36765550/1/2,36765550,case-control,36765550,10.3390/cancers15030594,NA,"Caleça T., Ribeiro P., Vitorino M., Menezes M., Sampaio-Alves M., Mendes A.D., Vicente R., Negreiros I., Faria A. , Costa D.A.","Breast Cancer Survivors and Healthy Women: Could Gut Microbiota Make a Difference?-""BiotaCancerSurvivors"": A Case-Control Study",Cancers,2023,"breast cancer, cancer, case-control study, microbiome, microbiota, survivors, survivorship",Experiment 1,"Portugal,United States of America",Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,Healthy female controls,BC survivors,"Women aged over 18 with a breast cancer (BC) diagnosis who had completed their core treatments (surgery, chemotherapy, and/or radiotherapy).",291,23,NA,16S,34,"Illumina,Ion Torrent",relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Table 2 & Section 3.3: Microbiota Analysis,11 July 2025,Ecsharp,Ecsharp,"Description: Table 2 consists of relative abundance of specific bacterial groups in stools of BC survivors and control group by specific primers and Section 3.3. Microbiota Analysis discusses further significant relative abundance results in text. (p value of ≤ 0.05, Mann-Whitney U test)",decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239;3379134|976|200643|171549|815|816|820;3379134|976;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|31979|1485|1502;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|216572|216851|853;3379134|74201;3379134|74201|203494|48461|1647988|239934;3379134|1224|1236|91347|543|561;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|2005525|375288;1783272|201174|1760|85009|31957|1743;1783272|201174|1760|85011|2062|1883;3379134|976|200643|171549|2005525|195950;3379134|976|200643|171549|815|816|46506,Complete,NA
bsdb:36774467/1/1,36774467,"cross-sectional observational, not case-control",36774467,10.1186/s12967-023-03953-7,NA,"Chen H., Ou R., Tang N., Su W., Yang R., Yu X., Zhang G., Jiao J. , Zhou X.",Alternation of the gut microbiota in irritable bowel syndrome: an integrated analysis based on multicenter amplicon sequencing data,Journal of translational medicine,2023,"Amplicon sequencing analysis, GMrepo database, Gut microbiota, Irritable bowel syndrome, Propensity score matching",Experiment 1,"United States of America,United Kingdom,Australia,Switzerland,Canada",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Controls,IBS (Irritable Bowel Syndrome) patients,"This group represents individuals diagnosed with irritable bowel syndrome (IBS), as identified from multicenter 16S rRNA sequencing data curated in the GMrepo database.",354,354,NA,16S,NA,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index,region,sex","age,body mass index,region,sex",NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,"Fig. 2b, c, d",3 May 2025,Joiejoie,"Joiejoie,Anne-mariesharp",The relative abundance of the taxa between the IBS and healthy controls.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|1224|1236|2887326|468|469;1783272|1239;1783272|1239|91061|1385|186817|1386;3379134|1224|1236|91347|543;1783272|1239|186801|3085636|186803|2719313;1783272|1239|526524|526525|128827|61170;3379134|1224|1236|2887326|468;3379134|976|117747|200666|84566;3379134|976|117747|200666|84566|28453;1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:36774467/1/2,36774467,"cross-sectional observational, not case-control",36774467,10.1186/s12967-023-03953-7,NA,"Chen H., Ou R., Tang N., Su W., Yang R., Yu X., Zhang G., Jiao J. , Zhou X.",Alternation of the gut microbiota in irritable bowel syndrome: an integrated analysis based on multicenter amplicon sequencing data,Journal of translational medicine,2023,"Amplicon sequencing analysis, GMrepo database, Gut microbiota, Irritable bowel syndrome, Propensity score matching",Experiment 1,"United States of America,United Kingdom,Australia,Switzerland,Canada",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Controls,IBS (Irritable Bowel Syndrome) patients,"This group represents individuals diagnosed with irritable bowel syndrome (IBS), as identified from multicenter 16S rRNA sequencing data curated in the GMrepo database.",354,354,NA,16S,NA,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index,region,sex","age,body mass index,region,sex",NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,"Fig. 2b, c, d, 6e",3 May 2025,Joiejoie,"Joiejoie,Anne-mariesharp",The relative abundance of the taxa between the IBS and healthy controls.,decreased,"k__Pseudomonadati|p__Acidobacteriota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium boum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium callitrichos,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium coryneforme,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium gallicum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium lemurum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pullorum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium saguini,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium tsurumiense,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Lentisphaerota,k__Methanobacteriati|p__Methanobacteriota,k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Planctomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Thermotogati|p__Synergistota,k__Pseudomonadati|p__Verrucomicrobiota",3379134|57723;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|78343;1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|1678|762209;1783272|201174|1760|85004|31953|1678|1687;1783272|201174|1760|85004|31953|1678|78342;1783272|201174|1760|85004|31953|1678|1603886;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|28026;1783272|201174|1760|85004|31953|1678|78448;1783272|201174|1760|85004|31953|1678|762210;1783272|201174|1760|85004|31953|1678|356829;1783272|201174|1760|85007|1653;1783272|1239|186801|186802|216572|216851;3379134|256845;3366610|28890;1783272|544448;1783272|1239|186801|186802|216572;3379134|203682;3379134|976|200643|171549|171552;3384194|508458;3379134|74201,Complete,KateRasheed
bsdb:36774467/2/1,36774467,"cross-sectional observational, not case-control",36774467,10.1186/s12967-023-03953-7,NA,"Chen H., Ou R., Tang N., Su W., Yang R., Yu X., Zhang G., Jiao J. , Zhou X.",Alternation of the gut microbiota in irritable bowel syndrome: an integrated analysis based on multicenter amplicon sequencing data,Journal of translational medicine,2023,"Amplicon sequencing analysis, GMrepo database, Gut microbiota, Irritable bowel syndrome, Propensity score matching",Experiment 2,"United States of America,United Kingdom,Australia,Canada,Switzerland",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS-C ( Irritable bowel syndrome with predominant constipation ),This group refers to patients diagnosed with irritable bowel syndrome complicated with predominant constipation.,354,79,NA,16S,NA,NA,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,"age,body mass index,region,sex","age,body mass index,region,sex",NA,unchanged,NA,unchanged,NA,NA,Signature 1,Fig. 4C,4 May 2025,Joiejoie,Joiejoie,Relative abundance of significantly enriched genera.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|186801|186802|216572|52784;1783272|1239|91061|1385|186817|1386;1783272|1239|186801|3085636|186803|2719313;1783272|1239|526524|526525|128827|61170;3379134|976|117747|200666|84566|28453;1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:36774467/2/2,36774467,"cross-sectional observational, not case-control",36774467,10.1186/s12967-023-03953-7,NA,"Chen H., Ou R., Tang N., Su W., Yang R., Yu X., Zhang G., Jiao J. , Zhou X.",Alternation of the gut microbiota in irritable bowel syndrome: an integrated analysis based on multicenter amplicon sequencing data,Journal of translational medicine,2023,"Amplicon sequencing analysis, GMrepo database, Gut microbiota, Irritable bowel syndrome, Propensity score matching",Experiment 2,"United States of America,United Kingdom,Australia,Canada,Switzerland",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS-C ( Irritable bowel syndrome with predominant constipation ),This group refers to patients diagnosed with irritable bowel syndrome complicated with predominant constipation.,354,79,NA,16S,NA,NA,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,"age,body mass index,region,sex","age,body mass index,region,sex",NA,unchanged,NA,unchanged,NA,NA,Signature 2,Fig. 4C,4 May 2025,Joiejoie,Joiejoie,Relative abundance of significantly depleted genera.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter",1783272|1239|186801|3120394|3120654|35829;1783272|1239|909932|1843488|909930|904;3379134|976|200643|171549|2005519|397864;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|33042;1783272|201174|1760|85007|1653|1716;1783272|1239|186801|186802|216572|216851;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;1783272|1239|1737404|1737405|1570339|162289;3379134|976|200643|171549|815|909656;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|31979|1266;1783272|1239|186801|186802|216572|44748,Complete,KateRasheed
bsdb:36774467/3/1,36774467,"cross-sectional observational, not case-control",36774467,10.1186/s12967-023-03953-7,NA,"Chen H., Ou R., Tang N., Su W., Yang R., Yu X., Zhang G., Jiao J. , Zhou X.",Alternation of the gut microbiota in irritable bowel syndrome: an integrated analysis based on multicenter amplicon sequencing data,Journal of translational medicine,2023,"Amplicon sequencing analysis, GMrepo database, Gut microbiota, Irritable bowel syndrome, Propensity score matching",Experiment 3,"Australia,Canada,Switzerland,United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS-D (Irritable bowel syndrome with predominant diarrhea ),This group refers to patients diagnosed with irritable bowel syndrome complicated with predominant diarrhea.,354,81,NA,16S,NA,NA,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,"age,body mass index,region,sex","age,body mass index,region,sex",NA,unchanged,NA,unchanged,NA,NA,Signature 1,Fig. 4C,4 May 2025,Joiejoie,Joiejoie,Relative abundance of significantly enriched genera.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster",3379134|1224|1236|135625|712|724;3379134|976|117747|200666|84566|28453;1783272|1239|526524|526525|128827|61170;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|1385|186817|1386;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|2719313,Complete,KateRasheed
bsdb:36774467/3/2,36774467,"cross-sectional observational, not case-control",36774467,10.1186/s12967-023-03953-7,NA,"Chen H., Ou R., Tang N., Su W., Yang R., Yu X., Zhang G., Jiao J. , Zhou X.",Alternation of the gut microbiota in irritable bowel syndrome: an integrated analysis based on multicenter amplicon sequencing data,Journal of translational medicine,2023,"Amplicon sequencing analysis, GMrepo database, Gut microbiota, Irritable bowel syndrome, Propensity score matching",Experiment 3,"Australia,Canada,Switzerland,United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS-D (Irritable bowel syndrome with predominant diarrhea ),This group refers to patients diagnosed with irritable bowel syndrome complicated with predominant diarrhea.,354,81,NA,16S,NA,NA,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,"age,body mass index,region,sex","age,body mass index,region,sex",NA,unchanged,NA,unchanged,NA,NA,Signature 2,Fig. 4C,4 May 2025,Joiejoie,Joiejoie,Relative abundance of significantly depleted genera.,decreased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina",3379134|200940|3031449|213115|194924|35832;1783272|201174|1760|85007|1653|1716;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|815|909656;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|52784;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3120394|3120654|35829;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572;1783272|1239|909932|1843488|909930|904;1783272|1239|186801|186802|31979|1266,Complete,KateRasheed
bsdb:36774467/4/1,36774467,"cross-sectional observational, not case-control",36774467,10.1186/s12967-023-03953-7,NA,"Chen H., Ou R., Tang N., Su W., Yang R., Yu X., Zhang G., Jiao J. , Zhou X.",Alternation of the gut microbiota in irritable bowel syndrome: an integrated analysis based on multicenter amplicon sequencing data,Journal of translational medicine,2023,"Amplicon sequencing analysis, GMrepo database, Gut microbiota, Irritable bowel syndrome, Propensity score matching",Experiment 4,"Australia,Canada,Switzerland,United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,IBS-C (Irritable bowel syndrome with predominant constipation),IBS-D (Irritable bowel syndrome with predominant diarrhea ),This refers to patients diagnosed with irritable bowel syndrome complicated with predominant diarrhea.,79,81,NA,16S,NA,NA,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,"age,body mass index,region,sex",NA,unchanged,NA,unchanged,NA,NA,Signature 1,Fig. 4C,4 May 2025,Joiejoie,Joiejoie,Relative abundance of significantly enriched genera.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster",3379134|1224|1236|135625|712|724;1783272|201174|1760|85007|1653|1716;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|28050;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|33042;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|2719313,Complete,KateRasheed
bsdb:36774467/4/2,36774467,"cross-sectional observational, not case-control",36774467,10.1186/s12967-023-03953-7,NA,"Chen H., Ou R., Tang N., Su W., Yang R., Yu X., Zhang G., Jiao J. , Zhou X.",Alternation of the gut microbiota in irritable bowel syndrome: an integrated analysis based on multicenter amplicon sequencing data,Journal of translational medicine,2023,"Amplicon sequencing analysis, GMrepo database, Gut microbiota, Irritable bowel syndrome, Propensity score matching",Experiment 4,"Australia,Canada,Switzerland,United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,IBS-C (Irritable bowel syndrome with predominant constipation),IBS-D (Irritable bowel syndrome with predominant diarrhea ),This refers to patients diagnosed with irritable bowel syndrome complicated with predominant diarrhea.,79,81,NA,16S,NA,NA,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,"age,body mass index,region,sex",NA,unchanged,NA,unchanged,NA,NA,Signature 2,Fig. 4C,4 May 2025,Joiejoie,Joiejoie,Relative abundance of significantly depleted genera,decreased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio",3379134|200940|3031449|213115|194924|35832;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|815|909656;1783272|1239|186801|186802|216572|52784;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|186802|31979|1266;1783272|1239|909932|1843488|909930|904;1783272|1239|186801|186802|216572;1783272|1239|91061|1385|186817|1386;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3120394|3120654|35829,Complete,KateRasheed
bsdb:36774467/5/1,36774467,"cross-sectional observational, not case-control",36774467,10.1186/s12967-023-03953-7,NA,"Chen H., Ou R., Tang N., Su W., Yang R., Yu X., Zhang G., Jiao J. , Zhou X.",Alternation of the gut microbiota in irritable bowel syndrome: an integrated analysis based on multicenter amplicon sequencing data,Journal of translational medicine,2023,"Amplicon sequencing analysis, GMrepo database, Gut microbiota, Irritable bowel syndrome, Propensity score matching",Experiment 5,"Australia,Canada,Switzerland,United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS-NPD ( Irritable Bowel Syndrome without psychiatric disorders ),This group refers to patients with irritable bowel syndrome without psychiatric disorders (IBS-NPD),354,214,NA,16S,NA,NA,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,"age,body mass index,region,sex","age,body mass index,region,sex",NA,unchanged,NA,unchanged,NA,NA,Signature 1,Fig. 5C,4 May 2025,Joiejoie,Joiejoie,The relative abundance of significantly enriched genera.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Niallia",3379134|976|117747|200666|84566|28453;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|3085636|186803|2719313;1783272|1239|91061|1385|186817|2837506,Complete,KateRasheed
bsdb:36774467/5/2,36774467,"cross-sectional observational, not case-control",36774467,10.1186/s12967-023-03953-7,NA,"Chen H., Ou R., Tang N., Su W., Yang R., Yu X., Zhang G., Jiao J. , Zhou X.",Alternation of the gut microbiota in irritable bowel syndrome: an integrated analysis based on multicenter amplicon sequencing data,Journal of translational medicine,2023,"Amplicon sequencing analysis, GMrepo database, Gut microbiota, Irritable bowel syndrome, Propensity score matching",Experiment 5,"Australia,Canada,Switzerland,United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS-NPD ( Irritable Bowel Syndrome without psychiatric disorders ),This group refers to patients with irritable bowel syndrome without psychiatric disorders (IBS-NPD),354,214,NA,16S,NA,NA,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,"age,body mass index,region,sex","age,body mass index,region,sex",NA,unchanged,NA,unchanged,NA,NA,Signature 2,Fig. 5C,4 May 2025,Joiejoie,Joiejoie,The relative abundance of significantly depleted genera.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter",1783272|1239|186801|3120394|3120654|35829;1783272|1239|909932|1843488|909930|904;1783272|201174|1760|85004|31953|1678;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|830;1783272|1239|186801|3085636|186803|33042;1783272|201174|1760|85007|1653|1716;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|815|909656;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|2304693;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|31979|1266;1783272|1239|186801|186802|216572|44748,Complete,KateRasheed
bsdb:36774467/6/1,36774467,"cross-sectional observational, not case-control",36774467,10.1186/s12967-023-03953-7,NA,"Chen H., Ou R., Tang N., Su W., Yang R., Yu X., Zhang G., Jiao J. , Zhou X.",Alternation of the gut microbiota in irritable bowel syndrome: an integrated analysis based on multicenter amplicon sequencing data,Journal of translational medicine,2023,"Amplicon sequencing analysis, GMrepo database, Gut microbiota, Irritable bowel syndrome, Propensity score matching",Experiment 6,"Australia,Canada,Switzerland,United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS-PD ( Irritable Bowel Syndrome with psychiatric disorders ),This group refers to patients with irritable bowel syndrome with psychiatric disorders (IBS-PD),354,140,NA,16S,NA,NA,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,"age,body mass index,region,sex","age,body mass index,region,sex",NA,unchanged,NA,unchanged,NA,NA,Signature 1,Fig. 5C,4 May 2025,Joiejoie,Joiejoie,The relative abundance of significantly enriched genera.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor",3379134|976|117747|200666|84566|28453;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|3085636|186803|2719313;1783272|1239|186801|186802|216572|1017280,Complete,KateRasheed
bsdb:36774467/6/2,36774467,"cross-sectional observational, not case-control",36774467,10.1186/s12967-023-03953-7,NA,"Chen H., Ou R., Tang N., Su W., Yang R., Yu X., Zhang G., Jiao J. , Zhou X.",Alternation of the gut microbiota in irritable bowel syndrome: an integrated analysis based on multicenter amplicon sequencing data,Journal of translational medicine,2023,"Amplicon sequencing analysis, GMrepo database, Gut microbiota, Irritable bowel syndrome, Propensity score matching",Experiment 6,"Australia,Canada,Switzerland,United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS-PD ( Irritable Bowel Syndrome with psychiatric disorders ),This group refers to patients with irritable bowel syndrome with psychiatric disorders (IBS-PD),354,140,NA,16S,NA,NA,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,"age,body mass index,region,sex","age,body mass index,region,sex",NA,unchanged,NA,unchanged,NA,NA,Signature 2,Fig. 5C,4 May 2025,Joiejoie,Joiejoie,The relative abundance of significantly depleted genera.,decreased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Niallia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus",3379134|200940|3031449|213115|194924|35832;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85007|1653|1716;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|815|909656;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|31979|1266;1783272|1239|186801|3120394|3120654|35829;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|186802|216572|2304693;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3085636|186803|830;1783272|1239|91061|1385|186817|2837506;1783272|1239|909932|1843488|909930|904,Complete,KateRasheed
bsdb:36774467/7/1,36774467,"cross-sectional observational, not case-control",36774467,10.1186/s12967-023-03953-7,NA,"Chen H., Ou R., Tang N., Su W., Yang R., Yu X., Zhang G., Jiao J. , Zhou X.",Alternation of the gut microbiota in irritable bowel syndrome: an integrated analysis based on multicenter amplicon sequencing data,Journal of translational medicine,2023,"Amplicon sequencing analysis, GMrepo database, Gut microbiota, Irritable bowel syndrome, Propensity score matching",Experiment 7,"Australia,Canada,Switzerland,United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,IBS-NPD (Irritable Bowel Syndrome without psychiatric disorders),IBS-PD (Irritable Bowel Syndrome with psychiatric disorders),This group refers to patients with irritable bowel syndrome with psychiatric disorders (IBS-PD),214,140,NA,16S,NA,NA,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,"age,body mass index,region,sex",NA,unchanged,NA,unchanged,NA,NA,Signature 1,Fig. 5C,5 May 2025,Joiejoie,Joiejoie,The relative abundance of significantly enriched genera.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio",1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549|815|909656;3379134|976|200643|171549|171552|838;3379134|976|117747|200666|84566|28453;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|2719313;1783272|1239|186801|186802|216572|1017280;1783272|1239|186801|3085636|186803|830,Complete,KateRasheed
bsdb:36774467/7/2,36774467,"cross-sectional observational, not case-control",36774467,10.1186/s12967-023-03953-7,NA,"Chen H., Ou R., Tang N., Su W., Yang R., Yu X., Zhang G., Jiao J. , Zhou X.",Alternation of the gut microbiota in irritable bowel syndrome: an integrated analysis based on multicenter amplicon sequencing data,Journal of translational medicine,2023,"Amplicon sequencing analysis, GMrepo database, Gut microbiota, Irritable bowel syndrome, Propensity score matching",Experiment 7,"Australia,Canada,Switzerland,United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,IBS-NPD (Irritable Bowel Syndrome without psychiatric disorders),IBS-PD (Irritable Bowel Syndrome with psychiatric disorders),This group refers to patients with irritable bowel syndrome with psychiatric disorders (IBS-PD),214,140,NA,16S,NA,NA,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,"age,body mass index,region,sex",NA,unchanged,NA,unchanged,NA,NA,Signature 2,Fig. 5C,5 May 2025,Joiejoie,Joiejoie,The relative abundance of significantly depleted genera.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Niallia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoclostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio",1783272|1239|909932|1843488|909930|904;1783272|1239|91061|1385|186817|2837506;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|186802|216572|2304693;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|186802|31979|1266;3379134|976|200643|171549|171552|577309;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|3120394|3120654|35829,Complete,KateRasheed
bsdb:36774467/8/1,36774467,"cross-sectional observational, not case-control",36774467,10.1186/s12967-023-03953-7,NA,"Chen H., Ou R., Tang N., Su W., Yang R., Yu X., Zhang G., Jiao J. , Zhou X.",Alternation of the gut microbiota in irritable bowel syndrome: an integrated analysis based on multicenter amplicon sequencing data,Journal of translational medicine,2023,"Amplicon sequencing analysis, GMrepo database, Gut microbiota, Irritable bowel syndrome, Propensity score matching",Experiment 8,"Australia,Canada,Switzerland,United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS Patients (Irritable Bowel Syndrome),"This group represents individuals diagnosed with irritable bowel syndrome (IBS), as identified from multicenter 16S rRNA sequencing data curated in the GMrepo database.",354,354,NA,16S,NA,NA,relative abundances,Random Forest Analysis,0.05,FALSE,NA,"age,body mass index,region,sex","age,body mass index,region,sex",NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Fig. 7A & B,4 May 2025,Joiejoie,"Joiejoie,Anne-mariesharp",The top-ranked biomarkers identified at the genus and species level to distinguish IBS from healthy controls on their mean decrease scores of the optimal model performance,increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales|f__Desulfosarcinaceae|g__Desulfosarcina,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania filiformis,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Trueperales|f__Trueperaceae|g__Truepera,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfomicrobiaceae|g__Desulfomicrobium|s__Desulfomicrobium norvegicum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus thuringiensis",3379134|200940|3024418|213118|3031624|2299;1783272|1239|186801|3085636|186803|2719313;1783272|201174|84998|1643822|1643826|644652|471189;1783272|1239|526524|526525|128827|61170|61171;3379134|976|117747|200666|84566|28453;1783272|1239|91061|186826|1300|1301;3384194|1297|188787|2762275|332247|332248;3379134|1224|1236|91347|1903409|53335;3379134|200940|3031449|213115|213116|898|52561;3379134|976|200643|171549|815|816|817;1783272|1239|91061|186826|1300|1301|1311;1783272|1239|91061|1385|186817|1386|1428,Complete,KateRasheed
bsdb:36774467/8/2,36774467,"cross-sectional observational, not case-control",36774467,10.1186/s12967-023-03953-7,NA,"Chen H., Ou R., Tang N., Su W., Yang R., Yu X., Zhang G., Jiao J. , Zhou X.",Alternation of the gut microbiota in irritable bowel syndrome: an integrated analysis based on multicenter amplicon sequencing data,Journal of translational medicine,2023,"Amplicon sequencing analysis, GMrepo database, Gut microbiota, Irritable bowel syndrome, Propensity score matching",Experiment 8,"Australia,Canada,Switzerland,United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS Patients (Irritable Bowel Syndrome),"This group represents individuals diagnosed with irritable bowel syndrome (IBS), as identified from multicenter 16S rRNA sequencing data curated in the GMrepo database.",354,354,NA,16S,NA,NA,relative abundances,Random Forest Analysis,0.05,FALSE,NA,"age,body mass index,region,sex","age,body mass index,region,sex",NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Fig. 7A & B,20 June 2025,Joiejoie,"Joiejoie,Anne-mariesharp",The top-ranked biomarkers identified at the genus and species level to distinguish IBS from healthy controls on their mean decrease scores of the optimal model performance,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus albus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus champanellensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum|s__Varibaculum cambriense,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] colinum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoclostridium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanosphaera,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium gallicum,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum",1783272|1239|186801|186802|216572|52784;1783272|201174|1760|85004|31953|1678|1680;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|33042|33043;1783272|1239|186801|186802|216572|253238;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|815|909656;3379134|976|200643|171549|815|909656|387090;1783272|1239|186801|186802|216572|1263|1264;1783272|1239|186801|186802|216572|1263|1161942;1783272|1239|186801|186802|31979|1266;1783272|1239|526524|526525|2810280|3025755|29348;1783272|201174|1760|2037|2049|184869|184870;3379134|256845|1313211|278082|255528|172900;1783272|1239|186801|3085636|186803|1506577|36835;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|2304693;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|216572|100175;3379134|1224|28216|80840|995019|40544;1783272|1239|526524|526525|2810280|3025755;3366610|28890|183925|2158|2159|2316;1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|1678|78342;3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|186802|216572|1263|40518;1783272|201174|1760|85004|31953|1678|216816,Complete,KateRasheed
bsdb:36774467/9/1,36774467,"cross-sectional observational, not case-control",36774467,10.1186/s12967-023-03953-7,NA,"Chen H., Ou R., Tang N., Su W., Yang R., Yu X., Zhang G., Jiao J. , Zhou X.",Alternation of the gut microbiota in irritable bowel syndrome: an integrated analysis based on multicenter amplicon sequencing data,Journal of translational medicine,2023,"Amplicon sequencing analysis, GMrepo database, Gut microbiota, Irritable bowel syndrome, Propensity score matching",Experiment 9,"Australia,Canada,Switzerland,United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS Patients (Irritable Bowel Syndrome),"This group represents individuals diagnosed with irritable bowel syndrome (IBS), as identified from multicenter 16S rRNA sequencing data curated in the GMrepo database.",354,354,NA,16S,NA,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,region,sex","age,body mass index,region,sex",NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table S7,9 July 2025,Anne-mariesharp,Anne-mariesharp,Differential analysis of microbial compositions between IBS and healthy controls at the species level,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania filiformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta",3379134|976|200643|171549|815|816|817;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|526524|526525|128827|61170|61171;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|186801|3085636|186803|2719313|358742;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|572511|33035,Complete,KateRasheed
bsdb:36774467/9/2,36774467,"cross-sectional observational, not case-control",36774467,10.1186/s12967-023-03953-7,NA,"Chen H., Ou R., Tang N., Su W., Yang R., Yu X., Zhang G., Jiao J. , Zhou X.",Alternation of the gut microbiota in irritable bowel syndrome: an integrated analysis based on multicenter amplicon sequencing data,Journal of translational medicine,2023,"Amplicon sequencing analysis, GMrepo database, Gut microbiota, Irritable bowel syndrome, Propensity score matching",Experiment 9,"Australia,Canada,Switzerland,United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS Patients (Irritable Bowel Syndrome),"This group represents individuals diagnosed with irritable bowel syndrome (IBS), as identified from multicenter 16S rRNA sequencing data curated in the GMrepo database.",354,354,NA,16S,NA,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,region,sex","age,body mass index,region,sex",NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,"Table S4, S5, S6, S7",9 July 2025,Anne-mariesharp,Anne-mariesharp,Differential analysis of microbial compositions between IBS and healthy controls at the different taxonomic levels,decreased,"k__Pseudomonadati|p__Lentisphaerota,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoclostridium,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanosphaera,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium tsurumiense",3379134|256845;3379134|256845|1313211|278082|255528;1783272|1239|186801|186802|216572|1263;3379134|256845|1313211|278082|255528|172900;1783272|1239|186801|186802|216572|2304693;3366610|28890|183925|2158|2159|2316;1783272|201174|1760|85004|31953|1678|356829,Complete,KateRasheed
bsdb:36790203/1/1,36790203,"cross-sectional observational, not case-control",36790203,10.1128/spectrum.02139-21,NA,"Kayongo A., Bartolomaeus T.U.P., Birkner T., Markó L., Löber U., Kigozi E., Atugonza C., Munana R., Mawanda D., Sekibira R., Uwimaana E., Alupo P., Kalyesubula R., Knauf F., Siddharthan T., Bagaya B.S., Kateete D.P., Joloba M.L., Sewankambo N.K., Jjingo D., Kirenga B., Checkley W. , Forslund S.K.",Sputum Microbiome and Chronic Obstructive Pulmonary Disease in a Rural Ugandan Cohort of Well-Controlled HIV Infection,Microbiology spectrum,2023,"AIDS, COPD, HIV, HIV-associated COPD, airway, airway microbiome, human immunodeficiency virus, microbiome, sputum",Experiment 1,Uganda,Homo sapiens,Sputum,UBERON:0007311,Chronic obstructive pulmonary disease,EFO:0000341,HIV-negative individuals with COPD,HIV-positive individuals diagnosed with COPD,The exposed group (Group 1) consists of individuals with both HIV infection and COPD.,50,50,2 weeks,16S,34,Illumina,raw counts,Linear Regression,0.05,NA,NA,"age,sex,smoking status",NA,increased,increased,decreased,increased,increased,NA,Signature 1,Table 4.,27 October 2023,Chinelsy,"Chinelsy,ChiomaBlessing,WikiWorks",Mean relative abundance of phyla and genera in HIV-positive individuals diagnosed with COPD versus HIV-negative individuals with COPD,increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,p__Candidatus Saccharimonadota|s__Candidatus Saccharimonadota bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Lentimicrobiaceae|g__Lentimicrobium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Pseudomonadati|p__Pseudomonadota,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Spirochaetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Thermotogati|p__Synergistota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,s__bacterium,p__Candidatus Saccharimonadota|s__uncultured Candidatus Saccharibacteria bacterium,k__Pseudomonadati|p__Pseudomonadota|s__unidentified proteobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.",1783272|201174;3379134|1224|1236|135625|712|416916;1783272|201174|1760|85009|31957|2801844;1783272|1239;1783272|1239|91061|1385|186817|1386;95818|2026720;3379134|1224|1236|135615|868|2717;1783272|201174|1760|85007|1653|1716;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3082720|3118655|44259;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378;3379134|976|200643|171549|1840213|1840214;3384189|32066|203490|203491|1129771|32067;1783272|1239|91061|186826|33958|2742598;3379134|1224|1236|2887326|468|475;1783272|1239|1737404|1737405|1570339|543311;3379134|976|200643|171549|171552|838;1783272|201174|1760|85009|31957|1743;3379134|1224;33090|35493|3398|72025|3803|3814|508215;1783272|1239|909932|909929|1843491|970;3379134|203691;1783272|1239|91061|186826|1300|1301;3384194|508458;3379134|976|200643|171549|2005525|195950;1869227;95818|179883;3379134|1224|2722;1783272|1239|186801|186802|186806|1730|142586,Complete,Chinelsy
bsdb:36790203/1/2,36790203,"cross-sectional observational, not case-control",36790203,10.1128/spectrum.02139-21,NA,"Kayongo A., Bartolomaeus T.U.P., Birkner T., Markó L., Löber U., Kigozi E., Atugonza C., Munana R., Mawanda D., Sekibira R., Uwimaana E., Alupo P., Kalyesubula R., Knauf F., Siddharthan T., Bagaya B.S., Kateete D.P., Joloba M.L., Sewankambo N.K., Jjingo D., Kirenga B., Checkley W. , Forslund S.K.",Sputum Microbiome and Chronic Obstructive Pulmonary Disease in a Rural Ugandan Cohort of Well-Controlled HIV Infection,Microbiology spectrum,2023,"AIDS, COPD, HIV, HIV-associated COPD, airway, airway microbiome, human immunodeficiency virus, microbiome, sputum",Experiment 1,Uganda,Homo sapiens,Sputum,UBERON:0007311,Chronic obstructive pulmonary disease,EFO:0000341,HIV-negative individuals with COPD,HIV-positive individuals diagnosed with COPD,The exposed group (Group 1) consists of individuals with both HIV infection and COPD.,50,50,2 weeks,16S,34,Illumina,raw counts,Linear Regression,0.05,NA,NA,"age,sex,smoking status",NA,increased,increased,decreased,increased,increased,NA,Signature 2,Table 4.,27 October 2023,Chinelsy,"Chinelsy,ChiomaBlessing,Welile,WikiWorks",Mean relative abundance of phyla and genera in HIV-positive individuals diagnosed with COPD versus HIV-negative individuals with COPD,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Acholeplasma,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,p__Candidatus Altimarinota,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|s__uncultured Clostridia bacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|s__uncultured actinomycete,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Nanosynbacterales|f__Candidatus Nanosynbacteraceae|g__Candidatus Nanosynbacter|s__Candidatus Nanosynbacter lyticus",1783272|1239|91061|186826|186827|46123;1783272|544448|31969|186329|2146|2147;3379134|1224|1236|135625|712|713;1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549|171552|1283313;1783272|1239|909932|1843489|31977|156454;1783272|201174|84998|84999|1643824|1380;3379134|976;3379134|976|117743|200644|2762318|59735;3379134|29547|3031852|213849|72294|194;3379134|29547;95818|2093818|2093825|2171986|1331051;3379134|976|117743|200644|49546|1016;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|186806|1730|142586;3384194|508458|649775|649776|3029087|1434006;3384189|32066;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|1164882;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|206351|481|482;1783272|1239|186801|3085636|186803|265975;;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838|59823;1783272|1239|909932|909929;3379134|1224|28216|206351|481|71;1783272|1239|526524|526525|128827|123375;1783272|1239|186801|3085636|186803|1213720;3384189|32066|203490|203491|1129771|34104;3379134|976|200643|171549|2005525|195950;3379134|203691|203692|136|2845253|157;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061;3379134|976|200643|171549;3379134|976|200643;363464;95818|2093818|2093825;95818|2093818;1783272|1239|526524|526525|128827;3379134|1224|1236;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171552;1783272|1239|909932|1843489|31977;1783272|1239|186801|244328;1783272|201174|1760|2037|100235;95818|2093818|2093819|2093822|2093823|2093824,Complete,Chinelsy
bsdb:36790203/2/1,36790203,"cross-sectional observational, not case-control",36790203,10.1128/spectrum.02139-21,NA,"Kayongo A., Bartolomaeus T.U.P., Birkner T., Markó L., Löber U., Kigozi E., Atugonza C., Munana R., Mawanda D., Sekibira R., Uwimaana E., Alupo P., Kalyesubula R., Knauf F., Siddharthan T., Bagaya B.S., Kateete D.P., Joloba M.L., Sewankambo N.K., Jjingo D., Kirenga B., Checkley W. , Forslund S.K.",Sputum Microbiome and Chronic Obstructive Pulmonary Disease in a Rural Ugandan Cohort of Well-Controlled HIV Infection,Microbiology spectrum,2023,"AIDS, COPD, HIV, HIV-associated COPD, airway, airway microbiome, human immunodeficiency virus, microbiome, sputum",Experiment 2,Uganda,Homo sapiens,Sputum,UBERON:0007311,Chronic obstructive pulmonary disease,EFO:0000341,HIV-negative individuals (without COPD),HIV-positive individuals (without COPD),The exposed group (Group 1) consists of individuals with HIV infection but without COPD.,50,50,2 weeks,16S,34,Illumina,raw counts,Linear Regression,0.05,NA,NA,"age,sex,smoking status",NA,increased,increased,decreased,increased,increased,NA,Signature 1,Table 4.,28 October 2023,Chinelsy,"Chinelsy,ChiomaBlessing,Welile,WikiWorks",Mean relative abundance of phyla and genera in HIV-positive individuals without COPD versus HIV-negative individuals without COPD,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Aminipila,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Pseudomonadati|p__Spirochaetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,k__Thermotogati|p__Synergistota,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,p__Candidatus Saccharimonadota|s__uncultured Candidatus Saccharibacteria bacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|s__uncultured actinomycete,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Nanosynbacterales|f__Candidatus Nanosynbacteraceae|g__Candidatus Nanosynbacter|s__Candidatus Nanosynbacter lyticus",3379134|1224|1236|135625|712|713;1783272|201174|1760|2037|2049|1654;1783272|201174;3379134|976|200643|171549|171552|1283313;1783272|1239|186801|3082720|543314|2060094;1783272|201174|84998|84999|1643824|1380;1783272|1239|91061|1385|186817|1386;3379134|976;1783272|1239|186801|3085636|186803|830;3379134|29547|3031852|213849|72294|194;3379134|29547;95818|2093818|2093825|2171986|1331051;3379134|976|117743|200644|49546|1016;1783272|1239|186801|3085636|186803|43996;1783272|201174|1760|85007|1653|1716;1783272|1117;1783272|1239|186801|186802|186806|1730;3384189|32066|203490|203491;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|1164882;3379134|1224|1236|2887326|468|475;1783272|1239|186801|3085636|186803|265975;;1783272|1239|186801|3082720|3118655|1913599;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838|59823;1783272|201174|1760|85009|31957|1743;3379134|1224;1783272|1239|909932|909929|1843491;1783272|1239|909932|909929;1783272|1239|909932|909929|1843491|970;1783272|1239|526524|526525|128827|123375;3379134|203691;1783272|1239|186801|3085636|186803|1213720;3384189|32066|203490|203491|1129771|34104;3384194|508458;3379134|203691|203692|136|2845253|157;1783272|1239|909932|1843489|31977|29465;95818|179883;1783272|201174|1760|2037|100235;95818|2093818|2093819|2093822|2093823|2093824,Complete,Chinelsy
bsdb:36790203/2/2,36790203,"cross-sectional observational, not case-control",36790203,10.1128/spectrum.02139-21,NA,"Kayongo A., Bartolomaeus T.U.P., Birkner T., Markó L., Löber U., Kigozi E., Atugonza C., Munana R., Mawanda D., Sekibira R., Uwimaana E., Alupo P., Kalyesubula R., Knauf F., Siddharthan T., Bagaya B.S., Kateete D.P., Joloba M.L., Sewankambo N.K., Jjingo D., Kirenga B., Checkley W. , Forslund S.K.",Sputum Microbiome and Chronic Obstructive Pulmonary Disease in a Rural Ugandan Cohort of Well-Controlled HIV Infection,Microbiology spectrum,2023,"AIDS, COPD, HIV, HIV-associated COPD, airway, airway microbiome, human immunodeficiency virus, microbiome, sputum",Experiment 2,Uganda,Homo sapiens,Sputum,UBERON:0007311,Chronic obstructive pulmonary disease,EFO:0000341,HIV-negative individuals (without COPD),HIV-positive individuals (without COPD),The exposed group (Group 1) consists of individuals with HIV infection but without COPD.,50,50,2 weeks,16S,34,Illumina,raw counts,Linear Regression,0.05,NA,NA,"age,sex,smoking status",NA,increased,increased,decreased,increased,increased,NA,Signature 2,Table 4.,28 October 2023,Chinelsy,"Chinelsy,ChiomaBlessing,WikiWorks",Mean relative abundance of phyla and genera in HIV-positive individuals without COPD versus HIV-negative individuals without COPD,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacillati|p__Bacillota,p__Candidatus Saccharimonadota|s__Candidatus Saccharimonadota bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.",1783272|1239|91061|186826|186827|46123;3379134|1224|1236|135625|712|416916;1783272|201174|1760|85009|31957|2801844;1783272|1239;95818|2026720;1783272|1239|186801|3082720|3118655|44259;3384194|508458|649775|649776|3029087|1434006;3384189|32066;3384189|32066|203490|203491|203492|848;3379134|1224|28216|80840|119060|47670;3384189|32066|203490|203491|1129771|32067;3379134|1224|28216|206351|481|482;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171552|838;33090|35493|3398|72025|3803|3814|508215;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|186806|1730|142586,Complete,Chinelsy
bsdb:36795141/1/1,36795141,case-control,36795141,10.1007/s00253-023-12410-w,NA,"Shi J., Wang Y., Chen D., Xu X., Li W., Li K., He J., Su W. , Luo Q.",The alteration of intestinal mucosal α-synuclein expression and mucosal microbiota in Parkinson's disease,Applied microbiology and biotechnology,2023,"Diagnosis, Intestinal mucosa, Mucosal microbiota, Parkinson’s disease, α-Synuclein",Experiment 1,China,Homo sapiens,Duodenal mucosa,UBERON:0000320,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's Disease (PD) Patients,Parkinson's disease (PD) patients diagnosed by an experienced neurologist (the stage of Hoehn and Yahr Scale < 5),22,19,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 5c,12 March 2024,Scholastica,"Scholastica,WikiWorks",Taxa significantly abundant in the duodenal mucosal microbiota composition in control versus Parkinson's disease (PD) patients,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia",3379134|1224|28216|80840|119060;3379134|1224|28216|80840;3379134|1224|1236;1783272|1239|91061|186826|1300|1357;3379134|1224|28216|80840|75682|149698;3379134|1224|28216|80840|75682;3379134|1224;3379134|1224|28216|80840|119060|48736,Complete,Svetlana up
bsdb:36795141/1/2,36795141,case-control,36795141,10.1007/s00253-023-12410-w,NA,"Shi J., Wang Y., Chen D., Xu X., Li W., Li K., He J., Su W. , Luo Q.",The alteration of intestinal mucosal α-synuclein expression and mucosal microbiota in Parkinson's disease,Applied microbiology and biotechnology,2023,"Diagnosis, Intestinal mucosa, Mucosal microbiota, Parkinson’s disease, α-Synuclein",Experiment 1,China,Homo sapiens,Duodenal mucosa,UBERON:0000320,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's Disease (PD) Patients,Parkinson's disease (PD) patients diagnosed by an experienced neurologist (the stage of Hoehn and Yahr Scale < 5),22,19,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 5c,12 March 2024,Scholastica,"Scholastica,WikiWorks",Taxa significantly abundant in the duodenal mucosal microbiota composition in control versus Parkinson's disease (PD) patients,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales",3379134|976|117743|200644|49546;3379134|1224|28211|204441,Complete,Svetlana up
bsdb:36795141/2/1,36795141,case-control,36795141,10.1007/s00253-023-12410-w,NA,"Shi J., Wang Y., Chen D., Xu X., Li W., Li K., He J., Su W. , Luo Q.",The alteration of intestinal mucosal α-synuclein expression and mucosal microbiota in Parkinson's disease,Applied microbiology and biotechnology,2023,"Diagnosis, Intestinal mucosa, Mucosal microbiota, Parkinson’s disease, α-Synuclein",Experiment 2,China,Homo sapiens,Mucosa of sigmoid colon,UBERON:0004993,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's Disease Patients,Parkinson's disease (PD) patients diagnosed by an experienced neurologist (the stage of Hoehn and Yahr Scale < 5),21,19,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 5d,12 March 2024,Scholastica,"Scholastica,WikiWorks",Taxa significantly abundant in the sigmoid mucosal microbiota composition in control versus Parkinson's disease (PD) patients,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",1783272|201174|1760|85004|31953|1678|216816;3379134|976|200643|171549|171552,Complete,Svetlana up
bsdb:36795141/2/2,36795141,case-control,36795141,10.1007/s00253-023-12410-w,NA,"Shi J., Wang Y., Chen D., Xu X., Li W., Li K., He J., Su W. , Luo Q.",The alteration of intestinal mucosal α-synuclein expression and mucosal microbiota in Parkinson's disease,Applied microbiology and biotechnology,2023,"Diagnosis, Intestinal mucosa, Mucosal microbiota, Parkinson’s disease, α-Synuclein",Experiment 2,China,Homo sapiens,Mucosa of sigmoid colon,UBERON:0004993,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's Disease Patients,Parkinson's disease (PD) patients diagnosed by an experienced neurologist (the stage of Hoehn and Yahr Scale < 5),21,19,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 5d,12 March 2024,Scholastica,"Scholastica,WikiWorks",Taxa significantly abundant in the sigmoid mucosal microbiota composition in control versus Parkinson's disease (PD) patients,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Thermoactinomycetaceae,1783272|1239|91061|1385|186824,Complete,Svetlana up
bsdb:36795141/3/NA,36795141,case-control,36795141,10.1007/s00253-023-12410-w,NA,"Shi J., Wang Y., Chen D., Xu X., Li W., Li K., He J., Su W. , Luo Q.",The alteration of intestinal mucosal α-synuclein expression and mucosal microbiota in Parkinson's disease,Applied microbiology and biotechnology,2023,"Diagnosis, Intestinal mucosa, Mucosal microbiota, Parkinson’s disease, α-Synuclein",Experiment 3,China,Homo sapiens,Mucosa of sigmoid colon,UBERON:0004993,Parkinson's disease,MONDO:0005180,Duodenal mucosa,Sigmoid mucosa,Samples from the sigmoid mucosa of Parkinson's disease (PD) patients,19,19,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,4,NA,NA,NA,increased,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:36803646/1/1,36803646,case-control,36803646,10.1186/s13041-023-01014-0,https://pubmed.ncbi.nlm.nih.gov/36803646/,"Kong G., Zhang W., Zhang S., Chen J., He K., Zhang C., Yuan X. , Xie B.",The gut microbiota and metabolite profiles are altered in patients with spinal cord injury,Molecular brain,2023,"16S rRNA gene sequencing, Gut microbiota, Spinal cord injury, Untargeted metabolomics",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Spinal cord injury,EFO:1001919,healthy control (without SCI),SCI (spinal cord injury),"Spinal cord injury (SCI), which is typically caused by severe trauma such as falls and traffic accidents, is one of the most severe forms of central nervous system injury (CNS).",10,11,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,"age,geographic area,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 1,Figure 2e,26 March 2023,Kahvecirem,"Kahvecirem,Atrayees,Boadiwaa,WikiWorks","The species with different abundances are listed in the genus, class, phylum, order, and family levels for each group.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239|186801|3085636|186803|1766253;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|2005519;1783272|1239|186801|3085636|186803|572511;3379134|1224|28216|80840;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801;1783272|1239|186801|186802|1898207;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|33042;1783272|201174|84998|84999|84107;1783272|1239|186801|3085636|186803|189330;1783272|1239|526524|526525|128827;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|1686313;1783272|1239|186801|3085636|186803|1407607;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|3085636|186803|1898203;1783272|1239|186801|3085636|186803|248744;3379134|1224|28216|80840|995019|577310;3379134|1224|1236|135625;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|201174|84998|1643822|1643826|84108;3379134|1224|28216|80840|995019|40544;3379134|1224|28216|80840|995019;1783272|1239|186801|186802|216572|39492;1783272|1239|186801;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802,Complete,Atrayees
bsdb:36803646/1/2,36803646,case-control,36803646,10.1186/s13041-023-01014-0,https://pubmed.ncbi.nlm.nih.gov/36803646/,"Kong G., Zhang W., Zhang S., Chen J., He K., Zhang C., Yuan X. , Xie B.",The gut microbiota and metabolite profiles are altered in patients with spinal cord injury,Molecular brain,2023,"16S rRNA gene sequencing, Gut microbiota, Spinal cord injury, Untargeted metabolomics",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Spinal cord injury,EFO:1001919,healthy control (without SCI),SCI (spinal cord injury),"Spinal cord injury (SCI), which is typically caused by severe trauma such as falls and traffic accidents, is one of the most severe forms of central nervous system injury (CNS).",10,11,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,"age,geographic area,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 2,Figure 2e,26 March 2023,Kahvecirem,"Kahvecirem,Atrayees,WikiWorks","The species with different abundances are listed in the genus, class, phylum, order, and family levels for each group.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",1783272|1239|186801|186802|216572|52784;1783272|1239|186801|3085636|186803|2383;1783272|1239|186801|3082768|990719|990721;3379134|976|200643|171549|2005520;3379134|976|200643|171549|2005520|156973;1783272|201174|84998|1643822|1643826|84111;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3082720|186804|1505657;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|3085636|186803|1769710;1783272|1239|526524|526525|2810280|3025755,Complete,Atrayees
bsdb:36803646/2/1,36803646,case-control,36803646,10.1186/s13041-023-01014-0,https://pubmed.ncbi.nlm.nih.gov/36803646/,"Kong G., Zhang W., Zhang S., Chen J., He K., Zhang C., Yuan X. , Xie B.",The gut microbiota and metabolite profiles are altered in patients with spinal cord injury,Molecular brain,2023,"16S rRNA gene sequencing, Gut microbiota, Spinal cord injury, Untargeted metabolomics",Experiment 2,United States of America,Homo sapiens,Venous blood,UBERON:0013756,Spinal cord injury,EFO:1001919,healthy control (without SCI),SCI (spinal cord injury),"Spinal cord injury (SCI), which is typically caused by severe trauma such as falls and traffic accidents, is one of the most severe forms of central nervous system injury (CNS).",10,10,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,geographic area,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 1,"Figure 2b, 2c",2 June 2023,Atrayees,"Atrayees,WikiWorks",Differential abundance of taxa at phylum and genus level,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|216851;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|3085636|186803|1766253;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|1407607;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|186802|216572|1263;1783272|1239|186801;1783272|1239|186801|3085636|186803,Complete,Atrayees
bsdb:36803646/2/2,36803646,case-control,36803646,10.1186/s13041-023-01014-0,https://pubmed.ncbi.nlm.nih.gov/36803646/,"Kong G., Zhang W., Zhang S., Chen J., He K., Zhang C., Yuan X. , Xie B.",The gut microbiota and metabolite profiles are altered in patients with spinal cord injury,Molecular brain,2023,"16S rRNA gene sequencing, Gut microbiota, Spinal cord injury, Untargeted metabolomics",Experiment 2,United States of America,Homo sapiens,Venous blood,UBERON:0013756,Spinal cord injury,EFO:1001919,healthy control (without SCI),SCI (spinal cord injury),"Spinal cord injury (SCI), which is typically caused by severe trauma such as falls and traffic accidents, is one of the most severe forms of central nervous system injury (CNS).",10,10,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,geographic area,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 2,"Figure 2b, 2c",2 June 2023,Atrayees,"Atrayees,WikiWorks",Differential abundance of taxa at phylum and genus level,increased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,1783272|201174|84998|1643822|1643826|84111,Complete,NA
bsdb:36803868/1/1,36803868,randomized controlled trial,36803868,10.1186/s40168-023-01460-x,NA,"Abotsi R.E., Dube F.S., Rehman A.M., Claassen-Weitz S., Xia Y., Simms V., Mwaikono K.S., Gardner-Lubbe S., McHugh G., Ngwira L.G., Kwambana-Adams B., Heyderman R.S., Odland J.Ø., Ferrand R.A. , Nicol M.P.",Sputum bacterial load and bacterial composition correlate with lung function and are altered by long-term azithromycin treatment in children with HIV-associated chronic lung disease,Microbiome,2023,"Adolescents, Africa, Bacteriome, FEV1z, HIV, Haemophilus, Microbiome, Moraxella, Obliterative bronchiolitis",Experiment 1,"Malawi,Zimbabwe",Homo sapiens,Sputum,UBERON:0007311,Response to antibiotic,GO:0046677,Placebo at 48 Weeks,Azithromycin(AZM) at 48 weeks,Participants with HIV-associated Chronic Lung Disease (HCLD) who received  azithromycin (AZM),150,154,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure S 24,11 October 2023,Chinelsy,"Chinelsy,Peace Sandy,ChiomaBlessing,WikiWorks","Heatmap displaying the q values of the genera detected as differentially abundant between AZM and placebo arms at 48 weeks by 10 statistical methods. For ANCOM2, taxa with w 0.6, 0.7, 0.8 and 0.9 were assigned q value of 0.01, 0.001, 0.0001 and 0.00001 respectively. Five genera were detected as differentially abundant by all methods (Lautropia, Moraxella, Rothia, Treponema and Veilonella).",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",3379134|1224|28216|80840|119060|47670;3379134|1224|1236|2887326|468|475;1783272|201174|1760|85006|1268|32207;3379134|203691|203692|136|2845253|157,Complete,Peace Sandy
bsdb:36803868/2/1,36803868,randomized controlled trial,36803868,10.1186/s40168-023-01460-x,NA,"Abotsi R.E., Dube F.S., Rehman A.M., Claassen-Weitz S., Xia Y., Simms V., Mwaikono K.S., Gardner-Lubbe S., McHugh G., Ngwira L.G., Kwambana-Adams B., Heyderman R.S., Odland J.Ø., Ferrand R.A. , Nicol M.P.",Sputum bacterial load and bacterial composition correlate with lung function and are altered by long-term azithromycin treatment in children with HIV-associated chronic lung disease,Microbiome,2023,"Adolescents, Africa, Bacteriome, FEV1z, HIV, Haemophilus, Microbiome, Moraxella, Obliterative bronchiolitis",Experiment 2,"Malawi,Zimbabwe",Homo sapiens,Sputum,UBERON:0007311,Azithromycin,CHEBI:2955,Placebo at 72 weeks,AZM at 72 weeks,Participants with HIV-associated Chronic Lung Disease (HCLD) who received  azithromycin (AZM),117,123,NA,16S,4,Illumina,relative abundances,"DESeq2,ANCOM",0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Tables S6 and S7,12 October 2023,Chinelsy,"Chinelsy,Peace Sandy,Davvve,Chloe,WikiWorks","Table S 6. Results of differential abundance testing of bacterial taxa from AZM and Placebo samples from 72 weeks using DESeq2.

Table S 7. Results of differential abundance testing of bacterial taxa from AZM and Placebo samples from 72 weeks using Ancom-II",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",3379134|1224|28216|80840|119060|47670;3379134|203691|203692|136|2845253|157,Complete,Chloe
bsdb:36803868/3/1,36803868,randomized controlled trial,36803868,10.1186/s40168-023-01460-x,NA,"Abotsi R.E., Dube F.S., Rehman A.M., Claassen-Weitz S., Xia Y., Simms V., Mwaikono K.S., Gardner-Lubbe S., McHugh G., Ngwira L.G., Kwambana-Adams B., Heyderman R.S., Odland J.Ø., Ferrand R.A. , Nicol M.P.",Sputum bacterial load and bacterial composition correlate with lung function and are altered by long-term azithromycin treatment in children with HIV-associated chronic lung disease,Microbiome,2023,"Adolescents, Africa, Bacteriome, FEV1z, HIV, Haemophilus, Microbiome, Moraxella, Obliterative bronchiolitis",Experiment 3,"Malawi,Zimbabwe",Homo sapiens,Sputum,UBERON:0007311,Azithromycin,CHEBI:2955,AZM at baseline - Azithromycin arm only,AZM at 48 weeks - Azithromycin arm only,Participants with HIV-associated Chronic Lung Disease (HCLD) who received  azithromycin (AZM) at 48weeks,173,154,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Table S 8.,12 October 2023,Chinelsy,"Chinelsy,Peace Sandy,WikiWorks",Results of differential abundance testing of bacterial taxa from samples from the AZM arm at baseline and 48 72 weeks using 10 methods.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium",3379134|1224|28216|80840|119060|47670;3379134|1224|1236|2887326|468|475;3379134|203691|203692|136|2845253|157;1783272|1239|186801|3085636|186803|265975,Complete,Peace Sandy
bsdb:36803868/4/1,36803868,randomized controlled trial,36803868,10.1186/s40168-023-01460-x,NA,"Abotsi R.E., Dube F.S., Rehman A.M., Claassen-Weitz S., Xia Y., Simms V., Mwaikono K.S., Gardner-Lubbe S., McHugh G., Ngwira L.G., Kwambana-Adams B., Heyderman R.S., Odland J.Ø., Ferrand R.A. , Nicol M.P.",Sputum bacterial load and bacterial composition correlate with lung function and are altered by long-term azithromycin treatment in children with HIV-associated chronic lung disease,Microbiome,2023,"Adolescents, Africa, Bacteriome, FEV1z, HIV, Haemophilus, Microbiome, Moraxella, Obliterative bronchiolitis",Experiment 4,"Malawi,Zimbabwe",Homo sapiens,Sputum,UBERON:0007311,Azithromycin,CHEBI:2955,Placebo at 48 Weeks - Arm Only,Placebo at 72 Weeks - Arm Only,Placebo treatment at 72 Weeks (arm only),174,174,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Table S 10.,24 February 2024,Peace Sandy,"Peace Sandy,WikiWorks",Results of differential abundance testing of bacterial taxa from Placebo samples from 48 and 72 weeks using DESeq2.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,3379134|1224|1236|2887326|468|475,Complete,Peace Sandy
bsdb:36803868/5/1,36803868,randomized controlled trial,36803868,10.1186/s40168-023-01460-x,NA,"Abotsi R.E., Dube F.S., Rehman A.M., Claassen-Weitz S., Xia Y., Simms V., Mwaikono K.S., Gardner-Lubbe S., McHugh G., Ngwira L.G., Kwambana-Adams B., Heyderman R.S., Odland J.Ø., Ferrand R.A. , Nicol M.P.",Sputum bacterial load and bacterial composition correlate with lung function and are altered by long-term azithromycin treatment in children with HIV-associated chronic lung disease,Microbiome,2023,"Adolescents, Africa, Bacteriome, FEV1z, HIV, Haemophilus, Microbiome, Moraxella, Obliterative bronchiolitis",Experiment 5,"Malawi,Zimbabwe",Homo sapiens,Sputum,UBERON:0007311,Response to antibiotic,GO:0046677,Placebo at baseline,Placebo at 72 weeks,Placebo at 72 weeks,174,117,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Table S 11,24 February 2024,Peace Sandy,"Peace Sandy,WikiWorks",Results of differential abundance testing of bacterial taxa from Placebo samples from baseline and 72 weeks using DESeq2.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,3379134|1224|1236|2887326|468|475,Complete,Peace Sandy
bsdb:36810115/1/1,36810115,laboratory experiment,36810115,10.1186/s40168-023-01471-8,NA,"Pan W., Zhao J., Wu J., Xu D., Meng X., Jiang P., Shi H., Ge X., Yang X., Hu M., Zhang P., Tang R., Nagaratnam N., Zheng K., Huang X.F. , Yu Y.",Dimethyl itaconate ameliorates cognitive impairment induced by a high-fat diet via the gut-brain axis in mice,Microbiome,2023,"Cognition, Gut microbiome, Gut-brain axis, Itaconate, Microglia, Obesity",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Metabolite,CHEBI:25212,HF+Veh (High fat and Vehicle treated mice),HF+DI (High fat and Dimethyl Itaconate treated mice),"Mice in this group received a high-fat diet (30% fat by weight) to induce cognitive impairment. Then, they were intraperitoneally injected with Dimethy Itaconate (25mg/kg) twice a week.",12,12,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Fig. 5g,30 July 2024,Victoria,"Victoria,WikiWorks",A Linear discriminant analysis (LDA) effect size (LEfSe) showing the most significantly abundant taxa enriched in microbiome from the HF+DI group compared to the HF+Veh group.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio",3379134|976|200643;3379134|976;3379134|976|200643|171549|171552;1783272|1239|526524|526525|128827|174708;3379134|976|200643|171549|171552|1283313;1783272|1239|91061;3379134|1224|28211|204441|2829815|191;3379134|1224|28211|204441|2829815;3379134|1224|1236|135624;3379134|1224|1236|135624|83763|83770,Complete,Svetlana up
bsdb:36810115/1/2,36810115,laboratory experiment,36810115,10.1186/s40168-023-01471-8,NA,"Pan W., Zhao J., Wu J., Xu D., Meng X., Jiang P., Shi H., Ge X., Yang X., Hu M., Zhang P., Tang R., Nagaratnam N., Zheng K., Huang X.F. , Yu Y.",Dimethyl itaconate ameliorates cognitive impairment induced by a high-fat diet via the gut-brain axis in mice,Microbiome,2023,"Cognition, Gut microbiome, Gut-brain axis, Itaconate, Microglia, Obesity",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Metabolite,CHEBI:25212,HF+Veh (High fat and Vehicle treated mice),HF+DI (High fat and Dimethyl Itaconate treated mice),"Mice in this group received a high-fat diet (30% fat by weight) to induce cognitive impairment. Then, they were intraperitoneally injected with Dimethy Itaconate (25mg/kg) twice a week.",12,12,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Fig. 5g,30 July 2024,Victoria,"Victoria,WikiWorks",A Linear discriminant analysis (LDA) effect size (LEfSe) showing the most significantly abundant taxa enriched in microbiome from the HF+DI group compared to the HF+Veh group.,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Pseudoxanthomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Candidatus Actinomarinales,k__Pseudomonadati|p__Acidobacteriota|c__Terriglobia|o__Bryobacterales|f__Solibacteraceae|g__Candidatus Solibacter",1783272|1239;1783272|1239|186801;28221;3379134|200940|3031449|213115;1783272|1239|186801|186802;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803;3379134|1224|1236|135614|32033|83618;1783272|1239|186801|186802|216572|1508657;1783272|201174|1760|1389450;3379134|57723|204432|332160|332161|332162,Complete,Svetlana up
bsdb:36810115/2/1,36810115,laboratory experiment,36810115,10.1186/s40168-023-01471-8,NA,"Pan W., Zhao J., Wu J., Xu D., Meng X., Jiang P., Shi H., Ge X., Yang X., Hu M., Zhang P., Tang R., Nagaratnam N., Zheng K., Huang X.F. , Yu Y.",Dimethyl itaconate ameliorates cognitive impairment induced by a high-fat diet via the gut-brain axis in mice,Microbiome,2023,"Cognition, Gut microbiome, Gut-brain axis, Itaconate, Microglia, Obesity",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Metabolite,CHEBI:25212,FMT-HF+Veh (Fecal microbiome transplantation-High fat and Vehicle treated mice),FMT-HF+DI (Fecal microbiome transplantation-High fat and Dimethyl Itaconate treated mice),"Mice in this group received a high-fat diet (30% fat by weight) to induce cognitive impairment. Then, they were intraperitoneally injected with Dimethy Itaconate (25mg/kg) twice a week. Afterward, they received fecal microbiome transplantation.",8,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Supplemental Figure S5,2 August 2024,Victoria,"Victoria,WikiWorks",Linear discriminant analysis (LDA) effect size (LEfSe) showing the most significantly abundant taxa enriched in microbiome from the FMT-HF+DI group compared to the FMT-HF+Veh group.,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Thermodesulfobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae",1783272|201174;1783272|201174|84998|84999;1783272|201174|84998;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115;3379134|200940|3031449;1783272|201174|84998|1643822|1643826;1783272|201174|84998|1643822|1643826|580024;1783272|1239|186801|3085636|186803;1783272|544448|31969|2085|2092|2093;1783272|1239|186801|3085636|186803|841;3379134|200940;1783272|1239|186801|3085636|186803|1506577;3379134|200940|3031449|213115|194924,Complete,Svetlana up
bsdb:36810115/2/2,36810115,laboratory experiment,36810115,10.1186/s40168-023-01471-8,NA,"Pan W., Zhao J., Wu J., Xu D., Meng X., Jiang P., Shi H., Ge X., Yang X., Hu M., Zhang P., Tang R., Nagaratnam N., Zheng K., Huang X.F. , Yu Y.",Dimethyl itaconate ameliorates cognitive impairment induced by a high-fat diet via the gut-brain axis in mice,Microbiome,2023,"Cognition, Gut microbiome, Gut-brain axis, Itaconate, Microglia, Obesity",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Metabolite,CHEBI:25212,FMT-HF+Veh (Fecal microbiome transplantation-High fat and Vehicle treated mice),FMT-HF+DI (Fecal microbiome transplantation-High fat and Dimethyl Itaconate treated mice),"Mice in this group received a high-fat diet (30% fat by weight) to induce cognitive impairment. Then, they were intraperitoneally injected with Dimethy Itaconate (25mg/kg) twice a week. Afterward, they received fecal microbiome transplantation.",8,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Supplemental Figure S5,2 August 2024,Victoria,"Victoria,WikiWorks",Linear discriminant analysis (LDA) effect size (LEfSe) showing the most significantly abundant taxa enriched in microbiome from the FMT-HF+DI group compared to the FMT-HF+Veh group.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Pseudochrobactrum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Ileibacterium,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales",3379134|1224|28211|356|118882|354349;3379134|1224|28211|356;3379134|1224|28211|356|82115;1783272|1239|526524|526525|128827|1937007;1783272|1239;1783272|1239|91061;1783272|1239|526524|526525|128827|1937008;1783272|1239|526524|526525|128827;1783272|1239|526524|526525,Complete,Svetlana up
bsdb:36864380/2/1,36864380,case-control,36864380,10.1186/s12866-023-02791-3,https://pubmed.ncbi.nlm.nih.gov/36864380/,"Mahdy M.S., Azmy A.F., Dishisha T., Mohamed W.R., Ahmed K.A., Hassan A., Aidy S.E. , El-Gendy A.O.",Irinotecan-gut microbiota interactions and the capability of probiotics to mitigate Irinotecan-associated toxicity,BMC microbiology,2023,"Anticancer, Beta-glucuronidase, Colon, Inflammation, Irinotecan, Probiotics",Experiment 2,Egypt,Homo sapiens,Feces,UBERON:0001988,Response to irinotecan,EFO:0004829,Healthy individuals and colon cancer (CRC) patients,Irinotecan treated patients,"Patients treated with Irinotecan, a chemotherapeutic agent used to treat a variety of tumors, including colorectal cancer (CRC).",10,5,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Fig. 4a,18 June 2024,Scholastica,"Scholastica,WikiWorks","The differences in the relative abundance of taxa between the colon cancer patients, Irinotecan treated, and healthy individuals as detected by the linear discriminant analysis effect size (LEfSe)",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|186801|186802|3085642|580596;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:36864380/3/1,36864380,case-control,36864380,10.1186/s12866-023-02791-3,https://pubmed.ncbi.nlm.nih.gov/36864380/,"Mahdy M.S., Azmy A.F., Dishisha T., Mohamed W.R., Ahmed K.A., Hassan A., Aidy S.E. , El-Gendy A.O.",Irinotecan-gut microbiota interactions and the capability of probiotics to mitigate Irinotecan-associated toxicity,BMC microbiology,2023,"Anticancer, Beta-glucuronidase, Colon, Inflammation, Irinotecan, Probiotics",Experiment 3,Egypt,Homo sapiens,Feces,UBERON:0001988,Response to irinotecan,EFO:0004829,Healthy individuals and Irinotecan treated patients,Colon cancer patients,Patients with colon cancer,10,5,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 4a,18 June 2024,Scholastica,"Scholastica,WikiWorks","The differences in the relative abundance of taxa between the colon cancer patients, Irinotecan treated, and healthy individuals as detected by the linear discriminant analysis effect size (LEfSe)",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales",1783272|1239|909932|1843489|31977|39948;3379134|1224|1236|91347|543;3379134|1224|1236|91347,Complete,Svetlana up
bsdb:36869345/1/1,36869345,case-control,36869345,https://doi.org/10.1186/s40168-022-01447-0,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01447-0,"Li J., Jing Q., Li J., Hua M., Di L., Song C., Huang Y., Wang J., Chen C. , Wu A.R.",Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection,Microbiome,2023,"COVID-19, Gut, Human microbiota, SARS-CoV-2, Upper respiratory tract",Experiment 1,China,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,samples from Healthy patients,Pharyngeal samples from COVID-19 patients,"The samples were collected from a cohort of patients diagnosed with COVID-19, classified into three severity degrees: mild, moderate, and severe illness, based on specific criteria.",39,174,NA,PCR,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 1,"Within Results text (""Alteration of microbial composition in COVID-19 patients is associated with disease severity"", lines 1-4)",27 October 2023,MyleeeA,"MyleeeA,Folakunmi,WikiWorks",Altered microbial composition associated with disease severity,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",3379134|1224|28216|80840|119060|32008;3379134|29547|3031852|213849|72294|194;3379134|1224|1236|91347|543|561;3384189|32066|203490|203491|203492|848;3379134|1224|1236|135625|712|724;1783272|201174|1760|85006|1268|1269;3379134|1224|28216|206351|481|482;1783272|1239|909932|909929|1843491|970;3379134|976|200643|171549|2005525|195950;3379134|203691|203692|136|2845253|157,Complete,Folakunmi
bsdb:36869345/1/2,36869345,case-control,36869345,https://doi.org/10.1186/s40168-022-01447-0,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01447-0,"Li J., Jing Q., Li J., Hua M., Di L., Song C., Huang Y., Wang J., Chen C. , Wu A.R.",Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection,Microbiome,2023,"COVID-19, Gut, Human microbiota, SARS-CoV-2, Upper respiratory tract",Experiment 1,China,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,samples from Healthy patients,Pharyngeal samples from COVID-19 patients,"The samples were collected from a cohort of patients diagnosed with COVID-19, classified into three severity degrees: mild, moderate, and severe illness, based on specific criteria.",39,174,NA,PCR,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 2,"Within Results text (""Alteration of microbial composition in COVID-19 patients is associated with disease severity"", lines 1-4)",27 October 2023,MyleeeA,"MyleeeA,Folakunmi,WikiWorks",Altered microbial composition associated with disease severity,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|1760|2037|2049|1654;33090|35493|3398|72025|3803|3814|508215;1783272|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:36869345/2/1,36869345,case-control,36869345,https://doi.org/10.1186/s40168-022-01447-0,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01447-0,"Li J., Jing Q., Li J., Hua M., Di L., Song C., Huang Y., Wang J., Chen C. , Wu A.R.",Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection,Microbiome,2023,"COVID-19, Gut, Human microbiota, SARS-CoV-2, Upper respiratory tract",Experiment 2,China,Homo sapiens,Sputum,UBERON:0007311,COVID-19,MONDO:0100096,samples from Healthy patients,Sputum samples from COVID-19 patients,"The samples were collected from a cohort of patients diagnosed with COVID-19, classified into three severity degrees: mild, moderate, and severe illness, based on specific criteria",15,235,NA,PCR,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 1,"Within Results text (""Alteration of microbial composition in COVID-19 patients is associated with disease severity"", lines 5-7)",27 October 2023,MyleeeA,"MyleeeA,Folakunmi,WikiWorks",Altered microbial composition associated with disease severity,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|976|117743|200644|49546|1016;1783272|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:36869345/2/2,36869345,case-control,36869345,https://doi.org/10.1186/s40168-022-01447-0,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01447-0,"Li J., Jing Q., Li J., Hua M., Di L., Song C., Huang Y., Wang J., Chen C. , Wu A.R.",Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection,Microbiome,2023,"COVID-19, Gut, Human microbiota, SARS-CoV-2, Upper respiratory tract",Experiment 2,China,Homo sapiens,Sputum,UBERON:0007311,COVID-19,MONDO:0100096,samples from Healthy patients,Sputum samples from COVID-19 patients,"The samples were collected from a cohort of patients diagnosed with COVID-19, classified into three severity degrees: mild, moderate, and severe illness, based on specific criteria",15,235,NA,PCR,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 2,"Within Results text (""Alteration of microbial composition in COVID-19 patients is associated with disease severity"", lines 5-7)",27 October 2023,MyleeeA,"MyleeeA,Folakunmi,WikiWorks",Altered microbial composition associated with disease severity,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",3379134|1224|28216|80840|80864|80865;3379134|1224|1236|135625|712|724;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|2005525|195950;3379134|203691|203692|136|2845253|157,Complete,Folakunmi
bsdb:36869345/3/1,36869345,case-control,36869345,https://doi.org/10.1186/s40168-022-01447-0,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01447-0,"Li J., Jing Q., Li J., Hua M., Di L., Song C., Huang Y., Wang J., Chen C. , Wu A.R.",Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection,Microbiome,2023,"COVID-19, Gut, Human microbiota, SARS-CoV-2, Upper respiratory tract",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,samples from Healthy patients,Feces samples from COVID-19 patients,"The samples were collected from a cohort of patients diagnosed with COVID-19, classified into three severity degrees: mild, moderate, and severe illness, based on specific criteria.",40,112,NA,PCR,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Within Results text (""Alteration of microbial composition in COVID-19 patients is associated with disease severity"", lines 13-16)  Description: Altered microbial composition associated with disease severity",27 October 2023,MyleeeA,"MyleeeA,Folakunmi,WikiWorks",Altered microbial composition associated with disease severity,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",3379134|1224|1236|135619|28256|2745;3379134|1224|1236|72274|135621|286,Complete,Folakunmi
bsdb:36869345/3/2,36869345,case-control,36869345,https://doi.org/10.1186/s40168-022-01447-0,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01447-0,"Li J., Jing Q., Li J., Hua M., Di L., Song C., Huang Y., Wang J., Chen C. , Wu A.R.",Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection,Microbiome,2023,"COVID-19, Gut, Human microbiota, SARS-CoV-2, Upper respiratory tract",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,samples from Healthy patients,Feces samples from COVID-19 patients,"The samples were collected from a cohort of patients diagnosed with COVID-19, classified into three severity degrees: mild, moderate, and severe illness, based on specific criteria.",40,112,NA,PCR,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Within Results text (""Alteration of microbial composition in COVID-19 patients is associated with disease severity"", lines 13-16)",27 October 2023,MyleeeA,"MyleeeA,Folakunmi,WikiWorks",Altered microbial composition associated with disease severity.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|3085636|186803|207244;1783272|201174|1760|85004|31953|1678;1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|3085636|186803|2719313;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3085636|186803|841,Complete,Folakunmi
bsdb:36870237/1/1,36870237,"cross-sectional observational, not case-control",36870237,https://doi.org/10.1016/j.semarthrit.2023.152185,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10148899/,"Nguyen A.D., Andréasson K., McMahan Z.H., Bukiri H., Howlett N., Lagishetty V., Lee S.M., Jacobs J.P. , Volkmann E.R.",Gastrointestinal tract involvement in systemic sclerosis: The roles of diet and the microbiome,Seminars in arthritis and rheumatism,2023,"FODMAP diet, Gastrointestinal microbiome, Systemic sclerosis, nutrition",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,"Adult Systemic Sclerosis patients on a low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP) diet.","Adult Systemic Sclerosis patients on a non-low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP) diet.","Adult patients with Systemic Sclerosis of any duration, as diagnosed according to the 2013 American College of Rheumatology/European League Against Rheumatism Classification Criteria for  Systemic Sclerosis, on a non-low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP) diet.",19,16,1 month,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 4,9 October 2023,Boadiwaa,"Boadiwaa,Chloe,Tolulopeo,WikiWorks",Differential abundance of specific genera between low versus non-low FODMAP groups.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales",1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|570;1783272|1239|909932|1843489|31977|906;3379134|1224|28211|204441,Complete,Folakunmi
bsdb:36870237/1/2,36870237,"cross-sectional observational, not case-control",36870237,https://doi.org/10.1016/j.semarthrit.2023.152185,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10148899/,"Nguyen A.D., Andréasson K., McMahan Z.H., Bukiri H., Howlett N., Lagishetty V., Lee S.M., Jacobs J.P. , Volkmann E.R.",Gastrointestinal tract involvement in systemic sclerosis: The roles of diet and the microbiome,Seminars in arthritis and rheumatism,2023,"FODMAP diet, Gastrointestinal microbiome, Systemic sclerosis, nutrition",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,"Adult Systemic Sclerosis patients on a low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP) diet.","Adult Systemic Sclerosis patients on a non-low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP) diet.","Adult patients with Systemic Sclerosis of any duration, as diagnosed according to the 2013 American College of Rheumatology/European League Against Rheumatism Classification Criteria for  Systemic Sclerosis, on a non-low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP) diet.",19,16,1 month,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 4,9 October 2023,Boadiwaa,"Boadiwaa,Chloe,WikiWorks",Differential abundance of specific genera between low versus non-low FODMAP groups.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp.,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptoclostridiaceae|g__Peptoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__Tyzzerella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",1783272|1239|186801|3085636|186803|33042|2049024;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|216572|216851|1946507;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|3082720|3120161|1481960;1783272|1239|186801|3082720|186804|1505652;1783272|1239|186801|3085636|186803|1506577|2053632;1783272|1239|186801|3085636|186803|297314,Complete,Folakunmi
bsdb:36870237/2/1,36870237,"cross-sectional observational, not case-control",36870237,https://doi.org/10.1016/j.semarthrit.2023.152185,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10148899/,"Nguyen A.D., Andréasson K., McMahan Z.H., Bukiri H., Howlett N., Lagishetty V., Lee S.M., Jacobs J.P. , Volkmann E.R.",Gastrointestinal tract involvement in systemic sclerosis: The roles of diet and the microbiome,Seminars in arthritis and rheumatism,2023,"FODMAP diet, Gastrointestinal microbiome, Systemic sclerosis, nutrition",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Systemic scleroderma,EFO:0000717,Not Applicable,Systemic Sclerosis patients with increased GIT 2.0 score,"Adult patients with Systemic Sclerosis of any duration, as diagnosed according to the 2013 American College of Rheumatology/European League Against Rheumatism Classification Criteria for Systemic Sclerosis, reporting more severe Gastrointestinal Tract symptoms",NA,66,1 month,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3,11 October 2023,Boadiwaa,"Boadiwaa,Chloe,Hodan Issah,WikiWorks",Differential abundance of specific genera based on GIT 2.0 Total Score,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium",1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|216572|216851|1946507;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|33958|1578;3379134|1224|28211|204457|3423717|165695,Complete,Folakunmi
bsdb:36870237/2/2,36870237,"cross-sectional observational, not case-control",36870237,https://doi.org/10.1016/j.semarthrit.2023.152185,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10148899/,"Nguyen A.D., Andréasson K., McMahan Z.H., Bukiri H., Howlett N., Lagishetty V., Lee S.M., Jacobs J.P. , Volkmann E.R.",Gastrointestinal tract involvement in systemic sclerosis: The roles of diet and the microbiome,Seminars in arthritis and rheumatism,2023,"FODMAP diet, Gastrointestinal microbiome, Systemic sclerosis, nutrition",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Systemic scleroderma,EFO:0000717,Not Applicable,Systemic Sclerosis patients with increased GIT 2.0 score,"Adult patients with Systemic Sclerosis of any duration, as diagnosed according to the 2013 American College of Rheumatology/European League Against Rheumatism Classification Criteria for Systemic Sclerosis, reporting more severe Gastrointestinal Tract symptoms",NA,66,1 month,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 3,11 October 2023,Boadiwaa,"Boadiwaa,Chloe,Peace Sandy,Hodan Issah,WikiWorks",Differential abundance of specific genera based on GIT 2.0 Total Score,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium DTU089,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:352,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Cuneatibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp.,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Orthornavirae|p__Pisuviricota|c__Pisoniviricetes|o__Picornavirales|f__Picornaviridae|s__Ensavirinae|g__Enterovirus|s__Enterovirus alpharhino,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae|s__uncultured Defluviitaleaceae bacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Viridiplantae|p__Chlorophyta|c__Chlorophyceae|o__Chlamydomonadales|s__uncultured Haematococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",3379134|976|200643|171549;1783272|1239|526524|526525|2810280|135858;1783272|1239|186801;1783272|1239|186801|186802|1898207;1783272|1239|186801|186802|1671661;1783272|1239|186801|186802|31979|1485|1262798;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|33042|2049024;1783272|1239|186801|3085636|186803|1918450;1783272|1239|526524|526525|128827|1937008;3366610|28890|183925|2158|2159|2172;1783272|544448|31969;3379134|976|200643|171549|171552|838;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|216572|292632|2053618;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3085636|186803|1506577;2732396|2732408|2732506|464095|12058|2946630|12059|3428501;1783272|1239|186801|3085636|1185407|2065077;1783272|1239|526524|526525|128827|331630;33090|3041|3166|3042|404784;1783272|1239|186801|186802|216572|707003,Complete,Folakunmi
bsdb:36870237/3/1,36870237,"cross-sectional observational, not case-control",36870237,https://doi.org/10.1016/j.semarthrit.2023.152185,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10148899/,"Nguyen A.D., Andréasson K., McMahan Z.H., Bukiri H., Howlett N., Lagishetty V., Lee S.M., Jacobs J.P. , Volkmann E.R.",Gastrointestinal tract involvement in systemic sclerosis: The roles of diet and the microbiome,Seminars in arthritis and rheumatism,2023,"FODMAP diet, Gastrointestinal microbiome, Systemic sclerosis, nutrition",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Systemic scleroderma,EFO:0000717,NA,Systemic Sclerosis patients with more severe diarrhoea,"Adult patients with Systemic Sclerosis of any duration, as diagnosed according to the 2013 American College of Rheumatology/European League Against Rheumatism Classification Criteria for  Systemic Sclerosis, reporting more severe diarrhea based on the diarrhea score.",NA,66,1 month,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Supplemental Figure 1,30 October 2023,Boadiwaa,"Boadiwaa,WikiWorks",Differential abundance of specific genera based on symptom score for the diarrhea domain.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium DTU089,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium",1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|1671661;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|33958|1578;3379134|1224|28211|204457|3423717|165695,Complete,Folakunmi
bsdb:36870237/3/2,36870237,"cross-sectional observational, not case-control",36870237,https://doi.org/10.1016/j.semarthrit.2023.152185,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10148899/,"Nguyen A.D., Andréasson K., McMahan Z.H., Bukiri H., Howlett N., Lagishetty V., Lee S.M., Jacobs J.P. , Volkmann E.R.",Gastrointestinal tract involvement in systemic sclerosis: The roles of diet and the microbiome,Seminars in arthritis and rheumatism,2023,"FODMAP diet, Gastrointestinal microbiome, Systemic sclerosis, nutrition",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Systemic scleroderma,EFO:0000717,NA,Systemic Sclerosis patients with more severe diarrhoea,"Adult patients with Systemic Sclerosis of any duration, as diagnosed according to the 2013 American College of Rheumatology/European League Against Rheumatism Classification Criteria for  Systemic Sclerosis, reporting more severe diarrhea based on the diarrhea score.",NA,66,1 month,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Supplemental Figure 1,30 October 2023,Boadiwaa,"Boadiwaa,Idiaru angela,WikiWorks",Differential abundance of specific genera based on symptom score for the diarrhea domain.,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae|s__uncultured Defluviitaleaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|201174|84998|1643822|1643826|447020;1783272|1239|186801|186802|216572|244127;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3082768|990719|990721|1935934;1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|1898207;1783272|1239|186801|3085636|186803|33042;1783272|201174|84998|84999;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|3082720|186804|1505657;3366610|28890|183925|2158|2159|2172;1783272|1239|186801|186802|216572|2485925;3379134|976|200643|171549|171552|838;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|1470353;1783272|1239|186801|186802|216572|292632;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|3085636|1185407|2065077;1783272|1239|186801|3085636|186803|297314;1783272|1239|186801|186802|216572|707003;1783272|1239|186801|186802|31979|1485,Complete,Folakunmi
bsdb:36870237/4/1,36870237,"cross-sectional observational, not case-control",36870237,https://doi.org/10.1016/j.semarthrit.2023.152185,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10148899/,"Nguyen A.D., Andréasson K., McMahan Z.H., Bukiri H., Howlett N., Lagishetty V., Lee S.M., Jacobs J.P. , Volkmann E.R.",Gastrointestinal tract involvement in systemic sclerosis: The roles of diet and the microbiome,Seminars in arthritis and rheumatism,2023,"FODMAP diet, Gastrointestinal microbiome, Systemic sclerosis, nutrition",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Systemic scleroderma,EFO:0000717,NA,Systemic Sclerosis patients with  worsened social functioning,"Adult patients with Systemic Sclerosis of any duration, as diagnosed according to the 2013 American College of Rheumatology/European League Against Rheumatism Classification Criteria for Systemic Sclerosis, reporting worsened social functioning",NA,66,1 month,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplemental Figure 2,30 October 2023,Boadiwaa,"Boadiwaa,Folakunmi,WikiWorks",Differential abundance of specific genera based on symptom score for the social functioning domain.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",1783272|201174|84998|1643822|1643826|84111;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|216572|216851|1946507;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|3085636|186803|1506553;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1357;1783272|1239|909932|1843489|31977|906;3379134|1224|28211|204457|3423717|165695;3379134|1224|1236|91347|543|1940338,Complete,Folakunmi
bsdb:36870237/4/2,36870237,"cross-sectional observational, not case-control",36870237,https://doi.org/10.1016/j.semarthrit.2023.152185,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10148899/,"Nguyen A.D., Andréasson K., McMahan Z.H., Bukiri H., Howlett N., Lagishetty V., Lee S.M., Jacobs J.P. , Volkmann E.R.",Gastrointestinal tract involvement in systemic sclerosis: The roles of diet and the microbiome,Seminars in arthritis and rheumatism,2023,"FODMAP diet, Gastrointestinal microbiome, Systemic sclerosis, nutrition",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Systemic scleroderma,EFO:0000717,NA,Systemic Sclerosis patients with  worsened social functioning,"Adult patients with Systemic Sclerosis of any duration, as diagnosed according to the 2013 American College of Rheumatology/European League Against Rheumatism Classification Criteria for Systemic Sclerosis, reporting worsened social functioning",NA,66,1 month,16S,4,Illumina,raw counts,DESeq2,0.1,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Supplemental Figure 2,30 October 2023,Boadiwaa,"Boadiwaa,Welile,WikiWorks",Differential abundance of specific genera based on symptom score for the social functioning domain.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:56,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|s__Christensenellaceae bacterium Phil7",1783272|1239|186801|3085636|186803|33042;1783272|1239|1263031;3366610|28890|183925|2158|2159|2172;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|292632;1783272|1239|526524|526525|2810281|191303;1783272|1239|526524|526525|128827|331630;1783272|1239|186801|186802|216572|707003;1783272|1239|186801|3082768|990719|1930013,Complete,Folakunmi
bsdb:36875281/1/1,36875281,case-control,36875281,https://doi.org/10.1177/17562848231154101,NA,"Yu T., Ding Y., Qian D., Lin L. , Tang Y.","Characteristics of fecal microbiota in different constipation subtypes and association with colon physiology, lifestyle factors, and psychological status",Therapeutic advances in gastroenterology,2023,"chronic constipation, colon physiology, microbiota, psychological distress",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy Controls (HC) participants,Chronic Constipation (CC) patients,Individuals diagnosed with conditions like Slow-Transit Constipation (STC) or Dyssynergic Defecation (DD).,31,53,1 month,16S,4,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,unchanged,decreased,NA,unchanged,Signature 1,Figure 2b and 2d,21 March 2025,Oriade-designs,"Oriade-designs,Aiyshaaaa",Statistical analysis of bacterium at the phylum and family level.,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|201174;1783272|1239;1783272|201174|1760|85004|31953;1783272|201174|84998|84999|84107;1783272|1239|526524|526525|128827;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:36875281/1/2,36875281,case-control,36875281,https://doi.org/10.1177/17562848231154101,NA,"Yu T., Ding Y., Qian D., Lin L. , Tang Y.","Characteristics of fecal microbiota in different constipation subtypes and association with colon physiology, lifestyle factors, and psychological status",Therapeutic advances in gastroenterology,2023,"chronic constipation, colon physiology, microbiota, psychological distress",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy Controls (HC) participants,Chronic Constipation (CC) patients,Individuals diagnosed with conditions like Slow-Transit Constipation (STC) or Dyssynergic Defecation (DD).,31,53,1 month,16S,4,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,unchanged,decreased,NA,unchanged,Signature 2,Figure 2b and 2d,21 March 2025,Oriade-designs,"Oriade-designs,Aiyshaaaa",Statistical analysis of bacterium at the phylum and family level.,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",3379134|976;3379134|976|200643|171549|171552;1783272|1239|91061|186826|1300,Complete,Svetlana up
bsdb:36875281/2/1,36875281,case-control,36875281,https://doi.org/10.1177/17562848231154101,NA,"Yu T., Ding Y., Qian D., Lin L. , Tang Y.","Characteristics of fecal microbiota in different constipation subtypes and association with colon physiology, lifestyle factors, and psychological status",Therapeutic advances in gastroenterology,2023,"chronic constipation, colon physiology, microbiota, psychological distress",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Normal-transit constipation (NTC),Slow-transit constipation (STC),Individuals diagnosed with Slow-Transit Constipation (STC).,22,31,1 month,16S,4,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a and 3b,1 April 2025,Oriade-designs,"Oriade-designs,Aiyshaaaa",Statistic analysis of bacterium in the family and phylum level in STC and NTC groups,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",1783272|1239;1783272|1239|186801|3082768|990719;1783272|201174|84998|84999|84107;1783272|1239|186801|3082720|186804,Complete,Svetlana up
bsdb:36875281/2/2,36875281,case-control,36875281,https://doi.org/10.1177/17562848231154101,NA,"Yu T., Ding Y., Qian D., Lin L. , Tang Y.","Characteristics of fecal microbiota in different constipation subtypes and association with colon physiology, lifestyle factors, and psychological status",Therapeutic advances in gastroenterology,2023,"chronic constipation, colon physiology, microbiota, psychological distress",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Normal-transit constipation (NTC),Slow-transit constipation (STC),Individuals diagnosed with Slow-Transit Constipation (STC).,22,31,1 month,16S,4,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3a and 3b,1 April 2025,Oriade-designs,"Oriade-designs,Aiyshaaaa,KateRasheed",Statistic analysis of bacterium in the phylum level in STC and NTC groups,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae",3379134|976|200643|171549|815;3379134|976;3379134|1224|28216|80840|506,Complete,Svetlana up
bsdb:36875281/3/1,36875281,case-control,36875281,https://doi.org/10.1177/17562848231154101,NA,"Yu T., Ding Y., Qian D., Lin L. , Tang Y.","Characteristics of fecal microbiota in different constipation subtypes and association with colon physiology, lifestyle factors, and psychological status",Therapeutic advances in gastroenterology,2023,"chronic constipation, colon physiology, microbiota, psychological distress",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy Controls (HC),Slow-Transit Constipation (STC),Individuals diagnosed with conditions like Slow-Transit Constipation (STC),31,31,1 month,16S,4,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a&3b,1 April 2025,Oriade-designs,"Oriade-designs,Aiyshaaaa",Statistic analysis of bacterium in the phylum and family level in STC and HC groups.,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|201174;1783272|1239;1783272|201174|1760|85004|31953;1783272|1239|91061|1385|186818;1783272|1239|186801|3082768|990719;1783272|201174|84998|84999|84107;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:36875281/3/2,36875281,case-control,36875281,https://doi.org/10.1177/17562848231154101,NA,"Yu T., Ding Y., Qian D., Lin L. , Tang Y.","Characteristics of fecal microbiota in different constipation subtypes and association with colon physiology, lifestyle factors, and psychological status",Therapeutic advances in gastroenterology,2023,"chronic constipation, colon physiology, microbiota, psychological distress",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy Controls (HC),Slow-Transit Constipation (STC),Individuals diagnosed with conditions like Slow-Transit Constipation (STC),31,31,1 month,16S,4,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3a and 3b,1 April 2025,Oriade-designs,"Oriade-designs,Aiyshaaaa",Statistic analysis of bacterium in the family and phylum level in STC and HC groups.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|1224|28216|80840|506;3379134|976;3379134|976|200643|171549|171552,Complete,Svetlana up
bsdb:36875281/4/1,36875281,case-control,36875281,https://doi.org/10.1177/17562848231154101,NA,"Yu T., Ding Y., Qian D., Lin L. , Tang Y.","Characteristics of fecal microbiota in different constipation subtypes and association with colon physiology, lifestyle factors, and psychological status",Therapeutic advances in gastroenterology,2023,"chronic constipation, colon physiology, microbiota, psychological distress",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy Controls (HC),Normal-transit constipation (NTC),Individuals diagnosed with Normal-transit constipation (NTC),31,22,1 month,16S,4,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a and 3b,1 April 2025,Oriade-designs,"Oriade-designs,Aiyshaaaa",Statistic analysis of bacterium in the phylum and family level in NTC and HC groups.,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|201174;1783272|1239;1783272|201174|1760|85004|31953;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:36875281/4/2,36875281,case-control,36875281,https://doi.org/10.1177/17562848231154101,NA,"Yu T., Ding Y., Qian D., Lin L. , Tang Y.","Characteristics of fecal microbiota in different constipation subtypes and association with colon physiology, lifestyle factors, and psychological status",Therapeutic advances in gastroenterology,2023,"chronic constipation, colon physiology, microbiota, psychological distress",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy Controls (HC),Normal-transit constipation (NTC),Individuals diagnosed with Normal-transit constipation (NTC),31,22,1 month,16S,4,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3a and 3b,1 April 2025,Oriade-designs,"Oriade-designs,Aiyshaaaa",Statistic analysis of bacterium in the phylum and family level in NTC and HC groups.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota",3379134|1224|28216|80840|506;3379134|976|200643|171549|171552;3379134|976,Complete,Svetlana up
bsdb:36875281/5/1,36875281,case-control,36875281,https://doi.org/10.1177/17562848231154101,NA,"Yu T., Ding Y., Qian D., Lin L. , Tang Y.","Characteristics of fecal microbiota in different constipation subtypes and association with colon physiology, lifestyle factors, and psychological status",Therapeutic advances in gastroenterology,2023,"chronic constipation, colon physiology, microbiota, psychological distress",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Non-dyssynergic defecation (non-DD),Dyssynergic defecation (DD),Individuals diagnosed with Dyssynergic Defecation (DD).,15,38,1 month,16S,4,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 3d,5 April 2025,Aiyshaaaa,"Aiyshaaaa,Oriade-designs",Statistic analysis of bacterium in the family level in DD and non-DD group.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",3379134|976|200643|171549|815;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171551,Complete,Svetlana up
bsdb:36875281/6/1,36875281,case-control,36875281,https://doi.org/10.1177/17562848231154101,NA,"Yu T., Ding Y., Qian D., Lin L. , Tang Y.","Characteristics of fecal microbiota in different constipation subtypes and association with colon physiology, lifestyle factors, and psychological status",Therapeutic advances in gastroenterology,2023,"chronic constipation, colon physiology, microbiota, psychological distress",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy Controls (HC),Dyssynergic defecation (DD),Individuals diagnosed with Dyssynergic Defecation (DD).,31,38,1 month,16S,4,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3c and 3d,5 April 2025,Aiyshaaaa,"Aiyshaaaa,Oriade-designs",Statistic analysis of bacterium in the phylum and family level in DD and HC groups.,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:36875281/6/2,36875281,case-control,36875281,https://doi.org/10.1177/17562848231154101,NA,"Yu T., Ding Y., Qian D., Lin L. , Tang Y.","Characteristics of fecal microbiota in different constipation subtypes and association with colon physiology, lifestyle factors, and psychological status",Therapeutic advances in gastroenterology,2023,"chronic constipation, colon physiology, microbiota, psychological distress",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy Controls (HC),Dyssynergic defecation (DD),Individuals diagnosed with Dyssynergic Defecation (DD).,31,38,1 month,16S,4,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 3c and 3d,5 April 2025,Aiyshaaaa,"Aiyshaaaa,Oriade-designs",Statistic analysis of bacterium in the phylum and family level in DD and HC groups.,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|976;3379134|976|200643|171549|171552,Complete,Svetlana up
bsdb:36875281/7/1,36875281,case-control,36875281,https://doi.org/10.1177/17562848231154101,NA,"Yu T., Ding Y., Qian D., Lin L. , Tang Y.","Characteristics of fecal microbiota in different constipation subtypes and association with colon physiology, lifestyle factors, and psychological status",Therapeutic advances in gastroenterology,2023,"chronic constipation, colon physiology, microbiota, psychological distress",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy Controls (HC),Non-dyssynergic defecation (non-DD),Individuals who has been catergorized as Non-Dyssynergic Defecation (non-DD).,31,15,1 month,16S,4,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3c and 3d,5 April 2025,Aiyshaaaa,"Aiyshaaaa,Oriade-designs",Statistic analysis of bacterium in the phylum level in non-DD and HC groups.,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:36875281/7/2,36875281,case-control,36875281,https://doi.org/10.1177/17562848231154101,NA,"Yu T., Ding Y., Qian D., Lin L. , Tang Y.","Characteristics of fecal microbiota in different constipation subtypes and association with colon physiology, lifestyle factors, and psychological status",Therapeutic advances in gastroenterology,2023,"chronic constipation, colon physiology, microbiota, psychological distress",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy Controls (HC),Non-dyssynergic defecation (non-DD),Individuals who has been catergorized as Non-Dyssynergic Defecation (non-DD).,31,15,1 month,16S,4,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 3c and 3d,5 April 2025,Aiyshaaaa,Aiyshaaaa,Statistic analysis of bacterium in the phylum and family level in non-DD and HC groups.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae",3379134|976|200643|171549|815;3379134|976;3379134|976|200643|171549|171552;3379134|200940|3031449|213115|194924,Complete,Svetlana up
bsdb:36894532/2/1,36894532,time series / longitudinal observational,36894532,10.1038/s41467-023-36781-w,https://pubmed.ncbi.nlm.nih.gov/36894532/,"Sukumar S., Wang F., Simpson C.A., Willet C.E., Chew T., Hughes T.E., Bockmann M.R., Sadsad R., Martin F.E., Lydecker H.W., Browne G.V., Davis K.M., Bui M., Martinez E. , Adler C.J.",Development of the oral resistome during the first decade of life,Nature communications,2023,NA,Experiment 2,Australia,Homo sapiens,Mouth,UBERON:0000165,Dental caries,EFO:0003819,T1 - Timepoint 1 - (T1. edentulous (no teeth)),T3 - Timepoint 3,"Samples at T3 (mixed dentition, 8.5 ± 1.2 years old)",139,211,3 months,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S4 C,23 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","Vector loadings for ARGs, functional pathways and species that contribute to discrimination of individuals by time point/stage of dental development from DIABLO analysis. For each data type, DIABLO was performed on features above 0.01% abundance that had been TSS and CLR transformed. For each data block, displayed are the top ten features (ARG, function and species) with the largest vector loadings.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces viscosus",1783272|201174|1760|2037|2049|1654|29317;1783272|201174|1760|2037|2049|1654|1656,Complete,Peace Sandy
bsdb:36894532/2/2,36894532,time series / longitudinal observational,36894532,10.1038/s41467-023-36781-w,https://pubmed.ncbi.nlm.nih.gov/36894532/,"Sukumar S., Wang F., Simpson C.A., Willet C.E., Chew T., Hughes T.E., Bockmann M.R., Sadsad R., Martin F.E., Lydecker H.W., Browne G.V., Davis K.M., Bui M., Martinez E. , Adler C.J.",Development of the oral resistome during the first decade of life,Nature communications,2023,NA,Experiment 2,Australia,Homo sapiens,Mouth,UBERON:0000165,Dental caries,EFO:0003819,T1 - Timepoint 1 - (T1. edentulous (no teeth)),T3 - Timepoint 3,"Samples at T3 (mixed dentition, 8.5 ± 1.2 years old)",139,211,3 months,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S4 C,23 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","Vector loadings for ARGs, functional pathways and species that contribute to discrimination of individuals by time point/stage of dental development from DIABLO analysis. For each data type, DIABLO was performed on features above 0.01% abundance that had been TSS and CLR transformed. For each data block, displayed are the top ten features (ARG, function and species) with the largest vector loadings.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus wangshanyuanii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus himalayensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus marmotae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parauberis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pluranimalium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus urinalis",1783272|1239|91061|186826|81852|1350|2005703;1783272|1239|91061|186826|1300|1301|1888195;1783272|1239|91061|186826|1300|1301|1825069;1783272|1239|91061|186826|1300|1301|1348;1783272|1239|91061|186826|1300|1301|82348;1783272|1239|91061|186826|1300|1301|149016,Complete,Peace Sandy
bsdb:36894532/3/1,36894532,time series / longitudinal observational,36894532,10.1038/s41467-023-36781-w,https://pubmed.ncbi.nlm.nih.gov/36894532/,"Sukumar S., Wang F., Simpson C.A., Willet C.E., Chew T., Hughes T.E., Bockmann M.R., Sadsad R., Martin F.E., Lydecker H.W., Browne G.V., Davis K.M., Bui M., Martinez E. , Adler C.J.",Development of the oral resistome during the first decade of life,Nature communications,2023,NA,Experiment 3,Australia,Homo sapiens,Mouth,UBERON:0000165,Dental caries,EFO:0003819,T2 - Timepoint 2,T3 - Timepoint 3,"Samples at T3 (mixed dentition, 8.5 ± 1.2 years old)",180,211,3 months,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S4 C,23 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","Vector loadings for ARGs, functional pathways and species that contribute to discrimination of individuals by time point/stage of dental development from DIABLO analysis. For each data type, DIABLO was performed on features above 0.01% abundance that had been TSS and CLR transformed.For each data block, displayed are the top ten features (ARG, function and species) with the largest vector loadings.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces viscosus",1783272|201174|1760|2037|2049|1654|29317;1783272|201174|1760|2037|2049|1654|1656,Complete,Peace Sandy
bsdb:36894986/1/1,36894986,case-control,36894986,https://doi.org/10.1186/s40168-023-01472-7,NA,"de Nies L., Galata V., Martin-Gallausiaux C., Despotovic M., Busi S.B., Snoeck C.J., Delacour L., Budagavi D.P., Laczny C.C., Habier J., Lupu P.C., Halder R., Fritz J.V., Marques T., Sandt E., O'Sullivan M.P., Ghosh S., Satagopam V., Krüger R., Fagherazzi G., Ollert M., Hefeng F.Q., May P. , Wilmes P.",Altered infective competence of the human gut microbiome in COVID-19,Microbiome,2023,"COVID-19, Gut microbiome, Metagenomics, Metatranscriptomics, SARS-CoV-2",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Control group,COVID-19 infection cases.,"These individuals had confirmed SARS-CoV-2 infection by a positive RT-PCR test result and presented with COVID-19 symptoms such as fever, cough, and difficulty breathing.",57,61,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),NA,TRUE,2,age,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 2B,11 March 2023,Busayo,"Busayo,Fatima,WikiWorks","Relative abundance of bacterial species
significantly enriched in COVID-19 patients compared to the control group",increased,"k__Bacillati|p__Bacillota|s__Firmicutes bacterium AM10-47,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:520,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:471,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea",1783272|1239|2292890;3379134|976|200643|171549|171552|838|1262929;1783272|1239|186801|3085636|186803|841|1262948;3379134|976|200643|171549|171552|2974265|363265,Complete,Fatima
bsdb:36894986/1/2,36894986,case-control,36894986,https://doi.org/10.1186/s40168-023-01472-7,NA,"de Nies L., Galata V., Martin-Gallausiaux C., Despotovic M., Busi S.B., Snoeck C.J., Delacour L., Budagavi D.P., Laczny C.C., Habier J., Lupu P.C., Halder R., Fritz J.V., Marques T., Sandt E., O'Sullivan M.P., Ghosh S., Satagopam V., Krüger R., Fagherazzi G., Ollert M., Hefeng F.Q., May P. , Wilmes P.",Altered infective competence of the human gut microbiome in COVID-19,Microbiome,2023,"COVID-19, Gut microbiome, Metagenomics, Metatranscriptomics, SARS-CoV-2",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Control group,COVID-19 infection cases.,"These individuals had confirmed SARS-CoV-2 infection by a positive RT-PCR test result and presented with COVID-19 symptoms such as fever, cough, and difficulty breathing.",57,61,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),NA,TRUE,2,age,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 2C,11 March 2023,Busayo,"Busayo,WikiWorks",Relative abundance of bacterial species significantly decreased in COVID-19 patients compared to the control group,decreased,"k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:145,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis",1783272|1239|1263005;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|526524|526525|2810281|191303|154288,Complete,Fatima
bsdb:36905309/1/1,36905309,case-control,36905309,https://doi.org/10.1111/ene.15776,NA,"Yang L., Liu G., Li S., Yao C., Zhao Z., Chen N., Zhang P., Shang Y., Wang Y., Zhang D., Tian X., Zhang J., Yao Z. , Hu B.",Association of aberrant brain network dynamics with gut microbial composition uncovers disrupted brain-gut-microbiome interactions in irritable bowel syndrome: Preliminary findings,European journal of neurology,2023,"brain-gut-microbiome axis, dynamic functional connectivity, gut microbiome, irritable bowel syndrome, resting-state functional MRI",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Controls (HC),IBS patients (Irritable Bowel Syndrome),Patients who have been diagnosed with irritable bowel syndrome (IBS),32,33,1 month,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,sex",NA,unchanged,decreased,NA,NA,NA,unchanged,Signature 1,Fig-5c and Table-S3,13 April 2025,Aiyshaaaa,Aiyshaaaa,Relative abundance in gut microbiota at genus and family level between healthy controls and irritable bowel syndrome patients,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|186801|3085636|186803|207244;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:36905309/1/2,36905309,case-control,36905309,https://doi.org/10.1111/ene.15776,NA,"Yang L., Liu G., Li S., Yao C., Zhao Z., Chen N., Zhang P., Shang Y., Wang Y., Zhang D., Tian X., Zhang J., Yao Z. , Hu B.",Association of aberrant brain network dynamics with gut microbial composition uncovers disrupted brain-gut-microbiome interactions in irritable bowel syndrome: Preliminary findings,European journal of neurology,2023,"brain-gut-microbiome axis, dynamic functional connectivity, gut microbiome, irritable bowel syndrome, resting-state functional MRI",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy Controls (HC),IBS patients (Irritable Bowel Syndrome),Patients who have been diagnosed with irritable bowel syndrome (IBS),32,33,1 month,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,sex",NA,unchanged,decreased,NA,NA,NA,unchanged,Signature 2,Fig-5c and Table-S3,13 April 2025,Aiyshaaaa,Aiyshaaaa,Relative abundance in gut microbiota at genus and family level between healthy controls and irritable bowel syndrome patients,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|976|200643|171549|2005519;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|171550;1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:36941248/1/1,36941248,case-control,36941248,10.1038/s41398-023-02325-5,NA,"Butler M.I., Bastiaanssen T.F.S., Long-Smith C., Morkl S., Berding K., Ritz N.L., Strain C., Patangia D., Patel S., Stanton C., O'Mahony S.M., Cryan J.F., Clarke G. , Dinan T.G.",The gut microbiome in social anxiety disorder: evidence of altered composition and function,Translational psychiatry,2023,NA,Experiment 1,Ireland,Homo sapiens,Feces,UBERON:0001988,Social anxiety disorder,EFO:1001917,Healthy controls,Patients with Social Anxiety Disorder (SAD),Patients with Social Anxiety Disorder (SAD),31,18,1 month,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex","age,body mass index,sex",NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Fig 2, Text",16 November 2023,Chinelsy,"Chinelsy,Peace Sandy,WikiWorks",Genus and species level differences between SAD and healthy controls.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. An250,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter",1783272|1239|186801|186802|3082771|1924093;1783272|1239|186801|186802|3082771|1924093|1965604;1783272|201174|84998|1643822|1643826|644652,Complete,Peace Sandy
bsdb:36941248/1/2,36941248,case-control,36941248,10.1038/s41398-023-02325-5,NA,"Butler M.I., Bastiaanssen T.F.S., Long-Smith C., Morkl S., Berding K., Ritz N.L., Strain C., Patangia D., Patel S., Stanton C., O'Mahony S.M., Cryan J.F., Clarke G. , Dinan T.G.",The gut microbiome in social anxiety disorder: evidence of altered composition and function,Translational psychiatry,2023,NA,Experiment 1,Ireland,Homo sapiens,Feces,UBERON:0001988,Social anxiety disorder,EFO:1001917,Healthy controls,Patients with Social Anxiety Disorder (SAD),Patients with Social Anxiety Disorder (SAD),31,18,1 month,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex","age,body mass index,sex",NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Fig 2, Text",28 December 2023,Peace Sandy,"Peace Sandy,WikiWorks",Genus and species level differences between SAD and healthy controls.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis",3379134|1224|28216|80840|995019|577310;3379134|1224|28216|80840|995019|577310|487175,Complete,Peace Sandy
bsdb:36943054/1/1,36943054,laboratory experiment,36943054,https://doi.org/10.1128/spectrum.03330-22,NA,"Zhou C., Wang Y., Li C., Xie Z. , Dai L.",Amelioration of Colitis by a Gut Bacterial Consortium Producing Anti-Inflammatory Secondary Bile Acids,Microbiology spectrum,2023,"bacterial consortium, colitis, gut microbiome, metabolomics, secondary bile acids, targeted metabolomics",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Colitis,EFO:0003872,DSS Group (Day 7),DSS + BAC Group (Day 7),Mice were given dextran sulfate sodium (DSS) to induce Colitis and then treated with Bile Acid Consortium (BAC).,7,7,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5C,15 March 2024,Victoria,"Victoria,WikiWorks",Bacterial taxa identified as differentially abundant between the untreated group (DSS) and the BAC treatment group (DSS + BAC) by LEfSe. Green indicates bacterial taxa whose abundance was higher in the DSS + BAC group; red indicates otherwise.,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella viscericola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum|s__Muribaculum intestinale,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus murinus",1783272|1239|91061;3379134|976|200643|171549;3379134|976|200643|171549|815|816|28116;3379134|976|200643;3379134|976;3379134|976|200643|171549|2005519|397864|397865;3379134|976|200643|171549|2005519;1783272|201174|1760|85004|31953|1678|28025;1783272|1239|91061|186826;3379134|976|200643|171549|2005473;3379134|976|200643|171549|2005473|1918540|1796646;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|2767887|1622,Complete,Svetlana up
bsdb:36943054/1/2,36943054,laboratory experiment,36943054,https://doi.org/10.1128/spectrum.03330-22,NA,"Zhou C., Wang Y., Li C., Xie Z. , Dai L.",Amelioration of Colitis by a Gut Bacterial Consortium Producing Anti-Inflammatory Secondary Bile Acids,Microbiology spectrum,2023,"bacterial consortium, colitis, gut microbiome, metabolomics, secondary bile acids, targeted metabolomics",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Colitis,EFO:0003872,DSS Group (Day 7),DSS + BAC Group (Day 7),Mice were given dextran sulfate sodium (DSS) to induce Colitis and then treated with Bile Acid Consortium (BAC).,7,7,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5C,15 March 2024,Victoria,"Victoria,WikiWorks",Bacterial taxa identified as differentially abundant between the untreated group (DSS) and the BAC treatment group (DSS + BAC) by LEfSe. Green indicates bacterial taxa whose abundance was higher in the DSS + BAC group; red indicates otherwise.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium YL45,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium CCNA10,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum|s__Faecalibaculum rodentium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium phocaeense,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium GAM79,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. PEA192,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|171550|239759|328814;1783272|1239;3379134|1224|28216;1783272|201174|1760|85004|31953|1678|1694;3379134|1224|28216|80840|1834205;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|2109688;1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|186801|186802|216572|216851|853;1783272|1239|526524|526525|128827|1729679|1702221;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|186802|1392389|1297617;1783272|1239|186801|3085636|186803|1506553|1871021;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|2109691;1783272|1239|186801|186802|216572|459786|2109687;1783272|1239|186801|3082720|186804;1783272|1239|186801|186802|216572|1017280;3379134|1224;3379134|976|200643|171549|171550;1783272|1239|186801|3085636|186803|841|301301;3379134|1224|1236|91347|543|590|28901;1783272|1239|186801|186802;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:36973353/1/1,36973353,"cross-sectional observational, not case-control",36973353,https://doi.org/10.1038/s41559-023-02013-z,https://pubmed.ncbi.nlm.nih.gov/36973353/,"Fackelmann G., Pham C.K., Rodríguez Y., Mallory M.L., Provencher J.F., Baak J.E. , Sommer S.",Current levels of microplastic pollution impact wild seabird gut microbiomes,Nature ecology & evolution,2023,NA,Experiment 1,"Portugal,Canada",Calonectris borealis,"Proventriculus,Cloaca","UBERON:0007357,UBERON:0000162",Exposure,EFO:0000487,ASVs negatively correlated with microplastic count,ASVs positively correlated with microplastic count,ASVs positively correlated with microplastic count in Cory’s shearwaters (C. borealis) and Northern fulmars(F. glacialis).,NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2(a),30 April 2024,Bolanle,"Bolanle,Aleru Divine,WikiWorks",Differentially abundant ASVs associated with microplastics (counts and mass) identified by ANCOM.,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium|s__Cetobacterium sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium xerosis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus aviarius,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp.",3384189|32066|203490|203491|203492|180162|2071632;1783272|201174|1760|85007|1653|1716|1725;1783272|1239|91061|186826|33958|2767887|1606;1783272|1239|1737404|1737405|1570339|543311|1944660,Complete,Svetlana up
bsdb:36973353/1/2,36973353,"cross-sectional observational, not case-control",36973353,https://doi.org/10.1038/s41559-023-02013-z,https://pubmed.ncbi.nlm.nih.gov/36973353/,"Fackelmann G., Pham C.K., Rodríguez Y., Mallory M.L., Provencher J.F., Baak J.E. , Sommer S.",Current levels of microplastic pollution impact wild seabird gut microbiomes,Nature ecology & evolution,2023,NA,Experiment 1,"Portugal,Canada",Calonectris borealis,"Proventriculus,Cloaca","UBERON:0007357,UBERON:0000162",Exposure,EFO:0000487,ASVs negatively correlated with microplastic count,ASVs positively correlated with microplastic count,ASVs positively correlated with microplastic count in Cory’s shearwaters (C. borealis) and Northern fulmars(F. glacialis).,NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2(a),30 April 2024,Bolanle,"Bolanle,Aleru Divine,WikiWorks",Differentially abundant ASVs associated with microplastics (counts and mass) identified by ANCOM.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae|g__Pseudoalteromonas|s__Pseudoalteromonas sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter|s__Psychrobacter sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Catellicoccus|s__Catellicoccus sp.",1783272|1239|91061|186826|81852|1350|35783;3379134|1224|1236|135622|267888|53246|53249;3379134|1224|1236|2887326|468|497;1783272|1239|91061|1385|90964|1279|29387;3379134|1224|1236|2887326|468|497|56811;1783272|1239|91061|186826|81852|300418|2828652,Complete,Svetlana up
bsdb:36973353/2/1,36973353,"cross-sectional observational, not case-control",36973353,https://doi.org/10.1038/s41559-023-02013-z,https://pubmed.ncbi.nlm.nih.gov/36973353/,"Fackelmann G., Pham C.K., Rodríguez Y., Mallory M.L., Provencher J.F., Baak J.E. , Sommer S.",Current levels of microplastic pollution impact wild seabird gut microbiomes,Nature ecology & evolution,2023,NA,Experiment 2,"Canada,Portugal",Calonectris borealis,"Proventriculus,Cloaca","UBERON:0007357,UBERON:0000162",Exposure,EFO:0000487,ASVs negatively correlated with microplastic mass,ASVs positively correlated with microplastic mass,ASVs positively correlated with microplastic mass in Cory’s shearwaters (C. borealis) and Northern fulmars(F. glacialis).,NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2(b),30 April 2024,Bolanle,"Bolanle,Aleru Divine,WikiWorks",Differentially abundant ASVs associated with microplastics (counts and mass) identified by ANCOM.,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Edwardsiella|s__Edwardsiella sp. (in: enterobacteria),k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae|g__Pseudoalteromonas|s__Pseudoalteromonas sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Catellicoccus|s__Catellicoccus sp.",3384189|32066|203490|203491|203492|848|68766;3379134|1224|1236|91347|1903412|635|1906663;3379134|1224|1236|135622|267888|53246|53249;1783272|1239|91061|186826|81852|300418|2828652,Complete,Svetlana up
bsdb:36973353/2/2,36973353,"cross-sectional observational, not case-control",36973353,https://doi.org/10.1038/s41559-023-02013-z,https://pubmed.ncbi.nlm.nih.gov/36973353/,"Fackelmann G., Pham C.K., Rodríguez Y., Mallory M.L., Provencher J.F., Baak J.E. , Sommer S.",Current levels of microplastic pollution impact wild seabird gut microbiomes,Nature ecology & evolution,2023,NA,Experiment 2,"Canada,Portugal",Calonectris borealis,"Proventriculus,Cloaca","UBERON:0007357,UBERON:0000162",Exposure,EFO:0000487,ASVs negatively correlated with microplastic mass,ASVs positively correlated with microplastic mass,ASVs positively correlated with microplastic mass in Cory’s shearwaters (C. borealis) and Northern fulmars(F. glacialis).,NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2(b),30 April 2024,Bolanle,"Bolanle,Aleru Divine,WikiWorks",Differentially abundant ASVs associated with microplastics (counts and mass) identified by ANCOM.,decreased,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium|s__Cetobacterium sp.,3384189|32066|203490|203491|203492|180162|2071632,Complete,Svetlana up
bsdb:36973353/3/1,36973353,"cross-sectional observational, not case-control",36973353,https://doi.org/10.1038/s41559-023-02013-z,https://pubmed.ncbi.nlm.nih.gov/36973353/,"Fackelmann G., Pham C.K., Rodríguez Y., Mallory M.L., Provencher J.F., Baak J.E. , Sommer S.",Current levels of microplastic pollution impact wild seabird gut microbiomes,Nature ecology & evolution,2023,NA,Experiment 3,"Portugal,Canada",Calonectris borealis,"Proventriculus,Cloaca","UBERON:0007357,UBERON:0000162",Exposure,EFO:0000487,Microplastic count and the Cloaca,Microplastic count and the Proventriculus,Interaction between Microplastic Count and the Proventriculus in Cory’s shearwaters (C. borealis) and Northern fulmars(F. glacialis).,84,85,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Figure 2(c),30 April 2024,Bolanle,"Bolanle,Aleru Divine,WikiWorks",Differentially abundant ASVs associated with microplastics (counts and mass) identified by ANCOM.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Edwardsiella|s__Edwardsiella sp. (in: enterobacteria),k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.",3379134|1224|1236|91347|1903412|635|1906663;1783272|201174|1760|85007|1653|1716|1720,Complete,Svetlana up
bsdb:36973353/3/2,36973353,"cross-sectional observational, not case-control",36973353,https://doi.org/10.1038/s41559-023-02013-z,https://pubmed.ncbi.nlm.nih.gov/36973353/,"Fackelmann G., Pham C.K., Rodríguez Y., Mallory M.L., Provencher J.F., Baak J.E. , Sommer S.",Current levels of microplastic pollution impact wild seabird gut microbiomes,Nature ecology & evolution,2023,NA,Experiment 3,"Portugal,Canada",Calonectris borealis,"Proventriculus,Cloaca","UBERON:0007357,UBERON:0000162",Exposure,EFO:0000487,Microplastic count and the Cloaca,Microplastic count and the Proventriculus,Interaction between Microplastic Count and the Proventriculus in Cory’s shearwaters (C. borealis) and Northern fulmars(F. glacialis).,84,85,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,Figure 2(c),27 September 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differentially abundant ASVs associated with microplastics (counts and mass) identified by ANCOM.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Flaviflexus|s__Flaviflexus sp.,1783272|201174|1760|2037|2049|1522056|1969482,Complete,Svetlana up
bsdb:36973353/4/1,36973353,"cross-sectional observational, not case-control",36973353,https://doi.org/10.1038/s41559-023-02013-z,https://pubmed.ncbi.nlm.nih.gov/36973353/,"Fackelmann G., Pham C.K., Rodríguez Y., Mallory M.L., Provencher J.F., Baak J.E. , Sommer S.",Current levels of microplastic pollution impact wild seabird gut microbiomes,Nature ecology & evolution,2023,NA,Experiment 4,"Canada,Portugal",Calonectris borealis,"Proventriculus,Cloaca","UBERON:0007357,UBERON:0000162",Exposure,EFO:0000487,Microplastic mass and the Cloaca,Microplastic mass and the Proventriculus,Interaction between Microplastic mass and the Proventriculus in Cory’s shearwaters (C. borealis) and Northern fulmars(F. glacialis).,84,85,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 2(d),27 September 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differentially abundant ASVs associated with microplastics (counts and mass) identified by ANCOM.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter sp.,3379134|1224|1236|2887326|468|469|472,Complete,Svetlana up
bsdb:36973353/4/2,36973353,"cross-sectional observational, not case-control",36973353,https://doi.org/10.1038/s41559-023-02013-z,https://pubmed.ncbi.nlm.nih.gov/36973353/,"Fackelmann G., Pham C.K., Rodríguez Y., Mallory M.L., Provencher J.F., Baak J.E. , Sommer S.",Current levels of microplastic pollution impact wild seabird gut microbiomes,Nature ecology & evolution,2023,NA,Experiment 4,"Canada,Portugal",Calonectris borealis,"Proventriculus,Cloaca","UBERON:0007357,UBERON:0000162",Exposure,EFO:0000487,Microplastic mass and the Cloaca,Microplastic mass and the Proventriculus,Interaction between Microplastic mass and the Proventriculus in Cory’s shearwaters (C. borealis) and Northern fulmars(F. glacialis).,84,85,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Figure 2(d),27 September 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differentially abundant ASVs associated with microplastics (counts and mass) identified by ANCOM.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,1783272|1239|186801|186802|31979|1485|1502,Complete,Svetlana up
bsdb:36973353/5/1,36973353,"cross-sectional observational, not case-control",36973353,https://doi.org/10.1038/s41559-023-02013-z,https://pubmed.ncbi.nlm.nih.gov/36973353/,"Fackelmann G., Pham C.K., Rodríguez Y., Mallory M.L., Provencher J.F., Baak J.E. , Sommer S.",Current levels of microplastic pollution impact wild seabird gut microbiomes,Nature ecology & evolution,2023,NA,Experiment 5,"Canada,Portugal",Calonectris borealis,"Proventriculus,Cloaca","UBERON:0007357,UBERON:0000162",Exposure,EFO:0000487,Microplastic count and Cory’s shearwaters (C. borealis),Microplastic count and Northern fulmars(F. glacialis),Interaction between Microplastic Counts and Northern fulmars(F. glacialis),58,27,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2(e),27 September 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differentially abundant ASVs associated with microplastics (counts and mass) identified by ANCOM.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Catellicoccus|s__Catellicoccus sp.,1783272|1239|91061|186826|81852|300418|2828652,Complete,Svetlana up
bsdb:36975801/1/NA,36975801,case-control,36975801,10.1128/msystems.01003-22,NA,"Carter K.A., Fodor A.A., Balkus J.E., Zhang A., Serrano M.G., Buck G.A., Engel S.M., Wu M.C. , Sun S.",Vaginal Microbiome Metagenome Inference Accuracy: Differential Measurement Error according to Community Composition,mSystems,2023,"Lactobacillus crispatus, Lactobacillus iners, measurement error, metagenome inference, vaginal microbiome",Experiment 1,United States of America,Homo sapiens,Vagina,UBERON:0000996,Premature birth,EFO:0003917,term birth(control),preterm birth (PTB),Cases were participants who experienced early preterm birth at <32 weeks of gestation.,37,35,NA,16S,123,Illumina,relative abundances,Mann-Whitney (Wilcoxon),NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:36975828/1/1,36975828,"cross-sectional observational, not case-control",36975828,10.1128/spectrum.03549-22,NA,"Sheng D., Yue K., Li H., Zhao L., Zhao G., Jin C. , Zhang L.",The Interaction between Intratumoral Microbiome and Immunity Is Related to the Prognosis of Ovarian Cancer,Microbiology spectrum,2023,"gynecological, microbiome, ovarian cancer, prognostic biomarkers, tumor microenvironment",Experiment 1,China,Homo sapiens,Ovary,UBERON:0000992,Ovarian cancer,MONDO:0008170,Immune-enriched subtype (clust2),Immune-deficient subtype (clust1),Patients with the ovarian cancer subtype which is characterized by the lack of immune infiltration and high tumor purity,191,182,NA,PCR,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 3C,25 March 2024,Scholastica,"Scholastica,WikiWorks",Significant differentially abundant taxonomic biomarkers between immune-deficient subtype (clust1) and immune-enriched subtype (clust2) identified by LEfSe,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas|s__Aeromonas dhakensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus subtilis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Coxiella|s__Coxiella endosymbiont of Amblyomma nuttalli,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium modestum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia|s__Delftia acidovorans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus|s__Dermacoccus nishinomiyaensis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Halopseudomonas|s__Halopseudomonas phragmitis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Halopseudomonas|s__Halopseudomonas sabulinigri,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacteroides|s__Mycobacteroides chelonae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Nitrospirillum|s__Nitrospirillum amazonense,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas asplenii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Aquipseudomonas|s__Aquipseudomonas campi,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas cavernae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas citronellolis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas congelans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas cremoricolorata,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Metapseudomonas|s__Metapseudomonas furukawaii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas glycinae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas iranensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas marincola,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas oryzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas promysalinigenes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. 02C 26,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. B10,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. DR 5-09,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. DY-1,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. LPB0260,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. R3-18-08,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. R84,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas tussilaginis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. St316,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. Z003-0.4C(8344-21),k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas syringae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas vanderleydeniana,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas viciae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas xanthosomatis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas zeae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Sinorhizobium|s__Sinorhizobium meliloti,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus capitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. CFSAN084952,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. A214,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. OST1909,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Legionellaceae|g__Legionella|s__Legionella longbeachae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. St29,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas tensinigenes",3379134|1224|1236|135624|84642|642|196024;1783272|1239|91061|1385|186817|1386|1423;3379134|1224|1236|118969|118968|776|2749996;1783272|201174|1760|85009|31957|1912216|2559073;3379134|1224|28216|80840|80864|80865|80866;1783272|201174|1760|85006|145357|57495|1274;3384189|32066|203490|203491|203492|848|851;3379134|1224|1236|72274|135621|2901189|1931241;3379134|1224|1236|72274|135621|2901189|472181;1783272|201174|1760|85007|1762|670516|1774;3379134|1224|28211|204441|2829815|1543705|28077;3379134|1224|1236|72274|135621|286|53407;3379134|1224|1236|72274|135621|3236652|2731681;3379134|1224|1236|72274|135621|286|2320867;3379134|1224|1236|72274|135621|286|53408;3379134|1224|1236|72274|135621|286|200452;3379134|1224|1236|72274|135621|286|157783;3379134|1224|1236|72274|135621|3236656|1149133;3379134|1224|1236|72274|135621|286|1785145;3379134|1224|1236|72274|135621|286|2745503;3379134|1224|1236|72274|135621|286|437900;3379134|1224|1236|72274|135621|286|1392877;3379134|1224|1236|72274|135621|286|485898;3379134|1224|1236|72274|135621|286|2054914;3379134|1224|1236|72274|135621|286|118613;3379134|1224|1236|72274|135621|286|1534110;3379134|1224|1236|72274|135621|286|1755504;3379134|1224|1236|72274|135621|286|2614442;3379134|1224|1236|72274|135621|286|1173283;3379134|1224|1236|72274|135621|286|1573712;3379134|1224|1236|72274|135621|286|2866277;3379134|1224|1236|72274|135621|286|2678257;3379134|1224|1236|72274|135621|286|1855380;3379134|1224|1236|72274|135621|286|317;3379134|1224|1236|72274|135621|286|2745495;3379134|1224|1236|72274|135621|286|2505979;3379134|1224|1236|72274|135621|286|2842356;3379134|1224|1236|72274|135621|286|2745510;3379134|1224|28211|356|82115|28105|382;1783272|1239|91061|1385|90964|1279|29388;1783272|1239|91061|186826|1300|1301|28037;3379134|1224|1236|72274|135621|286|2664899;3379134|1224|1236|72274|135621|286|1855331;3379134|1224|1236|72274|135621|286|2777367;3379134|1224|1236|118969|444|445|450;3379134|1224|1236|72274|135621|286|1500687;3379134|1224|1236|72274|135621|286|2745511,Complete,Svetlana up
bsdb:36975828/1/2,36975828,"cross-sectional observational, not case-control",36975828,10.1128/spectrum.03549-22,NA,"Sheng D., Yue K., Li H., Zhao L., Zhao G., Jin C. , Zhang L.",The Interaction between Intratumoral Microbiome and Immunity Is Related to the Prognosis of Ovarian Cancer,Microbiology spectrum,2023,"gynecological, microbiome, ovarian cancer, prognostic biomarkers, tumor microenvironment",Experiment 1,China,Homo sapiens,Ovary,UBERON:0000992,Ovarian cancer,MONDO:0008170,Immune-enriched subtype (clust2),Immune-deficient subtype (clust1),Patients with the ovarian cancer subtype which is characterized by the lack of immune infiltration and high tumor purity,191,182,NA,PCR,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig. 3C,25 March 2024,Scholastica,"Scholastica,WikiWorks",Significant differentially abundant taxonomic biomarkers between immune-deficient subtype (clust1) and immune-enriched subtype (clust2) identified by LEfSe,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hydrogenophaga|s__Hydrogenophaga sp. NH-16,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter junii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio anguillarum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas thiooxydans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia ubonensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. C27(2019),k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus|s__Cupriavidus metallidurans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter|s__Arthrobacter woluwensis,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Isosphaerales|f__Isosphaeraceae|g__Aquisphaera|s__Aquisphaera giovannonii",3379134|1224|1236|72274|135621|286|287;3379134|1224|1236|2887326|468|469|470;3379134|1224|28216|80840|80864|47420|2184519;3379134|1224|1236|2887326|468|469|40215;3379134|1224|1236|135623|641|662|55601;3379134|1224|28216|80840|80864|283|363952;3379134|1224|28216|80840|119060|32008|101571;3379134|1224|1236|72274|135621|286|2604941;3379134|1224|28216|80840|119060|106589|119219;1783272|201174|1760|85006|1268|1663|156980;3379134|203682|203683|2691356|1763524|1511635|406548,Complete,Svetlana up
bsdb:36983633/1/1,36983633,case-control,36983633,10.3390/jpm13030450,NA,"Kartti S., Bendani H., Boumajdi N., Bouricha E.M., Zarrik O., El Agouri H., Fokar M., Aghlallou Y., El Jaoudi R., Belyamani L., Elkhannoussi B. , Ibrahimi A.",Metagenomics Analysis of Breast Microbiome Highlights the Abundance of Rothia Genus in Tumor Tissues,Journal of personalized medicine,2023,"16s rRNA sequencing, breast cancer, metagenomics, microbiome, rhotia",Experiment 1,Morocco,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,Adjacent normal tissue of BC patients,Tumor tissue of BC patients,Breast cancer (BC) patients were pathologically diagnosed with primary BC and underwent surgery for a total or partial mastectomy. Tumor tissue samples were obtained from the cores of tumor tissues without any contamination of normal tissues.,47,47,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1 (C),10 July 2025,Ecsharp,Ecsharp,Significant biomarkers between the tumor and adjacent tissues performed by linear discriminant analysis effect size (LEfSe) scores.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia",1783272|201174|1760|85006|1268|32207;1783272|1239|1737404|1737405|1570339|150022,Complete,NA
bsdb:36983633/1/2,36983633,case-control,36983633,10.3390/jpm13030450,NA,"Kartti S., Bendani H., Boumajdi N., Bouricha E.M., Zarrik O., El Agouri H., Fokar M., Aghlallou Y., El Jaoudi R., Belyamani L., Elkhannoussi B. , Ibrahimi A.",Metagenomics Analysis of Breast Microbiome Highlights the Abundance of Rothia Genus in Tumor Tissues,Journal of personalized medicine,2023,"16s rRNA sequencing, breast cancer, metagenomics, microbiome, rhotia",Experiment 1,Morocco,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,Adjacent normal tissue of BC patients,Tumor tissue of BC patients,Breast cancer (BC) patients were pathologically diagnosed with primary BC and underwent surgery for a total or partial mastectomy. Tumor tissue samples were obtained from the cores of tumor tissues without any contamination of normal tissues.,47,47,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1 (C),10 July 2025,Ecsharp,Ecsharp,Significant biomarkers between the tumor and adjacent tissues performed by linear discriminant analysis effect size (LEfSe) scores.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",3379134|1224|1236|72274|135621;3379134|1224|1236|72274|135621|286,Complete,NA
bsdb:36983633/2/1,36983633,case-control,36983633,10.3390/jpm13030450,NA,"Kartti S., Bendani H., Boumajdi N., Bouricha E.M., Zarrik O., El Agouri H., Fokar M., Aghlallou Y., El Jaoudi R., Belyamani L., Elkhannoussi B. , Ibrahimi A.",Metagenomics Analysis of Breast Microbiome Highlights the Abundance of Rothia Genus in Tumor Tissues,Journal of personalized medicine,2023,"16s rRNA sequencing, breast cancer, metagenomics, microbiome, rhotia",Experiment 2,Morocco,Homo sapiens,Breast,UBERON:0000310,Breast cancer,MONDO:0007254,Adjacent normal tissue of BC patients,Tumor tissue of BC patients,Breast cancer (BC) patients were pathologically diagnosed with primary BC and underwent surgery for a total or partial mastectomy. Tumor tissue samples were obtained from the cores of tumor tissues without any contamination of normal tissues.,47,47,3 months,16S,34,Illumina,NA,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3 (A-E),10 July 2025,Ecsharp,Ecsharp,Individual differences in proportional abundances of the most significantly altered microbial communities between adjacent and breast tumor tissues at different levels. A p < 0.05 is considered statistically significant based on t-test measurements.,decreased,"k__Pseudomonadati|p__Bdellovibrionota,k__Pseudomonadati|p__Bdellovibrionota|c__Oligoflexia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",3379134|3018035;3379134|3018035|1553900;3379134|1224|1236|91347;3379134|1224|1236|91347|543,Complete,NA
bsdb:36983633/3/1,36983633,case-control,36983633,10.3390/jpm13030450,NA,"Kartti S., Bendani H., Boumajdi N., Bouricha E.M., Zarrik O., El Agouri H., Fokar M., Aghlallou Y., El Jaoudi R., Belyamani L., Elkhannoussi B. , Ibrahimi A.",Metagenomics Analysis of Breast Microbiome Highlights the Abundance of Rothia Genus in Tumor Tissues,Journal of personalized medicine,2023,"16s rRNA sequencing, breast cancer, metagenomics, microbiome, rhotia",Experiment 3,Morocco,Homo sapiens,Breast,UBERON:0000310,Luminal B breast carcinoma,MONDO:0021115,Adjacent normal tissue of BC patients,BC patients with Luminal B,Breast cancer (BC) patients were pathologically diagnosed with primary BC and underwent surgery for a total or partial mastectomy. Tumor tissue samples were obtained from the cores of Luminal B tumor tissues without any contamination of normal tissues.,22,22,3 months,16S,34,Illumina,NA,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4. (A),10 July 2025,Ecsharp,Ecsharp,Individual differences in proportional abundances of significantly altered microbial genus between adjacent and breast tumor tissues in the hormonal patients’ groups. A p < 0.05 is considered statistically significant based on t-test measurements.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Alloiococcus,1783272|1239|91061|186826|186828|1651,Complete,NA
bsdb:36983633/4/1,36983633,case-control,36983633,10.3390/jpm13030450,NA,"Kartti S., Bendani H., Boumajdi N., Bouricha E.M., Zarrik O., El Agouri H., Fokar M., Aghlallou Y., El Jaoudi R., Belyamani L., Elkhannoussi B. , Ibrahimi A.",Metagenomics Analysis of Breast Microbiome Highlights the Abundance of Rothia Genus in Tumor Tissues,Journal of personalized medicine,2023,"16s rRNA sequencing, breast cancer, metagenomics, microbiome, rhotia",Experiment 4,Morocco,Homo sapiens,Breast,UBERON:0000310,Luminal A breast carcinoma,MONDO:0021116,Adjacent normal tissue of BC patients,BC patients with Luminal A,Breast cancer (BC) patients were pathologically diagnosed with primary BC and underwent surgery for a total or partial mastectomy. Tumor tissue samples were obtained from the cores of Luminal A tumor tissues without any contamination of normal tissues.,14,14,3 months,16S,34,Illumina,NA,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4. (A),10 July 2025,Ecsharp,Ecsharp,Individual differences in proportional abundances of significantly altered microbial genus between adjacent and breast tumor tissues in the hormonal patients’ groups. A p < 0.05 is considered statistically significant based on t-test measurements.,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,1783272|201174|1760|85007|1653|1716,Complete,NA
bsdb:36983633/4/2,36983633,case-control,36983633,10.3390/jpm13030450,NA,"Kartti S., Bendani H., Boumajdi N., Bouricha E.M., Zarrik O., El Agouri H., Fokar M., Aghlallou Y., El Jaoudi R., Belyamani L., Elkhannoussi B. , Ibrahimi A.",Metagenomics Analysis of Breast Microbiome Highlights the Abundance of Rothia Genus in Tumor Tissues,Journal of personalized medicine,2023,"16s rRNA sequencing, breast cancer, metagenomics, microbiome, rhotia",Experiment 4,Morocco,Homo sapiens,Breast,UBERON:0000310,Luminal A breast carcinoma,MONDO:0021116,Adjacent normal tissue of BC patients,BC patients with Luminal A,Breast cancer (BC) patients were pathologically diagnosed with primary BC and underwent surgery for a total or partial mastectomy. Tumor tissue samples were obtained from the cores of Luminal A tumor tissues without any contamination of normal tissues.,14,14,3 months,16S,34,Illumina,NA,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4. (A),10 July 2025,Ecsharp,Ecsharp,Individual differences in proportional abundances of significantly altered microbial genus between adjacent and breast tumor tissues in the hormonal patients’ groups. A p < 0.05 is considered statistically significant based on t-test measurements.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,1783272|201174|1760|85007|2805586|1847725,Complete,NA
bsdb:36983633/5/1,36983633,case-control,36983633,10.3390/jpm13030450,NA,"Kartti S., Bendani H., Boumajdi N., Bouricha E.M., Zarrik O., El Agouri H., Fokar M., Aghlallou Y., El Jaoudi R., Belyamani L., Elkhannoussi B. , Ibrahimi A.",Metagenomics Analysis of Breast Microbiome Highlights the Abundance of Rothia Genus in Tumor Tissues,Journal of personalized medicine,2023,"16s rRNA sequencing, breast cancer, metagenomics, microbiome, rhotia",Experiment 5,Morocco,Homo sapiens,Breast,UBERON:0000310,Triple-negative breast cancer,NA,Adjacent normal tissue of BC patients,BC patients with TNBC,Breast cancer (BC) patients were pathologically diagnosed with primary BC and underwent surgery for a total or partial mastectomy. Tumor tissue samples were obtained from the cores of triple-negative breast cancer (TNBC) tumor tissues without any contamination of normal tissues.,7,7,3 months,16S,34,Illumina,NA,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4. (A),10 July 2025,Ecsharp,Ecsharp,Individual differences in proportional abundances of significantly altered microbial genus between adjacent and breast tumor tissues in the hormonal patients’ groups. A p < 0.05 is considered statistically significant based on t-test measurements.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Sporosarcina,1783272|1239|91061|1385|186818|1569,Complete,NA
bsdb:36983633/6/1,36983633,case-control,36983633,10.3390/jpm13030450,NA,"Kartti S., Bendani H., Boumajdi N., Bouricha E.M., Zarrik O., El Agouri H., Fokar M., Aghlallou Y., El Jaoudi R., Belyamani L., Elkhannoussi B. , Ibrahimi A.",Metagenomics Analysis of Breast Microbiome Highlights the Abundance of Rothia Genus in Tumor Tissues,Journal of personalized medicine,2023,"16s rRNA sequencing, breast cancer, metagenomics, microbiome, rhotia",Experiment 6,Morocco,Homo sapiens,Breast,UBERON:0000310,"Triple-negative breast cancer,HER2 Positive Breast Carcinoma",EFO:1000294,BC patients with HER2,BC patients with TNBC,Breast cancer (BC) patients were pathologically diagnosed with primary BC and underwent surgery for a total or partial mastectomy. Tumor tissue samples were obtained from the cores of triple-negative breast cancer (TNBC) tumor tissues without any contamination of normal tissues.,4,7,3 months,16S,34,Illumina,NA,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4 (B),6 August 2025,Ecsharp,Ecsharp,"LDA score computed on the microbial relative abundance between breast tumor subtypes. The TNBC group is illustrated as Group 1, and the HER2 group as Group 2.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Caldimonas,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus,k__Thermotogati|p__Deinococcota,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae,k__Thermotogati|p__Deinococcota|c__Deinococci",3379134|1224|28216|80840|80864;3379134|1224|28216|80840|2975441|196013;3384194|1297|188787|68933;3384194|1297|188787|68933|188786|270;3384194|1297;3384194|1297|188787|68933|188786;3384194|1297|188787,Complete,NA
bsdb:36983633/6/2,36983633,case-control,36983633,10.3390/jpm13030450,NA,"Kartti S., Bendani H., Boumajdi N., Bouricha E.M., Zarrik O., El Agouri H., Fokar M., Aghlallou Y., El Jaoudi R., Belyamani L., Elkhannoussi B. , Ibrahimi A.",Metagenomics Analysis of Breast Microbiome Highlights the Abundance of Rothia Genus in Tumor Tissues,Journal of personalized medicine,2023,"16s rRNA sequencing, breast cancer, metagenomics, microbiome, rhotia",Experiment 6,Morocco,Homo sapiens,Breast,UBERON:0000310,"Triple-negative breast cancer,HER2 Positive Breast Carcinoma",EFO:1000294,BC patients with HER2,BC patients with TNBC,Breast cancer (BC) patients were pathologically diagnosed with primary BC and underwent surgery for a total or partial mastectomy. Tumor tissue samples were obtained from the cores of triple-negative breast cancer (TNBC) tumor tissues without any contamination of normal tissues.,4,7,3 months,16S,34,Illumina,NA,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4 (B),6 August 2025,Ecsharp,Ecsharp,"LDA score computed on the microbial relative abundance between breast tumor subtypes. The TNBC group is illustrated as Group 1, and the HER2 group as Group 2.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales",3379134|1224|28211|204457|41297;3379134|1224|28211|204457,Complete,NA
bsdb:36995230/1/1,36995230,"cross-sectional observational, not case-control",36995230,10.1128/spectrum.03152-22,NA,"Zhao C., Li Y., Chen B., Yue K., Su Z., Xu J., Xue W., Zhao G. , Zhang L.",Mycobiome Study Reveals Different Pathogens of Vulvovaginal Candidiasis Shape Characteristic Vaginal Bacteriome,Microbiology spectrum,2023,"RTIs, candidiasis, fungal community, mycobiome, vulvovaginal candidiasis",Experiment 1,China,Homo sapiens,Vagina,UBERON:0000996,Vulvovaginal candidiasis,EFO:0007543,Other reproductive tracts Infection (RTI) subjects + Healthy Controls,Vulvovaginal candidiasis (VVC) (I),The participants in this group belong to the first community state type (CST) identified from the VVC subjects.,152,9,1 month,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,4 June 2025,Aleru Divine,Aleru Divine,Differentially abundant taxa between three RTIs and healthy control groups,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis",1783272|1239|91061|186826|186827|1375;3379134|976|200643|171549|815|816|820;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|1680,Complete,NA
bsdb:36995230/2/1,36995230,"cross-sectional observational, not case-control",36995230,10.1128/spectrum.03152-22,NA,"Zhao C., Li Y., Chen B., Yue K., Su Z., Xu J., Xue W., Zhao G. , Zhang L.",Mycobiome Study Reveals Different Pathogens of Vulvovaginal Candidiasis Shape Characteristic Vaginal Bacteriome,Microbiology spectrum,2023,"RTIs, candidiasis, fungal community, mycobiome, vulvovaginal candidiasis",Experiment 2,China,Homo sapiens,Vagina,UBERON:0000996,Vulvovaginal candidiasis,EFO:0007543,Other reproductive tracts Infection (RTI) subjects + Healthy Controls,Vulvovaginal candidiasis (VVC) (II),The participants in this group belong to the second community state type (CST) identified from the VVC subjects.,126,35,1 month,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,4 June 2025,Aleru Divine,Aleru Divine,Differentially abundant taxa between three RTIs and healthy control groups,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella",3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|2701,Complete,NA
bsdb:36995230/3/1,36995230,"cross-sectional observational, not case-control",36995230,10.1128/spectrum.03152-22,NA,"Zhao C., Li Y., Chen B., Yue K., Su Z., Xu J., Xue W., Zhao G. , Zhang L.",Mycobiome Study Reveals Different Pathogens of Vulvovaginal Candidiasis Shape Characteristic Vaginal Bacteriome,Microbiology spectrum,2023,"RTIs, candidiasis, fungal community, mycobiome, vulvovaginal candidiasis",Experiment 3,China,Homo sapiens,Vagina,UBERON:0000996,Bacterial vaginosis,EFO:0003932,Other reproductive tracts Infection (RTI) subjects + Healthy Controls,Bacterial Vaginosis (BV),The participants in this group were diagnosed with bacterial vaginosis,124,37,1 month,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,4 June 2025,Aleru Divine,Aleru Divine,Differentially abundant taxa between three RTIs and healthy control groups,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sporobacterium|s__Sporobacterium sp. WAL 1855D,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",1783272|201174|1760|2037|2049|28263;1783272|201174|84998|84999|1643824|1380;3379134|29547|3031852|213849|72294|194;1783272|1239|186801|186802|31979|1485;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3082720|3118655|44259;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|91061|1385|539738|1378;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843489|31977|906;1783272|201174|1760|2037|2049|2050;1783272|1239|186801|3085636|186803|437755;1783272|544448|31969|2085|2092|2093;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481|482|28449;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|3082720|186804|1257;1783272|1239|186801|3082720|186804|1257|1261;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|186801|3085636|186803|177971;3384189|32066|203490|203491|1129771|168808;1783272|1239|186801|3085636|186803|100132|507843;3379134|1224|28216|80840|995019|40544,Complete,NA
bsdb:36995230/4/1,36995230,"cross-sectional observational, not case-control",36995230,10.1128/spectrum.03152-22,NA,"Zhao C., Li Y., Chen B., Yue K., Su Z., Xu J., Xue W., Zhao G. , Zhang L.",Mycobiome Study Reveals Different Pathogens of Vulvovaginal Candidiasis Shape Characteristic Vaginal Bacteriome,Microbiology spectrum,2023,"RTIs, candidiasis, fungal community, mycobiome, vulvovaginal candidiasis",Experiment 4,China,Homo sapiens,Vagina,UBERON:0000996,Ureaplasma urealyticum urethritis,EFO:1001225,Other reproductive tracts Infection (RTI) subjects + Healthy Controls,Ureaplasma urealyticum (UU) infection,The participants in this group were women diagnosed with Ureaplasma urealyticum (UU) infection,128,33,1 month,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,4 June 2025,Aleru Divine,Aleru Divine,Differentially abundant taxa between three RTIs and healthy control groups,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Renibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",1783272|1239|91061|186826|1300|1301;1783272|1239|1737404|1737405|1570339|165779;1783272|544448|2790996|2790998|2129;1783272|1239|909932|1843489|31977|29465;3384189|32066|203490|203491|203492|848;1783272|1239|909932|1843489|31977|29465|39778;3379134|976|200643|171549|171551|836|28124;1783272|201174|1760|85004|31953|1678|216816;3379134|1224|1236|72274|135621|286;1783272|201174|1760|85007|1653|1716;3379134|1224|1236|2887326|468|469;1783272|201174|1760|85006|1268|1645;1783272|201174|1760|2037|2049|1654,Complete,NA
bsdb:36995230/5/1,36995230,"cross-sectional observational, not case-control",36995230,10.1128/spectrum.03152-22,NA,"Zhao C., Li Y., Chen B., Yue K., Su Z., Xu J., Xue W., Zhao G. , Zhang L.",Mycobiome Study Reveals Different Pathogens of Vulvovaginal Candidiasis Shape Characteristic Vaginal Bacteriome,Microbiology spectrum,2023,"RTIs, candidiasis, fungal community, mycobiome, vulvovaginal candidiasis",Experiment 5,China,Homo sapiens,Vagina,UBERON:0000996,Female reproductive system disease,EFO:0009549,Other reproductive tracts Infection (RTI) subjects,Healthy Controls,The participants in this group were healthy women,114,47,1 month,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,4 June 2025,Aleru Divine,Aleru Divine,Differentially abundant taxa between three RTIs and healthy control groups,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1301|1328,Complete,NA
bsdb:36995383/1/1,36995383,case-control,36995383,10.1007/s00253-023-12489-1,NA,"Nie S., Jing Z., Wang J., Deng Y., Zhang Y., Ye Z. , Ge Y.",The link between increased Desulfovibrio and disease severity in Parkinson's disease,Applied microbiology and biotechnology,2023,"Desulfovibrio, Disease severity, Gut microbiome, Hydrogen sulfide, Parkinson’s disease",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Untreated patients with Parkinson Disease (PD),Untreated patients with Parkinson Disease refers to patients with Parkinson’s disease (the second most common neurodegenerative disease with motor and non-motor symptoms).,43,47,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,increased,unchanged,NA,increased,Signature 1,"Table S3, Fig. S5",25 February 2025,KateRasheed,KateRasheed,Differential abundance of taxa with significant differences between PD and Healthy control,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|1760|85004|31953|1678;1783272|1239|909932|1843489|31977|906;1783272|1239|91061|186826|33958|1578;3379134|200940|3031449|213115|194924|872;3379134|1224|1236|72274|135621;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:36995383/1/2,36995383,case-control,36995383,10.1007/s00253-023-12489-1,NA,"Nie S., Jing Z., Wang J., Deng Y., Zhang Y., Ye Z. , Ge Y.",The link between increased Desulfovibrio and disease severity in Parkinson's disease,Applied microbiology and biotechnology,2023,"Desulfovibrio, Disease severity, Gut microbiome, Hydrogen sulfide, Parkinson’s disease",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Untreated patients with Parkinson Disease (PD),Untreated patients with Parkinson Disease refers to patients with Parkinson’s disease (the second most common neurodegenerative disease with motor and non-motor symptoms).,43,47,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,increased,unchanged,NA,increased,Signature 2,Table S3,25 February 2025,KateRasheed,KateRasheed,Differential abundance of taxa with significant differences between PD and Healthy control,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,1783272|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:36995383/2/1,36995383,case-control,36995383,10.1007/s00253-023-12489-1,NA,"Nie S., Jing Z., Wang J., Deng Y., Zhang Y., Ye Z. , Ge Y.",The link between increased Desulfovibrio and disease severity in Parkinson's disease,Applied microbiology and biotechnology,2023,"Desulfovibrio, Disease severity, Gut microbiome, Hydrogen sulfide, Parkinson’s disease",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Untreated patients with Parkinson Disease (PD),Untreated patients with Parkinson Disease refers to patients with Parkinson’s disease (the second most common neurodegenerative disease with motor and non-motor symptoms).,8,8,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,increased,unchanged,NA,increased,Signature 1,Fig. S6,25 February 2025,KateRasheed,KateRasheed,Metagenome assembled genome (MAG58) was significantly increased in PD compared to healthy controls,increased,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,3379134|200940|3031449|213115|194924|872,Complete,Svetlana up
bsdb:36995383/3/1,36995383,case-control,36995383,10.1007/s00253-023-12489-1,NA,"Nie S., Jing Z., Wang J., Deng Y., Zhang Y., Ye Z. , Ge Y.",The link between increased Desulfovibrio and disease severity in Parkinson's disease,Applied microbiology and biotechnology,2023,"Desulfovibrio, Disease severity, Gut microbiome, Hydrogen sulfide, Parkinson’s disease",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Untreated patients with Parkinson Disease (PD),Untreated patients with Parkinson Disease refers to patients with Parkinson’s disease (the second most common neurodegenerative disease with motor and non-motor symptoms). These patients were gotten from the National Center for Biotechnology Information (NCBI) SRA database (under project number PRJNA433459).,40,40,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,increased,unchanged,NA,increased,Signature 1,Fig. S7,25 February 2025,KateRasheed,KateRasheed,The key metagenome-assembled genome (MAG) was significantly increased in Parkinson’s disease (PD),increased,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,3379134|200940|3031449|213115|194924|872,Complete,Svetlana up
bsdb:36997838/1/1,36997838,time series / longitudinal observational,36997838,10.1186/s12866-023-02822-z,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-02822-z,"Jacky D., Bibi C., Meng L.M.C., Jason F., Gwendoline T., Jeremy L. , Wie C.C.",Effects of OsomeFood Clean Label plant-based meals on the gut microbiome,BMC microbiology,2023,"Intervention, Metagenomic, Microbiota, Nutrition",Experiment 1,Singapore,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Participants before the AWE diet - D0,Participants after the AWE diet - D21,Participants who strictly adhered to OsomeFoods plant-based meal plans for five consecutive days (Monday through to Friday; 'AWE') for 3 weeks.,10,10,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig 2c,25 March 2024,ModinatG,"ModinatG,WikiWorks",Species differentially abundant between baseline and day 21 (End of the intervention period),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc garlicum",3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|371601;1783272|1239|91061|186826|33958|1243|255248,Complete,Svetlana up
bsdb:36997838/1/2,36997838,time series / longitudinal observational,36997838,10.1186/s12866-023-02822-z,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-02822-z,"Jacky D., Bibi C., Meng L.M.C., Jason F., Gwendoline T., Jeremy L. , Wie C.C.",Effects of OsomeFood Clean Label plant-based meals on the gut microbiome,BMC microbiology,2023,"Intervention, Metagenomic, Microbiota, Nutrition",Experiment 1,Singapore,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Participants before the AWE diet - D0,Participants after the AWE diet - D21,Participants who strictly adhered to OsomeFoods plant-based meal plans for five consecutive days (Monday through to Friday; 'AWE') for 3 weeks.,10,10,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Fig 2c,25 March 2024,ModinatG,"ModinatG,WikiWorks",Species differentially abundant between baseline and day 21 (End of the intervention period),decreased,"k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|s__Bacteroides phage B124-14,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia ilealis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella confusa",2731360|2731618|2731619|1105171;1783272|201174|84998|84999|84107|102106|147207;1783272|1239|186801|3082720|186804|1501226|1115758;1783272|1239|91061|186826|33958|46255|1583,Complete,Svetlana up
bsdb:37026303/1/1,37026303,case-control,37026303,10.4103/IJO.IJO_2821_22,NA,"Pal S., Vani G., Donthineni P.R., Basu S. , Arunasri K.",Tear film microbiome in Sjogren's and non-Sjogren's aqueous deficiency dry eye,Indian journal of ophthalmology,2023,"Dry eye disease, Prevotella, Sjogren's syndrome, non-Sjogren's syndrome, tear film microbiome",Experiment 1,India,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,Healthy Controls,Dry Eye Disease patients,Both Sjogren's and non-Sjogren's patients with Dry Eye Disease,18,24,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Table S2A,18 November 2023,Mary Bearkland,"Mary Bearkland,WikiWorks",Table S2A: Discriminative genera in SS and NSS compared to HC,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Luteimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Marinococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Nocardia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phreatobacteraceae|g__Phreatobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|g__Rhodobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Tsukamurellaceae|g__Tsukamurella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Zoogloea",3379134|1224|1236|91347|543|547;1783272|1239|91061|186826|81852|1350;1783272|1239|1737404|1582879;1783272|1239|186801|186802|216572|236752;1783272|201174|1760|85004|31953|2701;3379134|1224|1236|135625|712|724;3379134|1224|28216|80840|119060|47670;3379134|1224|1236|135614|32033|83614;1783272|1239|91061|1385|186817|1370;1783272|201174|1760|85007|85025|1817;1783272|1239|1737404|1737405|1570339|543311;3379134|1224|28211|356|2843305|1632780;3379134|1224|1236|72274|135621|286;3379134|1224|28211|204455|1060;1783272|201174|84998|1643822|1643826|84108;3379134|1224|28211|204457|3423717|165695;3384189|32066|203490|203491|1129771|34104;1783272|201174|1760|85011|2062|1883;1783272|201174|1760|85007|85028|2060;3379134|1224|28216|206389|2008794|349,Complete,Peace Sandy
bsdb:37026303/1/2,37026303,case-control,37026303,10.4103/IJO.IJO_2821_22,NA,"Pal S., Vani G., Donthineni P.R., Basu S. , Arunasri K.",Tear film microbiome in Sjogren's and non-Sjogren's aqueous deficiency dry eye,Indian journal of ophthalmology,2023,"Dry eye disease, Prevotella, Sjogren's syndrome, non-Sjogren's syndrome, tear film microbiome",Experiment 1,India,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,Healthy Controls,Dry Eye Disease patients,Both Sjogren's and non-Sjogren's patients with Dry Eye Disease,18,24,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Table S2A,18 November 2023,Mary Bearkland,"Mary Bearkland,WikiWorks",Table S2A: Discriminative genera in SS and NSS compared to HC,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alishewanella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Aurantimonadaceae|g__Aureimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Cellvibrio,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Desemzia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Domibacillus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Empedobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Haematobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Janibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Kytococcaceae|g__Kytococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Streptosporangiales|f__Streptosporangiaceae|g__Microbispora|s__Microbispora rosea|s__Microbispora rosea subsp. aerata,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermatophilaceae|g__Piscicoccus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propioniciclava,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Pseudoxanthomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Qipengyuania,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Skermanella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",3379134|1224|28216|80840|80864|12916;3379134|1224|1236|2887326|468|469;3379134|1224|1236|135624|84642|642;3379134|1224|1236|135622|72275|111142;3379134|976|200643|171549|171552|1283313;1783272|201174|1760|85006|1268|1663;3379134|1224|28211|356|255475|414371;1783272|1239|91061|1385|186817|1386;3379134|976|117743|200644|2762318|59735;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85006|85020|43668;1783272|201174|1760|85006|85019|1696;3379134|1224|1236|1706369|1706371|10;3379134|976|117743|200644|2762318|59732;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85009|31957|1912216;3379134|1224|28216|80840|80864|80865;1783272|1239|91061|186826|186828|82800;1783272|201174|1760|85007|85029|37914;1783272|1239|91061|1385|186817|1433999;3379134|976|117743|200644|2762318|59734;3379134|1224|28211|356|212791;1783272|201174|1760|85007|85026|2053;1783272|1239|91061|186826|186828|117563;3379134|1224|28211|204455|31989|366614;3379134|1224|1236|135619|28256|2745;1783272|201174|1760|85006|85021|53457;3379134|1224|1236|91347|543|570;1783272|201174|1760|85006|1268|57493;1783272|201174|1760|85006|2805426|57499;1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85007|2805586|1847725;3384189|32066|203490|203491|1129771|32067;3379134|1224|1236|135614|32033|68;3379134|1224|28216|80840|75682|149698;3379134|1224|28211|356|119045|407;1783272|201174|1760|85006|85023|33882;1783272|201174|1760|85012|2004|2005|58117|2010;1783272|201174|1760|85006|1268|1269;1783272|201174|1760|85007|1762|1763;1783272|1239|91061|1385|186822|44249;3379134|1224|28211|204455|31989|265;3379134|1224|28211|356|69277|28100;1783272|201174|1760|85006|85018|985001;1783272|201174|1760|85009|31957|1085622;3379134|1224|1236|135614|32033|83618;3379134|1224|28211|204457|335929|1855416;1783272|201174|1760|85006|1268|32207;3379134|1224|1236|91347|1903411|613;3379134|1224|1236|135622|267890|22;3379134|1224|28211|204441|2829815|204447;3379134|1224|1236|135614|32033|40323,Complete,Peace Sandy
bsdb:37026303/2/1,37026303,case-control,37026303,10.4103/IJO.IJO_2821_22,NA,"Pal S., Vani G., Donthineni P.R., Basu S. , Arunasri K.",Tear film microbiome in Sjogren's and non-Sjogren's aqueous deficiency dry eye,Indian journal of ophthalmology,2023,"Dry eye disease, Prevotella, Sjogren's syndrome, non-Sjogren's syndrome, tear film microbiome",Experiment 2,India,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,Healthy Controls,Sjogren's patients with Dry Eye Disease,Sjogren's patients with Dry Eye Disease,18,9,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Table S2B,19 November 2023,Mary Bearkland,"Mary Bearkland,WikiWorks",Table S2B: Discriminative genera in SS compared to HC,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Marinococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phreatobacteraceae|g__Phreatobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|g__Rhodobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Tsukamurellaceae|g__Tsukamurella,s__uncultured bacterium",3379134|976|117743|200644|2762318|59735;3379134|1224|1236|91347|543|547;1783272|1239|91061|186826|81852|1350;1783272|1239|1737404|1582879;3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|33958|1578;3379134|1224|28216|80840|119060|47670;1783272|1239|91061|1385|186817|1370;1783272|1239|1737404|1737405|1570339|543311;3379134|1224|28211|356|2843305|1632780;3379134|1224|28211|356|69277|28100;3379134|1224|1236|72274|135621|286;3379134|1224|28211|204455|1060;3379134|1224|1236|91347|543|590;3379134|1224|28211|204457|3423717|165695;1783272|201174|1760|85011|2062|1883;1783272|201174|1760|85007|85028|2060;77133,Complete,Peace Sandy
bsdb:37026303/2/2,37026303,case-control,37026303,10.4103/IJO.IJO_2821_22,NA,"Pal S., Vani G., Donthineni P.R., Basu S. , Arunasri K.",Tear film microbiome in Sjogren's and non-Sjogren's aqueous deficiency dry eye,Indian journal of ophthalmology,2023,"Dry eye disease, Prevotella, Sjogren's syndrome, non-Sjogren's syndrome, tear film microbiome",Experiment 2,India,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,Healthy Controls,Sjogren's patients with Dry Eye Disease,Sjogren's patients with Dry Eye Disease,18,9,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Table S2B,19 November 2023,Mary Bearkland,"Mary Bearkland,WikiWorks",Table S2B: Discriminative genera in SS compared to HC,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alishewanella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Cellvibrio,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Desemzia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Domibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|g__Exiguobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Haematobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Kytococcaceae|g__Kytococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Luteimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermatophilaceae|g__Piscicoccus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propioniciclava,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Qipengyuania,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Skermanella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Zoogloea",3379134|1224|28216|80840|80864|12916;3379134|1224|1236|135622|72275|111142;3379134|976|200643|171549|171552|1283313;1783272|1239|1737404|1737405|1570339|165779;1783272|201174|1760|85006|1268|1663;1783272|201174|1760|85006|85020|43668;1783272|201174|1760|85006|85019|1696;3379134|1224|1236|1706369|1706371|10;3379134|976|117743|200644|2762318|59732;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85009|31957|1912216;3379134|1224|28216|80840|80864|80865;1783272|1239|91061|186826|186828|82800;1783272|201174|1760|85007|85029|37914;1783272|1239|91061|1385|186817|1433999;3379134|1224|28211|356|212791;1783272|1239|91061|1385|33986;1783272|1239|91061|1385|539738|1378;1783272|201174|1760|85007|85026|2053;1783272|1239|91061|186826|186828|117563;3379134|1224|28211|204455|31989|366614;3379134|1224|1236|135619|28256|2745;1783272|201174|1760|85006|2805426|57499;1783272|201174|1760|85007|2805586|1847725;3384189|32066|203490|203491|1129771|32067;3379134|1224|1236|135614|32033|83614;3379134|1224|1236|135614|32033|68;3379134|1224|28216|80840|75682|149698;3379134|1224|28211|356|119045|407;1783272|201174|1760|85006|85023|33882;1783272|201174|1760|85006|1268|1269;1783272|201174|1760|85007|1762|1763;3379134|1224|28211|204455|31989|265;1783272|201174|1760|85006|85018|985001;1783272|201174|1760|85009|31957|1085622;3379134|1224|28211|204457|335929|1855416;1783272|201174|1760|85006|1268|32207;3379134|1224|1236|91347|1903411|613;3379134|1224|1236|135622|267890|22;3379134|1224|28211|204441|2829815|204447;3379134|1224|1236|135614|32033|40323;3379134|1224|1236|135623|641|662;1783272|1239|91061|186826|33958|46255;3379134|1224|28216|206389|2008794|349,Complete,Peace Sandy
bsdb:37026303/3/1,37026303,case-control,37026303,10.4103/IJO.IJO_2821_22,NA,"Pal S., Vani G., Donthineni P.R., Basu S. , Arunasri K.",Tear film microbiome in Sjogren's and non-Sjogren's aqueous deficiency dry eye,Indian journal of ophthalmology,2023,"Dry eye disease, Prevotella, Sjogren's syndrome, non-Sjogren's syndrome, tear film microbiome",Experiment 3,India,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,Healthy Controls,Non-Sjogren's Syndrome patients with Dry Eye Disease,Non-Sjogren's patients with Dry Eye Disease,18,15,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Table S2C,19 November 2023,Mary Bearkland,"Mary Bearkland,Muqtadirat,WikiWorks",Table S2C: Discriminative genera in NSS compared to HC,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Luteimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Marinococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Nocardia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|g__Rhodobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Roseomonadaceae|g__Roseomonas|s__Roseomonas gilardii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Tsukamurellaceae|g__Tsukamurella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Zoogloea,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|s__Rhodobacteraceae bacterium HIMB11",3379134|976|117743|200644|2762318|59735;3379134|1224|1236|91347|543|547;1783272|1239|91061|186826|81852|1350;1783272|1239|1737404|1582879;1783272|1239|186801|186802|216572|236752;1783272|201174|1760|85004|31953|2701;3379134|1224|28216|80840|119060|47670;3379134|1224|1236|135614|32033|83614;1783272|1239|91061|1385|186817|1370;1783272|201174|1760|85006|85023|33882;1783272|201174|1760|85007|85025|1817;1783272|1239|1737404|1737405|1570339|543311;3379134|1224|28211|356|69277|28100;3379134|1224|1236|72274|135621|286;3379134|1224|28211|204455|1060;3379134|1224|28211|3120395|3385906|125216|257708;1783272|201174|1760|85006|1268|32207;3379134|1224|1236|91347|1903411|613;3379134|1224|28211|204457|3423717|165695;3384189|32066|203490|203491|1129771|34104;1783272|201174|1760|85011|2062|1883;1783272|1239|186801|186802|216572|292632;1783272|201174|1760|85007|85028|2060;3379134|1224|28216|206389|2008794|349;3379134|1224|28211|204455|31989|1366046,Complete,Peace Sandy
bsdb:37026303/3/2,37026303,case-control,37026303,10.4103/IJO.IJO_2821_22,NA,"Pal S., Vani G., Donthineni P.R., Basu S. , Arunasri K.",Tear film microbiome in Sjogren's and non-Sjogren's aqueous deficiency dry eye,Indian journal of ophthalmology,2023,"Dry eye disease, Prevotella, Sjogren's syndrome, non-Sjogren's syndrome, tear film microbiome",Experiment 3,India,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,Healthy Controls,Non-Sjogren's Syndrome patients with Dry Eye Disease,Non-Sjogren's patients with Dry Eye Disease,18,15,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Table S2C,19 November 2023,Mary Bearkland,"Mary Bearkland,WikiWorks",Table S2C: Discriminative genera in NSS compared to HC,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alishewanella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Anoxybacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Cellvibrio,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Desemzia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Domibacillus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Empedobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Haematobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Janibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Kytococcaceae|g__Kytococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Mangrovibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermatophilaceae|g__Piscicoccus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propioniciclava,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Pseudoxanthomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Qipengyuania,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Skermanella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",3379134|1224|28216|80840|80864|12916;3379134|1224|1236|2887326|468|469;3379134|1224|1236|135624|84642|642;3379134|1224|1236|135622|72275|111142;3379134|976|200643|171549|171552|1283313;1783272|1239|91061|1385|3120669|150247;1783272|1239|91061|1385|186817|1386;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85006|85020|43668;1783272|201174|1760|85006|85019|1696;3379134|1224|28211|204458|76892|41275;3379134|1224|1236|1706369|1706371|10;3379134|976|117743|200644|2762318|59732;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85009|31957|1912216;3379134|1224|28216|80840|80864|80865;1783272|1239|91061|186826|186828|82800;1783272|201174|1760|85007|85029|37914;1783272|1239|91061|1385|186817|1433999;3379134|976|117743|200644|2762318|59734;3379134|1224|28211|356|212791;1783272|201174|1760|85007|85026|2053;3379134|1224|28211|204455|31989|366614;3379134|1224|1236|135625|712|724;3379134|1224|1236|135619|28256|2745;1783272|201174|1760|85006|85021|53457;3379134|1224|1236|91347|543|570;1783272|201174|1760|85006|1268|57493;1783272|201174|1760|85006|2805426|57499;1783272|201174|1760|85007|2805586|1847725;3384189|32066|203490|203491|1129771|32067;3379134|1224|1236|135614|32033|68;3379134|1224|1236|91347|543|451512;3379134|1224|28216|80840|75682|149698;3379134|1224|28211|356|119045|407;1783272|201174|1760|85006|1268|1269;1783272|201174|1760|85007|1762|1763;1783272|1239|91061|1385|186822|44249;3379134|1224|28211|204455|31989|265;1783272|201174|1760|85006|85018|985001;1783272|201174|1760|85009|31957|1085622;3379134|1224|1236|135614|32033|83618;3379134|1224|28211|204457|335929|1855416;3379134|1224|1236|135622|267890|22;3379134|1224|28211|204441|2829815|204447;1783272|201174|84998|1643822|1643826|84108;3379134|1224|1236|135614|32033|40323,Complete,Peace Sandy
bsdb:37032359/1/2,37032359,time series / longitudinal observational,37032359,10.1186/s40168-023-01516-y,NA,"Spatz M., Da Costa G., Ventin-Holmberg R., Planchais J., Michaudel C., Wang Y., Danne C., Lapiere A., Michel M.L., Kolho K.L., Langella P., Sokol H. , Richard M.L.",Antibiotic treatment using amoxicillin-clavulanic acid impairs gut mycobiota development through modification of the bacterial ecosystem,Microbiome,2023,"Antibiotics, Enterobacteriaceae, Microbiota, Mycobiota",Experiment 1,France,Mus musculus,Feces,UBERON:0001988,"Antimicrobial agent,Amoxicillin","CHEBI:2676,CHEBI:33281",mouse before antibiotic treatment,mouse  after antibiotic treatment,Mouse sample fungal results post-antibiotic treatment using Amoxicillin/clavulanate acid,7,12,NA,ITS / ITS2,NA,NA,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,figure 2D,13 October 2023,Hodan Issah,"Hodan Issah,WikiWorks",Amoxicillin/clavulanate acid treatment alters the fungal microbiota,increased,"k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Cladosporium,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Diaporthales|f__Cytosporaceae|g__Valsa",4751|4890|147545|5042|1131492|5052;4751|4890|147541|2726946|452563|5498;4751|4890|147550|5114|5117|83174,Complete,Folakunmi
bsdb:37032359/2/2,37032359,time series / longitudinal observational,37032359,10.1186/s40168-023-01516-y,NA,"Spatz M., Da Costa G., Ventin-Holmberg R., Planchais J., Michaudel C., Wang Y., Danne C., Lapiere A., Michel M.L., Kolho K.L., Langella P., Sokol H. , Richard M.L.",Antibiotic treatment using amoxicillin-clavulanic acid impairs gut mycobiota development through modification of the bacterial ecosystem,Microbiome,2023,"Antibiotics, Enterobacteriaceae, Microbiota, Mycobiota",Experiment 2,France,Mus musculus,Feces,UBERON:0001988,"Antimicrobial agent,Amoxicillin","CHEBI:2676,CHEBI:33281",Mouse before antibiotic  treatment,Mouse after antibiotic treatment,Mouse sample bacterial results post-antibiotic treatment using amoxicillin-acid clavulanic,7,12,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,figure 3D,13 October 2023,Hodan Issah,"Hodan Issah,Folakunmi,WikiWorks",Amoxicillin/clavulanate acid treatment alters the bacterial microbiota,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|1940338;1783272|1239|91061|186826|81852|1350,Complete,Folakunmi
bsdb:37033494/1/1,37033494,"cross-sectional observational, not case-control",37033494,10.3389/fcimb.2023.1105366,NA,"Chen H., Wang J., Ouyang Q., Peng X., Yu Z., Wang J. , Huang J.",Alterations of gut microbes and their correlation with clinical features in middle and end-stages chronic kidney disease,Frontiers in cellular and infection microbiology,2023,"chronic kidney disease, clinical indicators, community composition, end-stage renal disease, gut microbe",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Chronic kidney disease (CKD),End-stage renal disease (ESRD),Patients with end-stage renal disease,7,6,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3,8 October 2025,EniolaAde,EniolaAde,Differential abundance between chronic kidney disease (CKD) and end-stage renal disease (ESRD),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Geobacterales|f__Geobacteraceae|g__Geobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Raoultibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|201174|1760|85007|1653|1716;1783272|1239|526524|526525|128827|1937008;1783272|1239|91061|186826|81852|1350;1783272|1239|526524|526525|128827|1573534;3379134|200940|3031651|3031668|213422|28231;3379134|29547|3031852|213849|72293|209;1783272|201174|84998|1643822|1643826|1926677;1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:37033494/1/2,37033494,"cross-sectional observational, not case-control",37033494,10.3389/fcimb.2023.1105366,NA,"Chen H., Wang J., Ouyang Q., Peng X., Yu Z., Wang J. , Huang J.",Alterations of gut microbes and their correlation with clinical features in middle and end-stages chronic kidney disease,Frontiers in cellular and infection microbiology,2023,"chronic kidney disease, clinical indicators, community composition, end-stage renal disease, gut microbe",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Chronic kidney disease (CKD),End-stage renal disease (ESRD),Patients with end-stage renal disease,7,6,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3,8 October 2025,EniolaAde,"EniolaAde,Tosin",Differential abundance between chronic kidney disease (CKD) and end-stage renal disease (ESRD),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843488|909930|33024,Complete,Svetlana up
bsdb:37033494/2/1,37033494,"cross-sectional observational, not case-control",37033494,10.3389/fcimb.2023.1105366,NA,"Chen H., Wang J., Ouyang Q., Peng X., Yu Z., Wang J. , Huang J.",Alterations of gut microbes and their correlation with clinical features in middle and end-stages chronic kidney disease,Frontiers in cellular and infection microbiology,2023,"chronic kidney disease, clinical indicators, community composition, end-stage renal disease, gut microbe",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,High density lipoprotein cholesterol measurement,EFO:0004612,Low HDL_C (high density lipoprotein cholesterol) in end-stage renal disease,High HDL_C (high density lipoprotein cholesterol) in end-stage renal disease,High HDL_C (high density lipoprotein cholesterol) in end-stage renal disease,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 5,10 October 2025,EniolaAde,EniolaAde,Correlation between genus relative abundance in low HDL_C (high density lipoprotein cholesterol) and high HDL_C (high density lipoprotein cholesterol)  in End-stage renal disease group,decreased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,1783272|1239|526524|526525|2810281|191303,Complete,Svetlana up
bsdb:37033494/3/1,37033494,"cross-sectional observational, not case-control",37033494,10.3389/fcimb.2023.1105366,NA,"Chen H., Wang J., Ouyang Q., Peng X., Yu Z., Wang J. , Huang J.",Alterations of gut microbes and their correlation with clinical features in middle and end-stages chronic kidney disease,Frontiers in cellular and infection microbiology,2023,"chronic kidney disease, clinical indicators, community composition, end-stage renal disease, gut microbe",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Triglyceride measurement,EFO:0004530,Low triglyceride (TG) in End-stage renal disease group,High triglyceride (TG) in End-stage renal disease group,High triglyceride in end-stage renal disease,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 5,10 October 2025,EniolaAde,"EniolaAde,Tosin",Correlation between genus relative abundance in low triglyceride and high triglyceride in End-stage renal disease group,decreased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,1783272|1239|526524|526525|2810281|191303,Complete,Svetlana up
bsdb:37033494/4/1,37033494,"cross-sectional observational, not case-control",37033494,10.3389/fcimb.2023.1105366,NA,"Chen H., Wang J., Ouyang Q., Peng X., Yu Z., Wang J. , Huang J.",Alterations of gut microbes and their correlation with clinical features in middle and end-stages chronic kidney disease,Frontiers in cellular and infection microbiology,2023,"chronic kidney disease, clinical indicators, community composition, end-stage renal disease, gut microbe",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Beta-2 microglobulin measurement,EFO:0005197,Low beta 2-microglobulin in end-stage renal disease,High beta 2-microglobulin in end-stage renal disease,High beta 2-MG (beta 2 microglobulin) in end-stage renal disease,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 5,10 October 2025,EniolaAde,"EniolaAde,Tosin",Correlation between genus relative abundance in low beta 2-microglobulin and high beta 2-microglobulin in end-stage renal disease group,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",1783272|1239|186801|3082720|186804|1505657;1783272|1239|909932|1843488|909930|33024,Complete,Svetlana up
bsdb:37033494/5/1,37033494,"cross-sectional observational, not case-control",37033494,10.3389/fcimb.2023.1105366,NA,"Chen H., Wang J., Ouyang Q., Peng X., Yu Z., Wang J. , Huang J.",Alterations of gut microbes and their correlation with clinical features in middle and end-stages chronic kidney disease,Frontiers in cellular and infection microbiology,2023,"chronic kidney disease, clinical indicators, community composition, end-stage renal disease, gut microbe",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Natriuretic peptides B measurement,EFO:0010628,Low B-type natriuretic peptides in chronic kidney disease,High B-type natriuretic peptides in chronic kidney disease,High B-type natriuretic peptides in chronic kidney disease group,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 5,26 October 2025,EniolaAde,EniolaAde,Correlation between genus relative abundance in low B-type natriuretic peptides and high B-type natriuretic peptides in Chronic kidney disease group,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:37033494/6/1,37033494,"cross-sectional observational, not case-control",37033494,10.3389/fcimb.2023.1105366,NA,"Chen H., Wang J., Ouyang Q., Peng X., Yu Z., Wang J. , Huang J.",Alterations of gut microbes and their correlation with clinical features in middle and end-stages chronic kidney disease,Frontiers in cellular and infection microbiology,2023,"chronic kidney disease, clinical indicators, community composition, end-stage renal disease, gut microbe",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Vitamin D measurement,EFO:0004631,Low vitamin D in chronic kidney disease,High vitamin D in chronic kidney disease,High vitamin D in chronic kidney disease group,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 5,26 October 2025,EniolaAde,"EniolaAde,Tosin",Correlation between genus relative abundance in low vitamin D and high vitamin D in Chronic kidney disease group,increased,",k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia",;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|3082720|186804|1501226,Complete,Svetlana up
bsdb:37033494/6/2,37033494,"cross-sectional observational, not case-control",37033494,10.3389/fcimb.2023.1105366,NA,"Chen H., Wang J., Ouyang Q., Peng X., Yu Z., Wang J. , Huang J.",Alterations of gut microbes and their correlation with clinical features in middle and end-stages chronic kidney disease,Frontiers in cellular and infection microbiology,2023,"chronic kidney disease, clinical indicators, community composition, end-stage renal disease, gut microbe",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Vitamin D measurement,EFO:0004631,Low vitamin D in chronic kidney disease,High vitamin D in chronic kidney disease,High vitamin D in chronic kidney disease group,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 5,26 October 2025,EniolaAde,"EniolaAde,Tosin",Correlation between genus relative abundance in low vitamin D and high vitamin D in Chronic kidney disease group,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|216851|1946507;1783272|1239|186801|3082720|186804|1505657;1783272|1239|186801|3085636|186803|1506553;3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:37033494/7/1,37033494,"cross-sectional observational, not case-control",37033494,10.3389/fcimb.2023.1105366,NA,"Chen H., Wang J., Ouyang Q., Peng X., Yu Z., Wang J. , Huang J.",Alterations of gut microbes and their correlation with clinical features in middle and end-stages chronic kidney disease,Frontiers in cellular and infection microbiology,2023,"chronic kidney disease, clinical indicators, community composition, end-stage renal disease, gut microbe",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Uric acid measurement,EFO:0004761,Low uric acid in end-stage renal disease,High uric acid in end-stage renal disease,High uric acid in end-stage renal disease group,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 5,26 October 2025,EniolaAde,"EniolaAde,Tosin",Correlation between genus relative abundance in low uric acid and high uric acid in End-stage renal disease group,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,1783272|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:37033494/8/1,37033494,"cross-sectional observational, not case-control",37033494,10.3389/fcimb.2023.1105366,NA,"Chen H., Wang J., Ouyang Q., Peng X., Yu Z., Wang J. , Huang J.",Alterations of gut microbes and their correlation with clinical features in middle and end-stages chronic kidney disease,Frontiers in cellular and infection microbiology,2023,"chronic kidney disease, clinical indicators, community composition, end-stage renal disease, gut microbe",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Natriuretic peptides B measurement,EFO:0010628,Low B-type natriuretic peptides in End-stage renal disease,High B-type natriuretic peptides in End-stage renal disease,High B-type natriuretic peptides in End-stage renal disease group,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 5,26 October 2025,EniolaAde,"EniolaAde,Tosin",Correlation between genus relative abundance in low B-type natriuretic peptides and high B-type natriuretic peptides in End-stage renal disease group,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|976|200643|171549|171550|239759;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|292632;3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:37033494/9/1,37033494,"cross-sectional observational, not case-control",37033494,10.3389/fcimb.2023.1105366,NA,"Chen H., Wang J., Ouyang Q., Peng X., Yu Z., Wang J. , Huang J.",Alterations of gut microbes and their correlation with clinical features in middle and end-stages chronic kidney disease,Frontiers in cellular and infection microbiology,2023,"chronic kidney disease, clinical indicators, community composition, end-stage renal disease, gut microbe",Experiment 9,China,Homo sapiens,Feces,UBERON:0001988,Vitamin D measurement,EFO:0004631,Low vitamin D in End-stage renal disease,High vitamin D in End-stage renal disease,High vitamin D in End-stage renal disease group,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 5,26 October 2025,EniolaAde,"EniolaAde,Tosin",Correlation between genus relative abundance in low vitamin D and high vitamin D in End-stage renal disease group,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:37047557/1/1,37047557,laboratory experiment,37047557,https://doi.org/10.3390/ijms24076585,https://pmc.ncbi.nlm.nih.gov/articles/PMC10095166/,"Bingyong Mao, Hao Zhang, Jianxin Zhao, Qiuxiang Zhang, Shumao Cui, Xin Zhou, Xin Tang",Exploring the Dose-Effect Relationship of <i>Bifidobacterium longum</i> in Relieving Loperamide Hydrochloride-Induced Constipation in Rats through Colon-Released Capsules,International journal of molecular sciences,2023,"constipation, dose–effect relationship, Bifidobacterium longum",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Constipation,HP:0002019,"Combination of 10M2-M (Medium-dose Bifidobacterium longum strain FJSWXJ10M2), Control, S3-Free (Free Bifidobacterium longum strain FSDJN6M3), S3-L (Low-dose Bifidobacterium longum strain FSDJN6M3), 10M2-H (High-dose Bifidobacterium longum strain FJSWXJ10M2), 6M4-L (Low-dose Bifidobacterium longum strain FGSZY6M4), Model, S3-H (High-dose Bifidobacterium longum strain FSDJN6M3), S3-M (Medium-dose Bifidobacterium longum strain FSDJN6M3), 10M2-L (Low-dose Bifidobacterium longum strain FJSWXJ10M2) and 6M4-M (Medium-dose Bifidobacterium longum strain FGSZY6M4)",10M2-Free (Free Bifidobacterium longum strain FJSWXJ10M2),Rats in this group were administered a free bacterial suspension of FJSWXJ10M2 (10⁸ CFU/mL) and loperamide hydrochloride.,66,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A and 6B,28 October 2025,Jamesonyebuchi,"Jamesonyebuchi,Tosin","The linear discriminant analysis effect size (LEfSe) analysis of fecal flora. Phylogenetic tree illustrating the taxonomic hierarchy of bacteria, which varies in terms of relative abundance between the various groupings.",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes",1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|3085636|186803|207244,Complete,KateRasheed
bsdb:37047557/2/1,37047557,laboratory experiment,37047557,https://doi.org/10.3390/ijms24076585,https://pmc.ncbi.nlm.nih.gov/articles/PMC10095166/,"Bingyong Mao, Hao Zhang, Jianxin Zhao, Qiuxiang Zhang, Shumao Cui, Xin Zhou, Xin Tang",Exploring the Dose-Effect Relationship of <i>Bifidobacterium longum</i> in Relieving Loperamide Hydrochloride-Induced Constipation in Rats through Colon-Released Capsules,International journal of molecular sciences,2023,"constipation, dose–effect relationship, Bifidobacterium longum",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Constipation,HP:0002019,"Combination of 10M2-Free (Free Bifidobacterium longum strain FJSWXJ10M2), Model, Control , S3-Free (Free Bifidobacterium longum strain FSDJN6M3), S3-L (Low-dose Bifidobacterium longum strain FSDJN6M3), 10M2-H (High-dose Bifidobacterium longum strain FJSWXJ10M2), 6M4-L (Low-dose Bifidobacterium longum strain FGSZY6M4), S3-H (High-dose Bifidobacterium longum strain FSDJN6M3), S3-M (Medium-dose Bifidobacterium longum strain FSDJN6M3), 10M2-L (Low-dose Bifidobacterium longum strain FJSWXJ10M2) and 6M4-M (Medium-dose Bifidobacterium longum strain FGSZY6M4)",10M2-Medium (Medium Bifidobacterium longum strain FJSWXJ10M2),Rats in this group were administered colon-released capsules containing FJSWXJ10M2 (10⁶ CFU/capsule) and loperamide hydrochloride.,66,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A,27 January 2026,Tosin,Tosin,"The linear discriminant analysis effect size (LEfSe) analysis of fecal flora. Phylogenetic tree illustrating the taxonomic hierarchy of bacteria, which varies in terms of relative abundance between the various groupings.",increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella",1783272|1239|526524|526525|128827|1573534;3379134|1224|28216|80840|995019|577310,Complete,KateRasheed
bsdb:37047557/3/1,37047557,laboratory experiment,37047557,https://doi.org/10.3390/ijms24076585,https://pmc.ncbi.nlm.nih.gov/articles/PMC10095166/,"Bingyong Mao, Hao Zhang, Jianxin Zhao, Qiuxiang Zhang, Shumao Cui, Xin Zhou, Xin Tang",Exploring the Dose-Effect Relationship of <i>Bifidobacterium longum</i> in Relieving Loperamide Hydrochloride-Induced Constipation in Rats through Colon-Released Capsules,International journal of molecular sciences,2023,"constipation, dose–effect relationship, Bifidobacterium longum",Experiment 3,China,Rattus norvegicus,Feces,UBERON:0001988,Constipation,HP:0002019,"Combination of 10M2-Free (Free Bifidobacterium longum strain FJSWXJ10M2), 10M2-M (Medium-dose Bifidobacterium longum strain FJSWXJ10M2), S3-Free (Free Bifidobacterium longum strain FSDJN6M3), S3-L (Low-dose Bifidobacterium longum strain FSDJN6M3), 10M2-H (High-dose Bifidobacterium longum strain FJSWXJ10M2), 6M4-L (Low-dose Bifidobacterium longum strain FGSZY6M4), Model, S3-H (High-dose Bifidobacterium longum strain FSDJN6M3), S3-M (Medium-dose Bifidobacterium longum strain FSDJN6M3), 10M2-L (Low-dose Bifidobacterium longum strain FJSWXJ10M2) and 6M4-M (Medium-dose Bifidobacterium longum strain FGSZY6M4)",Control,Rats in this group were administered normal saline only and were not induced with constipation,66,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A and 6B,7 January 2026,Tosin,Tosin,"The linear discriminant analysis effect size (LEfSe) analysis of fecal flora. Phylogenetic tree illustrating the taxonomic hierarchy of bacteria, which varies in terms of relative abundance between the various groupings.",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetitomaculum",1783272|1239|91061|1385;3379134|976|200643|171549|171552|1283313;1783272|1239|186801|3085636|186803|189330;1783272|1239|91061|186826|186827;1783272|1239|91061|1385|90964|227979;1783272|1239|91061|186826|186827|1375;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|3085636|186803|31980,Complete,KateRasheed
bsdb:37047557/4/1,37047557,laboratory experiment,37047557,https://doi.org/10.3390/ijms24076585,https://pmc.ncbi.nlm.nih.gov/articles/PMC10095166/,"Bingyong Mao, Hao Zhang, Jianxin Zhao, Qiuxiang Zhang, Shumao Cui, Xin Zhou, Xin Tang",Exploring the Dose-Effect Relationship of <i>Bifidobacterium longum</i> in Relieving Loperamide Hydrochloride-Induced Constipation in Rats through Colon-Released Capsules,International journal of molecular sciences,2023,"constipation, dose–effect relationship, Bifidobacterium longum",Experiment 4,China,Rattus norvegicus,Feces,UBERON:0001988,Constipation,HP:0002019,"Combination of 10M2-Free (Free Bifidobacterium longum strain FJSWXJ10M2), 10M2-M (Medium-dose Bifidobacterium longum strain FJSWXJ10M2), Control , S3-L (Low-dose Bifidobacterium longum strain FSDJN6M3), 10M2-H (High-dose Bifidobacterium longum strain FJSWXJ10M2), 6M4-L (Low-dose Bifidobacterium longum strain FGSZY6M4), Model, S3-H (High-dose Bifidobacterium longum strain FSDJN6M3), S3-M (Medium-dose Bifidobacterium longum strain FSDJN6M3), 10M2-L (Low-dose Bifidobacterium longum strain FJSWXJ10M2) and 6M4-M (Medium-dose Bifidobacterium longum strain FGSZY6M4)",S3-Free (Free Bifidobacterium longum strain FSDJN6M3),Rats in this group were administered a free bacterial suspension of FSDJN6M3 (10⁸ CFU/mL) and loperamide hydrochloride,66,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A and 6B,7 January 2026,Tosin,Tosin,"The linear discriminant analysis effect size (LEfSe) analysis of fecal flora. Phylogenetic tree illustrating the taxonomic hierarchy of bacteria, which varies in terms of relative abundance between the various groupings.",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales,k__Thermotogati|p__Deinococcota|c__Deinococci,k__Thermotogati|p__Deinococcota,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus",1783272|201174|84998|84999|1643824;3379134|1224|28216|80840|119060;3384194|1297|188787|118964|183710;3384194|1297|188787|118964;3384194|1297|188787;3384194|1297;3384194|1297|188787|118964|183710|1298;3379134|1224|1236|135614|32033;3379134|1224|1236|135614;3379134|1224|1236|72274|135621;3379134|1224|1236|72274|135621|286;1783272|1239|186801|3085636|186803|841;3379134|1224|1236|135614|32033|40323;3384194|1297|188787|68933|188786;3384194|1297|188787|68933;3384194|1297|188787|68933|188786|270,Complete,KateRasheed
bsdb:37047557/5/1,37047557,laboratory experiment,37047557,https://doi.org/10.3390/ijms24076585,https://pmc.ncbi.nlm.nih.gov/articles/PMC10095166/,"Bingyong Mao, Hao Zhang, Jianxin Zhao, Qiuxiang Zhang, Shumao Cui, Xin Zhou, Xin Tang",Exploring the Dose-Effect Relationship of <i>Bifidobacterium longum</i> in Relieving Loperamide Hydrochloride-Induced Constipation in Rats through Colon-Released Capsules,International journal of molecular sciences,2023,"constipation, dose–effect relationship, Bifidobacterium longum",Experiment 5,China,Rattus norvegicus,Feces,UBERON:0001988,Constipation,HP:0002019,"Combination of 10M2-Free (Free Bifidobacterium longum strain FJSWXJ10M2), 10M2-M (Medium-dose Bifidobacterium longum strain FJSWXJ10M2), Control , S3-Free (Free Bifidobacterium longum strain FSDJN6M3), 10M2-H (High-dose Bifidobacterium longum strain FJSWXJ10M2), 6M4-L (Low-dose Bifidobacterium longum strain FGSZY6M4), Model, S3-H (High-dose Bifidobacterium longum strain FSDJN6M3), S3-M (Medium-dose Bifidobacterium longum strain FSDJN6M3), 10M2-L (Low-dose Bifidobacterium longum strain FJSWXJ10M2) and 6M4-M (Medium-dose Bifidobacterium longum strain FGSZY6M4)",S3-L (Low-dose Bifidobacterium longum strain FSDJN6M3),Rats in this group were administered colon-released capsules containing FSDJN6M3 (10⁴ CFU/capsule) and loperamide hydrochloride,66,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A,7 January 2026,Tosin,Tosin,"The linear discriminant analysis effect size (LEfSe) analysis of fecal flora. Phylogenetic tree illustrating the taxonomic hierarchy of bacteria, which varies in terms of relative abundance between the various groupings.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Dokdonella",3379134|1224|1236|135614|1775411;3379134|1224|1236|135614|1775411|323413,Complete,KateRasheed
bsdb:37047557/7/1,37047557,laboratory experiment,37047557,https://doi.org/10.3390/ijms24076585,https://pmc.ncbi.nlm.nih.gov/articles/PMC10095166/,"Bingyong Mao, Hao Zhang, Jianxin Zhao, Qiuxiang Zhang, Shumao Cui, Xin Zhou, Xin Tang",Exploring the Dose-Effect Relationship of <i>Bifidobacterium longum</i> in Relieving Loperamide Hydrochloride-Induced Constipation in Rats through Colon-Released Capsules,International journal of molecular sciences,2023,"constipation, dose–effect relationship, Bifidobacterium longum",Experiment 7,China,Rattus norvegicus,Feces,UBERON:0001988,Constipation,HP:0002019,"Combination of 10M2-Free (Free Bifidobacterium longum strain FJSWXJ10M2), 10M2-M (Medium-dose Bifidobacterium longum strain FJSWXJ10M2), Control , S3-Free (Free Bifidobacterium longum strain FSDJN6M3), S3-L (Low-dose Bifidobacterium longum strain FSDJN6M3), 10M2-H (High-dose Bifidobacterium longum strain FJSWXJ10M2), Model, S3-H (High-dose Bifidobacterium longum strain FSDJN6M3), S3-M (Medium-dose Bifidobacterium longum strain FSDJN6M3), 10M2-L (Low-dose Bifidobacterium longum strain FJSWXJ10M2) and 6M4-M (Medium-dose Bifidobacterium longum strain FGSZY6M4)",6M4-L (Low-dose Bifidobacterium longum strain FGSZY6M4),Rats in this group were administered colon-released capsules containing FGSZY6M4 (10⁴ CFU/capsule) and loperamide hydrochloride,66,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A and 6B,25 January 2026,Tosin,Tosin,"The linear discriminant analysis effect size (LEfSe) analysis of fecal flora. Phylogenetic tree illustrating the taxonomic hierarchy of bacteria, which varies in terms of relative abundance between the various groupings.",increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|s__uncultured Paenibacillaceae bacterium,1783272|1239|91061|1385|186822|256850,Complete,KateRasheed
bsdb:37047557/8/1,37047557,laboratory experiment,37047557,https://doi.org/10.3390/ijms24076585,https://pmc.ncbi.nlm.nih.gov/articles/PMC10095166/,"Bingyong Mao, Hao Zhang, Jianxin Zhao, Qiuxiang Zhang, Shumao Cui, Xin Zhou, Xin Tang",Exploring the Dose-Effect Relationship of <i>Bifidobacterium longum</i> in Relieving Loperamide Hydrochloride-Induced Constipation in Rats through Colon-Released Capsules,International journal of molecular sciences,2023,"constipation, dose–effect relationship, Bifidobacterium longum",Experiment 8,China,Rattus norvegicus,Feces,UBERON:0001988,Constipation,HP:0002019,"Combination of 10M2-Free (Free Bifidobacterium longum strain FJSWXJ10M2), 10M2-M (Medium-dose Bifidobacterium longum strain FJSWXJ10M2), Control , S3-Free (Free Bifidobacterium longum strain FSDJN6M3), S3-L (Low-dose Bifidobacterium longum strain FSDJN6M3), 10M2-H (High-dose Bifidobacterium longum strain FJSWXJ10M2), 6M4-L (Low-dose Bifidobacterium longum strain FGSZY6M4), S3-H (High-dose Bifidobacterium longum strain FSDJN6M3), S3-M (Medium-dose Bifidobacterium longum strain FSDJN6M3), 10M2-L (Low-dose Bifidobacterium longum strain FJSWXJ10M2) and 6M4-M (Medium-dose Bifidobacterium longum strain FGSZY6M4)",Model group,Rats in this group were administered normal saline and loperamide hydrochloride (5 mg/kg) to induce constipation,66,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A and 6B,25 January 2026,Tosin,Tosin,"The linear discriminant analysis effect size (LEfSe) analysis of fecal flora. Phylogenetic tree illustrating the taxonomic hierarchy of bacteria, which varies in terms of relative abundance between the various groupings.",increased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|s__Coriobacteriaceae bacterium CHKCI002,1783272|201174|84998|84999|84107|1780377,Complete,KateRasheed
bsdb:37047557/9/1,37047557,laboratory experiment,37047557,https://doi.org/10.3390/ijms24076585,https://pmc.ncbi.nlm.nih.gov/articles/PMC10095166/,"Bingyong Mao, Hao Zhang, Jianxin Zhao, Qiuxiang Zhang, Shumao Cui, Xin Zhou, Xin Tang",Exploring the Dose-Effect Relationship of <i>Bifidobacterium longum</i> in Relieving Loperamide Hydrochloride-Induced Constipation in Rats through Colon-Released Capsules,International journal of molecular sciences,2023,"constipation, dose–effect relationship, Bifidobacterium longum",Experiment 9,China,Rattus norvegicus,Feces,UBERON:0001988,Constipation,HP:0002019,"Combination of 10M2-Free (Free Bifidobacterium longum strain FJSWXJ10M2), 10M2-M (Medium-dose Bifidobacterium longum strain FJSWXJ10M2), Control , S3-Free (Free Bifidobacterium longum strain FSDJN6M3), S3-L (Low-dose Bifidobacterium longum strain FSDJN6M3), 10M2-H (High-dose Bifidobacterium longum strain FJSWXJ10M2), 6M4-L (Low-dose Bifidobacterium longum strain FGSZY6M4), Model, S3-M (Medium-dose Bifidobacterium longum strain FSDJN6M3), 10M2-L (Low-dose Bifidobacterium longum strain FJSWXJ10M2) and 6M4-M (Medium-dose Bifidobacterium longum strain FGSZY6M4)",S3-H (High-dose Bifidobacterium longum strain FSDJN6M3),Rats in this group were administered colon-released capsules containing FSDJN6M3 (10⁸ CFU/capsule) and loperamide hydrochloride,66,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A and 6B,25 January 2026,Tosin,Tosin,"The linear discriminant analysis effect size (LEfSe) analysis of fecal flora. Phylogenetic tree illustrating the taxonomic hierarchy of bacteria, which varies in terms of relative abundance between the various groupings.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|201174|1760|85004;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678,Complete,KateRasheed
bsdb:37047557/10/1,37047557,laboratory experiment,37047557,https://doi.org/10.3390/ijms24076585,https://pmc.ncbi.nlm.nih.gov/articles/PMC10095166/,"Bingyong Mao, Hao Zhang, Jianxin Zhao, Qiuxiang Zhang, Shumao Cui, Xin Zhou, Xin Tang",Exploring the Dose-Effect Relationship of <i>Bifidobacterium longum</i> in Relieving Loperamide Hydrochloride-Induced Constipation in Rats through Colon-Released Capsules,International journal of molecular sciences,2023,"constipation, dose–effect relationship, Bifidobacterium longum",Experiment 10,China,Rattus norvegicus,Feces,UBERON:0001988,Constipation,HP:0002019,"Combination of 10M2-Free (Free Bifidobacterium longum strain FJSWXJ10M2), 10M2-M (Medium-dose Bifidobacterium longum strain FJSWXJ10M2), Control , S3-Free (Free Bifidobacterium longum strain FSDJN6M3), S3-L (Low-dose Bifidobacterium longum strain FSDJN6M3), 10M2-H (High-dose Bifidobacterium longum strain FJSWXJ10M2), 6M4-L (Low-dose Bifidobacterium longum strain FGSZY6M4), Model, S3-H (High-dose Bifidobacterium longum strain FSDJN6M3), 10M2-L (Low-dose Bifidobacterium longum strain FJSWXJ10M2) and 6M4-M (Medium-dose Bifidobacterium longum strain FGSZY6M4)",S3-M (Medium-dose Bifidobacterium longum strain FSDJN6M3),Rats in this group were administered colon-released capsules containing FSDJN6M3 (10⁶ CFU/capsule) and loperamide hydrochloride,66,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A and 6B,25 January 2026,Tosin,Tosin,"The linear discriminant analysis effect size (LEfSe) analysis of fecal flora. Phylogenetic tree illustrating the taxonomic hierarchy of bacteria, which varies in terms of relative abundance between the various groupings.",increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,1783272|1239|186801|3085636|186803|248744,Complete,KateRasheed
bsdb:37047557/11/1,37047557,laboratory experiment,37047557,https://doi.org/10.3390/ijms24076585,https://pmc.ncbi.nlm.nih.gov/articles/PMC10095166/,"Bingyong Mao, Hao Zhang, Jianxin Zhao, Qiuxiang Zhang, Shumao Cui, Xin Zhou, Xin Tang",Exploring the Dose-Effect Relationship of <i>Bifidobacterium longum</i> in Relieving Loperamide Hydrochloride-Induced Constipation in Rats through Colon-Released Capsules,International journal of molecular sciences,2023,"constipation, dose–effect relationship, Bifidobacterium longum",Experiment 11,China,Rattus norvegicus,Feces,UBERON:0001988,Constipation,HP:0002019,"Combination of 10M2-Free (Free Bifidobacterium longum strain FJSWXJ10M2), 10M2-M (Medium-dose Bifidobacterium longum strain FJSWXJ10M2), Control , S3-Free (Free Bifidobacterium longum strain FSDJN6M3), S3-L (Low-dose Bifidobacterium longum strain FSDJN6M3), 10M2-H (High-dose Bifidobacterium longum strain FJSWXJ10M2), 6M4-L (Low-dose Bifidobacterium longum strain FGSZY6M4), Model, S3-H (High-dose Bifidobacterium longum strain FSDJN6M3), S3-M (Medium-dose Bifidobacterium longum strain FSDJN6M3) and 6M4-M (Medium-dose Bifidobacterium longum strain FGSZY6M4)",10M2-L (Low-dose Bifidobacterium longum strain FJSWXJ10M2),Rats in this group were administered colon-released capsules containing FJSWXJ10M2 (10⁴ CFU/capsule) and loperamide hydrochloride,66,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A and 6B,25 January 2026,Tosin,Tosin,"The linear discriminant analysis effect size (LEfSe) analysis of fecal flora. Phylogenetic tree illustrating the taxonomic hierarchy of bacteria, which varies in terms of relative abundance between the various groupings.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",3379134|976|200643|1970189|1573805;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|119852,Complete,KateRasheed
bsdb:37047557/12/1,37047557,laboratory experiment,37047557,https://doi.org/10.3390/ijms24076585,https://pmc.ncbi.nlm.nih.gov/articles/PMC10095166/,"Bingyong Mao, Hao Zhang, Jianxin Zhao, Qiuxiang Zhang, Shumao Cui, Xin Zhou, Xin Tang",Exploring the Dose-Effect Relationship of <i>Bifidobacterium longum</i> in Relieving Loperamide Hydrochloride-Induced Constipation in Rats through Colon-Released Capsules,International journal of molecular sciences,2023,"constipation, dose–effect relationship, Bifidobacterium longum",Experiment 12,China,Rattus norvegicus,Feces,UBERON:0001988,Constipation,HP:0002019,"Combination of 10M2-Free (Free Bifidobacterium longum strain FJSWXJ10M2), 10M2-M (Medium-dose Bifidobacterium longum strain FJSWXJ10M2), Control , S3-Free (Free Bifidobacterium longum strain FSDJN6M3), S3-L (Low-dose Bifidobacterium longum strain FSDJN6M3), 10M2-H (High-dose Bifidobacterium longum strain FJSWXJ10M2), 6M4-L (Low-dose Bifidobacterium longum strain FGSZY6M4), Model, S3-H (High-dose Bifidobacterium longum strain FSDJN6M3), S3-M (Medium-dose Bifidobacterium longum strain FSDJN6M3) and 10M2-L (Low-dose Bifidobacterium longum strain FJSWXJ10M2)",6M4-M (Medium-dose Bifidobacterium longum strain FGSZY6M4),Rats in this group were administered colon-released capsules containing FGSZY6M4 (10⁶ CFU/capsule) and loperamide hydrochloride,66,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A and 6B,25 January 2026,Tosin,Tosin,"The linear discriminant analysis effect size (LEfSe) analysis of fecal flora. Phylogenetic tree illustrating the taxonomic hierarchy of bacteria, which varies in terms of relative abundance between the various groupings.",increased,s__uncultured bacterium,77133,Complete,KateRasheed
bsdb:37047557/13/1,37047557,laboratory experiment,37047557,https://doi.org/10.3390/ijms24076585,https://pmc.ncbi.nlm.nih.gov/articles/PMC10095166/,"Bingyong Mao, Hao Zhang, Jianxin Zhao, Qiuxiang Zhang, Shumao Cui, Xin Zhou, Xin Tang",Exploring the Dose-Effect Relationship of <i>Bifidobacterium longum</i> in Relieving Loperamide Hydrochloride-Induced Constipation in Rats through Colon-Released Capsules,International journal of molecular sciences,2023,"constipation, dose–effect relationship, Bifidobacterium longum",Experiment 13,China,Rattus norvegicus,Feces,UBERON:0001988,Constipation,HP:0002019,Model group,6M4-L (Low-dose Bifidobacterium longum strain FGSZY6M4),Rats in this group were administered colon-released capsules containing FGSZY6M4 (10⁴ CFU/capsule) and loperamide hydrochloride,6,6,NA,16S,34,Illumina,relative abundances,"ANOVA,Post-Hoc Pairwise",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5F and 5H,25 January 2026,Tosin,Tosin,Relative abundance of taxa between model group and Low-dose Bifidobacterium longum strain FGSZY6M4 (6M4-L),increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota",3379134|976;3379134|1224,Complete,KateRasheed
bsdb:37047557/13/2,37047557,laboratory experiment,37047557,https://doi.org/10.3390/ijms24076585,https://pmc.ncbi.nlm.nih.gov/articles/PMC10095166/,"Bingyong Mao, Hao Zhang, Jianxin Zhao, Qiuxiang Zhang, Shumao Cui, Xin Zhou, Xin Tang",Exploring the Dose-Effect Relationship of <i>Bifidobacterium longum</i> in Relieving Loperamide Hydrochloride-Induced Constipation in Rats through Colon-Released Capsules,International journal of molecular sciences,2023,"constipation, dose–effect relationship, Bifidobacterium longum",Experiment 13,China,Rattus norvegicus,Feces,UBERON:0001988,Constipation,HP:0002019,Model group,6M4-L (Low-dose Bifidobacterium longum strain FGSZY6M4),Rats in this group were administered colon-released capsules containing FGSZY6M4 (10⁴ CFU/capsule) and loperamide hydrochloride,6,6,NA,16S,34,Illumina,relative abundances,"ANOVA,Post-Hoc Pairwise",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5E,25 January 2026,Tosin,Tosin,Relative abundance of taxa between model group and Low-dose Bifidobacterium longum strain FGSZY6M4 (6M4-L),decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,KateRasheed
bsdb:37047557/14/1,37047557,laboratory experiment,37047557,https://doi.org/10.3390/ijms24076585,https://pmc.ncbi.nlm.nih.gov/articles/PMC10095166/,"Bingyong Mao, Hao Zhang, Jianxin Zhao, Qiuxiang Zhang, Shumao Cui, Xin Zhou, Xin Tang",Exploring the Dose-Effect Relationship of <i>Bifidobacterium longum</i> in Relieving Loperamide Hydrochloride-Induced Constipation in Rats through Colon-Released Capsules,International journal of molecular sciences,2023,"constipation, dose–effect relationship, Bifidobacterium longum",Experiment 14,China,Rattus norvegicus,Feces,UBERON:0001988,Constipation,HP:0002019,Model group,S3-Free (Free Bifidobacterium longum strain FSDJN6M3),Rats in this group were administered a free bacterial suspension of FSDJN6M3 (10⁸ CFU/mL) and loperamide hydrochloride,6,6,NA,16S,34,Illumina,relative abundances,"ANOVA,Post-Hoc Pairwise",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5F and 5H,25 January 2026,Tosin,Tosin,Relative abundance of taxa between Model group and Free Bifidobacterium longum strain FSDJN6M3 (S3-Free),increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota",3379134|976;3379134|1224,Complete,KateRasheed
bsdb:37047557/14/2,37047557,laboratory experiment,37047557,https://doi.org/10.3390/ijms24076585,https://pmc.ncbi.nlm.nih.gov/articles/PMC10095166/,"Bingyong Mao, Hao Zhang, Jianxin Zhao, Qiuxiang Zhang, Shumao Cui, Xin Zhou, Xin Tang",Exploring the Dose-Effect Relationship of <i>Bifidobacterium longum</i> in Relieving Loperamide Hydrochloride-Induced Constipation in Rats through Colon-Released Capsules,International journal of molecular sciences,2023,"constipation, dose–effect relationship, Bifidobacterium longum",Experiment 14,China,Rattus norvegicus,Feces,UBERON:0001988,Constipation,HP:0002019,Model group,S3-Free (Free Bifidobacterium longum strain FSDJN6M3),Rats in this group were administered a free bacterial suspension of FSDJN6M3 (10⁸ CFU/mL) and loperamide hydrochloride,6,6,NA,16S,34,Illumina,relative abundances,"ANOVA,Post-Hoc Pairwise",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5E,25 January 2026,Tosin,Tosin,Relative abundance of taxa between Model group and Free Bifidobacterium longum strain FSDJN6M3 (S3-Free),decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,KateRasheed
bsdb:37049619/1/1,37049619,case-control,37049619,https://doi.org/10.3390/nu15071779,NA,"Wang J., Wang L., Yu Q., Tang N., Mei C., Zhang H., Wang G., Lu J. , Chen W.",Characteristics of the Gut Microbiome and Serum Metabolome in Patients with Functional Constipation,Nutrients,2023,"arginine biosynthesis pathway, biomarker, functional constipation, gut microbiome, serum metabolome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Normal Control,Functional Constipation,Patients Diagnosed with Functional Constipation based on Rome IV criteria by medical doctors.,28,30,1 month,16S,34,Illumina,relative abundances,ANOSIM,0.05,TRUE,NA,NA,NA,unchanged,unchanged,increased,unchanged,NA,increased,Signature 1,Figure 1d,19 March 2025,Dorcas-od,"Dorcas-od,KateRasheed","Differential microbes of the FC and NC groups at the phylum, family, and genus levels.",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136",1783272|1239|909932|1843488|909930;1783272|1239|186801|186802|216572|244127;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|3085636|186803|1506553;3379134|976|200643|1970189|1573805;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3085636|186803|841;3379134|976|200643|171549|2005525;3379134|976;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|216851|1946507;1783272|1239|186801|3085636|186803|877420,Complete,Svetlana up
bsdb:37049619/1/2,37049619,case-control,37049619,https://doi.org/10.3390/nu15071779,NA,"Wang J., Wang L., Yu Q., Tang N., Mei C., Zhang H., Wang G., Lu J. , Chen W.",Characteristics of the Gut Microbiome and Serum Metabolome in Patients with Functional Constipation,Nutrients,2023,"arginine biosynthesis pathway, biomarker, functional constipation, gut microbiome, serum metabolome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Normal Control,Functional Constipation,Patients Diagnosed with Functional Constipation based on Rome IV criteria by medical doctors.,28,30,1 month,16S,34,Illumina,relative abundances,ANOSIM,0.05,TRUE,NA,NA,NA,unchanged,unchanged,increased,unchanged,NA,increased,Signature 2,Figure 1D,20 March 2025,Dorcas-od,"Dorcas-od,KateRasheed","Differential microbes of the FC and NC groups at the phylum, family, and genus levels.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",1783272|1239|186801|3085636|186803|572511;3379134|1224|1236|91347|543|544;1783272|201174|84998|1643822|1643826|84111;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543;1783272|201174|84998|1643822|1643826|644652;1783272|1239|186801|3085636|186803;3379134|1224|28211|356|69277|68287;1783272|1239|186801|3082720|186804;3379134|1224|1236|72274|135621;3379134|1224;3379134|1224|1236|72274|135621|286;3379134|1224|28211|356|82115;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|2316020|33038,Complete,Svetlana up
bsdb:37049619/2/1,37049619,case-control,37049619,https://doi.org/10.3390/nu15071779,NA,"Wang J., Wang L., Yu Q., Tang N., Mei C., Zhang H., Wang G., Lu J. , Chen W.",Characteristics of the Gut Microbiome and Serum Metabolome in Patients with Functional Constipation,Nutrients,2023,"arginine biosynthesis pathway, biomarker, functional constipation, gut microbiome, serum metabolome",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Normal Control,Functional Constipation,Patients Diagnosed with Functional Constipation based on Rome IV criteria by medical doctors.,28,30,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,increased,unchanged,NA,increased,Signature 1,Figure 2A,20 March 2025,Dorcas-od,"Dorcas-od,KateRasheed",LEfSe analysis for key genera selection. LDA score plot shows the differential genera.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|g__Negativibacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium DTU089,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae",1783272|201174|84998|1643822|1643826|447020;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|244127;3379134|976|200643|171549|815|816;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|3085642|580596;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803;1783272|1239|1980693;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|577310;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|3068309;1783272|1239|186801|186802|216572|216851|1946507;1783272|1239|186801|186802|1671661;1783272|1239|186801|3085636|186803|1649459;3379134|976|200643|171549|815;3379134|976|200643|1970189|1573805;3379134|976|200643|171549|171550;3379134|976|200643|171549|2005525;3379134|976|200643|171549;1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|216572;1783272|1239|909932|1843488|909930;3379134|1224|28216|80840|119060,Complete,Svetlana up
bsdb:37049619/2/2,37049619,case-control,37049619,https://doi.org/10.3390/nu15071779,NA,"Wang J., Wang L., Yu Q., Tang N., Mei C., Zhang H., Wang G., Lu J. , Chen W.",Characteristics of the Gut Microbiome and Serum Metabolome in Patients with Functional Constipation,Nutrients,2023,"arginine biosynthesis pathway, biomarker, functional constipation, gut microbiome, serum metabolome",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Normal Control,Functional Constipation,Patients Diagnosed with Functional Constipation based on Rome IV criteria by medical doctors.,28,30,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,increased,unchanged,NA,increased,Signature 2,Figure 2A,21 March 2025,Dorcas-od,"Dorcas-od,D-coder111,KateRasheed",LEfSe analysis for key genera selection. LDA score plot shows the differential genera.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales",1783272|1239|186801|3085636|186803|572511;3379134|1224|1236|91347|543|544;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|1643822|1643826|84111;3379134|1224|1236|91347|543|547;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|3085636|186803|1407607;1783272|201174|84998|1643822|1643826|644652;3379134|1224|1236|135625|712|724;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|1300|1357;1783272|1239|909932|1843489|31977|906;3379134|1224|28211|356|69277|68287;3379134|1224|1236|72274|135621|286;1783272|1239|91061|186826|33958|46255;3379134|1224|1236|91347|543|1940338;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|33958;1783272|1239|186801|3085636|186803;1783272|1239|186801|3082720|186804;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;3379134|1224|28211|356|82115;3379134|1224|28211|356;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|1224|1236|72274|135621;3379134|1224|1236|72274,Complete,Svetlana up
bsdb:37060052/1/1,37060052,case-control,37060052,10.1186/s12866-023-02852-7,NA,"Liu Y., Wang M., Li W., Gao Y., Li H., Cao N., Hao W. , Zhao L.",Differences in gut microbiota and its metabolic function among different fasting plasma glucose groups in Mongolian population of China,BMC microbiology,2023,"Carotene intake, Gut microbiota, Metabolic function, Mongolian population, Type 2 diabetes mellitus",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Control (Normal glucose control group),T2D (type II diabetes) group,Patients with type II diabetes,12,6,1 month,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3A, 3B",12 April 2025,Tosin,Tosin,LeFse analysis between control and T2D(type 2 diabetes) group,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:156,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:882,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii",1783272|1239|186801|186802|31979|1485;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|186801|186802|186806|1730|1262880;1783272|1239|1262991;1783272|1239|526524|526525|128827|1573535;1783272|1239|526524|526525|128827|1573535|1735;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|815|909656|357276;1783272|1239|186801|186802|31979|1485|59620;3379134|976|200643|171549|815|909656|204516;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|572511|40520;3379134|976|200643|171549|815|816|28111,Complete,Svetlana up
bsdb:37060097/1/1,37060097,laboratory experiment,37060097,https://doi.org/10.1186/s40168-023-01527-9,NA,"Maidment T.I., Bryan E.R., Pyne M., Barnes M., Eccleston S., Cunningham S., Whitlock E., Redman K., Nicolson V., Beagley K.W. , Pelzer E.",Characterisation of the koala (Phascolarctos cinereus) pouch microbiota in a captive population reveals a dysbiotic compositional profile associated with neonatal mortality,Microbiome,2023,"Dysbiosis, Endangered species, Enterobacteriaceae, Klebsiella pneumoniae, Koala, Marsupial, Muribaculaceae, Phascolarctos cinereus, Pluralibacter gergoviae, Pouch, Reproduction",Experiment 1,Australia,Phascolarctos cinereus,Marsupium,UBERON:0009118,Neonatal death,HP:0003811,Successful breeders,Unsuccessful breeders,Captive Koalas who lost their pouch young during lactation.,10,7,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,supplementary Table 11,7 March 2024,Ehi,"Ehi,Folakunmi,WikiWorks",Differentially abundant genera in the pouch microbiota of successful vs. unsuccessful breeding koalas during early lactation.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pluralibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Lonepinella",1783272|1239|909932|1843488|909930|33024|33025;3379134|1224|1236|72274|135621|286;3379134|1224|1236|91347|543|1940338;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|543|1330546;3379134|1224|1236|135625|712|53416,Complete,Folakunmi
bsdb:37060097/1/2,37060097,laboratory experiment,37060097,https://doi.org/10.1186/s40168-023-01527-9,NA,"Maidment T.I., Bryan E.R., Pyne M., Barnes M., Eccleston S., Cunningham S., Whitlock E., Redman K., Nicolson V., Beagley K.W. , Pelzer E.",Characterisation of the koala (Phascolarctos cinereus) pouch microbiota in a captive population reveals a dysbiotic compositional profile associated with neonatal mortality,Microbiome,2023,"Dysbiosis, Endangered species, Enterobacteriaceae, Klebsiella pneumoniae, Koala, Marsupial, Muribaculaceae, Phascolarctos cinereus, Pluralibacter gergoviae, Pouch, Reproduction",Experiment 1,Australia,Phascolarctos cinereus,Marsupium,UBERON:0009118,Neonatal death,HP:0003811,Successful breeders,Unsuccessful breeders,Captive Koalas who lost their pouch young during lactation.,10,7,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,supplementary Table 11,7 March 2024,Ehi,"Ehi,Folakunmi,WikiWorks",Differentially abundant genera in the pouch microbiota of successful vs. unsuccessful breeding koalas during early lactation.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium",3379134|976|200643|171549|2005473|1918540;1783272|1239|909932|1843488|909930|33024|33025,Complete,Folakunmi
bsdb:37065158/1/1,37065158,"cross-sectional observational, not case-control",37065158,doi.org/10.3389/fmicb.2023.1094800,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1094800/full#h3,"Kool J., Tymchenko L., Shetty S.A. , Fuentes S.",Reducing bias in microbiome research: Comparing methods from sample collection to sequencing,Frontiers in microbiology,2023,"16S rRNA gene sequencing, gut, human studies, microbiome, microbiota, reproducible analysis",Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Sample collection protocol,EFO:0005518,Frozen Zymo control (-80-ZYCON),Room temperature zymo buffer (RT-ZYBUF),Zymo buffer at room temperature.,13,13,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Supplementary Fig 2a,4 April 2025,Shulamite,Shulamite,"LEfSe analysis showing the significantly distinguishing taxa between the different storage methods based on an LDA score >4.0. Showing the effect of storage at RT, with or without a stabilization buffer In green, compared to the control samples in red.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota",3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976,Complete,Svetlana up
bsdb:37065158/1/2,37065158,"cross-sectional observational, not case-control",37065158,doi.org/10.3389/fmicb.2023.1094800,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1094800/full#h3,"Kool J., Tymchenko L., Shetty S.A. , Fuentes S.",Reducing bias in microbiome research: Comparing methods from sample collection to sequencing,Frontiers in microbiology,2023,"16S rRNA gene sequencing, gut, human studies, microbiome, microbiota, reproducible analysis",Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Sample collection protocol,EFO:0005518,Frozen Zymo control (-80-ZYCON),Room temperature zymo buffer (RT-ZYBUF),Zymo buffer at room temperature.,13,13,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Supplementary Fig 2a,4 April 2025,Shulamite,Shulamite,"LEfSe analysis showing the significantly distinguishing taxa between the different storage methods based on an LDA score >4.0. Showing the effect of storage at RT, with or without a stabilization buffer in green, compared to the control samples in red.",decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia",1783272|201174;1783272|1239|186801|3085636|186803|572511;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998,Complete,Svetlana up
bsdb:37065158/2/1,37065158,"cross-sectional observational, not case-control",37065158,doi.org/10.3389/fmicb.2023.1094800,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1094800/full#h3,"Kool J., Tymchenko L., Shetty S.A. , Fuentes S.",Reducing bias in microbiome research: Comparing methods from sample collection to sequencing,Frontiers in microbiology,2023,"16S rRNA gene sequencing, gut, human studies, microbiome, microbiota, reproducible analysis",Experiment 2,Netherlands,Homo sapiens,Feces,UBERON:0001988,Sample collection protocol,EFO:0005518,Frozen Zymo control (-80-ZYCON),Zymo control at room temperature (RT-ZYCON),Sample storage at room temperature without buffer,13,13,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Supplementary Fig 2b,4 April 2025,Shulamite,Shulamite,"LEfSe analysis showing the significantly distinguishing taxa between the different storage methods based on an LDA score >4.0. Showing the effect of storage at RT, with or without a stabilization buffer in green, compared to the control samples in red.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236;3379134|1224;3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:37065158/2/2,37065158,"cross-sectional observational, not case-control",37065158,doi.org/10.3389/fmicb.2023.1094800,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1094800/full#h3,"Kool J., Tymchenko L., Shetty S.A. , Fuentes S.",Reducing bias in microbiome research: Comparing methods from sample collection to sequencing,Frontiers in microbiology,2023,"16S rRNA gene sequencing, gut, human studies, microbiome, microbiota, reproducible analysis",Experiment 2,Netherlands,Homo sapiens,Feces,UBERON:0001988,Sample collection protocol,EFO:0005518,Frozen Zymo control (-80-ZYCON),Zymo control at room temperature (RT-ZYCON),Sample storage at room temperature without buffer,13,13,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Supplementary Fig 2b,4 April 2025,Shulamite,Shulamite,"LEfSe analysis showing the significantly distinguishing taxa between the different storage methods based on an LDA score >4.0. Showing the effect of storage at RT, with or without a stabilization buffer in green, compared to the control samples in red.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;1783272|1239|91061|1385|90964|1279;1783272|1239;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:37065158/3/1,37065158,"cross-sectional observational, not case-control",37065158,doi.org/10.3389/fmicb.2023.1094800,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1094800/full#h3,"Kool J., Tymchenko L., Shetty S.A. , Fuentes S.",Reducing bias in microbiome research: Comparing methods from sample collection to sequencing,Frontiers in microbiology,2023,"16S rRNA gene sequencing, gut, human studies, microbiome, microbiota, reproducible analysis",Experiment 3,Netherlands,Homo sapiens,Feces,UBERON:0001988,Sample collection protocol,EFO:0005518,Zymo control at room temperature (RT-ZYCON),Zymo buffer at room temperature (RT-ZYBUF).,Zymo buffer at room temperature.,13,13,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Supplementary Fig 2c,4 April 2025,Shulamite,Shulamite,"LEfSe analysis showing the significantly distinguishing taxa between the different storage methods based on an LDA score >4.0. Showing the effect of storage at RT, with or without a stabilization buffer in green, compared to the control samples in red.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota",3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976;1783272|1239|186801;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239,Complete,Svetlana up
bsdb:37065158/3/2,37065158,"cross-sectional observational, not case-control",37065158,doi.org/10.3389/fmicb.2023.1094800,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1094800/full#h3,"Kool J., Tymchenko L., Shetty S.A. , Fuentes S.",Reducing bias in microbiome research: Comparing methods from sample collection to sequencing,Frontiers in microbiology,2023,"16S rRNA gene sequencing, gut, human studies, microbiome, microbiota, reproducible analysis",Experiment 3,Netherlands,Homo sapiens,Feces,UBERON:0001988,Sample collection protocol,EFO:0005518,Zymo control at room temperature (RT-ZYCON),Zymo buffer at room temperature (RT-ZYBUF).,Zymo buffer at room temperature.,13,13,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Supplementary Fig 2c,4 April 2025,Shulamite,Shulamite,"LEfSe analysis showing the significantly distinguishing taxa between the different storage methods based on an LDA score >4.0. Showing the effect of storage at RT, with or without a stabilization buffer in green, compared to the control samples in red.",decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",1783272|201174;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:37065158/4/1,37065158,"cross-sectional observational, not case-control",37065158,doi.org/10.3389/fmicb.2023.1094800,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1094800/full#h3,"Kool J., Tymchenko L., Shetty S.A. , Fuentes S.",Reducing bias in microbiome research: Comparing methods from sample collection to sequencing,Frontiers in microbiology,2023,"16S rRNA gene sequencing, gut, human studies, microbiome, microbiota, reproducible analysis",Experiment 4,Netherlands,Homo sapiens,Feces,UBERON:0001988,Sample collection protocol,EFO:0005518,Frozen OMNIgene GUT control (-80-OMCON),Room temperature OMNIgene GUT buffer (RT-OMBUF),OMNIgene·GUT tube with a stabilization buffer and stored at RT for 3–5 days before freezing at −80°C,65,65,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Supplementary Fig 2d,4 April 2025,Shulamite,Shulamite,"LEfSe analysis showing the significantly distinguishing taxa between the different storage methods based on an LDA score >4.0. Showing the effect of storage at RT, with or without a stabilization buffer in green, compared to the control samples in red.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus",3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976;3379134|976|200643|171549|815|909656|821,Complete,Svetlana up
bsdb:37065158/4/2,37065158,"cross-sectional observational, not case-control",37065158,doi.org/10.3389/fmicb.2023.1094800,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1094800/full#h3,"Kool J., Tymchenko L., Shetty S.A. , Fuentes S.",Reducing bias in microbiome research: Comparing methods from sample collection to sequencing,Frontiers in microbiology,2023,"16S rRNA gene sequencing, gut, human studies, microbiome, microbiota, reproducible analysis",Experiment 4,Netherlands,Homo sapiens,Feces,UBERON:0001988,Sample collection protocol,EFO:0005518,Frozen OMNIgene GUT control (-80-OMCON),Room temperature OMNIgene GUT buffer (RT-OMBUF),OMNIgene·GUT tube with a stabilization buffer and stored at RT for 3–5 days before freezing at −80°C,65,65,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Supplementary Fig 2d,4 April 2025,Shulamite,Shulamite,"LEfSe analysis showing the significantly distinguishing taxa between the different storage methods based on an LDA score >4.0. Showing the effect of storage at RT, with or without a stabilization buffer in green, compared to the control samples in red.",decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia",1783272|201174;1783272|1239;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;1783272|201174|84992,Complete,Svetlana up
bsdb:37065158/5/1,37065158,"cross-sectional observational, not case-control",37065158,doi.org/10.3389/fmicb.2023.1094800,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1094800/full#h3,"Kool J., Tymchenko L., Shetty S.A. , Fuentes S.",Reducing bias in microbiome research: Comparing methods from sample collection to sequencing,Frontiers in microbiology,2023,"16S rRNA gene sequencing, gut, human studies, microbiome, microbiota, reproducible analysis",Experiment 5,Netherlands,Homo sapiens,Feces,UBERON:0001988,Sample collection protocol,EFO:0005518,Frozen zymo control (-80-ZYCON),Room temperature zymo buffer (RT-ZYBUF),Zymo buffer at room temperature.,13,13,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Fig 3B,12 April 2025,Shulamite,Shulamite,Boxplots show the relative abundance of the five most abundant phyla. The difference between the storage conditions was tested with the Wilcoxon test.,increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota",3379134|976;3379134|1224,Complete,Svetlana up
bsdb:37065158/5/2,37065158,"cross-sectional observational, not case-control",37065158,doi.org/10.3389/fmicb.2023.1094800,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1094800/full#h3,"Kool J., Tymchenko L., Shetty S.A. , Fuentes S.",Reducing bias in microbiome research: Comparing methods from sample collection to sequencing,Frontiers in microbiology,2023,"16S rRNA gene sequencing, gut, human studies, microbiome, microbiota, reproducible analysis",Experiment 5,Netherlands,Homo sapiens,Feces,UBERON:0001988,Sample collection protocol,EFO:0005518,Frozen zymo control (-80-ZYCON),Room temperature zymo buffer (RT-ZYBUF),Zymo buffer at room temperature.,13,13,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Fig 3B,12 April 2025,Shulamite,Shulamite,Boxplots showing the relative abundance of the five top most abundant phyla.,decreased,k__Bacillati|p__Actinomycetota,1783272|201174,Complete,Svetlana up
bsdb:37065158/6/1,37065158,"cross-sectional observational, not case-control",37065158,doi.org/10.3389/fmicb.2023.1094800,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1094800/full#h3,"Kool J., Tymchenko L., Shetty S.A. , Fuentes S.",Reducing bias in microbiome research: Comparing methods from sample collection to sequencing,Frontiers in microbiology,2023,"16S rRNA gene sequencing, gut, human studies, microbiome, microbiota, reproducible analysis",Experiment 6,Netherlands,Homo sapiens,Feces,UBERON:0001988,Sample collection protocol,EFO:0005518,Frozen zymo control (-80-ZYCON),Room temperature zymo control (RT-ZYCON),Room temperature zymo control,13,13,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Fig 3B,12 April 2025,Shulamite,"Shulamite,KateRasheed",Boxplots show the relative abundance of the five top most abundant phyla.,increased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Verrucomicrobiota",3379134|1224;3379134|74201,Complete,Svetlana up
bsdb:37065158/6/2,37065158,"cross-sectional observational, not case-control",37065158,doi.org/10.3389/fmicb.2023.1094800,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1094800/full#h3,"Kool J., Tymchenko L., Shetty S.A. , Fuentes S.",Reducing bias in microbiome research: Comparing methods from sample collection to sequencing,Frontiers in microbiology,2023,"16S rRNA gene sequencing, gut, human studies, microbiome, microbiota, reproducible analysis",Experiment 6,Netherlands,Homo sapiens,Feces,UBERON:0001988,Sample collection protocol,EFO:0005518,Frozen zymo control (-80-ZYCON),Room temperature zymo control (RT-ZYCON),Room temperature zymo control,13,13,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Fig 3B,12 April 2025,Shulamite,Shulamite,Boxplots show the relative abundance of the five top most abundant phyla.,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Svetlana up
bsdb:37065158/7/1,37065158,"cross-sectional observational, not case-control",37065158,doi.org/10.3389/fmicb.2023.1094800,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1094800/full#h3,"Kool J., Tymchenko L., Shetty S.A. , Fuentes S.",Reducing bias in microbiome research: Comparing methods from sample collection to sequencing,Frontiers in microbiology,2023,"16S rRNA gene sequencing, gut, human studies, microbiome, microbiota, reproducible analysis",Experiment 7,Netherlands,Homo sapiens,Feces,UBERON:0001988,Sample collection protocol,EFO:0005518,Frozen OMNIgene·GUT control (-80-OMCON),Room temperature OMNIgene·GUTbuffer (RT-OMBUF),OMNIgene·GUT tube with a stabilization buffer and stored at RT for 3–5 days before freezing at −80°C,65,65,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,3,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Fig 3B,6 April 2025,Shulamite,Shulamite,"Bacterial composition at the phylum level, showing the relative abundance of the phyla.",increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota",3379134|976;3379134|1224,Complete,Svetlana up
bsdb:37065158/7/2,37065158,"cross-sectional observational, not case-control",37065158,doi.org/10.3389/fmicb.2023.1094800,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1094800/full#h3,"Kool J., Tymchenko L., Shetty S.A. , Fuentes S.",Reducing bias in microbiome research: Comparing methods from sample collection to sequencing,Frontiers in microbiology,2023,"16S rRNA gene sequencing, gut, human studies, microbiome, microbiota, reproducible analysis",Experiment 7,Netherlands,Homo sapiens,Feces,UBERON:0001988,Sample collection protocol,EFO:0005518,Frozen OMNIgene·GUT control (-80-OMCON),Room temperature OMNIgene·GUTbuffer (RT-OMBUF),OMNIgene·GUT tube with a stabilization buffer and stored at RT for 3–5 days before freezing at −80°C,65,65,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,3,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Fig 3B,6 April 2025,Shulamite,Shulamite,"Bacterial composition at the phylum level, showing the relative abundance of the phyla.",decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota",1783272|201174;1783272|1239,Complete,Svetlana up
bsdb:37065158/8/1,37065158,"cross-sectional observational, not case-control",37065158,doi.org/10.3389/fmicb.2023.1094800,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1094800/full#h3,"Kool J., Tymchenko L., Shetty S.A. , Fuentes S.",Reducing bias in microbiome research: Comparing methods from sample collection to sequencing,Frontiers in microbiology,2023,"16S rRNA gene sequencing, gut, human studies, microbiome, microbiota, reproducible analysis",Experiment 8,Netherlands,Homo sapiens,Feces,UBERON:0001988,Nucleic acid extraction protocol,NA,Mechanical disruption blood kit (MD-BK),Enzymatical disruption blood kit (ED-BK),Enzymatical disruption blood kit refers to enzymatical disruption (ED) that was purified with the Maxwell RSC Blood DNA kit (BK).,14,14,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Fig 8A,12 April 2025,Shulamite,Shulamite,Boxplots show the relative abundance of the top most abundant phyla. The Wilcoxon test was used to calculate the adjusted p-values of the differences between the DNA extraction methods.,increased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Svetlana up
bsdb:37065158/8/2,37065158,"cross-sectional observational, not case-control",37065158,doi.org/10.3389/fmicb.2023.1094800,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1094800/full#h3,"Kool J., Tymchenko L., Shetty S.A. , Fuentes S.",Reducing bias in microbiome research: Comparing methods from sample collection to sequencing,Frontiers in microbiology,2023,"16S rRNA gene sequencing, gut, human studies, microbiome, microbiota, reproducible analysis",Experiment 8,Netherlands,Homo sapiens,Feces,UBERON:0001988,Nucleic acid extraction protocol,NA,Mechanical disruption blood kit (MD-BK),Enzymatical disruption blood kit (ED-BK),Enzymatical disruption blood kit refers to enzymatical disruption (ED) that was purified with the Maxwell RSC Blood DNA kit (BK).,14,14,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Fig 8A,12 April 2025,Shulamite,Shulamite,Boxplots show the relative abundance of the top most abundant phyla. The Wilcoxon test was used to calculate the adjusted p-values of the differences between the DNA extraction methods.,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota",1783272|201174;1783272|1239,Complete,Svetlana up
bsdb:37065158/9/1,37065158,"cross-sectional observational, not case-control",37065158,doi.org/10.3389/fmicb.2023.1094800,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1094800/full#h3,"Kool J., Tymchenko L., Shetty S.A. , Fuentes S.",Reducing bias in microbiome research: Comparing methods from sample collection to sequencing,Frontiers in microbiology,2023,"16S rRNA gene sequencing, gut, human studies, microbiome, microbiota, reproducible analysis",Experiment 9,Netherlands,Homo sapiens,Feces,UBERON:0001988,Nucleic acid extraction protocol,NA,Mechanical disruption fecal kit (MD-FK),Enzymatical disruption fecal kit (ED-FK),Enzymatical disruption fecal kit refers to enzymatical disruption (ED) that was purified with the Maxwell RSC Fecal Microbiome DNA kit (FK).,14,14,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Fig 8A,12 April 2025,Shulamite,Shulamite,Boxplots show the relative abundance of the top most abundant phyla. The Wilcoxon test was used to calculate the adjusted p-values of the differences between the DNA extraction methods.,increased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Svetlana up
bsdb:37065158/9/2,37065158,"cross-sectional observational, not case-control",37065158,doi.org/10.3389/fmicb.2023.1094800,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1094800/full#h3,"Kool J., Tymchenko L., Shetty S.A. , Fuentes S.",Reducing bias in microbiome research: Comparing methods from sample collection to sequencing,Frontiers in microbiology,2023,"16S rRNA gene sequencing, gut, human studies, microbiome, microbiota, reproducible analysis",Experiment 9,Netherlands,Homo sapiens,Feces,UBERON:0001988,Nucleic acid extraction protocol,NA,Mechanical disruption fecal kit (MD-FK),Enzymatical disruption fecal kit (ED-FK),Enzymatical disruption fecal kit refers to enzymatical disruption (ED) that was purified with the Maxwell RSC Fecal Microbiome DNA kit (FK).,14,14,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Fig 8A,12 April 2025,Shulamite,Shulamite,Boxplots show the relative abundance of the top most abundant phyla. The Wilcoxon test was used to calculate the adjusted p-values of the differences between the DNA extraction methods.,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota",1783272|201174;1783272|1239,Complete,Svetlana up
bsdb:37065158/10/1,37065158,"cross-sectional observational, not case-control",37065158,doi.org/10.3389/fmicb.2023.1094800,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1094800/full#h3,"Kool J., Tymchenko L., Shetty S.A. , Fuentes S.",Reducing bias in microbiome research: Comparing methods from sample collection to sequencing,Frontiers in microbiology,2023,"16S rRNA gene sequencing, gut, human studies, microbiome, microbiota, reproducible analysis",Experiment 10,Netherlands,Homo sapiens,Feces,UBERON:0001988,Sample collection protocol,EFO:0005518,Frozen zymo control (-80-ZYCON),Room temperature zymo control (RT-ZYCON),Room temperature zymo control,13,13,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Supplementary fig 3A,12 April 2025,Shulamite,"Shulamite,KateRasheed",Boxplots of the relative abundance of Enterobacteriaceae in all conditions.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,Svetlana up
bsdb:37065158/11/1,37065158,"cross-sectional observational, not case-control",37065158,doi.org/10.3389/fmicb.2023.1094800,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1094800/full#h3,"Kool J., Tymchenko L., Shetty S.A. , Fuentes S.",Reducing bias in microbiome research: Comparing methods from sample collection to sequencing,Frontiers in microbiology,2023,"16S rRNA gene sequencing, gut, human studies, microbiome, microbiota, reproducible analysis",Experiment 11,Netherlands,Homo sapiens,Feces,UBERON:0001988,Sample collection protocol,EFO:0005518,Room temperature zymo control(RT-ZYCON),Room temperature zymo buffer (RT-ZYBUF),Room temperature zymo buffer,13,13,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Supplementary fig 3A,12 April 2025,Shulamite,"Shulamite,KateRasheed",Boxplots of the relative abundance of Enterobacteriaceae in all storage conditions.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,Svetlana up
bsdb:37077242/1/1,37077242,case-control,37077242,10.3389/fmicb.2023.1113174,https://pubmed.ncbi.nlm.nih.gov/37077242/,"Huang D., Wang J., Zeng Y., Li Q. , Wang Y.",Identifying microbial signatures for patients with postmenopausal osteoporosis using gut microbiota analyses and feature selection approaches,Frontiers in microbiology,2023,"bone mineral density, feature selection, gut microbiota, microbial biomarker, postmenopausal osteoporosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Postmenopausal osteoporosis,EFO:0003854,Healthy controls,Postmenopausal osteoporosis (PMOP) patients,Patients with Postmenopausal osteoporosis (PMOP),37,21,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,NA,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Table S2, Figure 1",20 December 2023,Aleru002,"Aleru002,Folakunmi,WikiWorks",Gut microbiota compositions between healthy controls and patients with postmenopausal osteoporosis (PMOP),increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium disporicum,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239|91061;1783272|1239|186801|186802|31979|1485|84024;1783272|1239|526524;3384189|32066|203490;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|526524|526525;1783272|1239|91061|186826|33958|2767887|1624;1783272|1239|186801|186802,Complete,Folakunmi
bsdb:37077242/1/2,37077242,case-control,37077242,10.3389/fmicb.2023.1113174,https://pubmed.ncbi.nlm.nih.gov/37077242/,"Huang D., Wang J., Zeng Y., Li Q. , Wang Y.",Identifying microbial signatures for patients with postmenopausal osteoporosis using gut microbiota analyses and feature selection approaches,Frontiers in microbiology,2023,"bone mineral density, feature selection, gut microbiota, microbial biomarker, postmenopausal osteoporosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Postmenopausal osteoporosis,EFO:0003854,Healthy controls,Postmenopausal osteoporosis (PMOP) patients,Patients with Postmenopausal osteoporosis (PMOP),37,21,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,NA,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table S2,20 December 2023,Aleru002,"Aleru002,Folakunmi,WikiWorks",Gut microbiota compositions and statistical results between healthy controls and patients with postmenopausal osteoporosis (PMOP),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|976|200643|171549|815|816|28111;1783272|1239|186801|186802|216572,Complete,Folakunmi
bsdb:37089564/1/1,37089564,case-control,37089564,10.3389/fmicb.2023.1069325,NA,"Zhang Y., Wang T., Wan Z., Bai J., Xue Y., Dai R., Wang M. , Peng Q.",Alterations of the intestinal microbiota in age-related macular degeneration,Frontiers in microbiology,2023,"age-related macular degeneration, gut-retina axis, intestinal microbiota, metabolic pathway, microbial diversity",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Age-related macular degeneration,EFO:0001365,Control,AMD (Age-related macular degeneration),Patients diagnosed with age-related macular degeneration,17,30,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure 3A, B",24 July 2025,Anne-mariesharp,Anne-mariesharp,Fecal microbiota profile in the both groups at different taxonomic levels,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|186801|186802|216572|39492;1783272|1239|909932;3379134|1224;3379134|1224|1236;3379134|976;3379134|976|200643;3379134|976|200643|171549;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816,Complete,KateRasheed
bsdb:37089564/1/2,37089564,case-control,37089564,10.3389/fmicb.2023.1069325,NA,"Zhang Y., Wang T., Wan Z., Bai J., Xue Y., Dai R., Wang M. , Peng Q.",Alterations of the intestinal microbiota in age-related macular degeneration,Frontiers in microbiology,2023,"age-related macular degeneration, gut-retina axis, intestinal microbiota, metabolic pathway, microbial diversity",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Age-related macular degeneration,EFO:0001365,Control,AMD (Age-related macular degeneration),Patients diagnosed with age-related macular degeneration,17,30,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 3A, B",24 July 2025,Anne-mariesharp,Anne-mariesharp,Fecal microbiota profile in the both groups at different taxonomic levels,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales",1783272|1239|186801|3085636|186803|207244;1783272|1239;1783272|1239|186801|3085636|186803|572511;95818|2093818|2093825|2171986;1783272|1239|186801;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636,Complete,KateRasheed
bsdb:37089564/2/1,37089564,case-control,37089564,10.3389/fmicb.2023.1069325,NA,"Zhang Y., Wang T., Wan Z., Bai J., Xue Y., Dai R., Wang M. , Peng Q.",Alterations of the intestinal microbiota in age-related macular degeneration,Frontiers in microbiology,2023,"age-related macular degeneration, gut-retina axis, intestinal microbiota, metabolic pathway, microbial diversity",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Age-related macular degeneration,EFO:0001365,Enterotype 2 (enriched in healthy controls),Enterotype 1 (enriched in AMD patients),Individuals clustered into enterotype 1 based on genus-level gut microbiome profiles using PAM(Partitioning Around Medoids) clustering with Jensen-Shannon distance. This group was predominantly composed of AMD patients and showed higher relative abundance of Escherichia-Shigella.,NA,NA,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4C,24 July 2025,Anne-mariesharp,Anne-mariesharp,Comparison between the two enterotypes at the genus level.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",3379134|1224|1236|91347|543|1940338;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|81852|1350,Complete,KateRasheed
bsdb:37089564/2/2,37089564,case-control,37089564,10.3389/fmicb.2023.1069325,NA,"Zhang Y., Wang T., Wan Z., Bai J., Xue Y., Dai R., Wang M. , Peng Q.",Alterations of the intestinal microbiota in age-related macular degeneration,Frontiers in microbiology,2023,"age-related macular degeneration, gut-retina axis, intestinal microbiota, metabolic pathway, microbial diversity",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Age-related macular degeneration,EFO:0001365,Enterotype 2 (enriched in healthy controls),Enterotype 1 (enriched in AMD patients),Individuals clustered into enterotype 1 based on genus-level gut microbiome profiles using PAM(Partitioning Around Medoids) clustering with Jensen-Shannon distance. This group was predominantly composed of AMD patients and showed higher relative abundance of Escherichia-Shigella.,NA,NA,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4C,24 July 2025,Anne-mariesharp,Anne-mariesharp,Comparison between the two enterotypes at the genus level.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|572511;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803,Complete,KateRasheed
bsdb:37091735/1/1,37091735,prospective cohort,37091735,10.1099/acmi.0.000497.v3,NA,"Campos M., Cickovski T., Fernandez M., Jaric M., Wanner A., Holt G., Donna E., Mendes E., Silva-Herzog E., Schneper L., Segal J., Amador D.M., Riveros J.D., Aguiar-Pulido V., Banerjee S., Salathe M., Mathee K. , Narasimhan G.",Lower respiratory tract microbiome composition and community interactions in smokers,Access microbiology,2023,"clustering, co-occurrence networks, lower respiratory tract (LRT), microbiome, smoking",Experiment 1,United States of America,Homo sapiens,Lung,UBERON:0002048,Smoking status measurement,EFO:0006527,Never smokers,Active smokers,Participants who have smoked at least one cigarette within 3days of enrolment,9,22,3 months,16S,678,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,Signature 1,table 3,8 October 2023,OdigiriGreat,"OdigiriGreat,Folakunmi,WikiWorks",Genera that were found to be differentially more abundant in Never smokers vs Active smokers using  DESeq2.,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3384189|32066|203490|203491|203492|848;3379134|1224|1236|135625|712|724;3379134|1224|28211|356|119045|407;1783272|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:37091735/1/2,37091735,prospective cohort,37091735,10.1099/acmi.0.000497.v3,NA,"Campos M., Cickovski T., Fernandez M., Jaric M., Wanner A., Holt G., Donna E., Mendes E., Silva-Herzog E., Schneper L., Segal J., Amador D.M., Riveros J.D., Aguiar-Pulido V., Banerjee S., Salathe M., Mathee K. , Narasimhan G.",Lower respiratory tract microbiome composition and community interactions in smokers,Access microbiology,2023,"clustering, co-occurrence networks, lower respiratory tract (LRT), microbiome, smoking",Experiment 1,United States of America,Homo sapiens,Lung,UBERON:0002048,Smoking status measurement,EFO:0006527,Never smokers,Active smokers,Participants who have smoked at least one cigarette within 3days of enrolment,9,22,3 months,16S,678,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,Signature 2,table 3,8 October 2023,OdigiriGreat,"OdigiriGreat,Folakunmi,WikiWorks",Genera that were found to be differentially more abundant in Never smokers vs Active smokers using  DESeq2.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia sp. 1-6,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",3379134|1224|28216|80840|119060|32008|36773;3379134|1224|28216|80840|119060|48736|1221567;3379134|1224|28216|80840|2975441|335058;3379134|1224|1236|135614|32033|40323,Complete,Folakunmi
bsdb:37091735/2/1,37091735,prospective cohort,37091735,10.1099/acmi.0.000497.v3,NA,"Campos M., Cickovski T., Fernandez M., Jaric M., Wanner A., Holt G., Donna E., Mendes E., Silva-Herzog E., Schneper L., Segal J., Amador D.M., Riveros J.D., Aguiar-Pulido V., Banerjee S., Salathe M., Mathee K. , Narasimhan G.",Lower respiratory tract microbiome composition and community interactions in smokers,Access microbiology,2023,"clustering, co-occurrence networks, lower respiratory tract (LRT), microbiome, smoking",Experiment 2,United States of America,Homo sapiens,Lung,UBERON:0002048,Smoking status measurement,EFO:0006527,Never smokers,former smokers,Participants who have stopped smoking,9,24,3 months,16S,678,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,Signature 1,table 3,9 October 2023,OdigiriGreat,"OdigiriGreat,Folakunmi,WikiWorks",Genera that were found to be differentially more abundant in Never smokers vs former smokers using  DESeq2.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia sp. 1-6,3379134|1224|28216|80840|119060|48736|1221567,Complete,Folakunmi
bsdb:37091735/2/2,37091735,prospective cohort,37091735,10.1099/acmi.0.000497.v3,NA,"Campos M., Cickovski T., Fernandez M., Jaric M., Wanner A., Holt G., Donna E., Mendes E., Silva-Herzog E., Schneper L., Segal J., Amador D.M., Riveros J.D., Aguiar-Pulido V., Banerjee S., Salathe M., Mathee K. , Narasimhan G.",Lower respiratory tract microbiome composition and community interactions in smokers,Access microbiology,2023,"clustering, co-occurrence networks, lower respiratory tract (LRT), microbiome, smoking",Experiment 2,United States of America,Homo sapiens,Lung,UBERON:0002048,Smoking status measurement,EFO:0006527,Never smokers,former smokers,Participants who have stopped smoking,9,24,3 months,16S,678,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,Signature 2,table 3,9 October 2023,OdigiriGreat,"OdigiriGreat,Folakunmi,WikiWorks",Genera that were found to be differentially more abundant in Never smokers vs former smokers using  DESeq2.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.",3379134|1224|28216|80840|119060|47670;3384189|32066|203490|203491|1129771|32067;3379134|976|200643|171549|171552|838|59823,Complete,Folakunmi
bsdb:37091735/3/1,37091735,prospective cohort,37091735,10.1099/acmi.0.000497.v3,NA,"Campos M., Cickovski T., Fernandez M., Jaric M., Wanner A., Holt G., Donna E., Mendes E., Silva-Herzog E., Schneper L., Segal J., Amador D.M., Riveros J.D., Aguiar-Pulido V., Banerjee S., Salathe M., Mathee K. , Narasimhan G.",Lower respiratory tract microbiome composition and community interactions in smokers,Access microbiology,2023,"clustering, co-occurrence networks, lower respiratory tract (LRT), microbiome, smoking",Experiment 3,United States of America,Homo sapiens,Lung,UBERON:0002048,Smoking status measurement,EFO:0006527,former smokers,active smokers,Participants who have smoked at least one cigarette within 3days of enrolment,24,22,3 months,16S,678,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,Signature 1,table 3,9 October 2023,OdigiriGreat,"OdigiriGreat,Folakunmi,WikiWorks",Genera that were found to be differentially more abundant in former smokers vs Active smokers using  DESeq2.,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",3384189|32066|203490|203491|203492|848;3379134|1224|28216|206351|481|482,Complete,Folakunmi
bsdb:37091735/3/2,37091735,prospective cohort,37091735,10.1099/acmi.0.000497.v3,NA,"Campos M., Cickovski T., Fernandez M., Jaric M., Wanner A., Holt G., Donna E., Mendes E., Silva-Herzog E., Schneper L., Segal J., Amador D.M., Riveros J.D., Aguiar-Pulido V., Banerjee S., Salathe M., Mathee K. , Narasimhan G.",Lower respiratory tract microbiome composition and community interactions in smokers,Access microbiology,2023,"clustering, co-occurrence networks, lower respiratory tract (LRT), microbiome, smoking",Experiment 3,United States of America,Homo sapiens,Lung,UBERON:0002048,Smoking status measurement,EFO:0006527,former smokers,active smokers,Participants who have smoked at least one cigarette within 3days of enrolment,24,22,3 months,16S,678,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,Signature 2,table 3,9 October 2023,OdigiriGreat,"OdigiriGreat,Folakunmi,WikiWorks",Genera that were found to be differentially more abundant in former smokers vs active smokers using  DESeq2.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum",3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|1213720,Complete,Folakunmi
bsdb:37091735/4/1,37091735,prospective cohort,37091735,10.1099/acmi.0.000497.v3,NA,"Campos M., Cickovski T., Fernandez M., Jaric M., Wanner A., Holt G., Donna E., Mendes E., Silva-Herzog E., Schneper L., Segal J., Amador D.M., Riveros J.D., Aguiar-Pulido V., Banerjee S., Salathe M., Mathee K. , Narasimhan G.",Lower respiratory tract microbiome composition and community interactions in smokers,Access microbiology,2023,"clustering, co-occurrence networks, lower respiratory tract (LRT), microbiome, smoking",Experiment 4,United States of America,Homo sapiens,Lung,UBERON:0002048,Smoking status measurement,EFO:0006527,Active smokers & former smokers,Never smokers,Participants who have never smoked,46,9,3 months,16S,678,Roche454,relative abundances,LEfSe,0.05,TRUE,2.5,NA,NA,NA,NA,decreased,NA,decreased,NA,Signature 1,Fig 5,9 October 2023,OdigiriGreat,"OdigiriGreat,Folakunmi,WikiWorks",Genera that were found to be differentially more abundant in Active smokers and former smokers vs Never smokers using  LEFse.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|1224|28211;1783272|1239;3379134|976|200643|171549;3379134|976|200643;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|186806|1730;3379134|1224|1236|135625|712|724;3379134|1224|28211|356;3379134|1224|28216|80840|119060|47670;1783272|1239|909932|1843489|31977|906;3379134|1224|28211|356|119045;3379134|1224|28211|356|119045|407;1783272|1239|186801|3082720|543314|86331;1783272|1239|909932;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|909932|909929;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977,Complete,Folakunmi
bsdb:37091735/5/1,37091735,prospective cohort,37091735,10.1099/acmi.0.000497.v3,NA,"Campos M., Cickovski T., Fernandez M., Jaric M., Wanner A., Holt G., Donna E., Mendes E., Silva-Herzog E., Schneper L., Segal J., Amador D.M., Riveros J.D., Aguiar-Pulido V., Banerjee S., Salathe M., Mathee K. , Narasimhan G.",Lower respiratory tract microbiome composition and community interactions in smokers,Access microbiology,2023,"clustering, co-occurrence networks, lower respiratory tract (LRT), microbiome, smoking",Experiment 5,United States of America,Homo sapiens,Lung,UBERON:0002048,Smoking status measurement,EFO:0006527,never smokers & former smokers,Active smokers,Participants who have smoked at least one cigarette within 3days of enrolment,33,22,3 months,16S,678,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,Signature 1,table 3,9 October 2023,OdigiriGreat,"OdigiriGreat,WikiWorks",Genera that were found to be differentially more abundant in Never smokers and former smokers vs Active smokers using  DESeq2.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,3379134|1224|28216|80840|80864|80865,Complete,Folakunmi
bsdb:37091735/6/1,37091735,prospective cohort,37091735,10.1099/acmi.0.000497.v3,NA,"Campos M., Cickovski T., Fernandez M., Jaric M., Wanner A., Holt G., Donna E., Mendes E., Silva-Herzog E., Schneper L., Segal J., Amador D.M., Riveros J.D., Aguiar-Pulido V., Banerjee S., Salathe M., Mathee K. , Narasimhan G.",Lower respiratory tract microbiome composition and community interactions in smokers,Access microbiology,2023,"clustering, co-occurrence networks, lower respiratory tract (LRT), microbiome, smoking",Experiment 6,United States of America,Homo sapiens,Lung,UBERON:0002048,Smoking status measurement,EFO:0006527,Active smokers & former smokers,Never smokers,Participants who have smoked at least one cigarette within 3days of enrolment,46,9,3 months,16S,678,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,increased,NA,increased,NA,Signature 1,table 3,16 February 2024,Folakunmi,"Folakunmi,WikiWorks",Genera that were found to be differentially more abundant in Active  smokers and former smokers vs Never smokers using DESeq2.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,3379134|976|200643|171549|171552|838|59823,Complete,Folakunmi
bsdb:37091735/7/1,37091735,prospective cohort,37091735,10.1099/acmi.0.000497.v3,NA,"Campos M., Cickovski T., Fernandez M., Jaric M., Wanner A., Holt G., Donna E., Mendes E., Silva-Herzog E., Schneper L., Segal J., Amador D.M., Riveros J.D., Aguiar-Pulido V., Banerjee S., Salathe M., Mathee K. , Narasimhan G.",Lower respiratory tract microbiome composition and community interactions in smokers,Access microbiology,2023,"clustering, co-occurrence networks, lower respiratory tract (LRT), microbiome, smoking",Experiment 7,United States of America,Homo sapiens,Lung,UBERON:0002048,Smoking status measurement,EFO:0006527,Active smokers & former smokers,never smokers,Participants who have never smoked,46,9,3 months,16S,678,Roche454,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,increased,NA,increased,NA,Signature 1,table 3,16 February 2024,Folakunmi,"Folakunmi,WikiWorks",Genera that were found to be differentially more abundant in Active smokers and former smokers vs Never smokers using DESeq2.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,3379134|976|200643|171549|171552|838|59823,Complete,Folakunmi
bsdb:37119437/1/1,37119437,prospective cohort,37119437,10.1002/advs.202205058,https://pmc.ncbi.nlm.nih.gov/articles/PMC10323652/,"Hu X., Wang H., Yu B., Yu J., Lu H., Sun J., Sun Y., Zou Y., Luo H., Zeng Z., Liu S., Jiang Y., Wu Z. , Ren Z.",Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2023,"coronavirus disease 2019, mycobiome, non-invasive biomarkers, oral fungi, severe acute respiratory syndrome coronavirus 2",Experiment 1,China,Homo sapiens,Surface of tongue,UBERON:0007367,COVID-19,MONDO:0100096,Covid-19 and Post Covid-19 Groups,Healthy Controls Group,Participants in this group were 132 age- and sex-matched healthy individuals (controls),93,132,2 months,ITS / ITS2,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4g,19 April 2024,Victoria,"Victoria,Aleru Divine,WikiWorks","This figure shows the predominant oral fungal among the COVID-19, Post-COVID-19, and control groups.",increased,"k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Chaetosphaeriales|f__Chaetosphaeriaceae|g__Zanclospora|s__Zanclospora jonesii,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Chaetosphaeriales|f__Chaetosphaeriaceae|g__Zanclospora,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Cryptococcaceae|g__Cryptococcus,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae|g__Vanrija|s__Vanrija longa,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Erysiphales|f__Erysiphaceae|g__Blumeria,k__Fungi|p__Mucoromycota|c__Glomeromycetes|o__Diversisporales|f__Diversisporaceae|g__Diversispora|s__Diversispora spurca,k__Fungi|p__Mucoromycota|c__Glomeromycetes|o__Diversisporales|f__Diversisporaceae|g__Diversispora,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Eremomycetales|f__Eremomycetaceae|g__Arthrographis,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Eremomycetales|f__Eremomycetaceae|g__Arthrographis|s__Arthrographis grakistii,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Raffaelea,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Harringtonia|s__Harringtonia lauricola,k__Fungi|p__Ascomycota|g__Milospium|s__Milospium graphideorum,k__Fungi|p__Ascomycota|g__Milospium,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Cladosporium|s__Cladosporium kenpeggii,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Trichocomaceae|g__Talaromyces,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales|f__Russulaceae|g__Russula,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales|f__Russulaceae|g__Russula|s__Russula xerophila,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Diaporthales|f__Diaporthaceae|g__Diaporthe,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida parapsilosis,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus amstelodami,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Ophiostoma",4751|4890|147550|261460|103886|1323519|2040582;4751|4890|147550|261460|103886|1323519;4751|5204|155616|5234|1884633|5206;4751|5204|155616|1851469|1759442|1851468|181171;4751|4890|147548|5120|34371|34372;4751|1913637|214506|214509|308925|308926|308927;4751|1913637|214506|214509|308925|308926;4751|4890|147541|2714147|241722|241727;4751|4890|147541|2714147|241722|241727|2682943;4751|4890|147550|5151|5152|45340;4751|4890|147550|5151|5152|2933754|483707;4751|4890|1666919|1664392;4751|4890|1666919;4751|5204|1538075|162474|742845|55193|76775;4751|4890|147541|2726946|452563|5498|2016221;4751|4890|147545|5042|28568|5094;4751|5204|155619|452342|5401|5402;4751|5204|155619|452342|5401|5402|278596;4751|4890|147550|5114|767018|36922;4751|4890|3239874|2916678|766764|5475|5480;4751|4890|147545|5042|1131492|5052|5054;4751|4890|147550|5151|5152|5159,Complete,Svetlana up
bsdb:37119437/2/1,37119437,prospective cohort,37119437,10.1002/advs.202205058,https://pmc.ncbi.nlm.nih.gov/articles/PMC10323652/,"Hu X., Wang H., Yu B., Yu J., Lu H., Sun J., Sun Y., Zou Y., Luo H., Zeng Z., Liu S., Jiang Y., Wu Z. , Ren Z.",Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2023,"coronavirus disease 2019, mycobiome, non-invasive biomarkers, oral fungi, severe acute respiratory syndrome coronavirus 2",Experiment 2,China,Homo sapiens,Surface of tongue,UBERON:0007367,COVID-19,MONDO:0100096,Healthy Controls and Post-Covid-19 Groups,Covid-19 Group,Participants in this group were COVID-19 patients.,154,71,2 months,ITS / ITS2,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4g,19 April 2024,Victoria,"Victoria,Aleru Divine,WikiWorks","This figure shows the predominant oral fungal among the COVID-19, Post-COVID-19, and control groups.",increased,"k__Fungi|p__Ascomycota|c__Sordariomycetes|g__Acrodictys,k__Fungi|p__Ascomycota|c__Sordariomycetes|g__Acrodictys|s__Acrodictys fluminicola,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus subflavus,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Chrysosphaeria|s__Chrysosphaeria jannelii,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Chrysosphaeria,k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Pezizaceae|g__Hydnobolites,k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Pezizaceae|g__Hydnobolites|s__Hydnobolites roseus,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Amorosiaceae|g__Angustimassarina|s__Angustimassarina camporesii,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Cordycipitaceae|g__Simplicillium|s__Simplicillium sympodiophorum,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Cordycipitaceae|g__Simplicillium,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Amorosiaceae|g__Angustimassarina,k__Fungi|c__Entorrhizomycetes|o__Entorrhizales|f__Entorrhizaceae|g__Entorrhiza,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Coronophorales|f__Scortechiniaceae|g__Parasympodiella|s__Parasympodiella longispora,k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Tuberaceae|g__Tuber|s__Tuber alcaracense,k__Fungi|p__Ascomycota|c__Sordariomycetes|g__Fantasmomyces|s__Fantasmomyces hyalinus,k__Fungi|p__Ascomycota|c__Sordariomycetes|g__Fantasmomyces,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Coronophorales|f__Scortechiniaceae|g__Parasympodiella,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Fuscosporellales|f__Fuscosporellaceae|g__Parafuscosporella,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Filobasidiales|f__Filobasidiaceae|s__[Cryptococcus] ater,k__Fungi|p__Ascomycota|g__Vanakripa|s__Vanakripa mucosa,k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Tuberaceae|g__Tuber,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces",4751|4890|147550|1827388;4751|4890|147550|1827388|2571388;4751|4890|147545|5042|1131492|5052|2175223;4751|4890|147550|5151|5152|2875642|2745882;4751|4890|147550|5151|5152|2875642;4751|4890|147549|5185|5186|405928;4751|4890|147549|5185|5186|405928|2489165;4751|4890|4891|4892|4893|4930|4932;4751|4890|147541|92860|1859218|1762950|2599739;4751|4890|147550|5125|474943|292631|935215;4751|4890|147550|5125|474943|292631;4751|4890|147541|92860|1859218|1762950;4751|62907|62910|62911|63255;4751|4890|147550|252166|307582|673167|756022;4751|4890|147549|5185|40289|36048|2698902;4751|4890|147550|1932873|1925498;4751|4890|147550|1932873;4751|4890|147550|252166|307582|673167;4751|4890|147550|1963390|1963370|1963373;4751|5204|155616|90886|5408|104670;4751|4890|2081268|1963375;4751|4890|147549|5185|40289|36048;4751|4890|4891|4892|4893|4930,Complete,Svetlana up
bsdb:37119437/3/1,37119437,prospective cohort,37119437,10.1002/advs.202205058,https://pmc.ncbi.nlm.nih.gov/articles/PMC10323652/,"Hu X., Wang H., Yu B., Yu J., Lu H., Sun J., Sun Y., Zou Y., Luo H., Zeng Z., Liu S., Jiang Y., Wu Z. , Ren Z.",Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2023,"coronavirus disease 2019, mycobiome, non-invasive biomarkers, oral fungi, severe acute respiratory syndrome coronavirus 2",Experiment 3,China,Homo sapiens,Surface of tongue,UBERON:0007367,COVID-19,MONDO:0100096,Healthy Controls and Covid-19 Groups,Post-Covid-19 Group,This group consists of 22 patients who have recovered from Covid-19.,203,22,2 months,ITS / ITS2,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4g,24 April 2024,Victoria,"Victoria,WikiWorks","This figure shows the predominant oral fungal among the COVID-19, Post-COVID-19, and control groups.",increased,"k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Actinomucor,k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Actinomucor|s__Actinomucor elegans,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus penicillioides,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus versicolor,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Botryosphaeriales|f__Botryosphaeriaceae|g__Botryosphaeria,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Dipodascaceae|g__Dipodascus,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Dipodascaceae|g__Geotrichum,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Dipodascaceae|g__Geotrichum|s__Geotrichum pseudocandidum,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Dipodascaceae|g__Geotrichum|s__Geotrichum candidum,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Mucor,k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Mucor|s__Mucor circinelloides,k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Mucor|s__Mucor pseudolusitanicus,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Rhodotorula,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Rhodotorula|s__Rhodotorula mucilaginosa,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Trichocomaceae|g__Talaromyces|s__Talaromyces scorteus,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Udeniomyces,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Udeniomyces|s__Udeniomyces megalosporus,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Udeniomyces|s__Udeniomyces pyricola",4751|1913637|2212703|4827|34489|64644;4751|1913637|2212703|4827|34489|64644|64647;4751|4890|147545|5042|1131492|5052|41959;4751|4890|147545|5042|1131492|5052|46472;4751|4890|147541|451869|45131|45132;4751|4890|3239874|2916678|766764|5475;4751|4890|3239874|2916678|766764|5475|5476;4751|4890|3239873|3243772|34353|27314;4751|4890|3239873|3243772|34353|27316;4751|4890|3239873|3243772|34353|43987|1206149;4751|4890|3239873|3243772|34353|43987|1173061;4751|5204|1538075|162474|742845|55193;4751|1913637|2212703|4827|34489|4830;4751|1913637|2212703|4827|34489|4830|36080;4751|1913637|2212703|4827|34489|4830|2021227;4751|5204|162481|231213|1799696|5533;4751|5204|162481|231213|1799696|5533|5537;4751|4890|147545|5042|28568|5094|1400007;4751|5204|155616|90883|1851551|42658;4751|5204|155616|90883|1851551|42658|42659;4751|5204|155616|90883|1851551|42658|42661,Complete,Svetlana up
bsdb:37119437/4/1,37119437,prospective cohort,37119437,10.1002/advs.202205058,https://pmc.ncbi.nlm.nih.gov/articles/PMC10323652/,"Hu X., Wang H., Yu B., Yu J., Lu H., Sun J., Sun Y., Zou Y., Luo H., Zeng Z., Liu S., Jiang Y., Wu Z. , Ren Z.",Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2023,"coronavirus disease 2019, mycobiome, non-invasive biomarkers, oral fungi, severe acute respiratory syndrome coronavirus 2",Experiment 4,China,Homo sapiens,Surface of tongue,UBERON:0007367,COVID-19,MONDO:0100096,Control group,Covid-19-N group,This group consists of 56 Covid-19 patients without comorbidities.,132,56,2 months,ITS / ITS2,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,3,"age,sex",NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Supplemental Figure S4,3 June 2024,Victoria,"Victoria,WikiWorks","The 10 most abundant fungi among the differential fungi among the three groups
at the genus and species levels.",increased,"k__Fungi|p__Ascomycota|c__Sordariomycetes|g__Acrodictys,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida,k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Pezizaceae|g__Hydnobolites,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Raffaelea,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Harringtonia|s__Harringtonia lauricola,k__Fungi|p__Ascomycota|c__Sordariomycetes|g__Acrodictys|s__Acrodictys fluminicola,k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Pezizaceae|g__Hydnobolites|s__Hydnobolites roseus,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans",4751|4890|147550|1827388;4751|4890|3239874|2916678|766764|5475;4751|4890|147549|5185|5186|405928;4751|4890|147550|5151|5152|45340;4751|4890|147550|5151|5152|2933754|483707;4751|4890|147550|1827388|2571388;4751|4890|147549|5185|5186|405928|2489165;4751|4890|3239874|2916678|766764|5475|5476,Complete,Svetlana up
bsdb:37119437/4/2,37119437,prospective cohort,37119437,10.1002/advs.202205058,https://pmc.ncbi.nlm.nih.gov/articles/PMC10323652/,"Hu X., Wang H., Yu B., Yu J., Lu H., Sun J., Sun Y., Zou Y., Luo H., Zeng Z., Liu S., Jiang Y., Wu Z. , Ren Z.",Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2023,"coronavirus disease 2019, mycobiome, non-invasive biomarkers, oral fungi, severe acute respiratory syndrome coronavirus 2",Experiment 4,China,Homo sapiens,Surface of tongue,UBERON:0007367,COVID-19,MONDO:0100096,Control group,Covid-19-N group,This group consists of 56 Covid-19 patients without comorbidities.,132,56,2 months,ITS / ITS2,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,3,"age,sex",NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Supplemental Figure S4,3 June 2024,Victoria,"Victoria,WikiWorks","The 10 most abundant fungi among the differential fungi among the three groups
at the genus and species levels",decreased,"k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Chaetosphaeriales|f__Chaetosphaeriaceae|g__Zanclospora,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Erysiphales|f__Erysiphaceae|g__Blumeria,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Cryptococcaceae|g__Cryptococcus,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Cladosporium,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,k__Fungi|p__Mucoromycota|c__Glomeromycetes|o__Diversisporales|f__Diversisporaceae|g__Diversispora,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Chaetosphaeriales|f__Chaetosphaeriaceae|g__Zanclospora|s__Zanclospora jonesii,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae|g__Vanrija|s__Vanrija longa,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Fungi|p__Mucoromycota|c__Glomeromycetes|o__Diversisporales|f__Diversisporaceae|g__Diversispora|s__Diversispora spurca,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Cladosporium|s__Cladosporium kenpeggii",4751|4890|147550|261460|103886|1323519;4751|4890|147548|5120|34371|34372;4751|5204|155616|5234|1884633|5206;4751|4890|147541|2726946|452563|5498;4751|5204|1538075|162474|742845|55193;4751|1913637|214506|214509|308925|308926;4751|4890|147550|261460|103886|1323519|2040582;4751|5204|155616|1851469|1759442|1851468|181171;4751|5204|1538075|162474|742845|55193|76775;4751|1913637|214506|214509|308925|308926|308927;4751|4890|147541|2726946|452563|5498|2016221,Complete,Svetlana up
bsdb:37119437/5/1,37119437,prospective cohort,37119437,10.1002/advs.202205058,https://pmc.ncbi.nlm.nih.gov/articles/PMC10323652/,"Hu X., Wang H., Yu B., Yu J., Lu H., Sun J., Sun Y., Zou Y., Luo H., Zeng Z., Liu S., Jiang Y., Wu Z. , Ren Z.",Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2023,"coronavirus disease 2019, mycobiome, non-invasive biomarkers, oral fungi, severe acute respiratory syndrome coronavirus 2",Experiment 5,China,Homo sapiens,Surface of tongue,UBERON:0007367,COVID-19,MONDO:0100096,Control group,Covid-19-C group,This group consists of 15 Covid-19 patients with comorbidities.,132,15,2 months,ITS / ITS2,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,3,"age,sex",NA,NA,increased,NA,NA,NA,increased,Signature 1,Supplemental Figure S4,3 June 2024,Victoria,"Victoria,WikiWorks","The 10 most abundant fungi among the differential fungi among the three groups
at the genus and species levels.",increased,"k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Raffaelea,k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Pezizaceae|g__Hydnobolites,k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Pezizaceae|g__Hydnobolites|s__Hydnobolites roseus",4751|4890|3239874|2916678|766764|5475|5476;4751|4890|3239874|2916678|766764|5475;4751|4890|147550|5151|5152|45340;4751|4890|147549|5185|5186|405928;4751|4890|147549|5185|5186|405928|2489165,Complete,Svetlana up
bsdb:37119437/5/2,37119437,prospective cohort,37119437,10.1002/advs.202205058,https://pmc.ncbi.nlm.nih.gov/articles/PMC10323652/,"Hu X., Wang H., Yu B., Yu J., Lu H., Sun J., Sun Y., Zou Y., Luo H., Zeng Z., Liu S., Jiang Y., Wu Z. , Ren Z.",Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2023,"coronavirus disease 2019, mycobiome, non-invasive biomarkers, oral fungi, severe acute respiratory syndrome coronavirus 2",Experiment 5,China,Homo sapiens,Surface of tongue,UBERON:0007367,COVID-19,MONDO:0100096,Control group,Covid-19-C group,This group consists of 15 Covid-19 patients with comorbidities.,132,15,2 months,ITS / ITS2,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,3,"age,sex",NA,NA,increased,NA,NA,NA,increased,Signature 2,Supplemental Figure S4,3 June 2024,Victoria,"Victoria,WikiWorks","The 10 most abundant fungi among the differential fungi among the three groups
at the genus and species levels.",decreased,"k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Chaetosphaeriales|f__Chaetosphaeriaceae|g__Zanclospora,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Cryptococcaceae|g__Cryptococcus,k__Fungi|p__Mucoromycota|c__Glomeromycetes|o__Diversisporales|f__Diversisporaceae|g__Diversispora,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Chaetosphaeriales|f__Chaetosphaeriaceae|g__Zanclospora|s__Zanclospora jonesii,k__Fungi|p__Mucoromycota|c__Glomeromycetes|o__Diversisporales|f__Diversisporaceae|g__Diversispora|s__Diversispora spurca,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae|g__Vanrija|s__Vanrija longa",4751|4890|147550|261460|103886|1323519;4751|5204|155616|5234|1884633|5206;4751|1913637|214506|214509|308925|308926;4751|4890|147550|261460|103886|1323519|2040582;4751|1913637|214506|214509|308925|308926|308927;4751|5204|155616|1851469|1759442|1851468|181171,Complete,Svetlana up
bsdb:37119437/6/1,37119437,prospective cohort,37119437,10.1002/advs.202205058,https://pmc.ncbi.nlm.nih.gov/articles/PMC10323652/,"Hu X., Wang H., Yu B., Yu J., Lu H., Sun J., Sun Y., Zou Y., Luo H., Zeng Z., Liu S., Jiang Y., Wu Z. , Ren Z.",Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2023,"coronavirus disease 2019, mycobiome, non-invasive biomarkers, oral fungi, severe acute respiratory syndrome coronavirus 2",Experiment 6,China,Homo sapiens,Surface of tongue,UBERON:0007367,COVID-19,MONDO:0100096,Covid-19-N group,Covid-19-C group,This group consists of 15 Covid-19 patients with comorbidities.,56,15,2 months,ITS / ITS2,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,3,"age,sex",NA,NA,increased,NA,NA,NA,unchanged,Signature 1,Supplemental Figure S4,3 June 2024,Victoria,"Victoria,WikiWorks","The 10 most abundant fungi among the differential fungi among the three groups
at the genus and species levels.",increased,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Erysiphales|f__Erysiphaceae|g__Blumeria,4751|4890|147548|5120|34371|34372,Complete,Svetlana up
bsdb:37119437/7/1,37119437,prospective cohort,37119437,10.1002/advs.202205058,https://pmc.ncbi.nlm.nih.gov/articles/PMC10323652/,"Hu X., Wang H., Yu B., Yu J., Lu H., Sun J., Sun Y., Zou Y., Luo H., Zeng Z., Liu S., Jiang Y., Wu Z. , Ren Z.",Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2023,"coronavirus disease 2019, mycobiome, non-invasive biomarkers, oral fungi, severe acute respiratory syndrome coronavirus 2",Experiment 7,China,Homo sapiens,Surface of tongue,UBERON:0007367,COVID-19,MONDO:0100096,Healthy controls,Covid-19 Group,Participants in this group were Covid-19 patients from the test phase.,88,48,2 months,ITS / ITS2,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,3,"age,sex",NA,NA,unchanged,NA,NA,NA,increased,Signature 1,"Figure 1E, F and Figure S3B",21 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","The ten most abundant fungi among the differential fungi between COVID-19 and controls at the phylum, genus and species levels.",increased,"k__Fungi|p__Ascomycota|c__Sordariomycetes|g__Acrodictys,k__Fungi|p__Ascomycota|c__Sordariomycetes|g__Acrodictys|s__Acrodictys fluminicola,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Pezizaceae|g__Hydnobolites,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Cordycipitaceae|g__Simplicillium,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Cordycipitaceae|g__Simplicillium|s__Simplicillium sympodiophorum,k__Fungi|p__Zoopagomycota,k__Fungi|p__Ascomycota",4751|4890|147550|1827388;4751|4890|147550|1827388|2571388;4751|4890|3239874|2916678|766764|5475;4751|4890|3239874|2916678|766764|5475|5476;4751|4890|147549|5185|5186|405928;4751|4890|147550|5125|474943|292631;4751|4890|147550|5125|474943|292631|935215;4751|1913638;4751|4890,Complete,Svetlana up
bsdb:37119437/7/2,37119437,prospective cohort,37119437,10.1002/advs.202205058,https://pmc.ncbi.nlm.nih.gov/articles/PMC10323652/,"Hu X., Wang H., Yu B., Yu J., Lu H., Sun J., Sun Y., Zou Y., Luo H., Zeng Z., Liu S., Jiang Y., Wu Z. , Ren Z.",Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2023,"coronavirus disease 2019, mycobiome, non-invasive biomarkers, oral fungi, severe acute respiratory syndrome coronavirus 2",Experiment 7,China,Homo sapiens,Surface of tongue,UBERON:0007367,COVID-19,MONDO:0100096,Healthy controls,Covid-19 Group,Participants in this group were Covid-19 patients from the test phase.,88,48,2 months,ITS / ITS2,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,3,"age,sex",NA,NA,unchanged,NA,NA,NA,increased,Signature 2,"Figure 1E, F and Figure S3B",21 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","The ten most abundant fungi among the differential fungi between COVID-19 and controls at the phylum, genus and species levels.",decreased,"k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Eremomycetales|f__Eremomycetaceae|g__Arthrographis,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Eremomycetales|f__Eremomycetaceae|g__Arthrographis|s__Arthrographis grakistii,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Cladosporium,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Cladosporium|s__Cladosporium kenpeggii,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Cryptococcaceae|g__Cryptococcus,k__Fungi|p__Mucoromycota|c__Glomeromycetes|o__Diversisporales|f__Diversisporaceae|g__Diversispora,k__Fungi|p__Mucoromycota|c__Glomeromycetes|o__Diversisporales|f__Diversisporaceae|g__Diversispora|s__Diversispora spurca,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Harringtonia|s__Harringtonia lauricola,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Raffaelea,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae|g__Vanrija|s__Vanrija longa,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Chaetosphaeriales|f__Chaetosphaeriaceae|g__Zanclospora|s__Zanclospora jonesii,k__Fungi|p__Basidiomycota,k__Fungi|p__Mucoromycota,k__Fungi|p__Cryptomycota",4751|4890|147541|2714147|241722|241727;4751|4890|147541|2714147|241722|241727|2682943;4751|4890|147541|2726946|452563|5498;4751|4890|147541|2726946|452563|5498|2016221;4751|5204|155616|5234|1884633|5206;4751|1913637|214506|214509|308925|308926;4751|1913637|214506|214509|308925|308926|308927;4751|4890|147550|5151|5152|2933754|483707;4751|5204|1538075|162474|742845|55193;4751|5204|1538075|162474|742845|55193|76775;4751|4890|147550|5151|5152|45340;4751|5204|155616|1851469|1759442|1851468|181171;4751|4890|147550|261460|103886|1323519|2040582;4751|5204;4751|1913637;4751|1031332,Complete,Svetlana up
bsdb:37119437/8/1,37119437,prospective cohort,37119437,10.1002/advs.202205058,https://pmc.ncbi.nlm.nih.gov/articles/PMC10323652/,"Hu X., Wang H., Yu B., Yu J., Lu H., Sun J., Sun Y., Zou Y., Luo H., Zeng Z., Liu S., Jiang Y., Wu Z. , Ren Z.",Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2023,"coronavirus disease 2019, mycobiome, non-invasive biomarkers, oral fungi, severe acute respiratory syndrome coronavirus 2",Experiment 8,China,Homo sapiens,Surface of tongue,UBERON:0007367,COVID-19,MONDO:0100096,Healthy Controls,Covid-19 Group,Participants in this group were COVID-19 patients.,132,71,2 months,ITS / ITS2,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,3,"age,sex",NA,NA,unchanged,NA,NA,NA,increased,Signature 1,"Figure 4E, S6b and S6c",22 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","The differential fungi among Healthy controls, Covid-19 and Post-Covid-19 groups at the phyla, genus and species levels.",increased,"k__Fungi|p__Ascomycota,k__Fungi|p__Chytridiomycota,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Harringtonia|s__Harringtonia lauricola,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium|s__Fusarium fujikuroi,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Amphisphaeriales|f__Apiosporaceae|g__Nigrospora|s__Nigrospora oryzae,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Amphisphaeriales|f__Apiosporaceae|g__Nigrospora,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Penicillium|s__Penicillium hirsutum,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae|g__Ramularia|s__Ramularia coryli,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae|g__Ramularia,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus tennesseensis,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Raffaelea,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Diutina",4751|4890;4751|4761;4751|4890|147550|5151|5152|2933754|483707;4751|4890|147550|5125|110618|5506|5127;4751|4890|147550|3402561|106263|114230|335854;4751|4890|147550|3402561|106263|114230;4751|4890|147545|5042|1131492|5073|36648;4751|4890|147541|2726947|93133|112497|1873263;4751|4890|147541|2726947|93133|112497;4751|4890|147545|5042|1131492|5052|1220210;4751|4890|147550|5151|5152|45340;4751|4890|147550|5125|110618|5506;4751|4890|3239874|2916678|766764|1910789,Complete,Svetlana up
bsdb:37119437/8/2,37119437,prospective cohort,37119437,10.1002/advs.202205058,https://pmc.ncbi.nlm.nih.gov/articles/PMC10323652/,"Hu X., Wang H., Yu B., Yu J., Lu H., Sun J., Sun Y., Zou Y., Luo H., Zeng Z., Liu S., Jiang Y., Wu Z. , Ren Z.",Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2023,"coronavirus disease 2019, mycobiome, non-invasive biomarkers, oral fungi, severe acute respiratory syndrome coronavirus 2",Experiment 8,China,Homo sapiens,Surface of tongue,UBERON:0007367,COVID-19,MONDO:0100096,Healthy Controls,Covid-19 Group,Participants in this group were COVID-19 patients.,132,71,2 months,ITS / ITS2,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,3,"age,sex",NA,NA,unchanged,NA,NA,NA,increased,Signature 2,"Figure 4E, S6b and S6c",22 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","The differential fungi among Healthy controls, Covid-19 and Post-Covid-19 groups at the phyla, genus and species levels.",decreased,"k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Diaporthales|f__Diaporthaceae|g__Diaporthe,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Trichocomaceae|g__Talaromyces,k__Fungi|p__Ascomycota|g__Milospium,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Chaetosphaeriales|f__Chaetosphaeriaceae|g__Zanclospora,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Diaporthales|f__Diaporthaceae|g__Diaporthe|s__Diaporthe kochmanii,k__Fungi|p__Ascomycota|g__Milospium|s__Milospium graphideorum,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Chaetosphaeriales|f__Chaetosphaeriaceae|g__Zanclospora|s__Zanclospora jonesii,k__Fungi|p__Basidiomycota,k__Fungi|p__Mucoromycota,k__Fungi|p__Cryptomycota",4751|4890|147550|5114|767018|36922;4751|4890|147545|5042|28568|5094;4751|4890|1666919;4751|4890|147550|261460|103886|1323519;4751|4890|147550|5114|767018|36922|1116855;4751|4890|1666919|1664392;4751|5204|1538075|162474|742845|55193|76775;4751|4890|147550|261460|103886|1323519|2040582;4751|5204;4751|1913637;4751|1031332,Complete,Svetlana up
bsdb:37119437/9/1,37119437,prospective cohort,37119437,10.1002/advs.202205058,https://pmc.ncbi.nlm.nih.gov/articles/PMC10323652/,"Hu X., Wang H., Yu B., Yu J., Lu H., Sun J., Sun Y., Zou Y., Luo H., Zeng Z., Liu S., Jiang Y., Wu Z. , Ren Z.",Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2023,"coronavirus disease 2019, mycobiome, non-invasive biomarkers, oral fungi, severe acute respiratory syndrome coronavirus 2",Experiment 9,China,Homo sapiens,Surface of tongue,UBERON:0007367,COVID-19,MONDO:0100096,Healthy Controls,Post Covid-19 Group,Participants in this group were recovered COVID-19 patients.,132,22,2 months,ITS / ITS2,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,3,"age,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"Figure 4E, S6b and S6c",22 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","The differential fungi among Healthy controls, Covid-19 and Post Covid-19 groups at the phyla, genus and species levels.",increased,"k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Amphisphaeriales|f__Apiosporaceae|g__Nigrospora,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Xylariales|f__Diatrypaceae|g__Peroneutypa,k__Fungi|p__Mucoromycota,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium|s__Fusarium fujikuroi,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Amphisphaeriales|f__Apiosporaceae|g__Nigrospora|s__Nigrospora oryzae,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Penicillium|s__Penicillium hirsutum,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus tennesseensis",4751|4890|147550|5125|110618|5506;4751|4890|147550|3402561|106263|114230;4751|4890|147550|37989|42364|889755;4751|1913637;4751|4890|147550|5125|110618|5506|5127;4751|4890|147550|3402561|106263|114230|335854;4751|4890|147545|5042|1131492|5073|36648;4751|4890|147545|5042|1131492|5052|1220210,Complete,Svetlana up
bsdb:37119437/9/2,37119437,prospective cohort,37119437,10.1002/advs.202205058,https://pmc.ncbi.nlm.nih.gov/articles/PMC10323652/,"Hu X., Wang H., Yu B., Yu J., Lu H., Sun J., Sun Y., Zou Y., Luo H., Zeng Z., Liu S., Jiang Y., Wu Z. , Ren Z.",Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2023,"coronavirus disease 2019, mycobiome, non-invasive biomarkers, oral fungi, severe acute respiratory syndrome coronavirus 2",Experiment 9,China,Homo sapiens,Surface of tongue,UBERON:0007367,COVID-19,MONDO:0100096,Healthy Controls,Post Covid-19 Group,Participants in this group were recovered COVID-19 patients.,132,22,2 months,ITS / ITS2,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,3,"age,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 2,"Figure 4E, S6b and S6c",22 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","The differential fungi among Healthy controls, Covid-19 and Post-Covid-19 groups at the phyla, genus and species levels.",decreased,"k__Fungi|p__Ascomycota,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Diaporthales|f__Diaporthaceae|g__Diaporthe,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Diaporthales|f__Diaporthaceae|g__Diaporthe|s__Diaporthe kochmanii,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Harringtonia|s__Harringtonia lauricola,k__Fungi|p__Ascomycota|g__Milospium,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Raffaelea,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Trichocomaceae|g__Talaromyces,k__Fungi|p__Ascomycota|g__Milospium|s__Milospium graphideorum",4751|4890;4751|4890|147550|5114|767018|36922;4751|4890|147550|5114|767018|36922|1116855;4751|4890|147550|5151|5152|2933754|483707;4751|4890|1666919;4751|4890|147550|5151|5152|45340;4751|4890|147545|5042|28568|5094;4751|4890|1666919|1664392,Complete,Svetlana up
bsdb:37119437/10/1,37119437,prospective cohort,37119437,10.1002/advs.202205058,https://pmc.ncbi.nlm.nih.gov/articles/PMC10323652/,"Hu X., Wang H., Yu B., Yu J., Lu H., Sun J., Sun Y., Zou Y., Luo H., Zeng Z., Liu S., Jiang Y., Wu Z. , Ren Z.",Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2023,"coronavirus disease 2019, mycobiome, non-invasive biomarkers, oral fungi, severe acute respiratory syndrome coronavirus 2",Experiment 10,China,Homo sapiens,Surface of tongue,UBERON:0007367,COVID-19,MONDO:0100096,Covid-19 Group,Post Covid-19 Group,Participants in this group were recovered COVID-19 patients.,71,22,2 months,ITS / ITS2,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,3,"age,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"Figure 4E, S6b and S6c",22 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","The differential fungi among Healthy controls, Covid-19 and Post-Covid-19 groups at the phyla, genus and species levels.",increased,"k__Fungi|p__Ascomycota,k__Fungi|p__Ascomycota|g__Milospium,k__Fungi|p__Ascomycota|g__Milospium|s__Milospium graphideorum,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Trichocomaceae|g__Talaromyces,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Harringtonia|s__Harringtonia lauricola,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Raffaelea",4751|4890;4751|4890|1666919;4751|4890|1666919|1664392;4751|4890|147545|5042|28568|5094;4751|4890|147550|5151|5152|2933754|483707;4751|4890|147550|5151|5152|45340,Complete,Svetlana up
bsdb:37119437/10/2,37119437,prospective cohort,37119437,10.1002/advs.202205058,https://pmc.ncbi.nlm.nih.gov/articles/PMC10323652/,"Hu X., Wang H., Yu B., Yu J., Lu H., Sun J., Sun Y., Zou Y., Luo H., Zeng Z., Liu S., Jiang Y., Wu Z. , Ren Z.",Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2023,"coronavirus disease 2019, mycobiome, non-invasive biomarkers, oral fungi, severe acute respiratory syndrome coronavirus 2",Experiment 10,China,Homo sapiens,Surface of tongue,UBERON:0007367,COVID-19,MONDO:0100096,Covid-19 Group,Post Covid-19 Group,Participants in this group were recovered COVID-19 patients.,71,22,2 months,ITS / ITS2,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,3,"age,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 2,"Figure 4E, S6b and S6c",22 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","The differential fungi among Healthy controls, Covid-19 and Post-Covid-19 groups at the phyla, genus and species levels.",decreased,"k__Fungi|p__Mucoromycota,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Diaporthales|f__Diaporthaceae|g__Diaporthe|s__Diaporthe kochmanii,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta",4751|1913637;4751|4890|147550|5114|767018|36922|1116855;4751|5204|1538075|162474|742845|55193|76775,Complete,Svetlana up
bsdb:37119735/1/1,37119735,"cross-sectional observational, not case-control,prospective cohort",37119735,10.1016/j.ebiom.2023.104583,NA,"Palmu J., Börschel C.S., Ortega-Alonso A., Markó L., Inouye M., Jousilahti P., Salido R.A., Sanders K., Brennan C., Humphrey G.C., Sanders J.G., Gutmann F., Linz D., Salomaa V., Havulinna A.S., Forslund S.K., Knight R., Lahti L., Niiranen T. , Schnabel R.B.",Gut microbiome and atrial fibrillation-results from a large population-based study,EBioMedicine,2023,"Atrial fibrillation, Epidemiology, Gut microbiome, Metagenomics",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Atrial fibrillation,EFO:0000275,Individuals without Prevalent Atrial Fibrillation (AF),Individuals with Prevalent Atrial Fibrillation (AF),Participants with prevalent atrial fibrillation. Atrial fibrillation (AF) is an important heart rhythm disorder in aging populations,6647,116,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,alcohol consumption measurement,blood pressure,body mass index,diabetes mellitus,physical activity,sex,smoking status,total cholesterol measurement",NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 2, Table 2",15 October 2023,Iram jamshed,"Iram jamshed,Tolulopeo,ChiomaBlessing,WikiWorks",Abundant genera in individuals with Prevalent Atrial Fibrillation (AF) compared to individuals without Prevalent AF,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kluyvera",1783272|1239|186801|3085636|186803|1432051;1783272|201174|84998|84999|84107|1472762;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|579,Complete,ChiomaBlessing
bsdb:37119735/1/2,37119735,"cross-sectional observational, not case-control,prospective cohort",37119735,10.1016/j.ebiom.2023.104583,NA,"Palmu J., Börschel C.S., Ortega-Alonso A., Markó L., Inouye M., Jousilahti P., Salido R.A., Sanders K., Brennan C., Humphrey G.C., Sanders J.G., Gutmann F., Linz D., Salomaa V., Havulinna A.S., Forslund S.K., Knight R., Lahti L., Niiranen T. , Schnabel R.B.",Gut microbiome and atrial fibrillation-results from a large population-based study,EBioMedicine,2023,"Atrial fibrillation, Epidemiology, Gut microbiome, Metagenomics",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Atrial fibrillation,EFO:0000275,Individuals without Prevalent Atrial Fibrillation (AF),Individuals with Prevalent Atrial Fibrillation (AF),Participants with prevalent atrial fibrillation. Atrial fibrillation (AF) is an important heart rhythm disorder in aging populations,6647,116,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,alcohol consumption measurement,blood pressure,body mass index,diabetes mellitus,physical activity,sex,smoking status,total cholesterol measurement",NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 2, Table 2",15 October 2023,Iram jamshed,"Iram jamshed,Tolulopeo,ChiomaBlessing,WikiWorks",Abundant genera in individuals with Prevalent Atrial Fibrillation (AF) compared to individuals without Prevalent AF,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;1783272|1239|526524|526525|128827|1573535;3379134|976|200643|171549|2005525|375288;1783272|1239|526524|526525|2810281|191303,Complete,ChiomaBlessing
bsdb:37119735/2/1,37119735,"cross-sectional observational, not case-control,prospective cohort",37119735,10.1016/j.ebiom.2023.104583,NA,"Palmu J., Börschel C.S., Ortega-Alonso A., Markó L., Inouye M., Jousilahti P., Salido R.A., Sanders K., Brennan C., Humphrey G.C., Sanders J.G., Gutmann F., Linz D., Salomaa V., Havulinna A.S., Forslund S.K., Knight R., Lahti L., Niiranen T. , Schnabel R.B.",Gut microbiome and atrial fibrillation-results from a large population-based study,EBioMedicine,2023,"Atrial fibrillation, Epidemiology, Gut microbiome, Metagenomics",Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Atrial fibrillation,EFO:0000275,Individuals without Incident Atrial Fibrillation (AF),Individuals with Incident Atrial Fibrillation (AF),"Incident AF refers to new cases of atrial fibrillation that occurred during the follow-up period of the study, among individuals who did not have a history of atrial fibrillation at baseline.",6647,539,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,alcohol consumption measurement,blood pressure,body mass index,diabetes mellitus,sex,smoking status,total cholesterol measurement",NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 2, Table 3",17 October 2023,Iram jamshed,"Iram jamshed,Tolulopeo,ChiomaBlessing,WikiWorks",Abundant genera in individuals with Incident Atrial Fibrillation (AF) compared to individuals without Incident AF,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas",1783272|201174|1760|85004|31953|1678;1783272|201174|84998|84999|84107|1472762;1783272|1239|91061|186826|1300|1357;1783272|1239|909932|909929|1843491|52225;1783272|1239|186801|3085636|186803|1769710,Complete,ChiomaBlessing
bsdb:37119735/2/2,37119735,"cross-sectional observational, not case-control,prospective cohort",37119735,10.1016/j.ebiom.2023.104583,NA,"Palmu J., Börschel C.S., Ortega-Alonso A., Markó L., Inouye M., Jousilahti P., Salido R.A., Sanders K., Brennan C., Humphrey G.C., Sanders J.G., Gutmann F., Linz D., Salomaa V., Havulinna A.S., Forslund S.K., Knight R., Lahti L., Niiranen T. , Schnabel R.B.",Gut microbiome and atrial fibrillation-results from a large population-based study,EBioMedicine,2023,"Atrial fibrillation, Epidemiology, Gut microbiome, Metagenomics",Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Atrial fibrillation,EFO:0000275,Individuals without Incident Atrial Fibrillation (AF),Individuals with Incident Atrial Fibrillation (AF),"Incident AF refers to new cases of atrial fibrillation that occurred during the follow-up period of the study, among individuals who did not have a history of atrial fibrillation at baseline.",6647,539,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,alcohol consumption measurement,blood pressure,body mass index,diabetes mellitus,sex,smoking status,total cholesterol measurement",NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 2, Table 3",17 October 2023,Iram jamshed,"Iram jamshed,Tolulopeo,ChiomaBlessing,WikiWorks",Abundant genera in individuals with Incident Atrial Fibrillation (AF) compared to individuals without Incident AF,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Sanguibacteroides",1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|3085636|186803|1506577;3379134|976|200643|171549|171551|1635148,Complete,ChiomaBlessing
bsdb:37122038/1/1,37122038,laboratory experiment,37122038,10.1186/s40104-023-00865-w,NA,"Xu B., Qin W., Chen Y., Tang Y., Zhou S., Huang J., Ma L. , Yan X.",Multi-omics analysis reveals gut microbiota-ovary axis contributed to the follicular development difference between Meishan and Landrace × Yorkshire sows,Journal of animal science and biotechnology,2023,"Follicular development, Granulosa cells apoptosis, Gut microbiota, Short-chain fatty acids, Sows",Experiment 1,China,Sus scrofa domesticus,Feces,UBERON:0001988,Reproductive behaviour measurement,EFO:0007862,L×Y (Landrace × Yorkshire sows),MS (Meishan sows),"Meishan sows were defined as the case group based on their breed-specific reproductive characteristics, including a significantly greater number of antral follicles and higher serum estradiol levels compared to Landrace x Yorkshire sows.",7,7,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,unchanged,decreased,NA,unchanged,Signature 1,"Figure 5A, B",15 May 2025,Anne-mariesharp,Anne-mariesharp,LefSe analysis showing differentially abundant taxa between MS and L × Y sows,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Fibrobacterota|c__Fibrobacteria|o__Fibrobacterales|f__Fibrobacteraceae|g__Fibrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Pseudomonadati|p__Spirochaetota",3379134|976|200643|171549|815;1783272|1239|186801|186802|31979;3379134|65842|204430|218872|204431|832;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|171551;3379134|203691|203692|136;1783272|1239|526524|526525|2810281;3379134|203691,Complete,KateRasheed
bsdb:37122038/1/2,37122038,laboratory experiment,37122038,10.1186/s40104-023-00865-w,NA,"Xu B., Qin W., Chen Y., Tang Y., Zhou S., Huang J., Ma L. , Yan X.",Multi-omics analysis reveals gut microbiota-ovary axis contributed to the follicular development difference between Meishan and Landrace × Yorkshire sows,Journal of animal science and biotechnology,2023,"Follicular development, Granulosa cells apoptosis, Gut microbiota, Short-chain fatty acids, Sows",Experiment 1,China,Sus scrofa domesticus,Feces,UBERON:0001988,Reproductive behaviour measurement,EFO:0007862,L×Y (Landrace × Yorkshire sows),MS (Meishan sows),"Meishan sows were defined as the case group based on their breed-specific reproductive characteristics, including a significantly greater number of antral follicles and higher serum estradiol levels compared to Landrace x Yorkshire sows.",7,7,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,unchanged,decreased,NA,unchanged,Signature 2,"Figure 5A,B",15 May 2025,Ese,Ese,LefSe analysis showing differentially abundant taxa between MS and L × Y sows,decreased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|91061;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826;1783272|1239|91061|186826|1300;1783272|1239|909932|1843489|31977,Complete,KateRasheed
bsdb:37150399/1/1,37150399,"cross-sectional observational, not case-control",37150399,10.1016/j.neuropharm.2023.109566,NA,"Nuzum N.D., Szymlek-Gay E.A., Loke S., Dawson S.L., Teo W.P., Hendy A.M., Loughman A. , Macpherson H.",Differences in the gut microbiome across typical ageing and in Parkinson's disease,Neuropharmacology,2023,"Aging, Gut-brain-axis, Microbiome, Microbiota, PD, Short chain fatty acids",Experiment 1,Australia,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy younger (HY),Healthy older (HO),"Healthy older (HO) refers to patients who are 50-80 years and had no neurological or neurodegenerative conditions, no first-degree relatives with PD, scores of ≥24/30 on the Montreal Cognitive assessment (MoCA) or ≥ 17/22 for the MoCA-Blind (remote assessment).",22,33,3 months,WMS,NA,Illumina,centered log-ratio,MaAsLin2,0.1,TRUE,NA,sex,NA,NA,unchanged,NA,unchanged,unchanged,unchanged,Signature 1,"Fig. 2, Fig. S1B",28 February 2025,KateRasheed,KateRasheed,Significantly differential abundance of taxa between healthy young and healthy older groups,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,1783272|201174|1760|85004|31953|1678|1681,Complete,Svetlana up
bsdb:37150399/2/1,37150399,"cross-sectional observational, not case-control",37150399,10.1016/j.neuropharm.2023.109566,NA,"Nuzum N.D., Szymlek-Gay E.A., Loke S., Dawson S.L., Teo W.P., Hendy A.M., Loughman A. , Macpherson H.",Differences in the gut microbiome across typical ageing and in Parkinson's disease,Neuropharmacology,2023,"Aging, Gut-brain-axis, Microbiome, Microbiota, PD, Short chain fatty acids",Experiment 2,Australia,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy younger (HY),Healthy older (HO),"Healthy older (HO) refers to patients who are 50-80 years and had no neurological or neurodegenerative conditions, no first-degree relatives with PD, scores of ≥24/30 on the Montreal Cognitive assessment (MoCA) or ≥ 17/22 for the MoCA-Blind (remote assessment).",22,33,3 months,WMS,NA,Illumina,centered log-ratio,MaAsLin2,0.1,TRUE,NA,sex,"body mass index,sex",NA,unchanged,NA,unchanged,unchanged,unchanged,Signature 1,"Fig. 2, Fig. S1B",28 February 2025,KateRasheed,KateRasheed,Significantly differential abundance of taxa between healthy young and healthy older groups after adjusting for covariates.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,1783272|201174|1760|85004|31953|1678|1681,Complete,Svetlana up
bsdb:37150399/3/1,37150399,"cross-sectional observational, not case-control",37150399,10.1016/j.neuropharm.2023.109566,NA,"Nuzum N.D., Szymlek-Gay E.A., Loke S., Dawson S.L., Teo W.P., Hendy A.M., Loughman A. , Macpherson H.",Differences in the gut microbiome across typical ageing and in Parkinson's disease,Neuropharmacology,2023,"Aging, Gut-brain-axis, Microbiome, Microbiota, PD, Short chain fatty acids",Experiment 3,Australia,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy older (HO),Parkinson’s disease patients (PD),"PD refers to patients who are 50–80 years; having PD diagnosis which was determined through an independent neurologist. These individuals had to have mild-moderate PD as assessed via the Movement Disorder Society Unified Parkinson’s Disease Rating Scale stage-II form (MDS-UPDRS-II); which covers the motor experiences of daily living, no cases of early-onset PD i.e., diagnosis after 50 years of age, and MoCA scores for  the PD group were set at ≥ 21/30 and ≥ 15/22 for the standard and MoCA-Blind respectively.",33,18,3 months,WMS,NA,Illumina,centered log-ratio,MaAsLin2,0.1,TRUE,NA,"age,sex",NA,NA,unchanged,NA,unchanged,unchanged,unchanged,Signature 1,Fig. S1A,28 February 2025,KateRasheed,KateRasheed,Significantly differential abundance of taxa between PD and healthy older groups.,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,Svetlana up
bsdb:37150399/4/1,37150399,"cross-sectional observational, not case-control",37150399,10.1016/j.neuropharm.2023.109566,NA,"Nuzum N.D., Szymlek-Gay E.A., Loke S., Dawson S.L., Teo W.P., Hendy A.M., Loughman A. , Macpherson H.",Differences in the gut microbiome across typical ageing and in Parkinson's disease,Neuropharmacology,2023,"Aging, Gut-brain-axis, Microbiome, Microbiota, PD, Short chain fatty acids",Experiment 4,Australia,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy older (HO),Parkinson’s disease patients (PD),"PD refers to patients who are 50–80 years; having PD diagnosis which was determined through an independent neurologist. These individuals had to have mild-moderate PD as assessed via the Movement Disorder Society Unified Parkinson’s Disease Rating Scale stage-II form (MDS-UPDRS-II); which covers the motor experiences of daily living, no cases of early-onset PD i.e., diagnosis after 50 years of age, and MoCA scores for the PD group were set at ≥ 21/30 and ≥ 15/22 for the standard and MoCA-Blind respectively.",33,18,3 months,WMS,NA,Illumina,centered log-ratio,MaAsLin2,0.1,TRUE,NA,"age,sex","body mass index,sex",NA,unchanged,NA,unchanged,unchanged,unchanged,Signature 1,"In text of the ""Phylum level"" section",28 February 2025,KateRasheed,KateRasheed,Significantly differential abundance of taxa between PD and healthy older groups after adjusting for covariates.,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,Svetlana up
bsdb:37158877/1/1,37158877,case-control,37158877,10.1186/s12866-023-02872-3,NA,"Wei N., Zhu G., Zhao T., Wang Y., Lou H., Li H., Yang Z., Zhang Z., Wang Q., Han M., Lin Z. , Li S.",Characterization of oral bacterial and fungal microbiome in recovered COVID-19 patients,BMC microbiology,2023,"COVID-19, Oral bacteria, Oral fungi, Recovered patients, Virus clearance",Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,COVID-19,MONDO:0100096,HCs (Healthy Controls),RPs (Recovered Patients),This group consists of patients who have recovered from COVID-19.,29,23,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Fig. 3A & Fig. 6A,9 August 2024,Victoria,"Victoria,WikiWorks","Images showing the differences in taxa between RPs and HCs. (Fig. 3A shows oral bacterial taxa, while Fig. 6A shows oral fungi taxa).",increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Diaporthales|f__Diaporthaceae,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Diaporthales,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Diaporthales|f__Diaporthaceae|g__Diaporthe,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Fungi|p__Ascomycota|c__Sordariomycetes,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Trichocomaceae|g__Talaromyces,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Aquamicrobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Liberibacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Vogesella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella",3379134|29547|3031852|213849|2808963|28196;3379134|29547|3031852|213849|2808963;4751|4890|147550|5114|767018;4751|4890|147550|5114;4751|4890|147550|5114|767018|36922;1783272|1239|91061|186826|33958;1783272|1239|91061|1385|186822|44249;4751|4890|147550;4751|4890|147545|5042|28568|5094;3384194|1297|188787|68933|188786;3384194|1297|188787|68933|188786|270;1783272|1239|91061|186826|33958|46255;1783272|1239|186801|3085636|186803|43994;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|3085636|186803|1213720;1783272|1239|186801|3085636|186803;1783272|1239|526524|526525|128827|118747;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492;3384189|32066|203490|203491|1129771|168808;3379134|1224|28211|356|69277|69278;3379134|1224|28211|356|82115|34019;3379134|1224|28211|356|118882|528;3379134|1224|28211|356|82115;3379134|1224|28216|206351|1499392|57739;3379134|1224|28216|206351|1499392;3379134|1224|1236|2887326|468|475,Complete,Svetlana up
bsdb:37158877/1/2,37158877,case-control,37158877,10.1186/s12866-023-02872-3,NA,"Wei N., Zhu G., Zhao T., Wang Y., Lou H., Li H., Yang Z., Zhang Z., Wang Q., Han M., Lin Z. , Li S.",Characterization of oral bacterial and fungal microbiome in recovered COVID-19 patients,BMC microbiology,2023,"COVID-19, Oral bacteria, Oral fungi, Recovered patients, Virus clearance",Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,COVID-19,MONDO:0100096,HCs (Healthy Controls),RPs (Recovered Patients),This group consists of patients who have recovered from COVID-19.,29,23,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Fig. 3A & Fig. 6A,10 August 2024,Victoria,"Victoria,WikiWorks","Images showing the differences in taxa between RPs and HCs. (Fig. 3A shows oral bacterial taxa, while Fig. 6A shows oral fungi taxa).",decreased,"k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Elizabethkingia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Empedobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Anaplasmataceae|g__Wolbachia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Anaplasmataceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|g__Candidatus Profftella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae",4751|4890|3239874|2916678|766764|5475;1783272|201174|1760|85009|31957|2801844;1783272|201174|1760|85009|31957;3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|171552|838;3379134|976|117743|200644|2762318|308865;3379134|976|117743|200644|2762318|59734;1783272|1239|91061|186826|81852|2737;3379134|1224|28211|204458|76892;3379134|1224|28211|356|119045|407;3379134|1224|28211|356|69277|68287;3379134|1224|28211|356|41294|374;3379134|1224|28211|356|335928;3379134|1224|28211|766|942|953;3379134|1224|28211|766|942;3379134|1224|28216|1381133;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|80840|119060|48736;3379134|1224|28216|80840|119060;3379134|1224|1236|135625|712|416916;3379134|1224|1236|135623|641|662;3379134|1224|1236|135623|641,Complete,Svetlana up
bsdb:37179374/1/1,37179374,"cross-sectional observational, not case-control",37179374,10.1186/s13148-023-01487-9,https://pubmed.ncbi.nlm.nih.gov/37179374/,"Liu K., He X., Huang J., Yu S., Cui M., Gao M., Liu L., Qian Y., Xie Y., Hui M., Hong Y. , Nie X.",Short-chain fatty acid-butyric acid ameliorates granulosa cells inflammation through regulating METTL3-mediated N6-methyladenosine modification of FOSL2 in polycystic ovarian syndrome,Clinical epigenetics,2023,"Butyric acid, Gut microbiome, Inflammation, PCOS, m6A modification",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control + Hyperandrogenism group (HA),Obese group (FAT),The mere obese patients with polycystic ovary syndrome,12,6,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2B,12 May 2025,Shulamite,Shulamite,"Linear discriminant analysis (LDA) discriminant histogram of gut microbiota in three groups. Identification of the bacterial taxa with statistically significant difference between groups using LEfSe software and LDA. Taxa enriched in Control, FAT-PCOS, and HA-PCOS group are colored by red, green, and blue respectively (LDA > 2.0 and P < 0.05), the relative abundance of thesebiomarkers are shown in the histogram (mean and standard deviation values are plotted) under the corresponding cladogram.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Rhizobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|1224|28216|80840|506|222;3384189|32066|203490|203491|203492|848;3379134|1224|28216|80840|212743;1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:37179374/2/1,37179374,"cross-sectional observational, not case-control",37179374,10.1186/s13148-023-01487-9,https://pubmed.ncbi.nlm.nih.gov/37179374/,"Liu K., He X., Huang J., Yu S., Cui M., Gao M., Liu L., Qian Y., Xie Y., Hui M., Hong Y. , Nie X.",Short-chain fatty acid-butyric acid ameliorates granulosa cells inflammation through regulating METTL3-mediated N6-methyladenosine modification of FOSL2 in polycystic ovarian syndrome,Clinical epigenetics,2023,"Butyric acid, Gut microbiome, Inflammation, PCOS, m6A modification",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control + Mere obese group (FAT),Hyperandrogenism group (HA),The mere Hyperandrogenism group with polycystic ovary syndrome,12,6,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,2B,12 May 2025,Shulamite,Shulamite,"Linear discriminant analysis (LDA) discriminant histogram of gut microbiota in three groups. Identification of the bacterial taxa with statistically significant difference between groups using LEfSe software and LDA. Taxa enriched in Control, FAT-PCOS, and HA-PCOS group are colored by red, green, and blue respectively (LDA > 2.0 and P < 0.05), the relative abundance of thesebiomarkers are shown in the histogram (mean and standard deviation values are plotted) under the corresponding cladogram.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia",1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3082720|186804|1501226,Complete,KateRasheed
bsdb:37180435/1/1,37180435,laboratory experiment,37180435,10.3389/fcimb.2023.1135428,NA,"Fan Y., Liang L., Tang X., Zhu J., Mu L., Wang M., Huang X., Gong S., Xu J., Liu T. , Zhang T.",Changes in the gut microbiota structure and function in rats with doxorubicin-induced heart failure,Frontiers in cellular and infection microbiology,2023,"16S rRNA gene sequencing, animal model, doxorubicin, gut microbiota, heart failure, intestinal hypothesis",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Heart failure,EFO:0003144,Control (Con-J) group,Doxorubicin-A (Dox-A) group,"The rats in the DOX-A group were administered 2mg/kg of doxorubicin via the tail vein for 6 weeks to induce heart failure, and their body weights decreased to varying degrees.",9,9,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 8 & 9,26 June 2025,Victoria,Victoria,"Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae",3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|1283313;1783272|201174;1783272|201174;3379134|976|200643|171549|1853231|283168;3379134|976|200643|1970189|1573805,Complete,KateRasheed
bsdb:37180435/1/2,37180435,laboratory experiment,37180435,10.3389/fcimb.2023.1135428,NA,"Fan Y., Liang L., Tang X., Zhu J., Mu L., Wang M., Huang X., Gong S., Xu J., Liu T. , Zhang T.",Changes in the gut microbiota structure and function in rats with doxorubicin-induced heart failure,Frontiers in cellular and infection microbiology,2023,"16S rRNA gene sequencing, animal model, doxorubicin, gut microbiota, heart failure, intestinal hypothesis",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Heart failure,EFO:0003144,Control (Con-J) group,Doxorubicin-A (Dox-A) group,"The rats in the DOX-A group were administered 2mg/kg of doxorubicin via the tail vein for 6 weeks to induce heart failure, and their body weights decreased to varying degrees.",9,9,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 8 & 9,26 June 2025,Victoria,Victoria,"Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides rodentium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus murinus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota",1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|815|816|691816;1783272|1239|186801|186802;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|91061|186826|33958|2767887|1622;1783272|1239|91061|186826|33958|2767887;1783272|1239|91061|186826|33958;1783272|1239|186801;1783272|1239,Complete,KateRasheed
bsdb:37180435/2/1,37180435,laboratory experiment,37180435,10.3389/fcimb.2023.1135428,NA,"Fan Y., Liang L., Tang X., Zhu J., Mu L., Wang M., Huang X., Gong S., Xu J., Liu T. , Zhang T.",Changes in the gut microbiota structure and function in rats with doxorubicin-induced heart failure,Frontiers in cellular and infection microbiology,2023,"16S rRNA gene sequencing, animal model, doxorubicin, gut microbiota, heart failure, intestinal hypothesis",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Heart failure,EFO:0003144,Control (Con-J) group,Doxorubicin-B (Dox-B) group,"The rats in the DOX-B group were administered 2.5mg/kg of doxorubicin via the tail vein for 6 weeks to induce heart failure, and their body weights decreased to varying degrees.",9,8,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,decreased,decreased,unchanged,NA,decreased,Signature 1,Figure 8 & 9,27 June 2025,Victoria,Victoria,"Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae",3379134|976|200643|171549;3379134|976;3379134|976|200643;3379134|1224|1236|91347|543;3379134|1224|1236|91347;3379134|1224|1236|91347|543|1940338;3379134|1224|1236|91347|543|561|562;3379134|1224|1236;3379134|1224;3379134|976|200643|171549|171552;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|171552|1283313;3379134|976|200643|1970189|1573805,Complete,KateRasheed
bsdb:37180435/2/2,37180435,laboratory experiment,37180435,10.3389/fcimb.2023.1135428,NA,"Fan Y., Liang L., Tang X., Zhu J., Mu L., Wang M., Huang X., Gong S., Xu J., Liu T. , Zhang T.",Changes in the gut microbiota structure and function in rats with doxorubicin-induced heart failure,Frontiers in cellular and infection microbiology,2023,"16S rRNA gene sequencing, animal model, doxorubicin, gut microbiota, heart failure, intestinal hypothesis",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Heart failure,EFO:0003144,Control (Con-J) group,Doxorubicin-B (Dox-B) group,"The rats in the DOX-B group were administered 2.5mg/kg of doxorubicin via the tail vein for 6 weeks to induce heart failure, and their body weights decreased to varying degrees.",9,8,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,decreased,decreased,unchanged,NA,decreased,Signature 2,Figure 8 & 9,27 June 2025,Victoria,Victoria,"Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides rodentium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus murinus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota",1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|815|816|691816;1783272|1239|186801|186802;1783272|1239|91061|186826|33958|2767887|1622;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815;1783272|1239|91061|186826|33958|2767887;1783272|1239|186801;1783272|1239,Complete,KateRasheed
bsdb:37180435/3/1,37180435,laboratory experiment,37180435,10.3389/fcimb.2023.1135428,NA,"Fan Y., Liang L., Tang X., Zhu J., Mu L., Wang M., Huang X., Gong S., Xu J., Liu T. , Zhang T.",Changes in the gut microbiota structure and function in rats with doxorubicin-induced heart failure,Frontiers in cellular and infection microbiology,2023,"16S rRNA gene sequencing, animal model, doxorubicin, gut microbiota, heart failure, intestinal hypothesis",Experiment 3,China,Rattus norvegicus,Feces,UBERON:0001988,Heart failure,EFO:0003144,Control (Con-J) group,Doxorubicin-C (Dox-C) group,"The rats in the DOX-C group were administered 3mg/kg of doxorubicin via the tail vein for 6 weeks to induce heart failure, and their body weights decreased to varying degrees.",9,9,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,decreased,decreased,unchanged,NA,decreased,Signature 1,Figure 8 & 9,27 June 2025,Victoria,Victoria,"Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",1783272|201174|1760|85004|31953|1678|1694;3379134|1224|1236|91347|543|1940338;3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|543;3379134|1224|1236;3379134|1224;3379134|1224|1236|91347;3379134|976|200643|171549|171550;3379134|976|200643|171549|171550|239759,Complete,KateRasheed
bsdb:37180435/3/2,37180435,laboratory experiment,37180435,10.3389/fcimb.2023.1135428,NA,"Fan Y., Liang L., Tang X., Zhu J., Mu L., Wang M., Huang X., Gong S., Xu J., Liu T. , Zhang T.",Changes in the gut microbiota structure and function in rats with doxorubicin-induced heart failure,Frontiers in cellular and infection microbiology,2023,"16S rRNA gene sequencing, animal model, doxorubicin, gut microbiota, heart failure, intestinal hypothesis",Experiment 3,China,Rattus norvegicus,Feces,UBERON:0001988,Heart failure,EFO:0003144,Control (Con-J) group,Doxorubicin-C (Dox-C) group,"The rats in the DOX-C group were administered 3mg/kg of doxorubicin via the tail vein for 6 weeks to induce heart failure, and their body weights decreased to varying degrees.",9,9,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,decreased,decreased,unchanged,NA,decreased,Signature 2,Figure 8 & 9,27 June 2025,Victoria,Victoria,"Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.",decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides rodentium,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus murinus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|691816;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|91061|186826|33958|2767887;1783272|1239|91061|186826|33958|2767887|1622;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|1263,Complete,KateRasheed
bsdb:37180435/4/1,37180435,laboratory experiment,37180435,10.3389/fcimb.2023.1135428,NA,"Fan Y., Liang L., Tang X., Zhu J., Mu L., Wang M., Huang X., Gong S., Xu J., Liu T. , Zhang T.",Changes in the gut microbiota structure and function in rats with doxorubicin-induced heart failure,Frontiers in cellular and infection microbiology,2023,"16S rRNA gene sequencing, animal model, doxorubicin, gut microbiota, heart failure, intestinal hypothesis",Experiment 4,China,Rattus norvegicus,Feces,UBERON:0001988,Heart failure,EFO:0003144,Control (Con-J) group,Doxorubicin-D (Dox-D) group,"The rats in the DOX-D group were administered doxorubicin via the tail vein in the following concentrations: 3mg/kg in weeks 1, 3, and 5, and 1mg/kg in weeks 2, 4 & 6 to induce heart failure, and their body weights decreased to varying degrees.",9,9,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 8 & 9,27 June 2025,Victoria,Victoria,"Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae",3379134|1224|1236|91347|543;3379134|1224|1236|91347;3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|543|1940338;3379134|976|200643|171549|171550;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|1853231|283168;3379134|976|200643|1970189|1573805,Complete,KateRasheed
bsdb:37180435/4/2,37180435,laboratory experiment,37180435,10.3389/fcimb.2023.1135428,NA,"Fan Y., Liang L., Tang X., Zhu J., Mu L., Wang M., Huang X., Gong S., Xu J., Liu T. , Zhang T.",Changes in the gut microbiota structure and function in rats with doxorubicin-induced heart failure,Frontiers in cellular and infection microbiology,2023,"16S rRNA gene sequencing, animal model, doxorubicin, gut microbiota, heart failure, intestinal hypothesis",Experiment 4,China,Rattus norvegicus,Feces,UBERON:0001988,Heart failure,EFO:0003144,Control (Con-J) group,Doxorubicin-D (Dox-D) group,"The rats in the DOX-D group were administered doxorubicin via the tail vein in the following concentrations: 3mg/kg in weeks 1, 3, and 5, and 1mg/kg in weeks 2, 4 & 6 to induce heart failure, and their body weights decreased to varying degrees.",9,9,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 8 & 9,27 June 2025,Victoria,Victoria,"Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides rodentium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus murinus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota",1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|815|816|691816;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815;1783272|1239|91061|186826|33958|2767887|1622;1783272|1239|91061|186826|33958|2767887;1783272|1239,Complete,KateRasheed
bsdb:37180435/5/1,37180435,laboratory experiment,37180435,10.3389/fcimb.2023.1135428,NA,"Fan Y., Liang L., Tang X., Zhu J., Mu L., Wang M., Huang X., Gong S., Xu J., Liu T. , Zhang T.",Changes in the gut microbiota structure and function in rats with doxorubicin-induced heart failure,Frontiers in cellular and infection microbiology,2023,"16S rRNA gene sequencing, animal model, doxorubicin, gut microbiota, heart failure, intestinal hypothesis",Experiment 5,China,Rattus norvegicus,Feces,UBERON:0001988,Heart failure,EFO:0003144,Control (Con-J) group,Doxorubicin-E (Dox-E) group,"The rats in the DOX-E group were administered doxorubicin via the tail vein in the following concentrations: 3.5mg/kg in weeks 1, 3, and 5, and 1.5mg/kg in weeks 2, 4 & 6 to induce heart failure, and their body weights decreased to varying degrees.",9,9,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,decreased,unchanged,unchanged,NA,unchanged,Signature 1,Figure 8 & 9,27 June 2025,Victoria,Victoria,"Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",3379134|1224|1236|91347|543|1940338;3379134|1224|1236|91347|543;3379134|1224|1236|91347;3379134|1224|1236|91347|543|561|562;3379134|1224;3379134|1224|1236;3379134|976|200643|171549|1853231|283168;3379134|976|200643|1970189|1573805;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550,Complete,KateRasheed
bsdb:37180435/5/2,37180435,laboratory experiment,37180435,10.3389/fcimb.2023.1135428,NA,"Fan Y., Liang L., Tang X., Zhu J., Mu L., Wang M., Huang X., Gong S., Xu J., Liu T. , Zhang T.",Changes in the gut microbiota structure and function in rats with doxorubicin-induced heart failure,Frontiers in cellular and infection microbiology,2023,"16S rRNA gene sequencing, animal model, doxorubicin, gut microbiota, heart failure, intestinal hypothesis",Experiment 5,China,Rattus norvegicus,Feces,UBERON:0001988,Heart failure,EFO:0003144,Control (Con-J) group,Doxorubicin-E (Dox-E) group,"The rats in the DOX-E group were administered doxorubicin via the tail vein in the following concentrations: 3.5mg/kg in weeks 1, 3, and 5, and 1.5mg/kg in weeks 2, 4 & 6 to induce heart failure, and their body weights decreased to varying degrees.",9,9,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,decreased,unchanged,unchanged,NA,unchanged,Signature 2,Figure 8 & 9,27 June 2025,Victoria,Victoria,"Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides rodentium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus murinus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Clostridia",1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|815|816|691816;1783272|1239|186801|186802;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|91061|186826|33958|2767887|1622;1783272|1239|91061|186826|33958|2767887;1783272|1239|186801,Complete,KateRasheed
bsdb:37180435/6/1,37180435,laboratory experiment,37180435,10.3389/fcimb.2023.1135428,NA,"Fan Y., Liang L., Tang X., Zhu J., Mu L., Wang M., Huang X., Gong S., Xu J., Liu T. , Zhang T.",Changes in the gut microbiota structure and function in rats with doxorubicin-induced heart failure,Frontiers in cellular and infection microbiology,2023,"16S rRNA gene sequencing, animal model, doxorubicin, gut microbiota, heart failure, intestinal hypothesis",Experiment 6,China,Rattus norvegicus,Feces,UBERON:0001988,Heart failure,EFO:0003144,Control (Con-J) group,Doxorubicin-F (Dox-F) group,"The rats in the DOX-F group were administered doxorubicin via the tail vein in the following concentrations: 4mg/kg in weeks 1, 3, and 5, and 2mg/kg in weeks 2, 4 & 6 to induce heart failure, and their body weights decreased to varying degrees.",9,7,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,decreased,decreased,unchanged,NA,decreased,Signature 1,Figure 8 & 9,27 June 2025,Victoria,Victoria,"Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",3379134|1224|1236|91347|543|1940338;3379134|1224|1236|91347|543|561|562;3379134|1224;3379134|1224|1236;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|976|200643|171549|1853231|283168;3379134|976|200643|1970189|1573805;1783272|1239|91061|186826|33958|2742598;1783272|1239|91061|186826|33958|2742598|1598;1783272|1239|526524|526525|128827|1937008;3379134|976|200643|171549|171550;3379134|976|200643|171549|171550|239759,Complete,KateRasheed
bsdb:37180435/6/2,37180435,laboratory experiment,37180435,10.3389/fcimb.2023.1135428,NA,"Fan Y., Liang L., Tang X., Zhu J., Mu L., Wang M., Huang X., Gong S., Xu J., Liu T. , Zhang T.",Changes in the gut microbiota structure and function in rats with doxorubicin-induced heart failure,Frontiers in cellular and infection microbiology,2023,"16S rRNA gene sequencing, animal model, doxorubicin, gut microbiota, heart failure, intestinal hypothesis",Experiment 6,China,Rattus norvegicus,Feces,UBERON:0001988,Heart failure,EFO:0003144,Control (Con-J) group,Doxorubicin-F (Dox-F) group,"The rats in the DOX-F group were administered doxorubicin via the tail vein in the following concentrations: 4mg/kg in weeks 1, 3, and 5, and 2mg/kg in weeks 2, 4 & 6 to induce heart failure, and their body weights decreased to varying degrees.",9,7,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,decreased,decreased,unchanged,NA,decreased,Signature 2,Figure 8 & 9,27 June 2025,Victoria,Victoria,"Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides rodentium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus murinus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Clostridia",3379134|976|200643|171549|815|816|691816;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;1783272|1239|91061|186826|33958|2767887|1622;1783272|1239|91061|186826|33958|2767887;1783272|1239|186801,Complete,KateRasheed
bsdb:37180435/7/1,37180435,laboratory experiment,37180435,10.3389/fcimb.2023.1135428,NA,"Fan Y., Liang L., Tang X., Zhu J., Mu L., Wang M., Huang X., Gong S., Xu J., Liu T. , Zhang T.",Changes in the gut microbiota structure and function in rats with doxorubicin-induced heart failure,Frontiers in cellular and infection microbiology,2023,"16S rRNA gene sequencing, animal model, doxorubicin, gut microbiota, heart failure, intestinal hypothesis",Experiment 7,China,Rattus norvegicus,Feces,UBERON:0001988,Heart failure,EFO:0003144,Control (Con-K) group,Doxorubicin-G (Dox-G) group,"The rats in the DOX-G group were administered doxorubicin intraperitoneally in the following concentrations: 3mg/kg in weeks 1, 3, and 5, and 1mg/kg in weeks 2, 4 & 6 to induce heart failure, and their body weights increased to varying degrees.",9,9,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,decreased,unchanged,decreased,NA,increased,Signature 1,Figure 8 & 9,27 June 2025,Victoria,Victoria,"Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.",increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae",1783272|201174;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004;1783272|201174|84992;1783272|201174|1760|85004|31953|1678|1694;1783272|201174|1760|85004|31953,Complete,KateRasheed
bsdb:37180435/7/2,37180435,laboratory experiment,37180435,10.3389/fcimb.2023.1135428,NA,"Fan Y., Liang L., Tang X., Zhu J., Mu L., Wang M., Huang X., Gong S., Xu J., Liu T. , Zhang T.",Changes in the gut microbiota structure and function in rats with doxorubicin-induced heart failure,Frontiers in cellular and infection microbiology,2023,"16S rRNA gene sequencing, animal model, doxorubicin, gut microbiota, heart failure, intestinal hypothesis",Experiment 7,China,Rattus norvegicus,Feces,UBERON:0001988,Heart failure,EFO:0003144,Control (Con-K) group,Doxorubicin-G (Dox-G) group,"The rats in the DOX-G group were administered doxorubicin intraperitoneally in the following concentrations: 3mg/kg in weeks 1, 3, and 5, and 1mg/kg in weeks 2, 4 & 6 to induce heart failure, and their body weights increased to varying degrees.",9,9,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,decreased,unchanged,decreased,NA,increased,Signature 2,Figure 8 & 9,27 June 2025,Victoria,Victoria,"Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides rodentium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia",1783272|1239|186801|3085636;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|815|816|691816;1783272|1239|186801|186802|216572;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815;1783272|1239|186801|186802;1783272|1239|186801,Complete,KateRasheed
bsdb:37180435/8/1,37180435,laboratory experiment,37180435,10.3389/fcimb.2023.1135428,NA,"Fan Y., Liang L., Tang X., Zhu J., Mu L., Wang M., Huang X., Gong S., Xu J., Liu T. , Zhang T.",Changes in the gut microbiota structure and function in rats with doxorubicin-induced heart failure,Frontiers in cellular and infection microbiology,2023,"16S rRNA gene sequencing, animal model, doxorubicin, gut microbiota, heart failure, intestinal hypothesis",Experiment 8,China,Rattus norvegicus,Feces,UBERON:0001988,Heart failure,EFO:0003144,Control (Con-K) group,Doxorubicin-H (Dox-H) group,"The rats in the DOX-H group were administered doxorubicin intraperitoneally in the following concentrations: 3.5mg/kg in weeks 1, 3, and 5, and 1.5mg/kg in weeks 2, 4 & 6 to induce heart failure, and their body weights increased to varying degrees.",9,9,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,decreased,increased,decreased,NA,increased,Signature 1,Figure 8 & 9,27 June 2025,Victoria,Victoria,"Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.",increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum|s__Faecalibaculum rodentium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella",1783272|1239|91061;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|33959;1783272|1239|91061|186826;1783272|1239|91061|186826|33958;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|201174;1783272|201174|1760|85004|31953|1678|1694;1783272|201174|84992;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|201174|1760|85004;1783272|1239|526524|526525|128827|1729679|1702221;1783272|1239|526524|526525|128827|1729679;1783272|1239|526524|526525|128827|1937008,Complete,KateRasheed
bsdb:37180435/8/2,37180435,laboratory experiment,37180435,10.3389/fcimb.2023.1135428,NA,"Fan Y., Liang L., Tang X., Zhu J., Mu L., Wang M., Huang X., Gong S., Xu J., Liu T. , Zhang T.",Changes in the gut microbiota structure and function in rats with doxorubicin-induced heart failure,Frontiers in cellular and infection microbiology,2023,"16S rRNA gene sequencing, animal model, doxorubicin, gut microbiota, heart failure, intestinal hypothesis",Experiment 8,China,Rattus norvegicus,Feces,UBERON:0001988,Heart failure,EFO:0003144,Control (Con-K) group,Doxorubicin-H (Dox-H) group,"The rats in the DOX-H group were administered doxorubicin intraperitoneally in the following concentrations: 3.5mg/kg in weeks 1, 3, and 5, and 1.5mg/kg in weeks 2, 4 & 6 to induce heart failure, and their body weights increased to varying degrees.",9,9,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,decreased,increased,decreased,NA,increased,Signature 2,Figure 8 & 9,27 June 2025,Victoria,Victoria,"Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.",decreased,"k__Bacillati,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus murinus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136",1783272;3379134|976|200643|171549;3379134|976|200643;3379134|976;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;1783272|1239|91061|186826|33958|2767887;1783272|1239|91061|186826|33958|2767887|1622;3379134|976|200643|171549|2005473;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|877420,Complete,KateRasheed
bsdb:37180435/9/1,37180435,laboratory experiment,37180435,10.3389/fcimb.2023.1135428,NA,"Fan Y., Liang L., Tang X., Zhu J., Mu L., Wang M., Huang X., Gong S., Xu J., Liu T. , Zhang T.",Changes in the gut microbiota structure and function in rats with doxorubicin-induced heart failure,Frontiers in cellular and infection microbiology,2023,"16S rRNA gene sequencing, animal model, doxorubicin, gut microbiota, heart failure, intestinal hypothesis",Experiment 9,China,Rattus norvegicus,Feces,UBERON:0001988,Heart failure,EFO:0003144,Control (Con-K) group,Doxorubicin-I (Dox-I) group,"The rats in the DOX-I group were administered doxorubicin intraperitoneally in the following concentrations: 4mg/kg in weeks 1, 3, and 5, and 2mg/kg in weeks 2, 4 & 6 to induce heart failure, and their body weights increased to varying degrees.",9,7,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,Figure 8 & 9,27 June 2025,Victoria,Victoria,"Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.",increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,s__iron-reducing bacterium enrichment culture clone HN70,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium",1783272|201174|84992;1783272|201174;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|1694;1783272|1239|91061;1783272|1239|526524|526525|128827;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|33959;1783272|1239|526524|526525;1783272|1239|526524|526525|128827|1937008;1783272|201174|84998;1783272|201174|84998|84999;1783272|201174|84998|84999|1643824;569512;1783272|1239|526524|526525|128827|123375,Complete,KateRasheed
bsdb:37180435/9/2,37180435,laboratory experiment,37180435,10.3389/fcimb.2023.1135428,NA,"Fan Y., Liang L., Tang X., Zhu J., Mu L., Wang M., Huang X., Gong S., Xu J., Liu T. , Zhang T.",Changes in the gut microbiota structure and function in rats with doxorubicin-induced heart failure,Frontiers in cellular and infection microbiology,2023,"16S rRNA gene sequencing, animal model, doxorubicin, gut microbiota, heart failure, intestinal hypothesis",Experiment 9,China,Rattus norvegicus,Feces,UBERON:0001988,Heart failure,EFO:0003144,Control (Con-K) group,Doxorubicin-I (Dox-I) group,"The rats in the DOX-I group were administered doxorubicin intraperitoneally in the following concentrations: 4mg/kg in weeks 1, 3, and 5, and 2mg/kg in weeks 2, 4 & 6 to induce heart failure, and their body weights increased to varying degrees.",9,7,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 2,Figure 8 & 9,27 June 2025,Victoria,Victoria,"Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.",decreased,"k__Bacillati,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides rodentium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus murinus,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136",1783272;1783272|1239;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|691816;3379134|976|200643;3379134|976;3379134|1224|28211|204458|76892|41275;95818|2093818|2093825|2171986;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;1783272|1239|91061|186826|33958|2767887;1783272|1239|91061|186826|33958|2767887|1622;1783272|1239|186801|3085656|3085657;1783272|1239|186801|3085656;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|877420,Complete,KateRasheed
bsdb:37180439/1/1,37180439,case-control,37180439,10.3389/fcimb.2023.1157368,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2023.1157368/full,"Niu C., Tu Y., Jin Q., Chen Z., Yuan K., Wang M., Zhang P., Luo J., Li H., Yang Y., Liu X., Mao M., Dong T., Tan W., Hu X., Pan Y., Hou L., Ma R. , Huang Z.",Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease,Frontiers in cellular and infection microbiology,2023,"gut mycobiome, metabolic dysfunction-associated fatty liver disease, metagenomics, oral mycobiome, oral-gut axis",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Non-alcoholic fatty liver disease,EFO:0003095,Healthy Controls,Patients with Metabolic dysfunction-associated liver disease (MAFLD),"Patients diagnosed with Non-alcoholic fatty liver disease (now known as Metabolic dysfunction-associated fatty liver disease ""MAFLD"")",20,21,more than 5 days during 6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Fig. 2c,22 October 2025,Deborah-Fabusuyi,"WikiWorks,Deborah-Fabusuyi,Tosin",Differential fungal species in the saliva mycobiome between Metabolic dysfunction-associated fatty liver disease (MAFLD) patients and Healthy controls.,increased,"k__Fungi|p__Zoopagomycota|c__Basidiobolomycetes|o__Basidiobolales|f__Basidiobolaceae|g__Basidiobolus|s__Basidiobolus meristosporus,k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Mucor|s__Mucor ambiguus",4751|1913638|1399768|1264872|4858|4859|423460;4751|1913637|2212703|4827|34489|4830|91626,Complete,KateRasheed
bsdb:37180439/2/1,37180439,case-control,37180439,10.3389/fcimb.2023.1157368,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2023.1157368/full,"Niu C., Tu Y., Jin Q., Chen Z., Yuan K., Wang M., Zhang P., Luo J., Li H., Yang Y., Liu X., Mao M., Dong T., Tan W., Hu X., Pan Y., Hou L., Ma R. , Huang Z.",Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease,Frontiers in cellular and infection microbiology,2023,"gut mycobiome, metabolic dysfunction-associated fatty liver disease, metagenomics, oral mycobiome, oral-gut axis",Experiment 2,China,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Non-alcoholic fatty liver disease,EFO:0003095,Healthy Controls,Patients with Metabolic dysfunction-associated liver disease,"Patients diagnosed with Non-alcoholic fatty liver disease (now known as Metabolic dysfunction-associated fatty liver disease ""MAFLD"")",20,21,more than 5 days during 6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 2c,22 October 2025,Deborah-Fabusuyi,"WikiWorks,Deborah-Fabusuyi,Tosin",Differential fungal species in the supragingival mycobiome between Metabolic dysfunction-associated fatty liver disease (MAFLD) patients and Healthy controls.,increased,"k__Fungi|p__Mucoromycota|c__Glomeromycetes|o__Glomerales|f__Glomeraceae|g__Glomus|s__Glomus cerebriforme,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae x Saccharomyces kudriavzevii,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces paradoxus,k__Fungi|p__Ascomycota|c__Schizosaccharomycetes|o__Schizosaccharomycetales|f__Schizosaccharomycetaceae|g__Schizosaccharomyces|s__Schizosaccharomyces pombe,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Trichomonascaceae|g__Sugiyamaella|s__Sugiyamaella lignohabitans",4751|1913637|214506|36750|36751|4875|658196;4751|4890|4891|4892|4893|4930|4932;4751|4890|4891|4892|4893|4930|332112;4751|4890|4891|4892|4893|4930|27291;4751|4890|147554|34346|4894|4895|4896;4751|4890|3239873|3243772|410830|410829|796027,Complete,KateRasheed
bsdb:37180439/2/2,37180439,case-control,37180439,10.3389/fcimb.2023.1157368,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2023.1157368/full,"Niu C., Tu Y., Jin Q., Chen Z., Yuan K., Wang M., Zhang P., Luo J., Li H., Yang Y., Liu X., Mao M., Dong T., Tan W., Hu X., Pan Y., Hou L., Ma R. , Huang Z.",Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease,Frontiers in cellular and infection microbiology,2023,"gut mycobiome, metabolic dysfunction-associated fatty liver disease, metagenomics, oral mycobiome, oral-gut axis",Experiment 2,China,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Non-alcoholic fatty liver disease,EFO:0003095,Healthy Controls,Patients with Metabolic dysfunction-associated liver disease,"Patients diagnosed with Non-alcoholic fatty liver disease (now known as Metabolic dysfunction-associated fatty liver disease ""MAFLD"")",20,21,more than 5 days during 6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 2c,22 October 2025,Deborah-Fabusuyi,"WikiWorks,Deborah-Fabusuyi,Tosin",Differential fungal species in the supragingival mycobiome between Metabolic dysfunction-associated fatty liver disease (MAFLD) patients and Healthy controls.,decreased,"k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Onygenales|f__Arthrodermataceae|g__Arthroderma|s__Arthroderma uncinatum,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Diaporthales|f__Cytosporaceae|g__Cytospora|s__Cytospora leucostoma,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales|f__Peniophoraceae|g__Peniophora|s__Peniophora sp. CBMAI 1063,k__Fungi|p__Mucoromycota|c__Glomeromycetes|o__Glomerales|f__Glomeraceae|g__Rhizophagus|s__Rhizophagus sp. MUCL 43196",4751|4890|147545|33183|34384|63399|74035;4751|4890|147550|5114|5117|117544|1230097;4751|5204|155619|452342|103393|40463|718367;4751|1913637|214506|36750|36751|1129544|1803374,Complete,KateRasheed
bsdb:37180439/3/1,37180439,case-control,37180439,10.3389/fcimb.2023.1157368,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2023.1157368/full,"Niu C., Tu Y., Jin Q., Chen Z., Yuan K., Wang M., Zhang P., Luo J., Li H., Yang Y., Liu X., Mao M., Dong T., Tan W., Hu X., Pan Y., Hou L., Ma R. , Huang Z.",Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease,Frontiers in cellular and infection microbiology,2023,"gut mycobiome, metabolic dysfunction-associated fatty liver disease, metagenomics, oral mycobiome, oral-gut axis",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,Healthy Controls,Patients with Metabolic dysfunction-associated liver disease,"Patients diagnosed with Non-alcoholic fatty liver disease (now known as Metabolic dysfunction-associated fatty liver disease ""MAFLD"")",20,21,more than 5 days during 6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,decreased,unchanged,decreased,NA,NA,Signature 1,Figure 2c,22 October 2025,Deborah-Fabusuyi,"WikiWorks,Deborah-Fabusuyi,Saima-Younis,Tosin",Differential fungal species in the gut (feces) mycobiome between Metabolic dysfunction-associated fatty liver disease (MAFLD) patients and Healthy controls.,increased,k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Mucor|s__Mucor ambiguus,4751|1913637|2212703|4827|34489|4830|91626,Complete,KateRasheed
bsdb:37180439/3/2,37180439,case-control,37180439,10.3389/fcimb.2023.1157368,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2023.1157368/full,"Niu C., Tu Y., Jin Q., Chen Z., Yuan K., Wang M., Zhang P., Luo J., Li H., Yang Y., Liu X., Mao M., Dong T., Tan W., Hu X., Pan Y., Hou L., Ma R. , Huang Z.",Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease,Frontiers in cellular and infection microbiology,2023,"gut mycobiome, metabolic dysfunction-associated fatty liver disease, metagenomics, oral mycobiome, oral-gut axis",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,Healthy Controls,Patients with Metabolic dysfunction-associated liver disease,"Patients diagnosed with Non-alcoholic fatty liver disease (now known as Metabolic dysfunction-associated fatty liver disease ""MAFLD"")",20,21,more than 5 days during 6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,decreased,unchanged,decreased,NA,NA,Signature 2,Figure 2c,22 October 2025,Deborah-Fabusuyi,"WikiWorks,Deborah-Fabusuyi,Saima-Younis,Tosin",Differential fungal species in the gut (feces) mycobiome between Metabolic dysfunction-associated fatty liver disease (MAFLD) patients and Healthy controls.,decreased,"k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Ophiocordycipitaceae|g__Purpureocillium|s__Purpureocillium lilacinum,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae x Saccharomyces kudriavzevii,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces paradoxus,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces pastorianus,k__Fungi|p__Ascomycota|c__Schizosaccharomycetes|o__Schizosaccharomycetales|f__Schizosaccharomycetaceae|g__Schizosaccharomyces|s__Schizosaccharomyces pombe",4751|4890|147550|5125|474942|1052105|33203;4751|4890|4891|4892|4893|4930|4932;4751|4890|4891|4892|4893|4930|332112;4751|4890|4891|4892|4893|4930|27291;4751|4890|4891|4892|4893|4930|27292;4751|4890|147554|34346|4894|4895|4896,Complete,KateRasheed
bsdb:37180439/4/1,37180439,case-control,37180439,10.3389/fcimb.2023.1157368,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2023.1157368/full,"Niu C., Tu Y., Jin Q., Chen Z., Yuan K., Wang M., Zhang P., Luo J., Li H., Yang Y., Liu X., Mao M., Dong T., Tan W., Hu X., Pan Y., Hou L., Ma R. , Huang Z.",Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease,Frontiers in cellular and infection microbiology,2023,"gut mycobiome, metabolic dysfunction-associated fatty liver disease, metagenomics, oral mycobiome, oral-gut axis",Experiment 4,China,Homo sapiens,Saliva,UBERON:0001836,Body mass index,EFO:0004340,Healthy Controls,Patients with Metabolic dysfunction-associated liver disease,"Patients diagnosed with Non-alcoholic fatty liver disease (now known as Metabolic dysfunction-associated fatty liver disease ""MAFLD"")",20,21,more than 5 days during 6 months,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3a,25 October 2025,Deborah-Fabusuyi,"WikiWorks,Deborah-Fabusuyi,Tosin",Heatmap of Spearman correlation analysis of Body Mass Index (BMI) between participants with Metabolic dysfunction-associated fatty liver disease (MAFLD) and Healthy Controls in Saliva,increased,k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Mucor|s__Mucor ambiguus,4751|1913637|2212703|4827|34489|4830|91626,Complete,KateRasheed
bsdb:37180439/5/1,37180439,case-control,37180439,10.3389/fcimb.2023.1157368,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2023.1157368/full,"Niu C., Tu Y., Jin Q., Chen Z., Yuan K., Wang M., Zhang P., Luo J., Li H., Yang Y., Liu X., Mao M., Dong T., Tan W., Hu X., Pan Y., Hou L., Ma R. , Huang Z.",Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease,Frontiers in cellular and infection microbiology,2023,"gut mycobiome, metabolic dysfunction-associated fatty liver disease, metagenomics, oral mycobiome, oral-gut axis",Experiment 5,China,Homo sapiens,Saliva,UBERON:0001836,HbA1c measurement,EFO:0004541,Healthy Controls,Patients with Metabolic dysfunction-associated liver disease,"Patients diagnosed with Non-alcoholic fatty liver disease (now known as Metabolic dysfunction-associated fatty liver disease ""MAFLD"")",20,21,more than 5 days during 6 months,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3a,25 October 2025,Deborah-Fabusuyi,"WikiWorks,Deborah-Fabusuyi,Tosin",Heatmap of Spearman correlation analysis of glycosylated hemoglobin type A1C (HbA1C) between participants with Metabolic dysfunction-associated fatty liver disease (MAFLD) and Healthy Controls in Saliva,increased,k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Mucor|s__Mucor ambiguus,4751|1913637|2212703|4827|34489|4830|91626,Complete,KateRasheed
bsdb:37180439/6/1,37180439,case-control,37180439,10.3389/fcimb.2023.1157368,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2023.1157368/full,"Niu C., Tu Y., Jin Q., Chen Z., Yuan K., Wang M., Zhang P., Luo J., Li H., Yang Y., Liu X., Mao M., Dong T., Tan W., Hu X., Pan Y., Hou L., Ma R. , Huang Z.",Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease,Frontiers in cellular and infection microbiology,2023,"gut mycobiome, metabolic dysfunction-associated fatty liver disease, metagenomics, oral mycobiome, oral-gut axis",Experiment 6,China,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Triglyceride measurement,EFO:0004530,Healthy Controls,Patients with Metabolic dysfunction-associated liver disease,"Patients diagnosed with Non-alcoholic fatty liver disease (now known as Metabolic dysfunction-associated fatty liver disease ""MAFLD"")",20,21,more than 5 days during 6 months,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3b,26 October 2025,Deborah-Fabusuyi,"WikiWorks,Deborah-Fabusuyi,Tosin",Heatmap of Spearman correlation analysis of triglyceride (TG) between participants with Metabolic dysfunction-associated fatty liver disease (MAFLD) and Healthy controls in Supragingival dental plaques.,increased,"k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae,k__Fungi|p__Ascomycota|c__Schizosaccharomycetes|o__Schizosaccharomycetales|f__Schizosaccharomycetaceae|g__Schizosaccharomyces|s__Schizosaccharomyces pombe",4751|4890|4891|4892|4893|4930|4932;4751|4890|147554|34346|4894|4895|4896,Complete,KateRasheed
bsdb:37180439/6/2,37180439,case-control,37180439,10.3389/fcimb.2023.1157368,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2023.1157368/full,"Niu C., Tu Y., Jin Q., Chen Z., Yuan K., Wang M., Zhang P., Luo J., Li H., Yang Y., Liu X., Mao M., Dong T., Tan W., Hu X., Pan Y., Hou L., Ma R. , Huang Z.",Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease,Frontiers in cellular and infection microbiology,2023,"gut mycobiome, metabolic dysfunction-associated fatty liver disease, metagenomics, oral mycobiome, oral-gut axis",Experiment 6,China,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Triglyceride measurement,EFO:0004530,Healthy Controls,Patients with Metabolic dysfunction-associated liver disease,"Patients diagnosed with Non-alcoholic fatty liver disease (now known as Metabolic dysfunction-associated fatty liver disease ""MAFLD"")",20,21,more than 5 days during 6 months,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 3b,26 October 2025,Deborah-Fabusuyi,"WikiWorks,Deborah-Fabusuyi,Tosin",Heatmap of Spearman correlation analysis of triglyceride (TG) between participants with Metabolic dysfunction-associated fatty liver disease (MAFLD)  and Healthy controls in Supragingival dental plaques.,decreased,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Diaporthales|f__Cytosporaceae|g__Cytospora|s__Cytospora leucostoma,4751|4890|147550|5114|5117|117544|1230097,Complete,KateRasheed
bsdb:37180439/7/1,37180439,case-control,37180439,10.3389/fcimb.2023.1157368,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2023.1157368/full,"Niu C., Tu Y., Jin Q., Chen Z., Yuan K., Wang M., Zhang P., Luo J., Li H., Yang Y., Liu X., Mao M., Dong T., Tan W., Hu X., Pan Y., Hou L., Ma R. , Huang Z.",Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease,Frontiers in cellular and infection microbiology,2023,"gut mycobiome, metabolic dysfunction-associated fatty liver disease, metagenomics, oral mycobiome, oral-gut axis",Experiment 7,China,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Serum gamma-glutamyl transferase measurement,EFO:0004532,Healthy Controls,Patients with Metabolic dysfunction-associated liver disease,"Patients diagnosed with Non-alcoholic fatty liver disease (now known as Metabolic dysfunction-associated fatty liver disease ""MAFLD"")",20,21,more than 5 days during 6 months,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3b,26 October 2025,Deborah-Fabusuyi,"WikiWorks,Deborah-Fabusuyi,Tosin",Heatmap of Spearman correlation analysis of gamma-glutamyl transferase (GGT) between participants with Metabolic dysfunction-associated fatty liver disease (MAFLD) and Healthy controls in Supragingival dental plaques.,increased,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae,4751|4890|4891|4892|4893|4930|4932,Complete,KateRasheed
bsdb:37180439/7/2,37180439,case-control,37180439,10.3389/fcimb.2023.1157368,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2023.1157368/full,"Niu C., Tu Y., Jin Q., Chen Z., Yuan K., Wang M., Zhang P., Luo J., Li H., Yang Y., Liu X., Mao M., Dong T., Tan W., Hu X., Pan Y., Hou L., Ma R. , Huang Z.",Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease,Frontiers in cellular and infection microbiology,2023,"gut mycobiome, metabolic dysfunction-associated fatty liver disease, metagenomics, oral mycobiome, oral-gut axis",Experiment 7,China,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Serum gamma-glutamyl transferase measurement,EFO:0004532,Healthy Controls,Patients with Metabolic dysfunction-associated liver disease,"Patients diagnosed with Non-alcoholic fatty liver disease (now known as Metabolic dysfunction-associated fatty liver disease ""MAFLD"")",20,21,more than 5 days during 6 months,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 3b,26 October 2025,Deborah-Fabusuyi,"WikiWorks,Deborah-Fabusuyi,Tosin",Heatmap of Spearman correlation analysis of gamma-glutamyl transferase (GGT) between participants with Metabolic dysfunction-associated fatty liver disease (MAFLD) and Healthy controls in Supragingival dental plaques.,decreased,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Diaporthales|f__Cytosporaceae|g__Cytospora|s__Cytospora leucostoma,4751|4890|147550|5114|5117|117544|1230097,Complete,KateRasheed
bsdb:37180439/8/1,37180439,case-control,37180439,10.3389/fcimb.2023.1157368,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2023.1157368/full,"Niu C., Tu Y., Jin Q., Chen Z., Yuan K., Wang M., Zhang P., Luo J., Li H., Yang Y., Liu X., Mao M., Dong T., Tan W., Hu X., Pan Y., Hou L., Ma R. , Huang Z.",Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease,Frontiers in cellular and infection microbiology,2023,"gut mycobiome, metabolic dysfunction-associated fatty liver disease, metagenomics, oral mycobiome, oral-gut axis",Experiment 8,China,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Fasting blood insulin measurement,EFO:0004466,Healthy Controls,Patients with Metabolic dysfunction-associated liver disease,"Patients diagnosed with Non-alcoholic fatty liver disease (now known as Metabolic dysfunction-associated fatty liver disease ""MAFLD"")",20,21,more than 5 days during 6 months,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3b,26 October 2025,Deborah-Fabusuyi,"WikiWorks,Deborah-Fabusuyi,Saima-Younis,Tosin",Heatmap of Spearman correlation analysis fasting serum insulin (FSI) between participants with Metabolic dysfunction-associated fatty liver disease (MAFLD) and Healthy controls in Supragingival dental plaques.,decreased,"k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Diaporthales|f__Cytosporaceae|g__Cytospora|s__Cytospora leucostoma,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales|f__Peniophoraceae|g__Peniophora|s__Peniophora sp. CBMAI 1063",4751|4890|147550|5114|5117|117544|1230097;4751|5204|155619|452342|103393|40463|718367,Complete,KateRasheed
bsdb:37180439/9/1,37180439,case-control,37180439,10.3389/fcimb.2023.1157368,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2023.1157368/full,"Niu C., Tu Y., Jin Q., Chen Z., Yuan K., Wang M., Zhang P., Luo J., Li H., Yang Y., Liu X., Mao M., Dong T., Tan W., Hu X., Pan Y., Hou L., Ma R. , Huang Z.",Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease,Frontiers in cellular and infection microbiology,2023,"gut mycobiome, metabolic dysfunction-associated fatty liver disease, metagenomics, oral mycobiome, oral-gut axis",Experiment 9,China,Homo sapiens,Supragingival dental plaque,UBERON:0016485,C-reactive protein measurement,EFO:0004458,Healthy Controls,Patients with Metabolic dysfunction-associated liver disease,"Patients diagnosed with Non-alcoholic fatty liver disease (now known as Metabolic dysfunction-associated fatty liver disease ""MAFLD"")",20,21,more than 5 days during 6 months,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3b,27 October 2025,Saima-Younis,"WikiWorks,Saima-Younis,Tosin",Heatmap of Spearman correlation analysis of C-reactive protein between participants with Metabolic dysfunction-associated fatty liver disease(MAFLD)  and Healthy controls in Supragingival dental plaques.,decreased,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Diaporthales|f__Cytosporaceae|g__Cytospora|s__Cytospora leucostoma,4751|4890|147550|5114|5117|117544|1230097,Complete,KateRasheed
bsdb:37180439/10/1,37180439,case-control,37180439,10.3389/fcimb.2023.1157368,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2023.1157368/full,"Niu C., Tu Y., Jin Q., Chen Z., Yuan K., Wang M., Zhang P., Luo J., Li H., Yang Y., Liu X., Mao M., Dong T., Tan W., Hu X., Pan Y., Hou L., Ma R. , Huang Z.",Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease,Frontiers in cellular and infection microbiology,2023,"gut mycobiome, metabolic dysfunction-associated fatty liver disease, metagenomics, oral mycobiome, oral-gut axis",Experiment 10,China,Homo sapiens,Feces,UBERON:0001988,Body mass index,EFO:0004340,Healthy Controls,Patients with Metabolic dysfunction-associated liver disease,"Patients diagnosed with Non-alcoholic fatty liver disease (now known as Metabolic dysfunction-associated fatty liver disease ""MAFLD"")",20,21,more than 5 days during 6 months,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,"age,sex",NA,NA,decreased,unchanged,decreased,NA,NA,Signature 1,Figure 3c,27 October 2025,Saima-Younis,"WikiWorks,Saima-Younis,Tosin",Heatmap of Spearman correlation analysis of Body mass index (BMI) between participants with Metabolic dysfunction-associated fatty liver disease (MAFLD) and Healthy controls in Feces,decreased,"k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Ophiocordycipitaceae|g__Purpureocillium|s__Purpureocillium lilacinum,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae x Saccharomyces kudriavzevii,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces paradoxus,k__Fungi|p__Ascomycota|c__Schizosaccharomycetes|o__Schizosaccharomycetales|f__Schizosaccharomycetaceae|g__Schizosaccharomyces|s__Schizosaccharomyces pombe",4751|4890|147550|5125|474942|1052105|33203;4751|4890|4891|4892|4893|4930|332112;4751|4890|4891|4892|4893|4930|27291;4751|4890|147554|34346|4894|4895|4896,Complete,KateRasheed
bsdb:37180439/11/1,37180439,case-control,37180439,10.3389/fcimb.2023.1157368,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2023.1157368/full,"Niu C., Tu Y., Jin Q., Chen Z., Yuan K., Wang M., Zhang P., Luo J., Li H., Yang Y., Liu X., Mao M., Dong T., Tan W., Hu X., Pan Y., Hou L., Ma R. , Huang Z.",Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease,Frontiers in cellular and infection microbiology,2023,"gut mycobiome, metabolic dysfunction-associated fatty liver disease, metagenomics, oral mycobiome, oral-gut axis",Experiment 11,China,Homo sapiens,Feces,UBERON:0001988,Total cholesterol measurement,EFO:0004574,Healthy Controls,Patients with Metabolic dysfunction-associated liver disease,"Patients diagnosed with Non-alcoholic fatty liver disease (now known as Metabolic dysfunction-associated fatty liver disease ""MAFLD"")",20,21,more than 5 days during 6 months,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,"age,sex",NA,NA,decreased,unchanged,decreased,NA,NA,Signature 1,Figure 3c,27 October 2025,Saima-Younis,"WikiWorks,Saima-Younis,Tosin",Heatmap of Spearman correlation analysis of Total cholesterol (TC)  between participants with Metabolic dysfunction-associated fatty liver disease (MAFLD) and Healthy controls in Feces,increased,k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Mucor|s__Mucor ambiguus,4751|1913637|2212703|4827|34489|4830|91626,Complete,KateRasheed
bsdb:37180439/12/1,37180439,case-control,37180439,10.3389/fcimb.2023.1157368,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2023.1157368/full,"Niu C., Tu Y., Jin Q., Chen Z., Yuan K., Wang M., Zhang P., Luo J., Li H., Yang Y., Liu X., Mao M., Dong T., Tan W., Hu X., Pan Y., Hou L., Ma R. , Huang Z.",Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease,Frontiers in cellular and infection microbiology,2023,"gut mycobiome, metabolic dysfunction-associated fatty liver disease, metagenomics, oral mycobiome, oral-gut axis",Experiment 12,China,Homo sapiens,Feces,UBERON:0001988,Triglyceride measurement,EFO:0004530,Healthy Controls,Patients with Metabolic dysfunction-associated liver disease,"Patients diagnosed with Non-alcoholic fatty liver disease (now known as Metabolic dysfunction-associated fatty liver disease ""MAFLD"")",20,21,more than 5 days during 6 months,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,"age,sex",NA,NA,decreased,unchanged,decreased,NA,NA,Signature 1,Figure 3c,27 October 2025,Saima-Younis,"WikiWorks,Saima-Younis,Tosin",Heatmap of Spearman correlation analysis of Triglyceride (TG) between participants with Metabolic dysfunction-associated fatty liver disease (MAFLD) and Healthy controls in Feces,decreased,"k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae x Saccharomyces kudriavzevii,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces paradoxus,k__Fungi|p__Ascomycota|c__Schizosaccharomycetes|o__Schizosaccharomycetales|f__Schizosaccharomycetaceae|g__Schizosaccharomyces|s__Schizosaccharomyces pombe",4751|4890|4891|4892|4893|4930|332112;4751|4890|4891|4892|4893|4930|27291;4751|4890|147554|34346|4894|4895|4896,Complete,KateRasheed
bsdb:37180439/13/1,37180439,case-control,37180439,10.3389/fcimb.2023.1157368,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2023.1157368/full,"Niu C., Tu Y., Jin Q., Chen Z., Yuan K., Wang M., Zhang P., Luo J., Li H., Yang Y., Liu X., Mao M., Dong T., Tan W., Hu X., Pan Y., Hou L., Ma R. , Huang Z.",Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease,Frontiers in cellular and infection microbiology,2023,"gut mycobiome, metabolic dysfunction-associated fatty liver disease, metagenomics, oral mycobiome, oral-gut axis",Experiment 13,China,Homo sapiens,Feces,UBERON:0001988,Low density lipoprotein cholesterol measurement,EFO:0004611,Healthy Controls,Patients with Metabolic dysfunction-associated liver disease,"Patients diagnosed with Non-alcoholic fatty liver disease (now known as Metabolic dysfunction-associated fatty liver disease ""MAFLD"")",20,21,more than 5 days during 6 months,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,"age,sex",NA,NA,decreased,unchanged,decreased,NA,NA,Signature 1,Figure 3c,27 October 2025,Deborah-Fabusuyi,"WikiWorks,Saima-Younis,Deborah-Fabusuyi,Tosin",Heatmap of Spearman correlation analysis of Low-density lipoprotein cholesterol (LDL-C) between participants with Metabolic dysfunction-associated fatty liver disease (MAFLD) and Healthy controls in Feces,increased,k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Mucor|s__Mucor ambiguus,4751|1913637|2212703|4827|34489|4830|91626,Complete,KateRasheed
bsdb:37180439/14/1,37180439,case-control,37180439,10.3389/fcimb.2023.1157368,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2023.1157368/full,"Niu C., Tu Y., Jin Q., Chen Z., Yuan K., Wang M., Zhang P., Luo J., Li H., Yang Y., Liu X., Mao M., Dong T., Tan W., Hu X., Pan Y., Hou L., Ma R. , Huang Z.",Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease,Frontiers in cellular and infection microbiology,2023,"gut mycobiome, metabolic dysfunction-associated fatty liver disease, metagenomics, oral mycobiome, oral-gut axis",Experiment 14,China,Homo sapiens,Feces,UBERON:0001988,Serum alanine aminotransferase measurement,EFO:0004735,Healthy Controls,Patients with Metabolic dysfunction-associated liver disease,"Patients diagnosed with Non-alcoholic fatty liver disease (now known as Metabolic dysfunction-associated fatty liver disease ""MAFLD"")",20,21,more than 5 days during 6 months,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,"age,sex",NA,NA,decreased,unchanged,decreased,NA,NA,Signature 1,Figure 3c,27 October 2025,Deborah-Fabusuyi,"WikiWorks,Saima-Younis,Deborah-Fabusuyi,Tosin",Heatmap of Spearman correlation analysis of alanine transaminase (ALT) between participants with Metabolic dysfunction-associated fatty liver disease (MAFLD) and Healthy controls in Feces,increased,k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Mucor|s__Mucor ambiguus,4751|1913637|2212703|4827|34489|4830|91626,Complete,KateRasheed
bsdb:37180439/14/2,37180439,case-control,37180439,10.3389/fcimb.2023.1157368,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2023.1157368/full,"Niu C., Tu Y., Jin Q., Chen Z., Yuan K., Wang M., Zhang P., Luo J., Li H., Yang Y., Liu X., Mao M., Dong T., Tan W., Hu X., Pan Y., Hou L., Ma R. , Huang Z.",Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease,Frontiers in cellular and infection microbiology,2023,"gut mycobiome, metabolic dysfunction-associated fatty liver disease, metagenomics, oral mycobiome, oral-gut axis",Experiment 14,China,Homo sapiens,Feces,UBERON:0001988,Serum alanine aminotransferase measurement,EFO:0004735,Healthy Controls,Patients with Metabolic dysfunction-associated liver disease,"Patients diagnosed with Non-alcoholic fatty liver disease (now known as Metabolic dysfunction-associated fatty liver disease ""MAFLD"")",20,21,more than 5 days during 6 months,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,"age,sex",NA,NA,decreased,unchanged,decreased,NA,NA,Signature 2,Figure 3c,27 October 2025,Deborah-Fabusuyi,"WikiWorks,Saima-Younis,Deborah-Fabusuyi,Tosin",Heatmap of Spearman correlation analysis of alanine transaminase (ALT) between participants with Metabolic dysfunction-associated fatty liver disease (MAFLD) and Healthy controls in Feces,decreased,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Ophiocordycipitaceae|g__Purpureocillium|s__Purpureocillium lilacinum,4751|4890|147550|5125|474942|1052105|33203,Complete,KateRasheed
bsdb:37180439/15/1,37180439,case-control,37180439,10.3389/fcimb.2023.1157368,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2023.1157368/full,"Niu C., Tu Y., Jin Q., Chen Z., Yuan K., Wang M., Zhang P., Luo J., Li H., Yang Y., Liu X., Mao M., Dong T., Tan W., Hu X., Pan Y., Hou L., Ma R. , Huang Z.",Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease,Frontiers in cellular and infection microbiology,2023,"gut mycobiome, metabolic dysfunction-associated fatty liver disease, metagenomics, oral mycobiome, oral-gut axis",Experiment 15,China,Homo sapiens,Feces,UBERON:0001988,Fasting blood insulin measurement,EFO:0004466,Healthy Controls,Patients with Metabolic dysfunction-associated liver disease,"Patients diagnosed with Non-alcoholic fatty liver disease (now known as Metabolic dysfunction-associated fatty liver disease ""MAFLD"")",20,21,more than 5 days during 6 months,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,"age,sex",NA,NA,decreased,unchanged,decreased,NA,NA,Signature 1,Figure 3c,27 October 2025,Saima-Younis,"WikiWorks,Saima-Younis,Tosin",Heatmap of Spearman correlation analysis of Fasting serum insulin (FSI) between participants with Metabolic dysfunction-associated fatty liver disease (MAFLD) and Healthy controls in Feces,decreased,"k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae x Saccharomyces kudriavzevii,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces paradoxus,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces pastorianus,k__Fungi|p__Ascomycota|c__Schizosaccharomycetes|o__Schizosaccharomycetales|f__Schizosaccharomycetaceae|g__Schizosaccharomyces|s__Schizosaccharomyces pombe",4751|4890|4891|4892|4893|4930|4932;4751|4890|4891|4892|4893|4930|332112;4751|4890|4891|4892|4893|4930|27291;4751|4890|4891|4892|4893|4930|27292;4751|4890|147554|34346|4894|4895|4896,Complete,KateRasheed
bsdb:37180439/16/1,37180439,case-control,37180439,10.3389/fcimb.2023.1157368,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2023.1157368/full,"Niu C., Tu Y., Jin Q., Chen Z., Yuan K., Wang M., Zhang P., Luo J., Li H., Yang Y., Liu X., Mao M., Dong T., Tan W., Hu X., Pan Y., Hou L., Ma R. , Huang Z.",Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease,Frontiers in cellular and infection microbiology,2023,"gut mycobiome, metabolic dysfunction-associated fatty liver disease, metagenomics, oral mycobiome, oral-gut axis",Experiment 16,China,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Aspartate aminotransferase measurement,EFO:0004736,Healthy Controls,Patients with Metabolic dysfunction-associated liver disease,"Patients diagnosed with Non-alcoholic fatty liver disease (now known as Metabolic dysfunction-associated fatty liver disease ""MAFLD"")",20,21,more than 5 days during 6 months,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3b,29 December 2025,Tosin,Tosin,Heatmap of Spearman correlation analysis of aspartate transaminase (AST) between participants with Metabolic dysfunction-associated fatty liver disease (MAFLD) and Healthy controls in Supragingival dental plaques,increased,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae,4751|4890|4891|4892|4893|4930|4932,Complete,NA
bsdb:37180439/17/1,37180439,case-control,37180439,10.3389/fcimb.2023.1157368,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2023.1157368/full,"Niu C., Tu Y., Jin Q., Chen Z., Yuan K., Wang M., Zhang P., Luo J., Li H., Yang Y., Liu X., Mao M., Dong T., Tan W., Hu X., Pan Y., Hou L., Ma R. , Huang Z.",Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease,Frontiers in cellular and infection microbiology,2023,"gut mycobiome, metabolic dysfunction-associated fatty liver disease, metagenomics, oral mycobiome, oral-gut axis",Experiment 17,China,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Serum alanine aminotransferase measurement,EFO:0004735,Healthy Controls,Patients with Metabolic dysfunction-associated liver disease,"Patients diagnosed with Non-alcoholic fatty liver disease (now known as Metabolic dysfunction-associated fatty liver disease ""MAFLD"")",20,21,more than 5 days during 6 months,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3b,29 December 2025,Tosin,Tosin,Heatmap of Spearman correlation analysis of alanine transaminase (ALT) between participants with Metabolic dysfunction-associated fatty liver disease (MAFLD) and Healthy controls in Supragingival dental plaques,increased,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae,4751|4890|4891|4892|4893|4930|4932,Complete,KateRasheed
bsdb:37180439/18/1,37180439,case-control,37180439,10.3389/fcimb.2023.1157368,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2023.1157368/full,"Niu C., Tu Y., Jin Q., Chen Z., Yuan K., Wang M., Zhang P., Luo J., Li H., Yang Y., Liu X., Mao M., Dong T., Tan W., Hu X., Pan Y., Hou L., Ma R. , Huang Z.",Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease,Frontiers in cellular and infection microbiology,2023,"gut mycobiome, metabolic dysfunction-associated fatty liver disease, metagenomics, oral mycobiome, oral-gut axis",Experiment 18,China,Homo sapiens,Feces,UBERON:0001988,Serum gamma-glutamyl transferase measurement,EFO:0004532,Healthy Controls,Patients with Metabolic dysfunction-associated liver disease,"Patients diagnosed with Non-alcoholic fatty liver disease (now known as Metabolic dysfunction-associated fatty liver disease ""MAFLD"")",20,21,more than 5 days during 6 months,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,"age,sex",NA,NA,decreased,unchanged,decreased,NA,NA,Signature 1,Figure 3c,29 December 2025,Tosin,Tosin,Heatmap of Spearman correlation analysis of gamma-glutamyl transferase (GGT) between participants with Metabolic dysfunction-associated fatty liver disease (MAFLD) and Healthy controls in Feces,decreased,"k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Ophiocordycipitaceae|g__Purpureocillium|s__Purpureocillium lilacinum,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces eubayanus,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces paradoxus,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces pastorianus,k__Fungi|p__Ascomycota|c__Schizosaccharomycetes|o__Schizosaccharomycetales|f__Schizosaccharomycetaceae|g__Schizosaccharomyces|s__Schizosaccharomyces pombe",4751|4890|147550|5125|474942|1052105|33203;4751|4890|4891|4892|4893|4930|4932;4751|4890|4891|4892|4893|4930|1080349;4751|4890|4891|4892|4893|4930|27291;4751|4890|4891|4892|4893|4930|27292;4751|4890|147554|34346|4894|4895|4896,Complete,KateRasheed
bsdb:37180439/19/1,37180439,case-control,37180439,10.3389/fcimb.2023.1157368,https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2023.1157368/full,"Niu C., Tu Y., Jin Q., Chen Z., Yuan K., Wang M., Zhang P., Luo J., Li H., Yang Y., Liu X., Mao M., Dong T., Tan W., Hu X., Pan Y., Hou L., Ma R. , Huang Z.",Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease,Frontiers in cellular and infection microbiology,2023,"gut mycobiome, metabolic dysfunction-associated fatty liver disease, metagenomics, oral mycobiome, oral-gut axis",Experiment 19,China,Homo sapiens,Feces,UBERON:0001988,Aspartate aminotransferase measurement,EFO:0004736,Healthy Controls,Patients with Metabolic dysfunction-associated liver disease,"Patients diagnosed with Non-alcoholic fatty liver disease (now known as Metabolic dysfunction-associated fatty liver disease ""MAFLD"")",20,21,more than 5 days during 6 months,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,"age,sex",NA,NA,decreased,unchanged,decreased,NA,NA,Signature 1,Figure 3c,29 December 2025,Tosin,Tosin,Heatmap of Spearman correlation analysis of aspartate transaminase (AST) between participants with Metabolic dysfunction-associated fatty liver disease (MAFLD) and Healthy controls in Feces,increased,k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Mucor|s__Mucor ambiguus,4751|1913637|2212703|4827|34489|4830|91626,Complete,KateRasheed
bsdb:37182146/1/1,37182146,"case-control,time series / longitudinal observational",37182146,10.3389/fonc.2023.1183039,NA,"Bucher-Johannessen C., Birkeland E.E., Vinberg E., Bemanian V., Hoff G., Berstad P. , Rounge T.B.",Long-term follow-up of colorectal cancer screening attendees identifies differences in <i>Phascolarctobacterium</i> spp. using 16S rRNA and metagenome sequencing,Frontiers in oncology,2023,"16S rRNA, archived fecal samples, colorectal cancer screening, long term follow-up, metagenome, microbiome, sequencing",Experiment 1,Norway,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,Healthy controls,HRA (high-risk adenoma),"Individuals selected from available archive of fresh-frozen stool samples with high-risk adenomas were defined as those presenting with one or more adenomas of ≥10 mm, with high-grade dysplasia or villous components regardless of polyp size, or those with three or more adenomas regardless of size, dysplasia, and villosity.",53,63,NA,16S,34,Illumina,raw counts,Negative Binomial Regression,0.05,TRUE,NA,"age,sex,time","geographic area,sex",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Table 2,19 October 2023,Yjung24,"Yjung24,Davvve,Folakunmi,WikiWorks","Differential abundance analyses of taxa and pathways between CRC, HRA, and healthy controls.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum|s__Azospirillum sp. 47_25,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|28211|204441|2829815|191|1896971;3379134|1224|1236|91347|543|1940338;3379134|1224,Complete,Folakunmi
bsdb:37182146/1/2,37182146,"case-control,time series / longitudinal observational",37182146,10.3389/fonc.2023.1183039,NA,"Bucher-Johannessen C., Birkeland E.E., Vinberg E., Bemanian V., Hoff G., Berstad P. , Rounge T.B.",Long-term follow-up of colorectal cancer screening attendees identifies differences in <i>Phascolarctobacterium</i> spp. using 16S rRNA and metagenome sequencing,Frontiers in oncology,2023,"16S rRNA, archived fecal samples, colorectal cancer screening, long term follow-up, metagenome, microbiome, sequencing",Experiment 1,Norway,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,Healthy controls,HRA (high-risk adenoma),"Individuals selected from available archive of fresh-frozen stool samples with high-risk adenomas were defined as those presenting with one or more adenomas of ≥10 mm, with high-grade dysplasia or villous components regardless of polyp size, or those with three or more adenomas regardless of size, dysplasia, and villosity.",53,63,NA,16S,34,Illumina,raw counts,Negative Binomial Regression,0.05,TRUE,NA,"age,sex,time","geographic area,sex",NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,Table 2,19 October 2023,Yjung24,"Yjung24,Folakunmi,WikiWorks","Differential abundance analyses of taxa and pathways between CRC, HRA, and healthy controls.",increased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Folakunmi
bsdb:37182146/2/1,37182146,"case-control,time series / longitudinal observational",37182146,10.3389/fonc.2023.1183039,NA,"Bucher-Johannessen C., Birkeland E.E., Vinberg E., Bemanian V., Hoff G., Berstad P. , Rounge T.B.",Long-term follow-up of colorectal cancer screening attendees identifies differences in <i>Phascolarctobacterium</i> spp. using 16S rRNA and metagenome sequencing,Frontiers in oncology,2023,"16S rRNA, archived fecal samples, colorectal cancer screening, long term follow-up, metagenome, microbiome, sequencing",Experiment 2,Norway,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls,CRC (participants diagnosed with colorectal cancer),participants who were diagnosed with colorectal cancer at screening during the Norwegian Colorectal Prevention trial or by registry follow-up selected from available archive of fresh-frozen stool samples.,53,28,NA,16S,34,Illumina,raw counts,Negative Binomial Regression,0.05,TRUE,NA,"age,sex,time","geographic area,sex",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Table 2,22 October 2023,Yjung24,"Yjung24,Folakunmi,WikiWorks","Differential abundance analyses of taxa and pathways between CRC, HRA, and healthy controls.",increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",1783272|1239;1783272|1239|909932|1843488|909930|33024,Complete,Folakunmi
bsdb:37182146/3/1,37182146,"case-control,time series / longitudinal observational",37182146,10.3389/fonc.2023.1183039,NA,"Bucher-Johannessen C., Birkeland E.E., Vinberg E., Bemanian V., Hoff G., Berstad P. , Rounge T.B.",Long-term follow-up of colorectal cancer screening attendees identifies differences in <i>Phascolarctobacterium</i> spp. using 16S rRNA and metagenome sequencing,Frontiers in oncology,2023,"16S rRNA, archived fecal samples, colorectal cancer screening, long term follow-up, metagenome, microbiome, sequencing",Experiment 3,Norway,Homo sapiens,Feces,UBERON:0001988,"Colorectal adenoma,Colorectal cancer","EFO:0005406,EFO:0005842",Healthy controls,HRA (high-risk adenoma) group combined with CRC (colorectal cancer) group,"Individuals selected from available archive of fresh-frozen stool samples with high-risk adenomas were defined as those presenting with one or more adenomas of ≥10 mm, with high-grade dysplasia or villous components regardless of polyp size, or those with three or more adenomas regardless of size, dysplasia, and villosity. Combined with individuals selected from available archive of fresh-frozen stool samples diagnosed with colorectal cancer at screening or by registry follow-up.",53,91,NA,16S,34,Illumina,raw counts,Negative Binomial Regression,0.05,TRUE,NA,"age,sex,time","geographic area,sex",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Table 2,22 October 2023,Yjung24,"Yjung24,WikiWorks","Differential abundance analyses of taxa and pathways between CRC, HRA, and healthy controls.",increased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Folakunmi
bsdb:37182146/4/1,37182146,"case-control,time series / longitudinal observational",37182146,10.3389/fonc.2023.1183039,NA,"Bucher-Johannessen C., Birkeland E.E., Vinberg E., Bemanian V., Hoff G., Berstad P. , Rounge T.B.",Long-term follow-up of colorectal cancer screening attendees identifies differences in <i>Phascolarctobacterium</i> spp. using 16S rRNA and metagenome sequencing,Frontiers in oncology,2023,"16S rRNA, archived fecal samples, colorectal cancer screening, long term follow-up, metagenome, microbiome, sequencing",Experiment 4,Norway,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,Healthy controls,HRA (high-risk adenoma),"Individuals selected from available archive of fresh-frozen stool samples with high-risk adenomas were defined as those presenting with one or more adenomas of ≥10 mm, with high-grade dysplasia or villous components regardless of polyp size, or those with three or more adenomas regardless of size, dysplasia, and villosity.",53,63,NA,WMS,NA,Illumina,raw counts,Negative Binomial Regression,0.05,TRUE,NA,"age,sex,time","geographic area,sex",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Table 2,22 October 2023,Yjung24,"Yjung24,Folakunmi,WikiWorks",Differential abundance analyses of taxa and pathways between HRA and healthy controls.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora saccharolytica,1783272|1239|186801|3085636|186803|2719231|84030,Complete,Folakunmi
bsdb:37182146/4/2,37182146,"case-control,time series / longitudinal observational",37182146,10.3389/fonc.2023.1183039,NA,"Bucher-Johannessen C., Birkeland E.E., Vinberg E., Bemanian V., Hoff G., Berstad P. , Rounge T.B.",Long-term follow-up of colorectal cancer screening attendees identifies differences in <i>Phascolarctobacterium</i> spp. using 16S rRNA and metagenome sequencing,Frontiers in oncology,2023,"16S rRNA, archived fecal samples, colorectal cancer screening, long term follow-up, metagenome, microbiome, sequencing",Experiment 4,Norway,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,Healthy controls,HRA (high-risk adenoma),"Individuals selected from available archive of fresh-frozen stool samples with high-risk adenomas were defined as those presenting with one or more adenomas of ≥10 mm, with high-grade dysplasia or villous components regardless of polyp size, or those with three or more adenomas regardless of size, dysplasia, and villosity.",53,63,NA,WMS,NA,Illumina,raw counts,Negative Binomial Regression,0.05,TRUE,NA,"age,sex,time","geographic area,sex",NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,Table 2,22 October 2023,Yjung24,"Yjung24,Folakunmi,WikiWorks",Differential abundance analyses of taxa and pathways between HRA and healthy controls.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,3379134|1224|28216|80840|995019|577310,Complete,Folakunmi
bsdb:37182146/5/1,37182146,"case-control,time series / longitudinal observational",37182146,10.3389/fonc.2023.1183039,NA,"Bucher-Johannessen C., Birkeland E.E., Vinberg E., Bemanian V., Hoff G., Berstad P. , Rounge T.B.",Long-term follow-up of colorectal cancer screening attendees identifies differences in <i>Phascolarctobacterium</i> spp. using 16S rRNA and metagenome sequencing,Frontiers in oncology,2023,"16S rRNA, archived fecal samples, colorectal cancer screening, long term follow-up, metagenome, microbiome, sequencing",Experiment 5,Norway,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls,CRC (participants diagnosed with colorectal cancer),participants who were diagnosed with colorectal cancer at screening during the Norwegian Colorectal Prevention trial or by registry follow-up selected from available archive of fresh-frozen stool samples.,22,7,NA,WMS,NA,Illumina,raw counts,Negative Binomial Regression,0.05,TRUE,NA,"age,sex,time","geographic area,sex",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Table 2,22 October 2023,Yjung24,"Yjung24,WikiWorks","Differential abundance analyses of taxa and pathways between CRC, HRA, and healthy controls.",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:95,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__[Lactobacillus] rogosae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens",1783272|1239|909932|1843488|909930|904;1783272|1239|909932|1843488|909930|904|187327;1783272|1239|186801|3085636|186803|33042|33043;1783272|1239|1262988;1783272|1239|186801|3085636|186803|28050|706562;1783272|1239|909932|1843488|909930|33024|626940,Complete,Folakunmi
bsdb:37182146/5/2,37182146,"case-control,time series / longitudinal observational",37182146,10.3389/fonc.2023.1183039,NA,"Bucher-Johannessen C., Birkeland E.E., Vinberg E., Bemanian V., Hoff G., Berstad P. , Rounge T.B.",Long-term follow-up of colorectal cancer screening attendees identifies differences in <i>Phascolarctobacterium</i> spp. using 16S rRNA and metagenome sequencing,Frontiers in oncology,2023,"16S rRNA, archived fecal samples, colorectal cancer screening, long term follow-up, metagenome, microbiome, sequencing",Experiment 5,Norway,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls,CRC (participants diagnosed with colorectal cancer),participants who were diagnosed with colorectal cancer at screening during the Norwegian Colorectal Prevention trial or by registry follow-up selected from available archive of fresh-frozen stool samples.,22,7,NA,WMS,NA,Illumina,raw counts,Negative Binomial Regression,0.05,TRUE,NA,"age,sex,time","geographic area,sex",NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,Table 2,22 October 2023,Yjung24,"Yjung24,WikiWorks","Differential abundance analyses of taxa and pathways between CRC, HRA, and healthy controls.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus|s__Monoglobus pectinilyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:303,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula",3379134|976|200643|171549|815|816|338188;1783272|1239|186801|3085656|3085657|2039302|1981510;1783272|1239|186801|3085636|186803|841|1262944;1783272|1239|909932|1843489|31977|29465|29466,Complete,Folakunmi
bsdb:37182146/6/1,37182146,"case-control,time series / longitudinal observational",37182146,10.3389/fonc.2023.1183039,NA,"Bucher-Johannessen C., Birkeland E.E., Vinberg E., Bemanian V., Hoff G., Berstad P. , Rounge T.B.",Long-term follow-up of colorectal cancer screening attendees identifies differences in <i>Phascolarctobacterium</i> spp. using 16S rRNA and metagenome sequencing,Frontiers in oncology,2023,"16S rRNA, archived fecal samples, colorectal cancer screening, long term follow-up, metagenome, microbiome, sequencing",Experiment 6,Norway,Homo sapiens,Feces,UBERON:0001988,"Colorectal adenoma,Colorectal cancer","EFO:0005842,EFO:0005406",Healthy controls,HRA (high-risk adenoma) group combined with CRC (colorectal cancer) group,"Individuals selected from available archive of fresh-frozen stool samples with high-risk adenomas were defined as those presenting with one or more adenomas of ≥10 mm, with high-grade dysplasia or villous components regardless of polyp size, or those with three or more adenomas regardless of size, dysplasia, and villosity. Combined with individuals selected from available archive of fresh-frozen stool samples diagnosed with colorectal cancer at screening or by registry follow-up.",22,25,NA,WMS,NA,Illumina,raw counts,Negative Binomial Regression,0.05,TRUE,NA,"age,sex,time","geographic area,sex",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Table 2,22 October 2023,Yjung24,"Yjung24,WikiWorks","Differential abundance analyses of taxa and pathways between CRC, HRA, and healthy controls.",increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora saccharolytica,1783272|1239|186801|3085636|186803|2719231|84030,Complete,Folakunmi
bsdb:37182146/7/1,37182146,"case-control,time series / longitudinal observational",37182146,10.3389/fonc.2023.1183039,NA,"Bucher-Johannessen C., Birkeland E.E., Vinberg E., Bemanian V., Hoff G., Berstad P. , Rounge T.B.",Long-term follow-up of colorectal cancer screening attendees identifies differences in <i>Phascolarctobacterium</i> spp. using 16S rRNA and metagenome sequencing,Frontiers in oncology,2023,"16S rRNA, archived fecal samples, colorectal cancer screening, long term follow-up, metagenome, microbiome, sequencing",Experiment 7,Norway,Homo sapiens,Feces,UBERON:0001988,Time,EFO:0000721,Colorectal cancer diagnosed at time of screening,Colorectal cancer diagnosed during 17-year follow-up/post screening,Diagnosed with colorectal cancer at screening in the beginning of the Norwegian Colorectal Cancer Prevention Trial,5,23,NA,16S,34,Illumina,raw counts,Negative Binomial Regression,0.05,TRUE,NA,NA,"geographic area,sex",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Table 2,26 October 2023,Yjung24,"Yjung24,WikiWorks","Differential abundance analyses of taxa and pathways between CRC, HRA, and healthy controls.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803,Complete,Folakunmi
bsdb:37182146/7/2,37182146,"case-control,time series / longitudinal observational",37182146,10.3389/fonc.2023.1183039,NA,"Bucher-Johannessen C., Birkeland E.E., Vinberg E., Bemanian V., Hoff G., Berstad P. , Rounge T.B.",Long-term follow-up of colorectal cancer screening attendees identifies differences in <i>Phascolarctobacterium</i> spp. using 16S rRNA and metagenome sequencing,Frontiers in oncology,2023,"16S rRNA, archived fecal samples, colorectal cancer screening, long term follow-up, metagenome, microbiome, sequencing",Experiment 7,Norway,Homo sapiens,Feces,UBERON:0001988,Time,EFO:0000721,Colorectal cancer diagnosed at time of screening,Colorectal cancer diagnosed during 17-year follow-up/post screening,Diagnosed with colorectal cancer at screening in the beginning of the Norwegian Colorectal Cancer Prevention Trial,5,23,NA,16S,34,Illumina,raw counts,Negative Binomial Regression,0.05,TRUE,NA,NA,"geographic area,sex",NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,Table 2,26 October 2023,Yjung24,"Yjung24,WikiWorks","Differential abundance analyses of taxa and pathways between CRC, HRA, and healthy controls.",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,1783272|1239|186801|3085636|186803,Complete,Folakunmi
bsdb:37184522/1/1,37184522,time series / longitudinal observational,37184522,10.1097/HC9.0000000000000151,NA,"Waldner B., Aldrian D., Zöggeler T., Oberacher H., Oberhuber R., Schneeberger S., Messner F., Schneider A.M., Kohlmaier B., Lanzersdorfer R., Huber W.D., Entenmann A., Müller T. , Vogel G.F.",The influence of liver transplantation on the interplay between gut microbiome and bile acid homeostasis in children with biliary atresia,Hepatology communications,2023,NA,Experiment 1,Austria,Homo sapiens,Feces,UBERON:0001988,Biliary atresia,MONDO:0008867,Children with BA before - [pre],Post24 + m,The impact of LT and reestablishment of bile flow on gut microbiome–bile acid homeostasis in children with BA for more than 24 months (post24 + m) after liver transplantation (LT),10,12,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,age,NA,NA,increased,increased,increased,NA,increased,Signature 1,FIGURE 3,9 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","Differential abundances and linear discriminant effect size analysis (LEfSe) of gut microbiota. (C) Cladogram of LEfSe analysis results of pre and post24 + m groups on the taxonomic order level. Over-representation of taxa is color-coded in red (post24 + m) and green (pre). Radiating circle depicts phylum to order level. (E) Barchart of LDA values with significantly different abundances to order level is shown comparing pre versus post24 + m, and healthy versus post24 +m",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",3379134|976|200643|171549;3379134|976|200643;1783272|1239|186801;1783272|201174|84998|84999;1783272|201174|84998;28221;3379134|200940|3031449|213115;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|186801|186802,Complete,Peace Sandy
bsdb:37184522/1/2,37184522,time series / longitudinal observational,37184522,10.1097/HC9.0000000000000151,NA,"Waldner B., Aldrian D., Zöggeler T., Oberacher H., Oberhuber R., Schneeberger S., Messner F., Schneider A.M., Kohlmaier B., Lanzersdorfer R., Huber W.D., Entenmann A., Müller T. , Vogel G.F.",The influence of liver transplantation on the interplay between gut microbiome and bile acid homeostasis in children with biliary atresia,Hepatology communications,2023,NA,Experiment 1,Austria,Homo sapiens,Feces,UBERON:0001988,Biliary atresia,MONDO:0008867,Children with BA before - [pre],Post24 + m,The impact of LT and reestablishment of bile flow on gut microbiome–bile acid homeostasis in children with BA for more than 24 months (post24 + m) after liver transplantation (LT),10,12,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,age,NA,NA,increased,increased,increased,NA,increased,Signature 2,Fig 3,9 February 2024,Peace Sandy,"Peace Sandy,WikiWorks","Differential abundances and linear discriminant effect size analysis (LEfSe) of gut microbiota. (C) Cladogram of LEfSe analysis results of pre and post24 + m groups on the taxonomic order level. Over-representation of taxa is color-coded in red (post24 + m) and green (pre). Radiating circle depicts phylum to order level. (E) Barchart of LDA values with significantly different abundances to order level is shown comparing pre versus post24 + m, and healthy versus post24 +m",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli",1783272|201174|1760|85006;3379134|29547|3031852|213849;1783272|1239|91061|1385;1783272|1239|91061|186826;1783272|1239|91061,Complete,Peace Sandy
bsdb:37187470/1/1,37187470,case-control,37187470,10.3389/fcimb.2023.1127916,NA,"Wu C., Yi H., Hu Y., Luo D., Tang Z., Wen X., Zhang Y., Tang M., Zhang L., Wu S. , Chen M.",Effects of second-line anti-tuberculosis drugs on the intestinal microbiota of patients with rifampicin-resistant tuberculosis,Frontiers in cellular and infection microbiology,2023,"differential function, differential species, intestinal microbiota, rifampicin-resistant tuberculosis, second-line anti-tuberculosis drugs",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,"Drug-resistant tuberculosis,Multidrug-resistant tuberculosis","MONDO:0041806,EFO:0007381",Control (untreated Rifampicin-resistant TB),Intensive-phase treatment group (G1G2 group),Rifampicin-resistant tuberculosis patients within 6 months of second-line drugs,30,60,NA,PCR,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,FIGURE 4; Table 7,15 July 2025,Nuerteye,Nuerteye,"Significant differences in relative abundance identified by LEfSe analysis between the three groups (Control, G1G2 and G3G4). At the species level, the untreated group(control) is shown in blue, the intensive treatment group(G1G2) in red and the consolidation treatment group(G3G4) in green. The length of the column represents the influence of significantly different species in relative abundance (LDA scores > 2).",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter werkmanii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia fergusonii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella|s__Morganella morganii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella sonnei,k__Pseudomonadati|p__Pseudomonadota|s__Proteobacteria bacterium CAG:139",3379134|1224|1236|91347|543|544|546;3379134|1224|1236|91347|543|544|545;3379134|1224|1236|91347|543|544|67827;3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|543|561|564;3379134|1224|1236|91347|543|570|571;3379134|1224|1236|91347|543|570|573;3379134|1224|1236|91347|1903414|581|582;3379134|1224|1236|91347|543|590|28901;3379134|1224|1236|91347|543|620|624;3379134|1224|1262986,Complete,NA
bsdb:37187470/1/2,37187470,case-control,37187470,10.3389/fcimb.2023.1127916,NA,"Wu C., Yi H., Hu Y., Luo D., Tang Z., Wen X., Zhang Y., Tang M., Zhang L., Wu S. , Chen M.",Effects of second-line anti-tuberculosis drugs on the intestinal microbiota of patients with rifampicin-resistant tuberculosis,Frontiers in cellular and infection microbiology,2023,"differential function, differential species, intestinal microbiota, rifampicin-resistant tuberculosis, second-line anti-tuberculosis drugs",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,"Drug-resistant tuberculosis,Multidrug-resistant tuberculosis","MONDO:0041806,EFO:0007381",Control (untreated Rifampicin-resistant TB),Intensive-phase treatment group (G1G2 group),Rifampicin-resistant tuberculosis patients within 6 months of second-line drugs,30,60,NA,PCR,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 4; Table 6,15 July 2025,Nuerteye,Nuerteye,"Significant differences in relative abundance identified by LEfSe analysis between the three groups (Control, G1G2 and G3G4). At the species level, the untreated group(control) is shown in blue, the intensive treatment group(G1G2) in red and the consolidation treatment group(G3G4) in green. The length of the column represents the influence of significantly different species in relative abundance (LDA scores > 2).",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. ICM47,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. S6-Spd3,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum|s__Actinobaculum sp. oral taxon 183",1783272|201174|1760|2037|2049|1654|936548;1783272|201174|1760|2037|2049|1654|1284680;1783272|201174|1760|2037|2049|76833|712888,Complete,NA
bsdb:37187470/2/1,37187470,case-control,37187470,10.3389/fcimb.2023.1127916,NA,"Wu C., Yi H., Hu Y., Luo D., Tang Z., Wen X., Zhang Y., Tang M., Zhang L., Wu S. , Chen M.",Effects of second-line anti-tuberculosis drugs on the intestinal microbiota of patients with rifampicin-resistant tuberculosis,Frontiers in cellular and infection microbiology,2023,"differential function, differential species, intestinal microbiota, rifampicin-resistant tuberculosis, second-line anti-tuberculosis drugs",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,"Drug-resistant tuberculosis,Multidrug-resistant tuberculosis","MONDO:0041806,EFO:0007381",Control (untreated Rifampicin-resistant TB),continuation phase 12–14-month of the treatment (G3G4 group),patients who were at the 12–14-month continuation phase of the treatment with second-line anti-TB drugs,30,60,NA,PCR,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 4; Table 8,15 July 2025,Nuerteye,Nuerteye,"Significant differences in relative abundance identified by LEfSe analysis between the three groups (Control, G1G2 and G3G4). At the species level, the untreated group(control) is shown in blue, the intensive treatment group(G1G2) in red and the consolidation treatment group(G3G4) in green. The length of the column
represents the influence of significantly different species in relative
abundance (LDA scores > 2)",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus pullicaecorum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale",1783272|201174|1760|85004|31953|1678|1680;1783272|1239|186801|186802|3085642|580596|501571;1783272|1239|909932|909929|1843491|158846|158847,Complete,NA
bsdb:37187470/2/2,37187470,case-control,37187470,10.3389/fcimb.2023.1127916,NA,"Wu C., Yi H., Hu Y., Luo D., Tang Z., Wen X., Zhang Y., Tang M., Zhang L., Wu S. , Chen M.",Effects of second-line anti-tuberculosis drugs on the intestinal microbiota of patients with rifampicin-resistant tuberculosis,Frontiers in cellular and infection microbiology,2023,"differential function, differential species, intestinal microbiota, rifampicin-resistant tuberculosis, second-line anti-tuberculosis drugs",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,"Drug-resistant tuberculosis,Multidrug-resistant tuberculosis","MONDO:0041806,EFO:0007381",Control (untreated Rifampicin-resistant TB),continuation phase 12–14-month of the treatment (G3G4 group),patients who were at the 12–14-month continuation phase of the treatment with second-line anti-TB drugs,30,60,NA,PCR,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 4; Table 6,15 July 2025,Nuerteye,Nuerteye,"Significant differences in relative abundance identified by LEfSe analysis between the three groups (Control, G1G2 and G3G4). At the species level, the untreated group(control) is shown in blue, the intensive treatment group(G1G2) in red and the consolidation treatment group(G3G4) in green. The length of the column
represents the influence of significantly different species in relative abundance (LDA scores > 2).",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. ICM47,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. S6-Spd3,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum|s__Actinobaculum sp. oral taxon 183",1783272|201174|1760|2037|2049|1654|936548;1783272|201174|1760|2037|2049|1654|1284680;1783272|201174|1760|2037|2049|76833|712888,Complete,NA
bsdb:37197229/1/1,37197229,"cross-sectional observational, not case-control",37197229,10.1155/2023/6297653,NA,"Zhang X., Wang X., Zhao H., Cao R., Dang Y. , Yu B.",Imbalance of Microbacterial Diversity Is Associated with Functional Prognosis of Stroke,Neural plasticity,2023,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Healthy Control,Post Stroke Patients,Post Stroke patients,20,20,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Figure 2(b),10 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",Compositional changes in the gut microbiota of poststroke and healthy controls.,increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,s__uncultured Gram-positive bacterium",3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;3379134|200940|3031449;1783272|1239|186801|186802;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;1783272|1239|186801|186802|216572;38145,Complete,Svetlana up
bsdb:37197229/1/4,37197229,"cross-sectional observational, not case-control",37197229,10.1155/2023/6297653,NA,"Zhang X., Wang X., Zhao H., Cao R., Dang Y. , Yu B.",Imbalance of Microbacterial Diversity Is Associated with Functional Prognosis of Stroke,Neural plasticity,2023,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Healthy Control,Post Stroke Patients,Post Stroke patients,20,20,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 4,Figure 2(b),13 October 2024,Ifeanyisam,"Ifeanyisam,Rahila,WikiWorks",Compositional changes in the gut microbiota of poststroke and healthy controls,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales,k__Pseudomonadati|p__Bdellovibrionota|c__Bdellovibrionia|o__Bdellovibrionales,k__Pseudomonadati|p__Bdellovibrionota|c__Bdellovibrionia,k__Pseudomonadati|p__Acidobacteriota|c__Terriglobia|o__Bryobacterales|f__Bryobacteraceae,k__Pseudomonadati|p__Acidobacteriota|c__Terriglobia|o__Bryobacterales,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Frankiales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Pseudomonadati|p__Gemmatimonadota|c__Gemmatimonadia|o__Gemmatimonadales|f__Gemmatimonadaceae,k__Pseudomonadati|p__Gemmatimonadota|c__Gemmatimonadia|o__Gemmatimonadales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacillati|p__Chloroflexota|c__Ktedonobacteria|o__Ktedonobacterales|f__Ktedonobacteraceae,k__Bacillati|p__Chloroflexota|c__Ktedonobacteria|o__Ktedonobacterales,k__Bacillati|p__Chloroflexota|c__Ktedonobacteria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae,k__Pseudomonadati|p__Myxococcota,k__Pseudomonadati|p__Bdellovibrionota|c__Bdellovibrionia|o__Bdellovibrionales|f__Pseudobdellovibrionaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales,k__Pseudomonadati|p__Acidobacteriota|c__Terriglobia|o__Terriglobales,k__Bacillati|p__Actinomycetota|c__Thermoleophilia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Cyanobacteriota",3379134|1224|28211|3120395|433;3379134|1224|28211|3120395;3379134|3018035|3031418|213481;3379134|3018035|3031418;3379134|57723|204432|332160|1962910;3379134|57723|204432|332160;3379134|976|1853228|1853229;1783272|201174|1760|85013;3384189|32066|203490;3379134|142182|219685|219686|219687;3379134|142182|219685|219686;1783272|201174|1760|1643682|85030;3379134|1224|28211|356;1783272|200795|388447|388448|388449;1783272|200795|388447|388448;1783272|200795|388447;1783272|201174|1760|85006|85023;3379134|976|200643|171549|2005473;1783272|1239|91061|1385|186822;3379134|2818505;3379134|3018035|3031418|213481|213483;1783272|201174|1760|85010|2070;1783272|201174|1760|85010;3379134|1224|28211|766;3379134|57723|204432|204433;1783272|201174|1497346;3379134|1224|28211|356|335928;1783272|1117;1783272|1117,Complete,Svetlana up
bsdb:37197229/2/1,37197229,"cross-sectional observational, not case-control",37197229,10.1155/2023/6297653,NA,"Zhang X., Wang X., Zhao H., Cao R., Dang Y. , Yu B.",Imbalance of Microbacterial Diversity Is Associated with Functional Prognosis of Stroke,Neural plasticity,2023,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Healthy Control,Post Stroke Patients,Post Stroke patients,20,20,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Figure 2(a),16 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",The mean relative abundances of taxa at the phylum level in poststroke and control subjects,increased,"k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Thermodesulfobacteriota",3384189|32066;3379134|200940,Complete,Svetlana up
bsdb:37197229/2/2,37197229,"cross-sectional observational, not case-control",37197229,10.1155/2023/6297653,NA,"Zhang X., Wang X., Zhao H., Cao R., Dang Y. , Yu B.",Imbalance of Microbacterial Diversity Is Associated with Functional Prognosis of Stroke,Neural plasticity,2023,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Stroke,EFO:0000712,Healthy Control,Post Stroke Patients,Post Stroke patients,20,20,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,Figure 2(a),16 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",The mean relative abundances of taxa at the phylum level in poststroke and control subjects,decreased,"k__Pseudomonadati|p__Acidobacteriota,k__Bacillati|p__Chloroflexota,s__bacterium",3379134|57723;1783272|200795;1869227,Complete,Svetlana up
bsdb:37199608/1/1,37199608,randomized controlled trial,37199608,https://doi.org/10.1128/spectrum.05273-22,NA,"Finlayson-Trick E., Nearing J., Fischer J.A., Ma Y., Wang S., Krouen H., Goldfarb D.M. , Karakochuk C.D.","The Effect of Oral Iron Supplementation on Gut Microbial Composition: a Secondary Analysis of a Double-Blind, Randomized Controlled Trial among Cambodian Women of Reproductive Age",Microbiology spectrum,2023,"enteropathogen, gut microbiome, iron supplementation",Experiment 1,Cambodia,Homo sapiens,Feces,UBERON:0001988,Iron,CHEBI:18248,Placebo group - 0 week treatment (Baseline),Placebo group - 12 weeks treatment,Placebo group - 12 weeks treatment refers to patients in the placebo group who are receiving 12 weeks treatment.,47,47,3 months,16S,678,Illumina,relative abundances,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 4, Figure 5",29 March 2024,Manisha28,"Manisha28,KateRasheed,WikiWorks",Differentially abundant bacterial Taxa in the Placebo group.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:37199608/1/2,37199608,randomized controlled trial,37199608,https://doi.org/10.1128/spectrum.05273-22,NA,"Finlayson-Trick E., Nearing J., Fischer J.A., Ma Y., Wang S., Krouen H., Goldfarb D.M. , Karakochuk C.D.","The Effect of Oral Iron Supplementation on Gut Microbial Composition: a Secondary Analysis of a Double-Blind, Randomized Controlled Trial among Cambodian Women of Reproductive Age",Microbiology spectrum,2023,"enteropathogen, gut microbiome, iron supplementation",Experiment 1,Cambodia,Homo sapiens,Feces,UBERON:0001988,Iron,CHEBI:18248,Placebo group - 0 week treatment (Baseline),Placebo group - 12 weeks treatment,Placebo group - 12 weeks treatment refers to patients in the placebo group who are receiving 12 weeks treatment.,47,47,3 months,16S,678,Illumina,relative abundances,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4,29 March 2024,Manisha28,"Manisha28,KateRasheed,WikiWorks",Differentially abundant bacterial Taxa in the Placebo group.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,1783272|1239|91061|186826|33958|46255,Complete,Svetlana up
bsdb:37199608/2/1,37199608,randomized controlled trial,37199608,https://doi.org/10.1128/spectrum.05273-22,NA,"Finlayson-Trick E., Nearing J., Fischer J.A., Ma Y., Wang S., Krouen H., Goldfarb D.M. , Karakochuk C.D.","The Effect of Oral Iron Supplementation on Gut Microbial Composition: a Secondary Analysis of a Double-Blind, Randomized Controlled Trial among Cambodian Women of Reproductive Age",Microbiology spectrum,2023,"enteropathogen, gut microbiome, iron supplementation",Experiment 2,Cambodia,Homo sapiens,Feces,UBERON:0001988,Iron,CHEBI:18248,Ferrous sulfate group - 0 week treatment (Baseline),Ferrous sulfate group - 12 weeks treatment,Ferrous sulfate group - 12 weeks treatment refers to patients in the Ferrous sulfate group who are receiving 12 weeks treatment.,40,40,3 months,16S,678,Illumina,relative abundances,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4,29 March 2024,Manisha28,"Manisha28,KateRasheed,WikiWorks",Differentially abundant bacterial Taxa in the Ferrous sulfate group,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|33958|46255,Complete,Svetlana up
bsdb:37199608/2/2,37199608,randomized controlled trial,37199608,https://doi.org/10.1128/spectrum.05273-22,NA,"Finlayson-Trick E., Nearing J., Fischer J.A., Ma Y., Wang S., Krouen H., Goldfarb D.M. , Karakochuk C.D.","The Effect of Oral Iron Supplementation on Gut Microbial Composition: a Secondary Analysis of a Double-Blind, Randomized Controlled Trial among Cambodian Women of Reproductive Age",Microbiology spectrum,2023,"enteropathogen, gut microbiome, iron supplementation",Experiment 2,Cambodia,Homo sapiens,Feces,UBERON:0001988,Iron,CHEBI:18248,Ferrous sulfate group - 0 week treatment (Baseline),Ferrous sulfate group - 12 weeks treatment,Ferrous sulfate group - 12 weeks treatment refers to patients in the Ferrous sulfate group who are receiving 12 weeks treatment.,40,40,3 months,16S,678,Illumina,relative abundances,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 4, Figure 5",29 March 2024,Manisha28,"Manisha28,KateRasheed,WikiWorks",Differentially abundant bacterial Taxa in the Ferrous sulfate group,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:37199608/3/1,37199608,randomized controlled trial,37199608,https://doi.org/10.1128/spectrum.05273-22,NA,"Finlayson-Trick E., Nearing J., Fischer J.A., Ma Y., Wang S., Krouen H., Goldfarb D.M. , Karakochuk C.D.","The Effect of Oral Iron Supplementation on Gut Microbial Composition: a Secondary Analysis of a Double-Blind, Randomized Controlled Trial among Cambodian Women of Reproductive Age",Microbiology spectrum,2023,"enteropathogen, gut microbiome, iron supplementation",Experiment 3,Cambodia,Homo sapiens,Feces,UBERON:0001988,Iron,CHEBI:18248,Ferrous bisglycinate group - 0 week treatment (Baseline),Ferrous bisglycinate group - 12 weeks treatment,Ferrous bisglycinate group - 12 weeks treatment refers to patients in the Ferrous bisglycinate group who are receiving 12 weeks treatment.,46,46,3 months,16S,678,Illumina,relative abundances,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 4, Figure 5",9 January 2025,Manisha28,"Manisha28,KateRasheed,WikiWorks",Differentially abundant bacterial Taxa in the Ferrous bisglycinate group,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:37199608/3/2,37199608,randomized controlled trial,37199608,https://doi.org/10.1128/spectrum.05273-22,NA,"Finlayson-Trick E., Nearing J., Fischer J.A., Ma Y., Wang S., Krouen H., Goldfarb D.M. , Karakochuk C.D.","The Effect of Oral Iron Supplementation on Gut Microbial Composition: a Secondary Analysis of a Double-Blind, Randomized Controlled Trial among Cambodian Women of Reproductive Age",Microbiology spectrum,2023,"enteropathogen, gut microbiome, iron supplementation",Experiment 3,Cambodia,Homo sapiens,Feces,UBERON:0001988,Iron,CHEBI:18248,Ferrous bisglycinate group - 0 week treatment (Baseline),Ferrous bisglycinate group - 12 weeks treatment,Ferrous bisglycinate group - 12 weeks treatment refers to patients in the Ferrous bisglycinate group who are receiving 12 weeks treatment.,46,46,3 months,16S,678,Illumina,relative abundances,Beta Binomial Regression,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4,9 January 2025,Manisha28,"Manisha28,KateRasheed,WikiWorks",Differentially abundant bacterial Taxa in the Ferrous bisglycinate group,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|33958|46255,Complete,Svetlana up
bsdb:37208728/1/1,37208728,case-control,37208728,10.1186/s12974-023-02782-1,NA,"Yu J., Meng J., Qin Z., Yu Y., Liang Y., Wang Y. , Min D.",Dysbiosis of gut microbiota inhibits NMNAT2 to promote neurobehavioral deficits and oxidative stress response in the 6-OHDA-lesioned rat model of Parkinson's disease,Journal of neuroinflammation,2023,"Dysbiosis of gut microbiota, Fecal microbiota transplantation, NMNAT2, Neurobehavioral symptoms, Oxidative stress response, Parkinson’s disease",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy,Parkinson's Disease (PD)-patients,Individuals with early-stage Parkinson's disease,28,31,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,NA,NA,NA,decreased,NA,Signature 1,Figure 2B,13 March 2024,Barrakat,"Barrakat,WikiWorks",Difference in gut microbiota composition between Parkinson's Disease (PD)-patients and healthy individuals,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",1783272|201174|84998|1643822|1643826|447020;1783272|201174|84998|1643822|1643826|447020|446660;3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|2030927;3379134|74201|203494|48461|203557;3379134|74201|203494;3379134|74201|203494|48461;3379134|74201;3379134|976|200643|171549,Complete,Svetlana up
bsdb:37208728/1/2,37208728,case-control,37208728,10.1186/s12974-023-02782-1,NA,"Yu J., Meng J., Qin Z., Yu Y., Liang Y., Wang Y. , Min D.",Dysbiosis of gut microbiota inhibits NMNAT2 to promote neurobehavioral deficits and oxidative stress response in the 6-OHDA-lesioned rat model of Parkinson's disease,Journal of neuroinflammation,2023,"Dysbiosis of gut microbiota, Fecal microbiota transplantation, NMNAT2, Neurobehavioral symptoms, Oxidative stress response, Parkinson’s disease",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy,Parkinson's Disease (PD)-patients,Individuals with early-stage Parkinson's disease,28,31,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,NA,NA,NA,decreased,NA,Signature 2,Figure 2B,13 March 2024,Barrakat,"Barrakat,Scholastica,WikiWorks",Difference in gut microbiota composition between Parkinson's Disease (PD)-patients and healthy individuals,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium mitsuokai,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp. ART55_1",1783272|1239|909932|1843488|909930;1783272|201174|1760|2037;1783272|1239|91061;1783272|1239|526524|526525|2810280|135858|100886;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;3379134|1224|1236;1783272|1239|526524|526525|128827|1573535|1735;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826;3379134|976|200643|171549|171552|2974265|363265;1783272|1239|909932;3379134|976|200643|171549|171552|577309;1783272|1239|909932|1843488|909930|33024;1783272|1239|909932|1843488|909930|33024|626940;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|909932|909929;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|186801|186802|216572|1535;1783272|1239|526524|526525|128827;3379134|976|200643|171549|171552|577309;1783272|1239|526524|526525|2810280|135858;3379134|1224|1236|91347|543|561;1783272|1239|186801|3085636|186803|33042|2710826,Complete,Svetlana up
bsdb:37210496/1/1,37210496,case-control,37210496,10.1186/s12866-023-02880-3.,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-02880-3,"Li H., Xiao H.Y., Yuan L.P., Yan B., Pan Y., Tian P.P. , Zhang W.J.",Protective effect of L-pipecolic acid on constipation in C57BL/6 mice based on gut microbiome and serum metabolomic,BMC microbiology,2023,"Children, Functional constipation, Gut microbiota, L-pipecolic acid, Metabolite profiles",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,Healthy Controls,Functional Constipation(FC),"Patients (children) with functional constipation, with infrequent bowel movements and who fulfilled the Roman IV diagnostic criteria",28,26,3 months,16S,34,NA,relative abundances,"T-Test,Mann-Whitney (Wilcoxon)",0.05,NA,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,Figure 1F,16 March 2025,Mautin,"Mautin,Fiddyhamma,KateRasheed",The  Differential analysis between healthy Controls and Functional constipation using STAMP Analysis,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena fissicatena",1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|1392389;3379134|1224|1236|91347|543|570;1783272|1239|186801|186802|216572|3068309;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|186801|3085636|186803|2005359|290055,Complete,KateRasheed
bsdb:37210496/1/2,37210496,case-control,37210496,10.1186/s12866-023-02880-3.,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-02880-3,"Li H., Xiao H.Y., Yuan L.P., Yan B., Pan Y., Tian P.P. , Zhang W.J.",Protective effect of L-pipecolic acid on constipation in C57BL/6 mice based on gut microbiome and serum metabolomic,BMC microbiology,2023,"Children, Functional constipation, Gut microbiota, L-pipecolic acid, Metabolite profiles",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,Healthy Controls,Functional Constipation(FC),"Patients (children) with functional constipation, with infrequent bowel movements and who fulfilled the Roman IV diagnostic criteria",28,26,3 months,16S,34,NA,relative abundances,"T-Test,Mann-Whitney (Wilcoxon)",0.05,NA,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,Figure 1F,16 March 2025,Mautin,"Mautin,Fiddyhamma",The Differential analysis between healthy Controls and Functional constipation using STAMP Analysis,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",1783272|1239|91061|1385|186817|1386;3379134|1224|28211|356|118882|528;1783272|1239|909932|1843488|909930|33024,Complete,KateRasheed
bsdb:37220908/1/1,37220908,laboratory experiment,37220908,10.5483/BMBRep.2023-0068,NA,"Jeong S.M., Jin E.J., Wei S., Bae J.H., Ji Y., Jo Y., Jeong J.H., Im S.J. , Ryu D.",The impact of cancer cachexia on gut microbiota composition and short-chain fatty acid metabolism in a murine model,BMB reports,2023,NA,Experiment 1,Republic of Korea,Mus musculus,Feces,UBERON:0001988,Cachexia,HP:0004326,Healthy controls,cachexia-induced mice,All mice that were induced with cancer cachexia (Lewis lung cancer cells).,3,4,NA,16S,34,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Fig 3,8 October 2023,Grace og,"Grace og,Peace Sandy,WikiWorks",Differential abundance analysis of gut microbiota by DESeq2. (B) Microbes of significantly different abundance in genus level by DESeq2 analysis between groups expressed in log2 fold change.,increased,"s__rumen bacterium NK4A214,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Raoultibacter",877428;1783272|1239|186801|3085636|186803|248744;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|31979|49082;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|1643822|1643826|1926677,Complete,Peace Sandy
bsdb:37220908/1/2,37220908,laboratory experiment,37220908,10.5483/BMBRep.2023-0068,NA,"Jeong S.M., Jin E.J., Wei S., Bae J.H., Ji Y., Jo Y., Jeong J.H., Im S.J. , Ryu D.",The impact of cancer cachexia on gut microbiota composition and short-chain fatty acid metabolism in a murine model,BMB reports,2023,NA,Experiment 1,Republic of Korea,Mus musculus,Feces,UBERON:0001988,Cachexia,HP:0004326,Healthy controls,cachexia-induced mice,All mice that were induced with cancer cachexia (Lewis lung cancer cells).,3,4,NA,16S,34,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Fig 3,8 October 2023,Grace og,"Grace og,Hodan Issah,Peace Sandy,WikiWorks",Differential abundance analysis of gut microbiota by DESeq2. (B) Microbes of significantly different abundance in genus level by DESeq2 analysis between groups expressed in log2 fold change.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter",1783272|1239|186801|3082720|186804|1501226;1783272|1239|91061|186826|1300|1357;1783272|1239|526524|526525|2810281|191303;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|1980681,Complete,Peace Sandy
bsdb:37228368/1/1,37228368,"cross-sectional observational, not case-control",37228368,10.3389/fmicb.2023.1117905,NA,"Wang L., Lv W.Q., Yang J.T., Lin X., Liu H.M., Tan H.J., Quan R.P., Long P.P., Shen H., Shen J., Deng H.W. , Xiao H.M.",Enteric nervous system damage caused by abnormal intestinal butyrate metabolism may lead to functional constipation,Frontiers in microbiology,2023,"Fusobacterium, butyrate, enteric nervous system, functional constipation, metagenomics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Group 1,Group 2,Low risk people for Functional constipation (FC) whose defecation frequency was 1 time/day,38,360,NA,WMS,NA,BGISEQ-500 Sequencing,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,"Figure 1E, Table S4, Figure S3a, Figure S5e, Figure S5f",17 April 2025,Tosin,"Tosin,Victoria","Significant different bacteria genus, species among the four groups obtained via Deseq2 in the comparison between groups 1 and 2",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus sp. CAG:542,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. CAG:29,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp. CAG:528,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum|s__Azospirillum sp. CAG:239,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum|s__Azospirillum sp. CAG:260,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:927,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Apopatosoma|s__Candidatus Apopatosoma intestinale,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium VE202-14,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:138,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:217,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:226,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:302,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:343,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:349,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:352,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:417,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:440,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:492,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:571,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:62,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:678,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:780,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:798,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia fergusonii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:202,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:38,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:581,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. CAG:74,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:114,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:129,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:238,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:240,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:321,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:341,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:41,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas rupellensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1031,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:255,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:279,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:485,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:873,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:891,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:380,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:177,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:254,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:55,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:90,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp. 4_3_54A2FAA,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinatimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinatimonas|s__Succinatimonas sp. CAG:777,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella sp. CAG:397,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella sp. CAG:521,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella magna,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pectinovora",1783272|1239|909932|1843488|909930|904;1783272|1239|909932|1843488|909930|904|1262687;3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988|239934|239935;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759|1262694;1783272|1239|186801|186802|216572|244127|1262700;3379134|1224|28211|204441|2829815|191;3379134|1224|28211|204441|2829815|191|1262705;3379134|1224|28211|204441|2829815|191|1262706;3379134|976|200643|171549|815|816|1262753;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|1681;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|186801|186802|3082828|1262966;1783272|1239|186801|186802|1232452;1783272|1239|186801|186802|31979|1485|1262775;1783272|1239|186801|186802|31979|1485|1262779;1783272|1239|186801|186802|31979|1485|1262781;1783272|1239|186801|186802|31979|1485|1262793;1783272|1239|186801|186802|31979|1485|1262796;1783272|1239|186801|186802|31979|1485|1262797;1783272|1239|186801|186802|31979|1485|1262798;1783272|1239|186801|186802|31979|1485|1262804;1783272|1239|186801|186802|31979|1485|1262807;1783272|1239|186801|186802|31979|1485|1262813;1783272|1239|186801|186802|31979|1485|1262822;1783272|1239|186801|186802|31979|1485|1262828;1783272|1239|186801|186802|31979|1485|1262831;1783272|1239|186801|186802|31979|1485|1262839;1783272|1239|186801|186802|31979|1485|1262841;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|909932|1843489|31977|39948|487173;3379134|1224|1236|91347|543|561|564;1783272|1239|186801|186802|186806|1730|1262884;1783272|1239|186801|186802|186806|1730|1262889;1783272|1239|186801|186802|186806|1730|1262890;1783272|1239|186801|186802|216572|216851|1262897;1783272|1239|1263001;1783272|1239|1263003;1783272|1239|1263011;1783272|1239|1263013;1783272|1239|1263018;1783272|1239|1263019;1783272|1239|1263021;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|909929|1843491|158846|158847;1783272|1239|909932|909929|1843491|158846|491921;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|1853231|283168|28118;1783272|1239|909932|1843488|909930|33024|626940;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|171552|838|1262917;3379134|976|200643|171549|171552|838|1262923;3379134|976|200643|171549|171552|838|1262924;3379134|976|200643|171549|171552|838|1262927;3379134|976|200643|171549|171552|838|1262936;3379134|976|200643|171549|171552|838|1262937;1783272|1239|186801|3085636|186803|841|1262946;1783272|1239|186801|186802|216572|1263|1262952;1783272|1239|186801|186802|216572|1263|1262953;1783272|1239|186801|186802|216572|1263|1262960;1783272|1239|186801|186802|216572|1263|1262968;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|186801|186802|216572|292632|665956;3379134|1224|1236|135624|83763|674963;3379134|1224|1236|135624|83763|674963|1262974;3379134|1224|28216|80840|995019|40544|1262976;3379134|1224|28216|80840|995019|40544|1262977;3379134|1224|28216|80840|995019|40544|40545;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843489|31977|29465|464322;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|186801|186802|216572|1535;1783272|1239|909932|1843488|909930|904;3379134|74201|203494|48461|1647988|239934;1783272|201174|1760|85004|31953|1678;3379134|1224|1236|91347|543|547;3379134|976|200643|171549|1853231|283168;1783272|1239|91061|186826|1300|1301;3379134|1224|28216|80840|995019|40544;1783272|1239|909932|1843489|31977|29465;3379134|976|200643|171549|171552|838|1602169,Complete,KateRasheed
bsdb:37228368/1/2,37228368,"cross-sectional observational, not case-control",37228368,10.3389/fmicb.2023.1117905,NA,"Wang L., Lv W.Q., Yang J.T., Lin X., Liu H.M., Tan H.J., Quan R.P., Long P.P., Shen H., Shen J., Deng H.W. , Xiao H.M.",Enteric nervous system damage caused by abnormal intestinal butyrate metabolism may lead to functional constipation,Frontiers in microbiology,2023,"Fusobacterium, butyrate, enteric nervous system, functional constipation, metagenomics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Group 1,Group 2,Low risk people for Functional constipation (FC) whose defecation frequency was 1 time/day,38,360,NA,WMS,NA,BGISEQ-500 Sequencing,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,"Figure 1E, Table S4, Figure S3a, Figure S5e, Figure S5f",17 April 2025,Tosin,"Tosin,Victoria","Significant different bacteria genus, species among the four groups obtained via Deseq2 in the comparison between groups 1 and 2",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides graminisolvens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:98,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:127,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:56,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium ulcerans,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium varium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:254,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Schaedlerella|s__Schaedlerella arabinosiphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",3379134|976|200643|171549|815|816|477666;3379134|976|200643|171549|815|816|1262754;1783272|1239|186801|186802|31979|1485|1262774;1783272|1239|1263031;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492|848|851;3384189|32066|203490|203491|203492|848|861;3384189|32066|203490|203491|203492|848|856;1783272|1239|526524|526525|128827|1573535;1783272|1239|526524|526525|128827|1573535|1735;3379134|976|200643|171549|815|909656|204516;3379134|976|200643|171549|815|909656|671267;1783272|1239|186801|186802|216572|1263|1262953;1783272|1239|186801|3085636|186803|2676048|2044587;1783272|1239|186801|3085636|186803|2719313|1531;1783272|1239|526524|526525|128827,Complete,KateRasheed
bsdb:37228368/2/1,37228368,"cross-sectional observational, not case-control",37228368,10.3389/fmicb.2023.1117905,NA,"Wang L., Lv W.Q., Yang J.T., Lin X., Liu H.M., Tan H.J., Quan R.P., Long P.P., Shen H., Shen J., Deng H.W. , Xiao H.M.",Enteric nervous system damage caused by abnormal intestinal butyrate metabolism may lead to functional constipation,Frontiers in microbiology,2023,"Fusobacterium, butyrate, enteric nervous system, functional constipation, metagenomics",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Group 2,Group 3,High risk people for Functional constipation (FC) whose defecation frequency was 1 time/2 days,360,52,NA,WMS,NA,BGISEQ-500 Sequencing,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,increased,NA,NA,Signature 1,"Figure 1E, Table S4, Figure S3b",17 April 2025,Tosin,"Tosin,Victoria","Significant different bacteria genus, species among the four groups obtained via Deseq2 in the comparison between groups 2 and 3",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes ihumii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp. CAG:390,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp. G3(2012),k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea|s__Candidatus Soleaferrea massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium NK3B98,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium VE202-13,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium VE202-21,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:1013,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:1024,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:138,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:169,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:217,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:226,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:269,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:277,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:302,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:349,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:352,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:389,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:413,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:417,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:470,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:571,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:678,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:798,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister sp. CAG:486,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:202,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:841,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. CAG:74,k__Bacillati|p__Bacillota|s__Firmicutes bacterium ASF500,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:103,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:110,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:114,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:124,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:129,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:137,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:145,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:170,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:176,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:238,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:240,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:321,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:555,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:56,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:83,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:94,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 1-3,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. CAG:155,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. CAG:241,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. ER4,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. KLE 1728,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium VE202-24,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus albus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Wegman et al. 2014),k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus champanellensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus flavefaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:177,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:353,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:403,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:488,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:579,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:9,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] methylpentosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",3379134|976|200643|171549|171550|239759|1470347;3379134|976|200643|171549|171550|239759|626932;3379134|976|200643|171549|171550|239759|1465754;1783272|1239|186801|186802|216572|244127|169435;1783272|1239|186801|186802|216572|244127|1262703;1783272|1239|186801|186802|216572|244127|1235835;1783272|1239|186801|186802|1470353|1470354;1783272|1239|186801|186802|877414;1783272|1239|186801|186802|1232443;1783272|1239|186801|186802|1232453;1783272|1239|186801|186802|31979|1485|1262769;1783272|1239|186801|186802|31979|1485|1262770;1783272|1239|186801|186802|31979|1485|1262775;1783272|1239|186801|186802|31979|1485|1262778;1783272|1239|186801|186802|31979|1485|1262779;1783272|1239|186801|186802|31979|1485|1262781;1783272|1239|186801|186802|31979|1485|1262788;1783272|1239|186801|186802|31979|1485|1262790;1783272|1239|186801|186802|31979|1485|1262793;1783272|1239|186801|186802|31979|1485|1262797;1783272|1239|186801|186802|31979|1485|1262798;1783272|1239|186801|186802|31979|1485|1262801;1783272|1239|186801|186802|31979|1485|1262803;1783272|1239|186801|186802|31979|1485|1262804;1783272|1239|186801|186802|31979|1485|1262812;1783272|1239|186801|186802|31979|1485|1262822;1783272|1239|186801|186802|31979|1485|1262831;1783272|1239|186801|186802|31979|1485|1262841;3379134|200940|3031449|213115|194924|872|901;1783272|1239|909932|1843489|31977|39948|1262870;1783272|1239|186801|186802|186806|1730|1262884;1783272|1239|186801|186802|186806|1730|1262894;1783272|1239|186801|186802|216572|216851|1262897;1783272|1239|1378168;1783272|1239|1262999;1783272|1239|1263000;1783272|1239|1263001;1783272|1239|1263002;1783272|1239|1263003;1783272|1239|1263004;1783272|1239|1263005;1783272|1239|1263006;1783272|1239|1263007;1783272|1239|1263011;1783272|1239|1263013;1783272|1239|1263018;1783272|1239|1263030;1783272|1239|1263031;1783272|1239|1262992;1783272|1239|1262989;1783272|1239|186801|186802|1392389|1297617;1783272|544448|31969|2085|2092|2093;1783272|1239|186801|186802|216572|459786|1263547;1783272|1239|186801|186802|216572|459786|1235797;1783272|1239|186801|186802|216572|459786|1262910;1783272|1239|186801|186802|216572|459786|1262911;1783272|1239|186801|186802|216572|459786|1519439;1783272|1239|186801|186802|216572|459786|1226322;1783272|1239|186801|186802|216572|459786|351091;1783272|1239|186801|186802|216572|1232459;1783272|1239|186801|186802|216572|1017280|106588;1783272|1239|186801|186802|216572|1263|1264;1783272|1239|186801|186802|216572|1263|1160721;1783272|1239|186801|186802|216572|1263|1161942;1783272|1239|186801|186802|216572|1263|1265;1783272|1239|186801|186802|216572|1263|1262952;1783272|1239|186801|186802|216572|1263|1262955;1783272|1239|186801|186802|216572|1263|1262958;1783272|1239|186801|186802|216572|1263|1262959;1783272|1239|186801|186802|216572|1263|1262963;1783272|1239|186801|186802|216572|1263|1262967;1783272|1239|186801|186802|31979|1485|1522;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|186802|216572|84026;1783272|1239|186801|186802|216572|39492;1783272|1239|186801|186802|216572|39492;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|1263,Complete,KateRasheed
bsdb:37228368/2/2,37228368,"cross-sectional observational, not case-control",37228368,10.3389/fmicb.2023.1117905,NA,"Wang L., Lv W.Q., Yang J.T., Lin X., Liu H.M., Tan H.J., Quan R.P., Long P.P., Shen H., Shen J., Deng H.W. , Xiao H.M.",Enteric nervous system damage caused by abnormal intestinal butyrate metabolism may lead to functional constipation,Frontiers in microbiology,2023,"Fusobacterium, butyrate, enteric nervous system, functional constipation, metagenomics",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Group 2,Group 3,High risk people for Functional constipation (FC) whose defecation frequency was 1 time/2 days,360,52,NA,WMS,NA,BGISEQ-500 Sequencing,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,increased,NA,NA,Signature 2,"Figure 1E, Table S4, Figure S3b",17 April 2025,Tosin,"Tosin,Victoria","Significanf different bacteria genus, species among the four groups obtained via Deseq2 in the comparison between groups 2 and 3",decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus sp. CAG:542,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. CAG:435,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. CAG:831,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum|s__Azospirillum sp. CAG:239,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum|s__Azospirillum sp. CAG:260,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides gallinarum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides helcogenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides oleiciplenus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides pyogenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides reticulotermitis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 14(A),k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 1_1_30,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 2_1_22,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 2_2_4,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 3_1_23,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 3_1_33FAA,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 3_1_40A,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 4_1_36,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 4_3_47FAA,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 9_1_42FAA,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:189,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:462,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:530,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:598,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:633,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:702,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:714,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:754,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:875,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:98,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. D1,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. D2,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. D20,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. D22,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. HPS0048,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercorirosoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides timonensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella viscericola,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum|s__Bifidobacterium catenulatum subsp. kashiwanohense,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. CAG:257,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. CAG:37,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. CAG:52,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. KLE 1732,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter jejuni,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella morbi,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium 1_7_47FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium VE202-06,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium VE202-14,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium VE202-26,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium VE202-28,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium botulinum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium butyricum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:230,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:253,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:299,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:411,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:505,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:7,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:81,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:91,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. SS2/1,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus sp. CAG:235,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp. HPP0048,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp. HPP0074,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp. 5-2,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp. AGR2135,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp. CAG:317,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix|s__Erysipelothrix rhusiopathiae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia fergusonii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. 3_1_31,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:248,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:252,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:274,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:38,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:76,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:86,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:212,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:227,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:41,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:424,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:882,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium ulcerans,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium varium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella bergensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella multisaccharivorax,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella seregens,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Halobacillus|s__Halobacillus trueperi,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp. MS 92-3,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella variicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 1 4 56FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 2 1 46FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 2_1_58FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 5_1_63FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 6_1_37FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 9_1_43BFAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium A2,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium A4,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium CAG:25,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus delbrueckii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas rupellensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter laneus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp. CAG:409,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp. HGS0025,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium sp. CAG:207,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium sp. CAG:266,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola barnesiae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola salanitronis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella dentalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. AGR2160,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. BV3P1,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1092,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1124,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1185,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1320,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:255,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:386,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:474,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:5226,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:604,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:732,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:891,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:924,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. S7-1-8,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:303,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:45,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:50,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__Ruminiclostridium papyrosolvens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:17,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:55,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:60,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:90,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. SR1/5,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella albensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella baroniae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella buccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella maculosa,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella paludivivens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella dysenteriae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella flexneri,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinatimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinatimonas|s__Succinatimonas sp. CAG:777,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella parvirubra,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella sp. 6_1_58FAA_CT1,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella sp. CAG:51,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Thermobrachium|s__Thermobrachium celere,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella magna,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter oryzae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter ruminicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__[Bacteroides] pectinophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas nexilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas nexilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,s__bacterium LF-3,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__butyrate-producing bacterium SS3/4,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,,s__uncultured 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1|186802|186806|1730|1262885;1783272|1239|186801|186802|186806|1730|1262887;1783272|1239|186801|186802|186806|1730|1262888;1783272|1239|186801|186802|186806|1730|1262889;1783272|1239|186801|186802|186806|1730|1262892;1783272|1239|186801|186802|186806|1730|1262895;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|1263009;1783272|1239|1263010;1783272|1239|1263021;1783272|1239|1263022;1783272|1239|1262991;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492|848|850;3384189|32066|203490|203491|203492|848|851;3384189|32066|203490|203491|203492|848|861;3384189|32066|203490|203491|203492|848|856;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712|724|729;3379134|976|200643|171549|171552|52228|242750;3379134|976|200643|171549|171552|52228|310514;3379134|976|200643|171549|171552|52228|52229;1783272|1239|91061|1385|186817|45667|156205;3379134|976|200643|171549|171552|2974257|28127;3379134|976|200643|171549|171552|2974257|386414;1783272|1239|186801|3082720|186804|1505657|261299;3379134|1224|1236|91347|543|570|548;3379134|1224|1236|91347|543|570|573;3379134|1224|1236|91347|543|570|749535;3379134|1224|1236|91347|543|570|244366;1783272|1239|186801|3085636|186803|2683688;1783272|1239|186801|3085636|186803|2683689;1783272|1239|186801|3085636|186803|658082;1783272|1239|186801|3085636|186803|658089;1783272|1239|186801|3085636|186803|658656;1783272|1239|186801|3085636|186803|658088;1783272|1239|186801|3085636|186803|397290;1783272|1239|186801|3085636|186803|397291;1783272|1239|186801|3085636|186803|1262984;1783272|1239|91061|186826|33958|1578|1584;1783272|1239|91061|186826|33958|2767887|1623;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|909929|1843491|158846|437897;1783272|1239|909932|909929|1843491|158846|437897;1783272|1239|909932|909929|1843491|158846|158847;1783272|1239|909932|909929|1843491|158846|491921;1783272|1239|909932|1843489|31977|906|907;1783272|1239|909932|909929|1843491|52225|52226;3379134|976|200643|171549|1853231|283168|626933;3379134|976|200643|171549|2005525|375288|1262913;3379134|976|200643|171549|2005525|375288|1078087;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|1239|909932|1843488|909930|33024|1262914;1783272|1239|909932|1843488|909930|33024|1262915;3379134|976|200643|171549|815|909656|376804;3379134|976|200643|171549|815|909656|387090;3379134|976|200643|171549|815|909656|387090;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|204516;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|909656|376805;3379134|976|200643|171549|815|909656|671267;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|171552|838|419005;3379134|976|200643|171549|171552|838|28125;3379134|976|200643|171549|171552|838|52227;3379134|976|200643|171549|171552|838|28130;3379134|976|200643|171549|171552|838|470565;3379134|976|200643|171549|171552|838|1280674;3379134|976|200643|171549|171552|838|1111130;3379134|976|200643|171549|171552|838|1262919;3379134|976|200643|171549|171552|838|1262920;3379134|976|200643|171549|171552|838|1262921;3379134|976|200643|171549|171552|838|1262922;3379134|976|200643|171549|171552|838|1262923;3379134|976|200643|171549|171552|838|1262925;3379134|976|200643|171549|171552|838|1262926;3379134|976|200643|171549|171552|838|1262930;3379134|976|200643|171549|171552|838|1262932;3379134|976|200643|171549|171552|838|1262934;3379134|976|200643|171549|171552|838|1262937;3379134|976|200643|171549|171552|838|1262938;3379134|976|200643|171549|171552|838|1284775;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|3085636|186803|841|1262944;1783272|1239|186801|3085636|186803|841|1262947;1783272|1239|186801|3085636|186803|841|1262949;1783272|1239|186801|186802|216572|1508657|29362;1783272|1239|186801|186802|216572|1263|1262951;1783272|1239|186801|186802|216572|1263|1262960;1783272|1239|186801|186802|216572|1263|1262964;1783272|1239|186801|186802|216572|1263|1262968;1783272|1239|186801|186802|216572|1263|657323;3379134|1224|1236|91347|543|590|28901;3379134|976|200643|171549|171552|2974251|77768;3379134|976|200643|171549|171552|2974251|305719;3379134|976|200643|171549|171552|2974251|28126;3379134|976|200643|171549|171552|2974251|165179;3379134|976|200643|171549|171552|2974251|165179;3379134|976|200643|171549|171552|2974251|439703;3379134|976|200643|171549|171552|2974251|28135;3379134|976|200643|171549|171552|2974251|185294;3379134|976|200643|171549|171552|2974251|228604;3379134|1224|1236|91347|543|620;3379134|1224|1236|91347|543|620|622;3379134|1224|1236|91347|543|620|623;1783272|1239|91061|1385|90964|1279|1280;1783272|1239|91061|186826|1300|1301|1311;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1313;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|1300|1301|1308;3379134|1224|1236|135624|83763|674963;3379134|1224|1236|135624|83763|674963|1262974;3379134|1224|28216|80840|995019|40544|437898;3379134|1224|28216|80840|995019|40544|40545;3379134|1224|28216|80840|995019|40544|40545;3379134|976|200643|171549|2005525|195950|665949;3379134|976|200643|171549|2005525|195950|1262979;1783272|1239|186801|186802|31979|150333|53422;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843489|31977|29465|464322;1783272|1239|909932|1843489|31977|29465|29466;3379134|976|200643|171549|171552|558436|185293;3379134|976|200643|171549|171552|558436|839;1783272|1239|186801|186802|384638;1783272|1239|186801|3085636|186803|2719313|1531;1783272|1239|186801|3085636|186803|2005355|29361;1783272|1239|186801|3085636|186803|2005355|29361;1783272|1239|186801|3085636|186803|1506553|29347;1783272|1239|186801|3085636|186803|2316020|46228;1783272|1239|186801|3085636|186803|2316020|33039;1504823;1783272|1239|186801|186802|245014;1783272|1239|909932|1843488|909930|904;;3379134|976|200643|171549;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|189330;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543;1783272|1239|526524|526525|128827;3379134|1224|1236|91347|543|561;1783272|1239|186801|3085636|186803|1506553;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843489|31977|906;3379134|976|200643|171549|171551;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|841;1783272|1239|91061|186826|1300|1301;3379134|1224|28216|80840|995019|40544;1783272|1239|909932|1843489|31977|29465;;77133,Complete,KateRasheed
bsdb:37228368/3/1,37228368,"cross-sectional observational, not case-control",37228368,10.3389/fmicb.2023.1117905,NA,"Wang L., Lv W.Q., Yang J.T., Lin X., Liu H.M., Tan H.J., Quan R.P., Long P.P., Shen H., Shen J., Deng H.W. , Xiao H.M.",Enteric nervous system damage caused by abnormal intestinal butyrate metabolism may lead to functional constipation,Frontiers in microbiology,2023,"Fusobacterium, butyrate, enteric nervous system, functional constipation, metagenomics",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Group 3,Group 4,Patients with Functional constipation (FC) whose defecation frequency was 1 time/3 days,52,10,NA,WMS,NA,BGISEQ-500 Sequencing,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,"Figure 1E, Table S4, Figure S3C",17 April 2025,Tosin,"Tosin,Victoria","Significant different bacteria genus, species among the four groups obtained via Deseq2 in the comparison between groups 3 and 4",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. CAG:435,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp. CAG:317,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:76,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. CAG:82,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:65,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:891,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. S7-1-8,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella maculosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae,s__uncultured bacterium",3379134|976|200643|171549|171550|239759|1262695;1783272|1239|186801|3085636|186803|189330|1262873;1783272|1239|186801|186802|186806|1730|1262892;1783272|1239|186801|186802|216572|216851|1262898;1783272|1239|1262994;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|909929|1843491|158846|158847;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|419005;3379134|976|200643|171549|171552|838|470565;3379134|976|200643|171549|171552|838|1262937;3379134|976|200643|171549|171552|838|1284775;3379134|976|200643|171549|171552|2974251|439703;1783272|1239|91061|186826|1300|1301|1311;77133,Complete,KateRasheed
bsdb:37228368/3/2,37228368,"cross-sectional observational, not case-control",37228368,10.3389/fmicb.2023.1117905,NA,"Wang L., Lv W.Q., Yang J.T., Lin X., Liu H.M., Tan H.J., Quan R.P., Long P.P., Shen H., Shen J., Deng H.W. , Xiao H.M.",Enteric nervous system damage caused by abnormal intestinal butyrate metabolism may lead to functional constipation,Frontiers in microbiology,2023,"Fusobacterium, butyrate, enteric nervous system, functional constipation, metagenomics",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Group 3,Group 4,Patients with Functional constipation (FC) whose defecation frequency was 1 time/3 days,52,10,NA,WMS,NA,BGISEQ-500 Sequencing,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,"Figure 1E, Table S4, Figure S3C",17 April 2025,Tosin,"Tosin,Victoria","Significant different bacteria genus, species among the four groups obtained via Deseq2 in the comparison between groups 3 and 4",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Acetobacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp. CAG:344,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum|s__Azospirillum sp. CAG:239,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea|s__Candidatus Soleaferrea massiliensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:138,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:226,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:242,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:245,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:264,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:269,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:349,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:389,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:413,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:417,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:470,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:798,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:115,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:581,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:786,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:841,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:110,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:176,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:341,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. CAG:241,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:873,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:177,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:488,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:579,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",3379134|1224|28211|3120395|433|434;3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988|239934|239935;3379134|74201|203494|48461|1647988|239934|1262691;3379134|1224|28211|204441|2829815|191;3379134|1224|28211|204441|2829815|191|1262705;1783272|201174|1760|85004|31953|1678|1680;1783272|1239|186801|186802|1470353|1470354;3379134|1224|1236|91347|543|544;1783272|1239|186801|186802|31979|1485|1262775;1783272|1239|186801|186802|31979|1485|1262781;1783272|1239|186801|186802|31979|1485|1262783;1783272|1239|186801|186802|31979|1485|1262784;1783272|1239|186801|186802|31979|1485|1262786;1783272|1239|186801|186802|31979|1485|1262788;1783272|1239|186801|186802|31979|1485|1262797;1783272|1239|186801|186802|31979|1485|1262801;1783272|1239|186801|186802|31979|1485|1262803;1783272|1239|186801|186802|31979|1485|1262804;1783272|1239|186801|186802|31979|1485|1262812;1783272|1239|186801|186802|31979|1485|1262841;1783272|1239|909932|1843489|31977|39948|487173;1783272|1239|186801|186802|186806|1730|1262878;1783272|1239|186801|186802|186806|1730|1262890;1783272|1239|186801|186802|186806|1730|1262893;1783272|1239|186801|186802|186806|1730|1262894;1783272|1239|1263000;1783272|1239|1263007;1783272|1239|1263019;1783272|544448|31969|2085|2092|2093;1783272|1239|186801|186802|216572|459786|1262911;3379134|976|200643|171549|171552|838|1262936;1783272|1239|186801|186802|216572|1263|1262952;1783272|1239|186801|186802|216572|1263|1262959;1783272|1239|186801|186802|216572|1263|1262963;3379134|1224|1236|91347|543|620;3379134|1224|1236|91347|543,Complete,KateRasheed
bsdb:37228368/4/1,37228368,"cross-sectional observational, not case-control",37228368,10.3389/fmicb.2023.1117905,NA,"Wang L., Lv W.Q., Yang J.T., Lin X., Liu H.M., Tan H.J., Quan R.P., Long P.P., Shen H., Shen J., Deng H.W. , Xiao H.M.",Enteric nervous system damage caused by abnormal intestinal butyrate metabolism may lead to functional constipation,Frontiers in microbiology,2023,"Fusobacterium, butyrate, enteric nervous system, functional constipation, metagenomics",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy Controls,Functional constipation (FC) group,Patients with Functional constipation (FC),6,6,NA,WMS,NA,BGISEQ-500 Sequencing,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,"Figure 3E, Table S5",17 April 2025,Tosin,Tosin,Significant differential taxa between Healthy controls (HC) and Functional Constipation (FC) group using LeFse analysis,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF34-10BH,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF36-18BH,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. TF08-15,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium GAM79,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fluxus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. AM54-2NS,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 4_1_36,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AM34-9AC",1783272|1239|186801|3085636|186803|207244|105841;1783272|1239|186801|186802|31979|1485|2293011;1783272|1239|186801|186802|31979|1485|2293014;1783272|1239|186801|186802|31979|1485|2293052;1783272|1239|186801|3085636|186803|33042|33043;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|2109691;3379134|976|200643|171549|1853231|283168|28118;1783272|1239|909932|1843488|909930|33024|33025;1783272|1239|186801|3085636|186803|841|301301;;1783272|1239|186801|186802|186806|1730;3379134|976|200643|171549|815|816|626930;3379134|976|200643|171549|815|816|2292955;3379134|976|200643|171549|815|816|457393;1783272|1239|186801|186802|31979|1485|2293030,Complete,KateRasheed
bsdb:37228368/4/2,37228368,"cross-sectional observational, not case-control",37228368,10.3389/fmicb.2023.1117905,NA,"Wang L., Lv W.Q., Yang J.T., Lin X., Liu H.M., Tan H.J., Quan R.P., Long P.P., Shen H., Shen J., Deng H.W. , Xiao H.M.",Enteric nervous system damage caused by abnormal intestinal butyrate metabolism may lead to functional constipation,Frontiers in microbiology,2023,"Fusobacterium, butyrate, enteric nervous system, functional constipation, metagenomics",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy Controls,Functional constipation (FC) group,Patients with Functional constipation (FC),6,6,NA,WMS,NA,BGISEQ-500 Sequencing,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,"Figure 3E, Table S5",18 April 2025,Tosin,Tosin,Significant differential taxa between Healthy controls (HC) and Functional Constipation (FC) group using LeFse analysis,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium paraputrificum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium ulcerans,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:38,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium disporicum",1783272|1239|186801|186802|31979|1485|29363;3384189|32066|203490|203491|203492|848|861;3384189|32066|203490|203491|203492|848|850;1783272|1239|186801|186802|186806|1730|1262889;1783272|1239|186801|186802|31979|1485|84024,Complete,KateRasheed
bsdb:37228368/5/1,37228368,"cross-sectional observational, not case-control",37228368,10.3389/fmicb.2023.1117905,NA,"Wang L., Lv W.Q., Yang J.T., Lin X., Liu H.M., Tan H.J., Quan R.P., Long P.P., Shen H., Shen J., Deng H.W. , Xiao H.M.",Enteric nervous system damage caused by abnormal intestinal butyrate metabolism may lead to functional constipation,Frontiers in microbiology,2023,"Fusobacterium, butyrate, enteric nervous system, functional constipation, metagenomics",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Group 2,FCHR (Functional constipation high-risk) group,Combination of High risk people for Functional constipation (FC) whose defecation frequency was 1 time/2 days and High risk people for Functional constipation (FC) whose defecation frequency was 1 time/3 days.,360,62,NA,WMS,NA,BGISEQ-500 Sequencing,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure S5e, Figure S5f",20 April 2025,Tosin,Tosin,"Significant different bacterias among the three groups obtained by Deseq2, FC=log2 fold change at the genus and species levels.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:226,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:417,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:798,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma",1783272|1239|186801|186802|31979|1485|1262781;1783272|1239|186801|186802|31979|1485|1262804;1783272|1239|186801|186802|31979|1485|1262841;1783272|544448|31969|2085|2092|2093,Complete,KateRasheed
bsdb:37228368/5/2,37228368,"cross-sectional observational, not case-control",37228368,10.3389/fmicb.2023.1117905,NA,"Wang L., Lv W.Q., Yang J.T., Lin X., Liu H.M., Tan H.J., Quan R.P., Long P.P., Shen H., Shen J., Deng H.W. , Xiao H.M.",Enteric nervous system damage caused by abnormal intestinal butyrate metabolism may lead to functional constipation,Frontiers in microbiology,2023,"Fusobacterium, butyrate, enteric nervous system, functional constipation, metagenomics",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Group 2,FCHR (Functional constipation high-risk) group,Combination of High risk people for Functional constipation (FC) whose defecation frequency was 1 time/2 days and High risk people for Functional constipation (FC) whose defecation frequency was 1 time/3 days.,360,62,NA,WMS,NA,BGISEQ-500 Sequencing,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure S5e, Figure S5f",20 April 2025,Tosin,Tosin,"Significant different bacterias among the three groups obtained by Deseq2, FC=log2 fold change at the genus and species levels.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia fergusonii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium ulcerans,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium varium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinatimonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|1224|28211|204441|2829815|191;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|561|564;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492|848|850;3384189|32066|203490|203491|203492|848|861;3384189|32066|203490|203491|203492|848|856;3379134|1224|1236|135625|712|724;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|909929|1843491|158846|437897;3379134|1224|1236|91347|543|620;3379134|1224|1236|135624|83763|674963;1783272|1239|909932|1843488|909930|904;3379134|1224|1236|91347|543;1783272|1239|909932|1843489|31977|29465,Complete,KateRasheed
bsdb:37277785/1/1,37277785,laboratory experiment,37277785,https://doi.org/10.1186/s13048-023-01193-3,NA,"Yang J., Wang E., Jiang M., Tan Y., Yao F., Sun C., Pan L., Gao L. , Yao J.",Integrated fecal microbiota and metabolomics analysis of the orlistat intervention effect on polycystic ovary syndrome rats induced by letrozole combined with a high-fat diet,Journal of ovarian research,2023,"Gut microbiota, Metabolomics, Obesity, Orlistat, Polycystic ovary syndrome",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,PCOS (Polycystic ovary syndrome ) Control group,ORL-PCOS (Orlistat-Polycystic ovary syndrome) group,"The ORL-PCOS (Orlistat-Polycystic ovary syndrome) group was treated with different doses of orlistat (low-20 mg/kg/d; medium-40 mg/kg/d; high-80 mg/kg/d; Lunan Pharmaceutical Group Corporation; Shandong, Linyi, China.) over the next 12 weeks.",10,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Fig. 4A  and 4B,30 April 2025,PreciousChijioke,"PreciousChijioke,Victoria,KateRasheed",LEfSe of the gut microbiota of the ORL-PCOS and PCOS groups.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|g__Acidibacter,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Pseudomonadati|p__Acidobacteriota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Acidothermales|f__Acidothermaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Acidothermales|f__Acidothermaceae|g__Acidothermus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Myxococcota|c__Myxococcia|o__Myxococcales|f__Anaeromyxobacteraceae|g__Anaeromyxobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Aquicella,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Isosphaerales|f__Isosphaeraceae|g__Aquisphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Acidobacteriota|c__Terriglobia|o__Bryobacterales|f__Bryobacteraceae|g__Bryobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Acidobacteriota|c__Terriglobia|o__Terriglobales|f__Candidatus Korobacteraceae|g__Candidatus Korobacter,k__Pseudomonadati|p__Acidobacteriota|c__Terriglobia|o__Bryobacterales|f__Solibacteraceae|g__Candidatus Solibacter,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Frankiales,k__Pseudomonadati|p__Gemmatimonadota|c__Gemmatimonadia|o__Gemmatimonadales|f__Gemmatimonadaceae|g__Gemmatirosa,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Methanobacteriati|p__Methanobacteriota|c__Methanomicrobia|o__Methanocellales|f__Methanocellaceae|g__Methanocella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Pseudomonadati|p__Acidobacteriota|c__Terriglobia|o__Terriglobales|f__Acidobacteriaceae|g__Occallatibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Pasteuriaceae|g__Pasteuria,k__Pseudomonadati|p__Verrucomicrobiota|c__Pedosphaerae|o__Pedosphaerales|f__Pedosphaeraceae|g__Pedosphaera,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Roseiarcaceae|g__Roseiarcus,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Isosphaerales|f__Isosphaeraceae|g__Singulisphaera,k__Pseudomonadati|p__Acidobacteriota|c__Terriglobia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae,s__mouse gut metagenome,k__Pseudomonadati|p__Acidobacteriota|s__uncultured Acidobacteriota bacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|s__uncultured Actinomycetes bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|s__uncultured Alphaproteobacteria bacterium,k__Bacillati|p__Bacillota|s__uncultured Bacillota bacterium,s__uncultured bacterium,s__uncultured forest soil bacterium,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Gemmatales|f__Gemmataceae|g__Gemmata",3379134|1224|1236|1549619;1783272|201174|84992;3379134|57723;1783272|201174|1760|1643683|85032;1783272|201174|1760|1643683|85032|28048;3379134|1224|28211;3379134|2818505|32015|29|1524215|161492;3379134|1224|1236|118969|118968|254245;3379134|203682|203683|2691356|1763524|1511635;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976;3379134|57723|204432|332160|1962910|911113;3379134|976|200643|171549|1853231|574697;3379134|57723|204432|204433|3121618|658061;3379134|57723|204432|332160|332161|332162;3379134|200940|3031449|213115|194924|872;1783272|201174|1760|85013;3379134|142182|219685|219686|219687|1706036;3379134|1224|28211|356;3366610|28890|224756|570264|570265|570266;3379134|976|200643|171549|2005473;1783272|201174|1760|85007|1762|1763;3379134|57723|204432|204433|204434|1742983;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|577310;1783272|1239|91061|1385|538998|86004;3379134|74201|3440663|3440664|3440665|1032526;3379134|1224;3379134|1224|28211|356|1643957|1643958;3379134|203682|203683|2691356|1763524|466152;3379134|57723|204432;3379134|1224|28211|356|335928;410661;3379134|57723|171953;1783272|201174|1760|152507;3379134|976|200643;3379134|1224|28211|91750;1783272|1239|344338;77133;169009;3379134|203682|203683|2691355|1914233|113,Complete,KateRasheed
bsdb:37277785/1/2,37277785,laboratory experiment,37277785,https://doi.org/10.1186/s13048-023-01193-3,NA,"Yang J., Wang E., Jiang M., Tan Y., Yao F., Sun C., Pan L., Gao L. , Yao J.",Integrated fecal microbiota and metabolomics analysis of the orlistat intervention effect on polycystic ovary syndrome rats induced by letrozole combined with a high-fat diet,Journal of ovarian research,2023,"Gut microbiota, Metabolomics, Obesity, Orlistat, Polycystic ovary syndrome",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,PCOS (Polycystic ovary syndrome ) Control group,ORL-PCOS (Orlistat-Polycystic ovary syndrome) group,"The ORL-PCOS (Orlistat-Polycystic ovary syndrome) group was treated with different doses of orlistat (low-20 mg/kg/d; medium-40 mg/kg/d; high-80 mg/kg/d; Lunan Pharmaceutical Group Corporation; Shandong, Linyi, China.) over the next 12 weeks.",10,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Fig. 4A and 4B,1 May 2025,PreciousChijioke,"PreciousChijioke,KateRasheed",LEfSe of the gut microbiota of the ORL-PCOS and PCOS groups.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",1783272|1239|91061;1783272|1239;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|3068309;1783272|1239|186801|186802|216572|707003,Complete,KateRasheed
bsdb:37291572/2/1,37291572,"cross-sectional observational, not case-control",37291572,https://doi.org/10.1186/s12967-023-04119-1,https://translational-medicine.biomedcentral.com/articles/10.1186/s12967-023-04119-1,"Liu J., Huang X., Chen C., Wang Z., Huang Z., Qin M., He F., Tang B., Long C., Hu H., Pan S., Wu J. , Tang W.",Identification of colorectal cancer progression-associated intestinal microbiome and predictive signature construction,Journal of translational medicine,2023,"16S rRNA, Colorectal cancer, Immune infiltration, Intestinal microbiome, Staging prediction",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Early Colorectal Cancer (CRC) Stage I-II,Advanced Colorectal Cancer (CRC) Stage III-IV,Patients in stages III-IV were defined as those with advanced colorectal cancer,62,130,1 month,16S,34,Illumina,relative abundances,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,decreased,NA,unchanged,Signature 1,"Figure 2A, 2B and Additional file 9: Table S3",15 October 2025,Oladoye,"Oladoye,Fiddyhamma","Differential analysis of intestinal flora of CRC patients in stage I-II group and stage III-IV group. B LDA bar graph based on 16S rRNA gene sequencing, the table shows species with LDA score (log10) P value less than 0.05 and greater than the present value (default is 2).",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Aestuariispiraceae|g__Aestuariispira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes inops,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides chinchillae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus|s__Vagococcus teuberi,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__uncultured Eubacteriales bacterium,s__uncultured bacterium,s__uncultured organism",3379134|1224|28211|204441|3466454|1647175;3379134|976|200643|171549|171550|239759|626932;3379134|976|200643|171549|171550|239759|1501391;1783272|1239|186801|186802|3085642|580596;3379134|976|200643|171549|2005519|1348911;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288|871327;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|815|909656|310297;3379134|1224|1236|91347|1903414|583;3379134|1224|28211|204441|41295;3379134|1224|28211|204441;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|44748;1783272|1239|91061|186826|81852|2737;1783272|1239|91061|186826|81852|2737|519472;1783272|1239|186801|186802|172733;77133;155900,Complete,KateRasheed
bsdb:37291572/2/2,37291572,"cross-sectional observational, not case-control",37291572,https://doi.org/10.1186/s12967-023-04119-1,https://translational-medicine.biomedcentral.com/articles/10.1186/s12967-023-04119-1,"Liu J., Huang X., Chen C., Wang Z., Huang Z., Qin M., He F., Tang B., Long C., Hu H., Pan S., Wu J. , Tang W.",Identification of colorectal cancer progression-associated intestinal microbiome and predictive signature construction,Journal of translational medicine,2023,"16S rRNA, Colorectal cancer, Immune infiltration, Intestinal microbiome, Staging prediction",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Early Colorectal Cancer (CRC) Stage I-II,Advanced Colorectal Cancer (CRC) Stage III-IV,Patients in stages III-IV were defined as those with advanced colorectal cancer,62,130,1 month,16S,34,Illumina,relative abundances,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,decreased,NA,unchanged,Signature 2,"Figure 2A, 2B and Additional file 9: Table S3",15 October 2025,Oladoye,"Oladoye,Fiddyhamma","Differential analysis of intestinal flora of CRC patients in stage I-II group and stage III-IV group. B LDA bar graph based on 16S rRNA gene sequencing, the table shows species with LDA score (log10) P value less than 0.05 and greater than the present value (default is 2).",decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium|s__Atopobium minutum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium aurimucosum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. canine oral taxon 423,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermatophilaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermatophilaceae|g__Dermatophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Macrococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus russellii,s__bacterium,k__Pseudomonadati|p__Bdellovibrionota|c__Bdellovibrionia|o__Bdellovibrionales|f__Pseudobdellovibrionaceae|g__Bdellovibrio|s__uncultured Bdellovibrio sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|s__uncultured Eubacteriaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. oral clone FX028",1783272|201174|84998|84999|1643824|1380|1381;3379134|1224|28211|204458|76892|75;3379134|1224|1236|91347|543|544;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85007|1653|1716|169292;1783272|201174|1760|85007|1653|1716|1347145;1783272|201174|1760|85006|85018;1783272|201174|1760|85006|85018|1862;1783272|1239|91061|186826|186828|29393;3379134|1224|1236|135625|712|724|729;1783272|1239|91061|1385|90964|69965;3379134|1224|1236|91347|1903414|581;1783272|1239|186801|3082720|186804|1257|215200;1869227;3379134|3018035|3031418|213481|213483|958|239744;1783272|1239|186801|186802|186806|203524;1783272|1239|186801|186802|186806|1730|207551,Complete,KateRasheed
bsdb:37294364/1/1,37294364,case-control,37294364,10.1007/s00284-023-03361-6,NA,"Li Y., Liu G., Gong R. , Xi Y.",Gut Microbiome Dysbiosis in Patients with Endometrial Cancer vs. Healthy Controls Based on 16S rRNA Gene Sequencing,Current microbiology,2023,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Endometrial cancer,MONDO:0011962,Healthy controls (N),Endometrial Cancer (EC),"Patients pathologically diagnosed with endometrial cancer (type I endometrial cancer) who received surgical treatment, and their histological type was endometrioid cancer.",32,33,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 4B,16 April 2025,MyleeeA,MyleeeA,"Composition of the gut microbiota and the analysis of species differences at the phylum, class, order, family, genus and species levels between Endometrial cancer and Healthy Controls.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella",3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236;3379134|1224;3379134|1224|1236|91347|543|620,Complete,KateRasheed
bsdb:37294364/1/2,37294364,case-control,37294364,10.1007/s00284-023-03361-6,NA,"Li Y., Liu G., Gong R. , Xi Y.",Gut Microbiome Dysbiosis in Patients with Endometrial Cancer vs. Healthy Controls Based on 16S rRNA Gene Sequencing,Current microbiology,2023,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Endometrial cancer,MONDO:0011962,Healthy controls (N),Endometrial Cancer (EC),"Patients pathologically diagnosed with endometrial cancer (type I endometrial cancer) who received surgical treatment, and their histological type was endometrioid cancer.",32,33,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 4B,17 April 2025,MyleeeA,MyleeeA,"Composition of the gut microbiota and the analysis of species differences at the phylum, class, order, family, genus and species levels between Endometrial cancer and Healthy Controls.",decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis",1783272|1239;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|204475|745368,Complete,KateRasheed
bsdb:37294364/2/1,37294364,case-control,37294364,10.1007/s00284-023-03361-6,NA,"Li Y., Liu G., Gong R. , Xi Y.",Gut Microbiome Dysbiosis in Patients with Endometrial Cancer vs. Healthy Controls Based on 16S rRNA Gene Sequencing,Current microbiology,2023,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Endometrial cancer,MONDO:0011962,Healthy controls (N),Endometrial Cancer (EC),"Patients pathologically diagnosed with endometrial cancer (type I endometrial cancer) who received surgical treatment, and their histological type was endometrioid cancer.",32,33,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Fig 5A - 5B,18 April 2025,PreciousChijioke,PreciousChijioke,LEfSe analysis of the gut microbiota between Healthy Controls and Endometrial Cancer.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella",3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236;3379134|1224;3379134|1224|1236|91347|543|620,Complete,KateRasheed
bsdb:37294364/2/2,37294364,case-control,37294364,10.1007/s00284-023-03361-6,NA,"Li Y., Liu G., Gong R. , Xi Y.",Gut Microbiome Dysbiosis in Patients with Endometrial Cancer vs. Healthy Controls Based on 16S rRNA Gene Sequencing,Current microbiology,2023,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Endometrial cancer,MONDO:0011962,Healthy controls (N),Endometrial Cancer (EC),"Patients pathologically diagnosed with endometrial cancer (type I endometrial cancer) who received surgical treatment, and their histological type was endometrioid cancer.",32,33,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 2,Fig 5A - 5B,18 April 2025,PreciousChijioke,PreciousChijioke,LEfSe analysis of the gut microbiota between Healthy Controls and Endometrial Cancer.,decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Bacteroidota",1783272|1239;3379134|976|200643|171549;3379134|976|200643;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|204475;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803|841;3379134|976,Complete,KateRasheed
bsdb:37298483/1/1,37298483,"cross-sectional observational, not case-control",37298483,https://doi.org/10.3390/ijms24119533,NA,"Park S., Zhang T. , Kang S.","Fecal Microbiota Composition, Their Interactions, and Metagenome Function in US Adults with Type 2 Diabetes According to Enterotypes",International journal of molecular sciences,2023,"fecal bacteria, metagenome analysis, pooling data, type 2 diabetes, western diet",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls in Total participants,Type 2 diabetes (T2DM) in Total Participants,Participants were Caucasians with T2DM aged over 30 years.,872,1039,NA,16S,NA,Illumina,relative abundances,NA,0.001,TRUE,NA,NA,NA,NA,decreased,decreased,unchanged,NA,NA,Signature 1,Figures 2B,24 February 2025,Miss Lulu,Miss Lulu,Fecal bacteria composition in total participants.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia glucerasea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena fissicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] aminophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora xylanolytica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia luti",1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|572511|536633;1783272|1239|186801|3085636|186803|2005359|290055;1783272|1239|186801|3085636|186803|2941495|1512;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|1506553|1526;1783272|1239|186801|186802|216572|459786|351091;3379134|976|200643|171549|815|816|246787;1783272|1239|186801|3085636|186803|2719231|29375;1783272|1239|186801|3085636|186803|572511|89014,Complete,Svetlana up
bsdb:37298483/1/2,37298483,"cross-sectional observational, not case-control",37298483,https://doi.org/10.3390/ijms24119533,NA,"Park S., Zhang T. , Kang S.","Fecal Microbiota Composition, Their Interactions, and Metagenome Function in US Adults with Type 2 Diabetes According to Enterotypes",International journal of molecular sciences,2023,"fecal bacteria, metagenome analysis, pooling data, type 2 diabetes, western diet",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls in Total participants,Type 2 diabetes (T2DM) in Total Participants,Participants were Caucasians with T2DM aged over 30 years.,872,1039,NA,16S,NA,Illumina,relative abundances,NA,0.001,TRUE,NA,NA,NA,NA,decreased,decreased,unchanged,NA,NA,Signature 2,Figure 2B,24 February 2025,Miss Lulu,Miss Lulu,Fecal bacteria composition in total participants.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Kineothrix|s__Kineothrix alysoides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter ruminantium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",3379134|976|200643|171549|815|816|1912896;3379134|976|200643|171549|815|816|820;1783272|1239|186801|3085636|186803|572511|418240;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|186802|204475|745368;1783272|1239|186801|3085636|186803|2163168|1469948;1783272|1239|186801|186802|216572|459786|1263547;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|3085636|186803|2316020|33038,Complete,Svetlana up
bsdb:37298483/2/1,37298483,"cross-sectional observational, not case-control",37298483,https://doi.org/10.3390/ijms24119533,NA,"Park S., Zhang T. , Kang S.","Fecal Microbiota Composition, Their Interactions, and Metagenome Function in US Adults with Type 2 Diabetes According to Enterotypes",International journal of molecular sciences,2023,"fecal bacteria, metagenome analysis, pooling data, type 2 diabetes, western diet",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls in ET-B,Type 2 diabetes (T2DM) in ET-B,Participants were Caucasians with T2DM aged over 30 years (Enterotype Bacteroidaceae (ET-B)).,416,533,NA,16S,NA,Illumina,relative abundances,NA,0.001,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3B,24 February 2025,Miss Lulu,Miss Lulu,Fecal bacteria composition in Enterotype Bacteroidaceae (ET-B),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia glucerasea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora xylanolytica,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena fissicatena,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei",1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|572511|536633;1783272|1239|186801|3085636|186803|2719231|29375;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|2941495|1512;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|3085636|186803|2005359|290055;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|909656|357276,Complete,Svetlana up
bsdb:37298483/2/2,37298483,"cross-sectional observational, not case-control",37298483,https://doi.org/10.3390/ijms24119533,NA,"Park S., Zhang T. , Kang S.","Fecal Microbiota Composition, Their Interactions, and Metagenome Function in US Adults with Type 2 Diabetes According to Enterotypes",International journal of molecular sciences,2023,"fecal bacteria, metagenome analysis, pooling data, type 2 diabetes, western diet",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls in ET-B,Type 2 diabetes (T2DM) in ET-B,Participants were Caucasians with T2DM aged over 30 years (Enterotype Bacteroidaceae (ET-B)).,416,533,NA,16S,NA,Illumina,relative abundances,NA,0.001,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3B,24 February 2025,Miss Lulu,"Miss Lulu,Aleru Divine",Fecal bacteria composition in Enterotype Bacteroidaceae (ET-B),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia luti,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter ruminantium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans",3379134|976|200643|171549|815|816|1912896;3379134|976|200643|171549|815|816|371601;1783272|1239|186801|3085636|186803|572511|89014;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|186801|186802|216572|459786|1263547;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|3082720|186804|1501226|1776391;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|3085636|186803|841|360807,Complete,Svetlana up
bsdb:37298483/3/1,37298483,"cross-sectional observational, not case-control",37298483,https://doi.org/10.3390/ijms24119533,NA,"Park S., Zhang T. , Kang S.","Fecal Microbiota Composition, Their Interactions, and Metagenome Function in US Adults with Type 2 Diabetes According to Enterotypes",International journal of molecular sciences,2023,"fecal bacteria, metagenome analysis, pooling data, type 2 diabetes, western diet",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls in ET-L,Type 2 diabetes (T2DM) in ET-L,Participants were Caucasians with T2DM aged over 30 years in  Enterotype Lachnospiraceae (ET-L).,329,411,NA,16S,NA,Illumina,relative abundances,NA,0.001,TRUE,NA,NA,NA,NA,decreased,decreased,increased,NA,NA,Signature 1,Figure 4B,24 February 2025,Miss Lulu,"Miss Lulu,Aleru Divine",Fecal bacteria composition in Enterotype Lachnospiraceae (ET-L),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus senegalensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus rubiinfantis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia glucerasea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia luti,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena fissicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcoides|s__Ruminococcoides bili,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] aminophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] herbivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus",1783272|1239|186801|186802|3082771|1924093|1673717;1783272|1239|186801|186802|216572|244127|1720200;1783272|1239|186801|3085636|186803|572511|536633;1783272|1239|186801|3085636|186803|572511|89014;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|2005359|290055;1783272|1239|186801|186802|216572|2893095|2678306;1783272|1239|186801|3085636|186803|1506553|1526;1783272|1239|186801|3085636|186803|1506553|39479;1783272|1239|186801|3085636|186803|207244|649756,Complete,Svetlana up
bsdb:37298483/3/2,37298483,"cross-sectional observational, not case-control",37298483,https://doi.org/10.3390/ijms24119533,NA,"Park S., Zhang T. , Kang S.","Fecal Microbiota Composition, Their Interactions, and Metagenome Function in US Adults with Type 2 Diabetes According to Enterotypes",International journal of molecular sciences,2023,"fecal bacteria, metagenome analysis, pooling data, type 2 diabetes, western diet",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls in ET-L,Type 2 diabetes (T2DM) in ET-L,Participants were Caucasians with T2DM aged over 30 years in  Enterotype Lachnospiraceae (ET-L).,329,411,NA,16S,NA,Illumina,relative abundances,NA,0.001,TRUE,NA,NA,NA,NA,decreased,decreased,increased,NA,NA,Signature 2,Figure 4B,24 February 2025,Miss Lulu,"Miss Lulu,Aleru Divine",Fecal bacteria composition in Enterotype Lachnospiraceae (ET-L).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium pacaense,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella effluvii,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus|s__Monoglobus pectinilyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus champanellensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter|s__Sporobacter termitidis,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila",3379134|976|200643|171549|815|816|1912896;1783272|1239|186801|3085636|186803|572511|871665;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|186802|31979|1485|1917870;1783272|1239|186801|3085636|186803|1649459|1096246;1783272|1239|186801|3085656|3085657|2039302|1981510;1783272|1239|186801|186802|216572|459786|1263547;1783272|1239|186801|186802|216572|1263|1161942;1783272|1239|186801|186802|216572|44748|44749;3379134|74201|203494|48461|1647988|239934|239935,Complete,Svetlana up
bsdb:37298483/4/1,37298483,"cross-sectional observational, not case-control",37298483,https://doi.org/10.3390/ijms24119533,NA,"Park S., Zhang T. , Kang S.","Fecal Microbiota Composition, Their Interactions, and Metagenome Function in US Adults with Type 2 Diabetes According to Enterotypes",International journal of molecular sciences,2023,"fecal bacteria, metagenome analysis, pooling data, type 2 diabetes, western diet",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls in ET-P,Type 2 diabetes (T2DM) in ET-P,Participants were Caucasians with T2DM aged over 30 years in Enterotype Prevotellaceae (ET-P).,127,95,NA,16S,NA,Illumina,relative abundances,NA,0.001,TRUE,NA,NA,NA,NA,decreased,decreased,increased,NA,NA,Signature 1,Figure 5B,24 February 2025,Miss Lulu,Miss Lulu,Fecal bacteria composition in Enterotype Prevotellaceae (ET-P).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Kineothrix|s__Kineothrix alysoides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter ruminantium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae",3379134|976|200643|171549|815|816|674529;3379134|976|200643|171549|815|816|1912896;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|2163168|1469948;1783272|1239|186801|186802|216572|459786|1263547;3379134|976|200643|171549|2005525|375288|46503,Complete,Svetlana up
bsdb:37298483/4/2,37298483,"cross-sectional observational, not case-control",37298483,https://doi.org/10.3390/ijms24119533,NA,"Park S., Zhang T. , Kang S.","Fecal Microbiota Composition, Their Interactions, and Metagenome Function in US Adults with Type 2 Diabetes According to Enterotypes",International journal of molecular sciences,2023,"fecal bacteria, metagenome analysis, pooling data, type 2 diabetes, western diet",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls in ET-P,Type 2 diabetes (T2DM) in ET-P,Participants were Caucasians with T2DM aged over 30 years in Enterotype Prevotellaceae (ET-P).,127,95,NA,16S,NA,Illumina,relative abundances,NA,0.001,TRUE,NA,NA,NA,NA,decreased,decreased,increased,NA,NA,Signature 2,Figure 5B,24 February 2025,Miss Lulu,Miss Lulu,Fecal bacteria composition in Enterotype Prevotellaceae (ET-P).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia glucerasea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] herbivorans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] aminophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia luti,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara",1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|572511|536633;1783272|1239|186801|3085636|186803|1506553|39479;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|3085636|186803|1506553|1526;1783272|1239|186801|186802|216572|459786|351091;1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|841|360807;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|186801|3085636|186803|572511|89014;1783272|1239|186801|3085636|186803|33042|33043;3379134|976|200643|171549|171552|577309|454154,Complete,Svetlana up
bsdb:37314861/1/1,37314861,case-control,37314861,10.1002/ana.26719,NA,"Palacios N., Wilkinson J., Bjornevik K., Schwarzschild M.A., McIver L., Ascherio A. , Huttenhower C.",Metagenomics of the Gut Microbiome in Parkinson's Disease: Prodromal Changes,Annals of neurology,2023,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Recently diagnosed Parkinson's disease patients (PD),"Recently diagnosed PD refers to patients with onset Parkinson's disease (the second most common neurodegenerative disease globally, impacting approximately 1% of the population 65 years and older).",131,75,NA,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.2,TRUE,NA,age,"age,body mass index",NA,NA,NA,NA,NA,NA,Signature 1,"In text of the ""Individual Species and Functions Are Similarly Associated with Recently Onset PD and PPS"" section and PD_Dataverse_taxa",25 February 2025,KateRasheed,KateRasheed,Significantly differential abundance of taxa identified via feature-wise analyses (MaAsLin 2),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella tayi,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae",1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|186801|186802|216572|1535;1783272|201174|1760|85004|31953|1678|1689;1783272|1239|186801|3085636|186803|1432051|1432052;1783272|201174|84998|1643822|1643826|644652|471189,Complete,Svetlana up
bsdb:37314861/1/2,37314861,case-control,37314861,10.1002/ana.26719,NA,"Palacios N., Wilkinson J., Bjornevik K., Schwarzschild M.A., McIver L., Ascherio A. , Huttenhower C.",Metagenomics of the Gut Microbiome in Parkinson's Disease: Prodromal Changes,Annals of neurology,2023,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Recently diagnosed Parkinson's disease patients (PD),"Recently diagnosed PD refers to patients with onset Parkinson's disease (the second most common neurodegenerative disease globally, impacting approximately 1% of the population 65 years and older).",131,75,NA,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.2,TRUE,NA,age,"age,body mass index",NA,NA,NA,NA,NA,NA,Signature 2,"In text of the ""Individual Species and Functions Are Similarly Associated with Recently Onset PD and PPS"" section and PD_Dataverse_taxa",25 February 2025,KateRasheed,KateRasheed,Significantly differential abundance of taxa identified via feature-wise analyses (MaAsLin 2),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Lawsonibacter|s__Lawsonibacter asaccharolyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 57_20",1783272|1239|186801|186802|186806|1730|39490;1783272|1239|186801|186802|216572|2172004|2108523;3379134|976|200643|171549|815|816|371601;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|186802|216572|39492;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|459786|1897011,Complete,Svetlana up
bsdb:37314861/3/1,37314861,case-control,37314861,10.1002/ana.26719,NA,"Palacios N., Wilkinson J., Bjornevik K., Schwarzschild M.A., McIver L., Ascherio A. , Huttenhower C.",Metagenomics of the Gut Microbiome in Parkinson's Disease: Prodromal Changes,Annals of neurology,2023,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Prodromal (Premotor) Parkinson's syndrome (PPS),"Prodromal (Premotor) Parkinson's syndrome (PPS) refers to patients that had constipation, pRBD, and substantial loss of smell.",131,101,NA,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.2,TRUE,NA,age,"age,body mass index",NA,NA,NA,NA,NA,NA,Signature 1,PD_Dataverse_taxa,25 February 2025,KateRasheed,KateRasheed,Significantly differential abundance of taxa identified via feature-wise analyses (MaAsLin 2),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D5,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella tayi",1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|186802|216572|1520815;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|3085636|186803|1432051|1432052,Complete,Svetlana up
bsdb:37314861/3/2,37314861,case-control,37314861,10.1002/ana.26719,NA,"Palacios N., Wilkinson J., Bjornevik K., Schwarzschild M.A., McIver L., Ascherio A. , Huttenhower C.",Metagenomics of the Gut Microbiome in Parkinson's Disease: Prodromal Changes,Annals of neurology,2023,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Prodromal (Premotor) Parkinson's syndrome (PPS),"Prodromal (Premotor) Parkinson's syndrome (PPS) refers to patients that had constipation, pRBD, and substantial loss of smell.",131,101,NA,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.2,TRUE,NA,age,"age,body mass index",NA,NA,NA,NA,NA,NA,Signature 2,PD_Dataverse_taxa,25 February 2025,KateRasheed,KateRasheed,Significantly differential abundance of taxa identified via feature-wise analyses (MaAsLin 2),decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,1783272|1239|186801|186802|216572|216851|853,Complete,Svetlana up
bsdb:37329328/1/1,37329328,"cross-sectional observational, not case-control",37329328,https://doi.org/10.1111/ene.15931,NA,"Lledós M., Prats-Sánchez L., Llucià-Carol L., Cárcel-Márquez J., Muiño E., Cullell N., Gallego-Fabrega C., Martín-Campos J.M., Aguilera-Simón A., Guasch-Jiménez M., Guisado-Alonso D., Ramos-Pachón A., Martínez-Domeño A., Izquierdo A., Marín R., Camps-Renom P., Martí-Fàbregas J. , Fernández-Cadenas I.",Ischaemic stroke patients present sex differences in gut microbiota,European journal of neurology,2023,"gut microbiota, gut-brain axis, sex, stroke",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Ischemic stroke,HP:0002140,Male IS patients (Ischemic stroke),Female IS patients (Ischemic stroke),Female patients who have been diagnosed with Ischemic stroke,53,36,1 month,WMS,NA,Illumina,log transformation,Negative Binomial Regression,0.05,TRUE,NA,NA,age,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Fig-2b and Table-2,12 April 2025,Aiyshaaaa,Aiyshaaaa,Log-transformed and differential abundance of Fusobacteria (phylum to family level) in between male and female ischemic stroke patients.,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota",3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066,Complete,Svetlana up
bsdb:37334756/1/1,37334756,laboratory experiment,37334756,https://doi.org/10.1111/cns.14302,NA,"Yang C., Wang W., Deng P., Wang X., Zhu L., Zhao L., Li C. , Gao H.",Fibroblast growth factor 21 ameliorates behavior deficits in Parkinson's disease mouse model via modulating gut microbiota and metabolic homeostasis,CNS neuroscience & therapeutics,2023,"FGF21, Parkinson's disease, metabolism, microbiota-gut-brain metabolic axis, neurotransmitter",Experiment 1,China,Mus musculus,Colon,UBERON:0001155,Parkinson's disease,MONDO:0005180,Control (CON groups),MPTP (untreated PD mice),"1‐methyl‐4‐phenyl‐1,2,3,6‐tetrahydropyridine (MPTP) induced Parkinson's disease (PD) mice model.",10,10,NA,16S,4,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 1,"Figure 5A, Text",13 March 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",LEfSe analysis with LDA score representing statistical bacterial differences in colonic microbiota between the PD (positive score) and CON groups (negative score).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|976|200643|171549|2005473;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|2005525;3379134|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:37334756/1/2,37334756,laboratory experiment,37334756,https://doi.org/10.1111/cns.14302,NA,"Yang C., Wang W., Deng P., Wang X., Zhu L., Zhao L., Li C. , Gao H.",Fibroblast growth factor 21 ameliorates behavior deficits in Parkinson's disease mouse model via modulating gut microbiota and metabolic homeostasis,CNS neuroscience & therapeutics,2023,"FGF21, Parkinson's disease, metabolism, microbiota-gut-brain metabolic axis, neurotransmitter",Experiment 1,China,Mus musculus,Colon,UBERON:0001155,Parkinson's disease,MONDO:0005180,Control (CON groups),MPTP (untreated PD mice),"1‐methyl‐4‐phenyl‐1,2,3,6‐tetrahydropyridine (MPTP) induced Parkinson's disease (PD) mice model.",10,10,NA,16S,4,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 2,"Figure 5A, Text",13 March 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",LEfSe analysis with LDA score representing statistical bacterial differences in colonic microbiota between the PD (positive score) and CON groups (negative score).,decreased,"p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter mastomyrinus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,s__bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma",95818|2093818|2093825|2171986|1331051;1783272|1239|186801;1783272|1239|186801|186802;3379134|29547|3031852|213849|72293|209|287948;1783272|1239|186801|3085636|186803;3379134|976|200643|1970189|1573805;1783272|544448|31969;1783272|544448;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572;1869227;1783272|1239|186801|186802|216572;1783272|544448|2790996|2790998|2129,Complete,Svetlana up
bsdb:37334756/2/1,37334756,laboratory experiment,37334756,https://doi.org/10.1111/cns.14302,NA,"Yang C., Wang W., Deng P., Wang X., Zhu L., Zhao L., Li C. , Gao H.",Fibroblast growth factor 21 ameliorates behavior deficits in Parkinson's disease mouse model via modulating gut microbiota and metabolic homeostasis,CNS neuroscience & therapeutics,2023,"FGF21, Parkinson's disease, metabolism, microbiota-gut-brain metabolic axis, neurotransmitter",Experiment 2,China,Mus musculus,Colon,UBERON:0001155,Clinical treatment,EFO:0007056,FGF21 + MPTP mice (mice treated with Fibroblast growth factor 21 (FGF21)),MPTP (untreated PD mice),"1‐methyl‐4‐phenyl‐1,2,3,6‐tetrahydropyridine (MPTP) induced Parkinson's disease (PD) mice model.",10,10,NA,16S,4,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 5C, Text",13 March 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",LEfSe analysis with LDA score representing statistical bacterial differences in colonic microbiota between the PD (positive score) and FGF21 groups (negative score).,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Mammaliicoccus|s__Mammaliicoccus lentus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|1239|91061|1385;1783272|1239|91061|1385|90964|2803850|42858;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:37334756/2/2,37334756,laboratory experiment,37334756,https://doi.org/10.1111/cns.14302,NA,"Yang C., Wang W., Deng P., Wang X., Zhu L., Zhao L., Li C. , Gao H.",Fibroblast growth factor 21 ameliorates behavior deficits in Parkinson's disease mouse model via modulating gut microbiota and metabolic homeostasis,CNS neuroscience & therapeutics,2023,"FGF21, Parkinson's disease, metabolism, microbiota-gut-brain metabolic axis, neurotransmitter",Experiment 2,China,Mus musculus,Colon,UBERON:0001155,Clinical treatment,EFO:0007056,FGF21 + MPTP mice (mice treated with Fibroblast growth factor 21 (FGF21)),MPTP (untreated PD mice),"1‐methyl‐4‐phenyl‐1,2,3,6‐tetrahydropyridine (MPTP) induced Parkinson's disease (PD) mice model.",10,10,NA,16S,4,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 5C, Text",13 March 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",LEfSe analysis with LDA score representing statistical bacterial differences in colonic microbiota between the PD (positive score) and FGF21 groups (negative score).,decreased,"p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Clostridia,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__Ruminiclostridium papyrosolvens,s__bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",95818|2093818|2093825|2171986|1331051;1783272|1239|186801;28221;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|1508657|29362;1869227;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:37375044/1/1,37375044,"cross-sectional observational, not case-control",37375044,https://doi.org/10.3390/microorganisms11061542,https://www.mdpi.com/2076-2607/11/6/1542,"Scarafile D., Luise D., Motta V., Spiezio C., Modesto M., Porcu M.M., Yitzhak Y., Correa F., Sandri C., Trevisi P. , Mattarelli P.",Faecal Microbiota Characterisation of <i>Potamochoerus porcus</i> Living in a Controlled Environment,Microorganisms,2023,"Potamocherus porcus, beneficial microbes, bifidobacteria, diet, gut microbiota",Experiment 1,Italy,Potamochoerus porcus,Feces,UBERON:0001988,Environmental factor,EFO:0000469,Potamochoerus porcus housed in Verona,Potamochoerus porcus housed in Rome,"Potamochoerus porcus housed in Bioparco, Rome, Italy. This group included 2 adult individuals.",3,2,2 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,decreased,NA,Signature 1,Table 3 and Table S2,17 October 2024,Prolific,"Prolific,Aleru Divine,WikiWorks",Key microbial taxa that were differentially abundant in gut microbiota composition of Red River Hogs (Potamochoerus porcus) housed in  Rome and Verona parks.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Cellulosilyticaceae|g__Cellulosilyticum,k__Pseudomonadati|p__Elusimicrobiota,k__Pseudomonadati|p__Fibrobacterota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Pseudomonadati|p__Thermodesulfobacteriota,k__Methanobacteriati|p__Thermoplasmatota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__uncultured Eubacteriales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|s__uncultured Prevotellaceae bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Holosporales|f__Candidatus Paracaedibacteraceae",3379134|976|200643|171549|171552|1283313;3379134|976;1783272|1239|186801|3085636|3018741|698776;3379134|74152;3379134|65842;1783272|1239|186801|3085636|186803|28050;3379134|976|200643|171549|2005523;3379134|1224;3379134|1224|28216|80840|995019|40544;3379134|1224|28216|80840|995019;3379134|200940;3366610|2283796;1783272|1239|186801|186802|172733;1783272|1239|186801|3085636|186803|297314;3379134|976|200643|171549|171552|370804;3379134|1224|28211|1921002|1777752,Complete,Svetlana up
bsdb:37375044/1/2,37375044,"cross-sectional observational, not case-control",37375044,https://doi.org/10.3390/microorganisms11061542,https://www.mdpi.com/2076-2607/11/6/1542,"Scarafile D., Luise D., Motta V., Spiezio C., Modesto M., Porcu M.M., Yitzhak Y., Correa F., Sandri C., Trevisi P. , Mattarelli P.",Faecal Microbiota Characterisation of <i>Potamochoerus porcus</i> Living in a Controlled Environment,Microorganisms,2023,"Potamocherus porcus, beneficial microbes, bifidobacteria, diet, gut microbiota",Experiment 1,Italy,Potamochoerus porcus,Feces,UBERON:0001988,Environmental factor,EFO:0000469,Potamochoerus porcus housed in Verona,Potamochoerus porcus housed in Rome,"Potamochoerus porcus housed in Bioparco, Rome, Italy. This group included 2 adult individuals.",3,2,2 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,decreased,NA,Signature 2,Table 3 and Table S2,21 October 2024,Prolific,"Prolific,Aleru Divine,WikiWorks",Key microbial taxa that were differentially abundant in gut microbiota composition of Red River Hogs (Potamochoerus porcus) housed in  Rome and Verona parks.,decreased,"k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Spirochaetota,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Actinomycetota,k__Thermotogati|p__Synergistota,k__Methanobacteriati|p__Methanobacteriota,k__Pseudomonadati|p__Planctomycetota,",3379134|203691|203692|136|137;3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|1185407;3379134|976|200643|171549;1783272|1239|91061|186826|33958;1783272|201174|1760|85007|1653;3379134|203691|203692|136|2845253|157;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|1470353;1783272|1239|526524|526525|128827;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|100175;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|171550;1783272|201174|1760|85007|1653|1716;1783272|1239;3379134|203691;3379134|74201;1783272|201174;3384194|508458;3366610|28890;3379134|203682;,Complete,Svetlana up
bsdb:37399128/1/1,37399128,meta-analysis,37399128,https://doi.org/10.1111/ene.15961,NA,"Chen G., Zhou X., Zhu Y., Shi W. , Kong L.","Gut microbiome characteristics in subjective cognitive decline, mild cognitive impairment and Alzheimer's disease: a systematic review and meta-analysis",European journal of neurology,2023,"Alzheimer's disease, alpha diversity, gut microbes, relative abundance",Experiment 1,"China,United States of America",Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healthy Controls (HC),Alzheimer's disease (AD),Individuals who have been diagnosed with Alzheimer's disease (AD),128,129,NA,16S,34,Illumina,relative abundances,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,unchanged,NA,unchanged,Signature 1,Fig-1b,7 May 2025,Aiyshaaaa,Aiyshaaaa,"Forest plots of the estimated relative abundance of phylum Firmicutes, in patients with AD compared to HCs.",decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,KateRasheed
bsdb:37399128/2/1,37399128,meta-analysis,37399128,https://doi.org/10.1111/ene.15961,NA,"Chen G., Zhou X., Zhu Y., Shi W. , Kong L.","Gut microbiome characteristics in subjective cognitive decline, mild cognitive impairment and Alzheimer's disease: a systematic review and meta-analysis",European journal of neurology,2023,"Alzheimer's disease, alpha diversity, gut microbes, relative abundance",Experiment 2,"China,United States of America",Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Healthy Controls (HC),Mild cognitive impairment(MCI),Individuals who have been diagnosed with Mild cognitive impairment(MCI),131,137,NA,16S,34,Illumina,relative abundances,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,NA,Signature 1,Fig 1A,7 May 2025,Aiyshaaaa,"Aiyshaaaa,Fiddyhamma","Forest plots of the estimated relative abundance of phylum Bacteroidetes, phylum Firmicutes in patients with MCI compared to HCs",increased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,KateRasheed
bsdb:37399128/3/1,37399128,meta-analysis,37399128,https://doi.org/10.1111/ene.15961,NA,"Chen G., Zhou X., Zhu Y., Shi W. , Kong L.","Gut microbiome characteristics in subjective cognitive decline, mild cognitive impairment and Alzheimer's disease: a systematic review and meta-analysis",European journal of neurology,2023,"Alzheimer's disease, alpha diversity, gut microbes, relative abundance",Experiment 3,"China,United States of America",Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Healthy Controls (HC),Mild cognitive impairment(MCI),Individuals who have been diagnosed with Mild cognitive impairment(MCI),168,149,NA,16S,34,Illumina,relative abundances,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,NA,Signature 1,Figure 1B,11 June 2025,Fiddyhamma,Fiddyhamma,"Forest plots of the estimated relative abundance of phylum Bacteroidetes, phylum Firmicutes in patients with MCI compared to HCs",decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,KateRasheed
bsdb:37409975/1/1,37409975,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R., Kumari N., Gupta S., Jaiswal R., Mehrotra D., Singh S., Mukherjee S. , Kumar R.",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 1,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Adjacent normal tissue (AT),Tumor tissue (TT) samples,Tumor tissue (TT) specimens were obtained from the inner part of the tumor,20,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Supplementary Figure 3A,28 April 2024,MyleeeA,"MyleeeA,WikiWorks",Differential abundance of core bacterial genera among adjacent tumor tissue and tumor tissues.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,3379134|1224|28211|204458|76892|41275,Complete,Svetlana up
bsdb:37409975/1/2,37409975,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R., Kumari N., Gupta S., Jaiswal R., Mehrotra D., Singh S., Mukherjee S. , Kumar R.",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 1,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Adjacent normal tissue (AT),Tumor tissue (TT) samples,Tumor tissue (TT) specimens were obtained from the inner part of the tumor,20,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Supplementary Figure 2B, 3A and 3c",28 April 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundances of core bacterial phyla, genera and Species among adjacent tumor tissue and tumor tissues.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas|s__Brevundimonas diminuta,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria mucosa,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|28211|204458|76892|41275|293;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481|482|488;3379134|1224|28216|206351|481|482|28449;3379134|1224|28211|356|118882|528;33090|35493|3398|72025|3803|3814|508215;1783272|201174|1760|85006|1268|32207|2047;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|909932|1843489|31977|29465;3379134|1224,Complete,Svetlana up
bsdb:37409975/2/1,37409975,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R., Kumari N., Gupta S., Jaiswal R., Mehrotra D., Singh S., Mukherjee S. , Kumar R.",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 2,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Adjacent normal tissue (AT),Precancer,"Precancerous lesion samples were collected from patients with leukoplakia, fibrosis, and
erythroplakia.",20,15,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Supplementary Figure 2C, 3B and 3D",28 April 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundances of core bacterial phyla, genera and Species among adjacent tumor tissue and Precancer Samples.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,p__Candidatus Saccharimonadota,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema medium",1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549|815|816;3379134|976|200643;95818;3379134|976|117743|200644|49546|1016;3379134|976|117743|200644|49546|1016|45242;3379134|976|117743|200644|49546|1016|327575;3379134|976|117743|200644|49546|1016|1018;3379134|976|117743|200644|49546|1016|1019;1783272|201174|1760|85007|1653|1716;3379134|200940|3031449|213115|194924;1783272|1239|186801|3085636|186803;3384189|32066|203490|203491|1129771|32067;3379134|1224|28216|206351|481|482;1783272|1239|186801|186802|216572|119852;3379134|976|117747|200666|84566|84567;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836;3379134|203691|203692|136;3379134|203691|203692|136|2845253|157;3379134|203691|203692|136|2845253|157|158;3379134|203691|203692|136|2845253|157|58231,Complete,Svetlana up
bsdb:37409975/2/2,37409975,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R., Kumari N., Gupta S., Jaiswal R., Mehrotra D., Singh S., Mukherjee S. , Kumar R.",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 2,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Adjacent normal tissue (AT),Precancer,"Precancerous lesion samples were collected from patients with leukoplakia, fibrosis, and
erythroplakia.",20,15,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 3D,28 April 2024,MyleeeA,"MyleeeA,WikiWorks",Differential abundances of core bacterial Species among adjacent tumor tissue and Precancer lesions.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus periodonticum,1783272|1239|91061|186826|1300|1301|2490633,Complete,Svetlana up
bsdb:37409975/3/1,37409975,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R., Kumari N., Gupta S., Jaiswal R., Mehrotra D., Singh S., Mukherjee S. , Kumar R.",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 3,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Precancer,Early Stage Cancer,Cancer Samples subdivided into T1 and T2,20,30,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3B,28 April 2024,MyleeeA,"MyleeeA,WikiWorks",Differential abundances of core bacterial species between the precancer group with early (T1 and T2),increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium canifelinum,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola",3379134|976|117743|200644|49546|1016|1018;3379134|976|117743|200644|49546|1016|45242;3379134|976|117743|200644|49546|1016|327575;3384189|32066|203490|203491|203492|848|851;3384189|32066|203490|203491|203492|848|285729;3379134|203691|203692|136|2845253|157|158,Complete,Svetlana up
bsdb:37409975/3/2,37409975,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R., Kumari N., Gupta S., Jaiswal R., Mehrotra D., Singh S., Mukherjee S. , Kumar R.",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 3,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Precancer,Early Stage Cancer,Cancer Samples subdivided into T1 and T2,20,30,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3B,28 April 2024,MyleeeA,"MyleeeA,WikiWorks",Differential abundances of core bacterial species between the precancer group and early (T1 and T2),decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus periodonticum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus dysgalactiae",1783272|1239|91061|186826|1300|1301|2490633;1783272|201174|1760|85006|1268|32207|2047;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300|1301|1334,Complete,Svetlana up
bsdb:37409975/4/1,37409975,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R., Kumari N., Gupta S., Jaiswal R., Mehrotra D., Singh S., Mukherjee S. , Kumar R.",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 4,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Precancer,Late Stage Cancer,Cancer Samples subdivided into T3 and T4,20,30,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3B,28 April 2024,MyleeeA,"MyleeeA,WikiWorks",Differential abundances of core bacterial species between the precancer group and late cancer (T3 and T4) groups,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri",3379134|976|117743|200644|49546|1016|1018;3379134|976|117743|200644|49546|1016|45242;3379134|976|117743|200644|49546|1016|1019;3379134|976|117743|200644|49546|1016|327575,Complete,Svetlana up
bsdb:37409975/4/2,37409975,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R., Kumari N., Gupta S., Jaiswal R., Mehrotra D., Singh S., Mukherjee S. , Kumar R.",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 4,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Precancer,Late Stage Cancer,Cancer Samples subdivided into T3 and T4,20,30,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3B,28 April 2024,MyleeeA,"MyleeeA,WikiWorks",Differential abundances of core bacterial species between the precancer group and late cancer (T3 and T4) groups,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus dysgalactiae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus periodonticum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa",1783272|1239|91061|186826|1300|1301|1334;1783272|1239|91061|186826|1300|1301|2490633;1783272|201174|1760|85006|1268|32207|43675;1783272|201174|1760|85006|1268|32207|2047,Complete,Svetlana up
bsdb:37409975/5/1,37409975,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R., Kumari N., Gupta S., Jaiswal R., Mehrotra D., Singh S., Mukherjee S. , Kumar R.",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 5,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Precancer,Cancer,Participants at different stages of disease pathogenesis (T1 to T4).,15,60,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2B, 2C, 3A and Supplementary Fig 2D",29 April 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundances of core bacterial Phyla, Family, Genera and Species between Precancer and Cancer Samples.",increased,"p__Candidatus Altimarinota,k__Pseudomonadati|p__Verrucomicrobiota,p__Candidatus Saccharimonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa",363464;3379134|74201;95818;3379134|976|200643;3379134|203691|203692|136;3379134|976|200643|171549|171551;3379134|976|200643|171549|171552;1783272|1239|1737404|1737405|1737406;3379134|1224|1236|72274|135621;3379134|200940|3031449|213115|194924;1783272|1239|186801|3082720|186804;1783272|1239|186801|3085636|186803;3379134|203691|203692|136|137;3379134|976|117743|200644|49546;3379134|1224|28216|80840|80864;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3379134|1224|1236|72274|135621|286;3379134|203691|203692|136|2845253|157;3384189|32066|203490|203491|1129771|32067;3379134|976|117743|200644|49546|1016;1783272|1239|186801|186802|216572|119852;3379134|203691|203692|136|2845253|157|158;3379134|976|117743|200644|49546|1016|327575;3379134|976|117743|200644|49546|1016|1018;3379134|976|117743|200644|49546|1016|1019;3379134|976|117743|200644|49546|1016|45242,Complete,Svetlana up
bsdb:37409975/5/2,37409975,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R., Kumari N., Gupta S., Jaiswal R., Mehrotra D., Singh S., Mukherjee S. , Kumar R.",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 5,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Precancer,Cancer,Participants at different stages of disease pathogenesis (T1 to T4).,15,60,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2B, 2C, 3A and Supplementary Fig 2D",29 April 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundances of core bacterial Phyla, Family, Genera and Species between Precancer and Cancer Samples.",decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus dysgalactiae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus periodonticum,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia",1783272|201174;1783272|201174|1760|2037|2049|28263;1783272|1239;1783272|1239|186801|186802;1783272|1239|1737404|1737405|1570339|543311;1783272|201174|1760|85006|1268|32207|2047;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301|1334;1783272|1239|91061|186826|1300|1301|2490633;33090|35493|3398|72025|3803|3814|508215,Complete,Svetlana up
bsdb:37409975/6/1,37409975,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R., Kumari N., Gupta S., Jaiswal R., Mehrotra D., Singh S., Mukherjee S. , Kumar R.",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 6,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Early Stage Cancer,Late Stage Cancer,Cancer Samples subdivided into T3 and T4,30,30,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2D and Supplementary Figure 2A,29 April 2024,MyleeeA,"MyleeeA,WikiWorks",Differential abundances of core bacterial species between the Early stage cancer groups (T1 and T2) and Late Stage cancer (T3 and T4) groups,increased,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,3379134|976|117747|200666|84566|84567,Complete,Svetlana up
bsdb:37409975/6/2,37409975,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R., Kumari N., Gupta S., Jaiswal R., Mehrotra D., Singh S., Mukherjee S. , Kumar R.",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 6,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Early Stage Cancer,Late Stage Cancer,Cancer Samples subdivided into T3 and T4,30,30,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2D and Supplementary Figure 2A,29 April 2024,MyleeeA,"MyleeeA,WikiWorks",Differential abundances of core bacterial species between the Early stage cancer groups (T1 and T2) and Late Stage cancer (T3 and T4) groups,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",3384189|32066|203490;3384189|32066|203490|203491|1129771|32067;3379134|200940|3031449|213115|194924;1783272|1239|186801|186802,Complete,Svetlana up
bsdb:37409975/7/NA,37409975,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R., Kumari N., Gupta S., Jaiswal R., Mehrotra D., Singh S., Mukherjee S. , Kumar R.",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 7,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Precancer,T1,Early Stage Cancer Patients grouped as T1,15,15,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:37409975/8/NA,37409975,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R., Kumari N., Gupta S., Jaiswal R., Mehrotra D., Singh S., Mukherjee S. , Kumar R.",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 8,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Precancer,T2,Early Stage Cancer Patients grouped as T2,15,15,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:37409975/9/NA,37409975,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R., Kumari N., Gupta S., Jaiswal R., Mehrotra D., Singh S., Mukherjee S. , Kumar R.",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 9,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Precancer,T3,Late Stage Cancer Patients grouped as T3,15,15,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:37409975/10/NA,37409975,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R., Kumari N., Gupta S., Jaiswal R., Mehrotra D., Singh S., Mukherjee S. , Kumar R.",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 10,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,Precancer,T4,Late Stage Cancer Patients grouped as T4,15,15,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:37409975/11/NA,37409975,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R., Kumari N., Gupta S., Jaiswal R., Mehrotra D., Singh S., Mukherjee S. , Kumar R.",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 11,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,T1,T3,Late Stage Cancer Patients grouped as T3,15,15,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:37409975/12/NA,37409975,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R., Kumari N., Gupta S., Jaiswal R., Mehrotra D., Singh S., Mukherjee S. , Kumar R.",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 12,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,T2,T4,Late Stage Cancer Patients grouped as T4,15,15,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:37409975/13/NA,37409975,"cross-sectional observational, not case-control",37409975,10.1128/spectrum.04596-22,NA,"Pratap Singh R., Kumari N., Gupta S., Jaiswal R., Mehrotra D., Singh S., Mukherjee S. , Kumar R.",Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma,Microbiology spectrum,2023,"OSCC, biomarker, inflammation, microbiome, tumor microenvironment",Experiment 13,India,Homo sapiens,Mouth,UBERON:0000165,Oral cavity carcinoma,MONDO:0044925,T3,T4,Late Stage Cancer Patients grouped as T4,15,15,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:37422471/1/1,37422471,laboratory experiment,37422471,10.1038/s41522-023-00415-2,NA,"Li S., Zhai J., Chu W., Geng X., Wang D., Jiao L., Lu G., Chan W.Y., Sun K., Sun Y., Chen Z.J. , Du Y.",Alleviation of Limosilactobacillus reuteri in polycystic ovary syndrome protects against circadian dysrhythmia-induced dyslipidemia via capric acid and GALR1 signaling,NPJ biofilms and microbiomes,2023,NA,Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control,Darkness,Rats in this group were exposed to the darkness treatment for 8 weeks.,8,8,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Dunn's test",0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 5c & Supplementary Data 4,6 August 2025,Victoria,Victoria,"Relative abundance of differential genera (highly or lowly expressed in darkness rats compared with control and DL.reuteri rats, P < 0.05), calculated with Kruskal–Wallis test followed by Dunn’s multiple comparison test.",increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,1783272|1239|186801|186802|31979|1485,Complete,KateRasheed
bsdb:37422471/1/2,37422471,laboratory experiment,37422471,10.1038/s41522-023-00415-2,NA,"Li S., Zhai J., Chu W., Geng X., Wang D., Jiao L., Lu G., Chan W.Y., Sun K., Sun Y., Chen Z.J. , Du Y.",Alleviation of Limosilactobacillus reuteri in polycystic ovary syndrome protects against circadian dysrhythmia-induced dyslipidemia via capric acid and GALR1 signaling,NPJ biofilms and microbiomes,2023,NA,Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control,Darkness,Rats in this group were exposed to the darkness treatment for 8 weeks.,8,8,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Dunn's test",0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 5c & Supplementary Data 4,6 August 2025,Victoria,Victoria,"Relative abundance of differential genera (highly or lowly expressed in darkness rats compared with control and DL.reuteri rats, P < 0.05), calculated with Kruskal–Wallis test followed by Dunn’s multiple comparison test.",decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,KateRasheed
bsdb:37422471/2/1,37422471,laboratory experiment,37422471,10.1038/s41522-023-00415-2,NA,"Li S., Zhai J., Chu W., Geng X., Wang D., Jiao L., Lu G., Chan W.Y., Sun K., Sun Y., Chen Z.J. , Du Y.",Alleviation of Limosilactobacillus reuteri in polycystic ovary syndrome protects against circadian dysrhythmia-induced dyslipidemia via capric acid and GALR1 signaling,NPJ biofilms and microbiomes,2023,NA,Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Darkness,Darkness+Limosilactobacillus reuteri,"Rats in this group were exposed to the darkness treatment for 8 weeks, followed by Limosilactobacillus reuteri administration.",8,8,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Dunn's test",0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 5c & Supplementary Data 4,6 August 2025,Victoria,Victoria,"Relative abundance of differential genera (highly or lowly expressed in darkness rats compared with control and DL.reuteri rats, P < 0.05), calculated with Kruskal–Wallis test followed by Dunn’s multiple comparison test.",increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,KateRasheed
bsdb:37422471/2/2,37422471,laboratory experiment,37422471,10.1038/s41522-023-00415-2,NA,"Li S., Zhai J., Chu W., Geng X., Wang D., Jiao L., Lu G., Chan W.Y., Sun K., Sun Y., Chen Z.J. , Du Y.",Alleviation of Limosilactobacillus reuteri in polycystic ovary syndrome protects against circadian dysrhythmia-induced dyslipidemia via capric acid and GALR1 signaling,NPJ biofilms and microbiomes,2023,NA,Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Darkness,Darkness+Limosilactobacillus reuteri,"Rats in this group were exposed to the darkness treatment for 8 weeks, followed by Limosilactobacillus reuteri administration.",8,8,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Dunn's test",0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 5c & Supplementary Data 4,6 August 2025,Victoria,Victoria,"Relative abundance of differential genera (highly or lowly expressed in darkness rats compared with control and DL.reuteri rats, P < 0.05), calculated with Kruskal–Wallis test followed by Dunn’s multiple comparison test.",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,1783272|1239|186801|186802|31979|1485,Complete,KateRasheed
bsdb:37422471/3/1,37422471,laboratory experiment,37422471,10.1038/s41522-023-00415-2,NA,"Li S., Zhai J., Chu W., Geng X., Wang D., Jiao L., Lu G., Chan W.Y., Sun K., Sun Y., Chen Z.J. , Du Y.",Alleviation of Limosilactobacillus reuteri in polycystic ovary syndrome protects against circadian dysrhythmia-induced dyslipidemia via capric acid and GALR1 signaling,NPJ biofilms and microbiomes,2023,NA,Experiment 3,China,Rattus norvegicus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control & Darkness,Darkness+Limosilactobacillus reuteri,"Rats in this group were exposed to the darkness treatment for 8 weeks, followed by Limosilactobacillus reuteri administration.",16,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5d & e,6 August 2025,Victoria,Victoria,Cladogram and Genera biomarkers within groups identified by LDA effect size analysis with an LDA score > 2.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacillati|p__Candidatus Melainabacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|s__uncultured Erysipelotrichia bacterium,s__uncultured rumen bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",3379134|976|200643|171549|1853231|574697;1783272|1798710|1906119;1783272|1798710;1783272|1239|186801|186802|31979|49082;1783272|1239|186801|186802|186806|1730|42322;1783272|544448|31969;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|666559;136703;1783272|1239|186801|186802|216572|707003,Complete,KateRasheed
bsdb:37422471/4/1,37422471,laboratory experiment,37422471,10.1038/s41522-023-00415-2,NA,"Li S., Zhai J., Chu W., Geng X., Wang D., Jiao L., Lu G., Chan W.Y., Sun K., Sun Y., Chen Z.J. , Du Y.",Alleviation of Limosilactobacillus reuteri in polycystic ovary syndrome protects against circadian dysrhythmia-induced dyslipidemia via capric acid and GALR1 signaling,NPJ biofilms and microbiomes,2023,NA,Experiment 4,China,Rattus norvegicus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control & Darkness+Limosilactobacillus reuteri,Darkness,Rats in this group were exposed to the darkness treatment for 8 weeks.,16,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5d & e,6 August 2025,Victoria,Victoria,Cladogram and Genera biomarkers within groups identified by LDA effect size analysis with an LDA score > 2.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|31979|1485;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|526524|526525|128827|1573534;1783272|1239|186801|186802|216572|459786;3379134|1224|1236|135625|712|745;3379134|1224|1236|135625|712;3379134|1224|1236|135625;1783272|1239|186801|3082720|186804;1783272|1239|526524|526525|2810281|191303,Complete,KateRasheed
bsdb:37422471/5/1,37422471,laboratory experiment,37422471,10.1038/s41522-023-00415-2,NA,"Li S., Zhai J., Chu W., Geng X., Wang D., Jiao L., Lu G., Chan W.Y., Sun K., Sun Y., Chen Z.J. , Du Y.",Alleviation of Limosilactobacillus reuteri in polycystic ovary syndrome protects against circadian dysrhythmia-induced dyslipidemia via capric acid and GALR1 signaling,NPJ biofilms and microbiomes,2023,NA,Experiment 5,China,Rattus norvegicus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Darkness & Darkness+Limosilactobacillus reuteri,Control,Rats in this group were not exposed to the darkness treatment.,16,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5d & e,6 August 2025,Victoria,Victoria,Cladogram and Genera biomarkers within groups identified by LDA effect size analysis with an LDA score > 2.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Atopostipes,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Sporosarcina,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Myroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Amphibacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Oceanobacillus,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae",1783272|1239|91061|186826|186828|292480;1783272|1239|91061|1385|186818|1569;1783272|1239|91061|1385|90964|227979;1783272|1239|91061|186826|186827|66831;1783272|1239|91061|1385|186817|1386;3379134|1224|1236|2887326|468|497;1783272|1239|91061|186826|81852|2737;3379134|976|117743|200644|49546|76831;1783272|1239|91061|1385|186817|29331;1783272|201174|1760|85006|85020|43668;1783272|1239|91061|1385|186817|182709;1783272|1239|91061;1783272|1239|91061|186826;1783272|1239|91061|186826|186828;1783272|1239|91061|186826|186827;1783272|1239|91061|1385|186818;1783272|1239|91061|1385|186817;3379134|976|117743;3379134|976|117743|200644|49546;3379134|976|117743|200644;1783272|201174;1783272|201174|1760|85006|85020;1783272|201174|1760|85007;1783272|201174|1760|85007|1653,Complete,KateRasheed
bsdb:37428087/1/1,37428087,case-control,37428087,https://doi.org/10.1128/spectrum.00590-23,https://journals.asm.org/doi/10.1128/spectrum.00590-23,"Bai H., Liu T., Wang S., Gong W., Shen L., Zhang S. , Wang Z.",Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats,Microbiology spectrum,2023,"QIIME2, acute diarrhea, domestic cat, gut microbiota, metabolome, microbiome",Experiment 1,China,Felis catus,Feces,UBERON:0001988,Diarrhea,HP:0002014,Healthy American Shorthair (MH),Acutely diarrheic American Shorthair cats (MD),American Shorthair cats with acute diarrhea,12,12,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,unchanged,unchanged,increased,unchanged,NA,increased,Signature 1,FIG 3a,12 March 2024,Imaspecial,"Imaspecial,Scholastica,WikiWorks",Species analysis of differences in healthy (MH) versus acutely diarrheic (MD) American Shorthair cats using LEfSe,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri",3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|2974251|165179,Complete,Svetlana up
bsdb:37428087/1/2,37428087,case-control,37428087,https://doi.org/10.1128/spectrum.00590-23,https://journals.asm.org/doi/10.1128/spectrum.00590-23,"Bai H., Liu T., Wang S., Gong W., Shen L., Zhang S. , Wang Z.",Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats,Microbiology spectrum,2023,"QIIME2, acute diarrhea, domestic cat, gut microbiota, metabolome, microbiome",Experiment 1,China,Felis catus,Feces,UBERON:0001988,Diarrhea,HP:0002014,Healthy American Shorthair (MH),Acutely diarrheic American Shorthair cats (MD),American Shorthair cats with acute diarrhea,12,12,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,unchanged,unchanged,increased,unchanged,NA,increased,Signature 2,FIG 3a,12 March 2024,Imaspecial,"Imaspecial,Scholastica,WikiWorks",Species analysis of differences in healthy (MH) versus acutely diarrheic (MD) American Shorthair cats using LEfSe,decreased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales",1783272|1239|91061;1783272|1239;1783272|1239|526524|526525|2810280|135858;1783272|1239|909932|1843489|31977|39948;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|909932;1783272|1239|909932|909929;1783272|1239|526524|526525|128827|123375;1783272|1239|909932|1843489|31977;1783272|1239|909932|1843489,Complete,Svetlana up
bsdb:37428087/2/1,37428087,case-control,37428087,https://doi.org/10.1128/spectrum.00590-23,https://journals.asm.org/doi/10.1128/spectrum.00590-23,"Bai H., Liu T., Wang S., Gong W., Shen L., Zhang S. , Wang Z.",Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats,Microbiology spectrum,2023,"QIIME2, acute diarrhea, domestic cat, gut microbiota, metabolome, microbiome",Experiment 2,China,Felis catus,Feces,UBERON:0001988,Diarrhea,HP:0002014,Healthy British Shorthair (BH),Acutely diarrheic British Shorthair cats (BD),British Shorthair cats with acute diarrhea,12,12,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,FIG 3c,12 March 2024,Imaspecial,"Imaspecial,Scholastica,WikiWorks",Species analysis of differences in healthy (BH) versus acutely diarrheic (BD) British Shorthair cats using LEfSe,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri",3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|2974251|165179,Complete,Svetlana up
bsdb:37428087/2/2,37428087,case-control,37428087,https://doi.org/10.1128/spectrum.00590-23,https://journals.asm.org/doi/10.1128/spectrum.00590-23,"Bai H., Liu T., Wang S., Gong W., Shen L., Zhang S. , Wang Z.",Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats,Microbiology spectrum,2023,"QIIME2, acute diarrhea, domestic cat, gut microbiota, metabolome, microbiome",Experiment 2,China,Felis catus,Feces,UBERON:0001988,Diarrhea,HP:0002014,Healthy British Shorthair (BH),Acutely diarrheic British Shorthair cats (BD),British Shorthair cats with acute diarrhea,12,12,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,FIG 3c,12 March 2024,Imaspecial,"Imaspecial,Scholastica,WikiWorks",Species analysis of differences in healthy (BH) versus acutely diarrheic (BD) British Shorthair cats using LEfSe,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella tanakaei,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis",1783272|201174;1783272|201174|84998|84999|1643824;1783272|1239|91061;1783272|1239|186801|186802|3085642;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107|102106|626935;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|526524|526525;1783272|201174|84998|84999|1643824|2082587;1783272|1239|526524|526525|2810280|3025755;1783272|1239|526524|526525|2810280|3025755|29348,Complete,Svetlana up
bsdb:37428087/3/1,37428087,case-control,37428087,https://doi.org/10.1128/spectrum.00590-23,https://journals.asm.org/doi/10.1128/spectrum.00590-23,"Bai H., Liu T., Wang S., Gong W., Shen L., Zhang S. , Wang Z.",Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats,Microbiology spectrum,2023,"QIIME2, acute diarrhea, domestic cat, gut microbiota, metabolome, microbiome",Experiment 3,China,Felis catus,Feces,UBERON:0001988,Diarrhea,HP:0002014,Healthy British Shorthair (BH),Acutely diarrheic British Shorthair cats (BD),British Shorthair cats with acute diarrhea,12,12,1 month,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,FIG 3e,6 June 2024,Scholastica,"Scholastica,WikiWorks",Species analysis of differences in healthy (BH) versus acutely diarrheic (BD) British Shorthair cats using LEfSe,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri",3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|2974251|165179,Complete,Svetlana up
bsdb:37428087/3/2,37428087,case-control,37428087,https://doi.org/10.1128/spectrum.00590-23,https://journals.asm.org/doi/10.1128/spectrum.00590-23,"Bai H., Liu T., Wang S., Gong W., Shen L., Zhang S. , Wang Z.",Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats,Microbiology spectrum,2023,"QIIME2, acute diarrhea, domestic cat, gut microbiota, metabolome, microbiome",Experiment 3,China,Felis catus,Feces,UBERON:0001988,Diarrhea,HP:0002014,Healthy British Shorthair (BH),Acutely diarrheic British Shorthair cats (BD),British Shorthair cats with acute diarrhea,12,12,1 month,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,FIG 3e,6 June 2024,Scholastica,"Scholastica,WikiWorks",Species analysis of differences in healthy (BH) versus acutely diarrheic (BD) British Shorthair cats using LEfSe,decreased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella intestinalis,1783272|201174|84998|84999|84107|102106|147207,Complete,Svetlana up
bsdb:37428087/4/1,37428087,case-control,37428087,https://doi.org/10.1128/spectrum.00590-23,https://journals.asm.org/doi/10.1128/spectrum.00590-23,"Bai H., Liu T., Wang S., Gong W., Shen L., Zhang S. , Wang Z.",Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats,Microbiology spectrum,2023,"QIIME2, acute diarrhea, domestic cat, gut microbiota, metabolome, microbiome",Experiment 4,China,Felis catus,Feces,UBERON:0001988,Breed,EFO:0005238,Healthy British Shorthair (BH),Healthy American Shorthair (MH),Healthy American Shorthair (MH) cats,12,12,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,FIG 2a,6 June 2024,Scholastica,"Scholastica,WikiWorks",Species analysis of differences in healthy British Shorthair (BH) versus healthy American Shorthair (MH)  using LEfSe,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri",3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|1224|1236|91347;3379134|1224|1236;3379134|1224|1236|91347|1903414;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|1224|1236|91347|1903414|586;3379134|1224;3379134|976|200643|171549|171552|2974251|165179,Complete,Svetlana up
bsdb:37428087/4/2,37428087,case-control,37428087,https://doi.org/10.1128/spectrum.00590-23,https://journals.asm.org/doi/10.1128/spectrum.00590-23,"Bai H., Liu T., Wang S., Gong W., Shen L., Zhang S. , Wang Z.",Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats,Microbiology spectrum,2023,"QIIME2, acute diarrhea, domestic cat, gut microbiota, metabolome, microbiome",Experiment 4,China,Felis catus,Feces,UBERON:0001988,Breed,EFO:0005238,Healthy British Shorthair (BH),Healthy American Shorthair (MH),Healthy American Shorthair (MH) cats,12,12,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,FIG 2a,6 June 2024,Scholastica,"Scholastica,WikiWorks",Species analysis of differences in healthy British Shorthair (BH) versus healthy American Shorthair (MH) using LEfSe,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia glucerasea,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptoclostridiaceae|g__Peptoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] colinum",1783272|1239;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|536633;1783272|1239|186801;1783272|1117;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;1783272|1239|186801|186802|216572;1783272|1239|186801|3082720|3120161|1481960;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;1783272|1239|1737404|1737405;1783272|1239|186801|3085636|186803|1506577|36835,Complete,Svetlana up
bsdb:37428087/5/1,37428087,case-control,37428087,https://doi.org/10.1128/spectrum.00590-23,https://journals.asm.org/doi/10.1128/spectrum.00590-23,"Bai H., Liu T., Wang S., Gong W., Shen L., Zhang S. , Wang Z.",Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats,Microbiology spectrum,2023,"QIIME2, acute diarrhea, domestic cat, gut microbiota, metabolome, microbiome",Experiment 5,China,Felis catus,Feces,UBERON:0001988,Breed,EFO:0005238,Healthy British Shorthair (BH),Healthy American Shorthair (MH),Healthy American Shorthair (MH) cats,12,12,1 month,16S,4,Illumina,relative abundances,Metastats,0.05,FALSE,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Supplementary Table S3,6 June 2024,Scholastica,"Scholastica,WikiWorks",Species analysis of differences in healthy British Shorthair (BH) versus healthy American Shorthair (MH) using Metastat,increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota,k__Methanobacteriati|p__Methanobacteriota|c__Halobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera",3379134|976;3379134|1224;3366610|28890|183963;3379134|976|200643|171549|171552|838;3379134|1224|1236|91347|1903414|586;3379134|1224|28216|80840|995019|40544;1783272|1239|909932|1843489|31977|906,Complete,Svetlana up
bsdb:37428087/5/2,37428087,case-control,37428087,https://doi.org/10.1128/spectrum.00590-23,https://journals.asm.org/doi/10.1128/spectrum.00590-23,"Bai H., Liu T., Wang S., Gong W., Shen L., Zhang S. , Wang Z.",Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats,Microbiology spectrum,2023,"QIIME2, acute diarrhea, domestic cat, gut microbiota, metabolome, microbiome",Experiment 5,China,Felis catus,Feces,UBERON:0001988,Breed,EFO:0005238,Healthy British Shorthair (BH),Healthy American Shorthair (MH),Healthy American Shorthair (MH) cats,12,12,1 month,16S,4,Illumina,relative abundances,Metastats,0.05,FALSE,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Supplementary Table S3,6 June 2024,Scholastica,"Scholastica,WikiWorks",Species analysis of differences in healthy British Shorthair (BH) versus healthy American Shorthair (MH) using Metastat,decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Thermodesulfobacteriota,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Planctomycetota,k__Bacillati|p__Armatimonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptoclostridiaceae|g__Peptoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis",1783272|1239;3379134|200940;1783272|1117;3379134|74201;3379134|203682;1783272|67819;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3082720|3120161|1481960;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|186802|31979|1266;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|1407607;3379134|1224|1236|2887326|468|469;1783272|1239|91061|1385|186817|1386;1783272|1239|91061|1385|90964|1279;1783272|1239|186801|186802|186806|264995,Complete,Svetlana up
bsdb:37428087/6/1,37428087,case-control,37428087,https://doi.org/10.1128/spectrum.00590-23,https://journals.asm.org/doi/10.1128/spectrum.00590-23,"Bai H., Liu T., Wang S., Gong W., Shen L., Zhang S. , Wang Z.",Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats,Microbiology spectrum,2023,"QIIME2, acute diarrhea, domestic cat, gut microbiota, metabolome, microbiome",Experiment 6,China,Felis catus,Feces,UBERON:0001988,Diarrhea,HP:0002014,Healthy American Shorthair (MH),Acutely diarrheic American Shorthair cats (MD),American Shorthair cats with acute diarrhea,12,12,1 month,16S,4,Illumina,relative abundances,Metastats,0.05,FALSE,NA,NA,NA,unchanged,unchanged,increased,unchanged,NA,increased,Signature 1,Supplementary Table S3,6 June 2024,Scholastica,"Scholastica,WikiWorks",Species analysis of differences in healthy (MH) versus acutely diarrheic (MD) American Shorthair cats using Metastat,increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Acidobacteriota,k__Pseudomonadati|p__Thermodesulfobacteriota,k__Pseudomonadati|p__Gemmatimonadota,k__Bacillati|p__Chloroflexota|c__Chloroflexia,k__Pseudomonadati|p__Myxococcota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|s__uncultured Prevotellaceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Acidobacteriota|c__Thermoanaerobaculia|o__Thermoanaerobaculales|f__Thermoanaerobaculaceae|s__Thermoanaerobaculaceae bacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Blastococcus,k__Pseudomonadati|p__Acidobacteriota|c__Vicinamibacteria|s__Vicinamibacteria bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Arenimonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Skermanella",3379134|976;3379134|57723;3379134|200940;3379134|142182;1783272|200795|32061;3379134|2818505;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|2005473;3379134|1224|28216|80840|119060|48736;3379134|976|200643|171549|171552|370804;3379134|976|200643|171549|2005473|1918540;1783272|1239|91061|1385|186817|1386;3379134|57723|1562571|2562241|2562242|2699758;1783272|201174|1760|1643682|85030|38501;3379134|57723|1813735|2793154;3379134|1224|1236|135614|32033|490567;3379134|1224|28211|204441|2829815|204447,Complete,Svetlana up
bsdb:37428087/6/2,37428087,case-control,37428087,https://doi.org/10.1128/spectrum.00590-23,https://journals.asm.org/doi/10.1128/spectrum.00590-23,"Bai H., Liu T., Wang S., Gong W., Shen L., Zhang S. , Wang Z.",Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats,Microbiology spectrum,2023,"QIIME2, acute diarrhea, domestic cat, gut microbiota, metabolome, microbiome",Experiment 6,China,Felis catus,Feces,UBERON:0001988,Diarrhea,HP:0002014,Healthy American Shorthair (MH),Acutely diarrheic American Shorthair cats (MD),American Shorthair cats with acute diarrhea,12,12,1 month,16S,4,Illumina,relative abundances,Metastats,0.05,FALSE,NA,NA,NA,unchanged,unchanged,increased,unchanged,NA,increased,Signature 2,Supplementary Table S3,6 June 2024,Scholastica,"Scholastica,WikiWorks",Species analysis of differences in healthy (MH) versus acutely diarrheic (MD) American Shorthair cats using Metastat,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Catenisphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__Anaerovoracaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas",1783272|1239;1783272|1239|526524|526525|128827|123375;1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|3085636|186803|1506577;1783272|201174|84998|84999|1643824|2082587;1783272|1239|526524|526525|128827|1774107;1783272|1239|186801|3082720|543314|3030912;1783272|1239|186801|186802|1392389,Complete,Svetlana up
bsdb:37428087/7/1,37428087,case-control,37428087,https://doi.org/10.1128/spectrum.00590-23,https://journals.asm.org/doi/10.1128/spectrum.00590-23,"Bai H., Liu T., Wang S., Gong W., Shen L., Zhang S. , Wang Z.",Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats,Microbiology spectrum,2023,"QIIME2, acute diarrhea, domestic cat, gut microbiota, metabolome, microbiome",Experiment 7,China,Felis catus,Feces,UBERON:0001988,Diarrhea,HP:0002014,Healthy British Shorthair (BH),Acutely diarrheic British Shorthair cats (BD),British Shorthair cats with acute diarrhea,12,12,1 month,16S,4,Illumina,relative abundances,Metastats,0.05,FALSE,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Supplementary Table S3,6 June 2024,Scholastica,"Scholastica,WikiWorks",Species analysis of differences in healthy (BH) versus acutely diarrheic (BD) British Shorthair cats using Metastat,increased,"k__Pseudomonadati|p__Acidobacteriota,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|57723;3379134|976;3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:37428087/7/2,37428087,case-control,37428087,https://doi.org/10.1128/spectrum.00590-23,https://journals.asm.org/doi/10.1128/spectrum.00590-23,"Bai H., Liu T., Wang S., Gong W., Shen L., Zhang S. , Wang Z.",Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats,Microbiology spectrum,2023,"QIIME2, acute diarrhea, domestic cat, gut microbiota, metabolome, microbiome",Experiment 7,China,Felis catus,Feces,UBERON:0001988,Diarrhea,HP:0002014,Healthy British Shorthair (BH),Acutely diarrheic British Shorthair cats (BD),British Shorthair cats with acute diarrhea,12,12,1 month,16S,4,Illumina,relative abundances,Metastats,0.05,FALSE,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Supplementary Table S3,6 June 2024,Scholastica,"Scholastica,WikiWorks",Species analysis of differences in healthy (BH) versus acutely diarrheic (BD) British Shorthair cats using Metastat,decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Planctomycetota,k__Bacillati|p__Armatimonadota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella",1783272|201174;3379134|203682;1783272|67819;1783272|201174|84998|84999|84107|102106;1783272|1239|526524|526525|2810280|3025755;1783272|201174|84998|84999|1643824|2082587,Complete,Svetlana up
bsdb:37432374/1/1,37432374,case-control,37432374,10.3390/nu15092173,NA,"Silvano A., Meriggi N., Renzi S., Seravalli V., Torcia M.G., Cavalieri D. , Di Tommaso M.",Vaginal Microbiome in Pregnant Women with and without Short Cervix,Nutrients,2023,"Gardenerella vaginalis, Lactobacillus, aerobic vaginitis, microbiome, risk in pregnancy, shortened cervix",Experiment 1,Italy,Homo sapiens,Vagina,UBERON:0000996,Cervix erosion,EFO:1000862,Control,Short Cervix Length,Pregnant women of predominantly Caucasian ethnicity with singleton gestation and a cervical length ≤ 25 mm in their second or early third trimester (23–32 weeks’ gestation),29,68,At the time of recruitment,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,decreased,Signature 1,Figure 2a,6 April 2024,Ayibatari,"Ayibatari,Scholastica,WikiWorks",Linear discriminant analysis effect size (LEfSe) showing the significant taxonomic features in short cervix length versus control groups at different taxonomic levels,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Pseudoxanthomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Tabrizicola",3379134|1224|28211;3379134|1224|28211|204458|76892|41275;3379134|1224|28211|204458|76892;3379134|1224|28211|204458;1783272|201174|1760|85007|1653;3379134|1224|1236;3379134|1224|1236|135614|32033;3379134|1224|1236|135614;1783272|201174|1760|85007;3379134|1224|1236|72274|135621;3379134|1224|1236|72274;3379134|1224;3379134|1224|1236|72274|135621|286;3379134|1224|1236|135614|32033|83618;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;3379134|1224|28211|204455|31989|1443919,Complete,Svetlana up
bsdb:37432374/1/2,37432374,case-control,37432374,10.3390/nu15092173,NA,"Silvano A., Meriggi N., Renzi S., Seravalli V., Torcia M.G., Cavalieri D. , Di Tommaso M.",Vaginal Microbiome in Pregnant Women with and without Short Cervix,Nutrients,2023,"Gardenerella vaginalis, Lactobacillus, aerobic vaginitis, microbiome, risk in pregnancy, shortened cervix",Experiment 1,Italy,Homo sapiens,Vagina,UBERON:0000996,Cervix erosion,EFO:1000862,Control,Short Cervix Length,Pregnant women of predominantly Caucasian ethnicity with singleton gestation and a cervical length ≤ 25 mm in their second or early third trimester (23–32 weeks’ gestation),29,68,At the time of recruitment,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,decreased,Signature 2,Figure 2a,12 June 2024,Scholastica,"Scholastica,WikiWorks",Linear discriminant analysis effect size (LEfSe) showing the significant taxonomic features in short cervix length versus control groups at different taxonomic levels,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus",3379134|1224|28211|204455|31989;3379134|1224|28211|204455;1783272|201174|1760|2037;1783272|201174|1760|2037|2049;1783272|1239|186801;3379134|1224|28211|204455|31989|265;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171551;1783272|201174|1760|85006;1783272|201174|1760|2037|2049|2050,Complete,Svetlana up
bsdb:37438797/1/1,37438797,time series / longitudinal observational,37438797,10.1186/s13073-023-01202-6,NA,"Nguyen L.H., Okin D., Drew D.A., Battista V.M., Jesudasen S.J., Kuntz T.M., Bhosle A., Thompson K.N., Reinicke T., Lo C.H., Woo J.E., Caraballo A., Berra L., Vieira J., Huang C.Y., Das Adhikari U., Kim M., Sui H.Y., Magicheva-Gupta M., McIver L., Goldberg M.B., Kwon D.S., Huttenhower C., Chan A.T. , Lai P.S.",Metagenomic assessment of gut microbial communities and risk of severe COVID-19,Genome medicine,2023,"Machine learning, Microbiome, SARS-CoV-2",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Moderate COVID-19,Severe COVID-19,Hospitalized patients with severe Covid-19,48,79,NA,PCR,NA,Illumina,relative abundances,Random Forest Analysis,0.05,TRUE,NA,NA,"age,antibiotic exposure,body mass index,comorbidity,ethnic group,race,sequence read depth",NA,NA,NA,NA,decreased,NA,Signature 1,Fig. 3a,23 February 2024,Peace Sandy,"Peace Sandy,ChiomaBlessing,WikiWorks",Stool-based classifier for COVID-19 disease severity showing the differential abundance among patients with severe/critical COVID-19 compared to patients with mild/moderate COVID-19,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,1783272|1239|91061|186826|81852|1350|1351,Complete,Peace Sandy
bsdb:37438797/1/2,37438797,time series / longitudinal observational,37438797,10.1186/s13073-023-01202-6,NA,"Nguyen L.H., Okin D., Drew D.A., Battista V.M., Jesudasen S.J., Kuntz T.M., Bhosle A., Thompson K.N., Reinicke T., Lo C.H., Woo J.E., Caraballo A., Berra L., Vieira J., Huang C.Y., Das Adhikari U., Kim M., Sui H.Y., Magicheva-Gupta M., McIver L., Goldberg M.B., Kwon D.S., Huttenhower C., Chan A.T. , Lai P.S.",Metagenomic assessment of gut microbial communities and risk of severe COVID-19,Genome medicine,2023,"Machine learning, Microbiome, SARS-CoV-2",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Moderate COVID-19,Severe COVID-19,Hospitalized patients with severe Covid-19,48,79,NA,PCR,NA,Illumina,relative abundances,Random Forest Analysis,0.05,TRUE,NA,NA,"age,antibiotic exposure,body mass index,comorbidity,ethnic group,race,sequence read depth",NA,NA,NA,NA,decreased,NA,Signature 2,Fig. 3a,23 February 2024,Peace Sandy,"Peace Sandy,ChiomaBlessing,WikiWorks",Stool-based classifier for COVID-19 disease severity showing the differential abundance among patients with severe/critical COVID-19 compared to patients with mild/moderate COVID-19,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. HPA0247,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens|s__Adlercreutzia equolifaciens subsp. celatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum butyriciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella stercoris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:94,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:95,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus|s__Monoglobus pectinilyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Wegman et al. 2014),k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",1783272|201174|1760|2037|2049|1654|544580;1783272|201174|1760|2037|2049|1654|1203556;1783272|201174|84998|1643822|1643826|447020|446660;1783272|201174|84998|1643822|1643826|447020|446660|394340;1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|186802|3085642|2048137|1628085;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|207244|649756;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|572511|418240;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|84998|84999|84107|102106|147206;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|186802|186806|1730|39490;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|216572|216851|853;1783272|1239|1262989;1783272|1239|1262988;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|91061|1385|539738|1378|84135;1783272|1239|186801|186802|204475|745368;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|91061|186826|1300|1357|1358;1783272|1239|186801|3085656|3085657|2039302|1981510;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|841|360807;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|186801|186802|216572|1263|1160721;1783272|1239|186801|186802|216572|1263|40518;1783272|201174|1760|2037|2049|2529408|1660;1783272|1239|91061|186826|1300|1301|1302;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|186802|216572|39492;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Peace Sandy
bsdb:37439681/1/1,37439681,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa S.K., Antosca K., Beekman C.N., Peterson R.L., Penumutchu S. , Belenky P.",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 1,United States of America,Mus musculus,Cecum mucosa,UBERON:0000314,Response to diet,EFO:0010757,Always Dextrose oats Day 5 No Antibiotics (Abx),Always Dextrose oats Day 5 Abx,Cecal pellets collected on day 5 from mice that were fed diet supplemented with Always Dextrose oats as a preventive measure during amoxicillin treatment,10,10,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,20 March 2024,Barrakat,"Barrakat,KateRasheed,WikiWorks",Differential abundance in gut microbial taxa of mice placed on whole milled oats diet with amoxicillin mitigation (Day 5) as assessed by DeSeq2,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus rodentium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella|s__Dubosiella newyorkensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Ileibacterium|s__Ileibacterium valens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia ilealis",1783272|1239|91061|186826|33958|1578|947835;1783272|1239|526524|526525|128827|1937008|1862672;1783272|1239|91061|186826|33958|2742598|1598;1783272|1239|526524|526525|128827|1937007|1862668;1783272|1239|91061|186826|33958|1578|1203033;1783272|1239|186801|3082720|186804|1501226|1115758,Complete,Svetlana up
bsdb:37439681/1/2,37439681,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa S.K., Antosca K., Beekman C.N., Peterson R.L., Penumutchu S. , Belenky P.",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 1,United States of America,Mus musculus,Cecum mucosa,UBERON:0000314,Response to diet,EFO:0010757,Always Dextrose oats Day 5 No Antibiotics (Abx),Always Dextrose oats Day 5 Abx,Cecal pellets collected on day 5 from mice that were fed diet supplemented with Always Dextrose oats as a preventive measure during amoxicillin treatment,10,10,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,20 March 2024,Barrakat,"Barrakat,KateRasheed,WikiWorks",Differential abundance in microbial taxa of mice placed on whole milled oats diet with amoxicillin mitigation (Day 5) as assessed by DeSeq2,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides congonensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecichinchillae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus asini",3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|815|816|1871006;3379134|976|200643|171549|815|816|871325;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|371601;1783272|1239|91061|186826|81852|1350|57732,Complete,Svetlana up
bsdb:37439681/2/1,37439681,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa S.K., Antosca K., Beekman C.N., Peterson R.L., Penumutchu S. , Belenky P.",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 2,United States of America,Mus musculus,Cecum mucosa,UBERON:0000314,Response to diet,EFO:0010757,Prophylactic oats Day 5 No Abx,Prophylactic oats Day 5 Abx,Cecal pellets collected on day 5 from mice that were fed diet supplemented with Prophylactic oats as a preventive measure during amoxicillin treatment,3,3,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 3,11 February 2025,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in microbial taxa of mice placed on whole milled oats diet with amoxicillin mitigation (Day 5) as assessed by DeSeq2,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecichinchillae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus xylosus",3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|871325;3379134|976|200643|171549|815|816|371601;1783272|1239|91061|1385|90964|1279|1288,Complete,Svetlana up
bsdb:37439681/2/2,37439681,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa S.K., Antosca K., Beekman C.N., Peterson R.L., Penumutchu S. , Belenky P.",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 2,United States of America,Mus musculus,Cecum mucosa,UBERON:0000314,Response to diet,EFO:0010757,Prophylactic oats Day 5 No Abx,Prophylactic oats Day 5 Abx,Cecal pellets collected on day 5 from mice that were fed diet supplemented with Prophylactic oats as a preventive measure during amoxicillin treatment,3,3,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 3,11 February 2025,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in microbial taxa of mice placed on whole milled oats diet with amoxicillin mitigation (Day 5) as assessed by DeSeq2,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus hominis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus rodentium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella|s__Dubosiella newyorkensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus taiwanensis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Ileibacterium|s__Ileibacterium valens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus intestinalis",1783272|1239|91061|186826|33958|1578|1203033;1783272|1239|91061|186826|33958|1578|947835;1783272|1239|526524|526525|128827|1937008|1862672;1783272|1239|91061|186826|33958|1578|508451;1783272|1239|526524|526525|128827|1937007|1862668;1783272|1239|91061|186826|33958|1578|33959;1783272|1239|91061|186826|33958|2742598|1598;1783272|1239|91061|186826|33958|1578|151781,Complete,Svetlana up
bsdb:37439681/23/1,37439681,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa S.K., Antosca K., Beekman C.N., Peterson R.L., Penumutchu S. , Belenky P.",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 23,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Always Dextrose Day 5 No Abx,Always Dextrose Day 5 Abx,Fecal pellets collected on day 5 from mice that were fed diet supplemented with always dextrose oats as a preventive measure during amoxicillin treatment,10,10,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 2B,11 February 2025,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in gut microbial taxa of mice placed on whole milled oats diet with amoxicillin mitigation (Day 5) as assessed by Mann-whitney,increased,k__Pseudomonadati|p__Verrucomicrobiota,3379134|74201,Complete,Svetlana up
bsdb:37439681/23/2,37439681,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa S.K., Antosca K., Beekman C.N., Peterson R.L., Penumutchu S. , Belenky P.",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 23,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Always Dextrose Day 5 No Abx,Always Dextrose Day 5 Abx,Fecal pellets collected on day 5 from mice that were fed diet supplemented with always dextrose oats as a preventive measure during amoxicillin treatment,10,10,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 2B,11 February 2025,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in gut microbial taxa of mice placed on whole milled oats diet with amoxicillin mitigation (Day 5) as assessed by Mann-whitney,decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota",1783272|1239;3379134|976,Complete,Svetlana up
bsdb:37439681/24/1,37439681,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa S.K., Antosca K., Beekman C.N., Peterson R.L., Penumutchu S. , Belenky P.",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 24,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Prophylactic oats Day 5 No Abx,Prophylactic oats Day 5 Abx,Fecal pellets collected on day 5 from mice that were fed diet supplemented with Prophylactic oats as a preventive measure during amoxicillin treatment,3,3,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 2B,11 February 2025,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in gut microbial taxa of mice placed on whole milled oats diet with amoxicillin mitigation (Day 5) as assessed by Mann-whitney,increased,k__Pseudomonadati|p__Verrucomicrobiota,3379134|74201,Complete,Svetlana up
bsdb:37439681/24/2,37439681,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa S.K., Antosca K., Beekman C.N., Peterson R.L., Penumutchu S. , Belenky P.",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 24,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Prophylactic oats Day 5 No Abx,Prophylactic oats Day 5 Abx,Fecal pellets collected on day 5 from mice that were fed diet supplemented with Prophylactic oats as a preventive measure during amoxicillin treatment,3,3,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 2B,11 February 2025,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in gut microbial taxa of mice placed on whole milled oats diet with amoxicillin mitigation (Day 5) as assessed by Mann-whitney,decreased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota",3379134|1224;3379134|976,Complete,Svetlana up
bsdb:37439681/25/1,37439681,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa S.K., Antosca K., Beekman C.N., Peterson R.L., Penumutchu S. , Belenky P.",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 25,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Always oats Day 5 No Abx,Always oats Day 5 Abx,Fecal pellets collected on day 5 from mice that were fed diet supplemented with Always oats as a preventive measure during amoxicillin treatment,6,6,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 2B,11 February 2025,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in gut microbial taxa of mice placed on whole milled oats diet with amoxicillin mitigation (Day 5) as assessed by Mann-whitney,increased,k__Pseudomonadati|p__Verrucomicrobiota,3379134|74201,Complete,Svetlana up
bsdb:37439681/25/2,37439681,laboratory experiment,37439681,10.1128/spectrum.02376-23,NA,"Costa S.K., Antosca K., Beekman C.N., Peterson R.L., Penumutchu S. , Belenky P.",Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis,Microbiology spectrum,2023,"antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome",Experiment 25,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Always oats Day 5 No Abx,Always oats Day 5 Abx,Fecal pellets collected on day 5 from mice that were fed diet supplemented with Always oats as a preventive measure during amoxicillin treatment,6,6,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 2B,11 February 2025,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in gut microbial taxa of mice placed on whole milled oats diet with amoxicillin mitigation (Day 5) as assessed by Mann-whitney,decreased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota",3379134|1224;3379134|976;1783272|1239,Complete,Svetlana up
bsdb:37441825/1/1,37441825,laboratory experiment,37441825,10.1016/j.nut.2023.112127,NA,"Wang R., Zhao Y., Fang X., Miao C., Ren N., Chen Y., Cheng W. , Zhang Q.",Effect of the ketogenic diet on gut microbiome composition and metabolomics in polycystic ovarian syndrome rats induced by letrozole and a high-fat diet,"Nutrition (Burbank, Los Angeles County, Calif.)",2023,"Insulin resistance, Intestinal microbiota, Metabolites, Polycystic ovary syndrome, Steroid hormone biosynthesis pathway",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Polycystic Ovary Syndrome-Insulin Resistance (PCOS-IR) group,Polycystic Ovary Syndrome-Insulin Resistance-Ketonic Diet (PCOS-IR-KD) group,Rats in this group were given a high-fat diet and letrozole to induce Polycystic ovary syndrome (PCOS) and then treated (fed) with a ketonic diet (KD) for 8 weeks.,5,5,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,4.5,NA,NA,decreased,decreased,NA,decreased,NA,decreased,Signature 1,Figure 4 a&b,10 February 2025,Victoria,"Victoria,WikiWorks",Differences in the composition of the gut microbiota among PCOS-IR and PCOS-IR-KD groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster lavalensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__uncultured Bacteroides sp.",3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976;3379134|1224|28216|80840;1783272|1239|186801|3082720|186804|1870884;1783272|1239|186801|3085636|186803|2719313|460384;3379134|1224|1236;1783272|1239|186801|3085636|186803|1506553;3379134|1224|28216|80840|995019|577310;3379134|1224;3379134|1224|28216|80840|995019;1783272|1239|186801|3082720|186804|1870884;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|815|816|162156,Complete,Svetlana up
bsdb:37441825/1/2,37441825,laboratory experiment,37441825,10.1016/j.nut.2023.112127,NA,"Wang R., Zhao Y., Fang X., Miao C., Ren N., Chen Y., Cheng W. , Zhang Q.",Effect of the ketogenic diet on gut microbiome composition and metabolomics in polycystic ovarian syndrome rats induced by letrozole and a high-fat diet,"Nutrition (Burbank, Los Angeles County, Calif.)",2023,"Insulin resistance, Intestinal microbiota, Metabolites, Polycystic ovary syndrome, Steroid hormone biosynthesis pathway",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Polycystic Ovary Syndrome-Insulin Resistance (PCOS-IR) group,Polycystic Ovary Syndrome-Insulin Resistance-Ketonic Diet (PCOS-IR-KD) group,Rats in this group were given a high-fat diet and letrozole to induce Polycystic ovary syndrome (PCOS) and then treated (fed) with a ketonic diet (KD) for 8 weeks.,5,5,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,4.5,NA,NA,decreased,decreased,NA,decreased,NA,decreased,Signature 2,Figure 4 a&b,10 February 2025,Victoria,"Victoria,WikiWorks",Differences in the composition of the gut microbiota among PCOS-IR and PCOS-IR-KD groups.,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239;1783272|1239|186801;1783272|1239|186801|186802|1980681;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|1980681;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802,Complete,Svetlana up
bsdb:37441825/2/1,37441825,laboratory experiment,37441825,10.1016/j.nut.2023.112127,NA,"Wang R., Zhao Y., Fang X., Miao C., Ren N., Chen Y., Cheng W. , Zhang Q.",Effect of the ketogenic diet on gut microbiome composition and metabolomics in polycystic ovarian syndrome rats induced by letrozole and a high-fat diet,"Nutrition (Burbank, Los Angeles County, Calif.)",2023,"Insulin resistance, Intestinal microbiota, Metabolites, Polycystic ovary syndrome, Steroid hormone biosynthesis pathway",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Polycystic Ovary Syndrome-Insulin Resistance (PCOS-IR) group,Polycystic Ovary Syndrome-Insulin Resistance-Ketonic Diet (PCOS-IR-KD) group,Rats in this group were given a high-fat diet and letrozole to induce Polycystic ovary syndrome (PCOS) and then treated (fed) with a ketonic diet (KD) for 8 weeks.,5,5,NA,16S,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,decreased,decreased,NA,decreased,NA,decreased,Signature 1,Figure 4c,18 February 2025,Victoria,Victoria,Differences in the relative abundances of intestine microbiota between PCOS-IR and PCOS-IR-KD groups at the genus level.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",1783272|1239|186801|3085636|186803|1506553;3379134|976|200643|171549|815|816;3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|186803|572511,Complete,Svetlana up
bsdb:37441825/2/2,37441825,laboratory experiment,37441825,10.1016/j.nut.2023.112127,NA,"Wang R., Zhao Y., Fang X., Miao C., Ren N., Chen Y., Cheng W. , Zhang Q.",Effect of the ketogenic diet on gut microbiome composition and metabolomics in polycystic ovarian syndrome rats induced by letrozole and a high-fat diet,"Nutrition (Burbank, Los Angeles County, Calif.)",2023,"Insulin resistance, Intestinal microbiota, Metabolites, Polycystic ovary syndrome, Steroid hormone biosynthesis pathway",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Polycystic Ovary Syndrome-Insulin Resistance (PCOS-IR) group,Polycystic Ovary Syndrome-Insulin Resistance-Ketonic Diet (PCOS-IR-KD) group,Rats in this group were given a high-fat diet and letrozole to induce Polycystic ovary syndrome (PCOS) and then treated (fed) with a ketonic diet (KD) for 8 weeks.,5,5,NA,16S,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,decreased,decreased,NA,decreased,NA,decreased,Signature 2,Figure 4c,18 February 2025,Victoria,Victoria,Differences in the relative abundances of intestine microbiota between PCOS-IR and PCOS-IR-KD groups at the genus level.,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239;1783272|1239|186801|186802|1980681;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263,Complete,Svetlana up
bsdb:37443082/1/1,37443082,laboratory experiment,37443082,10.1186/s13048-023-01227-w,NA,"Zhang H., Zheng L., Li C., Jing J., Li Z., Sun S., Xue T., Zhang K., Xue M., Cao C., Ouyang L., Qian Z., Xu R., He Z., Ma R., Chen L. , Yao B.",Effects of gut microbiota on omega-3-mediated ovary and metabolic benefits in polycystic ovary syndrome mice,Journal of ovarian research,2023,"Gut microbiota, Inflammation, Omega-3 PUFAs, Polycystic ovary syndrome",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control group,Polycystic ovary syndrome (PCOS) group,"After 21 days of DHEA treatment, the mice in this group were treated with an equal volume of corn oil at 2 g/kg",3,3,NA,16S,34,NA,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,decreased,Signature 1,Figure 4G,25 April 2025,MyleeeA,MyleeeA,Differential microbial abundance between Polycystic ovary syndrome (PCOS) and Control,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,3379134|976|200643|171549|171552|1283313,Complete,KateRasheed
bsdb:37443082/1/2,37443082,laboratory experiment,37443082,10.1186/s13048-023-01227-w,NA,"Zhang H., Zheng L., Li C., Jing J., Li Z., Sun S., Xue T., Zhang K., Xue M., Cao C., Ouyang L., Qian Z., Xu R., He Z., Ma R., Chen L. , Yao B.",Effects of gut microbiota on omega-3-mediated ovary and metabolic benefits in polycystic ovary syndrome mice,Journal of ovarian research,2023,"Gut microbiota, Inflammation, Omega-3 PUFAs, Polycystic ovary syndrome",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control group,Polycystic ovary syndrome (PCOS) group,"After 21 days of DHEA treatment, the mice in this group were treated with an equal volume of corn oil at 2 g/kg",3,3,NA,16S,34,NA,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,decreased,Signature 2,Figure 4I,25 April 2025,MyleeeA,MyleeeA,Differential microbial abundance between Polycystic ovary syndrome (PCOS) and Control,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,3379134|976|200643|171549|171550|239759,Complete,KateRasheed
bsdb:37443082/2/1,37443082,laboratory experiment,37443082,10.1186/s13048-023-01227-w,NA,"Zhang H., Zheng L., Li C., Jing J., Li Z., Sun S., Xue T., Zhang K., Xue M., Cao C., Ouyang L., Qian Z., Xu R., He Z., Ma R., Chen L. , Yao B.",Effects of gut microbiota on omega-3-mediated ovary and metabolic benefits in polycystic ovary syndrome mice,Journal of ovarian research,2023,"Gut microbiota, Inflammation, Omega-3 PUFAs, Polycystic ovary syndrome",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Polycystic ovary syndrome (PCOS) mice,Omega-3 mice,"Omega-3-treated mice, after 3 weeks of DHEA treatment, the mice received another 8 weeks of treatment by gavage with omega-3 PUFAs (2 g/kg every 2 days)",3,3,NA,16S,34,NA,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,increased,NA,NA,increased,Signature 1,Figure 4G,25 April 2025,MyleeeA,"MyleeeA,Ese",Differential microbial abundance between Omega-3 mice and Polycystic ovary syndrome (PCOS) mice,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,3379134|976|200643|171549|171552|1283313,Complete,KateRasheed
bsdb:37460569/1/1,37460569,"cross-sectional observational, not case-control",37460569,https://doi.org/10.1038/s41531-023-00554-5,NA,"Huang P., Zhang P., Du J., Gao C., Liu J., Tan Y. , Chen S.",Association of fecal short-chain fatty acids with clinical severity and gut microbiota in essential tremor and its difference from Parkinson's disease,NPJ Parkinson's disease,2023,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Essential tremor,EFO:0003108,Healthy Control,Essential Tremor,"Participants face an action tremor of the upper limbs, possibly with the involvement of other parts of the body, such as the head, vocal cords, and lower limbs. Not only motor symptoms but also some nonmotor features, including gastrointestinal disorders, were experienced by them.",35,37,1 month,16S,34,NA,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4, Table S5",19 March 2024,Nityasinghal 14,"Nityasinghal 14,Svetlana up,WikiWorks",Exploration of discriminant gut microbiota using LEfSE analysis and the genus level of the relative abundance data was selected for further study.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,3379134|1224|1236|135614|32033|40323,Complete,Svetlana up
bsdb:37460569/1/2,37460569,"cross-sectional observational, not case-control",37460569,https://doi.org/10.1038/s41531-023-00554-5,NA,"Huang P., Zhang P., Du J., Gao C., Liu J., Tan Y. , Chen S.",Association of fecal short-chain fatty acids with clinical severity and gut microbiota in essential tremor and its difference from Parkinson's disease,NPJ Parkinson's disease,2023,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Essential tremor,EFO:0003108,Healthy Control,Essential Tremor,"Participants face an action tremor of the upper limbs, possibly with the involvement of other parts of the body, such as the head, vocal cords, and lower limbs. Not only motor symptoms but also some nonmotor features, including gastrointestinal disorders, were experienced by them.",35,37,1 month,16S,34,NA,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 4, Table S5",19 March 2024,Nityasinghal 14,"Nityasinghal 14,Svetlana up,WikiWorks","Exploration of discriminant gut microbiota using LEfSE analysis, and the genus level of the relative abundance data was selected for further study.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella",1783272|1239|186801|186802|31979|49082;1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|404402;1783272|1239|91061|186826|33958|1578;3379134|1224|1236|91347|543|160674,Complete,Svetlana up
bsdb:37460569/2/2,37460569,"cross-sectional observational, not case-control",37460569,https://doi.org/10.1038/s41531-023-00554-5,NA,"Huang P., Zhang P., Du J., Gao C., Liu J., Tan Y. , Chen S.",Association of fecal short-chain fatty acids with clinical severity and gut microbiota in essential tremor and its difference from Parkinson's disease,NPJ Parkinson's disease,2023,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Essential tremor,EFO:0003108,Parkinson's Disease,Essential Tremor,"Participants face an action tremor of the upper limbs, possibly with the involvement of other parts of the body, such as the head, vocal cords, and lower limbs. Not only motor symptoms but also some nonmotor features, including gastrointestinal disorders, were experienced by them.",37,37,1 month,16S,34,NA,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 4, Table S5",19 March 2024,Nityasinghal 14,"Nityasinghal 14,Svetlana up,WikiWorks",Examination of the fecal levels of SCFAs and linkage to changes in gut microbiota and symptom severity.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,1783272|1239|186801|3085636|186803|1506553,Complete,Svetlana up
bsdb:37468867/1/1,37468867,"cross-sectional observational, not case-control",37468867,10.1186/s12916-023-02972-x,NA,"Zhang D., Weng S., Xia C., Ren Y., Liu Z., Xu Y., Yang X., Wu R., Peng L., Sun L., Zhu J., Liang X., Jia Y., Wang H., Chen Q., Liu D., Chen Y., Guo H., Han X., Jin Z., Chen C., Yang X., Li Z. , Huang H.",Gastrointestinal symptoms of long COVID-19 related to the ectopic colonization of specific bacteria that move between the upper and lower alimentary tract and alterations in serum metabolites,BMC medicine,2023,"Coronavirus, Gut microbiome, Microbial functions, Serum metabolomics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Post-COVID-19 disorder,MONDO:0100320,healthy controls and mild COVID-19 patients,long COVID-19,patients with gastrointestinal symptoms associated with long COVID-19 at 3 months follow-up,70,45,3 months,WMS,NA,Illumina,relative abundances,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 3H,8 October 2023,Chiwendeee,"Chiwendeee,Folakunmi,WikiWorks",The top 20 microbial species with significantly lower relative abundance in fecal samples of follow-up patients compared with normal samples or mild patients.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp. oral taxon 473,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium pseudoperiodonticum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. ICM33,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella tobetsuensis,p__Candidatus Saccharimonadota|s__Candidatus Saccharimonadota bacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. ICM47,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp. KLE 1280",3379134|1224|1236|135625|712|724|729;3379134|976|200643|171549|171552|838|28132;3379134|1224|28216|206351|481|482|484;1783272|1239|91061|186826|1300|1301|28037;3379134|976|200643|171549|171552|1283313|1872471;3379134|1224|28216|206351|481|482|28449;3379134|976|200643|171549|171551|836|322095;3379134|976|200643|171549|171552|1283313|712469;3384189|32066|203490|203491|203492|848|2663009;3379134|976|200643|171549|171552|1283313|76122;3379134|976|200643|171549|171552|838|28131;1783272|1239|91061|186826|1300|1301|1303;3379134|976|200643|171549|171552|838|1161412;3379134|976|200643|171549|171552|838|60133;1783272|1239|91061|186826|1300|1301|1313;1783272|1239|909932|1843489|31977|29465|1110546;95818|2026720;1783272|1239|91061|186826|1300|1301|68892;1783272|201174|1760|2037|2049|1654|936548;3379134|976|200643|171549|171551|836|997829,Complete,Folakunmi
bsdb:37468867/2/1,37468867,"cross-sectional observational, not case-control",37468867,10.1186/s12916-023-02972-x,NA,"Zhang D., Weng S., Xia C., Ren Y., Liu Z., Xu Y., Yang X., Wu R., Peng L., Sun L., Zhu J., Liang X., Jia Y., Wang H., Chen Q., Liu D., Chen Y., Guo H., Han X., Jin Z., Chen C., Yang X., Li Z. , Huang H.",Gastrointestinal symptoms of long COVID-19 related to the ectopic colonization of specific bacteria that move between the upper and lower alimentary tract and alterations in serum metabolites,BMC medicine,2023,"Coronavirus, Gut microbiome, Microbial functions, Serum metabolomics",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Post-COVID-19 disorder,MONDO:0100320,healthy controls and mild COVID-19 patients,long COVID-19,patients with gastrointestinal symptoms associated with long COVID-19 at 3 months follow-up,70,45,3 months,WMS,NA,Illumina,relative abundances,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 4K,23 February 2024,Folakunmi,"Folakunmi,WikiWorks",The top 20 microbial species with significantly high relative abundance in saliva samples of follow-up patients compared to normal samples or mild patients.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella tobetsuensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella jejuni,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis",3379134|976|200643|171549|171551|836|1583331;3379134|1224|28216|206351|481|482|28449;3379134|1224|28216|206351|481|482|484;3379134|976|200643|171549|171552|838|28132;1783272|1239|909932|1843489|31977|29465|423477;3379134|1224|1236|135625|712|724|729;1783272|1239|909932|1843489|31977|29465|1110546;3379134|976|200643|171549|171552|838|60133;3379134|1224|28216|80840|119060|47670|47671;1783272|1239|91061|186826|1300|1301|1304;3379134|976|200643|171549|171552|838|1177574;1783272|201174|1760|85006|1268|32207|43675;3379134|1224|28216|206351|481|482|495;3379134|976|200643|171549|171551|836|837,Complete,Folakunmi
bsdb:37483698/1/1,37483698,"cross-sectional observational, not case-control",37483698,10.1016/j.heliyon.2023.e18035,https://www.sciencedirect.com/science/article/pii/S240584402305243X,"Elkholy A., Avuthu N., Abdalla M., Behring M., Bajpai P., Kim H.G., Header D., Abo Elwafa R.A., Saed H., Embaby A., El-Nikhely N., Obuya S., Mohamed M., Badawy A.A., Nawar A., Afaq F., Rogers L.Q., Bae S., Shikany J.M., Bateman L.B., Fouad M., Saleh M., Samuel T., Varambally S., Guda C., Arafat W. , Manne U.","Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients",Heliyon,2023,"African American, Colorectal cancer, Egyptian, European American, Microbiome",Experiment 1,Egypt,Homo sapiens,Colorectal mucosa,UBERON:0013067,Colorectal cancer,EFO:0005842,Normal samples free from Colorectal Cancer,Egyptian Samples with Colorectal Cancer,Egyptian Patients with colocrectal cancer,17,17,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2A,12 October 2023,Chloe 256,"Chloe 256,Peace Sandy,Folakunmi,WikiWorks","Fig.2A  shows histograms of differential microbial taxa, at the species level, between tumor (CRC) and normal samples in Egyptians.",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Abyssicoccaceae|g__Abyssicoccus|s__Abyssicoccus albus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium kroppenstedtii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus helveticus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae|g__Tissierella|s__Tissierella creatinophila",1783272|1239|91061|1385|3076164|1955413|1817405;1783272|201174|1760|85004|31953|1678|1694;1783272|201174|1760|85007|1653|1716|161879;1783272|201174|1760|85009|31957|1912216|1747;1783272|1239|186801|186802;1783272|201174|1760|85006|1268|57493;1783272|1239|91061|186826|33958|1578|1587;1783272|1239|1737404|1737405|1737406|41273|79681,Complete,Folakunmi
bsdb:37483698/1/2,37483698,"cross-sectional observational, not case-control",37483698,10.1016/j.heliyon.2023.e18035,https://www.sciencedirect.com/science/article/pii/S240584402305243X,"Elkholy A., Avuthu N., Abdalla M., Behring M., Bajpai P., Kim H.G., Header D., Abo Elwafa R.A., Saed H., Embaby A., El-Nikhely N., Obuya S., Mohamed M., Badawy A.A., Nawar A., Afaq F., Rogers L.Q., Bae S., Shikany J.M., Bateman L.B., Fouad M., Saleh M., Samuel T., Varambally S., Guda C., Arafat W. , Manne U.","Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients",Heliyon,2023,"African American, Colorectal cancer, Egyptian, European American, Microbiome",Experiment 1,Egypt,Homo sapiens,Colorectal mucosa,UBERON:0013067,Colorectal cancer,EFO:0005842,Normal samples free from Colorectal Cancer,Egyptian Samples with Colorectal Cancer,Egyptian Patients with colocrectal cancer,17,17,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2A,12 October 2023,Chloe 256,"Chloe 256,Peace Sandy,WikiWorks","Figure 2A shows histograms of differential microbial taxa, at the species level, between tumor (CRC) and normal samples in egyptians.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|g__Exiguobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria|s__Kocuria palustris,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas viridiflava,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria",1783272|201174|1760|2037;1783272|1239|91061|1385|33986;1783272|201174|1760|85006|1268|57493|71999;1783272|201174|1760|85006|1268|1269;3379134|1224|28216|206351|481|482;3379134|1224|1236|72274|135621|286|33069;1783272|201174|1760|85006|1268|32207|172042,Complete,Folakunmi
bsdb:37483698/2/1,37483698,"cross-sectional observational, not case-control",37483698,10.1016/j.heliyon.2023.e18035,https://www.sciencedirect.com/science/article/pii/S240584402305243X,"Elkholy A., Avuthu N., Abdalla M., Behring M., Bajpai P., Kim H.G., Header D., Abo Elwafa R.A., Saed H., Embaby A., El-Nikhely N., Obuya S., Mohamed M., Badawy A.A., Nawar A., Afaq F., Rogers L.Q., Bae S., Shikany J.M., Bateman L.B., Fouad M., Saleh M., Samuel T., Varambally S., Guda C., Arafat W. , Manne U.","Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients",Heliyon,2023,"African American, Colorectal cancer, Egyptian, European American, Microbiome",Experiment 2,United States of America,Homo sapiens,Colorectal mucosa,UBERON:0013067,Colorectal cancer,EFO:0005842,Normal samples free from Colorectal Cancer,African American Samples with Colorectal Cancer,African American Patients with Colorectal cancer.,18,18,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2B,13 October 2023,Chloe 256,"Chloe 256,WikiWorks","Figure 2B shows histogram of differential microbial taxa, at the species level, between tumor (CRC) and normal samples in African Americans.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|g__Rhodobacter",1783272|1239|186801|186802|31979|1485|1502;1783272|201174|1760|85004|31953|2701;1783272|1239|91061|186826|186828|117563;3379134|1224|28211|204455|1060,Complete,Folakunmi
bsdb:37483698/2/2,37483698,"cross-sectional observational, not case-control",37483698,10.1016/j.heliyon.2023.e18035,https://www.sciencedirect.com/science/article/pii/S240584402305243X,"Elkholy A., Avuthu N., Abdalla M., Behring M., Bajpai P., Kim H.G., Header D., Abo Elwafa R.A., Saed H., Embaby A., El-Nikhely N., Obuya S., Mohamed M., Badawy A.A., Nawar A., Afaq F., Rogers L.Q., Bae S., Shikany J.M., Bateman L.B., Fouad M., Saleh M., Samuel T., Varambally S., Guda C., Arafat W. , Manne U.","Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients",Heliyon,2023,"African American, Colorectal cancer, Egyptian, European American, Microbiome",Experiment 2,United States of America,Homo sapiens,Colorectal mucosa,UBERON:0013067,Colorectal cancer,EFO:0005842,Normal samples free from Colorectal Cancer,African American Samples with Colorectal Cancer,African American Patients with Colorectal cancer.,18,18,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2B,13 October 2023,Chloe 256,"Chloe 256,WikiWorks","Figure 2B shows histograms of differential microbial taxa, at the species level, between tumor (CRC) and normal samples in African American",decreased,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,3379134|1224|28211|356|41294|374,Complete,Folakunmi
bsdb:37483698/3/1,37483698,"cross-sectional observational, not case-control",37483698,10.1016/j.heliyon.2023.e18035,https://www.sciencedirect.com/science/article/pii/S240584402305243X,"Elkholy A., Avuthu N., Abdalla M., Behring M., Bajpai P., Kim H.G., Header D., Abo Elwafa R.A., Saed H., Embaby A., El-Nikhely N., Obuya S., Mohamed M., Badawy A.A., Nawar A., Afaq F., Rogers L.Q., Bae S., Shikany J.M., Bateman L.B., Fouad M., Saleh M., Samuel T., Varambally S., Guda C., Arafat W. , Manne U.","Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients",Heliyon,2023,"African American, Colorectal cancer, Egyptian, European American, Microbiome",Experiment 3,United States of America,Homo sapiens,Colorectal mucosa,UBERON:0013067,Colorectal cancer,EFO:0005842,Normal samples free from Colorectal Cancer,European American Samples with Colorectal Cancer,European American Patients with colorectal cancer,19,19,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2C,13 October 2023,Chloe 256,"Chloe 256,WikiWorks","Figure 2C shows histogram of differential microbial taxa, at the species level, between tumor (CRC) and normal samples in European Americans.",increased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,3379134|1224|28216|80840|75682|149698,Complete,Folakunmi
bsdb:37483698/3/2,37483698,"cross-sectional observational, not case-control",37483698,10.1016/j.heliyon.2023.e18035,https://www.sciencedirect.com/science/article/pii/S240584402305243X,"Elkholy A., Avuthu N., Abdalla M., Behring M., Bajpai P., Kim H.G., Header D., Abo Elwafa R.A., Saed H., Embaby A., El-Nikhely N., Obuya S., Mohamed M., Badawy A.A., Nawar A., Afaq F., Rogers L.Q., Bae S., Shikany J.M., Bateman L.B., Fouad M., Saleh M., Samuel T., Varambally S., Guda C., Arafat W. , Manne U.","Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients",Heliyon,2023,"African American, Colorectal cancer, Egyptian, European American, Microbiome",Experiment 3,United States of America,Homo sapiens,Colorectal mucosa,UBERON:0013067,Colorectal cancer,EFO:0005842,Normal samples free from Colorectal Cancer,European American Samples with Colorectal Cancer,European American Patients with colorectal cancer,19,19,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2C,13 October 2023,Chloe 256,"Chloe 256,Iram jamshed,WikiWorks","Figure 2C shows histogram of differential microbial taxa, at the species level, between tumor (CRC) and normal samples in European Americans.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Geobacterales|f__Geobacteraceae|g__Geobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",1783272|1239|186801|186802|204475|745368;3379134|200940|3031651|3031668|213422|28231;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|186801|3085636|186803|2316020|33038,Complete,Folakunmi
bsdb:37483698/4/1,37483698,"cross-sectional observational, not case-control",37483698,10.1016/j.heliyon.2023.e18035,https://www.sciencedirect.com/science/article/pii/S240584402305243X,"Elkholy A., Avuthu N., Abdalla M., Behring M., Bajpai P., Kim H.G., Header D., Abo Elwafa R.A., Saed H., Embaby A., El-Nikhely N., Obuya S., Mohamed M., Badawy A.A., Nawar A., Afaq F., Rogers L.Q., Bae S., Shikany J.M., Bateman L.B., Fouad M., Saleh M., Samuel T., Varambally S., Guda C., Arafat W. , Manne U.","Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients",Heliyon,2023,"African American, Colorectal cancer, Egyptian, European American, Microbiome",Experiment 4,United States of America,Homo sapiens,Colorectal mucosa,UBERON:0013067,Population,IDOMAL:0001254,"KeNyaN, African American and Egyptians patients",Tumor samples of European American,sample of European Americans patients,53,19,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3,14 November 2023,Chloe 256,"Chloe 256,MyleeeA,Folakunmi,WikiWorks",Differential microbial taxa between tumor (CRC) samples of different races at the species level,increased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Flexispira,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners",1783272|544448|31969|186332|186333|2086;3379134|976|200643|171549|815|816|28116;1783272|1239|186801|186802|31979|1485|1502;3379134|1224|28216|80840|80864;1783272|201174|84998|1643822|1643826|84111|84112;3379134|29547|3031852|213849|72293|2353;1783272|544448|31969|2085|2092|2093;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|33958|1578|147802,Complete,Folakunmi
bsdb:37483698/5/1,37483698,"cross-sectional observational, not case-control",37483698,10.1016/j.heliyon.2023.e18035,https://www.sciencedirect.com/science/article/pii/S240584402305243X,"Elkholy A., Avuthu N., Abdalla M., Behring M., Bajpai P., Kim H.G., Header D., Abo Elwafa R.A., Saed H., Embaby A., El-Nikhely N., Obuya S., Mohamed M., Badawy A.A., Nawar A., Afaq F., Rogers L.Q., Bae S., Shikany J.M., Bateman L.B., Fouad M., Saleh M., Samuel T., Varambally S., Guda C., Arafat W. , Manne U.","Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients",Heliyon,2023,"African American, Colorectal cancer, Egyptian, European American, Microbiome",Experiment 5,Kenya,Homo sapiens,Colorectal mucosa,UBERON:0013067,Population,IDOMAL:0001254,"Egyptian, African American and European American Patients",Tumor samples of kenyans,Tumor samples of kenyan patients,54,18,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3,14 November 2023,Chloe 256,"Chloe 256,MyleeeA,Folakunmi,Joan Chuks,WikiWorks",differential microbial taxa between tumor (CRC) samples of different races at the species level,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Alcanivoracaceae|g__Alloalcanivorax|s__Alloalcanivorax dieselolei,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|g__Denitrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae|g__Inquilinus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sporobacterium|s__Sporobacterium sp. WAL 1855D,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",3379134|74201|203494|48461|1647988|239934|239935;3379134|1224|1236|135619|224372|3020832|285091;3379134|1224|28216|59507;3379134|1224|28211|204441|41295|171673;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|28133;1783272|1239|186801|3085636|186803|100132|507843;3379134|74201|203494|48461|203557,Complete,Folakunmi
bsdb:37483698/6/1,37483698,"cross-sectional observational, not case-control",37483698,10.1016/j.heliyon.2023.e18035,https://www.sciencedirect.com/science/article/pii/S240584402305243X,"Elkholy A., Avuthu N., Abdalla M., Behring M., Bajpai P., Kim H.G., Header D., Abo Elwafa R.A., Saed H., Embaby A., El-Nikhely N., Obuya S., Mohamed M., Badawy A.A., Nawar A., Afaq F., Rogers L.Q., Bae S., Shikany J.M., Bateman L.B., Fouad M., Saleh M., Samuel T., Varambally S., Guda C., Arafat W. , Manne U.","Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients",Heliyon,2023,"African American, Colorectal cancer, Egyptian, European American, Microbiome",Experiment 6,United States of America,Homo sapiens,Colorectal mucosa,UBERON:0013067,Population,IDOMAL:0001254,"Egyptian, Kenyan and European American patients",Tumor samples of African Americans,Sample of African American patients,54,18,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3,14 November 2023,Chloe 256,"Chloe 256,MyleeeA,Folakunmi,WikiWorks",differential microbial taxa between tumor (CRC) samples of different races at the species level,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium succinicans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|g__Rhodobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",1783272|201174|1760|85007|1653|1716;3379134|1224|28211|356|212791;1783272|1239|91061|186826|186827|66831;3379134|976|117743|200644|49546|237|29536;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1357;3384189|32066|203490|203491|1129771|32067;1783272|1239|1737404|1737405|1570339|162289;3379134|1224|1236|72274|135621|286;3379134|1224|28211|204455|1060;1783272|201174|1760|85006|1268|32207|2047;1783272|1239|91061|186826|33958,Complete,Folakunmi
bsdb:37483698/7/1,37483698,"cross-sectional observational, not case-control",37483698,10.1016/j.heliyon.2023.e18035,https://www.sciencedirect.com/science/article/pii/S240584402305243X,"Elkholy A., Avuthu N., Abdalla M., Behring M., Bajpai P., Kim H.G., Header D., Abo Elwafa R.A., Saed H., Embaby A., El-Nikhely N., Obuya S., Mohamed M., Badawy A.A., Nawar A., Afaq F., Rogers L.Q., Bae S., Shikany J.M., Bateman L.B., Fouad M., Saleh M., Samuel T., Varambally S., Guda C., Arafat W. , Manne U.","Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients",Heliyon,2023,"African American, Colorectal cancer, Egyptian, European American, Microbiome",Experiment 7,Egypt,Homo sapiens,Colorectal mucosa,UBERON:0013067,Population,IDOMAL:0001254,"African American, Kenya and European American patients",Tumor samples of Egyptians,sample of Egyptian patients,55,17,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3,15 November 2023,Chloe 256,"Chloe 256,MyleeeA,Folakunmi,WikiWorks",differential microbial taxa between tumor (CRC) samples of different races at the species level,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter lwoffii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter schindleri,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas|s__Brevundimonas diminuta,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Heyndrickxia|s__Heyndrickxia acidicola,k__Pseudomonadati|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Hydrogenophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Meiothermus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia marcescens,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas geniculata",3379134|1224|1236|2887326|468|469;3379134|1224|1236|2887326|468|469|28090;3379134|1224|1236|2887326|468|469|108981;1783272|1239|91061|1385|186817;3379134|1224|28211|356|41294|374;3379134|1224|28211|204458|76892|41275|293;3379134|1224|28216|80840|75682|963;1783272|1239|91061|1385|186817|2837504|209389;3379134|1224|2008785|119069|206349|70774;3379134|1224|1236|135614|32033|68;3384194|1297|188787|68933|188786|65551;1783272|201174|1760|85006|1268|1269;1783272|1239|91061|1385|186822|44249;3379134|1224|28211|356|69277|28100;3379134|1224|1236|91347|1903414|583;3379134|1224|1236|91347|1903411|613|615;3379134|1224|28211|204457|41297|13687;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|135614|32033|40323|86188,Complete,Folakunmi
bsdb:37485373/1/1,37485373,prospective cohort,37485373,https://doi.org/10.1016/j.isci.2023.107188,NA,"Deng Y., Wang J., Xie G., Zou G., Li S., Zhang J., Cai W. , Xu J.",Correlation between gut microbiota and the development of Graves' disease: A prospective study,iScience,2023,"Human metabolism, Microbial physiology, Microbiome, Pathology",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Control group (Con),Graves’ disease (GD),Patients diagnosed with Graves’ disease (GD),33,65,3 months,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,unchanged,decreased,NA,NA,NA,decreased,Signature 1,Figure 2A,24 July 2025,Aleru Divine,Aleru Divine,"Differentially abundant taxa from the phylum to genus level were further analyzed between Con and GD groups by STAMP analysis using Welch’s t test (p < 0.05, q < 0.05).",increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",1783272|1239|91061;1783272|1239|91061|186826;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;1783272|1239|526524|526525|2810280|3025755,Complete,NA
bsdb:37485373/1/2,37485373,prospective cohort,37485373,https://doi.org/10.1016/j.isci.2023.107188,NA,"Deng Y., Wang J., Xie G., Zou G., Li S., Zhang J., Cai W. , Xu J.",Correlation between gut microbiota and the development of Graves' disease: A prospective study,iScience,2023,"Human metabolism, Microbial physiology, Microbiome, Pathology",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Control group (Con),Graves’ disease (GD),Patients diagnosed with Graves’ disease (GD),33,65,3 months,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,unchanged,decreased,NA,NA,NA,decreased,Signature 2,Figure 2A,24 July 2025,Aleru Divine,Aleru Divine,"Differentially abundant taxa from the phylum to genus level were further analyzed between Con and GD groups by STAMP analysis using Welch’s t test (p < 0.05, q < 0.05).",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira",3379134|976|200643|1970189|1573805;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082768|424536;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|216572|1263;1783272|201174|84998|1643822|1643826|447020;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|28050,Complete,NA
bsdb:37485373/2/1,37485373,prospective cohort,37485373,https://doi.org/10.1016/j.isci.2023.107188,NA,"Deng Y., Wang J., Xie G., Zou G., Li S., Zhang J., Cai W. , Xu J.",Correlation between gut microbiota and the development of Graves' disease: A prospective study,iScience,2023,"Human metabolism, Microbial physiology, Microbiome, Pathology",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Graves’ disease before treatment (GDT0),Graves’ disease after treatment (GDT3),Patients diagnosed with Graves’ disease (GD) 3 months after treatment.,37,37,3 months,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2B,24 July 2025,Aleru Divine,Aleru Divine,Differentially abundant taxa from the phylum to genus level were further analyzed between GDT0and GDT3 groups by STAMP analysis using Welch’s t test.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira",1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|28050,Complete,NA
bsdb:37485373/2/2,37485373,prospective cohort,37485373,https://doi.org/10.1016/j.isci.2023.107188,NA,"Deng Y., Wang J., Xie G., Zou G., Li S., Zhang J., Cai W. , Xu J.",Correlation between gut microbiota and the development of Graves' disease: A prospective study,iScience,2023,"Human metabolism, Microbial physiology, Microbiome, Pathology",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Graves’ disease before treatment (GDT0),Graves’ disease after treatment (GDT3),Patients diagnosed with Graves’ disease (GD) 3 months after treatment.,37,37,3 months,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2B,24 July 2025,Aleru Divine,Aleru Divine,Differentially abundant taxa from the phylum to genus level were further analyzed between GDT0 and GDT3 groups by STAMP analysis using Welch’s t test.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella",1783272|1239|91061;1783272|1239|91061|186826;1783272|1239|91061|186826|186828;1783272|1239|91061|186826|1300;1783272|1239|186801|3085636|186803|1506577;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|186828|117563,Complete,NA
bsdb:37485373/3/1,37485373,prospective cohort,37485373,https://doi.org/10.1016/j.isci.2023.107188,NA,"Deng Y., Wang J., Xie G., Zou G., Li S., Zhang J., Cai W. , Xu J.",Correlation between gut microbiota and the development of Graves' disease: A prospective study,iScience,2023,"Human metabolism, Microbial physiology, Microbiome, Pathology",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Control group (Con),Graves’ disease after treatment (GDT3),Patients diagnosed with Graves’ disease (GD) 3 months after treatment.,33,37,3 months,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 1,Figure 2C,24 July 2025,Aleru Divine,Aleru Divine,Differentially abundant taxa from the phylum to genus level were further analyzed between Con and GDT3 groups by STAMP analysis using Welch’s t test.,increased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,1783272|1239|526524|526525|2810280|3025755,Complete,NA
bsdb:37485373/3/2,37485373,prospective cohort,37485373,https://doi.org/10.1016/j.isci.2023.107188,NA,"Deng Y., Wang J., Xie G., Zou G., Li S., Zhang J., Cai W. , Xu J.",Correlation between gut microbiota and the development of Graves' disease: A prospective study,iScience,2023,"Human metabolism, Microbial physiology, Microbiome, Pathology",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Control group (Con),Graves’ disease after treatment (GDT3),Patients diagnosed with Graves’ disease (GD) 3 months after treatment.,33,37,3 months,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 2,Figure 2C,24 July 2025,Aleru Divine,Aleru Divine,Differentially abundant taxa from the phylum to genus level were further analyzed between Con and GDT3 groups by STAMP analysis using Welch’s t test.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,s__metagenome",1783272|1239|186801|3082768|990719;3379134|976|200643|1970189|1573805;1783272|201174|84998|1643822|1643826;3379134|976|200643|171549|2005473;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|3085636|186803|33042;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|570;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|216572|946234;1783272|201174|84998|1643822|1643826|447020;256318,Complete,NA
bsdb:37485373/4/1,37485373,prospective cohort,37485373,https://doi.org/10.1016/j.isci.2023.107188,NA,"Deng Y., Wang J., Xie G., Zou G., Li S., Zhang J., Cai W. , Xu J.",Correlation between gut microbiota and the development of Graves' disease: A prospective study,iScience,2023,"Human metabolism, Microbial physiology, Microbiome, Pathology",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Graves’ disease before treatment (GDT0),Graves’ disease after treatment (GDT3),Patients diagnosed with Graves’ disease (GD) 3 months after treatment.,37,37,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 5C,24 July 2025,Aleru Divine,Aleru Divine,LEfSe analysis shows bacterial taxa significantly enriched in the GDT0 (red) or GDT3(green) groups. Taxonomic cladogram and linear discriminant analysis (LDA) scores show differences among taxa between GDT0 and GDT3. Only taxa meeting a significant LDA threshold value of >3 are shown.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter",1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1505657;1783272|1239|186801|3082720|186804|1505652,Complete,NA
bsdb:37485373/4/2,37485373,prospective cohort,37485373,https://doi.org/10.1016/j.isci.2023.107188,NA,"Deng Y., Wang J., Xie G., Zou G., Li S., Zhang J., Cai W. , Xu J.",Correlation between gut microbiota and the development of Graves' disease: A prospective study,iScience,2023,"Human metabolism, Microbial physiology, Microbiome, Pathology",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Graves’ disease before treatment (GDT0),Graves’ disease after treatment (GDT3),Patients diagnosed with Graves’ disease (GD) 3 months after treatment.,37,37,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 5C,24 July 2025,Aleru Divine,Aleru Divine,LEfSe analysis shows bacterial taxa significantly enriched in the GDT0 (red) or GDT3(green) groups. Taxonomic cladogram and linear discriminant analysis (LDA) scores show differences among taxa between GDT0 and GDT3. Only taxa meeting a significant LDA threshold value of >3 are shown.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales",1783272|1239|91061|186826|186828|117563;1783272|1239|91061|186826|186828;1783272|1239|91061;1783272|1239|91061|186826,Complete,NA
bsdb:37485373/5/1,37485373,prospective cohort,37485373,https://doi.org/10.1016/j.isci.2023.107188,NA,"Deng Y., Wang J., Xie G., Zou G., Li S., Zhang J., Cai W. , Xu J.",Correlation between gut microbiota and the development of Graves' disease: A prospective study,iScience,2023,"Human metabolism, Microbial physiology, Microbiome, Pathology",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Graves’ disease without hepatic impairment (GDN),Graves’ disease with impaired liver function before treatment (GDH),Patients with confirmed Graves’ disease (GD) and impaired liver function before treatment (GDH),47,18,3 months,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4A,24 July 2025,Aleru Divine,Aleru Divine,"Differentially abundant taxa from the phylum to genus level were further analyzed between GDH and GDN subgroups by STAMP analysis using Welch’s ttest (p < 0.05, q < 0.05).",increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,1783272|1239|186801|3085636|186803|33042,Complete,NA
bsdb:37485373/5/2,37485373,prospective cohort,37485373,https://doi.org/10.1016/j.isci.2023.107188,NA,"Deng Y., Wang J., Xie G., Zou G., Li S., Zhang J., Cai W. , Xu J.",Correlation between gut microbiota and the development of Graves' disease: A prospective study,iScience,2023,"Human metabolism, Microbial physiology, Microbiome, Pathology",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Graves’ disease without hepatic impairment (GDN),Graves’ disease with impaired liver function before treatment (GDH),Patients with confirmed Graves’ disease (GD) and impaired liver function before treatment (GDH),47,18,3 months,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4A,24 July 2025,Aleru Divine,Aleru Divine,"Differentially abundant taxa from the phylum to genus level were further analyzed between GDH and GDN subgroups by STAMP analysis using Welch’s ttest (p < 0.05, q < 0.05).",decreased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",3379134|1224;3379134|1224|1236;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|46255,Complete,NA
bsdb:37485373/6/1,37485373,prospective cohort,37485373,https://doi.org/10.1016/j.isci.2023.107188,NA,"Deng Y., Wang J., Xie G., Zou G., Li S., Zhang J., Cai W. , Xu J.",Correlation between gut microbiota and the development of Graves' disease: A prospective study,iScience,2023,"Human metabolism, Microbial physiology, Microbiome, Pathology",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Graves’ disease without hepatic impairment (GDN),Graves’ disease with impaired liver function before treatment (GDH),Patients with confirmed Graves’ disease (GD) and impaired liver function before treatment (GDH),47,18,3 months,16S,34,Illumina,raw counts,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,24 July 2025,Aleru Divine,Aleru Divine,LEfSe analysis shows bacterial taxa significantly enriched in the GDH (red) or GDN(green) groups. Taxonomic cladogram and linear discriminant analysis (LDA) scores show differences among taxa between GDH and GDN. Only taxa meeting a significant LDA threshold value of >3 are shown.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales",1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|186802|186806|1730|39496;1783272|201174|84998|84999|1643824;1783272|201174|84998|84999|1643824|133925;1783272|1798710|1906119,Complete,NA
bsdb:37485373/6/2,37485373,prospective cohort,37485373,https://doi.org/10.1016/j.isci.2023.107188,NA,"Deng Y., Wang J., Xie G., Zou G., Li S., Zhang J., Cai W. , Xu J.",Correlation between gut microbiota and the development of Graves' disease: A prospective study,iScience,2023,"Human metabolism, Microbial physiology, Microbiome, Pathology",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Graves’ disease without hepatic impairment (GDN),Graves’ disease with impaired liver function before treatment (GDH),Patients with confirmed Graves’ disease (GD) and impaired liver function before treatment (GDH),47,18,3 months,16S,34,Illumina,raw counts,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4B,24 July 2025,Aleru Divine,Aleru Divine,LEfSe analysis shows bacterial taxa significantly enriched in the GDH (red) or GDN(green) groups. Taxonomic cladogram and linear discriminant analysis (LDA) scores show differences among taxa between GDH and GDN. Only taxa meeting a significant LDA threshold value of >3 are shown.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",1783272|1239|91061;3379134|1224|1236|91347;3379134|1224|1236;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;3379134|1224;1783272|1239|91061|186826|33958|46255,Complete,NA
bsdb:37502423/1/1,37502423,"cross-sectional observational, not case-control",37502423,10.3389/fnagi.2023.1148546,NA,"Zhang M., Zhai Z., Yang B., He L., Wang J., Dai W., Xue L., Yang X., Feng Y. , Wang H.",Exploring the alteration of gut microbiota and brain function in gender-specific Parkinson's disease based on metagenomic sequencing,Frontiers in aging neuroscience,2023,"Parkinson’s disease, fMRI, gender, gut microbiota, metagenomic sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Female Parkinson’s disease (PD_F) patients,Male Parkinson’s disease (PD_M) patients,Male patients with Parkinson’s disease (PD) diagnosed according to the primary Parkinson’s disease diagnostic criteria.,11,13,1 month,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,body weight",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Fig. 2C, 2E",14 March 2024,Keamy,"Keamy,Scholastica,WikiWorks",Significantly differential taxa identified between male and female Parkinson’s disease (PD) patients,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Alsobacteraceae|g__Alsobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Bacillati|p__Bacillota|c__Tissierellia|g__Dethiosulfatibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Halanaerobiales|f__Halanaerobiaceae|g__Halocella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Budviciaceae|g__Leminorella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Rhodocyclaceae|g__Propionivibrio,k__Bacillati|p__Bacillota|c__Clostridia|g__Thermosediminibacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota,,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988|239934|239935;3379134|74201|203494|48461|1647988;3379134|1224|28211|356|2792775|1502180;1783272|1239|186801|186802|1470353;1783272|1239|1737404|448125;1783272|1239|186801|53433|972|46466;3379134|1224|1236|91347|1903416|82980;3379134|1224|28216|206389|75787|83766;1783272|1239|186801|291988;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201;;3379134|976|117743|200644|49546,Complete,Svetlana up
bsdb:37502423/1/2,37502423,"cross-sectional observational, not case-control",37502423,10.3389/fnagi.2023.1148546,NA,"Zhang M., Zhai Z., Yang B., He L., Wang J., Dai W., Xue L., Yang X., Feng Y. , Wang H.",Exploring the alteration of gut microbiota and brain function in gender-specific Parkinson's disease based on metagenomic sequencing,Frontiers in aging neuroscience,2023,"Parkinson’s disease, fMRI, gender, gut microbiota, metagenomic sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Female Parkinson’s disease (PD_F) patients,Male Parkinson’s disease (PD_M) patients,Male patients with Parkinson’s disease (PD) diagnosed according to the primary Parkinson’s disease diagnostic criteria.,11,13,1 month,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,body weight",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Fig. 2C, 2E",14 March 2024,Keamy,"Keamy,Scholastica,WikiWorks",Significantly differential taxa identified between male and female Parkinson’s disease (PD) patients,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Propionicicella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:254,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|3085636|186803|33042;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|3085636|186803;1783272|201174|1760|85009|85015|348581;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|1262953;1783272|1239|186801|3085636|186803|2316020|33039;3379134|1224|1236|91347|543|561;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|1263,Complete,Svetlana up
bsdb:37507685/1/1,37507685,case-control,37507685,10.1186/s12876-023-02904-2,NA,"Alsulaiman R.M., Al-Quorain A.A., Al-Muhanna F.A., Piotrowski S., Kurdi E.A., Vatte C., Alquorain A.A., Alfaraj N.H., Alrezuk A.M., Robinson F., Dowdell A.K., Alamri T.A., Hamilton L., Lad H., Gao H., Gandla D., Keating B.J., Meng R., Piening B. , Al-Ali A.K.",Gut microbiota analyses of inflammatory bowel diseases from a representative Saudi population,BMC gastroenterology,2023,"Crohn’s disease, IBD, Inflammation, Microbiota, Saudi, Ulcerative colitis",Experiment 1,Saudi Arabia,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,healthy controls,ulcerative colitis (UC),"Patients diagnosed with inflammatory bowel disease (IBD) through colonoscopy examinations, for ulcerative colitis (UC)",124,84,2 months,16S,123456789,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary File 14: Table S2,5 October 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential microbial abundance between ulcerative colitis (UC) and healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|s__Bacteroidaceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Metazoa|p__Nematoda|c__Enoplea|o__Trichinellida|f__Trichuridae|g__Trichuris|s__Trichuris trichiura",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|3085636|186803|207244|649756;3379134|976|200643|171549|815|2212467;3379134|976|200643|171549|2030927;3379134|976|200643|171549|815|816|46506;1783272|1239|186801|3085636|186803|189330|39486;3379134|976|200643|171549|2005525|375288|328812;3379134|976|200643|171549|171552|577309|454154;3379134|976|200643|171549|815|909656|310298;3379134|976|200643|171549|171552|2974251|165179;33208|6231|119088|6329|119093|36086|36087,Complete,Svetlana up
bsdb:37507685/1/2,37507685,case-control,37507685,10.1186/s12876-023-02904-2,NA,"Alsulaiman R.M., Al-Quorain A.A., Al-Muhanna F.A., Piotrowski S., Kurdi E.A., Vatte C., Alquorain A.A., Alfaraj N.H., Alrezuk A.M., Robinson F., Dowdell A.K., Alamri T.A., Hamilton L., Lad H., Gao H., Gandla D., Keating B.J., Meng R., Piening B. , Al-Ali A.K.",Gut microbiota analyses of inflammatory bowel diseases from a representative Saudi population,BMC gastroenterology,2023,"Crohn’s disease, IBD, Inflammation, Microbiota, Saudi, Ulcerative colitis",Experiment 1,Saudi Arabia,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,healthy controls,ulcerative colitis (UC),"Patients diagnosed with inflammatory bowel disease (IBD) through colonoscopy examinations, for ulcerative colitis (UC)",124,84,2 months,16S,123456789,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary File 14: Table S2,5 October 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential microbial abundance between ulcerative colitis (UC) and healthy controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas kerstersii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister propionicifaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus durans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides johnsonii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Myrtales|f__Lythraceae|g__Punica|s__Punica granatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__Tyzzerella sp.,s__bacterium NLAE-zl-H31",3379134|976|200643|171549|815|816|28116;1783272|1239|186801|3085636|186803|572511|1322;1783272|1239|186801|186802|31979|1898204;1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|186801|186802|31979|1485|1502;3379134|1224|28216|80840|80864|283|225992;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|909932|1843489|31977|39948|309120;1783272|1239|909932|1843489|31977|39948|308994;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|91061|186826|81852|1350|53345;3379134|1224|1236|91347|543|561|1884818;1783272|1239|909932|909929|1843491|158846|437897;3379134|976|200643|171549|2005525|375288|387661;3379134|976|200643|171549|171551|836|28123;3379134|976|200643|171549|171552|2974251|28135;33090|35493|3398|41944|3928|22662|22663;1783272|1239|186801|3085636|186803|1506577|2053632;1201630,Complete,Svetlana up
bsdb:37507685/2/1,37507685,case-control,37507685,10.1186/s12876-023-02904-2,NA,"Alsulaiman R.M., Al-Quorain A.A., Al-Muhanna F.A., Piotrowski S., Kurdi E.A., Vatte C., Alquorain A.A., Alfaraj N.H., Alrezuk A.M., Robinson F., Dowdell A.K., Alamri T.A., Hamilton L., Lad H., Gao H., Gandla D., Keating B.J., Meng R., Piening B. , Al-Ali A.K.",Gut microbiota analyses of inflammatory bowel diseases from a representative Saudi population,BMC gastroenterology,2023,"Crohn’s disease, IBD, Inflammation, Microbiota, Saudi, Ulcerative colitis",Experiment 2,Saudi Arabia,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,healthy controls,Crohn's disease (CD),"Patients diagnosed with inflammatory bowel disease (IBD) through endoscopy examinations, for Crohn's disease (CD)",124,135,2 months,16S,123456789,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary File 15: Table S3,5 October 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential microbial abundance between Crohn's disease (CD) and healthy controls,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|s__Prevotellaceae bacterium,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Myrtales|f__Lythraceae|g__Punica|s__Punica granatum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Metazoa|p__Nematoda|c__Enoplea|o__Trichinellida|f__Trichuridae|g__Trichuris|s__Trichuris trichiura",1783272|1239|186801|3085636|186803|207244|649756;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|46506;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|91061|186826|33958|1578|1579;1783272|1239|91061|186826|33958|1578|1596;3379134|976|200643|171549|171552|2974265|363265;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|171552|2049047;33090|35493|3398|41944|3928|22662|22663;3379134|976|200643|171549|171552|2974251|165179;33208|6231|119088|6329|119093|36086|36087,Complete,Svetlana up
bsdb:37507685/2/2,37507685,case-control,37507685,10.1186/s12876-023-02904-2,NA,"Alsulaiman R.M., Al-Quorain A.A., Al-Muhanna F.A., Piotrowski S., Kurdi E.A., Vatte C., Alquorain A.A., Alfaraj N.H., Alrezuk A.M., Robinson F., Dowdell A.K., Alamri T.A., Hamilton L., Lad H., Gao H., Gandla D., Keating B.J., Meng R., Piening B. , Al-Ali A.K.",Gut microbiota analyses of inflammatory bowel diseases from a representative Saudi population,BMC gastroenterology,2023,"Crohn’s disease, IBD, Inflammation, Microbiota, Saudi, Ulcerative colitis",Experiment 2,Saudi Arabia,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,healthy controls,Crohn's disease (CD),"Patients diagnosed with inflammatory bowel disease (IBD) through endoscopy examinations, for Crohn's disease (CD)",124,135,2 months,16S,123456789,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Supplementary File 15: Table S3, Figure 4: left plot",5 October 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential microbial abundance between Crohn's disease (CD) and healthy controls,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium butyricum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister propionicifaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus durans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides johnsonii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Myrtales|f__Lythraceae|g__Punica|s__Punica granatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus lutetiensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__Tyzzerella sp.,s__bacterium NLAE-zl-H31,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",3379134|976|200643|171549|815|816|28116;1783272|1239|186801|3085636|186803|572511|1322;1783272|1239|186801|186802|31979|1898204;1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|186801|186802|31979|1485|1492;1783272|1239|186801|186802|31979|1485|1502;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|909932|1843489|31977|39948|309120;1783272|1239|909932|1843489|31977|39948|308994;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|91061|186826|81852|1350|53345;3379134|1224|1236|91347|543|561|1884818;1783272|1239|909932|909929|1843491|158846|437897;3379134|976|200643|171549|2005525|375288|387661;3379134|976|200643|171549|171551|836|28123;33090|35493|3398|41944|3928|22662|22663;1783272|1239|91061|186826|1300|1301|150055;1783272|1239|186801|3085636|186803|1506577|2053632;1201630;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|3085636|186803|1506553,Complete,Svetlana up
bsdb:37507685/3/1,37507685,case-control,37507685,10.1186/s12876-023-02904-2,NA,"Alsulaiman R.M., Al-Quorain A.A., Al-Muhanna F.A., Piotrowski S., Kurdi E.A., Vatte C., Alquorain A.A., Alfaraj N.H., Alrezuk A.M., Robinson F., Dowdell A.K., Alamri T.A., Hamilton L., Lad H., Gao H., Gandla D., Keating B.J., Meng R., Piening B. , Al-Ali A.K.",Gut microbiota analyses of inflammatory bowel diseases from a representative Saudi population,BMC gastroenterology,2023,"Crohn’s disease, IBD, Inflammation, Microbiota, Saudi, Ulcerative colitis",Experiment 3,Saudi Arabia,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,ulcerative colitis (UC),Crohn's disease (CD),"Patients diagnosed with inflammatory bowel disease (IBD) through endoscopy examinations, for Crohn's disease (CD)",84,135,2 months,16S,123456789,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4: right plot,8 October 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential microbial abundance between ulcerative colitis (UC) and Crohn's disease (CD),increased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,1783272|1239|526524|526525|2810281|191303,Complete,Svetlana up
bsdb:37507685/3/2,37507685,case-control,37507685,10.1186/s12876-023-02904-2,NA,"Alsulaiman R.M., Al-Quorain A.A., Al-Muhanna F.A., Piotrowski S., Kurdi E.A., Vatte C., Alquorain A.A., Alfaraj N.H., Alrezuk A.M., Robinson F., Dowdell A.K., Alamri T.A., Hamilton L., Lad H., Gao H., Gandla D., Keating B.J., Meng R., Piening B. , Al-Ali A.K.",Gut microbiota analyses of inflammatory bowel diseases from a representative Saudi population,BMC gastroenterology,2023,"Crohn’s disease, IBD, Inflammation, Microbiota, Saudi, Ulcerative colitis",Experiment 3,Saudi Arabia,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,ulcerative colitis (UC),Crohn's disease (CD),"Patients diagnosed with inflammatory bowel disease (IBD) through endoscopy examinations, for Crohn's disease (CD)",84,135,2 months,16S,123456789,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 4, Plot 2",8 October 2023,ChiomaBlessing,"ChiomaBlessing,Peace Sandy,WikiWorks",Differential microbial abundance between ulcerative colitis (UC) and Crohn's disease (CD),decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|s__Christensenellaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__uncultured Lachnospira sp.,s__uncultured bacterium,k__Thermoproteati|p__Candidatus Bathyarchaeota",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|186803|653683;3379134|976|200643|171549|1853231|574697;95818|2093818|2093825|2171986;1783272|1239|186801|3082768|990719|2054177;1783272|1239|186801|186802|186806|1730|290054;3384189|32066|203490|203491|203492|848;1783272|1239|186801|186802|216572|1892380;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843488|909930|33024;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|3085636|186803|28050|446043;77133;1783275|928852,Complete,Svetlana up
bsdb:37525095/1/1,37525095,time series / longitudinal observational,37525095,10.1186/s12866-023-02951-5,NA,"Konecna E., Videnska P., Buresova L., Urik M., Smetanova S., Smatana S., Prokes R., Lanickova B., Budinska E., Klanova J. , Borilova Linhartova P.",Enrichment of human nasopharyngeal bacteriome with bacteria from dust after short-term exposure to indoor environment: a pilot study,BMC microbiology,2023,"16S rRNA, Bacteriome, Dust, Exposure, Hospital, Household, Indoor environment, Nasopharynx, Sequencing",Experiment 1,Czechia,Homo sapiens,Nasopharyngeal gland,NA,Exposure,EFO:0000487,Indoor dust samples,Nasopharyngeal swab samples from workplaces,"The workplaces in the study were commercially used buildings characterized by higher levels of human occupancy and usage of HVAC (heating, ventilation, air conditioning) systems, both contributing to the higher abundance of microorganisms and their spread in the building . The participants working at NEO, ENT, or RCX workplaces were included in the study",44,43,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Additional file 2,19 October 2023,Iram jamshed,"Iram jamshed,Hodan Issah,ChiomaBlessing,WikiWorks",Comparison between indoor dust and nasopharyngeal bacteriome,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|1239;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|1385|90964|1279,Complete,ChiomaBlessing
bsdb:37525095/2/NA,37525095,time series / longitudinal observational,37525095,10.1186/s12866-023-02951-5,NA,"Konecna E., Videnska P., Buresova L., Urik M., Smetanova S., Smatana S., Prokes R., Lanickova B., Budinska E., Klanova J. , Borilova Linhartova P.",Enrichment of human nasopharyngeal bacteriome with bacteria from dust after short-term exposure to indoor environment: a pilot study,BMC microbiology,2023,"16S rRNA, Bacteriome, Dust, Exposure, Hospital, Household, Indoor environment, Nasopharynx, Sequencing",Experiment 2,Czechia,Homo sapiens,Nasopharyngeal gland,NA,Exposure,EFO:0000487,"Nasopharyngeal swab samples collected in the Morning from workplaces (NEO, ENT, RCX)","Nasopharyngeal swab samples collected in the afternoon from workplaces (NEO, ENT, RCX)","Nasopharyngeal swabs collected in the afternoon (after an 8 h exposure to the workplace environment). The participants were working at NEO, ENT, or RCX workplaces.",22,21,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:37529095/1/1,37529095,laboratory experiment,37529095,10.55730/1300-0152.2617,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10388120/,"Fan T., Li X., Zhang X., Zhang J., Sun L., Chen J. , Fu C.",Influence of aerobic exercise training on mice gut microbiota in Parkinson's disease,Turkish journal of biology = Turk biyoloji dergisi,2022,"16S rRNA gene sequencing, Parkinson’s disease, aerobic exercise training, gut microbiota",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Response to exercise,EFO:0007768,Sham group and parkison's disease (PD) group,Aerobic exercise training group (AET),"Mice group that received grasping, rotating, walking and balance training exercises once a day, 6 days a week, 30 min each time, a total of 4 weeks.",10,5,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 6,9 March 2024,EGO,"EGO,Welile,Folakunmi,WikiWorks","Discriminative taxon in sham, PD, and AET groups by linear discriminant analysis (LDA) integrated with effect size (LEfSe)",increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|g__Rhodobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__uncultured Prevotella sp.",1783272|1239|91061;1783272|1239|91061|186826;1783272|1239|91061|186826|81850;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|1385|186817|400634;3379134|1224|28216|80840|2975441|93681;1783272|1239|91061|1385|186818;1783272|1239|186801|186802|216572|216851;3379134|1224|28211|204455|1060;3379134|976|200643|171549|171552|838|159272,Complete,Folakunmi
bsdb:37529095/3/1,37529095,laboratory experiment,37529095,10.55730/1300-0152.2617,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10388120/,"Fan T., Li X., Zhang X., Zhang J., Sun L., Chen J. , Fu C.",Influence of aerobic exercise training on mice gut microbiota in Parkinson's disease,Turkish journal of biology = Turk biyoloji dergisi,2022,"16S rRNA gene sequencing, Parkinson’s disease, aerobic exercise training, gut microbiota",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Response to exercise,EFO:0007768,Aerobic exercise training group (AET) and parkison's disease (PD) group,Sham group,group of mice that were injected intraperitoneally with equivalent volumes of normal saline for 7 days and did not receive any training,10,5,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 6,1 April 2024,Folakunmi,"Folakunmi,WikiWorks","Discriminative taxon in sham, PD, and AET groups by linear discriminant analysis (LDA) integrated with effect size (LEfSe)",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Devosia",3379134|976|200643|171549;3379134|976|200643;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|186827;1783272|1239|186801|3085636|186803|297314;3379134|1224|28211|356|2831106|46913,Complete,Folakunmi
bsdb:37542310/3/1,37542310,case-control,37542310,10.1186/s40168-023-01613-y,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01613-y,"Mäkinen A.I., Pappalardo V.Y., Buijs M.J., Brandt B.W., Mäkitie A.A., Meurman J.H. , Zaura E.",Salivary microbiome profiles of oral cancer patients analyzed before and after treatment,Microbiome,2023,"Cancer treatment, Oral cancer, Oral microbiome",Experiment 3,Finland,Homo sapiens,Oral cavity,UBERON:0000167,Oral squamous cell carcinoma,EFO:0000199,pre-treatment OSCC patients,post-treatment OSCC patients,"OSCC patients who received cancer treatment, and seen after a mean follow-up of 47.8 months.",28,28,Not mentioned,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig 4,9 August 2023,Andre,"Andre,WikiWorks",Discriminatory zOTUs between baseline and post-therapy samples in 28 OSCC patients (output of LEfSe analysis).,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium diversum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp.,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella|s__Bergeyella sp. oral taxon 322,k__Pseudomonadati|p__Bacteroidota|s__Bacteroidetes bacterium oral taxon 511,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 417,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 313,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hongkongensis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium vincentii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella veroralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 180,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis|s__Streptococcus oralis subsp. dentisani",1783272|1239|526524|526525|128827|123375|102148;1783272|1239|186801|3082720|543314|86331|114527;1783272|1239|91061|186826|1300|1301|1306;3384189|32066|203490|203491|1129771|32067|104608;3379134|203691|203692|136|2845253|157|166;3379134|976|117743|200644|2762318|59735|712187;3379134|976|712911;3379134|976|200643|171549|171551|836|28124;1783272|201174|84998|84999|1643824|2767353|1382;3379134|1224|28216|80840|119060|47670|47671;3384189|32066|203490|203491|1129771|32067|712365;1783272|1239|186801|3082720|186804|1257|341694;1783272|1239|1737404|1737405|1570339|543311|33033;3379134|976|200643|171549|171552|838|652722;3384189|32066|203490|203491|1129771|32067|554406;3379134|976|117743|200644|49546|1016|327575;3384189|32066|203490|203491|203492|848|155615;1783272|1239|909932|1843489|31977|29465|423477;3379134|976|200643|171549|171552|838|28137;1783272|1239|91061|186826|186827|46123|46125;1783272|201174|1760|2037|2049|1654|651609;1783272|1239|91061|186826|1300|1301|1305;1783272|1239|91061|186826|1300|1301|1303|1458253,Complete,Peace Sandy
bsdb:37542310/3/2,37542310,case-control,37542310,10.1186/s40168-023-01613-y,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01613-y,"Mäkinen A.I., Pappalardo V.Y., Buijs M.J., Brandt B.W., Mäkitie A.A., Meurman J.H. , Zaura E.",Salivary microbiome profiles of oral cancer patients analyzed before and after treatment,Microbiome,2023,"Cancer treatment, Oral cancer, Oral microbiome",Experiment 3,Finland,Homo sapiens,Oral cavity,UBERON:0000167,Oral squamous cell carcinoma,EFO:0000199,pre-treatment OSCC patients,post-treatment OSCC patients,"OSCC patients who received cancer treatment, and seen after a mean follow-up of 47.8 months.",28,28,Not mentioned,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,4,9 August 2023,Andre,"Andre,WikiWorks",Discriminatory zOTUs between baseline and post-therapy samples in 28 OSCC patients (output of LEfSe analysis),decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus paracasei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus rhamnosus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces gerencseriae",1783272|201174|1760|85006|1268|32207|2047;1783272|1239|91061|186826|33958|2759736|1597;1783272|1239|91061|186826|33958|2759736|47715;1783272|201174|1760|2037|2049|1654|52769,Complete,Peace Sandy
bsdb:37556398/1/1,37556398,"cross-sectional observational, not case-control",37556398,10.1371/journal.pone.0287839,NA,"Holdsworth E.A., Williams J.E., Pace R.M., Lane A.A., Gartstein M., McGuire M.A., McGuire M.K. , Meehan C.L.","Breastfeeding patterns are associated with human milk microbiome composition: The Mother-Infant Microbiomes, Behavior, and Ecology Study (MIMBES)",PloS one,2023,NA,Experiment 1,United States of America,Homo sapiens,Milk,UBERON:0001913,Breastfeeding duration,EFO:0006864,Medium Total Time Breastfeeding,Low Total Time Breastfeeding,Breastfeeding pattern,28,10,1 month,16S,123,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3A,12 October 2023,Peace Sandy,"Peace Sandy,WikiWorks","Log-Fold Change estimates relative to the medium group of genera identified as differentially abundant across [A] total time breastfeeding group in the ANCOM-BC global test Low < -1 Z-score, medium [-1 1] Z-score high > 1 Z-Score",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Agreia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Rugamonas",1783272|201174|1760|85006|85023|110934;1783272|201174|1760|85004|31953|1678;3379134|976|117747|200666|84566|84567;3379134|1224|1236|135614|32033|40323;3379134|1224|28216|80840|75682|212744,Complete,Chloe
bsdb:37556398/2/1,37556398,"cross-sectional observational, not case-control",37556398,10.1371/journal.pone.0287839,NA,"Holdsworth E.A., Williams J.E., Pace R.M., Lane A.A., Gartstein M., McGuire M.A., McGuire M.K. , Meehan C.L.","Breastfeeding patterns are associated with human milk microbiome composition: The Mother-Infant Microbiomes, Behavior, and Ecology Study (MIMBES)",PloS one,2023,NA,Experiment 2,United States of America,Homo sapiens,Milk,UBERON:0001913,Breastfeeding duration,EFO:0006864,Medium Total Time Breastfeeding,High Total Time Breastfeeding,Breastfeeding pattern,28,8,1 month,16S,123,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3A,12 October 2023,Peace Sandy,"Peace Sandy,WikiWorks","Log-Fold Change estimates relative to the medium group of genera identified as differentially abundant across [A] total time breastfeeding group in the ANCOM-BC global test Low < -1 Z-score, medium [-1 1] Z-score high > 1 Z-Score",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Agreia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Rugamonas",1783272|201174|1760|85006|85023|110934;1783272|201174|1760|85004|31953|1678;3379134|976|117747|200666|84566|84567;3379134|1224|1236|135614|32033|40323;3379134|1224|28216|80840|75682|212744,Complete,Chloe
bsdb:37556398/3/1,37556398,"cross-sectional observational, not case-control",37556398,10.1371/journal.pone.0287839,NA,"Holdsworth E.A., Williams J.E., Pace R.M., Lane A.A., Gartstein M., McGuire M.A., McGuire M.K. , Meehan C.L.","Breastfeeding patterns are associated with human milk microbiome composition: The Mother-Infant Microbiomes, Behavior, and Ecology Study (MIMBES)",PloS one,2023,NA,Experiment 3,United States of America,Homo sapiens,Milk,UBERON:0001913,Breastfeeding duration,EFO:0006864,Medium Breastfeeding Bouts,Low Breastfeeding Bouts,Breastfeeding pattern,30,10,1 month,16S,123,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3B,12 October 2023,Peace Sandy,"Peace Sandy,WikiWorks","Log-Fold Change estimates relative to the medium group of genera identified as differentially abundant across [B] Breastfeeding bouts in the ANCOM-BC global test Low < -1 Z-score, medium [-1 1] Z-score high > 1 Z-Score",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus",1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85006|1268|1269,Complete,Chloe
bsdb:37556398/3/2,37556398,"cross-sectional observational, not case-control",37556398,10.1371/journal.pone.0287839,NA,"Holdsworth E.A., Williams J.E., Pace R.M., Lane A.A., Gartstein M., McGuire M.A., McGuire M.K. , Meehan C.L.","Breastfeeding patterns are associated with human milk microbiome composition: The Mother-Infant Microbiomes, Behavior, and Ecology Study (MIMBES)",PloS one,2023,NA,Experiment 3,United States of America,Homo sapiens,Milk,UBERON:0001913,Breastfeeding duration,EFO:0006864,Medium Breastfeeding Bouts,Low Breastfeeding Bouts,Breastfeeding pattern,30,10,1 month,16S,123,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3B,12 October 2023,Peace Sandy,"Peace Sandy,WikiWorks","Log-Fold Change estimates relative to the medium group of genera identified as differentially abundant across [B] Breastfeeding bouts in the ANCOM-BC global test Low < -1 Z-score, medium [-1 1] Z-score high > 1 Z-Score",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acidocellaceae|g__Acidocella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter",3379134|976|117747|200666|84566|84567;3379134|1224|28211|3120395|3385905|50709;3379134|1224|28216|80840|506|222,Complete,Chloe
bsdb:37556398/4/1,37556398,"cross-sectional observational, not case-control",37556398,10.1371/journal.pone.0287839,NA,"Holdsworth E.A., Williams J.E., Pace R.M., Lane A.A., Gartstein M., McGuire M.A., McGuire M.K. , Meehan C.L.","Breastfeeding patterns are associated with human milk microbiome composition: The Mother-Infant Microbiomes, Behavior, and Ecology Study (MIMBES)",PloS one,2023,NA,Experiment 4,United States of America,Homo sapiens,Milk,UBERON:0001913,Breastfeeding duration,EFO:0006864,Medium Breastfeeding Bouts,High Breastfeeding Bouts,Breastfeeding pattern,30,6,1 month,16S,123,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3B,12 October 2023,Peace Sandy,"Peace Sandy,WikiWorks","Log-fold change estimates relative to the medium group of genera identified as differentially abundant across [B] Breastfeeding bouts in the ANCOM-BC global test. Low < -1 Z-score, medium [-1 1] Z-score high > 1 Z-Score",increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Chloe
bsdb:37556398/4/2,37556398,"cross-sectional observational, not case-control",37556398,10.1371/journal.pone.0287839,NA,"Holdsworth E.A., Williams J.E., Pace R.M., Lane A.A., Gartstein M., McGuire M.A., McGuire M.K. , Meehan C.L.","Breastfeeding patterns are associated with human milk microbiome composition: The Mother-Infant Microbiomes, Behavior, and Ecology Study (MIMBES)",PloS one,2023,NA,Experiment 4,United States of America,Homo sapiens,Milk,UBERON:0001913,Breastfeeding duration,EFO:0006864,Medium Breastfeeding Bouts,High Breastfeeding Bouts,Breastfeeding pattern,30,6,1 month,16S,123,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3B,12 October 2023,Peace Sandy,"Peace Sandy,WikiWorks","Log-fold change estimates relative to the medium group of genera identified as differentially abundant across [B] Breastfeeding bouts in the ANCOM-BC global test. Low < -1 Z-score, medium [-1 1] Z-score high > 1 Z-Score",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acidocellaceae|g__Acidocella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter",1783272|201174|1760|85006|1268|1269;3379134|976|117747|200666|84566|84567;3379134|1224|28211|3120395|3385905|50709;3379134|1224|28216|80840|506|222,Complete,Chloe
bsdb:37576972/1/1,37576972,"cross-sectional observational, not case-control",37576972,https://doi.org/10.3389/fendo.2023.1190954,https://www.frontiersin.org/journals/endocrinology/articles/10.3389/fendo.2023.1190954/full,"Xing M., Gao H., Yao L., Wang L., Zhang C., Zhu L. , Cui D.",Profiles and diagnostic value of intestinal microbiota in schizophrenia patients with metabolic syndrome,Frontiers in endocrinology,2023,"16S rRNA, dyslipidemia, intestinal microbiota, metabolic syndrome, schizophrenia, type 2 diabetes",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Metabolic syndrome,EFO:0000195,Schizophrenia patients with MetS,Schizophrenia patients without MetS,Schizophrenia patients with metabolic syndrome (MetS),58,57,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,NA,increased,NA,NA,Signature 1,Figure 4A,12 July 2024,JoyceQ,"JoyceQ,Scholastica,WikiWorks",A Linear Discriminant Analysis (LDA) Effect Size (LEfSe) analysis of significant bacterial differences in the fecal microbiota of schizophrenia patients with versus without metabolic syndrome (MetS),increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Synechococcales|f__Prochlorococcaceae|g__Prochlorococcus",3379134|74201|203494|48461|1647988|239934;1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3082720|186804;1783272|1239|186801|186802|31979|1266;1783272|1239|526524|526525|2810281|191303;1783272|1239|526524|526525|2810281;3379134|74201|203494|48461|203557;1783272|1239|526524;3379134|74201|203494;3379134|74201|203494|48461;3379134|74201;1783272|1117|3028117|1890424|2881426|1218,Complete,Svetlana up
bsdb:37576972/1/2,37576972,"cross-sectional observational, not case-control",37576972,https://doi.org/10.3389/fendo.2023.1190954,https://www.frontiersin.org/journals/endocrinology/articles/10.3389/fendo.2023.1190954/full,"Xing M., Gao H., Yao L., Wang L., Zhang C., Zhu L. , Cui D.",Profiles and diagnostic value of intestinal microbiota in schizophrenia patients with metabolic syndrome,Frontiers in endocrinology,2023,"16S rRNA, dyslipidemia, intestinal microbiota, metabolic syndrome, schizophrenia, type 2 diabetes",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Metabolic syndrome,EFO:0000195,Schizophrenia patients with MetS,Schizophrenia patients without MetS,Schizophrenia patients with metabolic syndrome (MetS),58,57,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,NA,increased,NA,NA,Signature 2,Figure 4A,12 July 2024,JoyceQ,"JoyceQ,Scholastica,WikiWorks",A Linear Discriminant Analysis (LDA) Effect Size (LEfSe) analysis of significant bacterial differences in the fecal microbiota of schizophrenia patients with versus without metabolic syndrome (MetS),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota",3379134|1224|28216|80840|506;;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|1224|28216;3379134|1224|28216|80840|119060|32008;3379134|1224|28216|80840|119060;3379134|1224|28216|80840;1783272|1239|186801|186802|31979|1485;1783272|1239|909932|1843489|31977|39948;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|909929|1843491|158846;3379134|1224|1236|2887326|468;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;3379134|1224|1236|72274;1783272|1239|91061|1385|90964;1783272|1239|91061|186826|1300;3379134|1224|28216|80840|995019|40544;1783272|1239|909932|1843489|31977;1783272|1239|91061|186826|33958;3379134|1224;3379134|976,Complete,Svetlana up
bsdb:37577672/1/1,37577672,laboratory experiment,37577672,10.1101/2023.08.01.551491,https://journals.asm.org/doi/10.1128/spectrum.03566-23,"Real M.V.F., Colvin M.S., Sheehan M.J. , Moeller A.H.",Major urinary protein (<i>Mup</i>) gene family deletion drives sex-specific alterations on the house mouse gut microbiota,bioRxiv : the preprint server for biology,2023,NA,Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Gene deletion library,EFO:0007560,Wild Type Male Mice (WT male),Knock Out Male Mice (KO male),"Knockout male mice refers to laboratory mice whose gene has been genetically engineered to be inactive or ""knocked out"".",4,6,NA,WMS,NA,Illumina,NA,ANCOM,0.001,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,"Fig. 3A, Table S5",31 January 2025,KateRasheed,"KateRasheed,WikiWorks",Differential abundance analyses with ANCOM-BC2,decreased,NA,NA,Complete,Svetlana up
bsdb:37586456/1/1,37586456,prospective cohort,37586456,10.1016/j.exer.2023.109615,NA,"Ozkan J., Majzoub M.E., Coroneo M., Thomas T. , Willcox M.",Ocular microbiome changes in dry eye disease and meibomian gland dysfunction,Experimental eye research,2023,"16S rRNA gene sequencing, Dry eye disease, Meibomian gland dysfunction, Microbiome, Ocular microbiology",Experiment 1,Australia,Homo sapiens,Margin of eyelid,UBERON:0034772,Dry eye syndrome,EFO:1000906,Meibomian Gland Dysfunction,Meibomian Gland Dysfunction + Lacrimal Dysfunction,Participants with MGD + LD corresponding to both evaporative dry eye disease and aqueous deficient dry eye disease (severe DED).,15,17,3 months,16S,34,Illumina,raw counts,Linear Regression,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 4,22 August 2023,Mary Bearkland,"Mary Bearkland,Folakunmi,WikiWorks","Bacteria identified at the eyelid margin which showed significant differences in mean
relative abundance between the groups - MGD and MGD+LD. Analysis conducted using univariate GLMs with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05",increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas putida,3379134|1224|1236|72274|135621|286|303,Complete,Folakunmi
bsdb:37586456/1/2,37586456,prospective cohort,37586456,10.1016/j.exer.2023.109615,NA,"Ozkan J., Majzoub M.E., Coroneo M., Thomas T. , Willcox M.",Ocular microbiome changes in dry eye disease and meibomian gland dysfunction,Experimental eye research,2023,"16S rRNA gene sequencing, Dry eye disease, Meibomian gland dysfunction, Microbiome, Ocular microbiology",Experiment 1,Australia,Homo sapiens,Margin of eyelid,UBERON:0034772,Dry eye syndrome,EFO:1000906,Meibomian Gland Dysfunction,Meibomian Gland Dysfunction + Lacrimal Dysfunction,Participants with MGD + LD corresponding to both evaporative dry eye disease and aqueous deficient dry eye disease (severe DED).,15,17,3 months,16S,34,Illumina,raw counts,Linear Regression,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 4,22 August 2023,Mary Bearkland,"Mary Bearkland,Folakunmi,WikiWorks",Bacteria identified at the eyelid margin which showed significant differences in mean relative abundance between the groups - MGD and MGD+LD. Analysis conducted using univariate GLMs with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium accolens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium macginleyi,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium simulans",1783272|201174|1760|85007|1653|1716|38284;1783272|201174|1760|85007|1653|1716|38290;1783272|201174|1760|85007|1653|1716|146827,Complete,Folakunmi
bsdb:37586456/2/1,37586456,prospective cohort,37586456,10.1016/j.exer.2023.109615,NA,"Ozkan J., Majzoub M.E., Coroneo M., Thomas T. , Willcox M.",Ocular microbiome changes in dry eye disease and meibomian gland dysfunction,Experimental eye research,2023,"16S rRNA gene sequencing, Dry eye disease, Meibomian gland dysfunction, Microbiome, Ocular microbiology",Experiment 2,Australia,Homo sapiens,Margin of eyelid,UBERON:0034772,Dry eye syndrome,EFO:1000906,Healthy Control,Meibomian Gland Dysfunction + Lacrimal Dysfunction,Participants with MGD + LD corresponding to both evaporative dry eye disease and aqueous deficient dry eye disease (severe DED).,15,17,3 months,16S,34,Illumina,raw counts,Linear Regression,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 4,22 August 2023,Mary Bearkland,"Mary Bearkland,Folakunmi,WikiWorks",Bacteria identified at the eyelid margin which showed significant differences in mean relative abundance between the groups MGD+LD and healthy controls. Analysis conducted using univariate GLMs with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean.  *P < 0.05,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas putida,3379134|1224|1236|72274|135621|286|303,Complete,Folakunmi
bsdb:37586456/2/2,37586456,prospective cohort,37586456,10.1016/j.exer.2023.109615,NA,"Ozkan J., Majzoub M.E., Coroneo M., Thomas T. , Willcox M.",Ocular microbiome changes in dry eye disease and meibomian gland dysfunction,Experimental eye research,2023,"16S rRNA gene sequencing, Dry eye disease, Meibomian gland dysfunction, Microbiome, Ocular microbiology",Experiment 2,Australia,Homo sapiens,Margin of eyelid,UBERON:0034772,Dry eye syndrome,EFO:1000906,Healthy Control,Meibomian Gland Dysfunction + Lacrimal Dysfunction,Participants with MGD + LD corresponding to both evaporative dry eye disease and aqueous deficient dry eye disease (severe DED).,15,17,3 months,16S,34,Illumina,raw counts,Linear Regression,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 4,22 August 2023,Mary Bearkland,"Mary Bearkland,Folakunmi,WikiWorks",Bacteria identified at the eyelid margin which showed significant differences in mean relative abundance between the groups MGD+LD and healthy controls. Analysis conducted using univariate GLMs with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean.  *P < 0.05,decreased,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus nagyae,1783272|1239|1737404|1737405|1570339|165779|1755241,Complete,Folakunmi
bsdb:37586456/3/1,37586456,prospective cohort,37586456,10.1016/j.exer.2023.109615,NA,"Ozkan J., Majzoub M.E., Coroneo M., Thomas T. , Willcox M.",Ocular microbiome changes in dry eye disease and meibomian gland dysfunction,Experimental eye research,2023,"16S rRNA gene sequencing, Dry eye disease, Meibomian gland dysfunction, Microbiome, Ocular microbiology",Experiment 3,Australia,Homo sapiens,Margin of eyelid,UBERON:0034772,Dry eye syndrome,EFO:1000906,Control,Meibomian Gland Dysfunction,Participants with MGD corresponding to  evaporative dry eye disease (moderate).,15,15,3 months,16S,34,Illumina,raw counts,Linear Regression,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 4,23 August 2023,Mary Bearkland,"Mary Bearkland,Folakunmi,WikiWorks",Bacteria identified at the eyelid margin which showed significant differences in mean relative abundance between the groups - MGD and healthy controls. Analysis conducted using univariate GLMs with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium accolens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium macginleyi,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium simulans",1783272|201174|1760|85007|1653|1716|38284;1783272|201174|1760|85007|1653|1716|38290;1783272|201174|1760|85007|1653|1716|146827,Complete,Folakunmi
bsdb:37586456/3/2,37586456,prospective cohort,37586456,10.1016/j.exer.2023.109615,NA,"Ozkan J., Majzoub M.E., Coroneo M., Thomas T. , Willcox M.",Ocular microbiome changes in dry eye disease and meibomian gland dysfunction,Experimental eye research,2023,"16S rRNA gene sequencing, Dry eye disease, Meibomian gland dysfunction, Microbiome, Ocular microbiology",Experiment 3,Australia,Homo sapiens,Margin of eyelid,UBERON:0034772,Dry eye syndrome,EFO:1000906,Control,Meibomian Gland Dysfunction,Participants with MGD corresponding to  evaporative dry eye disease (moderate).,15,15,3 months,16S,34,Illumina,raw counts,Linear Regression,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 4,23 August 2023,Mary Bearkland,"Mary Bearkland,Folakunmi,WikiWorks",Bacteria identified at the eyelid margin which showed significant differences in mean relative abundance between the groups - MGD and healthy controls. Analysis conducted using univariate GLMs with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05,decreased,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus nagyae,1783272|1239|1737404|1737405|1570339|165779|1755241,Complete,Folakunmi
bsdb:37586456/4/1,37586456,prospective cohort,37586456,10.1016/j.exer.2023.109615,NA,"Ozkan J., Majzoub M.E., Coroneo M., Thomas T. , Willcox M.",Ocular microbiome changes in dry eye disease and meibomian gland dysfunction,Experimental eye research,2023,"16S rRNA gene sequencing, Dry eye disease, Meibomian gland dysfunction, Microbiome, Ocular microbiology",Experiment 4,Australia,Homo sapiens,Conjunctiva,UBERON:0001811,Dry eye syndrome,EFO:1000906,Meibomian Gland Dysfunction,Meibomian Gland Dysfunction + Lacrimal Dysfunction,Participants with MGD + LD corresponding to both evaporative dry eye disease and aqueous deficient dry eye disease (severe DED).,15,17,3 months,16S,34,Illumina,raw counts,Linear Regression,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3,23 August 2023,Mary Bearkland,"Mary Bearkland,Folakunmi,WikiWorks","Bacteria identified from the conjunctiva which showed significant differences in
mean relative abundance between the groups - MGD   and MGD+LD. Analysis conducted using univariate generalized linear models (GLMs) with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05, **P < 0.01",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Caballeronia|s__Caballeronia zhejiangensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas azotoformans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Ectopseudomonas|s__Ectopseudomonas oleovorans",3379134|1224|28216|80840|119060|1827195|871203;3379134|1224|1236|72274|135621|286|47878;3379134|1224|1236|72274|135621|3236654|301,Complete,Folakunmi
bsdb:37586456/4/2,37586456,prospective cohort,37586456,10.1016/j.exer.2023.109615,NA,"Ozkan J., Majzoub M.E., Coroneo M., Thomas T. , Willcox M.",Ocular microbiome changes in dry eye disease and meibomian gland dysfunction,Experimental eye research,2023,"16S rRNA gene sequencing, Dry eye disease, Meibomian gland dysfunction, Microbiome, Ocular microbiology",Experiment 4,Australia,Homo sapiens,Conjunctiva,UBERON:0001811,Dry eye syndrome,EFO:1000906,Meibomian Gland Dysfunction,Meibomian Gland Dysfunction + Lacrimal Dysfunction,Participants with MGD + LD corresponding to both evaporative dry eye disease and aqueous deficient dry eye disease (severe DED).,15,17,3 months,16S,34,Illumina,raw counts,Linear Regression,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 3,23 August 2023,Mary Bearkland,"Mary Bearkland,Folakunmi,WikiWorks","Bacteria identified from the conjunctiva which showed significant differences in
mean relative abundance between the groups - MGD and MGD+LD. Analysis conducted using univariate generalized linear models (GLMs) with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05, **P < 0.01",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium kroppenstedtii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium macginleyi",1783272|201174|1760|85007|1653|1716|161879;1783272|201174|1760|85007|1653|1716|38290,Complete,Folakunmi
bsdb:37586456/6/1,37586456,prospective cohort,37586456,10.1016/j.exer.2023.109615,NA,"Ozkan J., Majzoub M.E., Coroneo M., Thomas T. , Willcox M.",Ocular microbiome changes in dry eye disease and meibomian gland dysfunction,Experimental eye research,2023,"16S rRNA gene sequencing, Dry eye disease, Meibomian gland dysfunction, Microbiome, Ocular microbiology",Experiment 6,Australia,Homo sapiens,Conjunctiva,UBERON:0001811,Dry eye syndrome,EFO:1000906,control,Meibomian Gland Dysfunction,Participants with MGD  to  evaporative dry eye disease (moderate DED).,15,15,3 months,16S,34,Illumina,raw counts,Linear Regression,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3,23 August 2023,Mary Bearkland,"Mary Bearkland,Folakunmi,WikiWorks","Bacteria identified from the conjunctiva which showed significant differences in
mean relative abundance between the groups - MGD and healthy controls. Analysis conducted using univariate generalized linear models (GLMs) with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05, **P < 0.01",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium kroppenstedtii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium macginleyi",1783272|201174|1760|85007|1653|1716|161879;1783272|201174|1760|85007|1653|1716|38290,Complete,Folakunmi
bsdb:37587195/1/1,37587195,time series / longitudinal observational,37587195,10.1038/s41598-023-40102-y,NA,"Querdasi F.R., Vogel S.C., Thomason M.E., Callaghan B.L. , Brito N.H.",A comparison of the infant gut microbiome before versus after the start of the covid-19 pandemic,Scientific reports,2023,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,pre-pandemic group with covariates controlled for,pandemic group with covariates controlled for,"healthy 12-month old infants who provided stool samples during the first 9 months of the pandemic with covariates ( diet(average fat intake), child sex, still breastfeeding at sample collection, and birth mode) controlled for.",34,20,1 month,16S,NA,Illumina,arcsine square-root,MaAsLin2,0.25,TRUE,NA,NA,"breast feeding,delivery procedure,diet,sex",NA,unchanged,decreased,NA,NA,NA,Signature 1,"figure 6, figure 7",10 October 2023,Folakunmi,"Folakunmi,WikiWorks",differential analysis of gut microbiome by pandemic group with covariates controlled for.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712,Complete,ChiomaBlessing
bsdb:37587195/2/1,37587195,time series / longitudinal observational,37587195,10.1038/s41598-023-40102-y,NA,"Querdasi F.R., Vogel S.C., Thomason M.E., Callaghan B.L. , Brito N.H.",A comparison of the infant gut microbiome before versus after the start of the covid-19 pandemic,Scientific reports,2023,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,pre-pandemic group without covariates controlled for,pandemic group without covariates controlled for,healthy 12-month old infants who provided stool samples during the first 9 months of the pandemic without controlling for covariates.,34,20,1 month,16S,NA,Illumina,arcsine square-root,MaAsLin2,0.25,TRUE,NA,NA,"age,breast feeding,delivery procedure,diet",NA,unchanged,decreased,NA,NA,NA,Signature 1,"Supplementary information: Page 5, under sub-heading- “Differential abundance of gut microbiome by pandemic group without controlling for covariates”",10 October 2023,Folakunmi,"Folakunmi,ChiomaBlessing,WikiWorks",Differential abundance of gut microbiome by pandemic group without controlling for covariates.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,3379134|1224|1236|135625|712,Complete,ChiomaBlessing
bsdb:37587195/2/2,37587195,time series / longitudinal observational,37587195,10.1038/s41598-023-40102-y,NA,"Querdasi F.R., Vogel S.C., Thomason M.E., Callaghan B.L. , Brito N.H.",A comparison of the infant gut microbiome before versus after the start of the covid-19 pandemic,Scientific reports,2023,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,pre-pandemic group without covariates controlled for,pandemic group without covariates controlled for,healthy 12-month old infants who provided stool samples during the first 9 months of the pandemic without controlling for covariates.,34,20,1 month,16S,NA,Illumina,arcsine square-root,MaAsLin2,0.25,TRUE,NA,NA,"age,breast feeding,delivery procedure,diet",NA,unchanged,decreased,NA,NA,NA,Signature 2,"Supplementary information: Page 5, under sub-heading- “Differential abundance of gut microbiome by pandemic group without controlling for covariates”",11 October 2023,Folakunmi,"Folakunmi,ChiomaBlessing,WikiWorks",Differential abundance of gut microbiome by pandemic group without controlling for covariates.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,1783272|1239|91061|186826|33958,Complete,ChiomaBlessing
bsdb:37587195/3/1,37587195,time series / longitudinal observational,37587195,10.1038/s41598-023-40102-y,NA,"Querdasi F.R., Vogel S.C., Thomason M.E., Callaghan B.L. , Brito N.H.",A comparison of the infant gut microbiome before versus after the start of the covid-19 pandemic,Scientific reports,2023,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,pandemic group (without covariates),pandemic group according to the number of days,"Healthy 12-month old infants who provided stool samples during the first 9 months of the pandemic according to the number of days since the pandemic began. Due to the small sample size of the during pandemic group (N = 20), analyses restricted to this group did not include any covariates.",34,20,1 month,16S,NA,Illumina,arcsine square-root,MaAsLin2,0.25,TRUE,NA,NA,"breast feeding,delivery procedure,diet,sex",NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Results within text: Page 4, under sub-heading ""Differential abundance of gut microbiota by days since the start of the pandemic among the pandemic group"".",11 October 2023,Folakunmi,"Folakunmi,ChiomaBlessing,WikiWorks",Differential abundance of gut microbiota by days since the start of the pandemic among the pandemic group.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,1783272|201174|1760|85004|31953,Complete,ChiomaBlessing
bsdb:37593638/1/1,37593638,"prospective cohort,time series / longitudinal observational",37593638,10.1016/j.heliyon.2023.e18610,NA,"Woodall C.A., Hammond A., Cleary D., Preston A., Muir P., Pascoe B., Sheppard S.K. , Hay A.D.",Oral and gut microbial biomarkers of susceptibility to respiratory tract infection in adults: A feasibility study,Heliyon,2023,"Community, Feasibility, Longitudinal, Microbial biomarkers, Respiratory tract infection",Experiment 1,United Kingdom,Homo sapiens,Saliva,UBERON:0001836,Respiratory tract infectious disease,MONDO:0024355,healthy controls,respiratory tract infection(baseline),participants who acquired Respiratory Tract Infection symptoms at the baseline/start of the study,21,19,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 5,22 March 2025,UtibeIta,UtibeIta,Difference between microbial biomarkers in oral baseline samples from participants who acquired Respiratory Tract Infection symptoms compared to those who remained healthy.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sobrinus",1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|909929|1843491|158846|2049033;1783272|1239|91061|186826|1300|1301|1310,Complete,Svetlana up
bsdb:37593638/1/2,37593638,"prospective cohort,time series / longitudinal observational",37593638,10.1016/j.heliyon.2023.e18610,NA,"Woodall C.A., Hammond A., Cleary D., Preston A., Muir P., Pascoe B., Sheppard S.K. , Hay A.D.",Oral and gut microbial biomarkers of susceptibility to respiratory tract infection in adults: A feasibility study,Heliyon,2023,"Community, Feasibility, Longitudinal, Microbial biomarkers, Respiratory tract infection",Experiment 1,United Kingdom,Homo sapiens,Saliva,UBERON:0001836,Respiratory tract infectious disease,MONDO:0024355,healthy controls,respiratory tract infection(baseline),participants who acquired Respiratory Tract Infection symptoms at the baseline/start of the study,21,19,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 5,22 March 2025,UtibeIta,UtibeIta,Difference between microbial biomarkers in oral baseline samples from participants who acquired Respiratory Tract Infection symptoms compared to those who remained healthy.,decreased,"k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Dethiosulfovibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Thermotogati|p__Synergistota,k__Pseudomonadati|p__Verrucomicrobiota,k__Thermotogati|p__Synergistota|c__Synergistia|s__uncultured Synergistia bacterium",3384194|508458|649775|649776|3029088|47054;1783272|1239|91061|186826|33958|1578|1591;1783272|1239|91061|186826|33958|2767887|1624;3384194|508458;3379134|74201;3384194|508458|649775|1294150,Complete,Svetlana up
bsdb:37593638/2/1,37593638,"prospective cohort,time series / longitudinal observational",37593638,10.1016/j.heliyon.2023.e18610,NA,"Woodall C.A., Hammond A., Cleary D., Preston A., Muir P., Pascoe B., Sheppard S.K. , Hay A.D.",Oral and gut microbial biomarkers of susceptibility to respiratory tract infection in adults: A feasibility study,Heliyon,2023,"Community, Feasibility, Longitudinal, Microbial biomarkers, Respiratory tract infection",Experiment 2,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Respiratory tract infectious disease,MONDO:0024355,healthy controls,respiratory tract infection(baseline),participants who acquired Respiratory Tract Infection symptoms at the baseline/start of the study,21,19,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 5,25 March 2025,UtibeIta,UtibeIta,Difference between microbial biomarkers in gut baseline samples from participants who acquired Respiratory Tract Infection symptoms compared to those who remained healthy.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter|s__Enhydrobacter sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp.",1783272|201174|84998|1643822|1643826|84111|1929886;3379134|1224|28211|356|212791;3379134|1224|28211|356|212791|1894999;3379134|1224|1236|135614|32033;3379134|1224|1236|135614;3379134|976|200643|171549|171550;1783272|1239|909932|1843489|31977|29465|1926307,Complete,Svetlana up
bsdb:37593638/2/2,37593638,"prospective cohort,time series / longitudinal observational",37593638,10.1016/j.heliyon.2023.e18610,NA,"Woodall C.A., Hammond A., Cleary D., Preston A., Muir P., Pascoe B., Sheppard S.K. , Hay A.D.",Oral and gut microbial biomarkers of susceptibility to respiratory tract infection in adults: A feasibility study,Heliyon,2023,"Community, Feasibility, Longitudinal, Microbial biomarkers, Respiratory tract infection",Experiment 2,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Respiratory tract infectious disease,MONDO:0024355,healthy controls,respiratory tract infection(baseline),participants who acquired Respiratory Tract Infection symptoms at the baseline/start of the study,21,19,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 5,25 March 2025,UtibeIta,UtibeIta,Difference between microbial biomarkers in gut baseline samples from participants who acquired Respiratory Tract Infection symptoms compared to those who remained healthy.,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus sp.,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus|s__Desulfobulbus sp.",1783272|1239|526524|526525|2810280|100883|2137881;3379134|200940|3024418|213118;3379134|200940|3031451|3024411|213121;3379134|200940|3031451|3024411|213121|893;3379134|200940|3031451|3024411|213121|893|895,Complete,Svetlana up
bsdb:37593638/3/1,37593638,"prospective cohort,time series / longitudinal observational",37593638,10.1016/j.heliyon.2023.e18610,NA,"Woodall C.A., Hammond A., Cleary D., Preston A., Muir P., Pascoe B., Sheppard S.K. , Hay A.D.",Oral and gut microbial biomarkers of susceptibility to respiratory tract infection in adults: A feasibility study,Heliyon,2023,"Community, Feasibility, Longitudinal, Microbial biomarkers, Respiratory tract infection",Experiment 3,United Kingdom,Homo sapiens,Saliva,UBERON:0001836,Respiratory tract infectious disease,MONDO:0024355,healthy control,respiratory tract infection(end of study),participants who acquired Respiratory Tract Infection symptoms at the end of study,21,17,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure S3A,27 March 2025,UtibeIta,UtibeIta,Difference between microbial biomarkers in oral end-of-study samples from participants who acquired Respiratory Tract Infection symptoms compared to those who remained healthy.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|1760|2037;1783272|201174;1783272|1239|91061;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:37593638/3/2,37593638,"prospective cohort,time series / longitudinal observational",37593638,10.1016/j.heliyon.2023.e18610,NA,"Woodall C.A., Hammond A., Cleary D., Preston A., Muir P., Pascoe B., Sheppard S.K. , Hay A.D.",Oral and gut microbial biomarkers of susceptibility to respiratory tract infection in adults: A feasibility study,Heliyon,2023,"Community, Feasibility, Longitudinal, Microbial biomarkers, Respiratory tract infection",Experiment 3,United Kingdom,Homo sapiens,Saliva,UBERON:0001836,Respiratory tract infectious disease,MONDO:0024355,healthy control,respiratory tract infection(end of study),participants who acquired Respiratory Tract Infection symptoms at the end of study,21,17,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure S3A,27 March 2025,UtibeIta,UtibeIta,Difference between microbial biomarkers in oral end-of-study samples from participants who acquired Respiratory Tract Infection symptoms compared to those who remained healthy.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:37593638/4/1,37593638,"prospective cohort,time series / longitudinal observational",37593638,10.1016/j.heliyon.2023.e18610,NA,"Woodall C.A., Hammond A., Cleary D., Preston A., Muir P., Pascoe B., Sheppard S.K. , Hay A.D.",Oral and gut microbial biomarkers of susceptibility to respiratory tract infection in adults: A feasibility study,Heliyon,2023,"Community, Feasibility, Longitudinal, Microbial biomarkers, Respiratory tract infection",Experiment 4,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Respiratory tract infectious disease,MONDO:0024355,healthy control,respiratory tract infection(end of study),participants who acquired Respiratory Tract Infection symptoms at the end of study,21,17,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure S3B,27 March 2025,UtibeIta,"UtibeIta,Aleru Divine",Difference between microbial biomarkers in gut end-of-study samples from participants who acquired Respiratory Tract Infection symptoms compared to those who remained healthy.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium",1783272|1239|526524|526525|2810280|135858;1783272|1239|526524|526525|2810280|135858|2049022;1783272|1239|186801;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|2044939,Complete,Svetlana up
bsdb:37593638/4/2,37593638,"prospective cohort,time series / longitudinal observational",37593638,10.1016/j.heliyon.2023.e18610,NA,"Woodall C.A., Hammond A., Cleary D., Preston A., Muir P., Pascoe B., Sheppard S.K. , Hay A.D.",Oral and gut microbial biomarkers of susceptibility to respiratory tract infection in adults: A feasibility study,Heliyon,2023,"Community, Feasibility, Longitudinal, Microbial biomarkers, Respiratory tract infection",Experiment 4,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Respiratory tract infectious disease,MONDO:0024355,healthy control,respiratory tract infection(end of study),participants who acquired Respiratory Tract Infection symptoms at the end of study,21,17,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure S3B,27 March 2025,UtibeIta,UtibeIta,Difference between microbial biomarkers in gut end-of-study samples from participants who acquired Respiratory Tract Infection symptoms compared to those who remained healthy.,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis",1783272|1239|526524|526525|2810280|100883;1783272|1239|526524|526525;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|186806|1730|142586;1783272|1239|526524|526525|128827|1573535|1735,Complete,Svetlana up
bsdb:37596518/1/1,37596518,time series / longitudinal observational,37596518,https://doi.org/10.1186/s12879-023-08511-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10436399/,"Galperine T., Choi Y., Pagani J.L., Kritikos A., Papadimitriou-Olivgeris M., Méan M., Scherz V., Opota O., Greub G., Guery B. , Bertelli C.",Temporal changes in fecal microbiota of patients infected with COVID-19: a longitudinal cohort,BMC infectious diseases,2023,"COVID-19, Gut microbiota, Gut-lung axis, Microbiota profiling, SARS-CoV-2",Experiment 1,Switzerland,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Non-Covid 19 Patients - pneumonia patients,COVID-19 Patients,Patients admitted for COVID-19,19,57,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2.5,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,Fig. 1C,15 October 2023,Tolulopeo,"Tolulopeo,Peace Sandy,WikiWorks","C, D Differential abundance analysis and distance-based redundancy analysis (db-RDA) in COVID-19 and non-COVID-19 patients. COVID-19 and non-COVID-19 pneumonia patients were compared to evaluate the COVID-19 effect. C Differentially abundant taxa identified by linear discriminant analysis effect size (LEfSe) at genus level. The results with p-value < 0.01 and effect size (log10) > 2.5 for each group are presented as a bar plot (**p < 0.01, ***p < 0.001).",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|1017280;1783272|1239|186801|186802|216572|1905344,Complete,Peace Sandy
bsdb:37596518/1/2,37596518,time series / longitudinal observational,37596518,https://doi.org/10.1186/s12879-023-08511-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10436399/,"Galperine T., Choi Y., Pagani J.L., Kritikos A., Papadimitriou-Olivgeris M., Méan M., Scherz V., Opota O., Greub G., Guery B. , Bertelli C.",Temporal changes in fecal microbiota of patients infected with COVID-19: a longitudinal cohort,BMC infectious diseases,2023,"COVID-19, Gut microbiota, Gut-lung axis, Microbiota profiling, SARS-CoV-2",Experiment 1,Switzerland,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,Non-Covid 19 Patients - pneumonia patients,COVID-19 Patients,Patients admitted for COVID-19,19,57,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2.5,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,Fig. 1c,15 October 2023,Tolulopeo,"Tolulopeo,Peace Sandy,WikiWorks","C, D Differential abundance analysis and distance-based redundancy analysis (db-RDA) in COVID-19 and non-COVID-19 patients. COVID-19 and non-COVID-19 pneumonia patients were compared to evaluate the COVID-19 effect. C Differentially abundant taxa identified by linear discriminant analysis effect size (LEfSe) at genus level. The results with p-value < 0.01 and effect size (log10) > 2.5 for each group are presented as a bar plot (**p < 0.01, ***p < 0.001).",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus",1783272|1239|186801|186802|1686313;1783272|1239|1737404|1737405|1570339|150022;3379134|976|200643|171549|171551|836;1783272|201174|1760|85007|1653|1716;3379134|1224|28216|80840|995019|40544;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|909932|1843489|31977|909928,Complete,Peace Sandy
bsdb:37596518/2/1,37596518,time series / longitudinal observational,37596518,https://doi.org/10.1186/s12879-023-08511-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10436399/,"Galperine T., Choi Y., Pagani J.L., Kritikos A., Papadimitriou-Olivgeris M., Méan M., Scherz V., Opota O., Greub G., Guery B. , Bertelli C.",Temporal changes in fecal microbiota of patients infected with COVID-19: a longitudinal cohort,BMC infectious diseases,2023,"COVID-19, Gut microbiota, Gut-lung axis, Microbiota profiling, SARS-CoV-2",Experiment 2,Switzerland,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,COVID-19 patients - Non-Ventilated,COVID-19 patients - Ventilated,COVID-19 patients in Intensive Care Unit [ICU] - Ventilated,43,14,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig 2 A,16 October 2023,Tolulopeo,"Tolulopeo,Davvve,Peace Sandy,WikiWorks","Impact of COVID-19 severity on the taxa composition and longitudinal changes of the gut microbiota. A, B Differential abundance analysis and db-RDA analysis in ventilated and non-ventilated COVID-19 patients. A Genera differentially abundant among the two groups were identified by a complex model including ventilation, antibiotics and timepoint with longitudinal sampling correction using negative binomial and zero-inflated mixed model (NBZIMM). The taxa with p-value < 0.01 and effect size (log10) > 2.5 for each group are presented in the bar plot (**p < 0.01, ***p < 0.001).",increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",3379134|29547|3031852|213849|72294|194;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|31979|1485,Complete,Peace Sandy
bsdb:37596518/2/2,37596518,time series / longitudinal observational,37596518,https://doi.org/10.1186/s12879-023-08511-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10436399/,"Galperine T., Choi Y., Pagani J.L., Kritikos A., Papadimitriou-Olivgeris M., Méan M., Scherz V., Opota O., Greub G., Guery B. , Bertelli C.",Temporal changes in fecal microbiota of patients infected with COVID-19: a longitudinal cohort,BMC infectious diseases,2023,"COVID-19, Gut microbiota, Gut-lung axis, Microbiota profiling, SARS-CoV-2",Experiment 2,Switzerland,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,COVID-19 patients - Non-Ventilated,COVID-19 patients - Ventilated,COVID-19 patients in Intensive Care Unit [ICU] - Ventilated,43,14,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Fig 2 A,16 October 2023,Tolulopeo,"Tolulopeo,Peace Sandy,WikiWorks","Impact of COVID-19 severity on the taxa composition and longitudinal changes of the gut microbiota. A, B Differential abundance analysis and db-RDA analysis in ventilated and non-ventilated COVID-19 patients. A Genera differentially abundant among the two groups were identified by a complex model including ventilation, antibiotics and timepoint with longitudinal sampling correction using negative binomial and zero-inflated mixed model (NBZIMM). The taxa with p-value < 0.01 and effect size (log10) > 2.5 for each group are presented in the bar plot (**p < 0.01, ***p < 0.001).",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|841,Complete,Peace Sandy
bsdb:37596536/2/1,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 2,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kuvale,Himba,The Himba are also Bantu-speaking cattle herders of the Herero tradition. They reside in the same coastal lowlands as the Kuvale and share similar environmental conditions.,7,7,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Supplementary Table 4 and 5, Figure 5",23 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|1591;1783272|201174|1760|85009|31957|2801844|1750;1783272|201174|1760|85009|31957|2801844,Complete,Svetlana up
bsdb:37596536/2/2,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 2,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kuvale,Himba,The Himba are also Bantu-speaking cattle herders of the Herero tradition. They reside in the same coastal lowlands as the Kuvale and share similar environmental conditions.,7,7,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Supplementary Table 4 and 5, Figure 5",23 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae",3379134|1224|1236|91347|543|158483;3379134|1224|1236|91347|543|544|546;3379134|1224|1236|91347|543|544|545;3379134|1224|1236|91347|543|590;3379134|1224|1236|91347|543|590|599;3379134|1224|1236|91347|543|158483|158484,Complete,Svetlana up
bsdb:37596536/3/1,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 3,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kuvale,Tjimba,The Tjimba inhabit the same coastal lowlands as the Kuvale and Himba. They may represent a subgroup or offshoot of the Himba community.,7,4,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Supplementary Table 4 and 5, Figure 5",23 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter piscolens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae",3384194|508458|649775|649776|3029088|638847;3384194|508458|649775|649776|3029088|638847|638849;3379134|1224|1236|91347|543|544|133448,Complete,Svetlana up
bsdb:37596536/3/2,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 3,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kuvale,Tjimba,The Tjimba inhabit the same coastal lowlands as the Kuvale and Himba. They may represent a subgroup or offshoot of the Himba community.,7,4,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Supplementary Table 4 and 5, Figure 5",23 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp.",3379134|1224|1236|91347|543|158483;3379134|1224|1236|91347|543|158483|158484;3379134|1224|1236|91347|543|544|546;3379134|1224|1236|91347|543|544|1639133;3379134|1224|1236|91347|1903412|568;3379134|1224|1236|91347|1903412|568|1873498,Complete,Svetlana up
bsdb:37596536/4/1,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 4,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kuvale,Kwisi,The Kwisi are a marginalized group whose origins have been considered enigmatic. Their livelihoods also deviate from traditional food production or foraging patterns.,7,8,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Supplementary Table 4 and 5, Figure 5",23 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia|s__Eggerthia catenaformis",3379134|1224|1236|91347|543|544|133448;1783272|1239|526524|526525|2810280|1279384|31973,Complete,Svetlana up
bsdb:37596536/4/2,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 4,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kuvale,Kwisi,The Kwisi are a marginalized group whose origins have been considered enigmatic. Their livelihoods also deviate from traditional food production or foraging patterns.,7,8,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Supplementary Table 4 and 5, Figure 5",23 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between Population according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first Population of the comparison, and negative values represent taxa enriched in the second one.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.",3379134|1224|1236|91347|543|158483;3379134|1224|1236|91347|543|158483|158484;3379134|1224|1236|91347|543|544|1639133;3379134|1224|1236|91347|543|544|545;3379134|1224|1236|91347|543|544|1896336,Complete,Svetlana up
bsdb:37596536/5/1,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 5,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kuvale,Twa,"The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.",7,7,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Supplementary Table 4 and 5, Figure 5",23 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia|s__Eggerthia catenaformis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella rimae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia sp. (in: enterobacteria),k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium",3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543|544|133448;1783272|1239|526524|526525|2810280|1279384;1783272|1239|526524|526525|2810280|1279384|31973;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|547|42895;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|3082720|3118655|44259;1783272|1239|186801|3082720|3118655|44259|143361;3379134|1224|1236|91347|543|570|571;3379134|1224|1236|91347|543|570|573;3379134|1224|1236|91347|543|570|576;1783272|201174|84998|84999|1643824|2767353|1383;3379134|1224|1236|72274|135621|286;3379134|1224|1236|72274|135621|286|306;3379134|1224|1236|91347|543|590;3379134|1224|1236|91347|543|590|599;3379134|1224|1236|91347|1903411|613;3379134|1224|1236|91347|1903411|613|616;3379134|1224|1236|91347|543|158876;3379134|1224|1236|91347|543|158876|158877;1783272|201174|1760|85007|1653|1716,Complete,Svetlana up
bsdb:37596536/5/2,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 5,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kuvale,Twa,"The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.",7,7,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Supplementary Table 4 and 5, Figure 5",23 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",3384189|32066|203490|203491|203492|848|860;1783272|1239|91061|1385|539738|1378|84135;3379134|976|200643|171549|171552|577309|454154;3379134|976|200643|171549|171551|836|322095;3379134|976|200643|171549|171551|836|1924944;3379134|976|200643|171549|171552|577309;3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|171551|836,Complete,Svetlana up
bsdb:37596536/7/1,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 7,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kuvale,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups.",7,7,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Supplementary Table 4 and 5, Figure 5",24 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between Populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first Population of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia|s__Eggerthia catenaformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia",3379134|1224|1236|91347|543|544|133448;1783272|1239|526524|526525|2810280|1279384;1783272|1239|526524|526525|2810280|1279384|31973;1783272|1239|186801|3082720|3118655|1913599;1783272|201174|1760|85009|31957|1743;1783272|1239|186801|3085636|186803|177971;3379134|976|200643,Complete,Svetlana up
bsdb:37596536/7/2,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 7,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kuvale,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups.",7,7,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,24 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between Populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first Population of the comparison, and negative values represent taxa enriched in the second one.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus paraphrohaemolyticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia sp.",1783272|1239|91061|186826|186827|46123;1783272|1239|91061|186826|186827|46123|46125;1783272|1239|91061|1385|186817|1386;3379134|1224|1236|91347|543|544|546;1783272|1239|186801|3082720|186804|1870884;1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|1385|539738|1378|84135;3379134|1224|1236|135625|712|724|736;1783272|1239|91061|186826|186827|46123|76631,Complete,Svetlana up
bsdb:37596536/8/1,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 8,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwepe,Himba,the Himba are also Bantu-speaking cattle herders of the Herero tradition. They reside in the same coastal lowlands as the Kuvale and share similar environmental conditions.,7,7,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Supplementary Table 4 and 5, Figure 5",24 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between Populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first Population of the comparison, and negative values represent taxa enriched in the second one.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei",3379134|1224|1236|91347|543|158483;3379134|1224|1236|91347|543|158483|158484;3379134|1224|1236|91347|543|544|546;3379134|1224|1236|91347|543|570|573;3379134|1224|1236|91347|543|570|576;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|1898203;3379134|1224|1236|91347|543|590;3379134|1224|1236|91347|543|590|599;3379134|1224|1236|91347|543|158876;3379134|1224|1236|91347|543|158876|158877,Complete,Svetlana up
bsdb:37596536/8/2,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 8,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwepe,Himba,the Himba are also Bantu-speaking cattle herders of the Herero tradition. They reside in the same coastal lowlands as the Kuvale and share similar environmental conditions.,7,7,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Supplementary Table 4 and 5, Figure 5",24 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between Populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first Population of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|1591;1783272|1239|91061|186826|1300|1301|1305;1783272|201174|1760|85009|31957|2801844;1783272|201174|1760|85009|31957|2801844|1750,Complete,Svetlana up
bsdb:37596536/9/1,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 9,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwepe,Tjimba,The Tjimba inhabit the same coastal lowlands as the Kuvale and Himba. They may represent a subgroup or offshoot of the Himba community.,7,4,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Supplementary Table 4 and 5, Figure 5",24 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae,3379134|1224|1236|91347|543|544|133448,Complete,Svetlana up
bsdb:37596536/9/2,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 9,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwepe,Tjimba,The Tjimba inhabit the same coastal lowlands as the Kuvale and Himba. They may represent a subgroup or offshoot of the Himba community.,7,4,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Supplementary Table 4 and 5, Figure 5",24 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella",3379134|1224|1236|91347|543|544|546;3379134|1224|1236|91347|1903412|568|1873498;3379134|1224|1236|91347|543|544|1639133;3379134|1224|1236|91347|1903412|568;1783272|1239|526524|526525|128827|118747;3379134|1224|1236|91347|543|158483;3379134|1224|1236|91347|543|158876,Complete,Svetlana up
bsdb:37596536/10/1,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 10,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwepe,Kwisi,The Kwisi are a marginalized group whose origins have been considered enigmatic. Their livelihoods also deviate from traditional food production or foraging patterns.,7,8,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,24 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella sp.",3379134|1224|1236|91347|543|544|133448;3379134|1224|1236|2887326|468|475|479,Complete,Svetlana up
bsdb:37596536/10/2,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 10,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwepe,Kwisi,The Kwisi are a marginalized group whose origins have been considered enigmatic. Their livelihoods also deviate from traditional food production or foraging patterns.,7,8,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,24 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049|1654|29317;3379134|1224|1236|91347|543|158483|158484;3379134|1224|1236|91347|543|544|1639133;3379134|1224|1236|91347|543|544|1896336;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|1898203;1783272|1239|91061|186826|1300|1301|1318;3379134|1224|1236|91347|543|158876;3379134|1224|1236|91347|543|158876|158877;3379134|1224|1236|91347|543|158483,Complete,Svetlana up
bsdb:37596536/11/1,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 11,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwepe,Twa,"The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.",7,7,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,24 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae",3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543|547;3379134|1224|1236|72274|135621|286;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|547|42895;3379134|1224|1236|91347|543|544|545;3379134|1224|1236|91347|543|544|133448,Complete,Svetlana up
bsdb:37596536/12/1,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 12,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwepe,Tshwa,"Khoe-Kwadi-speaking foragers from the Tsholotsho District of western Zimbabwe. They traditionally relied on foraging but were forced to leave their hunting grounds in Hwange National Park during the early 20th century, leading to social marginalization.",7,5,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudopneumoniae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter|s__[Eubacterium] yurii",3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543|544|545;3379134|1224|1236|91347|543|544|133448;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|547|42895;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|561|562;3384189|32066|203490|203491|203492|848|851;1783272|1239|91061|186826|186828|117563|137732;3379134|1224|28216|206351|481|32257|505;3379134|1224|1236|91347|543|570|571;3379134|1224|1236|72274|135621|286|306;3379134|1224|1236|91347|543|590;3379134|1224|1236|91347|543|590|599;1783272|1239|91061|186826|1300|1301|1313;1783272|1239|91061|186826|1300|1301|257758;1783272|1239|186801|3082720|3118655|1913599|39498,Complete,Svetlana up
bsdb:37596536/12/2,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 12,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwepe,Tshwa,"Khoe-Kwadi-speaking foragers from the Tsholotsho District of western Zimbabwe. They traditionally relied on foraging but were forced to leave their hunting grounds in Hwange National Park during the early 20th century, leading to social marginalization.",7,5,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella kingae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049|1654|55565;1783272|201174|1760|2037|2049|1654|29317;3379134|1224|28216|206351|481|32257|504;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|1898203;1783272|1239|909932|1843489|31977|906;1783272|201174|1760|2037|2049|2529408|1660;1783272|1239|186801|3085636|186803|1164882,Complete,Svetlana up
bsdb:37596536/13/1,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 13,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwepe,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups",7,7,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae,3379134|1224|1236|91347|543|544|133448,Complete,Svetlana up
bsdb:37596536/13/2,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 13,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwepe,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups",7,7,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. (in: high G+C Gram-positive bacteria)",3379134|1224|1236|91347|543|544|546;1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|91061|1385|539738|1378|84135;3379134|1224|1236|91347|543|570|573;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|201174|1760|85006|1268|32207|1885016,Complete,Svetlana up
bsdb:37596536/14/1,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 14,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Himba,Tjimba,The Tjimba inhabit the same coastal lowlands as the Kuvale and Himba.,7,4,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella",3379134|1224|1236|91347|543|590|599;3379134|1224|1236|91347|543|590,Complete,Svetlana up
bsdb:37596536/14/2,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 14,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Himba,Tjimba,The Tjimba inhabit the same coastal lowlands as the Kuvale and Himba.,7,4,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia",3379134|1224|1236|91347|1903412|568|1873498;3379134|1224|1236|91347|1903412|568,Complete,Svetlana up
bsdb:37596536/15/1,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 15,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Himba,Kwisi,The Kwisi are a marginalized group whose origins have been considered enigmatic. Their livelihoods also deviate from traditional food production or foraging patterns.,7,8,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema lecithinolyticum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae",3379134|1224|1236|91347|543|590;3379134|1224|1236|91347|543|544|546;3379134|1224|1236|91347|543|590|599;3379134|203691|203692|136|2845253|157|53418;3379134|1224|1236|91347|543|570|573;3379134|1224|1236|91347|543|544|133448,Complete,Svetlana up
bsdb:37596536/15/2,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 15,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Himba,Kwisi,The Kwisi are a marginalized group whose origins have been considered enigmatic. Their livelihoods also deviate from traditional food production or foraging patterns.,7,8,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",3379134|1224|1236|91347|543|544|1639133;3379134|1224|1236|91347|543|544|1896336;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:37596536/16/1,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 16,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Himba,Twa,"The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.",7,7,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli",3379134|1224|1236|91347|543|590;3379134|1224|1236|91347|543|158483;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|158876;3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|1903412|568;3379134|29547|3031852|213849|72294|194;3379134|1224|1236|91347|1903411|613;1783272|1239|909932|909929|1843491|970;3379134|1224|1236|91347|543|544|546;3379134|1224|1236|91347|543|590|599;3379134|1224|1236|91347|543|547|42895;3379134|1224|1236|91347|543|158483|158484;3379134|1224|1236|91347|543|158876|158877;3379134|1224|1236|91347|543|544|133448;3379134|1224|1236|91347|543|570|576;3379134|1224|1236|91347|543|544|545;3379134|1224|1236|91347|543|570|571;3379134|1224|1236|91347|543|570|573;3379134|1224|1236|91347|543|561|562,Complete,Svetlana up
bsdb:37596536/16/2,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 16,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Himba,Twa,"The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.",7,7,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,"MyleeeA,KateRasheed,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara",1783272|201174|1760|85009|31957|2801844;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|171552|577309|454154,Complete,Svetlana up
bsdb:37596536/17/1,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 17,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Himba,Tshwa,"They traditionally relied on foraging but were forced to leave their hunting grounds in Hwange National Park during the early 20th century, leading to social marginalization.",7,5,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,"MyleeeA,KateRasheed,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Pseudomonadati|p__Bacteroidota|s__Bacteroidetes oral taxon 274,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp.,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema lecithinolyticum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter|s__[Eubacterium] yurii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae",3379134|976|652708;3379134|976|200643;3379134|1224|1236|91347|543|158483;3379134|1224|1236|91347|543|158483|158484;3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543|544|546;3379134|1224|1236|91347|543|544|545;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|547|42895;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|543|561|1884818;3384189|32066|203490|203491|203492|848|851;3379134|1224|1236|91347|1903412|568;3379134|1224|1236|91347|1903412|568|1873498;3379134|1224|1236|91347|543|570|571;3379134|1224|1236|91347|543|570|573;3379134|1224|1236|91347|543|570|576;1783272|1239|186801|3082720|186804;3379134|1224|1236|91347|543|590;3379134|1224|1236|91347|543|590|599;3379134|203691|203692|136|2845253|157|53418;3379134|1224|1236|91347|543|158876;3379134|1224|1236|91347|543|158876|158877;1783272|1239|186801|3082720|3118655|1913599|39498;3379134|1224|1236|91347|543|544|133448,Complete,Svetlana up
bsdb:37596536/17/2,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 17,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Himba,Tshwa,"They traditionally relied on foraging but were forced to leave their hunting grounds in Hwange National Park during the early 20th century, leading to social marginalization.",7,5,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.",1783272|201174|1760|2037|2049|1654|55565;1783272|201174|1760|85009|31957|2801844;1783272|201174|1760|85009|31957|2801844|1750;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|1591,Complete,Svetlana up
bsdb:37596536/18/1,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 18,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Himba,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups.",7,7,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae",3379134|29547|3031852|213849|72294|194;3379134|1224|1236|91347|543|590;3379134|1224|1236|91347|543|590|599;3379134|1224|1236|91347|543|544|133448,Complete,Svetlana up
bsdb:37596536/18/2,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 18,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Himba,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups.",7,7,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,"MyleeeA,KateRasheed,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. (in: firmicutes),k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. (in: high G+C Gram-positive bacteria),k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia georgiae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens",1783272|1239|91061|186826|186827|46123;1783272|1239|91061|186826|186827|46123|46125;1783272|1239|91061|186826|186827|46123|76631;1783272|201174|1760|85009|31957|2801844;1783272|201174|1760|85009|31957|2801844|1750;1783272|1239|91061|1385|186817|1386;1783272|1239|91061|1385|186817|1386|1409;3379134|1224|1236|91347|543|544|546;1783272|1239|186801|3082720|186804|1870884;1783272|1239|186801|3082720|186804|1870884|1496;1783272|201174|1760|85007|1653|1716|1720;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|81852|1350|35783;1783272|1239|91061|1385|539738|1378|84135;1783272|1239|91061|186826|186828|117563|2049028;1783272|1239|91061|186826|33958|1578|1591;1783272|201174|1760|85006|1268|32207|1885016;1783272|201174|1760|2037|2049|2529408|52768;1783272|1239|91061|186826|1300|1301|1305;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|186828|117563|46124,Complete,Svetlana up
bsdb:37596536/19/1,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 19,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Twa,Tshwa,"The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.",7,5,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter|s__[Eubacterium] yurii",3384189|32066|203490|203491|203492|848|851;1783272|1239|186801|3082720|3118655|1913599|39498,Complete,Svetlana up
bsdb:37596536/19/2,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 19,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Twa,Tshwa,"The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.",7,5,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,"Supplementary Table 4 and 5, Figure 5",25 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella|s__Simonsiella muelleri,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",3379134|1224|28216|206351|481|71|72;1783272|201174|1760|2037|2049|1654|55565;3379134|1224|28216|206351|481|71;1783272|201174|1760|2037|2049|1654,Complete,Svetlana up
bsdb:37596536/20/1,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 20,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Twa,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups.",7,7,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia georgiae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia sp. (in: enterobacteria),k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli",3379134|1224|1236|91347|543|158483;3379134|1224|1236|91347|543|158483|158484;3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543|544|546;3379134|1224|1236|91347|543|544|545;1783272|1239|186801|3082720|186804|1870884;1783272|201174|1760|85007|1653|1716|1720;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|547|42895;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|81852|1350|35783;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|570|571;3379134|1224|1236|91347|543|570|573;3379134|1224|1236|91347|543|570|576;3379134|1224|1236|72274|135621|286;33090|35493|3398|72025|3803|3814|508215;3379134|1224|1236|91347|543|590;1783272|201174|1760|2037|2049|2529408|52768;3379134|1224|1236|91347|1903411|613;3379134|1224|1236|91347|1903411|613|616;3379134|1224|1236|91347|543|158876;3379134|1224|1236|91347|543|158876|158877;3379134|1224|1236|91347|543|561|562,Complete,Svetlana up
bsdb:37596536/21/1,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 21,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Tshwa,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups.",5,7,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Supplementary Table 4 and 5, Figure 5",25 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella kingae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella|s__Simonsiella muelleri",3379134|1224|28216|206351|481|71;1783272|201174|1760|85009|31957|1743;1783272|201174|1760|2037|2049|1654|55565;3379134|1224|28216|206351|481|32257|504;3379134|1224|28216|206351|481|71|72,Complete,Svetlana up
bsdb:37596536/21/2,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 21,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Tshwa,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups.",5,7,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides",3379134|1224|1236|91347|543|544|546;1783272|1239|91061|186826|81852|1350|35783;3379134|1224|1236|91347|543|570|571;3379134|1224|1236|91347|543|570|576;3379134|1224|1236|91347|543|561|562;1783272|201174|1760|85006|1268|32207|172042;3379134|1224|1236|91347|543|570|573;3379134|1224|1236|91347|543|544|545;1783272|1239|186801|3082720|186804|1870884|1496;1783272|201174|1760|85007|1653|1716|1720;1783272|1239|91061|1385|539738|1378|84135;3379134|1224|1236|91347|543|590|599;3379134|1224|1236|91347|543|158876|158877;1783272|1239|91061|186826|1300|1301|1304;3379134|1224|1236|91347|543|158483|158484;1783272|1239|91061|1385|539738|1378|1379;3384189|32066|203490|203491|203492|848|851;3379134|1224|28216|80840|119060|47670|47671;3379134|1224|28216|206351|481|32257|505;3379134|1224|1236|91347|543|547|42895;1783272|1239|1737404|1737405|1570339|543311|33033;3379134|1224|1236|91347|1903411|613;1783272|1239|91061|1385|539738|1378;3379134|1224|28216|80840|119060|47670;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|590;3379134|1224|1236|91347|543|158876;3379134|1224|1236|91347|543|158483;1783272|1239|186801|3082720|186804|1870884,Complete,Svetlana up
bsdb:37596536/22/1,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 22,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Tjimba,Kwisi,The Kwisi are a marginalized group whose origins have been considered enigmatic. Their livelihoods also deviate from traditional food production or foraging patterns.,4,8,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia",3379134|1224|1236|91347|543|544|546;3379134|1224|1236|91347|1903412|568|1873498;3379134|1224|1236|91347|1903412|568,Complete,Svetlana up
bsdb:37596536/22/2,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 22,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Tjimba,Kwisi,The Kwisi are a marginalized group whose origins have been considered enigmatic. Their livelihoods also deviate from traditional food production or foraging patterns.,4,8,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter piscolens",3384194|508458|649775|649776|3029088|638847;3384194|508458|649775|649776|3029088|638847|638849,Complete,Svetlana up
bsdb:37596536/23/1,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 23,Angola,Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Tjimba,Twa,"The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.",4,7,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp.",3379134|1224|1236|91347|543|158483;3379134|1224|1236|91347|543|158483|158484;3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543|544|546;3379134|1224|1236|91347|543|544|545;3379134|1224|1236|91347|543|544|1639133;3379134|1224|1236|91347|543|544|1896336;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|547|42895;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|1903412|568;3379134|1224|1236|91347|543|570|571;3379134|1224|1236|91347|543|570|573;3379134|1224|1236|91347|543|570|576;3379134|1224|1236|91347|543|158876;3379134|1224|1236|91347|543|158876|158877;3379134|1224|1236|91347|1903412|568|1873498,Complete,Svetlana up
bsdb:37596536/24/1,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 24,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Tjimba,Tshwa,"Khoe-Kwadi-speaking foragers from the Tsholotsho District of western Zimbabwe. They traditionally relied on foraging but were forced to leave their hunting grounds in Hwange National Park during the early 20th century, leading to social marginalization.",4,5,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp.",3379134|1224|1236|91347|1903412|568;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|158483;3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543|158876;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|590;3379134|1224|1236|91347|543|590|599;3379134|1224|1236|91347|543|547|42895;3379134|1224|28216|206351|481|32257|505;3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|543|570|573;3379134|1224|1236|91347|543|158876|158877;3379134|1224|1236|91347|543|544|545;3379134|1224|1236|91347|543|158483|158484;3379134|1224|1236|91347|543|544|1896336;3379134|1224|1236|91347|543|544|546;3379134|1224|1236|91347|543|570|571;3379134|1224|1236|91347|543|570|576;3379134|1224|1236|91347|543|544|1639133;3379134|1224|1236|91347|1903412|568|1873498,Complete,Svetlana up
bsdb:37596536/24/2,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 24,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Tjimba,Tshwa,"Khoe-Kwadi-speaking foragers from the Tsholotsho District of western Zimbabwe. They traditionally relied on foraging but were forced to leave their hunting grounds in Hwange National Park during the early 20th century, leading to social marginalization.",4,5,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,1783272|201174|1760|2037|2049|1654|55565,Complete,Svetlana up
bsdb:37596536/25/1,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 25,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Tjimba,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups",4,7,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium",3379134|1224|1236|91347|1903412|568;3379134|1224|1236|91347|1903412|568|1873498;1783272|201174|1760|85009|31957|1743,Complete,Svetlana up
bsdb:37596536/26/1,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 26,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwisi,Twa,"The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.",8,7,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter",3379134|1224|1236|91347|543|158483|158484;3379134|1224|1236|91347|543|544|1639133;3379134|1224|1236|91347|543|547|42895;3379134|1224|1236|91347|543|158876|158877;3379134|1224|1236|91347|543|544|1896336;3379134|1224|1236|91347|543|544|545;3379134|1224|1236|91347|543|570|571;3379134|1224|1236|91347|543|158483;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|158876;3379134|1224|1236|91347|543|544,Complete,Svetlana up
bsdb:37596536/26/2,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 26,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwisi,Twa,"The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.",8,7,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella sp.,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis",3379134|1224|1236|2887326|468|475|479;3379134|976|117743|200644|49546|1016|1017,Complete,Svetlana up
bsdb:37596536/27/1,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 27,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwisi,Tshwa,"Khoe-Kwadi-speaking foragers from the Tsholotsho District of western Zimbabwe. They traditionally relied on foraging but were forced to leave their hunting grounds in Hwange National Park during the early 20th century, leading to social marginalization.",8,5,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter|s__[Eubacterium] yurii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella",3379134|1224|1236|91347|543|158483;3379134|1224|1236|91347|543|158483|158484;3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543|544|546;3379134|1224|1236|91347|543|544|545;3379134|1224|1236|91347|543|544|1639133;3379134|1224|1236|91347|543|544|1896336;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|547|42895;3384189|32066|203490|203491|203492|848|851;3379134|1224|28216|206351|481|32257|505;3379134|1224|1236|91347|543|570|571;3379134|1224|1236|91347|543|590|599;3379134|1224|1236|91347|543|158876|158877;1783272|1239|186801|3082720|3118655|1913599|39498;3379134|1224|1236|91347|543|158876;3379134|1224|1236|91347|543|590,Complete,Svetlana up
bsdb:37596536/27/2,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 27,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwisi,Tshwa,"Khoe-Kwadi-speaking foragers from the Tsholotsho District of western Zimbabwe. They traditionally relied on foraging but were forced to leave their hunting grounds in Hwange National Park during the early 20th century, leading to social marginalization.",8,5,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella kingae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella|s__Simonsiella muelleri,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella",3379134|976|117743|200644|49546|1016|1017;3379134|1224|1236|2887326|468|475|479;3379134|1224|28216|206351|481|32257|504;3379134|1224|28216|206351|481|71|72;3379134|1224|28216|206351|481|71;3379134|1224|1236|2887326|468|475,Complete,Svetlana up
bsdb:37596536/28/1,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 28,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwisi,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups",8,7,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium",3379134|1224|1236|91347|543|544|1639133;3379134|1224|1236|91347|543|544|1896336;1783272|201174|1760|85009|31957|1743,Complete,Svetlana up
bsdb:37596536/28/2,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 28,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwisi,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups",8,7,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] brachy,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. (in: firmicutes)",1783272|1239|91061|186826|186827|46123;1783272|1239|91061|186826|186827|46123|76631;1783272|1239|91061|1385|186817|1386;3379134|976|117743|200644|49546|1016|1017;3379134|1224|1236|91347|543|544|546;1783272|1239|186801|3082720|186804|1870884;1783272|1239|186801|3082720|186804|1870884|1496;1783272|201174|1760|85007|1653|1716|1720;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|561|562;1783272|1239|91061|1385|539738|1378|1379;1783272|1239|91061|1385|539738|1378|84135;3379134|1224|1236|135625|712|724|735;1783272|1239|186801|3082720|543314|35517;1783272|1239|91061|1385|186817|1386|1409,Complete,Svetlana up
bsdb:37596536/29/1,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 29,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Socioeconomic status,EXO:0000114,Pastoralists,Foragers,"They are the !Xun group from Kunene Province, Angola, they traditionally rely on hunting and gathering for subsistence in an area characterized by open savanna woodland.",21,7,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 6 and 7,26 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between subsistence patterns according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first subsistence method of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia|s__Eggerthia catenaformis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia",3379134|1224|1236|91347|543|544|133448;1783272|201174|1760|85004|31953|1678|1685;1783272|1239|526524|526525|2810280|1279384|31973;3379134|1224|1236|91347|543|547|42895;1783272|1239|526524|526525|2810280|1279384,Complete,Svetlana up
bsdb:37596536/29/2,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 29,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Socioeconomic status,EXO:0000114,Pastoralists,Foragers,"They are the !Xun group from Kunene Province, Angola, they traditionally rely on hunting and gathering for subsistence in an area characterized by open savanna woodland.",21,7,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 6 and 7,26 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between subsistence patterns according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first subsistence method of the comparison, and negative values represent taxa enriched in the second one.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. (in: high G+C Gram-positive bacteria),k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. (in: firmicutes),k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia georgiae",1783272|1239|91061|186826|186827|46123;1783272|1239|91061|186826|186827|46123|46125;1783272|1239|91061|186826|186827|46123|76631;1783272|1239|91061|1385|186817|1386;3379134|1224|1236|91347|543|158483|158484;1783272|201174|1760|85006|1268|32207|1885016;3379134|1224|1236|91347|543|544|546;1783272|1239|186801|3082720|186804|1870884;1783272|1239|186801|3082720|186804|1870884|1496;1783272|201174|1760|85007|1653|1716|1720;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|81852|1350|35783;1783272|1239|91061|1385|539738|1378|84135;1783272|1239|91061|186826|186828|117563|2049028;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|1385|186817|1386|1409;33090|35493|3398|72025|3803|3814|508215;1783272|201174|1760|2037|2049|2529408|52768,Complete,Svetlana up
bsdb:37596536/30/1,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 30,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Socioeconomic status,EXO:0000114,Pastoralists,Peripatetics,"Includes the Twa, Tjimba, Kwisi, and Kwepe in southwestern Angola, these groups have a mobile lifestyle without a fixed settlement. They inhabit coastal lowlands and may have mixed livelihoods, combining aspects of both pastoralism and foraging.",21,24,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 6 and 7,26 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between subsistence patterns according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first subsistence method of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cancerogenus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia|s__Eggerthia catenaformis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Weeksella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus|s__Proteus sp. (in: enterobacteria),k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella michiganensis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii",3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|590;3379134|1224|1236|91347|1903412|568|1873498;3379134|1224|1236|91347|1903412|568;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|547|42895;3379134|1224|1236|91347|543|547|158836;3379134|1224|1236|91347|543|547|69218;3379134|1224|1236|72274|135621|286;3379134|1224|1236|72274|135621|286|306;1783272|1239|526524|526525|2810280|1279384;1783272|1239|526524|526525|2810280|1279384|31973;3379134|976|117743|200644|2762318|1013;3379134|976|200643;1783272|1239|186801|3082720|186804;3379134|1224|1236|91347|1903414|583;3379134|1224|1236|91347|1903414|583|229037;3379134|1224|1236|91347|543|544|133448;3379134|1224|1236|91347|543|544|546;3379134|1224|1236|91347|543|544|1639133;3379134|1224|1236|91347|543|570|571;3379134|1224|1236|91347|543|570|573;3379134|1224|1236|91347|543|570|576;3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|543|590|599;3379134|1224|1236|91347|543|570|1134687;3384189|32066|203490|203491|1129771|32067|157688;1783272|201174|1760|85007|1653|1716|43768,Complete,Svetlana up
bsdb:37596536/30/2,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 30,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Socioeconomic status,EXO:0000114,Pastoralists,Peripatetics,"Includes the Twa, Tjimba, Kwisi, and Kwepe in southwestern Angola, these groups have a mobile lifestyle without a fixed settlement. They inhabit coastal lowlands and may have mixed livelihoods, combining aspects of both pastoralism and foraging.",21,24,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 6 and 7,26 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between subsistence patterns according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first subsistence method of the comparison, and negative values represent taxa enriched in the second one.",decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",1783272|1239|526524|526525|128827|123375;1783272|1239|186801|3085636|186803|1164882;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|171552|577309,Complete,Svetlana up
bsdb:37596536/31/1,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 31,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Socioeconomic status,EXO:0000114,Peripatetics,Foragers,"They are represented by the !Xun group from Kunene Province, Angola, they traditionally rely on hunting and gathering for subsistence in an area characterized by open savanna woodland.",24,7,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 6 and 7,26 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between subsistence patterns according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first subsistence method of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve",1783272|201174|1760|85009|31957|1743;1783272|201174|1760|85004|31953|1678|1685,Complete,Svetlana up
bsdb:37596536/31/2,37596536,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V., Fehn A.M., Phiri A., Wills J., Rocha J. , Gayà-Vidal M.",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 31,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Socioeconomic status,EXO:0000114,Peripatetics,Foragers,"They are represented by the !Xun group from Kunene Province, Angola, they traditionally rely on hunting and gathering for subsistence in an area characterized by open savanna woodland.",24,7,NA,16S,12,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 6 and 7,29 March 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance (FDR adjusted p_value <0.05) between subsistence methods according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first subsistence method of the comparison, and negative values represent taxa enriched in the second one.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. (in: firmicutes),k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cancerogenus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella michiganensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] brachy,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia georgiae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. (in: high G+C Gram-positive bacteria)",1783272|1239|91061|186826|186827|46123;1783272|1239|91061|186826|186827|46123|46125;1783272|1239|91061|186826|186827|46123|76631;1783272|1239|91061|1385|186817|1386;1783272|1239|91061|1385|186817|1386|1409;3379134|1224|1236|91347|543|158483|158484;3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543|544|546;3379134|1224|1236|91347|543|544|545;1783272|1239|186801|3082720|186804|1870884;1783272|1239|186801|3082720|186804|1870884|1496;1783272|201174|1760|85007|1653|1716|1720;3379134|1224|1236|91347|543|547|69218;3379134|1224|1236|91347|543|547|158836;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|81852|1350|35783;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|561|562;1783272|1239|91061|1385|539738|1378|1379;1783272|1239|91061|1385|539738|1378|84135;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|543|570|1134687;3379134|1224|1236|91347|543|570|571;3379134|1224|1236|91347|543|570|573;3379134|1224|1236|91347|543|570|576;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|80840|119060|47670|47671;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|43675;3379134|1224|1236|91347|543|590;3379134|1224|1236|91347|543|590|599;1783272|1239|186801|3082720|543314|35517;1783272|201174|1760|2037|2049|2529408|52768;1783272|201174|1760|85006|1268|32207|1885016,Complete,Svetlana up
bsdb:37597851/1/1,37597851,case-control,37597851,10.1136/jitc-2023-007420,NA,"Li J., Guo Y., Liu J., Guo F., Du L., Yang Y., Li X. , Ma Y.",Depicting the landscape of gut microbial-metabolic interaction and microbial-host immune heterogeneity in deficient and proficient DNA mismatch repair colorectal cancers,Journal for immunotherapy of cancer,2023,gastrointestinal neoplasms,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Mismatch repair cancer syndrome,MONDO:0031219,proficient DNA mismatch repair (pMMR) CRC,deficient DNA mismatch repair (dMMR) CRC,dMMR in colorectal cancer (CRC) characterized by robust immune environment,207,21,NA,WMS,NA,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,increased,NA,NA,NA,NA,Signature 1,"Table S2, Figure 2c",16 October 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential microbial abundance between deficient DNA mismatch repair (dMMR) and proficient DNA mismatch repair (pMMR) in CRC,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter|s__Achromobacter sp. AONIH1,k__Pseudomonadati|p__Pseudomonadota|c__Acidithiobacillia|o__Acidithiobacillales|f__Acidithiobacillaceae|g__Acidithiobacillus|s__Acidithiobacillus ferrivorans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax|s__Acidovorax sp. RAC01,s__Actinoalloteichus hoggarensis,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Aminobacter|s__Aminobacter aminovorans,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Aminobacter|s__Aminobacter sp. MSH1,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Amycolatopsis|s__Amycolatopsis albispora,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum propionicum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Aquitalea|s__Aquitalea sp. USM4,g__Arcticibacterium|s__Arcticibacterium luteifluviistationis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Azoarcus|s__Azoarcus sp. DN11,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Azoarcus|s__Azoarcus sp. KH32C,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Rhodocyclaceae|g__Azospira|s__Azospira oryzae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum|s__Azospirillum brasilense,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum|s__Azospirillum sp. TSH100,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum|s__Azospirillum thermophilum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus velezensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium CF,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella viscericola,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium angulatum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Bordetella|s__Bordetella genomosp. 8,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium diazoefficiens,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium erythrophlei,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium guangdongense,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium lablabi,s__Trinickia violacea,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia stabilis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia thailandensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium JOSHI_001,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|g__Candidatus Azobacteroides|s__Candidatus Azobacteroides pseudotrichonymphae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Candidatus Desulfovibrio trichonymphae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga haemolytica,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter|s__Caulobacter flavus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Cereibacter|s__Cereibacter sphaeroides,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Christiangramia|s__Christiangramia fulva,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Chromobacterium|s__Chromobacterium violaceum,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium shandongense,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium sp. 6424,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Collimonas|s__Collimonas pratensis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Coriobacterium|s__Coriobacterium glomerans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium jeikeium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Croceicoccus|s__Croceicoccus naphthovorans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus|s__Cupriavidus metallidurans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus|s__Cupriavidus necator,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus|s__Cupriavidus taiwanensis,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus actinosclerus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales|f__Desulfatibacillaceae|g__Desulfatibacillum|s__Desulfatibacillum aliphaticivorans,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus|s__Desulfobulbus oralis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales|g__Desulfococcus|s__Desulfococcus multivorans,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfocurvibacter|s__Desulfocurvibacter africanus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfomicrobiaceae|g__Desulfomicrobium|s__Desulfomicrobium baculatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfotomaculaceae|g__Desulfotomaculum|s__Desulfotomaculum nigrificans,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio desulfuricans,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio sp. G11,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Nitratidesulfovibrio|s__Nitratidesulfovibrio vulgaris,s__Devosia sp. A16,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Dickeya|s__Dickeya chrysanthemi,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Dickeya|s__Dickeya fangzhongdai,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Spirosomataceae|g__Dyadobacter|s__Dyadobacter fermentans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Elizabethkingia|s__Elizabethkingia miricola,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Ensifer|s__Ensifer adhaerens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter asburiae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter bugandensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae complex sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus gilvus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Erythrobacter|s__Erythrobacter litoralis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Ferrimonadaceae|g__Ferrimonas|s__Ferrimonas balearica,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Crocinitomicaceae|g__Fluviicola|s__Fluviicola taffensis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Frigidibacter|s__Frigidibacter mobilis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Desulfuromonadales|f__Geoalkalibacteraceae|s__Geoalkalibacter subterraneus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Geobacterales|f__Geobacteraceae|g__Geobacter|s__Geobacter sp. M18,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Geobacterales|f__Geobacteraceae|g__Geobacter|s__Geobacter sp. M21,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Geobacterales|f__Geobacteraceae|g__Geobacter|s__Geobacter sulfurreducens,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Geobacterales|f__Geobacteraceae|g__Geotalea|s__Geotalea daltonii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Gluconobacter|s__Gluconobacter oxydans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia|s__Gordonia sp. YC-JH1,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter massiliensis (ex Traore et al. 2017),k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter urolithinfaciens,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Halobacillus|s__Halobacillus halophilus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter pylori,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella enoeca,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter|s__Hymenobacter psoromatis,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter|s__Hymenobacter radiodurans,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter|s__Hymenobacter sedentarius,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter|s__Hymenobacter sp. APR13,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter|s__Hymenobacter sp. DG25A,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter|s__Hymenobacter sp. DG25B,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Immundisolibacterales|f__Immundisolibacteraceae|g__Immundisolibacter|s__Immundisolibacter cernigliae,k__Pseudomonadati|p__Kiritimatiellota|c__Kiritimatiellia|o__Kiritimatiellales|f__Kiritimatiellaceae|g__Kiritimatiella|s__Kiritimatiella glycovorans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Kitasatospora|s__Kitasatospora sp. MMS16-BH015,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus|s__Lactiplantibacillus pentosus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae|g__Magnetospirillum|s__Magnetospirillum gryphiswaldense,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Magnetospirillaceae|g__Paramagnetospirillum|s__Paramagnetospirillum magneticum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Marinobacteraceae|g__Marinobacter|s__Marinobacter nauticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae|g__Marinobacterium|s__Marinobacterium aestuarii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Aurantimonadaceae|g__Martelella|s__Martelella endophytica,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia|s__Massilia oculi,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia|s__Massilia sp. YMA4,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia|s__Massilia violaceinigra,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Megalodesulfovibrio|s__Megalodesulfovibrio gigas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium|s__Mesorhizobium ciceri,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium|s__Mesorhizobium loti,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium|s__Mesorhizobium sp. Pch-S,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Microvirga|s__Microvirga sp. 17 mud 1-3,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Aquaspirillaceae|g__Microvirgula|s__Microvirgula aerodenitrificans,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Mucilaginibacter|s__Mucilaginibacter sp. PAMC 26640,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum|s__Muribaculum intestinale,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria animaloris,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria meningitidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Neobacillus|s__Neobacillus mesonae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Streptosporangiales|f__Nocardiopsidaceae|g__Nocardiopsis|s__Nocardiopsis dassonvillei,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium|s__Novosphingobium resinovorum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Oleidesulfovibrio|s__Oleidesulfovibrio alaskensis,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae|s__Opitutaceae bacterium TAV5,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus chitinolyticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus ihbetae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus kribbensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus larvae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus lutimineralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus polymyxa,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus sp. CAA11,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Isosphaerales|f__Isosphaeraceae|g__Paludisphaera|s__Paludisphaera borealis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Pandoraea|s__Pandoraea oxalativorans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Pandoraea|s__Pandoraea sp. XY-2,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Pantoea agglomerans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Pantoea vagans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia terrae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia xenovorans,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Parvibaculaceae|g__Parvibaculum|s__Parvibaculum lavamentivorans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles|s__Paucibacter sp. KCTC 42545,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Pectobacterium|s__Pectobacterium carotovorum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Desulfuromonadales|f__Desulfuromonadaceae|g__Pelobacter|s__Pelobacter propionicus,k__Pseudomonadati|p__Chlorobiota|c__Chlorobiia|o__Chlorobiales|f__Chlorobiaceae|g__Pelodictyon|s__Pelodictyon luteolum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Aedoeadaptatus|s__Aedoeadaptatus ivorii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Phaeobacter|s__Phaeobacter gallaeciensis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phreatobacteraceae|g__Phreatobacter|s__Phreatobacter cathodiphilus,s__Pigmentiphaga sp. H8,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Planctomycetales|f__Planctomycetaceae|g__Planctomyces|s__Planctomyces sp. SH-PL62,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas cangingivalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas crevioricanis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella dentalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Pseudodesulfovibrio|s__Pseudodesulfovibrio aespoeensis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Pseudodesulfovibrio|s__Pseudodesulfovibrio profundus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Pseudoduganella|s__Pseudoduganella armeniaca,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas brassicacearum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas entomophila,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas fluorescens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas knackmussii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas oryzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas protegens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. LTJR-52,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium|s__Rhizobium etli,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium|s__Rhizobium jaguaris,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|g__Rhodobacter|s__Rhodobacter xanthinilyticus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Rhodopseudomonas|s__Rhodopseudomonas palustris,k__Pseudomonadati|p__Rhodothermota|c__Rhodothermia|o__Rhodothermales|f__Rhodothermaceae|s__Rhodothermaceae bacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Rufibacter|s__Rufibacter radiotolerans,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Spirosomataceae|g__Runella|s__Runella rosea,k__Pseudomonadati|p__Rhodothermota|c__Rhodothermia|o__Rhodothermales|f__Salinibacteraceae|g__Salinibacter|s__Salinibacter ruber,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Salipiger|s__Salipiger profundus,k__Pseudomonadati|p__Myxococcota|o__Polyangiales|f__Sandaracinaceae|g__Sandaracinus|s__Sandaracinus amylolyticus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia fonticola,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia marcescens,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Sinorhizobium|s__Sinorhizobium fredii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Sinorhizobium|s__Sinorhizobium meliloti,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Sinorhizobium|s__Sinorhizobium sp. RAC02,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Sphaerochaetaceae|g__Sphaerochaeta|s__Sphaerochaeta globosa,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium|s__Sphingobium baderi,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta|s__Spirochaeta africana,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae|g__Spirosoma|s__Spirosoma pollinicola,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae|g__Spirosoma|s__Spirosoma radiotolerans,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Thermoactinomycetaceae|g__Staphylospora|s__Staphylospora marina,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus equi,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus intermedius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus lutetiensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces bingchenggensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces cadmiisoli,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces dengpaensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces olivoreticuli,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces sp. endophyte_N2,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Stutzerimonas|s__Stutzerimonas stutzeri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiohalomonadales|f__Thiohalomonadaceae|g__Sulfurivermis|s__Sulfurivermis fontis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Syntrophobacteria|o__Syntrophobacterales|f__Syntrophobacteraceae|g__Syntrophobacter|s__Syntrophobacter fumaroxidans,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Desulfuromonadales|f__Syntrophotaleaceae|g__Syntrophotalea|s__Syntrophotalea acetylenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella serpentiformis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Thauera|s__Thauera humireducens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|g__Thiobacillus|s__Thiobacillus denitrificans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Thiomonas|s__Thiomonas intermedia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Geminicoccales|f__Geminicoccaceae|g__Tistrella|s__Tistrella mobilis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae|g__Tumebacillus|s__Tumebacillus avium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sp. H121,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax|s__Variovorax sp. HW608,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax|s__Variovorax sp. PMC12,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|s__Victivallales bacterium CCUG 44730,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae|g__Xanthobacter|s__Xanthobacter autotrophicus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas|s__Xanthomonas translucens",3379134|1224|28216|80840|506|222|1758194;3379134|1224|1807140|225057|225058|119977|160808;3379134|1224|28216|80840|80864|12916|1842533;1470176;3379134|74201|203494|48461|1647988|239934|239935;3379134|1224|28211|356|69277|31988|83263;3379134|1224|28211|356|69277|31988|374606;1783272|201174|1760|85010|2070|1813|1804986;1783272|1239|186801|3085636|3118652|2039240|28446;3379134|1224|28216|206351|1499392|407217|1590041;2173039|1784714;3379134|1224|28216|206389|2008794|12960|356837;3379134|1224|28216|206389|2008794|12960|748247;3379134|1224|28216|206389|75787|146937|146939;3379134|1224|28211|204441|2829815|191|192;3379134|1224|28211|204441|2829815|191|652764;3379134|1224|28211|204441|2829815|191|2202148;1783272|1239|91061|1385|186817|1386|492670;3379134|976|200643|171549|1400053;3379134|976|200643|171549|2005519|397864|397865;1783272|201174|1760|85004|31953|1678|1683;3379134|1224|28216|80840|506|517|1416806;3379134|1224|28211|356|41294|374|1355477;3379134|1224|28211|356|41294|374|1437360;3379134|1224|28211|356|41294|374|1325090;3379134|1224|28211|356|41294|374|722472;2571746;3379134|1224|28216|80840|119060|32008|95485;3379134|1224|28216|80840|119060|32008|57975;3379134|1224|28216|80840|864051;3379134|976|200643|171549|511434|511435;3379134|200940|3031449|213115|194924|872|1725232;3379134|976|117743|200644|49546|1016|45243;3379134|1224|28211|204458|76892|75|1679497;3379134|1224|28211|204455|31989|1653176|1063;3379134|976|117743|200644|49546|292691|2126553;3379134|1224|28216|206351|1499392|535|536;3379134|976|117743|200644|2762318|59732|1493872;3379134|976|117743|200644|2762318|59732|2039166;3379134|1224|28216|80840|75682|202907|279113;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|84998|84999|84107|33870|33871;1783272|201174|1760|85007|1653|1716|38289;3379134|1224|28211|204457|335929|1295327|1348774;3379134|1224|28216|80840|119060|106589|119219;3379134|1224|28216|80840|119060|106589|106590;3379134|1224|28216|80840|119060|106589|164546;3384194|1297|188787|118964|183710|1298|1768108;3379134|200940|3024418|213118|3031627|218207|218208;3379134|200940|3031451|3024411|213121|893|1986146;3379134|200940|3024418|213118|896|897;3379134|200940|3031449|213115|194924|2582840|873;3379134|200940|3031449|213115|213116|898|899;1783272|1239|186801|186802|2937910|1562|1565;3379134|200940|3031449|213115|194924|872|876;3379134|200940|3031449|213115|194924|872|631220;3379134|200940|3031449|213115|194924|2802295|881;1736675;3379134|1224|1236|91347|1903410|204037|556;3379134|1224|1236|91347|1903410|204037|1778540;3379134|976|768503|768507|2896860|120831|94254;3379134|1224|28216|206351|481|538|539;3379134|976|117743|200644|2762318|308865|172045;3379134|1224|28211|356|82115|106591|106592;3379134|1224|1236|91347|543|547|61645;3379134|1224|1236|91347|543|547|881260;3379134|1224|1236|91347|543|547|2027919;3379134|1224|1236|91347|543|547|158836;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|91061|186826|81852|1350|160453;3379134|1224|28211|204457|335929|1041|39960;3379134|1224|1236|135622|267892|44011|44012;1783272|1239|186801|3082720|3118655|44259|143361;3379134|976|117743|200644|1853230|332102|191579;3379134|1224|28211|204455|31989|1775705|1335048;3384189|32066|203490|203491|203492|848|851;3379134|200940|3031651|69541|3031665|483547;3379134|200940|3031651|3031668|213422|28231|443143;3379134|200940|3031651|3031668|213422|28231|443144;3379134|200940|3031651|3031668|213422|28231|35554;3379134|200940|3031651|3031668|213422|2910589|1203471;3379134|1224|28211|3120395|433|441|442;1783272|201174|1760|85007|85026|2053|2059875;1783272|201174|84998|1643822|1643826|644652|1841863;1783272|201174|84998|1643822|1643826|644652|471189;1783272|201174|84998|1643822|1643826|644652|1335613;1783272|1239|91061|1385|186817|45667|1570;3379134|29547|3031852|213849|72293|209|210;3379134|976|200643|171549|171552|2974257|76123;3379134|976|768503|768507|1853232|89966|1484116;3379134|976|768503|768507|1853232|89966|2496028;3379134|976|768503|768507|1853232|89966|1411621;3379134|976|768503|768507|1853232|89966|1356852;3379134|976|768503|768507|1853232|89966|1385663;3379134|976|768503|768507|1853232|89966|1385664;3379134|1224|1236|1934945|1934946|1934947|1810504;3379134|134625|1921781|1921782|1921783|1921784|1307763;1783272|201174|1760|85011|2062|2063|2018025;1783272|1239|91061|186826|33958|2767842|1589;3379134|1224|28216|80840|119060|47670|47671;3379134|1224|28211|204441|41295|13134|55518;3379134|1224|28211|204441|3036766|3031148|84159;3379134|1224|1236|72274|2887365|2742|2743;3379134|1224|1236|135619|135620|48075|1821621;3379134|1224|28211|356|255475|293088|1486262;3379134|1224|28216|80840|75682|149698|945844;3379134|1224|28216|80840|75682|149698|1593482;3379134|1224|28216|80840|75682|149698|2045208;3379134|200940|3031449|213115|194924|2910978|879;3379134|1224|28211|356|69277|68287|39645;3379134|1224|28211|356|69277|68287|381;3379134|1224|28211|356|69277|68287|2082387;3379134|1224|28211|356|119045|186650|2082949;3379134|1224|28216|206351|2897176|57479|57480;3379134|976|117747|200666|84566|423349|1300914;3379134|976|200643|171549|2005473|1918540|1796646;3379134|1224|28216|206351|481|482|326522;3379134|1224|28216|206351|481|482|487;1783272|1239|91061|1385|186817|2675232|1193713;1783272|201174|1760|85012|83676|2013|2014;3379134|1224|28211|204457|41297|165696|158500;3379134|976|200643|171549|1853231|283168|28118;3379134|200940|3031449|213115|194924|2909705|58180;3379134|74201|414999|415000|134623|794903;1783272|1239|91061|1385|186822|44249|79263;1783272|1239|91061|1385|186822|44249|1870820;1783272|1239|91061|1385|186822|44249|172713;1783272|1239|91061|1385|186822|44249|1464;1783272|1239|91061|1385|186822|44249|2707005;1783272|1239|91061|1385|186822|44249|1406;1783272|1239|91061|1385|186822|44249|1532905;3379134|203682|203683|2691356|1763524|1763521|1387353;3379134|1224|28216|80840|119060|93217|573737;3379134|1224|28216|80840|119060|93217|2518599;3379134|1224|1236|91347|1903409|53335|549;3379134|1224|1236|91347|1903409|53335|470934;3379134|1224|28216|80840|119060|1822464|311230;3379134|1224|28216|80840|119060|1822464|36873;3379134|1224|28211|356|2813035|256616|256618;3379134|1224|28216|80840|2975441|93681|1768242;3379134|1224|1236|91347|1903410|122277|554;3379134|200940|3031651|69541|213421|18|29543;3379134|1090|191410|191411|191412|1099|1100;1783272|1239|1737404|1737405|1570339|2981628|54006;3379134|1224|28211|204455|2854170|302485|60890;3379134|1224|28211|356|2843305|1632780|1868589;2488560;3379134|203682|203683|112|126|118|1636152;3379134|976|200643|171549|171551|836|36874;3379134|976|200643|171549|171551|836|393921;3379134|976|200643|171549|171552|838|52227;3379134|976|200643|171549|171552|838|28131;3379134|200940|3031449|213115|194924|2035811|182210;3379134|200940|3031449|213115|194924|2035811|57320;3379134|1224|28216|80840|75682|1522432|2072590;3379134|1224|1236|72274|135621|286|930166;3379134|1224|1236|72274|135621|286|312306;3379134|1224|1236|72274|135621|286|294;3379134|1224|1236|72274|135621|286|65741;3379134|1224|1236|72274|135621|286|1392877;3379134|1224|1236|72274|135621|286|380021;3379134|1224|1236|72274|135621|286|2479392;3379134|1224|28211|356|82115|379|29449;3379134|1224|28211|356|82115|379|1312183;3379134|1224|28211|204455|1060|1850250;3379134|1224|28211|356|41294|1073|1076;3379134|1853220|1853222|1853224|563843|2026787;1783272|201174|1760|85006|1268|32207|2047;3379134|976|768503|768507|1853232|1379908|1379910;3379134|976|768503|768507|2896860|105|2259595;3379134|1853220|1853222|1853224|1853225|146918|146919;3379134|1224|28211|204455|2854170|263377|1229727;3379134|2818505|3031712|1055686|1055688|927083;1783272|1239|909932|909929|1843491|970|69823;3379134|1224|1236|91347|1903411|613|47917;3379134|1224|1236|91347|1903411|613|615;3379134|1224|28211|356|82115|28105|380;3379134|1224|28211|356|82115|28105|382;3379134|1224|28211|356|82115|28105|1842534;3379134|203691|203692|136|2791015|399320|1131703;3379134|1224|28211|204457|3423717|165695|1332080;3379134|203691|203692|136|137|146|46355;3379134|976|768503|768507|89373|107|2057025;3379134|976|768503|768507|89373|107|1379870;1783272|1239|91061|1385|186824|2689589|2490858;1783272|1239|91061|186826|1300|1301|1336;1783272|1239|91061|186826|1300|1301|1338;1783272|1239|91061|186826|1300|1301|150055;1783272|1239|91061|186826|1300|1301|1305;1783272|201174|1760|85011|2062|1883|379067;1783272|201174|1760|85011|2062|1883|2184053;1783272|201174|1760|85011|2062|1883|2049881;1783272|201174|1760|85011|2062|1883|68246;1783272|201174|1760|85011|2062|1883|2153485;3379134|1224|1236|72274|135621|2901164|316;3379134|1224|1236|3084968|3084969|2034504|1972068;3379134|200940|3024408|213462|213465|29526|119484;3379134|200940|3031651|69541|2812024|2812025|29542;3379134|976|200643|171549|2005525|195950|712710;3379134|1224|28216|206389|2008794|33057|1134435;3379134|1224|28216|32003|919|36861;3379134|1224|28216|80840|32012|926;3379134|1224|28211|3108222|2066434|171436|171437;1783272|1239|91061|1385|186823|432330|1903704;1783272|1239|526524|526525|2810281|191303|1712675;3379134|1224|28216|80840|80864|34072|1034889;3379134|1224|28216|80840|80864|34072|2126319;3379134|256845|1313211|278082|2094242;3379134|1224|28211|356|335928|279|280;3379134|1224|1236|135614|32033|338|343,Complete,Folakunmi
bsdb:37597851/1/2,37597851,case-control,37597851,10.1136/jitc-2023-007420,NA,"Li J., Guo Y., Liu J., Guo F., Du L., Yang Y., Li X. , Ma Y.",Depicting the landscape of gut microbial-metabolic interaction and microbial-host immune heterogeneity in deficient and proficient DNA mismatch repair colorectal cancers,Journal for immunotherapy of cancer,2023,gastrointestinal neoplasms,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Mismatch repair cancer syndrome,MONDO:0031219,proficient DNA mismatch repair (pMMR) CRC,deficient DNA mismatch repair (dMMR) CRC,dMMR in colorectal cancer (CRC) characterized by robust immune environment,207,21,NA,WMS,NA,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,increased,NA,NA,NA,NA,Signature 2,Table S2,16 October 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential microbial abundance between deficient DNA mismatch repair (dMMR) and proficient DNA mismatch repair (pMMR) in CRC,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans",1783272|1239|186801|186802|216572|946234|292800;1783272|1239|91061|1385|539738|1378|1379,Complete,Folakunmi
bsdb:37597851/2/1,37597851,case-control,37597851,10.1136/jitc-2023-007420,NA,"Li J., Guo Y., Liu J., Guo F., Du L., Yang Y., Li X. , Ma Y.",Depicting the landscape of gut microbial-metabolic interaction and microbial-host immune heterogeneity in deficient and proficient DNA mismatch repair colorectal cancers,Journal for immunotherapy of cancer,2023,gastrointestinal neoplasms,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls (CTRL),deficient DNA mismatch repair (dMMR) CRC,dMMR in colorectal cancer (CRC) characterized by robust immune environment,227,21,NA,WMS,NA,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2c,16 October 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential microbial abundance between deficient DNA mismatch repair (dMMR) in CRC and healthy controls (CTRL),increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus velezensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella viscericola,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio desulfuricans,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella enoeca,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum|s__Muribaculum intestinale,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas cangingivalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia",1783272|1239|91061|1385|186817|1386|492670;3379134|976|200643|171549|2005519|397864|397865;3379134|200940|3031449|213115|194924|872|876;3384189|32066|203490|203491|203492|848|851;3379134|976|200643|171549|171552|2974257|76123;3379134|976|200643|171549|2005473|1918540|1796646;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|171551|836|36874;3379134|976|200643|171549|171552|838|28131,Complete,Folakunmi
bsdb:37597851/3/1,37597851,case-control,37597851,10.1136/jitc-2023-007420,NA,"Li J., Guo Y., Liu J., Guo F., Du L., Yang Y., Li X. , Ma Y.",Depicting the landscape of gut microbial-metabolic interaction and microbial-host immune heterogeneity in deficient and proficient DNA mismatch repair colorectal cancers,Journal for immunotherapy of cancer,2023,gastrointestinal neoplasms,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls (CTRL),proficient DNA mismatch repair (pMMR) CRC,pMMR in colorectal cancer (CRC) characterized by immunosuppressive tumor microenvironment,227,207,NA,WMS,NA,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,decreased,NA,NA,NA,NA,Signature 1,Figure 2c,16 October 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential microbial abundance between proficient DNA mismatch repair (pMMR) in CRC and healthy controls (CTRL),increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,1783272|1239|186801|186802|216572|946234|292800,Complete,Folakunmi
bsdb:37597851/3/2,37597851,case-control,37597851,10.1136/jitc-2023-007420,NA,"Li J., Guo Y., Liu J., Guo F., Du L., Yang Y., Li X. , Ma Y.",Depicting the landscape of gut microbial-metabolic interaction and microbial-host immune heterogeneity in deficient and proficient DNA mismatch repair colorectal cancers,Journal for immunotherapy of cancer,2023,gastrointestinal neoplasms,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls (CTRL),proficient DNA mismatch repair (pMMR) CRC,pMMR in colorectal cancer (CRC) characterized by immunosuppressive tumor microenvironment,227,207,NA,WMS,NA,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,decreased,NA,NA,NA,NA,Signature 2,Figure 2c,16 October 2023,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential microbial abundance between proficient DNA mismatch repair (pMMR) in CRC and healthy controls (CTRL),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum propionicum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae",1783272|1239|186801|3085636|3118652|2039240|28446;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|84998|1643822|1643826|644652|471189,Complete,Folakunmi
bsdb:37602324/1/1,37602324,meta-analysis,37602324,https://doi.org/10.3389/fmolb.2023.1210225,NA,"Suryavanshi M., Agudelo J. , Miller A.","Rare phylotypes in stone, stool, and urine microbiomes are associated with urinary stone disease",Frontiers in molecular biosciences,2023,"human microbiome, kidney stones, rare phylotype, reference database, urinary stone disease, urobiome, urology",Experiment 1,NA,Homo sapiens,Feces,UBERON:0001988,Urolithiasis,MONDO:0024647,healthy controls,urinary stone disease patients,patients with urinary stone disease,136,201,NA,NA,NA,NA,raw counts,DESeq2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,21 October 2023,Joju,"Joju,Iram jamshed,MyleeeA,WikiWorks",Bubble plot showing the fold change of differentially abundant common rare (B) taxa associated with health disparities (control and USD phenotypes) in stool samples. Selection of taxa is defined using DESeq2 differential abundance analysis with a false discovery rate-corrected p-value <0.05. Taxa are listed as the number of ASVs within the lowest assigned taxonomy as a means to elucidate the most important taxa associated with USD.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549|171550|239759;1783272|1239|909932|1843489|31977|209879;3379134|976|200643|171549|171552|1283313;1783272|1239|186801|186802|216572|244127;1783272|1239;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|1853231|574697;1783272|1239|526524|526525|2810280|135858;1783272|1239|186801;1783272|1239|186801|186802|1898207;1783272|1239|186801|186802|1980681;1783272|201174|84998|84999|84107|102106;3379134|976|200643|171549|2005519|1348911;1783272|201174|84998|84999;1783272|201174|1760|85007|1653|1716;3379134|200940|3031449|213115|194924|872;1783272|1239|909932|1843489|31977|39948;1783272|1239|526524|526525|128827;3384189|32066|203490|203491|203492|848;1783272|1239|186801|186802|216572|596767;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|248744;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|909929|1843491|52225;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|3085656|3085657|2039302;3379134|976|200643|171549|2005473;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300|1301;3379134|1224|28216|80840|995019|40544;3379134|203691|203692|136|2845253|157;1783272|1239|526524|526525|2810281|191303;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|216572,Complete,Peace Sandy
bsdb:37602324/2/1,37602324,meta-analysis,37602324,https://doi.org/10.3389/fmolb.2023.1210225,NA,"Suryavanshi M., Agudelo J. , Miller A.","Rare phylotypes in stone, stool, and urine microbiomes are associated with urinary stone disease",Frontiers in molecular biosciences,2023,"human microbiome, kidney stones, rare phylotype, reference database, urinary stone disease, urobiome, urology",Experiment 2,NA,Homo sapiens,Urine,UBERON:0001088,Urolithiasis,MONDO:0024647,healthy controls,urinary stone disease patients,patients with urinary stone disease,136,201,NA,NA,NA,NA,raw counts,DESeq2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7,30 October 2023,Joju,"Joju,WikiWorks",Bubble plot showing the fold change of differentially abundant rare (B) taxa associated with health disparities (control and USD phenotypes) in urine samples.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacillati|p__Bacillota|c__Clostridia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Elizabethkingia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Helcococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Tolumonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Undibacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Crocinitomicaceae|g__Fluviicola,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Chujaibacter,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia",3379134|1224|1236|2887326|468|469;1783272|201174|1760|2037|2049|1654;1783272|1239|1737404|1737405|1570339|165779;1783272|201174|84998|84999|1643824|1380;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;3379134|1224|28211|356|41294|374;1783272|201174|1760|85006|85019|1696;3379134|976|117743|200644|2762318|59732;1783272|1239|186801;3379134|1224|28216|80840|80864;1783272|201174|1760|85007|1653|1716;3379134|976|117743|200644|2762318|308865;1783272|1239|91061|186826|186827|66831;1783272|1239|186801|186802|216572|236752;3379134|976|117743|200644|49546|237;1783272|1239|186801|3085636|186803|1407607;3384189|32066|203490|203491|203492|848;1783272|1239|1737404|1737405|1570339|162290;1783272|1239|1737404|1737405|1570339|31983;1783272|201174|1760|85006|1268|57493;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85007|2805586|1847725;3379134|1224|28211|356|119045|407;1783272|1239|1737404|1737405|1570339|1161127;1783272|201174|84998|84999|1643824|133925;1783272|1239|186801|186802|186807|2740;1783272|1239|1737404|1737405|1570339|162289;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3379134|1224|1236|72274|135621|286;1783272|1239|186801|186802|216572|1263;3379134|1224|28211|204457|41297|13687;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|292632;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|135624|84642|43947;3379134|1224|28216|80840|75682|401469;3379134|976|117743|200644|1853230|332102;3379134|1224|28216|80840|75682|149698;3379134|1224|1236|135614|32033|1931224;33090|35493|3398|72025|3803|3814|508215,Complete,Peace Sandy
bsdb:37604954/1/1,37604954,"cross-sectional observational, not case-control",37604954,https://doi.org/10.1038/s41598-023-40872-5,NA,"Fongang B., Satizabal C., Kautz T.F., Wadop Y.N., Muhammad J.A.S., Vasquez E., Mathews J., Gireud-Goss M., Saklad A.R., Himali J., Beiser A., Cavazos J.E., Mahaney M.C., Maestre G., DeCarli C., Shipp E.L., Vasan R.S. , Seshadri S.",Cerebral small vessel disease burden is associated with decreased abundance of gut Barnesiella intestinihominis bacterium in the Framingham Heart Study,Scientific reports,2023,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Cerebral small vessel disease,EFO:0008493,Lower burden (Healthy),High burden (Unhealthy),Participants with Cerebral small vessel disease that were tested using the PSMD marker,674,108,NA,16S,4,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,"age,body mass index,education level,sex,time",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Table S4, S5, S6",14 October 2023,Sinmisoluwa Adesanya,"Sinmisoluwa Adesanya,Chinelsy,Peace Sandy,Folakunmi,Welile,WikiWorks","Difference between the gut microbiome of patients with cSVD marker PSMD and the Lower burden (Healthy) group at phylum, genus and species rank",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira|s__Oscillospira guilliermondii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",1783272|1239|186801|3082768|990719|270497;1783272|1239|186801|186802|31979|1485|1960653;1783272|1239|186801|3085636|186803|2719313|358742;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572|119852|119853;1783272|1239|526524|526525|128827,Complete,Folakunmi
bsdb:37604954/1/2,37604954,"cross-sectional observational, not case-control",37604954,https://doi.org/10.1038/s41598-023-40872-5,NA,"Fongang B., Satizabal C., Kautz T.F., Wadop Y.N., Muhammad J.A.S., Vasquez E., Mathews J., Gireud-Goss M., Saklad A.R., Himali J., Beiser A., Cavazos J.E., Mahaney M.C., Maestre G., DeCarli C., Shipp E.L., Vasan R.S. , Seshadri S.",Cerebral small vessel disease burden is associated with decreased abundance of gut Barnesiella intestinihominis bacterium in the Framingham Heart Study,Scientific reports,2023,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Cerebral small vessel disease,EFO:0008493,Lower burden (Healthy),High burden (Unhealthy),Participants with Cerebral small vessel disease that were tested using the PSMD marker,674,108,NA,16S,4,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,"age,body mass index,education level,sex,time",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Table S4, S5, S6",14 October 2023,Sinmisoluwa Adesanya,"Sinmisoluwa Adesanya,Chinelsy,Peace Sandy,Folakunmi,WikiWorks","Difference between the gut microbiome of patients with cSVD marker PSMD and the Lower burden (Healthy) group at phylum, genus and species rank",decreased,"p__Candidatus Poribacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis",265317;1783272|1239|186801|186802|31979|1485;3366610|28890|183925|2158|2159|2172;3379134|256845|1313211|278082|255528|172900,Complete,Folakunmi
bsdb:37604954/2/1,37604954,"cross-sectional observational, not case-control",37604954,https://doi.org/10.1038/s41598-023-40872-5,NA,"Fongang B., Satizabal C., Kautz T.F., Wadop Y.N., Muhammad J.A.S., Vasquez E., Mathews J., Gireud-Goss M., Saklad A.R., Himali J., Beiser A., Cavazos J.E., Mahaney M.C., Maestre G., DeCarli C., Shipp E.L., Vasan R.S. , Seshadri S.",Cerebral small vessel disease burden is associated with decreased abundance of gut Barnesiella intestinihominis bacterium in the Framingham Heart Study,Scientific reports,2023,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Cerebral small vessel disease,EFO:0008493,Lower burden (Healthy),High burden (Unhealthy),Participants with Cerebral small vessel disease that were tested using the WMH marker,832,136,NA,16S,4,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,"age,body mass index,education level,sex,time",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Table S4, S5, S6",15 October 2023,Sinmisoluwa Adesanya,"Sinmisoluwa Adesanya,Chinelsy,Folakunmi,WikiWorks","Difference between the gut microbiome of patients with cSVD marker PSMD and the Lower burden (Healthy) group at phylum, genus and species rank",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Pseudomonadati|p__Pseudomonadota",1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|3085636|186803|2719313|358742;3379134|1224,Complete,Folakunmi
bsdb:37604954/2/2,37604954,"cross-sectional observational, not case-control",37604954,https://doi.org/10.1038/s41598-023-40872-5,NA,"Fongang B., Satizabal C., Kautz T.F., Wadop Y.N., Muhammad J.A.S., Vasquez E., Mathews J., Gireud-Goss M., Saklad A.R., Himali J., Beiser A., Cavazos J.E., Mahaney M.C., Maestre G., DeCarli C., Shipp E.L., Vasan R.S. , Seshadri S.",Cerebral small vessel disease burden is associated with decreased abundance of gut Barnesiella intestinihominis bacterium in the Framingham Heart Study,Scientific reports,2023,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Cerebral small vessel disease,EFO:0008493,Lower burden (Healthy),High burden (Unhealthy),Participants with Cerebral small vessel disease that were tested using the WMH marker,832,136,NA,16S,4,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,"age,body mass index,education level,sex,time",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Table S4, S5, S6",15 October 2023,Sinmisoluwa Adesanya,"Sinmisoluwa Adesanya,Chinelsy,Folakunmi,Welile,WikiWorks","Difference between the gut microbiome of patients with cSVD marker PSMD and the Lower burden (Healthy) group at phylum, genus and species rank",decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae|g__Anaerosinus,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,p__Candidatus Parcubacteria,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium mitsuokai,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnotalea|s__Lachnotalea glycerini,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",1783272|201174;1783272|1239|909932|909929|1843490|151037;1783272|1239;3379134|976|200643;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|2005519|397864|487174;221216;1783272|1239|526524|526525|2810280|135858;1783272|1239|526524|526525|2810280|135858|100886;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|31979|1485|1960653;1783272|1239|186801|3085636|186803|1763508|1763509;3366610|28890|183925|2158|2159|2172;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|2316020|46228;1783272|1239|526524|526525|128827,Complete,Folakunmi
bsdb:37604954/3/1,37604954,"cross-sectional observational, not case-control",37604954,https://doi.org/10.1038/s41598-023-40872-5,NA,"Fongang B., Satizabal C., Kautz T.F., Wadop Y.N., Muhammad J.A.S., Vasquez E., Mathews J., Gireud-Goss M., Saklad A.R., Himali J., Beiser A., Cavazos J.E., Mahaney M.C., Maestre G., DeCarli C., Shipp E.L., Vasan R.S. , Seshadri S.",Cerebral small vessel disease burden is associated with decreased abundance of gut Barnesiella intestinihominis bacterium in the Framingham Heart Study,Scientific reports,2023,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Cerebral small vessel disease,EFO:0008493,Lower burden (Healthy),High burden (Unhealthy),Participants with Cerebral small vessel disease that were tested using the EF marker,822,121,NA,16S,4,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,"age,body mass index,education level,sex,time",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Table S4, S5, S6",15 October 2023,Sinmisoluwa Adesanya,"Sinmisoluwa Adesanya,Chinelsy,Folakunmi,WikiWorks","Difference between the gut microbiome of patients with cSVD marker PSMD and the Lower burden (Healthy) group at phylum, genus and species rank",increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium ruminantium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster lavalensis",1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|186802|31979|1485|1960653;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|3085636|186803|2719313|358742;1783272|1239|186801|3085636|186803|2719313|460384,Complete,Folakunmi
bsdb:37604954/3/2,37604954,"cross-sectional observational, not case-control",37604954,https://doi.org/10.1038/s41598-023-40872-5,NA,"Fongang B., Satizabal C., Kautz T.F., Wadop Y.N., Muhammad J.A.S., Vasquez E., Mathews J., Gireud-Goss M., Saklad A.R., Himali J., Beiser A., Cavazos J.E., Mahaney M.C., Maestre G., DeCarli C., Shipp E.L., Vasan R.S. , Seshadri S.",Cerebral small vessel disease burden is associated with decreased abundance of gut Barnesiella intestinihominis bacterium in the Framingham Heart Study,Scientific reports,2023,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Cerebral small vessel disease,EFO:0008493,Lower burden (Healthy),High burden (Unhealthy),Participants with Cerebral small vessel disease that were tested using the EF marker,822,121,NA,16S,4,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,"age,body mass index,education level,sex,time",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Table S4, S5, S6",15 October 2023,Sinmisoluwa Adesanya,"Sinmisoluwa Adesanya,Chinelsy,Folakunmi,WikiWorks","Difference between the gut microbiome of patients with cSVD marker PSMD and the Lower burden (Healthy) group at phylum, genus and species rank",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota,p__Candidatus Parcubacteria,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris",3379134|976|200643|171549|171550|239759;1783272|1239;221216;3366610|28890|183925|2158|2159|2172;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|2316020|46228,Complete,Folakunmi
bsdb:37605183/1/1,37605183,"cross-sectional observational, not case-control",37605183,https://doi.org/10.1186/s12902-023-01432-0,NA,"Gravdal K., Kirste K.H., Grzelak K., Kirubakaran G.T., Leissner P., Saliou A. , Casèn C.",Exploring the gut microbiota in patients with pre-diabetes and treatment naïve diabetes type 2 - a pilot study,BMC endocrine disorders,2023,"16S rRNA bacterial gene, Bacterial profiling, Microbiota signatures, Prediabetes, Type 2 diabetes",Experiment 1,Norway,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls - based on GA- map,Pre-Type 2 Diabetes,"Pre-Type 2 Diabetes patients are Individuals that have blood glucose levels higher than normal but below the threshold for T2D, are often overweight, and have an elevated risk of T2D and cardiovascular disease.",38,22,1 month,16S,3456789,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 October 2023,Kadeniyi,"Kadeniyi,Peace Sandy,WikiWorks","Differentially abundant bacteria – pre-T2D vs. healthy, GA-map® 131-plex",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",1783272|1239|186801|3085636|186803|189330;3379134|1224;3379134|1224|1236|91347;3379134|1224|1236|91347|543|1940338,Complete,Peace Sandy
bsdb:37605183/1/2,37605183,"cross-sectional observational, not case-control",37605183,https://doi.org/10.1186/s12902-023-01432-0,NA,"Gravdal K., Kirste K.H., Grzelak K., Kirubakaran G.T., Leissner P., Saliou A. , Casèn C.",Exploring the gut microbiota in patients with pre-diabetes and treatment naïve diabetes type 2 - a pilot study,BMC endocrine disorders,2023,"16S rRNA bacterial gene, Bacterial profiling, Microbiota signatures, Prediabetes, Type 2 diabetes",Experiment 1,Norway,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy controls - based on GA- map,Pre-Type 2 Diabetes,"Pre-Type 2 Diabetes patients are Individuals that have blood glucose levels higher than normal but below the threshold for T2D, are often overweight, and have an elevated risk of T2D and cardiovascular disease.",38,22,1 month,16S,3456789,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 2,10 October 2023,Kadeniyi,"Kadeniyi,Peace Sandy,WikiWorks","Differentially abundant bacteria – pre-T2D vs. healthy, GA-map® 131-plex",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis",1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|186802|216572|216851|853;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|909932|1843489|31977|29465;3379134|1224|28216|80840|995019|40544|40545,Complete,Peace Sandy
bsdb:37605183/2/1,37605183,"cross-sectional observational, not case-control",37605183,https://doi.org/10.1186/s12902-023-01432-0,NA,"Gravdal K., Kirste K.H., Grzelak K., Kirubakaran G.T., Leissner P., Saliou A. , Casèn C.",Exploring the gut microbiota in patients with pre-diabetes and treatment naïve diabetes type 2 - a pilot study,BMC endocrine disorders,2023,"16S rRNA bacterial gene, Bacterial profiling, Microbiota signatures, Prediabetes, Type 2 diabetes",Experiment 2,Norway,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy Controls - based on LUMI -Seq data,Pre-Type 2 Diabetes,"Pre-Type 2 Diabetes patients are Individuals that have blood glucose levels higher than normal but below the threshold for T2D, are often overweight, and have an elevated risk of T2D and cardiovascular disease.",48,22,1 month,16S,123456789,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 3,11 October 2023,Kadeniyi,"Kadeniyi,Peace Sandy,WikiWorks","Diferentially abundant bacteria — pre-T2D and T2D vs. healthy, LUMI-Seq™",increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Neglectibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Neglectibacter|s__Neglectibacter timonensis",1783272|1239|91061;1783272|1239|91061|186826;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|3085636|186803|1432051|1720294;1783272|1239|186801|186802|216572|1924105;1783272|1239|186801|186802|216572|1924105|1776382,Complete,Peace Sandy
bsdb:37605183/2/2,37605183,"cross-sectional observational, not case-control",37605183,https://doi.org/10.1186/s12902-023-01432-0,NA,"Gravdal K., Kirste K.H., Grzelak K., Kirubakaran G.T., Leissner P., Saliou A. , Casèn C.",Exploring the gut microbiota in patients with pre-diabetes and treatment naïve diabetes type 2 - a pilot study,BMC endocrine disorders,2023,"16S rRNA bacterial gene, Bacterial profiling, Microbiota signatures, Prediabetes, Type 2 diabetes",Experiment 2,Norway,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy Controls - based on LUMI -Seq data,Pre-Type 2 Diabetes,"Pre-Type 2 Diabetes patients are Individuals that have blood glucose levels higher than normal but below the threshold for T2D, are often overweight, and have an elevated risk of T2D and cardiovascular disease.",48,22,1 month,16S,123456789,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 3,11 October 2023,Kadeniyi,"Kadeniyi,Peace Sandy,WikiWorks","Diferentially abundant bacteria — pre-T2D and T2D vs. healthy, LUMI-Seq™",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola",1783272|1239|186801|186802|216572|459786|351091;3379134|976|200643|171549|815|909656|310298,Complete,Peace Sandy
bsdb:37605183/3/1,37605183,"cross-sectional observational, not case-control",37605183,https://doi.org/10.1186/s12902-023-01432-0,NA,"Gravdal K., Kirste K.H., Grzelak K., Kirubakaran G.T., Leissner P., Saliou A. , Casèn C.",Exploring the gut microbiota in patients with pre-diabetes and treatment naïve diabetes type 2 - a pilot study,BMC endocrine disorders,2023,"16S rRNA bacterial gene, Bacterial profiling, Microbiota signatures, Prediabetes, Type 2 diabetes",Experiment 3,Norway,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy Controls - based on LUMI -Seq data,Type 2 Diabetes - T2D,Patients with  Type 2 diabetes (T2D),48,16,1 month,16S,123456789,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 3,12 October 2023,Kadeniyi,"Kadeniyi,Peace Sandy,WikiWorks","Diferentially abundant bacteria — pre-T2D and T2D vs. healthy, LUMI-Seq™",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis",1783272|1239|186801|3085636|186803|189330;3379134|1224|1236|91347;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|526524;1783272|1239|526524|526525|128827;1783272|1239|526524|526525|2810281|191303;1783272|1239|526524|526525|2810281|191303|154288,Complete,Peace Sandy
bsdb:37605183/3/2,37605183,"cross-sectional observational, not case-control",37605183,https://doi.org/10.1186/s12902-023-01432-0,NA,"Gravdal K., Kirste K.H., Grzelak K., Kirubakaran G.T., Leissner P., Saliou A. , Casèn C.",Exploring the gut microbiota in patients with pre-diabetes and treatment naïve diabetes type 2 - a pilot study,BMC endocrine disorders,2023,"16S rRNA bacterial gene, Bacterial profiling, Microbiota signatures, Prediabetes, Type 2 diabetes",Experiment 3,Norway,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Healthy Controls - based on LUMI -Seq data,Type 2 Diabetes - T2D,Patients with  Type 2 diabetes (T2D),48,16,1 month,16S,123456789,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 3,12 October 2023,Kadeniyi,"Kadeniyi,Peace Sandy,WikiWorks","Diferentially abundant bacteria — pre-T2D and T2D vs. healthy, LUMI-Seq™",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,1783272|1239|186801|3085636|3118652|2039240,Complete,Peace Sandy
bsdb:37605183/4/1,37605183,"cross-sectional observational, not case-control",37605183,https://doi.org/10.1186/s12902-023-01432-0,NA,"Gravdal K., Kirste K.H., Grzelak K., Kirubakaran G.T., Leissner P., Saliou A. , Casèn C.",Exploring the gut microbiota in patients with pre-diabetes and treatment naïve diabetes type 2 - a pilot study,BMC endocrine disorders,2023,"16S rRNA bacterial gene, Bacterial profiling, Microbiota signatures, Prediabetes, Type 2 diabetes",Experiment 4,Norway,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Pre- Type 2 Diabetes individuals,Type 2 Diabetes - T2D Patients,Patients with Type 2 Diabetes,22,16,1 month,16S,123456789,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 3,24 January 2024,Peace Sandy,"Peace Sandy,WikiWorks","Diferentially abundant bacteria — pre-T2D and T2D vs. healthy, LUMI-Seq™",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis",1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|526524|526525|128827;1783272|1239|526524;1783272|1239|526524|526525|2810281|191303;1783272|1239|526524|526525|2810281|191303|154288,Complete,Peace Sandy
bsdb:37605183/4/2,37605183,"cross-sectional observational, not case-control",37605183,https://doi.org/10.1186/s12902-023-01432-0,NA,"Gravdal K., Kirste K.H., Grzelak K., Kirubakaran G.T., Leissner P., Saliou A. , Casèn C.",Exploring the gut microbiota in patients with pre-diabetes and treatment naïve diabetes type 2 - a pilot study,BMC endocrine disorders,2023,"16S rRNA bacterial gene, Bacterial profiling, Microbiota signatures, Prediabetes, Type 2 diabetes",Experiment 4,Norway,Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Pre- Type 2 Diabetes individuals,Type 2 Diabetes - T2D Patients,Patients with Type 2 Diabetes,22,16,1 month,16S,123456789,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 3,24 January 2024,Peace Sandy,"Peace Sandy,WikiWorks","Diferentially abundant bacteria — pre-T2D and T2D vs. healthy, LUMI-Seq™",decreased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella massiliensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Neglectibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Neglectibacter|s__Neglectibacter timonensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|3085636|186803|1432051|1720294;1783272|1239|91061|186826;1783272|1239|186801|186802|216572|1924105;1783272|1239|186801|186802|216572|1924105|1776382;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301,Complete,Peace Sandy
bsdb:37608830/1/1,37608830,case-control,37608830,10.3389/fmed.2023.1177990,NA,"Vidmar Šimic M., Maver A., Zimani A.N., Hočevar K., Peterlin B., Kovanda A. , Premru-Sršen T.",Oral microbiome and preterm birth,Frontiers in medicine,2023,"16S rDNA, 16S rRNA gene, microbiome, oral microbiome, pregnancy, preterm delivery",Experiment 1,Slovenia,Homo sapiens,Oral cavity,UBERON:0000167,Premature birth,EFO:0003917,Term birth (TB),Preterm birth (PTB),"Spontaneous onset of preterm labor (≤36 6/7 weeks) due to various causes, including spontaneous contractions, preterm premature rupture of membranes (PPROM), intrauterine infection, cervical insufficiency, and others",91,61,1 week,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,Signature 1,Figure 4,6 April 2024,Ayibatari,"Ayibatari,Scholastica,WikiWorks",Differential relative abundance of oral bacteria in term vs. preterm delivery groups,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella massiliensis",3379134|976|117743|200644|49546|1016;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|1936062,Complete,Svetlana up
bsdb:37608830/1/2,37608830,case-control,37608830,10.3389/fmed.2023.1177990,NA,"Vidmar Šimic M., Maver A., Zimani A.N., Hočevar K., Peterlin B., Kovanda A. , Premru-Sršen T.",Oral microbiome and preterm birth,Frontiers in medicine,2023,"16S rDNA, 16S rRNA gene, microbiome, oral microbiome, pregnancy, preterm delivery",Experiment 1,Slovenia,Homo sapiens,Oral cavity,UBERON:0000167,Premature birth,EFO:0003917,Term birth (TB),Preterm birth (PTB),"Spontaneous onset of preterm labor (≤36 6/7 weeks) due to various causes, including spontaneous contractions, preterm premature rupture of membranes (PPROM), intrauterine infection, cervical insufficiency, and others",91,61,1 week,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,Signature 2,Figure 4,11 June 2024,Scholastica,"Scholastica,WikiWorks",Differential relative abundance of oral bacteria in term vs. preterm delivery groups,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 848,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia wadei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sputorum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia trevisanii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum saburreum,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudopneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria cinerea,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria meningitidis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria mucosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus haemolyticus",1783272|201174|1760|85007|1653|1716;1783272|201174|1760|2037|2049|1654;1783272|1239|186801|3085636|186803|1164882;1783272|201174|1760|2037|2049|1654|649739;3379134|29547|3031852|213849|72294|194;3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|171551|836;1783272|1239|186801|3085636|186803|43996;3384189|32066|203490|203491|1129771|32067;1783272|1239|909932|1843489|31977|29465;3379134|1224|28216|206351|481|482;1783272|1239|91061|186826|1300|1301;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|2047;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|1300|1301|113107;1783272|1239|91061|186826|1300|1301|68892;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|91061|186826|1300|1301|1305;3379134|1224|1236|135625|712|724|727;3379134|1224|1236|135625|712|724|729;1783272|1239|91061|186826|1300|1301|45634;1783272|1239|91061|1385|539738|1378|84135;3384189|32066|203490|203491|1129771|32067|157687;3379134|1224|1236|135625|712|724|1078480;3384189|32066|203490|203491|1129771|32067|109328;1783272|1239|186801|3085636|186803|1164882|467210;3379134|29547|3031852|213849|72294|194|824;1783272|1239|91061|186826|1300|1301|1313;1783272|1239|91061|186826|1300|1301|257758;3379134|1224|28216|206351|481|482|1107316;3379134|1224|28216|206351|481|482|483;3379134|1224|28216|206351|481|482|487;3379134|1224|28216|206351|481|482|28449;3379134|1224|28216|206351|481|482|488;1783272|201174|1760|85006|1268|32207|43675;3379134|1224|1236|135625|712|724|726,Complete,Svetlana up
bsdb:37626573/1/1,37626573,"cross-sectional observational, not case-control",37626573,https://doi.org/10.3390/brainsci13081217,NA,"Li Z., Gu M., Sun H., Chen X., Zhou J. , Zhang Y.",The Potential of Gut Microbiota in Prediction of Stroke-Associated Pneumonia,Brain sciences,2023,"gut microbiota, predictor, short-chain fatty acids, stroke, stroke-associated pneumonia",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Ischemic stroke,HP:0002140,Patients without stroke-associated pneumonia (non-SAP),Patients with stroke-associated pneumonia (SAP),Patients who developed stroke-associated pneumonia after an acute ischemic stroke often due to immune suppression and difficulty swallowing.,92,43,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,increased,NA,unchanged,Signature 1,Figure 3b,4 October 2024,Tosin,"Tosin,WikiWorks","LEfSe of gut microbiota with significantly differential bacteria between two groups.(SAP and non-SAP). The analysis highlights the increased relative abundances of certain taxa in the SAP group. These taxa are identified as key microbial features distinguishing the SAP group from the NSAP group, potentially playing a role in the development of stroke-associated pneumonia.",increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,s__uncultured bacterium,s__uncultured organism",1783272|1239|91061;1783272|1239|186801|3085636|186803|830;1783272|1239|186801|186802|31979|1485|1502;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|186826;1783272|1239|186801|186802|31979|1485|1522;1783272|1239|186801|3085636|186803|297314;77133;155900,Complete,Svetlana up
bsdb:37626573/1/2,37626573,"cross-sectional observational, not case-control",37626573,https://doi.org/10.3390/brainsci13081217,NA,"Li Z., Gu M., Sun H., Chen X., Zhou J. , Zhang Y.",The Potential of Gut Microbiota in Prediction of Stroke-Associated Pneumonia,Brain sciences,2023,"gut microbiota, predictor, short-chain fatty acids, stroke, stroke-associated pneumonia",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Ischemic stroke,HP:0002140,Patients without stroke-associated pneumonia (non-SAP),Patients with stroke-associated pneumonia (SAP),Patients who developed stroke-associated pneumonia after an acute ischemic stroke often due to immune suppression and difficulty swallowing.,92,43,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,increased,NA,unchanged,Signature 2,Figure 3b,4 October 2024,Tosin,"Tosin,WikiWorks","LEfSe of gut microbiota with significantly differential between two groups.(SAP and Non SAP). The analysis highlights the decreased relative abundances of certain taxa in the SAP group, where they may indicate a protective role against the development of stroke-associated pneumonia.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__butyrate-producing bacterium L2-12,s__uncultured organism",3379134|976|200643|171549;3379134|976;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|1407607;1783272|1239|909932;1783272|1239|909932|909929;3379134|1224|28216|80840|995019;1783272|1239|186801|186802|136624;155900,Complete,Svetlana up
bsdb:37626573/2/1,37626573,"cross-sectional observational, not case-control",37626573,https://doi.org/10.3390/brainsci13081217,NA,"Li Z., Gu M., Sun H., Chen X., Zhou J. , Zhang Y.",The Potential of Gut Microbiota in Prediction of Stroke-Associated Pneumonia,Brain sciences,2023,"gut microbiota, predictor, short-chain fatty acids, stroke, stroke-associated pneumonia",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Ischemic stroke,HP:0002140,Patients without stroke-associated Pnuemonia(non-SAP),Patients with stroke-associated Pnuemonia(SAP),Patients who developed stroke-associated pneumonia after an acute ischemic stroke often due to immune suppression and difficulty swallowing.,92,43,1 month,16S,34,Illumina,relative abundances,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,increased,NA,unchanged,Signature 1,Figure 2,8 October 2024,Tosin,"Tosin,WikiWorks",Gut microbiota with significantly different relative abundance between the two groups (SAP and non-SAP) at genus level in Metastats analysis where certain taxas were more enriched in the SAP group potentially contributing to the altered gut microbiota observed in the patients.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|3085642|580596;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|1407607,Complete,Svetlana up
bsdb:37626573/2/2,37626573,"cross-sectional observational, not case-control",37626573,https://doi.org/10.3390/brainsci13081217,NA,"Li Z., Gu M., Sun H., Chen X., Zhou J. , Zhang Y.",The Potential of Gut Microbiota in Prediction of Stroke-Associated Pneumonia,Brain sciences,2023,"gut microbiota, predictor, short-chain fatty acids, stroke, stroke-associated pneumonia",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Ischemic stroke,HP:0002140,Patients without stroke-associated Pnuemonia(non-SAP),Patients with stroke-associated Pnuemonia(SAP),Patients who developed stroke-associated pneumonia after an acute ischemic stroke often due to immune suppression and difficulty swallowing.,92,43,1 month,16S,34,Illumina,relative abundances,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,increased,NA,unchanged,Signature 2,Figure S3,7 December 2024,Tosin,"Tosin,WikiWorks",Gut Microbiota with significantly different relative abundance between the SAP (stroke associated pneumonia) and non SAP groups at phylum and family level in Metastats analysis.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|976|200643|171549|815;3379134|976;3379134|1224|28216|80840|995019;1783272|1239|909932|1843489|31977,Complete,Svetlana up
bsdb:37639812/1/1,37639812,laboratory experiment,37639812,10.1016/j.phymed.2023.155013,NA,"Gao Y., Mo S., Cao H., Zhi Y., Ma X., Huang Z., Li B., Wu J., Zhang K. , Jin L.",The efficacy and mechanism of Angelica sinensis (Oliv.) Diels root aqueous extract based on RNA sequencing and 16S rDNA sequencing in alleviating polycystic ovary syndrome,Phytomedicine : international journal of phytotherapy and phytopharmacology,2023,"16S rDNA sequencing, Angelica sinensis (oliv.) Diels root, Polycystic ovary syndrome, RNA sequencing",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control,Polycystic ovary syndrome (PCOS),Rats with polycystic ovary syndrome (PCOS) were induced by letrozole and a high-fat diet.,5,5,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,Figure 9I,17 July 2025,Victoria,Victoria,The effects of WEA on the gut microbiota of PCOS rats using LEfSe.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae",1783272|1239|526524|526525;1783272|1239|526524|526525|128827;1783272|1239|526524|526525|128827|174708;3379134|976;3379134|976|200643;3379134|976|200643|171549;3379134|976|200643|171549|2005473;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815,Complete,KateRasheed
bsdb:37639812/1/2,37639812,laboratory experiment,37639812,10.1016/j.phymed.2023.155013,NA,"Gao Y., Mo S., Cao H., Zhi Y., Ma X., Huang Z., Li B., Wu J., Zhang K. , Jin L.",The efficacy and mechanism of Angelica sinensis (Oliv.) Diels root aqueous extract based on RNA sequencing and 16S rDNA sequencing in alleviating polycystic ovary syndrome,Phytomedicine : international journal of phytotherapy and phytopharmacology,2023,"16S rDNA sequencing, Angelica sinensis (oliv.) Diels root, Polycystic ovary syndrome, RNA sequencing",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control,Polycystic ovary syndrome (PCOS),Rats with polycystic ovary syndrome (PCOS) were induced by letrozole and a high-fat diet.,5,5,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 2,Figure 9I,17 July 2025,Victoria,Victoria,The effects of WEA on the gut microbiota of PCOS rats using LEfSe.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales",1783272|1239|91061|186826|33958|2742598|1598;1783272|1239|91061|186826|33958|1578|1579;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826,Complete,KateRasheed
bsdb:37639812/2/1,37639812,laboratory experiment,37639812,10.1016/j.phymed.2023.155013,NA,"Gao Y., Mo S., Cao H., Zhi Y., Ma X., Huang Z., Li B., Wu J., Zhang K. , Jin L.",The efficacy and mechanism of Angelica sinensis (Oliv.) Diels root aqueous extract based on RNA sequencing and 16S rDNA sequencing in alleviating polycystic ovary syndrome,Phytomedicine : international journal of phytotherapy and phytopharmacology,2023,"16S rDNA sequencing, Angelica sinensis (oliv.) Diels root, Polycystic ovary syndrome, RNA sequencing",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Polycystic ovary syndrome,Polycystic ovary syndrome + Water extract of Angelica sinensis root (PCOS+WEA),Rats with polycystic ovary syndrome (PCOS) were induced by letrozole and a high-fat diet and administered intragastrically with metformin (0.3g/kg) and WEA (8g/kg) for 4 weeks as treatment.,5,5,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,unchanged,increased,NA,unchanged,Signature 1,Figure 9J,17 July 2025,Victoria,Victoria,The effects of WEA on the gut microbiota of PCOS rats using LEfSe.,increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus murinus,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",1783272|201174|84992;1783272|201174|84998|84999|1643824;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|28025;1783272|1239|186801;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|526524|526525|128827|1937008;1783272|1239|186801|186802;1783272|1239|91061|186826|33958|2767887|1622;3379134|203691|203692|136|137;3379134|203691|203692|136;3379134|203691|203692;3379134|203691|203692|136|2845253|157,Complete,KateRasheed
bsdb:37639812/2/2,37639812,laboratory experiment,37639812,10.1016/j.phymed.2023.155013,NA,"Gao Y., Mo S., Cao H., Zhi Y., Ma X., Huang Z., Li B., Wu J., Zhang K. , Jin L.",The efficacy and mechanism of Angelica sinensis (Oliv.) Diels root aqueous extract based on RNA sequencing and 16S rDNA sequencing in alleviating polycystic ovary syndrome,Phytomedicine : international journal of phytotherapy and phytopharmacology,2023,"16S rDNA sequencing, Angelica sinensis (oliv.) Diels root, Polycystic ovary syndrome, RNA sequencing",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Polycystic ovary syndrome,Polycystic ovary syndrome + Water extract of Angelica sinensis root (PCOS+WEA),Rats with polycystic ovary syndrome (PCOS) were induced by letrozole and a high-fat diet and administered intragastrically with metformin (0.3g/kg) and WEA (8g/kg) for 4 weeks as treatment.,5,5,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,unchanged,increased,NA,unchanged,Signature 2,Figure 9J,17 July 2025,Victoria,Victoria,The effects of WEA on the gut microbiota of PCOS rats using LEfSe.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Pseudomonadati|p__Bacteroidota",3379134|976|200643|171549|2005473;3379134|976|200643|171549;3379134|976|200643;3379134|1224|1236;1783272|1239|91061|186826|33958|1578|33959;3379134|976,Complete,KateRasheed
bsdb:37644001/1/1,37644001,"prospective cohort,time series / longitudinal observational",37644001,10.1038/s41467-023-40336-4,NA,"Hoskinson C., Dai D.L.Y., Del Bel K.L., Becker A.B., Moraes T.J., Mandhane P.J., Finlay B.B., Simons E., Kozyrskyj A.L., Azad M.B., Subbarao P., Petersen C. , Turvey S.E.",Delayed gut microbiota maturation in the first year of life is a hallmark of pediatric allergic disease,Nature communications,2023,NA,Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,"Asthma,Allergic rhinitis,Food allergy,Dermatitis","MONDO:0004979,EFO:0005854,EFO:1001890,MONDO:0002406",Healthy controls,Allergic Children,Children diagnosed by an expert physician at the 5-year scheduled visit with one or more allergic disorders.,523,592,NA,WMS,NA,Illumina,relative abundances,Random Forest Analysis,0.05,FALSE,NA,age,NA,NA,decreased,NA,NA,NA,NA,Signature 1,figure 4C,11 October 2023,Nwajei Edgar,"Nwajei Edgar,Peace Sandy,Folakunmi,WikiWorks",Comparing species abundance within the 1-year microbiota between children who did or did not receive an allergic diagnosis at 5 years,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans",1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|3085636|186803|1407607|1150298,Complete,Folakunmi
bsdb:37644001/1/2,37644001,"prospective cohort,time series / longitudinal observational",37644001,10.1038/s41467-023-40336-4,NA,"Hoskinson C., Dai D.L.Y., Del Bel K.L., Becker A.B., Moraes T.J., Mandhane P.J., Finlay B.B., Simons E., Kozyrskyj A.L., Azad M.B., Subbarao P., Petersen C. , Turvey S.E.",Delayed gut microbiota maturation in the first year of life is a hallmark of pediatric allergic disease,Nature communications,2023,NA,Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,"Asthma,Allergic rhinitis,Food allergy,Dermatitis","MONDO:0004979,EFO:0005854,EFO:1001890,MONDO:0002406",Healthy controls,Allergic Children,Children diagnosed by an expert physician at the 5-year scheduled visit with one or more allergic disorders.,523,592,NA,WMS,NA,Illumina,relative abundances,Random Forest Analysis,0.05,FALSE,NA,age,NA,NA,decreased,NA,NA,NA,NA,Signature 2,figure 4C,11 October 2023,Nwajei Edgar,"Nwajei Edgar,Peace Sandy,Folakunmi,WikiWorks",Comparing species abundance within the 1-year microbiota between children who did or did not receive an allergic diagnosis at 5 years,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas nexilis",1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|91061|186826|81852|1350|1351;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|31979|1485|1522;1783272|1239|186801|3085636|186803|2005355|29361,Complete,Folakunmi
bsdb:37655887/1/1,37655887,laboratory experiment,37655887,https://doi.org/10.1128/spectrum.00189-23,NA,"Xu F., Li Q., Wang S., Dong M., Xiao G., Bai J., Wang J. , Sun X.",The efficacy of prevention for colon cancer based on the microbiota therapy and the antitumor mechanisms with intervention of dietary <i>Lactobacillus</i>,Microbiology spectrum,2023,"Lactobacillus, colon cancer, gut microbiota, serine, sphingosine 1-phosphate signaling",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Tumor control group (CK),Living bacteria group (LB),"BALB/c mice (male, 6 wk) purchased from Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences. These mice were given oral administration of living Lactobacillus bacteria.",30,30,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,increased,unchanged,NA,NA,Signature 1,Figure 3g,17 March 2024,Manisha28,"Manisha28,Svetlana up,WikiWorks",Effects of administration of Lactobacillus on living bacteria group(LB). The gut microbiota with the capacity of producing antitumor compounds are increased in living bacteria group.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Colwelliaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Myxococcota|c__Myxococcia|o__Myxococcales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,s__bacterium AF12",3379134|1224|1236|135624;1783272|1239|91061|1385|186817;1783272|1239|91061|1385;1783272|1239|91061;1783272|1239;1783272|1239|186801;3379134|1224|1236|135622|267889;1783272|1239|186801|3085636|186803|33042;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|561;1783272|1239|186801|186802;3379134|1224|1236;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;3379134|2818505|32015|29;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|841;1783272|1239|526524|526525|2810281|191303;1783272|1239|526524|526525|2810281;1729795,Complete,Svetlana up
bsdb:37655887/1/2,37655887,laboratory experiment,37655887,https://doi.org/10.1128/spectrum.00189-23,NA,"Xu F., Li Q., Wang S., Dong M., Xiao G., Bai J., Wang J. , Sun X.",The efficacy of prevention for colon cancer based on the microbiota therapy and the antitumor mechanisms with intervention of dietary <i>Lactobacillus</i>,Microbiology spectrum,2023,"Lactobacillus, colon cancer, gut microbiota, serine, sphingosine 1-phosphate signaling",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Tumor control group (CK),Living bacteria group (LB),"BALB/c mice (male, 6 wk) purchased from Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences. These mice were given oral administration of living Lactobacillus bacteria.",30,30,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,increased,unchanged,NA,NA,Signature 2,Figure 3g,17 March 2024,Manisha28,"Manisha28,Svetlana up,WikiWorks",Effects of administration of Lactobacillus on living bacteria group(LB). Some gut microbiota are decreased in living bacteria group.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Viridiplantae|p__Streptophyta",3379134|976|200643|171549;3379134|976|200643|171549|1853231|574697;1783272|1117;3379134|976|200643|171549|171550;3379134|1224|28211|204457|41297;3379134|1224|28211|204457|41297|13687;33090|35493,Complete,Svetlana up
bsdb:37655887/3/1,37655887,laboratory experiment,37655887,https://doi.org/10.1128/spectrum.00189-23,NA,"Xu F., Li Q., Wang S., Dong M., Xiao G., Bai J., Wang J. , Sun X.",The efficacy of prevention for colon cancer based on the microbiota therapy and the antitumor mechanisms with intervention of dietary <i>Lactobacillus</i>,Microbiology spectrum,2023,"Lactobacillus, colon cancer, gut microbiota, serine, sphingosine 1-phosphate signaling",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Inactivated bacteria group,Living bacteria group,"BALB/c mice (male, 6 wk) purchased from Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences. These mice were given oral administration of living Lactobacillus bacteria.",30,30,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3g,6 April 2024,Svetlana up,"Svetlana up,WikiWorks",LEfSe results of Inactivated vs Living Bacteria group,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",3379134|1224|28211;1783272|1117;1783272|1239|186801|186802|216572|2485925;3379134|1224|28211|766;3379134|976|200643|171549|171550,Complete,Svetlana up
bsdb:37655887/3/2,37655887,laboratory experiment,37655887,https://doi.org/10.1128/spectrum.00189-23,NA,"Xu F., Li Q., Wang S., Dong M., Xiao G., Bai J., Wang J. , Sun X.",The efficacy of prevention for colon cancer based on the microbiota therapy and the antitumor mechanisms with intervention of dietary <i>Lactobacillus</i>,Microbiology spectrum,2023,"Lactobacillus, colon cancer, gut microbiota, serine, sphingosine 1-phosphate signaling",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Inactivated bacteria group,Living bacteria group,"BALB/c mice (male, 6 wk) purchased from Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences. These mice were given oral administration of living Lactobacillus bacteria.",30,30,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 3g,6 April 2024,Svetlana up,"Svetlana up,WikiWorks",LEfSe results of Inactivated vs Living Bacteria group,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239|91061;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|561;3379134|1224|1236;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:37658443/1/1,37658443,case-control,37658443,https://doi.org/10.1186/s40168-023-01640-9,NA,"Paulo A.C., Lança J., Almeida S.T., Hilty M. , Sá-Leão R.","The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children",Microbiome,2023,"Healthy adults, Microbiota, Nasopharynx, Oropharynx, Streptococcus pneumoniae",Experiment 1,Portugal,Homo sapiens,"Nasopharyngeal gland,Saliva",UBERON:0001836,Streptococcus pneumoniae,NCBITAXON:1313,Pneumococcal non-carriers.,Pneumococcal carriers,Individuals who carry pneumococci in the nasopharynx,47,12,1 month,16S,4,MGISEQ-2000,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,Table S2.,9 October 2023,Karen254.,"Karen254.,Chloe,Peace Sandy,WikiWorks",Bacteria (ASV) differentially present in the nasopharyngeal microbiota of pneumococcal carriers and non-carriers.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudopneumoniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra",1783272|1239|91061|186826|1300|1301|1313;1783272|1239|91061|186826|1300|1301|257758;1783272|1239|91061|186826|1300|1301|28037;3379134|1224|1236|135625|712|724|727;3384189|32066|203490|203491|203492|848|851;1783272|1239|1737404|1737405|1570339|543311|33033,Complete,Peace Sandy
bsdb:37658443/1/2,37658443,case-control,37658443,https://doi.org/10.1186/s40168-023-01640-9,NA,"Paulo A.C., Lança J., Almeida S.T., Hilty M. , Sá-Leão R.","The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children",Microbiome,2023,"Healthy adults, Microbiota, Nasopharynx, Oropharynx, Streptococcus pneumoniae",Experiment 1,Portugal,Homo sapiens,"Nasopharyngeal gland,Saliva",UBERON:0001836,Streptococcus pneumoniae,NCBITAXON:1313,Pneumococcal non-carriers.,Pneumococcal carriers,Individuals who carry pneumococci in the nasopharynx,47,12,1 month,16S,4,MGISEQ-2000,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Table S2,9 October 2023,Karen254.,"Karen254.,Chloe,Peace Sandy,WikiWorks",Bacteria (ASV) differentially present in the nasopharyngeal microbiota of pneumococcal carriers and non-carriers.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sicca,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus lugdunensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis",3379134|1224|1236|135625|712|724|735;3379134|1224|28216|206351|481|482|490;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|91061|1385|90964|1279|28035;3379134|976|200643|171549|171552|2974257|28127,Complete,Peace Sandy
bsdb:37658443/2/1,37658443,case-control,37658443,https://doi.org/10.1186/s40168-023-01640-9,NA,"Paulo A.C., Lança J., Almeida S.T., Hilty M. , Sá-Leão R.","The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children",Microbiome,2023,"Healthy adults, Microbiota, Nasopharynx, Oropharynx, Streptococcus pneumoniae",Experiment 2,Portugal,Homo sapiens,"Nasopharyngeal gland,Saliva",UBERON:0001836,Streptococcus pneumoniae,NCBITAXON:1313,non- smokers,Smokers,The nasopharyngeal area of smokers,20,5,1 month,16S,4,MGISEQ-2000,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table S3,10 February 2024,Peace Sandy,"Peace Sandy,WikiWorks",Bacteria (ASV) differentially present in the nasopharyngeal microbiota of smokers and non-smokers.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium necrophorum",1783272|1239|91061|1385|186817|1386;3379134|976|200643|171549|171552|838|28132;1783272|1239|909932|1843489|31977|29465|39777;3379134|1224|28216|80840|119060|32008;3384189|32066|203490|203491|203492|848|859,Complete,Peace Sandy
bsdb:37658443/2/2,37658443,case-control,37658443,https://doi.org/10.1186/s40168-023-01640-9,NA,"Paulo A.C., Lança J., Almeida S.T., Hilty M. , Sá-Leão R.","The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children",Microbiome,2023,"Healthy adults, Microbiota, Nasopharynx, Oropharynx, Streptococcus pneumoniae",Experiment 2,Portugal,Homo sapiens,"Nasopharyngeal gland,Saliva",UBERON:0001836,Streptococcus pneumoniae,NCBITAXON:1313,non- smokers,Smokers,The nasopharyngeal area of smokers,20,5,1 month,16S,4,MGISEQ-2000,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Table S3,10 February 2024,Peace Sandy,"Peace Sandy,WikiWorks",Bacteria (ASV) differentially present in the nasopharyngeal microbiota of smokers and non-smokers,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sputorum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium propinquum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella|s__Lawsonella clevelandensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Curvibacter|s__Curvibacter gracilis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum pigrum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis",3379134|1224|1236|135625|712|724|735;3379134|1224|1236|135625|712|724|1078480;1783272|201174|1760|85007|1653|1716|43769;1783272|201174|1760|85007|2805586|1847725|1528099;3379134|1224|28216|80840|80864|281915|230310;1783272|1239|91061|186826|186828|29393|29394;3384189|32066|203490|203491|203492|848|851;1783272|1239|1737404|1737405|1570339|543311|33033;3379134|976|200643|171549|171552|2974257|28127,Complete,Peace Sandy
bsdb:37658443/3/1,37658443,case-control,37658443,https://doi.org/10.1186/s40168-023-01640-9,NA,"Paulo A.C., Lança J., Almeida S.T., Hilty M. , Sá-Leão R.","The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children",Microbiome,2023,"Healthy adults, Microbiota, Nasopharynx, Oropharynx, Streptococcus pneumoniae",Experiment 3,Portugal,Homo sapiens,"Nasopharyngeal gland,Saliva",UBERON:0001836,Streptococcus pneumoniae,NCBITAXON:1313,No contact with children,Contact with children,The nasopharyngeal microbiota of individuals that  regular contact with children.,22,10,1 month,16S,4,MGISEQ-2000,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,unchanged,NA,Signature 1,Table S4,10 February 2024,Peace Sandy,"Peace Sandy,WikiWorks",Bacteria (ASV) differentially present in the nasopharyngeal microbiota of individuals that have and do not have regular contact with children.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella catarrhalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum",1783272|1239|91061|186826|1300|1301|1313;1783272|1239|91061|186826|1300|1301|28037;3379134|1224|1236|2887326|468|475|480;3379134|1224|1236|135625|712|724|727;3384189|32066|203490|203491|203492|848|851,Complete,Peace Sandy
bsdb:37658443/3/2,37658443,case-control,37658443,https://doi.org/10.1186/s40168-023-01640-9,NA,"Paulo A.C., Lança J., Almeida S.T., Hilty M. , Sá-Leão R.","The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children",Microbiome,2023,"Healthy adults, Microbiota, Nasopharynx, Oropharynx, Streptococcus pneumoniae",Experiment 3,Portugal,Homo sapiens,"Nasopharyngeal gland,Saliva",UBERON:0001836,Streptococcus pneumoniae,NCBITAXON:1313,No contact with children,Contact with children,The nasopharyngeal microbiota of individuals that  regular contact with children.,22,10,1 month,16S,4,MGISEQ-2000,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,unchanged,NA,Signature 2,Table S4,10 February 2024,Peace Sandy,"Peace Sandy,WikiWorks",Bacteria (ASV) differentially present in the nasopharyngeal microbiota of individuals that have and do not have regular contact with children.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus lugdunensis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas sp. FARSPH,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus|s__Dermacoccus nishinomiyaensis",1783272|1239|91061|1385|90964|1279|28035;3379134|1224|28211|204457|41297|13687|2219696;1783272|201174|1760|85006|145357|57495|1274,Complete,Peace Sandy
bsdb:37658443/4/1,37658443,case-control,37658443,https://doi.org/10.1186/s40168-023-01640-9,NA,"Paulo A.C., Lança J., Almeida S.T., Hilty M. , Sá-Leão R.","The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children",Microbiome,2023,"Healthy adults, Microbiota, Nasopharynx, Oropharynx, Streptococcus pneumoniae",Experiment 4,Portugal,Homo sapiens,"Oropharyngeal gland,Saliva","UBERON:0003410,UBERON:0001836",Streptococcus pneumoniae,NCBITAXON:1313,Pneumococcal non-carriers.,Pneumococcal carriers,Oropharyngeal microbiota of pneumococcal carriers,47,12,1 month,16S,4,MGISEQ-2000,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,Table S5,10 February 2024,Peace Sandy,"Peace Sandy,WikiWorks",Bacteria (ASV) differentially present in the oropharyngeal microbiota of pneumococcal carriers and non-carriers.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",1783272|1239|91061|186826|1300|1301|1313;3379134|976|117743|200644|49546|1016;1783272|1239|1737404|1737405|1570339|543311|33033;3379134|29547|3031852|213849|72294|194|204;3379134|976|117743|200644|49546|1016|45242;1783272|1239|186801|3085636|186803|297314;3379134|976|117743|200644|49546|1016|1019;3379134|976|200643|171549|2005525|195950,Complete,Peace Sandy
bsdb:37658443/4/2,37658443,case-control,37658443,https://doi.org/10.1186/s40168-023-01640-9,NA,"Paulo A.C., Lança J., Almeida S.T., Hilty M. , Sá-Leão R.","The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children",Microbiome,2023,"Healthy adults, Microbiota, Nasopharynx, Oropharynx, Streptococcus pneumoniae",Experiment 4,Portugal,Homo sapiens,"Oropharyngeal gland,Saliva","UBERON:0003410,UBERON:0001836",Streptococcus pneumoniae,NCBITAXON:1313,Pneumococcal non-carriers.,Pneumococcal carriers,Oropharyngeal microbiota of pneumococcal carriers,47,12,1 month,16S,4,MGISEQ-2000,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Table S5,10 February 2024,Peace Sandy,"Peace Sandy,WikiWorks",Bacteria (ASV) differentially present in the oropharyngeal microbiota of pneumococcal carriers and non-carriers.,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,s__uncultured bacterium",3384189|32066|203490|203491|1129771|32067;3379134|976|200643|171549|171552|1283313|76122;77133,Complete,Peace Sandy
bsdb:37658443/5/1,37658443,case-control,37658443,https://doi.org/10.1186/s40168-023-01640-9,NA,"Paulo A.C., Lança J., Almeida S.T., Hilty M. , Sá-Leão R.","The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children",Microbiome,2023,"Healthy adults, Microbiota, Nasopharynx, Oropharynx, Streptococcus pneumoniae",Experiment 5,Portugal,Homo sapiens,"Oropharyngeal gland,Saliva","UBERON:0003410,UBERON:0001836",Streptococcus pneumoniae,NCBITAXON:1313,Non- smokers,Smokers,Oropharyngeal microbiota of smokers,20,5,1 month,16S,4,MGISEQ-2000,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table S6,10 February 2024,Peace Sandy,"Peace Sandy,WikiWorks",Bacteria (ASV) differentially present in the oropharyngeal microbiota of smokers and non-smokers.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus paraphrohaemolyticus",1783272|1239|91061|1385|186817|1386;1783272|1239|91061|186826|1300|1301|1313;3379134|1224|28216|80840|119060|32008;1783272|1239|909932|909929|1843491|970|69823;3379134|1224|1236|135625|712|724|736,Complete,Peace Sandy
bsdb:37658443/5/2,37658443,case-control,37658443,https://doi.org/10.1186/s40168-023-01640-9,NA,"Paulo A.C., Lança J., Almeida S.T., Hilty M. , Sá-Leão R.","The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children",Microbiome,2023,"Healthy adults, Microbiota, Nasopharynx, Oropharynx, Streptococcus pneumoniae",Experiment 5,Portugal,Homo sapiens,"Oropharyngeal gland,Saliva","UBERON:0003410,UBERON:0001836",Streptococcus pneumoniae,NCBITAXON:1313,Non- smokers,Smokers,Oropharyngeal microbiota of smokers,20,5,1 month,16S,4,MGISEQ-2000,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Table S6,10 February 2024,Peace Sandy,"Peace Sandy,WikiWorks",Bacteria (ASV) differentially present in the oropharyngeal microbiota of smokers and non-smokers.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella shahii,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia dentalis",3379134|1224|28216|206351|481|482;3379134|1224|1236|135625|712|724|735;3379134|976|200643|171549|171552|1283313|76122;3379134|976|200643|171549|171552|2974257|228603;3379134|29547|3031852|213849|72294|194|204;3379134|976|200643|171549|2005525|195950;3379134|203691|203692|136|2845253|157;3379134|1224|28216|80840|119060|47670|2490857,Complete,Peace Sandy
bsdb:37658443/6/1,37658443,case-control,37658443,https://doi.org/10.1186/s40168-023-01640-9,NA,"Paulo A.C., Lança J., Almeida S.T., Hilty M. , Sá-Leão R.","The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children",Microbiome,2023,"Healthy adults, Microbiota, Nasopharynx, Oropharynx, Streptococcus pneumoniae",Experiment 6,Portugal,Homo sapiens,"Oropharyngeal gland,Saliva","UBERON:0003410,UBERON:0001836",Streptococcus pneumoniae,NCBITAXON:1313,No Contact with Children,Contact with children,Oropharyngeal microbiota of individuals that have regular contact with children.,22,10,1 month,16S,4,MGISEQ-2000,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table S7,10 February 2024,Peace Sandy,"Peace Sandy,WikiWorks",Bacteria (ASV) differentially present in the oropharyngeal microbiota of individuals that have and do not have regular contact with children.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium asaccharolyticum",1783272|1239|91061|186826|1300|1301|1313;3379134|1224|1236|135625|712|724|735;3384189|32066|203490|203491|203492|848|851;1783272|201174|1760|85006|1268|32207|43675;3379134|1224|1236|135625|712|416916|739;3379134|1224|1236|135625|712|724|729;3379134|976|200643|171549|171552|838|28132;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|3085636|186803|265975|1501332,Complete,Peace Sandy
bsdb:37658443/6/2,37658443,case-control,37658443,https://doi.org/10.1186/s40168-023-01640-9,NA,"Paulo A.C., Lança J., Almeida S.T., Hilty M. , Sá-Leão R.","The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children",Microbiome,2023,"Healthy adults, Microbiota, Nasopharynx, Oropharynx, Streptococcus pneumoniae",Experiment 6,Portugal,Homo sapiens,"Oropharyngeal gland,Saliva","UBERON:0003410,UBERON:0001836",Streptococcus pneumoniae,NCBITAXON:1313,No Contact with Children,Contact with children,Oropharyngeal microbiota of individuals that have regular contact with children.,22,10,1 month,16S,4,MGISEQ-2000,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Table S7,10 February 2024,Peace Sandy,"Peace Sandy,WikiWorks",Bacteria (ASV) differentially present in the oropharyngeal microbiota of individuals that have and do not have regular contact with children,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",3379134|976|200643|171549|171551|836|837;3379134|976|200643|171549|171552|1283313|671218;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|28132;3379134|1224|28216|206351|481|482,Complete,Peace Sandy
bsdb:37659505/1/1,37659505,"cross-sectional observational, not case-control",37659505,https://doi.org/10.1016/j.jaci.2023.07.022,NA,"Chandrasekaran P., Han Y., Zerbe C.S., Heller T., DeRavin S.S., Kreuzberg S.A., Marciano B.E., Siu Y., Jones D.R., Abraham R.S., Stephens M.C., Tsou A.M., Snapper S., Conlan S., Subramanian P., Quinones M., Grou C., Calderon V., Deming C., Leiding J.W., Arnold D.E., Logan B.R., Griffith L.M., Petrovic A., Mousallem T.I., Kapoor N., Heimall J.R., Barnum J.L., Kapadia M., Wright N., Rayes A., Chandra S., Broglie L.A., Chellapandian D., Deal C.L., Grunebaum E., Lim S.S., Mallhi K., Marsh R.A., Murguia-Favela L., Parikh S., Touzot F., Cowan M.J., Dvorak C.C., Haddad E., Kohn D.B., Notarangelo L.D., Pai S.Y., Puck J.M., Pulsipher M.A., Torgerson T.R., Kang E.M., Malech H.L., Segre J.A., Bryant C.E., Holland S.M. , Falcone E.L.",Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease,The Journal of allergy and clinical immunology,2023,"CGD, Chronic granulomatous disease, IBD, NADPH oxidase, dysbiosis, inborn errors of immunity, inflammatory bowel disease, intestinal inflammation, metabolome, microbiome, primary immune deficiency",Experiment 1,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Chronic granulomatous disease,MONDO:0018305,Healthy controls,Chronic granulomatous disease,Patients with Chronic granulomatous disease and only receiving prophylactic antimicrobials and without a history of inflammatory bowel disease at the time of stool collection,16,17,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,"antibiotic,antimicrobial agent,inflammatory bowel disease",NA,decreased,decreased,NA,NA,NA,Signature 1,Fig 2,14 March 2024,Ifyohondu,"Ifyohondu,WikiWorks",Difference between the intestinal microbiome of patients with Chronic granulomatous disease and healthy controls by LEfSe.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__uncultured Roseburia sp.,s__uncultured bacterium",1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|1769710;1783272|1239|526524|526525|2810280|3025755;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|3085636|186803|841|512314;77133,Complete,Folakunmi
bsdb:37659505/1/2,37659505,"cross-sectional observational, not case-control",37659505,https://doi.org/10.1016/j.jaci.2023.07.022,NA,"Chandrasekaran P., Han Y., Zerbe C.S., Heller T., DeRavin S.S., Kreuzberg S.A., Marciano B.E., Siu Y., Jones D.R., Abraham R.S., Stephens M.C., Tsou A.M., Snapper S., Conlan S., Subramanian P., Quinones M., Grou C., Calderon V., Deming C., Leiding J.W., Arnold D.E., Logan B.R., Griffith L.M., Petrovic A., Mousallem T.I., Kapoor N., Heimall J.R., Barnum J.L., Kapadia M., Wright N., Rayes A., Chandra S., Broglie L.A., Chellapandian D., Deal C.L., Grunebaum E., Lim S.S., Mallhi K., Marsh R.A., Murguia-Favela L., Parikh S., Touzot F., Cowan M.J., Dvorak C.C., Haddad E., Kohn D.B., Notarangelo L.D., Pai S.Y., Puck J.M., Pulsipher M.A., Torgerson T.R., Kang E.M., Malech H.L., Segre J.A., Bryant C.E., Holland S.M. , Falcone E.L.",Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease,The Journal of allergy and clinical immunology,2023,"CGD, Chronic granulomatous disease, IBD, NADPH oxidase, dysbiosis, inborn errors of immunity, inflammatory bowel disease, intestinal inflammation, metabolome, microbiome, primary immune deficiency",Experiment 1,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Chronic granulomatous disease,MONDO:0018305,Healthy controls,Chronic granulomatous disease,Patients with Chronic granulomatous disease and only receiving prophylactic antimicrobials and without a history of inflammatory bowel disease at the time of stool collection,16,17,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,"antibiotic,antimicrobial agent,inflammatory bowel disease",NA,decreased,decreased,NA,NA,NA,Signature 2,Fig 2,14 March 2024,Ifyohondu,"Ifyohondu,Folakunmi,WikiWorks",Difference between the intestinal microbiome of patients with Chronic granulomatous disease and healthy controls by LEfSe .,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__uncultured Eubacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__uncultured Lachnospira sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|3085642|580596|2049021;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|1392389|1297617;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|526524|526525|2810281|191303;1783272|1239|526524|526525|128827|331630;1783272|1239|186801|186802|186806|1730|165185;1783272|1239|186801|3085636|186803|28050|446043;1783272|1239|186801|3085636|186803|297314,Complete,Folakunmi
bsdb:37659505/2/1,37659505,"cross-sectional observational, not case-control",37659505,https://doi.org/10.1016/j.jaci.2023.07.022,NA,"Chandrasekaran P., Han Y., Zerbe C.S., Heller T., DeRavin S.S., Kreuzberg S.A., Marciano B.E., Siu Y., Jones D.R., Abraham R.S., Stephens M.C., Tsou A.M., Snapper S., Conlan S., Subramanian P., Quinones M., Grou C., Calderon V., Deming C., Leiding J.W., Arnold D.E., Logan B.R., Griffith L.M., Petrovic A., Mousallem T.I., Kapoor N., Heimall J.R., Barnum J.L., Kapadia M., Wright N., Rayes A., Chandra S., Broglie L.A., Chellapandian D., Deal C.L., Grunebaum E., Lim S.S., Mallhi K., Marsh R.A., Murguia-Favela L., Parikh S., Touzot F., Cowan M.J., Dvorak C.C., Haddad E., Kohn D.B., Notarangelo L.D., Pai S.Y., Puck J.M., Pulsipher M.A., Torgerson T.R., Kang E.M., Malech H.L., Segre J.A., Bryant C.E., Holland S.M. , Falcone E.L.",Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease,The Journal of allergy and clinical immunology,2023,"CGD, Chronic granulomatous disease, IBD, NADPH oxidase, dysbiosis, inborn errors of immunity, inflammatory bowel disease, intestinal inflammation, metabolome, microbiome, primary immune deficiency",Experiment 2,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Chronic granulomatous disease,MONDO:0018305,Healthy individuals,Chronic granulomatous disease (CGD) patients,CGD patients without a history of IBD and only receiving prophylactic antimicrobials,17,16,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Fig. 2G,6 May 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Comparison of microbiome signatures between patients with CGD (without a history of IBD) VS Healthy individuals using LEfSe,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__uncultured Roseburia sp.,s__uncultured bacterium",1783272|1239|186801|3085636|186803|841|512314;77133,Complete,ChiomaBlessing
bsdb:37659505/2/2,37659505,"cross-sectional observational, not case-control",37659505,https://doi.org/10.1016/j.jaci.2023.07.022,NA,"Chandrasekaran P., Han Y., Zerbe C.S., Heller T., DeRavin S.S., Kreuzberg S.A., Marciano B.E., Siu Y., Jones D.R., Abraham R.S., Stephens M.C., Tsou A.M., Snapper S., Conlan S., Subramanian P., Quinones M., Grou C., Calderon V., Deming C., Leiding J.W., Arnold D.E., Logan B.R., Griffith L.M., Petrovic A., Mousallem T.I., Kapoor N., Heimall J.R., Barnum J.L., Kapadia M., Wright N., Rayes A., Chandra S., Broglie L.A., Chellapandian D., Deal C.L., Grunebaum E., Lim S.S., Mallhi K., Marsh R.A., Murguia-Favela L., Parikh S., Touzot F., Cowan M.J., Dvorak C.C., Haddad E., Kohn D.B., Notarangelo L.D., Pai S.Y., Puck J.M., Pulsipher M.A., Torgerson T.R., Kang E.M., Malech H.L., Segre J.A., Bryant C.E., Holland S.M. , Falcone E.L.",Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease,The Journal of allergy and clinical immunology,2023,"CGD, Chronic granulomatous disease, IBD, NADPH oxidase, dysbiosis, inborn errors of immunity, inflammatory bowel disease, intestinal inflammation, metabolome, microbiome, primary immune deficiency",Experiment 2,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Chronic granulomatous disease,MONDO:0018305,Healthy individuals,Chronic granulomatous disease (CGD) patients,CGD patients without a history of IBD and only receiving prophylactic antimicrobials,17,16,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Fig. 2G,6 May 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Comparison of microbiome signatures between patients with CGD (without a history of IBD) VS Healthy individuals using LEfSe,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,s__uncultured bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis",1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|28050|39485;77133;1783272|1239|186801|3085636|186803|297314;1783272|1239|186801|186802|1392389|1297617;1783272|1239|186801|3085636|186803|841|301301,Complete,ChiomaBlessing
bsdb:37659505/4/1,37659505,"cross-sectional observational, not case-control",37659505,https://doi.org/10.1016/j.jaci.2023.07.022,NA,"Chandrasekaran P., Han Y., Zerbe C.S., Heller T., DeRavin S.S., Kreuzberg S.A., Marciano B.E., Siu Y., Jones D.R., Abraham R.S., Stephens M.C., Tsou A.M., Snapper S., Conlan S., Subramanian P., Quinones M., Grou C., Calderon V., Deming C., Leiding J.W., Arnold D.E., Logan B.R., Griffith L.M., Petrovic A., Mousallem T.I., Kapoor N., Heimall J.R., Barnum J.L., Kapadia M., Wright N., Rayes A., Chandra S., Broglie L.A., Chellapandian D., Deal C.L., Grunebaum E., Lim S.S., Mallhi K., Marsh R.A., Murguia-Favela L., Parikh S., Touzot F., Cowan M.J., Dvorak C.C., Haddad E., Kohn D.B., Notarangelo L.D., Pai S.Y., Puck J.M., Pulsipher M.A., Torgerson T.R., Kang E.M., Malech H.L., Segre J.A., Bryant C.E., Holland S.M. , Falcone E.L.",Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease,The Journal of allergy and clinical immunology,2023,"CGD, Chronic granulomatous disease, IBD, NADPH oxidase, dysbiosis, inborn errors of immunity, inflammatory bowel disease, intestinal inflammation, metabolome, microbiome, primary immune deficiency",Experiment 4,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Cohort,EFO:0004445,PIDTC Cohort (CGD without IBD),NIHCC Cohort (CGD without IBD),Patients with Chronic granulomatous disease (CGD) without a history of Inflammatory bowel disease (IBD) and not receiving any medications other than prophylactic antimicrobials.,23,16,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Fig. 3C,18 March 2024,Ifyohondu,"Ifyohondu,Folakunmi,ChiomaBlessing,WikiWorks",Comparison of microbiome signatures between patients with CGD (without a history of IBD) from NIHCC VS PIDTC cohorts using LEfSe,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,1783272|1239|91061|186826|81852|1350,Complete,Folakunmi
bsdb:37659505/4/2,37659505,"cross-sectional observational, not case-control",37659505,https://doi.org/10.1016/j.jaci.2023.07.022,NA,"Chandrasekaran P., Han Y., Zerbe C.S., Heller T., DeRavin S.S., Kreuzberg S.A., Marciano B.E., Siu Y., Jones D.R., Abraham R.S., Stephens M.C., Tsou A.M., Snapper S., Conlan S., Subramanian P., Quinones M., Grou C., Calderon V., Deming C., Leiding J.W., Arnold D.E., Logan B.R., Griffith L.M., Petrovic A., Mousallem T.I., Kapoor N., Heimall J.R., Barnum J.L., Kapadia M., Wright N., Rayes A., Chandra S., Broglie L.A., Chellapandian D., Deal C.L., Grunebaum E., Lim S.S., Mallhi K., Marsh R.A., Murguia-Favela L., Parikh S., Touzot F., Cowan M.J., Dvorak C.C., Haddad E., Kohn D.B., Notarangelo L.D., Pai S.Y., Puck J.M., Pulsipher M.A., Torgerson T.R., Kang E.M., Malech H.L., Segre J.A., Bryant C.E., Holland S.M. , Falcone E.L.",Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease,The Journal of allergy and clinical immunology,2023,"CGD, Chronic granulomatous disease, IBD, NADPH oxidase, dysbiosis, inborn errors of immunity, inflammatory bowel disease, intestinal inflammation, metabolome, microbiome, primary immune deficiency",Experiment 4,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Cohort,EFO:0004445,PIDTC Cohort (CGD without IBD),NIHCC Cohort (CGD without IBD),Patients with Chronic granulomatous disease (CGD) without a history of Inflammatory bowel disease (IBD) and not receiving any medications other than prophylactic antimicrobials.,23,16,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Fig. 3C,18 March 2024,Ifyohondu,"Ifyohondu,Folakunmi,ChiomaBlessing,WikiWorks,Tosin",Comparison of microbiome signatures between patients with CGD (without a history of IBD) from NIHCC VS PIDTC cohorts using LEfSe,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|1769710;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|3085636|186803|2316020|33039;,Complete,Folakunmi
bsdb:37659505/5/1,37659505,"cross-sectional observational, not case-control",37659505,https://doi.org/10.1016/j.jaci.2023.07.022,NA,"Chandrasekaran P., Han Y., Zerbe C.S., Heller T., DeRavin S.S., Kreuzberg S.A., Marciano B.E., Siu Y., Jones D.R., Abraham R.S., Stephens M.C., Tsou A.M., Snapper S., Conlan S., Subramanian P., Quinones M., Grou C., Calderon V., Deming C., Leiding J.W., Arnold D.E., Logan B.R., Griffith L.M., Petrovic A., Mousallem T.I., Kapoor N., Heimall J.R., Barnum J.L., Kapadia M., Wright N., Rayes A., Chandra S., Broglie L.A., Chellapandian D., Deal C.L., Grunebaum E., Lim S.S., Mallhi K., Marsh R.A., Murguia-Favela L., Parikh S., Touzot F., Cowan M.J., Dvorak C.C., Haddad E., Kohn D.B., Notarangelo L.D., Pai S.Y., Puck J.M., Pulsipher M.A., Torgerson T.R., Kang E.M., Malech H.L., Segre J.A., Bryant C.E., Holland S.M. , Falcone E.L.",Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease,The Journal of allergy and clinical immunology,2023,"CGD, Chronic granulomatous disease, IBD, NADPH oxidase, dysbiosis, inborn errors of immunity, inflammatory bowel disease, intestinal inflammation, metabolome, microbiome, primary immune deficiency",Experiment 5,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Cohort,EFO:0004445,PIDTC Cohort (CGD Patients),NIHCC Cohort (CGD Patients),Patients with Chronic granulomatous disease (CGD) regardless of IBD status or antimicrobial use,36,79,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Fig E4C,19 March 2024,Ifyohondu,"Ifyohondu,Folakunmi,ChiomaBlessing,WikiWorks",Comparison of microbiome signatures between patients with CGD (regardless of IBD status) from NIHCC VS PIDTC cohorts using LEfSe,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|186801|186802|3085642|580596;1783272|1239|91061|186826|1300|1301,Complete,Folakunmi
bsdb:37659505/5/2,37659505,"cross-sectional observational, not case-control",37659505,https://doi.org/10.1016/j.jaci.2023.07.022,NA,"Chandrasekaran P., Han Y., Zerbe C.S., Heller T., DeRavin S.S., Kreuzberg S.A., Marciano B.E., Siu Y., Jones D.R., Abraham R.S., Stephens M.C., Tsou A.M., Snapper S., Conlan S., Subramanian P., Quinones M., Grou C., Calderon V., Deming C., Leiding J.W., Arnold D.E., Logan B.R., Griffith L.M., Petrovic A., Mousallem T.I., Kapoor N., Heimall J.R., Barnum J.L., Kapadia M., Wright N., Rayes A., Chandra S., Broglie L.A., Chellapandian D., Deal C.L., Grunebaum E., Lim S.S., Mallhi K., Marsh R.A., Murguia-Favela L., Parikh S., Touzot F., Cowan M.J., Dvorak C.C., Haddad E., Kohn D.B., Notarangelo L.D., Pai S.Y., Puck J.M., Pulsipher M.A., Torgerson T.R., Kang E.M., Malech H.L., Segre J.A., Bryant C.E., Holland S.M. , Falcone E.L.",Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease,The Journal of allergy and clinical immunology,2023,"CGD, Chronic granulomatous disease, IBD, NADPH oxidase, dysbiosis, inborn errors of immunity, inflammatory bowel disease, intestinal inflammation, metabolome, microbiome, primary immune deficiency",Experiment 5,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Cohort,EFO:0004445,PIDTC Cohort (CGD Patients),NIHCC Cohort (CGD Patients),Patients with Chronic granulomatous disease (CGD) regardless of IBD status or antimicrobial use,36,79,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Fig E4C,19 March 2024,Ifyohondu,"Ifyohondu,Folakunmi,ChiomaBlessing,WikiWorks,Tosin",Comparison of microbiome signatures between patients with CGD (regardless of IBD status) from NIHCC VS PIDTC cohorts using LEfSe,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium DTU089,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena fissicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|186802|1671661;1783272|1239|186801|3085636|186803|2005359|290055;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|186801|3085636|186803|437755;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|3085636|186803|1769710;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|3085636|186803|2316020|33039;,Complete,Folakunmi
bsdb:37659505/6/1,37659505,"cross-sectional observational, not case-control",37659505,https://doi.org/10.1016/j.jaci.2023.07.022,NA,"Chandrasekaran P., Han Y., Zerbe C.S., Heller T., DeRavin S.S., Kreuzberg S.A., Marciano B.E., Siu Y., Jones D.R., Abraham R.S., Stephens M.C., Tsou A.M., Snapper S., Conlan S., Subramanian P., Quinones M., Grou C., Calderon V., Deming C., Leiding J.W., Arnold D.E., Logan B.R., Griffith L.M., Petrovic A., Mousallem T.I., Kapoor N., Heimall J.R., Barnum J.L., Kapadia M., Wright N., Rayes A., Chandra S., Broglie L.A., Chellapandian D., Deal C.L., Grunebaum E., Lim S.S., Mallhi K., Marsh R.A., Murguia-Favela L., Parikh S., Touzot F., Cowan M.J., Dvorak C.C., Haddad E., Kohn D.B., Notarangelo L.D., Pai S.Y., Puck J.M., Pulsipher M.A., Torgerson T.R., Kang E.M., Malech H.L., Segre J.A., Bryant C.E., Holland S.M. , Falcone E.L.",Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease,The Journal of allergy and clinical immunology,2023,"CGD, Chronic granulomatous disease, IBD, NADPH oxidase, dysbiosis, inborn errors of immunity, inflammatory bowel disease, intestinal inflammation, metabolome, microbiome, primary immune deficiency",Experiment 6,"United States of America,Canada",Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,CGD patients less than or equal to 12 years,CGD patients above 12 years,CGD patients above 12 years old with no active IBD or history of IBD,26,12,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Fig E5D,19 March 2024,Ifyohondu,"Ifyohondu,Folakunmi,ChiomaBlessing,WikiWorks",Effect of age on microbiome signatures in CGD patients (with no active IBD or history of IBD) comparing participants less than or equal to 12 years VS above 12 years using LEfSe,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",3379134|976|200643|171549|171550|239759;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|3085636|186803|1769710;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Folakunmi
bsdb:37660163/1/NA,37660163,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N., Jinato T., Avihingsanon A., Nookaew I., Tanaka Y. , Tangkijvanich P.",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 1,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,Healthy controls,Patients at baseline - SVR,Patients at baseline with HCV monoinfection and HCV/HIV coinfection  who achieved sustained virological response (SVR),20,NA,2 weeks,16S,34,Illumina,relative abundances,NA,NA,NA,NA,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:37660163/3/NA,37660163,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N., Jinato T., Avihingsanon A., Nookaew I., Tanaka Y. , Tangkijvanich P.",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 3,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,Healthy controls,Follow-up at week 72 (FUw72) -SVR,Patients at week 72 after treatment completion who achieved sustained virological response (SVR),20,NA,2 weeks,16S,34,Illumina,relative abundances,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:37660163/4/NA,37660163,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N., Jinato T., Avihingsanon A., Nookaew I., Tanaka Y. , Tangkijvanich P.",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 4,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,Patients with mild fibrosis at baseline (F0–F1),Patients with mild fibrosis at FUw72 (F0–F1),Patients with mild fibrosis (F0–F1) at week 72 after treatment completion,NA,NA,2 weeks,16S,34,Illumina,relative abundances,NA,NA,NA,NA,NA,NA,NA,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:37660163/5/NA,37660163,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N., Jinato T., Avihingsanon A., Nookaew I., Tanaka Y. , Tangkijvanich P.",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 5,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,Patients with significant fibrosis to cirrhosis at baseline (F2–F4),Patients with significant fibrosis to cirrhosis at FUw72 (F2–F4),Patients with significant fibrosis to cirrhosis (F2–F4) at week 72 after treatment completion (FUw72),NA,NA,2 weeks,16S,34,Illumina,relative abundances,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:37660163/6/NA,37660163,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N., Jinato T., Avihingsanon A., Nookaew I., Tanaka Y. , Tangkijvanich P.",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 6,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,Patients with HCV monoinfection & (F2-F4) fibrosis at baseline,Patients with HCV monoinfection & (F2-F4) fibrosis at FUw72,Patients with HCV monoinfection and significant fibrosis to cirrhosis (F2-F4) at week 72 after treatment completion (FUw72).,NA,NA,2 weeks,16S,34,Illumina,relative abundances,NA,NA,NA,NA,NA,NA,NA,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:37660163/7/1,37660163,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N., Jinato T., Avihingsanon A., Nookaew I., Tanaka Y. , Tangkijvanich P.",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 7,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,Patients with HCV/HIV coinfection at baseline,Patients with HCV/HIV coinfection at FUw72,Patients with HCV/HIV coinfection at week 72 after treatment completion (FUw72),24,19,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,unchanged,increased,NA,NA,Signature 1,Table S4,4 April 2024,Idiaru angela,"Idiaru angela,WikiWorks,Tosin",Differential abundance at genus levels in baseline and follow-up week-72 (FUw72) of patients with HCV/HIV coinfection,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",1783272|1239|186801|3085636|186803|1766253;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|189330;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Svetlana up
bsdb:37660163/7/2,37660163,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N., Jinato T., Avihingsanon A., Nookaew I., Tanaka Y. , Tangkijvanich P.",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 7,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,Patients with HCV/HIV coinfection at baseline,Patients with HCV/HIV coinfection at FUw72,Patients with HCV/HIV coinfection at week 72 after treatment completion (FUw72),24,19,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,unchanged,increased,NA,NA,Signature 2,Table S3,4 April 2024,Idiaru angela,"Idiaru angela,WikiWorks,Tosin",Differential abundance at genus levels in baseline and follow-up week-72 (FUw72) of patients with HCV/HIV coinfection,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136",3379134|976|200643|171549|815|816;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|877420,Complete,Svetlana up
bsdb:37660163/8/NA,37660163,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N., Jinato T., Avihingsanon A., Nookaew I., Tanaka Y. , Tangkijvanich P.",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 8,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,Patients with HCV monoinfection + mild fibrosis at baseline,Patients with HCV monoinfection + mild fibrosis at FUw72,Patients with HCV monoinfection who had F0–F1 fibrosis stage at week 72 after treatment completion (FUw72),NA,NA,2 weeks,16S,34,Illumina,relative abundances,NA,NA,NA,NA,NA,NA,NA,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:37660163/9/NA,37660163,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N., Jinato T., Avihingsanon A., Nookaew I., Tanaka Y. , Tangkijvanich P.",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 9,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,Patients with HCV monoinfection + significant fibrosis at baseline,Patients with HCV monoinfection + significant fibrosis at FUw72,Patients with HCV monoinfection who had F2–F4 fibrosis stage at week 72 after treatment completion (FUw72),NA,NA,2 weeks,16S,34,Illumina,relative abundances,NA,NA,NA,NA,NA,NA,NA,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:37660163/10/NA,37660163,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N., Jinato T., Avihingsanon A., Nookaew I., Tanaka Y. , Tangkijvanich P.",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 10,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,Patients with HCV/HIV coinfection + mild fibrosis at baseline,Patients with HCV/HIV coinfection + mild fibrosis at FUw72,Patients with HCV/HIV coinfection who had F0–F1 fibrosis stage at week 72 after treatment completion (FUw72),NA,NA,2 weeks,16S,34,Illumina,relative abundances,NA,NA,NA,NA,NA,NA,NA,NA,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:37660163/11/1,37660163,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N., Jinato T., Avihingsanon A., Nookaew I., Tanaka Y. , Tangkijvanich P.",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 11,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,patients with HCV monoinfection at baseline,patients with HCV monoinfection at FUw72,patients with HCV monoinfection at week 72 after treatment completion (FUw72),62,50,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,increased,increased,NA,NA,Signature 1,Table S3,4 April 2024,Idiaru angela,"Idiaru angela,WikiWorks,Tosin",Differential abundance at genus levels in baseline and follow-up week-72 (FUw72) of patients with HCV monoinfection,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii",1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803|2569097|39488,Complete,Svetlana up
bsdb:37660163/11/2,37660163,time series / longitudinal observational,37660163,10.1038/s41598-023-41664-7,NA,"Chuaypen N., Jinato T., Avihingsanon A., Nookaew I., Tanaka Y. , Tangkijvanich P.",Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection,Scientific reports,2023,NA,Experiment 11,Thailand,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,patients with HCV monoinfection at baseline,patients with HCV monoinfection at FUw72,patients with HCV monoinfection at week 72 after treatment completion (FUw72),62,50,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,increased,increased,NA,NA,Signature 2,Table S3,4 April 2024,Idiaru angela,"Idiaru angela,WikiWorks",Differential abundance at genus levels in baseline and follow-up week-72 (FUw72) of patients with HCV monoinfection,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|1506553,Complete,Svetlana up
bsdb:37679873/1/1,37679873,time series / longitudinal observational,37679873,10.1097/MPG.0000000000003928,NA,"Menzies J., Sundararaj A., Cardamone M., McHarg A., Leach S. , Krishnan U.","Ketogenic Diets in Children With Intractable Epilepsy and its Effects on Gastrointestinal Function, Gut Microbiome, Inflammation, and Quality of Life",Journal of pediatric gastroenterology and nutrition,2023,NA,Experiment 1,Australia,Homo sapiens,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,pre-ketogenic diet,post-ketogenic diet,children with intractable epilepsy (IE) after ketogenic diet (KD) treatment,12,14,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Supplemental Digital Content 4,11 December 2024,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of post-ketogenic diet group compared to pre-ketogenic diet group,increased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,NA
bsdb:37679873/1/2,37679873,time series / longitudinal observational,37679873,10.1097/MPG.0000000000003928,NA,"Menzies J., Sundararaj A., Cardamone M., McHarg A., Leach S. , Krishnan U.","Ketogenic Diets in Children With Intractable Epilepsy and its Effects on Gastrointestinal Function, Gut Microbiome, Inflammation, and Quality of Life",Journal of pediatric gastroenterology and nutrition,2023,NA,Experiment 1,Australia,Homo sapiens,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,pre-ketogenic diet,post-ketogenic diet,children with intractable epilepsy (IE) after ketogenic diet (KD) treatment,12,14,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Supplemental Digital Content 4,11 December 2024,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of post-ketogenic diet group compared to pre-ketogenic diet group,decreased,k__Bacillati|p__Actinomycetota,1783272|201174,Complete,NA
bsdb:37686135/1/1,37686135,meta-analysis,37686135,10.3390/ijms241713329,NA,"Park S., Li C., Wu X. , Zhang T.",Gut Microbiota Alterations and Their Functional Differences in Depression According to Enterotypes in Asian Individuals,International journal of molecular sciences,2023,"enterotype, glucose metabolism, gut microbiota, gut–brain axis, network analysis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Depressive disorder,MONDO:0002050,Healthy group,Depressive group,patients with depressive disorder in the high bacteroidaceae enterotype (ET-B). Enterotypes were identified through PCA using gut microbiota from the collected fecal FASTA/Q files.,45,84,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 2C,9 March 2024,Idiat,"Idiat,Welile,Folakunmi,WikiWorks",Primary gut microbiota in Healthy and Depression groups in high bacteroidaceae  enterotype (ET-B) using linear discriminant analysis (LDA) scores.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pseudescherichia|s__Pseudescherichia vulneris,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Petroclostridium|s__Petroclostridium xylanilyticum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum",3379134|1224|1236|91347|543|2055880|566;1783272|1239|186801|186802|216572|2304687|1792311;1783272|1239|186801|186802|31979|1485|1522,Complete,Folakunmi
bsdb:37686135/1/2,37686135,meta-analysis,37686135,10.3390/ijms241713329,NA,"Park S., Li C., Wu X. , Zhang T.",Gut Microbiota Alterations and Their Functional Differences in Depression According to Enterotypes in Asian Individuals,International journal of molecular sciences,2023,"enterotype, glucose metabolism, gut microbiota, gut–brain axis, network analysis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Depressive disorder,MONDO:0002050,Healthy group,Depressive group,patients with depressive disorder in the high bacteroidaceae enterotype (ET-B). Enterotypes were identified through PCA using gut microbiota from the collected fecal FASTA/Q files.,45,84,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 2C,9 March 2024,Idiat,"Idiat,Folakunmi,Aananditaa,WikiWorks",Primary gut microbiota in Healthy and Depression groups in high bacteroidaceae enterotype (ET-B) using linear discriminant analysis (LDA) scores.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum butyriciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella massiliensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia albertii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Faecalibacillus|s__Faecalibacillus intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium hattorii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] colinum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia maritimum",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|186802|3085642|2048137|1628085;1783272|1239|186801|3085636|186803|43996|2799636;3379134|1224|1236|91347|543|561|208962;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|526524|526525|2810280|2678885|1982626;1783272|1239|186801|186802|216572|216851|2935520;1783272|1239|186801|186802|204475|745368;3379134|1224|28216|80840|995019|577310|487175;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|186801|3085636|186803|1506577|36835;1783272|1239|186801|3085636|186803|572511|2763028;1783272|1239|186801|3082720|186804|1501226|2020948,Complete,Folakunmi
bsdb:37686135/2/1,37686135,meta-analysis,37686135,10.3390/ijms241713329,NA,"Park S., Li C., Wu X. , Zhang T.",Gut Microbiota Alterations and Their Functional Differences in Depression According to Enterotypes in Asian Individuals,International journal of molecular sciences,2023,"enterotype, glucose metabolism, gut microbiota, gut–brain axis, network analysis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Depressive disorder,MONDO:0002050,Healthy group,Depressive group,patients with depression in the high lachnospiraceae enterotype (ET-L). Enterotypes were identified through PCA using gut microbiota from the collected fecal FASTA/Q files.,47,127,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,figure 3D,19 March 2024,Folakunmi,"Folakunmi,WikiWorks",Primary gut microbiota in Healthy and DP groups at the species level in high lachnospiraceae enterotype (ET-L) using linear discriminant analysis (LDA) scores.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia provencensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia luti,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia glucerasea,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea phocaeensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus senegalensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum faecicola,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Evtepia|s__Evtepia gabavorous,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii",1783272|1239|186801|3085636|186803|572511|1936059;1783272|1239|186801|3085636|186803|572511|89014;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|186801|3085636|186803|2316020|33038;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|3085636|186803|572511|536633;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|186801|3085636|186803|2719313|208479;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|3085636|186803|189330|2040291;1783272|1239|186801|3085636|186803|2719313|1531;1783272|1239|186801|186802|31979|1485|1522;1783272|1239|186801|3085636|186803|2316020|1720300;1783272|1239|186801|186802|3082771|1924093|1673717;1783272|1239|186801|3085636|3118652|2039240|2358141;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|186801|186802|2211178|2211183;1783272|1239|186801|186802|216572|946234|292800,Complete,Folakunmi
bsdb:37686135/2/2,37686135,meta-analysis,37686135,10.3390/ijms241713329,NA,"Park S., Li C., Wu X. , Zhang T.",Gut Microbiota Alterations and Their Functional Differences in Depression According to Enterotypes in Asian Individuals,International journal of molecular sciences,2023,"enterotype, glucose metabolism, gut microbiota, gut–brain axis, network analysis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Depressive disorder,MONDO:0002050,Healthy group,Depressive group,patients with depression in the high lachnospiraceae enterotype (ET-L). Enterotypes were identified through PCA using gut microbiota from the collected fecal FASTA/Q files.,47,127,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,figure 3D,19 March 2024,Folakunmi,"Folakunmi,Aananditaa,WikiWorks",Primary gut microbiota in Healthy and DP groups at the species level in high lachnospiraceae enterotype (ET-L) using linear discriminant analysis (LDA) scores.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum butyriciproducens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes faecalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia phocaeensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium saudiense,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella porci,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia albertii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Faecalibacillus|s__Faecalibacillus intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium hattorii,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Gehongia|s__Gehongia tenuis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas massiliensis (ex Afouda et al. 2020),k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium pacaense,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__[Lactobacillus] rogosae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Marseillibacter|s__Marseillibacter massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter faecis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Petroclostridium|s__Petroclostridium xylanilyticum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor gallinarum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Simiaoa|s__Simiaoa hominis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus periodonticum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Vescimonas|s__Vescimonas coprocola,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia maritimum",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|186802|3085642|2048137|1628085;3379134|976|200643|171549|171550|239759|328814;1783272|1239|186801|3085636|186803|207244|2738446;3379134|976|200643|171549|815|816|1912894;3379134|976|200643|171549|815|816|820;1783272|201174|1760|85004|31953|1678|1686;1783272|1239|186801|3085636|186803|572511|2025493;1783272|1239|186801|3085636|186803|572511|1917888;1783272|1239|186801|186802|31979|1485|1414720;1783272|1239|909932|1843489|31977|39948|2161821;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|1432051|2652274;3379134|1224|1236|91347|543|561|208962;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|526524|526525|2810280|2678885|1982626;1783272|1239|186801|186802|216572|216851|2935520;1783272|1239|186801|3082768|990719|2944147|2763655;1783272|1239|186801|186802|204475|745368;3379134|1224|1236|135625|712|724|729;1783272|1239|186801|186802|1392389|1673721;1783272|1239|186801|186802|31979|1485|1917870;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|28050|706562;1783272|1239|186801|186802|216572|1930587|1852369;1783272|1239|186801|3085636|186803|2316020|592978;3379134|1224|28216|80840|995019|577310|487175;1783272|1239|186801|186802|216572|2304687|1792311;1783272|1239|909932|1843488|909930|33024|33025;3379134|976|200643|171549|815|909656|204516;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|186802|216572|1017280|2779352;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|186802|216572|1263|40518;3379134|976|200643|171549|171552|2974251|2518605;1783272|1239|186801|3085636|186803|2944193|2763665;1783272|1239|91061|186826|1300|1301|2490633;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|186801|186802|216572|2892396|2714355;1783272|1239|186801|3085636|186803|572511|2763028;1783272|1239|186801|3082720|186804|1501226|2020948,Complete,Folakunmi
bsdb:37695126/1/1,37695126,case-control,37695126,10.1128/spectrum.00662-23,NA,"Eickhardt-Dalbøge C.S., Ingham A.C., Nielsen H.V., Fuursted K., Stensvold C.R., Andersen L.O., Larsen M.K., Kjær L., Christensen S.F., Knudsen T.A., Skov V., Ellervik C., Olsen L.R., Hasselbalch H.C., Elmer Christensen J.J. , Nielsen X.C.",Pronounced gut microbiota signatures in patients with <i>JAK2V617F-</i>positive essential thrombocythemia,Microbiology spectrum,2023,"ET, JAK2V617F, essential thrombocythemia, gut microbiome, gut microbiota, inflammation, myelofibrosis, myeloproliferative neoplasms, polycythemia vera",Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Essential thrombocythemia,EFO:0000479,Healthy Controls,Essential thrombocythemia (ET),"Patients with essential thrombocythemia (ET), a cancer characterized by thrombocyte overproduction",42,54,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,0.005,sex,NA,NA,NA,NA,NA,unchanged,increased,Signature 1,Fig 6a,12 March 2024,Deacme,"Deacme,WikiWorks",Differential abundance analysis identified using LEfSe between healthy controls and patients with Essential Thrombocythemia,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|526524|526525|128827;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:37695126/1/2,37695126,case-control,37695126,10.1128/spectrum.00662-23,NA,"Eickhardt-Dalbøge C.S., Ingham A.C., Nielsen H.V., Fuursted K., Stensvold C.R., Andersen L.O., Larsen M.K., Kjær L., Christensen S.F., Knudsen T.A., Skov V., Ellervik C., Olsen L.R., Hasselbalch H.C., Elmer Christensen J.J. , Nielsen X.C.",Pronounced gut microbiota signatures in patients with <i>JAK2V617F-</i>positive essential thrombocythemia,Microbiology spectrum,2023,"ET, JAK2V617F, essential thrombocythemia, gut microbiome, gut microbiota, inflammation, myelofibrosis, myeloproliferative neoplasms, polycythemia vera",Experiment 1,Denmark,Homo sapiens,Feces,UBERON:0001988,Essential thrombocythemia,EFO:0000479,Healthy Controls,Essential thrombocythemia (ET),"Patients with essential thrombocythemia (ET), a cancer characterized by thrombocyte overproduction",42,54,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,0.005,sex,NA,NA,NA,NA,NA,unchanged,increased,Signature 2,Fig 6a,12 March 2024,Deacme,"Deacme,Scholastica,WikiWorks",Differential abundance analysis identified using LEfSe between healthy controls and patients with Essential Thrombocythemia,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;1783272|1239|186801|186802|216572;1783272|1239,Complete,Svetlana up
bsdb:37695126/2/1,37695126,case-control,37695126,10.1128/spectrum.00662-23,NA,"Eickhardt-Dalbøge C.S., Ingham A.C., Nielsen H.V., Fuursted K., Stensvold C.R., Andersen L.O., Larsen M.K., Kjær L., Christensen S.F., Knudsen T.A., Skov V., Ellervik C., Olsen L.R., Hasselbalch H.C., Elmer Christensen J.J. , Nielsen X.C.",Pronounced gut microbiota signatures in patients with <i>JAK2V617F-</i>positive essential thrombocythemia,Microbiology spectrum,2023,"ET, JAK2V617F, essential thrombocythemia, gut microbiome, gut microbiota, inflammation, myelofibrosis, myeloproliferative neoplasms, polycythemia vera",Experiment 2,Denmark,Homo sapiens,Feces,UBERON:0001988,Essential thrombocythemia,EFO:0000479,Healthy Controls,Janus-kinase 2 (JAK2V617F)-positive,Essential thrombocythemia patients positive for the Janus-kinase 2 (JAK2V617F) mutation,42,36,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,0.005,sex,NA,NA,NA,NA,NA,unchanged,increased,Signature 1,Fig 6b,14 March 2024,Deacme,"Deacme,WikiWorks",Differential abundance analysis identified using LEfSe between healthy controls and Essential thrombocythemia patients positive for the JAK2V617F mutation,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524|526525|2810281|191303;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:37695126/2/2,37695126,case-control,37695126,10.1128/spectrum.00662-23,NA,"Eickhardt-Dalbøge C.S., Ingham A.C., Nielsen H.V., Fuursted K., Stensvold C.R., Andersen L.O., Larsen M.K., Kjær L., Christensen S.F., Knudsen T.A., Skov V., Ellervik C., Olsen L.R., Hasselbalch H.C., Elmer Christensen J.J. , Nielsen X.C.",Pronounced gut microbiota signatures in patients with <i>JAK2V617F-</i>positive essential thrombocythemia,Microbiology spectrum,2023,"ET, JAK2V617F, essential thrombocythemia, gut microbiome, gut microbiota, inflammation, myelofibrosis, myeloproliferative neoplasms, polycythemia vera",Experiment 2,Denmark,Homo sapiens,Feces,UBERON:0001988,Essential thrombocythemia,EFO:0000479,Healthy Controls,Janus-kinase 2 (JAK2V617F)-positive,Essential thrombocythemia patients positive for the Janus-kinase 2 (JAK2V617F) mutation,42,36,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,0.005,sex,NA,NA,NA,NA,NA,unchanged,increased,Signature 2,Fig 6b,14 March 2024,Deacme,"Deacme,Scholastica,WikiWorks",Differential abundance analysis identified using LEfSe between healthy controls and Essential thrombocythemia patients positive for the JAK2V617F mutation,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;1783272|1239|186801|186802|216572;1783272|1239;1783272|1239|186801|186802,Complete,Svetlana up
bsdb:37695126/3/1,37695126,case-control,37695126,10.1128/spectrum.00662-23,NA,"Eickhardt-Dalbøge C.S., Ingham A.C., Nielsen H.V., Fuursted K., Stensvold C.R., Andersen L.O., Larsen M.K., Kjær L., Christensen S.F., Knudsen T.A., Skov V., Ellervik C., Olsen L.R., Hasselbalch H.C., Elmer Christensen J.J. , Nielsen X.C.",Pronounced gut microbiota signatures in patients with <i>JAK2V617F-</i>positive essential thrombocythemia,Microbiology spectrum,2023,"ET, JAK2V617F, essential thrombocythemia, gut microbiome, gut microbiota, inflammation, myelofibrosis, myeloproliferative neoplasms, polycythemia vera",Experiment 3,Denmark,Homo sapiens,Feces,UBERON:0001988,Essential thrombocythemia,EFO:0000479,Healthy Controls,Janus-kinase 2 (JAK2V617F)-negative,Essential thrombocythemia patients negative for the Janus-kinase 2 (JAK2V617F) mutation,42,16,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,0.005,sex,NA,NA,NA,NA,NA,unchanged,unchanged,Signature 1,Fig 6c,14 March 2024,Deacme,"Deacme,WikiWorks",Differential abundance analysis identified using LEfSe between healthy controls and Essential thrombocythemia patients negative for the JAK2V617F mutation,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|292632,Complete,Svetlana up
bsdb:37695126/3/2,37695126,case-control,37695126,10.1128/spectrum.00662-23,NA,"Eickhardt-Dalbøge C.S., Ingham A.C., Nielsen H.V., Fuursted K., Stensvold C.R., Andersen L.O., Larsen M.K., Kjær L., Christensen S.F., Knudsen T.A., Skov V., Ellervik C., Olsen L.R., Hasselbalch H.C., Elmer Christensen J.J. , Nielsen X.C.",Pronounced gut microbiota signatures in patients with <i>JAK2V617F-</i>positive essential thrombocythemia,Microbiology spectrum,2023,"ET, JAK2V617F, essential thrombocythemia, gut microbiome, gut microbiota, inflammation, myelofibrosis, myeloproliferative neoplasms, polycythemia vera",Experiment 3,Denmark,Homo sapiens,Feces,UBERON:0001988,Essential thrombocythemia,EFO:0000479,Healthy Controls,Janus-kinase 2 (JAK2V617F)-negative,Essential thrombocythemia patients negative for the Janus-kinase 2 (JAK2V617F) mutation,42,16,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,0.005,sex,NA,NA,NA,NA,NA,unchanged,unchanged,Signature 2,Fig 6c,14 March 2024,Deacme,"Deacme,Scholastica,WikiWorks",Differential abundance analysis identified using LEfSe between healthy controls and Essential thrombocythemia patients negative for the JAK2V617F mutation,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:37695126/4/1,37695126,case-control,37695126,10.1128/spectrum.00662-23,NA,"Eickhardt-Dalbøge C.S., Ingham A.C., Nielsen H.V., Fuursted K., Stensvold C.R., Andersen L.O., Larsen M.K., Kjær L., Christensen S.F., Knudsen T.A., Skov V., Ellervik C., Olsen L.R., Hasselbalch H.C., Elmer Christensen J.J. , Nielsen X.C.",Pronounced gut microbiota signatures in patients with <i>JAK2V617F-</i>positive essential thrombocythemia,Microbiology spectrum,2023,"ET, JAK2V617F, essential thrombocythemia, gut microbiome, gut microbiota, inflammation, myelofibrosis, myeloproliferative neoplasms, polycythemia vera",Experiment 4,Denmark,Homo sapiens,Feces,UBERON:0001988,Essential thrombocythemia,EFO:0000479,Janus-kinase 2 (JAK2V617F)-negative,Janus-kinase 2 (JAK2V617F)-positive,Essential thrombocythemia patients positive for the Janus-kinase 2 (JAK2V617F) mutation,16,36,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,0.005,sex,NA,NA,NA,NA,NA,unchanged,unchanged,Signature 1,Fig 6d,14 March 2024,Deacme,"Deacme,WikiWorks",Differential abundance analysis identified using LEfSe between Essential thrombocythemia patients negative for the JAK2V617F mutation and patients positive for the JAK2V617F mutation,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales",1783272|1239|91061;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|526524|526525,Complete,Svetlana up
bsdb:37695126/4/2,37695126,case-control,37695126,10.1128/spectrum.00662-23,NA,"Eickhardt-Dalbøge C.S., Ingham A.C., Nielsen H.V., Fuursted K., Stensvold C.R., Andersen L.O., Larsen M.K., Kjær L., Christensen S.F., Knudsen T.A., Skov V., Ellervik C., Olsen L.R., Hasselbalch H.C., Elmer Christensen J.J. , Nielsen X.C.",Pronounced gut microbiota signatures in patients with <i>JAK2V617F-</i>positive essential thrombocythemia,Microbiology spectrum,2023,"ET, JAK2V617F, essential thrombocythemia, gut microbiome, gut microbiota, inflammation, myelofibrosis, myeloproliferative neoplasms, polycythemia vera",Experiment 4,Denmark,Homo sapiens,Feces,UBERON:0001988,Essential thrombocythemia,EFO:0000479,Janus-kinase 2 (JAK2V617F)-negative,Janus-kinase 2 (JAK2V617F)-positive,Essential thrombocythemia patients positive for the Janus-kinase 2 (JAK2V617F) mutation,16,36,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,0.005,sex,NA,NA,NA,NA,NA,unchanged,unchanged,Signature 2,Fig 6d,16 March 2024,Deacme,"Deacme,WikiWorks",Differential abundance analysis identified using LEfSe between Essential thrombocythemia patients negative for the JAK2V617F mutation and patients positive for the JAK2V617F mutation,decreased,NA,NA,Complete,Svetlana up
bsdb:37700874/1/1,37700874,case-control,37700874,10.2147/JAA.S422537,NA,"Wan J., Song J., Lv Q., Zhang H., Xiang Q., Dai H., Zheng H., Lin X. , Zhang W.",Alterations in the Gut Microbiome of Young Children with Airway Allergic Disease Revealed by Next-Generation Sequencing,Journal of asthma and allergy,2023,"allergic asthma, allergic rhinitis, childhood, gut microbiome, metagenomic sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Allergic asthma,MONDO:0004784,Healthy control,Allergic asthma,Children with allergic asthma,19,23,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,body mass index,sex",NA,NA,increased,NA,increased,NA,NA,Signature 1,"FIG 4A, 4B",8 April 2024,Rahila,"Rahila,Scholastica,WikiWorks",Linear discriminant analysis (LDA) scores for crucial bacteria classification with different abundances in allergic asthma versus healthy groups,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus macedonicus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales",1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|28026;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|186802|216572|1263|457412;1783272|1239|91061|186826|1300|1301|1304;1783272|201174|1760|2037|2049|1654|55565;1783272|201174|1760|2037|2049|2529408|1660;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|84998|1643822|1643826|84111|84112;1783272|201174|84998|1643822|1643826|84111;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|1239|91061|1385|539738|1378|1379;1783272|1239|91061|186826|1300|1301|59310;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300;1783272|1239|91061|186826;1783272|1239|909932|1843489|31977|906|907;4751|4890|3239874|2916678|766764|5475|5476;4751|4890|3239874|2916678|766764|5475;4751|4890|4891|4892,Complete,Svetlana up
bsdb:37700874/1/2,37700874,case-control,37700874,10.2147/JAA.S422537,NA,"Wan J., Song J., Lv Q., Zhang H., Xiang Q., Dai H., Zheng H., Lin X. , Zhang W.",Alterations in the Gut Microbiome of Young Children with Airway Allergic Disease Revealed by Next-Generation Sequencing,Journal of asthma and allergy,2023,"allergic asthma, allergic rhinitis, childhood, gut microbiome, metagenomic sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Allergic asthma,MONDO:0004784,Healthy control,Allergic asthma,Children with allergic asthma,19,23,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,body mass index,sex",NA,NA,increased,NA,increased,NA,NA,Signature 2,"FIG 4A, 4B",9 June 2024,Scholastica,"Scholastica,WikiWorks",Linear discriminant analysis (LDA) scores for crucial bacteria classification with different abundances in allergic asthma versus healthy groups,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae",3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|246787;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|2005519|397864|487174;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|815|909656|310298;3379134|976|200643|171549|815|909656|821;1783272|1239|909932|1843489|31977|906;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815;3379134|976|200643|171549|2005519|1348911|1099853;3379134|976|200643|171549|2005519|1348911;3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550;3379134|976|200643|171549;1783272|1239|91061|186826|33958|2742598|1613;1783272|1239|909932|1843488|909930|904;1783272|1239|909932|1843488|909930,Complete,Svetlana up
bsdb:37702484/2/1,37702484,case-control,37702484,10.1128/spectrum.02360-23,NA,"Chen K., Geng H., Liu J. , Ye C.",Alteration in gut mycobiota of patients with polycystic ovary syndrome,Microbiology spectrum,2023,"Aspergillus, Lentinula, Saccharomyces, gut mycobiota, polycystic ovary syndrome",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy Controls,Polycystic ovary syndrome (PCOS) patients,Women with PCOS diagnosed according to the 2003 Rotterdam criteria.,17,17,NA,PCR,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,decreased,decreased,unchanged,decreased,NA,decreased,Signature 1,"Figure 3b, 4b and 5b",4 July 2025,Victoria,Victoria,"Fecal microbial community composition at the phylum, family, and genus level. Results were analyzed by the Mann-Whitney U-test (n = 17).",increased,"k__Fungi|p__Ascomycota,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Marasmiaceae,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Trichocomaceae,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces",4751|4890;4751|4890|4891|4892|4893;4751|5204|155619|5338|654128;4751|4890|147545|5042|28568;4751|4890|4891|4892|4893|4930,Complete,Svetlana up
bsdb:37702484/2/2,37702484,case-control,37702484,10.1128/spectrum.02360-23,NA,"Chen K., Geng H., Liu J. , Ye C.",Alteration in gut mycobiota of patients with polycystic ovary syndrome,Microbiology spectrum,2023,"Aspergillus, Lentinula, Saccharomyces, gut mycobiota, polycystic ovary syndrome",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy Controls,Polycystic ovary syndrome (PCOS) patients,Women with PCOS diagnosed according to the 2003 Rotterdam criteria.,17,17,NA,PCR,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,decreased,decreased,unchanged,decreased,NA,decreased,Signature 2,Figure 3b and 5b,4 July 2025,Victoria,Victoria,"Fecal microbial community composition at the phylum, family, and genus level. Results were analyzed by the Mann-Whitney U-test (n = 17).",decreased,"k__Fungi|p__Basidiomycota,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Omphalotaceae|g__Lentinula",4751|5204;4751|4890|147545|5042|1131492|5052;4751|5204|155619|5338|72117|5352,Complete,Svetlana up
bsdb:37715296/1/1,37715296,"cross-sectional observational, not case-control",37715296,10.1186/s40168-023-01636-5,NA,"Mills M., Lee S., Piperata B.A., Garabed R., Choi B. , Lee J.",Household environment and animal fecal contamination are critical modifiers of the gut microbiome and resistome in young children from rural Nicaragua,Microbiome,2023,"Animals, Breastfeeding duration, Dirt floor, E. coli as antibiotic resistance host, Microbial source tracking, Multi-drug resistance, One Health",Experiment 1,Nicaragua,Homo sapiens,Feces,UBERON:0001988,Environmental factor,EFO:0000469,Infants,Children,Participants between 2.0 – 6.0 years of age,26,31,NA,WMS,NA,Nanopore,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,increased,increased,NA,NA,NA,NA,Signature 1,Figure 2b,23 March 2024,Aishat,"Aishat,Scholastica,WikiWorks",Bacterial families with different abundances in children versus infants identified with linear discriminant analysis effect size (LEfSe),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171552;3379134|203691|203692|136|137;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:37715296/1/2,37715296,"cross-sectional observational, not case-control",37715296,10.1186/s40168-023-01636-5,NA,"Mills M., Lee S., Piperata B.A., Garabed R., Choi B. , Lee J.",Household environment and animal fecal contamination are critical modifiers of the gut microbiome and resistome in young children from rural Nicaragua,Microbiome,2023,"Animals, Breastfeeding duration, Dirt floor, E. coli as antibiotic resistance host, Microbial source tracking, Multi-drug resistance, One Health",Experiment 1,Nicaragua,Homo sapiens,Feces,UBERON:0001988,Environmental factor,EFO:0000469,Infants,Children,Participants between 2.0 – 6.0 years of age,26,31,NA,WMS,NA,Nanopore,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,increased,increased,NA,NA,NA,NA,Signature 2,Figure 2b,23 March 2024,Aishat,"Aishat,Scholastica,WikiWorks",Bacterial families with different abundances in children versus infants identified with linear discriminant analysis effect size (LEfSe),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",3379134|976|200643|171549|815;1783272|201174|1760|85004|31953;3379134|1224|1236|91347|543,Complete,Svetlana up
bsdb:37715296/2/1,37715296,"cross-sectional observational, not case-control",37715296,10.1186/s40168-023-01636-5,NA,"Mills M., Lee S., Piperata B.A., Garabed R., Choi B. , Lee J.",Household environment and animal fecal contamination are critical modifiers of the gut microbiome and resistome in young children from rural Nicaragua,Microbiome,2023,"Animals, Breastfeeding duration, Dirt floor, E. coli as antibiotic resistance host, Microbial source tracking, Multi-drug resistance, One Health",Experiment 2,Nicaragua,Homo sapiens,Feces,UBERON:0001988,Exposure,EFO:0000487,No - antibiotics,Yes - antibiotics,Infants and young children (ages 4 days - 6 years) in rural Nicaragua who had ever received antibiotics,11,11,NA,WMS,NA,Nanopore,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S5,5 July 2024,Scholastica,"Scholastica,WikiWorks",Differentially abundant taxa identified in children and infants who had compared to those who had not received antibiotics using linear discriminant analysis effect size (LEfSe).,decreased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale",1783272|1239|1737404|1737405|1570339|543311|33033;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|91061|186826|33958|46255;1783272|1239|909932|909929|1843491|158846|158847,Complete,Svetlana up
bsdb:37715299/1/2,37715299,laboratory experiment,37715299,https://doi.org/10.1093/femspd/ftad025,NA,"Shaw C.G., Pavloudi C., Barela Hudgell M.A., Crow R.S., Saw J.H., Pyron R.A. , Smith L.C.",Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium,Pathogens and disease,2023,"16S rRNA high throughput sequencing, Strongylocentrotus purpuratus, bacterial infection, echinoderm, microbiome",Experiment 1,United States of America,Strongylocentrotus purpuratus,Anatomical surface,UBERON:0006984,Bacterial disease,EFO:0000771,Diseased + Recovered sea urchins,Healthy sea urchins,Healthy sea urchins refers to sea urchins in aquarium A and B that are healthy.,8,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 6 & Supplementary Data file 2,  Table S7.",16 April 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,KateRasheed,WikiWorks",Taxa with significantly different abundances in the microbiomes on sea urchins among the groups.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Agarivorans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Candidatus Tectimicrobiota|c__Candidatus Entotheonellia|o__Candidatus Entotheonellales|f__Candidatus Entotheonellaceae|g__Candidatus Entotheonella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae|g__Candidatus Riegeria,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfocapsaceae|g__Desulfotalea,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Devosia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Draconibacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flagellimonas,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Halieaceae|g__Halioglobus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Parvularculales|f__Parvularculaceae|g__Hyphococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomonadales|f__Hyphomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Jannaschia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Ahrensiaceae|g__Pseudahrensia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Psychroflexus,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Pirellulales|f__Pirellulaceae|g__Rhodopirellula,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Roseimarinus,k__Pseudomonadati|p__Bacteroidota|c__Saprospiria|o__Saprospirales|f__Saprospiraceae|g__Rubidimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Terasakiellaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Ulvibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Cyanobacteriota",3379134|1224|1236|135622|72275|261825;3379134|976|200643;3379134|1802339|3277336|3277337|3277338|93171;3379134|1224|28211|204441|41295|1068873;3379134|976|1853228|1853229;1783272|1239|186801|3082768|990719;1783272|1239|186801;3379134|200940|3031451|3024411|213121|893;3379134|200940|3031451|3024411|2886822|109168;3379134|1224|28211|356|2831106|46913;3379134|976|200643|1970189|1471398|1471399;3379134|976|117743|200644|49546|444459;3379134|976|117743|200644|49546;3379134|1224|1236|1706369|1706372|1217416;3379134|1224|28211|255473|255474|2038635;3379134|1224|28211|2800060|69657;3379134|1224|28211|204455|2854170|188905;1783272|1239|186801|3085636|186803;3379134|976|200643|1970189|1573805;3379134|1224|28211|356|2829814|1434035;3379134|976|117743|200644|49546|83612;3379134|203682|203683|2691354|2691357|265488;3379134|976|200643|1970189|1471398|1827484;3379134|976|1937959|1936988|89374|1147735;3379134|1224|1236|135622|267890|22;3379134|1224|28211|204441|2813951;3379134|976|117743|200644|49546|237444;3379134|1224|1236;1783272|1117,Complete,Svetlana up
bsdb:37715299/2/1,37715299,laboratory experiment,37715299,https://doi.org/10.1093/femspd/ftad025,NA,"Shaw C.G., Pavloudi C., Barela Hudgell M.A., Crow R.S., Saw J.H., Pyron R.A. , Smith L.C.",Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium,Pathogens and disease,2023,"16S rRNA high throughput sequencing, Strongylocentrotus purpuratus, bacterial infection, echinoderm, microbiome",Experiment 2,United States of America,Strongylocentrotus purpuratus,Anatomical surface,UBERON:0006984,Bacterial disease,EFO:0000771,Healthy + Diseased sea urchins,Recovered sea urchins,"A quality in which complete clearance of the disorder is attained; however, physiological 'memory' may persist.",8,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 6 & Supplementary Data file 2,  Table S7.",16 April 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,KateRasheed,WikiWorks",Taxa with significantly different abundances in the microbiomes on sea urchins among the groups.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Pseudomaricurvus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Pleioneaceae|g__Aliikangiella,k__Pseudomonadati|p__Bdellovibrionota|c__Bacteriovoracia|o__Bacteriovoracales|f__Bacteriovoracaceae,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Coxiella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales|f__Desulfobacteraceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfocapsaceae|g__Desulforhopalus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomonadales|f__Hyphomonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Spongiibacteraceae|g__Oceanicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Roseibacillus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Rubritaleaceae|g__Rubritalea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Spongiibacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Colwelliaceae|g__Thalassotalea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,p__Candidatus Absconditibacteriota",3379134|1224|1236|1706369|1706371|1635133;3379134|1224|1236|135619|2823145|1920241;3379134|3018035|3031419|2024979|263369;3379134|976|1853228|1853229;1783272|1239|186801|3082768|990719;1783272|1239|186801;3379134|1224|1236|118969|118968|776;3379134|200940|3024418|213118|213119;3379134|200940|3031451|3024411|2886822|40413;3379134|200940|3031449|213115|194924|872;3379134|1224|1236;3379134|1224|28211|2800060|69657;1783272|1239|186801|3085636|186803;3379134|1224|1236|1706369|1706375|1084558;1783272|1239|186801|186802|216572;3379134|1224|28211|766;3379134|74201|203494|48461|203557|518755;3379134|74201|203494|48461|1648490|361050;3379134|1224|1236|1706369|1706375;3379134|1224|1236|135622|267889|1518149;3379134|1224|1236|135623|641|662;221235,Complete,Svetlana up
bsdb:37715299/3/1,37715299,laboratory experiment,37715299,https://doi.org/10.1093/femspd/ftad025,NA,"Shaw C.G., Pavloudi C., Barela Hudgell M.A., Crow R.S., Saw J.H., Pyron R.A. , Smith L.C.",Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium,Pathogens and disease,2023,"16S rRNA high throughput sequencing, Strongylocentrotus purpuratus, bacterial infection, echinoderm, microbiome",Experiment 3,United States of America,Strongylocentrotus purpuratus,Anatomical surface,UBERON:0006984,Bacterial disease,EFO:0000771,Recovered + Healthy sea urchins,Diseased sea urchins,Bald sea urchin disease (BSUD) is a bacterial infection that occurs in a wide range of sea urchin species and causes the loss of surface appendages.,8,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 6 & Supplementary Data file 2, Table S7.",17 April 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,KateRasheed,WikiWorks",Taxa with significantly different abundances in the microbiomes on sea urchins among the groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Amoebophilaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Amylibacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Saprospiria|o__Saprospirales|f__Saprospiraceae|g__Aureispira,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Colwelliaceae|g__Colwellia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Cryomorphaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Donghicola,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Fusibacteraceae|g__Fusibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Granulosicoccaceae|g__Granulosicoccus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Halieaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Halocynthiibacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Haloferula,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Thiotrichaceae|g__Leucothrix,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Luteibaculaceae|g__Luteibaculum,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Lutimonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Planctomycetales|f__Planctomycetaceae|g__Planctomicrobium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Poseidonibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Pseudoteredinibacter,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Reichenbachiellaceae|g__Reichenbachiella,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Pirellulales|f__Pirellulaceae|g__Rhodopirellula,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Rickettsiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Roseimarinus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Roseobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Saccharospirillaceae,k__Pseudomonadati|p__Bacteroidota|c__Saprospiria|o__Saprospirales|f__Saprospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Spongiibacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Candidatus Berkiellales|f__Candidatus Berkiellaceae|g__Candidatus Berkiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria",3379134|976|768503|768507|1501348;3379134|1224|28211|204455|31989|1617805;3379134|29547|3031852|213849|2808963;3379134|976|1937959|1936988|89374|365032;3379134|1224|1236|135622|267889|28228;3379134|976|117743|200644|246874;3379134|1224|28211|204455|2854170|393277;3379134|976|117743|200644|49546;1783272|1239|186801|186802|3679999|76008;3379134|1224|1236|135613|449719|437504;3379134|1224|1236|1706369|1706372;3379134|1224|28211|204455|31989|1579315;3379134|74201|203494|48461|203557|574899;3379134|1224|1236|72273|135617|45247;3379134|976|117743|200644|2772533|1649465;3379134|976|117743|200644|49546|449810;3379134|1224|28211|204455|31989;3379134|203682|203683|112|126|1779141;3379134|29547|3031852|213849|2808963|2321187;3379134|1224|1236|1706369|1706371|1122284;3379134|976|768503|768507|2762302|156993;3379134|203682|203683|2691354|2691357|265488;3379134|1224|28211|766|775;3379134|1224|28211|766;3379134|976|200643|1970189|1471398|1827484;3379134|1224|28211|204455|2854170|2433;3379134|1224|1236|135619|255527;3379134|976|1937959|1936988|89374;3379134|1224|1236|1706369|1706375;3379134|1224|1236|3345221|3345222|1755683;3379134|1224|1236,Complete,Svetlana up
bsdb:37715299/4/1,37715299,laboratory experiment,37715299,https://doi.org/10.1093/femspd/ftad025,NA,"Shaw C.G., Pavloudi C., Barela Hudgell M.A., Crow R.S., Saw J.H., Pyron R.A. , Smith L.C.",Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium,Pathogens and disease,2023,"16S rRNA high throughput sequencing, Strongylocentrotus purpuratus, bacterial infection, echinoderm, microbiome",Experiment 4,United States of America,Strongylocentrotus purpuratus,Anatomical surface,UBERON:0006984,Bacterial disease,EFO:0000771,Recovered + Diseased sea urchins - ZymoResearch pipeline,Healthy sea urchins - ZymoResearch pipeline,Healthy sea urchins refers to healthy sea urchins in aquarium A and B,8,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Supplementary Data file 3, TableS4-5.",22 January 2025,KateRasheed,"KateRasheed,WikiWorks",Taxa have different abundances in microbiomes from samples collected from healthy sea urchins compared to recovered and diseased sea urchins,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas|s__Halomonas sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Marinobacteraceae|g__Marinobacter|s__Marinobacter salarius,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Marinosulfonomonas|s__Marinosulfonomonas methylotropha,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycolicibacterium|s__Mycolicibacterium hippocampi,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Echinimonadaceae|g__Neiella|s__Neiella sp.,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Oceanispirochaeta|s__Oceanispirochaeta litoralis,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Planctomycetales|f__Planctomycetaceae|g__Planctomyces|s__Planctomyces sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Prolixibacter|s__Prolixibacter sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella|s__Shewanella olleyana,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio litoralis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Psychromonadaceae|g__Psychromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Prolixibacter,k__Pseudomonadati|p__Myxococcota|o__Polyangiales|f__Sandaracinaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Oceaniovalibus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Marinobacteraceae|g__Marinobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Loktanella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Echinimonadaceae|g__Neiella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae|g__Litoribacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Marinosulfonomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae|g__Pseudoalteromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinilabiliaceae|g__Saccharicrinis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Sulfitobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Draconibacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Gilvibacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Psychroflexus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Pseudomonadati|p__Nitrospirota|c__Nitrospiria|o__Nitrospirales|f__Nitrospiraceae|g__Nitrospira,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Planctomycetales|f__Planctomycetaceae|g__Planctomyces",3379134|1224|1236|135619|28256|2745|1486246;3379134|1224|1236|72274|2887365|2742|1420917;3379134|1224|28211|204455|31989|50056|50058;1783272|201174|1760|85007|1762|1866885|659824;3379134|1224|1236|135622|3046600|1434025|2562652;3379134|203691|203692|136|137|2035349|151;3379134|203682|203683|112|126|118|37635;3379134|976|200643|1970189|1471398|314318|1954466;3379134|1224|1236|135622|267890|22|135626;3379134|1224|1236|135623|641|662|335972;3379134|1224|1236|135622|267894|67572;3379134|1224|1236|135622|267890|22;3379134|976|200643|1970189|1471398|314318;3379134|2818505|3031712|1055686;3379134|1224|28211|204455|2854170|1207070;3379134|1224|1236|72274|2887365|2742;3379134|1224|28211|204455|2854170|245186;3379134|1224|1236|135622|3046600|1434025;3379134|203691|203692|136|137|146;3379134|1224|1236|135619|135620|1264044;3379134|1224|28211|204455|31989|50056;3379134|1224|1236|135622|267888|53246;3379134|976|200643|1970189|558415|1618113;3379134|1224|28211|204455|2854170|60136;3379134|976|200643|1970189|1471398|1471399;3379134|976|117743|200644|49546|379070;3379134|976|117743|200644|49546|83612;1783272|201174|1760|85007|1762|1763;3379134|40117|203693|189778|189779|1234;3379134|203682|203683|112|126|118,Complete,Svetlana up
bsdb:37715299/6/1,37715299,laboratory experiment,37715299,https://doi.org/10.1093/femspd/ftad025,NA,"Shaw C.G., Pavloudi C., Barela Hudgell M.A., Crow R.S., Saw J.H., Pyron R.A. , Smith L.C.",Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium,Pathogens and disease,2023,"16S rRNA high throughput sequencing, Strongylocentrotus purpuratus, bacterial infection, echinoderm, microbiome",Experiment 6,United States of America,Strongylocentrotus purpuratus,Anatomical surface,UBERON:0006984,Bacterial disease,EFO:0000771,Recovered + Healthy sea urchins - ZymoResearch pipeline,Diseased sea urchins - ZymoResearch pipeline,Bald sea urchin disease (BSUD) is a bacterial infection that occurs in a wide range of sea urchin species and causes the loss of surface appendages.,8,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Supplementary Data file 3, TableS4-5.",17 April 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,KateRasheed,WikiWorks",Taxa have different abundances in microbiomes from samples collected from diseased sea urchins compared to recovered and healthy sea urchins,increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Pirellulales|f__Pirellulaceae|g__Blastopirellula,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Colwelliaceae|g__Colwellia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia|s__Erwinia rhapontici,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Crocinitomicaceae|g__Fluviicola,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Thiotrichaceae|g__Leucothrix,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Lutibacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Lutibacter|s__Lutibacter agarilyticus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Octadecabacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Polaribacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Crocinitomicaceae|g__Fluviicola|s__Fluviicola sp.,k__Pseudomonadati|p__Bdellovibrionota|c__Bdellovibrionia|o__Bdellovibrionales|f__Pseudobdellovibrionaceae,k__Pseudomonadati|p__Bacteroidota|c__Saprospiria|o__Saprospirales|f__Saprospiraceae",3379134|29547|3031852|213849|2808963|28196;3379134|203682|203683|2691354|2691357|265487;3379134|1224|1236|135622|267889|28228;3379134|1224|1236|91347|1903409|551;3379134|1224|1236|91347|1903409|551|55212;3379134|976|117743|200644|1853230|332102;3379134|1224|1236|72273|135617|45247;3379134|976|117743|200644|49546|358023;3379134|976|117743|200644|49546|358023|1109740;3379134|1224|28211|204455|2854170|53945;3379134|976|117743|200644|49546|52959;3379134|1224|1236|135619|135620;3379134|976|117743|200644|1853230|332102|1917219;3379134|3018035|3031418|213481|213483;3379134|976|1937959|1936988|89374,Complete,Svetlana up
bsdb:37715299/8/1,37715299,laboratory experiment,37715299,https://doi.org/10.1093/femspd/ftad025,NA,"Shaw C.G., Pavloudi C., Barela Hudgell M.A., Crow R.S., Saw J.H., Pyron R.A. , Smith L.C.",Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium,Pathogens and disease,2023,"16S rRNA high throughput sequencing, Strongylocentrotus purpuratus, bacterial infection, echinoderm, microbiome",Experiment 8,United States of America,Strongylocentrotus purpuratus,Anatomical surface,UBERON:0006984,Bacterial disease,EFO:0000771,Healthy + Diseased sea urchins - ZymoResearch pipeline,Recovered sea urchins - ZymoResearch pipeline,"A quality in which complete clearance of the disorder is attained; however, physiological 'memory' may persist.",8,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Supplementary Data file 3, TableS4-5.",17 April 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,KateRasheed,WikiWorks",Taxa have different abundances in microbiomes from samples collected from recovered sea urchins compared to healthy and diseased sea urchins,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Altererythrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alteromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alteromonas|s__Alteromonas sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Arenicellales|f__Arenicellaceae|g__Arenicella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Arenicellales|f__Arenicellaceae|g__Arenicella|s__Arenicella xantha,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Cobetia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Coxiella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Francisellaceae|g__Francisella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Kordiimonadales|f__Kordiimonadaceae|g__Kordiimonas,k__Thermoproteati|p__Nitrososphaerota|c__Nitrososphaeria|o__Nitrosopumilales|f__Nitrosopumilaceae|g__Nitrosarchaeum,k__Thermoproteati|p__Nitrososphaerota|c__Nitrososphaeria|o__Nitrosopumilales|f__Nitrosopumilaceae|g__Nitrosarchaeum|s__Nitrosarchaeum koreense,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Roseibacillus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Roseibacillus|s__Roseibacillus ponti,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Stappiaceae|g__Roseibium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Stappiaceae|g__Roseibium|s__Roseibium aquae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Rubritaleaceae|g__Rubritalea,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Sulfurimonadaceae|g__Sulfurimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiohalomonadales|f__Thiohalophilaceae|g__Thiohalophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio panuliri,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Winogradskyella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae,k__Pseudomonadati|p__Myxococcota|o__Nannocystales|f__Nannocystaceae",3379134|1224|28211|204457|335929|361177;3379134|1224|1236|135622|72275|226;3379134|1224|1236|135622|72275|226|232;3379134|1224|1236|1617890|1617891|904708;3379134|1224|1236|1617890|1617891|904708|644221;3379134|1224|1236|135619|28256|204286;3379134|1224|1236|118969|118968|776;3379134|200940|3031449|213115|194924|872;3379134|1224|1236|72273|34064|262;3379134|1224|28211|362534|1331809|288021;1783275|651137|1643678|31932|338190|1007082;1783275|651137|1643678|31932|338190|1007082|1088740;3379134|74201|203494|48461|203557|518755;3379134|74201|203494|48461|203557|518755|454147;3379134|1224|28211|356|2821832|150830;3379134|1224|28211|356|2821832|150830|1323746;3379134|74201|203494|48461|1648490|361050;3379134|29547|3031852|213849|2771471|202746;3379134|1224|1236|3084968|3084970|445670;3379134|1224|1236|135623|641|662|1381081;3379134|976|117743|200644|49546|286104;3379134|1224|1236|1706369|1706371;3379134|2818505|3031713|224463,Complete,Svetlana up
bsdb:37721699/1/1,37721699,time series / longitudinal observational,37721699,10.1007/s43032-023-01351-4,NA,"Li K.T., Li F., Jaspan H., Nyemba D., Myer L., Aldrovandi G. , Joseph-Davey D.",Changes in the Vaginal Microbiome During Pregnancy and the Postpartum Period in South African Women: a Longitudinal Study,"Reproductive sciences (Thousand Oaks, Calif.)",2024,"Microbiome in pregnancy, South Africa, Vaginal microbiome",Experiment 1,South Africa,Homo sapiens,Vagina,UBERON:0000996,HIV infection,EFO:0000764,Pregnant women ≥ 18 years of age without Human immunodeficiency virus (HIV) at Visit B,Pregnant women ≥ 18 years of age with Human immunodeficiency virus (HIV) at Visit B,Pregnant women ≥ 18 years of age with Human immunodeficiency virus (HIV) whose gestational age range at Visit B (third trimester visit) was 24–36 weeks.,135,107,NA,16S,4,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplement S6,8 March 2025,Tosin,"Lwaldron,Tosin","Differential abundance testing of microbial species in women with and without Human immunodeficiency virus, HIV (zero-inflated negative binomial model)",decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus jensenii,1783272|1239|91061|186826|33958|1578|109790,Complete,Svetlana up
bsdb:37721699/2/1,37721699,time series / longitudinal observational,37721699,10.1007/s43032-023-01351-4,NA,"Li K.T., Li F., Jaspan H., Nyemba D., Myer L., Aldrovandi G. , Joseph-Davey D.",Changes in the Vaginal Microbiome During Pregnancy and the Postpartum Period in South African Women: a Longitudinal Study,"Reproductive sciences (Thousand Oaks, Calif.)",2024,"Microbiome in pregnancy, South Africa, Vaginal microbiome",Experiment 2,South Africa,Homo sapiens,Vagina,UBERON:0000996,HIV infection,EFO:0000764,Pregnant women ≥ 18 years of age without Human immunodeficiency virus (HIV) at Postpartum (PPt) visit,Pregnant women ≥ 18 years of age with Human immunodeficiency virus (HIV) at Postpartum (PPt) visit.,Pregnant women ≥ 18 years of age with Human immunodeficiency virus (HIV) whose mean gestational age at the postpartum visit was 17 days after delivery.,135,107,NA,16S,4,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplement S6,8 March 2025,Tosin,"Lwaldron,Tosin","Differential abundance testing of microbial species in women with and without Human Imunodeficiency virus, HIV (zero-inflated negative binomial model)",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma hominis",1783272|201174|84998|84999|1643824|2767327|82135;1783272|544448|2790996|2895623|2895509|2098,Complete,Svetlana up
bsdb:37721699/2/2,37721699,time series / longitudinal observational,37721699,10.1007/s43032-023-01351-4,NA,"Li K.T., Li F., Jaspan H., Nyemba D., Myer L., Aldrovandi G. , Joseph-Davey D.",Changes in the Vaginal Microbiome During Pregnancy and the Postpartum Period in South African Women: a Longitudinal Study,"Reproductive sciences (Thousand Oaks, Calif.)",2024,"Microbiome in pregnancy, South Africa, Vaginal microbiome",Experiment 2,South Africa,Homo sapiens,Vagina,UBERON:0000996,HIV infection,EFO:0000764,Pregnant women ≥ 18 years of age without Human immunodeficiency virus (HIV) at Postpartum (PPt) visit,Pregnant women ≥ 18 years of age with Human immunodeficiency virus (HIV) at Postpartum (PPt) visit.,Pregnant women ≥ 18 years of age with Human immunodeficiency virus (HIV) whose mean gestational age at the postpartum visit was 17 days after delivery.,135,107,NA,16S,4,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplement S6,8 March 2025,Tosin,"Lwaldron,Tosin","Differential abundance testing of microbial species in women with and without Human Imunodeficiency virus, HIV (zero-inflated negative binomial model)",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella corporis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella bergensis",3379134|976|200643|171549|171552|838|28128;3379134|976|200643|171549|171552|52228|242750,Complete,Svetlana up
bsdb:37721699/3/1,37721699,time series / longitudinal observational,37721699,10.1007/s43032-023-01351-4,NA,"Li K.T., Li F., Jaspan H., Nyemba D., Myer L., Aldrovandi G. , Joseph-Davey D.",Changes in the Vaginal Microbiome During Pregnancy and the Postpartum Period in South African Women: a Longitudinal Study,"Reproductive sciences (Thousand Oaks, Calif.)",2024,"Microbiome in pregnancy, South Africa, Vaginal microbiome",Experiment 3,South Africa,Homo sapiens,Vagina,UBERON:0000996,Sexually transmitted disease,NA,Pregnant women ≥ 18 years of age without any sexually transmitted infection (STI) at Visit A,Pregnant women ≥ 18 years of age with any sexually transmitted infection (STI) at Visit A,"Pregnant women ≥ 18 years of age with any sexually transmitted infection (STI) diagnosis whose mean gestational age at Visit A [first antenatal clinic (ANC) visit] was 18.6 weeks [standard deviation (SD) 6.3], with a range of 6–30 weeks.",162,80,NA,16S,4,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplement S10 a,8 March 2025,Tosin,"Lwaldron,Tosin","Differential abundance testing  of vaginal microbial species in women with and without any sexually transmitted infection, STI diagnosis (zero-inflated negative binomial model)",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella colorans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma hominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia vaginalis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|s__Veillonellaceae bacterium",3379134|976|200643|171549|171552|52228|1703337;3379134|976|200643|171549|171552|2974257|28127;1783272|544448|2790996|2895623|2895509|2098;3379134|976|200643|171549|171552|838|419005;3379134|976|200643|171549|171552|838|28125;3384189|32066|203490|203491|1129771|168808|187101;1783272|1239|909932|1843489|31977|2049049,Complete,Svetlana up
bsdb:37721699/4/1,37721699,time series / longitudinal observational,37721699,10.1007/s43032-023-01351-4,NA,"Li K.T., Li F., Jaspan H., Nyemba D., Myer L., Aldrovandi G. , Joseph-Davey D.",Changes in the Vaginal Microbiome During Pregnancy and the Postpartum Period in South African Women: a Longitudinal Study,"Reproductive sciences (Thousand Oaks, Calif.)",2024,"Microbiome in pregnancy, South Africa, Vaginal microbiome",Experiment 4,South Africa,Homo sapiens,Vagina,UBERON:0000996,Sexually transmitted disease,NA,Pregnant women ≥ 18 years of age without any sexually transmitted infection (STI) at Visit B,Pregnant women ≥ 18 years of age with any sexually transmitted infection (STI) at Visit B,Pregnant women ≥ 18 years of age with any sexually transmitted infection (STI) diagnosis whose gestational age range at Visit B (third trimester visit) was 24–36 weeks.,162,80,NA,16S,4,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplement S10 a,8 March 2025,Tosin,"Lwaldron,Tosin","Differential abundance testing of vaginal microbial species in women with and without any sexually transmitted infection, STI diagnosis (zero-inflated negative binomial model)",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,3379134|976|200643|171549|171552|2974257|28127,Complete,Svetlana up
bsdb:37721699/5/1,37721699,time series / longitudinal observational,37721699,10.1007/s43032-023-01351-4,NA,"Li K.T., Li F., Jaspan H., Nyemba D., Myer L., Aldrovandi G. , Joseph-Davey D.",Changes in the Vaginal Microbiome During Pregnancy and the Postpartum Period in South African Women: a Longitudinal Study,"Reproductive sciences (Thousand Oaks, Calif.)",2024,"Microbiome in pregnancy, South Africa, Vaginal microbiome",Experiment 5,South Africa,Homo sapiens,Vagina,UBERON:0000996,Sexually transmitted disease,NA,Pregnant women ≥ 18 years of age without any sexually transmitted infection (STI) at Postpartum (PPt) visit,Pregnant women ≥ 18 years of age with any sexually transmitted infection (STI) at Postpartum (PPt) visit.,Pregnant women ≥ 18 years of age with any sexually transmitted infection (STI) diagnosis whose mean gestational age at the postpartum visit was 17 days after delivery.,162,80,NA,16S,4,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplement S10 a,9 March 2025,Tosin,"Lwaldron,Tosin","Differential abundance testing of vaginal microbial species in women with and without any sexually transmitted infection, STI diagnosis (zero-inflated negative binomial model)",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,3379134|976|200643|171549|171552|838|59823,Complete,Svetlana up
bsdb:37721699/6/1,37721699,time series / longitudinal observational,37721699,10.1007/s43032-023-01351-4,NA,"Li K.T., Li F., Jaspan H., Nyemba D., Myer L., Aldrovandi G. , Joseph-Davey D.",Changes in the Vaginal Microbiome During Pregnancy and the Postpartum Period in South African Women: a Longitudinal Study,"Reproductive sciences (Thousand Oaks, Calif.)",2024,"Microbiome in pregnancy, South Africa, Vaginal microbiome",Experiment 6,South Africa,Homo sapiens,Vagina,UBERON:0000996,Chlamydia trachomatis infectious disease,EFO:0007205,Pregnant women ≥ 18 years of age without Chlamydia trachomatis (CT) infection at Visit A,Pregnant women ≥ 18 years of age with Chlamydia trachomatis (CT) infection at Visit A,"Pregnant women ≥ 18 years of age with Chlamydia trachomatis (CT) infection diagnosis whose mean gestational age at Visit A [first antenatal clinic (ANC) visit] was 18.6 weeks [standard deviation (SD) 6.3], with a range of 6–30 weeks.",190,52,NA,16S,4,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplement S10 b,9 March 2025,Tosin,"Lwaldron,Tosin",Differential abundance testing of vaginal microbial species in women with and without Chlamydia trachomatis (CT) infection diagnosis (zero-inflated negative binomial model),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella colorans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia vaginalis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|s__Veillonellaceae bacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__uncultured Megasphaera sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",3379134|976|200643|171549|171552|52228|1703337;3379134|976|200643|171549|171552|2974257|28127;3379134|976|200643|171549|171552|838|419005;3384189|32066|203490|203491|1129771|168808|187101;1783272|1239|909932|1843489|31977|2049049;1783272|1239|909932|1843489|31977|906|165188;1783272|1239|186801|3085636|186803|297314,Complete,Svetlana up
bsdb:37721699/7/1,37721699,time series / longitudinal observational,37721699,10.1007/s43032-023-01351-4,NA,"Li K.T., Li F., Jaspan H., Nyemba D., Myer L., Aldrovandi G. , Joseph-Davey D.",Changes in the Vaginal Microbiome During Pregnancy and the Postpartum Period in South African Women: a Longitudinal Study,"Reproductive sciences (Thousand Oaks, Calif.)",2024,"Microbiome in pregnancy, South Africa, Vaginal microbiome",Experiment 7,South Africa,Homo sapiens,Vagina,UBERON:0000996,Chlamydia trachomatis infectious disease,EFO:0007205,Pregnant women ≥ 18 years of age without Chlamydia trachomatis (CT) infection at Visit B,Pregnant women ≥ 18 years of age with Chlamydia trachomatis (CT) infection at Visit B,Pregnant women ≥ 18 years of age with Chlamydia trachomatis (CT) infection diagnosis whose gestational age range at Visit B (third trimester visit) was 24–36 weeks.,190,52,NA,16S,4,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplement S10 b,9 March 2025,Tosin,"Lwaldron,Tosin",Differential abundance testing of vaginal microbial species in women with and without Chlamydia trachomatis (CT) infection diagnosis (zero-inflated negative binomial model),increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__uncultured Megasphaera sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis",1783272|1239|909932|1843489|31977|906|165188;3379134|976|200643|171549|171552|2974257|28127,Complete,Svetlana up
bsdb:37721699/8/1,37721699,time series / longitudinal observational,37721699,10.1007/s43032-023-01351-4,NA,"Li K.T., Li F., Jaspan H., Nyemba D., Myer L., Aldrovandi G. , Joseph-Davey D.",Changes in the Vaginal Microbiome During Pregnancy and the Postpartum Period in South African Women: a Longitudinal Study,"Reproductive sciences (Thousand Oaks, Calif.)",2024,"Microbiome in pregnancy, South Africa, Vaginal microbiome",Experiment 8,South Africa,Homo sapiens,Vagina,UBERON:0000996,Chlamydia trachomatis infectious disease,EFO:0007205,Pregnant women ≥ 18 years of age without Chlamydia trachomatis (CT) infection at postpartum (PPt) visit.,Pregnant women ≥ 18 years of age with Chlamydia trachomatis (CT) infection at postpartum (PPt) visit,Pregnant women ≥ 18 years of age with Chlamydia trachomatis (CT) infection diagnosis whose mean gestational age at the postpartum visit was 17 days after delivery.,190,52,NA,16S,4,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplement S10 b,9 March 2025,Tosin,"Lwaldron,Tosin",Differential abundance testing of vaginal microbial species in women with and without Chlamydia trachomatis (CT) infection diagnosis (zero-inflated negative binomial model),increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,3379134|976|200643|171549|171552|838|59823,Complete,Svetlana up
bsdb:37721699/9/1,37721699,time series / longitudinal observational,37721699,10.1007/s43032-023-01351-4,NA,"Li K.T., Li F., Jaspan H., Nyemba D., Myer L., Aldrovandi G. , Joseph-Davey D.",Changes in the Vaginal Microbiome During Pregnancy and the Postpartum Period in South African Women: a Longitudinal Study,"Reproductive sciences (Thousand Oaks, Calif.)",2024,"Microbiome in pregnancy, South Africa, Vaginal microbiome",Experiment 9,South Africa,Homo sapiens,Vagina,UBERON:0000996,Gonorrhea,DOID:7551,Pregnant women ≥ 18 years of age without Neisseria gonorrhoea (NG) infection at postpartum (PPt) visit.,Pregnant women ≥ 18 years of age with Neisseria gonorrhoea (NG) infection at postpartum (PPt) visit,Pregnant women ≥ 18 years of age with Neisseria gonorrhoea (NG) infection diagnosis whose mean gestational age at the postpartum visit was 17 days after delivery.,228,14,NA,16S,4,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplement S10 c,9 March 2025,Tosin,"Lwaldron,Tosin",Differential abundance testing of vaginal microbial species in women with and without Neisseria gonorrhoea (NG) infection diagnosis (zero-inflated negative binomial model),decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella bergensis,3379134|976|200643|171549|171552|52228|242750,Complete,Svetlana up
bsdb:37721699/10/1,37721699,time series / longitudinal observational,37721699,10.1007/s43032-023-01351-4,NA,"Li K.T., Li F., Jaspan H., Nyemba D., Myer L., Aldrovandi G. , Joseph-Davey D.",Changes in the Vaginal Microbiome During Pregnancy and the Postpartum Period in South African Women: a Longitudinal Study,"Reproductive sciences (Thousand Oaks, Calif.)",2024,"Microbiome in pregnancy, South Africa, Vaginal microbiome",Experiment 10,South Africa,Homo sapiens,Vagina,UBERON:0000996,Trichomonas vaginitis,EFO:0007521,Pregnant women ≥ 18 years of age without Trichomonas vaginalis (TV) infection at Visit A,Pregnant women ≥ 18 years of age with Trichomonas vaginalis (TV) infection at Visit A,"Pregnant women ≥ 18 years of age with Trichomonas vaginalis (TV) infection diagnosis whose mean gestational age at Visit A [first antenatal clinic (ANC) visit] was 18.6 weeks [standard deviation (SD) 6.3], with a range of 6–30 weeks.",204,38,NA,16S,4,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplement S10 d,9 March 2025,Tosin,"Lwaldron,Tosin",Differential abundance testing of vaginal microbial species in women with and without Trichomonas vaginalis (TV) infection diagnosis (zero-inflated negative binomial model),increased,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma hominis,1783272|544448|2790996|2895623|2895509|2098,Complete,Svetlana up
bsdb:37721699/11/1,37721699,time series / longitudinal observational,37721699,10.1007/s43032-023-01351-4,NA,"Li K.T., Li F., Jaspan H., Nyemba D., Myer L., Aldrovandi G. , Joseph-Davey D.",Changes in the Vaginal Microbiome During Pregnancy and the Postpartum Period in South African Women: a Longitudinal Study,"Reproductive sciences (Thousand Oaks, Calif.)",2024,"Microbiome in pregnancy, South Africa, Vaginal microbiome",Experiment 11,South Africa,Homo sapiens,Vagina,UBERON:0000996,Trichomonas vaginitis,EFO:0007521,Pregnant women ≥ 18 years of age without Trichomonas vaginalis (TV) infection at postpartum (PPt) visit.,Pregnant women ≥ 18 years of age with Trichomonas vaginalis (TV) infection at postpartum (PPt) visit,Pregnant women ≥ 18 years of age with Trichomonas vaginalis (TV) infection diagnosis whose mean gestational age at the postpartum visit was 17 days after delivery.,204,38,NA,16S,4,Illumina,raw counts,Zero-Inflated Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplement S10 d,9 March 2025,Tosin,"Lwaldron,Tosin",Differential abundance testing of vaginal microbial species in women with and without Trichomonas vaginalis (TV) infection diagnosis (zero-inflated negative binomial model),decreased,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,3384189|32066|203490|203491|1129771|168808|40543,Complete,Svetlana up
bsdb:37737154/1/1,37737154,case-control,37737154,10.1186/s12866-023-03020-7,NA,"Luan M., Niu M., Yang P., Han D., Zhang Y., Li W., He Q., Zhao Y., Mao B., Chen J., Mou K. , Li P.",Metagenomic sequencing reveals altered gut microbial compositions and gene functions in patients with non-segmental vitiligo,BMC microbiology,2023,"Gut microbiota, Metagenomic sequencing, Vitiligo",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Vitiligo,EFO:0004208,Healthy controls,Non-segmental Vitiligo patients,"Individuals characterized by the progressive loss of skin pigmentation in various areas of the body, resulting in depigmented white patches that is mostly widespread in distribution.",25,25,3 months,WMS,NA,BGISEQ-500 Sequencing,relative abundances,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,2,"age,body mass index,sex",NA,NA,decreased,NA,decreased,NA,NA,Signature 1,"Figure 2b, 3",16 October 2023,Deacme,"Deacme,WikiWorks",Increased abundant species in Non-segmental Vitiligo patients,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium OF09-6,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Massilioclostridium|s__Massilioclostridium coli,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 348,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister hominis",1783272|1239|186801|3085636|186803|1766253|39491;3379134|976|200643|171549|171550|239759|28117;1783272|1239|526524|526525|128827|2749846|31971;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|207244|649756;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|46506;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|2005519|397864|487174;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|186801|3085636|186803|572511|418240;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|3085636|186803|2293831;1783272|1239|186801|186802|31979|1935927|1870991;1783272|1239|909932|909929|1843491|158846|437897;3379134|976|200643|171549|815|909656|310298;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|186802|216572|1263|40518;95818|671231;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|909932|1843489|31977|39948|2582419,Complete,Chloe
bsdb:37737154/1/2,37737154,case-control,37737154,10.1186/s12866-023-03020-7,NA,"Luan M., Niu M., Yang P., Han D., Zhang Y., Li W., He Q., Zhao Y., Mao B., Chen J., Mou K. , Li P.",Metagenomic sequencing reveals altered gut microbial compositions and gene functions in patients with non-segmental vitiligo,BMC microbiology,2023,"Gut microbiota, Metagenomic sequencing, Vitiligo",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Vitiligo,EFO:0004208,Healthy controls,Non-segmental Vitiligo patients,"Individuals characterized by the progressive loss of skin pigmentation in various areas of the body, resulting in depigmented white patches that is mostly widespread in distribution.",25,25,3 months,WMS,NA,BGISEQ-500 Sequencing,relative abundances,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,2,"age,body mass index,sex",NA,NA,decreased,NA,decreased,NA,NA,Signature 2,"Figure 2d, 3",16 October 2023,Deacme,"Deacme,WikiWorks",Decreased abundant species in non-segmental Vitiligo patients,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. ICM58,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister histaminiformans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides bouchesdurhonensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF20-17LB,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter secundus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio desulfuricans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|s__Eggerthellaceae bacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae|g__Isoptericola|s__Isoptericola variabilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|s__Rikenellaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas intestinalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Trueperella|s__Trueperella pyogenes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena fissicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas umbilicata,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas faecalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Neobittarella (ex Bilen et al. 2018)|s__Neobittarella massiliensis (ex Bilen et al. 2018),k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes ihumii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis",1783272|201174|1760|2037|2049|1654|1105030;1783272|1239|909932|1843489|31977|39948|209880;3379134|976|200643|171549|815|816|1841855;3379134|976|200643|171549|815|816|28111;1783272|1239|186801|2044939;1783272|1239|186801|186802|31979|1485|2292205;3379134|976|200643|171549|2005519|1348911|1501392;1783272|1239|186801|3085636|186803|3569723|410072;3379134|200940|3031449|213115|194924|872|876;1783272|1239|186801|3085636|186803|189330|88431;1783272|201174|84998|1643822|1643826|1972561;1783272|201174|1760|85006|85017|254250|139208;1783272|1239|186801|186802|216572|2485925;1783272|1239|1737404|1737405|1570339|543311|33033;3379134|976|200643|171549|171550|2049048;1783272|1239|186801|3085636|186803|1769710|1653434;1783272|201174|1760|2037|2049|1069494|1661;1783272|1239|909932|1843489|31977|29465|423477;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|186801|3085636|186803|2005359|290055;1783272|1239|186801|3085636|186803|2005355|1912855;3379134|976|200643|171549|171550|239759|1288121;3379134|976|200643|171549|1853231|574697|2093856;1783272|1239|186801|186802|216572|2126544|2041842;3379134|976|200643|171549|171550|239759|1470347;1783272|1239|526524|526525|128827|1573535|1735,Complete,Chloe
bsdb:37740058/1/1,37740058,prospective cohort,37740058,10.1038/s41598-023-43108-8,https://pubmed.ncbi.nlm.nih.gov/37740058/,"Komori E., Kato-Kogoe N., Imai Y., Sakaguchi S., Taniguchi K., Omori M., Ohmichi M., Nakamura S., Nakano T., Lee S.W. , Ueno T.",Changes in salivary microbiota due to gastric cancer resection and its relation to gastric fluid microbiota,Scientific reports,2023,NA,Experiment 1,Japan,Homo sapiens,Saliva,UBERON:0001836,Gastric cancer,MONDO:0001056,Gastric cancer patients (Pre-gastrectomy),Gastric cancer patients (Post-gastrectomy),Patients diagnosed with primary gastric cancer who underwent distal gastrectomy and B1 or RY reconstruction,63,63,3 months,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 1,Figure 3a,19 October 2023,Aleru002,"Aleru002,WikiWorks",The differentially abundant bacterial genera between pre- and post-gastrectomy groups in the saliva sample identified by linear discriminant analysis effect size (LEfSe).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,s__uncultured bacterium",1783272|1239|186801|186802|404402;1783272|1239|91061|186826|33958|1578;77133,Complete,Chloe
bsdb:37740058/1/2,37740058,prospective cohort,37740058,10.1038/s41598-023-43108-8,https://pubmed.ncbi.nlm.nih.gov/37740058/,"Komori E., Kato-Kogoe N., Imai Y., Sakaguchi S., Taniguchi K., Omori M., Ohmichi M., Nakamura S., Nakano T., Lee S.W. , Ueno T.",Changes in salivary microbiota due to gastric cancer resection and its relation to gastric fluid microbiota,Scientific reports,2023,NA,Experiment 1,Japan,Homo sapiens,Saliva,UBERON:0001836,Gastric cancer,MONDO:0001056,Gastric cancer patients (Pre-gastrectomy),Gastric cancer patients (Post-gastrectomy),Patients diagnosed with primary gastric cancer who underwent distal gastrectomy and B1 or RY reconstruction,63,63,3 months,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 2,Figure 3a,19 October 2023,Aleru002,"Aleru002,WikiWorks",The differentially abundant bacterial genera between pre- and post-gastrectomy groups in the saliva sample identified by linear discriminant analysis effect size (LEfSe).,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Aminipila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral clone CW040,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter|s__[Eubacterium] yurii",1783272|201174|1760|2037|2049|1654;1783272|1239|186801|3085636|186803|1766253;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3082720|543314|2060094;1783272|1239|186801|3085636|186803|207244;1783272|201174|1760|85009|31957|2801844;1783272|1239|186801|3085636|186803|830;95818|2093818|2093825|2171986|1331051;3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|2005473;1783272|1239|186801|186802|186807|2740;3379134|1224|28216|80840|995019|40544;95818|163601;1783272|1239|186801|3082720|3118655|1913599|39498,Complete,Chloe
bsdb:37740058/2/1,37740058,prospective cohort,37740058,10.1038/s41598-023-43108-8,https://pubmed.ncbi.nlm.nih.gov/37740058/,"Komori E., Kato-Kogoe N., Imai Y., Sakaguchi S., Taniguchi K., Omori M., Ohmichi M., Nakamura S., Nakano T., Lee S.W. , Ueno T.",Changes in salivary microbiota due to gastric cancer resection and its relation to gastric fluid microbiota,Scientific reports,2023,NA,Experiment 2,Japan,Homo sapiens,Gastric juice,UBERON:0001971,Gastric cancer,MONDO:0001056,Gastric cancer patients (Pre-gastrectomy),Gastric cancer patients (Post-gastrectomy),Patients diagnosed with primary gastric cancer who underwent distal gastrectomy and B1 or RY reconstruction,63,63,3 months,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 3b,19 October 2023,Aleru002,"Aleru002,WikiWorks",The differentially abundant bacterial genera between pre- and post-gastrectomy groups in the gastric fluid sample identified by linear discriminant analysis effect size (LEfSe).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptoclostridiaceae|g__Peptoclostridium",3379134|976|117743|200644|2762318|59735;1783272|201174|1760|85004|31953|1678;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3082720|3120161|1481960,Complete,Chloe
bsdb:37740058/2/2,37740058,prospective cohort,37740058,10.1038/s41598-023-43108-8,https://pubmed.ncbi.nlm.nih.gov/37740058/,"Komori E., Kato-Kogoe N., Imai Y., Sakaguchi S., Taniguchi K., Omori M., Ohmichi M., Nakamura S., Nakano T., Lee S.W. , Ueno T.",Changes in salivary microbiota due to gastric cancer resection and its relation to gastric fluid microbiota,Scientific reports,2023,NA,Experiment 2,Japan,Homo sapiens,Gastric juice,UBERON:0001971,Gastric cancer,MONDO:0001056,Gastric cancer patients (Pre-gastrectomy),Gastric cancer patients (Post-gastrectomy),Patients diagnosed with primary gastric cancer who underwent distal gastrectomy and B1 or RY reconstruction,63,63,3 months,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Figure 3b,19 October 2023,Aleru002,"Aleru002,WikiWorks",The differentially abundant bacterial genera between pre- and post-gastrectomy groups in the gastric fluid sample identified by linear discriminant analysis effect size (LEfSe).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:352,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Marmoricola,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral clone CW040,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum,s__uncultured bacterium",3379134|976|200643|171549|171552|1283313;1783272|1239|186801|3085636|186803|830;95818|2093818|2093825|2171986|1331051;1783272|1239|186801|3085636|186803|43996;1783272|1239|186801|186802|31979|1485|1262798;1783272|1239|526524|526525|2810280|100883;1783272|1239|186801|3085636|186803|189330;1783272|1239|526524|526525|128827|1573534;3384189|32066|203490|203491|203492|848;3379134|29547|3031852|213849|72293|209;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|3085636|186803;1783272|201174|1760|85009|85015|86795;3379134|1224|28216|206351|481|482;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836;1783272|201174|1760|85004|31953|196081;95818|163601;1783272|1239|186801|3082720|543314|35518;77133,Complete,Chloe
bsdb:37750731/3/NA,37750731,time series / longitudinal observational,37750731,https://doi.org/10.1128/spectrum.02974-23,https://journals.asm.org/doi/10.1128/spectrum.02974-23,"Roche C.E., Montague M.J., Wang J., Dickey A.N., Ruiz-Lambides A., Brent L.J.N., Platt M.L. , Horvath J.E.",Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques,Microbiology spectrum,2023,"16S rRNA, Cayo Santiago, microbial diversity, primates, rhesus macaques, skin microbiome, social behavior, year-to-year environment",Experiment 3,United States of America,Macaca mulatta,Axilla skin,UBERON:0015474,Social interaction measurement,EFO:0009592,Core microbiome social groups (V),Core microbiome social groups (F),"The core features 1.0 list (e.g., features present in 100% of samples) was used to filter the complete microbiome table and output a “core” microbiome feature table, via q2-filter-features.",NA,NA,NA,16S,4,Illumina,centered log-ratio,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:37750731/11/1,37750731,time series / longitudinal observational,37750731,https://doi.org/10.1128/spectrum.02974-23,https://journals.asm.org/doi/10.1128/spectrum.02974-23,"Roche C.E., Montague M.J., Wang J., Dickey A.N., Ruiz-Lambides A., Brent L.J.N., Platt M.L. , Horvath J.E.",Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques,Microbiology spectrum,2023,"16S rRNA, Cayo Santiago, microbial diversity, primates, rhesus macaques, skin microbiome, social behavior, year-to-year environment",Experiment 11,United States of America,Macaca mulatta,Axilla skin,UBERON:0015474,Social interaction measurement,EFO:0009592,Complete microbiome social group V,Complete microbiome social group KK,"Colony members self-organize into social groups, demonstrate various forms of social behaviors, most notably grooming",12,8,NA,16S,4,Illumina,centered log-ratio,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Fig 2B, text",4 April 2024,Fiddyhamma,"Fiddyhamma,WikiWorks","Box plots representing the taxonomic differences for specific phyla among social groups, with significance assessed using a KW test on CLR transformed relative abundance values: Actinobacteria (KW P = 0.00013), Cyanobacteria (KW P = 0.12), Firmicutes (KW P = 0.044), and Proteobacteria (KW P = 0.0096). Pairwise comparisons between groups were assessed using t-tests; the symbolic number coding of P-values is as follows: *, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001; ****, P ≤ 0.0001.",increased,k__Bacillati|p__Actinomycetota,1783272|201174,Complete,Svetlana up
bsdb:37750731/12/1,37750731,time series / longitudinal observational,37750731,https://doi.org/10.1128/spectrum.02974-23,https://journals.asm.org/doi/10.1128/spectrum.02974-23,"Roche C.E., Montague M.J., Wang J., Dickey A.N., Ruiz-Lambides A., Brent L.J.N., Platt M.L. , Horvath J.E.",Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques,Microbiology spectrum,2023,"16S rRNA, Cayo Santiago, microbial diversity, primates, rhesus macaques, skin microbiome, social behavior, year-to-year environment",Experiment 12,United States of America,Macaca mulatta,Axilla skin,UBERON:0015474,Sampling time,EFO:0000689,2013 sampling period (Complete microbiome),2015 sampling period (Complete microbiome),The 2015 sampling period occurred from October 2015 through December 2015,42,33,NA,16S,4,Illumina,centered log-ratio,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Figure 4B, text",6 April 2024,Fiddyhamma,"Fiddyhamma,KateRasheed,WikiWorks","Box plots representing the significant pairwise taxa using Wilcoxon tests on CLR transformed relative abundance values on phyla: Actinobacteria, Firmicutes, Deinococcus-Thermus, Fusobacteria, and Proteobacteria.",decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Pseudomonadati|p__Pseudomonadota,k__Thermotogati|p__Deinococcota",1783272|201174;1783272|1239;3384189|32066|203490;3379134|1224;3384194|1297,Complete,Svetlana up
bsdb:37762390/1/1,37762390,case-control,37762390,10.3390/ijms241814091,NA,"Schlegel I., De Goüyon Matignon de Pontourade C.M.F., Lincke J.B., Keller I., Zinkernagel M.S. , Zysset-Burri D.C.",The Human Ocular Surface Microbiome and Its Associations with the Tear Proteome in Dry Eye Disease,International journal of molecular sciences,2023,"chromatography–tandem mass spectrometry, dry eye disease, ocular surface microbiome, tear proteome, whole-metagenome shotgun sequencing",Experiment 1,Switzerland,Homo sapiens,Eyelid,UBERON:0001711,Dry eye syndrome,EFO:1000906,healthy controls,Dry Eye,Dry Eye Disease diagnosis,10,10,3 months,WMS,NA,Illumina,relative abundances,Welch's T-Test,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4c,1 October 2023,Mary Bearkland,"Mary Bearkland,WikiWorks","Figure 4c. The distinct taxonomical and functional composition of the ocular surface microbiome between DED patients and healthy controls.  The relative abundances
of taxa associated with DED (Mann–Whitney test). Mean values and
standard deviations are shown.",increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,1783272|201174|1760|85009|31957,Complete,ChiomaBlessing
bsdb:37762390/2/1,37762390,case-control,37762390,10.3390/ijms241814091,NA,"Schlegel I., De Goüyon Matignon de Pontourade C.M.F., Lincke J.B., Keller I., Zinkernagel M.S. , Zysset-Burri D.C.",The Human Ocular Surface Microbiome and Its Associations with the Tear Proteome in Dry Eye Disease,International journal of molecular sciences,2023,"chromatography–tandem mass spectrometry, dry eye disease, ocular surface microbiome, tear proteome, whole-metagenome shotgun sequencing",Experiment 2,Switzerland,Homo sapiens,Palpebral conjunctiva,NA,Dry eye syndrome,EFO:1000906,healthy controls,Dry Eye,Dry Eye Disease diagnosis,10,10,3 months,WMS,NA,Illumina,relative abundances,Welch's T-Test,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4a,1 October 2023,Mary Bearkland,"Mary Bearkland,WikiWorks","Figure 4. The distinct taxonomical composition of the ocular surface microbiome between DED patients and healthy controls.  The relative abundances
of taxa (c) associated with DED (Mann–Whitney test). Mean values and
standard deviations are shown.",increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium tuberculostearicum,1783272|201174|1760|85007|1653|1716|38304,Complete,ChiomaBlessing
bsdb:37784178/1/1,37784178,laboratory experiment,37784178,10.1186/s40168-023-01588-w,https://pubmed.ncbi.nlm.nih.gov/37784178/,"Salvador A.C., Huda M.N., Arends D., Elsaadi A.M., Gacasan C.A., Brockmann G.A., Valdar W., Bennett B.J. , Threadgill D.W.","Analysis of strain, sex, and diet-dependent modulation of gut microbiota reveals candidate keystone organisms driving microbial diversity in response to American and ketogenic diets",Microbiome,2023,"diet, ketogenic, keystone species, microbiome, mouse",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,mice on American diet,mice on ketogenic diet,male and female mice placed on American diet during feeding trial,224,245,NA,16S,4,Illumina,relative abundances,ANOVA,0.001,TRUE,NA,NA,"diet,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 4A,18 October 2023,Winnie,"Winnie,Davvve,WikiWorks","Precision Nutrition through the integration of genetic 
variation, microbiota, and sex affecting microbiota variation",increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",3379134|200940|3031449|213115|194924|35832;3379134|976|200643|171549|171550|28138;1783272|1239|186801|186802|216572|1508657,Complete,NA
bsdb:37784178/1/2,37784178,laboratory experiment,37784178,10.1186/s40168-023-01588-w,https://pubmed.ncbi.nlm.nih.gov/37784178/,"Salvador A.C., Huda M.N., Arends D., Elsaadi A.M., Gacasan C.A., Brockmann G.A., Valdar W., Bennett B.J. , Threadgill D.W.","Analysis of strain, sex, and diet-dependent modulation of gut microbiota reveals candidate keystone organisms driving microbial diversity in response to American and ketogenic diets",Microbiome,2023,"diet, ketogenic, keystone species, microbiome, mouse",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,mice on American diet,mice on ketogenic diet,male and female mice placed on American diet during feeding trial,224,245,NA,16S,4,Illumina,relative abundances,ANOVA,0.001,TRUE,NA,NA,"diet,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,Fig. 4B,18 October 2023,Winnie,"Winnie,Iram jamshed,WikiWorks","Precision Nutrition through the integration of genetic 
variation, microbiota, and sex affecting microbiota variation",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171550,Complete,NA
bsdb:37789427/1/1,37789427,laboratory experiment,37789427,10.1186/s42523-023-00269-1,https://pubmed.ncbi.nlm.nih.gov/37789427/,"Wang J., Li Y., Jaramillo-Torres A., Einen O., Jakobsen J.V., Krogdahl Å. , Kortner T.M.",Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics,Animal microbiome,2023,"Atlantic salmon, Gut health, Gut microbiota, Lactic acid bacteria, Mycoplasma, Yeast cell wall based-prebiotics",Experiment 1,Norway,Salmo salar,Intestine,UBERON:0000160,Diet,EFO:0002755,Reference diet,Test diet,"Atlantic Salmon fed with Yeast cell-wall based prebiotics diet with average water temperature of 3.9, 3.4 and 9.6 degree celsius respectively.",36,36,NA,16S,12,Illumina,relative abundances,MaAsLin2,0.05,TRUE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,General Performance,11 March 2024,Bolanle,"Bolanle,WikiWorks",Effects of diets containing yeast cell-wall based prebiotics on the gut microbiota of Atlantic Salmon in September: Mycoplasma became more prominent as fish progressed towards April and September.,increased,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,1783272|544448|31969|2085|2092|2093,Complete,Svetlana up
bsdb:37789427/1/2,37789427,laboratory experiment,37789427,10.1186/s42523-023-00269-1,https://pubmed.ncbi.nlm.nih.gov/37789427/,"Wang J., Li Y., Jaramillo-Torres A., Einen O., Jakobsen J.V., Krogdahl Å. , Kortner T.M.",Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics,Animal microbiome,2023,"Atlantic salmon, Gut health, Gut microbiota, Lactic acid bacteria, Mycoplasma, Yeast cell wall based-prebiotics",Experiment 1,Norway,Salmo salar,Intestine,UBERON:0000160,Diet,EFO:0002755,Reference diet,Test diet,"Atlantic Salmon fed with Yeast cell-wall based prebiotics diet with average water temperature of 3.9, 3.4 and 9.6 degree celsius respectively.",36,36,NA,16S,12,Illumina,relative abundances,MaAsLin2,0.05,TRUE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Supplementary material 3,11 March 2024,Bolanle,"Bolanle,WikiWorks","Relative abundance of all Amplicon sequence variants (ASVs) for each sample; life stage dietary treatmet
LAB decreasing trend suggests a change in the gut microbiome composition of Atlantic Salmon in response to diets",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|33958|1243,Complete,Svetlana up
bsdb:37789427/2/1,37789427,laboratory experiment,37789427,10.1186/s42523-023-00269-1,https://pubmed.ncbi.nlm.nih.gov/37789427/,"Wang J., Li Y., Jaramillo-Torres A., Einen O., Jakobsen J.V., Krogdahl Å. , Kortner T.M.",Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics,Animal microbiome,2023,"Atlantic salmon, Gut health, Gut microbiota, Lactic acid bacteria, Mycoplasma, Yeast cell wall based-prebiotics",Experiment 2,Norway,Salmo salar,Intestine,UBERON:0000160,Diet,EFO:0002755,January Reference diet,January Test diet,"Atlantic Salmon fed with Yeast cell-wall based prebiotics diet with average water temperature of 3.9, 3.4 and 9.6 degree celsius respectively.",18,18,NA,16S,12,Illumina,relative abundances,MaAsLin2,0.05,TRUE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 7,18 April 2024,Bolanle,"Bolanle,WikiWorks",most abundant taxa at genus level of all samples relative abundance of each taxon,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Geobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Psychrilyobacter",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1243;1783272|1239|91061|186826|1300|1357;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1257;1783272|1239|91061|186826|33958|46255;1783272|1239|91061|1385|186817|1386;1783272|1239|91061|1385|3120669|129337;1783272|1239|186801|186802|31979|1485;3379134|1224|1236|135623|641|657;3379134|1224|1236|135619|28256|2745;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492|623282,Complete,Svetlana up
bsdb:37789427/2/2,37789427,laboratory experiment,37789427,10.1186/s42523-023-00269-1,https://pubmed.ncbi.nlm.nih.gov/37789427/,"Wang J., Li Y., Jaramillo-Torres A., Einen O., Jakobsen J.V., Krogdahl Å. , Kortner T.M.",Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics,Animal microbiome,2023,"Atlantic salmon, Gut health, Gut microbiota, Lactic acid bacteria, Mycoplasma, Yeast cell wall based-prebiotics",Experiment 2,Norway,Salmo salar,Intestine,UBERON:0000160,Diet,EFO:0002755,January Reference diet,January Test diet,"Atlantic Salmon fed with Yeast cell-wall based prebiotics diet with average water temperature of 3.9, 3.4 and 9.6 degree celsius respectively.",18,18,NA,16S,12,Illumina,relative abundances,MaAsLin2,0.05,TRUE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 7,18 April 2024,Bolanle,"Bolanle,WikiWorks",most abundant taxa at genus level of all samples relative abundance of each taxon,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Ureibacillus,1783272|1239|91061|1385|186818|160795,Complete,Svetlana up
bsdb:37789427/3/1,37789427,laboratory experiment,37789427,10.1186/s42523-023-00269-1,https://pubmed.ncbi.nlm.nih.gov/37789427/,"Wang J., Li Y., Jaramillo-Torres A., Einen O., Jakobsen J.V., Krogdahl Å. , Kortner T.M.",Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics,Animal microbiome,2023,"Atlantic salmon, Gut health, Gut microbiota, Lactic acid bacteria, Mycoplasma, Yeast cell wall based-prebiotics",Experiment 3,Norway,Salmo salar,Intestine,UBERON:0000160,Diet,EFO:0002755,Fishes fed with test diet in January,Fishes fed with test diet in April,Atlantic Salmon fed with yeast cell wall based-prebiotics diet in January,18,18,NA,16S,12,Illumina,relative abundances,MaAsLin2,0.05,TRUE,2,NA,NA,unchanged,unchanged,NA,unchanged,NA,NA,Signature 1,FIgure 7,14 March 2024,Bolanle,"Bolanle,WikiWorks","Compared to January fish, April fish showed a slight increase in genera Proteobacteria (15% and 10% in Reference fed and Test-fed fish, respectively) and Mycoplasma (4% and 29.5% in Reference fed and Test- fed fish, respectively)",increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium,3379134|1224|1236|135623|641|657,Complete,Svetlana up
bsdb:37789427/4/1,37789427,laboratory experiment,37789427,10.1186/s42523-023-00269-1,https://pubmed.ncbi.nlm.nih.gov/37789427/,"Wang J., Li Y., Jaramillo-Torres A., Einen O., Jakobsen J.V., Krogdahl Å. , Kortner T.M.",Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics,Animal microbiome,2023,"Atlantic salmon, Gut health, Gut microbiota, Lactic acid bacteria, Mycoplasma, Yeast cell wall based-prebiotics",Experiment 4,Norway,Salmo salar,Intestine,UBERON:0000160,Diet,EFO:0002755,Fishes fed with test diet in January,Fishes fed with test diet in September,Atlantic Salmon fed with yeast cell wall based-prebiotics diet in September,18,18,NA,16S,12,Illumina,relative abundances,MaAsLin2,0.001,TRUE,2,NA,NA,unchanged,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 7,17 March 2024,Bolanle,"Bolanle,WikiWorks","As fish subject progressed towards september, Mycoplasma (50% and 47% in Reference diet fish and Test dit fish respectively) became more prominent.",increased,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,1783272|544448|31969|2085|2092|2093,Complete,Svetlana up
bsdb:37789427/4/2,37789427,laboratory experiment,37789427,10.1186/s42523-023-00269-1,https://pubmed.ncbi.nlm.nih.gov/37789427/,"Wang J., Li Y., Jaramillo-Torres A., Einen O., Jakobsen J.V., Krogdahl Å. , Kortner T.M.",Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics,Animal microbiome,2023,"Atlantic salmon, Gut health, Gut microbiota, Lactic acid bacteria, Mycoplasma, Yeast cell wall based-prebiotics",Experiment 4,Norway,Salmo salar,Intestine,UBERON:0000160,Diet,EFO:0002755,Fishes fed with test diet in January,Fishes fed with test diet in September,Atlantic Salmon fed with yeast cell wall based-prebiotics diet in September,18,18,NA,16S,12,Illumina,relative abundances,MaAsLin2,0.001,TRUE,2,NA,NA,unchanged,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 7,17 March 2024,Bolanle,"Bolanle,WikiWorks","there was reduction in Lactic acid bacteria(LAB), for example Lactobacillus (12%), Leuconostoc (0.03%) and Lactococcus(0.02%) in Reference diet fish, and Lactobacillus (12%), Leuconostoc (0.05%) and Lactococcus (0.02%) in Test diet fish, respectively.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus",1783272|1239|91061|186826|33958|1243;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1357,Complete,Svetlana up
bsdb:37789427/5/1,37789427,laboratory experiment,37789427,10.1186/s42523-023-00269-1,https://pubmed.ncbi.nlm.nih.gov/37789427/,"Wang J., Li Y., Jaramillo-Torres A., Einen O., Jakobsen J.V., Krogdahl Å. , Kortner T.M.",Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics,Animal microbiome,2023,"Atlantic salmon, Gut health, Gut microbiota, Lactic acid bacteria, Mycoplasma, Yeast cell wall based-prebiotics",Experiment 5,Norway,Salmo salar,Intestine,UBERON:0000160,Diet,EFO:0002755,April Reference diet,April Test diet,"Atlantic Salmon fed with Yeast cell-wall based prebiotics diet with average water temperature of 3.9, 3.4 and 9.6 degree celsius respectively.",18,18,NA,16S,12,Illumina,relative abundances,MaAsLin2,0.05,TRUE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 7,18 April 2024,Bolanle,"Bolanle,WikiWorks",most abundant taxa at genus level of all samples relative abundance of each taxon,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Aliivibrio",3384189|32066|203490|203491|203492|848;3379134|1224|1236|135619|28256|2745;1783272|544448|31969|2085|2092|2093;3379134|1224|1236|135622|267890|22;1783272|1239|91061|186826|33958|46255;1783272|1239|186801|186802|216572|2485925;3379134|1224|1236|135623|641|511678,Complete,Svetlana up
bsdb:37789427/5/2,37789427,laboratory experiment,37789427,10.1186/s42523-023-00269-1,https://pubmed.ncbi.nlm.nih.gov/37789427/,"Wang J., Li Y., Jaramillo-Torres A., Einen O., Jakobsen J.V., Krogdahl Å. , Kortner T.M.",Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics,Animal microbiome,2023,"Atlantic salmon, Gut health, Gut microbiota, Lactic acid bacteria, Mycoplasma, Yeast cell wall based-prebiotics",Experiment 5,Norway,Salmo salar,Intestine,UBERON:0000160,Diet,EFO:0002755,April Reference diet,April Test diet,"Atlantic Salmon fed with Yeast cell-wall based prebiotics diet with average water temperature of 3.9, 3.4 and 9.6 degree celsius respectively.",18,18,NA,16S,12,Illumina,relative abundances,MaAsLin2,0.05,TRUE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 7,18 April 2024,Bolanle,"Bolanle,WikiWorks",most abundant taxa at genus level of all samples relative abundance of each taxon,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Ureibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Psychrilyobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1243;1783272|1239|91061|186826|1300|1357;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1257;1783272|1239|91061|1385|186817|1386;1783272|1239|91061|1385|186818|160795;3379134|1224|1236|135623|641|657;3384189|32066|203490|203491|203492|623282;1783272|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:37789427/6/1,37789427,laboratory experiment,37789427,10.1186/s42523-023-00269-1,https://pubmed.ncbi.nlm.nih.gov/37789427/,"Wang J., Li Y., Jaramillo-Torres A., Einen O., Jakobsen J.V., Krogdahl Å. , Kortner T.M.",Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics,Animal microbiome,2023,"Atlantic salmon, Gut health, Gut microbiota, Lactic acid bacteria, Mycoplasma, Yeast cell wall based-prebiotics",Experiment 6,Norway,Salmo salar,Intestine,UBERON:0000160,Diet,EFO:0002755,september Reference diet,september Test diet,"Atlantic Salmon fed with Yeast cell-wall based prebiotics diet with average water temperature of 3.9, 3.4 and 9.6 degree celsius respectively.",18,18,NA,16S,12,Illumina,relative abundances,MaAsLin2,0.05,TRUE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 7,18 April 2024,Bolanle,"Bolanle,WikiWorks",most abundant taxa at genus level of all samples relative abundance of each taxon,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Ureibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Psychrilyobacter",1783272|1239|91061|1385|186818|160795;3379134|1224|1236|135623|641|657;1783272|1239|91061|186826|33958|1578;3379134|1224|1236|135622|267890|22;3384189|32066|203490|203491|203492|623282,Complete,Svetlana up
bsdb:37789427/6/2,37789427,laboratory experiment,37789427,10.1186/s42523-023-00269-1,https://pubmed.ncbi.nlm.nih.gov/37789427/,"Wang J., Li Y., Jaramillo-Torres A., Einen O., Jakobsen J.V., Krogdahl Å. , Kortner T.M.",Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics,Animal microbiome,2023,"Atlantic salmon, Gut health, Gut microbiota, Lactic acid bacteria, Mycoplasma, Yeast cell wall based-prebiotics",Experiment 6,Norway,Salmo salar,Intestine,UBERON:0000160,Diet,EFO:0002755,september Reference diet,september Test diet,"Atlantic Salmon fed with Yeast cell-wall based prebiotics diet with average water temperature of 3.9, 3.4 and 9.6 degree celsius respectively.",18,18,NA,16S,12,Illumina,relative abundances,MaAsLin2,0.05,TRUE,2,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 7,18 April 2024,Bolanle,"Bolanle,WikiWorks",most abundant taxa at genus level of all samples relative abundance of each taxon,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma",3379134|1224|1236|135619|28256|2745;1783272|544448|31969|2085|2092|2093,Complete,Svetlana up
bsdb:37789856/1/1,37789856,laboratory experiment,37789856,10.3389/fmicb.2023.1214577,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1214577/full,"Peng X., Yi X., Deng N., Liu J., Tan Z. , Cai Y.",Zhishi Daozhi decoction alleviates constipation induced by a high-fat and high-protein diet via regulating intestinal mucosal microbiota and oxidative stress,Frontiers in microbiology,2023,"Zhishi Daozhi decoction, constipation, high-fat and high-protein diet, intestinal mucosal microbiota, microbial diversity",Experiment 1,China,Mus musculus,Intestinal mucosa,UBERON:0001242,Traditional Chinese medicine type,EFO:0007637,Normal (MN) group,Natural recovery (MR) group,"The model recovery group that receives the herbal (zhishi Daozhi decoction) after the disease model is established for mice that were on a high fat, high protein diet, induced constipation with Loperamide hydrochloride (LOP).",5,5,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 5A,4 November 2025,Chyono2,Chyono2,The LEfSe(linear discriminant analysis effect size) analysis of the characteristic bacteria of intestinal mucosa in mice between normal (MN)group and natural recovery (MR) group.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia",1783272|201174|1760|2037;1783272|1239|91061|186826|186827;1783272|1239|91061|186826|186827|1375;1783272|1239|91061|1385;1783272|1239|91061;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;1783272|201174|84992,Complete,KateRasheed
bsdb:37789856/1/2,37789856,laboratory experiment,37789856,10.3389/fmicb.2023.1214577,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1214577/full,"Peng X., Yi X., Deng N., Liu J., Tan Z. , Cai Y.",Zhishi Daozhi decoction alleviates constipation induced by a high-fat and high-protein diet via regulating intestinal mucosal microbiota and oxidative stress,Frontiers in microbiology,2023,"Zhishi Daozhi decoction, constipation, high-fat and high-protein diet, intestinal mucosal microbiota, microbial diversity",Experiment 1,China,Mus musculus,Intestinal mucosa,UBERON:0001242,Traditional Chinese medicine type,EFO:0007637,Normal (MN) group,Natural recovery (MR) group,"The model recovery group that receives the herbal (zhishi Daozhi decoction) after the disease model is established for mice that were on a high fat, high protein diet, induced constipation with Loperamide hydrochloride (LOP).",5,5,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 5A,5 November 2025,Chyono2,Chyono2,The LEfSe (linear discriminant analysis effect size) analysis of the characteristic bacteria of intestinal mucosa in mice between normal(MN) group and natural recovery(MR) group.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",1783272|1239|186801;1783272|1239|186801|186802|31979;3379134|74201|203494|48461|203557;3379134|74201|203494|48461;3379134|74201;1783272|1239|186801|186802|31979|49082;3379134|74201|203494;1783272|1239|186801|186802;3379134|74201|203494|48461|1647988|239934,Complete,KateRasheed
bsdb:37789856/2/1,37789856,laboratory experiment,37789856,10.3389/fmicb.2023.1214577,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1214577/full,"Peng X., Yi X., Deng N., Liu J., Tan Z. , Cai Y.",Zhishi Daozhi decoction alleviates constipation induced by a high-fat and high-protein diet via regulating intestinal mucosal microbiota and oxidative stress,Frontiers in microbiology,2023,"Zhishi Daozhi decoction, constipation, high-fat and high-protein diet, intestinal mucosal microbiota, microbial diversity",Experiment 2,China,Mus musculus,Intestinal mucosa,UBERON:0001242,Traditional Chinese medicine type,EFO:0007637,Natural recovery (MR) group,Model low dose (MLD) Group,"Mice that received the low dose of Zhishi Daozhi decoction on a high fat, high protein diet, induced constipation with Loperamide hydrochloride (LOP).",5,5,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 5B,4 November 2025,Chyono2,Chyono2,The LEfSe (linear discriminant analysis effect size) analysis of the  Characteristic bacteria of intestinal mucosa in mice between natural recovery(MR) group and model low-dose(MLD) group.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales",3379134|1224|28211|204458|76892;3379134|1224|28211|204458,Complete,KateRasheed
bsdb:37789856/2/2,37789856,laboratory experiment,37789856,10.3389/fmicb.2023.1214577,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1214577/full,"Peng X., Yi X., Deng N., Liu J., Tan Z. , Cai Y.",Zhishi Daozhi decoction alleviates constipation induced by a high-fat and high-protein diet via regulating intestinal mucosal microbiota and oxidative stress,Frontiers in microbiology,2023,"Zhishi Daozhi decoction, constipation, high-fat and high-protein diet, intestinal mucosal microbiota, microbial diversity",Experiment 2,China,Mus musculus,Intestinal mucosa,UBERON:0001242,Traditional Chinese medicine type,EFO:0007637,Natural recovery (MR) group,Model low dose (MLD) Group,"Mice that received the low dose of Zhishi Daozhi decoction on a high fat, high protein diet, induced constipation with Loperamide hydrochloride (LOP).",5,5,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 5B,6 November 2025,Chyono2,Chyono2,The LEfSe (linear discriminant analysis effect size) analysis of the characteristic bacteria of intestinal mucosa in mice between natural recovery(MR) group and model low-dose(MLD) group.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|201174|1760|2037;1783272|1239|91061|186826|186827|1375;1783272|1239|91061|1385;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279,Complete,KateRasheed
bsdb:37789856/3/1,37789856,laboratory experiment,37789856,10.3389/fmicb.2023.1214577,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1214577/full,"Peng X., Yi X., Deng N., Liu J., Tan Z. , Cai Y.",Zhishi Daozhi decoction alleviates constipation induced by a high-fat and high-protein diet via regulating intestinal mucosal microbiota and oxidative stress,Frontiers in microbiology,2023,"Zhishi Daozhi decoction, constipation, high-fat and high-protein diet, intestinal mucosal microbiota, microbial diversity",Experiment 3,China,Mus musculus,Intestinal mucosa,UBERON:0001242,Traditional Chinese medicine type,EFO:0007637,Natural recovery group (MR),Medium-dose group (MMD),"Mice given medium-dose treatment  and were on a high fat, high protein diet, induced constipation with Loperamide hydrochloride (LOP)",5,5,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 5C,4 November 2025,Chyono2,Chyono2,The LEfSe (linear discriminant analysis effect size) analysis of the characteristic bacteria of intestinal mucosa in mice between natural recovery(MR) group and model medium dose(MMD) group,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Bacteroidota",3379134|976|200643|171549;3379134|976|200643;3379134|74201;3379134|976,Complete,KateRasheed
bsdb:37789856/3/2,37789856,laboratory experiment,37789856,10.3389/fmicb.2023.1214577,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1214577/full,"Peng X., Yi X., Deng N., Liu J., Tan Z. , Cai Y.",Zhishi Daozhi decoction alleviates constipation induced by a high-fat and high-protein diet via regulating intestinal mucosal microbiota and oxidative stress,Frontiers in microbiology,2023,"Zhishi Daozhi decoction, constipation, high-fat and high-protein diet, intestinal mucosal microbiota, microbial diversity",Experiment 3,China,Mus musculus,Intestinal mucosa,UBERON:0001242,Traditional Chinese medicine type,EFO:0007637,Natural recovery group (MR),Medium-dose group (MMD),"Mice given medium-dose treatment  and were on a high fat, high protein diet, induced constipation with Loperamide hydrochloride (LOP)",5,5,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 5C,6 November 2025,Chyono2,Chyono2,The LEfSe (linear discriminant analysis effect size) analysis of the characteristic bacteria of intestinal mucosa in mice between natural recovery(MR) group and model medium dose (MMD) group.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae",1783272|1239|91061|186826|186827|1375;3379134|1224|1236|135624;1783272|1239|91061|1385|186817;1783272|1239|91061|1385;1783272|1239|91061|1385|186817|1386;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|135624|83763|83770;3379134|1224|1236|135624|83763,Complete,KateRasheed
bsdb:37789856/4/1,37789856,laboratory experiment,37789856,10.3389/fmicb.2023.1214577,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1214577/full,"Peng X., Yi X., Deng N., Liu J., Tan Z. , Cai Y.",Zhishi Daozhi decoction alleviates constipation induced by a high-fat and high-protein diet via regulating intestinal mucosal microbiota and oxidative stress,Frontiers in microbiology,2023,"Zhishi Daozhi decoction, constipation, high-fat and high-protein diet, intestinal mucosal microbiota, microbial diversity",Experiment 4,China,Mus musculus,Intestinal mucosa,UBERON:0001242,Traditional Chinese medicine type,EFO:0007637,Natural recovery (MR) group,Model high-dose (MHD) group,"Mice given high-dose treatment and were on a high fat, high protein diet, induced constipation with Loperamide hydrochloride (LOP)",5,5,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 5D,4 November 2025,Chyono2,Chyono2,The LEfSe (linear discriminant analysis effect size) analysis of characteristic bacteria of intestinal mucosa in mice between natural recovery (MR) group and model high-dose (MHD) group.,increased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus",1783272|1239|186801;1783272|1239|186801|186802|31979;3379134|1224|1236|91347|543|620;1783272|1239|186801|186802;1783272|1239|186801|186802|31979|49082,Complete,KateRasheed
bsdb:37789856/4/2,37789856,laboratory experiment,37789856,10.3389/fmicb.2023.1214577,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1214577/full,"Peng X., Yi X., Deng N., Liu J., Tan Z. , Cai Y.",Zhishi Daozhi decoction alleviates constipation induced by a high-fat and high-protein diet via regulating intestinal mucosal microbiota and oxidative stress,Frontiers in microbiology,2023,"Zhishi Daozhi decoction, constipation, high-fat and high-protein diet, intestinal mucosal microbiota, microbial diversity",Experiment 4,China,Mus musculus,Intestinal mucosa,UBERON:0001242,Traditional Chinese medicine type,EFO:0007637,Natural recovery (MR) group,Model high-dose (MHD) group,"Mice given high-dose treatment and were on a high fat, high protein diet, induced constipation with Loperamide hydrochloride (LOP)",5,5,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 5D,6 November 2025,Chyono2,Chyono2,The LEfSe (linear discriminant analysis effect size) analysis of the characteristic bacteria of intestinal mucosa in mice between natural recovery(MR) group and model high-dose(MHD) group,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia",1783272|201174|1760|2037;1783272|1239|91061|186826|186827|1375;1783272|1239|91061|1385|186817;1783272|1239|91061|1385;1783272|1239|91061;1783272|1239|91061|1385|186817|1386;1783272|1239|186801|186802|31979|1485;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;28221;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|201174;1783272|201174|84992,Complete,KateRasheed
bsdb:37789856/5/1,37789856,laboratory experiment,37789856,10.3389/fmicb.2023.1214577,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1214577/full,"Peng X., Yi X., Deng N., Liu J., Tan Z. , Cai Y.",Zhishi Daozhi decoction alleviates constipation induced by a high-fat and high-protein diet via regulating intestinal mucosal microbiota and oxidative stress,Frontiers in microbiology,2023,"Zhishi Daozhi decoction, constipation, high-fat and high-protein diet, intestinal mucosal microbiota, microbial diversity",Experiment 5,China,Mus musculus,Intestinal mucosa,UBERON:0001242,Oxidative Stress,EFO:1001905,Low superoxide dismutase(SOD) in natural recovery(MR) group and Normal (MN)group,High superoxide dismutase(SOD) in natural recovery (MR)group and Normal (MN)group,Samples with high superoxide dismutase(SOD) indicator for natural recovery(MR) group and normal(MN) group.,5,5,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 7A,5 November 2025,Chyono2,Chyono2,Heat maps of correlation between characteristic bacteria and superoxide dismutase(SOD) indicator in (A) MN and MR.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,1783272|1239|186801|186802|31979|49082,Complete,KateRasheed
bsdb:37789856/6/1,37789856,laboratory experiment,37789856,10.3389/fmicb.2023.1214577,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1214577/full,"Peng X., Yi X., Deng N., Liu J., Tan Z. , Cai Y.",Zhishi Daozhi decoction alleviates constipation induced by a high-fat and high-protein diet via regulating intestinal mucosal microbiota and oxidative stress,Frontiers in microbiology,2023,"Zhishi Daozhi decoction, constipation, high-fat and high-protein diet, intestinal mucosal microbiota, microbial diversity",Experiment 6,China,Mus musculus,Intestinal mucosa,UBERON:0001242,Oxidative Stress,EFO:1001905,Low malondialdehyde(MDA) in natural recovery(MR) and normal (MN) group,High malondialdehyde(MDA) in natural recovery (MR) and Normal (MN)group,Samples with high malondialdehyde(MDA) indicator for natural recovery(MR) group and normal(MN) group.,5,5,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 7A,5 November 2025,Chyono2,Chyono2,Heat maps of correlation between characteristic bacteria and malondialdehyde (MDA) indicator in (A) MN and MR.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium",1783272|1239|91061|186826|186827|1375;1783272|201174|1760|85007|1653|1716,Complete,KateRasheed
bsdb:37789856/6/2,37789856,laboratory experiment,37789856,10.3389/fmicb.2023.1214577,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1214577/full,"Peng X., Yi X., Deng N., Liu J., Tan Z. , Cai Y.",Zhishi Daozhi decoction alleviates constipation induced by a high-fat and high-protein diet via regulating intestinal mucosal microbiota and oxidative stress,Frontiers in microbiology,2023,"Zhishi Daozhi decoction, constipation, high-fat and high-protein diet, intestinal mucosal microbiota, microbial diversity",Experiment 6,China,Mus musculus,Intestinal mucosa,UBERON:0001242,Oxidative Stress,EFO:1001905,Low malondialdehyde(MDA) in natural recovery(MR) and normal (MN) group,High malondialdehyde(MDA) in natural recovery (MR) and Normal (MN)group,Samples with high malondialdehyde(MDA) indicator for natural recovery(MR) group and normal(MN) group.,5,5,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,fig 7A,6 November 2025,Chyono2,Chyono2,Heat maps of correlation between characteristic bacteria and malondialdehyde(MDA) indicator in (A) MN and MR.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,1783272|1239|186801|186802|31979|49082,Complete,KateRasheed
bsdb:37789856/7/1,37789856,laboratory experiment,37789856,10.3389/fmicb.2023.1214577,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1214577/full,"Peng X., Yi X., Deng N., Liu J., Tan Z. , Cai Y.",Zhishi Daozhi decoction alleviates constipation induced by a high-fat and high-protein diet via regulating intestinal mucosal microbiota and oxidative stress,Frontiers in microbiology,2023,"Zhishi Daozhi decoction, constipation, high-fat and high-protein diet, intestinal mucosal microbiota, microbial diversity",Experiment 7,China,Mus musculus,Intestinal mucosa,UBERON:0001242,Oxidative Stress,EFO:1001905,Low superoxide dismutase(SOD) in natural recovery (MR) and model low-dose (MLD) group,High superoxide dismutase(SOD) in natural recovery (MR) group and model low-dose (MLD) group,Samples with high superoxide dismutase(SOD) indicator for natural recovery(MR) group and model low-dose(MLD) group.,5,5,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 7B,5 November 2025,Chyono2,Chyono2,Heat maps of correlation between characteristic bacteria and superoxide dismutase (SOD) indicator group in (B) MR and MLD,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio",1783272|1239|91061|186826|186827|1375;1783272|1239|91061|1385|186817|1386;3379134|1224|1236|135624|83763|83770,Complete,KateRasheed
bsdb:37789856/8/1,37789856,laboratory experiment,37789856,10.3389/fmicb.2023.1214577,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1214577/full,"Peng X., Yi X., Deng N., Liu J., Tan Z. , Cai Y.",Zhishi Daozhi decoction alleviates constipation induced by a high-fat and high-protein diet via regulating intestinal mucosal microbiota and oxidative stress,Frontiers in microbiology,2023,"Zhishi Daozhi decoction, constipation, high-fat and high-protein diet, intestinal mucosal microbiota, microbial diversity",Experiment 8,China,Mus musculus,Intestinal mucosa,UBERON:0001242,Oxidative Stress,EFO:1001905,Low cholecystokinin (CCK) group in natural recovery(MR) and model medium-dose (MMD) group,High cholecystokinin (CCK) group in natural recovery (MR) and model medium-dose (MMD) group,Samples with high cholecystokinin(CCK) indicator for natural recovery(MR) group and model medium-dose(MMD) group.,5,5,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 7C,5 November 2025,Chyono2,Chyono2,Heat maps of correlation between characteristic bacteria and cholecystokinin (CCK) indicator in (C) MR & MMD,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,KateRasheed
bsdb:37789856/9/1,37789856,laboratory experiment,37789856,10.3389/fmicb.2023.1214577,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1214577/full,"Peng X., Yi X., Deng N., Liu J., Tan Z. , Cai Y.",Zhishi Daozhi decoction alleviates constipation induced by a high-fat and high-protein diet via regulating intestinal mucosal microbiota and oxidative stress,Frontiers in microbiology,2023,"Zhishi Daozhi decoction, constipation, high-fat and high-protein diet, intestinal mucosal microbiota, microbial diversity",Experiment 9,China,Mus musculus,Intestinal mucosa,UBERON:0001242,Oxidative Stress,EFO:1001905,Low cacitonin gene-related peptide(CGRP) group in natural recovery(MR) and model medium-dose(MMD),High  cacitonin gene-related peptide(CGRP) in natural recovery(MR) and model medium-dose (MMD) groupgroup,Samples with high cacitonin gene-related peptide(CGRP) indicator for natural recovery(MR) group and model medium dose(MMD) group.,5,5,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 7C,5 November 2025,Chyono2,Chyono2,Heat maps of correlation between characteristic bacteria and cacitonin gene-related peptides(CGRP) indicator group (C) MN and MMD,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:37789856/10/1,37789856,laboratory experiment,37789856,10.3389/fmicb.2023.1214577,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1214577/full,"Peng X., Yi X., Deng N., Liu J., Tan Z. , Cai Y.",Zhishi Daozhi decoction alleviates constipation induced by a high-fat and high-protein diet via regulating intestinal mucosal microbiota and oxidative stress,Frontiers in microbiology,2023,"Zhishi Daozhi decoction, constipation, high-fat and high-protein diet, intestinal mucosal microbiota, microbial diversity",Experiment 10,China,Mus musculus,Intestinal mucosa,UBERON:0001242,Oxidative Stress,EFO:1001905,Low malondialdehyde(MDA) group in natural recovery (MR) and model medium-dose(MMD) group,High malondialdehyde(MDA) group in natural recovery(MR) and model medium-dose (MMD) group,Samples with high malondialdehyde(MDA) indicator for natural recovery(MR) group and model medium-dose(MMD) group.,5,5,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 7C,5 November 2025,Chyono2,Chyono2,Heat maps of correlation between characteristic bacteria and malondialdehyde (MDA) indicator in (C) MR & MMD,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|91061|1385|186817|1386;3379134|976|200643|171549|171552|838,Complete,KateRasheed
bsdb:37789856/11/1,37789856,laboratory experiment,37789856,10.3389/fmicb.2023.1214577,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1214577/full,"Peng X., Yi X., Deng N., Liu J., Tan Z. , Cai Y.",Zhishi Daozhi decoction alleviates constipation induced by a high-fat and high-protein diet via regulating intestinal mucosal microbiota and oxidative stress,Frontiers in microbiology,2023,"Zhishi Daozhi decoction, constipation, high-fat and high-protein diet, intestinal mucosal microbiota, microbial diversity",Experiment 11,China,Mus musculus,Intestinal mucosa,UBERON:0001242,Oxidative Stress,EFO:1001905,Low superoxide dismutase(SOD) in natural recovery(MR) group and model medium-dose (MMD) group,High superoxide dismutase(SOD) in natural recovery(MR) group and model medium-dose (MMD) group,Samples with high superoxide dismutase (SOD) indicator for natural recovery(MR) group and model medium-dose(MMD) group.,5,5,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 7C,5 November 2025,Chyono2,Chyono2,Heat maps of correlation between characteristic bacteria and superoxide dismutase (SOD) indicator group in (C) MR & MMD,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio",1783272|1239|91061|186826|186827|1375;1783272|1239|91061|1385|186817|1386;1783272|201174|1760|85007|1653|1716;3379134|976|200643|171549|171552|838;3379134|1224|1236|135624|83763|83770,Complete,KateRasheed
bsdb:37789856/12/1,37789856,laboratory experiment,37789856,10.3389/fmicb.2023.1214577,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1214577/full,"Peng X., Yi X., Deng N., Liu J., Tan Z. , Cai Y.",Zhishi Daozhi decoction alleviates constipation induced by a high-fat and high-protein diet via regulating intestinal mucosal microbiota and oxidative stress,Frontiers in microbiology,2023,"Zhishi Daozhi decoction, constipation, high-fat and high-protein diet, intestinal mucosal microbiota, microbial diversity",Experiment 12,China,Mus musculus,Intestinal mucosa,UBERON:0001242,Oxidative Stress,EFO:1001905,Low cholecystokinin (CCK) in natural recovery (MR) group and model high-dose (MHD) group,High cholecystokinin (CCK) in natural recovery (MR) group and model high-dose (MHD) group,Samples with high cholecystokinin (CCK) indicator for natural recovery (MR) group and model high-dose (MHD) group.,5,5,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 7D,5 November 2025,Chyono2,Chyono2,Heat maps of correlation between characteristic bacteria and cholecystokinin (CCK) indicator in (D) MR & MHD,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|186801|186802|31979|1485;1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:37789856/13/1,37789856,laboratory experiment,37789856,10.3389/fmicb.2023.1214577,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1214577/full,"Peng X., Yi X., Deng N., Liu J., Tan Z. , Cai Y.",Zhishi Daozhi decoction alleviates constipation induced by a high-fat and high-protein diet via regulating intestinal mucosal microbiota and oxidative stress,Frontiers in microbiology,2023,"Zhishi Daozhi decoction, constipation, high-fat and high-protein diet, intestinal mucosal microbiota, microbial diversity",Experiment 13,China,Mus musculus,Intestinal mucosa,UBERON:0001242,Oxidative Stress,EFO:1001905,Low superoxide dismutase (SOD) in natural recovery (MR) group and model high-dose(MHD) group,High superoxide dismutase (SOD)  in natural recovery (MR) group and model high-dose(MHD) group,Samples with high superoxide dismutase (SOD) indicator for natural recovery (MR) group and model high-dose (MHD) group,5,5,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 7D,7 November 2025,Chyono2,Chyono2,Heat maps of correlation between characteristic bacteria and superoxide dismutase (SOD) indicator in (D) MR & MHD,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,3379134|1224|1236|91347|543|620,Complete,KateRasheed
bsdb:37789856/13/2,37789856,laboratory experiment,37789856,10.3389/fmicb.2023.1214577,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1214577/full,"Peng X., Yi X., Deng N., Liu J., Tan Z. , Cai Y.",Zhishi Daozhi decoction alleviates constipation induced by a high-fat and high-protein diet via regulating intestinal mucosal microbiota and oxidative stress,Frontiers in microbiology,2023,"Zhishi Daozhi decoction, constipation, high-fat and high-protein diet, intestinal mucosal microbiota, microbial diversity",Experiment 13,China,Mus musculus,Intestinal mucosa,UBERON:0001242,Oxidative Stress,EFO:1001905,Low superoxide dismutase (SOD) in natural recovery (MR) group and model high-dose(MHD) group,High superoxide dismutase (SOD)  in natural recovery (MR) group and model high-dose(MHD) group,Samples with high superoxide dismutase (SOD) indicator for natural recovery (MR) group and model high-dose (MHD) group,5,5,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 7D,7 November 2025,Chyono2,Chyono2,Heat maps of correlation between characteristic bacteria and superoxide dismutase (SOD) indicator in (D) MR & (MHD),decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",1783272|1239|91061|186826|186827|1375;1783272|1239|91061|1385|186817|1386;1783272|1239|186801|186802|31979|1485;3379134|200940|3031449|213115|194924|872;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|909929|1843491|970,Complete,KateRasheed
bsdb:37789856/14/1,37789856,laboratory experiment,37789856,10.3389/fmicb.2023.1214577,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1214577/full,"Peng X., Yi X., Deng N., Liu J., Tan Z. , Cai Y.",Zhishi Daozhi decoction alleviates constipation induced by a high-fat and high-protein diet via regulating intestinal mucosal microbiota and oxidative stress,Frontiers in microbiology,2023,"Zhishi Daozhi decoction, constipation, high-fat and high-protein diet, intestinal mucosal microbiota, microbial diversity",Experiment 14,China,Mus musculus,Intestinal mucosa,UBERON:0001242,Oxidative Stress,EFO:1001905,Low level malondialdehyde (MDA) in natural recovery (MR) group and model high-dose (MHD) group,High level malondialdehyde (MDA)  in natural recovery (MR) group and model high-dose (MHD) group,Samples with high malondialdehyde (MDA) indicator for natural recovery (MR) group and model high-dose (MHD) group.,5,5,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 7D,7 November 2025,Chyono2,Chyono2,Heat maps of correlation between characteristic bacteria and malondialdehyde (MDA) indicator in (D) MR & MHD,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,3379134|1224|1236|91347|543|620,Complete,KateRasheed
bsdb:37789856/15/1,37789856,laboratory experiment,37789856,10.3389/fmicb.2023.1214577,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1214577/full,"Peng X., Yi X., Deng N., Liu J., Tan Z. , Cai Y.",Zhishi Daozhi decoction alleviates constipation induced by a high-fat and high-protein diet via regulating intestinal mucosal microbiota and oxidative stress,Frontiers in microbiology,2023,"Zhishi Daozhi decoction, constipation, high-fat and high-protein diet, intestinal mucosal microbiota, microbial diversity",Experiment 15,China,Mus musculus,Intestinal mucosa,UBERON:0001242,Traditional Chinese medicine type,EFO:0007637,Normal (MN) group,Natural recovery (MR) group,"The model recovery group that receives the herbal (zhishi Daozhi decoction) after the disease model is established for mice that were on a high fat, high protein diet, induced constipation with Loperamide hydrochloride (LOP).",5,5,NA,16S,34,Illumina,relative abundances,"ANOVA,Post-Hoc Pairwise",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,fig 4c,9 November 2025,Chyono2,Chyono2,"Differential bacteria in genus level. n = 5, *p < 0.05, **p < 0.01.",increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,KateRasheed
bsdb:37789856/16/1,37789856,laboratory experiment,37789856,10.3389/fmicb.2023.1214577,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1214577/full,"Peng X., Yi X., Deng N., Liu J., Tan Z. , Cai Y.",Zhishi Daozhi decoction alleviates constipation induced by a high-fat and high-protein diet via regulating intestinal mucosal microbiota and oxidative stress,Frontiers in microbiology,2023,"Zhishi Daozhi decoction, constipation, high-fat and high-protein diet, intestinal mucosal microbiota, microbial diversity",Experiment 16,China,Mus musculus,Intestinal mucosa,UBERON:0001242,Traditional Chinese medicine type,EFO:0007637,Normal (MN) group,Medium-dose (MMD) group,"Mice given medium-dose treatment and were on a high fat, high protein diet, induced constipation with Loperamide hydrochloride (LOP).",5,5,NA,16S,34,Illumina,relative abundances,"ANOVA,Post-Hoc Pairwise",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,fig 4c,9 November 2025,Chyono2,Chyono2,"Differential bacteria in genus level. n = 5, *p < 0.05, **p < 0.01.",decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,1783272|1239|91061|1385|186817|1386,Complete,KateRasheed
bsdb:37789856/17/1,37789856,laboratory experiment,37789856,10.3389/fmicb.2023.1214577,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1214577/full,"Peng X., Yi X., Deng N., Liu J., Tan Z. , Cai Y.",Zhishi Daozhi decoction alleviates constipation induced by a high-fat and high-protein diet via regulating intestinal mucosal microbiota and oxidative stress,Frontiers in microbiology,2023,"Zhishi Daozhi decoction, constipation, high-fat and high-protein diet, intestinal mucosal microbiota, microbial diversity",Experiment 17,China,Mus musculus,Intestinal mucosa,UBERON:0001242,Traditional Chinese medicine type,EFO:0007637,Normal (MN) group,Model high-dose (MHD) group,"Mice given high-dose treatment and were on a high fat, high protein diet, induced constipation with Loperamide hydrochloride (LOP).",5,5,NA,16S,34,Illumina,relative abundances,"ANOVA,Post-Hoc Pairwise",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,fig 4c,9 November 2025,Chyono2,Chyono2,"Differential bacteria in genus level. n = 5, *p < 0.05, **p < 0.01.",decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,1783272|1239|91061|1385|186817|1386,Complete,KateRasheed
bsdb:37789856/18/1,37789856,laboratory experiment,37789856,10.3389/fmicb.2023.1214577,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1214577/full,"Peng X., Yi X., Deng N., Liu J., Tan Z. , Cai Y.",Zhishi Daozhi decoction alleviates constipation induced by a high-fat and high-protein diet via regulating intestinal mucosal microbiota and oxidative stress,Frontiers in microbiology,2023,"Zhishi Daozhi decoction, constipation, high-fat and high-protein diet, intestinal mucosal microbiota, microbial diversity",Experiment 18,China,Mus musculus,Intestinal mucosa,UBERON:0001242,Traditional Chinese medicine type,EFO:0007637,Natural recovery (MR) group,Model low-dose (MLD) group,"Mice given low-dose treatment and were on a high fat, high protein diet, induced constipation with Loperamide hydrochloride (LOP).",5,5,NA,16S,34,Illumina,relative abundances,"ANOVA,Post-Hoc Pairwise",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,fig 4c,9 November 2025,Chyono2,Chyono2,"Differential bacteria in genus level. n = 5, *p < 0.05, **p < 0.01.",decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,3379134|1224|1236|135624|83763|83770,Complete,KateRasheed
bsdb:37789856/19/1,37789856,laboratory experiment,37789856,10.3389/fmicb.2023.1214577,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1214577/full,"Peng X., Yi X., Deng N., Liu J., Tan Z. , Cai Y.",Zhishi Daozhi decoction alleviates constipation induced by a high-fat and high-protein diet via regulating intestinal mucosal microbiota and oxidative stress,Frontiers in microbiology,2023,"Zhishi Daozhi decoction, constipation, high-fat and high-protein diet, intestinal mucosal microbiota, microbial diversity",Experiment 19,China,Mus musculus,Intestinal mucosa,UBERON:0001242,Traditional Chinese medicine type,EFO:0007637,Natural recovery (MR) group,Model medium-dose (MMD) group,"Mice given medium-dose treatment and were on a high fat, high protein diet, induced constipation with Loperamide hydrochloride (LOP).",5,5,NA,16S,34,Illumina,relative abundances,"ANOVA,Post-Hoc Pairwise",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,fig 4c,9 November 2025,Chyono2,Chyono2,"Differential bacteria in genus level. n = 5, *p < 0.05, **p < 0.01.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio",1783272|201174|1760|85007|1653|1716;3379134|1224|1236|135624|83763|83770,Complete,KateRasheed
bsdb:37789856/20/1,37789856,laboratory experiment,37789856,10.3389/fmicb.2023.1214577,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1214577/full,"Peng X., Yi X., Deng N., Liu J., Tan Z. , Cai Y.",Zhishi Daozhi decoction alleviates constipation induced by a high-fat and high-protein diet via regulating intestinal mucosal microbiota and oxidative stress,Frontiers in microbiology,2023,"Zhishi Daozhi decoction, constipation, high-fat and high-protein diet, intestinal mucosal microbiota, microbial diversity",Experiment 20,China,Mus musculus,Intestinal mucosa,UBERON:0001242,Traditional Chinese medicine type,EFO:0007637,Natural recovery (MR) group,Model high-dose (MHD) group,"Mice given high-dose treatment and were on a high fat, high protein diet, induced constipation with Loperamide hydrochloride (LOP).",5,5,NA,16S,34,Illumina,relative abundances,"ANOVA,Post-Hoc Pairwise",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,fig 4c,9 November 2025,Chyono2,Chyono2,"Differential bacteria in genus level. n = 5, *p < 0.05, **p < 0.01.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:37789856/21/1,37789856,laboratory experiment,37789856,10.3389/fmicb.2023.1214577,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1214577/full,"Peng X., Yi X., Deng N., Liu J., Tan Z. , Cai Y.",Zhishi Daozhi decoction alleviates constipation induced by a high-fat and high-protein diet via regulating intestinal mucosal microbiota and oxidative stress,Frontiers in microbiology,2023,"Zhishi Daozhi decoction, constipation, high-fat and high-protein diet, intestinal mucosal microbiota, microbial diversity",Experiment 21,China,Mus musculus,Intestinal mucosa,UBERON:0001242,Traditional Chinese medicine type,EFO:0007637,Model medium-dose(MMD) group,Model high-dose (MHD) group,"Mice given high-dose treatment and were on a high fat, high protein diet, induced constipation with Loperamide hydrochloride (LOP).",5,5,NA,16S,34,Illumina,relative abundances,"ANOVA,Post-Hoc Pairwise",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,fig 4c,9 November 2025,Chyono2,Chyono2,"Differential bacteria in genus level. n = 5, *p < 0.05, **p < 0.01.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus",3379134|1224|1236|135624|83763|83770;1783272|1239|186801|186802|31979|49082,Complete,KateRasheed
bsdb:37789856/22/1,37789856,laboratory experiment,37789856,10.3389/fmicb.2023.1214577,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1214577/full,"Peng X., Yi X., Deng N., Liu J., Tan Z. , Cai Y.",Zhishi Daozhi decoction alleviates constipation induced by a high-fat and high-protein diet via regulating intestinal mucosal microbiota and oxidative stress,Frontiers in microbiology,2023,"Zhishi Daozhi decoction, constipation, high-fat and high-protein diet, intestinal mucosal microbiota, microbial diversity",Experiment 22,China,Mus musculus,Intestinal mucosa,UBERON:0001242,Oxidative Stress,EFO:1001905,Low cacitonin gene-related peptide(CGRP) in normal (MN) group and natural recovery(MR) group,High  cacitonin gene-related peptide(CGRP) in normal(MN) group and natural recovery(MR),Samples with high cacitonin gene-related peptide(CGRP) indicator for normal (MN) group and natural recovery (MR) group.,5,5,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 7A,11 November 2025,Chyono2,Chyono2,Heat maps of correlation between characteristic bacteria and cacitonin gene-related peptides (CGRP) indicator in (A) MN & MR,increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,1783272|1239|909932|909929|1843491|970,Complete,KateRasheed
bsdb:37789856/23/1,37789856,laboratory experiment,37789856,10.3389/fmicb.2023.1214577,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1214577/full,"Peng X., Yi X., Deng N., Liu J., Tan Z. , Cai Y.",Zhishi Daozhi decoction alleviates constipation induced by a high-fat and high-protein diet via regulating intestinal mucosal microbiota and oxidative stress,Frontiers in microbiology,2023,"Zhishi Daozhi decoction, constipation, high-fat and high-protein diet, intestinal mucosal microbiota, microbial diversity",Experiment 23,China,Mus musculus,Intestinal mucosa,UBERON:0001242,Oxidative Stress,EFO:1001905,Low cacitonin gene-related peptide(CGRP) in natural recovery(MR) group and model medium-high dose (MHD) group,High  cacitonin gene-related peptide(CGRP) in natural recovery(MR) and model high-dose (MHD) group,Samples with high cacitonin gene-related peptide(CGRP) indicator for natural recovery (MR) group and model high-dose (MHD) group.,5,5,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 7D,11 November 2025,Chyono2,Chyono2,Heat maps of correlation between characteristic bacteria and cacitonin gene-related peptides (CGRP) indicator in (D) MR & MHD,increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,1783272|1239|909932|909929|1843491|970,Complete,KateRasheed
bsdb:37798293/1/1,37798293,time series / longitudinal observational,37798293,10.1038/s41541-023-00745-4,NA,"Zhao S., Lok K.Y.W., Sin Z.Y., Peng Y., Fan H.S.L., Nagesh N., Choi M.S.L., Kwok J.Y.Y., Choi E.P.H., Zhang X., Wai H.K., Tsang L.C.H., Cheng S.S.M., Wong M.K.L., Zhu J., Mok C.K.P., Ng S.C., Chan F.K.L., Peiris M., Poon L.L.M. , Tun H.M.",COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition,NPJ vaccines,2023,NA,Experiment 1,China,Homo sapiens,"Breast,Milk","UBERON:0000310,UBERON:0001913","Response to vaccine,Timepoint","EFO:0000724,EFO:0004645",Mothers at pre-vaccination timepoint,Mothers at post vaccination timepoints,"Breastfeeding mothers at post vaccination timepoints; one week post-first dose, one week post second-dose, one month post-second dose.",44,44,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,1.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,figure 1g,22 October 2023,Folakunmi,"Folakunmi,WikiWorks","The most differentially abundant taxa in mothers throughout all post-vaccination timepoints; at one week post-first dose, one week post-second dose and one month post-second dose.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter ursingii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Roseomonadaceae|g__Roseomonas|s__Roseomonas gilardii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae",3379134|1224|1236|2887326|468|469|108980;3379134|1224|28211|3120395|3385906|125216|257708;3379134|1224|28211|204458|76892|41275;1783272|201174|1760|85007|85026|2053;3379134|1224|28211|204455|31989,Complete,ChiomaBlessing
bsdb:37798293/1/2,37798293,time series / longitudinal observational,37798293,10.1038/s41541-023-00745-4,NA,"Zhao S., Lok K.Y.W., Sin Z.Y., Peng Y., Fan H.S.L., Nagesh N., Choi M.S.L., Kwok J.Y.Y., Choi E.P.H., Zhang X., Wai H.K., Tsang L.C.H., Cheng S.S.M., Wong M.K.L., Zhu J., Mok C.K.P., Ng S.C., Chan F.K.L., Peiris M., Poon L.L.M. , Tun H.M.",COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition,NPJ vaccines,2023,NA,Experiment 1,China,Homo sapiens,"Breast,Milk","UBERON:0000310,UBERON:0001913","Response to vaccine,Timepoint","EFO:0000724,EFO:0004645",Mothers at pre-vaccination timepoint,Mothers at post vaccination timepoints,"Breastfeeding mothers at post vaccination timepoints; one week post-first dose, one week post second-dose, one month post-second dose.",44,44,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,1.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,figure 1g,22 October 2023,Folakunmi,"Folakunmi,WikiWorks","The most differentially abundant taxa in mothers throughout all post-vaccination timepoints; at one week post-first dose, one week post-second dose and one month post-second dose.",decreased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter rodentium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",3379134|29547|3031852|213849|72293|209|59617;1783272|1239|526524|526525|128827|174708;3379134|976|200643|171549|2005473;3379134|1224|28216|80840|119060|48736;1783272|1239|526524|526525|2810281|191303,Complete,ChiomaBlessing
bsdb:37798293/2/1,37798293,time series / longitudinal observational,37798293,10.1038/s41541-023-00745-4,NA,"Zhao S., Lok K.Y.W., Sin Z.Y., Peng Y., Fan H.S.L., Nagesh N., Choi M.S.L., Kwok J.Y.Y., Choi E.P.H., Zhang X., Wai H.K., Tsang L.C.H., Cheng S.S.M., Wong M.K.L., Zhu J., Mok C.K.P., Ng S.C., Chan F.K.L., Peiris M., Poon L.L.M. , Tun H.M.",COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition,NPJ vaccines,2023,NA,Experiment 2,China,Homo sapiens,"Breast,Milk","UBERON:0000310,UBERON:0001913",Response to vaccine,EFO:0004645,Low IgA mothers at Baseline,High IgA mothers at Baseline,Breastfeeding mothers with high IgA at baseline,25,18,NA,16S,34,Illumina,relative abundances,LEfSe,0.004,FALSE,2,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 1,Figure 2d,22 October 2023,Folakunmi,"Folakunmi,ChiomaBlessing,WikiWorks",Taxonomic differences in baseline microbiota between high- and low-IgA subjects.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces massiliensis,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium granulosum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Endobacter|s__Endobacter medicaginis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Stutzerimonas|s__Stutzerimonas balearica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alishewanella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Castellaniella,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter",1783272|201174|1760|2037|2049|1654|461393;1783272|1239;1783272|201174|1760|85009|31957|1912216|33011;3379134|1224|28211|3120395|433|1649268|1181271;3384189|32066|203490|203491|203492|848;3379134|1224|28216|206351|481|482|495;3379134|976|200643|171549|171552|838|470565;1783272|1239|186801|186802|216572|1263|40519;3379134|1224|1236|72274|135621|2901164|74829;3379134|1224|1236|135625|712|713;3379134|1224|1236|135625|712|416916;3379134|1224|1236|135622|72275|111142;1783272|201174|1760|85009|31957|2801844;3379134|1224|28216|80840|506|359336;1783272|1239|186801|3085656|3085657|2039302;3379134|1224|28216|206351|481|482;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803|1213720;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|3082720|186804|1505652,Complete,ChiomaBlessing
bsdb:37798293/2/2,37798293,time series / longitudinal observational,37798293,10.1038/s41541-023-00745-4,NA,"Zhao S., Lok K.Y.W., Sin Z.Y., Peng Y., Fan H.S.L., Nagesh N., Choi M.S.L., Kwok J.Y.Y., Choi E.P.H., Zhang X., Wai H.K., Tsang L.C.H., Cheng S.S.M., Wong M.K.L., Zhu J., Mok C.K.P., Ng S.C., Chan F.K.L., Peiris M., Poon L.L.M. , Tun H.M.",COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition,NPJ vaccines,2023,NA,Experiment 2,China,Homo sapiens,"Breast,Milk","UBERON:0000310,UBERON:0001913",Response to vaccine,EFO:0004645,Low IgA mothers at Baseline,High IgA mothers at Baseline,Breastfeeding mothers with high IgA at baseline,25,18,NA,16S,34,Illumina,relative abundances,LEfSe,0.004,FALSE,2,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 2,Figure 2d,15 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Taxonomic differences in baseline microbiota between high- and low-IgA subjects.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium kroppenstedtii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas",1783272|201174|1760|85007|1653|1716|161879;3379134|1224|1236|2887326|468|469;3379134|1224|28211|204458|76892|41275,Complete,ChiomaBlessing
bsdb:37798293/3/1,37798293,time series / longitudinal observational,37798293,10.1038/s41541-023-00745-4,NA,"Zhao S., Lok K.Y.W., Sin Z.Y., Peng Y., Fan H.S.L., Nagesh N., Choi M.S.L., Kwok J.Y.Y., Choi E.P.H., Zhang X., Wai H.K., Tsang L.C.H., Cheng S.S.M., Wong M.K.L., Zhu J., Mok C.K.P., Ng S.C., Chan F.K.L., Peiris M., Poon L.L.M. , Tun H.M.",COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition,NPJ vaccines,2023,NA,Experiment 3,China,Homo sapiens,"Breast,Milk","UBERON:0000310,UBERON:0001913",Response to vaccine,EFO:0004645,Low IgA mothers at one week post-second dose,High IgA mothers at one week post-second dose,Breastfeeding mothers with high IgA at one week after receiving the second dose of the SARS-CoV-2 mRNA vaccine (BNT162b2).,25,18,NA,16S,34,Illumina,relative abundances,LEfSe,0.004,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3d,22 October 2023,Folakunmi,"Folakunmi,ChiomaBlessing,WikiWorks",Taxonomic differences in microbiota one week post-second dose between high- and low-IgA subjects,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Candidatus Marinarcus|s__Candidatus Marinarcus aquaticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasuis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Gemmobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leucobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae|g__Neptunomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|g__Rhodobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio",1783272|201174|1760|85004|31953|1678|1681;3379134|29547|3031852|213849|2808963|2321204|2044504;1783272|1239|91061|186826|1300|1301|1501662;1783272|1239|909932|1843488|909930|904;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85007|1653|1716;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|186806|1730;3379134|1224|28211|204455|31989|204456;1783272|1239|526524|526525|128827|1573535;1783272|201174|1760|85006|85023|55968;3379134|1224|1236|135619|135620|75687;3379134|1224|28211|204455|1060;1783272|1239|186801|186802|216572|292632;3379134|1224|1236|135623|641|662,Complete,ChiomaBlessing
bsdb:37798293/3/2,37798293,time series / longitudinal observational,37798293,10.1038/s41541-023-00745-4,NA,"Zhao S., Lok K.Y.W., Sin Z.Y., Peng Y., Fan H.S.L., Nagesh N., Choi M.S.L., Kwok J.Y.Y., Choi E.P.H., Zhang X., Wai H.K., Tsang L.C.H., Cheng S.S.M., Wong M.K.L., Zhu J., Mok C.K.P., Ng S.C., Chan F.K.L., Peiris M., Poon L.L.M. , Tun H.M.",COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition,NPJ vaccines,2023,NA,Experiment 3,China,Homo sapiens,"Breast,Milk","UBERON:0000310,UBERON:0001913",Response to vaccine,EFO:0004645,Low IgA mothers at one week post-second dose,High IgA mothers at one week post-second dose,Breastfeeding mothers with high IgA at one week after receiving the second dose of the SARS-CoV-2 mRNA vaccine (BNT162b2).,25,18,NA,16S,34,Illumina,relative abundances,LEfSe,0.004,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 3d,15 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Taxonomic differences in microbiota one week post-second dose between high- and low-IgA subjects,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter soli,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas",3379134|1224|1236|2887326|468|469|487316;3379134|1224|28211|204458|76892|41275,Complete,ChiomaBlessing
bsdb:37798293/4/1,37798293,time series / longitudinal observational,37798293,10.1038/s41541-023-00745-4,NA,"Zhao S., Lok K.Y.W., Sin Z.Y., Peng Y., Fan H.S.L., Nagesh N., Choi M.S.L., Kwok J.Y.Y., Choi E.P.H., Zhang X., Wai H.K., Tsang L.C.H., Cheng S.S.M., Wong M.K.L., Zhu J., Mok C.K.P., Ng S.C., Chan F.K.L., Peiris M., Poon L.L.M. , Tun H.M.",COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition,NPJ vaccines,2023,NA,Experiment 4,China,Homo sapiens,"Breast,Milk","UBERON:0001913,UBERON:0000310",Response to vaccine,EFO:0004645,Mothers at pre-vaccination timepoint (baseline),Mothers at one week post-first dose,Breastfeeding mothers at one week after receiving the first dose of BNT162b2 vaccine.,44,44,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,1.5,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,supplementary table 3,24 October 2023,Folakunmi,"Folakunmi,ChiomaBlessing,WikiWorks",differential abundance of mothers one week after first dose of BNT162b2 when compared to baseline.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter radioresistens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter soli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter ursingii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Caldibacillus|s__Caldibacillus thermoamylovorans,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Empedobacter|s__Empedobacter brevis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus haemolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Roseomonadaceae|g__Roseomonas|s__Roseomonas gilardii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Anoxybacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Duganella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Empedobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Pseudarthrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium CHKCI001,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium",3379134|1224|1236|2887326|468|469|40216;3379134|1224|1236|2887326|468|469|487316;3379134|1224|1236|2887326|468|469|108980;1783272|1239|91061|1385|186817|1276290|35841;3379134|976|117743|200644|2762318|59734|247;1783272|1239|186801|186802|186806|1730|39496;3379134|1224|1236|135625|712|724|726;3379134|1224|1236|135625|712|724|735;3379134|1224|28211|3120395|3385906|125216|257708;3379134|1224|1236|135625|712|713;1783272|1239|91061|1385|3120669|150247;1783272|1239|91061|1385|186817|1386;3379134|976|117743|200644|2762318|59735;3379134|1224|28211|204458|76892|41275;3379134|1224|28216|80840|75682|75654;3379134|976|117743|200644|2762318|59734;3379134|1224|28211|356|212791;3379134|976|117743|200644|49546|237;3379134|1224|28216|80840|75682|29580;1783272|201174|1760|85006|85023|33882;3379134|1224|28211|204455|31989;3379134|1224|1236|91347|1903414|586;1783272|201174|1760|85006|1268|1742993;3379134|1224|1236|135622|267890|22;3379134|1224|28211|204457|41297;3379134|1224|28211|204457|41297|13687;1783272|1239|186801|186802|1780378;1783272|201174|1760|85007|85026|2053;3379134|976|117747|200666|84566|28453,Complete,ChiomaBlessing
bsdb:37798293/4/2,37798293,time series / longitudinal observational,37798293,10.1038/s41541-023-00745-4,NA,"Zhao S., Lok K.Y.W., Sin Z.Y., Peng Y., Fan H.S.L., Nagesh N., Choi M.S.L., Kwok J.Y.Y., Choi E.P.H., Zhang X., Wai H.K., Tsang L.C.H., Cheng S.S.M., Wong M.K.L., Zhu J., Mok C.K.P., Ng S.C., Chan F.K.L., Peiris M., Poon L.L.M. , Tun H.M.",COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition,NPJ vaccines,2023,NA,Experiment 4,China,Homo sapiens,"Breast,Milk","UBERON:0001913,UBERON:0000310",Response to vaccine,EFO:0004645,Mothers at pre-vaccination timepoint (baseline),Mothers at one week post-first dose,Breastfeeding mothers at one week after receiving the first dose of BNT162b2 vaccine.,44,44,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,1.5,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Supplementary Table 3,15 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential abundance of mothers one week after first dose of BNT162b2 when compared to baseline.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus intestinalis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",3379134|1224|1236|2887326|468|469|470;1783272|1239|91061|186826|33958|1578|151781;1783272|1239|526524|526525|128827|174708;1783272|1239|91061;3379134|1224|28216|80840|80864;1783272|1239|186801|3085636|186803|1407607;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|119060|48736;1783272|1239|526524|526525|2810281|191303;3379134|976|200643|171549|2005473,Complete,ChiomaBlessing
bsdb:37798293/5/1,37798293,time series / longitudinal observational,37798293,10.1038/s41541-023-00745-4,NA,"Zhao S., Lok K.Y.W., Sin Z.Y., Peng Y., Fan H.S.L., Nagesh N., Choi M.S.L., Kwok J.Y.Y., Choi E.P.H., Zhang X., Wai H.K., Tsang L.C.H., Cheng S.S.M., Wong M.K.L., Zhu J., Mok C.K.P., Ng S.C., Chan F.K.L., Peiris M., Poon L.L.M. , Tun H.M.",COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition,NPJ vaccines,2023,NA,Experiment 5,China,Homo sapiens,"Breast,Milk","UBERON:0001913,UBERON:0000310",Response to vaccine,EFO:0004645,Mothers at pre-vaccination timepoint (baseline),Mothers at one week post-second dose,Breastfeeding mothers at one week post-second dose of BNT162b2 vaccine.,44,43,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,1.5,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,supplementary table 3,24 October 2023,Folakunmi,"Folakunmi,ChiomaBlessing,WikiWorks",differential abundance of mothers at one week post second dose of BNT162b2 when compared to baseline.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter soli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter ursingii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas|s__Brevundimonas olei,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Epilithonimonas|s__Epilithonimonas hominis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Faucicola|s__Faucicola atlantae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella porci,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus macerans,k__Pseudomonadati|p__Bdellovibrionota|c__Bacteriovoracia|o__Bacteriovoracales|f__Bacteriovoracaceae|g__Peredibacter|s__Peredibacter starrii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Roseomonadaceae|g__Roseomonas|s__Roseomonas gilardii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Gemmobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Nautella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae|g__Neptunomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Vogesella,k__Bacillati|p__Bacillota|c__Clostridia|s__uncultured Clostridia bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__uncultured Paraburkholderia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Pseudarcobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingosinicellaceae|g__Sandaracinobacter",3379134|1224|1236|2887326|468|469|470;3379134|1224|1236|2887326|468|469|487316;3379134|1224|1236|2887326|468|469|108980;3379134|1224|28211|204458|76892|41275|657642;3379134|976|117743|200644|2762318|2782229|420404;3379134|1224|1236|2887326|468|1604696|34059;3379134|1224|1236|2887326|468|475|1288392;1783272|1239|91061|1385|186822|44249|44252;3379134|3018035|3031419|2024979|263369|263370|28202;3379134|976|200643|171549|171552|838|28132;3379134|1224|28211|3120395|3385906|125216|257708;3379134|1224|1236|2887326|468|469;3379134|1224|1236|135625|712|713;3379134|1224|28211|204458|76892|41275;3379134|976|1853228|1853229|563835;3379134|1224|28211|204455|31989|204456;1783272|201174|1760|85007|85026|2053;3379134|1224|1236|91347|543|570;3384189|32066|203490|203491|1129771|32067;1783272|1239|909932|909929|1843491|158846;3379134|1224|28211|204455|2854170|481445;3379134|1224|1236|135619|135620|75687;3379134|1224|28211|356|118882|528;3379134|1224|28211|204455|31989;1783272|1239|1737404|1737405|1570339|162289;3379134|1224|1236|91347|1903411|613;3379134|1224|28216|206351|1499392|57739;1783272|1239|186801|244328;3379134|1224|28216|80840|119060|1822464|1822466;1783272|1239|186801|186802|1898207;1783272|1239|186801|186802|186806|1730;3379134|29547|3031852|213849|2808963|2321113;3379134|1224|28211|204457|2820280|56358,Complete,ChiomaBlessing
bsdb:37798293/5/2,37798293,time series / longitudinal observational,37798293,10.1038/s41541-023-00745-4,NA,"Zhao S., Lok K.Y.W., Sin Z.Y., Peng Y., Fan H.S.L., Nagesh N., Choi M.S.L., Kwok J.Y.Y., Choi E.P.H., Zhang X., Wai H.K., Tsang L.C.H., Cheng S.S.M., Wong M.K.L., Zhu J., Mok C.K.P., Ng S.C., Chan F.K.L., Peiris M., Poon L.L.M. , Tun H.M.",COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition,NPJ vaccines,2023,NA,Experiment 5,China,Homo sapiens,"Breast,Milk","UBERON:0001913,UBERON:0000310",Response to vaccine,EFO:0004645,Mothers at pre-vaccination timepoint (baseline),Mothers at one week post-second dose,Breastfeeding mothers at one week post-second dose of BNT162b2 vaccine.,44,43,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,1.5,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Supplementary Table 3,15 February 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differential abundance of mothers one week after second dose of BNT162b2 when compared to baseline.,decreased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus nagyae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus octavius,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter|s__Arthrobacter russicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caecimuris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium granulosum,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter rodentium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus aviarius,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Pseudoxanthomonas|s__Pseudoxanthomonas kaohsiungensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. (in: high G+C Gram-positive bacteria),k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Castellaniella,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Myxococcota|o__Haliangiales|f__Kofleriaceae|g__Haliangium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Kurthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Quinella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__uncultured Odoribacter sp.",1783272|1239|1737404|1737405|1570339|165779|1755241;1783272|1239|1737404|1737405|1570339|165779|54007;1783272|201174|1760|85006|1268|1663|172040;3379134|976|200643|171549|815|816|1796613;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|186802|31979|1898204;1783272|1239|186801|186802|216572;1783272|201174|1760|85009|31957|1912216|33011;3379134|29547|3031852|213849|72293|209|59617;1783272|1239|91061|186826|33958|2767887|1606;3379134|1224|1236|135614|32033|83618|283923;1783272|201174|1760|85006|1268|32207|1885016;1783272|1239|186801|186802|186806|1730;3379134|74201|203494|48461|1647988|239934;3379134|1224|28216|80840|506|507;1783272|1239|526524|526525|128827|174708;1783272|1239|91061;3379134|976|200643|171549|815|816;3379134|1224|28216|80840|506|359336;1783272|1239;1783272|1239|186801|186802|1980681;1783272|201174|84998|84999|84107;3379134|200940|3031449|213115|194924;1783272|1239|526524|526525|128827|1937008;1783272|1239|186801|186802|216572|216851;3379134|2818505|3031714|224464|162027;3379134|1224|1236|135619|28256;3379134|1224|1236|135619|28256|2745;1783272|1239|91061|1385|186818|1649;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|2005473;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171552;1783272|1239|909932|1843489|31977|1567;3379134|1224|28216|80840|119060|48736;1783272|1239|186801|3082720|186804|1501226;3379134|1224|28216|80840|995019|40544;3379134|203691|203692|136|2845253|157;1783272|1239|526524|526525|2810281|191303;3379134|976|200643|171549|1853231|283168|876416,Complete,ChiomaBlessing
bsdb:37798293/6/1,37798293,time series / longitudinal observational,37798293,10.1038/s41541-023-00745-4,NA,"Zhao S., Lok K.Y.W., Sin Z.Y., Peng Y., Fan H.S.L., Nagesh N., Choi M.S.L., Kwok J.Y.Y., Choi E.P.H., Zhang X., Wai H.K., Tsang L.C.H., Cheng S.S.M., Wong M.K.L., Zhu J., Mok C.K.P., Ng S.C., Chan F.K.L., Peiris M., Poon L.L.M. , Tun H.M.",COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition,NPJ vaccines,2023,NA,Experiment 6,China,Homo sapiens,"Breast,Milk","UBERON:0001913,UBERON:0000310",Response to vaccine,EFO:0004645,Mothers at pre-vaccination timepoint (baseline),Mothers at one month post second-dose,Breastfeeding mothers at one month post second-dose of BNT162b2 vaccine.,44,44,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,1.5,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,supplementary table 3,24 October 2023,Folakunmi,"Folakunmi,Chinelsy,ChiomaBlessing,WikiWorks",differential abundance of mothers at one month post second dose of BNT162b2 when compared to baseline.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter ursingii,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella|s__Dubosiella newyorkensis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Epilithonimonas|s__Epilithonimonas hominis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae|g__Marinobacterium|s__Marinobacterium marisflavi,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Faucicola|s__Faucicola atlantae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Roseomonadaceae|g__Roseomonas|s__Teichococcus aestuarii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Roseomonadaceae|g__Roseomonas|s__Roseomonas gilardii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas acidaminiphila,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Aeromicrobium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Formosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Microvirga,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Pseudarcobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Skermanella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Tepidimonas,k__Bacillati|p__Bacillota|c__Clostridia|s__uncultured Clostridia bacterium",3379134|1224|1236|2887326|468|469|108980;3379134|29547|3031852|213849|72294|194|204;1783272|1239|186801|186802|1898207;1783272|1239|526524|526525|128827|1937008|1862672;3379134|976|117743|200644|2762318|2782229|420404;3379134|1224|1236|135619|135620|48075|434084;3379134|1224|1236|2887326|468|1604696|34059;3379134|1224|28216|206351|481|482|495;3379134|976|200643|171549|171552|838|470565;3379134|976|200643|171549|171552|838|28132;3379134|1224|28211|3120395|3385906|125216|568898;3379134|1224|28211|3120395|3385906|125216|257708;3379134|1224|1236|135614|32033|40323|128780;3379134|1224|28216|80840|80864|12916;1783272|201174|1760|85009|85015|2040;1783272|201174|84998|84999|1643824|1380;3379134|1224|28211|204458|76892|41275;1783272|201174|1760|85007|1653;1783272|201174|1760|85006|145357;3379134|976|117743|200644|49546|225842;1783272|201174|1760|85007|85026|2053;1783272|1239|186801|3085636|186803|1164882;3379134|1224|28211|356|119045|186650;3379134|1224|1236|2887326|468|475;3379134|1224|28216|206351|481;3379134|1224|28211|204457|41297|165696;3379134|1224|28211|204455|31989;3379134|1224|1236|135625|712;1783272|1239|91061|186826|33958|1253;1783272|1239|91061|1385|186818;3379134|29547|3031852|213849|2808963|2321113;3379134|1224|28211|356|82115;3379134|1224|1236|91347|1903411|613;3379134|1224|28211|204441|2829815|204447;3379134|1224|28211|204457|41297|13687;3379134|1224|28216|80840|114248;1783272|1239|186801|244328,Complete,ChiomaBlessing
bsdb:37798293/6/2,37798293,time series / longitudinal observational,37798293,10.1038/s41541-023-00745-4,NA,"Zhao S., Lok K.Y.W., Sin Z.Y., Peng Y., Fan H.S.L., Nagesh N., Choi M.S.L., Kwok J.Y.Y., Choi E.P.H., Zhang X., Wai H.K., Tsang L.C.H., Cheng S.S.M., Wong M.K.L., Zhu J., Mok C.K.P., Ng S.C., Chan F.K.L., Peiris M., Poon L.L.M. , Tun H.M.",COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition,NPJ vaccines,2023,NA,Experiment 6,China,Homo sapiens,"Breast,Milk","UBERON:0001913,UBERON:0000310",Response to vaccine,EFO:0004645,Mothers at pre-vaccination timepoint (baseline),Mothers at one month post second-dose,Breastfeeding mothers at one month post second-dose of BNT162b2 vaccine.,44,44,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,1.5,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Supplementary Table 3,16 February 2024,ChiomaBlessing,"ChiomaBlessing,Joan Chuks,WikiWorks",Differential abundance of mothers at one month post second dose of BNT162b2 when compared to baseline.,decreased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus octavius,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Aquabacterium|s__Aquabacterium citratiphilum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter|s__Arthrobacter russicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caecimuris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas aquatica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus cecorum,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter rodentium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus aviarius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Pseudoxanthomonas|s__Pseudoxanthomonas kaohsiungensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. (in: high G+C Gram-positive bacteria),k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus flavefaciens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota,,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bdellovibrionota|c__Bdellovibrionia|o__Bdellovibrionales|f__Pseudobdellovibrionaceae|g__Bdellovibrio,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Castellaniella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|g__Exiguobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Flaviflexus,k__Pseudomonadati|p__Myxococcota|o__Haliangiales|f__Kofleriaceae|g__Haliangium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Quinella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__uncultured Odoribacter sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__uncultured Muribaculaceae bacterium",1783272|1239|1737404|1737405|1570339|165779|54007;3379134|1224|28216|80840|92793|70582;1783272|201174|1760|85006|1268|1663|172040;3379134|976|200643|171549|815|816|1796613;3379134|976|200643|171549|815|816|817;1783272|1239|186801|186802|31979|1898204;3379134|1224|28216|80840|80864|283|225991;1783272|1239|91061|186826|81852|1350|44008;3379134|29547|3031852|213849|72293|209|59617;3384189|32066|203490|203491|1129771|32067|104608;1783272|1239|91061|186826|33958|2767887|1606;3379134|976|200643|171549|815|909656|310298;3379134|1224|1236|135614|32033|83618|283923;1783272|201174|1760|85006|1268|32207|1885016;1783272|1239|186801|186802|216572|1263|1265;1783272|1239|91061|186826|186827|1375;3379134|74201|203494|48461|1647988|239934;3379134|1224|28216|80840|506|507;3379134|976|200643|171549|171550|239759;1783272|1239|526524|526525|128827|174708;1783272|1239|1737404|1737405|1570339|165779;1783272|1239;;3379134|976|200643|171549|815|816;3379134|3018035|3031418|213481|213483|958;3379134|1224|28216|80840|506|359336;1783272|201174|84998|84999|84107;3379134|200940|3031449|213115|194924;1783272|1239|909932|1843489|31977|39948;1783272|1239|526524|526525|128827|1937008;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|1385|33986;1783272|1239|186801|186802|216572|216851;1783272|1239|526524|526525|128827|1573534;1783272|201174|1760|2037|2049|1522056;3379134|2818505|3031714|224464|162027;3379134|1224|1236|135619|28256;3379134|1224|1236|135619|28256|2745;1783272|1239|526524|526525|128827|1573535;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803;3379134|1224|28216|80840|119060|47670;1783272|201174|1760|85006|85023|33882;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|171552;1783272|1239|909932|1843489|31977|1567;3379134|1224|28216|80840|119060|48736;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1200657;3379134|203691|203692|136|2845253|157;1783272|1239|526524|526525|2810281|191303;3379134|976|200643|171549|1853231|283168|876416;3379134|976|200643|171549|2005473|2301481,Complete,ChiomaBlessing
bsdb:37800955/1/1,37800955,case-control,37800955,10.1128/spectrum.00234-23,NA,"Ji X., Li P., Guo Q., Guan L., Gao P., Wu B., Cheng H., Xiao J. , Ye L.",Salivary microbiome profiles for different clinical phenotypes of pituitary adenomas by single-molecular long-read sequencing,Microbiology spectrum,2023,"clinical phenotype, diagnostics, pituitary adenomas, saliva microbiome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Pituitary Gland Adenoma,EFO:1000478,Healthy controls,Patients with pituitary adenomas (PA),"Patients with pituitary adenomas (PA) which included four clinical phenotypes: adrenocorticotropic hormone-secreting PA (n = 6), growth hormone-secreting PA (n = 9), prolactin-secreting PA (n = 18), and nonfunctioning PA (n = 9)",20,42,6 months,16S,NA,NA,relative abundances,NA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Fig 2D,19 March 2024,Scholastica,"Scholastica,WikiWorks",Differential abundance of microbes in patients with pituitary adenomas (PA) versus healthy individual,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85009|31957|2801844;1783272|1239|186801|3085636|186803|830;3379134|1224|1236|135615|868|2717;1783272|201174|1760|85007|1653|1716;1783272|201174|84998|84999|1643824|2767353;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836;33090|35493|3398|72025|3803|3814|508215;1783272|201174|1760|2037|2049|2529408;1783272|1239|186801|3085636|186803|177971;3379134|976|200643|171549|2005525|195950,Complete,Svetlana up
bsdb:37800955/1/2,37800955,case-control,37800955,10.1128/spectrum.00234-23,NA,"Ji X., Li P., Guo Q., Guan L., Gao P., Wu B., Cheng H., Xiao J. , Ye L.",Salivary microbiome profiles for different clinical phenotypes of pituitary adenomas by single-molecular long-read sequencing,Microbiology spectrum,2023,"clinical phenotype, diagnostics, pituitary adenomas, saliva microbiome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Pituitary Gland Adenoma,EFO:1000478,Healthy controls,Patients with pituitary adenomas (PA),"Patients with pituitary adenomas (PA) which included four clinical phenotypes: adrenocorticotropic hormone-secreting PA (n = 6), growth hormone-secreting PA (n = 9), prolactin-secreting PA (n = 18), and nonfunctioning PA (n = 9)",20,42,6 months,16S,NA,NA,relative abundances,NA,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Fig 2D,19 March 2024,Scholastica,"Scholastica,WikiWorks",Differential abundance of microbes in patients with pituitary adenomas (PA) versus healthy individual,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Casaltella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotellamassilia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|1224|1236|135625|712|416916;3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|815|816;3379134|976|117743|200644|2762318|59735;3379134|29547|3031852|213849|72294|194;1783272|1239|186801|3082720|543314|1715793;1783272|1239|909932|909929|1843491|82202;1783272|1239|909932|1843489|31977|39948;3384189|32066|203490|203491|203492|848;3379134|1224|1236|135625|712|724;3379134|1224|1236|91347|543|570;1783272|1239|909932|1843489|31977|906;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|1926672;3379134|1224|1236|91347|543|620;3379134|1224|28216|206351|481|71;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:37803040/1/NA,37803040,"cross-sectional observational, not case-control",37803040,10.1038/s41598-023-43040-x,NA,"Bellato M., Cappellato M., Longhin F., Del Vecchio C., Brancaccio G., Cattelan A.M., Brun P., Salaris C., Castagliuolo I. , Di Camillo B.",Uncover a microbiota signature of upper respiratory tract in patients with SARS-CoV-2 + ,Scientific reports,2023,NA,Experiment 1,Italy,Homo sapiens,Nasal cavity,UBERON:0001707,COVID-19,MONDO:0100096,Asymptomatic patients,Symptomatic patients,Symptomatic patients with signs of COVID-19,36,156,1 month,16S,34,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,unchanged,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:37803040/2/1,37803040,"cross-sectional observational, not case-control",37803040,10.1038/s41598-023-43040-x,NA,"Bellato M., Cappellato M., Longhin F., Del Vecchio C., Brancaccio G., Cattelan A.M., Brun P., Salaris C., Castagliuolo I. , Di Camillo B.",Uncover a microbiota signature of upper respiratory tract in patients with SARS-CoV-2 + ,Scientific reports,2023,NA,Experiment 2,Italy,Homo sapiens,Nasal cavity,UBERON:0001707,"COVID-19,Pneumonia","MONDO:0100096,EFO:0003106",COVID-19 patients with mild pneumonia,COVID-19 patients with severe pneumonia,"COVID-19 patients with severe pneumonia. Severe pneumonia is a type of pneumonia that is characterized by inflammation of the lungs, difficulty breathing, and low oxygen levels in the blood. It can be a life-threatening condition. 

This was the most exposed group in the study",17,89,1 month,16S,34,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,unchanged,NA,NA,NA,NA,unchanged,Signature 1,Table 3,24 October 2023,Fortunehechi,"Fortunehechi,Folakunmi,WikiWorks",MaAsLin2 differentially abundant taxa analysis in COVID patients with pneumonia,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Ornithinimicrobiaceae|g__Ornithinimicrobium,1783272|201174|1760|85006|2805590|125287,Complete,Folakunmi
bsdb:37803040/3/1,37803040,"cross-sectional observational, not case-control",37803040,10.1038/s41598-023-43040-x,NA,"Bellato M., Cappellato M., Longhin F., Del Vecchio C., Brancaccio G., Cattelan A.M., Brun P., Salaris C., Castagliuolo I. , Di Camillo B.",Uncover a microbiota signature of upper respiratory tract in patients with SARS-CoV-2 + ,Scientific reports,2023,NA,Experiment 3,Italy,Homo sapiens,Nasal cavity,UBERON:0001707,"COVID-19,Respiratory failure requiring assisted ventilation","MONDO:0100096,HP:0004887",Non-intubated,Intubated,Patients unable to provide enough oxygen to their body.,0,18,1 month,16S,34,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,unchanged,NA,NA,NA,NA,unchanged,Signature 1,Table 3,17 February 2024,Folakunmi,"Folakunmi,WikiWorks",MaAsLin2 differentially abundant taxa analysis in COVID patients with and without intubation,increased,"k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Jonquetella|s__Jonquetella anthropi,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Ornithinimicrobiaceae|g__Ornithinimicrobium|s__Ornithinimicrobium pekingense,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Ornithinimicrobiaceae|g__Ornithinimicrobium",3384194|508458|649775|649776|3029088|428711|428712;1783272|201174|1760|85006|2805590|125287|384677;1783272|1239|91061|186826|81852|1350;1783272|201174|1760|85006|2805590|125287,Complete,Folakunmi
bsdb:37803040/4/NA,37803040,"cross-sectional observational, not case-control",37803040,10.1038/s41598-023-43040-x,NA,"Bellato M., Cappellato M., Longhin F., Del Vecchio C., Brancaccio G., Cattelan A.M., Brun P., Salaris C., Castagliuolo I. , Di Camillo B.",Uncover a microbiota signature of upper respiratory tract in patients with SARS-CoV-2 + ,Scientific reports,2023,NA,Experiment 4,Italy,Homo sapiens,Nasal cavity,UBERON:0001707,Response to supplemental oxygen,EFO:0009796,No Supplemental O2,Supplemental O2 (High/Low),Patients in need of supply of oxygen to help them breathe better and keep their blood oxygen levels up.,0,72,1 month,16S,34,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,unchanged,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:37803284/1/1,37803284,case-control,37803284,10.1186/s12866-023-03013-6,NA,"Chen Z., Xiao Y., Jia Y., Lin Q., Qian Y., Cui L., Xiang Z., Li M., Yang C. , Zou H.",Metagenomic analysis of microbiological changes on the ocular surface of diabetic children and adolescents with a dry eye,BMC microbiology,2023,"Children and adolescents, Diabetes mellitus, Dry eye, Metagenome, Microecology, Ocular surface",Experiment 1,China,Homo sapiens,Conjunctival sac,UBERON:0005908,Dry eye syndrome,EFO:1000906,Normal healthy (NDM) children,Diabetic children with Dry Eye Disease (DM-DE),Children aged 8-16 with Diabetes and Dry Eye Disease,10,10,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,NA,"age,body mass index,sex",NA,NA,NA,decreased,NA,NA,decreased,Signature 1,"Figure 3g and Results within text (Page 7, Last 6 lines, Under subheading: Composition and difference analysis of the ocular microbiome)",11 November 2023,Mary Bearkland,"Mary Bearkland,ChiomaBlessing,WikiWorks","Fig 3g: Species composition with significant difference
at the species level between the NDM and DM-DE groups (top 20)",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacteroides|s__Mycobacteroides abscessus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium|s__Novosphingobium nitrogenifigens,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium|s__Novosphingobium sp. Fuku2-ISO-50,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus odorifer,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio agarivorans",1783272|201174|1760|85007|1762|670516|36809;3379134|1224|28211|204457|41297|165696|378548;3379134|1224|28211|204457|41297|165696|1739114;1783272|1239|91061|1385|186822|44249|189426;1783272|1239|91061|1385|90964|1279|1280;1783272|1239|91061|186826|1300|1301|1302;3379134|1224|1236|135623|641|662|153622,Complete,ChiomaBlessing
bsdb:37803284/1/2,37803284,case-control,37803284,10.1186/s12866-023-03013-6,NA,"Chen Z., Xiao Y., Jia Y., Lin Q., Qian Y., Cui L., Xiang Z., Li M., Yang C. , Zou H.",Metagenomic analysis of microbiological changes on the ocular surface of diabetic children and adolescents with a dry eye,BMC microbiology,2023,"Children and adolescents, Diabetes mellitus, Dry eye, Metagenome, Microecology, Ocular surface",Experiment 1,China,Homo sapiens,Conjunctival sac,UBERON:0005908,Dry eye syndrome,EFO:1000906,Normal healthy (NDM) children,Diabetic children with Dry Eye Disease (DM-DE),Children aged 8-16 with Diabetes and Dry Eye Disease,10,10,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,NA,"age,body mass index,sex",NA,NA,NA,decreased,NA,NA,decreased,Signature 2,"Figure 3g and Results within text (Page 7, Last 6 lines, Under subheading: Composition and difference analysis of the ocular microbiome)",11 November 2023,Mary Bearkland,"Mary Bearkland,ChiomaBlessing,WikiWorks","Figure 3g Species composition with significant difference
at the species level between the NDM and DM-DE groups (top 20)",increased,"k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Cordycipitaceae|g__Cordyceps|s__Cordyceps militaris,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter mori,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc sp. DORA_2,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio vulnificus",4751|4890|147550|5125|474943|45234|73501;3379134|1224|1236|91347|543|547|539813;1783272|1239|91061|186826|33958|1243|1403934;3379134|1224|1236|91347|543|590|28901;3379134|1224|1236|135623|641|662|672,Complete,ChiomaBlessing
bsdb:37803284/2/1,37803284,case-control,37803284,10.1186/s12866-023-03013-6,NA,"Chen Z., Xiao Y., Jia Y., Lin Q., Qian Y., Cui L., Xiang Z., Li M., Yang C. , Zou H.",Metagenomic analysis of microbiological changes on the ocular surface of diabetic children and adolescents with a dry eye,BMC microbiology,2023,"Children and adolescents, Diabetes mellitus, Dry eye, Metagenome, Microecology, Ocular surface",Experiment 2,China,Homo sapiens,Conjunctival sac,UBERON:0005908,Dry eye syndrome,EFO:1000906,Normal healthy (NDM) children,Diabetic children with Dry Eye Disease (DM-DE),Children aged 8-16 with Diabetes and Dry Eye Disease,10,10,NA,WMS,NA,Illumina,relative abundances,ANOSIM,0.05,NA,NA,"age,body mass index,sex",NA,NA,NA,decreased,NA,NA,decreased,Signature 1,"Text on page 5; Under subheading ""Composition and difference analysis of the ocular microbiome""",18 November 2023,Mary Bearkland,"Mary Bearkland,ChiomaBlessing,WikiWorks",Composition and Differential analysis of the ocular microbiome between NDM and DM-DE groups,increased,"k__Bacillati|p__Actinomycetota,p__Apicomplexa,k__Fungi|p__Ascomycota,k__Pseudomonadati|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia|s__Chlamydia trachomatis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc sp. DORA_2,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium leprae,p__Apicomplexa|c__Aconoidasida|o__Haemosporida|f__Plasmodiidae|g__Plasmodium|s__Plasmodium ovale,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio",1783272|201174;5794;4751|4890;3379134|204428|204429|51291|809|810|813;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|561|562;1783272|1239|91061|186826|33958|1243|1403934;1783272|201174|1760|85007|1762|1763|1769;5794|422676|5819|1639119|5820|36330;3379134|1224|1236|91347|543|590|28901;3379134|1224|1236|135623|641|662,Complete,ChiomaBlessing
bsdb:37803284/2/2,37803284,case-control,37803284,10.1186/s12866-023-03013-6,NA,"Chen Z., Xiao Y., Jia Y., Lin Q., Qian Y., Cui L., Xiang Z., Li M., Yang C. , Zou H.",Metagenomic analysis of microbiological changes on the ocular surface of diabetic children and adolescents with a dry eye,BMC microbiology,2023,"Children and adolescents, Diabetes mellitus, Dry eye, Metagenome, Microecology, Ocular surface",Experiment 2,China,Homo sapiens,Conjunctival sac,UBERON:0005908,Dry eye syndrome,EFO:1000906,Normal healthy (NDM) children,Diabetic children with Dry Eye Disease (DM-DE),Children aged 8-16 with Diabetes and Dry Eye Disease,10,10,NA,WMS,NA,Illumina,relative abundances,ANOSIM,0.05,NA,NA,"age,body mass index,sex",NA,NA,NA,decreased,NA,NA,decreased,Signature 2,"Text on page 5; Under subheading ""Composition and difference analysis of the ocular microbiome""",18 November 2023,Mary Bearkland,"Mary Bearkland,ChiomaBlessing,WikiWorks",Composition and Differential analysis of the ocular microbiome between NDM and DM-DE groups,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter johnsonii,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae",3379134|1224|1236|2887326|468|469|40214;1783272|1239;1783272|1239|91061|186826|81852|1350|1351;3379134|1224;1783272|1239|91061|1385|90964|1279|1280;1783272|1239|91061|186826|1300|1301|1313,Complete,ChiomaBlessing
bsdb:37805557/1/1,37805557,case-control,37805557,https://doi.org/10.1186/s40168-023-01657-0,NA,"Huang G., Shi W., Wang L., Qu Q., Zuo Z., Wang J., Zhao F. , Wei F.","PandaGUT provides new insights into bacterial diversity, function, and resistome landscapes with implications for conservation",Microbiome,2023,"Adaptive evolution, Conservation, Diversity, Giant panda, Gut microbiome, Wild mammal",Experiment 1,China,Ailuropoda melanoleuca,Feces,UBERON:0001988,Diet,EFO:0002755,Pandas in shoot-eating season,Pandas in leaf-eating season,Pandas in leaf-eating season from the Qinling cohort of wild pandas,24,33,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A,15 March 2024,Svetlana up,"Svetlana up,Omojokunoluwatomisin,WikiWorks",A very challenging figure to interpret: Significantly differentially abundant taxa between diet seasons. Increased abundance in pandas leaf-eating season.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,1783272|1239|186801|186802|31979|1485|1506,Complete,Svetlana up
bsdb:37819112/1/1,37819112,laboratory experiment,37819112,10.1128/msphere.00431-23,NA,"Cui C., Song H., Han Y., Yu H., Li H., Yang Y. , Zhang B.",Gut microbiota-associated taurine metabolism dysregulation in a mouse model of Parkinson's disease,mSphere,2023,"Lactobacillus, Parkinson's disease, metabolism, microbiota, taurine",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control mice,MPTP-treated mice,"Mice were injected with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), to induce Parkinson's disease.",10,9,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 3I,12 March 2024,Victoria,"Victoria,WikiWorks","Cladogram of linear discriminant analysis scores for differentially abundant bacteria (phylum, class, order, and family). Only taxa meeting a linear discriminant analysis significant threshold of >2.0 are shown.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|201174|1760|2037;1783272|201174;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|84998|84999|84107;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85007|85025;3379134|976|200643|171549|1853231|283168;1783272|201174|1760|85007|85025|1827;3379134|976|200643|171549|171550|28138;1783272|201174|1760|85004|31953|1678,Complete,Svetlana up
bsdb:37819112/1/2,37819112,laboratory experiment,37819112,10.1128/msphere.00431-23,NA,"Cui C., Song H., Han Y., Yu H., Li H., Yang Y. , Zhang B.",Gut microbiota-associated taurine metabolism dysregulation in a mouse model of Parkinson's disease,mSphere,2023,"Lactobacillus, Parkinson's disease, metabolism, microbiota, taurine",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control mice,MPTP-treated mice,"Mice were injected with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), to induce Parkinson's disease.",10,9,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 3I,12 March 2024,Victoria,"Victoria,WikiWorks","Cladogram of linear discriminant analysis scores for differentially abundant bacteria (phylum, class, order, and family). Only taxa meeting a linear discriminant analysis significant threshold of >2.0 are shown.",decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",1783272|201174|84998|1643822|1643826|447020;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|976|200643|171549|1853231|574697;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;3379134|976|200643|171549|2005473;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|577309,Complete,Svetlana up
bsdb:37832478/1/1,37832478,case-control,37832478,10.1016/j.tube.2023.102413,NA,"Luo D., Shi C.Y., Wei N.S., Yang B.Y., Qin K., Liu G., Dong B.Q., Qin Y.X., Qin X.L., Chen S.Y., Guo X.J., Gan L., Xu R.L., Li H. , Li J.",The potential mechanism of the progression from latent to active tuberculosis based on the intestinal microbiota alterations,"Tuberculosis (Edinburgh, Scotland)",2023,"16S rDNA sequencing, Intestinal microbiota, LTBI, Tuberculosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Tuberculosis,MONDO:0018076,combination of active tuberculosis (ATB) and latent tuberculosis infection (LTBI),healthy controls,All cases had no previous history of tuberculosis,42,11,NA,16S,345,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,increased,increased,increased,NA,increased,Signature 1,Figure 5A-B,29 July 2025,Nuerteye,Nuerteye,"The enrichment deviation diagram of three groups based on LEfSe analysis (selection criteria: P<0.05; LDA score ≥ 4). Histogram of LDA value of intestinal microbiota in three groups. The column represents LDA Score, and the colors represent the microbiota in three groups, respectively. LEfSe cladogram of LEfSe analysis.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Negativicutes",3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|838;1783272|1239|526524|526525|128827|1573535;1783272|1239|909932,Complete,NA
bsdb:37832478/2/1,37832478,case-control,37832478,10.1016/j.tube.2023.102413,NA,"Luo D., Shi C.Y., Wei N.S., Yang B.Y., Qin K., Liu G., Dong B.Q., Qin Y.X., Qin X.L., Chen S.Y., Guo X.J., Gan L., Xu R.L., Li H. , Li J.",The potential mechanism of the progression from latent to active tuberculosis based on the intestinal microbiota alterations,"Tuberculosis (Edinburgh, Scotland)",2023,"16S rDNA sequencing, Intestinal microbiota, LTBI, Tuberculosis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Tuberculosis,MONDO:0018076,combination of healthy controls (HC) and latent tuberculosis infection (LTBI),active tuberculosis (ATB),Patents with ATB enrolled according to Technical Guidelines for Tuberculosis Prevention and Control in China [20] and all cases had no previous history of TB.,24,29,NA,16S,345,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 5A-B,29 July 2025,Nuerteye,Nuerteye,"The enrichment deviation diagram of three groups based on LEfSe analysis (selection criteria: P<0.05; LDA score ≥ 4). Histogram of LDA value of intestinal microbiota in three groups. The column represents LDA Score, and the colors represent the microbiota in three groups, respectively. LEfSe cladogram of LEfSe analysis.",increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",1783272|1239|91061;1783272|1239|91061|186826;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;3379134|1224|1236|91347;3379134|1224|1236|91347|543,Complete,NA
bsdb:37832478/3/1,37832478,case-control,37832478,10.1016/j.tube.2023.102413,NA,"Luo D., Shi C.Y., Wei N.S., Yang B.Y., Qin K., Liu G., Dong B.Q., Qin Y.X., Qin X.L., Chen S.Y., Guo X.J., Gan L., Xu R.L., Li H. , Li J.",The potential mechanism of the progression from latent to active tuberculosis based on the intestinal microbiota alterations,"Tuberculosis (Edinburgh, Scotland)",2023,"16S rDNA sequencing, Intestinal microbiota, LTBI, Tuberculosis",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Tuberculosis,MONDO:0018076,combination of healthy controls (HC) and active tuberculosis (ATB),latent tuberculosis infection (LTBI),"Positive IGRAs and/or TST (nodule ≥15 mm, blister or necrosis), but had no clinical symptoms of TB.",40,13,NA,16S,345,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 5A-B,29 July 2025,Nuerteye,Nuerteye,"The enrichment deviation diagram of three groups based on LEfSe analysis (selection criteria: P<0.05; LDA score ≥ 4). Histogram of LDA value of intestinal microbiota in three groups. The column represents LDA Score, and the colors represent the microbiota in three groups, respectively. LEfSe cladogram of LEfSe analysis.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia",1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004;1783272|201174|1760|85004|31953;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958;1783272|1239|186801|3082720|186804|1501226,Complete,NA
bsdb:37848699/1/1,37848699,"cross-sectional observational, not case-control",37848699,10.1038/s41598-023-44981-z,NA,"Klinsawat W., Uthaipaisanwong P., Jenjaroenpun P., Sripiboon S., Wongsurawat T. , Kusonmano K.",Microbiome variations among age classes and diets of captive Asian elephants (Elephas maximus) in Thailand using full-length 16S rRNA nanopore sequencing,Scientific reports,2023,NA,Experiment 1,Thailand,Elephas maximus,Feces,UBERON:0001988,Diet,EFO:0002755,Adult captive elephants without Caryota urens,Adult captive elephants fed with Caryota urens,Adult (> 10 years) captive elephants fed with the palm Caryota urens as a supplement.,6,6,NA,16S,123456789,Nanopore,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,25 October 2025,Tosin,"Tosin,Nina Takang",Boxplots display abundances of microbes that are significantly different (p-value < = 0.05) between adult captive elephants in Thailand fed with (n = 6) and without (n = 6) Caryota urens as a supplement,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,1783272|1239|186801|3085636|186803|297314,Complete,Svetlana up
bsdb:37848699/1/2,37848699,"cross-sectional observational, not case-control",37848699,10.1038/s41598-023-44981-z,NA,"Klinsawat W., Uthaipaisanwong P., Jenjaroenpun P., Sripiboon S., Wongsurawat T. , Kusonmano K.",Microbiome variations among age classes and diets of captive Asian elephants (Elephas maximus) in Thailand using full-length 16S rRNA nanopore sequencing,Scientific reports,2023,NA,Experiment 1,Thailand,Elephas maximus,Feces,UBERON:0001988,Diet,EFO:0002755,Adult captive elephants without Caryota urens,Adult captive elephants fed with Caryota urens,Adult (> 10 years) captive elephants fed with the palm Caryota urens as a supplement.,6,6,NA,16S,123456789,Nanopore,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6,25 October 2025,Tosin,Tosin,Boxplots display abundances of microbes that are significantly different (p-value < = 0.05) between adult captive elephants in Thailand fed with (n = 6) and without (n = 6) Caryota urens as a supplement,decreased,NA,NA,Complete,Svetlana up
bsdb:37848699/2/1,37848699,"cross-sectional observational, not case-control",37848699,10.1038/s41598-023-44981-z,NA,"Klinsawat W., Uthaipaisanwong P., Jenjaroenpun P., Sripiboon S., Wongsurawat T. , Kusonmano K.",Microbiome variations among age classes and diets of captive Asian elephants (Elephas maximus) in Thailand using full-length 16S rRNA nanopore sequencing,Scientific reports,2023,NA,Experiment 2,Thailand,Elephas maximus,Feces,UBERON:0001988,Age,EFO:0000246,Combination of Baby and Juvenile elephants,Adult elephant,Adult captive elephants in Thailand older than (>) 10 years of age,20,12,NA,16S,123456789,Nanopore,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,26 October 2025,Tosin,Tosin,"Differential abundant microbes between each age class of captive elephants, which are baby (green), juvenile (blue), and adult (red), respectively",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae|s__uncultured Marinifilaceae bacterium,3379134|976|200643|1970189|1573805|2934798,Complete,Svetlana up
bsdb:37848699/3/1,37848699,"cross-sectional observational, not case-control",37848699,10.1038/s41598-023-44981-z,NA,"Klinsawat W., Uthaipaisanwong P., Jenjaroenpun P., Sripiboon S., Wongsurawat T. , Kusonmano K.",Microbiome variations among age classes and diets of captive Asian elephants (Elephas maximus) in Thailand using full-length 16S rRNA nanopore sequencing,Scientific reports,2023,NA,Experiment 3,Thailand,Elephas maximus,Feces,UBERON:0001988,Age,EFO:0000246,Combination of Juvenile and Adult elephants,Baby elephants,Baby captive Asian elephants in Thailand aged 0-2 yearsc,26,6,NA,16S,123456789,Nanopore,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,25 October 2025,Nina Takang,"Nina Takang,Tosin","Differential abundant microbes between each age class of captive elephants, which are baby (green), juvenile (blue), and adult (red), respectively",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter hyointestinalis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas kerstersii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella flexneri",3379134|976|200643|171549|815|816|817;3379134|29547|3031852|213849|72294|194|198;3379134|1224|28216|80840|80864|283|225992;3379134|1224|1236|91347|543|561|562;1783272|1239|909932|1843488|909930|33024|33025;3379134|1224|1236|91347|543|620|623,Complete,Svetlana up
bsdb:37848699/4/1,37848699,"cross-sectional observational, not case-control",37848699,10.1038/s41598-023-44981-z,NA,"Klinsawat W., Uthaipaisanwong P., Jenjaroenpun P., Sripiboon S., Wongsurawat T. , Kusonmano K.",Microbiome variations among age classes and diets of captive Asian elephants (Elephas maximus) in Thailand using full-length 16S rRNA nanopore sequencing,Scientific reports,2023,NA,Experiment 4,Thailand,Elephas maximus,Feces,UBERON:0001988,Age,EFO:0000246,Combination of Baby and Adult elephants,Juvenile elephants,Juvenile captive Asian elephants in Thailand aged 2-10 years,18,14,NA,16S,123456789,Nanopore,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,25 October 2025,Nina Takang,"Nina Takang,Tosin","Differential abundant microbes between each age class of captive elephants, which are baby (green), juvenile (blue), and adult (red), respectively",increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,1783272|1239|186801|3085636|186803|297314,Complete,Svetlana up
bsdb:37856089/1/1,37856089,prospective cohort,37856089,https://doi.org/10.1182/blood.2023020026,https://ashpublications.org/blood/article/142/16/1387/497377/Gut-microbiota-diversity-before-allogeneic,"Masetti R., Leardini D., Muratore E., Fabbrini M., D'Amico F., Zama D., Baccelli F., Gottardi F., Belotti T., Ussowicz M., Fraczkiewicz J., Cesaro S., Zecca M., Merli P., Candela M., Pession A., Locatelli F., Prete A., Brigidi P. , Turroni S.",Gut microbiota diversity before allogeneic hematopoietic stem cell transplantation as a predictor of mortality in children,Blood,2023,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,"Gut microbiome measurement,Acute graft vs. host disease","EFO:0007874,EFO:0004599",Lower-diversity group (before allo-HSCT),Higher-diversity group (before allo-HSCT),"Patients whose pre-transplant gut microbiota alpha diversity (Shannon index) was above the median value (4.04) for the cohort, as measured from 16S rRNA gene sequencing.",45,45,NA,16S,34,Illumina,relative abundances,"Cox Proportional-Hazards Regression,Fisher's Exact Test,Mann-Whitney (Wilcoxon),PERMANOVA,T-Test",0.05,TRUE,NA,NA,age,NA,increased,NA,NA,NA,NA,Signature 1,Figure 4B–C,1 November 2025,Adiba Patel,Adiba Patel,Families and genera enriched in higher-diversity pediatric patients before allo-HSCT.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|s__Christensenellaceae bacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium AM28-23LB,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3082768|990719|270497;1783272|1239|186801|3082768|990719|2054177;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|33042;1783272|201174|84998|84999|84107;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|2485925;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|2292269;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|2005525,Complete,NA
bsdb:37856089/1/2,37856089,prospective cohort,37856089,https://doi.org/10.1182/blood.2023020026,https://ashpublications.org/blood/article/142/16/1387/497377/Gut-microbiota-diversity-before-allogeneic,"Masetti R., Leardini D., Muratore E., Fabbrini M., D'Amico F., Zama D., Baccelli F., Gottardi F., Belotti T., Ussowicz M., Fraczkiewicz J., Cesaro S., Zecca M., Merli P., Candela M., Pession A., Locatelli F., Prete A., Brigidi P. , Turroni S.",Gut microbiota diversity before allogeneic hematopoietic stem cell transplantation as a predictor of mortality in children,Blood,2023,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,"Gut microbiome measurement,Acute graft vs. host disease","EFO:0007874,EFO:0004599",Lower-diversity group (before allo-HSCT),Higher-diversity group (before allo-HSCT),"Patients whose pre-transplant gut microbiota alpha diversity (Shannon index) was above the median value (4.04) for the cohort, as measured from 16S rRNA gene sequencing.",45,45,NA,16S,34,Illumina,relative abundances,"Cox Proportional-Hazards Regression,Fisher's Exact Test,Mann-Whitney (Wilcoxon),PERMANOVA,T-Test",0.05,TRUE,NA,NA,age,NA,increased,NA,NA,NA,NA,Signature 2,Figure 4B–C,1 November 2025,Adiba Patel,Adiba Patel,Families and genera overrepresented in lower-diversity pediatric patients before allo-HSCT.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|1940338,Complete,NA
bsdb:37864204/1/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 1,Japan,Canis lupus familiaris,Skin of abdomen,UBERON:0001416,Atopic eczema,EFO:0000274,Healthy dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,NA,16S,12,Illumina,centered log-ratio,Beta Binomial Regression,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Table S4, Table S3",29 March 2024,Deacme,"Deacme,KateRasheed,WikiWorks",Differentially abundant bacterial taxa at the genus level between two groups; healthy dogs and cADtreat dogs,increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota",1783272|201174;3379134|976,Complete,Svetlana up
bsdb:37864204/1/2,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 1,Japan,Canis lupus familiaris,Skin of abdomen,UBERON:0001416,Atopic eczema,EFO:0000274,Healthy dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,NA,16S,12,Illumina,centered log-ratio,Beta Binomial Regression,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Table S4, Table S3",22 January 2025,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant bacterial taxa at the genus level between two groups; healthy dogs and cADtreat dogs,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota",1783272|201174|1760|85006|1268|1663;1783272|201174|1760|85007|1653|1716;3379134|1224,Complete,Svetlana up
bsdb:37864204/2/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 2,Japan,Canis lupus familiaris,Skin of abdomen,UBERON:0001416,Atopic eczema,EFO:0000274,cADpre dogs,cADpost dogs,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,10,10,NA,16S,12,Illumina,centered log-ratio,Beta Binomial Regression,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Table S4, Table S3",29 March 2024,Deacme,"Deacme,KateRasheed,WikiWorks",Differentially abundant bacterial taxa at the genus level between two groups; cADpre dogs and cADpost dogs,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Skermanella,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota,k__Thermotogati|p__Deinococcota",1783272|201174|1760|85006|1268|1663;1783272|1239|91061|1385|186817|1386;3384194|1297|188787|118964|183710|1298;3379134|1224|1236|72274|135621|286;3379134|1224|28211|204441|2829815|204447;3379134|1224;3379134|976;3384194|1297,Complete,Svetlana up
bsdb:37864204/2/2,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 2,Japan,Canis lupus familiaris,Skin of abdomen,UBERON:0001416,Atopic eczema,EFO:0000274,cADpre dogs,cADpost dogs,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,10,10,NA,16S,12,Illumina,centered log-ratio,Beta Binomial Regression,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Table S4, Table S3",29 March 2024,Deacme,"Deacme,KateRasheed,WikiWorks",Differentially abundant bacterial taxa at the genus level between two groups; cADpre dogs and cADpost dogs,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Roseomonadaceae|g__Roseomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Rubellimicrobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Acidobacteriota",1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85009|31957|1912216;3379134|1224|28211|356|119045|407;1783272|201174|1760|85009|85015|1839;3379134|1224|28211|204455|31989|265;3379134|1224|28211|3120395|3385906|125216;3379134|1224|28211|204455|2854170|295418;3379134|1224|28211|204457|41297|13687;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;1783272|201174;3379134|57723,Complete,Svetlana up
bsdb:37864204/3/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 3,Japan,Canis lupus familiaris,Forelimb skin,UBERON:0003531,Atopic eczema,EFO:0000274,Healthy dogs,cADPre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,NA,16S,12,Illumina,centered log-ratio,Beta Binomial Regression,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Table S4, Table S3",29 March 2024,Deacme,"Deacme,KateRasheed,WikiWorks",Differentially abundant bacterial taxa at the genus level between two groups; healthy dogs and cADpre dogs,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter,k__Pseudomonadati|p__Acidobacteriota,k__Thermotogati|p__Deinococcota,k__Pseudomonadati|p__Verrucomicrobiota",3379134|976|768503|768507|1853232|89966;3379134|57723;3384194|1297;3379134|74201,Complete,Svetlana up
bsdb:37864204/3/2,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 3,Japan,Canis lupus familiaris,Forelimb skin,UBERON:0003531,Atopic eczema,EFO:0000274,Healthy dogs,cADPre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,NA,16S,12,Illumina,centered log-ratio,Beta Binomial Regression,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Table S4, Table S3",29 March 2024,Deacme,"Deacme,KateRasheed,WikiWorks",Differentially abundant bacterial taxa at the genus level between two groups; healthy dogs and cADpre dogs,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Acetobacter,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|28211|3120395|433|434;3379134|1224,Complete,Svetlana up
bsdb:37864204/4/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 4,Japan,Canis lupus familiaris,Forelimb skin,UBERON:0003531,Atopic eczema,EFO:0000274,Healthy dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,NA,16S,12,Illumina,centered log-ratio,Beta Binomial Regression,0.1,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Table S4,29 March 2024,Deacme,"Deacme,KateRasheed,WikiWorks",Differentially abundant bacterial taxa at the genus level between two groups; healthy dogs and cADtreat dogs,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Frederiksenia",3379134|1224|1236|2887326|468|469;3379134|1224|1236|135625|712|1649317,Complete,Svetlana up
bsdb:37864204/4/2,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 4,Japan,Canis lupus familiaris,Forelimb skin,UBERON:0003531,Atopic eczema,EFO:0000274,Healthy dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,NA,16S,12,Illumina,centered log-ratio,Beta Binomial Regression,0.1,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Table S4,29 March 2024,Deacme,"Deacme,KateRasheed,WikiWorks",Differentially abundant bacterial taxa at the genus level between two groups; healthy dogs and cADtreat dogs,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Acetobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Marmoricola,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",3379134|1224|28211|3120395|433|434;3379134|976|117743|200644|49546|1016;1783272|201174|1760|85009|85015|86795;1783272|1239|909932|909929|1843491|158846,Complete,Svetlana up
bsdb:37864204/10/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 10,Japan,Canis lupus familiaris,Ventral side of post-anal tail,UBERON:0018691,Atopic eczema,EFO:0000274,Healthy dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,NA,16S,12,Illumina,centered log-ratio,Beta Binomial Regression,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table S4,29 March 2024,Deacme,"Deacme,KateRasheed,WikiWorks",Differentially abundant bacterial taxa at the genus level between two groups; Healthy dogs and cADtreat dogs,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium",1783272|201174|1760|2037|2049|1654;3379134|976|117743|200644|2762318|501783,Complete,Svetlana up
bsdb:37864204/10/2,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 10,Japan,Canis lupus familiaris,Ventral side of post-anal tail,UBERON:0018691,Atopic eczema,EFO:0000274,Healthy dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,NA,16S,12,Illumina,centered log-ratio,Beta Binomial Regression,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table S4,29 March 2024,Deacme,"Deacme,KateRasheed,WikiWorks",Differentially abundant bacterial taxa at the genus level between two groups; Healthy dogs and cADtreat dogs,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Roseomonadaceae|g__Roseomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",3379134|1224|28216|80840|75682|149698;3379134|976|200643|171549|171551|836;3379134|1224|28211|3120395|3385906|125216;1783272|1239|91061|1385|90964|1279;1783272|1239|526524|526525|2810281|191303,Complete,Svetlana up
bsdb:37864204/11/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 11,Japan,Canis lupus familiaris,Ventral side of post-anal tail,UBERON:0018691,Atopic eczema,EFO:0000274,cADpre dogs,cADpost dogs,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,10,10,NA,16S,12,Illumina,centered log-ratio,Beta Binomial Regression,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Table S4, Table S3",29 March 2024,Deacme,"Deacme,KateRasheed,WikiWorks",Differentially abundant bacterial taxa between two groups; cADpre dogs and cADpost dogs,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Blastococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Flavisolibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Rubellimicrobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Acidobacteriota,k__Bacillati|p__Actinomycetota,k__Thermotogati|p__Deinococcota",1783272|201174|1760|1643682|85030|38501;1783272|1239|186801|3085636|186803|572511;3384194|1297|188787|118964|183710|1298;3379134|976|1853228|1853229|563835|398041;3379134|1224|1236|91347|1903414|583;3379134|1224|28211|204455|2854170|295418;1783272|1239|91061|1385|90964|1279;3379134|57723;1783272|201174;3384194|1297,Complete,Svetlana up
bsdb:37864204/11/2,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 11,Japan,Canis lupus familiaris,Ventral side of post-anal tail,UBERON:0018691,Atopic eczema,EFO:0000274,cADpre dogs,cADpost dogs,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,10,10,NA,16S,12,Illumina,centered log-ratio,Beta Binomial Regression,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Table S4, Table S3",29 March 2024,Deacme,"Deacme,KateRasheed,WikiWorks",Differentially abundant bacterial taxa between two groups; cADpre dogs and cADpost dogs,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Microlunatus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Microvirga,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Nakamurellales|f__Nakamurellaceae|g__Nakamurella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Skermanella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Bacteroidota,p__Candidatus Saccharimonadota,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota",1783272|201174|1760|85006|1268|1663;3379134|976|200643|171549|815|816;3379134|1224|28211|204458|76892|41275;1783272|201174|1760|85009|31957|1912216;1783272|1239|186801|3085636|186803|2005355;3379134|976|117743|200644|49546|237;3379134|1224|28216|80840|119060|47670;3379134|1224|28211|356|119045|407;1783272|201174|1760|85009|31957|29404;3379134|1224|28211|356|119045|186650;1783272|201174|1760|1643684|85031|53460;1783272|201174|1760|85009|85015|1839;3379134|976|200643|171549|171551|836;3379134|1224|28211|204441|2829815|204447;3379134|1224|28211|204457|41297|13687;3379134|976;95818;1783272|1239;3379134|1224,Complete,Svetlana up
bsdb:37864204/12/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 12,Japan,Canis lupus familiaris,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,Healthy,cADpre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,NA,16S,34,Illumina,centered log-ratio,Beta Binomial Regression,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Table 2, Table 1",30 March 2024,Barrakat,"Barrakat,KateRasheed,WikiWorks",Differentially abundant faecal bacterial taxa between two groups cADpre and Healthy dogs,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota",3384189|32066|203490|203491|203492|848;3384189|32066,Complete,Svetlana up
bsdb:37864204/12/2,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 12,Japan,Canis lupus familiaris,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,Healthy,cADpre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,NA,16S,34,Illumina,centered log-ratio,Beta Binomial Regression,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 2,30 March 2024,Barrakat,"Barrakat,KateRasheed,WikiWorks",Differentially abundant faecal bacterial taxa at the genus level between two groups cADpre and Healthy dogs,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|1239|526524|526525|128827|2749267;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|216572|946234;3379134|976|200643|171549|171551|836;1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:37864204/14/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 14,Japan,Canis lupus familiaris,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,Healthy dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,NA,16S,34,Illumina,centered log-ratio,Beta Binomial Regression,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Table 2, Table 1",30 March 2024,Barrakat,"Barrakat,KateRasheed,WikiWorks",Differentially abundant bacterial taxa between two groups; healthy dogs and cADtreat dogs,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas,k__Pseudomonadati|p__Campylobacterota",1783272|1239|186801|3085636|3118652|2039240;1783272|201174|1760|85007|1653|1716;1783272|1239|186801|3085636|186803|2005355;3379134|29547,Complete,Svetlana up
bsdb:37864204/14/2,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 14,Japan,Canis lupus familiaris,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,Healthy dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,NA,16S,34,Illumina,centered log-ratio,Beta Binomial Regression,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 2,30 March 2024,Barrakat,"Barrakat,MyleeeA,KateRasheed,WikiWorks",Differentially abundant bacterial taxa at the genus level between two groups; healthy dogs and cADtreat dogs,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",1783272|1239|186801|186802|31979|1485;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3085636|186803|572511,Complete,Svetlana up
bsdb:37864204/17/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 17,Japan,Canis lupus familiaris,Skin of abdomen,UBERON:0001416,Atopic eczema,EFO:0000274,Healthy,cAD Treat,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,NA,16S,12,Illumina,NA,ANCOM,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Supplementary Table S7, Supplementary Table S4 and Fig 3",1 April 2024,MyleeeA,"MyleeeA,KateRasheed,WikiWorks",Statistical summary of differentially abundant of taxa between dog groups.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus equorum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Curvibacter",1783272|1239|91061|1385|90964|1279|246432;3379134|1224|28216|80840|80864|281915,Complete,Svetlana up
bsdb:37864204/17/2,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 17,Japan,Canis lupus familiaris,Skin of abdomen,UBERON:0001416,Atopic eczema,EFO:0000274,Healthy,cAD Treat,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,NA,16S,12,Illumina,NA,ANCOM,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table S7 and Fig 3,1 April 2024,MyleeeA,"MyleeeA,WikiWorks",Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,1783272|1239|91061|1385|90964|1279|1282,Complete,Svetlana up
bsdb:37864204/19/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 19,Japan,Canis lupus familiaris,Axilla skin,UBERON:0015474,Atopic eczema,EFO:0000274,cAD Pre,cAD post,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,10,10,NA,16S,12,Illumina,NA,ANCOM,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Fig 3,1 April 2024,MyleeeA,"MyleeeA,WikiWorks",Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus equorum,1783272|1239|91061|1385|90964|1279|246432,Complete,Svetlana up
bsdb:37864204/19/2,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 19,Japan,Canis lupus familiaris,Axilla skin,UBERON:0015474,Atopic eczema,EFO:0000274,cAD Pre,cAD post,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,10,10,NA,16S,12,Illumina,NA,ANCOM,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table S7 and Fig 3,1 April 2024,MyleeeA,"MyleeeA,WikiWorks",Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,1783272|1239|91061|1385|90964|1279|1290,Complete,Svetlana up
bsdb:37864204/20/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 20,Japan,Canis lupus familiaris,Axilla skin,UBERON:0015474,Atopic eczema,EFO:0000274,Healthy dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,NA,16S,12,Illumina,NA,ANCOM,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,2 April 2024,Deacme,"Deacme,KateRasheed,WikiWorks",Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus haemolyticus",1783272|1239|91061|1385|90964|1279|1282;1783272|1239|91061|1385|90964|1279|1283,Complete,Svetlana up
bsdb:37864204/21/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 21,Japan,Canis lupus familiaris,Brachialis muscle,UBERON:0001506,Atopic eczema,EFO:0000274,Healthy dogs,cADPre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,NA,16S,12,Illumina,NA,ANCOM,0.1,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,2 April 2024,Deacme,"Deacme,KateRasheed,WikiWorks",Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus pseudintermedius,1783272|1239|91061|1385|90964|1279|283734,Complete,Svetlana up
bsdb:37864204/22/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 22,Japan,Canis lupus familiaris,Brachialis muscle,UBERON:0001506,Atopic eczema,EFO:0000274,Healthy dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,NA,16S,12,Illumina,NA,ANCOM,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,2 April 2024,Deacme,"Deacme,KateRasheed,WikiWorks",Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus equorum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus schleiferi",1783272|1239|91061|1385|90964|1279|246432;1783272|1239|91061|1385|90964|1279|1295,Complete,Svetlana up
bsdb:37864204/23/2,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 23,Japan,Canis lupus familiaris,Lateral lumbar region of abdomen,UBERON:0000180,Atopic eczema,EFO:0000274,Healthy controls,cAD Pre,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,NA,16S,12,Illumina,NA,ANCOM,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table S7 and Fig 3,2 April 2024,Barrakat,"Barrakat,Deacme,KateRasheed,WikiWorks",Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus pseudintermedius,1783272|1239|91061|1385|90964|1279|283734,Complete,Svetlana up
bsdb:37864204/25/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 25,Japan,Canis lupus familiaris,Lateral lumbar region of abdomen,UBERON:0000180,Atopic eczema,EFO:0000274,cADpre,cAD Post,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,20,10,NA,16S,12,Illumina,NA,ANCOM,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Fig 3,2 April 2024,Barrakat,"Barrakat,Deacme,KateRasheed,WikiWorks",Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,1783272|1239|91061|1385|90964|1279|1290,Complete,Svetlana up
bsdb:37864204/26/2,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 26,Japan,Canis lupus familiaris,Forelimb skin,UBERON:0003531,Atopic eczema,EFO:0000274,Healthy controls,cAD Pre,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,NA,16S,12,Illumina,NA,ANCOM,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Supplementary Table S7, Supplementary Table S3-4 and Figure 3",2 April 2024,Barrakat,"Barrakat,KateRasheed,WikiWorks",Statistical summary of differentially abundant taxa between dog groups.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus pseudintermedius,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota",1783272|1239|91061|1385|90964|1279|283734;3384189|32066|203490|203491|203492|848;1783272|1239,Complete,Svetlana up
bsdb:37864204/27/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 27,Japan,Canis lupus familiaris,Forelimb skin,UBERON:0003531,Atopic eczema,EFO:0000274,Healthy controls,cAD Treat,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,NA,16S,12,Illumina,NA,ANCOM,0.1,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Supplementary Table S7, Supplementary Table S4 and Figure 3",2 April 2024,Barrakat,"Barrakat,Deacme,KateRasheed,WikiWorks",Statistical summary of differentially abundant taxa between dog groups.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus equorum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Curvibacter",1783272|1239|91061|1385|90964|1279|246432;3379134|1224|28216|80840|80864|281915,Complete,Svetlana up
bsdb:37864204/27/2,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 27,Japan,Canis lupus familiaris,Forelimb skin,UBERON:0003531,Atopic eczema,EFO:0000274,Healthy controls,cAD Treat,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,NA,16S,12,Illumina,NA,ANCOM,0.1,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Supplementary Table S3,23 January 2025,KateRasheed,"KateRasheed,WikiWorks",Statistical summary of differentially abundant taxa between dog groups.,increased,k__Pseudomonadati|p__Acidobacteriota,3379134|57723,Complete,Svetlana up
bsdb:37864204/31/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 31,Japan,Canis lupus familiaris,Hindlimb skin,UBERON:0003532,Atopic eczema,EFO:0000274,cADpre dogs,cADpost dogs,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,20,10,NA,16S,12,Illumina,NA,ANCOM,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,2 April 2024,Barrakat,"Barrakat,Deacme,KateRasheed,WikiWorks",Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus caprae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus lugdunensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus pseudintermedius,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus warneri",1783272|1239|91061|1385|90964|1279|29380;1783272|1239|91061|1385|90964|1279|1282;1783272|1239|91061|1385|90964|1279|28035;1783272|1239|91061|1385|90964|1279|283734;1783272|1239|91061|1385|90964|1279|1292,Complete,Svetlana up
bsdb:37864204/31/2,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 31,Japan,Canis lupus familiaris,Hindlimb skin,UBERON:0003532,Atopic eczema,EFO:0000274,cADpre dogs,cADpost dogs,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,20,10,NA,16S,12,Illumina,NA,ANCOM,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table S7 and Figure 3,2 April 2024,Barrakat,"Barrakat,Deacme,KateRasheed,WikiWorks",Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,1783272|1239|91061|1385|90964|1279|1280,Complete,Svetlana up
bsdb:37864204/34/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 34,Japan,Canis lupus familiaris,Pinna,UBERON:0001757,Atopic eczema,EFO:0000274,Healthy dogs,cADpre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,NA,16S,12,Illumina,NA,ANCOM,0.1,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,5 April 2024,Deacme,"Deacme,KateRasheed,WikiWorks",Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus equorum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus warneri",1783272|1239|91061|1385|90964|1279|246432;1783272|1239|91061|1385|90964|1279|1292,Complete,Svetlana up
bsdb:37864204/37/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 37,Japan,Canis lupus familiaris,Skin of palmar/plantar part of autopod,UBERON:0013776,Atopic eczema,EFO:0000274,Healthy dogs,cADPre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,NA,16S,12,Illumina,NA,ANCOM,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,6 April 2024,Deacme,"Deacme,KateRasheed,WikiWorks",Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus equorum",1783272|1239|91061|1385|90964|1279|1280;1783272|1239|91061|1385|90964|1279|246432,Complete,Svetlana up
bsdb:37864204/37/2,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 37,Japan,Canis lupus familiaris,Skin of palmar/plantar part of autopod,UBERON:0013776,Atopic eczema,EFO:0000274,Healthy dogs,cADPre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,NA,16S,12,Illumina,NA,ANCOM,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table S7 and Figure 3,6 April 2024,Deacme,"Deacme,KateRasheed,WikiWorks",Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus pseudintermedius,1783272|1239|91061|1385|90964|1279|283734,Complete,Svetlana up
bsdb:37864204/38/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 38,Japan,Canis lupus familiaris,Skin of palmar/plantar part of autopod,UBERON:0013776,Atopic eczema,EFO:0000274,Healthy dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,NA,16S,12,Illumina,NA,ANCOM,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,6 April 2024,Deacme,"Deacme,KateRasheed,WikiWorks",Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus equorum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus warneri",1783272|1239|91061|1385|90964|1279|246432;1783272|1239|91061|1385|90964|1279|1292,Complete,Svetlana up
bsdb:37864204/40/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 40,Japan,Canis lupus familiaris,Mouth,UBERON:0000165,Atopic eczema,EFO:0000274,Healthy dogs,cADpre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,NA,16S,12,Illumina,NA,ANCOM,0.1,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary Table S7 and Figure 3,6 April 2024,Deacme,"Deacme,KateRasheed,WikiWorks",Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Mammaliicoccus|s__Mammaliicoccus sciuri,1783272|1239|91061|1385|90964|2803850|1296,Complete,Svetlana up
bsdb:37864204/40/2,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 40,Japan,Canis lupus familiaris,Mouth,UBERON:0000165,Atopic eczema,EFO:0000274,Healthy dogs,cADpre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,NA,16S,12,Illumina,NA,ANCOM,0.1,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Supplementary Table S7 and Figure 3,6 April 2024,Deacme,"Deacme,KateRasheed,WikiWorks",Statistical summary of differentially abundant Staphylococcus spp. between dog groups.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus pseudintermedius,1783272|1239|91061|1385|90964|1279|283734,Complete,Svetlana up
bsdb:37864204/41/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 41,Japan,Canis lupus familiaris,Mouth,UBERON:0000165,Atopic eczema,EFO:0000274,cADpre dogs,cADpost dogs,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,10,10,NA,16S,12,Illumina,NA,ANCOM,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Supplementary Table S7, Supplementary Table S3 and Figure 3",6 April 2024,Deacme,"Deacme,KateRasheed,WikiWorks",Statistical summary of differentially abundant taxa between dog groups.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus coagulans,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus pseudintermedius,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus schleiferi,k__Bacillati|p__Actinomycetota",1783272|1239|91061|1385|90964|1279|74706;1783272|1239|91061|1385|90964|1279|283734;1783272|1239|91061|1385|90964|1279|1295;1783272|201174,Complete,Svetlana up
bsdb:37864204/41/2,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 41,Japan,Canis lupus familiaris,Mouth,UBERON:0000165,Atopic eczema,EFO:0000274,cADpre dogs,cADpost dogs,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,10,10,NA,16S,12,Illumina,NA,ANCOM,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table S4,23 January 2025,KateRasheed,"KateRasheed,WikiWorks",Statistical summary of differentially abundant taxa between dog groups.,increased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Acetobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium",3379134|1224;3379134|1224|28211|3120395|433|434;1783272|201174|1760|85009|31957|1912216,Complete,Svetlana up
bsdb:37864204/43/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 43,Japan,Canis lupus familiaris,Ventral side of post-anal tail,UBERON:0018691,Atopic eczema,EFO:0000274,Healthy dogs,cADpre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,NA,16S,12,Illumina,NA,ANCOM,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Supplementary Table S7, Supplementary Table S4 and Figure 3",6 April 2024,Deacme,"Deacme,KateRasheed,WikiWorks",Statistical summary of differentially abundant taxa between dog groups.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus pseudintermedius,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|1239|91061|1385|90964|1279|283734;1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:37864204/44/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 44,Japan,Canis lupus familiaris,Ventral side of post-anal tail,UBERON:0018691,Atopic eczema,EFO:0000274,Healthy dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,NA,16S,12,Illumina,NA,ANCOM,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Supplementary Table S7, Supplementary Table S4 and Figure 3",6 April 2024,Deacme,"Deacme,KateRasheed,WikiWorks",Statistical summary of differentially abundant taxa between dog groups.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus equorum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella",1783272|1239|91061|1385|90964|1279|246432;3379134|1224|1236|2887326|468|475,Complete,Svetlana up
bsdb:37864204/44/2,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 44,Japan,Canis lupus familiaris,Ventral side of post-anal tail,UBERON:0018691,Atopic eczema,EFO:0000274,Healthy dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,NA,16S,12,Illumina,NA,ANCOM,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Supplementary Table S7, Supplementary Table S4 and Figure 3",6 April 2024,Deacme,"Deacme,KateRasheed,WikiWorks",Statistical summary of differentially abundant taxa between dog groups.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia",1783272|1239|91061|1385|90964|1279|1282;1783272|1239|91061|1385|90964|1279|1290;3379134|1224|28216|80840|119060|47670,Complete,Svetlana up
bsdb:37864204/46/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 46,Japan,Canis lupus familiaris,Mouth,UBERON:0000165,Atopic eczema,EFO:0000274,Healthy dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,20,10,NA,16S,12,Illumina,NA,ANCOM,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S3,23 January 2025,KateRasheed,"KateRasheed,WikiWorks",Statistical summary of differentially abundant taxa between dog groups.,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,Svetlana up
bsdb:37864204/47/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 47,Japan,Canis lupus familiaris,Abdomen,UBERON:0000916,Atopic eczema,EFO:0000274,Healthy dogs,cADpre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,NA,16S,12,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 1C,23 January 2025,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between dogs using ANOVA,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:37864204/48/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 48,Japan,Canis lupus familiaris,Abdomen,UBERON:0000916,Atopic eczema,EFO:0000274,cADpre dogs,cADpost dogs,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,10,10,NA,16S,12,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 1C,23 January 2025,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between dogs using ANOVA,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:37864204/49/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 49,Japan,Canis lupus familiaris,Axilla,UBERON:0009472,Atopic eczema,EFO:0000274,Healthy dogs,cADpre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,NA,16S,12,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 1C,23 January 2025,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between dogs using ANOVA,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:37864204/50/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 50,Japan,Canis lupus familiaris,Brachialis muscle,UBERON:0001506,Atopic eczema,EFO:0000274,Healthy dogs,cADpre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,NA,16S,12,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Fig. 1C,23 January 2025,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between dogs using ANOVA,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:37864204/51/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 51,Japan,Canis lupus familiaris,Brachialis muscle,UBERON:0001506,Atopic eczema,EFO:0000274,cADpre dogs,cADpost dogs,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,10,10,NA,16S,12,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 1C,23 January 2025,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between dogs using ANOVA,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:37864204/52/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 52,Japan,Canis lupus familiaris,Brachialis muscle,UBERON:0001506,Atopic eczema,EFO:0000274,cADpre dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,10,10,NA,16S,12,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 1C,23 January 2025,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between dogs using ANOVA,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:37864204/53/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 53,Japan,Canis lupus familiaris,Inguinal part of abdomen,UBERON:0008337,Atopic eczema,EFO:0000274,Healthy dogs,cADpre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,NA,16S,12,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 1C,23 January 2025,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between dogs using ANOVA,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:37864204/54/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 54,Japan,Canis lupus familiaris,Carpal bone,UBERON:0001435,Atopic eczema,EFO:0000274,Healthy dogs,cADpre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,NA,16S,12,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 1C,23 January 2025,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between dogs using ANOVA,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:37864204/55/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 55,Japan,Canis lupus familiaris,Carpal bone,UBERON:0001435,Atopic eczema,EFO:0000274,cADpre dogs,cADpost dogs,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,10,10,NA,16S,12,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 1C,23 January 2025,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between dogs using ANOVA,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:37864204/56/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 56,Japan,Canis lupus familiaris,Carpal bone,UBERON:0001435,Atopic eczema,EFO:0000274,cADpre dogs,cADtreat dogs,Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment,10,10,NA,16S,12,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 1C,23 January 2025,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between dogs using ANOVA,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:37864204/57/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 57,Japan,Canis lupus familiaris,Mouth,UBERON:0000165,Atopic eczema,EFO:0000274,Healthy dogs,cADpre dogs,Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments,20,10,NA,16S,12,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Fig. 1C,23 January 2025,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between dogs using ANOVA,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:37864204/58/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 58,Japan,Canis lupus familiaris,Mouth,UBERON:0000165,Atopic eczema,EFO:0000274,cADpre dogs,cADpost dogs,cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis,10,10,NA,16S,12,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 1C,23 January 2025,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between dogs using ANOVA,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:37864204/59/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 59,Japan,Canis lupus familiaris,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,Mitochondrial haplogroups A,Mitochondrial haplogroups C,"Mitochondrial haplogroups C refers to dogs belonging to this haplogroup, determined using the Canis mtDNA HV1 database",20,14,NA,16S,34,Illumina,centered log-ratio,Beta Binomial Regression,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 10,23 January 2025,KateRasheed,"KateRasheed,WikiWorks",Statistical summary of differentially abundant faecal bacterial taxa between mtDNA haplogroups A and C,decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Campylobacterota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacterium",1783272|201174;3379134|29547;1783272|1239|186801|3085636|186803|207244;1783272|1239;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|3118652|2039240;1783272|1239|186801|3085636|186803|572511;1783272|1239|526524|526525|128827|2749267,Complete,Svetlana up
bsdb:37864204/60/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 60,Japan,Canis lupus familiaris,Axilla,UBERON:0009472,Atopic eczema,EFO:0000274,Mitochondrial haplogroups A,Mitochondrial haplogroups C,"Mitochondrial haplogroups C refers to dogs belonging to this haplogroup, determined using the Canis mtDNA HV1 database",20,14,NA,16S,12,Illumina,centered log-ratio,Beta Binomial Regression,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 10,23 January 2025,KateRasheed,"KateRasheed,WikiWorks",Statistical summary of differentially abundant skin bacterial taxa between mtDNA haplogroups A and C,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|201174;1783272|201174|1760|85006|1268|1663;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:37864204/61/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 61,Japan,Canis lupus familiaris,Axilla,UBERON:0009472,Atopic eczema,EFO:0000274,Mitochondrial haplogroups A,Mitochondrial haplogroups C,"Mitochondrial haplogroups C refers to dogs belonging to this haplogroup, determined using the Canis mtDNA HV1 database",20,14,NA,16S,12,Illumina,NA,ANCOM,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 10,23 January 2025,KateRasheed,"KateRasheed,WikiWorks",Statistical summary of differentially abundant skin bacterial taxa between mtDNA haplogroups A and C,increased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Svetlana up
bsdb:37864204/61/2,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 61,Japan,Canis lupus familiaris,Axilla,UBERON:0009472,Atopic eczema,EFO:0000274,Mitochondrial haplogroups A,Mitochondrial haplogroups C,"Mitochondrial haplogroups C refers to dogs belonging to this haplogroup, determined using the Canis mtDNA HV1 database",20,14,NA,16S,12,Illumina,NA,ANCOM,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 10,23 January 2025,KateRasheed,"KateRasheed,WikiWorks",Statistical summary of differentially abundant skin bacterial taxa between mtDNA haplogroups A and C,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Rubellimicrobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",3379134|1224|28211|204455|2854170|295418;3379134|1224|1236|135625|712|724,Complete,Svetlana up
bsdb:37864204/62/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 62,Japan,Canis lupus familiaris,Pinna,UBERON:0001757,Atopic eczema,EFO:0000274,Mitochondrial haplogroups A,Mitochondrial haplogroups C,"Mitochondrial haplogroups C refers to dogs belonging to this haplogroup, determined using the Canis mtDNA HV1 database",20,14,NA,16S,12,Illumina,centered log-ratio,Beta Binomial Regression,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 10,23 January 2025,KateRasheed,"KateRasheed,WikiWorks",Statistical summary of differentially abundant skin bacterial taxa between mtDNA haplogroups A and C,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",1783272|201174|1760|85006|1268|32207;3379134|976|200643|171549|2005525|195950;3379134|1224|1236|135614|32033|40323,Complete,Svetlana up
bsdb:37864204/62/2,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 62,Japan,Canis lupus familiaris,Pinna,UBERON:0001757,Atopic eczema,EFO:0000274,Mitochondrial haplogroups A,Mitochondrial haplogroups C,"Mitochondrial haplogroups C refers to dogs belonging to this haplogroup, determined using the Canis mtDNA HV1 database",20,14,NA,16S,12,Illumina,centered log-ratio,Beta Binomial Regression,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 10,23 January 2025,KateRasheed,"KateRasheed,WikiWorks",Statistical summary of differentially abundant skin bacterial taxa between mtDNA haplogroups A and C,decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella",1783272|201174;3379134|976|117743|200644|49546|237;3379134|1224|1236|135625|712|745,Complete,Svetlana up
bsdb:37864204/63/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 63,Japan,Canis lupus familiaris,Feces,UBERON:0001988,Atopic eczema,EFO:0000274,Mitochondrial haplogroups A,Mitochondrial haplogroups C,"Mitochondrial haplogroups C refers to dogs belonging to this haplogroup, determined using the Canis mtDNA HV1 database",20,14,NA,16S,34,Illumina,NA,ANCOM,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 10,23 January 2025,KateRasheed,"KateRasheed,WikiWorks",Statistical summary of differentially abundant faecal bacterial taxa between mtDNA haplogroups A and C,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,1783272|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:37864204/64/1,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 64,Japan,Canis lupus familiaris,Forelimb,UBERON:0002102,Atopic eczema,EFO:0000274,Mitochondrial haplogroups A,Mitochondrial haplogroups C,"Mitochondrial haplogroups C refers to dogs belonging to this haplogroup, determined using the Canis mtDNA HV1 database",20,14,NA,16S,12,Illumina,centered log-ratio,Beta Binomial Regression,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 10,23 January 2025,KateRasheed,"KateRasheed,WikiWorks",Statistical summary of differentially abundant skin bacterial taxa between mtDNA haplogroups A and C,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,3379134|1224|1236|135625|712|724,Complete,Svetlana up
bsdb:37864204/64/2,37864204,time series / longitudinal observational,37864204,10.1186/s40168-023-01671-2,NA,"Thomsen M., Künstner A., Wohlers I., Olbrich M., Lenfers T., Osumi T., Shimazaki Y., Nishifuji K., Ibrahim S.M., Watson A., Busch H. , Hirose M.",A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs,Microbiome,2023,"16S rRNA, Canine atopic dermatitis, Fusobacterium, JAK inhibitor, Megamonas, Mitochondrial DNA, Mitochondrial haplogroup, Shiba Inu dogs, Skin and gut microbiota, Staphylococcus",Experiment 64,Japan,Canis lupus familiaris,Forelimb,UBERON:0002102,Atopic eczema,EFO:0000274,Mitochondrial haplogroups A,Mitochondrial haplogroups C,"Mitochondrial haplogroups C refers to dogs belonging to this haplogroup, determined using the Canis mtDNA HV1 database",20,14,NA,16S,12,Illumina,centered log-ratio,Beta Binomial Regression,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 10,23 January 2025,KateRasheed,"KateRasheed,WikiWorks",Statistical summary of differentially abundant skin bacterial taxa between mtDNA haplogroups A and C,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",3379134|976|200643|171549|815|816;3379134|976|117743|200644|49546|1016;3379134|1224|28216|206351|481|482,Complete,Svetlana up
bsdb:37866373/1/1,37866373,randomized controlled trial,37866373,10.1016/S2666-5247(23)00213-6,NA,"Schwartz D.J., Langdon A., Sun X., Langendorf C., Berthé F., Grais R.F., Trehan I., Isanaka S. , Dantas G.","Effect of amoxicillin on the gut microbiome of children with severe acute malnutrition in Madarounfa, Niger: a retrospective metagenomic analysis of a placebo-controlled trial",The Lancet. Microbe,2023,NA,Experiment 1,Niger,Homo sapiens,Feces,UBERON:0001988,Treatment,EFO:0000727,Amoxicillin Week 0,Amoxicillin Week 1,Children with severe acute malnutrition who received amoxicillin for one week and had their fecal samples collected at the end of treatment (Week 1).,35,39,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 3E,17 July 2025,Anne-mariesharp,Anne-mariesharp,Significant taxonomic changes at the genus level with Benjamini-Hochberg-corrected q-values.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp.,3379134|1224|1236|91347|543|561|1884818,Complete,KateRasheed
bsdb:37866373/1/2,37866373,randomized controlled trial,37866373,10.1016/S2666-5247(23)00213-6,NA,"Schwartz D.J., Langdon A., Sun X., Langendorf C., Berthé F., Grais R.F., Trehan I., Isanaka S. , Dantas G.","Effect of amoxicillin on the gut microbiome of children with severe acute malnutrition in Madarounfa, Niger: a retrospective metagenomic analysis of a placebo-controlled trial",The Lancet. Microbe,2023,NA,Experiment 1,Niger,Homo sapiens,Feces,UBERON:0001988,Treatment,EFO:0000727,Amoxicillin Week 0,Amoxicillin Week 1,Children with severe acute malnutrition who received amoxicillin for one week and had their fecal samples collected at the end of treatment (Week 1).,35,39,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,"Figure 3A, B, C",17 July 2025,Anne-mariesharp,Anne-mariesharp,Significant taxonomic changes at the genus level with Benjamini-Hochberg-corrected q-values.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.",1783272|201174|1760|85004|31953|1678|41200;1783272|1239|526524|526525|128827|1573535|1971762;1783272|1239|91061|186826|33958|1578|1591,Complete,KateRasheed
bsdb:37866373/2/1,37866373,randomized controlled trial,37866373,10.1016/S2666-5247(23)00213-6,NA,"Schwartz D.J., Langdon A., Sun X., Langendorf C., Berthé F., Grais R.F., Trehan I., Isanaka S. , Dantas G.","Effect of amoxicillin on the gut microbiome of children with severe acute malnutrition in Madarounfa, Niger: a retrospective metagenomic analysis of a placebo-controlled trial",The Lancet. Microbe,2023,NA,Experiment 2,Niger,Homo sapiens,Feces,UBERON:0001988,Treatment,EFO:0000727,Placebo Week 1,Amoxicillin Week 1,Children with severe acute malnutrition who received amoxicillin for one week and had their fecal samples collected at the end of treatment (Week 1).,33,39,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3E,17 July 2025,Anne-mariesharp,Anne-mariesharp,Significant taxonomic changes at the genus level with Benjamini-Hochberg-corrected q-values.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp.,3379134|1224|1236|91347|543|561|1884818,Complete,KateRasheed
bsdb:37866373/2/2,37866373,randomized controlled trial,37866373,10.1016/S2666-5247(23)00213-6,NA,"Schwartz D.J., Langdon A., Sun X., Langendorf C., Berthé F., Grais R.F., Trehan I., Isanaka S. , Dantas G.","Effect of amoxicillin on the gut microbiome of children with severe acute malnutrition in Madarounfa, Niger: a retrospective metagenomic analysis of a placebo-controlled trial",The Lancet. Microbe,2023,NA,Experiment 2,Niger,Homo sapiens,Feces,UBERON:0001988,Treatment,EFO:0000727,Placebo Week 1,Amoxicillin Week 1,Children with severe acute malnutrition who received amoxicillin for one week and had their fecal samples collected at the end of treatment (Week 1).,33,39,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 3A, B",17 July 2025,Anne-mariesharp,Anne-mariesharp,Significant taxonomic changes at the genus level with Benjamini-Hochberg-corrected q-values.,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.",1783272|1239|526524|526525|128827|1573535|1971762;1783272|1239|91061|186826|33958|1578|1591,Complete,KateRasheed
bsdb:37866373/3/1,37866373,randomized controlled trial,37866373,10.1016/S2666-5247(23)00213-6,NA,"Schwartz D.J., Langdon A., Sun X., Langendorf C., Berthé F., Grais R.F., Trehan I., Isanaka S. , Dantas G.","Effect of amoxicillin on the gut microbiome of children with severe acute malnutrition in Madarounfa, Niger: a retrospective metagenomic analysis of a placebo-controlled trial",The Lancet. Microbe,2023,NA,Experiment 3,Niger,Homo sapiens,Feces,UBERON:0001988,Treatment,EFO:0000727,Placebo Week 0,Placebo Week 1,Children with severe acute malnutrition who received Placebo for one week and had their fecal samples collected at week 1,32,33,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3D,18 July 2025,Anne-mariesharp,Anne-mariesharp,Significant taxonomic changes at the genus level with Benjamini-Hochberg-corrected q-values.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.,3379134|1224|1236|91347|543|570|576,Complete,KateRasheed
bsdb:37866373/4/1,37866373,randomized controlled trial,37866373,10.1016/S2666-5247(23)00213-6,NA,"Schwartz D.J., Langdon A., Sun X., Langendorf C., Berthé F., Grais R.F., Trehan I., Isanaka S. , Dantas G.","Effect of amoxicillin on the gut microbiome of children with severe acute malnutrition in Madarounfa, Niger: a retrospective metagenomic analysis of a placebo-controlled trial",The Lancet. Microbe,2023,NA,Experiment 4,Niger,Homo sapiens,Feces,UBERON:0001988,Treatment,EFO:0000727,Placebo Week 1,Amoxicillin Week 1,Children with severe acute malnutrition who received amoxicillin for one week and had their fecal samples collected at the end of treatment (Week 1).,33,39,NA,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,age,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 3F, Appendix 3 (tab 3)",18 July 2025,Anne-mariesharp,Anne-mariesharp,Coefficients (effect size) and 95% confidence intervals for significant taxonomic enrichment and depletion,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp.,3379134|1224|1236|91347|543|561|1884818,Complete,KateRasheed
bsdb:37866373/4/2,37866373,randomized controlled trial,37866373,10.1016/S2666-5247(23)00213-6,NA,"Schwartz D.J., Langdon A., Sun X., Langendorf C., Berthé F., Grais R.F., Trehan I., Isanaka S. , Dantas G.","Effect of amoxicillin on the gut microbiome of children with severe acute malnutrition in Madarounfa, Niger: a retrospective metagenomic analysis of a placebo-controlled trial",The Lancet. Microbe,2023,NA,Experiment 4,Niger,Homo sapiens,Feces,UBERON:0001988,Treatment,EFO:0000727,Placebo Week 1,Amoxicillin Week 1,Children with severe acute malnutrition who received amoxicillin for one week and had their fecal samples collected at the end of treatment (Week 1).,33,39,NA,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,age,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 3F, Appendix 3 (tab 3)",18 July 2025,Anne-mariesharp,Anne-mariesharp,Coefficients (effect size) and 95% confidence intervals for significant taxonomic enrichment and depletion,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp.,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.",1783272|1239|186801|3085636|186803|189330|2040332;1783272|1239|526524|526525|128827|1573535|1971762;1783272|1239|91061|186826|33958|1578|1591;1783272|1239|91061|186826|1300|1301|1306,Complete,KateRasheed
bsdb:37866373/5/1,37866373,randomized controlled trial,37866373,10.1016/S2666-5247(23)00213-6,NA,"Schwartz D.J., Langdon A., Sun X., Langendorf C., Berthé F., Grais R.F., Trehan I., Isanaka S. , Dantas G.","Effect of amoxicillin on the gut microbiome of children with severe acute malnutrition in Madarounfa, Niger: a retrospective metagenomic analysis of a placebo-controlled trial",The Lancet. Microbe,2023,NA,Experiment 5,Niger,Homo sapiens,Feces,UBERON:0001988,Treatment,EFO:0000727,Amoxicillin Week 0,Amoxicillin Week 1,Children with severe acute malnutrition who received amoxicillin for one week and had their fecal samples collected at the end of treatment (Week 1).,35,39,NA,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"Figure 3F, Appendix 3 (tab 3)",18 July 2025,Anne-mariesharp,Anne-mariesharp,Coefficients (effect size) and 95% confidence intervals for significant taxonomic enrichment and depletion,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.",3379134|1224|1236|91347|543|561|1884818;3379134|1224|1236|91347|543|570|576,Complete,KateRasheed
bsdb:37866373/5/2,37866373,randomized controlled trial,37866373,10.1016/S2666-5247(23)00213-6,NA,"Schwartz D.J., Langdon A., Sun X., Langendorf C., Berthé F., Grais R.F., Trehan I., Isanaka S. , Dantas G.","Effect of amoxicillin on the gut microbiome of children with severe acute malnutrition in Madarounfa, Niger: a retrospective metagenomic analysis of a placebo-controlled trial",The Lancet. Microbe,2023,NA,Experiment 5,Niger,Homo sapiens,Feces,UBERON:0001988,Treatment,EFO:0000727,Amoxicillin Week 0,Amoxicillin Week 1,Children with severe acute malnutrition who received amoxicillin for one week and had their fecal samples collected at the end of treatment (Week 1).,35,39,NA,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,"Figure 3F, Appendix 3 (tab 3)",18 July 2025,Anne-mariesharp,Anne-mariesharp,Coefficients (effect size) and 95% confidence intervals for significant taxonomic enrichment and depletion,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.",1783272|201174|1760|85004|31953|1678|41200;1783272|1239|526524|526525|128827|1573535|1971762;1783272|1239|91061|186826|33958|1578|1591,Complete,KateRasheed
bsdb:37866373/6/1,37866373,randomized controlled trial,37866373,10.1016/S2666-5247(23)00213-6,NA,"Schwartz D.J., Langdon A., Sun X., Langendorf C., Berthé F., Grais R.F., Trehan I., Isanaka S. , Dantas G.","Effect of amoxicillin on the gut microbiome of children with severe acute malnutrition in Madarounfa, Niger: a retrospective metagenomic analysis of a placebo-controlled trial",The Lancet. Microbe,2023,NA,Experiment 6,Niger,Homo sapiens,Feces,UBERON:0001988,Treatment,EFO:0000727,Placebo-treated children (Week 104),Amoxicillin-treated children (Week 104),"Children with severe acute malnutrition who received amoxicillin for one week, and had their fecal samples collected at the 2-year follow-up (Week 104).",13,22,NA,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 5C, Appendix 3 (tab 10)",21 July 2025,Anne-mariesharp,Anne-mariesharp,Coefficients (effect size) and 95% CI for taxa significantly different between amoxicillin-treated and placebo-treated children,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium mitsuokai,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus animalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. 885,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus macedonicus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella cibaria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella confusa",1783272|1239|526524|526525|2810280|135858|100886;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|186802|204475|745368;1783272|1239|526524|526525|128827|1573535|1735;3379134|976|200643|171549|171552|2974265|363265;1783272|1239|91061|186826|33958|2767887|1605;3379134|976|200643|171549|171552|838|2022527;1783272|201174|1760|2037|2049|2529408|1660;1783272|201174|84998|1643822|1643826|84108|572010;1783272|1239|91061|186826|1300|1301|59310;1783272|1239|91061|186826|33958|46255|137591;1783272|1239|91061|186826|33958|46255|1583,Complete,KateRasheed
bsdb:37866373/6/2,37866373,randomized controlled trial,37866373,10.1016/S2666-5247(23)00213-6,NA,"Schwartz D.J., Langdon A., Sun X., Langendorf C., Berthé F., Grais R.F., Trehan I., Isanaka S. , Dantas G.","Effect of amoxicillin on the gut microbiome of children with severe acute malnutrition in Madarounfa, Niger: a retrospective metagenomic analysis of a placebo-controlled trial",The Lancet. Microbe,2023,NA,Experiment 6,Niger,Homo sapiens,Feces,UBERON:0001988,Treatment,EFO:0000727,Placebo-treated children (Week 104),Amoxicillin-treated children (Week 104),"Children with severe acute malnutrition who received amoxicillin for one week, and had their fecal samples collected at the 2-year follow-up (Week 104).",13,22,NA,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 5C, Appendix 3 (tab 10)",21 July 2025,Anne-mariesharp,Anne-mariesharp,Coefficients (effect size) and 95% CI for taxa significantly different between amoxicillin-treated and placebo-treated children,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum",1783272|201174|1760|85004|31953|1678|1681;1783272|201174|1760|85004|31953|1678|216816,Complete,KateRasheed
bsdb:37866373/7/1,37866373,randomized controlled trial,37866373,10.1016/S2666-5247(23)00213-6,NA,"Schwartz D.J., Langdon A., Sun X., Langendorf C., Berthé F., Grais R.F., Trehan I., Isanaka S. , Dantas G.","Effect of amoxicillin on the gut microbiome of children with severe acute malnutrition in Madarounfa, Niger: a retrospective metagenomic analysis of a placebo-controlled trial",The Lancet. Microbe,2023,NA,Experiment 7,Niger,Homo sapiens,Feces,UBERON:0001988,Treatment,EFO:0000727,non-SAM (Severe Acute Malnutrition) Week 104,SAM (Severe Acute Malnutrition) Placebo at Week 104,"Children with severe acute malnutrition who received placebo for one week, and had their fecal samples collected at the 2-year follow-up (Week 104).",6,13,NA,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,"Supplementary Figure 5, Appendix 3 (tab15)",22 July 2025,Anne-mariesharp,Anne-mariesharp,Coefficient of significantly increased species between placebo-treated and non-SAM children,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum",1783272|201174|1760|85004|31953|1678|1681;1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|1678|216816,Complete,KateRasheed
bsdb:37866373/7/2,37866373,randomized controlled trial,37866373,10.1016/S2666-5247(23)00213-6,NA,"Schwartz D.J., Langdon A., Sun X., Langendorf C., Berthé F., Grais R.F., Trehan I., Isanaka S. , Dantas G.","Effect of amoxicillin on the gut microbiome of children with severe acute malnutrition in Madarounfa, Niger: a retrospective metagenomic analysis of a placebo-controlled trial",The Lancet. Microbe,2023,NA,Experiment 7,Niger,Homo sapiens,Feces,UBERON:0001988,Treatment,EFO:0000727,non-SAM (Severe Acute Malnutrition) Week 104,SAM (Severe Acute Malnutrition) Placebo at Week 104,"Children with severe acute malnutrition who received placebo for one week, and had their fecal samples collected at the 2-year follow-up (Week 104).",6,13,NA,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 2,"Supplementary Figure 5, Appendix 3 (tab15)",22 July 2025,Anne-mariesharp,Anne-mariesharp,Coefficient of significantly increased species between placebo-treated and non-SAM children,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. 885,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. AM42-24",1783272|1239|186801|186802|216572|216851|853;3379134|976|200643|171549|171552|838|2022527;3379134|976|200643|171549|171552|2974251|165179;3379134|976|200643|171549|171552|838|2293125,Complete,KateRasheed
bsdb:37888992/1/1,37888992,laboratory experiment,37888992,10.1128/spectrum.02715-23,NA,"Ange-Stark M., Parise K.L., Cheng T.L., Hoyt J.R., Langwig K.E., Frick W.F., Kilpatrick A.M., Gillece J., MacManes M.D. , Foster J.T.",White-nose syndrome restructures bat skin microbiomes,Microbiology spectrum,2023,"Eptesicus fuscus, Myotis lucifugus, Perimyotis subflavus, Pseudogymnoascus destructans, bat populations, disease ecology, microbiome, white-nose syndrome",Experiment 1,United States of America,Myotis lucifugus,Skin epidermis,UBERON:0001003,Fungal infectious disease,MONDO:0002041,Pseudogymnoascus Destructans (PD) Negative,Pseudogymnoascus Destructans (PD) positive,Myotis lucifugus Bats species infected with Pseudogymnoascus destructans (Pd).,29,81,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 1,Results Text and Fig 4,21 March 2024,MyleeeA,"MyleeeA,WikiWorks",Taxonomic differential abundance analyses in Pseudogymnoascus destructans (Pd)-positive and Pseudogymnoascus destructans (Pd)-negative M.  lucifugus.,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae,1783272|201174|1760|85010|2070,Complete,Svetlana up
bsdb:37888992/1/2,37888992,laboratory experiment,37888992,10.1128/spectrum.02715-23,NA,"Ange-Stark M., Parise K.L., Cheng T.L., Hoyt J.R., Langwig K.E., Frick W.F., Kilpatrick A.M., Gillece J., MacManes M.D. , Foster J.T.",White-nose syndrome restructures bat skin microbiomes,Microbiology spectrum,2023,"Eptesicus fuscus, Myotis lucifugus, Perimyotis subflavus, Pseudogymnoascus destructans, bat populations, disease ecology, microbiome, white-nose syndrome",Experiment 1,United States of America,Myotis lucifugus,Skin epidermis,UBERON:0001003,Fungal infectious disease,MONDO:0002041,Pseudogymnoascus Destructans (PD) Negative,Pseudogymnoascus Destructans (PD) positive,Myotis lucifugus Bats species infected with Pseudogymnoascus destructans (Pd).,29,81,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 2,Results Text and Fig 4,21 March 2024,MyleeeA,"MyleeeA,WikiWorks",Taxonomic differential abundance analyses in Pseudogymnoascus destructans (Pd)-positive and Pseudogymnoascus destructans (Pd)-negative M. lucifugus.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae",3379134|1224|28211|356|118882;3379134|1224|1236|135613;3379134|976|768503|768507|89373;3379134|1224|28211|356|82115,Complete,Svetlana up
bsdb:37888992/2/NA,37888992,laboratory experiment,37888992,10.1128/spectrum.02715-23,NA,"Ange-Stark M., Parise K.L., Cheng T.L., Hoyt J.R., Langwig K.E., Frick W.F., Kilpatrick A.M., Gillece J., MacManes M.D. , Foster J.T.",White-nose syndrome restructures bat skin microbiomes,Microbiology spectrum,2023,"Eptesicus fuscus, Myotis lucifugus, Perimyotis subflavus, Pseudogymnoascus destructans, bat populations, disease ecology, microbiome, white-nose syndrome",Experiment 2,United States of America,Perimyotis subflavus,Skin epidermis,UBERON:0001003,Fungal infectious disease,MONDO:0002041,Pseudogymnoascus Destructans (PD) Negative,Pseudogymnoascus Destructans (PD) positive,Perimyotis subflavus Bats species infected with Pseudogymnoascus destructans (Pd).,43,95,NA,ITS / ITS2,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,increased,increased,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:37888992/3/1,37888992,laboratory experiment,37888992,10.1128/spectrum.02715-23,NA,"Ange-Stark M., Parise K.L., Cheng T.L., Hoyt J.R., Langwig K.E., Frick W.F., Kilpatrick A.M., Gillece J., MacManes M.D. , Foster J.T.",White-nose syndrome restructures bat skin microbiomes,Microbiology spectrum,2023,"Eptesicus fuscus, Myotis lucifugus, Perimyotis subflavus, Pseudogymnoascus destructans, bat populations, disease ecology, microbiome, white-nose syndrome",Experiment 3,United States of America,Myotis lucifugus,Skin epidermis,UBERON:0001003,Fungal infectious disease,MONDO:0002041,Batsskin swaps,Substrate (Environmental swaps),Substrate swab samples simultaneously collected from the ceiling or walls of each hibernaculum at least 10 cm from the bat species.,154,70,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure S8,21 March 2024,MyleeeA,"MyleeeA,WikiWorks",Bacterial differential abundance between bat and substrate samples.,increased,"k__Bacillati|p__Actinomycetota|c__Thermoleophilia|o__Gaiellales|f__Gaiellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae,k__Pseudomonadati|p__Nitrospirota|c__Nitrospiria|o__Nitrospirales|f__Nitrospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Syntrophobacteria|o__Syntrophobacterales|f__Syntrophobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Nevskiales|f__Nevskiaceae,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Gemmatales|f__Gemmataceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylocystaceae,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Pirellulales|f__Pirellulaceae,k__Pseudomonadati|p__Acidobacteriota|c__Terriglobia|o__Terriglobales|f__Acidobacteriaceae|s__bacterium Ellin6075",1783272|201174|1497346|1154584|1154585;3379134|1224|28211|356|45401;3379134|40117|203693|189778|189779;1783272|201174|1760|85010|2070;3379134|1224|28211|204441|41295;3379134|1224|28211|204457|41297;3379134|200940|3024408|213462|213465;3379134|1224|1236|1775403|568386;3379134|203682|203683|2691355|1914233;3379134|1224|28211|356|31993;3379134|203682|203683|2691354|2691357;3379134|57723|204432|204433|204434|234266,Complete,Svetlana up
bsdb:37888992/3/2,37888992,laboratory experiment,37888992,10.1128/spectrum.02715-23,NA,"Ange-Stark M., Parise K.L., Cheng T.L., Hoyt J.R., Langwig K.E., Frick W.F., Kilpatrick A.M., Gillece J., MacManes M.D. , Foster J.T.",White-nose syndrome restructures bat skin microbiomes,Microbiology spectrum,2023,"Eptesicus fuscus, Myotis lucifugus, Perimyotis subflavus, Pseudogymnoascus destructans, bat populations, disease ecology, microbiome, white-nose syndrome",Experiment 3,United States of America,Myotis lucifugus,Skin epidermis,UBERON:0001003,Fungal infectious disease,MONDO:0002041,Batsskin swaps,Substrate (Environmental swaps),Substrate swab samples simultaneously collected from the ceiling or walls of each hibernaculum at least 10 cm from the bat species.,154,70,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure S8,21 March 2024,MyleeeA,"MyleeeA,WikiWorks",Bacterial differential abundance between bat and substrate samples.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",3379134|1224|1236|72274|135621;3379134|1224|1236|91347|543;1783272|201174|1760|85006|1268;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|186818;1783272|1239|91061|186826|186828;1783272|1239|91061|186826|1300,Complete,Svetlana up
bsdb:37894412/1/1,37894412,case-control,37894412,10.3390/cancers15205045,NA,"Welham Z., Li J., Engel A.F. , Molloy M.P.",Mucosal Microbiome in Patients with Early Bowel Polyps: Inferences from Short-Read and Long-Read 16S rRNA Sequencing,Cancers,2023,"16S rRNA sequencing, PacBio long-read sequencing, bowel polyps, gut microbiome",Experiment 1,Australia,Homo sapiens,Colonic mucosa,UBERON:0000317,Intestinal polyp,EFO:0003855,Polyp-free control patients,Patients with low-grade colorectal polyps cohort,"Colorectal polyps were removed as standard clinical care during the colonoscopy procedure. For each polyp removed, two further 2 mm mucosal biopsies 20 mm and 50 mm adjacent to the polyp were collected.",27,27,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,"age,body mass index,sex",NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,"Figure 7a , 7c",29 November 2023,Yjung24,"Yjung24,Peace Sandy,WikiWorks",LEfSe differential abundance plot for short-read samples,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes inops,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum faecicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Flintibacter|s__Flintibacter butyricus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239|909932|1843488|909930|904|187327;3379134|976|200643|171549|171550|239759|1501391;1783272|1239|186801|3085636|3118652|2039240|2358141;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|820;1783272|201174|84998|84999|84107|102106|74426;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|1918454|1417852;1783272|1239|186801|3085636|186803|2316020|33038;3379134|976|200643|171549|2005525|375288|823;1783272|1239|186801|186802|216572|1263,Complete,Peace Sandy
bsdb:37894412/1/2,37894412,case-control,37894412,10.3390/cancers15205045,NA,"Welham Z., Li J., Engel A.F. , Molloy M.P.",Mucosal Microbiome in Patients with Early Bowel Polyps: Inferences from Short-Read and Long-Read 16S rRNA Sequencing,Cancers,2023,"16S rRNA sequencing, PacBio long-read sequencing, bowel polyps, gut microbiome",Experiment 1,Australia,Homo sapiens,Colonic mucosa,UBERON:0000317,Intestinal polyp,EFO:0003855,Polyp-free control patients,Patients with low-grade colorectal polyps cohort,"Colorectal polyps were removed as standard clinical care during the colonoscopy procedure. For each polyp removed, two further 2 mm mucosal biopsies 20 mm and 50 mm adjacent to the polyp were collected.",27,27,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,"age,body mass index,sex",NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 2,"Figure 7a , 7c",29 November 2023,Yjung24,"Yjung24,Peace Sandy,WikiWorks",LEfSe differential abundance plot for short read samples,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter faecis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Schaedlerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosacchariphilus",1783272|1239|186801|3085636|186803|207244|649756;3379134|976|200643|171549|815|816|820;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3082768|424536;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|2316020|592978;3379134|1224|28216|80840|995019|40544|40545;1783272|1239|186801|3085636|186803|2676048;1783272|1239|186801|3085636|186803|2678884,Complete,Peace Sandy
bsdb:37894412/2/1,37894412,case-control,37894412,10.3390/cancers15205045,NA,"Welham Z., Li J., Engel A.F. , Molloy M.P.",Mucosal Microbiome in Patients with Early Bowel Polyps: Inferences from Short-Read and Long-Read 16S rRNA Sequencing,Cancers,2023,"16S rRNA sequencing, PacBio long-read sequencing, bowel polyps, gut microbiome",Experiment 2,Australia,Homo sapiens,Colonic mucosa,UBERON:0000317,Intestinal polyp,EFO:0003855,Polyp-free control patients,Patients with low-grade colorectal polyps cohort,"Colorectal polyps were removed as standard clinical care during the colonoscopy procedure. For each polyp removed, two further 2 mm mucosal biopsies 20 mm and 50 mm adjacent to the polyp were collected.",27,27,1 month,16S,123456789,NA,relative abundances,LEfSe,0.05,FALSE,NA,"age,body mass index,sex",NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,"Figure 7b, 7d",29 November 2023,Yjung24,"Yjung24,Peace Sandy,WikiWorks",Pacbio Long Read LefSe differential abundance plot between polyp and no polyp specimens.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium",1783272|1239|186801|3085636|186803|2316020|33038;1783272|201174|1760|85004|31953|1678|216816;3379134|1224|28216|80840|995019|40544|40545;3379134|976|200643|171549|171552|1283313;1783272|1239|909932|1843488|909930|33024|33025,Complete,Peace Sandy
bsdb:37894412/2/2,37894412,case-control,37894412,10.3390/cancers15205045,NA,"Welham Z., Li J., Engel A.F. , Molloy M.P.",Mucosal Microbiome in Patients with Early Bowel Polyps: Inferences from Short-Read and Long-Read 16S rRNA Sequencing,Cancers,2023,"16S rRNA sequencing, PacBio long-read sequencing, bowel polyps, gut microbiome",Experiment 2,Australia,Homo sapiens,Colonic mucosa,UBERON:0000317,Intestinal polyp,EFO:0003855,Polyp-free control patients,Patients with low-grade colorectal polyps cohort,"Colorectal polyps were removed as standard clinical care during the colonoscopy procedure. For each polyp removed, two further 2 mm mucosal biopsies 20 mm and 50 mm adjacent to the polyp were collected.",27,27,1 month,16S,123456789,NA,relative abundances,LEfSe,0.05,FALSE,NA,"age,body mass index,sex",NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 2,"7b, 7d",29 November 2023,Yjung24,"Yjung24,Peace Sandy,WikiWorks",Pacbio Long Read LefSe differential abundance plot between polyp and no polyp specimens.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella nakazawae",3379134|976|200643|171549|2005525|375288|46503;1783272|1239|909932|1843489|31977|29465|2682456,Complete,Peace Sandy
bsdb:37900322/1/1,37900322,case-control,37900322,10.3389/fcimb.2023.1227581,NA,"Zhan D., Li D., Yuan K., Sun Y., He L., Zhong J. , Wang L.",Characteristics of the pulmonary microbiota in patients with mild and severe pulmonary infection,Frontiers in cellular and infection microbiology,2023,"pulmonary infection, biomarker, network, pulmonary microbiota, severity",Experiment 1,China,Homo sapiens,Sputum,UBERON:0007311,Abnormal lung morphology,HP:0002088,mild group,severe group,Patients who were at least 18 years of age with pulmonary infection.,140,80,NA,PCR,NA,MGISEQ-2000,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 4A,8 August 2025,Nuerteye,Nuerteye,"Bacterial biomarkers were identified by linear discriminant analysis effect size (LEfSe) algorithm. (A) Bacterial histograms of unique biomarkers based
on LEfSe (>2). The length of the bar chart represents the magnitude of the impact of significantly different genus.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Luteipulveratus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Steroidobacterales|f__Steroidobacteraceae|g__Steroidobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Bhargavaea,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella",1783272|201174|1760|85006|145357|745364;3379134|1224|1236|3060226|2689614|469322;1783272|1239|91061|1385|186818|941338;1783272|201174|84998|84999|1643824|133925,Complete,NA
bsdb:37900322/1/2,37900322,case-control,37900322,10.3389/fcimb.2023.1227581,NA,"Zhan D., Li D., Yuan K., Sun Y., He L., Zhong J. , Wang L.",Characteristics of the pulmonary microbiota in patients with mild and severe pulmonary infection,Frontiers in cellular and infection microbiology,2023,"pulmonary infection, biomarker, network, pulmonary microbiota, severity",Experiment 1,China,Homo sapiens,Sputum,UBERON:0007311,Abnormal lung morphology,HP:0002088,mild group,severe group,Patients who were at least 18 years of age with pulmonary infection.,140,80,NA,PCR,NA,MGISEQ-2000,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 4A,9 August 2025,Nuerteye,Nuerteye,Bacterial biomarkers were identified by linear discriminant analysis effect size (LEfSe) algorithm. (A) Bacterial histograms of unique biomarkers based on LEfSe (>2). The length of the bar chart represents the magnitude of the impact of significantly different genus.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium",3379134|976|117743|200644|2762318|501783;3379134|1224|28216|80840|119060|1822464;3379134|1224|28211|356|69277|68287;3379134|1224|1236|135623|641|657;3379134|1224|1236|91347|543|413496;1783272|201174|1760|85007|1762|1763,Complete,NA
bsdb:37905804/1/1,37905804,case-control,37905804,10.1128/spectrum.02368-23,NA,"Nath S., Sarkar M., Maddheshiya A., De D., Paul S., Dey S., Pal K., Roy S.K., Ghosh A., Sengupta S., Paine S.K., Biswas N.K., Basu A. , Mukherjee S.",Upper respiratory tract microbiome profiles in SARS-CoV-2 Delta and Omicron infected patients exhibit variant specific patterns and robust prediction of disease groups,Microbiology spectrum,2023,"COVID-19, Delta, Omicron, URT, microbiome, next generation sequencing",Experiment 1,India,Homo sapiens,Upper respiratory tract,UBERON:0001557,SARS-CoV-2-related disease,MONDO:0100318,Healthy Controls,COVID-19 patients,Patients infected with COVID-19 virus (Delta and Omicron),19,43,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,FIG 2,12 March 2024,ModinatG,"ModinatG,Folakunmi,WikiWorks",LEfSe analysis of core  species of COVID-19 patients and healthy controls.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae|g__Pseudoalteromonas|s__Pseudoalteromonas shioyasakiensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae|g__Pseudoalteromonas|s__Pseudoalteromonas gelatinilytica,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum|s__Ochrobactrum sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus caprae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae|g__Rheinheimera|s__Rheinheimera pleomorphica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio tritonius,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Vreelandella|s__Vreelandella piezotolerans,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Pelagibacterium|s__Pelagibacterium halotolerans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa",3379134|1224|1236|135614|32033|40323|40324;3379134|1224|1236|135622|267888|53246|1190813;3379134|1224|1236|135622|267888|53246|1703256;3379134|1224|28211|356|118882|528|42190;3379134|1224|1236|135614|32033|40323|69392;3379134|1224|1236|72274|135621|286|306;1783272|1239|91061|1385|90964|1279|29380;3379134|1224|1236|135613|1046|67575|2703963;3379134|1224|1236|135623|641|662|1435069;3379134|976|117743|200644|2762318|59732|1871047;3379134|1224|1236|135619|28256|3137766|2609667;3379134|1224|28211|356|2831106|1082930|531813;3379134|1224|1236|72274|135621|286|287,Complete,Folakunmi
bsdb:37905804/1/2,37905804,case-control,37905804,10.1128/spectrum.02368-23,NA,"Nath S., Sarkar M., Maddheshiya A., De D., Paul S., Dey S., Pal K., Roy S.K., Ghosh A., Sengupta S., Paine S.K., Biswas N.K., Basu A. , Mukherjee S.",Upper respiratory tract microbiome profiles in SARS-CoV-2 Delta and Omicron infected patients exhibit variant specific patterns and robust prediction of disease groups,Microbiology spectrum,2023,"COVID-19, Delta, Omicron, URT, microbiome, next generation sequencing",Experiment 1,India,Homo sapiens,Upper respiratory tract,UBERON:0001557,SARS-CoV-2-related disease,MONDO:0100318,Healthy Controls,COVID-19 patients,Patients infected with COVID-19 virus (Delta and Omicron),19,43,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,FIG 2,12 March 2024,ModinatG,"ModinatG,Folakunmi,WikiWorks",Relative abundances of bacteria in upper respiratory tract (URT) of Covid-19 patients and healthy group,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium pseudoperiodonticum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria perflava,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus symci,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella nakazawae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella tobetsuensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus|s__Actinobacillus sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium accolens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella equi,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus toyakuensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia wadei,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica",1783272|201174|1760|85004|31953|1678|216816;3384189|32066|203490|203491|203492|848|2663009;3379134|1224|1236|135625|712|724|729;3379134|1224|28216|206351|481|482|33053;3379134|976|200643|171549|171552|838|28132;1783272|1239|91061|186826|1300|1301|2588991;1783272|1239|909932|1843489|31977|29465|2682456;1783272|1239|909932|1843489|31977|29465|1110546;3379134|1224|1236|135625|712|713|41114;1783272|201174|1760|85007|1653|1716|38284;3379134|1224|1236|2887326|468|475|60442;1783272|1239|91061|186826|1300|1301|2819619;1783272|1239|909932|1843489|31977|29465|423477;3379134|1224|28216|206351|481|482|28449;3384189|32066|203490|203491|1129771|32067|157687;1783272|1239|909932|1843489|31977|29465|39777,Complete,Folakunmi
bsdb:37905804/2/1,37905804,case-control,37905804,10.1128/spectrum.02368-23,NA,"Nath S., Sarkar M., Maddheshiya A., De D., Paul S., Dey S., Pal K., Roy S.K., Ghosh A., Sengupta S., Paine S.K., Biswas N.K., Basu A. , Mukherjee S.",Upper respiratory tract microbiome profiles in SARS-CoV-2 Delta and Omicron infected patients exhibit variant specific patterns and robust prediction of disease groups,Microbiology spectrum,2023,"COVID-19, Delta, Omicron, URT, microbiome, next generation sequencing",Experiment 2,India,Homo sapiens,Upper respiratory tract,UBERON:0001557,SARS-CoV-2-related disease,MONDO:0100318,Healthy Controls,Delta and Omicron-infected patients,Patients infected with the Delta and Omicron variants of  SARS-CoV-2,19,43,1 month,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,FIG 6,14 March 2024,ModinatG,"ModinatG,Folakunmi,WikiWorks","Taxonomic difference among healthy controls, Delta-, and Omicron-infected patients.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria perflava,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium pseudoperiodonticum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella nakazawae",3379134|1224|1236|135625|712|724|729;3379134|1224|28216|206351|481|482|33053;3384189|32066|203490|203491|203492|848|2663009;3379134|1224|28216|206351|481|482|28449;1783272|1239|909932|1843489|31977|29465|423477;1783272|1239|909932|1843489|31977|29465|2682456,Complete,Folakunmi
bsdb:37905804/3/1,37905804,case-control,37905804,10.1128/spectrum.02368-23,NA,"Nath S., Sarkar M., Maddheshiya A., De D., Paul S., Dey S., Pal K., Roy S.K., Ghosh A., Sengupta S., Paine S.K., Biswas N.K., Basu A. , Mukherjee S.",Upper respiratory tract microbiome profiles in SARS-CoV-2 Delta and Omicron infected patients exhibit variant specific patterns and robust prediction of disease groups,Microbiology spectrum,2023,"COVID-19, Delta, Omicron, URT, microbiome, next generation sequencing",Experiment 3,India,Homo sapiens,Upper respiratory tract,UBERON:0001557,SARS-CoV-2-related disease,MONDO:0100318,Omicron-infected patients,Delta-infected patients,Patients infected with Delta virus,19,24,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,FIG 5,12 March 2024,ModinatG,"ModinatG,WikiWorks",Upper respiratory tract (URT) microbiome composition between Delta and Omicron infected patients.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter kobei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter mori,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter quasihormaechei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella quasipneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella variicola,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus toyakuensis",3379134|1224|1236|2887326|468|469|470;3379134|976|117743|200644|2762318|59732|1871047;3379134|1224|1236|91347|543|547|208224;3379134|1224|1236|91347|543|547|539813;3379134|1224|1236|91347|543|547|2529382;3379134|1224|1236|91347|543|570|573;3379134|1224|1236|91347|543|570|1463165;3379134|1224|1236|91347|543|570|244366;3379134|1224|1236|135614|32033|40323|69392;1783272|1239|91061|186826|1300|1301|2819619,Complete,Folakunmi
bsdb:37905804/3/2,37905804,case-control,37905804,10.1128/spectrum.02368-23,NA,"Nath S., Sarkar M., Maddheshiya A., De D., Paul S., Dey S., Pal K., Roy S.K., Ghosh A., Sengupta S., Paine S.K., Biswas N.K., Basu A. , Mukherjee S.",Upper respiratory tract microbiome profiles in SARS-CoV-2 Delta and Omicron infected patients exhibit variant specific patterns and robust prediction of disease groups,Microbiology spectrum,2023,"COVID-19, Delta, Omicron, URT, microbiome, next generation sequencing",Experiment 3,India,Homo sapiens,Upper respiratory tract,UBERON:0001557,SARS-CoV-2-related disease,MONDO:0100318,Omicron-infected patients,Delta-infected patients,Patients infected with Delta virus,19,24,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,FIG 5,12 March 2024,ModinatG,"ModinatG,WikiWorks",Upper respiratory tract (URT) microbiome composition between Delta and Omicron infected patients.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria perflava,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum|s__Ochrobactrum sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Pelagibacterium|s__Pelagibacterium halotolerans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus caprae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus ilei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus symci,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella nakazawae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella tobetsuensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio tritonius",3379134|1224|28216|206351|481|482|33053;3379134|1224|28211|356|118882|528|42190;3379134|1224|28211|356|2831106|1082930|531813;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|171551|836|1583331;3379134|976|200643|171549|171552|838|28132;3379134|1224|1236|72274|135621|286|287;3379134|1224|1236|72274|135621|286|306;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|1385|90964|1279|29380;1783272|1239|91061|186826|1300|1301|1156431;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|1300|1301|2588991;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843489|31977|29465|2682456;1783272|1239|909932|1843489|31977|29465|1110546;3379134|1224|1236|135623|641|662|1435069,Complete,Folakunmi
bsdb:37919319/1/1,37919319,"cross-sectional observational, not case-control",37919319,10.1038/s41598-023-42474-7,NA,"Antonello G., Blostein F., Bhaumik D., Davis E., Gögele M., Melotti R., Pramstaller P., Pattaro C., Segata N., Foxman B. , Fuchsberger C.",Smoking and salivary microbiota: a cross-sectional analysis of an Italian alpine population,Scientific reports,2023,NA,Experiment 1,Italy,Homo sapiens,Mouth,UBERON:0000165,Smoking status measurement,EFO:0006527,Never smokers,Current smokers,Individuals who reported being smokers at the day of examination with daily smoking intensity at least 1 month prior to the visit.,880,326,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,number of teeth measurement,sex",NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 1,figure 1,7 November 2023,OdigiriGreat,"OdigiriGreat,Folakunmi,WikiWorks",Heatmap of the 44 genera diferentially abundant between Current and Never smokers,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Cryptobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__uncultured Peptostreptococcus sp.",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85004|31953|419014;1783272|201174|84998|84999|1643824|1380;3379134|976|200643;1783272|201174|1760|85004|31953|1678;1783272|1239|526524|526525|128827|118747;1783272|201174|84998|1643822|1643826|84162;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3082720|3118655|44259;3384194|508458|649775|649776|3029087|1434006;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|909929|1843491|52225;1783272|544448|31969|2085|2092|2093;33090|35493|3398|72025|3803|3814|508215;1783272|1239|186801|3085636|186803|1213720;3379134|203691|203692|136|2845253|157;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|3082720|186804|1257|169971,Complete,Folakunmi
bsdb:37919319/1/2,37919319,"cross-sectional observational, not case-control",37919319,10.1038/s41598-023-42474-7,NA,"Antonello G., Blostein F., Bhaumik D., Davis E., Gögele M., Melotti R., Pramstaller P., Pattaro C., Segata N., Foxman B. , Fuchsberger C.",Smoking and salivary microbiota: a cross-sectional analysis of an Italian alpine population,Scientific reports,2023,NA,Experiment 1,Italy,Homo sapiens,Mouth,UBERON:0000165,Smoking status measurement,EFO:0006527,Never smokers,Current smokers,Individuals who reported being smokers at the day of examination with daily smoking intensity at least 1 month prior to the visit.,880,326,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,number of teeth measurement,sex",NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 2,figure 1,7 November 2023,OdigiriGreat,"OdigiriGreat,Folakunmi,WikiWorks",Result of the Heatmap of the 44 genera diferentially abundant between Current and Never smokers.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,p__Candidatus Absconditibacteriota,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ottowia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__uncultured Peptostreptococcus sp.,p__Candidatus Altimarinota",1783272|1239|91061|186826|186827|46123;3379134|1224|1236|135625|712|416916;3379134|976|200643|171549|171552|1283313;3379134|976|117743|200644|2762318|59735;221235;3379134|976|117743|200644|49546|1016;3379134|1224|1236|135615|868|2717;1783272|1239|186801|3085636|186803|43996;3384189|32066|203490|203491|203492|848;3379134|1224|1236|135625|712|724;3379134|1224|28216|206351|481|32257;3379134|1224|28216|80840|119060|47670;3384189|32066|203490|203491|1129771|32067;3379134|1224|28216|206351|481|482;3379134|1224|28216|80840|80864|219181;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836;1783272|1239|186801|3085636|186803|297314;1783272|1239|186801|3082720|186804|1257|169971;363464,Complete,Folakunmi
bsdb:37919319/2/NA,37919319,"cross-sectional observational, not case-control",37919319,10.1038/s41598-023-42474-7,NA,"Antonello G., Blostein F., Bhaumik D., Davis E., Gögele M., Melotti R., Pramstaller P., Pattaro C., Segata N., Foxman B. , Fuchsberger C.",Smoking and salivary microbiota: a cross-sectional analysis of an Italian alpine population,Scientific reports,2023,NA,Experiment 2,Italy,Homo sapiens,Mouth,UBERON:0000165,Smoking status measurement,EFO:0006527,Never smokers,Former smokers,Individuals who quit smoking 17.96 years on average,880,395,2 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,number of teeth measurement,sex",NA,unchanged,unchanged,NA,unchanged,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:37924005/1/1,37924005,case-control,37924005,10.1186/s12866-023-03071-w,NA,"Chen L., Mou X., Li J., Li M., Ye C., Gao X., Liu X., Ma Y., Xu Y. , Zhong Y.",Alterations in gut microbiota and host transcriptome of patients with coronary artery disease,BMC microbiology,2023,"Biomarkers, Coronary artery disease, Gut microbe, Risk genes, Transcriptome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Coronary artery disease,EFO:0001645,Healthy controls,Patient with coronary artery disease,patients with coronary artery disease between the age of 25 - 80 years and show greater than 70% stenosis in at least one major branch of the coronary artery.,21,31,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,figure 2 & supplementary figure S1,22 March 2024,Idiaru angela,"Idiaru angela,Scholastica,WikiWorks",Differential abundance of gut microbiota between coronary artery disease patients and controls at all taxa levels,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus rubiinfantis,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium CCNA10,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister propionicifaciens,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Fructilactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium GAM79,k__Bacillati|p__Bacillota|g__Negativibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii",1783272|201174|1760|2037|2049|1654|1655;1783272|1239|186801|186802|216572|244127|1720200;1783272|1239|186801;1783272|1239|186801|186802|2109688;1783272|1239|186801|186802|1980681;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|909932|1843489|31977|39948|308994;1783272|1239|526524|526525|128827|1573534;1783272|1239|91061|186826|33958|2767881;1783272|1239|186801|3085636|186803|2109691;1783272|1239|1980693;1783272|1239|186801|186802|216572;1783272|1239|1737404|1737405|1570339|162289;3379134|976|200643|171549|171551|836|281920;3379134|1224|28211|356|82115;1783272|1239|526524|526525|128827|123375;1783272|1239|526524|526525|128827|123375|102148;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|3085636|186803|2569097|39488,Complete,Svetlana up
bsdb:37924005/1/2,37924005,case-control,37924005,10.1186/s12866-023-03071-w,NA,"Chen L., Mou X., Li J., Li M., Ye C., Gao X., Liu X., Ma Y., Xu Y. , Zhong Y.",Alterations in gut microbiota and host transcriptome of patients with coronary artery disease,BMC microbiology,2023,"Biomarkers, Coronary artery disease, Gut microbe, Risk genes, Transcriptome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Coronary artery disease,EFO:0001645,Healthy controls,Patient with coronary artery disease,patients with coronary artery disease between the age of 25 - 80 years and show greater than 70% stenosis in at least one major branch of the coronary artery.,21,31,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,figure 2 & supplementary figure S1,23 March 2024,Idiaru angela,"Idiaru angela,WikiWorks",Differential abundance of gut microbiota between coronary artery disease patients and controls at all taxa levels,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium limosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|186806;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|186806|1730|1736;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085656|3085657;1783272|1239|186801|3085656;1783272|1239|186801|3085656|3085657|2039302;3379134|976|200643|171549|2005525|375288|46503,Complete,Svetlana up
bsdb:37925571/1/1,37925571,"cross-sectional observational, not case-control",37925571,10.1038/s41598-023-46566-2,NA,"He J., Gong X., Hu B., Lin L., Lin X., Gong W., Zhang B., Cao M., Xu Y., Xia R., Zheng G., Wu S. , Zhang Y.",Altered Gut Microbiota and Short-chain Fatty Acids in Chinese Children with Constipated Autism Spectrum Disorder,Scientific reports,2023,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Typically developing (TD) group,Constipated autism spectrum disorder (C-ASD) group,Children with autism spectrum disorder (ASD) while also experiencing constipation as an important gastrointestinal (GI) comorbidity.,40,40,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,body mass index,sex",NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Figure 3,7 November 2023,Deacme,"Deacme,Folakunmi,WikiWorks",Discriminative taxa between the typically developing (TD) group and constipated autism spectrum disorder (C-ASD) group  derived from LeFse analysis.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptoclostridiaceae|g__Peptoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",3379134|976|200643|171549|2005519|397864;1783272|1239|526524|526525|128827|1470349;3379134|1224|28216|80840|80864|283;3379134|976|200643|171549|2005519|1348911;1783272|1239|186801|3085636|186803|33042;3379134|200940|3031449|213115|194924|872;1783272|201174|84998|84999|84107|1472762;3384189|32066|203490|203491|203492|848;1783272|1239|909932|909929|1843491|158846;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|577309;1783272|1239|186801|3082720|3120161|1481960;1783272|1239|186801|186802|186807|2740;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|186802|216572|1508657;3379134|256845|1313211|278082|255528|172900;1783272|1239|186801|186802|216572|707003;1783272|1239|526524|526525|128827,Complete,Folakunmi
bsdb:37925571/1/2,37925571,"cross-sectional observational, not case-control",37925571,10.1038/s41598-023-46566-2,NA,"He J., Gong X., Hu B., Lin L., Lin X., Gong W., Zhang B., Cao M., Xu Y., Xia R., Zheng G., Wu S. , Zhang Y.",Altered Gut Microbiota and Short-chain Fatty Acids in Chinese Children with Constipated Autism Spectrum Disorder,Scientific reports,2023,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Typically developing (TD) group,Constipated autism spectrum disorder (C-ASD) group,Children with autism spectrum disorder (ASD) while also experiencing constipation as an important gastrointestinal (GI) comorbidity.,40,40,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,body mass index,sex",NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,Figure 3,7 November 2023,Deacme,"Deacme,Folakunmi,WikiWorks",Discriminative taxa between the typically developing (TD) group and constipated autism spectrum disorder (C-ASD) group derived from LeFse analysis.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Listeria,k__Bacillati|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae|g__Longilinea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Sphaerochaetaceae|g__Sphaerochaeta,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] brachy,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",1783272|1239|91061|186826|186827|1375;1783272|1239|186801|3085636|186803|207244;1783272|201174|1760|85007|1653|1716;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|877420;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|1385|186820|1637;1783272|200795|292625|292629|292628|475961;1783272|1239|186801|3085636|186803|248744;3379134|1224|28211|356|119045|407;1783272|201174|1760|85006|85023|33882;3379134|976|200643|171549|171552|838;3379134|1224|1236|72274|135621|286;3379134|1224|28216|80840|119060|48736;1783272|1239|186801|186802|216572|1263;3379134|203691|203692|136|2791015|399320;1783272|1239|91061|1385|90964|1279;1783272|1239|526524|526525|2810280|3025755;3379134|203691|203692|136|2845253|157;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|3082720|543314|35517;1783272|1239|186801|3085636|186803|2316020|33038;1783272|201174|84998|84999|84107;1783272|1239|526524|526525|128827;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171552,Complete,Folakunmi
bsdb:37926855/1/1,37926855,laboratory experiment,37926855,https://doi.org/10.1186/s40168-023-01691-y,NA,"Minnebo Y., Delbaere K., Goethals V., Raes J., Van de Wiele T. , De Paepe K.","Gut microbiota response to in vitro transit time variation is mediated by microbial growth rates, nutrient use efficiency and adaptation to in vivo transit time",Microbiome,2023,"Gastrointestinal transit, Gut microbial ecology, Gut residence time, Gut retention time, Personalised gut microbiome research, Quantitative microbiome profiling, SHIME in vitro gut simulator",Experiment 1,Belgium,Homo sapiens,Feces,UBERON:0001988,Increased intestinal transit time,HP:0410204,Short Transit Time (Proximal colon),Long Transit Time (Proximal colon),Proximal colon sample from SHIME model simulating long transit time (24hours),6,6,6 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,diet,health,life style,physical activity,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table S10,23 March 2025,Vanisha1606,"Vanisha1606,Anne-mariesharp",Significant differences of bacterial taxa between transit times in proximal colon,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|976|200643|171549|815|816;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|838,Complete,KateRasheed
bsdb:37926855/1/2,37926855,laboratory experiment,37926855,https://doi.org/10.1186/s40168-023-01691-y,NA,"Minnebo Y., Delbaere K., Goethals V., Raes J., Van de Wiele T. , De Paepe K.","Gut microbiota response to in vitro transit time variation is mediated by microbial growth rates, nutrient use efficiency and adaptation to in vivo transit time",Microbiome,2023,"Gastrointestinal transit, Gut microbial ecology, Gut residence time, Gut retention time, Personalised gut microbiome research, Quantitative microbiome profiling, SHIME in vitro gut simulator",Experiment 1,Belgium,Homo sapiens,Feces,UBERON:0001988,Increased intestinal transit time,HP:0410204,Short Transit Time (Proximal colon),Long Transit Time (Proximal colon),Proximal colon sample from SHIME model simulating long transit time (24hours),6,6,6 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,diet,health,life style,physical activity,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table S10,23 March 2025,Vanisha1606,"Vanisha1606,Anne-mariesharp",Significant differences of bacterial taxa between transit times in proximal colon,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|85004|31953|1678;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803|841;3379134|1224|1236|135614|32033|40323;1783272|1239|909932|1843489|31977|29465,Complete,KateRasheed
bsdb:37926855/2/1,37926855,laboratory experiment,37926855,https://doi.org/10.1186/s40168-023-01691-y,NA,"Minnebo Y., Delbaere K., Goethals V., Raes J., Van de Wiele T. , De Paepe K.","Gut microbiota response to in vitro transit time variation is mediated by microbial growth rates, nutrient use efficiency and adaptation to in vivo transit time",Microbiome,2023,"Gastrointestinal transit, Gut microbial ecology, Gut residence time, Gut retention time, Personalised gut microbiome research, Quantitative microbiome profiling, SHIME in vitro gut simulator",Experiment 2,Belgium,Homo sapiens,Feces,UBERON:0001988,Increased intestinal transit time,HP:0410204,Short Transit Time (Proximal colon),Medium Transit Time (Proximal colon),Proximal colon sample from SHIME model simulating medium transit time (16hours),6,6,6 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,diet,health,life style,physical activity,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table S10,16 July 2025,Anne-mariesharp,Anne-mariesharp,Significant differences of bacterial taxa between transit times in proximal colon,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",1783272|1239|909932|1843489|31977|156454;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;3384194|508458|649775|649776|649777|508459;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|2005525|375288,Complete,KateRasheed
bsdb:37926855/2/2,37926855,laboratory experiment,37926855,https://doi.org/10.1186/s40168-023-01691-y,NA,"Minnebo Y., Delbaere K., Goethals V., Raes J., Van de Wiele T. , De Paepe K.","Gut microbiota response to in vitro transit time variation is mediated by microbial growth rates, nutrient use efficiency and adaptation to in vivo transit time",Microbiome,2023,"Gastrointestinal transit, Gut microbial ecology, Gut residence time, Gut retention time, Personalised gut microbiome research, Quantitative microbiome profiling, SHIME in vitro gut simulator",Experiment 2,Belgium,Homo sapiens,Feces,UBERON:0001988,Increased intestinal transit time,HP:0410204,Short Transit Time (Proximal colon),Medium Transit Time (Proximal colon),Proximal colon sample from SHIME model simulating medium transit time (16hours),6,6,6 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,diet,health,life style,physical activity,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table S10,16 July 2025,Anne-mariesharp,Anne-mariesharp,Significant differences of bacterial taxa between transit times in proximal colon,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|85004|31953|1678;1783272|201174|84998|84999|84107|102106;3379134|1224|1236|135614|32033|40323;1783272|1239|909932|1843489|31977|29465,Complete,KateRasheed
bsdb:37926855/3/1,37926855,laboratory experiment,37926855,https://doi.org/10.1186/s40168-023-01691-y,NA,"Minnebo Y., Delbaere K., Goethals V., Raes J., Van de Wiele T. , De Paepe K.","Gut microbiota response to in vitro transit time variation is mediated by microbial growth rates, nutrient use efficiency and adaptation to in vivo transit time",Microbiome,2023,"Gastrointestinal transit, Gut microbial ecology, Gut residence time, Gut retention time, Personalised gut microbiome research, Quantitative microbiome profiling, SHIME in vitro gut simulator",Experiment 3,Belgium,Homo sapiens,Feces,UBERON:0001988,Increased intestinal transit time,HP:0410204,Medium Transit Time (Proximal colon),Long Transit Time (Proximal colon),Proximal colon sample from SHIME model simulating long transit time (24hours),6,6,6 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,diet,health,life style,physical activity,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table S10,16 July 2025,Anne-mariesharp,Anne-mariesharp,Significant differences of bacterial taxa between transit times in proximal colon,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|909932|1843489|31977|39948;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|838,Complete,KateRasheed
bsdb:37926855/3/2,37926855,laboratory experiment,37926855,https://doi.org/10.1186/s40168-023-01691-y,NA,"Minnebo Y., Delbaere K., Goethals V., Raes J., Van de Wiele T. , De Paepe K.","Gut microbiota response to in vitro transit time variation is mediated by microbial growth rates, nutrient use efficiency and adaptation to in vivo transit time",Microbiome,2023,"Gastrointestinal transit, Gut microbial ecology, Gut residence time, Gut retention time, Personalised gut microbiome research, Quantitative microbiome profiling, SHIME in vitro gut simulator",Experiment 3,Belgium,Homo sapiens,Feces,UBERON:0001988,Increased intestinal transit time,HP:0410204,Medium Transit Time (Proximal colon),Long Transit Time (Proximal colon),Proximal colon sample from SHIME model simulating long transit time (24hours),6,6,6 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,diet,health,life style,physical activity,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table S10,16 July 2025,Anne-mariesharp,Anne-mariesharp,Significant differences of bacterial taxa between transit times in proximal colon,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",1783272|1239|909932|1843489|31977|156454;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572;3379134|1224|1236|135614|32033|40323,Complete,KateRasheed
bsdb:37926855/4/1,37926855,laboratory experiment,37926855,https://doi.org/10.1186/s40168-023-01691-y,NA,"Minnebo Y., Delbaere K., Goethals V., Raes J., Van de Wiele T. , De Paepe K.","Gut microbiota response to in vitro transit time variation is mediated by microbial growth rates, nutrient use efficiency and adaptation to in vivo transit time",Microbiome,2023,"Gastrointestinal transit, Gut microbial ecology, Gut residence time, Gut retention time, Personalised gut microbiome research, Quantitative microbiome profiling, SHIME in vitro gut simulator",Experiment 4,Belgium,Homo sapiens,Feces,UBERON:0001988,Increased intestinal transit time,HP:0410204,Short Transit Time (Distal colon),Long Transit Time (Distal colon),Distal colon sample from SHIME model simulating long transit time (39hours),6,6,6 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,diet,health,life style,physical activity,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table S10,17 July 2025,Anne-mariesharp,Anne-mariesharp,Significant differences of bacterial taxa between transit times in distal colon,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|976|200643|171549|815|816;3384194|508458|649775|649776|649777|508459;1783272|1239|909932|1843489|31977|39948;3379134|976|200643|171549|2005525|375288;3379134|1224|1236|72274|135621|286;3379134|1224|28216|80840|995019|40544,Complete,KateRasheed
bsdb:37926855/4/2,37926855,laboratory experiment,37926855,https://doi.org/10.1186/s40168-023-01691-y,NA,"Minnebo Y., Delbaere K., Goethals V., Raes J., Van de Wiele T. , De Paepe K.","Gut microbiota response to in vitro transit time variation is mediated by microbial growth rates, nutrient use efficiency and adaptation to in vivo transit time",Microbiome,2023,"Gastrointestinal transit, Gut microbial ecology, Gut residence time, Gut retention time, Personalised gut microbiome research, Quantitative microbiome profiling, SHIME in vitro gut simulator",Experiment 4,Belgium,Homo sapiens,Feces,UBERON:0001988,Increased intestinal transit time,HP:0410204,Short Transit Time (Distal colon),Long Transit Time (Distal colon),Distal colon sample from SHIME model simulating long transit time (39hours),6,6,6 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,diet,health,life style,physical activity,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table S10,17 July 2025,Anne-mariesharp,Anne-mariesharp,Significant differences of bacterial taxa between transit times in distal colon,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|85004|31953|1678;1783272|201174|84998|84999|84107|102106;3379134|1224|1236|91347|543;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|841;3379134|1224|1236|135614|32033|40323;1783272|1239|909932|1843489|31977|29465,Complete,KateRasheed
bsdb:37926855/5/1,37926855,laboratory experiment,37926855,https://doi.org/10.1186/s40168-023-01691-y,NA,"Minnebo Y., Delbaere K., Goethals V., Raes J., Van de Wiele T. , De Paepe K.","Gut microbiota response to in vitro transit time variation is mediated by microbial growth rates, nutrient use efficiency and adaptation to in vivo transit time",Microbiome,2023,"Gastrointestinal transit, Gut microbial ecology, Gut residence time, Gut retention time, Personalised gut microbiome research, Quantitative microbiome profiling, SHIME in vitro gut simulator",Experiment 5,Belgium,Homo sapiens,Feces,UBERON:0001988,Increased intestinal transit time,HP:0410204,Short Transit Time (Distal colon),Medium Transit Time (Distal colon),Distal colon sample from SHIME model simulating medium transit time (26hours),6,6,6 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,diet,health,life style,physical activity,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table S10,17 July 2025,Anne-mariesharp,Anne-mariesharp,Significant differences of bacterial taxa between transit times in distal colon,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|976|200643|171549|171550|239759;1783272|1239|909932|1843489|31977|156454;3379134|976|200643|171549|815|816;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;3379134|1224|1236|72274|135621|286;3379134|1224|28216|80840|995019|40544,Complete,KateRasheed
bsdb:37926855/5/2,37926855,laboratory experiment,37926855,https://doi.org/10.1186/s40168-023-01691-y,NA,"Minnebo Y., Delbaere K., Goethals V., Raes J., Van de Wiele T. , De Paepe K.","Gut microbiota response to in vitro transit time variation is mediated by microbial growth rates, nutrient use efficiency and adaptation to in vivo transit time",Microbiome,2023,"Gastrointestinal transit, Gut microbial ecology, Gut residence time, Gut retention time, Personalised gut microbiome research, Quantitative microbiome profiling, SHIME in vitro gut simulator",Experiment 5,Belgium,Homo sapiens,Feces,UBERON:0001988,Increased intestinal transit time,HP:0410204,Short Transit Time (Distal colon),Medium Transit Time (Distal colon),Distal colon sample from SHIME model simulating medium transit time (26hours),6,6,6 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,diet,health,life style,physical activity,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table S10,17 July 2025,Anne-mariesharp,Anne-mariesharp,Significant differences of bacterial taxa between transit times in distal colon,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|85004|31953|1678;1783272|201174|84998|84999|84107|102106;1783272|1239|909932|1843489|31977|29465,Complete,KateRasheed
bsdb:37926855/6/1,37926855,laboratory experiment,37926855,https://doi.org/10.1186/s40168-023-01691-y,NA,"Minnebo Y., Delbaere K., Goethals V., Raes J., Van de Wiele T. , De Paepe K.","Gut microbiota response to in vitro transit time variation is mediated by microbial growth rates, nutrient use efficiency and adaptation to in vivo transit time",Microbiome,2023,"Gastrointestinal transit, Gut microbial ecology, Gut residence time, Gut retention time, Personalised gut microbiome research, Quantitative microbiome profiling, SHIME in vitro gut simulator",Experiment 6,Belgium,Homo sapiens,Feces,UBERON:0001988,Increased intestinal transit time,HP:0410204,Medium Transit Time (Distal colon),Long Transit Time (Distal colon),Distal colon sample from SHIME model simulating long transit time (39hours),6,6,6 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,diet,health,life style,physical activity,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table S10,17 July 2025,Anne-mariesharp,Anne-mariesharp,Significant differences of bacterial taxa between transit times in distal colon,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,KateRasheed
bsdb:37926855/6/2,37926855,laboratory experiment,37926855,https://doi.org/10.1186/s40168-023-01691-y,NA,"Minnebo Y., Delbaere K., Goethals V., Raes J., Van de Wiele T. , De Paepe K.","Gut microbiota response to in vitro transit time variation is mediated by microbial growth rates, nutrient use efficiency and adaptation to in vivo transit time",Microbiome,2023,"Gastrointestinal transit, Gut microbial ecology, Gut residence time, Gut retention time, Personalised gut microbiome research, Quantitative microbiome profiling, SHIME in vitro gut simulator",Experiment 6,Belgium,Homo sapiens,Feces,UBERON:0001988,Increased intestinal transit time,HP:0410204,Medium Transit Time (Distal colon),Long Transit Time (Distal colon),Distal colon sample from SHIME model simulating long transit time (39hours),6,6,6 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,body mass index,diet,health,life style,physical activity,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table S10,17 July 2025,Anne-mariesharp,Anne-mariesharp,Significant differences of bacterial taxa between transit times in distal colon,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",3379134|976|200643|171549|171550|239759;1783272|1239|909932|1843489|31977|156454;1783272|1239|186801|186802;1783272|201174|84998|84999|84107|102106;3379134|1224|1236|91347|543;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572;3379134|1224|1236|135614|32033|40323,Complete,KateRasheed
bsdb:37936065/1/1,37936065,laboratory experiment,37936065,10.1186/s12866-023-03079-2,NA,"Li Z., Cui R., Wang Y.B., Luo Y.B., Xue P.X., Tang Q.G. , Fang M.Y.",Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle,BMC microbiology,2023,"16S rDNA, Gut microbiota, Metagenomics, Tan sheep",Experiment 1,China,Ovis aries,Rumen,UBERON:0007365,Breed,EFO:0005238,Rumen of Dorper sheep (D_R),Rumen of Tan Sheep (T_R),"Rumen of Tan sheep bred in Ningxia, China",4,4,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 3A,11 April 2024,Scholastica,"Scholastica,WikiWorks",LEfSe analysis of ruminal microbiota in Tan sheep versus Dorper sheep from metagenomic data at the species level.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter|s__Achromobacter xylosoxidans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Mageeibacillus|s__Mageeibacillus indolicus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. PEA192,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Stutzerimonas|s__Stutzerimonas stutzeri",3379134|1224|28216|80840|506|222|85698;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|186802|216572|1637257|884684;1783272|1239|186801|186802|216572|459786|2109687;3379134|1224|1236|135614|32033|40323|40324;3379134|1224|1236|72274|135621|2901164|316,Complete,Svetlana up
bsdb:37936065/1/2,37936065,laboratory experiment,37936065,10.1186/s12866-023-03079-2,NA,"Li Z., Cui R., Wang Y.B., Luo Y.B., Xue P.X., Tang Q.G. , Fang M.Y.",Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle,BMC microbiology,2023,"16S rDNA, Gut microbiota, Metagenomics, Tan sheep",Experiment 1,China,Ovis aries,Rumen,UBERON:0007365,Breed,EFO:0005238,Rumen of Dorper sheep (D_R),Rumen of Tan Sheep (T_R),"Rumen of Tan sheep bred in Ningxia, China",4,4,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 3A,11 April 2024,Scholastica,"Scholastica,WikiWorks",LEfSe analysis of ruminal microbiota in Tan sheep versus Dorper sheep from metagenomic data at the species level.,decreased,"k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter millerae,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanosphaera|s__Methanosphaera sp. BMS",3366610|28890|183925|2158|2159|2172|230361;3366610|28890|183925|2158|2159|2316|1789762,Complete,Svetlana up
bsdb:37936065/2/1,37936065,laboratory experiment,37936065,10.1186/s12866-023-03079-2,NA,"Li Z., Cui R., Wang Y.B., Luo Y.B., Xue P.X., Tang Q.G. , Fang M.Y.",Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle,BMC microbiology,2023,"16S rDNA, Gut microbiota, Metagenomics, Tan sheep",Experiment 2,China,Ovis aries,Duodenum,UBERON:0002114,Breed,EFO:0005238,Duodenum of Dorper sheep (D_Du),Duodenum of Tan Sheep (T_Du),"Duodenum of Tan sheep bred in Ningxia, China",3,3,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 4A,11 April 2024,Scholastica,"Scholastica,WikiWorks",LEfSe analysis of differences in duodenal microbial composition in Tan sheep versus Dorper sheep from metagenomic data at the species level.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium|s__Agrobacterium tumefaciens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter|s__Arthrobacter alpinus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Friedmanniella|s__Friedmanniella luteola,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Modestobacter|s__Modestobacter marinus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium dioxanotrophicus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Ornithinimicrobiaceae|g__Ornithinimicrobium|s__Ornithinimicrobium avium",3379134|1224|28211|356|82115|357|358;1783272|201174|1760|85006|1268|1663|656366;1783272|201174|1760|85009|85015|53387|546871;1783272|201174|1760|1643682|85030|88138|477641;1783272|201174|1760|85007|1762|1763|482462;1783272|201174|1760|85006|2805590|125287|2283195,Complete,Svetlana up
bsdb:37936065/2/2,37936065,laboratory experiment,37936065,10.1186/s12866-023-03079-2,NA,"Li Z., Cui R., Wang Y.B., Luo Y.B., Xue P.X., Tang Q.G. , Fang M.Y.",Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle,BMC microbiology,2023,"16S rDNA, Gut microbiota, Metagenomics, Tan sheep",Experiment 2,China,Ovis aries,Duodenum,UBERON:0002114,Breed,EFO:0005238,Duodenum of Dorper sheep (D_Du),Duodenum of Tan Sheep (T_Du),"Duodenum of Tan sheep bred in Ningxia, China",3,3,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 4A,11 April 2024,Scholastica,"Scholastica,WikiWorks",LEfSe analysis of differences in duodenal microbial composition in Tan sheep versus Dorper sheep from metagenomic data at the species level.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Advenella|s__Advenella mimigardefordensis,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Nostocaceae|g__Nostoc|s__Nostoc sphaeroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Solibacillus|s__Solibacillus silvestris",3379134|1224|28216|80840|506|290425|302406;1783272|1117|3028117|1161|1162|1177|446679;1783272|1239|91061|1385|186818|648800|76853,Complete,Svetlana up
bsdb:37936065/4/1,37936065,laboratory experiment,37936065,10.1186/s12866-023-03079-2,NA,"Li Z., Cui R., Wang Y.B., Luo Y.B., Xue P.X., Tang Q.G. , Fang M.Y.",Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle,BMC microbiology,2023,"16S rDNA, Gut microbiota, Metagenomics, Tan sheep",Experiment 4,China,Ovis aries,Rumen,UBERON:0007365,Breed,EFO:0005238,Rumen of Dorper sheep (D_R),Rumen of Tan Sheep (T_R),"Rumen of Tan sheep bred in Ningxia, China",6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Fig. S6,11 April 2024,Scholastica,"Scholastica,WikiWorks",LEfSe analysis of ruminal microbiota in Tan sheep versus Dorper sheep from 16S data at the genus level.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium CG2,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|s__uncultured Prevotellaceae bacterium",1783272|1239|186801|3085636|186803|1394809;1783272|1239|186801|186802|216572|100175;1783272|1239|186801|186802|216572|1200657;3379134|976|200643|171549|171552|370804,Complete,Svetlana up
bsdb:37936065/5/1,37936065,laboratory experiment,37936065,10.1186/s12866-023-03079-2,NA,"Li Z., Cui R., Wang Y.B., Luo Y.B., Xue P.X., Tang Q.G. , Fang M.Y.",Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle,BMC microbiology,2023,"16S rDNA, Gut microbiota, Metagenomics, Tan sheep",Experiment 5,China,Ovis aries,Duodenum,UBERON:0002114,Breed,EFO:0005238,Duodenum of Dorper sheep (D_Du),Duodenum of Tan Sheep (T_Du),"Duodenum of Tan sheep bred in Ningxia, China",6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Fig. S7,11 April 2024,Scholastica,"Scholastica,WikiWorks",LEfSe analysis of duodenal microbiota in Tan sheep versus Dorper sheep from 16S data at the genus level.,increased,"k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacillati|p__Candidatus Melainabacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",1783272|1798710|1906119;1783272|1798710;1783272|1239|186801|186802|186807;1783272|1239|186801|186802|216572|1200657;1783272|201174|84998|84999|84107|1473205;1783272|1239|186801|3085636|186803|297314,Complete,Svetlana up
bsdb:37936065/6/1,37936065,laboratory experiment,37936065,10.1186/s12866-023-03079-2,NA,"Li Z., Cui R., Wang Y.B., Luo Y.B., Xue P.X., Tang Q.G. , Fang M.Y.",Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle,BMC microbiology,2023,"16S rDNA, Gut microbiota, Metagenomics, Tan sheep",Experiment 6,China,Ovis aries,Jejunum,UBERON:0002115,Breed,EFO:0005238,Jejunum of Dorper sheep (D_J),Jejunum of Tan Sheep (T_J),"Jejunum of Tan sheep bred in Ningxia, China",6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Fig. S8,11 April 2024,Scholastica,"Scholastica,WikiWorks",LEfSe analysis of jejunal microbiota in Tan sheep versus Dorper sheep from 16S data at the genus level.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|s__uncultured Prevotellaceae bacterium,3379134|976|200643|171549|171552|370804,Complete,Svetlana up
bsdb:37936065/6/2,37936065,laboratory experiment,37936065,10.1186/s12866-023-03079-2,NA,"Li Z., Cui R., Wang Y.B., Luo Y.B., Xue P.X., Tang Q.G. , Fang M.Y.",Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle,BMC microbiology,2023,"16S rDNA, Gut microbiota, Metagenomics, Tan sheep",Experiment 6,China,Ovis aries,Jejunum,UBERON:0002115,Breed,EFO:0005238,Jejunum of Dorper sheep (D_J),Jejunum of Tan Sheep (T_J),"Jejunum of Tan sheep bred in Ningxia, China",6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Fig. S8,11 April 2024,Scholastica,"Scholastica,WikiWorks",LEfSe analysis of jejunal microbiota in Tan sheep versus Dorper sheep from 16S data at the genus level.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli",1783272|1239|91061|1385;1783272|1239|91061,Complete,Svetlana up
bsdb:37936065/7/1,37936065,laboratory experiment,37936065,10.1186/s12866-023-03079-2,NA,"Li Z., Cui R., Wang Y.B., Luo Y.B., Xue P.X., Tang Q.G. , Fang M.Y.",Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle,BMC microbiology,2023,"16S rDNA, Gut microbiota, Metagenomics, Tan sheep",Experiment 7,China,Ovis aries,Colon,UBERON:0001155,Breed,EFO:0005238,Colon of Dorper sheep (D_Co),Colon of Tan Sheep (T_Co),"Colon of Tan sheep bred in Ningxia, China",6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Fig. S9,11 April 2024,Scholastica,"Scholastica,WikiWorks",LEfSe analysis of colonic microbiota in Tan sheep versus Dorper sheep from 16S data at the genus level.,increased,"k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacillati|p__Candidatus Melainabacteria,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",1783272|1798710|1906119;1783272|1798710;1783272|1117;3379134|256845|1313211|278082|255528|172900;1783272|1239|186801|186802|216572|707003,Complete,Svetlana up
bsdb:37936065/7/2,37936065,laboratory experiment,37936065,10.1186/s12866-023-03079-2,NA,"Li Z., Cui R., Wang Y.B., Luo Y.B., Xue P.X., Tang Q.G. , Fang M.Y.",Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle,BMC microbiology,2023,"16S rDNA, Gut microbiota, Metagenomics, Tan sheep",Experiment 7,China,Ovis aries,Colon,UBERON:0001155,Breed,EFO:0005238,Colon of Dorper sheep (D_Co),Colon of Tan Sheep (T_Co),"Colon of Tan sheep bred in Ningxia, China",6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Fig. S9,11 April 2024,Scholastica,"Scholastica,WikiWorks",LEfSe analysis of colonic microbiota in Tan sheep versus Dorper sheep from 16S data at the genus level.,decreased,",k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__uncultured Bacteroidales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",;3379134|976|200643|171549|171550;3379134|976|200643|171549|194843;1783272|1239|186801|3085636|186803|297314,Complete,Svetlana up
bsdb:37936065/8/1,37936065,laboratory experiment,37936065,10.1186/s12866-023-03079-2,NA,"Li Z., Cui R., Wang Y.B., Luo Y.B., Xue P.X., Tang Q.G. , Fang M.Y.",Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle,BMC microbiology,2023,"16S rDNA, Gut microbiota, Metagenomics, Tan sheep",Experiment 8,China,Ovis aries,Caecum,UBERON:0001153,Breed,EFO:0005238,Cecum of Dorper sheep (D_C),Cecum of Tan Sheep (T_C),"Cecum of Tan sheep bred in Ningxia, China",6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Fig. S10,11 April 2024,Scholastica,"Scholastica,WikiWorks",LEfSe analysis of cecal microbiota in Tan sheep versus Dorper sheep from 16S data at the genus level.,increased,"k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",3379134|1224;1783272|1239|186801|186802|216572|707003,Complete,Svetlana up
bsdb:37936065/8/2,37936065,laboratory experiment,37936065,10.1186/s12866-023-03079-2,NA,"Li Z., Cui R., Wang Y.B., Luo Y.B., Xue P.X., Tang Q.G. , Fang M.Y.",Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle,BMC microbiology,2023,"16S rDNA, Gut microbiota, Metagenomics, Tan sheep",Experiment 8,China,Ovis aries,Caecum,UBERON:0001153,Breed,EFO:0005238,Cecum of Dorper sheep (D_C),Cecum of Tan Sheep (T_C),"Cecum of Tan sheep bred in Ningxia, China",6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Fig. S10,11 April 2024,Scholastica,"Scholastica,WikiWorks",LEfSe analysis of cecal microbiota in Tan sheep versus Dorper sheep from 16S data at the genus level.,decreased,k__Bacillati|p__Actinomycetota,1783272|201174,Complete,Svetlana up
bsdb:37936084/1/1,37936084,case-control,37936084,10.1186/s12877-023-04417-9,https://pmc.ncbi.nlm.nih.gov/articles/PMC11055349/,"Hung C.C., Chao Y.P., Lee Y., Huang C.W., Huang S.H., Chang C.C. , Cheng C.H.",Cingulate white matter mediates the effects of fecal Ruminococcus on neuropsychiatric symptoms in patients with amyloid-positive amnestic mild cognitive impairment,BMC geriatrics,2023,"Amnestic mild cognitive impairment, Diffusion tensor imaging, Gut microbiota, Limbic system, Neuropsychiatric symptoms, Ruminococcus",Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,Cognitive impairment measurement,EFO:0007998,Healthy control (HC).,Amnestic mild cognitive impairment (aMCI+).,"Patients with amnestic mild cognitive impairment ""Amyloid positive"" (aMCI+).",20,20,2 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Fig 1A,26 April 2025,Shulamite,Shulamite,Mann-Whitney U test revealed significantly differential abundance of genera Ruminococcus and Lactococcus between aMCI + and HC groups.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239|91061|186826|1300|1357;1783272|1239|186801|186802|216572|1263,Complete,KateRasheed
bsdb:37936084/2/1,37936084,case-control,37936084,10.1186/s12877-023-04417-9,https://pmc.ncbi.nlm.nih.gov/articles/PMC11055349/,"Hung C.C., Chao Y.P., Lee Y., Huang C.W., Huang S.H., Chang C.C. , Cheng C.H.",Cingulate white matter mediates the effects of fecal Ruminococcus on neuropsychiatric symptoms in patients with amyloid-positive amnestic mild cognitive impairment,BMC geriatrics,2023,"Amnestic mild cognitive impairment, Diffusion tensor imaging, Gut microbiota, Limbic system, Neuropsychiatric symptoms, Ruminococcus",Experiment 2,Taiwan,Homo sapiens,Feces,UBERON:0001988,Cognitive impairment measurement,EFO:0007998,Healthy control (HC).,Amnestic mild cognitive impairment (aMCI+).,"Patients with amnestic mild cognitive impairment ""Amyloid positive"" (aMCI+).",20,20,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Fig 1B,26 April 2025,Shulamite,Shulamite,LEfSe analysis showed significantly differential abundance of genera Ruminococcus and Lactococcus between aMCI+ (positive scores) and HC (negative scores) groups.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239|91061|186826|1300|1357;1783272|1239|186801|186802|216572|1263,Complete,KateRasheed
bsdb:37936242/1/1,37936242,laboratory experiment,37936242,10.1186/s40168-023-01689-6,NA,"Pan C., Zhang H., Zhang L., Chen L., Xu L., Xu N., Liu X., Meng Q., Wang X. , Zhang Z.Y.",Surgery-induced gut microbial dysbiosis promotes cognitive impairment via regulation of intestinal function and the metabolite palmitic amide,Microbiome,2023,"Fecal microbiota transplantation, Gut microbiota, Intestinal permeability, Microbiota, Palmitic amide, Perioperative neurocognitive disorders",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Cognitive disorder,MONDO:0002039,"Young+Surgery, Aged+surgery and Aged",Young,Adult male C57BL/6 mice 2 months old were grouped as Young.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3D,1 May 2025,MyleeeA,"MyleeeA,Anne-mariesharp","Linear discriminant analysis Efect Size (LEfSe) was used to find species with significant differences at all taxonomic levels of the gut microbiota in the feces of Young, Aged, Young+surgery and Aged+surgery groups of mice",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Rhodocyclaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae",3379134|74201|203494|48461|1647988|239934;1783272|1239|526524|526525|128827|174708;3379134|1224|28216|206389|75787;3379134|1224|28216|206389;1783272|1239|526524|526525|2810281|191303;1783272|1239|526524|526525|2810281;3379134|74201|203494|48461|203557;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201;1783272|1239|91061|1385|186817,Complete,KateRasheed
bsdb:37936242/2/1,37936242,laboratory experiment,37936242,10.1186/s40168-023-01689-6,NA,"Pan C., Zhang H., Zhang L., Chen L., Xu L., Xu N., Liu X., Meng Q., Wang X. , Zhang Z.Y.",Surgery-induced gut microbial dysbiosis promotes cognitive impairment via regulation of intestinal function and the metabolite palmitic amide,Microbiome,2023,"Fecal microbiota transplantation, Gut microbiota, Intestinal permeability, Microbiota, Palmitic amide, Perioperative neurocognitive disorders",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Cognitive disorder,MONDO:0002039,"Young+Surgery, Aged+surgery and Young",Aged,Adult Male C57BL/6 mice 18 months old were grouped as Aged.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3D,1 May 2025,MyleeeA,MyleeeA,"Linear discriminant analysis Efect Size (LEfSe) was used to find species with significant differences at all taxonomic levels of the gut microbiota in the feces of Young, Aged, Young+surgery and Aged+surgery groups of mice",increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Idiomarinaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Idiomarinaceae|g__Idiomarina,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella",3379134|976;3379134|976|200643;3379134|1224|1236|135622;3379134|976|200643|171549;3379134|1224|1236|91347;3379134|976|200643|171549|171552;3379134|1224|1236|135622|267893;3379134|1224|1236|91347|543;3379134|976|200643|171549|171552|577309;3379134|1224|1236|135622|267893|135575;3379134|1224|1236|91347|543|620,Complete,KateRasheed
bsdb:37936242/3/1,37936242,laboratory experiment,37936242,10.1186/s40168-023-01689-6,NA,"Pan C., Zhang H., Zhang L., Chen L., Xu L., Xu N., Liu X., Meng Q., Wang X. , Zhang Z.Y.",Surgery-induced gut microbial dysbiosis promotes cognitive impairment via regulation of intestinal function and the metabolite palmitic amide,Microbiome,2023,"Fecal microbiota transplantation, Gut microbiota, Intestinal permeability, Microbiota, Palmitic amide, Perioperative neurocognitive disorders",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Response to surgery,EFO:0009951,"Young, Aged+surgery and Aged",Young+Surgery,Adult male C57BL/6 mice 2 months old that underwent surgery were grouped as Young+surgery,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3D,1 May 2025,MyleeeA,MyleeeA,"Linear discriminant analysis Efect Size (LEfSe) was used to find species with significant differences at all taxonomic levels of the gut microbiota in the feces of Young, Aged, Young+surgery and Aged+surgery groups of mice",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,3379134|976|200643|171549|2005473,Complete,KateRasheed
bsdb:37936242/4/1,37936242,laboratory experiment,37936242,10.1186/s40168-023-01689-6,NA,"Pan C., Zhang H., Zhang L., Chen L., Xu L., Xu N., Liu X., Meng Q., Wang X. , Zhang Z.Y.",Surgery-induced gut microbial dysbiosis promotes cognitive impairment via regulation of intestinal function and the metabolite palmitic amide,Microbiome,2023,"Fecal microbiota transplantation, Gut microbiota, Intestinal permeability, Microbiota, Palmitic amide, Perioperative neurocognitive disorders",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Response to surgery,EFO:0009951,"Young+Surgery, Young and Aged",Aged+surgery,Adult male C57BL/6 mice 18 months old that underwent surgery were grouped as Aged+surgery,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3D,1 May 2025,MyleeeA,"MyleeeA,Anne-mariesharp","Linear discriminant analysis Efect Size (LEfSe) was used to find species with significant differences at all taxonomic levels of the gut microbiota in the feces of Young, Aged, Young+surgery and Aged+surgery groups of mice",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",3379134|1224|1236;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|1300,Complete,KateRasheed
bsdb:37936242/5/1,37936242,laboratory experiment,37936242,10.1186/s40168-023-01689-6,NA,"Pan C., Zhang H., Zhang L., Chen L., Xu L., Xu N., Liu X., Meng Q., Wang X. , Zhang Z.Y.",Surgery-induced gut microbial dysbiosis promotes cognitive impairment via regulation of intestinal function and the metabolite palmitic amide,Microbiome,2023,"Fecal microbiota transplantation, Gut microbiota, Intestinal permeability, Microbiota, Palmitic amide, Perioperative neurocognitive disorders",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Response to surgery,EFO:0009951,Young mice,Young+surgery mice,Adult male C57BL/6 mice 2 months old that underwent surgery were grouped as Young+surgery,NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3H,1 May 2025,MyleeeA,"MyleeeA,Anne-mariesharp",Differential abundant microbial taxon significant between Young+surgery mice and Young mice.,decreased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,3379134|74201|203494|48461|1647988|239934,Complete,KateRasheed
bsdb:37936242/6/1,37936242,laboratory experiment,37936242,10.1186/s40168-023-01689-6,NA,"Pan C., Zhang H., Zhang L., Chen L., Xu L., Xu N., Liu X., Meng Q., Wang X. , Zhang Z.Y.",Surgery-induced gut microbial dysbiosis promotes cognitive impairment via regulation of intestinal function and the metabolite palmitic amide,Microbiome,2023,"Fecal microbiota transplantation, Gut microbiota, Intestinal permeability, Microbiota, Palmitic amide, Perioperative neurocognitive disorders",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Response to surgery,EFO:0009951,Aged mice,Aged+surgery mice,Adult male C57BL/6 mice 18 months old that underwent surgery were grouped as Aged+surgery,NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3G,1 May 2025,MyleeeA,"MyleeeA,Anne-mariesharp",Differential abundant microbial taxon significant between Aged+surgery mice and Aged mice.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,KateRasheed
bsdb:37936242/7/1,37936242,laboratory experiment,37936242,10.1186/s40168-023-01689-6,NA,"Pan C., Zhang H., Zhang L., Chen L., Xu L., Xu N., Liu X., Meng Q., Wang X. , Zhang Z.Y.",Surgery-induced gut microbial dysbiosis promotes cognitive impairment via regulation of intestinal function and the metabolite palmitic amide,Microbiome,2023,"Fecal microbiota transplantation, Gut microbiota, Intestinal permeability, Microbiota, Palmitic amide, Perioperative neurocognitive disorders",Experiment 7,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Aged+surgery+youngFecal Microbiota Transplantation mice,Aged+surgery+agedFecal Microbiota Transplantation mice,Adult male C57BL/6 mice 18 months old that underwent surgery and Fecal microbiota transplantation with aged samples were grouped as Aged+surgery+aFMT.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 5K,1 May 2025,MyleeeA,MyleeeA,Linear discriminant analysis Efect Size (LEfSe) was used to find species with significant differences at all taxonomic levels of the gut microbiota in the feces of  Aged+surgery+youngFMT and Aged+surgery+agedFMT groups of mice.,increased,"k__Bacillati|p__Cyanobacteriota,s__uncultured rumen bacterium 4C0d-2,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,s__rumen bacterium YS2,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter",1783272|1117;107058;3379134|29547|3031852;209265;3379134|29547|3031852|213849;3379134|29547|3031852|213849|72293;3379134|29547|3031852|213849|72293|209,Complete,KateRasheed
bsdb:37936242/7/2,37936242,laboratory experiment,37936242,10.1186/s40168-023-01689-6,NA,"Pan C., Zhang H., Zhang L., Chen L., Xu L., Xu N., Liu X., Meng Q., Wang X. , Zhang Z.Y.",Surgery-induced gut microbial dysbiosis promotes cognitive impairment via regulation of intestinal function and the metabolite palmitic amide,Microbiome,2023,"Fecal microbiota transplantation, Gut microbiota, Intestinal permeability, Microbiota, Palmitic amide, Perioperative neurocognitive disorders",Experiment 7,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Aged+surgery+youngFecal Microbiota Transplantation mice,Aged+surgery+agedFecal Microbiota Transplantation mice,Adult male C57BL/6 mice 18 months old that underwent surgery and Fecal microbiota transplantation with aged samples were grouped as Aged+surgery+aFMT.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 5K,1 May 2025,MyleeeA,"MyleeeA,Anne-mariesharp",Linear discriminant analysis Efect Size (LEfSe) was used to find species with significant differences at all taxonomic levels of the gut microbiota in the feces of  Aged+surgery+youngFMT and Aged+surgery+agedFMT groups of mice.,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Chitinophaga,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Saprospiria|o__Saprospirales,k__Pseudomonadati|p__Bacteroidota|c__Saprospiria,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota",3379134|74201|203494|48461|1647988|239934;3379134|976|1853228|1853229|563835|79328;3379134|976|1853228|1853229|563835;1783272|1239|186801|3082720|186804;3379134|976|1937959|1936988;3379134|976|1937959;3379134|74201|203494|48461|203557;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201,Complete,KateRasheed
bsdb:37936242/8/1,37936242,laboratory experiment,37936242,10.1186/s40168-023-01689-6,NA,"Pan C., Zhang H., Zhang L., Chen L., Xu L., Xu N., Liu X., Meng Q., Wang X. , Zhang Z.Y.",Surgery-induced gut microbial dysbiosis promotes cognitive impairment via regulation of intestinal function and the metabolite palmitic amide,Microbiome,2023,"Fecal microbiota transplantation, Gut microbiota, Intestinal permeability, Microbiota, Palmitic amide, Perioperative neurocognitive disorders",Experiment 8,China,Mus musculus,Feces,UBERON:0001988,Response to surgery,EFO:0009951,"Aged, Young+surgery before, Young+surgery after, Aged+surgery before and Aged+surgery after",Young,Adult male C57BL/6 mice 2 months old were grouped as Young.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 2F,1 May 2025,MyleeeA,"MyleeeA,Anne-mariesharp","Linear discriminant analysis Efect Size (LEfSe) was used to find species with significant differences at all taxonomic levels of the gut microbiota in the feces of Young, Aged, Young+surgery before, Young+surgery after, Aged+surgery before and Aged+surgery after groups of mice",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Viridiplantae|p__Streptophyta,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Synechococcales|f__Synechococcaceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Synechococcales,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Synechococcales|f__Synechococcaceae|g__Synechococcus",3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;33090|35493;1783272|1117|3028117|1890424|1890426;1783272|1117|3028117|1890424;1783272|1117|3028117|1890424|1890426|1129,Complete,KateRasheed
bsdb:37936242/9/1,37936242,laboratory experiment,37936242,10.1186/s40168-023-01689-6,NA,"Pan C., Zhang H., Zhang L., Chen L., Xu L., Xu N., Liu X., Meng Q., Wang X. , Zhang Z.Y.",Surgery-induced gut microbial dysbiosis promotes cognitive impairment via regulation of intestinal function and the metabolite palmitic amide,Microbiome,2023,"Fecal microbiota transplantation, Gut microbiota, Intestinal permeability, Microbiota, Palmitic amide, Perioperative neurocognitive disorders",Experiment 9,China,Mus musculus,Feces,UBERON:0001988,Response to surgery,EFO:0009951,"Young, Young+surgery before, Young+surgery after, Aged+surgery before and Aged+surgery after",Aged,C57BL/6 mice 18 months old were grouped as Aged.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 2F,1 May 2025,MyleeeA,"MyleeeA,Anne-mariesharp","Linear discriminant analysis Efect Size (LEfSe) was used to find species with significant differences at all taxonomic levels of the gut microbiota in the feces of Young, Aged, Young+surgery before, Young+surgery after, Aged+surgery before and Aged+surgery after groups of mice.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Sporosarcina,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Yaniella,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia",1783272|201174|1760|2037;1783272|1239|91061|186826|186827;3379134|1224|28216|80840|506|507;1783272|1239|91061|1385|186817;1783272|1239|91061|1385;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;3379134|200940|3031449|213115|194924|35832;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|186826|186827|66831;1783272|1239|91061|1385|90964|227979;1783272|201174|1760|85006|1268;3379134|1224|1236|2887326|468|497;1783272|1239|91061|1385|186818|1569;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;1783272|201174|1760|85006|1268|225447;1783272|201174|84992,Complete,KateRasheed
bsdb:37936242/10/1,37936242,laboratory experiment,37936242,10.1186/s40168-023-01689-6,NA,"Pan C., Zhang H., Zhang L., Chen L., Xu L., Xu N., Liu X., Meng Q., Wang X. , Zhang Z.Y.",Surgery-induced gut microbial dysbiosis promotes cognitive impairment via regulation of intestinal function and the metabolite palmitic amide,Microbiome,2023,"Fecal microbiota transplantation, Gut microbiota, Intestinal permeability, Microbiota, Palmitic amide, Perioperative neurocognitive disorders",Experiment 10,China,Mus musculus,Feces,UBERON:0001988,Exploratory behavior,EFO:0004316,"Aged, Young, Young+surgery after, Aged+surgery before and Aged+surgery after",Young+surgery before,Adult male C57BL/6 mice 2 months old that underwent surgery before behavioural testing,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 2F,1 May 2025,MyleeeA,MyleeeA,"Linear discriminant analysis Efect Size (LEfSe) was used to find species with significant differences at all taxonomic levels of the gut microbiota in the feces of Young, Aged, Young+surgery before, Young+surgery after, Aged+surgery before and Aged+surgery after groups of mice.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|s__Streptococcaceae bacterium RF32",3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|976|200643|171549|2005473;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|423432,Complete,KateRasheed
bsdb:37936242/11/1,37936242,laboratory experiment,37936242,10.1186/s40168-023-01689-6,NA,"Pan C., Zhang H., Zhang L., Chen L., Xu L., Xu N., Liu X., Meng Q., Wang X. , Zhang Z.Y.",Surgery-induced gut microbial dysbiosis promotes cognitive impairment via regulation of intestinal function and the metabolite palmitic amide,Microbiome,2023,"Fecal microbiota transplantation, Gut microbiota, Intestinal permeability, Microbiota, Palmitic amide, Perioperative neurocognitive disorders",Experiment 11,China,Mus musculus,Feces,UBERON:0001988,Exploratory behavior,EFO:0004316,"Young, Aged, Young+surgery before, Aged+surgery before and Aged+surgery after",Young+surgery after,Adult male C57BL/6 mice 2 months old that underwent surgery after behavioural tests.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 2F,1 May 2025,MyleeeA,"MyleeeA,Anne-mariesharp","Linear discriminant analysis Efect Size (LEfSe) was used to find species with significant differences at all taxonomic levels of the gut microbiota in the feces of Young, Aged, Young+surgery before, Young+surgery after, Aged+surgery before and Aged+surgery after groups of mice.",increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Chloroflexota|c__Ktedonobacteria",1783272|1239|526524|526525|128827|174708;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|200795|388447,Complete,KateRasheed
bsdb:37936242/12/1,37936242,laboratory experiment,37936242,10.1186/s40168-023-01689-6,NA,"Pan C., Zhang H., Zhang L., Chen L., Xu L., Xu N., Liu X., Meng Q., Wang X. , Zhang Z.Y.",Surgery-induced gut microbial dysbiosis promotes cognitive impairment via regulation of intestinal function and the metabolite palmitic amide,Microbiome,2023,"Fecal microbiota transplantation, Gut microbiota, Intestinal permeability, Microbiota, Palmitic amide, Perioperative neurocognitive disorders",Experiment 12,China,Mus musculus,Feces,UBERON:0001988,Exploratory behavior,EFO:0004316,"Young, Aged, Young+surgery before, Young+surgery after and Aged+surgery after",Aged+surgery before,Adult male C57BL/6 mice 18 months old that underwent surgery before behavioural tests.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 2F,1 May 2025,MyleeeA,"MyleeeA,Anne-mariesharp","Linear discriminant analysis Efect Size (LEfSe) was used to find species with significant differences at all taxonomic levels of the gut microbiota in the feces of Young, Aged, Young+surgery before, Young+surgery after, Aged+surgery before and Aged+surgery after groups of mice.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,k__Bacillati|p__Chloroflexota,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres,k__Pseudomonadati|p__Deferribacterota,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Flexispira,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Nitrospirota|c__Nitrospiria|o__Nitrospirales|f__Nitrospiraceae|g__Nitrospira,k__Pseudomonadati|p__Nitrospirota|c__Nitrospiria|o__Nitrospirales|f__Nitrospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,s__bacterium AF12",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|29547|3031852|213849;1783272|1239|186801|186802|31979|49082;1783272|200795;3379134|200930|68337|191393|191394;3379134|200930|68337|191393;3379134|200930|68337;3379134|200930;3379134|29547|3031852;3379134|29547|3031852|213849|72293|2353;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|1385|539738;3379134|29547|3031852|213849|72293|209;3379134|29547|3031852|213849|72293;3379134|200930|68337|191393|2945020|248038;3379134|40117|203693|189778|189779|1234;3379134|40117|203693|189778|189779;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|1853231;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;3379134|976|200643|171549|171550|28138;3379134|976|200643|171549|171550;3379134|1224|28211|204457|3423717|165695;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977;1729795,Complete,KateRasheed
bsdb:37936242/13/1,37936242,laboratory experiment,37936242,10.1186/s40168-023-01689-6,NA,"Pan C., Zhang H., Zhang L., Chen L., Xu L., Xu N., Liu X., Meng Q., Wang X. , Zhang Z.Y.",Surgery-induced gut microbial dysbiosis promotes cognitive impairment via regulation of intestinal function and the metabolite palmitic amide,Microbiome,2023,"Fecal microbiota transplantation, Gut microbiota, Intestinal permeability, Microbiota, Palmitic amide, Perioperative neurocognitive disorders",Experiment 13,China,Mus musculus,Feces,UBERON:0001988,Exploratory behavior,EFO:0004316,"Young, Aged, Young+surgery before, Aged+surgery before and Young+surgery after",Aged+surgery after,Adult male C57BL/6 mice 18 months old that underwent surgery after behavioural tests.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 2F,1 May 2025,MyleeeA,"MyleeeA,Anne-mariesharp","Linear discriminant analysis Efect Size (LEfSe) was used to find species with significant differences at all taxonomic levels of the gut microbiota in the feces of Young, Aged, Young+surgery before, Young+surgery after, Aged+surgery before and Aged+surgery after groups of mice.",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|201174|84998|1643822|1643826|447020;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|31979|1485,Complete,KateRasheed
bsdb:37936242/14/1,37936242,laboratory experiment,37936242,10.1186/s40168-023-01689-6,NA,"Pan C., Zhang H., Zhang L., Chen L., Xu L., Xu N., Liu X., Meng Q., Wang X. , Zhang Z.Y.",Surgery-induced gut microbial dysbiosis promotes cognitive impairment via regulation of intestinal function and the metabolite palmitic amide,Microbiome,2023,"Fecal microbiota transplantation, Gut microbiota, Intestinal permeability, Microbiota, Palmitic amide, Perioperative neurocognitive disorders",Experiment 14,China,Mus musculus,Feces,UBERON:0001988,Response to surgery,EFO:0009951,Aged+surgery and Aged+surgery+dexamethasone,Aged,Adult male C57BL/6 mice 18 months old were grouped as Aged.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 5G,30 April 2025,MyleeeA,"MyleeeA,Anne-mariesharp","Linear discriminant analysis Efect Size (LEfSe) was used to find species with significant differences at all taxonomic levels of the gut microbiota in the feces of Aged, Aged+surgery and Aged+surgery+dexamethasone groups of mice.",increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|s__Enterococcaceae bacterium RF39,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Gluconobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Yaniella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|201174|84992;1783272|201174|1760|2037;1783272|201174;1783272|201174|84998|1643822|1643826|447020;1783272|1239|91061|186826|186827;1783272|1239|91061|186826|186827|1375;3379134|1224|28216|80840|506;3379134|1224|28216|80840|506|507;1783272|1239|526524|526525|128827|174708;1783272|1239|186801|186802|186806|264995;1783272|1239|91061|1385|186817;1783272|1239|91061|1385;3379134|1224|28216;3379134|200940|3031449|213115|194924|35832;3379134|1224|28216|80840;1783272|1239|91061|1385|186818;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;1783272|1239|186801|186802|186807|51514;1783272|1239|186801|3085636|186803|189330;1783272|1239|91061|186826|81852|423410;1783272|1239|186801|186802|186806;1783272|1239|91061|186826|186827|66831;3379134|1224|28211|3120395|433|441;1783272|1239|91061|1385|90964|227979;1783272|1239|91061|186826|1300|1357;1783272|201174|1760|85006|1268;3379134|1224|1236|2887326|468;3379134|976|200643|171549|2005473;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572;3379134|1224|1236|72274;3379134|1224|1236|2887326|468|497;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|1385|90964|1279;1783272|1239|526524|526525|2810281|191303;1783272|1239|526524|526525|2810281;1783272|201174|1760|85006|1268|225447;1783272|1239|186801|186802|31979|1485,Complete,KateRasheed
bsdb:37936242/15/1,37936242,laboratory experiment,37936242,10.1186/s40168-023-01689-6,NA,"Pan C., Zhang H., Zhang L., Chen L., Xu L., Xu N., Liu X., Meng Q., Wang X. , Zhang Z.Y.",Surgery-induced gut microbial dysbiosis promotes cognitive impairment via regulation of intestinal function and the metabolite palmitic amide,Microbiome,2023,"Fecal microbiota transplantation, Gut microbiota, Intestinal permeability, Microbiota, Palmitic amide, Perioperative neurocognitive disorders",Experiment 15,China,Mus musculus,Feces,UBERON:0001988,Cognitive disorder,MONDO:0002039,Aged and Aged+surgery+dexamethasone,Aged+surgery,Adult male C57BL/6 mice 18 months old that underwent surgery were grouped as Aged+surgery,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 5G,30 April 2025,MyleeeA,"MyleeeA,Anne-mariesharp","Linear discriminant analysis Efect Size (LEfSe) was used to find species with significant differences at all taxonomic levels of the gut microbiota in the feces of Aged, Aged+surgery and Aged+surgery+dexamethasone groups of mice.",increased,"k__Bacillati|p__Chloroflexota|c__Anaerolineae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,k__Bacillati|p__Chloroflexota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres,k__Pseudomonadati|p__Deferribacterota,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,s__bacterium AF12",1783272|200795|292625;1783272|1239|186801|186802|31979|49082;1783272|200795;1783272|1239|186801|186802|31979;1783272|201174|84998|84999|84107|102106;3379134|200930|68337|191393|191394;3379134|200930|68337|191393;3379134|200930|68337;3379134|200930;3379134|200940|3031449|213115|194924|872;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|216851;3379134|1224|1236|91347|543|570;3379134|1224|1236|135614|32033;3379134|1224|1236|135614;3379134|200930|68337|191393|2945020|248038;1783272|544448|31969|2085|2092|2093;1783272|544448|31969|2085|2092;1783272|544448|31969|2085;3379134|976|200643|171549|171552|577309;3379134|1224;3379134|976|200643|171549|171550|28138;3379134|1224|28211|204457|3423717|165695;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977;1729795,Complete,KateRasheed
bsdb:37936242/16/1,37936242,laboratory experiment,37936242,10.1186/s40168-023-01689-6,NA,"Pan C., Zhang H., Zhang L., Chen L., Xu L., Xu N., Liu X., Meng Q., Wang X. , Zhang Z.Y.",Surgery-induced gut microbial dysbiosis promotes cognitive impairment via regulation of intestinal function and the metabolite palmitic amide,Microbiome,2023,"Fecal microbiota transplantation, Gut microbiota, Intestinal permeability, Microbiota, Palmitic amide, Perioperative neurocognitive disorders",Experiment 16,China,Mus musculus,Feces,UBERON:0001988,Cognitive disorder,MONDO:0002039,Aged and Aged+surgery,Aged+surgery+dexamethasone,Adult male C57BL/6 mice 18 months old that underwent surgery and were given Dexamethasone.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 5G,30 April 2025,MyleeeA,MyleeeA,"Linear discriminant analysis Efect Size (LEfSe) was used to find species with significant differences at all taxonomic levels of the gut microbiota in the feces of Aged, Aged+surgery and Aged+surgery+dexamethasone groups of mice.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Caryophyllales|f__Chenopodiaceae|s__Betoideae|g__Beta,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Solibacillus,s__rumen bacterium YS2,s__uncultured rumen bacterium 4C0d-2",3379134|1224|1236|2887326|468|469;33090|35493|3398|3524|1804623|1804621|3554;3379134|1224|28216|80840|119060|32008;3379134|1224|28216|80840|119060;1783272|1239|909932|909929|1843491|158846;3379134|1224|1236|72274|135621;3379134|1224|1236|72274|135621|286;1783272|1239|91061|1385|186818|648800;209265;107058,Complete,KateRasheed
bsdb:37936242/17/1,37936242,laboratory experiment,37936242,10.1186/s40168-023-01689-6,NA,"Pan C., Zhang H., Zhang L., Chen L., Xu L., Xu N., Liu X., Meng Q., Wang X. , Zhang Z.Y.",Surgery-induced gut microbial dysbiosis promotes cognitive impairment via regulation of intestinal function and the metabolite palmitic amide,Microbiome,2023,"Fecal microbiota transplantation, Gut microbiota, Intestinal permeability, Microbiota, Palmitic amide, Perioperative neurocognitive disorders",Experiment 17,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,"Young+Surgery+agedFMT, Aged+surgery+youngFMT and Aged+surgery+agedFMT.",Young+Surgery+youngFMT,Adult male C57BL/6 mice 2 months old that underwent surgery and Fecal microbiota transplantation with young samples.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 7G,30 April 2025,MyleeeA,MyleeeA,"Linear discriminant analysis Efect Size (LEfSe) was used to find species with significant differences at all taxonomic levels of the gut microbiota in the feces of Young+Surgery+youngFMT, Young+Surgery+agedFMT, Aged+surgery+youngFMT and Aged+surgery+agedFMT groups of mice.",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hydrogenophaga,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Rhodocyclaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota",3379134|74201|203494|48461|1647988|239934;3379134|1224|28216|80840|506;3379134|1224|28211;3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|1224|28216;3379134|1224|28216|80840;3379134|1224|28216|80840|80864;3379134|1224|28216|80840|80864|47420;3379134|976|200643|171549|2005473;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;3379134|1224|28216|206389|75787;3379134|1224|28216|206389;3379134|1224|28216|80840|995019|40544;3379134|74201|203494|48461|203557;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201,Complete,KateRasheed
bsdb:37936242/18/1,37936242,laboratory experiment,37936242,10.1186/s40168-023-01689-6,NA,"Pan C., Zhang H., Zhang L., Chen L., Xu L., Xu N., Liu X., Meng Q., Wang X. , Zhang Z.Y.",Surgery-induced gut microbial dysbiosis promotes cognitive impairment via regulation of intestinal function and the metabolite palmitic amide,Microbiome,2023,"Fecal microbiota transplantation, Gut microbiota, Intestinal permeability, Microbiota, Palmitic amide, Perioperative neurocognitive disorders",Experiment 18,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,"Young+Surgery+youngFMT, Aged+surgery+youngFMT and Aged+surgery+agedFMT.",Young+Surgery+agedFMT,Adult male C57BL/6 mice 2 months old that underwent surgery and Fecal microbiota transplantation with aged samples.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 7G,30 April 2025,MyleeeA,MyleeeA,"Linear discriminant analysis Efect Size (LEfSe) was used to find species with significant differences at all taxonomic levels of the gut microbiota in the feces of Young+Surgery+youngFMT, Young+Surgery+agedFMT, Aged+surgery+youngFMT and Aged+surgery+agedFMT groups of mice.",increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia",1783272|1239|526524|526525|128827|174708;1783272|1239|186801|3082768|990719;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524,Complete,KateRasheed
bsdb:37936242/19/1,37936242,laboratory experiment,37936242,10.1186/s40168-023-01689-6,NA,"Pan C., Zhang H., Zhang L., Chen L., Xu L., Xu N., Liu X., Meng Q., Wang X. , Zhang Z.Y.",Surgery-induced gut microbial dysbiosis promotes cognitive impairment via regulation of intestinal function and the metabolite palmitic amide,Microbiome,2023,"Fecal microbiota transplantation, Gut microbiota, Intestinal permeability, Microbiota, Palmitic amide, Perioperative neurocognitive disorders",Experiment 19,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,"Young+Surgery+youngFMT, Young+surgery+agedFMT and Aged+surgery+agedFMT.",Aged+surgery+youngFMT,Adult male C57BL/6 mice 18 months old that underwent surgery and Fecal microbiota transplantation with young samples.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 7G,30 April 2025,MyleeeA,MyleeeA,"Linear discriminant analysis Efect Size (LEfSe) was used to find species with significant differences at all taxonomic levels of the gut microbiota in the feces of Young+Surgery+youngFMT, Young+Surgery+agedFMT, Aged+surgery+youngFMT and Aged+surgery+agedFMT groups of mice.",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae",1783272|1239|91061|186826|186827|1375;1783272|1239;1783272|1239|526524|526525|2810281|191303;1783272|1239|526524|526525|2810281,Complete,KateRasheed
bsdb:37936242/20/1,37936242,laboratory experiment,37936242,10.1186/s40168-023-01689-6,NA,"Pan C., Zhang H., Zhang L., Chen L., Xu L., Xu N., Liu X., Meng Q., Wang X. , Zhang Z.Y.",Surgery-induced gut microbial dysbiosis promotes cognitive impairment via regulation of intestinal function and the metabolite palmitic amide,Microbiome,2023,"Fecal microbiota transplantation, Gut microbiota, Intestinal permeability, Microbiota, Palmitic amide, Perioperative neurocognitive disorders",Experiment 20,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,"Young+Surgery+youngFMT, Young+surgery+agedFMT and Aged+surgery+youngFMT.",Aged+surgery+agedFMT,Adult male C57BL/6 mice 18 months old that underwent surgery and Fecal microbiota transplantation with aged samples.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 7G,30 April 2025,MyleeeA,"MyleeeA,Anne-mariesharp","Linear discriminant analysis Efect Size (LEfSe) was used to find species with significant differences at all taxonomic levels of the gut microbiota in the feces of Young+Surgery+youngFMT, Young+Surgery+agedFMT, Aged+surgery+youngFMT and Aged+surgery+agedFMT groups of mice.",increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres,k__Pseudomonadati|p__Deferribacterota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",1783272|201174|84992;1783272|201174;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|31979|1485;1783272|1239|526524|526525|2810280|100883;3379134|200930|68337|191393|191394;3379134|200930|68337|191393;3379134|200930|68337;3379134|200930;1783272|1239|91061|186826|1300|1357;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|3082720|186804,Complete,KateRasheed
bsdb:37951857/1/1,37951857,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang D.Y., Park J.L., Yeo M.K., Kang S.B., Kim J.M., Kim J.S. , Kim S.Y.",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Healthy controls (HC),Crohn’s disease (CD) patients,Patients with Crohn's disease,50,69,NA,WMS,NA,MGISEQ-2000,raw counts,Linear Regression,1e-4,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Supplemental. file: Table S5,8 March 2024,Samreen-19,"Samreen-19,ChiomaBlessing,WikiWorks",Differences in the taxonomic composition of the gut microbiome in patients with Crohn's disease (CD) compared to healthy controls (HC),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces pacaensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 414,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Aurantimicrobium|s__Aurantimicrobium minutum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. WP8,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Bartonellaceae|g__Bartonella|s__Bartonella clarridgeiae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Bartonellaceae|g__Bartonella|s__Bartonella tribocorum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Metazoa|p__Arthropoda|c__Insecta|o__Blattodea|f__Blattellidae|g__Blattella|s__Blattella germanica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia argi,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter porcelli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Candidatus Johnevansiales|f__Candidatus Johnevansiaceae|g__Candidatus Johnevansia|s__Candidatus Johnevansia muelleri,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Liberibacter|s__Candidatus Liberibacter americanus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Candidatus Midichloriaceae|g__Candidatus Midichloria|s__Candidatus Midichloria mitochondrii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|f__Candidatus Pseudothioglobaceae|g__Candidatus Thioglobus|s__Candidatus Thioglobus autotrophicus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium|s__Carnobacterium maltaromaticum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium butyricum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus durans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus gilvus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus mundtii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia albertii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia fergusonii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia marmotae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Jeotgalibaca|s__Jeotgalibaca dankookensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Marinobacteraceae|g__Marinobacter|s__Marinobacter sp. CP1,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium sp. PYR15,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma|s__Mycoplasma wenyonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus|s__Pediococcus acidilactici,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus|s__Proteus mirabilis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus warneri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus dysgalactiae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus intermedius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus marmotae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pasteurianus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pluranimalium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus respiraculi,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. A12,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 431,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Synechococcales|f__Synechococcaceae|g__Synechococcus|s__Synechococcus sp. KORDI-52,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. YL32,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Companilactobacillus|s__Companilactobacillus zhachilii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|g__Exiguobacterium|s__Exiguobacterium sp. ZWU0009,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter werkmanii",1783272|201174|1760|2037|2049|1654|544580;1783272|201174|1760|2037|2049|1654|1852377;1783272|201174|1760|2037|2049|1654|712122;1783272|201174|1760|85006|85023|1705353|708131;1783272|1239|91061|1385|186817|1386|756828;3379134|1224|28211|356|772|773|56426;3379134|1224|28211|356|772|773|85701;1783272|201174|1760|85004|31953|1678|1685;33208|6656|50557|85823|3046527|6972|6973;1783272|1239|186801|3085636|186803|572511|1912897;3379134|29547|3031852|213849|72294|194|1660073;3379134|1224|1236|3399795|3399796|1495768|1495769;3379134|1224|28211|356|82115|34019|309868;3379134|1224|28211|766|1328881|411566|234827;3379134|1224|1236|3399801|655184|1705394;1783272|1239|91061|186826|186828|2747|2751;1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|186801|186802|31979|1485|1492;1783272|1239|186801|186802|31979|1485|1502;1783272|201174|1760|85009|31957|1912216|1747;1783272|1239|91061|186826|81852|1350|53345;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|91061|186826|81852|1350|1352;1783272|1239|91061|186826|81852|1350|160453;1783272|1239|91061|186826|81852|1350|53346;1783272|1239|526524|526525|128827|2049044;3379134|1224|1236|91347|543|561|208962;3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|543|561|564;3379134|1224|1236|91347|543|561|1499973;1783272|1239|91061|1385|539738|1378|29391;1783272|1239|91061|186826|186828|1470540|708126;3379134|1224|1236|91347|543|570|548;3379134|1224|1236|91347|543|570|571;1783272|1239|91061|186826|33958|1578|33959;1783272|201174|84998|84999|1643824|2767353|1382;3379134|1224|1236|72274|2887365|2742|1671721;1783272|201174|1760|85007|1762|1763|2051552;1783272|544448|31969|2085|2092|2093|65123;1783272|1239|91061|186826|33958|1253|1254;3379134|1224|1236|91347|1903414|583|584;3379134|1224|1236|91347|543|590|28901;1783272|1239|91061|1385|90964|1279|1292;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|91061|186826|1300|1301|113107;1783272|1239|91061|186826|1300|1301|45634;1783272|1239|91061|186826|1300|1301|1334;1783272|1239|91061|186826|1300|1301|1302;1783272|1239|91061|186826|1300|1301|1338;1783272|1239|91061|186826|1300|1301|1825069;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|91061|186826|1300|1301|197614;1783272|1239|91061|186826|1300|1301|82348;1783272|1239|91061|186826|1300|1301|2021971;1783272|1239|91061|186826|1300|1301|1305;1783272|1239|91061|186826|1300|1301|1759399;1783272|1239|91061|186826|1300|1301|712633;1783272|1117|3028117|1890424|1890426|1129|585425;1783272|1239|186801|3085636|186803|1506553|1834196;1783272|1239|91061|186826|33958|2767879|2304606;1783272|1239|91061|1385|33986|1224749;3379134|1224|1236|91347|543|544|67827,Complete,ChiomaBlessing
bsdb:37951857/1/2,37951857,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang D.Y., Park J.L., Yeo M.K., Kang S.B., Kim J.M., Kim J.S. , Kim S.Y.",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Healthy controls (HC),Crohn’s disease (CD) patients,Patients with Crohn's disease,50,69,NA,WMS,NA,MGISEQ-2000,raw counts,Linear Regression,1e-4,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Supplemental. file: Table S5,9 March 2024,Samreen-19,"Samreen-19,ChiomaBlessing,WikiWorks",Differences in the taxonomic composition of the gut microbiome in patients with Crohn's disease (CD) compared to healthy controls (HC),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii",3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|171550|239759|328814,Complete,ChiomaBlessing
bsdb:37951857/2/1,37951857,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang D.Y., Park J.L., Yeo M.K., Kang S.B., Kim J.M., Kim J.S. , Kim S.Y.",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Healthy controls (HC),Ulcerative colitis (UC) patients,Patients with ulcerative colitis,50,198,NA,WMS,NA,MGISEQ-2000,raw counts,Linear Regression,1e-4,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Supplemental. file: Table S8,9 March 2024,Samreen-19,"Samreen-19,ChiomaBlessing,WikiWorks",Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC) compared to healthy controls (HC),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces pacaensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 431,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus respiraculi,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. A12,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Lelliottia|s__Lelliottia nimipressuralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus|s__Pediococcus acidilactici",1783272|201174|1760|85006|1268|32207|43675;1783272|201174|1760|2037|2049|1654|1852377;1783272|1239|91061|186826|1300|1301|1302;1783272|1239|91061|186826|1300|1301|45634;1783272|1239|91061|186826|1300|1301|1305;1783272|1239|91061|186826|1300|1301|712633;1783272|1239|91061|186826|1300|1301|2021971;1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85009|31957|1912216|1747;1783272|1239|91061|186826|1300|1301|113107;1783272|1239|91061|186826|1300|1301|1759399;3379134|1224|1236|91347|543|1330545|69220;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|33958|1253|1254,Complete,ChiomaBlessing
bsdb:37951857/2/2,37951857,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang D.Y., Park J.L., Yeo M.K., Kang S.B., Kim J.M., Kim J.S. , Kim S.Y.",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Healthy controls (HC),Ulcerative colitis (UC) patients,Patients with ulcerative colitis,50,198,NA,WMS,NA,MGISEQ-2000,raw counts,Linear Regression,1e-4,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Supplemental. file: Table S8,9 March 2024,Samreen-19,"Samreen-19,ChiomaBlessing,WikiWorks",Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC) compared to healthy controls (HC),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio sp. G11,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|s__Victivallales bacterium CCUG 44730,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium sp. ORS 278,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila",3379134|976|200643|171549|171550|239759|328814;3379134|200940|3031449|213115|194924|872|631220;3379134|256845|1313211|278082|2094242;3379134|976|200643|171549|1853231|283168|28118;3379134|1224|28211|356|41294|374|114615;3379134|74201|203494|48461|1647988|239934|239935,Complete,ChiomaBlessing
bsdb:37951857/3/1,37951857,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang D.Y., Park J.L., Yeo M.K., Kang S.B., Kim J.M., Kim J.S. , Kim S.Y.",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,Inflammatory bowel disease,EFO:0003767,Ulcerative colitis (UC) patients,Crohn's disease (CD) patients,Patients with Crohn's disease,198,69,NA,WMS,NA,MGISEQ-2000,raw counts,Linear Regression,1e-4,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Supplemental. file: Table S2,9 March 2024,Samreen-19,"Samreen-19,ChiomaBlessing,WikiWorks",Differences in the taxonomic composition of the gut microbiome in patients with Crohn's disease (CD) compared to Ulcerative colitis (UC),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter werkmanii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia albertii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia fergusonii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia marmotae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella dysenteriae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella flexneri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Enterobacteriaceae bacterium strain FGI 57",3379134|1224|1236|91347|543|544|67827;3379134|1224|1236|91347|543|561|208962;3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|543|561|564;3379134|1224|1236|91347|543|561|1499973;3379134|1224|1236|91347|543|590|28901;3379134|1224|1236|91347|543|620|622;3379134|1224|1236|91347|543|620|623;3379134|1224|1236|91347|543|693444,Complete,ChiomaBlessing
bsdb:37951857/3/2,37951857,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang D.Y., Park J.L., Yeo M.K., Kang S.B., Kim J.M., Kim J.S. , Kim S.Y.",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 3,South Korea,Homo sapiens,Feces,UBERON:0001988,Inflammatory bowel disease,EFO:0003767,Ulcerative colitis (UC) patients,Crohn's disease (CD) patients,Patients with Crohn's disease,198,69,NA,WMS,NA,MGISEQ-2000,raw counts,Linear Regression,1e-4,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Supplemental. file: Table S2,9 March 2024,Samreen-19,"Samreen-19,ChiomaBlessing,WikiWorks",Differences in the taxonomic composition of the gut microbiome in patients with Crohn's disease (CD) compared to Ulcerative colitis (UC),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Alicycliphilus|s__Alicycliphilus denitrificans,k__Pseudomonadati|p__Myxococcota|c__Myxococcia|o__Myxococcales|f__Archangiaceae|g__Stigmatella|s__Stigmatella aurantiaca",1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|91061|186826|33958|2767887|1623;3379134|1224|28216|80840|80864|201096|179636;3379134|2818505|32015|29|39|40|41,Complete,ChiomaBlessing
bsdb:37951857/4/1,37951857,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang D.Y., Park J.L., Yeo M.K., Kang S.B., Kim J.M., Kim J.S. , Kim S.Y.",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 4,South Korea,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Health controls (HC),Crohn's disease patients- Mild group,Patients with Crohn's disease in the mild group according to disease activity,50,49,NA,WMS,NA,MGISEQ-2000,relative abundances,"Mann-Whitney (Wilcoxon),T-Test",0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Figure 2J,1 April 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differences in the taxonomic composition of the gut microbiome in patients with Crohn's disease (CD)- mild group compared to Healthy controls (HC),decreased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Pseudodesulfovibrio|s__Pseudodesulfovibrio aespoeensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii",3379134|200940|3031449|213115|194924|2035811|182210;3379134|976|200643|171549|171550|239759|328814,Complete,ChiomaBlessing
bsdb:37951857/5/1,37951857,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang D.Y., Park J.L., Yeo M.K., Kang S.B., Kim J.M., Kim J.S. , Kim S.Y.",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 5,South Korea,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Health controls (HC),Crohn's disease patients- Moderate group,Patients with Crohn's disease in the moderate group according to disease activity,50,19,NA,WMS,NA,MGISEQ-2000,relative abundances,"Mann-Whitney (Wilcoxon),T-Test",0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Figure 2J,1 April 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differences in the taxonomic composition of the gut microbiome in patients with Crohn's disease (CD)- moderate group compared to Healthy controls (HC),decreased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Pseudodesulfovibrio|s__Pseudodesulfovibrio aespoeensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii",3379134|200940|3031449|213115|194924|2035811|182210;3379134|976|200643|171549|171550|239759|328814,Complete,ChiomaBlessing
bsdb:37951857/5/2,37951857,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang D.Y., Park J.L., Yeo M.K., Kang S.B., Kim J.M., Kim J.S. , Kim S.Y.",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 5,South Korea,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Health controls (HC),Crohn's disease patients- Moderate group,Patients with Crohn's disease in the moderate group according to disease activity,50,19,NA,WMS,NA,MGISEQ-2000,relative abundances,"Mann-Whitney (Wilcoxon),T-Test",0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Figure 2J,1 April 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differences in the taxonomic composition of the gut microbiome in patients with Crohn's disease (CD)- moderate group compared to Healthy controls (HC),increased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Polynucleobacter|s__Polynucleobacter wuianus,3379134|1224|28216|80840|119060|44013|1743168,Complete,ChiomaBlessing
bsdb:37951857/6/1,37951857,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang D.Y., Park J.L., Yeo M.K., Kang S.B., Kim J.M., Kim J.S. , Kim S.Y.",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 6,South Korea,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Health controls (HC),"Ulcerative colitis disease patients- Mild, moderate and severe groups","Patients with Ulcerative colitis disease in the mild, moderate and severe groups according to disease activity",50,NA,NA,WMS,NA,MGISEQ-2000,relative abundances,"Mann-Whitney (Wilcoxon),T-Test",0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Figure 3J,1 April 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks","Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC)- mild, moderate and severe groups compared to Healthy controls (HC)",decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171551|836|28123;3379134|976|200643|171549|171550|239759|328814,Complete,ChiomaBlessing
bsdb:37951857/6/2,37951857,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang D.Y., Park J.L., Yeo M.K., Kang S.B., Kim J.M., Kim J.S. , Kim S.Y.",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 6,South Korea,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Health controls (HC),"Ulcerative colitis disease patients- Mild, moderate and severe groups","Patients with Ulcerative colitis disease in the mild, moderate and severe groups according to disease activity",50,NA,NA,WMS,NA,MGISEQ-2000,relative abundances,"Mann-Whitney (Wilcoxon),T-Test",0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Figure 3J,1 April 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks","Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC)- mild, moderate and severe groups compared to Healthy controls (HC)",increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Candidatus Pantoea carbekii,3379134|1224|1236|91347|1903409|53335|1235990,Complete,ChiomaBlessing
bsdb:37951857/7/1,37951857,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang D.Y., Park J.L., Yeo M.K., Kang S.B., Kim J.M., Kim J.S. , Kim S.Y.",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 7,South Korea,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Ulcerative colitis disease patients- Mild group,Ulcerative colitis disease patients- Severe group,Patients with Ulcerative colitis disease in the severe group according to disease activity,162,11,NA,WMS,NA,MGISEQ-2000,relative abundances,"Mann-Whitney (Wilcoxon),T-Test",0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Figure 3J,1 April 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC)- severe group compared to Ulcerative colitis disease (UC)- mild group (Mann-Whitney and T-test),decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171551|836|28123;3379134|976|200643|171549|171550|239759|328814,Complete,ChiomaBlessing
bsdb:37951857/7/2,37951857,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang D.Y., Park J.L., Yeo M.K., Kang S.B., Kim J.M., Kim J.S. , Kim S.Y.",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 7,South Korea,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Ulcerative colitis disease patients- Mild group,Ulcerative colitis disease patients- Severe group,Patients with Ulcerative colitis disease in the severe group according to disease activity,162,11,NA,WMS,NA,MGISEQ-2000,relative abundances,"Mann-Whitney (Wilcoxon),T-Test",0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Figure 3J,1 April 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC)- severe group compared to Ulcerative colitis disease (UC)- mild group (Mann-Whitney and T-test),increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Candidatus Pantoea carbekii,3379134|1224|1236|91347|1903409|53335|1235990,Complete,ChiomaBlessing
bsdb:37951857/9/1,37951857,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang D.Y., Park J.L., Yeo M.K., Kang S.B., Kim J.M., Kim J.S. , Kim S.Y.",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 9,South Korea,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Ulcerative colitis disease patients- Mild group,Ulcerative colitis disease patients- Severe group,Patients with Ulcerative colitis disease in the severe group according to disease activity,162,11,NA,WMS,NA,MGISEQ-2000,relative abundances,Linear Regression,0.01,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Supplemental. Table S9,1 April 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC)- severe group compared to Ulcerative colitis disease (UC)- mild group,decreased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfarculia|o__Desulfarculales|f__Desulfarculaceae|g__Desulfarculus|s__Desulfarculus baarsii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Denitrobacterium|s__Denitrobacterium detoxificans",3379134|200940|3031646|453227|453228|453229|453230;1783272|201174|84998|1643822|1643826|79603|79604,Complete,ChiomaBlessing
bsdb:37951857/9/2,37951857,case-control,37951857,10.1186/s12866-023-03084-5,NA,"Kang D.Y., Park J.L., Yeo M.K., Kang S.B., Kim J.M., Kim J.S. , Kim S.Y.",Diagnosis of Crohn's disease and ulcerative colitis using the microbiome,BMC microbiology,2023,"Crohn’s disease, Gut microbiome, Inflammatory bowel disease, Machine learning, Ulcerative colitis, Whole metagenome shotgun (WMS) sequencing",Experiment 9,South Korea,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Ulcerative colitis disease patients- Mild group,Ulcerative colitis disease patients- Severe group,Patients with Ulcerative colitis disease in the severe group according to disease activity,162,11,NA,WMS,NA,MGISEQ-2000,relative abundances,Linear Regression,0.01,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Supplemental. Table S9,1 April 2024,ChiomaBlessing,"ChiomaBlessing,WikiWorks",Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC)- severe group compared to Ulcerative colitis disease (UC)- mild group,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. SJ-10,k__Metazoa|p__Arthropoda|c__Insecta|o__Blattodea|f__Blattellidae|g__Blattella|s__Blattella germanica",1783272|1239|91061|1385|186817|1386|563169;33208|6656|50557|85823|3046527|6972|6973,Complete,ChiomaBlessing
bsdb:37953319/1/1,37953319,"cross-sectional observational, not case-control",37953319,10.1186/s40168-023-01694-9,NA,"Kaisanlahti A., Turunen J., Byts N., Samoylenko A., Bart G., Virtanen N., Tejesvi M.V., Zhyvolozhnyi A., Sarfraz S., Kumpula S., Hekkala J., Salmi S., Will O., Korvala J., Paalanne N., Erawijantari P.P., Suokas M., Medina T.P., Vainio S., Medina O.P., Lahti L., Tapiainen T. , Reunanen J.",Maternal microbiota communicates with the fetus through microbiota-derived extracellular vesicles,Microbiome,2023,"Amniotic fluid, Extracellular vesicles, Fetal environment, Fetal microbiota, Gut microbiota, Intestine",Experiment 1,Finland,Homo sapiens,Amniotic fluid,UBERON:0000173,Vesicle membrane,GO:0012506,Amniotic fluid (AM),Amniotic fluid-derived extracellular vesicles (AM EVs),Amniotic fluid-derived extracellular vesicles from Amniotic samples,10,24,NA,16S,45,Ion Torrent,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,increased,Signature 1,Additional file 1: Table 8,25 March 2024,Iman-Ngwepe,"Iman-Ngwepe,Fiddyhamma,MyleeeA,WikiWorks,Ese",The differentially abundant genera in the amniotic fluid (AM) vs. amniotic fluid-derived extracellular vesicles (AM EV),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Vibrionimonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Williamsia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|815|816;3379134|1224|28211|356|41294|374;3384194|1297|188787|118964|183710|1298;1783272|201174|1760|85006|145357|57495;1783272|1239|91061|186826|186828|29393;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563;1783272|201174|1760|85007|2805586|1847725;3379134|1224|28216|206351|481|482;1783272|1239|1737404|1737405|1570339|162289;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;3379134|976|1853228|1853229|563835|1649511;1783272|201174|1760|85007|85025|85043;3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:37953319/1/2,37953319,"cross-sectional observational, not case-control",37953319,10.1186/s40168-023-01694-9,NA,"Kaisanlahti A., Turunen J., Byts N., Samoylenko A., Bart G., Virtanen N., Tejesvi M.V., Zhyvolozhnyi A., Sarfraz S., Kumpula S., Hekkala J., Salmi S., Will O., Korvala J., Paalanne N., Erawijantari P.P., Suokas M., Medina T.P., Vainio S., Medina O.P., Lahti L., Tapiainen T. , Reunanen J.",Maternal microbiota communicates with the fetus through microbiota-derived extracellular vesicles,Microbiome,2023,"Amniotic fluid, Extracellular vesicles, Fetal environment, Fetal microbiota, Gut microbiota, Intestine",Experiment 1,Finland,Homo sapiens,Amniotic fluid,UBERON:0000173,Vesicle membrane,GO:0012506,Amniotic fluid (AM),Amniotic fluid-derived extracellular vesicles (AM EVs),Amniotic fluid-derived extracellular vesicles from Amniotic samples,10,24,NA,16S,45,Ion Torrent,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,increased,Signature 2,Additional file 1: Table 8,22 October 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",The differentially abundant genera in the amniotic fluid (AM) vs. amniotic fluid-derived extracellular vesicles (AM EV),decreased,k__Thermotogati|p__Deinococcota,3384194|1297,Complete,Svetlana up
bsdb:37953319/2/1,37953319,"cross-sectional observational, not case-control",37953319,10.1186/s40168-023-01694-9,NA,"Kaisanlahti A., Turunen J., Byts N., Samoylenko A., Bart G., Virtanen N., Tejesvi M.V., Zhyvolozhnyi A., Sarfraz S., Kumpula S., Hekkala J., Salmi S., Will O., Korvala J., Paalanne N., Erawijantari P.P., Suokas M., Medina T.P., Vainio S., Medina O.P., Lahti L., Tapiainen T. , Reunanen J.",Maternal microbiota communicates with the fetus through microbiota-derived extracellular vesicles,Microbiome,2023,"Amniotic fluid, Extracellular vesicles, Fetal environment, Fetal microbiota, Gut microbiota, Intestine",Experiment 2,Finland,Homo sapiens,"Amniotic fluid,Feces","UBERON:0000173,UBERON:0001988",Vesicle membrane,GO:0012506,Amniotic fluid (AM),Maternal feces (FE),Maternal feces collected before cesarean section,10,22,NA,16S,45,Ion Torrent,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Additional file 1: Table 8,25 March 2024,Iman-Ngwepe,"Iman-Ngwepe,Fiddyhamma,WikiWorks",The differentially abundant genera in the amniotic fluid (AM) vs. Maternal Feces (FE),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",3379134|1224|28211|356|41294|374;1783272|201174|1760|85006|145357|57495;1783272|1239|186801|186802|216572|216851;1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:37953319/2/2,37953319,"cross-sectional observational, not case-control",37953319,10.1186/s40168-023-01694-9,NA,"Kaisanlahti A., Turunen J., Byts N., Samoylenko A., Bart G., Virtanen N., Tejesvi M.V., Zhyvolozhnyi A., Sarfraz S., Kumpula S., Hekkala J., Salmi S., Will O., Korvala J., Paalanne N., Erawijantari P.P., Suokas M., Medina T.P., Vainio S., Medina O.P., Lahti L., Tapiainen T. , Reunanen J.",Maternal microbiota communicates with the fetus through microbiota-derived extracellular vesicles,Microbiome,2023,"Amniotic fluid, Extracellular vesicles, Fetal environment, Fetal microbiota, Gut microbiota, Intestine",Experiment 2,Finland,Homo sapiens,"Amniotic fluid,Feces","UBERON:0000173,UBERON:0001988",Vesicle membrane,GO:0012506,Amniotic fluid (AM),Maternal feces (FE),Maternal feces collected before cesarean section,10,22,NA,16S,45,Ion Torrent,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,Additional file 1: Table 8,22 October 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",The differentially abundant genera in the amniotic fluid (AM) vs. Maternal Feces (FE),decreased,"k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota",3379134|976;1783272|1239,Complete,Svetlana up
bsdb:37953319/3/NA,37953319,"cross-sectional observational, not case-control",37953319,10.1186/s40168-023-01694-9,NA,"Kaisanlahti A., Turunen J., Byts N., Samoylenko A., Bart G., Virtanen N., Tejesvi M.V., Zhyvolozhnyi A., Sarfraz S., Kumpula S., Hekkala J., Salmi S., Will O., Korvala J., Paalanne N., Erawijantari P.P., Suokas M., Medina T.P., Vainio S., Medina O.P., Lahti L., Tapiainen T. , Reunanen J.",Maternal microbiota communicates with the fetus through microbiota-derived extracellular vesicles,Microbiome,2023,"Amniotic fluid, Extracellular vesicles, Fetal environment, Fetal microbiota, Gut microbiota, Intestine",Experiment 3,Finland,Homo sapiens,"Amniotic fluid,Feces","UBERON:0000173,UBERON:0001988",Vesicle membrane,GO:0012506,Amniotic fluid (AM),Feces-derived extracellular vesicles (FE EV),Feces-derived extracellular vesicles from Feces samples,10,22,NA,16S,45,Ion Torrent,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:37953319/4/NA,37953319,"cross-sectional observational, not case-control",37953319,10.1186/s40168-023-01694-9,NA,"Kaisanlahti A., Turunen J., Byts N., Samoylenko A., Bart G., Virtanen N., Tejesvi M.V., Zhyvolozhnyi A., Sarfraz S., Kumpula S., Hekkala J., Salmi S., Will O., Korvala J., Paalanne N., Erawijantari P.P., Suokas M., Medina T.P., Vainio S., Medina O.P., Lahti L., Tapiainen T. , Reunanen J.",Maternal microbiota communicates with the fetus through microbiota-derived extracellular vesicles,Microbiome,2023,"Amniotic fluid, Extracellular vesicles, Fetal environment, Fetal microbiota, Gut microbiota, Intestine",Experiment 4,Finland,Homo sapiens,"Amniotic fluid,Feces","UBERON:0000173,UBERON:0001988",Vesicle membrane,GO:0012506,Amniotic fluid-derived extracellular vesicles (AM EV),Maternal feces (FE),Maternal feces collected before cesarean section,24,22,NA,16S,45,Ion Torrent,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:37953319/5/1,37953319,"cross-sectional observational, not case-control",37953319,10.1186/s40168-023-01694-9,NA,"Kaisanlahti A., Turunen J., Byts N., Samoylenko A., Bart G., Virtanen N., Tejesvi M.V., Zhyvolozhnyi A., Sarfraz S., Kumpula S., Hekkala J., Salmi S., Will O., Korvala J., Paalanne N., Erawijantari P.P., Suokas M., Medina T.P., Vainio S., Medina O.P., Lahti L., Tapiainen T. , Reunanen J.",Maternal microbiota communicates with the fetus through microbiota-derived extracellular vesicles,Microbiome,2023,"Amniotic fluid, Extracellular vesicles, Fetal environment, Fetal microbiota, Gut microbiota, Intestine",Experiment 5,Finland,Homo sapiens,"Amniotic fluid,Feces","UBERON:0000173,UBERON:0001988",Vesicle membrane,GO:0012506,Amniotic fluid-derived extracellular vesicles (AM EV),Feces-derived extracellular vesicles (FE EV),Feces-derived extracellular vesicles from Feces samples,24,22,NA,16S,45,Ion Torrent,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Additional file 1: Table 8,25 March 2024,Iman-Ngwepe,"Iman-Ngwepe,Fiddyhamma,WikiWorks",The differentially abundant genera in the amniotic fluid-derived extracellular vesicles (AM EV) vs. fecal-derived extracellular vesicles (FE EV),increased,k__Fusobacteriati|p__Fusobacteriota,3384189|32066,Complete,Svetlana up
bsdb:37953319/5/2,37953319,"cross-sectional observational, not case-control",37953319,10.1186/s40168-023-01694-9,NA,"Kaisanlahti A., Turunen J., Byts N., Samoylenko A., Bart G., Virtanen N., Tejesvi M.V., Zhyvolozhnyi A., Sarfraz S., Kumpula S., Hekkala J., Salmi S., Will O., Korvala J., Paalanne N., Erawijantari P.P., Suokas M., Medina T.P., Vainio S., Medina O.P., Lahti L., Tapiainen T. , Reunanen J.",Maternal microbiota communicates with the fetus through microbiota-derived extracellular vesicles,Microbiome,2023,"Amniotic fluid, Extracellular vesicles, Fetal environment, Fetal microbiota, Gut microbiota, Intestine",Experiment 5,Finland,Homo sapiens,"Amniotic fluid,Feces","UBERON:0000173,UBERON:0001988",Vesicle membrane,GO:0012506,Amniotic fluid-derived extracellular vesicles (AM EV),Feces-derived extracellular vesicles (FE EV),Feces-derived extracellular vesicles from Feces samples,24,22,NA,16S,45,Ion Torrent,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,Additional file 1: Table 8,22 October 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",The differentially abundant genera in the amniotic fluid-derived extracellular vesicles (AM EV) vs. fecal-derived extracellular vesicles (FE EV),decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia",3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|815|816;1783272|1239|1737404|1737405|1570339|150022,Complete,Svetlana up
bsdb:37953319/6/1,37953319,"cross-sectional observational, not case-control",37953319,10.1186/s40168-023-01694-9,NA,"Kaisanlahti A., Turunen J., Byts N., Samoylenko A., Bart G., Virtanen N., Tejesvi M.V., Zhyvolozhnyi A., Sarfraz S., Kumpula S., Hekkala J., Salmi S., Will O., Korvala J., Paalanne N., Erawijantari P.P., Suokas M., Medina T.P., Vainio S., Medina O.P., Lahti L., Tapiainen T. , Reunanen J.",Maternal microbiota communicates with the fetus through microbiota-derived extracellular vesicles,Microbiome,2023,"Amniotic fluid, Extracellular vesicles, Fetal environment, Fetal microbiota, Gut microbiota, Intestine",Experiment 6,Finland,Homo sapiens,Feces,UBERON:0001988,Vesicle membrane,GO:0012506,Maternal feces (FE),Feces-derived extracellular vesicles (FE EV),Feces-derived extracellular vesicles from Feces samples,22,22,NA,16S,45,Ion Torrent,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Additional file 1: Table 8,25 March 2024,Iman-Ngwepe,"Iman-Ngwepe,Fiddyhamma,WikiWorks",The differentially abundant genera in Maternal feces (FE) vs. fecal-derived extracellular vesicles (FE EV),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Eremococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Williamsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171552|1283313;1783272|1239|1737404|1737405|1570339|165779;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005519|397864;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|1980681;3384194|1297|188787|118964|183710|1298;1783272|1239|91061|186826|186828|29393;1783272|1239|91061|186826|186827|171412;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|1737404|1582879;1783272|1239|186801|186802|216572|216851;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563;1783272|1239|186801|3085636|186803;1783272|201174|1760|85007|2805586|1847725;1783272|201174|1760|85006|1268|1269;3379134|1224|28216|206351|481|482;1783272|1239|186801|186802|216572|459786;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|1737404|1737405|1570339|162289;3379134|976|200643|171549|171551|836;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|292632;1783272|1239|909932|1843489|31977|29465;1783272|201174|1760|85007|85025|85043;1783272|1239|186801|186802|216572|707003,Complete,Svetlana up
bsdb:37953319/6/2,37953319,"cross-sectional observational, not case-control",37953319,10.1186/s40168-023-01694-9,NA,"Kaisanlahti A., Turunen J., Byts N., Samoylenko A., Bart G., Virtanen N., Tejesvi M.V., Zhyvolozhnyi A., Sarfraz S., Kumpula S., Hekkala J., Salmi S., Will O., Korvala J., Paalanne N., Erawijantari P.P., Suokas M., Medina T.P., Vainio S., Medina O.P., Lahti L., Tapiainen T. , Reunanen J.",Maternal microbiota communicates with the fetus through microbiota-derived extracellular vesicles,Microbiome,2023,"Amniotic fluid, Extracellular vesicles, Fetal environment, Fetal microbiota, Gut microbiota, Intestine",Experiment 6,Finland,Homo sapiens,Feces,UBERON:0001988,Vesicle membrane,GO:0012506,Maternal feces (FE),Feces-derived extracellular vesicles (FE EV),Feces-derived extracellular vesicles from Feces samples,22,22,NA,16S,45,Ion Torrent,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Additional file 1: Table 8,22 October 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",The differentially abundant genera in Maternal feces (FE) vs. fecal-derived extracellular vesicles (FE EV),decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota,k__Thermotogati|p__Deinococcota,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobacteria,k__Fusobacteriati|p__Fusobacteriota",1783272|201174;3379134|976;3384194|1297;3379134|200940|3024418;3384189|32066,Complete,Svetlana up
bsdb:37960154/1/1,37960154,laboratory experiment,37960154,10.3390/nu15214502,NA,"Luo M., Xie P., Deng X., Fan J. , Xiong L.",Rifaximin Ameliorates Loperamide-Induced Constipation in Rats through the Regulation of Gut Microbiota and Serum Metabolites,Nutrients,2023,"5-HT, bile acids, constipation, gut microbiota, loperamide, metabolites, rifaximin",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Combination of LOP (loperamide) and RIF (rifaximin) group,CTR (control) group,Rats in this group were injected with 0.9% saline.,14,7,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3G and 3H,3 April 2025,Tosin,Tosin,Histogram of LDA value distribution generated by LEfSe indicating the differences of bacterial communities among three groups after LDA using a threshold score of LDA > 3.5,increased,"p__Candidatus Altimarinota,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus intestinalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus murinus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",363464;95818|2093818|2093825|2171986;95818|2093818|2093825;95818|2093818;95818|2093818|2093825|2171986|1331051;1783272|1239|91061|186826|33958|1578|151781;1783272|1239|91061|186826|33958|2767887|1622;3379134|976|200643|171549|171550;3379134|976|200643|171549|171550|239759,Complete,Svetlana up
bsdb:37960154/2/1,37960154,laboratory experiment,37960154,10.3390/nu15214502,NA,"Luo M., Xie P., Deng X., Fan J. , Xiong L.",Rifaximin Ameliorates Loperamide-Induced Constipation in Rats through the Regulation of Gut Microbiota and Serum Metabolites,Nutrients,2023,"5-HT, bile acids, constipation, gut microbiota, loperamide, metabolites, rifaximin",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Combination of CTR (control) and RIF (rifaximin) group,LOP (loperamide) group,Rats in this group were injected subcutaneously with 5 mg kg−1 of body weight loperamide in 0.9% saline solution twice daily at 09:00 am and 5:00 pm for 14 days,14,7,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3G and 3H,3 April 2025,Tosin,Tosin,Histogram of LDA value distribution generated by LEfSe indicating the differences of bacterial communities among three groups after LDA using a threshold score of LDA > 3.5,increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum|s__Faecalibaculum rodentium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum|s__uncultured Allobaculum sp.",1783272|201174|84992;1783272|201174;1783272|1239|526524|526525|128827|174708;1783272|201174|84998|84999|1643824;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|1694;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|526524|526525|128827|1937008;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|186801|186802;1783272|1239|526524|526525|128827|1729679;1783272|1239|526524|526525|128827|1729679|1702221;1783272|1239|526524|526525|2810281|191303;1783272|1239|526524|526525|128827|174708|1187017,Complete,Svetlana up
bsdb:37960154/3/1,37960154,laboratory experiment,37960154,10.3390/nu15214502,NA,"Luo M., Xie P., Deng X., Fan J. , Xiong L.",Rifaximin Ameliorates Loperamide-Induced Constipation in Rats through the Regulation of Gut Microbiota and Serum Metabolites,Nutrients,2023,"5-HT, bile acids, constipation, gut microbiota, loperamide, metabolites, rifaximin",Experiment 3,China,Rattus norvegicus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Combination of CTR (control) and LOP (loperamide) group,RIF (rifaximin) group,The rats in the RIF group were treated with rifaximin (75 mg kg−1 body weight) by gavage administration one hour after LOP was injected,14,7,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3G and 3H,3 April 2025,Tosin,Tosin,Histogram of LDA value distribution generated by LEfSe indicating the differences of bacterial communities among three groups after LDA using a threshold score of LDA > 3.5,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota,s__unidentified rumen bacterium RF39",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988|239934|239935;3379134|74201|203494|48461|1647988;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|1263|438033;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201;60681,Complete,Svetlana up
bsdb:37960154/4/1,37960154,laboratory experiment,37960154,10.3390/nu15214502,NA,"Luo M., Xie P., Deng X., Fan J. , Xiong L.",Rifaximin Ameliorates Loperamide-Induced Constipation in Rats through the Regulation of Gut Microbiota and Serum Metabolites,Nutrients,2023,"5-HT, bile acids, constipation, gut microbiota, loperamide, metabolites, rifaximin",Experiment 4,China,Rattus norvegicus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,CTR (control) group,LOP (loperamide) group,Rats in this group were injected subcutaneously with 5 mg kg−1 of body weight loperamide in 0.9% saline solution twice daily at 09:00 am and 5:00 pm for 14 days,7,7,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,T-Test",0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Figure 4A, 4B and 4C",3 April 2025,Tosin,Tosin,"Relative abundances of gut microbiota at the phylum, genus and species level among CTR (control) and LOP (loperamide) groups.",increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum|s__Faecalibaculum rodentium",1783272|201174;1783272|1239|526524|526525|128827|174708;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|1694;1783272|1239|186801|186802|31979|1485;1783272|1239|526524|526525|128827|1937008;1783272|1239|526524|526525|128827|1729679;1783272|1239|526524|526525|128827|1729679|1702221,Complete,Svetlana up
bsdb:37960154/4/2,37960154,laboratory experiment,37960154,10.3390/nu15214502,NA,"Luo M., Xie P., Deng X., Fan J. , Xiong L.",Rifaximin Ameliorates Loperamide-Induced Constipation in Rats through the Regulation of Gut Microbiota and Serum Metabolites,Nutrients,2023,"5-HT, bile acids, constipation, gut microbiota, loperamide, metabolites, rifaximin",Experiment 4,China,Rattus norvegicus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,CTR (control) group,LOP (loperamide) group,Rats in this group were injected subcutaneously with 5 mg kg−1 of body weight loperamide in 0.9% saline solution twice daily at 09:00 am and 5:00 pm for 14 days,7,7,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,T-Test",0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Figure 4A, 4B and 4C",3 April 2025,Tosin,Tosin,"Relative abundances of gut microbiota at the phylum, genus and species level among CTR (control) and LOP (loperamide) groups.",decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus murinus,1783272|1239|91061|186826|33958|2767887|1622,Complete,Svetlana up
bsdb:37960154/5/1,37960154,laboratory experiment,37960154,10.3390/nu15214502,NA,"Luo M., Xie P., Deng X., Fan J. , Xiong L.",Rifaximin Ameliorates Loperamide-Induced Constipation in Rats through the Regulation of Gut Microbiota and Serum Metabolites,Nutrients,2023,"5-HT, bile acids, constipation, gut microbiota, loperamide, metabolites, rifaximin",Experiment 5,China,Rattus norvegicus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,LOP (loperamide) group,RIF (rifaximin) group,The rats in the RIF group were treated with rifaximin (75 mg kg−1 body weight) by gavage administration one hour after LOP was injected,7,7,NA,16S,34,Illumina,relative abundances,"T-Test,Kruskall-Wallis",0.05,FALSE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,"Figure 4A, 4B, 4C, Table S1 and Table S2",3 April 2025,Tosin,Tosin,"Relative abundances of gut microbiota at the phylum, genus and species level among LOP (loperamide) and RIF (rifaximin) groups",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis|s__Anaerofustis stercorihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium elkanii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Globicatella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium MD335,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus murinus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola paurosaccharolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Plesiomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Plesiomonas|s__Plesiomonas shigelloides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|186802|186806|264995;1783272|1239|186801|186802|186806|264995|214853;1783272|1239|186801|3085636|186803|572511;3379134|1224|28211|356|41294|374;3379134|1224|28211|356|41294|374|29448;1783272|1239|526524|526525|2810280;1783272|201174|84998|1643822|1643826|580024;1783272|1239|526524|526525|128827|1573534;1783272|1239|91061|186826|186827|13075;1783272|201174|84998|1643822|1643826|644652;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|1235793;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|2767887|1622;3379134|976|200643|171549|815|909656|732242;3379134|1224|1236|91347|543|702;3379134|1224|1236|91347|543|702|703;1783272|201174|1760|85006|1268|32207;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|438033;1783272|1239|526524|526525|2810280|3025755;3379134|74201;1783272|1239|186801|186802|31979|1485|1522;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|3082720|543314|35518,Complete,Svetlana up
bsdb:37960154/5/2,37960154,laboratory experiment,37960154,10.3390/nu15214502,NA,"Luo M., Xie P., Deng X., Fan J. , Xiong L.",Rifaximin Ameliorates Loperamide-Induced Constipation in Rats through the Regulation of Gut Microbiota and Serum Metabolites,Nutrients,2023,"5-HT, bile acids, constipation, gut microbiota, loperamide, metabolites, rifaximin",Experiment 5,China,Rattus norvegicus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,LOP (loperamide) group,RIF (rifaximin) group,The rats in the RIF group were treated with rifaximin (75 mg kg−1 body weight) by gavage administration one hour after LOP was injected,7,7,NA,16S,34,Illumina,relative abundances,"T-Test,Kruskall-Wallis",0.05,FALSE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,"Figure 4A, 4B, 4C, Table S1 and Table S2",3 April 2025,Tosin,Tosin,"Relative abundances of gut microbiota at the phylum, genus and species level among LOP (loperamide) and RIF (rifaximin) groups",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. cv1,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Bacilli,,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,p__Candidatus Altimarinota,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella minuta,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Crenobacter,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|g__Exiguobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|g__Exiguobacterium|s__Exiguobacterium sp. AT1b,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum|s__Faecalibaculum rodentium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Ideonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus|s__Pediococcus pentosaceus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pygmaiobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia ilealis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] brachy,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__uncultured Eubacteriales bacterium",3379134|1224|28216|80840|506|222;1783272|201174;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550|239759|1622071;1783272|1239|526524|526525|128827|174708;1783272|1239|91061;;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|1694;363464;95818|2093818|2093825|2171986|1331051;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|3082768|990719|990721|626937;1783272|1239|186801|3082768|990719|990721|1816678;1783272|1239|186801|3082768|424536;1783272|1239|186801;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999;3379134|1224|28216|206351|481|1654931;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;1783272|1239|526524|526525|128827|1937008;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|91061|1385|33986;1783272|1239|91061|1385|33986|360911;1783272|1239|526524|526525|128827|1729679;1783272|1239|526524|526525|128827|1729679|1702221;3379134|1224|28216|80840|2975441|36862;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|995019|577310;1783272|1239|91061|186826|33958|1253;1783272|1239|91061|186826|33958|1253|1255;1783272|1239|186801|186802|186807|2740;3379134|1224;1783272|1239|186801|186802|216572|1929305;3379134|976|200643|171549|171550|28138;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3082720|186804|1501226|1115758;1783272|1239|186801|186802|216572|1508657;3379134|1224|28216|80840|995019;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|3082720|543314|35517;1783272|1239|186801|186802|31979|1485|59620;1783272|1239|186801|186802|172733,Complete,Svetlana up
bsdb:37960281/1/1,37960281,case-control,37960281,10.3390/nu15214628,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10649662/,"Altinok Dindar D., Chun B., Palma A., Cheney J., Krieger M., Kasschau K., Stagaman K., Mitri Z.I., Goodyear S.M., Shannon J., Karstens L., Sharpton T. , Zhang Z.",Association between Gut Microbiota and Breast Cancer: Diet as a Potential Modulating Factor,Nutrients,2023,"Acidaminococus, Hungatella, Tyzzerella, breast cancer, gut microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,Healthy controls,Breast cancer patients,"Biopsy-confirmed diagnosis of breast cancer prior to initiating any treatment, including surgery, chemotherapy, or radiation therapy.",44,42,Not mentioned,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,body mass index,decreased,decreased,NA,NA,decreased,NA,Signature 1,Figure 2,30 November 2023,Andre,"Andre,WikiWorks",Linear discriminant analysis effect size (LEfSe) analysis of fecal microbiome at genus level of the participants in the control and BCa group samples,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",1783272|1239|909932|1843488|909930|904;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|3085636|186803|1506577,Complete,Folakunmi
bsdb:37960281/1/2,37960281,case-control,37960281,10.3390/nu15214628,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10649662/,"Altinok Dindar D., Chun B., Palma A., Cheney J., Krieger M., Kasschau K., Stagaman K., Mitri Z.I., Goodyear S.M., Shannon J., Karstens L., Sharpton T. , Zhang Z.",Association between Gut Microbiota and Breast Cancer: Diet as a Potential Modulating Factor,Nutrients,2023,"Acidaminococus, Hungatella, Tyzzerella, breast cancer, gut microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,Healthy controls,Breast cancer patients,"Biopsy-confirmed diagnosis of breast cancer prior to initiating any treatment, including surgery, chemotherapy, or radiation therapy.",44,42,Not mentioned,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,body mass index,decreased,decreased,NA,NA,decreased,NA,Signature 2,Figure 2,30 November 2023,Andre,"Andre,Folakunmi,WikiWorks",Linear discriminant analysis effect size (LEfSe) analysis of fecal microbiome at genus level of the participants in the control and BCa group samples,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,g__Candidatus Galligastranaerophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A144,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,s__rumen bacterium NK4A214",1783272|1239|186801|186802|216572|52784;2840511;1783272|1239|186801|3082768|990719;1783272|201174|84998|84999;1783272|1239|909932|1843489|31977|39948;3379134|976|117743|200644;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|216572|3068309;1783272|1239|186801|3085636|186803|877421;1783272|1239|186801|186802|216572;877428,Complete,Folakunmi
bsdb:37975314/1/1,37975314,case-control,37975314,10.1021/acsinfecdis.3c00416,NA,"Liu H., Ji S., Fang Y., Yi X., Wu F., Xing F., Wang C., Zhou H., Xu J. , Sun W.",Microbiome Alteration in Lung Tissues of Tuberculosis Patients Revealed by Metagenomic Next-Generation Sequencing and Immune-Related Transcriptional Profile Identified by Transcriptome Sequencing,ACS infectious diseases,2023,"mNGS, microbiome, transcriptional profile, transcriptome sequencing, tuberculosis",Experiment 1,China,Homo sapiens,Lung,UBERON:0002048,Pulmonary tuberculosis,EFO:1000049,patients with Non-tuberculosis,patients with tuberculosis,"Mtb-positive in the bacteriological examination, including sputum smear or sputum
culture, mNGS, acid-fast staining, T-spot, adenosine deaminase, PCR, and interferon-gamma release assay; clinical manifestations such as constitutional symptoms and imaging
manifestations; improvement following initiation of anti-TB therapy.",25,110,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,Signature 1,Figure 2C,20 July 2025,Nuerteye,Nuerteye,Microbial distribution in lung tissues of TB and NonTB patients. LEfSe analyses were performed to determine the microbial features with significant differences in the relative abundance.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia|s__Delftia tsuruhatensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Streptosporangiales|f__Streptosporangiaceae|g__Streptosporangium|s__Streptosporangium violaceochromogenes",3379134|1224|28216|80840|80864|80865|180282;1783272|201174|1760|85012|2004|2000|46188,Complete,NA
bsdb:37975314/1/2,37975314,case-control,37975314,10.1021/acsinfecdis.3c00416,NA,"Liu H., Ji S., Fang Y., Yi X., Wu F., Xing F., Wang C., Zhou H., Xu J. , Sun W.",Microbiome Alteration in Lung Tissues of Tuberculosis Patients Revealed by Metagenomic Next-Generation Sequencing and Immune-Related Transcriptional Profile Identified by Transcriptome Sequencing,ACS infectious diseases,2023,"mNGS, microbiome, transcriptional profile, transcriptome sequencing, tuberculosis",Experiment 1,China,Homo sapiens,Lung,UBERON:0002048,Pulmonary tuberculosis,EFO:1000049,patients with Non-tuberculosis,patients with tuberculosis,"Mtb-positive in the bacteriological examination, including sputum smear or sputum
culture, mNGS, acid-fast staining, T-spot, adenosine deaminase, PCR, and interferon-gamma release assay; clinical manifestations such as constitutional symptoms and imaging
manifestations; improvement following initiation of anti-TB therapy.",25,110,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,Signature 2,Figure 2C,20 July 2025,Nuerteye,Nuerteye,Microbial distribution in lung tissues of TB and NonTB patients. LEfSe analyses were performed to determine the microbial features with significant differences in the relative abundance.,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia insidiosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus haemolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylorubrum|s__Methylorubrum populi",3384189|32066|203490|203491|203492|848|851;3379134|976|200643|171549|171552|838|28132;3379134|1224|28216|80840|119060|48736|190721;1783272|1239|91061|1385|90964|1279|1283;3379134|1224|28211|356|119045|2282523|223967,Complete,NA
bsdb:37978347/1/1,37978347,case-control,37978347,10.1186/s12866-023-03067-6,NA,"Xiaofeng N., Jian C., Jingjing W., Zhanbo Q., Yifei S., Jing Z. , Shuwen H.",Correlation of gut microbiota with leukopenia after chemotherapy in patients with colorectal cancer,BMC microbiology,2023,"Chemotherapy, Colorectal cancer, Gut microbiota, Leukopenia, Myelosuppression",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal carcinoma,EFO:1001951,Healthy,Colorectal cancer (CRC),Patients who has colorectal cancer (CRC),56,55,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Fig. 2B,20 March 2024,Ayibatari,"Ayibatari,Scholastica,WikiWorks",Gut microbiota with significant differences in colorectal cancer (CRC) patients compared to healthy individuals.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Aquabacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|g__Exiguobacterium,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales",3379134|1224|1236|2887326|468|469;1783272|201174|1760|2037|2049|1654;3379134|1224|1236|135624|84642|642;3379134|1224|1236|135625|712|416916;3379134|74201|203494|48461|1647988|239934;1783272|201174|1760|85004|31953|419014;1783272|1239|909932|1843489|31977|156454;3379134|1224|28216|80840|92793;1783272|201174|1760|85006|1268|1663;3379134|1224|28211|356|41294|374;3379134|1224|28211|204458|76892|41275;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|3082768|990719|990721;1783272|201174|1760|85007|1653|1716;3379134|1224|28216|206351|481|538;3379134|1224|1236|91347|543|547;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|1385|33986;3384194|508458|649775|649776|3029087|1434006;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|1506553;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|909929|1843491|52225;1783272|1239|186801|3082720|543314|86331;3379134|1224|1236|91347|1903414|581;1783272|201174|84998|84999|1643824|133925;3379134|976|200643|171549|2005525|375288;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;1783272|201174|1760|85009|31957|1743;1783272|1239|186801|186802|186806|113286;3379134|1224|28216|80840|119060|48736;3379134|1224|1236|91347|543|160674;1783272|201174|1760|85007|85025|1827;1783272|201174|1760|85004|31953|196081;1783272|1239|909932|909929|1843491|970;1783272|201174|84998|1643822|1643826|84108;1783272|1239|526524|526525|128827|123375;3379134|1224|28211|204457|41297|13687;1783272|1239|91061|186826|1300|1301;3379134|1224|28216|80840|80864;1783272|201174|84998|84999;3379134|1224|1236|91347|543;1783272|1239|91061|186826,Complete,Svetlana up
bsdb:37978347/1/2,37978347,case-control,37978347,10.1186/s12866-023-03067-6,NA,"Xiaofeng N., Jian C., Jingjing W., Zhanbo Q., Yifei S., Jing Z. , Shuwen H.",Correlation of gut microbiota with leukopenia after chemotherapy in patients with colorectal cancer,BMC microbiology,2023,"Chemotherapy, Colorectal cancer, Gut microbiota, Leukopenia, Myelosuppression",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal carcinoma,EFO:1001951,Healthy,Colorectal cancer (CRC),Patients who has colorectal cancer (CRC),56,55,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Fig. 2B,19 June 2024,Scholastica,"Scholastica,WikiWorks,Tosin",Gut microbiota with significant differences in colorectal cancer (CRC) patients compared to healthy individuals.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|g__Negativibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:352",1783272|1239|186801|3085636|186803|1766253;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815|816;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3082768|424536;1783272|1239|186801|186802|1980681;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|216572|216851;1783272|1239|526524|526525|128827|1573534;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|1407607;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|186802|216572|3028852;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|1980693;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|995019|577310;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;3384189|32066|203490|203491|1129771|168808;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|31979|1485|59620;1783272|1239|526524|526525|128827|331630;1783272|1239|186801|186802|31979|1485|1262798,Complete,Svetlana up
bsdb:37978347/2/1,37978347,case-control,37978347,10.1186/s12866-023-03067-6,NA,"Xiaofeng N., Jian C., Jingjing W., Zhanbo Q., Yifei S., Jing Z. , Shuwen H.",Correlation of gut microbiota with leukopenia after chemotherapy in patients with colorectal cancer,BMC microbiology,2023,"Chemotherapy, Colorectal cancer, Gut microbiota, Leukopenia, Myelosuppression",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Leukopenia,EFO:0004233,Normal leukocytes,Hypoleukocytes,Colorectal cancer patients with lower-than-normal levels of leukocytes (below 3.5 × 10^9/L) after chemotherapy,42,13,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Fig. 6B,20 March 2024,Ayibatari,"Ayibatari,Scholastica,WikiWorks",Gut microbiota with significant differences in colorectal cancer (CRC) patients with hypoleukocytes compared to normal leukocytes.,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,p__Candidatus Saccharimonadota",3384189|32066|203490|203491|203492|180162;1783272|1239|526524|526525|2810280|1279384;1783272|1239|91061|186826|186828|117563;95818,Complete,Svetlana up
bsdb:37978347/2/2,37978347,case-control,37978347,10.1186/s12866-023-03067-6,NA,"Xiaofeng N., Jian C., Jingjing W., Zhanbo Q., Yifei S., Jing Z. , Shuwen H.",Correlation of gut microbiota with leukopenia after chemotherapy in patients with colorectal cancer,BMC microbiology,2023,"Chemotherapy, Colorectal cancer, Gut microbiota, Leukopenia, Myelosuppression",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Leukopenia,EFO:0004233,Normal leukocytes,Hypoleukocytes,Colorectal cancer patients with lower-than-normal levels of leukocytes (below 3.5 × 10^9/L) after chemotherapy,42,13,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Fig. 6B,20 March 2024,Ayibatari,"Ayibatari,Scholastica,WikiWorks",Gut microbiota with significant differences in colorectal cancer (CRC) patients with hypoleukocytes compared to normal leukocytes.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,p__Rhodophyta|c__Florideophyceae|o__Batrachospermales|f__Batrachospermaceae|g__Paludicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Paraclostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium",1783272|1239|186801|3082768|990719|990721;1783272|1239|526524|526525|2810280|100883;1783272|201174|84998|84999|84107|1472762;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|1737404|1582879;3384189|32066|203490|203491|203492|848;3379134|1224|1236|91347|543|570;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|186802|216572|459786;2763|2806|31370|31371|2729669;1783272|1239|186801|3082720|186804|1849822;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|186802|216572;1783272|1239|526524|526525|128827|331630,Complete,Svetlana up
bsdb:37978427/1/1,37978427,case-control,37978427,10.1186/s12866-023-03061-y,NA,"Huang Q., Wu X., Zhou X., Sun Z., Shen J., Kong M., Chen N., Qiu J.G., Jiang B.H., Yuan C. , Zheng Y.",Association of cigarette smoking with oral bacterial microbiota and cardiometabolic health in Chinese adults,BMC microbiology,2023,"Cardiometabolic health, Chinese adults, Cigarette, Oral microbiome, Smoking",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Smoking status measurement,EFO:0006527,Non-smokers,Smokers,Participants who smoked one or more cigarettes every three days for at least 6 consecutive months were classified as smokers.,476,111,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,increased,increased,NA,NA,NA,increased,Signature 1,"Table S1, Figure 1B, Table S3",6 March 2025,Tosin,Tosin,Phylum and genus level composition of the oral microbiome by cigarette smoking status between non-smokers and smokers group.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia",1783272|201174|1760|2037|2049|1654;1783272|201174;1783272|1239|909932|1843489|31977|156454;1783272|201174|84998|84999|1643824|1380;1783272|1239;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|404402;1783272|1239|909932|1843489|31977|906;1783272|201174|1760|85006|1268|32207;1783272|1239|186801|3082720|186804|1501226,Complete,KateRasheed
bsdb:37978427/1/2,37978427,case-control,37978427,10.1186/s12866-023-03061-y,NA,"Huang Q., Wu X., Zhou X., Sun Z., Shen J., Kong M., Chen N., Qiu J.G., Jiang B.H., Yuan C. , Zheng Y.",Association of cigarette smoking with oral bacterial microbiota and cardiometabolic health in Chinese adults,BMC microbiology,2023,"Cardiometabolic health, Chinese adults, Cigarette, Oral microbiome, Smoking",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Smoking status measurement,EFO:0006527,Non-smokers,Smokers,Participants who smoked one or more cigarettes every three days for at least 6 consecutive months were classified as smokers.,476,111,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,increased,increased,NA,NA,NA,increased,Signature 2,"Table S1, Figure 1B, Table S3",7 March 2025,Tosin,Tosin,Phylum and genus level composition of the oral microbiome by cigarette smoking status between non-smokers and smokers group.,decreased,"k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella",3379134|1224;1783272|1239|186801|3085636|186803|43994,Complete,KateRasheed
bsdb:37978427/2/1,37978427,case-control,37978427,10.1186/s12866-023-03061-y,NA,"Huang Q., Wu X., Zhou X., Sun Z., Shen J., Kong M., Chen N., Qiu J.G., Jiang B.H., Yuan C. , Zheng Y.",Association of cigarette smoking with oral bacterial microbiota and cardiometabolic health in Chinese adults,BMC microbiology,2023,"Cardiometabolic health, Chinese adults, Cigarette, Oral microbiome, Smoking",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Smoking status measurement,EFO:0006527,Non-smokers,Smokers,Participants who smoked one or more cigarettes every three days for at least 6 consecutive months were classified as smokers.,476,111,NA,16S,4,Illumina,log transformation,MaAsLin2,0.2,TRUE,NA,NA,"age,alcohol drinking,body mass index,education level,sex",increased,increased,NA,NA,NA,increased,Signature 1,"Figure 3A, 3C and Table S2.",7 March 2025,Tosin,Tosin,Bacterial genera significantly associated with cigarette smoking status identified by MaAsLin2.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",1783272|201174|1760|2037|2049|1654;1783272|1239|909932|1843489|31977|156454;1783272|201174|84998|84999|1643824|1380;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|404402;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3082720|186804|1501226;1783272|201174|1760|85006|1268|32207,Complete,KateRasheed
bsdb:37978427/2/2,37978427,case-control,37978427,10.1186/s12866-023-03061-y,NA,"Huang Q., Wu X., Zhou X., Sun Z., Shen J., Kong M., Chen N., Qiu J.G., Jiang B.H., Yuan C. , Zheng Y.",Association of cigarette smoking with oral bacterial microbiota and cardiometabolic health in Chinese adults,BMC microbiology,2023,"Cardiometabolic health, Chinese adults, Cigarette, Oral microbiome, Smoking",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Smoking status measurement,EFO:0006527,Non-smokers,Smokers,Participants who smoked one or more cigarettes every three days for at least 6 consecutive months were classified as smokers.,476,111,NA,16S,4,Illumina,log transformation,MaAsLin2,0.2,TRUE,NA,NA,"age,alcohol drinking,body mass index,education level,sex",increased,increased,NA,NA,NA,increased,Signature 2,"Figure 3A, 3C and Table S2.",7 March 2025,Tosin,Tosin,Bacterial genera significantly associated with cigarette smoking status identified by MaAsLin2.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,1783272|1239|186801|3085636|186803|43994,Complete,KateRasheed
bsdb:37980506/1/1,37980506,case-control,37980506,0.1186/s12866-023-03115-1,https://doi.org/10.1186/s12866-023-03115-1,"Huijuan Ning, Jing Yuan, Jinghua Cui, Kunyu Yao, Meijuan Wang, Meng Jin, Wenwen Liu, Xuemei Zhong",Alterations in gut microbiota and metabolite profiles in patients with infantile cholestasis,BMC microbiology,2023,"Infantile cholestasis (IC), Gut microbiota, Microbiota-derived metabolites, Ruminococcus, Butyrivibrio,  Veillonella",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Cholestasis,NA,Healthy Control (CON),Infantile  cholestasis (IC),Infants aged less than 1 year with all diagnostic criteria for cholestasis met upon admission.,20,20,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,age,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 1 C,10 March 2024,Amara,"Amara,Ayibatari,Peace Sandy,WikiWorks",Characteristics of gut microbiota in infantile cholestasis (IC; n = 20) and control (CON; n = 20) groups. C. score plot of differential species showing linear discriminant analysis of differentially abundant genera between the two groups;,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|976|200643|171549|2005520;3379134|976|200643|171549|2005520|156973;3379134|1224|1236;1783272|1239|186801|3085636|186803|1506553;3379134|1224;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301,Complete,Peace Sandy
bsdb:37980506/1/2,37980506,case-control,37980506,0.1186/s12866-023-03115-1,https://doi.org/10.1186/s12866-023-03115-1,"Huijuan Ning, Jing Yuan, Jinghua Cui, Kunyu Yao, Meijuan Wang, Meng Jin, Wenwen Liu, Xuemei Zhong",Alterations in gut microbiota and metabolite profiles in patients with infantile cholestasis,BMC microbiology,2023,"Infantile cholestasis (IC), Gut microbiota, Microbiota-derived metabolites, Ruminococcus, Butyrivibrio,  Veillonella",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Cholestasis,NA,Healthy Control (CON),Infantile  cholestasis (IC),Infants aged less than 1 year with all diagnostic criteria for cholestasis met upon admission.,20,20,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,age,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 1 C,10 March 2024,Amara,"Amara,Welile,Peace Sandy,WikiWorks",Characteristics of gut microbiota in infantile cholestasis (IC; n = 20) and control (CON; n = 20) groups. C. score plot of differential species showing linear discriminant analysis of differentially abundant genera between the two groups;,decreased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Amorphaceae|g__Amorphus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhodobiaceae",1783272|1239|186801;1783272|1239|186801|186802|216572;1783272|1239|186801|3082720|186804|1501226;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;3379134|1224|28211|204458|76892|75;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|3082768|990719;1783272|1239|186801|3082768;3379134|1224|28211|356|2685818|580880;3379134|1224|28211|356|119043,Complete,Peace Sandy
bsdb:37986012/1/1,37986012,"cross-sectional observational, not case-control",37986012,10.1186/s42523-023-00281-5,NA,"Basbas C., Garzon A., Schlesener C., van Heule M., Profeta R., Weimer B.C., Silva-Del-Rio N., Byrne B.A., Karle B., Aly S.S., Lima F.S. , Pereira R.V.",Unveiling the microbiome during post-partum uterine infection: a deep shotgun sequencing approach to characterize the dairy cow uterine microbiome,Animal microbiome,2023,"Diversity, Metritis, Microbiota, Uterine microbiome",Experiment 1,United States of America,Bos taurus,Endocervix,UBERON:0000458,Uterine disease,NA,Control group (CT),Metritis group (MET),"Cows with Metritis typically occurring within 21 days post-partum, characterized by an enlarged uterus, fever, and fetid, watery red-brown uterine discharge.",32,33,NA,WMS,NA,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,decreased,increased,decreased,NA,NA,Signature 1,Table 1,23 February 2025,MyleeeA,MyleeeA,Most abundant genera for Metritis (MET regardless of antimicrobial treatment) vs. Control (CT),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979|1485;3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|815|909656;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:37986012/1/2,37986012,"cross-sectional observational, not case-control",37986012,10.1186/s42523-023-00281-5,NA,"Basbas C., Garzon A., Schlesener C., van Heule M., Profeta R., Weimer B.C., Silva-Del-Rio N., Byrne B.A., Karle B., Aly S.S., Lima F.S. , Pereira R.V.",Unveiling the microbiome during post-partum uterine infection: a deep shotgun sequencing approach to characterize the dairy cow uterine microbiome,Animal microbiome,2023,"Diversity, Metritis, Microbiota, Uterine microbiome",Experiment 1,United States of America,Bos taurus,Endocervix,UBERON:0000458,Uterine disease,NA,Control group (CT),Metritis group (MET),"Cows with Metritis typically occurring within 21 days post-partum, characterized by an enlarged uterus, fever, and fetid, watery red-brown uterine discharge.",32,33,NA,WMS,NA,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,decreased,increased,decreased,NA,NA,Signature 2,Table 1,23 February 2025,MyleeeA,MyleeeA,Most abundant genera for Metritis (MET regardless of antimicrobial treatment) vs. Control (CT),decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium",1783272|201174|1760|85007|85029|37914;1783272|201174|1760|85006|85023|33882,Complete,Svetlana up
bsdb:37986012/2/1,37986012,"cross-sectional observational, not case-control",37986012,10.1186/s42523-023-00281-5,NA,"Basbas C., Garzon A., Schlesener C., van Heule M., Profeta R., Weimer B.C., Silva-Del-Rio N., Byrne B.A., Karle B., Aly S.S., Lima F.S. , Pereira R.V.",Unveiling the microbiome during post-partum uterine infection: a deep shotgun sequencing approach to characterize the dairy cow uterine microbiome,Animal microbiome,2023,"Diversity, Metritis, Microbiota, Uterine microbiome",Experiment 2,United States of America,Bos taurus,Endocervix,UBERON:0000458,Uterine disease,NA,Control group (CT),Metritis group (MET_treatment),Cows with metritis that had received individual antimicrobial treatment in the last 14 days prior to sampling.,32,9,NA,WMS,NA,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4 and 5,23 February 2025,MyleeeA,MyleeeA,Heatmap of natural log fold changes in abundance of the phyla and genera with an adjusted p<0.05 for MET_Treatment when compared to control.,increased,"k__Pseudomonadati|p__Acidobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Halanaerobiales|g__Anoxybacter,k__Pseudomonadati|p__Aquificota,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Chlamydiota,k__Pseudomonadati|p__Chlorobiota,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cyclobacteriaceae|g__Cyclobacterium,k__Pseudomonadati|p__Deferribacterota,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Spirosomataceae|g__Dyadobacter,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Flavihumibacter,k__Pseudomonadati|p__Gemmatimonadota,k__Pseudomonadati|p__Ignavibacteriota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Liquorilactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Oceanobacillus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Owenweeksiaceae|g__Owenweeksia,k__Pseudomonadati|p__Planctomycetota,k__Thermotogati|p__Synergistota,k__Thermotogati|p__Thermotogota|c__Thermotogae,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Spirochaetota",3379134|57723;1783272|1239|186801|53433|1769008;3379134|200783;3379134|976;3379134|204428;3379134|1090;1783272|1117;3379134|976|768503|768507|563798|68288;3379134|200930;3379134|976|768503|768507|2896860|120831;3379134|976|1853228|1853229|563835|1004301;3379134|142182;3379134|1134404;1783272|1239|91061|186826|33958|2767888;1783272|1239|91061|1385|186817|182709;3379134|976|117743|200644|3024551|267986;3379134|203682;3384194|508458;3384194|200918|188708;3379134|74201;3379134|203691,Complete,Svetlana up
bsdb:37986012/2/2,37986012,"cross-sectional observational, not case-control",37986012,10.1186/s42523-023-00281-5,NA,"Basbas C., Garzon A., Schlesener C., van Heule M., Profeta R., Weimer B.C., Silva-Del-Rio N., Byrne B.A., Karle B., Aly S.S., Lima F.S. , Pereira R.V.",Unveiling the microbiome during post-partum uterine infection: a deep shotgun sequencing approach to characterize the dairy cow uterine microbiome,Animal microbiome,2023,"Diversity, Metritis, Microbiota, Uterine microbiome",Experiment 2,United States of America,Bos taurus,Endocervix,UBERON:0000458,Uterine disease,NA,Control group (CT),Metritis group (MET_treatment),Cows with metritis that had received individual antimicrobial treatment in the last 14 days prior to sampling.,32,9,NA,WMS,NA,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4 and 5,23 February 2025,MyleeeA,MyleeeA,Heatmap of natural log fold changes in abundance of the phyla and genera with an adjusted p<0.05 for MET_Treatment when compared to control.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Rathayibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Glutamicibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Pseudonocardia,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Kiritimatiellota,p__Evosea,p__Euglenozoa,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia,k__Methanobacteriati|p__Thermoplasmatota,k__Fungi|p__Basidiomycota,k__Pseudomonadati|p__Balneolota,p__Bacillariophyta,k__Fungi|p__Ascomycota,p__Apicomplexa,k__Bacillati|p__Actinomycetota",1783272|201174|1760|85006|85023|33886;1783272|201174|1760|85006|1268|1742989;1783272|201174|1760|85010|2070|1847;1783272|544448;3379134|134625;2605435;33682;3379134|74152|641853;3366610|2283796;4751|5204;3379134|1936987;2836;4751|4890;5794;1783272|201174,Complete,Svetlana up
bsdb:37986012/3/1,37986012,"cross-sectional observational, not case-control",37986012,10.1186/s42523-023-00281-5,NA,"Basbas C., Garzon A., Schlesener C., van Heule M., Profeta R., Weimer B.C., Silva-Del-Rio N., Byrne B.A., Karle B., Aly S.S., Lima F.S. , Pereira R.V.",Unveiling the microbiome during post-partum uterine infection: a deep shotgun sequencing approach to characterize the dairy cow uterine microbiome,Animal microbiome,2023,"Diversity, Metritis, Microbiota, Uterine microbiome",Experiment 3,United States of America,Bos taurus,Endocervix,UBERON:0000458,Clinical treatment,EFO:0007056,Control group (CT),Metritis group (MET_no treatment),Cows with metritis that had not received individual antimicrobial treatment in the last 14 days prior to sampling.,32,25,NA,WMS,NA,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4 and 5,24 February 2025,MyleeeA,MyleeeA,Heatmap of natural log fold changes in abundance of the phyla and genera with an adjusted p<0.05 for MET_no Treatment when compared to control.,increased,"k__Pseudomonadati|p__Ignavibacteriota,k__Pseudomonadati|p__Gemmatimonadota,k__Pseudomonadati|p__Deferribacterota,k__Pseudomonadati|p__Chlorobiota,k__Pseudomonadati|p__Chlamydiota,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Aquificota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Liquorilactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cyclobacteriaceae|g__Cyclobacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Owenweeksiaceae|g__Owenweeksia,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Flavihumibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Halanaerobiales|g__Anoxybacter,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Spirosomataceae|g__Dyadobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Oceanobacillus",3379134|1134404;3379134|142182;3379134|200930;3379134|1090;3379134|204428;3379134|976;3379134|200783;1783272|1239|91061|186826|33958|2767888;3379134|976|768503|768507|563798|68288;3379134|976|117743|200644|3024551|267986;3379134|976|1853228|1853229|563835|1004301;1783272|1239|186801|53433|1769008;3379134|976|768503|768507|2896860|120831;1783272|1239|91061|1385|186817|182709,Complete,Svetlana up
bsdb:37986012/3/2,37986012,"cross-sectional observational, not case-control",37986012,10.1186/s42523-023-00281-5,NA,"Basbas C., Garzon A., Schlesener C., van Heule M., Profeta R., Weimer B.C., Silva-Del-Rio N., Byrne B.A., Karle B., Aly S.S., Lima F.S. , Pereira R.V.",Unveiling the microbiome during post-partum uterine infection: a deep shotgun sequencing approach to characterize the dairy cow uterine microbiome,Animal microbiome,2023,"Diversity, Metritis, Microbiota, Uterine microbiome",Experiment 3,United States of America,Bos taurus,Endocervix,UBERON:0000458,Clinical treatment,EFO:0007056,Control group (CT),Metritis group (MET_no treatment),Cows with metritis that had not received individual antimicrobial treatment in the last 14 days prior to sampling.,32,25,NA,WMS,NA,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4 and 5,24 February 2025,MyleeeA,MyleeeA,Heatmap of natural log fold changes in abundance of the phyla and genera with an adjusted p<0.05 for MET_no Treatment when compared to control.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Rathayibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Glutamicibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Pseudonocardia,k__Bacillati|p__Actinomycetota",1783272|201174|1760|85006|85023|33886;1783272|201174|1760|85006|1268|1742989;1783272|201174|1760|85010|2070|1847;1783272|201174,Complete,Svetlana up
bsdb:37986012/4/1,37986012,"cross-sectional observational, not case-control",37986012,10.1186/s42523-023-00281-5,NA,"Basbas C., Garzon A., Schlesener C., van Heule M., Profeta R., Weimer B.C., Silva-Del-Rio N., Byrne B.A., Karle B., Aly S.S., Lima F.S. , Pereira R.V.",Unveiling the microbiome during post-partum uterine infection: a deep shotgun sequencing approach to characterize the dairy cow uterine microbiome,Animal microbiome,2023,"Diversity, Metritis, Microbiota, Uterine microbiome",Experiment 4,United States of America,Bos taurus,Endocervix,UBERON:0000458,Uterine disease,NA,Control group (CT),Pus Cows,Cows with purulent discharge (PUS); defined as a non-fetid purulent or mucopurulent vaginal discharge.,32,31,NA,WMS,NA,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,decreased,unchanged,decreased,NA,NA,Signature 1,Figure 4 and 5,24 February 2025,MyleeeA,MyleeeA,Heatmap of natural log fold changes in abundance of the phyla and genera with an adjusted p<0.05 for Pus when compared to control.,increased,"k__Pseudomonadati|p__Gemmatimonadota,k__Pseudomonadati|p__Chlorobiota,k__Pseudomonadati|p__Chlamydiota,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Liquorilactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cyclobacteriaceae|g__Cyclobacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Owenweeksiaceae|g__Owenweeksia,k__Bacillati|p__Bacillota|c__Clostridia|o__Halanaerobiales|g__Anoxybacter,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Flavihumibacter,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Spirosomataceae|g__Dyadobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Oceanobacillus",3379134|142182;3379134|1090;3379134|204428;3379134|976;1783272|1239|91061|186826|33958|2767888;3379134|976|768503|768507|563798|68288;3379134|976|117743|200644|3024551|267986;1783272|1239|186801|53433|1769008;3379134|976|1853228|1853229|563835|1004301;3379134|976|768503|768507|2896860|120831;1783272|1239|91061|1385|186817|182709,Complete,Svetlana up
bsdb:37986012/4/2,37986012,"cross-sectional observational, not case-control",37986012,10.1186/s42523-023-00281-5,NA,"Basbas C., Garzon A., Schlesener C., van Heule M., Profeta R., Weimer B.C., Silva-Del-Rio N., Byrne B.A., Karle B., Aly S.S., Lima F.S. , Pereira R.V.",Unveiling the microbiome during post-partum uterine infection: a deep shotgun sequencing approach to characterize the dairy cow uterine microbiome,Animal microbiome,2023,"Diversity, Metritis, Microbiota, Uterine microbiome",Experiment 4,United States of America,Bos taurus,Endocervix,UBERON:0000458,Uterine disease,NA,Control group (CT),Pus Cows,Cows with purulent discharge (PUS); defined as a non-fetid purulent or mucopurulent vaginal discharge.,32,31,NA,WMS,NA,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,decreased,unchanged,decreased,NA,NA,Signature 2,Figure 4 and 5,24 February 2025,MyleeeA,MyleeeA,Heatmap of natural log fold changes in abundance of the phyla and genera with an adjusted p<0.05 for Pus when compared to control.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Rathayibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Pseudonocardia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Glutamicibacter,k__Bacillati|p__Actinomycetota",1783272|201174|1760|85006|85023|33886;1783272|201174|1760|85010|2070|1847;1783272|201174|1760|85006|1268|1742989;1783272|201174,Complete,Svetlana up
bsdb:37986012/5/1,37986012,"cross-sectional observational, not case-control",37986012,10.1186/s42523-023-00281-5,NA,"Basbas C., Garzon A., Schlesener C., van Heule M., Profeta R., Weimer B.C., Silva-Del-Rio N., Byrne B.A., Karle B., Aly S.S., Lima F.S. , Pereira R.V.",Unveiling the microbiome during post-partum uterine infection: a deep shotgun sequencing approach to characterize the dairy cow uterine microbiome,Animal microbiome,2023,"Diversity, Metritis, Microbiota, Uterine microbiome",Experiment 5,United States of America,Bos taurus,Endocervix,UBERON:0000458,Clinical treatment,EFO:0007056,Control group (CT),Metritis group (MET_treatment),Clinical group comparison of metritis or uterine health by other studies for Cows with metritis that had received individual antimicrobial treatment in the last 14 days prior to sampling.,32,9,NA,WMS,NA,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6 and Supplementary Table 3,24 February 2025,MyleeeA,MyleeeA,ANCOM-BC heatmap of natural log fold changes of genera abundance for MET_Treatment vs Control (CT) compared to genera from other studies.,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Cryptococcaceae|g__Cryptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus",3384189|32066|203490|203491|1129771|34104;3379134|1224|1236|91347|543|590;1783272|1239|1737404|1737405|1570339|162289;3379134|976|117747|200666|84566|84567;3379134|29547|3031852|213849|72293|209;1783272|1239|186801|3082720|3118655|44259;4751|5204|155616|5234|1884633|5206;3379134|1224|1236|91347|543|544;1783272|201174|1760|2037|2049|28263;1783272|1239|1737404|1737405|1570339|165779,Complete,Svetlana up
bsdb:37986012/5/3,37986012,"cross-sectional observational, not case-control",37986012,10.1186/s42523-023-00281-5,NA,"Basbas C., Garzon A., Schlesener C., van Heule M., Profeta R., Weimer B.C., Silva-Del-Rio N., Byrne B.A., Karle B., Aly S.S., Lima F.S. , Pereira R.V.",Unveiling the microbiome during post-partum uterine infection: a deep shotgun sequencing approach to characterize the dairy cow uterine microbiome,Animal microbiome,2023,"Diversity, Metritis, Microbiota, Uterine microbiome",Experiment 5,United States of America,Bos taurus,Endocervix,UBERON:0000458,Clinical treatment,EFO:0007056,Control group (CT),Metritis group (MET_treatment),Clinical group comparison of metritis or uterine health by other studies for Cows with metritis that had received individual antimicrobial treatment in the last 14 days prior to sampling.,32,9,NA,WMS,NA,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 3,Figure 6 and Supplementary Table 3,25 February 2025,MyleeeA,MyleeeA,ANCOM-BC heatmap of natural log fold changes of genera abundance for MET_Treatment vs Control (CT) compared to genera from other studies.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Trueperella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Histophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus",1783272|201174|1760|2037|2049|1069494;1783272|201174|1760|85011|2062|1883;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|1385|90964|1279;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|171552|838;1783272|201174|1760|85007|1762|1763;1783272|201174|1760|85006|1268|1269;3379134|1224|1236|91347|543|570;3379134|1224|1236|135625|712|214906;3379134|1224|1236|91347|543|561;1783272|201174|1760|85007|1653|1716;3379134|1224|28211|356|118882|234;1783272|201174|1760|85006|85019|1696;1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549|815|816;1783272|1239|91061|1385|186817|1386,Complete,Svetlana up
bsdb:37986012/6/1,37986012,"cross-sectional observational, not case-control",37986012,10.1186/s42523-023-00281-5,NA,"Basbas C., Garzon A., Schlesener C., van Heule M., Profeta R., Weimer B.C., Silva-Del-Rio N., Byrne B.A., Karle B., Aly S.S., Lima F.S. , Pereira R.V.",Unveiling the microbiome during post-partum uterine infection: a deep shotgun sequencing approach to characterize the dairy cow uterine microbiome,Animal microbiome,2023,"Diversity, Metritis, Microbiota, Uterine microbiome",Experiment 6,United States of America,Bos taurus,Endocervix,UBERON:0000458,Clinical treatment,EFO:0007056,Control group (CT),Metritis group (MET_no treatment),Clinical group comparison of metritis or uterine health by other studies for Cows with metritis that had not received individual antimicrobial treatment in the last 14 days prior to sampling.,32,25,NA,WMS,NA,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6 and Supplementary Table 3,25 February 2025,MyleeeA,MyleeeA,ANCOM-BC heatmap of natural log fold changes of genera abundance for MET_no Treatment vs Control (CT) compared to genera from other studies.,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia",3384189|32066|203490|203491|1129771|34104;1783272|1239|186801|3082720|3118655|44259;3379134|1224|1236|91347|543|544;3379134|204428|204429|51291|809|810,Complete,Svetlana up
bsdb:37986012/6/2,37986012,"cross-sectional observational, not case-control",37986012,10.1186/s42523-023-00281-5,NA,"Basbas C., Garzon A., Schlesener C., van Heule M., Profeta R., Weimer B.C., Silva-Del-Rio N., Byrne B.A., Karle B., Aly S.S., Lima F.S. , Pereira R.V.",Unveiling the microbiome during post-partum uterine infection: a deep shotgun sequencing approach to characterize the dairy cow uterine microbiome,Animal microbiome,2023,"Diversity, Metritis, Microbiota, Uterine microbiome",Experiment 6,United States of America,Bos taurus,Endocervix,UBERON:0000458,Clinical treatment,EFO:0007056,Control group (CT),Metritis group (MET_no treatment),Clinical group comparison of metritis or uterine health by other studies for Cows with metritis that had not received individual antimicrobial treatment in the last 14 days prior to sampling.,32,25,NA,WMS,NA,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6 and Supplementary Table 3,25 February 2025,MyleeeA,MyleeeA,ANCOM-BC heatmap of natural log fold changes of genera abundance for MET_no Treatment vs Control (CT) compared to genera from other studies.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|201174|1760|85011|2062|1883;1783272|201174|1760|85006|1268|1269;1783272|201174|1760|85007|1653|1716;3379134|1224|28211|356|118882|234;1783272|201174|1760|85006|85019|1696;1783272|201174|1760|85004|31953|1678,Complete,Svetlana up
bsdb:37993728/1/1,37993728,case-control,37993728,10.1038/s43705-023-00332-7,https://pmc.ncbi.nlm.nih.gov/articles/PMC10665332,"Sun D., Herath J., Zhou S., Ellepola G. , Meegaskumbura M.",Associations of Batrachochytrium dendrobatidis with skin bacteria and fungi on Asian amphibian hosts,ISME communications,2023,NA,Experiment 1,China,Theloderma rhododiscus,Skin epidermis,UBERON:0001003,Fungal infectious disease,MONDO:0002041,Theloderma rhododiscus frog uninfected with Batrachocytrium dendrobatidis (Bd-),Theloderma rhododiscus frog infected with Batrachocytrium dendrobatidis (Bd+),Bacterial diversity of Theloderma rhododiscus frogs infected with Batrachocytrium dendrobatidis (Bd+),21,8,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3a,15 November 2025,Oladoye,"Oladoye,Tosin",Bacterial taxonomic biomarkers in infected individuals of the species Theloderma Rhododiscus,increased,"k__Bacillati|p__Chloroflexota|c__Anaerolineae,k__Bacillati|p__Chloroflexota,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales",1783272|200795|292625;1783272|200795;3379134|29547|3031852|213849|72293|209;3379134|29547|3031852|213849|72293;1783272|1239|91061|186826|1300|1357;1783272|1239|909932;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|1224|28216|80840,Complete,KateRasheed
bsdb:37993728/1/2,37993728,case-control,37993728,10.1038/s43705-023-00332-7,https://pmc.ncbi.nlm.nih.gov/articles/PMC10665332,"Sun D., Herath J., Zhou S., Ellepola G. , Meegaskumbura M.",Associations of Batrachochytrium dendrobatidis with skin bacteria and fungi on Asian amphibian hosts,ISME communications,2023,NA,Experiment 1,China,Theloderma rhododiscus,Skin epidermis,UBERON:0001003,Fungal infectious disease,MONDO:0002041,Theloderma rhododiscus frog uninfected with Batrachocytrium dendrobatidis (Bd-),Theloderma rhododiscus frog infected with Batrachocytrium dendrobatidis (Bd+),Bacterial diversity of Theloderma rhododiscus frogs infected with Batrachocytrium dendrobatidis (Bd+),21,8,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3a,15 November 2025,Oladoye,Oladoye,Bacterial taxonomic biomarkers in uninfected individuals of the species Theloderma Rhododiscus,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;1783272|201174|1760|85006|85020;1783272|201174|1760|85006|85020,Complete,KateRasheed
bsdb:37993728/2/1,37993728,case-control,37993728,10.1038/s43705-023-00332-7,https://pmc.ncbi.nlm.nih.gov/articles/PMC10665332,"Sun D., Herath J., Zhou S., Ellepola G. , Meegaskumbura M.",Associations of Batrachochytrium dendrobatidis with skin bacteria and fungi on Asian amphibian hosts,ISME communications,2023,NA,Experiment 2,China,Theloderma rhododiscus,Skin epidermis,UBERON:0001003,Fungal infectious disease,MONDO:0002041,Theloderma rhododiscus frog uninfected with Batrachocytrium dendrobatidis (Bd-),Theloderma rhododiscus frog infected with Batrachocytrium dendrobatidis (Bd+),Fungal diversity of Infected frogs with Batrachocytrium dendrobatidis (Bd+),21,8,NA,ITS / ITS2,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 1,Figure 3b,15 November 2025,Oladoye,"Oladoye,Tosin",Fungal taxonomic biomarkers in infected individuals of the species Theloderma Rhododiscus,increased,"k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae|g__Apiotrichum,k__Fungi|p__Chytridiomycota|c__Chytridiomycetes|o__Rhizophydiales|g__Batrachochytrium,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Cephalothecales|f__Cephalothecaceae,k__Fungi|p__Chytridiomycota,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Cephalothecales|f__Cephalothecaceae|g__Phialemonium,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Plectosphaerellaceae,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Thelebolales|f__Pseudeurotiaceae,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Thelebolales|f__Pseudeurotiaceae|g__Pseudeurotium,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Thelebolales|f__Thelebolaceae|g__Pseudogymnoascus,k__Fungi|p__Chytridiomycota|c__Chytridiomycetes|o__Rhizophydiales,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Thelebolales,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Plectosphaerellaceae|g__Verticillium",4751|5204|155616|1851469|1759442|105983;4751|4761|451435|451442|100474;4751|4890|147550|3036495|95343;4751|4761;4751|4890|147550|3036495|95343|83822;4751|4890|147550|1028384|1033978;4751|4890|147548|292491|34379;4751|4890|147548|292491|34379|95331;4751|4890|147548|292491|46451|78156;4751|4761|451435|451442;4751|4890|147548|292491;4751|5204|155616|1851469|1759442;4751|5204|155616|1851469;4751|4890|147550|1028384|1033978|1036719,Complete,KateRasheed
bsdb:37993728/2/2,37993728,case-control,37993728,10.1038/s43705-023-00332-7,https://pmc.ncbi.nlm.nih.gov/articles/PMC10665332,"Sun D., Herath J., Zhou S., Ellepola G. , Meegaskumbura M.",Associations of Batrachochytrium dendrobatidis with skin bacteria and fungi on Asian amphibian hosts,ISME communications,2023,NA,Experiment 2,China,Theloderma rhododiscus,Skin epidermis,UBERON:0001003,Fungal infectious disease,MONDO:0002041,Theloderma rhododiscus frog uninfected with Batrachocytrium dendrobatidis (Bd-),Theloderma rhododiscus frog infected with Batrachocytrium dendrobatidis (Bd+),Fungal diversity of Infected frogs with Batrachocytrium dendrobatidis (Bd+),21,8,NA,ITS / ITS2,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 2,Figure 3b,15 November 2025,Oladoye,Oladoye,Fungal taxonomic biomarkers in uninfected individuals of the species Theloderma Rhododiscus,decreased,"k__Fungi|p__Zoopagomycota|c__Basidiobolomycetes|o__Basidiobolales|f__Basidiobolaceae,k__Fungi|p__Zoopagomycota|c__Basidiobolomycetes|o__Basidiobolales,k__Fungi|p__Zoopagomycota|c__Basidiobolomycetes,k__Fungi|p__Zoopagomycota|c__Basidiobolomycetes|o__Basidiobolales|f__Basidiobolaceae|g__Basidiobolus,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales|f__Hyaloscyphaceae,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Capnodiales,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales|f__Hyaloscyphaceae,k__Fungi|p__Ascomycota|c__Saccharomycetes",4751|1913638|1399768|1264872|4858;4751|1913638|1399768|1264872;4751|1913638|1399768;4751|1913638|1399768|1264872|4858|4859;4751|4890|147548|5178;4751|4890|147548|5178|47743;4751|4890|4891|4892|4893|4930;4751|4890|4891|4892|4893;4751|4890|4891|4892;4751|4890|147541|134362;4751|4890|147548|5178|47743;4751|4890|4891,Complete,KateRasheed
bsdb:37993728/4/1,37993728,case-control,37993728,10.1038/s43705-023-00332-7,https://pmc.ncbi.nlm.nih.gov/articles/PMC10665332,"Sun D., Herath J., Zhou S., Ellepola G. , Meegaskumbura M.",Associations of Batrachochytrium dendrobatidis with skin bacteria and fungi on Asian amphibian hosts,ISME communications,2023,NA,Experiment 4,China,Leptobrachella liui,Skin epidermis,UBERON:0001003,Fungal infectious disease,MONDO:0002041,Leptobrachella liui frog uninfected with Batrachochytrium dendrobatidis (Bd-),Leptobrachella liui frog infected with Batrachochytrium dendrobatidis (Bd+),Bacterial diversity of infected frogs with Batrachocytrium dendrobatidis (Bd+),11,9,NA,16S,4,Illumina,relative abundances,Pearson Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S4a and Table S3,15 November 2025,Oladoye,Oladoye,The significant correlations of bacterial taxa and Bd infection intensity with Fujian metacarpal-tubercled toad (Leptobrachella liui) host species.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Acidobacteriota|c__Terriglobia|o__Bryobacterales|f__Solibacteraceae|g__Candidatus Solibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Cellvibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales,k__Bacillati|p__Chloroflexota|c__Chloroflexia|o__Chloroflexales|f__Chloroflexaceae,k__Bacillati|p__Chloroflexota|c__Chloroflexia|o__Chloroflexales,k__Bacillati|p__Chloroflexota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Pseudomonadati|p__Gemmatimonadota|c__Longimicrobiia|o__Longimicrobiales|f__Longimicrobiaceae|g__Longimicrobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Rhodocytophagaceae|g__Rhodocytophaga,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Rubellimicrobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Tahibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Bacteroidota|c__Saprospiria|o__Saprospirales|f__Saprospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Chloroflexota|c__Chloroflexia",1783272|201174|84998|84999|1643824|1380;3379134|57723|204432|332160|332161|332162;3379134|1224|1236|1706369|1706371|10;3379134|1224|1236|1706369|1706371;3379134|1224|1236|1706369;1783272|200795|32061|32064|1106;1783272|200795|32061|32064;1783272|200795;1783272|1239|186801|3082720|186804|1870884;3379134|142182|1804991|1804992|1804993|1804994;3379134|976|200643|171549|171552|838;3379134|976|768503|768507|3078917|455076;3379134|1224|28211|204455|2854170|295418;3379134|1224|1236|135614|1775411|1453544;3379134|1224|1236|135614|32033;3379134|1224|1236|72274|135621|286;3379134|976|1937959|1936988|89374;3379134|1224|28211|204457|41297;3379134|1224|1236|72274|135621|286;1783272|200795|32061,Complete,KateRasheed
bsdb:37993728/4/2,37993728,case-control,37993728,10.1038/s43705-023-00332-7,https://pmc.ncbi.nlm.nih.gov/articles/PMC10665332,"Sun D., Herath J., Zhou S., Ellepola G. , Meegaskumbura M.",Associations of Batrachochytrium dendrobatidis with skin bacteria and fungi on Asian amphibian hosts,ISME communications,2023,NA,Experiment 4,China,Leptobrachella liui,Skin epidermis,UBERON:0001003,Fungal infectious disease,MONDO:0002041,Leptobrachella liui frog uninfected with Batrachochytrium dendrobatidis (Bd-),Leptobrachella liui frog infected with Batrachochytrium dendrobatidis (Bd+),Bacterial diversity of infected frogs with Batrachocytrium dendrobatidis (Bd+),11,9,NA,16S,4,Illumina,relative abundances,Pearson Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure S4a and Table S3,20 November 2025,Oladoye,Oladoye,The significant correlations of bacterial taxa and Bd infection intensity with Fujian metacarpal-tubercled toad (Leptobrachella liui) host species.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",1783272|201174|1760|85009|85015|1839;1783272|1239|186801|186802|31979,Complete,KateRasheed
bsdb:37993728/6/1,37993728,case-control,37993728,10.1038/s43705-023-00332-7,https://pmc.ncbi.nlm.nih.gov/articles/PMC10665332,"Sun D., Herath J., Zhou S., Ellepola G. , Meegaskumbura M.",Associations of Batrachochytrium dendrobatidis with skin bacteria and fungi on Asian amphibian hosts,ISME communications,2023,NA,Experiment 6,China,Amolops chunganensis,Skin epidermis,UBERON:0001003,Fungal infectious disease,MONDO:0002041,Amolops chunganensis frog uninfected with Batrachochytrium dendrobatidis (Bd-),Amolops chunganensis frog infected with Batrachochytrium dendrobatidis (Bd+),Bacterial diversity of infected frogs with Batrachocytrium dendrobatidis (Bd+),16,15,NA,16S,4,Illumina,relative abundances,Pearson Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S4a and Table S3,15 November 2025,Oladoye,Oladoye,The significant correlations of bacterial taxa and Bd infection intensity with Chungan torrent frog (Amolops chunganensis) host species.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;1783272|1239|909932|1843489|31977|39948;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|186801|3082720|186804|1501226;3379134|1224|28216|80840|995019|40544;1783272|1239|909932|1843489|31977,Complete,KateRasheed
bsdb:37993728/8/1,37993728,case-control,37993728,10.1038/s43705-023-00332-7,https://pmc.ncbi.nlm.nih.gov/articles/PMC10665332,"Sun D., Herath J., Zhou S., Ellepola G. , Meegaskumbura M.",Associations of Batrachochytrium dendrobatidis with skin bacteria and fungi on Asian amphibian hosts,ISME communications,2023,NA,Experiment 8,China,Rhacophorus minimus,Skin epidermis,UBERON:0001003,Fungal infectious disease,MONDO:0002041,Rhacophorus minimus frog uninfected with Batrachochytrium dendrobatidis (Bd-),Rhacophorus minimus frog infected with Batrachochytrium dendrobatidis (Bd+),Bacterial diversity of infected frogs with Batrachocytrium dendrobatidis (Bd+),15,11,NA,16S,4,Illumina,relative abundances,Pearson Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S4a and Table S3,15 November 2025,Oladoye,Oladoye,The significant correlations of bacterial taxa and Bd infection intensity with Minimal treefrog (Rhacophorus minimus) host species.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae|g__Spirosoma,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae",3379134|1224|28211|204457|41297|13687;3379134|976|768503|768507|89373|107;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801;1783272|1239|186801|3085636|186803;3379134|1224|1236|91347|1903412,Complete,KateRasheed
bsdb:37993728/9/1,37993728,case-control,37993728,10.1038/s43705-023-00332-7,https://pmc.ncbi.nlm.nih.gov/articles/PMC10665332,"Sun D., Herath J., Zhou S., Ellepola G. , Meegaskumbura M.",Associations of Batrachochytrium dendrobatidis with skin bacteria and fungi on Asian amphibian hosts,ISME communications,2023,NA,Experiment 9,China,Theloderma rhododiscus,Skin epidermis,UBERON:0001003,Fungal infectious disease,MONDO:0002041,Theloderma rhododiscus frog uninfected with Batrachocytrium dendrobatidis (Bd-),Theloderma rhododiscus frog infected with Batrachocytrium dendrobatidis (Bd+),Bacterial diversity of infected frogs with Batrachocytrium dendrobatidis (Bd+),21,8,NA,16S,4,Illumina,relative abundances,Pearson Correlation,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary Figure S4a and Table S3,16 November 2025,Oladoye,Oladoye,The significant correlations of bacterial taxa and Bd infection intensity with Red-disked small treefrog (Theloderma rhododiscus) host species,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Klenkia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae",3379134|1224|1236|2887326|468|469;1783272|1239|186801|3085636|186803|1766253;3379134|976|200643|171549|171552|1283313;1783272|544448|31969|186332|186333|2152;1783272|1239|186801|186802|216572|216851;1783272|201174|1760|1643682|85030|2183612;1783272|1239|91061|186826|1300|1357;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843489|31977|906;1783272|1239|91061|1385|186822|44249;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|292632;3379134|1224|1236|91347|1903411,Complete,KateRasheed
bsdb:37993728/9/2,37993728,case-control,37993728,10.1038/s43705-023-00332-7,https://pmc.ncbi.nlm.nih.gov/articles/PMC10665332,"Sun D., Herath J., Zhou S., Ellepola G. , Meegaskumbura M.",Associations of Batrachochytrium dendrobatidis with skin bacteria and fungi on Asian amphibian hosts,ISME communications,2023,NA,Experiment 9,China,Theloderma rhododiscus,Skin epidermis,UBERON:0001003,Fungal infectious disease,MONDO:0002041,Theloderma rhododiscus frog uninfected with Batrachocytrium dendrobatidis (Bd-),Theloderma rhododiscus frog infected with Batrachocytrium dendrobatidis (Bd+),Bacterial diversity of infected frogs with Batrachocytrium dendrobatidis (Bd+),21,8,NA,16S,4,Illumina,relative abundances,Pearson Correlation,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplementary Figure S4a and Table S3,16 November 2025,Oladoye,Oladoye,The significant correlations of bacterial taxa and Bd infection intensity with Red-disked small treefrog (Theloderma rhododiscus) host species,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Flavisolibacter,k__Bacillati|p__Actinomycetota|c__Thermoleophilia|o__Solirubrobacterales|f__Solirubrobacteraceae|g__Solirubrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae",3379134|976|1853228|1853229|563835|398041;1783272|201174|1497346|588673|320599|207599;3379134|1224|28216|80840|80864,Complete,KateRasheed
bsdb:37993728/11/1,37993728,case-control,37993728,10.1038/s43705-023-00332-7,https://pmc.ncbi.nlm.nih.gov/articles/PMC10665332,"Sun D., Herath J., Zhou S., Ellepola G. , Meegaskumbura M.",Associations of Batrachochytrium dendrobatidis with skin bacteria and fungi on Asian amphibian hosts,ISME communications,2023,NA,Experiment 11,China,Theloderma rhododiscus,Skin epidermis,UBERON:0001003,Fungal infectious disease,MONDO:0002041,Theloderma rhododiscus frog uninfected with Batrachocytrium dendrobatidis (Bd-),Theloderma rhododiscus frog infected with Batrachocytrium dendrobatidis (Bd+),Fungal diversity of infected frogs with Batrachocytrium dendrobatidis (Bd+),21,8,NA,ITS / ITS2,NA,Illumina,relative abundances,Pearson Correlation,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 1,Supplementary Figure S4b and Table S4,16 November 2025,Oladoye,Oladoye,The significant correlations of fungal taxa and Bd infection intensity with Red-disked small treefrog (Theloderma rhododiscus) host species,increased,"k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Cucurbitariaceae,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Cucurbitariaceae|g__Pyrenochaeta",4751|4890|147541|92860|221670;4751|4890|147541|92860|221670|285810,Complete,KateRasheed
bsdb:37993728/14/1,37993728,case-control,37993728,10.1038/s43705-023-00332-7,https://pmc.ncbi.nlm.nih.gov/articles/PMC10665332,"Sun D., Herath J., Zhou S., Ellepola G. , Meegaskumbura M.",Associations of Batrachochytrium dendrobatidis with skin bacteria and fungi on Asian amphibian hosts,ISME communications,2023,NA,Experiment 14,China,Rhacophorus minimus,Skin epidermis,UBERON:0001003,Fungal infectious disease,MONDO:0002041,Rhacophorus minimus frog uninfected with Batrachochytrium dendrobatidis (Bd-),Rhacophorus minimus frog infected with Batrachochytrium dendrobatidis (Bd+),Fungal diversity of Infected frogs with Batrachocytrium dendrobatidis (Bd+),15,11,NA,ITS / ITS2,NA,Illumina,relative abundances,Pearson Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S4b and Table S4,16 November 2025,Oladoye,Oladoye,The significant correlations of fungal taxa and Bd infection intensity with Minimal treefrog (Rhacophorus minimus) host species.,increased,"k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Bulleribasidiaceae|g__Bulleribasidium,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales|f__Calloriaceae|g__Calloria,k__Fungi|p__Cryptomycota,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Diaporthales|f__Diaporthaceae,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Diaporthales|f__Diaporthaceae|g__Diaporthe,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales",4751|5204|155616|5234|1884640|189446;4751|4890|147548|5178|2576002|1763460;4751|1031332;4751|4890|147550|5114|767018;4751|4890|147550|5114|767018|36922;4751|4890|147550|5125,Complete,KateRasheed
bsdb:37993728/16/1,37993728,case-control,37993728,10.1038/s43705-023-00332-7,https://pmc.ncbi.nlm.nih.gov/articles/PMC10665332,"Sun D., Herath J., Zhou S., Ellepola G. , Meegaskumbura M.",Associations of Batrachochytrium dendrobatidis with skin bacteria and fungi on Asian amphibian hosts,ISME communications,2023,NA,Experiment 16,China,Amolops chunganensis,Skin epidermis,UBERON:0001003,Fungal infectious disease,MONDO:0002041,Amolops chunganensis frog uninfected with Batrachochytrium dendrobatidis (Bd-),Amolops chunganensis frog infected with Batrachochytrium dendrobatidis (Bd+),Fungal diversity of infected frogs with Batrachocytrium dendrobatidis (Bd+),16,15,NA,ITS / ITS2,NA,Illumina,relative abundances,Pearson Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S4b and Table S4,16 November 2025,Oladoye,"Oladoye,Tosin",The significant correlations of fungal taxa and Bd infection intensity with Chungan torrent frog (Amolops chunganensis) host species.,increased,"k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Amphisphaeriales|f__Castanediellaceae|g__Castanediella,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|f__Chrysozymaceae,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Filobasidiales|f__Piskurozymaceae|g__Piskurozyma,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|f__Chrysozymaceae|g__Pseudohyphozyma,k__Fungi|p__Chytridiomycota|c__Chytridiomycetes|o__Rhizophydiales,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Volutella,k__Fungi|p__Ascomycota,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae",4751|4890|147550|3402561|3402563|1671266;4751|5204|162481|1799785;4751|5204|155616|90886|1851565|1851566;4751|5204|162481|1799785|1801563;4751|4761|451435|451442;4751|4890|147550|5125|110618|145966;4751|4890;4751|4890|147550|5125|110618,Complete,KateRasheed
bsdb:37993728/16/2,37993728,case-control,37993728,10.1038/s43705-023-00332-7,https://pmc.ncbi.nlm.nih.gov/articles/PMC10665332,"Sun D., Herath J., Zhou S., Ellepola G. , Meegaskumbura M.",Associations of Batrachochytrium dendrobatidis with skin bacteria and fungi on Asian amphibian hosts,ISME communications,2023,NA,Experiment 16,China,Amolops chunganensis,Skin epidermis,UBERON:0001003,Fungal infectious disease,MONDO:0002041,Amolops chunganensis frog uninfected with Batrachochytrium dendrobatidis (Bd-),Amolops chunganensis frog infected with Batrachochytrium dendrobatidis (Bd+),Fungal diversity of infected frogs with Batrachocytrium dendrobatidis (Bd+),16,15,NA,ITS / ITS2,NA,Illumina,relative abundances,Pearson Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure S4b and Table S4,16 November 2025,Oladoye,Oladoye,The significant correlations of fungal taxa and Bd infection intensity with Chungan torrent frog (Amolops chunganensis) host species.,decreased,k__Fungi|p__Ascomycota,4751|4890,Complete,KateRasheed
bsdb:37993728/18/1,37993728,case-control,37993728,10.1038/s43705-023-00332-7,https://pmc.ncbi.nlm.nih.gov/articles/PMC10665332,"Sun D., Herath J., Zhou S., Ellepola G. , Meegaskumbura M.",Associations of Batrachochytrium dendrobatidis with skin bacteria and fungi on Asian amphibian hosts,ISME communications,2023,NA,Experiment 18,China,Leptobrachella liui,Skin epidermis,UBERON:0001003,Fungal infectious disease,MONDO:0002041,Leptobrachella liui frog uninfected with Batrachochytrium dendrobatidis (Bd-),Leptobrachella liui frog infected with Batrachochytrium dendrobatidis (Bd+),Fungal diversity of infected frogs with Batrachocytrium dendrobatidis (Bd+),11,9,NA,ITS / ITS2,NA,Illumina,relative abundances,Pearson Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S4b and Table S4,16 November 2025,Oladoye,Oladoye,The significant correlations of fungal taxa and Bd infection intensity with Fujian metacarpal-tubercled toad (Leptobrachella liui) host species.,increased,"k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus,k__Fungi|p__Ascomycota|c__Orbiliomycetes|o__Orbiliales|f__Orbiliaceae|g__Dactylella,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Teratosphaeriaceae|g__Devriesia,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales|f__Helotiaceae,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales,k__Fungi|p__Ascomycota|c__Leotiomycetes,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Myriangiales,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Diaporthales|g__Sirococcus,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Didymellaceae,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales,k__Fungi|p__Ascomycota",4751|4890|147545|5042|1131492|5052;4751|4890|189478|189479|47021|47025;4751|4890|147541|2726947|668547|286563;4751|4890|147548|5178|5181;4751|4890|147548|5178;4751|4890|147548;4751|4890|147541|45676;4751|4890|147550|5114|83884;4751|4890|147541|92860|683158;4751|4890|147541|92860;4751|4890,Complete,KateRasheed
bsdb:37993728/18/2,37993728,case-control,37993728,10.1038/s43705-023-00332-7,https://pmc.ncbi.nlm.nih.gov/articles/PMC10665332,"Sun D., Herath J., Zhou S., Ellepola G. , Meegaskumbura M.",Associations of Batrachochytrium dendrobatidis with skin bacteria and fungi on Asian amphibian hosts,ISME communications,2023,NA,Experiment 18,China,Leptobrachella liui,Skin epidermis,UBERON:0001003,Fungal infectious disease,MONDO:0002041,Leptobrachella liui frog uninfected with Batrachochytrium dendrobatidis (Bd-),Leptobrachella liui frog infected with Batrachochytrium dendrobatidis (Bd+),Fungal diversity of infected frogs with Batrachocytrium dendrobatidis (Bd+),11,9,NA,ITS / ITS2,NA,Illumina,relative abundances,Pearson Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure S4b and Table S4,16 November 2025,Oladoye,Oladoye,The significant correlations of fungal taxa and Bd infection intensity with Fujian metacarpal-tubercled toad (Leptobrachella liui) host species.,decreased,"k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales|f__Discinellaceae|g__Articulospora,k__Fungi|p__Ascomycota,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Didymellaceae",4751|4890|147548|5178|2794838|253308;4751|4890;4751|4890|147541|92860|683158,Complete,KateRasheed
bsdb:38006331/1/1,38006331,case-control,38006331,10.1093/bjsopen/zrad105,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10675991/,"Cao Y., Shang F., Jin M., Deng S., Gu J., Mao F., Qin L., Wang J., Xue Y., Jiang Z., Cheng D., Liu L., Nie X., Liu T., Liu H. , Cai K.",Changes in Bacteroides and the microbiota in patients with obstructed colorectal cancer: retrospective cohort study,BJS open,2023,NA,Experiment 1,China,Homo sapiens,Colon,UBERON:0001155,Intestinal obstruction,MONDO:0004565,Non-obstruction tumor group,Obstruction tumor group,"Obstruction tumor colorectal cancer (CRC) patients diagnosed with intestinal obstruction; the inability of bowel contents to pass through due to an intestinal tumour, accompanied by abdominal distension and pain.",42,42,1 week,16S,34,Illumina,relative abundances,Metastats,0.05,FALSE,NA,"age,body mass index,chemotherapy,sex",NA,increased,increased,increased,increased,NA,increased,Signature 1,Figure 5C,31 January 2024,Andre,"Andre,WikiWorks,Ese,Fiddyhamma","The enriched microbial communities in obstruction tumour tissues versus non-obstruction, at the phylum level",increased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,KateRasheed
bsdb:38006331/2/1,38006331,case-control,38006331,10.1093/bjsopen/zrad105,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10675991/,"Cao Y., Shang F., Jin M., Deng S., Gu J., Mao F., Qin L., Wang J., Xue Y., Jiang Z., Cheng D., Liu L., Nie X., Liu T., Liu H. , Cai K.",Changes in Bacteroides and the microbiota in patients with obstructed colorectal cancer: retrospective cohort study,BJS open,2023,NA,Experiment 2,China,Homo sapiens,Colon,UBERON:0001155,Intestinal obstruction,MONDO:0004565,Non-obstruction tumor group,Obstruction tumor group,"Obstruction tumor colorectal cancer (CRC) patients diagnosed with intestinal obstruction; the inability of bowel contents to pass through due to an intestinal tumour, accompanied by abdominal distension and pain.",42,42,1 week,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.45,"age,body mass index,chemotherapy,sex",NA,increased,increased,increased,increased,NA,increased,Signature 1,Figure 5G,5 August 2025,Ese,"Ese,Fiddyhamma",Linear discriminant analysis effect size (LEfSe)  analysis showing significant differences in species diversity between Non-obstruction tumor group and Obstruction tumor group,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alteromonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Anoxybacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bdellovibrionota|c__Bdellovibrionia|o__Bdellovibrionales|f__Pseudobdellovibrionaceae|g__Bdellovibrio,k__Pseudomonadati|p__Bdellovibrionota|c__Bdellovibrionia|o__Bdellovibrionales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Gemmatimonadota|c__Gemmatimonadia|o__Gemmatimonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Idiomarinaceae|g__Idiomarina,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Idiomarinaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Legionellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Leptothrix,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bdellovibrionota|c__Bdellovibrionia|o__Bdellovibrionales|f__Pseudobdellovibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Thermomonas,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Wautersiella,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia",3379134|1224|1236|2887326|468|469;1783272|201174|1760|2037;1783272|201174;3379134|1224|28211|356|82115|357;3379134|976|200643|171549|171550|239759;3379134|1224|28211;3379134|1224|1236|135622|72275;3379134|1224|1236|135622;3379134|1224|1236|135622|72275|226;1783272|1239|91061|1385|3120669|150247;1783272|201174|1760|85006|1268|1663;1783272|1239|91061|1385|186817;1783272|1239|91061|1385;1783272|1239|91061;1783272|1239;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976;3379134|3018035|3031418|213481|213483|958;3379134|3018035|3031418|213481;1783272|1239|186801|3085636|186803|572511;3379134|1224|28211|204458|76892|41275;1783272|1239|186801|186802|3085642|580596;3379134|1224|28211|204458|76892;3379134|1224|28211|204458;3379134|1224|28216|80840|80864;1783272|1239|186801|3085636|186803|33042;3379134|1224|28216|80840|80864|80865;28221;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;3379134|976|117743|200644|49546;3379134|976|117743|200644;3379134|976|117743;3379134|976|117743|200644|49546|237;3379134|1224|1236;3379134|142182|219685|219686;3379134|1224|1236|135622|267893|135575;3379134|1224|1236|135622|267893;3379134|1224|28216|80840|75682|29580;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;3379134|1224|1236|118969|444;3379134|1224|1236|118969;3379134|1224|28216|80840|2975441|88;1783272|201174|1760|85006|85023;1783272|201174|1760|85006|1268;3379134|1224|1236|2887326|468;3379134|976|200643|171549|2005473;3379134|1224|1236|135619|135620;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572;1783272|1239|186801|3082720|186804;3379134|3018035|3031418|213481|213483;3379134|1224|1236|72274|135621;3379134|1224|1236|72274;3379134|1224|1236|72274|135621|286;3379134|1224|28216|80840|119060|48736;3379134|1224|28211|356|82115;3379134|976|200643|171549|171550;3379134|1224|28216|80840|2975441|93681;1783272|1239|186801|186802|216572|1263;3379134|1224|28211|204457|3423717|165695;3379134|1224|28211|204457|41297;3379134|1224|28211|204457;1783272|1239|186801|186802|216572|292632;3379134|1224|1236|135614|32033|141948;3379134|976|117743|200644|2762318|343873;1783272|201174|84992,Complete,KateRasheed
bsdb:38006331/2/2,38006331,case-control,38006331,10.1093/bjsopen/zrad105,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10675991/,"Cao Y., Shang F., Jin M., Deng S., Gu J., Mao F., Qin L., Wang J., Xue Y., Jiang Z., Cheng D., Liu L., Nie X., Liu T., Liu H. , Cai K.",Changes in Bacteroides and the microbiota in patients with obstructed colorectal cancer: retrospective cohort study,BJS open,2023,NA,Experiment 2,China,Homo sapiens,Colon,UBERON:0001155,Intestinal obstruction,MONDO:0004565,Non-obstruction tumor group,Obstruction tumor group,"Obstruction tumor colorectal cancer (CRC) patients diagnosed with intestinal obstruction; the inability of bowel contents to pass through due to an intestinal tumour, accompanied by abdominal distension and pain.",42,42,1 week,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.45,"age,body mass index,chemotherapy,sex",NA,increased,increased,increased,increased,NA,increased,Signature 2,Figure 5G,5 August 2025,Ese,"Ese,Fiddyhamma",Linear discriminant analysis effect size (LEfSe) analysis showing significant differences in species diversity between Non-obstruction tumor group and Obstruction tumor group,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Aquabacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|28216|80840|92793;3379134|1224|28216;3379134|1224|28216|80840;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;3379134|1224|28216|80840|119060|106589;1783272|1239|186801|186802;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;3379134|29547|3031852|213849|72293;3384189|32066|203490|203491|1129771|32067;3384189|32066|203490|203491|1129771;3379134|1224|28216|80840|75682;3379134|1224,Complete,KateRasheed
bsdb:38006331/4/1,38006331,case-control,38006331,10.1093/bjsopen/zrad105,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10675991/,"Cao Y., Shang F., Jin M., Deng S., Gu J., Mao F., Qin L., Wang J., Xue Y., Jiang Z., Cheng D., Liu L., Nie X., Liu T., Liu H. , Cai K.",Changes in Bacteroides and the microbiota in patients with obstructed colorectal cancer: retrospective cohort study,BJS open,2023,NA,Experiment 4,China,Homo sapiens,Colon,UBERON:0001155,Intestinal obstruction,MONDO:0004565,Non-obstruction tumor group (fresh tumor tissue),Obstruction tumor group (fresh tumor tissue),"Fresh tumor tissue from obstruction tumor colorectal cancer (CRC) patients diagnosed with intestinal obstruction; the inability of bowel contents to pass through due to an intestinal tumour, accompanied by abdominal distension and pain.",NA,NA,1 week,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.3,NA,NA,increased,increased,increased,increased,NA,increased,Signature 1,Figure 7C,7 August 2025,Ese,"Ese,Fiddyhamma",Linear discriminant analysis effect size (LEfSe) analysis showing significant differences in species diversity between Non-obstruction tumor group (fresh tumor tissue) and Obstruction tumor group (fresh tumor tissue),increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinopolysporales|f__Actinopolysporaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Alkanindiges,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Anoxybacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Pseudomonadati|p__Bdellovibrionota|c__Bdellovibrionia|o__Bdellovibrionales|f__Pseudobdellovibrionaceae|g__Bdellovibrio,k__Pseudomonadati|p__Bdellovibrionota|c__Bdellovibrionia|o__Bdellovibrionales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Blastobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Geobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Legionellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Leptothrix,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Mycoplana,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Myxococcota|c__Myxococcia|o__Myxococcales,k__Pseudomonadati|p__Nitrospirota|c__Nitrospiria|o__Nitrospirales,k__Pseudomonadati|p__Nitrospirota|c__Nitrospiria,k__Pseudomonadati|p__Nitrospirota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Planctomycetota|c__Phycisphaerae,k__Pseudomonadati|p__Planctomycetota|c__Phycisphaerae|o__Phycisphaerales,k__Pseudomonadati|p__Planctomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae,k__Pseudomonadati|p__Bdellovibrionota|c__Bdellovibrionia|o__Bdellovibrionales|f__Pseudobdellovibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Xenorhabdus",1783272|201174|84992;3379134|1224|1236|2887326|468|469;1783272|201174|1760|2037;1783272|201174;1783272|201174|1760|622450|622451;3379134|976|200643|171549|171550|239759;3379134|1224|1236|2887326|468|222991;3379134|1224|1236|135622;1783272|1239|91061|1385|3120669|150247;1783272|201174|1760|85006|1268|1663;1783272|1239|91061|1385|186817;1783272|1239|91061|1385;1783272|1239|91061;1783272|1239;3379134|976;3379134|976|200643|171549|2005519;3379134|3018035|3031418|213481|213483|958;3379134|3018035|3031418|213481;3379134|1224|28211|356|41294|109;1783272|201174|1760|85006|85019;1783272|201174|1760|85006|85019|1696;3379134|1224|28211|204458|76892|41275;1783272|1239|186801|186802|3085642|580596;3379134|976|200643|171549|1853231|574697;3379134|1224|28211|204458|76892;3379134|1224|28211|204458;3379134|1224|1236|135613|1046;3379134|1224|28216|80840|80864;1783272|1239|186801|3085636|186803|33042;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|186801|186802|186807|51514;3379134|1224|28216|80840|80864|80865;28221;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;3379134|1224|1236|91347|543;1783272|1239|1737404|1737405|1570339|150022;3379134|976|117743|200644|49546;3379134|976|117743|200644|49546|237;3379134|1224|1236;1783272|1239|91061|1385|3120669|129337;3379134|1224|1236|135619|28256;3379134|1224|28216|80840|75682|29580;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;3379134|1224|1236|118969|444;3379134|1224|1236|118969;3379134|1224|28216|80840|2975441|88;1783272|201174|1760|85006|85023;1783272|201174|1760|85006|85023|33882;1783272|201174|1760|85006|1268;1783272|544448|31969;3379134|1224|1236|2887326|468;3379134|976|200643|171549|2005473;3379134|1224|28211|356|82115|13159;1783272|544448;3379134|2818505|32015|29;3379134|40117|203693|189778;3379134|40117|203693;3379134|40117;3379134|1224|1236|135619|135620;3379134|1224|1236|135619;3379134|976|200643|171549|1853231;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572;3379134|203682|666505;3379134|203682|666505|666506;3379134|203682;3379134|1224|1236|135622|267888;3379134|3018035|3031418|213481|213483;3379134|1224|1236|72274|135621;3379134|1224|1236|72274;3379134|1224|1236|72274|135621|286;3379134|976|200643|171549|171550;3379134|1224|28216|80840|2975441|93681;1783272|1239|186801|186802|216572|1263;3379134|976|117747|200666|84566;3379134|976|117747|200666;3379134|976|117747;3379134|976|117747|200666|84566|28453;3379134|1224|28211|204457|3423717|165695;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;1783272|1239|186801|186802|216572|292632;1783272|1239|1737404|1737405|1737406;3379134|1224|1236|91347|1903414|626,Complete,KateRasheed
bsdb:38006331/4/2,38006331,case-control,38006331,10.1093/bjsopen/zrad105,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10675991/,"Cao Y., Shang F., Jin M., Deng S., Gu J., Mao F., Qin L., Wang J., Xue Y., Jiang Z., Cheng D., Liu L., Nie X., Liu T., Liu H. , Cai K.",Changes in Bacteroides and the microbiota in patients with obstructed colorectal cancer: retrospective cohort study,BJS open,2023,NA,Experiment 4,China,Homo sapiens,Colon,UBERON:0001155,Intestinal obstruction,MONDO:0004565,Non-obstruction tumor group (fresh tumor tissue),Obstruction tumor group (fresh tumor tissue),"Fresh tumor tissue from obstruction tumor colorectal cancer (CRC) patients diagnosed with intestinal obstruction; the inability of bowel contents to pass through due to an intestinal tumour, accompanied by abdominal distension and pain.",NA,NA,1 week,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.3,NA,NA,increased,increased,increased,increased,NA,increased,Signature 2,Figure 7C,7 August 2025,Ese,"Ese,Fiddyhamma",Linear discriminant analysis effect size (LEfSe) analysis showing significant differences in species diversity between Non-obstruction tumor group (fresh tumor tissue) and Obstruction tumor group (fresh tumor tissue),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Aquabacterium,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|28216|80840|92793;3379134|1224,Complete,KateRasheed
bsdb:38006691/1/1,38006691,prospective cohort,38006691,10.1016/j.oraloncology.2023.106623,https://www.sciencedirect.com/science/article/abs/pii/S1368837523003196?via=ihub,"Hes C., Desilets A., Tonneau M., El Ouarzadi O., De Figueiredo Sousa M., Bahig H., Filion É., Nguyen-Tan P.F., Christopoulos A., Benlaïfaoui M., Derosa L., Alves Costa Silva C., Ponce M., Malo J., Belkad W., Charpentier D., Aubin F., Hamilou Z., Jamal R., Messaoudene M., Soulières D. , Routy B.",Gut microbiome predicts gastrointestinal toxicity outcomes from chemoradiation therapy in patients with head and neck squamous cell carcinoma,Oral oncology,2023,"Chemoradiation therapy, Head and neck squamous cell cancer, Microbiome, Mucositis",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Head and neck squamous cell carcinoma,EFO:0000181,Oral mucositis CTCAE grade 1-2 (mild),Oral mucositis CTCAE grade 3 (severe),Patients with severe mucositis following chemoradiation therapy,30,22,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Fig. 2.,20 December 2023,Andre,"Andre,WikiWorks",Fig. 2. Gut microbiome profiling with shotgun metagenomic sequencing by development of severe mucositis,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium UC5.1-1D1,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium paraputrificum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Massilicoli|s__Massilicoli timonensis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Massilimicrobiota|s__Massilimicrobiota timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas intestinalis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa",1783272|1239|186801|3085636|186803|207244|105841;1783272|1239|186801|1697794;1783272|1239|186801|186802|31979|1485|29363;1783272|1239|186801|3085636|186803|2719313|1531;1783272|1239|186801|3085636|186803|1649459|154046;1783272|1239|526524|526525|128827|2683202|2015901;1783272|1239|526524|526525|128827|1924110|1776392;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|186801|3085636|186803|1769710|1653434;1783272|1239|526524|526525|2810280|3025755|1547,Complete,Chloe
bsdb:38006691/1/2,38006691,prospective cohort,38006691,10.1016/j.oraloncology.2023.106623,https://www.sciencedirect.com/science/article/abs/pii/S1368837523003196?via=ihub,"Hes C., Desilets A., Tonneau M., El Ouarzadi O., De Figueiredo Sousa M., Bahig H., Filion É., Nguyen-Tan P.F., Christopoulos A., Benlaïfaoui M., Derosa L., Alves Costa Silva C., Ponce M., Malo J., Belkad W., Charpentier D., Aubin F., Hamilou Z., Jamal R., Messaoudene M., Soulières D. , Routy B.",Gut microbiome predicts gastrointestinal toxicity outcomes from chemoradiation therapy in patients with head and neck squamous cell carcinoma,Oral oncology,2023,"Chemoradiation therapy, Head and neck squamous cell cancer, Microbiome, Mucositis",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Head and neck squamous cell carcinoma,EFO:0000181,Oral mucositis CTCAE grade 1-2 (mild),Oral mucositis CTCAE grade 3 (severe),Patients with severe mucositis following chemoradiation therapy,30,22,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Fig. 2,20 December 2023,Andre,"Andre,WikiWorks",Fig. 2. Gut microbiome profiling with shotgun metagenomic sequencing by development of severe mucositis,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia|s__Alloscardovia omnicolens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium KLE1615,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF34-10BH,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. chh4-2,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella marseillensis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia|s__Senegalimassilia anaerobia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__Desulfovibrionaceae bacterium",1783272|1239|186801|3085636|186803|1766253|39491;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|171550|239759|1288121;1783272|201174|1760|85004|31953|419014|419015;1783272|1239|186801|186802|1715004;1783272|1239|186801|186802|31979|1485|2293011;1783272|1239|186801|186802|31979|1485|2067550;1783272|1239|186801|3085636|186803|28050|28052;3379134|976|200643|171549|815|909656|204516;3379134|976|200643|171549|171552|838|2479840;1783272|201174|84998|84999|84107|1473205|1473216;1783272|1239|186801|3085636|186803|2316020|46228;3379134|200940|3031449|213115|194924|2049043,Complete,Chloe
bsdb:38006691/2/1,38006691,prospective cohort,38006691,10.1016/j.oraloncology.2023.106623,https://www.sciencedirect.com/science/article/abs/pii/S1368837523003196?via=ihub,"Hes C., Desilets A., Tonneau M., El Ouarzadi O., De Figueiredo Sousa M., Bahig H., Filion É., Nguyen-Tan P.F., Christopoulos A., Benlaïfaoui M., Derosa L., Alves Costa Silva C., Ponce M., Malo J., Belkad W., Charpentier D., Aubin F., Hamilou Z., Jamal R., Messaoudene M., Soulières D. , Routy B.",Gut microbiome predicts gastrointestinal toxicity outcomes from chemoradiation therapy in patients with head and neck squamous cell carcinoma,Oral oncology,2023,"Chemoradiation therapy, Head and neck squamous cell cancer, Microbiome, Mucositis",Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Head and neck squamous cell carcinoma,EFO:0000181,No enteral feeding plus mild mucositis,Enteral feeding plus mucositis of any grade,Head and neck squamous cell carcinoma with severe mucositis and enteral feeding need,27,13,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Fig 3,3 January 2024,Andre,"Andre,WikiWorks",Gut microbiome profiling with shotgun metagenomic sequencing by co-occurrence of development of severe mucositis and enteral feeding,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella sp. YY7918,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Kytococcaceae|g__Kytococcus|s__Kytococcus sedentarius,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. An181,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas intestinalis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum",1783272|1239|186801|3085636|186803|207244|105841;1783272|201174|84998|1643822|1643826|84111|502558;1783272|1239|186801|3085636|186803|2719313|1531;1783272|1239|91061|186826|81852|1350|1351;1783272|201174|1760|85006|2805426|57499|1276;1783272|1239|186801|3085636|186803|1506553|1965575;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|186801|3085636|186803|1769710|1653434;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|186801|186802|31979|1485|1522,Complete,Chloe
bsdb:38006691/2/2,38006691,prospective cohort,38006691,10.1016/j.oraloncology.2023.106623,https://www.sciencedirect.com/science/article/abs/pii/S1368837523003196?via=ihub,"Hes C., Desilets A., Tonneau M., El Ouarzadi O., De Figueiredo Sousa M., Bahig H., Filion É., Nguyen-Tan P.F., Christopoulos A., Benlaïfaoui M., Derosa L., Alves Costa Silva C., Ponce M., Malo J., Belkad W., Charpentier D., Aubin F., Hamilou Z., Jamal R., Messaoudene M., Soulières D. , Routy B.",Gut microbiome predicts gastrointestinal toxicity outcomes from chemoradiation therapy in patients with head and neck squamous cell carcinoma,Oral oncology,2023,"Chemoradiation therapy, Head and neck squamous cell cancer, Microbiome, Mucositis",Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Head and neck squamous cell carcinoma,EFO:0000181,No enteral feeding plus mild mucositis,Enteral feeding plus mucositis of any grade,Head and neck squamous cell carcinoma with severe mucositis and enteral feeding need,27,13,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Fig3.,3 January 2024,Andre,"Andre,WikiWorks",NA,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium KLE1615,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF34-10BH,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia|s__Senegalimassilia anaerobia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis",3379134|976|200643|171549|171550|239759|28117;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|186802|1715004;1783272|1239|186801|186802|31979|1485|2293011;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|186802|186806|1730|39496;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|204516;1783272|1239|186801|3085636|186803|841|166486;1783272|201174|84998|84999|84107|1473205|1473216;3379134|1224|28216|80840|995019|40544|40545,Complete,Chloe
bsdb:38006691/3/1,38006691,prospective cohort,38006691,10.1016/j.oraloncology.2023.106623,https://www.sciencedirect.com/science/article/abs/pii/S1368837523003196?via=ihub,"Hes C., Desilets A., Tonneau M., El Ouarzadi O., De Figueiredo Sousa M., Bahig H., Filion É., Nguyen-Tan P.F., Christopoulos A., Benlaïfaoui M., Derosa L., Alves Costa Silva C., Ponce M., Malo J., Belkad W., Charpentier D., Aubin F., Hamilou Z., Jamal R., Messaoudene M., Soulières D. , Routy B.",Gut microbiome predicts gastrointestinal toxicity outcomes from chemoradiation therapy in patients with head and neck squamous cell carcinoma,Oral oncology,2023,"Chemoradiation therapy, Head and neck squamous cell cancer, Microbiome, Mucositis",Experiment 3,Canada,Homo sapiens,Feces,UBERON:0001988,Head and neck squamous cell carcinoma,EFO:0000181,No Enteral feeding tube placement,Enteral feeding tube placement,Patients needing enteral feeding,27,13,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Supplemental Figure 10,3 January 2024,Andre,"Andre,WikiWorks",Gut microbiome profiling in patients with enteral feeding versus without,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella sp. YY7918,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella sp. OF01-20,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena contorta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas umbilicata,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae|g__Isoptericola|s__Isoptericola variabilis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Kytococcaceae|g__Kytococcus|s__Kytococcus sedentarius,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. An181,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum",1783272|1239|186801|3085636|186803|207244|105841;1783272|1239|186801|3085636|186803|572511|1322;1783272|1239|186801|3085636|186803|572511|33035;1783272|201174|84998|1643822|1643826|84111|502558;1783272|1239|186801|3085636|186803|1432051|2292348;1783272|1239|186801|3085636|186803|2719313|1531;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|186801|3085636|186803|2005359|39482;1783272|1239|186801|3085636|186803|2005355|1912855;1783272|201174|1760|85006|85017|254250|139208;1783272|201174|1760|85006|2805426|57499|1276;1783272|1239|186801|3085636|186803|1506553|1965575;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|186801|186802|31979|1485|1522,Complete,Chloe
bsdb:38006691/3/2,38006691,prospective cohort,38006691,10.1016/j.oraloncology.2023.106623,https://www.sciencedirect.com/science/article/abs/pii/S1368837523003196?via=ihub,"Hes C., Desilets A., Tonneau M., El Ouarzadi O., De Figueiredo Sousa M., Bahig H., Filion É., Nguyen-Tan P.F., Christopoulos A., Benlaïfaoui M., Derosa L., Alves Costa Silva C., Ponce M., Malo J., Belkad W., Charpentier D., Aubin F., Hamilou Z., Jamal R., Messaoudene M., Soulières D. , Routy B.",Gut microbiome predicts gastrointestinal toxicity outcomes from chemoradiation therapy in patients with head and neck squamous cell carcinoma,Oral oncology,2023,"Chemoradiation therapy, Head and neck squamous cell cancer, Microbiome, Mucositis",Experiment 3,Canada,Homo sapiens,Feces,UBERON:0001988,Head and neck squamous cell carcinoma,EFO:0000181,No Enteral feeding tube placement,Enteral feeding tube placement,Patients needing enteral feeding,27,13,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Supplemental Figure 10,3 January 2024,Andre,"Andre,WikiWorks",Gut microbiome profiling in patients with enteral feeding versus without,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas faecihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium KLE1615,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF34-10BH,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp. AF36-15AT,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena fissicatena,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis",3379134|976|200643|171549|171550|239759|28117;1783272|1239|186801|3085636|186803|572511|40520;3379134|976|200643|171549|1853231|574697|1472416;1783272|1239|186801|186802|1715004;1783272|1239|186801|186802|31979|1485|2293011;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330|2292041;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|3085636|186803|2005359|290055;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|204516;1783272|1239|186801|3085636|186803|841|166486,Complete,Chloe
bsdb:38033462/1/1,38033462,"cross-sectional observational, not case-control",38033462,10.3389/froh.2023.1288499,NA,"Molli V.L.P., Kissa J., Baraniya D., Gharibi A., Chen T., Al-Hebshi N.N. , Albandar J.M.",Bacteriome analysis of <i>Aggregatibacter actinomycetemcomitans</i>-JP2 genotype-associated Grade C periodontitis in Moroccan adolescents,Frontiers in oral health,2023,"biofilm, dysbiosis, high-throughput nucleotide sequencing, microbiota, periodontitis",Experiment 1,Morocco,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Aggressive periodontitis,EFO:0006342,Healthy controls,Grade C (previously aggressive) Periodontitis- Shallow pocket,"Grade C (previously aggressive) Periodontitis- Shallow pocket refers to the depth of the periodontal pocket(PD ≤ 4 mm), which is the space between the tooth and the surrounding gum tissues. It also indicates mild periodontal disease.",13,8,3 months,16S,123,Illumina,centered log-ratio,MaAsLin2,0.1,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 1,"Supplementary Table 5,6",20 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between healthy controls and shallow pocket site.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kluyvera,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. oral taxon C61,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cancerogenus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas fluorescens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter lwoffii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium vrystaatense,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter sp. oral taxon C13,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|s__Veillonellaceae bacterium oral taxon 145,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. oral taxon C85,k__Bacillati|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae|s__Anaerolineaceae bacterium oral taxon 439,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium gwangjuense,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia|s__Erwinia aphidicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium oral taxon 500,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|s__Peptostreptococcaceae bacterium oral taxon 103,k__Pseudomonadati|p__Bacteroidota|s__Bacteroidetes bacterium oral taxon 365,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 355,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema maltophilum,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema lecithinolyticum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia alvei,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp. oral taxon 370,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|s__Peptostreptococcaceae bacterium oral taxon 369,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 349,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Pseudolactococcus|s__Pseudolactococcus raffinolactis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sinensis,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 350,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema parvum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia liquefaciens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia|s__Erwinia billingiae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia proteamaculans",3379134|1224|1236|2887326|468|469;3379134|976|117743|200644|2762318|59732;3379134|1224|1236|91347|543|547;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|1903409|551;3384194|508458|649775|649776|3029087|1434006;3379134|1224|1236|91347|1903412|568;3379134|1224|1236|91347|543|579;1783272|1239|91061|186826|1300|1357;3379134|1224|1236|72274|135621|286;3379134|1224|1236|91347|1903411|613;3379134|1224|1236|91347|543|547|550;3379134|1224|1236|72274|135621|286|712511;3379134|1224|1236|91347|543|547|69218;3379134|1224|1236|72274|135621|286|294;3379134|1224|1236|2887326|468|469|28090;3379134|1224|1236|91347|543|547|158836;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|2005525|195950|28112;3379134|976|117743|200644|2762318|59732|307480;3379134|1224|1236|2887326|468|469|712107;3379134|203691|203692|136|2845253|157|158;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|909932|1843489|31977|713068;3379134|1224|1236|72274|135621|286|712513;1783272|200795|292625|292629|292628|1889813;3379134|976|117743|200644|2762318|59732|1069980;3379134|1224|1236|91347|1903409|551|68334;1783272|1239|186801|3085636|186803|712991;1783272|1239|186801|3082720|186804|713018;3379134|976|712905;95818|713056;3379134|203691|203692|136|2845253|157|51160;3379134|203691|203692|136|2845253|157|53418;3379134|1224|1236|91347|1903412|568|569;3384189|32066|203490|203491|203492|848|712288;1783272|1239|186801|3082720|186804|713020;95818|713051;1783272|1239|91061|186826|1300|3436058|1366;1783272|1239|91061|186826|1300|1301|176090;95818|713052;3379134|203691|203692|136|2845253|157|138851;3379134|1224|1236|91347|1903411|613|614;3379134|1224|1236|91347|1903409|551|182337;3379134|1224|1236|91347|1903411|613|28151,Complete,Svetlana up
bsdb:38033462/1/2,38033462,"cross-sectional observational, not case-control",38033462,10.3389/froh.2023.1288499,NA,"Molli V.L.P., Kissa J., Baraniya D., Gharibi A., Chen T., Al-Hebshi N.N. , Albandar J.M.",Bacteriome analysis of <i>Aggregatibacter actinomycetemcomitans</i>-JP2 genotype-associated Grade C periodontitis in Moroccan adolescents,Frontiers in oral health,2023,"biofilm, dysbiosis, high-throughput nucleotide sequencing, microbiota, periodontitis",Experiment 1,Morocco,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Aggressive periodontitis,EFO:0006342,Healthy controls,Grade C (previously aggressive) Periodontitis- Shallow pocket,"Grade C (previously aggressive) Periodontitis- Shallow pocket refers to the depth of the periodontal pocket(PD ≤ 4 mm), which is the space between the tooth and the surrounding gum tissues. It also indicates mild periodontal disease.",13,8,3 months,16S,123,Illumina,centered log-ratio,MaAsLin2,0.1,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 2,"Supplementary Table 5,6",20 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between healthy controls and shallow pocket site,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga haemolytica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 431,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 219,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 064,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 223,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum umeaense,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp. oral taxon 078,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria mucosa,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Ectopseudomonas|s__Ectopseudomonas oleovorans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella|s__Bergeyella sp. oral taxon 322,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium polymorphum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 225,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hongkongensis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Pseudoleptotrichia|s__Pseudoleptotrichia goodfellowii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 423,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum|s__Actinobaculum sp. oral taxon 183,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae",1783272|1239|91061|186826|186827|46123;1783272|201174|1760|2037|2049|76833;3379134|1224|1236|135625|712|416916;3379134|976|117743|200644|2762318|59735;3379134|29547|3031852|213849|72294|194;3379134|976|117743|200644|49546|1016;3379134|1224|1236|135615|868|2717;1783272|201174|1760|85007|1653|1716;1783272|1239|909932|1843489|31977|39948;3379134|1224|28216|206351|481|538;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;3379134|1224|28216|206351|481|32257;1783272|1239|186801|3085636|186803|1164882;3379134|1224|28216|80840|119060|47670;3384189|32066|203490|203491|1129771|32067;3379134|1224|28216|206351|481|482;1783272|1239|186801|3085636|186803|265975;3379134|976|200643|171549|171552|838;1783272|201174|1760|85009|31957|1743;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85004|31953|196081;1783272|1239|186801|3085636|186803|177971;3379134|1224|1236|135614|32033|40323;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;3379134|976|117743|200644|49546|1016|45243;1783272|201174|1760|85007|1653|1716|43768;1783272|1239|91061|186826|1300|1301|712633;1783272|1239|91061|1385|539738|1378|84135;1783272|201174|1760|85009|31957|2801844|1750;1783272|1239|91061|186826|1300|1301|68892;1783272|201174|1760|85006|1268|32207|2047;3379134|1224|28216|206351|481|538|539;3384189|32066|203490|203491|1129771|32067|652714;3384189|32066|203490|203491|1129771|32067|157688;3379134|1224|28216|206351|481|482|1107316;1783272|1239|91061|186826|1300|1301|712624;3384189|32066|203490|203491|1129771|32067|712363;3379134|29547|3031852|213849|72294|194|204;1783272|201174|1760|85007|1653|1716|61592;1783272|1239|186801|3085636|186803|1164882|617123;1783272|1239|91061|186826|186828|117563|46124;1783272|1239|186801|3085636|186803|265975|652706;1783272|1239|91061|186826|1300|1301|45634;3379134|1224|28216|206351|481|482|488;3379134|1224|1236|135614|32033|40323|40324;3379134|1224|1236|72274|135621|3236654|301;3379134|1224|28216|206351|481|482|484;3379134|976|117743|200644|2762318|59735|712187;1783272|1239|91061|186826|1300|1301|113107;3379134|1224|1236|135615|868|2717|2718;3384189|32066|203490|203491|203492|848|76857;1783272|201174|1760|2037|2049|1654|1655;3384189|32066|203490|203491|1129771|32067|671213;1783272|1239|91061|1385|539738|1378|1379;3379134|29547|3031852|213849|72294|194|824;3384189|32066|203490|203491|1129771|32067|554406;3384189|32066|203490|203491|1129771|2755140|157692;1783272|1239|91061|186826|1300|1301|712632;3379134|1224|28216|206351|481|32257|505;1783272|201174|1760|2037|2049|76833|712888;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300|1301|1305;1783272|1239|909932|1843489|31977|29465|29466;3379134|976|117743|200644|49546|1016|1019;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|91061|186826|186827|46123|46125;1783272|1239|91061|186826|1300|1301|1302;1783272|201174|1760|85006|1268|32207|172042;3379134|1224|28216|80840|119060|47670|47671;3379134|1224|1236|135625|712|724|729,Complete,Svetlana up
bsdb:38033462/2/1,38033462,"cross-sectional observational, not case-control",38033462,10.3389/froh.2023.1288499,NA,"Molli V.L.P., Kissa J., Baraniya D., Gharibi A., Chen T., Al-Hebshi N.N. , Albandar J.M.",Bacteriome analysis of <i>Aggregatibacter actinomycetemcomitans</i>-JP2 genotype-associated Grade C periodontitis in Moroccan adolescents,Frontiers in oral health,2023,"biofilm, dysbiosis, high-throughput nucleotide sequencing, microbiota, periodontitis",Experiment 2,Morocco,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Aggressive periodontitis,EFO:0006342,Healthy controls,Grade C(previously aggressive) Periodontitis- Deep pocket,Grade C(previously aggressive) Periodontitis- Deep pocket refers to a periodontal pocket with a depth of 6 mm or more (PD ≥ 6 mm). It indicates moderate to severe periodontal disease.,13,8,3 months,16S,123,Illumina,centered log-ratio,MaAsLin2,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Supplementary Table 5,6",20 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between healthy controls and deep pocket site,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. oral taxon C61,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cancerogenus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|s__Veillonellaceae bacterium oral taxon 145,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema socranskii,k__Bacillati|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae|s__Anaerolineaceae bacterium oral taxon 439,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema maltophilum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter sp. oral taxon C13,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Pseudomonadati|p__Bacteroidota|s__Bacteroidetes bacterium oral taxon 365,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 349,k__Pseudomonadati|p__Bacteroidota|s__Bacteroidetes bacterium oral taxon 280,k__Fusobacteriati|p__Fusobacteriota|s__Fusobacteria bacterium oral taxon A71,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas fluorescens,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 350,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema parvum,k__Pseudomonadati|p__Bacteroidota|s__Bacteroidetes bacterium oral taxon 516,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp. oral taxon 270,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema lecithinolyticum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella uli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium oral taxon 500,k__Pseudomonadati|p__Bacteroidota|s__Bacteroidetes bacterium oral taxon 503,k__Pseudomonadati|p__Bacteroidota|s__Bacteroidetes bacterium oral taxon 511,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus|s__Desulfobulbus sp. oral taxon 041,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia|s__Delftia acidovorans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sinensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|s__Peptostreptococcaceae bacterium oral taxon 103,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|s__Veillonellaceae bacterium oral taxon 148,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia cardiffensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas tolaasii,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter rectus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 301,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 304,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia|s__Erwinia aphidicola,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|s__Veillonellaceae bacterium oral taxon 135,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp. oral taxon 268,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 300,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Prevotella heparinolytica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|s__Veillonellaceae bacterium oral taxon 132,k__Pseudomonadati|p__Bacteroidota|s__Bacteroidetes bacterium oral taxon 507,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 355,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia exigua,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|s__alpha proteobacterium oral taxon A28,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia alvei,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp. oral taxon G85,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp. oral taxon 237,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp. oral taxon 234,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|s__Veillonellaceae bacterium oral taxon 150,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|s__Veillonellaceae bacterium oral taxon 155,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella pleuritidis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella micans",3379134|1224|1236|2887326|468|469;3379134|976|200643|171549|815|816;3379134|1224|28216|80840|80864|80865;3379134|200940|3031451|3024411|213121|893;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|1903409|551;3384194|508458|649775|649776|3029087|1434006;3379134|1224|1236|72274|135621|286;1783272|201174|84998|1643822|1643826|84108;3379134|976|200643|171549|2005525|195950;3379134|203691|203692|136|2845253|157;3379134|1224|1236|72274|135621|286|712511;3379134|1224|1236|91347|543|547|69218;3379134|1224|1236|91347|543|547|550;3379134|1224|1236|91347|543|547|158836;3379134|976|200643|171549|171551|836|28124;1783272|1239|909932|1843489|31977|713068;3379134|976|200643|171549|2005525|195950|28112;3379134|203691|203692|136|2845253|157|158;3379134|203691|203692|136|2845253|157|53419;1783272|200795|292625|292629|292628|1889813;3379134|203691|203692|136|2845253|157|51160;3379134|1224|1236|2887326|468|469|712107;3379134|976|200643|171549|171551|836|837;3379134|976|712905;95818|713051;3379134|976|712900;3384189|32066|712973;3379134|1224|1236|72274|135621|286|294;95818|713052;3379134|203691|203692|136|2845253|157|138851;3379134|976|712912;3379134|203691|203692|136|2845253|157|671227;3379134|203691|203692|136|2845253|157|53418;1783272|201174|84998|84999|1643824|133925|133926;1783272|1239|186801|3085636|186803|712991;3379134|976|712907;3379134|976|712911;3379134|200940|3031451|3024411|213121|893|712258;3384194|508458|649775|649776|3029087|1434006|651822;3379134|1224|28216|80840|80864|80865|80866;1783272|1239|91061|186826|1300|1301|176090;1783272|1239|186801|3082720|186804|713018;1783272|1239|909932|1843489|31977|713069;1783272|201174|1760|2037|2049|2529408|181487;3379134|1224|1236|72274|135621|286|29442;3379134|29547|3031852|213849|72294|194|203;3379134|976|200643|171549|171552|838|712457;3379134|976|200643|171549|171552|838|712459;3379134|1224|1236|91347|1903409|551|68334;1783272|1239|909932|1843489|31977|713067;3379134|203691|203692|136|2845253|157|712745;3379134|976|200643|171549|171552|838|712456;3379134|976|200643|171549|815|816|28113;1783272|1239|909932|1843489|31977|713066;3379134|976|712909;95818|713056;1783272|201174|84998|1643822|1643826|84108|84109;3379134|1224|28211|712875;3379134|1224|1236|91347|1903412|568|569;3379134|203691|203692|136|2845253|157|712776;3379134|203691|203692|136|2845253|157|712724;3379134|203691|203692|136|2845253|157|712721;1783272|1239|909932|1843489|31977|671234;1783272|1239|909932|1843489|31977|671235;3379134|976|200643|171549|171552|2974257|407975;3379134|976|200643|171549|171552|838|189723,Complete,Svetlana up
bsdb:38033462/2/2,38033462,"cross-sectional observational, not case-control",38033462,10.3389/froh.2023.1288499,NA,"Molli V.L.P., Kissa J., Baraniya D., Gharibi A., Chen T., Al-Hebshi N.N. , Albandar J.M.",Bacteriome analysis of <i>Aggregatibacter actinomycetemcomitans</i>-JP2 genotype-associated Grade C periodontitis in Moroccan adolescents,Frontiers in oral health,2023,"biofilm, dysbiosis, high-throughput nucleotide sequencing, microbiota, periodontitis",Experiment 2,Morocco,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Aggressive periodontitis,EFO:0006342,Healthy controls,Grade C(previously aggressive) Periodontitis- Deep pocket,Grade C(previously aggressive) Periodontitis- Deep pocket refers to a periodontal pocket with a depth of 6 mm or more (PD ≥ 6 mm). It indicates moderate to severe periodontal disease.,13,8,3 months,16S,123,Illumina,centered log-ratio,MaAsLin2,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Supplementary Table 5,6",20 November 2024,KateRasheed,"KateRasheed,Aleru Divine,WikiWorks",Differentially abundant taxa between healthy controls and deep pocket site,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum|s__Actinobaculum sp. oral taxon 183,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces gerencseriae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces johnsonii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces massiliensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 169,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 175,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 877,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella|s__Bergeyella sp. oral taxon 322,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga haemolytica,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium valvarum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Ectopseudomonas|s__Ectopseudomonas oleovorans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium polymorphum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum umeaense,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hongkongensis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 212,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 215,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 223,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 225,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia trevisanii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria mucosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Pseudoleptotrichia|s__Pseudoleptotrichia goodfellowii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus intermedius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 058,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 064,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 423,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 431,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis",1783272|1239|91061|186826|186827|46123;1783272|1239|91061|186826|186827|46123|46125;1783272|201174|1760|2037|2049|76833;1783272|201174|1760|2037|2049|76833|712888;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049|1654|52769;1783272|201174|1760|2037|2049|1654|544581;1783272|201174|1760|2037|2049|1654|461393;1783272|201174|1760|2037|2049|1654|1655;1783272|201174|1760|2037|2049|1654|712116;1783272|201174|1760|2037|2049|1654|712119;1783272|201174|1760|2037|2049|1654|1227263;3379134|1224|1236|135625|712|416916;1783272|201174|1760|85009|31957|2801844|1750;3379134|976|117743|200644|2762318|59735;3379134|976|117743|200644|2762318|59735|712187;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294|194|204;3379134|976|117743|200644|49546|1016;3379134|976|117743|200644|49546|1016|45243;3379134|976|117743|200644|49546|1016|1019;3379134|1224|1236|135615|868|2717;3379134|1224|1236|135615|868|2717|2718;3379134|1224|1236|135615|868|2717|194702;1783272|1239|186801|3085636|186803|43996;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85007|1653|1716|61592;3379134|1224|1236|72274|135621|3236654|301;3379134|1224|28216|206351|481|538;3379134|1224|28216|206351|481|538|539;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492|848|860;3384189|32066|203490|203491|203492|848|76857;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|1385|539738|1378|1379;1783272|1239|91061|1385|539738|1378|29391;1783272|1239|91061|1385|539738|1378|84135;1783272|1239|91061|186826|186828|117563;1783272|1239|91061|186826|186828|117563|46124;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712|724|729;3379134|1224|28216|206351|481|32257;3379134|1224|28216|206351|481|32257|505;1783272|1239|186801|3085636|186803|1164882;1783272|1239|186801|3085636|186803|1164882|617123;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|80840|119060|47670|47671;3384189|32066|203490|203491|1129771|32067;3384189|32066|203490|203491|1129771|32067|40542;3384189|32066|203490|203491|1129771|32067|157688;3384189|32066|203490|203491|1129771|32067|554406;3384189|32066|203490|203491|1129771|32067|712357;3384189|32066|203490|203491|1129771|32067|712359;3384189|32066|203490|203491|1129771|32067|712363;3384189|32066|203490|203491|1129771|32067|671213;3384189|32066|203490|203491|1129771|32067|109328;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481|482|488;1783272|201174|1760|85009|31957|1743;3384189|32066|203490|203491|1129771|2755140|157692;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|172042;1783272|201174|1760|85006|1268|32207|2047;1783272|201174|1760|85006|1268|32207|43675;3379134|1224|1236|135614|32033|40323;3379134|1224|1236|135614|32033|40323|40324;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|113107;1783272|1239|91061|186826|1300|1301|45634;1783272|1239|91061|186826|1300|1301|1302;1783272|1239|91061|186826|1300|1301|68892;1783272|1239|91061|186826|1300|1301|1338;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|91061|186826|1300|1301|1305;1783272|1239|91061|186826|1300|1301|712622;1783272|1239|91061|186826|1300|1301|712624;1783272|1239|91061|186826|1300|1301|712632;1783272|1239|91061|186826|1300|1301|712633;1783272|1239|91061|186826|1300|1301|1343;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|29466;3379134|29547|3031852|213849|72294|194|824,Complete,Svetlana up
bsdb:38033462/3/1,38033462,"cross-sectional observational, not case-control",38033462,10.3389/froh.2023.1288499,NA,"Molli V.L.P., Kissa J., Baraniya D., Gharibi A., Chen T., Al-Hebshi N.N. , Albandar J.M.",Bacteriome analysis of <i>Aggregatibacter actinomycetemcomitans</i>-JP2 genotype-associated Grade C periodontitis in Moroccan adolescents,Frontiers in oral health,2023,"biofilm, dysbiosis, high-throughput nucleotide sequencing, microbiota, periodontitis",Experiment 3,Morocco,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Aggressive periodontitis,EFO:0006342,GCP- Shallow pocket,GCP- Deep pocket,"Grade C Periodontitis - Deep pocket refers to a periodontal pocket with a depth of 6 mm or more (PD ≥ 6 mm), indicating moderate to severe periodontal disease.",8,8,3 months,16S,123,Illumina,centered log-ratio,MaAsLin2,0.25,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 1,Supplementary Figure 2A,21 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between shallow pocket and deep pocket site.,increased,"k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",3379134|203691|203692|136|2845253|157;1783272|201174|84998|84999|1643824|1380;1783272|201174|84998|1643822|1643826|84108;3379134|976|200643|171549|2005525|195950,Complete,Svetlana up
bsdb:38033462/3/2,38033462,"cross-sectional observational, not case-control",38033462,10.3389/froh.2023.1288499,NA,"Molli V.L.P., Kissa J., Baraniya D., Gharibi A., Chen T., Al-Hebshi N.N. , Albandar J.M.",Bacteriome analysis of <i>Aggregatibacter actinomycetemcomitans</i>-JP2 genotype-associated Grade C periodontitis in Moroccan adolescents,Frontiers in oral health,2023,"biofilm, dysbiosis, high-throughput nucleotide sequencing, microbiota, periodontitis",Experiment 3,Morocco,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Aggressive periodontitis,EFO:0006342,GCP- Shallow pocket,GCP- Deep pocket,"Grade C Periodontitis - Deep pocket refers to a periodontal pocket with a depth of 6 mm or more (PD ≥ 6 mm), indicating moderate to severe periodontal disease.",8,8,3 months,16S,123,Illumina,centered log-ratio,MaAsLin2,0.25,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 2,Supplementary Figure 2A,21 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between shallow pocket and deep pocket site.,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",3384189|32066|203490|203491|203492|848;1783272|1239|91061|186826|186827|46123;1783272|1239|91061|186826|186828|117563;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135614|32033|40323,Complete,Svetlana up
bsdb:38033462/4/1,38033462,"cross-sectional observational, not case-control",38033462,10.3389/froh.2023.1288499,NA,"Molli V.L.P., Kissa J., Baraniya D., Gharibi A., Chen T., Al-Hebshi N.N. , Albandar J.M.",Bacteriome analysis of <i>Aggregatibacter actinomycetemcomitans</i>-JP2 genotype-associated Grade C periodontitis in Moroccan adolescents,Frontiers in oral health,2023,"biofilm, dysbiosis, high-throughput nucleotide sequencing, microbiota, periodontitis",Experiment 4,Morocco,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Aggressive periodontitis,EFO:0006342,GCP- Shallow pocket,GCP- Deep pocket,"Grade C Periodontitis - Deep pocket refers to a periodontal pocket with a depth of 6 mm or more (PD ≥ 6 mm), indicating moderate to severe periodontal disease.",8,8,3 months,16S,123,Illumina,centered log-ratio,MaAsLin2,0.01,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 1,Supplementary Figure 2B,3 January 2025,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between shallow pocket and deep pocket site.,increased,"k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema socranskii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella uli,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|s__Veillonellaceae bacterium oral taxon 135,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia exigua,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes",3379134|203691|203692|136|2845253|157|53419;1783272|201174|84998|84999|1643824|133925|133926;1783272|1239|909932|1843489|31977|713067;1783272|201174|84998|1643822|1643826|84108|84109;1783272|1239|909932|1843489|31977|39948|39950,Complete,Svetlana up
bsdb:38033462/4/2,38033462,"cross-sectional observational, not case-control",38033462,10.3389/froh.2023.1288499,NA,"Molli V.L.P., Kissa J., Baraniya D., Gharibi A., Chen T., Al-Hebshi N.N. , Albandar J.M.",Bacteriome analysis of <i>Aggregatibacter actinomycetemcomitans</i>-JP2 genotype-associated Grade C periodontitis in Moroccan adolescents,Frontiers in oral health,2023,"biofilm, dysbiosis, high-throughput nucleotide sequencing, microbiota, periodontitis",Experiment 4,Morocco,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Aggressive periodontitis,EFO:0006342,GCP- Shallow pocket,GCP- Deep pocket,"Grade C Periodontitis - Deep pocket refers to a periodontal pocket with a depth of 6 mm or more (PD ≥ 6 mm), indicating moderate to severe periodontal disease.",8,8,3 months,16S,123,Illumina,centered log-ratio,MaAsLin2,0.01,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 2,Supplementary Figure 2B,3 January 2025,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between shallow pocket and deep pocket site.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 175,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia",1783272|1239|91061|1385|539738|1378|1379;1783272|1239|91061|186826|186828|117563|46124;1783272|201174|1760|2037|2049|1654|712119;1783272|1239|91061|186826|1300|1301|28037;3379134|1224|1236|135614|32033|40323|40324,Complete,Svetlana up
bsdb:38034621/1/1,38034621,"cross-sectional observational, not case-control",38034621,10.1016/j.heliyon.2023.e21463,NA,"Jiang W., Lu G., Qiao T., Yu X., Luo Q., Tong J., Fan S., Chai L., Gao D., Wang R., Deng C., Lv Z. , Li D.",Integrated microbiome and metabolome analysis reveals a distinct microbial and metabolic signature in Graves' disease and hypothyroidism,Heliyon,2023,"16S rRNA gene sequencing, Clinical hypothyroidism, Graves' disease, Microbiota, Non-targeted metabolomics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Controls,Graves’ disease (GD),Patients diagnosed with Graves’ disease (GD),48,39,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,body mass index,sex",NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 3,24 July 2025,Aleru Divine,Aleru Divine,"Mann-Whitney U test plots of the pairwise comparisons between the HT, GD, and control groups. This figure presents the top 10 genera that differed between groups in each pairwise comparison (HT versus Control, GD versus Control, and HT versus GD) according to the Mann-Whitney U test.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",3379134|976|200643|171549|815|816;1783272|1239|91061|186826|33958|1578,Complete,NA
bsdb:38034621/1/2,38034621,"cross-sectional observational, not case-control",38034621,10.1016/j.heliyon.2023.e21463,NA,"Jiang W., Lu G., Qiao T., Yu X., Luo Q., Tong J., Fan S., Chai L., Gao D., Wang R., Deng C., Lv Z. , Li D.",Integrated microbiome and metabolome analysis reveals a distinct microbial and metabolic signature in Graves' disease and hypothyroidism,Heliyon,2023,"16S rRNA gene sequencing, Clinical hypothyroidism, Graves' disease, Microbiota, Non-targeted metabolomics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Controls,Graves’ disease (GD),Patients diagnosed with Graves’ disease (GD),48,39,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,body mass index,sex",NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 3,24 July 2025,Aleru Divine,Aleru Divine,"Mann-Whitney U test plots of the pairwise comparisons between the HT, GD, and control groups. This figure presents the top 10 genera that differed between groups in each pairwise comparison (HT versus Control, GD versus Control, and HT versus GD) according to the Mann-Whitney U test.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3082720|186804,Complete,NA
bsdb:38034621/2/1,38034621,"cross-sectional observational, not case-control",38034621,10.1016/j.heliyon.2023.e21463,NA,"Jiang W., Lu G., Qiao T., Yu X., Luo Q., Tong J., Fan S., Chai L., Gao D., Wang R., Deng C., Lv Z. , Li D.",Integrated microbiome and metabolome analysis reveals a distinct microbial and metabolic signature in Graves' disease and hypothyroidism,Heliyon,2023,"16S rRNA gene sequencing, Clinical hypothyroidism, Graves' disease, Microbiota, Non-targeted metabolomics",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Hypothyroidism,EFO:0004705,Controls,Hypothyroidism group (HT),Patients diagnosed with Hypothyroidism group (HT),48,78,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,body mass index,sex",NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 3,24 July 2025,Aleru Divine,Aleru Divine,"Mann-Whitney U test plots of the pairwise comparisons between the HT, GD, and control groups. This figure presents the top 10 genera that differed between groups in each pairwise comparison (HT versus Control, GD versus Control, and HT versus GD) according to the Mann-Whitney U test.",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,NA
bsdb:38034621/2/2,38034621,"cross-sectional observational, not case-control",38034621,10.1016/j.heliyon.2023.e21463,NA,"Jiang W., Lu G., Qiao T., Yu X., Luo Q., Tong J., Fan S., Chai L., Gao D., Wang R., Deng C., Lv Z. , Li D.",Integrated microbiome and metabolome analysis reveals a distinct microbial and metabolic signature in Graves' disease and hypothyroidism,Heliyon,2023,"16S rRNA gene sequencing, Clinical hypothyroidism, Graves' disease, Microbiota, Non-targeted metabolomics",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Hypothyroidism,EFO:0004705,Controls,Hypothyroidism group (HT),Patients diagnosed with Hypothyroidism group (HT),48,78,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,"age,body mass index,sex",NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 3,24 July 2025,Aleru Divine,Aleru Divine,"Mann-Whitney U test plots of the pairwise comparisons between the HT, GD, and control groups. This figure presents the top 10 genera that differed between groups in each pairwise comparison (HT versus Control, GD versus Control, and HT versus GD) according to the Mann-Whitney U test.",decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|292632,Complete,NA
bsdb:38034621/3/1,38034621,"cross-sectional observational, not case-control",38034621,10.1016/j.heliyon.2023.e21463,NA,"Jiang W., Lu G., Qiao T., Yu X., Luo Q., Tong J., Fan S., Chai L., Gao D., Wang R., Deng C., Lv Z. , Li D.",Integrated microbiome and metabolome analysis reveals a distinct microbial and metabolic signature in Graves' disease and hypothyroidism,Heliyon,2023,"16S rRNA gene sequencing, Clinical hypothyroidism, Graves' disease, Microbiota, Non-targeted metabolomics",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,"Hypothyroidism,Graves disease","EFO:0004705,EFO:0004237",Graves' disease (GD),Hypothyroidism group (HT),Patients diagnosed with Hypothyroidism group (HT),39,78,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3,24 July 2025,Aleru Divine,Aleru Divine,"Mann-Whitney U test plots of the pairwise comparisons between the HT, GD, and control groups. This figure presents the top 10 genera that differed between groups in each pairwise comparison (HT versus Control, GD versus Control, and HT versus GD) according to the Mann-Whitney U test.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera",1783272|1239|186801|186802|31979|1485;1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1505657;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|216572;1783272|1239|909932|1843489|31977|906,Complete,NA
bsdb:38034621/3/2,38034621,"cross-sectional observational, not case-control",38034621,10.1016/j.heliyon.2023.e21463,NA,"Jiang W., Lu G., Qiao T., Yu X., Luo Q., Tong J., Fan S., Chai L., Gao D., Wang R., Deng C., Lv Z. , Li D.",Integrated microbiome and metabolome analysis reveals a distinct microbial and metabolic signature in Graves' disease and hypothyroidism,Heliyon,2023,"16S rRNA gene sequencing, Clinical hypothyroidism, Graves' disease, Microbiota, Non-targeted metabolomics",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,"Hypothyroidism,Graves disease","EFO:0004705,EFO:0004237",Graves' disease (GD),Hypothyroidism group (HT),Patients diagnosed with Hypothyroidism group (HT),39,78,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 3,24 July 2025,Aleru Divine,Aleru Divine,"Mann-Whitney U test plots of the pairwise comparisons between the HT, GD, and control groups. This figure presents the top 10 genera that differed between groups in each pairwise comparison (HT versus Control, GD versus Control, and HT versus GD) according to the Mann-Whitney U test.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|216851,Complete,NA
bsdb:38037123/1/3,38037123,time series / longitudinal observational,38037123,10.1186/s40168-023-01677-w,NA,"Medeiros M.C., The S., Bellile E., Russo N., Schmitd L., Danella E., Singh P., Banerjee R., Bassis C., Murphy G.R., Sartor M.A., Lombaert I., Schmidt T.M., Eisbruch A., Murdoch-Kinch C.A., Rozek L., Wolf G.T., Li G., Chen G.Y. , D'Silva N.J.",Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer,Microbiome,2023,NA,Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Treatment,EFO:0000727,Pre-treatment (baseline),Post-treatment (6 months later),Saliva samples collected from patients with oral squamous cell carcinoma (SCC) at 6 months after treatment,106,72,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,decreased,decreased,Signature 3,Supplementary Fig. 1B,23 March 2024,Nityasinghal 14,"Nityasinghal 14,Scholastica,WikiWorks",Differentially abundant taxa at pre-treatment (0 month) compared to post-treatment (6 months later) by Linear discriminant analysis Effect Size (LEfSe) analysis,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|171552|838;1783272|201174|1760|85006|1268|32207;3379134|1224|1236|72274|135621|286;1783272|201174|1760|85004|31953|196081;1783272|1239|909932|1843489|31977,Complete,Svetlana up
bsdb:38037123/1/4,38037123,time series / longitudinal observational,38037123,10.1186/s40168-023-01677-w,NA,"Medeiros M.C., The S., Bellile E., Russo N., Schmitd L., Danella E., Singh P., Banerjee R., Bassis C., Murphy G.R., Sartor M.A., Lombaert I., Schmidt T.M., Eisbruch A., Murdoch-Kinch C.A., Rozek L., Wolf G.T., Li G., Chen G.Y. , D'Silva N.J.",Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer,Microbiome,2023,NA,Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Treatment,EFO:0000727,Pre-treatment (baseline),Post-treatment (6 months later),Saliva samples collected from patients with oral squamous cell carcinoma (SCC) at 6 months after treatment,106,72,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,decreased,decreased,Signature 4,Supplementary Fig. 1B,23 March 2024,Nityasinghal 14,"Nityasinghal 14,Scholastica,WikiWorks",Differentially abundant taxa at pre-treatment (0 month) compared to post-treatment (6 months later) by Linear discriminant analysis Effect Size (LEfSe) analysis,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",1783272|201174|1760|85007|1653|1716;3384189|32066|203490|203491|1129771|32067;3379134|976|117743|200644|49546|1016;3379134|976|117743|200644|49546;1783272|1239|186801|3085636|186803|265975;3379134|976|200643|171549|171552|838;1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549;1783272|1239|909932|1843489|31977|906;1783272|1239|91061|186826;3379134|976|200643|171549|171551|836;3384189|32066|203490|203491|203492|848;3379134|1224|28216|206351|481|482;3379134|1224|1236|135625|712,Complete,Svetlana up
bsdb:38045157/1/1,38045157,case-control,38045157,10.1016/j.heliyon.2023.e22124,NA,"Huang Y., Tang J., Cai Z., Qi Y., Jiang S., Ma T., Yue Y., Huang F., Yang H. , Ma Y.",Alterations in the intestinal microbiota associated with active tuberculosis and latent tuberculosis infection,Heliyon,2023,"16S rDNA sequencing, Active tuberculosis (ATB), Human gut microbiota, Latent tuberculosis infection (LTBI), Microbial diversity, Mycobacterium tuberculosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,Healthy controls,Active TB,"Clinical and microbiologically confirmed pulmonary TB, treatment-naïve.",20,19,1 week,PCR,NA,Illumina,relative abundances,"LEfSe,Linear Discriminant Analysis",0.05,NA,4,"age,sex",NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 5A and B,27 June 2025,Nuerteye,Nuerteye,"(A) Column diagram of LDA analysis of fecal microbiome in the three groups (HC, LTBI and ATB) (P < 0.05; LDA score >4.0). (B) Pairwise LDA effect size (LEfSe) analysis table of fecal microbiome. The phyla and subsequent taxonomic levels are sorted alphabetically, and the corresponding LDA score for each pairwise analysis is indicated in the column (P < 0.05; LDA score >4.0)",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria",3379134|1224|1236|91347|543;3379134|1224|1236,Complete,NA
bsdb:38045157/1/2,38045157,case-control,38045157,10.1016/j.heliyon.2023.e22124,NA,"Huang Y., Tang J., Cai Z., Qi Y., Jiang S., Ma T., Yue Y., Huang F., Yang H. , Ma Y.",Alterations in the intestinal microbiota associated with active tuberculosis and latent tuberculosis infection,Heliyon,2023,"16S rDNA sequencing, Active tuberculosis (ATB), Human gut microbiota, Latent tuberculosis infection (LTBI), Microbial diversity, Mycobacterium tuberculosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,Healthy controls,Active TB,"Clinical and microbiologically confirmed pulmonary TB, treatment-naïve.",20,19,1 week,PCR,NA,Illumina,relative abundances,"LEfSe,Linear Discriminant Analysis",0.05,NA,4,"age,sex",NA,NA,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 5A and B,27 June 2025,Nuerteye,Nuerteye,"(A) Column diagram of LDA analysis of fecal microbiome in the three groups (HC, LTBI and ATB) (P < 0.05; LDA score >4.0). (B) Pairwise LDA effect size (LEfSe) analysis table of fecal microbiome. The phyla and subsequent taxonomic levels are sorted alphabetically, and the corresponding LDA score for each pairwise analysis is indicated in the column (P < 0.05; LDA score >4.0).",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter",1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|1239|186801;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|1407607,Complete,NA
bsdb:38045684/1/1,38045684,time series / longitudinal observational,38045684,10.3389/fimmu.2023.1280262,NA,"Munjoma P.T., Chandiwana P., Wyss J., Mazhandu A.J., Jordi S.B.U., Gutsire R., Katsidzira L., Yilmaz B., Misselwitz B. , Duri K.",Immune activation and inflammation in lactating women on combination antiretroviral therapy: role of gut dysfunction and gut microbiota imbalance,Frontiers in immunology,2023,"HIV, fecal calprotectin, gut microbiota, lactating women, microbial translocation, resource limited setting, systemic inflammation",Experiment 1,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV - uninfected,HIV - infected,The HIV-infected group consists of HIV-infected lactating women who were followed up at 6 weeks postpartum.,48,25,NA,16S,56,Ion Torrent,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 6a,2 October 2024,Paavni Goyal,"Paavni Goyal,KateRasheed,Aleru Divine,WikiWorks",Differentially abundant taxa significantly associated with HIV infection status at 6 weeks postpartum.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia",1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999;1783272|201174|1760|85006|1268;1783272|201174|84998|1643822|1643826|84108,Complete,ChiomaBlessing
bsdb:38045684/1/2,38045684,time series / longitudinal observational,38045684,10.3389/fimmu.2023.1280262,NA,"Munjoma P.T., Chandiwana P., Wyss J., Mazhandu A.J., Jordi S.B.U., Gutsire R., Katsidzira L., Yilmaz B., Misselwitz B. , Duri K.",Immune activation and inflammation in lactating women on combination antiretroviral therapy: role of gut dysfunction and gut microbiota imbalance,Frontiers in immunology,2023,"HIV, fecal calprotectin, gut microbiota, lactating women, microbial translocation, resource limited setting, systemic inflammation",Experiment 1,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV - uninfected,HIV - infected,The HIV-infected group consists of HIV-infected lactating women who were followed up at 6 weeks postpartum.,48,25,NA,16S,56,Ion Torrent,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 6a,2 October 2024,Paavni Goyal,"Paavni Goyal,KateRasheed,Aleru Divine,WikiWorks",Differentially abundant taxa significantly associated with HIV infection status at 6 weeks postpartum.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485,Complete,ChiomaBlessing
bsdb:38045684/2/1,38045684,time series / longitudinal observational,38045684,10.3389/fimmu.2023.1280262,NA,"Munjoma P.T., Chandiwana P., Wyss J., Mazhandu A.J., Jordi S.B.U., Gutsire R., Katsidzira L., Yilmaz B., Misselwitz B. , Duri K.",Immune activation and inflammation in lactating women on combination antiretroviral therapy: role of gut dysfunction and gut microbiota imbalance,Frontiers in immunology,2023,"HIV, fecal calprotectin, gut microbiota, lactating women, microbial translocation, resource limited setting, systemic inflammation",Experiment 2,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV - uninfected,HIV - infected,The HIV-infected group consists of HIV-infected lactating women who were followed up at 6 months postpartum.,42,23,NA,16S,56,Ion Torrent,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 6b,20 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differentially abundant taxa significantly associated with HIV infection status at 6 months postpartum.,increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,1783272|1239|909932|909929|1843491,Complete,ChiomaBlessing
bsdb:38045684/2/2,38045684,time series / longitudinal observational,38045684,10.3389/fimmu.2023.1280262,NA,"Munjoma P.T., Chandiwana P., Wyss J., Mazhandu A.J., Jordi S.B.U., Gutsire R., Katsidzira L., Yilmaz B., Misselwitz B. , Duri K.",Immune activation and inflammation in lactating women on combination antiretroviral therapy: role of gut dysfunction and gut microbiota imbalance,Frontiers in immunology,2023,"HIV, fecal calprotectin, gut microbiota, lactating women, microbial translocation, resource limited setting, systemic inflammation",Experiment 2,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV - uninfected,HIV - infected,The HIV-infected group consists of HIV-infected lactating women who were followed up at 6 months postpartum.,42,23,NA,16S,56,Ion Torrent,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 6b,20 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differentially abundant taxa significantly associated with HIV infection status at 6 months postpartum.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|31979|1485,Complete,ChiomaBlessing
bsdb:38045684/3/1,38045684,time series / longitudinal observational,38045684,10.3389/fimmu.2023.1280262,NA,"Munjoma P.T., Chandiwana P., Wyss J., Mazhandu A.J., Jordi S.B.U., Gutsire R., Katsidzira L., Yilmaz B., Misselwitz B. , Duri K.",Immune activation and inflammation in lactating women on combination antiretroviral therapy: role of gut dysfunction and gut microbiota imbalance,Frontiers in immunology,2023,"HIV, fecal calprotectin, gut microbiota, lactating women, microbial translocation, resource limited setting, systemic inflammation",Experiment 3,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV - uninfected,HIV - infected,The HIV-infected group consists of HIV-infected lactating women who were followed up at 6 weeks postpartum.,48,25,NA,16S,56,Ion Torrent,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Table 3,20 October 2024,KateRasheed,"KateRasheed,Aleru Divine,WikiWorks",Differentially abundant taxa in gut microbiota associated with inflammatory and vascular injury biomarkers after stratification by HIV infection status.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae",1783272|1239|186801|3085636|186803|28050|39485;3379134|1224|28216|80840|75682,Complete,ChiomaBlessing
bsdb:38045684/3/2,38045684,time series / longitudinal observational,38045684,10.3389/fimmu.2023.1280262,NA,"Munjoma P.T., Chandiwana P., Wyss J., Mazhandu A.J., Jordi S.B.U., Gutsire R., Katsidzira L., Yilmaz B., Misselwitz B. , Duri K.",Immune activation and inflammation in lactating women on combination antiretroviral therapy: role of gut dysfunction and gut microbiota imbalance,Frontiers in immunology,2023,"HIV, fecal calprotectin, gut microbiota, lactating women, microbial translocation, resource limited setting, systemic inflammation",Experiment 3,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV - uninfected,HIV - infected,The HIV-infected group consists of HIV-infected lactating women who were followed up at 6 weeks postpartum.,48,25,NA,16S,56,Ion Torrent,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Table 3,21 October 2024,KateRasheed,"KateRasheed,Aleru Divine,WikiWorks",Differentially abundant taxa in gut microbiota associated with inflammatory and vascular injury biomarkers after stratification by HIV infection status.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,1783272|1239|91061|186826|33958|46255,Complete,ChiomaBlessing
bsdb:38045684/4/1,38045684,time series / longitudinal observational,38045684,10.3389/fimmu.2023.1280262,NA,"Munjoma P.T., Chandiwana P., Wyss J., Mazhandu A.J., Jordi S.B.U., Gutsire R., Katsidzira L., Yilmaz B., Misselwitz B. , Duri K.",Immune activation and inflammation in lactating women on combination antiretroviral therapy: role of gut dysfunction and gut microbiota imbalance,Frontiers in immunology,2023,"HIV, fecal calprotectin, gut microbiota, lactating women, microbial translocation, resource limited setting, systemic inflammation",Experiment 4,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV - uninfected,HIV - infected,The HIV-infected group consists of HIV-infected lactating women who were followed up at 6 months postpartum.,42,23,NA,16S,56,Ion Torrent,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Table 3,21 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differentially abundant taxa in gut microbiota associated with inflammatory and vascular injury biomarkers after stratification by HIV infection status.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens",1783272|1239|186801|3085636|3118652|2039240;1783272|1239|186801|3085636|186803|830;1783272|1239|526524|526525|2810280|135858;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|28050|39485,Complete,ChiomaBlessing
bsdb:38045684/4/2,38045684,time series / longitudinal observational,38045684,10.3389/fimmu.2023.1280262,NA,"Munjoma P.T., Chandiwana P., Wyss J., Mazhandu A.J., Jordi S.B.U., Gutsire R., Katsidzira L., Yilmaz B., Misselwitz B. , Duri K.",Immune activation and inflammation in lactating women on combination antiretroviral therapy: role of gut dysfunction and gut microbiota imbalance,Frontiers in immunology,2023,"HIV, fecal calprotectin, gut microbiota, lactating women, microbial translocation, resource limited setting, systemic inflammation",Experiment 4,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV - uninfected,HIV - infected,The HIV-infected group consists of HIV-infected lactating women who were followed up at 6 months postpartum.,42,23,NA,16S,56,Ion Torrent,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Table 3,21 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differentially abundant taxa in gut microbiota associated with inflammatory and vascular injury biomarkers after stratification by HIV infection status.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium",1783272|201174|1760|2037|2049|1654;1783272|201174;1783272|1239;1783272|1239|526524|526525|2810280;1783272|201174|84998|84999|84107;1783272|201174|84998|1643822|1643826|84111;3384189|32066|203490|203491|203492;1783272|1239|91061|186826|33958|1578;1783272|1239|526524|526525|128827|123375,Complete,ChiomaBlessing
bsdb:38049420/1/1,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 1,"Ethiopia,Madagascar",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Madagascar,Adadle,"2-5 year old children from the Adadle woreda district in Ethiopia, whose samples were sequenced using Primer 1 set (V4 501-508F/701-712R).",431,54,NA,16S,4,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S6 B,22 October 2024,YokoC,"YokoC,WikiWorks",LEfSe analysis using primer set 1 showing bacterial families associated with Adadle or Madagascar.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Beijerinckiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Pirellulales|f__Pirellulaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Puniceicoccaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",1783272|201174|1760|2037|2049;3379134|74201|203494|48461|1647988;1783272|1239|186801|3082720|3030910;1783272|201174|84998|84999|1643824;1783272|1239|91061|1385|186817;3379134|1224|28211|356|45404;1783272|201174|1760|85004|31953;1783272|1239|91061|186826|186828;1783272|1239|91061|1385|186818;1783272|1239|526524|526525|2810280;1783272|201174|84998|84999|84107;1783272|201174|84998|1643822|1643826;1783272|1239|91061|186826|81852;1783272|1239|526524|526525|128827;1783272|1239|91061|1385|539738;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958;1783272|201174|1760|85006|1268;1783272|1239|186801|3085656|3085657;1783272|1239|186801|3082720|186804;3379134|203682|203683|2691354|2691357;3379134|74201|414999|415001|415002;1783272|1239|91061|1385|90964;1783272|1239|91061|186826|1300,Complete,Svetlana up
bsdb:38049420/1/2,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 1,"Ethiopia,Madagascar",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Madagascar,Adadle,"2-5 year old children from the Adadle woreda district in Ethiopia, whose samples were sequenced using Primer 1 set (V4 501-508F/701-712R).",431,54,NA,16S,4,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S6 B,22 October 2024,YokoC,"YokoC,WikiWorks,Tosin",LEfSe analysis using primer set 1 showing bacterial families associated with Adadle or Madagascar.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes",1783272|1239|909932|1843488|909930;3379134|976|200643|171549|815;3379134|29547|3031852|213849|72294;3379134|200940|3031449|213115|194924;3379134|29547|3031852|213849|72293;3379134|976|200643|171549|2005473;1783272|544448|31969|2085|2092;3379134|1224|28216|206351|481;1783272|1239|186801|186802|216572;3379134|1224|1236|135625|712;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550;1783272|1239|909932|909929|1843491;3379134|1224|1236|135624|83763;3379134|1224|28216|80840|995019;1783272|1239|909932|1843489|31977;1783272|1239|186801|186802|186806|1730|290054,Complete,Svetlana up
bsdb:38049420/2/1,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 2,"Central African Republic,Ethiopia",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Central African Republic,Adadle,"2-5 year old children from the Adadle woreda district in Ethiopia, whose samples were sequenced using Primer 1 set (V4 501-508F/701-712R).",274,54,NA,16S,4,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S6 B,22 October 2024,YokoC,"YokoC,WikiWorks",LEfSe analysis using primer set 1 data showing bacterial families associated with Adadle or Central African Republic.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Beijerinckiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Pirellulales|f__Pirellulaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",1783272|201174|1760|2037|2049;3379134|74201|203494|48461|1647988;1783272|1239|186801|3082720|3030910;1783272|201174|84998|84999|1643824;1783272|1239|91061|1385|186817;3379134|1224|28211|356|45404;1783272|201174|1760|85004|31953;1783272|1239|91061|186826|186828;1783272|1239|526524|526525|2810280;1783272|201174|84998|84999|84107;1783272|201174|84998|1643822|1643826;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|186806;1783272|1239|91061|1385|539738;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958;1783272|201174|1760|85006|1268;1783272|1239|186801|3085656|3085657;1783272|1239|186801|3082720|186804;3379134|203682|203683|2691354|2691357;1783272|1239|91061|1385|186818;3379134|1224|28211|356|82115;1783272|1239|91061|1385|90964;1783272|1239|91061|186826|1300,Complete,Svetlana up
bsdb:38049420/2/2,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 2,"Central African Republic,Ethiopia",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Central African Republic,Adadle,"2-5 year old children from the Adadle woreda district in Ethiopia, whose samples were sequenced using Primer 1 set (V4 501-508F/701-712R).",274,54,NA,16S,4,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S6 B,22 October 2024,YokoC,"YokoC,WikiWorks,Tosin",LEfSe analysis using primer set 1 data showing bacterial families associated with Adadle or Central African Republic.,decreased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes",1783272|544448|31969|186329|2146;1783272|1239|909932|1843488|909930;3379134|976|200643|171549|815;3379134|976|200643|171549|2005519;3379134|29547|3031852|213849|72294;3379134|200940|3031449|213115|194924;3379134|29547|3031852|213849|72293;3379134|976|200643|1970189|1573805;3379134|976|200643|171549|2005473;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|75682;3379134|1224|1236|135625|712;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550;1783272|1239|909932|909929|1843491;3379134|1224|28216|80840|995019;3379134|976|200643|171549|2005525;1783272|1239|909932|1843489|31977;1783272|1239|186801|186802|186806|1730|290054,Complete,Svetlana up
bsdb:38049420/3/1,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 3,"Ethiopia,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Industrial Lifestyle,Adadle Agropastoral Lifestyle,"2-5 year old children from the Adadle woreda district in Ethiopia with an Agropastoral lifestyle, whose samples were sequenced using Primer 2 set (V4 515F/806R). Lifestyle classifications of the different populations were based on the publications used for the datasets.",484,13,NA,16S,4,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S6 D,23 October 2024,YokoC,"YokoC,WikiWorks",LEfSe analysis using primer set 2 showing bacterial families associated with agropastoral and industrial lifestyles.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae",1783272|1239|186801|3082720|3030910;1783272|201174|84998|84999|1643824;1783272|1239|91061|1385|186817;1783272|1239|526524|526525|2810280;1783272|201174|84998|84999|84107;1783272|1239|91061|186826|81852;1783272|1239|526524|526525|128827;1783272|1239|186801|3085656|3085657;3379134|976|200643|171549|171552;1783272|1239|91061|186826|1300;3379134|1224|1236|135624|83763,Complete,Svetlana up
bsdb:38049420/3/2,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 3,"Ethiopia,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Industrial Lifestyle,Adadle Agropastoral Lifestyle,"2-5 year old children from the Adadle woreda district in Ethiopia with an Agropastoral lifestyle, whose samples were sequenced using Primer 2 set (V4 515F/806R). Lifestyle classifications of the different populations were based on the publications used for the datasets.",484,13,NA,16S,4,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S6 D,23 October 2024,YokoC,"YokoC,WikiWorks",LEfSe analysis using primer set 2 showing bacterial families associated with agropastoral and industrial lifestyles.,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|74201|203494|48461|1647988;3379134|976|200643|171549|815;3379134|976|200643|171549|2005519;1783272|201174|1760|85004|31953;1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|1185407;3379134|200940|3031449|213115|194924;3379134|976|200643|1970189|1573805;1783272|1239|186801|186802|216572;3379134|1224|1236|135625|712;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171551;3379134|976|200643|171549|171550;3379134|1224|28216|80840|995019;3379134|976|200643|171549|2005525;1783272|1239|909932|1843489|31977,Complete,Svetlana up
bsdb:38049420/4/1,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 4,"Cameroon,China,Ethiopia,Malawi,Peru,United Republic of Tanzania,Venezuela",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Traditional Lifestyle,Adadle Agropastoral Lifestyle,"2-5 year old children from the Adadle woreda district in Ethiopia with an Agropastoral lifestyle, whose samples were sequenced using Primer 2 set (V4 515F/806R). Lifestyle classifications of the different populations were based on the publications used for the datasets.",107,13,NA,16S,4,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S6 D,23 October 2024,YokoC,"YokoC,WikiWorks",LEfSe analysis using primer set 2 showing bacterial families associated with children from an Adadle agropastoral lifestyle or with a traditional lifestyle.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",1783272|1239|186801|3082720|3030910;1783272|1239|526524|526525|2810280;1783272|201174|84998|84999|84107;1783272|201174|84998|1643822|1643826;3379134|1224|1236|91347|543;1783272|1239|526524|526525|128827;1783272|1239|91061|186826|1300,Complete,Svetlana up
bsdb:38049420/4/2,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 4,"Cameroon,China,Ethiopia,Malawi,Peru,United Republic of Tanzania,Venezuela",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Traditional Lifestyle,Adadle Agropastoral Lifestyle,"2-5 year old children from the Adadle woreda district in Ethiopia with an Agropastoral lifestyle, whose samples were sequenced using Primer 2 set (V4 515F/806R). Lifestyle classifications of the different populations were based on the publications used for the datasets.",107,13,NA,16S,4,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S6 D,23 October 2024,YokoC,"YokoC,WikiWorks",LEfSe analysis using primer set 2 showing bacterial families associated with children from an Adadle agropastoral lifestyle or with a traditional lifestyle.,decreased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Lentisphaerota",1783272|544448|31969|186329|2146;1783272|1239|909932|1843488|909930;3379134|976|200643|171549|815;3379134|29547|3031852|213849|72294;1783272|1239|186801|186802|31979;3379134|200940|3031449|213115|194924;3379134|74152|641853|641854|641876;3366610|28890|183925|2158|2159;3379134|976|200643|171549|2005473;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|75682;3379134|1224|1236|135625|712;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550;1783272|1239|909932|909929|1843491;3379134|203691|203692|136|137;3379134|1224|1236|135624|83763;3379134|1224|28216|80840|995019;3379134|976|200643|171549|2005525;1783272|1239|909932|1843489|31977;3379134|256845,Complete,Svetlana up
bsdb:38049420/5/1,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 5,"Bangladesh,El Salvador,Ethiopia,Peru",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Transitional Lifestyle,Adadle Agropastoral Lifestyle,"2-5 year old children from the Adadle woreda district in Ethiopia with an Agropastoral lifestyle, whose samples were sequenced using Primer 2 set (V4 515F/806R). Lifestyle classifications of the different populations were based on the publications used for the datasets.",88,13,NA,16S,4,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S6 D,23 October 2024,YokoC,"YokoC,WikiWorks",LEfSe analysis using primer set 2 showing bacterial families associated with children from an Adadle agropastoral lifestyle or with a transitional lifestyle.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Puniceicoccales|f__Puniceicoccaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",1783272|1239|91061|1385|186817;1783272|1239|91061|186826|186828;1783272|1239|526524|526525|2810280;1783272|201174|84998|84999|84107;1783272|1239|526524|526525|128827;3384189|32066|203490|203491|1129771;3379134|74201|414999|415001|415002;1783272|1239|91061|186826|1300,Complete,Svetlana up
bsdb:38049420/5/2,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 5,"Bangladesh,El Salvador,Ethiopia,Peru",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Transitional Lifestyle,Adadle Agropastoral Lifestyle,"2-5 year old children from the Adadle woreda district in Ethiopia with an Agropastoral lifestyle, whose samples were sequenced using Primer 2 set (V4 515F/806R). Lifestyle classifications of the different populations were based on the publications used for the datasets.",88,13,NA,16S,4,Illumina,relative abundances,LEfSe,NA,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S6 D,23 October 2024,YokoC,"YokoC,WikiWorks",LEfSe analysis using primer set 2 showing bacterial families associated with children from an Adadle agropastoral lifestyle or with a transitional lifestyle.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|201174|1760|85004|31953;1783272|1239|186801|186802|31979;1783272|1239|91061|186826|33958;1783272|1239|186801|186802|216572;1783272|1239|186801|3082720|186804;1783272|1239|909932|1843489|31977,Complete,Svetlana up
bsdb:38049420/6/1,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 6,Ethiopia,Homo sapiens,Feces,UBERON:0001988,COPRO-seq,EFO:0008696,mOTUs2,MetaPhlAn3,MetaPhlan3 taxonomic profiling of shotgun metagenomic samples from Adadle woreda 2-5 year old children.,15,15,NA,WMS,NA,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S7 A,24 October 2024,YokoC,"YokoC,WikiWorks","Boxplots of species with a significantly different abundance (Wilcoxon rank test) between the two profiling tools, mOTUs2 and MetaPhlAn3.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. HMSC035G02,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 181,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum butyriciproducens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella intestinalis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella stercoris,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:471,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma|s__[Collinsella] massiliensis",1783272|201174|1760|2037|2049|1654|544580;1783272|201174|1760|2037|2049|1654|1739406;1783272|201174|1760|2037|2049|1654|712121;1783272|1239|186801|186802|3085642|2048137|1628085;3379134|976|200643|171549|815|816|820;1783272|201174|84998|84999|84107|102106|147207;1783272|201174|84998|84999|84107|102106|147206;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|186802|204475|745368;3379134|976|200643|171549|2005525|375288|823;1783272|1239|186801|3085636|186803|841|1262948;1783272|1239|186801|186802|216572|1905344|1550024;1783272|201174|84998|1643822|1643826|84108|572010;1783272|201174|84998|84999|84107|1472762|1232426,Complete,Svetlana up
bsdb:38049420/6/2,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 6,Ethiopia,Homo sapiens,Feces,UBERON:0001988,COPRO-seq,EFO:0008696,mOTUs2,MetaPhlAn3,MetaPhlan3 taxonomic profiling of shotgun metagenomic samples from Adadle woreda 2-5 year old children.,15,15,NA,WMS,NA,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S7 A,24 October 2024,YokoC,"YokoC,WikiWorks","Boxplots of species with a significantly different abundance (Wilcoxon rank test) between the two profiling tools, mOTUs2 and MetaPhlAn3.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces dentalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. ICM39,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces viscosus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica,k__Bacillati|p__Bacillota|c__Bacilli|s__Bacilli bacterium,k__Bacillati|p__Bacillota|s__Bacillota bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. KLE 1732,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Nanosynbacterales|f__Candidatus Nanosynbacteraceae|g__Candidatus Nanosynbacter|s__Candidatus Nanosynbacter lyticus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|s__Eggerthellaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|s__Lactobacillales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|s__Peptostreptococcaceae bacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia|s__Senegalimassilia anaerobia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus intermedius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HSISM1,s__bacterium LF-3,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__uncultured Butyricicoccus sp.,p__Candidatus Saccharimonadota|s__uncultured Candidatus Saccharibacteria bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__uncultured Collinsella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__uncultured Eubacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__uncultured Faecalibacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__uncultured Mogibacterium sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__uncultured Prevotella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__uncultured Streptococcus sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__uncultured Sutterella sp.",1783272|201174|1760|2037|2049|1654|272548;1783272|201174|1760|2037|2049|1654|1105029;1783272|201174|1760|2037|2049|1654|1656;1783272|201174|1760|85009|31957|2801844|1750;1783272|1239|91061|1903720;1783272|1239|1879010;1783272|1239|186801|3085636|186803|572511|1226324;95818|2093818|2093819|2093822|2093823|1476577;1783272|201174|84998|1643822|1643826|1972561;1783272|1239|186801|3085636|186803|1898203;1783272|1239|91061|186826|1993866;1783272|1239|186801|186802|216572|2485925;1783272|1239|186801|3082720|186804|1904861;1783272|201174|84998|84999|84107|1473205|1473216;1783272|1239|91061|186826|1300|1301|1338;1783272|1239|91061|186826|1300|1301|1316408;1504823;1783272|1239|186801|186802|3085642|580596|1193532;95818|179883;1783272|1239|186801|186802|31979|1485|59620;1783272|201174|84998|84999|84107|102106|165190;1783272|1239|186801|186802|186806|1730|165185;1783272|1239|186801|186802|216572|216851|259315;1783272|1239|186801|3082720|543314|86331|278065;3379134|976|200643|171549|171552|838|159272;1783272|1239|91061|186826|1300|1301|83427;3379134|1224|28216|80840|995019|40544|286133,Complete,Svetlana up
bsdb:38049420/7/1,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 7,Ethiopia,Homo sapiens,Feces,UBERON:0001988,COPRO-seq,EFO:0008696,Primer set 1,MetaPhlAn3,MetaPhlan3 taxonomic profiling of shotgun metagenomic samples from Adadle woreda 2-5 year old children.,6,6,NA,WMS,NA,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S8 B,24 October 2024,YokoC,"YokoC,WikiWorks",Boxplots of families with a significantly different abundance (Wilcoxon rank test) between primer set 1 and MetaPhlAn3.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae",1783272|1239|186801|186802|186806;1783272|1239|91061|1385;1783272|1239|186801|3082720|543314,Complete,Svetlana up
bsdb:38049420/7/2,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 7,Ethiopia,Homo sapiens,Feces,UBERON:0001988,COPRO-seq,EFO:0008696,Primer set 1,MetaPhlAn3,MetaPhlan3 taxonomic profiling of shotgun metagenomic samples from Adadle woreda 2-5 year old children.,6,6,NA,WMS,NA,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S8 B,24 October 2024,YokoC,"YokoC,WikiWorks,Tosin",Boxplots of families with a significantly different abundance (Wilcoxon rank test) between primer set 1 and MetaPhlAn3.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes",1783272|1239|186801|3082720|3030910;1783272|1239|186801|186802|3085642;1783272|1239|526524|526525|2810280;1783272|1239|91061|1385|539738;1783272|1239|186801|186802|186806|1730|290054,Complete,Svetlana up
bsdb:38049420/8/1,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 8,Ethiopia,Homo sapiens,Feces,UBERON:0001988,COPRO-seq,EFO:0008696,Primer set 2,MetaPhlAn3,MetaPhlan3 taxonomic profiling of shotgun metagenomic samples from Adadle woreda 2-5 year old children.,6,6,NA,WMS,NA,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S8 B,24 October 2024,YokoC,"YokoC,WikiWorks",Boxplots of families with a significantly different abundance (Wilcoxon rank test) between primer set 2 and MetaPhlAn3.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae",1783272|201174|1760|85007|1653;1783272|1239|186801|186802|186806;1783272|201174|1760|85006|1268;1783272|1239|91061|1385;1783272|1239|186801|3082720|543314,Complete,Svetlana up
bsdb:38049420/8/2,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 8,Ethiopia,Homo sapiens,Feces,UBERON:0001988,COPRO-seq,EFO:0008696,Primer set 2,MetaPhlAn3,MetaPhlan3 taxonomic profiling of shotgun metagenomic samples from Adadle woreda 2-5 year old children.,6,6,NA,WMS,NA,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S8 B,24 October 2024,YokoC,"YokoC,WikiWorks",Boxplots of families with a significantly different abundance (Wilcoxon rank test) between primer set 2 and MetaPhlAn3.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae",1783272|1239|186801|3082720|3030910;1783272|1239|526524|526525|2810280,Complete,Svetlana up
bsdb:38049420/9/1,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 9,Ethiopia,Homo sapiens,Feces,UBERON:0001988,COPRO-seq,EFO:0008696,Primer set 1,mOTUs2,mOTUs2 taxonomic profiling of shotgun metagenomic samples from Adadle woreda 2-5 year old children.,6,6,NA,WMS,NA,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S8 B,25 October 2024,YokoC,"YokoC,WikiWorks",Boxplots of families with a significantly different abundance (Wilcoxon rank test) between primer set 1 and mOTUs2.,increased,",k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,p__Candidatus Saccharimonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales",;1783272|1239|186801|186802|186806;1783272|1239|186801|3082720|543314;1783272|1239|186801|186802;1783272|1239|91061|1385|539738;1783272|201174|1760|85009|31957;1783272|1239|91061;1783272|1239;95818;1783272|1239|186801|186802;1783272|1239|91061|186826,Complete,Svetlana up
bsdb:38049420/9/2,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 9,Ethiopia,Homo sapiens,Feces,UBERON:0001988,COPRO-seq,EFO:0008696,Primer set 1,mOTUs2,mOTUs2 taxonomic profiling of shotgun metagenomic samples from Adadle woreda 2-5 year old children.,6,6,NA,WMS,NA,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S8 B,25 October 2024,YokoC,"YokoC,WikiWorks,Tosin",Boxplots of families with a significantly different abundance (Wilcoxon rank test) between primer set 1 and mOTUs2.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes",1783272|1239|186801|3082720|3030910;1783272|1239|186801|186802|3085642;1783272|1239|526524|526525|2810280;1783272|1239|91061|1385|539738;1783272|1239|186801|186802|186806|1730|290054,Complete,Svetlana up
bsdb:38049420/10/1,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 10,Ethiopia,Homo sapiens,Feces,UBERON:0001988,COPRO-seq,EFO:0008696,Primer set 2,mOTUs2,mOTUs2 taxonomic profiling of shotgun metagenomic samples from Adadle woreda 2-5 year old children.,6,6,NA,WMS,NA,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S8 B,25 October 2024,YokoC,"YokoC,WikiWorks",Boxplots of families with a significantly different abundance (Wilcoxon rank test) between primer set 2 and mOTUs2.,increased,",k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,,p__Candidatus Saccharimonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales",;1783272|1239|186801|186802|31979;1783272|201174|1760|85007|1653;1783272|1239|186801|186802|186806;1783272|1239|186801|3082720|543314;1783272|1239|186801|186802;1783272|1239|91061|1385|539738;1783272|201174|1760|85006|1268;1783272|201174|1760|85009|31957;3379134|1224|28216|80840|995019;1783272|1239|91061;1783272|1239;;95818;1783272|1239|186801|186802;1783272|1239|91061|186826,Complete,Svetlana up
bsdb:38049420/10/2,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 10,Ethiopia,Homo sapiens,Feces,UBERON:0001988,COPRO-seq,EFO:0008696,Primer set 2,mOTUs2,mOTUs2 taxonomic profiling of shotgun metagenomic samples from Adadle woreda 2-5 year old children.,6,6,NA,WMS,NA,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S8 B,25 October 2024,YokoC,"YokoC,WikiWorks",Boxplots of families with a significantly different abundance (Wilcoxon rank test) between primer set 2 and mOTUs2.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae",1783272|1239|186801|3082720|3030910;1783272|1239|526524|526525|2810280,Complete,Svetlana up
bsdb:38049420/13/1,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 13,"Ethiopia,United States of America",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Industrial Lifestyle,Adadle Agropastoral Lifestyle,"2-5 year old children from the Adadle woreda district in Ethiopia with an agropastoral lifestyle, whose samples were taxonomically profiled using mOTUs2.",29,15,NA,WMS,NA,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S9 B,2 November 2024,YokoC,"YokoC,WikiWorks",Boxplots of significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories in an industrial lifestyle and the Adadle agropastoral lifestyle.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae",1783272|1239|526524|526525|128827;1783272|1239|91061|186826|33958;3379134|976|200643|171549|171552;1783272|1239|91061|186826|1300;3379134|1224|1236|135624|83763,Complete,Svetlana up
bsdb:38049420/13/2,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 13,"Ethiopia,United States of America",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Industrial Lifestyle,Adadle Agropastoral Lifestyle,"2-5 year old children from the Adadle woreda district in Ethiopia with an agropastoral lifestyle, whose samples were taxonomically profiled using mOTUs2.",29,15,NA,WMS,NA,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S9 B,2 November 2024,YokoC,"YokoC,WikiWorks",Boxplots of significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories in an industrial lifestyle and the Adadle agropastoral lifestyle.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,3379134|976|200643|171549|815,Complete,Svetlana up
bsdb:38049420/14/1,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 14,"Ethiopia,Peru,United Republic of Tanzania,Zimbabwe",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Traditional Lifestyle,Adadle Agropastoral Lifestyle,"2-5 year old children from the Adadle woreda district in Ethiopia with an agropastoral lifestyle, whose samples were taxonomically profiled using mOTUs2.",40,15,NA,WMS,NA,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S9 B,3 November 2024,YokoC,"YokoC,WikiWorks",Boxplots of significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories in a traditional lifestyle and the Adadle agropastoral lifestyle.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",1783272|201174|1760|85004|31953;1783272|1239|526524|526525|128827;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|1300,Complete,Svetlana up
bsdb:38049420/14/2,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 14,"Ethiopia,Peru,United Republic of Tanzania,Zimbabwe",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Traditional Lifestyle,Adadle Agropastoral Lifestyle,"2-5 year old children from the Adadle woreda district in Ethiopia with an agropastoral lifestyle, whose samples were taxonomically profiled using mOTUs2.",40,15,NA,WMS,NA,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S9 B,3 November 2024,YokoC,"YokoC,WikiWorks",Boxplots of significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories in a traditional lifestyle and the Adadle agropastoral lifestyle.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae",3379134|976|200643|171549|815;3379134|976|200643|171549|171552;3379134|1224|1236|135624|83763,Complete,Svetlana up
bsdb:38049420/15/1,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 15,"El Salvador,Ethiopia,Peru",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Transitional Lifestyle,Adadle Agropastoral Lifestyle,"2-5 year old children from the Adadle woreda district in Ethiopia with an agropastoral lifestyle, whose samples were taxonomically profiled using mOTUs2.",18,15,NA,WMS,NA,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S9 B,4 November 2024,YokoC,"YokoC,WikiWorks",Boxplots of significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories in a transitional lifestyle and the Adadle agropastoral lifestyle.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",1783272|1239|526524|526525|128827;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|1300,Complete,Svetlana up
bsdb:38049420/15/2,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 15,"El Salvador,Ethiopia,Peru",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Transitional Lifestyle,Adadle Agropastoral Lifestyle,"2-5 year old children from the Adadle woreda district in Ethiopia with an agropastoral lifestyle, whose samples were taxonomically profiled using mOTUs2.",18,15,NA,WMS,NA,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S9 B,4 November 2024,YokoC,"YokoC,KateRasheed,WikiWorks",Boxplots of significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories in a transitional lifestyle and the Adadle agropastoral lifestyle.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|976|200643|171549|815;3379134|976|200643|171549|171552,Complete,Svetlana up
bsdb:38049420/16/1,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 16,"Ethiopia,Peru,United Republic of Tanzania,Zimbabwe,United States of America",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Industrial Lifestyle,Traditional Lifestyle,"2-5 year old children with a traditional lifestyle, whose samples were taxonomically profiled using mOTUs2.",29,40,NA,WMS,NA,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S9 B,4 November 2024,YokoC,"YokoC,WikiWorks",Boxplots of significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories in an industrial lifestyle and a traditional lifestyle.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae",1783272|1239|91061|186826|33958;3379134|976|200643|171549|171552;3379134|1224|1236|135624|83763,Complete,Svetlana up
bsdb:38049420/16/2,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 16,"Ethiopia,Peru,United Republic of Tanzania,Zimbabwe,United States of America",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Industrial Lifestyle,Traditional Lifestyle,"2-5 year old children with a traditional lifestyle, whose samples were taxonomically profiled using mOTUs2.",29,40,NA,WMS,NA,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S9 B,4 November 2024,YokoC,"YokoC,WikiWorks",Significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories and those with higher relative abundance in Adadle woreda.,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae",3379134|74201|203494|48461|1647988;3379134|976|200643|171549|815;1783272|201174|1760|85004|31953,Complete,Svetlana up
bsdb:38049420/17/1,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 17,"El Salvador,Ethiopia,Peru,United States of America",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Industrial Lifestyle,Transitional Lifestyle,"2-5 year old children with a transitional lifestyle, whose samples were taxonomically profiled using mOTUs2.",29,18,NA,WMS,NA,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S9 B,4 November 2024,YokoC,"YokoC,WikiWorks",Boxplots of significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories in an industrial lifestyle and a transitional lifestyle.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae",1783272|201174|1760|85004|31953;3379134|976|200643|171549|171552;3379134|1224|1236|135624|83763,Complete,Svetlana up
bsdb:38049420/17/2,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 17,"El Salvador,Ethiopia,Peru,United States of America",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Industrial Lifestyle,Transitional Lifestyle,"2-5 year old children with a transitional lifestyle, whose samples were taxonomically profiled using mOTUs2.",29,18,NA,WMS,NA,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S9 B,4 November 2024,YokoC,"YokoC,WikiWorks",Boxplots of significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories in an industrial lifestyle and a transitional lifestyle.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",3379134|976|200643|171549|815;1783272|1239|91061|186826|33958,Complete,Svetlana up
bsdb:38049420/18/1,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 18,"El Salvador,Peru,United Republic of Tanzania,Zimbabwe",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Traditional Lifestyle,Transitional Lifestyle,"2-5 year old children with a transitional lifestyle, whose samples were taxonomically profiled using mOTUs2.",40,18,NA,WMS,NA,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S9 B,4 November 2024,YokoC,"YokoC,WikiWorks",Boxplots of significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories in a traditional lifestyle and a transitional lifestyle.,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,1783272|201174|1760|85004|31953,Complete,Svetlana up
bsdb:38049420/18/2,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 18,"El Salvador,Peru,United Republic of Tanzania,Zimbabwe",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Traditional Lifestyle,Transitional Lifestyle,"2-5 year old children with a transitional lifestyle, whose samples were taxonomically profiled using mOTUs2.",40,18,NA,WMS,NA,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S9 B,4 November 2024,YokoC,"YokoC,WikiWorks",Boxplots of significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories in a traditional lifestyle and a transitional lifestyle.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae",3379134|976|200643|171549|171552;3379134|1224|1236|135624|83763,Complete,Svetlana up
bsdb:38049420/19/1,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 19,"Central African Republic,Ethiopia",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Central African Republic,Adadle,"2-5 year old children from the Adadle woreda district in Ethiopia, with an agropastoral lifestyle, whose samples were sequenced using Primer 1 set (V4 501-508F/701-712R). Lifestyle classifications of the different populations were based on the publications used for the datasets.",274,54,NA,16S,4,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3D,15 January 2025,YokoC,"YokoC,WikiWorks",Boxplots of significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories in Central African Republic (transitional lifestyle) and Adadle woreda (agropastoral lifestyle).,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",1783272|201174|1760|85004|31953;1783272|1239|526524|526525|2810280;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|1300,Complete,Svetlana up
bsdb:38049420/19/2,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 19,"Central African Republic,Ethiopia",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Central African Republic,Adadle,"2-5 year old children from the Adadle woreda district in Ethiopia, with an agropastoral lifestyle, whose samples were sequenced using Primer 1 set (V4 501-508F/701-712R). Lifestyle classifications of the different populations were based on the publications used for the datasets.",274,54,NA,16S,4,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3D,15 January 2025,YokoC,"YokoC,WikiWorks",Boxplots of significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories in Central African Republic (transitional lifestyle) and Adadle woreda (agropastoral lifestyle).,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|74201|203494|48461|1647988;3379134|976|200643|171549|815;3379134|976|200643|171549|171552,Complete,Svetlana up
bsdb:38049420/20/1,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 20,"Ethiopia,Madagascar",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Madagascar,Adadle,"2-5 year old children from the Adadle woreda district in Ethiopia, with an agropastoral lifestyle, whose samples were sequenced using Primer 1 set (V4 501-508F/701-712R). Lifestyle classifications of the different populations were based on the publications used for the datasets.",431,54,NA,16S,4,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3D,15 January 2025,YokoC,"YokoC,WikiWorks",Significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories in Madagascar (transitional lifestyle) and Adadle woreda (agropastoral lifestyle).,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae",3379134|74201|203494|48461|1647988;1783272|201174|1760|85004|31953;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|33958;1783272|1239|526524|526525|2810280,Complete,Svetlana up
bsdb:38049420/20/2,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 20,"Ethiopia,Madagascar",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Madagascar,Adadle,"2-5 year old children from the Adadle woreda district in Ethiopia, with an agropastoral lifestyle, whose samples were sequenced using Primer 1 set (V4 501-508F/701-712R). Lifestyle classifications of the different populations were based on the publications used for the datasets.",431,54,NA,16S,4,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3D,15 January 2025,YokoC,"YokoC,WikiWorks",Significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories in Madagascar (transitional lifestyel) and Adadle woreda (agropastoral lifestyle).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae",3379134|976|200643|171549|815;3379134|976|200643|171549|171552;3379134|1224|1236|135624|83763,Complete,Svetlana up
bsdb:38049420/21/1,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 21,"Central African Republic,Madagascar",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Madagascar,Central African Republic,"2-5 year old children with a transitional lifestyle from the Bangui region in the Central African Republic, whose samples were sequenced using Primer 1 set (V4 501-508F/701-712R). Lifestyle classifications of the different populations were based on the publications used for the datasets.",431,274,NA,16S,4,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3D,15 January 2025,YokoC,"YokoC,WikiWorks",Boxplots (Wilcoxon) of significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories in two transitional lifestyle populations: Central African Republic and Madagascar.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae",3379134|74201|203494|48461|1647988;3379134|976|200643|171549|815,Complete,Svetlana up
bsdb:38049420/21/2,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 21,"Central African Republic,Madagascar",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Madagascar,Central African Republic,"2-5 year old children with a transitional lifestyle from the Bangui region in the Central African Republic, whose samples were sequenced using Primer 1 set (V4 501-508F/701-712R). Lifestyle classifications of the different populations were based on the publications used for the datasets.",431,274,NA,16S,4,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3D,15 January 2025,YokoC,"YokoC,WikiWorks",Boxplots (Wilcoxon) of significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories in two transitional lifestyle populations: Central African Republic and Madagascar.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae",1783272|201174|1760|85004|31953;1783272|1239|91061|186826|33958;3379134|976|200643|171549|171552;1783272|1239|91061|186826|1300;3379134|1224|1236|135624|83763,Complete,Svetlana up
bsdb:38049420/22/1,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 22,"Ethiopia,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Industrial Lifestyle,Adadle Agropastoral Lifestyle,"2-5 year old children from the Adadle woreda district in Ethiopia with an agropastoral lifestyle, whose samples were sequenced using Primer 2 set (V4 515F/806R). Lifestyle classifications of the different populations were based on the publications used for the datasets.",484,13,NA,16S,4,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3D,16 January 2025,YokoC,"YokoC,WikiWorks",Boxplots of significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories in the Adadle woreda agropastoral lifestyle and the industrial lifestyle.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae",1783272|1239|91061|186826|1300;1783272|1239|526524|526525|2810280,Complete,Svetlana up
bsdb:38049420/22/2,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 22,"Ethiopia,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Industrial Lifestyle,Adadle Agropastoral Lifestyle,"2-5 year old children from the Adadle woreda district in Ethiopia with an agropastoral lifestyle, whose samples were sequenced using Primer 2 set (V4 515F/806R). Lifestyle classifications of the different populations were based on the publications used for the datasets.",484,13,NA,16S,4,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3D,16 January 2025,YokoC,"YokoC,WikiWorks",Boxplots of significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories in the Adadle woreda lifestyle and the industrial lifestyle.,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae",3379134|74201|203494|48461|1647988;3379134|976|200643|171549|815,Complete,Svetlana up
bsdb:38049420/23/1,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 23,"Cameroon,China,Ethiopia,Malawi,Peru,United Republic of Tanzania,Venezuela",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Traditional Lifestyle,Adadle Agropastoral Lifestyle,"2-5 year old children from the Adadle woreda district in Ethiopia with an Agropastoral lifestyle, whose samples were sequenced using Primer 2 set (V4 515F/806R). Lifestyle classifications of the different populations were based on the publications used for the datasets.",107,13,NA,16S,4,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3D,19 January 2025,YokoC,"YokoC,WikiWorks",Boxplots of significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories in a traditional lifestyle and the Adadle agropastoral lifestyle.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",1783272|1239|526524|526525|2810280;1783272|1239|91061|186826|1300,Complete,Svetlana up
bsdb:38049420/23/2,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 23,"Cameroon,China,Ethiopia,Malawi,Peru,United Republic of Tanzania,Venezuela",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Traditional Lifestyle,Adadle Agropastoral Lifestyle,"2-5 year old children from the Adadle woreda district in Ethiopia with an Agropastoral lifestyle, whose samples were sequenced using Primer 2 set (V4 515F/806R). Lifestyle classifications of the different populations were based on the publications used for the datasets.",107,13,NA,16S,4,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3D,19 January 2025,YokoC,"YokoC,WikiWorks",Boxplots of significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories in a traditional lifestyle and the Adadle agropastoral lifestyle.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae",3379134|976|200643|171549|815;3379134|976|200643|171549|171552;3379134|1224|1236|135624|83763,Complete,Svetlana up
bsdb:38049420/24/1,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 24,"Bangladesh,El Salvador,Ethiopia,Peru",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Transitional Lifestyle,Adadle Agropastoral Lifestyle,"2-5 year old children from the Adadle woreda district in Ethiopia with an Agropastoral lifestyle, whose samples were sequenced using Primer 2 set (V4 515F/806R). Lifestyle classifications of the different populations were based on the publications used for the datasets.",88,13,NA,16S,4,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3D,17 January 2025,YokoC,"YokoC,WikiWorks",Boxplots of significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories in the Adadle agropastoral lifestyle and a transitional lifestyle.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae",1783272|1239|91061|186826|1300;1783272|1239|526524|526525|2810280,Complete,Svetlana up
bsdb:38049420/24/2,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 24,"Bangladesh,El Salvador,Ethiopia,Peru",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Transitional Lifestyle,Adadle Agropastoral Lifestyle,"2-5 year old children from the Adadle woreda district in Ethiopia with an Agropastoral lifestyle, whose samples were sequenced using Primer 2 set (V4 515F/806R). Lifestyle classifications of the different populations were based on the publications used for the datasets.",88,13,NA,16S,4,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3D,17 January 2025,YokoC,"YokoC,WikiWorks",Boxplots of significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories in the Adadle agropastoral lifestyle and the transitional lifestyle.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,1783272|201174|1760|85004|31953,Complete,Svetlana up
bsdb:38049420/25/1,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 25,"Ethiopia,Peru,United States of America,Sweden,Cameroon,China,Malawi,United Republic of Tanzania,Venezuela",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Industrial Lifestyle,Traditional Lifestyle,"2-5 year old children from different regions with a traditional lifestyle, whose samples were sequenced using Primer 2 set (V4 515F/806R). Lifestyle classifications of the different populations were based on the publications used for the datasets.",484,107,NA,16S,4,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3D,17 January 2025,YokoC,"YokoC,WikiWorks",Boxplots of significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories in an industrial lifestyle and a traditional lifestyle.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",3379134|976|200643|171549|171552;3379134|1224|1236|135624|83763;1783272|1239|91061|186826|33958,Complete,Svetlana up
bsdb:38049420/25/2,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 25,"Ethiopia,Peru,United States of America,Sweden,Cameroon,China,Malawi,United Republic of Tanzania,Venezuela",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Industrial Lifestyle,Traditional Lifestyle,"2-5 year old children from different regions with a traditional lifestyle, whose samples were sequenced using Primer 2 set (V4 515F/806R). Lifestyle classifications of the different populations were based on the publications used for the datasets.",484,107,NA,16S,4,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3D,17 January 2025,YokoC,"YokoC,WikiWorks",Boxplots of significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories in an industrial lifestyle and a traditional lifestyle.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae",3379134|976|200643|171549|815;1783272|201174|1760|85004|31953;3379134|74201|203494|48461|1647988,Complete,Svetlana up
bsdb:38049420/26/1,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 26,"Ethiopia,Peru,Sweden,United States of America,El Salvador,Bangladesh",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Industrial Lifestyle,Transitional Lifestyle,"2-5 year old children from different regions with a transitional lifestyle, whose samples were sequenced using Primer 2 set (V4 515F/806R). Lifestyle classifications of the different populations were based on the publications used for the datasets.",484,88,NA,16S,4,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3D,17 January 2025,YokoC,"YokoC,WikiWorks",Boxplots of significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories in an industrial lifestyle and a transitional lifestyle.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",1783272|201174|1760|85004|31953;3379134|976|200643|171549|171552;1783272|1239|91061|186826|1300;1783272|1239|526524|526525|2810280;1783272|1239|91061|186826|33958,Complete,Svetlana up
bsdb:38049420/26/2,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 26,"Ethiopia,Peru,Sweden,United States of America,El Salvador,Bangladesh",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Industrial Lifestyle,Transitional Lifestyle,"2-5 year old children from different regions with a transitional lifestyle, whose samples were sequenced using Primer 2 set (V4 515F/806R). Lifestyle classifications of the different populations were based on the publications used for the datasets.",484,88,NA,16S,4,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3D,17 January 2025,YokoC,"YokoC,WikiWorks",Boxplots of significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories in an industrial lifestyle and a transitional lifestyle.,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae",3379134|74201|203494|48461|1647988;3379134|976|200643|171549|815;3379134|1224|1236|135624|83763,Complete,Svetlana up
bsdb:38049420/27/1,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 27,"Ethiopia,Peru,Cameroon,China,Malawi,United Republic of Tanzania,Venezuela,El Salvador,Bangladesh",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Traditional Lifestyle,Transitional Lifestyle,"2-5 year old children from different regions with a transitional lifestyle, whose samples were sequenced using Primer 2 set (V4 515F/806R). Lifestyle classifications of the different populations were based on the publications used for the datasets.",107,88,NA,16S,4,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3D,18 January 2025,YokoC,"YokoC,WikiWorks",Boxplots of significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories in traditional and transitional lifestyles.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",1783272|1239|526524|526525|2810280;1783272|1239|91061|186826|33958;1783272|201174|1760|85004|31953;1783272|1239|91061|186826|1300,Complete,Svetlana up
bsdb:38049420/27/2,38049420,"cross-sectional observational, not case-control",38049420,10.1038/s41598-023-47748-8,NA,"Yersin S., Garneau J.R., Schneeberger P.H.H., Osman K.A., Cercamondi C.I., Muhummed A.M., Tschopp R., Zinsstag J. , Vonaesch P.",Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits,Scientific reports,2023,NA,Experiment 27,"Ethiopia,Peru,Cameroon,China,Malawi,United Republic of Tanzania,Venezuela,El Salvador,Bangladesh",Homo sapiens,Feces,UBERON:0001988,Population,IDOMAL:0001254,Traditional Lifestyle,Transitional Lifestyle,"2-5 year old children from different regions with a transitional lifestyle, whose samples were sequenced using Primer 2 set (V4 515F/806R). Lifestyle classifications of the different populations were based on the publications used for the datasets.",107,88,NA,16S,4,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3D,18 January 2025,YokoC,"YokoC,WikiWorks",Boxplots of significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories in traditional and transitional lifestyles.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae",3379134|976|200643|171549|171552;3379134|976|200643|171549|815;3379134|1224|1236|135624|83763,Complete,Svetlana up
bsdb:38057705/1/1,38057705,time series / longitudinal observational,38057705,10.1186/s12866-023-03123-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC10701952/,"Yang C., Hu T., Xue X., Su X., Zhang X., Fan Y., Shen X. , Dong X.",Multi-omics analysis of fecal microbiota transplantation's impact on functional constipation and comorbid depression and anxiety,BMC microbiology,2023,"5-hydroxytryptamine, Constipation, Depression and anxiety, Fecal microbiota transplantation, Metabolomics, Metagenomics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Fb (Patients before FMT - Fecal microbiota transplantation),Fa (Patients After FMT - Fecal microbiota transplantation),Patients with functional constipation and comorbid depression/anxiety after undergoing fecal microbiota transplantation (FMT).,4,4,2 weeks,WMS,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Fig 2C,17 April 2025,Shulamite,"Shulamite,Anne-mariesharp",The shift in gut microbiota before and after FMT based on metagenomic sequencing data.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus hermanniensis,1783272|1239|91061|186826|81852|1350|249189,Complete,KateRasheed
bsdb:38057705/1/2,38057705,time series / longitudinal observational,38057705,10.1186/s12866-023-03123-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC10701952/,"Yang C., Hu T., Xue X., Su X., Zhang X., Fan Y., Shen X. , Dong X.",Multi-omics analysis of fecal microbiota transplantation's impact on functional constipation and comorbid depression and anxiety,BMC microbiology,2023,"5-hydroxytryptamine, Constipation, Depression and anxiety, Fecal microbiota transplantation, Metabolomics, Metagenomics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Fb (Patients before FMT - Fecal microbiota transplantation),Fa (Patients After FMT - Fecal microbiota transplantation),Patients with functional constipation and comorbid depression/anxiety after undergoing fecal microbiota transplantation (FMT).,4,4,2 weeks,WMS,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Fig 2E,17 April 2025,Shulamite,"Shulamite,Anne-mariesharp",The shift in gut microbiota before and after FMT based on metagenomic sequencing data.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides pyogenes,3379134|976|200643|171549|815|816|310300,Complete,KateRasheed
bsdb:38057705/4/1,38057705,time series / longitudinal observational,38057705,10.1186/s12866-023-03123-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC10701952/,"Yang C., Hu T., Xue X., Su X., Zhang X., Fan Y., Shen X. , Dong X.",Multi-omics analysis of fecal microbiota transplantation's impact on functional constipation and comorbid depression and anxiety,BMC microbiology,2023,"5-hydroxytryptamine, Constipation, Depression and anxiety, Fecal microbiota transplantation, Metabolomics, Metagenomics",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Fb (Patients before FMT - Fecal microbiota transplantation),Fa (Patients After FMT - Fecal microbiota transplantation),Patients with functional constipation and comorbid depression/anxiety after undergoing fecal microbiota transplantation (FMT).,4,4,2 weeks,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table S2 and Table 3,17 April 2025,Shulamite,"Shulamite,Anne-mariesharp",Differential relative abundance of species between the Fb and Fa groups,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Acetobacterium|s__Acetobacterium bakii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella|s__Allofournierella massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus senegalensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. An200,k__Fungi|p__Chytridiomycota|c__Neocallimastigomycetes|o__Neocallimastigales|f__Neocallimastigaceae|g__Anaeromyces|s__Anaeromyces robustus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum neopropionicum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio|s__Anaerovibrio lipolyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Anaerovirgula|s__Anaerovirgula multivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Angelakisella|s__Angelakisella massiliensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus wiedmannii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium 55_9,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 2_1_22,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp. N4G05,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Brevibacillus|s__Brevibacillus laterosporus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio sp. AE2032,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio sp. NC2002,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Marispirochaeta|s__Candidatus Marispirochaeta associata,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus|s__Cloacibacillus evryensis,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus|s__Cloacibacillus porcorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium 59_14,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium VE202-13,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium formicaceticum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:169,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:217_53_7,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:253,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:302,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:448,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. HGF2,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. MD294,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. W14A,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Cohnella|s__Cohnella sp. OV330,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella sp. An268,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Curtobacterium|s__Curtobacterium sp. ER1/6,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium|s__Dehalobacterium formicoaceticum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfotomaculaceae|g__Desulfotomaculum|s__Desulfotomaculum nigrificans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Drancourtella|s__Drancourtella massiliensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus hermanniensis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 5_2_54FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. CAG:1138,k__Pseudomonadati|p__Fibrobacterota|c__Fibrobacteria|o__Fibrobacterales|f__Fibrobacteraceae|g__Fibrobacter|s__Fibrobacter sp. UWB3,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:24053_14,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:882,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium psychrophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor sp. An91,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger sp. An87,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Gorillibacterium|s__Gorillibacterium massiliense,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium A10,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium C10,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus|s__Lactiplantibacillus plantarum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gallinarum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Aquaspirillaceae|g__Laribacter|s__Laribacter hongkongensis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 879,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc citreum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus coleohominis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus|s__Lysinibacillus sphaericus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Marinimicrobium|s__Marinimicrobium agarilyticum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Massilimicrobiota|s__Massilimicrobiota sp. An105,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Massilimicrobiota|s__Massilimicrobiota sp. An80,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera massiliensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Pseudomonadati|p__Thermomicrobiota|c__Thermomicrobia|o__Sphaerobacterales|f__Sphaerobacteraceae|g__Nitrolancea|s__Nitrolancea hollandica,k__Bacillati|p__Bacillota|c__Clostridia|o__Halanaerobiales|f__Halobacteroidaceae|g__Orenia|s__Orenia metallireducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp. oral taxon 078,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp. oral taxon 108,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 1-3,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. ER4,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|s__Paenibacillaceae bacterium ZCTH02-B3,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus amylolyticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus apiarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus chondroitinus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|s__Peptococcaceae bacterium 1109,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella falsenii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:474,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Propionispira|s__Propionispira arboris,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae|g__Propionispora|s__Propionispora sp. 2/2-37,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter sp. C12-8,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D16,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium cv2,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:353,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Schwartzia|s__Schwartzia succinivorans,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas artemidis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas bovis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. FC4001,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. oral taxon 136,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae|g__Sporomusa|s__Sporomusa sphaeroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus ilei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus ovis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HSISS3,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp. 4_3_54A2FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp. 60_17,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum variabile,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Traorella|s__Traorella massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] hylemonae,s__bacterium OL-1,s__uncultured bacterium EB5",1783272|1239|186801|186802|186806|33951|52689;1783272|1239|186801|186802|216572|1940255|1650663;1783272|1239|186801|186802|3082771|1924093|1673717;1783272|1239|186801|186802|3082771|1924093|1965587;4751|4761|451455|29006|29007|105135|1754192;1783272|1239|186801|3085636|3118652|2039240|36847;1783272|1239|909932|909929|1843491|82373|82374;1783272|1239|186801|3082720|3118656|561442|312168;1783272|1239|186801|186802|216572|1935176|1871018;1783272|1239|91061|1385|186817|1386|1890302;3379134|976|200643|171549|1897041;3379134|976|200643|171549|815|816|469588;1783272|201174|1760|85004|31953|1678|2013020;1783272|1239|91061|1385|186822|55080|1465;1783272|1239|186801|3085636|186803|830|1458463;1783272|1239|186801|3085636|186803|830|1410610;3379134|203691|203692|136|137|1911565|1560235;3384194|508458|649775|649776|649777|508459|508460;3384194|508458|649775|649776|649777|508459|1197717;1783272|1239|186801|186802|1897049;1783272|1239|186801|186802|1232443;1783272|1239|186801|186802|31979|1485|1497;1783272|1239|186801|186802|31979|1485|1262778;1783272|1239|186801|186802|31979|1485|1896992;1783272|1239|186801|186802|31979|1485|1262785;1783272|1239|186801|186802|31979|1485|1262793;1783272|1239|186801|186802|31979|1485|1262808;1783272|1239|186801|186802|31979|1485|908340;1783272|1239|186801|186802|31979|1485|97138;1783272|1239|186801|186802|31979|1485|1849176;1783272|1239|91061|1385|186822|329857|1855288;1783272|201174|84998|84999|84107|102106|1965612;1783272|201174|1760|85006|85023|2034|1891920;1783272|1239|186801|186802|186807|51514|51515;1783272|1239|186801|186802|2937910|1562|1565;1783272|1239|186801|186802|216572|1903506|1632013;1783272|1239|91061|186826|81852|1350|249189;1783272|1239|526524|526525|128827|552396;1783272|1239|186801|186802|216572|216851|1262896;3379134|65842|204430|218872|204431|832|1964357;1783272|1239|1897032;1783272|1239|1262991;3379134|976|117743|200644|49546|237|96345;1783272|1239|186801|186802|216572|946234|1965665;1783272|1239|186801|186802|204475|745368;1783272|1239|186801|186802|204475|1965662;1783272|1239|91061|1385|186822|1689250|1280390;1783272|1239|186801|3085636|186803|28050|28052;1783272|1239|186801|3085636|186803|1520821;1783272|1239|186801|3085636|186803|1520822;1783272|1239|91061|186826|33958|2767842|1590;1783272|1239|91061|186826|33958|1578|1579;1783272|1239|91061|186826|33958|1578|52242;3379134|1224|28216|206351|2897176|168470|168471;3384189|32066|203490|203491|1129771|32067|1227267;1783272|1239|91061|186826|33958|1243|33964;1783272|1239|91061|186826|33958|2742598|181675;1783272|1239|91061|1385|186817|400634|1421;3379134|1224|1236|1706369|1706371|359337|306546;1783272|1239|526524|526525|128827|1924110|1965540;1783272|1239|526524|526525|128827|1924110|1965658;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|909932|1843489|31977|906|1232428;1783272|1239|909932|909929|1843491|52225|52226;3379134|3027942|189775|85001|85002|1206748|1206749;1783272|1239|186801|53433|53434|46468|1413210;1783272|1239|186801|3085636|186803|265975|237576;1783272|1239|186801|3085636|186803|265975|652706;1783272|1239|186801|3085636|186803|265975|712414;1783272|1239|186801|186802|216572|459786|1263547;1783272|1239|186801|186802|216572|459786|1235797;1783272|1239|186801|186802|216572|459786|1519439;1783272|1239|91061|1385|186822|1861638;1783272|1239|91061|1385|186822|44249|1451;1783272|1239|91061|1385|186822|44249|46240;1783272|1239|91061|1385|186822|44249|59842;1783272|1239|186801|186802|186807|1655638;3379134|976|200643|171549|171552|838|515414;3379134|976|200643|171549|171552|838|1262926;1783272|1239|909932|909929|1843491|84034|84035;1783272|1239|909932|909929|1843490|112902|1677858;3384194|508458|649775|649776|3029088|638847|1943580;1783272|1239|186801|186802|216572|552398;1783272|1239|186801|186802|216572|1627893;1783272|1239|186801|186802|216572|1263|1262955;1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|909932|909929|1843491|55506|55507;1783272|1239|909932|909929|1843491|970|671224;1783272|1239|909932|909929|1843491|970|416586;1783272|1239|909932|909929|1843491|970|1408313;1783272|1239|909932|909929|1843491|970|713030;1783272|1239|909932|909929|1843490|2375|47679;1783272|1239|91061|1385|90964|1279|1290;1783272|1239|91061|186826|1300|1301|45634;1783272|1239|91061|186826|1300|1301|1156431;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|91061|186826|1300|1301|82806;1783272|1239|91061|186826|1300|1301|1316412;1783272|1239|91061|186826|1300|1301|1343;1783272|1239|186801|186802|216572|292632|665956;1783272|1239|186801|186802|216572|292632|1897022;1783272|1239|186801|186802|216572|292632|214851;1783272|1239|526524|526525|128827|1929045|1903263;1783272|1239|186801|3085636|186803|1506553|89153;1504822;1348858,Complete,KateRasheed
bsdb:38057705/4/2,38057705,time series / longitudinal observational,38057705,10.1186/s12866-023-03123-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC10701952/,"Yang C., Hu T., Xue X., Su X., Zhang X., Fan Y., Shen X. , Dong X.",Multi-omics analysis of fecal microbiota transplantation's impact on functional constipation and comorbid depression and anxiety,BMC microbiology,2023,"5-hydroxytryptamine, Constipation, Depression and anxiety, Fecal microbiota transplantation, Metabolomics, Metagenomics",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Fb (Patients before FMT - Fecal microbiota transplantation),Fa (Patients After FMT - Fecal microbiota transplantation),Patients with functional constipation and comorbid depression/anxiety after undergoing fecal microbiota transplantation (FMT).,4,4,2 weeks,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Table S2 and Table 3,17 April 2025,Shulamite,"Shulamite,Anne-mariesharp",Differential relative abundance of species between the Fb and Fa groups,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acidocellaceae|g__Acidiphilium|s__Acidiphilium sp. CAG:727,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. BO,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. UNC41MFS5,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecichinchillae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides pyogenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. An51A,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercorirosoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. An81,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Thermohalobacteraceae|g__Caloranaerobacter|s__Caloranaerobacter sp. TR13,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium botulinum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. D5,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium|s__Dehalobacterium formicoaceticum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena contorta,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp. HMSC16C06,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella variicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 2_1_58FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 6_1_37FAA,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Listeria|s__Listeria monocytogenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Natronincola|s__Natronincola peptidivorans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus algorifonticola,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus ferrarius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides gordonii,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus russellii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio|s__Pseudobutyrivibrio sp. UC1225,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter sp. C12-8,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella genomosp. SF-2015,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella sonnei,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia sp. CM382",3379134|1224|28211|3120395|3385905|522|1262689;1783272|1239|91061|1385|186817|1386|1476855;1783272|1239|91061|1385|186817|1386|1449046;3379134|976|200643|171549|815|816|871325;3379134|976|200643|171549|815|816|674529;3379134|976|200643|171549|815|816|310300;3379134|976|200643|171549|815|816|1965640;3379134|976|200643|171549|815|816|871324;3379134|976|200643|171549|815|816|818;1783272|1239|186801|3085636|186803|572511|1965659;1783272|1239|1737404|1737405|2848916|171003|1302151;1783272|1239|186801|186802|31979|1485|1491;1783272|1239|186801|186802|31979|1485|556261;1783272|1239|186801|186802|186807|51514|51515;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|3085636|186803|2005359|39482;3379134|1224|1236|91347|543|570|573;3379134|1224|1236|91347|543|570|1581110;3379134|1224|1236|91347|543|570|244366;1783272|1239|186801|3085636|186803|658082;1783272|1239|186801|3085636|186803|658656;1783272|1239|91061|1385|186820|1637|1639;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3082720|3118656|89958|426128;3379134|976|200643|171549|1853231|283168|28118;1783272|1239|91061|1385|186822|44249|684063;1783272|1239|91061|1385|186822|44249|1469647;3379134|976|200643|171549|2005525|375288|574930;1783272|1239|186801|3082720|186804|1257|215200;1783272|1239|186801|3085636|186803|46205|1798185;3384194|508458|649775|649776|3029088|638847|1943580;3379134|1224|1236|91347|543|620|1776082;3379134|1224|1236|91347|543|620|624;1783272|201174|84998|1643822|1643826|84108|1111137,Complete,KateRasheed
bsdb:38087200/1/1,38087200,prospective cohort,38087200,https://doi.org/10.1186/s12866-023-03042-1,NA,"Zhang J., Lu X., Cheng Z., Zou D., Shi W. , Wang T.",Alterations of conjunctival microbiota associated with orthokeratology lens wearing in myopic children,BMC microbiology,2023,"16S rDNA gene sequencing, Acinetobacter, Brevundimonas, Conjunctiva sac, Genomics, Microbiome, Orthokeratology lenses, Proteus",Experiment 1,China,Homo sapiens,Conjunctival sac,UBERON:0005908,Myopia,HP:0000545,N group -  Non-wearer group,L group -  Ok Lens group,Myopic patients who had been wearing OK lenses for 12–13 months,22,28,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Fig 4,8 March 2024,Ebere,"Ebere,Peace Sandy,WikiWorks","Linear Discriminant Analysis (LDA) Effect Size (LEfSe) multilevel discriminant analysis of the species differences (LDA > 3, P < 0.05, Mann–Whitney U-tests). A: Cladogram. The circle radiating from inside to outside represents the classification level from the kingdom to the genus (or species). Species with no significant differences are uniformly colored in yellow, the red nodes represent the microbial group that plays an important role in the OK group, and the green nodes represent the non-wearer group. B: Histogram of LDA value distribution shows the biomarkers with statistical difference. The LDA value represents the influence of bacterial species, and the longer the length, the higher the degree of influence. L: the OK lens group, N: the non-wearer group",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Acidobacteriota,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Planctomycetales|f__Planctomycetaceae|g__Planctomyces|s__Planctomyces sp. SH-PL62,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacillati|p__Chloroflexota|c__Chloroflexia",3379134|1224|28211;3379134|1224|28211|204458|76892;3379134|1224|28211|204458;3379134|1224|28211|204458|76892|41275;1783272|201174;1783272|1239|91061;3379134|1224|28211|204457;3379134|1224|28211|204457|41297;1783272|201174|1760|85007|1653;1783272|201174|1760|85007;3379134|1224|1236|2887326|468;3379134|1224|1236|2887326|468|469;1783272|1239|91061|1385;1783272|1239|91061|1385|90964;3379134|1224|1236|91347|1903414|583;3379134|1224|1236|91347;1783272|201174|1760|85006;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|91347|1903414|583;1783272|1117;3379134|1224|1236|135614|32033;1783272|1239|91061|186826|1300;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|186826|1300|1301;1783272|201174|1760|85007|1653|1716;3379134|57723;3379134|203682|203683|112|126|118|1636152;1783272|1239|91061|186826|81852;1783272|201174|1760|85006|1268;3379134|1224|1236|91347|543|547;1783272|1239|91061|186826|81852|1350;3379134|976|1853228|1853229;1783272|201174|1760|85009;3379134|1224|1236|91347|543|547;3379134|976|117743|200644;3379134|976|1853228|1853229|563835;1783272|1239|186801|3085636|186803|572511;1783272|1239|91061|1385|186817;1783272|201174|1760|85009|31957;1783272|201174|1760|85009|31957|1912216;1783272|200795|32061,Complete,Peace Sandy
bsdb:38087200/1/2,38087200,prospective cohort,38087200,https://doi.org/10.1186/s12866-023-03042-1,NA,"Zhang J., Lu X., Cheng Z., Zou D., Shi W. , Wang T.",Alterations of conjunctival microbiota associated with orthokeratology lens wearing in myopic children,BMC microbiology,2023,"16S rDNA gene sequencing, Acinetobacter, Brevundimonas, Conjunctiva sac, Genomics, Microbiome, Orthokeratology lenses, Proteus",Experiment 1,China,Homo sapiens,Conjunctival sac,UBERON:0005908,Myopia,HP:0000545,N group -  Non-wearer group,L group -  Ok Lens group,Myopic patients who had been wearing OK lenses for 12–13 months,22,28,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Fig 4,8 March 2024,Ebere,"Ebere,Peace Sandy,WikiWorks","Linear Discriminant Analysis (LDA) Effect Size (LEfSe) multilevel discriminant analysis of the species differences (LDA > 3, P < 0.05, Mann–Whitney U-tests). A: Cladogram. The circle radiating from inside to outside represents the classification level from the kingdom to the genus (or species). Species with no significant differences are uniformly colored in yellow, the red nodes represent the microbial group that plays an important role in the OK group, and the green nodes represent the non-wearer group. B: Histogram of LDA value distribution shows the biomarkers with statistical difference. The LDA value represents the influence of bacterial species, and the longer the length, the higher the degree of influence. L: the OK lens group, N: the non-wearer group",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",1783272|1239|91061|1385|186817|1386;;3379134|74201|203494|48461|1647988|239934|1872421;3379134|976|200643|171549|2005473;3379134|976|200643|171549|2005473,Complete,Peace Sandy
bsdb:38111925/1/1,38111925,case-control,38111925,10.18240/ijo.2023.12.10,NA,"Zou X.R., Zhang P., Zhou Y. , Yin Y.",Ocular surface microbiota in patients with varying degrees of dry eye severity,International journal of ophthalmology,2023,"dry eye, microbiota, ocular surface, tear film break up time",Experiment 1,China,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,control,Mild and Moderate to Severe Dry Eye,2s<TFBUT<5s (Tear Film Breakup Time between 2 and 5 sec) and TFBUT<2s,61,138,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2.92,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a,28 September 2024,Mary Bearkland,"Mary Bearkland,WikiWorks",Linear Discriminant Analysis of the three groups,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae|g__Pseudoalteromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Viridiplantae|p__Streptophyta,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae",1783272|201174|1760|2037;1783272|201174|1760;3379134|1224|28211|356|82115|357;1783272|1239|91061;3379134|976|200643|171549;3379134|976|200643;1783272|201174|1760|85006|85019;3379134|1224|28211|356|118882;3379134|976|1853228|1853229|563835;3379134|976|117743|200644|2762318|59732;1783272|1239|186801;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;3384194|1297|188787|118964|183710;3384194|1297|188787|118964|183710|1298;3379134|1224|28211|356|212791;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;3379134|1224|28211|356|119045;3379134|1224|28211|356|119045|407;3379134|1224|1236|2887326|468;3379134|1224|28211|356|118882|528;3379134|1224|28211|204455|31989|265;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|201174|1760|85009|31957;1783272|201174|1760|85009|31957|1743;3379134|1224|1236|135622|267888;3379134|1224|1236|135622|267888|53246;3379134|1224|1236|72274;1783272|201174|1760|85010|2070;3379134|1224|28211|356|82115;3379134|976|1853228|1853229|563835|504481;3379134|1224|1236|91347|543|620;1783272|1239|91061|1385|90964;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;33090|35493;1783272|1239|1737404|1737405;1783272|1239|909932|1843489|31977;3379134|1224|1236|135623;3379134|976|117743|200644|2762318,Complete,NA
bsdb:38111925/1/2,38111925,case-control,38111925,10.18240/ijo.2023.12.10,NA,"Zou X.R., Zhang P., Zhou Y. , Yin Y.",Ocular surface microbiota in patients with varying degrees of dry eye severity,International journal of ophthalmology,2023,"dry eye, microbiota, ocular surface, tear film break up time",Experiment 1,China,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,control,Mild and Moderate to Severe Dry Eye,2s<TFBUT<5s (Tear Film Breakup Time between 2 and 5 sec) and TFBUT<2s,61,138,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2.92,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,28 September 2024,Mary Bearkland,"Mary Bearkland,WikiWorks",Linear Discriminant Analysis of the three groups,increased,NA,NA,Complete,NA
bsdb:38111925/2/1,38111925,case-control,38111925,10.18240/ijo.2023.12.10,NA,"Zou X.R., Zhang P., Zhou Y. , Yin Y.",Ocular surface microbiota in patients with varying degrees of dry eye severity,International journal of ophthalmology,2023,"dry eye, microbiota, ocular surface, tear film break up time",Experiment 2,China,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,Control and moderate-to-severe dry eye,Mild Dry Eye,Tear Film Breakup Time less than 2 sec and Tear Film Breakup Time >/=5 sec,143,56,3 months,16S,34,Illumina,NA,LEfSe,0.05,NA,2.92,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a,4 October 2024,Mary Bearkland,"Mary Bearkland,WikiWorks",Linear Discriminant Analysis of the three groups,increased,"k__Bacillati|p__Chloroflexota|c__Anaerolineae,c__Deltaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Nostocaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Rhodocyclaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Nesterenkonia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Sporosarcina,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas",1783272|200795|292625;28221;3379134|1224|28211|204457;3379134|1224|28216|206389;1783272|1117|3028117|1161|1162;3379134|1224|1236|72274;1783272|201174|1760|85006|1268;1783272|1239|91061|1385|186818;3379134|1224|28211|204457|41297;3379134|1224|28216|80840|80864;3379134|1224|28216|206389|75787;1783272|201174|1760|85006|1268|1663;1783272|201174|1760|85006|1268|57494;1783272|1239|91061|1385|186818|1569;3379134|1224|28211|204457|41297|13687,Complete,NA
bsdb:38111925/2/2,38111925,case-control,38111925,10.18240/ijo.2023.12.10,NA,"Zou X.R., Zhang P., Zhou Y. , Yin Y.",Ocular surface microbiota in patients with varying degrees of dry eye severity,International journal of ophthalmology,2023,"dry eye, microbiota, ocular surface, tear film break up time",Experiment 2,China,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,Control and moderate-to-severe dry eye,Mild Dry Eye,Tear Film Breakup Time less than 2 sec and Tear Film Breakup Time >/=5 sec,143,56,3 months,16S,34,Illumina,NA,LEfSe,0.05,NA,2.92,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3a,4 October 2024,Mary Bearkland,"Mary Bearkland,WikiWorks",Linear Discriminant Analysis of the three groups,decreased,NA,NA,Complete,NA
bsdb:38111925/3/1,38111925,case-control,38111925,10.18240/ijo.2023.12.10,NA,"Zou X.R., Zhang P., Zhou Y. , Yin Y.",Ocular surface microbiota in patients with varying degrees of dry eye severity,International journal of ophthalmology,2023,"dry eye, microbiota, ocular surface, tear film break up time",Experiment 3,China,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,control and mild dry eye,Moderate-to-severe dry eye,Tear Film Breakup Time less than 2 sec,117,82,3 months,16S,34,Illumina,NA,LEfSe,0.05,NA,2.92,NA,NA,decreased,decreased,decreased,decreased,NA,NA,Signature 1,Figure 3a,4 October 2024,Mary Bearkland,"Mary Bearkland,WikiWorks",Linear Discriminant Analysis of the three groups,increased,",k__Thermotogati|p__Deinococcota|c__Deinococci,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Beijerinckiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Anoxybacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Chelatococcaceae|g__Chelatococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Chelativorans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Sterolibacteriaceae|g__Methyloversatilis",;3384194|1297|188787;1783272|1239|526524|526525;3379134|1224|28211|204458;3379134|1224|28211|204441;3379134|1224|28216|80840;3384194|1297|188787|68933|188786;1783272|1239|91061|1385|186817;1783272|1239|526524|526525|128827;3379134|1224|28211|204458|76892;3379134|1224|28211|356|45404;3379134|1224|28211|3120395|433;3379134|1224|28216|80840|75682;3384194|1297|188787|68933|188786|270;1783272|1239|91061|1385|3120669|150247;1783272|1239|526524|526525|128827|174708;3379134|1224|28211|356|2036754|28209;3379134|1224|28211|356|69277|449972;3379134|1224|28216|80840|119060|106589;3379134|1224|28216|32003|2008793|378210,Complete,NA
bsdb:38111925/3/2,38111925,case-control,38111925,10.18240/ijo.2023.12.10,NA,"Zou X.R., Zhang P., Zhou Y. , Yin Y.",Ocular surface microbiota in patients with varying degrees of dry eye severity,International journal of ophthalmology,2023,"dry eye, microbiota, ocular surface, tear film break up time",Experiment 3,China,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,control and mild dry eye,Moderate-to-severe dry eye,Tear Film Breakup Time less than 2 sec,117,82,3 months,16S,34,Illumina,NA,LEfSe,0.05,NA,2.92,NA,NA,decreased,decreased,decreased,decreased,NA,NA,Signature 2,Figure 3a,4 October 2024,Mary Bearkland,"Mary Bearkland,WikiWorks",Linear Discriminant Analysis of the three groups,decreased,NA,NA,Complete,NA
bsdb:38113233/1/1,38113233,"cross-sectional observational, not case-control",38113233,https://doi.org/10.1371/journal.pone.0292645,NA,"Troth T.D., McInnes R.S., Dunn S.J., Mirza J., Whittaker A.H., Goodchild S.A., Loman N.J., Harding S.V. , van Schaik W.",Differences in the gut microbiota between Gurkhas and soldiers of British origin,PloS one,2023,NA,Experiment 1,United Kingdom,Homo sapiens,Feces,UBERON:0001988,NA,NA,British soldiers,Gurkhas,"This field could be left blank or potentially used to describe factors related to the differences observed, if any are known and being controlled for, although the core ""condition"" is the origin (Gurkhas vs. British soldiers).",22,16,3 months,16S,1234,Illumina,relative abundances,MaAsLin2,0.05,TRUE,3,NA,NA,decreased,decreased,unchanged,decreased,decreased,decreased,Signature 1,Figure 1,22 September 2025,SheikhAlMamun,SheikhAlMamun,"British soldiers' gut microbiota included 41 unique genera over 1% abundance. The most common were Bacteroides, Blautia, Dorea, Eubacterium, and Roseburia, present in all samples, while Anaerotruncus was least common, found in just one sample.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium",1783272|1239|186801|3085636|186803|28050;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|186806|1730,Complete,NA
bsdb:38113233/1/2,38113233,"cross-sectional observational, not case-control",38113233,https://doi.org/10.1371/journal.pone.0292645,NA,"Troth T.D., McInnes R.S., Dunn S.J., Mirza J., Whittaker A.H., Goodchild S.A., Loman N.J., Harding S.V. , van Schaik W.",Differences in the gut microbiota between Gurkhas and soldiers of British origin,PloS one,2023,NA,Experiment 1,United Kingdom,Homo sapiens,Feces,UBERON:0001988,NA,NA,British soldiers,Gurkhas,"This field could be left blank or potentially used to describe factors related to the differences observed, if any are known and being controlled for, although the core ""condition"" is the origin (Gurkhas vs. British soldiers).",22,16,3 months,16S,1234,Illumina,relative abundances,MaAsLin2,0.05,TRUE,3,NA,NA,decreased,decreased,unchanged,decreased,decreased,decreased,Signature 2,Figure 1,22 September 2025,SheikhAlMamun,SheikhAlMamun,"British soldiers' gut microbiota included 41 unique genera over 1% abundance. The most common were Bacteroides, Blautia, Dorea, Eubacterium, and Roseburia, present in all samples, while Anaerotruncus was least common, found in just one sample.",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium",1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|186806|1730,Complete,NA
bsdb:38113233/2/NA,38113233,"cross-sectional observational, not case-control",38113233,https://doi.org/10.1371/journal.pone.0292645,NA,"Troth T.D., McInnes R.S., Dunn S.J., Mirza J., Whittaker A.H., Goodchild S.A., Loman N.J., Harding S.V. , van Schaik W.",Differences in the gut microbiota between Gurkhas and soldiers of British origin,PloS one,2023,NA,Experiment 2,United Kingdom,Homo sapiens,Feces,UBERON:0001988,NA,NA,British soldiers,Gurkhas,"This field could be left blank or potentially used to describe factors related to the differences observed, if any are known and being controlled for, although the core ""condition"" is the origin (Gurkhas vs. British soldiers).",22,16,3 months,16S,1234,Illumina,relative abundances,MaAsLin2,0.05,TRUE,3,NA,NA,increased,increased,unchanged,increased,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:38115159/1/1,38115159,laboratory experiment,38115159,10.1186/s40104-023-00959-5,NA,"Liu M., Zhang J., Zhou Y., Xiong S., Zhou M., Wu L., Liu Q., Chen Z., Jiang H., Yang J., Liu Y., Wang Y., Chen C. , Huang L.",Gut microbiota affects the estrus return of sows by regulating the metabolism of sex steroid hormones,Journal of animal science and biotechnology,2023,"Estrus return, Fecal metabolome, Gut microbiota, Metagenomics, Sex steroid hormones, Sow",Experiment 1,China,Sus scrofa domesticus,Feces,UBERON:0001988,Sex hormone,CHEBI:50112,Non-return sows (Discovery cohort),Normal Return sows (Discovery cohort),This group comprises sows that returned to estrus within 7 days of weaning in the discovery cohort.,40,45,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 1,"Figure 1D, Additional file1: Figure S5D & Additional file 2: Table S4",25 April 2025,Victoria,Victoria,Differential bacterial species between normal return and non-return sows in 85 faecal samples with metagenomic sequencing data.,increased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Fibrobacterota|c__Fibrobacteria|o__Fibrobacterales|f__Fibrobacteraceae|g__Fibrobacter,k__Pseudomonadati|p__Fibrobacterota|c__Fibrobacteria|o__Fibrobacterales|f__Fibrobacteraceae|g__Hallerella|s__Hallerella succinigenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter olleyae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P2-180,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P3-122,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P5-92,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella bryantii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp.,k__Pseudomonadati|p__Verrucomicrobiota|s__Verrucomicrobiota bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter ruminicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|g__Candidatus Alcium|s__Candidatus Alcium sp. P201,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas|s__uncultured Dysgonomonas sp.",1783272|1239;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|28116;3379134|976;3379134|65842|204430|218872|204431|832;3379134|65842|204430|218872|204431|2815788|1896222;1783272|1239|186801|3085636|186803|1898203;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|91061|186826|33958|1578|33959;1783272|1239|91061|186826|33958|2742598|1598;3366610|28890|183925|2158|2159|2172;3366610|28890|183925|2158|2159|2172|294671;3379134|976|200643|171549|2005473;3379134|976|200643|171549|2005525|375288|328812;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|28130;3379134|976|200643|171549|171552|838|28131;3379134|976|200643|171549|171552|838|2024224;3379134|976|200643|171549|171552|838|2024223;3379134|976|200643|171549|171552|838|2024222;3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|2974251|77095;3379134|976|200643|171549|171552|2974251|165179;3379134|203691|203692|136|2845253|157|166;3379134|74201|2026799;3379134|976|200643|171549|171552|558436|839;3379134|976|200643|171549|3443717|1768112;1783272|1239;3379134|976|200643|171549|2005473;3379134|976|200643|171549|2005520|156973|206096,Complete,KateRasheed
bsdb:38115159/1/2,38115159,laboratory experiment,38115159,10.1186/s40104-023-00959-5,NA,"Liu M., Zhang J., Zhou Y., Xiong S., Zhou M., Wu L., Liu Q., Chen Z., Jiang H., Yang J., Liu Y., Wang Y., Chen C. , Huang L.",Gut microbiota affects the estrus return of sows by regulating the metabolism of sex steroid hormones,Journal of animal science and biotechnology,2023,"Estrus return, Fecal metabolome, Gut microbiota, Metagenomics, Sex steroid hormones, Sow",Experiment 1,China,Sus scrofa domesticus,Feces,UBERON:0001988,Sex hormone,CHEBI:50112,Non-return sows (Discovery cohort),Normal Return sows (Discovery cohort),This group comprises sows that returned to estrus within 7 days of weaning in the discovery cohort.,40,45,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 2,"Figure 1D, Additional file1: Figure S5D & Additional file 2: Table S4",25 April 2025,Victoria,Victoria,Differential bacterial species between normal return and non-return sows in 85 faecal samples with metagenomic sequencing data.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter amalonaticus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium xerosis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus cecorum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|f__Andersonviridae|s__Ounavirinae|g__Felixounavirus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus|s__Pediococcus pentosaceus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus equinus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gallolyticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus suis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa",3379134|976|200643|171549|815|816|817;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|1694;3379134|1224|1236|91347|543|544|35703;1783272|201174|1760|85007|1653|1716|1725;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|81852|1350|44008;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|91061|186826|81852|1350|1352;2731360|2731618|2731619|3424631|1985285|1198140;1783272|1239|91061|186826;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|1300|1357|1358;3366610|28890|183925|2158|2159|2172|2173;1783272|1239|91061|186826|33958|1253|1255;3379134|976|200643|171549|815|909656|310297;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1335;1783272|1239|91061|186826|1300|1301|315405;1783272|1239|91061|186826|1300|1301|1313;1783272|1239|91061|186826|1300|1301|1307;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|526524|526525|2810280|3025755|1547,Complete,KateRasheed
bsdb:38115159/2/1,38115159,laboratory experiment,38115159,10.1186/s40104-023-00959-5,NA,"Liu M., Zhang J., Zhou Y., Xiong S., Zhou M., Wu L., Liu Q., Chen Z., Jiang H., Yang J., Liu Y., Wang Y., Chen C. , Huang L.",Gut microbiota affects the estrus return of sows by regulating the metabolism of sex steroid hormones,Journal of animal science and biotechnology,2023,"Estrus return, Fecal metabolome, Gut microbiota, Metagenomics, Sex steroid hormones, Sow",Experiment 2,China,Sus scrofa domesticus,Feces,UBERON:0001988,Sex hormone,CHEBI:50112,Non-return sows (Discovery cohort),Normal Return sows (Discovery cohort),This group comprises sows that returned to estrus within 7 days of weaning in the discovery cohort.,40,167,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,"Additional file 1: Figure S4 D&E, Additional file2: Table S2",25 April 2025,Victoria,Victoria,Differential ASVs and genera between normal return and non-return sows in 207 fecal samples.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|g__Candidatus Alcium|s__Candidatus Alcium sp. F082,k__Pseudomonadati|p__Kiritimatiellota|s__uncultured eubacterium WCHB1-41",3379134|976|200643|171549;1783272|1239|91061|186826|33958|1578|33959;3379134|976|200643|171549|2005473;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|3068309;3379134|976|200643|171549|3443717|1768115;3379134|134625|74206,Complete,KateRasheed
bsdb:38115159/2/2,38115159,laboratory experiment,38115159,10.1186/s40104-023-00959-5,NA,"Liu M., Zhang J., Zhou Y., Xiong S., Zhou M., Wu L., Liu Q., Chen Z., Jiang H., Yang J., Liu Y., Wang Y., Chen C. , Huang L.",Gut microbiota affects the estrus return of sows by regulating the metabolism of sex steroid hormones,Journal of animal science and biotechnology,2023,"Estrus return, Fecal metabolome, Gut microbiota, Metagenomics, Sex steroid hormones, Sow",Experiment 2,China,Sus scrofa domesticus,Feces,UBERON:0001988,Sex hormone,CHEBI:50112,Non-return sows (Discovery cohort),Normal Return sows (Discovery cohort),This group comprises sows that returned to estrus within 7 days of weaning in the discovery cohort.,40,167,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,"Additional file 1: Figure S4 D&E, Additional file2: Table S2",25 April 2025,Victoria,"Victoria,KateRasheed",Differential ASVs and genera between normal return and non-return sows in 207 fecal samples.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Cellulosilyticaceae|g__Cellulosilyticum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium bornimense,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium septicum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium XBB1006,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium sp.,k__Bacillati|p__Bacillota|g__Negativibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005",3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|817;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|1694;1783272|1239|186801|3085636|3018741|698776;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|31979|1485|1216932;1783272|1239|186801|186802|31979|1485|1502;1783272|1239|186801|186802|31979|1485|1504;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|1520827;1783272|1239|186801|3082720|543314|86331|2049035;1783272|1239|1980693;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|186807;3379134|976|200643|171549|815|909656|310297;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3082720|186804|1505652;1783272|1239|186801|186802|216572|3068309,Complete,KateRasheed
bsdb:38115159/3/1,38115159,laboratory experiment,38115159,10.1186/s40104-023-00959-5,NA,"Liu M., Zhang J., Zhou Y., Xiong S., Zhou M., Wu L., Liu Q., Chen Z., Jiang H., Yang J., Liu Y., Wang Y., Chen C. , Huang L.",Gut microbiota affects the estrus return of sows by regulating the metabolism of sex steroid hormones,Journal of animal science and biotechnology,2023,"Estrus return, Fecal metabolome, Gut microbiota, Metagenomics, Sex steroid hormones, Sow",Experiment 3,China,Sus scrofa domesticus,Feces,UBERON:0001988,Sex hormone,CHEBI:50112,Non-return Sows (Validation cohort),Normal Return Sows (Validation cohort),This group comprises sows that returned to estrus within 7 days of weaning in the validation cohort.,11,18,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.1,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Additional file1: Figure S6D,11 May 2025,Victoria,Victoria,Differential bacterial species between normal return and non-return sows with metagenomic sequencing data in the validation cohort.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|s__Rikenellaceae bacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus delbrueckii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Pseudomonadati|p__Verrucomicrobiota|s__Verrucomicrobiota bacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|s__Porphyromonadaceae bacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus helveticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus taiwanensis,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Jonquetella|s__Jonquetella anthropi",1783272|1239|91061|186826|33958|1578|33959;3379134|976|200643|171549|171550|2049048;1783272|1239|91061|186826|33958|1578|1584;1783272|1239|91061|186826|33958|1578|47770;3379134|74201|2026799;1783272|1239|91061|186826|33958|1578|1596;3379134|976|200643|171549|171551|2049046;1783272|1239|91061|186826|33958|1578|1587;1783272|1239|91061|186826|33958|2742598|1613;1783272|1239|91061|186826|33958|1578|508451;3384194|508458|649775|649776|3029088|428711|428712,Complete,KateRasheed
bsdb:38115159/3/2,38115159,laboratory experiment,38115159,10.1186/s40104-023-00959-5,NA,"Liu M., Zhang J., Zhou Y., Xiong S., Zhou M., Wu L., Liu Q., Chen Z., Jiang H., Yang J., Liu Y., Wang Y., Chen C. , Huang L.",Gut microbiota affects the estrus return of sows by regulating the metabolism of sex steroid hormones,Journal of animal science and biotechnology,2023,"Estrus return, Fecal metabolome, Gut microbiota, Metagenomics, Sex steroid hormones, Sow",Experiment 3,China,Sus scrofa domesticus,Feces,UBERON:0001988,Sex hormone,CHEBI:50112,Non-return Sows (Validation cohort),Normal Return Sows (Validation cohort),This group comprises sows that returned to estrus within 7 days of weaning in the validation cohort.,11,18,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.1,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Additional file1: Figure S6D,11 May 2025,Victoria,Victoria,Differential bacterial species between normal return and non-return sows with metagenomic sequencing data in the validation cohort.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus suis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus equinus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,s__bacterium D16-59,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Criibacterium|s__Criibacterium bergeronii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter|s__Psychrobacter piechaudii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium tertium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus viridans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes|s__Synergistes jonesii",1783272|1239|186801|186802|216572|39492;1783272|201174|1760|85004|31953|1678|1694;1783272|1239|91061|186826|1300|1301|1307;1783272|1239|186801|3085636|186803|2316020|46228;1783272|1239|91061|186826|1300|1301|1335;1783272|201174|84998|84999|84107|102106|74426;2320098;1783272|1239|186801|3082720|3118655|1937664|1871336;3379134|1224|1236|2887326|468|497|1945521;3379134|976|200643|171549|2030927;3379134|976|200643|171549|815|816|674529;1783272|1239|186801|186802|31979|1485|1559;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|91061|186826|186827|1375|1377;1783272|1239|91061|186826|1300|1301|76860;3384194|508458|649775|649776|649777|2753|2754,Complete,KateRasheed
bsdb:38125567/1/1,38125567,"cross-sectional observational, not case-control",38125567,10.3389/fmicb.2023.1320567,NA,"Li Y.Q., Yan X.Y., Xiao X.J., Ma P.T., Wang S.Q., Liu H.L., Zhang W., Chen M., Yao J.P. , Li Y.",The gut microbiome and metabolites are altered and interrelated in patients with functional constipation,Frontiers in microbiology,2023,"clinical trial, correlation analysis, fecal metabolites, functional constipation, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy control,Functional Constipation,Patients diagnosed with Functional Constipation by physicians according to the Rome IV diagnostic criteria.,21,21,1 month,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,"age,body mass index,sex",NA,NA,increased,increased,increased,NA,NA,Signature 1,Figure 1E and Table S1,18 March 2025,Daberechi,"Daberechi,Tosin",Differential microbiome of the FC (Functional constipation) and HC (Healthy control) groups at the genus levels,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|186803|2569097|39488;;3379134|976|200643|171549|2005519|397864;1783272|1239|186801|186802|1980681;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3082720|186804|1505657;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|216572|39492,Complete,Svetlana up
bsdb:38125567/1/2,38125567,"cross-sectional observational, not case-control",38125567,10.3389/fmicb.2023.1320567,NA,"Li Y.Q., Yan X.Y., Xiao X.J., Ma P.T., Wang S.Q., Liu H.L., Zhang W., Chen M., Yao J.P. , Li Y.",The gut microbiome and metabolites are altered and interrelated in patients with functional constipation,Frontiers in microbiology,2023,"clinical trial, correlation analysis, fecal metabolites, functional constipation, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy control,Functional Constipation,Patients diagnosed with Functional Constipation by physicians according to the Rome IV diagnostic criteria.,21,21,1 month,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,"age,body mass index,sex",NA,NA,increased,increased,increased,NA,NA,Signature 2,Figure 1E and Table S1,18 March 2025,Daberechi,"Daberechi,Tosin",Differential microbiome of the FC (Functional constipation) and HC (Healthy control) groups at the genus levels,decreased,NA,NA,Complete,Svetlana up
bsdb:38125567/2/1,38125567,"cross-sectional observational, not case-control",38125567,10.3389/fmicb.2023.1320567,NA,"Li Y.Q., Yan X.Y., Xiao X.J., Ma P.T., Wang S.Q., Liu H.L., Zhang W., Chen M., Yao J.P. , Li Y.",The gut microbiome and metabolites are altered and interrelated in patients with functional constipation,Frontiers in microbiology,2023,"clinical trial, correlation analysis, fecal metabolites, functional constipation, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy control,Functional Constipation,Patients diagnosed with Functional Constipation by physicians according to the Rome IV diagnostic criteria.,21,21,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,body mass index,sex",NA,NA,increased,increased,increased,NA,NA,Signature 1,"Figure 2A, 2B",7 April 2025,Anne-mariesharp,"Anne-mariesharp,Daberechi",LDA score diagram and Phylogenetic tree in the cladogram showing significantly differential taxa,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:352",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;1783272|1239|186801|3085636|186803|2569097|39488;;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|2005519;3379134|1224|28211|204458|76892|41275;3379134|1224|28211|204458|76892;3379134|1224|28211|204458;1783272|1239|186801|3082768|990719;1783272|1239|186801|3082768;1783272|1239|186801|186802|1980681;1783272|1239|909932|1843489|31977|39948;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|3082720|186804|1505657;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|292632;3379134|1224|28216|80840|995019|40544;3379134|976|200643|171549|2005525;1783272|1239|909932|1843489|31977;3379134|74201|203494|48461;3379134|74201|203494;1783272|1239|186801|186802|31979|1485|1262798,Complete,Svetlana up
bsdb:38125567/2/2,38125567,"cross-sectional observational, not case-control",38125567,10.3389/fmicb.2023.1320567,NA,"Li Y.Q., Yan X.Y., Xiao X.J., Ma P.T., Wang S.Q., Liu H.L., Zhang W., Chen M., Yao J.P. , Li Y.",The gut microbiome and metabolites are altered and interrelated in patients with functional constipation,Frontiers in microbiology,2023,"clinical trial, correlation analysis, fecal metabolites, functional constipation, gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy control,Functional Constipation,Patients diagnosed with Functional Constipation by physicians according to the Rome IV diagnostic criteria.,21,21,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,body mass index,sex",NA,NA,increased,increased,increased,NA,NA,Signature 2,"Figure 2A, 2B",7 April 2025,Anne-mariesharp,"Anne-mariesharp,Tosin",LDA score diagram and Phylogenetic tree in the cladogram showing significantly differential taxa,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Orbales|f__Orbaceae|g__Gilliamella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Orbales|f__Orbaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Orbales",3379134|976|200643|171549|171550|239759;3379134|1224|1236|1240482|1240483|1193503;3379134|976|200643|171549|2005473;3379134|1224|1236|1240482|1240483;3379134|1224|1236|1240482,Complete,Svetlana up
bsdb:38125567/3/1,38125567,"cross-sectional observational, not case-control",38125567,10.3389/fmicb.2023.1320567,NA,"Li Y.Q., Yan X.Y., Xiao X.J., Ma P.T., Wang S.Q., Liu H.L., Zhang W., Chen M., Yao J.P. , Li Y.",The gut microbiome and metabolites are altered and interrelated in patients with functional constipation,Frontiers in microbiology,2023,"clinical trial, correlation analysis, fecal metabolites, functional constipation, gut microbiota",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Bowel dysfunction,MONDO:0004880,Low levels of complete spontaneous bowel movements (CSBMs),High levels of complete spontaneous bowel movements (CSBMs),Patients with high levels of complete spontaneous bowel movements,NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S2,9 April 2025,Tosin,"Tosin,Daberechi",The correlations between differential genera and clinical parameters.,increased,NA,NA,Complete,Svetlana up
bsdb:38125567/3/2,38125567,"cross-sectional observational, not case-control",38125567,10.3389/fmicb.2023.1320567,NA,"Li Y.Q., Yan X.Y., Xiao X.J., Ma P.T., Wang S.Q., Liu H.L., Zhang W., Chen M., Yao J.P. , Li Y.",The gut microbiome and metabolites are altered and interrelated in patients with functional constipation,Frontiers in microbiology,2023,"clinical trial, correlation analysis, fecal metabolites, functional constipation, gut microbiota",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Bowel dysfunction,MONDO:0004880,Low levels of complete spontaneous bowel movements (CSBMs),High levels of complete spontaneous bowel movements (CSBMs),Patients with high levels of complete spontaneous bowel movements,NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S2,9 April 2025,Tosin,"Tosin,Daberechi",The correlations between differential genera and clinical parameters.,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|186803|2569097|39488;;3379134|976|200643|171549|2005519|397864;1783272|1239|186801|186802|1980681;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|3082720|186804|1505657;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|877420;3379134|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:38125567/4/1,38125567,"cross-sectional observational, not case-control",38125567,10.3389/fmicb.2023.1320567,NA,"Li Y.Q., Yan X.Y., Xiao X.J., Ma P.T., Wang S.Q., Liu H.L., Zhang W., Chen M., Yao J.P. , Li Y.",The gut microbiome and metabolites are altered and interrelated in patients with functional constipation,Frontiers in microbiology,2023,"clinical trial, correlation analysis, fecal metabolites, functional constipation, gut microbiota",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Complicated disease course,EFO:0006820,Low course of disease,High course of disease,Patients with high course of the disease (Functional Constipation),NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S2,9 April 2025,Anne-mariesharp,Anne-mariesharp,The correlations between differential genera and clinical parameters,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|186803|2569097|39488;;3379134|976|200643|171549|2005519|397864;1783272|1239|186801|186802|1980681;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|3082720|186804|1505657;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|877420;3379134|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:38125567/4/2,38125567,"cross-sectional observational, not case-control",38125567,10.3389/fmicb.2023.1320567,NA,"Li Y.Q., Yan X.Y., Xiao X.J., Ma P.T., Wang S.Q., Liu H.L., Zhang W., Chen M., Yao J.P. , Li Y.",The gut microbiome and metabolites are altered and interrelated in patients with functional constipation,Frontiers in microbiology,2023,"clinical trial, correlation analysis, fecal metabolites, functional constipation, gut microbiota",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Complicated disease course,EFO:0006820,Low course of disease,High course of disease,Patients with high course of the disease (Functional Constipation),NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S2,9 April 2025,Anne-mariesharp,"Anne-mariesharp,Tosin",The correlations between differential genera and clinical parameters,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Orbales|f__Orbaceae|g__Gilliamella,3379134|1224|1236|1240482|1240483|1193503,Complete,Svetlana up
bsdb:38125567/5/1,38125567,"cross-sectional observational, not case-control",38125567,10.3389/fmicb.2023.1320567,NA,"Li Y.Q., Yan X.Y., Xiao X.J., Ma P.T., Wang S.Q., Liu H.L., Zhang W., Chen M., Yao J.P. , Li Y.",The gut microbiome and metabolites are altered and interrelated in patients with functional constipation,Frontiers in microbiology,2023,"clinical trial, correlation analysis, fecal metabolites, functional constipation, gut microbiota",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,Low level of straining during defecation,High level of straining during defecation,Patients with high level of straining during defecation,NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S2,9 April 2025,Anne-mariesharp,"Anne-mariesharp,Daberechi",The correlations between differential genera and clinical parameters,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|186803|2569097|39488;;1783272|1239|186801|186802|1980681;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|3082720|186804|1505657;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|877420;3379134|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:38125567/5/2,38125567,"cross-sectional observational, not case-control",38125567,10.3389/fmicb.2023.1320567,NA,"Li Y.Q., Yan X.Y., Xiao X.J., Ma P.T., Wang S.Q., Liu H.L., Zhang W., Chen M., Yao J.P. , Li Y.",The gut microbiome and metabolites are altered and interrelated in patients with functional constipation,Frontiers in microbiology,2023,"clinical trial, correlation analysis, fecal metabolites, functional constipation, gut microbiota",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,Low level of straining during defecation,High level of straining during defecation,Patients with high level of straining during defecation,NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S2,9 April 2025,Anne-mariesharp,"Anne-mariesharp,Tosin",The correlations between differential genera and clinical parameters,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Orbales|f__Orbaceae|g__Gilliamella,3379134|1224|1236|1240482|1240483|1193503,Complete,Svetlana up
bsdb:38125567/6/1,38125567,"cross-sectional observational, not case-control",38125567,10.3389/fmicb.2023.1320567,NA,"Li Y.Q., Yan X.Y., Xiao X.J., Ma P.T., Wang S.Q., Liu H.L., Zhang W., Chen M., Yao J.P. , Li Y.",The gut microbiome and metabolites are altered and interrelated in patients with functional constipation,Frontiers in microbiology,2023,"clinical trial, correlation analysis, fecal metabolites, functional constipation, gut microbiota",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Anxiety,EFO:0005230,Low level of self-rating anxiety scale (SAS),High level of self-rating anxiety scale (SAS),Patients with high level of self-rating anxiety scale (SAS),NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S2,9 April 2025,Anne-mariesharp,"Anne-mariesharp,Daberechi",The correlations between differential genera and clinical parameters,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|186803|2569097|39488;;1783272|1239|186801|186802|1980681;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|3082720|186804|1505657;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|877420;3379134|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:38125567/6/2,38125567,"cross-sectional observational, not case-control",38125567,10.3389/fmicb.2023.1320567,NA,"Li Y.Q., Yan X.Y., Xiao X.J., Ma P.T., Wang S.Q., Liu H.L., Zhang W., Chen M., Yao J.P. , Li Y.",The gut microbiome and metabolites are altered and interrelated in patients with functional constipation,Frontiers in microbiology,2023,"clinical trial, correlation analysis, fecal metabolites, functional constipation, gut microbiota",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Anxiety,EFO:0005230,Low level of self-rating anxiety scale (SAS),High level of self-rating anxiety scale (SAS),Patients with high level of self-rating anxiety scale (SAS),NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S2,9 April 2025,Anne-mariesharp,"Anne-mariesharp,Tosin,Daberechi",The correlations between differential genera and clinical parameters,decreased,NA,NA,Complete,Svetlana up
bsdb:38125567/7/1,38125567,"cross-sectional observational, not case-control",38125567,10.3389/fmicb.2023.1320567,NA,"Li Y.Q., Yan X.Y., Xiao X.J., Ma P.T., Wang S.Q., Liu H.L., Zhang W., Chen M., Yao J.P. , Li Y.",The gut microbiome and metabolites are altered and interrelated in patients with functional constipation,Frontiers in microbiology,2023,"clinical trial, correlation analysis, fecal metabolites, functional constipation, gut microbiota",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Depressive disorder,MONDO:0002050,Low self-rating depression scale (SDS),High self-rating depression scale (SDS),Patients with high self-rating depression scale (SDS),NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S2,9 April 2025,Anne-mariesharp,"Anne-mariesharp,Tosin,Daberechi",The correlations between differential genera and clinical parameters,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|186803|2569097|39488;;1783272|1239|186801|186802|1980681;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|3082720|186804|1505657;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;3379134|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:38125567/7/2,38125567,"cross-sectional observational, not case-control",38125567,10.3389/fmicb.2023.1320567,NA,"Li Y.Q., Yan X.Y., Xiao X.J., Ma P.T., Wang S.Q., Liu H.L., Zhang W., Chen M., Yao J.P. , Li Y.",The gut microbiome and metabolites are altered and interrelated in patients with functional constipation,Frontiers in microbiology,2023,"clinical trial, correlation analysis, fecal metabolites, functional constipation, gut microbiota",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Depressive disorder,MONDO:0002050,Low self-rating depression scale (SDS),High self-rating depression scale (SDS),Patients with high self-rating depression scale (SDS),NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S2,9 April 2025,Anne-mariesharp,"Anne-mariesharp,Tosin",The correlations between differential genera and clinical parameters,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Orbales|f__Orbaceae|g__Gilliamella,3379134|1224|1236|1240482|1240483|1193503,Complete,Svetlana up
bsdb:38125567/8/1,38125567,"cross-sectional observational, not case-control",38125567,10.3389/fmicb.2023.1320567,NA,"Li Y.Q., Yan X.Y., Xiao X.J., Ma P.T., Wang S.Q., Liu H.L., Zhang W., Chen M., Yao J.P. , Li Y.",The gut microbiome and metabolites are altered and interrelated in patients with functional constipation,Frontiers in microbiology,2023,"clinical trial, correlation analysis, fecal metabolites, functional constipation, gut microbiota",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Low levels of bristol stool form scale (BSFS),High levels of bristol stool form scale (BSFS),Patients with high levels of bristol stool form scale,NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S2,9 April 2025,Daberechi,Daberechi,The correlations between differential genera and clinical parameters.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Orbales|f__Orbaceae|g__Gilliamella,3379134|1224|1236|1240482|1240483|1193503,Complete,Svetlana up
bsdb:38125567/8/2,38125567,"cross-sectional observational, not case-control",38125567,10.3389/fmicb.2023.1320567,NA,"Li Y.Q., Yan X.Y., Xiao X.J., Ma P.T., Wang S.Q., Liu H.L., Zhang W., Chen M., Yao J.P. , Li Y.",The gut microbiome and metabolites are altered and interrelated in patients with functional constipation,Frontiers in microbiology,2023,"clinical trial, correlation analysis, fecal metabolites, functional constipation, gut microbiota",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Low levels of bristol stool form scale (BSFS),High levels of bristol stool form scale (BSFS),Patients with high levels of bristol stool form scale,NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S2,9 April 2025,Daberechi,"Daberechi,Tosin",The correlations between differential genera and clinical parameters.,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|186803|2569097|39488;;1783272|1239|186801|186802|1980681;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|3082720|186804|1505657;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|877420;3379134|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:38125567/9/1,38125567,"cross-sectional observational, not case-control",38125567,10.3389/fmicb.2023.1320567,NA,"Li Y.Q., Yan X.Y., Xiao X.J., Ma P.T., Wang S.Q., Liu H.L., Zhang W., Chen M., Yao J.P. , Li Y.",The gut microbiome and metabolites are altered and interrelated in patients with functional constipation,Frontiers in microbiology,2023,"clinical trial, correlation analysis, fecal metabolites, functional constipation, gut microbiota",Experiment 9,China,Homo sapiens,Feces,UBERON:0001988,Health-related quality of life measurement,EFO:0011014,Low levels of patient assessment of constipation quality of life (PAC-QOL) index,High levels of patient assessment of constipation quality of life (PAC-QOL) index,Patients with high levels of patient assessment of constipation quality of life (PAC-QOL) index,NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S2,9 April 2025,Daberechi,Daberechi,The correlations between differential genera and clinical parameters,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Orbales|f__Orbaceae|g__Gilliamella,3379134|1224|1236|1240482|1240483|1193503,Complete,Svetlana up
bsdb:38125567/9/2,38125567,"cross-sectional observational, not case-control",38125567,10.3389/fmicb.2023.1320567,NA,"Li Y.Q., Yan X.Y., Xiao X.J., Ma P.T., Wang S.Q., Liu H.L., Zhang W., Chen M., Yao J.P. , Li Y.",The gut microbiome and metabolites are altered and interrelated in patients with functional constipation,Frontiers in microbiology,2023,"clinical trial, correlation analysis, fecal metabolites, functional constipation, gut microbiota",Experiment 9,China,Homo sapiens,Feces,UBERON:0001988,Health-related quality of life measurement,EFO:0011014,Low levels of patient assessment of constipation quality of life (PAC-QOL) index,High levels of patient assessment of constipation quality of life (PAC-QOL) index,Patients with high levels of patient assessment of constipation quality of life (PAC-QOL) index,NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S2,9 April 2025,Daberechi,"Daberechi,Tosin",The correlations between differential genera and clinical parameters,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136",3379134|74201|203494|48461|1647988|239934;;3379134|976|200643|171549|2005519|397864;1783272|1239|186801|186802|1980681;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|3082720|186804|1505657;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|877420,Complete,Svetlana up
bsdb:38162648/1/1,38162648,"cross-sectional observational, not case-control",38162648,10.3389/fimmu.2023.1297378,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10755913/,"Martínez-Sanz J., Talavera-Rodríguez A., Díaz-Álvarez J., Rosas Cancio-Suárez M., Rodríguez J.M., Alba C., Montes M.L., Martín-Mateos R., Burgos-Santamaría D., Moreno S., Serrano-Villar S. , Sánchez-Conde M.",A gut microbiome signature for HIV and metabolic dysfunction-associated steatotic liver disease,Frontiers in immunology,2023,"HIV, MASLD, NAFLD, gut microbiome, microbiome",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,HIV- MASLD+,HIV+ MASLD+,Participants living with HIV (PLWH) and Metabolic dysfunction-associated steatotic liver disease (MASLD).,20,30,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure S2,5 May 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe analysis graph indicating differentially abundant bacterial genera between the different study groups. Only those genus whose LDA score was greater than 4 have been represented.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK3A20,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,s__uncultured bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",1783272|1239|186801|3085636|186803|877406;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|3082720|543314|86331;1783272|1239|526524|526525|128827|123375;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|216572|1263|438033;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|186802|186807|2740;3366610|28890|183925|2158|2159|2172;1783272|1239|186801|3085636|186803|248744;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|3085636|186803|572511;77133;1783272|1239|186801|3085636|186803|1506553,Complete,Svetlana up
bsdb:38162648/1/2,38162648,"cross-sectional observational, not case-control",38162648,10.3389/fimmu.2023.1297378,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10755913/,"Martínez-Sanz J., Talavera-Rodríguez A., Díaz-Álvarez J., Rosas Cancio-Suárez M., Rodríguez J.M., Alba C., Montes M.L., Martín-Mateos R., Burgos-Santamaría D., Moreno S., Serrano-Villar S. , Sánchez-Conde M.",A gut microbiome signature for HIV and metabolic dysfunction-associated steatotic liver disease,Frontiers in immunology,2023,"HIV, MASLD, NAFLD, gut microbiome, microbiome",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,HIV- MASLD+,HIV+ MASLD+,Participants living with HIV (PLWH) and Metabolic dysfunction-associated steatotic liver disease (MASLD).,20,30,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure S2,5 May 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe analysis graph indicating differentially abundant bacterial genera between the different study groups. Only those genus whose LDA score was greater than 4 have been represented.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:352,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes",1783272|1239|186801|186802|216572|1508657;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|1903409|53335;1783272|1239|186801|186802|31979|1485|1262798;3379134|1224|1236|91347|1903411|629;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|1766253;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|841;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|292632;1783272|1239|91061|186826|33958|46255;1783272|1239|186801|3085636|186803|207244,Complete,Svetlana up
bsdb:38162648/2/1,38162648,"cross-sectional observational, not case-control",38162648,10.3389/fimmu.2023.1297378,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10755913/,"Martínez-Sanz J., Talavera-Rodríguez A., Díaz-Álvarez J., Rosas Cancio-Suárez M., Rodríguez J.M., Alba C., Montes M.L., Martín-Mateos R., Burgos-Santamaría D., Moreno S., Serrano-Villar S. , Sánchez-Conde M.",A gut microbiome signature for HIV and metabolic dysfunction-associated steatotic liver disease,Frontiers in immunology,2023,"HIV, MASLD, NAFLD, gut microbiome, microbiome",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,HIV+ MASLD-,HIV+ MASLD+,Participants living with HIV (PLWH) and Metabolic dysfunction-associated steatotic liver disease (MASLD).,30,30,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure S2,5 May 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe analysis graph indicating differentially abundant bacterial genera between the different study groups. Only those genus whose LDA score was greater than 4 have been represented.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK3A20,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,s__uncultured bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",1783272|1239|186801|3085636|186803|877406;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|3082720|543314|86331;1783272|1239|526524|526525|128827|123375;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|216572|1263|438033;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|186802|186807|2740;3366610|28890|183925|2158|2159|2172;1783272|1239|186801|3085636|186803|248744;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|3085636|186803|572511;77133;1783272|1239|186801|3085636|186803|1506553,Complete,Svetlana up
bsdb:38162648/2/2,38162648,"cross-sectional observational, not case-control",38162648,10.3389/fimmu.2023.1297378,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10755913/,"Martínez-Sanz J., Talavera-Rodríguez A., Díaz-Álvarez J., Rosas Cancio-Suárez M., Rodríguez J.M., Alba C., Montes M.L., Martín-Mateos R., Burgos-Santamaría D., Moreno S., Serrano-Villar S. , Sánchez-Conde M.",A gut microbiome signature for HIV and metabolic dysfunction-associated steatotic liver disease,Frontiers in immunology,2023,"HIV, MASLD, NAFLD, gut microbiome, microbiome",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,HIV+ MASLD-,HIV+ MASLD+,Participants living with HIV (PLWH) and Metabolic dysfunction-associated steatotic liver disease (MASLD).,30,30,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure S2,5 May 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe analysis graph indicating differentially abundant bacterial genera between the different study groups. Only those genus whose LDA score was greater than 4 have been represented.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. 2-3,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|909932|1843488|909930|904;3379134|976|200643|171549|171552|1283313;1783272|1239|909932|909929|1843491|82373;1783272|544448|31969|186332|186333|2152;1783272|1239|526524|526525|2810280|135858;1783272|201174|84998|84999|84107|102106;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|909929|1843491|52225;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|577309;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|59823;3379134|976|200643|171549|171552|838|1486938;3379134|1224|1236|135624|83763|83770;3379134|1224|28216|80840|995019|40544;1783272|1239|909932|1843489|31977|39948;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:38162648/3/1,38162648,"cross-sectional observational, not case-control",38162648,10.3389/fimmu.2023.1297378,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10755913/,"Martínez-Sanz J., Talavera-Rodríguez A., Díaz-Álvarez J., Rosas Cancio-Suárez M., Rodríguez J.M., Alba C., Montes M.L., Martín-Mateos R., Burgos-Santamaría D., Moreno S., Serrano-Villar S. , Sánchez-Conde M.",A gut microbiome signature for HIV and metabolic dysfunction-associated steatotic liver disease,Frontiers in immunology,2023,"HIV, MASLD, NAFLD, gut microbiome, microbiome",Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,HIV+ MASLD-,HIV- MASLD+,Participants with Metabolic dysfunction-associated steatotic liver disease (MASLD) without HIV infection.,30,20,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure S2,5 May 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe analysis graph indicating differentially abundant bacterial genera between the different study groups. Only those genus whose LDA score was greater than 4 have been represented.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:352,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",1783272|1239|186801|186802|216572|1508657;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|1903409|53335;1783272|1239|186801|186802|31979|1485|1262798;3379134|1224|1236|91347|1903411|629;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|1766253;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|841;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|216572|292632;1783272|1239|91061|186826|33958|46255,Complete,Svetlana up
bsdb:38162648/3/2,38162648,"cross-sectional observational, not case-control",38162648,10.3389/fimmu.2023.1297378,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10755913/,"Martínez-Sanz J., Talavera-Rodríguez A., Díaz-Álvarez J., Rosas Cancio-Suárez M., Rodríguez J.M., Alba C., Montes M.L., Martín-Mateos R., Burgos-Santamaría D., Moreno S., Serrano-Villar S. , Sánchez-Conde M.",A gut microbiome signature for HIV and metabolic dysfunction-associated steatotic liver disease,Frontiers in immunology,2023,"HIV, MASLD, NAFLD, gut microbiome, microbiome",Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,HIV+ MASLD-,HIV- MASLD+,Participants with Metabolic dysfunction-associated steatotic liver disease (MASLD) without HIV infection.,30,20,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure S2,5 May 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe analysis graph indicating differentially abundant bacterial genera between the different study groups. Only those genus whose LDA score was greater than 4 have been represented.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. 2-3,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|909932|1843488|909930|904;3379134|976|200643|171549|171552|1283313;1783272|1239|909932|909929|1843491|82373;1783272|544448|31969|186332|186333|2152;1783272|1239|526524|526525|2810280|135858;1783272|201174|84998|84999|84107|102106;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|909929|1843491|52225;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|577309;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|59823;3379134|976|200643|171549|171552|838|1486938;3379134|1224|1236|135624|83763|83770;3379134|1224|28216|80840|995019|40544;1783272|1239|909932|1843489|31977|39948;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:38166904/1/1,38166904,"cross-sectional observational, not case-control",38166904,10.1186/s12890-023-02825-6,NA,"Luan J., Zhang F., Suo L., Zhang W., Li Y., Yu X., Liu B. , Cao H.",Analyzing lung cancer risks in patients with impaired pulmonary function through characterization of gut microbiome and metabolites,BMC pulmonary medicine,2024,"Biomarkers, Gut microbiota, Lung cancer, Metabolomics, Pulmonary function",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Lung cancer,MONDO:0008903,Benign pulmonary diseases (N group),Lung cancer (L group),"Lung cancer patients graded according to the American Thoracic Society/ European Respiratory Society (ATS/ERS) five level classification method for pulmonary ventilation impairment and divided into 3 groups, including 20 patients with normal lung ventilation, 23 patients with mild pulmonary ventilation dysfunction and 12 patients with moderate or above pulmonary ventilation dysfunction.",28,55,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,figure 2b,21 March 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,Scholastica,WikiWorks",Differential taxa at the genus level analyzed by linear discriminant analysis (LDA) scores in lung cancer patients (C) versus benign diseases patients(N),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:38166904/1/2,38166904,"cross-sectional observational, not case-control",38166904,10.1186/s12890-023-02825-6,NA,"Luan J., Zhang F., Suo L., Zhang W., Li Y., Yu X., Liu B. , Cao H.",Analyzing lung cancer risks in patients with impaired pulmonary function through characterization of gut microbiome and metabolites,BMC pulmonary medicine,2024,"Biomarkers, Gut microbiota, Lung cancer, Metabolomics, Pulmonary function",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Lung cancer,MONDO:0008903,Benign pulmonary diseases (N group),Lung cancer (L group),"Lung cancer patients graded according to the American Thoracic Society/ European Respiratory Society (ATS/ERS) five level classification method for pulmonary ventilation impairment and divided into 3 groups, including 20 patients with normal lung ventilation, 23 patients with mild pulmonary ventilation dysfunction and 12 patients with moderate or above pulmonary ventilation dysfunction.",28,55,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,figure 2b,21 March 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,Scholastica,WikiWorks,Tosin",Differential taxa at the genus level analyzed by linear discriminant analysis (LDA) scores in lung cancer patients (C) versus benign diseases patients(N),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Kurthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:352",1783272|1239|186801|3085636|186803|572511;1783272|1239|91061|186826|186828|2747;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|1407607;1783272|1239|91061|1385|186818|1649;1783272|1239|186801|3085636|186803|1164882;1783272|201174|1760|85009|31957|1743;1783272|1239|186801|186802|216572|1263|438033;1783272|1239|186801|186802|216572|292632;1783272|201174|84998|84999|1643824;1783272|1239|186801|186802|31979|1485|1262798,Complete,Svetlana up
bsdb:38171017/1/1,38171017,laboratory experiment,38171017,https://doi.org/10.1128/spectrum.02037-23,NA,"Matějková T., Dodoková A., Kreisinger J., Stopka P. , Stopková R.","Microbial, proteomic, and metabolomic profiling of the estrous cycle in wild house mice",Microbiology spectrum,2024,"16S RNA sequencing, Mus musculus, Pasteurellaceae, estrous cycle, estrus, microbiome, oral, proteome, saliva, vaginal",Experiment 1,Czechia,Mus musculus,"Vagina,Saliva","UBERON:0000996,UBERON:0001836",Sampling site,EFO:0000688,Oral (saliva),Vagina,Vaginal samples of lived-trapped females of Mus musculus musculus mice,18,18,NA,16S,34,Illumina,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 1,Figure 3B,20 March 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,Scholastica,WikiWorks",Bacterial taxa identified by ANCOM exhibiting significant abundance in oral compared to vaginal samples,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",1783272|1239|91061|186826|81852|1350;3379134|976|200643|171549|2005473,Complete,Svetlana up
bsdb:38171017/1/2,38171017,laboratory experiment,38171017,https://doi.org/10.1128/spectrum.02037-23,NA,"Matějková T., Dodoková A., Kreisinger J., Stopka P. , Stopková R.","Microbial, proteomic, and metabolomic profiling of the estrous cycle in wild house mice",Microbiology spectrum,2024,"16S RNA sequencing, Mus musculus, Pasteurellaceae, estrous cycle, estrus, microbiome, oral, proteome, saliva, vaginal",Experiment 1,Czechia,Mus musculus,"Vagina,Saliva","UBERON:0000996,UBERON:0001836",Sampling site,EFO:0000688,Oral (saliva),Vagina,Vaginal samples of lived-trapped females of Mus musculus musculus mice,18,18,NA,16S,34,Illumina,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 2,Figure 3B,20 March 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,Scholastica,WikiWorks",Bacterial taxa identified by ANCOM exhibiting significant abundance in oral compared to vaginal samples,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Muribacter",1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|1300|1301;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|186826|33958|1578;3379134|1224|28211|356|119045|407;3379134|1224|28211|356|41294|374;3379134|1224|1236|135625|712|1857532,Complete,Svetlana up
bsdb:38171017/2/1,38171017,laboratory experiment,38171017,https://doi.org/10.1128/spectrum.02037-23,NA,"Matějková T., Dodoková A., Kreisinger J., Stopka P. , Stopková R.","Microbial, proteomic, and metabolomic profiling of the estrous cycle in wild house mice",Microbiology spectrum,2024,"16S RNA sequencing, Mus musculus, Pasteurellaceae, estrous cycle, estrus, microbiome, oral, proteome, saliva, vaginal",Experiment 2,Czechia,Mus musculus,Vagina,UBERON:0000996,Sampling time,EFO:0000689,Vaginal estrus samples,Vaginal metestrus samples,Vaginal samples collected during the metestrus phase,18,18,NA,16S,34,Illumina,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 1,Figure 5D,20 March 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,Scholastica,WikiWorks",Bacterial taxa identified by ANCOM exhibiting significant abundance in estrus compared to metestrus phase,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",3379134|1224|28216|80840|75682|149698;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:38171017/2/2,38171017,laboratory experiment,38171017,https://doi.org/10.1128/spectrum.02037-23,NA,"Matějková T., Dodoková A., Kreisinger J., Stopka P. , Stopková R.","Microbial, proteomic, and metabolomic profiling of the estrous cycle in wild house mice",Microbiology spectrum,2024,"16S RNA sequencing, Mus musculus, Pasteurellaceae, estrous cycle, estrus, microbiome, oral, proteome, saliva, vaginal",Experiment 2,Czechia,Mus musculus,Vagina,UBERON:0000996,Sampling time,EFO:0000689,Vaginal estrus samples,Vaginal metestrus samples,Vaginal samples collected during the metestrus phase,18,18,NA,16S,34,Illumina,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 2,Figure 5D,20 March 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,Scholastica,WikiWorks",Bacterial taxa identified by ANCOM exhibiting significant abundance in estrus compared to metestrus phase,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Muribacter,3379134|1224|1236|135625|712|1857532,Complete,Svetlana up
bsdb:38172649/1/1,38172649,laboratory experiment,38172649,https://doi.org/10.1186/s12866-023-03161-9,NA,"Shaw C.G., Pavloudi C., Crow R.S., Saw J.H. , Smith L.C.","Spotting disease disrupts the microbiome of infected purple sea urchins, Strongylocentrotus purpuratus",BMC microbiology,2024,"16S rRNA, Disease, Infection, Lesion, Microbiome, Pathogenic",Experiment 1,United States of America,Strongylocentrotus purpuratus,Body external integument structure,UBERON:3000977,Animal disease,EFO:0005932,Healthy sea urchins,Diseased sea urchins,Sea urchins with spotting disease,4,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,Supplementary Table S3,20 March 2024,Ndruscilla,"Ndruscilla,Scholastica,WikiWorks",Significantly differentially abundant taxa as identified by LEfSe for diseased versus healthy global surface microbiome samples,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Lutibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Pseudoteredinibacter,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cyclobacteriaceae",3379134|976|117743|200644|49546|358023;3379134|1224|1236|1706369|1706371|1122284;3379134|976|768503|768507|563798,Complete,Svetlana up
bsdb:38172649/1/2,38172649,laboratory experiment,38172649,https://doi.org/10.1186/s12866-023-03161-9,NA,"Shaw C.G., Pavloudi C., Crow R.S., Saw J.H. , Smith L.C.","Spotting disease disrupts the microbiome of infected purple sea urchins, Strongylocentrotus purpuratus",BMC microbiology,2024,"16S rRNA, Disease, Infection, Lesion, Microbiome, Pathogenic",Experiment 1,United States of America,Strongylocentrotus purpuratus,Body external integument structure,UBERON:3000977,Animal disease,EFO:0005932,Healthy sea urchins,Diseased sea urchins,Sea urchins with spotting disease,4,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 2,Supplementary Table S3,20 March 2024,Ndruscilla,"Ndruscilla,Scholastica,WikiWorks",Significantly differentially abundant taxa as identified by LEfSe for diseased versus healthy global surface microbiome samples,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales",3379134|1224|1236|91347;1783272|1798710|1906119,Complete,Svetlana up
bsdb:38172649/2/1,38172649,laboratory experiment,38172649,https://doi.org/10.1186/s12866-023-03161-9,NA,"Shaw C.G., Pavloudi C., Crow R.S., Saw J.H. , Smith L.C.","Spotting disease disrupts the microbiome of infected purple sea urchins, Strongylocentrotus purpuratus",BMC microbiology,2024,"16S rRNA, Disease, Infection, Lesion, Microbiome, Pathogenic",Experiment 2,United States of America,Strongylocentrotus purpuratus,Body external integument structure,UBERON:3000977,Sampling site,EFO:0000688,Lesion surface samples (LS),Lesion body wall samples (LBW),Lesion body wall samples from sea urchins with spotting disease,5,7,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,Supplementary Table S6,1 August 2024,Scholastica,"Scholastica,WikiWorks",Significantly differentially abundant taxa as identified by LEFSe for the lesion surface (LS) versus lesion body wall (LBW) microbiome samples,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Candidatus Photodesmus,3379134|1224|1236|135623|641|1076727,Complete,Svetlana up
bsdb:38172649/2/2,38172649,laboratory experiment,38172649,https://doi.org/10.1186/s12866-023-03161-9,NA,"Shaw C.G., Pavloudi C., Crow R.S., Saw J.H. , Smith L.C.","Spotting disease disrupts the microbiome of infected purple sea urchins, Strongylocentrotus purpuratus",BMC microbiology,2024,"16S rRNA, Disease, Infection, Lesion, Microbiome, Pathogenic",Experiment 2,United States of America,Strongylocentrotus purpuratus,Body external integument structure,UBERON:3000977,Sampling site,EFO:0000688,Lesion surface samples (LS),Lesion body wall samples (LBW),Lesion body wall samples from sea urchins with spotting disease,5,7,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 2,Supplementary Table S6,1 August 2024,Scholastica,"Scholastica,WikiWorks",Significantly differentially abundant taxa as identified by LEFSe for the lesion surface (LS) versus lesion body wall (LBW) microbiome samples,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Pseudophaeobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Roseobacter",3379134|1224|1236|1706369|1706371;3379134|1224|28211|204455|31989|1541822;3379134|1224|1236;3379134|1224|28211|204455|2854170|2433,Complete,Svetlana up
bsdb:38172649/3/1,38172649,laboratory experiment,38172649,https://doi.org/10.1186/s12866-023-03161-9,NA,"Shaw C.G., Pavloudi C., Crow R.S., Saw J.H. , Smith L.C.","Spotting disease disrupts the microbiome of infected purple sea urchins, Strongylocentrotus purpuratus",BMC microbiology,2024,"16S rRNA, Disease, Infection, Lesion, Microbiome, Pathogenic",Experiment 3,United States of America,Strongylocentrotus purpuratus,"Coelomic fluid,Body wall","UBERON:0036217,UBERON:0000309",Sampling site,EFO:0000688,Healthy coelomic fluid (HCF),Diseased coelomic fluid (DCF) and lesion body wall (LBW),Diseased coelomic fluid (DCF) and lesion body wall (LBW) samples from sea urchins with spotting disease,3,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table S9,1 August 2024,Scholastica,"Scholastica,WikiWorks",Significantly differentially abundance taxa as identified by LEfSe in the tissue microbiome samples,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium",1783272|201174|1760|85006|85023|33882;3379134|976|200643;1783272|201174|1760|85006|85019|1696,Complete,Svetlana up
bsdb:38172649/4/1,38172649,laboratory experiment,38172649,https://doi.org/10.1186/s12866-023-03161-9,NA,"Shaw C.G., Pavloudi C., Crow R.S., Saw J.H. , Smith L.C.","Spotting disease disrupts the microbiome of infected purple sea urchins, Strongylocentrotus purpuratus",BMC microbiology,2024,"16S rRNA, Disease, Infection, Lesion, Microbiome, Pathogenic",Experiment 4,United States of America,Strongylocentrotus purpuratus,"Coelomic fluid,Body wall","UBERON:0036217,UBERON:0000309",Sampling site,EFO:0000688,Healthy coelomic fluid (HCF) and diseased coelomic fluid (DCF),Lesion body wall (LBW),Lesion body wall (LBW) samples from sea urchins with spotting disease,6,7,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table S9,1 August 2024,Scholastica,"Scholastica,WikiWorks",Significantly differentially abundance taxa as identified by LEfSe in the tissue microbiome samples,increased,"k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cyclobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Candidatus Photodesmus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Cryomorphaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Pseudoteredinibacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Lutibacter",3379134|976|768503|768507|563798;3379134|1224|1236|135623|641|1076727;3379134|976|117743|200644|246874;3379134|1224|1236|135623|641|662;3379134|1224|1236|1706369|1706371|1122284;3379134|976|117743|200644|49546|358023,Complete,Svetlana up
bsdb:38172649/5/1,38172649,laboratory experiment,38172649,https://doi.org/10.1186/s12866-023-03161-9,NA,"Shaw C.G., Pavloudi C., Crow R.S., Saw J.H. , Smith L.C.","Spotting disease disrupts the microbiome of infected purple sea urchins, Strongylocentrotus purpuratus",BMC microbiology,2024,"16S rRNA, Disease, Infection, Lesion, Microbiome, Pathogenic",Experiment 5,United States of America,Strongylocentrotus purpuratus,"Coelomic fluid,Body wall","UBERON:0036217,UBERON:0000309",Sampling site,EFO:0000688,Healthy coelomic fluid (HCF) and lesion body wall (LBW),Diseased coelomic fluid (DCF),Diseased coelomic fluid (DCF) samples from sea urchins with spotting disease,10,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table S9,1 August 2024,Scholastica,"Scholastica,WikiWorks",Significantly differentially abundance taxa as identified by LEfSe in the tissue microbiome samples,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae|g__Pseudoalteromonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Pseudophaeobacter",3379134|1224|1236|135622|267888|53246;3379134|1224|28211|204455|31989|1541822,Complete,Svetlana up
bsdb:38172680/1/1,38172680,case-control,38172680,https://doi.org/10.1186/s12866-023-03157-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-03157-5,"Aya Ishizaka, Eisuke Adachi, Hiroshi Yotsuyanagi, Kiyoko Iwatsuki-Horimoto, Michiko Koga, Seiya Yamayoshi, Taketoshi Mizutani, Yoshihiro Kawaoka, Yutaka Suzuki",Association of gut microbiota with the pathogenesis of SARS-CoV-2 Infection in people living with HIV,BMC microbiology,2024,"SARS-CoV-2, COVID-19, HIV, Microbiota, Post-acute COVID-19 syndrome",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,SARS coronavirus,NCBITAXON:694009,SARS-CoV-2-uninfected PLWH (< 8 days),SARS-CoV-2-infected PLWH (< 8 days),Hospitalized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected PLWH  (People living with HIV) within 7 days of COVID-19 onset (< 8 days),10,10,NA,16S,34,Illumina,relative abundances,"LEfSe,MaAsLin2",0.05,FALSE,3,NA,body mass index,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2C,21 March 2024,Ardeybisi,"Ardeybisi,Adenike Oladimeji-Kasumu,WikiWorks",Changes in gut microbiota in SARS-CoV-2 infected PLWH were analyzed using linear discriminant analysis (LDA) effect size in comparison with the SARS-CoV-2 uninfected PLWH within 7 days of COVID-19 onset.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae",1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|186802|216572|1263|41978;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815,Complete,Svetlana up
bsdb:38172680/1/2,38172680,case-control,38172680,https://doi.org/10.1186/s12866-023-03157-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-03157-5,"Aya Ishizaka, Eisuke Adachi, Hiroshi Yotsuyanagi, Kiyoko Iwatsuki-Horimoto, Michiko Koga, Seiya Yamayoshi, Taketoshi Mizutani, Yoshihiro Kawaoka, Yutaka Suzuki",Association of gut microbiota with the pathogenesis of SARS-CoV-2 Infection in people living with HIV,BMC microbiology,2024,"SARS-CoV-2, COVID-19, HIV, Microbiota, Post-acute COVID-19 syndrome",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,SARS coronavirus,NCBITAXON:694009,SARS-CoV-2-uninfected PLWH (< 8 days),SARS-CoV-2-infected PLWH (< 8 days),Hospitalized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected PLWH  (People living with HIV) within 7 days of COVID-19 onset (< 8 days),10,10,NA,16S,34,Illumina,relative abundances,"LEfSe,MaAsLin2",0.05,FALSE,3,NA,body mass index,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2C,21 March 2024,Ardeybisi,"Ardeybisi,Adenike Oladimeji-Kasumu,WikiWorks",Changes in gut microbiota in SARS-CoV-2 infected PLWH were analyzed using linear discriminant analysis (LDA) effect size in comparison with the SARS-CoV-2 uninfected PLWH within 7 days of COVID-19 onset.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|s__Peptostreptococcaceae bacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|3085636|186803|1407607;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|909929|1843491|52225;1783272|1239|186801|3082720|186804|1904861;1783272|1239|909932|1843489|31977,Complete,Svetlana up
bsdb:38172680/2/1,38172680,case-control,38172680,https://doi.org/10.1186/s12866-023-03157-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-03157-5,"Aya Ishizaka, Eisuke Adachi, Hiroshi Yotsuyanagi, Kiyoko Iwatsuki-Horimoto, Michiko Koga, Seiya Yamayoshi, Taketoshi Mizutani, Yoshihiro Kawaoka, Yutaka Suzuki",Association of gut microbiota with the pathogenesis of SARS-CoV-2 Infection in people living with HIV,BMC microbiology,2024,"SARS-CoV-2, COVID-19, HIV, Microbiota, Post-acute COVID-19 syndrome",Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,SARS coronavirus,NCBITAXON:694009,SARS-CoV-2-uninfected PLWH (8–14 days),SARS-CoV-2-infected PLWH (8–14 days),Hospitalized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected PLWH (People living with HIV) 8 − 14 days after COVID-19 onset,9,9,NA,16S,34,Illumina,relative abundances,"LEfSe,MaAsLin2",0.05,FALSE,3,NA,body mass index,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2D,8 April 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,WikiWorks",Changes in gut microbiota in SARS-CoV-2 infected PLWH were analyzed using linear discriminant analysis (LDA) effect size in comparison with the SARS-CoV-2 uninfected PLWH  8−14 days after COVID-19 onset.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae",1783272|1239|186801|3085636|186803|1164882;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|3082720|543314|86331;1783272|1239|526524|526525|128827|1472649;1783272|201174|84998|1643822|1643826;1783272|201174|1760|85007|1653|1716;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815,Complete,Svetlana up
bsdb:38172680/2/2,38172680,case-control,38172680,https://doi.org/10.1186/s12866-023-03157-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-03157-5,"Aya Ishizaka, Eisuke Adachi, Hiroshi Yotsuyanagi, Kiyoko Iwatsuki-Horimoto, Michiko Koga, Seiya Yamayoshi, Taketoshi Mizutani, Yoshihiro Kawaoka, Yutaka Suzuki",Association of gut microbiota with the pathogenesis of SARS-CoV-2 Infection in people living with HIV,BMC microbiology,2024,"SARS-CoV-2, COVID-19, HIV, Microbiota, Post-acute COVID-19 syndrome",Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,SARS coronavirus,NCBITAXON:694009,SARS-CoV-2-uninfected PLWH (8–14 days),SARS-CoV-2-infected PLWH (8–14 days),Hospitalized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected PLWH (People living with HIV) 8 − 14 days after COVID-19 onset,9,9,NA,16S,34,Illumina,relative abundances,"LEfSe,MaAsLin2",0.05,FALSE,3,NA,body mass index,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2D,8 April 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,WikiWorks",Changes in gut microbiota in SARS-CoV-2 infected PLWH were analyzed using linear discriminant analysis (LDA) effect size in comparison with the SARS-CoV-2 uninfected PLWH  8−14 days after COVID-19 onset.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes",1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843488|909930|904;1783272|1239|909932|1843489|31977;1783272|1239|909932|909929;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|207244,Complete,Svetlana up
bsdb:38172680/3/1,38172680,case-control,38172680,https://doi.org/10.1186/s12866-023-03157-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-03157-5,"Aya Ishizaka, Eisuke Adachi, Hiroshi Yotsuyanagi, Kiyoko Iwatsuki-Horimoto, Michiko Koga, Seiya Yamayoshi, Taketoshi Mizutani, Yoshihiro Kawaoka, Yutaka Suzuki",Association of gut microbiota with the pathogenesis of SARS-CoV-2 Infection in people living with HIV,BMC microbiology,2024,"SARS-CoV-2, COVID-19, HIV, Microbiota, Post-acute COVID-19 syndrome",Experiment 3,Japan,Homo sapiens,Feces,UBERON:0001988,SARS coronavirus,NCBITAXON:694009,SARS-CoV-2-uninfected PLWH (>1 M),SARS-CoV-2-infected PLWH (>1 M),Hospitalized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected PLWH (People living with HIV) over 1 month after COVID-19 onset,7,7,NA,16S,34,Illumina,relative abundances,"LEfSe,MaAsLin2",0.05,FALSE,3,NA,body mass index,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2E,8 April 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,WikiWorks",Changes in gut microbiota in SARS-CoV-2 infected PLWH were analyzed using linear discriminant analysis (LDA) effect size in comparison with the SARS-CoV-2 uninfected PLWH over 1 month after COVID-19 onset.,increased,"p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Dickeya,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Enterobacteriaceae bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",95818|2093818|2093825|2171986|1331051;3379134|1224|1236|91347|1903410|204037;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|1849603;3379134|1224|1236;3379134|1224|28211|356|82115;3379134|1224|1236|91347;3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:38172680/3/2,38172680,case-control,38172680,https://doi.org/10.1186/s12866-023-03157-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-03157-5,"Aya Ishizaka, Eisuke Adachi, Hiroshi Yotsuyanagi, Kiyoko Iwatsuki-Horimoto, Michiko Koga, Seiya Yamayoshi, Taketoshi Mizutani, Yoshihiro Kawaoka, Yutaka Suzuki",Association of gut microbiota with the pathogenesis of SARS-CoV-2 Infection in people living with HIV,BMC microbiology,2024,"SARS-CoV-2, COVID-19, HIV, Microbiota, Post-acute COVID-19 syndrome",Experiment 3,Japan,Homo sapiens,Feces,UBERON:0001988,SARS coronavirus,NCBITAXON:694009,SARS-CoV-2-uninfected PLWH (>1 M),SARS-CoV-2-infected PLWH (>1 M),Hospitalized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected PLWH (People living with HIV) over 1 month after COVID-19 onset,7,7,NA,16S,34,Illumina,relative abundances,"LEfSe,MaAsLin2",0.05,FALSE,3,NA,body mass index,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2E,8 April 2024,Adenike Oladimeji-Kasumu,"Adenike Oladimeji-Kasumu,Scholastica,WikiWorks",Changes in gut microbiota in SARS-CoV-2 infected PLWH were analyzed using linear discriminant analysis (LDA) effect size in comparison with the SARS-CoV-2 uninfected PLWH over 1 month after COVID-19 onset.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802,Complete,Svetlana up
bsdb:38172680/4/1,38172680,case-control,38172680,https://doi.org/10.1186/s12866-023-03157-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-03157-5,"Aya Ishizaka, Eisuke Adachi, Hiroshi Yotsuyanagi, Kiyoko Iwatsuki-Horimoto, Michiko Koga, Seiya Yamayoshi, Taketoshi Mizutani, Yoshihiro Kawaoka, Yutaka Suzuki",Association of gut microbiota with the pathogenesis of SARS-CoV-2 Infection in people living with HIV,BMC microbiology,2024,"SARS-CoV-2, COVID-19, HIV, Microbiota, Post-acute COVID-19 syndrome",Experiment 4,Japan,Homo sapiens,Feces,UBERON:0001988,Illness severity status,EFO:0007863,Mildly ill SARS-CoV-2-infected PLWH (8–14 days),Moderately/severely ill SARS-CoV-2-infected PLWH (8–14 days),Moderately (n = 4) and severely (n = 1) ill hospitalized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected PLWH  (People living with HIV) within 7 days of COVID-19 onset (8–14 days),6,5,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,body mass index,NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 3F,20 June 2024,Scholastica,"Scholastica,WikiWorks","Changes in the gut microbiota in PLWH-CoV (8-14 days) analyzed by linear discriminant analysis (LDA) effect size, compared by disease severity (mild, n = 6 vs. moderate/severe, n = 5)",increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,1783272|1239|186801|186802|216572|244127,Complete,Svetlana up
bsdb:38172680/4/2,38172680,case-control,38172680,https://doi.org/10.1186/s12866-023-03157-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-03157-5,"Aya Ishizaka, Eisuke Adachi, Hiroshi Yotsuyanagi, Kiyoko Iwatsuki-Horimoto, Michiko Koga, Seiya Yamayoshi, Taketoshi Mizutani, Yoshihiro Kawaoka, Yutaka Suzuki",Association of gut microbiota with the pathogenesis of SARS-CoV-2 Infection in people living with HIV,BMC microbiology,2024,"SARS-CoV-2, COVID-19, HIV, Microbiota, Post-acute COVID-19 syndrome",Experiment 4,Japan,Homo sapiens,Feces,UBERON:0001988,Illness severity status,EFO:0007863,Mildly ill SARS-CoV-2-infected PLWH (8–14 days),Moderately/severely ill SARS-CoV-2-infected PLWH (8–14 days),Moderately (n = 4) and severely (n = 1) ill hospitalized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected PLWH  (People living with HIV) within 7 days of COVID-19 onset (8–14 days),6,5,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,body mass index,NA,decreased,NA,NA,NA,decreased,Signature 2,Figure 3F,20 June 2024,Scholastica,"Scholastica,WikiWorks","Changes in the gut microbiota in PLWH-CoV (8-14 days) analyzed by linear discriminant analysis (LDA) effect size, compared by disease severity (mild, n = 6 vs. moderate/severe, n = 5)",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",3379134|976|200643|171549|171552|1283313;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;3379134|1224|1236|135625|712;3379134|1224|1236|135625;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801;1783272|1239|186801|186802;3379134|1224|1236|135625|712,Complete,Svetlana up
bsdb:38183473/1/1,38183473,case-control,38183473,10.1007/s00253-023-12845-1,NA,"Jinato T., Anuntakarun S., Satthawiwat N., Chuaypen N. , Tangkijvanich P.",Distinct alterations of gut microbiota between viral- and non-viral-related hepatocellular carcinoma,Applied microbiology and biotechnology,2024,"16 s rRNA, Biomarker, Gut dysbiosis, HCC, NAFLD, Viral hepatitis",Experiment 1,Thailand,Homo sapiens,Feces,UBERON:0001988,Hepatocellular carcinoma,EFO:0000182,Healthy controls,Patients with Hepatocellular carcinoma (HCC),"patients with viral related hepatocellular carcinoma or non-hepatitis B-, non-hepatitis C-related hepatocellular carcinoma whose diagnosis of HCC was documented by dynamic computed tomography (CT) and/or magnetic resonance imaging (MRI) regarding the clinical guideline of the American Association for the Study of Liver Diseases (AASLD)",16,51,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,25 April 2024,Idiaru angela,"Idiaru angela,WikiWorks",The significant taxa from the top 50 relative abundance genus level compared between healthy controls and Hepatocellular carcinoma patients.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",3379134|976|200643|171549|815|816;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|909932|1843489|31977|29465;1783272|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:38183473/1/2,38183473,case-control,38183473,10.1007/s00253-023-12845-1,NA,"Jinato T., Anuntakarun S., Satthawiwat N., Chuaypen N. , Tangkijvanich P.",Distinct alterations of gut microbiota between viral- and non-viral-related hepatocellular carcinoma,Applied microbiology and biotechnology,2024,"16 s rRNA, Biomarker, Gut dysbiosis, HCC, NAFLD, Viral hepatitis",Experiment 1,Thailand,Homo sapiens,Feces,UBERON:0001988,Hepatocellular carcinoma,EFO:0000182,Healthy controls,Patients with Hepatocellular carcinoma (HCC),"patients with viral related hepatocellular carcinoma or non-hepatitis B-, non-hepatitis C-related hepatocellular carcinoma whose diagnosis of HCC was documented by dynamic computed tomography (CT) and/or magnetic resonance imaging (MRI) regarding the clinical guideline of the American Association for the Study of Liver Diseases (AASLD)",16,51,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,25 April 2024,Idiaru angela,"Idiaru angela,WikiWorks",The significant taxa from the top 50 relative abundance genus level compared between healthy controls and Hepatocellular carcinoma patients.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136",1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3082720|186804|1501226;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|877420,Complete,Svetlana up
bsdb:38183473/2/1,38183473,case-control,38183473,10.1007/s00253-023-12845-1,NA,"Jinato T., Anuntakarun S., Satthawiwat N., Chuaypen N. , Tangkijvanich P.",Distinct alterations of gut microbiota between viral- and non-viral-related hepatocellular carcinoma,Applied microbiology and biotechnology,2024,"16 s rRNA, Biomarker, Gut dysbiosis, HCC, NAFLD, Viral hepatitis",Experiment 2,Thailand,Homo sapiens,Feces,UBERON:0001988,Hepatitis virus-related hepatocellular carcinoma,EFO:0008505,viral-related Hepatocellular carcinoma,"non-hepatitis B-, non-hepatitis C-related Hepatocellular carcinoma","Patients with non-hepatitis B-, non-hepatitis C-related Hepatocellular carcinoma whose  diagnosis of HCC was documented by dynamic computed tomography (CT) and/or magnetic resonance imaging (MRI) regarding the clinical guideline of the American Association for the Study of Liver Diseases (AASLD)",33,18,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,decreased,NA,NA,Signature 1,Table 3,26 April 2024,Idiaru angela,"Idiaru angela,WikiWorks",The significant taxa from the top 50 relative abundance genus level compared between Viral- and NBNC-HCC,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",3379134|976|200643|171549|815|816;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|2316020|33038;3379134|976|200643|171549|2005525|375288;1783272|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:38183473/2/2,38183473,case-control,38183473,10.1007/s00253-023-12845-1,NA,"Jinato T., Anuntakarun S., Satthawiwat N., Chuaypen N. , Tangkijvanich P.",Distinct alterations of gut microbiota between viral- and non-viral-related hepatocellular carcinoma,Applied microbiology and biotechnology,2024,"16 s rRNA, Biomarker, Gut dysbiosis, HCC, NAFLD, Viral hepatitis",Experiment 2,Thailand,Homo sapiens,Feces,UBERON:0001988,Hepatitis virus-related hepatocellular carcinoma,EFO:0008505,viral-related Hepatocellular carcinoma,"non-hepatitis B-, non-hepatitis C-related Hepatocellular carcinoma","Patients with non-hepatitis B-, non-hepatitis C-related Hepatocellular carcinoma whose  diagnosis of HCC was documented by dynamic computed tomography (CT) and/or magnetic resonance imaging (MRI) regarding the clinical guideline of the American Association for the Study of Liver Diseases (AASLD)",33,18,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,decreased,NA,NA,Signature 2,Table 3,26 April 2024,Idiaru angela,"Idiaru angela,WikiWorks",The significant taxa from the top 50 relative abundance genus level compared between Viral- and NBNC-HCC,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1766253;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|292632;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|186802|216572|1263|438033,Complete,Svetlana up
bsdb:38183473/3/1,38183473,case-control,38183473,10.1007/s00253-023-12845-1,NA,"Jinato T., Anuntakarun S., Satthawiwat N., Chuaypen N. , Tangkijvanich P.",Distinct alterations of gut microbiota between viral- and non-viral-related hepatocellular carcinoma,Applied microbiology and biotechnology,2024,"16 s rRNA, Biomarker, Gut dysbiosis, HCC, NAFLD, Viral hepatitis",Experiment 3,Thailand,Homo sapiens,Feces,UBERON:0001988,Hepatitis virus-related hepatocellular carcinoma,EFO:0008505,viral-related Hepatocellular carcinoma,"non-hepatitis B-, non-hepatitis C-related Hepatocellular carcinoma","Patients with non-hepatitis B-, non-hepatitis C-related Hepatocellular carcinoma whose  diagnosis of HCC was documented by dynamic computed tomography (CT) and/or magnetic resonance imaging (MRI) regarding the clinical guideline of the American Association for the Study of Liver Diseases (AASLD)",33,18,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,unchanged,decreased,NA,NA,Signature 1,Figure 4B,26 April 2024,Idiaru angela,"Idiaru angela,WikiWorks",LEfSe identifies the microbiota that differed the most between NBNC-HCC and Viral-HCC,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",1783272|1239|186801|186802|31979;1783272|1239|186801|186802;1783272|1239|186801|186802|216572;1783272|1239|91061|186826;1783272|1239|91061|186826|186828;1783272|1239|91061|186826|186828|117563;1783272|1239;1783272|1239|186801|3082720|186804,Complete,Svetlana up
bsdb:38183473/3/2,38183473,case-control,38183473,10.1007/s00253-023-12845-1,NA,"Jinato T., Anuntakarun S., Satthawiwat N., Chuaypen N. , Tangkijvanich P.",Distinct alterations of gut microbiota between viral- and non-viral-related hepatocellular carcinoma,Applied microbiology and biotechnology,2024,"16 s rRNA, Biomarker, Gut dysbiosis, HCC, NAFLD, Viral hepatitis",Experiment 3,Thailand,Homo sapiens,Feces,UBERON:0001988,Hepatitis virus-related hepatocellular carcinoma,EFO:0008505,viral-related Hepatocellular carcinoma,"non-hepatitis B-, non-hepatitis C-related Hepatocellular carcinoma","Patients with non-hepatitis B-, non-hepatitis C-related Hepatocellular carcinoma whose  diagnosis of HCC was documented by dynamic computed tomography (CT) and/or magnetic resonance imaging (MRI) regarding the clinical guideline of the American Association for the Study of Liver Diseases (AASLD)",33,18,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,unchanged,decreased,NA,NA,Signature 2,Figure 4B,26 April 2024,Idiaru angela,"Idiaru angela,WikiWorks",LEfSe identifies the microbiota that differed the most between NBNC-HCC and Viral-HCC,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",1783272|1239|186801|3085636;1783272|1239|186801|3085636|186803;3379134|976;3379134|976|200643;3379134|976|200643|171549;3379134|976|200643|171549|171552,Complete,Svetlana up
bsdb:38183473/4/NA,38183473,case-control,38183473,10.1007/s00253-023-12845-1,NA,"Jinato T., Anuntakarun S., Satthawiwat N., Chuaypen N. , Tangkijvanich P.",Distinct alterations of gut microbiota between viral- and non-viral-related hepatocellular carcinoma,Applied microbiology and biotechnology,2024,"16 s rRNA, Biomarker, Gut dysbiosis, HCC, NAFLD, Viral hepatitis",Experiment 4,Thailand,Homo sapiens,Feces,UBERON:0001988,Hepatocellular carcinoma,EFO:0000182,Healthy controls,"non-hepatitis B-, non-hepatitis C-related Hepatocellular carcinoma","Patients with non-hepatitis B-, non-hepatitis C-related Hepatocellular carcinoma whose diagnosis of HCC was documented by dynamic computed tomography (CT) and/or magnetic resonance imaging (MRI) regarding the clinical guideline of the American Association for the Study of Liver Diseases (AASLD)",16,18,2 weeks,16S,34,Illumina,relative abundances,NA,0.05,NA,NA,NA,NA,NA,decreased,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:38183473/5/NA,38183473,case-control,38183473,10.1007/s00253-023-12845-1,NA,"Jinato T., Anuntakarun S., Satthawiwat N., Chuaypen N. , Tangkijvanich P.",Distinct alterations of gut microbiota between viral- and non-viral-related hepatocellular carcinoma,Applied microbiology and biotechnology,2024,"16 s rRNA, Biomarker, Gut dysbiosis, HCC, NAFLD, Viral hepatitis",Experiment 5,Thailand,Homo sapiens,Feces,UBERON:0001988,Hepatitis virus-related hepatocellular carcinoma,EFO:0008505,Hepatitis-B virus related Hepatocellular carcinoma,"non-hepatitis B-, non-hepatitis C-related Hepatocellular carcinoma","Patients with non-hepatitis B-, non-hepatitis C-related Hepatocellular carcinoma whose diagnosis of HCC was documented by dynamic computed tomography (CT) and/or magnetic resonance imaging (MRI) regarding the clinical guideline of the American Association for the Study of Liver Diseases (AASLD)",17,18,2 weeks,16S,34,Illumina,relative abundances,NA,0.05,NA,NA,NA,NA,NA,decreased,unchanged,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:38189294/1/1,38189294,case-control,38189294,https://doi.org/10.1128/spectrum.01006-23,NA,"Zhang J., Shi M., Zhao C., Liang G., Li C., Ge X., Pei C., Kong Y., Li D., Yang W., Cao B., Fu L., Yan Y., Wu J., Zhou J., Fang Y., Meng X., Li Y. , Wang L.",Role of intestinal flora in the development of nonalcoholic fatty liver disease in children,Microbiology spectrum,2024,"BMI, NAFLD, NASH, children, gut microbiota, metabolism",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,Healthy controls,Non-alcoholic fatty liver disease (NAFLD),Pediatric patients with non-alcoholic fatty liver disease (NAFLD) whose body mass index (BMI) was higher than the 95th percentile and defined through a clinical evaluation and liver ultrasonography,35,79,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Fig 3,14 March 2024,Scholastica,"Scholastica,WikiWorks",Multiple bacterial species with significantly different abundance found in the intestinal flora of patients with non-alcoholic fatty liver disease (NAFLD) versus healthy controls (HCs),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota|c__Bacilli,,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__Tyzzerella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|1224|28216|80840|506;1783272|1239|91061;;3379134|1224|28216;3379134|1224|28216|80840;1783272|1239|186801|186802|3085642|580596;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|216572|946234;3384189|32066|203490|203491;3384189|32066|203490;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|2316020|33038;3379134|1224;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|3085636|186803|1506577|2053632;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:38189294/1/2,38189294,case-control,38189294,https://doi.org/10.1128/spectrum.01006-23,NA,"Zhang J., Shi M., Zhao C., Liang G., Li C., Ge X., Pei C., Kong Y., Li D., Yang W., Cao B., Fu L., Yan Y., Wu J., Zhou J., Fang Y., Meng X., Li Y. , Wang L.",Role of intestinal flora in the development of nonalcoholic fatty liver disease in children,Microbiology spectrum,2024,"BMI, NAFLD, NASH, children, gut microbiota, metabolism",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic fatty liver disease,EFO:0003095,Healthy controls,Non-alcoholic fatty liver disease (NAFLD),Pediatric patients with non-alcoholic fatty liver disease (NAFLD) whose body mass index (BMI) was higher than the 95th percentile and defined through a clinical evaluation and liver ultrasonography,35,79,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Fig 3,14 March 2024,Scholastica,"Scholastica,Ayibatari,WikiWorks",Multiple bacterial species with significantly different abundance found in the intestinal flora of patients with non-alcoholic fatty liver disease (NAFLD) versus healthy controls (HCs),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Methanobacteriati|p__Methanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptoclostridiaceae|g__Peptoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. 2-3,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae sp. B_A14,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,s__uncultured bacterium",1783272|1239|186801|3085636|186803|207244;;3379134|976|200643|171549|2005519|397864;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|1239|186801|3082768|424536;1783272|1239|186801|3082768|990719;3379134|1224|28216|80840|80864;3379134|1224|28216|80840|80864|283;1783272|1239|186801|3085636|186803|33042;1783272|1239|909932|1843489|31977|39948;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|39496;3366610|28890;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;3379134|1224|1236|135625|712|724;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843489|31977|906;3366610|28890|183925;3366610|28890|183925|2158|2159;3366610|28890|183925|2158;3366610|28890|183925|2158|2159|2172;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171552|577309;3379134|1224|1236|135625|712;3379134|1224|1236|135625;1783272|1239|186801|3082720|3120161|1481960;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|1486938;3379134|976|200643|171549|171552;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|186802|216572|3023528;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977;1783272|1239|526524|526525|128827|331630;1783272|1239|186801|186802|216572|707003;77133,Complete,Svetlana up
bsdb:38189294/2/1,38189294,case-control,38189294,https://doi.org/10.1128/spectrum.01006-23,NA,"Zhang J., Shi M., Zhao C., Liang G., Li C., Ge X., Pei C., Kong Y., Li D., Yang W., Cao B., Fu L., Yan Y., Wu J., Zhou J., Fang Y., Meng X., Li Y. , Wang L.",Role of intestinal flora in the development of nonalcoholic fatty liver disease in children,Microbiology spectrum,2024,"BMI, NAFLD, NASH, children, gut microbiota, metabolism",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic steatohepatitis,EFO:1001249,NAFL (Non-alcoholic fatty liver) patients,NASH (Non-alcoholic steatohepatitis) patients,Non-alcoholic fatty liver disease (NAFLD) patients with the presence of hepatic steatosis with necroinflammation and hepatocellular injury with or without fibrosis,5,8,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,increased,increased,NA,increased,NA,increased,Signature 1,"Fig 4C, Fig 4D",15 March 2024,Scholastica,"Scholastica,WikiWorks",Differential diversity and multiple bacterial species with significantly different abundance found in the intestinal flora of patients with NAFL (Non-alcoholic fatty liver) compared to NASH (Non-alcoholic steatohepatitis),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 7_1_58FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",3379134|976|200643|171549|815|816|820;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|3085636|186803|658087;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3082720|186804,Complete,Svetlana up
bsdb:38189294/2/2,38189294,case-control,38189294,https://doi.org/10.1128/spectrum.01006-23,NA,"Zhang J., Shi M., Zhao C., Liang G., Li C., Ge X., Pei C., Kong Y., Li D., Yang W., Cao B., Fu L., Yan Y., Wu J., Zhou J., Fang Y., Meng X., Li Y. , Wang L.",Role of intestinal flora in the development of nonalcoholic fatty liver disease in children,Microbiology spectrum,2024,"BMI, NAFLD, NASH, children, gut microbiota, metabolism",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Non-alcoholic steatohepatitis,EFO:1001249,NAFL (Non-alcoholic fatty liver) patients,NASH (Non-alcoholic steatohepatitis) patients,Non-alcoholic fatty liver disease (NAFLD) patients with the presence of hepatic steatosis with necroinflammation and hepatocellular injury with or without fibrosis,5,8,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,increased,increased,NA,increased,NA,increased,Signature 2,"Fig 4C, Fig 4D",15 March 2024,Scholastica,"Scholastica,WikiWorks",Differential diversity and multiple bacterial species with significantly different abundance found in the intestinal flora of patients with NAFL (Non-alcoholic fatty liver) compared to NASH (Non-alcoholic steatohepatitis),decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,3379134|976|200643|171549|171550|239759,Complete,Svetlana up
bsdb:38225541/1/1,38225541,case-control,38225541,https://doi.org/10.1186/s12866-023-03173-5,NA,"Li Liu, Shangren Wang, Xiaoqiang Liu, Yang Pan",Characteristics of gut microbiota in patients with asthenozoospermia: a Chinese pilot study,BMC microbiology,2024,"16s rrna, Asthenozoospermia, Semen quality, dysbiosis, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Abnormal sperm morphology,HP:0012864,Healthy Control,Asthenozoospermia,Patients with reduced sperm mortility,60,48,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 1,Figure 5B,10 March 2024,Eve10111,"Eve10111,Folakunmi,WikiWorks",The differentially expressed gut microbiota identified by LEfSe analysis,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Pseudomonadati|p__Thermodesulfobacteriota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",1783272|1239|909932|1843488|909930;1783272|1239|909932|1843488;3379134|1224|1236|135625|712|416916;3379134|976|200643|171549|171552|1283313;3379134|1224|28211|204441|2829815|191;3379134|976|200643|171549|815|816|817;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|28026;3379134|1224|28216|80840;3379134|1224|1236|91347|543|544|546;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;3379134|200940|3031449;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|526524|526525|128827;3379134|1224|1236|91347|543|1940338;3379134|1224|1236;1783272|1239|526524|526525|128827|61170;1783272|1239|91061|186826|81850;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|2767887|1624;3379134|976|200643|171549|2005473;3379134|1224|28216|80840|995019|577310;3379134|1224|1236|135625|712;1783272|1239|909932|1843488|909930|33024;1783272|1239|909932|1843488|909930|33024|33025;3379134|1224;1783272|1239|91061|186826|1300|1301|28037;3379134|1224|28216|80840|995019;3379134|200940;1783272|1239|526524|526525|128827,Complete,Folakunmi
bsdb:38225541/1/2,38225541,case-control,38225541,https://doi.org/10.1186/s12866-023-03173-5,NA,"Li Liu, Shangren Wang, Xiaoqiang Liu, Yang Pan",Characteristics of gut microbiota in patients with asthenozoospermia: a Chinese pilot study,BMC microbiology,2024,"16s rrna, Asthenozoospermia, Semen quality, dysbiosis, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Abnormal sperm morphology,HP:0012864,Healthy Control,Asthenozoospermia,Patients with reduced sperm mortility,60,48,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 2,Figure 5B,10 March 2024,Eve10111,"Eve10111,Folakunmi,WikiWorks",The differentially expressed gut microbiota identified by LEfSe analysis,decreased,"k__Pseudomonadati|p__Acidobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales,k__Bacillati|p__Actinomycetota|c__Thermoleophilia,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|57723;3379134|1224|28211;1783272|1239;1783272|1239|526524|526525|128827;3379134|1224|28211|356;1783272|201174|1760|85009|85015;3379134|976|200643|171549|815|909656|387090;3379134|976|200643|171549|171552|838|59823;1783272|201174|1760|85009;1783272|201174|1497346;3379134|74201;3379134|976|200643|171549|171552,Complete,Folakunmi
bsdb:38226659/1/1,38226659,laboratory experiment,38226659,10.1039/d3fo04714h,NA,"He D., Gao X., Wen J., Zhang Y., Yang S., Sun X., Cui M., Li Z., Fu S., Liu J. , Liu D.",Orally administered neohesperidin attenuates MPTP-induced neurodegeneration by inhibiting inflammatory responses and regulating intestinal flora in mice,Food & function,2024,NA,Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Treatment,EFO:0000727,Saline,"1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)","1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) group administered with MPTP 25 mg kg−1 dissolved in saline, intraperitoneally",6,6,NA,16S,NA,NA,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,"Figure 5D, F and H",25 March 2025,MyleeeA,MyleeeA,Differences in the abundance of microbial taxa between Saline and MPTP groups.,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter",1783272|201174;1783272|201174|84998|1643822|1643826|447020;1783272|1239|526524|526525|128827|174708;3379134|200940|3031449|213115|194924;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|216572|119852;3379134|1224;3379134|1224|1236|2887326|468|497,Complete,Svetlana up
bsdb:38226659/1/2,38226659,laboratory experiment,38226659,10.1039/d3fo04714h,NA,"He D., Gao X., Wen J., Zhang Y., Yang S., Sun X., Cui M., Li Z., Fu S., Liu J. , Liu D.",Orally administered neohesperidin attenuates MPTP-induced neurodegeneration by inhibiting inflammatory responses and regulating intestinal flora in mice,Food & function,2024,NA,Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Treatment,EFO:0000727,Saline,"1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)","1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) group administered with MPTP 25 mg kg−1 dissolved in saline, intraperitoneally",6,6,NA,16S,NA,NA,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 2,Figure 5F and H,25 March 2025,MyleeeA,MyleeeA,Differences in the abundance of microbial taxa between Saline and MPTP groups.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:38226659/2/1,38226659,laboratory experiment,38226659,10.1039/d3fo04714h,NA,"He D., Gao X., Wen J., Zhang Y., Yang S., Sun X., Cui M., Li Z., Fu S., Liu J. , Liu D.",Orally administered neohesperidin attenuates MPTP-induced neurodegeneration by inhibiting inflammatory responses and regulating intestinal flora in mice,Food & function,2024,NA,Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Treatment,EFO:0000727,MPTP,(Neo+MPTP) NM,Donor Mice group treated with MPTP 25 mg kg−1 intraperitoneally and Neo 25 mg kg−1.,6,6,NA,16S,NA,NA,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,increased,NA,NA,increased,Signature 1,"Figure 5D, F and H",25 March 2025,MyleeeA,MyleeeA,Differences in the abundance of microbial taxa between MPTP and Neo+MPTP groups.,increased,"k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",3379134|976;1783272|1239|91061|186826|33958;3379134|976|200643|171549|2005473;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:38226659/2/2,38226659,laboratory experiment,38226659,10.1039/d3fo04714h,NA,"He D., Gao X., Wen J., Zhang Y., Yang S., Sun X., Cui M., Li Z., Fu S., Liu J. , Liu D.",Orally administered neohesperidin attenuates MPTP-induced neurodegeneration by inhibiting inflammatory responses and regulating intestinal flora in mice,Food & function,2024,NA,Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Treatment,EFO:0000727,MPTP,(Neo+MPTP) NM,Donor Mice group treated with MPTP 25 mg kg−1 intraperitoneally and Neo 25 mg kg−1.,6,6,NA,16S,NA,NA,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,increased,NA,NA,increased,Signature 2,"Figure 5D, F and H",25 March 2025,MyleeeA,MyleeeA,Differences in the abundance of microbial taxa between MPTP and Neo+MPTP groups.,decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",1783272|201174;3379134|1224;1783272|1239|526524|526525|128827;3379134|200940|3031449|213115|194924;1783272|1239|186801|186802|216572;3379134|1224|1236|2887326|468|497;1783272|201174|84998|1643822|1643826|447020;1783272|1239|526524|526525|128827|174708;1783272|1239|186801|186802|216572|119852,Complete,Svetlana up
bsdb:38226659/3/1,38226659,laboratory experiment,38226659,10.1039/d3fo04714h,NA,"He D., Gao X., Wen J., Zhang Y., Yang S., Sun X., Cui M., Li Z., Fu S., Liu J. , Liu D.",Orally administered neohesperidin attenuates MPTP-induced neurodegeneration by inhibiting inflammatory responses and regulating intestinal flora in mice,Food & function,2024,NA,Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Treatment,EFO:0000727,Saline and Neo+MPTP,MPTP,"1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) group administered with MPTP 25 mg kg−1 dissolved in saline, intraperitoneally",12,6,NA,16S,NA,NA,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,25 March 2025,MyleeeA,MyleeeA,Differences in the abundance of microbial taxa between Saline/Neo+MPTP and MPTP.,increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Macrococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Bacteroidota|c__Saprospiria|o__Saprospirales|f__Saprospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Saprospiria|o__Saprospirales,k__Pseudomonadati|p__Bacteroidota|c__Saprospiria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Sporosarcina,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae",1783272|201174|84992;1783272|201174|1760|2037;1783272|201174;1783272|201174|84998|1643822|1643826|447020;3379134|1224|28216|80840|506;1783272|1239|526524|526525|128827|174708;1783272|1239|91061|1385;3379134|1224|28216;3379134|1224|28216|80840;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;28221;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115;1783272|201174|1760|85007|85029|37914;1783272|201174|1760|85007|85029;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;3379134|1224|1236;1783272|1239|91061|1385|90964|227979;1783272|1239|91061|1385|90964|69965;3379134|1224|1236|2887326|468;3379134|1224|28216|80840|75682;3379134|1224|1236|72274;3379134|1224|1236|2887326|468|497;3379134|1224|28216|80840|119060|48736;3379134|976|1937959|1936988|89374;3379134|976|1937959|1936988;3379134|976|1937959;3379134|1224|1236|91347|543|620;1783272|1239|91061|1385|186818|1569;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;3379134|200940|3031449|213115|194924,Complete,Svetlana up
bsdb:38226659/4/1,38226659,laboratory experiment,38226659,10.1039/d3fo04714h,NA,"He D., Gao X., Wen J., Zhang Y., Yang S., Sun X., Cui M., Li Z., Fu S., Liu J. , Liu D.",Orally administered neohesperidin attenuates MPTP-induced neurodegeneration by inhibiting inflammatory responses and regulating intestinal flora in mice,Food & function,2024,NA,Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Treatment,EFO:0000727,Saline and MPTP,Neo+MPTP (NM),Donor Mice group treated with MPTP 25 mg kg−1 intraperitoneally and Neo 25 mg kg−1.,12,6,NA,16S,NA,NA,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,25 March 2025,MyleeeA,MyleeeA,Differences in the abundance of microbial taxa between Saline/MPTP and Neo+MPTP.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552,Complete,Svetlana up
bsdb:38226659/5/1,38226659,laboratory experiment,38226659,10.1039/d3fo04714h,NA,"He D., Gao X., Wen J., Zhang Y., Yang S., Sun X., Cui M., Li Z., Fu S., Liu J. , Liu D.",Orally administered neohesperidin attenuates MPTP-induced neurodegeneration by inhibiting inflammatory responses and regulating intestinal flora in mice,Food & function,2024,NA,Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Treatment,EFO:0000727,MPTP and Neo + MPTP (NM),Saline,The mice in the Saline group were administered Saline orally.,12,6,NA,16S,NA,NA,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,26 March 2025,MyleeeA,MyleeeA,Differences in the abundance of microbial taxa between Saline and MPTP/Neo+MPTP.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacillati|p__Chloroflexota|c__Chloroflexia,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Verrucomicrobiota",3379134|74201|203494|48461|1647988|239934;1783272|544448|31969|186332|186333|2086;1783272|1239|91061|186826|33958|1253;1783272|1239|91061|186826|33958|1578;3379134|74201|203494|48461|203557;1783272|544448|31969|186332|186333;3379134|1224|1236|72274|135621;3379134|74201|203494|48461;1783272|1239|91061|186826|33958;1783272|544448|31969|186332;1783272|1239|91061|186826;3379134|74201|203494;1783272|200795|32061;1783272|544448|31969;1783272|544448;3379134|74201,Complete,Svetlana up
bsdb:38229613/1/1,38229613,case-control,38229613,10.4103/aian.aian_460_23,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10789430/,"Pavan S., Gorthi S.P., Prabhu A.N., Das B., Mutreja A., Vasudevan K., Shetty V., Ramamurthy T. , Ballal M.",Dysbiosis of the Beneficial Gut Bacteria in Patients with Parkinson's Disease from India,Annals of Indian Academy of Neurology,2023,"16S rRNA gene sequencing, Parkinson's disease, dysbiosis, gut microbiota, neurodegenerative disease, stool",Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's disease,Patients with Parkinson's disease from India,13,23,1 month,16S,NA,Nanopore,relative abundances,LEfSe,0.01,TRUE,2,NA,NA,NA,increased,unchanged,increased,NA,unchanged,Signature 1,Figure 5,18 March 2024,Kaycee,"Kaycee,Peace Sandy,WikiWorks","The differences between the groups were evaluated using the linear discrimination analysis effect size (LEfSe). The bar graph shows the LDA scores of significant bacteria. The colors (Healthy = red, Parkinson = blue) represent which group was more abundant compared with the other group at the genus and family level.",increased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801;1783272|1239|186801|3082768|424536;1783272|1239|186801|186802|216572,Complete,Peace Sandy
bsdb:38229613/1/2,38229613,case-control,38229613,10.4103/aian.aian_460_23,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10789430/,"Pavan S., Gorthi S.P., Prabhu A.N., Das B., Mutreja A., Vasudevan K., Shetty V., Ramamurthy T. , Ballal M.",Dysbiosis of the Beneficial Gut Bacteria in Patients with Parkinson's Disease from India,Annals of Indian Academy of Neurology,2023,"16S rRNA gene sequencing, Parkinson's disease, dysbiosis, gut microbiota, neurodegenerative disease, stool",Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's disease,Patients with Parkinson's disease from India,13,23,1 month,16S,NA,Nanopore,relative abundances,LEfSe,0.01,TRUE,2,NA,NA,NA,increased,unchanged,increased,NA,unchanged,Signature 2,Figure 5,18 March 2024,Kaycee,"Kaycee,Peace Sandy,WikiWorks","The differences between the groups were evaluated using the linear discrimination analysis effect size (LEfSe). The bar graph shows the LDA scores of significant bacteria. The colors (Healthy = red, Parkinson = blue) represent which group was more abundant compared with the other group at the genus and family level.",decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium",1783272|201174|84998|84999|84107;1783272|1239|186801|3085636|186803;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1898203,Complete,Peace Sandy
bsdb:38230936/2/1,38230936,time series / longitudinal observational,38230936,10.1128/spectrum.03190-23,NA,"Iwase S.C., Osawe S., Happel A.-.U., Gray C.M., Holmes S.P., Blackburn J.M., Abimiku A. , Jaspan H.B.",Longitudinal gut microbiota composition of South African and Nigerian infants in relation to tetanus vaccine responses,Microbiology spectrum,2024,"HIV-exposed uninfected infants, Nigeria, South Africa, gut microbiota, tetanus toxoid, vaccine response",Experiment 2,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Infants who are HIV unexposed and uninfected (iHUU) at week 15,Infants who are HIV exposed but uninfected (iHEU) at week 15,Infants at 15 weeks of age born to mothers from South Africa who have HIV but are not themselves infected with HIV adjusted by mode of feeding,21,61,NA,16S,34,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 2,24 June 2024,Scholastica,"Scholastica,WikiWorks",Differentially abundant ASVs (adj P < 0.05) among iHEU (infants who are HIV exposed but uninfected) relative to iHUU (infants who are HIV unexposed and uninfected) at 15 weeks of age in South Africa adjusted by mode of feeding,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus gilvus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus raffinosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella quasipneumoniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gallolyticus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|201174|1760|85004|31953|1678|1680;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|91061|186826|81852|1350|160453;1783272|1239|91061|186826|81852|1350|71452;1783272|1239|186801|186802|216572|216851|853;3379134|1224|1236|91347|543|570|1463165;1783272|1239|91061|186826|1300|1357|1358;1783272|1239|91061|186826|1300|1301|315405;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|186828|117563;1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:38230936/2/2,38230936,time series / longitudinal observational,38230936,10.1128/spectrum.03190-23,NA,"Iwase S.C., Osawe S., Happel A.-.U., Gray C.M., Holmes S.P., Blackburn J.M., Abimiku A. , Jaspan H.B.",Longitudinal gut microbiota composition of South African and Nigerian infants in relation to tetanus vaccine responses,Microbiology spectrum,2024,"HIV-exposed uninfected infants, Nigeria, South Africa, gut microbiota, tetanus toxoid, vaccine response",Experiment 2,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Infants who are HIV unexposed and uninfected (iHUU) at week 15,Infants who are HIV exposed but uninfected (iHEU) at week 15,Infants at 15 weeks of age born to mothers from South Africa who have HIV but are not themselves infected with HIV adjusted by mode of feeding,21,61,NA,16S,34,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 2,24 June 2024,Scholastica,"Scholastica,WikiWorks",Differentially abundant ASVs (adj P < 0.05) among iHEU (infants who are HIV exposed but uninfected) relative to iHUU (infants who are HIV unexposed and uninfected) at 15 weeks of age in South Africa adjusted by mode of feeding,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella michiganensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus rhamnosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|976|200643|171549|815|816|47678;3379134|1224|1236|91347|543|570|1134687;1783272|1239|91061|186826|33958|2759736|47715;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|909932|1843489|31977|906|907;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|186801|3085636|186803|2316020|33039;1783272|201174|84998|84999|1643824|133925;3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:38230936/3/1,38230936,time series / longitudinal observational,38230936,10.1128/spectrum.03190-23,NA,"Iwase S.C., Osawe S., Happel A.-.U., Gray C.M., Holmes S.P., Blackburn J.M., Abimiku A. , Jaspan H.B.",Longitudinal gut microbiota composition of South African and Nigerian infants in relation to tetanus vaccine responses,Microbiology spectrum,2024,"HIV-exposed uninfected infants, Nigeria, South Africa, gut microbiota, tetanus toxoid, vaccine response",Experiment 3,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Infants who are HIV unexposed and uninfected (iHUU) at week 15,Infants who are HIV exposed but uninfected (iHEU) at week 15,Infants at 15 weeks of age born to mothers from South Africa who have HIV but are not themselves infected with HIV when adjusted for reported antibiotic (co-trimoxazole) prophylaxis history adjusted by mode of feeding and reported antibiotics history,21,61,NA,16S,34,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,antibiotic exposure,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table S2,24 June 2024,Scholastica,"Scholastica,WikiWorks",Differentially abundant ASVs (adj P < 0.05) among iHEU (infants who are HIV exposed but uninfected) relative to iHUU (infants who are HIV unexposed and uninfected) at 15 weeks of age in South Africa adjusted by mode of feeding and reported antibiotics history,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella quasipneumoniae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gallolyticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus gilvus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus raffinosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium propinquum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc lactis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus peroris",1783272|201174|84998|84999|84107|102106|74426;3379134|1224|1236|91347|543|570|1463165;1783272|201174|1760|85004|31953|1678|1680;1783272|1239|91061|186826|1300|1301|315405;1783272|1239|91061|186826|81852|1350|160453;1783272|1239|91061|186826|1300|1357|1358;1783272|1239|91061|186826|81852|1350|71452;1783272|1239|186801|3085636|186803|189330|39486;1783272|201174|1760|85007|1653|1716|43769;1783272|1239|186801|186802|216572|216851|853;1783272|1239|91061|186826|33958|1243|1246;1783272|1239|91061|186826|186828|117563;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|1300|1301|68891,Complete,Svetlana up
bsdb:38230936/3/2,38230936,time series / longitudinal observational,38230936,10.1128/spectrum.03190-23,NA,"Iwase S.C., Osawe S., Happel A.-.U., Gray C.M., Holmes S.P., Blackburn J.M., Abimiku A. , Jaspan H.B.",Longitudinal gut microbiota composition of South African and Nigerian infants in relation to tetanus vaccine responses,Microbiology spectrum,2024,"HIV-exposed uninfected infants, Nigeria, South Africa, gut microbiota, tetanus toxoid, vaccine response",Experiment 3,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Infants who are HIV unexposed and uninfected (iHUU) at week 15,Infants who are HIV exposed but uninfected (iHEU) at week 15,Infants at 15 weeks of age born to mothers from South Africa who have HIV but are not themselves infected with HIV when adjusted for reported antibiotic (co-trimoxazole) prophylaxis history adjusted by mode of feeding and reported antibiotics history,21,61,NA,16S,34,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,antibiotic exposure,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table S2,24 June 2024,Scholastica,"Scholastica,WikiWorks",Differentially abundant ASVs (adj P < 0.05) among iHEU (infants who are HIV exposed but uninfected) relative to iHUU (infants who are HIV unexposed and uninfected) at 15 weeks of age in South Africa adjusted by mode of feeding and reported antibiotics history,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus vaginalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus rhamnosus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus gilvus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella michiganensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",1783272|1239|91061|186826|33958|2742598|1633;1783272|1239|91061|186826|33958|2742598|1613;3379134|976|200643|171549|2005525|375288|823;1783272|1239|91061|186826|33958|2759736|47715;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|81852|1350|160453;1783272|1239|909932|1843489|31977|906|907;1783272|201174|84998|84999|1643824|133925;1783272|201174|84998|84999|84107|1473205;3379134|1224|1236|91347|543|570|1134687;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|171552|838;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Svetlana up
bsdb:38243297/1/1,38243297,case-control,38243297,10.1186/s13293-024-00582-7,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10797902/,"Garcia-Fernandez H., Arenas-de Larriva A.P., Lopez-Moreno J., Gutierrez-Mariscal F.M., Romero-Cabrera J.L., Molina-Abril H., Torres-Peña J.D., Rodriguez-Cano D., Malagon M.M., Ordovas J.M., Delgado-Lista J., Perez-Martinez P., Lopez-Miranda J. , Camargo A.",Sex-specific differences in intestinal microbiota associated with cardiovascular diseases,Biology of sex differences,2024,"CORDIOPREV, Cardiovascular diseases, Dysbiosis, Gut microbiota, Sexual dimorphism",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Cardiovascular disease,EFO:0000319,Men with coronary heart disease (CHD),Women with coronary heart disease (CHD),"Women with coronary heart disease, and enrolled in the CORDIOPREV study.",567,112,1 month,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Fig.1 B,23 January 2024,Andre,"Andre,WikiWorks","Differently abundant taxa in CHD patients according to the sex, based on LEfSe analysis.",decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum",1783272|1239|526524|526525|128827;1783272|1239|186801|3085636|186803|28050;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|39492,Complete,Chloe
bsdb:38243297/1/2,38243297,case-control,38243297,10.1186/s13293-024-00582-7,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10797902/,"Garcia-Fernandez H., Arenas-de Larriva A.P., Lopez-Moreno J., Gutierrez-Mariscal F.M., Romero-Cabrera J.L., Molina-Abril H., Torres-Peña J.D., Rodriguez-Cano D., Malagon M.M., Ordovas J.M., Delgado-Lista J., Perez-Martinez P., Lopez-Miranda J. , Camargo A.",Sex-specific differences in intestinal microbiota associated with cardiovascular diseases,Biology of sex differences,2024,"CORDIOPREV, Cardiovascular diseases, Dysbiosis, Gut microbiota, Sexual dimorphism",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Cardiovascular disease,EFO:0000319,Men with coronary heart disease (CHD),Women with coronary heart disease (CHD),"Women with coronary heart disease, and enrolled in the CORDIOPREV study.",567,112,1 month,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Fig.1 B,24 January 2024,Andre,"Andre,WikiWorks,Tosin","Differently abundant taxa in CHD patients according to sex, based on LEfSe analysis.",increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia",1783272|201174;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|2005519;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;3379134|200940|3031449|213115|194924|35832;1783272|201174|84998|84999;1783272|201174|84998;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525;;1783272|1239|186801|186802|216572|216851|1946507;1783272|201174|84992,Complete,Chloe
bsdb:38243297/2/1,38243297,case-control,38243297,10.1186/s13293-024-00582-7,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10797902/,"Garcia-Fernandez H., Arenas-de Larriva A.P., Lopez-Moreno J., Gutierrez-Mariscal F.M., Romero-Cabrera J.L., Molina-Abril H., Torres-Peña J.D., Rodriguez-Cano D., Malagon M.M., Ordovas J.M., Delgado-Lista J., Perez-Martinez P., Lopez-Miranda J. , Camargo A.",Sex-specific differences in intestinal microbiota associated with cardiovascular diseases,Biology of sex differences,2024,"CORDIOPREV, Cardiovascular diseases, Dysbiosis, Gut microbiota, Sexual dimorphism",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Cardiovascular disease,EFO:0000319,Men without cardiovascular disease,Women without cardiovascular disease,"Women without cardiovascular disease, and enrolled in the ONCOVER study",242,87,1 month,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Fig. 2 B,24 January 2024,Andre,"Andre,WikiWorks","Differently abundant taxa in non‑CVD patients according to sex, based on LEfSe analysis",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",3379134|976|200643|171549;3379134|976|200643;3379134|976;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107,Complete,Chloe
bsdb:38243297/2/2,38243297,case-control,38243297,10.1186/s13293-024-00582-7,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10797902/,"Garcia-Fernandez H., Arenas-de Larriva A.P., Lopez-Moreno J., Gutierrez-Mariscal F.M., Romero-Cabrera J.L., Molina-Abril H., Torres-Peña J.D., Rodriguez-Cano D., Malagon M.M., Ordovas J.M., Delgado-Lista J., Perez-Martinez P., Lopez-Miranda J. , Camargo A.",Sex-specific differences in intestinal microbiota associated with cardiovascular diseases,Biology of sex differences,2024,"CORDIOPREV, Cardiovascular diseases, Dysbiosis, Gut microbiota, Sexual dimorphism",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Cardiovascular disease,EFO:0000319,Men without cardiovascular disease,Women without cardiovascular disease,"Women without cardiovascular disease, and enrolled in the ONCOVER study",242,87,1 month,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Fig. 2 B,24 January 2024,Andre,"Andre,WikiWorks","Differently abundant taxa in non‑CVD patients according to sex, based on LEfSe analysis",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;1783272|1239;1783272|1239|186801|3082768|990719;1783272|1239|186801|3082768;1783272|1239|186801|186802|216572;3379134|74201|203494;3379134|74201|203494|48461;3379134|74201,Complete,Chloe
bsdb:38243297/3/1,38243297,case-control,38243297,10.1186/s13293-024-00582-7,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10797902/,"Garcia-Fernandez H., Arenas-de Larriva A.P., Lopez-Moreno J., Gutierrez-Mariscal F.M., Romero-Cabrera J.L., Molina-Abril H., Torres-Peña J.D., Rodriguez-Cano D., Malagon M.M., Ordovas J.M., Delgado-Lista J., Perez-Martinez P., Lopez-Miranda J. , Camargo A.",Sex-specific differences in intestinal microbiota associated with cardiovascular diseases,Biology of sex differences,2024,"CORDIOPREV, Cardiovascular diseases, Dysbiosis, Gut microbiota, Sexual dimorphism",Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Cardiovascular disease,EFO:0000319,Men without cardiovascular disease,Men with coronary heart disease (CHD),"Men with coronary heart disease, and enrolled in the CORDIOPREV study.",242,567,1 month,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,decreased,NA,unchanged,Signature 1,Fig. 4,24 January 2024,Andre,"Andre,WikiWorks",Linear discriminant analysis between CHD patients and non‑CVD subjects in Men,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Thermodesulfobacteriota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales",1783272|1239|909932|1843488|909930;1783272|1239|909932|1843488;1783272|201174;3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;1783272|1239|91061;1783272|1239;95818|2093818|2093825;95818|2093818;1783272|1239|186801;1783272|201174|84998|84999;1783272|201174|84998;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;3379134|200940|3031449;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|561;3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|909932;1783272|1239|186801|186802|216572;3379134|1224|1236|135625|712;3379134|1224|1236|135625;;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3085636|186803|841;1783272|1239|909932|909929;3379134|1224|1236|91347|543|620;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|292632;3379134|200940;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977;1783272|1239|909932|1843489;3379134|74201|203494|48461,Complete,Chloe
bsdb:38243297/3/2,38243297,case-control,38243297,10.1186/s13293-024-00582-7,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10797902/,"Garcia-Fernandez H., Arenas-de Larriva A.P., Lopez-Moreno J., Gutierrez-Mariscal F.M., Romero-Cabrera J.L., Molina-Abril H., Torres-Peña J.D., Rodriguez-Cano D., Malagon M.M., Ordovas J.M., Delgado-Lista J., Perez-Martinez P., Lopez-Miranda J. , Camargo A.",Sex-specific differences in intestinal microbiota associated with cardiovascular diseases,Biology of sex differences,2024,"CORDIOPREV, Cardiovascular diseases, Dysbiosis, Gut microbiota, Sexual dimorphism",Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Cardiovascular disease,EFO:0000319,Men without cardiovascular disease,Men with coronary heart disease (CHD),"Men with coronary heart disease, and enrolled in the CORDIOPREV study.",242,567,1 month,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,decreased,NA,unchanged,Signature 2,Figure 4,24 January 2024,Andre,"Andre,MyleeeA,WikiWorks",Linear discriminant analysis between CHD patients and non‑CVD subjects in Men,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|2005519;1783272|1239|186801|3085636|186803|572511;3379134|1224|28216|80840;3379134|976|200643|171549|1853231|574697;3379134|976|200643|171549|2005519|1348911;1783272|1239|526524|526525;3379134|976|200643|1970189|1573805;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|577309;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|3082720;3379134|1224;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|1263;3379134|1224|28216|80840|995019|40544;3379134|1224|28216|80840|995019;3379134|976|200643|171549|2005525;1783272|1239|526524|526525|2810280|3025755;1783272|1239|1737404|1737405;1783272|1239|186801|186802|216572|39492,Complete,Chloe
bsdb:38243297/4/1,38243297,case-control,38243297,10.1186/s13293-024-00582-7,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10797902/,"Garcia-Fernandez H., Arenas-de Larriva A.P., Lopez-Moreno J., Gutierrez-Mariscal F.M., Romero-Cabrera J.L., Molina-Abril H., Torres-Peña J.D., Rodriguez-Cano D., Malagon M.M., Ordovas J.M., Delgado-Lista J., Perez-Martinez P., Lopez-Miranda J. , Camargo A.",Sex-specific differences in intestinal microbiota associated with cardiovascular diseases,Biology of sex differences,2024,"CORDIOPREV, Cardiovascular diseases, Dysbiosis, Gut microbiota, Sexual dimorphism",Experiment 4,Spain,Homo sapiens,Feces,UBERON:0001988,Cardiovascular disease,EFO:0000319,Women without cardiovascular disease,Women with coronary heart disease (CHD),"Women with coronary heart disease, and enrolled in the CORDIOPREV study",87,112,1 month,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,decreased,NA,unchanged,Signature 1,Figure 4,24 January 2024,Andre,"Andre,WikiWorks,Tosin",Linear discriminant analysis between CHD patients and non‑CVD subjects in Women,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Thermodesulfobacteriota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,",1783272|1239|909932|1843488|909930;1783272|1239|909932|1843488;1783272|201174;1783272|1239|91061;3379134|200940|3031449|213115|194924|35832;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;3379134|200940|3031449;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|561;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|909932;1783272|1239|909932|1843488|909930|33024;3379134|1224|1236|91347|543|620;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;3379134|200940;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|186802|216572|216851|1946507;,Complete,Chloe
bsdb:38243297/4/2,38243297,case-control,38243297,10.1186/s13293-024-00582-7,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10797902/,"Garcia-Fernandez H., Arenas-de Larriva A.P., Lopez-Moreno J., Gutierrez-Mariscal F.M., Romero-Cabrera J.L., Molina-Abril H., Torres-Peña J.D., Rodriguez-Cano D., Malagon M.M., Ordovas J.M., Delgado-Lista J., Perez-Martinez P., Lopez-Miranda J. , Camargo A.",Sex-specific differences in intestinal microbiota associated with cardiovascular diseases,Biology of sex differences,2024,"CORDIOPREV, Cardiovascular diseases, Dysbiosis, Gut microbiota, Sexual dimorphism",Experiment 4,Spain,Homo sapiens,Feces,UBERON:0001988,Cardiovascular disease,EFO:0000319,Women without cardiovascular disease,Women with coronary heart disease (CHD),"Women with coronary heart disease, and enrolled in the CORDIOPREV study",87,112,1 month,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,decreased,NA,unchanged,Signature 2,Figure 4,24 January 2024,Andre,"Andre,WikiWorks",Linear discriminant analysis between CHD patients and non‑CVD subjects in Women,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum",3379134|976|200643|171549;3379134|976|200643;3379134|976;1783272|1239|186801|3085636|186803|572511;3379134|1224|28216|80840;3379134|976|200643|171549|1853231|574697;1783272|1239|526524|526525;3379134|976|200643|1970189|1573805;3379134|976|200643|171549|1853231|283168;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|3082720;1783272|1239|186801|186802|216572|1263;3379134|1224|28216|80840|995019;1783272|1239|1737404|1737405;1783272|1239|186801|186802|216572|39492,Complete,Chloe
bsdb:38245675/1/1,38245675,"cross-sectional observational, not case-control",38245675,10.1186/s12866-023-03149-5,NA,"Bayardo-González R.A., Peña-Rodríguez M., Pereira-Suárez A.L., Rubio-Sánchez A.X., García-Chagollán M., Valenzuela-Orozco D.N., Lizarazo-Taborda M.D.R., Mora-Mora J. , Vega-Magaña N.",Insights into estrogen impact in oral health & microbiome in COVID-19,BMC microbiology,2024,"COVID-19, Cytokines, Inflammation, Microbiome, Women-s health",Experiment 1,Mexico,Homo sapiens,Saliva,UBERON:0001836,Menopause,EFO:0003922,Premenopausal women group,Postmenopausal women group,Postmenopausal women with COVID-19,20,18,1 month,16S,34,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 3c,20 March 2024,EniolaAde,"EniolaAde,Scholastica,WikiWorks",DeSeq2 deferentially abundant taxa in premenopausal women compared to postmenopausal women group,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica",3379134|976|200643|171549|171552|1283313;3379134|1224|1236|135625|712|724;3379134|976|200643|171549|171552|2974257|425941;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|838|28132,Complete,Svetlana up
bsdb:38245675/1/2,38245675,"cross-sectional observational, not case-control",38245675,10.1186/s12866-023-03149-5,NA,"Bayardo-González R.A., Peña-Rodríguez M., Pereira-Suárez A.L., Rubio-Sánchez A.X., García-Chagollán M., Valenzuela-Orozco D.N., Lizarazo-Taborda M.D.R., Mora-Mora J. , Vega-Magaña N.",Insights into estrogen impact in oral health & microbiome in COVID-19,BMC microbiology,2024,"COVID-19, Cytokines, Inflammation, Microbiome, Women-s health",Experiment 1,Mexico,Homo sapiens,Saliva,UBERON:0001836,Menopause,EFO:0003922,Premenopausal women group,Postmenopausal women group,Postmenopausal women with COVID-19,20,18,1 month,16S,34,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 3c,26 March 2024,EniolaAde,"EniolaAde,Scholastica,WikiWorks",DeSeq2 deferentially abundant taxa in premenopausal women compared to postmenopausal women group,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,3379134|1224|28216|206351|481|482,Complete,Svetlana up
bsdb:38245675/2/1,38245675,"cross-sectional observational, not case-control",38245675,10.1186/s12866-023-03149-5,NA,"Bayardo-González R.A., Peña-Rodríguez M., Pereira-Suárez A.L., Rubio-Sánchez A.X., García-Chagollán M., Valenzuela-Orozco D.N., Lizarazo-Taborda M.D.R., Mora-Mora J. , Vega-Magaña N.",Insights into estrogen impact in oral health & microbiome in COVID-19,BMC microbiology,2024,"COVID-19, Cytokines, Inflammation, Microbiome, Women-s health",Experiment 2,Mexico,Homo sapiens,Saliva,UBERON:0001836,Health trait,EFO:0007652,Adequate oral health group,Poor oral health group,"COVID-19 patients with poor oral health status. Patients were classified as having poor oral health when there were more than two caries, hygiene index higher than 2.5, gingival inflammation between 2–3 and bleeding when toothbrushing.",NA,NA,1 month,16S,34,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 3f,22 March 2024,EniolaAde,"EniolaAde,Scholastica,WikiWorks",DESeq2 differentially abundant taxa in poor oral health group compared to adequate oral health group,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria perflava,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",3379134|1224|28216|206351|481|482|33053;3379134|1224|28216|206351|481|482,Complete,Svetlana up
bsdb:38245675/2/2,38245675,"cross-sectional observational, not case-control",38245675,10.1186/s12866-023-03149-5,NA,"Bayardo-González R.A., Peña-Rodríguez M., Pereira-Suárez A.L., Rubio-Sánchez A.X., García-Chagollán M., Valenzuela-Orozco D.N., Lizarazo-Taborda M.D.R., Mora-Mora J. , Vega-Magaña N.",Insights into estrogen impact in oral health & microbiome in COVID-19,BMC microbiology,2024,"COVID-19, Cytokines, Inflammation, Microbiome, Women-s health",Experiment 2,Mexico,Homo sapiens,Saliva,UBERON:0001836,Health trait,EFO:0007652,Adequate oral health group,Poor oral health group,"COVID-19 patients with poor oral health status. Patients were classified as having poor oral health when there were more than two caries, hygiene index higher than 2.5, gingival inflammation between 2–3 and bleeding when toothbrushing.",NA,NA,1 month,16S,34,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 3f,22 March 2024,EniolaAde,"EniolaAde,Scholastica,WikiWorks",DESeq2 differentially abundant taxa in poor oral health group compared to adequate oral health group,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|s__uncultured Bacteroidota bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",3379134|976|200643|171549|171552|1283313;3379134|976;1783272|1239|186801|186802|1898207;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552|1283313;3384189|32066|203490|203491|1129771|32067;3379134|1224|28216|206351|481|482;3379134|976|152509;3379134|1224|1236|135625|712|724;3379134|976|200643|171549|2005525|195950,Complete,Svetlana up
bsdb:38245675/3/1,38245675,"cross-sectional observational, not case-control",38245675,10.1186/s12866-023-03149-5,NA,"Bayardo-González R.A., Peña-Rodríguez M., Pereira-Suárez A.L., Rubio-Sánchez A.X., García-Chagollán M., Valenzuela-Orozco D.N., Lizarazo-Taborda M.D.R., Mora-Mora J. , Vega-Magaña N.",Insights into estrogen impact in oral health & microbiome in COVID-19,BMC microbiology,2024,"COVID-19, Cytokines, Inflammation, Microbiome, Women-s health",Experiment 3,Mexico,Homo sapiens,Saliva,UBERON:0001836,Viral load,EFO:0010125,Moderate SARS-CoV-2 viral load group,High SARS-CoV-2 viral load group,COVID-19 patients with high SARS-CoV-2 viral load,11,41,1 month,16S,34,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 3i,22 March 2024,EniolaAde,"EniolaAde,Scholastica,WikiWorks",DESeq2 differentially abundant taxa in moderate compared to high SARS-CoV-2 viral load group,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|s__uncultured Bacteroidota bacterium",3379134|976|200643|171549|171552|1283313;3379134|1224|1236|135625|712|724;3379134|976|200643|171549|171552|2974257|425941;3384189|32066|203490|203491|1129771|32067;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|171552|838|28132;3379134|976|152509,Complete,Svetlana up
bsdb:38262927/1/1,38262927,"cross-sectional observational, not case-control",38262927,https://doi.org/10.1186/s12866-023-03150-y,NA,"Liu S., Imad S., Hussain S., Xiao S., Yu X. , Cao H.","Sex, health status and habitat alter the community composition and assembly processes of symbiotic bacteria in captive frogs",BMC microbiology,2024,"Assembly, Frog, Habitat, Health status, Network structure, Sex",Experiment 1,China,Pelophylax nigromaculatus,Intestine,UBERON:0000160,Sex design,EFO:0001752,male,female,female black spotted frog,8,8,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,figure 3a,20 March 2024,Idiaru angela,"Idiaru angela,Scholastica,WikiWorks",differential abundance of bacteria genera in frog guts between female and male frog samples.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:38262927/1/2,38262927,"cross-sectional observational, not case-control",38262927,https://doi.org/10.1186/s12866-023-03150-y,NA,"Liu S., Imad S., Hussain S., Xiao S., Yu X. , Cao H.","Sex, health status and habitat alter the community composition and assembly processes of symbiotic bacteria in captive frogs",BMC microbiology,2024,"Assembly, Frog, Habitat, Health status, Network structure, Sex",Experiment 1,China,Pelophylax nigromaculatus,Intestine,UBERON:0000160,Sex design,EFO:0001752,male,female,female black spotted frog,8,8,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,figure 3a,20 March 2024,Idiaru angela,"Idiaru angela,Scholastica,WikiWorks",Differential abundance of bacterial genera in frog guts between male and female frog samples.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Aquaspirillaceae|g__Laribacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae|g__Tumebacillus",3379134|1224|28216|206351|2897176|168470;1783272|1239|91061|1385|186823|432330,Complete,Svetlana up
bsdb:38262927/2/1,38262927,"cross-sectional observational, not case-control",38262927,https://doi.org/10.1186/s12866-023-03150-y,NA,"Liu S., Imad S., Hussain S., Xiao S., Yu X. , Cao H.","Sex, health status and habitat alter the community composition and assembly processes of symbiotic bacteria in captive frogs",BMC microbiology,2024,"Assembly, Frog, Habitat, Health status, Network structure, Sex",Experiment 2,China,Pelophylax nigromaculatus,Intestine,UBERON:0000160,Infectious meningitis,NA,H: uninfected individuals,NH: infected individuals,frogs found to be infected with Meningitis-like infectious diseases.,8,8,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,figure 3b,20 March 2024,Idiaru angela,"Idiaru angela,WikiWorks",comparison of gut bacterial communities in frogs between healthy and unhealthy frog samples,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,3379134|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:38262927/2/2,38262927,"cross-sectional observational, not case-control",38262927,https://doi.org/10.1186/s12866-023-03150-y,NA,"Liu S., Imad S., Hussain S., Xiao S., Yu X. , Cao H.","Sex, health status and habitat alter the community composition and assembly processes of symbiotic bacteria in captive frogs",BMC microbiology,2024,"Assembly, Frog, Habitat, Health status, Network structure, Sex",Experiment 2,China,Pelophylax nigromaculatus,Intestine,UBERON:0000160,Infectious meningitis,NA,H: uninfected individuals,NH: infected individuals,frogs found to be infected with Meningitis-like infectious diseases.,8,8,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,figure 3b,20 March 2024,Idiaru angela,"Idiaru angela,WikiWorks",comparison of gut bacterial communities in frogs between healthy and unhealthy frog samples,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|1853231|283168,Complete,Svetlana up
bsdb:38271852/1/1,38271852,case-control,38271852,10.1016/j.nicl.2024.103567,NA,"Liang L., Li S., Huang Y., Zhou J., Xiong D., Li S., Li H., Zhu B., Li X., Ning Y., Hou X., Wu F. , Wu K.","Relationships among the gut microbiome, brain networks, and symptom severity in schizophrenia patients: A mediation analysis",NeuroImage. Clinical,2024,"Brain networks, Gut microbiome, Mediation analysis, Microbiome-gut-brain axis, Schizophrenia, Symptom severity",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Normal controls (NC),Schizophrenia patients (SZ),Patients with schizophrenia (SZ),38,38,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2,24 November 2025,Arnold Pakis,"Arnold Pakis,Tosin",Taxonomic differences between schizophrenia (SZ) patients and normal controls (NCs) according to the LEfSe (Linear Discriminant Analysis effect size) method.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia",1783272|1239|186801|186802|216572|946234;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490|203491|203492|848;1783272|1239|909932|1843489|31977|29465;1783272|201174|84998|1643822|1643826|447020,Complete,KateRasheed
bsdb:38271852/1/2,38271852,case-control,38271852,10.1016/j.nicl.2024.103567,NA,"Liang L., Li S., Huang Y., Zhou J., Xiong D., Li S., Li H., Zhu B., Li X., Ning Y., Hou X., Wu F. , Wu K.","Relationships among the gut microbiome, brain networks, and symptom severity in schizophrenia patients: A mediation analysis",NeuroImage. Clinical,2024,"Brain networks, Gut microbiome, Mediation analysis, Microbiome-gut-brain axis, Schizophrenia, Symptom severity",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Normal controls (NC),Schizophrenia patients (SZ),Patients with schizophrenia (SZ),38,38,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2,24 November 2025,Arnold Pakis,"Arnold Pakis,Tosin",Taxonomic differences between schizophrenia (SZ) patients and normal controls (NCs) according to the LEfSe (Linear Discriminant Analysis effect size) method.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|g__Negativibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005",1783272|1239|186801|3085636|186803|1766253;3379134|976|200643|171549|2005519|397864;1783272|1798710|1906119;1783272|1239|909932|1843489|31977|39948;1783272|1239|1980693;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|216572|3068309,Complete,KateRasheed
bsdb:38274754/1/1,38274754,case-control,38274754,10.3389/fmicb.2023.1323877,NA,"Yao J., Yan X., Li Y., Chen Y., Xiao X., Zhou S., Zhang W., Wang L., Chen M., Zeng F. , Li Y.",Altered gut microbial profile is associated with differentially expressed fecal microRNAs in patients with functional constipation,Frontiers in microbiology,2023,"16S rRNA, functional constipation, gut microbiota, microRNA, microRNA sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy Controls,Functional constipation (FC) group,Patients diagnosed with functional constipation (FC),30,30,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,"age,body mass index,sex",NA,increased,increased,increased,increased,decreased,increased,Signature 1,Figure 2A,18 March 2025,Tosin,Tosin,Differentially abundant taxa between Functional constipation (FC) group and Healthy Controls (HC),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,",3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005519|397864;1783272|1239|186801|186802|1980681;3379134|976|200643|171549|2005519|1348911;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3082720|186804|1505657;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;,Complete,Svetlana up
bsdb:38274754/1/2,38274754,case-control,38274754,10.3389/fmicb.2023.1323877,NA,"Yao J., Yan X., Li Y., Chen Y., Xiao X., Zhou S., Zhang W., Wang L., Chen M., Zeng F. , Li Y.",Altered gut microbial profile is associated with differentially expressed fecal microRNAs in patients with functional constipation,Frontiers in microbiology,2023,"16S rRNA, functional constipation, gut microbiota, microRNA, microRNA sequencing",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy Controls,Functional constipation (FC) group,Patients diagnosed with functional constipation (FC),30,30,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,"age,body mass index,sex",NA,increased,increased,increased,increased,decreased,increased,Signature 2,Figure 2A,18 March 2025,Tosin,Tosin,Differentially abundant taxa between Functional constipation (FC) group and Healthy Controls (HC),decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",1783272|1239|909932|909929|1843491|158846;1783272|201174|84998|84999|84107|102106,Complete,Svetlana up
bsdb:38274754/2/1,38274754,case-control,38274754,10.3389/fmicb.2023.1323877,NA,"Yao J., Yan X., Li Y., Chen Y., Xiao X., Zhou S., Zhang W., Wang L., Chen M., Zeng F. , Li Y.",Altered gut microbial profile is associated with differentially expressed fecal microRNAs in patients with functional constipation,Frontiers in microbiology,2023,"16S rRNA, functional constipation, gut microbiota, microRNA, microRNA sequencing",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy Controls,Functional constipation (FC) group,Patients diagnosed with functional constipation (FC),30,30,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,"age,body mass index,sex",NA,increased,increased,increased,increased,decreased,increased,Signature 1,Figure 2B. 2C,18 March 2025,Tosin,Tosin,Differentially abundant taxa between Functional constipation (FC) group and Healthy Controls (HC),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|46506;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730|290054;3379134|1224|1236;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|815|909656|310298;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|821;3379134|1224;1783272|1239|186801|186802|216572|292632;3379134|976|200643|171549|2005525,Complete,Svetlana up
bsdb:38274754/2/2,38274754,case-control,38274754,10.3389/fmicb.2023.1323877,NA,"Yao J., Yan X., Li Y., Chen Y., Xiao X., Zhou S., Zhang W., Wang L., Chen M., Zeng F. , Li Y.",Altered gut microbial profile is associated with differentially expressed fecal microRNAs in patients with functional constipation,Frontiers in microbiology,2023,"16S rRNA, functional constipation, gut microbiota, microRNA, microRNA sequencing",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy Controls,Functional constipation (FC) group,Patients diagnosed with functional constipation (FC),30,30,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,"age,body mass index,sex",NA,increased,increased,increased,increased,decreased,increased,Signature 2,"Figure 2B, 2C",18 March 2025,Tosin,Tosin,Differentially abundant taxa between Functional constipation (FC) group and Healthy Controls (HC),decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|s__Prevotellaceae bacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales",1783272|1239|909932|909929|1843491;1783272|1239|909932|909929|1843491|158846;3379134|976|200643|171549|171552|2049047;1783272|1239|909932|909929|1843491|158846|437897;1783272|201174|84998;1783272|201174|84998|84999,Complete,Svetlana up
bsdb:38274754/3/1,38274754,case-control,38274754,10.3389/fmicb.2023.1323877,NA,"Yao J., Yan X., Li Y., Chen Y., Xiao X., Zhou S., Zhang W., Wang L., Chen M., Zeng F. , Li Y.",Altered gut microbial profile is associated with differentially expressed fecal microRNAs in patients with functional constipation,Frontiers in microbiology,2023,"16S rRNA, functional constipation, gut microbiota, microRNA, microRNA sequencing",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Low Bristol stool form scale (BSFS) scores,High Bristol stool form scale (BSFS) scores,Patients with exertion in defecation and dry stool at baseline of a high Bristol stool form scale (BSFS),NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4, Table S2",21 March 2025,Tosin,Tosin,Heatmap showing bacterial genera that were significantly correlated with the constipated-indicators.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,3379134|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:38274754/4/1,38274754,case-control,38274754,10.3389/fmicb.2023.1323877,NA,"Yao J., Yan X., Li Y., Chen Y., Xiao X., Zhou S., Zhang W., Wang L., Chen M., Zeng F. , Li Y.",Altered gut microbial profile is associated with differentially expressed fecal microRNAs in patients with functional constipation,Frontiers in microbiology,2023,"16S rRNA, functional constipation, gut microbiota, microRNA, microRNA sequencing",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Health-related quality of life measurement,EFO:0011014,Low Patient-Assessment of Constipation Quality of Life (PAC_QOL),High Patient-Assessment of Constipation Quality of Life (PAC_QOL),Patients with High levels of Patient-Assessment of Constipation Quality of Life (PAC_QOL),NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4, Table S2",21 March 2025,Tosin,Tosin,Heatmap showing bacterial genera that were significantly correlated with the constipated-indicators.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter",1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|186802|1980681,Complete,Svetlana up
bsdb:38274754/4/2,38274754,case-control,38274754,10.3389/fmicb.2023.1323877,NA,"Yao J., Yan X., Li Y., Chen Y., Xiao X., Zhou S., Zhang W., Wang L., Chen M., Zeng F. , Li Y.",Altered gut microbial profile is associated with differentially expressed fecal microRNAs in patients with functional constipation,Frontiers in microbiology,2023,"16S rRNA, functional constipation, gut microbiota, microRNA, microRNA sequencing",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Health-related quality of life measurement,EFO:0011014,Low Patient-Assessment of Constipation Quality of Life (PAC_QOL),High Patient-Assessment of Constipation Quality of Life (PAC_QOL),Patients with High levels of Patient-Assessment of Constipation Quality of Life (PAC_QOL),NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 4, Table S2",22 March 2025,Tosin,Tosin,Heatmap showing bacterial genera that were significantly correlated with the constipated-indicators.,decreased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,1783272|1239|909932|909929|1843491|158846,Complete,Svetlana up
bsdb:38274754/5/1,38274754,case-control,38274754,10.3389/fmicb.2023.1323877,NA,"Yao J., Yan X., Li Y., Chen Y., Xiao X., Zhou S., Zhang W., Wang L., Chen M., Zeng F. , Li Y.",Altered gut microbial profile is associated with differentially expressed fecal microRNAs in patients with functional constipation,Frontiers in microbiology,2023,"16S rRNA, functional constipation, gut microbiota, microRNA, microRNA sequencing",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,Low levels of straining during defecation,High levels of straining during defecation,Patients with high levels of straining during defecation,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4, Table S2",21 March 2025,Tosin,Tosin,Heatmap showing bacterial genera that were significantly correlated with the constipated-indicators.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:38274754/5/2,38274754,case-control,38274754,10.3389/fmicb.2023.1323877,NA,"Yao J., Yan X., Li Y., Chen Y., Xiao X., Zhou S., Zhang W., Wang L., Chen M., Zeng F. , Li Y.",Altered gut microbial profile is associated with differentially expressed fecal microRNAs in patients with functional constipation,Frontiers in microbiology,2023,"16S rRNA, functional constipation, gut microbiota, microRNA, microRNA sequencing",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,Low levels of straining during defecation,High levels of straining during defecation,Patients with high levels of straining during defecation,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 4, Table S2",21 March 2025,Tosin,Tosin,Heatmap showing bacterial genera that were significantly correlated with the constipated-indicators.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",3379134|976|200643|171549|2005519|397864;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|909932|909929|1843491|158846,Complete,Svetlana up
bsdb:38274754/6/1,38274754,case-control,38274754,10.3389/fmicb.2023.1323877,NA,"Yao J., Yan X., Li Y., Chen Y., Xiao X., Zhou S., Zhang W., Wang L., Chen M., Zeng F. , Li Y.",Altered gut microbial profile is associated with differentially expressed fecal microRNAs in patients with functional constipation,Frontiers in microbiology,2023,"16S rRNA, functional constipation, gut microbiota, microRNA, microRNA sequencing",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Bowel dysfunction,MONDO:0004880,Low levels of Average complete spontaneous bowel movements (CSBM),High levels of Average complete spontaneous bowel movements (CSBM),"Patients with High frequency of Average complete spontaneous bowel movements (CSBMs) ≤ 2 times per week, which lasted for more than 3 months",NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4, Table S2",21 March 2025,Tosin,Tosin,Heatmap showing bacterial genera that were significantly correlated with the constipated-indicators.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:38274754/7/1,38274754,case-control,38274754,10.3389/fmicb.2023.1323877,NA,"Yao J., Yan X., Li Y., Chen Y., Xiao X., Zhou S., Zhang W., Wang L., Chen M., Zeng F. , Li Y.",Altered gut microbial profile is associated with differentially expressed fecal microRNAs in patients with functional constipation,Frontiers in microbiology,2023,"16S rRNA, functional constipation, gut microbiota, microRNA, microRNA sequencing",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Bowel dysfunction,MONDO:0004880,Low levels of spontaneous bowel movement (SBM),High levels of spontaneous bowel movement (SBM),Patients with High levels of spontaneous bowel movement (SBM),NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4, Table S2",21 March 2025,Tosin,Tosin,Heatmap showing bacterial genera that were significantly correlated with the constipated-indicators,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:38274754/8/1,38274754,case-control,38274754,10.3389/fmicb.2023.1323877,NA,"Yao J., Yan X., Li Y., Chen Y., Xiao X., Zhou S., Zhang W., Wang L., Chen M., Zeng F. , Li Y.",Altered gut microbial profile is associated with differentially expressed fecal microRNAs in patients with functional constipation,Frontiers in microbiology,2023,"16S rRNA, functional constipation, gut microbiota, microRNA, microRNA sequencing",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Depressive disorder,MONDO:0002050,Low levels of self-rating depression scale (SDS),High levels of self-rating depression scale (SDS),Patients with mental disorder (depression) of a high self-rating depression scale (SDS) standard score,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4, Table S2",21 March 2025,Tosin,Tosin,Heatmap showing bacterial genera that were significantly correlated with the constipated-indicators,decreased,NA,NA,Complete,Svetlana up
bsdb:38289047/1/1,38289047,prospective cohort,38289047,https://doi.org/10.1128/spectrum.03009-23,https://journals.asm.org/doi/10.1128/spectrum.03009-23,"Romani L., Del Chierico F., Pane S., Ristori M.V., Pirona I., Guarrasi V., Cotugno N., Bernardi S., Lancella L., Perno C.F., Rossi P., Villani A., Campana A., Palma P. , Putignani L.",Exploring nasopharyngeal microbiota profile in children affected by SARS-CoV-2 infection,Microbiology spectrum,2024,"COVID-19, SARS-CoV-2, children, nasopharyngeal microbiota, respiratory tract",Experiment 1,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,healthy controls,COVID-19 patients,"Children whose Nasopharyngeal swab were positive for SARS-CoV-2 infection, as assayed by a molecular test.",59,71,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 3,14 March 2024,Ndruscilla,"Ndruscilla,Ayibatari,Joan Chuks,WikiWorks",Differences in bacterial taxa abundance of nasopharyngeal (NP) microbiota in COVID-19 patients VS Control (CTRL) groups,increased,"k__Bacillati|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae|g__Anaerolinea,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Gulbenkiania,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|200795|292625|292629|292628|233189;1783272|1239|91061|1385|186817|1386;3379134|1224|28216|80840|119060|32008;3379134|1224|28216|80840|119060;3379134|976|117743|200644|49546|1016;1783272|1239|91061|186826|186828;3379134|1224|28216|206351|1499392;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|1385|539738;3379134|1224|28216|206351|1499392|397456;3379134|1224|1236|135625|712|724;3384189|32066|203490|203491|1129771|32067;3384189|32066|203490|203491|1129771;1783272|201174|1760|85006|1268;3379134|1224|1236|2887326|468|475;3379134|1224|1236|2887326|468;1783272|1239|909932;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977,Complete,ChiomaBlessing
bsdb:38289047/1/2,38289047,prospective cohort,38289047,https://doi.org/10.1128/spectrum.03009-23,https://journals.asm.org/doi/10.1128/spectrum.03009-23,"Romani L., Del Chierico F., Pane S., Ristori M.V., Pirona I., Guarrasi V., Cotugno N., Bernardi S., Lancella L., Perno C.F., Rossi P., Villani A., Campana A., Palma P. , Putignani L.",Exploring nasopharyngeal microbiota profile in children affected by SARS-CoV-2 infection,Microbiology spectrum,2024,"COVID-19, SARS-CoV-2, children, nasopharyngeal microbiota, respiratory tract",Experiment 1,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,healthy controls,COVID-19 patients,"Children whose Nasopharyngeal swab were positive for SARS-CoV-2 infection, as assayed by a molecular test.",59,71,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 3,14 March 2024,Ndruscilla,"Ndruscilla,Ayibatari,Joan Chuks,WikiWorks",Differences in bacterial taxa abundance of nasopharyngeal (NP) microbiota in COVID-19 patients Vs Control (CTRL) groups,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Frisingicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",1783272|1239|186801|3085636|186803|1766253;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3082768|424536;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1918511;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|292632,Complete,ChiomaBlessing
bsdb:38289047/2/1,38289047,prospective cohort,38289047,https://doi.org/10.1128/spectrum.03009-23,https://journals.asm.org/doi/10.1128/spectrum.03009-23,"Romani L., Del Chierico F., Pane S., Ristori M.V., Pirona I., Guarrasi V., Cotugno N., Bernardi S., Lancella L., Perno C.F., Rossi P., Villani A., Campana A., Palma P. , Putignani L.",Exploring nasopharyngeal microbiota profile in children affected by SARS-CoV-2 infection,Microbiology spectrum,2024,"COVID-19, SARS-CoV-2, children, nasopharyngeal microbiota, respiratory tract",Experiment 2,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,NO COVID-19 (Patients with diagnosis different from COVID-19),COVID-19 patients,"Children whose Nasopharyngeal swab were positive for SARS-CoV-2 infection, as assayed by a molecular test.",7,71,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure S4,11 April 2024,Joan Chuks,"Joan Chuks,WikiWorks",Differences in bacterial taxa abundance of nasopharyngeal (NP) microbiota in COVID-19 patients Vs NO COVID-19 (Patients with diagnosis different from COVID-19),increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,1783272|1239|909932|1843489|31977|39948,Complete,ChiomaBlessing
bsdb:38289047/2/2,38289047,prospective cohort,38289047,https://doi.org/10.1128/spectrum.03009-23,https://journals.asm.org/doi/10.1128/spectrum.03009-23,"Romani L., Del Chierico F., Pane S., Ristori M.V., Pirona I., Guarrasi V., Cotugno N., Bernardi S., Lancella L., Perno C.F., Rossi P., Villani A., Campana A., Palma P. , Putignani L.",Exploring nasopharyngeal microbiota profile in children affected by SARS-CoV-2 infection,Microbiology spectrum,2024,"COVID-19, SARS-CoV-2, children, nasopharyngeal microbiota, respiratory tract",Experiment 2,United States of America,Homo sapiens,Nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,NO COVID-19 (Patients with diagnosis different from COVID-19),COVID-19 patients,"Children whose Nasopharyngeal swab were positive for SARS-CoV-2 infection, as assayed by a molecular test.",7,71,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,age,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure S4,11 April 2024,Joan Chuks,"Joan Chuks,ChiomaBlessing,WikiWorks",Differences in bacterial taxa abundance of nasopharyngeal (NP) microbiota in COVID-19 patients Vs NO COVID-19 (Patients with diagnosis different from COVID-19),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Beijerinckiaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,s__unidentified,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",3379134|976|200643|171549|171552|1283313;3379134|1224|28211;3379134|1224|28211|356|45404;3384189|32066|203490|203491|203492;3384189|32066|203490|203491|203492|848;3379134|1224|28216|80840|119060|47670;3379134|1224|1236|2887326|468;3379134|1224|28211|204455|31989;3379134|1224|28211|204455|31989|265;3379134|1224|1236|72274|135621;3379134|1224|1236|72274;3379134|1224|28211|204455;3379134|1224|28211|204457|41297;3379134|1224|28211|204457;3379134|1224|28211|204457|41297|13687;32644;3379134|1224|1236|72274|135621|286,Complete,ChiomaBlessing
bsdb:38291301/1/1,38291301,randomized controlled trial,38291301,10.1038/s41591-023-02761-2,https://pubmed.ncbi.nlm.nih.gov/38291301/,"Link V.M., Subramanian P., Cheung F., Han K.L., Stacy A., Chi L., Sellers B.A., Koroleva G., Courville A.B., Mistry S., Burns A., Apps R., Hall K.D. , Belkaid Y.",Differential peripheral immune signatures elicited by vegan versus ketogenic diets in humans,Nature medicine,2024,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Participants on vegan diet,Participants on ketogenic diet,"To determine the impact of dietary intervention on human immunity and microbiota, this group of participants were placed on a ketogenic diet, and would later be switched to a vegan diet.",10,10,NA,WMS,NA,Illumina,centered log-ratio,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Fig. 4e,10 March 2024,Johnpaul,"Johnpaul,Aleru Divine,Scholastica,WikiWorks","Differentially abundant species between ketogenic and vegan diets for all significant taxa, showing the impact of a ketogenic diet on participants compared to a vegan diet.",increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas faecihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma|s__Dielma fastidiosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Neobittarella (ex Bilen et al. 2018)|s__Neobittarella massiliensis (ex Bilen et al. 2018),k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] sulci",3379134|200940|3031449|213115|194924|35832|35833;3379134|976|200643|171549|1853231|574697|1472416;3379134|976|200643|171549|1853231|574697|544645;1783272|1239|526524|526525|128827|1472649|1034346;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|2719313|358743;1783272|1239|186801|186802|186806|1730|39490;1783272|1239|91061|186826|1300|1357|1358;1783272|1239|186801|186802|216572|2126544|2041842;3379134|976|200643|171549|1853231|283168|28118;1783272|1239|909932|1843488|909930|33024|33025;3379134|976|200643|171549|815|909656|671267;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|3082720|543314|143393,Complete,Svetlana up
bsdb:38291301/1/2,38291301,randomized controlled trial,38291301,10.1038/s41591-023-02761-2,https://pubmed.ncbi.nlm.nih.gov/38291301/,"Link V.M., Subramanian P., Cheung F., Han K.L., Stacy A., Chi L., Sellers B.A., Koroleva G., Courville A.B., Mistry S., Burns A., Apps R., Hall K.D. , Belkaid Y.",Differential peripheral immune signatures elicited by vegan versus ketogenic diets in humans,Nature medicine,2024,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Participants on vegan diet,Participants on ketogenic diet,"To determine the impact of dietary intervention on human immunity and microbiota, this group of participants were placed on a ketogenic diet, and would later be switched to a vegan diet.",10,10,NA,WMS,NA,Illumina,centered log-ratio,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Fig. 4e,10 March 2024,Johnpaul,"Johnpaul,Aleru Divine,Scholastica,WikiWorks","Differentially abundant species between ketogenic and vegan diets for all significant taxa, showing the impact of a ketogenic diet on participants compared to a vegan diet.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum butyriciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis|s__Anaerofustis stercorihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|s__Bacillota bacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia massiliensis (ex Durand et al. 2017),k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella morbi,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|186802|3085642|2048137|1628085;1783272|1239|186801|186802|186806|264995|214853;1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|1879010;1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|1678|1686;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|186801|3085636|186803|572511|1737424;1783272|1239|186801|186802|3085642|580596|2049021;1783272|1239|186801|186802|186806|1730|142586;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|3082720|186804|1505657|261299;1783272|1239|186801|3085636|186803|1898203;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|1263|41978;1783272|1239|186801|186802|216572|292632|2053618;1783272|1239|186801|3085636|186803|43996|43997;1783272|1239|186801|3085636|186803|572511|1955243,Complete,Svetlana up
bsdb:38294805/1/4,38294805,case-control,38294805,10.1001/jamapsychiatry.2023.5371,NA,"Vasileva S.S., Yang Y., Baker A., Siskind D., Gratten J. , Eyles D.",Associations of the Gut Microbiome With Treatment Resistance in Schizophrenia,JAMA psychiatry,2024,NA,Experiment 1,Australia,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,control individuals without a psychiatric diagnosis (past or present),SCZ: individuals with a psychiatric diagnosis of schizophrenia,"Participants with a schizophrenia diagnosis categorized as follows:
1. AAP: individuals with treatment-responsive schizophrenia taking atypical antipsychotics (not clozapine) with a total Positive and Negative Symptom Scale (PANSS) score of 60 or low.
2. CR: individuals with treatment-resistant schizophrenia who were clozapine responsive total PANSS score ≤60).
3. CNR: individuals with treatment-resistant schizophrenia who were clozapine nonresponsive
(total PANSS score >60).",25,72,2 months,WMS,NA,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,unchanged,NA,unchanged,NA,decreased,Signature 4,Figure 3,29 June 2024,Jacob A. De Jesus,"Jacob A. De Jesus,WikiWorks","Differentially abundant species identified for control individuals and SCZ group comparisons. Analyses were performed using ANCOM-BC, adjusting for age, sex, and body mass index.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter urolithinfaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella effluvii",1783272|1239|186801|186802|216572|244127|169435;1783272|1239|186801|3085636|186803|572511|33035;1783272|201174|84998|1643822|1643826|84111|84112;3379134|1224|1236|91347|543|561|562;1783272|201174|84998|1643822|1643826|644652|1335613;1783272|1239|186801|3085636|186803|1649459|1096246,Complete,Svetlana up
bsdb:38294805/1/5,38294805,case-control,38294805,10.1001/jamapsychiatry.2023.5371,NA,"Vasileva S.S., Yang Y., Baker A., Siskind D., Gratten J. , Eyles D.",Associations of the Gut Microbiome With Treatment Resistance in Schizophrenia,JAMA psychiatry,2024,NA,Experiment 1,Australia,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,control individuals without a psychiatric diagnosis (past or present),SCZ: individuals with a psychiatric diagnosis of schizophrenia,"Participants with a schizophrenia diagnosis categorized as follows:
1. AAP: individuals with treatment-responsive schizophrenia taking atypical antipsychotics (not clozapine) with a total Positive and Negative Symptom Scale (PANSS) score of 60 or low.
2. CR: individuals with treatment-resistant schizophrenia who were clozapine responsive total PANSS score ≤60).
3. CNR: individuals with treatment-resistant schizophrenia who were clozapine nonresponsive
(total PANSS score >60).",25,72,2 months,WMS,NA,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,unchanged,NA,unchanged,NA,decreased,Signature 5,Figure 3,29 June 2024,Jacob A. De Jesus,"Jacob A. De Jesus,WikiWorks","Differentially abundant species identified for control individuals and SCZ group comparisons. Analyses were performed using ANCOM-BC, adjusting for age, sex, and body mass index.",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,1783272|1239|186801|3082720|186804|1501226|1776391,Complete,Svetlana up
bsdb:38294805/2/1,38294805,case-control,38294805,10.1001/jamapsychiatry.2023.5371,NA,"Vasileva S.S., Yang Y., Baker A., Siskind D., Gratten J. , Eyles D.",Associations of the Gut Microbiome With Treatment Resistance in Schizophrenia,JAMA psychiatry,2024,NA,Experiment 2,Australia,Homo sapiens,Feces,UBERON:0001988,Response to antipsychotic drug,GO:0097332,control individuals without a psychiatric diagnosis of schizophrenia,AAP: individuals with treatment-responsive schizophrenia taking atypical antipsychotics (not clozapine),AAP: individuals with treatment-responsive schizophrenia taking atypical antipsychotics (not clozapine) with a total Positive and Negative Symptom Scale (PANSS) score of 60 or low.,25,24,2 months,WMS,NA,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,unchanged,NA,unchanged,NA,decreased,Signature 1,Figure 3,4 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,WikiWorks","Differentially abundant species identified for control individuals and AAP group comparisons. Analyses were performed using ANCOM-BC, adjusting for age, sex, and body mass index.",decreased,NA,NA,Complete,Svetlana up
bsdb:38294805/3/1,38294805,case-control,38294805,10.1001/jamapsychiatry.2023.5371,NA,"Vasileva S.S., Yang Y., Baker A., Siskind D., Gratten J. , Eyles D.",Associations of the Gut Microbiome With Treatment Resistance in Schizophrenia,JAMA psychiatry,2024,NA,Experiment 3,Australia,Homo sapiens,Feces,UBERON:0001988,Treatment refractory schizophrenia,EFO:0004609,AAP: individuals with treatment-responsive schizophrenia taking atypical antipsychotics (not clozapine),TRS: individuals with treatment-resistant schizophrenia taking clozapine,"Participants with treatment-resistant schizophrenia categorized as follows: 1. CR: individuals with treatment-resistant schizophrenia who were clozapine responsive total PANSS score ≤60).
2. CNR: individuals with treatment-resistant schizophrenia who were clozapine nonresponsive
(total PANSS score >60).",24,48,2 months,WMS,NA,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 3,1 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,WikiWorks","Differentially abundant species identified for AAP and TRS group comparisons. Analyses were performed using ANCOM-BC, adjusting for age, sex, and body mass index.",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella tayi,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella effluvii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans",1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|3085636|186803|1432051|1432052;1783272|1239|186801|3085636|186803|1649459|1096246;1783272|1239|186801|186802|216572|1905344|1550024,Complete,Svetlana up
bsdb:38294805/3/2,38294805,case-control,38294805,10.1001/jamapsychiatry.2023.5371,NA,"Vasileva S.S., Yang Y., Baker A., Siskind D., Gratten J. , Eyles D.",Associations of the Gut Microbiome With Treatment Resistance in Schizophrenia,JAMA psychiatry,2024,NA,Experiment 3,Australia,Homo sapiens,Feces,UBERON:0001988,Treatment refractory schizophrenia,EFO:0004609,AAP: individuals with treatment-responsive schizophrenia taking atypical antipsychotics (not clozapine),TRS: individuals with treatment-resistant schizophrenia taking clozapine,"Participants with treatment-resistant schizophrenia categorized as follows: 1. CR: individuals with treatment-resistant schizophrenia who were clozapine responsive total PANSS score ≤60).
2. CNR: individuals with treatment-resistant schizophrenia who were clozapine nonresponsive
(total PANSS score >60).",24,48,2 months,WMS,NA,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 3,1 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,WikiWorks","Differentially abundant species identified for AAP and TRS group comparisons. Analyses were performed using ANCOM-BC, adjusting for age, sex, and body mass index.",decreased,NA,NA,Complete,Svetlana up
bsdb:38294805/4/1,38294805,case-control,38294805,10.1001/jamapsychiatry.2023.5371,NA,"Vasileva S.S., Yang Y., Baker A., Siskind D., Gratten J. , Eyles D.",Associations of the Gut Microbiome With Treatment Resistance in Schizophrenia,JAMA psychiatry,2024,NA,Experiment 4,Australia,Homo sapiens,Feces,UBERON:0001988,Treatment refractory schizophrenia,EFO:0004609,control individuals without a psychiatric diagnosis of schizophrenia,TRS: individuals with treatment-resistant schizophrenia taking clozapine,Participants with treatment-resistant schizophrenia categorized as follows: 1. CR: individuals with treatment-resistant schizophrenia who were clozapine responsive total PANSS score ≤60). 2. CNR: individuals with treatment-resistant schizophrenia who were clozapine nonresponsive (total PANSS score >60).,25,48,2 months,WMS,NA,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,4 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,WikiWorks","Differentially abundant species identified for control individuals and TRS group comparisons. Analyses were performed using ANCOM-BC, adjusting for age, sex, and body mass index.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter urolithinfaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella effluvii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans",1783272|1239|186801|186802|216572|244127|169435;1783272|201174|84998|1643822|1643826|84111|84112;3379134|1224|1236|91347|543|561|562;1783272|201174|84998|1643822|1643826|644652|1335613;1783272|1239|186801|3085636|186803|1649459|1096246;1783272|1239|186801|186802|216572|1905344|1550024,Complete,Svetlana up
bsdb:38294805/4/2,38294805,case-control,38294805,10.1001/jamapsychiatry.2023.5371,NA,"Vasileva S.S., Yang Y., Baker A., Siskind D., Gratten J. , Eyles D.",Associations of the Gut Microbiome With Treatment Resistance in Schizophrenia,JAMA psychiatry,2024,NA,Experiment 4,Australia,Homo sapiens,Feces,UBERON:0001988,Treatment refractory schizophrenia,EFO:0004609,control individuals without a psychiatric diagnosis of schizophrenia,TRS: individuals with treatment-resistant schizophrenia taking clozapine,Participants with treatment-resistant schizophrenia categorized as follows: 1. CR: individuals with treatment-resistant schizophrenia who were clozapine responsive total PANSS score ≤60). 2. CNR: individuals with treatment-resistant schizophrenia who were clozapine nonresponsive (total PANSS score >60).,25,48,2 months,WMS,NA,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,4 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,WikiWorks","Differentially abundant species identified for control individuals and TRS group comparisons. Analyses were performed using ANCOM-BC, adjusting for age, sex, and body mass index.",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,1783272|1239|186801|3082720|186804|1501226|1776391,Complete,Svetlana up
bsdb:38294805/5/1,38294805,case-control,38294805,10.1001/jamapsychiatry.2023.5371,NA,"Vasileva S.S., Yang Y., Baker A., Siskind D., Gratten J. , Eyles D.",Associations of the Gut Microbiome With Treatment Resistance in Schizophrenia,JAMA psychiatry,2024,NA,Experiment 5,Australia,Homo sapiens,Feces,UBERON:0001988,Response to clozapine,NA,control individuals without a psychiatric diagnosis of schizophrenia,CR: individuals with treatment-resistant schizophrenia responsive to clozapine,CR: individuals with treatment-resistant schizophrenia who were clozapine responsive (total PANSS score ≤60).,25,26,2 months,WMS,NA,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,unchanged,NA,unchanged,NA,decreased,Signature 1,Figure 3,4 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,WikiWorks","Differentially abundant species identified for control individuals and CR group comparisons. Analyses were performed using ANCOM-BC, adjusting for age, sex, and body mass index.",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella effluvii",1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|3085636|186803|1649459|1096246,Complete,Svetlana up
bsdb:38294805/5/2,38294805,case-control,38294805,10.1001/jamapsychiatry.2023.5371,NA,"Vasileva S.S., Yang Y., Baker A., Siskind D., Gratten J. , Eyles D.",Associations of the Gut Microbiome With Treatment Resistance in Schizophrenia,JAMA psychiatry,2024,NA,Experiment 5,Australia,Homo sapiens,Feces,UBERON:0001988,Response to clozapine,NA,control individuals without a psychiatric diagnosis of schizophrenia,CR: individuals with treatment-resistant schizophrenia responsive to clozapine,CR: individuals with treatment-resistant schizophrenia who were clozapine responsive (total PANSS score ≤60).,25,26,2 months,WMS,NA,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,unchanged,NA,unchanged,NA,decreased,Signature 2,Figure 3,4 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,WikiWorks","Differentially abundant species identified for control individuals and CR group comparisons. Analyses were performed using ANCOM-BC, adjusting for age, sex, and body mass index.",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,1783272|1239|186801|3082720|186804|1501226|1776391,Complete,Svetlana up
bsdb:38294805/6/1,38294805,case-control,38294805,10.1001/jamapsychiatry.2023.5371,NA,"Vasileva S.S., Yang Y., Baker A., Siskind D., Gratten J. , Eyles D.",Associations of the Gut Microbiome With Treatment Resistance in Schizophrenia,JAMA psychiatry,2024,NA,Experiment 6,Australia,Homo sapiens,Feces,UBERON:0001988,Treatment refractory schizophrenia,EFO:0004609,control individuals without a psychiatric diagnosis of schizophrenia,CNR: individuals with treatment-resistant schizophrenia nonresponsive to clozapine,CNR: individuals with treatment-resistant schizophrenia who were clozapine nonresponsive (total PANSS score >60).,25,22,2 months,WMS,NA,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 3,4 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,WikiWorks","Differentially abundant species identified for CR and CNR group comparisons. Analyses were performed using ANCOM-BC, adjusting for age, sex, and body mass index.",increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,1783272|1239|186801|186802|216572|1905344|1550024,Complete,Svetlana up
bsdb:38294805/6/2,38294805,case-control,38294805,10.1001/jamapsychiatry.2023.5371,NA,"Vasileva S.S., Yang Y., Baker A., Siskind D., Gratten J. , Eyles D.",Associations of the Gut Microbiome With Treatment Resistance in Schizophrenia,JAMA psychiatry,2024,NA,Experiment 6,Australia,Homo sapiens,Feces,UBERON:0001988,Treatment refractory schizophrenia,EFO:0004609,control individuals without a psychiatric diagnosis of schizophrenia,CNR: individuals with treatment-resistant schizophrenia nonresponsive to clozapine,CNR: individuals with treatment-resistant schizophrenia who were clozapine nonresponsive (total PANSS score >60).,25,22,2 months,WMS,NA,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 3,4 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,WikiWorks","Differentially abundant species identified for CR and CNR group comparisons. Analyses were performed using ANCOM-BC, adjusting for age, sex, and body mass index.",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,1783272|1239|186801|3082720|186804|1501226|1776391,Complete,Svetlana up
bsdb:38306898/1/1,38306898,"cross-sectional observational, not case-control",38306898,10.1016/j.ebiom.2024.104980,NA,"Barot S.V., Sangwan N., Nair K.G., Schmit S.L., Xiang S., Kamath S., Liska D. , Khorana A.A.",Distinct intratumoral microbiome of young-onset and average-onset colorectal cancer,EBioMedicine,2024,"16S, Colorectal cancer, Dysbiosis, Early-onset, Microbiome, Young-onset",Experiment 1,United States of America,Homo sapiens,Colorectum,UBERON:0012652,Colorectal cancer,EFO:0005842,Average-Onset Colorectal Cancer(aoCRC)(tumor tissue),Young-Onset Colorectal Cancer(yoCRC)(tumor tissue),Tumor tissue of patients diagnosed with colorectal cancer before the age of 50 years,140,136,NA,16S,4,Illumina,relative abundances,Random Forest Analysis,0.05,TRUE,NA,NA,"race,sex,smoking status",NA,increased,NA,NA,NA,increased,Signature 1,Table 2,14 October 2025,Adenike Awotunde,Adenike Awotunde,Relative abundance (%) between yoCRC and aoCRC tumor tissue,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:38306898/1/2,38306898,"cross-sectional observational, not case-control",38306898,10.1016/j.ebiom.2024.104980,NA,"Barot S.V., Sangwan N., Nair K.G., Schmit S.L., Xiang S., Kamath S., Liska D. , Khorana A.A.",Distinct intratumoral microbiome of young-onset and average-onset colorectal cancer,EBioMedicine,2024,"16S, Colorectal cancer, Dysbiosis, Early-onset, Microbiome, Young-onset",Experiment 1,United States of America,Homo sapiens,Colorectum,UBERON:0012652,Colorectal cancer,EFO:0005842,Average-Onset Colorectal Cancer(aoCRC)(tumor tissue),Young-Onset Colorectal Cancer(yoCRC)(tumor tissue),Tumor tissue of patients diagnosed with colorectal cancer before the age of 50 years,140,136,NA,16S,4,Illumina,relative abundances,Random Forest Analysis,0.05,TRUE,NA,NA,"race,sex,smoking status",NA,increased,NA,NA,NA,increased,Signature 2,Table 2,14 October 2025,Adenike Awotunde,Adenike Awotunde,Relative abundance (%) between yoCRC and aoCRC tumor tissue.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Listeria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",1783272|1239|91061|1385|186817|1386;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|1940338;3384189|32066|203490|203491|203492|848;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|1385|186820|1637;3379134|976|200643|171549|2005525|375288;3379134|1224|1236|72274|135621|286;3379134|1224|1236|91347|543|590;1783272|1239|91061|1385|90964|1279;3379134|976|200643|171549|171550|239759,Complete,Svetlana up
bsdb:38306898/2/1,38306898,"cross-sectional observational, not case-control",38306898,10.1016/j.ebiom.2024.104980,NA,"Barot S.V., Sangwan N., Nair K.G., Schmit S.L., Xiang S., Kamath S., Liska D. , Khorana A.A.",Distinct intratumoral microbiome of young-onset and average-onset colorectal cancer,EBioMedicine,2024,"16S, Colorectal cancer, Dysbiosis, Early-onset, Microbiome, Young-onset",Experiment 2,United States of America,Homo sapiens,Colorectum,UBERON:0012652,Colorectal cancer,EFO:0005842,Average-Onset Colorectal Cancer(aoCRC)(Adjacent non-malignant tissue),Young-Onset Colorectal Cancer(yoCRC) (Adjacent non-malignant tissue),Adjacent non malignant(normal) tissue of patients diagnosed with colorectal cancer before the age of 50 years.,140,136,NA,16S,4,Illumina,relative abundances,Random Forest Analysis,0.05,TRUE,NA,NA,"race,sex,smoking status",NA,increased,NA,NA,NA,increased,Signature 1,Table 2,15 October 2025,Adenike Awotunde,Adenike Awotunde,Relative abundance (%) between yoCRC and aoCRC adjacent non-malignant tissue.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|976|200643|171549|815|816;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:38306898/2/2,38306898,"cross-sectional observational, not case-control",38306898,10.1016/j.ebiom.2024.104980,NA,"Barot S.V., Sangwan N., Nair K.G., Schmit S.L., Xiang S., Kamath S., Liska D. , Khorana A.A.",Distinct intratumoral microbiome of young-onset and average-onset colorectal cancer,EBioMedicine,2024,"16S, Colorectal cancer, Dysbiosis, Early-onset, Microbiome, Young-onset",Experiment 2,United States of America,Homo sapiens,Colorectum,UBERON:0012652,Colorectal cancer,EFO:0005842,Average-Onset Colorectal Cancer(aoCRC)(Adjacent non-malignant tissue),Young-Onset Colorectal Cancer(yoCRC) (Adjacent non-malignant tissue),Adjacent non malignant(normal) tissue of patients diagnosed with colorectal cancer before the age of 50 years.,140,136,NA,16S,4,Illumina,relative abundances,Random Forest Analysis,0.05,TRUE,NA,NA,"race,sex,smoking status",NA,increased,NA,NA,NA,increased,Signature 2,Table 2,15 October 2025,Adenike Awotunde,Adenike Awotunde,Relative abundance (%) between yoCRC and aoCRC adjacent non-malignant tissue.,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Listeria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;1783272|1239|91061|1385|186817|1386;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|1940338;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|186820|1637;3379134|1224|1236|72274|135621|286;3379134|1224|1236|91347|543|590;1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:38306898/3/1,38306898,"cross-sectional observational, not case-control",38306898,10.1016/j.ebiom.2024.104980,NA,"Barot S.V., Sangwan N., Nair K.G., Schmit S.L., Xiang S., Kamath S., Liska D. , Khorana A.A.",Distinct intratumoral microbiome of young-onset and average-onset colorectal cancer,EBioMedicine,2024,"16S, Colorectal cancer, Dysbiosis, Early-onset, Microbiome, Young-onset",Experiment 3,United States of America,Homo sapiens,Colorectum,UBERON:0012652,Colorectal cancer,EFO:0005842,Small-sized colorectal cancer tumors in aoCRC,Large-sized colorectal cancer tumors in aoCRC,Tumor samples from patients whose colorectal tumors are classified as large in size in aoCRC cohort,NA,NA,NA,16S,4,Illumina,relative abundances,metagenomeSeq,0.05,TRUE,NA,NA,"race,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4A,20 October 2025,Adenike Awotunde,Adenike Awotunde,Correlation analysis of yoCRC and aoCRC tumors depicting the linear association between specific microbial genera and tumor size,increased,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,3384189|32066|203490|203491|203492|848,Complete,Svetlana up
bsdb:38306898/3/2,38306898,"cross-sectional observational, not case-control",38306898,10.1016/j.ebiom.2024.104980,NA,"Barot S.V., Sangwan N., Nair K.G., Schmit S.L., Xiang S., Kamath S., Liska D. , Khorana A.A.",Distinct intratumoral microbiome of young-onset and average-onset colorectal cancer,EBioMedicine,2024,"16S, Colorectal cancer, Dysbiosis, Early-onset, Microbiome, Young-onset",Experiment 3,United States of America,Homo sapiens,Colorectum,UBERON:0012652,Colorectal cancer,EFO:0005842,Small-sized colorectal cancer tumors in aoCRC,Large-sized colorectal cancer tumors in aoCRC,Tumor samples from patients whose colorectal tumors are classified as large in size in aoCRC cohort,NA,NA,NA,16S,4,Illumina,relative abundances,metagenomeSeq,0.05,TRUE,NA,NA,"race,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 2,Figure 4A,20 October 2025,Adenike Awotunde,Adenike Awotunde,Correlation analysis of yoCRC and aoCRC tumors depicting the linear association between specific microbial genera and tumor size,decreased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,3379134|74201|203494|48461|1647988|239934,Complete,Svetlana up
bsdb:38306898/4/1,38306898,"cross-sectional observational, not case-control",38306898,10.1016/j.ebiom.2024.104980,NA,"Barot S.V., Sangwan N., Nair K.G., Schmit S.L., Xiang S., Kamath S., Liska D. , Khorana A.A.",Distinct intratumoral microbiome of young-onset and average-onset colorectal cancer,EBioMedicine,2024,"16S, Colorectal cancer, Dysbiosis, Early-onset, Microbiome, Young-onset",Experiment 4,United States of America,Homo sapiens,Colorectum,UBERON:0012652,Colorectal cancer,EFO:0005842,Short overall survival in yoCRC,Long overall survival in yoCRC,Young-onset colorectal cancer patients with longer overall survival.,NA,NA,NA,16S,4,Illumina,relative abundances,metagenomeSeq,0.05,TRUE,NA,NA,"race,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,20 October 2025,Adenike Awotunde,Adenike Awotunde,Correlation analysis of yoCRC tumors depicting the linear association between specific microbial genera and overall survival,increased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,3379134|74201|203494|48461|1647988|239934,Complete,Svetlana up
bsdb:38306898/4/2,38306898,"cross-sectional observational, not case-control",38306898,10.1016/j.ebiom.2024.104980,NA,"Barot S.V., Sangwan N., Nair K.G., Schmit S.L., Xiang S., Kamath S., Liska D. , Khorana A.A.",Distinct intratumoral microbiome of young-onset and average-onset colorectal cancer,EBioMedicine,2024,"16S, Colorectal cancer, Dysbiosis, Early-onset, Microbiome, Young-onset",Experiment 4,United States of America,Homo sapiens,Colorectum,UBERON:0012652,Colorectal cancer,EFO:0005842,Short overall survival in yoCRC,Long overall survival in yoCRC,Young-onset colorectal cancer patients with longer overall survival.,NA,NA,NA,16S,4,Illumina,relative abundances,metagenomeSeq,0.05,TRUE,NA,NA,"race,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 2,Figure 4B,21 October 2025,Adenike Awotunde,Adenike Awotunde,Correlation analysis of yoCRC tumors depicting the linear association between specific microbial genera and overall survival.,decreased,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,3384189|32066|203490|203491|203492|848,Complete,Svetlana up
bsdb:38306898/5/1,38306898,"cross-sectional observational, not case-control",38306898,10.1016/j.ebiom.2024.104980,NA,"Barot S.V., Sangwan N., Nair K.G., Schmit S.L., Xiang S., Kamath S., Liska D. , Khorana A.A.",Distinct intratumoral microbiome of young-onset and average-onset colorectal cancer,EBioMedicine,2024,"16S, Colorectal cancer, Dysbiosis, Early-onset, Microbiome, Young-onset",Experiment 5,United States of America,Homo sapiens,Colorectum,UBERON:0012652,Colorectal cancer,EFO:0005842,Colon tumors in yoCRC patients,Rectal tumors in yoCRC patients,Rectal tumors in patients with Young-onset colorectal cancer.,NA,NA,NA,16S,4,Illumina,relative abundances,metagenomeSeq,0.05,TRUE,NA,NA,"race,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table S1,21 October 2025,Adenike Awotunde,Adenike Awotunde,"Microbial taxa associated with tumor location in yoCRC, comparing rectal and colon tumors, showing a positive correlation between Fusobacterium abundance and rectal tumors, and a negative correlation between Akkermansia abundance and rectal tumors.",increased,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,3384189|32066|203490|203491|203492|848,Complete,Svetlana up
bsdb:38306898/5/2,38306898,"cross-sectional observational, not case-control",38306898,10.1016/j.ebiom.2024.104980,NA,"Barot S.V., Sangwan N., Nair K.G., Schmit S.L., Xiang S., Kamath S., Liska D. , Khorana A.A.",Distinct intratumoral microbiome of young-onset and average-onset colorectal cancer,EBioMedicine,2024,"16S, Colorectal cancer, Dysbiosis, Early-onset, Microbiome, Young-onset",Experiment 5,United States of America,Homo sapiens,Colorectum,UBERON:0012652,Colorectal cancer,EFO:0005842,Colon tumors in yoCRC patients,Rectal tumors in yoCRC patients,Rectal tumors in patients with Young-onset colorectal cancer.,NA,NA,NA,16S,4,Illumina,relative abundances,metagenomeSeq,0.05,TRUE,NA,NA,"race,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table S1,21 October 2025,Adenike Awotunde,Adenike Awotunde,"Microbial taxa associated with tumor location in yoCRC, comparing rectal and colon tumors, showing a positive correlation between Fusobacterium abundance and rectal tumors, and a negative correlation between Akkermansia abundance and rectal tumors.",decreased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,3379134|74201|203494|48461|1647988|239934,Complete,Svetlana up
bsdb:38306898/6/1,38306898,"cross-sectional observational, not case-control",38306898,10.1016/j.ebiom.2024.104980,NA,"Barot S.V., Sangwan N., Nair K.G., Schmit S.L., Xiang S., Kamath S., Liska D. , Khorana A.A.",Distinct intratumoral microbiome of young-onset and average-onset colorectal cancer,EBioMedicine,2024,"16S, Colorectal cancer, Dysbiosis, Early-onset, Microbiome, Young-onset",Experiment 6,United States of America,Homo sapiens,Colorectum,UBERON:0012652,Colorectal cancer,EFO:0005842,Colon tumors in aoCRC patients,Rectal tumors in aoCRC patients,Rectal tumors in patients with Average-onset colorectal cancer,NA,NA,NA,16S,4,Illumina,relative abundances,metagenomeSeq,0.05,TRUE,NA,NA,"race,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table S1,21 October 2025,Adenike Awotunde,Adenike Awotunde,"Microbial taxa associated with tumor location in aoCRC, comparing rectal and colon tumors, showing a positive correlation between Fusobacterium abundance and rectal tumors, and a negative correlation between Akkermansia abundance and rectal tumors.",increased,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,3384189|32066|203490|203491|203492|848,Complete,Svetlana up
bsdb:38306898/6/2,38306898,"cross-sectional observational, not case-control",38306898,10.1016/j.ebiom.2024.104980,NA,"Barot S.V., Sangwan N., Nair K.G., Schmit S.L., Xiang S., Kamath S., Liska D. , Khorana A.A.",Distinct intratumoral microbiome of young-onset and average-onset colorectal cancer,EBioMedicine,2024,"16S, Colorectal cancer, Dysbiosis, Early-onset, Microbiome, Young-onset",Experiment 6,United States of America,Homo sapiens,Colorectum,UBERON:0012652,Colorectal cancer,EFO:0005842,Colon tumors in aoCRC patients,Rectal tumors in aoCRC patients,Rectal tumors in patients with Average-onset colorectal cancer,NA,NA,NA,16S,4,Illumina,relative abundances,metagenomeSeq,0.05,TRUE,NA,NA,"race,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table S1,21 October 2025,Adenike Awotunde,Adenike Awotunde,"Microbial taxa associated with tumor location in aoCRC, comparing rectal and colon tumors, showing a positive correlation between Fusobacterium abundance and rectal tumors, and a negative correlation between Akkermansia abundance and rectal tumors.",decreased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,3379134|74201|203494|48461|1647988|239934,Complete,Svetlana up
bsdb:38310301/1/1,38310301,time series / longitudinal observational,38310301,10.1186/s40168-023-01718-4,NA,"Burkhart Colorado A.S., Lazzaro A., Neff C.P., Nusbacher N., Boyd K., Fiorillo S., Martin C., Siebert J.C., Campbell T.B., Borok M., Palmer B.E. , Lozupone C.",Differential effects of antiretroviral treatment on immunity and gut microbiome composition in people living with HIV in rural versus urban Zimbabwe,Microbiome,2024,"ART response, HIV, Immune activation and exhaustion, Inflammation, Intestinal microbiome, Rural, Urban",Experiment 1,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Healthy controls (HC),Antiretroviral therapy (ART) Naïve at baseline,PLWH (people living with HIV) who were not on ART at the first timepoint but who subsequently commenced first-line ART with efavirenz/lamivudine/tenofovir disoproxil fumarate (EFV/3TC/TDF) and the prophylactic antibiotic cotrimoxazole (ART Naïve) - Baseline,42,67,2 months,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 4A,11 March 2024,Nwajei Edgar,"Nwajei Edgar,Ayibatari,Keamy,WikiWorks","Differential abundance of genera in ART-naïve compared to HC using ANCOM-BC, significant differential log-fold changes between microbes were calculated relative to healthy controls using only baseline values.",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,1783272|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:38310301/2/2,38310301,time series / longitudinal observational,38310301,10.1186/s40168-023-01718-4,NA,"Burkhart Colorado A.S., Lazzaro A., Neff C.P., Nusbacher N., Boyd K., Fiorillo S., Martin C., Siebert J.C., Campbell T.B., Borok M., Palmer B.E. , Lozupone C.",Differential effects of antiretroviral treatment on immunity and gut microbiome composition in people living with HIV in rural versus urban Zimbabwe,Microbiome,2024,"ART response, HIV, Immune activation and exhaustion, Inflammation, Intestinal microbiome, Rural, Urban",Experiment 2,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,Healthy controls (HC),Antiretroviral therapy (ART) naïve at baseline and after 24 weeks of first-line ART,PLWH (people living with HIV) who were not on antiretroviral therapy (ART) at the first timepoint but who subsequently commenced first-line ART with efavirenz/lamivudine/tenofovir disoproxil fumarate (EFV/3TC/TDF) and the prophylactic antibiotic cotrimoxazole (ART Naïve) - two time points.,42,52,2 months,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,time,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 4B,13 March 2024,Nwajei Edgar,"Nwajei Edgar,Ayibatari,Keamy,WikiWorks",ART-naïve compared to HC with Model using two time points.,decreased,"c__Bigyra|o__Opalinata|f__Blastocystidae|g__Blastocystis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2683628|42740|2547934|12967;1783272|1239|186801|3085636|186803|830;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:38310301/3/1,38310301,time series / longitudinal observational,38310301,10.1186/s40168-023-01718-4,NA,"Burkhart Colorado A.S., Lazzaro A., Neff C.P., Nusbacher N., Boyd K., Fiorillo S., Martin C., Siebert J.C., Campbell T.B., Borok M., Palmer B.E. , Lozupone C.",Differential effects of antiretroviral treatment on immunity and gut microbiome composition in people living with HIV in rural versus urban Zimbabwe,Microbiome,2024,"ART response, HIV, Immune activation and exhaustion, Inflammation, Intestinal microbiome, Rural, Urban",Experiment 3,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,Healthy controls (HC),Antiretroviral therapy (ART) experienced at baseline,PLWH (people living with HIV) who were on  ART regimen and cotrimoxazole at baseline,42,33,2 months,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 4A,13 April 2024,Keamy,"Keamy,WikiWorks","Differential abundance of genera in ART experienced compared to HC using ANCOM-BC, significant differential log-fold changes between microbes were calculated relative to healthy controls using only baseline values.",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|3085636|186803|1506553,Complete,Svetlana up
bsdb:38310301/3/2,38310301,time series / longitudinal observational,38310301,10.1186/s40168-023-01718-4,NA,"Burkhart Colorado A.S., Lazzaro A., Neff C.P., Nusbacher N., Boyd K., Fiorillo S., Martin C., Siebert J.C., Campbell T.B., Borok M., Palmer B.E. , Lozupone C.",Differential effects of antiretroviral treatment on immunity and gut microbiome composition in people living with HIV in rural versus urban Zimbabwe,Microbiome,2024,"ART response, HIV, Immune activation and exhaustion, Inflammation, Intestinal microbiome, Rural, Urban",Experiment 3,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,Healthy controls (HC),Antiretroviral therapy (ART) experienced at baseline,PLWH (people living with HIV) who were on  ART regimen and cotrimoxazole at baseline,42,33,2 months,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 4A,13 April 2024,Keamy,"Keamy,WikiWorks","Differential abundance of genera in ART experienced compared to HC using ANCOM-BC, significant differential log-fold changes between microbes were calculated relative to healthy controls using only baseline values.",decreased,"c__Bigyra|o__Opalinata|f__Blastocystidae|g__Blastocystis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2683628|42740|2547934|12967;1783272|1239|186801|3085636|186803|830;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:38310301/4/1,38310301,time series / longitudinal observational,38310301,10.1186/s40168-023-01718-4,NA,"Burkhart Colorado A.S., Lazzaro A., Neff C.P., Nusbacher N., Boyd K., Fiorillo S., Martin C., Siebert J.C., Campbell T.B., Borok M., Palmer B.E. , Lozupone C.",Differential effects of antiretroviral treatment on immunity and gut microbiome composition in people living with HIV in rural versus urban Zimbabwe,Microbiome,2024,"ART response, HIV, Immune activation and exhaustion, Inflammation, Intestinal microbiome, Rural, Urban",Experiment 4,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,Healthy controls (HC),Antiretroviral therapy (ART) experienced at baseline and after 24 weeks,PLWH (people living with HIV) who were on ART regimen and cotrimoxazole at both time points,42,NA,2 months,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,time,NA,decreased,NA,NA,NA,NA,Signature 1,4B,13 April 2024,Keamy,"Keamy,WikiWorks","Differential abundance of genera in ART experienced compared to HC using ANCOM-BC, significant differential log-fold changes between microbes were calculated relative to healthy controls using both time points.",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|3085636|186803|1506553;3379134|200940|3031449|213115|194924|35832,Complete,Svetlana up
bsdb:38310301/4/2,38310301,time series / longitudinal observational,38310301,10.1186/s40168-023-01718-4,NA,"Burkhart Colorado A.S., Lazzaro A., Neff C.P., Nusbacher N., Boyd K., Fiorillo S., Martin C., Siebert J.C., Campbell T.B., Borok M., Palmer B.E. , Lozupone C.",Differential effects of antiretroviral treatment on immunity and gut microbiome composition in people living with HIV in rural versus urban Zimbabwe,Microbiome,2024,"ART response, HIV, Immune activation and exhaustion, Inflammation, Intestinal microbiome, Rural, Urban",Experiment 4,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,Response to antiviral drug,EFO:0010123,Healthy controls (HC),Antiretroviral therapy (ART) experienced at baseline and after 24 weeks,PLWH (people living with HIV) who were on ART regimen and cotrimoxazole at both time points,42,NA,2 months,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,time,NA,decreased,NA,NA,NA,NA,Signature 2,4B,13 April 2024,Keamy,"Keamy,WikiWorks","Differential abundance of genera in ART experienced compared to HC using ANCOM-BC, significant differential log-fold changes between microbes were calculated relative to healthy controls using both time points.",decreased,"c__Bigyra|o__Opalinata|f__Blastocystidae|g__Blastocystis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2683628|42740|2547934|12967;1783272|1239|186801|3085636|186803|830;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:38317217/1/1,38317217,laboratory experiment,38317217,10.1186/s40168-023-01734-4,NA,"Xing J.H., Niu T.M., Zou B.S., Yang G.L., Shi C.W., Yan Q.S., Sun M.J., Yu T., Zhang S.M., Feng X.Z., Fan S.H., Huang H.B., Wang J.H., Li M.H., Jiang Y.L., Wang J.Z., Cao X., Wang N., Zeng Y., Hu J.T., Zhang D., Sun W.S., Yang W.T. , Wang C.F.",Gut microbiota-derived LCA mediates the protective effect of PEDV infection in piglets,Microbiome,2024,"Gut microbiota, Infection resistance, Macrogenomic, Metabolomic, T cell response",Experiment 1,China,Sus scrofa domesticus,Feces,UBERON:0001988,Infectious diarrheal disease,MONDO:0001517,"Combination of M-PEDV(min-Porcine epidemic diarrhea virus), L-CON(landrace-control) and L-PEDV(landrace-  Porcine epidemic diarrhea virus) pigs",M-CON (min-control) pigs,Min pigs in china challenged with porcine backfat syndrome (PBS).,30,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 2G,7 November 2024,Nathcynthia,"Nathcynthia,Tosin,WikiWorks,Ese","Taxa differentially abundant between M-CON (min-control), M-PEDV(min-Porcine epidemic diarrhea virus), L-CON (landrace-control) and L-PEDV(Landrace Porcine epidemic diarrhea virus) pigs.",increased,"k__Bacillati|p__Actinomycetota,,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Actinomycetota",1783272|201174;;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|292632;1783272|201174,Complete,Svetlana up
bsdb:38317217/2/1,38317217,laboratory experiment,38317217,10.1186/s40168-023-01734-4,NA,"Xing J.H., Niu T.M., Zou B.S., Yang G.L., Shi C.W., Yan Q.S., Sun M.J., Yu T., Zhang S.M., Feng X.Z., Fan S.H., Huang H.B., Wang J.H., Li M.H., Jiang Y.L., Wang J.Z., Cao X., Wang N., Zeng Y., Hu J.T., Zhang D., Sun W.S., Yang W.T. , Wang C.F.",Gut microbiota-derived LCA mediates the protective effect of PEDV infection in piglets,Microbiome,2024,"Gut microbiota, Infection resistance, Macrogenomic, Metabolomic, T cell response",Experiment 2,China,Sus scrofa domesticus,Feces,UBERON:0001988,Infectious diarrheal disease,MONDO:0001517,"Combination of M-CON (min-control) , L-CON (landrace-control) and L-PEDV (landrace- Porcine epidemic diarrhea virus) pigs",M-PEDV(min- pigs Porcine epidemic diarrhea virus),Min pigs challenged with PEDV (Porcine epidemic diarrhea virus).,30,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 2G,7 November 2024,Nathcynthia,"Nathcynthia,Tosin,WikiWorks","Taxa differentially abundant between M-CON (min-control), M-PEDV(min- Porcine epidemic diarrhea virus), L-CON (landrace control) and L-PEDV(Landrace Porcine epidemic diarrhea virus) pigs",increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus",1783272|1239|526524|526525;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;1783272|1239|91061|186826|33958|2742598,Complete,Svetlana up
bsdb:38317217/3/1,38317217,laboratory experiment,38317217,10.1186/s40168-023-01734-4,NA,"Xing J.H., Niu T.M., Zou B.S., Yang G.L., Shi C.W., Yan Q.S., Sun M.J., Yu T., Zhang S.M., Feng X.Z., Fan S.H., Huang H.B., Wang J.H., Li M.H., Jiang Y.L., Wang J.Z., Cao X., Wang N., Zeng Y., Hu J.T., Zhang D., Sun W.S., Yang W.T. , Wang C.F.",Gut microbiota-derived LCA mediates the protective effect of PEDV infection in piglets,Microbiome,2024,"Gut microbiota, Infection resistance, Macrogenomic, Metabolomic, T cell response",Experiment 3,China,Sus scrofa domesticus,Feces,UBERON:0001988,Infectious diarrheal disease,MONDO:0001517,"Combination of M-CON (min-control), M-PEDV(min-Porcine epidemic diarrhea virus) and L-PEDV(landrace-Porcine epidemic diarrhea virus) pigs.",L-CON (landrace-control) pigs,Landrace pigs challenged with PBS.,30,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 2G,12 November 2024,Tosin,"Tosin,WikiWorks","Taxa differentially abundant between M-CON (min-control), M-PEDV(min-Porcine epidemic diarrhea virus), L-CON (landrace-control) and L-PEDV(landrace Porcine epidemic diarrhea virus) pigs",increased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia,k__Pseudomonadati|p__Spirochaetota,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,s__unidentified,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|186802;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171550;3379134|203691|203692|136|137;3379134|203691|203692|136;3379134|203691|203692;3379134|203691;3379134|203691|203692|136|2845253|157;32644;1783272|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:38317217/4/1,38317217,laboratory experiment,38317217,10.1186/s40168-023-01734-4,NA,"Xing J.H., Niu T.M., Zou B.S., Yang G.L., Shi C.W., Yan Q.S., Sun M.J., Yu T., Zhang S.M., Feng X.Z., Fan S.H., Huang H.B., Wang J.H., Li M.H., Jiang Y.L., Wang J.Z., Cao X., Wang N., Zeng Y., Hu J.T., Zhang D., Sun W.S., Yang W.T. , Wang C.F.",Gut microbiota-derived LCA mediates the protective effect of PEDV infection in piglets,Microbiome,2024,"Gut microbiota, Infection resistance, Macrogenomic, Metabolomic, T cell response",Experiment 4,China,Sus scrofa domesticus,Feces,UBERON:0001988,Infectious diarrheal disease,MONDO:0001517,"Combination of M-CON (min-control), M-PEDV(min-Porcine epidemic diarrhea virus) and L-CON (landrace-control) pigs.",L-PEDV(landrace- Porcine epidemic diarrhea virus) pigs,Landrace pigs challenged with PEDV (Porcine epidemic diarrhea virus).,30,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 2G,11 November 2024,Nathcynthia,"Nathcynthia,Tosin,WikiWorks","Taxa differentially abundant between M-CON (min-control), M-PEDV(min-Porcine epidemic diarrhea virus), L-CON (landrace-control) and L-PEDV(landrace-Porcine epidemic diarrhea virus) pigs.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales",1783272|1239|186801|3085636|186803|1766253;1783272|1239|91061;1783272|1239;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|906;1783272|1239|909932;1783272|1239|909932|1843489|31977;1783272|1239|909932|1843489;1783272|1239|909932|909929,Complete,Svetlana up
bsdb:38317217/5/1,38317217,laboratory experiment,38317217,10.1186/s40168-023-01734-4,NA,"Xing J.H., Niu T.M., Zou B.S., Yang G.L., Shi C.W., Yan Q.S., Sun M.J., Yu T., Zhang S.M., Feng X.Z., Fan S.H., Huang H.B., Wang J.H., Li M.H., Jiang Y.L., Wang J.Z., Cao X., Wang N., Zeng Y., Hu J.T., Zhang D., Sun W.S., Yang W.T. , Wang C.F.",Gut microbiota-derived LCA mediates the protective effect of PEDV infection in piglets,Microbiome,2024,"Gut microbiota, Infection resistance, Macrogenomic, Metabolomic, T cell response",Experiment 5,China,Sus scrofa domesticus,Feces,UBERON:0001988,Infectious diarrheal disease,MONDO:0001517,M-CON (min-control) pigs,M-PEDV(min-Porcine epidemic diarrhea virus) pigs,Min pigs in china challenged with PEDV (Porcine epidemic diarrhea virus).,10,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,increased,increased,increased,NA,increased,Signature 1,Figure 4D,12 November 2024,Tosin,"Tosin,WikiWorks",Taxa differentially abundant between M-CON (min-control) and M-PEDV(Porcine epidemic diarrhea virus) pigs.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:709,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:770,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:927,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Bariatricus|s__Bariatricus massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus porcorum,k__Pseudomonadati|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia|s__Chlamydia trachomatis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium 52_15,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:127,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:221,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:451,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:180,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:114,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:646,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:124,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:170,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:791,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus amylovorus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus amylovorus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus helveticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus kitasatonis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus pontis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mobilibacterium|s__Mobilibacterium timonense,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma|s__Mycoplasma sp. CAG:956,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. CAG:241,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:386,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:485,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:604,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:873,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:891,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P2-180,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P3-122,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P5-92,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. S7-1-8,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:197,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus flavefaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:254,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. JC304,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum variabile,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema porcinum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__uncultured Blautia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__uncultured Butyricicoccus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__uncultured Eubacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__uncultured Ruminococcus sp.",1783272|1239|186801|3085636|186803|2569097|39488;3379134|976|200643|171549|815|816|1262748;3379134|976|200643|171549|815|816|1262751;3379134|976|200643|171549|815|816|1262753;1783272|1239|186801|3085636|186803|1924081|1745713;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|186802|3085642|580596|1945634;3379134|204428|204429|51291|809|810|813;1783272|1239|186801|186802|1897048;1783272|1239|186801|186802|31979|1485|1262774;1783272|1239|186801|186802|31979|1485|1262780;1783272|1239|186801|186802|31979|1485|1262809;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|1262882;1783272|1239|186801|186802|216572|216851|853;1783272|1239|1263001;1783272|1239|1262995;1783272|1239|1263002;1783272|1239|1263006;1783272|1239|1262993;1783272|1239|526524|526525|128827|1573535|1735;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|91061|186826|33958|1578|1604;1783272|1239|91061|186826|33958|1578|1604;1783272|1239|91061|186826|33958|1578|1587;1783272|1239|91061|186826|33958|1578|33959;1783272|1239|91061|186826|33958|1578|237446;1783272|1239|91061|186826|33958|2742598|97478;1783272|1239|91061|186826|33958|2742598|35787;1783272|1239|91061|186826|33958|2742598|1598;1783272|1239|909932|1843489|31977|906|907;1783272|1239|186801|3082720|543314|1935192|1871012;1783272|544448|31969|2085|2092|2093|1262908;1783272|1239|186801|186802|216572|459786|1262911;3379134|976|200643|171549|171552|838|1262925;3379134|976|200643|171549|171552|838|1262927;3379134|976|200643|171549|171552|838|1262932;3379134|976|200643|171549|171552|838|1262936;3379134|976|200643|171549|171552|838|1262937;3379134|976|200643|171549|171552|838|2024224;3379134|976|200643|171549|171552|838|2024223;3379134|976|200643|171549|171552|838|2024222;3379134|976|200643|171549|171552|838|1284775;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|3085636|186803|841|1262943;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|186801|186802|216572|1263|1265;1783272|1239|186801|186802|216572|1263|1262953;1783272|1239|186801|186802|216572|1263|1095771;1783272|1239|186801|186802|216572|292632|214851;3379134|203691|203692|136|2845253|157|261392;1783272|1239|186801|3085636|186803|572511|765821;1783272|1239|186801|186802|3085642|580596|1193532;1783272|1239|186801|186802|31979|1485|59620;1783272|1239|186801|186802|186806|1730|165185;1783272|1239|186801|186802|216572|1263|165186,Complete,Svetlana up
bsdb:38317217/5/2,38317217,laboratory experiment,38317217,10.1186/s40168-023-01734-4,NA,"Xing J.H., Niu T.M., Zou B.S., Yang G.L., Shi C.W., Yan Q.S., Sun M.J., Yu T., Zhang S.M., Feng X.Z., Fan S.H., Huang H.B., Wang J.H., Li M.H., Jiang Y.L., Wang J.Z., Cao X., Wang N., Zeng Y., Hu J.T., Zhang D., Sun W.S., Yang W.T. , Wang C.F.",Gut microbiota-derived LCA mediates the protective effect of PEDV infection in piglets,Microbiome,2024,"Gut microbiota, Infection resistance, Macrogenomic, Metabolomic, T cell response",Experiment 5,China,Sus scrofa domesticus,Feces,UBERON:0001988,Infectious diarrheal disease,MONDO:0001517,M-CON (min-control) pigs,M-PEDV(min-Porcine epidemic diarrhea virus) pigs,Min pigs in china challenged with PEDV (Porcine epidemic diarrhea virus).,10,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,increased,increased,increased,NA,increased,Signature 2,Figure 4D,12 November 2024,Tosin,"Tosin,WikiWorks",Taxa differentially abundant between M-CON (min-control) and M-PEDV(Porcine epidemic diarrhea virus) pigs.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fluxus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides mediterraneensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 43_108,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:443,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:875,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus cecorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor sp. An306,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor sp. An82,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger sp. An120,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger sp. An50,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:279,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:520,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. tc2-28,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D16,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gallolyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp. 60_17,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella magna,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__uncultured Bacteroides sp.,s__uncultured bacterium",3379134|976|200643|171549|815|816|28111;3379134|976|200643|171549|815|816|626930;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|1841856;3379134|976|200643|171549|815|816|1896974;3379134|976|200643|171549|815|816|1262739;3379134|976|200643|171549|815|816|1262752;3379134|976|200643|171549|815|816|820;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|91061|186826|81852|1350|44008;1783272|1239|186801|186802|216572|946234|1965629;1783272|1239|186801|186802|216572|946234|1965660;1783272|1239|186801|186802|204475|745368;1783272|1239|186801|186802|204475|1965549;1783272|1239|186801|186802|204475|1965639;1783272|1239|186801|186802|1392389|1297617;3379134|976|200643|171549|171552|2974265|363265;1783272|1239|909932|1843488|909930|33024|626940;3379134|976|200643|171549|815|909656|310298;3379134|976|200643|171549|815|909656|387090;3379134|976|200643|171549|815|909656|204516;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|171552|838|1262924;3379134|976|200643|171549|171552|838|1262929;3379134|976|200643|171549|171552|838|1761888;1783272|1239|186801|186802|216572|552398;3379134|976|200643|171549|171552|2974251|165179;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|91061|186826|1300|1301|315405;1783272|1239|186801|186802|216572|292632|1897022;1783272|1239|909932|1843489|31977|29465|464322;3379134|976|200643|171549|815|816|162156;77133,Complete,Svetlana up
bsdb:38317217/6/1,38317217,laboratory experiment,38317217,10.1186/s40168-023-01734-4,NA,"Xing J.H., Niu T.M., Zou B.S., Yang G.L., Shi C.W., Yan Q.S., Sun M.J., Yu T., Zhang S.M., Feng X.Z., Fan S.H., Huang H.B., Wang J.H., Li M.H., Jiang Y.L., Wang J.Z., Cao X., Wang N., Zeng Y., Hu J.T., Zhang D., Sun W.S., Yang W.T. , Wang C.F.",Gut microbiota-derived LCA mediates the protective effect of PEDV infection in piglets,Microbiome,2024,"Gut microbiota, Infection resistance, Macrogenomic, Metabolomic, T cell response",Experiment 6,China,Sus scrofa domesticus,Feces,UBERON:0001988,Infectious diarrheal disease,MONDO:0001517,M-CON (min-control) pigs,M-PEDV(min-Porcine epidemic diarrhea virus) pigs,Min pigs in china challenged with PEDV (Porcine epidemic diarrhea virus).,10,10,NA,16S,34,Illumina,relative abundances,Metastats,0.05,FALSE,NA,NA,NA,NA,increased,increased,increased,NA,increased,Signature 1,Figure 4B,15 November 2024,Tosin,"Tosin,WikiWorks",Analysis of significantly upregulated (top 4) and downregulated (top 4) species in the abundance table between M-CON (min-control) and M-PEDV (min- porcine epidemic diarrhea virus) pigs.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus amylovorus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:604",1783272|1239|186801|186802|216572|216851|853;1783272|1239|91061|186826|33958|1578|1604;1783272|1239|91061|186826|33958|2742598|1598;3379134|976|200643|171549|171552|838|1262932,Complete,Svetlana up
bsdb:38317217/6/2,38317217,laboratory experiment,38317217,10.1186/s40168-023-01734-4,NA,"Xing J.H., Niu T.M., Zou B.S., Yang G.L., Shi C.W., Yan Q.S., Sun M.J., Yu T., Zhang S.M., Feng X.Z., Fan S.H., Huang H.B., Wang J.H., Li M.H., Jiang Y.L., Wang J.Z., Cao X., Wang N., Zeng Y., Hu J.T., Zhang D., Sun W.S., Yang W.T. , Wang C.F.",Gut microbiota-derived LCA mediates the protective effect of PEDV infection in piglets,Microbiome,2024,"Gut microbiota, Infection resistance, Macrogenomic, Metabolomic, T cell response",Experiment 6,China,Sus scrofa domesticus,Feces,UBERON:0001988,Infectious diarrheal disease,MONDO:0001517,M-CON (min-control) pigs,M-PEDV(min-Porcine epidemic diarrhea virus) pigs,Min pigs in china challenged with PEDV (Porcine epidemic diarrhea virus).,10,10,NA,16S,34,Illumina,relative abundances,Metastats,0.05,FALSE,NA,NA,NA,NA,increased,increased,increased,NA,increased,Signature 2,Figure 4B,15 November 2024,Tosin,"Tosin,WikiWorks",Analysis of significantly upregulated (top 4) and downregulated (top 4) species in the abundance table between M-CON and M-PEDV (min- porcine epidemic diarrhea virus) pigs.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:520,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius",3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|171552|2974251|165179;3379134|976|200643|171549|171552|838|1262929;3379134|976|200643|171549|815|909656|310297,Complete,Svetlana up
bsdb:38319728/1/1,38319728,"case-control,laboratory experiment",38319728,10.1080/19490976.2024.2307542,NA,"Yu X., Ou J., Wang L., Li Z., Ren Y., Xie L., Chen Z., Liang J., Shen G., Zou Z., Zhao C., Li G. , Hu Y.",Gut microbiota modulate CD8<sup>+</sup> T cell immunity in gastric cancer through Butyrate/GPR109A/HOPX,Gut microbes,2024,"CD8+ T cell immunity, Gut microbiota, butyrate, gastric cancer",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,Normal Individuals (N),Gastric Cancer patients (GC),Patients admitted to the hospital with Gastric cancer.,20,20,3 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,decreased,NA,NA,Signature 1,"Figure 1A, Supplementary Figure 2A and Supplementary Figure 3A",6 May 2025,MyleeeA,MyleeeA,Differential analysis of microbial community composition between Gastric Cancer-patients (GC) and Normal Individuals (N).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Chloroflexota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella|s__Morganella morganii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__uncultured Streptococcus sp.",3379134|1224|28216|80840|80864|12916;3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;1783272|1239|91061;1783272|200795;1783272|1239|186801|186802|31979|1485;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|2742598;3379134|1224|1236|91347|1903414|581;3379134|1224|1236|91347|1903414|581|582;3379134|1224|1236|91347|1903414;1783272|1239|186801|3082720|186804|1257;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1306;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201;1783272|1239|186801|3085636|186803|2316020|33039;3379134|1224|28216|80840|80864|12916;3379134|74201|203494|48461|1647988|239934;1783272|1239|186801;1783272|1239|91061|186826|33958|2742598;1783272|1239|186801|3082720|186804|1257;1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|2005525;1783272|1239|91061|186826|1300|1301|83427,Complete,KateRasheed
bsdb:38319728/1/2,38319728,"case-control,laboratory experiment",38319728,10.1080/19490976.2024.2307542,NA,"Yu X., Ou J., Wang L., Li Z., Ren Y., Xie L., Chen Z., Liang J., Shen G., Zou Z., Zhao C., Li G. , Hu Y.",Gut microbiota modulate CD8<sup>+</sup> T cell immunity in gastric cancer through Butyrate/GPR109A/HOPX,Gut microbes,2024,"CD8+ T cell immunity, Gut microbiota, butyrate, gastric cancer",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,Normal Individuals (N),Gastric Cancer patients (GC),Patients admitted to the hospital with Gastric cancer.,20,20,3 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,decreased,NA,NA,Signature 2,"Figure 1A, Supplementary Figure 2A and Supplementary Figure 3A",6 May 2025,MyleeeA,MyleeeA,Differential analysis of microbial community composition between Gastric Cancer-patients (GC) and Normal Individuals (N).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,,,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium edouardi,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|207244;;;1783272|1239|186801|186802|3085642;1783272|1239|186801|186802|3085642|580596;1783272|1239|526524|526525|2810280|135858;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|526524|526525|2810280;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|1506553|1926283;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;1783272|1239|186801|3085656|3085657;1783272|1239|186801|3085656;1783272|1239|186801|3085656|3085657|2039302;3379134|976|200643|171549|2005473;1783272|1239|186801|186802|216572;1783272|1239|186801|3082720|186804;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|207244;1783272|1239;1783272|1239|186801|186802|3085642|580596;1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085656|3085657|2039302;3379134|976|200643|171549|2005473;1783272|1239|186801|186802|216572|100175;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|292632,Complete,KateRasheed
bsdb:38319728/2/1,38319728,"case-control,laboratory experiment",38319728,10.1080/19490976.2024.2307542,NA,"Yu X., Ou J., Wang L., Li Z., Ren Y., Xie L., Chen Z., Liang J., Shen G., Zou Z., Zhao C., Li G. , Hu Y.",Gut microbiota modulate CD8<sup>+</sup> T cell immunity in gastric cancer through Butyrate/GPR109A/HOPX,Gut microbes,2024,"CD8+ T cell immunity, Gut microbiota, butyrate, gastric cancer",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Normal-Fecal Microbiota Transplant (F-N),Gastric Cancer-Fecal Microbiota Transplant (F-CA),Mice given Antibiotic (ABX) and transplanted with Gastric Cancer microbiota (F-CA) from human.,6,6,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 2H and Supplementary Figure 9A,6 May 2025,MyleeeA,"MyleeeA,Anne-mariesharp",Differential analysis of microbial community composition between Gastric Cancer-Fecal Microbiota Transplant (F-CA) and Normal-Fecal Microbiota Transplant (F-N).,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. XB44A,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,p__Candidatus Methylomirabilota|c__Candidatus Methylomirabilia,p__Candidatus Methylomirabilota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. Clone-7,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;3379134|976|200643|171549|815|816|371600;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|1955243;640293|3159502;640293;1783272|1239|186801|186802|31979|1485|1003363;1783272|544448|31969|2085|2092;1783272|544448|31969|2085;1783272|1239|526524|526525|2810281|191303;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201;1783272|201174|1760|2037|2049|1654;3379134|74201|203494|48461|1647988|239934;3384189|32066|203490|203491|203492|180162;3379134|200940|3031449|213115|194924;1783272|544448|31969|2085|2092;1783272|1239|186801|3082720|186804|1501226;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3082720|543314,Complete,KateRasheed
bsdb:38319728/2/2,38319728,"case-control,laboratory experiment",38319728,10.1080/19490976.2024.2307542,NA,"Yu X., Ou J., Wang L., Li Z., Ren Y., Xie L., Chen Z., Liang J., Shen G., Zou Z., Zhao C., Li G. , Hu Y.",Gut microbiota modulate CD8<sup>+</sup> T cell immunity in gastric cancer through Butyrate/GPR109A/HOPX,Gut microbes,2024,"CD8+ T cell immunity, Gut microbiota, butyrate, gastric cancer",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Normal-Fecal Microbiota Transplant (F-N),Gastric Cancer-Fecal Microbiota Transplant (F-CA),Mice given Antibiotic (ABX) and transplanted with Gastric Cancer microbiota (F-CA) from human.,6,6,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 2H and Supplementary Figure 9A,6 May 2025,MyleeeA,"MyleeeA,Anne-mariesharp",Differential analysis of microbial community composition between Gastric Cancer-Fecal Microbiota Transplant (F-CA) and Normal-Fecal Microbiota Transplant (F-N).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor|s__Acetatifactor sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum sp.,,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Bittarella (ex Durand et al. 2017),k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Bittarella (ex Durand et al. 2017)|s__Bittarella massiliensis (ex Durand et al. 2017),k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Pleomorphomonadaceae|g__Chthonobacter,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Actinomycetota|c__Thermoleophilia|o__Gaiellales|f__Gaiellaceae|g__Gaiella,k__Bacillati|p__Actinomycetota|c__Thermoleophilia|o__Gaiellales|f__Gaiellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter|s__Paludibacter propionicigenes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Pantoea agglomerans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Paramuribaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Paramuribaculum|s__Paramuribaculum intestinale,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola paurosaccharolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Pleomorphomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Pseudaeromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Pseudaeromonas|s__Pseudaeromonas sharmana,k__Pseudomonadati|p__Thermodesulfobacteriota,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Pleomorphomonadaceae|g__Chthonobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Actinomycetota|c__Thermoleophilia|o__Gaiellales|f__Gaiellaceae|g__Gaiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Chloroflexota|c__Ktedonobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__uncultured Bacteroides sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__uncultured Eubacterium sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides provencensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum",1783272|1239|186801|3085636|186803|1427378|1872090;1783272|1239|186801|3085636|3118652|2039240;1783272|1239|186801|3085636|3118652|2039240|2039241;;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|216572|1929297;1783272|1239|186801|186802|216572|1929297|1720313;1783272|1239|186801|186802|3085642;1783272|1239|186801|186802|3085642|580596;3379134|1224|28211|356|2843308|1926253;1783272|1239|186801;1783272|1239|186801|186802|1980681;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;3379134|200940|3031449;1783272|1239|186801|186802|186806;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730;1783272|201174|1497346|1154584|1154585|1154586;1783272|201174|1497346|1154584|1154585;1783272|1239|186801|186802|1392389;1783272|201174|1760|85006|85021;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|3085636;1783272|1239|186801|186802|216572|459786|1945593;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005523|346096|185300;3379134|1224|1236|91347|1903409|53335|549;3379134|976|200643|171549|2005473|2518497;3379134|976|200643|171549|2005473|2518497|2094151;1783272|1239|186801|186802|186807;3379134|976|200643|171549|815|909656|732242;3379134|1224|28211|356|2843308;3379134|1224|1236|135624|84642|1929090;3379134|1224|1236|135624|84642|1929090|328412;3379134|200940;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|3085642|580596;3379134|1224|28211|356|2843308|1926253;1783272|1239|186801|186802|1980681;1783272|1239|186801|186802;1783272|201174|1497346|1154584|1154585|1154586;1783272|1239|186801|186802|216572|1892380;1783272|1239|186801|186802|1392389;1783272|200795|388447;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|186807;3379134|976|200643|171549|815|816|162156;1783272|1239|186801|186802|31979|1485|59620;1783272|1239|186801|186802|186806|1730|165185;3379134|976|200643|171549|2005525|375288|1944636;1783272|1239|186801|186802|186806|1730|39497,Complete,KateRasheed
bsdb:38319728/3/1,38319728,"case-control,laboratory experiment",38319728,10.1080/19490976.2024.2307542,NA,"Yu X., Ou J., Wang L., Li Z., Ren Y., Xie L., Chen Z., Liang J., Shen G., Zou Z., Zhao C., Li G. , Hu Y.",Gut microbiota modulate CD8<sup>+</sup> T cell immunity in gastric cancer through Butyrate/GPR109A/HOPX,Gut microbes,2024,"CD8+ T cell immunity, Gut microbiota, butyrate, gastric cancer",Experiment 3,China,Mus musculus,Gastric juice,UBERON:0001971,Response to transplant,EFO:0007043,Normal mouse (N),Gastric Cancer Mouse (Ca),"Gastric cancer mouse- 20 g C57BL/6J mice at 6 weeks of age infected with Helicobacter pylori and given N-methyl-N-nitrosourea (MNU) plus abnormal feeding cycles, to induce gastric cancer.",4,5,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 4A,6 May 2025,MyleeeA,MyleeeA,Differential analysis of microbial community composition of gastric fluids between Gastric Cancer mouse and Normal mouse.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,s__bacterium A2,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.",3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|244127;;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|1980681;3379134|29547|3031852|213849|72293|209;3379134|200930|68337|191393|2945020|248038;3379134|976|200643|171549|2005473|1918540;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3085636|186803|1506577;166648;3379134|976;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|31979|1485|59620,Complete,KateRasheed
bsdb:38319728/3/2,38319728,"case-control,laboratory experiment",38319728,10.1080/19490976.2024.2307542,NA,"Yu X., Ou J., Wang L., Li Z., Ren Y., Xie L., Chen Z., Liang J., Shen G., Zou Z., Zhao C., Li G. , Hu Y.",Gut microbiota modulate CD8<sup>+</sup> T cell immunity in gastric cancer through Butyrate/GPR109A/HOPX,Gut microbes,2024,"CD8+ T cell immunity, Gut microbiota, butyrate, gastric cancer",Experiment 3,China,Mus musculus,Gastric juice,UBERON:0001971,Response to transplant,EFO:0007043,Normal mouse (N),Gastric Cancer Mouse (Ca),"Gastric cancer mouse- 20 g C57BL/6J mice at 6 weeks of age infected with Helicobacter pylori and given N-methyl-N-nitrosourea (MNU) plus abnormal feeding cycles, to induce gastric cancer.",4,5,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 4A,6 May 2025,MyleeeA,MyleeeA,Differential analysis of microbial community composition of gastric fluids between Gastric Cancer mouse and Normal mouse.,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Sterolibacteriaceae|g__Methyloversatilis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio",1783272|1239|526524|526525|128827|1937008;1783272|1239|91061|186826|33958|2767887;3379134|1224|28216|32003|2008793|378210;3379134|1224|1236|72274|135621|286;3379134|1224|1236|135623|641|662,Complete,KateRasheed
bsdb:38326891/1/1,38326891,prospective cohort,38326891,https://doi.org/10.1186/s40168-023-01735-3,NA,"Mercer E.M., Ramay H.R., Moossavi S., Laforest-Lapointe I., Reyna M.E., Becker A.B., Simons E., Mandhane P.J., Turvey S.E., Moraes T.J., Sears M.R., Subbarao P., Azad M.B. , Arrieta M.C.",Divergent maturational patterns of the infant bacterial and fungal gut microbiome in the first year of life are associated with inter-kingdom community dynamics and infant nutrition,Microbiome,2024,"Alpha diversity, Colonization patterns, Early life, Gut fungi, Gut microbiome, Gut mycobiome, Inter-kingdom dynamics, Microbial succession, Microbiome maturation",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Development or differentiation design,EFO:0001746,3 months,12 months,infants when they are 12 months of age,99,99,3 months,16S,4,Illumina,raw counts,DESeq2,0.001,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Fig 3C,23 March 2024,Tayk26,"Tayk26,Svetlana up,WikiWorks",Comparison of bacterial growth  at 3 and 12 months,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|171552|2974251|165179;3379134|976|200643|171549|171550,Complete,Svetlana up
bsdb:38326891/1/2,38326891,prospective cohort,38326891,https://doi.org/10.1186/s40168-023-01735-3,NA,"Mercer E.M., Ramay H.R., Moossavi S., Laforest-Lapointe I., Reyna M.E., Becker A.B., Simons E., Mandhane P.J., Turvey S.E., Moraes T.J., Sears M.R., Subbarao P., Azad M.B. , Arrieta M.C.",Divergent maturational patterns of the infant bacterial and fungal gut microbiome in the first year of life are associated with inter-kingdom community dynamics and infant nutrition,Microbiome,2024,"Alpha diversity, Colonization patterns, Early life, Gut fungi, Gut microbiome, Gut mycobiome, Inter-kingdom dynamics, Microbial succession, Microbiome maturation",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Development or differentiation design,EFO:0001746,3 months,12 months,infants when they are 12 months of age,99,99,3 months,16S,4,Illumina,raw counts,DESeq2,0.001,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Fig 3C,23 March 2024,Tayk26,"Tayk26,Svetlana up,WikiWorks",Comparison of bacterial growth at 3 and 12 months,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:38326891/2/1,38326891,prospective cohort,38326891,https://doi.org/10.1186/s40168-023-01735-3,NA,"Mercer E.M., Ramay H.R., Moossavi S., Laforest-Lapointe I., Reyna M.E., Becker A.B., Simons E., Mandhane P.J., Turvey S.E., Moraes T.J., Sears M.R., Subbarao P., Azad M.B. , Arrieta M.C.",Divergent maturational patterns of the infant bacterial and fungal gut microbiome in the first year of life are associated with inter-kingdom community dynamics and infant nutrition,Microbiome,2024,"Alpha diversity, Colonization patterns, Early life, Gut fungi, Gut microbiome, Gut mycobiome, Inter-kingdom dynamics, Microbial succession, Microbiome maturation",Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Development or differentiation design,EFO:0001746,3 months,12 months,infants when they are 12 months of age,95,95,3 months,ITS / ITS2,NA,Illumina,raw counts,DESeq2,0.001,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Fig 3F,23 March 2024,Tayk26,"Tayk26,Svetlana up,WikiWorks",Comparison of differential fungal growth in 3 and 12 months,decreased,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida parapsilosis,4751|4890|3239874|2916678|766764|5475|5480,Complete,Svetlana up
bsdb:38326891/2/2,38326891,prospective cohort,38326891,https://doi.org/10.1186/s40168-023-01735-3,NA,"Mercer E.M., Ramay H.R., Moossavi S., Laforest-Lapointe I., Reyna M.E., Becker A.B., Simons E., Mandhane P.J., Turvey S.E., Moraes T.J., Sears M.R., Subbarao P., Azad M.B. , Arrieta M.C.",Divergent maturational patterns of the infant bacterial and fungal gut microbiome in the first year of life are associated with inter-kingdom community dynamics and infant nutrition,Microbiome,2024,"Alpha diversity, Colonization patterns, Early life, Gut fungi, Gut microbiome, Gut mycobiome, Inter-kingdom dynamics, Microbial succession, Microbiome maturation",Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Development or differentiation design,EFO:0001746,3 months,12 months,infants when they are 12 months of age,95,95,3 months,ITS / ITS2,NA,Illumina,raw counts,DESeq2,0.001,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Fig 3F,23 March 2024,Tayk26,"Tayk26,Svetlana up,MyleeeA,WikiWorks",Comparison of differential fungal growth in 3 and 12 months,increased,"k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Phaffomycetales|f__Phaffomycetaceae|g__Cyberlindnera|s__Cyberlindnera jadinii,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Meyerozyma|s__Meyerozyma guilliermondii",4751|4890|4891|3243778|115784|604195|4903;4751|4890|4891|4892|4893|4930|4932;4751|4890|3239874|2916678|766764|766728|4929,Complete,Svetlana up
bsdb:38327745/1/1,38327745,case-control,38327745,10.3389/fonc.2024.1279132,NA,"Zeber-Lubecka N., Kulecka M., Jagiełło-Gruszfeld A., Dąbrowska M., Kluska A., Piątkowska M., Bagińska K., Głowienka M., Surynt P., Tenderenda M., Mikula M. , Ostrowski J.",Breast cancer but not the menopausal status is associated with small changes of the gut microbiota,Frontiers in oncology,2024,"breast cancer, gut dysbiosis, menopausal status, microbiome, shotgun",Experiment 1,Poland,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,pre-menopausal controls,pre-menopausal breast cancer (BC) patients,Newly diagnosed pre- or perimenopausal breast cancer patients at the Maria Sklodowska-Curie National Research Institute of Oncology.,51,47,2 months,WMS,NA,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 3,31 March 2024,Keamy,"Keamy,Scholastica,WikiWorks",Taxa differentiating premenopausal breast cancer (BC) patients from premenopausal controls assessed using the LInear model for Differential Abundance (LINDA) method for compositional data,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma|s__[Collinsella] massiliensis",1783272|201174|1760|2037|2049;1783272|201174;1783272|1239|186801|186802|3082771|1924093;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|201174|84998|84999|84107;1783272|201174|84998|1643822|1643826;1783272|1239|186801|186802|204475;1783272|1239|186801|186802|204475|745368;1783272|1239|186801|186802|216572|1905344;1783272|201174|84998|84999|84107|1472762|1232426,Complete,Svetlana up
bsdb:38327745/2/1,38327745,case-control,38327745,10.3389/fonc.2024.1279132,NA,"Zeber-Lubecka N., Kulecka M., Jagiełło-Gruszfeld A., Dąbrowska M., Kluska A., Piątkowska M., Bagińska K., Głowienka M., Surynt P., Tenderenda M., Mikula M. , Ostrowski J.",Breast cancer but not the menopausal status is associated with small changes of the gut microbiota,Frontiers in oncology,2024,"breast cancer, gut dysbiosis, menopausal status, microbiome, shotgun",Experiment 2,Poland,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,post-menopausal controls,post-menopausal BC patients,Newly diagnosed postmenopausal breast cancer patients at the Maria Sklodowska-Curie National Research Institute of Oncology.,35,41,2 months,WMS,NA,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,Table 4,31 March 2024,Keamy,"Keamy,Scholastica,WikiWorks",Taxa differentiating postmenopausal breast cancer (BC) patients from postmenopausal controls assessed using the Linear model for Differential Abundance (LINDA) method for compositional data,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae",1783272|1239|186801|186802|3085642|2048137;1783272|201174|84998|84999|84107|102106|147207;1783272|1239|186801|186802|216572|1892380;1783272|201174|1760|85006|1268,Complete,Svetlana up
bsdb:38327745/2/2,38327745,case-control,38327745,10.3389/fonc.2024.1279132,NA,"Zeber-Lubecka N., Kulecka M., Jagiełło-Gruszfeld A., Dąbrowska M., Kluska A., Piątkowska M., Bagińska K., Głowienka M., Surynt P., Tenderenda M., Mikula M. , Ostrowski J.",Breast cancer but not the menopausal status is associated with small changes of the gut microbiota,Frontiers in oncology,2024,"breast cancer, gut dysbiosis, menopausal status, microbiome, shotgun",Experiment 2,Poland,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,post-menopausal controls,post-menopausal BC patients,Newly diagnosed postmenopausal breast cancer patients at the Maria Sklodowska-Curie National Research Institute of Oncology.,35,41,2 months,WMS,NA,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,Table 4,31 March 2024,Keamy,"Keamy,Scholastica,WikiWorks",Taxa differentiating postmenopausal breast cancer (BC) patients from postmenopausal controls assessed using the Linear model for Differential Abundance (LINDA) method for compositional data,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium",3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|2005519;1783272|1239|186801|3085636|186803|572511|40520;3379134|976|200643|171549|2005519|1348911;3379134|976|200643|171549|2005519|1348911|1099853;1783272|1239|186801|3085636|186803|189330;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|823;1783272|1239|909932|1843488|909930|33024|33025,Complete,Svetlana up
bsdb:38331563/1/1,38331563,randomized controlled trial,38331563,10.1136/gutjnl-2023-330521,NA,"Budden K.F., Shukla S.D., Bowerman K.L., Vaughan A., Gellatly S.L., Wood D.L.A., Lachner N., Idrees S., Rehman S.F., Faiz A., Patel V.K., Donovan C., Alemao C.A., Shen S., Amorim N., Majumder R., Vanka K.S., Mason J., Haw T.J., Tillet B., Fricker M., Keely S., Hansbro N., Belz G.T., Horvat J., Ashhurst T., van Vreden C., McGuire H., Fazekas de St Groth B., King N.J.C., Crossett B., Cordwell S.J., Bonaguro L., Schultze J.L., Hamilton-Williams E.E., Mann E., Forster S.C., Cooper M.A., Segal L.N., Chotirmall S.H., Collins P., Bowman R., Fong K.M., Yang I.A., Wark P.A.B., Dennis P.G., Hugenholtz P. , Hansbro P.M.",Faecal microbial transfer and complex carbohydrates mediate protection against COPD,Gut,2024,"BASIC SCIENCES, COLONIC MICROFLORA, DIETARY FIBRE, IMMUNOLOGY, INFLAMMATORY DISEASES",Experiment 1,Australia,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Air-exposed FMT mice - 12 weeks,Cigarette Smoke exposed FMT mice (CS-exposed 12 weeks),"Cigarette Smoke exposed FMT mice (CS-exposed 12 weeks) refers to ""in vivo"" female mouse model of cigarette smoke (CS)-induced COPD and faecal microbial transfer (FMT) who underwent 3 weeks of baseline microbiome normalisation by transferring soiled bedding and co-housing, before exposure to mainstream CS through the nose only for 12 weeks (12 wk CS).",8,8,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,age,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 1,Supplementary Table 6,22 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between air-exposed FMT mice and CS-exposed FMT mice at 12 weeks,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Kineothrix|s__Kineothrix sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Muricomes|s__Muricomes sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 14-2",1783272|1239|186801|3085636|186803|2163168|2163169;1783272|1239|186801|3085636|186803|1918542|1918608;1783272|1239|186801|3085636|186803|397286,Complete,Svetlana up
bsdb:38331563/1/2,38331563,randomized controlled trial,38331563,10.1136/gutjnl-2023-330521,NA,"Budden K.F., Shukla S.D., Bowerman K.L., Vaughan A., Gellatly S.L., Wood D.L.A., Lachner N., Idrees S., Rehman S.F., Faiz A., Patel V.K., Donovan C., Alemao C.A., Shen S., Amorim N., Majumder R., Vanka K.S., Mason J., Haw T.J., Tillet B., Fricker M., Keely S., Hansbro N., Belz G.T., Horvat J., Ashhurst T., van Vreden C., McGuire H., Fazekas de St Groth B., King N.J.C., Crossett B., Cordwell S.J., Bonaguro L., Schultze J.L., Hamilton-Williams E.E., Mann E., Forster S.C., Cooper M.A., Segal L.N., Chotirmall S.H., Collins P., Bowman R., Fong K.M., Yang I.A., Wark P.A.B., Dennis P.G., Hugenholtz P. , Hansbro P.M.",Faecal microbial transfer and complex carbohydrates mediate protection against COPD,Gut,2024,"BASIC SCIENCES, COLONIC MICROFLORA, DIETARY FIBRE, IMMUNOLOGY, INFLAMMATORY DISEASES",Experiment 1,Australia,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Air-exposed FMT mice - 12 weeks,Cigarette Smoke exposed FMT mice (CS-exposed 12 weeks),"Cigarette Smoke exposed FMT mice (CS-exposed 12 weeks) refers to ""in vivo"" female mouse model of cigarette smoke (CS)-induced COPD and faecal microbial transfer (FMT) who underwent 3 weeks of baseline microbiome normalisation by transferring soiled bedding and co-housing, before exposure to mainstream CS through the nose only for 12 weeks (12 wk CS).",8,8,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,age,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 2,Supplementary Table 6,22 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between air-exposed FMT mice and CS-exposed FMT mice at 12 weeks,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Candidatus Amulumruptor|s__Candidatus Amulumruptor sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Duncaniella|s__Duncaniella sp.,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Mailhella|s__Mailhella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum|s__Muribaculum sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:485",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|2005473|2510710|2854024;3379134|976|200643|171549|2005473|2518495|2518496;3379134|200940|3031449|213115|194924|1981028|1981029;3379134|976|200643|171549|2005473|1918540|1918611;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|171552|838|1262927,Complete,Svetlana up
bsdb:38331563/2/1,38331563,randomized controlled trial,38331563,10.1136/gutjnl-2023-330521,NA,"Budden K.F., Shukla S.D., Bowerman K.L., Vaughan A., Gellatly S.L., Wood D.L.A., Lachner N., Idrees S., Rehman S.F., Faiz A., Patel V.K., Donovan C., Alemao C.A., Shen S., Amorim N., Majumder R., Vanka K.S., Mason J., Haw T.J., Tillet B., Fricker M., Keely S., Hansbro N., Belz G.T., Horvat J., Ashhurst T., van Vreden C., McGuire H., Fazekas de St Groth B., King N.J.C., Crossett B., Cordwell S.J., Bonaguro L., Schultze J.L., Hamilton-Williams E.E., Mann E., Forster S.C., Cooper M.A., Segal L.N., Chotirmall S.H., Collins P., Bowman R., Fong K.M., Yang I.A., Wark P.A.B., Dennis P.G., Hugenholtz P. , Hansbro P.M.",Faecal microbial transfer and complex carbohydrates mediate protection against COPD,Gut,2024,"BASIC SCIENCES, COLONIC MICROFLORA, DIETARY FIBRE, IMMUNOLOGY, INFLAMMATORY DISEASES",Experiment 2,Australia,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Air-exposed FMT mice - 12 weeks,8weeks CS exposed + 4weeks rest FMT mice,8weeks CS exposed + 4weeks rest FMT mice refers to mice who were induced with cigarette-smoke(CS) for 8weeks after which they were exposed to normal air for 4weeks.,8,8,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,age,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 1,Supplementary Table 6,22 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between 12 weeks air-exposed FMT mice and 8weeks CS exposed + 4weeks rest FMT mice,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Muricomes|s__Muricomes sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium MD335",3379134|976|200643|171549|171550|239759|1872444;1783272|1239|91061|186826|33958|1578|33959;1783272|1239|186801|3085636|186803|1918542|1918608;1783272|1239|186801|3085636|186803|1235793,Complete,Svetlana up
bsdb:38331563/2/2,38331563,randomized controlled trial,38331563,10.1136/gutjnl-2023-330521,NA,"Budden K.F., Shukla S.D., Bowerman K.L., Vaughan A., Gellatly S.L., Wood D.L.A., Lachner N., Idrees S., Rehman S.F., Faiz A., Patel V.K., Donovan C., Alemao C.A., Shen S., Amorim N., Majumder R., Vanka K.S., Mason J., Haw T.J., Tillet B., Fricker M., Keely S., Hansbro N., Belz G.T., Horvat J., Ashhurst T., van Vreden C., McGuire H., Fazekas de St Groth B., King N.J.C., Crossett B., Cordwell S.J., Bonaguro L., Schultze J.L., Hamilton-Williams E.E., Mann E., Forster S.C., Cooper M.A., Segal L.N., Chotirmall S.H., Collins P., Bowman R., Fong K.M., Yang I.A., Wark P.A.B., Dennis P.G., Hugenholtz P. , Hansbro P.M.",Faecal microbial transfer and complex carbohydrates mediate protection against COPD,Gut,2024,"BASIC SCIENCES, COLONIC MICROFLORA, DIETARY FIBRE, IMMUNOLOGY, INFLAMMATORY DISEASES",Experiment 2,Australia,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Air-exposed FMT mice - 12 weeks,8weeks CS exposed + 4weeks rest FMT mice,8weeks CS exposed + 4weeks rest FMT mice refers to mice who were induced with cigarette-smoke(CS) for 8weeks after which they were exposed to normal air for 4weeks.,8,8,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,age,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 2,Supplementary Table 6,22 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between 12 weeks air-exposed FMT mice and 8weeks CS exposed + 4weeks rest FMT mice,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Candidatus Amulumruptor|s__Candidatus Amulumruptor sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Duncaniella|s__Duncaniella sp.,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Mailhella|s__Mailhella sp.,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum|s__Mucispirillum schaedleri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium UBA3282,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium MD335",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|2005473|2510710|2854024;3379134|976|200643|171549|2005473|2518495|2518496;3379134|200940|3031449|213115|194924|1981028|1981029;3379134|200930|68337|191393|2945020|248038|248039;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|3085636|186803|1952023;1783272|1239|186801|3085636|186803|1235793,Complete,Svetlana up
bsdb:38331563/3/1,38331563,randomized controlled trial,38331563,10.1136/gutjnl-2023-330521,NA,"Budden K.F., Shukla S.D., Bowerman K.L., Vaughan A., Gellatly S.L., Wood D.L.A., Lachner N., Idrees S., Rehman S.F., Faiz A., Patel V.K., Donovan C., Alemao C.A., Shen S., Amorim N., Majumder R., Vanka K.S., Mason J., Haw T.J., Tillet B., Fricker M., Keely S., Hansbro N., Belz G.T., Horvat J., Ashhurst T., van Vreden C., McGuire H., Fazekas de St Groth B., King N.J.C., Crossett B., Cordwell S.J., Bonaguro L., Schultze J.L., Hamilton-Williams E.E., Mann E., Forster S.C., Cooper M.A., Segal L.N., Chotirmall S.H., Collins P., Bowman R., Fong K.M., Yang I.A., Wark P.A.B., Dennis P.G., Hugenholtz P. , Hansbro P.M.",Faecal microbial transfer and complex carbohydrates mediate protection against COPD,Gut,2024,"BASIC SCIENCES, COLONIC MICROFLORA, DIETARY FIBRE, IMMUNOLOGY, INFLAMMATORY DISEASES",Experiment 3,Australia,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Fecal samples baseline(Week 0),Fecal samples at the end of the experiment(Week 12),Fecal samples at the end of the experiment(Week 12) refers to fecal samples collected at the completion of the experiment.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,increased,NA,Signature 1,Supplementary Table 5,23 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between fecal samples at baseline(Week 0) and at completion of the experiment(Week 12),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Candidatus Amulumruptor|s__Candidatus Amulumruptor sp.,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella|s__Dubosiella newyorkensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Duncaniella|s__Duncaniella dubosii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Duncaniella|s__Duncaniella sp.,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Mailhella|s__Mailhella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum|s__Muribaculum intestinale,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Schaedlerella|s__Schaedlerella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Schaedlerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:485,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:873,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium UBA3282,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:303",3379134|976|200643|171549|171550|239759|1872444;3379134|976|200643|171549|2005473|2510710|2854024;1783272|1239|526524|526525|128827|1937008|1862672;3379134|976|200643|171549|2005473|2518495|2518971;3379134|976|200643|171549|2005473|2518495|2518496;3379134|200940|3031449|213115|194924|1981028|1981029;3379134|976|200643|171549|2005473|1918540|1796646;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|171552|838|59823;1783272|1239|186801|3085636|186803|2676048|2676057;1783272|1239|186801|3085636|186803|2676048;3379134|976|200643|171549|171552|838|1262927;3379134|976|200643|171549|171552|838|1262936;1783272|1239|186801|3085636|186803|1952023;1783272|1239|186801|3085636|186803|841|1262944,Complete,Svetlana up
bsdb:38331563/3/2,38331563,randomized controlled trial,38331563,10.1136/gutjnl-2023-330521,NA,"Budden K.F., Shukla S.D., Bowerman K.L., Vaughan A., Gellatly S.L., Wood D.L.A., Lachner N., Idrees S., Rehman S.F., Faiz A., Patel V.K., Donovan C., Alemao C.A., Shen S., Amorim N., Majumder R., Vanka K.S., Mason J., Haw T.J., Tillet B., Fricker M., Keely S., Hansbro N., Belz G.T., Horvat J., Ashhurst T., van Vreden C., McGuire H., Fazekas de St Groth B., King N.J.C., Crossett B., Cordwell S.J., Bonaguro L., Schultze J.L., Hamilton-Williams E.E., Mann E., Forster S.C., Cooper M.A., Segal L.N., Chotirmall S.H., Collins P., Bowman R., Fong K.M., Yang I.A., Wark P.A.B., Dennis P.G., Hugenholtz P. , Hansbro P.M.",Faecal microbial transfer and complex carbohydrates mediate protection against COPD,Gut,2024,"BASIC SCIENCES, COLONIC MICROFLORA, DIETARY FIBRE, IMMUNOLOGY, INFLAMMATORY DISEASES",Experiment 3,Australia,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Fecal samples baseline(Week 0),Fecal samples at the end of the experiment(Week 12),Fecal samples at the end of the experiment(Week 12) refers to fecal samples collected at the completion of the experiment.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,increased,NA,Signature 2,Supplementary Table 5,23 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between fecal samples at baseline(Week 0) and at completion of the experiment(Week 12),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum|s__Bifidobacterium pseudolongum subsp. globosum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Duncaniella|s__Duncaniella dubosii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Duncaniella|s__Duncaniella muris,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum|s__Faecalibaculum rodentium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Ileibacterium|s__Ileibacterium valens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium MD335,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:180,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:115,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium UBA7001,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. MD294",1783272|1239|186801|3085636|186803|1427378;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759|1872444;1783272|201174|1760|85004|31953|1678|1694;1783272|201174|1760|85004|31953|1678|1694|1690;3379134|976|200643|171549|2005473|2518495|2518971;3379134|976|200643|171549|2005473|2518495|2094150;1783272|1239|186801|186802|186806|1730;1783272|1239|526524|526525|128827|1729679|1702221;1783272|1239|526524|526525|128827|1937007|1862668;1783272|1239|186801|3085636|186803|1235793;1783272|1239|186801|186802|186806|1730|1262882;1783272|1239|186801|186802|186806|1730|1262878;1783272|1239|186801|186802|1950920;1783272|1239|186801|186802|31979|1485|97138,Complete,Svetlana up
bsdb:38331563/4/1,38331563,randomized controlled trial,38331563,10.1136/gutjnl-2023-330521,NA,"Budden K.F., Shukla S.D., Bowerman K.L., Vaughan A., Gellatly S.L., Wood D.L.A., Lachner N., Idrees S., Rehman S.F., Faiz A., Patel V.K., Donovan C., Alemao C.A., Shen S., Amorim N., Majumder R., Vanka K.S., Mason J., Haw T.J., Tillet B., Fricker M., Keely S., Hansbro N., Belz G.T., Horvat J., Ashhurst T., van Vreden C., McGuire H., Fazekas de St Groth B., King N.J.C., Crossett B., Cordwell S.J., Bonaguro L., Schultze J.L., Hamilton-Williams E.E., Mann E., Forster S.C., Cooper M.A., Segal L.N., Chotirmall S.H., Collins P., Bowman R., Fong K.M., Yang I.A., Wark P.A.B., Dennis P.G., Hugenholtz P. , Hansbro P.M.",Faecal microbial transfer and complex carbohydrates mediate protection against COPD,Gut,2024,"BASIC SCIENCES, COLONIC MICROFLORA, DIETARY FIBRE, IMMUNOLOGY, INFLAMMATORY DISEASES",Experiment 4,Australia,Homo sapiens,Feces,UBERON:0001988,Treatment,EFO:0000727,Pre-inulin,Post-inulin,"Post-inulin refers to the period after inulin supplementation. Human patients with COPD received supplements of inulin, a common fermentable fibre, for 4 weeks.",7,9,NA,16S,5678,Roche454,centered log-ratio,PLS-DA (Partial least square discriminant analysis),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 1,Figure 9D,23 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between pre-inulin and post inulin,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,s__uncultured bacterium,s__uncultured organism,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae",1783272|1239|186801|3082720|186804|1505657;77133;155900;1783272|1239|526524|526525|2810280,Complete,Svetlana up
bsdb:38331563/5/1,38331563,randomized controlled trial,38331563,10.1136/gutjnl-2023-330521,NA,"Budden K.F., Shukla S.D., Bowerman K.L., Vaughan A., Gellatly S.L., Wood D.L.A., Lachner N., Idrees S., Rehman S.F., Faiz A., Patel V.K., Donovan C., Alemao C.A., Shen S., Amorim N., Majumder R., Vanka K.S., Mason J., Haw T.J., Tillet B., Fricker M., Keely S., Hansbro N., Belz G.T., Horvat J., Ashhurst T., van Vreden C., McGuire H., Fazekas de St Groth B., King N.J.C., Crossett B., Cordwell S.J., Bonaguro L., Schultze J.L., Hamilton-Williams E.E., Mann E., Forster S.C., Cooper M.A., Segal L.N., Chotirmall S.H., Collins P., Bowman R., Fong K.M., Yang I.A., Wark P.A.B., Dennis P.G., Hugenholtz P. , Hansbro P.M.",Faecal microbial transfer and complex carbohydrates mediate protection against COPD,Gut,2024,"BASIC SCIENCES, COLONIC MICROFLORA, DIETARY FIBRE, IMMUNOLOGY, INFLAMMATORY DISEASES",Experiment 5,Australia,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Air-exposed control mice - 8 weeks,Cigarette Smoke exposed control mice (CS-exposed control mice - 8 weeks),Cigarette Smoke exposed control mice (CS-exposed control mice - 8 weeks) refers to mice model who received their own soiled bedding mixed with clean bedding for eight weeks.,NA,NA,NA,16S,5678,Roche454,centered log-ratio,PLS-DA (Partial least square discriminant analysis),0.05,FALSE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S7e,23 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between air-exposed control mice and CS-exposed control mice,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,3379134|976|200643|171549|2005473,Complete,Svetlana up
bsdb:38331563/5/2,38331563,randomized controlled trial,38331563,10.1136/gutjnl-2023-330521,NA,"Budden K.F., Shukla S.D., Bowerman K.L., Vaughan A., Gellatly S.L., Wood D.L.A., Lachner N., Idrees S., Rehman S.F., Faiz A., Patel V.K., Donovan C., Alemao C.A., Shen S., Amorim N., Majumder R., Vanka K.S., Mason J., Haw T.J., Tillet B., Fricker M., Keely S., Hansbro N., Belz G.T., Horvat J., Ashhurst T., van Vreden C., McGuire H., Fazekas de St Groth B., King N.J.C., Crossett B., Cordwell S.J., Bonaguro L., Schultze J.L., Hamilton-Williams E.E., Mann E., Forster S.C., Cooper M.A., Segal L.N., Chotirmall S.H., Collins P., Bowman R., Fong K.M., Yang I.A., Wark P.A.B., Dennis P.G., Hugenholtz P. , Hansbro P.M.",Faecal microbial transfer and complex carbohydrates mediate protection against COPD,Gut,2024,"BASIC SCIENCES, COLONIC MICROFLORA, DIETARY FIBRE, IMMUNOLOGY, INFLAMMATORY DISEASES",Experiment 5,Australia,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Air-exposed control mice - 8 weeks,Cigarette Smoke exposed control mice (CS-exposed control mice - 8 weeks),Cigarette Smoke exposed control mice (CS-exposed control mice - 8 weeks) refers to mice model who received their own soiled bedding mixed with clean bedding for eight weeks.,NA,NA,NA,16S,5678,Roche454,centered log-ratio,PLS-DA (Partial least square discriminant analysis),0.05,FALSE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S7e,23 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa between air-exposed control mice and CS-exposed control mice at 8weeks.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",3379134|976|200643|171549|2005473;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|186801|186802|216572|1263,Complete,Svetlana up
bsdb:38344423/1/1,38344423,laboratory experiment,38344423,10.2147/NDT.S448940,NA,"Li Y. , Liu P.",Characteristics of Oral-Gut Microbiota in Model Rats with CUMS-Induced Depression,Neuropsychiatric disease and treatment,2024,"16SrRNA sequencing, gut microbiota, major depressive disorder, oral microbiota",Experiment 1,China,Rattus norvegicus,Oral cavity,UBERON:0000167,Major depressive disorder,MONDO:0002009,Control group (Rats without CUMS - induced depression,CUMS group (Rats with chronic unpredictable mild stress- induced depression),This group consisted of rats subjected to a Chronic Unpredictable Mild Stress (CUMS) protocol to induce depressive-like symptoms.,10,10,NA,16S,34,NA,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,NA,increased,NA,NA,increased,Signature 1,Figure 5A,2 April 2025,Montana-D,"Montana-D,Francisca",Comparison of oral microbiota composition between between CUMS-induced depressed rats and control rats.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Isobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota",1783272|1239|91061|186826|186827|1375;3379134|74201|203494|48461|1647988|239934;1783272|201174|1760|85006|1268|1663;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|200940|3031449|213115|194924|872;3379134|1224|1236;1783272|1239|91061|186826|186828|142587;1783272|1239|91061|186826|1300|1357;3379134|1224|1236|2887326|468;3379134|1224|1236|72274;3379134|1224;3379134|1224|1236|2887326|468|497;3379134|74201|203494|48461|203557;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201,Complete,Svetlana up
bsdb:38344423/1/2,38344423,laboratory experiment,38344423,10.2147/NDT.S448940,NA,"Li Y. , Liu P.",Characteristics of Oral-Gut Microbiota in Model Rats with CUMS-Induced Depression,Neuropsychiatric disease and treatment,2024,"16SrRNA sequencing, gut microbiota, major depressive disorder, oral microbiota",Experiment 1,China,Rattus norvegicus,Oral cavity,UBERON:0000167,Major depressive disorder,MONDO:0002009,Control group (Rats without CUMS - induced depression,CUMS group (Rats with chronic unpredictable mild stress- induced depression),This group consisted of rats subjected to a Chronic Unpredictable Mild Stress (CUMS) protocol to induce depressive-like symptoms.,10,10,NA,16S,34,NA,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,NA,increased,NA,NA,increased,Signature 2,Figure 5A,2 April 2025,Montana-D,"Montana-D,Francisca",Comparison of oral microbiota composition between CUMS-induced depressed rats and control rats,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae",1783272|201174|1760|2037;1783272|201174|1760;1783272|201174;1783272|1239|91061|186826|186827|66831;1783272|201174|1760|85006|1268;3379134|1224|28211|204455|31989|265;3379134|1224|28211|204455;1783272|201174|1760|85006|1268|32207;3379134|1224|1236|135614|32033|40323;3379134|1224|1236|135623|641|662;3379134|1224|1236|135623|641;3379134|1224|1236|135623;3379134|1224|28211|204455|31989,Complete,Svetlana up
bsdb:38344423/2/1,38344423,laboratory experiment,38344423,10.2147/NDT.S448940,NA,"Li Y. , Liu P.",Characteristics of Oral-Gut Microbiota in Model Rats with CUMS-Induced Depression,Neuropsychiatric disease and treatment,2024,"16SrRNA sequencing, gut microbiota, major depressive disorder, oral microbiota",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Control group (Rats without CUMS - induced depression,CUMS group (Rats with chronic unpredictable mild stress- induced depression),This group consisted of rats subjected to a Chronic Unpredictable Mild Stress (CUMS) protocol to induce depressive-like symptoms.,10,10,NA,16S,34,NA,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,Figure 5B,2 April 2025,Montana-D,Montana-D,Comparison of gut microbiota between CUMS-induced depressed rats and control rats.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,1783272|1239|186801|186802|3085642|580596,Complete,Svetlana up
bsdb:38344423/2/2,38344423,laboratory experiment,38344423,10.2147/NDT.S448940,NA,"Li Y. , Liu P.",Characteristics of Oral-Gut Microbiota in Model Rats with CUMS-Induced Depression,Neuropsychiatric disease and treatment,2024,"16SrRNA sequencing, gut microbiota, major depressive disorder, oral microbiota",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Control group (Rats without CUMS - induced depression,CUMS group (Rats with chronic unpredictable mild stress- induced depression),This group consisted of rats subjected to a Chronic Unpredictable Mild Stress (CUMS) protocol to induce depressive-like symptoms.,10,10,NA,16S,34,NA,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 2,Figure 5B,2 April 2025,Montana-D,"Montana-D,Francisca",Comparison of gut microbiota between CUMS-induced depressed rats and control rats,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|s__Enterococcaceae bacterium RF39,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Bacillati|p__Mycoplasmatota",1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|423410;1783272|1239|91061|186826|81852|1350;1783272|1239|526524|526525;1783272|544448|31969;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810281|191303;1783272|1239|526524|526525|2810281;1783272|544448,Complete,Svetlana up
bsdb:38344423/3/1,38344423,laboratory experiment,38344423,10.2147/NDT.S448940,NA,"Li Y. , Liu P.",Characteristics of Oral-Gut Microbiota in Model Rats with CUMS-Induced Depression,Neuropsychiatric disease and treatment,2024,"16SrRNA sequencing, gut microbiota, major depressive disorder, oral microbiota",Experiment 3,China,Rattus norvegicus,"Feces,Oral cavity","UBERON:0000167,UBERON:0001988",Major depressive disorder,MONDO:0002009,Lower body weight,Increased body weight,Rats exposed to chronic unpredictable mild stress (CUMS) exhibiting increased body weight and altered oral and gut microbiota profiles.,NA,NA,NA,16S,34,NA,relative abundances,Spearman Correlation,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,4 April 2025,Montana-D,Montana-D,Differentially abundant bacteria between oral and gut flora with respect to their body weight indicator,increased,"k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",33090|35493|3398|72025|3803|3814|508215;1783272|1239|91061|186826|186827|66831;3379134|1224|1236|135623|641|662;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:38344423/3/2,38344423,laboratory experiment,38344423,10.2147/NDT.S448940,NA,"Li Y. , Liu P.",Characteristics of Oral-Gut Microbiota in Model Rats with CUMS-Induced Depression,Neuropsychiatric disease and treatment,2024,"16SrRNA sequencing, gut microbiota, major depressive disorder, oral microbiota",Experiment 3,China,Rattus norvegicus,"Feces,Oral cavity","UBERON:0000167,UBERON:0001988",Major depressive disorder,MONDO:0002009,Lower body weight,Increased body weight,Rats exposed to chronic unpredictable mild stress (CUMS) exhibiting increased body weight and altered oral and gut microbiota profiles.,NA,NA,NA,16S,34,NA,relative abundances,Spearman Correlation,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6,4 April 2025,Montana-D,Montana-D,Differentially abundant bacteria between oral and gut flora with respect to their body weight indicator,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus",3379134|1224|1236|2887326|468|497;1783272|1239|91061|186826|186827|1375;3379134|200940|3031449|213115|194924|872;1783272|1239|91061|186826|1300|1357,Complete,Svetlana up
bsdb:38344423/4/1,38344423,laboratory experiment,38344423,10.2147/NDT.S448940,NA,"Li Y. , Liu P.",Characteristics of Oral-Gut Microbiota in Model Rats with CUMS-Induced Depression,Neuropsychiatric disease and treatment,2024,"16SrRNA sequencing, gut microbiota, major depressive disorder, oral microbiota",Experiment 4,China,Rattus norvegicus,"Feces,Oral cavity","UBERON:0001988,UBERON:0000167",Major depressive disorder,MONDO:0002009,Higher sucrose preference,Lower sucrose preference,"Rats subjected to chronic unpredictable mild stress (CUMS) exhibiting reduced sucrose preference, indicative of anhedonia and depression-like behavior",NA,NA,NA,16S,34,NA,relative abundances,Spearman Correlation,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,4 April 2025,Montana-D,Montana-D,Differentially abundant bacteria between oral and gut flora with respect to their sucrose preference indicator,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,3379134|1224|1236|135623|641|662,Complete,Svetlana up
bsdb:38344423/5/1,38344423,laboratory experiment,38344423,10.2147/NDT.S448940,NA,"Li Y. , Liu P.",Characteristics of Oral-Gut Microbiota in Model Rats with CUMS-Induced Depression,Neuropsychiatric disease and treatment,2024,"16SrRNA sequencing, gut microbiota, major depressive disorder, oral microbiota",Experiment 5,China,Rattus norvegicus,"Feces,Oral cavity","UBERON:0000167,UBERON:0001988",Major depressive disorder,MONDO:0002009,Higher total distance traveled,Lower total distance traveled,"Rats exposed to chronic unpredictable mild stress (CUMS) exhibiting reduced locomotor activity, indicative of depression-like behavior.",NA,NA,NA,16S,34,NA,relative abundances,Spearman Correlation,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,4 April 2025,Montana-D,Montana-D,Differentially abundant bacteria between oral and gut flora with respect to their Total distance indicator,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter",1783272|1239|91061|186826|186827|1375;3379134|1224|1236|2887326|468|497,Complete,Svetlana up
bsdb:38344423/5/2,38344423,laboratory experiment,38344423,10.2147/NDT.S448940,NA,"Li Y. , Liu P.",Characteristics of Oral-Gut Microbiota in Model Rats with CUMS-Induced Depression,Neuropsychiatric disease and treatment,2024,"16SrRNA sequencing, gut microbiota, major depressive disorder, oral microbiota",Experiment 5,China,Rattus norvegicus,"Feces,Oral cavity","UBERON:0000167,UBERON:0001988",Major depressive disorder,MONDO:0002009,Higher total distance traveled,Lower total distance traveled,"Rats exposed to chronic unpredictable mild stress (CUMS) exhibiting reduced locomotor activity, indicative of depression-like behavior.",NA,NA,NA,16S,34,NA,relative abundances,Spearman Correlation,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6,5 April 2025,Francisca,Francisca,Differentially abundant bacteria between oral and gut flora with respect to their Total distance indicator,decreased,"k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",33090|35493|3398|72025|3803|3814|508215;1783272|1239|91061|186826|186827|66831;3379134|1224|1236|135623|641|662;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:38344423/6/1,38344423,laboratory experiment,38344423,10.2147/NDT.S448940,NA,"Li Y. , Liu P.",Characteristics of Oral-Gut Microbiota in Model Rats with CUMS-Induced Depression,Neuropsychiatric disease and treatment,2024,"16SrRNA sequencing, gut microbiota, major depressive disorder, oral microbiota",Experiment 6,China,Rattus norvegicus,"Feces,Oral cavity","UBERON:0000167,UBERON:0001988",Major depressive disorder,MONDO:0002009,Higher mean speed,Lower mean speed,"Rats exposed to chronic unpredictable mild stress (CUMS) displaying reduced average movement speed, indicative of depression-like behavior.",NA,NA,NA,16S,34,NA,relative abundances,Spearman Correlation,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,4 April 2025,Montana-D,Montana-D,Differentially abundant bacteria between oral and gut flora with respect to their Mean speed indicator,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus",3379134|1224|1236|2887326|468|497;1783272|1239|91061|186826|186827|1375,Complete,Svetlana up
bsdb:38344423/6/2,38344423,laboratory experiment,38344423,10.2147/NDT.S448940,NA,"Li Y. , Liu P.",Characteristics of Oral-Gut Microbiota in Model Rats with CUMS-Induced Depression,Neuropsychiatric disease and treatment,2024,"16SrRNA sequencing, gut microbiota, major depressive disorder, oral microbiota",Experiment 6,China,Rattus norvegicus,"Feces,Oral cavity","UBERON:0000167,UBERON:0001988",Major depressive disorder,MONDO:0002009,Higher mean speed,Lower mean speed,"Rats exposed to chronic unpredictable mild stress (CUMS) displaying reduced average movement speed, indicative of depression-like behavior.",NA,NA,NA,16S,34,NA,relative abundances,Spearman Correlation,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6,5 April 2025,Francisca,Francisca,Differentially abundant bacteria between oral and gut flora with respect to their Mean speed indicator,decreased,"k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",33090|35493|3398|72025|3803|3814|508215;1783272|1239|91061|186826|186827|66831;3379134|1224|1236|135623|641|662;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:38344423/7/1,38344423,laboratory experiment,38344423,10.2147/NDT.S448940,NA,"Li Y. , Liu P.",Characteristics of Oral-Gut Microbiota in Model Rats with CUMS-Induced Depression,Neuropsychiatric disease and treatment,2024,"16SrRNA sequencing, gut microbiota, major depressive disorder, oral microbiota",Experiment 7,China,Rattus norvegicus,"Feces,Oral cavity","UBERON:0001988,UBERON:0000167",Major depressive disorder,MONDO:0002009,Higher number of rearing events,Lower number of rearing events,"Rats subjected to chronic unpredictable mild stress (CUMS) exhibiting reduced exploratory behavior, as indicated by fewer rearing events, consistent with depression-like symptoms.",NA,NA,NA,16S,34,NA,relative abundances,Spearman Correlation,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,5 April 2025,Francisca,Francisca,Differentially abundant bacteria between oral and gut flora with respect to their Number of rearing indicator,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus",3379134|1224|1236|2887326|468|497;1783272|1239|91061|186826|186827|1375,Complete,Svetlana up
bsdb:38344423/7/2,38344423,laboratory experiment,38344423,10.2147/NDT.S448940,NA,"Li Y. , Liu P.",Characteristics of Oral-Gut Microbiota in Model Rats with CUMS-Induced Depression,Neuropsychiatric disease and treatment,2024,"16SrRNA sequencing, gut microbiota, major depressive disorder, oral microbiota",Experiment 7,China,Rattus norvegicus,"Feces,Oral cavity","UBERON:0001988,UBERON:0000167",Major depressive disorder,MONDO:0002009,Higher number of rearing events,Lower number of rearing events,"Rats subjected to chronic unpredictable mild stress (CUMS) exhibiting reduced exploratory behavior, as indicated by fewer rearing events, consistent with depression-like symptoms.",NA,NA,NA,16S,34,NA,relative abundances,Spearman Correlation,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6,5 April 2025,Francisca,Francisca,Differentially abundant bacteria between oral and gut flora with respect to their Number of rearing indicator,decreased,"k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",33090|35493|3398|72025|3803|3814|508215;1783272|1239|91061|186826|186827|66831;3379134|1224|1236|135623|641|662;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:38366600/1/1,38366600,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang K.D., Amend L., Gálvez E.J.C., Lesker T.R., de Oliveira R., Bielecka A., Blanco-Míguez A., Valles-Colomer M., Ruf I., Pasolli E., Buer J., Segata N., Esser S., Strowig T. , Kehrmann J.",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 1,"Germany,China",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,Men with 0-3 sexual partners,Men with >3 sexual partners,Men in the risk increasing category with more than 3 sexual partners (in the last 12 months).,38,29,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,figure 4 (c) and Supplementary Table S4,5 March 2024,Uhabiba14,"Uhabiba14,Fiddyhamma,MyleeeA,WikiWorks",Species-level taxonomic biomarkers identified using LEfSe to associate with behaviors having >3 (and 0–3) sexual partners.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia massiliensis (ex Durand et al. 2017),k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Neoanaerotignum|s__Candidatus Neoanaerotignum tabaqchaliae,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Methanobacteriati|p__Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|s__Methanomassiliicoccales archaeon,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Clostridia",1783272|1239|186801|3085636|186803|572511|1737424;1783272|1239|186801|2721109|2721136;1783272|1239|186801|2044939;1783272|1239|186801|3085636|186803|28050|28052;3366610|2283796|183967|1235850|1906667;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549;1783272|1239|186801,Complete,Svetlana up
bsdb:38366600/1/2,38366600,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang K.D., Amend L., Gálvez E.J.C., Lesker T.R., de Oliveira R., Bielecka A., Blanco-Míguez A., Valles-Colomer M., Ruf I., Pasolli E., Buer J., Segata N., Esser S., Strowig T. , Kehrmann J.",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 1,"Germany,China",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,Men with 0-3 sexual partners,Men with >3 sexual partners,Men in the risk increasing category with more than 3 sexual partners (in the last 12 months).,38,29,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,figure 4C and SupplementaryTable S4,5 March 2024,Uhabiba14,"Uhabiba14,MyleeeA,Fiddyhamma,WikiWorks","Species-level taxonomic biomarkers identified using LEfSe58 to associate with behaviors having ( 0–3) sexual partners. Only taxonomically known
species are displayed",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum faecicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|s__Bacteroidaceae bacterium,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira pilosicoli,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|s__Campylobacteraceae bacterium,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales|s__Candidatus Gastranaerophilales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora amygdalina,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pectinovora,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotellamassilia|s__Prevotellamassilia timonensis",1783272|1239|186801|3085636|3118652|2039240|2358141;3379134|976|200643|171549|815|2212467;3379134|203691|203692|1643686|143786|29521|52584;3379134|29547|3031852|213849|72294|2268179;1783272|1798710|1906119|2137880;1783272|1239|186801|3085636|186803|2719231|253257;1783272|1239|186801|186802|216572|2485925;3379134|976|200643|171549|171552|838|1602169;3379134|976|200643|171549|171552|1926672|1852370,Complete,Svetlana up
bsdb:38366600/3/1,38366600,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang K.D., Amend L., Gálvez E.J.C., Lesker T.R., de Oliveira R., Bielecka A., Blanco-Míguez A., Valles-Colomer M., Ruf I., Pasolli E., Buer J., Segata N., Esser S., Strowig T. , Kehrmann J.",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 3,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,No Oral Sex,Yes Oral Sex,Men in the risk increasing category who practice Oral sex.,21,42,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary Table S4,13 April 2024,MyleeeA,"MyleeeA,WikiWorks",Species-level taxonomic biomarkers identified using LEfSe to associate with No Oral sex and Yes Oral sex.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|s__Bacteroidaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pectinovora,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",3379134|976|200643|171549|815|2212467;1783272|1239|186801|2044939;3379134|200940|3031449|213115|194924|872|901;1783272|1239|909932|1843488|909930|33024|626940;3379134|976|200643|171549|171552|838|1602169;3379134|976|200643|171549|171552|838|59823;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|2485925;1783272|1239|186801;3379134|976|200643|171549|171550;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Svetlana up
bsdb:38366600/3/2,38366600,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang K.D., Amend L., Gálvez E.J.C., Lesker T.R., de Oliveira R., Bielecka A., Blanco-Míguez A., Valles-Colomer M., Ruf I., Pasolli E., Buer J., Segata N., Esser S., Strowig T. , Kehrmann J.",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 3,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,No Oral Sex,Yes Oral Sex,Men in the risk increasing category who practice Oral sex.,21,42,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplementary Table S4,13 April 2024,MyleeeA,"MyleeeA,WikiWorks",Species-level taxonomic biomarkers identified using LEfSe to associate with No Oral sex and Yes Oral sex.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Avimicrobium|s__Candidatus Avimicrobium caecorum,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium disporicum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Merdimonas|s__Merdimonas faecis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Mesosutterella|s__Mesosutterella multiformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Bacilli",3379134|976|200643|171549|815|816|818;1783272|201174|1760|85004|31953|1678|1681;3379134|200940|3031449|213115|194924|35832|35833;3379134|29547|3031852|213849|72294|194|824;1783272|1239|186801|2720800|2720821;1783272|1239|186801|2044939;1783272|1239|186801|186802|31979|1485|84024;1783272|1239|526524|526525|128827|2049044;1783272|1239|186801|3085636|186803|1898203;1783272|1239|909932|1843488|909930|33024|33025;3379134|976|200643|171549|815|909656|204516;1783272|1239|186801|186802|3082771|1924093|1924094;1783272|1239|186801|3085636|186803|2023266|1653435;3379134|1224|28216|80840|995019|2494213|2259133;1783272|1239|186801|3085636|186803|2316020|46228;1783272|1239|186801|186802|216572|2485925;1783272|1239|91061,Complete,Svetlana up
bsdb:38366600/4/NA,38366600,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang K.D., Amend L., Gálvez E.J.C., Lesker T.R., de Oliveira R., Bielecka A., Blanco-Míguez A., Valles-Colomer M., Ruf I., Pasolli E., Buer J., Segata N., Esser S., Strowig T. , Kehrmann J.",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 4,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,condom use (Sometimes during RAI),no condom use (during RAI),Men in the risk increasing category who never use condom during Receptive Anal Intercourse.,15,37,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:38366600/5/NA,38366600,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang K.D., Amend L., Gálvez E.J.C., Lesker T.R., de Oliveira R., Bielecka A., Blanco-Míguez A., Valles-Colomer M., Ruf I., Pasolli E., Buer J., Segata N., Esser S., Strowig T. , Kehrmann J.",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 5,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,condom use (Always during RAI),condom use (Sometimes during RAI),Men in the risk increasing category who sometimes use Condom during Receptive Anal Intercourse,12,15,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:38366600/7/1,38366600,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang K.D., Amend L., Gálvez E.J.C., Lesker T.R., de Oliveira R., Bielecka A., Blanco-Míguez A., Valles-Colomer M., Ruf I., Pasolli E., Buer J., Segata N., Esser S., Strowig T. , Kehrmann J.",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 7,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,No RAI,Yes RAI,Men in the risk increasing category who practice Receptive Anal intercourse.,21,46,6 Months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary Table S4,15 April 2024,MyleeeA,"MyleeeA,WikiWorks",Species-level taxonomic biomarkers identified using LEfSe to associate with No Receptive Anal Intercourse and Yes Receptive Anal Intercourse.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",1783272|1239|186801|186802|31979|1485|1506;1783272|1239|909932|1843488|909930|33024|626940;3379134|976|200643|171549|171550,Complete,Svetlana up
bsdb:38366600/7/2,38366600,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang K.D., Amend L., Gálvez E.J.C., Lesker T.R., de Oliveira R., Bielecka A., Blanco-Míguez A., Valles-Colomer M., Ruf I., Pasolli E., Buer J., Segata N., Esser S., Strowig T. , Kehrmann J.",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 7,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,No RAI,Yes RAI,Men in the risk increasing category who practice Receptive Anal intercourse.,21,46,6 Months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplementary Table S4,15 April 2024,MyleeeA,"MyleeeA,WikiWorks",Species-level taxonomic biomarkers identified using LEfSe to associate with No Receptive Anal Intercourse and Yes Receptive Anal Intercourse.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Avimicrobium|s__Candidatus Avimicrobium caecorum,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Mesosutterella|s__Mesosutterella multiformis,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|s__Mycoplasmatales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas nexilis,k__Bacillati|p__Bacillota|c__Clostridia",3379134|976|200643|171549|171550|239759|214856;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|2720800|2720821;1783272|1239|186801|2044939;3379134|1224|28216|80840|995019|2494213|2259133;1783272|1239|91061;1783272|544448|31969|2085|2023991;1783272|1239|186801|186802|216572|2485925;1783272|1239|186801|3085636|186803|2005355|29361;1783272|1239|186801,Complete,Svetlana up
bsdb:38366600/9/1,38366600,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang K.D., Amend L., Gálvez E.J.C., Lesker T.R., de Oliveira R., Bielecka A., Blanco-Míguez A., Valles-Colomer M., Ruf I., Pasolli E., Buer J., Segata N., Esser S., Strowig T. , Kehrmann J.",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 9,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,Non MSM,MSM,Men who have sex with Men (Prevotella Family comparison),24,84,6 Months,WMS,NA,Illumina,relative abundances,Fisher's Exact Test,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary Table S2,17 April 2024,MyleeeA,"MyleeeA,WikiWorks",Species differentially enriched in MSM relative to non-MSM. Log2-transformed abundances of Prevotellaceae members with a minimum abundance of 0.1 at 90th percentile in all subjects.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pectinovora,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.",3379134|976|200643|171549|171552|577309|454154;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|1602169;3379134|976|200643|171549|171552|838|59823,Complete,Svetlana up
bsdb:38366600/10/1,38366600,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang K.D., Amend L., Gálvez E.J.C., Lesker T.R., de Oliveira R., Bielecka A., Blanco-Míguez A., Valles-Colomer M., Ruf I., Pasolli E., Buer J., Segata N., Esser S., Strowig T. , Kehrmann J.",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 10,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,Non MSM,MSM,Men who have sex with Men,31,93,6 Months,WMS,NA,Illumina,relative abundances,Fisher's Exact Test,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 1,Supplementary Table S3,17 April 2024,MyleeeA,"MyleeeA,WikiWorks",Species enriched in MSM and Non MSM.,increased,"k__Bacillati|p__Bacillota|s__Bacillota bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|s__Bacteroidaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|s__Lentisphaeria bacterium,k__Methanobacteriati|p__Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|s__Methanomassiliicoccales archaeon,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella jalaludinii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pectinovora,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|s__Rikenellaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp.,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. Marseille,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira aalborgi,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sp.,k__Bacillati|p__Bacillota|c__Bacilli|s__Bacilli bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella hominis",1783272|1239|1879010;3379134|976|200643|171549|815|2212467;1783272|1239|186801|2044939;3379134|200940|3031449|213115|194924|872|901;1783272|1239|186801|186802|186806|1730|142586;1783272|1239|186801|186802|216572|216851|853;3384189|32066|203490|203491|203492|848|850;1783272|1239|186801|3085636|186803|1898203;1783272|1239|526524|526525|128827|1573535|1735;3379134|256845|1313211|2053569;3366610|2283796|183967|1235850|1906667;1783272|1239|909932|909929|1843491|52225|187979;1783272|1239|909932|1843488|909930|33024|626940;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|1602169;3379134|976|200643|171549|171550|2049048;1783272|1239|186801|3085636|186803|841|2049040;1783272|201174|84998|1643822|1643826|84108|572010;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|186801;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171550;3379134|976|200643|171549|171552|838|304215;1783272|1239|526524|526525|2810280|135858|2049022;3379134|976|200643|171549|171552|838|59823;3379134|203691|203692|1643686|143786|29521|29522;1783272|1239|909932|1843489|31977|906|2023260;1783272|1239|91061|1903720;3379134|976|200643|171549|171552|2974251|2518605,Complete,Svetlana up
bsdb:38366600/10/2,38366600,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang K.D., Amend L., Gálvez E.J.C., Lesker T.R., de Oliveira R., Bielecka A., Blanco-Míguez A., Valles-Colomer M., Ruf I., Pasolli E., Buer J., Segata N., Esser S., Strowig T. , Kehrmann J.",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 10,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,Non MSM,MSM,Men who have sex with Men,31,93,6 Months,WMS,NA,Illumina,relative abundances,Fisher's Exact Test,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 2,Supplementary Table S3,18 April 2024,MyleeeA,"MyleeeA,WikiWorks",Species enriched in MSM and Non MSM.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|s__Acidaminococcaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum butyriciproducens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes inops,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum faecicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales|s__Candidatus Gastranaerophilales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Evtepia|s__Evtepia gabavorous,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Mesosutterella|s__Mesosutterella multiformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Liu et al. 2021),k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium fessum",1783272|1239|909932|1843488|909930|2049052;1783272|1239|186801|186802|3085642|2048137|1628085;3379134|976|200643|171549|171550|239759|2585118;3379134|976|200643|171549|171550|239759|1501391;3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|171550|239759|28117;1783272|1239|186801|3085636|3118652|2039240|2358141;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|246787;3379134|976|200643|171549|815|816|338188;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|2005519|397864|487174;1783272|201174|1760|85004|31953|1678|1681;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|186801|3085636|186803|572511|871665;1783272|1239|186801|3085636|186803|572511|418240;1783272|1798710|1906119|2137880;1783272|1239|186801|2044939;1783272|1239|186801|186802|31979|1898204;1783272|1239|186801|186802|31979|1485|1506;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|186801|186802|2211178|2211183;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|186802|204475;1783272|1239|186801|3085636|186803|2316020|33038;3379134|1224|28216|80840|995019|2494213|2259133;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|171552|577309|454154;3379134|1224|28216|80840|995019|577310;3379134|1224|28216|80840|995019|577310|487175;1783272|1239|909932|1843488|909930|33024|33025;3379134|976|200643|171549|815|909656|310298;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|186802|216572|1263|3062497;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|186801|3085636|186803|2316020|46228;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801;1783272|1239|186801|186802|31979|1485|2126740,Complete,Svetlana up
bsdb:38366600/11/1,38366600,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang K.D., Amend L., Gálvez E.J.C., Lesker T.R., de Oliveira R., Bielecka A., Blanco-Míguez A., Valles-Colomer M., Ruf I., Pasolli E., Buer J., Segata N., Esser S., Strowig T. , Kehrmann J.",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 11,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,MSM,Non Westernized,"Non-Westernized describes a population practicing a traditional lifestyle relating to factors such as diet, hygiene, and with limited access to modern medical healthcare and pharmaceuticals (e.g., antibiotics).",93,481,6 Months,WMS,NA,Illumina,relative abundances,Fisher's Exact Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table S3,18 April 2024,MyleeeA,"MyleeeA,WikiWorks",Species enriched in MSM and Non Westernized.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus massiliensis (ex Liu et al. 2021),k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Angelakisella|s__Angelakisella massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira pilosicoli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Alangreenwoodia|s__Candidatus Alangreenwoodia gallinarii,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Allobutyricicoccus|s__Candidatus Allobutyricicoccus pentlandensis,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Allochristensenella|s__Candidatus Allochristensenella caecavium,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Avimonas|s__Candidatus Avimonas narfae,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Geddesella|s__Candidatus Geddesella stercoravicola,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Metalachnospira|s__Candidatus Metalachnospira gallinarum,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Neochristensenella|s__Candidatus Neochristensenella gallicola,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Neoruminococcus|s__Candidatus Neoruminococcus faecicola,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Pseudolachnospira|s__Candidatus Pseudolachnospira avium,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella tayi,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor sp.,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania filiformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Hydrogeniiclostridium|s__Hydrogeniiclostridium mannosilyticum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas massiliensis (ex Afouda et al. 2020),k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Massiliimalia|s__Massiliimalia timonensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis|s__Merdimmobilis hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Merdimonas|s__Merdimonas faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium freudenreichii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Sanguibacteroides|s__Sanguibacteroides justesenii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Massilimicrobiota|s__Massilimicrobiota sp.",1783272|1239|186801|186802|216572|244127|2321404;1783272|1239|186801|186802|216572|1935176|1871018;3379134|976|200643|171549|815|816|291644;1783272|201174|1760|85004|31953|1678|1686;3379134|203691|203692|1643686|143786|29521|52584;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|2720809|2720823;1783272|1239|186801|2720794|2720824;1783272|1239|186801|2720795|2720825;1783272|1239|186801|2720801|2720820;1783272|1239|186801|2720808|2720834;1783272|1239|186801|2721107|2721132;1783272|1239|186801|2721110|2721137;1783272|1239|186801|2721112|2721139;1783272|1239|186801|2721118|2721148;1783272|1239|186801|2044939;1783272|1239|186801|186802|31979|1898204;1783272|1239|186801|186802|1898207;1783272|1239|186801|186802|31979|1485|1506;3379134|976|200643|171549|2005519|1348911|1099853;1783272|1239|186801|3085636|186803|1432051|1432052;1783272|1239|526524|526525|128827|2049044;1783272|1239|186801|186802|186806|1730|142586;1783272|1239|186801|186802|216572|946234|2049025;1783272|1239|526524|526525|128827|61170|61171;1783272|1239|186801|186802|3082771|2764317|2764322;1783272|1239|186801|186802|1392389|1673721;1783272|1239|186801|186802|1392389|1689270;1783272|1239|186801|3085636|186803|1506553|2028282;1783272|1239|186801|3085636|186803|1898203;1783272|1239|186801|186802|216572|2895461|1987501;1783272|1239|909932|1843489|31977|906|907;1783272|1239|186801|186802|216572|3028852|2897707;1783272|1239|186801|3085636|186803|2023266|1653435;1783272|1239|186801|186802|216572|459786|1945593;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|171552|838|28125;1783272|201174|1760|85009|31957|1743|1744;1783272|201174|1760|85006|1268|32207|43675;3379134|976|200643|171549|171551|1635148|1547597;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|2485925;1783272|1239|526524|526525|128827|1924110|1924111,Complete,Svetlana up
bsdb:38366600/11/2,38366600,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang K.D., Amend L., Gálvez E.J.C., Lesker T.R., de Oliveira R., Bielecka A., Blanco-Míguez A., Valles-Colomer M., Ruf I., Pasolli E., Buer J., Segata N., Esser S., Strowig T. , Kehrmann J.",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 11,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,MSM,Non Westernized,"Non-Westernized describes a population practicing a traditional lifestyle relating to factors such as diet, hygiene, and with limited access to modern medical healthcare and pharmaceuticals (e.g., antibiotics).",93,481,6 Months,WMS,NA,Illumina,relative abundances,Fisher's Exact Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table S3,19 April 2024,MyleeeA,"MyleeeA,WikiWorks",Species enriched in MSM and Non Westernized.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|s__Bacteroidaceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotellamassilia|s__Prevotellamassilia timonensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales|s__Candidatus Gastranaerophilales bacterium,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 348,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Nanosynsacchari|s__Candidatus Nanosynsacchari sp. TM7_ANC_38.39_G1_1,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|s__Elusimicrobiales bacterium,k__Bacillati|p__Bacillota|c__Bacilli|s__Bacilli bacterium,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus petauri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Pseudolactococcus|s__Pseudolactococcus plantarum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium disporicum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium diversum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|s__Eubacteriaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Liu et al. 2021),k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|s__Lentisphaeria bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia marmotae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|s__Spirochaetia bacterium",1783272|201174|1760|2037|2049|1654|29317;3379134|976|200643|171549|815|2212467;3379134|976|200643|171549|171552|1926672|1852370;3379134|976|200643|171549|171552|838|59823;1783272|1798710|1906119|2137880;95818|671231;95818|2093818|2093825|2171986|2789662|1986206;3379134|74152|641853|641854|2478488;1783272|1239|91061|1903720;1783272|1239|91061;1783272|1239|91061|186826|33958|1243;1783272|1239|91061|186826|1300|1357|1940789;1783272|1239|91061|186826|1300|3436058|1365;1783272|1239|91061|186826|1300|1301|1306;1783272|1239|186801|2044939;1783272|1239|186801;1783272|1239|186801|186802|31979|1485|84024;1783272|1239|186801|186802|31979|1485|1506;1783272|1239|186801|3082720|543314|86331|114527;1783272|1239|186801|186802|186806|2049045;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|871665;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|1898203;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|2316020|46228;1783272|1239|186801|3085636|186803|841|2049040;1783272|1239|186801|186802|216572|2485925;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|1263|3062497;1783272|1239|526524|526525|128827|2049044;1783272|1239|909932|909929|1843491|970;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|909932|1843489|31977|29465|423477;3379134|256845|1313211|2053569;3379134|1224|1236|91347|543|561|1499973;3379134|203691|203692|2053615,Complete,Svetlana up
bsdb:38366600/12/1,38366600,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang K.D., Amend L., Gálvez E.J.C., Lesker T.R., de Oliveira R., Bielecka A., Blanco-Míguez A., Valles-Colomer M., Ruf I., Pasolli E., Buer J., Segata N., Esser S., Strowig T. , Kehrmann J.",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 12,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,MSM,Westernized,"Westernization describes a population with incremental urbanization, profound lifestyle changes, including but not limited to, transition from autarchic means of producing food to controlled food production chain, increased hygiene and accessibility to modern medicals, introduction of food sterilization, increased exposure to pollutants, and switch from high-fiber simple diets to high-fat high-protein processes that has been undergoing for centuries.",93,481,6 Months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A,17 April 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance of Bacteroidaceae and Prevotellaceae families and Bacteroides and Segatella/Prevotella genera between MSM (n = 93), Westernized (n = 481), non-Westernized (n = 389), and urban Chinese (n= 66) samples (Wilcoxon rank-sum test with FDR correction).",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,3379134|976|200643|171549|171552,Complete,Svetlana up
bsdb:38366600/12/2,38366600,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang K.D., Amend L., Gálvez E.J.C., Lesker T.R., de Oliveira R., Bielecka A., Blanco-Míguez A., Valles-Colomer M., Ruf I., Pasolli E., Buer J., Segata N., Esser S., Strowig T. , Kehrmann J.",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 12,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,MSM,Westernized,"Westernization describes a population with incremental urbanization, profound lifestyle changes, including but not limited to, transition from autarchic means of producing food to controlled food production chain, increased hygiene and accessibility to modern medicals, introduction of food sterilization, increased exposure to pollutants, and switch from high-fiber simple diets to high-fat high-protein processes that has been undergoing for centuries.",93,481,6 Months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3A,17 April 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance of Bacteroidaceae and Prevotellaceae families and Bacteroides and Segatella/Prevotella genera between MSM (n = 93), Westernized (n = 481), non-Westernized (n = 389), and urban Chinese (n= 66) samples (Wilcoxon rank-sum test with FDR correction).",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:38366600/13/1,38366600,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang K.D., Amend L., Gálvez E.J.C., Lesker T.R., de Oliveira R., Bielecka A., Blanco-Míguez A., Valles-Colomer M., Ruf I., Pasolli E., Buer J., Segata N., Esser S., Strowig T. , Kehrmann J.",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 13,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,MSM,Non Westernized,"Non-Westernized describes a population practicing a traditional lifestyle relating to factors such as diet, hygiene, and with limited access to modern medical healthcare and pharmaceuticals (e.g., antibiotics).",93,389,6 Months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A,17 April 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance of Bacteroidaceae and Prevotellaceae families and Bacteroides and Segatella/Prevotella genera between MSM (n = 93), Westernized (n = 481), non-Westernized (n = 389), and urban Chinese (n= 66) samples (Wilcoxon rank-sum test with FDR correction).",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:38366600/13/2,38366600,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang K.D., Amend L., Gálvez E.J.C., Lesker T.R., de Oliveira R., Bielecka A., Blanco-Míguez A., Valles-Colomer M., Ruf I., Pasolli E., Buer J., Segata N., Esser S., Strowig T. , Kehrmann J.",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 13,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,MSM,Non Westernized,"Non-Westernized describes a population practicing a traditional lifestyle relating to factors such as diet, hygiene, and with limited access to modern medical healthcare and pharmaceuticals (e.g., antibiotics).",93,389,6 Months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3A,17 April 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance of Bacteroidaceae and Prevotellaceae families and Bacteroides and Segatella/Prevotella genera between MSM (n = 93), Westernized (n = 481), non-Westernized (n = 389), and urban Chinese (n= 66) samples (Wilcoxon rank-sum test with FDR correction).",decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,3379134|976|200643|171549|171552,Complete,Svetlana up
bsdb:38366600/14/1,38366600,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang K.D., Amend L., Gálvez E.J.C., Lesker T.R., de Oliveira R., Bielecka A., Blanco-Míguez A., Valles-Colomer M., Ruf I., Pasolli E., Buer J., Segata N., Esser S., Strowig T. , Kehrmann J.",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 14,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,MSM,China (Urban),Two Chinese cities - GuangDong and TangShan - which are located in Southern China and have been experiencing rapid urbanization in the last decade. They were used to represent populations from non-Western but relatively urbanized communities.,93,66,6 Months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A,17 April 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance of Bacteroidaceae and Prevotellaceae families and Bacteroides and Segatella/Prevotella genera between MSM (n = 93), Westernized (n = 481), non-Westernized (n = 389), and urban Chinese (n= 66) samples (Wilcoxon rank-sum test with FDR correction).",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,3379134|976|200643|171549|171552,Complete,Svetlana up
bsdb:38366600/14/2,38366600,case-control,38366600,https://doi.org/10.1016/j.xcrm.2024.101426,https://pubmed.ncbi.nlm.nih.gov/38366600/,"Huang K.D., Amend L., Gálvez E.J.C., Lesker T.R., de Oliveira R., Bielecka A., Blanco-Míguez A., Valles-Colomer M., Ruf I., Pasolli E., Buer J., Segata N., Esser S., Strowig T. , Kehrmann J.",Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices,Cell reports. Medicine,2024,"MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation",Experiment 14,"China,Germany",Homo sapiens,Feces,UBERON:0001988,Male homosexuality,EFO:0008486,MSM,China (Urban),Two Chinese cities - GuangDong and TangShan - which are located in Southern China and have been experiencing rapid urbanization in the last decade. They were used to represent populations from non-Western but relatively urbanized communities.,93,66,6 Months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3A,17 April 2024,MyleeeA,"MyleeeA,WikiWorks","Differential abundance of Bacteroidaceae and Prevotellaceae families and Bacteroides and Segatella/Prevotella genera between MSM (n = 93), Westernized (n = 481), non-Westernized (n = 389), and urban Chinese (n= 66) samples (Wilcoxon rank-sum test with FDR correction).",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:38374114/1/NA,38374114,time series / longitudinal observational,38374114,https://doi.org/10.1038/s41522-024-00482-z,NA,"Bazzani D., Heidrich V., Manghi P., Blanco-Miguez A., Asnicar F., Armanini F., Cavaliere S., Bertelle A., Dell'Acqua F., Dellasega E., Waldner R., Vicentini D., Bolzan M., Tomasi C., Segata N., Pasolli E. , Ghensi P.",Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases,NPJ biofilms and microbiomes,2024,NA,Experiment 1,Italy,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Peri-Implantitis,EFO:1001390,Healthy group (case samples),Mucositis group (case samples),Healthy species/ biomarkers enriched or significant in mucositis patients compared with healthy group patients who underwent surgical (n=9) or non-surgical treatment (n=22) as decided by clinical practitioners,32,28,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:38374114/2/1,38374114,time series / longitudinal observational,38374114,https://doi.org/10.1038/s41522-024-00482-z,NA,"Bazzani D., Heidrich V., Manghi P., Blanco-Miguez A., Asnicar F., Armanini F., Cavaliere S., Bertelle A., Dell'Acqua F., Dellasega E., Waldner R., Vicentini D., Bolzan M., Tomasi C., Segata N., Pasolli E. , Ghensi P.",Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases,NPJ biofilms and microbiomes,2024,NA,Experiment 2,Italy,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Peri-Implantitis,EFO:1001390,Healthy group (case samples),Peri-implantitis group (case samples),Healthy species/ biomarkers enriched or significant in peri-implantitis patients compared with healthy group patients who underwent surgical (n=9) or non-surgical treatment (n=22) as decided by clinical practitioners,32,31,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2a and text (paragraph 4),7 March 2024,EniolaAde,"EniolaAde,Folakunmi,WikiWorks",LEFSE-identified healthy microbiome composition significantly enriched after treatment  in healthy group patients compared with peri-implantitis patients,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria",1783272|201174|1760|2037|2049|1654|544580;1783272|201174|1760|85007|1653|1716|43768;1783272|201174|1760|85006|1268|32207|172042,Complete,Folakunmi
bsdb:38374114/3/1,38374114,time series / longitudinal observational,38374114,https://doi.org/10.1038/s41522-024-00482-z,NA,"Bazzani D., Heidrich V., Manghi P., Blanco-Miguez A., Asnicar F., Armanini F., Cavaliere S., Bertelle A., Dell'Acqua F., Dellasega E., Waldner R., Vicentini D., Bolzan M., Tomasi C., Segata N., Pasolli E. , Ghensi P.",Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases,NPJ biofilms and microbiomes,2024,NA,Experiment 3,Italy,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Peri-Implantitis,EFO:1001390,Healthy group (case samples),Peri-implantitis group (case samples),Peri-implantitis species/ biomarkers enriched or significant in peri-implantitis patients compared with healthy group patients who underwent surgical (n=9) or non-surgical treatment (n=22) as decided by clinical practitioners,32,31,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2c,7 March 2024,EniolaAde,"EniolaAde,Folakunmi,WikiWorks",LEFSE-identified peri-implantitis biomarkers/microbiome composition significantly enriched after treatment in healthy group patients compared with peri-implantitis patients,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacillati|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae",3384189|32066|203490|203491|203492|848|851;3379134|976|200643|171549|171551|836|837;1783272|200795|292625|292629|292628,Complete,Folakunmi
bsdb:38374114/4/1,38374114,time series / longitudinal observational,38374114,https://doi.org/10.1038/s41522-024-00482-z,NA,"Bazzani D., Heidrich V., Manghi P., Blanco-Miguez A., Asnicar F., Armanini F., Cavaliere S., Bertelle A., Dell'Acqua F., Dellasega E., Waldner R., Vicentini D., Bolzan M., Tomasi C., Segata N., Pasolli E. , Ghensi P.",Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases,NPJ biofilms and microbiomes,2024,NA,Experiment 4,Italy,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Peri-Implantitis,EFO:1001390,Healthy group (contralateral site samples),Mucositis group (contralateral site samples),Healthy species/ biomarkers enriched or significant in mucositis patients compared with healthy group patients who underwent surgical (n=9) or non-surgical treatment (n=22) as decided by clinical practitioners,32,28,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2b,23 March 2024,Folakunmi,"Folakunmi,WikiWorks",LEFSE-identified healthy microbiome composition significantly enriched after treatment in  mucositis patients compared with healthy group patients,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,1783272|1239|91061|186826|1300|1301|1303,Complete,Folakunmi
bsdb:38374114/5/1,38374114,time series / longitudinal observational,38374114,https://doi.org/10.1038/s41522-024-00482-z,NA,"Bazzani D., Heidrich V., Manghi P., Blanco-Miguez A., Asnicar F., Armanini F., Cavaliere S., Bertelle A., Dell'Acqua F., Dellasega E., Waldner R., Vicentini D., Bolzan M., Tomasi C., Segata N., Pasolli E. , Ghensi P.",Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases,NPJ biofilms and microbiomes,2024,NA,Experiment 5,Italy,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Peri-Implantitis,EFO:1001390,Healthy group (contralateral site samples),Peri-implantitis group (contralateral site samples),Healthy species/ biomarkers enriched or significant in Peri-implantitis patients compared with healthy group patients who underwent surgical (n=9) or non-surgical treatment (n=22) as decided by clinical practitioners,32,31,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2b,23 March 2024,Folakunmi,"Folakunmi,WikiWorks",LEFSE-identified peri-implantitis biomarkers/microbiome composition significantly enriched after treatment in healthy group patients compared with peri-implantitis patients,decreased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,1783272|1239|909932|1843489|31977|29465|29466,Complete,Folakunmi
bsdb:38374114/6/1,38374114,time series / longitudinal observational,38374114,https://doi.org/10.1038/s41522-024-00482-z,NA,"Bazzani D., Heidrich V., Manghi P., Blanco-Miguez A., Asnicar F., Armanini F., Cavaliere S., Bertelle A., Dell'Acqua F., Dellasega E., Waldner R., Vicentini D., Bolzan M., Tomasi C., Segata N., Pasolli E. , Ghensi P.",Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases,NPJ biofilms and microbiomes,2024,NA,Experiment 6,Italy,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Peri-Implantitis,EFO:1001390,Healthy group  (contralteral samples),Peri-implantitis and mucositis groups (contralteral samples),Peri-implantitis species/ biomarkers enriched or significant in peri-implantitis and mucositis patients compared with healthy group patients who underwent surgical (n=9) or non-surgical treatment (n=22) as decided by clinical practitioners,32,59,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2d,28 March 2024,Folakunmi,"Folakunmi,WikiWorks",LEFSE-identified peri-implantitis biomarkers/microbiome composition significantly enriched after treatment in healthy group patients compared with peri-implantitis and mucositis patients,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,3379134|976|200643|171549|171552|838|28131,Complete,Folakunmi
bsdb:38378622/1/1,38378622,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W., Ma Q., Wang L., Yuan N., Gan H., He L., Li X., Huang J. , Chen J.",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Response to antidepressant,GO:0036276,"Chronic Unpredictable Mild Stress (CUMS), CUMS + Xiaoyaosan (XYS) and CUMS + fluoxetine (FLX) groups",Control Group,Samples collected from the mice groups without any intervention or drug administration.,18,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4F and Figure S2d,22 March 2024,Aleru Divine,"Aleru Divine,WikiWorks","LEfSe analysis of the microbiome data showing differentially abundant bacterial taxa in the control, CUMS, (CUMS + XYS) and (CUMS + FLX) groups.",increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Armatimonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota,k__Bacillati|p__Chloroflexota,k__Thermotogati|p__Deinococcota,k__Pseudomonadati|p__Gemmatimonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|201174|84992;1783272|201174;1783272|67819;1783272|1239|91061|1385;1783272|1239;1783272|200795;3384194|1297;3379134|142182;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:38378622/2/1,38378622,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W., Ma Q., Wang L., Yuan N., Gan H., He L., Li X., Huang J. , Chen J.",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Response to antidepressant,GO:0036276,"Control, (CUMS + XYS) and (CUMS + FLX) groups",CUMS group,Mice group induced with chronic unpredictable mild stress (CUMS),18,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4F and Figure S2d,22 March 2024,Aleru Divine,"Aleru Divine,WikiWorks","LEfSe analysis of the microbiome data showing differentially abundant bacterial taxa in the control, CUMS, (CUMS + XYS) and (CUMS + FLX) groups.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Verrucomicrobiota",3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3384189|32066;3379134|1224|1236;3379134|1224|1236|91347|543|570;3379134|1224;3379134|74201,Complete,Svetlana up
bsdb:38378622/4/1,38378622,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W., Ma Q., Wang L., Yuan N., Gan H., He L., Li X., Huang J. , Chen J.",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Response to antidepressant,GO:0036276,"Control, CUMS, and (CUMS + FLX) groups",CUMS + XYS group,"Mice group induced with chronic unpredictable mild stress (CUMS) for 8 weeks, followed by daily oral administration of Xiaoyaosan (XYS).",18,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4F and Figure S2d,22 March 2024,Aleru Divine,"Aleru Divine,WikiWorks","LEfSe analysis of the microbiome data showing differentially abundant bacterial taxa in the control, CUMS, (CUMS + XYS) and (CUMS + FLX) groups.",increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Mycoplasmatota",1783272|1239|91061;1783272|1239;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|544448,Complete,Svetlana up
bsdb:38378622/5/1,38378622,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W., Ma Q., Wang L., Yuan N., Gan H., He L., Li X., Huang J. , Chen J.",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Environmental stress treatment,EFO:0000470,Control group,CUMS Group,Mice group induced with chronic unpredictable mild stress (CUMS),6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,decreased,unchanged,unchanged,NA,unchanged,Signature 1,Figure 8g,22 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe analysis of the microbiome data showing differentially abundant bacterial taxa in the control and CUMS group,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|577309,Complete,Svetlana up
bsdb:38378622/5/2,38378622,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W., Ma Q., Wang L., Yuan N., Gan H., He L., Li X., Huang J. , Chen J.",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Environmental stress treatment,EFO:0000470,Control group,CUMS Group,Mice group induced with chronic unpredictable mild stress (CUMS),6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,decreased,unchanged,unchanged,NA,unchanged,Signature 2,Figure 8G,22 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe analysis of the microbiome data showing differentially abundant bacterial taxa in the control and CUMS group,decreased,",k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",;1783272|1239|186801|186802|216572|216851,Complete,Svetlana up
bsdb:38378622/6/1,38378622,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W., Ma Q., Wang L., Yuan N., Gan H., He L., Li X., Huang J. , Chen J.",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Control group,Control + FMT(CUMS) group,Mice group that received fecal microbiota transplantation from host induced with chronic unpredictable mild stress (CUMS).,6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,decreased,unchanged,unchanged,NA,unchanged,Signature 1,Figure 8i,22 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe analysis of the microbiome data showing differentially abundant bacterial taxa in the control and Control + FMT(CUMS) group.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",1783272|1239|526524|526525|128827|174708;3379134|976|200643|171549;3379134|976|200643;3379134|976;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|577309,Complete,Svetlana up
bsdb:38378622/6/2,38378622,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W., Ma Q., Wang L., Yuan N., Gan H., He L., Li X., Huang J. , Chen J.",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Control group,Control + FMT(CUMS) group,Mice group that received fecal microbiota transplantation from host induced with chronic unpredictable mild stress (CUMS).,6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,decreased,unchanged,unchanged,NA,unchanged,Signature 2,Figure 8i,22 March 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe analysis of the microbiome data showing differentially abundant bacterial taxa in the control and Control + FMT(CUMS) group.,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Svetlana up
bsdb:38378622/8/1,38378622,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W., Ma Q., Wang L., Yuan N., Gan H., He L., Li X., Huang J. , Chen J.",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 8,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Control group,Control + FMT(CUMS) group,Mice group that received fecal microbiota transplantation (FMT) from host induced with chronic unpredictable mild stress (CUMS).,6,6,NA,16S,34,Illumina,relative abundances,Pearson Correlation,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,unchanged,NA,unchanged,Signature 1,Figure S5F,7 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Gut microbiota change at genus level (Control versus Control+FMT(CUMS)),increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|526524|526525|128827|174708;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|40544;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:38378622/8/2,38378622,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W., Ma Q., Wang L., Yuan N., Gan H., He L., Li X., Huang J. , Chen J.",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 8,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Control group,Control + FMT(CUMS) group,Mice group that received fecal microbiota transplantation (FMT) from host induced with chronic unpredictable mild stress (CUMS).,6,6,NA,16S,34,Illumina,relative abundances,Pearson Correlation,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,unchanged,NA,unchanged,Signature 2,Figure S5F,7 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Gut microbiota change at genus level (Control versus Control+FMT(CUMS)),decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,s__unidentified,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",1783272|201174|1760|85004|31953|2701;1783272|1239|186801|186802|31979|1485;1783272|1239|91061|1385|90964|1279;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|31979|49082;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572|1263;3379134|29547|3031852|213849|72293|209;1783272|1239|186801|186802|216572|216851;32644;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|171552|838;3379134|74201|203494|48461|1647988|239934,Complete,Svetlana up
bsdb:38378622/9/1,38378622,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W., Ma Q., Wang L., Yuan N., Gan H., He L., Li X., Huang J. , Chen J.",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 9,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,CUMS group,CUMS + FMT(XYS) group,Mice group that received fecal microbiota transplantation from host treated with Xiaoyaosan (XYS).,6,6,NA,16S,34,Illumina,relative abundances,Pearson Correlation,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure S5d,7 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Gut microbiota change at genus level (CUMS versus CUMS+FMT(XYS)).,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|74201|203494|48461|1647988|239934;1783272|1239|91061|186826|33958|1578;3379134|1224|28216|80840|995019|40544;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:38378622/9/2,38378622,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W., Ma Q., Wang L., Yuan N., Gan H., He L., Li X., Huang J. , Chen J.",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 9,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,CUMS group,CUMS + FMT(XYS) group,Mice group that received fecal microbiota transplantation from host treated with Xiaoyaosan (XYS).,6,6,NA,16S,34,Illumina,relative abundances,Pearson Correlation,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure S5d,7 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Gut microbiota change at genus level (CUMS versus CUMS+FMT(XYS)).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,s__unidentified,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|31979|1485;1783272|201174|1760|85004|31953|2701;1783272|1239|526524|526525|128827|174708;32644;1783272|1239|186801|3085636|186803|841;3379134|29547|3031852|213849|72293|209;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|31979|49082;1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:38378622/10/1,38378622,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W., Ma Q., Wang L., Yuan N., Gan H., He L., Li X., Huang J. , Chen J.",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 10,China,Mus musculus,Feces,UBERON:0001988,Environmental stress treatment,EFO:0000470,Control group,CUMS Group,Mice group induced with chronic unpredictable mild stress (CUMS),6,6,NA,16S,34,Illumina,relative abundances,Pearson Correlation,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,unchanged,NA,unchanged,Signature 1,Figure S5E,7 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Gut microbiota change at genus level (Control versus CUMS).,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.",1783272|1239|526524|526525|128827|174708;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|31979|1485;3379134|976|200643|171549|171552|838;1783272|201174|1760|85004|31953|2701;3379134|976|200643|171549|2005525|375288;3379134|29547|3031852|213849|72293|209;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171552|838|59823,Complete,Svetlana up
bsdb:38378622/10/2,38378622,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W., Ma Q., Wang L., Yuan N., Gan H., He L., Li X., Huang J. , Chen J.",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 10,China,Mus musculus,Feces,UBERON:0001988,Environmental stress treatment,EFO:0000470,Control group,CUMS Group,Mice group induced with chronic unpredictable mild stress (CUMS),6,6,NA,16S,34,Illumina,relative abundances,Pearson Correlation,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,unchanged,NA,unchanged,Signature 2,Figure S5E,7 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Gut microbiota change at genus level (Control versus CUMS).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,s__unidentified,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",1783272|1239|186801|186802|31979|49082;3379134|976|200643|171549|815|816;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|1385|90964|1279;1783272|1239|186801|3085636|186803|33042;32644;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|572511,Complete,Svetlana up
bsdb:38378622/11/1,38378622,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W., Ma Q., Wang L., Yuan N., Gan H., He L., Li X., Huang J. , Chen J.",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 11,China,Mus musculus,Feces,UBERON:0001988,Depressive disorder,MONDO:0002050,Control group,CUMS group,Mice group induced with chronic unpredictable mild stress (CUMS) for 8 weeks.,6,6,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 4(G-I),11 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","The relative abundances of selected bacterial signatures in the control, CUMS, (CUMS + XYS) and (CUMS + FLX) groups.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella",3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|570,Complete,Svetlana up
bsdb:38378622/11/2,38378622,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W., Ma Q., Wang L., Yuan N., Gan H., He L., Li X., Huang J. , Chen J.",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 11,China,Mus musculus,Feces,UBERON:0001988,Depressive disorder,MONDO:0002050,Control group,CUMS group,Mice group induced with chronic unpredictable mild stress (CUMS) for 8 weeks.,6,6,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 4(G-I),11 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","The relative abundances of selected bacterial signatures in the control, CUMS, (CUMS + XYS) and (CUMS + FLX) groups.",decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:38378622/12/1,38378622,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W., Ma Q., Wang L., Yuan N., Gan H., He L., Li X., Huang J. , Chen J.",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 12,China,Mus musculus,Feces,UBERON:0001988,Response to antidepressant,GO:0036276,CUMS group,CUMS + XYS group,"Mice group induced with chronic unpredictable mild stress (CUMS) for 8 weeks, followed by daily oral administration of Xiaoyaosan (XYS).",6,6,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 4(G-I),11 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","The relative abundances of selected bacterial signatures in the control, CUMS, (CUMS + XYS) and (CUMS + FLX) groups.",increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:38378622/12/2,38378622,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W., Ma Q., Wang L., Yuan N., Gan H., He L., Li X., Huang J. , Chen J.",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 12,China,Mus musculus,Feces,UBERON:0001988,Response to antidepressant,GO:0036276,CUMS group,CUMS + XYS group,"Mice group induced with chronic unpredictable mild stress (CUMS) for 8 weeks, followed by daily oral administration of Xiaoyaosan (XYS).",6,6,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 4(G-I),11 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","The relative abundances of selected bacterial signatures in the control, CUMS, (CUMS + XYS) and (CUMS + FLX) groups.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella",3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|570,Complete,Svetlana up
bsdb:38378622/13/1,38378622,laboratory experiment,38378622,10.1186/s40168-024-01756-6,https://pubmed.ncbi.nlm.nih.gov/38378622/,"Hao W., Ma Q., Wang L., Yuan N., Gan H., He L., Li X., Huang J. , Chen J.",Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3,Microbiome,2024,"Complement C3, Depression, Fecal microbiota transplantation, Gut microbiota, Microglia, Synaptic pruning",Experiment 13,China,Mus musculus,Feces,UBERON:0001988,Response to antidepressant,GO:0036276,CUMS group,CUMS + FLX group,"Mice group induced with chronic unpredictable mild stress (CUMS) for 8 weeks, followed by daily oral administration of fluoxetine (FLX).",6,6,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 4(G-I),11 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","The relative abundances of selected bacterial signatures in the control, CUMS, (CUMS + XYS) and (CUMS + FLX) groups.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella",3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|570,Complete,Svetlana up
bsdb:38381714/1/1,38381714,case-control,38381714,10.1371/journal.pone.0297858,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0297858,"Humińska-Lisowska K., Zielińska K., Mieszkowski J., Michałowska-Sawczyn M., Cięszczyk P., Łabaj P.P., Wasąg B., Frączek B., Grzywacz A., Kochanowicz A. , Kosciolek T.",Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study,PloS one,2024,NA,Experiment 1,Poland,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Non-athletes,Strength athletes,Athletes engaged in strength athletics at timepoint B0 (in the morning before the Bruce Treadmill Test),19,15,6 months,PCR,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,diet,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table 2,7 March 2024,Aleru Divine,"Aleru Divine,Folakunmi,WikiWorks",Species identified as specific per group after being identified as significantly more abundant in the group of interest in comparison to the other two groups by LEfSe at Timepoint B0 (in the morning before the Bruce Treadmill Test),increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium sp. AM22-15,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium phoceensis",1783272|1239|526524|526525|2810280|135858|2292991;1783272|1239|186801|186802|31979|1485|1650661,Complete,Folakunmi
bsdb:38381714/2/1,38381714,case-control,38381714,10.1371/journal.pone.0297858,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0297858,"Humińska-Lisowska K., Zielińska K., Mieszkowski J., Michałowska-Sawczyn M., Cięszczyk P., Łabaj P.P., Wasąg B., Frączek B., Grzywacz A., Kochanowicz A. , Kosciolek T.",Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study,PloS one,2024,NA,Experiment 2,Poland,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Non-athletes,Endurance athletes,Athletes engaged in endurance athletics (in the morning before the Bruce Treadmill Test),19,13,6 months,PCR,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,diet,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table 2,7 March 2024,Aleru Divine,"Aleru Divine,Folakunmi,WikiWorks",Species identified as specific per group after being identified as significantly more abundant in the group of interest in comparison to the other two groups by LEfSe at time point B0(in the morning before the Bruce Treadmill Test),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. AF19-10LB,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena",1783272|1239|186801|3085636|186803|572511|2292961;1783272|1239|186801|3085636|186803|189330|88431,Complete,Folakunmi
bsdb:38381714/3/1,38381714,case-control,38381714,10.1371/journal.pone.0297858,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0297858,"Humińska-Lisowska K., Zielińska K., Mieszkowski J., Michałowska-Sawczyn M., Cięszczyk P., Łabaj P.P., Wasąg B., Frączek B., Grzywacz A., Kochanowicz A. , Kosciolek T.",Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study,PloS one,2024,NA,Experiment 3,Poland,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Non-athletes,Strength athletes,Athletes engaged in strength athletics at timepoint W1 (the same day after the repeated lower body 30s-all-out wingate's test),19,15,6 months,PCR,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,diet,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table 2,8 March 2024,Aleru Divine,"Aleru Divine,Folakunmi,WikiWorks",Species identified as specific per group after being identified as significantly more abundant in the group of interest in comparison to the other two groups by LEfSe at Timepoint W1 (the same day after the repeated lower body 30s-all-out wingate's test),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. AF41-9",1783272|1239|186801|3085636|186803|3570277|116085;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|186801|186802|216572|1263|2292069,Complete,Folakunmi
bsdb:38381714/3/2,38381714,case-control,38381714,10.1371/journal.pone.0297858,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0297858,"Humińska-Lisowska K., Zielińska K., Mieszkowski J., Michałowska-Sawczyn M., Cięszczyk P., Łabaj P.P., Wasąg B., Frączek B., Grzywacz A., Kochanowicz A. , Kosciolek T.",Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study,PloS one,2024,NA,Experiment 3,Poland,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Non-athletes,Strength athletes,Athletes engaged in strength athletics at timepoint W1 (the same day after the repeated lower body 30s-all-out wingate's test),19,15,6 months,PCR,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,diet,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Table 2,8 March 2024,Aleru Divine,"Aleru Divine,Folakunmi,WikiWorks",Species identified as specific per group after being identified as significantly more abundant in the group of interest in comparison to the other two groups by LEfSe at Timepoint W1 (the same day after the repeated lower body 30s-all-out wingate's test),decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecis,3379134|976|200643|171549|815|816|674529,Complete,Folakunmi
bsdb:38381714/4/1,38381714,case-control,38381714,10.1371/journal.pone.0297858,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0297858,"Humińska-Lisowska K., Zielińska K., Mieszkowski J., Michałowska-Sawczyn M., Cięszczyk P., Łabaj P.P., Wasąg B., Frączek B., Grzywacz A., Kochanowicz A. , Kosciolek T.",Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study,PloS one,2024,NA,Experiment 4,Poland,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Non-athletes,Endurance athletes,Athletes engaged in endurance athletics at time point W1 (the same day after the repeated lower body 30s-all-out wingate's test),19,13,6 months,PCR,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,diet,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table 2,8 March 2024,Aleru Divine,"Aleru Divine,Folakunmi,WikiWorks",Species identified as specific per group after being identified as significantly more abundant in the group of interest in comparison to the other two groups by LEfSe at time point W1 (the same day after the repeated lower body 30s-all-out wingate's test),increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,1783272|1239|186801|3085636|186803|1407607|1150298,Complete,Folakunmi
bsdb:38381714/4/2,38381714,case-control,38381714,10.1371/journal.pone.0297858,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0297858,"Humińska-Lisowska K., Zielińska K., Mieszkowski J., Michałowska-Sawczyn M., Cięszczyk P., Łabaj P.P., Wasąg B., Frączek B., Grzywacz A., Kochanowicz A. , Kosciolek T.",Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study,PloS one,2024,NA,Experiment 4,Poland,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Non-athletes,Endurance athletes,Athletes engaged in endurance athletics at time point W1 (the same day after the repeated lower body 30s-all-out wingate's test),19,13,6 months,PCR,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,diet,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Table 2,8 March 2024,Aleru Divine,"Aleru Divine,Folakunmi,WikiWorks",Species identified as specific per group after being identified as significantly more abundant in the group of interest in comparison to the other two groups by LEfSe at Timepoint W1  (the same day after the repeated lower body 30s-all-out wingate's test),decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecis,3379134|976|200643|171549|815|816|674529,Complete,Folakunmi
bsdb:38381714/5/1,38381714,case-control,38381714,10.1371/journal.pone.0297858,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0297858,"Humińska-Lisowska K., Zielińska K., Mieszkowski J., Michałowska-Sawczyn M., Cięszczyk P., Łabaj P.P., Wasąg B., Frączek B., Grzywacz A., Kochanowicz A. , Kosciolek T.",Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study,PloS one,2024,NA,Experiment 5,Poland,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Non-athletes,Strength athletes,Athletes engaged in strength athletics at timepoint W2 (morning fasting after the WT on an empty stomach),19,15,6 months,PCR,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,diet,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table 2,8 March 2024,Aleru Divine,"Aleru Divine,Folakunmi,WikiWorks",Species identified as specific per group after being identified as significantly more abundant in the group of interest in comparison to the other two groups by LEfSe at Timepoint W2 (morning fasting after the WT on an empty stomach),decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,3379134|976|200643|171549|815|909656|204516,Complete,Folakunmi
bsdb:38381714/6/1,38381714,case-control,38381714,10.1371/journal.pone.0297858,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0297858,"Humińska-Lisowska K., Zielińska K., Mieszkowski J., Michałowska-Sawczyn M., Cięszczyk P., Łabaj P.P., Wasąg B., Frączek B., Grzywacz A., Kochanowicz A. , Kosciolek T.",Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study,PloS one,2024,NA,Experiment 6,Poland,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Non-athletes,Endurance athletes,Athletes engaged in endurance athletics at timepoint W2 (morning fasting after the WT on an empty stomach),19,13,6 months,PCR,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,diet,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table 2,8 March 2024,Aleru Divine,"Aleru Divine,Folakunmi,WikiWorks",Species identified as specific per group after being identified as significantly more abundant in the group of interest in comparison to the other two groups by LEfSe at Timepoint W2  (morning fasting after the WT on an empty stomach),increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. AF19-10LB,1783272|1239|186801|3085636|186803|572511|2292961,Complete,Folakunmi
bsdb:38381714/6/2,38381714,case-control,38381714,10.1371/journal.pone.0297858,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0297858,"Humińska-Lisowska K., Zielińska K., Mieszkowski J., Michałowska-Sawczyn M., Cięszczyk P., Łabaj P.P., Wasąg B., Frączek B., Grzywacz A., Kochanowicz A. , Kosciolek T.",Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study,PloS one,2024,NA,Experiment 6,Poland,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Non-athletes,Endurance athletes,Athletes engaged in endurance athletics at timepoint W2 (morning fasting after the WT on an empty stomach),19,13,6 months,PCR,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,diet,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Table 2,8 March 2024,Aleru Divine,"Aleru Divine,Folakunmi,WikiWorks",Species identified as specific per group after being identified as significantly more abundant in the group of interest in comparison to the other two groups by LEfSe at Timepoint W2  (morning fasting after the WT on an empty stomach),decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,3379134|976|200643|171549|815|909656|204516,Complete,Folakunmi
bsdb:38381714/7/1,38381714,case-control,38381714,10.1371/journal.pone.0297858,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0297858,"Humińska-Lisowska K., Zielińska K., Mieszkowski J., Michałowska-Sawczyn M., Cięszczyk P., Łabaj P.P., Wasąg B., Frączek B., Grzywacz A., Kochanowicz A. , Kosciolek T.",Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study,PloS one,2024,NA,Experiment 7,Poland,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Non-athletes,Strength athletes,Athletes engaged in strength athletics at timepoint B1 (the same day after the Bruce Treadmill Test),19,15,6 months,PCR,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,diet,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table 2,8 March 2024,Aleru Divine,"Aleru Divine,Folakunmi,WikiWorks",Species identified as specific per group after being identified as significantly more abundant in the group of interest in comparison to the other two groups by LEfSe at timepoint B1 (the same day after the Bruce Treadmill Test),increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,1783272|1239|186801|186802|1898207,Complete,Folakunmi
bsdb:38381714/8/1,38381714,case-control,38381714,10.1371/journal.pone.0297858,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0297858,"Humińska-Lisowska K., Zielińska K., Mieszkowski J., Michałowska-Sawczyn M., Cięszczyk P., Łabaj P.P., Wasąg B., Frączek B., Grzywacz A., Kochanowicz A. , Kosciolek T.",Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study,PloS one,2024,NA,Experiment 8,Poland,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Non-athletes,Endurance athletes,Athletes engaged in endurance athletics  at timepoint B1 (the same day after the Bruce Treadmill Test),19,13,6 months,PCR,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,diet,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table 2,8 March 2024,Aleru Divine,"Aleru Divine,Folakunmi,WikiWorks",Species identified as specific per group after being identified as significantly more abundant in the group of interest in comparison to the other two groups by LEfSe at timepoint B1 (the same day after the Bruce Treadmill Test),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. AF19-10LB,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus paracasei",1783272|1239|186801|3085636|186803|572511|2292961;1783272|1239|91061|186826|33958|2759736|1597,Complete,Folakunmi
bsdb:38381714/9/1,38381714,case-control,38381714,10.1371/journal.pone.0297858,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0297858,"Humińska-Lisowska K., Zielińska K., Mieszkowski J., Michałowska-Sawczyn M., Cięszczyk P., Łabaj P.P., Wasąg B., Frączek B., Grzywacz A., Kochanowicz A. , Kosciolek T.",Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study,PloS one,2024,NA,Experiment 9,Poland,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Non-athletes,Strength athletes,Athletes engaged in strength athletics  at timepoint B2 (morning after the Bruce Treadmill Test on an empty stomach),19,15,6 months,PCR,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,diet,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table 2,8 March 2024,Aleru Divine,"Aleru Divine,Folakunmi,WikiWorks",Species identified as specific per group after being identified as significantly more abundant in the group of interest in comparison to the other two groups by LEfSe at Timepoint B2 (morning after the Bruce Treadmill Test on an empty stomach),increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. MSK.20.85,1783272|1239|186801|3085636|186803|572511|2709718,Complete,Folakunmi
bsdb:38381714/10/1,38381714,case-control,38381714,10.1371/journal.pone.0297858,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0297858,"Humińska-Lisowska K., Zielińska K., Mieszkowski J., Michałowska-Sawczyn M., Cięszczyk P., Łabaj P.P., Wasąg B., Frączek B., Grzywacz A., Kochanowicz A. , Kosciolek T.",Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study,PloS one,2024,NA,Experiment 10,Poland,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Non-athletes,Endurance athletes,Athletes engaged in endurance athletics  at timepoint B2 (morning after the Bruce Treadmill Test on an empty stomach),19,13,6 months,PCR,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,diet,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table 2,8 March 2024,Aleru Divine,"Aleru Divine,Folakunmi,WikiWorks",Species identified as specific per group after being identified as significantly more abundant in the group of interest in comparison to the other two groups by LEfSe at Timepoint B2 (morning after the Bruce Treadmill Test),increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. AF19-10LB,1783272|1239|186801|3085636|186803|572511|2292961,Complete,Folakunmi
bsdb:38382594/1/1,38382594,laboratory experiment,38382594,https://doi.org/10.1016/j.jare.2024.02.014,https://www.sciencedirect.com/science/article/pii/S2090123224000766?via=ihub#s0010,"Wu J.J., Zheng X., Wu C., Ma W., Wang Y., Wang J., Wei Y., Zeng X., Zhang S., Guan W. , Chen F.",Melatonin alleviates high temperature exposure induced fetal growth restriction via the gut-placenta-fetus axis in pregnant mice,Journal of advanced research,2025,"Gut microbial dysbiosis, Heat stress, LPS, Melatonin administration, Placental barrier",Experiment 1,China,Mus musculus,Cecum mucosa,UBERON:0000314,Fetal growth restriction,EFO:0000495,Control + Heat Stress (Con + HS),Heat Stress + Melatonin Administration (Hs + Mel),Pregnant mice were exposed to heat stress (HS) and supplemented with melatonin (Mel).,17,10,NA,16S,34,NA,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 3E,20 March 2025,Shulamite,"Shulamite,KateRasheed",The cladogram representation (D) and LDA score bar (E) show that bacterial taxa differed significantly among different treated groups by analysing LEfSe.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium UBA1381,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:41,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:95,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Luxibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Candidatus Amulumruptor,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Fimenecus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 14-2,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. 1XD42-69",3379134|1224|1236|2887326|468|469;1783272|1239|186801|186802|1950820;1783272|1239|526524|526525|2810280;1783272|1239|526524|526525|128827|1729679;1783272|1239|1263021;1783272|1239|1262988;1783272|1239|186801|3085636|186803|2813348;3379134|1224|1236|2887326|468;3379134|976|200643|171549|171552|838;3379134|976|1853228|1853229|563835|504481;3379134|1224|28216|80840|995019|1918598;3379134|976|200643|171549|2005473|2510710;1783272|1239|186801|2840564;1783272|1239|186801|3085636|186803|397286;1783272|1239|186801|3085636|186803|841|2320088,Complete,Svetlana up
bsdb:38382594/2/1,38382594,laboratory experiment,38382594,https://doi.org/10.1016/j.jare.2024.02.014,https://www.sciencedirect.com/science/article/pii/S2090123224000766?via=ihub#s0010,"Wu J.J., Zheng X., Wu C., Ma W., Wang Y., Wang J., Wei Y., Zeng X., Zhang S., Guan W. , Chen F.",Melatonin alleviates high temperature exposure induced fetal growth restriction via the gut-placenta-fetus axis in pregnant mice,Journal of advanced research,2025,"Gut microbial dysbiosis, Heat stress, LPS, Melatonin administration, Placental barrier",Experiment 2,China,Mus musculus,Cecum mucosa,UBERON:0000314,Fetal growth restriction,EFO:0000495,Control + Heat Stress + Melatonin Administration (Con + HS +Mel),Heat Stress. (HS),Heat Stress,18,9,NA,16S,34,NA,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 3E,21 March 2025,Shulamite,"Shulamite,KateRasheed",The cladogram representation (D) and LDA score bar (E) show that bacterial taxa differed significantly among different treated groups by performing the analysis of LEfSe.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Aliivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Emergencia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Merdisoma",3379134|1224|1236|135623|641|511678;1783272|1239|186801|3082720|543314|1926556;3379134|1224|1236|135623|641|657;1783272|1239|186801|3085636|186803|841;3379134|976|200643|171549|2005525;3379134|1224|1236|135623|641;3379134|976|200643|171549|171550;1783272|1239|186801|3085636|186803|2840622,Complete,Svetlana up
bsdb:38382594/3/1,38382594,laboratory experiment,38382594,https://doi.org/10.1016/j.jare.2024.02.014,https://www.sciencedirect.com/science/article/pii/S2090123224000766?via=ihub#s0010,"Wu J.J., Zheng X., Wu C., Ma W., Wang Y., Wang J., Wei Y., Zeng X., Zhang S., Guan W. , Chen F.",Melatonin alleviates high temperature exposure induced fetal growth restriction via the gut-placenta-fetus axis in pregnant mice,Journal of advanced research,2025,"Gut microbial dysbiosis, Heat stress, LPS, Melatonin administration, Placental barrier",Experiment 3,China,Mus musculus,Cecum mucosa,UBERON:0000314,Fetal growth restriction,EFO:0000495,"Heat Stress, Heat Stress + Melatonin Administration. (HS, HS + Mel)",Control. (Con),Mice in the Con group were maintained under 25 ± 2 °C.,19,8,NA,16S,34,NA,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 3E,21 March 2025,Shulamite,"Shulamite,KateRasheed",The cladogram representation (D) and LDA score bar (E) show that bacterial taxa differed significantly among different treated groups by performing the analysis of LEfSe.,increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Massilioclostridium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Tidjanibacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia sp. ZJ304,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Actinomycetota",3379134|29547|3031852|213849|2808963;3379134|1224|28216|80840|119060|32008;3379134|976|200643|171549|1853231|574697;1783272|201174|84998|1643822|1643826;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;3379134|976|117743|200644|49546;3379134|976|117743|200644|49546|237;3379134|1224|1236;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|2767887;3379134|976|200643|1970189|1573805;1783272|1239|186801|186802|31979|1935927;3379134|1224|28216|80840|995019|577310;3379134|1224|1236|72274|135621;3379134|976|200643|171549|171550|1929083;3379134|29547|3031852|213849|2808963;1783272|201174|84998|1643822|1643826|447020|2709791;1783272|1239|186801|186802|216572;3379134|1224;1783272|201174,Complete,Svetlana up
bsdb:38383483/3/1,38383483,case-control,38383483,doi: 10.1186/s40168-024-01758-4.,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01758-4,"Singh S., Giron L.B., Shaikh M.W., Shankaran S., Engen P.A., Bogin Z.R., Bambi S.A., Goldman A.R., Azevedo J.L.L.C., Orgaz L., de Pedro N., González P., Giera M., Verhoeven A., Sánchez-López E., Pandrea I., Kannan T., Tanes C.E., Bittinger K., Landay A.L., Corley M.J., Keshavarzian A. , Abdel-Mohsen M.",Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging,Microbiome,2024,"Aging clocks, Biological aging, Gut, HIV, Intestines, Metabolome, Microbiome",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Controls/ People living without HIV (PLWOH),People living with HIV on Antiretroviral Therapy (PLWH on ART),People with HIV infection on Anti-Retroviral Therapy(ART),23,25,NA,16S,12,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,"age,body mass index,ethnic group,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig 4D,22 March 2024,Imaspecial,"Imaspecial,Fiddyhamma,WikiWorks",Log-scale differences in bacterial abundance across feces (circle) between PLWOH and PLWH on ART.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|526524|526525|2810280|135858;3379134|976|200643|171549|171552|838|59823;3379134|976|200643|171549|171552|1283313;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:38383483/3/2,38383483,case-control,38383483,doi: 10.1186/s40168-024-01758-4.,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01758-4,"Singh S., Giron L.B., Shaikh M.W., Shankaran S., Engen P.A., Bogin Z.R., Bambi S.A., Goldman A.R., Azevedo J.L.L.C., Orgaz L., de Pedro N., González P., Giera M., Verhoeven A., Sánchez-López E., Pandrea I., Kannan T., Tanes C.E., Bittinger K., Landay A.L., Corley M.J., Keshavarzian A. , Abdel-Mohsen M.",Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging,Microbiome,2024,"Aging clocks, Biological aging, Gut, HIV, Intestines, Metabolome, Microbiome",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Controls/ People living without HIV (PLWOH),People living with HIV on Antiretroviral Therapy (PLWH on ART),People with HIV infection on Anti-Retroviral Therapy(ART),23,25,NA,16S,12,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,"age,body mass index,ethnic group,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig 4D,22 March 2024,Imaspecial,"Imaspecial,Fiddyhamma,WikiWorks",Log-scale differences in bacterial abundance across feces (circle) between PLWOH and PLWH on ART.,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii",1783272|1239|526524|526525|128827|331630;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|1263|438033,Complete,Svetlana up
bsdb:38383483/5/1,38383483,case-control,38383483,doi: 10.1186/s40168-024-01758-4.,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01758-4,"Singh S., Giron L.B., Shaikh M.W., Shankaran S., Engen P.A., Bogin Z.R., Bambi S.A., Goldman A.R., Azevedo J.L.L.C., Orgaz L., de Pedro N., González P., Giera M., Verhoeven A., Sánchez-López E., Pandrea I., Kannan T., Tanes C.E., Bittinger K., Landay A.L., Corley M.J., Keshavarzian A. , Abdel-Mohsen M.",Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging,Microbiome,2024,"Aging clocks, Biological aging, Gut, HIV, Intestines, Metabolome, Microbiome",Experiment 5,United States of America,Homo sapiens,"Ileum,Feces","UBERON:0002116,UBERON:0001988",Aging,GO:0007568,Ileum Tissue Sample,Fecal Sample,Fecal sample collected from participants,NA,NA,NA,16S,12,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,"age,body mass index,ethnic group,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 4C,22 March 2024,Imaspecial,"Imaspecial,Fiddyhamma,WikiWorks",Differential bacterial abundance between tissue and fecal samples on a logarithmic scale. Comparisons include Ileum vs. feces (blue).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|572511;1783272|1239|526524|526525|2810280|135858;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|1407607;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|216572|1263|438033;1783272|1239|526524|526525|128827|331630;1783272|1239|186801|186802|216572|1263|41978,Complete,Svetlana up
bsdb:38383483/5/2,38383483,case-control,38383483,doi: 10.1186/s40168-024-01758-4.,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01758-4,"Singh S., Giron L.B., Shaikh M.W., Shankaran S., Engen P.A., Bogin Z.R., Bambi S.A., Goldman A.R., Azevedo J.L.L.C., Orgaz L., de Pedro N., González P., Giera M., Verhoeven A., Sánchez-López E., Pandrea I., Kannan T., Tanes C.E., Bittinger K., Landay A.L., Corley M.J., Keshavarzian A. , Abdel-Mohsen M.",Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging,Microbiome,2024,"Aging clocks, Biological aging, Gut, HIV, Intestines, Metabolome, Microbiome",Experiment 5,United States of America,Homo sapiens,"Ileum,Feces","UBERON:0002116,UBERON:0001988",Aging,GO:0007568,Ileum Tissue Sample,Fecal Sample,Fecal sample collected from participants,NA,NA,NA,16S,12,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,"age,body mass index,ethnic group,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 4C,22 March 2024,Imaspecial,"Imaspecial,Fiddyhamma,WikiWorks",Differential bacterial abundance between tissue and fecal samples on a logarithmic scale. Comparisons include Ileum vs. feces (blue).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. 1-8,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|2316020|33038;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|3085636|186803|2316020|33039;3379134|976|200643|171549|171552|838|59823;3379134|976|200643|171549|171552|838|1486937;3379134|976|200643|171549,Complete,Svetlana up
bsdb:38383483/6/1,38383483,case-control,38383483,doi: 10.1186/s40168-024-01758-4.,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01758-4,"Singh S., Giron L.B., Shaikh M.W., Shankaran S., Engen P.A., Bogin Z.R., Bambi S.A., Goldman A.R., Azevedo J.L.L.C., Orgaz L., de Pedro N., González P., Giera M., Verhoeven A., Sánchez-López E., Pandrea I., Kannan T., Tanes C.E., Bittinger K., Landay A.L., Corley M.J., Keshavarzian A. , Abdel-Mohsen M.",Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging,Microbiome,2024,"Aging clocks, Biological aging, Gut, HIV, Intestines, Metabolome, Microbiome",Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Controls/ People living without HIV (PLWOH),People living with HIV on Antiretroviral Therapy (PLWH on ART),People with HIV infection on Anti-Retroviral Therapy(ART),NA,NA,NA,16S,12,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,"age,body mass index,ethnic group,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 1,Additional figure 10E,13 November 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",Estimated log difference between heterosexual PLWH on ART and heterosexual PLWoH,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|186801|186802|216572|1263|41978;1783272|1239|186801|186802|216572;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:38383483/7/1,38383483,case-control,38383483,doi: 10.1186/s40168-024-01758-4.,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01758-4,"Singh S., Giron L.B., Shaikh M.W., Shankaran S., Engen P.A., Bogin Z.R., Bambi S.A., Goldman A.R., Azevedo J.L.L.C., Orgaz L., de Pedro N., González P., Giera M., Verhoeven A., Sánchez-López E., Pandrea I., Kannan T., Tanes C.E., Bittinger K., Landay A.L., Corley M.J., Keshavarzian A. , Abdel-Mohsen M.",Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging,Microbiome,2024,"Aging clocks, Biological aging, Gut, HIV, Intestines, Metabolome, Microbiome",Experiment 7,United States of America,Homo sapiens,Ileum,UBERON:0002116,HIV infection,EFO:0000764,Controls/ People living without HIV (PLWOH),People living with HIV on Antiretroviral Therapy (PLWH on ART),People with HIV infection on Anti-Retroviral Therapy(ART),NA,NA,NA,16S,12,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,"age,body mass index,ethnic group,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 1,Additional figure 10E,13 November 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",Estimated log difference between heterosexual PLWH on ART and heterosexual PLWoH,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,Svetlana up
bsdb:38383483/7/2,38383483,case-control,38383483,doi: 10.1186/s40168-024-01758-4.,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01758-4,"Singh S., Giron L.B., Shaikh M.W., Shankaran S., Engen P.A., Bogin Z.R., Bambi S.A., Goldman A.R., Azevedo J.L.L.C., Orgaz L., de Pedro N., González P., Giera M., Verhoeven A., Sánchez-López E., Pandrea I., Kannan T., Tanes C.E., Bittinger K., Landay A.L., Corley M.J., Keshavarzian A. , Abdel-Mohsen M.",Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging,Microbiome,2024,"Aging clocks, Biological aging, Gut, HIV, Intestines, Metabolome, Microbiome",Experiment 7,United States of America,Homo sapiens,Ileum,UBERON:0002116,HIV infection,EFO:0000764,Controls/ People living without HIV (PLWOH),People living with HIV on Antiretroviral Therapy (PLWH on ART),People with HIV infection on Anti-Retroviral Therapy(ART),NA,NA,NA,16S,12,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,"age,body mass index,ethnic group,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 2,Additional figure 10E,13 November 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",Estimated log difference between heterosexual PLWH on ART and heterosexual PLWoH,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|33042|2049024;1783272|1239|186801|186802|216572|1263|41978,Complete,Svetlana up
bsdb:38383483/8/1,38383483,case-control,38383483,doi: 10.1186/s40168-024-01758-4.,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01758-4,"Singh S., Giron L.B., Shaikh M.W., Shankaran S., Engen P.A., Bogin Z.R., Bambi S.A., Goldman A.R., Azevedo J.L.L.C., Orgaz L., de Pedro N., González P., Giera M., Verhoeven A., Sánchez-López E., Pandrea I., Kannan T., Tanes C.E., Bittinger K., Landay A.L., Corley M.J., Keshavarzian A. , Abdel-Mohsen M.",Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging,Microbiome,2024,"Aging clocks, Biological aging, Gut, HIV, Intestines, Metabolome, Microbiome",Experiment 8,United States of America,Homo sapiens,Colon,UBERON:0001155,HIV infection,EFO:0000764,Controls/ People living without HIV (PLWOH),People living with HIV on Antiretroviral Therapy (PLWH on ART),People with HIV infection on Anti-Retroviral Therapy(ART),NA,NA,NA,16S,12,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,"age,body mass index,ethnic group,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 1,Additional figure 10E,13 November 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",Estimated log difference between heterosexual PLWH on ART and heterosexual PLWoH,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,Svetlana up
bsdb:38383483/8/2,38383483,case-control,38383483,doi: 10.1186/s40168-024-01758-4.,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01758-4,"Singh S., Giron L.B., Shaikh M.W., Shankaran S., Engen P.A., Bogin Z.R., Bambi S.A., Goldman A.R., Azevedo J.L.L.C., Orgaz L., de Pedro N., González P., Giera M., Verhoeven A., Sánchez-López E., Pandrea I., Kannan T., Tanes C.E., Bittinger K., Landay A.L., Corley M.J., Keshavarzian A. , Abdel-Mohsen M.",Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging,Microbiome,2024,"Aging clocks, Biological aging, Gut, HIV, Intestines, Metabolome, Microbiome",Experiment 8,United States of America,Homo sapiens,Colon,UBERON:0001155,HIV infection,EFO:0000764,Controls/ People living without HIV (PLWOH),People living with HIV on Antiretroviral Therapy (PLWH on ART),People with HIV infection on Anti-Retroviral Therapy(ART),NA,NA,NA,16S,12,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,"age,body mass index,ethnic group,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 2,Additional figure 10E,13 November 2024,Fiddyhamma,"Fiddyhamma,WikiWorks",Estimated log difference between heterosexual PLWH on ART and heterosexual PLWoH,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|33042|2049024;1783272|1239|186801|186802|216572|1263|41978,Complete,Svetlana up
bsdb:38384431/1/1,38384431,randomized controlled trial,38384431,10.1093/femsmc/xtae001,https://pmc.ncbi.nlm.nih.gov/articles/PMC10880814/,"Pihelgas S., Ehala-Aleksejev K., Kuldjärv R., Jõeleht A., Kazantseva J. , Adamberg K.",Short-term pectin-enriched smoothie consumption has beneficial effects on the gut microbiota of low-fiber consumers,FEMS microbes,2024,"16S rRNA sequencing, dietary fibre, gut microbiota, intervention trial, pectin",Experiment 1,Estonia,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Base (Pre-intervention point of diet) (Group 1),HPect (High Pectin smoothie) (Group 1),"Participants in group 1 who consumed a higher amount of dietary fiber, especially high pectin smoothies first before a washout period and a low pectin smoothies consumption period",17,17,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,28 April 2025,Shulamite,"Shulamite,Anne-mariesharp",Bacterial up and down shifts after smoothie periods and recoveries of abundance after WO periods.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,1783272|1239|186801|3085636|186803|28050,Complete,KateRasheed
bsdb:38384431/1/2,38384431,randomized controlled trial,38384431,10.1093/femsmc/xtae001,https://pmc.ncbi.nlm.nih.gov/articles/PMC10880814/,"Pihelgas S., Ehala-Aleksejev K., Kuldjärv R., Jõeleht A., Kazantseva J. , Adamberg K.",Short-term pectin-enriched smoothie consumption has beneficial effects on the gut microbiota of low-fiber consumers,FEMS microbes,2024,"16S rRNA sequencing, dietary fibre, gut microbiota, intervention trial, pectin",Experiment 1,Estonia,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Base (Pre-intervention point of diet) (Group 1),HPect (High Pectin smoothie) (Group 1),"Participants in group 1 who consumed a higher amount of dietary fiber, especially high pectin smoothies first before a washout period and a low pectin smoothies consumption period",17,17,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2,28 April 2025,Shulamite,"Shulamite,Anne-mariesharp",Bacterial up and down shifts after smoothie periods and recoveries of abundance after washout periods.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|2316020|33039,Complete,KateRasheed
bsdb:38384431/2/1,38384431,randomized controlled trial,38384431,10.1093/femsmc/xtae001,https://pmc.ncbi.nlm.nih.gov/articles/PMC10880814/,"Pihelgas S., Ehala-Aleksejev K., Kuldjärv R., Jõeleht A., Kazantseva J. , Adamberg K.",Short-term pectin-enriched smoothie consumption has beneficial effects on the gut microbiota of low-fiber consumers,FEMS microbes,2024,"16S rRNA sequencing, dietary fibre, gut microbiota, intervention trial, pectin",Experiment 2,Estonia,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,LF-intake (Low-fiber intake),HF-intake (High fiber-intake),Participants who regularly consumed >23 g of dietary fiber per day,22,9,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3B,28 April 2025,Shulamite,"Shulamite,Anne-mariesharp","At lower levels of abundance, four genera show the difference between LF and HF intake groups in the base period.",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus",3379134|74201|203494|48461|1647988|239934;3384194|508458|649775|649776|649777|508459;1783272|1239|186801|3085636|186803|33042;1783272|1239|91061|186826|1300|1357,Complete,KateRasheed
bsdb:38384431/3/1,38384431,randomized controlled trial,38384431,10.1093/femsmc/xtae001,https://pmc.ncbi.nlm.nih.gov/articles/PMC10880814/,"Pihelgas S., Ehala-Aleksejev K., Kuldjärv R., Jõeleht A., Kazantseva J. , Adamberg K.",Short-term pectin-enriched smoothie consumption has beneficial effects on the gut microbiota of low-fiber consumers,FEMS microbes,2024,"16S rRNA sequencing, dietary fibre, gut microbiota, intervention trial, pectin",Experiment 3,Estonia,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Base (LF intake group),HPect (LF intake group),"Participants consuming a low-fiber diet (<23 g/day, LF intake group), who received the high-pectin (HPect) smoothie during the intervention period.",NA,22,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4A, 6A, Table S3",28 April 2025,Shulamite,"Shulamite,Anne-mariesharp",Altered genera in LF intake group (Base vs HPect). The pairwise comparison was performed using the Wilcoxon signed-rank test for statistical analysis to compare LPect and HPect effects on base period microbiota at the genus level,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|28050;3379134|976|200643|171549|171552|577309,Complete,KateRasheed
bsdb:38384431/3/2,38384431,randomized controlled trial,38384431,10.1093/femsmc/xtae001,https://pmc.ncbi.nlm.nih.gov/articles/PMC10880814/,"Pihelgas S., Ehala-Aleksejev K., Kuldjärv R., Jõeleht A., Kazantseva J. , Adamberg K.",Short-term pectin-enriched smoothie consumption has beneficial effects on the gut microbiota of low-fiber consumers,FEMS microbes,2024,"16S rRNA sequencing, dietary fibre, gut microbiota, intervention trial, pectin",Experiment 3,Estonia,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Base (LF intake group),HPect (LF intake group),"Participants consuming a low-fiber diet (<23 g/day, LF intake group), who received the high-pectin (HPect) smoothie during the intervention period.",NA,22,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 4A, 4C, 6A, Table S3",1 May 2025,Shulamite,"Shulamite,Anne-mariesharp",Altered genera in LF intake group (Base vs HPect). The pairwise comparison was performed using the Wilcoxon signed-rank test for statistical analysis to compare LPect and HPect effects on base period microbiota at the genus level.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena fissicatena,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Evtepia",1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|189330;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|3085636|186803|2005359|290055;1783272|1239|526524|526525|128827|1573535;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|91061|186826|1300|1357;1783272|1239|186801|186802|2211178,Complete,KateRasheed
bsdb:38384431/4/1,38384431,randomized controlled trial,38384431,10.1093/femsmc/xtae001,https://pmc.ncbi.nlm.nih.gov/articles/PMC10880814/,"Pihelgas S., Ehala-Aleksejev K., Kuldjärv R., Jõeleht A., Kazantseva J. , Adamberg K.",Short-term pectin-enriched smoothie consumption has beneficial effects on the gut microbiota of low-fiber consumers,FEMS microbes,2024,"16S rRNA sequencing, dietary fibre, gut microbiota, intervention trial, pectin",Experiment 4,Estonia,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Base (LF intake group),LPect (Low pectin smoothie) (LF intake group),Participants in the low-fiber intake group (<23 g/day) who received the low-pectin (LPect) smoothie as part of the intervention.,NA,22,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4B, 6A, Table S3",28 April 2025,Shulamite,"Shulamite,Anne-mariesharp",Altered genera in LF intake group (Base vs LPect). The pairwise comparison was performed using the Wilcoxon signed-rank test for statistical analysis to compare LPect and HPect effects on base period microbiota at the genus level.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:352,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",1783272|1239|186801|186802|31979|1485|1262798;1783272|1239|186801|186802|1980681;1783272|1239|186801|186802|216572|459786;3379134|1224|28216|80840|75682|846;3379134|976|200643|171549|171552|577309,Complete,KateRasheed
bsdb:38384431/4/2,38384431,randomized controlled trial,38384431,10.1093/femsmc/xtae001,https://pmc.ncbi.nlm.nih.gov/articles/PMC10880814/,"Pihelgas S., Ehala-Aleksejev K., Kuldjärv R., Jõeleht A., Kazantseva J. , Adamberg K.",Short-term pectin-enriched smoothie consumption has beneficial effects on the gut microbiota of low-fiber consumers,FEMS microbes,2024,"16S rRNA sequencing, dietary fibre, gut microbiota, intervention trial, pectin",Experiment 4,Estonia,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Base (LF intake group),LPect (Low pectin smoothie) (LF intake group),Participants in the low-fiber intake group (<23 g/day) who received the low-pectin (LPect) smoothie as part of the intervention.,NA,22,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 4B, 4C, 6A, Table S3",28 April 2025,Shulamite,"Shulamite,Anne-mariesharp",Altered genera in LF intake group (Base vs LPect). The pairwise comparison was performed using the Wilcoxon signed-rank test for statistical analysis to compare LPect and HPect effects on base period microbiota at the genus level,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Merdibacter",1783272|1239|186801|186802|186806|1730|39496;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|186802|186807|2740;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810281|191303;1783272|1239|526524|526525|128827|1935200,Complete,KateRasheed
bsdb:38384431/5/1,38384431,randomized controlled trial,38384431,10.1093/femsmc/xtae001,https://pmc.ncbi.nlm.nih.gov/articles/PMC10880814/,"Pihelgas S., Ehala-Aleksejev K., Kuldjärv R., Jõeleht A., Kazantseva J. , Adamberg K.",Short-term pectin-enriched smoothie consumption has beneficial effects on the gut microbiota of low-fiber consumers,FEMS microbes,2024,"16S rRNA sequencing, dietary fibre, gut microbiota, intervention trial, pectin",Experiment 5,Estonia,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Base (HF intake group),HPect (HF intake group),Participants in the high-fiber intake group (>23 g/day) during the high-pectin (HPect) smoothie intervention period.,NA,9,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 5A, Table S3",28 April 2025,Shulamite,"Shulamite,Anne-mariesharp",Altered genera in the HF intake group (Base vs HPect). The pairwise comparison was performed using the Wilcoxon signed-rank test for statistical analysis to compare LPect and HPect effects on base period microbiota at the genus level.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella",1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|877420;3379134|1224|28216|80840|995019|577310,Complete,KateRasheed
bsdb:38384431/5/2,38384431,randomized controlled trial,38384431,10.1093/femsmc/xtae001,https://pmc.ncbi.nlm.nih.gov/articles/PMC10880814/,"Pihelgas S., Ehala-Aleksejev K., Kuldjärv R., Jõeleht A., Kazantseva J. , Adamberg K.",Short-term pectin-enriched smoothie consumption has beneficial effects on the gut microbiota of low-fiber consumers,FEMS microbes,2024,"16S rRNA sequencing, dietary fibre, gut microbiota, intervention trial, pectin",Experiment 5,Estonia,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Base (HF intake group),HPect (HF intake group),Participants in the high-fiber intake group (>23 g/day) during the high-pectin (HPect) smoothie intervention period.,NA,9,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 5A, 5C, 6B, Table S3",28 April 2025,Shulamite,"Shulamite,Anne-mariesharp",Altered genera in the HF intake group (Base vs HPect). The pairwise comparison was performed using the Wilcoxon signed-rank test for statistical analysis to compare LPect and HPect effects on base period microbiota at the genus level.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes",1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803|207244,Complete,KateRasheed
bsdb:38384431/6/1,38384431,randomized controlled trial,38384431,10.1093/femsmc/xtae001,https://pmc.ncbi.nlm.nih.gov/articles/PMC10880814/,"Pihelgas S., Ehala-Aleksejev K., Kuldjärv R., Jõeleht A., Kazantseva J. , Adamberg K.",Short-term pectin-enriched smoothie consumption has beneficial effects on the gut microbiota of low-fiber consumers,FEMS microbes,2024,"16S rRNA sequencing, dietary fibre, gut microbiota, intervention trial, pectin",Experiment 6,Estonia,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Base (HF intake group),LPect (HF intake group),Participants in the high-fiber intake group (>23 g/day) during the low-pectin (LPect) smoothie intervention period.,NA,9,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 5B, 6B, Table S3",28 April 2025,Shulamite,"Shulamite,Anne-mariesharp",Altered genera in the HF intake group (Base vs LPect). The pairwise comparison was performed using the Wilcoxon signed-rank test for statistical analysis to compare LPect and HPect effects on base period microbiota at the genus level.,increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|171552|577309,Complete,KateRasheed
bsdb:38384431/6/2,38384431,randomized controlled trial,38384431,10.1093/femsmc/xtae001,https://pmc.ncbi.nlm.nih.gov/articles/PMC10880814/,"Pihelgas S., Ehala-Aleksejev K., Kuldjärv R., Jõeleht A., Kazantseva J. , Adamberg K.",Short-term pectin-enriched smoothie consumption has beneficial effects on the gut microbiota of low-fiber consumers,FEMS microbes,2024,"16S rRNA sequencing, dietary fibre, gut microbiota, intervention trial, pectin",Experiment 6,Estonia,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Base (HF intake group),LPect (HF intake group),Participants in the high-fiber intake group (>23 g/day) during the low-pectin (LPect) smoothie intervention period.,NA,9,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 5B, 5C, 6B, Table S3",28 April 2025,Shulamite,"Shulamite,Anne-mariesharp",Altered genera in the HF intake group (Base vs LPect). The pairwise comparison was performed using the Wilcoxon signed-rank test for statistical analysis to compare LPect and HPect effects on base period microbiota at the genus level.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|216572|1263,Complete,KateRasheed
bsdb:38384431/7/1,38384431,randomized controlled trial,38384431,10.1093/femsmc/xtae001,https://pmc.ncbi.nlm.nih.gov/articles/PMC10880814/,"Pihelgas S., Ehala-Aleksejev K., Kuldjärv R., Jõeleht A., Kazantseva J. , Adamberg K.",Short-term pectin-enriched smoothie consumption has beneficial effects on the gut microbiota of low-fiber consumers,FEMS microbes,2024,"16S rRNA sequencing, dietary fibre, gut microbiota, intervention trial, pectin",Experiment 7,Estonia,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,WO LPect (Wash out low pectin smoothie) (Group 2),HPect (Group 2),"Participants in group 2 who consumed the high-pectin smoothie during their second intervention period, following the low-pectin smoothie consumption period and a washout period.",14,14,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,28 April 2025,Shulamite,"Shulamite,Anne-mariesharp",Bacterial up- and down-shifts after smoothie periods and recoveries of abundances after WO periods.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|2316020|33039,Complete,KateRasheed
bsdb:38384431/9/1,38384431,randomized controlled trial,38384431,10.1093/femsmc/xtae001,https://pmc.ncbi.nlm.nih.gov/articles/PMC10880814/,"Pihelgas S., Ehala-Aleksejev K., Kuldjärv R., Jõeleht A., Kazantseva J. , Adamberg K.",Short-term pectin-enriched smoothie consumption has beneficial effects on the gut microbiota of low-fiber consumers,FEMS microbes,2024,"16S rRNA sequencing, dietary fibre, gut microbiota, intervention trial, pectin",Experiment 9,Estonia,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,WO-HPect (Washout - high pectin smoothie) (Group 1),LPect (Group 1),"Participants in group 1 who consumed the low-pectin smoothie during their second intervention period, following the high-pectin smoothie consumption period and wash-out period",14,14,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,30 April 2025,Shulamite,"Shulamite,Anne-mariesharp",Bacterial up- and down-shifts after smoothie periods and recoveries of abundances after WO periods.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,1783272|1239|186801|3085636|186803|33042,Complete,KateRasheed
bsdb:38384431/10/1,38384431,randomized controlled trial,38384431,10.1093/femsmc/xtae001,https://pmc.ncbi.nlm.nih.gov/articles/PMC10880814/,"Pihelgas S., Ehala-Aleksejev K., Kuldjärv R., Jõeleht A., Kazantseva J. , Adamberg K.",Short-term pectin-enriched smoothie consumption has beneficial effects on the gut microbiota of low-fiber consumers,FEMS microbes,2024,"16S rRNA sequencing, dietary fibre, gut microbiota, intervention trial, pectin",Experiment 10,Estonia,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,HPect (Group 1),WO HPect (Group 1),Participants in group 1 during the washout period after completing the high-pectin smoothie intervention.,17,17,3 months,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,30 April 2025,Shulamite,"Shulamite,Anne-mariesharp",Bacterial up- and down-shifts after smoothie periods and recoveries of abundances after WO periods.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,1783272|1239|186801|3085636|186803|28050,Complete,KateRasheed
bsdb:38385646/1/1,38385646,time series / longitudinal observational,38385646,https://doi.org/10.1128/spectrum.03142-23,https://journals.asm.org/doi/pdf/10.1128/spectrum.03142-23,"Bo Wu, Peng Wang, Tangjuan Zhang, Ting Qian, Xiangnan Li, Xue Pan, Zheng Ding, Zhichao Hou",Analysis on the change of gut microbiota and metabolome in lung transplant patients,American Society for Microbiology,2024,"gut microbiota, metabolome, lung transplantation, transplant rejection",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Lung transplantation,EFO:0010721,No lung transplant group (NT),Lung transplant event-free group (EF),cases without any symptoms and with negative pathology were considered event-free patients after transplantation.,20,15,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,figure 3 A,13 March 2024,Glorious,"Glorious,Fiddyhamma,Folakunmi,MyleeeA,WikiWorks",Lefse analysis to identify the microbial species that exhibited the most significant differences between NT and EF,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae",1783272|1239|91061;1783272|1239|91061|1385|186817|1386;1783272|1239|186801|186802|31979;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810280|3025755;1783272|1239|526524|526525|2810280,Complete,Folakunmi
bsdb:38385646/1/2,38385646,time series / longitudinal observational,38385646,https://doi.org/10.1128/spectrum.03142-23,https://journals.asm.org/doi/pdf/10.1128/spectrum.03142-23,"Bo Wu, Peng Wang, Tangjuan Zhang, Ting Qian, Xiangnan Li, Xue Pan, Zheng Ding, Zhichao Hou",Analysis on the change of gut microbiota and metabolome in lung transplant patients,American Society for Microbiology,2024,"gut microbiota, metabolome, lung transplantation, transplant rejection",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Lung transplantation,EFO:0010721,No lung transplant group (NT),Lung transplant event-free group (EF),cases without any symptoms and with negative pathology were considered event-free patients after transplantation.,20,15,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,figure 3 A,18 March 2024,Glorious,"Glorious,Fiddyhamma,Folakunmi,WikiWorks",Lefse analysis to identify the microbial species that exhibited the most significant differences between NT and EF,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",1783272|1239|186801|3085636|186803|1766253;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976;1783272|1239|186801|3085636|186803|2383;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;3379134|976|200643|171549|171552|2974265|363265;1783272|1239|909932;1783272|1239|186801|186802|216572;3379134|976|200643|171549|815|909656|310298;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552,Complete,Folakunmi
bsdb:38385646/2/1,38385646,time series / longitudinal observational,38385646,https://doi.org/10.1128/spectrum.03142-23,https://journals.asm.org/doi/pdf/10.1128/spectrum.03142-23,"Bo Wu, Peng Wang, Tangjuan Zhang, Ting Qian, Xiangnan Li, Xue Pan, Zheng Ding, Zhichao Hou",Analysis on the change of gut microbiota and metabolome in lung transplant patients,American Society for Microbiology,2024,"gut microbiota, metabolome, lung transplantation, transplant rejection",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Lung transplantation,EFO:0010721,No lung transplant group (NT),Lung transplant chronic rejection group (CR),The lung transplant rejection participants were patients who survived more than 6 months after transplant and were all cases of chronic rejection.,20,17,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 3B,13 March 2024,Glorious,"Glorious,Fiddyhamma,WikiWorks","From the LEfSe analysis, CR group exhibited a higher abundance of Lacticaseibacillus, Enterococcus, Streptococcus and other significant taxas",increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",1783272|1239|91061;1783272|1239|91061|1385|186817|1386;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|33958|2759736;1783272|1239|91061|186826;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300;3379134|1224|1236|91347|543;1783272|1239|91061|186826|33958,Complete,Folakunmi
bsdb:38385646/2/2,38385646,time series / longitudinal observational,38385646,https://doi.org/10.1128/spectrum.03142-23,https://journals.asm.org/doi/pdf/10.1128/spectrum.03142-23,"Bo Wu, Peng Wang, Tangjuan Zhang, Ting Qian, Xiangnan Li, Xue Pan, Zheng Ding, Zhichao Hou",Analysis on the change of gut microbiota and metabolome in lung transplant patients,American Society for Microbiology,2024,"gut microbiota, metabolome, lung transplantation, transplant rejection",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Lung transplantation,EFO:0010721,No lung transplant group (NT),Lung transplant chronic rejection group (CR),The lung transplant rejection participants were patients who survived more than 6 months after transplant and were all cases of chronic rejection.,20,17,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Figure 3B,18 March 2024,Glorious,"Glorious,Fiddyhamma,WikiWorks","Within the lung transplant cohort, a significant decrease in Bacteroides, Epulopiscium, Faecalibacterium, Prevotella and other significant taxas was observed.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976;1783272|1239|186801|3085636|186803|2383;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;3379134|976|200643|171549|171552|2974265|363265;1783272|1239|909932;1783272|1239|186801|186802|216572;3379134|976|200643|171549|815|909656|310298;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552,Complete,Folakunmi
bsdb:38385646/3/1,38385646,time series / longitudinal observational,38385646,https://doi.org/10.1128/spectrum.03142-23,https://journals.asm.org/doi/pdf/10.1128/spectrum.03142-23,"Bo Wu, Peng Wang, Tangjuan Zhang, Ting Qian, Xiangnan Li, Xue Pan, Zheng Ding, Zhichao Hou",Analysis on the change of gut microbiota and metabolome in lung transplant patients,American Society for Microbiology,2024,"gut microbiota, metabolome, lung transplantation, transplant rejection",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Lung transplantation,EFO:0010721,Lung transplant event-free group (EF),Lung transplant chronic rejection group (CR),The lung transplant rejection participants were patients who survived more than 6 months after transplant and were all cases of chronic rejection.,15,17,1 month,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 3c,10 April 2024,Fiddyhamma,"Fiddyhamma,Folakunmi,WikiWorks","In analyzing the EF and CR cohorts (Fig. 3C), only Ruminococcus gnavus group was
found dominant in the EF group.",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,1783272|1239|186801|3085636|186803|2316020|33038,Complete,Folakunmi
bsdb:38387693/1/1,38387693,"cross-sectional observational, not case-control",38387693,10.1016/j.alcohol.2024.02.003,NA,"Qiao N.N., Fang Q., Zhang X.H., Ke S.S., Wang Z.W., Tang G., Leng R.X. , Fan Y.G.",Effects of alcohol on the composition and metabolism of the intestinal microbiota among people with HIV: a cross-sectional study,"Alcohol (Fayetteville, N.Y.)",2024,"Alcohol, Cross-sectional study, HIV/AIDS, Intestinal microbiota, Metabolism",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Alcohol consumption measurement,EFO:0007878,Non Drinking,Low to Moderate drinking,HIV infected persons who consume alcohol ≥1 time/month or ≥12 times/year in the last year. Individuals in the low to moderate drinking group consumed <210 g of alcohol per week.,72,21,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 4C,21 April 2024,MyleeeA,"MyleeeA,WikiWorks",Differentially enriched bacterial taxa between low to moderate drinking and non-drinking groups in HIV-infected patients.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",1783272|1239|526524|526525|2810280|100883;1783272|1239|186801|3085636|186803|46205;3384189|32066|203490|203491|203492|180162;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3082720|186804,Complete,Svetlana up
bsdb:38387693/1/2,38387693,"cross-sectional observational, not case-control",38387693,10.1016/j.alcohol.2024.02.003,NA,"Qiao N.N., Fang Q., Zhang X.H., Ke S.S., Wang Z.W., Tang G., Leng R.X. , Fan Y.G.",Effects of alcohol on the composition and metabolism of the intestinal microbiota among people with HIV: a cross-sectional study,"Alcohol (Fayetteville, N.Y.)",2024,"Alcohol, Cross-sectional study, HIV/AIDS, Intestinal microbiota, Metabolism",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Alcohol consumption measurement,EFO:0007878,Non Drinking,Low to Moderate drinking,HIV infected persons who consume alcohol ≥1 time/month or ≥12 times/year in the last year. Individuals in the low to moderate drinking group consumed <210 g of alcohol per week.,72,21,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 4C,21 April 2024,MyleeeA,"MyleeeA,WikiWorks",Differentially enriched bacterial taxa between low to moderate drinking and non-drinking groups in HIV-infected patients.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Tessaracoccus",3379134|1224|1236|135614|32033;3379134|1224|1236|135614|32033|40323;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|1224|1236|135614;3379134|1224|1236|135625|712|724;1783272|201174|1760|85009|31957|72763,Complete,Svetlana up
bsdb:38406269/1/1,38406269,laboratory experiment,38406269,10.2147/DMSO.S451129,NA,"Xiong C., Wu J., Ma Y., Li N., Wang X., Li Y. , Ding X.",Effects of Glucagon-Like Peptide-1 Receptor Agonists on Gut Microbiota in Dehydroepiandrosterone-Induced Polycystic Ovary Syndrome Mice: Compared Evaluation of Liraglutide and Semaglutide Intervention,"Diabetes, metabolic syndrome and obesity : targets and therapy",2024,"GLP-1 receptor agonists, PCOS, gut microbiota, metabolism",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy control group,Polycystic ovary syndrome group (PCOS),Mice with Dehydroepiandrosterone (DHEA)-induced Polycystic ovary syndrome (PCOS).,6,6,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3B,3 January 2025,Victoria,"Victoria,WikiWorks",LDA (linear discriminant analysis) scores for the species abundance in the control and PCOS groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Duncaniella|s__Duncaniella dubosii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Lepagella|s__Lepagella muris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__Muribaculaceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Paramuribaculum|s__Paramuribaculum intestinale,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__Muribaculaceae bacterium Isolate-104 (HZI),k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__Muribaculaceae bacterium Isolate-110 (HZI),k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__Muribaculaceae bacterium Isolate-037 (Harlan),k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__Muribaculaceae bacterium Isolate-105 (HZI),k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella sp. CU968,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__Muribaculaceae bacterium Isolate-114 (HZI),k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__Muribaculaceae bacterium Isolate-004 (NCI),k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__Muribaculaceae bacterium Isolate-036 (Harlan)",3379134|976|200643|171549|815|816|85831;3379134|976|200643|171549|2005473|2518495|2518971;3379134|1224|1236|91347|543|561|562;3379134|976|200643|171549|2005473|3032807|3032870;3379134|976|200643|171549|2005473|2498093;3379134|976|200643|171549|2005473|2518497|2094151;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543;3379134|976|200643|171549|2005473|2486471;3379134|976|200643|171549|2005473|2486473;3379134|976|200643|171549|2005473|2486461;3379134|976|200643|171549|2005473|2486472;3379134|976|200643|171549|2005519|397864|2780099;3379134|976|200643|171549|2005473|2486475;3379134|976|200643|171549|2005473|2489216;3379134|976|200643|171549|2005473|2486460,Complete,Svetlana up
bsdb:38406269/1/2,38406269,laboratory experiment,38406269,10.2147/DMSO.S451129,NA,"Xiong C., Wu J., Ma Y., Li N., Wang X., Li Y. , Ding X.",Effects of Glucagon-Like Peptide-1 Receptor Agonists on Gut Microbiota in Dehydroepiandrosterone-Induced Polycystic Ovary Syndrome Mice: Compared Evaluation of Liraglutide and Semaglutide Intervention,"Diabetes, metabolic syndrome and obesity : targets and therapy",2024,"GLP-1 receptor agonists, PCOS, gut microbiota, metabolism",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy control group,Polycystic ovary syndrome group (PCOS),Mice with Dehydroepiandrosterone (DHEA)-induced Polycystic ovary syndrome (PCOS).,6,6,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3B,3 January 2025,Victoria,"Victoria,WikiWorks",LDA (linear discriminant analysis) scores for the species abundance in the control and PCOS groups.,decreased,"s__bacterium 1xD42-87,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium MD335,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum|s__Muribaculum intestinale,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Taurinivorans|s__Taurinivorans muris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes muris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 10-1,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium A4,s__bacterium 0.1xD8-71,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|s__Caudoviricetes sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor|s__Acetatifactor muris,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 28-4,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor|s__Acetatifactor aquisgranensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Flintibacter|s__Flintibacter muris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sporofaciens|s__Sporofaciens musculi,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__Muribaculaceae bacterium Isolate-042 (Harlan),k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Schaedlerella|s__Schaedlerella arabinosiphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. CU971,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 1-3,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|s__Firmicutes bacterium ASF500,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. 14-2,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium plexicaudatum,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter sp. MIT 03-1616",2320113;1783272|1239|186801|3085636|186803|1235793;1783272|1239|186801|3085636|186803|1898203;3379134|976|200643|171549|2005473|1918540|1796646;3379134|200940|3031449|213115|194924|3126915|2787751;3379134|976|200643|171549|171550|239759|2941326;1783272|1239|186801|3085636|186803|1235800;1783272|1239|186801|3085636|186803|397291;2320099;2731360|2731618|2731619|2832643;1783272|1239|186801|3085636|186803|1427378|879566;3379134|29547|3031852|213849|72293|209;1783272|1239|186801|3085636|186803|397287;1783272|1239|186801|3085636|186803|1427378|2941233;1783272|1239|186801|186802|1918454|2941327;1783272|1239|186801|3085636|186803|2811390|2681861;3379134|976|200643|171549|2005473|2486462;1783272|1239|186801|3085636|186803|2676048|2044587;1783272|1239|186801|186802|216572|459786|2780102;1783272|1239|186801|186802|216572|459786|1235797;1783272|1239|186801|186802;1783272|1239|1378168;1783272|1239|186801|186802|186806|1730|1235790;1783272|1239|186801|186802|186806|1730|97253;3379134|29547|3031852|213849|72293|209|1548148,Complete,Svetlana up
bsdb:38406269/2/1,38406269,laboratory experiment,38406269,10.2147/DMSO.S451129,NA,"Xiong C., Wu J., Ma Y., Li N., Wang X., Li Y. , Ding X.",Effects of Glucagon-Like Peptide-1 Receptor Agonists on Gut Microbiota in Dehydroepiandrosterone-Induced Polycystic Ovary Syndrome Mice: Compared Evaluation of Liraglutide and Semaglutide Intervention,"Diabetes, metabolic syndrome and obesity : targets and therapy",2024,"GLP-1 receptor agonists, PCOS, gut microbiota, metabolism",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Polycystic ovary syndrome (PCOS) group,Polycystic ovary syndrome + Liraglutide group (PCOS + Liraglutide),Mice with Dehydroepiandrosterone (DHEA)-induced Polycystic ovary syndrome (PCOS) and then treated with liraglitude GLP-1RAs for 4 weeks.,6,6,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,decreased,NA,decreased,Signature 1,Figure 3C,3 January 2025,Victoria,"Victoria,WikiWorks",LDA scores for the species abundance in the PCOS and PCOS+Liraglutide groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Duncaniella|s__Duncaniella dubosii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium A4,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter ganmani,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. 14-2,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Ileibacterium|s__Ileibacterium valens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,s__bacterium 1xD42-87,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes muris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp. 5-2,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium A2,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Flintibacter|s__Flintibacter muris,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Acutalibacter|s__Acutalibacter muris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 10-1,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 1-3,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. CU971,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__Muribaculaceae bacterium Isolate-080 (Janvier),k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|s__Firmicutes bacterium ASF500,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Schaedlerella|s__Schaedlerella arabinosiphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sporofaciens|s__Sporofaciens musculi,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor sp. 60,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__Otoolea muris,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter|s__Colidextribacter sp. OB.20,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Petralouisia|s__Petralouisia muris,s__bacterium 1xD42-67,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum|s__Faecalibaculum rodentium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 3-1,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor|s__Acetatifactor muris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|976|200643|171549|2005473|2518495|2518971;1783272|1239|186801|3085636|186803|397291;1783272|1239|186801|3085636|186803|1898203;3379134|29547|3031852|213849|72293|209|60246;1783272|201174|1760|85004|31953|1678|1694;1783272|1239|186801|186802|186806|1730|1235790;1783272|1239|526524|526525|128827|1937007|1862668;1783272|1239|91061|186826|33958|1578|33959;2320113;3379134|976|200643|171549|171550|239759|2941326;1783272|1239|186801|3085636|186803|189330|1235798;1783272|1239|186801|3085636|186803|397290;1783272|1239|186801|186802|1918454|2941327;1783272|1239|186801|186802|3082771|1918385|1796620;1783272|1239|186801|3085636|186803|1235800;1783272|1239|186801|186802|216572|459786|1235797;1783272|1239|186801|186802|216572|459786|2780102;3379134|976|200643|171549|2005473|2486468;1783272|1239|186801|186802;1783272|1239|1378168;1783272|1239|186801|3085636|186803|2676048|2044587;1783272|1239|186801|3085636|186803|2811390|2681861;1783272|1239|186801|186802|216572|1017280|2304576;1783272|1239|186801|3085636|186803|2941495|2941515;1783272|1239|186801|186802|1980681|2304568;1783272|1239|186801|3085636|186803|3032809|3032872;2320107;1783272|1239|526524|526525|128827|1729679|1702221;1783272|1239|186801|3085636|186803|397288;1783272|1239|186801|3085636|186803|1427378|879566;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:38406269/2/2,38406269,laboratory experiment,38406269,10.2147/DMSO.S451129,NA,"Xiong C., Wu J., Ma Y., Li N., Wang X., Li Y. , Ding X.",Effects of Glucagon-Like Peptide-1 Receptor Agonists on Gut Microbiota in Dehydroepiandrosterone-Induced Polycystic Ovary Syndrome Mice: Compared Evaluation of Liraglutide and Semaglutide Intervention,"Diabetes, metabolic syndrome and obesity : targets and therapy",2024,"GLP-1 receptor agonists, PCOS, gut microbiota, metabolism",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Polycystic ovary syndrome (PCOS) group,Polycystic ovary syndrome + Liraglutide group (PCOS + Liraglutide),Mice with Dehydroepiandrosterone (DHEA)-induced Polycystic ovary syndrome (PCOS) and then treated with liraglitude GLP-1RAs for 4 weeks.,6,6,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,decreased,NA,decreased,Signature 2,Figure 3C,3 January 2025,Victoria,"Victoria,WikiWorks",LDA scores for the species abundance in the PCOS and PCOS+Liraglutide groups.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Lepagella|s__Lepagella muris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__Muribaculaceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__Muribaculaceae bacterium Isolate-110 (HZI),k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__Muribaculaceae bacterium Isolate-013 (NCI),k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__Muribaculaceae bacterium Isolate-002 (NCI),k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__Muribaculaceae bacterium Isolate-004 (NCI),k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__Muribaculaceae bacterium Isolate-104 (HZI),k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__Muribaculaceae bacterium Isolate-102 (HZI),k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__Muribaculaceae bacterium Isolate-105 (HZI),k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__Muribaculaceae bacterium Isolate-037 (Harlan),k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Duncaniella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum|s__Muribaculum sp. NM65_B17,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Paramuribaculum|s__Paramuribaculum intestinale,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. MGM2,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Duncaniella|s__Duncaniella muris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Duncaniella|s__Duncaniella freteri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercorirosoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum|s__Muribaculum gordoncarteri",3379134|976|200643|171549|2005473|3032807|3032870;3379134|976|200643|171549|2005473|2498093;3379134|976|200643|171549|2005473|2486473;3379134|976|200643|171549|2005473|2489218;3379134|976|200643|171549|2005473|2489215;3379134|976|200643|171549|2005473|2489216;3379134|976|200643|171549|2005473|2486471;3379134|976|200643|171549|2005473|2486470;3379134|976|200643|171549|2005473|2486472;3379134|976|200643|171549|2005473|2486461;3379134|976|200643|171549;3379134|976|200643|171549|815|816|85831;3379134|976|200643|171549|2005473|2518495;3379134|976|200643|171549|2005473|1918540|2516961;3379134|1224|1236|91347|543;3379134|976|200643|171549|2005473|2518497|2094151;3379134|1224|1236|91347|543|561|562;3379134|976|200643|171549|171552|838|2033406;3379134|976|200643|171549|2005473|2518495|2094150;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005473|2518495|2530391;3379134|976|200643|171549|815|816|871324;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005473|1918540|2530390,Complete,Svetlana up
bsdb:38406269/3/1,38406269,laboratory experiment,38406269,10.2147/DMSO.S451129,NA,"Xiong C., Wu J., Ma Y., Li N., Wang X., Li Y. , Ding X.",Effects of Glucagon-Like Peptide-1 Receptor Agonists on Gut Microbiota in Dehydroepiandrosterone-Induced Polycystic Ovary Syndrome Mice: Compared Evaluation of Liraglutide and Semaglutide Intervention,"Diabetes, metabolic syndrome and obesity : targets and therapy",2024,"GLP-1 receptor agonists, PCOS, gut microbiota, metabolism",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Polycystic ovary syndrome (PCOS) group,Polycystic ovary syndrome + Semaglutide group (PCOS + Semaglutide),Mice with Dehydroepiandrosterone (DHEA)-induced Polycystic ovary syndrome (PCOS) and then treated with Semaglutide GLP-1RAs for 4 weeks.,6,6,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,decreased,NA,decreased,Signature 1,Figure 3D,3 January 2025,Victoria,"Victoria,WikiWorks",LDA scores for the species abundance in the PCOS and PCOS+Semaglutide groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Duncaniella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes muris,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter sp. MIT 03-1616,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter typhlonius,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter japonicus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum|s__Faecalibaculum rodentium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__Otoolea muris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella|s__Rikenella microfusus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium M18-1,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. MD294,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Millionella|s__Millionella massiliensis,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter hepaticus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter sp. MIT 03-1614,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Senimuribacter|s__Senimuribacter intestinalis",3379134|976|200643|171549|2005473|2518495;3379134|29547|3031852|213849|72293|209;3379134|976|200643|171549|171550|239759|2941326;3379134|29547|3031852|213849|72293|209|1548148;3379134|29547|3031852|213849|72293|209|76936;3379134|29547|3031852|213849|72293|209|425400;1783272|1239|526524|526525|128827|1729679|1702221;1783272|1239|186801|3085636|186803|2941495|2941515;3379134|976|200643|171549|171550|28138|28139;1783272|1239|186801|3085636|186803|1235792;1783272|1239|186801|186802|31979|1485|97138;3379134|976|200643|171549|171550|1980038|1871023;3379134|29547|3031852|213849|72293|209|32025;3379134|29547|3031852|213849|72293|209|1548147;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|3082720|543314|2941520|2941507,Complete,Svetlana up
bsdb:38406269/3/2,38406269,laboratory experiment,38406269,10.2147/DMSO.S451129,NA,"Xiong C., Wu J., Ma Y., Li N., Wang X., Li Y. , Ding X.",Effects of Glucagon-Like Peptide-1 Receptor Agonists on Gut Microbiota in Dehydroepiandrosterone-Induced Polycystic Ovary Syndrome Mice: Compared Evaluation of Liraglutide and Semaglutide Intervention,"Diabetes, metabolic syndrome and obesity : targets and therapy",2024,"GLP-1 receptor agonists, PCOS, gut microbiota, metabolism",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Polycystic ovary syndrome (PCOS) group,Polycystic ovary syndrome + Semaglutide group (PCOS + Semaglutide),Mice with Dehydroepiandrosterone (DHEA)-induced Polycystic ovary syndrome (PCOS) and then treated with Semaglutide GLP-1RAs for 4 weeks.,6,6,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,decreased,NA,decreased,Signature 2,Figure 3D,3 January 2025,Victoria,"Victoria,WikiWorks",LDA scores for the species abundance in the PCOS and PCOS+Semaglutide groups.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio|s__Acetivibrio sp. MSJd-27,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes ihumii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. CAG:268,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|s__Bacteroidaceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecichinchillae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:927,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercorirosoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia pseudococcoides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__Muribaculaceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__Muribaculaceae bacterium Isolate-002 (NCI),k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__Muribaculaceae bacterium Isolate-037 (Harlan),k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__Muribaculaceae bacterium Isolate-110 (HZI),k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum|s__Muribaculum intestinale,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides gordonii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella xylaniphila,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1185,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. MGM2,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus|s__Proteus mirabilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia ilealis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes timonensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides chinchillae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Gallalistipes|s__Gallalistipes aquisgranensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Marseilla|s__Marseilla massiliensis,s__uncultured bacterium BAC10G6,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas massiliensis (ex Liu et al. 2021),k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. An66,k__Bacillati|p__Bacillota|c__Dethiobacteria|o__Dethiobacterales|f__Dethiobacteraceae|g__Candidatus Contubernalis|s__Candidatus Contubernalis alkaliaceticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Lawsonibacter|s__Lawsonibacter celer",1783272|1239|186801|3120394|3120654|35829|2841523;3379134|74201|203494|48461|1647988|239934|239935;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759|2585118;3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|171550|239759|1470347;3379134|976|200643|171549|171550|239759|1288121;3379134|976|200643|171549|171550|239759|1262693;3379134|976|200643|171549|815|2212467;3379134|976|200643|171549|2030927;3379134|976|200643|171549|815|816|85831;3379134|976|200643|171549|815|816|871325;3379134|976|200643|171549|815|816|338188;3379134|976|200643|171549|815|816|291645;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|1262753;3379134|976|200643|171549|815|816|871324;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|815|816|371601;1783272|1239|186801|3085636|186803|572511|1796616;3379134|1224|28216|80840|1891238;3379134|1224|1236|91347|543|561|562;3379134|976|200643|171549|2005473|2498093;3379134|976|200643|171549|2005473|2489215;3379134|976|200643|171549|2005473|2486461;3379134|976|200643|171549|2005473|2486473;3379134|976|200643|171549|2005473|1918540|1796646;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|2005525|375288|328812;3379134|976|200643|171549|2005525|375288|574930;3379134|976|200643|171549|171552|577309|454154;3379134|976|200643|171549|171552|577309|454155;3379134|1224|28216|80840|995019|577310|487175;3379134|976|200643|171549|815|909656|671267;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|171552|838|1262921;3379134|976|200643|171549|171552|838|2033406;3379134|1224|1236|91347|1903414|583|584;1783272|1239|186801|3082720|186804|1501226|1115758;3379134|976|200643|171549|171552|2974251|165179;3379134|976|200643|171549|2005525|195950|28112;1783272|1239;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|561;3379134|1224|1236;3379134|976|200643|171549|2005525|375288;3379134|1224|1236|91347|1903414|583;3379134|976|200643|171549|171550;1783272|1239|526524|526525|2810281|191303;3379134|976|200643|171549|171550|239759|1465754;3379134|976|200643|171549|815;3379134|976|200643|171549|2005525|375288|871327;3379134|976|200643|171549|171550|2884610|2779358;3379134|976|200643|171549|171552|1926655|1841864;1329522;1783272|1239|186801|186802|1392389|3062493;3379134|976|200643|171549|171550|239759|1965650;1783272|1239|3086086|3086087|3086088|338648|338645;1783272|1239|186801|186802|216572|2172004|2986526,Complete,Svetlana up
bsdb:38406269/4/1,38406269,laboratory experiment,38406269,10.2147/DMSO.S451129,NA,"Xiong C., Wu J., Ma Y., Li N., Wang X., Li Y. , Ding X.",Effects of Glucagon-Like Peptide-1 Receptor Agonists on Gut Microbiota in Dehydroepiandrosterone-Induced Polycystic Ovary Syndrome Mice: Compared Evaluation of Liraglutide and Semaglutide Intervention,"Diabetes, metabolic syndrome and obesity : targets and therapy",2024,"GLP-1 receptor agonists, PCOS, gut microbiota, metabolism",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy control group,Polycystic ovary syndrome group (PCOS),Mice with Dehydroepiandrosterone (DHEA)-induced Polycystic ovary syndrome (PCOS).,6,6,NA,WMS,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2b, c, d & Figure 3e",14 January 2025,Victoria,"Victoria,WikiWorks","Microbiota composition at the phylum, family, and genus level and the relative abundance of signatures among four groups.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__Muribaculaceae bacterium Isolate-037 (Harlan),k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Lepagella|s__Lepagella muris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Lepagella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens",3379134|976|200643|171549|2005473|2486461;3379134|976;3379134|976|200643|171549|2005473;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005473|3032807|3032870;3379134|976|200643|171549|2005473|3032807;3379134|976|200643|171549|815|816|85831,Complete,Svetlana up
bsdb:38406269/4/2,38406269,laboratory experiment,38406269,10.2147/DMSO.S451129,NA,"Xiong C., Wu J., Ma Y., Li N., Wang X., Li Y. , Ding X.",Effects of Glucagon-Like Peptide-1 Receptor Agonists on Gut Microbiota in Dehydroepiandrosterone-Induced Polycystic Ovary Syndrome Mice: Compared Evaluation of Liraglutide and Semaglutide Intervention,"Diabetes, metabolic syndrome and obesity : targets and therapy",2024,"GLP-1 receptor agonists, PCOS, gut microbiota, metabolism",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy control group,Polycystic ovary syndrome group (PCOS),Mice with Dehydroepiandrosterone (DHEA)-induced Polycystic ovary syndrome (PCOS).,6,6,NA,WMS,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2b,14 January 2025,Victoria,"Victoria,WikiWorks","Microbiota composition at the phylum, family, and genus level and the relative abundance of signatures among four groups.",decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Svetlana up
bsdb:38406269/5/1,38406269,laboratory experiment,38406269,10.2147/DMSO.S451129,NA,"Xiong C., Wu J., Ma Y., Li N., Wang X., Li Y. , Ding X.",Effects of Glucagon-Like Peptide-1 Receptor Agonists on Gut Microbiota in Dehydroepiandrosterone-Induced Polycystic Ovary Syndrome Mice: Compared Evaluation of Liraglutide and Semaglutide Intervention,"Diabetes, metabolic syndrome and obesity : targets and therapy",2024,"GLP-1 receptor agonists, PCOS, gut microbiota, metabolism",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Polycystic ovary syndrome (PCOS) group,Polycystic ovary syndrome + Liraglutide group (PCOS + Liraglutide),Mice with Dehydroepiandrosterone (DHEA)-induced Polycystic ovary syndrome (PCOS) and then treated with liraglutide GLP-1RAs for 4 weeks.,6,6,NA,WMS,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,decreased,NA,decreased,Signature 1,"Figure 2b, c & d",14 January 2025,Victoria,"Victoria,WikiWorks","Microbiota composition at the phylum, family, and genus level and the relative abundance of signatures among four groups.",increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Ileibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239;1783272|201174|1760|85004|31953|1678;1783272|1239|526524|526525|128827|1937007;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:38406269/5/2,38406269,laboratory experiment,38406269,10.2147/DMSO.S451129,NA,"Xiong C., Wu J., Ma Y., Li N., Wang X., Li Y. , Ding X.",Effects of Glucagon-Like Peptide-1 Receptor Agonists on Gut Microbiota in Dehydroepiandrosterone-Induced Polycystic Ovary Syndrome Mice: Compared Evaluation of Liraglutide and Semaglutide Intervention,"Diabetes, metabolic syndrome and obesity : targets and therapy",2024,"GLP-1 receptor agonists, PCOS, gut microbiota, metabolism",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Polycystic ovary syndrome (PCOS) group,Polycystic ovary syndrome + Liraglutide group (PCOS + Liraglutide),Mice with Dehydroepiandrosterone (DHEA)-induced Polycystic ovary syndrome (PCOS) and then treated with liraglutide GLP-1RAs for 4 weeks.,6,6,NA,WMS,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,decreased,NA,decreased,Signature 2,"Figure 2b, c, d & Figure 3e",14 January 2025,Victoria,"Victoria,WikiWorks","Microbiota composition at the phylum, family, and genus level and the relative abundance of signatures among four groups.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__Muribaculaceae bacterium Isolate-037 (Harlan),k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Lepagella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Lepagella|s__Lepagella muris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens",3379134|976|200643|171549|2005473|2486461;3379134|976;3379134|976|200643|171549|2005473;3379134|976|200643|171549|815;3379134|976|200643|171549|2005473|3032807;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005473|3032807|3032870;3379134|976|200643|171549|815|816|85831,Complete,Svetlana up
bsdb:38406269/6/1,38406269,laboratory experiment,38406269,10.2147/DMSO.S451129,NA,"Xiong C., Wu J., Ma Y., Li N., Wang X., Li Y. , Ding X.",Effects of Glucagon-Like Peptide-1 Receptor Agonists on Gut Microbiota in Dehydroepiandrosterone-Induced Polycystic Ovary Syndrome Mice: Compared Evaluation of Liraglutide and Semaglutide Intervention,"Diabetes, metabolic syndrome and obesity : targets and therapy",2024,"GLP-1 receptor agonists, PCOS, gut microbiota, metabolism",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Polycystic ovary syndrome (PCOS) group,Polycystic ovary syndrome + Semaglutide group (PCOS + Semaglutide),Mice with Dehydroepiandrosterone (DHEA)-induced Polycystic ovary syndrome (PCOS) and then treated with Semaglutide GLP-1RAs for 4 weeks.,6,6,NA,WMS,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,decreased,NA,decreased,Signature 1,"Figure 2b, c, d & Figure 3e",14 January 2025,Victoria,"Victoria,WikiWorks","Microbiota composition at the phylum, family, and genus level and the relative abundance of signatures among four groups.",increased,"k__Pseudomonadati|p__Campylobacterota,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes muris",3379134|29547;3379134|29547|3031852|213849|72293;3379134|29547|3031852|213849|72293|209;3379134|976|200643|171549|171550|239759|2941326,Complete,Svetlana up
bsdb:38406269/6/2,38406269,laboratory experiment,38406269,10.2147/DMSO.S451129,NA,"Xiong C., Wu J., Ma Y., Li N., Wang X., Li Y. , Ding X.",Effects of Glucagon-Like Peptide-1 Receptor Agonists on Gut Microbiota in Dehydroepiandrosterone-Induced Polycystic Ovary Syndrome Mice: Compared Evaluation of Liraglutide and Semaglutide Intervention,"Diabetes, metabolic syndrome and obesity : targets and therapy",2024,"GLP-1 receptor agonists, PCOS, gut microbiota, metabolism",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Polycystic ovary syndrome (PCOS) group,Polycystic ovary syndrome + Semaglutide group (PCOS + Semaglutide),Mice with Dehydroepiandrosterone (DHEA)-induced Polycystic ovary syndrome (PCOS) and then treated with Semaglutide GLP-1RAs for 4 weeks.,6,6,NA,WMS,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,decreased,NA,decreased,Signature 2,Figure 2d & Figure 3e,14 January 2025,Victoria,"Victoria,WikiWorks","Microbiota composition at the phylum, family, and genus level and the relative abundance of signatures among four groups.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Lepagella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Lepagella|s__Lepagella muris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__Muribaculaceae bacterium Isolate-037 (Harlan)",3379134|976|200643|171549|2005473|3032807;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005473|3032807|3032870;3379134|976|200643|171549|815|816|85831;3379134|976|200643|171549|2005473|2486461,Complete,Svetlana up
bsdb:38420215/1/1,38420215,case-control,38420215,10.3389/fmicb.2023.1326870,NA,"Li H., Guo W., Li S., Sun B., Li N., Xie D., Dong Z., Luo D., Chen W., Fu W., Zheng J. , Zhu J.",Alteration of the gut microbiota profile in children with autism spectrum disorder in China,Frontiers in microbiology,2023,"Chinese children, autism spectrum disorder, gut microbiota, gut-brain axis, metabolic pathways",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Healthy children,Children with Autism Spectrum Disorder (ASD),Diagnosed with ASD according to DSM-5 (Diagnostic and Statistical Manual of Mental Disorders - 5th Edition),161,957,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,Figures 3A-E,25 October 2024,AlishaM,"AlishaM,WikiWorks",The shift of gut microbiota in ASD and HC groups,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia",1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|186802|216572|216851;1783272|1239|909932|1843489|31977|39948;3379134|1224|28216|80840|995019|577310;3384189|32066|203490;1783272|1239;3379134|74201|203494;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802;1783272|1239|186801,Complete,NA
bsdb:38420215/1/2,38420215,case-control,38420215,10.3389/fmicb.2023.1326870,NA,"Li H., Guo W., Li S., Sun B., Li N., Xie D., Dong Z., Luo D., Chen W., Fu W., Zheng J. , Zhu J.",Alteration of the gut microbiota profile in children with autism spectrum disorder in China,Frontiers in microbiology,2023,"Chinese children, autism spectrum disorder, gut microbiota, gut-brain axis, metabolic pathways",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Healthy children,Children with Autism Spectrum Disorder (ASD),Diagnosed with ASD according to DSM-5 (Diagnostic and Statistical Manual of Mental Disorders - 5th Edition),161,957,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,Figures 3A-E,25 October 2024,AlishaM,"AlishaM,WikiWorks",The shift of gut microbiota in ASD and HC groups,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Lentisphaerota,k__Methanobacteriati|p__Methanobacteriota,",3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|186802|216572|292632;3379134|976|200643|171549|171552;3379134|976|200643|171549;3379134|976|200643;3379134|1224|1236|91347|543;3379134|1224|1236|91347;1783272|1239|909932|909929|1843491|158846;3379134|256845;3366610|28890;,Complete,NA
bsdb:38421192/1/1,38421192,laboratory experiment,38421192,https://doi.org/10.1128/spectrum.01437-23,NA,"Zhang N., Gao X., Li D., Xu L., Zhou G., Xu M., Peng L., Sun G., Pan F., Li Y., Ren R., Huang R., Yang Y. , Wang Z.",Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites,Microbiology spectrum,2024,"anxiety, gut microbiota, metabolomics, probiotics, sleep deprivation",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,Baseline samples (BSL),Post sleep deprivation samples (7d-SD),Samples collected from rats after being subjected to 7 days of sleep deprivation (7d-SD).,30,29,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Fig.3d,18 March 2024,Iman-Ngwepe,"Iman-Ngwepe,Aleru Divine,Scholastica,WikiWorks",LEfSe analysis identified bacteria species that significantly differed in baseline (BSL) versus 7 days of sleep deprivation (7d-SD) samples.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__Desulfovibrionaceae bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Oligella|s__Oligella ureolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. MGM2,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus hyointestinalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus|s__Vagococcus lutrae",1783272|201174|84998|1643822|1643826|447020|446660;3379134|976|200643|171549|815|816|820;1783272|201174|1760|85004|31953|1678|1694;3379134|200940|3031449|213115|194924|2049043;3379134|1224|1236|91347|543|561|562;3379134|1224|28216|80840|506|90243|90244;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|171552|838|2033406;1783272|1239|91061|186826|1300|1301|1337;1783272|1239|91061|186826|81852|2737|81947,Complete,Svetlana up
bsdb:38421192/1/2,38421192,laboratory experiment,38421192,https://doi.org/10.1128/spectrum.01437-23,NA,"Zhang N., Gao X., Li D., Xu L., Zhou G., Xu M., Peng L., Sun G., Pan F., Li Y., Ren R., Huang R., Yang Y. , Wang Z.",Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites,Microbiology spectrum,2024,"anxiety, gut microbiota, metabolomics, probiotics, sleep deprivation",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,Baseline samples (BSL),Post sleep deprivation samples (7d-SD),Samples collected from rats after being subjected to 7 days of sleep deprivation (7d-SD).,30,29,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Fig.3d,18 March 2024,Iman-Ngwepe,"Iman-Ngwepe,Aleru Divine,Scholastica,WikiWorks",LEfSe analysis identified bacteria species that significantly differed in baseline (BSL) versus 7 days of sleep deprivation (7d-SD) samples.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|s__Aerococcaceae bacterium,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caecimuris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium stationis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1031,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P2-180,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter|s__Psychrobacter pasteurii",1783272|1239|91061|186826|186827|2053495;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|815|816|1796613;3379134|976|200643|171549|815|816|818;1783272|201174|1760|85007|1653|1716|1705;1783272|1239|91061|186826|33958|1578|33959;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|671267;3379134|976|200643|171549|171552|838|1262917;3379134|976|200643|171549|171552|838|2024224;3379134|1224|1236|2887326|468|497|1945520,Complete,Svetlana up
bsdb:38421192/2/1,38421192,laboratory experiment,38421192,https://doi.org/10.1128/spectrum.01437-23,NA,"Zhang N., Gao X., Li D., Xu L., Zhou G., Xu M., Peng L., Sun G., Pan F., Li Y., Ren R., Huang R., Yang Y. , Wang Z.",Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites,Microbiology spectrum,2024,"anxiety, gut microbiota, metabolomics, probiotics, sleep deprivation",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,Baseline samples (BSL),Saline supplementation - SA (21d-SA),Samples collected from rats after 14 days of saline supplementation (21d-SA).,30,15,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Fig.3d,11 April 2024,Aleru Divine,"Aleru Divine,Scholastica,WikiWorks",LEfSe analysis identified bacteria species that significantly differed in baseline (BSL) versus 14 days of saline supplementation (21d-SA) samples,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|s__Aerococcaceae bacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium stationis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__Desulfovibrionaceae bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Oligella|s__Oligella ureolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1031,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. MGM2,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P2-180,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus hyointestinalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus|s__Vagococcus lutrae",1783272|201174|84998|1643822|1643826|447020|446660;1783272|1239|91061|186826|186827|2053495;1783272|201174|1760|85004|31953|1678|1694;1783272|201174|1760|85007|1653|1716|1705;3379134|200940|3031449|213115|194924|2049043;3379134|1224|28216|80840|506|90243|90244;3379134|976|200643|171549|171552|838|1262917;3379134|976|200643|171549|171552|838|2033406;3379134|976|200643|171549|171552|838|2024224;1783272|1239|91061|186826|1300|1301|1337;1783272|1239|91061|186826|81852|2737|81947,Complete,Svetlana up
bsdb:38421192/2/2,38421192,laboratory experiment,38421192,https://doi.org/10.1128/spectrum.01437-23,NA,"Zhang N., Gao X., Li D., Xu L., Zhou G., Xu M., Peng L., Sun G., Pan F., Li Y., Ren R., Huang R., Yang Y. , Wang Z.",Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites,Microbiology spectrum,2024,"anxiety, gut microbiota, metabolomics, probiotics, sleep deprivation",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,Baseline samples (BSL),Saline supplementation - SA (21d-SA),Samples collected from rats after 14 days of saline supplementation (21d-SA).,30,15,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Fig.3d,11 April 2024,Aleru Divine,"Aleru Divine,Scholastica,WikiWorks",LEfSe analysis identified bacteria species that significantly differed in baseline (BSL) versus 14 days of saline supplementation (21d-SA) samples,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caecimuris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter|s__Psychrobacter pasteurii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus|s__Vagococcus lutrae",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|815|816|1796613;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|820;1783272|201174|1760|85004|31953|1678|1694;3379134|1224|1236|91347|543|561|562;1783272|1239|91061|186826|33958|1578|33959;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|671267;3379134|976|200643|171549|815|909656|821;3379134|1224|1236|2887326|468|497|1945520;1783272|1239|91061|186826|81852|2737|81947,Complete,Svetlana up
bsdb:38421192/4/1,38421192,laboratory experiment,38421192,https://doi.org/10.1128/spectrum.01437-23,NA,"Zhang N., Gao X., Li D., Xu L., Zhou G., Xu M., Peng L., Sun G., Pan F., Li Y., Ren R., Huang R., Yang Y. , Wang Z.",Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites,Microbiology spectrum,2024,"anxiety, gut microbiota, metabolomics, probiotics, sleep deprivation",Experiment 4,China,Rattus norvegicus,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,Post sleep deprivation samples (7d-SD),Saline supplementation - SA (21d-SA),Samples collected from rats after 14 days of saline supplementation (21d-SA).,29,15,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Fig.3d,11 April 2024,Aleru Divine,"Aleru Divine,Scholastica,WikiWorks",LEfSe analysis identified bacteria species that significantly differed in post sleep deprivation (7d-SD) versus 14 days of saline supplementation (21d-SA) samples,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|s__Aerococcaceae bacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium stationis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1031,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. MGM2,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P2-180,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus hyointestinalis",1783272|1239|91061|186826|186827|2053495;1783272|201174|1760|85007|1653|1716|1705;1783272|1239|91061|186826|33958|1578|33959;3379134|976|200643|171549|171552|838|1262917;3379134|976|200643|171549|171552|838|2033406;3379134|976|200643|171549|171552|838|2024224;1783272|1239|91061|186826|1300|1301|1337,Complete,Svetlana up
bsdb:38421192/4/2,38421192,laboratory experiment,38421192,https://doi.org/10.1128/spectrum.01437-23,NA,"Zhang N., Gao X., Li D., Xu L., Zhou G., Xu M., Peng L., Sun G., Pan F., Li Y., Ren R., Huang R., Yang Y. , Wang Z.",Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites,Microbiology spectrum,2024,"anxiety, gut microbiota, metabolomics, probiotics, sleep deprivation",Experiment 4,China,Rattus norvegicus,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,Post sleep deprivation samples (7d-SD),Saline supplementation - SA (21d-SA),Samples collected from rats after 14 days of saline supplementation (21d-SA).,29,15,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Fig.3d,11 April 2024,Aleru Divine,"Aleru Divine,Scholastica,WikiWorks",LEfSe analysis identified bacteria species that significantly differed in post sleep deprivation (7d-SD) versus 14 days of saline supplementation (21d-SA) samples,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caecimuris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__Desulfovibrionaceae bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Oligella|s__Oligella ureolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter|s__Psychrobacter pasteurii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus|s__Vagococcus lutrae",1783272|201174|84998|1643822|1643826|447020|446660;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|815|816|1796613;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|820;1783272|201174|1760|85004|31953|1678|1694;3379134|200940|3031449|213115|194924|2049043;3379134|1224|1236|91347|543|561|562;3379134|1224|28216|80840|506|90243|90244;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|671267;3379134|976|200643|171549|815|909656|821;3379134|1224|1236|2887326|468|497|1945520;1783272|1239|91061|186826|81852|2737|81947,Complete,Svetlana up
bsdb:38421192/5/1,38421192,laboratory experiment,38421192,https://doi.org/10.1128/spectrum.01437-23,NA,"Zhang N., Gao X., Li D., Xu L., Zhou G., Xu M., Peng L., Sun G., Pan F., Li Y., Ren R., Huang R., Yang Y. , Wang Z.",Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites,Microbiology spectrum,2024,"anxiety, gut microbiota, metabolomics, probiotics, sleep deprivation",Experiment 5,China,Rattus norvegicus,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,Post sleep deprivation samples (7d-SD),Multi-probiotic supplementation - MP (21d-MP),Samples collected from rats after 14 days of multi-probiotic supplementation (21d-MP).,29,14,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Fig.3d,11 April 2024,Aleru Divine,"Aleru Divine,Scholastica,WikiWorks",LEfSe analysis identified bacteria species that significantly differed in post sleep deprivation (7d-SD) versus 14 days of multi-probiotic supplementation (21d-MP) samples,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|s__Aerococcaceae bacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium stationis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Oligella|s__Oligella ureolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1031,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. MGM2,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P2-180,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter|s__Psychrobacter pasteurii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus hyointestinalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus|s__Vagococcus lutrae",1783272|201174|84998|1643822|1643826|447020|446660;1783272|1239|91061|186826|186827|2053495;1783272|201174|1760|85007|1653|1716|1705;1783272|1239|91061|186826|33958|1578|33959;3379134|1224|28216|80840|506|90243|90244;3379134|976|200643|171549|171552|838|1262917;3379134|976|200643|171549|171552|838|2033406;3379134|976|200643|171549|171552|838|2024224;3379134|1224|1236|2887326|468|497|1945520;1783272|1239|91061|186826|1300|1301|1337;1783272|1239|91061|186826|81852|2737|81947,Complete,Svetlana up
bsdb:38421192/5/2,38421192,laboratory experiment,38421192,https://doi.org/10.1128/spectrum.01437-23,NA,"Zhang N., Gao X., Li D., Xu L., Zhou G., Xu M., Peng L., Sun G., Pan F., Li Y., Ren R., Huang R., Yang Y. , Wang Z.",Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites,Microbiology spectrum,2024,"anxiety, gut microbiota, metabolomics, probiotics, sleep deprivation",Experiment 5,China,Rattus norvegicus,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,Post sleep deprivation samples (7d-SD),Multi-probiotic supplementation - MP (21d-MP),Samples collected from rats after 14 days of multi-probiotic supplementation (21d-MP).,29,14,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Fig.3d,11 April 2024,Aleru Divine,"Aleru Divine,Scholastica,WikiWorks",LEfSe analysis identified bacteria species that significantly differed in post sleep deprivation (7d-SD) versus 14 days of multi-probiotic supplementation (21d-MP) samples,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caecimuris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__Desulfovibrionaceae bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|815|816|1796613;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|820;1783272|201174|1760|85004|31953|1678|1694;3379134|200940|3031449|213115|194924|2049043;3379134|1224|1236|91347|543|561|562;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|671267;3379134|976|200643|171549|815|909656|821,Complete,Svetlana up
bsdb:38421192/6/1,38421192,laboratory experiment,38421192,https://doi.org/10.1128/spectrum.01437-23,NA,"Zhang N., Gao X., Li D., Xu L., Zhou G., Xu M., Peng L., Sun G., Pan F., Li Y., Ren R., Huang R., Yang Y. , Wang Z.",Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites,Microbiology spectrum,2024,"anxiety, gut microbiota, metabolomics, probiotics, sleep deprivation",Experiment 6,China,Rattus norvegicus,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,Saline supplementation - SA (21d-SA),Multi-probiotic supplementation - MP (21d-MP),Samples collected from rats after 14 days of multi-probiotic supplementation (21d-MP).,15,14,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Fig.3d,11 April 2024,Aleru Divine,"Aleru Divine,Scholastica,WikiWorks",LEfSe analysis identified bacteria species that significantly differed in 14 days of saline supplementation (21d-SA)  versus 14 days of multi-probiotic supplementation (21d-MP) samples,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|s__Aerococcaceae bacterium,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium stationis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Oligella|s__Oligella ureolytica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter|s__Psychrobacter pasteurii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus hyointestinalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus|s__Vagococcus lutrae",1783272|201174|84998|1643822|1643826|447020|446660;1783272|1239|91061|186826|186827|2053495;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|815|816|818;1783272|201174|1760|85004|31953|1678|1694;1783272|201174|1760|85007|1653|1716|1705;3379134|1224|1236|91347|543|561|562;1783272|1239|91061|186826|33958|1578|33959;3379134|1224|28216|80840|506|90243|90244;3379134|1224|1236|2887326|468|497|1945520;1783272|1239|91061|186826|1300|1301|1337;1783272|1239|91061|186826|81852|2737|81947,Complete,Svetlana up
bsdb:38421192/6/2,38421192,laboratory experiment,38421192,https://doi.org/10.1128/spectrum.01437-23,NA,"Zhang N., Gao X., Li D., Xu L., Zhou G., Xu M., Peng L., Sun G., Pan F., Li Y., Ren R., Huang R., Yang Y. , Wang Z.",Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites,Microbiology spectrum,2024,"anxiety, gut microbiota, metabolomics, probiotics, sleep deprivation",Experiment 6,China,Rattus norvegicus,Feces,UBERON:0001988,Anxiety disorder,EFO:0006788,Saline supplementation - SA (21d-SA),Multi-probiotic supplementation - MP (21d-MP),Samples collected from rats after 14 days of multi-probiotic supplementation (21d-MP).,15,14,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Fig.3d,11 April 2024,Aleru Divine,"Aleru Divine,Scholastica,WikiWorks",LEfSe analysis identified bacteria species that significantly differed in 14 days of saline supplementation (21d-SA)  versus 14 days of multi-probiotic supplementation (21d-MP) samples,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caecimuris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__Desulfovibrionaceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1031,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. MGM2,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P2-180",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|815|816|1796613;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|820;3379134|200940|3031449|213115|194924|2049043;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|671267;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|171552|838|1262917;3379134|976|200643|171549|171552|838|2033406;3379134|976|200643|171549|171552|838|2024224,Complete,Svetlana up
bsdb:38424099/1/1,38424099,randomized controlled trial,38424099,https://doi.org/10.1038/s41467-024-46116-y,NA,"Ni Lochlainn M., Bowyer R.C.E., Moll J.M., García M.P., Wadge S., Baleanu A.F., Nessa A., Sheedy A., Akdag G., Hart D., Raffaele G., Seed P.T., Murphy C., Harridge S.D.R., Welch A.A., Greig C., Whelan K. , Steves C.J.",Effect of gut microbiome modulation on muscle function and cognition: the PROMOTe randomised controlled trial,Nature communications,2024,NA,Experiment 1,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Placebo group (End of study),Prebiotic group (End of study),Subjects who received prebiotic supplements (inulin and fructo-oligosaccharides) along with BCAA (branched-chain amino acid) supplementation and resistance exercise and follow up was done after 12 weeks.,34,32,3 months,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.05,TRUE,NA,NA,"age,diet,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,7 October 2024,Rukaya-lab,"Rukaya-lab,Rahila,Chrisawoke,Chloe,WikiWorks","Twin-paired group comparisons between prebiotic and placebo supplements, including data from the end of the study",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota",1783272|201174|1760;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|201174,Complete,Chloe
bsdb:38424099/1/2,38424099,randomized controlled trial,38424099,https://doi.org/10.1038/s41467-024-46116-y,NA,"Ni Lochlainn M., Bowyer R.C.E., Moll J.M., García M.P., Wadge S., Baleanu A.F., Nessa A., Sheedy A., Akdag G., Hart D., Raffaele G., Seed P.T., Murphy C., Harridge S.D.R., Welch A.A., Greig C., Whelan K. , Steves C.J.",Effect of gut microbiome modulation on muscle function and cognition: the PROMOTe randomised controlled trial,Nature communications,2024,NA,Experiment 1,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Placebo group (End of study),Prebiotic group (End of study),Subjects who received prebiotic supplements (inulin and fructo-oligosaccharides) along with BCAA (branched-chain amino acid) supplementation and resistance exercise and follow up was done after 12 weeks.,34,32,3 months,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.05,TRUE,NA,NA,"age,diet,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 2,11 October 2024,Rukaya-lab,"Rukaya-lab,Rahila,Chrisawoke,MyleeeA,Chloe,WikiWorks","Twin-paired group comparisons between prebiotic and placebo supplements, including data from the end of the study or the difference between baseline and end of study.",decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis|s__Merdimmobilis hominis,k__Pseudomonadati|p__Bacteroidota",1783272|1239;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|3028852;1783272|1239|186801|186802|216572|3028852|2897707;3379134|976,Complete,Chloe
bsdb:38424099/2/1,38424099,randomized controlled trial,38424099,https://doi.org/10.1038/s41467-024-46116-y,NA,"Ni Lochlainn M., Bowyer R.C.E., Moll J.M., García M.P., Wadge S., Baleanu A.F., Nessa A., Sheedy A., Akdag G., Hart D., Raffaele G., Seed P.T., Murphy C., Harridge S.D.R., Welch A.A., Greig C., Whelan K. , Steves C.J.",Effect of gut microbiome modulation on muscle function and cognition: the PROMOTe randomised controlled trial,Nature communications,2024,NA,Experiment 2,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Placebo (change between baseline and study end),Prebiotic(change between baseline and study end),Subjects who received prebiotic supplements (inulin and fructo-oligosaccharides) along with BCAA (branched-chain amino acid) supplementation and resistance exercise and follow up was done after 12 weeks. Study end was adjusted for baseline in this experiment.,34,32,3 months,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,8 October 2024,Rukaya-lab,"Rukaya-lab,Rahila,Chrisawoke,MyleeeA,WikiWorks","Twin-paired group comparisons between prebiotic and placebo supplements, including data from the end of the study or the difference between baseline and end of study.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes",1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760,Complete,Chloe
bsdb:38424099/2/2,38424099,randomized controlled trial,38424099,https://doi.org/10.1038/s41467-024-46116-y,NA,"Ni Lochlainn M., Bowyer R.C.E., Moll J.M., García M.P., Wadge S., Baleanu A.F., Nessa A., Sheedy A., Akdag G., Hart D., Raffaele G., Seed P.T., Murphy C., Harridge S.D.R., Welch A.A., Greig C., Whelan K. , Steves C.J.",Effect of gut microbiome modulation on muscle function and cognition: the PROMOTe randomised controlled trial,Nature communications,2024,NA,Experiment 2,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Placebo (change between baseline and study end),Prebiotic(change between baseline and study end),Subjects who received prebiotic supplements (inulin and fructo-oligosaccharides) along with BCAA (branched-chain amino acid) supplementation and resistance exercise and follow up was done after 12 weeks. Study end was adjusted for baseline in this experiment.,34,32,3 months,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2,11 October 2024,Rukaya-lab,"Rukaya-lab,Rahila,Chrisawoke,MyleeeA,Chloe,WikiWorks","Twin-paired group comparisons between prebiotic and placebo supplements, including data from the end of the study or the difference between baseline and end of study.",decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Clostridia,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. AF17-7,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis|s__Merdimmobilis hominis",1783272|1239|909932|1843488;1783272|1239|186801|186802|3082771|1924093;3379134|976|200643|171549;1783272|1239|186801;28221;3379134|200940|3031449|213115;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730|2293105;1783272|1239|91061|186826;1783272|1239|186801|186802|216572|3028852;1783272|1239|186801|186802|216572|3028852|2897707,Complete,Chloe
bsdb:38424099/3/1,38424099,randomized controlled trial,38424099,https://doi.org/10.1038/s41467-024-46116-y,NA,"Ni Lochlainn M., Bowyer R.C.E., Moll J.M., García M.P., Wadge S., Baleanu A.F., Nessa A., Sheedy A., Akdag G., Hart D., Raffaele G., Seed P.T., Murphy C., Harridge S.D.R., Welch A.A., Greig C., Whelan K. , Steves C.J.",Effect of gut microbiome modulation on muscle function and cognition: the PROMOTe randomised controlled trial,Nature communications,2024,NA,Experiment 3,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Baseline Placebo,End of Study Placebo,Week 12 (End of study) participants who received protein (BCAA) supplement powder combined with a placebo supplement (maltodextrin).,36,34,3 months,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure S6,11 October 2024,Rukaya-lab,"Rukaya-lab,Rahila,Chrisawoke,WikiWorks",Significant Microbiota Features between Baseline and Study End,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,1783272|201174|1760|2037|2049|1654|55565,Complete,Chloe
bsdb:38424099/4/1,38424099,randomized controlled trial,38424099,https://doi.org/10.1038/s41467-024-46116-y,NA,"Ni Lochlainn M., Bowyer R.C.E., Moll J.M., García M.P., Wadge S., Baleanu A.F., Nessa A., Sheedy A., Akdag G., Hart D., Raffaele G., Seed P.T., Murphy C., Harridge S.D.R., Welch A.A., Greig C., Whelan K. , Steves C.J.",Effect of gut microbiome modulation on muscle function and cognition: the PROMOTe randomised controlled trial,Nature communications,2024,NA,Experiment 4,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Baseline Prebiotic,End of study Prebiotic,Week 12 (End of study) participants who received daily prebiotic supplementation (inulin and fructo-oligosaccharides) along with branched-chain amino acids (BCAA) and resistance exercise.,36,32,3 months,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,increased,NA,NA,NA,increased,Signature 1,Supplementary Figure S6,11 October 2024,Rukaya-lab,"Rukaya-lab,Rahila,Chrisawoke,MyleeeA,WikiWorks",Significant Microbiota Features identified between Baseline Prebiotic and Study End Prebiotic using Linear models.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Nanosynbacterales|f__Candidatus Nanosynbacteraceae|g__Candidatus Nanosynbacter,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Nanosynbacterales|f__Candidatus Nanosynbacteraceae,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Nanosynbacterales,p__Candidatus Saccharimonadota,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas sp. MSJ-38",1783272|201174|1760|2037|2049|1654|55565;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;1783272|201174|1760;1783272|201174;1783272|1239|186801|3085636|186803|207244|649756;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|1689;1783272|201174|1760|85004|31953|1678|216816;95818|2093818|2093819|2093822|2093823;95818|2093818|2093819|2093822;95818|2093818|2093819;95818;95818|2093818;1783272|1239|1737404|1737405|1570339|543311;1783272|201174|1760|2037|2049|2529408;1783272|201174|1760|2037|2049|2529408|1660;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|1392389|2841532,Complete,Chloe
bsdb:38424099/4/2,38424099,randomized controlled trial,38424099,https://doi.org/10.1038/s41467-024-46116-y,NA,"Ni Lochlainn M., Bowyer R.C.E., Moll J.M., García M.P., Wadge S., Baleanu A.F., Nessa A., Sheedy A., Akdag G., Hart D., Raffaele G., Seed P.T., Murphy C., Harridge S.D.R., Welch A.A., Greig C., Whelan K. , Steves C.J.",Effect of gut microbiome modulation on muscle function and cognition: the PROMOTe randomised controlled trial,Nature communications,2024,NA,Experiment 4,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Baseline Prebiotic,End of study Prebiotic,Week 12 (End of study) participants who received daily prebiotic supplementation (inulin and fructo-oligosaccharides) along with branched-chain amino acids (BCAA) and resistance exercise.,36,32,3 months,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,increased,NA,NA,NA,increased,Signature 2,Supplementary Figure S6,11 October 2024,Rukaya-lab,"Rukaya-lab,Rahila,Chrisawoke,MyleeeA,WikiWorks",Significant Microbiota Features identified between Baseline Prebiotic and Study End Prebiotic using Linear models.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus,c__Bigyra,k__Bacillati|p__Bacillota|c__Clostridia,c__Deltaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis|s__Merdimmobilis hominis,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Waltera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF34-10BH,k__Methanobacteriati|p__Methanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. AF17-7",1783272|1239|186801|186802|3082771|1924093;2683628;1783272|1239|186801;28221;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|3028852;1783272|1239|186801|186802|216572|3028852|2897707;3366610|28890|183925;1783272|1239|909932;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|2815781;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|186802|31979|1485|2293011;3366610|28890;1783272|1239|186801|186802|186806|1730|2293105,Complete,Chloe
bsdb:38424099/5/1,38424099,randomized controlled trial,38424099,https://doi.org/10.1038/s41467-024-46116-y,NA,"Ni Lochlainn M., Bowyer R.C.E., Moll J.M., García M.P., Wadge S., Baleanu A.F., Nessa A., Sheedy A., Akdag G., Hart D., Raffaele G., Seed P.T., Murphy C., Harridge S.D.R., Welch A.A., Greig C., Whelan K. , Steves C.J.",Effect of gut microbiome modulation on muscle function and cognition: the PROMOTe randomised controlled trial,Nature communications,2024,NA,Experiment 5,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Baseline prebiotics and placebo,End of study prebiotics and placebo,Week 12 (End of study) participants who received protein (BCAA) supplement powder combined with a placebo supplement (maltodextrin) and daily prebiotic supplementation (inulin and fructo-oligosaccharides) along with branched-chain amino acids (BCAA) and resistance exercise.,70,68,3 months,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure S6,27 October 2024,Chrisawoke,"Chrisawoke,Chloe,WikiWorks",Significant Microbiota Features Between Baseline and Study End,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum",1783272|201174|1760|2037|2049|1654|55565;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|1239|186801|186802|186806|1730|39496,Complete,Chloe
bsdb:38424099/5/2,38424099,randomized controlled trial,38424099,https://doi.org/10.1038/s41467-024-46116-y,NA,"Ni Lochlainn M., Bowyer R.C.E., Moll J.M., García M.P., Wadge S., Baleanu A.F., Nessa A., Sheedy A., Akdag G., Hart D., Raffaele G., Seed P.T., Murphy C., Harridge S.D.R., Welch A.A., Greig C., Whelan K. , Steves C.J.",Effect of gut microbiome modulation on muscle function and cognition: the PROMOTe randomised controlled trial,Nature communications,2024,NA,Experiment 5,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Baseline prebiotics and placebo,End of study prebiotics and placebo,Week 12 (End of study) participants who received protein (BCAA) supplement powder combined with a placebo supplement (maltodextrin) and daily prebiotic supplementation (inulin and fructo-oligosaccharides) along with branched-chain amino acids (BCAA) and resistance exercise.,70,68,3 months,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure S6,22 November 2024,Chloe,"Chloe,WikiWorks","2.6 Supplementary Figure S6: Significant Microbiota Features between Baseline
and Study End Paired group comparison of relative abundance (a) and prevalence (p) of bacterial taxa between baseline and end of study, including data from both study arms.",decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma|s__[Collinsella] massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio|s__Acetivibrio sp. MSJd-27,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF23-8,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes dispar,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor hominis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella",1783272|1239|909932|1843488|909930|33024;1783272|201174|84998|84999|84107|1472762|1232426;1783272|1239|186801|3085636|186803|2316020|46228;1783272|1239|186801|3120394|3120654|35829|2841523;1783272|1239|186801|3120394|3120654|35829;1783272|1239|186801|186802|31979|1485|2293006;3379134|976|200643|171549|171550|239759|2585119;1783272|1239|186801|186802|216572|1017280|2763059;1783272|201174|84998|84999|1643824|133925,Complete,Chloe
bsdb:38424099/6/1,38424099,randomized controlled trial,38424099,https://doi.org/10.1038/s41467-024-46116-y,NA,"Ni Lochlainn M., Bowyer R.C.E., Moll J.M., García M.P., Wadge S., Baleanu A.F., Nessa A., Sheedy A., Akdag G., Hart D., Raffaele G., Seed P.T., Murphy C., Harridge S.D.R., Welch A.A., Greig C., Whelan K. , Steves C.J.",Effect of gut microbiome modulation on muscle function and cognition: the PROMOTe randomised controlled trial,Nature communications,2024,NA,Experiment 6,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Placebo (Correlated with Cognition Factor),Prebiotic (Correlated with Cognition Factor),Week 12 (End of study) participants in prebiotic group positively correlated with Cognition Factor.,34,32,3 months,WMS,NA,Illumina,centered log-ratio,Pearson Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 9 and 10,25 October 2024,MyleeeA,"MyleeeA,WikiWorks",Microbiota features that positively correlated with Cognition Factor.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota",1783272|1239|909932|1843489|31977;1783272|1239|909932|1843489;1783272|201174|84998|84999;1783272|201174,Complete,Chloe
bsdb:38424099/6/2,38424099,randomized controlled trial,38424099,https://doi.org/10.1038/s41467-024-46116-y,NA,"Ni Lochlainn M., Bowyer R.C.E., Moll J.M., García M.P., Wadge S., Baleanu A.F., Nessa A., Sheedy A., Akdag G., Hart D., Raffaele G., Seed P.T., Murphy C., Harridge S.D.R., Welch A.A., Greig C., Whelan K. , Steves C.J.",Effect of gut microbiome modulation on muscle function and cognition: the PROMOTe randomised controlled trial,Nature communications,2024,NA,Experiment 6,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Placebo (Correlated with Cognition Factor),Prebiotic (Correlated with Cognition Factor),Week 12 (End of study) participants in prebiotic group positively correlated with Cognition Factor.,34,32,3 months,WMS,NA,Illumina,centered log-ratio,Pearson Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 9 and 10,25 October 2024,MyleeeA,"MyleeeA,WikiWorks",Microbiota features that Negatively correlated with Cognition Factor.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora,1783272|1239|186801|3085636|186803|2719231,Complete,Chloe
bsdb:38424099/7/1,38424099,randomized controlled trial,38424099,https://doi.org/10.1038/s41467-024-46116-y,NA,"Ni Lochlainn M., Bowyer R.C.E., Moll J.M., García M.P., Wadge S., Baleanu A.F., Nessa A., Sheedy A., Akdag G., Hart D., Raffaele G., Seed P.T., Murphy C., Harridge S.D.R., Welch A.A., Greig C., Whelan K. , Steves C.J.",Effect of gut microbiome modulation on muscle function and cognition: the PROMOTe randomised controlled trial,Nature communications,2024,NA,Experiment 7,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Placebo (Correlated with Chair Rise time),Prebiotic (Correlated with Chair Rise time),Week 12 (End of study) participants in prebiotic group positively correlated with Chair Rise time (CST).,34,32,3 months,WMS,NA,Illumina,centered log-ratio,Pearson Correlation,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Supplementary Figure 8,25 October 2024,MyleeeA,"MyleeeA,Chrisawoke,WikiWorks",Microbiota features that Positively correlated with Physical Activity (Chair Rise Time).,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. An250,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Bittarella (ex Durand et al. 2017)|s__Bittarella massiliensis (ex Durand et al. 2017),k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium CCNA10,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AT4,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter|s__Dysosmobacter welbionis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea|s__Faecalitalea cylindroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Hydrogeniiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Hydrogeniiclostridium|s__Hydrogeniiclostridium mannosilyticum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus|s__Lactiplantibacillus paraplantarum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Merdimonas|s__Merdimonas faecis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella corporis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Rubneribacter|s__Rubneribacter badeniensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia turicensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas intestinalis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma|s__[Collinsella] massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Wansuia|s__Wansuia hejianensis",1783272|1239|909932|1843488|909930|904;1783272|1239|909932|1843488|909930|904|187327;1783272|1239|186801|186802|3082771|1924093|1965604;1783272|1239|91061|1385;1783272|1239|186801|186802|216572|1929297|1720313;1783272|1239|186801|3085636|186803|572511|33035;3379134|1224|1236|91347|543|544|546;1783272|1239|186801|186802|2109688;1783272|1239|186801|186802|31979|1485|1720194;1783272|1239|526524|526525|2810280|100883;1783272|1239|526524|526525|2810280|100883|100884;1783272|1239|186801|186802|216572|2591381|2093857;1783272|1239|186801|3085636|186803|2719313;1783272|1239|186801|3085636|186803|2719313|358742;1783272|1239|186801|3082720|543314;1783272|1239|186801|3085636|186803|2005359;1783272|1239|526524|526525|128827|1573534;1783272|1239|526524|526525|128827|1573534|39483;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|216572|946234|292800;3379134|976|200643|171549|171552|2974257|386414;1783272|1239|186801|3085636|186803|1649459|154046;1783272|1239|186801|186802|3082771|2764317;1783272|1239|186801|186802|3082771|2764317|2764322;3379134|1224|1236|91347|543|570|571;1783272|1239|91061|186826|33958|2767842;1783272|1239|91061|186826|33958|2767842|60520;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|91061|186826|33958|2742598;1783272|1239|91061|186826|33958|2742598|1613;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|186803|2023266|1653435;3379134|976|200643|171549|171551|836|322095;3379134|976|200643|171549|171552|838|28128;1783272|201174|84998|1643822|1643826|2126002|2070688;1783272|1239|186801|186802|216572|1905344;1783272|1239|186801|186802|216572|1905344|1550024;1783272|201174|1760|2037|2049|2529408|131111;1783272|1239|186801|3085636|186803|1769710;1783272|1239|186801|3085636|186803|1769710|1653434;1783272|1239|526524|526525|128827|123375;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|91061|186826|1300|1301|1309;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|526524|526525|2810280|3025755|29348;1783272|1239|186801|186802|31979|1485|1522;1783272|1239|186801|3085636|186803|1506553|29347;1783272|1239|186801|3085636|186803|2941495|1512;1783272|201174|84998|84999|84107|1472762|1232426;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|186802|3085642|2048137|2763013;1783272|1239|186801|3085636|186803|2944198|2763667,Complete,Chloe
bsdb:38424099/7/2,38424099,randomized controlled trial,38424099,https://doi.org/10.1038/s41467-024-46116-y,NA,"Ni Lochlainn M., Bowyer R.C.E., Moll J.M., García M.P., Wadge S., Baleanu A.F., Nessa A., Sheedy A., Akdag G., Hart D., Raffaele G., Seed P.T., Murphy C., Harridge S.D.R., Welch A.A., Greig C., Whelan K. , Steves C.J.",Effect of gut microbiome modulation on muscle function and cognition: the PROMOTe randomised controlled trial,Nature communications,2024,NA,Experiment 7,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Placebo (Correlated with Chair Rise time),Prebiotic (Correlated with Chair Rise time),Week 12 (End of study) participants in prebiotic group positively correlated with Chair Rise time (CST).,34,32,3 months,WMS,NA,Illumina,centered log-ratio,Pearson Correlation,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Supplementary Figure 8,25 October 2024,MyleeeA,"MyleeeA,WikiWorks",Microbiota features that Negatively correlated with Physical Activity (Chair Rise Time).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum butyriciproducens,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum faecicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia glucerasea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp. AF36-15AT,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. AF17-7,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas umbilicata,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. AF34-10,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF37-5,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium longum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia saccharogumia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas sp. MSJ-38,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. OM04-15AA,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. TM06-18,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. SG-772,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. OF03-18AA,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp. APC924/74,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Candidatus Borkfalkia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Massilicoli,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Faecalibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Waltera",1783272|1239|186801|3120394|3120654|35829;1783272|1239|186801|186802|3085642|2048137|1628085;3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|3118652|2039240;1783272|1239|186801|3085636|3118652|2039240|2358141;1783272|1239|186801|3085636|186803|572511|536633;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|3082768;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|33042|33043;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330|2292041;1783272|1239|186801|186802|186806|1730|39490;1783272|1239|186801|186802|186806|1730|2293105;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|2005355;1783272|1239|186801|3085636|186803|2005355|1912855;1783272|1239|186801|186802|204475;1783272|1239|186801|186802|204475|745368;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|815|909656;1783272|1239|186801|186802|216572|292632;3379134|74201|203494|48461;3379134|256845|1313211|278082;3379134|256845|1313211|278082|255528|172900;1783272|1239|186801|3085636|186803|572511|2292968;1783272|1239|186801|186802|31979|1485|2293016;1783272|1239|186801|186802|216572|216851|1851428;1783272|1239|526524|526525|2810280|3025755|341225;1783272|1239|186801|186802|1392389|2841532;1783272|1239|186801|3085636|186803|841|2293143;1783272|1239|186801|186802|31979|1485|2293054;1783272|1239|186801|3085636|186803|572511|2109334;1783272|1239|186801|186802|31979|1485|2292308;1783272|1239|186801|186802|216572|292632|2086273;1783272|1239|186801|3082768|990719|2508948;1783272|1239|526524|526525|128827|2683202;1783272|1239|526524|526525|2810280|2678885;1783272|1239|186801|3085636|186803|2815781,Complete,Chloe
bsdb:38431030/1/1,38431030,case-control,38431030,10.1016/j.ygeno.2024.110816,NA,"Shahzad M., Saeed M., Amin H., Binmadi N., Ullah Z., Bibi S. , Andrew S.C.",The oral microbiome of newly diagnosed tuberculosis patients; a pilot study,Genomics,2024,"Bacterial diversity, Dysbiosis, Metabolic potential, Microbiota, Respiratory diseases",Experiment 1,Pakistan,Homo sapiens,Oral cavity,UBERON:0000167,Pulmonary tuberculosis,EFO:1000049,Healthy controls,"Newly diagnosed, treatment‑naive pulmonary TB patients","Confirmed active pulmonary TB (sputum smear microscopy and Xpert MTB/RIF assay, per national guidelines)",10,20,Current use of antibiotics,16S,34,Illumina,relative abundances,"PERMANOVA,DESeq2,LEfSe",0.05,TRUE,2,age,"education level,oral hygiene,socioeconomic status",NA,increased,NA,increased,increased,increased,Signature 1,Figure 4A and B,7 June 2025,Nuerteye,Nuerteye,Linear discriminant analysis Effect Size (LEfSe) at genus and phylum level between the two groups.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549|815|816;3379134|1224|28216|80840|80864|283;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300|1301,Complete,NA
bsdb:38431030/1/2,38431030,case-control,38431030,10.1016/j.ygeno.2024.110816,NA,"Shahzad M., Saeed M., Amin H., Binmadi N., Ullah Z., Bibi S. , Andrew S.C.",The oral microbiome of newly diagnosed tuberculosis patients; a pilot study,Genomics,2024,"Bacterial diversity, Dysbiosis, Metabolic potential, Microbiota, Respiratory diseases",Experiment 1,Pakistan,Homo sapiens,Oral cavity,UBERON:0000167,Pulmonary tuberculosis,EFO:1000049,Healthy controls,"Newly diagnosed, treatment‑naive pulmonary TB patients","Confirmed active pulmonary TB (sputum smear microscopy and Xpert MTB/RIF assay, per national guidelines)",10,20,Current use of antibiotics,16S,34,Illumina,relative abundances,"PERMANOVA,DESeq2,LEfSe",0.05,TRUE,2,age,"education level,oral hygiene,socioeconomic status",NA,increased,NA,increased,increased,increased,Signature 2,Figure 4A and B,7 June 2025,Nuerteye,Nuerteye,Linear discriminant analysis Effect Size (LEfSe) at genus and phylum level between the two groups.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Spirochaetota,k__Thermotogati|p__Synergistota",3379134|976|200643|171549|171552|1283313;3379134|1224|28216|80840|119060|48736;3379134|1224|28211|204457|41297|13687;3379134|203691;3384194|508458,Complete,NA
bsdb:38431030/2/NA,38431030,case-control,38431030,10.1016/j.ygeno.2024.110816,NA,"Shahzad M., Saeed M., Amin H., Binmadi N., Ullah Z., Bibi S. , Andrew S.C.",The oral microbiome of newly diagnosed tuberculosis patients; a pilot study,Genomics,2024,"Bacterial diversity, Dysbiosis, Metabolic potential, Microbiota, Respiratory diseases",Experiment 2,Pakistan,Homo sapiens,Oral cavity,UBERON:0000167,Extrapulmonary tuberculosis,NA,Healthy controls,"Newly diagnosed, treatment‑naive pulmonary TB patients","Confirmed active pulmonary TB (sputum smear microscopy and Xpert MTB/RIF assay, per national guidelines).",10,20,Current use of antibiotics,16S,34,Illumina,relative abundances,"PERMANOVA,DESeq2,LEfSe",0.05,TRUE,2,age,"education level,oral hygiene,socioeconomic status",NA,increased,NA,increased,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:38436093/1/1,38436093,time series / longitudinal observational,38436093,https://doi.org/10.1080/19490976.2024.2323234,NA,"Peng Y., Tun H.M., Ng S.C., Wai H.K., Zhang X., Parks J., Field C.J., Mandhane P., Moraes T.J., Simons E., Turvey S.E., Subbarao P., Brook J.R., Takaro T.K., Scott J.A., Chan F.K. , Kozyrskyj A.L.",Maternal smoking during pregnancy increases the risk of gut microbiome-associated childhood overweight and obesity,Gut microbes,2024,"Maternal smoking, butyrate production, childhood obesity, gut microbiota",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Smoking behaviour measurement,EFO:0005671,Early infants (3 months) with maternal history of  'NO' 'smoking,Early infants (3 months) with maternal history of  'YES' 'smoking,"Infants (3 months old) whose mothers quit smoking during pregnancy, reduced the number of cigarettes, or had the same number of cigarettes (as before conception) during pregnancy.",1458,134,NA,16S,4,NA,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,increased,increased,NA,increased,Signature 1,"Figure 2B, Supplementary Table S8",21 April 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,Scholastica,WikiWorks",Differentially abundant taxa identified by LEfSe in smoke exposed versus non-smoke exposed early infants (3 months old),increased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",1783272|1239;3379134|1224|28216|80840;1783272|1239|186801;1783272|1239|186801|3082720|186804|1870884;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|909932|1843489|31977|906;1783272|1239|909932;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720;1783272|1239|909932|909929;3379134|1224|28216|80840|995019|40544;3379134|1224|28216|80840|995019;1783272|1239|1737404|1737405;1783272|1239|909932|1843489|31977;1783272|1239|909932|1843489;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Svetlana up
bsdb:38436093/1/2,38436093,time series / longitudinal observational,38436093,https://doi.org/10.1080/19490976.2024.2323234,NA,"Peng Y., Tun H.M., Ng S.C., Wai H.K., Zhang X., Parks J., Field C.J., Mandhane P., Moraes T.J., Simons E., Turvey S.E., Subbarao P., Brook J.R., Takaro T.K., Scott J.A., Chan F.K. , Kozyrskyj A.L.",Maternal smoking during pregnancy increases the risk of gut microbiome-associated childhood overweight and obesity,Gut microbes,2024,"Maternal smoking, butyrate production, childhood obesity, gut microbiota",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Smoking behaviour measurement,EFO:0005671,Early infants (3 months) with maternal history of  'NO' 'smoking,Early infants (3 months) with maternal history of  'YES' 'smoking,"Infants (3 months old) whose mothers quit smoking during pregnancy, reduced the number of cigarettes, or had the same number of cigarettes (as before conception) during pregnancy.",1458,134,NA,16S,4,NA,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,increased,increased,NA,increased,Signature 2,"Figure 2B, Supplementary Table S8",21 April 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,Scholastica,WikiWorks",Differentially abundant taxa identified by LEfSe in smoke exposed versus non-smoke exposed early infants (3 months old),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",1783272|1239|186801|3085636|186803|572511;3379134|1224|1236|135625|712|724;1783272|201174|1760|85006|1268;1783272|201174|1760|85006;1783272|1239|186801|186802|216572;3379134|1224|1236|135625|712;3379134|1224|1236|135625;1783272|201174|1760|85006|1268|32207,Complete,Svetlana up
bsdb:38436093/2/1,38436093,time series / longitudinal observational,38436093,https://doi.org/10.1080/19490976.2024.2323234,NA,"Peng Y., Tun H.M., Ng S.C., Wai H.K., Zhang X., Parks J., Field C.J., Mandhane P., Moraes T.J., Simons E., Turvey S.E., Subbarao P., Brook J.R., Takaro T.K., Scott J.A., Chan F.K. , Kozyrskyj A.L.",Maternal smoking during pregnancy increases the risk of gut microbiome-associated childhood overweight and obesity,Gut microbes,2024,"Maternal smoking, butyrate production, childhood obesity, gut microbiota",Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Smoking behaviour measurement,EFO:0005671,Late infants (12months) with maternal history of  'NO' 'smoking,Late infants (12months) with maternal history of  'YES' 'smoking,"Infants (12 months old) whose mothers quit smoking during pregnancy, reduced the number of cigarettes, or had the same number of cigarettes (as before conception) during pregnancy.",1458,134,NA,16S,4,NA,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,increased,increased,NA,increased,Signature 1,"Figure 2B, Supplementary Table S8",22 April 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,Scholastica,MyleeeA,WikiWorks",Differentially abundant taxa identified by LEfSe in smoke exposed versus non-smoke exposed late infants (12 months old),increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Thermodesulfobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae",3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|3085642;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|1980681;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;3379134|200940|3031449;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|995019|40544;3379134|200940;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803|297314;1783272|1239|526524|526525|2810280,Complete,Svetlana up
bsdb:38436093/2/2,38436093,time series / longitudinal observational,38436093,https://doi.org/10.1080/19490976.2024.2323234,NA,"Peng Y., Tun H.M., Ng S.C., Wai H.K., Zhang X., Parks J., Field C.J., Mandhane P., Moraes T.J., Simons E., Turvey S.E., Subbarao P., Brook J.R., Takaro T.K., Scott J.A., Chan F.K. , Kozyrskyj A.L.",Maternal smoking during pregnancy increases the risk of gut microbiome-associated childhood overweight and obesity,Gut microbes,2024,"Maternal smoking, butyrate production, childhood obesity, gut microbiota",Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Smoking behaviour measurement,EFO:0005671,Late infants (12months) with maternal history of  'NO' 'smoking,Late infants (12months) with maternal history of  'YES' 'smoking,"Infants (12 months old) whose mothers quit smoking during pregnancy, reduced the number of cigarettes, or had the same number of cigarettes (as before conception) during pregnancy.",1458,134,NA,16S,4,NA,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,increased,increased,NA,increased,Signature 2,"Figure 2B, Supplementary Table S8",22 April 2024,Omojokunoluwatomisin,"Omojokunoluwatomisin,Scholastica,WikiWorks",Differentially abundant taxa identified by LEfSe in smoke exposed versus non-smoke exposed late infants (12 months old),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|28050;3379134|1224|1236|135625|712;3379134|1224|1236|135625;1783272|1239|909932|909929;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977,Complete,Svetlana up
bsdb:38440790/1/1,38440790,case-control,38440790,10.3389/fcimb.2024.1331521,NA,"Yunusbaeva M., Borodina L., Terentyeva D., Bogdanova A., Zakirova A., Bulatov S., Altinbaev R., Bilalov F. , Yunusbayev B.",Excess fermentation and lactic acidosis as detrimental functions of the gut microbes in treatment-naive TB patients,Frontiers in cellular and infection microbiology,2024,"anaerobic fermentation, dysbiosis, gut microbiome, gut-derived lactic acidosis, tuberculosis",Experiment 1,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,healthy controls (HCs),Treatment‑naïve tuberculosis (TB) patients,"pulmonary TB as confirmed by chest radiography and a positive sputum smear or
were positive for M. tuberculosis based on the GeneXpert MTB/RIF
test without evidence of rifampin resistance.",47,23,1 month,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,4.5,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2B,26 July 2025,Nuerteye,Nuerteye,Taxonomic composition of the fecal microbiota of TB patients and healthy controls. Barplot depicting top bacterial species (LDA scores > 4.5) discriminating between groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis",3379134|976|200643|171549|815|909656|357276;3379134|1224|1236|91347|543|561|562;3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|909932|909929|1843491|158846|437897,Complete,NA
bsdb:38440790/1/2,38440790,case-control,38440790,10.3389/fcimb.2024.1331521,NA,"Yunusbaeva M., Borodina L., Terentyeva D., Bogdanova A., Zakirova A., Bulatov S., Altinbaev R., Bilalov F. , Yunusbayev B.",Excess fermentation and lactic acidosis as detrimental functions of the gut microbes in treatment-naive TB patients,Frontiers in cellular and infection microbiology,2024,"anaerobic fermentation, dysbiosis, gut microbiome, gut-derived lactic acidosis, tuberculosis",Experiment 1,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,healthy controls (HCs),Treatment‑naïve tuberculosis (TB) patients,"pulmonary TB as confirmed by chest radiography and a positive sputum smear or
were positive for M. tuberculosis based on the GeneXpert MTB/RIF
test without evidence of rifampin resistance.",47,23,1 month,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,4.5,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2B,26 July 2025,Nuerteye,Nuerteye,Taxonomic composition of the fecal microbiota of TB patients and healthy controls. Barplot depicting top bacterial species (LDA scores > 4.5) discriminating between groups.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola",3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|815|909656|310298,Complete,NA
bsdb:38446304/1/1,38446304,laboratory experiment,38446304,10.1007/s10620-024-08334-8,NA,"Wang H., Zhao D., Wang S., Liu H., Zhao S., Li Z., Qin X. , Liu X.",Gastrointestinal Characteristics of Constipation from the Perspectives of Microbiome and Metabolome,Digestive diseases and sciences,2024,"Constipation, Correlation networks, Diagnose, Fecal metabolomics, Intestinal microbiota",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Constipation,HP:0002019,Negative Control,Constipation Group,"The Constipation Group were Sprague–Dawley male rats that had a constipation-like phenotype induced by intragastrical administration of white vinegar and activated carbon-cold water for 5 weeks. 

The diagnostic Criteria are:
1. Longer gastrointestinal transit time: Rats with constipation-like phenotype took significantly longer to complete gastrointestinal propulsion compared to controls.
2. Reduced small intestinal propulsion rate: The propulsion rate of the small intestine was significantly lower in constipated rats.
3. Decreased defecation frequency and volume: The frequency and amount of defecation were significantly reduced, mimicking clinical constipation symptoms in humans.",4,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,increased,increased,increased,increased,NA,increased,Signature 1,Figures 2B and 2D,20 March 2025,Thelee98,"Thelee98,MyleeeA",Represents the LDA Effect Size (LEfSe) analysis results comparing the Negative Control and Constipation Group.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|201174|84998|1643822|1643826|447020;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|186802|216572|1263;1783272|1239|909932|1843489|31977,Complete,KateRasheed
bsdb:38446304/1/2,38446304,laboratory experiment,38446304,10.1007/s10620-024-08334-8,NA,"Wang H., Zhao D., Wang S., Liu H., Zhao S., Li Z., Qin X. , Liu X.",Gastrointestinal Characteristics of Constipation from the Perspectives of Microbiome and Metabolome,Digestive diseases and sciences,2024,"Constipation, Correlation networks, Diagnose, Fecal metabolomics, Intestinal microbiota",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Constipation,HP:0002019,Negative Control,Constipation Group,"The Constipation Group were Sprague–Dawley male rats that had a constipation-like phenotype induced by intragastrical administration of white vinegar and activated carbon-cold water for 5 weeks. 

The diagnostic Criteria are:
1. Longer gastrointestinal transit time: Rats with constipation-like phenotype took significantly longer to complete gastrointestinal propulsion compared to controls.
2. Reduced small intestinal propulsion rate: The propulsion rate of the small intestine was significantly lower in constipated rats.
3. Decreased defecation frequency and volume: The frequency and amount of defecation were significantly reduced, mimicking clinical constipation symptoms in humans.",4,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,increased,increased,increased,increased,NA,increased,Signature 2,Figures 2B and 2D,20 March 2025,Thelee98,"Thelee98,MyleeeA,KateRasheed",Represents the LDA Effect Size (LEfSe) analysis results comparing the Negative Control and Constipation Group.,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,p__Candidatus Saccharimonadota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral clone CW040,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae",1783272|201174;1783272|201174|84998|1643822|1643826|447020;1783272|1239|186801|186802|186806|264995;1783272|1239|91061;3379134|1224|28211|204458|76892|41275;95818;3379134|1224|28211|204458|76892;3379134|1224|28211|204458;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|186801|186802|186806;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|3082720|186804;95818|163601;1783272|1239|526524|526525|2810281|191303;1783272|1239|526524|526525|2810281,Complete,KateRasheed
bsdb:38459054/1/1,38459054,"cross-sectional observational, not case-control",38459054,10.1038/s41598-024-54782-7,NA,"García-Gamboa R., Díaz-Torres O., Senés-Guerrero C., Gradilla-Hernández M.S., Moya A., Pérez-Brocal V., Garcia-Gonzalez A. , González-Avila M.",Associations between bacterial and fungal communities in the human gut microbiota and their implications for nutritional status and body weight,Scientific reports,2024,"Candida, Bacillota/Bacteroidota (Firmicutes/Bacteroidetes) ratio, Gut bacteriota, Gut dysbiosis, Gut mycobiota, Obesity",Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Overweight body mass index status,EFO:0005935,Healthy-weight group,Overweight group,Individuals displaying BMIs (body mass index) between 25.0 and 29.9,10,10,3 months,16S,34,Illumina,relative abundances,Linear Discriminant Analysis,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3a,7 March 2025,Tosin,Tosin,Statistically significant bacterial genera between overweight and healthy-weight groups by Volcano plots.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor",1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|186802|216572|946234,Complete,KateRasheed
bsdb:38459054/1/2,38459054,"cross-sectional observational, not case-control",38459054,10.1038/s41598-024-54782-7,NA,"García-Gamboa R., Díaz-Torres O., Senés-Guerrero C., Gradilla-Hernández M.S., Moya A., Pérez-Brocal V., Garcia-Gonzalez A. , González-Avila M.",Associations between bacterial and fungal communities in the human gut microbiota and their implications for nutritional status and body weight,Scientific reports,2024,"Candida, Bacillota/Bacteroidota (Firmicutes/Bacteroidetes) ratio, Gut bacteriota, Gut dysbiosis, Gut mycobiota, Obesity",Experiment 1,Mexico,Homo sapiens,Feces,UBERON:0001988,Overweight body mass index status,EFO:0005935,Healthy-weight group,Overweight group,Individuals displaying BMIs (body mass index) between 25.0 and 29.9,10,10,3 months,16S,34,Illumina,relative abundances,Linear Discriminant Analysis,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 3a,8 March 2025,Tosin,Tosin,Statistically significant bacterial genera between overweight and healthy-weight groups by Volcano plots.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Histophilus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella",1783272|1239|186801|186802|216572|216851;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712|214906;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|186802|216572|596767;1783272|1239|186801|3085636|186803|28050;3379134|976|200643|171549|171550|28138,Complete,KateRasheed
bsdb:38459054/2/1,38459054,"cross-sectional observational, not case-control",38459054,10.1038/s41598-024-54782-7,NA,"García-Gamboa R., Díaz-Torres O., Senés-Guerrero C., Gradilla-Hernández M.S., Moya A., Pérez-Brocal V., Garcia-Gonzalez A. , González-Avila M.",Associations between bacterial and fungal communities in the human gut microbiota and their implications for nutritional status and body weight,Scientific reports,2024,"Candida, Bacillota/Bacteroidota (Firmicutes/Bacteroidetes) ratio, Gut bacteriota, Gut dysbiosis, Gut mycobiota, Obesity",Experiment 2,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Healthy-weight group,Obese group,Individuals with BMIs (body mass index) in the range of 30.0–34.9,10,10,3 months,16S,34,Illumina,relative abundances,Linear Discriminant Analysis,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3b,8 March 2025,Tosin,Tosin,Statistically significant bacterial genera between the obese and healthy-weight groups by Volcano plots.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma",1783272|1239|909932|1843489|31977|209879;1783272|1239|186801|186802|216572|292632;1783272|1239|526524|526525|128827|1472649,Complete,KateRasheed
bsdb:38459054/2/2,38459054,"cross-sectional observational, not case-control",38459054,10.1038/s41598-024-54782-7,NA,"García-Gamboa R., Díaz-Torres O., Senés-Guerrero C., Gradilla-Hernández M.S., Moya A., Pérez-Brocal V., Garcia-Gonzalez A. , González-Avila M.",Associations between bacterial and fungal communities in the human gut microbiota and their implications for nutritional status and body weight,Scientific reports,2024,"Candida, Bacillota/Bacteroidota (Firmicutes/Bacteroidetes) ratio, Gut bacteriota, Gut dysbiosis, Gut mycobiota, Obesity",Experiment 2,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Healthy-weight group,Obese group,Individuals with BMIs (body mass index) in the range of 30.0–34.9,10,10,3 months,16S,34,Illumina,relative abundances,Linear Discriminant Analysis,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 3b,8 March 2025,Tosin,Tosin,Statistically significant bacterial genera between the obese and healthy-weight groups by Volcano plots.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Histophilus",3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|28050;3379134|976|200643|171549|171550|28138;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|3085636|186803|248744;3379134|1224|1236|135625|712|214906,Complete,KateRasheed
bsdb:38459054/3/1,38459054,"cross-sectional observational, not case-control",38459054,10.1038/s41598-024-54782-7,NA,"García-Gamboa R., Díaz-Torres O., Senés-Guerrero C., Gradilla-Hernández M.S., Moya A., Pérez-Brocal V., Garcia-Gonzalez A. , González-Avila M.",Associations between bacterial and fungal communities in the human gut microbiota and their implications for nutritional status and body weight,Scientific reports,2024,"Candida, Bacillota/Bacteroidota (Firmicutes/Bacteroidetes) ratio, Gut bacteriota, Gut dysbiosis, Gut mycobiota, Obesity",Experiment 3,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Overweight group,Obese group,Individuals with BMIs (body mass index) in the range of 30.0–34.9.,10,10,3 months,16S,34,Illumina,relative abundances,Linear Discriminant Analysis,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3c,8 March 2025,Tosin,Tosin,Statistically significant bacterial genera between the obese and overweight groups by Volcano plots.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia",1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3082720|186804|1501226,Complete,KateRasheed
bsdb:38459054/3/2,38459054,"cross-sectional observational, not case-control",38459054,10.1038/s41598-024-54782-7,NA,"García-Gamboa R., Díaz-Torres O., Senés-Guerrero C., Gradilla-Hernández M.S., Moya A., Pérez-Brocal V., Garcia-Gonzalez A. , González-Avila M.",Associations between bacterial and fungal communities in the human gut microbiota and their implications for nutritional status and body weight,Scientific reports,2024,"Candida, Bacillota/Bacteroidota (Firmicutes/Bacteroidetes) ratio, Gut bacteriota, Gut dysbiosis, Gut mycobiota, Obesity",Experiment 3,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Overweight group,Obese group,Individuals with BMIs (body mass index) in the range of 30.0–34.9.,10,10,3 months,16S,34,Illumina,relative abundances,Linear Discriminant Analysis,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 3c,8 March 2025,Tosin,Tosin,Statistically significant bacterial genera between the obese and overweight groups by Volcano plots.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor",3379134|976|200643|171549|171552|1283313;1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|186802|216572|946234,Complete,KateRasheed
bsdb:38459054/4/1,38459054,"cross-sectional observational, not case-control",38459054,10.1038/s41598-024-54782-7,NA,"García-Gamboa R., Díaz-Torres O., Senés-Guerrero C., Gradilla-Hernández M.S., Moya A., Pérez-Brocal V., Garcia-Gonzalez A. , González-Avila M.",Associations between bacterial and fungal communities in the human gut microbiota and their implications for nutritional status and body weight,Scientific reports,2024,"Candida, Bacillota/Bacteroidota (Firmicutes/Bacteroidetes) ratio, Gut bacteriota, Gut dysbiosis, Gut mycobiota, Obesity",Experiment 4,Mexico,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Healthy-weight group,Obese group,Individuals with BMIs (body mass index) in the range of 30.0–34.9,10,10,3 months,16S,34,Illumina,relative abundances,Linear Discriminant Analysis,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3d,8 March 2025,Tosin,Tosin,Statistically significant fungal genera between the obese and healthy-weight groups by Volcano plots.,increased,"k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia",4751|4890|147545|5042|1131492|5052;4751|5204|1538075|162474|742845|55193,Complete,KateRasheed
bsdb:38459431/1/1,38459431,prospective cohort,38459431,10.1186/s12866-024-03230-7,NA,"Fang L., Tuohuti A., Cai W. , Chen X.",Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study,BMC microbiology,2024,"16S rRNA sequencing, Biomarker, Microbiome, Pediatric OSA, Upper airway",Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,Obstructive sleep apnea,EFO:0003918,"Combination of non-OSA group B(surface of palatine tonsil), C (palatine tonsillar capsule after tonsillectomy) and D (adenoid: nasopharynx site)",Non-OSA group A (oropharynx site),Participants (children) with obstructive apnea hypopnea index [OAHI] categorized into severity (< 1 events/h) whose sample was obtained from the tongue base (oropharynx site).,NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,1 November 2024,Tosin,"Tosin,WikiWorks","Species differentially abundant in non- OSA group A(mucosa of the patient’s tongue base: oropharynx site), B(surface of palatine tonsil), C( palatine tonsillar capsule after tonsillectomy) and D(adenoid :nasopharynx site).",increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:38459431/1/2,38459431,prospective cohort,38459431,10.1186/s12866-024-03230-7,NA,"Fang L., Tuohuti A., Cai W. , Chen X.",Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study,BMC microbiology,2024,"16S rRNA sequencing, Biomarker, Microbiome, Pediatric OSA, Upper airway",Experiment 1,China,Homo sapiens,Throat,UBERON:0000341,Obstructive sleep apnea,EFO:0003918,"Combination of non-OSA group B(surface of palatine tonsil), C (palatine tonsillar capsule after tonsillectomy) and D (adenoid: nasopharynx site)",Non-OSA group A (oropharynx site),Participants (children) with obstructive apnea hypopnea index [OAHI] categorized into severity (< 1 events/h) whose sample was obtained from the tongue base (oropharynx site).,NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5A,1 November 2024,Tosin,"Tosin,WikiWorks","Species differentially abundant in non- OSA group A(mucosa of the patient’s tongue base: oropharynx site), B(surface of palatine tonsil), C( palatine tonsillar capsule after tonsillectomy) and D(adenoid :nasopharynx site).",decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",3384189|32066|203490;3379134|203691|203692|136|2845253|157,Complete,Svetlana up
bsdb:38459431/2/1,38459431,prospective cohort,38459431,10.1186/s12866-024-03230-7,NA,"Fang L., Tuohuti A., Cai W. , Chen X.",Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study,BMC microbiology,2024,"16S rRNA sequencing, Biomarker, Microbiome, Pediatric OSA, Upper airway",Experiment 2,China,Homo sapiens,Throat,UBERON:0000341,Obstructive sleep apnea,EFO:0003918,Non Obstructive sleep apnea (OSA),Obstructive sleep apnea (OSA),"Participants (Children)with Obstructive sleep apnea categorized into mild OSA (OAHI, 1–5 events/h), moderate OSA (OAHI, 6–10 events/h), and severe OSA (OAHI>10 events/h).",10,30,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5E,1 November 2024,MyleeeA,"MyleeeA,WikiWorks",Species differentially abundant in the Obstructive Sleep Apnea (OSA) group and the Non-Obstructive Sleep Apnea group (OSA),increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,3379134|976|200643|171549|171552|1283313,Complete,Svetlana up
bsdb:38459431/2/2,38459431,prospective cohort,38459431,10.1186/s12866-024-03230-7,NA,"Fang L., Tuohuti A., Cai W. , Chen X.",Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study,BMC microbiology,2024,"16S rRNA sequencing, Biomarker, Microbiome, Pediatric OSA, Upper airway",Experiment 2,China,Homo sapiens,Throat,UBERON:0000341,Obstructive sleep apnea,EFO:0003918,Non Obstructive sleep apnea (OSA),Obstructive sleep apnea (OSA),"Participants (Children)with Obstructive sleep apnea categorized into mild OSA (OAHI, 1–5 events/h), moderate OSA (OAHI, 6–10 events/h), and severe OSA (OAHI>10 events/h).",10,30,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5E,1 November 2024,MyleeeA,"MyleeeA,WikiWorks",Species differentially abundant in the Obstructive Sleep Apnea (OSA) group and the Non-Obstructive Sleep Apnea group (OSA),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",3379134|1224|28216|206351|481|482;3379134|1224|1236|135625|712|724,Complete,Svetlana up
bsdb:38459431/3/1,38459431,prospective cohort,38459431,10.1186/s12866-024-03230-7,NA,"Fang L., Tuohuti A., Cai W. , Chen X.",Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study,BMC microbiology,2024,"16S rRNA sequencing, Biomarker, Microbiome, Pediatric OSA, Upper airway",Experiment 3,China,Homo sapiens,Throat,UBERON:0000341,Obstructive sleep apnea,EFO:0003918,"Combination of Mild OSA group B(surface of palatine tonsil), C(palatine tonsillar capsule after tonsillectomy) and D(adenoid: nasopharynx site)",Mild OSA group A (oropharynx site),Participants (children) with obstructive apnea hypopnea index [OAHI] categorized into severity (1–5 events/h) whose sample was obtained from the tongue base (oropharynx site).,NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5B,1 November 2024,Tosin,"Tosin,Aleru Divine,WikiWorks","Species differentially abundant in Mild OSA group A(mucosa of the patient’s tongue base: oropharynx site), B(surface of palatine tonsil), C( palatine tonsillar capsule after tonsillectomy) and D(adenoid :nasopharynx site).",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",1783272|1239|909932|1843489|31977|29465;3379134|1224|28216|206351|481|482,Complete,Svetlana up
bsdb:38459431/3/2,38459431,prospective cohort,38459431,10.1186/s12866-024-03230-7,NA,"Fang L., Tuohuti A., Cai W. , Chen X.",Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study,BMC microbiology,2024,"16S rRNA sequencing, Biomarker, Microbiome, Pediatric OSA, Upper airway",Experiment 3,China,Homo sapiens,Throat,UBERON:0000341,Obstructive sleep apnea,EFO:0003918,"Combination of Mild OSA group B(surface of palatine tonsil), C(palatine tonsillar capsule after tonsillectomy) and D(adenoid: nasopharynx site)",Mild OSA group A (oropharynx site),Participants (children) with obstructive apnea hypopnea index [OAHI] categorized into severity (1–5 events/h) whose sample was obtained from the tongue base (oropharynx site).,NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5B,1 November 2024,Tosin,"Tosin,Aleru Divine,WikiWorks","Species differentially abundant in Mild OSA group A(mucosa of the patient’s tongue base: oropharynx site), B(surface of palatine tonsil), C( palatine tonsillar capsule after tonsillectomy) and D(adenoid :nasopharynx site).",decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",3384189|32066|203490|203491|203492|848;3379134|203691|203692|136|2845253|157,Complete,Svetlana up
bsdb:38459431/4/1,38459431,prospective cohort,38459431,10.1186/s12866-024-03230-7,NA,"Fang L., Tuohuti A., Cai W. , Chen X.",Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study,BMC microbiology,2024,"16S rRNA sequencing, Biomarker, Microbiome, Pediatric OSA, Upper airway",Experiment 4,China,Homo sapiens,Throat,UBERON:0000341,Obstructive sleep apnea,EFO:0003918,"Non-OSA, mild OSA and severe OSA",Moderate OSA,"Participants (Children) in the moderate OSA group were categorized based on (OAHI, 6–10 events/h)",30,10,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5f,1 November 2024,MyleeeA,"MyleeeA,WikiWorks","Species differentially abundant in the Moderate Obstructive Sleep Apnea (OSA) group and the None, Mild and Severe Obstructive Sleep Apnea groups (OSA)",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",3379134|1224|1236|135625|712|724;3379134|1224|28216|206351|481|482,Complete,Svetlana up
bsdb:38459431/5/1,38459431,prospective cohort,38459431,10.1186/s12866-024-03230-7,NA,"Fang L., Tuohuti A., Cai W. , Chen X.",Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study,BMC microbiology,2024,"16S rRNA sequencing, Biomarker, Microbiome, Pediatric OSA, Upper airway",Experiment 5,China,Homo sapiens,Throat,UBERON:0000341,Obstructive sleep apnea,EFO:0003918,"Combination of Moderate OSA group B(surface of palatine tonsil), C(palatine tonsillar capsule after tonsillectomy) and D(adenoid: nasopharynx site)",Moderate OSA group A (oropharynx site),Participants (children) with obstructive apnea hypopnea index [OAHI] categorized into severity (6–10 events/h) whose sample was obtained from the tongue base (oropharynx site)(Part A).,NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5C,2 November 2024,Tosin,"Tosin,WikiWorks","Species differentially abundant in Moderate OSA group A(mucosa of the patient’s tongue base: oropharynx site), B(surface of palatine tonsil), C( palatine tonsillar capsule after tonsillectomy) and D(adenoid :nasopharynx site).",increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:38459431/6/1,38459431,prospective cohort,38459431,10.1186/s12866-024-03230-7,NA,"Fang L., Tuohuti A., Cai W. , Chen X.",Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study,BMC microbiology,2024,"16S rRNA sequencing, Biomarker, Microbiome, Pediatric OSA, Upper airway",Experiment 6,China,Homo sapiens,Throat,UBERON:0000341,Obstructive sleep apnea,EFO:0003918,"Combination of Severe OSA group B(surface of palatine tonsil), C(palatine tonsillar capsule after tonsillectomy) and D(adenoid: nasopharynx site)",Severe OSA group A (oropharynx site).,"Participants (children) with obstructive apnea hypopnea index [OAHI], severity > 10 events/h whose sample was obtained from tongue base (oropharynx site)(Part A).",NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5D,2 November 2024,Tosin,"Tosin,WikiWorks","Species differentially abundant in Severe OSA group A(mucosa of the patient’s tongue base: oropharynx site), B(surface of palatine tonsil), C( palatine tonsillar capsule after tonsillectomy) and D(adenoid :nasopharynx site).",increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:38459431/6/2,38459431,prospective cohort,38459431,10.1186/s12866-024-03230-7,NA,"Fang L., Tuohuti A., Cai W. , Chen X.",Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study,BMC microbiology,2024,"16S rRNA sequencing, Biomarker, Microbiome, Pediatric OSA, Upper airway",Experiment 6,China,Homo sapiens,Throat,UBERON:0000341,Obstructive sleep apnea,EFO:0003918,"Combination of Severe OSA group B(surface of palatine tonsil), C(palatine tonsillar capsule after tonsillectomy) and D(adenoid: nasopharynx site)",Severe OSA group A (oropharynx site).,"Participants (children) with obstructive apnea hypopnea index [OAHI], severity > 10 events/h whose sample was obtained from tongue base (oropharynx site)(Part A).",NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5D,2 November 2024,Tosin,"Tosin,WikiWorks","Species differentially abundant in Severe OSA group A(mucosa of the patient’s tongue base: oropharynx site), B(surface of palatine tonsil), C( palatine tonsillar capsule after tonsillectomy) and D(adenoid :nasopharynx site).",decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,1783272|201174|1760|85007|1653|1716,Complete,Svetlana up
bsdb:38459431/7/1,38459431,prospective cohort,38459431,10.1186/s12866-024-03230-7,NA,"Fang L., Tuohuti A., Cai W. , Chen X.",Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study,BMC microbiology,2024,"16S rRNA sequencing, Biomarker, Microbiome, Pediatric OSA, Upper airway",Experiment 7,China,Homo sapiens,Throat,UBERON:0000341,Obstructive sleep apnea,EFO:0003918,Non OSA group B,"Combination of Mild OSA group B, Moderate OSA group B and Severe OSA group B.","Patients in the Mild, Moderate and Severe groups who completed the collection of oral microbiota samples in surface of palatine tonsils (Part B).",NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S5B,2 November 2024,Tosin,"Tosin,WikiWorks","The differences in the relative abundance of key bacterias among four groups (None, Mild, Moderate, Severe) in surface of palatine tonsils (Part B).",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",3379134|1224|1236|135625|712|724;3379134|1224|28216|206351|481|482;3379134|203691|203692|136|2845253|157,Complete,Svetlana up
bsdb:38459431/8/1,38459431,prospective cohort,38459431,10.1186/s12866-024-03230-7,NA,"Fang L., Tuohuti A., Cai W. , Chen X.",Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study,BMC microbiology,2024,"16S rRNA sequencing, Biomarker, Microbiome, Pediatric OSA, Upper airway",Experiment 8,China,Homo sapiens,Throat,UBERON:0000341,Obstructive sleep apnea,EFO:0003918,Non OSA group C,"Combination of Mild OSA group C, Moderate OSA group C and Severe OSA group C.","Patients in the Mild, Moderate and Severe groups who completed the collection of oral microbiota samples in palatine tonsillar capsule after tonsillectomy (Part C).",NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S5C,2 November 2024,Tosin,"Tosin,WikiWorks","The differences in the relative abundance of key bacterias among four groups (None, Mild, Moderate, Severe) in palatine tonsillar capsule after tonsillectomy (Part C).",decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:38459431/9/1,38459431,prospective cohort,38459431,10.1186/s12866-024-03230-7,NA,"Fang L., Tuohuti A., Cai W. , Chen X.",Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study,BMC microbiology,2024,"16S rRNA sequencing, Biomarker, Microbiome, Pediatric OSA, Upper airway",Experiment 9,China,Homo sapiens,Throat,UBERON:0000341,Obstructive sleep apnea,EFO:0003918,Preoperative Severe OSA patients,Postoperative Severe OSA patients,Patients who completed the collection of oral microbiota samples in tongue base (oropharynx site) after surgery one month after undergoing adeno-tonsillectomy,NA,NA,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 6F,2 November 2024,MyleeeA,"MyleeeA,WikiWorks",Species differentially abundant in the Preoperative Severe Obstructive Sleep Apnea (OSA) patient and Postoperative Severe Obstructive Sleep Apnea (OSA) patients.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",3379134|976|200643|171549|171551|836;3379134|203691|203692|136|2845253|157,Complete,Svetlana up
bsdb:38459431/9/2,38459431,prospective cohort,38459431,10.1186/s12866-024-03230-7,NA,"Fang L., Tuohuti A., Cai W. , Chen X.",Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study,BMC microbiology,2024,"16S rRNA sequencing, Biomarker, Microbiome, Pediatric OSA, Upper airway",Experiment 9,China,Homo sapiens,Throat,UBERON:0000341,Obstructive sleep apnea,EFO:0003918,Preoperative Severe OSA patients,Postoperative Severe OSA patients,Patients who completed the collection of oral microbiota samples in tongue base (oropharynx site) after surgery one month after undergoing adeno-tonsillectomy,NA,NA,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 6F,28 November 2024,MyleeeA,"MyleeeA,WikiWorks",Species differentially abundant in the Preoperative Severe Obstructive Sleep Apnea (OSA) patient and Postoperative Severe Obstructive Sleep Apnea (OSA) patients.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,3379134|1224|1236|2887326|468|475,Complete,Svetlana up
bsdb:38459431/10/1,38459431,prospective cohort,38459431,10.1186/s12866-024-03230-7,NA,"Fang L., Tuohuti A., Cai W. , Chen X.",Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study,BMC microbiology,2024,"16S rRNA sequencing, Biomarker, Microbiome, Pediatric OSA, Upper airway",Experiment 10,China,Homo sapiens,Throat,UBERON:0000341,Obstructive sleep apnea,EFO:0003918,Non Obstructive sleep apnea (OSA),Obstructive sleep apnea (OSA) Severe,Participants (Children) with Obstructive sleep apnea categorized into severe OSA (OAHI>10 events/h).,10,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 7C,3 November 2024,MyleeeA,"MyleeeA,WikiWorks",Species differentially abundant in the Obstructive sleep apnea (OSA) Severe and None Obstructive sleep apnea (OSA) patients.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Alcanivoracaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Alcanivoracaceae|g__Alcanivorax,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Flectobacillaceae|g__Arcicella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Devosia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hydrogenophaga,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Legionellaceae|g__Legionella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Legionellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae|g__Opitutus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Ornithinimicrobiaceae|g__Ornithinimicrobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Pseudochrobactrum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Pseudoxanthomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Rhodocista,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax,k__Pseudomonadati|p__Verrucomicrobiota",3379134|1224|28211|3120395|433;3379134|1224|1236|135619|224372;3379134|1224|1236|135619|224372|59753;1783272|1239|91061|1385|186823;3379134|976|768503|768507|3141701|217140;1783272|201174|1760|85006|85020|43668;3379134|1224|28211|356|118882;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85006|85020;3379134|1224|28211|356|2831106|46913;3379134|1224|28216|80840|80864|47420;3379134|1224|1236|118969|444|445;3379134|1224|1236|118969|444;3379134|1224|1236|118969;1783272|544448|31969;1783272|544448|31969|2085|2092|2093;1783272|544448|31969|2085|2092;1783272|544448|31969|2085;1783272|544448;3379134|74201|414999|415000|134623;3379134|74201|414999|415000;3379134|74201|414999|415000|134623|178440;1783272|201174|1760|85006|2805590|125287;3379134|1224|28211|356|118882|354349;3379134|1224|1236|135614|32033|83618;3379134|1224|28211|204441|2829815|34023;1783272|201174|84998|1643822|1643826|84108;3379134|1224|28216|80840|80864|34072;3379134|74201,Complete,Svetlana up
bsdb:38459431/10/2,38459431,prospective cohort,38459431,10.1186/s12866-024-03230-7,NA,"Fang L., Tuohuti A., Cai W. , Chen X.",Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study,BMC microbiology,2024,"16S rRNA sequencing, Biomarker, Microbiome, Pediatric OSA, Upper airway",Experiment 10,China,Homo sapiens,Throat,UBERON:0000341,Obstructive sleep apnea,EFO:0003918,Non Obstructive sleep apnea (OSA),Obstructive sleep apnea (OSA) Severe,Participants (Children) with Obstructive sleep apnea categorized into severe OSA (OAHI>10 events/h).,10,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 7C,3 November 2024,MyleeeA,"MyleeeA,WikiWorks",Species differentially abundant in the Obstructive sleep apnea (OSA) Severe and None Obstructive sleep apnea (OSA) patients.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum",3379134|1224|28216|206351|481|538;3379134|1224|28216|80840|119060|47670;3379134|1224|1236|2887326|468|475;1783272|201174|1760|85006|1268|32207;1783272|1239|186801|3085636|186803|1213720,Complete,Svetlana up
bsdb:38459431/11/1,38459431,prospective cohort,38459431,10.1186/s12866-024-03230-7,NA,"Fang L., Tuohuti A., Cai W. , Chen X.",Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study,BMC microbiology,2024,"16S rRNA sequencing, Biomarker, Microbiome, Pediatric OSA, Upper airway",Experiment 11,China,Homo sapiens,Throat,UBERON:0000341,Obstructive sleep apnea,EFO:0003918,Non Obstructive sleep apnea (OSA),Obstructive sleep apnea (OSA) Mild,Participants (children) with obstructive apnea hypopnea index [OAHI] categorized into severity (1–5 events/h).,10,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S7A,3 November 2024,Tosin,"Tosin,WikiWorks",Species differentially abundant in the non-Obstructive sleep apnea (OSA) and Obstructive sleep apnea (OSA) Mild patients.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Altererythrobacter,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Curvibacter,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Schwartzia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae|g__Rheinheimera,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia,k__Pseudomonadati|p__Spirochaetota,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",3379134|1224|28211|204457|335929|361177;3379134|200940|3031449|213115|194924|872;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|526524|526525|128827|118747;3379134|1224|28216|80840|80864|281915;28221;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;3379134|1224|28216|206351|481|538;3379134|1224|28211|204457|335929;1783272|1239|186801|3082720|3118655|44259;1783272|201174|1760|85009|85015;1783272|201174|1760|85009|85015|1839;3379134|1224|28211|204457|41297|165696;3379134|1224|1236|91347|1903414|583;1783272|1239|909932|909929|1843491|55506;3379134|1224|1236|135613|1046;3379134|1224|1236|135613;3379134|976|200643|171549|171552|1283313;3379134|1224|1236|135613|1046|67575;3379134|203691|203692|136;3379134|203691|203692;3379134|203691;3379134|203691|203692|136|137;3379134|203691|203692|136|2845253|157,Complete,Svetlana up
bsdb:38459431/11/2,38459431,prospective cohort,38459431,10.1186/s12866-024-03230-7,NA,"Fang L., Tuohuti A., Cai W. , Chen X.",Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study,BMC microbiology,2024,"16S rRNA sequencing, Biomarker, Microbiome, Pediatric OSA, Upper airway",Experiment 11,China,Homo sapiens,Throat,UBERON:0000341,Obstructive sleep apnea,EFO:0003918,Non Obstructive sleep apnea (OSA),Obstructive sleep apnea (OSA) Mild,Participants (children) with obstructive apnea hypopnea index [OAHI] categorized into severity (1–5 events/h).,10,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S7A,3 November 2024,Tosin,"Tosin,WikiWorks",Species differentially abundant in the non-Obstructive sleep apnea (OSA) and Obstructive sleep apnea (OSA) Mild participants.,decreased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax",3379134|1224;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|1224|1236|135625|712|724;3379134|1224|28216;3379134|1224|28216|206351;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481;3379134|1224|1236;1783272|1239|91061;1783272|1239|91061|186826;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300;1783272|201174|1760|2037;33090|35493|3398|72025|3803|3814|508215;1783272|201174|1760|85006|1268;3379134|976|117743|200644;3379134|976|117743;3379134|976|117743|200644|49546;3379134|976|117743|200644|49546|1016;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|3082720|543314|109326,Complete,Svetlana up
bsdb:38459431/12/1,38459431,prospective cohort,38459431,10.1186/s12866-024-03230-7,NA,"Fang L., Tuohuti A., Cai W. , Chen X.",Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study,BMC microbiology,2024,"16S rRNA sequencing, Biomarker, Microbiome, Pediatric OSA, Upper airway",Experiment 12,China,Homo sapiens,Throat,UBERON:0000341,Obstructive sleep apnea,EFO:0003918,Non Obstructive sleep apnea (OSA),Obstructive sleep apnea (OSA) Moderate,Participants (children) with obstructive apnea hypopnea index [OAHI] severity 6-10 events/h.,10,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S7B,3 November 2024,Tosin,"Tosin,WikiWorks",Species differentially abundant in the non-Obstructive sleep apnea (OSA) and Obstructive sleep apnea (OSA) Moderate participants.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Cellulomonadaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Cellulomonadaceae|g__Cellulomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae|g__Rheinheimera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Rubellimicrobium,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|526524|526525|128827|118747;1783272|201174|1760|85006|85016;1783272|201174|1760|85006|85016|1707;3379134|1224|1236|135613|1046;3379134|1224|1236|135613;1783272|1239|186801|3085636|186803;3379134|1224|28211|204457|41297|165696;1783272|1239|186801|186802|216572|459786;3379134|1224|1236|135613|1046|67575;1783272|1239|186801|3085636|186803|841;3379134|1224|28211|204455|2854170|295418;3379134|74201;1783272|1239|186801|186802|216572|1263,Complete,Svetlana up
bsdb:38459431/12/2,38459431,prospective cohort,38459431,10.1186/s12866-024-03230-7,NA,"Fang L., Tuohuti A., Cai W. , Chen X.",Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study,BMC microbiology,2024,"16S rRNA sequencing, Biomarker, Microbiome, Pediatric OSA, Upper airway",Experiment 12,China,Homo sapiens,Throat,UBERON:0000341,Obstructive sleep apnea,EFO:0003918,Non Obstructive sleep apnea (OSA),Obstructive sleep apnea (OSA) Moderate,Participants (children) with obstructive apnea hypopnea index [OAHI] severity 6-10 events/h.,10,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S7B,3 November 2024,Tosin,"Tosin,WikiWorks",Species differentially abundant in the non-Obstructive sleep apnea (OSA) and Obstructive sleep apnea (OSA) Moderate participants.,decreased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae",3379134|1224;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|1224|1236|135625|712|724;3379134|1224|28216;3379134|1224|28216|206351;3379134|1224|28216|206351|481;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171551;3384189|32066|203490|203491|1129771|32067;3379134|976|117743|200644|49546|1016;3379134|1224|28216|80840|119060,Complete,Svetlana up
bsdb:38459431/13/1,38459431,prospective cohort,38459431,10.1186/s12866-024-03230-7,NA,"Fang L., Tuohuti A., Cai W. , Chen X.",Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study,BMC microbiology,2024,"16S rRNA sequencing, Biomarker, Microbiome, Pediatric OSA, Upper airway",Experiment 13,China,Homo sapiens,Throat,UBERON:0000341,Obstructive sleep apnea,EFO:0003918,Non OSA ( Postoperative),"Mild OSA, Moderate OSA and severe OSA (Postoperative)","Patients in the Mild, Moderate and Severe groups who completed the collection of oral microbiota samples in tongue base (oropharynx site) one month after undergoing adeno-tonsillectomy.",NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6B,4 November 2024,MyleeeA,"MyleeeA,WikiWorks","Genus abundance of predominant bacteria between the Non-Obstructive sleep apnea (OSA) and Obstructive sleep apnea (OSA) Mild, Moderate and Severe in the postoperative groups.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|1224|28216|206351|481|482;1783272|1239|909932|1843489|31977|29465;3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:38459431/13/2,38459431,prospective cohort,38459431,10.1186/s12866-024-03230-7,NA,"Fang L., Tuohuti A., Cai W. , Chen X.",Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study,BMC microbiology,2024,"16S rRNA sequencing, Biomarker, Microbiome, Pediatric OSA, Upper airway",Experiment 13,China,Homo sapiens,Throat,UBERON:0000341,Obstructive sleep apnea,EFO:0003918,Non OSA ( Postoperative),"Mild OSA, Moderate OSA and severe OSA (Postoperative)","Patients in the Mild, Moderate and Severe groups who completed the collection of oral microbiota samples in tongue base (oropharynx site) one month after undergoing adeno-tonsillectomy.",NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6B,4 November 2024,MyleeeA,"MyleeeA,WikiWorks","Genus abundance of predominant bacteria between the Non-Obstructive sleep apnea (OSA) and Obstructive sleep apnea (OSA) Mild, Moderate and Severe in the postoperative groups.",decreased,"k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|203691|203692|136|2845253|157;3384189|32066|203490|203491|203492|848;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:38461361/1/1,38461361,"cross-sectional observational, not case-control",38461361,10.1038/s41598-024-56585-2,NA,"Mok K., Poolsawat T., Somnuk S., Wanikorn B., Patumcharoenpol P., Nitisinprasert S., Vongsangnak W. , Nakphaichit M.",Preliminary characterization of gut mycobiome enterotypes reveals the correlation trends between host metabolic parameter and diet: a case study in the Thai Cohort,Scientific reports,2024,NA,Experiment 1,Thailand,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Saccharomyces enterotype (enterotype SA),Aspergillus/Penicillium enterotype (enterotype AP/Pe),"Individuals whose gut mycobiome composition was dominated by Aspergillus and Penicillium genera, identified through hierarchical clustering of ITS2 fungal profiles.",15,45,3 months,ITS / ITS2,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,increased,increased,unchanged,NA,NA,NA,Signature 1,Figure 1b,21 July 2025,Ese,Ese,Results of linear discriminant analysis effect size (LEfSe) analysis showing specific taxa significantly abundant between Saccharomyces enterotype (enterotype SA) and Aspergillus/Penicillium enterotype (enterotype AP/Pe),increased,"k__Fungi|p__Basidiomycota|c__Agaricomycetes,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus,k__Fungi|p__Basidiomycota,k__Fungi|p__Basidiomycota|c__Cystobasidiomycetes,k__Fungi|p__Ascomycota|c__Dothideomycetes,k__Fungi|p__Ascomycota|c__Eurotiomycetes,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Penicillium,k__Fungi|p__Ascomycota|c__Sordariomycetes,k__Fungi|p__Basidiomycota|c__Tremellomycetes,k__Fungi|p__Basidiomycota|c__Ustilaginomycetes",4751|5204|155619;4751|4890|147545|5042|1131492|5052;4751|5204;4751|5204|432005;4751|4890|147541;4751|4890|147545;4751|4890|147545|5042|1131492|5073;4751|4890|147550;4751|5204|155616;4751|5204|5257,Complete,NA
bsdb:38461361/1/2,38461361,"cross-sectional observational, not case-control",38461361,10.1038/s41598-024-56585-2,NA,"Mok K., Poolsawat T., Somnuk S., Wanikorn B., Patumcharoenpol P., Nitisinprasert S., Vongsangnak W. , Nakphaichit M.",Preliminary characterization of gut mycobiome enterotypes reveals the correlation trends between host metabolic parameter and diet: a case study in the Thai Cohort,Scientific reports,2024,NA,Experiment 1,Thailand,Homo sapiens,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Saccharomyces enterotype (enterotype SA),Aspergillus/Penicillium enterotype (enterotype AP/Pe),"Individuals whose gut mycobiome composition was dominated by Aspergillus and Penicillium genera, identified through hierarchical clustering of ITS2 fungal profiles.",15,45,3 months,ITS / ITS2,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,increased,increased,unchanged,NA,NA,NA,Signature 2,Figure 1b,22 July 2025,Ese,Ese,Results of linear discriminant analysis effect size (LEfSe) analysis showing specific taxa significantly abundant between Saccharomyces enterotype (enterotype SA)  and Aspergillus/Penicillium enterotype (enterotype AP/Pe),decreased,"k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces,k__Fungi|p__Ascomycota|c__Saccharomycetes",4751|4890|4891|4892|4893|4930;4751|4890|4891,Complete,NA
bsdb:38468206/1/1,38468206,case-control,38468206,10.1186/s12866-024-03239-y,NA,"Watai K., Suda W., Kurokawa R., Sekiya K., Hayashi H., Iwata M., Nagayama K., Nakamura Y., Hamada Y., Kamide Y., Fukutomi Y., Nakabayashi T., Tanaka K., Kamita M., Taniguchi M. , Hattori M.",Metagenomic gut microbiome analysis of Japanese patients with multiple chemical sensitivity/idiopathic environmental intolerance,BMC microbiology,2024,"Central nervous system, Gut microbiome, Multiple chemical sensitivity, Shotgun metagenomic sequencing",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Multiple chemical sensitivity,EFO:0007382,Healthy Control (HC),Multiple Chemical Sensitivity (MCS),Japanese female patients with Multiple Chemical Sensitivity (MCS),24,30,6 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Fig. 2b, Fig. 3a, Fig. 4a, Additional File Fig. S1a",13 February 2025,Taofeecoh,"Taofeecoh,WikiWorks","Relative abundances of species that differed significantly between multiple chemical sensitivity (MCS, n = 30) patients and healthy controls (HC, n = 24).",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp. CAG:344,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis|s__Bifidobacterium animalis subsp. animalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:217,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:264,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:273,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:352,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister sp. CAG:357,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus durans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:192,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:202,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:251,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus delbrueckii|s__Lactobacillus delbrueckii subsp. jakobsenii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:177,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:254,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:57,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. JC304,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus lutetiensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. C150,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HSISS1,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp. CAG:933,k__Pseudomonadati|p__Verrucomicrobiota",1783272|201174|1760|2037|2049|1654;3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988|239934|239935;3379134|74201|203494|48461|1647988|239934|1262691;3379134|976|200643|171549|815|816|817;1783272|201174|1760|85004|31953|1678|28025|302912;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|186802|31979|1485|1262779;1783272|1239|186801|186802|31979|1485|1262786;1783272|1239|186801|186802|31979|1485|1262789;1783272|1239|186801|186802|31979|1485|1262798;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|909932|1843489|31977|39948|1262869;1783272|1239|91061|186826|81852|1350|53345;1783272|1239|186801|186802|186806|1730|1262883;1783272|1239|186801|186802|186806|1730|1262884;1783272|1239|186801|186802|186806|1730|1262886;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|1584|1537158;3379134|976|200643|171549|815|909656|357276;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|1263|1262952;1783272|1239|186801|186802|216572|1263|1262953;1783272|1239|186801|186802|216572|1263|1262962;1783272|1239|186801|186802|216572|1263|1095771;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|150055;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|1300|1301|435842;1783272|1239|91061|186826|1300|1301|1316410;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|91061|186826|1300|1301|1343;1783272|1239|526524|526525|2810280|3025755;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|1262980;3379134|74201,Complete,Svetlana up
bsdb:38468206/1/2,38468206,case-control,38468206,10.1186/s12866-024-03239-y,NA,"Watai K., Suda W., Kurokawa R., Sekiya K., Hayashi H., Iwata M., Nagayama K., Nakamura Y., Hamada Y., Kamide Y., Fukutomi Y., Nakabayashi T., Tanaka K., Kamita M., Taniguchi M. , Hattori M.",Metagenomic gut microbiome analysis of Japanese patients with multiple chemical sensitivity/idiopathic environmental intolerance,BMC microbiology,2024,"Central nervous system, Gut microbiome, Multiple chemical sensitivity, Shotgun metagenomic sequencing",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Multiple chemical sensitivity,EFO:0007382,Healthy Control (HC),Multiple Chemical Sensitivity (MCS),Japanese female patients with Multiple Chemical Sensitivity (MCS),24,30,6 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Fig. 2a, Fig. 3b, Fig. 4b, Additional File Fig. S1b",13 February 2025,Taofeecoh,"Taofeecoh,WikiWorks","Relative abundances of species that differed significantly between multiple chemical sensitivity (MCS, n = 30) patients and healthy controls (HC, n = 24).",decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. CAG:37,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:127,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:138,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister sp. CAG:486,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium duncaniae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas rupellensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium VE202-27,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens",1783272|201174;1783272|1239|186801|3085636|186803|572511|1262757;1783272|1239|186801|186802|31979|1485|1262774;1783272|1239|186801|186802|31979|1485|1262775;1783272|1239|909932|1843489|31977|39948|1262870;1783272|1239|186801|186802|216572|216851|411483;1783272|1239|186801|3085636|186803|1649459|154046;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|909929|1843491|158846|158847;1783272|1239|909932|909929|1843491|158846|491921;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|186802|1232457;1783272|1239|909932|909929|1843491|52225|52226;1783272|1239|526524|526525|128827;1783272|1239|909932|1843488|909930|33024|626940,Complete,Svetlana up
bsdb:38477534/1/1,38477534,"cross-sectional observational, not case-control,laboratory experiment",38477534,10.1002/advs.202306297,NA,"Zhang Y., Song F., Yang M., Chen C., Cui J., Xing M., Dai Y., Li M., Cao Y., Lu L., Zhu H., Liu Y., Ma C., Wei Q., Qin H. , Li J.",Gastrointestinal Dysmotility Predisposes to Colitis through Regulation of Gut Microbial Composition and Linoleic Acid Metabolism,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2024,"gut microbiota, gut motility, immune cell, inflammatory bowel disease, linoleic acid",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Colitis,EFO:0003872,Wild Type (WT) Mice,Kit wsh/wsh mice,"c-Kit receptor dysfunction-based ICC-deficient murine model (Kitwsh/wsh) before Dextran Sulfate Sodium (DSS) treatment. Kitwsh/wsh C57BL/6J mice were from Jackson Laboratory (BarHarbor, ME).",6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,"age,sex",NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 3C,14 April 2025,MyleeeA,MyleeeA,Differences in microbial taxa at species levels between Wild Type (WT) and Kit wsh/wsh mice were calculated by LDA effect size (LEfSe).,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium MD335,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter ganmani,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter hepaticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium CIEAF 020,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA,s__bacterium mpn-isolate group 9",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|3085636|186803|1235793;3379134|29547|3031852|213849|72293|209|60246;3379134|976|200643|171549|815|816|85831;1783272|1239|91061|186826|33958|1578|151781;3379134|976|200643|171549|815|909656|671267;3379134|29547|3031852|213849|72293|209|32025;1783272|1239|186801|186802|1159215;1783272|1239|186801|186802|216572|1263|457412;157940,Complete,Svetlana up
bsdb:38477534/1/2,38477534,"cross-sectional observational, not case-control,laboratory experiment",38477534,10.1002/advs.202306297,NA,"Zhang Y., Song F., Yang M., Chen C., Cui J., Xing M., Dai Y., Li M., Cao Y., Lu L., Zhu H., Liu Y., Ma C., Wei Q., Qin H. , Li J.",Gastrointestinal Dysmotility Predisposes to Colitis through Regulation of Gut Microbial Composition and Linoleic Acid Metabolism,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2024,"gut microbiota, gut motility, immune cell, inflammatory bowel disease, linoleic acid",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Colitis,EFO:0003872,Wild Type (WT) Mice,Kit wsh/wsh mice,"c-Kit receptor dysfunction-based ICC-deficient murine model (Kitwsh/wsh) before Dextran Sulfate Sodium (DSS) treatment. Kitwsh/wsh C57BL/6J mice were from Jackson Laboratory (BarHarbor, ME).",6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,"age,sex",NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 3C,14 April 2025,MyleeeA,MyleeeA,Differences in microbial taxa at species levels between Wild Type (WT) and Kit wsh/wsh mice were calculated by LDA effect size (LEfSe).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. Culture-54,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus animalis,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum|s__Mucispirillum schaedleri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia mucosicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium A4",1783272|1239|186801|186802|31979|1485|1003352;1783272|1239|91061|186826|33958|2767887|1605;3379134|200930|68337|191393|2945020|248038|248039;3379134|976|200643|171549|2005525|375288|328812;1783272|201174|84998|1643822|1643826|447020|580026;1783272|1239|186801|3085636|186803|397291,Complete,Svetlana up
bsdb:38477534/2/1,38477534,"cross-sectional observational, not case-control,laboratory experiment",38477534,10.1002/advs.202306297,NA,"Zhang Y., Song F., Yang M., Chen C., Cui J., Xing M., Dai Y., Li M., Cao Y., Lu L., Zhu H., Liu Y., Ma C., Wei Q., Qin H. , Li J.",Gastrointestinal Dysmotility Predisposes to Colitis through Regulation of Gut Microbial Composition and Linoleic Acid Metabolism,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2024,"gut microbiota, gut motility, immune cell, inflammatory bowel disease, linoleic acid",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Colitis,EFO:0003872,Wild Type (WT) Mice,Kit wsh/wsh mice,"c-Kit receptor dysfunction-based ICC-deficient murine model (Kitwsh/wsh) before Dextran Sulfate Sodium (DSS) treatment. Kitwsh/wsh C57BL/6J mice were from Jackson Laboratory (BarHarbor, ME).",6,6,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,"age,sex",NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 3D,14 April 2025,MyleeeA,MyleeeA,Differences in microbial taxa at the genus and species levels between Wild Type (WT) and Kit wsh/wsh mice.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988|239934|239935,Complete,Svetlana up
bsdb:38477534/2/2,38477534,"cross-sectional observational, not case-control,laboratory experiment",38477534,10.1002/advs.202306297,NA,"Zhang Y., Song F., Yang M., Chen C., Cui J., Xing M., Dai Y., Li M., Cao Y., Lu L., Zhu H., Liu Y., Ma C., Wei Q., Qin H. , Li J.",Gastrointestinal Dysmotility Predisposes to Colitis through Regulation of Gut Microbial Composition and Linoleic Acid Metabolism,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2024,"gut microbiota, gut motility, immune cell, inflammatory bowel disease, linoleic acid",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Colitis,EFO:0003872,Wild Type (WT) Mice,Kit wsh/wsh mice,"c-Kit receptor dysfunction-based ICC-deficient murine model (Kitwsh/wsh) before Dextran Sulfate Sodium (DSS) treatment. Kitwsh/wsh C57BL/6J mice were from Jackson Laboratory (BarHarbor, ME).",6,6,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,"age,sex",NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 3D,14 April 2025,MyleeeA,MyleeeA,Differences in microbial taxa at the genus and species levels between Wild Type (WT) and Kit wsh/wsh mice.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus animalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|2767887|1605;1783272|1239|91061|186826|33958|1578|33959,Complete,Svetlana up
bsdb:38477534/3/1,38477534,"cross-sectional observational, not case-control,laboratory experiment",38477534,10.1002/advs.202306297,NA,"Zhang Y., Song F., Yang M., Chen C., Cui J., Xing M., Dai Y., Li M., Cao Y., Lu L., Zhu H., Liu Y., Ma C., Wei Q., Qin H. , Li J.",Gastrointestinal Dysmotility Predisposes to Colitis through Regulation of Gut Microbial Composition and Linoleic Acid Metabolism,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2024,"gut microbiota, gut motility, immune cell, inflammatory bowel disease, linoleic acid",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Colitis,EFO:0003872,Wild Type (WT) Mice (No DSS),Kit wsh/wsh mice (No DSS),"c-Kit receptor dysfunction-based ICC-deficient murine model (Kitwsh/wsh) without Dextran Sulfate Sodium (DSS) treatment. Kitwsh/wsh C57BL/6J mice were from Jackson Laboratory (BarHarbor, ME).",6,6,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,"age,sex",NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 3E,14 April 2025,MyleeeA,MyleeeA,Differences in microbial taxa at the species levels between Wild Type (WT) and Kit wsh/wsh mice not treated with DSS.,increased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,3379134|74201|203494|48461|1647988|239934|239935,Complete,Svetlana up
bsdb:38477534/3/2,38477534,"cross-sectional observational, not case-control,laboratory experiment",38477534,10.1002/advs.202306297,NA,"Zhang Y., Song F., Yang M., Chen C., Cui J., Xing M., Dai Y., Li M., Cao Y., Lu L., Zhu H., Liu Y., Ma C., Wei Q., Qin H. , Li J.",Gastrointestinal Dysmotility Predisposes to Colitis through Regulation of Gut Microbial Composition and Linoleic Acid Metabolism,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2024,"gut microbiota, gut motility, immune cell, inflammatory bowel disease, linoleic acid",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Colitis,EFO:0003872,Wild Type (WT) Mice (No DSS),Kit wsh/wsh mice (No DSS),"c-Kit receptor dysfunction-based ICC-deficient murine model (Kitwsh/wsh) without Dextran Sulfate Sodium (DSS) treatment. Kitwsh/wsh C57BL/6J mice were from Jackson Laboratory (BarHarbor, ME).",6,6,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,"age,sex",NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 3E,14 April 2025,MyleeeA,MyleeeA,Differences in microbial taxa at the species levels between Wild Type (WT) and Kit wsh/wsh mice not treated with DSS.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus animalis",1783272|1239|91061|186826|33958|1578|33959;1783272|1239|91061|186826|33958|2767887|1605,Complete,Svetlana up
bsdb:38477534/4/1,38477534,"cross-sectional observational, not case-control,laboratory experiment",38477534,10.1002/advs.202306297,NA,"Zhang Y., Song F., Yang M., Chen C., Cui J., Xing M., Dai Y., Li M., Cao Y., Lu L., Zhu H., Liu Y., Ma C., Wei Q., Qin H. , Li J.",Gastrointestinal Dysmotility Predisposes to Colitis through Regulation of Gut Microbial Composition and Linoleic Acid Metabolism,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2024,"gut microbiota, gut motility, immune cell, inflammatory bowel disease, linoleic acid",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Healthy controls - Fecal Microbiota Transplantation (HC-FMT),Chronic Constipation - Fecal Microbiota Transplantation (CC-FMT),"Fecal microbiota transplant (FMT), recipient mice were pre-treated with a cocktail of antibiotics (ABX) in drinking water for 2 weeks. Mice were administered filtered donor fecal homogenate by oral gavage (300 μl per mouse) one day after ABX treatment every other day over a period of 10 days.",6,6,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 8F,15 April 2025,MyleeeA,MyleeeA,Differences in microbial taxa significant between Chronic Constipation - Fecal Microbiota Transplantation (CC-FMT) and Healthy controls - Fecal Microbiota Transplantation (HC-FMT).,increased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,3379134|74201|203494|48461|1647988|239934|239935,Complete,Svetlana up
bsdb:38477534/4/2,38477534,"cross-sectional observational, not case-control,laboratory experiment",38477534,10.1002/advs.202306297,NA,"Zhang Y., Song F., Yang M., Chen C., Cui J., Xing M., Dai Y., Li M., Cao Y., Lu L., Zhu H., Liu Y., Ma C., Wei Q., Qin H. , Li J.",Gastrointestinal Dysmotility Predisposes to Colitis through Regulation of Gut Microbial Composition and Linoleic Acid Metabolism,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2024,"gut microbiota, gut motility, immune cell, inflammatory bowel disease, linoleic acid",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Healthy controls - Fecal Microbiota Transplantation (HC-FMT),Chronic Constipation - Fecal Microbiota Transplantation (CC-FMT),"Fecal microbiota transplant (FMT), recipient mice were pre-treated with a cocktail of antibiotics (ABX) in drinking water for 2 weeks. Mice were administered filtered donor fecal homogenate by oral gavage (300 μl per mouse) one day after ABX treatment every other day over a period of 10 days.",6,6,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 8F,15 April 2025,MyleeeA,MyleeeA,Differences in microbial taxa significant between Chronic Constipation - Fecal Microbiota Transplantation (CC-FMT) and Healthy controls - Fecal Microbiota Transplantation (HC-FMT).,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:38477534/5/1,38477534,"cross-sectional observational, not case-control,laboratory experiment",38477534,10.1002/advs.202306297,NA,"Zhang Y., Song F., Yang M., Chen C., Cui J., Xing M., Dai Y., Li M., Cao Y., Lu L., Zhu H., Liu Y., Ma C., Wei Q., Qin H. , Li J.",Gastrointestinal Dysmotility Predisposes to Colitis through Regulation of Gut Microbial Composition and Linoleic Acid Metabolism,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2024,"gut microbiota, gut motility, immune cell, inflammatory bowel disease, linoleic acid",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Treatment,EFO:0000727,Wild Type (WT) Mice (DSS),Kit wsh/wsh mice (DSS),"c-Kit receptor dysfunction-based ICC-deficient murine model (Kitwsh/wsh) with Dextran Sulfate Sodium (DSS) treatment. Kitwsh/wsh C57BL/6J mice were from Jackson Laboratory (BarHarbor, ME).",6,6,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,"age,sex",NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 3E,15 April 2025,MyleeeA,MyleeeA,Differences in microbial taxa at the species levels between Wild Type (WT) and Kit wsh/wsh mice treated with DSS.,increased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,3379134|74201|203494|48461|1647988|239934|239935,Complete,Svetlana up
bsdb:38477534/5/2,38477534,"cross-sectional observational, not case-control,laboratory experiment",38477534,10.1002/advs.202306297,NA,"Zhang Y., Song F., Yang M., Chen C., Cui J., Xing M., Dai Y., Li M., Cao Y., Lu L., Zhu H., Liu Y., Ma C., Wei Q., Qin H. , Li J.",Gastrointestinal Dysmotility Predisposes to Colitis through Regulation of Gut Microbial Composition and Linoleic Acid Metabolism,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2024,"gut microbiota, gut motility, immune cell, inflammatory bowel disease, linoleic acid",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Treatment,EFO:0000727,Wild Type (WT) Mice (DSS),Kit wsh/wsh mice (DSS),"c-Kit receptor dysfunction-based ICC-deficient murine model (Kitwsh/wsh) with Dextran Sulfate Sodium (DSS) treatment. Kitwsh/wsh C57BL/6J mice were from Jackson Laboratory (BarHarbor, ME).",6,6,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,"age,sex",NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 3E,15 April 2025,MyleeeA,MyleeeA,Differences in microbial taxa at the species levels between Wild Type (WT) and Kit wsh/wsh mice treated with DSS.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus animalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii",1783272|1239|91061|186826|33958|2767887|1605;1783272|1239|91061|186826|33958|1578|33959,Complete,Svetlana up
bsdb:38477534/6/1,38477534,"cross-sectional observational, not case-control,laboratory experiment",38477534,10.1002/advs.202306297,NA,"Zhang Y., Song F., Yang M., Chen C., Cui J., Xing M., Dai Y., Li M., Cao Y., Lu L., Zhu H., Liu Y., Ma C., Wei Q., Qin H. , Li J.",Gastrointestinal Dysmotility Predisposes to Colitis through Regulation of Gut Microbial Composition and Linoleic Acid Metabolism,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2024,"gut microbiota, gut motility, immune cell, inflammatory bowel disease, linoleic acid",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Control Diet (CD) mice,Low-carbohydrate and high-protein diet (LCHD) mice,"WT mice fed with an isocaloric low-carbohydrate and high-protein diet (LCHD, 28.9% carbohydrate, 60.0% protein, and 11.1% fat as percentages of calories) for 4 weeks",NA,NA,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 4C,15 April 2025,MyleeeA,MyleeeA,Differences in microbial taxa significant between mice fed with Low-carbohydrate and high-protein diet (LCHD) and Control Diet (CD).,increased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,3379134|74201|203494|48461|1647988|239934|239935,Complete,Svetlana up
bsdb:38477534/6/2,38477534,"cross-sectional observational, not case-control,laboratory experiment",38477534,10.1002/advs.202306297,NA,"Zhang Y., Song F., Yang M., Chen C., Cui J., Xing M., Dai Y., Li M., Cao Y., Lu L., Zhu H., Liu Y., Ma C., Wei Q., Qin H. , Li J.",Gastrointestinal Dysmotility Predisposes to Colitis through Regulation of Gut Microbial Composition and Linoleic Acid Metabolism,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2024,"gut microbiota, gut motility, immune cell, inflammatory bowel disease, linoleic acid",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Control Diet (CD) mice,Low-carbohydrate and high-protein diet (LCHD) mice,"WT mice fed with an isocaloric low-carbohydrate and high-protein diet (LCHD, 28.9% carbohydrate, 60.0% protein, and 11.1% fat as percentages of calories) for 4 weeks",NA,NA,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 4C,15 April 2025,MyleeeA,MyleeeA,Differences in microbial taxa significant between mice fed with Low-carbohydrate and high-protein diet (LCHD) and Control Diet (CD).,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:38477534/7/1,38477534,"cross-sectional observational, not case-control,laboratory experiment",38477534,10.1002/advs.202306297,NA,"Zhang Y., Song F., Yang M., Chen C., Cui J., Xing M., Dai Y., Li M., Cao Y., Lu L., Zhu H., Liu Y., Ma C., Wei Q., Qin H. , Li J.",Gastrointestinal Dysmotility Predisposes to Colitis through Regulation of Gut Microbial Composition and Linoleic Acid Metabolism,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2024,"gut microbiota, gut motility, immune cell, inflammatory bowel disease, linoleic acid",Experiment 7,China,Mus musculus,Feces,UBERON:0001988,Colitis,EFO:0003872,Wild Type (WT) Mice,Kit wsh/wsh Mice,"c-Kit receptor dysfunction-based ICC-deficient murine model (Kitwsh/wsh). Kitwsh/wsh C57BL/6J mice were from Jackson Laboratory (BarHarbor, ME).",6,6,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,"age,sex",NA,NA,increased,increased,NA,NA,NA,Signature 1,Supplementary Figure 5A,15 April 2025,MyleeeA,MyleeeA,Differences in microbial taxa at the species levels between Wild Type (WT) and Kit wsh/wsh mice.,increased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,3379134|74201|203494|48461|1647988|239934|239935,Complete,Svetlana up
bsdb:38477534/7/2,38477534,"cross-sectional observational, not case-control,laboratory experiment",38477534,10.1002/advs.202306297,NA,"Zhang Y., Song F., Yang M., Chen C., Cui J., Xing M., Dai Y., Li M., Cao Y., Lu L., Zhu H., Liu Y., Ma C., Wei Q., Qin H. , Li J.",Gastrointestinal Dysmotility Predisposes to Colitis through Regulation of Gut Microbial Composition and Linoleic Acid Metabolism,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2024,"gut microbiota, gut motility, immune cell, inflammatory bowel disease, linoleic acid",Experiment 7,China,Mus musculus,Feces,UBERON:0001988,Colitis,EFO:0003872,Wild Type (WT) Mice,Kit wsh/wsh Mice,"c-Kit receptor dysfunction-based ICC-deficient murine model (Kitwsh/wsh). Kitwsh/wsh C57BL/6J mice were from Jackson Laboratory (BarHarbor, ME).",6,6,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,"age,sex",NA,NA,increased,increased,NA,NA,NA,Signature 2,Supplementary Figure 5A,15 April 2025,MyleeeA,MyleeeA,Differences in microbial taxa at the species levels between Wild Type (WT) and Kit wsh/wsh mice.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus animalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii",1783272|1239|91061|186826|33958|2767887|1605;1783272|1239|91061|186826|33958|1578|33959,Complete,Svetlana up
bsdb:38477534/8/1,38477534,"cross-sectional observational, not case-control,laboratory experiment",38477534,10.1002/advs.202306297,NA,"Zhang Y., Song F., Yang M., Chen C., Cui J., Xing M., Dai Y., Li M., Cao Y., Lu L., Zhu H., Liu Y., Ma C., Wei Q., Qin H. , Li J.",Gastrointestinal Dysmotility Predisposes to Colitis through Regulation of Gut Microbial Composition and Linoleic Acid Metabolism,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2024,"gut microbiota, gut motility, immune cell, inflammatory bowel disease, linoleic acid",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy controls (HC),Chronic Constipation (CC),Patients with Chronic Constipation,30,30,2 months,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 8C,15 April 2025,MyleeeA,MyleeeA,Relative abundance of microbial taxa in stool samples from Chronic constipation patients (CC) and Healthy controls (HC).,increased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,3379134|74201|203494|48461|1647988|239934|239935,Complete,Svetlana up
bsdb:38477534/8/2,38477534,"cross-sectional observational, not case-control,laboratory experiment",38477534,10.1002/advs.202306297,NA,"Zhang Y., Song F., Yang M., Chen C., Cui J., Xing M., Dai Y., Li M., Cao Y., Lu L., Zhu H., Liu Y., Ma C., Wei Q., Qin H. , Li J.",Gastrointestinal Dysmotility Predisposes to Colitis through Regulation of Gut Microbial Composition and Linoleic Acid Metabolism,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2024,"gut microbiota, gut motility, immune cell, inflammatory bowel disease, linoleic acid",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy controls (HC),Chronic Constipation (CC),Patients with Chronic Constipation,30,30,2 months,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 8C,15 April 2025,MyleeeA,MyleeeA,Relative abundance of microbial taxa in stool samples from Chronic constipation patients (CC) and Healthy controls (HC).,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:38477534/9/1,38477534,"cross-sectional observational, not case-control,laboratory experiment",38477534,10.1002/advs.202306297,NA,"Zhang Y., Song F., Yang M., Chen C., Cui J., Xing M., Dai Y., Li M., Cao Y., Lu L., Zhu H., Liu Y., Ma C., Wei Q., Qin H. , Li J.",Gastrointestinal Dysmotility Predisposes to Colitis through Regulation of Gut Microbial Composition and Linoleic Acid Metabolism,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2024,"gut microbiota, gut motility, immune cell, inflammatory bowel disease, linoleic acid",Experiment 9,China,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Healthy controls (HC),Crohn's Disease (CD),Patients with Crohn's disease,30,32,2 months,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 8C,15 April 2025,MyleeeA,MyleeeA,Relative abundance of microbial taxa in stool samples from Crohn's Disease patients (CD) and Healthy controls (HC).,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:38477534/10/1,38477534,"cross-sectional observational, not case-control,laboratory experiment",38477534,10.1002/advs.202306297,NA,"Zhang Y., Song F., Yang M., Chen C., Cui J., Xing M., Dai Y., Li M., Cao Y., Lu L., Zhu H., Liu Y., Ma C., Wei Q., Qin H. , Li J.",Gastrointestinal Dysmotility Predisposes to Colitis through Regulation of Gut Microbial Composition and Linoleic Acid Metabolism,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2024,"gut microbiota, gut motility, immune cell, inflammatory bowel disease, linoleic acid",Experiment 10,China,Homo sapiens,Feces,UBERON:0001988,Ulcerative colitis,EFO:0000729,Healthy controls (HC),Ulcerative colitis,Patients with Ulcerative colitis,30,25,2 months,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 8C,15 April 2025,MyleeeA,MyleeeA,Relative abundance of microbial taxa in stool samples from Ulcerative colitis patients (UC) and Healthy controls (HC).,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:38479397/1/1,38479397,time series / longitudinal observational,38479397,https://doi.org/10.1016/j.chom.2024.02.012,NA,"Zhou X., Shen X., Johnson J.S., Spakowicz D.J., Agnello M., Zhou W., Avina M., Honkala A., Chleilat F., Chen S.J., Cha K., Leopold S., Zhu C., Chen L., Lyu L., Hornburg D., Wu S., Zhang X., Jiang C., Jiang L., Jiang L., Jian R., Brooks A.W., Wang M., Contrepois K., Gao P., Rose S.M.S., Tran T.D.B., Nguyen H., Celli A., Hong B.Y., Bautista E.J., Dorsett Y., Kavathas P.B., Zhou Y., Sodergren E., Weinstock G.M. , Snyder M.P.",Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease,Cell host & microbe,2024,"insulin resistance, longitudinal profiling, microbiome host interaction, microbiome stability, nasal microbiome, oral microbiome, precision medicine, prediabetes, skin microbiome, stool microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Insulin sensitivity measurement,EFO:0004471,Insulin Sensitive (IS) Individuals,Insulin Resistant (IR) Individuals,"Individuals who are at risk for type 2 diabetes or  voluntarily interested in diabetes-related research, whose steady-state plasma glucose (SSPG) was greater than or equal to 150 mg/dl after undergoing Glucose control assessments, comprising an annual oral glucose tolerance test and a gold-standard steady-state plasma glucose (SSPG) measurement.",28,30,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,date,NA,unchanged,decreased,NA,NA,NA,NA,Signature 1,Table S1D + Figure S1M,8 April 2024,Joan Chuks,"Joan Chuks,Adeitan,Aleru Divine,WikiWorks",Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|3118652|2039240;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816|818;3379134|976|200643;3379134|976;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|2719313;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|815|909656;3379134|976|200643|171549|815;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|815|909656;1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|3118652|2039240;1783272|1239|186801|3085636|186803|2719313,Complete,Svetlana up
bsdb:38479397/1/2,38479397,time series / longitudinal observational,38479397,https://doi.org/10.1016/j.chom.2024.02.012,NA,"Zhou X., Shen X., Johnson J.S., Spakowicz D.J., Agnello M., Zhou W., Avina M., Honkala A., Chleilat F., Chen S.J., Cha K., Leopold S., Zhu C., Chen L., Lyu L., Hornburg D., Wu S., Zhang X., Jiang C., Jiang L., Jiang L., Jian R., Brooks A.W., Wang M., Contrepois K., Gao P., Rose S.M.S., Tran T.D.B., Nguyen H., Celli A., Hong B.Y., Bautista E.J., Dorsett Y., Kavathas P.B., Zhou Y., Sodergren E., Weinstock G.M. , Snyder M.P.",Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease,Cell host & microbe,2024,"insulin resistance, longitudinal profiling, microbiome host interaction, microbiome stability, nasal microbiome, oral microbiome, precision medicine, prediabetes, skin microbiome, stool microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Insulin sensitivity measurement,EFO:0004471,Insulin Sensitive (IS) Individuals,Insulin Resistant (IR) Individuals,"Individuals who are at risk for type 2 diabetes or  voluntarily interested in diabetes-related research, whose steady-state plasma glucose (SSPG) was greater than or equal to 150 mg/dl after undergoing Glucose control assessments, comprising an annual oral glucose tolerance test and a gold-standard steady-state plasma glucose (SSPG) measurement.",28,30,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,date,NA,unchanged,decreased,NA,NA,NA,NA,Signature 2,Table S1D + Figure S1M,8 April 2024,Joan Chuks,"Joan Chuks,Aleru Divine,WikiWorks",Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe),decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Acutalibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Beduinibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio desulfuricans,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Ihubacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Kiloniellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Kineothrix,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnotalea,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Mailhella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales,k__Thermotogati|p__Synergistota|c__Synergistia,k__Thermotogati|p__Synergistota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Acutalibacter,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Ihubacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Kineothrix,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnotalea,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Mailhella,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae",1783272|201174|1760;1783272|1239|186801|186802|3082771|1918385;3379134|976|200643|171549|2005519;1783272|1239|186801|3082768|990719|1987009;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|186802|1980681;1783272|1239|526524|526525|2810280|100883;1783272|1239|186801|3085636|186803|33042;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924|872|876;1783272|1239|186801|3082720|543314;1783272|1239|186801|3085636|186803|2005359;3379134|1224|1236|135625|712|724;1783272|1239|186801|3082720|543314|1926667;3379134|1224|28211|204441|597359;1783272|1239|186801|3085636|186803|2163168;1783272|1239|186801|3085636|186803|1763508;3379134|200940|3031449|213115|194924|1981028;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|3085656|3085657|2039302;1783272|201174|1760|85007;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|1853231;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|75682|846;3379134|1224|28216|80840|75682;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171551|836|837;3379134|1224|28211|204441;3384194|508458|649775|649776|649777;3384194|508458|649775|649776;3384194|508458|649775;3384194|508458;1783272|1239|526524|526525|2810281|191303;1783272|1239|526524|526525|2810281|191303|154288;1783272|1239|186801|186802|3082771|1918385;1783272|1239;3379134|976|200643|171549;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|1980681;1783272|1239|526524|526525|2810280|100883;1783272|1239|186801|3085636|186803|33042;3379134|200940|3031449|213115|194924|872;1783272|201174|84998|1643822|1643826;1783272|1239|526524|526525|128827;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803|2005359;3379134|1224|1236|135625|712|724;1783272|1239|186801|3082720|543314|1926667;1783272|1239|186801|3085636|186803|2163168;1783272|1239|186801|3085636|186803|1763508;3379134|200940|3031449|213115|194924|1981028;1783272|1239|186801|3085656|3085657|2039302;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|75682|846;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3082768|990719,Complete,Svetlana up
bsdb:38479397/2/1,38479397,time series / longitudinal observational,38479397,https://doi.org/10.1016/j.chom.2024.02.012,NA,"Zhou X., Shen X., Johnson J.S., Spakowicz D.J., Agnello M., Zhou W., Avina M., Honkala A., Chleilat F., Chen S.J., Cha K., Leopold S., Zhu C., Chen L., Lyu L., Hornburg D., Wu S., Zhang X., Jiang C., Jiang L., Jiang L., Jian R., Brooks A.W., Wang M., Contrepois K., Gao P., Rose S.M.S., Tran T.D.B., Nguyen H., Celli A., Hong B.Y., Bautista E.J., Dorsett Y., Kavathas P.B., Zhou Y., Sodergren E., Weinstock G.M. , Snyder M.P.",Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease,Cell host & microbe,2024,"insulin resistance, longitudinal profiling, microbiome host interaction, microbiome stability, nasal microbiome, oral microbiome, precision medicine, prediabetes, skin microbiome, stool microbiome",Experiment 2,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Insulin sensitivity measurement,EFO:0004471,Insulin Sensitive (IS) Individuals,Insulin Resistant (IR) Individuals,"Individuals who are at risk for type 2 diabetes or  voluntarily interested in diabetes-related research, whose steady-state plasma glucose (SSPG) was greater than or equal to 150 mg/dl after undergoing Glucose control assessments, comprising an annual oral glucose tolerance test and a gold-standard steady-state plasma glucose (SSPG) measurement.",28,30,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,date,NA,increased,increased,NA,NA,NA,NA,Signature 1,Table S1D + Figure S1M,12 April 2024,Joan Chuks,"Joan Chuks,Aleru Divine,WikiWorks",Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alishewanella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus octavius,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus provencensis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia|o__Acidimicrobiales|f__Iamiaceae|g__Aquihabitans|s__Aquihabitans daechungensis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter ureolyticus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota,p__Candidatus Saccharimonadota,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Empedobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia|s__Facklamia languida,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium lindanitolerans,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Fulvivirgaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Gemmatales|f__Gemmataceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Intrasporangium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Methylophilaceae|g__Methylophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Micropruina,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Fulvivirgaceae|g__Ohtaekwangia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus|s__Paracoccus siganidrum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas bennonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Rickettsiella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia koreensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Tepidimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Thermoactinomycetaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Empedobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Tepidimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Intrasporangium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Methylophilaceae|g__Methylophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Fulvivirgaceae|g__Ohtaekwangia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Rickettsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alishewanella,k__Pseudomonadati|p__Acidobacteriota|c__Blastocatellia|o__Blastocatellales|f__Blastocatellaceae,p__Candidatus Saccharimonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium",3379134|1224|1236|135625|712|416916|739;3379134|1224|1236|135622|72275|111142;3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|171552|1283313|76122;1783272|1239|1737404|1737405|1570339|165779|54007;1783272|1239|1737404|1737405|1570339|165779|938293;1783272|1239|1737404|1737405|1570339|165779|33037;1783272|201174|84992|84993|633392|1648491|1052257;1783272|201174|84998|84999|1643824|1380;3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294|194|204;3379134|29547|3031852|213849|72294|194|827;3379134|29547|3031852|213849|72294;3379134|29547|3031852|213849;3379134|29547;95818;3379134|976|117743|200644|49546|1016|1019;1783272|1239|186801;1783272|201174|84998;3379134|200940|3031449|213115|194924;1783272|1239|909932|1843489|31977|39948|309120;1783272|201174|1760|85007|85029|37914;1783272|201174|1760|85007|85029;3379134|976|117743|200644|2762318|59734;3379134|29547|3031852;1783272|1239|186801|186802|216572|253238;1783272|1239|186801|186802|186806;1783272|1239|186801|186802;1783272|1239|186801|3082720|543314;1783272|1239|186801|186802|186806|1730;1783272|1239|91061|186826|186827|66831|82347;3379134|976|117743|200644;3379134|976|117743;3379134|976|117743|200644|49546|237|428988;3379134|976|768503|768507|2762286;1783272|201174|1760|85004|31953|2701;3379134|203682|203683|2691355|1914233;1783272|201174|1760|85006|85021;1783272|201174|1760|85006|85021|53357;3379134|1224|28216|206351|481|32257;3379134|1224|28216|206351|481|32257|505;1783272|201174|1760|85007|2805586|1847725;1783272|201174|1760|85007|2805586;3379134|1224|1236|135614|32033|68;1783272|1239|909932|1843489|31977|906;3379134|1224|28216|32003|32011|16;1783272|201174|1760|85009|85015|116071;1783272|1239|186801|3082720|543314|86331;1783272|1239|909932|1843489|31977|909928;1783272|1239|909932;3379134|976|768503|768507|2762286|1210119;3379134|1224|28211|204455|31989|265|1276757;1783272|1239|1737404|1737405|1570339;1783272|1239|1737404|1737405|1570339|162289;3379134|976|200643|171549|171551|836|501496;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|28125;3379134|976|200643|171549|171552|838|470565;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552|838|28133;3379134|976|200643|171549|171552;3379134|1224|1236|118969|118968|59195;1783272|201174|1760|85006|1268|32207|592378;3379134|976|200643|171549|171552|2974251|228604;3379134|1224|28216|80840|114248;1783272|1239|91061|1385|186824;1783272|1239|909932|1843489|31977;1783272|1239|909932|1843489;3379134|976|117743|200644|2762318;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|3085636|186803|265975;3379134|1224|28211|204441;1783272|1239|186801|186802|186806|1730;3379134|976|117743|200644|2762318|59734;3379134|1224|28216|80840|114248;3379134|1224|1236|135625|712|416916;1783272|201174|1760|85006|85021|53357;3379134|1224|28216|32003|32011|16;1783272|201174|1760|85007|2805586|1847725;1783272|1239|909932|1843489|31977|909928;3379134|976|768503|768507|2762286|1210119;3379134|1224|1236|135614|32033|68;3379134|1224|1236|118969|118968|59195;3379134|1224|1236|135622|72275|111142;3379134|57723|1562566|1748771|1748772;95818;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|1164882;1783272|1239|186801|3082720|543314|86331,Complete,Svetlana up
bsdb:38479397/2/2,38479397,time series / longitudinal observational,38479397,https://doi.org/10.1016/j.chom.2024.02.012,NA,"Zhou X., Shen X., Johnson J.S., Spakowicz D.J., Agnello M., Zhou W., Avina M., Honkala A., Chleilat F., Chen S.J., Cha K., Leopold S., Zhu C., Chen L., Lyu L., Hornburg D., Wu S., Zhang X., Jiang C., Jiang L., Jiang L., Jian R., Brooks A.W., Wang M., Contrepois K., Gao P., Rose S.M.S., Tran T.D.B., Nguyen H., Celli A., Hong B.Y., Bautista E.J., Dorsett Y., Kavathas P.B., Zhou Y., Sodergren E., Weinstock G.M. , Snyder M.P.",Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease,Cell host & microbe,2024,"insulin resistance, longitudinal profiling, microbiome host interaction, microbiome stability, nasal microbiome, oral microbiome, precision medicine, prediabetes, skin microbiome, stool microbiome",Experiment 2,United States of America,Homo sapiens,Skin of body,UBERON:0002097,Insulin sensitivity measurement,EFO:0004471,Insulin Sensitive (IS) Individuals,Insulin Resistant (IR) Individuals,"Individuals who are at risk for type 2 diabetes or  voluntarily interested in diabetes-related research, whose steady-state plasma glucose (SSPG) was greater than or equal to 150 mg/dl after undergoing Glucose control assessments, comprising an annual oral glucose tolerance test and a gold-standard steady-state plasma glucose (SSPG) measurement.",28,30,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,date,NA,increased,increased,NA,NA,NA,NA,Signature 2,Table S1D + Figure S1M,12 April 2024,Joan Chuks,"Joan Chuks,Adeitan,Aleru Divine,WikiWorks",Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe),decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinotignum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Aurantimonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Beijerinckiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Flavisolibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus|s__Paracoccus yeei,k__Bacillati|p__Actinomycetota|c__Thermoleophilia|o__Solirubrobacterales|f__Patulibacteraceae|g__Patulibacter|s__Patulibacter minatonensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Gemmatimonadota|c__Gemmatimonadia|o__Gemmatimonadales|f__Gemmatimonadaceae|g__Roseisolibacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas ginsengisoli (ex Hoang et al. 2012),k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus haemolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinotignum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Beijerinckiaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Gemmatimonadota|c__Gemmatimonadia|o__Gemmatimonadales|f__Gemmatimonadaceae|g__Roseisolibacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Flavisolibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae",1783272|201174;1783272|201174|1760|2037|2049|1653174;3379134|1224|28211|356|255475;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|2005519;3379134|1224|28211|356|45404;1783272|201174|1760|85009|31957|1912216;1783272|1239|909932|1843489|31977|39948;3379134|976|1853228|1853229|563835|398041;1783272|1239|186801|3085636|186803|140625;1783272|201174|1760|85006;3379134|1224|28211|204455|31989;3379134|1224|28211|204455|31989|265;3379134|1224|28211|204455|31989|265|147645;1783272|201174|1497346|588673|361606|361607|298163;1783272|201174|1760|85009;3379134|1224|28216|80840|119060|48736;3379134|1224|28211|204455;1783272|1239|186801|3085636|186803|841;3379134|142182|219685|219686|219687|2093335;3379134|1224|28211|204457|41297;3379134|1224|28211|204457;3379134|1224|28211|204457|41297|13687;3379134|1224|28211|204457|41297|13687|1706000;1783272|1239|91061|1385|90964|1279|1283;3379134|1224|1236|135614|32033|338;1783272|201174|1760|2037|2049|1653174;3379134|976|200643|171549|2005519|397864;3379134|1224|28211|356|45404;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|140625;3379134|1224|28216|80840|119060|48736;1783272|1239|186801|3085636|186803|841;3379134|142182|219685|219686|219687|2093335;3379134|1224|28211|204457|41297|13687;3379134|1224|1236|135614|32033|338;3379134|976|1853228|1853229|563835|398041;1783272|201174|1760|85009|31957|1912216;1783272|201174|1760|85009|31957,Complete,Svetlana up
bsdb:38479397/3/1,38479397,time series / longitudinal observational,38479397,https://doi.org/10.1016/j.chom.2024.02.012,NA,"Zhou X., Shen X., Johnson J.S., Spakowicz D.J., Agnello M., Zhou W., Avina M., Honkala A., Chleilat F., Chen S.J., Cha K., Leopold S., Zhu C., Chen L., Lyu L., Hornburg D., Wu S., Zhang X., Jiang C., Jiang L., Jiang L., Jian R., Brooks A.W., Wang M., Contrepois K., Gao P., Rose S.M.S., Tran T.D.B., Nguyen H., Celli A., Hong B.Y., Bautista E.J., Dorsett Y., Kavathas P.B., Zhou Y., Sodergren E., Weinstock G.M. , Snyder M.P.",Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease,Cell host & microbe,2024,"insulin resistance, longitudinal profiling, microbiome host interaction, microbiome stability, nasal microbiome, oral microbiome, precision medicine, prediabetes, skin microbiome, stool microbiome",Experiment 3,United States of America,Homo sapiens,Anterior naris,UBERON:2001427,Insulin sensitivity measurement,EFO:0004471,Insulin Sensitive (IS) Individuals,Insulin Resistant (IR) Individuals,"Individuals who are at risk for type 2 diabetes or  voluntarily interested in diabetes-related research, whose steady-state plasma glucose (SSPG) was greater than or equal to 150 mg/dl after undergoing Glucose control assessments, comprising an annual oral glucose tolerance test and a gold-standard steady-state plasma glucose (SSPG) measurement.",28,30,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,date,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 1,Table S1D,12 April 2024,Joan Chuks,"Joan Chuks,Adeitan,Aleru Divine,WikiWorks",Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe),increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus senegalensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus luteus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Salinimicrobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus capitis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Salinimicrobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae",1783272|1239|1737404|1737405|1570339|165779|1288120;1783272|201174|1760|85006|85019|1696;3379134|1224|28211|204458|76892;3379134|976|768503|768507|89373;1783272|201174|1760|85006|1268|1269|1270;3379134|976|200643|171549|171551|836|28124;3379134|976|117743|200644|49546|561367;1783272|1239|91061|1385|90964|1279|29388;1783272|201174|1760|85007|1762|1763;3379134|976|117743|200644|49546|561367;1783272|201174|1760|85006|85019|1696;3379134|1224|28211|204458|76892,Complete,Svetlana up
bsdb:38479397/3/2,38479397,time series / longitudinal observational,38479397,https://doi.org/10.1016/j.chom.2024.02.012,NA,"Zhou X., Shen X., Johnson J.S., Spakowicz D.J., Agnello M., Zhou W., Avina M., Honkala A., Chleilat F., Chen S.J., Cha K., Leopold S., Zhu C., Chen L., Lyu L., Hornburg D., Wu S., Zhang X., Jiang C., Jiang L., Jiang L., Jian R., Brooks A.W., Wang M., Contrepois K., Gao P., Rose S.M.S., Tran T.D.B., Nguyen H., Celli A., Hong B.Y., Bautista E.J., Dorsett Y., Kavathas P.B., Zhou Y., Sodergren E., Weinstock G.M. , Snyder M.P.",Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease,Cell host & microbe,2024,"insulin resistance, longitudinal profiling, microbiome host interaction, microbiome stability, nasal microbiome, oral microbiome, precision medicine, prediabetes, skin microbiome, stool microbiome",Experiment 3,United States of America,Homo sapiens,Anterior naris,UBERON:2001427,Insulin sensitivity measurement,EFO:0004471,Insulin Sensitive (IS) Individuals,Insulin Resistant (IR) Individuals,"Individuals who are at risk for type 2 diabetes or  voluntarily interested in diabetes-related research, whose steady-state plasma glucose (SSPG) was greater than or equal to 150 mg/dl after undergoing Glucose control assessments, comprising an annual oral glucose tolerance test and a gold-standard steady-state plasma glucose (SSPG) measurement.",28,30,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,2,date,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 2,Table S1D,12 April 2024,Joan Chuks,"Joan Chuks,Aleru Divine,WikiWorks",Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe),decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Allorhizobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Azonexaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Blastococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga canimorsus,k__Bacillati|p__Chloroflexota|c__Chloroflexia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemelliphila|s__Gemelliphila palaticanis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Ihubacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Methylophilaceae|g__Methylobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium|s__Microbacterium oleivorans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium|s__Microbacterium testaceum,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Bacillati|p__Actinomycetota|c__Nitriliruptoria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Sanguibacteraceae|g__Sanguibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingosinicellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Allorhizobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Blastococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Ihubacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Microvirga,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Cyanobacteriota,k__Viridiplantae|p__Streptophyta,k__Viridiplantae|p__Streptophyta",1783272|1239|91061|186826|186827|1375;3379134|1224|28211|356|82115|78526;1783272|1239|186801|3085636|186803|2569097;1783272|1239|186801|3085636|186803|207244;3379134|1224|28216|206389|2008795;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|371601;1783272|201174|1760|1643682|85030|38501;3379134|976|200643|171549|1853231|574697;3379134|976|117743|200644|49546|1016|28188;1783272|200795|32061;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|2719313;3379134|1224|1236;1783272|1239|91061|1385|539738|3076174|81950;1783272|201174|1760|1643682|85030;1783272|201174|1760|1643682;3379134|1224|1236|135619|28256;3379134|1224|1236|135619|28256|2745;3379134|29547|3031852|213849|72293;1783272|1239|186801|3082720|543314|1926667;3379134|1224|28216|32003|32011|404;1783272|201174|1760|85006|85023|33882|273677;1783272|201174|1760|85006|85023|33882|2033;1783272|544448|31969;1783272|1239|186801|3085656|3085657|2039302;3379134|1224|1236|2887326|468|475;3379134|1224|1236|2887326|468;1783272|544448;3379134|1224|28216|206351|481|482|484;1783272|201174|908620;3379134|1224|1236|135619;3379134|976|200643|171549|1853231;3379134|976|200643|171549|2005523|346096;3379134|976|200643|171549|2005523;3379134|1224|28216|206389;3379134|1224|28211|204441|41295;1783272|201174|1760|85006|145360|60919;3379134|976|200643|171549|171552|2974251|228604;3379134|1224|28211|204457|2820280;1783272|1239|186801|186802|216572|292632;3379134|1224|1236|135614|32033|338;1783272|1239|91061|186826|186827|1375;3379134|1224|28211|356|82115|78526;1783272|1239|186801|3085636|186803|2569097;1783272|1239|186801|3085636|186803|207244;1783272|201174|1760|1643682|85030|38501;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|2719313;3379134|1224|1236|135619|28256|2745;1783272|1239|186801|3082720|543314|1926667;1783272|1239|91061|186826|33958|1243;1783272|201174|1760|85006;3379134|1224|28211|356|119045|186650;1783272|1239|186801|3085656|3085657|2039302;3379134|1224|1236|2887326|468|475;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|2005523|346096;1783272|1239|186801|186802|216572|292632;1783272|1117;33090|35493;33090|35493,Complete,Svetlana up
bsdb:38479397/4/1,38479397,time series / longitudinal observational,38479397,https://doi.org/10.1016/j.chom.2024.02.012,NA,"Zhou X., Shen X., Johnson J.S., Spakowicz D.J., Agnello M., Zhou W., Avina M., Honkala A., Chleilat F., Chen S.J., Cha K., Leopold S., Zhu C., Chen L., Lyu L., Hornburg D., Wu S., Zhang X., Jiang C., Jiang L., Jiang L., Jian R., Brooks A.W., Wang M., Contrepois K., Gao P., Rose S.M.S., Tran T.D.B., Nguyen H., Celli A., Hong B.Y., Bautista E.J., Dorsett Y., Kavathas P.B., Zhou Y., Sodergren E., Weinstock G.M. , Snyder M.P.",Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease,Cell host & microbe,2024,"insulin resistance, longitudinal profiling, microbiome host interaction, microbiome stability, nasal microbiome, oral microbiome, precision medicine, prediabetes, skin microbiome, stool microbiome",Experiment 4,United States of America,Homo sapiens,Posterior wall of oropharynx,UBERON:0035240,Insulin sensitivity measurement,EFO:0004471,Insulin Sensitive (IS) Individuals,Insulin Resistant (IR) Individuals,"Individuals who are at risk for type 2 diabetes or  voluntarily interested in diabetes-related research, whose steady-state plasma glucose (SSPG) was greater than or equal to 150 mg/dl after undergoing Glucose control assessments, comprising an annual oral glucose tolerance test and a gold-standard steady-state plasma glucose (SSPG) measurement.",28,30,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,date,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 1,Table S1D,12 April 2024,Joan Chuks,"Joan Chuks,Aleru Divine,WikiWorks",Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe),increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum umeaense,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella micans,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter",1783272|1239|91061|186826|186827|46123;1783272|1239|91061|186826|186827|46123|46125;1783272|1239|91061|186826|186827;3379134|976|768503|768507;3379134|976|768503;3379134|1224|28211|204457|335929;1783272|1239|186801|3085636|186803|1164882|617123;1783272|201174|84998|84999|1643824|133925;3379134|976|200643|171549|171552|838|189723;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|1385|90964|1279;1783272|201174|84998|84999|1643824|133925;3379134|1224|1236|135625|712|416916,Complete,Svetlana up
bsdb:38479397/4/2,38479397,time series / longitudinal observational,38479397,https://doi.org/10.1016/j.chom.2024.02.012,NA,"Zhou X., Shen X., Johnson J.S., Spakowicz D.J., Agnello M., Zhou W., Avina M., Honkala A., Chleilat F., Chen S.J., Cha K., Leopold S., Zhu C., Chen L., Lyu L., Hornburg D., Wu S., Zhang X., Jiang C., Jiang L., Jiang L., Jian R., Brooks A.W., Wang M., Contrepois K., Gao P., Rose S.M.S., Tran T.D.B., Nguyen H., Celli A., Hong B.Y., Bautista E.J., Dorsett Y., Kavathas P.B., Zhou Y., Sodergren E., Weinstock G.M. , Snyder M.P.",Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease,Cell host & microbe,2024,"insulin resistance, longitudinal profiling, microbiome host interaction, microbiome stability, nasal microbiome, oral microbiome, precision medicine, prediabetes, skin microbiome, stool microbiome",Experiment 4,United States of America,Homo sapiens,Posterior wall of oropharynx,UBERON:0035240,Insulin sensitivity measurement,EFO:0004471,Insulin Sensitive (IS) Individuals,Insulin Resistant (IR) Individuals,"Individuals who are at risk for type 2 diabetes or  voluntarily interested in diabetes-related research, whose steady-state plasma glucose (SSPG) was greater than or equal to 150 mg/dl after undergoing Glucose control assessments, comprising an annual oral glucose tolerance test and a gold-standard steady-state plasma glucose (SSPG) measurement.",28,30,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,date,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 2,Table S1D,12 April 2024,Joan Chuks,"Joan Chuks,Adeitan,Aleru Divine,WikiWorks",Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Pseudoleptotrichia|s__Pseudoleptotrichia goodfellowii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda",1783272|1239|186801|3085636|186803|43996;1783272|1239|186801;1783272|1117;1783272|1239|186801|186802;1783272|1239|186801|3082720|3118655|44259;1783272|1239|186801|3082720|3118655|44259|143361;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|3085636|186803|265975|237576;3384189|32066|203490|203491|1129771|2755140|157692;1783272|1239|186801|3085636|186803|43996;1783272|1239|909932|909929|1843491|82202,Complete,Svetlana up
bsdb:38479554/1/NA,38479554,laboratory experiment,38479554,https://doi.org/10.1016/j.neulet.2024.137714,NA,"Wang Y., Ullah H., Deng T., Ren X., Zhao Z., Xin Y. , Qiu J.",Social isolation induces intestinal barrier disorder and imbalances gut microbiota in mice,Neuroscience letters,2024,"Gut microbiota, Intestinal barrier, Social isolation",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Social deprivation,EFO:0009696,Normal Control NCd (8-week normal control group),Socially Isolated SId (8-week socially isolated group),Individually housed mice without any sensory communication with other mice for 8 weeks,10,10,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:38479554/2/1,38479554,laboratory experiment,38479554,https://doi.org/10.1016/j.neulet.2024.137714,NA,"Wang Y., Ullah H., Deng T., Ren X., Zhao Z., Xin Y. , Qiu J.",Social isolation induces intestinal barrier disorder and imbalances gut microbiota in mice,Neuroscience letters,2024,"Gut microbiota, Intestinal barrier, Social isolation",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Social deprivation,EFO:0009696,Normal Control NCc (15-week normal control group),Socially Isolated SIc (15-week socially isolated group),Individually housed mice without any sensory communication with other mice for 15 weeks,10,10,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,NA,increased,NA,increased,NA,NA,Signature 1,Figure 9B,18 April 2024,Barrakat,"Barrakat,Peace Sandy,WikiWorks",Differentially abundant bacterial in Normal control (NCc) and Socially isolated (SIc) mice housed for 15 weeks,increased,"k__Pseudomonadati|p__Acidobacteriota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|57723;1783272|201174|84998|1643822|1643826|447020;3379134|74201|203494|48461|1647988|239934;3379134|1224|28216|80840|506;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3082720|3030910;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|1224|28216|80840|80864;1783272|201174|84998|84999;1783272|201174|84998;3379134|200930|68337|191393|191394;3379134|200930|68337|191393;3379134|200930|68337;1783272|1239|91061|186826|1300|1357;3379134|200930|68337|191393|2945020|248038;3379134|1224|28211|204457|41297|13687;3379134|1224|28216|80840|995019|40544,Complete,Peace Sandy
bsdb:38479554/2/2,38479554,laboratory experiment,38479554,https://doi.org/10.1016/j.neulet.2024.137714,NA,"Wang Y., Ullah H., Deng T., Ren X., Zhao Z., Xin Y. , Qiu J.",Social isolation induces intestinal barrier disorder and imbalances gut microbiota in mice,Neuroscience letters,2024,"Gut microbiota, Intestinal barrier, Social isolation",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Social deprivation,EFO:0009696,Normal Control NCc (15-week normal control group),Socially Isolated SIc (15-week socially isolated group),Individually housed mice without any sensory communication with other mice for 15 weeks,10,10,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,NA,increased,NA,increased,NA,NA,Signature 2,Figure 9B,18 April 2024,Barrakat,"Barrakat,Peace Sandy,WikiWorks",Differentially abundant bacterial taxa in Normal control (NCc) and Socially isolated (SIc) mice housed for 15 weeks,decreased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae|g__Marinomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae",1783272|1239|91061;1783272|1239;1783272|1117;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;3379134|1224|1236|135619|135620|28253;3379134|1224|28211|356|119045;3379134|1224|28211|356|119045|407;3379134|1224|1236|135619|135620;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|1853231,Complete,Peace Sandy
bsdb:38481313/1/1,38481313,"cross-sectional observational, not case-control",38481313,10.1186/s13098-024-01298-9,NA,"Wang J., Teng M., Feng R., Su X., Xu K., Wang J., Wang G., Zhang Y. , Xu P.",Large-scale causal analysis of gut microbiota and six common complications of diabetes: a mendelian randomization study,Diabetology & metabolic syndrome,2024,"Complications of diabetes, Genome-wise association studies, Gut microbiota, Mendelian randomization study, Single-nucleotide polymorphism",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Hypoglycemia,NA,Controls,Diabetic hypoglycemia,Patients with diabetic hypoglycemia obtained from the FinnGen consortium.,271817,7332,NA,NA,NA,Illumina,NA,NA,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Significant results between the gut microbiota and the six common complications of diabetes.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales",3379134|976|200643;1783272|1239|526524|526525|2810280|135858;1783272|201174|84998|1643822|1643826|84111;3379134|976|200643|171549;3379134|74201|203494|48461,Complete,Svetlana up
bsdb:38481313/1/2,38481313,"cross-sectional observational, not case-control",38481313,10.1186/s13098-024-01298-9,NA,"Wang J., Teng M., Feng R., Su X., Xu K., Wang J., Wang G., Zhang Y. , Xu P.",Large-scale causal analysis of gut microbiota and six common complications of diabetes: a mendelian randomization study,Diabetology & metabolic syndrome,2024,"Complications of diabetes, Genome-wise association studies, Gut microbiota, Mendelian randomization study, Single-nucleotide polymorphism",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Hypoglycemia,NA,Controls,Diabetic hypoglycemia,Patients with diabetic hypoglycemia obtained from the FinnGen consortium.,271817,7332,NA,NA,NA,Illumina,NA,NA,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,10 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Significant results between the gut microbiota and the six common complications of diabetes.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae",3379134|1224|28216|80840|506;1783272|1239|186801|186802|216572|216851;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3085636|1185407,Complete,Svetlana up
bsdb:38481313/2/1,38481313,"cross-sectional observational, not case-control",38481313,10.1186/s13098-024-01298-9,NA,"Wang J., Teng M., Feng R., Su X., Xu K., Wang J., Wang G., Zhang Y. , Xu P.",Large-scale causal analysis of gut microbiota and six common complications of diabetes: a mendelian randomization study,Diabetology & metabolic syndrome,2024,"Complications of diabetes, Genome-wise association studies, Gut microbiota, Mendelian randomization study, Single-nucleotide polymorphism",Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Diabetic ketoacidosis,EFO:1000897,Controls,Diabetic ketoacidosis,Patients with diabetic ketoacidosis obtained from the FinnGen consortium.,271817,7841,NA,NA,NA,Illumina,NA,NA,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Significant results between the gut microbiota and the six common complications of diabetes.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella",1783272|201174|84998|1643822|1643826|447020;1783272|1239|909932|1843489|31977|209879;3379134|976|200643|171549|171550|239759;1783272|201174|84998|84999|1643824|133925,Complete,Svetlana up
bsdb:38481313/2/2,38481313,"cross-sectional observational, not case-control",38481313,10.1186/s13098-024-01298-9,NA,"Wang J., Teng M., Feng R., Su X., Xu K., Wang J., Wang G., Zhang Y. , Xu P.",Large-scale causal analysis of gut microbiota and six common complications of diabetes: a mendelian randomization study,Diabetology & metabolic syndrome,2024,"Complications of diabetes, Genome-wise association studies, Gut microbiota, Mendelian randomization study, Single-nucleotide polymorphism",Experiment 2,Finland,Homo sapiens,Feces,UBERON:0001988,Diabetic ketoacidosis,EFO:1000897,Controls,Diabetic ketoacidosis,Patients with diabetic ketoacidosis obtained from the FinnGen consortium.,271817,7841,NA,NA,NA,Illumina,NA,NA,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,10 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Significant results between the gut microbiota and the six common complications of diabetes.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales",1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|216572|3068309;3379134|200940|3031449|213115,Complete,Svetlana up
bsdb:38481313/3/1,38481313,"cross-sectional observational, not case-control",38481313,10.1186/s13098-024-01298-9,NA,"Wang J., Teng M., Feng R., Su X., Xu K., Wang J., Wang G., Zhang Y. , Xu P.",Large-scale causal analysis of gut microbiota and six common complications of diabetes: a mendelian randomization study,Diabetology & metabolic syndrome,2024,"Complications of diabetes, Genome-wise association studies, Gut microbiota, Mendelian randomization study, Single-nucleotide polymorphism",Experiment 3,Finland,Homo sapiens,Feces,UBERON:0001988,Diabetic nephropathy,EFO:0000401,Controls,Diabetic Nephropathy,Patients with diabetic nephropathy obtained from the FinnGen consortium.,308539,4111,NA,NA,NA,Illumina,NA,NA,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Significant results between the gut microbiota and the six common complications of diabetes.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales",3379134|976|200643;3379134|74201|203494|48461|203557;3379134|74201|203494;3379134|74201|203494|48461|1647988|239934;1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|3085636|186803|1506553;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549;3379134|976;3379134|74201|203494|48461,Complete,Svetlana up
bsdb:38481313/3/2,38481313,"cross-sectional observational, not case-control",38481313,10.1186/s13098-024-01298-9,NA,"Wang J., Teng M., Feng R., Su X., Xu K., Wang J., Wang G., Zhang Y. , Xu P.",Large-scale causal analysis of gut microbiota and six common complications of diabetes: a mendelian randomization study,Diabetology & metabolic syndrome,2024,"Complications of diabetes, Genome-wise association studies, Gut microbiota, Mendelian randomization study, Single-nucleotide polymorphism",Experiment 3,Finland,Homo sapiens,Feces,UBERON:0001988,Diabetic nephropathy,EFO:0000401,Controls,Diabetic Nephropathy,Patients with diabetic nephropathy obtained from the FinnGen consortium.,308539,4111,NA,NA,NA,Illumina,NA,NA,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,10 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Significant results between the gut microbiota and the six common complications of diabetes.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|91061|186826|1300|1357;3379134|256845|1313211|278082|255528,Complete,Svetlana up
bsdb:38481313/4/1,38481313,"cross-sectional observational, not case-control",38481313,10.1186/s13098-024-01298-9,NA,"Wang J., Teng M., Feng R., Su X., Xu K., Wang J., Wang G., Zhang Y. , Xu P.",Large-scale causal analysis of gut microbiota and six common complications of diabetes: a mendelian randomization study,Diabetology & metabolic syndrome,2024,"Complications of diabetes, Genome-wise association studies, Gut microbiota, Mendelian randomization study, Single-nucleotide polymorphism",Experiment 4,Finland,Homo sapiens,Feces,UBERON:0001988,Diabetic retinopathy,EFO:0003770,Controls,Diabetic Retinopathy,Patients with diabetic retinopathy obtained from the FinnGen consortium.,308633,10413,NA,NA,NA,Illumina,NA,NA,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Significant results between the gut microbiota and the six common complications of diabetes.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota",3379134|976|200643|171549|171550|239759;1783272|201174|84998|1643822|1643826|84111;1783272|1239,Complete,Svetlana up
bsdb:38481313/4/2,38481313,"cross-sectional observational, not case-control",38481313,10.1186/s13098-024-01298-9,NA,"Wang J., Teng M., Feng R., Su X., Xu K., Wang J., Wang G., Zhang Y. , Xu P.",Large-scale causal analysis of gut microbiota and six common complications of diabetes: a mendelian randomization study,Diabetology & metabolic syndrome,2024,"Complications of diabetes, Genome-wise association studies, Gut microbiota, Mendelian randomization study, Single-nucleotide polymorphism",Experiment 4,Finland,Homo sapiens,Feces,UBERON:0001988,Diabetic retinopathy,EFO:0003770,Controls,Diabetic Retinopathy,Patients with diabetic retinopathy obtained from the FinnGen consortium.,308633,10413,NA,NA,NA,Illumina,NA,NA,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,10 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Significant results between the gut microbiota and the six common complications of diabetes.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes",1783272|1239|909932|1843488|909930;1783272|1239|186801|186802|186807;1783272|1239|186801|186802|186806|1730|290054,Complete,Svetlana up
bsdb:38481313/5/1,38481313,"cross-sectional observational, not case-control",38481313,10.1186/s13098-024-01298-9,NA,"Wang J., Teng M., Feng R., Su X., Xu K., Wang J., Wang G., Zhang Y. , Xu P.",Large-scale causal analysis of gut microbiota and six common complications of diabetes: a mendelian randomization study,Diabetology & metabolic syndrome,2024,"Complications of diabetes, Genome-wise association studies, Gut microbiota, Mendelian randomization study, Single-nucleotide polymorphism",Experiment 5,Finland,Homo sapiens,Feces,UBERON:0001988,Diabetic neuropathy,EFO:1000783,Controls,Diabetic Neuropathy,Patients with diabetic neuropathy obtained from the FinnGen consortium.,271817,2843,NA,NA,NA,Illumina,NA,NA,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Significant results between the gut microbiota and the six common complications of diabetes.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549;3379134|976|200643;1783272|1239|909932|1843489|31977|39948;1783272|201174|84998|84999|1643824|133925;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|543314|35518;3379134|976|200643|171549|2005473,Complete,Svetlana up
bsdb:38481313/5/2,38481313,"cross-sectional observational, not case-control",38481313,10.1186/s13098-024-01298-9,NA,"Wang J., Teng M., Feng R., Su X., Xu K., Wang J., Wang G., Zhang Y. , Xu P.",Large-scale causal analysis of gut microbiota and six common complications of diabetes: a mendelian randomization study,Diabetology & metabolic syndrome,2024,"Complications of diabetes, Genome-wise association studies, Gut microbiota, Mendelian randomization study, Single-nucleotide polymorphism",Experiment 5,Finland,Homo sapiens,Feces,UBERON:0001988,Diabetic neuropathy,EFO:1000783,Controls,Diabetic Neuropathy,Patients with diabetic neuropathy obtained from the FinnGen consortium.,271817,2843,NA,NA,NA,Illumina,NA,NA,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,10 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Significant results between the gut microbiota and the six common complications of diabetes.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,1783272|1239|186801|3085636|186803|1432051,Complete,Svetlana up
bsdb:38481313/6/1,38481313,"cross-sectional observational, not case-control",38481313,10.1186/s13098-024-01298-9,NA,"Wang J., Teng M., Feng R., Su X., Xu K., Wang J., Wang G., Zhang Y. , Xu P.",Large-scale causal analysis of gut microbiota and six common complications of diabetes: a mendelian randomization study,Diabetology & metabolic syndrome,2024,"Complications of diabetes, Genome-wise association studies, Gut microbiota, Mendelian randomization study, Single-nucleotide polymorphism",Experiment 6,Finland,Homo sapiens,Feces,UBERON:0001988,Diabetic foot,EFO:1001459,Controls,Charcot foot,Patients with Charcot foot obtained from the FinnGen consortium.,271817,473,NA,NA,NA,Illumina,NA,NA,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,10 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Significant results between the gut microbiota and the six common complications of diabetes.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota",1783272|1239|186801|3085636|186803|207244;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|3085636|186803|1649459;1783272|1239,Complete,Svetlana up
bsdb:38481313/6/2,38481313,"cross-sectional observational, not case-control",38481313,10.1186/s13098-024-01298-9,NA,"Wang J., Teng M., Feng R., Su X., Xu K., Wang J., Wang G., Zhang Y. , Xu P.",Large-scale causal analysis of gut microbiota and six common complications of diabetes: a mendelian randomization study,Diabetology & metabolic syndrome,2024,"Complications of diabetes, Genome-wise association studies, Gut microbiota, Mendelian randomization study, Single-nucleotide polymorphism",Experiment 6,Finland,Homo sapiens,Feces,UBERON:0001988,Diabetic foot,EFO:1001459,Controls,Charcot foot,Patients with Charcot foot obtained from the FinnGen consortium.,271817,473,NA,NA,NA,Illumina,NA,NA,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,10 February 2025,Aleru Divine,"Aleru Divine,WikiWorks",Significant results between the gut microbiota and the six common complications of diabetes.,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales",1783272|1239|526524|526525|128827;1783272|1239|526524;1783272|1239|186801|186802|186807;1783272|1239|909932|1843488|909930|33024;1783272|1239|526524|526525,Complete,Svetlana up
bsdb:38481313/7/1,38481313,"cross-sectional observational, not case-control",38481313,10.1186/s13098-024-01298-9,NA,"Wang J., Teng M., Feng R., Su X., Xu K., Wang J., Wang G., Zhang Y. , Xu P.",Large-scale causal analysis of gut microbiota and six common complications of diabetes: a mendelian randomization study,Diabetology & metabolic syndrome,2024,"Complications of diabetes, Genome-wise association studies, Gut microbiota, Mendelian randomization study, Single-nucleotide polymorphism",Experiment 7,Finland,Homo sapiens,Feces,UBERON:0001988,Hypoglycemia,HP:0001943,Controls,Diabetic hypoglycemia,Patients with diabetic hypoglycemia obtained from the FinnGen consortium.,271817,7332,NA,NA,NA,Illumina,NA,NA,0.05,TRUE,NA,NA,"age,alcohol drinking,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,10 February 2025,Aleru Divine,"Aleru Divine,WikiWorks","Multivariate Mendelian Randomization (MR) results: After adjusting for confounding factors, including consumption of alcoholic drinks, LDL levels, TG levels, and smoking.",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,3379134|976|200643,Complete,Svetlana up
bsdb:38491387/1/1,38491387,case-control,38491387,10.1186/s12866-024-03233-4,NA,"Chen H., Jiang X., Zhu F., Yang R., Yu X., Zhou X. , Tang N.",Characteristics of the oral and gastric microbiome in patients with early-stage intramucosal esophageal squamous cell carcinoma,BMC microbiology,2024,"Amplicon sequencing analysis, Early esophageal cancer, Gastric microbiome, Intramucosal esophageal squamous carcinoma, Oral microbiome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Esophageal squamous cell carcinoma,EFO:0005922,NC_oral - No carcinoma.,EIESC_oral - Early-stage intramucosal esophageal squamous carcinoma.,Patients diagnosed with Early-stage Intramucosal Esophageal Squamous Carcinoma (EIESC) who provided Oral samples (saliva).,21,31,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Fig. 5A,20 March 2024,Victoria,"Victoria,WikiWorks","LEfSe analysis. Plot of LDA Effect Size. The length of the bar column represents the LDA score.
The figure shows the oral microbial taxa with significant differences between the EIESC (orange) and Control (green) (LDA score>2)",increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter",3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;3384189|32066|203490|203491|1129771|32067;3384189|32066|203490|203491|1129771;1783272|1239|1737404|1737405|1570339|543311;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836;3384194|508458|649775|649776|3029088|638847,Complete,Svetlana up
bsdb:38491387/1/2,38491387,case-control,38491387,10.1186/s12866-024-03233-4,NA,"Chen H., Jiang X., Zhu F., Yang R., Yu X., Zhou X. , Tang N.",Characteristics of the oral and gastric microbiome in patients with early-stage intramucosal esophageal squamous cell carcinoma,BMC microbiology,2024,"Amplicon sequencing analysis, Early esophageal cancer, Gastric microbiome, Intramucosal esophageal squamous carcinoma, Oral microbiome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Esophageal squamous cell carcinoma,EFO:0005922,NC_oral - No carcinoma.,EIESC_oral - Early-stage intramucosal esophageal squamous carcinoma.,Patients diagnosed with Early-stage Intramucosal Esophageal Squamous Carcinoma (EIESC) who provided Oral samples (saliva).,21,31,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Fig. 5A,20 March 2024,Victoria,"Victoria,WikiWorks","LEfSe analysis. Plot of LDA Effect Size. The length of the bar column represents the LDA score.
The figure shows the oral microbial taxa with significant differences between the EIESC (orange) and Control (green) (LDA score > 2).",decreased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,k__Pseudomonadati|p__Gemmatimonadota|c__Gemmatimonadia|o__Gemmatimonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae,k__Pseudomonadati|p__Thermomicrobiota|c__Thermomicrobia",3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294;3379134|29547|3031852|213849;1783272|1239|186801|186802|31979|1485;3379134|29547|3031852;3379134|142182|219685|219686;3379134|1224|1236|135614|32033|68;1783272|201174|1760|85006|85017;3379134|3027942|189775,Complete,Svetlana up
bsdb:38491387/2/NA,38491387,case-control,38491387,10.1186/s12866-024-03233-4,NA,"Chen H., Jiang X., Zhu F., Yang R., Yu X., Zhou X. , Tang N.",Characteristics of the oral and gastric microbiome in patients with early-stage intramucosal esophageal squamous cell carcinoma,BMC microbiology,2024,"Amplicon sequencing analysis, Early esophageal cancer, Gastric microbiome, Intramucosal esophageal squamous carcinoma, Oral microbiome",Experiment 2,China,Homo sapiens,Mucosa of body of stomach,UBERON:0004995,Esophageal squamous cell carcinoma,EFO:0005922,No Carcinoma (NC)_gastric,Early-stage Intramucosal Esophageal Squamous Carcinoma  (EIESC)_gastric,Patients diagnosed with Early-stage Intramucosal Esophageal Squamous Carcinoma (EIESC) who provided Gastric biopsy samples.,21,31,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:38517896/1/1,38517896,laboratory experiment,38517896,https://doi.org/10.1016/j.celrep.2024.113953,NA,"Griffiths J.A., Yoo B.B., Thuy-Boun P., Cantu V.J., Weldon K.C., Challis C., Sweredoski M.J., Chan K.Y., Thron T.M., Sharon G., Moradian A., Humphrey G., Zhu Q., Shaffer J.P., Wolan D.W., Dorrestein P.C., Knight R., Gradinaru V. , Mazmanian S.K.",Peripheral neuronal activation shapes the microbiome and alters gut physiology,Cell reports,2024,"Akkermansia muciniphila, CP: Microbiology, CP: Neuroscience, cholinergic, dopaminergic, enteric nervous system, gut microbiome, gut motility, noradrenergic, peripheral nervous system",Experiment 1,United States of America,Mus musculus,Cecum mucosa,UBERON:0000314,Peripheral neuron,CL:2000032,Control mice,ChAT+ (Choline acetyltransferase) -activated mice,ChAT+ (Choline acetyltransferase) -activated mice were treated with C21 ( compound 21) (3 mg/kg) administered daily for 10 consecutive days.,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 2K,17 April 2025,PreciousChijioke,"PreciousChijioke,KateRasheed",Gut-associated ChAT+ and TH+ neuronal activation alters the gut microbiome,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinilabiliaceae",3379134|74201|203494|48461|1647988;1783272|201174|1760|85004|31953;3379134|976|200643|1970189|558415,Complete,KateRasheed
bsdb:38517896/1/2,38517896,laboratory experiment,38517896,https://doi.org/10.1016/j.celrep.2024.113953,NA,"Griffiths J.A., Yoo B.B., Thuy-Boun P., Cantu V.J., Weldon K.C., Challis C., Sweredoski M.J., Chan K.Y., Thron T.M., Sharon G., Moradian A., Humphrey G., Zhu Q., Shaffer J.P., Wolan D.W., Dorrestein P.C., Knight R., Gradinaru V. , Mazmanian S.K.",Peripheral neuronal activation shapes the microbiome and alters gut physiology,Cell reports,2024,"Akkermansia muciniphila, CP: Microbiology, CP: Neuroscience, cholinergic, dopaminergic, enteric nervous system, gut microbiome, gut motility, noradrenergic, peripheral nervous system",Experiment 1,United States of America,Mus musculus,Cecum mucosa,UBERON:0000314,Peripheral neuron,CL:2000032,Control mice,ChAT+ (Choline acetyltransferase) -activated mice,ChAT+ (Choline acetyltransferase) -activated mice were treated with C21 ( compound 21) (3 mg/kg) administered daily for 10 consecutive days.,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 2K,17 April 2025,PreciousChijioke,PreciousChijioke,Gut-associated ChAT+ and TH+ neuronal activation alters the gut microbiome,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__Eubacteriales Family XIII. Incertae Sedis bacterium",3379134|976|200643|171549|2005519;1783272|1239|186801|186802|31979;1783272|1239|91061|186826|81852;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|186806;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|1853231;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550;1783272|1239|186801|3082720|543314|2137877,Complete,KateRasheed
bsdb:38517896/2/1,38517896,laboratory experiment,38517896,https://doi.org/10.1016/j.celrep.2024.113953,NA,"Griffiths J.A., Yoo B.B., Thuy-Boun P., Cantu V.J., Weldon K.C., Challis C., Sweredoski M.J., Chan K.Y., Thron T.M., Sharon G., Moradian A., Humphrey G., Zhu Q., Shaffer J.P., Wolan D.W., Dorrestein P.C., Knight R., Gradinaru V. , Mazmanian S.K.",Peripheral neuronal activation shapes the microbiome and alters gut physiology,Cell reports,2024,"Akkermansia muciniphila, CP: Microbiology, CP: Neuroscience, cholinergic, dopaminergic, enteric nervous system, gut microbiome, gut motility, noradrenergic, peripheral nervous system",Experiment 2,United States of America,Mus musculus,Cecum mucosa,UBERON:0000314,Peripheral neuron,CL:2000032,Control mice,TH+ (Tyrosine hydroxylase) -activated mice,TH+ (Tyrosine hydroxylase) -activated mice were treated with C21 ( compound 21) (3 mg/kg) administered daily for 10 consecutive days.,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 2M,17 April 2025,PreciousChijioke,PreciousChijioke,Gut-associated ChAT+ and TH+ neuronal activation alters the gut microbiome,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae",3379134|976|200643|171549|815;3379134|976|200643|171549|171552;3379134|976|200643|171549|2005525,Complete,KateRasheed
bsdb:38517896/2/2,38517896,laboratory experiment,38517896,https://doi.org/10.1016/j.celrep.2024.113953,NA,"Griffiths J.A., Yoo B.B., Thuy-Boun P., Cantu V.J., Weldon K.C., Challis C., Sweredoski M.J., Chan K.Y., Thron T.M., Sharon G., Moradian A., Humphrey G., Zhu Q., Shaffer J.P., Wolan D.W., Dorrestein P.C., Knight R., Gradinaru V. , Mazmanian S.K.",Peripheral neuronal activation shapes the microbiome and alters gut physiology,Cell reports,2024,"Akkermansia muciniphila, CP: Microbiology, CP: Neuroscience, cholinergic, dopaminergic, enteric nervous system, gut microbiome, gut motility, noradrenergic, peripheral nervous system",Experiment 2,United States of America,Mus musculus,Cecum mucosa,UBERON:0000314,Peripheral neuron,CL:2000032,Control mice,TH+ (Tyrosine hydroxylase) -activated mice,TH+ (Tyrosine hydroxylase) -activated mice were treated with C21 ( compound 21) (3 mg/kg) administered daily for 10 consecutive days.,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 2M,17 April 2025,PreciousChijioke,PreciousChijioke,Gut-associated ChAT+ and TH+ neuronal activation alters the gut microbiome,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|201174|84998|1643822|1643826;1783272|1239|186801|3085636|186803,Complete,KateRasheed
bsdb:38517896/3/1,38517896,laboratory experiment,38517896,https://doi.org/10.1016/j.celrep.2024.113953,NA,"Griffiths J.A., Yoo B.B., Thuy-Boun P., Cantu V.J., Weldon K.C., Challis C., Sweredoski M.J., Chan K.Y., Thron T.M., Sharon G., Moradian A., Humphrey G., Zhu Q., Shaffer J.P., Wolan D.W., Dorrestein P.C., Knight R., Gradinaru V. , Mazmanian S.K.",Peripheral neuronal activation shapes the microbiome and alters gut physiology,Cell reports,2024,"Akkermansia muciniphila, CP: Microbiology, CP: Neuroscience, cholinergic, dopaminergic, enteric nervous system, gut microbiome, gut motility, noradrenergic, peripheral nervous system",Experiment 3,United States of America,Mus musculus,Cecum mucosa,UBERON:0000314,Peripheral neuron,CL:2000032,Contol mice on day 10,ChAT+ (Choline acetyltransferase) -activated mice on day 10,ChAT+ (Choline acetyltransferase) -activated mice were treated with C21 ( compound 21) (3 mg/kg) administered daily for 10 consecutive days.,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig S6,17 April 2025,PreciousChijioke,PreciousChijioke,Annotated changes in gut bacteria,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|526524|526525|2810280|3025755|29348;1783272|1239|91061|1385|186817|1386;3379134|976|200643|171549|171552|2974257|386414;1783272|201174|1760|85004|31953|1678|1694;1783272|1239|186801|3085636|186803|207244|105841,Complete,KateRasheed
bsdb:38517896/3/2,38517896,laboratory experiment,38517896,https://doi.org/10.1016/j.celrep.2024.113953,NA,"Griffiths J.A., Yoo B.B., Thuy-Boun P., Cantu V.J., Weldon K.C., Challis C., Sweredoski M.J., Chan K.Y., Thron T.M., Sharon G., Moradian A., Humphrey G., Zhu Q., Shaffer J.P., Wolan D.W., Dorrestein P.C., Knight R., Gradinaru V. , Mazmanian S.K.",Peripheral neuronal activation shapes the microbiome and alters gut physiology,Cell reports,2024,"Akkermansia muciniphila, CP: Microbiology, CP: Neuroscience, cholinergic, dopaminergic, enteric nervous system, gut microbiome, gut motility, noradrenergic, peripheral nervous system",Experiment 3,United States of America,Mus musculus,Cecum mucosa,UBERON:0000314,Peripheral neuron,CL:2000032,Contol mice on day 10,ChAT+ (Choline acetyltransferase) -activated mice on day 10,ChAT+ (Choline acetyltransferase) -activated mice were treated with C21 ( compound 21) (3 mg/kg) administered daily for 10 consecutive days.,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig S6,17 April 2025,PreciousChijioke,PreciousChijioke,Annotated changes in gut bacteria,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum desmolans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella|s__Allofournierella massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum lactatifermentans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp. G3(2012),k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella viscericola,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. KLE 1732,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas synergistica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. L2-50,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. SY8519,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp. 5-2,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella tayi,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium plexicaudatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. 14-2,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena contorta,k__Bacillati|p__Bacillota|s__Firmicutes bacterium ASF500,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas massiliensis (ex Afouda et al. 2020),k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 3-1,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium A2,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia|s__Marvinbryantia formatexigens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis|s__Merdimmobilis hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 1-3,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum variabile,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] methylpentosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas nexilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus|s__Candidatus Stoquefichus sp. SB1,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 10-1,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium MA2020,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium M18-1,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 28-4",1783272|1239|186801|186802|3085642|2048137|39484;3379134|976|200643|171549|171550|239759|2585118;3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|171550|239759|1288121;1783272|1239|186801|186802|216572|1940255|1650663;1783272|1239|186801|3085636|3118652|2039240|160404;1783272|1239|186801|186802|216572|244127|1235835;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|2005519|397864|397865;1783272|1239|186801|3085636|186803|572511|1322;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|572511|1226324;3379134|976|200643|171549|1853231|574697|544644;3379134|976|200643|171549|1853231|574697|544645;1783272|1239|186801|186802|31979|1485|411489;1783272|1239|186801|186802|31979|1485|1042156;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|33042|33043;1783272|1239|186801|3085636|186803|189330|1235798;1783272|1239|186801|3085636|186803|1432051|1432052;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|186801|186802|186806|1730|97253;1783272|1239|186801|186802|186806|1730|1235790;1783272|1239|186801|3085636|186803|2005359|39482;1783272|1239|1378168;1783272|1239|186801|186802|216572|946234|292800;3379134|976|200643|171549|171552|2974257|28127;1783272|1239|186801|186802|1392389|1673721;1783272|1239|186801|3085636|186803|397288;1783272|1239|186801|3085636|186803|397290;1783272|1239|186801|3085636|186803|248744|168384;1783272|1239|186801|186802|216572|3028852|2897707;1783272|1239|186801|186802|216572|459786|1235797;1783272|1239|186801|186802|216572|459786|351091;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|186802|216572|1263|438033;1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|186801|186802|216572|292632|214851;1783272|1239|186801|186802|216572|84026;1783272|1239|186801|3085636|186803|2005355|29361;1783272|1239|186801|3085636|186803|2941495|1512;1783272|1239|526524|526525|128827|1470349|1658109;1783272|1239|186801|3085636|186803|1235800;1783272|1239|186801|3085636|186803|1408323;1783272|1239|186801|3085636|186803|1235792;1783272|1239|186801|3085636|186803|397287,Complete,KateRasheed
bsdb:38517896/4/1,38517896,laboratory experiment,38517896,https://doi.org/10.1016/j.celrep.2024.113953,NA,"Griffiths J.A., Yoo B.B., Thuy-Boun P., Cantu V.J., Weldon K.C., Challis C., Sweredoski M.J., Chan K.Y., Thron T.M., Sharon G., Moradian A., Humphrey G., Zhu Q., Shaffer J.P., Wolan D.W., Dorrestein P.C., Knight R., Gradinaru V. , Mazmanian S.K.",Peripheral neuronal activation shapes the microbiome and alters gut physiology,Cell reports,2024,"Akkermansia muciniphila, CP: Microbiology, CP: Neuroscience, cholinergic, dopaminergic, enteric nervous system, gut microbiome, gut motility, noradrenergic, peripheral nervous system",Experiment 4,United States of America,Mus musculus,Cecum mucosa,UBERON:0000314,Peripheral neuron,CL:2000032,Control mice on day 10,TH+ (Tyrosine hydroxylase) -activated mice on day 10,TH+ (Tyrosine hydroxylase) -activated mice were treated with C21 ( compound 21) (3 mg/kg) administered daily for 10 consecutive days.,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig S6,18 April 2025,PreciousChijioke,PreciousChijioke,Annotated changes in gut bacteria,increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. KLE 1745,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter laneus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes timonensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides pyogenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella dentalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella enoeca",3379134|200940|3031449|213115|194924|872|901;1783272|1239|526524|526525|2810280|3025755|29348;1783272|1239|186801|186802|216572|459786|1226323;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|186802|1392389|1297617;3379134|976|200643|171549|2005525|375288|328812;3379134|976|200643|171549|1853231|283168|626933;3379134|976|200643|171549|171550|239759|2585118;3379134|976|200643|171549|171550|239759|1465754;3379134|976|200643|171549|171550|239759|1288121;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|815|816|46506;3379134|976|200643|171549|815|816|291644;3379134|976|200643|171549|815|816|310300;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|171552|838|52227;3379134|976|200643|171549|171552|2974257|76123,Complete,KateRasheed
bsdb:38517896/4/2,38517896,laboratory experiment,38517896,https://doi.org/10.1016/j.celrep.2024.113953,NA,"Griffiths J.A., Yoo B.B., Thuy-Boun P., Cantu V.J., Weldon K.C., Challis C., Sweredoski M.J., Chan K.Y., Thron T.M., Sharon G., Moradian A., Humphrey G., Zhu Q., Shaffer J.P., Wolan D.W., Dorrestein P.C., Knight R., Gradinaru V. , Mazmanian S.K.",Peripheral neuronal activation shapes the microbiome and alters gut physiology,Cell reports,2024,"Akkermansia muciniphila, CP: Microbiology, CP: Neuroscience, cholinergic, dopaminergic, enteric nervous system, gut microbiome, gut motility, noradrenergic, peripheral nervous system",Experiment 4,United States of America,Mus musculus,Cecum mucosa,UBERON:0000314,Peripheral neuron,CL:2000032,Control mice on day 10,TH+ (Tyrosine hydroxylase) -activated mice on day 10,TH+ (Tyrosine hydroxylase) -activated mice were treated with C21 ( compound 21) (3 mg/kg) administered daily for 10 consecutive days.,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig S6,18 April 2025,PreciousChijioke,PreciousChijioke,Annotated changes in gut bacteria,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia caecimuris,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia mucosicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium A2,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium MD335,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 28-4,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 2_1_46FAA",1783272|201174|84998|1643822|1643826|447020|671266;1783272|201174|84998|1643822|1643826|447020|580026;1783272|1239|186801|3085636|186803|397290;1783272|1239|186801|3085636|186803|1235793;1783272|1239|186801|3085636|186803|2316020|1720300;1783272|1239|186801|3085636|186803|397287;1783272|1239|186801|3085636|186803|742723,Complete,KateRasheed
bsdb:38517896/5/1,38517896,laboratory experiment,38517896,https://doi.org/10.1016/j.celrep.2024.113953,NA,"Griffiths J.A., Yoo B.B., Thuy-Boun P., Cantu V.J., Weldon K.C., Challis C., Sweredoski M.J., Chan K.Y., Thron T.M., Sharon G., Moradian A., Humphrey G., Zhu Q., Shaffer J.P., Wolan D.W., Dorrestein P.C., Knight R., Gradinaru V. , Mazmanian S.K.",Peripheral neuronal activation shapes the microbiome and alters gut physiology,Cell reports,2024,"Akkermansia muciniphila, CP: Microbiology, CP: Neuroscience, cholinergic, dopaminergic, enteric nervous system, gut microbiome, gut motility, noradrenergic, peripheral nervous system",Experiment 5,United States of America,Mus musculus,Feces,UBERON:0001988,Peripheral neuron,CL:2000032,Control mice on day 10,ChAT+ (Choline acetyltransferase) -activated mice on day 10,ChAT+ (Choline acetyltransferase) -activated mice were treated with C21 ( compound 21) (3 mg/kg) administered daily for 10 consecutive days.,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig S7,18 April 2025,PreciousChijioke,PreciousChijioke,Gut-Associated Activation-Meditated Changes in the Fecal Microbiome,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;3379134|74201|203494|48461,Complete,KateRasheed
bsdb:38517896/5/2,38517896,laboratory experiment,38517896,https://doi.org/10.1016/j.celrep.2024.113953,NA,"Griffiths J.A., Yoo B.B., Thuy-Boun P., Cantu V.J., Weldon K.C., Challis C., Sweredoski M.J., Chan K.Y., Thron T.M., Sharon G., Moradian A., Humphrey G., Zhu Q., Shaffer J.P., Wolan D.W., Dorrestein P.C., Knight R., Gradinaru V. , Mazmanian S.K.",Peripheral neuronal activation shapes the microbiome and alters gut physiology,Cell reports,2024,"Akkermansia muciniphila, CP: Microbiology, CP: Neuroscience, cholinergic, dopaminergic, enteric nervous system, gut microbiome, gut motility, noradrenergic, peripheral nervous system",Experiment 5,United States of America,Mus musculus,Feces,UBERON:0001988,Peripheral neuron,CL:2000032,Control mice on day 10,ChAT+ (Choline acetyltransferase) -activated mice on day 10,ChAT+ (Choline acetyltransferase) -activated mice were treated with C21 ( compound 21) (3 mg/kg) administered daily for 10 consecutive days.,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig S7,19 April 2025,PreciousChijioke,PreciousChijioke,Gut-Associated Activation-Meditated Changes in the Fecal Microbiome,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Cellulomonadaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Cellulomonadaceae|g__Cellulomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Lawsonia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Heunggongvirae|p__Peploviricota|c__Herviviricetes|o__Herpesvirales|f__Orthoherpesviridae|s__Alphaherpesvirinae|g__Varicellovirus",1783272|201174|84998|1643822|1643826|447020;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|186806|264995;1783272|1239|186801|186802|216572|244127;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|2005519;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;3379134|1224|28216|80840;1783272|1239|526524|526525|128827|1470349;1783272|201174|1760|85006|85016;1783272|201174|1760|85006|85016|1707;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;3379134|976|200643|171549|2005519|1348911;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|1432051;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|186801|186802|186806;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803|2005359;1783272|1239|526524|526525|128827|1573534;3379134|976|117743|200644;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803;3379134|200940|3031449|213115|194924|41707;3379134|976|200643|1970189;1783272|1239|186801|3085636|186803|248744;1783272|201174|1760|85006;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|186801|186802|216572|1017280;3379134|976|200643|171549|171550|28138;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1905344;1783272|1239|186801|3085636|186803|1769710;3379134|203691|203692|136|137;3379134|203691|203692|136;3379134|1224|28216|80840|995019;3379134|976|200643|171549|2005525;3379134|203691|203692|136|2845253|157;1783272|1239|186801|3085636|186803|1506577;2731360|2731361|2731363|548681|3044472|10293|10319,Complete,KateRasheed
bsdb:38517896/6/1,38517896,laboratory experiment,38517896,https://doi.org/10.1016/j.celrep.2024.113953,NA,"Griffiths J.A., Yoo B.B., Thuy-Boun P., Cantu V.J., Weldon K.C., Challis C., Sweredoski M.J., Chan K.Y., Thron T.M., Sharon G., Moradian A., Humphrey G., Zhu Q., Shaffer J.P., Wolan D.W., Dorrestein P.C., Knight R., Gradinaru V. , Mazmanian S.K.",Peripheral neuronal activation shapes the microbiome and alters gut physiology,Cell reports,2024,"Akkermansia muciniphila, CP: Microbiology, CP: Neuroscience, cholinergic, dopaminergic, enteric nervous system, gut microbiome, gut motility, noradrenergic, peripheral nervous system",Experiment 6,United States of America,Mus musculus,Feces,UBERON:0001988,Peripheral neuron,CL:2000032,Control mice on day 6,TH+ (Tyrosine hydroxylase) -activated mice on day 6,TH+ (Tyrosine hydroxylase) -activated mice were treated with C21 ( compound 21) (3 mg/kg) administered daily for 10 consecutive days.,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig S7,18 April 2025,PreciousChijioke,PreciousChijioke,Gut-Associated Activation-Meditated Changes in the Fecal Microbiome,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae",3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525,Complete,KateRasheed
bsdb:38517896/6/2,38517896,laboratory experiment,38517896,https://doi.org/10.1016/j.celrep.2024.113953,NA,"Griffiths J.A., Yoo B.B., Thuy-Boun P., Cantu V.J., Weldon K.C., Challis C., Sweredoski M.J., Chan K.Y., Thron T.M., Sharon G., Moradian A., Humphrey G., Zhu Q., Shaffer J.P., Wolan D.W., Dorrestein P.C., Knight R., Gradinaru V. , Mazmanian S.K.",Peripheral neuronal activation shapes the microbiome and alters gut physiology,Cell reports,2024,"Akkermansia muciniphila, CP: Microbiology, CP: Neuroscience, cholinergic, dopaminergic, enteric nervous system, gut microbiome, gut motility, noradrenergic, peripheral nervous system",Experiment 6,United States of America,Mus musculus,Feces,UBERON:0001988,Peripheral neuron,CL:2000032,Control mice on day 6,TH+ (Tyrosine hydroxylase) -activated mice on day 6,TH+ (Tyrosine hydroxylase) -activated mice were treated with C21 ( compound 21) (3 mg/kg) administered daily for 10 consecutive days.,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig S7,18 April 2025,PreciousChijioke,PreciousChijioke,Gut-Associated Activation-Meditated Changes in the Fecal Microbiome,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Metazoa|p__Chordata|c__Aves|o__Passeriformes|f__Tyrannidae|g__Fluvicola",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3082720|186804|1870884;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|1432051;3379134|976|117743|200644;1783272|1239|186801|186802|216572|1017280;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;33208|7711|8782|9126|28728|196029,Complete,KateRasheed
bsdb:38517896/7/1,38517896,laboratory experiment,38517896,https://doi.org/10.1016/j.celrep.2024.113953,NA,"Griffiths J.A., Yoo B.B., Thuy-Boun P., Cantu V.J., Weldon K.C., Challis C., Sweredoski M.J., Chan K.Y., Thron T.M., Sharon G., Moradian A., Humphrey G., Zhu Q., Shaffer J.P., Wolan D.W., Dorrestein P.C., Knight R., Gradinaru V. , Mazmanian S.K.",Peripheral neuronal activation shapes the microbiome and alters gut physiology,Cell reports,2024,"Akkermansia muciniphila, CP: Microbiology, CP: Neuroscience, cholinergic, dopaminergic, enteric nervous system, gut microbiome, gut motility, noradrenergic, peripheral nervous system",Experiment 7,United States of America,Mus musculus,Cecum mucosa,UBERON:0000314,Peripheral neuron,CL:2000032,Control mice on day 10,ChAT+ (Choline acetyltransferase) -activated mice on day 10,ChAT+ (Choline acetyltransferase) -activated mice were treated with C21 ( compound 21) (3 mg/kg) administered daily for 10 consecutive days.,NA,NA,NA,WMS,NA,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 2N,30 April 2025,PreciousChijioke,PreciousChijioke,Gut-associated ChAT+ and TH+ neuronal activation alters the gut microbiome,increased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,3379134|74201|203494|48461|1647988|239934,Complete,KateRasheed
bsdb:38517896/8/1,38517896,laboratory experiment,38517896,https://doi.org/10.1016/j.celrep.2024.113953,NA,"Griffiths J.A., Yoo B.B., Thuy-Boun P., Cantu V.J., Weldon K.C., Challis C., Sweredoski M.J., Chan K.Y., Thron T.M., Sharon G., Moradian A., Humphrey G., Zhu Q., Shaffer J.P., Wolan D.W., Dorrestein P.C., Knight R., Gradinaru V. , Mazmanian S.K.",Peripheral neuronal activation shapes the microbiome and alters gut physiology,Cell reports,2024,"Akkermansia muciniphila, CP: Microbiology, CP: Neuroscience, cholinergic, dopaminergic, enteric nervous system, gut microbiome, gut motility, noradrenergic, peripheral nervous system",Experiment 8,United States of America,Mus musculus,Feces,UBERON:0001988,Peripheral neuron,CL:2000032,Control mice on day 10,ChAT+ (Choline acetyltransferase) -activated mice on day 10,ChAT+ (Choline acetyltransferase) -activated mice were treated with C21 ( compound 21) (3 mg/kg) administered daily for 10 consecutive days.,NA,NA,NA,WMS,NA,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 2N,30 April 2025,PreciousChijioke,PreciousChijioke,Gut-associated ChAT+ and TH+ neuronal activation alters the gut microbiome,increased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,3379134|74201|203494|48461|1647988|239934,Complete,KateRasheed
bsdb:38528960/1/1,38528960,"cross-sectional observational, not case-control",38528960,https://doi.org/10.1080/20002297.2024.2331264,https://www.tandfonline.com/doi/full/10.1080/20002297.2024.2331264,"Yay E., Yilmaz M., Toygar H., Balci N., Alvarez Rivas C., Bolluk Kılıç B., Zirh A., Paster B.J. , Kantarci A.",Oral and gut microbial profiling in periodontitis and Parkinson's disease,Journal of oral microbiology,2024,"Parkinson’s disease, Periodontitis, microbiome, next-generation sequencing, pathogenesis",Experiment 1,Turkey,Homo sapiens,Saliva,UBERON:0001836,Periodontitis,EFO:0000649,Healthy controls (HC),Periodontitis group (P),"Participants in this group were diagnosed with Stage III, Grade B periodontitis.",17,18,3 months,16S,123,Illumina,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 4 and Figure 6,2 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","Differential abundance in the oral microbiome profiles of the healthy control, Parkinson’s and non-Parkinson’s groups.",increased,"k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma faucium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 346,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 349,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 355,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 356,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia",1783272|544448|2790996|2895623|2895509|56142;1783272|1239|1737404|1737405|1570339|543311|33033;95818|713049;95818|713051;95818|713056;95818|713057;3379134|976|200643|171549|2005525|195950|28112,Complete,Svetlana up
bsdb:38528960/1/2,38528960,"cross-sectional observational, not case-control",38528960,https://doi.org/10.1080/20002297.2024.2331264,https://www.tandfonline.com/doi/full/10.1080/20002297.2024.2331264,"Yay E., Yilmaz M., Toygar H., Balci N., Alvarez Rivas C., Bolluk Kılıç B., Zirh A., Paster B.J. , Kantarci A.",Oral and gut microbial profiling in periodontitis and Parkinson's disease,Journal of oral microbiology,2024,"Parkinson’s disease, Periodontitis, microbiome, next-generation sequencing, pathogenesis",Experiment 1,Turkey,Homo sapiens,Saliva,UBERON:0001836,Periodontitis,EFO:0000649,Healthy controls (HC),Periodontitis group (P),"Participants in this group were diagnosed with Stage III, Grade B periodontitis.",17,18,3 months,16S,123,Illumina,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 4 and Figure 6,2 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","Differential abundance in the oral microbiome profiles of the healthy control, Parkinson’s and non-Parkinson’s groups.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|s__Prevotellaceae bacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp.",1783272|1239|91061|1385|539738|1378|84135;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552|838|60133;3379134|976|200643|171549|171552|2049047;1783272|201174|1760|85006|1268|32207|2047;3379134|1224|28216|206351|481|482|192066,Complete,Svetlana up
bsdb:38528960/2/1,38528960,"cross-sectional observational, not case-control",38528960,https://doi.org/10.1080/20002297.2024.2331264,https://www.tandfonline.com/doi/full/10.1080/20002297.2024.2331264,"Yay E., Yilmaz M., Toygar H., Balci N., Alvarez Rivas C., Bolluk Kılıç B., Zirh A., Paster B.J. , Kantarci A.",Oral and gut microbial profiling in periodontitis and Parkinson's disease,Journal of oral microbiology,2024,"Parkinson’s disease, Periodontitis, microbiome, next-generation sequencing, pathogenesis",Experiment 2,Turkey,Homo sapiens,Saliva,UBERON:0001836,Periodontitis,EFO:0000649,Healthy controls (HC),Parkinson's disease + Periodontitis group (PA + P),"Participants in this group had Parkinson's disease and were also diagnosed with Stage III, Grade B periodontitis.",17,16,3 months,16S,123,Illumina,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,NA,increased,NA,increased,NA,increased,Signature 1,Figure 4 and Figure 6,2 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","Differential abundance in the oral microbiome profiles of the healthy control, Parkinson’s and non-Parkinson’s groups.",increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|s__Prevotellaceae bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp.,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma faucium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 346,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 349,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 355,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 356",1783272|1239|1737404|1737405|1570339|543311|33033;3379134|976|200643|171549|171552|2049047;3379134|1224|28216|206351|481|482|192066;1783272|544448|2790996|2895623|2895509|56142;3379134|976|200643|171549|2005525|195950|28112;95818|713049;95818|713051;95818|713056;95818|713057,Complete,Svetlana up
bsdb:38528960/2/2,38528960,"cross-sectional observational, not case-control",38528960,https://doi.org/10.1080/20002297.2024.2331264,https://www.tandfonline.com/doi/full/10.1080/20002297.2024.2331264,"Yay E., Yilmaz M., Toygar H., Balci N., Alvarez Rivas C., Bolluk Kılıç B., Zirh A., Paster B.J. , Kantarci A.",Oral and gut microbial profiling in periodontitis and Parkinson's disease,Journal of oral microbiology,2024,"Parkinson’s disease, Periodontitis, microbiome, next-generation sequencing, pathogenesis",Experiment 2,Turkey,Homo sapiens,Saliva,UBERON:0001836,Periodontitis,EFO:0000649,Healthy controls (HC),Parkinson's disease + Periodontitis group (PA + P),"Participants in this group had Parkinson's disease and were also diagnosed with Stage III, Grade B periodontitis.",17,16,3 months,16S,123,Illumina,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,NA,increased,NA,increased,NA,increased,Signature 2,Figure 4 and Figure 6,2 November 2024,Aleru Divine,"Aleru Divine,WikiWorks","Differential abundance in the oral microbiome profiles of the healthy control, Parkinson’s and non-Parkinson’s groups.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica",1783272|201174|1760|85006|1268|32207|2047;3379134|976|200643|171549|171552|838|60133;1783272|1239|91061|1385|539738|1378|84135;3379134|976|200643|171549|171552|838|28132,Complete,Svetlana up
bsdb:38528960/4/1,38528960,"cross-sectional observational, not case-control",38528960,https://doi.org/10.1080/20002297.2024.2331264,https://www.tandfonline.com/doi/full/10.1080/20002297.2024.2331264,"Yay E., Yilmaz M., Toygar H., Balci N., Alvarez Rivas C., Bolluk Kılıç B., Zirh A., Paster B.J. , Kantarci A.",Oral and gut microbial profiling in periodontitis and Parkinson's disease,Journal of oral microbiology,2024,"Parkinson’s disease, Periodontitis, microbiome, next-generation sequencing, pathogenesis",Experiment 4,Turkey,Homo sapiens,Feces,UBERON:0001988,Periodontitis,EFO:0000649,Healthy controls (HC),Periodontitis group (P),"Participants in this group were diagnosed with Stage III, Grade B periodontitis.",17,18,3 months,16S,123,Illumina,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 7A,4 November 2024,MyleeeA,"MyleeeA,WikiWorks",Differential abundance in the oral microbiome profiles of the Healthy controls and Periodontitis groups.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus",1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|186801|3085636|186803|3342669|45851;3379134|976|200643|171549|171552|1283313|76122;1783272|1239|909932|1843489|31977|39948|487173,Complete,Svetlana up
bsdb:38528960/4/2,38528960,"cross-sectional observational, not case-control",38528960,https://doi.org/10.1080/20002297.2024.2331264,https://www.tandfonline.com/doi/full/10.1080/20002297.2024.2331264,"Yay E., Yilmaz M., Toygar H., Balci N., Alvarez Rivas C., Bolluk Kılıç B., Zirh A., Paster B.J. , Kantarci A.",Oral and gut microbial profiling in periodontitis and Parkinson's disease,Journal of oral microbiology,2024,"Parkinson’s disease, Periodontitis, microbiome, next-generation sequencing, pathogenesis",Experiment 4,Turkey,Homo sapiens,Feces,UBERON:0001988,Periodontitis,EFO:0000649,Healthy controls (HC),Periodontitis group (P),"Participants in this group were diagnosed with Stage III, Grade B periodontitis.",17,18,3 months,16S,123,Illumina,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 7A,4 November 2024,MyleeeA,"MyleeeA,WikiWorks",Differential abundance in the oral microbiome profiles of the Healthy controls and Periodontitis groups.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,3379134|976|200643|171549|2005525|375288|823,Complete,Svetlana up
bsdb:38528960/5/1,38528960,"cross-sectional observational, not case-control",38528960,https://doi.org/10.1080/20002297.2024.2331264,https://www.tandfonline.com/doi/full/10.1080/20002297.2024.2331264,"Yay E., Yilmaz M., Toygar H., Balci N., Alvarez Rivas C., Bolluk Kılıç B., Zirh A., Paster B.J. , Kantarci A.",Oral and gut microbial profiling in periodontitis and Parkinson's disease,Journal of oral microbiology,2024,"Parkinson’s disease, Periodontitis, microbiome, next-generation sequencing, pathogenesis",Experiment 5,Turkey,Homo sapiens,Feces,UBERON:0001988,Periodontitis,EFO:0000649,Healthy controls (HC),Parkinson's disease + Periodontitis group (PA + P),"Participants in this group had Parkinson's disease and were also diagnosed with Stage III, Grade B periodontitis.",17,16,3 months,16S,123,Illumina,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,NA,increased,NA,increased,NA,NA,Signature 1,Figure 7A,4 November 2024,MyleeeA,"MyleeeA,WikiWorks",Differential abundance in the oral microbiome profiles of the Healthy controls and Parkinson's disease + Periodontitis group (PA + P).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae",1783272|1239|186801|3085636|186803|3342669|45851;3379134|976|200643|171549|171552|1283313|76122,Complete,Svetlana up
bsdb:38528960/5/2,38528960,"cross-sectional observational, not case-control",38528960,https://doi.org/10.1080/20002297.2024.2331264,https://www.tandfonline.com/doi/full/10.1080/20002297.2024.2331264,"Yay E., Yilmaz M., Toygar H., Balci N., Alvarez Rivas C., Bolluk Kılıç B., Zirh A., Paster B.J. , Kantarci A.",Oral and gut microbial profiling in periodontitis and Parkinson's disease,Journal of oral microbiology,2024,"Parkinson’s disease, Periodontitis, microbiome, next-generation sequencing, pathogenesis",Experiment 5,Turkey,Homo sapiens,Feces,UBERON:0001988,Periodontitis,EFO:0000649,Healthy controls (HC),Parkinson's disease + Periodontitis group (PA + P),"Participants in this group had Parkinson's disease and were also diagnosed with Stage III, Grade B periodontitis.",17,16,3 months,16S,123,Illumina,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,NA,increased,NA,increased,NA,NA,Signature 2,Figure 7A,4 November 2024,MyleeeA,"MyleeeA,WikiWorks",Differential abundance in the oral microbiome profiles of the Healthy controls and Parkinson's disease + Periodontitis group (PA + P).,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,3379134|976|200643|171549|2005525|375288|823,Complete,Svetlana up
bsdb:38528960/6/1,38528960,"cross-sectional observational, not case-control",38528960,https://doi.org/10.1080/20002297.2024.2331264,https://www.tandfonline.com/doi/full/10.1080/20002297.2024.2331264,"Yay E., Yilmaz M., Toygar H., Balci N., Alvarez Rivas C., Bolluk Kılıç B., Zirh A., Paster B.J. , Kantarci A.",Oral and gut microbial profiling in periodontitis and Parkinson's disease,Journal of oral microbiology,2024,"Parkinson’s disease, Periodontitis, microbiome, next-generation sequencing, pathogenesis",Experiment 6,Turkey,Homo sapiens,Feces,UBERON:0001988,Periodontitis,EFO:0000649,Periodontitis group (P),Parkinson's disease + Periodontitis group (PA + P),"Participants in this group had Parkinson's disease and were also diagnosed with Stage III, Grade B periodontitis.",18,16,3 months,16S,123,Illumina,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 7A,4 November 2024,MyleeeA,"MyleeeA,WikiWorks",Differential abundance in the oral microbiome profiles of the Periodontitis and Parkinson's disease + Periodontitis group (PA + P).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae",1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|186801|3085636|186803|3342669|45851;3379134|976|200643|171549|171552|1283313|76122,Complete,Svetlana up
bsdb:38528960/6/2,38528960,"cross-sectional observational, not case-control",38528960,https://doi.org/10.1080/20002297.2024.2331264,https://www.tandfonline.com/doi/full/10.1080/20002297.2024.2331264,"Yay E., Yilmaz M., Toygar H., Balci N., Alvarez Rivas C., Bolluk Kılıç B., Zirh A., Paster B.J. , Kantarci A.",Oral and gut microbial profiling in periodontitis and Parkinson's disease,Journal of oral microbiology,2024,"Parkinson’s disease, Periodontitis, microbiome, next-generation sequencing, pathogenesis",Experiment 6,Turkey,Homo sapiens,Feces,UBERON:0001988,Periodontitis,EFO:0000649,Periodontitis group (P),Parkinson's disease + Periodontitis group (PA + P),"Participants in this group had Parkinson's disease and were also diagnosed with Stage III, Grade B periodontitis.",18,16,3 months,16S,123,Illumina,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 7A,4 November 2024,MyleeeA,"MyleeeA,WikiWorks",Differential abundance in the oral microbiome profiles of the Periodontitis and Parkinson's disease + Periodontitis group (PA + P).,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,1783272|1239|186801|186802|216572|1905344|1550024,Complete,Svetlana up
bsdb:38528960/7/1,38528960,"cross-sectional observational, not case-control",38528960,https://doi.org/10.1080/20002297.2024.2331264,https://www.tandfonline.com/doi/full/10.1080/20002297.2024.2331264,"Yay E., Yilmaz M., Toygar H., Balci N., Alvarez Rivas C., Bolluk Kılıç B., Zirh A., Paster B.J. , Kantarci A.",Oral and gut microbial profiling in periodontitis and Parkinson's disease,Journal of oral microbiology,2024,"Parkinson’s disease, Periodontitis, microbiome, next-generation sequencing, pathogenesis",Experiment 7,Turkey,Homo sapiens,"Saliva,Feces","UBERON:0001836,UBERON:0001988",Sampling site,EFO:0000688,Healthy controls (Feces),Healthy controls (Saliva),Saliva samples collected from healthy control participants.,17,17,3 months,16S,123,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary File 2a,5 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",LefSe results representing significant difference in relative abundance in fecal and saliva samples from healthy controls.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli,,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,p__Candidatus Altimarinota,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Nanosynbacterales|f__Candidatus Nanosynbacteraceae|g__Candidatus Nanosynbacter|s__Candidatus Nanosynbacter sp. HMT-352,p__Candidatus Saccharimonadota,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma faucium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia,k__Pseudomonadati|p__Spirochaetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus lactarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 346,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 349,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 351,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 355,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 356,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] brachy,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] sulci,p__Candidatus Absconditibacteriota|s__candidate division SR1 bacterium,p__Candidatus Altimarinota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|91061|186826|186827|46123;1783272|1239|91061|186826|186827|46123|46125;1783272|201174|84992;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;1783272|201174;1783272|1239|91061|186826|186827;1783272|1239|91061|1385;1783272|1239|91061;;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|117743|200644|2762318|59735;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294;3379134|29547|3031852|213849;363464;95818|2093818|2093819|2093822|2093823|2899133;95818;3379134|976|117743|200644|49546|1016;3379134|976|117743|200644|49546|1016|327575;3379134|1224|1236|135615|868;3379134|1224|1236|135615;3379134|1224|1236|135615|868|2717;3379134|1224|1236|135615|868|2717|2718;1783272|1239|91061|186826|186828;3379134|29547|3031852;1783272|1239|186801|3082720|3118655|44259;1783272|1239|186801|3082720|3118655|44259|143361;3379134|976|117743|200644|49546;3379134|976|117743|200644;3379134|976|117743;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;3384189|32066|203490|203491|203492|848;3379134|1224|1236;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|1385|539738|1378|1379;1783272|1239|91061|1385|539738;1783272|1239|91061|186826|186828|117563;1783272|1239|91061|186826;1783272|544448|2790996|2895623|2895509|56142;1783272|201174|1760|85006|1268;1783272|1239|186801|3082720|543314|86331;1783272|544448|31969;1783272|544448|31969|2085|2092|2093;1783272|544448|31969|2085|2092;1783272|544448|31969|2085;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481;3379134|1224|28216|206351;1783272|1239|186801|186802|216572;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|1737404|1737405|1570339;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1257|341694;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|171551|836|1583331;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|43675;1783272|201174|1760|2037|2049|2529408;1783272|1239|909932|909929|1843491|970;1783272|1239|526524|526525|128827|123375;1783272|1239|526524|526525|128827|123375|102148;3379134|203691|203692|136|137;3379134|203691|203692|136;3379134|203691|203692;3379134|203691;1783272|1239|91061|1385|90964;1783272|1239|186801|3085636|186803|1213720;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|684066;1783272|1239|91061|186826|1300|1301|1305;95818|713049;95818|713051;95818|713053;95818|713056;95818|713057;3379134|976|200643|171549|2005525|195950;3379134|976|200643|171549|2005525|195950|28112;3379134|976|200643|171549|2005525;3379134|203691|203692|136|2845253|157;3379134|203691|203692|136|2845253|157|166;1783272|1239|186801|3082720|543314|35517;1783272|1239|186801|3082720|543314|143393;221235|2044938;363464;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:38528960/7/2,38528960,"cross-sectional observational, not case-control",38528960,https://doi.org/10.1080/20002297.2024.2331264,https://www.tandfonline.com/doi/full/10.1080/20002297.2024.2331264,"Yay E., Yilmaz M., Toygar H., Balci N., Alvarez Rivas C., Bolluk Kılıç B., Zirh A., Paster B.J. , Kantarci A.",Oral and gut microbial profiling in periodontitis and Parkinson's disease,Journal of oral microbiology,2024,"Parkinson’s disease, Periodontitis, microbiome, next-generation sequencing, pathogenesis",Experiment 7,Turkey,Homo sapiens,"Saliva,Feces","UBERON:0001836,UBERON:0001988",Sampling site,EFO:0000688,Healthy controls (Feces),Healthy controls (Saliva),Saliva samples collected from healthy control participants.,17,17,3 months,16S,123,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary File 2a,5 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",LefSe results representing significant difference in relative abundance in fecal and saliva samples from healthy controls.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Acutalibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Acutalibacter|s__Acutalibacter muris,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia muris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum desmolans,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella|s__Allofournierella massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Alteracholeplasma|s__Alteracholeplasma parvum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales,,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma|s__Asteroleplasma anaerobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides hominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia caccae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia luti,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Breznakia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Caproiciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Caproiciproducens|s__Caproiciproducens galactitolivorans,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium mitsuokai,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Duncaniella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Duncaniella|s__Duncaniella freteri,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Duodenibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Duodenibacillus|s__Duodenibacillus massiliensis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae|g__Elusimicrobium,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae|g__Elusimicrobium|s__Elusimicrobium minutum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium pacaense,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea|s__Faecalitalea cylindroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella oralis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella shahii,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Ihubacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Kineothrix,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Kineothrix|s__Kineothrix alysoides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora xylanolytica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Massiliprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Massiliprevotella|s__Massiliprevotella massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter massiliensis,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales,k__Methanobacteriati|p__Methanobacteriota,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus|s__Monoglobus pectinilyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Metazoa|p__Arthropoda|c__Insecta|o__Hemiptera|f__Aphididae|s__Aphidinae|g__Ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides faecis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotellamassilia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio|s__Pseudobutyrivibrio ruminis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter|s__Sporobacter termitidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus 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massiliensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] methylpentosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|91061|186826|186827|46123|76631;1783272|1239|186801|186802|3082771|1918385;1783272|1239|186801|186802|3082771|1918385|1796620;1783272|201174|84998|1643822|1643826|447020;1783272|201174|84998|1643822|1643826|447020|1796610;1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|186802|3085642|2048137;1783272|1239|186801|186802|3085642|2048137|39484;3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988|239934|239935;3379134|74201|203494|48461|1647988;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|1940255;1783272|1239|186801|186802|216572|1940255|1650663;3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|171552|1283313|671218;3379134|976|200643|171549|171552|1283313|76122;1783272|544448|31969|186329|2146|2903105|264639;1783272|1239|186801|3085636|186803|2569097|39488;1783272|544448|31969|186332|186333;1783272|544448|31969|186332;;1783272|544448|31969|186332|186333|2152;1783272|544448|31969|186332|186333|2152|2153;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|2763023;3379134|976|200643;3379134|976;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|216816;3379134|200940|3031449|213115|194924|35832;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|3133175;1783272|1239|186801|3085636|186803|572511|89014;1783272|1239|186801|3085636|186803|572511|1955243;1783272|1239|526524|526525|128827|1854458;3379134|1224|28216|80840;1783272|1239|186801|3085636|186803|830;1783272|1239|186801|3085636|186803|830|28121;1783272|1239|186801|186802|3082771|1738645;1783272|1239|186801|186802|3082771|1738645|642589;1783272|1239|526524|526525|2810280|135858;1783272|1239|526524|526525|2810280|135858|100886;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|3082768|990719|990721|1805714;1783272|1239|186801|3082768|990719;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|31979|1485|1506;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|84998|84999|84107|102106|147207;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|33042|33043;1783272|201174|84998|84999|84107;28221;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|39948|487173;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330|88431;3379134|976|200643|171549|2005473|2518495;3379134|976|200643|171549|2005473|2518495|2530391;3379134|1224|28216|80840|995019|1980697;3379134|1224|28216|80840|995019|1980697|1852381;1783272|201174|84998|1643822|1643826;1783272|201174|84998|1643822;3379134|74152|641853;3379134|74152|641853|641854;3379134|74152|641853|641854|641876|423604;3379134|74152|641853|641854|641876|423604|423605;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|186801|186802|31979|1485|1917870;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|186801|3085636|186803|3342669|45851;1783272|1239|186801|186802|186806;1783272|1239|186801|186802;1783272|1239|186801|3082720|543314;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|142586;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|526524|526525|128827|1573534;1783272|1239|526524|526525|128827|1573534|39483;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|526524|526525|128827|1573535;1783272|1239|526524|526525|128827|1573535|1735;3379134|976|200643|171549|171552|2974257|28134;3379134|976|200643|171549|171552|2974257|228603;1783272|1239|186801|3082720|543314|1926667;1783272|1239|186801|3085636|186803|2163168;1783272|1239|186801|3085636|186803|2163168|1469948;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|2719231;1783272|1239|186801|3085636|186803|2719231|29375;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;3384189|32066|203490|203491|1129771|32067|157691;3379134|976|200643|171549|171552|2974265|363265;3379134|976|200643|171549|171552|1981037;3379134|976|200643|171549|171552|1981037|1816687;1783272|1239|186801|3085636|186803|2316020;1783272|1239|186801|3085636|186803|2316020|592978;1783272|1239|186801|3085636|186803|2316020|1720300;3366610|28890|183925;3366610|28890|183925|2158|2159;3366610|28890|183925|2158;3366610|28890;3366610|28890|183925|2158|2159|2172;3366610|28890|183925|2158|2159|2172|2173;1783272|1239|909932|909929|1843491|52225;1783272|544448|31969;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|186801|3085656|3085657|2039302|1981510;3379134|976|200643|171549|2005473;1783272|544448;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|1853231;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|459786|1263547;1783272|1239|186801|186802|216572|459786|1945593;1783272|1239|186801|186802|216572|459786|351091;1783272|1239|186801|186802|216572;33208|6656|50557|7524|27482|133076|666060;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|1217282;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|171552|577309|454154;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|815|909656;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|1926672;1783272|1239|186801|3085636|186803|46205|46206;3379134|976|200643|171549|171550;1783272|1239|186801|3082720|186804|1501226|1776391;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|3085636|186803|841|2049040;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|186801|186802|216572|1263|41978;1783272|1239|186801|186802|216572|1905344;1783272|1239|186801|186802|216572|1905344|1550024;3379134|976|200643|171549|171552|2974251|165179;3379134|976|200643|171549|171552|2974251|28135;1783272|1239|909932|909929|1843491|970|2058293;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|186802|216572|44748|44749;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|216572|292632|214851;3379134|1224|1236|135624|83763|83770;3379134|1224|1236|135624|83763|83770|83771;3379134|1224|1236|135624|83763;3379134|1224|28216|80840|995019|40544;3379134|1224|28216|80840|995019|40544|1816689;3379134|1224|28216|80840|995019;1783272|1239|526524|526525|2810280|3025755;1783272|1239|526524|526525|2810280|3025755|29348;1783272|1239|909932|1843489|31977|29465|423477;1783272|1239|909932|1843489|31977;3379134|74201|203494|48461|203557;3379134|74201|203494|48461;3379134|74201;1783272|1239|186801|186802|216572|84026;1783272|1239|186801|186802|216572|39492;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:38528960/8/1,38528960,"cross-sectional observational, not case-control",38528960,https://doi.org/10.1080/20002297.2024.2331264,https://www.tandfonline.com/doi/full/10.1080/20002297.2024.2331264,"Yay E., Yilmaz M., Toygar H., Balci N., Alvarez Rivas C., Bolluk Kılıç B., Zirh A., Paster B.J. , Kantarci A.",Oral and gut microbial profiling in periodontitis and Parkinson's disease,Journal of oral microbiology,2024,"Parkinson’s disease, Periodontitis, microbiome, next-generation sequencing, pathogenesis",Experiment 8,Turkey,Homo sapiens,"Saliva,Feces","UBERON:0001836,UBERON:0001988",Periodontitis,EFO:0000649,Periodontitis group (P) Feces,Periodontitis group (P) Saliva,Saliva samples collected from Periodontitis participants.,18,18,3 months,16S,123,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary File 2,5 November 2024,MyleeeA,"MyleeeA,Aleru Divine,WikiWorks",LefSe results representing significant difference in relative abundance in fecal and saliva samples from Periodontitis patients.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli,,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma faucium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia,k__Pseudomonadati|p__Spirochaetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus lactarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] brachy,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] sulci",1783272|1239|91061|186826|186827|46123;1783272|1239|91061|186826|186827|46123|46125;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;1783272|201174|1760;1783272|201174;1783272|1239|91061|186826|186827;1783272|1239|91061|1385;1783272|1239|91061;;3379134|976|200643|171549|815;3379134|976|117743|200644|2762318|59735;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294;3379134|29547|3031852|213849;3379134|976|117743|200644|49546|1016;3379134|976|117743|200644|49546|1016|327575;3379134|1224|1236|135615|868;3379134|1224|1236|135615;3379134|1224|1236|135615|868|2717;3379134|1224|1236|135615|868|2717|2718;1783272|1239|91061|186826|186828;3379134|29547|3031852;1783272|1239|186801|3082720|3118655|44259;1783272|1239|186801|3082720|3118655|44259|143361;3379134|976|117743|200644|49546;3379134|976|117743|200644;3379134|976|117743;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;3384189|32066|203490|203491|203492|848;3379134|1224|1236;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|1385|539738|1378|1379;1783272|1239|91061|1385|539738|1378|84135;1783272|1239|91061|1385|539738;1783272|1239|91061|186826|186828|117563;1783272|1239|91061|186826;1783272|544448|2790996|2895623|2895509|56142;1783272|201174|1760|85006|1268;1783272|1239|186801|3082720|543314|86331;1783272|544448|31969;1783272|544448|31969|2085;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|1737404|1737405|1570339;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1257;1783272|1239|186801|3082720|186804|1257|341694;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|171551|836|1583331;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|43675;1783272|201174|1760|2037|2049|2529408;1783272|1239|909932|909929|1843491|970;1783272|1239|526524|526525|128827|123375|102148;3379134|203691|203692|136|137;3379134|203691|203692|136;3379134|203691|203692;3379134|203691;1783272|1239|91061|1385|90964;1783272|1239|186801|3085636|186803|1213720;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|684066;1783272|1239|91061|186826|1300|1301|1305;3379134|976|200643|171549|2005525|195950;3379134|976|200643|171549|2005525|195950|28112;3379134|976|200643|171549|2005525;3379134|203691|203692|136|2845253|157;1783272|1239|526524|526525|2810281|191303|154288;1783272|1239|186801|3082720|543314|35517;1783272|1239|186801|3082720|543314|143393,Complete,Svetlana up
bsdb:38528960/8/2,38528960,"cross-sectional observational, not case-control",38528960,https://doi.org/10.1080/20002297.2024.2331264,https://www.tandfonline.com/doi/full/10.1080/20002297.2024.2331264,"Yay E., Yilmaz M., Toygar H., Balci N., Alvarez Rivas C., Bolluk Kılıç B., Zirh A., Paster B.J. , Kantarci A.",Oral and gut microbial profiling in periodontitis and Parkinson's disease,Journal of oral microbiology,2024,"Parkinson’s disease, Periodontitis, microbiome, next-generation sequencing, pathogenesis",Experiment 8,Turkey,Homo sapiens,"Saliva,Feces","UBERON:0001836,UBERON:0001988",Periodontitis,EFO:0000649,Periodontitis group (P) Feces,Periodontitis group (P) Saliva,Saliva samples collected from Periodontitis participants.,18,18,3 months,16S,123,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary File 2,5 November 2024,MyleeeA,"MyleeeA,Aleru Divine,WikiWorks",LefSe results representing significant difference in relative abundance in fecal and saliva samples from Periodontitis patients.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Acutalibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Acutalibacter|s__Acutalibacter muris,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia muris,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum desmolans,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella|s__Allofournierella massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Alteracholeplasma|s__Alteracholeplasma parvum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales,,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma|s__Asteroleplasma anaerobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia caccae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia luti,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Breznakia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Caproiciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Caproiciproducens|s__Caproiciproducens galactitolivorans,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium mitsuokai,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Duncaniella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Duncaniella|s__Duncaniella freteri,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Duodenibacillus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales,k__Pseudomonadati|p__Elusimicrobiota,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae|g__Elusimicrobium,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae|g__Elusimicrobium|s__Elusimicrobium minutum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium pacaense,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea|s__Faecalitalea cylindroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella oralis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella shahii,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Ihubacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Ihubacter|s__Ihubacter massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Kineothrix,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Kineothrix|s__Kineothrix alysoides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora xylanolytica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Massiliprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Massiliprevotella|s__Massiliprevotella massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter faecis,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales,k__Methanobacteriati|p__Methanobacteriota,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus|s__Monoglobus pectinilyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotellamassilia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio|s__Pseudobutyrivibrio ruminis,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Hymenochaetales|f__Rickenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter|s__Sporobacter termitidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum variabile,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio|s__Succinivibrio dextrinosolvens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella massiliensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|186802|3082771|1918385;1783272|1239|186801|186802|3082771|1918385|1796620;1783272|201174|84998|1643822|1643826|447020;1783272|201174|84998|1643822|1643826|447020|1796610;3379134|1224|1236|135624;1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|186802|3085642|2048137;1783272|1239|186801|186802|3085642|2048137|39484;3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988|239934|239935;3379134|74201|203494|48461|1647988;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|1940255;1783272|1239|186801|186802|216572|1940255|1650663;3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|171552|1283313|671218;3379134|976|200643|171549|171552|1283313|76122;1783272|544448|31969|186329|2146|2903105|264639;1783272|1239|186801|3085636|186803|2569097|39488;1783272|544448|31969|186332|186333;1783272|544448|31969|186332;;1783272|544448|31969|186332|186333|2152;1783272|544448|31969|186332|186333|2152|2153;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|674529;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|329854;3379134|976|200643|171549|815|816|28116;3379134|976|200643;3379134|976;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|216816;3379134|200940|3031449|213115|194924|35832;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|3133175;1783272|1239|186801|3085636|186803|572511|2025493;1783272|1239|186801|3085636|186803|572511|89014;1783272|1239|526524|526525|128827|1854458;3379134|1224|28216|80840;1783272|1239|186801|3085636|186803|830;1783272|1239|186801|186802|3082771|1738645;1783272|1239|186801|186802|3082771|1738645|642589;1783272|1239|526524|526525|2810280|135858;1783272|1239|526524|526525|2810280|135858|100886;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|3082768|990719|990721|1805714;1783272|1239|186801|3082768|990719;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|33042|33043;1783272|201174|84998|84999|84107;28221;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|39948|487173;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330|88431;3379134|976|200643|171549|2005473|2518495;3379134|976|200643|171549|2005473|2518495|2530391;3379134|1224|28216|80840|995019|1980697;1783272|201174|84998|1643822|1643826;1783272|201174|84998|1643822;3379134|74152|641853|641854|641876;3379134|74152|641853|641854;3379134|74152;3379134|74152|641853|641854|641876|423604;3379134|74152|641853|641854|641876|423604|423605;3379134|1224|1236|91347|543;1783272|1239|186801|186802|31979|1485|1917870;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|186801|3085636|186803|3342669|45851;1783272|1239|186801|186802|186806;1783272|1239|186801|186802;1783272|1239|186801|3082720|543314;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|526524|526525|128827|1573534;1783272|1239|526524|526525|128827|1573534|39483;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|526524|526525|128827|1573535;1783272|1239|526524|526525|128827|1573535|1735;3379134|976|200643|171549|171552|2974257|28134;3379134|976|200643|171549|171552|2974257|228603;1783272|1239|186801|3082720|543314|1926667;1783272|1239|186801|3082720|543314|1926667|1852367;1783272|1239|186801|3085636|186803|2163168;1783272|1239|186801|3085636|186803|2163168|1469948;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|2719231;1783272|1239|186801|3085636|186803|2719231|29375;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;3384189|32066|203490|203491|1129771|32067|157691;3379134|976|200643|171549|171552|2974265|363265;3379134|976|200643|171549|171552|1981037;3379134|976|200643|171549|171552|1981037|1816687;1783272|1239|186801|3085636|186803|2316020;1783272|1239|186801|3085636|186803|2316020|592978;3366610|28890|183925;3366610|28890|183925|2158|2159;3366610|28890|183925|2158;3366610|28890;3366610|28890|183925|2158|2159|2172;3366610|28890|183925|2158|2159|2172|2173;1783272|1239|909932|909929|1843491|52225;1783272|544448|31969;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|186801|3085656|3085657|2039302|1981510;3379134|976|200643|171549|2005473;1783272|544448;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|1853231;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|459786|1263547;1783272|1239|186801|186802|216572|459786|351091;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|171552|577309|454154;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|815|909656;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|1926672;1783272|1239|186801|3085636|186803|46205|46206;4751|5204|155619|139380|1124673;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3082720|186804|1501226|1776391;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|186801|186802|216572|1905344;1783272|1239|186801|186802|216572|1905344|1550024;3379134|976|200643|171549|171552|2974251|165179;3379134|976|200643|171549|171552|2974251|28135;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|186802|216572|44748|44749;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|186801|186802|216572|292632|214851;3379134|1224|1236|135624|83763|83770;3379134|1224|1236|135624|83763|83770|83771;3379134|1224|1236|135624|83763;3379134|1224|28216|80840|995019|40544|1816689;3379134|1224|28216|80840|995019;1783272|1239|526524|526525|2810280|3025755;1783272|1239|526524|526525|2810280|3025755|29348;1783272|1239|909932|1843489|31977;3379134|74201|203494|48461;3379134|74201|203494;1783272|1239|186801|186802|216572|39492;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:38528960/9/1,38528960,"cross-sectional observational, not case-control",38528960,https://doi.org/10.1080/20002297.2024.2331264,https://www.tandfonline.com/doi/full/10.1080/20002297.2024.2331264,"Yay E., Yilmaz M., Toygar H., Balci N., Alvarez Rivas C., Bolluk Kılıç B., Zirh A., Paster B.J. , Kantarci A.",Oral and gut microbial profiling in periodontitis and Parkinson's disease,Journal of oral microbiology,2024,"Parkinson’s disease, Periodontitis, microbiome, next-generation sequencing, pathogenesis",Experiment 9,Turkey,Homo sapiens,"Saliva,Feces","UBERON:0001836,UBERON:0001988",Periodontitis,EFO:0000649,Parkinson's disease + Periodontitis group (PA + P) (Feces),Parkinson's disease + Periodontitis group (PA + P) (Saliva),Saliva samples collected from Parkinson's disease + Periodontitis group (PA + P) participants.,16,16,3 months,16S,123,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary File 2c,5 November 2024,Aleru Divine,"Aleru Divine,Svetlana up,WikiWorks",LefSe results representing significant difference in relative abundance in fecal and saliva samples from Periodontitis patients with Parkinson's disease (PA + P).,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli,,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,p__Candidatus Absconditibacteriota|s__Candidatus Absconditabacteria bacterium,p__Candidatus Altimarinota,p__Candidatus Saccharimonadota,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma faucium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia exigua,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia,k__Pseudomonadati|p__Spirochaetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae|g__Tissierella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] brachy,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] sulci",1783272|1239|91061|186826|186827|46123;1783272|1239|91061|186826|186827|46123|46125;1783272|201174|84992;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;1783272|201174;1783272|1239|91061|186826|186827;1783272|1239|91061|1385;1783272|1239|91061;;3379134|976|117743|200644|2762318|59735;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294|194|199;3379134|29547|3031852|213849|72294;3379134|29547|3031852|213849;221235|3018262;363464;95818;3379134|976|117743|200644|49546|1016;1783272|1239|91061|186826|186828;3379134|29547|3031852;3379134|976|117743|200644|49546;3379134|976|117743|200644;3379134|976|117743;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|1385|539738|1378|1379;1783272|1239|91061|1385|539738|1378|1966354;1783272|1239|91061|1385|539738;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712|724|729;1783272|1239|91061|186826;1783272|544448|2790996|2895623|2895509|56142;1783272|201174|1760|85006|1268;1783272|1239|186801|3082720|543314|86331;1783272|544448|31969;1783272|544448|31969|2085|2092|2093;1783272|544448|31969|2085|2092;1783272|544448|31969|2085;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481|482|28449;3379134|1224|28216|206351|481;3379134|1224|28216|206351;1783272|1239|186801|186802|216572;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|1239|1737404|1737405|1570339|543311|1944660;3379134|1224|1236|135625|712;3379134|1224|1236|135625;1783272|1239|1737404|1737405|1570339;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1257;1783272|1239|186801|3082720|186804|1257|341694;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171551|836|1583331;3379134|976|200643|171549|171552|838|28132;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|909932|909929|1843491|970;1783272|201174|84998|1643822|1643826|84108;1783272|201174|84998|1643822|1643826|84108|84109;1783272|1239|526524|526525|128827|123375;1783272|1239|526524|526525|128827|123375|102148;3379134|203691|203692|136|137;3379134|203691|203692|136;3379134|203691|203692;3379134|203691;1783272|1239|91061|1385|90964;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1328;3379134|976|200643|171549|2005525|195950;3379134|976|200643|171549|2005525|195950|28112;3379134|976|200643|171549|2005525;1783272|1239|1737404|1737405|1737406|41273;1783272|1239|1737404|1737405;3379134|203691|203692|136|2845253|157;3379134|203691|203692|136|2845253|157|158;1783272|1239|909932|1843489|31977;1783272|1239|186801|3082720|543314|35517;1783272|1239|186801|3082720|543314|143393,Complete,Svetlana up
bsdb:38528960/9/2,38528960,"cross-sectional observational, not case-control",38528960,https://doi.org/10.1080/20002297.2024.2331264,https://www.tandfonline.com/doi/full/10.1080/20002297.2024.2331264,"Yay E., Yilmaz M., Toygar H., Balci N., Alvarez Rivas C., Bolluk Kılıç B., Zirh A., Paster B.J. , Kantarci A.",Oral and gut microbial profiling in periodontitis and Parkinson's disease,Journal of oral microbiology,2024,"Parkinson’s disease, Periodontitis, microbiome, next-generation sequencing, pathogenesis",Experiment 9,Turkey,Homo sapiens,"Saliva,Feces","UBERON:0001836,UBERON:0001988",Periodontitis,EFO:0000649,Parkinson's disease + Periodontitis group (PA + P) (Feces),Parkinson's disease + Periodontitis group (PA + P) (Saliva),Saliva samples collected from Parkinson's disease + Periodontitis group (PA + P) participants.,16,16,3 months,16S,123,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary File 2,6 November 2024,MyleeeA,"MyleeeA,Aleru Divine,WikiWorks",LefSe results representing significant difference in relative abundance in fecal and saliva samples from Periodontitis patients with Parkinson's disease (PA + P).,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia sp. HMSC24B09,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium|s__Acetanaerobacterium elongatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Acutalibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Acutalibacter|s__Acutalibacter muris,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum desmolans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella|s__Allofournierella massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Alteracholeplasma|s__Alteracholeplasma parvum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus senegalensis,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum faecicola,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma|s__Asteroleplasma anaerobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia caccae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia intestinihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia luti,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Breznakia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Breznakia|s__Breznakia pachnodae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus pullicaecorum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Caecibacter|s__Caecibacter massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Casaltella|s__Casaltella massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae|g__Defluviitalea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Duodenibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Duodenibacillus|s__Duodenibacillus massiliensis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea|s__Faecalitalea cylindroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Thermotaleaceae|g__Geosporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Thermotaleaceae|g__Geosporobacter|s__Geosporobacter ferrireducens,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella oralis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella shahii,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Ihubacter|s__Ihubacter massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Intestinibacillus|s__Intestinibacillus massiliensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kineosporiales|f__Kineosporiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kineosporiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Kineothrix|s__Kineothrix alysoides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium|s__Lachnobacterium bovis,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia shahii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter massiliensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus|s__Monoglobus pectinilyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella|s__Parolsenella catena,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio|s__Pseudobutyrivibrio ruminis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia|s__Senegalimassilia anaerobia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter|s__Sporobacter termitidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum variabile,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis|s__Victivallis vadensis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma|s__[Collinsella] massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum",1783272|1239|91061|186826|186827|46123|1581061;1783272|1239|186801|186802|216572|258514;1783272|1239|186801|186802|216572|258514|258515;1783272|1239|186801|186802|3082771|1918385;1783272|1239|186801|186802|3082771|1918385|1796620;1783272|1239|186801|186802|3085642|2048137|39484;3379134|1224|28216|80840|506;3379134|976|200643|171549|171550|239759|2585118;3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|171550|239759|328814;1783272|1239|186801|186802|216572|1940255|1650663;3379134|976|200643|171549|171552|1283313|76122;1783272|544448|31969|186329|2146|2903105|264639;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|186802|3082771|1924093;1783272|1239|186801|186802|3082771|1924093|1673717;1783272|544448|31969|186332|186333;1783272|544448|31969|186332;1783272|1239|186801|3085636|3118652|2039240;1783272|1239|186801|3085636|3118652|2039240|2358141;1783272|544448|31969|186332|186333|2152;1783272|544448|31969|186332|186333|2152|2153;3379134|976|200643|171549|815|816|329854;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|2005519;3379134|200940|3031449|213115|194924|35832;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|3133175;1783272|1239|186801|3085636|186803|572511|3133152;1783272|1239|186801|3085636|186803|572511|89014;1783272|1239|186801|3085636|186803|572511|1955243;1783272|1239|526524|526525|128827|1854458;1783272|1239|526524|526525|128827|1854458|265178;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|3085642|580596|501571;3379134|976|200643|171549|1853231|574697;1783272|1239|909932|1843489|31977|1980685|1852378;1783272|1239|186801|3082720|543314|1715793|938278;1783272|1239|186801|3082768|990719|990721|1805714;1783272|1239|186801|186802|31979|1485;3379134|976|200643|171549|2005519|1348911;3379134|976|200643|171549|2005519|1348911|1099853;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|33042|33043;1783272|1239|186801|3085636|1185407|1185408;1783272|1239|186801|3085636|1185407;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924|872|901;1783272|1239|909932|1843489|31977|39948|487173;1783272|1239|186801|3085636|186803|189330|39486;3379134|1224|28216|80840|995019|1980697;3379134|1224|28216|80840|995019|1980697|1852381;1783272|201174|84998|1643822|1643826|84111;1783272|201174|84998|1643822|1643826|84111|84112;1783272|201174|84998|1643822|1643826;1783272|201174|84998|1643822;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|186801|3085636|186803|3342669|45851;1783272|1239|186801|3082720|543314;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|216572|216851|853;1783272|1239|526524|526525|128827|1573534;1783272|1239|526524|526525|128827|1573534|39483;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|3082720|3118657|390805;1783272|1239|186801|3082720|3118657|390805|1424294;1783272|1239|526524|526525|128827|1573535;1783272|1239|526524|526525|128827|1573535|1735;3379134|976|200643|171549|171552|2974257|28134;3379134|976|200643|171549|171552|2974257|228603;1783272|1239|186801|3082720|543314|1926667|1852367;1783272|1239|186801|186802|3085642|1928820|1871029;1783272|201174|1760|622452|83778;1783272|201174|1760|622452;1783272|1239|186801|3085636|186803|2163168|1469948;1783272|1239|186801|3085636|186803|140625;1783272|1239|186801|3085636|186803|140625|140626;3379134|256845|1313211;3384189|32066|203490|203491|1129771|32067|157691;1783272|1239|91061|186826|33958|2742598;1783272|1239|91061|186826|33958|2742598|97478;1783272|1239|186801|3085636|186803|2316020|1720300;1783272|1239|909932|1843489|31977|906|907;1783272|1239|909932|1843489|31977|906|1232428;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|186801|3085656|3085657|2039302|1981510;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|1853231;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|459786|1263547;1783272|1239|186801|186802|216572|459786|351091;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|171552|577309|454154;1783272|201174|84998|84999|1643824|2082587;1783272|201174|84998|84999|1643824|2082587|2003188;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|815|909656|204516;1783272|1239|186801|3085636|186803|46205|46206;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3082720|186804|1501226|1776391;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|186802|216572|1263|40518;3379134|976|200643|171549|171552|2974251|165179;1783272|201174|84998|84999|84107|1473205;1783272|201174|84998|84999|84107|1473205|1473216;1783272|201174|84998|1643822|1643826|84108;1783272|201174|84998|1643822|1643826|84108|572010;1783272|1239|186801|186802|216572|44748|44749;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|186801|186802|216572|292632|214851;3379134|1224|28216|80840|995019|40544;3379134|1224|28216|80840|995019|40544|40545;1783272|1239|526524|526525|2810280|3025755;1783272|1239|526524|526525|2810280|3025755|29348;1783272|1239|526524|526525|2810281|191303;1783272|1239|526524|526525|2810281|191303|154288;1783272|1239|526524|526525|2810281;3379134|256845|1313211|278082;3379134|256845|1313211|278082|255528|172900;3379134|256845|1313211|278082|255528|172900|172901;1783272|201174|84998|84999|84107|1472762|1232426;1783272|1239|186801|186802|216572|39492,Complete,Svetlana up
bsdb:38533382/1/1,38533382,case-control,38533382,https://doi.org/10.3389/fcimb.2024.1349397,NA,"Liu Y., Tang S., Feng Y., Xue B., Cheng C., Su Y., Wei W., Zhang L., Huang Z., Shi X., Fang Y., Yang J., Zhang Y., Deng X., Wang L., Ren H., Wang C. , Yuan H.",Alteration in gut microbiota is associated with immune imbalance in Graves' disease,Frontiers in cellular and infection microbiology,2024,"B cells, Graves’ disease, LPS, cytokines, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Healthy Controls (HCs),Graves’ disease (GD),Patients diagnosed with Graves' disease,32,33,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2C,24 July 2025,Aleru Divine,Aleru Divine,"Linear discriminant analysis (LEfSe, LDA>3) showing alternation of gut microbiota compared with HCs.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|1239|186801|186802|216572|1263|438033;1783272|1239|91061|186826|33958|46255;1783272|201174|84998|84999|84107|102106;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|572511;1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85004|31953|1678,Complete,NA
bsdb:38533382/1/2,38533382,case-control,38533382,https://doi.org/10.3389/fcimb.2024.1349397,NA,"Liu Y., Tang S., Feng Y., Xue B., Cheng C., Su Y., Wei W., Zhang L., Huang Z., Shi X., Fang Y., Yang J., Zhang Y., Deng X., Wang L., Ren H., Wang C. , Yuan H.",Alteration in gut microbiota is associated with immune imbalance in Graves' disease,Frontiers in cellular and infection microbiology,2024,"B cells, Graves’ disease, LPS, cytokines, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Healthy Controls (HCs),Graves’ disease (GD),Patients diagnosed with Graves' disease,32,33,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2C,24 July 2025,Aleru Divine,Aleru Divine,"Linear discriminant analysis (LEfSe, LDA>3) showing alternation of gut microbiota compared with HCs.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,s__rumen bacterium NK4A214,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|976|200643|171549|815|816;1783272|1239|909932|1843489|31977|39948;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|1407607;877428;3379134|976|200643|171549|2005525|375288,Complete,NA
bsdb:38548910/1/1,38548910,case-control,38548910,10.1038/s41598-024-58118-3,NA,"Prasanchit P., Pongchaikul P., Lertsittichai P., Tantitham C. , Manonai J.",Vaginal microbiomes of breast cancer survivors treated with aromatase inhibitors with and without vulvovaginal symptoms,Scientific reports,2024,NA,Experiment 1,Thailand,Homo sapiens,Vaginal fluid,UBERON:0036243,Vulvovaginitis,EFO:1001240,Non-vulvovaginal symptoms (control),Vulvovaginal symptoms,Breast cancer survivors treated with aromatase inhibitors with vulvovaginal symptoms,20,20,Within 7 days,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,FIG 3 (A),9 April 2024,Rahila,"Rahila,Scholastica,WikiWorks",Linear discriminant analysis effect size (LEfSe) analysis of microbial abundance between breast cancer survivors treated with aromatase inhibitors with versus without vulvovaginal symptoms.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia|s__Alloscardovia omnicolens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium riegelii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemelliphila|s__Gemelliphila asaccharolytica,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila|s__Fastidiosipila sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp.",1783272|201174|1760|85004|31953|419014;1783272|201174|1760|85004|31953|419014|419015;1783272|201174|1760|85007|1653|1716|156976;1783272|1239|186801|186802|216572|236752;1783272|201174|1760|85004|31953|2701;1783272|201174|1760|85004|31953|2701|2702;1783272|1239|91061|1385|539738|3076174|502393;3384189|32066|203490|203491|1129771;3384189|32066|203490|203491|1129771|168808;3384189|32066|203490|203491|1129771|168808|40543;1783272|1239|186801|186802|216572|236752|1938886;1783272|1239|1737404|1737405|1570339|162289|1971214,Complete,Svetlana up
bsdb:38548910/1/2,38548910,case-control,38548910,10.1038/s41598-024-58118-3,NA,"Prasanchit P., Pongchaikul P., Lertsittichai P., Tantitham C. , Manonai J.",Vaginal microbiomes of breast cancer survivors treated with aromatase inhibitors with and without vulvovaginal symptoms,Scientific reports,2024,NA,Experiment 1,Thailand,Homo sapiens,Vaginal fluid,UBERON:0036243,Vulvovaginitis,EFO:1001240,Non-vulvovaginal symptoms (control),Vulvovaginal symptoms,Breast cancer survivors treated with aromatase inhibitors with vulvovaginal symptoms,20,20,Within 7 days,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,FIG 3 (A),9 April 2024,Rahila,"Rahila,Scholastica,WikiWorks",Linear discriminant analysis effect size (LEfSe) analysis of microbial abundance between breast cancer survivors treated with aromatase inhibitors with versus without vulvovaginal symptoms.,decreased,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,1783272|1239|1737404|1737405|1570339|543311|33033,Complete,Svetlana up
bsdb:38551926/1/1,38551926,"cross-sectional observational, not case-control",38551926,10.1371/journal.pone.0299349,NA,"Surono I.S., Popov I., Verbruggen S., Verhoeven J., Kusumo P.D. , Venema K.","Gut microbiota differences in stunted and normal-lenght children aged 36-45 months in East Nusa Tenggara, Indonesia",PloS one,2024,NA,Experiment 1,Indonesia,Homo sapiens,Feces,UBERON:0001988,Short stature,HP:0004322,Normal Length children,Stunted Length children,Stunted length children aged 36–45 months,100,100,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,unchanged,decreased,NA,NA,NA,unchanged,Signature 1,Figure 4.,23 February 2025,An05hka,An05hka,Boxplots of the 3 taxa at genus level that were significantly different between non-stunted  and stunted children.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1506553;1783272|1239|909932|1843489|31977|29465,Complete,KateRasheed
bsdb:38551926/2/1,38551926,"cross-sectional observational, not case-control",38551926,10.1371/journal.pone.0299349,NA,"Surono I.S., Popov I., Verbruggen S., Verhoeven J., Kusumo P.D. , Venema K.","Gut microbiota differences in stunted and normal-lenght children aged 36-45 months in East Nusa Tenggara, Indonesia",PloS one,2024,NA,Experiment 2,Indonesia,Homo sapiens,Feces,UBERON:0001988,Short stature,HP:0004322,Normal Length children in Kupang,Stunted Length children in Kupang,Stunted length children aged 36–45 months from Kupang,NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,unchanged,decreased,NA,NA,NA,unchanged,Signature 1,Figure 4.,24 February 2025,An05hka,An05hka,"Boxplots of the 3 taxa at genus level that were significantly different (Kruskal-Wallis analysis, with Benjamini-Hochberg FDR correction) between non-stunted  and stunted  children of Kupang.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",1783272|1239|186801|186802|216572|216851;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|3085636|186803|1506553,Complete,KateRasheed
bsdb:38551926/3/1,38551926,"cross-sectional observational, not case-control",38551926,10.1371/journal.pone.0299349,NA,"Surono I.S., Popov I., Verbruggen S., Verhoeven J., Kusumo P.D. , Venema K.","Gut microbiota differences in stunted and normal-lenght children aged 36-45 months in East Nusa Tenggara, Indonesia",PloS one,2024,NA,Experiment 3,Indonesia,Homo sapiens,Feces,UBERON:0001988,Short stature,HP:0004322,Normal Length children from North Kodi,Stunted Length children from North Kodi,Stunted length children aged 36–45 months from North Kodi,NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4.,24 February 2025,An05hka,An05hka,"Boxplots of the 3 taxa at genus level that were significantly different (Kruskal-Wallis analysis, with Benjamini-Hochberg FDR correction) between non-stunted and stunted children from North Kodi",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1506553,Complete,KateRasheed
bsdb:38551926/4/1,38551926,"cross-sectional observational, not case-control",38551926,10.1371/journal.pone.0299349,NA,"Surono I.S., Popov I., Verbruggen S., Verhoeven J., Kusumo P.D. , Venema K.","Gut microbiota differences in stunted and normal-lenght children aged 36-45 months in East Nusa Tenggara, Indonesia",PloS one,2024,NA,Experiment 4,Indonesia,Homo sapiens,Feces,UBERON:0001988,Short stature,HP:0004322,Normal Length children,Stunted Length children,Stunted length children aged 36–45 months,100,100,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3.,24 February 2025,An05hka,"An05hka,Victoria",Gut microbiota composition in stunted and normal-length children at the phylum level.,increased,"k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Bacteroidota",1783272|1117;3379134|976,Complete,KateRasheed
bsdb:38551926/5/2,38551926,"cross-sectional observational, not case-control",38551926,10.1371/journal.pone.0299349,NA,"Surono I.S., Popov I., Verbruggen S., Verhoeven J., Kusumo P.D. , Venema K.","Gut microbiota differences in stunted and normal-lenght children aged 36-45 months in East Nusa Tenggara, Indonesia",PloS one,2024,NA,Experiment 5,Indonesia,Homo sapiens,Feces,UBERON:0001988,Body weight,EFO:0004338,low Weight,High Weight,Children with high weight aged 36-45 months,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6a,10 March 2025,An05hka,"An05hka,Victoria",Heatmap of the taxa at genus level that were different (q < 0.05) when correlated by Spearman correlation analysis to the weight. Blue: Positive correlation; red: Negative correlation,decreased,NA,NA,Complete,KateRasheed
bsdb:38551926/6/1,38551926,"cross-sectional observational, not case-control",38551926,10.1371/journal.pone.0299349,NA,"Surono I.S., Popov I., Verbruggen S., Verhoeven J., Kusumo P.D. , Venema K.","Gut microbiota differences in stunted and normal-lenght children aged 36-45 months in East Nusa Tenggara, Indonesia",PloS one,2024,NA,Experiment 6,Indonesia,Homo sapiens,Feces,UBERON:0001988,Body height,EFO:0004339,Low Height,High Height,Children with high body Height aged 36-45 months,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6a,12 March 2025,An05hka,"An05hka,Victoria",Heatmap of the taxa at genus level that were different (q < 0.05) when correlated by Spearman correlation analysis to the Height.  Blue: Positive correlation; red: Negative correlation.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|572511;1783272|1239|91061|186826|186828;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|216572;1783272|1239|186801|3082720|186804;1783272|1239|186801|186802|216572|292632;1783272|1239|526524|526525|2810280|3025755,Complete,KateRasheed
bsdb:38551926/6/2,38551926,"cross-sectional observational, not case-control",38551926,10.1371/journal.pone.0299349,NA,"Surono I.S., Popov I., Verbruggen S., Verhoeven J., Kusumo P.D. , Venema K.","Gut microbiota differences in stunted and normal-lenght children aged 36-45 months in East Nusa Tenggara, Indonesia",PloS one,2024,NA,Experiment 6,Indonesia,Homo sapiens,Feces,UBERON:0001988,Body height,EFO:0004339,Low Height,High Height,Children with high body Height aged 36-45 months,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6a,12 March 2025,An05hka,"An05hka,Victoria",Heatmap of the taxa at genus level that were different (q < 0.05) when correlated by Spearman correlation analysis to the Height. Positive correlation; red: Negative correlation,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1506553;3379134|1224|1236|135624|83763|83770;1783272|1239|909932|1843489|31977|29465,Complete,KateRasheed
bsdb:38551926/7/1,38551926,"cross-sectional observational, not case-control",38551926,10.1371/journal.pone.0299349,NA,"Surono I.S., Popov I., Verbruggen S., Verhoeven J., Kusumo P.D. , Venema K.","Gut microbiota differences in stunted and normal-lenght children aged 36-45 months in East Nusa Tenggara, Indonesia",PloS one,2024,NA,Experiment 7,Indonesia,Homo sapiens,Feces,UBERON:0001988,Body mass index,EFO:0004340,Low Body Mass Index,High Body Mass Index,Children with high Body Mass Index (BMI) aged 36-45 months,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6a,12 March 2025,An05hka,"An05hka,Victoria",Heatmap of the taxa at genus level that were different (q < 0.05) when correlated by Spearman correlation analysis to the BMI. Positive correlation; red: Negative correlation,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium",3379134|976|200643|171549|171552|1283313;1783272|1798710|1906119;1783272|1239|186801|186802|1392389;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|31979|1266;3379134|1224|1236|135624|83763|83770;1783272|1239|526524|526525|2810280|135858,Complete,KateRasheed
bsdb:38551926/7/2,38551926,"cross-sectional observational, not case-control",38551926,10.1371/journal.pone.0299349,NA,"Surono I.S., Popov I., Verbruggen S., Verhoeven J., Kusumo P.D. , Venema K.","Gut microbiota differences in stunted and normal-lenght children aged 36-45 months in East Nusa Tenggara, Indonesia",PloS one,2024,NA,Experiment 7,Indonesia,Homo sapiens,Feces,UBERON:0001988,Body mass index,EFO:0004340,Low Body Mass Index,High Body Mass Index,Children with high Body Mass Index (BMI) aged 36-45 months,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6a,12 March 2025,An05hka,"An05hka,Victoria",Heatmap of the taxa at genus level that were different (q < 0.05) when correlated by Spearman correlation analysis to the BMI. Positive correlation; red: Negative correlation,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|91061|186826|186828;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|1407607;1783272|1239|91061|1385|539738|1378;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|909932|909929|1843491|158846;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3082720|186804;1783272|1239|186801|186802|216572|292632,Complete,KateRasheed
bsdb:38582855/1/1,38582855,case-control,38582855,10.1038/s41531-024-00687-1,https://www.nature.com/articles/s41531-024-00687-1,"Aho V.T.E., Klee M., Landoulsi Z., Heintz-Buschart A., Pavelka L., Leist A.K., Krüger R., May P. , Wilmes P.",Gut microbiome is not associated with mild cognitive impairment in Parkinson's disease,NPJ Parkinson's disease,2024,NA,Experiment 1,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control Subjects,Cognitively Unimpaired PD (PD-NC),Parkinson’s disease (PD) patients without cognitive impairment (NC).,90,60,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,Signature 1,Supplementary Figure 1d,16 July 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap summarizing differentially abundant taxa.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium DTU089,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Methanobacteriati|p__Methanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|s__Selenomonadales bacterium Marseille-P2399",1783272|1239|186801|186802|216572|244127;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|1671661;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|186806|1730|290054;3366610|28890;1783272|1239|186801|186802|216572|216851|1946507;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|3085636|186803|1649459|2613924;1783272|1239|186801|186802|216572|596767;3379134|1224|1236|91347|543|570|573;3366610|28890|183925|2158|2159|2172;3379134|976|200643|171549|815|909656|357276;1783272|1239|909932|909929|1806836,Complete,Shaimaa Elsafoury
bsdb:38582855/1/2,38582855,case-control,38582855,10.1038/s41531-024-00687-1,https://www.nature.com/articles/s41531-024-00687-1,"Aho V.T.E., Klee M., Landoulsi Z., Heintz-Buschart A., Pavelka L., Leist A.K., Krüger R., May P. , Wilmes P.",Gut microbiome is not associated with mild cognitive impairment in Parkinson's disease,NPJ Parkinson's disease,2024,NA,Experiment 1,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control Subjects,Cognitively Unimpaired PD (PD-NC),Parkinson’s disease (PD) patients without cognitive impairment (NC).,90,60,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,Signature 2,Supplementary Figure 1d,20 June 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap summarizing differentially abundant taxa.,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 10-1,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005",1783272|1239;1783272|1239|186801|186802|3085642;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|1235800;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171552|838;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|3068309,Complete,Svetlana up
bsdb:38582855/2/1,38582855,case-control,38582855,10.1038/s41531-024-00687-1,https://www.nature.com/articles/s41531-024-00687-1,"Aho V.T.E., Klee M., Landoulsi Z., Heintz-Buschart A., Pavelka L., Leist A.K., Krüger R., May P. , Wilmes P.",Gut microbiome is not associated with mild cognitive impairment in Parkinson's disease,NPJ Parkinson's disease,2024,NA,Experiment 2,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Cognitively Unimpaired-PD (PD-NC),Mild Cognitive Impairment-PD,Parkinson’s disease (PD) patients with mild cognitive impairment (MCI).,60,58,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,Signature 1,Supplementary Figure 1d and table 3c,20 June 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap summarizing differentially abundant taxa.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061|186826;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:38582855/2/2,38582855,case-control,38582855,10.1038/s41531-024-00687-1,https://www.nature.com/articles/s41531-024-00687-1,"Aho V.T.E., Klee M., Landoulsi Z., Heintz-Buschart A., Pavelka L., Leist A.K., Krüger R., May P. , Wilmes P.",Gut microbiome is not associated with mild cognitive impairment in Parkinson's disease,NPJ Parkinson's disease,2024,NA,Experiment 2,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Cognitively Unimpaired-PD (PD-NC),Mild Cognitive Impairment-PD,Parkinson’s disease (PD) patients with mild cognitive impairment (MCI).,60,58,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,Signature 2,Supplementary Figure 1d and table 3c,20 June 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap summarizing differentially abundant taxa.,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma",3379134|74201|203494|48461|1647988|239934|239935;1783272|544448|31969|186332|186333|2152,Complete,Svetlana up
bsdb:38582855/3/1,38582855,case-control,38582855,10.1038/s41531-024-00687-1,https://www.nature.com/articles/s41531-024-00687-1,"Aho V.T.E., Klee M., Landoulsi Z., Heintz-Buschart A., Pavelka L., Leist A.K., Krüger R., May P. , Wilmes P.",Gut microbiome is not associated with mild cognitive impairment in Parkinson's disease,NPJ Parkinson's disease,2024,NA,Experiment 3,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control Subjects,Mild Cognitive Impairment -PD (PD-MCI),Parkinson’s disease (PD) patients with Mild Cognitive Impairment (MCI).,90,58,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,Signature 1,Supplementary Figure 1d,20 June 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap summarizing differentially abundant taxa.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium DTU089,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Methanobacteriati|p__Methanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|s__Selenomonadales bacterium Marseille-P2399",1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|1671661;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|186806|1730|290054;3366610|28890;1783272|1239|186801|186802|216572|216851|1946507;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|3085636|186803|1649459|2613924;1783272|1239|186801|186802|216572|596767;3379134|1224|1236|91347|543|570|573;3366610|28890|183925|2158|2159|2172;3379134|976|200643|171549|815|909656|357276;1783272|1239|909932|909929|1806836,Complete,Svetlana up
bsdb:38582855/3/2,38582855,case-control,38582855,10.1038/s41531-024-00687-1,https://www.nature.com/articles/s41531-024-00687-1,"Aho V.T.E., Klee M., Landoulsi Z., Heintz-Buschart A., Pavelka L., Leist A.K., Krüger R., May P. , Wilmes P.",Gut microbiome is not associated with mild cognitive impairment in Parkinson's disease,NPJ Parkinson's disease,2024,NA,Experiment 3,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control Subjects,Mild Cognitive Impairment -PD (PD-MCI),Parkinson’s disease (PD) patients with Mild Cognitive Impairment (MCI).,90,58,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,Signature 2,Supplementary Figure 1d,16 July 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap summarizing differentially abundant taxa.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 10-1,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005",1783272|1239|186801|186802|3085642;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|1235800;3379134|976|200643|171549|171552|838;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|216572|3068309,Complete,Svetlana up
bsdb:38582855/4/1,38582855,case-control,38582855,10.1038/s41531-024-00687-1,https://www.nature.com/articles/s41531-024-00687-1,"Aho V.T.E., Klee M., Landoulsi Z., Heintz-Buschart A., Pavelka L., Leist A.K., Krüger R., May P. , Wilmes P.",Gut microbiome is not associated with mild cognitive impairment in Parkinson's disease,NPJ Parkinson's disease,2024,NA,Experiment 4,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control Subjects,Cognitively Unimpaired PD (PD-NC),Parkinson’s disease (PD) patients without cognitive impairment (NC).,90,60,NA,16S,34,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,Signature 1,Supplementary Figure 1d,17 July 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap summarizing differentially abundant taxa.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium DTU089,1783272|1239|186801|186802|1671661,Complete,Svetlana up
bsdb:38582855/4/2,38582855,case-control,38582855,10.1038/s41531-024-00687-1,https://www.nature.com/articles/s41531-024-00687-1,"Aho V.T.E., Klee M., Landoulsi Z., Heintz-Buschart A., Pavelka L., Leist A.K., Krüger R., May P. , Wilmes P.",Gut microbiome is not associated with mild cognitive impairment in Parkinson's disease,NPJ Parkinson's disease,2024,NA,Experiment 4,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control Subjects,Cognitively Unimpaired PD (PD-NC),Parkinson’s disease (PD) patients without cognitive impairment (NC).,90,60,NA,16S,34,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,Signature 2,Supplementary Figure 1d,17 July 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap summarizing differentially abundant taxa.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 10-1",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|3068309;1783272|1239|186801|3085636|186803|1235800,Complete,Svetlana up
bsdb:38582855/5/1,38582855,case-control,38582855,10.1038/s41531-024-00687-1,https://www.nature.com/articles/s41531-024-00687-1,"Aho V.T.E., Klee M., Landoulsi Z., Heintz-Buschart A., Pavelka L., Leist A.K., Krüger R., May P. , Wilmes P.",Gut microbiome is not associated with mild cognitive impairment in Parkinson's disease,NPJ Parkinson's disease,2024,NA,Experiment 5,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control Subjects,Mild Cognitive Impairment PD (PD-MCI),Parkinson’s disease (PD) patients with Mild Cognitive Impairment (NC).,90,58,NA,16S,34,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,Signature 1,Supplementary Figure 1d,17 July 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap summarizing differentially abundant taxa.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|186802|3085642;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:38582855/6/1,38582855,case-control,38582855,10.1038/s41531-024-00687-1,https://www.nature.com/articles/s41531-024-00687-1,"Aho V.T.E., Klee M., Landoulsi Z., Heintz-Buschart A., Pavelka L., Leist A.K., Krüger R., May P. , Wilmes P.",Gut microbiome is not associated with mild cognitive impairment in Parkinson's disease,NPJ Parkinson's disease,2024,NA,Experiment 6,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control Subjects,Cognitively Unimpaired PD (PD-NC),Parkinson’s disease (PD) patients without cognitive impairment (NC).,90,60,NA,16S,34,Illumina,centered log-ratio,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,Signature 1,Supplementary Figure 1d,17 July 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap summarizing differentially abundant taxa.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|s__Selenomonadales bacterium Marseille-P2399,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium DTU089,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus",1783272|1239|186801|186802|216572|596767;1783272|1239|186801|186802|216572|216851|1946507;1783272|1239|909932|909929|1806836;1783272|1239|186801|186802|1671661;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|216572|244127,Complete,Svetlana up
bsdb:38582855/6/2,38582855,case-control,38582855,10.1038/s41531-024-00687-1,https://www.nature.com/articles/s41531-024-00687-1,"Aho V.T.E., Klee M., Landoulsi Z., Heintz-Buschart A., Pavelka L., Leist A.K., Krüger R., May P. , Wilmes P.",Gut microbiome is not associated with mild cognitive impairment in Parkinson's disease,NPJ Parkinson's disease,2024,NA,Experiment 6,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control Subjects,Cognitively Unimpaired PD (PD-NC),Parkinson’s disease (PD) patients without cognitive impairment (NC).,90,60,NA,16S,34,Illumina,centered log-ratio,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,Signature 2,Supplementary Figure 1d,17 July 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap summarizing differentially abundant taxa.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 10-1",1783272|1239|186801|3085636|186803|1766253;1783272|1239;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|3068309;1783272|1239|186801|3085636|186803|1235800,Complete,Svetlana up
bsdb:38582855/7/1,38582855,case-control,38582855,10.1038/s41531-024-00687-1,https://www.nature.com/articles/s41531-024-00687-1,"Aho V.T.E., Klee M., Landoulsi Z., Heintz-Buschart A., Pavelka L., Leist A.K., Krüger R., May P. , Wilmes P.",Gut microbiome is not associated with mild cognitive impairment in Parkinson's disease,NPJ Parkinson's disease,2024,NA,Experiment 7,Luxembourg,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control Subjects,Mild Cognitive Impairment PD (PD-MCI),Parkinson’s disease (PD) patients with Mild Cognitive Impairment (NC).,90,58,NA,16S,34,Illumina,centered log-ratio,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,Signature 1,Supplementary Figure 1d,17 July 2024,Aleru Divine,"Aleru Divine,WikiWorks",Heatmap summarizing differentially abundant taxa.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|186802|3085642;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:38589361/1/1,38589361,"cross-sectional observational, not case-control",38589361,10.1038/s41467-024-47182-y,NA,"Barker-Tejeda T.C., Zubeldia-Varela E., Macías-Camero A., Alonso L., Martín-Antoniano I.A., Rey-Stolle M.F., Mera-Berriatua L., Bazire R., Cabrera-Freitag P., Shanmuganathan M., Britz-McKibbin P., Ubeda C., Francino M.P., Barber D., Ibáñez-Sandín M.D., Barbas C., Pérez-Gordo M. , Villaseñor A.",Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach,Nature communications,2024,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Mothers,Infants,Infants (0 - 12 months old),43,38,3 months,16S,34,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Supplemental data 4 and 5,21 July 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differential abundance results at the phylum and genus levels for 16S rRNA gene sequencing in infants compared to mothers.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,",1783272|1239|186801|186802|216572|258514;1783272|201174|84998|1643822|1643826|447020;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|3082720|543314|109326;1783272|1239;3379134|976;3379134|976|200643|171549|2005519|397864;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;3379134|976|200643|171549|2005519|1348911;1783272|1239|186801|3085636|186803|33042;1783272|201174|84998|84999|84107;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|204475;1783272|201174|84998|1643822|1643826|644652;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|186802|1392389;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|41978;,Complete,Svetlana up
bsdb:38589361/1/2,38589361,"cross-sectional observational, not case-control",38589361,10.1038/s41467-024-47182-y,NA,"Barker-Tejeda T.C., Zubeldia-Varela E., Macías-Camero A., Alonso L., Martín-Antoniano I.A., Rey-Stolle M.F., Mera-Berriatua L., Bazire R., Cabrera-Freitag P., Shanmuganathan M., Britz-McKibbin P., Ubeda C., Francino M.P., Barber D., Ibáñez-Sandín M.D., Barbas C., Pérez-Gordo M. , Villaseñor A.",Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach,Nature communications,2024,NA,Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Mothers,Infants,Infants (0 - 12 months old),43,38,3 months,16S,34,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Supplemental data 4 and 5,21 July 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differential abundance results at the phylum and genus levels for 16S rRNA gene sequencing in infants compared to mothers.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,p__Bacillariophyta,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,p__Candidatus Parcubacteria,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Viridiplantae|p__Streptophyta,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|2037|2049|1654;1783272|201174;1783272|201174|84998|84999|1643824|1380;2836;1783272|201174|1760|85004|31953|1678;221216;1783272|1117;1783272|201174|84998|1643822|1643826|84111;3379134|1224|1236|91347|543|547;1783272|1239|91061|186826|81852|1350;1783272|1239|526524|526525|128827;3379134|1224|1236|91347|543|1940338;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|33958|1578;3379134|1224|28211|356|69277|68287;3379134|1224;1783272|201174|1760|85006|1268|32207;3379134|1224|28211|204457|41297|13687;1783272|1239|91061|1385|90964|1279;33090|35493;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:38589361/2/1,38589361,"cross-sectional observational, not case-control",38589361,10.1038/s41467-024-47182-y,NA,"Barker-Tejeda T.C., Zubeldia-Varela E., Macías-Camero A., Alonso L., Martín-Antoniano I.A., Rey-Stolle M.F., Mera-Berriatua L., Bazire R., Cabrera-Freitag P., Shanmuganathan M., Britz-McKibbin P., Ubeda C., Francino M.P., Barber D., Ibáñez-Sandín M.D., Barbas C., Pérez-Gordo M. , Villaseñor A.",Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach,Nature communications,2024,NA,Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Grandmothers,Infants,Infants (0 - 12 months old),40,38,3 months,16S,34,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Supplemental data 4 and 5,21 July 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differential abundance results at the phylum and genus levels for 16S rRNA gene sequencing in infants compared to grandmothers.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Aestuariispiraceae|g__Aestuariispira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Methanobacteriati|p__Methanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,",1783272|1239|186801|186802|216572|258514;1783272|201174|84998|1643822|1643826|447020;3379134|1224|28211|204441|3466454|1647175;3379134|976|200643|171549|171550|239759;1783272|1239;3379134|976;3379134|976|200643|171549|2005519|397864;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801;3379134|976|200643|171549|2005519|1348911;1783272|1239|186801|3085636|186803|33042;1783272|201174|84998|84999|84107;1783272|1239|186801|186802;3366610|28890;1783272|1239|186801|186802|216572|216851;1783272|1239|526524|526525|128827|1573536;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|204475;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|186802|1392389;3366610|28890|183925|2158|2159|2172;1783272|201174|84998|84999|1643824|133925;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|44748;1783272|1239|526524|526525|2810281|191303;,Complete,Svetlana up
bsdb:38589361/2/2,38589361,"cross-sectional observational, not case-control",38589361,10.1038/s41467-024-47182-y,NA,"Barker-Tejeda T.C., Zubeldia-Varela E., Macías-Camero A., Alonso L., Martín-Antoniano I.A., Rey-Stolle M.F., Mera-Berriatua L., Bazire R., Cabrera-Freitag P., Shanmuganathan M., Britz-McKibbin P., Ubeda C., Francino M.P., Barber D., Ibáñez-Sandín M.D., Barbas C., Pérez-Gordo M. , Villaseñor A.",Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach,Nature communications,2024,NA,Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Grandmothers,Infants,Infants (0 - 12 months old),40,38,3 months,16S,34,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Supplemental data 4 and 5,21 July 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differential abundance results at the phylum and genus levels for 16S rRNA gene sequencing in infants compared to grandmothers.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|2037|2049|1654;1783272|201174;1783272|201174|84998|84999|1643824|1380;1783272|201174|1760|85004|31953|1678;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|1940338;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;3379134|1224|1236|91347|543|570;3379134|1224|28211|356|69277|68287;3379134|1224;3379134|1224|28211|204457|41297|13687;1783272|1239|91061|1385|90964|1279;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:38589361/3/1,38589361,"cross-sectional observational, not case-control",38589361,10.1038/s41467-024-47182-y,NA,"Barker-Tejeda T.C., Zubeldia-Varela E., Macías-Camero A., Alonso L., Martín-Antoniano I.A., Rey-Stolle M.F., Mera-Berriatua L., Bazire R., Cabrera-Freitag P., Shanmuganathan M., Britz-McKibbin P., Ubeda C., Francino M.P., Barber D., Ibáñez-Sandín M.D., Barbas C., Pérez-Gordo M. , Villaseñor A.",Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach,Nature communications,2024,NA,Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Mothers,Infants,Infants (0 - 12 months old),43,38,3 months,WMS,NA,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"Supplemental data 4, 5 and 6",21 July 2024,Aleru Divine,"Aleru Divine,WikiWorks","Differential abundance results at phylum, genus and species level for Shotgun metagenomics sequencing in infants compared to mothers.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Acutalibacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens|s__Adlercreutzia equolifaciens subsp. celatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum butyriciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Angelakisella|s__Angelakisella massiliensis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Asaccharobacter,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|s__Bacillota bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Bittarella (ex Durand et al. 2017),k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia massiliensis (ex Durand et al. 2017),k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catenibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catenibacillus|s__Catenibacillus scindens,k__Bacillati|p__Chloroflexota,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium phoceensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister sp.,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma|s__Dielma fastidiosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XII. Incertae Sedis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Evtepia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena fissicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Flintibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Flintibacter|s__Flintibacter sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Hydrogeniiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas massiliensis (ex Afouda et al. 2020),k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnotalea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Lactonifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Lawsonibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Massiliimalia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Massiliimalia|s__Massiliimalia timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Raoultibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Liu et al. 2021),k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Pseudomonadati|p__Spirochaetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum variabile,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella tobetsuensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas nexilis,k__Bacillati|p__Bacillota,,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae",1783272|1239|186801|186802|3082771|1918385;1783272|201174|84998|1643822|1643826|447020;1783272|201174|84998|1643822|1643826|447020|446660;1783272|201174|84998|1643822|1643826|447020|446660|394340;1783272|1239|186801|186802|3085642|2048137;1783272|1239|186801|186802|3085642|2048137|1628085;1783272|1239|186801|186802|3085642|2048137|2048138;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550|239759|1288121;3379134|976|200643|171549|171550|239759|328814;1783272|1239|186801|186802|3082771|1924093;1783272|1239|186801|186802|3082771|1924093|1924094;1783272|1239|186801|3085636|3118652|2039240;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|186802|216572|244127|169435;1783272|1239|186801|186802|216572|1935176|1871018;1783272|201174|84998|1643822|1643826|553372;1783272|1239;1783272|1239|1879010;3379134|976|200643|171549|815|816|338188;3379134|976|200643|171549|815|816|46506;3379134|976|200643|171549|2005519|397864;1783272|1239|186801|186802|216572|1929297;1783272|1239|186801|3085636|186803|572511|1737424;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|2316203;1783272|1239|186801|3085636|186803|2316203|673271;1783272|200795;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|2044939;1783272|1239|186801|186802|31979|1898204;1783272|1239|186801|186802|31979|1485|1650661;1783272|1239|186801|3085636|186803|33042;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|39948|1955814;1783272|1239|526524|526525|128827|1472649;1783272|1239|526524|526525|128827|1472649|1034346;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|189330|2040332;1783272|1239|186801|186802|216572|2591381;1783272|1239|186801|186802|543313;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|2211178;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|2005359;1783272|1239|186801|3085636|186803|2005359|290055;1783272|1239|186801|186802|216572|946234|2049025;1783272|1239|186801|186802|1918454;1783272|1239|186801|186802|1918454|1918624;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|204475;1783272|201174|84998|1643822|1643826|644652;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|186802|3082771|2764317;1783272|1239|186801|186802|1392389|1673721;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|1763508;1783272|1239|186801|186802|31979|420345;1783272|1239|186801|186802|216572|2172004;1783272|1239|186801|186802|216572|2895461;1783272|1239|186801|186802|216572|2895461|1987501;1783272|1239|186801|186802|216572|3028852;1783272|1239|186801|3082720|543314|86331;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|1853231|283168|28118;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|459786|1945593;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572|2485925;1783272|1239|91061|1385|186822|44249;1783272|1239|186801|186802|216572|1017280|106588;1783272|201174|84998|1643822|1643826|1926677;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|3085636|186803|841|2049040;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|3062497;1783272|1239|186801|186802|216572|1263|40519;3379134|203691;1783272|1239|91061|186826|1300|1301|1313;1783272|1239|91061|186826|1300|1301|1306;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|216572|292632|214851;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843489|31977|29465|1110546;3379134|1224|1236|135614|32033|338;1783272|1239|186801|3085636|186803|2005355|29361;1783272|1239;;1783272|1239|186801;1783272|201174|84998;1783272|201174|84998|1643822|1643826;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;3379134|256845|1313211;1783272|1239|186801|186802|216572;1783272|1239|91061|1385|186822,Complete,Svetlana up
bsdb:38589361/3/2,38589361,"cross-sectional observational, not case-control",38589361,10.1038/s41467-024-47182-y,NA,"Barker-Tejeda T.C., Zubeldia-Varela E., Macías-Camero A., Alonso L., Martín-Antoniano I.A., Rey-Stolle M.F., Mera-Berriatua L., Bazire R., Cabrera-Freitag P., Shanmuganathan M., Britz-McKibbin P., Ubeda C., Francino M.P., Barber D., Ibáñez-Sandín M.D., Barbas C., Pérez-Gordo M. , Villaseñor A.",Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach,Nature communications,2024,NA,Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Mothers,Infants,Infants (0 - 12 months old),43,38,3 months,WMS,NA,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,"Supplemental data 4, 5 and 6",21 July 2024,Aleru Divine,"Aleru Divine,WikiWorks","Differential abundance results at phylum, genus and species level for Shotgun metagenomics sequencing in infants compared to mothers.",decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Bittarella (ex Liu et al. 2021)|s__Bittarella massiliensis (ex Liu et al. 2021),k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia glucerasea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter|s__Dysosmobacter sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania filiformis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania massiliensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnotalea|s__Lachnotalea sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter butyricigenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium sp.,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Viridiplantae|p__Streptophyta,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",1783272|201174;3379134|976|200643|171549|171550|239759|2585118;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|1681;1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|186802|216572|3062447|3062437;1783272|1239|186801|3085636|186803|572511|536633;1783272|1239|186801|186802|1898207;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|186802|216572|2591381|2591382;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|186806|1730|39490;1783272|1239|186801|186802|186806|1730|142586;1783272|201174|1760|85004|31953|2701;1783272|1239|526524|526525|128827|61170|61171;1783272|1239|526524|526525|128827|61170|1468449;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|1763508|2021453;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|2316020|2316025;1783272|1239|186801|3082720|543314|86331|2049035;3379134|1224;3379134|1224|1236|91347|543|620;1783272|1239|91061|186826|1300|1301|28037;33090|35493;1783272|1239|909932|1843489|31977|29465;1783272|201174|1760|2037|2049;1783272|201174|1760|85004|31953;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|91061|186826|1300,Complete,Svetlana up
bsdb:38589361/4/1,38589361,"cross-sectional observational, not case-control",38589361,10.1038/s41467-024-47182-y,NA,"Barker-Tejeda T.C., Zubeldia-Varela E., Macías-Camero A., Alonso L., Martín-Antoniano I.A., Rey-Stolle M.F., Mera-Berriatua L., Bazire R., Cabrera-Freitag P., Shanmuganathan M., Britz-McKibbin P., Ubeda C., Francino M.P., Barber D., Ibáñez-Sandín M.D., Barbas C., Pérez-Gordo M. , Villaseñor A.",Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach,Nature communications,2024,NA,Experiment 4,Spain,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Grandmothers,Infants,Infants (0 - 12 months old),40,38,3 months,WMS,NA,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"Supplemental data 4, 5 and 6",21 July 2024,Aleru Divine,"Aleru Divine,WikiWorks","Differential abundance results at phylum, genus and species level for Shotgun metagenomics sequencing in infants compared to grandmothers.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Acutalibacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens|s__Adlercreutzia equolifaciens subsp. celatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes dispar,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Angelakisella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Angelakisella|s__Angelakisella massiliensis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Asaccharobacter,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|s__Bacillota bacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Chloroflexota,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium phoceensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Methanobacteriati|p__Methanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Evtepia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena fissicatena,k__Pseudomonadati|p__Fibrobacterota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Flintibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Flintibacter|s__Flintibacter sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas gabonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnotalea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Lawsonibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Massiliimalia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|s__Porphyromonadaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Pseudomonadati|p__Spirochaetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum variabile,k__Metazoa|p__Nematoda|c__Enoplea|o__Trichinellida|f__Trichuridae|g__Trichuris,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella tobetsuensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas nexilis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae",1783272|1239|186801|186802|3082771|1918385;1783272|201174|84998|1643822|1643826|447020;1783272|201174|84998|1643822|1643826|447020|446660;1783272|201174|84998|1643822|1643826|447020|446660|394340;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550|239759|2585119;3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|171550|239759|1288121;3379134|976|200643|171549|171550|239759|328814;1783272|1239|186801|3085636|186803|2569097;1783272|1239|186801|186802|3082771|1924093;1783272|1239|186801|186802|3082771|1924093|1924094;1783272|1239|186801|3085636|3118652|2039240;1783272|1239|186801|186802|216572|1935176;1783272|1239|186801|186802|216572|1935176|1871018;1783272|201174|84998|1643822|1643826|553372;1783272|1239;1783272|1239|1879010;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|3085642|580596;1783272|200795;1783272|1239|186801|2044939;1783272|1239|186801|186802|31979|1898204;1783272|1239|186801|186802|1898207;1783272|1239|186801|186802|31979|1485|1650661;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|189330|2040332;1783272|1239|186801|186802|216572|2591381;1783272|1239|186801|186802|186806|1730;3366610|28890;1783272|1239|186801|186802|2211178;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|2005359;1783272|1239|186801|3085636|186803|2005359|290055;3379134|65842;1783272|1239|186801|186802|216572|946234|2049025;1783272|1239|186801|186802|1918454;1783272|1239|186801|186802|1918454|1918624;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|204475;1783272|1239|186801|186802|216572|1892380;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|186802|1392389|1702285;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|1506553|2028282;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|1763508;1783272|1239|186801|186802|216572|2172004;1783272|1239|186801|186802|216572|2895461;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|3082720|543314|86331|2049035;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|459786|1945593;1783272|1239|186801|186802|216572;1783272|1239|91061|1385|186822|44249;1783272|1239|909932|1843488|909930|33024;1783272|1239|909932|1843488|909930|33024|33025;3379134|976|200643|171549|171551|2049046;1783272|1239|186801|186802|216572|1017280;1783272|1239|186801|186802|216572|1017280|106588;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3082720|186804|1501226|1776391;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|3085636|186803|841|2049040;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|1263|40519;3379134|203691;1783272|1239|91061|186826|1300|1301|1313;1783272|1239|91061|186826|1300|1301|1306;1783272|1239|186801|186802|216572|292632|214851;33208|6231|119088|6329|119093|36086;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843489|31977|29465|1110546;3379134|1224|1236|135614|32033|338;1783272|1239|186801|3085636|186803|2005355|29361;1783272|1239|909932|1843488|909930;1783272|1239|91061;1783272|1239;;3379134|976;1783272|1239|186801;1783272|201174|84998|84999;1783272|201174|84998;1783272|201174|84998|1643822|1643826;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;1783272|1239|91061|1385|186822,Complete,Svetlana up
bsdb:38589361/4/2,38589361,"cross-sectional observational, not case-control",38589361,10.1038/s41467-024-47182-y,NA,"Barker-Tejeda T.C., Zubeldia-Varela E., Macías-Camero A., Alonso L., Martín-Antoniano I.A., Rey-Stolle M.F., Mera-Berriatua L., Bazire R., Cabrera-Freitag P., Shanmuganathan M., Britz-McKibbin P., Ubeda C., Francino M.P., Barber D., Ibáñez-Sandín M.D., Barbas C., Pérez-Gordo M. , Villaseñor A.",Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach,Nature communications,2024,NA,Experiment 4,Spain,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Grandmothers,Infants,Infants (0 - 12 months old),40,38,3 months,WMS,NA,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,"Supplemental data 4, 5 and 6",21 July 2024,Aleru Divine,"Aleru Divine,WikiWorks","Differential abundance results at phylum, genus and species level for Shotgun metagenomics sequencing in infants compared to grandmothers.",decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter|s__Dysosmobacter sp.,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|s__Eggerthellaceae bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnotalea|s__Lachnotalea sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|s__Lentisphaeria bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter butyricigenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Viridiplantae|p__Streptophyta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",1783272|201174;3379134|976|200643|171549|171550|239759|28117;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|1681;1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|186802|216572|2591381|2591382;1783272|201174|84998|1643822|1643826|1972561;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|201174|1760|85004|31953|2701;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|1763508|2021453;1783272|1239|91061|186826|33958|1578;3379134|256845|1313211|2053569;1783272|1239|186801|3085636|186803|2316020|2316025;3379134|976|200643|171549|1853231|283168|28118;3379134|1224;3379134|1224|1236|91347|543|620;33090|35493;1783272|1239|186801|3085636|186803|1506577;1783272|1239|909932|1843489|31977|29465;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|91061|186826|1300,Complete,Svetlana up
bsdb:38589361/5/1,38589361,"cross-sectional observational, not case-control",38589361,10.1038/s41467-024-47182-y,NA,"Barker-Tejeda T.C., Zubeldia-Varela E., Macías-Camero A., Alonso L., Martín-Antoniano I.A., Rey-Stolle M.F., Mera-Berriatua L., Bazire R., Cabrera-Freitag P., Shanmuganathan M., Britz-McKibbin P., Ubeda C., Francino M.P., Barber D., Ibáñez-Sandín M.D., Barbas C., Pérez-Gordo M. , Villaseñor A.",Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach,Nature communications,2024,NA,Experiment 5,Spain,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Mothers and Grandmothers,Infants,Infants (0 - 12 months old),83,38,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7E,23 September 2024,Aleru Divine,"Aleru Divine,WikiWorks",Linear discriminant analysis (LDA) effect size (LEfSe) results showing the taxa enriched in the Infants – compared to the other two groups (Mothers and Grandmothers),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:38589361/6/1,38589361,"cross-sectional observational, not case-control",38589361,10.1038/s41467-024-47182-y,NA,"Barker-Tejeda T.C., Zubeldia-Varela E., Macías-Camero A., Alonso L., Martín-Antoniano I.A., Rey-Stolle M.F., Mera-Berriatua L., Bazire R., Cabrera-Freitag P., Shanmuganathan M., Britz-McKibbin P., Ubeda C., Francino M.P., Barber D., Ibáñez-Sandín M.D., Barbas C., Pérez-Gordo M. , Villaseñor A.",Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach,Nature communications,2024,NA,Experiment 6,Spain,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Infants and Grandmothers,Mothers,Mothers of the infants,78,43,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7E,23 September 2024,Aleru Divine,"Aleru Divine,WikiWorks",Linear discriminant analysis (LDA) effect size (LEfSe) results showing the taxa enriched in the Mothers – compared to the other two groups (Infants and Grandmothers),increased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",1783272|1239|186801;1783272|1239|186801|186802;1783272|1239;1783272|1239|186801|3085636|186803|572511;1783272|1239|909932|1843489|31977|39948;1783272|1239|526524|526525|128827|61170;3379134|1224|28216|80840|995019|40544,Complete,Svetlana up
bsdb:38589361/7/1,38589361,"cross-sectional observational, not case-control",38589361,10.1038/s41467-024-47182-y,NA,"Barker-Tejeda T.C., Zubeldia-Varela E., Macías-Camero A., Alonso L., Martín-Antoniano I.A., Rey-Stolle M.F., Mera-Berriatua L., Bazire R., Cabrera-Freitag P., Shanmuganathan M., Britz-McKibbin P., Ubeda C., Francino M.P., Barber D., Ibáñez-Sandín M.D., Barbas C., Pérez-Gordo M. , Villaseñor A.",Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach,Nature communications,2024,NA,Experiment 7,Spain,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Infants and Mothers,Grandmothers,Grandmothers of the infants.,81,40,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7E,23 September 2024,Aleru Divine,"Aleru Divine,WikiWorks",Linear discriminant analysis (LDA) effect size (LEfSe) results showing the taxa enriched in the Grandmothers – compared to the other two groups (Infants and Mothers),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Coriobacterium,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfobaculum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Parvibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota",1783272|1239|186801|186802|216572|258514;3379134|74201|203494|48461|1647988|239934;3379134|200940|3031449|213115|194924|35832;1783272|201174|84998|84999|84107|33870;28221;3379134|200940|3031449|213115|194924|1433996;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;1783272|201174|84998|84999|1643824|133925;1783272|201174|84998|84999|84107|1427376;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171551;3379134|74201|203494|48461|203557;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201,Complete,Svetlana up
bsdb:38589368/1/1,38589368,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P., Liu Z., Wang J., Wang J., Gao M., Zhang Y., Yang C., Zhang A., Li G., Li X., Liu S., Liu L., Sun N. , Zhang K.",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Healthy controls (HC),Major depressive disorder (MDD),"First-episode, drug-naïve patients with major depressive disorder (MDD) ages of 18–55.",85,85,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,unchanged,unchanged,increased,unchanged,NA,increased,Signature 1,FIG 1 (C),18 April 2024,Rahila,"Rahila,Scholastica,WikiWorks",A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant in patients with major depressive disorder (MDD) compared to healthy controls (HC),increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Chloroflexota|c__Anaerolineae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae,k__Pseudomonadati|p__Myxococcota|c__Myxococcia|o__Myxococcales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacillati|p__Actinomycetota|c__Thermoleophilia",1783272|201174|84998|1643822|1643826|447020;1783272|200795|292625;1783272|201174|1760|85008|28056;3379134|2818505|32015|29;3379134|1224|28211|204441|41295;3379134|1224|28211|204441;1783272|201174|1497346,Complete,Svetlana up
bsdb:38589368/1/2,38589368,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P., Liu Z., Wang J., Wang J., Gao M., Zhang Y., Yang C., Zhang A., Li G., Li X., Liu S., Liu L., Sun N. , Zhang K.",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Healthy controls (HC),Major depressive disorder (MDD),"First-episode, drug-naïve patients with major depressive disorder (MDD) ages of 18–55.",85,85,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,unchanged,unchanged,increased,unchanged,NA,increased,Signature 2,FIG 1 (C),2 August 2024,Scholastica,"Scholastica,WikiWorks",A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant in patients with major depressive disorder (MDD) compared to healthy controls (HC),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|1224|1236|135625|712|724;1783272|1239|526524|526525|2810281|191303;1783272|1239|526524|526525|2810281;1783272|1239|186801|3082720|186804,Complete,Svetlana up
bsdb:38589368/2/1,38589368,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P., Liu Z., Wang J., Wang J., Gao M., Zhang Y., Yang C., Zhang A., Li G., Li X., Liu S., Liu L., Sun N. , Zhang K.",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Depressive disorder,MONDO:0002050,Healthy controls (HC) and inflammatory depression group,Non-inflammatory depression,Patients with major depressive disorder (MDD) who had non-inflammatory depression,127,43,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2.72,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 3 (A1),18 April 2024,Rahila,"Rahila,Scholastica,WikiWorks",A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant among three groups,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales",1783272|1239;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;3379134|1224|1236|135625|712|724;1783272|1239|186801|186802|216572;3379134|1224|1236|135625|712;3379134|1224|1236|135625,Complete,Svetlana up
bsdb:38589368/3/1,38589368,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P., Liu Z., Wang J., Wang J., Gao M., Zhang Y., Yang C., Zhang A., Li G., Li X., Liu S., Liu L., Sun N. , Zhang K.",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Depressive disorder,MONDO:0002050,Healthy controls (HC) and non-inflammatory depression group,Inflammatory depression,Patients with major depressive disorder (MDD) who had inflammatory depression,128,42,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2.72,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 3 (A1),18 April 2024,Rahila,"Rahila,Scholastica,WikiWorks",A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant among three groups,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Aquincola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Candidatus Tectimicrobiota|c__Candidatus Entotheonellia|o__Candidatus Entotheonellales|f__Candidatus Entotheonellaceae|g__Candidatus Entotheonella|s__Candidatus Entotheonella sp.,k__Pseudomonadati|p__Verrucomicrobiota|c__Spartobacteria|g__Candidatus Xiphinematobacter,k__Pseudomonadati|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia,k__Pseudomonadati|p__Chlamydiota,k__Bacillati|p__Chloroflexota|c__Chloroflexia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae,k__Bacillati|p__Actinomycetota|c__Thermoleophilia|o__Gaiellales|f__Gaiellaceae|g__Gaiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Kaistibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Nakamurellales|f__Nakamurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Noviherbaspirillum|s__Noviherbaspirillum malthae,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales|f__Peniophoraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Skermanella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Steroidobacterales|f__Steroidobacteraceae|g__Steroidobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Streptosporangiales|f__Streptosporangiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Maricaulales|f__Maricaulaceae|g__Woodsholea",3379134|1224|28216|80840|2975441|391952;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|1224|28211|204458|76892|41275;3379134|1802339|3277336|3277337|3277338|93171|2066855;3379134|74201|134549|134550;3379134|204428|204429|51291|809|810;3379134|204428;1783272|200795|32061;3379134|1224|28211|204457|335929;1783272|201174|1497346|1154584|1154585|1154586;3379134|1224|1236|135614|32033|505691;1783272|1239|91061|186826|1300|1357;1783272|201174|1760|85008|28056;1783272|201174|1760|1643684|85031;3379134|1224|28216|80840|75682|1344552|1260987;4751|5204|155619|452342|103393;3379134|1224|28211|204441|2829815|204447;3379134|1224|1236|3060226|2689614|469322;1783272|201174|1760|85012|2004;3379134|1224|28211|2800059|2800061|240236,Complete,Svetlana up
bsdb:38589368/4/1,38589368,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P., Liu Z., Wang J., Wang J., Gao M., Zhang Y., Yang C., Zhang A., Li G., Li X., Liu S., Liu L., Sun N. , Zhang K.",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Depressive disorder,MONDO:0002050,Non-inflammatory depression,Inflammatory depression,Patients with major depressive disorder (MDD) who had inflammatory depression,43,42,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2.45,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 3 (A1),18 April 2024,Rahila,"Rahila,Scholastica,WikiWorks",A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant in patients with inflammatory versus non-inflammatory depression,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae,k__Bacillati|p__Actinomycetota|c__Thermoleophilia|o__Solirubrobacterales|f__Solirubrobacteraceae|g__Solirubrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae",3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|1300|1357;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;1783272|201174|1760|85006|85017;1783272|201174|1497346|588673|320599|207599;3379134|1224|28211|356|335928,Complete,Svetlana up
bsdb:38589368/4/2,38589368,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P., Liu Z., Wang J., Wang J., Gao M., Zhang Y., Yang C., Zhang A., Li G., Li X., Liu S., Liu L., Sun N. , Zhang K.",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Depressive disorder,MONDO:0002050,Non-inflammatory depression,Inflammatory depression,Patients with major depressive disorder (MDD) who had inflammatory depression,43,42,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2.45,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,FIG 3 (A2),18 April 2024,Rahila,"Rahila,Scholastica,WikiWorks",A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant in patients with inflammatory versus non-inflammatory depression,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales",1783272|1239;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;3379134|1224|1236|135625|712|724;1783272|1239|186801|186802|216572;3379134|1224|1236|135625|712;3379134|1224|1236|135625,Complete,Svetlana up
bsdb:38589368/5/1,38589368,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P., Liu Z., Wang J., Wang J., Gao M., Zhang Y., Yang C., Zhang A., Li G., Li X., Liu S., Liu L., Sun N. , Zhang K.",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Healthy controls (HC),Inflammatory depression,Patients with major depressive disorder (MDD) who had inflammatory depression,20,20,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 3 (C),18 April 2024,Rahila,"Rahila,Scholastica,WikiWorks",A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant in patients with inflammatory depression compared to healthy controls (HC) at species level using shotgun metagenomic sequencing,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces bouchesdurhonensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. ICM47,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:138,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium diversum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae",1783272|201174|1760|2037|2049|1654|1852361;1783272|201174|1760|2037|2049|1654|55565;1783272|201174|1760|2037|2049|1654|936548;1783272|1239|186801|186802|31979|1485|1262775;1783272|1239|186801|3082720|543314|86331|114527;1783272|201174|1760|2037|2049|2529408|1660;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1313,Complete,Svetlana up
bsdb:38589368/5/2,38589368,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P., Liu Z., Wang J., Wang J., Gao M., Zhang Y., Yang C., Zhang A., Li G., Li X., Liu S., Liu L., Sun N. , Zhang K.",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Healthy controls (HC),Inflammatory depression,Patients with major depressive disorder (MDD) who had inflammatory depression,20,20,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,FIG 3 (C),2 August 2024,Scholastica,"Scholastica,WikiWorks",A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant in patients with inflammatory depression compared to healthy controls (HC) at species level using shotgun metagenomic sequencing,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina|s__Sarcina ventriculi,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp. 60_17,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Thermotaleaceae|g__Geosporobacter|s__Geosporobacter subterraneus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:417,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. AF28-13AC,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. AF22-5LB,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. AF17-7,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium butyricum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. AF19-1,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. AF36-5BH,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:343,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. CAG:37_48_57,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. AF10-46,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. AF14-40,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. OF03-13,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. AF32-4BH,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. AF19-13LB,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. AF27-11BH,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:413,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. OM07-7,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. AF17-9LB,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. OM04-11BH,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. AF34-35BH,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 57_20,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:18,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:192,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes ihumii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. CAG:241,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella|s__Allofournierella massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. AM43-5AT,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus sp. AM42-5AC,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. CAG:74_58_120,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. CAG:241_62_21,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. CAG:37",1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|204475|745368;1783272|1239|186801|186802|31979|1266|1267;1783272|1239|186801|186802|216572|292632|1897022;1783272|1239|186801|3082720|3118657|390805|390806;1783272|1239|186801|186802|31979|1485|1262804;1783272|1239|186801|186802|216572|216851|2292234;1783272|1239|186801|3085636|186803|572511|2292964;1783272|1239|186801|186802|186806|1730|2293105;3379134|976|200643|171549|171550|239759|2585118;1783272|1239|186801|186802|31979|1485|1502;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|186802|31979|1485|1492;1783272|1239|186801|3085636|186803|572511|2292960;1783272|1239|186801|186802|186806|1730|2293108;1783272|1239|186801|3082720|186804|1501226|1776391;1783272|1239|186801|186802|31979|1485|1262796;1783272|1239|186801|3085636|186803|572511|1896976;1783272|1239|186801|186802|216572|216851|2302955;1783272|1239|186801|3085636|186803|572511|2292958;1783272|1239|186801|3085636|186803|572511|2292980;1783272|1239|186801|3085636|186803|572511|2292967;1783272|1239|186801|3085636|186803|572511|2292962;1783272|1239|186801|186802|216572|216851|2302956;1783272|1239|186801|186802|31979|1485|1262803;1783272|1239|186801|186802|216572|1263|2293234;1783272|1239|186801|3085636|186803|572511|2292959;1783272|1239|186801|186802|216572|216851|2292357;1783272|1239|186801|186802|186806|1730|2293107;1783272|1239|186801|186802|216572|459786|1897011;1783272|1239|186801|3085636|186803|841|1262941;1783272|1239|186801|186802|186806|1730|1262883;3379134|976|200643|171549|171550|239759|1470347;1783272|1239|186801|186802|216572|459786|1262911;1783272|1239|186801|186802|31979|1485|1506;1783272|1239|186801|186802|216572|459786|1945593;1783272|1239|186801|186802|216572|1940255|1650663;1783272|1239|186801|186802|216572|216851|2302957;1783272|1239|186801|186802|3085642|580596|2292297;1783272|1239|186801|186802|216572|216851|1897005;1783272|1239|186801|186802|216572|459786|1897012;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|3085636|186803|572511|1262757,Complete,Svetlana up
bsdb:38589368/6/1,38589368,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P., Liu Z., Wang J., Wang J., Gao M., Zhang Y., Yang C., Zhang A., Li G., Li X., Liu S., Liu L., Sun N. , Zhang K.",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Healthy control (HC),Inflammatory and non-inflammatory depression,Patients with major depressive disorder (MDD) grouped into inflammatory and non-inflammatory depression groups,85,85,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2.72,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 3 (A1),18 April 2024,Rahila,"Rahila,Scholastica,WikiWorks",A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant among three groups,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|31979;1783272|1239|186801|3082720|186804;1783272|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:38589368/7/1,38589368,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P., Liu Z., Wang J., Wang J., Gao M., Zhang Y., Yang C., Zhang A., Li G., Li X., Liu S., Liu L., Sun N. , Zhang K.",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 7,China,Mus musculus,Feces,UBERON:0001988,Depressive disorder,MONDO:0002050,"Low-inflammatory, healthy control and blank groups",High-inflammatory group,Mice classified into the high-inflammatory group,24,20,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4.31,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 4 (D3),18 April 2024,Rahila,"Rahila,Scholastica,WikiWorks",A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant among four mice groups,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",1783272|1239|526524|526525|128827|174708;1783272|1239|526524;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524|526525|2810281;1783272|1239|526524|526525|2810281|191303,Complete,Svetlana up
bsdb:38589368/9/1,38589368,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P., Liu Z., Wang J., Wang J., Gao M., Zhang Y., Yang C., Zhang A., Li G., Li X., Liu S., Liu L., Sun N. , Zhang K.",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 9,China,Mus musculus,Feces,UBERON:0001988,Depressive disorder,MONDO:0002050,Healthy control (HC) group,"High-inflammatory, low-inflammatory and blank groups","Mice classified into the high-inflammatory, low-inflammatory and blank groups",7,37,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4.31,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 4 (D3),18 April 2024,Rahila,"Rahila,Scholastica,WikiWorks",A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant among four mice groups,decreased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales",3379134|1224;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|1224|1236;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|620;3379134|1224|1236|91347,Complete,Svetlana up
bsdb:38589368/10/1,38589368,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P., Liu Z., Wang J., Wang J., Gao M., Zhang Y., Yang C., Zhang A., Li G., Li X., Liu S., Liu L., Sun N. , Zhang K.",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 10,China,Mus musculus,Feces,UBERON:0001988,Depressive disorder,MONDO:0002050,"High-inflammatory, low-inflammatory and healthy control groups",Blank group,Mice administered normal saline and classified into the blank group,35,9,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4.31,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 4 (D3),18 April 2024,Rahila,"Rahila,Scholastica,WikiWorks",A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant among four mice groups,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",3379134|976|200643|171549|2005473;1783272|1239|186801|3085636|186803;3379134|200940|3031449|213115|194924|872,Complete,Svetlana up
bsdb:38589368/11/1,38589368,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P., Liu Z., Wang J., Wang J., Gao M., Zhang Y., Yang C., Zhang A., Li G., Li X., Liu S., Liu L., Sun N. , Zhang K.",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 11,China,Mus musculus,Feces,UBERON:0001988,Clostridium butyricum,NCBITAXON:1492,Clostridium butyricum (CB) and normal saline (NS) groups,High-inflammatory group,Mice classified into the high-inflammatory group,13,7,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4.22,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 6 (C),5 August 2024,Scholastica,"Scholastica,WikiWorks",A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant among three mice groups,increased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,c__Deltaproteobacteria",1783272|1239|186801;1783272|1239|186801|186802;1783272|1239;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;3379134|200940|3031449|213115|194924|872;28221,Complete,Svetlana up
bsdb:38589368/12/1,38589368,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P., Liu Z., Wang J., Wang J., Gao M., Zhang Y., Yang C., Zhang A., Li G., Li X., Liu S., Liu L., Sun N. , Zhang K.",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 12,China,Mus musculus,Feces,UBERON:0001988,Clostridium butyricum,NCBITAXON:1492,High-inflammatory and normal saline (NS) groups,Clostridium butyricum (CB),Mice administered probiotics (Clostridium butyricum),13,7,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4.22,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 6 (C),5 August 2024,Scholastica,"Scholastica,WikiWorks",A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant among three mice groups,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae",3379134|1224|1236;3379134|1224;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543;3379134|1224|1236|91347;3379134|1224|1236|91347|543|620;3379134|976|200643|171549|1853231|574697;3379134|976|200643|171549|1853231,Complete,Svetlana up
bsdb:38589368/13/1,38589368,"case-control,laboratory experiment",38589368,10.1038/s41467-024-47273-w,NA,"Liu P., Liu Z., Wang J., Wang J., Gao M., Zhang Y., Yang C., Zhang A., Li G., Li X., Liu S., Liu L., Sun N. , Zhang K.",Immunoregulatory role of the gut microbiota in inflammatory depression,Nature communications,2024,NA,Experiment 13,China,Mus musculus,Feces,UBERON:0001988,Clostridium butyricum,NCBITAXON:1492,Normal saline (NS),High-inflammatory and Clostridium butyricum (CB) groups,Mice administered normal saline (NS),6,14,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4.22,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 6 (C),5 August 2024,Scholastica,"Scholastica,WikiWorks",A linear discriminant analysis (LDA) effect size (LEfSe) analysis showing taxa differentially abundant among three mice groups,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",3379134|976|200643|171549|2005473;3379134|976|200643;3379134|976;3379134|976|200643|171549,Complete,Svetlana up
bsdb:38589392/1/1,38589392,laboratory experiment,38589392,https://doi.org/10.1038/s41467-024-47072-3,NA,"Dokoshi T., Chen Y., Cavagnero K.J., Rahman G., Hakim D., Brinton S., Schwarz H., Brown E.A., O'Neill A., Nakamura Y., Li F., Salzman N.H., Knight R. , Gallo R.L.",Dermal injury drives a skin to gut axis that disrupts the intestinal microbiome and intestinal immune homeostasis in mice,Nature communications,2024,NA,Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Skin wound,EFO:0005756,Control group(mice without skin wounds),Experimental group/Wound (with skin wounds),Experimental group of mice subjected to either dermal injury or skin injury,32,32,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,FALSE,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 3D,12 November 2024,Prolific,"Prolific,KateRasheed,WikiWorks",Differential abundance of bacterial species between the group with skin wounds and the control group (without skin injuries).,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia caecimuris,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia mucosicola,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|s__Firmicutes bacterium ASF500,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium A2,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium A4,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium M18-1,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp. G3,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp. 5-2,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 3-1,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium MD308,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 1-3",1783272|201174|84998|1643822|1643826|447020|671266;1783272|201174|84998|1643822|1643826|447020|446660;1783272|201174|84998|1643822|1643826|447020|580026;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|818;1783272|201174|1760|85004|31953|1678|1694;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|1378168;1783272|1239|186801|3085636|186803|397290;1783272|1239|186801|3085636|186803|397291;1783272|1239|186801|3085636|186803|1235792;1783272|1239|91061|186826|33958|1578|1579;1783272|1239|91061|186826|33958|1578|1596;3379134|1224|28216|80840|995019|577310|487175;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|186802|216572|244127|397284;1783272|1239|186801|3085636|186803|189330|1235798;1783272|1239|186801|3085636|186803|397288;1783272|1239|186801|3085636|186803|1235799;1783272|1239|186801|186802|216572|459786|1235797,Complete,Svetlana up
bsdb:38589392/1/2,38589392,laboratory experiment,38589392,https://doi.org/10.1038/s41467-024-47072-3,NA,"Dokoshi T., Chen Y., Cavagnero K.J., Rahman G., Hakim D., Brinton S., Schwarz H., Brown E.A., O'Neill A., Nakamura Y., Li F., Salzman N.H., Knight R. , Gallo R.L.",Dermal injury drives a skin to gut axis that disrupts the intestinal microbiome and intestinal immune homeostasis in mice,Nature communications,2024,NA,Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Skin wound,EFO:0005756,Control group(mice without skin wounds),Experimental group/Wound (with skin wounds),Experimental group of mice subjected to either dermal injury or skin injury,32,32,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,FALSE,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 3D,12 November 2024,Prolific,"Prolific,KateRasheed,WikiWorks",Differential abundance of bacterial species between the group with skin wounds and the control group (without skin injuries).,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Curtobacterium|s__Curtobacterium flaccumfaciens,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella|s__Dubosiella newyorkensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus murinus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Mammaliicoccus|s__Mammaliicoccus lentus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus|s__Pediococcus damnosus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia pickettii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Saccharomonospora|s__Saccharomonospora viridis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Saccharopolyspora|s__Saccharopolyspora rectivirgula,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia marcescens,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Shouchella|s__Shouchella clausii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus xylosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Thermoactinomycetaceae|g__Thermoactinomyces|s__Thermoactinomyces sp. Gus2-1",1783272|201174|1760|85006|85023|2034|2035;1783272|1239|526524|526525|128827|1937008|1862672;3379134|1224|1236|91347|543|561|562;1783272|1239|91061|186826|33958|2767887|1622;1783272|1239|91061|1385|90964|2803850|42858;1783272|1239|91061|186826|33958|1253|51663;3379134|1224|28216|80840|119060|48736|329;1783272|201174|1760|85010|2070|1851|1852;1783272|201174|1760|85010|2070|1835|28042;3379134|1224|1236|91347|1903411|613|615;1783272|1239|91061|1385|186817|2893057|79880;1783272|1239|91061|1385|90964|1279|1288;1783272|1239|91061|1385|186824|2023|1535750,Complete,Svetlana up
bsdb:38589392/2/1,38589392,laboratory experiment,38589392,https://doi.org/10.1038/s41467-024-47072-3,NA,"Dokoshi T., Chen Y., Cavagnero K.J., Rahman G., Hakim D., Brinton S., Schwarz H., Brown E.A., O'Neill A., Nakamura Y., Li F., Salzman N.H., Knight R. , Gallo R.L.",Dermal injury drives a skin to gut axis that disrupts the intestinal microbiome and intestinal immune homeostasis in mice,Nature communications,2024,NA,Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Skin wound,EFO:0005756,Control group,Experimental group/Wound (after skin wounding),Experimental group of mice who were subjected to either dermal injury or skin injury.,5,5,NA,WMS,NA,Illumina,relative abundances,T-Test,0.05,FALSE,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplementary Figure 7,20 December 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of bacterial species between the group with skin wounds and the control group (after skin wounding).,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|91061|186826|33958|1578|1596;3379134|976|200643|171549|815|816|818,Complete,Svetlana up
bsdb:38589422/1/1,38589422,"case-control,laboratory experiment",38589422,https://doi.org/10.1038/s41537-024-00460-6,NA,"Wei N., Ju M., Su X., Zhang Y., Huang Y., Rao X., Cui L., Lin Z. , Dong Y.",Transplantation of gut microbiota derived from patients with schizophrenia induces schizophrenia-like behaviors and dysregulated brain transcript response in mice,"Schizophrenia (Heidelberg, Germany)",2024,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,HCF: healthy controls (no psychiatric diagnosis of schizophrenia),SCZF: patients with schizophrenia,antipsychotic-treated patients with schizophrenia,15,20,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,decreased,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 2B,10 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,Scholastica,WikiWorks",LEfSe comparison of gut microbiota in antipsychotic-treated patients with schizophrenia (SCZF group) versus healthy controls (HCF group),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Leptothrix,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Mycoplana,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Pseudochrobactrum,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;1783272|201174|1760|85006|1268|1663;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;3379134|1224|28216|80840|119060|106589;3379134|1224|1236|91347|543;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|186806|1730;3379134|1224|1236;3379134|1224|28216|80840|2975441|88;1783272|201174|1760|85006|1268;3379134|1224|28211|356|82115|13159;3379134|1224|28211|356|118882|354349;3379134|1224;3379134|1224|1236|72274|135621|286;1783272|1239|186801|186802|186806|113286;3379134|1224|1236|91347|543|620;1783272|201174;3379134|1224|1236|91347,Complete,Svetlana up
bsdb:38589422/1/2,38589422,"case-control,laboratory experiment",38589422,https://doi.org/10.1038/s41537-024-00460-6,NA,"Wei N., Ju M., Su X., Zhang Y., Huang Y., Rao X., Cui L., Lin Z. , Dong Y.",Transplantation of gut microbiota derived from patients with schizophrenia induces schizophrenia-like behaviors and dysregulated brain transcript response in mice,"Schizophrenia (Heidelberg, Germany)",2024,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,HCF: healthy controls (no psychiatric diagnosis of schizophrenia),SCZF: patients with schizophrenia,antipsychotic-treated patients with schizophrenia,15,20,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,decreased,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 2B,10 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,Scholastica,WikiWorks",LEfSe comparison of gut microbiota in antipsychotic-treated patients with schizophrenia (SCZF group) versus healthy controls (HCF group),decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Aquabacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Macellibacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|201174|84998|1643822|1643826|447020;3379134|976|200643|171549|171550|239759;3379134|1224|28216|80840|92793;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;1783272|1239|186801;1783272|1239|186801|3085636|186803|33042;1783272|201174|84998|84999|84107;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|216572|216851;3379134|1224|1236|135625|712|724;3379134|976|200643|171549|171551|1159323;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|2005525|375288;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|976|200643|171549|171551;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|186801|3085636|186803|46205;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|1263;3379134|976;1783272|1239;1783272|1239|186801|186802;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:38589422/2/1,38589422,"case-control,laboratory experiment",38589422,https://doi.org/10.1038/s41537-024-00460-6,NA,"Wei N., Ju M., Su X., Zhang Y., Huang Y., Rao X., Cui L., Lin Z. , Dong Y.",Transplantation of gut microbiota derived from patients with schizophrenia induces schizophrenia-like behaviors and dysregulated brain transcript response in mice,"Schizophrenia (Heidelberg, Germany)",2024,NA,Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,HC: healthy control fecal microbiota-recipient mice,SCZ: schizophrenia fecal microbiota-recipient mice,Male C57BL/6 mice which transplanted fecal microbiota from a human patient with a schizophrenia psychiatric disorder.,5,5,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4D,16 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,Scholastica,WikiWorks",Bacterial genera differentially expressed in mice transplanted with schizophrenia versus healthy control fecal microbiota,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",1783272|201174|1760|85007|1653|1716;3379134|29547|3031852|213849|72293|209;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|171552|577309;1783272|1239|186801|186802|216572|1508657,Complete,Svetlana up
bsdb:38589422/2/2,38589422,"case-control,laboratory experiment",38589422,https://doi.org/10.1038/s41537-024-00460-6,NA,"Wei N., Ju M., Su X., Zhang Y., Huang Y., Rao X., Cui L., Lin Z. , Dong Y.",Transplantation of gut microbiota derived from patients with schizophrenia induces schizophrenia-like behaviors and dysregulated brain transcript response in mice,"Schizophrenia (Heidelberg, Germany)",2024,NA,Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,HC: healthy control fecal microbiota-recipient mice,SCZ: schizophrenia fecal microbiota-recipient mice,Male C57BL/6 mice which transplanted fecal microbiota from a human patient with a schizophrenia psychiatric disorder.,5,5,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4D,16 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,Scholastica,WikiWorks",Bacterial genera differentially expressed in mice transplanted with schizophrenia versus healthy control fecal microbiota,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;1783272|1239|186801|3082768|990719|990721;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|2005525|375288;1783272|1239|526524|526525|2810280|1505663,Complete,Svetlana up
bsdb:38594374/1/1,38594374,case-control,38594374,10.1038/s41598-024-58642-2,NA,"Kwiatkowska M., Gołębiewski M., Sikora M., Rycharska E.Ł. , Krogulska A.",The oral cavity and intestinal microbiome in children with functional constipation,Scientific reports,2024,NA,Experiment 1,Poland,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Children without Functional constipation,Children with Functional constipation,Children over three years of age with Functional constipation,34,57,1 month,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Table 3,14 March 2025,Tosin,Tosin,Taxonomic changes in the gut microbiome in children with functional constipation (FC) compared to children without functional constipation (FC),increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,3379134|976|200643|171549|2005525,Complete,KateRasheed
bsdb:38594374/1/2,38594374,case-control,38594374,10.1038/s41598-024-58642-2,NA,"Kwiatkowska M., Gołębiewski M., Sikora M., Rycharska E.Ł. , Krogulska A.",The oral cavity and intestinal microbiome in children with functional constipation,Scientific reports,2024,NA,Experiment 1,Poland,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Children without Functional constipation,Children with Functional constipation,Children over three years of age with Functional constipation,34,57,1 month,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Table 3,14 March 2025,Tosin,Tosin,Taxonomic changes in the gut microbiome in children with functional constipation (FC) compared to children without functional constipation (FC).,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",3379134|1224|28216|80840|119060;1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|186803|1407607;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|216572|292632,Complete,KateRasheed
bsdb:38596264/1/1,38596264,"cross-sectional observational, not case-control",38596264,10.3892/ol.2024.14368,https://www.spandidos-publications.com/10.3892/ol.2024.14368,"Jin M., Fan Q., Shang F., Zhang T., Ogino S. , Liu H.",Fusobacteria alterations are associated with colorectal cancer liver metastasis and a poor prognosis,Oncology letters,2024,"colorectal cancer, fusobacteria, gut microbiota, liver metastasis",Experiment 1,China,Homo sapiens,Colorectum,UBERON:0012652,Metastatic colorectal cancer,EFO:1001480,No liver metastasis (NLM),Liver metastasis (LM),Colorectal patients with liver metastasis (LM) in the supplementary discovery cohort (cohort 1),10,8,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,increased,unchanged,NA,NA,increased,Signature 1,"Figure 4a, 4b and Figure 5c",20 April 2024,Aleru Divine,"Aleru Divine,WikiWorks","Taxonomic tree, histogram and heatmap (fig 5) displaying differentially abundant taxa in the cladogram in cohort 1.",increased,"k__Pseudomonadati|p__Acidobacteriota,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Armatimonadota,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,p__Candidatus Saccharimonadota,k__Bacillati|p__Chloroflexota|c__Chloroflexia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacillati|p__Cyanobacteriota,k__Thermotogati|p__Deinococcota|c__Deinococci,k__Thermotogati|p__Deinococcota,k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Gemmatimonadota|c__Gemmatimonadia,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Nitrospirota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Planctomycetota,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Thermotogati|p__Synergistota,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Bacteroidota",3379134|57723;1783272|201174;1783272|67819;1783272|1239;3379134|1224|28216;3379134|1224|28216|80840;95818;1783272|200795|32061;3379134|1224|28216|80840|119060|106589;1783272|1117;3384194|1297|188787;3384194|1297;3384189|32066;3379134|142182|219685;1783272|544448;3379134|40117;3379134|1224|28216|80840|75682;3379134|203682;3379134|203691|203692|136;3384194|508458;3384194|1297|188787|68933|188786;3384194|1297|188787|68933;3384194|1297|188787|68933|188786|270;3379134|74201;3379134|976,Complete,Svetlana up
bsdb:38596264/1/2,38596264,"cross-sectional observational, not case-control",38596264,10.3892/ol.2024.14368,https://www.spandidos-publications.com/10.3892/ol.2024.14368,"Jin M., Fan Q., Shang F., Zhang T., Ogino S. , Liu H.",Fusobacteria alterations are associated with colorectal cancer liver metastasis and a poor prognosis,Oncology letters,2024,"colorectal cancer, fusobacteria, gut microbiota, liver metastasis",Experiment 1,China,Homo sapiens,Colorectum,UBERON:0012652,Metastatic colorectal cancer,EFO:1001480,No liver metastasis (NLM),Liver metastasis (LM),Colorectal patients with liver metastasis (LM) in the supplementary discovery cohort (cohort 1),10,8,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,increased,unchanged,NA,NA,increased,Signature 2,"Figure 4a, 4b and Figure 5c",20 April 2024,Aleru Divine,"Aleru Divine,WikiWorks","Taxonomic tree, histogram and heatmap (fig 5) displaying differentially abundant taxa in the cladogram in cohort 1.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas",3379134|1224|1236|2887326|468|469;3379134|1224|28211;3379134|74152|641853;3379134|1224|1236;3379134|1224|1236|2887326|468;;3379134|1224|1236|72274;3379134|1224;3379134|1224|28211|204457|41297;3379134|1224|28211|204457;3379134|1224|28211|204457|41297|13687,Complete,Svetlana up
bsdb:38596264/2/1,38596264,"cross-sectional observational, not case-control",38596264,10.3892/ol.2024.14368,https://www.spandidos-publications.com/10.3892/ol.2024.14368,"Jin M., Fan Q., Shang F., Zhang T., Ogino S. , Liu H.",Fusobacteria alterations are associated with colorectal cancer liver metastasis and a poor prognosis,Oncology letters,2024,"colorectal cancer, fusobacteria, gut microbiota, liver metastasis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Metastatic colorectal cancer,EFO:1001480,No liver metastasis (NLM),Liver metastasis (LM),Colorectal patients with liver metastasis (LM) in the discovery cohort (cohort 2),36,18,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,"Figure 4c, 4d and Figure 5d",20 April 2024,Aleru Divine,"Aleru Divine,WikiWorks","Taxonomic tree, histogram and heatmap (fig 5) displaying differentially abundant taxa in the cladogram in cohort 2.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,p__Candidatus Saccharimonadota,k__Pseudomonadati|p__Chlorobiota,k__Bacillati|p__Chloroflexota|c__Chloroflexia,k__Bacillati|p__Cyanobacteriota,k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Gemmatimonadota|c__Gemmatimonadia,k__Pseudomonadati|p__Lentisphaerota,,k__Pseudomonadati|p__Planctomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Spirochaetota,k__Thermotogati|p__Synergistota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Verrucomicrobiota",3379134|976|200643|171549|171550|239759;1783272|1239;3379134|976|200643;95818;3379134|1090;1783272|200795|32061;1783272|1117;3384189|32066;3379134|142182|219685;3379134|256845;;3379134|203682;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550;3379134|203691;3384194|508458;1783272|1239|909932|1843489|31977;3379134|74201,Complete,Svetlana up
bsdb:38596264/2/2,38596264,"cross-sectional observational, not case-control",38596264,10.3892/ol.2024.14368,https://www.spandidos-publications.com/10.3892/ol.2024.14368,"Jin M., Fan Q., Shang F., Zhang T., Ogino S. , Liu H.",Fusobacteria alterations are associated with colorectal cancer liver metastasis and a poor prognosis,Oncology letters,2024,"colorectal cancer, fusobacteria, gut microbiota, liver metastasis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Metastatic colorectal cancer,EFO:1001480,No liver metastasis (NLM),Liver metastasis (LM),Colorectal patients with liver metastasis (LM) in the discovery cohort (cohort 2),36,18,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,"Figure 4c, 4d and Figure 5d",20 April 2024,Aleru Divine,"Aleru Divine,WikiWorks","Taxonomic tree, histogram and heatmap (fig 5) displaying differentially abundant taxa in the cladogram in cohort 2.",decreased,"k__Pseudomonadati|p__Acidobacteriota,k__Bacillati|p__Actinomycetota,k__Thermotogati|p__Deinococcota,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Nitrospirota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Pseudomonadota",3379134|57723;1783272|201174;3384194|1297;1783272|544448;3379134|40117;3379134|976|200643|171549|171551|836;3379134|1224,Complete,Svetlana up
bsdb:38596264/3/1,38596264,"cross-sectional observational, not case-control",38596264,10.3892/ol.2024.14368,https://www.spandidos-publications.com/10.3892/ol.2024.14368,"Jin M., Fan Q., Shang F., Zhang T., Ogino S. , Liu H.",Fusobacteria alterations are associated with colorectal cancer liver metastasis and a poor prognosis,Oncology letters,2024,"colorectal cancer, fusobacteria, gut microbiota, liver metastasis",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Metastatic colorectal cancer,EFO:1001480,No liver metastasis (NLM),Liver metastasis (LM),Colorectal patients with liver metastasis (LM) in the validation cohort (cohort 3),41,13,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,"Figure 4e, 4f and Figure 5e",21 April 2024,Aleru Divine,"Aleru Divine,WikiWorks","Taxonomic tree, histogram and heatmap (fig 5) displaying differentially abundant taxa in the cladogram in cohort 3.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Pseudomonadati|p__Chlorobiota,k__Bacillati|p__Chloroflexota,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Devosia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales,k__Pseudomonadati|p__Elusimicrobiota,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Crocinitomicaceae|g__Fluviicola,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Pseudomonadati|p__Gemmatimonadota|c__Gemmatimonadia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hydrogenophaga,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Isosphaerales|f__Isosphaeraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnobacterium,k__Pseudomonadati|p__Lentisphaerota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Methylophilaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Planctomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae|g__Promicromonospora,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Pseudoxanthomonas,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae|g__Rhodomicrobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Spirochaetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Synechococcales|f__Synechococcaceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Synechococcales,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Synechococcales|f__Synechococcaceae|g__Synechococcus,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales,k__Thermotogati|p__Synergistota|c__Synergistia,k__Thermotogati|p__Synergistota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota",3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|207244;1783272|1239;1783272|1239|526524|526525|128827|118747;3379134|1090;1783272|200795;1783272|1239|186801|3082768|990719;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|33042;3379134|1224|1236|118969|118968;1783272|1117|3028117;28221;3379134|200940|3031449|213115|194924|872;3384194|508458|649775|649776|3029088;3379134|1224|28211|356|2831106|46913;1783272|1239|186801|3085636|186803|189330;3379134|74152|641853;3379134|74152|641853|641854|641876;3379134|74152|641853|641854;3379134|74152;3379134|976|117743|200644|1853230|332102;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738;3379134|142182|219685;1783272|1239|186801|186802|204475;3379134|1224|28216|80840|80864|47420;3379134|203682|203683|2691356|1763524;1783272|1239|186801|3085636|186803|140625;3379134|256845;3379134|1224|28216|32003|32011;3379134|976|200643|171549|2005473;3379134|1224|28216|32003;1783272|1239|186801|186802|216572|119852;3379134|976|200643|171549|171552|577309;;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;1783272|1239|909932|1843488|909930|33024;3379134|203682;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|201174|1760|85006|85017|43676;3379134|1224|1236|135614|32033|83618;3384194|508458|649775|649776|3029088|638847;3379134|1224|28211|356|45401|1068;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|1263;3379134|203691;1783272|1239|186801|186802|216572|292632;1783272|1117|3028117|1890424|1890426;1783272|1117|3028117|1890424;1783272|1117|3028117|1890424|1890426|1129;3384194|508458|649775|649776;3384194|508458|649775;3384194|508458;3379134|1224|1236|72273;1783272|1239|1737404|1737405|1737406;1783272|1239|909932|1843489|31977;3379134|976,Complete,Svetlana up
bsdb:38596264/3/2,38596264,"cross-sectional observational, not case-control",38596264,10.3892/ol.2024.14368,https://www.spandidos-publications.com/10.3892/ol.2024.14368,"Jin M., Fan Q., Shang F., Zhang T., Ogino S. , Liu H.",Fusobacteria alterations are associated with colorectal cancer liver metastasis and a poor prognosis,Oncology letters,2024,"colorectal cancer, fusobacteria, gut microbiota, liver metastasis",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Metastatic colorectal cancer,EFO:1001480,No liver metastasis (NLM),Liver metastasis (LM),Colorectal patients with liver metastasis (LM) in the validation cohort (cohort 3),41,13,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,"Figure 4e, 4f and Figure 5e",21 April 2024,Aleru Divine,"Aleru Divine,WikiWorks","Taxonomic tree, histogram and heatmap (fig 5) displaying differentially abundant taxa in the cladogram in cohort 3.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Verrucomicrobiota,p__Candidatus Saccharimonadota,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Nitrospirota,k__Bacillati|p__Actinomycetota,k__Thermotogati|p__Deinococcota,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Acidobacteriota",3379134|976|200643|171549|1853231;3379134|976|200643|171549|171551|836;3379134|74201;95818;1783272|544448;3379134|40117;1783272|201174;3384194|1297;3379134|1224;1783272|1117;3379134|57723,Complete,Svetlana up
bsdb:38627869/1/1,38627869,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán J.M., Argüello H., Cabrera-Rubio R., Crispie F., Cotter P.D., Garrido J.J., Ekhlas D., Burgess C.M. , Manzanilla E.G.",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 1,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Therapeutic zinc oxide (Zn) treatment + non-medicated control diet (Ct diet) - Global data set,Antibiotic (Ab) treatment - Global data set,Piglets treated with antibiotics. Global data set involves both consistency and Day post weaning (dpw) factors,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 5A, 5B and Text",20 April 2024,Fiddyhamma,"Fiddyhamma,KateRasheed,WikiWorks","Differences in species abundance, returned by LEfSe, most likely explaining the differences among dietary treatments. (A) Species associated with each dietary treatment in the analysis of global species data.",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii",1783272|1239|91061|186826|33958|2742598|1598;1783272|1239|909932|1843489|31977|906|907,Complete,Svetlana up
bsdb:38627869/2/2,38627869,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán J.M., Argüello H., Cabrera-Rubio R., Crispie F., Cotter P.D., Garrido J.J., Ekhlas D., Burgess C.M. , Manzanilla E.G.",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 2,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,CT diet + Ab treatment global data set,Therapeutic Zinc oxide (Zn) global data set,Piglets treated with Therapeutic Zinc oxide. Global data set involves both consistency and Day post weaning (dpw) factors,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 5A, 5B",21 April 2024,Fiddyhamma,"Fiddyhamma,KateRasheed,WikiWorks","Differences in species abundance, returned by LEfSe, most likely explaining the differences among dietary treatments. (A) Species associated with each dietary treatment in the analysis of global species data.",decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister massiliensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera hexanoica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera stantonii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas ruminantium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. oral taxon 920,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena",1783272|1239|909932|1843489|31977|39948|2161821;3379134|1224|1236|91347|543|561|562;1783272|1239|909932|909929|1843491|158846|158847;1783272|1239|909932|1843489|31977|906|1675036;1783272|1239|909932|1843489|31977|906|2144175;3379134|976|200643|171549|1853231|283168|28118;1783272|1239|909932|909929|1843491|970|971;1783272|1239|909932|909929|1843491|970|1884263;1783272|1239|909932|909929|1843491|970|69823,Complete,Svetlana up
bsdb:38627869/3/1,38627869,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán J.M., Argüello H., Cabrera-Rubio R., Crispie F., Cotter P.D., Garrido J.J., Ekhlas D., Burgess C.M. , Manzanilla E.G.",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 3,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Antibiotics (Ab) global data set + Zn global data set,Ct diet global data set,Piglets with non-medicated control diet. Global data set involves both consistency and Day post weaning (dpw) factors,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 5A, 5B and Text",21 April 2024,Fiddyhamma,"Fiddyhamma,KateRasheed,WikiWorks","Differences in species abundance, returned by LEfSe, most likely explaining the differences among dietary treatments. (A) Species associated with each dietary treatment in the analysis of global species data.
	  
		  
		  
		  
		  
		  
		  
		  
		  
		  
	  
		  ",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caecimuris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulolyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides helcogenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Prevotella heparinolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides zoogleoformans,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium callanderi,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Methanobacteriati|p__Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomethylophilaceae|g__Methanomethylophilus|s__Methanomethylophilus alvi,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp. CT06,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola salanitronis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella serpentiformis",3379134|976|200643|171549|815|816|1796613;3379134|976|200643|171549|815|816|2981780;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|290053;3379134|976|200643|171549|815|816|28113;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|28119;1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|186801|186802|186806|1730|53442;1783272|1239|186801|186802|216572|946234|292800;3366610|2283796|183967|1235850|2517203|1291539|1291540;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|2005525|375288|2025876;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|376805;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|2005525|195950|28112;3379134|976|200643|171549|2005525|195950|712710,Complete,Svetlana up
bsdb:38627869/4/NA,38627869,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán J.M., Argüello H., Cabrera-Rubio R., Crispie F., Cotter P.D., Garrido J.J., Ekhlas D., Burgess C.M. , Manzanilla E.G.",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 4,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Sampling time,EFO:0000689,Day 0 post weaning (0dpw),Day 7 post weaning (7dpw),"The dietary treatments were administered in the first two weeks post weaning and samplings were scheduled at days 0, 7 and 14 post weaning (0dpw, 7dpw, and 14dpw. respectively).",NA,NA,NA,WMS,NA,Illumina,NA,NA,0.05,FALSE,NA,NA,NA,decreased,decreased,decreased,decreased,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:38627869/7/2,38627869,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán J.M., Argüello H., Cabrera-Rubio R., Crispie F., Cotter P.D., Garrido J.J., Ekhlas D., Burgess C.M. , Manzanilla E.G.",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 7,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Therapeutic zinc oxide (Zn) treatment + non-medicated control diet (Ct diet) - Faecal 7 days post weaning (7 dpw),Antibiotic (Ab) treatment - Faecal 7 days post weaning (7 dpw),Piglets treated with antibiotics at Faecal 7 days post weaning.,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 5C,24 April 2024,Fiddyhamma,"Fiddyhamma,KateRasheed,WikiWorks",Taxa associated with each dietary treatment in the analysis of Faecal_7dpw data.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio|s__Acetivibrio clariflavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio|s__Acetivibrio saccincola,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Acetobacterium|s__Acetobacterium woodii,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus|s__Alkaliphilus oremlandii,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Aminipila|s__Aminipila luticellarii,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. BNL1100,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium thermosuccinogenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium|s__Dehalobacterium formicoaceticum,k__Bacillati|p__Chloroflexota|c__Dehalococcoidia|o__Dehalococcoidales|f__Dehalococcoidaceae|g__Dehalococcoides|s__Dehalococcoides mccartyi,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Hungateiclostridiaceae bacterium KB18,k__Bacillati|p__Bacillota|c__Clostridia|o__Mahellales|f__Mahellaceae|g__Mahella|s__Mahella australiensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium diversum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella|s__Murdochiella vaginalis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella sp. oral taxon 807,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus albus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Liu et al. 2021),k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus suis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Acidilutibacteraceae|g__Acidilutibacter|s__Acidilutibacter cellobiosedens,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] sulci",1783272|1239|186801|3120394|3120654|35829|288965;1783272|1239|186801|3120394|3120654|35829|1677857;1783272|1239|186801|186802|186806|33951|33952;3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|3082720|3118656|114627|461876;1783272|1239|186801|3082720|543314|2060094|2507160;1783272|1239|186801|3082768|990719|990721|1805714;1783272|1239|186801|186802|31979|1485|755731;1783272|1239|186801|186802|31979|1485|84032;1783272|1239|186801|186802|186807|51514|51515;1783272|200795|301297|1202465|1202464|61434|61435;3379134|200940|3031449|213115|194924|872|901;1783272|1239|91061|186826|81852|1350|1352;1783272|1239|186801|186802|216572|1834198;1783272|1239|186801|3120428|3120709|252965|252966;1783272|1239|186801|3082720|543314|86331|114527;1783272|1239|1737404|1737405|1570339|1161127|1852373;1783272|201174|84998|84999|1643824|133925|712411;1783272|1239|186801|186802|216572|1263|1264;1783272|1239|186801|186802|216572|1263|3062497;1783272|1239|91061|186826|1300|1301|1307;1783272|1239|1737404|1737405|2992717|2992720|2507161;1783272|1239|186801|3082720|543314|143393,Complete,Svetlana up
bsdb:38627869/8/2,38627869,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán J.M., Argüello H., Cabrera-Rubio R., Crispie F., Cotter P.D., Garrido J.J., Ekhlas D., Burgess C.M. , Manzanilla E.G.",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 8,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Faecal_7dpw Ct + Zn groups,Faecal_7dpw AB(antibiotics) group,Diarrhoea samples collected at day 7 post weaning from piglets treated with antibiotics,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 5C,22 April 2024,Fiddyhamma,"Fiddyhamma,KateRasheed,WikiWorks",Taxa associated with each dietary treatment in the analysis of Faecal_7dpw data.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister massiliensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena",1783272|1239|909932|1843489|31977|39948|2161821;1783272|1239|91061|186826|33958|2742598|1598;1783272|1239|909932|909929|1843491|970|69823,Complete,Svetlana up
bsdb:38627869/9/2,38627869,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán J.M., Argüello H., Cabrera-Rubio R., Crispie F., Cotter P.D., Garrido J.J., Ekhlas D., Burgess C.M. , Manzanilla E.G.",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 9,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Faecal_7dpw Ab + Ct groups,Faecal_7dpw Zn(Zinc Oxide) group,Faecal samples collected at day 7 post weaning from piglets treated with Zinc Oxide,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 5C,22 April 2024,Fiddyhamma,"Fiddyhamma,KateRasheed,WikiWorks","Taxa associated with each dietary treatment in the analysis of Faecal_7dpw data. Significant species are coloured according to the treatment to which they are associated to, and are annotated in the cladogram as letters, which can be identified below it.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium callanderi,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas ruminantium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. oral taxon 920",1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|186801|186802|186806|1730|53442;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|821;1783272|1239|909932|909929|1843491|970|971;1783272|1239|909932|909929|1843491|970|1884263,Complete,Svetlana up
bsdb:38627869/10/1,38627869,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán J.M., Argüello H., Cabrera-Rubio R., Crispie F., Cotter P.D., Garrido J.J., Ekhlas D., Burgess C.M. , Manzanilla E.G.",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 10,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Faecal_0dpw Ct + Zn groups,Faecal_0dpw Ab(antibiotics) group,Faecal samples collected at day 0 post weaning from piglets treated with antibiotics,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Suppl fig 3A and text,22 April 2024,Fiddyhamma,"Fiddyhamma,KateRasheed,WikiWorks","Species associated with each dietary treatment in the analysis of Faecal_0dpw species data, according to LEfSe(Linear discriminant analysis Effect Size), most likely explaining the differences among dietary treatments.",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola salanitronis,3379134|976|200643|171549|815|909656|376805,Complete,Svetlana up
bsdb:38627869/11/1,38627869,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán J.M., Argüello H., Cabrera-Rubio R., Crispie F., Cotter P.D., Garrido J.J., Ekhlas D., Burgess C.M. , Manzanilla E.G.",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 11,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Faecal_14dpw Ab + Zn groups,Faecal_14pw CT(no medication) group,Faecal samples collected at day 14 post weaning from piglets not treated with medication,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 5D,27 April 2024,Fiddyhamma,"Fiddyhamma,KateRasheed,WikiWorks",Taxa associated with each dietary treatment in the analysis of Faecal_14dpw data.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sporogenes,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio fairfieldensis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister massiliensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Intestinibaculum|s__Intestinibaculum porci,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus delbrueckii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera hexanoica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera stantonii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae|g__Methylomusa|s__Methylomusa anaerophila,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae|g__Pelosinus|s__Pelosinus fermentans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Vallitaleaceae|g__Petrocella|s__Petrocella atlantisensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Liu et al. 2021),k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas ruminantium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. oral taxon 920,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena",1783272|1239|909932|1843488|909930|904|187327;1783272|1239|186801|186802|31979|1485|1509;3379134|200940|3031449|213115|194924|872|44742;3379134|200940|3031449|213115|194924|872|901;1783272|1239|909932|1843489|31977|39948|2161821;3379134|1224|1236|91347|543|561|562;1783272|1239|526524|526525|128827|2679910|2487118;1783272|1239|91061|186826|33958|1578|1584;1783272|1239|909932|909929|1843491|158846|158847;1783272|1239|909932|1843489|31977|906|907;1783272|1239|909932|1843489|31977|906|1675036;1783272|1239|909932|1843489|31977|906|2144175;1783272|1239|909932|909929|1843490|2093783|1930071;1783272|1239|909932|909929|1843490|365348|365349;1783272|1239|186801|3085636|2603322|2603323|2173034;1783272|1239|186801|186802|216572|1263|3062497;1783272|1239|909932|909929|1843491|970|971;1783272|1239|909932|909929|1843491|970|1884263;1783272|1239|909932|909929|1843491|970|69823,Complete,Svetlana up
bsdb:38627869/12/1,38627869,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán J.M., Argüello H., Cabrera-Rubio R., Crispie F., Cotter P.D., Garrido J.J., Ekhlas D., Burgess C.M. , Manzanilla E.G.",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 12,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Faecal_14dpw Ct + Zn groups,Faecal_14dpw AB(antibiotics) group,Faecal samples collected at day 14 post weaning from piglets treated with antibiotics,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 5D,27 April 2024,Fiddyhamma,"Fiddyhamma,KateRasheed,WikiWorks",Taxa associated with each dietary treatment in the analysis of Faecal_14dpw data.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus fermentans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. SY8519",1783272|1239|909932|1843488|909930|904|905;1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|186802|31979|1485|1042156,Complete,Svetlana up
bsdb:38627869/13/1,38627869,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán J.M., Argüello H., Cabrera-Rubio R., Crispie F., Cotter P.D., Garrido J.J., Ekhlas D., Burgess C.M. , Manzanilla E.G.",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 13,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Faecal_14dpw Ct + Ab groups,Faecal_14dpw Zn(Zinc Oxide) group,Faecal samples collected at day 14 post weaning from piglets treated with Zinc Oxide,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 5D,27 April 2024,Fiddyhamma,"Fiddyhamma,KateRasheed,WikiWorks",Taxa associated with each dietary treatment in the analysis of Faecal_14dpw data.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caecimuris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides helcogenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Prevotella heparinolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Draconibacterium|s__Draconibacterium orientale,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Fermentimonas|s__Fermentimonas caenicola,k__Methanobacteriati|p__Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomethylophilaceae|g__Methanomethylophilus|s__Methanomethylophilus alvi,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Ornithobacterium|s__Ornithobacterium rhinotracheale,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter|s__Paludibacter propionicigenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola salanitronis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella serpentiformis",3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|1796613;3379134|976|200643|171549|815|816|246787;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|290053;3379134|976|200643|171549|815|816|28113;3379134|976|200643|171549|815|816|818;1783272|1239|186801|3082720|186804|1870884|1496;3379134|976|200643|1970189|1471398|1471399|1168034;3379134|976|200643|171549|2005520|1784836|1562970;3366610|2283796|183967|1235850|2517203|1291539|1291540;3379134|976|117743|200644|2762318|28250|28251;3379134|976|200643|171549|2005523|346096|185300;3379134|976|200643|171549|2005525|375288|823;1783272|1239|909932|1843488|909930|33024|33025;3379134|976|200643|171549|815|909656|376805;3379134|976|200643|171549|2005525|195950|28112;3379134|976|200643|171549|2005525|195950|712710,Complete,Svetlana up
bsdb:38627869/14/1,38627869,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán J.M., Argüello H., Cabrera-Rubio R., Crispie F., Cotter P.D., Garrido J.J., Ekhlas D., Burgess C.M. , Manzanilla E.G.",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 14,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Diarrhoea_7dpw Ct + Zn groups,Diarrhoea_7dpw Ab(antibiotics) group,Diarrhoea samples collected at day 14 post weaning from piglets treated with antibiotics,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 5E,21 January 2025,KateRasheed,"KateRasheed,WikiWorks",Taxa associated with each dietary treatment in the analysis of Diarrhoea_14dpw data.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,1783272|1239|91061|186826|33958|2742598|1598,Complete,Svetlana up
bsdb:38627869/15/1,38627869,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán J.M., Argüello H., Cabrera-Rubio R., Crispie F., Cotter P.D., Garrido J.J., Ekhlas D., Burgess C.M. , Manzanilla E.G.",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 15,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Diarrhoea_7dpw Ct + Ab groups,Diarrhoea_7dpw Zn group,Diarrhoea samples collected at day 14 post weaning from piglets treated with Zinc Oxide,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 5E,21 January 2025,KateRasheed,"KateRasheed,WikiWorks",Taxa associated with each dietary treatment in the analysis of Diarrhoea_14dpw data.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus",3379134|976|200643|171549|815|816|28116;1783272|1239|186801|186802|1392389|1297617;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|821,Complete,Svetlana up
bsdb:38627869/16/1,38627869,laboratory experiment,38627869,10.1186/s42523-024-00306-7,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00306-7,"Ortiz Sanjuán J.M., Argüello H., Cabrera-Rubio R., Crispie F., Cotter P.D., Garrido J.J., Ekhlas D., Burgess C.M. , Manzanilla E.G.",Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs,Animal microbiome,2024,"Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine",Experiment 16,Ireland,Sus scrofa domesticus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Diarrhoea_7dpw Ab + Zn groups,Diarrhoea_7dpw Ct group,Diarrhoea samples collected at day 14 post weaning from piglets not treated with medication,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 5E,21 January 2025,KateRasheed,"KateRasheed,WikiWorks",Taxa associated with each dietary treatment in the analysis of Diarrhoea_14dpw data.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella megalosphaeroides",3379134|1224|1236|91347|543|561|562;3379134|1224|28216|80840|995019|40544|2494234,Complete,Svetlana up
bsdb:38643180/1/1,38643180,"cross-sectional observational, not case-control",38643180,10.1038/s41467-024-46265-0,NA,"Ramaboli M.C., Ocvirk S., Khan Mirzaei M., Eberhart B.L., Valdivia-Garcia M., Metwaly A., Neuhaus K., Barker G., Ru J., Nesengani L.T., Mahdi-Joest D., Wilson A.S., Joni S.K., Layman D.C., Zheng J., Mandal R., Chen Q., Perez M.R., Fortuin S., Gaunt B., Wishart D., Methé B., Haller D., Li J.V., Deng L., Swart R. , O'Keefe S.J.D.",Diet changes due to urbanization in South Africa are linked to microbiome and metabolome signatures of Westernization and colorectal cancer,Nature communications,2024,NA,Experiment 1,South Africa,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Rural Xhosa Cohort,Urban Xhosa Cohort,People from Urban Xhosa of South Africa transitioning from traditional high-fiber to Western diets,21,20,6 weeks,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Fig. 1D,28 April 2024,Scholastica,"Scholastica,WikiWorks,Tosin",Significantly differential bacterial genera identified by linear discriminant analysis (LDA) effect size (LEfSe) in fecal samples of Rural Xhosa versus Urban Xhosa cohorts,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|g__Negativibacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:56",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005519|397864;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|830;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|186802|216572|946234;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|1980693;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;1783272|1239|909932|1843488|909930|33024;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|186802|31979|1485|1522;1783272|1239|1263031,Complete,Svetlana up
bsdb:38643180/1/2,38643180,"cross-sectional observational, not case-control",38643180,10.1038/s41467-024-46265-0,NA,"Ramaboli M.C., Ocvirk S., Khan Mirzaei M., Eberhart B.L., Valdivia-Garcia M., Metwaly A., Neuhaus K., Barker G., Ru J., Nesengani L.T., Mahdi-Joest D., Wilson A.S., Joni S.K., Layman D.C., Zheng J., Mandal R., Chen Q., Perez M.R., Fortuin S., Gaunt B., Wishart D., Methé B., Haller D., Li J.V., Deng L., Swart R. , O'Keefe S.J.D.",Diet changes due to urbanization in South Africa are linked to microbiome and metabolome signatures of Westernization and colorectal cancer,Nature communications,2024,NA,Experiment 1,South Africa,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Rural Xhosa Cohort,Urban Xhosa Cohort,People from Urban Xhosa of South Africa transitioning from traditional high-fiber to Western diets,21,20,6 weeks,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Fig. 1D,28 April 2024,Scholastica,"Scholastica,WikiWorks",Significantly differential bacterial genera identified by linear discriminant analysis (LDA) effect size (LEfSe) in fecal samples of Rural Xhosa versus Urban Xhosa cohorts,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae|g__Elusimicrobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|s__uncultured Prevotellaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK3A20,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|186802|1470353;3379134|74152|641853|641854|641876|423604;3379134|976|200643|171549|171552|370804;1783272|1239|186801|3085636|186803|877406;1783272|1239|909932|909929|1843491|970;3379134|203691|203692|136|2845253|157;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:38643180/3/1,38643180,"cross-sectional observational, not case-control",38643180,10.1038/s41467-024-46265-0,NA,"Ramaboli M.C., Ocvirk S., Khan Mirzaei M., Eberhart B.L., Valdivia-Garcia M., Metwaly A., Neuhaus K., Barker G., Ru J., Nesengani L.T., Mahdi-Joest D., Wilson A.S., Joni S.K., Layman D.C., Zheng J., Mandal R., Chen Q., Perez M.R., Fortuin S., Gaunt B., Wishart D., Methé B., Haller D., Li J.V., Deng L., Swart R. , O'Keefe S.J.D.",Diet changes due to urbanization in South Africa are linked to microbiome and metabolome signatures of Westernization and colorectal cancer,Nature communications,2024,NA,Experiment 3,South Africa,Homo sapiens,Ingested food,UBERON:0012112,Diet,EFO:0002755,Frozen food samples from rural Xhosa households,Frozen food samples from urban Xhosa households,Frozen food samples collected from representative households of urban Xhosa of South Africa,7,6,6 weeks,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Figure 4D,30 April 2024,Idiaru angela,"Idiaru angela,WikiWorks",Significantly different abundance at the genus level. Statistical analysis using a two-sided Wilcoxon test corrected for multiple testing by the Benjamini–Hochberg method using normalized samples,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Rosenbergiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",3379134|1224|1236|91347|1903409|1356488;1783272|1239|91061|186826|33958|46255,Complete,Svetlana up
bsdb:38643180/4/1,38643180,"cross-sectional observational, not case-control",38643180,10.1038/s41467-024-46265-0,NA,"Ramaboli M.C., Ocvirk S., Khan Mirzaei M., Eberhart B.L., Valdivia-Garcia M., Metwaly A., Neuhaus K., Barker G., Ru J., Nesengani L.T., Mahdi-Joest D., Wilson A.S., Joni S.K., Layman D.C., Zheng J., Mandal R., Chen Q., Perez M.R., Fortuin S., Gaunt B., Wishart D., Methé B., Haller D., Li J.V., Deng L., Swart R. , O'Keefe S.J.D.",Diet changes due to urbanization in South Africa are linked to microbiome and metabolome signatures of Westernization and colorectal cancer,Nature communications,2024,NA,Experiment 4,South Africa,Homo sapiens,Manual digit skin,UBERON:0003533,Diet,EFO:0002755,Rural Xhosa Cohort,Urban Xhosa Cohort,Hand skin swabs from urban Xhosa cohort of South Africa,7,6,Oral or I.V antibiotic therapy within the last 6 weeks,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Supplementary Table 3,28 April 2024,Scholastica,"Scholastica,WikiWorks",Significantly different abundant bacterial genera or families on hand skin swabs from rural versus urban Xhosa cohorts,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Alkanindiges,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Aquabacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Desemzia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Flaviflexus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Planomicrobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Thermomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Trichococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio",3379134|1224|1236|2887326|468|469;1783272|1239|91061|186826|186827|1375;3379134|1224|1236|2887326|468|222991;3379134|1224|28216|80840|92793;1783272|201174|84998|84999|84107|102106;1783272|1239|91061|186826|186828|82800;1783272|201174|1760|2037|2049|1522056;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|91061|1385|90964|227979;3379134|1224|28211|204455|31989|265;3379134|976|200643|171549|171552|838;1783272|1239|91061|1385|186818|162291;3379134|1224|1236|2887326|468|497;1783272|1239|186801|186802|216572|1263;3379134|1224|1236|135614|32033|141948;1783272|1239|91061|186826|186828|82802;3379134|1224|1236|135624|83763|83770;3379134|1224|1236|135623|641|662,Complete,Svetlana up
bsdb:38643180/4/2,38643180,"cross-sectional observational, not case-control",38643180,10.1038/s41467-024-46265-0,NA,"Ramaboli M.C., Ocvirk S., Khan Mirzaei M., Eberhart B.L., Valdivia-Garcia M., Metwaly A., Neuhaus K., Barker G., Ru J., Nesengani L.T., Mahdi-Joest D., Wilson A.S., Joni S.K., Layman D.C., Zheng J., Mandal R., Chen Q., Perez M.R., Fortuin S., Gaunt B., Wishart D., Methé B., Haller D., Li J.V., Deng L., Swart R. , O'Keefe S.J.D.",Diet changes due to urbanization in South Africa are linked to microbiome and metabolome signatures of Westernization and colorectal cancer,Nature communications,2024,NA,Experiment 4,South Africa,Homo sapiens,Manual digit skin,UBERON:0003533,Diet,EFO:0002755,Rural Xhosa Cohort,Urban Xhosa Cohort,Hand skin swabs from urban Xhosa cohort of South Africa,7,6,Oral or I.V antibiotic therapy within the last 6 weeks,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Supplementary Table 3,28 April 2024,Scholastica,"Scholastica,WikiWorks",Significantly different abundant bacterial genera or families on hand skin swabs from rural versus urban Xhosa cohorts,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Actinomycetospora,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Marmoricola,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Williamsia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",1783272|201174|1760|85010|2070|402649;1783272|1239|91061|1385|186817|1386;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|1385|186817|400634;1783272|201174|1760|85009|85015|86795;3379134|1224|28211|204457|41297|165696;3379134|1224|28211|356|118882|528;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|3082720|186804;3379134|1224|1236|91347|1903411|613;3379134|1224|28211|204457|41297|13687;3379134|976|117743|200644|2762318;1783272|201174|1760|85007|85025|85043;1783272|1239|91061|186826|33958|46255,Complete,Svetlana up
bsdb:38650928/3/1,38650928,case-control,38650928,10.3389/fimmu.2024.1323723,NA,"Chai Y., Liu X., Bai G., Zhou N., Liu D., Zhang X., Li M., Li K. , Lei H.","Gut microbiome, T cell subsets, and cytokine analysis identify differential biomarkers in tuberculosis",Frontiers in immunology,2024,"T cell subsets, biomarkers, cytokines, gut microbiome, tuberculosis",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Tuberculosis,NA,Combination of TB patients (cz group) and healthy controls (jk group),retreated patients (fz group),"patients with recurrent TB in the fz
group",60,30,1 month,16S,NA,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,decreased,decreased,decreased,decreased,decreased,decreased,Signature 1,Figure 3A and 3B,29 July 2025,Nuerteye,Nuerteye,"Identification of different genera as biomarkers by relative abundance. (A) The column length signifies the impact of distinct species in terms of relative abundance (linear discriminant analysis scores > 4). (B) The clado-gram displays the species that are markedly distinct. Each circle symbolizes the phylogenetic progression from phylum to genus, encompassing both the interior and exterior. The size of each circle is linked to the number of taxa present, and the biomarker is in agreement with the group indicated by the color.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus",3379134|1224|1236;3379134|1224|1236|91347|543;3379134|1224|1236|91347;1783272|1239|526524|526525|128827;1783272|1239|526524|526525|2810280|100883;1783272|1239|909932|1843488|909930|904,Complete,NA
bsdb:38658829/1/1,38658829,case-control,38658829,10.1186/s12866-024-03275-8,NA,"Han M., Wang X., Zhang J., Su L., Ishaq H.M., Li D., Cui J., Zhao H. , Yang F.",Gut bacterial and fungal dysbiosis in tuberculosis patients,BMC microbiology,2024,"Dysbiosis, Gut microbiota, Gut mycobiota, IFN-γ, IL-17, Tuberculosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,Healthy controls,Tuberculosis (TB) patients,Smear/culture-confirmed pulmonary tuberculosis.,20,33,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,4,"age,sex",NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 1e and 2e,27 June 2025,Nuerteye,Nuerteye,"1e) Identified the differentially abundant taxa between the TB patients and HC (LDA > 4, P < 0.05). The taxa enriched in the HC were characterized by a positive LDA score (red), and the TB-enriched taxa were indicated with a negative LDA score (blue).
2e) The LEfSe analysis identified the differentially abundant taxa between the TB patients and HC (LDA > 4, P < 0.05).",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|976|200643|171549|171552|838;4751|4890|4891|4892|4893|4930;3379134|976|200643|171549|815|816,Complete,NA
bsdb:38658829/1/2,38658829,case-control,38658829,10.1186/s12866-024-03275-8,NA,"Han M., Wang X., Zhang J., Su L., Ishaq H.M., Li D., Cui J., Zhao H. , Yang F.",Gut bacterial and fungal dysbiosis in tuberculosis patients,BMC microbiology,2024,"Dysbiosis, Gut microbiota, Gut mycobiota, IFN-γ, IL-17, Tuberculosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,Healthy controls,Tuberculosis (TB) patients,Smear/culture-confirmed pulmonary tuberculosis.,20,33,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,4,"age,sex",NA,NA,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 1e and 2e,27 June 2025,Nuerteye,Nuerteye,"1e) Identified the differentially abundant taxa between the TB patients and HC (LDA > 4, P < 0.05). The taxa enriched in the HC were characterized by a positive LDA score (red), and the TB-enriched taxa were indicated with a negative LDA score (blue).
2e) The LEfSe analysis identified the differentially abundant taxa between the TB patients and HC (LDA > 4, P < 0.05).",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Fungi|p__Ascomycota,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus",1783272|1239|186801|3085636|186803|572511;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|3085636|186803|1407607;3379134|1224|1236|91347|543|570;4751|4890;4751|4890|147545|5042|1131492|5052,Complete,NA
bsdb:38658841/1/1,38658841,"cross-sectional observational, not case-control",38658841,https://doi.org/10.1186/s12866-024-03219-2,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-024-03219-2,"Jeong S., Liao Y.T., Tsai M.H., Wang Y.K., Wu I.C., Liu C.J., Wu M.S., Chan T.S., Chen M.Y., Hu P.J., Kao W.Y., Liu H.C., Tsai M.J., Liu C.Y., Chang C.C., Wu D.C. , Hsu Y.H.",Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study,BMC microbiology,2024,"Bacteroides_caccae, Bifidobacterium_longum, Fusobacteria, GLCMANNANAUT-PWY, Lachnospiraceae_bacterium_5_1_63FAA, Streptococcus_anginosus",Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,Chronic gastritis,Gastric Cancer,Participants diagnosed with early and late stage gastric cancer.,33,32,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,4.27,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2(a) and Supplementary Table 7,21 July 2024,Shulamite,"Shulamite,Aleru Divine,WikiWorks",Comparative analysis of differential abundance between chronic gastritis and gastric cancer at the genus levels using LEfSe.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae",1783272|1239|186801|3085636|186803|33042;3384189|32066|203490|203491|203492|848;3379134|1224|1236|135625|712|724;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;1783272|1239|909932|1843488|909930|33024;3379134|1224|28216|80840|995019|40544;1783272|1239|909932|1843489|31977|29465;3379134|1224|28216|80840|995019,Complete,Svetlana up
bsdb:38658841/1/2,38658841,"cross-sectional observational, not case-control",38658841,https://doi.org/10.1186/s12866-024-03219-2,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-024-03219-2,"Jeong S., Liao Y.T., Tsai M.H., Wang Y.K., Wu I.C., Liu C.J., Wu M.S., Chan T.S., Chen M.Y., Hu P.J., Kao W.Y., Liu H.C., Tsai M.J., Liu C.Y., Chang C.C., Wu D.C. , Hsu Y.H.",Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study,BMC microbiology,2024,"Bacteroides_caccae, Bifidobacterium_longum, Fusobacteria, GLCMANNANAUT-PWY, Lachnospiraceae_bacterium_5_1_63FAA, Streptococcus_anginosus",Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,Chronic gastritis,Gastric Cancer,Participants diagnosed with early and late stage gastric cancer.,33,32,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,4.27,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2(a) and Supplementary Table 7,21 July 2024,Shulamite,"Shulamite,Aleru Divine,WikiWorks",Comparative analysis of differential abundance between chronic gastritis and gastric cancer at the genus levels using LEfSe.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",3379134|1224|1236|2887326|468|469;1783272|201174|84998|1643822|1643826|447020;1783272|201174|1760|85004|31953|1678;1783272|201174|84998|84999|84107|102106;1783272|1239|91061|186826|81852|1350;3384189|32066;3379134|1224|1236|72274|135621|286,Complete,Svetlana up
bsdb:38658841/2/1,38658841,"cross-sectional observational, not case-control",38658841,https://doi.org/10.1186/s12866-024-03219-2,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-024-03219-2,"Jeong S., Liao Y.T., Tsai M.H., Wang Y.K., Wu I.C., Liu C.J., Wu M.S., Chan T.S., Chen M.Y., Hu P.J., Kao W.Y., Liu H.C., Tsai M.J., Liu C.Y., Chang C.C., Wu D.C. , Hsu Y.H.",Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study,BMC microbiology,2024,"Bacteroides_caccae, Bifidobacterium_longum, Fusobacteria, GLCMANNANAUT-PWY, Lachnospiraceae_bacterium_5_1_63FAA, Streptococcus_anginosus",Experiment 2,Taiwan,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,"Other sub-groups (Non-Intestinal Metaplasia (NIM), Intestinal Metaplasia (IM) and late-stage gastric cancer))",Early-stage gastric cancer,Participants diagnosed with early-stage gastric cancer (Phase I and II).,52,13,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,4.47,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2(b) and Supplementary Table 8,1 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Comparative analysis of differential abundance between chronic gastritis sub-groups and gastric cancer sub-groups using LEfSe.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae",1783272|1239|91061|186826|81852|1350;3379134|976|200643|171549|1853231|283168;1783272|1239|909932|1843488|909930|33024;1783272|1239|909932|1843489|31977|29465;3379134|1224|28216|80840|995019,Complete,Svetlana up
bsdb:38658841/3/1,38658841,"cross-sectional observational, not case-control",38658841,https://doi.org/10.1186/s12866-024-03219-2,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-024-03219-2,"Jeong S., Liao Y.T., Tsai M.H., Wang Y.K., Wu I.C., Liu C.J., Wu M.S., Chan T.S., Chen M.Y., Hu P.J., Kao W.Y., Liu H.C., Tsai M.J., Liu C.Y., Chang C.C., Wu D.C. , Hsu Y.H.",Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study,BMC microbiology,2024,"Bacteroides_caccae, Bifidobacterium_longum, Fusobacteria, GLCMANNANAUT-PWY, Lachnospiraceae_bacterium_5_1_63FAA, Streptococcus_anginosus",Experiment 3,Taiwan,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,"Other sub-groups (Non-Intestinal Metaplasia (NIM), Intestinal Metaplasia (IM) and early-stage gastric cancer)",Late-stage gastric cancer,Participants diagnosed with late-stage gastric cancer (Phase III and IV).,46,19,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,4.47,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2(b) and Supplementary Table 8,1 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Comparative analysis of differential abundance between chronic gastritis sub-groups and gastric cancer sub-groups using LEfSe.,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3384189|32066|203490|203491|203492|848;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|40544,Complete,Svetlana up
bsdb:38658841/4/1,38658841,"cross-sectional observational, not case-control",38658841,https://doi.org/10.1186/s12866-024-03219-2,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-024-03219-2,"Jeong S., Liao Y.T., Tsai M.H., Wang Y.K., Wu I.C., Liu C.J., Wu M.S., Chan T.S., Chen M.Y., Hu P.J., Kao W.Y., Liu H.C., Tsai M.J., Liu C.Y., Chang C.C., Wu D.C. , Hsu Y.H.",Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study,BMC microbiology,2024,"Bacteroides_caccae, Bifidobacterium_longum, Fusobacteria, GLCMANNANAUT-PWY, Lachnospiraceae_bacterium_5_1_63FAA, Streptococcus_anginosus",Experiment 4,Taiwan,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,"Other sub-groups (Non-Intestinal Metaplasia (NIM), early-stage gastric cancer and late-stage gastric cancer)",Intestinal metaplasia (IM),Participants diagnosed with chronic gastritis with pre-cancer lesions (intestinal metaplasia (IM).,50,15,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,4.47,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2(b) and Supplementary Table 8,1 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Comparative analysis of differential abundance between chronic gastritis sub-groups and gastric cancer sub-groups using LEfSe.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes",1783272|201174|84998|1643822|1643826|447020;1783272|1239|186801|3085636|186803|207244,Complete,Svetlana up
bsdb:38658841/5/1,38658841,"cross-sectional observational, not case-control",38658841,https://doi.org/10.1186/s12866-024-03219-2,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-024-03219-2,"Jeong S., Liao Y.T., Tsai M.H., Wang Y.K., Wu I.C., Liu C.J., Wu M.S., Chan T.S., Chen M.Y., Hu P.J., Kao W.Y., Liu H.C., Tsai M.J., Liu C.Y., Chang C.C., Wu D.C. , Hsu Y.H.",Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study,BMC microbiology,2024,"Bacteroides_caccae, Bifidobacterium_longum, Fusobacteria, GLCMANNANAUT-PWY, Lachnospiraceae_bacterium_5_1_63FAA, Streptococcus_anginosus",Experiment 5,Taiwan,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,"Other sub-groups (Intestinal Metaplasia (IM), early-stage gastric cancer and late-stage gastric cancer)",Non-intestinal metaplasia (NIM),Participants diagnosed with chronic gastritis without pre-cancer lesions (non-intestinal metaplasia (NIM).,47,18,6 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,4.47,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2(b) and Supplementary Table 8,1 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Comparative analysis of differential abundance between chronic gastritis sub-groups and gastric cancer sub-groups using LEfSe.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,3379134|1224|1236|2887326|468|469,Complete,Svetlana up
bsdb:38658841/6/1,38658841,"cross-sectional observational, not case-control",38658841,https://doi.org/10.1186/s12866-024-03219-2,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-024-03219-2,"Jeong S., Liao Y.T., Tsai M.H., Wang Y.K., Wu I.C., Liu C.J., Wu M.S., Chan T.S., Chen M.Y., Hu P.J., Kao W.Y., Liu H.C., Tsai M.J., Liu C.Y., Chang C.C., Wu D.C. , Hsu Y.H.",Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study,BMC microbiology,2024,"Bacteroides_caccae, Bifidobacterium_longum, Fusobacteria, GLCMANNANAUT-PWY, Lachnospiraceae_bacterium_5_1_63FAA, Streptococcus_anginosus",Experiment 6,Taiwan,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,Chronic gastritis,Gastric Cancer,Participants diagnosed with early and late stage gastric cancer.,33,32,6 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Table 1, Supplementary Table 6 and 10",8 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differential abundance by Wilcoxon Rank-Sum Test between chronic gastritis and gastric cancer in Phylum,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976|200643|171549|815|816|47678;1783272|201174|1760|85004|31953|1678|1689;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|189330|39486;3384189|32066;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492|848|850;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712|724|729;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|91061|186826|33958|2767887|1624;1783272|1239|91061|186826|33958|2742598|1613;1783272|1239|91061|186826|33958|2742598|97478;1783272|1239|91061|186826|33958|2742598|1598;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|823;1783272|1239|909932|1843488|909930|33024;1783272|1239|909932|1843488|909930|33024|626940;1783272|1239|91061|186826|1300|1301|1328;3379134|1224|28216|80840|995019|40544;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:38658841/6/2,38658841,"cross-sectional observational, not case-control",38658841,https://doi.org/10.1186/s12866-024-03219-2,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-024-03219-2,"Jeong S., Liao Y.T., Tsai M.H., Wang Y.K., Wu I.C., Liu C.J., Wu M.S., Chan T.S., Chen M.Y., Hu P.J., Kao W.Y., Liu H.C., Tsai M.J., Liu C.Y., Chang C.C., Wu D.C. , Hsu Y.H.",Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study,BMC microbiology,2024,"Bacteroides_caccae, Bifidobacterium_longum, Fusobacteria, GLCMANNANAUT-PWY, Lachnospiraceae_bacterium_5_1_63FAA, Streptococcus_anginosus",Experiment 6,Taiwan,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,Chronic gastritis,Gastric Cancer,Participants diagnosed with early and late stage gastric cancer.,33,32,6 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Table 1, Supplementary Table 6 and 10",8 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differential abundance by Wilcoxon Rank-Sum Test between chronic gastritis and gastric cancer in Phylum,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baylyi,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",3379134|1224|1236|2887326|468|469;1783272|201174;1783272|201174|84998|1643822|1643826|447020;1783272|201174|1760|85004|31953|1678;1783272|201174|84998|84999|84107|102106;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|72274|135621|286;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|28026;1783272|201174|84998|1643822|1643826|447020|446660;1783272|201174|84998|84999|84107|102106|74426;3379134|976|200643|171549|171550|239759;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|91061|186826|81852|1350|1352;3379134|1224|1236|2887326|468|469|202950;3379134|1224|1236|72274|135621|286,Complete,Svetlana up
bsdb:38658841/7/1,38658841,"cross-sectional observational, not case-control",38658841,https://doi.org/10.1186/s12866-024-03219-2,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-024-03219-2,"Jeong S., Liao Y.T., Tsai M.H., Wang Y.K., Wu I.C., Liu C.J., Wu M.S., Chan T.S., Chen M.Y., Hu P.J., Kao W.Y., Liu H.C., Tsai M.J., Liu C.Y., Chang C.C., Wu D.C. , Hsu Y.H.",Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study,BMC microbiology,2024,"Bacteroides_caccae, Bifidobacterium_longum, Fusobacteria, GLCMANNANAUT-PWY, Lachnospiraceae_bacterium_5_1_63FAA, Streptococcus_anginosus",Experiment 7,Taiwan,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,Chronic gastritis,Gastric Cancer,Participants diagnosed with early and late stage gastric cancer.,33,32,6 months,WMS,NA,Illumina,raw counts,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 2,8 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Significant genera by EdgeR analysis,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:38658841/7/2,38658841,"cross-sectional observational, not case-control",38658841,https://doi.org/10.1186/s12866-024-03219-2,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-024-03219-2,"Jeong S., Liao Y.T., Tsai M.H., Wang Y.K., Wu I.C., Liu C.J., Wu M.S., Chan T.S., Chen M.Y., Hu P.J., Kao W.Y., Liu H.C., Tsai M.J., Liu C.Y., Chang C.C., Wu D.C. , Hsu Y.H.",Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study,BMC microbiology,2024,"Bacteroides_caccae, Bifidobacterium_longum, Fusobacteria, GLCMANNANAUT-PWY, Lachnospiraceae_bacterium_5_1_63FAA, Streptococcus_anginosus",Experiment 7,Taiwan,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,Chronic gastritis,Gastric Cancer,Participants diagnosed with early and late stage gastric cancer.,33,32,6 months,WMS,NA,Illumina,raw counts,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 2,8 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Significant genera by EdgeR analysis,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella",1783272|1239|186801|186802|186806|1730;1783272|201174|84998|84999|84107|102106;3379134|1224|1236|72274|135621|286;3379134|1224|1236|91347|1903414|581,Complete,Svetlana up
bsdb:38658841/8/1,38658841,"cross-sectional observational, not case-control",38658841,https://doi.org/10.1186/s12866-024-03219-2,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-024-03219-2,"Jeong S., Liao Y.T., Tsai M.H., Wang Y.K., Wu I.C., Liu C.J., Wu M.S., Chan T.S., Chen M.Y., Hu P.J., Kao W.Y., Liu H.C., Tsai M.J., Liu C.Y., Chang C.C., Wu D.C. , Hsu Y.H.",Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study,BMC microbiology,2024,"Bacteroides_caccae, Bifidobacterium_longum, Fusobacteria, GLCMANNANAUT-PWY, Lachnospiraceae_bacterium_5_1_63FAA, Streptococcus_anginosus",Experiment 8,Taiwan,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,"Other sub-groups (Non-Intestinal Metaplasia (NIM), early-stage gastric cancer and late-stage gastric cancer))",Intestinal metaplasia (IM),Participants diagnosed with chronic gastritis with pre-cancer lesions (intestinal metaplasia (IM).,50,15,6 months,WMS,NA,Illumina,raw counts,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Table 2, text",8 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Significant genera by EdgeR analysis,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803|1766253|39491,Complete,Svetlana up
bsdb:38658841/9/1,38658841,"cross-sectional observational, not case-control",38658841,https://doi.org/10.1186/s12866-024-03219-2,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-024-03219-2,"Jeong S., Liao Y.T., Tsai M.H., Wang Y.K., Wu I.C., Liu C.J., Wu M.S., Chan T.S., Chen M.Y., Hu P.J., Kao W.Y., Liu H.C., Tsai M.J., Liu C.Y., Chang C.C., Wu D.C. , Hsu Y.H.",Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study,BMC microbiology,2024,"Bacteroides_caccae, Bifidobacterium_longum, Fusobacteria, GLCMANNANAUT-PWY, Lachnospiraceae_bacterium_5_1_63FAA, Streptococcus_anginosus",Experiment 9,Taiwan,Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,"Other sub-groups (Intestinal Metaplasia (IM), early-stage gastric cancer and late-stage gastric cancer))",Non-intestinal metaplasia (NIM),Participants diagnosed with chronic gastritis without pre-cancer lesions (non-intestinal metaplasia (NIM).,47,18,6 months,WMS,NA,Illumina,raw counts,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 2,8 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Significant genera by EdgeR analysis,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",1783272|1239|909932|909929|1843491|158846;3379134|1224|1236|72274|135621|286,Complete,Svetlana up
bsdb:38668545/1/1,38668545,laboratory experiment,38668545,10.3390/tropicalmed9040084,NA,"Chen C.Y., Chan W.Y., Ismail A. , Oliver S.V.",Characterization of the Tissue and Strain-Specific Microbiota of <i>Anopheles funestus</i> Giles (Diptera: Culicidae),Tropical medicine and infectious disease,2024,"16S rRNA, microbiota, midgut, mosquito, ovaries, paratransgenesis, salivary glands, vector control",Experiment 1,South Africa,Anopheles funestus,"Midgut,Saliva-secreting gland","UBERON:0001045,UBERON:0001044",Sampling site,EFO:0000688,Anopheles funestus (Midgut),Anopheles funestus (Salivary gland),Adult Anopheles funestus that were 15 days old and had had 3 blood meals.,25,30,NA,16S,34,Illumina,raw counts,DESeq2,0.01,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 5a,19 November 2024,MyleeeA,"MyleeeA,WikiWorks",Differential abundance of genera in Anopheles funestus tissues between midgut (left) and salivary glands (right).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Agromyces",3379134|1224|1236|72274|135621|286;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|543|158483;3379134|1224|28211|204441|2829815|191;1783272|201174|1760|85006|85023|33877,Complete,Svetlana up
bsdb:38668545/1/2,38668545,laboratory experiment,38668545,10.3390/tropicalmed9040084,NA,"Chen C.Y., Chan W.Y., Ismail A. , Oliver S.V.",Characterization of the Tissue and Strain-Specific Microbiota of <i>Anopheles funestus</i> Giles (Diptera: Culicidae),Tropical medicine and infectious disease,2024,"16S rRNA, microbiota, midgut, mosquito, ovaries, paratransgenesis, salivary glands, vector control",Experiment 1,South Africa,Anopheles funestus,"Midgut,Saliva-secreting gland","UBERON:0001045,UBERON:0001044",Sampling site,EFO:0000688,Anopheles funestus (Midgut),Anopheles funestus (Salivary gland),Adult Anopheles funestus that were 15 days old and had had 3 blood meals.,25,30,NA,16S,34,Illumina,raw counts,DESeq2,0.01,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 5a,19 November 2024,MyleeeA,"MyleeeA,WikiWorks",Differential abundance of genera in Anopheles funestus tissues between midgut (left) and salivary glands (right).,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Flectobacillaceae|g__Flectobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|1224|1236|2887326|468|469;1783272|201174|1760|85009|31957|1912216;3379134|976|768503|768507|3141701|101;3379134|1224|1236|135624|84642|642;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:38668545/2/1,38668545,laboratory experiment,38668545,10.3390/tropicalmed9040084,NA,"Chen C.Y., Chan W.Y., Ismail A. , Oliver S.V.",Characterization of the Tissue and Strain-Specific Microbiota of <i>Anopheles funestus</i> Giles (Diptera: Culicidae),Tropical medicine and infectious disease,2024,"16S rRNA, microbiota, midgut, mosquito, ovaries, paratransgenesis, salivary glands, vector control",Experiment 2,South Africa,Anopheles funestus,"Midgut,Ovary","UBERON:0001045,UBERON:0000992",Sampling site,EFO:0000688,Anopheles funestus (Midgut),Anopheles funestus (Ovaries),Anopheles funestus ovaries were dissected from female adults that were 15 days old and had had 3 blood meals.,25,25,NA,16S,34,Illumina,raw counts,DESeq2,0.01,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 5b,19 November 2024,MyleeeA,"MyleeeA,WikiWorks",Differential abundance of genera in Anopheles funestus tissues between midgut (left) and Ovaries (right).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Agromyces,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",3379134|1224|1236|91347|543|570;3379134|1224|28211|204441|2829815|191;1783272|201174|1760|85006|85023|33877;3379134|1224|1236|135624|84642|642;3379134|1224|1236|72274|135621|286,Complete,Svetlana up
bsdb:38668545/2/2,38668545,laboratory experiment,38668545,10.3390/tropicalmed9040084,NA,"Chen C.Y., Chan W.Y., Ismail A. , Oliver S.V.",Characterization of the Tissue and Strain-Specific Microbiota of <i>Anopheles funestus</i> Giles (Diptera: Culicidae),Tropical medicine and infectious disease,2024,"16S rRNA, microbiota, midgut, mosquito, ovaries, paratransgenesis, salivary glands, vector control",Experiment 2,South Africa,Anopheles funestus,"Midgut,Ovary","UBERON:0001045,UBERON:0000992",Sampling site,EFO:0000688,Anopheles funestus (Midgut),Anopheles funestus (Ovaries),Anopheles funestus ovaries were dissected from female adults that were 15 days old and had had 3 blood meals.,25,25,NA,16S,34,Illumina,raw counts,DESeq2,0.01,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 5b,19 November 2024,MyleeeA,"MyleeeA,WikiWorks",Differential abundance of genera in Anopheles funestus tissues between midgut (left) and Ovaries (right).,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,3379134|1224|1236|91347|543|570,Complete,Svetlana up
bsdb:38668545/3/1,38668545,laboratory experiment,38668545,10.3390/tropicalmed9040084,NA,"Chen C.Y., Chan W.Y., Ismail A. , Oliver S.V.",Characterization of the Tissue and Strain-Specific Microbiota of <i>Anopheles funestus</i> Giles (Diptera: Culicidae),Tropical medicine and infectious disease,2024,"16S rRNA, microbiota, midgut, mosquito, ovaries, paratransgenesis, salivary glands, vector control",Experiment 3,South Africa,Anopheles funestus,"Saliva-secreting gland,Ovary","UBERON:0001044,UBERON:0000992",Sampling site,EFO:0000688,Anopheles funestus (Ovaries),Anopheles funestus (Salivary gland),Anopheles funestus Salivary gland were dissected from female adults that were 15 days old and had had 3 blood meals.,25,30,NA,16S,34,Illumina,raw counts,DESeq2,0.01,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 5c,21 November 2024,MyleeeA,"MyleeeA,WikiWorks",Differential abundance of genera in Anopheles funestus tissues between Ovaries (left) and Salivary gland (right).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea",3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|543|158483,Complete,Svetlana up
bsdb:38668545/3/2,38668545,laboratory experiment,38668545,10.3390/tropicalmed9040084,NA,"Chen C.Y., Chan W.Y., Ismail A. , Oliver S.V.",Characterization of the Tissue and Strain-Specific Microbiota of <i>Anopheles funestus</i> Giles (Diptera: Culicidae),Tropical medicine and infectious disease,2024,"16S rRNA, microbiota, midgut, mosquito, ovaries, paratransgenesis, salivary glands, vector control",Experiment 3,South Africa,Anopheles funestus,"Saliva-secreting gland,Ovary","UBERON:0001044,UBERON:0000992",Sampling site,EFO:0000688,Anopheles funestus (Ovaries),Anopheles funestus (Salivary gland),Anopheles funestus Salivary gland were dissected from female adults that were 15 days old and had had 3 blood meals.,25,30,NA,16S,34,Illumina,raw counts,DESeq2,0.01,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 5c,21 November 2024,MyleeeA,"MyleeeA,WikiWorks",Differential abundance of genera in Anopheles funestus tissues between Ovaries (left) and Salivary gland (right).,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Flectobacillaceae|g__Flectobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia",1783272|201174|1760|85009|31957|1912216;3379134|1224|1236|2887326|468|469;3379134|976|117743|200644|2762318|59732;3379134|1224|1236|135624|84642|642;3379134|976|768503|768507|3141701|101;3379134|1224|1236|91347|1903411|629,Complete,Svetlana up
bsdb:38668545/4/1,38668545,laboratory experiment,38668545,10.3390/tropicalmed9040084,NA,"Chen C.Y., Chan W.Y., Ismail A. , Oliver S.V.",Characterization of the Tissue and Strain-Specific Microbiota of <i>Anopheles funestus</i> Giles (Diptera: Culicidae),Tropical medicine and infectious disease,2024,"16S rRNA, microbiota, midgut, mosquito, ovaries, paratransgenesis, salivary glands, vector control",Experiment 4,South Africa,Anopheles funestus,"Midgut,Saliva-secreting gland,Ovary","UBERON:0001045,UBERON:0001044,UBERON:0000992",Strain,EFO:0005135,Anopheles funestus (FANG),Anopheles funestus (FUMOZ),The FUMOZ strain originated from Southern Mozambique in 2000,NA,NA,NA,16S,34,Illumina,raw counts,DESeq2,0.01,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 6a,21 November 2024,MyleeeA,"MyleeeA,WikiWorks",Differential abundance of genera in Anopheles funestus tissues between FANG (left) and FUMOZ (right).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea",3379134|1224|1236|2887326|468|469;3379134|1224|1236|72274|135621|286;3379134|1224|1236|91347|543|158483,Complete,Svetlana up
bsdb:38668545/4/2,38668545,laboratory experiment,38668545,10.3390/tropicalmed9040084,NA,"Chen C.Y., Chan W.Y., Ismail A. , Oliver S.V.",Characterization of the Tissue and Strain-Specific Microbiota of <i>Anopheles funestus</i> Giles (Diptera: Culicidae),Tropical medicine and infectious disease,2024,"16S rRNA, microbiota, midgut, mosquito, ovaries, paratransgenesis, salivary glands, vector control",Experiment 4,South Africa,Anopheles funestus,"Midgut,Saliva-secreting gland,Ovary","UBERON:0001045,UBERON:0001044,UBERON:0000992",Strain,EFO:0005135,Anopheles funestus (FANG),Anopheles funestus (FUMOZ),The FUMOZ strain originated from Southern Mozambique in 2000,NA,NA,NA,16S,34,Illumina,raw counts,DESeq2,0.01,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 6a,21 November 2024,MyleeeA,"MyleeeA,Aleru Divine,WikiWorks",Differential abundance of genera in Anopheles funestus tissues between FANG (left) and FUMOZ (right).,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Agromyces,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rahnella",1783272|201174|1760|85006|85023|33877;3379134|1224|28211|204441|2829815|191;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|1903411|34037,Complete,Svetlana up
bsdb:38668545/5/1,38668545,laboratory experiment,38668545,10.3390/tropicalmed9040084,NA,"Chen C.Y., Chan W.Y., Ismail A. , Oliver S.V.",Characterization of the Tissue and Strain-Specific Microbiota of <i>Anopheles funestus</i> Giles (Diptera: Culicidae),Tropical medicine and infectious disease,2024,"16S rRNA, microbiota, midgut, mosquito, ovaries, paratransgenesis, salivary glands, vector control",Experiment 5,South Africa,Anopheles funestus,"Midgut,Saliva-secreting gland,Ovary","UBERON:0001045,UBERON:0001044,UBERON:0000992",Strain,EFO:0005135,Anopheles funestus (FANG),Anopheles funestus (FUMOZ-R),The FUMOZ-R strain was selected from FUMOZ by λ-cyhalothrin exposure. Both FUMOZ and FUMOZ-R display pyrethroid resistance as well as carbamate resistance,NA,NA,NA,16S,34,Illumina,raw counts,DESeq2,0.01,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 6b,21 November 2024,MyleeeA,"MyleeeA,WikiWorks",Differential abundance of genera in Anopheles funestus tissues between FANG (left) and FUMOZ-R (right).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea",3379134|1224|1236|2887326|468|469;3379134|1224|1236|72274|135621|286;3379134|1224|1236|91347|543|158483,Complete,Svetlana up
bsdb:38668545/5/2,38668545,laboratory experiment,38668545,10.3390/tropicalmed9040084,NA,"Chen C.Y., Chan W.Y., Ismail A. , Oliver S.V.",Characterization of the Tissue and Strain-Specific Microbiota of <i>Anopheles funestus</i> Giles (Diptera: Culicidae),Tropical medicine and infectious disease,2024,"16S rRNA, microbiota, midgut, mosquito, ovaries, paratransgenesis, salivary glands, vector control",Experiment 5,South Africa,Anopheles funestus,"Midgut,Saliva-secreting gland,Ovary","UBERON:0001045,UBERON:0001044,UBERON:0000992",Strain,EFO:0005135,Anopheles funestus (FANG),Anopheles funestus (FUMOZ-R),The FUMOZ-R strain was selected from FUMOZ by λ-cyhalothrin exposure. Both FUMOZ and FUMOZ-R display pyrethroid resistance as well as carbamate resistance,NA,NA,NA,16S,34,Illumina,raw counts,DESeq2,0.01,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 6b,21 November 2024,MyleeeA,"MyleeeA,WikiWorks",Differential abundance of genera in Anopheles funestus tissues between FANG (left) and FUMOZ-R (right).,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella",3379134|1224|1236|91347|1903411|629;3379134|1224|1236|135624|84642|642;3379134|1224|1236|91347|543|570,Complete,Svetlana up
bsdb:38668545/6/1,38668545,laboratory experiment,38668545,10.3390/tropicalmed9040084,NA,"Chen C.Y., Chan W.Y., Ismail A. , Oliver S.V.",Characterization of the Tissue and Strain-Specific Microbiota of <i>Anopheles funestus</i> Giles (Diptera: Culicidae),Tropical medicine and infectious disease,2024,"16S rRNA, microbiota, midgut, mosquito, ovaries, paratransgenesis, salivary glands, vector control",Experiment 6,South Africa,Anopheles funestus,"Midgut,Saliva-secreting gland,Ovary","UBERON:0001045,UBERON:0001044,UBERON:0000992",Strain,EFO:0005135,Anopheles funestus (FUMOZ),Anopheles funestus (FUMOZ-R),The FUMOZ-R strain was selected from FUMOZ by λ-cyhalothrin exposure. Both FUMOZ and FUMOZ-R display pyrethroid resistance as well as carbamate resistance,NA,NA,NA,16S,34,Illumina,raw counts,DESeq2,0.01,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 6c,21 November 2024,MyleeeA,"MyleeeA,Aleru Divine,WikiWorks",Differential abundance of genera in Anopheles funestus tissues between FUMOZ(left) and FUMOZ-R (right).,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Agromyces,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rahnella",1783272|201174|1760|85006|85023|33877;3379134|1224|28211|204441|2829815|191;3379134|1224|1236|91347|543|158483;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|1903411|629;3379134|1224|1236|91347|1903411|34037,Complete,Svetlana up
bsdb:38668545/6/2,38668545,laboratory experiment,38668545,10.3390/tropicalmed9040084,NA,"Chen C.Y., Chan W.Y., Ismail A. , Oliver S.V.",Characterization of the Tissue and Strain-Specific Microbiota of <i>Anopheles funestus</i> Giles (Diptera: Culicidae),Tropical medicine and infectious disease,2024,"16S rRNA, microbiota, midgut, mosquito, ovaries, paratransgenesis, salivary glands, vector control",Experiment 6,South Africa,Anopheles funestus,"Midgut,Saliva-secreting gland,Ovary","UBERON:0001045,UBERON:0001044,UBERON:0000992",Strain,EFO:0005135,Anopheles funestus (FUMOZ),Anopheles funestus (FUMOZ-R),The FUMOZ-R strain was selected from FUMOZ by λ-cyhalothrin exposure. Both FUMOZ and FUMOZ-R display pyrethroid resistance as well as carbamate resistance,NA,NA,NA,16S,34,Illumina,raw counts,DESeq2,0.01,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 6c,21 November 2024,MyleeeA,"MyleeeA,WikiWorks",Differential abundance of genera in Anopheles funestus tissues between FUMOZ(left) and FUMOZ-R (right).,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella",3379134|1224|1236|72274|135621|286;3379134|1224|1236|135624|84642|642;3379134|1224|1236|91347|1903411|629;3379134|1224|1236|91347|543|570,Complete,Svetlana up
bsdb:38669829/1/1,38669829,laboratory experiment,38669829,10.1016/j.nut.2024.112450,NA,"Pieczyńska-Zając J.M., Malinowska A.M., Pruszyńska-Oszmałek E., Kołodziejski P.A., Drzymała-Czyż S. , Bajerska J.",Effect of a high-fat high-fructose diet on the composition of the intestinal microbiota and its association with metabolic and anthropometric parameters in a letrozole-induced mouse model of polycystic ovary syndrome,"Nutrition (Burbank, Los Angeles County, Calif.)",2024,"Intestinal microbiota, Lipopolysaccharide, Reproductive disorders, Short-chain fatty acids",Experiment 1,Poland,Mus musculus,Caecum,UBERON:0001153,Response to diet,EFO:0010757,Placebo,Placebo+high-fat/high-fructose (HF/HFr) diet,Mice in this group were injected with a placebo pellet and fed a high-fat/high-fructose diet.,8,8,NA,16S,34,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,increased,NA,increased,NA,NA,Signature 1,Table 1 & Supplementary Table S1,24 July 2025,Victoria,Victoria,The relative abundances of selected taxa at all taxonomic levels in intestinal microbiota of prepubertal female C57BL/6 mice.,increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.",1783272|201174|84992;1783272|201174;3379134|976|200643|171549|171552|1283313;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;3379134|1224|28216|80840;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730|290054;3379134|1224|1236;3379134|976|200643|171549|2005473|1918540;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550|28138;1783272|1239|186801|3082720|186804|1501226;3379134|1224|28216|80840|995019;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|216572|39492;1783272|1239|186801|186802|31979|1485|59620,Complete,KateRasheed
bsdb:38669829/1/2,38669829,laboratory experiment,38669829,10.1016/j.nut.2024.112450,NA,"Pieczyńska-Zając J.M., Malinowska A.M., Pruszyńska-Oszmałek E., Kołodziejski P.A., Drzymała-Czyż S. , Bajerska J.",Effect of a high-fat high-fructose diet on the composition of the intestinal microbiota and its association with metabolic and anthropometric parameters in a letrozole-induced mouse model of polycystic ovary syndrome,"Nutrition (Burbank, Los Angeles County, Calif.)",2024,"Intestinal microbiota, Lipopolysaccharide, Reproductive disorders, Short-chain fatty acids",Experiment 1,Poland,Mus musculus,Caecum,UBERON:0001153,Response to diet,EFO:0010757,Placebo,Placebo+high-fat/high-fructose (HF/HFr) diet,Mice in this group were injected with a placebo pellet and fed a high-fat/high-fructose diet.,8,8,NA,16S,34,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,increased,NA,increased,NA,NA,Signature 2,Table 1 & Supplementary Table S1,24 July 2025,Victoria,Victoria,The relative abundances of selected taxa at all taxonomic levels in intestinal microbiota of prepubertal female C57BL/6 mice.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958,Complete,KateRasheed
bsdb:38669829/2/1,38669829,laboratory experiment,38669829,10.1016/j.nut.2024.112450,NA,"Pieczyńska-Zając J.M., Malinowska A.M., Pruszyńska-Oszmałek E., Kołodziejski P.A., Drzymała-Czyż S. , Bajerska J.",Effect of a high-fat high-fructose diet on the composition of the intestinal microbiota and its association with metabolic and anthropometric parameters in a letrozole-induced mouse model of polycystic ovary syndrome,"Nutrition (Burbank, Los Angeles County, Calif.)",2024,"Intestinal microbiota, Lipopolysaccharide, Reproductive disorders, Short-chain fatty acids",Experiment 2,Poland,Mus musculus,Caecum,UBERON:0001153,Polycystic ovary syndrome,EFO:0000660,Placebo,letrozole-induced polycystic ovary syndrome (LET),Mice in this group were injected with a Letrozole (LET) pellet to induce polycystic ovary syndrome (PCOS) and fed a standard diet.,8,8,NA,16S,34,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Table 1 & Supplementary Table S1,24 July 2025,Victoria,Victoria,The relative abundances of selected taxa at all taxonomic levels in intestinal microbiota of prepubertal female C57BL/6 mice.,increased,NA,NA,Complete,KateRasheed
bsdb:38669829/3/1,38669829,laboratory experiment,38669829,10.1016/j.nut.2024.112450,NA,"Pieczyńska-Zając J.M., Malinowska A.M., Pruszyńska-Oszmałek E., Kołodziejski P.A., Drzymała-Czyż S. , Bajerska J.",Effect of a high-fat high-fructose diet on the composition of the intestinal microbiota and its association with metabolic and anthropometric parameters in a letrozole-induced mouse model of polycystic ovary syndrome,"Nutrition (Burbank, Los Angeles County, Calif.)",2024,"Intestinal microbiota, Lipopolysaccharide, Reproductive disorders, Short-chain fatty acids",Experiment 3,Poland,Mus musculus,Caecum,UBERON:0001153,Response to diet,EFO:0010757,Letrozole-induced polycystic ovary syndrome (LET),Placebo+high-fat/high-fructose (HF/HFr) diet,Mice in this group were injected with a placebo pellet and fed a high-fat/high-fructose diet.,8,8,NA,16S,34,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Table 1 & Supplementary Table S1,24 July 2025,Victoria,Victoria,The relative abundances of selected taxa at all taxonomic levels in intestinal microbiota of prepubertal female C57BL/6 mice.,increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|201174|84992;1783272|201174;3379134|976|200643|171549|171552|1283313;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|186801|186802|186806|1730|290054;3379134|976|200643|171549|2005473|1918540;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550|28138;1783272|1239|186801|3082720|186804|1501226;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|216572|39492;1783272|1239|186801|186802,Complete,KateRasheed
bsdb:38669829/3/2,38669829,laboratory experiment,38669829,10.1016/j.nut.2024.112450,NA,"Pieczyńska-Zając J.M., Malinowska A.M., Pruszyńska-Oszmałek E., Kołodziejski P.A., Drzymała-Czyż S. , Bajerska J.",Effect of a high-fat high-fructose diet on the composition of the intestinal microbiota and its association with metabolic and anthropometric parameters in a letrozole-induced mouse model of polycystic ovary syndrome,"Nutrition (Burbank, Los Angeles County, Calif.)",2024,"Intestinal microbiota, Lipopolysaccharide, Reproductive disorders, Short-chain fatty acids",Experiment 3,Poland,Mus musculus,Caecum,UBERON:0001153,Response to diet,EFO:0010757,Letrozole-induced polycystic ovary syndrome (LET),Placebo+high-fat/high-fructose (HF/HFr) diet,Mice in this group were injected with a placebo pellet and fed a high-fat/high-fructose diet.,8,8,NA,16S,34,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Table 1 & Supplementary Table S1,24 July 2025,Victoria,Victoria,The relative abundances of selected taxa at all taxonomic levels in intestinal microbiota of prepubertal female C57BL/6 mice.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales",1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|3085642|580596;1783272|1239|91061|186826|33958;1783272|1239|91061|186826,Complete,KateRasheed
bsdb:38669829/4/1,38669829,laboratory experiment,38669829,10.1016/j.nut.2024.112450,NA,"Pieczyńska-Zając J.M., Malinowska A.M., Pruszyńska-Oszmałek E., Kołodziejski P.A., Drzymała-Czyż S. , Bajerska J.",Effect of a high-fat high-fructose diet on the composition of the intestinal microbiota and its association with metabolic and anthropometric parameters in a letrozole-induced mouse model of polycystic ovary syndrome,"Nutrition (Burbank, Los Angeles County, Calif.)",2024,"Intestinal microbiota, Lipopolysaccharide, Reproductive disorders, Short-chain fatty acids",Experiment 4,Poland,Mus musculus,Caecum,UBERON:0001153,Response to diet,EFO:0010757,Letrozole-induced polycystic ovary syndrome (LET)+high-fat/high-fructose (HF/HFr) diet,Placebo+high-fat/high-fructose (HF/HFr) diet,Mice in this group were injected with a placebo pellet and fed a high-fat/high-fructose diet.,8,8,NA,16S,34,Illumina,relative abundances,"Dunn's test,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Table 1 & Supplementary Table S1,24 July 2025,Victoria,Victoria,The relative abundances of selected taxa at all taxonomic levels in intestinal microbiota of prepubertal female C57BL/6 mice.,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum",1783272|201174;1783272|201174|84992;1783272|1239|526524|526525;1783272|1239|186801|186802;1783272|201174|1760|85004;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|31979;1783272|201174|1760|85004|31953;3379134|976|200643|171549|2005473|1918540;1783272|1239|186801|3082720|186804|1501226;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|31979|1485;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|216572|39492,Complete,KateRasheed
bsdb:38669829/5/1,38669829,laboratory experiment,38669829,10.1016/j.nut.2024.112450,NA,"Pieczyńska-Zając J.M., Malinowska A.M., Pruszyńska-Oszmałek E., Kołodziejski P.A., Drzymała-Czyż S. , Bajerska J.",Effect of a high-fat high-fructose diet on the composition of the intestinal microbiota and its association with metabolic and anthropometric parameters in a letrozole-induced mouse model of polycystic ovary syndrome,"Nutrition (Burbank, Los Angeles County, Calif.)",2024,"Intestinal microbiota, Lipopolysaccharide, Reproductive disorders, Short-chain fatty acids",Experiment 5,Poland,Mus musculus,Caecum,UBERON:0001153,Response to diet,EFO:0010757,Letrozole-induced polycystic ovary syndrome (LET)+high-fat/high-fructose (HF/HFr) & Placebo+high-fat/high-fructose (HF/HFr) & Letrozole-induced polycystic ovary syndrome (LET),Placebo,Mice in this group were injected with a placebo pellet and fed a standard diet.,24,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S1 & S2,23 July 2025,Victoria,Victoria,"Cladogram of LEfSe analysis of gut microbiota in different groups. The microbial compositions were compared at five taxonomic levels (phylum, class, order, family, genus).",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres,k__Pseudomonadati|p__Deferribacterota,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239|186801|3085636;3379134|200930|68337;3379134|200930;3379134|200930|68337|191393;3379134|200930|68337|191393|191394;3379134|200930|68337|191393|2945020|248038;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578,Complete,KateRasheed
bsdb:38669829/6/1,38669829,laboratory experiment,38669829,10.1016/j.nut.2024.112450,NA,"Pieczyńska-Zając J.M., Malinowska A.M., Pruszyńska-Oszmałek E., Kołodziejski P.A., Drzymała-Czyż S. , Bajerska J.",Effect of a high-fat high-fructose diet on the composition of the intestinal microbiota and its association with metabolic and anthropometric parameters in a letrozole-induced mouse model of polycystic ovary syndrome,"Nutrition (Burbank, Los Angeles County, Calif.)",2024,"Intestinal microbiota, Lipopolysaccharide, Reproductive disorders, Short-chain fatty acids",Experiment 6,Poland,Mus musculus,Caecum,UBERON:0001153,Polycystic ovary syndrome,EFO:0000660,Letrozole-induced polycystic ovary syndrome (LET)+high-fat/high-fructose (HF/HFr) & Placebo+high-fat/high-fructose (HF/HFr) & Placebo,Letrozole-induced polycystic ovary syndrome (LET),Mice in this group were injected with a Letrozole (LET) pellet to induce polycystic ovary syndrome (PCOS) and fed a standard diet.,24,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S1 & S2,23 July 2025,Victoria,Victoria,"Cladogram of LEfSe analysis of gut microbiota in different groups. The microbial compositions were compared at five taxonomic levels (phylum, class, order, family, genus).",increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,1783272|1239|186801|186802|3085642|580596,Complete,KateRasheed
bsdb:38669829/7/1,38669829,laboratory experiment,38669829,10.1016/j.nut.2024.112450,NA,"Pieczyńska-Zając J.M., Malinowska A.M., Pruszyńska-Oszmałek E., Kołodziejski P.A., Drzymała-Czyż S. , Bajerska J.",Effect of a high-fat high-fructose diet on the composition of the intestinal microbiota and its association with metabolic and anthropometric parameters in a letrozole-induced mouse model of polycystic ovary syndrome,"Nutrition (Burbank, Los Angeles County, Calif.)",2024,"Intestinal microbiota, Lipopolysaccharide, Reproductive disorders, Short-chain fatty acids",Experiment 7,Poland,Mus musculus,Caecum,UBERON:0001153,Response to diet,EFO:0010757,Letrozole-induced polycystic ovary syndrome (LET)+high-fat/high-fructose (HF/HFr) & Placebo & Letrozole-induced polycystic ovary syndrome (LET),Placebo+high-fat/high-fructose (HF/HFr),Mice in this group were injected with a placebo pellet and fed a high-fat/high-fructose diet.,24,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S1 & S2,23 July 2025,Victoria,Victoria,"Cladogram of LEfSe analysis of gut microbiota in different groups. The microbial compositions were compared at five taxonomic levels (phylum, class, order, family, genus).",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.",3379134|976|200643|171549|171552|1283313;3379134|1224|28216|80840;3379134|1224|1236;3379134|976|200643|171549|2005473|1918540;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|171552;3379134|1224;3379134|976|200643|171549|171550|28138;3379134|1224|28216|80840|995019;1783272|1239|186801|186802|31979|1485|59620,Complete,KateRasheed
bsdb:38669829/8/1,38669829,laboratory experiment,38669829,10.1016/j.nut.2024.112450,NA,"Pieczyńska-Zając J.M., Malinowska A.M., Pruszyńska-Oszmałek E., Kołodziejski P.A., Drzymała-Czyż S. , Bajerska J.",Effect of a high-fat high-fructose diet on the composition of the intestinal microbiota and its association with metabolic and anthropometric parameters in a letrozole-induced mouse model of polycystic ovary syndrome,"Nutrition (Burbank, Los Angeles County, Calif.)",2024,"Intestinal microbiota, Lipopolysaccharide, Reproductive disorders, Short-chain fatty acids",Experiment 8,Poland,Mus musculus,Caecum,UBERON:0001153,Response to diet,EFO:0010757,Placebo+high-fat/high-fructose (HF/HFr) & Placebo & Letrozole-induced polycystic ovary syndrome (LET),Letrozole-induced polycystic ovary syndrome (LET)+high-fat/high-fructose (HF/HFr),Mice in this group were injected with a Letrozole pellet and fed a high-fat/high-fructose diet.,24,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S1 & S2,23 July 2025,Victoria,Victoria,"Cladogram of LEfSe analysis of gut microbiota in different groups. The microbial compositions were compared at five taxonomic levels (phylum, class, order, family, genus).",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",3379134|976|200643|171549;3379134|976;3379134|976|200643;3379134|976|200643|171549|2005473;3379134|976|200643|171549|2005473|1918540;3379134|200940|3031449|213115|194924|35832,Complete,KateRasheed
bsdb:38678197/1/1,38678197,"cross-sectional observational, not case-control",38678197,10.1186/s12866-024-03279-4,https://pmc.ncbi.nlm.nih.gov/articles/PMC11055349/,"Fu P., Wang C., Zheng S., Qiao L., Gao W. , Gong L.",Connection of pre-competition anxiety with gut microbiota and metabolites in wrestlers with varying sports performances based on brain-gut axis theory,BMC microbiology,2024,"Brain-gut axis, Gut microbiota, Pre-competition anxiety, Untargeted metabonomics, Wrestlers",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Physical activity measurement,EFO:0008002,No- achievement group (CnP group),Achievement group (CP group),"Wrestlers who ranked 3rd, 9th, 11th, and 15th in the female division and 11th and 16th in the male division. (Top rank).",6,6,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig 3B1 and 3B2,25 April 2025,Shulamite,Shulamite,Histogram of the distribution of lda values.,decreased,"p__Candidatus Altimarinota,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Nanosynbacterales|f__Candidatus Nanosynbacteraceae|g__Candidatus Nanosynbacter|s__Candidatus Nanosynbacter lyticus,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia",363464;95818|2093818|2093819|2093822|2093823|2093824;95818|2093818|2093825|2171986;95818|2093818|2093825;95818|2093818,Complete,KateRasheed
bsdb:38678197/1/3,38678197,"cross-sectional observational, not case-control",38678197,10.1186/s12866-024-03279-4,https://pmc.ncbi.nlm.nih.gov/articles/PMC11055349/,"Fu P., Wang C., Zheng S., Qiao L., Gao W. , Gong L.",Connection of pre-competition anxiety with gut microbiota and metabolites in wrestlers with varying sports performances based on brain-gut axis theory,BMC microbiology,2024,"Brain-gut axis, Gut microbiota, Pre-competition anxiety, Untargeted metabonomics, Wrestlers",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Physical activity measurement,EFO:0008002,No- achievement group (CnP group),Achievement group (CP group),"Wrestlers who ranked 3rd, 9th, 11th, and 15th in the female division and 11th and 16th in the male division. (Top rank).",6,6,6 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 3,Fig 3B1 and 3B2,25 April 2025,Shulamite,Shulamite,Histogram of the distribution of lda values.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|171552|577309;1783272|1239|186801|186802|216572|3068309;1783272|1239|186801|186802|216572,Complete,KateRasheed
bsdb:38684759/1/1,38684759,prospective cohort,38684759,10.1038/s41598-024-60386-y,NA,"Gupta A., Chan S.Y., Toh R., Low J.M., Liu I.M.Z., Lim S.L., Lee L.Y. , Swarup S.",Gestational diabetes-related gut microbiome dysbiosis is not influenced by different Asian ethnicities and dietary interventions: a pilot study,Scientific reports,2024,NA,Experiment 1,Singapore,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Non-Gestational diabetes mellitus (non-GDM),Gestational diabetes mellitus (GDM),"Women diagnosed with Gestational diabetes mellitus (GDM) using WHO (World Health Organization) 2013 criteria: fasting plasma glucose ≥ 5.1 mmol/L, or a 1-h glucose ≥ 10.0 mmol/L, or a 2-h glucose ≥ 8.5 mmol/L.",16,53,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"body height,body mass index,body weight,maternal age",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 2A,25 October 2024,Rahila,"Rahila,Aleru Divine,WikiWorks",Change in bacterial composition at phylum level between women with and without GDM.,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota,k__Fusobacteriati|p__Fusobacteriota",1783272|201174;1783272|1239;3384189|32066,Complete,Svetlana up
bsdb:38684759/1/2,38684759,prospective cohort,38684759,10.1038/s41598-024-60386-y,NA,"Gupta A., Chan S.Y., Toh R., Low J.M., Liu I.M.Z., Lim S.L., Lee L.Y. , Swarup S.",Gestational diabetes-related gut microbiome dysbiosis is not influenced by different Asian ethnicities and dietary interventions: a pilot study,Scientific reports,2024,NA,Experiment 1,Singapore,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Non-Gestational diabetes mellitus (non-GDM),Gestational diabetes mellitus (GDM),"Women diagnosed with Gestational diabetes mellitus (GDM) using WHO (World Health Organization) 2013 criteria: fasting plasma glucose ≥ 5.1 mmol/L, or a 1-h glucose ≥ 10.0 mmol/L, or a 2-h glucose ≥ 8.5 mmol/L.",16,53,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"body height,body mass index,body weight,maternal age",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 2A,27 October 2024,Rahila,"Rahila,Aleru Divine,WikiWorks",Change in bacterial composition at phylum level between women with and without GDM.,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Verrucomicrobiota",3379134|976;3379134|1224;3379134|74201,Complete,Svetlana up
bsdb:38684759/2/1,38684759,prospective cohort,38684759,10.1038/s41598-024-60386-y,NA,"Gupta A., Chan S.Y., Toh R., Low J.M., Liu I.M.Z., Lim S.L., Lee L.Y. , Swarup S.",Gestational diabetes-related gut microbiome dysbiosis is not influenced by different Asian ethnicities and dietary interventions: a pilot study,Scientific reports,2024,NA,Experiment 2,Singapore,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Control_Chinese (non-GDM),GDM_Chinese,Pregnant women with gestational diabetes mellitus (GDM) of Chinese ethnicity.,6,27,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"body height,body mass index,body weight,maternal age",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 2B,27 October 2024,Rahila,"Rahila,Aleru Divine,WikiWorks",Change in bacterial composition at the phylum level between women with and without GDM in the different ethnic groups.,increased,k__Bacillati|p__Actinomycetota,1783272|201174,Complete,Svetlana up
bsdb:38684759/2/2,38684759,prospective cohort,38684759,10.1038/s41598-024-60386-y,NA,"Gupta A., Chan S.Y., Toh R., Low J.M., Liu I.M.Z., Lim S.L., Lee L.Y. , Swarup S.",Gestational diabetes-related gut microbiome dysbiosis is not influenced by different Asian ethnicities and dietary interventions: a pilot study,Scientific reports,2024,NA,Experiment 2,Singapore,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Control_Chinese (non-GDM),GDM_Chinese,Pregnant women with gestational diabetes mellitus (GDM) of Chinese ethnicity.,6,27,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"body height,body mass index,body weight,maternal age",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 2B,27 October 2024,Rahila,"Rahila,Aleru Divine,WikiWorks",Change in bacterial composition at the phylum level between women with and without GDM in the different ethnic groups.,decreased,"k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Pseudomonadota",3379134|74201;3379134|1224,Complete,Svetlana up
bsdb:38684759/3/1,38684759,prospective cohort,38684759,10.1038/s41598-024-60386-y,NA,"Gupta A., Chan S.Y., Toh R., Low J.M., Liu I.M.Z., Lim S.L., Lee L.Y. , Swarup S.",Gestational diabetes-related gut microbiome dysbiosis is not influenced by different Asian ethnicities and dietary interventions: a pilot study,Scientific reports,2024,NA,Experiment 3,Singapore,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Control_Malay (non-GDM),GDM_Malay,Pregnant women with gestational diabetes mellitus (GDM) of Malay ethnicity.,5,15,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"body height,body mass index,body weight,maternal age",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 2B,27 October 2024,Rahila,"Rahila,Aleru Divine,WikiWorks",Change in bacterial composition at the phylum level between women with and without GDM in the different ethnic groups.,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota",1783272|201174;1783272|1239,Complete,Svetlana up
bsdb:38684759/3/2,38684759,prospective cohort,38684759,10.1038/s41598-024-60386-y,NA,"Gupta A., Chan S.Y., Toh R., Low J.M., Liu I.M.Z., Lim S.L., Lee L.Y. , Swarup S.",Gestational diabetes-related gut microbiome dysbiosis is not influenced by different Asian ethnicities and dietary interventions: a pilot study,Scientific reports,2024,NA,Experiment 3,Singapore,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Control_Malay (non-GDM),GDM_Malay,Pregnant women with gestational diabetes mellitus (GDM) of Malay ethnicity.,5,15,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"body height,body mass index,body weight,maternal age",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 2B,27 October 2024,Rahila,"Rahila,Aleru Divine,WikiWorks",Change in bacterial composition at the phylum level between women with and without GDM in the different ethnic groups.,decreased,"k__Pseudomonadati|p__Acidobacteriota,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota",3379134|57723;3379134|976;3379134|1224,Complete,Svetlana up
bsdb:38684759/4/1,38684759,prospective cohort,38684759,10.1038/s41598-024-60386-y,NA,"Gupta A., Chan S.Y., Toh R., Low J.M., Liu I.M.Z., Lim S.L., Lee L.Y. , Swarup S.",Gestational diabetes-related gut microbiome dysbiosis is not influenced by different Asian ethnicities and dietary interventions: a pilot study,Scientific reports,2024,NA,Experiment 4,Singapore,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Control_Indian (non-GDM),GDM_Indian,Pregnant women with gestational diabetes mellitus (GDM) of Indian ethnicity.,5,11,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"body height,body mass index,body weight,maternal age",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 2B,28 October 2024,Rahila,"Rahila,Aleru Divine,WikiWorks",Change in bacterial composition at the phylum level between women with and without GDM in the different ethnic groups.,increased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Svetlana up
bsdb:38684759/4/2,38684759,prospective cohort,38684759,10.1038/s41598-024-60386-y,NA,"Gupta A., Chan S.Y., Toh R., Low J.M., Liu I.M.Z., Lim S.L., Lee L.Y. , Swarup S.",Gestational diabetes-related gut microbiome dysbiosis is not influenced by different Asian ethnicities and dietary interventions: a pilot study,Scientific reports,2024,NA,Experiment 4,Singapore,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Control_Indian (non-GDM),GDM_Indian,Pregnant women with gestational diabetes mellitus (GDM) of Indian ethnicity.,5,11,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"body height,body mass index,body weight,maternal age",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 2B,28 October 2024,Rahila,"Rahila,Aleru Divine,WikiWorks",Change in bacterial composition at the phylum level between women with and without GDM in the different ethnic groups.,decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Svetlana up
bsdb:38684759/5/1,38684759,prospective cohort,38684759,10.1038/s41598-024-60386-y,NA,"Gupta A., Chan S.Y., Toh R., Low J.M., Liu I.M.Z., Lim S.L., Lee L.Y. , Swarup S.",Gestational diabetes-related gut microbiome dysbiosis is not influenced by different Asian ethnicities and dietary interventions: a pilot study,Scientific reports,2024,NA,Experiment 5,Singapore,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Non-Gestational diabetes mellitus (non-GDM),Gestational diabetes mellitus (GDM),"Women diagnosed with Gestational diabetes mellitus (GDM) using WHO (World Health Organization) 2013 criteria: fasting plasma glucose ≥ 5.1 mmol/L, or a 1-h glucose ≥ 10.0 mmol/L, or a 2-h glucose ≥ 8.5 mmol/L.",16,53,1 month,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"body height,body mass index,body weight,maternal age",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Supplementary Table S3,28 October 2024,Rahila,"Rahila,Aleru Divine,WikiWorks",Detailed list of differentially ASVs between GDM and control pregnant women identified through DeSeq2. ,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:352,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena fissicatena,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalicoccus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:56,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Pseudomonadati|p__Nitrospirota|c__Nitrospiria|o__Nitrospirales|f__Nitrospiraceae|g__Nitrospira,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ottowia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] brachy,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,s__bacterium FCS020",1783272|201174|84998|1643822|1643826|447020;1783272|1239|186801|3085636|186803|1766253;3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|186802|216572|1940255;3379134|976|200643|171549|171552|1283313;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|207244;1783272|201174|84998|84999|1643824|1380;1783272|1239|91061|1385|186817|1386;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005519|397864;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|31979|1485|1262798;1783272|201174|84998|84999|84107|102106;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85009|31957|1912216;3379134|200940|3031449|213115|194924|872;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|189330;1783272|201174|84998|1643822|1643826|84111;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|2005359|290055;1783272|1239|526524|526525|128827|1573536;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|1263031;1783272|1239|186801|3085636|186803|1407607;3384189|32066|203490|203491|203492|848;1783272|201174|1760|85004|31953|2701;1783272|1239|186801|3082720|186804|1505657;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|1506553;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|33958|2767887;1783272|1239|91061|186826|33958|2742598;1783272|1239|186801|3085636|186803|248744;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|909929|1843491|52225;3379134|40117|203693|189778|189779|1234;1783272|201174|84998|84999|1643824|133925;3379134|1224|28216|80840|80864|219181;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|577309;1783272|1239|1737404|1737405|1570339|543311;3379134|1224|1236|72274|135621|286;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|1769710;1783272|201174|84998|84999|84107|1473205;1783272|1239|186801|3085636|186803|177971;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|292632;3379134|1224|28216|80840|995019|40544;1783272|1239|526524|526525|2810280|3025755;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3085636|186803|1506577;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|33958|46255;1783272|1239|186801|3082720|543314|35517;1783272|1239|186801|3085636|186803|2316020|33039;1451755,Complete,Svetlana up
bsdb:38684759/5/2,38684759,prospective cohort,38684759,10.1038/s41598-024-60386-y,NA,"Gupta A., Chan S.Y., Toh R., Low J.M., Liu I.M.Z., Lim S.L., Lee L.Y. , Swarup S.",Gestational diabetes-related gut microbiome dysbiosis is not influenced by different Asian ethnicities and dietary interventions: a pilot study,Scientific reports,2024,NA,Experiment 5,Singapore,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Non-Gestational diabetes mellitus (non-GDM),Gestational diabetes mellitus (GDM),"Women diagnosed with Gestational diabetes mellitus (GDM) using WHO (World Health Organization) 2013 criteria: fasting plasma glucose ≥ 5.1 mmol/L, or a 1-h glucose ≥ 10.0 mmol/L, or a 2-h glucose ≥ 8.5 mmol/L.",16,53,1 month,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"body height,body mass index,body weight,maternal age",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Supplementary Table S3,28 October 2024,Rahila,"Rahila,Aleru Divine,WikiWorks",Detailed list of differentially ASVs between GDM and control pregnant women identified through DeSeq2. ,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Acidothermales|f__Acidothermaceae|g__Acidothermus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Actinomycetospora,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Afipia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Amycolatopsis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Aquimonas,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Blastococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Acidobacteriota|c__Terriglobia|o__Bryobacterales|f__Bryobacteraceae|g__Bryobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Pseudomonadati|p__Acidobacteriota|c__Terriglobia|o__Bryobacterales|f__Solibacteraceae|g__Candidatus Solibacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Spartobacteria|o__Chthoniobacterales|f__Chthoniobacteraceae|g__Candidatus Udaeobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Cellvibrio,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Crossiella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae|g__Dactylosporangium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Fictibacillaceae|g__Fictibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Actinomycetota|c__Thermoleophilia|o__Gaiellales|f__Gaiellaceae|g__Gaiella,k__Pseudomonadati|p__Gemmatimonadota|c__Gemmatimonadia|o__Gemmatimonadales|f__Gemmatimonadaceae|g__Gemmatimonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Geodermatophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae|g__Hyphomicrobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Jatrophihabitantales|f__Jatrophihabitantaceae|g__Jatrophihabitans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Lelliottia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Marmoricola,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Microvirga,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacillati|p__Bacillota|g__Negativibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Nitrosomonadaceae|g__Nitrosospira,k__Pseudomonadati|p__Nitrospirota|c__Nitrospiria|o__Nitrospirales|f__Nitrospiraceae|g__Nitrospira,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Paenarthrobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Pseudarthrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Pseudoduganella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Pseudonocardia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ramlibacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Reyranellaceae|g__Reyranella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Skermanella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Steroidobacterales|f__Steroidobacteraceae|g__Steroidobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,s__bacterium FCS020,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Rhodoplanes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Lapillicoccus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Kitasatospora,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae|g__Pedomicrobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae|g__Pseudolabrys,k__Bacillati|p__Actinomycetota|c__Thermoleophilia|o__Solirubrobacterales|f__Conexibacteraceae|g__Conexibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Kribbellaceae|g__Kribbella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae|g__Rugosimonospora,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kineosporiales|f__Kineosporiaceae|g__Quadrisphaera,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Dongiaceae|g__Dongia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|s__bacterium Ellin6055,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae|g__Labrys,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Psychroglaciecola,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|g__Acidibacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Nordella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Rhodopila,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae|g__Luedemannella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Rhizobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Dokdonella,k__Pseudomonadati|p__Myxococcota|c__Myxococcia|o__Myxococcales|f__Anaeromyxobacteraceae|g__Anaeromyxobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|s__uncultured bacterium mle1-7,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia|o__Acidimicrobiales|f__Iamiaceae|g__Iamia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae|g__Krasilnikovia",1783272|1239|909932|1843488|909930|904;1783272|201174|1760|1643683|85032|28048;3379134|1224|1236|2887326|468|469;1783272|201174|1760|85010|2070|402649;3379134|1224|28211|356|41294|1033;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;1783272|1239|526524|526525|128827|174708;3379134|976|200643|171549|171552|1283313;1783272|201174|1760|85010|2070|1813;1783272|1239|186801|3085636|186803|207244;3379134|1224|1236|135614|32033|265718;1783272|544448|31969|186332|186333|2152;1783272|1239|91061|1385|186817|1386;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005519|397864;1783272|201174|1760|1643682|85030|38501;3379134|1224|28211|356|41294|374;3379134|57723|204432|332160|1962910|911113;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|3085636|186803|830;3379134|57723|204432|332160|332161|332162;3379134|74201|134549|1836787|1836792|1921511;3379134|1224|1236|1706369|1706371|10;3384194|508458|649775|649776|649777|508459;1783272|1239|186801|186802|31979|1485;3379134|1224|28216|80840|80864|283;3379134|976|200643|171549|2005519|1348911;1783272|1239|186801|3085636|186803|33042;3379134|1224|1236|91347|543|413496;1783272|201174|1760|85010|2070|130795;1783272|201174|1760|85008|28056|35753;3379134|200940|3031449|213115|194924|872;1783272|1239|909932|1843489|31977|39948;1783272|1239|526524|526525|128827|1937008;3379134|1224|1236|91347|543|547;1783272|201174|84998|1643822|1643826|580024;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|216572|216851;1783272|1239|91061|1385|3120697|1329200;1783272|1239|186801|3085636|186803|1407607;1783272|201174|1497346|1154584|1154585|1154586;3379134|142182|219685|219686|219687|173479;1783272|201174|1760|1643682|85030|1860;3379134|1224|1236|135625|712|724;3379134|29547|3031852|213849|72293|209;1783272|1239|186801|186802|404402;3379134|1224|28211|356|45401|81;1783272|201174|1760|2805415|2805416|1434010;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|877420;1783272|1239|91061|186826|33958|1578;3379134|1224|1236|91347|543|1330545;1783272|1239|91061|186826|33958|2767887;1783272|1239|91061|1385|186817|400634;1783272|201174|1760|85009|85015|86795;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843489|31977|906;3379134|1224|28211|356|69277|68287;3379134|1224|28211|356|119045|186650;1783272|1239|909932|909929|1843491|52225;3379134|976|200643|171549|2005473|1918540;1783272|201174|1760|85007|1762|1763;1783272|1239|1980693;3379134|1224|28216|32003|206379|35798;3379134|40117|203693|189778|189779|1234;1783272|201174|1760|85009|85015|1839;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|119852;1783272|201174|1760|85006|1268|1742992;3379134|976|200643|171549|2005525|375288;1783272|1239|91061|186826|33958|1253;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171552|838;1783272|201174|1760|85006|1268|1742993;3379134|1224|28216|80840|75682|1522432;3379134|1224|1236|72274|135621|286;1783272|201174|1760|85010|2070|1847;3379134|1224|28216|80840|119060|48736;3379134|1224|28216|80840|80864|174951;3379134|1224|28211|356|2844375|445219;3379134|1224|28216|80840|2975441|93681;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|438033;3379134|1224|1236|91347|543|590;3379134|1224|28211|204441|2829815|204447;3379134|1224|28211|204457|41297|13687;3379134|1224|1236|135614|32033|40323;3379134|1224|1236|3060226|2689614|469322;1783272|201174|1760|85011|2062|1883;3379134|1224|28216|80840|995019|40544;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|135623|641|662;1451755;3379134|1224|28211|356|41294|29407;1783272|201174|1760|85006|85021|402170;1783272|201174|1760|85011|2062|2063;3379134|1224|28211|356|45401|47494;3379134|1224|28211|356|335928|556257;1783272|201174|1497346|588673|320583|191494;1783272|201174|1760|85009|2726069|182639;1783272|201174|1760|85008|28056|1198243;1783272|201174|1760|622452|83778|317661;3379134|1224|28211|204441|3031144|1146845;3379134|1224|28211|204457|41297|234356;3379134|1224|28211|356|335928|204476;3379134|1224|28211|356|119045|1649484;3379134|1224|1236|1549619;3379134|1224|28211|356|169055;3379134|1224|28211|3120395|433|1070;1783272|201174|1760|85008|28056|349314;3379134|1224|28216|80840|212743;3379134|1224|1236|135614|1775411|323413;3379134|2818505|32015|29|1524215|161492;3379134|1224|28216|137401;1783272|201174|84992|84993|633392|467975;1783272|201174|1760|85008|28056|349312,Complete,Svetlana up
bsdb:38684759/6/1,38684759,prospective cohort,38684759,10.1038/s41598-024-60386-y,NA,"Gupta A., Chan S.Y., Toh R., Low J.M., Liu I.M.Z., Lim S.L., Lee L.Y. , Swarup S.",Gestational diabetes-related gut microbiome dysbiosis is not influenced by different Asian ethnicities and dietary interventions: a pilot study,Scientific reports,2024,NA,Experiment 6,Singapore,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Control_Chinese (non-GDM),GDM_Chinese,Pregnant women with gestational diabetes mellitus (GDM) of Chinese ethnicity.,6,27,1 month,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"body height,body mass index,body weight,maternal age",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Supplementary Figure S1A,28 October 2024,Rahila,"Rahila,Aleru Divine,WikiWorks",Differentially abundant ASVs identified from DeSeq2 based analysis between GDM and non GDM mothers belonging to the Chinese ethnic group.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] brachy,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3082720|543314|35517;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|186801|3085636|186803|841;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|3085636|186803|2569097|39488;1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|3085636|186803|2316020|33039;3379134|1224|28216|80840|995019|577310;1783272|1239|91061|186826|33958|46255;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|3082720|186804|1505657;1783272|1239|909932|1843489|31977|906;3379134|1224|28216|80840|995019|40544;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|207244;1783272|201174|1760|85009|31957|1912216;1783272|1239|186801|3085636|186803|28050|39485;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|1385|90964|1279;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3085636|186803|1769710;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|815|816;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:38684759/6/2,38684759,prospective cohort,38684759,10.1038/s41598-024-60386-y,NA,"Gupta A., Chan S.Y., Toh R., Low J.M., Liu I.M.Z., Lim S.L., Lee L.Y. , Swarup S.",Gestational diabetes-related gut microbiome dysbiosis is not influenced by different Asian ethnicities and dietary interventions: a pilot study,Scientific reports,2024,NA,Experiment 6,Singapore,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Control_Chinese (non-GDM),GDM_Chinese,Pregnant women with gestational diabetes mellitus (GDM) of Chinese ethnicity.,6,27,1 month,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"body height,body mass index,body weight,maternal age",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Supplementary Figure S1A,28 October 2024,Rahila,"Rahila,Aleru Divine,WikiWorks",Differentially abundant ASVs identified from DeSeq2 based analysis between GDM and non GDM mothers belonging to the Chinese ethnic group.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacillati|p__Bacillota|g__Negativibacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Lelliottia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Denitrobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Aquimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pluralibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|1224|1236|72274|135621|286;3379134|1224|28216|80840|80864|283;3379134|74201|203494|48461|1647988|239934;3379134|1224|1236|91347|543|590;1783272|1239|1980693;1783272|1239|909932|909929|1843491|52225;1783272|1239|186801|186802|216572|292632;3379134|1224|1236|91347|543|570;3379134|976|117743|200644|2762318|59732;3379134|1224|1236|91347|543|1330545;1783272|1239|186801|3085636|186803|1766253;3379134|976|200643|171549|171552|1283313;1783272|1239|186801|186802|216572|39492;1783272|1239|909932|1843488|909930|904;3379134|1224|28216|80840|119060|48736;3379134|1224|1236|91347|543|547;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|1853231|283168;;3379134|1224|1236|135614|32033|40323;3379134|976|200643|171549|2005519|1348911;1783272|1239|526524|526525|128827|1937008;1783272|1239|909932|1843488|909930|33024;3379134|1224|1236|135625|712|724;1783272|201174|84998|1643822|1643826|79603;1783272|1239|909932|1843489|31977|39948;3379134|1224|1236|135614|32033|265718;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|2005519|397864;1783272|1239|186801|3085636|186803|877420;1783272|1239|91061|186826|33958|1253;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|404402;1783272|1239|526524|526525|128827|174708;3379134|976|200643|171549|2005473|1918540;3379134|256845|1313211|278082|255528|172900;3379134|29547|3031852|213849|72293|209;3379134|976|200643|171549|171550|239759;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|1980681;1783272|544448|31969|186332|186333|2152;1783272|1239|186801|186802|1686313;1783272|1239|186801|3085636|186803|28050;3379134|1224|1236|91347|543|1330546;1783272|1239|186801|186802|216572|119852;1783272|201174|84998|84999|1643824|133925;3384194|508458|649775|649776|649777|508459;1783272|1239|91061|186826|33958|2767887;3379134|1224|28216|80840|75682|846;1783272|1239|186801|3085636|186803|1506553;3379134|976|200643|171549|1853231|574697;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|186802|216572|459786;3379134|1224|1236|91347|543|413496;1783272|1239|91061|1385|539738|1378;1783272|1239|186801|186802|1392389;3379134|1224|1236|135623|641|662;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|2316020|33039;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|3085636|186803|1649459;1783272|1239|909932|1843489|31977|906;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:38684759/7/1,38684759,prospective cohort,38684759,10.1038/s41598-024-60386-y,NA,"Gupta A., Chan S.Y., Toh R., Low J.M., Liu I.M.Z., Lim S.L., Lee L.Y. , Swarup S.",Gestational diabetes-related gut microbiome dysbiosis is not influenced by different Asian ethnicities and dietary interventions: a pilot study,Scientific reports,2024,NA,Experiment 7,Singapore,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Control_Malay (non-GDM),GDM_Malay,Pregnant women with gestational diabetes mellitus (GDM) of Malay ethnicity.,5,15,1 month,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"body height,body mass index,body weight,maternal age",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Supplementary Figure S1B,29 October 2024,Rahila,"Rahila,Aleru Divine,WikiWorks",Differentially abundant ASVs identified from DeSeq2 based analysis between GDM and non GDM mothers belonging to the Malay ethnic group.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] brachy,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|186801|3082720|543314|35517;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|3085636|186803|1506553;1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|3085636|186803|841;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|33958|46255;3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|572511;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843489|31977|906;1783272|1239|91061|186826|33958|2767887;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:38684759/7/2,38684759,prospective cohort,38684759,10.1038/s41598-024-60386-y,NA,"Gupta A., Chan S.Y., Toh R., Low J.M., Liu I.M.Z., Lim S.L., Lee L.Y. , Swarup S.",Gestational diabetes-related gut microbiome dysbiosis is not influenced by different Asian ethnicities and dietary interventions: a pilot study,Scientific reports,2024,NA,Experiment 7,Singapore,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Control_Malay (non-GDM),GDM_Malay,Pregnant women with gestational diabetes mellitus (GDM) of Malay ethnicity.,5,15,1 month,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"body height,body mass index,body weight,maternal age",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Supplementary Figure S1B,29 October 2024,Rahila,"Rahila,Aleru Divine,WikiWorks",Differentially abundant ASVs identified from DeSeq2 based analysis between GDM and non GDM mothers belonging to the Malay ethnic group.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,p__Rhodophyta|c__Florideophyceae|o__Batrachospermales|f__Batrachospermaceae|g__Paludicola,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Nitrospirota|c__Nitrospiria|o__Nitrospirales|f__Nitrospiraceae|g__Nitrospira,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Lelliottia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|1224|28216|80840|80864|283;3379134|1224|1236|135614|32033|40323;1783272|1239|91061|186826|33958|1253;3379134|976|200643|171549|171550|239759;3379134|1224|28216|80840|506|222;3379134|200940|3031449|213115|194924|872;1783272|1239|909932|1843488|909930|904;3379134|976|200643|171549|2005519|397864;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|1506577;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|216572|216851;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|186802|186806|1730|39496;2763|2806|31370|31371|2729669;3379134|1224|1236|91347|543|1940338;3379134|976|200643|171549|2005519|1348911;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|3085636|186803|877420;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|1283313;1783272|1239|909932|1843489|31977|39948;3379134|1224|1236|135625|712|724;3379134|1224|28211|204457|41297|13687;3379134|40117|203693|189778|189779|1234;3379134|1224|1236|91347|543|570;1783272|1239|186801|3082720|186804|1501226;1783272|1239|526524|526525|128827|1937008;3379134|1224|28211|356|41294|374;1783272|1239|186801|186802|216572|946234;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|1766253;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|186802|31979|1485|1522;1783272|1239|186801|3085636|186803|830;1783272|1239|186801|3085636|186803|1432051;3379134|1224|1236|72274|135621|286;3379134|1224|1236|91347|543|547;1783272|1239|186801|3085636|186803|28050;3379134|1224|1236|91347|543|1330545;3379134|976|200643|171549|1853231|574697;3379134|1224|1236|91347|543|544;1783272|1239|909932|1843488|909930|33024;1783272|1239|91061|1385|186817|1386;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|186802|216572|1263;3379134|74201|203494|48461|1647988|239934;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843489|31977|906;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:38684759/8/1,38684759,prospective cohort,38684759,10.1038/s41598-024-60386-y,NA,"Gupta A., Chan S.Y., Toh R., Low J.M., Liu I.M.Z., Lim S.L., Lee L.Y. , Swarup S.",Gestational diabetes-related gut microbiome dysbiosis is not influenced by different Asian ethnicities and dietary interventions: a pilot study,Scientific reports,2024,NA,Experiment 8,Singapore,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Control_Indian (non-GDM),GDM_Indian,Pregnant women with gestational diabetes mellitus (GDM) of Indian ethnicity.,5,11,1 month,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"body height,body mass index,body weight,maternal age",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Supplementary Figure S1C,29 October 2024,Rahila,"Rahila,Aleru Divine,WikiWorks",Differentially abundant ASVs identified from DeSeq2 based analysis between GDM and non GDM mothers belonging to the Indian ethnic group.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,s__bacterium FCS020,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|186801|3085656|3085657|2039302;1783272|1239|186801|3085636|186803|1407607;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|572511;1783272|1239|909932|909929|1843491|158846;1451755;1783272|1239|186801|3085636|186803|841;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|1769710;1783272|1239|186801|3082720|186804|1505657;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|171550|239759;1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:38684759/8/2,38684759,prospective cohort,38684759,10.1038/s41598-024-60386-y,NA,"Gupta A., Chan S.Y., Toh R., Low J.M., Liu I.M.Z., Lim S.L., Lee L.Y. , Swarup S.",Gestational diabetes-related gut microbiome dysbiosis is not influenced by different Asian ethnicities and dietary interventions: a pilot study,Scientific reports,2024,NA,Experiment 8,Singapore,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Control_Indian (non-GDM),GDM_Indian,Pregnant women with gestational diabetes mellitus (GDM) of Indian ethnicity.,5,11,1 month,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"body height,body mass index,body weight,maternal age",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Supplementary Figure S1C,29 October 2024,Rahila,"Rahila,Aleru Divine,WikiWorks",Differentially abundant ASVs identified from DeSeq2 based analysis between GDM and non GDM mothers belonging to the Indian ethnic group.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Acidothermales|f__Acidothermaceae|g__Acidothermus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|909932|1843489|31977|39948;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|2005525|375288;3379134|1224|1236|135623|641|662;1783272|1239|186801|3085636|186803|877420;1783272|1239|526524|526525|128827|1937008;1783272|1239|186801|186802|216572|216851;3379134|29547|3031852|213849|72293|209;1783272|201174|1760|85011|2062|1883;3379134|976|200643|171549|171552|838;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3085636|186803|265975;1783272|201174|1760|1643683|85032|28048;1783272|1239|909932|1843489|31977|29465;3379134|976|200643|171549|171552|1283313;3379134|1224|1236|91347|543|570;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|3085636|186803|2316020|33039;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:38689063/1/1,38689063,"cross-sectional observational, not case-control",38689063,https://doi.org/10.1038/s41591-024-02963-2,NA,"Tito R.Y., Verbandt S., Aguirre Vazquez M., Lahti L., Verspecht C., Lloréns-Rico V., Vieira-Silva S., Arts J., Falony G., Dekker E., Reumers J., Tejpar S. , Raes J.",Microbiome confounders and quantitative profiling challenge predicted microbial targets in colorectal cancer development,Nature medicine,2024,NA,Experiment 1,Belgium,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Controls (CTLs),Colorectal Cancer (CRC),Patients with Colorectal Cancer (CRC),205,47,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 7,2 March 2025,Aleru Divine,Aleru Divine,"Differences in relative (RMP) species abundances over diagnostic groups LCMP cohort (n=589, Kruskal-Wallis and adjusted for multiple testing (AdjP, BH method)).",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium pumilum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei",3379134|976|200643|171549|171550|239759|328813;1783272|1239|1737404|1737405|1570339|165779|33037;1783272|1239|909932|1843489|31977|39948|39950;3384189|32066|203490|203491|203492|848|851;1783272|1239|186801|3082720|543314|86331|86332;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|1239|186801|3082720|186804|1257|1261;3379134|976|200643|171549|171551|836|28123;3379134|976|200643|171549|171552|838|28131;1783272|1239|526524|526525|128827|123375|102148,Complete,Svetlana up
bsdb:38689063/2/1,38689063,"cross-sectional observational, not case-control",38689063,https://doi.org/10.1038/s41591-024-02963-2,NA,"Tito R.Y., Verbandt S., Aguirre Vazquez M., Lahti L., Verspecht C., Lloréns-Rico V., Vieira-Silva S., Arts J., Falony G., Dekker E., Reumers J., Tejpar S. , Raes J.",Microbiome confounders and quantitative profiling challenge predicted microbial targets in colorectal cancer development,Nature medicine,2024,NA,Experiment 2,Belgium,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Controls (CTLs) with normal levels of calprotectin,Colorectal Cancer (CRC),Patients with Colorectal Cancer (CRC) with normal levels of calprotectin,112,12,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 10,2 March 2025,Aleru Divine,Aleru Divine,"Differences in relative (RMP) species abundances over diagnostic groups in LCMP cohort subset with normal levels of fecal calprotectin (n=340 (112 PWoL, 216 PWP and 12 PWT, Kruskal-Wallis and adjusted for multiple testing (AdjP, BH method)).",increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia|s__Harryflintia acetispora,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia",1783272|1239|1737404|1737405|1570339|165779|33037;1783272|1239|186801|186802|216572|1892380|1849041;1783272|1239|1737404|1737405|1570339|543311|33033;3379134|976|200643|171549|171552|838|28131,Complete,Svetlana up
bsdb:38689063/3/1,38689063,"cross-sectional observational, not case-control",38689063,https://doi.org/10.1038/s41591-024-02963-2,NA,"Tito R.Y., Verbandt S., Aguirre Vazquez M., Lahti L., Verspecht C., Lloréns-Rico V., Vieira-Silva S., Arts J., Falony G., Dekker E., Reumers J., Tejpar S. , Raes J.",Microbiome confounders and quantitative profiling challenge predicted microbial targets in colorectal cancer development,Nature medicine,2024,NA,Experiment 3,Belgium,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Polyps (ADE),Colorectal Cancer (CRC),Patients with Colorectal Cancer (CRC),337,47,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 7,7 March 2025,Aleru Divine,Aleru Divine,"Differences in relative (RMP) species abundances over diagnostic groups LCMP cohort (n=589, Kruskal-Wallis and adjusted for multiple testing (AdjP, BH method)).",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium pumilum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei",3379134|976|200643|171549|171550|239759|328813;1783272|1239|1737404|1737405|1570339|165779|33037;1783272|1239|909932|1843489|31977|39948|39950;3384189|32066|203490|203491|203492|848|851;1783272|1239|186801|3082720|543314|86331|86332;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|1239|186801|3082720|186804|1257|1261;3379134|976|200643|171549|171551|836|28123;3379134|976|200643|171549|171552|838|28131;1783272|1239|526524|526525|128827|123375|102148,Complete,Svetlana up
bsdb:38689063/5/1,38689063,"cross-sectional observational, not case-control",38689063,https://doi.org/10.1038/s41591-024-02963-2,NA,"Tito R.Y., Verbandt S., Aguirre Vazquez M., Lahti L., Verspecht C., Lloréns-Rico V., Vieira-Silva S., Arts J., Falony G., Dekker E., Reumers J., Tejpar S. , Raes J.",Microbiome confounders and quantitative profiling challenge predicted microbial targets in colorectal cancer development,Nature medicine,2024,NA,Experiment 5,Belgium,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Polyps (ADE) with normal levels of calprotectin,Colorectal Cancer (CRC),Patients with Colorectal Cancer (CRC) with normal levels of calprotectin,216,12,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 10,7 March 2025,Aleru Divine,Aleru Divine,"Differences in relative (RMP) species abundances over diagnostic groups in LCMP cohort subset with normal levels of fecal calprotectin (n=340 (112 PWoL, 216 PWP and 12 PWT, Kruskal-Wallis and adjusted for multiple testing (AdjP, BH method)).",increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia|s__Harryflintia acetispora,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia",1783272|1239|1737404|1737405|1570339|165779|33037;1783272|1239|186801|186802|216572|1892380|1849041;1783272|1239|1737404|1737405|1570339|543311|33033;3379134|976|200643|171549|171552|838|28131,Complete,Svetlana up
bsdb:38709933/1/1,38709933,"cross-sectional observational, not case-control,laboratory experiment",38709933,10.1073/pnas.2306776121,NA,"Chen J., Liu X., Zou Y., Gong J., Ge Z., Lin X., Zhang W., Huang H., Zhao J., Saw P.E., Lu Y., Hu H. , Song E.",A high-fat diet promotes cancer progression by inducing gut microbiota-mediated leucine production and PMN-MDSC differentiation,Proceedings of the National Academy of Sciences of the United States of America,2024,"breast cancer, gut microbiota, high-fat diet, myeloid-derived suppressor cells",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Body mass index,EFO:0004340,Breast cancer patients with body mass index (BMI) ≤ 24,Breast cancer patients with body mass index (BMI) > 24,Female patients with breast cancer and a body mass index (BMI) greater than 24,41,20,NA,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 1D,27 October 2025,Adenike Awotunde,"Adenike Awotunde,Fiddyhamma",Linear discriminant analysis effect size (LEfSE) analysis showed statistically differential gut microbes between patients with breast cancer with BMI > 24 (n = 20) and those with BMI ≤ 24 (n = 41). This signature represents taxa with a significant linear discriminant analysis (LDA) threshold value > 2.,increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales",3379134|200940|3031449|213115|194924|872;3379134|1224|28211|204441,Complete,NA
bsdb:38709933/1/2,38709933,"cross-sectional observational, not case-control,laboratory experiment",38709933,10.1073/pnas.2306776121,NA,"Chen J., Liu X., Zou Y., Gong J., Ge Z., Lin X., Zhang W., Huang H., Zhao J., Saw P.E., Lu Y., Hu H. , Song E.",A high-fat diet promotes cancer progression by inducing gut microbiota-mediated leucine production and PMN-MDSC differentiation,Proceedings of the National Academy of Sciences of the United States of America,2024,"breast cancer, gut microbiota, high-fat diet, myeloid-derived suppressor cells",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Body mass index,EFO:0004340,Breast cancer patients with body mass index (BMI) ≤ 24,Breast cancer patients with body mass index (BMI) > 24,Female patients with breast cancer and a body mass index (BMI) greater than 24,41,20,NA,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 1D,27 October 2025,Adenike Awotunde,Adenike Awotunde,Linear discriminant analysis effect size (LEfSE) analysis showed statistically differential gut microbes between patients with breast cancer with BMI > 24 (n = 20) and those with BMI ≤ 24 (n = 41). This signature represents taxa with a significant linear discriminant analysis (LDA) threshold value > 2.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium",1783272|1239|186801|3085636|186803|2005355;1783272|1239|91061|1385|539738|1378;1783272|1239|526524|526525|128827|123375,Complete,NA
bsdb:38709933/2/1,38709933,"cross-sectional observational, not case-control,laboratory experiment",38709933,10.1073/pnas.2306776121,NA,"Chen J., Liu X., Zou Y., Gong J., Ge Z., Lin X., Zhang W., Huang H., Zhao J., Saw P.E., Lu Y., Hu H. , Song E.",A high-fat diet promotes cancer progression by inducing gut microbiota-mediated leucine production and PMN-MDSC differentiation,Proceedings of the National Academy of Sciences of the United States of America,2024,"breast cancer, gut microbiota, high-fat diet, myeloid-derived suppressor cells",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Body mass index,EFO:0004340,Breast cancer patients with body mass index (BMI) ≤ 24,Breast cancer patients with body mass index (BMI) > 24,Female patients with breast cancer and a body mass index (BMI) greater than 24,41,20,NA,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 1E,27 October 2025,Adenike Awotunde,"Adenike Awotunde,Fiddyhamma",Correlation analysis between differential gut genus and BMI in breast cancer patients. This signature represents microbial taxa having positive correlation with patients' body mass index.,increased,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,3379134|200940|3031449|213115|194924|872,Complete,NA
bsdb:38709933/2/2,38709933,"cross-sectional observational, not case-control,laboratory experiment",38709933,10.1073/pnas.2306776121,NA,"Chen J., Liu X., Zou Y., Gong J., Ge Z., Lin X., Zhang W., Huang H., Zhao J., Saw P.E., Lu Y., Hu H. , Song E.",A high-fat diet promotes cancer progression by inducing gut microbiota-mediated leucine production and PMN-MDSC differentiation,Proceedings of the National Academy of Sciences of the United States of America,2024,"breast cancer, gut microbiota, high-fat diet, myeloid-derived suppressor cells",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Body mass index,EFO:0004340,Breast cancer patients with body mass index (BMI) ≤ 24,Breast cancer patients with body mass index (BMI) > 24,Female patients with breast cancer and a body mass index (BMI) greater than 24,41,20,NA,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 1E,27 October 2025,Adenike Awotunde,"Adenike Awotunde,Fiddyhamma",Correlation analysis between differential gut genus and BMI in breast cancer patients. This signature represents microbial taxa having negative correlation with patients' body mass index.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas,1783272|1239|186801|3085636|186803|2005355,Complete,NA
bsdb:38709933/3/1,38709933,"cross-sectional observational, not case-control,laboratory experiment",38709933,10.1073/pnas.2306776121,NA,"Chen J., Liu X., Zou Y., Gong J., Ge Z., Lin X., Zhang W., Huang H., Zhao J., Saw P.E., Lu Y., Hu H. , Song E.",A high-fat diet promotes cancer progression by inducing gut microbiota-mediated leucine production and PMN-MDSC differentiation,Proceedings of the National Academy of Sciences of the United States of America,2024,"breast cancer, gut microbiota, high-fat diet, myeloid-derived suppressor cells",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,High fat diet,EFO:0002757,Mice fed with Normal-Fat Diet (NFD),Mice fed with High-Fat Diet (HFD),"Female transgenic wild-type mice fed with high-fat diet (D12492, Rodent Diet with 60 kcal% Fat, Research Diets, Inc).",6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 2B,27 October 2025,Adenike Awotunde,"Adenike Awotunde,Fiddyhamma",LEfSe analysis showing statistically differential gut microbes between normal-fat diet (NFD) and high fat diet (HFD) mice at the genus level. Taxa with a significant LDA threshold value > 2 are represented.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|3085636|186803|572511;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|186802|216572,Complete,NA
bsdb:38709933/3/2,38709933,"cross-sectional observational, not case-control,laboratory experiment",38709933,10.1073/pnas.2306776121,NA,"Chen J., Liu X., Zou Y., Gong J., Ge Z., Lin X., Zhang W., Huang H., Zhao J., Saw P.E., Lu Y., Hu H. , Song E.",A high-fat diet promotes cancer progression by inducing gut microbiota-mediated leucine production and PMN-MDSC differentiation,Proceedings of the National Academy of Sciences of the United States of America,2024,"breast cancer, gut microbiota, high-fat diet, myeloid-derived suppressor cells",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,High fat diet,EFO:0002757,Mice fed with Normal-Fat Diet (NFD),Mice fed with High-Fat Diet (HFD),"Female transgenic wild-type mice fed with high-fat diet (D12492, Rodent Diet with 60 kcal% Fat, Research Diets, Inc).",6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 2B,27 October 2025,Adenike Awotunde,"Adenike Awotunde,Fiddyhamma",LEfSe analysis showing statistically differential gut microbes between NFD and HFD mice at the genus level. Taxa with a significant LDA threshold value > 2 are represented.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|2005473,Complete,NA
bsdb:38709933/4/1,38709933,"cross-sectional observational, not case-control,laboratory experiment",38709933,10.1073/pnas.2306776121,NA,"Chen J., Liu X., Zou Y., Gong J., Ge Z., Lin X., Zhang W., Huang H., Zhao J., Saw P.E., Lu Y., Hu H. , Song E.",A high-fat diet promotes cancer progression by inducing gut microbiota-mediated leucine production and PMN-MDSC differentiation,Proceedings of the National Academy of Sciences of the United States of America,2024,"breast cancer, gut microbiota, high-fat diet, myeloid-derived suppressor cells",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Tumor size,EFO:0004134,Ki-67 in breast cancer patients with BMI ≤ 24,Ki-67 in breast cancer patients with BMI > 24,"Indicator of tumor growth rate, Ki-67 in breast cancer patients with BMI > 24.",41,20,NA,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 1E,28 October 2025,Adenike Awotunde,Adenike Awotunde,Correlation analysis between differential gut genus and Ki67 in breast cancer patients. This signature represents microbial taxa having positive correlation with Ki67.,increased,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,3379134|200940|3031449|213115|194924|872,Complete,NA
bsdb:38709933/5/1,38709933,"cross-sectional observational, not case-control,laboratory experiment",38709933,10.1073/pnas.2306776121,NA,"Chen J., Liu X., Zou Y., Gong J., Ge Z., Lin X., Zhang W., Huang H., Zhao J., Saw P.E., Lu Y., Hu H. , Song E.",A high-fat diet promotes cancer progression by inducing gut microbiota-mediated leucine production and PMN-MDSC differentiation,Proceedings of the National Academy of Sciences of the United States of America,2024,"breast cancer, gut microbiota, high-fat diet, myeloid-derived suppressor cells",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Tumor size,EFO:0004134,Tumor size in breast cancer patients with BMI ≤ 24,Tumor size in breast cancer patients with BMI > 24,"Indicator of tumor growth rate, tumor size in breast cancer patients with BMI > 24",41,20,NA,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 1E,28 October 2025,Adenike Awotunde,"Adenike Awotunde,Fiddyhamma",Correlation analysis between differential gut genus and tumor size in breast cancer patients. This signature represents microbial taxa having positive correlation with tumor size.,increased,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,3379134|200940|3031449|213115|194924|872,Complete,NA
bsdb:38709933/6/1,38709933,"cross-sectional observational, not case-control,laboratory experiment",38709933,10.1073/pnas.2306776121,NA,"Chen J., Liu X., Zou Y., Gong J., Ge Z., Lin X., Zhang W., Huang H., Zhao J., Saw P.E., Lu Y., Hu H. , Song E.",A high-fat diet promotes cancer progression by inducing gut microbiota-mediated leucine production and PMN-MDSC differentiation,Proceedings of the National Academy of Sciences of the United States of America,2024,"breast cancer, gut microbiota, high-fat diet, myeloid-derived suppressor cells",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,Lean donors-derived fecal microbiota transplantation (FMT) mice,Obese donors-derived fecal microbiota transplantation (FMT) mice,Mice that received fecal microbiota transplantation (FMT) from obese human donors.,6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. S7I,28 October 2025,Adenike Awotunde,Adenike Awotunde,LEfSe analysis showing statistically differential gut microbes between lean donors-derived FMT and obese donors-derived FMT mice at the genus level.Taxa with a significant LDA threshold value > 2 are represented.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",1783272|1239|91061|186826|33958|1578;3379134|200940|3031449|213115|194924|872,Complete,NA
bsdb:38709933/6/2,38709933,"cross-sectional observational, not case-control,laboratory experiment",38709933,10.1073/pnas.2306776121,NA,"Chen J., Liu X., Zou Y., Gong J., Ge Z., Lin X., Zhang W., Huang H., Zhao J., Saw P.E., Lu Y., Hu H. , Song E.",A high-fat diet promotes cancer progression by inducing gut microbiota-mediated leucine production and PMN-MDSC differentiation,Proceedings of the National Academy of Sciences of the United States of America,2024,"breast cancer, gut microbiota, high-fat diet, myeloid-derived suppressor cells",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Obesity,EFO:0001073,Lean donors-derived fecal microbiota transplantation (FMT) mice,Obese donors-derived fecal microbiota transplantation (FMT) mice,Mice that received fecal microbiota transplantation (FMT) from obese human donors.,6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. S7I,28 October 2025,Adenike Awotunde,"Adenike Awotunde,Fiddyhamma",LEfSe analysis showing statistically differential gut microbes between lean donors-derived FMT and obese donors-derived FMT mice at the genus level.Taxa with a significant LDA threshold value > 2 are represented.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",1783272|1239|186801|186802|1980681;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|1506577,Complete,NA
bsdb:38710815/1/1,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 1,United States of America,Homo sapiens,Buccal mucosa,UBERON:0006956,Smoking behaviour measurement,EFO:0005671,Non-tobacco users (NU),Cigarettes users (CG ),"Participants in this group smoked 6–10 cigarettes per day and smoked filtered, menthol, and full-flavour cigarettes.",43,24,6 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 4,30 April 2025,Shulamite,"Shulamite,Victoria","Box plots of relative abundance of the top 14 bacterial genera by user group: cigarette user (CG, orange), smokeless tobacco user (ST, green), and non-user (NU). (*) represents p-value < 0.05.",increased,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,3384189|32066|203490|203491|1129771|32067,Complete,KateRasheed
bsdb:38710815/1/2,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 1,United States of America,Homo sapiens,Buccal mucosa,UBERON:0006956,Smoking behaviour measurement,EFO:0005671,Non-tobacco users (NU),Cigarettes users (CG ),"Participants in this group smoked 6–10 cigarettes per day and smoked filtered, menthol, and full-flavour cigarettes.",43,24,6 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 4,30 April 2025,Shulamite,"Shulamite,Victoria","Box plots of relative abundance of the top 14 bacterial genera by user group: cigarette user (CG, orange), smokeless tobacco user (ST, green), and non-user (NU). (*) represents p-value < 0.05.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|201174|1760|2037|2049|1654;1783272|1239|91061|186826|186828|117563;3379134|1224|28216|206351|481|482;1783272|1239|186801|3085636|186803|265975;3379134|976|200643|171549|171552|838;1783272|1239|909932|1843489|31977|29465,Complete,KateRasheed
bsdb:38710815/2/1,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 2,United States of America,Homo sapiens,Buccal mucosa,UBERON:0006956,Smoking behaviour measurement,EFO:0005671,Smokeless tobacco users (ST),Cigarettes users (CG ),"Participants in this group smoked 6–10 cigarettes per day and smoked filtered, menthol, and full-flavour cigarettes.",18,24,6 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4,30 April 2025,Shulamite,"Shulamite,Victoria","Box plots of relative abundance of the top 14 bacterial genera by user group: cigarette user (CG, orange), smokeless tobacco user (ST, green), and non-user (NU). (*) represents p-value < 0.05.",increased,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,3384189|32066|203490|203491|1129771|32067,Complete,KateRasheed
bsdb:38710815/2/2,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 2,United States of America,Homo sapiens,Buccal mucosa,UBERON:0006956,Smoking behaviour measurement,EFO:0005671,Smokeless tobacco users (ST),Cigarettes users (CG ),"Participants in this group smoked 6–10 cigarettes per day and smoked filtered, menthol, and full-flavour cigarettes.",18,24,6 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4,29 July 2025,Victoria,Victoria,"Box plots of relative abundance of the top 14 bacterial genera by user group: cigarette user (CG, orange), smokeless tobacco user (ST, green), and non-user (NU). (*) represents p-value < 0.05.",decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,3379134|1224|1236|72274|135621|286,Complete,KateRasheed
bsdb:38710815/3/2,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 3,United States of America,Homo sapiens,Buccal mucosa,UBERON:0006956,Smoking behaviour measurement,EFO:0005671,Non-tobacco users (NU ),Smokeless tobacco users (ST),Participants in this group had used tobacco at least once per week for the previous year.,43,18,6 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,"age,race,sex",NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 4,30 April 2025,Shulamite,"Shulamite,Victoria","Box plots of relative abundance of the top 14 bacterial genera by user group: cigarette user (CG, orange), smokeless tobacco user (ST, green), and non-user (NU). (*) represents p-value < 0.05.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171551|836;1783272|1239|186801|3085636|186803|265975;3384189|32066|203490|203491|1129771|32067;1783272|1239|91061|186826|186828|117563;1783272|201174|1760|2037|2049|1654,Complete,KateRasheed
bsdb:38710815/4/1,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behaviour measurement,EFO:0005671,Non-tobacco users (NU),Cigarettes users (CG ),"Participants in this group smoked 6–10 cigarettes per day and smoked filtered, menthol, and full-flavour cigarettes.",43,24,6 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 4,30 April 2025,Shulamite,"Shulamite,Victoria","Box plots of relative abundance of the top 14 bacterial genera by user group: cigarette user (CG, orange), smokeless tobacco user (ST, green), and non-user (NU). (*) represents p-value < 0.05.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",1783272|201174|1760|2037|2049|1654;3384189|32066|203490|203491|1129771|32067;3379134|976|200643|171549|171551|836,Complete,KateRasheed
bsdb:38710815/4/2,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behaviour measurement,EFO:0005671,Non-tobacco users (NU),Cigarettes users (CG ),"Participants in this group smoked 6–10 cigarettes per day and smoked filtered, menthol, and full-flavour cigarettes.",43,24,6 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 4,30 April 2025,Shulamite,"Shulamite,Victoria","Box plots of relative abundance of the top 14 bacterial genera by user group: cigarette user (CG, orange), smokeless tobacco user (ST, green), and non-user (NU). (*) represents p-value < 0.05.",decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia",3384189|32066|203490|203491|203492|848;3379134|1224|1236|135625|712|724;3379134|1224|1236|72274|135621|286;33090|35493|3398|72025|3803|3814|508215,Complete,KateRasheed
bsdb:38710815/5/1,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 5,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behaviour measurement,EFO:0005671,Smokeless tobacco users (ST),Cigarette users (CG),"Participants in this group smoked 6–10 cigarettes per day and smoked filtered, menthol, and full-flavour cigarettes.",18,24,6 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4,30 April 2025,Shulamite,"Shulamite,Victoria","Box plots of relative abundance of the top 14 bacterial genera by user group: cigarette user (CG, orange), smokeless tobacco user (ST, green), and non-user (NU). (*) represents p-value < 0.05.",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,KateRasheed
bsdb:38710815/5/2,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 5,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behaviour measurement,EFO:0005671,Smokeless tobacco users (ST),Cigarette users (CG),"Participants in this group smoked 6–10 cigarettes per day and smoked filtered, menthol, and full-flavour cigarettes.",18,24,6 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4,30 April 2025,Shulamite,"Shulamite,Victoria","Box plots of relative abundance of the top 14 bacterial genera by user group: cigarette user (CG, orange), smokeless tobacco user (ST, green), and non-user (NU). (*) represents p-value < 0.05.",decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",3384189|32066|203490|203491|203492|848;3379134|1224|1236|135625|712|724;3384189|32066|203490|203491|1129771|32067;1783272|1239|186801|3085636|186803|265975;3379134|976|200643|171549|171551|836,Complete,KateRasheed
bsdb:38710815/6/1,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 6,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behaviour measurement,EFO:0005671,Non-tobacco users (NU),Smokeless tobacco user (ST),Participants in this group had used tobacco at least once per week for the previous year.,43,18,6 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,"age,race,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4,30 April 2025,Shulamite,"Shulamite,Victoria","Box plots of relative abundance of the top 14 bacterial genera by user group: cigarette user (CG, orange), smokeless tobacco user (ST, green), and non-user (NU). (*) represents p-value < 0.05.",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,KateRasheed
bsdb:38710815/6/2,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 6,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behaviour measurement,EFO:0005671,Non-tobacco users (NU),Smokeless tobacco user (ST),Participants in this group had used tobacco at least once per week for the previous year.,43,18,6 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,"age,race,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4,30 April 2025,Shulamite,"Shulamite,Victoria","Box plots of relative abundance of the top 14 bacterial genera by user group: cigarette user (CG, orange), smokeless tobacco user (ST, green), and non-user (NU). (*) represents p-value < 0.05.",decreased,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,3384189|32066|203490|203491|203492|848,Complete,KateRasheed
bsdb:38710815/7/1,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 7,United States of America,Homo sapiens,Buccal mucosa,UBERON:0006956,Smoking behaviour measurement,EFO:0005671,Non-tobacco users at Time 1 (NU),Non-tobacco users at Time 4 (NU),Participants who had either never used tobacco products or had smoked less than 20 cigarettes or used smokeless tobacco less than 20 times in their lifetime at time point 4.,43,43,6 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2a,30 April 2025,Shulamite,"Shulamite,Victoria","Differential abundance of bacterial OTUs in buccal swab samples that were statistically significantly different (α = 0.001) between time-points 1 and 4. The OTUs are colored by user groups (cigarette user (CG), orange; smokeless tobacco user (ST), green; non-user (NU), grey). A positive log2-fold change value denotes an OTU that is significantly higher in time-point 1 samples, while a negative log2-fold change indicates an OTU that is significantly higher in time-point 4 samples.",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum",1783272|1239|91061|186826|186828|117563;3384189|32066|203490|203491|1129771|32067;3379134|976|200643|171549|171552|838;3379134|1224|28216|206351|481|482|28449;1783272|201174|1760|85007|85025|1827;3379134|1224|28211|356|118882|528,Complete,KateRasheed
bsdb:38710815/7/2,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 7,United States of America,Homo sapiens,Buccal mucosa,UBERON:0006956,Smoking behaviour measurement,EFO:0005671,Non-tobacco users at Time 1 (NU),Non-tobacco users at Time 4 (NU),Participants who had either never used tobacco products or had smoked less than 20 cigarettes or used smokeless tobacco less than 20 times in their lifetime at time point 4.,43,43,6 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2a,29 July 2025,Victoria,Victoria,"Differential abundance of bacterial OTUs in buccal swab samples that were statistically significantly different (α = 0.001) between time-points 1 and 4. The OTUs are colored by user groups (cigarette user (CG), orange; smokeless tobacco user (ST), green; non-user (NU), grey). A positive log2-fold change value denotes an OTU that is significantly higher in time-point 1 samples, while a negative log2-fold change indicates an OTU that is significantly higher in time-point 4 samples.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus lutetiensis",1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|572511;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|91347|543|547|550;1783272|1239|91061|186826|1300|1301|150055,Complete,KateRasheed
bsdb:38710815/8/1,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 8,United States of America,Homo sapiens,Buccal mucosa,UBERON:0006956,Smoking behaviour measurement,EFO:0005671,Cigarette users at time 1 (CG),Cigarette users at time 4 (CG),"Participants who smoked 6–10 cigarettes per day and smoked filtered, menthol, and full-flavour cigarettes at time point 4.",24,24,6 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2a,30 April 2025,Shulamite,"Shulamite,Victoria","Differential abundance of bacterial OTUs in buccal swab samples that were statistically significantly different (α = 0.001) between time-points 1 and 4. The OTUs are colored by user groups (cigarette user (CG), orange; smokeless tobacco user (ST), green; non-user (NU), grey). A positive log2-fold change value denotes an OTU that is significantly higher in time-point 1 samples, while a negative log2-fold change indicates an OTU that is significantly higher in time-point 4 samples.",increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter ureolyticus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum",1783272|1239|1737404|1737405|1570339|162289;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|1737404|1737405|1570339|165779;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3379134|29547|3031852|213849|72294|194|827;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|2037|2049|184869,Complete,KateRasheed
bsdb:38710815/8/2,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 8,United States of America,Homo sapiens,Buccal mucosa,UBERON:0006956,Smoking behaviour measurement,EFO:0005671,Cigarette users at time 1 (CG),Cigarette users at time 4 (CG),"Participants who smoked 6–10 cigarettes per day and smoked filtered, menthol, and full-flavour cigarettes at time point 4.",24,24,6 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2a,30 April 2025,Shulamite,"Shulamite,Victoria","Differential abundance of bacterial OTUs in buccal swab samples that were statistically significantly different (α = 0.001) between time-points 1 and 4. The OTUs are colored by user groups (cigarette user (CG), orange; smokeless tobacco user (ST), green; non-user (NU), grey). A positive log2-fold change value denotes an OTU that is significantly higher in time-point 1 samples, while a negative log2-fold change indicates an OTU that is significantly higher in time-point 4 samples.",decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,3379134|1224|1236|72274|135621|286,Complete,KateRasheed
bsdb:38710815/9/1,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 9,United States of America,Homo sapiens,Buccal mucosa,UBERON:0006956,Smoking behaviour measurement,EFO:0005671,Smokeless tobacco users at time 1 (ST),Smokeless tobacco users at time 4 (ST),Participants who had used tobacco at least once per week for the previous year at time point 4.,18,18,6 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2a,30 April 2025,Shulamite,"Shulamite,Victoria","Differential abundance of bacterial OTUs in buccal swab samples that were statistically significantly different (α = 0.001) between time-points 1 and 4. The OTUs are colored by user groups (cigarette user (CG), orange; smokeless tobacco user (ST), green; non-user (NU), grey). A positive log2-fold change value denotes an OTU that is significantly higher in time-point 1 samples, while a negative log2-fold change indicates an OTU that is significantly higher in time-point 4 samples.",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,KateRasheed
bsdb:38710815/10/1,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 10,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behaviour measurement,EFO:0005671,Cigarette users at time 1 (CG),Cigarette users at time 4 (CG),"Participants who smoked 6–10 cigarettes per day and smoked filtered, menthol, and full-flavour cigarettes at time point 4.",24,24,6 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2b,30 April 2025,Shulamite,"Shulamite,Victoria","Differential abundance of bacterial OTUs in saliva samples that were statistically significantly different (α = 0.001) between time-points 1 and 4. The OTUs are colored by user groups (cigarette user (CG), orange; smokeless tobacco user (ST), green; non-user (NU), grey). A positive log2-fold change value denotes an OTU that is significantly higher in time-point 1 samples, while a negative log2-fold change indicates an OTU that is significantly higher in time-point 4 samples.",increased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,3379134|1224|28216|80840|506|222,Complete,KateRasheed
bsdb:38710815/10/2,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 10,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behaviour measurement,EFO:0005671,Cigarette users at time 1 (CG),Cigarette users at time 4 (CG),"Participants who smoked 6–10 cigarettes per day and smoked filtered, menthol, and full-flavour cigarettes at time point 4.",24,24,6 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2b,30 April 2025,Shulamite,"Shulamite,Victoria","Differential abundance of bacterial OTUs in saliva samples that were statistically significantly different (α = 0.001) between time-points 1 and 4. The OTUs are colored by user groups (cigarette user (CG), orange; smokeless tobacco user (ST), green; non-user (NU), grey). A positive log2-fold change value denotes an OTU that is significantly higher in time-point 1 samples, while a negative log2-fold change indicates an OTU that is significantly higher in time-point 4 samples.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus",3379134|1224|1236|72274|135621|286;1783272|201174|1760|85007|85025|1827,Complete,KateRasheed
bsdb:38710815/11/1,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 11,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behaviour measurement,EFO:0005671,Smokeless tobacco users at time 1 (ST),Smokeless tobacco users at time 4 (ST),Participants who had used tobacco at least once per week for the previous year at time point 4.,43,18,6 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2b,30 April 2025,Shulamite,"Shulamite,Victoria","Differential abundance of bacterial OTUs in saliva samples that were statistically significantly different (α = 0.001) between time-points 1 and 4. The OTUs are colored by user groups (cigarette user (CG), orange; smokeless tobacco user (ST), green; non-user (NU), grey). A positive log2-fold change value denotes an OTU that is significantly higher in time-point 1 samples, while a negative log2-fold change indicates an OTU that is significantly higher in time-point 4 samples.",increased,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,1783272|544448|31969|2085|2092,Complete,KateRasheed
bsdb:38710815/12/1,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 12,United States of America,Homo sapiens,"Saliva,Buccal mucosa","UBERON:0001836,UBERON:0006956",Specimen,OBI:0100051,Cigarettes users (CG - Buccal),Cigarettes users (CG - Saliva),"Saliva samples of participants who smoked 6–10 cigarettes per day and smoked filtered, menthol, and full-flavour cigarettes.",24,24,6 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 9,30 April 2025,Shulamite,"Shulamite,Victoria","Box plots of relative abundance of the top 14 bacterial genera by sample type (buccal swab (red), saliva (blue) across each user group: cigarette users (CG), smokeless tobacco users (ST), and non-users (NU).",increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3384189|32066|203490|203491|203492|848;1783272|201174|1760|2037|2049|1654;3384189|32066|203490|203491|1129771|32067;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,KateRasheed
bsdb:38710815/12/2,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 12,United States of America,Homo sapiens,"Saliva,Buccal mucosa","UBERON:0001836,UBERON:0006956",Specimen,OBI:0100051,Cigarettes users (CG - Buccal),Cigarettes users (CG - Saliva),"Saliva samples of participants who smoked 6–10 cigarettes per day and smoked filtered, menthol, and full-flavour cigarettes.",24,24,6 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 9,30 July 2025,Victoria,Victoria,"Box plots of relative abundance of the top 14 bacterial genera by sample type (buccal swab (red), saliva (blue) across each user group: cigarette users (CG), smokeless tobacco users (ST), and non-users (NU).",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella",3379134|1224|1236|72274|135621|286;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|186828|117563,Complete,KateRasheed
bsdb:38710815/13/1,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 13,United States of America,Homo sapiens,"Saliva,Buccal mucosa","UBERON:0001836,UBERON:0006956",Specimen,OBI:0100051,Non-users (NU - Buccal),Non-users (NU - Saliva),Saliva samples of participants who had either never used tobacco products or had smoked less than 20 cigarettes or used smokeless tobacco less than 20 times in their lifetime.,43,43,6 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 9,30 April 2025,Shulamite,"Shulamite,Victoria","Box plots of relative abundance of the top 14 bacterial genera by sample type (buccal swab (red), saliva (blue) across each user group: cigarette users (CG), smokeless tobacco users (ST), and non-users (NU).",increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3384189|32066|203490|203491|1129771|32067;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171551|836;1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549|171552|838,Complete,KateRasheed
bsdb:38710815/13/2,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 13,United States of America,Homo sapiens,"Saliva,Buccal mucosa","UBERON:0001836,UBERON:0006956",Specimen,OBI:0100051,Non-users (NU - Buccal),Non-users (NU - Saliva),Saliva samples of participants who had either never used tobacco products or had smoked less than 20 cigarettes or used smokeless tobacco less than 20 times in their lifetime.,43,43,6 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 9,30 April 2025,Shulamite,"Shulamite,Victoria","Box plots of relative abundance of the top 14 bacterial genera by sample type (buccal swab (red), saliva (blue) across each user group: cigarette users (CG), smokeless tobacco users (ST), and non-users (NU).",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella",1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|1300|1301;1783272|201174|1760|85006|1268|32207;3379134|1224|1236|72274|135621|286;1783272|1239|91061|186826|186828|117563,Complete,KateRasheed
bsdb:38710815/14/1,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 14,United States of America,Homo sapiens,"Saliva,Buccal mucosa","UBERON:0001836,UBERON:0006956",Specimen,OBI:0100051,Smokeless tobacco users (ST - Buccal),Smokeless tobacco users (ST - Saliva),Saliva samples of participants who had used tobacco at least once per week for the previous year.,18,18,6 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 9,30 July 2025,Victoria,Victoria,"Box plots of relative abundance of the top 14 bacterial genera by sample type (buccal swab (red), saliva (blue) across each user group: cigarette users (CG), smokeless tobacco users (ST), and non-users (NU).",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|1760|2037|2049|1654;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|1129771|32067;3379134|1224|28216|206351|481|482;1783272|1239|186801|3085636|186803|265975;1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:38710815/14/2,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 14,United States of America,Homo sapiens,"Saliva,Buccal mucosa","UBERON:0001836,UBERON:0006956",Specimen,OBI:0100051,Smokeless tobacco users (ST - Buccal),Smokeless tobacco users (ST - Saliva),Saliva samples of participants who had used tobacco at least once per week for the previous year.,18,18,6 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 9,30 July 2025,Victoria,Victoria,"Box plots of relative abundance of the top 14 bacterial genera by sample type (buccal swab (red), saliva (blue) across each user group: cigarette users (CG), smokeless tobacco users (ST), and non-users (NU).",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",1783272|1239|91061|186826|186828|117563;1783272|1239|91061|186826|33958|1578;3379134|1224|1236|72274|135621|286,Complete,KateRasheed
bsdb:38710815/15/1,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 15,United States of America,Homo sapiens,Buccal mucosa,UBERON:0006956,Smoking behaviour measurement,EFO:0005671,Non-tobacco users (NU),Cigarettes users (CG ),"Participants in this group smoked 6–10 cigarettes per day and smoked filtered, menthol, and full-flavour cigarettes.",43,24,6 months,16S,34,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 5a,30 July 2025,Victoria,Victoria,Relative abundance of bacterial OTUs in buccal swab samples that were statistically significantly different (α = 0.001) between non-users (NU) and cigarette users (CG).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis",1783272|1239|186801|3082720|186804;3379134|1224|28211|356|118882|528;3384189|32066|203490|203491|1129771|32067;3379134|1224|28216|206351|481|482;1783272|1239|186801|3082720|543314|109326;3379134|1224|1236|135625|712|416916;3379134|1224|1236|135625|712|724;3379134|1224|28216|206351|481|482|28449;1783272|201174|1760|85007|85025|1827;3379134|1224|1236|72274|135621|286;1783272|1239|526524|526525|128827|123375|102148;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301|68892,Complete,KateRasheed
bsdb:38710815/15/2,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 15,United States of America,Homo sapiens,Buccal mucosa,UBERON:0006956,Smoking behaviour measurement,EFO:0005671,Non-tobacco users (NU),Cigarettes users (CG ),"Participants in this group smoked 6–10 cigarettes per day and smoked filtered, menthol, and full-flavour cigarettes.",43,24,6 months,16S,34,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 5a,30 July 2025,Victoria,Victoria,Relative abundance of bacterial OTUs in buccal swab samples that were statistically significantly different (α = 0.001) between non-users (NU) and cigarette users (CG).,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae",1783272|201174|1760|2037|2049|1654;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|91061|186826|186827|46123;3379134|1224|1236|135625|712|416916;3384189|32066|203490|203491|1129771,Complete,KateRasheed
bsdb:38710815/16/1,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 16,United States of America,Homo sapiens,Buccal mucosa,UBERON:0006956,Smoking behaviour measurement,EFO:0005671,Non-tobacco users (NU ),Smokeless tobacco users (ST),Participants in this group had used tobacco at least once per week for the previous year.,43,18,6 months,16S,34,Illumina,raw counts,DESeq2,0.05,FALSE,NA,"age,race,sex",NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 5b,30 July 2025,Victoria,Victoria,Relative abundance of bacterial OTUs in buccal swab samples that were statistically significantly different (α = 0.001) between non-users (NU) and smokeless tobacco users (ST).,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,1783272|1239|186801|3085636|186803|33042,Complete,KateRasheed
bsdb:38710815/16/2,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 16,United States of America,Homo sapiens,Buccal mucosa,UBERON:0006956,Smoking behaviour measurement,EFO:0005671,Non-tobacco users (NU ),Smokeless tobacco users (ST),Participants in this group had used tobacco at least once per week for the previous year.,43,18,6 months,16S,34,Illumina,raw counts,DESeq2,0.05,FALSE,NA,"age,race,sex",NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 5b,30 July 2025,Victoria,Victoria,Relative abundance of bacterial OTUs in buccal swab samples that were statistically significantly different (α = 0.001) between non-users (NU) and smokeless tobacco users (ST).,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|1224|1236|135625|712|724|729;3379134|1224|28216|206351|481|482|28449;3379134|1224|28216|80840|506|222;1783272|201174|1760|2037|2049|1654;3379134|1224|28216|206351|481|482;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|3082720|186804;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977,Complete,KateRasheed
bsdb:38710815/17/1,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 17,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behaviour measurement,EFO:0005671,Non-tobacco users (NU),Cigarettes users (CG ),"Participants in this group smoked 6–10 cigarettes per day and smoked filtered, menthol, and full-flavour cigarettes.",43,24,6 months,16S,34,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 6a,30 July 2025,Victoria,Victoria,Relative abundance of bacterial OTUs in saliva samples that was statistically significantly different (α = 0.001) between non-users (NU) and cigarette users (CG).,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium",1783272|201174|1760|85007|1653|1716;3384189|32066|203490|203491|1129771|32067;1783272|201174|1760|85009|31957;1783272|1239|186801|3082720|543314|109326;3379134|1224|28211|356;3379134|1224|1236|135625|712|724;3379134|1224|28216|206351|481|482;1783272|1239|186801|3082720|186804;3379134|1224|28211|356|118882|528;3379134|976|117743|200644|2762318;3379134|1224|1236|135625|712|416916;3379134|1224|1236|72274|135621|286;1783272|1239|91061|186826|1300|1301;3384189|32066|203490|203491|203492|848;3379134|1224|1236|135625|712|724|729;1783272|201174|1760|2037|2049|1654;3379134|1224|28216|206351|481|482|28449;3379134|976|200643|171549|171551|836;3379134|1224|1236|135623|641;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|28132;3379134|1224|28216|206351|481;1783272|1239|909932|1843489|31977|29465|29466;1783272|201174|1760|85006|1268|32207|172042;3379134|1224|28216|80840|119060|47670;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712;1783272|1239|186801|3085636|186803;3379134|976|117743|200644|49546|1016;1783272|1239|91061|186826|1300|1301|68892;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|909932|1843489|31977|29465|39778;3379134|1224|1236|135615|868|2717;1783272|1239|186801|3085636|186803|265975,Complete,KateRasheed
bsdb:38710815/17/2,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 17,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behaviour measurement,EFO:0005671,Non-tobacco users (NU),Cigarettes users (CG ),"Participants in this group smoked 6–10 cigarettes per day and smoked filtered, menthol, and full-flavour cigarettes.",43,24,6 months,16S,34,Illumina,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 6a,30 July 2025,Victoria,Victoria,Relative abundance of bacterial OTUs in saliva samples that was statistically significantly different (α = 0.001) between non-users (NU) and cigarette users (CG).,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Acidaminobacteraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Sharpea,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema socranskii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae",1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1328;1783272|201174|1760|2037|2049|1654;1783272|201174|84998|1643822|1643826|84108;3379134|976|200643|171549|171552|838|28133;3379134|976|200643|171549|171552|838|28132;1783272|1239|909932|1843489|31977|39948;3379134|976|200643|171549|171551|836|28124;1783272|1239|909932|1843489|31977|906;1783272|1239|91061|186826|33958|2742598|1598;3384189|32066|203490|203491|1129771|32067;1783272|1239|186801|3082720|3118655|44259;3379134|203691|203692|136|2845253|157|59892;1783272|1239|186801|3082720|3118653;1783272|1239|91061|186826|33958|1578;1783272|1239|526524|526525|2810280|519427;3379134|1224|28211|356|212791;1783272|1239|526524|526525|128827|118747;1783272|1239|186801|186802;1783272|201174|1760|85004|31953|196081;3379134|976|200643|171549|171551|836;3379134|203691|203692|136|2845253|157|53419;1783272|1239|186801|3085636|186803|43996;1783272|1239|91061|186826|33958|2767887|1624;1783272|201174|1760|85004|31953|1678;1783272|1239|909932|1843489|31977|29465;3384189|32066|203490|203491|1129771,Complete,KateRasheed
bsdb:38710815/18/1,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 18,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behaviour measurement,EFO:0005671,Non-tobacco users (NU),Smokeless tobacco user (ST),Participants in this group had used tobacco at least once per week for the previous year.,43,18,6 months,16S,34,Illumina,raw counts,DESeq2,0.05,FALSE,NA,"age,race,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 6b,30 July 2025,Victoria,Victoria,Relative abundance of bacterial OTUs in saliva samples that was statistically significantly different (α = 0.001) between non-users (NU) and smokeless tobacco users (ST).,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",3384189|32066|203490|203491|1129771|32067;3379134|203691|203692|136|2845253|157|59892;3379134|976|200643|171549|171551|836|28124;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300,Complete,KateRasheed
bsdb:38710815/18/2,38710815,"case-control,time series / longitudinal observational",38710815,10.1038/s41598-024-60730-2,https://pmc.ncbi.nlm.nih.gov/articles/PMC11074290/,"Chattopadhyay S., Malayil L., Chopyk J., Smyth E., Kulkarni P., Raspanti G., Thomas S.B., Sapkota A., Mongodin E.F. , Sapkota A.R.",Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users,Scientific reports,2024,NA,Experiment 18,United States of America,Homo sapiens,Saliva,UBERON:0001836,Smoking behaviour measurement,EFO:0005671,Non-tobacco users (NU),Smokeless tobacco user (ST),Participants in this group had used tobacco at least once per week for the previous year.,43,18,6 months,16S,34,Illumina,raw counts,DESeq2,0.05,FALSE,NA,"age,race,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 6b,30 July 2025,Victoria,Victoria,Relative abundance of bacterial OTUs in saliva samples that was statistically significantly different (α = 0.001) between non-users (NU) and smokeless tobacco users (ST).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium",3379134|976|200643|171549|171552|838;1783272|201174|1760|2037|2049|1654;3379134|1224|1236|91347|543|561|562;3379134|1224|28216|206351|481|482;1783272|201174|1760|85007|1653|1716,Complete,KateRasheed
bsdb:38720776/1/1,38720776,laboratory experiment,38720776,10.3389/fphar.2024.1343755,NA,"Chen D., Wang Y., Yang J., Ou W., Lin G., Zeng Z., Lu X., Chen Z., Zou L., Tian Y., Wu A., Keating S.E., Yang Q., Lin C. , Liang Y.",Shenling Baizhu San ameliorates non-alcoholic fatty liver disease in mice by modulating gut microbiota and metabolites,Frontiers in pharmacology,2024,"gut microbiota, metabolic-associated steatotic liver disease, metabolites, non-alcoholic fatty liver disease, traditional Chinese medicine",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,"Combination of ND [normal diet, no CCl₄ (Carbon tetrachloride) injection] and WDC_SLBZS [Western diet, CCl₄ (Carbon tetrachloride) injection + Shenling Baizhu San” (SLBZS)]","WDC [Western diet, CCl₄ (Carbon tetrachloride) injection]",Mice that were fed the Western diet with high sugar and received weekly intraperitoneal CCl₄ (Carbon tetrachloride) injections to induce NAFLD (non-alcoholic fatty liver disease) model.,12,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Supplementary Figure S2C, Table S4",9 October 2025,Tosin,Tosin,"Cladogram showing the significant differentially abundant taxa between groups: ND [normal diet, no CCl₄ (carbon tetrachloride) injection], WDC [Western diet,  CCl₄ (carbon tetrachloride) injection], and WDC+SLBZS [Western diet, CCl₄ (carbon tetrachloride) injection + SLBZS (Shenling Baizhu San)]",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Bordetella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Bordetella|s__Bordetella petrii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium YL45,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium CIEAF 022,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Enterobacteriaceae bacterium bta3-1,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacillati|p__Bacillota|g__Negativibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Thermocrispum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Thermocrispum|s__Thermocrispum municipale,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",3379134|1224|28216|80840|506;1783272|1239|186801|3085636|186803|572511;3379134|1224|28216|80840|506|517;3379134|1224|28216|80840|506|517|94624;3379134|1224|28216|80840|1834205;1783272|1239|186801|186802|1159224;1783272|1239|526524|526525|2810280;1783272|1239|526524|526525|2810280|100883;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|1265478;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|1903412;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;1783272|1239|91061|186826|33958|1578|33959;1783272|1239|1980693;3379134|1224|28216|80840|995019|577310;3379134|1224|28216|80840|995019;1783272|201174|1760|85010|2070|37924;1783272|201174|1760|85010|2070|37924|37926;1783272|1239|526524|526525|2810280|3025755,Complete,KateRasheed
bsdb:38720776/2/1,38720776,laboratory experiment,38720776,10.3389/fphar.2024.1343755,NA,"Chen D., Wang Y., Yang J., Ou W., Lin G., Zeng Z., Lu X., Chen Z., Zou L., Tian Y., Wu A., Keating S.E., Yang Q., Lin C. , Liang Y.",Shenling Baizhu San ameliorates non-alcoholic fatty liver disease in mice by modulating gut microbiota and metabolites,Frontiers in pharmacology,2024,"gut microbiota, metabolic-associated steatotic liver disease, metabolites, non-alcoholic fatty liver disease, traditional Chinese medicine",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,"Combination of WDC [Western diet, CCl₄ (Carbon tetrachloride) injection] and WDC_SLBZS [Western diet, CCl₄ (Carbon tetrachloride) injection + Shenling Baizhu San” (SLBZS)]","ND [normal diet, no CCl₄ (Carbon Tetrachloride) injection]","Mice fed with a normal chow diet [Lab diet 5C02 (5carbondioxide)] with regular drinking water, and injected intraperitoneally with the vehicle control [corn oil only, no CCl₄ (carbon tetrachloride) once per week.",12,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S2C,9 October 2025,Tosin,Tosin,"Cladogram showing the significant differentially abundant taxa between groups: ND [normal diet, no CCl₄ (carbon tetrachloride) injection], WDC [Western diet, CCl₄ (carbon tetrachloride) injection], and WDC+SLBZS [Western diet, CCl₄ (carbon tetrachloride) injection + SLBZS (Shenling Baizhu San)]",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter venetianus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes inops,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Arachidicoccus,,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus|s__Candidatus Arthromitus sp. SFB-mouse,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Elizabethkingia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus murinus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Mucilaginibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Ruegeria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus lutetiensis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Tritonibacter|s__Tritonibacter mobilis,k__Bacillati|p__Candidatus Melainabacteria|c__Vampirovibriophyceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae",3379134|1224|1236|2887326|468|469|52133;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550|239759|1501391;1783272|1239|526524|526525|128827|174708;3379134|976|200643|171549|171552|1283313;3379134|976|1853228|1853229|563835|1769012;;3379134|976|200643|171549;3379134|976|200643;3379134|1224|28216|80840;3379134|29547|3031852|213849;1783272|1239|186801|186802|31979|49082|49118;1783272|1798710|1906119;1783272|1239|186801|186802|31979|49082;1783272|1239|186801|3082768|990719;1783272|1239|186801|3082768;3379134|1224|28216|80840|80864;3379134|1224|28216|80840|80864|283;1783272|1239|186801|3085636|1185407;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;3379134|200940|3031449;3379134|976|117743|200644|2762318|308865;3379134|29547|3031852;1783272|1239|186801|186802|216572|216851|1946507;3379134|976|117743|200644|49546;3379134|976|117743|200644;3379134|1224|1236|135619|28256;3379134|1224|1236|135619|28256|2745;1783272|1239|186801|186802|216572|1892380;1783272|1239|91061|186826|33958|2767887|1622;3379134|1224|1236|135614|32033;3379134|1224|1236|135614;1783272|201174|1760|85006;3379134|976|117747|200666|84566|423349;3379134|976|200643|171549|2005473;3379134|1224|1236|135619;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|75682;3379134|1224|1236|135623|641|657;3379134|976|200643|171549|171552;3379134|1224|28211|204441;3379134|976|200643|171549|171550;3379134|1224|28211|204455|2854170|97050;1783272|1239|186801|186802|216572|3068309;3379134|976|117747|200666;1783272|1239|91061|186826|1300|1301|150055;3379134|1224|28211|204455|31989|2083206|379347;1783272|1798710|3118680;3379134|1224|1236|135623|641;3379134|1224|1236|135623;3379134|976|117743|200644|2762318,Complete,KateRasheed
bsdb:38720776/3/1,38720776,laboratory experiment,38720776,10.3389/fphar.2024.1343755,NA,"Chen D., Wang Y., Yang J., Ou W., Lin G., Zeng Z., Lu X., Chen Z., Zou L., Tian Y., Wu A., Keating S.E., Yang Q., Lin C. , Liang Y.",Shenling Baizhu San ameliorates non-alcoholic fatty liver disease in mice by modulating gut microbiota and metabolites,Frontiers in pharmacology,2024,"gut microbiota, metabolic-associated steatotic liver disease, metabolites, non-alcoholic fatty liver disease, traditional Chinese medicine",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,"Combination of ND [normal diet, no CCl₄ (Carbon Tetrachloride) injection] and WDC [Western diet, CCl₄ (Carbon tetrachloride) injection]","WDC_SLBZS [Western diet, CCl₄ (Carbon tetrachloride) injection + Shenling Baizhu San” (SLBZS)]","Mice that were fed the Western diet (high fat, carbohydrate, and protein content) with a high-sugar drinking solution (fructose + glucose) and given weekly intraperitoneal CCl₄ (carbon tetrachloride) injections to induce NAFLD (non-alcoholic fatty liver disease) like disease, while also receiving daily oral administration of Shenling Baizhu San (SLBZS, 21.8 g/kg) for 6 weeks.",12,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Supplementary Figure S2C, Table S4",10 October 2025,Tosin,Tosin,"Cladogram showing the significant differentially abundant taxa between groups: ND [normal diet, no CCl₄ (carbon tetrachloride) injection], WDC [Western diet, CCl₄ (carbon tetrachloride) injection], and WDC+SLBZS [Western diet, CCl₄ (carbon tetrachloride) injection + SLBZS (Shenling Baizhu San)]",increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum|s__Faecalibaculum rodentium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Parvibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Pirellulales|f__Pirellulaceae,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Pirellulales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia ilealis,k__Metazoa|p__Nematoda|c__Enoplea|o__Trichinellida|f__Trichinellidae|g__Trichinella|s__Trichinella pseudospiralis",1783272|201174|84992;1783272|201174|84998|84999|1643824;1783272|1239|91061;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|526524|526525|128827|1937008;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524|526525|128827|1729679;1783272|1239|526524|526525|128827|1729679|1702221;1783272|201174|84998|84999|84107|1427376;1783272|1239|186801|3082720|186804;3379134|203682|203683|2691354|2691357;3379134|203682|203683|2691354;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3082720|186804|1501226|1115758;33208|6231|119088|6329|6332|6333|6337,Complete,KateRasheed
bsdb:38720776/4/1,38720776,laboratory experiment,38720776,10.3389/fphar.2024.1343755,NA,"Chen D., Wang Y., Yang J., Ou W., Lin G., Zeng Z., Lu X., Chen Z., Zou L., Tian Y., Wu A., Keating S.E., Yang Q., Lin C. , Liang Y.",Shenling Baizhu San ameliorates non-alcoholic fatty liver disease in mice by modulating gut microbiota and metabolites,Frontiers in pharmacology,2024,"gut microbiota, metabolic-associated steatotic liver disease, metabolites, non-alcoholic fatty liver disease, traditional Chinese medicine",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,"ND [normal diet, no CCl₄ (Carbon tetrachloride) injection]","WDC [Western diet, CCl₄ (Carbon tetrachloride) injection]",Mice that were fed the Western diet with high sugar and received weekly intraperitoneal CCl₄ (Carbon tetrachloride) injections to induce NAFLD (non-alcoholic fatty liver disease) model.,6,6,NA,16S,34,Illumina,relative abundances,"ANOVA,Post-Hoc Pairwise",0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 4G and 4H,10 October 2025,Tosin,Tosin,"The relative abundance of significant different taxa between ND [normal diet, no CCl₄ (Carbon tetrachloride) injection] and WDC [Western diet, CCl₄ (Carbon tetrachloride) injection]",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",1783272|1239|186801|3085636|186803|1506553;1783272|1239|526524|526525|2810280|3025755,Complete,KateRasheed
bsdb:38720776/5/1,38720776,laboratory experiment,38720776,10.3389/fphar.2024.1343755,NA,"Chen D., Wang Y., Yang J., Ou W., Lin G., Zeng Z., Lu X., Chen Z., Zou L., Tian Y., Wu A., Keating S.E., Yang Q., Lin C. , Liang Y.",Shenling Baizhu San ameliorates non-alcoholic fatty liver disease in mice by modulating gut microbiota and metabolites,Frontiers in pharmacology,2024,"gut microbiota, metabolic-associated steatotic liver disease, metabolites, non-alcoholic fatty liver disease, traditional Chinese medicine",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,"WDC [Western diet, CCl₄ (Carbon tetrachloride) injection]","WDC_SLBZS [Western diet, CCl₄ (Carbon tetrachloride) injection + Shenling Baizhu San” (SLBZS)]","Mice that were fed the Western diet (high fat, carbohydrate, and protein content) with a high-sugar drinking solution (fructose + glucose) and given weekly intraperitoneal CCl₄ (carbon tetrachloride) injections to induce NAFLD-like disease, while also receiving daily oral administration of Shenling Baizhu San (SLBZS, 21.8 g/kg) for 6 weeks.",6,6,NA,16S,34,Illumina,relative abundances,"ANOVA,Post-Hoc Pairwise",0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 4E and 4F,10 October 2025,Tosin,Tosin,"Relative abundance of significant different taxa between WDC [Western diet, CCl₄ (Carbon tetrachloride) injection] and WDC_SLBZS [Western diet, CCl₄ (Carbon tetrachloride) injection + Shenling Baizhu San” (SLBZS)]",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Parvibacter",1783272|201174|1760|85004|31953|1678;1783272|201174|84998|84999|84107|1427376,Complete,KateRasheed
bsdb:38720776/5/2,38720776,laboratory experiment,38720776,10.3389/fphar.2024.1343755,NA,"Chen D., Wang Y., Yang J., Ou W., Lin G., Zeng Z., Lu X., Chen Z., Zou L., Tian Y., Wu A., Keating S.E., Yang Q., Lin C. , Liang Y.",Shenling Baizhu San ameliorates non-alcoholic fatty liver disease in mice by modulating gut microbiota and metabolites,Frontiers in pharmacology,2024,"gut microbiota, metabolic-associated steatotic liver disease, metabolites, non-alcoholic fatty liver disease, traditional Chinese medicine",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,"WDC [Western diet, CCl₄ (Carbon tetrachloride) injection]","WDC_SLBZS [Western diet, CCl₄ (Carbon tetrachloride) injection + Shenling Baizhu San” (SLBZS)]","Mice that were fed the Western diet (high fat, carbohydrate, and protein content) with a high-sugar drinking solution (fructose + glucose) and given weekly intraperitoneal CCl₄ (carbon tetrachloride) injections to induce NAFLD-like disease, while also receiving daily oral administration of Shenling Baizhu San (SLBZS, 21.8 g/kg) for 6 weeks.",6,6,NA,16S,34,Illumina,relative abundances,"ANOVA,Post-Hoc Pairwise",0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 4H,10 October 2025,Tosin,Tosin,"Relative abundance of significant different taxa between WDC [Western diet, CCl₄ (Carbon tetrachloride) injection] and WDC_SLBZS [Western diet, CCl₄ (Carbon tetrachloride) injection + Shenling Baizhu San” (SLBZS)]",decreased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,1783272|1239|526524|526525|2810280|3025755,Complete,KateRasheed
bsdb:38740280/1/1,38740280,time series / longitudinal observational,38740280,10.1016/j.ijid.2024.107085,NA,"Huang H.L., Lin C.H., Lee M.R., Huang W.C., Sheu C.C., Cheng M.H., Lu P.L., Huang C.H., Yeh Y.T., Yang J.M., Chong I.W., Liao Y.C. , Wang J.Y.",Sputum bacterial microbiota signature as a surrogate for predicting disease progression of nontuberculous mycobacterial lung disease,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2024,"Lung disease, Nontuberculous mycobacterium, Prediction, Progression, Sputum microbiota",Experiment 1,Taiwan,Homo sapiens,Sputum,UBERON:0007311,Pulmonary non-tuberculous mycobacterial infection,MONDO:0018469,Nonprogression,Progression,Nontuberculous mycobacterial lung disease (NTM-LD) progression was defined as either radiographic score increasing or Clinical assessment using COPD assessment score (CAT score) increasing due to Nontuberculous mycobacteria (NTM) and the initiation of antimycobacterial therapy being deemed necessary by the primary care physician.,77,49,3 months,16S,34,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),Kruskall-Wallis",0.001,FALSE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 3B,17 October 2025,Nina Takang,"Nina Takang,Fiddyhamma",Differential abundance of selected genera in progression and nonprogression samples. Box plots represent relative abundances of seven selected genera that differed significantly across progression and nonprogression samples.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles",3379134|1224|28216|80840|119060|32008;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|815|909656;3379134|1224|1236|72274|135621|286;3379134|1224|28211|204457|41297|13687;3379134|1224|28216|80840|2975441|93681,Complete,NA
bsdb:38740280/1/2,38740280,time series / longitudinal observational,38740280,10.1016/j.ijid.2024.107085,NA,"Huang H.L., Lin C.H., Lee M.R., Huang W.C., Sheu C.C., Cheng M.H., Lu P.L., Huang C.H., Yeh Y.T., Yang J.M., Chong I.W., Liao Y.C. , Wang J.Y.",Sputum bacterial microbiota signature as a surrogate for predicting disease progression of nontuberculous mycobacterial lung disease,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2024,"Lung disease, Nontuberculous mycobacterium, Prediction, Progression, Sputum microbiota",Experiment 1,Taiwan,Homo sapiens,Sputum,UBERON:0007311,Pulmonary non-tuberculous mycobacterial infection,MONDO:0018469,Nonprogression,Progression,Nontuberculous mycobacterial lung disease (NTM-LD) progression was defined as either radiographic score increasing or Clinical assessment using COPD assessment score (CAT score) increasing due to Nontuberculous mycobacteria (NTM) and the initiation of antimycobacterial therapy being deemed necessary by the primary care physician.,77,49,3 months,16S,34,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),Kruskall-Wallis",0.001,FALSE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Figure 3B,17 October 2025,Nina Takang,"Nina Takang,Fiddyhamma",Differential abundance of selected genera in progression and nonprogression samples. Box plots represent relative abundances of seven selected genera that differed significantly across progression and nonprogression samples.,decreased,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,95818|2093818|2093825|2171986|1331051,Complete,NA
bsdb:38740280/2/1,38740280,time series / longitudinal observational,38740280,10.1016/j.ijid.2024.107085,NA,"Huang H.L., Lin C.H., Lee M.R., Huang W.C., Sheu C.C., Cheng M.H., Lu P.L., Huang C.H., Yeh Y.T., Yang J.M., Chong I.W., Liao Y.C. , Wang J.Y.",Sputum bacterial microbiota signature as a surrogate for predicting disease progression of nontuberculous mycobacterial lung disease,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2024,"Lung disease, Nontuberculous mycobacterium, Prediction, Progression, Sputum microbiota",Experiment 2,Taiwan,Homo sapiens,Lung,UBERON:0002048,Pulmonary non-tuberculous mycobacterial infection,MONDO:0018469,Nonprogressors,Progressors,"Patients with newly diagnosed NTM-LD (Mycobacterium avium complex, M. abscessus complex, or M. kansasii) who developed disease progression during 2-year follow-up, defined as increasing radiographic score or CAT score due to NTM with initiation of antimycobacterial therapy deemed necessary by primary care physician",77,49,3months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.001,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,"Figure 2B, Table S2",28 October 2025,Nina Takang,Nina Takang,Bacterial genera with significantly increased relative abundance in sputum samples from NTM-LD progressors compared to nonprogressors. These genera show strong statistical significance (P < 0.001) and are associated with disease progression and worse clinical outcomes.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",3379134|1224|28216|80840|119060|32008;3379134|1224|1236|72274|135621|286,Complete,NA
bsdb:38740280/2/2,38740280,time series / longitudinal observational,38740280,10.1016/j.ijid.2024.107085,NA,"Huang H.L., Lin C.H., Lee M.R., Huang W.C., Sheu C.C., Cheng M.H., Lu P.L., Huang C.H., Yeh Y.T., Yang J.M., Chong I.W., Liao Y.C. , Wang J.Y.",Sputum bacterial microbiota signature as a surrogate for predicting disease progression of nontuberculous mycobacterial lung disease,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2024,"Lung disease, Nontuberculous mycobacterium, Prediction, Progression, Sputum microbiota",Experiment 2,Taiwan,Homo sapiens,Lung,UBERON:0002048,Pulmonary non-tuberculous mycobacterial infection,MONDO:0018469,Nonprogressors,Progressors,"Patients with newly diagnosed NTM-LD (Mycobacterium avium complex, M. abscessus complex, or M. kansasii) who developed disease progression during 2-year follow-up, defined as increasing radiographic score or CAT score due to NTM with initiation of antimycobacterial therapy deemed necessary by primary care physician",77,49,3months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.001,NA,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,"Figure 2B, Table S2",28 October 2025,Nina Takang,Nina Takang,"Bacterial genera with decreased relative abundance in sputum samples from NTM-LD progressors compared to nonprogressors. These genera are commonly detected in healthy individuals and their reduced abundance indicates dysbiosis associated with disease progression. Paper text states these organisms ""were more abundant in the nonprogression group.""",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|171552|838;1783272|1239|909932|1843489|31977|29465;3384189|32066|203490|203491|203492|848,Complete,NA
bsdb:38745393/1/1,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 1,Germany,Homo sapiens,Saliva,UBERON:0001836,Phenylketonuria,MONDO:0009861,Control Saliva (Ctrl-S) patients,Phenylketonuria Saliva (PKU-S) patients,Patients diagnosed with Phenylketonuria (PKU) and who stimulated Saliva samples were gotten from.,114,109,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,increased,decreased,NA,NA,NA,decreased,Signature 1,"Appendix Table 5, Figure 2D",13 August 2024,MyleeeA,"MyleeeA,Tosin,WikiWorks",Differential abundant genera in Phenylketonuria (PKU-S) and Control (Ctrl-S) Saliva Patients.,increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|29547|3031852|213849|72294|194;3379134|1224|1236|135625|712|724;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:38745393/1/2,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 1,Germany,Homo sapiens,Saliva,UBERON:0001836,Phenylketonuria,MONDO:0009861,Control Saliva (Ctrl-S) patients,Phenylketonuria Saliva (PKU-S) patients,Patients diagnosed with Phenylketonuria (PKU) and who stimulated Saliva samples were gotten from.,114,109,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,increased,decreased,NA,NA,NA,decreased,Signature 2,"Appendix Table 5, Figure 2D",13 August 2024,MyleeeA,"MyleeeA,Tosin,WikiWorks",Differential abundant genera in Phenylketonuria (PKU-S) and Control (Ctrl-S) Saliva Patients.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum",1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549|171552|1283313;1783272|201174|1760|85009|31957|2801844;3379134|1224|1236|135615|868|2717;1783272|1239|186801|3085636|186803|43996;1783272|201174|84998|84999|1643824|133925;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3082720|186804|1257;1783272|1239|186801|3085636|186803|1213720,Complete,Svetlana up
bsdb:38745393/2/1,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 2,Germany,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Phenylketonuria,MONDO:0009861,Control Subgingival plaque (Ctrl-SP) patients,Phenylketonuria Subgingival plaque (PKU-SP) patients,Patients diagnosed with Phenylketonuria (PKU) and who stimulated Sub gingival plaque samples were gotten from.,113,96,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,decreased,decreased,NA,NA,NA,decreased,Signature 1,"Appendix Table 5, Figure 2D",13 August 2024,MyleeeA,"MyleeeA,Tosin,WikiWorks",Differential abundant genera in Phenylketonuria (PKU-SP) and Control (Ctrl-SP) Subgingival Patients.,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,1783272|201174|1760|2037|2049|1654,Complete,Svetlana up
bsdb:38745393/2/2,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 2,Germany,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Phenylketonuria,MONDO:0009861,Control Subgingival plaque (Ctrl-SP) patients,Phenylketonuria Subgingival plaque (PKU-SP) patients,Patients diagnosed with Phenylketonuria (PKU) and who stimulated Sub gingival plaque samples were gotten from.,113,96,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,decreased,decreased,NA,NA,NA,decreased,Signature 2,"Appendix Table 5, Figure 2D",13 August 2024,MyleeeA,"MyleeeA,Tosin,WikiWorks",Differential abundant genera in Phenylketonuria (PKU-SP) and Control (Ctrl-SP) Subgingival Patients.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",3379134|1224|1236|135625|712|416916;3379134|976|117743|200644|49546|1016;1783272|1239|91061|1385|539738|1378;3384189|32066|203490|203491|1129771|32067,Complete,Svetlana up
bsdb:38745393/3/2,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 3,Germany,Homo sapiens,Saliva,UBERON:0001836,Phenylketonuria,MONDO:0009861,Control Adults Saliva (Ctrl-Adults-S) patients,Phenylketonuria Adults Saliva  (PKU-Adults-S) patients,Adult Patients diagnosed with Phenylketonuria (PKU) and who stimulated Saliva samples were gotten from.,52,50,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,unchanged,decreased,NA,NA,NA,decreased,Signature 2,"Appendix Table 5, Figure 2D",13 August 2024,MyleeeA,"MyleeeA,Tosin,WikiWorks",Differential abundant genera in Phenylketonuria (PKU-Adults-S) and Control (Ctrl-Adults-S) Adult Saliva patients.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum",1783272|201174|1760|2037|2049|1654;1783272|1239|186801|3085636|186803|43996;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3085636|186803|1213720,Complete,Svetlana up
bsdb:38745393/4/1,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 4,Germany,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Phenylketonuria,MONDO:0009861,Control Adults subgingival plaque (Ctrl-Adults-SP) patients,Phenylketonuria Adults subgingival plaque (PKU-Adults-SP) patients,Adult Patients diagnosed with Phenylketonuria (PKU) and who stimulated Sub gingival plaque samples were gotten from.,52,45,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,"Appendix Table 5, Figure 2D",13 August 2024,MyleeeA,"MyleeeA,Tosin,WikiWorks",Differential abundant genera in Phenylketonuria (PKU-Adults-SP) and Control (Ctrl-Adults-SP) Adults Subgingival plaque Patients.,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,1783272|201174|1760|2037|2049|1654,Complete,Svetlana up
bsdb:38745393/5/1,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 5,Germany,Homo sapiens,Saliva,UBERON:0001836,Phenylketonuria,MONDO:0009861,Control Children Saliva (Ctrl-Ch-S) patients,Phenylketonuria Children Saliva (PKU-Ch-S) patients,Children Patients diagnosed with Phenylketonuria (PKU) and who stimulated Saliva samples were gotten from.,62,59,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,"Appendix Table 5 , Figure 2D",13 August 2024,MyleeeA,"MyleeeA,Tosin,WikiWorks",Differential abundant genera in Phenylketonuria Children Saliva (PKU-Ch-S) and Control Children Saliva (Ctrl-Ch-S) Patients,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,3379134|1224|1236|135625|712|724,Complete,Svetlana up
bsdb:38745393/5/2,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 5,Germany,Homo sapiens,Saliva,UBERON:0001836,Phenylketonuria,MONDO:0009861,Control Children Saliva (Ctrl-Ch-S) patients,Phenylketonuria Children Saliva (PKU-Ch-S) patients,Children Patients diagnosed with Phenylketonuria (PKU) and who stimulated Saliva samples were gotten from.,62,59,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,"Appendix Table 5, Figure 2D",13 August 2024,MyleeeA,"MyleeeA,Tosin,WikiWorks",Differential abundant genera in Phenylketonuria Children Saliva (PKU-Ch-S) and Control Children Saliva (Ctrl-Ch-S) Patients,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85009|31957|2801844;1783272|201174|84998|84999|1643824|133925;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3082720|186804|1257;1783272|1239|909932|909929|1843491|970,Complete,Svetlana up
bsdb:38745393/6/1,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 6,Germany,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Phenylketonuria,MONDO:0009861,Control Children subgingival plaque (Ctrl-Ch-SP) patients,Phenylketonuria Children subgingival plaque (PKU-Ch-SP) patients,Children Patients diagnosed with Phenylketonuria (PKU) and who stimulated Sub gingival plaque samples were gotten from.,61,51,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,"Appendix Table 5 , Figure 2D",12 August 2024,MyleeeA,"MyleeeA,Tosin,WikiWorks",Differential abundant genera in Phenylketonuria (PKU-Ch-SP) and Control (Ctrl-Ch-SP) Children Subgingival plague Patients.,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,1783272|201174|1760|2037|2049|1654,Complete,Svetlana up
bsdb:38745393/6/2,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 6,Germany,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Phenylketonuria,MONDO:0009861,Control Children subgingival plaque (Ctrl-Ch-SP) patients,Phenylketonuria Children subgingival plaque (PKU-Ch-SP) patients,Children Patients diagnosed with Phenylketonuria (PKU) and who stimulated Sub gingival plaque samples were gotten from.,61,51,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,"Appendix Table 5 , Figure 2D",12 August 2024,MyleeeA,"MyleeeA,Tosin,WikiWorks",Differential abundant genera in Phenylketonuria (PKU-Ch-SP) and Control (Ctrl-Ch-SP) Children Subgingival plague Patients.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",3379134|1224|1236|135625|712|416916;3379134|976|117743|200644|49546|1016;1783272|1239|91061|1385|539738|1378;3384189|32066|203490|203491|1129771|32067,Complete,Svetlana up
bsdb:38745393/7/2,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 7,Germany,Homo sapiens,Saliva,UBERON:0001836,Phenylketonuria,MONDO:0009861,ChCtrlRel-S [related control children saliva (Healthy siblings of PKU patients)],ChCtrlUnrel-S (unrelated control children saliva) patients,Control Children unrelated to Phenylketonuria (PKU) patients who stimulated saliva samples were gotten from.,12,26,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,decreased,increased,NA,NA,NA,increased,Signature 2,"Appendix Table 5, Figure 2D",13 August 2024,MyleeeA,"Tosin,MyleeeA,WikiWorks",Differential abundant genera in ChCtrlRel-S (related control children saliva) and ChCtrlUnrel-S (unrelated control children saliva) to Phenylketonuria Patients.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,1783272|201174|1760|2037|2049|1654,Complete,NA
bsdb:38745393/8/NA,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 8,Germany,Homo sapiens,Saliva,UBERON:0001836,Phenylketonuria,MONDO:0009861,ChCtrlRel-S [related control children saliva (Healthy siblings of PKU patients)],ChPKU-S (PKU children saliva) patients,Children diagnosed with Phenylketonuria (PKU) and who stimulated Saliva samples were gotten from.,12,59,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,unchanged,unchanged,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:38745393/9/1,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 9,Germany,Homo sapiens,Oral cavity,UBERON:0000167,Phenylketonuria,MONDO:0009861,Control Saliva (Ctrl-S) patients,Control Subgingival plaque (Ctrl-SP) patients,Healthy Controls who stimulated Subgingival plaque samples were gotten from.,114,113,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Appendix Table 10 , Figure 2D",12 August 2024,MyleeeA,"MyleeeA,Tosin,WikiWorks",Differential abundant genera in Control Saliva (Ctrl-S) and Control Subgingival Plague (Ctrl-SP) patients,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976|200643|171549|171552|1283313;1783272|201174|84998|84999|1643824|1380;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|1164882;3379134|1224|28216|206351|481|482;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;33090|35493|3398|72025|3803|3814|508215;1783272|1239|186801|3085636|186803|1213720;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:38745393/9/2,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 9,Germany,Homo sapiens,Oral cavity,UBERON:0000167,Phenylketonuria,MONDO:0009861,Control Saliva (Ctrl-S) patients,Control Subgingival plaque (Ctrl-SP) patients,Healthy Controls who stimulated Subgingival plaque samples were gotten from.,114,113,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Appendix Table 10 , Figure 2D",12 August 2024,MyleeeA,"MyleeeA,Tosin,WikiWorks",Differential abundant genera in Control Saliva (Ctrl-S) and Control Subgingival plague (Ctrl-SP) patients,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",3379134|1224|1236|135625|712|416916;1783272|201174|1760|85009|31957|2801844;3379134|29547|3031852|213849|72294|194;3379134|976|117743|200644|49546|1016;3379134|1224|1236|135615|868|2717;1783272|201174|1760|85007|1653|1716;3384189|32066|203490|203491|203492|848;3379134|1224|28216|206351|481|32257;3384189|32066|203490|203491|1129771|32067;1783272|201174|84998|84999|1643824|133925;1783272|1239|909932|909929|1843491|970;3379134|976|200643|171549|2005525|195950,Complete,Svetlana up
bsdb:38745393/10/1,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 10,Germany,Homo sapiens,Oral cavity,UBERON:0000167,Phenylketonuria,MONDO:0009861,Control Adults Saliva (Ctrl-Adults-S) patients,Control Adults Subgingival plaque (Ctrl-Adults-SP) patients,Healthy Control adults who stimulated Sub gingival plaque samples were gotten from,52,52,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Appendix Table 10 , Figure 2D",12 August 2024,MyleeeA,"MyleeeA,Tosin,WikiWorks",Differential abundant genera in Control Adults Saliva (Ctrl-Adults-S) and Control Adults Subgingival plague (Ctrl-Adults-SP) patients,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976|200643|171549|171552|1283313;1783272|201174|84998|84999|1643824|1380;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135625|712|724;3379134|1224|28216|206351|481|482;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;33090|35493|3398|72025|3803|3814|508215;1783272|1239|186801|3085636|186803|1213720;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:38745393/10/2,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 10,Germany,Homo sapiens,Oral cavity,UBERON:0000167,Phenylketonuria,MONDO:0009861,Control Adults Saliva (Ctrl-Adults-S) patients,Control Adults Subgingival plaque (Ctrl-Adults-SP) patients,Healthy Control adults who stimulated Sub gingival plaque samples were gotten from,52,52,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Appendix Table 10 , Figure 2D",12 August 2024,MyleeeA,"MyleeeA,Tosin,WikiWorks",Differential abundant genera in Control Adults Saliva (Ctrl-Adults-S) and Control Adults Subgingival plague (Ctrl-Adults-SP) patients.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",3379134|1224|1236|135625|712|416916;1783272|201174|1760|85009|31957|2801844;3379134|29547|3031852|213849|72294|194;3379134|976|117743|200644|49546|1016;3379134|1224|1236|135615|868|2717;1783272|201174|1760|85007|1653|1716;3384189|32066|203490|203491|203492|848;1783272|1239|909932|909929|1843491|970;3379134|976|200643|171549|2005525|195950,Complete,Svetlana up
bsdb:38745393/11/1,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 11,Germany,Homo sapiens,Oral cavity,UBERON:0000167,Phenylketonuria,MONDO:0009861,Control Children Saliva (Ctrl-Ch-S) patients,Control Children Subgingival plaque (Ctrl-Ch-SP) patients,Healthy Control Children without PKU who stimulated Sub gingival plaque samples were gotten from.,62,61,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Appendix Table 10, Figure 2D",12 August 2024,MyleeeA,"MyleeeA,Tosin,WikiWorks",Differential abundant genera in Control Children Saliva (Ctrl-Ch-S) and Control children Subgingival plague (Ctrl-Ch-SP) patients.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976|200643|171549|171552|1283313;1783272|201174|84998|84999|1643824|1380;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135625|712|724;3379134|1224|28216|206351|481|482;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;33090|35493|3398|72025|3803|3814|508215;1783272|1239|186801|3085636|186803|1213720;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:38745393/11/2,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 11,Germany,Homo sapiens,Oral cavity,UBERON:0000167,Phenylketonuria,MONDO:0009861,Control Children Saliva (Ctrl-Ch-S) patients,Control Children Subgingival plaque (Ctrl-Ch-SP) patients,Healthy Control Children without PKU who stimulated Sub gingival plaque samples were gotten from.,62,61,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Appendix Table 10 , Figure 2D",12 August 2024,MyleeeA,"MyleeeA,Tosin,WikiWorks",Differential abundant genera in Control Children Saliva (Ctrl-Ch-S) and Control children Subgingival plague (Ctrl-Ch-SP) patients.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",3379134|1224|1236|135625|712|416916;1783272|201174|1760|85009|31957|2801844;3379134|29547|3031852|213849|72294|194;3379134|976|117743|200644|49546|1016;3379134|1224|1236|135615|868|2717;1783272|201174|1760|85007|1653|1716;3384189|32066|203490|203491|203492|848;1783272|1239|909932|909929|1843491|970;3379134|976|200643|171549|2005525|195950,Complete,Svetlana up
bsdb:38745393/12/1,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 12,Germany,Homo sapiens,Oral cavity,UBERON:0000167,Phenylketonuria,MONDO:0009861,Phenylketonuria Saliva (PKU-S) patients,Phenylketonuria Subgingival plaque (PKU-SP) patients,Patients diagnosed with Phenylketonuria (PKU) and who stimulated Sub gingival plaque samples were gotten from.,109,96,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Appendix Table 10 , Figure 2D",12 August 2024,MyleeeA,"MyleeeA,Tosin,WikiWorks",Differential abundant genera in PKU Saliva (PKU-S) and PKU Subgingival plague (PKU-SP) Patient s,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976|200643|171549|171552|1283313;1783272|201174|84998|84999|1643824|1380;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|1164882;3379134|1224|28216|206351|481|482;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;33090|35493|3398|72025|3803|3814|508215;1783272|1239|186801|3085636|186803|1213720;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:38745393/12/2,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 12,Germany,Homo sapiens,Oral cavity,UBERON:0000167,Phenylketonuria,MONDO:0009861,Phenylketonuria Saliva (PKU-S) patients,Phenylketonuria Subgingival plaque (PKU-SP) patients,Patients diagnosed with Phenylketonuria (PKU) and who stimulated Sub gingival plaque samples were gotten from.,109,96,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Appendix Table 10 , Figure 2D",12 August 2024,MyleeeA,"MyleeeA,Tosin,WikiWorks",Differneti abundant genera in PKU Saliva (PKU-S) and PKU Subgingival plague (PKU-SP) Patients.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85009|31957|2801844;3379134|29547|3031852|213849|72294|194;3379134|976|117743|200644|49546|1016;3379134|1224|1236|135615|868|2717;1783272|201174|1760|85007|1653|1716;3384194|508458|649775|649776|3029087|1434006;3384189|32066|203490|203491|203492|848;3379134|1224|28216|206351|481|32257;1783272|201174|84998|84999|1643824|133925;1783272|1239|186801|186802|186807|2740;1783272|1239|909932|909929|1843491|970;3379134|976|200643|171549|2005525|195950,Complete,Svetlana up
bsdb:38745393/13/1,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 13,Germany,Homo sapiens,Oral cavity,UBERON:0000167,Phenylketonuria,MONDO:0009861,Phenylketonuria Adults Saliva (PKU-Adults-S),Phenylketonuria Adults Subgingival plaque (PKU-Adults-SP),Adult Patients diagnosed with Phenylketonuria (PKU) and who stimulated Subgingival plaque samples were gotten from.,50,45,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Appendix Table 10 , Figure 2D",12 August 2024,MyleeeA,"MyleeeA,Tosin,WikiWorks",Differential abundant genera in PKU Adults Saliva (PKU-Adults-S) and PKU Subgingival plague (PKU-Adults-SP) patients.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976|200643|171549|171552|1283313;1783272|201174|84998|84999|1643824|1380;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|1164882;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171552|838;33090|35493|3398|72025|3803|3814|508215;1783272|1239|186801|3085636|186803|1213720;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:38745393/13/2,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 13,Germany,Homo sapiens,Oral cavity,UBERON:0000167,Phenylketonuria,MONDO:0009861,Phenylketonuria Adults Saliva (PKU-Adults-S),Phenylketonuria Adults Subgingival plaque (PKU-Adults-SP),Adult Patients diagnosed with Phenylketonuria (PKU) and who stimulated Subgingival plaque samples were gotten from.,50,45,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Appendix Table 10, Figure 2D",12 August 2024,MyleeeA,"MyleeeA,Tosin,WikiWorks",Differential abundant genera in PKU Adults Saliva (PKU-Adults-S) and PKU Subgingival plague (PKU-Adults-SP) patients.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85009|31957|2801844;3379134|29547|3031852|213849|72294|194;3379134|976|117743|200644|49546|1016;3379134|1224|1236|135615|868|2717;1783272|201174|1760|85007|1653|1716;3384189|32066|203490|203491|203492|848;1783272|201174|84998|84999|1643824|133925;1783272|1239|909932|909929|1843491|970;3379134|976|200643|171549|2005525|195950,Complete,Svetlana up
bsdb:38745393/14/1,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 14,Germany,Homo sapiens,Oral cavity,UBERON:0000167,Phenylketonuria,MONDO:0009861,Phenylketonuria Children Saliva (PKU-Ch-S) patients,Phenylketonuria Children subgingival plaque (PKU-Ch-SP) patients,Children diagnosed with Phenylketonuria (PKU) and who stimulated Subgingival plaque samples were gotten from.,59,51,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Appendix Table 10 , Figure 2D",12 August 2024,MyleeeA,"MyleeeA,Tosin,WikiWorks",Differential abundant genera in PKU children Saliva (PKU-Ch-S) and PKU Children Subgingival plague (PKU-Ch-SP) patients,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976|200643|171549|171552|1283313;1783272|201174|84998|84999|1643824|1380;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|1164882;3379134|1224|28216|206351|481|482;1783272|1239|186801|3085636|186803|265975;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;33090|35493|3398|72025|3803|3814|508215;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:38745393/14/2,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 14,Germany,Homo sapiens,Oral cavity,UBERON:0000167,Phenylketonuria,MONDO:0009861,Phenylketonuria Children Saliva (PKU-Ch-S) patients,Phenylketonuria Children subgingival plaque (PKU-Ch-SP) patients,Children diagnosed with Phenylketonuria (PKU) and who stimulated Subgingival plaque samples were gotten from.,59,51,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Appendix Table 10 , Figure 2D",12 August 2024,MyleeeA,"MyleeeA,Tosin,WikiWorks",Differential abundant genera in PKU children Saliva (PKU-Ch-S) and PKU Children Subgingival plague (PKU-Ch-SP) patients,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85009|31957|2801844;3379134|29547|3031852|213849|72294|194;3379134|976|117743|200644|49546|1016;3379134|1224|1236|135615|868|2717;1783272|201174|1760|85007|1653|1716;3384194|508458|649775|649776|3029087|1434006;3384189|32066|203490|203491|203492|848;3379134|1224|28216|206351|481|32257;1783272|201174|84998|84999|1643824|133925;1783272|1239|909932|909929|1843491|970;3379134|976|200643|171549|2005525|195950,Complete,Svetlana up
bsdb:38745393/15/NA,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 15,Germany,Homo sapiens,Saliva,UBERON:0001836,Phenylketonuria,MONDO:0009861,Control No period (CTRL-S),Phenylketonuria No Period (PKU-S),Patients diagnosed with Phenylketonuria (PKU) without suspected Periodontitis and who stimulated Saliva samples were gotten from.,NA,NA,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:38745393/16/NA,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 16,Germany,Homo sapiens,Saliva,UBERON:0001836,Phenylketonuria,MONDO:0009861,Control Period (CTRL-S),Phenylketonuria Period (PKU-S),Patients diagnosed with Phenylketonuria (PKU) with suspected Periodontitis and who stimulated Saliva samples were gotten from.,NA,NA,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:38745393/17/NA,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 17,Germany,Homo sapiens,Saliva,UBERON:0001836,Phenylketonuria,MONDO:0009861,Phenylketonuria No Period (PKU-S),Phenylketonuria Period (PKU-S),Patients diagnosed with Phenylketonuria (PKU) with suspected Periodontitis and who stimulated Saliva samples were gotten from.,NA,NA,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:38745393/18/1,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 18,Germany,Homo sapiens,Saliva,UBERON:0001836,Phenylketonuria,MONDO:0009861,CtrlRel-S (control related saliva),PKU-Rel-S (Phenylketonuria related saliva) patients,Controls related to Phenylketonuria (PKU) patients who stimulated saliva samples were gotten from.,NA,NA,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Appendix Table 4,14 January 2025,Tosin,"Tosin,WikiWorks",Differential abundant phylum between Ctrl-Rel-S (Control related saliva) patients and PKU-Rel-S (Phenylketonuria related saliva) patients,increased,"k__Pseudomonadati|p__Campylobacterota,,k__Pseudomonadati|p__Spirochaetota",3379134|29547;;3379134|203691,Complete,Svetlana up
bsdb:38745393/18/2,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 18,Germany,Homo sapiens,Saliva,UBERON:0001836,Phenylketonuria,MONDO:0009861,CtrlRel-S (control related saliva),PKU-Rel-S (Phenylketonuria related saliva) patients,Controls related to Phenylketonuria (PKU) patients who stimulated saliva samples were gotten from.,NA,NA,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Appendix Table 4,14 January 2025,Tosin,"Tosin,WikiWorks",Differential abundant phylum between Ctrl-Rel-S (Control related saliva) patients and PKU-Rel-S (Phenylketonuria related saliva) patients.,decreased,k__Bacillati|p__Actinomycetota,1783272|201174,Complete,Svetlana up
bsdb:38745393/19/1,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 19,Germany,Homo sapiens,Saliva,UBERON:0001836,Phenylketonuria,MONDO:0009861,CtrlRel-SP (control related subgingival plaque) patients,PKU-Rel-SP (Phenylketonuria related subgingival plaque) patients,Controls related to Phenylketonuria (PKU) patients who stimulated subgingival plaque samples were gotten from.,NA,NA,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Appendix Table 4,14 January 2025,Tosin,"Tosin,WikiWorks",Differential abundant phylum between Ctrl-Rel-SP (Control related subgingival plaque) patients and PKU-Rel-SP (Phenylketonuria related subgingival plaque) patients.,increased,k__Bacillati|p__Actinomycetota,1783272|201174,Complete,Svetlana up
bsdb:38745393/19/2,38745393,"cross-sectional observational, not case-control",38745393,10.1111/jcpe.13998,NA,"Bingöl M., Cardilli A., Bingöl A.C., Löber U., Bang C., Franke A., Bartzela T., Beblo S., Mönch E., Stolz S., Schaefer A.S., Forslund S.K. , Richter G.M.",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 19,Germany,Homo sapiens,Saliva,UBERON:0001836,Phenylketonuria,MONDO:0009861,CtrlRel-SP (control related subgingival plaque) patients,PKU-Rel-SP (Phenylketonuria related subgingival plaque) patients,Controls related to Phenylketonuria (PKU) patients who stimulated subgingival plaque samples were gotten from.,NA,NA,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Appendix Table 4,14 January 2025,Tosin,"Tosin,WikiWorks",Differential abundant phylum between Ctrl-Rel-SP (Control related subgingival plaque) patients and PKU-Rel-SP (Phenylketonuria related subgingival plaque) patients.,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Fusobacteriati|p__Fusobacteriota",3379134|976;3384189|32066,Complete,Svetlana up
bsdb:38760705/1/1,38760705,case-control,38760705,10.1186/s12866-024-03329-x,NA,"Yang T., Li G., Xu Y., He X., Song B. , Cao Y.",Characterization of the gut microbiota in polycystic ovary syndrome with dyslipidemia,BMC microbiology,2024,"Dyslipidemia, Gut microbiota, Polycystic ovary syndrome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control,Polycystic ovary syndrome (PCOS),Patients with Polycystic ovary syndrome (PCOS) as diagnosed by the revised 2003 Rotterdam criteria.,16,18,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 1,Figure 3A,17 July 2025,Victoria,"Victoria,Tosin",Linear discriminant analysis effect size (LEfSe) and Cladogram analyses of significantly different classification units between Control and Polycystic ovary syndrome (PCOS).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter ursingii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:56,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium GAM79,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae",3379134|1224|1236|2887326|468|469;3379134|1224|1236|2887326|468|469|108980;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171552|1283313;1783272|1239|186801|3085636|186803|207244;1783272|1239;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|28111;3379134|976|200643|171549|815|816|338188;3379134|976|200643|171549|815|816|46506;3379134|976|200643;3379134|976;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|871665;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|186802|3085642;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801;1783272|201174|84998|84999|84107|102106;3379134|1224|28216|80840|80864|283;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|3570277|116085;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|186801|3085636|186803|189330;3379134|1224|1236|91347|543|547;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|1263031;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|1407607;1783272|1239|1737404|1737405|1570339|162290;1783272|1239|186801|3082720|186804|1505657;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|2109691;1783272|1239|186801|3085636;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|909929|1843491|158846|437897;3379134|1224|1236|2887326|468;1783272|1239|909932;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|815|909656|310298;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|171552;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|360807;3379134|1224|28216|80840|995019,Complete,KateRasheed
bsdb:38760705/1/2,38760705,case-control,38760705,10.1186/s12866-024-03329-x,NA,"Yang T., Li G., Xu Y., He X., Song B. , Cao Y.",Characterization of the gut microbiota in polycystic ovary syndrome with dyslipidemia,BMC microbiology,2024,"Dyslipidemia, Gut microbiota, Polycystic ovary syndrome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control,Polycystic ovary syndrome (PCOS),Patients with Polycystic ovary syndrome (PCOS) as diagnosed by the revised 2003 Rotterdam criteria.,16,18,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 2,Figure 3A,17 July 2025,Victoria,"Victoria,Tosin",Linear discriminant analysis effect size (LEfSe) and Cladogram analyses of significantly different classification units between Control and Polycystic ovary syndrome (PCOS).,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",1783272|1239|526524|526525|128827;3379134|1224|1236;3379134|1224|1236|72274|135621;3379134|1224|1236|72274;3379134|1224;3379134|1224|1236|72274|135621|286,Complete,KateRasheed
bsdb:38760705/2/1,38760705,case-control,38760705,10.1186/s12866-024-03329-x,NA,"Yang T., Li G., Xu Y., He X., Song B. , Cao Y.",Characterization of the gut microbiota in polycystic ovary syndrome with dyslipidemia,BMC microbiology,2024,"Dyslipidemia, Gut microbiota, Polycystic ovary syndrome",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,"Rare dyslipidemia,Polycystic ovary syndrome","ORPHANET:101953,EFO:0000660",Control,Polycystic ovary syndrome & Dyslipidemia (PCOS.D),Patients with Dyslipidemia and Polycystic ovary syndrome (PCOS) as diagnosed by the revised 2003 Rotterdam criteria.,16,18,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3B,17 July 2025,Victoria,"Victoria,Tosin",LEfSe and Cladogram analyses of significantly different classification units between Control and PCOS.D.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,s__swine fecal bacterium SD-Pec10",3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549;3379134|976|200643|171549|815|816|46506;3379134|976|200643;3379134|976;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|33042;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3082720|186804|1505657;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|28050;3379134|976|200643|171549|171552|2974265|363265;3379134|976|200643|171549|2005525|375288|46503;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|815|909656|310298;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|216572|292632;3379134|1224|28216|80840|995019;1783272|1239|186801|3082720|186804|1505652;1783272|1239|526524|526525|2810281|191303;1783272|1239|909932|1843489|31977;621360,Complete,KateRasheed
bsdb:38760705/2/2,38760705,case-control,38760705,10.1186/s12866-024-03329-x,NA,"Yang T., Li G., Xu Y., He X., Song B. , Cao Y.",Characterization of the gut microbiota in polycystic ovary syndrome with dyslipidemia,BMC microbiology,2024,"Dyslipidemia, Gut microbiota, Polycystic ovary syndrome",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,"Rare dyslipidemia,Polycystic ovary syndrome","ORPHANET:101953,EFO:0000660",Control,Polycystic ovary syndrome & Dyslipidemia (PCOS.D),Patients with Dyslipidemia and Polycystic ovary syndrome (PCOS) as diagnosed by the revised 2003 Rotterdam criteria.,16,18,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 3B,17 July 2025,Victoria,"Victoria,Tosin",LEfSe and Cladogram analyses of significantly different classification units between Control and PCOS.D.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Bacilli|o__Staphylococcales",1783272|1239|186801|3085636|186803|1766253;3379134|976|117743|200644|49546;3379134|976|117743|200644;3379134|976|117743|200644|49546|237;3379134|1224|1236;3379134|1224;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;1783272|1239|186801|186802|216572|1535;1783272|1239|91061|3120442,Complete,KateRasheed
bsdb:38760705/3/1,38760705,case-control,38760705,10.1186/s12866-024-03329-x,NA,"Yang T., Li G., Xu Y., He X., Song B. , Cao Y.",Characterization of the gut microbiota in polycystic ovary syndrome with dyslipidemia,BMC microbiology,2024,"Dyslipidemia, Gut microbiota, Polycystic ovary syndrome",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,"Polycystic ovary syndrome,Rare dyslipidemia","EFO:0000660,ORPHANET:101953",Polycystic ovary syndrome (PCOS),Polycystic ovary syndrome & Dyslipidemia(PCOS.D),Patients with Dyslipidemia and Polycystic ovary syndrome (PCOS) as diagnosed by the revised 2003 Rotterdam criteria.,18,18,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3C,17 July 2025,Victoria,Victoria,LEfSe and Cladogram analyses of significantly different classification units between PCOS and PCOS.D.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,s__swine fecal bacterium SD-Pec10,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella",1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802;1783272|1239|186801|186802|31979;621360;1783272|1239|909932|909929|1843491|52225,Complete,KateRasheed
bsdb:38760705/3/2,38760705,case-control,38760705,10.1186/s12866-024-03329-x,NA,"Yang T., Li G., Xu Y., He X., Song B. , Cao Y.",Characterization of the gut microbiota in polycystic ovary syndrome with dyslipidemia,BMC microbiology,2024,"Dyslipidemia, Gut microbiota, Polycystic ovary syndrome",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,"Polycystic ovary syndrome,Rare dyslipidemia","EFO:0000660,ORPHANET:101953",Polycystic ovary syndrome (PCOS),Polycystic ovary syndrome & Dyslipidemia(PCOS.D),Patients with Dyslipidemia and Polycystic ovary syndrome (PCOS) as diagnosed by the revised 2003 Rotterdam criteria.,18,18,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 3C,17 July 2025,Victoria,Victoria,LEfSe and Cladogram analyses of significantly different classification units between PCOS and PCOS.D.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter ursingii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia",1783272|1239|186801|3085636|186803|1506553;3379134|1224|1236|135614|32033;3379134|1224|1236|135614|32033|40323;3379134|1224|1236|2887326|468;3379134|1224|1236|91347|543|547;3379134|1224|1236|135614;1783272|1239|186801|3085636|186803|841|360807;3379134|1224|1236|2887326|468|469;3379134|1224|1236|2887326|468|469|108980;1783272|1239|526524|526525|128827|1573535;3379134|1224|28216|80840|80864|283;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572;1783272|1239|186801|186802;1783272|1239|186801,Complete,KateRasheed
bsdb:38760705/4/1,38760705,case-control,38760705,10.1186/s12866-024-03329-x,NA,"Yang T., Li G., Xu Y., He X., Song B. , Cao Y.",Characterization of the gut microbiota in polycystic ovary syndrome with dyslipidemia,BMC microbiology,2024,"Dyslipidemia, Gut microbiota, Polycystic ovary syndrome",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Aspartate aminotransferase measurement,EFO:0004736,Aspartate aminotransferase__AST (Decreased),Aspartate aminotransferase__AST (Increased),High levels of Aspartate aminotransferase(AST).,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,21 July 2025,Victoria,Victoria,Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,3379134|1224|1236|72274|135621|286,Complete,KateRasheed
bsdb:38760705/5/1,38760705,case-control,38760705,10.1186/s12866-024-03329-x,NA,"Yang T., Li G., Xu Y., He X., Song B. , Cao Y.",Characterization of the gut microbiota in polycystic ovary syndrome with dyslipidemia,BMC microbiology,2024,"Dyslipidemia, Gut microbiota, Polycystic ovary syndrome",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Low density lipoprotein cholesterol measurement,EFO:0004611,Low-density lipoprotein cholesterol__LDL-C (Decreased),Low-density lipoprotein cholesterol__LDL-C (Increased),"Increased levels of Low-density lipoprotein cholesterol (LDL-C), short-chain fatty acids(SCFAs).",NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,21 July 2025,Victoria,Victoria,Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,1783272|1239|186801|3085636|186803|1766253,Complete,KateRasheed
bsdb:38760705/5/2,38760705,case-control,38760705,10.1186/s12866-024-03329-x,NA,"Yang T., Li G., Xu Y., He X., Song B. , Cao Y.",Characterization of the gut microbiota in polycystic ovary syndrome with dyslipidemia,BMC microbiology,2024,"Dyslipidemia, Gut microbiota, Polycystic ovary syndrome",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Low density lipoprotein cholesterol measurement,EFO:0004611,Low-density lipoprotein cholesterol__LDL-C (Decreased),Low-density lipoprotein cholesterol__LDL-C (Increased),"Increased levels of Low-density lipoprotein cholesterol (LDL-C), short-chain fatty acids(SCFAs).",NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5A,21 July 2025,Victoria,Victoria,Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella",3379134|1224|1236|72274|135621|286;1783272|1239|526524|526525|128827|1573535;3379134|1224|28216|80840|995019|577310,Complete,KateRasheed
bsdb:38760705/6/1,38760705,case-control,38760705,10.1186/s12866-024-03329-x,NA,"Yang T., Li G., Xu Y., He X., Song B. , Cao Y.",Characterization of the gut microbiota in polycystic ovary syndrome with dyslipidemia,BMC microbiology,2024,"Dyslipidemia, Gut microbiota, Polycystic ovary syndrome",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,High density lipoprotein cholesterol measurement,EFO:0004612,High-density lipoprotein cholesterol__HDL-C (Decreased),High-density lipoprotein cholesterol__HDL-C (Increased),Increased levels of High-density lipoprotein cholesterol (HDL-C).,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,21 July 2025,Victoria,Victoria,Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,3379134|1224|28216|80840|506|222,Complete,KateRasheed
bsdb:38760705/6/2,38760705,case-control,38760705,10.1186/s12866-024-03329-x,NA,"Yang T., Li G., Xu Y., He X., Song B. , Cao Y.",Characterization of the gut microbiota in polycystic ovary syndrome with dyslipidemia,BMC microbiology,2024,"Dyslipidemia, Gut microbiota, Polycystic ovary syndrome",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,High density lipoprotein cholesterol measurement,EFO:0004612,High-density lipoprotein cholesterol__HDL-C (Decreased),High-density lipoprotein cholesterol__HDL-C (Increased),Increased levels of High-density lipoprotein cholesterol (HDL-C).,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5A,21 July 2025,Victoria,Victoria,Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella",1783272|201174|1760|85004|31953|1678;3379134|1224|28216|80840|995019|577310,Complete,KateRasheed
bsdb:38760705/7/1,38760705,case-control,38760705,10.1186/s12866-024-03329-x,NA,"Yang T., Li G., Xu Y., He X., Song B. , Cao Y.",Characterization of the gut microbiota in polycystic ovary syndrome with dyslipidemia,BMC microbiology,2024,"Dyslipidemia, Gut microbiota, Polycystic ovary syndrome",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Triglyceride measurement,EFO:0004530,Triglyceride__TG (Decreased),Triglyceride__TG (Increased),Increased levels of Triglyceride (TG).,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,21 July 2025,Victoria,Victoria,Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|1263,Complete,KateRasheed
bsdb:38760705/8/1,38760705,case-control,38760705,10.1186/s12866-024-03329-x,NA,"Yang T., Li G., Xu Y., He X., Song B. , Cao Y.",Characterization of the gut microbiota in polycystic ovary syndrome with dyslipidemia,BMC microbiology,2024,"Dyslipidemia, Gut microbiota, Polycystic ovary syndrome",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Total cholesterol measurement,EFO:0004574,Total cholesterol__TC (Decreased),Total cholesterol__TC (Increased),Increased levels of Triglyceride (TC).,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,21 July 2025,Victoria,Victoria,Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,3379134|1224|28216|80840|506|222,Complete,KateRasheed
bsdb:38760705/8/2,38760705,case-control,38760705,10.1186/s12866-024-03329-x,NA,"Yang T., Li G., Xu Y., He X., Song B. , Cao Y.",Characterization of the gut microbiota in polycystic ovary syndrome with dyslipidemia,BMC microbiology,2024,"Dyslipidemia, Gut microbiota, Polycystic ovary syndrome",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Total cholesterol measurement,EFO:0004574,Total cholesterol__TC (Decreased),Total cholesterol__TC (Increased),Increased levels of Triglyceride (TC).,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5A,21 July 2025,Victoria,Victoria,Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella",1783272|1239|186801|186802|216572|216851;1783272|1239|526524|526525|128827|1573535;3379134|1224|28216|80840|995019|577310,Complete,KateRasheed
bsdb:38760705/9/1,38760705,case-control,38760705,10.1186/s12866-024-03329-x,NA,"Yang T., Li G., Xu Y., He X., Song B. , Cao Y.",Characterization of the gut microbiota in polycystic ovary syndrome with dyslipidemia,BMC microbiology,2024,"Dyslipidemia, Gut microbiota, Polycystic ovary syndrome",Experiment 9,China,Homo sapiens,Feces,UBERON:0001988,HOMA-IR,EFO:0004501,Homeostatic model assessment for insulin resistance__HOMA-IR (Decreased),Homeostatic model assessment for insulin resistance__HOMA-IR (Increased),Increased levels of Homeostatic model assessment for insulin resistance (HOMA-IR).,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,21 July 2025,Victoria,Victoria,Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,3379134|976|200643|171549|2005525|375288,Complete,KateRasheed
bsdb:38760705/10/1,38760705,case-control,38760705,10.1186/s12866-024-03329-x,NA,"Yang T., Li G., Xu Y., He X., Song B. , Cao Y.",Characterization of the gut microbiota in polycystic ovary syndrome with dyslipidemia,BMC microbiology,2024,"Dyslipidemia, Gut microbiota, Polycystic ovary syndrome",Experiment 10,China,Homo sapiens,Feces,UBERON:0001988,Hyperproinsulinemia,EFO:0009650,Fasting plasma insulin__FINS (Decreased),Fasting plasma insulin__FINS (Increased),Increased levels of Fasting plasma insulin (FINS).,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,21 July 2025,Victoria,Victoria,Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,3379134|976|200643|171549|2005525|375288,Complete,KateRasheed
bsdb:38760705/11/1,38760705,case-control,38760705,10.1186/s12866-024-03329-x,NA,"Yang T., Li G., Xu Y., He X., Song B. , Cao Y.",Characterization of the gut microbiota in polycystic ovary syndrome with dyslipidemia,BMC microbiology,2024,"Dyslipidemia, Gut microbiota, Polycystic ovary syndrome",Experiment 11,China,Homo sapiens,Feces,UBERON:0001988,Dehydroepiandrosterone measurement,EFO:0010240,Dehydroepiandrosterone__DHEA (Decreased),Dehydroepiandrosterone__DHEA (Increased),Increased levels of Dehydroepiandrosterone (DHEA).,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,21 July 2025,Victoria,Victoria,Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|572511,Complete,KateRasheed
bsdb:38760705/12/1,38760705,case-control,38760705,10.1186/s12866-024-03329-x,NA,"Yang T., Li G., Xu Y., He X., Song B. , Cao Y.",Characterization of the gut microbiota in polycystic ovary syndrome with dyslipidemia,BMC microbiology,2024,"Dyslipidemia, Gut microbiota, Polycystic ovary syndrome",Experiment 12,China,Homo sapiens,Feces,UBERON:0001988,Sex hormone-binding globulin measurement,EFO:0004696,Sex hormone-binding globulin__SHBG (Decreased),Sex hormone-binding globulin__SHBG (Increased),Increased levels of Sex hormone-binding globulin (SHBG).,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,21 July 2025,Victoria,Victoria,Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|1239|186801|186802|216572|216851;1783272|201174|1760|85004|31953|1678,Complete,KateRasheed
bsdb:38760705/12/2,38760705,case-control,38760705,10.1186/s12866-024-03329-x,NA,"Yang T., Li G., Xu Y., He X., Song B. , Cao Y.",Characterization of the gut microbiota in polycystic ovary syndrome with dyslipidemia,BMC microbiology,2024,"Dyslipidemia, Gut microbiota, Polycystic ovary syndrome",Experiment 12,China,Homo sapiens,Feces,UBERON:0001988,Sex hormone-binding globulin measurement,EFO:0004696,Sex hormone-binding globulin__SHBG (Decreased),Sex hormone-binding globulin__SHBG (Increased),Increased levels of Sex hormone-binding globulin (SHBG).,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5A,21 July 2025,Victoria,Victoria,Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,3379134|1224|28216|80840|119060|48736,Complete,KateRasheed
bsdb:38760705/13/1,38760705,case-control,38760705,10.1186/s12866-024-03329-x,NA,"Yang T., Li G., Xu Y., He X., Song B. , Cao Y.",Characterization of the gut microbiota in polycystic ovary syndrome with dyslipidemia,BMC microbiology,2024,"Dyslipidemia, Gut microbiota, Polycystic ovary syndrome",Experiment 13,China,Homo sapiens,Feces,UBERON:0001988,Hyperpituitarism,EFO:1000973,Luteinizing hormone/Follicle-stimulating hormone__LH/FSH (Decreased),Luteinizing hormone/Follicle-stimulating hormone__LH/FSH (Increased),Increased levels of Luteinizing hormone/Follicle-stimulating hormone (LH/FSH).,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,21 July 2025,Victoria,Victoria,Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|2005525|375288,Complete,KateRasheed
bsdb:38760705/13/2,38760705,case-control,38760705,10.1186/s12866-024-03329-x,NA,"Yang T., Li G., Xu Y., He X., Song B. , Cao Y.",Characterization of the gut microbiota in polycystic ovary syndrome with dyslipidemia,BMC microbiology,2024,"Dyslipidemia, Gut microbiota, Polycystic ovary syndrome",Experiment 13,China,Homo sapiens,Feces,UBERON:0001988,Hyperpituitarism,EFO:1000973,Luteinizing hormone/Follicle-stimulating hormone__LH/FSH (Decreased),Luteinizing hormone/Follicle-stimulating hormone__LH/FSH (Increased),Increased levels of Luteinizing hormone/Follicle-stimulating hormone (LH/FSH).,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5A,22 July 2025,Victoria,Victoria,Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,3379134|1224|1236|72274|135621|286,Complete,KateRasheed
bsdb:38760705/14/1,38760705,case-control,38760705,10.1186/s12866-024-03329-x,NA,"Yang T., Li G., Xu Y., He X., Song B. , Cao Y.",Characterization of the gut microbiota in polycystic ovary syndrome with dyslipidemia,BMC microbiology,2024,"Dyslipidemia, Gut microbiota, Polycystic ovary syndrome",Experiment 14,China,Homo sapiens,Feces,UBERON:0001988,Follicle stimulating hormone measurement,EFO:0004768,Follicle-stimulating hormone__FSH (Decreased),Follicle-stimulating hormone__FSH (Increased),Increased levels of Follicle-stimulating hormone (FSH).,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,22 July 2025,Victoria,Victoria,Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|31979|1485,Complete,KateRasheed
bsdb:38760705/15/1,38760705,case-control,38760705,10.1186/s12866-024-03329-x,NA,"Yang T., Li G., Xu Y., He X., Song B. , Cao Y.",Characterization of the gut microbiota in polycystic ovary syndrome with dyslipidemia,BMC microbiology,2024,"Dyslipidemia, Gut microbiota, Polycystic ovary syndrome",Experiment 15,China,Homo sapiens,Feces,UBERON:0001988,Luteinizing hormone measurement,EFO:0007002,Luteinizing hormone__LH (Decreased),Luteinizing hormone__LH (Increased),Increased levels of Luteinizing hormone (LH).,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,22 July 2025,Victoria,Victoria,Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|216572|1263,Complete,KateRasheed
bsdb:38760705/15/2,38760705,case-control,38760705,10.1186/s12866-024-03329-x,NA,"Yang T., Li G., Xu Y., He X., Song B. , Cao Y.",Characterization of the gut microbiota in polycystic ovary syndrome with dyslipidemia,BMC microbiology,2024,"Dyslipidemia, Gut microbiota, Polycystic ovary syndrome",Experiment 15,China,Homo sapiens,Feces,UBERON:0001988,Luteinizing hormone measurement,EFO:0007002,Luteinizing hormone__LH (Decreased),Luteinizing hormone__LH (Increased),Increased levels of Luteinizing hormone (LH).,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5A,22 July 2025,Victoria,Victoria,Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,3379134|1224|1236|72274|135621|286,Complete,KateRasheed
bsdb:38760705/16/1,38760705,case-control,38760705,10.1186/s12866-024-03329-x,NA,"Yang T., Li G., Xu Y., He X., Song B. , Cao Y.",Characterization of the gut microbiota in polycystic ovary syndrome with dyslipidemia,BMC microbiology,2024,"Dyslipidemia, Gut microbiota, Polycystic ovary syndrome",Experiment 16,China,Homo sapiens,Feces,UBERON:0001988,Estradiol measurement,EFO:0004697,Estradiol__E2 (Decreased),Estradiol__E2 (Increased),Increased levels of Estradiol (E2),NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,21 December 2025,Tosin,Tosin,Correlations of gut microbial genera and clinical parameters. Spot colors indicate the R value of Spearman correlation between clinical parameters and gut microbial compositions.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,3379134|1224|28216|80840|80864|283,Complete,KateRasheed
bsdb:38772541/1/1,38772541,laboratory experiment,38772541,10.5534/wjmh.230337,NA,"Xu Z., Wang S., Liu C., Kang J., Pan Y., Zhang Z., Zhou H., Xu M., Li X., Wang H., Niu S., Liu L., Sun D. , Liu X.",The Role of Gut Microbiota in Male Erectile Dysfunction of Rats,The world journal of men's health,2025,"Diet, high-fat, Erectile dysfunction, Gastrointestinal microbiome, Inflammation, Metabolomics",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Normal Diet (ND),Long-term high-fat diet (HFD),"The mice in the high-fat diet (HFD) groups were fed a HFD (carbohydrate, 20%; protein, 20%; fat, 60%; Research Diets). The treatment lasted for 24 weeks",6,6,NA,16S,34,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),T-Test",0.05,FALSE,NA,NA,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 1,Figure 2K,18 March 2025,MyleeeA,MyleeeA,Comparison of genus abundance between Normal Diet and High Fat Diet groups.,increased,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,3379134|200940|3031449|213115|194924|872,Complete,Svetlana up
bsdb:38772541/1/4,38772541,laboratory experiment,38772541,10.5534/wjmh.230337,NA,"Xu Z., Wang S., Liu C., Kang J., Pan Y., Zhang Z., Zhou H., Xu M., Li X., Wang H., Niu S., Liu L., Sun D. , Liu X.",The Role of Gut Microbiota in Male Erectile Dysfunction of Rats,The world journal of men's health,2025,"Diet, high-fat, Erectile dysfunction, Gastrointestinal microbiome, Inflammation, Metabolomics",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Normal Diet (ND),Long-term high-fat diet (HFD),"The mice in the high-fat diet (HFD) groups were fed a HFD (carbohydrate, 20%; protein, 20%; fat, 60%; Research Diets). The treatment lasted for 24 weeks",6,6,NA,16S,34,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),T-Test",0.05,FALSE,NA,NA,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 4,Figure 2 (H and J),18 March 2025,MyleeeA,MyleeeA,Comparison of genus abundance between Normal Diet and High Fat Diet groups.,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",3379134|976;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:38772541/3/1,38772541,laboratory experiment,38772541,10.5534/wjmh.230337,NA,"Xu Z., Wang S., Liu C., Kang J., Pan Y., Zhang Z., Zhou H., Xu M., Li X., Wang H., Niu S., Liu L., Sun D. , Liu X.",The Role of Gut Microbiota in Male Erectile Dysfunction of Rats,The world journal of men's health,2025,"Diet, high-fat, Erectile dysfunction, Gastrointestinal microbiome, Inflammation, Metabolomics",Experiment 3,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Normal Diet-Fecal Microbiota Transplantation (ND-FMT),High-fat diet-Fecal Microbiota Transplantation (HFD-FMT),The mice in the High Fat Diet Fecal Microbiota Transplantation (HFD-FMT) group were fed fecal microbiota liquid prepared from the feces of rats on HFD.,5,5,NA,16S,34,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),T-Test",0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,"Figure 4 G, H and I",18 March 2025,MyleeeA,MyleeeA,Genus analysis of intestinal microbiota in Normal Diet FMT and High Fat Diet FMT.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum",1783272|1239|186801|186802|31979|1485;3379134|200940|3031449|213115|194924|872;3379134|200930|68337|191393|2945020|248038,Complete,Svetlana up
bsdb:38772541/3/2,38772541,laboratory experiment,38772541,10.5534/wjmh.230337,NA,"Xu Z., Wang S., Liu C., Kang J., Pan Y., Zhang Z., Zhou H., Xu M., Li X., Wang H., Niu S., Liu L., Sun D. , Liu X.",The Role of Gut Microbiota in Male Erectile Dysfunction of Rats,The world journal of men's health,2025,"Diet, high-fat, Erectile dysfunction, Gastrointestinal microbiome, Inflammation, Metabolomics",Experiment 3,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Normal Diet-Fecal Microbiota Transplantation (ND-FMT),High-fat diet-Fecal Microbiota Transplantation (HFD-FMT),The mice in the High Fat Diet Fecal Microbiota Transplantation (HFD-FMT) group were fed fecal microbiota liquid prepared from the feces of rats on HFD.,5,5,NA,16S,34,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),T-Test",0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,"Figure 4 J, K, L and M",19 March 2025,MyleeeA,MyleeeA,Genus analysis of intestinal microbiota in Normal Diet FMT and High Fat Diet FMT.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1253;3379134|976|200643|171549|1853231|283168;3379134|29547|3031852|213849|72293|209,Complete,Svetlana up
bsdb:38772541/4/1,38772541,laboratory experiment,38772541,10.5534/wjmh.230337,NA,"Xu Z., Wang S., Liu C., Kang J., Pan Y., Zhang Z., Zhou H., Xu M., Li X., Wang H., Niu S., Liu L., Sun D. , Liu X.",The Role of Gut Microbiota in Male Erectile Dysfunction of Rats,The world journal of men's health,2025,"Diet, high-fat, Erectile dysfunction, Gastrointestinal microbiome, Inflammation, Metabolomics",Experiment 4,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Normal Diet-Fecal Microbiota Transplantation (ND-FMT),High-fat diet-Fecal Microbiota Transplantation (HFD-FMT),The mice in the High Fat Diet Fecal Microbiota Transplantation (HFD-FMT) group were fed fecal microbiota liquid prepared from the feces of rats on HFD.,5,5,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 4F,19 March 2025,MyleeeA,MyleeeA,Differential analysis of intestinal microbiota in Normal Diet FMT and High Fat Diet FMT.,increased,",k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales,k__Pseudomonadati|p__Deferribacterota,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum",;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;3379134|200930|68337|191393|191394;3379134|200930|68337;28221;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;1783272|1239|186801|186802;1783272|201174|1760|85006|1268;1783272|1239|186801|186802|216572;3379134|200930|68337|191393;3379134|200930;3379134|200930|68337|191393|2945020|248038,Complete,Svetlana up
bsdb:38772541/4/2,38772541,laboratory experiment,38772541,10.5534/wjmh.230337,NA,"Xu Z., Wang S., Liu C., Kang J., Pan Y., Zhang Z., Zhou H., Xu M., Li X., Wang H., Niu S., Liu L., Sun D. , Liu X.",The Role of Gut Microbiota in Male Erectile Dysfunction of Rats,The world journal of men's health,2025,"Diet, high-fat, Erectile dysfunction, Gastrointestinal microbiome, Inflammation, Metabolomics",Experiment 4,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Normal Diet-Fecal Microbiota Transplantation (ND-FMT),High-fat diet-Fecal Microbiota Transplantation (HFD-FMT),The mice in the High Fat Diet Fecal Microbiota Transplantation (HFD-FMT) group were fed fecal microbiota liquid prepared from the feces of rats on HFD.,5,5,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 4F,20 March 2025,MyleeeA,MyleeeA,Differential analysis of intestinal microbiota in Normal Diet FMT and High Fat Diet FMT.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae",1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|91061;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1253;3379134|29547|3031852|213849|72293|209;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|1853231,Complete,Svetlana up
bsdb:38773112/1/1,38773112,meta-analysis,38773112,10.1038/s41531-024-00724-z,NA,"Nishiwaki H., Ueyama J., Ito M., Hamaguchi T., Takimoto K., Maeda T., Kashihara K., Tsuboi Y., Mori H., Kurokawa K., Katsuno M., Hirayama M. , Ohno K.",Meta-analysis of shotgun sequencing of gut microbiota in Parkinson's disease,NPJ Parkinson's disease,2024,NA,Experiment 1,"Japan,United States of America,China,Germany,Taiwan",Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson’s disease patients (PD patients),Parkinson’s disease patients (PD patients) refers to patients with idiopathic PD and was diagnosed according to the Movement Disorder Society’s (MDS) PD criteria.,73,94,1 month,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplementary Table 7,26 February 2025,KateRasheed,KateRasheed,Meta-analysis of species and genera in six datasets,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes ihumii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. An250,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus rubiinfantis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Cibiobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Cibiobacter|s__Candidatus Cibiobacter qucibialis,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|s__Christensenellaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium UC5.1-1D1,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium phoceensis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp. AF36-15AT,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter|s__Dysosmobacter hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter|s__Dysosmobacter welbionis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|s__Eubacteriaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Evtepia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena contorta,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Massiliimalia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. AF02-12,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|201174|84998|1643822|1643826|447020;1783272|201174|84998|1643822|1643826|447020|446660;3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550|239759|2585118;3379134|976|200643|171549|171550|239759|1470347;3379134|976|200643|171549|171550|239759|626932;3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|171550|239759|328814;1783272|1239|186801|186802|3082771|1924093;1783272|1239|186801|186802|3082771|1924093|1965604;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|186802|216572|244127|169435;1783272|1239|186801|186802|216572|244127|1720200;3379134|976|200643|171549|815|816|246787;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|2005519|397864|487174;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|216816;3379134|200940|3031449|213115|194924|35832;3379134|200940|3031449|213115|194924|35832|35833;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802|2527773;1783272|1239|186801|186802|2527773|2500537;1783272|1239|186801|3082768|990719|2054177;1783272|1239|186801|2044939;1783272|1239|186801|1697794;1783272|1239|186801|186802|1898207;1783272|1239|186801|186802|31979|1485|1650661;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|3085636|186803|189330|2292041;1783272|1239|186801|186802|216572|2591381;1783272|1239|186801|186802|216572|2591381|2763041;1783272|1239|186801|186802|216572|2591381|2093857;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|3085636|186803|2719313;1783272|1239|186801|3085636|186803|2719313|358742;1783272|1239|186801|3085636|186803|2719313|333367;1783272|1239|186801|3085636|186803|2719313|358743;1783272|1239|186801|186802|186806|2049045;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|2211178;1783272|1239|186801|3085636|186803|2005359;1783272|1239|186801|3085636|186803|2005359|39482;1783272|201174|84998|1643822|1643826|644652;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|3085636|186803|1649459|154046;1783272|1239|186801|186802|1392389;1783272|1239|186801|186802|1392389|1297617;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|186802|216572|2895461;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|1853231|283168|28118;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|2485925;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|2005525|375288|328812;3379134|976|200643|171549|2005525|375288|46503;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|3085636|186803|841|2293126;1783272|1239|186801|186802|216572|1905344;1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|186801|186802|31979|1485|1522;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|3085636|186803|2941495|1512;1783272|1239|186801|186802|216572|39492;1783272|1239|91061;1783272|1239|186801|3082768|990719;1783272|1239|186801;1783272|201174|84998|1643822|1643826;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:38773112/1/2,38773112,meta-analysis,38773112,10.1038/s41531-024-00724-z,NA,"Nishiwaki H., Ueyama J., Ito M., Hamaguchi T., Takimoto K., Maeda T., Kashihara K., Tsuboi Y., Mori H., Kurokawa K., Katsuno M., Hirayama M. , Ohno K.",Meta-analysis of shotgun sequencing of gut microbiota in Parkinson's disease,NPJ Parkinson's disease,2024,NA,Experiment 1,"Japan,United States of America,China,Germany,Taiwan",Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson’s disease patients (PD patients),Parkinson’s disease patients (PD patients) refers to patients with idiopathic PD and was diagnosed according to the Movement Disorder Society’s (MDS) PD criteria.,73,94,1 month,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Supplementary Table 7,26 February 2025,KateRasheed,KateRasheed,Meta-analysis of species and genera in six datasets,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum butyriciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora amygdalina,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AM22-11AC,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Liu et al. 2021),k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia massiliensis (ex Liu et al. 2021),k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",1783272|1239|186801|186802|3085642|2048137|1628085;1783272|1239|186801|186802|216572|216851|853;3379134|1224|1236|135625|712|724|729;1783272|1239|186801|3085636|186803|2719231|253257;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|186801|3085636|186803|841|166486;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|186802|31979|1485|2293024;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|186802|216572|1263|3062497;1783272|1239|186801|3085636|186803|572511|3062492;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|2719231;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|3085642|2048137;3379134|976|200643|171549|815|909656;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|2316020;1783272|1239|186801|3085636|186803|572511,Complete,Svetlana up
bsdb:38773112/2/1,38773112,meta-analysis,38773112,10.1038/s41531-024-00724-z,NA,"Nishiwaki H., Ueyama J., Ito M., Hamaguchi T., Takimoto K., Maeda T., Kashihara K., Tsuboi Y., Mori H., Kurokawa K., Katsuno M., Hirayama M. , Ohno K.",Meta-analysis of shotgun sequencing of gut microbiota in Parkinson's disease,NPJ Parkinson's disease,2024,NA,Experiment 2,"China,Germany,Japan,United States of America,Taiwan",Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson’s disease patients (PD patients),Parkinson’s disease patients (PD patients) refers to patients with idiopathic PD and was diagnosed according to the Movement Disorder Society’s (MDS) PD criteria.,73,94,1 month,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplementary Table 8,27 February 2025,KateRasheed,KateRasheed,Confounding factor analysis of the species and the genera that were significantly changed in meta-analysis of six datasets,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|s__Christensenellaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter|s__Dysosmobacter welbionis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter|s__Dysosmobacter hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus rubiinfantis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",1783272|201174|1760|85004|31953|1678|216816;3379134|976|200643|171549|171550|239759|626932;1783272|1239|186801|2044939;1783272|1239|186801|3082768|990719|2054177;1783272|1239|186801|3085636|186803|1649459|154046;1783272|1239|186801|186802|216572|2591381|2093857;1783272|1239|186801|186802|216572|2591381|2763041;1783272|1239|186801|186802|216572|244127|169435;1783272|1239|186801|186802|216572|244127|1720200;1783272|1239|186801|186802|216572|2485925;1783272|1239|186801|186802|216572|1905344|1550024;3379134|74201|203494|48461|1647988|239934|239935;1783272|201174|1760|85004|31953|1678;1783272|201174|84998|1643822|1643826|644652;1783272|1239|91061;1783272|1239|186801;1783272|1239|186801|3082768|990719;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|186802|216572|2591381;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|186802|216572|1905344;1783272|1239|526524|526525|128827|61170;3379134|200940|3031449|213115|194924|872;3379134|74201|203494|48461|1647988|239934,Complete,Svetlana up
bsdb:38773112/2/2,38773112,meta-analysis,38773112,10.1038/s41531-024-00724-z,NA,"Nishiwaki H., Ueyama J., Ito M., Hamaguchi T., Takimoto K., Maeda T., Kashihara K., Tsuboi Y., Mori H., Kurokawa K., Katsuno M., Hirayama M. , Ohno K.",Meta-analysis of shotgun sequencing of gut microbiota in Parkinson's disease,NPJ Parkinson's disease,2024,NA,Experiment 2,"China,Germany,Japan,United States of America,Taiwan",Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson’s disease patients (PD patients),Parkinson’s disease patients (PD patients) refers to patients with idiopathic PD and was diagnosed according to the Movement Disorder Society’s (MDS) PD criteria.,73,94,1 month,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Supplementary Table 8,27 February 2025,KateRasheed,KateRasheed,Confounding factor analysis of the species and the genera that were significantly changed in meta-analysis of six datasets,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum butyriciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora amygdalina,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis",1783272|1239|186801|186802|3085642|2048137;1783272|1239|186801|186802|3085642|2048137|1628085;1783272|1239|186801|186802|3082771|1924093;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|2719231|253257;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|186801|3085636|186803|841|166486,Complete,Svetlana up
bsdb:38798019/1/1,38798019,time series / longitudinal observational,38798019,10.1080/19490976.2024.2357176,NA,"Samarra A., Cabrera-Rubio R., Martínez-Costa C. , Collado M.C.",The role of <i>Bifidobacterium</i> genus in modulating the neonate microbiota: implications for antibiotic resistance acquisition in early life,Gut microbes,2024,"Bifidobacterium, antibiotic, gut, infant, microbiota, resistance",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Drug resistance,EFO:0020001,Low-Bifidobacterium group,High-Bifidobacterium group,High-Bifidobacterium group in the seven (7) day-old infants.,57,42,NA,16S,34,Illumina,log transformation,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,3,NA,"antibiotic exposure,feeding practices,mode of birth",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,9 June 2024,Aleru Divine,"Aleru Divine,WikiWorks","Microbial composition according to Bifidobacterium-abundance groups, indicating differences in relative abundance and identified taxonomic biomarkers.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:38798019/1/2,38798019,time series / longitudinal observational,38798019,10.1080/19490976.2024.2357176,NA,"Samarra A., Cabrera-Rubio R., Martínez-Costa C. , Collado M.C.",The role of <i>Bifidobacterium</i> genus in modulating the neonate microbiota: implications for antibiotic resistance acquisition in early life,Gut microbes,2024,"Bifidobacterium, antibiotic, gut, infant, microbiota, resistance",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Drug resistance,EFO:0020001,Low-Bifidobacterium group,High-Bifidobacterium group,High-Bifidobacterium group in the seven (7) day-old infants.,57,42,NA,16S,34,Illumina,log transformation,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,3,NA,"antibiotic exposure,feeding practices,mode of birth",NA,NA,NA,NA,NA,NA,Signature 2,Figure 2,9 June 2024,Aleru Divine,"Aleru Divine,WikiWorks","Microbial composition according to Bifidobacterium-abundance groups, indicating differences in relative abundance and identified taxonomic biomarkers.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|570;1783272|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:38798019/2/1,38798019,time series / longitudinal observational,38798019,10.1080/19490976.2024.2357176,NA,"Samarra A., Cabrera-Rubio R., Martínez-Costa C. , Collado M.C.",The role of <i>Bifidobacterium</i> genus in modulating the neonate microbiota: implications for antibiotic resistance acquisition in early life,Gut microbes,2024,"Bifidobacterium, antibiotic, gut, infant, microbiota, resistance",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Drug resistance,EFO:0020001,Low-Bifidobacterium group,High-Bifidobacterium group,High-Bifidobacterium group in the one (1) month-old infants.,58,43,NA,16S,34,Illumina,log transformation,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,3,NA,"antibiotic exposure,feeding practices,mode of birth",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2 and 3,9 June 2024,Aleru Divine,"Aleru Divine,WikiWorks","Microbial composition according to Bifidobacterium-abundance groups, indicating differences in relative abundance and identified taxonomic biomarkers.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|81852|1350;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|186826|1300|1301;1783272|201174|1760|85004|31953|1678|41200,Complete,Svetlana up
bsdb:38798019/2/2,38798019,time series / longitudinal observational,38798019,10.1080/19490976.2024.2357176,NA,"Samarra A., Cabrera-Rubio R., Martínez-Costa C. , Collado M.C.",The role of <i>Bifidobacterium</i> genus in modulating the neonate microbiota: implications for antibiotic resistance acquisition in early life,Gut microbes,2024,"Bifidobacterium, antibiotic, gut, infant, microbiota, resistance",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Drug resistance,EFO:0020001,Low-Bifidobacterium group,High-Bifidobacterium group,High-Bifidobacterium group in the one (1) month-old infants.,58,43,NA,16S,34,Illumina,log transformation,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,3,NA,"antibiotic exposure,feeding practices,mode of birth",NA,NA,NA,NA,NA,NA,Signature 2,Figure 2 and 3,9 June 2024,Aleru Divine,"Aleru Divine,WikiWorks","Microbial composition according to Bifidobacterium-abundance groups, indicating differences in relative abundance and identified taxonomic biomarkers.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp.",3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678|1689;1783272|1239|186801|186802|31979|1485;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|91347|543|570;3379134|976|200643|171549|2005525|375288|1869337,Complete,Svetlana up
bsdb:38841824/1/1,38841824,case-control,38841824,https://doi.org/10.1002/brb3.3579,NA,"Chen Y.H., Yu H., Xue F., Bai J., Guo L. , Peng Z.W.",16S rRNA gene sequencing reveals altered gut microbiota in young adults with schizophrenia and prominent negative symptoms,Brain and behavior,2024,"gut microbiota, negative symptoms, schizophrenia, young adults",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Healthy controls,Schizophrenia patients with prominent negative symptoms (SCH-N),Patients with schizophrenia with prominent negative symptoms (SCH-N) who met the diagnostic criteria of schizophrenia with a total positive and negative syndrome scale (PANSS) score ≥60 according to the Statistical Clinical Interview for DSM-5 by two psychiatrists.,36,30,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 2B,11 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,Scholastica,WikiWorks",Differential species abundance in gut microbiome between healthy controls versus schizophrenia patients with prominent negative symptoms (SCH-N) based on (LEfSe) analysis.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Rodentibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales",3379134|1224|28216|80840|506|222;1783272|1239|526524|526525|2810280|100883;1783272|201174|1760|85007|1653;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|1940338;1783272|1239|526524|526525|128827|1573534;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;3384189|32066|203490|203491|203492|848;3379134|1224|1236;1783272|1239|186801|3085636|186803|1506553;3379134|976|200643|171549|2005473;3379134|1224|1236|135625|712|1960084;1783272|1239|186801|186802|31979|1266;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;3379134|976|200643|171549|2005473;3379134|1224;1783272|201174|1760|85007,Complete,Svetlana up
bsdb:38841824/1/2,38841824,case-control,38841824,https://doi.org/10.1002/brb3.3579,NA,"Chen Y.H., Yu H., Xue F., Bai J., Guo L. , Peng Z.W.",16S rRNA gene sequencing reveals altered gut microbiota in young adults with schizophrenia and prominent negative symptoms,Brain and behavior,2024,"gut microbiota, negative symptoms, schizophrenia, young adults",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Healthy controls,Schizophrenia patients with prominent negative symptoms (SCH-N),Patients with schizophrenia with prominent negative symptoms (SCH-N) who met the diagnostic criteria of schizophrenia with a total positive and negative syndrome scale (PANSS) score ≥60 according to the Statistical Clinical Interview for DSM-5 by two psychiatrists.,36,30,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 2B,11 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,Scholastica,WikiWorks,Tosin",Differential species abundance in gut microbiome between healthy controls versus schizophrenia patients with prominent negative symptoms (SCH-N) based on (LEfSe) analysis.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:352",1783272|1239|186801|3085636|186803|1766253;3379134|1224|28216|80840|506|507;1783272|1239;1783272|1239|186801|186802|3085642;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|33042;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|186802|216572|216851;3379134|976|117743|200644|49546;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|3085636;1783272|1239|909932|909929|1843491|52225;1783272|1239|186801|3085656|3085657;1783272|1239|186801|3085656;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|31979|1485|1262798,Complete,Svetlana up
bsdb:38841824/2/1,38841824,case-control,38841824,https://doi.org/10.1002/brb3.3579,NA,"Chen Y.H., Yu H., Xue F., Bai J., Guo L. , Peng Z.W.",16S rRNA gene sequencing reveals altered gut microbiota in young adults with schizophrenia and prominent negative symptoms,Brain and behavior,2024,"gut microbiota, negative symptoms, schizophrenia, young adults",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Schizophrenia patients with prominent negative symptoms (SCH-N),Schizophrenia patients with prominent positive symptoms (SCH-P),"Patients with schizophrenia with prominent positive symptoms (SCH-P) who met the diagnostic criteria of schizophrenia with a total positive and negative syndrome scale (PANSS) score ≥60; at least three out of seven items of PANSS positive subscale score ≥4, or at least two items score ≥5, and a total PANSS positive subscale score ≥20, and at least 3 points more than the total PANSS negative subscale score.",30,32,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,1.5,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 3B,11 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,Scholastica,WikiWorks",Differential species abundance in gut microbiome between schizophrenia patients with prominent negative (SCH-N) versus positive (SCH-P) symptoms based on (LEfSe) analysis.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina",3379134|976|200643|171549;3379134|1224|28211|204458|76892|41275;3379134|1224|1236|72274;1783272|1239|186801|186802|31979|1266,Complete,Svetlana up
bsdb:38841824/2/2,38841824,case-control,38841824,https://doi.org/10.1002/brb3.3579,NA,"Chen Y.H., Yu H., Xue F., Bai J., Guo L. , Peng Z.W.",16S rRNA gene sequencing reveals altered gut microbiota in young adults with schizophrenia and prominent negative symptoms,Brain and behavior,2024,"gut microbiota, negative symptoms, schizophrenia, young adults",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Schizophrenia patients with prominent negative symptoms (SCH-N),Schizophrenia patients with prominent positive symptoms (SCH-P),"Patients with schizophrenia with prominent positive symptoms (SCH-P) who met the diagnostic criteria of schizophrenia with a total positive and negative syndrome scale (PANSS) score ≥60; at least three out of seven items of PANSS positive subscale score ≥4, or at least two items score ≥5, and a total PANSS positive subscale score ≥20, and at least 3 points more than the total PANSS negative subscale score.",30,32,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,1.5,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 3B,11 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,Scholastica,WikiWorks",Differential species abundance in gut microbiome between schizophrenia patients with prominent negative (SCH-N) versus positive (SCH-P) symptoms based on (LEfSe) analysis.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales",3379134|1224|28211;1783272|1239|1737404|1582879;3379134|1224|28211|356|82115;3379134|1224|28211|204457|41297;3379134|1224|28211|204457;3379134|1224|28211|356,Complete,Svetlana up
bsdb:38846566/1/1,38846566,laboratory experiment,38846566,10.3389/fmicb.2024.1373077,NA,"Yang M., Deng H., Zhou S., Lu D., Shen X., Huang L., Chen Y. , Xu L.",Irisin alleviated the reproductive endocrinal disorders of PCOS mice accompanied by changes in gut microbiota and metabolomic characteristics,Frontiers in microbiology,2024,"fecal metabolomics, folliculogenesis, gut microbiota, irisin, polycystic ovary syndrome",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Polycystic ovary syndrome & Polycystic ovary syndrome+Irisin (PCOS & PCOS+Irisin),Vehicle,Animals in this group were injected daily with corn oil subcutaneously along with a control diet.,14,5,NA,16S,NA,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5C,14 July 2025,Victoria,Victoria,Cladogram and bar plot of the LEfSe analysis showing the most characteristic taxa in each group of mice (taxa with LDA score > 2.0).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia ilealis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia",1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1501226|1115758;1783272|1239|186801|3082720|186804|1501226,Complete,Svetlana up
bsdb:38846566/2/1,38846566,laboratory experiment,38846566,10.3389/fmicb.2024.1373077,NA,"Yang M., Deng H., Zhou S., Lu D., Shen X., Huang L., Chen Y. , Xu L.",Irisin alleviated the reproductive endocrinal disorders of PCOS mice accompanied by changes in gut microbiota and metabolomic characteristics,Frontiers in microbiology,2024,"fecal metabolomics, folliculogenesis, gut microbiota, irisin, polycystic ovary syndrome",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Vehicle & Polycystic ovary syndrome+Irisin (PCOS+Irisin),Polycystic ovary syndrome (PCOS),"Animals in this group were subcutaneously injected daily with DHEA (D4000; Sigma–Aldrich; 6 mg per 100 g, dissolved in corn oil) and were fed with a high-fat diet (HFD).",13,6,NA,16S,NA,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5C,14 July 2025,Victoria,Victoria,Cladogram and bar plot of the LEfSe analysis showing the most characteristic taxa in each group of mice (taxa with LDA score > 2.0).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",1783272|1239|186801|3085636|186803|572511|33035;3379134|200940|3031449|213115|194924|872,Complete,Svetlana up
bsdb:38846566/3/1,38846566,laboratory experiment,38846566,10.3389/fmicb.2024.1373077,NA,"Yang M., Deng H., Zhou S., Lu D., Shen X., Huang L., Chen Y. , Xu L.",Irisin alleviated the reproductive endocrinal disorders of PCOS mice accompanied by changes in gut microbiota and metabolomic characteristics,Frontiers in microbiology,2024,"fecal metabolomics, folliculogenesis, gut microbiota, irisin, polycystic ovary syndrome",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Vehicle & Polycystic ovary syndrome (PCOS),Polycystic ovary syndrome+Irisin (PCOS+Irisin),"Animals in this group were injected daily with DHEA subcutaneously, 400 μg/kg r-irisin intraperitoneally every other day, and were fed with a high-fat diet (HFD).",11,8,NA,16S,NA,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5C,14 July 2025,Victoria,Victoria,Cladogram and bar plot of the LEfSe analysis showing the most characteristic taxa in each group of mice (taxa with LDA score > 2.0).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 10-1,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136",3379134|1224|1236;1783272|1239|186801|3085636|186803|1235800;1783272|1239|91061|186826|33958|2742598|1598;1783272|1239|186801|3085636|186803|877420,Complete,Svetlana up
bsdb:38846566/4/1,38846566,laboratory experiment,38846566,10.3389/fmicb.2024.1373077,NA,"Yang M., Deng H., Zhou S., Lu D., Shen X., Huang L., Chen Y. , Xu L.",Irisin alleviated the reproductive endocrinal disorders of PCOS mice accompanied by changes in gut microbiota and metabolomic characteristics,Frontiers in microbiology,2024,"fecal metabolomics, folliculogenesis, gut microbiota, irisin, polycystic ovary syndrome",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Vehicle,Polycystic ovary syndrome+Irisin (PCOS+Irisin),"Animals in this group were injected daily with DHEA subcutaneously, 400 μg/kg r-irisin intraperitoneally every other day, and were fed with a high-fat diet (HFD).",5,8,NA,16S,NA,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5D,15 July 2025,Victoria,Victoria,The variance analysis of abundant taxa at the genus level among the three groups of mice.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,1783272|1239|186801|3082768|990719|990721,Complete,Svetlana up
bsdb:38846566/5/1,38846566,laboratory experiment,38846566,10.3389/fmicb.2024.1373077,NA,"Yang M., Deng H., Zhou S., Lu D., Shen X., Huang L., Chen Y. , Xu L.",Irisin alleviated the reproductive endocrinal disorders of PCOS mice accompanied by changes in gut microbiota and metabolomic characteristics,Frontiers in microbiology,2024,"fecal metabolomics, folliculogenesis, gut microbiota, irisin, polycystic ovary syndrome",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Polycystic ovary syndrome (PCOS),Polycystic ovary syndrome (PCOS) Polycystic ovary syndrome+Irisin (PCOS+Irisin),"Animals in this group were injected daily with DHEA subcutaneously, 400 μg/kg r-irisin intraperitoneally every other day, and were fed with a high-fat diet (HFD).",6,8,NA,16S,NA,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5D,15 July 2025,Victoria,Victoria,The variance analysis of abundant taxa at the genus level among three groups of mice.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,1783272|1239|186801|3082768|990719|990721,Complete,Svetlana up
bsdb:38866797/2/1,38866797,"cross-sectional observational, not case-control",38866797,https://doi.org/10.1038/s41598-024-60683-6,NA,"Ren J., Ren Y., Mu Y., Zhang L., Chen B., Li S., Fang Q., Zhang Z., Zhang K., Li S., Liu W., Cui Y. , Li X.",Microbial imbalance in Chinese children with diarrhea or constipation,Scientific reports,2024,"16S rRNA sequencing, Childhood constipation, Childhood diarrhea, Cross-sectional study, Gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Healthy children (HC) of the discovery cohort,Children with diarrhea (CD) of the discovery cohort,"Children with diarrhea experience a range of health impacts, such as difficulty in feeding, reduced immunity, malnutrition, and foodborne illness, with potential complications like viral myocarditis.",414,66,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,decreased,unchanged,NA,NA,Signature 1,Fig. 2D,21 March 2025,Jesulolufemi,"Jesulolufemi,Ameenatoloko",LEfSe (Linear Discriminant Analysis Effect Size) cladogram illustrating different bacterial taxa's phylogenetic relationships that are differentially abundant between the CD and HC groups.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Brevibacillus|s__Brevibacillus invocatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Isobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Isobaculum|s__Isobaculum melis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Jannaschia,k__Methanobacteriati|p__Methanobacteriota|c__Methanomicrobia|o__Methanomicrobiales|f__Methanoregulaceae|g__Methanolinea,k__Methanobacteriati|p__Methanobacteriota|c__Methanomicrobia|o__Methanomicrobiales,k__Methanobacteriati|p__Methanobacteriota|c__Methanomicrobia|o__Methanomicrobiales|f__Methanoregulaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycolicibacter|s__Mycolicibacter arupensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Natronobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Nitrobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Sinomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Virgibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Fulvimonas",1783272|201174|1760|2037;1783272|1239|91061|1385|186822|55080|173959;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|31979|1485|1502;1783272|1239|91061|186826|186828|142587;1783272|1239|91061|186826|186828|142587|142588;3379134|1224|28211|204455|2854170|188905;3366610|28890|224756|2191|1198451|499551;3366610|28890|224756|2191;3366610|28890|224756|2191|1198451;1783272|201174|1760|85006|1268;1783272|201174|1760|85007|1762|1073531|342002;1783272|1239|91061|1385|186817|472977;3379134|1224|28211|356|41294|911;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|43675;1783272|201174|1760|85006|1268|596707;1783272|1239|91061|1385|186817|84406;3379134|1224|1236|135614|1775411|155196,Complete,KateRasheed
bsdb:38866797/2/2,38866797,"cross-sectional observational, not case-control",38866797,https://doi.org/10.1038/s41598-024-60683-6,NA,"Ren J., Ren Y., Mu Y., Zhang L., Chen B., Li S., Fang Q., Zhang Z., Zhang K., Li S., Liu W., Cui Y. , Li X.",Microbial imbalance in Chinese children with diarrhea or constipation,Scientific reports,2024,"16S rRNA sequencing, Childhood constipation, Childhood diarrhea, Cross-sectional study, Gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Healthy children (HC) of the discovery cohort,Children with diarrhea (CD) of the discovery cohort,"Children with diarrhea experience a range of health impacts, such as difficulty in feeding, reduced immunity, malnutrition, and foodborne illness, with potential complications like viral myocarditis.",414,66,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,decreased,unchanged,NA,NA,Signature 2,Fig. 2D,21 March 2025,Jesulolufemi,"Jesulolufemi,Ameenatoloko",LEfSe (Linear Discriminant Analysis Effect Size) cladogram illustrating the phylogenetic relationships of bacterial taxa that are differentially abundant between the CD and HC groups.,decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Pseudomonadati|p__Bacteroidota",1783272|201174;3379134|1224|28216|80840|506;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|1681;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|2383;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;3379134|976|200643|171549|2005520|156973;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|1263;1783272|201174|84992;3379134|976,Complete,KateRasheed
bsdb:38866797/4/1,38866797,"cross-sectional observational, not case-control",38866797,https://doi.org/10.1038/s41598-024-60683-6,NA,"Ren J., Ren Y., Mu Y., Zhang L., Chen B., Li S., Fang Q., Zhang Z., Zhang K., Li S., Liu W., Cui Y. , Li X.",Microbial imbalance in Chinese children with diarrhea or constipation,Scientific reports,2024,"16S rRNA sequencing, Childhood constipation, Childhood diarrhea, Cross-sectional study, Gut microbiota",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,Healthy children (HC) of the discovery cohort,Children with constipation (CC) of the discovery cohort,"Children with constipation are at risk of various health issues, including mental, behavioral, social, and physical challenges.",414,138,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,increased,increased,NA,NA,Signature 1,Fig. 2C,21 March 2025,Jesulolufemi,"Jesulolufemi,Ameenatoloko",LEfSe (Linear Discriminant Analysis Effect Size) cladogram illustrating different bacterial taxa's phylogenetic relationships that are differentially abundant between the CC and HC groups.,increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Lentisphaerota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Trichococcus,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis|s__Victivallis vadensis,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Poales|f__Poaceae|s__Panicoideae|g__Zea,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Poales|f__Poaceae|s__Panicoideae|g__Zea|s__Zea luxurians",1783272|201174;3379134|976|200643|171549|815|816|820;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|28050;3379134|256845;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|171551;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|186828|82802;3379134|256845|1313211|278082|255528;3379134|256845|1313211|278082;3379134|256845|1313211|278082|255528|172900;3379134|256845|1313211|278082|255528|172900|172901;33090|35493|3398|38820|4479|147369|4575;33090|35493|3398|38820|4479|147369|4575|15945,Complete,KateRasheed
bsdb:38866797/4/2,38866797,"cross-sectional observational, not case-control",38866797,https://doi.org/10.1038/s41598-024-60683-6,NA,"Ren J., Ren Y., Mu Y., Zhang L., Chen B., Li S., Fang Q., Zhang Z., Zhang K., Li S., Liu W., Cui Y. , Li X.",Microbial imbalance in Chinese children with diarrhea or constipation,Scientific reports,2024,"16S rRNA sequencing, Childhood constipation, Childhood diarrhea, Cross-sectional study, Gut microbiota",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,Healthy children (HC) of the discovery cohort,Children with constipation (CC) of the discovery cohort,"Children with constipation are at risk of various health issues, including mental, behavioral, social, and physical challenges.",414,138,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,increased,increased,NA,NA,Signature 2,Fig. 2C,21 March 2025,Jesulolufemi,"Jesulolufemi,Ameenatoloko",LEfSe (Linear Discriminant Analysis Effect Size) cladogram illustrating different bacterial taxa's phylogenetic relationships that are differentially abundant between the CC and HC groups.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium butyricum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium neonatale,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota",1783272|1239|186801|186802|31979|1485|1492;1783272|1239|186801|186802|31979|1485|137838;3379134|1224|1236|91347|543|544;1783272|1239|186801|186802|31979;3379134|1224|1236|91347|543;3379134|1224|1236|91347;3379134|1224|1236;3379134|1224,Complete,KateRasheed
bsdb:38866797/5/1,38866797,"cross-sectional observational, not case-control",38866797,https://doi.org/10.1038/s41598-024-60683-6,NA,"Ren J., Ren Y., Mu Y., Zhang L., Chen B., Li S., Fang Q., Zhang Z., Zhang K., Li S., Liu W., Cui Y. , Li X.",Microbial imbalance in Chinese children with diarrhea or constipation,Scientific reports,2024,"16S rRNA sequencing, Childhood constipation, Childhood diarrhea, Cross-sectional study, Gut microbiota",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,Healthy Controls (HC),Children with constipation (CC),"Children with constipation are at risk of various health issues, including mental, behavioral, social, and physical challenges.",398,129,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,increased,increased,NA,NA,Signature 1,"Fig. S3, Table S7",30 April 2025,Ameenatoloko,Ameenatoloko,A cladogram made by LEfSe demonstrates different bacterial taxa between the CC and HC groups.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Fimenecus,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium UBA1381,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:138,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. CAG:74,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Lawsonibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Liu et al. 2021),k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae",1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815|816|28116;1783272|201174|1760|85004|31953|1678|1689;1783272|1239|186801|2840564;1783272|1239|186801|3082768|990719;1783272|1239|186801|3082768;1783272|1239|186801|186802|1950820;1783272|1239|186801|186802|31979|1485|1262775;1783272|201174|84998|84999;1783272|201174|84998;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;3379134|200940|3031449;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|1262897;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|216572|2172004;3379134|976|200643|1970189|1573805;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|3062497;3379134|976|200643|171549|2005525,Complete,KateRasheed
bsdb:38866797/5/2,38866797,"cross-sectional observational, not case-control",38866797,https://doi.org/10.1038/s41598-024-60683-6,NA,"Ren J., Ren Y., Mu Y., Zhang L., Chen B., Li S., Fang Q., Zhang Z., Zhang K., Li S., Liu W., Cui Y. , Li X.",Microbial imbalance in Chinese children with diarrhea or constipation,Scientific reports,2024,"16S rRNA sequencing, Childhood constipation, Childhood diarrhea, Cross-sectional study, Gut microbiota",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,Healthy Controls (HC),Children with constipation (CC),"Children with constipation are at risk of various health issues, including mental, behavioral, social, and physical challenges.",398,129,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,increased,increased,NA,NA,Signature 2,"Fig. S3, Table S7",30 April 2025,Ameenatoloko,"Ameenatoloko,KateRasheed",A cladogram made by LEfSe demonstrates different bacterial taxa between the CC and HC groups.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium neonatale,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. HMSC078H08",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|91061;3379134|976|200643|171549|815|816|820;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|31979|1485|137838;1783272|1239|186801|186802|31979|1485|1502;1783272|1239|186801|186802;3379134|1224|1236;1783272|201174|1760|85006|1268;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|1715008,Complete,KateRasheed
bsdb:38866797/6/1,38866797,"cross-sectional observational, not case-control",38866797,https://doi.org/10.1038/s41598-024-60683-6,NA,"Ren J., Ren Y., Mu Y., Zhang L., Chen B., Li S., Fang Q., Zhang Z., Zhang K., Li S., Liu W., Cui Y. , Li X.",Microbial imbalance in Chinese children with diarrhea or constipation,Scientific reports,2024,"16S rRNA sequencing, Childhood constipation, Childhood diarrhea, Cross-sectional study, Gut microbiota",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Healthy Controls (HC),Children with diarrhea (CD),"Children with diarrhea experience a range of health impacts, such as difficulty in feeding, reduced immunity, malnutrition, and foodborne illness, with potential complications like viral myocarditis.",398,60,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,decreased,unchanged,NA,NA,Signature 1,"Fig. S4, Table S8",30 April 2025,Ameenatoloko,Ameenatoloko,A cladogram made by LEfSe demonstrates different bacterial taxa between the CD and HC groups.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] piliforme",1783272|1239|186801|3085636|1185407;1783272|1239|186801|186802;3379134|1224|1236;1783272|1239|91061|1385|539738;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|1506577|1524,Complete,KateRasheed
bsdb:38866797/6/2,38866797,"cross-sectional observational, not case-control",38866797,https://doi.org/10.1038/s41598-024-60683-6,NA,"Ren J., Ren Y., Mu Y., Zhang L., Chen B., Li S., Fang Q., Zhang Z., Zhang K., Li S., Liu W., Cui Y. , Li X.",Microbial imbalance in Chinese children with diarrhea or constipation,Scientific reports,2024,"16S rRNA sequencing, Childhood constipation, Childhood diarrhea, Cross-sectional study, Gut microbiota",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Healthy Controls (HC),Children with diarrhea (CD),"Children with diarrhea experience a range of health impacts, such as difficulty in feeding, reduced immunity, malnutrition, and foodborne illness, with potential complications like viral myocarditis.",398,60,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,decreased,unchanged,NA,NA,Signature 2,"Fig. S4, Table S8",30 April 2025,Ameenatoloko,Ameenatoloko,A cladogram made by LEfSe demonstrates different bacterial taxa between the CD and HC groups.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter faecis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis",1783272|201174|1760|2037;1783272|201174|1760;3379134|976|200643;1783272|201174|1760|85004|31953;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;1783272|201174|84998|1643822|1643826;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|2316020|592978;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|3085636|186803|1649459;1783272|1239|91061|186826|1300|1301|1343,Complete,KateRasheed
bsdb:38866797/7/1,38866797,"cross-sectional observational, not case-control",38866797,https://doi.org/10.1038/s41598-024-60683-6,NA,"Ren J., Ren Y., Mu Y., Zhang L., Chen B., Li S., Fang Q., Zhang Z., Zhang K., Li S., Liu W., Cui Y. , Li X.",Microbial imbalance in Chinese children with diarrhea or constipation,Scientific reports,2024,"16S rRNA sequencing, Childhood constipation, Childhood diarrhea, Cross-sectional study, Gut microbiota",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,Healthy Controls (HC),Children with Constipation (CC),"Children with constipation are at risk of various health issues, including mental, behavioral, social, and physical challenges.",414,138,1 month,16S,34,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,age,NA,increased,increased,increased,NA,NA,Signature 1,Table S3,30 April 2025,Ameenatoloko,Ameenatoloko,The significantly altered genera determined by MaAsLin2 after adjusting for age and gender between the CC and HC groups.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|3085636|186803|33042;3379134|976|200643|171549|2005525|375288,Complete,KateRasheed
bsdb:38866797/7/2,38866797,"cross-sectional observational, not case-control",38866797,https://doi.org/10.1038/s41598-024-60683-6,NA,"Ren J., Ren Y., Mu Y., Zhang L., Chen B., Li S., Fang Q., Zhang Z., Zhang K., Li S., Liu W., Cui Y. , Li X.",Microbial imbalance in Chinese children with diarrhea or constipation,Scientific reports,2024,"16S rRNA sequencing, Childhood constipation, Childhood diarrhea, Cross-sectional study, Gut microbiota",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,Healthy Controls (HC),Children with Constipation (CC),"Children with constipation are at risk of various health issues, including mental, behavioral, social, and physical challenges.",414,138,1 month,16S,34,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,age,NA,increased,increased,increased,NA,NA,Signature 2,Table S3,30 April 2025,Ameenatoloko,Ameenatoloko,The significantly altered genera determined by MaAsLin2 after adjusting for age and gender between the CC and HC groups.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,1783272|201174|1760|85006|1268|32207,Complete,KateRasheed
bsdb:38866797/8/1,38866797,"cross-sectional observational, not case-control",38866797,https://doi.org/10.1038/s41598-024-60683-6,NA,"Ren J., Ren Y., Mu Y., Zhang L., Chen B., Li S., Fang Q., Zhang Z., Zhang K., Li S., Liu W., Cui Y. , Li X.",Microbial imbalance in Chinese children with diarrhea or constipation,Scientific reports,2024,"16S rRNA sequencing, Childhood constipation, Childhood diarrhea, Cross-sectional study, Gut microbiota",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Healthy Controls (HC),Children with Diarrhea (CD),"Children with diarrhea experience a range of health impacts, such as difficulty in feeding, reduced immunity, malnutrition, and foodborne illness, with potential complications like viral myocarditis.",414,66,1 month,16S,34,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,age,NA,decreased,decreased,decreased,NA,NA,Signature 1,Table S3,30 April 2025,Ameenatoloko,Ameenatoloko,The significantly altered genera determined by MaAsLin2 after adjusting for age and gender between the CD and HC groups.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella",1783272|1239|186801|186802|31979|1485;1783272|1239|91061|1385|539738|1378,Complete,KateRasheed
bsdb:38866797/8/2,38866797,"cross-sectional observational, not case-control",38866797,https://doi.org/10.1038/s41598-024-60683-6,NA,"Ren J., Ren Y., Mu Y., Zhang L., Chen B., Li S., Fang Q., Zhang Z., Zhang K., Li S., Liu W., Cui Y. , Li X.",Microbial imbalance in Chinese children with diarrhea or constipation,Scientific reports,2024,"16S rRNA sequencing, Childhood constipation, Childhood diarrhea, Cross-sectional study, Gut microbiota",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Healthy Controls (HC),Children with Diarrhea (CD),"Children with diarrhea experience a range of health impacts, such as difficulty in feeding, reduced immunity, malnutrition, and foodborne illness, with potential complications like viral myocarditis.",414,66,1 month,16S,34,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,age,NA,decreased,decreased,decreased,NA,NA,Signature 2,Table S3,30 April 2025,Ameenatoloko,Ameenatoloko,The significantly altered genera determined by MaAsLin2 after adjusting for age and gender between the CD and HC groups.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|201174|1760|85004|31953|1678;1783272|201174|84998|1643822|1643826|84111;1783272|201174|84998|84999|84107|102106;1783272|1239|526524|526525|2810280|100883;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|1263,Complete,KateRasheed
bsdb:38872962/1/1,38872962,laboratory experiment,38872962,https://doi.org/10.3389/fendo.2024.1397402,NA,"Wang L., Li T., Cao W.X., Zhao J.Y., Xu X.H., Chai J.P., Zhang J.X., Liu J. , Wang F.C.",To explore the mechanism of acupoint application in the treatment of primary dysmenorrhea by 16S rDNA sequencing and metabolomics,Frontiers in endocrinology,2024,"16S r DNA sequencing, acupoint application, graphene-based warm uterus acupoint paste, non-targeted metabolomics, primary dysmenorrhea",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Dysmenorrhea,HP:0100607,Control group,Model group,The subjects used estradiol benzoate combined with oxytocin.,4,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,increased,NA,NA,NA,Signature 1,Figure 3F,27 July 2025,Aleru Divine,Aleru Divine,The significantly enriched bacterial taxa in different groups as determined by LEfSe analysis.,increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Kribbellaceae|g__Kribbella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,s__uncultured bacterium,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia|o__Acidimicrobiales|f__Acidimicrobiaceae",1783272|201174|84992;1783272|1239|91061|186826|186827|1375;1783272|1239|526524|526525|128827|1937008;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|201174|1760|85009|2726069|182639;1783272|1239|186801|186802|216572|100175;77133;1783272|201174|84992|84993|84994,Complete,NA
bsdb:38872962/1/2,38872962,laboratory experiment,38872962,https://doi.org/10.3389/fendo.2024.1397402,NA,"Wang L., Li T., Cao W.X., Zhao J.Y., Xu X.H., Chai J.P., Zhang J.X., Liu J. , Wang F.C.",To explore the mechanism of acupoint application in the treatment of primary dysmenorrhea by 16S rDNA sequencing and metabolomics,Frontiers in endocrinology,2024,"16S r DNA sequencing, acupoint application, graphene-based warm uterus acupoint paste, non-targeted metabolomics, primary dysmenorrhea",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Dysmenorrhea,HP:0100607,Control group,Model group,The subjects used estradiol benzoate combined with oxytocin.,4,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,increased,NA,NA,NA,Signature 2,Figure 3F,27 July 2025,Aleru Divine,Aleru Divine,The significantly enriched bacterial taxa in different groups as determined by LEfSe analysis.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Holosporales|f__Candidatus Paracaedibacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,s__mouse gut metagenome,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales",1783272|1239|186801|186802|31979|49082;1783272|1239|186801|3085636|186803|1164882;3379134|1224|28211|1921002|1777752;1783272|1239|186801|186802|186807|2740;3379134|1224|1236|135625|712|724;410661;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958;1783272|1239|91061;1783272|1239|91061|186826,Complete,NA
bsdb:38872962/2/1,38872962,laboratory experiment,38872962,https://doi.org/10.3389/fendo.2024.1397402,NA,"Wang L., Li T., Cao W.X., Zhao J.Y., Xu X.H., Chai J.P., Zhang J.X., Liu J. , Wang F.C.",To explore the mechanism of acupoint application in the treatment of primary dysmenorrhea by 16S rDNA sequencing and metabolomics,Frontiers in endocrinology,2024,"16S r DNA sequencing, acupoint application, graphene-based warm uterus acupoint paste, non-targeted metabolomics, primary dysmenorrhea",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Dysmenorrhea,HP:0100607,Model group,Treatment group,The subjects used estradiol benzoate combined with oxytocin and were treated wth Graphene-based warm uterus acupoint paste (GWUAP).,4,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,decreased,NA,NA,NA,Signature 1,Figure 3G,27 July 2025,Aleru Divine,Aleru Divine,The significantly enriched bacterial taxa in different groups as determined by LEfSe analysis.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Pseudomonadota|s__unidentified proteobacterium",3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525;1783272|1239|91061|1385|186817;1783272|1239|91061|1385|186817|1386;3379134|1224|2722,Complete,NA
bsdb:38872962/2/2,38872962,laboratory experiment,38872962,https://doi.org/10.3389/fendo.2024.1397402,NA,"Wang L., Li T., Cao W.X., Zhao J.Y., Xu X.H., Chai J.P., Zhang J.X., Liu J. , Wang F.C.",To explore the mechanism of acupoint application in the treatment of primary dysmenorrhea by 16S rDNA sequencing and metabolomics,Frontiers in endocrinology,2024,"16S r DNA sequencing, acupoint application, graphene-based warm uterus acupoint paste, non-targeted metabolomics, primary dysmenorrhea",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Dysmenorrhea,HP:0100607,Model group,Treatment group,The subjects used estradiol benzoate combined with oxytocin and were treated wth Graphene-based warm uterus acupoint paste (GWUAP).,4,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,decreased,NA,NA,NA,Signature 2,Figure 3G,27 July 2025,Aleru Divine,Aleru Divine,The significantly enriched bacterial taxa in different groups as determined by LEfSe analysis.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia",1783272|1239|186801|3085636|186803|1766253;1783272|201174|1760|85007|1653|1716;28221;3379134|200940|3031449|213115;1783272|1239|91061|186826|1300|1301;3379134|200940|3031449|213115|194924;1783272|1239|91061|186826|1300;1783272|1239|186801|3085636|186803|877420;1783272|544448|31969|186332|186333;1783272|544448|31969|186332;1783272|544448|31969|186332|186333|2086;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1501226,Complete,NA
bsdb:38890302/1/1,38890302,randomized controlled trial,38890302,10.1038/s41467-024-49093-4,NA,"Seyoum Y., Greffeuille V., Kouadio D.K.D., Kuong K., Turpin W., M'Rabt R., Chochois V., Fortin S., Perignon M., Fiorentino M., Berger J., Burja K., Ponce M.C., Chamnan C., Wieringa F.T. , Humblot C.",Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice,Nature communications,2024,NA,Experiment 1,Cambodia,Homo sapiens,Feces,UBERON:0001988,Anemia,MONDO:0002280,Non anaemic,Anaemic,This Group includes children diagnosed with anemia with hemoglobin levels below the threshold (typically less than 11g/dl).,304,76,1 month,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,decreased,unchanged,NA,NA,NA,NA,Signature 1,Fig. 2A,16 December 2024,Joiejoie,"Joiejoie,WikiWorks",Differential ASVs between the children grouped according to anaemia.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Svetlana up
bsdb:38890302/1/2,38890302,randomized controlled trial,38890302,10.1038/s41467-024-49093-4,NA,"Seyoum Y., Greffeuille V., Kouadio D.K.D., Kuong K., Turpin W., M'Rabt R., Chochois V., Fortin S., Perignon M., Fiorentino M., Berger J., Burja K., Ponce M.C., Chamnan C., Wieringa F.T. , Humblot C.",Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice,Nature communications,2024,NA,Experiment 1,Cambodia,Homo sapiens,Feces,UBERON:0001988,Anemia,MONDO:0002280,Non anaemic,Anaemic,This Group includes children diagnosed with anemia with hemoglobin levels below the threshold (typically less than 11g/dl).,304,76,1 month,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,decreased,unchanged,NA,NA,NA,NA,Signature 2,Fig. 2A,16 December 2024,Joiejoie,"Joiejoie,WikiWorks",Differential ASVs between the children grouped according to their anaemic status.,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii",1783272|1239|526524|526525|2810280;1783272|1239|186801|186802|216572|216851;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958|2742598;1783272|1239|186801|3085636|186803|2569097|39488,Complete,Svetlana up
bsdb:38890302/2/1,38890302,randomized controlled trial,38890302,10.1038/s41467-024-49093-4,NA,"Seyoum Y., Greffeuille V., Kouadio D.K.D., Kuong K., Turpin W., M'Rabt R., Chochois V., Fortin S., Perignon M., Fiorentino M., Berger J., Burja K., Ponce M.C., Chamnan C., Wieringa F.T. , Humblot C.",Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice,Nature communications,2024,NA,Experiment 2,Cambodia,Homo sapiens,Feces,UBERON:0001988,Iron deficiency anemia,HP:0001891,No iron deficiency anaemia,Iron deficient anaemia,This group includes children diagnosed with iron deficient anemia with ferritin levels below 12 µg/L in children,333,47,1 month,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,decreased,unchanged,NA,NA,NA,NA,Signature 1,Fig. 2B,16 December 2024,Joiejoie,"Joiejoie,WikiWorks",Differential ASVs between the children grouped according to Iron deficiency anaemia.,increased,NA,NA,Complete,Svetlana up
bsdb:38890302/2/2,38890302,randomized controlled trial,38890302,10.1038/s41467-024-49093-4,NA,"Seyoum Y., Greffeuille V., Kouadio D.K.D., Kuong K., Turpin W., M'Rabt R., Chochois V., Fortin S., Perignon M., Fiorentino M., Berger J., Burja K., Ponce M.C., Chamnan C., Wieringa F.T. , Humblot C.",Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice,Nature communications,2024,NA,Experiment 2,Cambodia,Homo sapiens,Feces,UBERON:0001988,Iron deficiency anemia,HP:0001891,No iron deficiency anaemia,Iron deficient anaemia,This group includes children diagnosed with iron deficient anemia with ferritin levels below 12 µg/L in children,333,47,1 month,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,decreased,unchanged,NA,NA,NA,NA,Signature 2,Fig. 2B,16 December 2024,Joiejoie,"Joiejoie,WikiWorks",Differential ASVs between the children grouped according to their nutritional status. Iron deficiency anaemia.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium callanderi",1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;1783272|1239|186801|3085656|3085657;1783272|1239|186801|3085656;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|186806|1730|53442,Complete,Svetlana up
bsdb:38890302/3/1,38890302,randomized controlled trial,38890302,10.1038/s41467-024-49093-4,NA,"Seyoum Y., Greffeuille V., Kouadio D.K.D., Kuong K., Turpin W., M'Rabt R., Chochois V., Fortin S., Perignon M., Fiorentino M., Berger J., Burja K., Ponce M.C., Chamnan C., Wieringa F.T. , Humblot C.",Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice,Nature communications,2024,NA,Experiment 3,Cambodia,Homo sapiens,Feces,UBERON:0001988,Vitamin A deficiency,EFO:1001237,Sufficient vitamin A,Vitamin A deficiency,This group includes children diagnosed with Vitamin A deficiency with level less than 20 micrograms per deciliter [mcg/dL],350,30,1 month,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,decreased,decreased,NA,NA,NA,NA,Signature 1,Fig. 2C,16 December 2024,Joiejoie,"Joiejoie,WikiWorks",Differential ASVs between the children grouped according to Vitamin A deficiency.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,s__unidentified,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",1783272|1239|186801|3082720|186804|1501226;32644;1783272|201174|84998|1643822|1643826|644652;1783272|1239|91061|186826|33958,Complete,Svetlana up
bsdb:38890302/3/2,38890302,randomized controlled trial,38890302,10.1038/s41467-024-49093-4,NA,"Seyoum Y., Greffeuille V., Kouadio D.K.D., Kuong K., Turpin W., M'Rabt R., Chochois V., Fortin S., Perignon M., Fiorentino M., Berger J., Burja K., Ponce M.C., Chamnan C., Wieringa F.T. , Humblot C.",Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice,Nature communications,2024,NA,Experiment 3,Cambodia,Homo sapiens,Feces,UBERON:0001988,Vitamin A deficiency,EFO:1001237,Sufficient vitamin A,Vitamin A deficiency,This group includes children diagnosed with Vitamin A deficiency with level less than 20 micrograms per deciliter [mcg/dL],350,30,1 month,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,decreased,decreased,NA,NA,NA,NA,Signature 2,Fig. 2C,16 December 2024,Joiejoie,"Joiejoie,WikiWorks",Differential ASVs between the children grouped according to Vitamin A deficiency,decreased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum",3379134|200940|3031449|213115|194924;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|186802|216572|216851|1946507;1783272|1239|186801|186802|216572|39492,Complete,Svetlana up
bsdb:38890302/4/1,38890302,randomized controlled trial,38890302,10.1038/s41467-024-49093-4,NA,"Seyoum Y., Greffeuille V., Kouadio D.K.D., Kuong K., Turpin W., M'Rabt R., Chochois V., Fortin S., Perignon M., Fiorentino M., Berger J., Burja K., Ponce M.C., Chamnan C., Wieringa F.T. , Humblot C.",Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice,Nature communications,2024,NA,Experiment 4,Cambodia,Homo sapiens,Feces,UBERON:0001988,Growth delay,HP:0001510,Non-stunted children,Stunted children,This group includes children diagnosed with stunting with anthropometry measurement showing its prevalence at 40.0% at baseline,208,172,1 month,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 1,Fig. 2D,17 December 2024,Joiejoie,"Joiejoie,WikiWorks",Differential ASVs between the children grouped according to Stunting,increased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,1783272|1239|526524|526525|128827|1573535,Complete,Svetlana up
bsdb:38890302/4/2,38890302,randomized controlled trial,38890302,10.1038/s41467-024-49093-4,NA,"Seyoum Y., Greffeuille V., Kouadio D.K.D., Kuong K., Turpin W., M'Rabt R., Chochois V., Fortin S., Perignon M., Fiorentino M., Berger J., Burja K., Ponce M.C., Chamnan C., Wieringa F.T. , Humblot C.",Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice,Nature communications,2024,NA,Experiment 4,Cambodia,Homo sapiens,Feces,UBERON:0001988,Growth delay,HP:0001510,Non-stunted children,Stunted children,This group includes children diagnosed with stunting with anthropometry measurement showing its prevalence at 40.0% at baseline,208,172,1 month,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 2,Fig. 2D,17 December 2024,Joiejoie,"Joiejoie,WikiWorks",Differential ASVs between the children grouped according to stunting,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Raoultibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae",3379134|976|200643|171549|171550|239759;3379134|976|200643|1970189|1573805;3379134|976|200643|171549|1853231|283168;1783272|201174|84998|1643822|1643826|1926677;3379134|1224|1236|135624|83763|83770;3379134|1224|1236|135624|83763,Complete,Svetlana up
bsdb:38890302/5/1,38890302,randomized controlled trial,38890302,10.1038/s41467-024-49093-4,NA,"Seyoum Y., Greffeuille V., Kouadio D.K.D., Kuong K., Turpin W., M'Rabt R., Chochois V., Fortin S., Perignon M., Fiorentino M., Berger J., Burja K., Ponce M.C., Chamnan C., Wieringa F.T. , Humblot C.",Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice,Nature communications,2024,NA,Experiment 5,Cambodia,Homo sapiens,Feces,UBERON:0001988,Nutritional deficiency disease,EFO:1001067,Placebo,UR-Improved,"This group includes children placed on the more diverse micronutrient-fortified rice (FORISCA) fortified with vitamins A, B3, and B12 as additional vitamins.",114,122,1 month,16S,345,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,2,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 1,Fig. 4,17 December 2024,Joiejoie,"Joiejoie,KateRasheed,WikiWorks","Impact of the nutritional intervention on the taxonomic composition of
the faecal microbiota of the 380 children",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|572511;1783272|201174|84998|1643822|1643826|580024;3379134|976|200643|171549|2005473;1783272|1239|91061|186826|33958|1253;1783272|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:38890302/5/2,38890302,randomized controlled trial,38890302,10.1038/s41467-024-49093-4,NA,"Seyoum Y., Greffeuille V., Kouadio D.K.D., Kuong K., Turpin W., M'Rabt R., Chochois V., Fortin S., Perignon M., Fiorentino M., Berger J., Burja K., Ponce M.C., Chamnan C., Wieringa F.T. , Humblot C.",Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice,Nature communications,2024,NA,Experiment 5,Cambodia,Homo sapiens,Feces,UBERON:0001988,Nutritional deficiency disease,EFO:1001067,Placebo,UR-Improved,"This group includes children placed on the more diverse micronutrient-fortified rice (FORISCA) fortified with vitamins A, B3, and B12 as additional vitamins.",114,122,1 month,16S,345,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,2,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 2,Fig. 4,17 December 2024,Joiejoie,"Joiejoie,KateRasheed,WikiWorks,Tosin","Impact of the nutritional intervention on the taxonomic composition of
the faecal microbiota of the 380 children",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Sporanaerobacteraceae|g__Anaerosalibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:56,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Rummeliibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,",3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|1940255;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|1737404|1737405|2992718|1347386;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815|816;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802|1980681;1783272|1239|526524|526525|2810280;1783272|1239|186801|3085636|186803|33042;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|1946507;1783272|1239|1263031;1783272|1239|186801|3085636|186803|1407607;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958|2767887;1783272|1239|91061|186826|33958|2742598;1783272|1239|186801|3085636|186803|248744;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|186802|216572|1263|438033;1783272|1239|91061|1385|186818|648802;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|3085636|186803|2316020|33039;,Complete,Svetlana up
bsdb:38890302/6/1,38890302,randomized controlled trial,38890302,10.1038/s41467-024-49093-4,NA,"Seyoum Y., Greffeuille V., Kouadio D.K.D., Kuong K., Turpin W., M'Rabt R., Chochois V., Fortin S., Perignon M., Fiorentino M., Berger J., Burja K., Ponce M.C., Chamnan C., Wieringa F.T. , Humblot C.",Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice,Nature communications,2024,NA,Experiment 6,Cambodia,Homo sapiens,Feces,UBERON:0001988,Inflammation,MP:0001845,No inflammation,Inflammation,This group includes children grouped according to  systemic inflammation,240,140,1 month,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 1,S Fig. 2,17 December 2024,Joiejoie,"Joiejoie,WikiWorks","Differential ASVs between the children grouped according to their systemic
inflammation.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania",3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|1853231|574697;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|526524|526525|128827|61170,Complete,Svetlana up
bsdb:38890302/6/2,38890302,randomized controlled trial,38890302,10.1038/s41467-024-49093-4,NA,"Seyoum Y., Greffeuille V., Kouadio D.K.D., Kuong K., Turpin W., M'Rabt R., Chochois V., Fortin S., Perignon M., Fiorentino M., Berger J., Burja K., Ponce M.C., Chamnan C., Wieringa F.T. , Humblot C.",Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice,Nature communications,2024,NA,Experiment 6,Cambodia,Homo sapiens,Feces,UBERON:0001988,Inflammation,MP:0001845,No inflammation,Inflammation,This group includes children grouped according to  systemic inflammation,240,140,1 month,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 2,S Fig. 2,17 December 2024,Joiejoie,"Joiejoie,KateRasheed,WikiWorks","Differential ASVs between the children grouped according to their systemic
inflammation.",decreased,"k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter bugandensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|s__Enterococcaceae bacterium RF39,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lapidilactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lentilactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,s__unidentified,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:352",1783272|1798710|1906119;3379134|1224|1236|91347|543|547|881260;1783272|1239|91061|186826|81852|423410;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|33958|2767884;1783272|1239|91061|186826|33958|2767893;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1501226;3379134|1224|1236|135624|83763|83770;3379134|1224|1236|135624|83763;32644;1783272|1239|186801|186802|31979|1485|1262798,Complete,Svetlana up
bsdb:38890302/7/1,38890302,randomized controlled trial,38890302,10.1038/s41467-024-49093-4,NA,"Seyoum Y., Greffeuille V., Kouadio D.K.D., Kuong K., Turpin W., M'Rabt R., Chochois V., Fortin S., Perignon M., Fiorentino M., Berger J., Burja K., Ponce M.C., Chamnan C., Wieringa F.T. , Humblot C.",Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice,Nature communications,2024,NA,Experiment 7,Cambodia,Homo sapiens,Feces,UBERON:0001988,Parasitic infection,EFO:0001067,No parasitic infection,Parasitic infection,This group includes children grouped according to parasitic infection,276,104,1 month,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 1,S Fig. 2B,18 December 2024,Joiejoie,"Joiejoie,WikiWorks","Differential ASVs between the children grouped according to parasite infection,",increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|200940|3031449|213115|194924;1783272|1239|526524|526525|128827;1783272|1239|526524|526525|128827|1573535;1783272|1239|91061|186826|33958|46255;1783272|1239|186801|186802|31979|1266;1783272|1239|186801|186802|216572|236752;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:38890302/7/2,38890302,randomized controlled trial,38890302,10.1038/s41467-024-49093-4,NA,"Seyoum Y., Greffeuille V., Kouadio D.K.D., Kuong K., Turpin W., M'Rabt R., Chochois V., Fortin S., Perignon M., Fiorentino M., Berger J., Burja K., Ponce M.C., Chamnan C., Wieringa F.T. , Humblot C.",Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice,Nature communications,2024,NA,Experiment 7,Cambodia,Homo sapiens,Feces,UBERON:0001988,Parasitic infection,EFO:0001067,No parasitic infection,Parasitic infection,This group includes children grouped according to parasitic infection,276,104,1 month,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 2,S Fig. 2B,18 December 2024,Joiejoie,"Joiejoie,WikiWorks","Differential ASVs between the children grouped according to parasite infection,",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Kurthia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter",1783272|1239|91061|1385|186818|1649;1783272|201174|84998|1643822|1643826|644652,Complete,Svetlana up
bsdb:38890302/8/1,38890302,randomized controlled trial,38890302,10.1038/s41467-024-49093-4,NA,"Seyoum Y., Greffeuille V., Kouadio D.K.D., Kuong K., Turpin W., M'Rabt R., Chochois V., Fortin S., Perignon M., Fiorentino M., Berger J., Burja K., Ponce M.C., Chamnan C., Wieringa F.T. , Humblot C.",Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice,Nature communications,2024,NA,Experiment 8,Cambodia,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,10-14 years old,6-9 years old,This group includes children grouped according to age (6-9 years old),168,212,1 month,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,decreased,decreased,NA,NA,NA,NA,Signature 1,S Fig. 2C,18 December 2024,Joiejoie,"Joiejoie,WikiWorks",Differential ASVs between the children grouped according to age,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus",1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|3085642;1783272|1239|1737404|1737405|1570339|165779,Complete,Svetlana up
bsdb:38890302/8/2,38890302,randomized controlled trial,38890302,10.1038/s41467-024-49093-4,NA,"Seyoum Y., Greffeuille V., Kouadio D.K.D., Kuong K., Turpin W., M'Rabt R., Chochois V., Fortin S., Perignon M., Fiorentino M., Berger J., Burja K., Ponce M.C., Chamnan C., Wieringa F.T. , Humblot C.",Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice,Nature communications,2024,NA,Experiment 8,Cambodia,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,10-14 years old,6-9 years old,This group includes children grouped according to age (6-9 years old),168,212,1 month,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,decreased,decreased,NA,NA,NA,NA,Signature 2,S Fig. 2C,18 December 2024,Joiejoie,"Joiejoie,KateRasheed,WikiWorks",Differential ASVs between the children grouped according to age,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Agrilactobacillus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,s__unidentified,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136",1783272|1239|91061|186826|33958|2767875;3384189|32066|203490|203491|203492|180162;1783272|1239|186801|186802|1980681;1783272|1239|909932|1843489|31977|39948;3384189|32066|203490|203491|203492;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|91061|186826|33958|2759736;1783272|1239|186801|3085636|186803|248744;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|841;1783272|1239|909932|1843489|31977;32644;1783272|1239|186801|3085636|186803|877420,Complete,Svetlana up
bsdb:38890302/9/1,38890302,randomized controlled trial,38890302,10.1038/s41467-024-49093-4,NA,"Seyoum Y., Greffeuille V., Kouadio D.K.D., Kuong K., Turpin W., M'Rabt R., Chochois V., Fortin S., Perignon M., Fiorentino M., Berger J., Burja K., Ponce M.C., Chamnan C., Wieringa F.T. , Humblot C.",Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice,Nature communications,2024,NA,Experiment 9,Cambodia,Homo sapiens,Feces,UBERON:0001988,Biological sex,PATO:0000047,Girl,Boy,This group includes children identified on sex as a covariate feature.,180,200,1 month,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 1,S Fig. 2D,19 December 2024,Joiejoie,"Joiejoie,WikiWorks",Differential ASVs between the children grouped according to their sex,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,s__unidentified",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3082720|3030910;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|33042;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|91061|186826|33958|2767887;1783272|1239|186801|186802|216572;32644,Complete,Svetlana up
bsdb:38890302/9/2,38890302,randomized controlled trial,38890302,10.1038/s41467-024-49093-4,NA,"Seyoum Y., Greffeuille V., Kouadio D.K.D., Kuong K., Turpin W., M'Rabt R., Chochois V., Fortin S., Perignon M., Fiorentino M., Berger J., Burja K., Ponce M.C., Chamnan C., Wieringa F.T. , Humblot C.",Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice,Nature communications,2024,NA,Experiment 9,Cambodia,Homo sapiens,Feces,UBERON:0001988,Biological sex,PATO:0000047,Girl,Boy,This group includes children identified on sex as a covariate feature.,180,200,1 month,16S,345,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 2,S Fig. 2D,19 December 2024,Joiejoie,"Joiejoie,KateRasheed,WikiWorks",Differential ASVs between the children grouped according to their sex.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239|186801|186802|31979;1783272|1239|186801|186802;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|1385|539738;1783272|1239|91061|1385|90964;1783272|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:38904070/1/1,38904070,"prospective cohort,time series / longitudinal observational",38904070,10.1016/j.isci.2024.110142,NA,"Kayongo A., Ntayi M.L., Olweny G., Kyalo E., Ndawula J., Ssengooba W., Kigozi E., Kalyesubula R., Munana R., Namaganda J., Caroline M., Sekibira R., Bagaya B.S., Kateete D.P., Joloba M.L., Jjingo D., Sande O.J. , Mayanja-Kizza H.",Airway microbiome signature accurately discriminates <i>Mycobacterium tuberculosis</i> infection status,iScience,2024,"Bacteriology, Microbiology, Microbiome",Experiment 1,Uganda,Homo sapiens,Sputum,UBERON:0007311,Pulmonary tuberculosis,EFO:1000049,Non‑Tuberculosis (M.tb-uninfected),Active tuberculosis patients (PTB),Active tuberculosis defined by GeneXpert,NA,NA,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,"age,sex,smoking status",NA,decreased,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 4C,17 July 2025,Nuerteye,Nuerteye,Bar plots showing linear discriminant analysis (LDA) effect size scores of OTUs in active TB versus LTBI and M.tb-uninfected groups.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Brevibacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Beijerinckiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium tuberculosis",1783272|1239|91061|1385|186822|55080;1783272|201174|1760|85006|85023|33882;1783272|201174|1760|85011|2062|1883;3379134|1224|28211|356|45404;1783272|201174|1760|85007|1762|1763|1773,Complete,NA
bsdb:38904070/1/2,38904070,"prospective cohort,time series / longitudinal observational",38904070,10.1016/j.isci.2024.110142,NA,"Kayongo A., Ntayi M.L., Olweny G., Kyalo E., Ndawula J., Ssengooba W., Kigozi E., Kalyesubula R., Munana R., Namaganda J., Caroline M., Sekibira R., Bagaya B.S., Kateete D.P., Joloba M.L., Jjingo D., Sande O.J. , Mayanja-Kizza H.",Airway microbiome signature accurately discriminates <i>Mycobacterium tuberculosis</i> infection status,iScience,2024,"Bacteriology, Microbiology, Microbiome",Experiment 1,Uganda,Homo sapiens,Sputum,UBERON:0007311,Pulmonary tuberculosis,EFO:1000049,Non‑Tuberculosis (M.tb-uninfected),Active tuberculosis patients (PTB),Active tuberculosis defined by GeneXpert,NA,NA,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,"age,sex,smoking status",NA,decreased,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 4C,17 July 2025,Nuerteye,Nuerteye,Bar plots showing linear discriminant analysis (LDA) effect size scores of OTUs in active TB versus LTBI and M.tb-uninfected groups.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella",1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|815|816;3379134|976|200643|171549|171552|838;3379134|1224|1236|135614|32033|40323;3384189|32066|203490|203491|203492|848;1783272|1239|909932;3379134|1224|28216|206351|481|482;3379134|1224|28216|80840|119060|32008;3379134|1224|1236|135625|712|745;3379134|1224|28211|204457|41297|13687;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|135625|712|724;3379134|976|200643|171549|171552|1283313;3384189|32066|203490|203491|1129771|32067;1783272|1239|91061|186826|186828|117563,Complete,NA
bsdb:38908272/1/1,38908272,case-control,38908272,10.1016/j.envint.2024.108806,NA,"Deng Z., Li L., Jing Z., Luo X., Yu F., Zeng W., Bi W. , Zou J.",Association between environmental phthalates exposure and gut microbiota and metabolome in dementia with Lewy bodies,Environment international,2024,"Dementia with Lewy bodies, Gut microbiota, Metabolites, Multi-omics, Phthalates",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Lewy body dementia,EFO:0006792,Healthy controls,DLB patients,Patients diagnosed with Dementia with Lewy bodies,45,43,1 month,16S,34,Illumina,relative abundances,"ANOVA,T-Test",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,30 July 2025,Kristin.abraham,Kristin.abraham,Taxa enriched in DLB patients,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|815|816|329854;3379134|976|200643|171549|815|816|46506;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|459786|351091;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|186802|216572|1263,Complete,NA
bsdb:38908272/1/2,38908272,case-control,38908272,10.1016/j.envint.2024.108806,NA,"Deng Z., Li L., Jing Z., Luo X., Yu F., Zeng W., Bi W. , Zou J.",Association between environmental phthalates exposure and gut microbiota and metabolome in dementia with Lewy bodies,Environment international,2024,"Dementia with Lewy bodies, Gut microbiota, Metabolites, Multi-omics, Phthalates",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Lewy body dementia,EFO:0006792,Healthy controls,DLB patients,Patients diagnosed with Dementia with Lewy bodies,45,43,1 month,16S,34,Illumina,relative abundances,"ANOVA,T-Test",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5,30 July 2025,Kristin.abraham,Kristin.abraham,Taxa depleted in DLB patients,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|976|200643|171549|2005519|397864|487174;1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|1678|216816;3379134|976|200643|171549|171552|838,Complete,NA
bsdb:38918632/1/1,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 1,"United States of America,Israel,China,Sweden,Finland,Denmark,Germany,France",Homo sapiens,Feces,UBERON:0001988,Response to metformin,GO:1901558,Metformin naive T2D (type 2 diabetes) patients,Metformin treated T2D (type 2 diabetes) patients,Species confounded by metformin use in T2D (type 2 diabetes) cases,3,7,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Extended Data Figure 4B,15 October 2025,Tosin,Tosin,Meta-analyzed and cohort-specific associations of microbial species with metformin use among T2D (type 2 diabetes) patients,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia",1783272|1239|909932|1843488|909930|904|187327;3379134|200940|3031449|213115|194924|35832|35833,Complete,NA
bsdb:38918632/1/2,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 1,"United States of America,Israel,China,Sweden,Finland,Denmark,Germany,France",Homo sapiens,Feces,UBERON:0001988,Response to metformin,GO:1901558,Metformin naive T2D (type 2 diabetes) patients,Metformin treated T2D (type 2 diabetes) patients,Species confounded by metformin use in T2D (type 2 diabetes) cases,3,7,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Extended Data Figure 4B,15 October 2025,Tosin,Tosin,Meta-analyzed and cohort-specific associations of microbial species with metformin use among type 2 diabetes (T2D) patients,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:95,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:309",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|186802|216572|216851|853;1783272|1239|1262988;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|3082720|186804|1505657|261299;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|841|1262945,Complete,NA
bsdb:38918632/2/1,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 2,"China,Denmark,Finland,France,Germany,Israel,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Response to metformin,GO:1901558,Metformin naive T2D (type 2 diabetes) patients,Metformin treated T2D (type 2 diabetes) patients,Species associated with both metformin use and T2D (type 2 diabetes) cases,3,7,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Extended data Fig. 4B,15 October 2025,Fiddyhamma,"Fiddyhamma,Tosin",Meta-analyzed and cohort-specific associations of microbial species associated with both metformin use and T2D (type 2 diabetes),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli",1783272|1239|186801|3085636|186803|2719313|208479;3379134|1224|1236|91347|543|561|562,Complete,NA
bsdb:38918632/2/2,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 2,"China,Denmark,Finland,France,Germany,Israel,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Response to metformin,GO:1901558,Metformin naive T2D (type 2 diabetes) patients,Metformin treated T2D (type 2 diabetes) patients,Species associated with both metformin use and T2D (type 2 diabetes) cases,3,7,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Extended data Fig. 4B,15 October 2025,Fiddyhamma,Fiddyhamma,Meta-analyzed and cohort-specific associations of microbial species associated with both metformin use and T2D (type 2 diabetes),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:167,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:182",1783272|1239|186801|186802|31979|1485|1262777;1783272|1239|186801|3085636|186803|841|1262942,Complete,NA
bsdb:38918632/3/1,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 3,"China,Denmark,Finland,France,Germany,Israel,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Increased normoglycemic,Decreased normoglycemic,"People with decreasing normoglycemic condition, which finalizes in type 2 diabetes (diabetes mellitus).",10,10,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,"Supplementary Table 3, Extended data figure 3a",16 October 2025,YokoC,YokoC,"Heatmap for the meta-analyzed associations of microbial species with T2D (type 2 diabetes). The blue-to-red gradient represents the magnitude and direction of the associations quantified by a linear mixed model that includes disease status as an ordinal variable (normoglycemic controls, prediabetes or T2D).",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. CAG:257,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp. CAG:317,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius",1783272|1239|909932|1843488|909930|904|187327;1783272|1239|186801|186802|216572|244127|169435;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|818;1783272|201174|1760|85004|31953|1678|1681;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|3085636|186803|572511|1262756;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330|1262873;1783272|1239|186801|3085636|186803|1432051|1720294;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|2719313|358743;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|909932|909929|1843491|158846|437897;1783272|1239|909932|1843489|31977|906|907;1783272|1239|909932|1843488|909930|33024|33025;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1302;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1304,Complete,NA
bsdb:38918632/3/2,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 3,"China,Denmark,Finland,France,Germany,Israel,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Increased normoglycemic,Decreased normoglycemic,"People with decreasing normoglycemic condition, which finalizes in type 2 diabetes (diabetes mellitus).",10,10,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,"Supplementary Table 3, Extended data figure 3a",16 October 2025,YokoC,YokoC,"Heatmap for the meta-analyzed associations of microbial species with T2D (type 2 diabetes). The blue-to-red gradient represents the magnitude and direction of the associations quantified by a linear mixed model that includes disease status as an ordinal variable (normoglycemic controls, prediabetes or T2D).",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes inops,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. An250,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:144,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:167,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:253,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter secundus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:38,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:110,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:170,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:238,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:94,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:95,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 57_20,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. CAG:241,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:182,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:309,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D5,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Liu et al. 2021),k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis|s__Victivallis vadensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris",3379134|976|200643|171549|171550|239759|1501391;3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|171550|239759|328814;1783272|1239|186801|186802|3082771|1924093|1965604;1783272|1239|186801|3085636|186803|207244|649756;3379134|976|200643|171549|815|816|1262736;3379134|976|200643|171549|2005519|397864|487174;1783272|1239|186801|186802|31979|1485|1262777;1783272|1239|186801|186802|31979|1485|1262785;3379134|976|200643|171549|2005519|1348911|1501392;1783272|1239|186801|3085636|186803|33042|33043;3379134|200940|3031449|213115|194924|872|901;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|3342669|45851;1783272|1239|186801|186802|186806|1730|1262889;1783272|1239|186801|186802|216572|216851|853;1783272|1239|1263000;1783272|1239|1263006;1783272|1239|1263011;1783272|1239|1262989;1783272|1239|1262988;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|3082720|186804|1505657|261299;1783272|1239|186801|3085636|186803|28050|39485;3366610|28890|183925|2158|2159|2172|2173;1783272|1239|186801|186802|216572|459786|1897011;1783272|1239|186801|186802|216572|459786|1262911;3379134|1224|28216|80840|995019|577310|487175;3379134|976|200643|171549|815|909656|310297;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|841|1262942;1783272|1239|186801|3085636|186803|841|1262945;1783272|1239|186801|186802|216572|1520815;1783272|1239|186801|186802|216572|1263|3062497;1783272|1239|526524|526525|2810281|191303|154288;3379134|256845|1313211|278082|255528|172900|172901;1783272|1239|186801|186802|216572|39492;1783272|1239|186801|3085636|186803|2316020|46228,Complete,NA
bsdb:38918632/4/1,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 4,"China,Denmark,Finland,France,Germany,Israel,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Increased normoglycemic,Decreased normoglycemic,"People with decreasing normoglycemic condition, which finalizes in type 2 diabetes (diabetes mellitus).",10,10,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2a, Supplementary Table 3 and Extended Data Figure 3a",16 October 2025,YokoC,YokoC,"Heatmap for the meta-analyzed associations of microbial species with T2D (type 2 diabetes). The blue-to-red gradient represents the magnitude and direction of the associations quantified by a linear mixed model that includes disease status as an ordinal variable (normoglycemic controls, prediabetes or T2D).",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. CAG:257,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius",1783272|1239|909932|1843488|909930|904|187327;1783272|1239|186801|186802|216572|244127|169435;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|818;1783272|201174|1760|85004|31953|1678|1681;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|3085636|186803|572511|1262756;1783272|1239|186801|3085636|186803|1432051|1720294;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|2719313|358743;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|186802|1392389|1297617;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|909932|1843488|909930|33024|33025;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1302;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1304,Complete,NA
bsdb:38918632/4/2,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 4,"China,Denmark,Finland,France,Germany,Israel,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Increased normoglycemic,Decreased normoglycemic,"People with decreasing normoglycemic condition, which finalizes in type 2 diabetes (diabetes mellitus).",10,10,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2a, Supplementary Table 3 and Extended Data Figure 3a",16 October 2025,YokoC,YokoC,"Heatmap for the meta-analyzed associations of microbial species with T2D (type 2 diabetes). The blue-to-red gradient represents the magnitude and direction of the associations quantified by a linear mixed model that includes disease status as an ordinal variable (normoglycemic controls, prediabetes or T2D).",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:167,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:253,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:170,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:238,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:95,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 57_20,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. CAG:241,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:182,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:309,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Liu et al. 2021),k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris",1783272|1239|186801|3085636|186803|1766253|39491;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|2005519|397864|487174;1783272|1239|186801|186802|31979|1485|1262777;1783272|1239|186801|186802|31979|1485|1262785;1783272|1239|186801|3085636|186803|33042|33043;3379134|200940|3031449|213115|194924|872|901;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|3342669|45851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|1263006;1783272|1239|1263011;1783272|1239|1262988;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|3082720|186804|1505657|261299;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|186802|216572|459786|1897011;1783272|1239|186801|186802|216572|459786|1262911;3379134|1224|28216|80840|995019|577310|487175;3379134|976|200643|171549|815|909656|310297;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|841|1262942;1783272|1239|186801|3085636|186803|841|1262945;1783272|1239|186801|186802|216572|1263|3062497;1783272|1239|526524|526525|2810281|191303|154288;1783272|1239|186801|3085636|186803|2316020|46228,Complete,NA
bsdb:38918632/5/1,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 5,"China,Denmark,Finland,France,Germany,Israel,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic controls,Type 2 diabetes (T2D),People with type 2 diabetes (diabetes mellitus).,2277,1851,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Extended data Figure 3B and Supplementary Table 2,17 October 2025,Fiddyhamma,Fiddyhamma,"Meta- analyzed associations of individual microbial species with type 2 diabetes
(T2D) phenotype from the binary (b) models.The binary model modeled the disease status as a binary variable (T2D or controls) and used data from T2D patients and normoglycemic controls.",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum lactatifermentans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. CAG:257,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp. CAG:317,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster lavalensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum",1783272|1239|909932|1843488|909930|904|187327;1783272|1239|186801|3085636|3118652|2039240|160404;1783272|1239|186801|186802|216572|244127|169435;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|818;1783272|201174|1760|85004|31953|1678|1681;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|3085636|186803|572511|1262756;1783272|1239|186801|3085636|186803|189330|1262873;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|2719313|358743;1783272|1239|186801|3085636|186803|2719313|460384;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|909932|909929|1843491|158846|437897;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1302;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|186801|3085636|186803|2941495|1512,Complete,NA
bsdb:38918632/5/2,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 5,"China,Denmark,Finland,France,Germany,Israel,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic controls,Type 2 diabetes (T2D),People with type 2 diabetes (diabetes mellitus).,2277,1851,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Extended Data Figure 3B and Supplementary Table 2,20 October 2025,Tosin,"Tosin,Fiddyhamma",Meta- analyzed associations of individual microbial species with type 2 diabetes (T2D) phenotype from the binary (b) models.The binary model modeled the disease status as a binary variable (T2D or controls) and used data from T2D patients and normoglycemic controls.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes inops,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. An250,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:144,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:167,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:253,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter secundus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:110,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:170,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:238,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:94,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:95,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 57_20,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. CAG:241,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:182,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:309,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D5,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis|s__Victivallis vadensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Liu et al. 2021)",3379134|976|200643|171549|171550|239759|1501391;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|171550|239759|328814;1783272|1239|186801|186802|3082771|1924093|1965604;1783272|1239|186801|3085636|186803|207244|649756;3379134|976|200643|171549|815|816|1262736;3379134|976|200643|171549|2005519|397864|487174;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|186802|31979|1485|1262777;1783272|1239|186801|186802|31979|1485|1262785;3379134|976|200643|171549|2005519|1348911|1501392;1783272|1239|186801|3085636|186803|33042|33043;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|3342669|45851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|1263000;1783272|1239|1263006;1783272|1239|1263011;1783272|1239|1262989;1783272|1239|1262988;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|3085636|186803|28050|39485;3366610|28890|183925|2158|2159|2172|2173;3379134|976|200643|171549|1853231|283168|28118;1783272|1239|186801|186802|216572|459786|1897011;1783272|1239|186801|186802|216572|459786|1262911;3379134|1224|28216|80840|995019|577310|487175;3379134|976|200643|171549|815|909656|310297;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|841|1262942;1783272|1239|186801|3085636|186803|841|1262945;1783272|1239|186801|186802|216572|1520815;3379134|256845|1313211|278082|255528|172900|172901;1783272|1239|186801|186802|216572|39492;1783272|1239|186801|3085636|186803|2316020|46228;1783272|1239|186801|186802|216572|1263|3062497,Complete,NA
bsdb:38918632/6/1,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 6,"China,Denmark,Finland,France,Germany,Israel,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic controls,Type 2 diabetes (T2D),People with type 2 diabetes (diabetes mellitus).,2277,1851,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Extended data Figure 3B and Supplementary Table 2,17 October 2025,Fiddyhamma,Fiddyhamma,Meta- analyzed associations of individual microbial species with type 2 diabetes (T2D) phenotype from the binary (b) models.The binary model modeled the disease status as a binary variable (T2D or controls) and used data from T2D patients and normoglycemic controls.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius",1783272|1239|909932|1843488|909930|904|187327;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|818;1783272|201174|1760|85004|31953|1678|1681;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|2719313|358743;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1302;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1304,Complete,NA
bsdb:38918632/6/2,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 6,"China,Denmark,Finland,France,Germany,Israel,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic controls,Type 2 diabetes (T2D),People with type 2 diabetes (diabetes mellitus).,2277,1851,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Extended Data Figure 3B and Supplementary Table 2,20 October 2025,Tosin,"Tosin,Fiddyhamma",Meta- analyzed associations of individual microbial species with type 2 diabetes (T2D) phenotype from the binary (b) models.The binary model modeled the disease status as a binary variable (T2D or controls) and used data from T2D patients and normoglycemic controls.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes inops,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:167,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:253,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:238,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:95,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 57_20,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:182,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:309,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris",3379134|976|200643|171549|171550|239759|1501391;1783272|1239|186801|3085636|186803|207244|649756;3379134|976|200643|171549|2005519|397864|487174;1783272|1239|186801|186802|31979|1485|1262777;1783272|1239|186801|186802|31979|1485|1262785;1783272|1239|186801|3085636|186803|33042|33043;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|3342669|45851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|1263011;1783272|1239|1262988;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|186802|216572|459786|1897011;3379134|1224|28216|80840|995019|577310|487175;3379134|976|200643|171549|815|909656|310297;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|841|1262942;1783272|1239|186801|3085636|186803|841|1262945;1783272|1239|186801|3085636|186803|2316020|46228,Complete,NA
bsdb:38918632/7/1,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 7,"China,Denmark,Finland,France,Germany,Israel,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic controls,Type 2 diabetes (T2D),People with type 2 diabetes (diabetes mellitus).,2277,1851,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Extended data Figure 3B and Supplementary Table 2,17 October 2025,Fiddyhamma,Fiddyhamma,Meta- analyzed associations of individual microbial species with type 2 diabetes (T2D) phenotype from the binary (b) models.The binary model modeled the disease status as a binary variable (T2D or controls) and used data from T2D patients and normoglycemic controls.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp. CAG:317,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania filiformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa",1783272|1239|909932|1843488|909930|904|187327;3379134|976|200643|171549|815|816|817;1783272|201174|1760|85004|31953|1678|1681;1783272|1239|186801|3085636|186803|189330|1262873;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|2719313|358743;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|526524|526525|128827|61170|61171;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|526524|526525|2810280|3025755|1547,Complete,NA
bsdb:38918632/7/2,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 7,"China,Denmark,Finland,France,Germany,Israel,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic controls,Type 2 diabetes (T2D),People with type 2 diabetes (diabetes mellitus).,2277,1851,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Extended Data Figure 3B and Supplementary Table 2,21 October 2025,Tosin,"Tosin,Fiddyhamma",Meta- analyzed associations of individual microbial species with type 2 diabetes (T2D) phenotype from the binary (b) models.The binary model modeled the disease status as a binary variable (T2D or controls) and used data from T2D patients and normoglycemic controls.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes inops,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:167,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter secundus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:110,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:238,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:95,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 57_20,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:182,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:309,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis|s__Victivallis vadensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris",3379134|976|200643|171549|171550|239759|1501391;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|171550|239759|328814;1783272|1239|186801|186802|31979|1485|1262777;3379134|976|200643|171549|2005519|1348911|1501392;1783272|1239|186801|3085636|186803|33042|33043;1783272|1239|186801|3085636|186803|3342669|45851;1783272|1239|1263000;1783272|1239|1263011;1783272|1239|1262988;1783272|1239|186801|3085636|186803|1407607|1150298;3379134|976|200643|171549|1853231|283168|28118;1783272|1239|186801|186802|216572|459786|1897011;3379134|1224|28216|80840|995019|577310|487175;1783272|1239|186801|3085636|186803|841|1262942;1783272|1239|186801|3085636|186803|841|1262945;3379134|256845|1313211|278082|255528|172900|172901;1783272|1239|186801|3085636|186803|2316020|46228,Complete,NA
bsdb:38918632/8/1,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 8,"China,Denmark,Finland,France,Germany,Israel,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic controls,Type 2 diabetes (T2D),People with type 2 diabetes (diabetes mellitus).,2277,1851,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Extended data Figure 3B and Supplementary Table 2,17 October 2025,Fiddyhamma,Fiddyhamma,Meta- analyzed associations of individual microbial species with type 2 diabetes (T2D) phenotype from the binary (b) models.The binary model modeled the disease status as a binary variable (T2D or controls) and used data from T2D patients and normoglycemic controls.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp. CAG:317,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius",3379134|976|200643|171549|815|816|817;1783272|201174|1760|85004|31953|1678|1681;1783272|1239|186801|3085636|186803|189330|1262873;1783272|1239|186801|3085636|186803|2719313|358743;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1304,Complete,NA
bsdb:38918632/8/2,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 8,"China,Denmark,Finland,France,Germany,Israel,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic controls,Type 2 diabetes (T2D),People with type 2 diabetes (diabetes mellitus).,2277,1851,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Extended data Figure 3B and Supplementary Table 2,21 October 2025,Fiddyhamma,Fiddyhamma,Meta- analyzed associations of individual microbial species with type 2 diabetes (T2D) phenotype from the binary (b) models.The binary model modeled the disease status as a binary variable (T2D or controls) and used data from T2D patients and normoglycemic controls.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:238,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:182,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris",1783272|1239|186801|3085636|186803|33042|33043;1783272|1239|186801|3085636|186803|3342669|45851;1783272|1239|1263011;3379134|976|200643|171549|815|909656|310297;1783272|1239|186801|3085636|186803|841|1262942;1783272|1239|186801|3085636|186803|2316020|46228,Complete,NA
bsdb:38918632/9/1,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 9,"China,Denmark,Finland,France,Germany,Israel,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic controls,Type 2 diabetes (T2D),People with type 2 diabetes (diabetes mellitus).,2277,1851,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Extended data Figure 3B and Supplementary Table 2,17 October 2025,Fiddyhamma,Fiddyhamma,"Meta- analyzed associations of individual microbial species with type 2 diabetes (T2D) phenotype from the binary (b) models.The binary model modeled the disease status as a binary variable (T2D or controls) and used data from T2D patients and normoglycemic controls.	  
		  
		  ",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp. CAG:317,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius",1783272|1239|186801|3085636|186803|189330|1262873;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1304,Complete,NA
bsdb:38918632/9/2,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 9,"China,Denmark,Finland,France,Germany,Israel,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic controls,Type 2 diabetes (T2D),People with type 2 diabetes (diabetes mellitus).,2277,1851,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Extended data Figure 3B and Supplementary Table 2,21 October 2025,Fiddyhamma,Fiddyhamma,Meta- analyzed associations of individual microbial species with type 2 diabetes (T2D) phenotype from the binary (b) models.The binary model modeled the disease status as a binary variable (T2D or controls) and used data from T2D patients and normoglycemic controls.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:238,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:182,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris",1783272|1239|186801|3085636|186803|33042|33043;1783272|1239|186801|3085636|186803|3342669|45851;1783272|1239|1263011;1783272|1239|186801|3085636|186803|841|1262942;1783272|1239|186801|3085636|186803|2316020|46228,Complete,NA
bsdb:38918632/10/1,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 10,"China,Denmark,Finland,France,Germany,Israel,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Increased normoglycemic,Decreased normoglycemic,"People with decreasing normoglycemic condition, which finalizes in type 2 diabetes (T2D) mellitus",10,10,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2A, Extended Data Figure 3A and Supplementary Table 3",18 October 2025,Tosin,Tosin,"Meta-analyzed associations of microbial species with type 2 diabetes (T2D) based on 8,117 metagenomes from 1,851 T2D patients, 2,770 individuals with prediabetes, and 2,277 normoglycemic controls. The blue-to-red gradient represents the magnitude and direction of the associations quantified by linear mixed models that include disease status as an ordinal variable (normoglycemic controls, prediabetes, or T2D) and adjust for age, sex, body mass index (BMI), and metformin use (metf). For multiple comparison correction, we controlled the false discovery rate (FDR) with a target rate of 0.10.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius",3379134|976|200643|171549|815|816|817;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|2719313|358743;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1304,Complete,NA
bsdb:38918632/10/2,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 10,"China,Denmark,Finland,France,Germany,Israel,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Increased normoglycemic,Decreased normoglycemic,"People with decreasing normoglycemic condition, which finalizes in type 2 diabetes (T2D) mellitus",10,10,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2A, Extended Data Figure 3A and Supplementary Table 3",18 October 2025,Tosin,Tosin,"Meta-analyzed associations of microbial species with type 2 diabetes (T2D) based on 8,117 metagenomes from 1,851 T2D patients, 2,770 individuals with prediabetes, and 2,277 normoglycemic controls. The blue-to-red gradient represents the magnitude and direction of the associations quantified by linear mixed models that include disease status as an ordinal variable (normoglycemic controls, prediabetes, or T2D) and adjust for age, sex, body mass index (BMI), and metformin use (metf). For multiple comparison correction, we controlled the false discovery rate (FDR) with a target rate of 0.10.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:167,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:238,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 57_20,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:182,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis",1783272|1239|186801|186802|31979|1485|1262777;1783272|1239|186801|3085636|186803|33042|33043;3379134|200940|3031449|213115|194924|872|901;1783272|1239|1263011;1783272|1239|186801|186802|216572|459786|1897011;1783272|1239|186801|3085636|186803|841|1262942;1783272|1239|526524|526525|2810281|191303|154288,Complete,NA
bsdb:38918632/11/1,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 11,"China,Denmark,Finland,France,Germany,Israel,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Increased normoglycemic,Decreased normoglycemic,"People with decreasing normoglycemic condition, which finalizes in type 2 diabetes (diabetes mellitus).",10,10,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,"Extended Data Figure 3A, Supplementary Table 3",20 October 2025,Tosin,Tosin,"Meta-analyzed associations of microbial species with type 2 diabetes (T2D) based on 8,117 metagenomes from 1,851 T2D patients, 2,770 individuals with prediabetes, and 2,277 normoglycemic controls. The blue-to-red gradient represents the magnitude and direction of the associations quantified by linear mixed models that include disease status as an ordinal variable (normoglycemic controls, prediabetes, or T2D) and adjust for age, sex, body mass index (BMI),metformin use (metf) and insulin use. For multiple comparison correction, we controlled the false discovery rate (FDR) with a target rate of 0.10.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius",3379134|976|200643|171549|815|816|817;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|2719313|358743;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1304,Complete,NA
bsdb:38918632/11/2,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 11,"China,Denmark,Finland,France,Germany,Israel,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Increased normoglycemic,Decreased normoglycemic,"People with decreasing normoglycemic condition, which finalizes in type 2 diabetes (diabetes mellitus).",10,10,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,"Extended Data Figure 3A, Supplementary Table 3",20 October 2025,Tosin,Tosin,"Meta-analyzed associations of microbial species with type 2 diabetes (T2D) based on 8,117 metagenomes from 1,851 T2D patients, 2,770 individuals with prediabetes, and 2,277 normoglycemic controls. The blue-to-red gradient represents the magnitude and direction of the associations quantified by linear mixed models that include disease status as an ordinal variable (normoglycemic controls, prediabetes, or T2D) and adjust for age, sex, body mass index (BMI),metformin use (metf) and insulin use. For multiple comparison correction, we controlled the false discovery rate (FDR) with a target rate of 0.10.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:167,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:238,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 57_20,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:182,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis",1783272|1239|186801|186802|31979|1485|1262777;1783272|1239|186801|3085636|186803|33042|33043;3379134|200940|3031449|213115|194924|872|901;1783272|1239|1263011;1783272|1239|186801|186802|216572|459786|1897011;1783272|1239|186801|3085636|186803|841|1262942;1783272|1239|526524|526525|2810281|191303|154288,Complete,NA
bsdb:38918632/12/1,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 12,"China,Denmark,Finland,France,Germany,Israel,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Increased normoglycemic,Decreased normoglycemic,"People with decreasing normoglycemic condition, which finalizes in type 2 diabetes (T2D) mellitus",10,10,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2A, Extended Data Figure 3A and Supplementary Table 3",20 October 2025,Tosin,"Tosin,Fiddyhamma","Meta-analyzed associations of microbial species with type 2 diabetes (T2D) based on 8,117 metagenomes from 1,851 T2D patients, 2,770 individuals with prediabetes, and 2,277 normoglycemic controls. The blue-to-red gradient represents the magnitude and direction of the associations quantified by linear mixed models that include disease status as an ordinal variable (normoglycemic controls, prediabetes, or T2D) and adjust for age, sex and metformin use (metf). For multiple comparison correction, we controlled the false discovery rate (FDR) with a target rate of 0.10.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. CAG:257,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:58,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp. CAG:317,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius",1783272|1239|186801|186802|216572|244127|169435;3379134|976|200643|171549|815|816|817;1783272|1239|186801|3085636|186803|572511|1262756;1783272|1239|186801|186802|31979|1485|1262824;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|3085636|186803|189330|1262873;1783272|1239|186801|3085636|186803|1432051|1720294;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|2719313|358743;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|909932|909929|1843491|158846|437897;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1304,Complete,NA
bsdb:38918632/12/2,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 12,"China,Denmark,Finland,France,Germany,Israel,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Increased normoglycemic,Decreased normoglycemic,"People with decreasing normoglycemic condition, which finalizes in type 2 diabetes (T2D) mellitus",10,10,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2A, Extended Data Figure 3A and Supplementary Table 3",20 October 2025,Tosin,Tosin,"Meta-analyzed associations of microbial species with type 2 diabetes (T2D) based on 8,117 metagenomes from 1,851 T2D patients, 2,770 individuals with prediabetes, and 2,277 normoglycemic controls. The blue-to-red gradient represents the magnitude and direction of the associations quantified by linear mixed models that include disease status as an ordinal variable (normoglycemic controls, prediabetes, or T2D) and adjust for age, sex and metformin use (metf). For multiple comparison correction, we controlled the false discovery rate (FDR) with a target rate of 0.10.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:167,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter secundus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:110,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:238,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:95,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 57_20,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:182,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:309,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D5,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis|s__Victivallis vadensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris",3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|2005519|397864|487174;1783272|1239|186801|186802|31979|1485|1262777;3379134|976|200643|171549|2005519|1348911|1501392;1783272|1239|186801|3085636|186803|33042|33043;3379134|200940|3031449|213115|194924|872|901;1783272|1239|186801|3085636|186803|3342669|45851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|1263000;1783272|1239|1263011;1783272|1239|1262988;1783272|1239|186801|3085636|186803|28050|39485;3366610|28890|183925|2158|2159|2172|2173;3379134|976|200643|171549|1853231|283168|28118;1783272|1239|186801|186802|216572|459786|1897011;3379134|1224|28216|80840|995019|577310|487175;3379134|976|200643|171549|815|909656|310297;1783272|1239|186801|3085636|186803|841|1262942;1783272|1239|186801|3085636|186803|841|1262945;1783272|1239|186801|186802|216572|1520815;1783272|1239|526524|526525|2810281|191303|154288;3379134|256845|1313211|278082|255528|172900|172901;1783272|1239|186801|3085636|186803|2316020|46228,Complete,NA
bsdb:38918632/13/1,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 13,"China,Denmark,Finland,France,Germany,Israel,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Increased normoglycemic,Decreased normoglycemic,"Female patients with decreasing normoglycemic condition, which finalizes in type 2 diabetes (T2D) mellitus",10,10,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,"age,body mass index",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 11,21 October 2025,YokoC,YokoC,"Heatmap of meta-analyzed associations of microbial species with T2D (type 2 diabetes). The blue-to-red gradient represents the magnitude and direction of the associations quantified by Maaslin2, where the disease status is an ordinal variable (normoglycemic controls, prediabetes or T2D). FDR < 0.10.",increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,3379134|1224|1236|91347|543|561|562,Complete,NA
bsdb:38918632/13/2,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 13,"China,Denmark,Finland,France,Germany,Israel,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Increased normoglycemic,Decreased normoglycemic,"Female patients with decreasing normoglycemic condition, which finalizes in type 2 diabetes (T2D) mellitus",10,10,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,"age,body mass index",NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 11,21 October 2025,YokoC,YokoC,"Heatmap of meta-analyzed associations of microbial species with T2D (type 2 diabetes). The blue-to-red gradient represents the magnitude and direction of the associations quantified by Maaslin2, where the disease status is an ordinal variable (normoglycemic controls, prediabetes or T2D). FDR < 0.10.",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:167,1783272|1239|186801|186802|31979|1485|1262777,Complete,NA
bsdb:38918632/14/1,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 14,"China,Denmark,Finland,France,Germany,Israel,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic (control),T2D (type 2 diabetes),Female patients with type 2 diabetes (diabetes mellitus) from a binomial model (type 2 diabetes and normoglycemic controls).,10,10,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,"age,body mass index",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 11,21 October 2025,YokoC,YokoC,"Heatmap of meta-analyzed associations of microbial species with T2D (type 2 diabetes). The blue-to-red gradient represents the magnitude and direction of the associations quantified by Maaslin2, where the disease status is an binomial variable (normoglycemic controls or T2D). FDR < 0.10.",increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,3379134|1224|1236|91347|543|561|562,Complete,NA
bsdb:38918632/15/1,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 15,"China,Denmark,Finland,France,Germany,Israel,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Increased normoglycemic,Decreased normoglycemic,"Male patients with decreasing normoglycemic condition, which finalizes in type 2 diabetes (T2D) mellitus",10,10,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,"age,body mass index",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 11,21 October 2025,YokoC,YokoC,"Heatmap of meta-analyzed associations of microbial species with T2D (type 2 diabetes). The blue-to-red gradient represents the magnitude and direction of the associations quantified by Maaslin2, where the disease status is an ordinal variable (normoglycemic controls, prediabetes or T2D). FDR < 0.10.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii",1783272|1239|186801|186802|216572|244127|169435;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|3085636|186803|2719313|333367;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|2719313|358743;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|216572|946234|292800,Complete,NA
bsdb:38918632/15/2,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 15,"China,Denmark,Finland,France,Germany,Israel,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Increased normoglycemic,Decreased normoglycemic,"Male patients with decreasing normoglycemic condition, which finalizes in type 2 diabetes (T2D) mellitus",10,10,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,"age,body mass index",NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 11,21 October 2025,YokoC,YokoC,"Heatmap of meta-analyzed associations of microbial species with T2D (type 2 diabetes). The blue-to-red gradient represents the magnitude and direction of the associations quantified by Maaslin2, where the disease status is an ordinal variable (normoglycemic controls, prediabetes or T2D). FDR < 0.10.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:253,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 57_20,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:238",1783272|1239|186801|186802|31979|1485|1262785;3379134|200940|3031449|213115|194924|872|901;1783272|1239|186801|186802|216572|459786|1897011;1783272|1239|1263011,Complete,NA
bsdb:38918632/16/1,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 16,"China,Denmark,Finland,France,Germany,Israel,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic (control),T2D (type 2 diabetes),"Male patients with type 2 diabetes (diabetes mellitus), from a model where the disease status was treated as a binomial variable (type 2 diabetes or normoglycemic controls).",10,10,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,"age,body mass index",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 11,21 October 2025,YokoC,YokoC,"Heatmap of meta-analyzed associations of microbial species with T2D (type 2 diabetes). The blue-to-red gradient represents the magnitude and direction of the associations quantified by Maaslin2, where the disease status is an binomial variable (normoglycemic controls or T2D). FDR < 0.10.",increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,1783272|1239|186801|3085636|186803|2719313|358743,Complete,NA
bsdb:38918632/16/2,38918632,meta-analysis,38918632,10.1038/s41591-024-03067-7,NA,"Mei Z., Wang F., Bhosle A., Dong D., Mehta R., Ghazi A., Zhang Y., Liu Y., Rinott E., Ma S., Rimm E.B., Daviglus M., Willett W.C., Knight R., Hu F.B., Qi Q., Chan A.T., Burk R.D., Stampfer M.J., Shai I., Kaplan R.C., Huttenhower C. , Wang D.D.","Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes",Nature medicine,2024,NA,Experiment 16,"China,Denmark,Finland,France,Germany,Israel,Sweden,United States of America",Homo sapiens,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,Normoglycemic (control),T2D (type 2 diabetes),"Male patients with type 2 diabetes (diabetes mellitus), from a model where the disease status was treated as a binomial variable (type 2 diabetes or normoglycemic controls).",10,10,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina,Ion Torrent",log transformation,MaAsLin2,0.1,TRUE,NA,NA,"age,body mass index",NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 11,21 October 2025,YokoC,YokoC,"Description: Heatmap of meta-analyzed associations of microbial species with T2D (type 2 diabetes). The blue-to-red gradient represents the magnitude and direction of the associations quantified by Maaslin2, where the disease status is an binomial variable (normoglycemic controls or T2D). FDR < 0.10.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:238",1783272|1239|186801|3085636|186803|33042|33043;1783272|1239|1263011,Complete,NA
bsdb:38927243/1/1,38927243,"cross-sectional observational, not case-control",38927243,10.3390/biology13060363,NA,"Mena Canata D.A., Benfato M.S., Pereira F.D., Ramos Pereira M.J., Hackenhaar F.S., Mann M.B., Frazzon A.P.G. , Rampelotto P.H.",Comparative Analysis of the Gut Microbiota of Bat Species with Different Feeding Habits,Biology,2024,"diet, frugivore, insectivore, microbiome, nectarivore, vampire bat",Experiment 1,Brazil,Glossophaga soricina,Material entity in digestive tract,UBERON:0035118,Diet,EFO:0002755,"Combination of frugivorous, insectivorous and hematophagous bats.",Nectarivorous,"Nectarivorous adult male bats caught in southern Brazil. Nectarivorous bats have a specialized nectar based diet, adaptations include long, slender snouts and tongues.",26,7,NA,16S,4,Illumina,relative abundances,LEfSe,0.1,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"""3.3 Microbial Composition"" second paragraph text.",18 December 2024,YokoC,"YokoC,WikiWorks",LEfSe analysis of bacteria genera from four bat species with different feeding habits.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae",1783272|201174|1760|2037|2049|1654;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3082720|186804|1505652;1783272|544448|2790996|2790998|2129;1783272|1239|186801|186802|31979;3379134|1224|1236|91347|543;3379134|1224|28216|206351|481,Complete,Svetlana up
bsdb:38927243/1/2,38927243,"cross-sectional observational, not case-control",38927243,10.3390/biology13060363,NA,"Mena Canata D.A., Benfato M.S., Pereira F.D., Ramos Pereira M.J., Hackenhaar F.S., Mann M.B., Frazzon A.P.G. , Rampelotto P.H.",Comparative Analysis of the Gut Microbiota of Bat Species with Different Feeding Habits,Biology,2024,"diet, frugivore, insectivore, microbiome, nectarivore, vampire bat",Experiment 1,Brazil,Glossophaga soricina,Material entity in digestive tract,UBERON:0035118,Diet,EFO:0002755,"Combination of frugivorous, insectivorous and hematophagous bats.",Nectarivorous,"Nectarivorous adult male bats caught in southern Brazil. Nectarivorous bats have a specialized nectar based diet, adaptations include long, slender snouts and tongues.",26,7,NA,16S,4,Illumina,relative abundances,LEfSe,0.1,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"""3.3 Microbial Composition"" second paragraph text.",18 December 2024,YokoC,"YokoC,WikiWorks",LEfSe analysis of bacteria genera from four bat species with different feeding habits.,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Edwardsiella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",1783272|201174|84998|84999|1643824|1380;3379134|29547|3031852|213849|72294|194;1783272|1239|186801|186802|31979|49082;3379134|1224|1236|91347|1903412|635;3384189|32066|203490|203491|203492|848;3379134|29547|3031852|213849|72293|209;1783272|1239|91061|186826|33958|2767887;1783272|1239|186801|3082720|186804;1783272|544448|31969|186329|2146;1783272|201174;1783272|1239|91061;1783272|1239|526524|526525;1783272|1239|91061|186826;3379134|1224|1236|135625|712,Complete,Svetlana up
bsdb:38927243/2/1,38927243,"cross-sectional observational, not case-control",38927243,10.3390/biology13060363,NA,"Mena Canata D.A., Benfato M.S., Pereira F.D., Ramos Pereira M.J., Hackenhaar F.S., Mann M.B., Frazzon A.P.G. , Rampelotto P.H.",Comparative Analysis of the Gut Microbiota of Bat Species with Different Feeding Habits,Biology,2024,"diet, frugivore, insectivore, microbiome, nectarivore, vampire bat",Experiment 2,Brazil,Sturnira lilium,Material entity in digestive tract,UBERON:0035118,Diet,EFO:0002755,"Combination of nectarivorous, insectivorous and hematophagous bats.",Frugivorous,"Frugivorous adult male bats caught in southern Brazil. Frugivorous bats have a specialized fruit based diet, adaptations in neo-tropical species include short snouts and strong jaws.",23,10,NA,16S,4,Illumina,relative abundances,LEfSe,0.1,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"""3.3 Microbial Composition"" second paragraph text.",18 December 2024,YokoC,"YokoC,WikiWorks",LEfSe analysis of bacteria genera from four bat species with different feeding habits.,increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae",3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72293|209;1783272|544448|31969|186329|2146,Complete,Svetlana up
bsdb:38927243/2/2,38927243,"cross-sectional observational, not case-control",38927243,10.3390/biology13060363,NA,"Mena Canata D.A., Benfato M.S., Pereira F.D., Ramos Pereira M.J., Hackenhaar F.S., Mann M.B., Frazzon A.P.G. , Rampelotto P.H.",Comparative Analysis of the Gut Microbiota of Bat Species with Different Feeding Habits,Biology,2024,"diet, frugivore, insectivore, microbiome, nectarivore, vampire bat",Experiment 2,Brazil,Sturnira lilium,Material entity in digestive tract,UBERON:0035118,Diet,EFO:0002755,"Combination of nectarivorous, insectivorous and hematophagous bats.",Frugivorous,"Frugivorous adult male bats caught in southern Brazil. Frugivorous bats have a specialized fruit based diet, adaptations in neo-tropical species include short snouts and strong jaws.",23,10,NA,16S,4,Illumina,relative abundances,LEfSe,0.1,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"""3.3 Microbial Composition"" second paragraph text.",18 December 2024,YokoC,"YokoC,WikiWorks",LEfSe analysis of bacteria genera from four bat species with different feeding habits.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Edwardsiella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",1783272|201174|1760|2037|2049|1654;1783272|201174|84998|84999|1643824|1380;1783272|1239|186801|186802|31979|49082;1783272|1239|186801|186802|31979|1485;3379134|1224|1236|91347|1903412|635;3384189|32066|203490|203491|203492|848;1783272|1239|91061|186826|33958|2767887;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1505652;1783272|544448|2790996|2790998|2129;1783272|201174;1783272|1239|91061;1783272|1239|186801|186802|31979;3379134|1224|1236|91347|543;1783272|1239|526524|526525;1783272|1239|91061|186826;3379134|1224|28216|206351|481;3379134|1224|1236|135625|712,Complete,Svetlana up
bsdb:38927243/3/1,38927243,"cross-sectional observational, not case-control",38927243,10.3390/biology13060363,NA,"Mena Canata D.A., Benfato M.S., Pereira F.D., Ramos Pereira M.J., Hackenhaar F.S., Mann M.B., Frazzon A.P.G. , Rampelotto P.H.",Comparative Analysis of the Gut Microbiota of Bat Species with Different Feeding Habits,Biology,2024,"diet, frugivore, insectivore, microbiome, nectarivore, vampire bat",Experiment 3,Brazil,Molossus molossus,Material entity in digestive tract,UBERON:0035118,Diet,EFO:0002755,"Combination of frugivorous, nectarivorous and hematophagous bats.",Insectivorous,"Insectivorous adult male bats caught in southern Brazil. Insectivorous bats have a specialized diet based on arthropods, adaptations include echolocation calls that allow tracking and capturing small fast-moving prey.",23,10,NA,16S,4,Illumina,relative abundances,LEfSe,0.1,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"""3.3 Microbial Composition"" second paragraph text",18 December 2024,YokoC,"YokoC,WikiWorks",LEfSe analysis of bacteria genera from four bat species with different feeding habits.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia",1783272|201174|84998|84999|1643824|1380;1783272|1239|186801|186802|31979|49082;3384189|32066|203490|203491|203492|848;1783272|1239|91061|186826|33958|2767887;1783272|201174;1783272|1239|91061;1783272|1239|526524|526525;1783272|1239|91061|186826;3379134|1224|1236|135625|712;3379134|204428|204429|51291|809|810,Complete,Svetlana up
bsdb:38927243/3/2,38927243,"cross-sectional observational, not case-control",38927243,10.3390/biology13060363,NA,"Mena Canata D.A., Benfato M.S., Pereira F.D., Ramos Pereira M.J., Hackenhaar F.S., Mann M.B., Frazzon A.P.G. , Rampelotto P.H.",Comparative Analysis of the Gut Microbiota of Bat Species with Different Feeding Habits,Biology,2024,"diet, frugivore, insectivore, microbiome, nectarivore, vampire bat",Experiment 3,Brazil,Molossus molossus,Material entity in digestive tract,UBERON:0035118,Diet,EFO:0002755,"Combination of frugivorous, nectarivorous and hematophagous bats.",Insectivorous,"Insectivorous adult male bats caught in southern Brazil. Insectivorous bats have a specialized diet based on arthropods, adaptations include echolocation calls that allow tracking and capturing small fast-moving prey.",23,10,NA,16S,4,Illumina,relative abundances,LEfSe,0.1,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"""3.3 Microbial Composition"" second paragraph text.",18 December 2024,YokoC,"YokoC,WikiWorks",LEfSe analysis of bacteria genera from four bat species with different feeding habits.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Edwardsiella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae",1783272|201174|1760|2037|2049|1654;3379134|29547|3031852|213849|72294|194;1783272|1239|186801|186802|31979|1485;3379134|1224|1236|91347|1903412|635;3379134|29547|3031852|213849|72293|209;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1505652;1783272|544448|2790996|2790998|2129;1783272|544448|31969|186329|2146;1783272|1239|186801|186802|31979;3379134|1224|1236|91347|543;3379134|1224|28216|206351|481,Complete,Svetlana up
bsdb:38927243/4/1,38927243,"cross-sectional observational, not case-control",38927243,10.3390/biology13060363,NA,"Mena Canata D.A., Benfato M.S., Pereira F.D., Ramos Pereira M.J., Hackenhaar F.S., Mann M.B., Frazzon A.P.G. , Rampelotto P.H.",Comparative Analysis of the Gut Microbiota of Bat Species with Different Feeding Habits,Biology,2024,"diet, frugivore, insectivore, microbiome, nectarivore, vampire bat",Experiment 4,Brazil,Desmodus rotundus,Material entity in digestive tract,UBERON:0035118,Diet,EFO:0002755,"Combination of frugivorous, nectarivorous and insectivorous bats.",Hematophagous,"Hematophagous adult male bats caught in southern Brazil. Hematophagous bats have a blood specilized diet, adaptations include sharp incisors and heat sensors on their noses.",27,6,NA,16S,4,Illumina,relative abundances,LEfSe,0.1,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"""3.3 Microbial Composition"" second paragraph text.",18 December 2024,YokoC,"YokoC,WikiWorks",LEfSe analysis of bacteria genera from four bat species with different feeding habits.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Edwardsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",3379134|1224|1236|91347|1903412|635;1783272|1239|186801|3082720|186804,Complete,Svetlana up
bsdb:38927243/4/2,38927243,"cross-sectional observational, not case-control",38927243,10.3390/biology13060363,NA,"Mena Canata D.A., Benfato M.S., Pereira F.D., Ramos Pereira M.J., Hackenhaar F.S., Mann M.B., Frazzon A.P.G. , Rampelotto P.H.",Comparative Analysis of the Gut Microbiota of Bat Species with Different Feeding Habits,Biology,2024,"diet, frugivore, insectivore, microbiome, nectarivore, vampire bat",Experiment 4,Brazil,Desmodus rotundus,Material entity in digestive tract,UBERON:0035118,Diet,EFO:0002755,"Combination of frugivorous, nectarivorous and insectivorous bats.",Hematophagous,"Hematophagous adult male bats caught in southern Brazil. Hematophagous bats have a blood specilized diet, adaptations include sharp incisors and heat sensors on their noses.",27,6,NA,16S,4,Illumina,relative abundances,LEfSe,0.1,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"""3.3 Microbial Composition"" second paragraph text.",18 December 2024,YokoC,"YokoC,WikiWorks",LEfSe analysis of bacteria genera from four bat species with different feeding habits.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae",1783272|201174|1760|2037|2049|1654;1783272|201174|84998|84999|1643824|1380;3379134|29547|3031852|213849|72294|194;1783272|1239|186801|186802|31979|49082;1783272|1239|186801|186802|31979|1485;3384189|32066|203490|203491|203492|848;3379134|29547|3031852|213849|72293|209;1783272|1239|91061|186826|33958|2767887;1783272|1239|186801|3082720|186804|1505652;1783272|544448|2790996|2790998|2129;1783272|544448|31969|186329|2146;1783272|201174;1783272|1239|91061;1783272|1239|186801|186802|31979;3379134|1224|1236|91347|543;1783272|1239|526524|526525;1783272|1239|91061|186826;3379134|1224|28216|206351|481;3379134|1224|1236|135625|712,Complete,Svetlana up
bsdb:38935224/1/1,38935224,laboratory experiment,38935224,10.1007/s11064-024-04168-y,NA,"Li B., Ma Y., Wang X., Zhao D., Wang Z., Wang G., Li C., Yang L., Ji H., Liu K., Chen Q., Yang Y., Ma W., Du J., Ma L., Zhang L. , Qiang Y.","Ketogenic Diets Alter the Gut Microbiome, Resulting in Decreased Susceptibility to and Cognitive Impairment in Rats with Pilocarpine-Induced Status Epilepticus",Neurochemical research,2024,"Cognitive function, Gut microbiota, Ketogenic diet, Lithium-pilocarpine, Status epilepticus, Temporal lobe epilepsy",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,normal diet status epilepticus model (SE group),ketogenic diet (SE + KD group),male rats fed ketogenic diet for three weeks before undergoing pilocarpine-induced status epilepticus,6,6,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,Figure 7B,17 December 2024,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of SE + KD group compared to SE group,increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota",1783272|201174;3379134|1224,Complete,NA
bsdb:38935224/1/2,38935224,laboratory experiment,38935224,10.1007/s11064-024-04168-y,NA,"Li B., Ma Y., Wang X., Zhao D., Wang Z., Wang G., Li C., Yang L., Ji H., Liu K., Chen Q., Yang Y., Ma W., Du J., Ma L., Zhang L. , Qiang Y.","Ketogenic Diets Alter the Gut Microbiome, Resulting in Decreased Susceptibility to and Cognitive Impairment in Rats with Pilocarpine-Induced Status Epilepticus",Neurochemical research,2024,"Cognitive function, Gut microbiota, Ketogenic diet, Lithium-pilocarpine, Status epilepticus, Temporal lobe epilepsy",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,normal diet status epilepticus model (SE group),ketogenic diet (SE + KD group),male rats fed ketogenic diet for three weeks before undergoing pilocarpine-induced status epilepticus,6,6,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,Figure 7B,17 December 2024,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of SE + KD group compared to SE group,decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,NA
bsdb:38935224/2/1,38935224,laboratory experiment,38935224,10.1007/s11064-024-04168-y,NA,"Li B., Ma Y., Wang X., Zhao D., Wang Z., Wang G., Li C., Yang L., Ji H., Liu K., Chen Q., Yang Y., Ma W., Du J., Ma L., Zhang L. , Qiang Y.","Ketogenic Diets Alter the Gut Microbiome, Resulting in Decreased Susceptibility to and Cognitive Impairment in Rats with Pilocarpine-Induced Status Epilepticus",Neurochemical research,2024,"Cognitive function, Gut microbiota, Ketogenic diet, Lithium-pilocarpine, Status epilepticus, Temporal lobe epilepsy",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,normal diet healthy controls (NC group),ketogenic diet (SE + KD group),male rats fed ketogenic diet for three weeks before undergoing pilocarpine-induced status epilepticus,6,6,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,Figure 7B,3 January 2025,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of SE + KD group compared to NC group,increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota",1783272|201174;3379134|1224,Complete,NA
bsdb:38935224/2/2,38935224,laboratory experiment,38935224,10.1007/s11064-024-04168-y,NA,"Li B., Ma Y., Wang X., Zhao D., Wang Z., Wang G., Li C., Yang L., Ji H., Liu K., Chen Q., Yang Y., Ma W., Du J., Ma L., Zhang L. , Qiang Y.","Ketogenic Diets Alter the Gut Microbiome, Resulting in Decreased Susceptibility to and Cognitive Impairment in Rats with Pilocarpine-Induced Status Epilepticus",Neurochemical research,2024,"Cognitive function, Gut microbiota, Ketogenic diet, Lithium-pilocarpine, Status epilepticus, Temporal lobe epilepsy",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,normal diet healthy controls (NC group),ketogenic diet (SE + KD group),male rats fed ketogenic diet for three weeks before undergoing pilocarpine-induced status epilepticus,6,6,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,Figure 7B,3 January 2025,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of SE + KD group compared to NC group,decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,NA
bsdb:38935224/3/1,38935224,laboratory experiment,38935224,10.1007/s11064-024-04168-y,NA,"Li B., Ma Y., Wang X., Zhao D., Wang Z., Wang G., Li C., Yang L., Ji H., Liu K., Chen Q., Yang Y., Ma W., Du J., Ma L., Zhang L. , Qiang Y.","Ketogenic Diets Alter the Gut Microbiome, Resulting in Decreased Susceptibility to and Cognitive Impairment in Rats with Pilocarpine-Induced Status Epilepticus",Neurochemical research,2024,"Cognitive function, Gut microbiota, Ketogenic diet, Lithium-pilocarpine, Status epilepticus, Temporal lobe epilepsy",Experiment 3,China,Rattus norvegicus,Feces,UBERON:0001988,"Response to ketogenic diet,Response to antibiotic","EFO:0009372,GO:0046677",normal diet healthy controls (NC group),ketogenic diet and antibiotics (SE + KD + Ab group),male rats receiving antibiotic treatment and fed ketogenic diet for three weeks before undergoing pilocarpine-induced status epilepticus,6,6,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7B,3 January 2025,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of SE + KD + Ab group compared to NC group,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,NA
bsdb:38935224/3/2,38935224,laboratory experiment,38935224,10.1007/s11064-024-04168-y,NA,"Li B., Ma Y., Wang X., Zhao D., Wang Z., Wang G., Li C., Yang L., Ji H., Liu K., Chen Q., Yang Y., Ma W., Du J., Ma L., Zhang L. , Qiang Y.","Ketogenic Diets Alter the Gut Microbiome, Resulting in Decreased Susceptibility to and Cognitive Impairment in Rats with Pilocarpine-Induced Status Epilepticus",Neurochemical research,2024,"Cognitive function, Gut microbiota, Ketogenic diet, Lithium-pilocarpine, Status epilepticus, Temporal lobe epilepsy",Experiment 3,China,Rattus norvegicus,Feces,UBERON:0001988,"Response to ketogenic diet,Response to antibiotic","EFO:0009372,GO:0046677",normal diet healthy controls (NC group),ketogenic diet and antibiotics (SE + KD + Ab group),male rats receiving antibiotic treatment and fed ketogenic diet for three weeks before undergoing pilocarpine-induced status epilepticus,6,6,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 7B,3 January 2025,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of SE + KD + Ab group compared to NC group,decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,NA
bsdb:38935224/4/1,38935224,laboratory experiment,38935224,10.1007/s11064-024-04168-y,NA,"Li B., Ma Y., Wang X., Zhao D., Wang Z., Wang G., Li C., Yang L., Ji H., Liu K., Chen Q., Yang Y., Ma W., Du J., Ma L., Zhang L. , Qiang Y.","Ketogenic Diets Alter the Gut Microbiome, Resulting in Decreased Susceptibility to and Cognitive Impairment in Rats with Pilocarpine-Induced Status Epilepticus",Neurochemical research,2024,"Cognitive function, Gut microbiota, Ketogenic diet, Lithium-pilocarpine, Status epilepticus, Temporal lobe epilepsy",Experiment 4,China,Rattus norvegicus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,ketogenic diet (SE + KD group),ketogenic diet and antibiotics (SE + KD + Ab group),male rats receiving antibiotic treatment and fed ketogenic diet for three weeks before undergoing pilocarpine-induced status epilepticus,6,6,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7B,3 January 2025,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of SE + KD + Ab group compared to SE + KD group,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,NA
bsdb:38935224/4/2,38935224,laboratory experiment,38935224,10.1007/s11064-024-04168-y,NA,"Li B., Ma Y., Wang X., Zhao D., Wang Z., Wang G., Li C., Yang L., Ji H., Liu K., Chen Q., Yang Y., Ma W., Du J., Ma L., Zhang L. , Qiang Y.","Ketogenic Diets Alter the Gut Microbiome, Resulting in Decreased Susceptibility to and Cognitive Impairment in Rats with Pilocarpine-Induced Status Epilepticus",Neurochemical research,2024,"Cognitive function, Gut microbiota, Ketogenic diet, Lithium-pilocarpine, Status epilepticus, Temporal lobe epilepsy",Experiment 4,China,Rattus norvegicus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,ketogenic diet (SE + KD group),ketogenic diet and antibiotics (SE + KD + Ab group),male rats receiving antibiotic treatment and fed ketogenic diet for three weeks before undergoing pilocarpine-induced status epilepticus,6,6,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 7B,3 January 2025,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of SE + KD + Ab group compared to SE + KD group,decreased,k__Bacillati|p__Actinomycetota,1783272|201174,Complete,NA
bsdb:38935224/5/1,38935224,laboratory experiment,38935224,10.1007/s11064-024-04168-y,NA,"Li B., Ma Y., Wang X., Zhao D., Wang Z., Wang G., Li C., Yang L., Ji H., Liu K., Chen Q., Yang Y., Ma W., Du J., Ma L., Zhang L. , Qiang Y.","Ketogenic Diets Alter the Gut Microbiome, Resulting in Decreased Susceptibility to and Cognitive Impairment in Rats with Pilocarpine-Induced Status Epilepticus",Neurochemical research,2024,"Cognitive function, Gut microbiota, Ketogenic diet, Lithium-pilocarpine, Status epilepticus, Temporal lobe epilepsy",Experiment 5,China,Rattus norvegicus,Feces,UBERON:0001988,"Response to ketogenic diet,Response to antibiotic","EFO:0009372,GO:0046677",normal diet status epilepticus model (SE group),ketogenic diet and antibiotics (SE + KD + Ab group),male rats receiving antibiotic treatment and fed ketogenic diet for three weeks before undergoing pilocarpine-induced status epilepticus,6,6,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7B,3 January 2025,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of SE + KD + Ab group compared to SE group,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,NA
bsdb:38935224/5/2,38935224,laboratory experiment,38935224,10.1007/s11064-024-04168-y,NA,"Li B., Ma Y., Wang X., Zhao D., Wang Z., Wang G., Li C., Yang L., Ji H., Liu K., Chen Q., Yang Y., Ma W., Du J., Ma L., Zhang L. , Qiang Y.","Ketogenic Diets Alter the Gut Microbiome, Resulting in Decreased Susceptibility to and Cognitive Impairment in Rats with Pilocarpine-Induced Status Epilepticus",Neurochemical research,2024,"Cognitive function, Gut microbiota, Ketogenic diet, Lithium-pilocarpine, Status epilepticus, Temporal lobe epilepsy",Experiment 5,China,Rattus norvegicus,Feces,UBERON:0001988,"Response to ketogenic diet,Response to antibiotic","EFO:0009372,GO:0046677",normal diet status epilepticus model (SE group),ketogenic diet and antibiotics (SE + KD + Ab group),male rats receiving antibiotic treatment and fed ketogenic diet for three weeks before undergoing pilocarpine-induced status epilepticus,6,6,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 7B,3 January 2025,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of SE + KD + Ab group compared to SE group,increased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,NA
bsdb:38935224/6/1,38935224,laboratory experiment,38935224,10.1007/s11064-024-04168-y,NA,"Li B., Ma Y., Wang X., Zhao D., Wang Z., Wang G., Li C., Yang L., Ji H., Liu K., Chen Q., Yang Y., Ma W., Du J., Ma L., Zhang L. , Qiang Y.","Ketogenic Diets Alter the Gut Microbiome, Resulting in Decreased Susceptibility to and Cognitive Impairment in Rats with Pilocarpine-Induced Status Epilepticus",Neurochemical research,2024,"Cognitive function, Gut microbiota, Ketogenic diet, Lithium-pilocarpine, Status epilepticus, Temporal lobe epilepsy",Experiment 6,China,Rattus norvegicus,Feces,UBERON:0001988,Ketogenic diet,EFO:0009371,"(SE + KD + Ab), SE, and NC groups",ketogenic diet (SE + KD group),male rats fed ketogenic diet for three weeks before undergoing pilocarpine-induced status epilepticus,18,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7C,5 January 2025,Kavyaayala,"Kavyaayala,WikiWorks","Fecal microbiome of SE + KD group compared to (SE + KD + Ab), SE, and NC groups",increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum|s__uncultured Allobaculum sp.",1783272|201174;1783272|201174|84998|84999|1643824;1783272|1239|186801|3085636|186803|572511;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|186801|186802|186807;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|186807;1783272|1239|526524|526525|128827|174708|1187017,Complete,NA
bsdb:38935224/7/1,38935224,laboratory experiment,38935224,10.1007/s11064-024-04168-y,NA,"Li B., Ma Y., Wang X., Zhao D., Wang Z., Wang G., Li C., Yang L., Ji H., Liu K., Chen Q., Yang Y., Ma W., Du J., Ma L., Zhang L. , Qiang Y.","Ketogenic Diets Alter the Gut Microbiome, Resulting in Decreased Susceptibility to and Cognitive Impairment in Rats with Pilocarpine-Induced Status Epilepticus",Neurochemical research,2024,"Cognitive function, Gut microbiota, Ketogenic diet, Lithium-pilocarpine, Status epilepticus, Temporal lobe epilepsy",Experiment 7,China,Rattus norvegicus,Feces,UBERON:0001988,Ketogenic diet,EFO:0009371,"(SE + KD + Ab), (SE + KD), and NC groups",normal diet status epilepticus model (SE group),male rats fed normal diet and having pilocarpine-induced status epilepticus,18,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7C,5 January 2025,Kavyaayala,"Kavyaayala,WikiWorks","Fecal microbiome of SE group compared to (SE + KD + Ab), (SE + KD), and NC groups",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,k__Metazoa|p__Nematoda|c__Enoplea|o__Trichinellida|f__Trichinellidae|g__Trichinella|s__Trichinella pseudospiralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|186801|3082768|990719;1783272|1239|186801|3082768;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|2767887;3379134|976|200643|171549|815|909656|671267;33208|6231|119088|6329|6332|6333|6337;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|2767887,Complete,NA
bsdb:38935224/8/1,38935224,laboratory experiment,38935224,10.1007/s11064-024-04168-y,NA,"Li B., Ma Y., Wang X., Zhao D., Wang Z., Wang G., Li C., Yang L., Ji H., Liu K., Chen Q., Yang Y., Ma W., Du J., Ma L., Zhang L. , Qiang Y.","Ketogenic Diets Alter the Gut Microbiome, Resulting in Decreased Susceptibility to and Cognitive Impairment in Rats with Pilocarpine-Induced Status Epilepticus",Neurochemical research,2024,"Cognitive function, Gut microbiota, Ketogenic diet, Lithium-pilocarpine, Status epilepticus, Temporal lobe epilepsy",Experiment 8,China,Rattus norvegicus,Feces,UBERON:0001988,Ketogenic diet,EFO:0009371,"(SE + KD), SE, and NC groups",ketogenic diet and antibiotics (SE + KD + Ab group),male rats fed ketogenic diet for three weeks and receiving antibiotic treatment before undergoing pilocarpine-induced status epilepticus,18,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7C,5 January 2025,Kavyaayala,"Kavyaayala,WikiWorks","Fecal microbiome of SE + KD + Ab group compared to (SE + KD), SE, and NC groups",increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum",1783272|1239|526524|526525|2810280;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|186801|186802|216572|946234;3379134|1224|1236;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|186802|216572;3379134|1224;1783272|1239|526524|526525|2810280|3025755;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|1506553;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|186802|31979|1485|1522;1783272|1239|186801|3082720|543314|35518,Complete,NA
bsdb:38935224/9/1,38935224,laboratory experiment,38935224,10.1007/s11064-024-04168-y,NA,"Li B., Ma Y., Wang X., Zhao D., Wang Z., Wang G., Li C., Yang L., Ji H., Liu K., Chen Q., Yang Y., Ma W., Du J., Ma L., Zhang L. , Qiang Y.","Ketogenic Diets Alter the Gut Microbiome, Resulting in Decreased Susceptibility to and Cognitive Impairment in Rats with Pilocarpine-Induced Status Epilepticus",Neurochemical research,2024,"Cognitive function, Gut microbiota, Ketogenic diet, Lithium-pilocarpine, Status epilepticus, Temporal lobe epilepsy",Experiment 9,China,Rattus norvegicus,Feces,UBERON:0001988,Ketogenic diet,EFO:0009371,"(SE + KD + Ab), (SE + KD), and SE groups",normal diet controls (NC group),healthy male rats fed normal diet,18,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7C,5 January 2025,Kavyaayala,"Kavyaayala,WikiWorks","Fecal microbiome of NC group compared to (SE + KD + Ab), (SE + KD), and SE groups",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",3379134|976|200643|171549;3379134|976|200643;3379134|976;1783272|1239|186801|3085636|186803|877420;3379134|976|200643|171549|2005473;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|2005473;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802,Complete,NA
bsdb:38942886/1/1,38942886,case-control,38942886,10.1038/s41598-024-65869-6,NA,"Fo X., Pei M.L., Liu P.J., Zhu F., Zhang Y. , Mu X.",Metagenomic analysis revealed the association between gut microbiota and different ovary responses to controlled ovarian stimulation,Scientific reports,2024,"Controlled ovarian stimulation, FOI, Gut microbiome, Metagenomic analysis, Ovary responses",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Hormone replacement therapy,EFO:0003961,Follicle to Oocyte Index (FOI) >=0.5,Low Ovarian Sensitivity Follicle to Oocyte Index(FOI)<0.5,Patients who were hypo responsive with follicle-to-oocyte index <0.5.,25,22,1 month,WMS,NA,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 1,Figure 3,17 April 2025,Nithya,Nithya,"Significantly different microbiomes between two groups at
species level",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:58,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus|s__Proteus mirabilis",3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|291644;3379134|976|200643|171549|2005519|397864|487174;1783272|1239|186801|186802|31979|1485|1262824;1783272|1239|186801|3085636|186803|33042|33043;1783272|201174|1760|85007|1653|1716|61592;3379134|1224|1236|91347|1903414|583|584,Complete,KateRasheed
bsdb:38942886/1/2,38942886,case-control,38942886,10.1038/s41598-024-65869-6,NA,"Fo X., Pei M.L., Liu P.J., Zhu F., Zhang Y. , Mu X.",Metagenomic analysis revealed the association between gut microbiota and different ovary responses to controlled ovarian stimulation,Scientific reports,2024,"Controlled ovarian stimulation, FOI, Gut microbiome, Metagenomic analysis, Ovary responses",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Hormone replacement therapy,EFO:0003961,Follicle to Oocyte Index (FOI) >=0.5,Low Ovarian Sensitivity Follicle to Oocyte Index(FOI)<0.5,Patients who were hypo responsive with follicle-to-oocyte index <0.5.,25,22,1 month,WMS,NA,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 2,Figure 3,21 April 2025,Nithya,Nithya,Significantly different microbiomes between two groups at species level,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces johnsonii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris",1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|2037|2049|1654|55565;1783272|201174|1760|2037|2049|1654|544581;1783272|201174|1760|2037|2049|1654|544580,Complete,KateRasheed
bsdb:38946731/1/1,38946731,laboratory experiment,38946731,10.1093/pcmedi/pbae013,NA,"Li J.H., Chen Y., Ye Z.H., Chen L.P., Xu J.X., Han J., Xie L., Xing S., Tian D.A., Seidler U., Liao J.Z. , Xiao F.",Suppression of MyD88 disturbs gut microbiota and activates the NLR pathway and hence fails to ameliorate DSS-induced colitis,Precision clinical medicine,2024,"NOD-like receptor, inflammatory bowel disease, innate immunity, microbiota, myeloid differentiation factor 88, MyD88 inhibitor",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Colitis,EFO:0003872,DSS + PBS (dextran sulphate sodium + phosphate buffered saline) group,DSS + TJ5 [dextran sulphate sodium + Myeloid differentiation factor 88 (MyD88) inhibitor] group,A treatment group that received DSS (dextran sulphate sodium) and TJ5 [Myeloid differentiation factor 88 (MyD88) inhibitor],NA,NA,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 3F,5 May 2025,Tosin,Tosin,Relative abundances of indicated bacterial taxa in feces between DSS + PBS (dextran sulphate sodium + phosphate buffered saline) and DSS + TJ5 [dextran sulphate sodium + Myeloid differentiation factor 88 (MyD88) inhibitor] groups,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|1236|91347;3379134|1224|1236;3379134|1224,Complete,NA
bsdb:38946731/2/1,38946731,laboratory experiment,38946731,10.1093/pcmedi/pbae013,NA,"Li J.H., Chen Y., Ye Z.H., Chen L.P., Xu J.X., Han J., Xie L., Xing S., Tian D.A., Seidler U., Liao J.Z. , Xiao F.",Suppression of MyD88 disturbs gut microbiota and activates the NLR pathway and hence fails to ameliorate DSS-induced colitis,Precision clinical medicine,2024,"NOD-like receptor, inflammatory bowel disease, innate immunity, microbiota, myeloid differentiation factor 88, MyD88 inhibitor",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Colitis,EFO:0003872,"Combination of DSS + TJ5 [dextran sulphate sodium + Myeloid differentiation factor 88 (MyD88) inhibitor], DSS + PBS (dextran sulphate sodium + phosphate buffered saline) and H20 + TJ5 [water + Myeloid differentiation factor 88 (MyD88) inhibitor] groups",H20 + PBS (water + phosphate buffered saline) group,A treatment group that received H20 (water) and PBS (phosphate buffered saline),NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 3,5 May 2025,Tosin,Tosin,Significant changes in functional profiles were suggested based on phylogenetic investigations of communities through Linear Discriminant Analysis Effect Size (LEfSe) analysis.,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,p__Candidatus Saccharimonadota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral clone CW040,k__Bacillati|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae|g__Thermacetogenium,k__Bacillati|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales,s__bacterium F16",1783272|201174;1783272|1239|526524|526525|128827|174708;95818;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;3379134|200940|3031449|213115|194924|872;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|186801|186802|204475;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550|28138;95818|163601;1783272|1239|186801|68295|186814|140458;1783272|1239|186801|68295|186814;1783272|1239|186801|68295;1932694,Complete,NA
bsdb:38946731/3/1,38946731,laboratory experiment,38946731,10.1093/pcmedi/pbae013,NA,"Li J.H., Chen Y., Ye Z.H., Chen L.P., Xu J.X., Han J., Xie L., Xing S., Tian D.A., Seidler U., Liao J.Z. , Xiao F.",Suppression of MyD88 disturbs gut microbiota and activates the NLR pathway and hence fails to ameliorate DSS-induced colitis,Precision clinical medicine,2024,"NOD-like receptor, inflammatory bowel disease, innate immunity, microbiota, myeloid differentiation factor 88, MyD88 inhibitor",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Colitis,EFO:0003872,"Combination of DSS + TJ5 [dextran sulphate sodium + Myeloid differentiation factor 88 (MyD88) inhibitor], H20 + PBS [water + phosphate buffered saline) and H20 + TJ5 (water + Myeloid differentiation factor 88 (MyD88) inhibitor] groups",DSS + PBS (dextran sulphate sodium + phosphate buffered saline) group,A treatment group that received DSS (dextran sulphate sodium) and PBS (phosphate buffered saline),NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 3,5 May 2025,Tosin,Tosin,Significant changes in functional profiles were suggested based on phylogenetic investigations of communities through Linear Discriminant Analysis Effect Size (LEfSe) analysis.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|g__Exiguobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Macellibacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota",3379134|74201|203494|48461|1647988|239934;3379134|1224|28216|80840|506;1783272|1239|186801|186802|216572|244127;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|33042;1783272|1239|91061|1385|33986;3379134|976|200643|171549|171551|1159323;3379134|1224|28211|356|41294;3379134|1224|1236|72274|135621;3379134|1224|1236|72274;3379134|1224|1236|72274|135621|286;3379134|1224|28216|80840|995019|40544;3379134|74201|203494|48461|203557;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201,Complete,NA
bsdb:38946731/4/1,38946731,laboratory experiment,38946731,10.1093/pcmedi/pbae013,NA,"Li J.H., Chen Y., Ye Z.H., Chen L.P., Xu J.X., Han J., Xie L., Xing S., Tian D.A., Seidler U., Liao J.Z. , Xiao F.",Suppression of MyD88 disturbs gut microbiota and activates the NLR pathway and hence fails to ameliorate DSS-induced colitis,Precision clinical medicine,2024,"NOD-like receptor, inflammatory bowel disease, innate immunity, microbiota, myeloid differentiation factor 88, MyD88 inhibitor",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Colitis,EFO:0003872,"Combination of H20 + PBS (water + phosphate buffered saline), DSS + PBS [dextran sulphate sodium + phosphate buffered saline) and DSS + TJ5 (dextran sulphate sodium + Myeloid differentiation factor 88 (MyD88) inhibitor] groups",H20 + TJ5 [water + Myeloid differentiation factor 88 (MyD88) inhibitor] group,A treatment group that received H20 (water) and TJ5 [Myeloid differentiation factor 88  (MyD88) inhibitor],NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 3,5 May 2025,PreciousChijioke,"PreciousChijioke,Tosin",Significant changes in functional profiles were suggested based on phylogenetic investigations of communities through Linear Discriminant Analysis Effect Size (LEfSe) analysis.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|84998|1643822|1643826|447020;3379134|976|200643|171549;3379134|976|200643;3379134|976;1783272|1239|186801|186802|31979;1783272|1117;3379134|976|200643|171549|2005473;1783272|544448|31969|2085|2092;1783272|544448|31969|2085;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300|1301,Complete,NA
bsdb:38946731/5/1,38946731,laboratory experiment,38946731,10.1093/pcmedi/pbae013,NA,"Li J.H., Chen Y., Ye Z.H., Chen L.P., Xu J.X., Han J., Xie L., Xing S., Tian D.A., Seidler U., Liao J.Z. , Xiao F.",Suppression of MyD88 disturbs gut microbiota and activates the NLR pathway and hence fails to ameliorate DSS-induced colitis,Precision clinical medicine,2024,"NOD-like receptor, inflammatory bowel disease, innate immunity, microbiota, myeloid differentiation factor 88, MyD88 inhibitor",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Colitis,EFO:0003872,"Combination of H20 + PBS (water + phosphate buffered saline), DSS + PBS (dextran sulphate sodium+ Phosphate buffered saline) and H20 + TJ5 [water + Myeloid differentiation factor 88 (MyD88) inhibitor] groups",DSS + TJ5 [dextran sulphate sodium + Myeloid differentiation factor 88 (MyD88) inhibitor] group,A treatment group that received DSS (dextran sulphate sodium) and TJ5 [Myeloid differentiation factor 88 (MyD88) inhibitor],NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 3,5 May 2025,PreciousChijioke,PreciousChijioke,Significant changes in functional profiles were suggested based on phylogenetic investigations of communities through Linear Discriminant Analysis Effect Size (LEfSe) analysis.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota",1783272|1239|91061|186826|81852;3379134|1224|1236;3379134|1224,Complete,NA
bsdb:38951925/1/1,38951925,laboratory experiment,38951925,10.1186/s40168-024-01820-1,NA,"Rasmussen T.S., Mao X., Forster S., Larsen S.B., Von Münchow A., Tranæs K.D., Brunse A., Larsen F., Mejia J.L.C., Adamberg S., Hansen A.K., Adamberg K., Hansen C.H.F. , Nielsen D.S.",Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments,Microbiome,2024,NA,Experiment 1,Denmark,Mus musculus,Feces,UBERON:0001988,Clostridium difficile infection,EFO:0009130,Mice Before Clostridioides difficile infection (CDI),Survived mice,"Mice that survived a Clostridioides difficile infection (CDI) followed by one of 4 FVT (fecal virome transplantation), FMT (fecal microbiota transplantaiton) or saline treatments until study termination.",48,24,NA,16S,3,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 7A,16 November 2024,Tosin,"Tosin,WikiWorks",Differential abundance of significantly different bacterial taxa between Before CDI (Clostridioides difficile Infection) and Survived mice.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239;1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|186801|186802|31979|1485;1783272|1239|526524|526525|2810281|191303|154288,Complete,Svetlana up
bsdb:38951925/1/2,38951925,laboratory experiment,38951925,10.1186/s40168-024-01820-1,NA,"Rasmussen T.S., Mao X., Forster S., Larsen S.B., Von Münchow A., Tranæs K.D., Brunse A., Larsen F., Mejia J.L.C., Adamberg S., Hansen A.K., Adamberg K., Hansen C.H.F. , Nielsen D.S.",Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments,Microbiome,2024,NA,Experiment 1,Denmark,Mus musculus,Feces,UBERON:0001988,Clostridium difficile infection,EFO:0009130,Mice Before Clostridioides difficile infection (CDI),Survived mice,"Mice that survived a Clostridioides difficile infection (CDI) followed by one of 4 FVT (fecal virome transplantation), FMT (fecal microbiota transplantaiton) or saline treatments until study termination.",48,24,NA,16S,3,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 7A,16 November 2024,Tosin,"Tosin,WikiWorks",Differential abundance of significantly different bacterial taxa Between Before CDI (Clostridioides difficile infection) and Survived mice.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus canintestini,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia fergusonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus taiwanensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus vaginalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis",3379134|976|200643|171549|815|816|818;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|81852|1350|317010;3379134|1224|1236|91347|543|561|564;1783272|1239|91061|186826|33958|1578|508451;1783272|1239|91061|186826|33958|2742598|1633;3379134|976|200643|171549|2005525|375288|328812;3379134|1224|28216|80840|995019|577310|487175,Complete,Svetlana up
bsdb:38951925/2/1,38951925,laboratory experiment,38951925,10.1186/s40168-024-01820-1,NA,"Rasmussen T.S., Mao X., Forster S., Larsen S.B., Von Münchow A., Tranæs K.D., Brunse A., Larsen F., Mejia J.L.C., Adamberg S., Hansen A.K., Adamberg K., Hansen C.H.F. , Nielsen D.S.",Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments,Microbiome,2024,NA,Experiment 2,Denmark,Mus musculus,Feces,UBERON:0001988,Clostridium difficile infection,EFO:0009130,Mice Before Clostridioides difficile infection (CDI),Euthanized mice,Mice that reached a humane endpoint and were euthanized before the intended study termination date.,48,23,NA,16S,3,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 7B,16 November 2024,Tosin,"Tosin,WikiWorks",Differential abundance of significantly different bacterial taxa between Before CDI (Clostridioides difficile Infection) and euthanized mice.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|815|816;1783272|1239|186801|3082720|186804|1870884|1496,Complete,Svetlana up
bsdb:38951925/2/2,38951925,laboratory experiment,38951925,10.1186/s40168-024-01820-1,NA,"Rasmussen T.S., Mao X., Forster S., Larsen S.B., Von Münchow A., Tranæs K.D., Brunse A., Larsen F., Mejia J.L.C., Adamberg S., Hansen A.K., Adamberg K., Hansen C.H.F. , Nielsen D.S.",Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments,Microbiome,2024,NA,Experiment 2,Denmark,Mus musculus,Feces,UBERON:0001988,Clostridium difficile infection,EFO:0009130,Mice Before Clostridioides difficile infection (CDI),Euthanized mice,Mice that reached a humane endpoint and were euthanized before the intended study termination date.,48,23,NA,16S,3,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 7B,16 November 2024,Tosin,"Tosin,WikiWorks",Differential abundance of significantly different bacterial taxa between Before CDI (Clostridioides difficile Infection) and euthanized mice.,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus taiwanensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus animalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus vaginalis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis",1783272|1239;1783272|1239|91061|186826|33958|1578|508451;1783272|1239|91061|186826|33958|2767887|1605;1783272|1239|91061|186826|33958|2742598|1633;3379134|1224|28216|80840|995019|577310|487175;1783272|1239|526524|526525|2810281|191303|154288,Complete,Svetlana up
bsdb:38951925/3/1,38951925,laboratory experiment,38951925,10.1186/s40168-024-01820-1,NA,"Rasmussen T.S., Mao X., Forster S., Larsen S.B., Von Münchow A., Tranæs K.D., Brunse A., Larsen F., Mejia J.L.C., Adamberg S., Hansen A.K., Adamberg K., Hansen C.H.F. , Nielsen D.S.",Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments,Microbiome,2024,NA,Experiment 3,Denmark,Mus musculus,Feces,UBERON:0001988,Clostridium difficile infection,EFO:0009130,Euthanized mice,Survived mice,"Mice that survived a Clostridioides difficile infection (CDI) followed by one of 4 FVT (fecal virome transplantation), FMT (fecal microbiota transplantaiton) or saline treatments until study termination.",23,24,NA,16S,3,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 7C,17 November 2024,Tosin,"Tosin,WikiWorks",Differential abundance of significantly different bacterial taxa between euthanized and survived mice.,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus taiwanensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus animalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus vaginalis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis",1783272|1239;1783272|1239|186801|186802|31979|1485;1783272|1239|91061|186826|33958|1578|508451;1783272|1239|91061|186826|33958|2767887|1605;1783272|1239|91061|186826|33958|2742598|1633;1783272|1239|526524|526525|2810281|191303|154288,Complete,Svetlana up
bsdb:38951925/3/2,38951925,laboratory experiment,38951925,10.1186/s40168-024-01820-1,NA,"Rasmussen T.S., Mao X., Forster S., Larsen S.B., Von Münchow A., Tranæs K.D., Brunse A., Larsen F., Mejia J.L.C., Adamberg S., Hansen A.K., Adamberg K., Hansen C.H.F. , Nielsen D.S.",Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments,Microbiome,2024,NA,Experiment 3,Denmark,Mus musculus,Feces,UBERON:0001988,Clostridium difficile infection,EFO:0009130,Euthanized mice,Survived mice,"Mice that survived a Clostridioides difficile infection (CDI) followed by one of 4 FVT (fecal virome transplantation), FMT (fecal microbiota transplantaiton) or saline treatments until study termination.",23,24,NA,16S,3,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 7C,17 November 2024,Tosin,"Tosin,WikiWorks",Differential abundance of significantly different bacterial taxa between euthanized and survived mice.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia fergusonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus canintestini,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila",3379134|1224|28216|80840|995019|577310|487175;3379134|976|200643|171549|2005525|375288|328812;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|561|564;1783272|1239|91061|186826|81852|1350|317010;1783272|1239|186801|3082720|186804|1870884|1496;3379134|976|200643|171549|815|816|818;3379134|74201|203494|48461|1647988|239934|239935,Complete,Svetlana up
bsdb:38951925/4/1,38951925,laboratory experiment,38951925,10.1186/s40168-024-01820-1,NA,"Rasmussen T.S., Mao X., Forster S., Larsen S.B., Von Münchow A., Tranæs K.D., Brunse A., Larsen F., Mejia J.L.C., Adamberg S., Hansen A.K., Adamberg K., Hansen C.H.F. , Nielsen D.S.",Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments,Microbiome,2024,NA,Experiment 4,Denmark,Mus musculus,Feces,UBERON:0001988,Clostridium difficile infection,EFO:0009130,Mice before Clostridioides difficile infection (CDI),Survived mice,"Mice that survived a Clostridioides difficile infection (CDI) followed by one of 4 FVT (fecal virome transplantation), FMT (fecal microbiota transplantaiton) or saline treatments until study termination.",48,21,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 7D,17 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differential abundance of significantly different viral taxa between Before CDI (Clostridioides difficile Infection) and Survived mice.,increased,"k__Loebvirae|p__Hofneiviricota|c__Faserviricetes|o__Tubulavirales,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|o__Crassvirales",2732090|2732410|2732411|2732094;2731360|2731618|2731619|1978007,Complete,Svetlana up
bsdb:38951925/4/2,38951925,laboratory experiment,38951925,10.1186/s40168-024-01820-1,NA,"Rasmussen T.S., Mao X., Forster S., Larsen S.B., Von Münchow A., Tranæs K.D., Brunse A., Larsen F., Mejia J.L.C., Adamberg S., Hansen A.K., Adamberg K., Hansen C.H.F. , Nielsen D.S.",Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments,Microbiome,2024,NA,Experiment 4,Denmark,Mus musculus,Feces,UBERON:0001988,Clostridium difficile infection,EFO:0009130,Mice before Clostridioides difficile infection (CDI),Survived mice,"Mice that survived a Clostridioides difficile infection (CDI) followed by one of 4 FVT (fecal virome transplantation), FMT (fecal microbiota transplantaiton) or saline treatments until study termination.",48,21,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 7D,17 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differential abundance of significantly different viral taxa between Before CDI (Clostridioides difficile Infection) and Survived mice.,decreased,"s__unidentified virus,,k__Orthornavirae|p__Lenarviricota|c__Leviviricetes|o__Norzivirales,k__Orthornavirae|p__Pisuviricota|c__Duplopiviricetes|o__Durnavirales",1214906;;2732396|2732407|2842243|2842247;2732396|2732408|2732505|2732549,Complete,Svetlana up
bsdb:38951925/5/1,38951925,laboratory experiment,38951925,10.1186/s40168-024-01820-1,NA,"Rasmussen T.S., Mao X., Forster S., Larsen S.B., Von Münchow A., Tranæs K.D., Brunse A., Larsen F., Mejia J.L.C., Adamberg S., Hansen A.K., Adamberg K., Hansen C.H.F. , Nielsen D.S.",Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments,Microbiome,2024,NA,Experiment 5,Denmark,Mus musculus,Feces,UBERON:0001988,Clostridium difficile infection,EFO:0009130,Mice before Clostridioides difficile infection (CDI),Euthanized mice,Mice that reached a humane endpoint and were euthanized before the intended study termination date.,48,24,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 7E,17 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differential abundance of significantly different viral taxa between Before CDI (Clostridioides difficile Infection) and Euthanized mice.,increased,"k__Loebvirae|p__Hofneiviricota|c__Faserviricetes|o__Tubulavirales,k__Sangervirae|p__Phixviricota|c__Malgrandaviricetes|o__Petitvirales",2732090|2732410|2732411|2732094;2732091|2732412|2732413|2732414,Complete,Svetlana up
bsdb:38951925/5/2,38951925,laboratory experiment,38951925,10.1186/s40168-024-01820-1,NA,"Rasmussen T.S., Mao X., Forster S., Larsen S.B., Von Münchow A., Tranæs K.D., Brunse A., Larsen F., Mejia J.L.C., Adamberg S., Hansen A.K., Adamberg K., Hansen C.H.F. , Nielsen D.S.",Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments,Microbiome,2024,NA,Experiment 5,Denmark,Mus musculus,Feces,UBERON:0001988,Clostridium difficile infection,EFO:0009130,Mice before Clostridioides difficile infection (CDI),Euthanized mice,Mice that reached a humane endpoint and were euthanized before the intended study termination date.,48,24,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 7E,18 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differential abundance of significantly different viral taxa between Before CDI (Clostridioides difficile Infection) and Euthanized mice.,decreased,"s__unidentified virus,k__Orthornavirae|p__Lenarviricota|c__Leviviricetes|o__Norzivirales,k__Orthornavirae|p__Pisuviricota|c__Duplopiviricetes|o__Durnavirales",1214906;2732396|2732407|2842243|2842247;2732396|2732408|2732505|2732549,Complete,Svetlana up
bsdb:38951925/6/1,38951925,laboratory experiment,38951925,10.1186/s40168-024-01820-1,NA,"Rasmussen T.S., Mao X., Forster S., Larsen S.B., Von Münchow A., Tranæs K.D., Brunse A., Larsen F., Mejia J.L.C., Adamberg S., Hansen A.K., Adamberg K., Hansen C.H.F. , Nielsen D.S.",Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments,Microbiome,2024,NA,Experiment 6,Denmark,Mus musculus,Feces,UBERON:0001988,Clostridium difficile infection,EFO:0009130,Euthanized mice,Survived mice,"Mice that survived a Clostridioides difficile infection (CDI) followed by one of 4 FVT (fecal virome transplantation), FMT (fecal microbiota transplantaiton) or saline treatments until study termination.",24,21,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 7F,18 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differential abundance of significantly different viral taxa between Euthanized and Survived mice.,increased,NA,NA,Complete,Svetlana up
bsdb:38951925/6/2,38951925,laboratory experiment,38951925,10.1186/s40168-024-01820-1,NA,"Rasmussen T.S., Mao X., Forster S., Larsen S.B., Von Münchow A., Tranæs K.D., Brunse A., Larsen F., Mejia J.L.C., Adamberg S., Hansen A.K., Adamberg K., Hansen C.H.F. , Nielsen D.S.",Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments,Microbiome,2024,NA,Experiment 6,Denmark,Mus musculus,Feces,UBERON:0001988,Clostridium difficile infection,EFO:0009130,Euthanized mice,Survived mice,"Mice that survived a Clostridioides difficile infection (CDI) followed by one of 4 FVT (fecal virome transplantation), FMT (fecal microbiota transplantaiton) or saline treatments until study termination.",24,21,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 7F,18 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differential abundance of significantly different viral taxa between Euthanized and Survived mice.,decreased,"k__Sangervirae|p__Phixviricota|c__Malgrandaviricetes|o__Petitvirales,k__Orthornavirae|p__Pisuviricota|c__Duplopiviricetes|o__Durnavirales",2732091|2732412|2732413|2732414;2732396|2732408|2732505|2732549,Complete,Svetlana up
bsdb:38951925/7/1,38951925,laboratory experiment,38951925,10.1186/s40168-024-01820-1,NA,"Rasmussen T.S., Mao X., Forster S., Larsen S.B., Von Münchow A., Tranæs K.D., Brunse A., Larsen F., Mejia J.L.C., Adamberg S., Hansen A.K., Adamberg K., Hansen C.H.F. , Nielsen D.S.",Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments,Microbiome,2024,NA,Experiment 7,Denmark,Mus musculus,Feces,UBERON:0001988,Clostridium difficile,NCBITAXON:1496,Saline,FVT-UnT (Untreated Fecal Virome Transplantation),Mice that received untreated donor fecal virome material (before second FVT treatment).,7,7,NA,PCR,NA,RT-qPCR,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,20 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Evaluation of C. difficile abundance by qPCR.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,1783272|1239|186801|3082720|186804|1870884|1496,Complete,Svetlana up
bsdb:38951925/8/1,38951925,laboratory experiment,38951925,10.1186/s40168-024-01820-1,NA,"Rasmussen T.S., Mao X., Forster S., Larsen S.B., Von Münchow A., Tranæs K.D., Brunse A., Larsen F., Mejia J.L.C., Adamberg S., Hansen A.K., Adamberg K., Hansen C.H.F. , Nielsen D.S.",Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments,Microbiome,2024,NA,Experiment 8,Denmark,Mus musculus,Feces,UBERON:0001988,Clostridium difficile,NCBITAXON:1496,Saline,FVT-ChP (Chemostat-propagated fecal virome transplantation),Mice that received Chemostat-propagated fecal virome (before second FVT treatment).,7,8,NA,PCR,NA,RT-qPCR,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,20 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Evaluation of C. difficile abundance by qPCR.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,1783272|1239|186801|3082720|186804|1870884|1496,Complete,Svetlana up
bsdb:38951925/9/1,38951925,laboratory experiment,38951925,10.1186/s40168-024-01820-1,NA,"Rasmussen T.S., Mao X., Forster S., Larsen S.B., Von Münchow A., Tranæs K.D., Brunse A., Larsen F., Mejia J.L.C., Adamberg S., Hansen A.K., Adamberg K., Hansen C.H.F. , Nielsen D.S.",Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments,Microbiome,2024,NA,Experiment 9,Denmark,Mus musculus,Feces,UBERON:0001988,Clostridium difficile,NCBITAXON:1496,Saline,FVT-SDT (Solvent-Detergent Treated Fecal Virome Transplantation),Mice that received fecal virome material subjected to solvent-detergent treatment (before second FVT treatment).,7,8,NA,PCR,NA,RT-qPCR,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,20 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Evaluation of C. difficile abundance by qPCR.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,1783272|1239|186801|3082720|186804|1870884|1496,Complete,Svetlana up
bsdb:38951925/10/1,38951925,laboratory experiment,38951925,10.1186/s40168-024-01820-1,NA,"Rasmussen T.S., Mao X., Forster S., Larsen S.B., Von Münchow A., Tranæs K.D., Brunse A., Larsen F., Mejia J.L.C., Adamberg S., Hansen A.K., Adamberg K., Hansen C.H.F. , Nielsen D.S.",Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments,Microbiome,2024,NA,Experiment 10,Denmark,Mus musculus,Feces,UBERON:0001988,Clostridium difficile,NCBITAXON:1496,Saline,FVT-SDT (Solvent-Detergent Treated Fecal Virome Transplantation),Mice that received fecal virome material subjected to solvent-detergent treatment (at the experiment termination phase).,2,8,NA,PCR,NA,RT-qPCR,raw counts,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,20 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Evaluation of C. difficile abundance by qPCR.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,1783272|1239|186801|3082720|186804|1870884|1496,Complete,Svetlana up
bsdb:38956672/1/1,38956672,time series / longitudinal observational,38956672,https://doi.org/10.1186/s13048-024-01444-x,NA,"Hu L., Hong G., Li J., Chen M., Chang C.J., Cheng P.J., Zhang Z., Zhang X., Chen H., Zhuang Y. , Li Y.",Metformin modifies plasma microbial-derived extracellular vesicles in polycystic ovary syndrome with insulin resistance,Journal of ovarian research,2024,"EVs, Full-length 16S rRNA, Metformin, Microbial community, PCOS, PCOS-IR",Experiment 1,China,Homo sapiens,Blood plasma,UBERON:0001969,Polycystic ovary syndrome,EFO:0000660,EBF (EVs extracted from patients before treatment) group,EAF (EVs extracted from patients after treatment) group,"Polycystic ovary syndrome- Insulin-resistant patients of childbearing age, whose plasma EVs(extracellular vesicles) were extracted after 3 months of metformin treatment.",5,5,6 months,16S,123456789,NA,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,decreased,NA,NA,Signature 1,Figure 6B,18 April 2025,ShadeAkinremi,"ShadeAkinremi,Victoria",Analysis of microbial species diversity. Microbial cladogram (LEfSe).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium",3379134|1224|28211|356|69277|68287;3379134|1224|28211|356|69277|68287,Complete,KateRasheed
bsdb:38956672/1/2,38956672,time series / longitudinal observational,38956672,https://doi.org/10.1186/s13048-024-01444-x,NA,"Hu L., Hong G., Li J., Chen M., Chang C.J., Cheng P.J., Zhang Z., Zhang X., Chen H., Zhuang Y. , Li Y.",Metformin modifies plasma microbial-derived extracellular vesicles in polycystic ovary syndrome with insulin resistance,Journal of ovarian research,2024,"EVs, Full-length 16S rRNA, Metformin, Microbial community, PCOS, PCOS-IR",Experiment 1,China,Homo sapiens,Blood plasma,UBERON:0001969,Polycystic ovary syndrome,EFO:0000660,EBF (EVs extracted from patients before treatment) group,EAF (EVs extracted from patients after treatment) group,"Polycystic ovary syndrome- Insulin-resistant patients of childbearing age, whose plasma EVs(extracellular vesicles) were extracted after 3 months of metformin treatment.",5,5,6 months,16S,123456789,NA,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,decreased,NA,NA,Signature 2,Figure 6B,19 April 2025,ShadeAkinremi,"ShadeAkinremi,Victoria",Analysis of microbial species diversity. Microbial cladogram (LEfSe).,decreased,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium|s__Sphingobacterium hotanense,3379134|976|117747|200666|84566|28453|649196,Complete,KateRasheed
bsdb:38956672/2/1,38956672,time series / longitudinal observational,38956672,https://doi.org/10.1186/s13048-024-01444-x,NA,"Hu L., Hong G., Li J., Chen M., Chang C.J., Cheng P.J., Zhang Z., Zhang X., Chen H., Zhuang Y. , Li Y.",Metformin modifies plasma microbial-derived extracellular vesicles in polycystic ovary syndrome with insulin resistance,Journal of ovarian research,2024,"EVs, Full-length 16S rRNA, Metformin, Microbial community, PCOS, PCOS-IR",Experiment 2,China,Homo sapiens,Blood plasma,UBERON:0001969,Polycystic ovary syndrome,EFO:0000660,EBF (EVs extracted from patients before treatment) group,EAF (EVs extracted from patients after treatment) group,"Polycystic ovary syndrome- Insulin-resistant patients of childbearing age, whose plasma EVs(extracellular vesicles) were extracted after 3 months of metformin treatment.",5,5,6 months,16S,123456789,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,2,NA,NA,NA,NA,NA,decreased,NA,NA,Signature 1,Figure 6C,10 June 2025,Victoria,Victoria,Analysis of microbial species diversity. Microbial cladogram (Wilcoxon rank-sum test).,increased,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,3379134|1224|28211|356|69277|68287,Complete,KateRasheed
bsdb:38956672/2/2,38956672,time series / longitudinal observational,38956672,https://doi.org/10.1186/s13048-024-01444-x,NA,"Hu L., Hong G., Li J., Chen M., Chang C.J., Cheng P.J., Zhang Z., Zhang X., Chen H., Zhuang Y. , Li Y.",Metformin modifies plasma microbial-derived extracellular vesicles in polycystic ovary syndrome with insulin resistance,Journal of ovarian research,2024,"EVs, Full-length 16S rRNA, Metformin, Microbial community, PCOS, PCOS-IR",Experiment 2,China,Homo sapiens,Blood plasma,UBERON:0001969,Polycystic ovary syndrome,EFO:0000660,EBF (EVs extracted from patients before treatment) group,EAF (EVs extracted from patients after treatment) group,"Polycystic ovary syndrome- Insulin-resistant patients of childbearing age, whose plasma EVs(extracellular vesicles) were extracted after 3 months of metformin treatment.",5,5,6 months,16S,123456789,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,2,NA,NA,NA,NA,NA,decreased,NA,NA,Signature 2,Figure 6C,10 June 2025,Victoria,Victoria,Analysis of microbial species diversity. Microbial cladogram (Wilcoxon rank-sum test).,decreased,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium|s__Sphingobacterium hotanense,3379134|976|117747|200666|84566|28453|649196,Complete,KateRasheed
bsdb:38959253/1/1,38959253,case-control,38959253,10.1371/journal.pone.0306582,NA,"Wang Y., Bi S., Li X., Zhong Y. , Qi D.",Perturbations in gut microbiota composition in schizophrenia,PloS one,2024,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,NC: normal controls,SZ: patients with schizophrenia,"individuals with schizophrenia diagnosed by a clinician using the systematic structured clinical interview method and detailed background information approach detailed in the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition.",30,29,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,age,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 3A, 3B",23 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,WikiWorks",Differential abundance of microbial composition between normal controls and individuals with schizophrenia.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Acidithiobacillia|o__Acidithiobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Acidithiobacillia|o__Acidithiobacillales|f__Acidithiobacillaceae|g__Acidithiobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Coriobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Pseudomonadati|p__Nitrospirota|c__Nitrospiria|o__Nitrospirales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiales Family XVII. Incertae Sedis|g__Sulfobacillus,k__Pseudomonadati|p__Nitrospirota|c__Nitrospiria|o__Nitrospirales|f__Nitrospiraceae|g__Leptospirillum",1783272|1239|909932|1843488|909930|904;3379134|1224|1807140|225057;3379134|1224|1807140|225057|225058|119977;3379134|1224|1236|135624;1783272|1239|186801|186802|216572|244127;1783272|1239|91061|1385;1783272|1239|526524|526525|128827|118747;1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999;1783272|201174|84998|84999|84107|33870;1783272|201174|1760|85007|1653|1716;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|909929|1843491|52225;1783272|1239|186801|3082720|543314|86331;3379134|40117|203693|189778;3379134|1224|1236|91347|1903414|583;1783272|1239|186801|186802|31979|1266;1783272|1239|909932|909929|1843491|970;3379134|1224|1236|135624|83763|83770;1783272|1239|186801|186802|539000|28033;3379134|40117|203693|189778|189779|179,Complete,Svetlana up
bsdb:38959253/1/2,38959253,case-control,38959253,10.1371/journal.pone.0306582,NA,"Wang Y., Bi S., Li X., Zhong Y. , Qi D.",Perturbations in gut microbiota composition in schizophrenia,PloS one,2024,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,NC: normal controls,SZ: patients with schizophrenia,"individuals with schizophrenia diagnosed by a clinician using the systematic structured clinical interview method and detailed background information approach detailed in the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition.",30,29,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,age,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 3A, 3B",24 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,WikiWorks",Differential abundance of microbial composition between normal controls and individuals with schizophrenia.,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|186802|3085642|580596;3384194|508458|649775|649776|649777|508459;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|91061|186826|1300|1357;1783272|1239|909932|1843489|31977|906;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351;3384194|508458|649775|649776|3029088|638847;1783272|1239|909932|1843489|31977|29465;3379134|74201|203494|48461,Complete,Svetlana up
bsdb:38959253/2/1,38959253,case-control,38959253,10.1371/journal.pone.0306582,NA,"Wang Y., Bi S., Li X., Zhong Y. , Qi D.",Perturbations in gut microbiota composition in schizophrenia,PloS one,2024,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,NC: normal controls,SZ: patients with schizophrenia,"individuals with schizophrenia diagnosed by a clinician using the systematic structured clinical interview method and detailed background information approach detailed in the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition.",6,6,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,age,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 3C, 3D",24 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,WikiWorks",Differential abundance of microbial composition between normal controls and individuals with schizophrenia.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes ihumii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:413,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus pontis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Massiliimalia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Massiliimalia|s__Massiliimalia timonensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas rupellensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|s__Prevotellaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:177,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550|239759|1470347;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|31979|1485|1262803;1783272|1239|91061|186826|33958|2742598;1783272|1239|91061|186826|33958|2742598|35787;1783272|1239|186801|186802|216572|2895461;1783272|1239|186801|186802|216572|2895461|1987501;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|909929|1843491|158846|158847;1783272|1239|909932|909929|1843491|158846|491921;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843489|31977|906|907;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171552|2049047;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|1262952;1783272|1239|909932|909929|1843491|970,Complete,Svetlana up
bsdb:38959253/2/2,38959253,case-control,38959253,10.1371/journal.pone.0306582,NA,"Wang Y., Bi S., Li X., Zhong Y. , Qi D.",Perturbations in gut microbiota composition in schizophrenia,PloS one,2024,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,NC: normal controls,SZ: patients with schizophrenia,"individuals with schizophrenia diagnosed by a clinician using the systematic structured clinical interview method and detailed background information approach detailed in the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition.",6,6,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,age,NA,unchanged,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 3C, 3D",24 July 2024,Jacob A. De Jesus,"Jacob A. De Jesus,WikiWorks",Differential abundance of microbial composition between normal controls and individuals with schizophrenia.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides galacturonicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:443,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia massiliensis (ex Durand et al. 2017),k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. TM05-53,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella porci,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. TF10-5,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Wujia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Wujia|s__Wujia chipingensis",3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|384639;3379134|976|200643|171549|815|816|1262739;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|1737424;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|186806|1730|2292353;1783272|1239|526524|526525|128827|1573535;1783272|1239|526524|526525|128827|1573535|2652276;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|28050|28052;1783272|1239|186801|3085636|186803|28050|2049031;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|2293144;1783272|1239|186801|3085636|186803|2944152;1783272|1239|186801|3085636|186803|2944152|2763670,Complete,Svetlana up
bsdb:38968070/1/1,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 1,Honduras,Homo sapiens,Feces,UBERON:0001988,Health-related quality of life measurement,EFO:0011014,Health associated(Healthy),Disease associated(Chronically diseased individuals),"Disease associated has to do with chronically diseased individuals who had at least one
chronic condition. Examples of the chronic conditions include: diabetes, asthma, heart disease, arthritis, etc",NA,468,NA,WMS,NA,Illumina,centered log-ratio,MaAsLin2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. S4B,16 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in healthy vs chronically diseased individuals using MaAsLin2.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,1783272|1239|186801|3085636|186803|1898203,Complete,Svetlana up
bsdb:38968070/1/2,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 1,Honduras,Homo sapiens,Feces,UBERON:0001988,Health-related quality of life measurement,EFO:0011014,Health associated(Healthy),Disease associated(Chronically diseased individuals),"Disease associated has to do with chronically diseased individuals who had at least one
chronic condition. Examples of the chronic conditions include: diabetes, asthma, heart disease, arthritis, etc",NA,468,NA,WMS,NA,Illumina,centered log-ratio,MaAsLin2,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,Fig. S4B,16 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in healthy vs chronically diseased individuals using MaAsLin2,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|s__Spirochaetia bacterium,k__Bacillati|p__Bacillota|c__Clostridia",1783272|1239|186801|3085636|186803|33042;3379134|203691|203692|2053615;1783272|1239|186801,Complete,Svetlana up
bsdb:38968070/2/1,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 2,Honduras,Homo sapiens,Feces,UBERON:0001988,Health-related quality of life measurement,EFO:0011014,Healthy individuals,Unhealthy individuals based on Physiological Variables,"Unhealthy individuals refers to those with unhealthy phenotypes like BMI <18 and BMI >25 to account for underweight and overweight individuals; diastolic pressure >89 to account for hypertensive individuals; Haemoglobin A1c, Haemoglobin total, heart disease, oxygen saturation.",NA,NA,NA,WMS,NA,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,"body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table S1,16 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between healthy and unhealthy individuals based on physiological variables,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF27-2AA,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AM22-11AC,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sp. BL7,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF20-17LB,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister histaminiformans,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium fessum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF34-10BH,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora amygdalina,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",1783272|1239|909932|1843488|909930|33024|33025;1783272|1239|186801|186802|31979|1485|2292206;1783272|1239|186801|186802|31979|1485|2293024;3379134|1224|28216|80840|995019|40544|40545;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|909932|1843489|31977|906|1285585;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|909932|1843489|31977|906|907;1783272|1239|186801|186802|31979|1485|2292205;1783272|1239|909932|1843489|31977|39948|209880;1783272|1239|186801|3082720|186804|1501226|1776391;1783272|1239|186801|186802|31979|1485|2126740;1783272|1239|909932|909929|1843491|52225|52226;1783272|1239|91061|186826|1300|1301|1304;3379134|1224|1236|135625|712|724|729;1783272|1239|186801|3085636|186803|1898203;1783272|1239|186801|186802|31979|1485|2293011;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|2719231|253257;1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|186802|216572|216851|853,Complete,Svetlana up
bsdb:38968070/2/2,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 2,Honduras,Homo sapiens,Feces,UBERON:0001988,Health-related quality of life measurement,EFO:0011014,Healthy individuals,Unhealthy individuals based on Physiological Variables,"Unhealthy individuals refers to those with unhealthy phenotypes like BMI <18 and BMI >25 to account for underweight and overweight individuals; diastolic pressure >89 to account for hypertensive individuals; Haemoglobin A1c, Haemoglobin total, heart disease, oxygen saturation.",NA,NA,NA,WMS,NA,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,"body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table S1,16 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between healthy and unhealthy individuals based on physiological variables,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum|s__Agathobaculum butyriciproducens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira aalborgi,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas faecalis,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales|s__Candidatus Gastranaerophilales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|s__Elusimicrobiales bacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium OM04-12BH,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. ER4,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella|s__Parolsenella massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|s__Rikenellaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus champanellensis,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema succinifaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__[Bacteroides] pectinophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium lentum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium OM08-6BH,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF36-4,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bovis,k__Pseudomonadati|p__Kiritimatiellota|c__Kiritimatiellia|o__Kiritimatiellales|f__Kiritimatiellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp. OM04-5BH,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Pseudoruminococcus|s__Pseudoruminococcus massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus sp. AM29-23AC,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales",1783272|1239|186801|186802|3085642|2048137|1628085;3379134|976|200643|171549|2030927;3379134|203691|203692|1643686|143786|29521|29522;3379134|976|200643|171549|1853231|574697|2093856;1783272|1798710|1906119|2137880;1783272|1239|186801|2044939;1783272|1239|186801|186802|31979|1485|1502;3379134|74152|641853|641854|2478488;1783272|1239|526524|526525|128827|2049044;1783272|1239|186801|3085636|186803|3342669|45851;1783272|1239|186801|3085636|186803|2292272;3366610|28890|183925|2158|2159|2172|2173;1783272|1239|186801|186802|216572|459786|1519439;1783272|1239|186801|186802|216572|2485925;1783272|201174|84998|84999|1643824|2082587|1871022;3379134|976|200643|171549|171550|2049048;1783272|1239|186801|186802|216572|1263|1161942;3379134|203691|203692|136|2845253|157|167;1783272|1239|186801|186802|384638;1783272|1239|186801|186802|216572|39492;3379134|1224|28211;1783272|1239|91061;1783272|1239|186801|186802|31979|1485|2763037;1783272|1239|186801|186802|31979|2292274;1783272|1239|186801|186802|31979|1485|2293015;1783272|1239|186801|186802|216572|1263|2564099;3379134|134625|1921781|1921782|1921783;1783272|1239|186801|3085636|186803|33042|2293093;1783272|1239|186801|186802|3082771|2721119|2086583;1783272|1239|186801|186802|3085642|580596|2292295;1783272|544448|31969|186329,Complete,Svetlana up
bsdb:38968070/3/1,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 3,Honduras,Homo sapiens,Feces,UBERON:0001988,Health-related quality of life measurement,EFO:0011014,Healthy individuals,Unhealthy individuals based on acute conditions,"Unhealthy individuals refers to those with unhealthy phenotypes like Bristol, diarrhea, cough.",NA,NA,NA,WMS,NA,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,"body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table S1,16 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between healthy and unhealthy individuals based on acute conditions,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium",1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|186801|3085636|186803|1898203,Complete,Svetlana up
bsdb:38968070/3/2,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 3,Honduras,Homo sapiens,Feces,UBERON:0001988,Health-related quality of life measurement,EFO:0011014,Healthy individuals,Unhealthy individuals based on acute conditions,"Unhealthy individuals refers to those with unhealthy phenotypes like Bristol, diarrhea, cough.",NA,NA,NA,WMS,NA,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,"body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table S1,16 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between healthy and unhealthy individuals based on acute conditions,decreased,NA,NA,Complete,Svetlana up
bsdb:38968070/4/1,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 4,Honduras,Homo sapiens,Feces,UBERON:0001988,Health-related quality of life measurement,EFO:0011014,Healthy individuals,Unhealthy individuals based on Chronic conditions,"Unhealthy individuals based on Chronic conditions refers to those with unhealthy phenotypes like diabetes, allergies, heart disease, asthma, stomach illness, intestinal illness, arthritis",NA,688,NA,WMS,NA,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,"body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table S1,16 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between healthy and unhealthy individuals based on chronic conditions,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora amygdalina,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AM22-11AC,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae",3379134|976|200643|171549|815|909656|310297;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|2719231|253257;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|816|371601;1783272|1239|186801|3085636|186803|1898203;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|246787;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|186802|31979|1485|2293024;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|171550|239759|214856;1783272|1239|186801|3085636|186803|2316020|46228;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|171552|577309|454154;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|2005519|397864|487174;3379134|976|200643|171549|2005525|375288|46503,Complete,Svetlana up
bsdb:38968070/4/2,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 4,Honduras,Homo sapiens,Feces,UBERON:0001988,Health-related quality of life measurement,EFO:0011014,Healthy individuals,Unhealthy individuals based on Chronic conditions,"Unhealthy individuals based on Chronic conditions refers to those with unhealthy phenotypes like diabetes, allergies, heart disease, asthma, stomach illness, intestinal illness, arthritis",NA,688,NA,WMS,NA,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,"body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table S1,16 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between healthy and unhealthy individuals based on chronic conditions,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|s__Bacilli bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|s__Bacteroidaceae bacterium,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales|s__Candidatus Gastranaerophilales bacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium sp. AM22-15,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium lentum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella|s__Parolsenella massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pectinovora,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella hominis,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|s__Spirochaetia bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P3-120,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P4-51,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. 885,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. AF22-8LB",1783272|1239|91061|1903720;3379134|976|200643|171549|815|2212467;1783272|1798710|1906119|2137880;1783272|1239|526524|526525|2810280|135858|2292991;1783272|1239|186801|2044939;1783272|1239|186801|186802|31979|1485|2763037;1783272|1239|526524|526525|128827|2049044;1783272|1239|186801|186802|216572|216851|853;3379134|1224|1236|135625|712|724|729;1783272|1239|526524|526525|128827|1573535|1735;1783272|1239|186801|186802|216572|2485925;1783272|201174|84998|84999|1643824|2082587|1871022;3379134|976|200643|171549|171552|838|1602169;3379134|976|200643|171549|171552|2974251|2518605;3379134|203691|203692|2053615;1783272|1239|186801|3085636|186803|2316020|33039;3379134|1224|28211;3379134|976|200643|171549|171552|838|2024220;3379134|976|200643|171549|171552|838|2024228;3379134|976|200643|171549|171552|838|2022527;1783272|1239|186801|186802|186806|1730|2292232,Complete,Svetlana up
bsdb:38968070/5/1,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 5,Honduras,Homo sapiens,Feces,UBERON:0001988,Health-related quality of life measurement,EFO:0011014,Healthy individuals,Unhealthy individuals based on medication use,"Unhealthy individuals based on medication use refers to those with unhealthy phenotypes like antibiotics, painkillers, anti-diarreal, anti-fungal, anti-parasitic, anti-hypertensive and vitamins",NA,NA,NA,WMS,NA,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,"body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table S1,17 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between healthy and unhealthy individuals based on medication use.,increased,"k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales|s__Candidatus Gastranaerophilales bacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|s__Selenomonadales bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AM22-11AC",1783272|1798710|1906119|2137880;1783272|1239|909932|909929|2137878;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|371601;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|815|816|820;1783272|1239|186801|186802|31979|1485|2293024,Complete,Svetlana up
bsdb:38968070/5/2,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 5,Honduras,Homo sapiens,Feces,UBERON:0001988,Health-related quality of life measurement,EFO:0011014,Healthy individuals,Unhealthy individuals based on medication use,"Unhealthy individuals based on medication use refers to those with unhealthy phenotypes like antibiotics, painkillers, anti-diarreal, anti-fungal, anti-parasitic, anti-hypertensive and vitamins",NA,NA,NA,WMS,NA,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,"body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table S1,17 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between healthy and unhealthy individuals based on medication use.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium OM08-6BH,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium KLE1615,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium OM04-12BH,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF34-13,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pectinovora,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. OM07-10AC,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. AF22-8LB,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema succinifaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella sp. GAM18,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella|s__Parolsenella massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bovis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris",1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|186802|31979|2292274;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|1715004;1783272|1239|186801|3085636|186803|2292272;1783272|1239|186801|186802|31979|1485|2293012;1783272|201174|84998|1643822|1643826|84108|572010;1783272|1239|186801|3085636|186803|841|301302;3379134|976|200643|171549|171552|838|1602169;1783272|1239|186801|186802|216572|1263|2763066;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|186802|31979|1485|2293047;1783272|1239|186801|186802|186806|1730|2292232;3379134|203691|203692|136|2845253|157|167;1783272|201174|84998|84999|1643824|133925|2109685;3379134|1224|1236|135625|712|724|729;1783272|201174|84998|84999|1643824|2082587|1871022;1783272|1239|186801|186802|216572|1263|2564099;1783272|1239|186801|3085636|186803|2316020|46228,Complete,Svetlana up
bsdb:38968070/6/1,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 6,Honduras,Homo sapiens,Feces,UBERON:0001988,Health-related quality of life measurement,EFO:0011014,Healthy individuals,Unhealthy individuals based on mental health,"Unhealthy individuals based on mental health refers to those with unhealthy phenotypes like dementia, reserved, anxiety, depression, openness, nervous, cognitive impairment.",NA,NA,NA,WMS,NA,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,"body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table S1,17 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between healthy and unhealthy individuals based on mental health,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P4-51,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bovis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella hominis,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|s__Victivallales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",3379134|976|200643|171549|171552|838|2079531;3379134|976|200643|171549|171552|838|2024228;1783272|1239|186801|186802|216572|1263|2564099;3379134|976|200643|171549|171552|2974251|2518605;3379134|256845|1313211|278082|2212475;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|186802|216572|216851|853,Complete,Svetlana up
bsdb:38968070/6/2,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 6,Honduras,Homo sapiens,Feces,UBERON:0001988,Health-related quality of life measurement,EFO:0011014,Healthy individuals,Unhealthy individuals based on mental health,"Unhealthy individuals based on mental health refers to those with unhealthy phenotypes like dementia, reserved, anxiety, depression, openness, nervous, cognitive impairment.",NA,NA,NA,WMS,NA,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,"body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table S1,17 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between healthy and unhealthy individuals based on mental health,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Cibiobacter|s__Candidatus Cibiobacter qucibialis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AM22-11AC,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AM33-3,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella|s__Parolsenella massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella merdae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. 885",3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|171550|239759|1288121;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|46506;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|820;1783272|1239|186801|186802|2527773|2500537;1783272|1239|186801|186802|31979|1485|2293024;1783272|1239|186801|186802|31979|1485|2292304;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|2005525|375288|46503;1783272|201174|84998|84999|1643824|2082587|1871022;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|171552|838|2079531;3379134|1224|28216|80840|995019|40544|40545;3379134|976|200643|171549|171552|838|2022527,Complete,Svetlana up
bsdb:38968070/7/1,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 7,Honduras,Homo sapiens,Feces,UBERON:0001988,Health-related quality of life measurement,EFO:0011014,Healthy individuals,Unhealthy individuals based on alcohol and cigarette,"Unhealthy individuals based on unfavourable habits(alcohol and cigarette) refers to those with unhealthy phenotypes like alcohol daily frequency, cigarette use, cigarette frequency.",NA,972,NA,WMS,NA,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,"body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table S1,17 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between healthy and unhealthy individuals based on alcohol and cigarette.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii",3379134|1224|28216|80840|995019|40544|40545;1783272|1239|186801|186802|216572|946234|292800,Complete,Svetlana up
bsdb:38968070/7/2,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 7,Honduras,Homo sapiens,Feces,UBERON:0001988,Health-related quality of life measurement,EFO:0011014,Healthy individuals,Unhealthy individuals based on alcohol and cigarette,"Unhealthy individuals based on unfavourable habits(alcohol and cigarette) refers to those with unhealthy phenotypes like alcohol daily frequency, cigarette use, cigarette frequency.",NA,972,NA,WMS,NA,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,"body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table S1,17 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between healthy and unhealthy individuals based on alcohol and cigarette.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bovis,1783272|1239|186801|186802|216572|1263|2564099,Complete,Svetlana up
bsdb:38968070/8/1,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 8,Honduras,Homo sapiens,Feces,UBERON:0001988,Health-related quality of life measurement,EFO:0011014,Healthy individuals,Overall health phenotype sub-category,"Overall health phenotype sub-category refers to those with phenotypes like fair, poor, very good, excellent",NA,1394,NA,WMS,NA,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,"body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table S1,17 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between healthy and overall healthy phenotype sub-category(fair).,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,3379134|976|200643|171549|171550|239759|214856,Complete,Svetlana up
bsdb:38968070/9/1,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 9,Honduras,Homo sapiens,Feces,UBERON:0001988,Environmental exposure measurement,EFO:0008360,Individual unexposed to animals,Individual exposed to animals,"Individual exposed to animals refers to the villagers who reported having exposure to different types of animals, including wild animals, farm animals, and pets, affording possible zoonotic transmission.",NA,NA,NA,WMS,NA,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,"body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table S1,17 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between individuals exposed or unexposed to animals,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__Desulfovibrionaceae bacterium,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|s__Elusimicrobiales bacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Faecalibacillus|s__Faecalibacillus intestinalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. ER4,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotellamassilia|s__Prevotellamassilia timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Liu et al. 2021),k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",3379134|976|200643|171549|171550|239759|2585118;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|171550|239759|1288121;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|815|816|329854;3379134|976|200643|171549|815|816|46506;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|371601;1783272|1239|186801|3085636|186803|572511|871665;1783272|1239|186801|3085636|186803|572511|418240;3379134|200940|3031449|213115|194924|2049043;3379134|74152|641853|641854|2478488;1783272|1239|526524|526525|2810280|2678885|1982626;1783272|1239|91061|186826|1300|1357|1358;3379134|976|200643|171549|1853231|283168|28118;1783272|1239|186801|186802|216572|459786|1519439;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|171552|1926672|1852370;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|186802|216572|1263|3062497;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|909932|1843489|31977|29465|39778,Complete,Svetlana up
bsdb:38968070/9/2,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 9,Honduras,Homo sapiens,Feces,UBERON:0001988,Environmental exposure measurement,EFO:0008360,Individual unexposed to animals,Individual exposed to animals,"Individual exposed to animals refers to the villagers who reported having exposure to different types of animals, including wild animals, farm animals, and pets, affording possible zoonotic transmission.",NA,NA,NA,WMS,NA,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,"body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table S1,17 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between individuals exposed or unexposed to animals,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AM22-11AC,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella merdae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis",3379134|976|200643|171549|171550|239759|28117;1783272|201174|1760|85004|31953|1678|28026;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|186802|31979|1485|2293024;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|171552|838|2079531;3379134|1224|28216|80840|995019|40544|40545,Complete,Svetlana up
bsdb:38968070/10/1,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 10,Honduras,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Food frequency consumption(Never/Rarely),Food frequency consumption(Everyday),Food frequency consumption(Everyday) refers to individuals who consumed various categories of food everyday especially Beans and Tortillas,NA,NA,NA,WMS,NA,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,"body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table S1,18 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between food frequency consumption(never/rarely) and food frequency consumption(always).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. AM28-29,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella|s__Parolsenella massiliensis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella sp. GAM18,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella hominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sp. BL7,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia massiliensis (ex Liu et al. 2021),k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum faecicola,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AM22-11AC,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae",1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|1263|2763066;1783272|1239|186801|186802|186806|1730|2292349;1783272|201174|84998|84999|1643824|2082587|1871022;1783272|201174|84998|84999|1643824|133925|2109685;3379134|976|200643|171549|171552|2974251|2518605;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|815|816|46506;3379134|976|200643|171549|815|909656|821;1783272|201174|1760|85004|31953|1678|216816;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|171550|239759|328814;1783272|1239|909932|1843488|909930|33024|33025;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|171552|577309|454154;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|329854;3379134|976|200643|171549|815|816|371601;1783272|1239|909932|1843489|31977|906|1285585;3379134|1224|1236|91347|543|544|546;1783272|1239|186801|3085636|186803|1407607|1150298;3379134|976|200643|171549|815|909656|387090;1783272|1239|91061|186826|1300|1357|1358;3379134|976|200643|171549|171550|239759|328813;3379134|1224|1236|91347|543|547|158836;1783272|201174|1760|85004|31953|1678|1680;1783272|1239|91061|186826|81852|1350|1352;3379134|1224|1236|91347|543|570|573;3379134|976|200643|171549|2005519|397864|487174;1783272|1239|186801|3085636|186803|572511|3062492;1783272|1239|186801|3085636|3118652|2039240|2358141;3379134|200940|3031449|213115|194924|35832|35833;3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|815|816|246787;1783272|1239|909932|1843489|31977|906|907;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803|572511|871665;1783272|1239|186801|186802|31979|1485|2293024;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|3085636|186803|572511|418240,Complete,Svetlana up
bsdb:38968070/10/2,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 10,Honduras,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Food frequency consumption(Never/Rarely),Food frequency consumption(Everyday),Food frequency consumption(Everyday) refers to individuals who consumed various categories of food everyday especially Beans and Tortillas,NA,NA,NA,WMS,NA,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,"body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table S1,18 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between food frequency consumption(never/rarely) and food frequency consumption(always).,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium sp. AM22-15,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium lentum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp. OM04-5BH,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|s__Lentisphaeria bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. ER4,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella|s__Parolsenella massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. 885,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P3-120,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P4-51,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotellamassilia|s__Prevotellamassilia timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. AM59-24XD,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bovis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina|s__Sarcina ventriculi,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella hominis,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema berlinense,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema succinifaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",1783272|1239|526524|526525|2810280|135858|2292991;1783272|1239|186801|186802|31979|1485|2763037;1783272|1239|186801|3085636|186803|33042|2293093;3379134|256845|1313211|2053569;1783272|1239|186801|186802|216572|459786|1519439;1783272|201174|84998|84999|1643824|2082587|1871022;3379134|976|200643|171549|171552|838|2079531;3379134|976|200643|171549|171552|838|2022527;3379134|976|200643|171549|171552|838|2024220;3379134|976|200643|171549|171552|838|2024228;3379134|976|200643|171549|171552|1926672|1852370;1783272|1239|186801|3085636|186803|841|2293138;1783272|1239|186801|186802|216572|1263|2564099;1783272|1239|186801|186802|31979|1266|1267;3379134|976|200643|171549|171552|2974251|2518605;3379134|203691|203692|136|2845253|157|225004;3379134|203691|203692|136|2845253|157|167;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|815|816|329854;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Svetlana up
bsdb:38968070/11/1,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 11,Honduras,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,Subjects from the least well-off households based on economic factors,Subjects from the wealthier households based on economic factors,"Subjects from the wealthier households based on economic factors such as income(travel, monthly expenditure)  and household essentials(Household size, Household wealth index, TV, No electronics, Earth/sand floor, Ceramic floor, Glass windows, Unfinished windows, Clay/mud walls, Cement walls, Concrete roof, Sleeping rooms). The household wealth index is constructed based on these household essentials.",NA,NA,NA,WMS,NA,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,"body mass index,sex",NA,decreased,NA,NA,NA,NA,Signature 1,Table S1,19 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between subjects from the least well-off households and subjects from the wealthier households.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum faecicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia massiliensis (ex Durand et al. 2017),k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira aalborgi,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Cibiobacter|s__Candidatus Cibiobacter qucibialis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium sp. AM22-15,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium KLE1615,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF27-2AA,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AM22-11AC,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp. OM04-5BH,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. AF22-8LB,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. AM28-29,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella sp. GAM18,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella|s__Parolsenella massiliensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pectinovora,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. 885,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P3-120,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P4-51,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina|s__Sarcina ventriculi,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella hominis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|s__Selenomonadales bacterium,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|s__Spirochaetia bacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus lutetiensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema succinifaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|s__Firmicutes bacterium AF16-15,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella lascolaii,k__Pseudomonadati|p__Kiritimatiellota|c__Kiritimatiellia|s__Kiritimatiellia bacterium",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759|2585118;3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|171550|239759|1288121;3379134|976|200643|171549|171550|239759|328814;1783272|1239|186801|3085636|3118652|2039240|2358141;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|246787;3379134|976|200643|171549|815|816|28111;3379134|976|200643|171549|815|816|338188;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|329854;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|46506;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|815|816|371601;3379134|976|200643|171549|2005519|397864|487174;1783272|201174|1760|85004|31953|1678|216816;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|3085636|186803|572511|871665;1783272|1239|186801|3085636|186803|572511|1737424;1783272|1239|186801|3085636|186803|572511|418240;3379134|203691|203692|1643686|143786|29521|29522;1783272|1239|186801|186802|2527773|2500537;1783272|1239|526524|526525|2810280|135858|2292991;3379134|1224|1236|91347|543|544|546;1783272|1239|186801|186802|1715004;1783272|1239|186801|186802|31979|1485|2292206;1783272|1239|186801|186802|31979|1485|2293024;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|3085636|186803|33042|33043;1783272|1239|186801|3085636|186803|33042|2293093;1783272|1239|186801|3085636|186803|189330|39486;3379134|1224|1236|91347|543|547|158836;1783272|1239|186801|186802|186806|1730|2292232;1783272|1239|186801|186802|186806|1730|2292349;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|526524|526525|128827|1573535|1735;1783272|1239|91061|186826|1300|1357|1358;3379134|976|200643|171549|1853231|283168|28118;1783272|201174|84998|84999|1643824|133925|2109685;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|171552|577309|454154;1783272|201174|84998|84999|1643824|2082587|1871022;1783272|1239|909932|1843488|909930|33024|33025;1783272|1239|909932|1843488|909930|33024|626940;3379134|976|200643|171549|815|909656|387090;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|204516;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|171552|838|2079531;3379134|976|200643|171549|171552|838|1602169;3379134|976|200643|171549|171552|838|2022527;3379134|976|200643|171549|171552|838|2024220;3379134|976|200643|171549|171552|838|2024228;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|186802|31979|1266|1267;3379134|976|200643|171549|171552|2974251|2518605;1783272|1239|909932|909929|2137878;3379134|203691|203692|2053615;1783272|1239|91061|186826|1300|1301|150055;3379134|1224|28216|80840|995019|40544|40545;3379134|203691|203692|136|2845253|157|167;1783272|1239|186801|3085636|186803|2316020|46228;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|2292885;3379134|976|200643|171549|171552|2974265|1776379;3379134|134625|1921781|2212473,Complete,Svetlana up
bsdb:38968070/11/2,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 11,Honduras,Homo sapiens,Feces,UBERON:0001988,Socioeconomic status,EXO:0000114,Subjects from the least well-off households based on economic factors,Subjects from the wealthier households based on economic factors,"Subjects from the wealthier households based on economic factors such as income(travel, monthly expenditure)  and household essentials(Household size, Household wealth index, TV, No electronics, Earth/sand floor, Ceramic floor, Glass windows, Unfinished windows, Clay/mud walls, Cement walls, Concrete roof, Sleeping rooms). The household wealth index is constructed based on these household essentials.",NA,NA,NA,WMS,NA,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,"body mass index,sex",NA,decreased,NA,NA,NA,NA,Signature 2,Table S1,20 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between subjects from the least well-off households and subjects from the wealthier households based on economic factors.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira aalborgi,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Cibiobacter|s__Candidatus Cibiobacter qucibialis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium sp. AM22-15,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF34-13,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AM22-11AC,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp. OM04-5BH,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Duodenibacillus|s__Duodenibacillus massiliensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. AF22-8LB,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. AM28-29,k__Bacillati|p__Bacillota|s__Firmicutes bacterium AF16-15,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Pseudomonadati|p__Kiritimatiellota|c__Kiritimatiellia|s__Kiritimatiellia bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella sp. GAM18,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella|s__Parolsenella massiliensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pectinovora,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. 885,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P3-120,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P4-51,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotellamassilia|s__Prevotellamassilia timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bovis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina|s__Sarcina ventriculi,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella hominis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|s__Selenomonadales bacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|s__Spirochaetia bacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus lutetiensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema berlinense,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema succinifaciens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|s__Victivallales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales",3379134|976|200643|171549|171550|239759|2585118;3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|171550|239759|1288121;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|329854;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|46506;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|815|816|371601;3379134|976|200643|171549|2005519|397864|487174;1783272|201174|1760|85004|31953|1678|216816;3379134|200940|3031449|213115|194924|35832|35833;3379134|203691|203692|1643686|143786|29521|29522;1783272|1239|186801|186802|2527773|2500537;1783272|1239|526524|526525|2810280|135858|2292991;3379134|1224|1236|91347|543|544|546;1783272|1239|186801|186802|31979|1485|2293012;1783272|1239|186801|186802|31979|1485|2293024;1783272|1239|186801|3085636|186803|33042|2293093;3379134|1224|28216|80840|995019|1980697|1852381;3379134|1224|1236|91347|543|547|158836;1783272|1239|186801|3085636|186803|3342669|45851;1783272|1239|186801|186802|186806|1730|2292232;1783272|1239|186801|186802|186806|1730|2292349;1783272|1239|2292885;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|1407607|1150298;3379134|1224|1236|135625|712|724|729;1783272|1239|526524|526525|128827|1573535|1735;3379134|134625|1921781|2212473;3379134|1224|1236|91347|543|570|573;3379134|976|200643|171549|171552|2974265|363265;3379134|976|200643|171549|1853231|283168|28118;1783272|201174|84998|84999|1643824|133925|2109685;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|171552|577309|454154;1783272|201174|84998|84999|1643824|2082587|1871022;1783272|1239|909932|1843488|909930|33024|33025;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|204516;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|171552|838|2079531;3379134|976|200643|171549|171552|838|1602169;3379134|976|200643|171549|171552|838|2022527;3379134|976|200643|171549|171552|838|2024220;3379134|976|200643|171549|171552|838|2024228;3379134|976|200643|171549|171552|1926672|1852370;1783272|1239|186801|186802|216572|1263|2564099;1783272|1239|186801|186802|31979|1266|1267;3379134|976|200643|171549|171552|2974251|2518605;1783272|1239|909932|909929|2137878;1783272|201174|84998|1643822|1643826|84108|572010;3379134|203691|203692|2053615;1783272|1239|91061|186826|1300|1301|150055;3379134|1224|28216|80840|995019|40544|40545;3379134|203691|203692|136|2845253|157|225004;3379134|203691|203692|136|2845253|157|167;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843489|31977|29465|39778;3379134|256845|1313211|278082|2212475;1783272|1239|186801|3085636|186803|2316020|33039;1783272|544448|31969|186329,Complete,Svetlana up
bsdb:38968070/12/1,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 12,Honduras,Homo sapiens,Feces,UBERON:0001988,Self reported educational attainment,EFO:0004784,Subjects from the least well-off households based on educational attainment,Subjects from wealthier households based on educational attainment,"Subjects from wealthier households based on educational attainment refers to those that attained Primary(1-3), Middle (4–6), and Secondary (>6)",NA,1620,NA,WMS,NA,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,"body mass index,sex",NA,decreased,NA,NA,NA,NA,Signature 1,Table S1,19 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between Primary (1–3) and Middle (4–6)/Secondary (>6) educational levels.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AM22-11AC,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium",3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|815|816|371601;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|338188;3379134|976|200643|171549|815|816|329854;3379134|976|200643|171549|171550|239759|28117;1783272|1239|186801|186802|31979|1485|2293024;1783272|1239|186801|3085636|186803|572511|871665;3379134|200940|3031449|213115|194924|35832|35833;3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|171550|239759|328813;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|186802|216572|946234|292800;3379134|1224|1236|91347|543|544|546;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|909932|1843488|909930|33024|33025,Complete,Svetlana up
bsdb:38968070/12/2,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 12,Honduras,Homo sapiens,Feces,UBERON:0001988,Self reported educational attainment,EFO:0004784,Subjects from the least well-off households based on educational attainment,Subjects from wealthier households based on educational attainment,"Subjects from wealthier households based on educational attainment refers to those that attained Primary(1-3), Middle (4–6), and Secondary (>6)",NA,1620,NA,WMS,NA,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,"body mass index,sex",NA,decreased,NA,NA,NA,NA,Signature 2,Table S1,19 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between Primary (1–3) and Middle (4–6)/Secondary (>6) educational levels.,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium sp. AM22-15,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Waltera|s__Waltera intestinalis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P3-120,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella|s__Parolsenella massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P4-51,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella hominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pectinovora,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. 885",1783272|1239|526524|526525|2810280|135858|2292991;1783272|1239|186801|3085636|186803|2815781|2606635;1783272|1239|526524|526525|128827|1573535|1735;3379134|976|200643|171549|171552|838|2024220;1783272|201174|84998|84999|1643824|2082587|1871022;1783272|1239|186801|186802|216572|216851|853;3379134|976|200643|171549|171552|838|2024228;3379134|976|200643|171549|171552|2974251|2518605;3379134|976|200643|171549|171552|838|1602169;3379134|976|200643|171549|171552|838|2022527,Complete,Svetlana up
bsdb:38968070/13/1,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 13,Honduras,Homo sapiens,Feces,UBERON:0001988,Social interaction measurement,EFO:0009592,Subjects from the least well-off households based on social factors,Subjects from the wealthier households based on social factors,"Subjects from the wealthier households refers to those with these social phenotypes: Friend ties (same building), Friend ties (different building), Betweeness (friendship), Transitivity (friendship), Familial ties (same building), Familial ties (different building), Transitivity (familial), Betweeness (familial), Degree (all ties), Kin percentage (to the third degree), Altruism, washing hands, living with partners, number of partners.",NA,NA,NA,WMS,NA,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,"body mass index,sex",NA,decreased,NA,NA,NA,NA,Signature 1,Table S1,19 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between Subjects from the least well-off households and Subjects from the wealthier households based on social factors.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum|s__Anaerotignum faecicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|s__Lentisphaeria bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|s__Selenomonadales bacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus equinus",3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|171550|239759|1288121;1783272|1239|186801|3085636|3118652|2039240|2358141;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|371601;3379134|256845|1313211|2053569;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|909656|387090;3379134|976|200643|171549|815|909656|821;1783272|1239|909932|909929|2137878;1783272|1239|91061|186826|1300|1301|1335,Complete,Svetlana up
bsdb:38968070/13/2,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 13,Honduras,Homo sapiens,Feces,UBERON:0001988,Social interaction measurement,EFO:0009592,Subjects from the least well-off households based on social factors,Subjects from the wealthier households based on social factors,"Subjects from the wealthier households refers to those with these social phenotypes: Friend ties (same building), Friend ties (different building), Betweeness (friendship), Transitivity (friendship), Familial ties (same building), Familial ties (different building), Transitivity (familial), Betweeness (familial), Degree (all ties), Kin percentage (to the third degree), Altruism, washing hands, living with partners, number of partners.",NA,NA,NA,WMS,NA,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,"body mass index,sex",NA,decreased,NA,NA,NA,NA,Signature 2,Table S1,19 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between Subjects from the least well-off households and Subjects from the wealthier households based on social factors.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira aalborgi,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema succinifaciens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula",3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|815|816|820;1783272|1239|186801|3085636|186803|572511|418240;3379134|203691|203692|1643686|143786|29521|29522;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330|88431;3379134|203691|203692|136|2845253|157|167;1783272|1239|909932|1843489|31977|29465|29466,Complete,Svetlana up
bsdb:38968070/14/1,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 14,Honduras,Homo sapiens,Feces,UBERON:0001988,Environmental factor,EFO:0000469,Subjects from the least well-off households based on village factors,Subjects from wealthier households based on village factors,"Subjects from wealthier households based on village factors such as Distance to village center, Distance to main road, Number of churches, Altitude.",NA,NA,NA,WMS,NA,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,"body mass index,sex",NA,decreased,NA,NA,NA,NA,Signature 1,Table S1,19 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between Subjects from the least well-off households and Subjects from the wealthier households based on village factors.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens",3379134|1224|1236|91347|543|547|158836;1783272|1239|186801|3085636|186803|28050|28052;1783272|201174|84998|84999|84107|102106|74426,Complete,Svetlana up
bsdb:38968070/14/2,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 14,Honduras,Homo sapiens,Feces,UBERON:0001988,Environmental factor,EFO:0000469,Subjects from the least well-off households based on village factors,Subjects from wealthier households based on village factors,"Subjects from wealthier households based on village factors such as Distance to village center, Distance to main road, Number of churches, Altitude.",NA,NA,NA,WMS,NA,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,"body mass index,sex",NA,decreased,NA,NA,NA,NA,Signature 2,Table S1,19 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between Subjects from the least well-off households and Subjects from the wealthier households based on village factors.,decreased,NA,NA,Complete,Svetlana up
bsdb:38968070/15/1,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 15,Honduras,Homo sapiens,Feces,UBERON:0001988,Water,CHEBI:15377,Subjects from the least well-off households based on water sources,Subjects from wealthier households based on water sources,"Subjects from wealthier households based on water sources refers to those with water sources such as: dug well, spring, tube well",NA,1610,NA,WMS,NA,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,"body mass index,sex",NA,decreased,NA,NA,NA,NA,Signature 1,Table S1,19 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between Subjects from the least well-off households and Subjects from the wealthier households based on water sources.,increased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium sp. AM22-15,1783272|1239|526524|526525|2810280|135858|2292991,Complete,Svetlana up
bsdb:38968070/15/2,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 15,Honduras,Homo sapiens,Feces,UBERON:0001988,Water,CHEBI:15377,Subjects from the least well-off households based on water sources,Subjects from wealthier households based on water sources,"Subjects from wealthier households based on water sources refers to those with water sources such as: dug well, spring, tube well",NA,1610,NA,WMS,NA,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,"body mass index,sex",NA,decreased,NA,NA,NA,NA,Signature 2,Table S1,19 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between Subjects from the least well-off households and Subjects from the wealthier households based on village sources.,decreased,NA,NA,Complete,Svetlana up
bsdb:38968070/16/1,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 16,Honduras,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Phenotypes without strain-phylogenetic information,Phenotypes with strain-phylogenetic information,"Phenotypes with strain-phylogenetic information refers to samples having strain-phylogenetic information, which were constructed by StrainPhlAn for each species, resulting in a tree comprising of individuals based on the genetic makeup of the species in their respective guts",NA,NA,NA,WMS,NA,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,body mass index,NA,NA,NA,NA,NA,NA,Signature 1,Table S9,19 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between phenotypes with strain effect and phenotypes without strain effect.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus petauri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella|s__Parolsenella massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pectinovora,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella hominis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Faecalibacillus|s__Faecalibacillus intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotellamassilia|s__Prevotellamassilia timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AM49-4BH,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. AM28-29,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium OM08-6BH,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Cibiobacter|s__Candidatus Cibiobacter qucibialis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. AM59-24XD,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium fessum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora amygdalina,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",1783272|1239|91061|186826|1300|1357|1940789;3379134|976|200643|171549|815|816|817;1783272|1239|186801|3085636|186803|33042|33043;1783272|201174|84998|84999|1643824|2082587|1871022;3379134|976|200643|171549|171552|838|1602169;1783272|201174|1760|85004|31953|1678|1680;3379134|976|200643|171549|815|816|46506;1783272|201174|84998|1643822|1643826|84108|572010;3379134|976|200643|171549|171552|2974251|2518605;1783272|1239|526524|526525|2810280|2678885|1982626;1783272|1239|186801|3085636|186803|28050|39485;3379134|976|200643|171549|171552|577309|454154;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|186801|3085636|186803|1407607|1150298;3379134|976|200643|171549|171552|1926672|1852370;1783272|1239|186801|186802|31979|1485|2293035;1783272|1239|186801|186802|186806|1730|2292349;1783272|1239|186801|186802|31979|2292274;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|186802|2527773|2500537;1783272|1239|186801|3085636|186803|841|2293138;3379134|200940|3031449|213115|194924|872|901;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|186802|31979|1485|2126740;1783272|1239|186801|3085636|186803|2719231|253257;3379134|1224|1236|135625|712|724|729;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3082720|186804|1501226|1776391;1783272|1239|186801|3085636|186803|1766253|39491,Complete,Svetlana up
bsdb:38968070/16/2,38968070,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar S.V., Beghini F., Alexander M., Singh A., Juárez R.M., Brito I.L. , Christakis N.A.","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 16,Honduras,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Phenotypes without strain-phylogenetic information,Phenotypes with strain-phylogenetic information,"Phenotypes with strain-phylogenetic information refers to samples having strain-phylogenetic information, which were constructed by StrainPhlAn for each species, resulting in a tree comprising of individuals based on the genetic makeup of the species in their respective guts",NA,NA,NA,WMS,NA,Illumina,centered log-ratio,Mixed-Effects Regression,0.05,TRUE,NA,NA,body mass index,NA,NA,NA,NA,NA,NA,Signature 2,Table S9,19 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundant taxa between phenotypes with strain effect and phenotypes without strain effect.,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Cibiobacter|s__Candidatus Cibiobacter qucibialis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF27-2AA,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF36-4,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Faecalibacillus|s__Faecalibacillus intestinalis,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|s__Lentisphaeria bacterium,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. ER4,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pectinovora,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella hominis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759|1288121;1783272|1239|186801|186802|2527773|2500537;1783272|1239|186801|186802|31979|1485|2292206;1783272|1239|186801|186802|31979|1485|2293015;1783272|1239|526524|526525|2810280|2678885|1982626;3379134|256845|1313211|2053569;3366610|28890|183925|2158|2159|2172|2173;1783272|1239|909932|909929|1843491|52225|52226;1783272|1239|186801|186802|216572|459786|1519439;3379134|976|200643|171549|171552|838|1602169;3379134|976|200643|171549|171552|2974251|2518605;1783272|201174|84998|1643822|1643826|84108|572010,Complete,Svetlana up
bsdb:38977240/1/1,38977240,"cross-sectional observational, not case-control",38977240,10.1016/j.ijid.2024.107165,NA,"Chac D., Slater D.M., Guillaume Y., Dunmire C.N., Ternier R., Vissières K., Juin S., Lucien M.A.B., Boncy J., Sanchez V.M., Dumayas M.G., Augustin G.C., Bhuiyan T.R., Qadri F., Chowdhury F., Khan A.I., Weil A.A., Ivers L.C. , Harris J.B.","Association between chlorine-treated drinking water, the gut microbiome, and enteric pathogen burden in young children in Haiti: An observational study",International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2024,"Chlorine, Free chlorine residual, Gut microbiome, Infant microbiome",Experiment 1,Haiti,Homo sapiens,Rectum,UBERON:0001052,Age,EFO:0000246,Infants,Young Children,These are children defined as > 12 to 59 months.,7,32,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,NA,NA,NA,increased,NA,Signature 1,Figure S3B,27 October 2025,Mautin,Mautin,"Individual relative abundance at the phylum level. Inf = Infants, YC = Young Children.",increased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Folakunmi
bsdb:38977240/1/2,38977240,"cross-sectional observational, not case-control",38977240,10.1016/j.ijid.2024.107165,NA,"Chac D., Slater D.M., Guillaume Y., Dunmire C.N., Ternier R., Vissières K., Juin S., Lucien M.A.B., Boncy J., Sanchez V.M., Dumayas M.G., Augustin G.C., Bhuiyan T.R., Qadri F., Chowdhury F., Khan A.I., Weil A.A., Ivers L.C. , Harris J.B.","Association between chlorine-treated drinking water, the gut microbiome, and enteric pathogen burden in young children in Haiti: An observational study",International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2024,"Chlorine, Free chlorine residual, Gut microbiome, Infant microbiome",Experiment 1,Haiti,Homo sapiens,Rectum,UBERON:0001052,Age,EFO:0000246,Infants,Young Children,These are children defined as > 12 to 59 months.,7,32,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,NA,NA,NA,increased,NA,Signature 2,Figure S3b,28 October 2025,Mautin,Mautin,"Individual relative abundance at the phylum level. Inf = Infants, YC = Young Children.",decreased,k__Bacillati|p__Actinomycetota,1783272|201174,Complete,Folakunmi
bsdb:38977240/2/2,38977240,"cross-sectional observational, not case-control",38977240,10.1016/j.ijid.2024.107165,NA,"Chac D., Slater D.M., Guillaume Y., Dunmire C.N., Ternier R., Vissières K., Juin S., Lucien M.A.B., Boncy J., Sanchez V.M., Dumayas M.G., Augustin G.C., Bhuiyan T.R., Qadri F., Chowdhury F., Khan A.I., Weil A.A., Ivers L.C. , Harris J.B.","Association between chlorine-treated drinking water, the gut microbiome, and enteric pathogen burden in young children in Haiti: An observational study",International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2024,"Chlorine, Free chlorine residual, Gut microbiome, Infant microbiome",Experiment 2,Haiti,Homo sapiens,Rectum,UBERON:0001052,Environmental exposure measurement,EFO:0008360,Infants in households with undetectable free chlorine residue (FCR.),Infants in households with High free chlorine residue (FCR.),"Infants ≤ 12 Months of age, living in households with drinking water free chlorine residue (FCR) greater than > 0.5mg/L.",32,6,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,decreased,Signature 2,Figure 3B,28 October 2025,Mautin,Mautin,Relative abundance of 3 abundant microbial families shown by FCR levels. Mann-Whitney test of Undetected (Und.) FCR and >0·5 High FCR.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,1783272|1239|91061|186826|1300,Complete,Folakunmi
bsdb:38980075/1/1,38980075,case-control,38980075,10.1128/msphere.00059-24,NA,"Feng Z., Zhu J., Zhang L., Li C., Su D., Wang H., Yu Y. , Song L.",Microbiological and functional traits of peri-implant mucositis and correlation with disease severity,mSphere,2024,"dental implant, dysbiosis, metagenomics, sulcus bleeding index, whole-genome sequencing",Experiment 1,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Mucositis,EFO:1001898,Healthy Implant (HI),Peri-implant mucositis (PM),"Patients with peri-implant mucositis (PM); a reversible inflammation of the soft tissue around dental implants, caused by plaque-induced microbial dysbiosis, and occurs without bone loss.",12,20,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,decreased,NA,NA,Signature 1,"Figure 2A, Figure 7A, Figure S3A",10 January 2026,Tosin,Tosin,"Identification of biomarkers between the Peri-implant mucositis (PM) and Healthy implants (HI) groups. The cladogram plots show discriminating taxa at different levels of taxonomic classification (phylum, class, order, family, genus, and species).",increased,"k__Bacillati|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae,k__Bacillati|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae|s__Anaerolineaceae bacterium oral taxon 439,k__Bacillati|p__Chloroflexota|c__Anaerolineae,k__Bacillati|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter rectus,p__Candidatus Saccharimonadota|s__Candidatus Saccharibacteria bacterium oral taxon 488,k__Bacillati|p__Chloroflexota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus|s__Desulfobulbus oralis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella enoeca,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium oral taxon 500,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella sp. oral taxon 807,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella uli,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella dentalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella fusca,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella multiformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia cardiffensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia,k__Pseudomonadati|p__Spirochaetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus milleri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. NSJ-72,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales,k__Thermotogati|p__Synergistota|c__Synergistia,k__Thermotogati|p__Synergistota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales,k__Bacillati|p__Bacillota|c__Tissierellia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema medium,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema parvum,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema socranskii,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp. OMZ 305,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp. OMZ 803,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp. OMZ 906,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema vincentii,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] minutum,k__Bacillati|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae|g__Anaerolinea,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae",1783272|200795|292625|292629|292628;1783272|200795|292625|292629|292628|1889813;1783272|200795|292625;1783272|200795|292625|292629;1783272|201174|84998|84999|1643824;3379134|976|200643|171549;3379134|976|200643;3379134|29547|3031852|213849|72294|194|203;95818|713059;1783272|200795;1783272|1239|186801;1783272|201174|84998|84999;1783272|201174|84998;3379134|200940|3024418|213118;3379134|200940|3031451|3024411|213121;3379134|200940|3031451|3024411|213121|893;3379134|200940|3031451|3024411|213121|893|1986146;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|39948|39950;1783272|1239|186801|186802;1783272|1239|186801|3082720|3118655|44259;1783272|1239|186801|3082720|3118655|44259|143361;3384194|508458|649775|649776|3029087|1434006;3384194|508458|649775|649776|3029087|1434006|651822;3384189|32066|203490|203491|203492;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492|848|851;3379134|976|200643|171549|171552|2974257|76123;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|712991;1783272|201174|84998|84999|1643824|133925;1783272|201174|84998|84999|1643824|133925|712411;1783272|201174|84998|84999|1643824|133925|133926;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|1239|1737404|1737405|1570339;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|171551|836|837;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|52227;3379134|976|200643|171549|171552|838|28129;3379134|976|200643|171549|171552|838|589436;3379134|976|200643|171549|171552|838|28131;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552|838|282402;3379134|976|200643|171549|171552|838|28133;3379134|976|200643|171549|171552;1783272|201174|1760|2037|2049|2529408|181487;3379134|976|200643|171549|171552|2974251|28135;3379134|203691|203692|136;3379134|203691|203692;3379134|203691;1783272|1239|91061|186826|1300|1301|1311;1783272|1239|91061|186826|1300|1301|76860;1783272|1239|91061|186826|1300|1301|33040;1783272|1239|91061|186826|1300|1301|2763068;3384194|508458|649775|649776|649777;3384194|508458|649775|649776;3384194|508458|649775;3384194|508458;3379134|976|200643|171549|2005525|195950;3379134|976|200643|171549|2005525|195950|28112;3379134|976|200643|171549|2005525;1783272|1239|1737404|1737405;1783272|1239|1737404;3379134|203691|203692|136|2845253|157;3379134|203691|203692|136|2845253|157|158;3379134|203691|203692|136|2845253|157|58231;3379134|203691|203692|136|2845253|157|138851;3379134|203691|203692|136|2845253|157|53419;3379134|203691|203692|136|2845253|157|1659192;3379134|203691|203692|136|2845253|157|120682;3379134|203691|203692|136|2845253|157|2563662;3379134|203691|203692|136|2845253|157|69710;3379134|203691|203692|136|2845253;1783272|1239|186801|3082720|543314|76124;1783272|200795|292625|292629|292628|233189;1783272|1239|186801|3082720|543314;1783272|1239|186801|3085636|186803|28050;3384194|508458|649775|649776|649777;3384194|508458|649775|649776|649777|2753;3379134|976|200643|171549|2005525|195950;1783272|1239|186801|3082720|543314,Complete,NA
bsdb:38980075/1/2,38980075,case-control,38980075,10.1128/msphere.00059-24,NA,"Feng Z., Zhu J., Zhang L., Li C., Su D., Wang H., Yu Y. , Song L.",Microbiological and functional traits of peri-implant mucositis and correlation with disease severity,mSphere,2024,"dental implant, dysbiosis, metagenomics, sulcus bleeding index, whole-genome sequencing",Experiment 1,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Mucositis,EFO:1001898,Healthy Implant (HI),Peri-implant mucositis (PM),"Patients with peri-implant mucositis (PM); a reversible inflammation of the soft tissue around dental implants, caused by plaque-induced microbial dysbiosis, and occurs without bone loss.",12,20,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,decreased,NA,NA,Signature 2,"Figure 2A, Figure 7A, Figure S3A",11 January 2026,Tosin,Tosin,"Identification of biomarkers between the Peri-implant mucositis (PM) and Healthy implants (HI) groups. The cladogram plots show discriminating taxa at different levels of taxonomic classification (phylum, class, order, family, genus, and species).",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria bacilliformis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria macacae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria mucosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella",3379134|1224|28216|80840|119060;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712|724|729;3379134|1224|28216|206351|481|32257;3379134|1224|28216|206351|481|32257|505;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|80840|119060|47670|47671;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481|482|267212;3379134|1224|28216|206351|481|482|495;3379134|1224|28216|206351|481|482|496;3379134|1224|28216|206351|481|482|488;1783272|1239|91061|186826|1300|1301|1305;3379134|1224|28216|206351|481|32257,Complete,NA
bsdb:38980075/2/1,38980075,case-control,38980075,10.1128/msphere.00059-24,NA,"Feng Z., Zhu J., Zhang L., Li C., Su D., Wang H., Yu Y. , Song L.",Microbiological and functional traits of peri-implant mucositis and correlation with disease severity,mSphere,2024,"dental implant, dysbiosis, metagenomics, sulcus bleeding index, whole-genome sequencing",Experiment 2,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Mucositis,EFO:1001898,Gingivitis,Peri-implant mucositis (PM),"Patients with peri-implant mucositis (PM); a reversible inflammation of the soft tissue around dental implants, caused by plaque-induced microbial dysbiosis, and occurs without bone loss.",10,20,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4, Figure S3B",11 January 2026,Tosin,Tosin,"Biomarkers indicated by LEfSe analysis between the peri-implant mucositis (PM) and gingivitis (G) groups. The cladogram plots show discriminating taxa at different levels of taxonomic classification (phylum, class, order, family, genus, and species).",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. HMT897,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 897,k__Bacillati|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae,k__Bacillati|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae|s__Anaerolineaceae bacterium oral taxon 439,k__Bacillati|p__Chloroflexota|c__Anaerolineae,k__Bacillati|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter rectus,k__Bacillati|p__Chloroflexota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium hwasookii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella enoeca,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium oral taxon 500,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia trevisanii,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella sp. oral taxon 807,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella uli,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella dentalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella fusca,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia cardiffensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. oral taxon 126,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia,k__Pseudomonadati|p__Spirochaetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus milleri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. NSJ-72,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales,k__Thermotogati|p__Synergistota|c__Synergistia,k__Thermotogati|p__Synergistota,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 349,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales,k__Bacillati|p__Bacillota|c__Tissierellia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema medium,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema parvum,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema socranskii,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp. OMZ 305,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp. OMZ 803,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema vincentii,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] minutum,k__Bacillati|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae|g__Anaerolinea,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia,p__Candidatus Saccharimonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp. OMZ 906",1783272|201174|1760|2037|2049|1654|2789424;1783272|201174|1760|2037|2049|1654|2081702;1783272|200795|292625|292629|292628;1783272|200795|292625|292629|292628|1889813;1783272|200795|292625;1783272|200795|292625|292629;1783272|1239|186801|3082720|543314;1783272|201174|84998|84999|1643824;3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|29547|3031852|213849|72294|194|203;1783272|200795;1783272|1239|186801;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|39948|39950;1783272|1239|186801|186802;1783272|1239|186801|3082720|3118655|44259;1783272|1239|186801|3082720|3118655|44259|143361;3384194|508458|649775|649776|3029087|1434006;3384194|508458|649775|649776|3029087|1434006|651822;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492|848|1583098;3384189|32066|203490|203491|203492|848|851;3379134|976|200643|171549|171552|2974257|76123;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|712991;3384189|32066|203490|203491|1129771|32067|109328;1783272|1239|186801|3082720|543314|86331;1783272|201174|84998|84999|1643824|133925;1783272|201174|84998|84999|1643824|133925|712411;1783272|201174|84998|84999|1643824|133925|133926;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|1239|1737404|1737405|1570339;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|171551|836|837;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|52227;3379134|976|200643|171549|171552|838|589436;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552|838|28133;3379134|976|200643|171549|171552;1783272|201174|1760|2037|2049|2529408|181487;1783272|1239|909932|909929|1843491;1783272|1239|909932|909929;1783272|1239|909932|909929|1843491|970;1783272|1239|909932|909929|1843491|970|712528;1783272|1239|909932|909929|1843491|970|69823;3379134|203691|203692|136;3379134|203691|203692;3379134|203691;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|91061|186826|1300|1301|76860;1783272|1239|91061|186826|1300|1301|33040;1783272|1239|91061|186826|1300|1301|2763068;3384194|508458|649775|649776|649777;3384194|508458|649775|649776;3384194|508458|649775;3384194|508458;95818|713051;3379134|976|200643|171549|2005525|195950;3379134|976|200643|171549|2005525|195950|28112;3379134|976|200643|171549|2005525;1783272|1239|1737404|1737405;1783272|1239|1737404;3379134|203691|203692|136|2845253|157;3379134|203691|203692|136|2845253|157|158;3379134|203691|203692|136|2845253|157|58231;3379134|203691|203692|136|2845253|157|138851;3379134|203691|203692|136|2845253|157|53419;3379134|203691|203692|136|2845253|157|1659192;3379134|203691|203692|136|2845253|157|120682;3379134|203691|203692|136|2845253|157|69710;3379134|203691|203692|136|2845253;1783272|1239|186801|3082720|543314|76124;1783272|200795|292625|292629|292628|233189;1783272|1239|186801|3082720|543314|109326;95818|2093818|2093825|2171986;95818|2093818|2093825;95818|2093818;95818;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3082720|543314|86331;1783272|1239|909932|909929|1843491|970;3384194|508458|649775|649776|649777;3384194|508458|649775|649776|649777|2753;3379134|976|200643|171549|2005525|195950;3379134|203691|203692|136|2845253|157|2563662,Complete,NA
bsdb:38980075/3/1,38980075,case-control,38980075,10.1128/msphere.00059-24,NA,"Feng Z., Zhu J., Zhang L., Li C., Su D., Wang H., Yu Y. , Song L.",Microbiological and functional traits of peri-implant mucositis and correlation with disease severity,mSphere,2024,"dental implant, dysbiosis, metagenomics, sulcus bleeding index, whole-genome sequencing",Experiment 3,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Mucositis,EFO:1001898,Sulcus bleeding index (SBI) in Healthy implant (HI) patients,Sulcus bleeding index (SBI) in patients with Peri-implant mucositis (PM),Sulcus bleeding index (SBI) in Patients with peri-implant mucositis (PM),10,20,3 months,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 7A, 7B",11 January 2026,Tosin,Tosin,"Relationship between the SBI in patients with PM and 15 differentially abundant genera identified in LEfSe analysis when comparing the PM with HIs, based on Spearman correlation analysis",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,NA
bsdb:38980075/3/2,38980075,case-control,38980075,10.1128/msphere.00059-24,NA,"Feng Z., Zhu J., Zhang L., Li C., Su D., Wang H., Yu Y. , Song L.",Microbiological and functional traits of peri-implant mucositis and correlation with disease severity,mSphere,2024,"dental implant, dysbiosis, metagenomics, sulcus bleeding index, whole-genome sequencing",Experiment 3,China,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Mucositis,EFO:1001898,Sulcus bleeding index (SBI) in Healthy implant (HI) patients,Sulcus bleeding index (SBI) in patients with Peri-implant mucositis (PM),Sulcus bleeding index (SBI) in Patients with peri-implant mucositis (PM),10,20,3 months,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 7A, 7C, 7D and 7E",11 January 2026,Tosin,Tosin,"Relationship between the Sulcus bleeding index (SBI) in patients with Peri-implant mucositis (PM) and 15 differentially abundant genera identified in Linear discriminant analysis effect size (LEfSe) analysis when comparing the Peri-implant mucositis (PM! with (Healthy Impants) HIs, based on Spearman correlation analysis",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",3379134|1224|1236|135625|712|724;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|206351|481|482,Complete,NA
bsdb:38990031/1/1,38990031,case-control,38990031,10.1128/spectrum.04291-23,NA,"Chen K., Geng H., Ye C. , Liu J.",Dysbiotic alteration in the fecal microbiota of patients with polycystic ovary syndrome,Microbiology spectrum,2024,"Bacteroides, Bifidobacterium, gut microbiota, metabolism, polycystic ovary syndrome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy control group,Polycystic ovary syndrome group (PCOS),This group consists of women who were diagnosed with polycystic ovary syndrome according to the 2003 Rotterdam criteria.,17,17,NA,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,decreased,decreased,decreased,decreased,NA,decreased,Signature 1,"Figure 3d, 4b and Result text.",4 July 2025,Victoria,Victoria,"Comparison of intestinal microbiota abundance of PCOS patients and healthy group at the phylum and family level (Mann-Whitney U-test, n = 17).",increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Rhodocyclaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae",1783272|201174;1783272|1239|91061|186826|186827;1783272|201174|1760|85004|31953;1783272|1239|91061|186826|186828;3379134|1224|28216|206389|75787;1783272|1239|91061|1385|539738,Complete,KateRasheed
bsdb:38990031/1/2,38990031,case-control,38990031,10.1128/spectrum.04291-23,NA,"Chen K., Geng H., Ye C. , Liu J.",Dysbiotic alteration in the fecal microbiota of patients with polycystic ovary syndrome,Microbiology spectrum,2024,"Bacteroides, Bifidobacterium, gut microbiota, metabolism, polycystic ovary syndrome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy control group,Polycystic ovary syndrome group (PCOS),This group consists of women who were diagnosed with polycystic ovary syndrome according to the 2003 Rotterdam criteria.,17,17,NA,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,decreased,decreased,decreased,decreased,NA,decreased,Signature 2,"Figure 3d, 4b, 5b and Result text.",4 July 2025,Victoria,Victoria,"Comparison of intestinal microbiota abundance of PCOS patients and healthy group at the phylum, family, and genus level (Mann-Whitney U-test, n = 17).",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family IV. Incertae Sedis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Gracilibacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae",1783272|1239|91061|186826|186827|46123;1783272|1239|909932|1843488|909930;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|3082771|1924093;1783272|1239;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|2005519;1783272|1239|186801|186802|3085642;1783272|1239|186801|186802|3085642|580596;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|1689151;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|541019;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803;3379134|976|200643|1970189|1573805;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|75682;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|577309;1783272|1239|186801|186802|186807;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|3068309;3379134|1224|28216|80840|995019|40544;3379134|976|200643|171549|2005525;1783272|201174|84998|84999|1643824;1783272|1239;3379134|976;1783272|1239|186801|3082768|990719;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|186807,Complete,KateRasheed
bsdb:38990031/2/1,38990031,case-control,38990031,10.1128/spectrum.04291-23,NA,"Chen K., Geng H., Ye C. , Liu J.",Dysbiotic alteration in the fecal microbiota of patients with polycystic ovary syndrome,Microbiology spectrum,2024,"Bacteroides, Bifidobacterium, gut microbiota, metabolism, polycystic ovary syndrome",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy control group,Polycystic ovary syndrome group (PCOS),This group consists of women who were diagnosed with polycystic ovary syndrome according to the 2003 Rotterdam criteria.,17,17,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,4,age,NA,decreased,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 7a & b,4 July 2025,Victoria,Victoria,PCOS patient-associated microbial species and different bacterial genera identified by LEfSe (LDA score (log 10) ＞4).,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. NJ-64",1783272|201174;1783272|201174|84992;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|1239|91061|186826;;3379134|1224|1236|91347|543|547|418640,Complete,KateRasheed
bsdb:38990031/2/2,38990031,case-control,38990031,10.1128/spectrum.04291-23,NA,"Chen K., Geng H., Ye C. , Liu J.",Dysbiotic alteration in the fecal microbiota of patients with polycystic ovary syndrome,Microbiology spectrum,2024,"Bacteroides, Bifidobacterium, gut microbiota, metabolism, polycystic ovary syndrome",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Healthy control group,Polycystic ovary syndrome group (PCOS),This group consists of women who were diagnosed with polycystic ovary syndrome according to the 2003 Rotterdam criteria.,17,17,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,4,age,NA,decreased,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 7a & b,4 July 2025,Victoria,Victoria,PCOS patient-associated microbial species and different bacterial genera identified by LEfSe (LDA score (log 10) ＞4).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota,,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__uncultured Bacteroides sp.",3379134|976|200643|171549|171550|239759;1783272|1239;;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976;1783272|1239|186801|3082768|990719;1783272|1239|186801|3082768;1783272|1239|186801;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|171550|239759;1783272|1239;3379134|976|200643|171549|815|816;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|815|816|162156,Complete,KateRasheed
bsdb:39020289/1/1,39020289,case-control,39020289,10.1186/s12916-024-03503-y,NA,"Pérez-Prieto I., Vargas E., Salas-Espejo E., Lüll K., Canha-Gouveia A., Pérez L.A., Fontes J., Salumets A., Andreson R., Aasmets O., Whiteson K., Org E. , Altmäe S.",Gut microbiome in endometriosis: a cohort study on 1000 individuals,BMC medicine,2024,"Endometriosis, Estrobolome, Gut microbiota, Metagenomics, Microbiome, Microbiota, Shotgun sequencing",Experiment 1,Estonia,Homo sapiens,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Control,Endometriosis Cases,Study participants diagnosed with endometriosis,864,136,NA,WMS,NA,Illumina,log transformation,ANCOM-BC,0.05,FALSE,NA,NA,"age,body mass index,proton-pump inhibitor",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Additional file 2: Table S2,24 April 2025,Montana-D,Montana-D,Significant differential abundant taxa in endometriosis and control groups,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter sp. CAG:196,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:307,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:307_30_263,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:557,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. 36_13,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:313,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp. CAG:815,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella multisaccharivorax,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Paraclostridium|s__Paraclostridium sordellii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:474,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P4-51,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:254,p__Parabasalia|o__Trichomonadida|f__Trichomonadidae|g__Trichomonas|s__Trichomonas vaginalis,p__Parabasalia|o__Tritrichomonadida|f__Tritrichomonadidae|g__Tritrichomonas|s__Tritrichomonas foetus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|g__Candidatus Hemicellulosilyticus|s__Candidatus Hemicellulosilyticus sp. P3",3379134|1224|1236|2887326|468|469|1262690;1783272|1239|186801|186802|31979|1485|1262795;1783272|1239|186801|186802|31979|1485|1896987;1783272|1239|186801|186802|31979|1485|1262819;1783272|1239|186801|186802|186806|1730|1897001;1783272|1239|1263017;3384189|32066|203490|203491|203492|848|1262901;3379134|976|200643|171549|171552|52228|310514;1783272|1239|186801|3082720|186804|1849822|1505;3379134|976|200643|171549|171552|838|1262926;3379134|976|200643|171549|171552|838|2024228;1783272|1239|186801|3082720|186804|1501226|1776391;1783272|1239|186801|186802|216572|1263|1262953;5719|37104|181550|5721|5722;5719|740972|740983|5723|1144522;3379134|976|200643|171549|3443719|1768113,Complete,KateRasheed
bsdb:39020289/1/2,39020289,case-control,39020289,10.1186/s12916-024-03503-y,NA,"Pérez-Prieto I., Vargas E., Salas-Espejo E., Lüll K., Canha-Gouveia A., Pérez L.A., Fontes J., Salumets A., Andreson R., Aasmets O., Whiteson K., Org E. , Altmäe S.",Gut microbiome in endometriosis: a cohort study on 1000 individuals,BMC medicine,2024,"Endometriosis, Estrobolome, Gut microbiota, Metagenomics, Microbiome, Microbiota, Shotgun sequencing",Experiment 1,Estonia,Homo sapiens,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Control,Endometriosis Cases,Study participants diagnosed with endometriosis,864,136,NA,WMS,NA,Illumina,log transformation,ANCOM-BC,0.05,FALSE,NA,NA,"age,body mass index,proton-pump inhibitor",NA,unchanged,NA,NA,NA,unchanged,Signature 2,Additional file 2: Table S2,24 April 2025,Montana-D,Montana-D,Significant differential abundant taxa in endometriosis and control groups,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas vaginalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF34-10BH,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF36-4,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF37-5,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:58,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:62,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:91,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea|s__Faecalitalea cylindroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium GAM79,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp. D26,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:45,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:177",3379134|976|200643|171549|1853231|574697|2042309;1783272|1239|186801|186802|31979|1485|2293011;1783272|1239|186801|186802|31979|1485|2293015;1783272|1239|186801|186802|31979|1485|2293016;1783272|1239|186801|186802|31979|1485|1262824;1783272|1239|186801|186802|31979|1485|1262828;1783272|1239|186801|186802|31979|1485|1262845;1783272|1239|526524|526525|128827|1573534|39483;1783272|1239|186801|3085636|186803|2109691;3379134|976|200643|171549|2005525|375288|658662;1783272|1239|186801|3085636|186803|841|1262947;1783272|1239|186801|186802|216572|1263|1262952,Complete,KateRasheed
bsdb:39020289/2/1,39020289,case-control,39020289,10.1186/s12916-024-03503-y,NA,"Pérez-Prieto I., Vargas E., Salas-Espejo E., Lüll K., Canha-Gouveia A., Pérez L.A., Fontes J., Salumets A., Andreson R., Aasmets O., Whiteson K., Org E. , Altmäe S.",Gut microbiome in endometriosis: a cohort study on 1000 individuals,BMC medicine,2024,"Endometriosis, Estrobolome, Gut microbiota, Metagenomics, Microbiome, Microbiota, Shotgun sequencing",Experiment 2,Estonia,Homo sapiens,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Control,Endometriosis Cases,Women with endometriosis at their reproductive age (≤ 50 years),525,66,NA,WMS,NA,Illumina,log transformation,ANCOM-BC,0.05,FALSE,NA,NA,"age,body mass index,proton-pump inhibitor",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Additional File 2: Supplementary Table 5,24 April 2025,MyleeeA,MyleeeA,"Sensitivity differential abundance analysis in endometriosis and control groups. Species with a prevalence >10% and relative abundance ≥0.1% were compared in endometriosis and control groups after excluding women with age >50, using an Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC).",increased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma|s__Anaeroplasma bactoclasticum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:307,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:964,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella sp. CAG:166,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Pseudomonadati|p__Myxococcota|c__Myxococcia|o__Myxococcales|f__Myxococcaceae|g__Corallococcus|s__Corallococcus sp. CAG:1435,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:345,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:449,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella|s__Hallella multisaccharivorax,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Neglectibacter|s__Neglectibacter timonensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pectinovora,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. AGR2160,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:5226,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:254,p__Parabasalia|o__Trichomonadida|f__Trichomonadidae|g__Trichomonas|s__Trichomonas vaginalis,p__Parabasalia|o__Tritrichomonadida|f__Tritrichomonadidae|g__Tritrichomonas|s__Tritrichomonas foetus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter ruminicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:474",1783272|544448|31969|186332|186333|2086|2088;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|186802|31979|1485|1262795;1783272|1239|186801|186802|31979|1485|1262848;1783272|201174|84998|84999|84107|102106|1262850;1783272|1239|186801|3085636|186803|33042|33043;3379134|2818505|32015|29|31|83461|1262867;1783272|1239|1263020;1783272|1239|1263023;3379134|976|200643|171549|171552|52228|310514;3379134|976|200643|171549|171552|2974265|363265;1783272|1239|186801|186802|216572|1924105|1776382;3379134|976|200643|171549|171552|838|28131;3379134|976|200643|171549|171552|838|1602169;3379134|976|200643|171549|171552|838|1280674;3379134|976|200643|171549|171552|838|1262930;1783272|1239|186801|3082720|186804|1501226|1776391;1783272|1239|186801|186802|216572|1263|1262953;5719|37104|181550|5721|5722;5719|740972|740983|5723|1144522;3379134|976|200643|171549|171552|558436|839;3379134|976|200643|171549|171552|838|1262926,Complete,KateRasheed
bsdb:39020289/2/2,39020289,case-control,39020289,10.1186/s12916-024-03503-y,NA,"Pérez-Prieto I., Vargas E., Salas-Espejo E., Lüll K., Canha-Gouveia A., Pérez L.A., Fontes J., Salumets A., Andreson R., Aasmets O., Whiteson K., Org E. , Altmäe S.",Gut microbiome in endometriosis: a cohort study on 1000 individuals,BMC medicine,2024,"Endometriosis, Estrobolome, Gut microbiota, Metagenomics, Microbiome, Microbiota, Shotgun sequencing",Experiment 2,Estonia,Homo sapiens,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Control,Endometriosis Cases,Women with endometriosis at their reproductive age (≤ 50 years),525,66,NA,WMS,NA,Illumina,log transformation,ANCOM-BC,0.05,FALSE,NA,NA,"age,body mass index,proton-pump inhibitor",NA,unchanged,NA,NA,NA,unchanged,Signature 2,Additional File 2: Supplementary Table 5,24 April 2025,MyleeeA,MyleeeA,"Sensitivity differential abundance analysis in endometriosis and control groups. Species with a prevalence >10% and relative abundance ≥0.1% were compared in endometriosis and control groups after excluding women with age >50, using an Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC).",decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium sp.,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__Desulfovibrionaceae bacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila sp. 4_1_30,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:1193,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Acetobacter|s__Acetobacter sp. CAG:977,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter sp. 43_10,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:45,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium sp. CAG:266,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF36-4,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:62,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:609,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium CCNA10",1783272|1239|909932|1843488|909930|33024|2049039;3379134|200940|3031449|213115|194924|2049043;3379134|200940|3031449|213115|194924|35832|693988;1783272|1239|186801|186802|31979|1485|1262771;3379134|1224|28211|3120395|433|434|1262685;3379134|200940|3031449|213115|194924|35832|35833;3379134|976|200643|171549|1853231|283168|1897010;3379134|976|200643|171549|171550|239759|2585118;1783272|1239|186801|3085636|186803|841|1262947;1783272|1239|909932|1843488|909930|33024|1262915;1783272|1239|186801|186802|31979|1485|2293015;1783272|1239|186801|186802|31979|1485|1262828;1783272|1239|186801|186802|31979|1485|1262827;1783272|1239|186801|186802|2109688,Complete,KateRasheed
bsdb:39034613/1/1,39034613,"cross-sectional observational, not case-control",39034613,10.1080/19490976.2024.2377570,NA,"Krigul K.L., Feeney R.H., Wongkuna S., Aasmets O., Holmberg S.M., Andreson R., Puértolas-Balint F., Pantiukh K., Sootak L., Org T., Tenson T., Org E. , Schroeder B.O.",A history of repeated antibiotic usage leads to microbiota-dependent mucus defects,Gut microbes,2024,"Akkermansia, Antibiotics, colonic mucosa, fecal microbiota transplantation, gut microbiome, intestinal barrier, mucus, short-chain fatty acids",Experiment 1,Estonia,Homo sapiens,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,hCTRL (No antibiotic use humans),hABX (Repeated antibiotic use humans),Human adults who had not taken any antibiotics in the 6 months prior to stool sample collection but had used antibiotics at least 5 times within the last 5 years.,4,4,6 months,WMS,NA,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,"age,body mass index,diet,sex",NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Supplementary table 4,2 December 2024,YokoC,"YokoC,WikiWorks",ANCOM-BC differential analysis of gut microbial composition at genus level between hABX and hCTRL samples including those with a mean relative abundance below 1%.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Candidatus Borkfalkia,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Geddesella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Lawsonibacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|216572|244127;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3082768|990719|2508948;1783272|1239|186801|2720808;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|2591381;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|1407607;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803|1506553;1783272|1239|91061|186826|1300|1357;1783272|1239|186801|186802|216572|2172004;3379134|1224|28211|356|119045|407;3379134|1224|28216|80840|75682|846;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|815|909656;1783272|1239|186801|186802|216572|1017280;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|841;1783272|1239|186801;1783272|1239|186801|186802|31979;3379134|200940|3031449|213115|194924;1783272|1239|186801|3085636|186803;1783272|544448;1783272|1239|186801|186802,Complete,Svetlana up
bsdb:39034613/1/2,39034613,"cross-sectional observational, not case-control",39034613,10.1080/19490976.2024.2377570,NA,"Krigul K.L., Feeney R.H., Wongkuna S., Aasmets O., Holmberg S.M., Andreson R., Puértolas-Balint F., Pantiukh K., Sootak L., Org T., Tenson T., Org E. , Schroeder B.O.",A history of repeated antibiotic usage leads to microbiota-dependent mucus defects,Gut microbes,2024,"Akkermansia, Antibiotics, colonic mucosa, fecal microbiota transplantation, gut microbiome, intestinal barrier, mucus, short-chain fatty acids",Experiment 1,Estonia,Homo sapiens,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,hCTRL (No antibiotic use humans),hABX (Repeated antibiotic use humans),Human adults who had not taken any antibiotics in the 6 months prior to stool sample collection but had used antibiotics at least 5 times within the last 5 years.,4,4,6 months,WMS,NA,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,"age,body mass index,diet,sex",NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,Supplementary table 4,2 December 2024,YokoC,"YokoC,WikiWorks",ANCOM-BC differential analysis of gut microbial composition at genus level between hABX and hCTRL samples including those with a mean relative abundance below 1%.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae",1783272|1239|186801|186802|3085642|580596;3379134|1224|1236|91347|543|561;1783272;1783272|1239|186801|186802|31979;1783272|544448;1783272|1239|186801|186802|216572;3379134|1224|28211|204457|41297,Complete,Svetlana up
bsdb:39034613/2/1,39034613,"cross-sectional observational, not case-control",39034613,10.1080/19490976.2024.2377570,NA,"Krigul K.L., Feeney R.H., Wongkuna S., Aasmets O., Holmberg S.M., Andreson R., Puértolas-Balint F., Pantiukh K., Sootak L., Org T., Tenson T., Org E. , Schroeder B.O.",A history of repeated antibiotic usage leads to microbiota-dependent mucus defects,Gut microbes,2024,"Akkermansia, Antibiotics, colonic mucosa, fecal microbiota transplantation, gut microbiome, intestinal barrier, mucus, short-chain fatty acids",Experiment 2,Estonia,Mus musculus,Colon,UBERON:0001155,Response to transplant,EFO:0007043,FMT-C (control transplant mice),FMT- ABX (antibiotic transplant mice),Mice that received a fecal microbiota transplant (FMT) from the hABX (humans with a history of repeated antibiotic used) pool.,8,8,6 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 4e,3 December 2024,YokoC,"YokoC,WikiWorks","Boxplots of significant differentially abundant species (using ALDEX) in the distal colon of mouse microbiota between FMT-C and FMT-ABX, with at least a 0.1% mean relative abundance in either group.",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas paravirosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster lavalensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|3085636|186803|207244|105841;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|291644;1783272|1239|186801|3085636|186803|572511|33035;3379134|976|200643|171549|1853231|574697|1472417;1783272|1239|186801|3085636|186803|2719313|358742;1783272|1239|186801|3085636|186803|2719313|460384;3379134|1224|28216|80840|995019|577310|487175;1783272|1239|186801|3085636|186803|2941495|1512,Complete,Svetlana up
bsdb:39034613/2/2,39034613,"cross-sectional observational, not case-control",39034613,10.1080/19490976.2024.2377570,NA,"Krigul K.L., Feeney R.H., Wongkuna S., Aasmets O., Holmberg S.M., Andreson R., Puértolas-Balint F., Pantiukh K., Sootak L., Org T., Tenson T., Org E. , Schroeder B.O.",A history of repeated antibiotic usage leads to microbiota-dependent mucus defects,Gut microbes,2024,"Akkermansia, Antibiotics, colonic mucosa, fecal microbiota transplantation, gut microbiome, intestinal barrier, mucus, short-chain fatty acids",Experiment 2,Estonia,Mus musculus,Colon,UBERON:0001155,Response to transplant,EFO:0007043,FMT-C (control transplant mice),FMT- ABX (antibiotic transplant mice),Mice that received a fecal microbiota transplant (FMT) from the hABX (humans with a history of repeated antibiotic used) pool.,8,8,6 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 4e,3 December 2024,YokoC,"YokoC,WikiWorks","Boxplots of significant differentially abundant species (using ALDEX) in the distal colon of mouse microbiota between FMT-C and FMT-ABX, with at least a 0.1% mean relative abundance in either group.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas sp. Marseille-P2440,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium cochlearium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium limosum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii",3379134|976|200643|171549|815|816|626929;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|1853231|574697|1816677;1783272|1239|186801|186802|31979|1485|1494;1783272|1239|186801|186802|186806|1730|1736;3379134|976|200643|171549|2005525|375288|328812,Complete,Svetlana up
bsdb:39044127/1/1,39044127,time series / longitudinal observational,39044127,10.1186/s12866-024-03431-0,NA,"Ishizaka A., Koga M., Mizutani T., Suzuki Y., Matano T. , Yotsuyanagi H.",Sustained gut dysbiosis and intestinal inflammation show correlation with weight gain in person with chronic HIV infection on antiretroviral therapy,BMC microbiology,2024,"Chronic inflammation, HIV, Microbiota",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,HIV-1 infection,EFO:0000180,Baseline,Follow up,"Follow up refers to the study conducted four years after the initial gut microbiota analysis in 2018, where stool and blood samples were collected and analyzed for gut microbiota in 46 PWH(Person with human immunodeficiency virus type-1) receiving ART treatment. It is also referred to as second stool collection timepoint.",46,46,NA,16S,34,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,"age,alcohol drinking,body mass index,proton-pump inhibitor,sex,smoking behavior",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 1B,21 October 2024,KateRasheed,"KateRasheed,WikiWorks,Ese",Significant abundance of gut microbiota in PWH ( patients with human immunodeficiency virus (HIV) type-1); from baseline to follow-up period.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",1783272|201174|1760|85009|31957|1912216;1783272|1239|91061|1385|90964|1279;3379134|1224|28216|80840|119060;1783272|201174|1760|85007|1653|1716;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|1940338,Complete,Folakunmi
bsdb:39044127/1/2,39044127,time series / longitudinal observational,39044127,10.1186/s12866-024-03431-0,NA,"Ishizaka A., Koga M., Mizutani T., Suzuki Y., Matano T. , Yotsuyanagi H.",Sustained gut dysbiosis and intestinal inflammation show correlation with weight gain in person with chronic HIV infection on antiretroviral therapy,BMC microbiology,2024,"Chronic inflammation, HIV, Microbiota",Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,HIV-1 infection,EFO:0000180,Baseline,Follow up,"Follow up refers to the study conducted four years after the initial gut microbiota analysis in 2018, where stool and blood samples were collected and analyzed for gut microbiota in 46 PWH(Person with human immunodeficiency virus type-1) receiving ART treatment. It is also referred to as second stool collection timepoint.",46,46,NA,16S,34,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,"age,alcohol drinking,body mass index,proton-pump inhibitor,sex,smoking behavior",NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig. 1B,21 October 2024,KateRasheed,"KateRasheed,WikiWorks",Significant abundance of gut microbiota in PWH ( patients with human immunodeficiency virus (HIV) type-1); from baseline to follow-up period.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii",1783272|1239|186801|3085636|186803|572511;1783272|1239|526524|526525|2810280|135858;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|1407607;3379134|1224|1236|135614|32033|68;1783272|1239|186801|186802|216572|1263|438033,Complete,Folakunmi
bsdb:39044127/3/1,39044127,time series / longitudinal observational,39044127,10.1186/s12866-024-03431-0,NA,"Ishizaka A., Koga M., Mizutani T., Suzuki Y., Matano T. , Yotsuyanagi H.",Sustained gut dysbiosis and intestinal inflammation show correlation with weight gain in person with chronic HIV infection on antiretroviral therapy,BMC microbiology,2024,"Chronic inflammation, HIV, Microbiota",Experiment 3,Japan,Homo sapiens,Feces,UBERON:0001988,HIV-1 infection,EFO:0000180,Low BMI group,High BMI group,High BMI group refers to patients having BMI over 25 at baseline.,30,16,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,alcohol drinking,body mass index,proton-pump inhibitor,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,Fig. 3A,25 October 2024,KateRasheed,"KateRasheed,WikiWorks",Significant abundance of gut microbiota in BMI levels of PWH ( patients with human immunodeficiency virus (HIV) type-1); from baseline to follow-up period.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171550|239759,Complete,Folakunmi
bsdb:39044244/1/1,39044244,"cross-sectional observational, not case-control",39044244,10.1186/s40168-024-01847-4,NA,"Glendinning L., Jia X., Kebede A., Oyola S.O., Park J.E., Park W., Assiri A., Holm J.B., Kristiansen K., Han J. , Hanotte O.",Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia,Microbiome,2024,"Agro-ecology, Chicken, Ethiopia, Metagenomics, Microbiota, Poultry",Experiment 1,Ethiopia,Gallus gallus,Cecum mucosa,UBERON:0000314,Social environment measurement,EFO:0010552,Enterotype 2 + Enterotype 3,Enterotype 1,"Enterotype 1 refers to the Ethiopian chicken caecal microbiota from the gene catalogue, that was classified under Enterotype 1",NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 3C,22 February 2025,KateRasheed,KateRasheed,Differential enrichment of genera between enterotypes using LEfSe analysis,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Sphaerochaetaceae|g__Sphaerochaeta",3379134|976|200643|171549|171550|239759;3379134|203691|203692|136|2845253|157;3379134|203691|203692|1643686|143786|29521;3379134|200930|68337|191393|2945020|248038;3379134|976|200643|171549|2005473|1918540;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|40544;1783272|1239|909932|1843488|909930|904;3379134|74201|203494|48461|1647988|239934;3379134|203691|203692|136|2791015|399320,Complete,Svetlana up
bsdb:39044244/2/2,39044244,"cross-sectional observational, not case-control",39044244,10.1186/s40168-024-01847-4,NA,"Glendinning L., Jia X., Kebede A., Oyola S.O., Park J.E., Park W., Assiri A., Holm J.B., Kristiansen K., Han J. , Hanotte O.",Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia,Microbiome,2024,"Agro-ecology, Chicken, Ethiopia, Metagenomics, Microbiota, Poultry",Experiment 2,Ethiopia,Gallus gallus,Cecum mucosa,UBERON:0000314,Social environment measurement,EFO:0010552,Enterotype 1 + Enterotype 3,Enterotype 2,"Enterotype 2 refers to the Ethiopian chicken caecal microbiota from the gene catalogue, that was classified under Enterotype 2.",NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 3C,23 February 2025,KateRasheed,KateRasheed,Differential enrichment of genera between enterotypes using LEfSe analysis,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Merdimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",3379134|1224|28211|204441|2829815|191;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|204475;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|2023266;1783272|1239|186801|186802|216572|1017280;1783272|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:39044244/3/1,39044244,"cross-sectional observational, not case-control",39044244,10.1186/s40168-024-01847-4,NA,"Glendinning L., Jia X., Kebede A., Oyola S.O., Park J.E., Park W., Assiri A., Holm J.B., Kristiansen K., Han J. , Hanotte O.",Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia,Microbiome,2024,"Agro-ecology, Chicken, Ethiopia, Metagenomics, Microbiota, Poultry",Experiment 3,Ethiopia,Gallus gallus,Cecum mucosa,UBERON:0000314,Social environment measurement,EFO:0010552,Enterotype 1 + Enterotype 2,Enterotype 3,"Enterotype 3 refers to the Ethiopian chicken caecal microbiota from the gene catalogue, that was classified under Enterotype 3. They were particularly distinct from enterotypes 1 and 2 and clearly dominated by Climate zone 1.",NA,148,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 3C,23 February 2025,KateRasheed,KateRasheed,Differential enrichment of genera between enterotypes using LEfSe analysis,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Mediterranea,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",3379134|976|200643|171549|171552|838;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|186802|216572|216851;1783272|201174|84998|84999|1643824|133925;1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549|815|1926659;1783272|201174|84998|84999|84107|102106;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843489|31977|39948,Complete,Svetlana up
bsdb:39068488/1/1,39068488,laboratory experiment,39068488,10.1186/s40168-024-01852-7,NA,"van den Elsen L.J.W., Rekima A., Lynn M.A., Isnard C., Machado S., Divakara N., Patalwala D., Middleton A., Stevens N., Servant F., Burcelin R., Lynn D.J. , Verhasselt V.","Diet at birth is critical for healthy growth, independent of effects on the gut microbiota",Microbiome,2024,"Breast milk, Colostrum, Growth failure, Growth hormone resistance, Neonatal microbiota",Experiment 1,Australia,Mus musculus,Feces,UBERON:0001988,Postnatal growth retardation,HP:0008897,Control,Colostrum-deprived mice,"Newborn mice deprived of colostrum, fed with mature milk.",NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,increased,increased,NA,Signature 1,Figure 4D,8 October 2024,Princess Ben,"Princess Ben,Svetlana up,WikiWorks",Differential abundance in colostrum-deprived mice compared to the control mice.,increased,"p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae",95818|2093818|2093825|2171986|1331051;1783272|1239|186801|3085636|186803|248744;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572;95818|2093818|2093825|2171986,Complete,Svetlana up
bsdb:39068488/1/2,39068488,laboratory experiment,39068488,10.1186/s40168-024-01852-7,NA,"van den Elsen L.J.W., Rekima A., Lynn M.A., Isnard C., Machado S., Divakara N., Patalwala D., Middleton A., Stevens N., Servant F., Burcelin R., Lynn D.J. , Verhasselt V.","Diet at birth is critical for healthy growth, independent of effects on the gut microbiota",Microbiome,2024,"Breast milk, Colostrum, Growth failure, Growth hormone resistance, Neonatal microbiota",Experiment 1,Australia,Mus musculus,Feces,UBERON:0001988,Postnatal growth retardation,HP:0008897,Control,Colostrum-deprived mice,"Newborn mice deprived of colostrum, fed with mature milk.",NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,increased,increased,NA,Signature 2,Figure 4D,8 October 2024,Princess Ben,"Princess Ben,Svetlana up,WikiWorks",Differential abundance in colostrum-deprived mice compared to the control mice.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena fissicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales",1783272|1239|186801|3085636|186803|2005359|290055;1783272|1239|186801|3085636|186803|1506577;3379134|1224|28211|204441,Complete,Svetlana up
bsdb:39103909/1/1,39103909,case-control,39103909,10.1186/s12967-024-05533-9,NA,"Ling Z., Lan Z., Cheng Y., Liu X., Li Z., Yu Y., Wang Y., Shao L., Zhu Z., Gao J., Lei W., Ding W. , Liao R.",Altered gut microbiota and systemic immunity in Chinese patients with schizophrenia comorbid with metabolic syndrome,Journal of translational medicine,2024,"Gut dysbiosis, Gut-brain axis, Immunological dysfunction, Metabolic syndrome, Schizophrenia",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,"Schizophrenia,Metabolic syndrome","MONDO:0005090,EFO:0000195",Con (Healthy controls),SZ-MetS (Schizophrenia comorbid with metabolic syndrome),Patients aged 28-64 with both schizophrenia and metabolic syndrome,111,114,1 month,16S,34,Illumina,relative abundances,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,3.5,"age,sex",NA,NA,decreased,decreased,unchanged,NA,decreased,Signature 1,"Figure 3A, 3B",11 November 2025,Tosin,Tosin,Significant differential bacterial taxa in the fecal microbiota between the schizophrenia comorbid with metabolic syndrome (SZ-MetS) patients and healthy controls(HC) using linear discriminant analysis effect size (Lefse),increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|201174;1783272|201174|84998|84999|1643824;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;28221;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;3379134|1224|1236|91347|543|1940338;1783272|1239|526524|526525|128827|1573535;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843489|31977|906;1783272|1239|909932;1783272|201174|84998|84999|1643824|133925;3379134|976|200643|171549|171552;3379134|1224;1783272|1239|909932|909929;1783272|1239|909932|1843489|31977;1783272|1239|186801|186802|216572,Complete,KateRasheed
bsdb:39103909/1/2,39103909,case-control,39103909,10.1186/s12967-024-05533-9,NA,"Ling Z., Lan Z., Cheng Y., Liu X., Li Z., Yu Y., Wang Y., Shao L., Zhu Z., Gao J., Lei W., Ding W. , Liao R.",Altered gut microbiota and systemic immunity in Chinese patients with schizophrenia comorbid with metabolic syndrome,Journal of translational medicine,2024,"Gut dysbiosis, Gut-brain axis, Immunological dysfunction, Metabolic syndrome, Schizophrenia",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,"Schizophrenia,Metabolic syndrome","MONDO:0005090,EFO:0000195",Con (Healthy controls),SZ-MetS (Schizophrenia comorbid with metabolic syndrome),Patients aged 28-64 with both schizophrenia and metabolic syndrome,111,114,1 month,16S,34,Illumina,relative abundances,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,3.5,"age,sex",NA,NA,decreased,decreased,unchanged,NA,decreased,Signature 2,"Figure 3A, 3B",11 November 2025,Tosin,Tosin,Significant differential bacterial taxa in the fecal microbiota between the schizophrenia comorbid with metabolic syndrome (SZ-MetS) patients and healthy controls(HC) using linear discriminant analysis effect size (Lefse),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",1783272|1239|186801|3085636|186803|207244;1783272|1239;1783272|1239|186801|3085636|186803|572511;3379134|1224|28216|80840|119060;1783272|1239|186801;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;3379134|1224|1236|135625;1783272|1239|186801|3085636|186803|841;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|292632,Complete,KateRasheed
bsdb:39103909/2/1,39103909,case-control,39103909,10.1186/s12967-024-05533-9,NA,"Ling Z., Lan Z., Cheng Y., Liu X., Li Z., Yu Y., Wang Y., Shao L., Zhu Z., Gao J., Lei W., Ding W. , Liao R.",Altered gut microbiota and systemic immunity in Chinese patients with schizophrenia comorbid with metabolic syndrome,Journal of translational medicine,2024,"Gut dysbiosis, Gut-brain axis, Immunological dysfunction, Metabolic syndrome, Schizophrenia",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,"Schizophrenia,Metabolic syndrome","MONDO:0005090,EFO:0000195",Con (Healthy controls),SZ-MetS (Schizophrenia comorbid with metabolic syndrome),Patients aged 28-64 with both schizophrenia and metabolic syndrome,111,114,1 month,16S,34,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),Metastats",0.05,TRUE,NA,"age,sex",NA,NA,decreased,decreased,unchanged,NA,decreased,Signature 1,"Figure 4A, 4B, 4C",11 November 2025,Tosin,Tosin,"Comparisons of the relative abundance of abundant bacterial taxa in the fecal microbiota between SZ-MetS (schizophrenia comorbid with metabolic syndrome) patients and healthy controls in phylum, family and genus levels",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Thermotogati|p__Synergistota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|909932|1843488|909930;1783272|201174;1783272|1239|909932|1843489|31977|209879;3384194|508458|649775|649776|649777|508459;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;1783272|1239|909932|1843489|31977|39948;1783272|201174|84998|1643822|1643826;1783272|201174|84998|1643822|1643826|580024;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|186802|404402;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;3379134|976|200643|1970189|1573805;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843489|31977|906;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;3379134|976|200643|171549|171552;3379134|1224|1236|135624|83763;3379134|1224|28216|80840|995019|40544;3384194|508458|649775|649776|649777;3384194|508458;3379134|976|200643|171549|2005525;1783272|1239|909932|1843489|31977,Complete,KateRasheed
bsdb:39103909/2/2,39103909,case-control,39103909,10.1186/s12967-024-05533-9,NA,"Ling Z., Lan Z., Cheng Y., Liu X., Li Z., Yu Y., Wang Y., Shao L., Zhu Z., Gao J., Lei W., Ding W. , Liao R.",Altered gut microbiota and systemic immunity in Chinese patients with schizophrenia comorbid with metabolic syndrome,Journal of translational medicine,2024,"Gut dysbiosis, Gut-brain axis, Immunological dysfunction, Metabolic syndrome, Schizophrenia",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,"Schizophrenia,Metabolic syndrome","MONDO:0005090,EFO:0000195",Con (Healthy controls),SZ-MetS (Schizophrenia comorbid with metabolic syndrome),Patients aged 28-64 with both schizophrenia and metabolic syndrome,111,114,1 month,16S,34,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),Metastats",0.05,TRUE,NA,"age,sex",NA,NA,decreased,decreased,unchanged,NA,decreased,Signature 2,"Figure 4A, 4B, 4C",11 November 2025,Tosin,Tosin,"Comparisons of the relative abundance of abundant bacterial taxa in the fecal microbiota between SZ-MetS (schizophrenia comorbid with metabolic syndrome) patients and healthy controls in phylum, family and genus levels",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",1783272|1239|186801|3085636|186803|207244;1783272|1239;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;95818|2093818|2093825|2171986;1783272|1239|91061|186826|186828;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;1783272|201174|1760|85006|85023;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803|841;3379134|976|117747|200666|84566;1783272|1239|186801|186802|216572|292632,Complete,KateRasheed
bsdb:39103909/3/1,39103909,case-control,39103909,10.1186/s12967-024-05533-9,NA,"Ling Z., Lan Z., Cheng Y., Liu X., Li Z., Yu Y., Wang Y., Shao L., Zhu Z., Gao J., Lei W., Ding W. , Liao R.",Altered gut microbiota and systemic immunity in Chinese patients with schizophrenia comorbid with metabolic syndrome,Journal of translational medicine,2024,"Gut dysbiosis, Gut-brain axis, Immunological dysfunction, Metabolic syndrome, Schizophrenia",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Vascular endothelial growth factor measurement,EFO:0004762,Decreased VEGF (vascular endothelial growth factor),Increased VEGF (vascular endothelial growth factor),Increased levels of Vascular endothelial growth factor (VEGF),NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 10,11 November 2025,Tosin,Tosin,Spearman correlation heatmap between key functional differential genera and circulating inflammatory markers in SZ-MetS (schizophrenia comorbid with metabolic syndrome) patients,increased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,1783272|1239|526524|526525|128827|1573535,Complete,KateRasheed
bsdb:39103909/3/2,39103909,case-control,39103909,10.1186/s12967-024-05533-9,NA,"Ling Z., Lan Z., Cheng Y., Liu X., Li Z., Yu Y., Wang Y., Shao L., Zhu Z., Gao J., Lei W., Ding W. , Liao R.",Altered gut microbiota and systemic immunity in Chinese patients with schizophrenia comorbid with metabolic syndrome,Journal of translational medicine,2024,"Gut dysbiosis, Gut-brain axis, Immunological dysfunction, Metabolic syndrome, Schizophrenia",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Vascular endothelial growth factor measurement,EFO:0004762,Decreased VEGF (vascular endothelial growth factor),Increased VEGF (vascular endothelial growth factor),Increased levels of Vascular endothelial growth factor (VEGF),NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 10,11 November 2025,Tosin,Tosin,Spearman correlation heatmap between key functional differential genera and circulating inflammatory markers in SZ-MetS (schizophrenia comorbid with metabolic syndrome) patients,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,1783272|1239|186801|3085636|186803|1407607,Complete,KateRasheed
bsdb:39103909/4/1,39103909,case-control,39103909,10.1186/s12967-024-05533-9,NA,"Ling Z., Lan Z., Cheng Y., Liu X., Li Z., Yu Y., Wang Y., Shao L., Zhu Z., Gao J., Lei W., Ding W. , Liao R.",Altered gut microbiota and systemic immunity in Chinese patients with schizophrenia comorbid with metabolic syndrome,Journal of translational medicine,2024,"Gut dysbiosis, Gut-brain axis, Immunological dysfunction, Metabolic syndrome, Schizophrenia",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Monocyte chemotactic protein 1 measurement,EFO:0010596,Decreased MCP-1 (monocyte chemoattractant protein 1),Increased MCP-1 (monocyte chemoattractant protein 1),Increased levels of monocyte chemoattractant protein 1 (MCP-1),NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 10,11 November 2025,Tosin,Tosin,Spearman correlation heatmap between key functional differential genera and circulating inflammatory markers in SZ-MetS (schizophrenia comorbid with schizophrenia) patients,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter",1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|3085636|186803|1407607,Complete,KateRasheed
bsdb:39103909/4/2,39103909,case-control,39103909,10.1186/s12967-024-05533-9,NA,"Ling Z., Lan Z., Cheng Y., Liu X., Li Z., Yu Y., Wang Y., Shao L., Zhu Z., Gao J., Lei W., Ding W. , Liao R.",Altered gut microbiota and systemic immunity in Chinese patients with schizophrenia comorbid with metabolic syndrome,Journal of translational medicine,2024,"Gut dysbiosis, Gut-brain axis, Immunological dysfunction, Metabolic syndrome, Schizophrenia",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Monocyte chemotactic protein 1 measurement,EFO:0010596,Decreased MCP-1 (monocyte chemoattractant protein 1),Increased MCP-1 (monocyte chemoattractant protein 1),Increased levels of monocyte chemoattractant protein 1 (MCP-1),NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 10,11 November 2025,Tosin,Tosin,Spearman correlation heatmap between key functional differential genera and circulating inflammatory markers in SZ-MetS (schizophrenia comorbid with schizophrenia) patients,decreased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,1783272|1239|909932|909929|1843491|158846,Complete,KateRasheed
bsdb:39103909/5/1,39103909,case-control,39103909,10.1186/s12967-024-05533-9,NA,"Ling Z., Lan Z., Cheng Y., Liu X., Li Z., Yu Y., Wang Y., Shao L., Zhu Z., Gao J., Lei W., Ding W. , Liao R.",Altered gut microbiota and systemic immunity in Chinese patients with schizophrenia comorbid with metabolic syndrome,Journal of translational medicine,2024,"Gut dysbiosis, Gut-brain axis, Immunological dysfunction, Metabolic syndrome, Schizophrenia",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Platelet-derived growth factor BB measurement,EFO:0008264,Decreased PDGF-bb (platelet-derived growth factor bb),Increased PDGF-bb (platelet-derived growth factor bb),Increased levels of platelet-derived growth factor bb (PDGF-bb),NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 10,11 November 2025,Tosin,Tosin,Spearman correlation heatmap between key functional differential genera and circulating inflammatory markers in SZ-MetS (schizohprenia comorbid with metabolic syndrome) patients,increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,1783272|1239|909932|1843489|31977|906,Complete,KateRasheed
bsdb:39103909/5/2,39103909,case-control,39103909,10.1186/s12967-024-05533-9,NA,"Ling Z., Lan Z., Cheng Y., Liu X., Li Z., Yu Y., Wang Y., Shao L., Zhu Z., Gao J., Lei W., Ding W. , Liao R.",Altered gut microbiota and systemic immunity in Chinese patients with schizophrenia comorbid with metabolic syndrome,Journal of translational medicine,2024,"Gut dysbiosis, Gut-brain axis, Immunological dysfunction, Metabolic syndrome, Schizophrenia",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Platelet-derived growth factor BB measurement,EFO:0008264,Decreased PDGF-bb (platelet-derived growth factor bb),Increased PDGF-bb (platelet-derived growth factor bb),Increased levels of platelet-derived growth factor bb (PDGF-bb),NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 10,11 November 2025,Tosin,Tosin,Spearman correlation heatmap between key functional differential genera and circulating inflammatory markers in SZ-MetS (schizohprenia comorbid with metabolic syndrome) patients,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,KateRasheed
bsdb:39103909/7/1,39103909,case-control,39103909,10.1186/s12967-024-05533-9,NA,"Ling Z., Lan Z., Cheng Y., Liu X., Li Z., Yu Y., Wang Y., Shao L., Zhu Z., Gao J., Lei W., Ding W. , Liao R.",Altered gut microbiota and systemic immunity in Chinese patients with schizophrenia comorbid with metabolic syndrome,Journal of translational medicine,2024,"Gut dysbiosis, Gut-brain axis, Immunological dysfunction, Metabolic syndrome, Schizophrenia",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Interleukin 4 measurement,EFO:0008184,Decreased IL-4 (interleukin-4),Increased IL-4 (interleukin-4),Increased levels of interleukin-4 (IL-4),NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 10,11 November 2025,Tosin,Tosin,Spearman correlation heatmap between key functional differential genera and circulating inflammatory markers in SZ-MetS (schizohprenia comorbid with metabolic syndrome) patients,increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,1783272|1239|909932|1843489|31977|39948,Complete,KateRasheed
bsdb:39103909/7/2,39103909,case-control,39103909,10.1186/s12967-024-05533-9,NA,"Ling Z., Lan Z., Cheng Y., Liu X., Li Z., Yu Y., Wang Y., Shao L., Zhu Z., Gao J., Lei W., Ding W. , Liao R.",Altered gut microbiota and systemic immunity in Chinese patients with schizophrenia comorbid with metabolic syndrome,Journal of translational medicine,2024,"Gut dysbiosis, Gut-brain axis, Immunological dysfunction, Metabolic syndrome, Schizophrenia",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Interleukin 4 measurement,EFO:0008184,Decreased IL-4 (interleukin-4),Increased IL-4 (interleukin-4),Increased levels of interleukin-4 (IL-4),NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 10,11 November 2025,Tosin,Tosin,Spearman correlation heatmap between key functional differential genera and circulating inflammatory markers in SZ-MetS (schizohprenia comorbid with metabolic syndrome) patients,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,1783272|1239|186801|3085636|186803|841,Complete,KateRasheed
bsdb:39103909/8/1,39103909,case-control,39103909,10.1186/s12967-024-05533-9,NA,"Ling Z., Lan Z., Cheng Y., Liu X., Li Z., Yu Y., Wang Y., Shao L., Zhu Z., Gao J., Lei W., Ding W. , Liao R.",Altered gut microbiota and systemic immunity in Chinese patients with schizophrenia comorbid with metabolic syndrome,Journal of translational medicine,2024,"Gut dysbiosis, Gut-brain axis, Immunological dysfunction, Metabolic syndrome, Schizophrenia",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Fibroblast growth factor basic measurement,EFO:0008130,Decreased FGF basic (Fibroblast growth factor basic),Increased FGF basic (Fibroblast growth factor basic),Increased levels of Fibroblast growth factor basic (FGF basic),NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 10,11 November 2025,Tosin,Tosin,Spearman correlation heatmap between key functional differential genera and circulating inflammatory markers in SZ-MetS (schizohprenia comorbid with metabolic syndrome) patients,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|186802|216572|292632;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|841,Complete,KateRasheed
bsdb:39103909/9/1,39103909,case-control,39103909,10.1186/s12967-024-05533-9,NA,"Ling Z., Lan Z., Cheng Y., Liu X., Li Z., Yu Y., Wang Y., Shao L., Zhu Z., Gao J., Lei W., Ding W. , Liao R.",Altered gut microbiota and systemic immunity in Chinese patients with schizophrenia comorbid with metabolic syndrome,Journal of translational medicine,2024,"Gut dysbiosis, Gut-brain axis, Immunological dysfunction, Metabolic syndrome, Schizophrenia",Experiment 9,China,Homo sapiens,Feces,UBERON:0001988,Macrophage inflammatory protein 1b measurement,EFO:0008219,Decreased MIP-1b (macrophage inflammatory protein 1 beta),Increased MIP-1b (macrophage inflammatory protein 1 beta),Increased levels of macrophage inflammatory protein 1 beta (MIP-1b),NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 10,11 November 2025,Tosin,Tosin,Spearman correlation heatmap between key functional differential genera and circulating inflammatory markers in SZ-MetS (schizohprenia comorbid with metabolic syndrome) patients,increased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,1783272|201174|84998|84999|84107|102106,Complete,KateRasheed
bsdb:39103909/9/2,39103909,case-control,39103909,10.1186/s12967-024-05533-9,NA,"Ling Z., Lan Z., Cheng Y., Liu X., Li Z., Yu Y., Wang Y., Shao L., Zhu Z., Gao J., Lei W., Ding W. , Liao R.",Altered gut microbiota and systemic immunity in Chinese patients with schizophrenia comorbid with metabolic syndrome,Journal of translational medicine,2024,"Gut dysbiosis, Gut-brain axis, Immunological dysfunction, Metabolic syndrome, Schizophrenia",Experiment 9,China,Homo sapiens,Feces,UBERON:0001988,Macrophage inflammatory protein 1b measurement,EFO:0008219,Decreased MIP-1b (macrophage inflammatory protein 1 beta),Increased MIP-1b (macrophage inflammatory protein 1 beta),Increased levels of macrophage inflammatory protein 1 beta (MIP-1b),NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 10,12 November 2025,Tosin,Tosin,Spearman correlation heatmap between key functional differential genera and circulating inflammatory markers in SZ-MetS (schizohprenia comorbid with metabolic syndrome) patients,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,1783272|1239|186801|3085636|186803|841,Complete,KateRasheed
bsdb:39103909/10/1,39103909,case-control,39103909,10.1186/s12967-024-05533-9,NA,"Ling Z., Lan Z., Cheng Y., Liu X., Li Z., Yu Y., Wang Y., Shao L., Zhu Z., Gao J., Lei W., Ding W. , Liao R.",Altered gut microbiota and systemic immunity in Chinese patients with schizophrenia comorbid with metabolic syndrome,Journal of translational medicine,2024,"Gut dysbiosis, Gut-brain axis, Immunological dysfunction, Metabolic syndrome, Schizophrenia",Experiment 10,China,Homo sapiens,Feces,UBERON:0001988,C-X-C motif chemokine 10 measurement,EFO:0008056,Decreased IP-10 (interferon gamma-induced protein 10),Increased IP-10 (interferon gamma-induced protein 10),Increased levels of interferon gamma-induced protein 10 (IP-10),NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 10,12 November 2025,Tosin,Tosin,Spearman correlation heatmap between key functional differential genera and circulating inflammatory markers in SZ-MetS (schizohprenia comorbid with metabolic syndrome) patients,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,1783272|1239|186801|186802|216572|292632,Complete,KateRasheed
bsdb:39103909/11/1,39103909,case-control,39103909,10.1186/s12967-024-05533-9,NA,"Ling Z., Lan Z., Cheng Y., Liu X., Li Z., Yu Y., Wang Y., Shao L., Zhu Z., Gao J., Lei W., Ding W. , Liao R.",Altered gut microbiota and systemic immunity in Chinese patients with schizophrenia comorbid with metabolic syndrome,Journal of translational medicine,2024,"Gut dysbiosis, Gut-brain axis, Immunological dysfunction, Metabolic syndrome, Schizophrenia",Experiment 11,China,Homo sapiens,Feces,UBERON:0001988,Interleukin-6 measurement,EFO:0004810,Decreased IL-6 (interleukin-6),Increased IL-6 (interleukin-6),Increased levels of interleukin-6 (IL-6),NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 10,12 November 2025,Tosin,Tosin,Spearman correlation heatmap between key functional differential genera and circulating inflammatory markers in SZ-MetS (schizohprenia comorbid with metabolic syndrome) patients,increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,1783272|1239|909932|1843489|31977|906,Complete,KateRasheed
bsdb:39103909/12/1,39103909,case-control,39103909,10.1186/s12967-024-05533-9,NA,"Ling Z., Lan Z., Cheng Y., Liu X., Li Z., Yu Y., Wang Y., Shao L., Zhu Z., Gao J., Lei W., Ding W. , Liao R.",Altered gut microbiota and systemic immunity in Chinese patients with schizophrenia comorbid with metabolic syndrome,Journal of translational medicine,2024,"Gut dysbiosis, Gut-brain axis, Immunological dysfunction, Metabolic syndrome, Schizophrenia",Experiment 12,China,Homo sapiens,Feces,UBERON:0001988,Interleukin 8 measurement,EFO:0008191,Decreased IL-8 (interleukin-8),Increased IL-8 (interleukin-8),Increased levels of interleukin-8 (IL-8),NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 10,12 November 2025,Tosin,Tosin,Spearman correlation heatmap between key functional differential genera and circulating inflammatory markers in SZ-MetS (schizohprenia comorbid with metabolic syndrome) patients,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,1783272|1239|186801|3085636|186803|1407607,Complete,KateRasheed
bsdb:39103909/12/2,39103909,case-control,39103909,10.1186/s12967-024-05533-9,NA,"Ling Z., Lan Z., Cheng Y., Liu X., Li Z., Yu Y., Wang Y., Shao L., Zhu Z., Gao J., Lei W., Ding W. , Liao R.",Altered gut microbiota and systemic immunity in Chinese patients with schizophrenia comorbid with metabolic syndrome,Journal of translational medicine,2024,"Gut dysbiosis, Gut-brain axis, Immunological dysfunction, Metabolic syndrome, Schizophrenia",Experiment 12,China,Homo sapiens,Feces,UBERON:0001988,Interleukin 8 measurement,EFO:0008191,Decreased IL-8 (interleukin-8),Increased IL-8 (interleukin-8),Increased levels of interleukin-8 (IL-8),NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 10,12 November 2025,Tosin,Tosin,Spearman correlation heatmap between key functional differential genera and circulating inflammatory markers in SZ-MetS (schizohprenia comorbid with metabolic syndrome) patients,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes",1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|207244,Complete,KateRasheed
bsdb:39103909/13/1,39103909,case-control,39103909,10.1186/s12967-024-05533-9,NA,"Ling Z., Lan Z., Cheng Y., Liu X., Li Z., Yu Y., Wang Y., Shao L., Zhu Z., Gao J., Lei W., Ding W. , Liao R.",Altered gut microbiota and systemic immunity in Chinese patients with schizophrenia comorbid with metabolic syndrome,Journal of translational medicine,2024,"Gut dysbiosis, Gut-brain axis, Immunological dysfunction, Metabolic syndrome, Schizophrenia",Experiment 13,China,Homo sapiens,Feces,UBERON:0001988,Granulocyte colony-stimulating factor measurement,EFO:0008142,Decreased GCSF (granulocute colony-stimulating factor),Increased GCSF (granulocute colony-stimulating factor),Increased levels of granulocute colony-stimulating factor (GCSF),NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 10,12 November 2025,Tosin,Tosin,Spearman correlation heatmap between key functional differential genera and circulating inflammatory markers in SZ-MetS (schizohprenia comorbid with metabolic syndrome) patients,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|186802|216572|292632;1783272|1239|186801|3085636|186803|841,Complete,KateRasheed
bsdb:39103909/14/1,39103909,case-control,39103909,10.1186/s12967-024-05533-9,NA,"Ling Z., Lan Z., Cheng Y., Liu X., Li Z., Yu Y., Wang Y., Shao L., Zhu Z., Gao J., Lei W., Ding W. , Liao R.",Altered gut microbiota and systemic immunity in Chinese patients with schizophrenia comorbid with metabolic syndrome,Journal of translational medicine,2024,"Gut dysbiosis, Gut-brain axis, Immunological dysfunction, Metabolic syndrome, Schizophrenia",Experiment 14,China,Homo sapiens,Feces,UBERON:0001988,Macrophage inflammatory protein 1a measurement,EFO:0008218,Decreased MIP-1a (macrophage inflammatory protein 1 alpha),Increased MIP-1a (macrophage inflammatory protein 1 alpha),Increased levels of macrophage inflammatory protein 1 alpha (MIP-1a),NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 10,12 November 2025,Tosin,Tosin,Spearman correlation heatmap between key functional differential genera and circulating inflammatory markers in SZ-MetS (schizohprenia comorbid with metabolic syndrome) patients,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|186802|216572|292632;1783272|1239|186801|3085636|186803|841,Complete,KateRasheed
bsdb:39103909/15/1,39103909,case-control,39103909,10.1186/s12967-024-05533-9,NA,"Ling Z., Lan Z., Cheng Y., Liu X., Li Z., Yu Y., Wang Y., Shao L., Zhu Z., Gao J., Lei W., Ding W. , Liao R.",Altered gut microbiota and systemic immunity in Chinese patients with schizophrenia comorbid with metabolic syndrome,Journal of translational medicine,2024,"Gut dysbiosis, Gut-brain axis, Immunological dysfunction, Metabolic syndrome, Schizophrenia",Experiment 15,China,Homo sapiens,Feces,UBERON:0001988,Interleukin 1 receptor antagonist measurement,EFO:0004754,Decreased IL-1ra (interleukin-1 receptor antagonist alpha),Increased IL-1ra (interleukin-1 receptor antagonist alpha),Increased levels of interleukin-1 receptor antagonist alpha (IL-1ra),NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 10,12 November 2025,Tosin,Tosin,Spearman correlation heatmap between key functional differential genera and circulating inflammatory markers in SZ-MetS (schizohprenia comorbid with metabolic syndrome) patients,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,1783272|1239|186801|186802|216572|292632,Complete,KateRasheed
bsdb:39103909/16/1,39103909,case-control,39103909,10.1186/s12967-024-05533-9,NA,"Ling Z., Lan Z., Cheng Y., Liu X., Li Z., Yu Y., Wang Y., Shao L., Zhu Z., Gao J., Lei W., Ding W. , Liao R.",Altered gut microbiota and systemic immunity in Chinese patients with schizophrenia comorbid with metabolic syndrome,Journal of translational medicine,2024,"Gut dysbiosis, Gut-brain axis, Immunological dysfunction, Metabolic syndrome, Schizophrenia",Experiment 16,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia symptom severity measurement,EFO:0007927,Decreased Scale for Assessment of Negative Symptoms (SANS),Increased Scale for Assessment of Negative Symptoms (SANS),Increased levels of Scale for Assessment of Negative Symptoms (SANS),NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 6A, 6B",12 November 2025,Tosin,Tosin,Significant associations between specific bacterial genera and clinical indicators in SZ-MetS patients (schizophrenia comorbid with metabolic syndrome) using Spearman rank correlation analyses,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella",1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|3085636|186803|1649459,Complete,KateRasheed
bsdb:39103909/16/2,39103909,case-control,39103909,10.1186/s12967-024-05533-9,NA,"Ling Z., Lan Z., Cheng Y., Liu X., Li Z., Yu Y., Wang Y., Shao L., Zhu Z., Gao J., Lei W., Ding W. , Liao R.",Altered gut microbiota and systemic immunity in Chinese patients with schizophrenia comorbid with metabolic syndrome,Journal of translational medicine,2024,"Gut dysbiosis, Gut-brain axis, Immunological dysfunction, Metabolic syndrome, Schizophrenia",Experiment 16,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia symptom severity measurement,EFO:0007927,Decreased Scale for Assessment of Negative Symptoms (SANS),Increased Scale for Assessment of Negative Symptoms (SANS),Increased levels of Scale for Assessment of Negative Symptoms (SANS),NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6C,12 November 2025,Tosin,Tosin,Significant associations between specific bacterial genera and clinical indicators in SZ-MetS patients (schizophrenia comorbid with metabolic syndrome) using Spearman rank correlation analyses,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,1783272|1239|186801|186802|216572|292632,Complete,KateRasheed
bsdb:39103909/17/1,39103909,case-control,39103909,10.1186/s12967-024-05533-9,NA,"Ling Z., Lan Z., Cheng Y., Liu X., Li Z., Yu Y., Wang Y., Shao L., Zhu Z., Gao J., Lei W., Ding W. , Liao R.",Altered gut microbiota and systemic immunity in Chinese patients with schizophrenia comorbid with metabolic syndrome,Journal of translational medicine,2024,"Gut dysbiosis, Gut-brain axis, Immunological dysfunction, Metabolic syndrome, Schizophrenia",Experiment 17,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia symptom severity measurement,EFO:0007927,Decreased Scale for Assessment of Positive Symptoms (SAPS),Increased Scale for Assessment of Positive Symptoms (SAPS),Increased levels of Scale for Assessment of Positive Symptoms (SAPS),NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6C,12 November 2025,Tosin,Tosin,Significant associations between specific bacterial genera and clinical indicators in SZ-MetS patients (schizophrenia comorbid with metabolic syndrome) using Spearman rank correlation analyses,increased,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,3379134|200940|3031449|213115|194924|872,Complete,KateRasheed
bsdb:39103909/18/1,39103909,case-control,39103909,10.1186/s12967-024-05533-9,NA,"Ling Z., Lan Z., Cheng Y., Liu X., Li Z., Yu Y., Wang Y., Shao L., Zhu Z., Gao J., Lei W., Ding W. , Liao R.",Altered gut microbiota and systemic immunity in Chinese patients with schizophrenia comorbid with metabolic syndrome,Journal of translational medicine,2024,"Gut dysbiosis, Gut-brain axis, Immunological dysfunction, Metabolic syndrome, Schizophrenia",Experiment 18,China,Homo sapiens,Feces,UBERON:0001988,Body mass index,EFO:0004340,Decreased body mass index (BMI),Increased body mass index (BMI),Increased levels of body mass index (BMI),NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6E,12 November 2025,Tosin,Tosin,Significant associations between specific bacterial genera and clinical indicators in SZ-MetS patients (schizophrenia comorbid with metabolic syndrome) using Spearman rank correlation analyses,increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,1783272|1239|909932|909929|1843491|158846,Complete,KateRasheed
bsdb:39103909/18/2,39103909,case-control,39103909,10.1186/s12967-024-05533-9,NA,"Ling Z., Lan Z., Cheng Y., Liu X., Li Z., Yu Y., Wang Y., Shao L., Zhu Z., Gao J., Lei W., Ding W. , Liao R.",Altered gut microbiota and systemic immunity in Chinese patients with schizophrenia comorbid with metabolic syndrome,Journal of translational medicine,2024,"Gut dysbiosis, Gut-brain axis, Immunological dysfunction, Metabolic syndrome, Schizophrenia",Experiment 18,China,Homo sapiens,Feces,UBERON:0001988,Body mass index,EFO:0004340,Decreased body mass index (BMI),Increased body mass index (BMI),Increased levels of body mass index (BMI),NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 6F, 6G",12 November 2025,Tosin,Tosin,Significant associations between specific bacterial genera and clinical indicators in SZ-MetS patients (schizophrenia comorbid with metabolic syndrome) using Spearman rank correlation analyses,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,1783272|1239|186801|3085636|186803|841,Complete,KateRasheed
bsdb:39103909/19/1,39103909,case-control,39103909,10.1186/s12967-024-05533-9,NA,"Ling Z., Lan Z., Cheng Y., Liu X., Li Z., Yu Y., Wang Y., Shao L., Zhu Z., Gao J., Lei W., Ding W. , Liao R.",Altered gut microbiota and systemic immunity in Chinese patients with schizophrenia comorbid with metabolic syndrome,Journal of translational medicine,2024,"Gut dysbiosis, Gut-brain axis, Immunological dysfunction, Metabolic syndrome, Schizophrenia",Experiment 19,China,Homo sapiens,Feces,UBERON:0001988,Triglyceride measurement,EFO:0004530,Decreased Triglyceride (TG),Increased Triglyceride (TG),Increased levels of Triglyceride (TG),NA,NA,1 month,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6H,12 November 2025,Tosin,Tosin,Significant associations between specific bacterial genera and clinical indicators in SZ-MetS patients (schizophrenia comorbid with metabolic syndrome) using Spearman rank correlation analyses,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,KateRasheed
bsdb:39131354/1/1,39131354,randomized controlled trial,39131354,10.1101/2024.07.31.606041,NA,"Özcan E., Yu K.B., Dinh L., Lum G.R., Lau K., Hsu J., Arino M., Paramo J., Lopez-Romero A. , Hsiao E.Y.",Dietary fiber content in clinical ketogenic diets modifies the gut microbiome and seizure resistance in mice,bioRxiv : the preprint server for biology,2024,NA,Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,control diet (CD) group,KD4:1 group,Mice fed a ketogenic diet of 4:1 fat to protein ratio,14,14,NA,PCR,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,NA,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Supplementary Figure 2a,17 December 2024,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of KD4:1 group compared to CD group,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,",3379134|976|200643;1783272|201174|84998;3379134|200930|68337;1783272|1239|91061|186826|1300;,Complete,NA
bsdb:39131354/1/2,39131354,randomized controlled trial,39131354,10.1101/2024.07.31.606041,NA,"Özcan E., Yu K.B., Dinh L., Lum G.R., Lau K., Hsu J., Arino M., Paramo J., Lopez-Romero A. , Hsiao E.Y.",Dietary fiber content in clinical ketogenic diets modifies the gut microbiome and seizure resistance in mice,bioRxiv : the preprint server for biology,2024,NA,Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,control diet (CD) group,KD4:1 group,Mice fed a ketogenic diet of 4:1 fat to protein ratio,14,14,NA,PCR,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,NA,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,Supplementary Figure 2a,17 December 2024,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of KD4:1 group compared to CD group,decreased,k__Bacillati|p__Bacillota|c__Erysipelotrichia,1783272|1239|526524,Complete,NA
bsdb:39131354/2/1,39131354,randomized controlled trial,39131354,10.1101/2024.07.31.606041,NA,"Özcan E., Yu K.B., Dinh L., Lum G.R., Lau K., Hsu J., Arino M., Paramo J., Lopez-Romero A. , Hsiao E.Y.",Dietary fiber content in clinical ketogenic diets modifies the gut microbiome and seizure resistance in mice,bioRxiv : the preprint server for biology,2024,NA,Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,control diet (CD) group,KD3:1 group,Mice fed a ketogenic diet of 3:1 fat to protein ratio,14,14,NA,PCR,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Supplementary Figure 2a,17 December 2024,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of KD3:1 group compared to CD group,decreased,k__Bacillati|p__Actinomycetota,1783272|201174,Complete,NA
bsdb:39131354/2/2,39131354,randomized controlled trial,39131354,10.1101/2024.07.31.606041,NA,"Özcan E., Yu K.B., Dinh L., Lum G.R., Lau K., Hsu J., Arino M., Paramo J., Lopez-Romero A. , Hsiao E.Y.",Dietary fiber content in clinical ketogenic diets modifies the gut microbiome and seizure resistance in mice,bioRxiv : the preprint server for biology,2024,NA,Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,control diet (CD) group,KD3:1 group,Mice fed a ketogenic diet of 3:1 fat to protein ratio,14,14,NA,PCR,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Supplementary Figure 2a,17 December 2024,Kavyaayala,"Kavyaayala,WikiWorks",Fecal microbiome of KD3:1 group compared to CD group,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Mammaliicoccus|s__Mammaliicoccus sciuri,k__Pseudomonadati|p__Pseudomonadota",1783272|1239|91061|1385|90964|2803850|1296;3379134|1224,Complete,NA
bsdb:39131354/3/1,39131354,randomized controlled trial,39131354,10.1101/2024.07.31.606041,NA,"Özcan E., Yu K.B., Dinh L., Lum G.R., Lau K., Hsu J., Arino M., Paramo J., Lopez-Romero A. , Hsiao E.Y.",Dietary fiber content in clinical ketogenic diets modifies the gut microbiome and seizure resistance in mice,bioRxiv : the preprint server for biology,2024,NA,Experiment 3,United States of America,Mus musculus,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,control diet (CD) group,MCT2.5:1 group,"Mice fed a medium chain triglyceride (MCT) diet, a variation of the ketogenic diet using only MCT fats",14,14,NA,PCR,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,NA,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Supplementary Figure 2a,2 March 2025,Kavyaayala,Kavyaayala,Fecal microbiome of MCT2.5:1 group compared to CD group,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,",3379134|976|200643;1783272|201174|84998;3379134|200930|68337;1783272|1239|91061|186826|1300;,Complete,NA
bsdb:39131354/3/2,39131354,randomized controlled trial,39131354,10.1101/2024.07.31.606041,NA,"Özcan E., Yu K.B., Dinh L., Lum G.R., Lau K., Hsu J., Arino M., Paramo J., Lopez-Romero A. , Hsiao E.Y.",Dietary fiber content in clinical ketogenic diets modifies the gut microbiome and seizure resistance in mice,bioRxiv : the preprint server for biology,2024,NA,Experiment 3,United States of America,Mus musculus,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,control diet (CD) group,MCT2.5:1 group,"Mice fed a medium chain triglyceride (MCT) diet, a variation of the ketogenic diet using only MCT fats",14,14,NA,PCR,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,NA,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,Supplementary Figure 2a,2 March 2025,Kavyaayala,Kavyaayala,Fecal microbiome of MDT2.5:1 group compared to CD group,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Erysipelotrichia",1783272|201174;1783272|1239|526524,Complete,NA
bsdb:39131354/4/1,39131354,randomized controlled trial,39131354,10.1101/2024.07.31.606041,NA,"Özcan E., Yu K.B., Dinh L., Lum G.R., Lau K., Hsu J., Arino M., Paramo J., Lopez-Romero A. , Hsiao E.Y.",Dietary fiber content in clinical ketogenic diets modifies the gut microbiome and seizure resistance in mice,bioRxiv : the preprint server for biology,2024,NA,Experiment 4,United States of America,Mus musculus,Feces,UBERON:0001988,Ketogenic diet,EFO:0009371,KD3:1 group,MCT2.5:1 group,"Mice fed a medium chain triglyceride (MCT) diet, a variation of the ketogenic diet using only MCT fats",14,14,NA,PCR,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,NA,NA,NA,NA,increased,increased,NA,NA,NA,NA,Signature 1,Supplementary Figure 2a,2 March 2025,Kavyaayala,Kavyaayala,Fecal microbiome of MDT2.5:1 group compared to KD3:1 group,increased,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres,3379134|200930|68337,Complete,NA
bsdb:39131354/4/2,39131354,randomized controlled trial,39131354,10.1101/2024.07.31.606041,NA,"Özcan E., Yu K.B., Dinh L., Lum G.R., Lau K., Hsu J., Arino M., Paramo J., Lopez-Romero A. , Hsiao E.Y.",Dietary fiber content in clinical ketogenic diets modifies the gut microbiome and seizure resistance in mice,bioRxiv : the preprint server for biology,2024,NA,Experiment 4,United States of America,Mus musculus,Feces,UBERON:0001988,Ketogenic diet,EFO:0009371,KD3:1 group,MCT2.5:1 group,"Mice fed a medium chain triglyceride (MCT) diet, a variation of the ketogenic diet using only MCT fats",14,14,NA,PCR,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,NA,NA,NA,NA,increased,increased,NA,NA,NA,NA,Signature 2,Supplementary Figure 2a,2 March 2025,Kavyaayala,Kavyaayala,Fecal microbiome of MDT2.5:1 group compared to KD3:1 group,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Mammaliicoccus|s__Mammaliicoccus sciuri,k__Pseudomonadati|p__Pseudomonadota",1783272|1239|91061|186826|81852|1350|1351;3379134|1224|1236|91347|543|561|562;1783272|1239|91061|1385|90964|2803850|1296;3379134|1224,Complete,NA
bsdb:39131354/5/1,39131354,randomized controlled trial,39131354,10.1101/2024.07.31.606041,NA,"Özcan E., Yu K.B., Dinh L., Lum G.R., Lau K., Hsu J., Arino M., Paramo J., Lopez-Romero A. , Hsiao E.Y.",Dietary fiber content in clinical ketogenic diets modifies the gut microbiome and seizure resistance in mice,bioRxiv : the preprint server for biology,2024,NA,Experiment 5,United States of America,Mus musculus,Feces,UBERON:0001988,Ketogenic diet,EFO:0009371,KD4:1 group,KD3:1 group,Mice fed a ketogenic diet of 3:1 fat to protein ratio,14,14,NA,PCR,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Figure 2a,2 March 2025,Kavyaayala,Kavyaayala,Fecal microbiome of KD3:1 group compared to KD4:1 group,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Mammaliicoccus|s__Mammaliicoccus sciuri",1783272|1239|91061|186826|81852|1350|1351;3379134|1224|1236|91347|543|561|562;1783272|1239|91061|1385|90964|2803850|1296,Complete,NA
bsdb:39131354/5/2,39131354,randomized controlled trial,39131354,10.1101/2024.07.31.606041,NA,"Özcan E., Yu K.B., Dinh L., Lum G.R., Lau K., Hsu J., Arino M., Paramo J., Lopez-Romero A. , Hsiao E.Y.",Dietary fiber content in clinical ketogenic diets modifies the gut microbiome and seizure resistance in mice,bioRxiv : the preprint server for biology,2024,NA,Experiment 5,United States of America,Mus musculus,Feces,UBERON:0001988,Ketogenic diet,EFO:0009371,KD4:1 group,KD3:1 group,Mice fed a ketogenic diet of 3:1 fat to protein ratio,14,14,NA,PCR,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Figure 2a,2 March 2025,Kavyaayala,Kavyaayala,Fecal microbiome of KD3:1 group compared to KD4:1 group,decreased,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres,3379134|200930|68337,Complete,NA
bsdb:39143178/1/1,39143178,case-control,39143178,10.1038/s41598-024-69742-4,NA,"Duru I.C., Lecomte A., Shishido T.K., Laine P., Suppula J., Paulin L., Scheperjans F., Pereira P.A.B. , Auvinen P.",Metagenome-assembled microbial genomes from Parkinson's disease fecal samples,Scientific reports,2024,"Ruminococcus bromii, Metagenome, Microdiversity, Parkinson’s disease",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control,Parkinson’s disease (PD) patients,Parkinson’s disease (PD) patients refers to patients diagnosed of Parkinson’s disease (PD) - a common neurodegenerative disease.,68,68,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 14,3 March 2025,KateRasheed,KateRasheed,Differential abundance of taxa between Control and PD patients using DESeq2,increased,"k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Methanobacteriati|p__Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomethylophilaceae|g__Methanomethylophilus|s__Methanomethylophilus alvi",3366610|28890|183925|2158|2159|2172|2173;3366610|2283796|183967|1235850|2517203|1291539|1291540,Complete,Svetlana up
bsdb:39143178/1/2,39143178,case-control,39143178,10.1038/s41598-024-69742-4,NA,"Duru I.C., Lecomte A., Shishido T.K., Laine P., Suppula J., Paulin L., Scheperjans F., Pereira P.A.B. , Auvinen P.",Metagenome-assembled microbial genomes from Parkinson's disease fecal samples,Scientific reports,2024,"Ruminococcus bromii, Metagenome, Microdiversity, Parkinson’s disease",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Control,Parkinson’s disease (PD) patients,Parkinson’s disease (PD) patients refers to patients diagnosed of Parkinson’s disease (PD) - a common neurodegenerative disease.,68,68,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 14,3 March 2025,KateRasheed,KateRasheed,Differential abundance of taxa between Control and PD patients using DESeq2,decreased,k__Methanobacteriati|p__Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus|s__Candidatus Methanomassiliicoccus intestinalis,3366610|2283796|183967|1235850|1577788|1080709|1406512,Complete,Svetlana up
bsdb:39191760/1/1,39191760,"randomized controlled trial,time series / longitudinal observational",39191760,10.1038/s41522-024-00549-x,https://www.nature.com/articles/s41522-024-00549-x,"Hartikainen A.K., Jalanka J., Lahtinen P., Ponsero A.J., Mertsalmi T., Finnegan L., Crispie F., Cotter P.D., Arkkila P. , Satokari R.",Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients,NPJ biofilms and microbiomes,2024,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Autologous transplant (placebo) group,Fecal microbiota transplantation (FMT) from universal healthy donor group at 4 weeks,Patients that received a single fecal microbiota transplant (FMT) from a universal healthy donor at 4 weeks,26,23,NA,16S,34,Illumina,log transformation,MaAsLin2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,fig 2A & Supplementary table 2,13 November 2025,Chyono2,Chyono2,"Differential abundance testing on luminal 16S rRNA gene amplicon
sequencing at family-level with Maaslin2.",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",1783272|1239|909932|1843488|909930;3379134|976|200643|171549|171552,Complete,NA
bsdb:39191760/1/2,39191760,"randomized controlled trial,time series / longitudinal observational",39191760,10.1038/s41522-024-00549-x,https://www.nature.com/articles/s41522-024-00549-x,"Hartikainen A.K., Jalanka J., Lahtinen P., Ponsero A.J., Mertsalmi T., Finnegan L., Crispie F., Cotter P.D., Arkkila P. , Satokari R.",Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients,NPJ biofilms and microbiomes,2024,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Autologous transplant (placebo) group,Fecal microbiota transplantation (FMT) from universal healthy donor group at 4 weeks,Patients that received a single fecal microbiota transplant (FMT) from a universal healthy donor at 4 weeks,26,23,NA,16S,34,Illumina,log transformation,MaAsLin2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,fig 2A & Supplementary table 2,14 November 2025,Chyono2,Chyono2,Differential abundance testing on luminal 16S rRNA gene amplicon sequencing at family-level with Maaslin2,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|976|200643|171549|815;1783272|1239|186801|3085636|186803,Complete,NA
bsdb:39191760/2/1,39191760,"randomized controlled trial,time series / longitudinal observational",39191760,10.1038/s41522-024-00549-x,https://www.nature.com/articles/s41522-024-00549-x,"Hartikainen A.K., Jalanka J., Lahtinen P., Ponsero A.J., Mertsalmi T., Finnegan L., Crispie F., Cotter P.D., Arkkila P. , Satokari R.",Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients,NPJ biofilms and microbiomes,2024,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Autologous transplant (placebo) group,Fecal microbiota transplantation (FMT) from universal healthy donor group at 12 weeks,Patients that received a single fecal microbiota transplant (FMT) from a universal healthy donor at 12 weeks,26,23,NA,16S,34,Illumina,log transformation,MaAsLin2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,fig 2A & Supplementary table 2,13 November 2025,Chyono2,Chyono2,". Differential abundance testing on luminal 16S rRNA gene amplicon
sequencing at family-level with Maaslin2",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae",1783272|1239|909932|1843488|909930;3379134|976|200643|171549|171552;1783272|1239|91061|1385|90964,Complete,NA
bsdb:39191760/2/2,39191760,"randomized controlled trial,time series / longitudinal observational",39191760,10.1038/s41522-024-00549-x,https://www.nature.com/articles/s41522-024-00549-x,"Hartikainen A.K., Jalanka J., Lahtinen P., Ponsero A.J., Mertsalmi T., Finnegan L., Crispie F., Cotter P.D., Arkkila P. , Satokari R.",Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients,NPJ biofilms and microbiomes,2024,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Autologous transplant (placebo) group,Fecal microbiota transplantation (FMT) from universal healthy donor group at 12 weeks,Patients that received a single fecal microbiota transplant (FMT) from a universal healthy donor at 12 weeks,26,23,NA,16S,34,Illumina,log transformation,MaAsLin2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,fig 2A & Supplementary table 2,14 November 2025,Chyono2,Chyono2,Differential abundance testing on luminal 16S rRNA gene amplicon sequencing at family-level with Maaslin2,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,3379134|976|200643|171549|815,Complete,NA
bsdb:39191760/3/1,39191760,"randomized controlled trial,time series / longitudinal observational",39191760,10.1038/s41522-024-00549-x,https://www.nature.com/articles/s41522-024-00549-x,"Hartikainen A.K., Jalanka J., Lahtinen P., Ponsero A.J., Mertsalmi T., Finnegan L., Crispie F., Cotter P.D., Arkkila P. , Satokari R.",Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients,NPJ biofilms and microbiomes,2024,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Autologous transplant (placebo) group,Fecal microbiota transplantation (FMT) from universal healthy donor group at 52 weeks,Patients that received a single fecal microbiota (FMT) transplant from a universal healthy donor at 52 weeks,26,23,NA,16S,34,Illumina,log transformation,MaAsLin2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,fig 2A & Supplementary table 2,13 November 2025,Chyono2,Chyono2,"Differential abundance testing on luminal 16S rRNA gene amplicon
sequencing at family-level with Maaslin2 at 52 weeks",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",1783272|1239|909932|1843488|909930;3379134|976|117743|200644|49546;3379134|976|200643|171549|171552,Complete,NA
bsdb:39191760/4/1,39191760,"randomized controlled trial,time series / longitudinal observational",39191760,10.1038/s41522-024-00549-x,https://www.nature.com/articles/s41522-024-00549-x,"Hartikainen A.K., Jalanka J., Lahtinen P., Ponsero A.J., Mertsalmi T., Finnegan L., Crispie F., Cotter P.D., Arkkila P. , Satokari R.",Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients,NPJ biofilms and microbiomes,2024,NA,Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Baseline (BL) group,Fecal microbiota transplantation (FMT) from universal healthy donor group at 4 weeks,Patients who received a single fecal microbiota transplantation (FMT)  from a universal donor at 4 weeks,49,23,NA,16S,34,Illumina,log transformation,MaAsLin2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,fig 2A & Supplementary table 2,14 November 2025,Chyono2,Chyono2,Differential abundance testing on luminal 16S rRNA gene amplicon sequencing at family- level with Maaslin2,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae",3379134|976|117743|200644|49546;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550;3384194|508458|649775|649776|649777,Complete,NA
bsdb:39191760/4/2,39191760,"randomized controlled trial,time series / longitudinal observational",39191760,10.1038/s41522-024-00549-x,https://www.nature.com/articles/s41522-024-00549-x,"Hartikainen A.K., Jalanka J., Lahtinen P., Ponsero A.J., Mertsalmi T., Finnegan L., Crispie F., Cotter P.D., Arkkila P. , Satokari R.",Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients,NPJ biofilms and microbiomes,2024,NA,Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Baseline (BL) group,Fecal microbiota transplantation (FMT) from universal healthy donor group at 4 weeks,Patients who received a single fecal microbiota transplantation (FMT)  from a universal donor at 4 weeks,49,23,NA,16S,34,Illumina,log transformation,MaAsLin2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,fig 2A & Supplementary table 2,14 November 2025,Chyono2,Chyono2,Differential abundance testing on luminal 16S rRNA gene amplicon sequencing at family- level with Maaslin2,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae",3379134|976|200643|171549|815;1783272|1239|91061|186826|186828,Complete,NA
bsdb:39191760/5/1,39191760,"randomized controlled trial,time series / longitudinal observational",39191760,10.1038/s41522-024-00549-x,https://www.nature.com/articles/s41522-024-00549-x,"Hartikainen A.K., Jalanka J., Lahtinen P., Ponsero A.J., Mertsalmi T., Finnegan L., Crispie F., Cotter P.D., Arkkila P. , Satokari R.",Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients,NPJ biofilms and microbiomes,2024,NA,Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Baseline (BL) group,Fecal microbiota transplantation (FMT) from universal healthy donor group at 8 weeks,Patients who received a single fecal microbiota transplantation (FMT)  from a universal donor at 8 weeks,49,23,NA,16S,34,Illumina,log transformation,MaAsLin2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,fig 2A & Supplementary table 2,14 November 2025,Chyono2,Chyono2,Differential abundance testing on luminal 16S rRNA gene amplicon sequencing at family- level with Maaslin2,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Syntrophia|o__Syntrophales|f__Syntrophaceae",3379134|976|117743|200644|49546;1783272|201174|1760|85006|1268;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550;1783272|1239|91061|1385|90964;3384194|508458|649775|649776|649777;3379134|200940|3031648|2914038|213468,Complete,NA
bsdb:39191760/5/2,39191760,"randomized controlled trial,time series / longitudinal observational",39191760,10.1038/s41522-024-00549-x,https://www.nature.com/articles/s41522-024-00549-x,"Hartikainen A.K., Jalanka J., Lahtinen P., Ponsero A.J., Mertsalmi T., Finnegan L., Crispie F., Cotter P.D., Arkkila P. , Satokari R.",Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients,NPJ biofilms and microbiomes,2024,NA,Experiment 5,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Baseline (BL) group,Fecal microbiota transplantation (FMT) from universal healthy donor group at 8 weeks,Patients who received a single fecal microbiota transplantation (FMT)  from a universal donor at 8 weeks,49,23,NA,16S,34,Illumina,log transformation,MaAsLin2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,fig 2A & Supplementary table 2,14 November 2025,Chyono2,Chyono2,Differential abundance testing on luminal 16S rRNA gene amplicon sequencing at family- level with Maaslin2,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,3379134|976|200643|171549|815,Complete,NA
bsdb:39191760/6/1,39191760,"randomized controlled trial,time series / longitudinal observational",39191760,10.1038/s41522-024-00549-x,https://www.nature.com/articles/s41522-024-00549-x,"Hartikainen A.K., Jalanka J., Lahtinen P., Ponsero A.J., Mertsalmi T., Finnegan L., Crispie F., Cotter P.D., Arkkila P. , Satokari R.",Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients,NPJ biofilms and microbiomes,2024,NA,Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Baseline (BL) group,Fecal microbiota transplantation (FMT) from universal healthy donor group at 12 weeks,Patients who received a single fecal microbiota transplantation (FMT)  from a universal donor at 12 weeks,49,23,NA,16S,34,Illumina,log transformation,MaAsLin2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,fig 2A & Supplementary table 2,14 November 2025,Chyono2,Chyono2,Differential abundance testing on luminal 16S rRNA gene amplicon sequencing at family- level with Maaslin2,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae",3379134|976|117743|200644|49546;3379134|976|200643|171549|171552;1783272|1239|91061|1385|90964;3384194|508458|649775|649776|649777,Complete,NA
bsdb:39191760/6/2,39191760,"randomized controlled trial,time series / longitudinal observational",39191760,10.1038/s41522-024-00549-x,https://www.nature.com/articles/s41522-024-00549-x,"Hartikainen A.K., Jalanka J., Lahtinen P., Ponsero A.J., Mertsalmi T., Finnegan L., Crispie F., Cotter P.D., Arkkila P. , Satokari R.",Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients,NPJ biofilms and microbiomes,2024,NA,Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Baseline (BL) group,Fecal microbiota transplantation (FMT) from universal healthy donor group at 12 weeks,Patients who received a single fecal microbiota transplantation (FMT)  from a universal donor at 12 weeks,49,23,NA,16S,34,Illumina,log transformation,MaAsLin2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,fig 2A & Supplementary table 2,14 November 2025,Chyono2,Chyono2,Differential abundance testing on luminal 16S rRNA gene amplicon sequencing at family- level with Maaslin2,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae",3379134|976|200643|171549|815;3379134|1224|1236|72274|135621,Complete,NA
bsdb:39191760/7/1,39191760,"randomized controlled trial,time series / longitudinal observational",39191760,10.1038/s41522-024-00549-x,https://www.nature.com/articles/s41522-024-00549-x,"Hartikainen A.K., Jalanka J., Lahtinen P., Ponsero A.J., Mertsalmi T., Finnegan L., Crispie F., Cotter P.D., Arkkila P. , Satokari R.",Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients,NPJ biofilms and microbiomes,2024,NA,Experiment 7,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Baseline (BL) group,Fecal microbiota transplantation (FMT) from universal healthy donor group at 26 weeks,Patients who received a single fecal microbiota transplantation (FMT)  from a universal donor at 26 weeks,49,23,NA,16S,34,Illumina,log transformation,MaAsLin2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,fig 2A & Supplementary table 2,14 November 2025,Chyono2,Chyono2,Differential abundance testing on luminal 16S rRNA gene amplicon sequencing at family- level with Maaslin2,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae",3379134|976|117743|200644|49546;3379134|976|200643|171549|171552;3384194|508458|649775|649776|649777,Complete,NA
bsdb:39191760/7/2,39191760,"randomized controlled trial,time series / longitudinal observational",39191760,10.1038/s41522-024-00549-x,https://www.nature.com/articles/s41522-024-00549-x,"Hartikainen A.K., Jalanka J., Lahtinen P., Ponsero A.J., Mertsalmi T., Finnegan L., Crispie F., Cotter P.D., Arkkila P. , Satokari R.",Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients,NPJ biofilms and microbiomes,2024,NA,Experiment 7,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Baseline (BL) group,Fecal microbiota transplantation (FMT) from universal healthy donor group at 26 weeks,Patients who received a single fecal microbiota transplantation (FMT)  from a universal donor at 26 weeks,49,23,NA,16S,34,Illumina,log transformation,MaAsLin2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,fig 2A & Supplementary table 2,14 November 2025,Chyono2,Chyono2,Differential abundance testing on luminal 16S rRNA gene amplicon sequencing at family- level with Maaslin2,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,3379134|976|200643|171549|815,Complete,NA
bsdb:39191760/8/1,39191760,"randomized controlled trial,time series / longitudinal observational",39191760,10.1038/s41522-024-00549-x,https://www.nature.com/articles/s41522-024-00549-x,"Hartikainen A.K., Jalanka J., Lahtinen P., Ponsero A.J., Mertsalmi T., Finnegan L., Crispie F., Cotter P.D., Arkkila P. , Satokari R.",Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients,NPJ biofilms and microbiomes,2024,NA,Experiment 8,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Baseline (BL) group,Fecal microbiota transplantation (FMT) from universal healthy donor group at 52 weeks,Patients who received a single fecal microbiota transplantation (FMT)  from a universal donor at 52 weeks,49,23,NA,16S,34,Illumina,log transformation,MaAsLin2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,fig 2A & Supplemenntary table 2,14 November 2025,Chyono2,Chyono2,Differential abundance testing on luminal 16S rRNA gene amplicon sequencing at family- level with Maaslin2,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae",3379134|976|117743|200644|49546;3384194|508458|649775|649776|649777,Complete,NA
bsdb:39191760/8/2,39191760,"randomized controlled trial,time series / longitudinal observational",39191760,10.1038/s41522-024-00549-x,https://www.nature.com/articles/s41522-024-00549-x,"Hartikainen A.K., Jalanka J., Lahtinen P., Ponsero A.J., Mertsalmi T., Finnegan L., Crispie F., Cotter P.D., Arkkila P. , Satokari R.",Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients,NPJ biofilms and microbiomes,2024,NA,Experiment 8,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Baseline (BL) group,Fecal microbiota transplantation (FMT) from universal healthy donor group at 52 weeks,Patients who received a single fecal microbiota transplantation (FMT)  from a universal donor at 52 weeks,49,23,NA,16S,34,Illumina,log transformation,MaAsLin2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,fig 2A & Supplementary table 2,14 November 2025,Chyono2,Chyono2,Differential abundance testing on luminal 16S rRNA gene amplicon sequencing at family- level with Maaslin2,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,3379134|976|200643|171549|815,Complete,NA
bsdb:39191760/10/1,39191760,"randomized controlled trial,time series / longitudinal observational",39191760,10.1038/s41522-024-00549-x,https://www.nature.com/articles/s41522-024-00549-x,"Hartikainen A.K., Jalanka J., Lahtinen P., Ponsero A.J., Mertsalmi T., Finnegan L., Crispie F., Cotter P.D., Arkkila P. , Satokari R.",Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients,NPJ biofilms and microbiomes,2024,NA,Experiment 10,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Baseline (BL) group,Fecal microbiota transplantation (FMT) from universal healthy donor group at 4 weeks,Patients who received a single fecal microbiota transplantation (FMT)  from a universal donor at 4 weeks,49,23,NA,16S,34,Illumina,log transformation,MaAsLin2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"fig Supplementary 3a, Supplementary 3b, Supplementary Table 3",14 November 2025,Chyono2,Chyono2,"Differential abundance testing on luminal metagenomics at species-level with Maaslin2
fecal microbiota transplant(FMT) group follow-up time points vs. baseline group",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister histaminiformans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella bouchesdurhonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Evtepia|s__Evtepia gabavorous,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri",3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|171550|239759|1288121;3379134|976|200643|171549|171550|239759|328814;1783272|1239|909932|1843489|31977|39948|209880;1783272|1239|186801|3085636|186803|207244|649756;3379134|976|200643|171549|2005519|397864|487174;3379134|976|200643|171549|1853231|574697|544645;1783272|201174|84998|84999|84107|102106|1907654;1783272|1239|186801|186802|2211178|2211183;3379134|976|200643|171549|2005525|375288|328812;3379134|976|200643|171549|171552|2974251|165179,Complete,NA
bsdb:39191760/10/2,39191760,"randomized controlled trial,time series / longitudinal observational",39191760,10.1038/s41522-024-00549-x,https://www.nature.com/articles/s41522-024-00549-x,"Hartikainen A.K., Jalanka J., Lahtinen P., Ponsero A.J., Mertsalmi T., Finnegan L., Crispie F., Cotter P.D., Arkkila P. , Satokari R.",Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients,NPJ biofilms and microbiomes,2024,NA,Experiment 10,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Baseline (BL) group,Fecal microbiota transplantation (FMT) from universal healthy donor group at 4 weeks,Patients who received a single fecal microbiota transplantation (FMT)  from a universal donor at 4 weeks,49,23,NA,16S,34,Illumina,log transformation,MaAsLin2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"fig Supplementary 3a, Supplementary 3b, Supplementary Table 3",14 November 2025,Chyono2,Chyono2,"Differential abundance testing on luminal metagenomics at species-level with Maaslin2
FMT group follow-up time points vs. baseline",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CS29,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella sp. CB20,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Metazoa|p__Arthropoda|c__Insecta|o__Hymenoptera|f__Eulophidae|s__Eulophinae|s__Eulophinae gen. euloHansson01 sp. Hansson53,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Massilioclostridium|s__Massilioclostridium coli",1783272|1239|186801|3085636|186803|207244|649756;3379134|976|200643|171549|815|816|817;1783272|1239|186801|186802|31979|1485|165176;1783272|201174|84998|84999|84107|102106|165181;1783272|201174|84998|1643822|1643826|84111|84112;33208|6656|50557|7399|107755|150275|1139886;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|186802|31979|1935927|1870991,Complete,NA
bsdb:39191760/11/1,39191760,"randomized controlled trial,time series / longitudinal observational",39191760,10.1038/s41522-024-00549-x,https://www.nature.com/articles/s41522-024-00549-x,"Hartikainen A.K., Jalanka J., Lahtinen P., Ponsero A.J., Mertsalmi T., Finnegan L., Crispie F., Cotter P.D., Arkkila P. , Satokari R.",Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients,NPJ biofilms and microbiomes,2024,NA,Experiment 11,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Baseline (BL) group,Fecal microbiota transplantation (FMT) from universal healthy donor group at 12weeks,Patients who received a single fecal microbiota transplantation (FMT)  from a universal donor at 12 weeks,49,23,NA,16S,34,Illumina,log transformation,MaAsLin2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"fig Supplementary 3a, Supplementary 3b, Supplementary Table 3",15 November 2025,Chyono2,Chyono2,"Differential abundance testing on luminal metagenomics at species-level with Maaslin2
FMT group follow-up time points vs. baseline",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri",3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|2005525|375288|328812;3379134|976|200643|171549|171552|2974251|165179,Complete,NA
bsdb:39191760/11/2,39191760,"randomized controlled trial,time series / longitudinal observational",39191760,10.1038/s41522-024-00549-x,https://www.nature.com/articles/s41522-024-00549-x,"Hartikainen A.K., Jalanka J., Lahtinen P., Ponsero A.J., Mertsalmi T., Finnegan L., Crispie F., Cotter P.D., Arkkila P. , Satokari R.",Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients,NPJ biofilms and microbiomes,2024,NA,Experiment 11,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Baseline (BL) group,Fecal microbiota transplantation (FMT) from universal healthy donor group at 12weeks,Patients who received a single fecal microbiota transplantation (FMT)  from a universal donor at 12 weeks,49,23,NA,16S,34,Illumina,log transformation,MaAsLin2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"fig Supplementary 3a, Supplementary 3b, Supplementary Table 3",15 November 2025,Chyono2,Chyono2,"Differential abundance testing on luminal metagenomics at species-level with Maaslin2
FMT group follow-up time points vs. baseline",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,1783272|1239|186801|186802|216572|946234|292800,Complete,NA
bsdb:39191760/12/1,39191760,"randomized controlled trial,time series / longitudinal observational",39191760,10.1038/s41522-024-00549-x,https://www.nature.com/articles/s41522-024-00549-x,"Hartikainen A.K., Jalanka J., Lahtinen P., Ponsero A.J., Mertsalmi T., Finnegan L., Crispie F., Cotter P.D., Arkkila P. , Satokari R.",Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients,NPJ biofilms and microbiomes,2024,NA,Experiment 12,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Baseline (BL) group,Fecal microbiota transplantation (FMT) from universal healthy donor group at 26 weeks,Patients who received a single fecal microbiota transplantation (FMT)  from a universal donor at 26 weeks,49,23,NA,16S,34,Illumina,log transformation,MaAsLin2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"fig Supplementary 3a, Supplementary 3b, Supplementary Table 3",15 November 2025,Chyono2,Chyono2,"Differential abundance testing on luminal metagenomics at species-level with Maaslin2
FMT group follow-up time points vs. baseline",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister histaminiformans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri",3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|171550|239759|1288121;3379134|976|200643|171549|171550|239759|328814;1783272|1239|909932|1843489|31977|39948|209880;3379134|976|200643|171549|171552|2974251|165179,Complete,NA
bsdb:39191760/12/2,39191760,"randomized controlled trial,time series / longitudinal observational",39191760,10.1038/s41522-024-00549-x,https://www.nature.com/articles/s41522-024-00549-x,"Hartikainen A.K., Jalanka J., Lahtinen P., Ponsero A.J., Mertsalmi T., Finnegan L., Crispie F., Cotter P.D., Arkkila P. , Satokari R.",Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients,NPJ biofilms and microbiomes,2024,NA,Experiment 12,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Baseline (BL) group,Fecal microbiota transplantation (FMT) from universal healthy donor group at 26 weeks,Patients who received a single fecal microbiota transplantation (FMT)  from a universal donor at 26 weeks,49,23,NA,16S,34,Illumina,log transformation,MaAsLin2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"fig Supplementary 3a, Supplementary 3b, Supplementary Table 3",15 November 2025,Chyono2,Chyono2,"Differential abundance testing on luminal metagenomics at species-level with Maaslin2
FMT group follow-up time points vs. baseline",decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella sp. CB20,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Massilioclostridium|s__Massilioclostridium coli",1783272|201174|84998|84999|84107|102106|165181;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|186802|31979|1935927|1870991,Complete,NA
bsdb:39191760/13/1,39191760,"randomized controlled trial,time series / longitudinal observational",39191760,10.1038/s41522-024-00549-x,https://www.nature.com/articles/s41522-024-00549-x,"Hartikainen A.K., Jalanka J., Lahtinen P., Ponsero A.J., Mertsalmi T., Finnegan L., Crispie F., Cotter P.D., Arkkila P. , Satokari R.",Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients,NPJ biofilms and microbiomes,2024,NA,Experiment 13,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Baseline (BL) group,Fecal microbiota transplantation (FMT) from universal healthy donor group at 52 weeks,Patients who received a single fecal microbiota transplantation (FMT)  from a universal donor at 52 weeks,49,23,NA,16S,34,Illumina,log transformation,MaAsLin2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"fig Supplementary 3a, Supplementary 3b, Supplementary Table 3",15 November 2025,Chyono2,Chyono2,"Differential abundance testing on luminal metagenomics at species-level with Maaslin2
FMT group follow-up time points vs. baseline",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ndongoniae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella xylaniphila",3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|171550|239759|1288121;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|815|816|1903262;3379134|976|200643|171549|1853231|574697|544645;1783272|1239|526524|526525|128827|1573535|1735;3379134|976|200643|171549|2005525|375288|328812;3379134|976|200643|171549|171552|577309|454155,Complete,NA
bsdb:39191760/13/2,39191760,"randomized controlled trial,time series / longitudinal observational",39191760,10.1038/s41522-024-00549-x,https://www.nature.com/articles/s41522-024-00549-x,"Hartikainen A.K., Jalanka J., Lahtinen P., Ponsero A.J., Mertsalmi T., Finnegan L., Crispie F., Cotter P.D., Arkkila P. , Satokari R.",Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients,NPJ biofilms and microbiomes,2024,NA,Experiment 13,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Baseline (BL) group,Fecal microbiota transplantation (FMT) from universal healthy donor group at 52 weeks,Patients who received a single fecal microbiota transplantation (FMT)  from a universal donor at 52 weeks,49,23,NA,16S,34,Illumina,log transformation,MaAsLin2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"fig Supplementary 3a, Supplementary 3b, Supplementary Table 3",15 November 2025,Chyono2,Chyono2,"Differential abundance testing on luminal metagenomics at species-level with Maaslin2
FMT group follow-up time points vs. baseline",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella sp. CB20,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii",3379134|976|200643|171549|815|816|371601;1783272|201174|84998|84999|84107|102106|165181;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|186802|216572|946234|292800,Complete,NA
bsdb:39192744/1/1,39192744,case-control,39192744,10.1002/mds.29959,NA,"Metcalfe-Roach A., Cirstea M.S., Yu A.C., Ramay H.R., Coker O., Boroomand S., Kharazyan F., Martino D., Sycuro L.K., Appel-Cresswell S. , Finlay B.B.",Metagenomic Analysis Reveals Large-Scale Disruptions of the Gut Microbiome in Parkinson's Disease,Movement disorders : official journal of the Movement Disorder Society,2024,"Parkinson's disease, metagenomics, microbiome",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls (Ctrl),Parkinson’s disease patients (PD patients - Assymetric),"Parkinson’s disease patients (PD patients) refers to participants with PD; who had developed motor symptoms ≤12 years before initial study participation (mean, 6 ± 3 years).  Asymmetric motor phenotypes were defined as those with absolute differences above the median.",100,NA,3 months,WMS,NA,Illumina,centered log-ratio,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. S3,26 February 2025,KateRasheed,KateRasheed,Differential abundance of taxa between Control and PD,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum",1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|186801|3085636|186803|572511|40520,Complete,Svetlana up
bsdb:39192744/1/2,39192744,case-control,39192744,10.1002/mds.29959,NA,"Metcalfe-Roach A., Cirstea M.S., Yu A.C., Ramay H.R., Coker O., Boroomand S., Kharazyan F., Martino D., Sycuro L.K., Appel-Cresswell S. , Finlay B.B.",Metagenomic Analysis Reveals Large-Scale Disruptions of the Gut Microbiome in Parkinson's Disease,Movement disorders : official journal of the Movement Disorder Society,2024,"Parkinson's disease, metagenomics, microbiome",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls (Ctrl),Parkinson’s disease patients (PD patients - Assymetric),"Parkinson’s disease patients (PD patients) refers to participants with PD; who had developed motor symptoms ≤12 years before initial study participation (mean, 6 ± 3 years).  Asymmetric motor phenotypes were defined as those with absolute differences above the median.",100,NA,3 months,WMS,NA,Illumina,centered log-ratio,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. S3,26 February 2025,KateRasheed,KateRasheed,Differential abundance of taxa between Control and PD,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|186802|216572|216851|853,Complete,Svetlana up
bsdb:39192744/2/1,39192744,case-control,39192744,10.1002/mds.29959,NA,"Metcalfe-Roach A., Cirstea M.S., Yu A.C., Ramay H.R., Coker O., Boroomand S., Kharazyan F., Martino D., Sycuro L.K., Appel-Cresswell S. , Finlay B.B.",Metagenomic Analysis Reveals Large-Scale Disruptions of the Gut Microbiome in Parkinson's Disease,Movement disorders : official journal of the Movement Disorder Society,2024,"Parkinson's disease, metagenomics, microbiome",Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls (Ctrl),Parkinson’s disease patients (PD patients - Symmetric),"A ""symmetric motor phenotype"" in Parkinson's disease (PD) refers to a presentation where the motor symptoms like tremor, rigidity, and bradykinesia are equally present on both sides of the body, meaning the disease affects both sides of the body almost identically",100,NA,3 months,WMS,NA,Illumina,centered log-ratio,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. S3,26 February 2025,KateRasheed,KateRasheed,Differential abundance of taxa between Control and PD,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans",1783272|1239|186801|3085636|186803|572511|40520;1783272|201174|84998|84999|84107|102106|74426;3379134|976|200643|171549|171550|239759|626932;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|186802|216572|1905344|1550024,Complete,Svetlana up
bsdb:39192744/2/2,39192744,case-control,39192744,10.1002/mds.29959,NA,"Metcalfe-Roach A., Cirstea M.S., Yu A.C., Ramay H.R., Coker O., Boroomand S., Kharazyan F., Martino D., Sycuro L.K., Appel-Cresswell S. , Finlay B.B.",Metagenomic Analysis Reveals Large-Scale Disruptions of the Gut Microbiome in Parkinson's Disease,Movement disorders : official journal of the Movement Disorder Society,2024,"Parkinson's disease, metagenomics, microbiome",Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls (Ctrl),Parkinson’s disease patients (PD patients - Symmetric),"A ""symmetric motor phenotype"" in Parkinson's disease (PD) refers to a presentation where the motor symptoms like tremor, rigidity, and bradykinesia are equally present on both sides of the body, meaning the disease affects both sides of the body almost identically",100,NA,3 months,WMS,NA,Illumina,centered log-ratio,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. S3,26 February 2025,KateRasheed,KateRasheed,Differential abundance of taxa between Control and PD,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|186802|216572|216851|853,Complete,Svetlana up
bsdb:39192744/3/1,39192744,case-control,39192744,10.1002/mds.29959,NA,"Metcalfe-Roach A., Cirstea M.S., Yu A.C., Ramay H.R., Coker O., Boroomand S., Kharazyan F., Martino D., Sycuro L.K., Appel-Cresswell S. , Finlay B.B.",Metagenomic Analysis Reveals Large-Scale Disruptions of the Gut Microbiome in Parkinson's Disease,Movement disorders : official journal of the Movement Disorder Society,2024,"Parkinson's disease, metagenomics, microbiome",Experiment 3,Canada,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls (Ctrl),Parkinson’s disease patients (PD patients),"Parkinson’s disease patients (PD patients) refers to participants with PD; who had developed motor symptoms ≤12 years before initial study participation (mean, 6 ± 3 years).",100,176,3 months,WMS,NA,Illumina,centered log-ratio,"Kruskall-Wallis,ANCOM-BC,MaAsLin2",0.05,TRUE,NA,age,"sequence read depth,sex",NA,NA,NA,NA,NA,NA,Signature 1,Fig. 2A,27 February 2025,KateRasheed,KateRasheed,"Differentially abundance of species between healthy controls and PD patients using ANCOM-BC, MaAsLin2, and ALDEx2 (after controlling for confounders).",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum",1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|186802|216572|1905344|1550024;3379134|976|200643|171549|171550|239759|626932;1783272|1239|186801|3085636|186803|572511|40520,Complete,Svetlana up
bsdb:39192744/3/2,39192744,case-control,39192744,10.1002/mds.29959,NA,"Metcalfe-Roach A., Cirstea M.S., Yu A.C., Ramay H.R., Coker O., Boroomand S., Kharazyan F., Martino D., Sycuro L.K., Appel-Cresswell S. , Finlay B.B.",Metagenomic Analysis Reveals Large-Scale Disruptions of the Gut Microbiome in Parkinson's Disease,Movement disorders : official journal of the Movement Disorder Society,2024,"Parkinson's disease, metagenomics, microbiome",Experiment 3,Canada,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls (Ctrl),Parkinson’s disease patients (PD patients),"Parkinson’s disease patients (PD patients) refers to participants with PD; who had developed motor symptoms ≤12 years before initial study participation (mean, 6 ± 3 years).",100,176,3 months,WMS,NA,Illumina,centered log-ratio,"Kruskall-Wallis,ANCOM-BC,MaAsLin2",0.05,TRUE,NA,age,"sequence read depth,sex",NA,NA,NA,NA,NA,NA,Signature 2,Fig. 2A,27 February 2025,KateRasheed,KateRasheed,"Differentially abundance of species between healthy controls and PD patients using ANCOM-BC, MaAsLin2, and ALDEx2 (after controlling for confounders).",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae",1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|572511|418240,Complete,Svetlana up
bsdb:39192744/4/1,39192744,case-control,39192744,10.1002/mds.29959,NA,"Metcalfe-Roach A., Cirstea M.S., Yu A.C., Ramay H.R., Coker O., Boroomand S., Kharazyan F., Martino D., Sycuro L.K., Appel-Cresswell S. , Finlay B.B.",Metagenomic Analysis Reveals Large-Scale Disruptions of the Gut Microbiome in Parkinson's Disease,Movement disorders : official journal of the Movement Disorder Society,2024,"Parkinson's disease, metagenomics, microbiome",Experiment 4,Canada,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls (Ctrl),Parkinson’s disease patients (PD patients),"Parkinson’s disease patients (PD patients) refers to participants with PD; who had developed motor symptoms ≤12 years before initial study participation (mean, 6 ± 3 years).",100,176,3 months,WMS,NA,Illumina,centered log-ratio,"Kruskall-Wallis,MaAsLin2,ANCOM-BC",0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 2A,27 February 2025,KateRasheed,KateRasheed,"Differentially abundance of species between healthy controls and PD patients using ANCOM-BC, MaAsLin2, and ALDEx2.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans",3379134|976|200643|171549|171550|239759|626932;1783272|1239|186801|3085636|186803|572511|40520;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|186802|216572|1905344|1550024,Complete,Svetlana up
bsdb:39192744/4/2,39192744,case-control,39192744,10.1002/mds.29959,NA,"Metcalfe-Roach A., Cirstea M.S., Yu A.C., Ramay H.R., Coker O., Boroomand S., Kharazyan F., Martino D., Sycuro L.K., Appel-Cresswell S. , Finlay B.B.",Metagenomic Analysis Reveals Large-Scale Disruptions of the Gut Microbiome in Parkinson's Disease,Movement disorders : official journal of the Movement Disorder Society,2024,"Parkinson's disease, metagenomics, microbiome",Experiment 4,Canada,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls (Ctrl),Parkinson’s disease patients (PD patients),"Parkinson’s disease patients (PD patients) refers to participants with PD; who had developed motor symptoms ≤12 years before initial study participation (mean, 6 ± 3 years).",100,176,3 months,WMS,NA,Illumina,centered log-ratio,"Kruskall-Wallis,MaAsLin2,ANCOM-BC",0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 2A,27 February 2025,KateRasheed,KateRasheed,"Differentially abundance of species between healthy controls and PD patients using ANCOM-BC, MaAsLin2, and ALDEx2.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans",1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|841|360807,Complete,Svetlana up
bsdb:39194187/1/1,39194187,"cross-sectional observational, not case-control",39194187,https://doi.org/10.1128/mbio.02023-24,https://journals.asm.org/doi/10.1128/mbio.02023-24,"Wang L., Xu Y., Li L., Yang B., Zhao D., Ye C., Lin Z., Cui J., Liu Y., Zhu W., Li N., Tian H. , Chen Q.",The impact of small intestinal bacterial overgrowth on the efficacy of fecal microbiota transplantation in patients with chronic constipation,mBio,2024,"chronic constipation, efficacy, fecal microbiota transplantation, small intestinal bacterial overgrowth",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,PosF0 - Fecal sample in Small intestinal bacterial overgrowth group (SIBO group) at pre-FMT,PosF7 - Fecal sample in Small intestinal bacterial overgrowth group (SIBO group) seven days after FMT,Small intestinal bacterial overgrowth (SIBO) group seven days after FMT,88,88,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3A,21 March 2025,Miss Lulu,Miss Lulu,Represents the LEfSe analysis of the colon microbiota and small intestinal microbiota for two groups of patients.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:39194187/1/2,39194187,"cross-sectional observational, not case-control",39194187,https://doi.org/10.1128/mbio.02023-24,https://journals.asm.org/doi/10.1128/mbio.02023-24,"Wang L., Xu Y., Li L., Yang B., Zhao D., Ye C., Lin Z., Cui J., Liu Y., Zhu W., Li N., Tian H. , Chen Q.",The impact of small intestinal bacterial overgrowth on the efficacy of fecal microbiota transplantation in patients with chronic constipation,mBio,2024,"chronic constipation, efficacy, fecal microbiota transplantation, small intestinal bacterial overgrowth",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,PosF0 - Fecal sample in Small intestinal bacterial overgrowth group (SIBO group) at pre-FMT,PosF7 - Fecal sample in Small intestinal bacterial overgrowth group (SIBO group) seven days after FMT,Small intestinal bacterial overgrowth (SIBO) group seven days after FMT,88,88,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3A,21 March 2025,Miss Lulu,Miss Lulu,Represents the LEfSe analysis of the colon microbiota and small intestinal microbiota for two groups of patients.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236;3379134|1224;3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:39194187/2/1,39194187,"cross-sectional observational, not case-control",39194187,https://doi.org/10.1128/mbio.02023-24,https://journals.asm.org/doi/10.1128/mbio.02023-24,"Wang L., Xu Y., Li L., Yang B., Zhao D., Ye C., Lin Z., Cui J., Liu Y., Zhu W., Li N., Tian H. , Chen Q.",The impact of small intestinal bacterial overgrowth on the efficacy of fecal microbiota transplantation in patients with chronic constipation,mBio,2024,"chronic constipation, efficacy, fecal microbiota transplantation, small intestinal bacterial overgrowth",Experiment 2,China,Homo sapiens,Small intestine,UBERON:0002108,Response to transplant,EFO:0007043,NegI7-small intestine sample in Small intestinal bacterial overgrowth group (Non-SIBO group) 7 days after FMT,POSI0-small intestine sample in Small intestinal bacterial overgrowth group (SIBO group) at pre-FMT,Small intestinal bacterial overgrowth (SIBO) group before FMT,130,88,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 3D,21 March 2025,Miss Lulu,Miss Lulu,Represents the LEfSe analysis of the colon microbiota and small intestinal microbiota for two groups of patients.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|1940338;3379134|1224|1236;3379134|1224,Complete,Svetlana up
bsdb:39194187/2/2,39194187,"cross-sectional observational, not case-control",39194187,https://doi.org/10.1128/mbio.02023-24,https://journals.asm.org/doi/10.1128/mbio.02023-24,"Wang L., Xu Y., Li L., Yang B., Zhao D., Ye C., Lin Z., Cui J., Liu Y., Zhu W., Li N., Tian H. , Chen Q.",The impact of small intestinal bacterial overgrowth on the efficacy of fecal microbiota transplantation in patients with chronic constipation,mBio,2024,"chronic constipation, efficacy, fecal microbiota transplantation, small intestinal bacterial overgrowth",Experiment 2,China,Homo sapiens,Small intestine,UBERON:0002108,Response to transplant,EFO:0007043,NegI7-small intestine sample in Small intestinal bacterial overgrowth group (Non-SIBO group) 7 days after FMT,POSI0-small intestine sample in Small intestinal bacterial overgrowth group (SIBO group) at pre-FMT,Small intestinal bacterial overgrowth (SIBO) group before FMT,130,88,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 3D,21 March 2025,Miss Lulu,Miss Lulu,Changes in gut microbiota after FMT in two groups of patients: the SIBO group and the non-SIBO group,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061;1783272|1239;1783272|1239|91061|186826;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:39194187/3/1,39194187,"cross-sectional observational, not case-control",39194187,https://doi.org/10.1128/mbio.02023-24,https://journals.asm.org/doi/10.1128/mbio.02023-24,"Wang L., Xu Y., Li L., Yang B., Zhao D., Ye C., Lin Z., Cui J., Liu Y., Zhu W., Li N., Tian H. , Chen Q.",The impact of small intestinal bacterial overgrowth on the efficacy of fecal microbiota transplantation in patients with chronic constipation,mBio,2024,"chronic constipation, efficacy, fecal microbiota transplantation, small intestinal bacterial overgrowth",Experiment 3,China,Homo sapiens,Small intestine,UBERON:0002108,Response to transplant,EFO:0007043,NegI0-small intestine sample in Small intestinal bacterial overgrowth group (Non-SIBO group) at pre-FMT,POSI0-small intestine sample in Small intestinal bacterial overgrowth group (SIBO group) at pre-FMT,Small intestinal bacterial overgrowth (SIBO) group before FMT,130,88,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 5A,21 March 2025,Miss Lulu,Miss Lulu,Gut microbiota differences between the small intestinal microbiota of two groups were identified with a LEfSe analysis with an LDA score threshold >2.0.,decreased,"k__Pseudomonadati|p__Acidobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Obscuribacterales|f__Candidatus Obscuribacteraceae|g__Candidatus Obscuribacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus geothermalis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Devosia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia|s__Eggerthia catenaformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Geminicoccales|f__Geminicoccaceae,k__Pseudomonadati|p__Gemmatimonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Gracilibacteraceae|g__Gracilibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Gracilibacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK3A20,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter|s__Psychrobacter sanguinis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Salinarimonadaceae|g__Salinarimonas|s__Salinarimonas sp.,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Sphaerochaetaceae|g__Sphaerochaeta",3379134|57723;1783272|1239|186801|3085636|186803|207244;1783272|1798710|1906152|3121626|1906156;3379134|976|117743|200644|2762318|59732;3384194|1297|188787|118964|183710|1298|68909;3379134|1224|28211|356|2831106|46913;3379134|1224|28211|356|2831106;1783272|1239|526524|526525|2810280|1279384;1783272|1239|526524|526525|2810280|1279384|31973;1783272|1239|186801|186802;3379134|1224|28211|3108222|2066434;3379134|142182;1783272|1239|186801|186802|541019|342658;1783272|1239|186801|186802|541019;1783272|1239|186801|3085636|186803|877406;3379134|1224|1236|2887326|468|497|861445;3379134|1224|28211|356|2137278|690086|2766526;3379134|203691|203692|136|2791015|399320,Complete,Svetlana up
bsdb:39194187/3/2,39194187,"cross-sectional observational, not case-control",39194187,https://doi.org/10.1128/mbio.02023-24,https://journals.asm.org/doi/10.1128/mbio.02023-24,"Wang L., Xu Y., Li L., Yang B., Zhao D., Ye C., Lin Z., Cui J., Liu Y., Zhu W., Li N., Tian H. , Chen Q.",The impact of small intestinal bacterial overgrowth on the efficacy of fecal microbiota transplantation in patients with chronic constipation,mBio,2024,"chronic constipation, efficacy, fecal microbiota transplantation, small intestinal bacterial overgrowth",Experiment 3,China,Homo sapiens,Small intestine,UBERON:0002108,Response to transplant,EFO:0007043,NegI0-small intestine sample in Small intestinal bacterial overgrowth group (Non-SIBO group) at pre-FMT,POSI0-small intestine sample in Small intestinal bacterial overgrowth group (SIBO group) at pre-FMT,Small intestinal bacterial overgrowth (SIBO) group before FMT,130,88,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 5A,21 March 2025,Miss Lulu,Miss Lulu,Gut microbiota differences between the small intestinal microbiota of two groups were identified with a LEfSe analysis with an LDA score threshold >2.0.,increased,"k__Thermotogati|p__Deinococcota|c__Deinococci,k__Thermotogati|p__Deinococcota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Meiothermus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales",3384194|1297|188787;3384194|1297;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;3384194|1297|188787|68933|188786|65551;3379134|1224|28211|204457|41297;3379134|1224|28211|204457;3379134|1224|28211|204457|41297|13687;3384194|1297|188787|68933|188786;3384194|1297|188787|68933,Complete,Svetlana up
bsdb:39198450/1/1,39198450,"cross-sectional observational, not case-control",39198450,10.1038/s41522-024-00542-4,https://pubmed.ncbi.nlm.nih.gov/39198450/,"Licht P., Dominelli N., Kleemann J., Pastore S., Müller E.S., Haist M., Hartmann K.S., Stege H., Bros M., Meissner M., Grabbe S., Heermann R. , Mailänder V.",The skin microbiome stratifies patients with cutaneous T cell lymphoma and determines event-free survival,NPJ biofilms and microbiomes,2024,NA,Experiment 1,Germany,Homo sapiens,Skin epidermis,UBERON:0001003,Cutaneous T-cell lymphoma,EFO:0002913,Healthy control( ΔSA-neutral subgroup),Mycosis fungoides( ΔSA-positive),"Patients with significant dysbiosis on MF lesions exhibiting S. aureus expansion. Antimicrobial peptides (AMPs) were probably less prevalent when the overgrowth occurred, and S. aureus was able to adapt to these peptides to become a more virulent strain on the lesions.",20,20,1 month,PCR,NA,Illumina,raw counts,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"fig 2b, d-g",3 October 2024,Jayybb,"Jayybb,Peace Sandy,WikiWorks",Differential abundance analysis of microbial species for N = 65 metagenomic samples.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,1783272|1239|91061|1385|90964|1279|1280,Complete,Peace Sandy
bsdb:39198450/1/2,39198450,"cross-sectional observational, not case-control",39198450,10.1038/s41522-024-00542-4,https://pubmed.ncbi.nlm.nih.gov/39198450/,"Licht P., Dominelli N., Kleemann J., Pastore S., Müller E.S., Haist M., Hartmann K.S., Stege H., Bros M., Meissner M., Grabbe S., Heermann R. , Mailänder V.",The skin microbiome stratifies patients with cutaneous T cell lymphoma and determines event-free survival,NPJ biofilms and microbiomes,2024,NA,Experiment 1,Germany,Homo sapiens,Skin epidermis,UBERON:0001003,Cutaneous T-cell lymphoma,EFO:0002913,Healthy control( ΔSA-neutral subgroup),Mycosis fungoides( ΔSA-positive),"Patients with significant dysbiosis on MF lesions exhibiting S. aureus expansion. Antimicrobial peptides (AMPs) were probably less prevalent when the overgrowth occurred, and S. aureus was able to adapt to these peptides to become a more virulent strain on the lesions.",20,20,1 month,PCR,NA,Illumina,raw counts,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,"fig 2b, d-g",3 October 2024,Jayybb,"Jayybb,Peace Sandy,WikiWorks",Differential abundance analysis of microbial species for N = 65 metagenomic samples.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes",1783272|1239|91061|1385|90964|1279|1282;1783272|1239|91061|1385|90964|1279|1290;1783272|201174|1760|85009|31957|1912216|1747,Complete,Peace Sandy
bsdb:39217395/1/1,39217395,"case-control,time series / longitudinal observational",39217395,10.1186/s40001-024-02034-9,https://link.springer.com/article/10.1186/s40001-024-02034-9,"Li X., Jiang B., Gao T., Nian Y., Bai X., Zhong J., Qin L., Gao Z., Wang H. , Ma X.",Effects of inulin on intestinal flora and metabolism-related indicators in obese polycystic ovary syndrome patients,European journal of medical research,2024,"Gut microbiota, Inflammatory, Inulin, Obesity, Polycystic ovary syndrome (PCOS)",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Non-obese control group (NSD),Obese control group (NFD),This group consists of obese patients with ≥ 25 kg/m2 body mass index (BMI).,20,16,3 months,16S,NA,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3E,4 August 2025,Victoria,Victoria,Analysis of Biomarkers with significant differences between groups based on LDA Effect Size.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces massiliensis,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral clone FR058,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",1783272|1239|909932|1843489|31977|209879;3379134|976|200643|171549|2005525|375288|823;1783272|1239|186801|186802|404402;1783272|1239|186801|3085636|186803|2316020|33039;1783272|201174|1760|2037|2049|1654|461393;95818|175646;1783272|1239|909932|909929|1843491|158846,Complete,KateRasheed
bsdb:39217395/1/2,39217395,"case-control,time series / longitudinal observational",39217395,10.1186/s40001-024-02034-9,https://link.springer.com/article/10.1186/s40001-024-02034-9,"Li X., Jiang B., Gao T., Nian Y., Bai X., Zhong J., Qin L., Gao Z., Wang H. , Ma X.",Effects of inulin on intestinal flora and metabolism-related indicators in obese polycystic ovary syndrome patients,European journal of medical research,2024,"Gut microbiota, Inflammatory, Inulin, Obesity, Polycystic ovary syndrome (PCOS)",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Non-obese control group (NSD),Obese control group (NFD),This group consists of obese patients with ≥ 25 kg/m2 body mass index (BMI).,20,16,3 months,16S,NA,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3E,4 August 2025,Victoria,Victoria,Analysis of Biomarkers with significant differences between groups based on LDA Effect Size.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus",3379134|976|200643|171549|815|909656|310297;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803|33042|33043,Complete,KateRasheed
bsdb:39217395/2/1,39217395,"case-control,time series / longitudinal observational",39217395,10.1186/s40001-024-02034-9,https://link.springer.com/article/10.1186/s40001-024-02034-9,"Li X., Jiang B., Gao T., Nian Y., Bai X., Zhong J., Qin L., Gao Z., Wang H. , Ma X.",Effects of inulin on intestinal flora and metabolism-related indicators in obese polycystic ovary syndrome patients,European journal of medical research,2024,"Gut microbiota, Inflammatory, Inulin, Obesity, Polycystic ovary syndrome (PCOS)",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Obese control group (NFD),Obese Polycystic Ovary Syndrome patients (FDB),This group consists of obese patients with ≥ 25 kg/m2 body mass index (BMI) who have polycystic ovary syndrome (PCOS).,16,19,3 months,16S,NA,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3F,4 August 2025,Victoria,Victoria,Analysis of Biomarkers with significant differences between groups based on LDA Effect Size.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella corporis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Beijerinckiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius",1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|91061|186826|1300|1357;3379134|976|200643|171549|171552|838|28128;3379134|1224|28211|356|119045|407;3379134|1224|28211|356|45404;3379134|976|200643|171549|815|909656|310297,Complete,KateRasheed
bsdb:39217395/2/2,39217395,"case-control,time series / longitudinal observational",39217395,10.1186/s40001-024-02034-9,https://link.springer.com/article/10.1186/s40001-024-02034-9,"Li X., Jiang B., Gao T., Nian Y., Bai X., Zhong J., Qin L., Gao Z., Wang H. , Ma X.",Effects of inulin on intestinal flora and metabolism-related indicators in obese polycystic ovary syndrome patients,European journal of medical research,2024,"Gut microbiota, Inflammatory, Inulin, Obesity, Polycystic ovary syndrome (PCOS)",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Obese control group (NFD),Obese Polycystic Ovary Syndrome patients (FDB),This group consists of obese patients with ≥ 25 kg/m2 body mass index (BMI) who have polycystic ovary syndrome (PCOS).,16,19,3 months,16S,NA,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3F,4 August 2025,Victoria,Victoria,Analysis of Biomarkers with significant differences between groups based on LDA Effect Size.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,s__bacterium LD2013,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. MC 40,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii",1783272|1239|91061|186826|33958|2767887|1623;3379134|976|200643|171549|171552|1283313;1451860;1783272|1239|186801|186802|31979|1485|2683682;1783272|1239|526524|526525|128827|1573535;3379134|976|200643|171549|815|816|28111,Complete,KateRasheed
bsdb:39217395/3/1,39217395,"case-control,time series / longitudinal observational",39217395,10.1186/s40001-024-02034-9,https://link.springer.com/article/10.1186/s40001-024-02034-9,"Li X., Jiang B., Gao T., Nian Y., Bai X., Zhong J., Qin L., Gao Z., Wang H. , Ma X.",Effects of inulin on intestinal flora and metabolism-related indicators in obese polycystic ovary syndrome patients,European journal of medical research,2024,"Gut microbiota, Inflammatory, Inulin, Obesity, Polycystic ovary syndrome (PCOS)",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Obese Polycystic Ovary Syndrome patients (FDB) before inulin intervention,Obese Polycystic Ovary Syndrome patients (FDA) after inulin intervention,This group consists of obese patients with ≥ 25 kg/m2 body mass index (BMI) who have polycystic ovary syndrome (PCOS) after 3 months of inulin intervention.,19,13,3 months,16S,NA,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3G,4 August 2025,Victoria,Victoria,Analysis of Biomarkers with significant differences between groups based on LDA Effect Size.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,1783272|1239|186801|3085636|186803|28050,Complete,KateRasheed
bsdb:39217395/3/2,39217395,"case-control,time series / longitudinal observational",39217395,10.1186/s40001-024-02034-9,https://link.springer.com/article/10.1186/s40001-024-02034-9,"Li X., Jiang B., Gao T., Nian Y., Bai X., Zhong J., Qin L., Gao Z., Wang H. , Ma X.",Effects of inulin on intestinal flora and metabolism-related indicators in obese polycystic ovary syndrome patients,European journal of medical research,2024,"Gut microbiota, Inflammatory, Inulin, Obesity, Polycystic ovary syndrome (PCOS)",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Obese Polycystic Ovary Syndrome patients (FDB) before inulin intervention,Obese Polycystic Ovary Syndrome patients (FDA) after inulin intervention,This group consists of obese patients with ≥ 25 kg/m2 body mass index (BMI) who have polycystic ovary syndrome (PCOS) after 3 months of inulin intervention.,19,13,3 months,16S,NA,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3G,4 August 2025,Victoria,Victoria,Analysis of Biomarkers with significant differences between groups based on LDA Effect Size.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis",3379134|1224|28216|80840|995019|40544;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1357;3379134|1224|1236|91347|543|547;3379134|1224|28211|204441;1783272|1239|91061|186826|1300|1357|1358,Complete,KateRasheed
bsdb:39217395/4/1,39217395,"case-control,time series / longitudinal observational",39217395,10.1186/s40001-024-02034-9,https://link.springer.com/article/10.1186/s40001-024-02034-9,"Li X., Jiang B., Gao T., Nian Y., Bai X., Zhong J., Qin L., Gao Z., Wang H. , Ma X.",Effects of inulin on intestinal flora and metabolism-related indicators in obese polycystic ovary syndrome patients,European journal of medical research,2024,"Gut microbiota, Inflammatory, Inulin, Obesity, Polycystic ovary syndrome (PCOS)",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Obese control group (NFD),Obese Polycystic Ovary Syndrome patients (FDA) after inulin intervention,This group consists of obese patients with ≥ 25 kg/m2 body mass index (BMI) who have polycystic ovary syndrome (PCOS) after 3 months of inulin intervention.,16,13,3 months,16S,NA,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3H,4 August 2025,Victoria,Victoria,Analysis of Biomarkers with significant differences between groups based on LDA Effect Size.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Beijerinckiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides johnsonii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacterium|s__Amedibacterium intestinale,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium varium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",3379134|1224|28211|356|45404;3379134|1224|28211|356|119045|407;3379134|976|200643|171549|2005525|375288|387661;3379134|1224|1236|135625|712|416916;1783272|1239|526524|526525|128827|2749267|2583452;3379134|1224|1236|135625|712|416916|739;3384189|32066|203490|203491|203492|848|856;1783272|1239|186801|3085636|186803|207244;3384189|32066|203490|203491|203492|848|850;3384189|32066;3384189|32066|203490;3384189|32066|203490|203491;3384189|32066|203490|203491|203492;3384189|32066|203490|203491|203492|848,Complete,KateRasheed
bsdb:39217395/4/2,39217395,"case-control,time series / longitudinal observational",39217395,10.1186/s40001-024-02034-9,https://link.springer.com/article/10.1186/s40001-024-02034-9,"Li X., Jiang B., Gao T., Nian Y., Bai X., Zhong J., Qin L., Gao Z., Wang H. , Ma X.",Effects of inulin on intestinal flora and metabolism-related indicators in obese polycystic ovary syndrome patients,European journal of medical research,2024,"Gut microbiota, Inflammatory, Inulin, Obesity, Polycystic ovary syndrome (PCOS)",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Obese control group (NFD),Obese Polycystic Ovary Syndrome patients (FDA) after inulin intervention,This group consists of obese patients with ≥ 25 kg/m2 body mass index (BMI) who have polycystic ovary syndrome (PCOS) after 3 months of inulin intervention.,16,13,3 months,16S,NA,Ion Torrent,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3H,4 August 2025,Victoria,"Victoria,Fiddyhamma",Analysis of Biomarkers with significant differences between groups based on LDA Effect Size.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Liu et al. 2021),k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii",1783272|1239|909932|1843488|909930;3379134|976|200643|171549|815|816|246787;1783272|1239|186801|3082768|990719;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|186802|216572|1263|3062497;1783272|1239|186801|3085636|186803|2316020|33039;3379134|976|200643|171549|815|816|28111,Complete,KateRasheed
bsdb:39223134/1/1,39223134,case-control,39223134,10.1038/s41467-024-51464-w,NA,"Tesfaw G., Siraj D.S., Abdissa A., Jakobsen R.R., Johansen Ø.H., Zangenberg M., Hanevik K., Mekonnen Z., Langeland N., Bjørang O., Safdar N., Mapes A.C., Kates A., Krych L., Castro-Mejía J.L. , Nielsen D.S.",Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia,Nature communications,2024,NA,Experiment 1,Ethiopia,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,healthy controls,Diarrhea,Children under 5 years with Acute(AD) and Prolonged or persistent diarrhea(ProPD),663,650,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,region of residence,sex,time","age,breast feeding,education level,geographic area,sex,time",NA,increased,NA,NA,NA,increased,Signature 1,Supplementary Table 1,4 October 2024,Cateline Ouma,"Cateline Ouma,Peace Sandy,WikiWorks",This is a box plot that compares the relative abundance of bacterial taxa in Ethiopian children with diarrhea (both acute and prolonged/persistent) to that in non-diarrheal controls.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|1224|1236|91347|543|561|1884818;3379134|1224|1236|135625|712|724|729;1783272|1239|91061|186826|33958|2767887|1623;1783272|1239|909932|1843489|31977|29465|39778;;3379134|29547|3031852|213849|72294|194;3379134|1224|1236|91347|543;1783272|1239|91061|186826|1300|1301,Complete,Peace Sandy
bsdb:39223134/1/2,39223134,case-control,39223134,10.1038/s41467-024-51464-w,NA,"Tesfaw G., Siraj D.S., Abdissa A., Jakobsen R.R., Johansen Ø.H., Zangenberg M., Hanevik K., Mekonnen Z., Langeland N., Bjørang O., Safdar N., Mapes A.C., Kates A., Krych L., Castro-Mejía J.L. , Nielsen D.S.",Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia,Nature communications,2024,NA,Experiment 1,Ethiopia,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,healthy controls,Diarrhea,Children under 5 years with Acute(AD) and Prolonged or persistent diarrhea(ProPD),663,650,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,region of residence,sex,time","age,breast feeding,education level,geographic area,sex,time",NA,increased,NA,NA,NA,increased,Signature 2,"Figure 4a, Supplementary Table 1",9 October 2024,Cateline Ouma,"Cateline Ouma,Peace Sandy,WikiWorks",This is a box plot that shows the differential abundance between children with diarrhea (AD and ProPD) and healthy controls.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio|s__Succinivibrio dextrinosolvens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|976|200643|171549|815|816|817;1783272|1239|909932|1843489|31977|39948|487173;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|204475|745368;1783272|1239|91061|186826|33958|2767887|1623;3379134|976|200643|171549|171552|2974251|165179;3379134|1224|1236|135624|83763|83770|83771;1783272|201174|84998|84999|84107;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|909929|1843491|52225;3379134|976|200643|171549|171552,Complete,Peace Sandy
bsdb:39223134/2/1,39223134,case-control,39223134,10.1038/s41467-024-51464-w,NA,"Tesfaw G., Siraj D.S., Abdissa A., Jakobsen R.R., Johansen Ø.H., Zangenberg M., Hanevik K., Mekonnen Z., Langeland N., Bjørang O., Safdar N., Mapes A.C., Kates A., Krych L., Castro-Mejía J.L. , Nielsen D.S.",Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia,Nature communications,2024,NA,Experiment 2,Ethiopia,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Healthy Controls,Acute Diarrhea,Children under 5 years with acute diarrhea that lasted less than 7 days prior to enrollment into the study,663,554,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,region of residence,sex,time","age,breast feeding,education level,geographic area,sex,time",NA,increased,NA,NA,NA,increased,Signature 1,"Figure 4b, Supplementary Table 2",9 October 2024,Cateline Ouma,"Cateline Ouma,Peace Sandy,WikiWorks",A box plot comparing the relative abundance of taxa in children with acute diarrhea (AD) and non-diarrheal controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis",3379134|1224|1236|91347|543|561|1884818;3379134|1224|1236|135625|712|724|729;1783272|1239|909932|1843489|31977|29465|39778;;1783272|201174|1760|85004|31953|1678;3379134|29547|3031852|213849|72294|194;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|33958|2767887|1623,Complete,Peace Sandy
bsdb:39223134/2/2,39223134,case-control,39223134,10.1038/s41467-024-51464-w,NA,"Tesfaw G., Siraj D.S., Abdissa A., Jakobsen R.R., Johansen Ø.H., Zangenberg M., Hanevik K., Mekonnen Z., Langeland N., Bjørang O., Safdar N., Mapes A.C., Kates A., Krych L., Castro-Mejía J.L. , Nielsen D.S.",Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia,Nature communications,2024,NA,Experiment 2,Ethiopia,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Healthy Controls,Acute Diarrhea,Children under 5 years with acute diarrhea that lasted less than 7 days prior to enrollment into the study,663,554,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,region of residence,sex,time","age,breast feeding,education level,geographic area,sex,time",NA,increased,NA,NA,NA,increased,Signature 2,"Figure 4b, Supplementary Table 2",9 October 2024,Cateline Ouma,"Cateline Ouma,Peace Sandy,WikiWorks",A box plot comparing the relative abundance of taxa in children with acute diarrhea (AD) and non-diarrheal controls,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio|s__Succinivibrio dextrinosolvens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella",3379134|976|200643|171549|815|816|817;1783272|1239|909932|1843489|31977|39948|487173;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|204475|745368;3379134|976|200643|171549|171552|2974251|165179;3379134|1224|1236|135624|83763|83770|83771;1783272|201174|84998|84999|84107;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|909929|1843491|52225,Complete,Peace Sandy
bsdb:39223134/3/1,39223134,case-control,39223134,10.1038/s41467-024-51464-w,NA,"Tesfaw G., Siraj D.S., Abdissa A., Jakobsen R.R., Johansen Ø.H., Zangenberg M., Hanevik K., Mekonnen Z., Langeland N., Bjørang O., Safdar N., Mapes A.C., Kates A., Krych L., Castro-Mejía J.L. , Nielsen D.S.",Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia,Nature communications,2024,NA,Experiment 3,Ethiopia,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Healthy Controls,Prolonged or Persistent Diarrhea,A combination of   children whose diarrhea lasted for 7-13 days (Prolonged Diarrhea) and those whose diarrhea lasted for 14 days or longer (Persistent Diarrhea).,663,95,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,region of residence,sex,time","age,breast feeding,geographic area,sex,time",NA,increased,NA,NA,NA,increased,Signature 1,"Figure 4c, Supplementary table 3",11 October 2024,Cateline Ouma,"Cateline Ouma,Rahila,WikiWorks",DESEq2 differential abundance of taxa in children with prolonged or persistent diarrhea (ProPD) and non-diarrheal controls.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",3379134|1224|1236|91347|543|561|1884818;1783272|1239|91061|186826|33958|2742598|97478;1783272|1239|909932|1843489|31977|29465|39778;;3379134|29547|3031852|213849|72294|194;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|2316020|33038,Complete,Peace Sandy
bsdb:39223134/3/2,39223134,case-control,39223134,10.1038/s41467-024-51464-w,NA,"Tesfaw G., Siraj D.S., Abdissa A., Jakobsen R.R., Johansen Ø.H., Zangenberg M., Hanevik K., Mekonnen Z., Langeland N., Bjørang O., Safdar N., Mapes A.C., Kates A., Krych L., Castro-Mejía J.L. , Nielsen D.S.",Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia,Nature communications,2024,NA,Experiment 3,Ethiopia,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Healthy Controls,Prolonged or Persistent Diarrhea,A combination of   children whose diarrhea lasted for 7-13 days (Prolonged Diarrhea) and those whose diarrhea lasted for 14 days or longer (Persistent Diarrhea).,663,95,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,region of residence,sex,time","age,breast feeding,geographic area,sex,time",NA,increased,NA,NA,NA,increased,Signature 2,"Figure 4c, Supplementary table 3",11 October 2024,Cateline Ouma,"Cateline Ouma,Rahila,Peace Sandy,WikiWorks",DESeq2 analysis of differentially abundant taxa,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239|186801|3085636|186803|207244|649756;3379134|976|200643|171549|815|816|817;1783272|1239|909932|1843489|31977|39948|487173;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|204475|745368;3379134|976|200643|171549|171552|2974265|363265;1783272|1239|186801|3085636|186803|841|360807;3379134|976|200643|171549|815|816;1783272|201174|84998|84999|84107;1783272|1239|909932|909929|1843491|52225;1783272|1239|186801|186802|31979|1485,Complete,Peace Sandy
bsdb:39223134/4/1,39223134,case-control,39223134,10.1038/s41467-024-51464-w,NA,"Tesfaw G., Siraj D.S., Abdissa A., Jakobsen R.R., Johansen Ø.H., Zangenberg M., Hanevik K., Mekonnen Z., Langeland N., Bjørang O., Safdar N., Mapes A.C., Kates A., Krych L., Castro-Mejía J.L. , Nielsen D.S.",Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia,Nature communications,2024,NA,Experiment 4,Ethiopia,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Acute Diarrhea,Prolonged or Persistent Diarrhea,Combined cases of prolonged diarrhea (7-13 days) and persistent diarrhea (≥14 days),554,95,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,region of residence,sex,time","age,breast feeding,education level,geographic area,sex,time",NA,decreased,NA,NA,NA,decreased,Signature 1,"Figure 4d, Supplementary Table 4",15 October 2024,Cateline Ouma,"Cateline Ouma,WikiWorks",A box plot showing differential abundance of taxa in ProPD cases versus AD cases.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Peace Sandy
bsdb:39223134/4/2,39223134,case-control,39223134,10.1038/s41467-024-51464-w,NA,"Tesfaw G., Siraj D.S., Abdissa A., Jakobsen R.R., Johansen Ø.H., Zangenberg M., Hanevik K., Mekonnen Z., Langeland N., Bjørang O., Safdar N., Mapes A.C., Kates A., Krych L., Castro-Mejía J.L. , Nielsen D.S.",Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia,Nature communications,2024,NA,Experiment 4,Ethiopia,Homo sapiens,Feces,UBERON:0001988,Diarrhea,HP:0002014,Acute Diarrhea,Prolonged or Persistent Diarrhea,Combined cases of prolonged diarrhea (7-13 days) and persistent diarrhea (≥14 days),554,95,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,region of residence,sex,time","age,breast feeding,education level,geographic area,sex,time",NA,decreased,NA,NA,NA,decreased,Signature 2,"Figure 4d, Supplementary Table 4",15 October 2024,Cateline Ouma,"Cateline Ouma,Peace Sandy,WikiWorks",A box plot comparing the relative abundance of taxa in ProPD cases versus AD cases,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|186801|186802|216572|216851|853;1783272|201174|84998|84999|84107;3379134|976|200643|171549|815|816,Complete,Peace Sandy
bsdb:39235366/1/NA,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,Control Group,LPS-induced SIRS (systemic inflammatory response syndrome) group,Lipopolysaccharide-induced SIRS group represent the disease model receiving treatment. They serve as the primary target for testing the efficacy of therapeutic interventions  aimed at reducing inflammation and restoring gut microbiota balance.,6,6,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:39235366/2/1,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,LPS-induced SIRS (systemic inflammatory response syndrome) group,FMT-L Group,The (Xuanfei Baidu)XFBD-fed group containing live microbiota,6,6,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure S2D,21 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",Specific genus variations used for Fecal Microbiota Transplantation effects of SIRS mice.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:39235366/3/1,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,FMT-L Group,FMT-HK Group,The (Xuanfei Baidu)XFBD-fed group containing heat-killed microbiota,6,6,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure S2A,21 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",Specific genus variations used for the Fecal Microbiota Transplantation effects on microbiota in SIRS mice.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:39235366/4/1,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,LPS-induced SIRS (systemic inflammatory response syndrome) group,FMT-HK Group,The (Xuanfei Baidu)XFBD-fed group containing heat-killed microbiota,6,6,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S2A,21 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",Specific genus variations used for the Fecal Microbiota Transplantation effects on microbiota in SIRS mice.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:39235366/4/2,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,LPS-induced SIRS (systemic inflammatory response syndrome) group,FMT-HK Group,The (Xuanfei Baidu)XFBD-fed group containing heat-killed microbiota,6,6,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S2D,21 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",Specific genus variations used for the Fecal Microbiota Transplantation effects on microbiota in SIRS mice.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:39235366/5/NA,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,N (uncultured control),M (Uncultured Model),SIRS fecal sample before in vitro culture,3,3,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:39235366/6/NA,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,M (Uncultured Model Group),MD (Cultured Model Group),Microbial composition from the fecal content of LPS-induced SIRS mice after the in vitro culturing process.,3,3,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:39235366/7/2,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 7,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,ND (cultured control),MD (cultured model),Microbial composition from the fecal content of LPS-induced SIRS mice after the in vitro culturing process,3,3,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S5D,23 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",The relative abundance in genus levels after cocktail treatment,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:39235366/10/1,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 10,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,N,M,Uncultured Model,3,3,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 5B,23 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",A waterfall plot of significantly altered genus between model and control showing consistent trend in uncultured groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Asaccharospora,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",3379134|976|200643|171549|815|816;3379134|1224|1236|91347|1903414|583;3379134|976|200643|171549|1853231|574697;3379134|1224|1236|91347|543|1940338;3379134|976|200643|171549|2005525|375288;3379134|200940|3031449|213115|194924|35832;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3082720|186804|1505660;1783272|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:39235366/10/2,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 10,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,N,M,Uncultured Model,3,3,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 5B,23 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",A waterfall plot of significantly altered genus between model and control showing consistent trend in uncultured groups,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",1783272|1239|526524|526525|128827|174708;95818|2093818|2093825|2171986|1331051;1783272|1239|186801|186802|216572|1508657;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|216572|707003,Complete,Svetlana up
bsdb:39235366/11/1,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 11,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,ND,MD,Cultured model,3,3,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5B,23 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",A waterfall plot of significantly altered genus between model and control showing consistent trend in  cultured groups,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Asaccharospora,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",3379134|976|200643|171549|815|816;3379134|1224|1236|91347|1903414|583;3379134|976|200643|171549|1853231|574697;3379134|1224|1236|91347|543|1940338;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|31979|1485;3379134|200940|3031449|213115|194924|35832;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|3082720|186804|1505660;1783272|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:39235366/11/2,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 11,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,ND,MD,Cultured model,3,3,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5B,23 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",A waterfall plot of significantly altered genus between model and control showing consistent trend in  cultured groups,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",1783272|1239|186801|186802|216572|1508657;1783272|1239|526524|526525|128827|174708;1783272|1239|526524|526525|2810281|191303;95818|2093818|2093825|2171986|1331051;1783272|1239|186801|186802|216572|707003,Complete,Svetlana up
bsdb:39235366/12/2,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 12,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,MD (cultured model),A2.1 (gut microbiome remodeling compound),Gut Microbiome Remodeling Compound cocktail concentrations simplified from XFBD formula,3,3,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,Figure S5D,24 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",The relative abundance in genus levels after cocktail treatment,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:39235366/13/1,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 13,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,MD (cultured model),A2.2(gut microbiome remodeling compound),Gut Microbiome Remodeling Compound cocktail concentrations simplified from XFBD formula,3,3,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 1,Figure S5D,23 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",The relative abundance in genus levels after cocktail treatment,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:39235366/14/2,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 14,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,MD (cultured model),B2.1 (gut microbiome remodeling compound),Gut Microbiome Remodeling Compound cocktail concentrations simplified from XFBD formula,3,3,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,Figure S5D,24 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",The relative abundance in genus levels after cocktail treatment,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:39235366/15/1,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 15,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,PD1 (Patient sample 1 with DMSO),PC1 (Patient sample 1 treated with cocktail c),Patient sample treated with cocktail c,3,3,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 1,Figure S6A,23 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",The relative abundance in Phylum Levels,decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter",1783272|1239;3379134|1224|1236|91347|543|547,Complete,Svetlana up
bsdb:39235366/15/2,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 15,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,PD1 (Patient sample 1 with DMSO),PC1 (Patient sample 1 treated with cocktail c),Patient sample treated with cocktail c,3,3,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 2,Figure S6A,23 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",The relative abundance in Phylum Levels,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,Svetlana up
bsdb:39235366/16/1,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 16,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,PD2 (Patient sample 2 with DMSO),PC2 (Patient sample 2 treated with cocktail c),Patient sample treated with cocktail c,3,3,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure S6A and S6C,23 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",The relative abundance in Phylum and genera levels,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota",3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976|200643|171549|2005525|375288;3379134|1224,Complete,Svetlana up
bsdb:39235366/16/2,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 16,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,PD2 (Patient sample 2 with DMSO),PC2 (Patient sample 2 treated with cocktail c),Patient sample treated with cocktail c,3,3,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure S6A,23 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",The relative abundance level in Phylum levels,increased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Svetlana up
bsdb:39235366/17/1,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 17,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,PD4 (Patient sample 4 with DMSO),PC4 (Patient sample 4 treated with cocktail c),Patient sample treated with cocktail c,3,3,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,Figure S6A and S6C,23 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",the relative abundance in Phylum and genera levels,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia",3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|547;3379134|1224;3379134|976|200643,Complete,Svetlana up
bsdb:39235366/17/2,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 17,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,PD4 (Patient sample 4 with DMSO),PC4 (Patient sample 4 treated with cocktail c),Patient sample treated with cocktail c,3,3,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,figure S6A and S6C,23 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",The relative abundance in Phylum and genera levels,increased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",1783272|1239;3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:39235366/18/1,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 18,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,PD5 (Patient sample 5 with DMSO),PC5 (Patient sample 5 treated with cocktail c),Patient sample treated with cocktail c,3,3,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure S6A,23 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",The relative abundance in phylum levels,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Svetlana up
bsdb:39235366/18/2,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 18,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,PD5 (Patient sample 5 with DMSO),PC5 (Patient sample 5 treated with cocktail c),Patient sample treated with cocktail c,3,3,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure S6A,23 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",The relative abundance in phylum levels,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,Svetlana up
bsdb:39235366/19/1,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 19,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,PD6 (Patient sample 6 with DMSO),PC6 (Patient sample 6 treated with cocktail c),Patient sample treated with cocktail c,3,3,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure S6A and S6C,23 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",The relative abundance in Phylum and genera levels,decreased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|1224;3379134|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:39235366/19/2,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 19,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,PD6 (Patient sample 6 with DMSO),PC6 (Patient sample 6 treated with cocktail c),Patient sample treated with cocktail c,3,3,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure S6A,23 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",The relative abundance in Phylum levels,increased,k__Bacillati|p__Bacillota,1783272|1239,Complete,Svetlana up
bsdb:39235366/20/1,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 20,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,PD8 (Patient sample 8 with DMSO),PC8 (Patient sample 8 treated with cocktail c),Patient sample treated with cocktail c,3,3,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure S6A and S6C,23 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",The relative abundance in Phylum and genera levels,decreased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|1224;3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:39235366/20/2,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 20,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,PD8 (Patient sample 8 with DMSO),PC8 (Patient sample 8 treated with cocktail c),Patient sample treated with cocktail c,3,3,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure S6A and S6C,23 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",The relative abundance in Phylum and genera levels,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|1239;1783272|201174|1760|85004|31953|1678,Complete,Svetlana up
bsdb:39235366/21/1,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 21,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,H (Healthy Volunteers),P (Patients with SIRS),Patients with SIRS,10,8,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 8C,23 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",Abundance comparison of key genera between SIRS patients and healthy volunteers.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas",1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|547;1783272|1239|186801|3085636|186803|1506553;3379134|1224|1236|91347|543|1940338;3379134|74201|203494|48461|1647988|239934;3379134|1224|1236|72274|135621|286;3379134|1224|28216|80840|119060|48736;3379134|976|200643|171549|2005520|156973,Complete,Svetlana up
bsdb:39235366/21/2,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 21,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,H (Healthy Volunteers),P (Patients with SIRS),Patients with SIRS,10,8,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 8C,23 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",Abundance comparison of key genera between SIRS patients and healthy volunteers,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia",1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3082720|186804|1501226,Complete,Svetlana up
bsdb:39235366/22/2,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 22,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,MD (cultured model),B2.2 (gut microbiome remodeling compound),Gut Microbiome Remodeling Compound cocktail concentrations simplified from XFBD formula,3,3,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,Figure S5D,24 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",The relative abundance in genus levels after cocktail treatment,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:39235366/23/2,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 23,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,MD (cultured model),C2.1 (gut microbiome remodeling compound),Gut Microbiome Remodeling Compound cocktail concentrations simplified from XFBD formula,3,3,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,Figure S5D,24 October 2024,Ifeanyisam,"Ifeanyisam,Victoria,WikiWorks",The relative abundance in genus levels after cocktail treatment,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|1940338;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:39235366/24/1,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 24,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,MD (cultured model),C2.2 (gut microbiome remodeling compound),Gut Microbiome Remodeling Compound cocktail concentrations simplified from XFBD formula,3,3,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 1,Figure S5D,24 October 2024,Ifeanyisam,"Ifeanyisam,Victoria,WikiWorks",The relative abundance in genus levels after cocktail treatment,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:39235366/24/2,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 24,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,MD (cultured model),C2.2 (gut microbiome remodeling compound),Gut Microbiome Remodeling Compound cocktail concentrations simplified from XFBD formula,3,3,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 2,Figure S5D,24 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",The relative abundance in genus levels after cocktail treatment,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,1783272|1239|91061|186826|81852|1350,Complete,Svetlana up
bsdb:39235366/25/2,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 25,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,MD (cultured model),D2.1 (gut microbiome remodeling compound),Gut Microbiome Remodeling Compound cocktail concentrations simplified from XFBD formula,3,3,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,Figure S5D,24 October 2024,Ifeanyisam,"Ifeanyisam,Victoria,WikiWorks",the relative abundance in genus levels after cocktail treatment,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:39235366/26/1,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 26,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,MD (cultured model),D2.2 (gut microbiome remodeling compound),Gut Microbiome Remodeling Compound cocktail concentrations simplified from XFBD formula,3,3,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 1,Figure S5D,24 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",The relative abundance in genus levels after cocktail treatment,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,1783272|1239|91061|186826|81852|1350,Complete,Svetlana up
bsdb:39235366/26/2,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 26,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,MD (cultured model),D2.2 (gut microbiome remodeling compound),Gut Microbiome Remodeling Compound cocktail concentrations simplified from XFBD formula,3,3,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 2,Figure S5D,24 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",The relative abundance in genus levels after cocktail treatment,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:39235366/27/2,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 27,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,MD (cultured model),E2.1 (gut microbiome remodeling compound),Gut Microbiome Remodeling Compound cocktail concentrations simplified from XFBD formula,3,3,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,Figure S5D,24 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",The relative abundance in genus levels after cocktail treatment,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter",3379134|1224|1236|91347|543|1940338;3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|547,Complete,Svetlana up
bsdb:39235366/28/1,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 28,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,MD (cultured model),E2.2 (gut microbiome remodeling compound),Gut Microbiome Remodeling Compound cocktail concentrations simplified from XFBD formula,3,3,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,Figure S5D,24 October 2024,Ifeanyisam,"Ifeanyisam,Victoria,WikiWorks",the relative abundance in genus levels after cocktail treatment,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|1940338;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:39235366/29/1,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 29,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,MD (cultured model),F2.1 (gut microbiome remodeling compound),Gut Microbiome Remodeling Compound cocktail concentrations simplified from XFBD formula,3,3,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,Figure S5D,24 October 2024,Ifeanyisam,"Ifeanyisam,WikiWorks",The relative abundance in genus levels after cocktail treatment,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter",3379134|1224|1236|91347|543|1940338;3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|547,Complete,Svetlana up
bsdb:39235366/30/1,39235366,laboratory experiment,39235366,https://doi.org/10.1128/msystems.00788-24,NA,"Liu L., Ma L., Liu H., Zhao F., Li P., Zhang J., Lü X., Zhao X. , Yi Y.",Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome,mSystems,2024,"gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome",Experiment 30,China,Mus musculus,Feces,UBERON:0001988,Systemic inflammatory response syndrome,EFO:1001478,MD (cultured model),F2.2 (gut microbiome remodeling compound),Gut Microbiome Remodeling Compound cocktail concentrations simplified from XFBD formula,3,3,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure S5D,24 October 2024,Ifeanyisam,"Ifeanyisam,Victoria,WikiWorks",The relative abundance in genus levels after cocktail treatment,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:39237540/1/1,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 1,"Singapore,China",Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,61-70 years (Younger Age Group),71-80 years (Older Age Group),"Participants aged 71-80 years, representing an older age group used to assess age-related changes in the gut microbiome compared to the younger group.",57,33,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,age,increased,decreased,NA,increased,NA,decreased,Signature 1,Figure 1E,21 October 2024,MaryAgekameh,"MaryAgekameh,MyleeeA,WikiWorks",Microbial taxa Significantly associated with age in 61-70 and 71-80 age groups,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei",3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|909656|357276,Complete,ChiomaBlessing
bsdb:39237540/2/1,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 2,"China,Singapore",Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,Singapore Platinum Metagenomes Project (SPMP),SG90,"Dataset of Octogenarians community-living participants (not living in a nursing home,
 no diagnosis of dementia and not physically unfit) who consented to
 providing their stool and blood samples (SG90).",50,213,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 4,21 October 2024,MaryAgekameh,"MaryAgekameh,MyleeeA,WikiWorks",Significantly increased in the SG90 group compared to Singapore Platinum Metagenomes Project (SPMP).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|815|816|371601;3379134|1224|1236|91347|543|561|562;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|171550|239759;3379134|1224|1236|91347|543|561,Complete,ChiomaBlessing
bsdb:39237540/2/2,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 2,"China,Singapore",Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,Singapore Platinum Metagenomes Project (SPMP),SG90,"Dataset of Octogenarians community-living participants (not living in a nursing home,
 no diagnosis of dementia and not physically unfit) who consented to
 providing their stool and blood samples (SG90).",50,213,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 4,21 October 2024,MaryAgekameh,"MaryAgekameh,MyleeeA,WikiWorks",Significantly associated with age in the SG90 group compared to Singapore Platinum Metagenomes Project (SPMP),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|3085636|186803|2316020|33039;3379134|200940|3031449|213115|194924|35832;1783272|201174|84998|1643822|1643826|84111;1783272|1239|909932|909929|1843491|158846,Complete,ChiomaBlessing
bsdb:39237540/3/1,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 3,Singapore,Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,T2D,SG90,"Dataset of Octogenarians community-living participants (not living in a nursing home, no diagnosis of dementia and not physically unfit) who consented to providing their stool and blood samples (SG90).",171,213,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 4,23 October 2024,MyleeeA,"MyleeeA,WikiWorks",Significantly associated with age in the SG90 group compared to T2D,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",3379134|976|200643|171549|171550|239759|626932;3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|171550|239759|1288121;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550|239759|2585118;3379134|976|200643|171549|815|816|371601;3379134|976|200643|171549|815|909656|357276;3379134|1224|1236|91347|543|570|573;3379134|1224|1236|91347|543|561,Complete,ChiomaBlessing
bsdb:39237540/3/2,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 3,Singapore,Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,T2D,SG90,"Dataset of Octogenarians community-living participants (not living in a nursing home, no diagnosis of dementia and not physically unfit) who consented to providing their stool and blood samples (SG90).",171,213,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 4,23 October 2024,MyleeeA,"MyleeeA,WikiWorks",Significantly associated with age in the SG90 group compared to T2D,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 1_1_57FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 5_1_63FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA",1783272|201174|1760|85004|31953|1678|28026;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|3085636|186803|658081;1783272|1239|186801|3085636|186803|658089;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|186801|3085636|186803|2316020|46228;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|186802|216572|1263|457412,Complete,ChiomaBlessing
bsdb:39237540/4/1,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 4,"Singapore,China",Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,All Cohorts (Decreased age group),All Cohorts (Increased age group),"All cohorts (SG90, T2D, SPMP and CPE) in the older age group i.e 71-80, 81-90 and 91-100.",288,228,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Data File 3,23 October 2024,MyleeeA,"MyleeeA,WikiWorks","Phylum, Genus and species Significantly associated with age in All cohort groups.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550|239759|2585118;3379134|976|200643|171549|171550|239759|626932;3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|171550|239759|1288121;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|626929;3379134|976|200643|171549|815|816|371601;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|543|570|573;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|2005525|375288|46503;3379134|1224;1783272|1239|909932|1843488|909930;3379134|976|200643|171549|171550|239759;3379134|1224|1236|91347|543|561;3379134|976|200643|171549|815|909656|357276;3379134|976|200643,Complete,ChiomaBlessing
bsdb:39237540/4/2,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 4,"Singapore,China",Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,All Cohorts (Decreased age group),All Cohorts (Increased age group),"All cohorts (SG90, T2D, SPMP and CPE) in the older age group i.e 71-80, 81-90 and 91-100.",288,228,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Data File 3,23 October 2024,MyleeeA,"MyleeeA,WikiWorks","Phylum, Genus and species Significantly associated with age in All cohort groups",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 1_1_57FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 5_1_63FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides johnsonii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|3085636|186803|2569097|39488;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|28026;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|40520;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|526524|526525|2810280|100883;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|658081;1783272|1239|186801|3085636|186803|658089;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|909929|1843491|158846|437897;3379134|976|200643|171549|2005525|375288|387661;3379134|976|200643|171549|171552|577309;3379134|1224|28216|80840|995019|577310;3379134|1224|28216|80840|995019|577310|487175;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|186801|186802|216572|1263|457412;1783272|1239|186801|3085636|186803|2316020|46228;1783272|1239|186801|3085636|186803|2316020|33039;3379134|200940|3031449|213115|194924|35832;1783272|201174|84998|1643822|1643826|84111;1783272|1239|909932|909929|1843491|158846;3384189|32066|203490;1783272|201174;1783272|1239,Complete,ChiomaBlessing
bsdb:39237540/5/1,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 5,"China,Singapore",Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,Fasting Blood glucose Decreased age group(Age Corrected),Fasting Blood glucose increased age group(Age corrected),"Asian octogenarians in the older age group i.e 71-80, 81-90 and 91-100 with age correction. Clinical phenotype associated with age (Fasting Blood glucose)",288,228,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Data File 6,23 October 2024,MyleeeA,"MyleeeA,WikiWorks",Microbial Species Significantly associated with Fasting Blood glucose after age correction,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae",1783272|201174|1760|85004|31953|1678|1680;3379134|976|200643|171549|2005525|375288|328812;1783272|1239|91061|186826|33958|2742598|97478,Complete,ChiomaBlessing
bsdb:39237540/6/1,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 6,"China,Singapore",Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,Triglycerides Decreased age group(Age Corrected),Triglycerides Increased age group(Age Corrected),"Asian octogenarians in the older age group i.e 71-80, 81-90 and 91-100 with age correction. Clinical phenotype associated with age (Triglycirides)",288,228,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Data File 6,23 October 2024,MyleeeA,"MyleeeA,WikiWorks",Microbial Species Significantly associated with Triglycerides after age correction,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,3379134|1224|1236|135625|712|724|729,Complete,ChiomaBlessing
bsdb:39237540/7/1,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 7,"China,Singapore",Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,Total cholesterol Decreased age group(Age Corrected),Total cholesterol Increased age group(Age Corrected),"Asian octogenarians in the older age group i.e 71-80, 81-90 and 91-100 with age correction. Clinical phenotype associated with age (Total cholesterol).",288,228,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Data File 6,23 October 2024,MyleeeA,"MyleeeA,WikiWorks",Microbial Species Significantly associated with Total Cholesterol after age correction,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 1 4 56FAA,1783272|1239|186801|3085636|186803|2683688,Complete,ChiomaBlessing
bsdb:39237540/7/2,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 7,"China,Singapore",Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,Total cholesterol Decreased age group(Age Corrected),Total cholesterol Increased age group(Age Corrected),"Asian octogenarians in the older age group i.e 71-80, 81-90 and 91-100 with age correction. Clinical phenotype associated with age (Total cholesterol).",288,228,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Data File 6,23 October 2024,MyleeeA,"MyleeeA,WikiWorks",Microbial Species Significantly associated with Total Cholesterol after age correction,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,3379134|1224|1236|135625|712|724|729,Complete,ChiomaBlessing
bsdb:39237540/8/1,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 8,"China,Singapore",Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,LDL Decreased age group(Age Corrected),LDL Increased age group(Age Corrected),"Asian octogenarians in the older age group i.e 71-80, 81-90 and 91-100 with age correction. Clinical phenotype associated with age (Low-Density Lipoprotein (LDL) Levels)",288,228,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Data File 6,23 October 2024,MyleeeA,"MyleeeA,WikiWorks",Microbial Species Significantly associated with Low-Density Lipoprotein (LDL) Levels after age correction,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,3379134|1224|1236|135625|712|724|729,Complete,ChiomaBlessing
bsdb:39237540/8/2,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 8,"China,Singapore",Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,LDL Decreased age group(Age Corrected),LDL Increased age group(Age Corrected),"Asian octogenarians in the older age group i.e 71-80, 81-90 and 91-100 with age correction. Clinical phenotype associated with age (Low-Density Lipoprotein (LDL) Levels)",288,228,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Data File 6,23 October 2024,MyleeeA,"MyleeeA,WikiWorks",Microbial Species Significantly associated with Low-Density Lipoprotein (LDL) Levels after age correction,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 1 4 56FAA,1783272|1239|186801|3085636|186803|2683688,Complete,ChiomaBlessing
bsdb:39237540/9/1,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 9,"Singapore,China",Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,hs-CRP Decreased age group(Age Corrected),hs-CRP Increased age group(Age Corrected),"Asian octogenarians in the older age group i.e 71-80, 81-90 and 91-100 with age correction. Clinical phenotype associated with age (high-sensitivity C-Reactive Protein {hs-CRP})",288,228,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Data File 6,23 October 2024,MyleeeA,"MyleeeA,WikiWorks",Microbial Species Significantly associated with high-sensitivity C-Reactive Protein {hs-CRP} after age correction,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius",3379134|1224|1236|91347|543|561|562;1783272|201174|84998|1643822|1643826|84111;1783272|1239|91061|186826|1300|1301|1304,Complete,ChiomaBlessing
bsdb:39237540/10/1,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 10,"China,Singapore",Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,AST Decreased age group(Age Corrected),AST Increased age group(Age Corrected),"Asian octogenarians in the older age group i.e 71-80, 81-90 and 91-100 with age correction. Clinical phenotype associated with age (Aspartate Aminotransferase {AST})",288,228,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Data File 6,23 October 2024,MyleeeA,"MyleeeA,WikiWorks",Microbial Species Significantly associated with Aspartate Aminotransferase {AST} after age correction,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,3379134|1224|1236|91347|543|570|573,Complete,ChiomaBlessing
bsdb:39237540/11/1,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 11,"Singapore,China",Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,Vitamin B12 Decreased age group(Age Corrected),Vitamin B12 Increased age group(Age corrected),"Asian octogenarians in the older age group i.e 71-80, 81-90 and 91-100 with age correction. Clinical phenotype associated with age (Vitamin B12).",288,228,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Data File 6,23 October 2024,MyleeeA,"MyleeeA,WikiWorks",Microbial Species Significantly associated with Vitamin B12 after age correction,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola",1783272|1239|91061|186826|1300|1301|1318;3379134|976|200643|171549|815|909656|310298,Complete,ChiomaBlessing
bsdb:39237540/12/1,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 12,"China,Singapore",Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,All cohorts (Decreased age group),All cohorts (Increased age group),"All cohorts (SG90, T2D, SPMP and CPE) in the older age group i.e 71-80, 81-90 and 91-100.",288,228,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 3,27 October 2024,MaryAgekameh,"MaryAgekameh,MyleeeA,WikiWorks","Microbial abundance enriched in All cohorts (SG90, T2D, SPMP and CPE) with decease in Age. Using TSS Normalization and Linear model.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",3379134|976|200643|171549|171550|239759|2585118;3379134|976|200643|171549|171550|239759|626932;3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|171550|239759|1288121;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|815|816|626929;3379134|976|200643|171549|815|816|371601;3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|543|570|573;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|171550|239759;3379134|1224|1236|91347|543|561,Complete,ChiomaBlessing
bsdb:39237540/12/2,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 12,"China,Singapore",Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,All cohorts (Decreased age group),All cohorts (Increased age group),"All cohorts (SG90, T2D, SPMP and CPE) in the older age group i.e 71-80, 81-90 and 91-100.",288,228,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 3,27 October 2024,MaryAgekameh,"MaryAgekameh,MyleeeA,WikiWorks","Microbial abundance enriched in All cohorts (SG90, T2D, SPMP and CPE) with decease in Age. Using TSS Normalization and Linear model.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 1_1_57FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 5_1_63FAA,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|3085636|186803|2569097|39488;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|658081;1783272|1239|186801|3085636|186803|658089;1783272|1239|909932|909929|1843491|158846|437897;3379134|1224|28216|80840|995019|577310|487175;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|186801|186802|216572|1263|457412;1783272|1239|186801|3085636|186803|2316020|46228;1783272|1239|186801|3085636|186803|2316020|33039;3379134|200940|3031449|213115|194924|35832;1783272|1239|909932|909929|1843491|158846,Complete,ChiomaBlessing
bsdb:39237540/13/1,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 13,"China,Singapore",Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,All cohorts (Decreased age group),All cohorts (Increased age group),"All cohorts (SG90, T2D, SPMP and CPE) in the older age group i.e 71-80, 81-90 and 91-100.",288,228,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 3,27 October 2024,MaryAgekameh,"MaryAgekameh,MyleeeA,WikiWorks","Microbial abundance enriched in All cohorts (SG90, T2D, SPMP and CPE) with increase in Age. Using CSS Normalization and Linear model.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",3379134|976|200643|171549|171550|239759|2585118;3379134|976|200643|171549|171550|239759|626932;3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|171550|239759|1288121;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|815|816|626929;3379134|976|200643|171549|815|816|371601;3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|543|570|573;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|171550|239759;3379134|1224|1236|91347|543|561,Complete,ChiomaBlessing
bsdb:39237540/13/2,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 13,"China,Singapore",Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,All cohorts (Decreased age group),All cohorts (Increased age group),"All cohorts (SG90, T2D, SPMP and CPE) in the older age group i.e 71-80, 81-90 and 91-100.",288,228,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 3,27 October 2024,MaryAgekameh,"MaryAgekameh,MyleeeA,WikiWorks","Microbial abundance enriched in All cohorts (SG90, T2D, SPMP and CPE) with decrease in Age. Using TSS Normalization and Linear model.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 1_1_57FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 5_1_63FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|3085636|186803|658081;1783272|1239|186801|3085636|186803|658089;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|186801|186802|216572|1263|457412;1783272|1239|186801|3085636|186803|2316020|46228;1783272|1239|186801|3085636|186803|2316020|33039;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|841|301301;3379134|1224|28216|80840|995019|577310|487175;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|909929|1843491|158846|437897;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|3569723|410072;3379134|200940|3031449|213115|194924|35832,Complete,ChiomaBlessing
bsdb:39237540/14/1,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 14,"China,Singapore",Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,All Cohorts (Decreasing age group),All cohorts (Increased age group),"All cohorts (SG90, T2D, SPMP and CPE) in the older age group i.e 71-80, 81-90 and 91-100.",288,228,NA,WMS,NA,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 3,27 October 2024,MaryAgekameh,"MaryAgekameh,MyleeeA,WikiWorks","Microbial abundance enriched in All cohorts (SG90, T2D, SPMP and CPE) with increase in Age. Using ANCOM and Centered Log Ratio.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",3379134|976|200643|171549|171550|239759|2585118;3379134|976|200643|171549|171550|239759|626932;3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|171550|239759|1288121;3379134|976|200643|171549|815|816|371601;3379134|1224|1236|91347|543|561|562;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|171550|239759;3379134|1224|1236|91347|543|561,Complete,ChiomaBlessing
bsdb:39237540/14/2,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 14,"China,Singapore",Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,All Cohorts (Decreasing age group),All cohorts (Increased age group),"All cohorts (SG90, T2D, SPMP and CPE) in the older age group i.e 71-80, 81-90 and 91-100.",288,228,NA,WMS,NA,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 3,27 October 2024,MaryAgekameh,"MaryAgekameh,MyleeeA,WikiWorks","Microbial abundance enriched in All cohorts (SG90, T2D, SPMP and CPE) with decrease in Age. Using ANCOM and Centered Log Ratio.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 1_1_57FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 5_1_63FAA,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris",1783272|1239|186801|3085636|186803|2569097|39488;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|3085636|186803|658081;1783272|1239|186801|3085636|186803|658089;3379134|1224|28216|80840|995019|577310|487175;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|186801|186802|216572|1263|457412;1783272|1239|186801|3085636|186803|2316020|46228,Complete,ChiomaBlessing
bsdb:39237540/15/1,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 15,"China,Singapore",Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,All Cohorts (Decreasing age group),All cohorts (Increased age group),"All cohorts (SG90, T2D, SPMP and CPE) in the older age group i.e 71-80, 81-90 and 91-100.",288,228,NA,WMS,NA,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 3,27 October 2024,MaryAgekameh,"MaryAgekameh,MyleeeA,WikiWorks","Microbial abundance enriched in All cohorts (SG90, T2D, SPMP and CPE) with increase in Age. Using TSS Normalization and MaAslin2.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Metazoa|p__Nemertea|c__Enopla|o__Monostilifera|f__Tetrastemmatidae|g__Prostoma,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",3379134|976|200643|171549|171550|239759|2585118;3379134|976|200643|171549|171550|239759|626932;3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|171550|239759|1288121;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|815|816|626929;3379134|976|200643|171549|815|816|371601;3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|543|570|573;33208|6217|6225|6227|35726|35727;3379134|976|200643|171549|171550|239759;3379134|1224|1236|91347|543|561,Complete,ChiomaBlessing
bsdb:39237540/15/2,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 15,"China,Singapore",Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,All Cohorts (Decreasing age group),All cohorts (Increased age group),"All cohorts (SG90, T2D, SPMP and CPE) in the older age group i.e 71-80, 81-90 and 91-100.",288,228,NA,WMS,NA,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 3,27 October 2024,MaryAgekameh,"MaryAgekameh,MyleeeA,WikiWorks","Microbial abundance enriched in All cohorts (SG90, T2D, SPMP and CPE) with decrease in Age. Using TSS Normalization and MaAslin2.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 1_1_57FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 5_1_63FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum",1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|3085636|186803|658081;1783272|1239|186801|3085636|186803|658089;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|186801|186802|216572|1263|457412;1783272|1239|186801|3085636|186803|2316020|46228;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|841|301301;3379134|1224|28216|80840|995019|577310|487175;1783272|1239|909932|909929|1843491|158846|437897;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|3569723|410072;3379134|200940|3031449|213115|194924|35832;1783272|201174|1760|85004|31953|1678|28026,Complete,ChiomaBlessing
bsdb:39237540/16/1,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 16,"China,Singapore",Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,SG90+CPE (Decreasing age group),SG90+CPE (Increased age group),"Dataset of Octogenarians community-living participants (not living in a nursing home, no diagnosis of dementia and not physically unfit) who consented to providing their stool and blood samples (SG90) and  CPE-colonized subjects and their healthy family members (21–80 years old) with Chinese ethnicity.",69,226,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 3,26 October 2024,MyleeeA,"MyleeeA,WikiWorks",Microbial abundance in the SG90+CPE datasets significantly enriched with increase in Age. Using TSS Normalization and Linear model.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",3379134|976|200643|171549|171550|239759|626932;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|815|816|371601;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|171550|239759,Complete,ChiomaBlessing
bsdb:39237540/16/2,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 16,"China,Singapore",Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,SG90+CPE (Decreasing age group),SG90+CPE (Increased age group),"Dataset of Octogenarians community-living participants (not living in a nursing home, no diagnosis of dementia and not physically unfit) who consented to providing their stool and blood samples (SG90) and  CPE-colonized subjects and their healthy family members (21–80 years old) with Chinese ethnicity.",69,226,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary File 3,26 October 2024,MyleeeA,"MyleeeA,MaryAgekameh,WikiWorks",Microbial abundance in the SG90+CPE datasets enriched with decease in Age. Using TSS Normalization and Linear model.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|3085636|186803|2569097|39488;3379134|976|200643|171549|815|816|371601;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|186802|216572|1263|40518;3379134|200940|3031449|213115|194924|35832;1783272|201174|84998|1643822|1643826|84111;1783272|1239|909932|909929|1843491|158846,Complete,ChiomaBlessing
bsdb:39237540/17/1,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 17,"Singapore,China",Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,SG90+CPE (Decreasing age group),SG90+CPE (Increased age group),"Dataset of Octogenarians community-living participants (not living in a nursing home, no diagnosis of dementia and not physically unfit) who consented to providing their stool and blood samples (SG90) and CPE-colonized subjects and their healthy family members (21–80 years old) with Chinese ethnicity.",69,226,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 3,26 October 2024,MyleeeA,"MyleeeA,WikiWorks",Microbial abundance in the SG90+CPE datasets enriched with increase in Age. Using CSS Normalization and Linear model.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei",3379134|976|200643|171549|815|816|371601;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|171550|239759|626932;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|909656|357276,Complete,ChiomaBlessing
bsdb:39237540/17/2,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 17,"Singapore,China",Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,SG90+CPE (Decreasing age group),SG90+CPE (Increased age group),"Dataset of Octogenarians community-living participants (not living in a nursing home, no diagnosis of dementia and not physically unfit) who consented to providing their stool and blood samples (SG90) and CPE-colonized subjects and their healthy family members (21–80 years old) with Chinese ethnicity.",69,226,NA,WMS,NA,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 3,26 October 2024,MyleeeA,"MyleeeA,WikiWorks",Microbial abundance in the SG90+CPE datasets enriched with decease in Age. Using CSS Normalization and Linear model.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|3085636|186803|2569097|39488;3379134|976|200643|171549|815|816|371601;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|186802|216572|1263|40518;3379134|200940|3031449|213115|194924|35832;1783272|201174|84998|1643822|1643826|84111;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|3085636|186803|2316020|33038,Complete,ChiomaBlessing
bsdb:39237540/18/1,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 18,"China,Singapore",Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,SG90+CPE (Decreasing age group),SG90+CPE (Increased age group),"Dataset of Octogenarians community-living participants (not living in a nursing home, no diagnosis of dementia and not physically unfit) who consented to providing their stool and blood samples (SG90) and CPE-colonized subjects and their healthy family members (21–80 years old) with Chinese ethnicity.",69,226,NA,WMS,NA,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 3,26 October 2024,MyleeeA,"MyleeeA,WikiWorks",Microbial abundance in the SG90+CPE datasets enriched with increase in Age. Using Center log Ratio Normalization and ANCOM BC.,increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus",3379134|200940|3031449|213115|194924|35832;3379134|1224|1236|91347|543|570|573;3379134|976|200643|171549|815|816|371601;3379134|976|200643|171549|171550|239759|2585118;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|171550|239759|1288121;3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|171550|239759|626932,Complete,ChiomaBlessing
bsdb:39237540/18/2,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 18,"China,Singapore",Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,SG90+CPE (Decreasing age group),SG90+CPE (Increased age group),"Dataset of Octogenarians community-living participants (not living in a nursing home, no diagnosis of dementia and not physically unfit) who consented to providing their stool and blood samples (SG90) and CPE-colonized subjects and their healthy family members (21–80 years old) with Chinese ethnicity.",69,226,NA,WMS,NA,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 3,26 October 2024,MyleeeA,"MyleeeA,WikiWorks",Microbial abundance in the SG90+CPE datasets enriched with decrease in Age. Using Center log Ratio Normalization and ANCOM BC.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|186803|2569097|39488;1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330|88431;1783272|201174|1760|85004|31953|1678|28026;3379134|200940|3031449|213115|194924|35832,Complete,ChiomaBlessing
bsdb:39237540/19/1,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 19,"China,Singapore",Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,SG90+CPE (Decreasing age group),SG90+CPE (Increased age group),"Dataset of Octogenarians community-living participants (not living in a nursing home, no diagnosis of dementia and not physically unfit) who consented to providing their stool and blood samples (SG90) and CPE-colonized subjects and their healthy family members (21–80 years old) with Chinese ethnicity.",69,226,NA,WMS,NA,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 3,26 October 2024,MyleeeA,"MyleeeA,WikiWorks",Microbial abundance in the SG90+CPE datasets enriched with increase in Age.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae",3379134|976|200643|171549|171550|239759|626932;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816|371601;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|2005525|375288|46503,Complete,ChiomaBlessing
bsdb:39237540/19/2,39237540,"cross-sectional observational, not case-control",39237540,10.1038/s41467-024-52097-9,NA,"Ravikrishnan A., Wijaya I., Png E., Chng K.R., Ho E.X.P., Ng A.H.Q., Mohamed Naim A.N., Gounot J.S., Guan S.P., Hanqing J.L., Guan L., Li C., Koh J.Y., de Sessions P.F., Koh W.P., Feng L., Ng T.P., Larbi A., Maier A.B., Kennedy B.K. , Nagarajan N.",Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes,Nature communications,2024,NA,Experiment 19,"China,Singapore",Homo sapiens,Feces,UBERON:0001988,Aging,GO:0007568,SG90+CPE (Decreasing age group),SG90+CPE (Increased age group),"Dataset of Octogenarians community-living participants (not living in a nursing home, no diagnosis of dementia and not physically unfit) who consented to providing their stool and blood samples (SG90) and CPE-colonized subjects and their healthy family members (21–80 years old) with Chinese ethnicity.",69,226,NA,WMS,NA,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 3,26 October 2024,MyleeeA,"MyleeeA,WikiWorks",Microbial abundance in the SG90+CPE datasets enriched with decease in Age.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|1766253|39491;1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|189330|39486;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|186801|3085636|186803|3569723|410072;3379134|200940|3031449|213115|194924|35832,Complete,ChiomaBlessing
bsdb:39242653/1/1,39242653,prospective cohort,39242653,10.1038/s41598-024-71684-w,https://www.nature.com/articles/s41598-024-71684-w,"Urban S., Chmura O., Wątor J., Panek P. , Zapała B.",The intensive physical activity causes changes in the composition of gut and oral microbiota,Scientific reports,2024,"Exercises, Microbiome, Professional football player",Experiment 1,Poland,Homo sapiens,Mouth,UBERON:0000165,Physical activity,EFO:0003940,Amateurs,Professional football players,Participants in group 1 are professional football players who had oral swabs taken.,12,20,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,health",NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,Figure 9a,2 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Linear discriminant analysis (LDA) scores of differentially abundant species among amateurs and professional football players.,increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium canifelinum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia shahii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas noxia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella tobetsuensis",3379134|29547|3031852|213849|72294|194|824;1783272|201174|1760|85007|1653|1716|43768;3384189|32066|203490|203491|203492|848|285729;3384189|32066|203490|203491|1129771|32067|157691;1783272|201174|1760|85006|1268|32207|2047;1783272|1239|909932|909929|1843491|970|135083;1783272|1239|91061|186826|1300|1301|1305;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|909932|1843489|31977|29465|1110546,Complete,ChiomaBlessing
bsdb:39242653/1/2,39242653,prospective cohort,39242653,10.1038/s41598-024-71684-w,https://www.nature.com/articles/s41598-024-71684-w,"Urban S., Chmura O., Wątor J., Panek P. , Zapała B.",The intensive physical activity causes changes in the composition of gut and oral microbiota,Scientific reports,2024,"Exercises, Microbiome, Professional football player",Experiment 1,Poland,Homo sapiens,Mouth,UBERON:0000165,Physical activity,EFO:0003940,Amateurs,Professional football players,Participants in group 1 are professional football players who had oral swabs taken.,12,20,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,health",NA,NA,NA,unchanged,NA,NA,unchanged,Signature 2,Figure 9a,2 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Linear discriminant analysis (LDA) scores of differentially abundant species among amateurs and professional football players.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sputorum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica",3379134|976|200643|171549|171552|838|470565;3379134|976|200643|171549|171552|838|28132;1783272|201174|1760|2037|2049|1654|55565;3379134|1224|1236|135625|712|724|1078480;1783272|201174|1760|2037|2049|2529408|1660,Complete,ChiomaBlessing
bsdb:39242653/2/1,39242653,prospective cohort,39242653,10.1038/s41598-024-71684-w,https://www.nature.com/articles/s41598-024-71684-w,"Urban S., Chmura O., Wątor J., Panek P. , Zapała B.",The intensive physical activity causes changes in the composition of gut and oral microbiota,Scientific reports,2024,"Exercises, Microbiome, Professional football player",Experiment 2,Poland,Homo sapiens,Feces,UBERON:0001988,Physical activity,EFO:0003940,Amateurs,Professional football players,Participants in group 1 are professional football players who had stool samples taken.,12,20,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,health",NA,NA,NA,increased,NA,NA,increased,Signature 1,Figure 9b,2 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Linear discriminant analysis (LDA) scores of differentially abundant species among amateurs and professional football players,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Neglectibacter|s__Neglectibacter timonensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides johnsonii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris",1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|526524|526525|128827|1573535|1735;1783272|1239|186801|3085636|186803|2316020|592978;1783272|1239|186801|186802|216572|1924105|1776382;3379134|976|200643|171549|2005525|375288|387661;1783272|1239|909932|1843488|909930|33024|33025;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|186801|3085636|186803|2316020|46228,Complete,ChiomaBlessing
bsdb:39242653/2/2,39242653,prospective cohort,39242653,10.1038/s41598-024-71684-w,https://www.nature.com/articles/s41598-024-71684-w,"Urban S., Chmura O., Wątor J., Panek P. , Zapała B.",The intensive physical activity causes changes in the composition of gut and oral microbiota,Scientific reports,2024,"Exercises, Microbiome, Professional football player",Experiment 2,Poland,Homo sapiens,Feces,UBERON:0001988,Physical activity,EFO:0003940,Amateurs,Professional football players,Participants in group 1 are professional football players who had stool samples taken.,12,20,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,health",NA,NA,NA,increased,NA,NA,increased,Signature 2,Figure 9b,2 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Linear discriminant analysis (LDA) scores of differentially abundant species among amateurs and professional football players.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans",1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|909932|1843489|31977|39948|487173;1783272|1239|186801|3085636|186803|1898203;3379134|976|200643|171549|815|909656|310298;3379134|976|200643|171549|815|909656|387090;1783272|1239|186801|3085636|186803|841|360807,Complete,ChiomaBlessing
bsdb:39242653/3/1,39242653,prospective cohort,39242653,10.1038/s41598-024-71684-w,https://www.nature.com/articles/s41598-024-71684-w,"Urban S., Chmura O., Wątor J., Panek P. , Zapała B.",The intensive physical activity causes changes in the composition of gut and oral microbiota,Scientific reports,2024,"Exercises, Microbiome, Professional football player",Experiment 3,Poland,Homo sapiens,Feces,UBERON:0001988,Physical activity,EFO:0003940,Professional football players before intensive training,Professional football players after intensive training,Participants in group 1 are professional football players who had stool samples taken after intensive training.,20,20,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,health",NA,NA,NA,increased,NA,NA,increased,Signature 1,Figure 10,3 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe algorithm showing the features with significant differential abundance in the gut microbiota of professional football players before intensive training and after intensive training.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061|186826;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301,Complete,ChiomaBlessing
bsdb:39242653/3/2,39242653,prospective cohort,39242653,10.1038/s41598-024-71684-w,https://www.nature.com/articles/s41598-024-71684-w,"Urban S., Chmura O., Wątor J., Panek P. , Zapała B.",The intensive physical activity causes changes in the composition of gut and oral microbiota,Scientific reports,2024,"Exercises, Microbiome, Professional football player",Experiment 3,Poland,Homo sapiens,Feces,UBERON:0001988,Physical activity,EFO:0003940,Professional football players before intensive training,Professional football players after intensive training,Participants in group 1 are professional football players who had stool samples taken after intensive training.,20,20,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,health",NA,NA,NA,increased,NA,NA,increased,Signature 2,Figure 10,3 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe algorithm showing the features with significant differential abundance in the gut microbiota of professional football players before intensive training and after intensive training.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae",3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|2005519,Complete,ChiomaBlessing
bsdb:39242653/4/1,39242653,prospective cohort,39242653,10.1038/s41598-024-71684-w,https://www.nature.com/articles/s41598-024-71684-w,"Urban S., Chmura O., Wątor J., Panek P. , Zapała B.",The intensive physical activity causes changes in the composition of gut and oral microbiota,Scientific reports,2024,"Exercises, Microbiome, Professional football player",Experiment 4,Poland,Homo sapiens,Mouth,UBERON:0000165,Physical activity,EFO:0003940,Professional football players before intensive training,Professional football players after intensive training,Participants in group 1 are professional football players who had oral swabs taken after intensive training.,20,20,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,health",NA,NA,NA,decreased,NA,NA,decreased,Signature 1,Figure 11,3 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe algorithm showing the features with significant differential abundance in the oral microbiota of professional football players before intensive training and after intensive training.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales",1783272|1239|91061|186826|186827|46123;1783272|1239|91061|186826|186827;3379134|1224|1236|135625|712|416916;3379134|1224|28216|80840|119060;3379134|1224|28216|80840;3379134|976|117743|200644|49546|1016;3379134|1224|1236|135615|868;3379134|1224|1236|135615;3379134|1224|1236|135615|868|2717;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;1783272|1239|909932|1843489|31977|39948;3379134|976|117743|200644|49546;3379134|976|117743|200644;3379134|1224|28216|80840|119060|47670;1783272|201174|1760|85006|1268;1783272|201174|1760|85006;1783272|201174|1760|85007;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|1737404|1737405|1570339;1783272|201174|1760|85006|1268|32207;3379134|976|200643|171549|2005525|195950;3379134|976|200643|171549|2005525;1783272|1239|1737404|1737405,Complete,ChiomaBlessing
bsdb:39242653/4/2,39242653,prospective cohort,39242653,10.1038/s41598-024-71684-w,https://www.nature.com/articles/s41598-024-71684-w,"Urban S., Chmura O., Wątor J., Panek P. , Zapała B.",The intensive physical activity causes changes in the composition of gut and oral microbiota,Scientific reports,2024,"Exercises, Microbiome, Professional football player",Experiment 4,Poland,Homo sapiens,Mouth,UBERON:0000165,Physical activity,EFO:0003940,Professional football players before intensive training,Professional football players after intensive training,Participants in group 1 are professional football players who had oral swabs taken after intensive training.,20,20,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,body mass index,health",NA,NA,NA,decreased,NA,NA,decreased,Signature 2,Figure 11,3 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe algorithm showing the features with significant differential abundance in the oral microbiota of professional football players before intensive training and after intensive training.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria perflava,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|976|200643|171549;1783272|1239|91061|186826|186828;1783272|1239|186801|186802;1783272|1239|91061|186826|186828|117563;1783272|1239|186801|3085636|186803;3379134|1224|28216|206351|481|482|33053;3379134|1224|28216|206351|481;3379134|1224|28216|206351;1783272|1239|186801|3085636|186803|265975;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552,Complete,ChiomaBlessing
bsdb:39266570/1/1,39266570,case-control,39266570,10.1038/s41522-024-00548-y,https://www.nature.com/articles/s41522-024-00548-y,"Chen H., Qi T., Guo S., Zhang X., Zhan M., Liu S., Yin Y., Guo Y., Zhang Y., Zhao C., Wang X. , Wang H.",Integrating respiratory microbiome and host immune response through machine learning for respiratory tract infection diagnosis,NPJ biofilms and microbiomes,2024,NA,Experiment 1,China,Homo sapiens,Lung,UBERON:0002048,Lower respiratory tract disease,EFO:0009433,Non-lower respiratory tract infections (LRTIs),Lower respiratory tract infections (LRTIs),Subjects who met clinical or microbiologic diagnosis criteria for lower respiratory tract infections (LRTIs).,27,41,NA,WMS,NA,Illumina,raw counts,edgeR,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 2D and Dataset S4,21 October 2024,Martha KJ,"Martha KJ,Aleru Divine,WikiWorks",Barplot of the differential ambulance of micro-species between LRTIs and Non-LRTIs plotted by R,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus fumigatus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium striatum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella catarrhalis,k__Fungi|p__Ascomycota|c__Pneumocystomycetes|o__Pneumocystales|f__Pneumocystaceae|g__Pneumocystis|s__Pneumocystis jirovecii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Tropherymataceae|g__Tropheryma|s__Tropheryma whipplei",3379134|1224|1236|2887326|468|469;4751|4890|147545|5042|1131492|5052|746128;1783272|201174|1760|85007|1653|1716|43770;3379134|1224|1236|135625|712|724|727;3379134|1224|1236|91347|543|570|548;3379134|1224|1236|91347|543|570|573;3379134|1224|1236|2887326|468|475|480;4751|4890|147553|37987|44281|4753|42068;3379134|1224|1236|72274|135621|286|287;1783272|1239|91061|186826|1300|1301|1313;1783272|201174|1760|85006|2805591|2038|2039,Complete,Folakunmi
bsdb:39266570/1/2,39266570,case-control,39266570,10.1038/s41522-024-00548-y,https://www.nature.com/articles/s41522-024-00548-y,"Chen H., Qi T., Guo S., Zhang X., Zhan M., Liu S., Yin Y., Guo Y., Zhang Y., Zhao C., Wang X. , Wang H.",Integrating respiratory microbiome and host immune response through machine learning for respiratory tract infection diagnosis,NPJ biofilms and microbiomes,2024,NA,Experiment 1,China,Homo sapiens,Lung,UBERON:0002048,Lower respiratory tract disease,EFO:0009433,Non-lower respiratory tract infections (LRTIs),Lower respiratory tract infections (LRTIs),Subjects who met clinical or microbiologic diagnosis criteria for lower respiratory tract infections (LRTIs).,27,41,NA,WMS,NA,Illumina,raw counts,edgeR,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 2D and Dataset S4,21 October 2024,Martha KJ,"Martha KJ,Aleru Divine,WikiWorks",Barplot of the differential abundance of micro species between LTRIs and Non-LTRIs plotted by R,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Bowdeniella|s__Bowdeniella nasicola,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium dentalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii",1783272|201174|1760|2037|2049|2767322|208480;1783272|201174|1760|85007|1653|1716|2014528;1783272|1239|186801|3082720|3118655|44259|143361;3379134|976|200643|171549|171551|836|837;3379134|203691|203692|136|2845253|157|158;3384189|32066|203490|203491|1129771|32067|157688,Complete,Folakunmi
bsdb:39277573/1/1,39277573,time series / longitudinal observational,39277573,https://doi.org/10.1038/s41522-024-00562-0,NA,"Dalby M.J., Kiu R., Serghiou I.R., Miyazaki A., Acford-Palmer H., Tung R., Caim S., Phillips S., Kujawska M., Matsui M., Iwamoto A., Taking B., Cox S.E. , Hall L.J.",Faecal microbiota and cytokine profiles of rural Cambodian infants linked to diet and diarrhoeal episodes,NPJ biofilms and microbiomes,2024,NA,Experiment 1,Cambodia,Homo sapiens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,Infants who are not breast-fed,Infants who are breast-fed,Infants that are being breastfed at the time of the research/sample collection,9,23,NA,16S,12,Illumina,centered log-ratio,MaAsLin2,0.25,TRUE,NA,NA,time,NA,decreased,NA,NA,NA,NA,Signature 1,"Figure 2D, 3D, Supplementary Data 3, Supplementary Data 6",16 October 2024,Aishat,"Aishat,KateRasheed,WikiWorks",Bacterial genera differentially abundant between breastfed infants and infants who were not breastfed at all timepoints.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|91061|186826|1300|1301|1313;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|81852|1350,Complete,Svetlana up
bsdb:39277573/1/2,39277573,time series / longitudinal observational,39277573,https://doi.org/10.1038/s41522-024-00562-0,NA,"Dalby M.J., Kiu R., Serghiou I.R., Miyazaki A., Acford-Palmer H., Tung R., Caim S., Phillips S., Kujawska M., Matsui M., Iwamoto A., Taking B., Cox S.E. , Hall L.J.",Faecal microbiota and cytokine profiles of rural Cambodian infants linked to diet and diarrhoeal episodes,NPJ biofilms and microbiomes,2024,NA,Experiment 1,Cambodia,Homo sapiens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,Infants who are not breast-fed,Infants who are breast-fed,Infants that are being breastfed at the time of the research/sample collection,9,23,NA,16S,12,Illumina,centered log-ratio,MaAsLin2,0.25,TRUE,NA,NA,time,NA,decreased,NA,NA,NA,NA,Signature 2,"Figure 2E, 3E, Supplementary Data 3, Supplementary Data 6",16 October 2024,Aishat,"Aishat,KateRasheed,WikiWorks",Bacterial species differentially abundant between breastfed infants and infants who were not breastfed at all timepoints.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium butyricum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium paraputrificum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__uncultured Akkermansia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus",3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|543|570|573;1783272|1239|186801|3085636|186803|2719313|208479;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|2941495|1512;3379134|976|200643|171549|171552|2974251|165179;3384189|32066|203490|203491|203492|848|850;3379134|976|200643|171549|815|816|818;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|186801|186802|31979|1485|1492;1783272|1239|186801|186802|31979|1485|29363;1783272|1239|186801|3082720|186804|1505657|261299;3379134|74201|203494|48461|1647988|239934|512294;1783272|1239|186801|3085636|186803|2316020|33038;3379134|1224|1236|135625|712|724;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3082720|186804|1505657;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|189330;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|572511;1783272|1239|526524|526525|2810280|3025755;3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3082720|186804|1870884;3379134|1224|1236|91347|543|547;3379134|976|200643|171549|171552|1283313;1783272|1239|91061|186826|1300|1357,Complete,Svetlana up
bsdb:39277573/2/1,39277573,time series / longitudinal observational,39277573,https://doi.org/10.1038/s41522-024-00562-0,NA,"Dalby M.J., Kiu R., Serghiou I.R., Miyazaki A., Acford-Palmer H., Tung R., Caim S., Phillips S., Kujawska M., Matsui M., Iwamoto A., Taking B., Cox S.E. , Hall L.J.",Faecal microbiota and cytokine profiles of rural Cambodian infants linked to diet and diarrhoeal episodes,NPJ biofilms and microbiomes,2024,NA,Experiment 2,Cambodia,Homo sapiens,Feces,UBERON:0001988,"Diarrhea, Infantile",EFO:1001306,Infants without diarrhea - Timepoint 1,Infants with diarrhea - Timepoint 1,Infants who experienced diarrhea within the 7 days prior to sample collection.,26,6,NA,16S,12,Illumina,centered log-ratio,MaAsLin2,0.25,TRUE,NA,NA,time,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3G,16 October 2024,Aishat,"Aishat,KateRasheed,WikiWorks",Bacterial genera differentially abundant between infants with diarrheal illness and infants without diarrheal illness at time point 1.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,1783272|1239|186801|186802|31979|1485|1502,Complete,Svetlana up
bsdb:39277573/2/2,39277573,time series / longitudinal observational,39277573,https://doi.org/10.1038/s41522-024-00562-0,NA,"Dalby M.J., Kiu R., Serghiou I.R., Miyazaki A., Acford-Palmer H., Tung R., Caim S., Phillips S., Kujawska M., Matsui M., Iwamoto A., Taking B., Cox S.E. , Hall L.J.",Faecal microbiota and cytokine profiles of rural Cambodian infants linked to diet and diarrhoeal episodes,NPJ biofilms and microbiomes,2024,NA,Experiment 2,Cambodia,Homo sapiens,Feces,UBERON:0001988,"Diarrhea, Infantile",EFO:1001306,Infants without diarrhea - Timepoint 1,Infants with diarrhea - Timepoint 1,Infants who experienced diarrhea within the 7 days prior to sample collection.,26,6,NA,16S,12,Illumina,centered log-ratio,MaAsLin2,0.25,TRUE,NA,NA,time,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2F-H, 3F",16 October 2024,Aishat,"Aishat,KateRasheed,WikiWorks",Bacterial genera differentially abundant between infants with diarrheal illness and infants without diarrheal illness at time point 1.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella flexneri",3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|620;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|543|620|623,Complete,Svetlana up
bsdb:39277573/3/1,39277573,time series / longitudinal observational,39277573,https://doi.org/10.1038/s41522-024-00562-0,NA,"Dalby M.J., Kiu R., Serghiou I.R., Miyazaki A., Acford-Palmer H., Tung R., Caim S., Phillips S., Kujawska M., Matsui M., Iwamoto A., Taking B., Cox S.E. , Hall L.J.",Faecal microbiota and cytokine profiles of rural Cambodian infants linked to diet and diarrhoeal episodes,NPJ biofilms and microbiomes,2024,NA,Experiment 3,Cambodia,Homo sapiens,Feces,UBERON:0001988,Sample treatment protocol,EFO:0003809,Frozen Samples,Deoxyribonucleic Acid Shield (DNA Shield),"Deoxyribonucleic Acid Shield (DNA Shield) is a reagent that preserves the genetic integrity of samples during collection, transport, and storage.",70,94,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,increased,NA,Signature 1,"Fig. 1D, 1F, 1G",19 December 2024,KateRasheed,"KateRasheed,WikiWorks",Differences in genus abundance between paired frozen samples and DNAShield stored samples.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3085636|186803|1506553,Complete,Svetlana up
bsdb:39277573/3/2,39277573,time series / longitudinal observational,39277573,https://doi.org/10.1038/s41522-024-00562-0,NA,"Dalby M.J., Kiu R., Serghiou I.R., Miyazaki A., Acford-Palmer H., Tung R., Caim S., Phillips S., Kujawska M., Matsui M., Iwamoto A., Taking B., Cox S.E. , Hall L.J.",Faecal microbiota and cytokine profiles of rural Cambodian infants linked to diet and diarrhoeal episodes,NPJ biofilms and microbiomes,2024,NA,Experiment 3,Cambodia,Homo sapiens,Feces,UBERON:0001988,Sample treatment protocol,EFO:0003809,Frozen Samples,Deoxyribonucleic Acid Shield (DNA Shield),"Deoxyribonucleic Acid Shield (DNA Shield) is a reagent that preserves the genetic integrity of samples during collection, transport, and storage.",70,94,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,increased,NA,Signature 2,"Fig. 1E, H-K",19 December 2024,KateRasheed,"KateRasheed,WikiWorks",Differences in genus abundance between paired frozen samples and DNAShield stored samples.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",3379134|1224|1236|91347|543|561;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|81852|1350;1783272|201174|1760|2037|2049|1654,Complete,Svetlana up
bsdb:39277573/4/1,39277573,time series / longitudinal observational,39277573,https://doi.org/10.1038/s41522-024-00562-0,NA,"Dalby M.J., Kiu R., Serghiou I.R., Miyazaki A., Acford-Palmer H., Tung R., Caim S., Phillips S., Kujawska M., Matsui M., Iwamoto A., Taking B., Cox S.E. , Hall L.J.",Faecal microbiota and cytokine profiles of rural Cambodian infants linked to diet and diarrhoeal episodes,NPJ biofilms and microbiomes,2024,NA,Experiment 4,Cambodia,Homo sapiens,Feces,UBERON:0001988,"Diarrhea, Infantile",EFO:1001306,Infants without diarrhea - Timepoint 2,Infants with diarrhea - Timepoint 2,Infants who experienced diarrhea within the 7 days prior to sample collection.,26,6,NA,16S,12,Illumina,centered log-ratio,MaAsLin2,0.25,TRUE,NA,NA,time,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 2F,19 December 2024,KateRasheed,"KateRasheed,WikiWorks",Bacterial genera differentially abundant between infants with diarrheal illness and infants without diarrheal illness at time point 2.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:39277573/4/2,39277573,time series / longitudinal observational,39277573,https://doi.org/10.1038/s41522-024-00562-0,NA,"Dalby M.J., Kiu R., Serghiou I.R., Miyazaki A., Acford-Palmer H., Tung R., Caim S., Phillips S., Kujawska M., Matsui M., Iwamoto A., Taking B., Cox S.E. , Hall L.J.",Faecal microbiota and cytokine profiles of rural Cambodian infants linked to diet and diarrhoeal episodes,NPJ biofilms and microbiomes,2024,NA,Experiment 4,Cambodia,Homo sapiens,Feces,UBERON:0001988,"Diarrhea, Infantile",EFO:1001306,Infants without diarrhea - Timepoint 2,Infants with diarrhea - Timepoint 2,Infants who experienced diarrhea within the 7 days prior to sample collection.,26,6,NA,16S,12,Illumina,centered log-ratio,MaAsLin2,0.25,TRUE,NA,NA,time,NA,NA,NA,NA,NA,NA,Signature 2,"Fig. 2G-H, 3F-G",19 December 2024,KateRasheed,"KateRasheed,WikiWorks",Bacterial genera differentially abundant between infants with diarrheal illness and infants without diarrheal illness at time point 2.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella flexneri",1783272|1239|186801|186802|31979|1485|1502;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|543|620;3379134|1224|1236|91347|543|620|623,Complete,Svetlana up
bsdb:39277573/5/1,39277573,time series / longitudinal observational,39277573,https://doi.org/10.1038/s41522-024-00562-0,NA,"Dalby M.J., Kiu R., Serghiou I.R., Miyazaki A., Acford-Palmer H., Tung R., Caim S., Phillips S., Kujawska M., Matsui M., Iwamoto A., Taking B., Cox S.E. , Hall L.J.",Faecal microbiota and cytokine profiles of rural Cambodian infants linked to diet and diarrhoeal episodes,NPJ biofilms and microbiomes,2024,NA,Experiment 5,Cambodia,Homo sapiens,Feces,UBERON:0001988,"Diarrhea, Infantile",EFO:1001306,Infants without diarrhea - Timepoint 3,Infants with diarrhea - Timepoint 3,Infants who experienced diarrhea within the 7 days prior to sample collection.,26,6,NA,16S,12,Illumina,centered log-ratio,MaAsLin2,0.25,TRUE,NA,NA,time,NA,NA,NA,NA,NA,NA,Signature 1,"Fig. 2G-H, 3G",19 December 2024,KateRasheed,"KateRasheed,WikiWorks",Bacterial genera differentially abundant between infants with diarrheal illness and infants without diarrheal illness at time point 3,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens",3379134|1224|1236|91347|543|620;3379134|1224|1236|91347|543|570;1783272|1239|186801|186802|31979|1485|1502,Complete,Svetlana up
bsdb:39277573/5/2,39277573,time series / longitudinal observational,39277573,https://doi.org/10.1038/s41522-024-00562-0,NA,"Dalby M.J., Kiu R., Serghiou I.R., Miyazaki A., Acford-Palmer H., Tung R., Caim S., Phillips S., Kujawska M., Matsui M., Iwamoto A., Taking B., Cox S.E. , Hall L.J.",Faecal microbiota and cytokine profiles of rural Cambodian infants linked to diet and diarrhoeal episodes,NPJ biofilms and microbiomes,2024,NA,Experiment 5,Cambodia,Homo sapiens,Feces,UBERON:0001988,"Diarrhea, Infantile",EFO:1001306,Infants without diarrhea - Timepoint 3,Infants with diarrhea - Timepoint 3,Infants who experienced diarrhea within the 7 days prior to sample collection.,26,6,NA,16S,12,Illumina,centered log-ratio,MaAsLin2,0.25,TRUE,NA,NA,time,NA,NA,NA,NA,NA,NA,Signature 2,"Fig. 2F, 3F",19 December 2024,KateRasheed,"KateRasheed,WikiWorks",Bacterial genera differentially abundant between infants with diarrheal illness and infants without diarrheal illness at time point 3.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella flexneri",3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|620|623,Complete,Svetlana up
bsdb:39277616/1/1,39277616,laboratory experiment,39277616,doi: 10.1038/s41598-024-72057-z,NA,"Hanyue Wang, Honghui Liu, Jie Peng, Jie Wang, Ya Liu, Yan Jia, Yilin Huang, Yuxin Shi",Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis,Scientific Reports 14,2024,"Acute pancreatitis, gut microbiota, metabolomics, metagenomics",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Acute pancreatitis,EFO:1000652,Control group,Caeurulein group,"Caerulein group was induced by hourly intraperitoneal (i.p.) injection of caerulein (200 μg/kg, once an hour for a total of 10 times).",NA,NA,NA,WMS,NA,MGISEQ-2000,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,unchanged,NA,NA,Signature 1,Table S1,31 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in the gut microbiota between control group and caerulein group,increased,"k__Pseudomonadati|p__Kiritimatiellota,k__Pseudomonadati|p__Ignavibacteriota,k__Fungi|p__Basidiomycota,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Calditrichota,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia,k__Pseudomonadati|p__Gemmatimonadota,k__Pseudomonadati|p__Candidatus Cloacimonadota,k__Pseudomonadati|p__Chrysiogenota,k__Pseudomonadati|p__Lentisphaerota,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Chlorobiota,k__Pseudomonadati|p__Fibrobacterota,k__Pseudomonadati|p__Candidatus Zixiibacteriota,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Planctomycetota,k__Pseudomonadati|p__Balneolota,k__Bacillati|p__Armatimonadota,k__Pseudomonadati|p__Acidobacteriota",3379134|134625;3379134|1134404;4751|5204;3379134|1224;3379134|1930617;3379134|74152|641853;3379134|142182;3379134|456828;3379134|200938;3379134|256845;3379134|74201;3379134|1090;3379134|65842;3379134|1379697;3379134|976;3379134|203682;3379134|1936987;1783272|67819;3379134|57723,Complete,Folakunmi
bsdb:39277616/1/2,39277616,laboratory experiment,39277616,doi: 10.1038/s41598-024-72057-z,NA,"Hanyue Wang, Honghui Liu, Jie Peng, Jie Wang, Ya Liu, Yan Jia, Yilin Huang, Yuxin Shi",Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis,Scientific Reports 14,2024,"Acute pancreatitis, gut microbiota, metabolomics, metagenomics",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Acute pancreatitis,EFO:1000652,Control group,Caeurulein group,"Caerulein group was induced by hourly intraperitoneal (i.p.) injection of caerulein (200 μg/kg, once an hour for a total of 10 times).",NA,NA,NA,WMS,NA,MGISEQ-2000,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,unchanged,NA,NA,Signature 2,Table S1,31 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in the gut microbiota between control group and caerulein group,decreased,"k__Thermoproteati|p__Thermoproteota,k__Pseudomonadati|p__Aquificota,k__Metazoa|p__Chordata,k__Pseudomonadati|p__Thermodesulfobacteriota,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Caldisericota,k__Thermoproteati|p__Nitrososphaerota,k__Promethearchaeati|p__Promethearchaeota,p__Candidatus Altimarinota,k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Dictyoglomota,k__Bacillati|p__Bacillota",1783275|28889;3379134|200783;33208|7711;3379134|200940;1783272|544448;3379134|67814;1783275|651137;1935183|3366641;363464;3384189|32066;3379134|68297;1783272|1239,Complete,Folakunmi
bsdb:39277616/2/1,39277616,laboratory experiment,39277616,doi: 10.1038/s41598-024-72057-z,NA,"Hanyue Wang, Honghui Liu, Jie Peng, Jie Wang, Ya Liu, Yan Jia, Yilin Huang, Yuxin Shi",Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis,Scientific Reports 14,2024,"Acute pancreatitis, gut microbiota, metabolomics, metagenomics",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Acute pancreatitis,EFO:1000652,Control group,Caeurulein group,"Caerulein group was induced by hourly intraperitoneal (i.p.) injection of caerulein (200 μg/kg, once an hour for a total of 10 times).",NA,NA,NA,WMS,NA,MGISEQ-2000,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,unchanged,unchanged,NA,NA,Signature 1,Fig. 4C,9 October 2024,KateRasheed,"KateRasheed,Folakunmi,WikiWorks",Differential abundance in the gut microbiota between control group and caerulein group,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium YL45,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas faecalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum|s__Muribaculum gordoncarteri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum|s__Muribaculum intestinale,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Sodaliphilus|s__Sodaliphilus pleomorphus",3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|818;3379134|1224|28216|80840|1834205;3379134|976|200643|171549|1853231|574697|2093856;3379134|976|200643|171549|2005473|1918540|2530390;3379134|976|200643|171549|2005473|1918540|1796646;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|2005473|2815786|2606626,Complete,Folakunmi
bsdb:39277616/2/2,39277616,laboratory experiment,39277616,doi: 10.1038/s41598-024-72057-z,NA,"Hanyue Wang, Honghui Liu, Jie Peng, Jie Wang, Ya Liu, Yan Jia, Yilin Huang, Yuxin Shi",Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis,Scientific Reports 14,2024,"Acute pancreatitis, gut microbiota, metabolomics, metagenomics",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Acute pancreatitis,EFO:1000652,Control group,Caeurulein group,"Caerulein group was induced by hourly intraperitoneal (i.p.) injection of caerulein (200 μg/kg, once an hour for a total of 10 times).",NA,NA,NA,WMS,NA,MGISEQ-2000,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,unchanged,unchanged,NA,NA,Signature 2,Fig. 4C,9 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in the gut microbiota between control group and caerulein group,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium CCNA10,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Flintibacter|s__Flintibacter sp. KGMB00164,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium phocaeense,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. YL32,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium GAM79,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Massilistercora|s__Massilistercora timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta",1783272|1239|186801|186802|2109688;1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|186802|1918454|2610895;1783272|1239|186801|3085636|186803|1506553|1871021;1783272|1239|186801|3085636|186803|1506553|1834196;1783272|1239|186801|3085636|186803|2109691;1783272|1239|186801|186802|2717089|2086584;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|1506553|29347;1783272|1239|186801|3085636|186803|572511|33035,Complete,Folakunmi
bsdb:39277616/3/1,39277616,laboratory experiment,39277616,doi: 10.1038/s41598-024-72057-z,NA,"Hanyue Wang, Honghui Liu, Jie Peng, Jie Wang, Ya Liu, Yan Jia, Yilin Huang, Yuxin Shi",Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis,Scientific Reports 14,2024,"Acute pancreatitis, gut microbiota, metabolomics, metagenomics",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Acute pancreatitis,EFO:1000652,Control group,Caeurulein+LPS group,"Caerulein + LPS group was administered by hourly i.p. injection of caerulein (200 μg/kg, once an hour for a total of 10 times) combined with a dose of 5 mg/kg lipopolysaccharide (LPS).",NA,NA,NA,WMS,NA,MGISEQ-2000,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,increased,NA,NA,Signature 1,Fig. 4D,9 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in the gut microbiota between control group and caerulein+LPS group,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium YL45,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas faecalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum|s__Muribaculum intestinale,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum|s__Muribaculum gordoncarteri",3379134|1224|28216|80840|1834205;3379134|976|200643|171549|1853231|574697|2093856;3379134|1224|1236|91347|543|561|562;3379134|976|200643|171549|2005473|1918540|1796646;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|2005473|1918540|2530390,Complete,Folakunmi
bsdb:39277616/3/2,39277616,laboratory experiment,39277616,doi: 10.1038/s41598-024-72057-z,NA,"Hanyue Wang, Honghui Liu, Jie Peng, Jie Wang, Ya Liu, Yan Jia, Yilin Huang, Yuxin Shi",Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis,Scientific Reports 14,2024,"Acute pancreatitis, gut microbiota, metabolomics, metagenomics",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Acute pancreatitis,EFO:1000652,Control group,Caeurulein+LPS group,"Caerulein + LPS group was administered by hourly i.p. injection of caerulein (200 μg/kg, once an hour for a total of 10 times) combined with a dose of 5 mg/kg lipopolysaccharide (LPS).",NA,NA,NA,WMS,NA,MGISEQ-2000,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,increased,NA,NA,Signature 2,Fig. 4D,9 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in the gut microbiota between control group and caerulein+LPS group,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes dispar,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes megaguti,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Duncaniella|s__Duncaniella dubosii",3379134|976|200643|171549|171550|239759|2585118;3379134|976|200643|171549|171550|239759|2585119;3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|171550|239759|2364787;3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|2005473|2518495|2518971,Complete,Folakunmi
bsdb:39277616/4/1,39277616,laboratory experiment,39277616,doi: 10.1038/s41598-024-72057-z,NA,"Hanyue Wang, Honghui Liu, Jie Peng, Jie Wang, Ya Liu, Yan Jia, Yilin Huang, Yuxin Shi",Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis,Scientific Reports 14,2024,"Acute pancreatitis, gut microbiota, metabolomics, metagenomics",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Acute pancreatitis,EFO:1000652,Control group,L-arginine group,"Mice in the L-arginine group received 2 times i.p. injection of L-arginine (4 g/kg, once an hour, twice in total).",NA,NA,NA,WMS,NA,MGISEQ-2000,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,unchanged,NA,NA,Signature 1,Fig. 4E,9 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in the gut microbiota between control group and L-arginine group,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium YL45,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus murinus",3379134|1224|28216|80840|1834205;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|91061|186826|33958|1578|33959;1783272|1239|91061|186826|33958|2767887|1622,Complete,Folakunmi
bsdb:39277616/4/2,39277616,laboratory experiment,39277616,doi: 10.1038/s41598-024-72057-z,NA,"Hanyue Wang, Honghui Liu, Jie Peng, Jie Wang, Ya Liu, Yan Jia, Yilin Huang, Yuxin Shi",Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis,Scientific Reports 14,2024,"Acute pancreatitis, gut microbiota, metabolomics, metagenomics",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Acute pancreatitis,EFO:1000652,Control group,L-arginine group,"Mice in the L-arginine group received 2 times i.p. injection of L-arginine (4 g/kg, once an hour, twice in total).",NA,NA,NA,WMS,NA,MGISEQ-2000,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,unchanged,NA,NA,Signature 2,Fig. 4E,9 October 2024,KateRasheed,"KateRasheed,Folakunmi,WikiWorks",Differential abundance in the gut microbiota between control group and L-arginine group,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes dispar,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes megaguti,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium CCNA10,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Flintibacter|s__Flintibacter sp. KGMB00164,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium phocaeense,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium GAM79,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens",3379134|976|200643|171549|171550|239759|2585118;3379134|976|200643|171549|171550|239759|2585119;3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|171550|239759|2364787;3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|171550|239759|328814;1783272|1239|186801|3085636|186803|572511|33035;1783272|1239|186801|186802|2109688;1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|186802|1918454|2610895;1783272|1239|186801|3085636|186803|1506553|1871021;1783272|1239|186801|3085636|186803|2109691;1783272|1239|186801|3085636|186803|1506553|29347,Complete,Folakunmi
bsdb:39277616/5/1,39277616,laboratory experiment,39277616,doi: 10.1038/s41598-024-72057-z,NA,"Hanyue Wang, Honghui Liu, Jie Peng, Jie Wang, Ya Liu, Yan Jia, Yilin Huang, Yuxin Shi",Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis,Scientific Reports 14,2024,"Acute pancreatitis, gut microbiota, metabolomics, metagenomics",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Acute pancreatitis,EFO:1000652,Control group,Caeurulein+LPS group,"Caerulein + LPS group was administered by hourly i.p. injection of caerulein (200 μg/kg, once an hour for a total of 10 times) combined with a dose of 5 mg/kg lipopolysaccharide (LPS).",NA,NA,NA,WMS,NA,MGISEQ-2000,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,increased,NA,NA,Signature 1,Table S1,1 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in the gut microbiota between control group and caerulein+LPS group,increased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Candidatus Zixiibacteriota,k__Pseudomonadati|p__Fibrobacterota,k__Pseudomonadati|p__Deferribacterota,k__Pseudomonadati|p__Coprothermobacterota,k__Pseudomonadati|p__Verrucomicrobiota",3379134|1224;3379134|1379697;3379134|65842;3379134|200930;3379134|2138240;3379134|74201,Complete,Folakunmi
bsdb:39277616/5/2,39277616,laboratory experiment,39277616,doi: 10.1038/s41598-024-72057-z,NA,"Hanyue Wang, Honghui Liu, Jie Peng, Jie Wang, Ya Liu, Yan Jia, Yilin Huang, Yuxin Shi",Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis,Scientific Reports 14,2024,"Acute pancreatitis, gut microbiota, metabolomics, metagenomics",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Acute pancreatitis,EFO:1000652,Control group,Caeurulein+LPS group,"Caerulein + LPS group was administered by hourly i.p. injection of caerulein (200 μg/kg, once an hour for a total of 10 times) combined with a dose of 5 mg/kg lipopolysaccharide (LPS).",NA,NA,NA,WMS,NA,MGISEQ-2000,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,increased,NA,NA,Signature 2,Table S1,1 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in the gut microbiota between control group and caerulein+LPS group,decreased,"k__Pseudomonadati|p__Caldisericota,p__Candidatus Saccharimonadota,p__Candidatus Altimarinota,k__Thermoproteati|p__Thermoproteota",3379134|67814;95818;363464;1783275|28889,Complete,Folakunmi
bsdb:39277616/6/1,39277616,laboratory experiment,39277616,doi: 10.1038/s41598-024-72057-z,NA,"Hanyue Wang, Honghui Liu, Jie Peng, Jie Wang, Ya Liu, Yan Jia, Yilin Huang, Yuxin Shi",Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis,Scientific Reports 14,2024,"Acute pancreatitis, gut microbiota, metabolomics, metagenomics",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Acute pancreatitis,EFO:1000652,Control group,L-arginine group,"Mice in the L-arginine group received 2 times i.p. injection of L-arginine (4 g/kg, once an hour, twice in total).",NA,NA,NA,WMS,NA,MGISEQ-2000,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,unchanged,NA,NA,Signature 1,Table S1,1 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in the gut microbiota between control group and L-arginine group,decreased,"p__Candidatus Bipolaricaulota,k__Pseudomonadati|p__Caldisericota,k__Promethearchaeati|p__Promethearchaeota,k__Thermoproteati|p__Nitrososphaerota,k__Methanobacteriati|p__Methanobacteriota",67810;3379134|67814;1935183|3366641;1783275|651137;3366610|28890,Complete,Folakunmi
bsdb:39277616/6/2,39277616,laboratory experiment,39277616,doi: 10.1038/s41598-024-72057-z,NA,"Hanyue Wang, Honghui Liu, Jie Peng, Jie Wang, Ya Liu, Yan Jia, Yilin Huang, Yuxin Shi",Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis,Scientific Reports 14,2024,"Acute pancreatitis, gut microbiota, metabolomics, metagenomics",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Acute pancreatitis,EFO:1000652,Control group,L-arginine group,"Mice in the L-arginine group received 2 times i.p. injection of L-arginine (4 g/kg, once an hour, twice in total).",NA,NA,NA,WMS,NA,MGISEQ-2000,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,unchanged,NA,NA,Signature 2,Table S1,1 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance in the gut microbiota between control group and L-arginine group,increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Chlorobiota,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Candidatus Zixiibacteriota,k__Nanobdellati|p__Microcaldota,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Fibrobacterota",3379134|976;3379134|1090;1783272|1239;3379134|1379697;1783276|1801631;3379134|1224;3379134|65842,Complete,Folakunmi
bsdb:39282716/1/1,39282716,case-control,39282716,10.1002/ppul.27253,NA,"Yang X., Jiao W., Zeng X., Yu J., Xiao J., Jiang T., Tang H., Bi J., Chen Y., Li X., Chen W., Chen Y., Shen A. , Sun L.",Assessment of lower respiratory tract microbiota associated with pulmonary tuberculosis in children,Pediatric pulmonology,2024,"child, lower respiratory tract, respiratory microbiota, tuberculosis",Experiment 1,China,Homo sapiens,Sputum,UBERON:0007311,Pulmonary tuberculosis,EFO:1000049,non severe group TB (DC group),Active pulmonary tuberculosis (severe TB),children with active pulmonary TB (bacteriologically confirmed or clinically diagnosed),70,15,3 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 2C,28 July 2025,Nuerteye,Nuerteye,"Comparisons of respiratory microbiota in severe TB and non‐severe TB groups. (A) Relative abundance of the top 10 respiratory microbiota at the phylum level. Relative abundance of the top 10 respiratory microbiota at the genus level. Linear discriminant analysis
(LDA) score histogram",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Chloroflexota|c__Chloroflexia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Frankiales,k__Bacillati|p__Actinomycetota|c__Thermoleophilia|o__Gaiellales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Bacillati|p__Chloroflexota|c__Ktedonobacteria|o__Ktedonobacterales|f__Ktedonobacteraceae,k__Bacillati|p__Chloroflexota|c__Ktedonobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae,k__Bacillati|p__Actinomycetota|c__Thermoleophilia|o__Solirubrobacterales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Sporolactobacillaceae,k__Bacillati|p__Actinomycetota|c__Thermoleophilia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae",1783272|201174|1760|2037|2049|1654|55565;1783272|1239|91061|1385|186823;1783272|1239|91061|1385|186817;1783272|1239|91061|1385;1783272|1239|91061|1385|186817|1386;1783272|1239|91061|186826|186828;1783272|200795|32061;1783272|201174|1760|85013;1783272|201174|1497346|1154584;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724|727;1783272|200795|388447|388448|388449;1783272|200795|388447;1783272|1239|91061|1385|186822;1783272|201174|1497346|588673;1783272|1239|91061|1385|186821;1783272|201174|1497346;1783272|201174|1760|85011|2062,Complete,NA
bsdb:39282716/1/2,39282716,case-control,39282716,10.1002/ppul.27253,NA,"Yang X., Jiao W., Zeng X., Yu J., Xiao J., Jiang T., Tang H., Bi J., Chen Y., Li X., Chen W., Chen Y., Shen A. , Sun L.",Assessment of lower respiratory tract microbiota associated with pulmonary tuberculosis in children,Pediatric pulmonology,2024,"child, lower respiratory tract, respiratory microbiota, tuberculosis",Experiment 1,China,Homo sapiens,Sputum,UBERON:0007311,Pulmonary tuberculosis,EFO:1000049,non severe group TB (DC group),Active pulmonary tuberculosis (severe TB),children with active pulmonary TB (bacteriologically confirmed or clinically diagnosed),70,15,3 months,16S,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 2C,28 July 2025,Nuerteye,Nuerteye,"Comparisons of respiratory microbiota in severe TB and non‐severe TB groups. (A) Relative abundance of the top 10 respiratory microbiota at the phylum level. Relative abundance of the top 10 respiratory microbiota at the genus level. Linear discriminant analysis
(LDA) score histogram",decreased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,3379134|1224|28216|80840,Complete,NA
bsdb:39282716/2/1,39282716,case-control,39282716,10.1002/ppul.27253,NA,"Yang X., Jiao W., Zeng X., Yu J., Xiao J., Jiang T., Tang H., Bi J., Chen Y., Li X., Chen W., Chen Y., Shen A. , Sun L.",Assessment of lower respiratory tract microbiota associated with pulmonary tuberculosis in children,Pediatric pulmonology,2024,"child, lower respiratory tract, respiratory microbiota, tuberculosis",Experiment 2,China,Homo sapiens,Sputum,UBERON:0007311,Pulmonary tuberculosis,EFO:1000049,clinical diagnosis (negative),bacteriologically confirmed TB (positive),children with active pulmonary TB (bacteriologically confirmed or clinically diagnosed),34,51,3 months,16S,NA,Illumina,NA,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 3D,28 July 2025,Nuerteye,Nuerteye,"Association of respiratory microbiota with bacteriologically confirmed TB. (D) Identification of species with significant differences in abundance between the two groups
using LEfSe (LDA effect size) analysis.",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus",1783272|1239|91061|1385|186822;1783272|1239|91061|1385|186822|44249,Complete,NA
bsdb:39282716/2/2,39282716,case-control,39282716,10.1002/ppul.27253,NA,"Yang X., Jiao W., Zeng X., Yu J., Xiao J., Jiang T., Tang H., Bi J., Chen Y., Li X., Chen W., Chen Y., Shen A. , Sun L.",Assessment of lower respiratory tract microbiota associated with pulmonary tuberculosis in children,Pediatric pulmonology,2024,"child, lower respiratory tract, respiratory microbiota, tuberculosis",Experiment 2,China,Homo sapiens,Sputum,UBERON:0007311,Pulmonary tuberculosis,EFO:1000049,clinical diagnosis (negative),bacteriologically confirmed TB (positive),children with active pulmonary TB (bacteriologically confirmed or clinically diagnosed),34,51,3 months,16S,NA,Illumina,NA,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 3D,28 July 2025,Nuerteye,Nuerteye,Association of respiratory microbiota with bacteriologically confirmed TB. (D) Identification of species with significant differences in abundance between the two groups using LEfSe (LDA effect size) analysis.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|s__Christensenellaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella",1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|33042;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|1263;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3082768;1783272|1239|186801|3082768|990719|2054177;1783272|1239|186801|186802|216572|292632;1783272|201174|1760|85004|31953|1678|1680;1783272|1239|91061|186826|186828;1783272|1239|91061|186826|186828|117563,Complete,NA
bsdb:39287377/1/1,39287377,"cross-sectional observational, not case-control",39287377,10.1128/msystems.00968-24,NA,"Xu Y., Yu M., Huang X., Wang G., Wang H., Zhang F., Zhang J. , Gao X.",Differences in salivary microbiome among children with tonsillar hypertrophy and/or adenoid hypertrophy,mSystems,2024,"16s rRNA sequencing, oral microbiome, tonsillar hypertrophy",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Hypertrophy,EFO:0002460,Control + Adenotonsillar hypertrophy (ATH) group,Tonsillar hypertrophy (TH),These are children diagnosed with severe tonsillar hypertrophy (TH). It was divided into larger tonsillar hypertrophy group THL (n = 26) and smaller tonsillar hypertrophy group THS (n = 20),45,46,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 2A-B,8 October 2024,Rahila,"Rahila,KateRasheed,WikiWorks,Ese",Linear discriminant analysis (LDA)  scores showing significant taxonomic differences among the Tonsillar hypertrophy (TH) group and ATH + control groups.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces dentalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera geminata,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,p__Candidatus Saccharimonadota|c__Candidatus Nanoperiomorbia|o__Candidatus Nanoperiomorbales|f__Candidatus Nanoperiomorbaceae,p__Candidatus Saccharimonadota|c__Candidatus Nanoperiomorbia|o__Candidatus Nanoperiomorbales|f__Candidatus Nanoperiomorbaceae|g__Candidatus Nanoperiomorbus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium valvarum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Elizabethkingia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Elizabethkingia|s__Elizabethkingia anophelis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor villosus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sputorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium UBA3282,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Pauljensenia|s__Pauljensenia hongkongensis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella micans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Tatumella|s__Tatumella ptyseos,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Dialisteraceae",1783272|201174|1760|2037|2049|1654|272548;1783272|201174|1760|2037|2049|1654|544580;1783272|1239|909932|1843489|31977|906|156456;1783272|1239|91061|1385|186817;1783272|1239|91061|1385;1783272|1239|91061|1385|186817|1386;3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;95818|2171981|2171983|2171987;95818|2171981|2171983|2171987|2171988;3379134|976|117743|200644|49546|1016|1018;3379134|1224|1236|135615|868|2717|194702;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|39948|218538;3379134|976|117743|200644|2762318|308865;3379134|976|117743|200644|2762318|308865|1117645;1783272|1239|186801|3082720|3118655|44259;1783272|1239|186801|3082720|3118655|44259|29374;3384189|32066|203490|203491|203492|848|851;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|1385|539738|1378|29391;1783272|1239|91061|1385|539738;1783272|1239|91061|186826|186828|117563|137732;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712|724|1078480;1783272|1239|186801|3085636|186803|1952023;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;3384189|32066|203490|203491|1129771|32067|40542;1783272|1239|186801|3085636|186803|265975|1969407;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|201174|1760|2037|2049|2740557|178339;1783272|1239|1737404|1737405|1570339;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|171552|838|28131;3379134|976|200643|171549|171552|838|189723;3379134|976|200643|171549|171552|838|28133;1783272|1239|91061|186826|1300|1301|76860;3379134|1224|1236|91347|1903409|82986|82987;1783272|1239|1737404|1737405;3379134|203691|203692|136|2845253|157|158;1783272|1239|909932|1843489|3120688,Complete,Svetlana up
bsdb:39287377/2/1,39287377,"cross-sectional observational, not case-control",39287377,10.1128/msystems.00968-24,NA,"Xu Y., Yu M., Huang X., Wang G., Wang H., Zhang F., Zhang J. , Gao X.",Differences in salivary microbiome among children with tonsillar hypertrophy and/or adenoid hypertrophy,mSystems,2024,"16s rRNA sequencing, oral microbiome, tonsillar hypertrophy",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Hypertrophy,EFO:0002460,Control + Tonsillar Hypertrophy (TH) group,Adenotonsillar hypertrophy (ATH),The adenotonsillar hypertrophy (ATH) group consists of children who are diagnosed with Grade III tonsillar hypertrophy and Grade III or IV adenoid hypertrophy simultaneously,68,23,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,FIG 2A-B,8 October 2024,Rahila,"Rahila,MyleeeA,KateRasheed,WikiWorks",Linear discriminant analysis (LDA)  scores showing significant taxonomic differences among the adenotonsillar hypertrophy (ATH) group and TH + control groups.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella sp.",1783272|201174|84998|84999|1643824;1783272|201174|84998|84999|1643824|2767353;1783272|1239|909932|1843489|31977|906|187326;3379134|976|200643|171549|171552|2974251|228604;1783272|1239|909932|1843489|31977|29465|39777;1783272|201174|84998|84999|1643824|2767353|3088136,Complete,Svetlana up
bsdb:39287377/3/1,39287377,"cross-sectional observational, not case-control",39287377,10.1128/msystems.00968-24,NA,"Xu Y., Yu M., Huang X., Wang G., Wang H., Zhang F., Zhang J. , Gao X.",Differences in salivary microbiome among children with tonsillar hypertrophy and/or adenoid hypertrophy,mSystems,2024,"16s rRNA sequencing, oral microbiome, tonsillar hypertrophy",Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Hypertrophy,EFO:0002460,TH + ATH groups,Control group,Control group refers to children without tonsillar and/or adenoid hypertrophy.,69,22,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 2A-B,6 January 2025,KateRasheed,"KateRasheed,WikiWorks",Linear discriminant analysis (LDA)  scores showing significant taxonomic differences among the adenotonsillar hypertrophy (ATH) + TH groups and control group.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda|s__Centipeda periodontii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oulorum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella loescheii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum saburreum",1783272|1239|909932|909929|1843491|82202|82203;3379134|976|200643|171549|171552|2974251|28136;3379134|976|200643|171549|171552|2974257|840;1783272|1239|186801|3085636|186803|1164882|467210,Complete,Svetlana up
bsdb:39287377/4/1,39287377,"cross-sectional observational, not case-control",39287377,10.1128/msystems.00968-24,NA,"Xu Y., Yu M., Huang X., Wang G., Wang H., Zhang F., Zhang J. , Gao X.",Differences in salivary microbiome among children with tonsillar hypertrophy and/or adenoid hypertrophy,mSystems,2024,"16s rRNA sequencing, oral microbiome, tonsillar hypertrophy",Experiment 4,China,Homo sapiens,Saliva,UBERON:0001836,Hypertrophy,EFO:0002460,Control group,Tonsillar Hypertrophy (TH),Salivary microbial profile in children with a larger tonsillar hypertrophy group diagnosed with Grade III tonsillar hypertrophy,22,46,3 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,age,NA,NA,increased,increased,NA,NA,increased,Signature 1,Fig. 3A,6 January 2025,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between control group and tonsillar hypertrophy; using Kruskal-wallis test,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",1783272|1239|91061|1385|539738|1378;1783272|1239|909932|1843489|31977|39948;3379134|1224|1236|135625|712|724,Complete,Svetlana up
bsdb:39287377/5/1,39287377,"cross-sectional observational, not case-control",39287377,10.1128/msystems.00968-24,NA,"Xu Y., Yu M., Huang X., Wang G., Wang H., Zhang F., Zhang J. , Gao X.",Differences in salivary microbiome among children with tonsillar hypertrophy and/or adenoid hypertrophy,mSystems,2024,"16s rRNA sequencing, oral microbiome, tonsillar hypertrophy",Experiment 5,China,Homo sapiens,Saliva,UBERON:0001836,Hypertrophy,EFO:0002460,Adenotonsillar hypertrophy (ATH),Tonsillar hypertrophy (TH),The salivary microbial profile in children diagnosed with severe tonsillar hypertrophy (TH).,23,46,3 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,age,NA,NA,unchanged,increased,NA,NA,increased,Signature 1,Fig. 3A,9 October 2024,Rahila,"Rahila,KateRasheed,WikiWorks",Differential abundance of taxa between adenoid tonsillar group and tonsillar hypertrophy; using Kruskal-wallis test,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",1783272|1239|91061|1385|186817|1386;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3082720|3118655|44259;1783272|1239|91061|1385|539738|1378;1783272|1239|1737404|1737405|1570339|543311;3379134|203691|203692|136|2845253|157,Complete,Svetlana up
bsdb:39287377/5/2,39287377,"cross-sectional observational, not case-control",39287377,10.1128/msystems.00968-24,NA,"Xu Y., Yu M., Huang X., Wang G., Wang H., Zhang F., Zhang J. , Gao X.",Differences in salivary microbiome among children with tonsillar hypertrophy and/or adenoid hypertrophy,mSystems,2024,"16s rRNA sequencing, oral microbiome, tonsillar hypertrophy",Experiment 5,China,Homo sapiens,Saliva,UBERON:0001836,Hypertrophy,EFO:0002460,Adenotonsillar hypertrophy (ATH),Tonsillar hypertrophy (TH),The salivary microbial profile in children diagnosed with severe tonsillar hypertrophy (TH).,23,46,3 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,age,NA,NA,unchanged,increased,NA,NA,increased,Signature 2,Fig. 3B,6 January 2025,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between adenoid tonsillar group and tonsillar hypertrophy; using Kruskal-wallis test,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera",1783272|1239|909932|1843489|31977|29465;3379134|976|200643|171549|171552|838;1783272|1239|909932|1843489|31977|156454,Complete,Svetlana up
bsdb:39287377/6/1,39287377,"cross-sectional observational, not case-control",39287377,10.1128/msystems.00968-24,NA,"Xu Y., Yu M., Huang X., Wang G., Wang H., Zhang F., Zhang J. , Gao X.",Differences in salivary microbiome among children with tonsillar hypertrophy and/or adenoid hypertrophy,mSystems,2024,"16s rRNA sequencing, oral microbiome, tonsillar hypertrophy",Experiment 6,China,Homo sapiens,Saliva,UBERON:0001836,Hypertrophy,EFO:0002460,Adenoid hypertrophy (AH),Tonsillar hypertrophy (TH),The salivary microbial profile in children diagnosed with severe tonsillar hypertrophy (TH).,21,46,3 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,age,NA,NA,unchanged,increased,NA,NA,increased,Signature 1,FIG 3A,9 October 2024,Rahila,"Rahila,KateRasheed,WikiWorks",Significant taxonomic differences among the tonsillar hypertrophy (TH) group and adenoid hypertrophy (AH) group using Kruskal-Wallis test.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus",1783272|201174|1760|85004|31953|1678;1783272|1239|909932|1843489|31977|39948;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|1385|186817|1386,Complete,Svetlana up
bsdb:39287377/7/1,39287377,"cross-sectional observational, not case-control",39287377,10.1128/msystems.00968-24,NA,"Xu Y., Yu M., Huang X., Wang G., Wang H., Zhang F., Zhang J. , Gao X.",Differences in salivary microbiome among children with tonsillar hypertrophy and/or adenoid hypertrophy,mSystems,2024,"16s rRNA sequencing, oral microbiome, tonsillar hypertrophy",Experiment 7,China,Homo sapiens,Saliva,UBERON:0001836,Hypertrophy,EFO:0002460,Control group,Adenoid hypertrophy (AH),"The adenoid hypertrophy (AH) group, comprises 21 children diagnosed with Grade III or IV adenoid hypertrophy through fibro-laryngoscopic examination",22,21,3 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,age,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Fig. 3A,6 January 2025,KateRasheed,"KateRasheed,WikiWorks",Significant taxonomic differences among the control group and adenoid hypertrophy (AH) group using Kruskal-Wallis test.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,3379134|1224|1236|135625|712|724,Complete,Svetlana up
bsdb:39287377/8/1,39287377,"cross-sectional observational, not case-control",39287377,10.1128/msystems.00968-24,NA,"Xu Y., Yu M., Huang X., Wang G., Wang H., Zhang F., Zhang J. , Gao X.",Differences in salivary microbiome among children with tonsillar hypertrophy and/or adenoid hypertrophy,mSystems,2024,"16s rRNA sequencing, oral microbiome, tonsillar hypertrophy",Experiment 8,China,Homo sapiens,Saliva,UBERON:0001836,Hypertrophy,EFO:0002460,Control group,Adenotonsillar hypertrophy (ATH),The adenotonsillar hypertrophy (ATH) group consists of children who are diagnosed with Grade III tonsillar hypertrophy and Grade III or IV adenoid hypertrophy simultaneously,22,23,3 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,age,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Fig. 3A,6 January 2025,KateRasheed,"KateRasheed,WikiWorks",Significant taxonomic differences among the ATH  and control groups.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,3379134|1224|1236|135625|712|724,Complete,Svetlana up
bsdb:39293692/1/1,39293692,laboratory experiment,39293692,https://doi.org/10.1016/j.bbi.2024.09.020,https://pubmed.ncbi.nlm.nih.gov/39293692/,"Masson B.A., Kiridena P., Lu D., Kleeman E.A., Reisinger S.N., Qin W., Davies W.J., Muralitharan R.R., Jama H.A., Antonacci S., Marques F.Z., Gubert C. , Hannan A.J.",Depletion of the paternal gut microbiome alters sperm small RNAs and impacts offspring physiology and behavior in mice,"Brain, behavior, and immunity",2024,"Antibiotics, Anxiety, Behavior, Depression, Dysbiosis, Gut microbiota, Microbiome, Noncoding RNAs, Paternal epigenetic inheritance",Experiment 1,Australia,Mus musculus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Male Mice that received drinking water without any antibiotics.,Male Mice that were administered a cocktail of non-absorbable antibiotics to deplete their gut microbiota,"This group was defined by the condition where the male mice were exposed to antibiotics, leading to significant depletion of their gut microbiota. This was intended to assess the impact of gut microbiome depletion on their offspring",NA,NA,NA,16S,4,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,sex,NA,decreased,NA,NA,NA,NA,Signature 1,Table 1,7 October 2024,Wendy640,"Wendy640,Shulamite,WikiWorks","Taxas significantly higher in the control group compared to antibiotic treated
males after adjusting for cohort effects.",increased,NA,NA,Complete,Svetlana up
bsdb:39300532/1/1,39300532,laboratory experiment,39300532,10.1186/s40168-024-01896-9,NA,"Zhang S., Nie Q., Sun Y., Zuo S., Chen C., Li S., Yang J., Hu J., Zhou X., Yu Y., Huang P., Lian L., Xie M. , Nie S.",Bacteroides uniformis degrades β-glucan to promote Lactobacillus johnsonii improving indole-3-lactic acid levels in alleviating colitis,Microbiome,2024,"Bacteroides uniformis, Lactobacillus johnsonii, β-glucan, Aryl hydrocarbon receptor, Cross-feeding, Indole-3-lactic acid, Inflammatory bowel disease, Nicotinamide",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Colitis,EFO:0003872,DSS group,BG + DSS group,Mice treated with β-glucan (BG) alongside dextran sulfate sodium (DSS) to study the potential therapeutic effects of BG on DSS-induced colitis.,6,6,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,figure 2d,25 October 2024,Appleeyes,"Appleeyes,WikiWorks",Comparison of relative abundance of bacteria between DSS and BG + DSS group was calculated by linear discriminant analysis effect size (LEfSe). Taxa meeting an LDA score threshold > 2.0 is shown.,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",1783272|1239|91061;3379134|976|200643|171549|815|816|820;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|171551,Complete,Svetlana up
bsdb:39300532/1/2,39300532,laboratory experiment,39300532,10.1186/s40168-024-01896-9,NA,"Zhang S., Nie Q., Sun Y., Zuo S., Chen C., Li S., Yang J., Hu J., Zhou X., Yu Y., Huang P., Lian L., Xie M. , Nie S.",Bacteroides uniformis degrades β-glucan to promote Lactobacillus johnsonii improving indole-3-lactic acid levels in alleviating colitis,Microbiome,2024,"Bacteroides uniformis, Lactobacillus johnsonii, β-glucan, Aryl hydrocarbon receptor, Cross-feeding, Indole-3-lactic acid, Inflammatory bowel disease, Nicotinamide",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Colitis,EFO:0003872,DSS group,BG + DSS group,Mice treated with β-glucan (BG) alongside dextran sulfate sodium (DSS) to study the potential therapeutic effects of BG on DSS-induced colitis.,6,6,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,figure 2d,25 October 2024,Appleeyes,"Appleeyes,WikiWorks",Comparison of relative abundance of bacteria between DSS and BG + DSS group was calculated by linear discriminant analysis effect size (LEfSe). Taxa meeting an LDA score threshold > 2.0 is shown.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota",1783272|1239|186801;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|186801|3085636|186803;1783272|201174,Complete,Svetlana up
bsdb:39300532/2/1,39300532,laboratory experiment,39300532,10.1186/s40168-024-01896-9,NA,"Zhang S., Nie Q., Sun Y., Zuo S., Chen C., Li S., Yang J., Hu J., Zhou X., Yu Y., Huang P., Lian L., Xie M. , Nie S.",Bacteroides uniformis degrades β-glucan to promote Lactobacillus johnsonii improving indole-3-lactic acid levels in alleviating colitis,Microbiome,2024,"Bacteroides uniformis, Lactobacillus johnsonii, β-glucan, Aryl hydrocarbon receptor, Cross-feeding, Indole-3-lactic acid, Inflammatory bowel disease, Nicotinamide",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Colitis,EFO:0003872,0-h fermented samples,24-h fermented samples,Samples taken 24 hours after the intervention has been administered.,3,3,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,figure 2i,25 October 2024,Appleeyes,"Appleeyes,WikiWorks",Comparison of relative abundance of bacteria between 0 and 24 h in the fermented sample by LEfSe.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis",1783272|1239|526524|526525|128827|174708;1783272|1239|91061;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|820;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|1694;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|823,Complete,Svetlana up
bsdb:39300532/2/2,39300532,laboratory experiment,39300532,10.1186/s40168-024-01896-9,NA,"Zhang S., Nie Q., Sun Y., Zuo S., Chen C., Li S., Yang J., Hu J., Zhou X., Yu Y., Huang P., Lian L., Xie M. , Nie S.",Bacteroides uniformis degrades β-glucan to promote Lactobacillus johnsonii improving indole-3-lactic acid levels in alleviating colitis,Microbiome,2024,"Bacteroides uniformis, Lactobacillus johnsonii, β-glucan, Aryl hydrocarbon receptor, Cross-feeding, Indole-3-lactic acid, Inflammatory bowel disease, Nicotinamide",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Colitis,EFO:0003872,0-h fermented samples,24-h fermented samples,Samples taken 24 hours after the intervention has been administered.,3,3,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,figure 2i,25 October 2024,Appleeyes,"Appleeyes,WikiWorks",Comparison of relative abundance of bacteria between 0 and 24 h in the fermented sample by LEfSe.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum|s__Mucispirillum schaedleri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Bacteroidota",3379134|976|200643|171549;3379134|976|200643|171549|815|816|85831;3379134|976|200643|171549|815|816|28116;3379134|976|200643;3379134|200940|3031449|213115|194924|35832;3379134|200940|3031449|213115|194924|872;3379134|200930|68337|191393|2945020|248038;3379134|200930|68337|191393|2945020|248038|248039;3379134|976|200643|171549|1853231|283168;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810281|191303;3379134|976,Complete,Svetlana up
bsdb:39315776/1/1,39315776,laboratory experiment,39315776,10.1128/msystems.01015-24,NA,"Li S., Liu M., Han Y., Liu C., Cao S., Cui Y., Zhu X., Wang Z., Liu B. , Shi Y.",Gut microbiota-derived gamma-aminobutyric acid improves host appetite by inhibiting satiety hormone secretion,mSystems,2024,"appetite hormones, feeding regulation, gamma-aminobutyric acid, microbiota-gut-brain axis",Experiment 1,China,Oryctolagus cuniculus,Material entity in digestive tract,UBERON:0035118,Eating behaviour,NA,Low feed intake,High feed intake,The six rabbits with the highest feed intake from a group of 100 rabbits.,6,6,NA,16S,123456789,NA,relative abundances,LEfSe,0.01,FALSE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Fig 4H,14 October 2024,YokoC,"YokoC,Scholastica,WikiWorks",Differences in gut microbiota at genus level between High Feed Intake and Low Feed Intake rabbit groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Mediterranea,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia",3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|1926659;1783272|201174;1783272|201174|84998,Complete,Svetlana up
bsdb:39315776/1/2,39315776,laboratory experiment,39315776,10.1128/msystems.01015-24,NA,"Li S., Liu M., Han Y., Liu C., Cao S., Cui Y., Zhu X., Wang Z., Liu B. , Shi Y.",Gut microbiota-derived gamma-aminobutyric acid improves host appetite by inhibiting satiety hormone secretion,mSystems,2024,"appetite hormones, feeding regulation, gamma-aminobutyric acid, microbiota-gut-brain axis",Experiment 1,China,Oryctolagus cuniculus,Material entity in digestive tract,UBERON:0035118,Eating behaviour,NA,Low feed intake,High feed intake,The six rabbits with the highest feed intake from a group of 100 rabbits.,6,6,NA,16S,123456789,NA,relative abundances,LEfSe,0.01,FALSE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Fig 4H,14 October 2024,YokoC,"YokoC,Rahila,Scholastica,WikiWorks",Differences in gut microbiota at genus level between High Feed Intake and Low Feed Intake rabbit groups.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Breznakia,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Entomoplasmatales|f__Spiroplasmataceae|g__Spiroplasma,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|3120394|3120654|35829;1783272|1239|526524|526525|128827|1854458;1783272|544448|31969|186328|2131|2132;1783272|1239|526524|526525|128827;3379134|1224|1236;1783272|544448|31969;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:39315776/2/1,39315776,laboratory experiment,39315776,10.1128/msystems.01015-24,NA,"Li S., Liu M., Han Y., Liu C., Cao S., Cui Y., Zhu X., Wang Z., Liu B. , Shi Y.",Gut microbiota-derived gamma-aminobutyric acid improves host appetite by inhibiting satiety hormone secretion,mSystems,2024,"appetite hormones, feeding regulation, gamma-aminobutyric acid, microbiota-gut-brain axis",Experiment 2,China,Oryctolagus cuniculus,Material entity in digestive tract,UBERON:0035118,Eating behaviour,NA,Low feed intake,High feed intake,The six rabbits with the highest feed intake from a group of 100 rabbits.,6,6,NA,16S,123456789,NA,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 4G,18 October 2024,YokoC,"YokoC,Scholastica,WikiWorks",Differential analysis at species level in High Feed Intake versus Low Feed Intake rabbit groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides rodentium",3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|691816,Complete,Svetlana up
bsdb:39320101/1/1,39320101,case-control,39320101,https://doi.org/10.1128/msystems.00839-24,https://journals.asm.org/doi/10.1128/msystems.00839-24,"Xue H., Wang Y., Mei C., Han L., Lu M., Li X., Chen T., Wang F. , Tang X.",Gut microbiome and serum metabolome alterations associated with lactose intolerance (LI): a case‒control study and paired-sample study based on the American Gut Project (AGP),mSystems,2024,"16S rRNA, fecal microbiota transplantation (FMT), gut microbiome, lactose intolerance, metagenomics, serum metabolome",Experiment 1,"Canada,United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Lactose intolerance,EFO:1000062,Participants without Lactose Intolerance(Non-LI),Participants with Lactose Intolerance(LI),"Participants with condition, Lactose intolerance (LI) which is a prevalent condition characterized by gastrointestinal symptoms that arise following lactose consumption.",562,562,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,alcohol consumption measurement,body mass index,diet,geographic area,sex",NA,NA,unchanged,decreased,NA,NA,decreased,Signature 1,Fig 1c,11 October 2024,Nathcynthia,"Nathcynthia,Rahila,Tosin,WikiWorks",Gut microbiota alterations between LI cohort and non-LI cohort assessed using the linear discriminative analysis (LDA) effect size (LEfSe).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Spirochaetota|s__Spirochaetota bacterium,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",3379134|1224|28216|80840|506;3379134|1224|28216;1783272|1239|186801|3085636|186803|572511;3379134|1224|28216|80840;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;3379134|1224|28216|80840|80864|283;1783272|1239|909932|1843489|31977|39948;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803;1783272|1239|909932|1843489|31977|906;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|976|200643|171549|171551;3379134|203691|203692|136|137;3379134|203691|203692|136;3379134|203691|2202144;3379134|203691|203692|136|2845253|157,Complete,Svetlana up
bsdb:39320101/1/2,39320101,case-control,39320101,https://doi.org/10.1128/msystems.00839-24,https://journals.asm.org/doi/10.1128/msystems.00839-24,"Xue H., Wang Y., Mei C., Han L., Lu M., Li X., Chen T., Wang F. , Tang X.",Gut microbiome and serum metabolome alterations associated with lactose intolerance (LI): a case‒control study and paired-sample study based on the American Gut Project (AGP),mSystems,2024,"16S rRNA, fecal microbiota transplantation (FMT), gut microbiome, lactose intolerance, metagenomics, serum metabolome",Experiment 1,"Canada,United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Lactose intolerance,EFO:1000062,Participants without Lactose Intolerance(Non-LI),Participants with Lactose Intolerance(LI),"Participants with condition, Lactose intolerance (LI) which is a prevalent condition characterized by gastrointestinal symptoms that arise following lactose consumption.",562,562,6 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,alcohol consumption measurement,body mass index,diet,geographic area,sex",NA,NA,unchanged,decreased,NA,NA,decreased,Signature 2,Fig 1c,13 October 2024,Nathcynthia,"Nathcynthia,Rahila,Tosin,WikiWorks",Gut microbiota alterations between LI cohort and non-LI cohort assessed using the linear discriminative analysis (LDA) effect size (LEfSe)'.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|s__Leuconostocaceae bacterium,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|s__Enterococcaceae bacterium RF39",3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|830;1783272|1117;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|186806|1730;1783272|1239|91061|186826|33958|2590211;1783272|544448|31969;1783272|544448;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|1263;3379134|1224|1236|135624|83763|83770;1783272|1239|91061|186826|81852|423410,Complete,Svetlana up
bsdb:39320101/2/1,39320101,case-control,39320101,https://doi.org/10.1128/msystems.00839-24,https://journals.asm.org/doi/10.1128/msystems.00839-24,"Xue H., Wang Y., Mei C., Han L., Lu M., Li X., Chen T., Wang F. , Tang X.",Gut microbiome and serum metabolome alterations associated with lactose intolerance (LI): a case‒control study and paired-sample study based on the American Gut Project (AGP),mSystems,2024,"16S rRNA, fecal microbiota transplantation (FMT), gut microbiome, lactose intolerance, metagenomics, serum metabolome",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Lactose intolerance,EFO:1000062,Healthy controls (HC),Participants with Lactose Intolerance(LI),"Participants with condition, Lactose intolerance (LI) which is a prevalent condition characterized by gastrointestinal symptoms that arise following lactose consumption.",41,41,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Fig 3b,14 October 2024,Nathcynthia,"Nathcynthia,Rahila,Tosin,WikiWorks",LeFSe analysis reveals significant taxonomic differences between LI Patients and HCs.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:313,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp. AF19-14,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. AF12-5,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:177,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota",3379134|976|200643|171549|815|816|817;3379134|1224|28216|80840;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|547|158836;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|561|562;1783272|1239|1263017;3379134|1224|1236;1783272|1239|186801|3085636|186803|28050;1783272|1239|91061|186826|33958|1243;3379134|976|200643|171549|2005525|375288|2293114;3379134|1224;1783272|1239|186801|186802|216572|1263|2293146;1783272|1239|186801|186802|216572|1263|1262952;3379134|1224|1236|91347|543|590;3379134|1224|1236|91347|543|590|28901;3379134|1224|1236|91347|543|620;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|570;3379134|976|200643|171549|2005525|375288;3379134|1224,Complete,Svetlana up
bsdb:39320101/2/2,39320101,case-control,39320101,https://doi.org/10.1128/msystems.00839-24,https://journals.asm.org/doi/10.1128/msystems.00839-24,"Xue H., Wang Y., Mei C., Han L., Lu M., Li X., Chen T., Wang F. , Tang X.",Gut microbiome and serum metabolome alterations associated with lactose intolerance (LI): a case‒control study and paired-sample study based on the American Gut Project (AGP),mSystems,2024,"16S rRNA, fecal microbiota transplantation (FMT), gut microbiome, lactose intolerance, metagenomics, serum metabolome",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Lactose intolerance,EFO:1000062,Healthy controls (HC),Participants with Lactose Intolerance(LI),"Participants with condition, Lactose intolerance (LI) which is a prevalent condition characterized by gastrointestinal symptoms that arise following lactose consumption.",41,41,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Fig 3b,14 October 2024,Nathcynthia,"Nathcynthia,Rahila,Tosin,WikiWorks",LeFSe analysis reveals significant taxonomic differences between LI Patients and HCs.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF36-18BH,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. CAG:82,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__uncultured Ruminococcus sp.",1783272|1239|186801|186802|31979|1485|2293014;1783272|1239|186801|186802|186806|1730|142586;1783272|1239|186801|186802|216572|216851|1262898;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|1263|165186,Complete,Svetlana up
bsdb:39320101/3/1,39320101,case-control,39320101,https://doi.org/10.1128/msystems.00839-24,https://journals.asm.org/doi/10.1128/msystems.00839-24,"Xue H., Wang Y., Mei C., Han L., Lu M., Li X., Chen T., Wang F. , Tang X.",Gut microbiome and serum metabolome alterations associated with lactose intolerance (LI): a case‒control study and paired-sample study based on the American Gut Project (AGP),mSystems,2024,"16S rRNA, fecal microbiota transplantation (FMT), gut microbiome, lactose intolerance, metagenomics, serum metabolome",Experiment 3,China,Rattus norvegicus,Feces,UBERON:0001988,Lactose intolerance,EFO:1000062,FMT-Healthy Controls group,FMT-Lactose Intolerance group,Rats receiving gut microbiota from LI patients .,6,6,NA,16S,34,Illumina,relative abundances,Spearman Correlation,NA,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 1,Figure 7D,18 October 2024,Nathcynthia,"Nathcynthia,Tosin,WikiWorks",Heatmap based on the relative abundance of the genera between FMT-HC (FMT-Healthy control group) and FMT-LI (FMT-Lactose intolerance group).,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",1783272|1239|526524|526525|2810280|100883;1783272|1239|526524|526525|128827|1472649;3379134|1224|1236|91347|543|1940338;3379134|1224|28216|80840|995019|40544,Complete,Svetlana up
bsdb:39320101/3/2,39320101,case-control,39320101,https://doi.org/10.1128/msystems.00839-24,https://journals.asm.org/doi/10.1128/msystems.00839-24,"Xue H., Wang Y., Mei C., Han L., Lu M., Li X., Chen T., Wang F. , Tang X.",Gut microbiome and serum metabolome alterations associated with lactose intolerance (LI): a case‒control study and paired-sample study based on the American Gut Project (AGP),mSystems,2024,"16S rRNA, fecal microbiota transplantation (FMT), gut microbiome, lactose intolerance, metagenomics, serum metabolome",Experiment 3,China,Rattus norvegicus,Feces,UBERON:0001988,Lactose intolerance,EFO:1000062,FMT-Healthy Controls group,FMT-Lactose Intolerance group,Rats receiving gut microbiota from LI patients .,6,6,NA,16S,34,Illumina,relative abundances,Spearman Correlation,NA,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 2,Figure 7D,18 October 2024,Nathcynthia,"Nathcynthia,Tosin,WikiWorks",Heatmap based on the relative abundance of the genera between FMT-HC (Healthy control group) and FMT-LI (Lactose intolerance group).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter",1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607,Complete,Svetlana up
bsdb:39320101/4/1,39320101,case-control,39320101,https://doi.org/10.1128/msystems.00839-24,https://journals.asm.org/doi/10.1128/msystems.00839-24,"Xue H., Wang Y., Mei C., Han L., Lu M., Li X., Chen T., Wang F. , Tang X.",Gut microbiome and serum metabolome alterations associated with lactose intolerance (LI): a case‒control study and paired-sample study based on the American Gut Project (AGP),mSystems,2024,"16S rRNA, fecal microbiota transplantation (FMT), gut microbiome, lactose intolerance, metagenomics, serum metabolome",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Lactose intolerance,EFO:1000062,Healthy Controls,Participants with Lactose intolerance (LI),"Participants with condition, Lactose intolerance (LI) which is a prevalent condition characterized by gastrointestinal symptoms that arise following lactose consumption.",41,41,3 months,WMS,NA,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3d-I.,20 October 2024,Tosin,"Tosin,Nathcynthia,WikiWorks",Comparison of the relative abundances at the species level according to metagenomic sequencing between the two groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister massiliensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella flexneri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius",3379134|976|200643|171549|815|816|817;1783272|1239|909932|1843489|31977|39948|2161821;3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|543|620|623;1783272|1239|91061|186826|1300|1301|1304,Complete,Svetlana up
bsdb:39320101/4/2,39320101,case-control,39320101,https://doi.org/10.1128/msystems.00839-24,https://journals.asm.org/doi/10.1128/msystems.00839-24,"Xue H., Wang Y., Mei C., Han L., Lu M., Li X., Chen T., Wang F. , Tang X.",Gut microbiome and serum metabolome alterations associated with lactose intolerance (LI): a case‒control study and paired-sample study based on the American Gut Project (AGP),mSystems,2024,"16S rRNA, fecal microbiota transplantation (FMT), gut microbiome, lactose intolerance, metagenomics, serum metabolome",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Lactose intolerance,EFO:1000062,Healthy Controls,Participants with Lactose intolerance (LI),"Participants with condition, Lactose intolerance (LI) which is a prevalent condition characterized by gastrointestinal symptoms that arise following lactose consumption.",41,41,3 months,WMS,NA,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 3d-I,20 October 2024,Tosin,"Tosin,Nathcynthia,WikiWorks",Comparison of the relative abundances at the species level according to metagenomic sequencing between the two groups.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.,1783272|1239|186801|186802|186806|1730|142586,Complete,Svetlana up
bsdb:39320101/5/1,39320101,case-control,39320101,https://doi.org/10.1128/msystems.00839-24,https://journals.asm.org/doi/10.1128/msystems.00839-24,"Xue H., Wang Y., Mei C., Han L., Lu M., Li X., Chen T., Wang F. , Tang X.",Gut microbiome and serum metabolome alterations associated with lactose intolerance (LI): a case‒control study and paired-sample study based on the American Gut Project (AGP),mSystems,2024,"16S rRNA, fecal microbiota transplantation (FMT), gut microbiome, lactose intolerance, metagenomics, serum metabolome",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Lactose intolerance,EFO:1000062,Healthy Controls,Participants with Lactose Intolerance,"Participants with condition, Lactose intolerance (LI) which is prevalent condition characterized by gastrointestinal symptoms that arise following lactose consumption.",41,41,3 months,WMS,NA,Illumina,relative abundances,Spearman Correlation,NA,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3c,21 October 2024,Tosin,"Tosin,Nathcynthia,WikiWorks",Heatmap based on the relative abundance of the genera between Healthy control group and Lactose Intolerance group.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,3379134|1224|1236|91347|543|561,Complete,Svetlana up
bsdb:39320101/5/2,39320101,case-control,39320101,https://doi.org/10.1128/msystems.00839-24,https://journals.asm.org/doi/10.1128/msystems.00839-24,"Xue H., Wang Y., Mei C., Han L., Lu M., Li X., Chen T., Wang F. , Tang X.",Gut microbiome and serum metabolome alterations associated with lactose intolerance (LI): a case‒control study and paired-sample study based on the American Gut Project (AGP),mSystems,2024,"16S rRNA, fecal microbiota transplantation (FMT), gut microbiome, lactose intolerance, metagenomics, serum metabolome",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Lactose intolerance,EFO:1000062,Healthy Controls,Participants with Lactose Intolerance,"Participants with condition, Lactose intolerance (LI) which is prevalent condition characterized by gastrointestinal symptoms that arise following lactose consumption.",41,41,3 months,WMS,NA,Illumina,relative abundances,Spearman Correlation,NA,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 3c,21 October 2024,Tosin,"Tosin,Nathcynthia,WikiWorks",Heatmap based on the relative abundance of the genera between Healthy control group and Lactose Intolerance group.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|91061|186826|81852|1350;1783272|1239|526524|526525|2810280|3025755;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:39325441/1/1,39325441,meta-analysis,39325441,10.1001/jamaoncol.2024.4006,NA,"Kwak S., Wang C., Usyk M., Wu F., Freedman N.D., Huang W.Y., McCullough M.L., Um C.Y., Shrubsole M.J., Cai Q., Li H., Ahn J. , Hayes R.B.",Oral Microbiome and Subsequent Risk of Head and Neck Squamous Cell Cancer,JAMA oncology,2024,NA,Experiment 1,United States of America,Homo sapiens,Oral cavity,UBERON:0000167,Head and neck squamous cell carcinoma,EFO:0000181,Healthy Controls,Head and neck squamous cell cancer (HNSCC) participants,"Case participants with Head and Neck Squamous Cell Cancer (HNSCC; cancers of the oral cavity, pharynx, and larynx).",458,236,NA,WMS,NA,Illumina,log transformation,ANCOM-BC,0.05,FALSE,NA,"age,ethnic group,race,sex,time","age,ethnic group,race,sex,smoking status",unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 1a, eTable 4, Figure 2",28 January 2025,Tosin,"Tosin,WikiWorks",Associations between bacteria species and risk of overall Head and Neck squamous cell cancer (HNSCC),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas cangingivalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. HUN102,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter piscolens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Secundilactobacillus|s__Secundilactobacillus paracollinoides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gallolyticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus plurextorum",3379134|976|200643|171549|171551|836|36874;3379134|976|200643|171549|171552|838|1392486;3384194|508458|649775|649776|3029088|638847|638849;1783272|1239|91061|186826|33958|2767892|240427;1783272|1239|91061|186826|1300|1301|315405;1783272|1239|91061|186826|1300|1301|456876,Complete,KateRasheed
bsdb:39325441/1/2,39325441,meta-analysis,39325441,10.1001/jamaoncol.2024.4006,NA,"Kwak S., Wang C., Usyk M., Wu F., Freedman N.D., Huang W.Y., McCullough M.L., Um C.Y., Shrubsole M.J., Cai Q., Li H., Ahn J. , Hayes R.B.",Oral Microbiome and Subsequent Risk of Head and Neck Squamous Cell Cancer,JAMA oncology,2024,NA,Experiment 1,United States of America,Homo sapiens,Oral cavity,UBERON:0000167,Head and neck squamous cell carcinoma,EFO:0000181,Healthy Controls,Head and neck squamous cell cancer (HNSCC) participants,"Case participants with Head and Neck Squamous Cell Cancer (HNSCC; cancers of the oral cavity, pharynx, and larynx).",458,236,NA,WMS,NA,Illumina,log transformation,ANCOM-BC,0.05,FALSE,NA,"age,ethnic group,race,sex,time","age,ethnic group,race,sex,smoking status",unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 1a, eTable 4, Figure 2",26 February 2025,Tosin,Tosin,Associations between bacteria species and risk of overall Head and Neck squamous cell cancer (HNSCC),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 212,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella|s__Pasteurella multocida,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Rodentibacter|s__Rodentibacter pneumotropicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella|s__Simonsiella muelleri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis",3379134|1224|28216|206351|481|538|539;3384189|32066|203490|203491|1129771|32067|712357;3379134|1224|1236|135625|712|745|747;3379134|1224|1236|135625|712|1960084|758;3379134|976|200643|171549|171552|2974251|228604;3379134|1224|28216|206351|481|71|72;1783272|1239|91061|186826|1300|1301|1305,Complete,KateRasheed
bsdb:39325441/2/1,39325441,meta-analysis,39325441,10.1001/jamaoncol.2024.4006,NA,"Kwak S., Wang C., Usyk M., Wu F., Freedman N.D., Huang W.Y., McCullough M.L., Um C.Y., Shrubsole M.J., Cai Q., Li H., Ahn J. , Hayes R.B.",Oral Microbiome and Subsequent Risk of Head and Neck Squamous Cell Cancer,JAMA oncology,2024,NA,Experiment 2,United States of America,Homo sapiens,Oral cavity,UBERON:0000167,Head and neck squamous cell carcinoma,EFO:0000181,Healthy Controls,Head and neck squamous cell cancer (HNSCC) participants,"Case participants with Head and Neck Squamous Cell Cancer (HNSCC; cancers of the oral cavity, pharynx, and larynx).",458,62,NA,WMS,NA,Illumina,log transformation,ANCOM-BC,0.05,FALSE,NA,"age,ethnic group,race,sex","age,ethnic group,race,sex,smoking status",unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,eTable 4,26 February 2025,Tosin,Tosin,Associations between bacteria species and site-specific Head and Neck squamous cell cancer (HNSCC),increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter curvus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sp. oral taxon 338,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Schleiferilactobacillus|s__Schleiferilactobacillus harbinensis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus|s__Streptobacillus moniliformis,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema medium",3379134|29547|3031852|213849|72294|194|200;3379134|976|117743|200644|49546|1016|710239;1783272|1239|91061|186826|33958|2767891|304207;3384189|32066|203490|203491|1129771|34104|34105;3379134|203691|203692|136|2845253|157|58231,Complete,KateRasheed
bsdb:39325441/2/2,39325441,meta-analysis,39325441,10.1001/jamaoncol.2024.4006,NA,"Kwak S., Wang C., Usyk M., Wu F., Freedman N.D., Huang W.Y., McCullough M.L., Um C.Y., Shrubsole M.J., Cai Q., Li H., Ahn J. , Hayes R.B.",Oral Microbiome and Subsequent Risk of Head and Neck Squamous Cell Cancer,JAMA oncology,2024,NA,Experiment 2,United States of America,Homo sapiens,Oral cavity,UBERON:0000167,Head and neck squamous cell carcinoma,EFO:0000181,Healthy Controls,Head and neck squamous cell cancer (HNSCC) participants,"Case participants with Head and Neck Squamous Cell Cancer (HNSCC; cancers of the oral cavity, pharynx, and larynx).",458,62,NA,WMS,NA,Illumina,log transformation,ANCOM-BC,0.05,FALSE,NA,"age,ethnic group,race,sex","age,ethnic group,race,sex,smoking status",unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,eTable 4,26 February 2025,Tosin,Tosin,Associations between bacteria species and site-specific Head and Neck squamous cell cancer (HNSCC),decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium argentoratense,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium aurimucosum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium granulosum,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Gemmatales|f__Gemmataceae|g__Gemmata|s__Gemmata obscuriglobus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Sanguibacteroides|s__Sanguibacteroides justesenii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oulorum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces specialis",1783272|201174|1760|85007|1653|1716|42817;1783272|201174|1760|85007|1653|1716|169292;1783272|201174|1760|85009|31957|1912216|1747;1783272|201174|1760|85009|31957|1912216|33011;3379134|203682|203683|2691355|1914233|113|114;3379134|976|200643|171549|171551|1635148|1547597;3379134|976|200643|171549|171552|2974251|28136;1783272|1239|91061|1385|90964|1279|1290;1783272|201174|1760|85011|2062|1883|498367,Complete,KateRasheed
bsdb:39325441/3/1,39325441,meta-analysis,39325441,10.1001/jamaoncol.2024.4006,NA,"Kwak S., Wang C., Usyk M., Wu F., Freedman N.D., Huang W.Y., McCullough M.L., Um C.Y., Shrubsole M.J., Cai Q., Li H., Ahn J. , Hayes R.B.",Oral Microbiome and Subsequent Risk of Head and Neck Squamous Cell Cancer,JAMA oncology,2024,NA,Experiment 3,United States of America,Homo sapiens,Oral cavity,UBERON:0000167,Head and neck squamous cell carcinoma,EFO:0000181,Healthy Controls,Head and neck squamous cell cancer (HNSCC) participants,"Case participants with Head and Neck Squamous Cell Cancer (HNSCC; cancers of the oral cavity, pharynx, and larynx).",458,63,NA,WMS,NA,Illumina,log transformation,ANCOM-BC,0.05,FALSE,NA,"age,ethnic group,race,sex","age,ethnic group,race,sex,smoking status",unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,eTable 4,2 March 2025,Tosin,Tosin,Associations between bacteria species and site-specific Head and Neck squamous cell cancer (HNSCC),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|s__Coriobacteriaceae bacterium BV3Ac1,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella enoeca,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella uli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola abscessus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas cangingivalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivicanis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp. COT-290 OH3588,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella dentasini,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. HUN102,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium sp. oral taxon 192,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter piscolens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella buccae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus|s__Streptobacillus moniliformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema putidum",3379134|976|200643|171549|171552|1283313|671218;3379134|976|200643|171549|171552|1283313|76122;1783272|201174|84998|84999|84107|1111135;1783272|1239|909932|1843489|31977|39948|218538;3379134|976|200643|171549|171552|2974257|76123;1783272|201174|84998|84999|1643824|133925|133926;3379134|976|200643|171549|815|909656|555313;3379134|976|200643|171549|171551|836|36874;3379134|976|200643|171549|171551|836|266762;3379134|976|200643|171549|171551|836|1515617;3379134|976|200643|171549|171552|838|28125;3379134|976|200643|171549|171552|838|589537;3379134|976|200643|171549|171552|838|28131;3379134|976|200643|171549|171552|838|1392486;1783272|201174|1760|85009|31957|1743|671222;3384194|508458|649775|649776|3029088|638847|638849;3379134|976|200643|171549|171552|2974251|28126;3384189|32066|203490|203491|1129771|34104|34105;1783272|1239|91061|186826|1300|1301|1302;1783272|1239|91061|186826|1300|1301|28037;3379134|203691|203692|136|2845253|157|158;3379134|203691|203692|136|2845253|157|221027,Complete,KateRasheed
bsdb:39325441/3/2,39325441,meta-analysis,39325441,10.1001/jamaoncol.2024.4006,NA,"Kwak S., Wang C., Usyk M., Wu F., Freedman N.D., Huang W.Y., McCullough M.L., Um C.Y., Shrubsole M.J., Cai Q., Li H., Ahn J. , Hayes R.B.",Oral Microbiome and Subsequent Risk of Head and Neck Squamous Cell Cancer,JAMA oncology,2024,NA,Experiment 3,United States of America,Homo sapiens,Oral cavity,UBERON:0000167,Head and neck squamous cell carcinoma,EFO:0000181,Healthy Controls,Head and neck squamous cell cancer (HNSCC) participants,"Case participants with Head and Neck Squamous Cell Cancer (HNSCC; cancers of the oral cavity, pharynx, and larynx).",458,63,NA,WMS,NA,Illumina,log transformation,ANCOM-BC,0.05,FALSE,NA,"age,ethnic group,race,sex","age,ethnic group,race,sex,smoking status",unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,eTable 4,3 March 2025,Tosin,Tosin,Associations between bacteria species and site-specific Head and Neck squamous cell cancer (HNSCC),decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 448,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium reuteri,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Candidatus Burkholderia crenata,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus paracasei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus rhamnosus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium sp. Root265,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium acidifaciens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus macacae",1783272|201174|1760|2037|2049|1654|712124;1783272|201174|1760|85004|31953|1678|983706;3379134|1224|28216|80840|119060|32008|1074049;1783272|1239|91061|186826|33958|2759736|1597;1783272|1239|91061|186826|33958|2759736|47715;1783272|201174|1760|85007|1762|1763|1736504;1783272|201174|1760|85009|31957|1743|556499;1783272|1239|91061|186826|1300|1301|1339,Complete,KateRasheed
bsdb:39325441/4/1,39325441,meta-analysis,39325441,10.1001/jamaoncol.2024.4006,NA,"Kwak S., Wang C., Usyk M., Wu F., Freedman N.D., Huang W.Y., McCullough M.L., Um C.Y., Shrubsole M.J., Cai Q., Li H., Ahn J. , Hayes R.B.",Oral Microbiome and Subsequent Risk of Head and Neck Squamous Cell Cancer,JAMA oncology,2024,NA,Experiment 4,United States of America,Homo sapiens,Oral cavity,UBERON:0000167,Head and neck squamous cell carcinoma,EFO:0000181,Healthy Controls,Head and neck squamous cell cancer (HNSCC) participants,"Case participants with Head and Neck Squamous Cell Cancer (HNSCC; cancers of the oral cavity, pharynx, and larynx).",458,111,NA,WMS,NA,Illumina,log transformation,ANCOM-BC,0.05,FALSE,NA,"age,ethnic group,race,sex","age,ethnic group,race,sex,smoking status",unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,eTable 4,3 March 2025,Tosin,Tosin,Associations between bacteria species and site-specific Head and Neck squamous cell cancer (HNSCC),increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus rhamnosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus hominis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus vaginalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Secundilactobacillus|s__Secundilactobacillus paracollinoides",1783272|1239|91061|186826|33958|2759736|47715;1783272|1239|91061|186826|33958|1578|1203033;1783272|1239|91061|186826|33958|2767887|1624;1783272|1239|91061|186826|33958|2742598|1613;1783272|1239|91061|186826|33958|2742598|1633;1783272|1239|91061|186826|33958|2767892|240427,Complete,KateRasheed
bsdb:39325441/4/2,39325441,meta-analysis,39325441,10.1001/jamaoncol.2024.4006,NA,"Kwak S., Wang C., Usyk M., Wu F., Freedman N.D., Huang W.Y., McCullough M.L., Um C.Y., Shrubsole M.J., Cai Q., Li H., Ahn J. , Hayes R.B.",Oral Microbiome and Subsequent Risk of Head and Neck Squamous Cell Cancer,JAMA oncology,2024,NA,Experiment 4,United States of America,Homo sapiens,Oral cavity,UBERON:0000167,Head and neck squamous cell carcinoma,EFO:0000181,Healthy Controls,Head and neck squamous cell cancer (HNSCC) participants,"Case participants with Head and Neck Squamous Cell Cancer (HNSCC; cancers of the oral cavity, pharynx, and larynx).",458,111,NA,WMS,NA,Illumina,log transformation,ANCOM-BC,0.05,FALSE,NA,"age,ethnic group,race,sex","age,ethnic group,race,sex,smoking status",unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,eTable 4,3 March 2025,Tosin,Tosin,Associations between bacteria species and site-specific Head and Neck squamous cell cancer (HNSCC),decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium aesculapii,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sputorum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria mucosa,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella scopos,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella|s__Simonsiella muelleri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis",1783272|201174|1760|85004|31953|1678|1329411;3379134|29547|3031852|213849|72294|194|199;3379134|29547|3031852|213849|72294|194|204;3379134|976|117743|200644|49546|1016|1017;3384189|32066|203490|203491|203492|848|860;3379134|1224|1236|135625|712|724|727;3379134|1224|1236|135625|712|724|1078480;3379134|976|200643|171549|171552|2974257|425941;3379134|1224|28216|206351|481|482|488;3379134|976|200643|171549|171551|836|322095;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552|838|60133;3379134|976|200643|171549|171552|838|589437;1783272|201174|1760|2037|2049|2529408|1660;3379134|976|200643|171549|171552|2974251|228604;3379134|1224|28216|206351|481|71|72;1783272|1239|91061|186826|1300|1301|1305,Complete,KateRasheed
bsdb:39325441/5/1,39325441,meta-analysis,39325441,10.1001/jamaoncol.2024.4006,NA,"Kwak S., Wang C., Usyk M., Wu F., Freedman N.D., Huang W.Y., McCullough M.L., Um C.Y., Shrubsole M.J., Cai Q., Li H., Ahn J. , Hayes R.B.",Oral Microbiome and Subsequent Risk of Head and Neck Squamous Cell Cancer,JAMA oncology,2024,NA,Experiment 5,United States of America,Homo sapiens,Oral cavity,UBERON:0000167,Head and neck squamous cell carcinoma,EFO:0000181,Healthy Controls,Head and neck squamous cell cancer (HNSCC) participants,"Case participants with Head and Neck Squamous Cell Cancer (HNSCC; cancers of the oral cavity, pharynx, and larynx).",458,62,NA,ITS / ITS2,NA,Illumina,log transformation,ANCOM-BC,0.05,FALSE,NA,"age,ethnic group,race,sex","age,ethnic group,race,sex,smoking status",unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,eTable 5,3 March 2025,Tosin,Tosin,Associations between fungal species and site-specific Head and Neck squamous cell cancer (HNSCC),increased,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Penicillium|s__Penicillium neocrassum,4751|4890|147545|5042|1131492|5073|1167569,Complete,KateRasheed
bsdb:39325441/6/1,39325441,meta-analysis,39325441,10.1001/jamaoncol.2024.4006,NA,"Kwak S., Wang C., Usyk M., Wu F., Freedman N.D., Huang W.Y., McCullough M.L., Um C.Y., Shrubsole M.J., Cai Q., Li H., Ahn J. , Hayes R.B.",Oral Microbiome and Subsequent Risk of Head and Neck Squamous Cell Cancer,JAMA oncology,2024,NA,Experiment 6,United States of America,Homo sapiens,Oral cavity,UBERON:0000167,Head and neck squamous cell carcinoma,EFO:0000181,Healthy Controls,Head and neck squamous cell cancer (HNSCC) participants,"Case participants with Head and Neck Squamous Cell Cancer (HNSCC; cancers of the oral cavity, pharynx, and larynx).",458,63,NA,ITS / ITS2,NA,Illumina,log transformation,ANCOM-BC,0.05,FALSE,NA,"age,ethnic group,race,sex","age,ethnic group,race,sex,smoking status",unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,eTable 5,3 March 2025,Tosin,Tosin,Associations between fungal species and site-specific Head and Neck squamous cell cancer (HNSCC),increased,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia sympodialis,4751|5204|1538075|162474|742845|55193|76777,Complete,KateRasheed
bsdb:39325441/6/2,39325441,meta-analysis,39325441,10.1001/jamaoncol.2024.4006,NA,"Kwak S., Wang C., Usyk M., Wu F., Freedman N.D., Huang W.Y., McCullough M.L., Um C.Y., Shrubsole M.J., Cai Q., Li H., Ahn J. , Hayes R.B.",Oral Microbiome and Subsequent Risk of Head and Neck Squamous Cell Cancer,JAMA oncology,2024,NA,Experiment 6,United States of America,Homo sapiens,Oral cavity,UBERON:0000167,Head and neck squamous cell carcinoma,EFO:0000181,Healthy Controls,Head and neck squamous cell cancer (HNSCC) participants,"Case participants with Head and Neck Squamous Cell Cancer (HNSCC; cancers of the oral cavity, pharynx, and larynx).",458,63,NA,ITS / ITS2,NA,Illumina,log transformation,ANCOM-BC,0.05,FALSE,NA,"age,ethnic group,race,sex","age,ethnic group,race,sex,smoking status",unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,eTable 5,3 March 2025,Tosin,Tosin,Associations between fungal species and site-specific Head and Neck squamous cell cancer (HNSCC),decreased,k__Fungi|p__Ascomycota|c__Orbiliomycetes|o__Orbiliales|f__Orbiliaceae|g__Orbilia|s__Orbilia sp.,4751|4890|189478|189479|47021|47022|1955109,Complete,KateRasheed
bsdb:39325441/7/1,39325441,meta-analysis,39325441,10.1001/jamaoncol.2024.4006,NA,"Kwak S., Wang C., Usyk M., Wu F., Freedman N.D., Huang W.Y., McCullough M.L., Um C.Y., Shrubsole M.J., Cai Q., Li H., Ahn J. , Hayes R.B.",Oral Microbiome and Subsequent Risk of Head and Neck Squamous Cell Cancer,JAMA oncology,2024,NA,Experiment 7,United States of America,Homo sapiens,Oral cavity,UBERON:0000167,Head and neck squamous cell carcinoma,EFO:0000181,Healthy Controls,Head and neck squamous cell cancer (HNSCC) participants,"Case participants with Head and Neck Squamous Cell Cancer (HNSCC; cancers of the oral cavity, pharynx, and larynx).",458,111,NA,ITS / ITS2,NA,Illumina,log transformation,ANCOM-BC,0.05,FALSE,NA,"age,ethnic group,race,sex,time","age,ethnic group,race,sex,smoking status",unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,eTable 5,3 March 2025,Tosin,Tosin,Associations between fungal species and site-specific Head and Neck squamous cell cancer (HNSCC),increased,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales,4751|4890|147541|92860,Complete,KateRasheed
bsdb:39325441/7/2,39325441,meta-analysis,39325441,10.1001/jamaoncol.2024.4006,NA,"Kwak S., Wang C., Usyk M., Wu F., Freedman N.D., Huang W.Y., McCullough M.L., Um C.Y., Shrubsole M.J., Cai Q., Li H., Ahn J. , Hayes R.B.",Oral Microbiome and Subsequent Risk of Head and Neck Squamous Cell Cancer,JAMA oncology,2024,NA,Experiment 7,United States of America,Homo sapiens,Oral cavity,UBERON:0000167,Head and neck squamous cell carcinoma,EFO:0000181,Healthy Controls,Head and neck squamous cell cancer (HNSCC) participants,"Case participants with Head and Neck Squamous Cell Cancer (HNSCC; cancers of the oral cavity, pharynx, and larynx).",458,111,NA,ITS / ITS2,NA,Illumina,log transformation,ANCOM-BC,0.05,FALSE,NA,"age,ethnic group,race,sex,time","age,ethnic group,race,sex,smoking status",unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,eTable 5,3 March 2025,Tosin,Tosin,Associations between fungal species and site-specific Head and Neck squamous cell cancer (HNSCC),decreased,"k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Pleosporaceae|g__Alternaria|s__Alternaria malorum,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Bulleribasidiaceae|g__Vishniacozyma|s__Vishniacozyma victoriae",4751|4890|147541|92860|28556|5598|652027;4751|5204|155616|5234|1884640|1891946|1895944,Complete,KateRasheed
bsdb:39333864/2/1,39333864,laboratory experiment,39333864,https://doi.org/10.1186/s12866-024-03513-z,NA,"Huang F., Deng Y., Zhou M., Tang R., Zhang P. , Chen R.",Fecal microbiota transplantation from patients with polycystic ovary syndrome induces metabolic disorders and ovarian dysfunction in germ-free mice,BMC microbiology,2024,"Fecal microbiota transplantation, Gut microbiota, Polycystic ovary syndrome",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,Mice transplanted from the healthy controls on Day 14,Mice transplanted from PCOS (Polycystic ovary syndrome) patients on Day 14,The Mice transplanted from PCOS (Polycystic ovary syndrome) patients on Day 14 was given 100 µl of the fecal microbiota suspension from the PCOS patients.,6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Fig. 2D - 2E,1 May 2025,PreciousChijioke,PreciousChijioke,Results of LEfSe analysis and Cladogram showing bacterial taxa whose abundance in the gut significantly differed between D14-P and D14-H (upper and left).,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201,Complete,KateRasheed
bsdb:39333864/3/1,39333864,laboratory experiment,39333864,https://doi.org/10.1186/s12866-024-03513-z,NA,"Huang F., Deng Y., Zhou M., Tang R., Zhang P. , Chen R.",Fecal microbiota transplantation from patients with polycystic ovary syndrome induces metabolic disorders and ovarian dysfunction in germ-free mice,BMC microbiology,2024,"Fecal microbiota transplantation, Gut microbiota, Polycystic ovary syndrome",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,Mice transplanted from the healthy controls on Day 28,Mice transplanted from PCOS (Polycystic ovary syndrome) patients on Day 28,The Mice transplanted from PCOS (Polycystic ovary syndrome) patients on Day 28 was given 100 µl of the fecal microbiota suspension from the PCOS patients.,6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Fig. 2D - 2E,1 May 2025,PreciousChijioke,PreciousChijioke,Results of LEfSe analysis and Cladogram showing bacterial taxa whose abundance in the gut significantly differed between D28-H and D28-P (lower and right).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Lawsonibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",1783272|1239|186801|186802|216572|2172004;3379134|976|200643|171549|171550,Complete,KateRasheed
bsdb:39333864/4/1,39333864,laboratory experiment,39333864,https://doi.org/10.1186/s12866-024-03513-z,NA,"Huang F., Deng Y., Zhou M., Tang R., Zhang P. , Chen R.",Fecal microbiota transplantation from patients with polycystic ovary syndrome induces metabolic disorders and ovarian dysfunction in germ-free mice,BMC microbiology,2024,"Fecal microbiota transplantation, Gut microbiota, Polycystic ovary syndrome",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Insulin resistance,EFO:0002614,Low HOMAIR (insulin resistance index) of colonized GF mice,High HOMAIR (insulin resistance index) of colonized GF mice,The High HOMA-IR (insulin resistance index) of colonized GF mice.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 5,2 May 2025,PreciousChijioke,PreciousChijioke,"Heatmap of Spearman’s correlations between key bacteria of mice on Day 28 (genus level) and clinical factor HOMAIR, insulin resistance index.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae|g__Candidatus Scatocola,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catenibacillus",3379134|1224|28211|204441|41295|2840645;1783272|1239|186801|3085636|186803|2316203,Complete,KateRasheed
bsdb:39333864/4/2,39333864,laboratory experiment,39333864,https://doi.org/10.1186/s12866-024-03513-z,NA,"Huang F., Deng Y., Zhou M., Tang R., Zhang P. , Chen R.",Fecal microbiota transplantation from patients with polycystic ovary syndrome induces metabolic disorders and ovarian dysfunction in germ-free mice,BMC microbiology,2024,"Fecal microbiota transplantation, Gut microbiota, Polycystic ovary syndrome",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Insulin resistance,EFO:0002614,Low HOMAIR (insulin resistance index) of colonized GF mice,High HOMAIR (insulin resistance index) of colonized GF mice,The High HOMA-IR (insulin resistance index) of colonized GF mice.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 5,2 May 2025,PreciousChijioke,PreciousChijioke,"Heatmap of Spearman’s correlations between key bacteria of mice on Day 28 (genus level) and clinical factor HOMAIR, insulin resistance index.",decreased,NA,NA,Complete,KateRasheed
bsdb:39333864/5/1,39333864,laboratory experiment,39333864,https://doi.org/10.1186/s12866-024-03513-z,NA,"Huang F., Deng Y., Zhou M., Tang R., Zhang P. , Chen R.",Fecal microbiota transplantation from patients with polycystic ovary syndrome induces metabolic disorders and ovarian dysfunction in germ-free mice,BMC microbiology,2024,"Fecal microbiota transplantation, Gut microbiota, Polycystic ovary syndrome",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Testosterone measurement,EFO:0004908,Low T (testosterone) of colonized GF mice,High T (testosterone) of colonized GF mice,The High T (testosterone) of colonized GF mice.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 5,2 May 2025,PreciousChijioke,PreciousChijioke,"Heatmap of Spearman’s correlations between key bacteria of mice on Day 28 (genus level) and clinical factor T, testosterone.",increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catenibacillus,1783272|1239|186801|3085636|186803|2316203,Complete,KateRasheed
bsdb:39333864/5/2,39333864,laboratory experiment,39333864,https://doi.org/10.1186/s12866-024-03513-z,NA,"Huang F., Deng Y., Zhou M., Tang R., Zhang P. , Chen R.",Fecal microbiota transplantation from patients with polycystic ovary syndrome induces metabolic disorders and ovarian dysfunction in germ-free mice,BMC microbiology,2024,"Fecal microbiota transplantation, Gut microbiota, Polycystic ovary syndrome",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Testosterone measurement,EFO:0004908,Low T (testosterone) of colonized GF mice,High T (testosterone) of colonized GF mice,The High T (testosterone) of colonized GF mice.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 5,2 May 2025,PreciousChijioke,PreciousChijioke,"Heatmap of Spearman’s correlations between key bacteria of mice on Day 28 (genus level) and clinical factor T, testosterone.",decreased,k__Bacillati|p__Bacillota|g__Negativibacillus,1783272|1239|1980693,Complete,KateRasheed
bsdb:39333864/6/1,39333864,laboratory experiment,39333864,https://doi.org/10.1186/s12866-024-03513-z,NA,"Huang F., Deng Y., Zhou M., Tang R., Zhang P. , Chen R.",Fecal microbiota transplantation from patients with polycystic ovary syndrome induces metabolic disorders and ovarian dysfunction in germ-free mice,BMC microbiology,2024,"Fecal microbiota transplantation, Gut microbiota, Polycystic ovary syndrome",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Increased body weight,HP:0004324,Low SF/Wt (subcutaneous fat weight/body weight) of colonized GF mice,High SF/Wt (subcutaneous fat weight/body weight) of colonized GF mice,The High SF/Wt (subcutaneous fat weight/body weight) of colonized GF mice.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 5,2 May 2025,PreciousChijioke,PreciousChijioke,"Heatmap of Spearman’s correlations between key bacteria of mice on Day 28 (genus level) and clinical factor SF/Wt, subcutaneous fat weight/body weight.",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,KateRasheed
bsdb:39333864/6/2,39333864,laboratory experiment,39333864,https://doi.org/10.1186/s12866-024-03513-z,NA,"Huang F., Deng Y., Zhou M., Tang R., Zhang P. , Chen R.",Fecal microbiota transplantation from patients with polycystic ovary syndrome induces metabolic disorders and ovarian dysfunction in germ-free mice,BMC microbiology,2024,"Fecal microbiota transplantation, Gut microbiota, Polycystic ovary syndrome",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Increased body weight,HP:0004324,Low SF/Wt (subcutaneous fat weight/body weight) of colonized GF mice,High SF/Wt (subcutaneous fat weight/body weight) of colonized GF mice,The High SF/Wt (subcutaneous fat weight/body weight) of colonized GF mice.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 5,2 May 2025,PreciousChijioke,PreciousChijioke,"Heatmap of Spearman’s correlations between key bacteria of mice on Day 28 (genus level) and clinical factor SF/Wt, subcutaneous fat weight/body weight.",decreased,NA,NA,Complete,KateRasheed
bsdb:39333864/7/1,39333864,laboratory experiment,39333864,https://doi.org/10.1186/s12866-024-03513-z,NA,"Huang F., Deng Y., Zhou M., Tang R., Zhang P. , Chen R.",Fecal microbiota transplantation from patients with polycystic ovary syndrome induces metabolic disorders and ovarian dysfunction in germ-free mice,BMC microbiology,2024,"Fecal microbiota transplantation, Gut microbiota, Polycystic ovary syndrome",Experiment 7,China,Mus musculus,Feces,UBERON:0001988,Triglyceride measurement,EFO:0004530,Low TG (triglycerides) of colonized GF mice,High TG (triglycerides) of colonized GF mice,The High TG (triglycerides) of colonized GF mice.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 5,2 May 2025,PreciousChijioke,PreciousChijioke,"Heatmap of Spearman’s correlations between key bacteria of mice on Day 28 (genus level) and clinical factor TG, triglycerides.",increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae|g__Candidatus Scatocola,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Extibacter",3379134|200940|3031449|213115|194924|35832;3379134|976|200643|171549|1853231|574697;3379134|1224|28211|204441|41295|2840645;1783272|1239|186801|186802|216572|2591381;1783272|1239|186801|3085636|186803|1918452,Complete,KateRasheed
bsdb:39333864/7/2,39333864,laboratory experiment,39333864,https://doi.org/10.1186/s12866-024-03513-z,NA,"Huang F., Deng Y., Zhou M., Tang R., Zhang P. , Chen R.",Fecal microbiota transplantation from patients with polycystic ovary syndrome induces metabolic disorders and ovarian dysfunction in germ-free mice,BMC microbiology,2024,"Fecal microbiota transplantation, Gut microbiota, Polycystic ovary syndrome",Experiment 7,China,Mus musculus,Feces,UBERON:0001988,Triglyceride measurement,EFO:0004530,Low TG (triglycerides) of colonized GF mice,High TG (triglycerides) of colonized GF mice,The High TG (triglycerides) of colonized GF mice.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 5,2 May 2025,PreciousChijioke,PreciousChijioke,"Heatmap of Spearman’s correlations between key bacteria of mice on Day 28 (genus level) and clinical factor TG, triglycerides.",decreased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,1783272|1239|526524|526525|2810280|100883,Complete,KateRasheed
bsdb:39333864/8/1,39333864,laboratory experiment,39333864,https://doi.org/10.1186/s12866-024-03513-z,NA,"Huang F., Deng Y., Zhou M., Tang R., Zhang P. , Chen R.",Fecal microbiota transplantation from patients with polycystic ovary syndrome induces metabolic disorders and ovarian dysfunction in germ-free mice,BMC microbiology,2024,"Fecal microbiota transplantation, Gut microbiota, Polycystic ovary syndrome",Experiment 8,China,Mus musculus,Feces,UBERON:0001988,Low density lipoprotein cholesterol measurement,EFO:0004611,Decreasing low-density lipoprotein cholesterol (LDL-C) of colonized GF mice,Increasing low-density lipoprotein cholesterol (LDL-C) of colonized GF mice,The Increasing low-density lipoprotein cholesterol (LDL-C) of colonized GF mice.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 5,2 May 2025,PreciousChijioke,PreciousChijioke,Heatmap of Spearman’s correlations between key bacteria of mice on Day 28 (genus level) and clinical factor LDL-C; low-density lipoprotein cholesterol.,increased,NA,NA,Complete,KateRasheed
bsdb:39333864/9/1,39333864,laboratory experiment,39333864,https://doi.org/10.1186/s12866-024-03513-z,NA,"Huang F., Deng Y., Zhou M., Tang R., Zhang P. , Chen R.",Fecal microbiota transplantation from patients with polycystic ovary syndrome induces metabolic disorders and ovarian dysfunction in germ-free mice,BMC microbiology,2024,"Fecal microbiota transplantation, Gut microbiota, Polycystic ovary syndrome",Experiment 9,China,Mus musculus,Feces,UBERON:0001988,Total cholesterol measurement,EFO:0004574,Low TC (total cholesterol) of colonized GF mice,High TC (total cholesterol) of colonized GF mice,The High TC (total cholesterol) of colonized GF mice.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 5,2 May 2025,PreciousChijioke,PreciousChijioke,"Heatmap of Spearman’s correlations between key bacteria of mice on Day 28 (genus level) and clinical factor TC, total cholesterol.",increased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,3379134|1224|28216|80840|995019|577310,Complete,KateRasheed
bsdb:39333864/9/2,39333864,laboratory experiment,39333864,https://doi.org/10.1186/s12866-024-03513-z,NA,"Huang F., Deng Y., Zhou M., Tang R., Zhang P. , Chen R.",Fecal microbiota transplantation from patients with polycystic ovary syndrome induces metabolic disorders and ovarian dysfunction in germ-free mice,BMC microbiology,2024,"Fecal microbiota transplantation, Gut microbiota, Polycystic ovary syndrome",Experiment 9,China,Mus musculus,Feces,UBERON:0001988,Total cholesterol measurement,EFO:0004574,Low TC (total cholesterol) of colonized GF mice,High TC (total cholesterol) of colonized GF mice,The High TC (total cholesterol) of colonized GF mice.,NA,NA,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 5,2 May 2025,PreciousChijioke,PreciousChijioke,"Heatmap of Spearman’s correlations between key bacteria of mice on Day 28 (genus level) and clinical factor TC, total cholesterol.",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella sp. UBA3402,1783272|1239|186801|3085636|186803|1649459|1946595,Complete,KateRasheed
bsdb:39355268/1/1,39355268,meta-analysis,39355268,10.3389/fcimb.2024.1397466,NA,"Wang Y., Wang Y., Han W., Han M., Liu X., Dai J., Dong Y., Sun T. , Xu J.",Intratumoral and fecal microbiota reveals microbial markers associated with gastric carcinogenesis,Frontiers in cellular and infection microbiology,2024,"fecal microbiota, gastric cancer, intratumoral microbiota, microbial marker, non-invasive prediction",Experiment 1,"China,South Korea,Colombia",Homo sapiens,Mucosa of body of stomach,UBERON:0004995,Gastric cancer,MONDO:0001056,Combination of Benign and Normal group,Gastric cancer (GC) group.,Patients with Gastric cancer (GC).,1163,479,1 month,16S,12345,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2D, Figure S6A and Table S4",6 November 2025,Reddicx,"Reddicx,Tosin",Taxonomic composition of gastric tissue samples at the genus level.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Alloiococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Anoxybacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Polymorphum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae|g__Salinispora,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Tsukamurellaceae|g__Tsukamurella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Tsukamurellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales,k__Thermotogati|p__Deinococcota|c__Deinococci",1783272|1239|91061|186826|186828|1651;1783272|1239|91061|1385|3120669|150247;1783272|201174|1760|85006|1268|1663;3379134|1224|28211|356|212791;1783272|1239|91061|186826|186828|117563;1783272|1239|91061|186826|33958|1578;3379134|1224|28211|356|118882|528;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;3379134|1224|28211|204455|31989|991903;1783272|201174|1760|85009|31957|1743;1783272|201174|1760|85008|28056|168694;1783272|1239|91061|186826|1300|1301;3384194|1297|188787|68933|188786|270;1783272|201174|1760|85007|85028|2060;1783272|1239|909932|1843489|31977|29465;1783272|201174|1760|85006|1268;1783272|201174|1760|85009|31957;1783272|201174|1760|85007|85028;1783272|201174|1760|2037;1783272|201174|84992;1783272|1239|91061|1385|539738;1783272|1239|91061|186826|186827;1783272|1239|91061|186826|186828;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|1300;1783272|1239|91061|186826;1783272|1239|91061;1783272|1239|186801|3082720|186804;1783272|1239|1737404|1737405|1737406;3379134|1224|28211|204458|76892;3379134|1224|28211|204458;3379134|1224|28211|356|118882;3379134|1224|28211|356|45401;3379134|1224|28211|356;3379134|1224|28211;3379134|1224|28216|80840|119060;3384194|1297|188787|68933|188786;3384194|1297|188787|68933;3384194|1297|188787,Complete,KateRasheed
bsdb:39355268/2/1,39355268,meta-analysis,39355268,10.3389/fcimb.2024.1397466,NA,"Wang Y., Wang Y., Han W., Han M., Liu X., Dai J., Dong Y., Sun T. , Xu J.",Intratumoral and fecal microbiota reveals microbial markers associated with gastric carcinogenesis,Frontiers in cellular and infection microbiology,2024,"fecal microbiota, gastric cancer, intratumoral microbiota, microbial marker, non-invasive prediction",Experiment 2,"China,Colombia,South Korea",Homo sapiens,Mucosa of body of stomach,UBERON:0004995,Gastric cancer,MONDO:0001056,Combination of Normal and Gastric cancer (GC) group,Benign group,Patients with non-cancerous tumour.,813,829,1 month,16S,12345,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2D, Figure S6A and Table S4",6 November 2025,Reddicx,"Reddicx,Tosin",Taxonomic composition of gastric tissue samples at the phylum to genus level.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Curvibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Geobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Sporosarcina,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Virgibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria",3379134|1224|1236|135625|712|713;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|1239|91061|1385|186817;1783272|1239|91061|1385;3379134|1224|28211|356|41294|374;1783272|1239|526524|526525|128827|118747;1783272|1239|91061|186826|186828|2747;1783272|1239|91061|1385|186818;3379134|1224|28216|80840|80864;3379134|1224|28216|80840|80864|281915;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|3120669|129337;3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|33958|1243;3379134|976|200643|171549|2005473;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481;3379134|1224|28216|206351;3379134|1224|28211|356|41294;1783272|201174|1760|85007|85025;3379134|1224|1236|135625|712;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|201174|1760|85007|85025|1827;3379134|1224|28211|766;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|1385|186818|1569;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;3379134|1224|28216|80840|80864|34072;1783272|1239|91061|1385|186817|84406;3379134|1224|1236|135625;3379134|1224|1236,Complete,KateRasheed
bsdb:39355268/3/1,39355268,meta-analysis,39355268,10.3389/fcimb.2024.1397466,NA,"Wang Y., Wang Y., Han W., Han M., Liu X., Dai J., Dong Y., Sun T. , Xu J.",Intratumoral and fecal microbiota reveals microbial markers associated with gastric carcinogenesis,Frontiers in cellular and infection microbiology,2024,"fecal microbiota, gastric cancer, intratumoral microbiota, microbial marker, non-invasive prediction",Experiment 3,"China,Colombia,South Korea",Homo sapiens,Mucosa of body of stomach,UBERON:0004995,Gastric cancer,MONDO:0001056,Combination of Benign and Gastric cancer (GC) group.,Normal group.,Healthy people that are free of both benign and gastric cancer.,1308,334,1 month,16S,12345,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2D, Figure S6A and Table S4",6 November 2025,Reddicx,"Reddicx,Tosin",Taxonomic composition of gastric tissue samples at the genus level.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Natronincolaceae|g__Alkaliphilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Legionellaceae|g__Legionella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Legionellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales",3379134|1224|1236|2887326|468|469;1783272|1239|186801|3082720|3118656|114627;1783272|1239|91061|1385|186817|1386;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;3379134|976|117743|200644|2762318|59732;3379134|1224|1236|91347|543|544;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;3379134|1224|28216|80840|119060|106589;3379134|1224|1236|91347|543|547;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|561;1783272|1239|186801|186802|216572|216851;3379134|976|117743|200644;3379134|976|117743;3379134|1224|1236|118969|444|445;1783272|1239|909932|1843488|909930|33024;3379134|1224|1236|72274|135621|286;1783272|1239|186801|3085636|186803|841;3379134|976|117743|200644|2762318;1783272|1239|91061|186826|81852;1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;1783272|1239|909932|1843489|31977;1783272|1239|186801;1783272|1239|186801|186802;3379134|1224|28211|356|119045;3379134|1224|28216|80840|75682;3379134|1224|28216|80840;3379134|1224|28216;3379134|1224|1236|91347|543;3379134|1224|1236|91347;3379134|1224|1236|118969|444;3379134|1224|1236|118969;3379134|1224|1236|2887326|468;3379134|1224|1236|72274|135621;3379134|1224|1236|72274,Complete,KateRasheed
bsdb:39355268/4/1,39355268,meta-analysis,39355268,10.3389/fcimb.2024.1397466,NA,"Wang Y., Wang Y., Han W., Han M., Liu X., Dai J., Dong Y., Sun T. , Xu J.",Intratumoral and fecal microbiota reveals microbial markers associated with gastric carcinogenesis,Frontiers in cellular and infection microbiology,2024,"fecal microbiota, gastric cancer, intratumoral microbiota, microbial marker, non-invasive prediction",Experiment 4,"China,Colombia,South Korea",Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,Normal group,Gastric Cancer,These are patients with a confirmed diagnosis of Gastric Cancer.,188,206,1 month,16S,12345,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,"Figure 5D, Table S9 and Figure S4B",9 November 2025,Mautin,"Mautin,Tosin",The LEfSe (Linear discriminant analysis Effecf Size) method identified the bacterial taxa in fecal samples that differed most significantly between normal groups and gastric cancer.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria",3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1301;3379134|1224|1236|135624|83763|83770;3379134|976|200643|171549|171550;3379134|976|200643|171549;3379134|976|200643;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|1300;1783272|1239|91061|186826;1783272|1239|91061;1783272|1239|186801|3082768|990719;3379134|1224|1236|135624|83763;3379134|1224|1236|135624;3379134|1224|1236|91347|543;3379134|1224|1236|91347;3379134|1224|1236,Complete,KateRasheed
bsdb:39355268/4/2,39355268,meta-analysis,39355268,10.3389/fcimb.2024.1397466,NA,"Wang Y., Wang Y., Han W., Han M., Liu X., Dai J., Dong Y., Sun T. , Xu J.",Intratumoral and fecal microbiota reveals microbial markers associated with gastric carcinogenesis,Frontiers in cellular and infection microbiology,2024,"fecal microbiota, gastric cancer, intratumoral microbiota, microbial marker, non-invasive prediction",Experiment 4,"China,Colombia,South Korea",Homo sapiens,Feces,UBERON:0001988,Gastric cancer,MONDO:0001056,Normal group,Gastric Cancer,These are patients with a confirmed diagnosis of Gastric Cancer.,188,206,1 month,16S,12345,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,"Figure 5D, Table S9 and Figure S4B",9 November 2025,Mautin,"Mautin,Tosin",The LEfSe (Linear discriminant analysis Effect Size) method identified the bacterial taxa in fecal samples that differed most significantly between normal groups and gastric cancer.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria",1783272|1239|186801|186802|31979|1485;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3085636|186803|841;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;1783272|1239|909932|1843489|31977;1783272|1239|186801|186802;1783272|1239|186801;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;3379134|1224|28216|80840|506;3379134|1224|28216|80840;3379134|1224|28216,Complete,KateRasheed
bsdb:39355268/5/1,39355268,meta-analysis,39355268,10.3389/fcimb.2024.1397466,NA,"Wang Y., Wang Y., Han W., Han M., Liu X., Dai J., Dong Y., Sun T. , Xu J.",Intratumoral and fecal microbiota reveals microbial markers associated with gastric carcinogenesis,Frontiers in cellular and infection microbiology,2024,"fecal microbiota, gastric cancer, intratumoral microbiota, microbial marker, non-invasive prediction",Experiment 5,"China,Colombia,South Korea",Homo sapiens,Mucosa of body of stomach,UBERON:0004995,Gastric cancer,MONDO:0001056,Hp-Normal group,Hp-Gastric Cancer,These are patients with a confirmed diagnosis of non-Helicobacter pylori Gastric Cancer.,NA,NA,1 month,16S,12345,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Figure 4D, Table S7",9 November 2025,Mautin,Mautin,The LEfSe method identified the bacterial taxa that differed most significantly between the HP-normal groups and the HP-gastric cancer groups.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Geobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",1783272|201174|1760|85006|1268|1663;1783272|1239|91061|1385|3120669|129337;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3082720|186804|1257;3384189|32066|203490|203491|203492|848;3379134|1224|28211|356|118882|528;3379134|1224|28216|206351|481|482,Complete,KateRasheed
bsdb:39355268/5/2,39355268,meta-analysis,39355268,10.3389/fcimb.2024.1397466,NA,"Wang Y., Wang Y., Han W., Han M., Liu X., Dai J., Dong Y., Sun T. , Xu J.",Intratumoral and fecal microbiota reveals microbial markers associated with gastric carcinogenesis,Frontiers in cellular and infection microbiology,2024,"fecal microbiota, gastric cancer, intratumoral microbiota, microbial marker, non-invasive prediction",Experiment 5,"China,Colombia,South Korea",Homo sapiens,Mucosa of body of stomach,UBERON:0004995,Gastric cancer,MONDO:0001056,Hp-Normal group,Hp-Gastric Cancer,These are patients with a confirmed diagnosis of non-Helicobacter pylori Gastric Cancer.,NA,NA,1 month,16S,12345,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"Figure 4D, Table S7",10 November 2025,Mautin,Mautin,The LEfSe method identified the bacterial taxa that differed most significantly between the HP-normal groups and the HP-gastric cancer groups.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549|815|816;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|216851;1783272|1239|909932|1843488|909930|33024;3379134|1224|28216|80840|119060|106589;3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|561;3379134|1224|1236|2887326|468|469;3379134|1224|1236|72274|135621|286,Complete,KateRasheed
bsdb:39355268/6/1,39355268,meta-analysis,39355268,10.3389/fcimb.2024.1397466,NA,"Wang Y., Wang Y., Han W., Han M., Liu X., Dai J., Dong Y., Sun T. , Xu J.",Intratumoral and fecal microbiota reveals microbial markers associated with gastric carcinogenesis,Frontiers in cellular and infection microbiology,2024,"fecal microbiota, gastric cancer, intratumoral microbiota, microbial marker, non-invasive prediction",Experiment 6,"China,Colombia,South Korea",Homo sapiens,Mucosa of body of stomach,UBERON:0004995,Gastric cancer,MONDO:0001056,Hp+Normal group,Hp+Gastric Cancer,These are patients with a confirmed diagnosis of non-Helicobacter pylori Gastric Cancer.,NA,NA,1 month,16S,12345,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Figure 4H, Table S8",10 November 2025,Mautin,Mautin,The LEfSe method identified the bacterial taxa that differed most significantly between HP+ normal and HP+ gastric groups.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3082720|186804|1257;3379134|1224|28211|356|118882|528,Complete,KateRasheed
bsdb:39355268/6/2,39355268,meta-analysis,39355268,10.3389/fcimb.2024.1397466,NA,"Wang Y., Wang Y., Han W., Han M., Liu X., Dai J., Dong Y., Sun T. , Xu J.",Intratumoral and fecal microbiota reveals microbial markers associated with gastric carcinogenesis,Frontiers in cellular and infection microbiology,2024,"fecal microbiota, gastric cancer, intratumoral microbiota, microbial marker, non-invasive prediction",Experiment 6,"China,Colombia,South Korea",Homo sapiens,Mucosa of body of stomach,UBERON:0004995,Gastric cancer,MONDO:0001056,Hp+Normal group,Hp+Gastric Cancer,These are patients with a confirmed diagnosis of non-Helicobacter pylori Gastric Cancer.,NA,NA,1 month,16S,12345,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"Figure 4H, Table S8",10 November 2025,Mautin,Mautin,The LEfSe method identified the bacterial taxa that differed most significantly between HP+ normal and HP+ gastric groups.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",3379134|976|200643|171549|815|816;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|216572|216851;3379134|1224|28211|204457|41297|13687;3379134|1224|28216|80840|119060|106589;3379134|1224|1236|72274|135621|286,Complete,KateRasheed
bsdb:39367431/1/1,39367431,"cross-sectional observational, not case-control",39367431,10.1186/s40168-024-01901-1,https://pubmed.ncbi.nlm.nih.gov/39367431/,"Gaber M., Wilson A.S., Millen A.E., Hovey K.M., LaMonte M.J., Wactawski-Wende J., Ochs-Balcom H.M. , Cook K.L.",Visceral adiposity in postmenopausal women is associated with a pro-inflammatory gut microbiome and immunogenic metabolic endotoxemia,Microbiome,2024,"Aging, Inflammation, Leaky gut, Lipopolysaccharide, Menopause, Metabolic endotoxemia, Microbiome, Obesity, Women’s Health Initiative",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Visceral adipose tissue measurement,EFO:0004765,Low Visceral Adiposity Tissue (VAT) group (Control/Unexposed group).,High Visceral Adiposity Tissue (VAT) group (Case/Exposed group),"The high visceral adiposity tissue (VAT) group represents women with elevated visceral adipose tissue, which is associated with pro-inflammatory gut microbiome characteristics and metabolic endotoxemia",25,25,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Fig. 3E, Fig. 4b",24 October 2024,Vandana Maddi,"Vandana Maddi,KateRasheed,WikiWorks",Differential abundant taxa between women with Low Visceral Adiposity Tissue and High Visceral Adiposity Tissue,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Emergencia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__uncultured Burkholderia sp.",1783272|1239|186801|3082720|543314|1926556;3379134|1224|1236|91347|543|570;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|577310;3379134|1224;3379134|1224|1236|91347|543|620;3379134|1224|28216|80840|119060|32008|188058,Complete,Svetlana up
bsdb:39367431/1/2,39367431,"cross-sectional observational, not case-control",39367431,10.1186/s40168-024-01901-1,https://pubmed.ncbi.nlm.nih.gov/39367431/,"Gaber M., Wilson A.S., Millen A.E., Hovey K.M., LaMonte M.J., Wactawski-Wende J., Ochs-Balcom H.M. , Cook K.L.",Visceral adiposity in postmenopausal women is associated with a pro-inflammatory gut microbiome and immunogenic metabolic endotoxemia,Microbiome,2024,"Aging, Inflammation, Leaky gut, Lipopolysaccharide, Menopause, Metabolic endotoxemia, Microbiome, Obesity, Women’s Health Initiative",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Visceral adipose tissue measurement,EFO:0004765,Low Visceral Adiposity Tissue (VAT) group (Control/Unexposed group).,High Visceral Adiposity Tissue (VAT) group (Case/Exposed group),"The high visceral adiposity tissue (VAT) group represents women with elevated visceral adipose tissue, which is associated with pro-inflammatory gut microbiome characteristics and metabolic endotoxemia",25,25,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Fig. 4b,24 October 2024,Vandana Maddi,"Vandana Maddi,KateRasheed,WikiWorks",Differential abundant taxa between women with Low Visceral Adiposity Tissue and High Visceral Adiposity Tissue,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Massiliimalia,k__Bacillati|p__Bacillota|g__Negativibacillus",1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|2005519|397864;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|1392389;1783272|1239|186801|186802|216572|2895461;1783272|1239|1980693,Complete,ChiomaBlessing
bsdb:39367431/2/1,39367431,"cross-sectional observational, not case-control",39367431,10.1186/s40168-024-01901-1,https://pubmed.ncbi.nlm.nih.gov/39367431/,"Gaber M., Wilson A.S., Millen A.E., Hovey K.M., LaMonte M.J., Wactawski-Wende J., Ochs-Balcom H.M. , Cook K.L.",Visceral adiposity in postmenopausal women is associated with a pro-inflammatory gut microbiome and immunogenic metabolic endotoxemia,Microbiome,2024,"Aging, Inflammation, Leaky gut, Lipopolysaccharide, Menopause, Metabolic endotoxemia, Microbiome, Obesity, Women’s Health Initiative",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Visceral adipose tissue measurement,EFO:0004765,Low Visceral Adiposity Tissue (VAT) group with Lipopolysaccharide (LPS)-containing bacteria,High Visceral Adiposity Tissue (VAT) group with Lipopolysaccharide (LPS)-containing bacteria,High Visceral Adiposity Tissue (VAT) group with Lipopolysaccharide (LPS)-containing bacteria represents women with elevated visceral adipose tissue having LPS-containing bacteria as defined by lpxA and lpxB gene expression.,25,25,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 6E,24 October 2024,Vandana Maddi,"Vandana Maddi,KateRasheed,WikiWorks",Differential abundant taxa between women with Low Visceral Adiposity Tissue and High Visceral Adiposity Tissue with LPS-containing bacteria,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,Svetlana up
bsdb:39367431/2/2,39367431,"cross-sectional observational, not case-control",39367431,10.1186/s40168-024-01901-1,https://pubmed.ncbi.nlm.nih.gov/39367431/,"Gaber M., Wilson A.S., Millen A.E., Hovey K.M., LaMonte M.J., Wactawski-Wende J., Ochs-Balcom H.M. , Cook K.L.",Visceral adiposity in postmenopausal women is associated with a pro-inflammatory gut microbiome and immunogenic metabolic endotoxemia,Microbiome,2024,"Aging, Inflammation, Leaky gut, Lipopolysaccharide, Menopause, Metabolic endotoxemia, Microbiome, Obesity, Women’s Health Initiative",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Visceral adipose tissue measurement,EFO:0004765,Low Visceral Adiposity Tissue (VAT) group with Lipopolysaccharide (LPS)-containing bacteria,High Visceral Adiposity Tissue (VAT) group with Lipopolysaccharide (LPS)-containing bacteria,High Visceral Adiposity Tissue (VAT) group with Lipopolysaccharide (LPS)-containing bacteria represents women with elevated visceral adipose tissue having LPS-containing bacteria as defined by lpxA and lpxB gene expression.,25,25,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 6B,24 October 2024,Vandana Maddi,"Vandana Maddi,KateRasheed,WikiWorks",Differential abundant taxa between women with Low Visceral Adiposity Tissue and High Visceral Adiposity Tissue with LPS-containing bacteria,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,3379134|976|200643|171549|171550|239759,Complete,Svetlana up
bsdb:39367431/3/1,39367431,"cross-sectional observational, not case-control",39367431,10.1186/s40168-024-01901-1,https://pubmed.ncbi.nlm.nih.gov/39367431/,"Gaber M., Wilson A.S., Millen A.E., Hovey K.M., LaMonte M.J., Wactawski-Wende J., Ochs-Balcom H.M. , Cook K.L.",Visceral adiposity in postmenopausal women is associated with a pro-inflammatory gut microbiome and immunogenic metabolic endotoxemia,Microbiome,2024,"Aging, Inflammation, Leaky gut, Lipopolysaccharide, Menopause, Metabolic endotoxemia, Microbiome, Obesity, Women’s Health Initiative",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Visceral adipose tissue measurement,EFO:0004765,Low Visceral Adiposity Tissue (VAT) group (Control/Unexposed group).,High Visceral Adiposity Tissue (VAT) group (Case/Exposed group),"The high visceral adiposity tissue (VAT) group represents women with elevated visceral adipose tissue, which is associated with pro-inflammatory gut microbiome characteristics and metabolic endotoxemia",25,25,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Fig. 4D,24 October 2024,Vandana Maddi,"Vandana Maddi,KateRasheed,WikiWorks",Differential abundant taxa between women with Low Visceral Adiposity Tissue and High Visceral Adiposity Tissue using LEfSe,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__uncultured Burkholderia sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__uncultured Paraburkholderia sp.",3379134|1224|28216|80840|119060|32008|188058;3379134|1224|28216|80840|995019|577310|487175;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|2005525|375288|823;3379134|1224|28216|80840|119060|1822464|1822466,Complete,ChiomaBlessing
bsdb:39367431/3/2,39367431,"cross-sectional observational, not case-control",39367431,10.1186/s40168-024-01901-1,https://pubmed.ncbi.nlm.nih.gov/39367431/,"Gaber M., Wilson A.S., Millen A.E., Hovey K.M., LaMonte M.J., Wactawski-Wende J., Ochs-Balcom H.M. , Cook K.L.",Visceral adiposity in postmenopausal women is associated with a pro-inflammatory gut microbiome and immunogenic metabolic endotoxemia,Microbiome,2024,"Aging, Inflammation, Leaky gut, Lipopolysaccharide, Menopause, Metabolic endotoxemia, Microbiome, Obesity, Women’s Health Initiative",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Visceral adipose tissue measurement,EFO:0004765,Low Visceral Adiposity Tissue (VAT) group (Control/Unexposed group).,High Visceral Adiposity Tissue (VAT) group (Case/Exposed group),"The high visceral adiposity tissue (VAT) group represents women with elevated visceral adipose tissue, which is associated with pro-inflammatory gut microbiome characteristics and metabolic endotoxemia",25,25,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Fig. 4D,24 October 2024,Vandana Maddi,"Vandana Maddi,KateRasheed,WikiWorks",Differential abundant taxa between women with Low Visceral Adiposity Tissue and High Visceral Adiposity Tissue using LEfSe,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter rarus,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis|s__Victivallis vadensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas massiliensis (ex Afouda et al. 2020),k__Bacillati|p__Bacillota|g__Negativibacillus|s__Negativibacillus massiliensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__uncultured Bifidobacterium sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides timonensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Bacillota|s__uncultured Bacillota bacterium",3379134|976|200643|171549|171552|558436|1676614;3379134|256845|1313211|278082|255528|172900|172901;1783272|1239|186801|186802|1392389|1673721;1783272|1239|1980693|1871035;1783272|201174|1760|85004|31953|1678|165187;3379134|976|200643|171549|815|816|1470345;3379134|976|200643|171549|815|816|246787;3379134|976|200643|171549|2005519|397864|487174;1783272|1239|344338,Complete,ChiomaBlessing
bsdb:39367431/4/1,39367431,"cross-sectional observational, not case-control",39367431,10.1186/s40168-024-01901-1,https://pubmed.ncbi.nlm.nih.gov/39367431/,"Gaber M., Wilson A.S., Millen A.E., Hovey K.M., LaMonte M.J., Wactawski-Wende J., Ochs-Balcom H.M. , Cook K.L.",Visceral adiposity in postmenopausal women is associated with a pro-inflammatory gut microbiome and immunogenic metabolic endotoxemia,Microbiome,2024,"Aging, Inflammation, Leaky gut, Lipopolysaccharide, Menopause, Metabolic endotoxemia, Microbiome, Obesity, Women’s Health Initiative",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Visceral adipose tissue measurement,EFO:0004765,Low Visceral Adiposity Tissue (VAT) group (Control/Unexposed group).,High Visceral Adiposity Tissue (VAT) group (Case/Exposed group),"The high visceral adiposity tissue (VAT) group represents women with elevated visceral adipose tissue, which is associated with pro-inflammatory gut microbiome characteristics and metabolic endotoxemia",25,25,3 months,WMS,NA,Illumina,relative abundances,Pearson Correlation,0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Figure 4C + Within text (Under 'Results' section, Paragraph 4, Line 2)",24 October 2024,Vandana Maddi,"Vandana Maddi,KateRasheed,WikiWorks",Differential abundant taxa between women with Low Visceral Adiposity Tissue and High Visceral Adiposity Tissue using Pearson Heatmap,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella",1783272|1239|186801|3085636|186803|189330|88431;3379134|976|200643|171549|2005525|375288|823;1783272|1239|186801|3085636|186803|841|166486;3379134|1224|1236|91347|543|620,Complete,Svetlana up
bsdb:39367431/4/2,39367431,"cross-sectional observational, not case-control",39367431,10.1186/s40168-024-01901-1,https://pubmed.ncbi.nlm.nih.gov/39367431/,"Gaber M., Wilson A.S., Millen A.E., Hovey K.M., LaMonte M.J., Wactawski-Wende J., Ochs-Balcom H.M. , Cook K.L.",Visceral adiposity in postmenopausal women is associated with a pro-inflammatory gut microbiome and immunogenic metabolic endotoxemia,Microbiome,2024,"Aging, Inflammation, Leaky gut, Lipopolysaccharide, Menopause, Metabolic endotoxemia, Microbiome, Obesity, Women’s Health Initiative",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Visceral adipose tissue measurement,EFO:0004765,Low Visceral Adiposity Tissue (VAT) group (Control/Unexposed group).,High Visceral Adiposity Tissue (VAT) group (Case/Exposed group),"The high visceral adiposity tissue (VAT) group represents women with elevated visceral adipose tissue, which is associated with pro-inflammatory gut microbiome characteristics and metabolic endotoxemia",25,25,3 months,WMS,NA,Illumina,relative abundances,Pearson Correlation,0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Figure 4C + Within text (Under 'Results' section, Paragraph 4, Line 2)",24 October 2024,Vandana Maddi,"Vandana Maddi,KateRasheed,WikiWorks",Differential abundant taxa between women with Low Visceral Adiposity Tissue and High Visceral Adiposity Tissue using Pearson heatmap,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium AF42-6,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium OF09-1,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium AM21-21,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium AM26-1LB,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium GAM79,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium OF09-33XD,k__Bacillati|p__Bacillota|g__Negativibacillus|s__Negativibacillus massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium AM28-23LB",3379134|976|200643|171549|171550|239759|328814;1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|186802|31979|2291990;1783272|1239|186801|186802|31979|2292276;1783272|1239|186801|3085636|186803|2292903;1783272|1239|186801|3085636|186803|2292906;1783272|1239|186801|3085636|186803|2109691;1783272|1239|186801|3085636|186803|2292273;1783272|1239|1980693|1871035;1783272|1239|186801|186802|216572|2292269,Complete,ChiomaBlessing
bsdb:39377587/1/1,39377587,time series / longitudinal observational,39377587,10.1128/msphere.00706-24,NA,"McMillan A.S., Zhang G., Dougherty M.K., McGill S.K., Gulati A.S., Baker E.S. , Theriot C.M.","Metagenomic, metabolomic, and lipidomic shifts associated with fecal microbiota transplantation for recurrent <i>Clostridioides difficile</i> infection",mSphere,2024,"Clostridioides difficile, acylcarnitines, amino acids, bile acids, bile salt hydrolase, fecal microbiota transplant, lipids, microbial conjugated bile acids",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Clostridium difficile infection,EFO:0009130,pre-Fecal Microbiota Transplant (pre-FMT),post-Fecal Microbiota Transplant (post-FMT - 2 weeks),post-FMT (2 weeks) refers to samples from patients at 2weeks of fecal microbiota transplant (FMT).,16,11,NA,WMS,NA,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Table S1,24 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of microbiota between pre-FMT patients and 2-weeks post-FMT patients.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|186802|3082771;1783272|1239|186801|3082720|3030910;3379134|976|200643|171549|815;1783272|201174|1760|85004|31953;1783272|1239|186801|186802|3085642;1783272|201174|84998|84999|84107;1783272|201174|84998|1643822|1643826;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:39377587/1/2,39377587,time series / longitudinal observational,39377587,10.1128/msphere.00706-24,NA,"McMillan A.S., Zhang G., Dougherty M.K., McGill S.K., Gulati A.S., Baker E.S. , Theriot C.M.","Metagenomic, metabolomic, and lipidomic shifts associated with fecal microbiota transplantation for recurrent <i>Clostridioides difficile</i> infection",mSphere,2024,"Clostridioides difficile, acylcarnitines, amino acids, bile acids, bile salt hydrolase, fecal microbiota transplant, lipids, microbial conjugated bile acids",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Clostridium difficile infection,EFO:0009130,pre-Fecal Microbiota Transplant (pre-FMT),post-Fecal Microbiota Transplant (post-FMT - 2 weeks),post-FMT (2 weeks) refers to samples from patients at 2weeks of fecal microbiota transplant (FMT).,16,11,NA,WMS,NA,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Table S1,24 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of microbiota between pre-FMT patients and 2-weeks post-FMT patients.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|1224|1236|91347|543;1783272|1239|909932|1843489|31977,Complete,Svetlana up
bsdb:39377587/2/1,39377587,time series / longitudinal observational,39377587,10.1128/msphere.00706-24,NA,"McMillan A.S., Zhang G., Dougherty M.K., McGill S.K., Gulati A.S., Baker E.S. , Theriot C.M.","Metagenomic, metabolomic, and lipidomic shifts associated with fecal microbiota transplantation for recurrent <i>Clostridioides difficile</i> infection",mSphere,2024,"Clostridioides difficile, acylcarnitines, amino acids, bile acids, bile salt hydrolase, fecal microbiota transplant, lipids, microbial conjugated bile acids",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Clostridium difficile infection,EFO:0009130,pre-FMT,post-FMT (2 months),post-FMT (2 months) refers to samples from patients at 2 months of fecal microbiota transplant (FMT).,16,10,NA,WMS,NA,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Table S1,27 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of microbiota between pre-FMT patients and 2-months post-FMT patients.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae",1783272|1239|186801|186802|3082771;1783272|1239|186801|186802|216572;1783272|201174|84998|1643822|1643826;1783272|201174|84998|84999|84107;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|815;1783272|1239|186801|3082720|3030910;1783272|1239|186801|186802|3085642,Complete,Svetlana up
bsdb:39377587/2/2,39377587,time series / longitudinal observational,39377587,10.1128/msphere.00706-24,NA,"McMillan A.S., Zhang G., Dougherty M.K., McGill S.K., Gulati A.S., Baker E.S. , Theriot C.M.","Metagenomic, metabolomic, and lipidomic shifts associated with fecal microbiota transplantation for recurrent <i>Clostridioides difficile</i> infection",mSphere,2024,"Clostridioides difficile, acylcarnitines, amino acids, bile acids, bile salt hydrolase, fecal microbiota transplant, lipids, microbial conjugated bile acids",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Clostridium difficile infection,EFO:0009130,pre-FMT,post-FMT (2 months),post-FMT (2 months) refers to samples from patients at 2 months of fecal microbiota transplant (FMT).,16,10,NA,WMS,NA,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Table S1,27 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of microbiota between pre-FMT patients and 2-months post-FMT patients.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",3379134|1224|1236|91347|543;1783272|1239|909932|1843489|31977;1783272|1239|91061|186826|33958,Complete,Svetlana up
bsdb:39377587/3/1,39377587,time series / longitudinal observational,39377587,10.1128/msphere.00706-24,NA,"McMillan A.S., Zhang G., Dougherty M.K., McGill S.K., Gulati A.S., Baker E.S. , Theriot C.M.","Metagenomic, metabolomic, and lipidomic shifts associated with fecal microbiota transplantation for recurrent <i>Clostridioides difficile</i> infection",mSphere,2024,"Clostridioides difficile, acylcarnitines, amino acids, bile acids, bile salt hydrolase, fecal microbiota transplant, lipids, microbial conjugated bile acids",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Clostridium difficile infection,EFO:0009130,pre-FMT,post-FMT (6 months),post-FMT (6 months) refers to samples from patients at 6 months of fecal microbiota transplant (FMT).,16,8,NA,WMS,NA,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Table S1,26 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of microbiota between pre-FMT patients and 6-months post-FMT patients.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. CAG:74",1783272|1239|186801|186802|3082771;1783272|1239|186801|3082720|3030910;3379134|976|200643|171549|815;1783272|201174|84998|84999|84107;1783272|201174|84998|1643822|1643826;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|216851|1262897,Complete,Svetlana up
bsdb:39377587/3/2,39377587,time series / longitudinal observational,39377587,10.1128/msphere.00706-24,NA,"McMillan A.S., Zhang G., Dougherty M.K., McGill S.K., Gulati A.S., Baker E.S. , Theriot C.M.","Metagenomic, metabolomic, and lipidomic shifts associated with fecal microbiota transplantation for recurrent <i>Clostridioides difficile</i> infection",mSphere,2024,"Clostridioides difficile, acylcarnitines, amino acids, bile acids, bile salt hydrolase, fecal microbiota transplant, lipids, microbial conjugated bile acids",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Clostridium difficile infection,EFO:0009130,pre-FMT,post-FMT (6 months),post-FMT (6 months) refers to samples from patients at 6 months of fecal microbiota transplant (FMT).,16,8,NA,WMS,NA,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Table S1,26 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of microbiota between pre-FMT patients and 6-months post-FMT patients.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",3379134|1224|1236|91347|543;1783272|1239|91061|186826|33958,Complete,Svetlana up
bsdb:39377587/4/1,39377587,time series / longitudinal observational,39377587,10.1128/msphere.00706-24,NA,"McMillan A.S., Zhang G., Dougherty M.K., McGill S.K., Gulati A.S., Baker E.S. , Theriot C.M.","Metagenomic, metabolomic, and lipidomic shifts associated with fecal microbiota transplantation for recurrent <i>Clostridioides difficile</i> infection",mSphere,2024,"Clostridioides difficile, acylcarnitines, amino acids, bile acids, bile salt hydrolase, fecal microbiota transplant, lipids, microbial conjugated bile acids",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Clostridium difficile infection,EFO:0009130,pre-FMT,post-FMT (all time points),"post-FMT refers to all post-FMT time points (2 week, 2 months, and 6 months)",16,29,NA,WMS,NA,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Table S1,30 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of microbiota between pre-FMT and all post-FMT patients.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",1783272|1239|186801|186802|3082771;1783272|1239|186801|3082720|3030910;3379134|976|200643|171549|815;1783272|201174|1760|85004|31953;1783272|1239|186801|186802|3085642;1783272|201174|84998|84999|84107;1783272|201174|84998|1643822|1643826;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171550,Complete,Svetlana up
bsdb:39377587/4/2,39377587,time series / longitudinal observational,39377587,10.1128/msphere.00706-24,NA,"McMillan A.S., Zhang G., Dougherty M.K., McGill S.K., Gulati A.S., Baker E.S. , Theriot C.M.","Metagenomic, metabolomic, and lipidomic shifts associated with fecal microbiota transplantation for recurrent <i>Clostridioides difficile</i> infection",mSphere,2024,"Clostridioides difficile, acylcarnitines, amino acids, bile acids, bile salt hydrolase, fecal microbiota transplant, lipids, microbial conjugated bile acids",Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,Clostridium difficile infection,EFO:0009130,pre-FMT,post-FMT (all time points),"post-FMT refers to all post-FMT time points (2 week, 2 months, and 6 months)",16,29,NA,WMS,NA,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Table S1,30 October 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of microbiota between pre-FMT and all post-FMT patients.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|909932|1843489|31977;1783272|1239|91061|186826|33958,Complete,Svetlana up
bsdb:39387592/1/1,39387592,prospective cohort,39387592,10.1128/spectrum.00962-24,NA,"Fang Y., Liu X., Ren J., Wang X., Zhou F., Huang S., You L. , Zhao Y.",Integrated analysis of microbiome and metabolome reveals signatures in PDAC tumorigenesis and prognosis,Microbiology spectrum,2024,"PDAC, carcinogenesis, metabolome, microbial metabolism, microbiota, pancreatic ductal adenocarcinoma",Experiment 1,China,Homo sapiens,Pancreas,UBERON:0001264,Pancreatic ductal adenocarcinoma,EFO:0002517,Normal Adjacent Tissue (NAT),Pancreatic ductal adenocarcinoma  (PDAC),Patients with Pancreatic ductal adenocarcinoma tumor samples,105,103,NA,NA,NA,2b-RAD,relative abundances,MaAsLin2,0.25,TRUE,NA,NA,body mass index,NA,decreased,decreased,decreased,NA,NA,Signature 1,"Figure 2A,B and Table S1",1 April 2025,MyleeeA,MyleeeA,Differential taxa at the species and genus level identified by MaAsLin2 (*q < 0.25).,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium granulosum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus",1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85009|31957|1912216;1783272|201174|1760|85009|31957|1912216|1747;1783272|201174|1760|85009|31957|1912216|33011;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|1385|90964|1279|1280,Complete,Svetlana up
bsdb:39387592/1/2,39387592,prospective cohort,39387592,10.1128/spectrum.00962-24,NA,"Fang Y., Liu X., Ren J., Wang X., Zhou F., Huang S., You L. , Zhao Y.",Integrated analysis of microbiome and metabolome reveals signatures in PDAC tumorigenesis and prognosis,Microbiology spectrum,2024,"PDAC, carcinogenesis, metabolome, microbial metabolism, microbiota, pancreatic ductal adenocarcinoma",Experiment 1,China,Homo sapiens,Pancreas,UBERON:0001264,Pancreatic ductal adenocarcinoma,EFO:0002517,Normal Adjacent Tissue (NAT),Pancreatic ductal adenocarcinoma  (PDAC),Patients with Pancreatic ductal adenocarcinoma tumor samples,105,103,NA,NA,NA,2b-RAD,relative abundances,MaAsLin2,0.25,TRUE,NA,NA,body mass index,NA,decreased,decreased,decreased,NA,NA,Signature 2,"Figure 2A, B and Table S1",1 April 2025,MyleeeA,MyleeeA,Differential taxa at the species and genus level identified by MaAsLin2 (*q < 0.25).,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus bombysepticus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister hominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Limnohabitans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium intermedium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycolicibacillus|s__Mycolicibacillus koreensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles|s__Roseateles sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas aquatilis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|s__Opitutia bacterium UBA953",1783272|1239|91061|1385|186817|1386;1783272|1239|91061|1385|186817|1386|658666;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|39948|2582419;1783272|201174|1760|85007|85029|37914;3379134|1224|28216|80840|80864|665874;1783272|201174|1760|85006|85023|33882;1783272|201174|1760|85007|1762|1763;1783272|201174|1760|85007|1762|1763|28445;1783272|201174|1760|85007|1762|2126281|1069220;3379134|1224|28216|80840|2975441|93681;3379134|1224|28216|80840|2975441|93681|1971397;3379134|1224|28211|204457|41297|13687;3379134|1224|28211|204457|41297|13687|93063;1783272|1239|91061|186826|1300|1301;3379134|74201|414999|1948744,Complete,Svetlana up
bsdb:39387592/2/1,39387592,prospective cohort,39387592,10.1128/spectrum.00962-24,NA,"Fang Y., Liu X., Ren J., Wang X., Zhou F., Huang S., You L. , Zhao Y.",Integrated analysis of microbiome and metabolome reveals signatures in PDAC tumorigenesis and prognosis,Microbiology spectrum,2024,"PDAC, carcinogenesis, metabolome, microbial metabolism, microbiota, pancreatic ductal adenocarcinoma",Experiment 2,China,Homo sapiens,Pancreas,UBERON:0001264,Pancreatic ductal adenocarcinoma,EFO:0002517,Normal Adjacent Tissue (NAT),Pancreatic ductal adenocarcinoma  (PDAC),Patients with Pancreatic ductal adenocarcinoma tumor samples.,105,103,NA,NA,NA,2b-RAD,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,Figure 2C and D,1 April 2025,MyleeeA,MyleeeA,Differential taxa at the species and genus level identified by LefSe.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus",1783272|1239|91061|1385|90964|1279;1783272|1239|91061|1385|90964|1279|1280,Complete,Svetlana up
bsdb:39387592/2/2,39387592,prospective cohort,39387592,10.1128/spectrum.00962-24,NA,"Fang Y., Liu X., Ren J., Wang X., Zhou F., Huang S., You L. , Zhao Y.",Integrated analysis of microbiome and metabolome reveals signatures in PDAC tumorigenesis and prognosis,Microbiology spectrum,2024,"PDAC, carcinogenesis, metabolome, microbial metabolism, microbiota, pancreatic ductal adenocarcinoma",Experiment 2,China,Homo sapiens,Pancreas,UBERON:0001264,Pancreatic ductal adenocarcinoma,EFO:0002517,Normal Adjacent Tissue (NAT),Pancreatic ductal adenocarcinoma  (PDAC),Patients with Pancreatic ductal adenocarcinoma tumor samples.,105,103,NA,NA,NA,2b-RAD,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,Figure 2C and D,1 April 2025,MyleeeA,MyleeeA,Differential taxa at the species and genus level identified by LefSe.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus bombysepticus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister hominis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Limnohabitans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium intermedium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycolicibacillus|s__Mycolicibacillus koreensis,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|s__Opitutia bacterium UBA953,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas aquatilis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061|1385|186817|1386|658666;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|39948|2582419;3379134|1224|28216|80840|80864|665874;1783272|201174|1760|85007|1762|1763;1783272|201174|1760|85007|1762|1763|28445;1783272|201174|1760|85007|1762|2126281|1069220;3379134|74201|414999|1948744;3379134|1224|28211|204457|41297|13687;3379134|1224|28211|204457|41297|13687|93063;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:39387592/3/1,39387592,prospective cohort,39387592,10.1128/spectrum.00962-24,NA,"Fang Y., Liu X., Ren J., Wang X., Zhou F., Huang S., You L. , Zhao Y.",Integrated analysis of microbiome and metabolome reveals signatures in PDAC tumorigenesis and prognosis,Microbiology spectrum,2024,"PDAC, carcinogenesis, metabolome, microbial metabolism, microbiota, pancreatic ductal adenocarcinoma",Experiment 3,China,Homo sapiens,Pancreas,UBERON:0001264,M1 distant metastasis stage,EFO:0004930,M1 stage (Decreased),M1 stage (Increased),The tumor stage was evaluated based on the TNM staging system. M1 Stage (Metastasis stage) is the Distant Metastasis stage where cancer has spread to other part of the body.,3,3,NA,NA,NA,2b-RAD,relative abundances,MaAsLin2,0.25,TRUE,NA,NA,body mass index,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 1,1 April 2025,MyleeeA,MyleeeA,Differential taxa at the species level identified by MaAsLin2 (*q < 0.25).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia|s__Massilia timonae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas|s__Brevundimonas diminuta,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas fulva,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia|s__Dietzia maris",3379134|1224|28216|80840|75682|149698|47229;3379134|1224|28211|204458|76892|41275|293;3379134|1224|1236|72274|135621|286|47880;1783272|201174|1760|85007|85029|37914|37915,Complete,Svetlana up
bsdb:39387592/3/2,39387592,prospective cohort,39387592,10.1128/spectrum.00962-24,NA,"Fang Y., Liu X., Ren J., Wang X., Zhou F., Huang S., You L. , Zhao Y.",Integrated analysis of microbiome and metabolome reveals signatures in PDAC tumorigenesis and prognosis,Microbiology spectrum,2024,"PDAC, carcinogenesis, metabolome, microbial metabolism, microbiota, pancreatic ductal adenocarcinoma",Experiment 3,China,Homo sapiens,Pancreas,UBERON:0001264,M1 distant metastasis stage,EFO:0004930,M1 stage (Decreased),M1 stage (Increased),The tumor stage was evaluated based on the TNM staging system. M1 Stage (Metastasis stage) is the Distant Metastasis stage where cancer has spread to other part of the body.,3,3,NA,NA,NA,2b-RAD,relative abundances,MaAsLin2,0.25,TRUE,NA,NA,body mass index,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 1,1 April 2025,MyleeeA,MyleeeA,Differential taxa at the species level identified by MaAsLin2 (*q < 0.25).,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,3379134|1224|1236|72274|135621|286|306,Complete,Svetlana up
bsdb:39387592/5/1,39387592,prospective cohort,39387592,10.1128/spectrum.00962-24,NA,"Fang Y., Liu X., Ren J., Wang X., Zhou F., Huang S., You L. , Zhao Y.",Integrated analysis of microbiome and metabolome reveals signatures in PDAC tumorigenesis and prognosis,Microbiology spectrum,2024,"PDAC, carcinogenesis, metabolome, microbial metabolism, microbiota, pancreatic ductal adenocarcinoma",Experiment 5,China,Homo sapiens,Pancreas,UBERON:0001264,Cancer or benign tumor,MONDO:0045024,Node Stage (N),Tumor Stage (T),The tumor stage was evaluated based on the TNM staging system.,105,105,NA,NA,NA,2b-RAD,relative abundances,LEfSe,0.05,FALSE,2,NA,body mass index,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 2,1 April 2025,MyleeeA,MyleeeA,Differential Microbial taxa between T stage and N stage identified by LefSe.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum|s__Faecalibaculum rodentium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Friedmanniella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus",3379134|1224|28216|80840|80864|12916;1783272|1239|186801|186802|216572|216851;1783272|1239|526524|526525|128827|1729679|1702221;1783272|201174|1760|85009|85015|53387;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|1385|90964|1279|1280,Complete,Svetlana up
bsdb:39387592/5/2,39387592,prospective cohort,39387592,10.1128/spectrum.00962-24,NA,"Fang Y., Liu X., Ren J., Wang X., Zhou F., Huang S., You L. , Zhao Y.",Integrated analysis of microbiome and metabolome reveals signatures in PDAC tumorigenesis and prognosis,Microbiology spectrum,2024,"PDAC, carcinogenesis, metabolome, microbial metabolism, microbiota, pancreatic ductal adenocarcinoma",Experiment 5,China,Homo sapiens,Pancreas,UBERON:0001264,Cancer or benign tumor,MONDO:0045024,Node Stage (N),Tumor Stage (T),The tumor stage was evaluated based on the TNM staging system.,105,105,NA,NA,NA,2b-RAD,relative abundances,LEfSe,0.05,FALSE,2,NA,body mass index,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 2,1 April 2025,MyleeeA,MyleeeA,Differential Microbial taxa between T stage and N stage identified by LefSe.,decreased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia|o__Acidimicrobiales,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax|s__Acidovorax soli,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus bombysepticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae|g__Cellulosimicrobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae|g__Cellulosimicrobium|s__Cellulosimicrobium funkei,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister hominis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Dialisteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Duncaniella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Duncaniella|s__Duncaniella muris,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia|o__Acidimicrobiales|f__Ilumatobacteraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Janibacter|s__Janibacter anophelis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium UBA3282,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Limnohabitans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Luteimonas|s__Luteimonas sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium intermedium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycolicibacillus|s__Mycolicibacillus koreensis,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Opitutaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|s__Opitutia bacterium Tous-C4FEB,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|s__Opitutia bacterium UBA953,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus|s__Paracoccus marcusii,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Pirellulales,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Planctomycetales|f__Planctomycetaceae|s__Planctomycetaceae bacterium UBA1268,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia,k__Pseudomonadati|p__Planctomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:485,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:873,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas aquatilis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota",1783272|201174|84992|84993;1783272|201174|84992;3379134|1224|28216|80840|80864|12916|592050;1783272|201174;3379134|976|200643|171549|171550|239759|1872444;3379134|1224|28211;1783272|1239|91061|1385;1783272|1239;1783272|1239|91061|1385|186817|1386|658666;3379134|976|200643;3379134|976;3379134|1224|28216|80840|119060;1783272|201174|1760|85006|85017|157920;1783272|201174|1760|85006|85017|157920|264251;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|39948|2582419;1783272|1239|909932|1843489|3120688;3379134|976|200643|171549|2005473|2518495;3379134|976|200643|171549|2005473|2518495|2094150;3379134|1224|1236|91347|543|561|562;3379134|976|117743|200644;1783272|201174|84992|84993|2448023;1783272|201174|1760|85006|85021|53457|319054;1783272|1239|186801|3085636|186803|1952023;1783272|1239|91061|186826;3379134|1224|28216|80840|80864|665874;1783272|1239|91061|186826|33958|2742598;1783272|1239|91061|186826|33958|2742598|1613;3379134|1224|1236|135614|32033|83614|1873125;1783272|201174|1760|85007|1762;1783272|201174|1760|85007;1783272|201174|1760|85007|1762|1763;1783272|201174|1760|85007|1762|1763|28445;1783272|201174|1760|85007|1762|2126281|1069220;1783272|1239|909932;3379134|74201|414999|415000|134623;3379134|74201|414999|415000;3379134|74201|414999|1982321;3379134|74201|414999|1948744;3379134|1224|28211|204455|31989|265|59779;3379134|203682|203683|2691354;3379134|203682|203683|112|126|1952726;3379134|203682|203683;3379134|203682;3379134|976|200643|171549|171552|838|1262927;3379134|976|200643|171549|171552|838|1262936;3379134|1224|28211|204457|41297;3379134|1224|28211|204457;3379134|1224|28211|204457|41297|13687;3379134|1224|28211|204457|41297|13687|93063;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1311;1783272|1239|91061|186826|1300|1301|1309;1783272|1239|909932|1843489;3379134|74201|203494;3379134|74201,Complete,Svetlana up
bsdb:39390034/1/1,39390034,case-control,39390034,https://doi.org/10.1038/s41598-024-74513-2,https://www.nature.com/articles/s41598-024-74513-2,"Delanghe L., De Boeck I., Van Malderen J., Allonsius C.N., Van Rillaer T., Bron P.A., Claes I., Hagendorens M., Lebeer S. , Leysen J.",Mild atopic dermatitis is characterized by increase in non-staphylococcus pathobionts and loss of specific species,Scientific reports,2024,NA,Experiment 1,Belgium,Homo sapiens,Skin of body,UBERON:0002097,Dermatitis,MONDO:0002406,healthy controls,mild atopic dermatitis (AD),"Participants diagnosed with mild atopic dermatitis (AD). 
This group specifically includes individuals who exhibit mild lesions characterized by limited symptoms.",49,28,NA,WMS,NA,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a,12 October 2024,Joiejoie,"Joiejoie,Aleru Divine,WikiWorks",Differential abundance analysis for mild AD patients compared to healthy participants using Maaslin2,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pullorum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium ostraviense,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Paeniglutamicibacter|s__Paeniglutamicibacter antarcticus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter|s__Pedobacter panaciterrae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium|s__Photobacterium chitinilyticum,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Sodaliphilus|s__Sodaliphilus pleomorphus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces fumigatiscleroticus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Streptosporangiales|f__Streptosporangiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Streptosporangiales|f__Streptosporangiaceae|g__Streptosporangium|s__Streptosporangium violaceochromogenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium Barb7,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces malachitofuscus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces griseoincarnatus,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Chroococcales|f__Aphanothecaceae|g__Crocosphaera|s__Crocosphaera chwakensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces kurssanovii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus alvi,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Aestuariibaculum|s__Aestuariibaculum marinum,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium hauense,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Caproicibacter|s__Caproicibacter sp.,k__Pseudomonadati|p__Pseudomonadota|c__Candidatius Mariprofundia|o__Mariprofundales|f__Mariprofundaceae|g__Mariprofundus|s__Mariprofundus erugo,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae|g__Chromatium|s__Chromatium weissei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus schweitzeri,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia sp.",1783272|201174|1760|85004|31953|1678|78448;3379134|1224|28216|80840|119060|32008;3379134|1224|28216|80840|119060|32008|36773;3379134|1224|1236|135625|712|724|729;1783272|201174|1760|85007|1762|1763|2738409;1783272|201174|1760|85006|1268|1742990|494023;3379134|1224|28216|80840|119060|1822464;3379134|976|117747|200666|84566|84567|363849;3379134|1224|1236|135623|641|657|2485123;3384194|508458|649775|649776|3029088|638847|1943581;3379134|976|200643|171549|2005473|2815786|2606626;1783272|1239|91061|1385|90964|1279|1280;1783272|1239|91061|1385|90964|1279|1282;3379134|1224|1236|135614|32033|40323|40324;1783272|1239|91061|186826|1300|1301|1303;1783272|201174|1760|85011|2062|1883;1783272|201174|1760|85011|2062|1883|66371;1783272|201174|1760|85012|2004;1783272|201174|1760|85012|2004|2000|46188;3379134|976|200643|171549|1633203;1783272|201174|1760|85011|2062|1883|67322;1783272|201174|1760|85011|2062|1883|29305;1783272|1117|3028117|1118|1890450|263510|2546361;1783272|201174|1760|85011|2062|1883|67312;1783272|1239|91061|186826|33958|2742598|990412;3379134|976|117743|200644|49546|1386924|2683592;3379134|976|117743|200644|49546|237|1204512;1783272|1239|186801|186802|3082771|2576755|2814884;3379134|1224|580370|580371|580372|377315|2528639;1783272|201174|1760|85007|1762|1763|1785;3379134|1224|1236|135613|1046|1047|626372;3379134|976|200643|171549|1853231|574697|1969738;1783272|1239|91061|1385|90964|1279|1654388;3379134|1224|28216|80840|119060|1822464|1926495,Complete,Svetlana up
bsdb:39390034/1/2,39390034,case-control,39390034,https://doi.org/10.1038/s41598-024-74513-2,https://www.nature.com/articles/s41598-024-74513-2,"Delanghe L., De Boeck I., Van Malderen J., Allonsius C.N., Van Rillaer T., Bron P.A., Claes I., Hagendorens M., Lebeer S. , Leysen J.",Mild atopic dermatitis is characterized by increase in non-staphylococcus pathobionts and loss of specific species,Scientific reports,2024,NA,Experiment 1,Belgium,Homo sapiens,Skin of body,UBERON:0002097,Dermatitis,MONDO:0002406,healthy controls,mild atopic dermatitis (AD),"Participants diagnosed with mild atopic dermatitis (AD). 
This group specifically includes individuals who exhibit mild lesions characterized by limited symptoms.",49,28,NA,WMS,NA,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3a,12 October 2024,Joiejoie,"Joiejoie,Aleru Divine,WikiWorks",Differential abundance analysis for mild AD patients compared to healthy participants using Maaslin2,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter lwoffii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Epilithonimonas|s__Epilithonimonas hominis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Kaistella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Kaistella|s__Kaistella haifensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria|s__Kocuria palustris,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus endophyticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Faucicola|s__Faucicola osloensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria cinerea,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingopyxidaceae|g__Sphingopyxis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium|s__Agrobacterium pusense,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus cohnii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria|s__Kocuria salsicia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas|s__Brevundimonas bullata,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter idrijaensis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Haematobacter|s__Haematobacter massiliensis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus|s__Paracoccus marcusii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus|s__Paracoccus aeridis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax|s__Acidovorax temperans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium|s__Microbacterium lacticum",3379134|1224|1236|2887326|468|469;3379134|1224|1236|2887326|468|469|28090;3379134|1224|28211;3379134|976|200643;3379134|1224|28211|356|41294|374;3379134|1224|28211|204458|76892|41275;3379134|976|117743|200644|2762318|2782229|420404;3379134|1224|28211|356;3379134|976|117743|200644|2762318|2782231;3379134|976|117743|200644|2762318|2782231|421525;1783272|201174|1760|85006|1268|57493;1783272|201174|1760|85006|1268|57493|71999;1783272|201174|1760|85006|85023;1783272|201174|1760|85006|1268;1783272|201174|1760|85006|1268|1269|455343;3379134|1224|1236|2887326|468|475;3379134|1224|1236|2887326|468|1604696|34062;3379134|1224|1236|2887326|468|475|479;3379134|1224|1236|2887326|468;3379134|1224|28216|206351|481|482|483;1783272|201174|1760|85009|85015|1839;3379134|1224|28211|204455|31989;3379134|1224|28211|204455|31989|265;3379134|1224|1236|72274;1783272|201174|1760|85006|1268|32207;3379134|1224|28211|204457|41297|13687;3379134|1224|28211|204457|3423718|165697;3379134|1224|28211|356|335928;3379134|1224|28211|356|82115|357|648995;1783272|201174|1760|85006|1268|1269|993416;1783272|201174|1760|85006|1268|57493|664639;3379134|1224|28211|204458|76892|41275|13160;3379134|1224|1236|2887326|468|469|1507807;3379134|1224|28211|204455|31989|366614|195105;3379134|1224|28211|204455|31989|265|59779;3379134|1224|28211|204455|31989|265|1966466;3379134|1224|28216|80840|80864|12916|80878;1783272|201174|1760|85006|85023|33882|33885,Complete,Svetlana up
bsdb:39390034/2/1,39390034,case-control,39390034,https://doi.org/10.1038/s41598-024-74513-2,https://www.nature.com/articles/s41598-024-74513-2,"Delanghe L., De Boeck I., Van Malderen J., Allonsius C.N., Van Rillaer T., Bron P.A., Claes I., Hagendorens M., Lebeer S. , Leysen J.",Mild atopic dermatitis is characterized by increase in non-staphylococcus pathobionts and loss of specific species,Scientific reports,2024,NA,Experiment 2,Belgium,Homo sapiens,Skin of body,UBERON:0002097,Dermatitis,MONDO:0002406,healthy controls under 12 years,mild atopic dermatitis (AD) under 12 years,Participants diagnosed with mild atopic dermatitis (AD) who are under 12 years old.,30,11,NA,WMS,NA,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,unchanged,Signature 1,Figure 3a,23 October 2024,Joiejoie,"Joiejoie,Aleru Divine,WikiWorks",Differences in skin taxa relative abundance based on health condition (healthy or mild AD) and age (under 12 years old),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium|s__Photobacterium chitinilyticum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Streptosporangiales|f__Streptosporangiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Streptosporangiales|f__Streptosporangiaceae|g__Streptosporangium|s__Streptosporangium violaceochromogenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium Barb7,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces kurssanovii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter|s__Pedobacter panaciterrae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Sodaliphilus|s__Sodaliphilus pleomorphus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus alvi,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter sp.,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Aestuariibaculum|s__Aestuariibaculum marinum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium ostraviense,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Paeniglutamicibacter|s__Paeniglutamicibacter antarcticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces fumigatiscleroticus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces malachitofuscus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces griseoincarnatus",3379134|1224|1236|135623|641|657|2485123;1783272|1239|91061|1385|90964|1279|1280;1783272|201174|1760|85012|2004;1783272|201174|1760|85012|2004|2000|46188;3379134|976|200643|171549|1633203;1783272|201174|1760|85011|2062|1883|67312;3379134|1224|1236|135614|32033|40323|40324;3379134|976|117747|200666|84566|84567|363849;3379134|976|200643|171549|2005473|2815786|2606626;1783272|1239|91061|186826|33958|2742598|990412;3384194|508458|649775|649776|3029088|638847|1943581;3379134|976|117743|200644|49546|1386924|2683592;1783272|201174|1760|85007|1762|1763|2738409;1783272|201174|1760|85006|1268|1742990|494023;3379134|1224|1236|135625|712|724|729;1783272|201174|1760|85007|1762|1763|1785;1783272|201174|1760|85011|2062|1883;1783272|201174|1760|85011|2062|1883|66371;1783272|201174|1760|85011|2062|1883|67322;1783272|201174|1760|85011|2062|1883|29305,Complete,Svetlana up
bsdb:39390034/2/2,39390034,case-control,39390034,https://doi.org/10.1038/s41598-024-74513-2,https://www.nature.com/articles/s41598-024-74513-2,"Delanghe L., De Boeck I., Van Malderen J., Allonsius C.N., Van Rillaer T., Bron P.A., Claes I., Hagendorens M., Lebeer S. , Leysen J.",Mild atopic dermatitis is characterized by increase in non-staphylococcus pathobionts and loss of specific species,Scientific reports,2024,NA,Experiment 2,Belgium,Homo sapiens,Skin of body,UBERON:0002097,Dermatitis,MONDO:0002406,healthy controls under 12 years,mild atopic dermatitis (AD) under 12 years,Participants diagnosed with mild atopic dermatitis (AD) who are under 12 years old.,30,11,NA,WMS,NA,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,unchanged,Signature 2,Figure 3a,23 October 2024,Joiejoie,"Joiejoie,Aleru Divine,WikiWorks",Differences in skin taxa relative abundance based on health condition (healthy or mild AD) and age (under 12 years old),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus|s__Paracoccus denitrificans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus endophyticus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Kaistella|s__Kaistella haifensis",3379134|1224|28211|204455|31989|265|266;1783272|201174|1760|85006|85023;3379134|1224|28211|356;1783272|201174|1760|85006|1268;1783272|201174|1760|85006|1268|1269|455343;3379134|976|117743|200644|2762318|2782231|421525,Complete,Svetlana up
bsdb:39390034/3/1,39390034,case-control,39390034,https://doi.org/10.1038/s41598-024-74513-2,https://www.nature.com/articles/s41598-024-74513-2,"Delanghe L., De Boeck I., Van Malderen J., Allonsius C.N., Van Rillaer T., Bron P.A., Claes I., Hagendorens M., Lebeer S. , Leysen J.",Mild atopic dermatitis is characterized by increase in non-staphylococcus pathobionts and loss of specific species,Scientific reports,2024,NA,Experiment 3,Belgium,Homo sapiens,Skin of body,UBERON:0002097,Dermatitis,MONDO:0002406,healthy controls above 12 years,mild atopic dermatitis (AD) above 12 years Old,Participants diagnosed with mild atopic dermatitis (AD) who are above 12 years old.,19,17,NA,WMS,NA,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,unchanged,Signature 1,Figure 3a,24 October 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differences in skin taxa relative abundance based on health condition (healthy or mild AD) and age (above 12 years old),increased,"k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces fumigatiscleroticus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium ostraviense,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Paeniglutamicibacter|s__Paeniglutamicibacter antarcticus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia sp.",3384194|508458|649775|649776|3029088|638847|1943581;1783272|201174|1760|85011|2062|1883|66371;1783272|201174|1760|85007|1762|1763|2738409;1783272|201174|1760|85006|1268|1742990|494023;3379134|1224|28216|80840|119060|32008|36773;3379134|1224|28216|80840|119060|1822464|1926495,Complete,Svetlana up
bsdb:39390034/3/2,39390034,case-control,39390034,https://doi.org/10.1038/s41598-024-74513-2,https://www.nature.com/articles/s41598-024-74513-2,"Delanghe L., De Boeck I., Van Malderen J., Allonsius C.N., Van Rillaer T., Bron P.A., Claes I., Hagendorens M., Lebeer S. , Leysen J.",Mild atopic dermatitis is characterized by increase in non-staphylococcus pathobionts and loss of specific species,Scientific reports,2024,NA,Experiment 3,Belgium,Homo sapiens,Skin of body,UBERON:0002097,Dermatitis,MONDO:0002406,healthy controls above 12 years,mild atopic dermatitis (AD) above 12 years Old,Participants diagnosed with mild atopic dermatitis (AD) who are above 12 years old.,19,17,NA,WMS,NA,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,unchanged,Signature 2,Figure 3a,24 October 2024,Aleru Divine,"Aleru Divine,Scholastica,WikiWorks",Differences in skin taxa relative abundance based on health condition (healthy or mild AD) and age (above 12 years old),decreased,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Kaistella,3379134|976|117743|200644|2762318|2782231,Complete,Svetlana up
bsdb:39394588/1/1,39394588,laboratory experiment,39394588,10.1186/s12986-024-00855-3,NA,"Dou J., Wu Y., Hu R., Liu J., Zhang Y., Zhen X., Wu T., Zhang C., Liu Y., Zheng R. , Jiang G.",Quinoa ameliorates polycystic ovary syndrome via regulating gut microbiota through PI3K/AKT/mTOR pathway and autophagy,Nutrition & metabolism,2024,"Autophagy, Gut microbiota, PI3K/AKT/mTOR, Polycystic ovary syndrome, Quinoa, Sex hormone",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Quinoa group and Control group,Polycystic ovary syndrome (PCOS) group,"Letrozole-induced polycystic ovary syndrome (PCOS) rats, confirmed by estrous cycle disruption and increased body weight, and maintained on an ordinary diet.",15,5,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6H,3 November 2025,Adiba Patel,"Adiba Patel,Firdaws","Linear discriminant analysis Effect Size (LEfSe) analysis was used to evaluate fecal microbiota with a statistically significant difference at the Phylum, Class, Order, Family, and Genus levels. [PCOS vs (Quinoa & Control)]",increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;3384189|32066|203490|203491|203492|848;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171551|836;1783272|1239|186801|186802|216572|1263,Complete,KateRasheed
bsdb:39394588/2/1,39394588,laboratory experiment,39394588,10.1186/s12986-024-00855-3,NA,"Dou J., Wu Y., Hu R., Liu J., Zhang Y., Zhen X., Wu T., Zhang C., Liu Y., Zheng R. , Jiang G.",Quinoa ameliorates polycystic ovary syndrome via regulating gut microbiota through PI3K/AKT/mTOR pathway and autophagy,Nutrition & metabolism,2024,"Autophagy, Gut microbiota, PI3K/AKT/mTOR, Polycystic ovary syndrome, Quinoa, Sex hormone",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Polycystic ovary syndrome (PCOS) group and Control group,Quinoa group,"Letrozole-induced polycystic ovary syndrome (PCOS) rats, confirmed by estrous cycle disorder and increased body weight, fed a quinoa-supplemented diet (20 g/kg/day) in combination with an ordinary diet for 8 weeks.",15,5,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6H,19 January 2026,Firdaws,Firdaws,"Linear discriminant analysis Effect Size (LEfSe) analysis was used to evaluate fecal microbiota with a statistically significant difference at the Phylum, Class, Order, Family, and Genus levels. [Quinoa vs (PCOS & Control)]",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,p__Candidatus Saccharimonadota",3379134|1224|28216|80840|506;1783272|1239;1783272|1239|91061|186826|33958|1578;1783272|544448;3379134|1224|28216|80840|995019|40544;95818,Complete,KateRasheed
bsdb:39394588/3/1,39394588,laboratory experiment,39394588,10.1186/s12986-024-00855-3,NA,"Dou J., Wu Y., Hu R., Liu J., Zhang Y., Zhen X., Wu T., Zhang C., Liu Y., Zheng R. , Jiang G.",Quinoa ameliorates polycystic ovary syndrome via regulating gut microbiota through PI3K/AKT/mTOR pathway and autophagy,Nutrition & metabolism,2024,"Autophagy, Gut microbiota, PI3K/AKT/mTOR, Polycystic ovary syndrome, Quinoa, Sex hormone",Experiment 3,China,Rattus norvegicus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Polycystic ovary syndrome (PCOS) group and Quinoa group,Control group,Rats with regular estrous cycles that did not receive letrozole and were fed an ordinary diet.,10,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6H,19 January 2026,Firdaws,Firdaws,"Linear discriminant analysis Effect Size (LEfSe) analysis was used to evaluate fecal microbiota with a statistically significant difference at the Phylum, Class, Order, Family, and Genus levels. [Control vs (PCOS & Quinoa)]",increased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales,k__Pseudomonadati|p__Elusimicrobiota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239|186801;3379134|200940|3031449|213115|194924;3379134|74152|641853;3379134|74152|641853|641854|641876;3379134|74152|641853|641854;3379134|74152;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|119852;1783272|1239|186801|186802|31979|1485,Complete,KateRasheed
bsdb:39399065/1/1,39399065,case-control,39399065,10.2147/CCID.S473237,NA,"Zhao K., Zhao Y., Guo A., Xiao S. , Tu C.",Oral Microbiota Variations in Psoriasis Patients Without Comorbidity,"Clinical, cosmetic and investigational dermatology",2024,"16s rRNA, comorbidity, dysbiosis, oral microbiota, psoriasis",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Psoriasis,EFO:0000676,Healthy subjects (N),Psoriasis subjects (P),"Subjects diagnosed with plaque psoriasis by two dermatologists, aged between 18 and 60 years old, and belonging to the Chinese Han population.",20,20,3 months,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,log transformation,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,increased,NA,NA,Signature 1,"Figures 3a, 3b, 3c",30 October 2025,YokoC,YokoC,"Bar plots from a Wilcoxon test, showing the significant differences in relative abundance of taxa between the psoriasis group (P) and the healthy control group (N).",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|976|200643|171549|171551|836|837;3379134|976|200643|171549|171552|838,Complete,KateRasheed
bsdb:39399065/1/2,39399065,case-control,39399065,10.2147/CCID.S473237,NA,"Zhao K., Zhao Y., Guo A., Xiao S. , Tu C.",Oral Microbiota Variations in Psoriasis Patients Without Comorbidity,"Clinical, cosmetic and investigational dermatology",2024,"16s rRNA, comorbidity, dysbiosis, oral microbiota, psoriasis",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Psoriasis,EFO:0000676,Healthy subjects (N),Psoriasis subjects (P),"Subjects diagnosed with plaque psoriasis by two dermatologists, aged between 18 and 60 years old, and belonging to the Chinese Han population.",20,20,3 months,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,log transformation,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,increased,NA,NA,Signature 2,Figure 3d,30 October 2025,YokoC,"YokoC,Tosin","Bar plots from a Wilcoxon test, showing the significant differences in relative abundance of taxa between the psoriasis group (P) and the healthy control group (N).",decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,3379134|1224|1236|135625|712|724,Complete,KateRasheed
bsdb:39399065/2/1,39399065,case-control,39399065,10.2147/CCID.S473237,NA,"Zhao K., Zhao Y., Guo A., Xiao S. , Tu C.",Oral Microbiota Variations in Psoriasis Patients Without Comorbidity,"Clinical, cosmetic and investigational dermatology",2024,"16s rRNA, comorbidity, dysbiosis, oral microbiota, psoriasis",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Psoriasis,EFO:0000676,Healthy subjects (N),Psoriasis subjects (P),"Subjects diagnosed with plaque psoriasis by two dermatologists, aged between 18 and 60 years old, and belonging to the Chinese Han population.",20,20,3 months,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,increased,NA,NA,Signature 1,Figure 4,30 October 2025,YokoC,"YokoC,Tosin","LEfSe analysis of the psoriasis group and the healthy control group. Psoriasis patients (P), Healthy subjects (N).",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,p__Candidatus Altimarinota",3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552;363464,Complete,KateRasheed
bsdb:39399065/2/2,39399065,case-control,39399065,10.2147/CCID.S473237,NA,"Zhao K., Zhao Y., Guo A., Xiao S. , Tu C.",Oral Microbiota Variations in Psoriasis Patients Without Comorbidity,"Clinical, cosmetic and investigational dermatology",2024,"16s rRNA, comorbidity, dysbiosis, oral microbiota, psoriasis",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Psoriasis,EFO:0000676,Healthy subjects (N),Psoriasis subjects (P),"Subjects diagnosed with plaque psoriasis by two dermatologists, aged between 18 and 60 years old, and belonging to the Chinese Han population.",20,20,3 months,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,increased,NA,NA,Signature 2,Figure 4,30 October 2025,YokoC,YokoC,"LEfSe analysis of the psoriasis group and the healthy control group. Psoriasis patients (P), Healthy subjects (N).",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|1236|91347;3379134|1224|1236;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712;3379134|1224,Complete,KateRasheed
bsdb:39399065/3/1,39399065,case-control,39399065,10.2147/CCID.S473237,NA,"Zhao K., Zhao Y., Guo A., Xiao S. , Tu C.",Oral Microbiota Variations in Psoriasis Patients Without Comorbidity,"Clinical, cosmetic and investigational dermatology",2024,"16s rRNA, comorbidity, dysbiosis, oral microbiota, psoriasis",Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Psoriasis,EFO:0000676,Low Physician Global Assessment (PGA) score,High Physician Global Assessment (PGA) score,Severity of psoriasis as scored by the Physician Global Assessment (PGA),NA,NA,3 months,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,31 October 2025,YokoC,YokoC,Heatmap  of a Spearman correlation analysis between the severity of psoriasis and the oral microbiota at the genus level.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,3379134|1224|28216|206351|481|482,Complete,KateRasheed
bsdb:39399065/3/2,39399065,case-control,39399065,10.2147/CCID.S473237,NA,"Zhao K., Zhao Y., Guo A., Xiao S. , Tu C.",Oral Microbiota Variations in Psoriasis Patients Without Comorbidity,"Clinical, cosmetic and investigational dermatology",2024,"16s rRNA, comorbidity, dysbiosis, oral microbiota, psoriasis",Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Psoriasis,EFO:0000676,Low Physician Global Assessment (PGA) score,High Physician Global Assessment (PGA) score,Severity of psoriasis as scored by the Physician Global Assessment (PGA),NA,NA,3 months,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5,31 October 2025,YokoC,YokoC,Heatmap  of a Spearman correlation analysis between the severity of psoriasis and the oral microbiota at the genus level.,decreased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,1783272|1239|909932|1843489|31977|29465,Complete,KateRasheed
bsdb:39399065/4/1,39399065,case-control,39399065,10.2147/CCID.S473237,NA,"Zhao K., Zhao Y., Guo A., Xiao S. , Tu C.",Oral Microbiota Variations in Psoriasis Patients Without Comorbidity,"Clinical, cosmetic and investigational dermatology",2024,"16s rRNA, comorbidity, dysbiosis, oral microbiota, psoriasis",Experiment 4,China,Homo sapiens,Saliva,UBERON:0001836,Psoriasis,EFO:0000676,Low Psoriasis Area and Severity Index (PASI) score,High Psoriasis Area and Severity Index (PASI) score,Severity of psoriasis as scored by the Psoriasis Area and Severity Index (PASI).,NA,NA,3 months,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,31 October 2025,YokoC,YokoC,Heatmap of a Spearman correlation analysis between the severity of psoriasis and the oral microbiota at the genus level.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,3379134|976|200643|171549|171551|836,Complete,KateRasheed
bsdb:39399065/5/1,39399065,case-control,39399065,10.2147/CCID.S473237,NA,"Zhao K., Zhao Y., Guo A., Xiao S. , Tu C.",Oral Microbiota Variations in Psoriasis Patients Without Comorbidity,"Clinical, cosmetic and investigational dermatology",2024,"16s rRNA, comorbidity, dysbiosis, oral microbiota, psoriasis",Experiment 5,China,Homo sapiens,Saliva,UBERON:0001836,Psoriasis,EFO:0000676,Low Body Surface Area (BSA) score,High Body Surface Area (BSA) score,Severity of psoriasis as scored by the Body Surface Area (BSA).,NA,NA,3 months,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,31 October 2025,YokoC,YokoC,Heatmap of a Spearman correlation analysis between the severity of psoriasis and the oral microbiota at the genus level.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,3379134|976|200643|171549|171552|1283313,Complete,KateRasheed
bsdb:39417117/1/1,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 1,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low lead exposure,High lead exposure,Participants with high lead exposure,NA,NA,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2A,28 July 2025,Anne-mariesharp,"WikiWorks,Chloe,Tosin,Anne-mariesharp",Differential taxa by metal (lead) exposure. High lead exposure characterized by several taxa. Low lead exposure not characterized by any taxa. Lead denoted as “highpb_all” with high lead categorized as “1”; low as “0”.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|292632,Complete,Poornima
bsdb:39417117/2/1,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 2,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low arsenic exposure,High arsenic exposure,Participants with high arsenic exposure,NA,NA,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2B,28 July 2025,Anne-mariesharp,"WikiWorks,Chloe,Tosin,Anne-mariesharp",Differential taxa by metal (arsenic) exposure. High arsenic-exposed communities are unique compared with lower exposure. Arsenic is “highas_all” with high arsenic categorized as “1”; low as “0”.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota",3379134|976|200643|171549|171552|1283313;1783272|1239|186801|3082768|990719;1783272|1239|186801|3082768;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;3379134|1224|1236|91347;1783272|1239|186801|186802;3379134|1224|1236;3379134|976|200643|171549|171552;3379134|1224,Complete,Svetlana up
bsdb:39417117/2/2,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 2,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low arsenic exposure,High arsenic exposure,Participants with high arsenic exposure,NA,NA,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2B,28 July 2025,Anne-mariesharp,"WikiWorks,Chloe,Tosin,Anne-mariesharp",Differential taxa by metal (arsenic) exposure. High arsenic-exposed communities are unique compared with lower exposure. Arsenic is “highas_all” with high arsenic categorized as “1”; low as “0”.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|3085636|186803|207244;1783272|1239|526524|526525|2810280;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:39417117/3/1,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 3,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low Mercury exposure,High Mercury exposure,Participants with high mercury exposure,NA,NA,3 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2C,28 July 2025,Anne-mariesharp,"WikiWorks,Chloe,Tosin,Anne-mariesharp",Differential taxa by metal (mercury) exposure. Low mercury-exposed microbial communities were only differentially characterized by one taxon. High mercury exposure not characterized by any taxa. Mercury is “highhg” with high mercury categorized as “1”; low “0”.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,1783272|1239|186801|3085636|186803|207244,Complete,Svetlana up
bsdb:39417117/4/1,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 4,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Non-diabetic (high lead exposure),Diabetic (high lead exposure),Participants diagnosed with T2DM (Type 2 Diabetes Mellitus) within the high lead exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A,28 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (lead) exposure and cardiometabolic disease(CMD) factors,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas massiliensis (ex Liu et al. 2021),k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|186801|186802|31979|1485;3379134|1224|1236|135625|712|724;1783272|1239|186801|186802|1392389|3062493;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|577309;1783272|1239|91061|186826|33958|1253;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:39417117/4/2,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 4,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Non-diabetic (high lead exposure),Diabetic (high lead exposure),Participants diagnosed with T2DM (Type 2 Diabetes Mellitus) within the high lead exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 3A,28 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (lead) exposure and cardiometabolic disease (CMD) factors,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",3379134|976|200643|171549|171550|239759|626932;3379134|976|200643|171549|815|816|47678;1783272|1239|909932|1843489|31977|39948|218538;1783272|201174|84998|1643822|1643826|580024;1783272|1239|909932|909929|1843491|158846|437897;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|3085636|186803|84036;1783272|1239|186801|3085636|186803|1506577,Complete,Svetlana up
bsdb:39417117/5/1,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 5,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low diastolic blood pressure (DBP) (high lead exposure),High diastolic blood pressure (DBP) (high lead exposure),Participants with high diastolic blood pressure (DBP) within the high lead exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A,28 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (lead) exposure and cardiometabolic disease (CMD) factors,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas massiliensis (ex Liu et al. 2021),k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759|626932;1783272|1239|186801|186802|404402|404403;1783272|1239|186801|186802|1392389|3062493;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|186801|3085636|186803|1506577,Complete,Svetlana up
bsdb:39417117/5/2,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 5,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low diastolic blood pressure (DBP) (high lead exposure),High diastolic blood pressure (DBP) (high lead exposure),Participants with high diastolic blood pressure (DBP) within the high lead exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 3A,28 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (lead) exposure and cardiometabolic disease (CMD) factors,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|186801|186802|31979|1485;1783272|1239|909932|1843489|31977|39948;1783272|201174|84998|1643822|1643826|580024;1783272|1239|909932|909929|1843491|52225|52226;1783272|1239|91061|186826|33958|1253;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:39417117/6/1,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 6,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low body mass index (BMI) (high lead exposure),High body mass index (BMI) (high lead exposure),Participants with high body mass index (BMI) within the high lead exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A,28 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (lead) exposure and cardiometabolic disease (CMD) factors,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",3379134|976|200643|171549|171552|1283313;1783272|1239|186801|186802|31979|1485;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|39948|218538;1783272|201174|84998|1643822|1643826|580024;1783272|1239|909932|909929|1843491|52225|52226;1783272|1239|186801|3085636|186803|1506577,Complete,Svetlana up
bsdb:39417117/6/2,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 6,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low body mass index (BMI) (high lead exposure),High body mass index (BMI) (high lead exposure),Participants with high body mass index (BMI) within the high lead exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 3A,28 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (lead) exposure and cardiometabolic disease (CMD) factors,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas massiliensis (ex Liu et al. 2021),k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759|626932;1783272|1239|186801|3085636|186803|207244|649756;3379134|976|200643|171549|815|816|47678;1783272|201174|84998|1643822|1643826|580024;3379134|1224|1236|135625|712|724;1783272|1239|186801|186802|1392389|3062493;1783272|1239|909932|909929|1843491|158846|437897;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|815|909656|821;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:39417117/7/1,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 7,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Non-hypertensive (high lead exposure),Hypertensive (high lead exposure),Participants with hypertension within the high lead exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A,29 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (lead) exposure and cardiometabolic disease (CMD) factors,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus",1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|186801|186802|31979|1485;1783272|1239|909932|1843489|31977|39948|218538;1783272|201174|84998|1643822|1643826|580024;1783272|1239|909932|909929|1843491|158846|437897;1783272|1239|91061|186826|33958|1253,Complete,Svetlana up
bsdb:39417117/7/2,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 7,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Non-hypertensive (high lead exposure),Hypertensive (high lead exposure),Participants with hypertension within the high lead exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 3A,29 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (lead) exposure and cardiometabolic disease (CMD) factors,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas massiliensis (ex Liu et al. 2021),k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",3379134|976|200643|171549|171550|239759|626932;1783272|1239|186801|186802|404402|404403;1783272|1239|186801|186802|1392389|3062493;3379134|976|200643|171549|171552|577309;1783272|1239|186801|3085636|186803|1506577,Complete,Svetlana up
bsdb:39417117/8/1,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 8,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low glucose result (high lead exposure),High glucose result (high lead exposure),Participants with high glucose result within the high lead exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A,29 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal exposure (lead) and cardiometabolic disease (CMD) factors,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759|626932;1783272|1239|186801|186802|31979|1485;3379134|1224|1236|135625|712|724;1783272|1239|909932|909929|1843491|158846|437897;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|577309;1783272|201174|1760|85006|1268|32207;1783272|201174|84998|1643822|1643826|580024,Complete,Svetlana up
bsdb:39417117/8/2,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 8,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low glucose result (high lead exposure),High glucose result (high lead exposure),Participants with high glucose result within the high lead exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 3A,29 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (lead) exposure and cardiometabolic disease (CMD) factors,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas massiliensis (ex Liu et al. 2021),k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",3379134|976|200643|171549|171552|1283313;1783272|201174|84998|1643822|1643826|580024;1783272|1239|186801|186802|404402|404403;1783272|1239|186801|186802|1392389|3062493;1783272|1239|91061|186826|33958|1253;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|1506577,Complete,Svetlana up
bsdb:39417117/9/1,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 9,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low lead exposure,High lead exposure,Participants with high lead exposure,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3A, 5A",29 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (lead) exposure and cardiometabolic disease (CMD) factors,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus",3379134|976|200643|171549|171552|1283313;1783272|1239|186801|186802|31979|1485;1783272|1239|909932|1843489|31977|39948;3379134|1224|1236|135625|712|724;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|186802|404402|404403;1783272|1239|186801|186802|1392389|1297617;1783272|1239|91061|186826|33958|1243;3379134|1224|28216|206351|481|482;1783272|1239|91061|186826|33958|1253;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|84036,Complete,Svetlana up
bsdb:39417117/9/2,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 9,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low lead exposure,High lead exposure,Participants with high lead exposure,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3A, 5A",29 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (lead) exposure and cardiometabolic disease (CMD) factors,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas massiliensis (ex Liu et al. 2021),k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",1783272|1239|186801|3085636|186803|207244|649756;3379134|976|200643|171549|815|816|47678;1783272|201174|84998|1643822|1643826|580024;1783272|1239|186801|186802|1392389|3062493;1783272|1239|909932|1843489|31977|906|187326;3379134|976|200643|171549|171552|577309;1783272|1239|186801|186802|186807|2740;3379134|976|200643|171549|815|909656|821;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|3085636|186803|1506577,Complete,Svetlana up
bsdb:39417117/10/1,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 10,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low glucose result (high arsenic exposure),High glucose result (high arsenic exposure),Participants with high glucose result within the high arsenic exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 3B,30 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (arsenic) exposure and cardiometabolic disease (CMD) factors,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",1783272|1239|186801|3085636|186803|1766253;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759|626932;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|1980681;1783272|1239|909932|909929|1843491|158846|437897;1783272|1239|909932|1843489|31977|906;3379134|976|200643|171549|171552|577309;1783272|1239|186801|186802|186807|2740;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|3085636|186803|84036;1783272|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:39417117/10/2,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 10,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low glucose result (high arsenic exposure),High glucose result (high arsenic exposure),Participants with high glucose result within the high arsenic exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 3B,30 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (arsenic) exposure and cardiometabolic disease (CMD) factors,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella|s__Parolsenella massiliensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|976|200643|171549|171552|1283313;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|1643822|1643826|580024;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|186802|404402|404403;1783272|201174|84998|84999|1643824|2082587|1871022;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:39417117/11/1,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 11,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Non-hypertensive (high arsenic exposure),Hypertensive (high arsenic exposure),Participants with hypertension within the high arsenic exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 3B,30 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (arsenic) exposure and cardiometabolic disease (CMD) factors,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|207244|649756;;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|1643822|1643826|580024;1783272|1239|909932|909929|1843491|158846|437897;1783272|1239|909932|1843489|31977|906;3379134|1224|28216|206351|481|482;1783272|1239|186801|186802|186807|2740;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:39417117/11/2,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 11,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Non-hypertensive (high arsenic exposure),Hypertensive (high arsenic exposure),Participants with hypertension within the high arsenic exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 3B,30 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (arsenic) exposure and cardiometabolic disease (CMD) factors,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio",3379134|976|200643|171549|171550|239759|626932;1783272|1239|186801|186802|404402|404403;3379134|976|200643|171549|171552|577309;3379134|1224|1236|135624|83763|83770,Complete,Svetlana up
bsdb:39417117/12/1,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 12,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low body mass index (BMI) (high arsenic exposure),High body mass index (BMI) (high arsenic exposure),Participants with high body mass index (BMI) within the high arsenic exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 3B,30 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (arsenic) exposure and cardiometabolic disease (CMD) factors,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",1783272|1239|186801|3085636|186803|1766253;3379134|976|200643|171549|171552|1283313;1783272|1239|186801|186802|31979|1485;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|186801|186802|186807|2740;1783272|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:39417117/12/2,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 12,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low body mass index (BMI) (high arsenic exposure),High body mass index (BMI) (high arsenic exposure),Participants with high body mass index (BMI) within the high arsenic exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 3B,30 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (arsenic) exposure and cardiometabolic disease (CMD) factors,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella tayi,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759|626932;1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|186801|186802|1980681;1783272|1239|186801|3085636|186803|1432051|1432052;1783272|201174|84998|1643822|1643826|580024;3379134|1224|1236|135625|712|724;1783272|1239|526524|526525|128827|1573535;1783272|1239|909932|909929|1843491|158846|437897;1783272|1239|909932|1843489|31977|906;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|815|909656|821;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:39417117/13/1,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 13,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low diastolic blood pressure (DBP) (high arsenic exposure),High diastolic blood pressure (DBP) (high arsenic exposure),Participants with high diastolic blood pressure (DBP) within the high arsenic exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 3B,30 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (arsenic) exposure and cardiometabolic disease (CMD) factors,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759|626932;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|186802|404402|404403;1783272|201174|1760|85006|1268|32207|43675,Complete,Svetlana up
bsdb:39417117/13/2,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 13,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low diastolic blood pressure (DBP) (high arsenic exposure),High diastolic blood pressure (DBP) (high arsenic exposure),Participants with high diastolic blood pressure (DBP) within the high arsenic exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 3B,30 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (arsenic) exposure and cardiometabolic disease (CMD) factors,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella|s__Parolsenella massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|207244|649756;;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|1643822|1643826|580024;1783272|201174|84998|84999|1643824|2082587|1871022;1783272|1239|186801|186802|186807|2740;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:39417117/14/1,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 14,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low arsenic exposure,High arsenic exposure,Participants with high arsenic exposure,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3B, Figure 5A",30 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (arsenic) exposure and cardiometabolic disease (CMD) factors,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,p__Rhodophyta|c__Florideophyceae|o__Batrachospermales|f__Batrachospermaceae|g__Paludicola,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella|s__Parolsenella massiliensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",1783272|1239|186801|3085636|186803|1766253;3379134|976|200643|171549|171552|1283313;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|404402|404403;1783272|1239|91061|186826|33958|1243;3379134|1224|28216|206351|481|482;2763|2806|31370|31371|2729669;1783272|201174|84998|84999|1643824|2082587|1871022;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300|1301;3379134|1224|1236|135624|83763|83770;3379134|1224|1236|135625|712|724,Complete,Svetlana up
bsdb:39417117/14/2,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 14,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low arsenic exposure,High arsenic exposure,Participants with high arsenic exposure,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3B, Figure 5A",30 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (arsenic) exposure and cardiometabolic disease (CMD) factors,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella tayi,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",1783272|1239|186801|3085636|186803|207244|649756;;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|3085636|186803|1432051|1432052;1783272|201174|84998|1643822|1643826|580024;1783272|1239|526524|526525|128827|1573535;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843489|31977|906|187326;1783272|1239|186801|186802|186807|2740;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|84036;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|3085636|186803|1506577,Complete,Svetlana up
bsdb:39417117/15/1,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 15,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Non-diabetic (high arsenic exposure),Diabetic (high arsenic exposure),Participants diagnosed with T2DM (Type 2 Diabetes Mellitus) within the high arsenic exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 3B,30 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (arsenic) exposure and cardiometabolic disease (CMD) factors,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella|s__Parolsenella massiliensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|976|200643|171549|171552|1283313;1783272|1239|186801|186802|31979|1485;3379134|1224|1236|135625|712|724;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|186802|404402|404403;3379134|1224|28216|206351|481|482;1783272|201174|84998|84999|1643824|2082587|1871022;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:39417117/15/2,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 15,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Non-diabetic (high arsenic exposure),Diabetic (high arsenic exposure),Participants diagnosed with T2DM (Type 2 Diabetes Mellitus) within the high arsenic exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 3B,30 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (arsenic) exposure and cardiometabolic disease (CMD) factors,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",1783272|1239|186801|3085636|186803|1766253;3379134|976|200643|171549|171550|239759|626932;1783272|1239|186801|186802|1980681;1783272|201174|84998|84999|84107|102106;1783272|1239|909932|1843489|31977|39948|218538;1783272|201174|84998|1643822|1643826|580024;1783272|1239|909932|909929|1843491|158846|437897;1783272|1239|909932|1843489|31977|906;3379134|976|200643|171549|171552|577309;1783272|1239|186801|186802|186807|2740;3379134|976|200643|171549|815|909656|821;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|84036;1783272|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:39417117/16/1,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 16,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Non-diabetic (high cadmium exposure),Diabetic (high cadmium exposure),Participants diagnosed with T2DM (Type 2 Diabetes Mellitus) within the high cadmium exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 3C,31 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (cadmium) exposure and cardiometabolic disease (CMD) factors,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;3379134|1224|1236|135625|712|724;1783272|1239|186801|186802|1392389;3379134|1224|28216|206351|481|482;1783272|1239|91061|186826|33958|1253;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|43675,Complete,Svetlana up
bsdb:39417117/16/2,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 16,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Non-diabetic (high cadmium exposure),Diabetic (high cadmium exposure),Participants diagnosed with T2DM (Type 2 Diabetes Mellitus) within the high cadmium exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 3C,31 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (cadmium) exposure and cardiometabolic disease (CMD) factors,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus",3379134|976|200643|171549|171550|239759|626932;1783272|1239|186801|186802|1980681;1783272|201174|1760|85007|1653|1716;1783272|1239|909932|1843489|31977|39948|218538;1783272|201174|84998|1643822|1643826|580024;1783272|1239|909932|909929|1843491|158846|437897;3379134|976|200643|171549|171552|577309;1783272|1239|186801|186802|186807|2740;1783272|1239|909932|1843488|909930|33024|626940;3379134|976|200643|171549|815|909656|821;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|84036,Complete,Svetlana up
bsdb:39417117/17/1,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 17,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low diastolic blood pressure (high cadmium exposure),High diastolic blood pressure (high cadmium exposure),Participants with high diastolic blood pressure (dpb) within the high cadmium exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 3C,31 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (cadmium) exposure and cardiometabolic disease (CMD) factors,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759|626932;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|1980681;1783272|1239|186801|186802|404402|404403;1783272|1239|91061|186826|1300|1357;3379134|1224|28216|206351|481|482;1783272|201174|1760|85006|1268|32207|43675,Complete,Svetlana up
bsdb:39417117/17/2,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 17,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low diastolic blood pressure (high cadmium exposure),High diastolic blood pressure (high cadmium exposure),Participants with high diastolic blood pressure (dpb) within the high cadmium exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 3C,31 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (cadmium) exposure and cardiometabolic disease (CMD) factors,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;1783272|201174|1760|85007|1653|1716;1783272|201174|84998|1643822|1643826|580024;1783272|1239|186801|186802|1392389;1783272|1239|909932|909929|1843491|52225|52226;1783272|1239|91061|186826|33958|1253;1783272|1239|186801|186802|186807|2740;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:39417117/18/1,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 18,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low cadmium exposure,High cadmium exposure,Participants with high cadmium exposure,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 3C,31 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (cadmium) exposure and cardiometabolic disease (CMD) factors,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|186801|186802|1392389;1783272|1239|91061|186826|33958|1253;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:39417117/18/2,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 18,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low cadmium exposure,High cadmium exposure,Participants with high cadmium exposure,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 3C,31 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (cadmium) exposure and cardiometabolic disease (CMD) factors,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus",3379134|976|200643|171549|171550|239759|626932;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|1980681;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|1643822|1643826|580024;3379134|1224|1236|135625|712|724;1783272|1239|186801|186802|404402|404403;1783272|1239|91061|186826|1300|1357;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3085636|186803|84036,Complete,Svetlana up
bsdb:39417117/19/1,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 19,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low glucose result (high cadmium exposure),High glucose result (high cadmium exposure),Participants with high glucose result within the high cadmium exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 3C,31 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (cadmium) exposure and cardiometabolic disease (CMD) factors,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759|626932;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|1980681;1783272|201174|84998|84999|84107|102106;1783272|201174|1760|85007|1653|1716;3379134|1224|1236|135625|712|724;1783272|1239|186801|186802|1392389;1783272|1239|909932|909929|1843491|158846|437897;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|577309;1783272|1239|186801|186802|186807|2740;1783272|1239|909932|1843488|909930|33024|626940;3379134|976|200643|171549|815|909656|310297;1783272|201174|1760|85006|1268|32207;1783272|1239|186801|3085636|186803|84036,Complete,Svetlana up
bsdb:39417117/19/2,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 19,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low glucose result (high cadmium exposure),High glucose result (high cadmium exposure),Participants with high glucose result within the high cadmium exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 3C,31 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (cadmium) exposure and cardiometabolic disease (CMD) factors,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus",1783272|1239|186801|3085636|186803|572511;1783272|201174|84998|1643822|1643826|580024,Complete,Svetlana up
bsdb:39417117/20/1,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 20,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Non-hypertensive (high cadmium exposure),Hypertensive (high cadmium exposure),Participants with hypertension within the high cadmium exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 3C,31 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (cadmium) exposure and cardiometabolic disease (CMD) factors,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;1783272|201174|1760|85007|1653|1716;1783272|201174|84998|1643822|1643826|580024;1783272|1239|909932|909929|1843491|158846|437897;1783272|1239|91061|186826|33958|1253;1783272|1239|186801|186802|186807|2740;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:39417117/20/2,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 20,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Non-hypertensive (high cadmium exposure),Hypertensive (high cadmium exposure),Participants with hypertension within the high cadmium exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 3C,31 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (cadmium) exposure and cardiometabolic disease (CMD) factors,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",3379134|976|200643|171549|171550|239759|626932;1783272|1239|186801|186802|1980681;1783272|1239|186801|186802|404402|404403;1783272|1239|186801|186802|1392389;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|577309,Complete,Svetlana up
bsdb:39417117/21/1,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 21,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low body mass index (BMI) (high cadmium exposure),High body mass index (BMI) (high cadmium exposure),Participants with high body mass index within the high cadmium exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 3C,31 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (cadmium) exposure and cardiometabolic disease (CMD) factors,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|186801|186802|31979|1485;1783272|201174|1760|85007|1653|1716;1783272|1239|909932|909929|1843491|52225|52226;1783272|1239|186801|186802|186807|2740;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:39417117/21/2,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 21,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low body mass index (BMI) (high cadmium exposure),High body mass index (BMI) (high cadmium exposure),Participants with high body mass index within the high cadmium exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 3C,31 July 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (cadmium) exposure and cardiometabolic disease (CMD) factors,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759|626932;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|1980681;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|1643822|1643826|580024;3379134|1224|1236|135625|712|724;1783272|1239|186801|186802|1392389;1783272|1239|91061|186826|1300|1357;1783272|1239|909932|909929|1843491|158846|437897;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|909656|821;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|43675,Complete,Svetlana up
bsdb:39417117/22/1,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 22,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low body mass index (BMI) (high mercury exposure),High body mass index (BMI) (high mercury exposure),Participants with high body mass index within the high mercury exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 3D,1 August 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (mercury) exposure and cardiometabolic disease (CMD) factors,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",3384189|32066|203490|203491|203492|848;1783272|201174|1760|85006|1268|32207,Complete,Svetlana up
bsdb:39417117/23/1,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 23,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low glucose result (high mercury exposure),High glucose result (high mercury exposure),Participants with high glucose result within the high mercury exposure group,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 3D,1 August 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (mercury) exposure and cardiometabolic disease (CMD) factors,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella",3379134|976|200643|171549|171550|239759|626932;;1783272|201174|84998|84999|1643824|2082587,Complete,Svetlana up
bsdb:39417117/24/1,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 24,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low mercury exposure,High mercury exposure,Participants with high mercury exposure,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 3D,1 August 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp",Differential taxa by individual metal (mercury) exposure and cardiometabolic disease (CMD) factors,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus",1783272|1239|186801|186802|1470353;1783272|1239|186801|186802|216572|44748;1783272|1239|186801|3085636|186803|84036,Complete,Svetlana up
bsdb:39417117/25/1,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 25,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low diastolic blood pressure (dpb),High diastolic blood pressure (dpb),Participants with high diastolic blood pressure (dpb),NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,5 August 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp","Top 50 taxa associated with all high metals exposures (lead, arsenic, cadmium, and mercury) and cardiometabolic factors, controlling for site, sex, and age.",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|526524|526525|128827|61170|1468449;1783272|1239|186801|186802|404402|404403;1783272|1239|186801|186802|1392389|1297617;1783272|1239|909932|1843489|31977|906|187326;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|186801|3085636|186803|1506577,Complete,Svetlana up
bsdb:39417117/25/2,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 25,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low diastolic blood pressure (dpb),High diastolic blood pressure (dpb),Participants with high diastolic blood pressure (dpb),NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 5A,5 August 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp","Top 50 taxa associated with all high metals exposures (lead, arsenic, cadmium, and mercury) and cardiometabolic factors, controlling for site, sex, and age.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",1783272|1239|186801|3085636|186803|207244|649756;;1783272|1239|186801|186802|31979|1485;1783272|1239|909932|1843489|31977|39948;1783272|201174|84998|1643822|1643826|580024;1783272|1239|91061|186826|33958|1243;1783272|1239|186801|186802|186807|2740;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:39417117/26/1,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 26,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Non-diabetic,Diabetic,Participants diagnosed with T2DM (Type 2 Diabetes Mellitus),NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,5 August 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp","Top 50 taxa associated with all high metals exposures (lead, arsenic, cadmium, and mercury) and cardiometabolic factors, controlling for site, sex, and age.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella|s__Parolsenella massiliensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|186801|186802|31979|1485;3379134|1224|1236|135625|712|724;1783272|1239|186801|186802|404402|404403;1783272|1239|91061|186826|33958|1243;1783272|1239|909932|1843489|31977|906|187326;3379134|1224|28216|206351|481|482;1783272|201174|84998|84999|1643824|2082587|1871022;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:39417117/26/2,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 26,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Non-diabetic,Diabetic,Participants diagnosed with T2DM (Type 2 Diabetes Mellitus),NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 5A,5 August 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp","Top 50 taxa associated with all high metals exposures (lead, arsenic, cadmium, and mercury) and cardiometabolic factors, controlling for site, sex, and age.",decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|909932|1843489|31977|39948|218538;1783272|201174|84998|1643822|1643826|580024;1783272|1239|186801|186802|1392389|1297617;1783272|1239|909932|909929|1843491|158846|437897;3379134|976|200643|171549|171552|577309;1783272|1239|186801|186802|186807|2740;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|84036;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|3085636|186803|1506577,Complete,Svetlana up
bsdb:39417117/27/1,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 27,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Non-hypertensive,Hypertensive,Participants with hypertension,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,5 August 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp","Top 50 taxa associated with all high metals exposures (lead, arsenic, cadmium, and mercury) and cardiometabolic factors, controlling for site, sex, and age.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",1783272|1239|186801|3085636|186803|207244|649756;;1783272|1239|186801|186802|31979|1485;1783272|1239|909932|1843489|31977|39948|218538;1783272|201174|84998|1643822|1643826|580024;1783272|1239|91061|186826|33958|1243;1783272|1239|909932|909929|1843491|158846|437897;1783272|1239|909932|1843489|31977|906|187326;3379134|1224|28216|206351|481|482;1783272|1239|186801|186802|186807|2740;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:39417117/27/2,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 27,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Non-hypertensive,Hypertensive,Participants with hypertension,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 5A,5 August 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp","Top 50 taxa associated with all high metals exposures (lead, arsenic, cadmium, and mercury) and cardiometabolic factors, controlling for site, sex, and age.",decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",1783272|1239|526524|526525|128827|1573535;1783272|1239|526524|526525|128827|61170|1468449;1783272|1239|186801|186802|404402|404403;1783272|1239|186801|186802|1392389|1297617;3379134|976|200643|171549|171552|577309;3379134|1224|1236|135624|83763|83770;1783272|1239|186801|3085636|186803|1506577,Complete,Svetlana up
bsdb:39417117/28/1,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 28,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low body mass index (BMI),High body mass index (BMI),Participants with high body mass index (BMI),NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,5 August 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp","Top 50 taxa associated with all high metals exposures (lead, arsenic, cadmium, and mercury) and cardiometabolic factors, controlling for site, sex, and age.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",1783272|1239|186801|186802|31979|1485;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|186801|186802|186807|2740;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|3085636|186803|1506577,Complete,Svetlana up
bsdb:39417117/28/2,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 28,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low body mass index (BMI),High body mass index (BMI),Participants with high body mass index (BMI),NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 5A,5 August 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp","Top 50 taxa associated with all high metals exposures (lead, arsenic, cadmium, and mercury) and cardiometabolic factors, controlling for site, sex, and age.",decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|3085636|186803|207244|649756;1783272|201174|84998|1643822|1643826|580024;3379134|1224|1236|135625|712|724;1783272|1239|186801|186802|1392389|1297617;1783272|1239|91061|186826|33958|1243;1783272|1239|909932|909929|1843491|158846|437897;1783272|1239|909932|1843489|31977|906|187326;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|577309;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:39417117/29/1,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 29,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low glucose result,High glucose result,Participants with high glucose result,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 5A,5 August 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp","Top 50 taxa associated with all high metals exposures (lead, arsenic, cadmium, and mercury) and cardiometabolic factors, controlling for site, sex, and age.",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|186802|31979|1485;1783272|1239|909932|909929|1843491|158846|437897;3379134|976|200643|171549|171552|577309;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3085636|186803|84036;1783272|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:39417117/29/2,39417117,"cross-sectional observational, not case-control",39417117,10.1080/29933935.2025.2481442,NA,"Amy Luke, Brian T. Layden, Candice Choo-Kang, Dale Rae, Estelle V. Lambert, Gertrude Ecklu-Mensah, Jack A. Gilbert, Julianne A. Jorgensen, Kweku Bedu-Addo, Lara R. Dugas, Lina Issa, Luyu Wang, Maria Argos, Pascal Bovet, Robert M. Sargis, Tanika N. Kelly, Terrence Forrester, Yang Dai",Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations,Gut Microbes Reports,2025,"African-origin populations, Cardiometabolic risk, Toxic metals, gut microbiome, obesity, type 2 diabetes",Experiment 29,"Ghana,Jamaica,Seychelles,South Africa,United States of America",Homo sapiens,Feces,UBERON:0001988,Metabolic toxicity,EFO:0011054,Low glucose result,High glucose result,Participants with high glucose result,NA,NA,3 months,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 5A,5 August 2025,Anne-mariesharp,"WikiWorks,Tosin,Anne-mariesharp","Top 50 taxa associated with all high metals exposures (lead, arsenic, cadmium, and mercury) and cardiometabolic factors, controlling for site, sex, and age.",decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella|s__Parolsenella massiliensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",1783272|201174|84998|1643822|1643826|580024;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|186802|404402|404403;1783272|1239|186801|186802|1392389|1297617;1783272|1239|91061|186826|33958|1243;1783272|1239|909932|1843489|31977|906|187326;1783272|201174|84998|84999|1643824|2082587|1871022;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|1506577,Complete,Svetlana up
bsdb:39426329/1/1,39426329,case-control,39426329,10.1016/j.parkreldis.2024.107176,https://doi.org/10.1016/j.parkreldis.2024.107176,"Teigen L.M., McCarter S.J., Ziegert Z., Staley C., Grant K.M., Gupta V.K., Zhao X., St Louis E.K., Kantarci K., Lowe V.J., Forsberg L.K., Savica R., Ramanan V.K., Jones D.T., Petersen R.C., Sung J., Khoruts A., Boeve B.F. , Ross O.A.",Taxonomic intestinal microbiota differences in Lewy body spectrum disease and cohabitant controls,Parkinsonism & related disorders,2024,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,REM sleep behavior disorder,EFO:0007462,cohabitant controls,cases with iRBD,isolated REM sleep behavior disorder (iRBD) cases,39,11,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.0083,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 1,26 July 2025,Kristin.abraham,Kristin.abraham,Taxa depleted in iRBD cases.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,NA
bsdb:39426329/2/1,39426329,case-control,39426329,10.1016/j.parkreldis.2024.107176,https://doi.org/10.1016/j.parkreldis.2024.107176,"Teigen L.M., McCarter S.J., Ziegert Z., Staley C., Grant K.M., Gupta V.K., Zhao X., St Louis E.K., Kantarci K., Lowe V.J., Forsberg L.K., Savica R., Ramanan V.K., Jones D.T., Petersen R.C., Sung J., Khoruts A., Boeve B.F. , Ross O.A.",Taxonomic intestinal microbiota differences in Lewy body spectrum disease and cohabitant controls,Parkinsonism & related disorders,2024,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Lewy body dementia,EFO:0006792,Healthy cohort,LBD patients,Patients with Lewy Body Dementia (LBD),19,27,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.0083,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 1,26 July 2025,Kristin.abraham,Kristin.abraham,Taxa enriched in LBD patients.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,1783272|1239|186801|3085636|186803|572511,Complete,NA
bsdb:39426329/2/2,39426329,case-control,39426329,10.1016/j.parkreldis.2024.107176,https://doi.org/10.1016/j.parkreldis.2024.107176,"Teigen L.M., McCarter S.J., Ziegert Z., Staley C., Grant K.M., Gupta V.K., Zhao X., St Louis E.K., Kantarci K., Lowe V.J., Forsberg L.K., Savica R., Ramanan V.K., Jones D.T., Petersen R.C., Sung J., Khoruts A., Boeve B.F. , Ross O.A.",Taxonomic intestinal microbiota differences in Lewy body spectrum disease and cohabitant controls,Parkinsonism & related disorders,2024,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Lewy body dementia,EFO:0006792,Healthy cohort,LBD patients,Patients with Lewy Body Dementia (LBD),19,27,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.0083,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 1,26 July 2025,Kristin.abraham,Kristin.abraham,Taxa depleted in LBD patients.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803,Complete,NA
bsdb:39426329/3/1,39426329,case-control,39426329,10.1016/j.parkreldis.2024.107176,https://doi.org/10.1016/j.parkreldis.2024.107176,"Teigen L.M., McCarter S.J., Ziegert Z., Staley C., Grant K.M., Gupta V.K., Zhao X., St Louis E.K., Kantarci K., Lowe V.J., Forsberg L.K., Savica R., Ramanan V.K., Jones D.T., Petersen R.C., Sung J., Khoruts A., Boeve B.F. , Ross O.A.",Taxonomic intestinal microbiota differences in Lewy body spectrum disease and cohabitant controls,Parkinsonism & related disorders,2024,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,REM sleep behavior disorder,EFO:0007462,Healthy cohort,iRBD cases,isolated REM sleep behavior disorder (iRBD) cases,19,11,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.0083,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,26 July 2025,Kristin.abraham,Kristin.abraham,Taxa enriched in iRBD cases,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,1783272|1239|186801|3085636|186803|572511,Complete,NA
bsdb:39426329/3/2,39426329,case-control,39426329,10.1016/j.parkreldis.2024.107176,https://doi.org/10.1016/j.parkreldis.2024.107176,"Teigen L.M., McCarter S.J., Ziegert Z., Staley C., Grant K.M., Gupta V.K., Zhao X., St Louis E.K., Kantarci K., Lowe V.J., Forsberg L.K., Savica R., Ramanan V.K., Jones D.T., Petersen R.C., Sung J., Khoruts A., Boeve B.F. , Ross O.A.",Taxonomic intestinal microbiota differences in Lewy body spectrum disease and cohabitant controls,Parkinsonism & related disorders,2024,NA,Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,REM sleep behavior disorder,EFO:0007462,Healthy cohort,iRBD cases,isolated REM sleep behavior disorder (iRBD) cases,19,11,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.0083,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1,26 July 2025,Kristin.abraham,Kristin.abraham,Taxa depleted in iRBD cases,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816,Complete,NA
bsdb:39426329/4/1,39426329,case-control,39426329,10.1016/j.parkreldis.2024.107176,https://doi.org/10.1016/j.parkreldis.2024.107176,"Teigen L.M., McCarter S.J., Ziegert Z., Staley C., Grant K.M., Gupta V.K., Zhao X., St Louis E.K., Kantarci K., Lowe V.J., Forsberg L.K., Savica R., Ramanan V.K., Jones D.T., Petersen R.C., Sung J., Khoruts A., Boeve B.F. , Ross O.A.",Taxonomic intestinal microbiota differences in Lewy body spectrum disease and cohabitant controls,Parkinsonism & related disorders,2024,NA,Experiment 4,United States of America,Homo sapiens,Feces,UBERON:0001988,"Lewy body dementia,REM sleep behavior disorder","EFO:0007462,EFO:0006792",Healthy cohort,Cohabitant controls,Cohabitants of Lewy Body Dementia (LBD) and isolated REM Sleep Behavior Disorder (iRBD) cases,19,39,NA,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.0083,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 1,26 July 2025,Kristin.abraham,Kristin.abraham,Taxa enriched in cohabitant controls,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,1783272|1239|186801|3085636|186803|572511,Complete,NA
bsdb:39428055/1/1,39428055,case-control,39428055,10.1016/j.micinf.2024.105432,NA,"Hazra D., Chawla K., S M F., Sintchenko V., Magazine R., Martinez E. , Pandey A.",The impact of anti-tuberculosis treatment on respiratory tract microbiome in pulmonary tuberculosis,Microbes and infection,2025,"16S metagenomics, Anti-tuberculosis treatment, Respiratory microbiome, Sputum, Tuberculosis",Experiment 1,India,Homo sapiens,Sputum,UBERON:0007311,Pulmonary tuberculosis,EFO:1000049,Healthy controls,Untreated TB,"Newly diagnosed, Xpert MTB/RIF Ultra+ and sputum AFB+; no prior ATT",16,50,1 month,16S,34,Illumina,relative abundances,"Kruskall-Wallis,LEfSe",0.05,TRUE,2,"age,sex",NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,Figure 2D and E,21 June 2025,Nuerteye,Nuerteye,LEfSe genus plot showing UTB/CTB/HC discriminative taxa,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis",3379134|1224|1236|135625|712|724|727;1783272|201174|1760|85007|1762|1763;3379134|1224|1236|72274|135621|286|287;1783272|1239|91061|186826|1300|1301|28037,Complete,NA
bsdb:39428055/1/2,39428055,case-control,39428055,10.1016/j.micinf.2024.105432,NA,"Hazra D., Chawla K., S M F., Sintchenko V., Magazine R., Martinez E. , Pandey A.",The impact of anti-tuberculosis treatment on respiratory tract microbiome in pulmonary tuberculosis,Microbes and infection,2025,"16S metagenomics, Anti-tuberculosis treatment, Respiratory microbiome, Sputum, Tuberculosis",Experiment 1,India,Homo sapiens,Sputum,UBERON:0007311,Pulmonary tuberculosis,EFO:1000049,Healthy controls,Untreated TB,"Newly diagnosed, Xpert MTB/RIF Ultra+ and sputum AFB+; no prior ATT",16,50,1 month,16S,34,Illumina,relative abundances,"Kruskall-Wallis,LEfSe",0.05,TRUE,2,"age,sex",NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 2,Figure 2D and E,21 June 2025,Nuerteye,Nuerteye,LEfSe genus plot showing UTB/CTB/HC discriminative taxa,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|171551;3379134|976|200643|171549|171552|838,Complete,NA
bsdb:39431364/1/1,39431364,prospective cohort,39431364,10.1111/1471-0528.17979,https://obgyn.onlinelibrary.wiley.com/doi/10.1111/1471-0528.17979,"Hicks C., Leonardi M., Chua X.Y., Mari-Breedt L., Espanda M., El-Omar E.M., Condous G. , El-Assaad F.","Oral, Vaginal, and Stool Microbial Signatures in Patients With Endometriosis as Potential Diagnostic Non-Invasive Biomarkers: A Prospective Cohort Study",BJOG : an international journal of obstetrics and gynaecology,2024,"bacteria, biomarker, diagnostic, dysbiosis, endometriosis, inflammation, microbiome, microbiota, oral",Experiment 1,Australia,Homo sapiens,Mouth,UBERON:0000165,Endometriosis,EFO:0001065,Endometriosis and Non-endometriosis cohorts,Healthy control cohort,Participants in the healthy control cohort were women with no known gynaecological symptoms or infertility concerns.,45,18,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,8 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Microbial features that were detected to be differentially abundant between the three cohorts using LEfSe analysis,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|1224|1236|135625|712|713;1783272|1239|186801|3085636|186803|830;1783272|1239|91061|186826|1300|1357;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:39431364/2/1,39431364,prospective cohort,39431364,10.1111/1471-0528.17979,https://obgyn.onlinelibrary.wiley.com/doi/10.1111/1471-0528.17979,"Hicks C., Leonardi M., Chua X.Y., Mari-Breedt L., Espanda M., El-Omar E.M., Condous G. , El-Assaad F.","Oral, Vaginal, and Stool Microbial Signatures in Patients With Endometriosis as Potential Diagnostic Non-Invasive Biomarkers: A Prospective Cohort Study",BJOG : an international journal of obstetrics and gynaecology,2024,"bacteria, biomarker, diagnostic, dysbiosis, endometriosis, inflammation, microbiome, microbiota, oral",Experiment 2,Australia,Homo sapiens,Mouth,UBERON:0000165,Endometriosis,EFO:0001065,Healthy control and Non-endometriosis cohorts,Endometriosis cohort,Participants in the endometriosis cohort were women who were confirmed to have endometriosis.,42,21,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,8 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Microbial features that were detected to be differentially abundant between the three cohorts using LEfSe analysis,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,s__bacterium F16,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae",1783272|1239|909932|1843489|31977|29465;1932694;1783272|201174|1760|2037|2049,Complete,Svetlana up
bsdb:39431364/3/1,39431364,prospective cohort,39431364,10.1111/1471-0528.17979,https://obgyn.onlinelibrary.wiley.com/doi/10.1111/1471-0528.17979,"Hicks C., Leonardi M., Chua X.Y., Mari-Breedt L., Espanda M., El-Omar E.M., Condous G. , El-Assaad F.","Oral, Vaginal, and Stool Microbial Signatures in Patients With Endometriosis as Potential Diagnostic Non-Invasive Biomarkers: A Prospective Cohort Study",BJOG : an international journal of obstetrics and gynaecology,2024,"bacteria, biomarker, diagnostic, dysbiosis, endometriosis, inflammation, microbiome, microbiota, oral",Experiment 3,Australia,Homo sapiens,Mouth,UBERON:0000165,Endometriosis,EFO:0001065,Healthy control and endometriosis cohorts,Non-endometriosis cohorts,"Participants in the non-endometriosis cohort were women who had confirmed gynaecological pathologies such as fibroids, abnormal uterine bleeding and ovarian cysts.",39,24,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,8 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Microbial features that were detected to be differentially abundant between the three cohorts using LEfSe analysis,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239|909932|1843489|31977|906;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:39431364/4/1,39431364,prospective cohort,39431364,10.1111/1471-0528.17979,https://obgyn.onlinelibrary.wiley.com/doi/10.1111/1471-0528.17979,"Hicks C., Leonardi M., Chua X.Y., Mari-Breedt L., Espanda M., El-Omar E.M., Condous G. , El-Assaad F.","Oral, Vaginal, and Stool Microbial Signatures in Patients With Endometriosis as Potential Diagnostic Non-Invasive Biomarkers: A Prospective Cohort Study",BJOG : an international journal of obstetrics and gynaecology,2024,"bacteria, biomarker, diagnostic, dysbiosis, endometriosis, inflammation, microbiome, microbiota, oral",Experiment 4,Australia,Homo sapiens,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Endometriosis and Non-endometriosis cohorts,Healthy control cohort,Participants in the healthy control cohort were women with no known gynaecological symptoms or infertility concerns.,45,19,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,8 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Microbial features that were detected to be differentially abundant between the three cohorts using LEfSe analysis,increased,",k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|s__Streptococcaceae bacterium RF32,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|s__Enterococcaceae bacterium RF39",;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|186802|186807;3379134|256845|1313211|278082|255528;1783272|1239|91061|186826|1300|423432;1783272|1239|91061|186826|81852|423410,Complete,Svetlana up
bsdb:39431364/6/1,39431364,prospective cohort,39431364,10.1111/1471-0528.17979,https://obgyn.onlinelibrary.wiley.com/doi/10.1111/1471-0528.17979,"Hicks C., Leonardi M., Chua X.Y., Mari-Breedt L., Espanda M., El-Omar E.M., Condous G. , El-Assaad F.","Oral, Vaginal, and Stool Microbial Signatures in Patients With Endometriosis as Potential Diagnostic Non-Invasive Biomarkers: A Prospective Cohort Study",BJOG : an international journal of obstetrics and gynaecology,2024,"bacteria, biomarker, diagnostic, dysbiosis, endometriosis, inflammation, microbiome, microbiota, oral",Experiment 6,Australia,Homo sapiens,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Healthy control and endometriosis cohorts,Non-endometriosis cohorts,"Participants in the non-endometriosis cohort were women who had confirmed gynaecological pathologies such as fibroids, abnormal uterine bleeding and ovarian cysts.",40,24,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,8 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Microbial features that were detected to be differentially abundant between the three cohorts using LEfSe analysis,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",1783272|1239|186801|186802|186806|1730;3379134|976|200643|171549,Complete,Svetlana up
bsdb:39431364/7/1,39431364,prospective cohort,39431364,10.1111/1471-0528.17979,https://obgyn.onlinelibrary.wiley.com/doi/10.1111/1471-0528.17979,"Hicks C., Leonardi M., Chua X.Y., Mari-Breedt L., Espanda M., El-Omar E.M., Condous G. , El-Assaad F.","Oral, Vaginal, and Stool Microbial Signatures in Patients With Endometriosis as Potential Diagnostic Non-Invasive Biomarkers: A Prospective Cohort Study",BJOG : an international journal of obstetrics and gynaecology,2024,"bacteria, biomarker, diagnostic, dysbiosis, endometriosis, inflammation, microbiome, microbiota, oral",Experiment 7,Australia,Homo sapiens,Vagina,UBERON:0000996,Endometriosis,EFO:0001065,Endometriosis and Non-endometriosis cohorts,Healthy control cohort,Participants in the healthy control cohort were women with no known gynaecological symptoms or infertility concerns.,45,19,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,12 November 2024,MyleeeA,"MyleeeA,WikiWorks",Microbial features that were detected to be differentially abundant between the three cohorts using LEfSe analysis.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Listeria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus",3379134|1224|1236|91347|543|590;1783272|1239|91061|1385|186820|1637;3379134|1224|1236|72274|135621|286;1783272|1239|91061|1385|186817|1386,Complete,Svetlana up
bsdb:39431364/8/1,39431364,prospective cohort,39431364,10.1111/1471-0528.17979,https://obgyn.onlinelibrary.wiley.com/doi/10.1111/1471-0528.17979,"Hicks C., Leonardi M., Chua X.Y., Mari-Breedt L., Espanda M., El-Omar E.M., Condous G. , El-Assaad F.","Oral, Vaginal, and Stool Microbial Signatures in Patients With Endometriosis as Potential Diagnostic Non-Invasive Biomarkers: A Prospective Cohort Study",BJOG : an international journal of obstetrics and gynaecology,2024,"bacteria, biomarker, diagnostic, dysbiosis, endometriosis, inflammation, microbiome, microbiota, oral",Experiment 8,Australia,Homo sapiens,Vagina,UBERON:0000996,Endometriosis,EFO:0001065,Healthy control and Non-endometriosis cohorts,Endometriosis cohort,Participants in the endometriosis cohort were women who were confirmed to have endometriosis.,43,21,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,12 November 2024,MyleeeA,"MyleeeA,WikiWorks",Microbial features that were detected to be differentially abundant between the three cohorts using LEfSe analysis.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Tepidimonas,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus",3379134|1224|1236|91347|543|561;1783272|1239|91061|186826|81852|1350;3379134|1224|28216|80840|114248;3384194|1297|188787|68933|188786|270,Complete,Svetlana up
bsdb:39431364/9/1,39431364,prospective cohort,39431364,10.1111/1471-0528.17979,https://obgyn.onlinelibrary.wiley.com/doi/10.1111/1471-0528.17979,"Hicks C., Leonardi M., Chua X.Y., Mari-Breedt L., Espanda M., El-Omar E.M., Condous G. , El-Assaad F.","Oral, Vaginal, and Stool Microbial Signatures in Patients With Endometriosis as Potential Diagnostic Non-Invasive Biomarkers: A Prospective Cohort Study",BJOG : an international journal of obstetrics and gynaecology,2024,"bacteria, biomarker, diagnostic, dysbiosis, endometriosis, inflammation, microbiome, microbiota, oral",Experiment 9,Australia,Homo sapiens,Vagina,UBERON:0000996,Endometriosis,EFO:0001065,Healthy control and endometriosis cohorts,Non-endometriosis cohorts,"Participants in the non-endometriosis cohort were women who had confirmed gynaecological pathologies such as fibroids, abnormal uterine bleeding and ovarian cysts.",40,24,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,12 November 2024,MyleeeA,"MyleeeA,WikiWorks",Microbial features that were detected to be differentially abundant between the three cohorts using LEfSe analysis.,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae",3384189|32066|203490|203491|1129771|168808;3379134|1224|1236|135625|712|724;3379134|976|200643|171549|171552|838;3379134|976|117743|200644|2762318,Complete,Svetlana up
bsdb:39431364/11/1,39431364,prospective cohort,39431364,10.1111/1471-0528.17979,https://obgyn.onlinelibrary.wiley.com/doi/10.1111/1471-0528.17979,"Hicks C., Leonardi M., Chua X.Y., Mari-Breedt L., Espanda M., El-Omar E.M., Condous G. , El-Assaad F.","Oral, Vaginal, and Stool Microbial Signatures in Patients With Endometriosis as Potential Diagnostic Non-Invasive Biomarkers: A Prospective Cohort Study",BJOG : an international journal of obstetrics and gynaecology,2024,"bacteria, biomarker, diagnostic, dysbiosis, endometriosis, inflammation, microbiome, microbiota, oral",Experiment 11,Australia,Homo sapiens,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Minimal/Mild endometriosis,Moderate/Severe endometriosis,Patients who underwent laparoscopy with confirmed endometriosis (ENDO) Stages 3 and 4 further grouped as Moderate/Severe endometriosis.,12,9,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,12 November 2024,MyleeeA,"MyleeeA,WikiWorks",Microbial features that were detected to be differentially abundant using LEfSe analysis between patients with Minimal/Mild stage endometriosis and patients with Moderate/Severe endometriosis in stool samples.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,3379134|976|200643|171549|171552|577309,Complete,Svetlana up
bsdb:39431364/11/2,39431364,prospective cohort,39431364,10.1111/1471-0528.17979,https://obgyn.onlinelibrary.wiley.com/doi/10.1111/1471-0528.17979,"Hicks C., Leonardi M., Chua X.Y., Mari-Breedt L., Espanda M., El-Omar E.M., Condous G. , El-Assaad F.","Oral, Vaginal, and Stool Microbial Signatures in Patients With Endometriosis as Potential Diagnostic Non-Invasive Biomarkers: A Prospective Cohort Study",BJOG : an international journal of obstetrics and gynaecology,2024,"bacteria, biomarker, diagnostic, dysbiosis, endometriosis, inflammation, microbiome, microbiota, oral",Experiment 11,Australia,Homo sapiens,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Minimal/Mild endometriosis,Moderate/Severe endometriosis,Patients who underwent laparoscopy with confirmed endometriosis (ENDO) Stages 3 and 4 further grouped as Moderate/Severe endometriosis.,12,9,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6,12 November 2024,MyleeeA,"MyleeeA,WikiWorks",Microbial features that were detected to be differentially abundant using LEfSe analysis between patients with Minimal/Mild stage endometriosis and patients with Moderate/Severe endometriosis in stool samples.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,1783272|201174|1760|2037|2049|1654,Complete,Svetlana up
bsdb:39431364/12/1,39431364,prospective cohort,39431364,10.1111/1471-0528.17979,https://obgyn.onlinelibrary.wiley.com/doi/10.1111/1471-0528.17979,"Hicks C., Leonardi M., Chua X.Y., Mari-Breedt L., Espanda M., El-Omar E.M., Condous G. , El-Assaad F.","Oral, Vaginal, and Stool Microbial Signatures in Patients With Endometriosis as Potential Diagnostic Non-Invasive Biomarkers: A Prospective Cohort Study",BJOG : an international journal of obstetrics and gynaecology,2024,"bacteria, biomarker, diagnostic, dysbiosis, endometriosis, inflammation, microbiome, microbiota, oral",Experiment 12,Australia,Homo sapiens,Vagina,UBERON:0000996,Endometriosis,EFO:0001065,Minimal/Mild endometriosis,Moderate/Severe endometriosis,Patients who underwent laparoscopy with confirmed endometriosis (ENDO) Stages 3 and 4 further grouped as Moderate/Severe endometriosis.,12,9,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,12 November 2024,MyleeeA,"MyleeeA,WikiWorks",Microbial features that were detected to be differentially abundant using LEfSe analysis between patients with Minimal/Mild stage endometriosis and patients with Moderate/Severe endometriosis in vaginal samples.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|189330;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|186802|186806|1730,Complete,Svetlana up
bsdb:39443634/1/1,39443634,case-control,39443634,10.1038/s43856-024-00630-8,NA,"Stagaman K., Kmiecik M.J., Wetzel M., Aslibekyan S., Sonmez T.F., Fontanillas P., Tung J., Holmes M.V., Walk S.T., Houser M.C. , Norcliffe-Kaufmann L.",Oral and gut microbiome profiles in people with early idiopathic Parkinson's disease,Communications medicine,2024,NA,Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson’s disease patients (PD patients),"Parkinson’s disease patients (PD patients) refers to patients with Parkinson disease - a neurodegenerative disease that is characterized by both motor symptoms, such as tremors, and non-motor symptoms, such as constipation.",220,438,6 months,WMS,NA,NA,NA,ANCOM,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,increased,NA,Signature 1,"Figure 6b, Supplementary Data 2",6 November 2024,KateRasheed,"KateRasheed,Chrisawoke,WikiWorks",Significant differentially abundant OTU-level microbial taxa(oral microbiota) between controls and PD cases using ANCOM statistical test.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces gerencseriae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 448,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. HMSC064D08,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. HMSC065D09,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oulorum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas artemidis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas infelix,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. FDAARGOS_192,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC064D12,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC068F04,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC072D03,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp. DNF00869",1783272|201174|1760|2037|2049|1654|52769;1783272|201174|1760|2037|2049|1654|712124;3379134|976|200643|171549|171552|838|28129;3379134|976|200643|171549|171552|838|28129;1783272|201174|1760|85006|1268|32207|1715104;1783272|201174|1760|85006|1268|32207|1739511;3379134|976|200643|171549|171552|2974251|28136;1783272|1239|909932|909929|1843491|970|671224;1783272|1239|909932|909929|1843491|970|135082;1783272|1239|91061|186826|1300|1301|1309;1783272|1239|91061|186826|1300|1301|1309;1783272|1239|91061|186826|1300|1301|1839799;1783272|1239|91061|186826|1300|1301|1715176;1783272|1239|91061|186826|1300|1301|1715051;1783272|1239|91061|186826|1300|1301|1739381;1783272|1239|91061|186826|1300|1301|1343;1783272|1239|909932|1843489|31977|29465|1384081,Complete,Svetlana up
bsdb:39443634/1/2,39443634,case-control,39443634,10.1038/s43856-024-00630-8,NA,"Stagaman K., Kmiecik M.J., Wetzel M., Aslibekyan S., Sonmez T.F., Fontanillas P., Tung J., Holmes M.V., Walk S.T., Houser M.C. , Norcliffe-Kaufmann L.",Oral and gut microbiome profiles in people with early idiopathic Parkinson's disease,Communications medicine,2024,NA,Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson’s disease patients (PD patients),"Parkinson’s disease patients (PD patients) refers to patients with Parkinson disease - a neurodegenerative disease that is characterized by both motor symptoms, such as tremors, and non-motor symptoms, such as constipation.",220,438,6 months,WMS,NA,NA,NA,ANCOM,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,increased,NA,Signature 2,"Figure 6b, Supplementary Data 2",6 November 2024,KateRasheed,"KateRasheed,Chrisawoke,WikiWorks",Significant differentially abundant OTU-level microbial taxa(oral microbiota) between controls and PD cases using ANCOM statistical test.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. HMSC035G02,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium|s__Atopobium sp. HMSC064B08,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella sp. 572.rep1_STHE,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella loescheii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum sp. OBRC5-5,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 215,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC061B04,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC063B05,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC066F04,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC067H04,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC068C04,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC068C12,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC071A01,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC072F04,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC075C12,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC078C12,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC15G01,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. HMSC061E04,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. HMSC068E02,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. HMSC069C03,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. HMSC076D04,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. 1171_SSPC,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. 263_SSPC,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. 400_SSPC,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. A12,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC057E02,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC062D07,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC067H01,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HPH0090",1783272|201174|1760|2037|2049|1654|1739406;1783272|201174|84998|84999|1643824|1380|1739402;3384189|32066|203490|203491|203492|848|860;3384189|32066|203490|203491|203492|848|860;3384189|32066|203490|203491|203492|848|860;1783272|1239|91061|186826|186828|117563|1725361;3379134|976|200643|171549|171552|2974257|840;1783272|1239|186801|3085636|186803|1164882|936595;3384189|32066|203490|203491|1129771|32067|712359;3379134|1224|28216|206351|481|482|1715140;3379134|1224|28216|206351|481|482|1739328;3379134|1224|28216|206351|481|482|1715148;3379134|1224|28216|206351|481|482|1739338;3379134|1224|28216|206351|481|482|1715179;3379134|1224|28216|206351|481|482|1739456;3379134|1224|28216|206351|481|482|1739332;3379134|1224|28216|206351|481|482|1739348;3379134|1224|28216|206351|481|482|1739282;3379134|1224|28216|206351|481|482|1715075;3379134|1224|28216|206351|481|482|1581107;1783272|1239|186801|3085636|186803|265975|1501329;1783272|201174|1760|85006|1268|32207|1739431;1783272|201174|1760|85006|1268|32207|1739423;1783272|201174|1760|85006|1268|32207|1739283;1783272|201174|1760|85006|1268|32207|1739484;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|91061|186826|1300|1301|113107;1783272|1239|91061|186826|1300|1301|68892;1783272|1239|91061|186826|1300|1301|1579348;1783272|1239|91061|186826|1300|1301|1579343;1783272|1239|91061|186826|1300|1301|1579341;1783272|1239|91061|186826|1300|1301|1759399;1783272|1239|91061|186826|1300|1301|1739265;1783272|1239|91061|186826|1300|1301|1739461;1783272|1239|91061|186826|1300|1301|1739491;1783272|1239|91061|186826|1300|1301|1203590,Complete,Svetlana up
bsdb:39443634/2/1,39443634,case-control,39443634,10.1038/s43856-024-00630-8,NA,"Stagaman K., Kmiecik M.J., Wetzel M., Aslibekyan S., Sonmez T.F., Fontanillas P., Tung J., Holmes M.V., Walk S.T., Houser M.C. , Norcliffe-Kaufmann L.",Oral and gut microbiome profiles in people with early idiopathic Parkinson's disease,Communications medicine,2024,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson’s disease patients (PD patients),"Parkinson’s disease patients (PD patients) refer to patients with Parkinson's disease - a neurodegenerative disease that is characterized by both motor symptoms, such as tremors, and non-motor symptoms, such as constipation.",221,445,6 months,WMS,NA,NA,NA,ANCOM,0.05,TRUE,NA,"age,sex",NA,NA,NA,increased,NA,NA,NA,Signature 1,Supplementary Data 2,7 November 2024,KateRasheed,"KateRasheed,Chrisawoke,WikiWorks",Significantly differentially abundant OTU-level microbial taxa in the gut microbiota between controls and PD cases identified using the ANCOM statistical test.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium 1_1_47,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D16,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC064D12,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC072D03",1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|1686;1783272|201174|1760|85004|31953|1678|1689;3379134|1224|28216|80840|469610;1783272|1239|186801|186802|216572|552398;1783272|1239|91061|186826|1300|1301|1715176;1783272|1239|91061|186826|1300|1301|1739381,Complete,Svetlana up
bsdb:39443634/2/2,39443634,case-control,39443634,10.1038/s43856-024-00630-8,NA,"Stagaman K., Kmiecik M.J., Wetzel M., Aslibekyan S., Sonmez T.F., Fontanillas P., Tung J., Holmes M.V., Walk S.T., Houser M.C. , Norcliffe-Kaufmann L.",Oral and gut microbiome profiles in people with early idiopathic Parkinson's disease,Communications medicine,2024,NA,Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson’s disease patients (PD patients),"Parkinson’s disease patients (PD patients) refer to patients with Parkinson's disease - a neurodegenerative disease that is characterized by both motor symptoms, such as tremors, and non-motor symptoms, such as constipation.",221,445,6 months,WMS,NA,NA,NA,ANCOM,0.05,TRUE,NA,"age,sex",NA,NA,NA,increased,NA,NA,NA,Signature 2,Supplementary Data 2,7 November 2024,KateRasheed,"KateRasheed,Chrisawoke,WikiWorks",Significantly differentially abundant OTU-level microbial taxa in the gut microbiota between controls and PD cases identified using the ANCOM statistical test.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 3_1_13,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. HMSC067B03,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides gordonii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp. 20_3,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis",3379134|976|200643|171549|815|816|457389;3379134|976|200643|171549|815|816|1739298;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|2005525|375288|574930;3379134|976|200643|171549|2005525|375288|469591;1783272|1239|186801|3085636|186803|841|166486,Complete,Svetlana up
bsdb:39443634/3/1,39443634,case-control,39443634,10.1038/s43856-024-00630-8,NA,"Stagaman K., Kmiecik M.J., Wetzel M., Aslibekyan S., Sonmez T.F., Fontanillas P., Tung J., Holmes M.V., Walk S.T., Houser M.C. , Norcliffe-Kaufmann L.",Oral and gut microbiome profiles in people with early idiopathic Parkinson's disease,Communications medicine,2024,NA,Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson’s disease patients (PD patients),"Parkinson’s disease patients (PD patients) refers to patients with Parkinson disease - a neurodegenerative disease that is characterized by both motor symptoms, such as tremors, and non-motor symptoms, such as constipation.",220,438,6 months,WMS,NA,NA,NA,ANCOM,0.05,TRUE,NA,"age,sex","age,body mass index,smoking status",NA,NA,NA,NA,unchanged,NA,Signature 1,Supplementary Data 2,7 November 2024,KateRasheed,"KateRasheed,Chrisawoke,WikiWorks",Significantly differentially abundant OTU-level microbial taxa (oral microbiota) between controls and PD cases (after adjustment for covariates) identified using the ANCOM statistical test.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. HMSC035G02,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella sp. 572.rep1_STHE,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella loescheii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum sp. OBRC5-5,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC063B05,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC066F04,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC072F04,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC075C12,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. HMSC061E04,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. HMSC069C03,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. 1171_SSPC,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. 263_SSPC,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. 400_SSPC,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. A12",1783272|201174|1760|2037|2049|1654|1739406;3384189|32066|203490|203491|203492|848|860;1783272|1239|91061|186826|186828|117563|1725361;3379134|976|200643|171549|171552|2974257|840;1783272|1239|186801|3085636|186803|1164882|936595;3379134|1224|28216|206351|481|482|1739328;3379134|1224|28216|206351|481|482|1715148;3379134|1224|28216|206351|481|482|1739348;3379134|1224|28216|206351|481|482|1739282;1783272|1239|186801|3085636|186803|265975|1501329;1783272|201174|1760|85006|1268|32207|1739431;1783272|201174|1760|85006|1268|32207|1739283;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|91061|186826|1300|1301|113107;1783272|1239|91061|186826|1300|1301|1579348;1783272|1239|91061|186826|1300|1301|1579343;1783272|1239|91061|186826|1300|1301|1579341;1783272|1239|91061|186826|1300|1301|1759399,Complete,Svetlana up
bsdb:39443634/3/2,39443634,case-control,39443634,10.1038/s43856-024-00630-8,NA,"Stagaman K., Kmiecik M.J., Wetzel M., Aslibekyan S., Sonmez T.F., Fontanillas P., Tung J., Holmes M.V., Walk S.T., Houser M.C. , Norcliffe-Kaufmann L.",Oral and gut microbiome profiles in people with early idiopathic Parkinson's disease,Communications medicine,2024,NA,Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson’s disease patients (PD patients),"Parkinson’s disease patients (PD patients) refers to patients with Parkinson disease - a neurodegenerative disease that is characterized by both motor symptoms, such as tremors, and non-motor symptoms, such as constipation.",220,438,6 months,WMS,NA,NA,NA,ANCOM,0.05,TRUE,NA,"age,sex","age,body mass index,smoking status",NA,NA,NA,NA,unchanged,NA,Signature 2,Supplementary Data 2,7 November 2024,KateRasheed,"KateRasheed,WikiWorks",Significant differentially abundant OTU-level microbial taxa(oral microbiota) between controls and PD cases (after adjustment for covariates) using ANCOM statistical test.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 448,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. HMSC065D09,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC072D03",1783272|201174|1760|2037|2049|1654|712124;1783272|201174|1760|85006|1268|32207|1739511;1783272|1239|91061|186826|1300|1301|1309;1783272|1239|91061|186826|1300|1301|1309;1783272|1239|91061|186826|1300|1301|1739381,Complete,Svetlana up
bsdb:39443634/4/1,39443634,case-control,39443634,10.1038/s43856-024-00630-8,NA,"Stagaman K., Kmiecik M.J., Wetzel M., Aslibekyan S., Sonmez T.F., Fontanillas P., Tung J., Holmes M.V., Walk S.T., Houser M.C. , Norcliffe-Kaufmann L.",Oral and gut microbiome profiles in people with early idiopathic Parkinson's disease,Communications medicine,2024,NA,Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson’s disease patients (PD patients),"Parkinson’s disease patients (PD patients) refers to patients with Parkinson disease - a neurodegenerative disease that is characterized by both motor symptoms, such as tremors, and non-motor symptoms, such as constipation.",220,438,6 months,WMS,NA,NA,relative abundances,Linear Regression,0.05,TRUE,NA,"age,sex","age,body mass index,smoking status",NA,NA,NA,NA,unchanged,NA,Signature 1,Supplementary Data 2,7 November 2024,KateRasheed,"KateRasheed,WikiWorks",Significant differentially abundant OTU-level microbial taxa (oral microbiota) between controls and PD cases (after adjustment for covariates) using linear models statistical test.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 448,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC06F02,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. HMSC064D08,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. HMSC065D09,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas artemidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. FDAARGOS_192,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC064D12,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC068F04,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC072D03,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis",1783272|201174|1760|2037|2049|1654|712124;3379134|1224|28216|206351|481|482|1581124;3379134|976|200643|171549|171552|838|28129;3379134|976|200643|171549|171552|838|28129;1783272|201174|1760|85006|1268|32207|1715104;1783272|201174|1760|85006|1268|32207|1739511;1783272|1239|909932|909929|1843491|970|671224;1783272|1239|91061|186826|1300|1301|1309;1783272|1239|91061|186826|1300|1301|1309;1783272|1239|91061|186826|1300|1301|1839799;1783272|1239|91061|186826|1300|1301|1715176;1783272|1239|91061|186826|1300|1301|1715051;1783272|1239|91061|186826|1300|1301|1739381;1783272|1239|91061|186826|1300|1301|1343,Complete,Svetlana up
bsdb:39443634/4/2,39443634,case-control,39443634,10.1038/s43856-024-00630-8,NA,"Stagaman K., Kmiecik M.J., Wetzel M., Aslibekyan S., Sonmez T.F., Fontanillas P., Tung J., Holmes M.V., Walk S.T., Houser M.C. , Norcliffe-Kaufmann L.",Oral and gut microbiome profiles in people with early idiopathic Parkinson's disease,Communications medicine,2024,NA,Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson’s disease patients (PD patients),"Parkinson’s disease patients (PD patients) refers to patients with Parkinson disease - a neurodegenerative disease that is characterized by both motor symptoms, such as tremors, and non-motor symptoms, such as constipation.",220,438,6 months,WMS,NA,NA,relative abundances,Linear Regression,0.05,TRUE,NA,"age,sex","age,body mass index,smoking status",NA,NA,NA,NA,unchanged,NA,Signature 2,Supplementary Data 2,7 November 2024,KateRasheed,"KateRasheed,WikiWorks",Significant differentially abundant OTU-level microbial taxa (oral microbiota) between controls and PD cases (after adjustment for covariates) using linear models statistical test.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. HMSC035G02,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella sp. 572.rep1_STHE,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella loescheii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum sp. OBRC5-5,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC063B05,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC066F04,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC075C12,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. HMSC061E04,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. HMSC069C03,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. 1171_SSPC,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. 263_SSPC,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. 400_SSPC,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. A12,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HPH0090",1783272|201174|1760|2037|2049|1654|1739406;3384189|32066|203490|203491|203492|848|860;1783272|1239|91061|186826|186828|117563|1725361;3379134|976|200643|171549|171552|2974257|840;1783272|1239|186801|3085636|186803|1164882|936595;3379134|1224|28216|206351|481|482|1739328;3379134|1224|28216|206351|481|482|1715148;3379134|1224|28216|206351|481|482|1739282;1783272|1239|186801|3085636|186803|265975|1501329;1783272|201174|1760|85006|1268|32207|1739431;1783272|201174|1760|85006|1268|32207|1739283;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|91061|186826|1300|1301|113107;1783272|1239|91061|186826|1300|1301|1579348;1783272|1239|91061|186826|1300|1301|1579343;1783272|1239|91061|186826|1300|1301|1579341;1783272|1239|91061|186826|1300|1301|1759399;1783272|1239|91061|186826|1300|1301|1203590,Complete,Svetlana up
bsdb:39443634/5/1,39443634,case-control,39443634,10.1038/s43856-024-00630-8,NA,"Stagaman K., Kmiecik M.J., Wetzel M., Aslibekyan S., Sonmez T.F., Fontanillas P., Tung J., Holmes M.V., Walk S.T., Houser M.C. , Norcliffe-Kaufmann L.",Oral and gut microbiome profiles in people with early idiopathic Parkinson's disease,Communications medicine,2024,NA,Experiment 5,United States of America,Homo sapiens,Saliva,UBERON:0001836,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson’s disease patients (PD patients),"Parkinson’s disease patients (PD patients) refers to patients with Parkinson disease - a neurodegenerative disease that is characterized by both motor symptoms, such as tremors, and non-motor symptoms, such as constipation.",220,438,6 months,WMS,NA,NA,relative abundances,Linear Regression,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,increased,NA,Signature 1,Supplementary Data 2,7 November 2024,KateRasheed,"KateRasheed,WikiWorks",Significant differentially abundant OTU-level microbial taxa(oral microbiota) between controls and PD cases using linear models statistical test.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces gerencseriae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. HMSC08A09,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 448,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium|s__Atopobium sp. HMSC064B08,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC06F02,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. HMSC069G02,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. HMSC064D08,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. HMSC065D09,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas artemidis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas infelix,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. FDAARGOS_192,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC064D12,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC068F04,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC072D03,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC078H12,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp. DNF00869,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. 449_SSPC,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces johnsonii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces dentalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. C150,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces viscosus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp. 6_1_27,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp. 3_1_44,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas noxia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus",1783272|201174|1760|2037|2049|1654|52769;1783272|201174|1760|2037|2049|1654|1581133;1783272|201174|1760|2037|2049|1654|712124;1783272|201174|84998|84999|1643824|1380|1739402;3379134|1224|28216|206351|481|482|1581124;3379134|976|200643|171549|171552|838|28129;3379134|976|200643|171549|171552|838|28129;3379134|976|200643|171549|171552|838|1739496;1783272|201174|1760|85006|1268|32207|1715104;1783272|201174|1760|85006|1268|32207|1739511;1783272|1239|909932|909929|1843491|970|671224;1783272|1239|909932|909929|1843491|970|135082;1783272|1239|91061|186826|1300|1301|1309;1783272|1239|91061|186826|1300|1301|1309;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|1300|1301|1839799;1783272|1239|91061|186826|1300|1301|1715176;1783272|1239|91061|186826|1300|1301|1715051;1783272|1239|91061|186826|1300|1301|1739381;1783272|1239|91061|186826|1300|1301|1739483;1783272|1239|91061|186826|1300|1301|1343;1783272|1239|909932|1843489|31977|29465|1384081;1783272|1239|91061|186826|1300|1301|1579339;1783272|201174|1760|2037|2049|1654|544581;1783272|201174|1760|2037|2049|1654|272548;1783272|1239|91061|186826|1300|1301|1305;1783272|1239|91061|186826|1300|1301|435842;1783272|201174|1760|2037|2049|1654|1656;1783272|1239|909932|1843489|31977|29465|450749;1783272|1239|909932|1843489|31977|29465|457416;1783272|1239|909932|909929|1843491|970|135083;1783272|1239|909932|1843489|31977|39948|218538,Complete,Svetlana up
bsdb:39443634/5/2,39443634,case-control,39443634,10.1038/s43856-024-00630-8,NA,"Stagaman K., Kmiecik M.J., Wetzel M., Aslibekyan S., Sonmez T.F., Fontanillas P., Tung J., Holmes M.V., Walk S.T., Houser M.C. , Norcliffe-Kaufmann L.",Oral and gut microbiome profiles in people with early idiopathic Parkinson's disease,Communications medicine,2024,NA,Experiment 5,United States of America,Homo sapiens,Saliva,UBERON:0001836,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson’s disease patients (PD patients),"Parkinson’s disease patients (PD patients) refers to patients with Parkinson disease - a neurodegenerative disease that is characterized by both motor symptoms, such as tremors, and non-motor symptoms, such as constipation.",220,438,6 months,WMS,NA,NA,relative abundances,Linear Regression,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,increased,NA,Signature 2,Supplementary Data 2,7 November 2024,KateRasheed,"KateRasheed,WikiWorks",Significant differentially abundant OTU-level microbial taxa(oral microbiota) between controls and PD cases using linear models statistical test.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. HMSC035G02,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 172,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella sp. 572.rep1_STHE,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp. HMSC71H05,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella loescheii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum sp. OBRC5-5,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 215,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC061B04,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC061H08,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC063B05,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC064F03,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC066F04,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC067H04,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC068C04,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC068C12,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC071A01,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC072F04,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC075C12,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC078C12,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC15G01,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium asaccharolyticum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp. KLE 1280,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. HMSC061E04,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. HMSC068E02,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. HMSC069C03,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. HMSC076D04,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus peroris,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. 1171_SSPC,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. 263_SSPC,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. 400_SSPC,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. A12,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC034E03,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC057E02,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC062D07,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC067H01,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC34B10,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HPH0090,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. HMSC061C12,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp. HMSC068C11,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC073G10,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC071D03,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC056C01,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp. HMSC061E01,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC070A01,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. HMSC058F07,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella scopos,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp. CCUG 60358,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] sulci,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica",1783272|201174|1760|2037|2049|1654|1739406;1783272|201174|1760|2037|2049|1654|712118;3384189|32066|203490|203491|203492|848|860;3384189|32066|203490|203491|203492|848|860;3384189|32066|203490|203491|203492|848|860;1783272|1239|91061|186826|186828|117563|1725361;3379134|1224|1236|135625|712|724|1608898;3379134|976|200643|171549|171552|2974257|840;3379134|976|200643|171549|171552|2974257|425941;1783272|1239|186801|3085636|186803|1164882|936595;3384189|32066|203490|203491|1129771|32067|712359;3379134|1224|28216|206351|481|482|1715140;3379134|1224|28216|206351|481|482|1715154;3379134|1224|28216|206351|481|482|1739328;3379134|1224|28216|206351|481|482|1715037;3379134|1224|28216|206351|481|482|1715148;3379134|1224|28216|206351|481|482|1739338;3379134|1224|28216|206351|481|482|1715179;3379134|1224|28216|206351|481|482|1739456;3379134|1224|28216|206351|481|482|1739332;3379134|1224|28216|206351|481|482|1739348;3379134|1224|28216|206351|481|482|1739282;3379134|1224|28216|206351|481|482|1715075;3379134|1224|28216|206351|481|482|1581107;1783272|1239|186801|3085636|186803|265975|1501332;1783272|1239|186801|3085636|186803|265975|1501329;3379134|976|200643|171549|171551|836|997829;1783272|201174|1760|85006|1268|32207|1739431;1783272|201174|1760|85006|1268|32207|1739423;1783272|201174|1760|85006|1268|32207|1739283;1783272|201174|1760|85006|1268|32207|1739484;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|91061|186826|1300|1301|113107;1783272|1239|91061|186826|1300|1301|68892;1783272|1239|91061|186826|1300|1301|68891;1783272|1239|91061|186826|1300|1301|1579348;1783272|1239|91061|186826|1300|1301|1579343;1783272|1239|91061|186826|1300|1301|1579341;1783272|1239|91061|186826|1300|1301|1759399;1783272|1239|91061|186826|1300|1301|1739309;1783272|1239|91061|186826|1300|1301|1739265;1783272|1239|91061|186826|1300|1301|1739461;1783272|1239|91061|186826|1300|1301|1739491;1783272|1239|91061|186826|1300|1301|1608856;1783272|1239|91061|186826|1300|1301|1203590;1783272|201174|1760|85006|1268|32207|1739547;3379134|1224|1236|135625|712|724|1739522;3379134|1224|28216|206351|481|482|1739369;1783272|1239|91061|186826|1300|1301|1739341;1783272|1239|91061|186826|1300|1301|1739299;3379134|1224|1236|135625|712|724|1715211;3379134|1224|28216|206351|481|482|1715190;3379134|1224|28216|206351|481|482|1715175;3379134|976|200643|171549|171552|838|589437;3379134|1224|1236|135625|712|724|1859695;1783272|1239|186801|3082720|543314|143393;1783272|1239|91061|1385|539738|1378|84135;3379134|976|200643|171549|171552|838|28132;1783272|1239|91061|186826|186828|117563|46124;1783272|1239|909932|1843489|31977|29465|39778;3379134|976|200643|171549|171552|838|28132,Complete,Svetlana up
bsdb:39443634/6/1,39443634,case-control,39443634,10.1038/s43856-024-00630-8,NA,"Stagaman K., Kmiecik M.J., Wetzel M., Aslibekyan S., Sonmez T.F., Fontanillas P., Tung J., Holmes M.V., Walk S.T., Houser M.C. , Norcliffe-Kaufmann L.",Oral and gut microbiome profiles in people with early idiopathic Parkinson's disease,Communications medicine,2024,NA,Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson’s disease patients (PD patients),"Parkinson’s disease patients (PD patients) refer to patients with Parkinson's disease - a neurodegenerative disease that is characterized by both motor symptoms, such as tremors, and non-motor symptoms, such as constipation.",221,445,6 months,WMS,NA,NA,NA,ANCOM,0.05,TRUE,NA,"age,sex","age,body mass index,smoking status",NA,NA,increased,NA,NA,NA,Signature 1,Supplementary Data 2,7 November 2024,KateRasheed,"KateRasheed,Chrisawoke,WikiWorks",Significantly differentially abundant OTU-level microbial taxa (gut microbiota) between controls and PD cases (after adjustment for covariates) were identified using the ANCOM statistical test.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium 1_1_47,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D16,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC064D12,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC064H09,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC072D03",1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|1689;3379134|1224|28216|80840|469610;1783272|1239|186801|186802|216572|552398;1783272|1239|91061|186826|1300|1301|1715176;1783272|1239|91061|186826|1300|1301|1739371;1783272|1239|91061|186826|1300|1301|1739381,Complete,Svetlana up
bsdb:39443634/6/2,39443634,case-control,39443634,10.1038/s43856-024-00630-8,NA,"Stagaman K., Kmiecik M.J., Wetzel M., Aslibekyan S., Sonmez T.F., Fontanillas P., Tung J., Holmes M.V., Walk S.T., Houser M.C. , Norcliffe-Kaufmann L.",Oral and gut microbiome profiles in people with early idiopathic Parkinson's disease,Communications medicine,2024,NA,Experiment 6,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson’s disease patients (PD patients),"Parkinson’s disease patients (PD patients) refer to patients with Parkinson's disease - a neurodegenerative disease that is characterized by both motor symptoms, such as tremors, and non-motor symptoms, such as constipation.",221,445,6 months,WMS,NA,NA,NA,ANCOM,0.05,TRUE,NA,"age,sex","age,body mass index,smoking status",NA,NA,increased,NA,NA,NA,Signature 2,Supplementary Data 2,7 November 2024,KateRasheed,"KateRasheed,Chrisawoke,WikiWorks",Significantly differentially abundant OTU-level microbial taxa (gut microbiota) between controls and PD cases (after adjustment for covariates) were identified using the ANCOM statistical test.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,3379134|976|200643|171549|2005525|375288|823,Complete,Svetlana up
bsdb:39443634/7/1,39443634,case-control,39443634,10.1038/s43856-024-00630-8,NA,"Stagaman K., Kmiecik M.J., Wetzel M., Aslibekyan S., Sonmez T.F., Fontanillas P., Tung J., Holmes M.V., Walk S.T., Houser M.C. , Norcliffe-Kaufmann L.",Oral and gut microbiome profiles in people with early idiopathic Parkinson's disease,Communications medicine,2024,NA,Experiment 7,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson’s disease patients (PD patients),"Parkinson’s disease patients (PD patients) refer to patients with Parkinson's disease - a neurodegenerative disease that is characterized by both motor symptoms, such as tremors, and non-motor symptoms, such as constipation.",221,445,6 months,WMS,NA,NA,relative abundances,Linear Regression,0.05,TRUE,NA,"age,sex",NA,NA,NA,increased,NA,NA,NA,Signature 1,Supplementary Data 2,7 November 2024,KateRasheed,"KateRasheed,WikiWorks",Significant differentially abundant OTU-level microbial taxa(gut microbiota) between controls and PD cases using linear models statistical test.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium 1_1_47,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. A4-5,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC064H09,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC072D03,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC064D12",1783272|201174|1760|85004|31953|1678|1680;3379134|1224|28216|80840|469610;1783272|1239|186801|186802|216572|1535;1783272|201174|1760|85004|31953|1678|1686;1783272|1239|186801|186802|31979|1485|352071;1783272|1239|91061|186826|1300|1301|1739371;1783272|1239|91061|186826|1300|1301|1739381;1783272|1239|91061|186826|1300|1301|1715176,Complete,Svetlana up
bsdb:39443634/7/2,39443634,case-control,39443634,10.1038/s43856-024-00630-8,NA,"Stagaman K., Kmiecik M.J., Wetzel M., Aslibekyan S., Sonmez T.F., Fontanillas P., Tung J., Holmes M.V., Walk S.T., Houser M.C. , Norcliffe-Kaufmann L.",Oral and gut microbiome profiles in people with early idiopathic Parkinson's disease,Communications medicine,2024,NA,Experiment 7,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson’s disease patients (PD patients),"Parkinson’s disease patients (PD patients) refer to patients with Parkinson's disease - a neurodegenerative disease that is characterized by both motor symptoms, such as tremors, and non-motor symptoms, such as constipation.",221,445,6 months,WMS,NA,NA,relative abundances,Linear Regression,0.05,TRUE,NA,"age,sex",NA,NA,NA,increased,NA,NA,NA,Signature 2,Supplementary Data 2,7 November 2024,KateRasheed,"KateRasheed,WikiWorks",Significant differentially abundant OTU-level microbial taxa(gut microbiota) between controls and PD cases using linear models statistical test.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 2_1_22,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp. 20_3,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 3_1_40A,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 1_1_30,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides gordonii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 3_1_13,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. HMSC067B03,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. HMSC073E02",3379134|976|200643|171549|815|909656|821;3379134|976|200643|171549|815|909656|357276;1783272|1239|186801|3085636|186803|841|166486;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|815|816|469588;3379134|976|200643|171549|2005525|375288|469591;3379134|976|200643|171549|815|816|469593;3379134|976|200643|171549|815|816|457387;3379134|976|200643|171549|815|816|246787;3379134|976|200643|171549|815|816|371601;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|909656|671267;3379134|976|200643|171549|2005525|375288|574930;3379134|976|200643|171549|815|816|457389;3379134|976|200643|171549|815|816|1739298;3379134|976|200643|171549|815|816|1739517,Complete,Svetlana up
bsdb:39443634/8/1,39443634,case-control,39443634,10.1038/s43856-024-00630-8,NA,"Stagaman K., Kmiecik M.J., Wetzel M., Aslibekyan S., Sonmez T.F., Fontanillas P., Tung J., Holmes M.V., Walk S.T., Houser M.C. , Norcliffe-Kaufmann L.",Oral and gut microbiome profiles in people with early idiopathic Parkinson's disease,Communications medicine,2024,NA,Experiment 8,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson’s disease patients (PD patients),"Parkinson’s disease patients (PD patients) refer to patients with Parkinson's disease - a neurodegenerative disease that is characterized by both motor symptoms, such as tremors, and non-motor symptoms, such as constipation.",221,445,6 months,WMS,NA,NA,relative abundances,Linear Regression,0.05,TRUE,NA,"age,sex","age,body mass index,smoking status",NA,NA,increased,NA,NA,NA,Signature 1,Supplementary Data 2,7 November 2024,KateRasheed,"KateRasheed,WikiWorks",Significant differentially abundant OTU-level microbial taxa (gut microbiota) between controls and PD cases (after adjustment for covariates) using linear models statistical test.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC072D03,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D16,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium 1_1_47",1783272|1239|91061|186826|1300|1301|1739381;1783272|1239|186801|186802|216572|552398;1783272|201174|1760|85004|31953|1678|1689;3379134|1224|28216|80840|469610,Complete,Svetlana up
bsdb:39443634/8/2,39443634,case-control,39443634,10.1038/s43856-024-00630-8,NA,"Stagaman K., Kmiecik M.J., Wetzel M., Aslibekyan S., Sonmez T.F., Fontanillas P., Tung J., Holmes M.V., Walk S.T., Houser M.C. , Norcliffe-Kaufmann L.",Oral and gut microbiome profiles in people with early idiopathic Parkinson's disease,Communications medicine,2024,NA,Experiment 8,United States of America,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy Controls,Parkinson’s disease patients (PD patients),"Parkinson’s disease patients (PD patients) refer to patients with Parkinson's disease - a neurodegenerative disease that is characterized by both motor symptoms, such as tremors, and non-motor symptoms, such as constipation.",221,445,6 months,WMS,NA,NA,relative abundances,Linear Regression,0.05,TRUE,NA,"age,sex","age,body mass index,smoking status",NA,NA,increased,NA,NA,NA,Signature 2,Supplementary Data 2,7 November 2024,KateRasheed,"KateRasheed,WikiWorks",Significant differentially abundant OTU-level microbial taxa (gut microbiota) between controls and PD cases (after adjustment for covariates) using linear models statistical test.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. SN20,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. HMSC067B03,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 3_1_13,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides gordonii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola sartorii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp. 20_3,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis",1783272|1239|186801|186802|31979|1485|1776383;3379134|976|200643|171549|815|816|1739298;3379134|976|200643|171549|815|816|246787;3379134|976|200643|171549|815|816|457389;3379134|976|200643|171549|2005525|375288|574930;3379134|976|200643|171549|815|909656|671267;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|816|246787;3379134|976|200643|171549|2005525|375288|469591;1783272|1239|186801|3085636|186803|841|166486,Complete,Svetlana up
bsdb:39454570/1/1,39454570,randomized controlled trial,39454570,10.1016/j.xcrm.2024.101801,NA,"Li L., Li R., Tian Q., Luo Y., Li R., Lin X., Ou Y., Guo T., Chen X., Pan A., Manson J.E. , Liu G.",Effects of healthy low-carbohydrate diet and time-restricted eating on weight and gut microbiome in adults with overweight or obesity: Feeding RCT,Cell reports. Medicine,2024,"body composition, feeding trial, gut microbiome, healthy low-carbohydrate diet, metabolome, obesity, overweight, time-restricted eating, weight, weight regain",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Healthy Low Carbohydrate Diet at Baseline (HLCD),Healthy Low Carbohydrate Diet at Endpoint (HLCD),"The participants in the Healthy Low Carbohydrate Diet (HLCD) alone group were
provided with HLCD and instructed to follow their usual eating regimens during the 12 week feeding trial. The HLCD was a relatively healthy type of LCD consisting of approximately 30%, 50%, and 20% of total energy from carbohydrates, fats, and proteins, emphasizing the consumption of unsaturated fatty acids, plant proteins, and high-quality carbohydrates including whole grains, fresh vegetables, and fruits.",48,43,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2c and Supplementary Figure 2,12 April 2025,MyleeeA,MyleeeA,Significant taxonomic changes between Healthy Low Carbohydrate Diet (HLCD) at baseline and Endpoint as accessed using LefSe.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella confusa",3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|1224|28216;3379134|1224|28216|80840;3379134|1224|1236|91347|543|547|158836;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|561|562;3379134|1224|1236;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|543|570|573;3379134|1224;3379134|1224|28216|80840|995019;1783272|1239|91061|186826|33958|46255|1583,Complete,ChiomaBlessing
bsdb:39454570/1/2,39454570,randomized controlled trial,39454570,10.1016/j.xcrm.2024.101801,NA,"Li L., Li R., Tian Q., Luo Y., Li R., Lin X., Ou Y., Guo T., Chen X., Pan A., Manson J.E. , Liu G.",Effects of healthy low-carbohydrate diet and time-restricted eating on weight and gut microbiome in adults with overweight or obesity: Feeding RCT,Cell reports. Medicine,2024,"body composition, feeding trial, gut microbiome, healthy low-carbohydrate diet, metabolome, obesity, overweight, time-restricted eating, weight, weight regain",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Healthy Low Carbohydrate Diet at Baseline (HLCD),Healthy Low Carbohydrate Diet at Endpoint (HLCD),"The participants in the Healthy Low Carbohydrate Diet (HLCD) alone group were
provided with HLCD and instructed to follow their usual eating regimens during the 12 week feeding trial. The HLCD was a relatively healthy type of LCD consisting of approximately 30%, 50%, and 20% of total energy from carbohydrates, fats, and proteins, emphasizing the consumption of unsaturated fatty acids, plant proteins, and high-quality carbohydrates including whole grains, fresh vegetables, and fruits.",48,43,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2c and Supplementary Figure 2,12 April 2025,MyleeeA,MyleeeA,Significant taxonomic changes between Healthy Low Carbohydrate Diet (HLCD) at baseline and Endpoint as accessed using LefSe.,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. A12,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia",1783272|1239;1783272|1239|186801;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|2316020;1783272|1239|186801|186802|216572;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3082720|186804|1501226|1776391;1783272|1239|91061|186826|1300|1301|1759399;1783272|1239|526524|526525|2810281|191303|154288;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801,Complete,ChiomaBlessing
bsdb:39454570/2/1,39454570,randomized controlled trial,39454570,10.1016/j.xcrm.2024.101801,NA,"Li L., Li R., Tian Q., Luo Y., Li R., Lin X., Ou Y., Guo T., Chen X., Pan A., Manson J.E. , Liu G.",Effects of healthy low-carbohydrate diet and time-restricted eating on weight and gut microbiome in adults with overweight or obesity: Feeding RCT,Cell reports. Medicine,2024,"body composition, feeding trial, gut microbiome, healthy low-carbohydrate diet, metabolome, obesity, overweight, time-restricted eating, weight, weight regain",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Non-Healthy Low Carbohydrate Diet at Baseline (Non-HLCD),Non-Healthy Low Carbohydrate Diet at Endpoint (Non-HLCD),"The participants in the Non-Healthy Low Carbohydrate Diet (HLCD) alone group were not
provided with HLCD and instructed to follow their usual eating regimens during the 12 week feeding trial.",48,44,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2c and Supplementary Figure 2,12 April 2025,MyleeeA,MyleeeA,Significant taxonomic changes between Non-Healthy Low Carbohydrate Diet (Non-HLCD) at baseline and Endpoint as accessed using LefSe.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella confusa",3379134|1224|1236|91347|543|544;1783272|1239|186801|186802|216572|2591381;3379134|1224|1236|91347|543|547|158836;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|186801|3085636|186803|2719313|358743;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|561|562;3379134|1224|1236;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|543|570|573;1783272|1239|91061|186826|33958|46255|1583,Complete,ChiomaBlessing
bsdb:39454570/2/2,39454570,randomized controlled trial,39454570,10.1016/j.xcrm.2024.101801,NA,"Li L., Li R., Tian Q., Luo Y., Li R., Lin X., Ou Y., Guo T., Chen X., Pan A., Manson J.E. , Liu G.",Effects of healthy low-carbohydrate diet and time-restricted eating on weight and gut microbiome in adults with overweight or obesity: Feeding RCT,Cell reports. Medicine,2024,"body composition, feeding trial, gut microbiome, healthy low-carbohydrate diet, metabolome, obesity, overweight, time-restricted eating, weight, weight regain",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Non-Healthy Low Carbohydrate Diet at Baseline (Non-HLCD),Non-Healthy Low Carbohydrate Diet at Endpoint (Non-HLCD),"The participants in the Non-Healthy Low Carbohydrate Diet (HLCD) alone group were not
provided with HLCD and instructed to follow their usual eating regimens during the 12 week feeding trial.",48,44,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2c and Supplementary Figure 2,12 April 2025,MyleeeA,MyleeeA,Significant taxonomic changes between Non-Healthy Low Carbohydrate Diet (Non-HLCD) at baseline and Endpoint as accessed using LefSe.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus rubneri",1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|2316020;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3082720|186804|1501226|1776391;1783272|1239|91061|186826|1300|1301|1234680,Complete,ChiomaBlessing
bsdb:39454570/3/1,39454570,randomized controlled trial,39454570,10.1016/j.xcrm.2024.101801,NA,"Li L., Li R., Tian Q., Luo Y., Li R., Lin X., Ou Y., Guo T., Chen X., Pan A., Manson J.E. , Liu G.",Effects of healthy low-carbohydrate diet and time-restricted eating on weight and gut microbiome in adults with overweight or obesity: Feeding RCT,Cell reports. Medicine,2024,"body composition, feeding trial, gut microbiome, healthy low-carbohydrate diet, metabolome, obesity, overweight, time-restricted eating, weight, weight regain",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Fasting,EFO:0002756,Time-Restricted eating (TRE) at Baseline,Time-Restricted eating (TRE) at Endpoint,The participants in the Time Restricted eating (TRE) alone group were provided with control diets and instructed to follow the 10-h TRE during the 12 week feeding trial. The 10-h TRE required participants to consume the provided meals within a 10-h window each day.,48,43,3 months,WMS,NA,Illumina,relative abundances,"T-Test,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Figure 4A,12 April 2025,MyleeeA,MyleeeA,Significant taxonomic changes between Time-Restricted eating (TRE) at baseline and Endpoint.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|s__Eubacteriaceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis",3379134|976|200643|171549|2005525|375288|823;1783272|1239|186801|186802|186806|2049045;3379134|976|200643|171549|815|816|329854;3379134|1224|1236|91347|543|561|562;3379134|976|200643|171549|2005519|397864|487174,Complete,ChiomaBlessing
bsdb:39454570/6/1,39454570,randomized controlled trial,39454570,10.1016/j.xcrm.2024.101801,NA,"Li L., Li R., Tian Q., Luo Y., Li R., Lin X., Ou Y., Guo T., Chen X., Pan A., Manson J.E. , Liu G.",Effects of healthy low-carbohydrate diet and time-restricted eating on weight and gut microbiome in adults with overweight or obesity: Feeding RCT,Cell reports. Medicine,2024,"body composition, feeding trial, gut microbiome, healthy low-carbohydrate diet, metabolome, obesity, overweight, time-restricted eating, weight, weight regain",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Fasting,EFO:0002756,Time Restricted Eating at Baseline (TRE),Time Restricted Eating at Endpoint (TRE),"The participants in the Time Restricted Eating (TRE) alone group were provided with control diets and instructed to follow the 10-h TRE. The control diet was the traditional Chinese diet designed according to Dietary Guidelines for Chinese Resident characterized by approximately 50%, 34%, and 16% of energy from carbohydrates, fat, and protein. The 10-h TRE required participants to consume the provided meals within a 10-h window each day.",48,43,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2D and Supplementary Figure 2,14 April 2025,Daberechi,Daberechi,Significant taxonomic changes between Time Restricted Eating (TRE) at baseline and Endpoint as accessed using LefSe.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella confusa,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543|547|158836;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|561|562;3379134|1224|1236;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|543|570|573;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|2005525;1783272|1239|91061|186826|33958|46255|1583;3379134|1224,Complete,ChiomaBlessing
bsdb:39454570/6/2,39454570,randomized controlled trial,39454570,10.1016/j.xcrm.2024.101801,NA,"Li L., Li R., Tian Q., Luo Y., Li R., Lin X., Ou Y., Guo T., Chen X., Pan A., Manson J.E. , Liu G.",Effects of healthy low-carbohydrate diet and time-restricted eating on weight and gut microbiome in adults with overweight or obesity: Feeding RCT,Cell reports. Medicine,2024,"body composition, feeding trial, gut microbiome, healthy low-carbohydrate diet, metabolome, obesity, overweight, time-restricted eating, weight, weight regain",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Fasting,EFO:0002756,Time Restricted Eating at Baseline (TRE),Time Restricted Eating at Endpoint (TRE),"The participants in the Time Restricted Eating (TRE) alone group were provided with control diets and instructed to follow the 10-h TRE. The control diet was the traditional Chinese diet designed according to Dietary Guidelines for Chinese Resident characterized by approximately 50%, 34%, and 16% of energy from carbohydrates, fat, and protein. The 10-h TRE required participants to consume the provided meals within a 10-h window each day.",48,43,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2D and Supplementary Figure 2,14 April 2025,Daberechi,Daberechi,Significant taxonomic changes between Time Restricted Eating (TRE) at baseline and Endpoint as accessed using LefSe.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus rubneri,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|186802|186806|1730|39490;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|2316020;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3082720|186804|1501226|1776391;1783272|1239|91061|186826|1300|1301|1234680;1783272|1239|186801|186802|216572,Complete,ChiomaBlessing
bsdb:39454570/7/1,39454570,randomized controlled trial,39454570,10.1016/j.xcrm.2024.101801,NA,"Li L., Li R., Tian Q., Luo Y., Li R., Lin X., Ou Y., Guo T., Chen X., Pan A., Manson J.E. , Liu G.",Effects of healthy low-carbohydrate diet and time-restricted eating on weight and gut microbiome in adults with overweight or obesity: Feeding RCT,Cell reports. Medicine,2024,"body composition, feeding trial, gut microbiome, healthy low-carbohydrate diet, metabolome, obesity, overweight, time-restricted eating, weight, weight regain",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Binge eating,EFO:0005924,Non-Time Restricted Eating at Baseline (Non-TRE),Non-Time Restricted Eating at Endpoint (Non-TRE),The participants in the Non-Time Restricted Eating (TRE) alone group were provided with control diets and not instructed to follow the 10-h TRE.  The 10-h TRE required participants to consume the provided meals within a 10-h window each day.,48,44,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2D and Supplementary Figure 2,14 April 2025,Daberechi,Daberechi,Significant taxonomic changes between Non-Time Restricted Eating (Non-TRE) at baseline and Endpoint as accessed using LefSe.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF34-10BH,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella confusa,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",3379134|1224|1236|91347|543|570|573;3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|543|547|158836;1783272|1239|186801|186802|31979|1485|2293011;1783272|1239|91061|186826|33958|46255|1583;3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347;3379134|1224|1236|91347|543,Complete,ChiomaBlessing
bsdb:39454570/7/2,39454570,randomized controlled trial,39454570,10.1016/j.xcrm.2024.101801,NA,"Li L., Li R., Tian Q., Luo Y., Li R., Lin X., Ou Y., Guo T., Chen X., Pan A., Manson J.E. , Liu G.",Effects of healthy low-carbohydrate diet and time-restricted eating on weight and gut microbiome in adults with overweight or obesity: Feeding RCT,Cell reports. Medicine,2024,"body composition, feeding trial, gut microbiome, healthy low-carbohydrate diet, metabolome, obesity, overweight, time-restricted eating, weight, weight regain",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Binge eating,EFO:0005924,Non-Time Restricted Eating at Baseline (Non-TRE),Non-Time Restricted Eating at Endpoint (Non-TRE),The participants in the Non-Time Restricted Eating (TRE) alone group were provided with control diets and not instructed to follow the 10-h TRE.  The 10-h TRE required participants to consume the provided meals within a 10-h window each day.,48,44,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2D and Supplementary Figure 2,14 April 2025,Daberechi,Daberechi,Significant taxonomic changes between Non-Time Restricted Eating (Non-TRE) at baseline and Endpoint as accessed using LefSe.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter",1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|2316020,Complete,ChiomaBlessing
bsdb:39454570/8/1,39454570,randomized controlled trial,39454570,10.1016/j.xcrm.2024.101801,NA,"Li L., Li R., Tian Q., Luo Y., Li R., Lin X., Ou Y., Guo T., Chen X., Pan A., Manson J.E. , Liu G.",Effects of healthy low-carbohydrate diet and time-restricted eating on weight and gut microbiome in adults with overweight or obesity: Feeding RCT,Cell reports. Medicine,2024,"body composition, feeding trial, gut microbiome, healthy low-carbohydrate diet, metabolome, obesity, overweight, time-restricted eating, weight, weight regain",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Healthy Low Carbohydrate Diet at Baseline (HLCD),Healthy Low Carbohydrate Diet at Endpoint (HLCD),"The participants in the Healthy Low Carbohydrate Diet (HLCD) alone group were
provided with HLCD and instructed to follow their usual eating regimens during the 12 week feeding trial. The HLCD was a relatively healthy type of LCD consisting of approximately 30%, 50%, and 20% of total energy from carbohydrates, fats, and proteins, emphasizing the consumption of unsaturated fatty acids, plant proteins, and high-quality carbohydrates including whole grains, fresh vegetables, and fruits.",48,43,3 months,WMS,NA,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),T-Test",0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Figure 3A,14 April 2025,Daberechi,Daberechi,Significant taxonomic changes between Healthy Low Carbohydrate Diet (HLCD) at baseline and Endpoint as accessed.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus",3379134|976|200643|171549|815|909656|357276;1783272|1239|186801|186802|216572|1263|40519,Complete,ChiomaBlessing
bsdb:39454570/9/1,39454570,randomized controlled trial,39454570,10.1016/j.xcrm.2024.101801,NA,"Li L., Li R., Tian Q., Luo Y., Li R., Lin X., Ou Y., Guo T., Chen X., Pan A., Manson J.E. , Liu G.",Effects of healthy low-carbohydrate diet and time-restricted eating on weight and gut microbiome in adults with overweight or obesity: Feeding RCT,Cell reports. Medicine,2024,"body composition, feeding trial, gut microbiome, healthy low-carbohydrate diet, metabolome, obesity, overweight, time-restricted eating, weight, weight regain",Experiment 9,China,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Non-Healthy Low Carbohydrate Diet at Baseline (Non-HLCD),Non-Healthy Low Carbohydrate Diet at Endpoint (Non-HLCD),The participants in the Non-Healthy Low Carbohydrate Diet (HLCD) alone group were not provided with HLCD and instructed to follow their usual eating regimens during the 12 week feeding trial.,48,44,3 months,WMS,NA,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),T-Test",0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Figure 3B,14 April 2025,Daberechi,Daberechi,Significant taxonomic changes between Non-Healthy Low Carbohydrate Diet (Non-HLCD) at baseline and Endpoint as accessed.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter|s__Dysosmobacter hominis,1783272|1239|186801|186802|216572|2591381|2763041,Complete,ChiomaBlessing
bsdb:39454570/9/2,39454570,randomized controlled trial,39454570,10.1016/j.xcrm.2024.101801,NA,"Li L., Li R., Tian Q., Luo Y., Li R., Lin X., Ou Y., Guo T., Chen X., Pan A., Manson J.E. , Liu G.",Effects of healthy low-carbohydrate diet and time-restricted eating on weight and gut microbiome in adults with overweight or obesity: Feeding RCT,Cell reports. Medicine,2024,"body composition, feeding trial, gut microbiome, healthy low-carbohydrate diet, metabolome, obesity, overweight, time-restricted eating, weight, weight regain",Experiment 9,China,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Non-Healthy Low Carbohydrate Diet at Baseline (Non-HLCD),Non-Healthy Low Carbohydrate Diet at Endpoint (Non-HLCD),The participants in the Non-Healthy Low Carbohydrate Diet (HLCD) alone group were not provided with HLCD and instructed to follow their usual eating regimens during the 12 week feeding trial.,48,44,3 months,WMS,NA,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),T-Test",0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Figure 3B,14 April 2025,Daberechi,Daberechi,Significant taxonomic changes between Non-Healthy Low Carbohydrate Diet (Non-HLCD) at baseline and Endpoint as accessed.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Mesosutterella|s__Mesosutterella multiformis,3379134|1224|28216|80840|995019|2494213|2259133,Complete,ChiomaBlessing
bsdb:39455736/1/1,39455736,laboratory experiment,39455736,10.1038/s42003-024-07087-4,NA,"Gupta S., Vera-Ponce de León A., Kodama M., Hoetzinger M., Clausen C.G., Pless L., Verissimo A.R.A., Stengel B., Calabuig V., Kvingedal R., Skugor S., Westereng B., Harvey T.N., Nordborg A., Bertilsson S., Limborg M.T., Mørkøre T., Sandve S.R., Pope P.B., Hvidsten T.R. , La Rosa S.L.",The need for high-resolution gut microbiome characterization to design efficient strategies for sustainable aquaculture production,Communications biology,2024,NA,Experiment 1,Norway,Salmo salar,Hindgut,UBERON:0001046,Response to diet,EFO:0010757,0.2% CTR Diet T2,0.2% MC2 Diet T2,"Salmon fed a standard commercial diet supplemented with 0.2% MC2 (a 0.2% w/w α-mannan supplement produced by Cargill) at 10 weeks (T2, smolt stage) after the experiment started.",30,30,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 1G,18 November 2024,YokoC,"YokoC,WikiWorks","Significant differential abundances (Wilcoxon test) for bacterial genera in salmons fed a 0.2% MC2 diet or a CTR (control) diet at 10 weeks (T2, smolt stage) after the experiment began.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Nitrospirillum",3379134|1224|28216|80840|119060|106589;3379134|1224|28216|80840|75682|963;3379134|1224|28211|204441|2829815|1543705,Complete,Svetlana up
bsdb:39455736/2/1,39455736,laboratory experiment,39455736,10.1038/s42003-024-07087-4,NA,"Gupta S., Vera-Ponce de León A., Kodama M., Hoetzinger M., Clausen C.G., Pless L., Verissimo A.R.A., Stengel B., Calabuig V., Kvingedal R., Skugor S., Westereng B., Harvey T.N., Nordborg A., Bertilsson S., Limborg M.T., Mørkøre T., Sandve S.R., Pope P.B., Hvidsten T.R. , La Rosa S.L.",The need for high-resolution gut microbiome characterization to design efficient strategies for sustainable aquaculture production,Communications biology,2024,NA,Experiment 2,Norway,Salmo salar,Hindgut,UBERON:0001046,Response to diet,EFO:0010757,0.2% CTR Diet T2,0.2% MN3 Diet T2,"Salmon fed with a standard commercial diet supplemented with 0.2% MN3 (0.2% w/w acetylated β-galactoglucomannan) at 10 weeks (T2, smolt stage) after the experiment started.",30,30,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Fig. 1G,18 November 2024,YokoC,"YokoC,WikiWorks","Significant differential abundances (Wilcoxon test) for bacterial genera in salmons fed a 0.2% MN3 diet or a CTR (control) diet at 10 weeks (T2, smolt stage) after the experiment began.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Nitrospirillum",3379134|1224|28216|80840|119060|106589;3379134|1224|28216|80840|75682|963;3379134|1224|28211|204441|2829815|1543705,Complete,Svetlana up
bsdb:39455736/3/1,39455736,laboratory experiment,39455736,10.1038/s42003-024-07087-4,NA,"Gupta S., Vera-Ponce de León A., Kodama M., Hoetzinger M., Clausen C.G., Pless L., Verissimo A.R.A., Stengel B., Calabuig V., Kvingedal R., Skugor S., Westereng B., Harvey T.N., Nordborg A., Bertilsson S., Limborg M.T., Mørkøre T., Sandve S.R., Pope P.B., Hvidsten T.R. , La Rosa S.L.",The need for high-resolution gut microbiome characterization to design efficient strategies for sustainable aquaculture production,Communications biology,2024,NA,Experiment 3,Norway,Salmo salar,Actinopterygian pyloric caecum,UBERON:4300174,Response to diet,EFO:0010757,4% CTR Diet Pyloric caecum,4% MN3 Pyloric caecum,Salmon fed with a standard commercial diet supplemented with 4% MN3 ( 4% w/w acetylated β-galactoglucomannan) for 4 weeks.,18,18,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 2F,18 November 2024,YokoC,"YokoC,Aleru Divine,WikiWorks",Significant differential abundances (Wilcoxon test) for bacterial genera in samples collected from the pyloric caecum of salmons fed a 4% MN3 diet or a CTR diet.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",3379134|1224|28216|80840|80864;3379134|1224|1236|72274|135621|286,Complete,Svetlana up
bsdb:39455736/3/2,39455736,laboratory experiment,39455736,10.1038/s42003-024-07087-4,NA,"Gupta S., Vera-Ponce de León A., Kodama M., Hoetzinger M., Clausen C.G., Pless L., Verissimo A.R.A., Stengel B., Calabuig V., Kvingedal R., Skugor S., Westereng B., Harvey T.N., Nordborg A., Bertilsson S., Limborg M.T., Mørkøre T., Sandve S.R., Pope P.B., Hvidsten T.R. , La Rosa S.L.",The need for high-resolution gut microbiome characterization to design efficient strategies for sustainable aquaculture production,Communications biology,2024,NA,Experiment 3,Norway,Salmo salar,Actinopterygian pyloric caecum,UBERON:4300174,Response to diet,EFO:0010757,4% CTR Diet Pyloric caecum,4% MN3 Pyloric caecum,Salmon fed with a standard commercial diet supplemented with 4% MN3 ( 4% w/w acetylated β-galactoglucomannan) for 4 weeks.,18,18,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Fig. 2F,18 November 2024,YokoC,"YokoC,WikiWorks",Significant differential abundances (Wilcoxon test) for bacterial genera in samples collected from the pyloric caecum of salmons fed a 4% MN3 diet or a CTR diet.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tepidimicrobiaceae|g__Tepidimicrobium",1783272|1239|91061|186826|81852|1350;1783272|1239|1737404|1737405|1570339|162290;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|2742598;1783272|1239|186801|3082720|186804|1257;1783272|1239|1737404|1737405|2992719|285105,Complete,Svetlana up
bsdb:39455736/4/1,39455736,laboratory experiment,39455736,10.1038/s42003-024-07087-4,NA,"Gupta S., Vera-Ponce de León A., Kodama M., Hoetzinger M., Clausen C.G., Pless L., Verissimo A.R.A., Stengel B., Calabuig V., Kvingedal R., Skugor S., Westereng B., Harvey T.N., Nordborg A., Bertilsson S., Limborg M.T., Mørkøre T., Sandve S.R., Pope P.B., Hvidsten T.R. , La Rosa S.L.",The need for high-resolution gut microbiome characterization to design efficient strategies for sustainable aquaculture production,Communications biology,2024,NA,Experiment 4,Norway,Salmo salar,Hindgut,UBERON:0001046,Response to diet,EFO:0010757,4% CTR Diet hindgut,4% MN3 Diet hindgut,Salmon fed a standard commercial diet supplemented with 4% MN3 (4% w/w acetylated β-galactoglucomannan) for 4 weeks.,18,18,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Fig. 2F,18 November 2024,YokoC,"YokoC,Aleru Divine,WikiWorks",Significant differential abundances (Wilcoxon test) for bacterial genera in samples collected from the hindgut of salmons fed a 4% MN3 diet or a CTR (control) diet.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",3379134|1224|28216|80840|80864;3379134|1224|1236|72274|135621|286,Complete,Svetlana up
bsdb:39455736/4/2,39455736,laboratory experiment,39455736,10.1038/s42003-024-07087-4,NA,"Gupta S., Vera-Ponce de León A., Kodama M., Hoetzinger M., Clausen C.G., Pless L., Verissimo A.R.A., Stengel B., Calabuig V., Kvingedal R., Skugor S., Westereng B., Harvey T.N., Nordborg A., Bertilsson S., Limborg M.T., Mørkøre T., Sandve S.R., Pope P.B., Hvidsten T.R. , La Rosa S.L.",The need for high-resolution gut microbiome characterization to design efficient strategies for sustainable aquaculture production,Communications biology,2024,NA,Experiment 4,Norway,Salmo salar,Hindgut,UBERON:0001046,Response to diet,EFO:0010757,4% CTR Diet hindgut,4% MN3 Diet hindgut,Salmon fed a standard commercial diet supplemented with 4% MN3 (4% w/w acetylated β-galactoglucomannan) for 4 weeks.,18,18,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Fig. 2F,18 November 2024,YokoC,"YokoC,WikiWorks",Significant differential abundances (Wilcoxon test) for bacterial genera in samples collected from the hindgut of salmons fed a 4% MN3 diet or a CTR diet.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|2767887;1783272|1239|91061|186826|33958|2742598;1783272|1239|186801|3082720|186804|1257;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:39461337/1/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 1,Germany,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Model Patient 1 (MP1) with inactive disease,Model Patient 1 (MP1) with active disease,"Gnotobiotic Il10−/− mice subjected to fecal microbiota transplantation (FMT) from Model Patient 1 (MP1), resulting in recipients exhibiting inflammation",NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5D,2 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","LEfSe (Linear discriminant analysis Effect Size) analysis of differentially abundant bacteria at species level in all recipient inflamed (active, red) or non-inflamed (inactive, green) Il10-/- mice from all FMTs performed with abundance of strains in model patient 1 (MP1).",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. infantis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium KLE1615,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Lawsonibacter|s__Lawsonibacter asaccharolyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas intestinalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus lutetiensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:41,k__Pseudomonadati|p__Pseudomonadota|s__Proteobacteria bacterium CAG:495",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759|2585118;3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005519|397864|487174;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|216816|1682;1783272|1239|186801|3085636|186803|572511|1955243;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|186802|1715004;1783272|1239|186801|186802|31979|1485|1506;1783272|201174|84998|84999|84107|102106;1783272|1239|526524|526525|2810280|100883|100884;1783272|1239|186801|3085636|186803|33042|33043;1783272|1239|186801|186802|216572|2172004|2108523;1783272|1239|186801|3085636|186803|2316020|33038;3379134|976|200643|171549|1853231|283168|28118;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|995019|577310|487175;3379134|1224|28216|80840|995019|577310|2049037;3379134|976|200643|171549|815|909656|204516;1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|186801|3085636|186803|1769710|1653434;1783272|1239|91061|186826|1300|1301|150055;1783272|1239|186801|186802|31979|1485|1522;1783272|1239|186801|3085636|186803|1506553|29347;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|1263021;3379134|1224|1262987,Complete,Svetlana up
bsdb:39461337/1/2,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 1,Germany,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Model Patient 1 (MP1) with inactive disease,Model Patient 1 (MP1) with active disease,"Gnotobiotic Il10−/− mice subjected to fecal microbiota transplantation (FMT) from Model Patient 1 (MP1), resulting in recipients exhibiting inflammation",NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5D,2 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","LEfSe (Linear discriminant analysis Effect Size) analysis of differentially abundant bacteria at species level in all recipient inflamed (active, red) or non-inflamed (inactive, green) Il10-/- mice from all FMTs performed with abundance of strains in model patient 1 (MP1).",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum|s__Varibaculum cambriense,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii",1783272|1239|186801|3085636|186803|2719313|1531;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|371601;1783272|1239|186801|3085636|186803|2719313|208479;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|3085636|186803|2941495|1512;1783272|201174|1760|2037|2049|184869|184870;3379134|1224|1236|91347|543|544|546,Complete,Svetlana up
bsdb:39461337/2/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 2,Germany,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Model Patient 2 (MP2) with inactive disease,Model Patient 2 (MP2) with active disease,"Gnotobiotic Il10−/− mice subjected to fecal microbiota transplantation (FMT) from Model Patient 2 (MP2), resulting in recipients exhibiting inflammation",NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5E,2 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","LEfSe (Linear discriminant analysis Effect Size) analysis of differentially abundant bacteria at species level in all recipient inflamed (active, red) or non-inflamed (inactive, green) Il10-/- mice from all FMTs performed with abundance of strains in model patient 2 (MP2).",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus gallinarum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella sp.",1783272|1239|186801|3085636|186803|207244|105841;1783272|1239|186801|3085636|186803|207244|1872530;3379134|976|200643|171549|815|816|674529;3379134|976|200643|171549|815|816|338188;3379134|976|200643|171549|815|816|818;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|91061|186826|81852|1350|1353;3379134|1224|28216|80840|995019|577310|487175;3379134|1224|28216|80840|995019|577310|2049037,Complete,Svetlana up
bsdb:39461337/2/2,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 2,Germany,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Model Patient 2 (MP2) with inactive disease,Model Patient 2 (MP2) with active disease,"Gnotobiotic Il10−/− mice subjected to fecal microbiota transplantation (FMT) from Model Patient 2 (MP2), resulting in recipients exhibiting inflammation",NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5E,2 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","LEfSe (Linear discriminant analysis Effect Size) analysis of differentially abundant bacteria at species level in all recipient inflamed (active, red) or non-inflamed (inactive, green) Il10-/- mice from all FMTs performed with abundance of strains in model patient 2 (MP2).",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens",3379134|976|200643|171549|815|816|820;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|2719313|1531;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|526524|526525|2810280|3025755|29348;1783272|1239|186801|3085636|186803|1506553|29347,Complete,Svetlana up
bsdb:39461337/3/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 3,Germany,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Model Patient 3 (MP3) with inactive disease,Model Patient 3 (MP3) with active disease,"Gnotobiotic Il10−/− mice subjected to fecal microbiota transplantation (FMT) from Model Patient 3 (MP3), resulting in recipients exhibiting inflammation",NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5F,2 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","LEfSe (Linear discriminant analysis Effect Size) analysis of differentially abundant bacteria at species level in all recipient inflamed (active, red) or non-inflamed (inactive, green) Il10-/- mice from all FMTs performed with abundance of strains in model patient 3 (MP3).",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",1783272|1239|186801|3085636|186803|2719313|1531;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|186801|3085636|186803|2316020|33038,Complete,Svetlana up
bsdb:39461337/3/2,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 3,Germany,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Model Patient 3 (MP3) with inactive disease,Model Patient 3 (MP3) with active disease,"Gnotobiotic Il10−/− mice subjected to fecal microbiota transplantation (FMT) from Model Patient 3 (MP3), resulting in recipients exhibiting inflammation",NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5F,2 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","LEfSe (Linear discriminant analysis Effect Size) analysis of differentially abundant bacteria at species level in all recipient inflamed (active, red) or non-inflamed (inactive, green) Il10-/- mice from all FMTs performed with abundance of strains in model patient 3 (MP3).",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Niameybacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum",1783272|1239|186801|186802|31979|1485|1502;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|186801|3085636|186803|1973274;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|186801|186802|31979|1485|1522,Complete,Svetlana up
bsdb:39461337/4/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 4,Germany,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Inactive group,Active group,"Gnotobiotic Il10−/− mice subjected to fecal microbiota transplantation (FMT) from MP1 - MP3, resulting in recipients exhibiting inflammation",NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Figure S9A,2 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","LEfSe (Linear discriminant analysis Effect Size) analysis of differentially abundant bacteria at species level in all recipient inflamed (active, red) or non-inflamed (inactive, green) Il10-/- mice from all FMTs performed with abundance of strains in each model patient (MP).",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium KLE1615,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus casseliflavus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella michiganensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Lawsonibacter|s__Lawsonibacter asaccharolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella|s__Morganella morganii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759|2585118;3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|171550|239759|328814;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|1681;1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|186801|3085636|186803|572511|1955243;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|186802|1715004;1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|186801|186802|31979|1485|1506;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|33042|33043;1783272|1239|91061|186826|81852|1350|37734;1783272|1239|91061|186826|81852|1350|35783;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3082720|186804|1505657|261299;3379134|1224|1236|91347|543|570|1134687;3379134|1224|1236|91347|543|570|573;1783272|1239|186801|186802|216572|2172004|2108523;3379134|1224|1236|91347|1903414|581|582;1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|186801|3085636|186803|1769710|1653434;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Svetlana up
bsdb:39461337/4/2,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 4,Germany,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Inactive group,Active group,"Gnotobiotic Il10−/− mice subjected to fecal microbiota transplantation (FMT) from MP1 - MP3, resulting in recipients exhibiting inflammation",NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,Figure S9A,2 December 2024,Aleru Divine,"Aleru Divine,WikiWorks","LEfSe (Linear discriminant analysis Effect Size) analysis of differentially abundant bacteria at species level in all recipient inflamed (active, red) or non-inflamed (inactive, green) Il10-/- mice from all FMTs performed with abundance of strains in each model patient (MP).",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum|s__Varibaculum cambriense",3379134|976|200643|171549|171550|239759|626932;3379134|976|200643|171549|815|816|246787;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|329854;3379134|976|200643|171549|815|816|291645;3379134|976|200643|171549|815|816|291644;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|371601;3379134|976|200643|171549|1853231|574697|1969738;3379134|976|200643|171549|1853231|574697|544645;3379134|1224|1236|91347|543|544|546;1783272|1239|186801|186802|31979|1485|1502;1783272|1239|186801|3085636|186803|2719313|1531;1783272|1239|91061|186826|81852|1350|1352;3379134|976|200643|171549|2005525|375288|46503;1783272|1239|526524|526525|2810280|3025755|29348;1783272|201174|1760|2037|2049|184869|184870,Complete,Svetlana up
bsdb:39461337/5/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 5,Germany,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Chow diet,Exclusive enteral nutrition (EEN)-like diet,Mice fed with exclusive enteral nutrition (EEN)-like diet for 4 weeks after getting Fecal microbiota from MP3 (Model Patient 3),NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S9B,2 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe analysis of differentially abundant bacteria at species level based on metagenomic data in mouse experiments from MP1- MP3 (including relapse) based on mouse diet.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Niameybacter|s__Niameybacter massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella effluvii,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus avium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium paraputrificum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus|s__Proteus mirabilis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus casseliflavus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus hirae",1783272|1239|186801|186802|31979|1485|1522;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|3085636|186803|1973274|1658108;1783272|1239|186801|3085636|186803|1649459|1096246;1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|186801|186802|216572|946234|292800;3379134|1224|1236|135625|712|724|729;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|81852|1350|33945;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|91061|186826|1300|1301|1302;1783272|1239|91061|186826|81852|1350|35783;1783272|1239|186801|186802|31979|1485|29363;1783272|1239|526524|526525|2810280|3025755|29348;3379134|1224|1236|91347|1903414|583|584;1783272|1239|91061|186826|81852|1350|37734;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|186801|186802|31979|1485|1502;1783272|1239|91061|186826|81852|1350|1354,Complete,Svetlana up
bsdb:39461337/5/2,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 5,Germany,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Chow diet,Exclusive enteral nutrition (EEN)-like diet,Mice fed with exclusive enteral nutrition (EEN)-like diet for 4 weeks after getting Fecal microbiota from MP3 (Model Patient 3),NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S9B,2 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",LEfSe analysis of differentially abundant bacteria at species level based on metagenomic data in mouse experiments from MP1- MP3 (including relapse) based on mouse diet.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas sp.,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella grimontii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. infantis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes sp.,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei",3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|815|816|28111;3379134|976|200643|171549|815|816|46506;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171550|239759|214856;1783272|1239|186801|3085636|186803|207244|105841;3379134|976|200643|171549|815|816|674529;1783272|1239|186801|186802|1392389|1297617;3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|1853231|574697|1969738;1783272|1239|526524|526525|2810280|100883|100884;3379134|976|200643|171549|815|909656|204516;3379134|1224|1236|91347|543|544|546;3379134|976|200643|171549|815|816|338188;3379134|1224|1236|91347|543|570|2058152;1783272|1239|186801|3085636|186803|1506553|29347;3379134|976|200643|171549|1853231|574697|544645;3379134|976|200643|171549|171550|239759|28117;3379134|1224|28216|80840|995019|40544|40545;1783272|201174|1760|85004|31953|1678|216816|1682;3379134|976|200643|171549|815|816|626929;1783272|1239|186801|186802|216572|1905344|1550024;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|207244|1872530;3379134|200940|3031449|213115|194924|35832|35833;3379134|976|200643|171549|815|816|371601;1783272|1239|186801|3085636|186803|2719313|208479;3379134|976|200643|171549|815|816|820;1783272|1239|186801|3085636|186803|2719313|1531;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|909656|357276,Complete,Svetlana up
bsdb:39461337/6/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 6,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Unsorted cells,Ethanol (EtOH),Model Patient 1 (MP1) samples dissolved in ethanol.,NA,NA,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2E,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significantly enriched zOTUs in MP1.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,3379134|1224|1236|91347|543|561|562,Complete,Svetlana up
bsdb:39461337/7/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 7,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Unsorted cells,Lauric Acid (LA),Model Patient 1 (MP1) samples after exposure to Lauric Acid (LA).,NA,NA,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2E,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significantly enriched zOTUs in MP1.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,3379134|1224|1236|91347|543|561|562,Complete,Svetlana up
bsdb:39461337/8/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 8,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Unsorted cells,Decanoic Acid (DA),Model Patient 1 (MP1) samples after exposure to Decanoic Acid (DA).,NA,NA,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2E,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significantly enriched zOTUs in MP1.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,3379134|1224|1236|91347|543|561|562,Complete,Svetlana up
bsdb:39461337/9/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 9,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Unsorted cells,Octanoic Acid (OA),Model Patient 1 (MP1) samples after exposure to Octanoic Acid (OA).,NA,NA,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2E,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significantly enriched zOTUs in MP1,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,3379134|1224|1236|91347|543|561|562,Complete,Svetlana up
bsdb:39461337/10/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 10,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Ethanol (EtOH),Lauric Acid (LA),Model Patient 1 (MP1) samples after exposure to Lauric Acid (LA).,NA,NA,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2E,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significantly enriched zOTUs in MP1,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,3379134|1224|1236|91347|543|561|562,Complete,Svetlana up
bsdb:39461337/11/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 11,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Ethanol (EtOH),Decanoic Acid (DA),Model Patient 1 (MP1) samples after exposure to Decanoic Acid (DA).,NA,NA,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2E,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significantly enriched zOTUs in MP1.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,3379134|1224|1236|91347|543|561|562,Complete,Svetlana up
bsdb:39461337/12/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 12,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Ethanol (EtOH),Octanoic Acid (OA),Model Patient 1 (MP1) samples after exposure to Octanoic Acid (OA).,NA,NA,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2E,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significantly enriched zOTUs in MP1,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|1224|1236|91347|543|561|562;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:39461337/13/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 13,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Unsorted cells,Ethanol (EtOH),Model Patient 3 (MP3) samples dissolved in ethanol.,NA,NA,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2E,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significantly enriched zOTUs in MP3.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,3379134|1224|1236|91347|543|561|562,Complete,Svetlana up
bsdb:39461337/14/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 14,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Unsorted cells,Lauric Acid (LA),Model Patient 3 (MP3) samples after exposure to Lauric Acid (LA).,NA,NA,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2E,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significantly enriched zOTUs in MP3.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,3379134|1224|1236|91347|543|561|562,Complete,Svetlana up
bsdb:39461337/15/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 15,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Unsorted cells,Decanoic Acid (DA),Model Patient 3 (MP3) samples after exposure to Decanoic Acid (DA).,NA,NA,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2E,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significantly enriched zOTUs in MP3.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,3379134|1224|1236|91347|543|561|562,Complete,Svetlana up
bsdb:39461337/16/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 16,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Unsorted cells,Octanoic Acid (OA),Model Patient 3 (MP3) samples after exposure to Octanoic Acid (OA).,NA,NA,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2E,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significantly enriched zOTUs in MP3.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,3379134|1224|1236|91347|543|561|562,Complete,Svetlana up
bsdb:39461337/17/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 17,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Ethanol (EtOH),Octanoic Acid (OA),Model Patient 3 (MP3) samples after exposure to Octanoic Acid (OA).,NA,NA,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2E,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significantly enriched zOTUs in MP3.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,3379134|1224|1236|91347|543|561|562,Complete,Svetlana up
bsdb:39461337/18/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 18,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Unsorted cells,Ethanol (EtOH),Model Patient 2 (MP2) samples dissolved in ethanol.,NA,NA,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2E,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significantly enriched and depleted zOTUs in MP2.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,1783272|1239|186801|3082720|186804|1257|1261,Complete,Svetlana up
bsdb:39461337/18/2,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 18,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Unsorted cells,Ethanol (EtOH),Model Patient 2 (MP2) samples dissolved in ethanol.,NA,NA,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2E,2 January 2025,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significantly enriched and depleted zOTUs in MP2.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus",1783272|1239|186801|3085636|186803|1506553|29347;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|186801|186802|216572|1905344|1550024;3379134|976|200643|171549|815|909656|821,Complete,NA
bsdb:39461337/19/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 19,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Unsorted cells,Lauric Acid (LA),Model Patient 2 (MP2) samples after exposure to Lauric Acid (LA).,NA,NA,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2E,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significantly enriched and depleted zOTUs in MP2.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta",1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|2719313|358742;1783272|201174|84998|1643822|1643826|84111|84112,Complete,Svetlana up
bsdb:39461337/19/2,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 19,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Unsorted cells,Lauric Acid (LA),Model Patient 2 (MP2) samples after exposure to Lauric Acid (LA).,NA,NA,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2E,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significantly enriched and depleted zOTUs in MP2.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens",1783272|1239|186801|3085636|186803|1649459|2763050;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|186801|3085636|186803|1506553|29347,Complete,Svetlana up
bsdb:39461337/20/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 20,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Unsorted cells,Decanoic Acid (DA),Model Patient 2 (MP2) samples after exposure to Decanoic Acid (DA).,NA,NA,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2E,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significantly enriched and depleted zOTUs in MP2.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis",1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|2719313|358742,Complete,Svetlana up
bsdb:39461337/20/2,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 20,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Unsorted cells,Decanoic Acid (DA),Model Patient 2 (MP2) samples after exposure to Decanoic Acid (DA).,NA,NA,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2E,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significantly enriched and depleted zOTUs in MP2.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius",1783272|1239|186801|3085636|186803|1649459|2763050;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|186801|3085636|186803|1506553|29347;1783272|1239|186801|3082720|186804|1257|1261,Complete,Svetlana up
bsdb:39461337/21/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 21,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Unsorted cells,Octanoic Acid (OA),Model Patient 2 (MP2) samples after exposure to Octanoic Acid (OA).,NA,NA,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2E,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significantly enriched and depleted zOTUs in MP2.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae",1783272|1239|186801|3085636|186803|2719313|358742;1783272|1239|186801|3085636|186803|2719313|208479,Complete,Svetlana up
bsdb:39461337/21/2,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 21,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Unsorted cells,Octanoic Acid (OA),Model Patient 2 (MP2) samples after exposure to Octanoic Acid (OA).,NA,NA,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2E,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significantly enriched and depleted zOTUs in MP2.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens",1783272|1239|186801|3085636|186803|1649459|2763050;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|186801|3085636|186803|1506553|29347,Complete,Svetlana up
bsdb:39461337/22/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 22,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Ethanol (EtOH),Lauric Acid (LA),Model Patient 2 (MP2) samples after exposure to Lauric Acid (LA).,NA,NA,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2E,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significantly enriched and depleted zOTUs in MP2.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta",1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|2719313|358742;1783272|201174|84998|1643822|1643826|84111|84112,Complete,Svetlana up
bsdb:39461337/22/2,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 22,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Ethanol (EtOH),Lauric Acid (LA),Model Patient 2 (MP2) samples after exposure to Lauric Acid (LA).,NA,NA,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2E,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significantly enriched and depleted zOTUs in MP2.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,1783272|1239|186801|3082720|186804|1257|1261,Complete,Svetlana up
bsdb:39461337/23/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 23,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Ethanol (EtOH),Decanoic Acid (DA),Model Patient 2 (MP2) samples after exposure to Decanoic Acid (DA).,NA,NA,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2E,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significantly enriched and depleted zOTUs in MP2.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis",1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|2719313|358742,Complete,Svetlana up
bsdb:39461337/23/2,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 23,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Ethanol (EtOH),Decanoic Acid (DA),Model Patient 2 (MP2) samples after exposure to Decanoic Acid (DA).,NA,NA,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2E,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significantly enriched and depleted zOTUs in MP2.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens",1783272|1239|186801|3082720|186804|1257|1261;1783272|1239|186801|3085636|186803|1506553|29347,Complete,Svetlana up
bsdb:39461337/24/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 24,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Ethanol (EtOH),Octanoic Acid (OA),Model Patient 2 (MP2) samples after exposure to Octanoic Acid (OA).,NA,NA,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2E,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significantly enriched and depleted zOTUs in MP2.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis",1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|2719313|358742,Complete,Svetlana up
bsdb:39461337/24/2,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 24,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Ethanol (EtOH),Octanoic Acid (OA),Model Patient 2 (MP2) samples after exposure to Octanoic Acid (OA).,NA,NA,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2E,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significantly enriched and depleted zOTUs in MP2.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa",1783272|1239|186801|3085636|186803|1649459|2763050;1783272|1239|186801|3082720|186804|1257|1261;1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|526524|526525|2810280|3025755|1547,Complete,Svetlana up
bsdb:39461337/25/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 25,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Unsorted cells,Lauric Acid (LA),Model Patient 2 (MP2) relapse samples after exposure to Lauric Acid (LA).,NA,19,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S4,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significant enriched and depleted zOTUs in MP2 relapse,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens",1783272|1239|909932|1843489|31977|39948|218538;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803|1506553|29347,Complete,Svetlana up
bsdb:39461337/25/2,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 25,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Unsorted cells,Lauric Acid (LA),Model Patient 2 (MP2) relapse samples after exposure to Lauric Acid (LA).,NA,19,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S4,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significant enriched and depleted zOTUs in MP2 relapse,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hominenteromicrobium|s__Hominenteromicrobium mulieris,1783272|1239|186801|186802|216572|3073575|2885357,Complete,Svetlana up
bsdb:39461337/26/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 26,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Unsorted cells,Decanoic Acid (DA),Model Patient 2 (MP2) relapse samples after exposure to Decanoic Acid (DA).,NA,19,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S4,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significant enriched and depleted zOTUs in MP2 relapse.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,3379134|1224|1236|91347|543|561|562,Complete,Svetlana up
bsdb:39461337/26/2,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 26,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Unsorted cells,Decanoic Acid (DA),Model Patient 2 (MP2) relapse samples after exposure to Decanoic Acid (DA).,NA,19,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S4,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significant enriched and depleted zOTUs in MP2 relapse.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hominenteromicrobium|s__Hominenteromicrobium mulieris",1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|186801|186802|216572|3073575|2885357,Complete,Svetlana up
bsdb:39461337/27/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 27,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Unsorted cells,Octanoic Acid (OA),Model Patient 2 (MP2) relapse samples after exposure to Octanoic Acid (OA).,NA,20,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S4,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significant enriched and depleted zOTUs in MP2 relapse.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus",3379134|1224|1236|91347|543|561|562;1783272|1239|909932|1843489|31977|39948|218538,Complete,Svetlana up
bsdb:39461337/27/2,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 27,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Unsorted cells,Octanoic Acid (OA),Model Patient 2 (MP2) relapse samples after exposure to Octanoic Acid (OA).,NA,20,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S4,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significant enriched and depleted zOTUs in MP2 relapse.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hominenteromicrobium|s__Hominenteromicrobium mulieris",1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|186801|186802|216572|3073575|2885357,Complete,Svetlana up
bsdb:39461337/28/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 28,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Ethanol (EtOH),Lauric Acid (LA),Model Patient 2 (MP2) samples after exposure to Lauric Acid (LA).,20,19,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S4,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significant enriched and depleted zOTUs in MP2 relapse.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens",1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803|1506553|29347,Complete,Svetlana up
bsdb:39461337/29/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 29,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Ethanol (EtOH),Decanoic Acid (DA),Model Patient 2 (MP2) samples after exposure to Decanoic Acid (DA).,20,19,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S4,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significant enriched and depleted zOTUs in MP2 relapse.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,3379134|1224|1236|91347|543|561|562,Complete,Svetlana up
bsdb:39461337/29/2,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 29,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Ethanol (EtOH),Decanoic Acid (DA),Model Patient 2 (MP2) samples after exposure to Decanoic Acid (DA).,20,19,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S4,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significant enriched and depleted zOTUs in MP2 relapse.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hominenteromicrobium|s__Hominenteromicrobium mulieris",1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|186801|186802|216572|3073575|2885357,Complete,Svetlana up
bsdb:39461337/30/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 30,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Ethanol (EtOH),Octanoic Acid (OA),Model Patient 2 (MP2) relapse samples after exposure to Octanoic Acid (OA).,20,20,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S4,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significant enriched and depleted zOTUs in MP2 relapse.,increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,1783272|1239|909932|1843489|31977|39948|218538,Complete,Svetlana up
bsdb:39461337/30/2,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 30,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Ethanol (EtOH),Octanoic Acid (OA),Model Patient 2 (MP2) relapse samples after exposure to Octanoic Acid (OA).,20,20,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S4,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significant enriched and depleted zOTUs in MP2 relapse.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hominenteromicrobium|s__Hominenteromicrobium mulieris,1783272|1239|186801|186802|216572|3073575|2885357,Complete,Svetlana up
bsdb:39461337/31/1,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 31,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Unsorted cells,Ethanol (EtOH),Model Patient 2 (MP2) relapse samples dissolved in ethanol.,NA,20,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S4,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significant enriched and depleted zOTUs in MP2 relapse.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,3379134|1224|1236|91347|543|561|562,Complete,Svetlana up
bsdb:39461337/31/2,39461337,time series / longitudinal observational,39461337,10.1016/j.chom.2024.10.001,NA,"Häcker D., Siebert K., Smith B.J., Köhler N., Riva A., Mahapatra A., Heimes H., Nie J., Metwaly A., Hölz H., Manz Q., De Zen F., Heetmeyer J., Socas K., Le Thi G., Meng C., Kleigrewe K., Pauling J.K., Neuhaus K., List M., Pollard K.S., Schwerd T. , Haller D.",Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease,Cell host & microbe,2024,"EEN, FMT, bacterial strain dynamics, exclusive enteral nutrition, ex vivo gut chemostat model, fiber, medium-chain fatty acids, metagenomics, microbiome, multi-omics data integration, pediatric Crohn’s disease",Experiment 31,Germany,Mus musculus,Feces,UBERON:0001988,Exposure,EFO:0000487,Unsorted cells,Ethanol (EtOH),Model Patient 2 (MP2) relapse samples dissolved in ethanol.,NA,20,NA,WMS,NA,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S4,18 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Relative abundances of significant enriched and depleted zOTUs in MP2 relapse.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hominenteromicrobium|s__Hominenteromicrobium mulieris,1783272|1239|186801|186802|216572|3073575|2885357,Complete,Svetlana up
bsdb:39468434/1/1,39468434,case-control,39468434,10.1186/s12866-024-03529-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-024-03529-5#data-availability,"Kumar S., Mahajan S., Kale D., Chourasia N., Khan A., Asati D., Kotnis A. , Sharma V.K.",Insights into the gut microbiome of vitiligo patients from India,BMC microbiology,2024,"Autoimmune disease, Dysbiosis, Gut Microbiome, Gut-skin axis, Vitiligo",Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Vitiligo,EFO:0004208,Healthy Control,Vitiligo Patients,Patients diagnosed with Vitiligo,10,22,NA,16S,3,Illumina,relative abundances,LEfSe,NA,NA,2,"age,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Table S7,15 November 2024,Shulamite,"Shulamite,Ifeanyisam,WikiWorks",Differentially abundant  genera and species identified by LEfSe analysis in the control and vitiligo groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri",3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|2974251|165179,Complete,Svetlana up
bsdb:39468434/1/2,39468434,case-control,39468434,10.1186/s12866-024-03529-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-024-03529-5#data-availability,"Kumar S., Mahajan S., Kale D., Chourasia N., Khan A., Asati D., Kotnis A. , Sharma V.K.",Insights into the gut microbiome of vitiligo patients from India,BMC microbiology,2024,"Autoimmune disease, Dysbiosis, Gut Microbiome, Gut-skin axis, Vitiligo",Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Vitiligo,EFO:0004208,Healthy Control,Vitiligo Patients,Patients diagnosed with Vitiligo,10,22,NA,16S,3,Illumina,relative abundances,LEfSe,NA,NA,2,"age,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Table S7,15 November 2024,Shulamite,"Shulamite,Ifeanyisam,WikiWorks",Differentially abundant genera and species identified by LEfSe analysis in the control and vitiligo groups.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum soehngenii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Caecibacter,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Nanosynbacterales|f__Candidatus Nanosynbacteraceae|g__Candidatus Nanosynbacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Cellvibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|g__Exiguobacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kosakonia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Lactimicrobium|s__Lactimicrobium massiliense,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Paraclostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parafannyhessea,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parafannyhessea|s__Parafannyhessea umbonata,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Pectobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Pectobacterium|s__Pectobacterium parmentieri,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Peptidiphaga,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Pseudonocardia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pygmaiobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Reyranellaceae|g__Reyranella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia ilealis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Paraclostridium|s__Paraclostridium sordellii",1783272|1239|186801|3085636|186803|2569097;1783272|1239|186801|3085636|186803|2569097|105843;1783272|1239|526524|526525|128827|118747;1783272|1239|909932|1843489|31977|1980685;95818|2093818|2093819|2093822|2093823;3379134|976|117743|200644|49546|1016;3379134|1224|1236|1706369|1706371|10;1783272|1239|186801|3082720|186804|1870884;1783272|1239|186801|3082720|186804|1870884|1496;3379134|1224|1236|91347|543|547|158836;1783272|1239|186801|186802|186806|1730;1783272|1239|91061|1385|33986;3379134|976|117743|200644|49546|237;1783272|1239|91061|1385|539738|1378;1783272|1239|186801|186802|404402;1783272|1239|186801|186802|404402|404403;3379134|1224|28216|206351|481|32257;3379134|1224|1236|91347|543|1330547;1783272|1239|186801|3085636|186803|28050;1783272|1239|526524|526525|128827|2563777|2161814;1783272|1239|186801|3082720|186804|1849822;1783272|201174|84998|84999|1643824|2847312;1783272|201174|84998|84999|1643824|2847312|604330;3379134|1224|1236|91347|1903410|122277;3379134|1224|1236|91347|1903410|122277|1905730;1783272|201174|1760|2037|2049|2739835;1783272|1239|186801|3082720|186804|1257|341694;3379134|1224|1236|72274|135621|286;1783272|201174|1760|85010|2070|1847;1783272|1239|186801|186802|216572|1929305;3379134|1224|28211|356|2844375|445219;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3082720|186804|1501226|1507512;1783272|1239|186801|3082720|186804|1501226|1115758;3379134|1224|1236|91347|543|547;1783272|1239|186801|3082720|186804|1849822|1505,Complete,Svetlana up
bsdb:39468837/1/1,39468837,"cross-sectional observational, not case-control",39468837,10.1080/19490976.2024.2418984,https://doi.org/10.1080/19490976.2024.2418984,"Wan Y., Wong O.W.H., Tun H.M., Su Q., Xu Z., Tang W., Ma S.L., Chan S., Chan F.K.L. , Ng S.C.",Fecal microbial marker panel for aiding diagnosis of autism spectrum disorders,Gut microbes,2024,"Autism spectrum disorder, bacteria, diagnosis, microbiome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Typical Developing (TD) Children,Autism Spectrum Disorder (ASD) Children,Children with a clinician-confirmed diagnosis of ASD based on the DSM-4 or DSM-5 diagnostic criteria.,144,129,1 month,WMS,NA,Illumina,centered log-ratio,ANCOM,0.05,FALSE,NA,"age,sex","age,body mass index,sex",unchanged,unchanged,NA,NA,NA,increased,Signature 1,Table S3,16 October 2025,Kyaw,Kyaw,Significant differential abundant bacteria between Children with autism spectrum disorder and typically developing controls.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",3379134|976|200643|171549|815|816|291645;1783272|1239|186801|186802|31979|1485,Complete,KateRasheed
bsdb:39468837/1/2,39468837,"cross-sectional observational, not case-control",39468837,10.1080/19490976.2024.2418984,https://doi.org/10.1080/19490976.2024.2418984,"Wan Y., Wong O.W.H., Tun H.M., Su Q., Xu Z., Tang W., Ma S.L., Chan S., Chan F.K.L. , Ng S.C.",Fecal microbial marker panel for aiding diagnosis of autism spectrum disorders,Gut microbes,2024,"Autism spectrum disorder, bacteria, diagnosis, microbiome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Typical Developing (TD) Children,Autism Spectrum Disorder (ASD) Children,Children with a clinician-confirmed diagnosis of ASD based on the DSM-4 or DSM-5 diagnostic criteria.,144,129,1 month,WMS,NA,Illumina,centered log-ratio,ANCOM,0.05,FALSE,NA,"age,sex","age,body mass index,sex",unchanged,unchanged,NA,NA,NA,increased,Signature 2,Table S3,16 October 2025,Kyaw,Kyaw,Significant differential abundant bacteria between Children with autism spectrum disorder and typically developing controls.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica",1783272|1239|91061|1385|539738|1378|29391;1783272|1239|91061|186826|1300|1357;1783272|201174|1760|2037|2049|2529408|1660,Complete,KateRasheed
bsdb:39469457/1/1,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 1,Australia,Homo sapiens,Rectum,UBERON:0001052,Ulcerative colitis,EFO:0000729,Controls (rectum),Ulcerative colitis patients (UC) (rectum),"Individuals with the inflammatory bowel disease (IBD), Ulcerative colitis patients (UC).",22,28,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2B, Supplementary Table 3",1 May 2025,Tosin,Tosin,"Biogeography of significantly enriched and depleted bacterial genera in (ulcerative colitis) UC patients (rectum samples) relative to controls, across the lower (gastrointestinal) GI tract, measured in terms of relative abundance [upper and lower gastrointestinal (GI) tract]",increased,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,1783272|1239|1737404|1737405|1570339|165779,Complete,KateRasheed
bsdb:39469457/1/2,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 1,Australia,Homo sapiens,Rectum,UBERON:0001052,Ulcerative colitis,EFO:0000729,Controls (rectum),Ulcerative colitis patients (UC) (rectum),"Individuals with the inflammatory bowel disease (IBD), Ulcerative colitis patients (UC).",22,28,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2B, Supplementary Table 3",1 May 2025,Tosin,Tosin,"Biogeography of significantly enriched and depleted bacterial genera in (ulcerative colitis) UC patients (rectum samples) relative to controls, across the lower (gastrointestinal) GI tract, measured in terms of relative abundance [upper and lower gastrointestinal (GI) tract]",decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|1263,Complete,KateRasheed
bsdb:39469457/2/1,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 2,Australia,Homo sapiens,Right colon,UBERON:0008972,Ulcerative colitis,EFO:0000729,Controls (right colon),Ulcerative colitis patients (UC) (right colon),"Individuals with the inflammatory bowel disease (IBD), Ulcerative colitis patients (UC).",21,22,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2B and Supplementary Table 3,1 May 2025,Tosin,Tosin,"Biogeography of significantly enriched and depleted bacterial genera in (Ulcerative colitis) UC patients [right colon (RC) samples] relative to controls, across the lower (gastrointestinal) GI tract, measured in terms of relative abundance [upper and lower gastrointestinal (GI) tract]",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|1224|1236|91347|543|1940338;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|437755;1783272|1239|526524|526525|2810280|3025755;1783272|1239|909932|1843489|31977|29465,Complete,KateRasheed
bsdb:39469457/2/2,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 2,Australia,Homo sapiens,Right colon,UBERON:0008972,Ulcerative colitis,EFO:0000729,Controls (right colon),Ulcerative colitis patients (UC) (right colon),"Individuals with the inflammatory bowel disease (IBD), Ulcerative colitis patients (UC).",21,22,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2B, Supplementary Table 3",1 May 2025,Tosin,Tosin,"Biogeography of significantly enriched and depleted bacterial genera in (ulcerative colitis) UC patients [right colon (RC) samples] relative to controls, across the lower (gastrointestinal) GI tract, measured in terms of relative abundance [upper and lower gastrointestinal (GI) tract]",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",1783272|1239|186801|3085636|186803|207244;1783272|1239|909932|1843488|909930|33024,Complete,KateRasheed
bsdb:39469457/3/1,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 3,Australia,Homo sapiens,Ileum,UBERON:0002116,Ulcerative colitis,EFO:0000729,Controls (Terminal ileum),Ulcerative colitis patients (UC) (Terminal ileum),"Individuals with the inflammatory bowel disease (IBD), Ulcerative colitis patients (UC).",24,41,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2B, Supplementary Table 3",1 May 2025,Tosin,Tosin,"Biogeography of significantly enriched and depleted bacterial genera in (ulcerative colitis) UC patients [Terminal ileum (TI) samples] relative to controls, across the lower (gastrointestinal) GI tract, measured in terms of relative abundance [upper and lower gastrointestinal (GI) tract]",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|437755;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|186802|216572|707003,Complete,KateRasheed
bsdb:39469457/3/2,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 3,Australia,Homo sapiens,Ileum,UBERON:0002116,Ulcerative colitis,EFO:0000729,Controls (Terminal ileum),Ulcerative colitis patients (UC) (Terminal ileum),"Individuals with the inflammatory bowel disease (IBD), Ulcerative colitis patients (UC).",24,41,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2B, Supplementary Table 3",1 May 2025,Tosin,Tosin,"Biogeography of significantly enriched and depleted bacterial genera in (ulcerative colitis) UC patients [Terminal ileum (TI) samples] relative to controls, across the lower (gastrointestinal) GI tract, measured in terms of relative abundance [upper and lower gastrointestinal (GI) tract]",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|572511,Complete,KateRasheed
bsdb:39469457/4/1,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 4,Australia,Homo sapiens,Duodenum,UBERON:0002114,Crohn's disease,EFO:0000384,Controls (duodenum),Crohn’s disease (CD) (duodenum),"Individuals with the inflammatory bowel disease (IBD), Crohn’s disease (CD)",41,21,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2A, Supplementary Table 3",1 May 2025,Tosin,Tosin,"Biogeography of significantly enriched and depleted bacterial genera in Crohn’s disease (CD) patients [duodenum samples (DU) ] relative to controls, across the lower (gastrointestinal) GI tract, measured in terms of relative abundance [upper and lower gastrointestinal (GI) tract]",increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacillati|p__Cyanobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",3379134|976|117743|200644|2762318|59735;3379134|1224|28211|356|41294|374;1783272|1117;3384189|32066|203490|203491|1129771|32067;3379134|203691|203692|136|2845253|157,Complete,KateRasheed
bsdb:39469457/4/2,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 4,Australia,Homo sapiens,Duodenum,UBERON:0002114,Crohn's disease,EFO:0000384,Controls (duodenum),Crohn’s disease (CD) (duodenum),"Individuals with the inflammatory bowel disease (IBD), Crohn’s disease (CD)",41,21,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2A, Supplementary Table 3",2 May 2025,Tosin,Tosin,"Biogeography of significantly enriched and depleted bacterial genera in Crohn’s disease (CD) patients [duodenum samples (DU) ] relative to controls, across the lower (gastrointestinal) GI tract, measured in terms of relative abundance [upper and lower gastrointestinal (GI) tract]",decreased,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,3379134|1224|28211|204457|41297|13687,Complete,KateRasheed
bsdb:39469457/5/1,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 5,Australia,Homo sapiens,Mucosa of pyloric antrum,UBERON:0004997,Crohn's disease,EFO:0000384,Controls (gastric antrum),Crohn’s disease (CD) (gastric antrum),"Individuals with the inflammatory bowel disease (IBD), Crohn’s disease (CD)",32,20,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2A, Supplementary Table 3",1 May 2025,Tosin,Tosin,"Biogeography of significantly enriched and depleted bacterial genera in Crohn’s disease (CD) patients [gastric antrum (G) samples] relative to controls, across the lower (gastrointestinal) GI tract, measured in terms of relative abundance [upper and lower gastrointestinal (GI) tract]",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",1783272|1239|909932|1843489|31977|906;3379134|1224|28216|206351|481;3379134|976|200643|171549|2005525|195950,Complete,KateRasheed
bsdb:39469457/5/2,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 5,Australia,Homo sapiens,Mucosa of pyloric antrum,UBERON:0004997,Crohn's disease,EFO:0000384,Controls (gastric antrum),Crohn’s disease (CD) (gastric antrum),"Individuals with the inflammatory bowel disease (IBD), Crohn’s disease (CD)",32,20,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2A, Supplementary Table 3",1 May 2025,Tosin,Tosin,"Biogeography of significantly enriched and depleted bacterial genera in Crohn’s disease (CD) patients [gastric antrum (G) samples] relative to controls, across the lower (gastrointestinal) GI tract, measured in terms of relative abundance [upper and lower gastrointestinal (GI) tract]",decreased,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,3379134|29547|3031852|213849|72293|209,Complete,KateRasheed
bsdb:39469457/6/1,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 6,Australia,Homo sapiens,Esophagus,UBERON:0001043,Crohn's disease,EFO:0000384,Controls (oesophagus),Crohn’s disease (CD) (oesophagus),"Individuals with the inflammatory bowel disease (IBD), Crohn’s disease (CD)",30,21,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2A, Supplementary Table 3",1 May 2025,Tosin,Tosin,"Biogeography of significantly enriched and depleted bacterial genera in Crohn’s disease (CD) patients [oesophagus (O) samples] relative to controls, across the lower (gastrointestinal) GI tract, measured in terms of relative abundance [upper and lower gastrointestinal (GI) tract]",increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",3379134|976|117743|200644|2762318|501783;1783272|1239|186801|186802,Complete,KateRasheed
bsdb:39469457/6/2,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 6,Australia,Homo sapiens,Esophagus,UBERON:0001043,Crohn's disease,EFO:0000384,Controls (oesophagus),Crohn’s disease (CD) (oesophagus),"Individuals with the inflammatory bowel disease (IBD), Crohn’s disease (CD)",30,21,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2A, Supplementary Table 3",2 May 2025,Tosin,Tosin,"Biogeography of significantly enriched and depleted bacterial genera in Crohn’s disease (CD) patients [oesophagus (O) samples] relative to controls, across the lower (gastrointestinal) GI tract, measured in terms of relative abundance [upper and lower gastrointestinal (GI) tract]",decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,1783272|1239|91061|186826,Complete,KateRasheed
bsdb:39469457/7/1,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 7,Australia,Homo sapiens,Rectum,UBERON:0001052,Crohn's disease,EFO:0000384,Controls (rectum),Crohn’s disease (CD) (rectum),"Individuals with the inflammatory bowel disease (IBD), Crohn’s disease (CD)",22,4,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2A, Supplementary Table 3",1 May 2025,Tosin,Tosin,"Biogeography of significantly enriched and depleted bacterial genera in Crohn’s disease (CD) patients [rectum (R) samples] relative to controls, across the lower (gastrointestinal) GI tract, measured in terms of relative abundance [upper and lower gastrointestinal (GI) tract]",increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",3379134|200940|3031449|213115|194924|35832;3379134|976|200643|171549|2005519|1348911;1783272|1239|909932|1843489|31977|39948;1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|3085636|186803|437755;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|186802|216572|707003,Complete,KateRasheed
bsdb:39469457/7/2,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 7,Australia,Homo sapiens,Rectum,UBERON:0001052,Crohn's disease,EFO:0000384,Controls (rectum),Crohn’s disease (CD) (rectum),"Individuals with the inflammatory bowel disease (IBD), Crohn’s disease (CD)",22,4,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2A, Supplementary Table 3",1 May 2025,Tosin,Tosin,"Biogeography of significantly enriched and depleted bacterial genera in Crohn’s disease (CD) patients [rectum (R) samples] relative to controls, across the lower (gastrointestinal) GI tract, measured in terms of relative abundance [upper and lower gastrointestinal (GI) tract]",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|216851;3379134|1224|28216|80840|995019|40544,Complete,KateRasheed
bsdb:39469457/8/1,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 8,Australia,Homo sapiens,Right colon,UBERON:0008972,Crohn's disease,EFO:0000384,Controls (right colon),Crohn’s disease (CD) (right colon),"Individuals with the inflammatory bowel disease (IBD), Crohn’s disease (CD)",21,3,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2A, Supplementary Table 3",2 May 2025,Tosin,Tosin,Biogeography of significantly enriched and depleted bacterial genera in Crohn’s disease (CD) patients [right colon (RC) samples],increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",1783272|1239|1737404|1737405|1570339|165779;3379134|200940|3031449|213115|194924|35832;3379134|976|200643|171549|2005519|1348911;1783272|1239|186801|3085636|186803|437755;1783272|1239|186801|3085636|186803|2316020|33039,Complete,KateRasheed
bsdb:39469457/8/2,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 8,Australia,Homo sapiens,Right colon,UBERON:0008972,Crohn's disease,EFO:0000384,Controls (right colon),Crohn’s disease (CD) (right colon),"Individuals with the inflammatory bowel disease (IBD), Crohn’s disease (CD)",21,3,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2A, Supplementary Table 3",2 May 2025,Tosin,Tosin,"Biogeography of significantly enriched and depleted bacterial genera in Crohn’s disease (CD) patients [right colon (RC) samples] relative to controls, across the lower (gastrointestinal) GI tract, measured in terms of relative abundance [upper and lower gastrointestinal (GI) tract]",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|216572|216851,Complete,KateRasheed
bsdb:39469457/9/1,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 9,Australia,Homo sapiens,Ileum,UBERON:0002116,Crohn's disease,EFO:0000384,Controls (Terminal ileum),Crohn’s disease (CD) (Terminal ileum),"Individuals with the inflammatory bowel disease (IBD), Crohn’s disease (CD)",24,12,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2A, Supplementary Table 3",2 May 2025,Tosin,Tosin,"Biogeography of significantly enriched and depleted bacterial genera in Crohn’s disease (CD) patients [terminal ileum (TI) samples ] relative to controls, across the lower (gastrointestinal) GI tract, measured in terms of relative abundance [upper and lower gastrointestinal (GI) tract]",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819",1783272|1239|909932|1843488|909930|904;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|1980681;1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|186802|216572|946234;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|186802|31979|1485|1522;1783272|1239|186801|3085636|186803|297314;1783272|1239|186801|186802|216572|216851|1946507,Complete,KateRasheed
bsdb:39469457/9/2,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 9,Australia,Homo sapiens,Ileum,UBERON:0002116,Crohn's disease,EFO:0000384,Controls (Terminal ileum),Crohn’s disease (CD) (Terminal ileum),"Individuals with the inflammatory bowel disease (IBD), Crohn’s disease (CD)",24,12,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2A, Supplementary Table 3",2 May 2025,Tosin,Tosin,"Biogeography of significantly enriched and depleted bacterial genera in Crohn’s disease (CD) patients [terminal ileum (TI) samples ] relative to controls, across the lower (gastrointestinal) GI tract, measured in terms of relative abundance [upper and lower gastrointestinal (GI) tract]",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|216572|216851;1783272|201174|84998|84999|84107|102106,Complete,KateRasheed
bsdb:39469457/10/1,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 10,Australia,Homo sapiens,"Ileum,Right colon,Rectum","UBERON:0001052,UBERON:0002116,UBERON:0008972",Crohn's disease,EFO:0000384,Controls (lower gastrointestinal tract),Crohn’s disease (CD) (lower gastrointestinal tract),"Individuals with the inflammatory bowel disease (IBD), Crohn’s disease (CD) across the lower gastrointestinal tract",16,10,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3C,3 May 2025,Tosin,Tosin,"Significantly enriched and depleted bacterial genera in the Comparison of the microbiome composition of CD patients and controls, as measured by relative abundance (lower GI tract).",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas",3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|186801|186802|3085642|580596;3379134|976|200643|171549|2005525|375288;;1783272|201174|84998|1643822|1643826|84111;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|1980681;1783272|1239|186801|3085636|186803|297314;1783272|1239|909932|1843488|909930|904;1783272|1239|186801|3085636|186803|437755;3379134|976|200643|171549|2005519|1348911;1783272|1239|526524|526525|2810280|3025755;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|216572|946234;1783272|1239|526524|526525|128827|1573534;3379134|976|200643|171549|1853231|574697,Complete,KateRasheed
bsdb:39469457/10/2,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 10,Australia,Homo sapiens,"Ileum,Right colon,Rectum","UBERON:0001052,UBERON:0002116,UBERON:0008972",Crohn's disease,EFO:0000384,Controls (lower gastrointestinal tract),Crohn’s disease (CD) (lower gastrointestinal tract),"Individuals with the inflammatory bowel disease (IBD), Crohn’s disease (CD) across the lower gastrointestinal tract",16,10,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3C,3 May 2025,Tosin,Tosin,"Significantly enriched and depleted bacterial genera in the Comparison of the microbiome composition of CD patients and controls, as measured by relative abundance (lower GI tract).",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|1239|186801|186802|31979|1485|59620;1783272|201174|84998|1643822|1643826|447020;1783272|1239|186801|3085636|186803|33042;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3082768|990719;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|216572|216851,Complete,KateRasheed
bsdb:39469457/11/1,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 11,Australia,Homo sapiens,"Ileum,Right colon,Rectum","UBERON:0002116,UBERON:0008972,UBERON:0001052",Ulcerative colitis,EFO:0000729,Controls (lower gastrointestinal tract),Ulcerative colitis patients (UC) (lower gastrointestinal tract),"Individuals with the inflammatory bowel disease (IBD), ulcerative colitis (UC) across the lower gastrointestinal tract",16,39,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3C,3 May 2025,Tosin,Tosin,"Significantly enriched and depleted bacterial genera in the Comparison of the microbiome composition of (ulcerative colitis) UC patients and controls, as measured by relative abundance (lower GI tract).",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas",1783272|201174|84998|1643822|1643826|84111;1783272|1239|909932|1843488|909930|904;1783272|1239|186801|3085636|186803|437755;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|186802|216572|946234;3379134|976|200643|171549|1853231|574697,Complete,KateRasheed
bsdb:39469457/11/2,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 11,Australia,Homo sapiens,"Ileum,Right colon,Rectum","UBERON:0002116,UBERON:0008972,UBERON:0001052",Ulcerative colitis,EFO:0000729,Controls (lower gastrointestinal tract),Ulcerative colitis patients (UC) (lower gastrointestinal tract),"Individuals with the inflammatory bowel disease (IBD), ulcerative colitis (UC) across the lower gastrointestinal tract",16,39,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,decreased,NA,NA,NA,NA,Signature 2,Figure 3C,3 May 2025,Tosin,Tosin,"Significantly enriched and depleted bacterial genera in the Comparison of the microbiome composition of (ulcerative colitis) UC patients and controls, as measured by relative abundance (lower GI tract).",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|1263;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3082768|990719;3379134|1224|28216|80840|995019|40544;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|171552|838,Complete,KateRasheed
bsdb:39469457/12/1,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 12,Australia,Homo sapiens,"Ileum,Right colon,Rectum","UBERON:0002116,UBERON:0008972,UBERON:0001052",Response to proton-pump inhibitor,EFO:0010235,Low proton pump inhibitor (PPI) (lower gastrointestinal tract),High proton pump inhibitor (PPI) (lower gastrointestinal tract),Increased proton pump inhibitor in the lower gastrointestinal tract (GI),NA,NA,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4, supplementary Table 4",3 May 2025,Tosin,Tosin,Differentially abundant bacterial taxa associated with proton pump inhibitor (PPI) usage measured by relative abundance (lower gastrointestinal tract).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|g__Negativibacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter",1783272|1239|186801|186802|216572|216851;1783272|201174|84998|84999|84107|102106;1783272|1239|1980693;3379134|976|200643|171549|2005519|1348911;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|3085636|186803|877420;3379134|976|200643|171549|1853231|283168,Complete,KateRasheed
bsdb:39469457/12/2,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 12,Australia,Homo sapiens,"Ileum,Right colon,Rectum","UBERON:0002116,UBERON:0008972,UBERON:0001052",Response to proton-pump inhibitor,EFO:0010235,Low proton pump inhibitor (PPI) (lower gastrointestinal tract),High proton pump inhibitor (PPI) (lower gastrointestinal tract),Increased proton pump inhibitor in the lower gastrointestinal tract (GI),NA,NA,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 4B, Supplementary Table 4",3 May 2025,Tosin,Tosin,Differentially abundant bacterial taxa associated with proton pump inhibitor (PPI) usage measured by relative abundance (lower gastrointestinal tract).,decreased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",3379134|200940|3031449|213115|194924|35832;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|3085636|186803|1407607;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|3085636|186803|2316020|33038,Complete,KateRasheed
bsdb:39469457/13/1,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 13,Australia,Homo sapiens,"Mucosa of pyloric antrum,Duodenum,Esophagus","UBERON:0004997,UBERON:0002114,UBERON:0001043",Response to proton-pump inhibitor,EFO:0010235,Low proton pump inhibitor (PPI) (upper gastrointestinal tract),High proton pump inhibitor (PPI) (upper gastrointestinal tract),Increased proton pump inhibitor in the upper gastrointestinal tract (GI),NA,NA,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4B, Supplementary Table 4",3 May 2025,Tosin,Tosin,Differentially abundant bacterial taxa associated with proton pump inhibitor (PPI) usage measured by relative abundance (higher gastrointestinal tract).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|1224|1236|135625|712|713;3379134|1224|1236|135625|712|416916;3379134|1224|28216|80840|506;1783272|1239|526524|526525|128827|174708;95818|2093818|2093825|2171986|1331051;3379134|976|200643|171549|2005519|1348911;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|2005473|1918540;3379134|1224|28216|206351|481|482;1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:39469457/13/2,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 13,Australia,Homo sapiens,"Mucosa of pyloric antrum,Duodenum,Esophagus","UBERON:0004997,UBERON:0002114,UBERON:0001043",Response to proton-pump inhibitor,EFO:0010235,Low proton pump inhibitor (PPI) (upper gastrointestinal tract),High proton pump inhibitor (PPI) (upper gastrointestinal tract),Increased proton pump inhibitor in the upper gastrointestinal tract (GI),NA,NA,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 4B, Supplementary Table 4",3 May 2025,Tosin,Tosin,Differentially abundant bacterial taxa associated with proton pump inhibitor (PPI) usage measured by relative abundance (higher gastrointestinal tract).,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Cellulomonadaceae|g__Cellulomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",1783272|201174|1760|85006|85016|1707;3379134|1224|1236|72274|135621|286,Complete,KateRasheed
bsdb:39469457/14/1,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 14,Australia,Homo sapiens,"Ileum,Right colon,Rectum","UBERON:0001052,UBERON:0002116,UBERON:0008972",Abnormality of the gastrointestinal tract,HP:0011024,Low structural assessment of gastrointestinal symptom (SAGIS) scores (lower gastrointestinal tract),High structural assessment of gastrointestinal symptom (SAGIS) scores (lower gastrointestinal tract),Increased structural assessment of gastrointestinal symptom (SAGIS) scores in the lower gastrointestinal tract (GI),NA,NA,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 5B, Supplementary Table 5",3 May 2025,Tosin,Tosin,Differentially abundant bacterial taxa associated with higher structured assessment of gastrointestinal symptom (SAGIS) scores measured by relative abundance (lower gastrointestinal tract).,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171552|838;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3082720|186804,Complete,KateRasheed
bsdb:39469457/14/2,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 14,Australia,Homo sapiens,"Ileum,Right colon,Rectum","UBERON:0001052,UBERON:0002116,UBERON:0008972",Abnormality of the gastrointestinal tract,HP:0011024,Low structural assessment of gastrointestinal symptom (SAGIS) scores (lower gastrointestinal tract),High structural assessment of gastrointestinal symptom (SAGIS) scores (lower gastrointestinal tract),Increased structural assessment of gastrointestinal symptom (SAGIS) scores in the lower gastrointestinal tract (GI),NA,NA,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 5B, Supplementary Table 5",3 May 2025,Tosin,Tosin,Differentially abundant bacterial taxa associated with higher structured assessment of gastrointestinal symptom (SAGIS) scores measured by relative abundance (lower gastrointestinal tract).,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii",1783272|1239|909932|1843488|909930|904;3379134|976|200643|171549|2005519|1348911;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|3082720|186804|1505657;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|186802|216572|1263|438033,Complete,KateRasheed
bsdb:39469457/15/1,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 15,Australia,Homo sapiens,"Duodenum,Mucosa of pyloric antrum,Esophagus","UBERON:0002114,UBERON:0001043,UBERON:0004997",Abnormality of the gastrointestinal tract,HP:0011024,Low structural assessment of gastrointestinal symptom (SAGIS) scores (upper gastrointestinal tract),High structural assessment of gastrointestinal symptom (SAGIS) scores (upper gastrointestinal tract),Increased structural assessment of gastrointestinal symptom (SAGIS) scores  ≥12 in the upper gastrointestinal tract (GI),NA,NA,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 5B, Supplementary Table 5",3 May 2025,Tosin,Tosin,Differentially abundant bacterial taxa associated with higher structured assessment of gastrointestinal symptom (SAGIS) scores measured by relative abundance (upper gastrointestinal tract).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Azonexaceae|g__Dechloromonas",3379134|1224|28216|206351|481|482;3379134|1224|28216|80840|2975441|93681;3379134|1224|28216|206389|2008795|73029,Complete,NA
bsdb:39469457/15/2,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 15,Australia,Homo sapiens,"Duodenum,Mucosa of pyloric antrum,Esophagus","UBERON:0002114,UBERON:0001043,UBERON:0004997",Abnormality of the gastrointestinal tract,HP:0011024,Low structural assessment of gastrointestinal symptom (SAGIS) scores (upper gastrointestinal tract),High structural assessment of gastrointestinal symptom (SAGIS) scores (upper gastrointestinal tract),Increased structural assessment of gastrointestinal symptom (SAGIS) scores  ≥12 in the upper gastrointestinal tract (GI),NA,NA,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 5B, Supplementary Table 5",3 May 2025,Tosin,Tosin,Differentially abundant bacterial taxa associated with higher structured assessment of gastrointestinal symptom (SAGIS) scores measured by relative abundance (upper gastrointestinal tract).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] brachy,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Lentimicrobiaceae|g__Lentimicrobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella",1783272|1239|186801|3082720|543314|35517;3379134|976|200643|171549|1840213|1840214;3379134|976|200643|171549|171552|838;1783272|1239|186801|3082720|3118655|44259;1783272|1239|909932|1843489|31977|906;1783272|201174|84998|84999|1643824|1380;3379134|976|200643|171549|171552|1283313,Complete,KateRasheed
bsdb:39469457/16/1,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 16,Australia,Homo sapiens,"Ileum,Right colon,Rectum","UBERON:0002116,UBERON:0008972,UBERON:0001052",Malnutrition,EFO:0008572,Low nutrient challenge (NC) total scores (lower gastrointestinal tract),High nutrient challenge (NC) total scores (lower gastrointestinal tract),"Increased nutrient challenge (NC) total scores across the lower (gastrointestinal) GI tract for (Crohn’s disease) CD patients, (ulcerative colitis) UC patients and non-IBD (non-inflammatory bowel disease) controls",NA,NA,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 6B, Supplementary Table 6",3 May 2025,Tosin,Tosin,Differentially abundant bacterial taxa associated with standardized nutrient challenge (SNC) scores measured by relative abundance,increased,",k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.",;3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|186801|3085636|186803|841;1783272|201174|84998|84999|84107|1473205;1783272|1239|186801|186802|216572|292632;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|186802|31979|1485|59620,Complete,KateRasheed
bsdb:39469457/16/2,39469457,"cross-sectional observational, not case-control",39469457,10.3389/fmicb.2024.1454910,NA,"Sternes P.R., Shah A., Ayala Pintos C., Fairlie T., Koloski N., Kang S., Tousignant K.D., McIlroy S.J., Morrison M., Tyson G.W. , Holtmann G.J.",The biogeography of the mucosa-associated microbiome in health and disease,Frontiers in microbiology,2024,"Crohn’s disease, gut-brain, microbiome, proton pump inhibitor, symptom severity, ulcerative colitis",Experiment 16,Australia,Homo sapiens,"Ileum,Right colon,Rectum","UBERON:0002116,UBERON:0008972,UBERON:0001052",Malnutrition,EFO:0008572,Low nutrient challenge (NC) total scores (lower gastrointestinal tract),High nutrient challenge (NC) total scores (lower gastrointestinal tract),"Increased nutrient challenge (NC) total scores across the lower (gastrointestinal) GI tract for (Crohn’s disease) CD patients, (ulcerative colitis) UC patients and non-IBD (non-inflammatory bowel disease) controls",NA,NA,2 months,16S,678,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 6B, Supplementary Table 6",3 May 2025,Tosin,Tosin,Differentially abundant bacterial taxa associated with standardized nutrient challenge (SNC) scores measured by relative abundance,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",3379134|976|200643|171549|2005519|397864;1783272|1239|186801|3085636|186803|207244;3379134|1224|1236|91347|543;1783272|1239|186801|186802|216572|216851,Complete,KateRasheed
bsdb:39470189/1/1,39470189,"cross-sectional observational, not case-control",39470189,10.1128/msystems.01237-24,NA,"McCune E., Sharma A., Johnson B., O'Meara T., Theiner S., Campos M., Heditsian D., Brain S., Gilbert J.A., Esserman L. , Campbell M.J.","Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma <i>in situ</i>, and healthy women",mSystems,2024,"DCIS, breast cancer, gut microbiota, oral microbiota",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,Healthy women (Control),Breast cancer (BC),"Women with early-stage of breast cancer (BC),",42,66,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,NA,3,age,NA,NA,unchanged,NA,decreased,NA,NA,Signature 1,FIG 2 (A),19 November 2024,Rahila,"Rahila,Aleru Divine,WikiWorks",Identification of microbial taxa that differentiate breast cancer (BC) and healthy groups of gut microbiota using LEfSe discriminant analysis.,increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae",1783272|201174|84992;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|1737404|1737405|1570339|150022;1783272|544448;1783272|1239|1737404|1737405|1737406,Complete,Svetlana up
bsdb:39470189/1/2,39470189,"cross-sectional observational, not case-control",39470189,10.1128/msystems.01237-24,NA,"McCune E., Sharma A., Johnson B., O'Meara T., Theiner S., Campos M., Heditsian D., Brain S., Gilbert J.A., Esserman L. , Campbell M.J.","Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma <i>in situ</i>, and healthy women",mSystems,2024,"DCIS, breast cancer, gut microbiota, oral microbiota",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,Healthy women (Control),Breast cancer (BC),"Women with early-stage of breast cancer (BC),",42,66,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,NA,3,age,NA,NA,unchanged,NA,decreased,NA,NA,Signature 2,FIG 2 (A),19 November 2024,Rahila,"Rahila,WikiWorks",Identification of microbial taxa that differentiate breast cancer (BC) and healthy groups of gut microbiota using LEfSe discriminant analysis.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|1239|186801|3085636|186803|207244;1783272|1239;1783272|1239|186801;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802,Complete,Svetlana up
bsdb:39470189/2/1,39470189,"cross-sectional observational, not case-control",39470189,10.1128/msystems.01237-24,NA,"McCune E., Sharma A., Johnson B., O'Meara T., Theiner S., Campos M., Heditsian D., Brain S., Gilbert J.A., Esserman L. , Campbell M.J.","Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma <i>in situ</i>, and healthy women",mSystems,2024,"DCIS, breast cancer, gut microbiota, oral microbiota",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Breast ductal carcinoma in situ,EFO:0000432,Healthy women (Control),Ductal carcinoma in situ (DCIS),Women with ductal carcinoma in situ (DCIS),42,29,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,NA,3,age,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,FIG 2 (B),19 November 2024,Rahila,"Rahila,WikiWorks",Identification of microbial taxa that differentiate ductal carcinoma in situ (DCIS) and healthy groups of gut microbiota using LEfSe discriminant analysis.,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",1783272|201174;1783272|201174|84992;1783272|201174|1760|2037;1783272|1239|909932|909929|1843491|158846;1783272|201174|1760|2037|2049;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|2037|2049|184869;1783272|1239|909932|1843489|31977|39948,Complete,Svetlana up
bsdb:39470189/2/2,39470189,"cross-sectional observational, not case-control",39470189,10.1128/msystems.01237-24,NA,"McCune E., Sharma A., Johnson B., O'Meara T., Theiner S., Campos M., Heditsian D., Brain S., Gilbert J.A., Esserman L. , Campbell M.J.","Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma <i>in situ</i>, and healthy women",mSystems,2024,"DCIS, breast cancer, gut microbiota, oral microbiota",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Breast ductal carcinoma in situ,EFO:0000432,Healthy women (Control),Ductal carcinoma in situ (DCIS),Women with ductal carcinoma in situ (DCIS),42,29,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,NA,3,age,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,FIG 2 (B),19 November 2024,Rahila,"Rahila,WikiWorks",Identification of microbial taxa that differentiate ductal carcinoma in situ (DCIS) and healthy groups of gut microbiota using LEfSe discriminant analysis.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:39470189/3/1,39470189,"cross-sectional observational, not case-control",39470189,10.1128/msystems.01237-24,NA,"McCune E., Sharma A., Johnson B., O'Meara T., Theiner S., Campos M., Heditsian D., Brain S., Gilbert J.A., Esserman L. , Campbell M.J.","Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma <i>in situ</i>, and healthy women",mSystems,2024,"DCIS, breast cancer, gut microbiota, oral microbiota",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,Ductal carcinoma in situ (DCIS),Breast cancer (BC),"Women with early-stage of breast cancer (BC),",29,66,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,FIG 2 (C),19 November 2024,Rahila,"Rahila,WikiWorks",Identification of microbial taxa that differentiate BC and DCIS groups of gut microbiota using LEfSe discriminant analysis.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",1783272|1239|909932|1843488|909930|33024;1783272|1239|909932|909929|1843491|158846,Complete,Svetlana up
bsdb:39470189/3/2,39470189,"cross-sectional observational, not case-control",39470189,10.1128/msystems.01237-24,NA,"McCune E., Sharma A., Johnson B., O'Meara T., Theiner S., Campos M., Heditsian D., Brain S., Gilbert J.A., Esserman L. , Campbell M.J.","Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma <i>in situ</i>, and healthy women",mSystems,2024,"DCIS, breast cancer, gut microbiota, oral microbiota",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,Ductal carcinoma in situ (DCIS),Breast cancer (BC),"Women with early-stage of breast cancer (BC),",29,66,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,FIG 2 (C),19 November 2024,Rahila,"Rahila,WikiWorks",Identification of microbial taxa that differentiate BC and DCIS groups of gut microbiota using LEfSe discriminant analysis.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae",1783272|1239|909932|1843489|31977|39948;1783272|201174|1760|2037|2049,Complete,Svetlana up
bsdb:39470189/4/1,39470189,"cross-sectional observational, not case-control",39470189,10.1128/msystems.01237-24,NA,"McCune E., Sharma A., Johnson B., O'Meara T., Theiner S., Campos M., Heditsian D., Brain S., Gilbert J.A., Esserman L. , Campbell M.J.","Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma <i>in situ</i>, and healthy women",mSystems,2024,"DCIS, breast cancer, gut microbiota, oral microbiota",Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,Breast cancer,MONDO:0007254,Healthy women (Control),Breast cancer (BC),"Women with early-stage of breast cancer (BC),",31,47,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,NA,3,age,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,FIG 2 (D),19 November 2024,Rahila,"Rahila,WikiWorks",Identification of microbial taxa that differentiate breast cancer (BC) and healthy groups of oral microbiota using LEfSe discriminant analysis.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:39470189/5/1,39470189,"cross-sectional observational, not case-control",39470189,10.1128/msystems.01237-24,NA,"McCune E., Sharma A., Johnson B., O'Meara T., Theiner S., Campos M., Heditsian D., Brain S., Gilbert J.A., Esserman L. , Campbell M.J.","Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma <i>in situ</i>, and healthy women",mSystems,2024,"DCIS, breast cancer, gut microbiota, oral microbiota",Experiment 5,United States of America,Homo sapiens,Saliva,UBERON:0001836,Breast ductal carcinoma in situ,EFO:0000432,Healthy women (Control),Ductal carcinoma in situ (DCIS),Women with ductal carcinoma in situ (DCIS),31,15,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,NA,3,age,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,FIG 2 (E),19 November 2024,Rahila,"Rahila,WikiWorks",Identification of microbial taxa that differentiate ductal carcinoma in situ (DCIS) and healthy groups of oral microbiota using LEfSe discriminant analysis.,increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter",3379134|29547|3031852;3379134|29547|3031852|213849;3379134|29547|3031852|213849|72294;3379134|29547|3031852|213849|72294|194,Complete,Svetlana up
bsdb:39470189/6/2,39470189,"cross-sectional observational, not case-control",39470189,10.1128/msystems.01237-24,NA,"McCune E., Sharma A., Johnson B., O'Meara T., Theiner S., Campos M., Heditsian D., Brain S., Gilbert J.A., Esserman L. , Campbell M.J.","Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma <i>in situ</i>, and healthy women",mSystems,2024,"DCIS, breast cancer, gut microbiota, oral microbiota",Experiment 6,United States of America,Homo sapiens,Saliva,UBERON:0001836,Breast cancer,MONDO:0007254,Ductal carcinoma in situ (DCIS),Breast cancer (BC),"Women with early-stage of breast cancer (BC),",15,47,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,FIG 2 (F),19 November 2024,Rahila,"Rahila,Aleru Divine,WikiWorks",Identification of microbial taxa that differentiate BC and DCIS groups of oral microbiota using LEfSe discriminant analysis.,decreased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria",3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294;3379134|29547|3031852|213849;3379134|29547|3031852,Complete,Svetlana up
bsdb:39470189/7/1,39470189,"cross-sectional observational, not case-control",39470189,10.1128/msystems.01237-24,NA,"McCune E., Sharma A., Johnson B., O'Meara T., Theiner S., Campos M., Heditsian D., Brain S., Gilbert J.A., Esserman L. , Campbell M.J.","Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma <i>in situ</i>, and healthy women",mSystems,2024,"DCIS, breast cancer, gut microbiota, oral microbiota",Experiment 7,United States of America,Homo sapiens,"Feces,Saliva","UBERON:0001988,UBERON:0001836",Breast cancer,MONDO:0007254,Oral,Gut,Gut samples from all participants in the study.,93,137,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,increased,NA,increased,NA,NA,Signature 1,Supplementary Figure S5C,20 November 2024,Rahila,"Rahila,Aleru Divine,WikiWorks","LEfSe analysis comparing gut and oral microbiota at the genus (C) levels. The top 10 differentially abundant taxa, based on LDA score, are shown.",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacillati|p__Mycoplasmatota,k__Methanobacteriati|p__Methanobacteriota,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Bacteroidota",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|815;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803;3379134|74201|203494|48461|203557;1783272|544448;3366610|28890;1783272|1117;3379134|74201;3379134|976,Complete,Svetlana up
bsdb:39470189/7/2,39470189,"cross-sectional observational, not case-control",39470189,10.1128/msystems.01237-24,NA,"McCune E., Sharma A., Johnson B., O'Meara T., Theiner S., Campos M., Heditsian D., Brain S., Gilbert J.A., Esserman L. , Campbell M.J.","Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma <i>in situ</i>, and healthy women",mSystems,2024,"DCIS, breast cancer, gut microbiota, oral microbiota",Experiment 7,United States of America,Homo sapiens,"Feces,Saliva","UBERON:0001988,UBERON:0001836",Breast cancer,MONDO:0007254,Oral,Gut,Gut samples from all participants in the study.,93,137,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,increased,NA,increased,NA,NA,Signature 2,Supplementary Figure S5C,20 November 2024,Rahila,"Rahila,Aleru Divine,WikiWorks","LEfSe analysis comparing gut and oral microbiota at the genus (C) levels. The top 10 differentially abundant taxa, based on LDA score, are shown.",decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,p__Candidatus Saccharimonadota",1783272|201174;1783272|1239;1783272|1239|91061|186826|186828;3384189|32066;1783272|1239|91061|1385|539738;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481;3379134|1224|1236|135625|712;3379134|1224;1783272|1239|909932|909929|1843491|970;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977;95818,Complete,Svetlana up
bsdb:39470189/8/1,39470189,"cross-sectional observational, not case-control",39470189,10.1128/msystems.01237-24,NA,"McCune E., Sharma A., Johnson B., O'Meara T., Theiner S., Campos M., Heditsian D., Brain S., Gilbert J.A., Esserman L. , Campbell M.J.","Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma <i>in situ</i>, and healthy women",mSystems,2024,"DCIS, breast cancer, gut microbiota, oral microbiota",Experiment 8,United States of America,Homo sapiens,Feces,UBERON:0001988,Mammographic density measurement,EFO:0005941,Low breast density,High breast density,Patients with mammographic breast density categorized as high,50,104,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,FIG 6 (C),20 November 2024,Rahila,"Rahila,Aleru Divine,WikiWorks",Differentially enriched taxa abundance in fecal samples between high and low breast density was identified using LEfSe analysis (logarithmic LDA score threshold = 3; P < 0.05).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,s__rumen bacterium YS2,s__uncultured rumen bacterium 4C0d-2",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1117;1783272|1239|909932|1843488|909930|33024;209265;107058,Complete,Svetlana up
bsdb:39470189/8/2,39470189,"cross-sectional observational, not case-control",39470189,10.1128/msystems.01237-24,NA,"McCune E., Sharma A., Johnson B., O'Meara T., Theiner S., Campos M., Heditsian D., Brain S., Gilbert J.A., Esserman L. , Campbell M.J.","Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma <i>in situ</i>, and healthy women",mSystems,2024,"DCIS, breast cancer, gut microbiota, oral microbiota",Experiment 8,United States of America,Homo sapiens,Feces,UBERON:0001988,Mammographic density measurement,EFO:0005941,Low breast density,High breast density,Patients with mammographic breast density categorized as high,50,104,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,FIG 6 (C),20 November 2024,Rahila,"Rahila,WikiWorks",Differentially enriched taxa abundance in fecal samples between high and low breast density was identified using LEfSe analysis (logarithmic LDA score threshold = 3; P < 0.05).,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,1783272|1239|186801|3082768|990719,Complete,Svetlana up
bsdb:39470189/9/1,39470189,"cross-sectional observational, not case-control",39470189,10.1128/msystems.01237-24,NA,"McCune E., Sharma A., Johnson B., O'Meara T., Theiner S., Campos M., Heditsian D., Brain S., Gilbert J.A., Esserman L. , Campbell M.J.","Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma <i>in situ</i>, and healthy women",mSystems,2024,"DCIS, breast cancer, gut microbiota, oral microbiota",Experiment 9,United States of America,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,Healthy women (Control),Breast cancer (BC),"Women with early-stage of breast cancer (BC),",42,66,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,age,NA,NA,unchanged,NA,decreased,NA,NA,Signature 1,FIG 3 (A),20 November 2024,Rahila,"Rahila,WikiWorks",DESeq2 differential abundance analysis. Volcano plots of log2 fold differences in genera abundance in the gut microbiota between BC and healthy cohort,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|909932|1843488|909930|904;1783272|1239|1737404|1737405|1570339|165779;3379134|976|200643|171549|815|816;1783272|1239|526524|526525|2810280|100883;1783272|201174|1760|85007|1653|1716;1783272|201174|84998|1643822|1643826|84111;1783272|1239|1737404|1737405|1570339|150022;3379134|976|200643|171549|2005525|375288;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:39470189/9/2,39470189,"cross-sectional observational, not case-control",39470189,10.1128/msystems.01237-24,NA,"McCune E., Sharma A., Johnson B., O'Meara T., Theiner S., Campos M., Heditsian D., Brain S., Gilbert J.A., Esserman L. , Campbell M.J.","Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma <i>in situ</i>, and healthy women",mSystems,2024,"DCIS, breast cancer, gut microbiota, oral microbiota",Experiment 9,United States of America,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,Healthy women (Control),Breast cancer (BC),"Women with early-stage of breast cancer (BC),",42,66,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,age,NA,NA,unchanged,NA,decreased,NA,NA,Signature 2,FIG 3 (A),20 November 2024,Rahila,"Rahila,WikiWorks",DESeq2 differential abundance analysis. Volcano plots of log2 fold differences in genera abundance in the gut microbiota between BC and healthy cohort,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,1783272|1239|186801|3085636|186803|207244,Complete,Svetlana up
bsdb:39470189/10/1,39470189,"cross-sectional observational, not case-control",39470189,10.1128/msystems.01237-24,NA,"McCune E., Sharma A., Johnson B., O'Meara T., Theiner S., Campos M., Heditsian D., Brain S., Gilbert J.A., Esserman L. , Campbell M.J.","Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma <i>in situ</i>, and healthy women",mSystems,2024,"DCIS, breast cancer, gut microbiota, oral microbiota",Experiment 10,United States of America,Homo sapiens,Feces,UBERON:0001988,Breast ductal carcinoma in situ,EFO:0000432,Healthy women (Control),Ductal carcinoma in situ (DCIS),Women with ductal carcinoma in situ (DCIS),42,29,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,age,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,FIG 3 (B),20 November 2024,Rahila,"Rahila,Aleru Divine,WikiWorks",DESeq2 differential abundance analysis. Volcano plots of log2 fold differences in genera abundance in the gut microbiota between DCIS and healthy cohort,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,s__bacterium PH2",1783272|201174|1760|2037|2049|1654;1783272|1239|1737404|1737405|1570339|165779;1783272|201174|1760|85007|1653|1716;1783272|1239|909932|1843489|31977|39948;1783272|201174|84998|1643822|1643826|84111;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|909932|909929|1843491|158846;3379134|976|200643|171549|1853231|283168;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836;1783272|1239|91061|186826|1300|1301;1783272|201174|1760|2037|2049|184869;239775,Complete,Svetlana up
bsdb:39470189/10/2,39470189,"cross-sectional observational, not case-control",39470189,10.1128/msystems.01237-24,NA,"McCune E., Sharma A., Johnson B., O'Meara T., Theiner S., Campos M., Heditsian D., Brain S., Gilbert J.A., Esserman L. , Campbell M.J.","Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma <i>in situ</i>, and healthy women",mSystems,2024,"DCIS, breast cancer, gut microbiota, oral microbiota",Experiment 10,United States of America,Homo sapiens,Feces,UBERON:0001988,Breast ductal carcinoma in situ,EFO:0000432,Healthy women (Control),Ductal carcinoma in situ (DCIS),Women with ductal carcinoma in situ (DCIS),42,29,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,age,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,FIG 3 (B),20 November 2024,Rahila,"Rahila,WikiWorks",DESeq2 differential abundance analysis. Volcano plots of log2 fold differences in genera abundance in the gut microbiota between DCIS and healthy cohort,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:39470189/11/1,39470189,"cross-sectional observational, not case-control",39470189,10.1128/msystems.01237-24,NA,"McCune E., Sharma A., Johnson B., O'Meara T., Theiner S., Campos M., Heditsian D., Brain S., Gilbert J.A., Esserman L. , Campbell M.J.","Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma <i>in situ</i>, and healthy women",mSystems,2024,"DCIS, breast cancer, gut microbiota, oral microbiota",Experiment 11,United States of America,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,Ductal carcinoma in situ (DCIS),Breast cancer (BC),"Women with early-stage of breast cancer (BC),",29,66,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,FIG 3 (C),20 November 2024,Rahila,"Rahila,WikiWorks",DESeq2 differential abundance analysis. Volcano plots of log2 fold differences in genera abundance in the gut microbiota between BC and DCIS cohort,increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,1783272|1239|909932|1843488|909930|33024,Complete,Svetlana up
bsdb:39470189/11/2,39470189,"cross-sectional observational, not case-control",39470189,10.1128/msystems.01237-24,NA,"McCune E., Sharma A., Johnson B., O'Meara T., Theiner S., Campos M., Heditsian D., Brain S., Gilbert J.A., Esserman L. , Campbell M.J.","Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma <i>in situ</i>, and healthy women",mSystems,2024,"DCIS, breast cancer, gut microbiota, oral microbiota",Experiment 11,United States of America,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,Ductal carcinoma in situ (DCIS),Breast cancer (BC),"Women with early-stage of breast cancer (BC),",29,66,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,FIG 3 (C),20 November 2024,Rahila,"Rahila,WikiWorks",DESeq2 differential abundance analysis. Volcano plots of log2 fold differences in genera abundance in the gut microbiota between BC and DCIS cohort,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus",1783272|201174|1760|2037|2049|184869;1783272|1239|186801|3085636|186803|207244;1783272|201174|1760|2037|2049|1654;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|1737404|1737405|1570339|150022;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|1853231|283168;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|3085636|186803|33042,Complete,Svetlana up
bsdb:39470189/12/NA,39470189,"cross-sectional observational, not case-control",39470189,10.1128/msystems.01237-24,NA,"McCune E., Sharma A., Johnson B., O'Meara T., Theiner S., Campos M., Heditsian D., Brain S., Gilbert J.A., Esserman L. , Campbell M.J.","Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma <i>in situ</i>, and healthy women",mSystems,2024,"DCIS, breast cancer, gut microbiota, oral microbiota",Experiment 12,United States of America,Homo sapiens,Saliva,UBERON:0001836,Breast cancer,MONDO:0007254,Healthy women (Control),Breast cancer (BC),"Women with early-stage of breast cancer (BC),",31,47,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,age,NA,NA,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:39470189/13/1,39470189,"cross-sectional observational, not case-control",39470189,10.1128/msystems.01237-24,NA,"McCune E., Sharma A., Johnson B., O'Meara T., Theiner S., Campos M., Heditsian D., Brain S., Gilbert J.A., Esserman L. , Campbell M.J.","Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma <i>in situ</i>, and healthy women",mSystems,2024,"DCIS, breast cancer, gut microbiota, oral microbiota",Experiment 13,United States of America,Homo sapiens,Saliva,UBERON:0001836,Breast ductal carcinoma in situ,EFO:0000432,Healthy women (Control),Ductal carcinoma in situ (DCIS),Women with ductal carcinoma in situ (DCIS),31,15,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,age,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,FIG 3 (E),21 November 2024,Rahila,"Rahila,WikiWorks",DESeq2 differential abundance analysis. Volcano plots of log2 fold differences in genera abundance in the oral microbiota between DCIS and healthy cohort,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",3379134|1224|1236|135625|712|713;1783272|1239|186801|3085636|186803|572511,Complete,Svetlana up
bsdb:39470189/14/NA,39470189,"cross-sectional observational, not case-control",39470189,10.1128/msystems.01237-24,NA,"McCune E., Sharma A., Johnson B., O'Meara T., Theiner S., Campos M., Heditsian D., Brain S., Gilbert J.A., Esserman L. , Campbell M.J.","Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma <i>in situ</i>, and healthy women",mSystems,2024,"DCIS, breast cancer, gut microbiota, oral microbiota",Experiment 14,United States of America,Homo sapiens,Saliva,UBERON:0001836,Breast cancer,MONDO:0007254,Ductal carcinoma in situ (DCIS),Breast cancer (BC),"Women with early-stage of breast cancer (BC),",15,47,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
bsdb:39470277/1/2,39470277,case-control,39470277,https://doi.org/10.1128/spectrum.01808-24,https://journals.asm.org/doi/10.1128/spectrum.01808-24,"Xie J., Zhang X., Cheng L., Deng Y., Ren H., Mu M., Zhao L., Mu C., Chen J., Liu K. , Ma R.",Integrated multi-omics analysis of the microbial profile characteristics associated with pulmonary arterial hypertension in congenital heart disease,Microbiology spectrum,2024,"PAH-CHD, growth failure, human microbiota, inflammation, metabolome, reprogramming of energy metabolism",Experiment 1,China,Homo sapiens,Bronchoalveolar duct junction,UBERON:0004903,Pulmonary arterial hypertension associated with congenital heart disease,EFO:0009054,Healthy Control (HC),Pulmonary Arterial Hypertension associated with Congenital Heart Disease involving body-lung shunt (PAH-CHD),Children with Pulmonary Arterial Hypertension associated with Congenital Heart Disease involving body-lung shunt (PAH-CHD),15,15,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,unchanged,unchanged,NA,NA,NA,NA,Signature 2,Figure 1D,22 December 2025,Blessdamy,Blessdamy,"Linear Discriminant Analysis Effect Size (LEfSe) analysis reveals significant differences in the enrichment of lung bacterial taxa between the pulmonary arterial hypertension associated with congenital heart disease involving body-lung shunt (PAH-CHD) group and healthy controls, along with their phylogenetic tree (LDA > 3).",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus peroris,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans",1783272|1239|91061|186826|1300|1301|68891;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|360807,Complete,NA
bsdb:39470277/1/3,39470277,case-control,39470277,https://doi.org/10.1128/spectrum.01808-24,https://journals.asm.org/doi/10.1128/spectrum.01808-24,"Xie J., Zhang X., Cheng L., Deng Y., Ren H., Mu M., Zhao L., Mu C., Chen J., Liu K. , Ma R.",Integrated multi-omics analysis of the microbial profile characteristics associated with pulmonary arterial hypertension in congenital heart disease,Microbiology spectrum,2024,"PAH-CHD, growth failure, human microbiota, inflammation, metabolome, reprogramming of energy metabolism",Experiment 1,China,Homo sapiens,Bronchoalveolar duct junction,UBERON:0004903,Pulmonary arterial hypertension associated with congenital heart disease,EFO:0009054,Healthy Control (HC),Pulmonary Arterial Hypertension associated with Congenital Heart Disease involving body-lung shunt (PAH-CHD),Children with Pulmonary Arterial Hypertension associated with Congenital Heart Disease involving body-lung shunt (PAH-CHD),15,15,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,unchanged,unchanged,NA,NA,NA,NA,Signature 3,Figure 1D,23 December 2025,Blessdamy,Blessdamy,"Linear Discriminant Analysis Effect Size (LEfSe) analysis reveals significant differences in the enrichment of lung bacterial taxa between the pulmonary arterial hypertension associated with congenital heart disease involving body-lung shunt (PAH-CHD) group and healthy controls, along with their phylogenetic tree (LDA > 3).",decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Thermoactinomycetaceae|g__Thermoactinomyces,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Thermoactinomycetaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria lactamica",3384189|32066|203490|203491|1129771|32067;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|1385|186824|2023;1783272|1239|91061|1385|186824;3379134|1224|28216|206351|481|482|486,Complete,NA
bsdb:39470277/2/1,39470277,case-control,39470277,https://doi.org/10.1128/spectrum.01808-24,https://journals.asm.org/doi/10.1128/spectrum.01808-24,"Xie J., Zhang X., Cheng L., Deng Y., Ren H., Mu M., Zhao L., Mu C., Chen J., Liu K. , Ma R.",Integrated multi-omics analysis of the microbial profile characteristics associated with pulmonary arterial hypertension in congenital heart disease,Microbiology spectrum,2024,"PAH-CHD, growth failure, human microbiota, inflammation, metabolome, reprogramming of energy metabolism",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary arterial hypertension associated with congenital heart disease,EFO:0009054,Healthy Control (HC),Pulmonary Arterial Hypertension associated with Congenital Heart Disease involving body-lung shunt (PAH-CHD),Children with Pulmonary Arterial Hypertension associated with Congenital Heart Disease involving body-lung shunt (PAH-CHD).,15,15,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,increased,increased,NA,NA,NA,NA,Signature 1,Figure 1C,26 December 2025,Blessdamy,Blessdamy,"Linear Discriminant Analysis Effect Size (LEfSe) analysis reveals significant differences in the enrichment of gut bacterial taxa between the pulmonary arterial hypertension associated with congenital heart disease involving body-lung shunt (PAH-CHD) group and healthy controls, along with their phylogenetic tree Linear Discriminant Analysis (LDA > 3).",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium butyricum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecis,k__Pseudomonadati|p__Planctomycetota",1783272|201174|1760|85004|31953|1678|1685;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|909932|909929|1843491;1783272|1239|186801|186802|31979|1485|1492;1783272|201174|1760|85004|31953|1678|28025;3379134|976|200643|171549|815|816|674529;3379134|203682,Complete,NA
bsdb:39470277/2/2,39470277,case-control,39470277,https://doi.org/10.1128/spectrum.01808-24,https://journals.asm.org/doi/10.1128/spectrum.01808-24,"Xie J., Zhang X., Cheng L., Deng Y., Ren H., Mu M., Zhao L., Mu C., Chen J., Liu K. , Ma R.",Integrated multi-omics analysis of the microbial profile characteristics associated with pulmonary arterial hypertension in congenital heart disease,Microbiology spectrum,2024,"PAH-CHD, growth failure, human microbiota, inflammation, metabolome, reprogramming of energy metabolism",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary arterial hypertension associated with congenital heart disease,EFO:0009054,Healthy Control (HC),Pulmonary Arterial Hypertension associated with Congenital Heart Disease involving body-lung shunt (PAH-CHD),Children with Pulmonary Arterial Hypertension associated with Congenital Heart Disease involving body-lung shunt (PAH-CHD).,15,15,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,"age,sex",NA,increased,increased,NA,NA,NA,NA,Signature 2,Figure 1C,26 December 2025,Blessdamy,Blessdamy,"Linear Discriminant Analysis Effect Size (LEfSe) analysis reveals significant differences in the enrichment of gut bacterial taxa between the pulmonary arterial hypertension associated with congenital heart disease involving body-lung shunt (PAH-CHD) group and healthy controls, along with their phylogenetic tree Linear Discriminant Analysis (LDA > 3).",decreased,",k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Frisingicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus",;3379134|1224|28216|80840;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;1783272|201174|1760|85007|1653|1716|61592;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|1918511;1783272|1239|91061|186826|33958|1578|147802;1783272|1239|909932;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|91061|186826|1300|1301|1318;3379134|1224|28216|80840|995019;1783272|1239|909932|1843489|31977;1783272|1239|186801|186802;1783272|1239|186801|186802|216572;1783272|1239|909932|1843489|31977|39948|218538,Complete,NA
bsdb:39470277/3/2,39470277,case-control,39470277,https://doi.org/10.1128/spectrum.01808-24,https://journals.asm.org/doi/10.1128/spectrum.01808-24,"Xie J., Zhang X., Cheng L., Deng Y., Ren H., Mu M., Zhao L., Mu C., Chen J., Liu K. , Ma R.",Integrated multi-omics analysis of the microbial profile characteristics associated with pulmonary arterial hypertension in congenital heart disease,Microbiology spectrum,2024,"PAH-CHD, growth failure, human microbiota, inflammation, metabolome, reprogramming of energy metabolism",Experiment 3,China,Homo sapiens,Bronchoalveolar duct junction,UBERON:0004903,Pulmonary arterial hypertension associated with congenital heart disease,EFO:0009054,Healthy Control (HC),Pulmonary Arterial Hypertension associated with Congenital Heart Disease involving body-lung shunt (PAH-CHD),Children with Pulmonary Arterial Hypertension associated with Congenital Heart Disease involving body-lung shunt (PAH-CHD),15,15,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Figure 3C,6 February 2026,Blessdamy,"Blessdamy,Fiddyhamma","Linear Discriminant Analysis Effect Size (LEfSe) analysis indicates differences in genus-level enriched microbiota between the pulmonary arterial hypertension associated with congenital heart disease involving body-lung shunt (PAH-CHD) group and healthy controls, (LDA > 2).",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",3379134|1224|1236|2887326|468|469;4751|4890|147545|5042|1131492|5052;1783272|1239|91061|1385|186817|1386;1783272|201174|1760|85007|1653|1716;3379134|976|117743|200644|49546|237;1783272|1239|526524|526525|128827|1573535;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1243;3379134|1224|28211|356|119045|407;1783272|201174|1760|85007|1762|1763;3379134|1224;3379134|1224|28211|204457|41297|13687;1783272|1239|91061|1385|90964|1279,Complete,NA
bsdb:39470277/3/3,39470277,case-control,39470277,https://doi.org/10.1128/spectrum.01808-24,https://journals.asm.org/doi/10.1128/spectrum.01808-24,"Xie J., Zhang X., Cheng L., Deng Y., Ren H., Mu M., Zhao L., Mu C., Chen J., Liu K. , Ma R.",Integrated multi-omics analysis of the microbial profile characteristics associated with pulmonary arterial hypertension in congenital heart disease,Microbiology spectrum,2024,"PAH-CHD, growth failure, human microbiota, inflammation, metabolome, reprogramming of energy metabolism",Experiment 3,China,Homo sapiens,Bronchoalveolar duct junction,UBERON:0004903,Pulmonary arterial hypertension associated with congenital heart disease,EFO:0009054,Healthy Control (HC),Pulmonary Arterial Hypertension associated with Congenital Heart Disease involving body-lung shunt (PAH-CHD),Children with Pulmonary Arterial Hypertension associated with Congenital Heart Disease involving body-lung shunt (PAH-CHD),15,15,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 3,Supplementary Figure S3C,6 February 2026,Fiddyhamma,Fiddyhamma,"Linear Discriminant Analysis Effect Size (LEfSe) analysis indicates differences in genus-level enriched microbiota between the pulmonary arterial hypertension associated with congenital heart disease involving body-lung shunt (PAH-CHD) group and healthy controls, (LDA > 2).",increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Edwardsiella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Nostocoides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Listeria",3379134|29547|3031852|213849|72294|194;3379134|1224|1236|91347|1903412|635;3379134|29547|3031852|213849|72293|209;1783272|1239|909932|909929|1843491|158846;1783272|201174|1760|85006|85023|33882;3379134|1224|1236|2887326|468|475;1783272|201174|1760|85007|1762|1763;3379134|1224|28216|206351|481|482;1783272|201174|1760|85006|85021|99479;3379134|1224|1236|135614|32033|40323;1783272|1239|91061|186826|1300|1301;3379134|1224|1236|135623|641|662;1783272|1239|91061|1385|186820|1637,Complete,NA
bsdb:39481388/1/1,39481388,time series / longitudinal observational,39481388,10.1016/j.chom.2024.10.006,NA,"Macandog A.D.G., Catozzi C., Capone M., Nabinejad A., Nanaware P.P., Liu S., Vinjamuri S., Stunnenberg J.A., Galiè S., Jodice M.G., Montani F., Armanini F., Cassano E., Madonna G., Mallardo D., Mazzi B., Pece S., Tagliamonte M., Vanella V., Barberis M., Ferrucci P.F., Blank C.U., Bouvier M., Andrews M.C., Xu X., Santambrogio L., Segata N., Buonaguro L., Cocorocchio E., Ascierto P.A., Manzo T. , Nezi L.",Longitudinal analysis of the gut microbiota during anti-PD-1 therapy reveals stable microbial features of response in melanoma patients,Cell host & microbe,2024,"antigen mimicry, gut microbiome, immunotherapy, longitudinal, melanoma",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Melanoma,EFO:0000756,non-complete responders (nCR),complete responders (CR),This group represents the Complete Responders (CR) to anti-PD-1 therapy in melanoma patients for 2-6 months (early therapy) .,7,25,1 month,16S,34,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S2D,19 November 2024,Joiejoie,"Joiejoie,Aleru Divine,WikiWorks","Differential abundance of CR (blue) and ncR (red) stable taxa on log-transformed relative abundance, based on Maaslin2 linear model (LM) coefficient.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pullorum,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Heteroscillospira|s__Candidatus Heteroscillospira lomanii,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Metalachnospira|s__Candidatus Metalachnospira gallinarum,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Metaruminococcus|s__Candidatus Metaruminococcus gallistercoris,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Roslinia|s__Candidatus Roslinia caecavium,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Gallimonas|s__Candidatus Gallimonas caecicola",3379134|976|200643|171549|815|816|291645;1783272|201174|1760|85004|31953|1678|1694;1783272|201174|1760|85004|31953|1678|78448;1783272|1239|186801|2721105|2721130;1783272|1239|186801|2721107|2721132;1783272|1239|186801|2721108|2721134;1783272|1239|186801|2721121|2721153;1783272|1239|186801|2720806|2720810,Complete,Svetlana up
bsdb:39481388/1/2,39481388,time series / longitudinal observational,39481388,10.1016/j.chom.2024.10.006,NA,"Macandog A.D.G., Catozzi C., Capone M., Nabinejad A., Nanaware P.P., Liu S., Vinjamuri S., Stunnenberg J.A., Galiè S., Jodice M.G., Montani F., Armanini F., Cassano E., Madonna G., Mallardo D., Mazzi B., Pece S., Tagliamonte M., Vanella V., Barberis M., Ferrucci P.F., Blank C.U., Bouvier M., Andrews M.C., Xu X., Santambrogio L., Segata N., Buonaguro L., Cocorocchio E., Ascierto P.A., Manzo T. , Nezi L.",Longitudinal analysis of the gut microbiota during anti-PD-1 therapy reveals stable microbial features of response in melanoma patients,Cell host & microbe,2024,"antigen mimicry, gut microbiome, immunotherapy, longitudinal, melanoma",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Melanoma,EFO:0000756,non-complete responders (nCR),complete responders (CR),This group represents the Complete Responders (CR) to anti-PD-1 therapy in melanoma patients for 2-6 months (early therapy) .,7,25,1 month,16S,34,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S2D,29 January 2025,Aleru Divine,"Aleru Divine,WikiWorks","Differential abundance of CR (blue) and ncR (red) stable taxa on log-transformed relative abundance, based on Maaslin2 linear model (LM) coefficient.",decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. An66,3379134|976|200643|171549|171550|239759|1965650,Complete,Svetlana up
bsdb:39481388/2/1,39481388,time series / longitudinal observational,39481388,10.1016/j.chom.2024.10.006,NA,"Macandog A.D.G., Catozzi C., Capone M., Nabinejad A., Nanaware P.P., Liu S., Vinjamuri S., Stunnenberg J.A., Galiè S., Jodice M.G., Montani F., Armanini F., Cassano E., Madonna G., Mallardo D., Mazzi B., Pece S., Tagliamonte M., Vanella V., Barberis M., Ferrucci P.F., Blank C.U., Bouvier M., Andrews M.C., Xu X., Santambrogio L., Segata N., Buonaguro L., Cocorocchio E., Ascierto P.A., Manzo T. , Nezi L.",Longitudinal analysis of the gut microbiota during anti-PD-1 therapy reveals stable microbial features of response in melanoma patients,Cell host & microbe,2024,"antigen mimicry, gut microbiome, immunotherapy, longitudinal, melanoma",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Melanoma,EFO:0000756,non-complete responders (nCR),complete responders (CR),This group represents the Complete Responders (CR) to anti-PD-1 therapy in melanoma patients for 7-13 months (late therapy).,7,25,1 month,WMS,NA,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S2D,27 November 2024,Joiejoie,"Joiejoie,Aleru Divine,WikiWorks","Differential abundance of CR (blue) and ncR (red) stable taxa on log-transformed relative abundance, based on Maaslin2 linear model (LM) coefficient.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Metaruminococcus|s__Candidatus Metaruminococcus gallistercoris,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Metalachnospira|s__Candidatus Metalachnospira gallinarum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Evtepia|s__Evtepia gabavorous,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pullorum",1783272|1239|186801|2721108|2721134;1783272|1239|186801|2721107|2721132;3379134|976|200643|171549|815|816|291645;1783272|1239|186801|186802|2211178|2211183;1783272|201174|1760|85004|31953|1678|78448,Complete,Svetlana up
bsdb:39481388/2/2,39481388,time series / longitudinal observational,39481388,10.1016/j.chom.2024.10.006,NA,"Macandog A.D.G., Catozzi C., Capone M., Nabinejad A., Nanaware P.P., Liu S., Vinjamuri S., Stunnenberg J.A., Galiè S., Jodice M.G., Montani F., Armanini F., Cassano E., Madonna G., Mallardo D., Mazzi B., Pece S., Tagliamonte M., Vanella V., Barberis M., Ferrucci P.F., Blank C.U., Bouvier M., Andrews M.C., Xu X., Santambrogio L., Segata N., Buonaguro L., Cocorocchio E., Ascierto P.A., Manzo T. , Nezi L.",Longitudinal analysis of the gut microbiota during anti-PD-1 therapy reveals stable microbial features of response in melanoma patients,Cell host & microbe,2024,"antigen mimicry, gut microbiome, immunotherapy, longitudinal, melanoma",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Melanoma,EFO:0000756,non-complete responders (nCR),complete responders (CR),This group represents the Complete Responders (CR) to anti-PD-1 therapy in melanoma patients for 7-13 months (late therapy).,7,25,1 month,WMS,NA,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S2D,29 January 2025,Aleru Divine,"Aleru Divine,WikiWorks","Differential abundance of CR (blue) and ncR (red) stable taxa on log-transformed relative abundance, based on Maaslin2 linear model (LM) coefficient.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. An66,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. Marseille-P3684",3379134|976|200643|171549|171550|239759|1965650;3379134|976|200643|171549|815|816|2086579,Complete,Svetlana up
bsdb:39497165/1/1,39497165,"cross-sectional observational, not case-control",39497165,10.1186/s40168-024-01941-7,NA,"Ryu E.P., Gautam Y., Proctor D.M., Bhandari D., Tandukar S., Gupta M., Gautam G.P., Relman D.A., Shibl A.A., Sherchand J.B., Jha A.R. , Davenport E.R.",Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized,Microbiome,2024,"Lifestyle, Nepali populations, Oral microbiome, Oral microbiota, Salivary microbiome",Experiment 1,"Nepal,United States of America",Homo sapiens,Saliva,UBERON:0001836,Lifestyle measurement,EFO:0010724,Lifestyle Gradient,Increasing Lifestyle Gradient,Lifestyles transitioning from more traditional to industrial.,91,91,currently on antibiotics,16S,4,Illumina,relative abundances,Jonckheere's trend test,0.05,TRUE,NA,NA,sex,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,24 November 2024,Tosin,"Tosin,WikiWorks","Abundances of genera significantly following the lifestyle gradient ordered from most traditional (foragers) to most industrialized (American industrialists), left to right.",increased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,1783272|201174|84998|84999|1643824|1380,Complete,Svetlana up
bsdb:39497165/1/2,39497165,"cross-sectional observational, not case-control",39497165,10.1186/s40168-024-01941-7,NA,"Ryu E.P., Gautam Y., Proctor D.M., Bhandari D., Tandukar S., Gupta M., Gautam G.P., Relman D.A., Shibl A.A., Sherchand J.B., Jha A.R. , Davenport E.R.",Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized,Microbiome,2024,"Lifestyle, Nepali populations, Oral microbiome, Oral microbiota, Salivary microbiome",Experiment 1,"Nepal,United States of America",Homo sapiens,Saliva,UBERON:0001836,Lifestyle measurement,EFO:0010724,Lifestyle Gradient,Increasing Lifestyle Gradient,Lifestyles transitioning from more traditional to industrial.,91,91,currently on antibiotics,16S,4,Illumina,relative abundances,Jonckheere's trend test,0.05,TRUE,NA,NA,sex,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,24 November 2024,Tosin,"Tosin,WikiWorks","Abundances of genera significantly following the lifestyle gradient ordered from most traditional (foragers) to most industrialized (American industrialists), left to right.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Brachymonas",1783272|1239|91061|186826|186828|117563;3379134|1224|1236|2887326|468|475;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481|71;3384189|32066|203490|203491|1129771|34104;3379134|976;3379134|976|200643|171549|171551;3379134|1224|28216|80840|80864|28219,Complete,Svetlana up
bsdb:39497165/2/1,39497165,"cross-sectional observational, not case-control",39497165,10.1186/s40168-024-01941-7,NA,"Ryu E.P., Gautam Y., Proctor D.M., Bhandari D., Tandukar S., Gupta M., Gautam G.P., Relman D.A., Shibl A.A., Sherchand J.B., Jha A.R. , Davenport E.R.",Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized,Microbiome,2024,"Lifestyle, Nepali populations, Oral microbiome, Oral microbiota, Salivary microbiome",Experiment 2,Nepal,Homo sapiens,Saliva,UBERON:0001836,Lifestyle measurement,EFO:0010724,Wheat/Rice,Barley/Maize,Barley/Maize a grain type considered as a lifestyle factor associated with the oral microbiome of individuals.,NA,NA,currently on antibiotics,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 5B, 5C",24 November 2024,Tosin,"Tosin,WikiWorks","Grain, a lifestyle factor associated with significant individual oral genera.",increased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Brachymonas,3379134|1224|28216|80840|80864|28219,Complete,Svetlana up
bsdb:39497165/3/1,39497165,"cross-sectional observational, not case-control",39497165,10.1186/s40168-024-01941-7,NA,"Ryu E.P., Gautam Y., Proctor D.M., Bhandari D., Tandukar S., Gupta M., Gautam G.P., Relman D.A., Shibl A.A., Sherchand J.B., Jha A.R. , Davenport E.R.",Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized,Microbiome,2024,"Lifestyle, Nepali populations, Oral microbiome, Oral microbiota, Salivary microbiome",Experiment 3,Nepal,Homo sapiens,Saliva,UBERON:0001836,Lifestyle measurement,EFO:0010724,Non-smokers,Smokers,Individuals engaged in smoking,NA,NA,currently on antibiotics,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,S11A,27 November 2024,Tosin,"Tosin,WikiWorks",Differentially abundant taxa between smokers and Non-smokers group,increased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,1783272|201174|84998|84999|1643824|1380,Complete,Svetlana up
bsdb:39497165/3/2,39497165,"cross-sectional observational, not case-control",39497165,10.1186/s40168-024-01941-7,NA,"Ryu E.P., Gautam Y., Proctor D.M., Bhandari D., Tandukar S., Gupta M., Gautam G.P., Relman D.A., Shibl A.A., Sherchand J.B., Jha A.R. , Davenport E.R.",Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized,Microbiome,2024,"Lifestyle, Nepali populations, Oral microbiome, Oral microbiota, Salivary microbiome",Experiment 3,Nepal,Homo sapiens,Saliva,UBERON:0001836,Lifestyle measurement,EFO:0010724,Non-smokers,Smokers,Individuals engaged in smoking,NA,NA,currently on antibiotics,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure S11A,27 November 2024,Tosin,"Tosin,WikiWorks",Differentially abundant taxa between smokers and Non-smokers group.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",1783272|1239|91061|186826|186828|117563;3379134|976|200643|171549|171551;3379134|1224|28216|206351|481|482,Complete,Svetlana up
bsdb:39497165/4/1,39497165,"cross-sectional observational, not case-control",39497165,10.1186/s40168-024-01941-7,NA,"Ryu E.P., Gautam Y., Proctor D.M., Bhandari D., Tandukar S., Gupta M., Gautam G.P., Relman D.A., Shibl A.A., Sherchand J.B., Jha A.R. , Davenport E.R.",Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized,Microbiome,2024,"Lifestyle, Nepali populations, Oral microbiome, Oral microbiota, Salivary microbiome",Experiment 4,Nepal,Homo sapiens,Saliva,UBERON:0001836,Lifestyle measurement,EFO:0010724,Non-sinsu consumers,Sinsu comsumers,Individuals that consume sinsu.,NA,NA,currently on antibiotics,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure S11B,27 November 2024,Tosin,"Tosin,WikiWorks",Differentially abundant taxa between non-sinsu consumers and sinsu consumers.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Brachymonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",3379134|1224|28216|80840|80864|28219;3379134|1224|1236|2887326|468|475;3379134|976|200643|171549|171551,Complete,Svetlana up
bsdb:39497165/5/1,39497165,"cross-sectional observational, not case-control",39497165,10.1186/s40168-024-01941-7,NA,"Ryu E.P., Gautam Y., Proctor D.M., Bhandari D., Tandukar S., Gupta M., Gautam G.P., Relman D.A., Shibl A.A., Sherchand J.B., Jha A.R. , Davenport E.R.",Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized,Microbiome,2024,"Lifestyle, Nepali populations, Oral microbiome, Oral microbiota, Salivary microbiome",Experiment 5,"Nepal,United States of America",Homo sapiens,Saliva,UBERON:0001836,Lifestyle measurement,EFO:0010724,Traditional populations,Industrialized populations,American industrialists and Expats were categorized as Industralized populations.,73,18,currently on antibiotics,16S,4,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,sex,NA,NA,NA,NA,NA,NA,Signature 1,Figure S16B,27 November 2024,Tosin,"Tosin,WikiWorks",Abundance of Fusobacterium contributing to platinum resistance significantly differs between the traditional and industrialized populations.,decreased,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,3384189|32066|203490|203491|203492|848,Complete,Svetlana up
bsdb:39528484/1/1,39528484,"cross-sectional observational, not case-control",39528484,https://doi.org/10.1038/s41467-024-53934-7,NA,"Manghi P., Filosi M., Zolfo M., Casten L.G., Garcia-Valiente A., Mattevi S., Heidrich V., Golzato D., Perini S., Thomas A.M., Montalbano S., Cancellieri S., Waldron L., Hall J.B., Xu S., Volfovsky N., Green Snyder L., Feliciano P., Asnicar F., Valles-Colomer M., Michaelson J.J., Segata N. , Domenici E.",Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders,Nature communications,2024,NA,Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Autism spectrum disorder,EFO:0003756,Neurotypical Siblings(NTs),Autism Spectrum Disorders Children (ASD Children),Autism Spectrum Disorders Children (ASD Children) refers to children who show repetitive behaviours and sensory hyper-sensibility.,1646,2154,NA,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.005,TRUE,NA,NA,"age,sequence read depth,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,"Supplementary Data 3, 5",13 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in oral samples between Autism Spectrum Disorders children and Neurotypical Siblings..,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces johnsonii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces massiliensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 180,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 414,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter curvus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium valvarum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella halliae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter|s__Enhydrobacter aerosaccus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium oral taxon 096,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 225,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 847,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 879,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus luteus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium pumilum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Faucicola|s__Faucicola osloensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sicca,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Pauljensenia|s__Pauljensenia hongkongensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia georgiae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas noxia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. oral taxon 920,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sobrinus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 056,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ottowia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter",1783272|1239|91061|186826|186827|46123|46125;1783272|201174|1760|2037|2049|1654|544581;1783272|201174|1760|2037|2049|1654|461393;1783272|201174|1760|2037|2049|1654|1655;1783272|201174|1760|2037|2049|1654|544580;1783272|201174|1760|2037|2049|1654|651609;1783272|201174|1760|2037|2049|1654|712122;3379134|976|200643|171549|171552|1283313|671218;1783272|201174|1760|85009|31957|2801844|1750;3379134|29547|3031852|213849|72294|194|200;3379134|29547|3031852|213849|72294|194|824;3379134|976|117743|200644|49546|1016|45242;3379134|976|117743|200644|49546|1016|327575;3379134|976|117743|200644|49546|1016|1018;3379134|976|117743|200644|49546|1016|1019;3379134|1224|1236|135615|868|2717|2718;3379134|1224|1236|135615|868|2717|194702;1783272|201174|1760|85007|1653|1716|61592;1783272|201174|1760|85007|1653|1716|43768;1783272|201174|1760|85009|31957|1912216|1747;3379134|1224|28216|206351|481|538|539;3379134|1224|28216|206351|481|538|1795832;3379134|1224|28211|356|212791|225324;3384189|32066|203490|203491|203492|848|851;1783272|1239|91061|1385|539738|1378|29391;3379134|1224|28216|206351|481|32257|505;1783272|1239|186801|3085636|186803|712982;3384189|32066|203490|203491|1129771|32067|40542;3384189|32066|203490|203491|1129771|32067|157688;3384189|32066|203490|203491|1129771|32067|671213;3384189|32066|203490|203491|1129771|32067|1785996;3384189|32066|203490|203491|1129771|32067|1227267;4751|5204|1538075|162474|742845|55193|76775;1783272|201174|1760|85006|1268|1269|1270;1783272|1239|186801|3082720|543314|86331|86332;3379134|1224|1236|2887326|468|1604696|34062;3379134|1224|28216|206351|481|482|490;1783272|201174|1760|2037|2049|2740557|178339;1783272|201174|1760|85006|1268|32207|172042;1783272|201174|1760|85006|1268|32207|2047;1783272|201174|1760|2037|2049|2529408|52768;1783272|1239|909932|909929|1843491|970|135083;1783272|1239|909932|909929|1843491|970|1884263;1783272|1239|91061|1385|90964|1279|1282;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|91061|186826|1300|1301|45634;1783272|1239|91061|186826|1300|1301|1302;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|91061|186826|1300|1301|1309;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|91061|186826|1300|1301|1305;1783272|1239|91061|186826|1300|1301|1310;1783272|1239|91061|186826|1300|1301|712620;1783272|1239|91061|186826|1300|1301|1343;1783272|1239|909932|1843489|31977|29465|29466;1783272|201174|1760|85007|1653|1716;3379134|1224|28216|206351|481|32257;1783272|201174|1760|85009|31957|1912216;1783272|201174|1760|85009|31957|2801844;3379134|1224|1236|135615|868|2717;3379134|1224|28216|206351|481|538;3379134|976|117743|200644|49546|1016;3379134|1224|28216|80840|80864|219181;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|186827|46123;1783272|1239|909932|909929|1843491|970;3379134|976|200643|171549|2005525|195950;3384189|32066|203490|203491|1129771|32067;1783272|1239|91061|186826|1300|1301;1783272|201174|1760|85006|1268|1269;3379134|1224|28211|356|212791,Complete,Svetlana up
bsdb:39528484/1/2,39528484,"cross-sectional observational, not case-control",39528484,https://doi.org/10.1038/s41467-024-53934-7,NA,"Manghi P., Filosi M., Zolfo M., Casten L.G., Garcia-Valiente A., Mattevi S., Heidrich V., Golzato D., Perini S., Thomas A.M., Montalbano S., Cancellieri S., Waldron L., Hall J.B., Xu S., Volfovsky N., Green Snyder L., Feliciano P., Asnicar F., Valles-Colomer M., Michaelson J.J., Segata N. , Domenici E.",Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders,Nature communications,2024,NA,Experiment 1,United States of America,Homo sapiens,Saliva,UBERON:0001836,Autism spectrum disorder,EFO:0003756,Neurotypical Siblings(NTs),Autism Spectrum Disorders Children (ASD Children),Autism Spectrum Disorders Children (ASD Children) refers to children who show repetitive behaviours and sensory hyper-sensibility.,1646,2154,NA,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.005,TRUE,NA,NA,"age,sequence read depth,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,"Supplementary Data 3, 5",13 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in oral samples between Autism Spectrum Disorders children and Neurotypical Siblings..,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. HMSC035G02,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. HPA0247,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. ICM47,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. S6-Spd3,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 181,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp. oral taxon 473,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella shahii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella rimae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 215,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium diversum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium asaccharolyticum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella jejuni,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella scopos,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. F0091,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 299,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 306,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella veroralis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas flueggei,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum longum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. A12,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. F0442,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC034E03,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC067H01,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC071D03,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella infantium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp. T11011-6,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella tobetsuensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] infirmum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] sulci,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava",1783272|201174|1760|2037|2049|1654|55565;1783272|201174|1760|2037|2049|1654|1739406;1783272|201174|1760|2037|2049|1654|1203556;1783272|201174|1760|2037|2049|1654|936548;1783272|201174|1760|2037|2049|1654|1284680;1783272|201174|1760|2037|2049|1654|712121;3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|171552|1283313|712469;1783272|201174|84998|84999|1643824|1380;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294|194|199;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|186801|3082720|543314;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492|848|860;3379134|976|200643|171549|171552|2974257|228603;1783272|201174|84998|84999|1643824|2767353|1382;1783272|201174|84998|84999|1643824|2767353|1383;3384189|32066|203490|203491|1129771|32067|712359;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843489|31977|906|187326;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|3082720|543314|86331|114527;3379134|1224|28216|206351|481|482|484;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|3085636|186803|265975|1501332;1783272|1239|186801|3085636|186803|265975|1501329;1783272|1239|186801|3085636|186803|265975|237576;3379134|976|200643|171549|171551|836|322095;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|470565;3379134|976|200643|171549|171552|838|1177574;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552|838|60133;3379134|976|200643|171549|171552|838|589437;3379134|976|200643|171549|171552|838|1227276;3379134|976|200643|171549|171552|838|652716;3379134|976|200643|171549|171552|838|712461;3379134|976|200643|171549|171552|838|28137;1783272|201174|1760|85006|1268|32207|43675;1783272|201174|1760|2037|2049|2529408|1660;3379134|976|200643|171549|171552|2974251|228604;1783272|1239|909932|909929|1843491|970|135080;1783272|1239|526524|526525|128827|123375;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|186801|3085636|186803|1213720;1783272|1239|186801|3085636|186803|1213720|796942;1783272|1239|91061|186826|1300|1301|113107;1783272|1239|91061|186826|1300|1301|68892;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1759399;1783272|1239|91061|186826|1300|1301|999425;1783272|1239|91061|186826|1300|1301|1739309;1783272|1239|91061|186826|1300|1301|1739491;1783272|1239|91061|186826|1300|1301|1739341;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|909932|1843489|31977|29465|1911679;1783272|1239|909932|1843489|31977|29465|423477;1783272|1239|909932|1843489|31977|29465|2027459;1783272|1239|909932|1843489|31977|29465|1110546;1783272|1239|186801|3082720|543314|56774;1783272|1239|186801|3082720|543314|143393;1783272|1239|186801|3085636|186803;3379134|1224|28216|206351|481|482|28449,Complete,Svetlana up
bsdb:39528484/2/1,39528484,"cross-sectional observational, not case-control",39528484,https://doi.org/10.1038/s41467-024-53934-7,NA,"Manghi P., Filosi M., Zolfo M., Casten L.G., Garcia-Valiente A., Mattevi S., Heidrich V., Golzato D., Perini S., Thomas A.M., Montalbano S., Cancellieri S., Waldron L., Hall J.B., Xu S., Volfovsky N., Green Snyder L., Feliciano P., Asnicar F., Valles-Colomer M., Michaelson J.J., Segata N. , Domenici E.",Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders,Nature communications,2024,NA,Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,Autism spectrum disorder,EFO:0003756,Subset of Neurotypical Siblings(NTs),Subset of Autism Spectrum Disorders Children (ASD Children),Subset of Autism Spectrum Disorders Children (ASD Children) refers to a part of the ASD children(out of the 2154 in the study)  who show repetitive behaviours and sensory hyper-sensibility.,241,291,NA,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.2,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,"Fig. 3C, Supplementary Data 14",13 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in oral samples between Subset of Autism Spectrum Disorders children and Subset of Neurotypical Siblings,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces massiliensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium valvarum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella halliae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ottowia|s__Ottowia sp. oral taxon 894,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas catoniae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 056",1783272|201174|1760|2037|2049|1654|461393;1783272|201174|1760|2037|2049|1654|1655;1783272|201174|1760|2037|2049|1654|544580;1783272|201174|1760|85009|31957|2801844|1750;3379134|29547|3031852|213849|72294|194|824;3379134|1224|1236|135615|868|2717|2718;3379134|1224|1236|135615|868|2717|194702;3379134|1224|28216|206351|481|538|539;3379134|1224|28216|206351|481|538|1795832;3379134|1224|28216|206351|481|32257|505;3379134|1224|28216|80840|80864|219181|1658672;3379134|976|200643|171549|171551|836|41976;1783272|201174|1760|85006|1268|32207|172042;1783272|201174|1760|85006|1268|32207|2047;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|91061|186826|1300|1301|1305;1783272|1239|91061|186826|1300|1301|712620,Complete,Svetlana up
bsdb:39528484/2/2,39528484,"cross-sectional observational, not case-control",39528484,https://doi.org/10.1038/s41467-024-53934-7,NA,"Manghi P., Filosi M., Zolfo M., Casten L.G., Garcia-Valiente A., Mattevi S., Heidrich V., Golzato D., Perini S., Thomas A.M., Montalbano S., Cancellieri S., Waldron L., Hall J.B., Xu S., Volfovsky N., Green Snyder L., Feliciano P., Asnicar F., Valles-Colomer M., Michaelson J.J., Segata N. , Domenici E.",Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders,Nature communications,2024,NA,Experiment 2,United States of America,Homo sapiens,Saliva,UBERON:0001836,Autism spectrum disorder,EFO:0003756,Subset of Neurotypical Siblings(NTs),Subset of Autism Spectrum Disorders Children (ASD Children),Subset of Autism Spectrum Disorders Children (ASD Children) refers to a part of the ASD children(out of the 2154 in the study)  who show repetitive behaviours and sensory hyper-sensibility.,241,291,NA,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.2,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,"Fig. 3C, Supplementary Data 14",13 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in oral samples between Subset of Autism Spectrum Disorders children and Subset of Neurotypical Siblings,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. HMSC035G02,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. ICM47,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. S6-Spd3,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Pseudomonadati|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia|s__Chlamydia ibidis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella shahii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 215,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium diversum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium asaccharolyticum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella scopos,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. F0091,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC034E03,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC067H01,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC071D03,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella infantium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella tobetsuensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] sulci,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum",1783272|201174|1760|2037|2049|1654|55565;1783272|201174|1760|2037|2049|1654|1739406;1783272|201174|1760|2037|2049|1654|936548;1783272|201174|1760|2037|2049|1654|1284680;3379134|29547|3031852|213849|72294|194|199;3379134|204428|204429|51291|809|810|1405396;3379134|976|200643|171549|171552|2974257|228603;3384189|32066|203490|203491|1129771|32067|712359;1783272|1239|909932|1843489|31977|906|187326;1783272|1239|186801|3082720|543314|86331|114527;1783272|1239|186801|3085636|186803|265975|1501332;1783272|1239|186801|3085636|186803|265975|1501329;1783272|1239|186801|3085636|186803|265975|237576;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552|838|60133;3379134|976|200643|171549|171552|838|589437;3379134|976|200643|171549|171552|838|1227276;3379134|976|200643|171549|171552|2974251|228604;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|91061|186826|1300|1301|1739309;1783272|1239|91061|186826|1300|1301|1739491;1783272|1239|91061|186826|1300|1301|1739341;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|909932|1843489|31977|29465|1911679;1783272|1239|909932|1843489|31977|29465|1110546;1783272|1239|186801|3082720|543314|143393;3384189|32066|203490|203491|203492|848|860,Complete,Svetlana up
bsdb:39528484/3/1,39528484,"cross-sectional observational, not case-control",39528484,https://doi.org/10.1038/s41467-024-53934-7,NA,"Manghi P., Filosi M., Zolfo M., Casten L.G., Garcia-Valiente A., Mattevi S., Heidrich V., Golzato D., Perini S., Thomas A.M., Montalbano S., Cancellieri S., Waldron L., Hall J.B., Xu S., Volfovsky N., Green Snyder L., Feliciano P., Asnicar F., Valles-Colomer M., Michaelson J.J., Segata N. , Domenici E.",Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders,Nature communications,2024,NA,Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Autism spectrum disorder,EFO:0003756,Low Microbial Load,High Microbial Load,High Microbial Load is linked to poor oral hygiene and compromised oral health. It was found in both ASDs and NTs.,NA,NA,NA,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.005,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,"Fig. 2E, Supplementary Data 7",13 November 2024,KateRasheed,"KateRasheed,Aleru Divine,WikiWorks",Differentially abundant taxa in oral samples between High microbial load and low microbial load.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces johnsonii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces massiliensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 180,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 414,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp. oral taxon 473,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter curvus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium valvarum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella halliae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter|s__Enhydrobacter aerosaccus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium hwasookii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella bergeri,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella saccharolytica,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 215,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 225,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 847,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 879,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus luteus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Faucicola|s__Faucicola osloensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria cinerea,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sicca,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ottowia|s__Ottowia sp. oral taxon 894,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Pauljensenia|s__Pauljensenia hongkongensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 299,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia georgiae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas artemidis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas noxia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. FOBRC6,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. oral taxon 138,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. oral taxon 892,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. oral taxon 920,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sobrinus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. A12,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 056,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula",1783272|1239|91061|186826|186827|46123|46125;1783272|201174|1760|2037|2049|1654|544581;1783272|201174|1760|2037|2049|1654|461393;1783272|201174|1760|2037|2049|1654|1655;1783272|201174|1760|2037|2049|1654|544580;1783272|201174|1760|2037|2049|1654|651609;1783272|201174|1760|2037|2049|1654|712122;3379134|976|200643|171549|171552|1283313|712469;1783272|201174|1760|85009|31957|2801844|1750;3379134|29547|3031852|213849|72294|194|200;3379134|29547|3031852|213849|72294|194|824;3379134|976|117743|200644|49546|1016|45242;3379134|976|117743|200644|49546|1016|327575;3379134|976|117743|200644|49546|1016|1018;3379134|976|117743|200644|49546|1016|1019;3379134|1224|1236|135615|868|2717|2718;3379134|1224|1236|135615|868|2717|194702;1783272|201174|1760|85007|1653|1716|61592;1783272|201174|1760|85007|1653|1716|43768;1783272|201174|1760|85009|31957|1912216|1747;3379134|1224|28216|206351|481|538|539;3379134|1224|28216|206351|481|538|1795832;3379134|1224|28211|356|212791|225324;3384189|32066|203490|203491|203492|848|1583098;3384189|32066|203490|203491|203492|848|851;3384189|32066|203490|203491|203492|848|860;1783272|1239|91061|1385|539738|1378|84136;1783272|1239|91061|1385|539738|1378|1379;1783272|1239|91061|1385|539738|1378|29391;3379134|976|200643|171549|171552|2974257|633701;3379134|1224|28216|206351|481|32257|505;3384189|32066|203490|203491|1129771|32067|40542;3384189|32066|203490|203491|1129771|32067|157688;3384189|32066|203490|203491|1129771|32067|712359;3384189|32066|203490|203491|1129771|32067|671213;3384189|32066|203490|203491|1129771|32067|1785996;3384189|32066|203490|203491|1129771|32067|1227267;4751|5204|1538075|162474|742845|55193|76775;1783272|201174|1760|85006|1268|1269|1270;3379134|1224|1236|2887326|468|1604696|34062;3379134|1224|28216|206351|481|482|483;3379134|1224|28216|206351|481|482|490;3379134|1224|28216|80840|80864|219181|1658672;1783272|201174|1760|2037|2049|2740557|178339;3379134|976|200643|171549|171551|836|322095;3379134|976|200643|171549|171552|838|652716;1783272|201174|1760|85006|1268|32207|172042;1783272|201174|1760|85006|1268|32207|2047;1783272|201174|1760|2037|2049|2529408|52768;1783272|1239|909932|909929|1843491|970|671224;1783272|1239|909932|909929|1843491|970|135083;1783272|1239|909932|909929|1843491|970|936572;1783272|1239|909932|909929|1843491|970|712532;1783272|1239|909932|909929|1843491|970|1321785;1783272|1239|909932|909929|1843491|970|1884263;1783272|1239|91061|1385|90964|1279|1282;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|45634;1783272|1239|91061|186826|1300|1301|1302;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|91061|186826|1300|1301|1309;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|91061|186826|1300|1301|1313;1783272|1239|91061|186826|1300|1301|1305;1783272|1239|91061|186826|1300|1301|1310;1783272|1239|91061|186826|1300|1301|1759399;1783272|1239|91061|186826|1300|1301|712620;1783272|1239|91061|186826|1300|1301|1343;1783272|1239|909932|1843489|31977|29465|29466,Complete,Svetlana up
bsdb:39528484/3/2,39528484,"cross-sectional observational, not case-control",39528484,https://doi.org/10.1038/s41467-024-53934-7,NA,"Manghi P., Filosi M., Zolfo M., Casten L.G., Garcia-Valiente A., Mattevi S., Heidrich V., Golzato D., Perini S., Thomas A.M., Montalbano S., Cancellieri S., Waldron L., Hall J.B., Xu S., Volfovsky N., Green Snyder L., Feliciano P., Asnicar F., Valles-Colomer M., Michaelson J.J., Segata N. , Domenici E.",Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders,Nature communications,2024,NA,Experiment 3,United States of America,Homo sapiens,Saliva,UBERON:0001836,Autism spectrum disorder,EFO:0003756,Low Microbial Load,High Microbial Load,High Microbial Load is linked to poor oral hygiene and compromised oral health. It was found in both ASDs and NTs.,NA,NA,NA,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.005,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,"Fig. 2E, Supplementary Data 7",13 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in oral samples between High microbial load and low microbial load.,decreased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter rectus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella pleuritidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella rimae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. oral taxon 014,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Pseudoleptotrichia|s__Pseudoleptotrichia goodfellowii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] brachy,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] sulci,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella jejuni,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella shahii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium diversum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. ICM47,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. S6-Spd3,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 306,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium asaccharolyticum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella scopos,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC034E03,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC067H01,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. HMSC035G02,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. HPA0247,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium oral taxon 096,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 299,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella tobetsuensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. F0091,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum longum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. F0442,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp. oral taxon 473,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 215,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas flueggei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC071D03,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. A12,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 181,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella veroralis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp. T11011-6,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella infantium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] infirmum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum umeaense,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium pumilum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa",3379134|29547|3031852|213849|72294|194|203;3379134|976|117743|200644|49546|1016|1018;3379134|1224|1236|135625|712|724|735;3379134|976|200643|171549|171552|2974257|407975;1783272|1239|91061|186826|1300|1357|1358;1783272|201174|84998|84999|1643824|2767353|1383;3379134|1224|28216|80840|119060|47670|47671;3379134|1224|28216|206351|481|482|641148;1783272|1239|1737404|1737405|1570339|543311|33033;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|171552|838|28129;3379134|976|200643|171549|171552|838|28133;3384189|32066|203490|203491|1129771|2755140|157692;1783272|201174|1760|85006|1268|32207|172042;1783272|201174|1760|85006|1268|32207|2047;1783272|201174|1760|85004|31953|196081|230143;3379134|976|200643|171549|171552|2974251|28135;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|186801|3082720|543314|35517;1783272|1239|186801|3085636|186803|265975|1501329;1783272|1239|186801|3082720|543314|143393;3379134|976|200643|171549|171552|838|1177574;3379134|976|200643|171549|171552|838|60133;3379134|976|200643|171549|171552|2974257|228603;1783272|1239|909932|1843489|31977|906|187326;1783272|201174|1760|2037|2049|1654|55565;1783272|1239|186801|3082720|543314|86331|114527;1783272|201174|1760|2037|2049|1654|936548;1783272|201174|1760|2037|2049|1654|1284680;3379134|976|200643|171549|171552|838|712461;1783272|1239|186801|3085636|186803|265975|1501332;3379134|976|200643|171549|171552|2974251|228604;3379134|976|200643|171549|171552|838|470565;3379134|976|200643|171549|171552|838|589437;1783272|1239|526524|526525|128827|123375|102148;3379134|1224|28216|206351|481|482|28449;1783272|1239|91061|186826|1300|1301|1739309;1783272|1239|91061|186826|1300|1301|1739491;3379134|976|200643|171549|171552|1283313|671218;1783272|1239|909932|1843489|31977|29465|39777;1783272|201174|1760|2037|2049|1654|1739406;1783272|201174|84998|84999|1643824|2767353|1382;1783272|201174|1760|2037|2049|1654|1203556;3384189|32066|203490|203491|203492|848|860;1783272|1239|186801|3085636|186803|712982;1783272|1239|909932|1843489|31977|29465|423477;3379134|976|200643|171549|171552|838|652716;1783272|1239|909932|1843489|31977|29465|1110546;3379134|976|200643|171549|171552|838|1227276;1783272|1239|186801|3085636|186803|1213720|796942;1783272|1239|91061|186826|1300|1301|999425;3379134|976|200643|171549|171552|1283313|712469;1783272|1239|186801|3085636|186803|265975|237576;3384189|32066|203490|203491|1129771|32067|712359;3379134|976|200643|171549|171552|838|28132;1783272|1239|909932|909929|1843491|970|135080;1783272|1239|91061|186826|1300|1301|113107;1783272|1239|91061|186826|1300|1301|1739341;1783272|1239|91061|186826|1300|1301|1759399;1783272|201174|1760|2037|2049|1654|712121;3379134|29547|3031852|213849|72294|194|199;3379134|976|200643|171549|171552|838|28137;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|909932|1843489|31977|29465|2027459;1783272|1239|909932|1843489|31977|29465|1911679;3379134|976|200643|171549|171551|836|322095;1783272|1239|186801|3082720|543314|56774;3379134|1224|28216|206351|481|482|484;1783272|1239|909932|1843489|31977|39948|218538;1783272|201174|1760|2037|2049|2529408|1660;1783272|1239|186801|3085636|186803|1164882|617123;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|186801|3082720|543314|86331|86332;1783272|1239|91061|186826|1300|1301|68892;1783272|201174|1760|85006|1268|32207|43675,Complete,Svetlana up
bsdb:39528484/4/1,39528484,"cross-sectional observational, not case-control",39528484,https://doi.org/10.1038/s41467-024-53934-7,NA,"Manghi P., Filosi M., Zolfo M., Casten L.G., Garcia-Valiente A., Mattevi S., Heidrich V., Golzato D., Perini S., Thomas A.M., Montalbano S., Cancellieri S., Waldron L., Hall J.B., Xu S., Volfovsky N., Green Snyder L., Feliciano P., Asnicar F., Valles-Colomer M., Michaelson J.J., Segata N. , Domenici E.",Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders,Nature communications,2024,NA,Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,Cognitive impairment,HP:0100543,Low Intelligence Quotients(Low IQ ≤70),High Intelligence Quotients(High IQ > 85),High Intelligence Quotients(High IQ) was estimated from parent-reported data by an algorithm developed to estimate with high accuracy cognitive levels in large cohorts of ASD children. High IQ refers to intelligent quotients greater than 85.,413,784,NA,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.2,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,"Fig. 3C, Supplementary Data 17",14 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in oral samples between Autism Spectrum Disorders children with Low IQ and High IQ,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. HMSC035G02,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. ICM47,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. S6-Spd3,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 181,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium|s__Atopobium deltae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium argentoratense,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium diversum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium asaccharolyticum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella jejuni,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella scopos,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas flueggei,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC034E03,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC067H01,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella infantium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp. T11011-6,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] sulci",1783272|201174|1760|2037|2049|1654|55565;1783272|201174|1760|2037|2049|1654|1739406;1783272|201174|1760|2037|2049|1654|936548;1783272|201174|1760|2037|2049|1654|1284680;1783272|201174|1760|2037|2049|1654|712121;1783272|201174|84998|84999|1643824|1380|1393034;3379134|29547|3031852|213849|72294|194|199;1783272|201174|1760|85007|1653|1716|42817;3379134|976|200643|171549|171552|2974257|228603;3379134|976|200643|171549|171552|2974257|386414;1783272|201174|84998|84999|1643824|2767353|1382;1783272|1239|909932|1843489|31977|906|187326;1783272|1239|186801|3082720|543314|86331|114527;1783272|1239|186801|3085636|186803|265975|1501332;1783272|1239|186801|3085636|186803|265975|1501329;1783272|1239|186801|3085636|186803|265975|237576;3379134|976|200643|171549|171552|838|470565;3379134|976|200643|171549|171552|838|1177574;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552|838|60133;3379134|976|200643|171549|171552|838|589437;1783272|201174|1760|2037|2049|2529408|1660;3379134|976|200643|171549|171552|2974251|228604;1783272|1239|909932|909929|1843491|970|135080;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|91061|186826|1300|1301|1739309;1783272|1239|91061|186826|1300|1301|1739491;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|909932|1843489|31977|29465|1911679;1783272|1239|909932|1843489|31977|29465|423477;1783272|1239|909932|1843489|31977|29465|2027459;1783272|1239|186801|3082720|543314|143393,Complete,Svetlana up
bsdb:39528484/4/2,39528484,"cross-sectional observational, not case-control",39528484,https://doi.org/10.1038/s41467-024-53934-7,NA,"Manghi P., Filosi M., Zolfo M., Casten L.G., Garcia-Valiente A., Mattevi S., Heidrich V., Golzato D., Perini S., Thomas A.M., Montalbano S., Cancellieri S., Waldron L., Hall J.B., Xu S., Volfovsky N., Green Snyder L., Feliciano P., Asnicar F., Valles-Colomer M., Michaelson J.J., Segata N. , Domenici E.",Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders,Nature communications,2024,NA,Experiment 4,United States of America,Homo sapiens,Saliva,UBERON:0001836,Cognitive impairment,HP:0100543,Low Intelligence Quotients(Low IQ ≤70),High Intelligence Quotients(High IQ > 85),High Intelligence Quotients(High IQ) was estimated from parent-reported data by an algorithm developed to estimate with high accuracy cognitive levels in large cohorts of ASD children. High IQ refers to intelligent quotients greater than 85.,413,784,NA,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.2,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,"Fig. 3C, Supplementary Data 17",14 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in oral samples between Autism Spectrum Disorders children with Low IQ and High IQ,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus terreus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:83,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria|s__Kocuria palustris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda|s__Centipeda periodontii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria bacilliformis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 225,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema lecithinolyticum,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Acaryochloridales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium valvarum,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. FOBRC6,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella saccharolytica,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 879,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 897,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 414,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella halliae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces johnsonii",1783272|1239|186801|186802|216572|216851|853;3384194|508458|649775|649776|3029087|1434006|651822;1783272|201174|1760|85006|1268|32207|172042;1783272|1239|526524|526525|2810280|3025755|29348;1783272|201174|1760|85006|1268|1269|574650;3379134|976|200643|171549|2005525|375288|46503;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|28050|39485;3379134|976|200643|171549|815|909656|204516;1783272|1239|186801|186802|204475|745368;1783272|1239|186801|186802|216572|39492;3379134|976|200643|171549|171550|239759|214856;1783272|1239|186801|3082720|186804|1505657|261299;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|1262992;3379134|976|200643|171549|2005525|375288|823;1783272|201174|1760|85004|31953|1678|1681;1783272|1239|186801|3085636|186803|572511|40520;1783272|201174|1760|85004|31953|1678|28026;3379134|976|200643|171549|815|816|47678;1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|186801|186802|216572|1263|40518;1783272|201174|1760|85004|31953|1678|1680;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803|1407607|1150298;3379134|976|200643|171549|815|909656|821;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|1760|85006|1268|57493|71999;1783272|1239|186801|3085636|186803|1766253|39491;3379134|976|200643|171549|171552|2974257|28134;1783272|1239|91061|1385|539738|1378|29391;1783272|1239|91061|186826|186827|46123|46125;1783272|201174|1760|2037|2049|1654|544580;3379134|976|117743|200644|49546|1016|327575;1783272|1239|909932|909929|1843491|82202|82203;3379134|1224|28216|206351|481|482|267212;3384189|32066|203490|203491|1129771|32067|671213;3379134|203691|203692|136|2845253|157|53418;1783272|1117|3028117|3079744;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|91061|186826|1300|1301|1305;3379134|1224|1236|135615|868|2717|194702;3379134|29547|3031852|213849|72294|194|824;3379134|1224|28216|206351|481|538|539;3379134|1224|28216|206351|481|32257|505;3384189|32066|203490|203491|1129771|32067|157688;1783272|1239|91061|1385|90964|1279|1282;3379134|976|117743|200644|49546|1016|1017;1783272|201174|1760|85007|1653|1716|43768;1783272|1239|909932|909929|1843491|970|936572;1783272|201174|1760|2037|2049|1654|461393;3379134|976|200643|171549|171552|2974257|633701;3384189|32066|203490|203491|1129771|32067|1227267;1783272|201174|1760|2037|2049|1654|2081702;1783272|201174|1760|2037|2049|1654|712122;3379134|1224|28216|206351|481|538|1795832;1783272|1239|91061|186826|1300|1301|1302;1783272|201174|1760|85009|31957|1912216|1747;3379134|976|117743|200644|49546|1016|45242;1783272|201174|1760|85009|31957|2801844|1750;1783272|201174|1760|2037|2049|1654|544581,Complete,Svetlana up
bsdb:39528484/5/1,39528484,"cross-sectional observational, not case-control",39528484,https://doi.org/10.1038/s41467-024-53934-7,NA,"Manghi P., Filosi M., Zolfo M., Casten L.G., Garcia-Valiente A., Mattevi S., Heidrich V., Golzato D., Perini S., Thomas A.M., Montalbano S., Cancellieri S., Waldron L., Hall J.B., Xu S., Volfovsky N., Green Snyder L., Feliciano P., Asnicar F., Valles-Colomer M., Michaelson J.J., Segata N. , Domenici E.",Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders,Nature communications,2024,NA,Experiment 5,United States of America,Homo sapiens,Saliva,UBERON:0001836,Cognitive impairment,HP:0100543,Low Intelligence Quotients(Low IQ ≤70) by diet,High Intelligence Quotients(High IQ > 85) by diet,High Intelligence Quotients(High IQ) was estimated from parent-reported data by an algorithm developed to estimate with high accuracy cognitive levels in large cohorts of ASD children. High IQ refers to intelligent quotients greater than 85. This was adjusted for picky factor(diet).,413,784,NA,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.2,TRUE,NA,NA,"age,diet,sex",NA,NA,NA,NA,NA,NA,Signature 1,"Fig. 3C, Supplementary Data 18",14 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in oral samples between Autism Spectrum Disorders children with Low IQ and High IQ after adjusting for diet.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. HMSC035G02,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. ICM47,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. S6-Spd3,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 181,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium argentoratense,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella shahii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium diversum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium asaccharolyticum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella jejuni,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella scopos,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas flueggei,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC034E03,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC067H01,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella infantium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp. T11011-6,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] sulci",1783272|201174|1760|2037|2049|1654|55565;1783272|201174|1760|2037|2049|1654|1739406;1783272|201174|1760|2037|2049|1654|936548;1783272|201174|1760|2037|2049|1654|1284680;1783272|201174|1760|2037|2049|1654|712121;3379134|29547|3031852|213849|72294|194|199;1783272|201174|1760|85007|1653|1716|42817;3379134|976|200643|171549|171552|2974257|228603;1783272|201174|84998|84999|1643824|2767353|1382;1783272|1239|909932|1843489|31977|906|187326;1783272|1239|186801|3082720|543314|86331|114527;1783272|1239|186801|3085636|186803|265975|1501332;1783272|1239|186801|3085636|186803|265975|1501329;1783272|1239|186801|3085636|186803|265975|237576;3379134|976|200643|171549|171552|838|470565;3379134|976|200643|171549|171552|838|1177574;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552|838|60133;3379134|976|200643|171549|171552|838|589437;1783272|201174|1760|2037|2049|2529408|1660;3379134|976|200643|171549|171552|2974251|228604;1783272|1239|909932|909929|1843491|970|135080;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|91061|186826|1300|1301|1739309;1783272|1239|91061|186826|1300|1301|1739491;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|909932|1843489|31977|29465|1911679;1783272|1239|909932|1843489|31977|29465|423477;1783272|1239|909932|1843489|31977|29465|2027459;1783272|1239|186801|3082720|543314|143393,Complete,Svetlana up
bsdb:39528484/5/2,39528484,"cross-sectional observational, not case-control",39528484,https://doi.org/10.1038/s41467-024-53934-7,NA,"Manghi P., Filosi M., Zolfo M., Casten L.G., Garcia-Valiente A., Mattevi S., Heidrich V., Golzato D., Perini S., Thomas A.M., Montalbano S., Cancellieri S., Waldron L., Hall J.B., Xu S., Volfovsky N., Green Snyder L., Feliciano P., Asnicar F., Valles-Colomer M., Michaelson J.J., Segata N. , Domenici E.",Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders,Nature communications,2024,NA,Experiment 5,United States of America,Homo sapiens,Saliva,UBERON:0001836,Cognitive impairment,HP:0100543,Low Intelligence Quotients(Low IQ ≤70) by diet,High Intelligence Quotients(High IQ > 85) by diet,High Intelligence Quotients(High IQ) was estimated from parent-reported data by an algorithm developed to estimate with high accuracy cognitive levels in large cohorts of ASD children. High IQ refers to intelligent quotients greater than 85. This was adjusted for picky factor(diet).,413,784,NA,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.2,TRUE,NA,NA,"age,diet,sex",NA,NA,NA,NA,NA,NA,Signature 2,"Fig. 3C, Supplementary Data 18",14 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in oral samples between Autism Spectrum Disorders children with Low IQ and High IQ after adjusting for diet.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces johnsonii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces massiliensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella halliae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 215,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus terreus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:83,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria|s__Kocuria palustris,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella oralis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 225,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium valvarum,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda|s__Centipeda periodontii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria bacilliformis,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema lecithinolyticum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. FOBRC6,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella morbi,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella saccharolytica,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 879,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 897,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 414,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa",1783272|201174|1760|2037|2049|1654|544581;1783272|201174|1760|2037|2049|1654|461393;1783272|201174|1760|85009|31957|2801844|1750;1783272|201174|1760|85007|1653|1716|43768;1783272|201174|1760|85009|31957|1912216|1747;3379134|1224|28216|206351|481|538|1795832;3384189|32066|203490|203491|1129771|32067|157688;3384189|32066|203490|203491|1129771|32067|712359;1783272|1239|91061|186826|1300|1301|1305;1783272|201174|1760|85006|1268|1269|574650;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|186802|204475|745368;3379134|976|200643|171549|815|909656|204516;3379134|976|200643|171549|171550|239759|214856;1783272|1239|186801|3082720|186804|1505657|261299;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|572511|40520;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|1262992;3379134|976|200643|171549|815|816|47678;1783272|201174|1760|85004|31953|1678|1680;1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|91061|186826|1300|1301|28037;3379134|976|200643|171549|815|909656|821;3384194|508458|649775|649776|3029087|1434006|651822;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|1760|85006|1268|57493|71999;1783272|1239|91061|1385|539738|1378|29391;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|1766253|39491;3379134|976|200643|171549|171552|2974257|28134;1783272|201174|1760|2037|2049|1654|544580;1783272|201174|1760|2037|2049|1654|1655;3384189|32066|203490|203491|1129771|32067|671213;3379134|1224|28216|206351|481|538|539;3379134|1224|1236|135615|868|2717|194702;3379134|29547|3031852|213849|72294|194|824;1783272|1239|909932|909929|1843491|82202|82203;3379134|1224|28216|206351|481|32257|505;3379134|1224|28216|206351|481|482|267212;3379134|203691|203692|136|2845253|157|53418;1783272|1239|909932|909929|1843491|970|936572;3379134|976|117743|200644|49546|1016|1017;1783272|1239|91061|1385|90964|1279|1282;1783272|1239|186801|3085636|186803|43996|43997;3379134|976|200643|171549|171552|2974257|633701;3384189|32066|203490|203491|1129771|32067|1227267;1783272|201174|1760|2037|2049|1654|2081702;1783272|201174|1760|2037|2049|1654|712122;3379134|976|117743|200644|49546|1016|45242,Complete,Svetlana up
bsdb:39528484/6/1,39528484,"cross-sectional observational, not case-control",39528484,https://doi.org/10.1038/s41467-024-53934-7,NA,"Manghi P., Filosi M., Zolfo M., Casten L.G., Garcia-Valiente A., Mattevi S., Heidrich V., Golzato D., Perini S., Thomas A.M., Montalbano S., Cancellieri S., Waldron L., Hall J.B., Xu S., Volfovsky N., Green Snyder L., Feliciano P., Asnicar F., Valles-Colomer M., Michaelson J.J., Segata N. , Domenici E.",Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders,Nature communications,2024,NA,Experiment 6,United States of America,Homo sapiens,Saliva,UBERON:0001836,Cognitive function measurement,EFO:0008354,Lower Social Communication Questionnaire (Low SCQ) scale scale,Upper Social Communication Questionnaire (Upper SCQ) scale,Upper Social Communication Questionnaire (SCQ) scale is an ASD screening measures used to explore phenotypic aspects capable of explaining the observed differences in cognitive abilities. It reads greater than 95 interval.,NA,NA,NA,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.005,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Data 11,14 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in oral samples between Autism Spectrum Disorders children with Lower SCQ and Upper SCQ scale,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp. oral taxon 278,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,k__Pseudomonadati|p__Bacteroidota|s__Bacteroidetes oral taxon 274,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 498,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 414,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella morbi,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella maculosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella saccharolytica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces massiliensis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia|s__Bulleidia extructa,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 225,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 879,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus haemolyticus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis",1783272|1239|91061|186826|1300|1301|1302;3379134|976|200643|171549|171551|836|712437;3384189|32066|203490|203491|1129771|32067|40542;3379134|976|652708;1783272|201174|1760|85004|31953|196081|230143;3384189|32066|203490|203491|1129771|32067|712368;3379134|976|117743|200644|49546|1016|45242;1783272|201174|1760|2037|2049|1654|712122;1783272|1239|186801|3085636|186803|43996|43997;3379134|203691|203692|136|2845253|157|158;3379134|976|200643|171549|171552|2974251|439703;1783272|201174|1760|85009|31957|2801844|1750;1783272|201174|1760|85007|1653|1716|43768;3379134|976|200643|171549|171552|2974257|633701;1783272|201174|1760|2037|2049|1654|461393;1783272|1239|526524|526525|128827|118747|118748;3379134|29547|3031852|213849|72294|194|824;3384189|32066|203490|203491|1129771|32067|671213;3384189|32066|203490|203491|1129771|32067|1227267;3379134|1224|1236|135625|712|724|726;3384189|32066|203490|203491|1129771|32067|157688;1783272|201174|1760|2037|2049|1654|544580;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|91061|186826|1300|1301|28037,Complete,Svetlana up
bsdb:39528484/6/2,39528484,"cross-sectional observational, not case-control",39528484,https://doi.org/10.1038/s41467-024-53934-7,NA,"Manghi P., Filosi M., Zolfo M., Casten L.G., Garcia-Valiente A., Mattevi S., Heidrich V., Golzato D., Perini S., Thomas A.M., Montalbano S., Cancellieri S., Waldron L., Hall J.B., Xu S., Volfovsky N., Green Snyder L., Feliciano P., Asnicar F., Valles-Colomer M., Michaelson J.J., Segata N. , Domenici E.",Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders,Nature communications,2024,NA,Experiment 6,United States of America,Homo sapiens,Saliva,UBERON:0001836,Cognitive function measurement,EFO:0008354,Lower Social Communication Questionnaire (Low SCQ) scale scale,Upper Social Communication Questionnaire (Upper SCQ) scale,Upper Social Communication Questionnaire (SCQ) scale is an ASD screening measures used to explore phenotypic aspects capable of explaining the observed differences in cognitive abilities. It reads greater than 95 interval.,NA,NA,NA,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.005,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Data 11,14 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in oral samples between Autism Spectrum Disorders children with Lower SCQ and Upper SCQ scale,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter|s__Achromobacter sp. AONIH1,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax|s__Acidovorax temperans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. ICM47,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. S6-Spd3,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus christensenii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium|s__Agrobacterium pusense,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus versicolor,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides galacturonicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:144,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides zoogleoformans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium angulatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Bowdeniella|s__Bowdeniella nasicola,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga canimorsus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter|s__Caulobacter vibrioides,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella minuta,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium gleum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium neonatale,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:253,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas thiooxydans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium ammoniagenes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium resistens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium striatum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter|s__Cronobacter sakazakii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Curtobacterium|s__Curtobacterium flaccumfaciens,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio fairfieldensis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|s__Desulfovibrionaceae bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Dickeya|s__Dickeya chrysanthemi,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter bugandensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter soli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus hirae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus saccharolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia|s__Erwinia billingiae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium anhuiense,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium varium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia alvei,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Jonquetella|s__Jonquetella anthropi,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus|s__Lactiplantibacillus paraplantarum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus|s__Lactiplantibacillus pentosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus amylovorus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus equicursoris,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus garvieae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus petauri,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus aviarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus antri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus coleohominis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus panis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Liquorilactobacillus|s__Liquorilactobacillus nagelii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus|s__Lysinibacillus fusiformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma hominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium|s__Microbacterium oleivorans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus curtisii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus mulieris,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium diversum,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mycoplasmopsis|s__Mycoplasmopsis agalactiae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium asaccharolyticum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Ornithinimicrobiaceae|g__Ornithinimicrobium|s__Ornithinimicrobium pekingense,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus odorifer,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella|s__Pasteurella dagmatis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus grossensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas cangingivalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas circumdentaria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas crevioricanis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Priestia|s__Priestia flexa,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Priestia|s__Priestia megaterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus|s__Proteus mirabilis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles|s__Roseateles puraquae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus champanellensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Shouchella|s__Shouchella clausii,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium|s__Sphingobacterium sp. B29,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas acidaminiphila,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gallolyticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parauberis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pasteurianus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus troglodytae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus uberis,k__Bacillati|p__Bacillota|c__Tissierellia|s__Tissierellia bacterium KA00581,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma urealyticum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella infantium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella montpellierensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas|s__Xanthomonas arboricola,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas|s__Xanthomonas translucens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia|s__Yersinia frederiksenii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia|s__Yersinia intermedia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma|s__[Collinsella] massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] sulci,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus|s__Jeotgalicoccus sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leifsonia|s__Leifsonia sp. 71-9,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium|s__Microbacterium laevaniformans,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|g__Exiguobacterium|s__Exiguobacterium sp. RIT594,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia sympodialis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Acidipropionibacterium|s__Acidipropionibacterium acidipropionici,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. NS1(2017),k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Ewingella|s__Ewingella americana,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas gingeri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Pantoea allii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Suttonella|s__Suttonella indologenes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium singulare,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas yamanorum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter|s__Achromobacter piechaudii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia mannitolilytica,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas koreensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. AFS040349,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas|s__Xanthomonas hortorum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|s__Alphaproteobacteria bacterium HGW-Alphaproteobacteria-17,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium|s__Microbacterium sp. SMR1,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Tetragenococcus|s__Tetragenococcus muriaticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Apilactobacillus|s__Apilactobacillus kunkeei,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|s__Sphingomonadales bacterium RIFCSPHIGHO2_01_FULL_65_20,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Bruguierivoracaceae|g__Sodalis|s__Sodalis praecaptivus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Duganella|s__Duganella phyllosphaerae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Cytobacillus|s__Cytobacillus horneckiae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia gladioli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. HMWF006,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomonadales|f__Hyphomonadaceae|g__Hyphomonas|s__Hyphomonas atlantica corrig.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas|s__Xanthomonas sacchari,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas sanguinis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium|s__Methylobacterium phyllosphaerae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Gluconobacter|s__Gluconobacter frateurii,k__Thermotogati|p__Thermotogota|c__Thermotogae|o__Thermotogales|f__Fervidobacteriaceae|g__Fervidobacterium|s__Fervidobacterium pennivorans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium pollutisoli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Jeotgalibaca|s__Jeotgalibaca sp. PTS2502,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas granadensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus nuruki,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella negevensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Tepidimonas|s__Tepidimonas fonticaldi,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Parageobacillus|s__Parageobacillus thermoglucosidasius,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus reticulitermitis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chishuiella|s__Chishuiella changwenlii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium|s__Agrobacterium salinitolerans,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mycoplasmopsis|s__Mycoplasmopsis canis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Canicola|s__Canicola haemoglobinophilus,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus proteolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Rodentibacter|s__Rodentibacter caecimuris,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus hongkongensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Aeriscardovia|s__Aeriscardovia aeriphila,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Pantoea sp. AS-PWVM4,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella pluranimalium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas lurida,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas indicatrix,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Companilactobacillus|s__Companilactobacillus futsaii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus|s__Jeotgalicoccus aerolatus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Winkia|s__Winkia neuii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium avium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia paralvei,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium|s__Brevibacterium iodinum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Liquorilactobacillus|s__Liquorilactobacillus mali,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. OV508,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rouxiella|s__Rouxiella silvae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. 2822_17,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella soli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella hellenica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella paramesenteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium|s__Microbacterium hominis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Geobacillus|s__Geobacillus kaustophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Geobacillus|s__Geobacillus thermoleovorans,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Geobacillus|s__Geobacillus thermocatenulatus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium scophthalmum,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter sp. C12-8,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Acetobacter|s__Acetobacter orientalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas cerasi,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Boseaceae|g__Bosea|s__Bosea vaviloviae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas ginsenosidimutans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella grimontii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lentilactobacillus|s__Lentilactobacillus parabuchneri,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Macrococcoides|s__Macrococcoides bohemicum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. Choline-02u-1,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas chlororaphis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia proteamaculans,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sp. DISK 18,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum|s__Herbaspirillum frisingense,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium|s__Sphingobacterium nematocida,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium|s__Microbacterium paraoxydans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Glutamicibacter|s__Glutamicibacter sp.,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium balustinum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas soli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kluyvera|s__Kluyvera intermedia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus amylolyticus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria zoodegmatis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter|s__Arthrobacter pityocampae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rahnella|s__Rahnella sikkimica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus saerimneri,k__Pseudomonadati|p__Myxococcota|c__Myxococcia|o__Myxococcales|f__Archangiaceae|g__Hyalangium|s__Hyalangium minutum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Pantoea latae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Duganella|s__Duganella sp. Leaf61,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium freneyi,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus safensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus|s__Pediococcus sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus|s__Pediococcus parvulus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Secundilactobacillus|s__Secundilactobacillus collinoides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus|s__Pediococcus ethanolidurans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lentilactobacillus|s__Lentilactobacillus parafarraginis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lentilactobacillus|s__Lentilactobacillus rapi,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus haynesii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium|s__Microbacterium sp. Leaf151,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium|s__Photobacterium phosphoreum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus devriesei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alteromonas|s__Alteromonas macleodii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas sp. SPM,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Siccibacter|s__Siccibacter turicensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Sanguibacteraceae|g__Sanguibacter|s__Sanguibacter sp. Leaf3,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. kpr-6,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Neorhizobium|s__Neorhizobium sp. SOG26,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Criibacterium|s__Criibacterium bergeronii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter|s__Lysobacter enzymogenes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces gaoshouyii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas|s__Xanthomonas euvesicatoria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas|s__Xanthomonas citri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Schleiferilactobacillus|s__Schleiferilactobacillus harbinensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Shouchella|s__Shouchella rhizosphaerae,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus glaucus,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia pachydermatis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Epilithonimonas|s__Epilithonimonas hispanica,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Blattabacteriaceae|g__Blattabacterium|s__Blattabacterium punctulatus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes|s__Alcaligenes aquatilis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Helcococcus|s__Helcococcus kunzii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium glaucum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Eremococcus|s__Eremococcus coleocola,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Tanticharoenia|s__Tanticharoenia sakaeratensis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Gluconobacter|s__Gluconobacter albidus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Pandoraea|s__Pandoraea pnomenusa,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Rickettsiaceae|g__Rickettsia|s__Rickettsia bellii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Pseudonocardia|s__Pseudonocardia autotrophica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium moukalabense,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus hominis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia sp. Leaf51,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Tetzosporium|s__Tetzosporium hominis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Companilactobacillus|s__Companilactobacillus alimentarius,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Tersicoccus|s__Tersicoccus sp. Bi-70,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Dickeya|s__Dickeya dadantii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Pseudorhodobacter|s__Pseudorhodobacter sp. MZDSW-24AT,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium aquidurense,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Companilactobacillus|s__Companilactobacillus crustorum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Fructilactobacillus|s__Fructilactobacillus fructivorans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium|s__Arcanobacterium haemolyticum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Bordetella|s__Bordetella bronchiseptica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia radingae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia grimesii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium|s__Janthinobacterium lividum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium vitaeruminis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus|s__Cupriavidus sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Gulbenkiania|s__Gulbenkiania indica,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium gambrini,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus condimenti,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Candidatus Phytoplasma|s__Aster yellows witches'-broom phytoplasma,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Candidatus Phytoplasma|s__Onion yellows phytoplasma,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia ficaria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia|s__Dietzia timorensis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingopyxidaceae|g__Sphingopyxis|s__Sphingopyxis terrae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister sp. CAG:357,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Acetobacter|s__Acetobacter senegalensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter|s__Achromobacter ruhlandii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae|g__Alicyclobacillus|s__Alicyclobacillus acidocaldarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus frumenti,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Peribacillus|s__Peribacillus simplex,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium tyrobutyricum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia|s__Yersinia ruckeri,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium|s__Brachybacterium sp. UMB0905,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Blastomonadaceae|g__Blastomonas|s__Blastomonas sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium|s__Novosphingobium sp. AAP93,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rahnella|s__Rahnella sp. AA,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Rickettsiaceae|g__Rickettsia|s__Rickettsia asembonensis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Rickettsiaceae|g__Rickettsia|s__Rickettsia hoogstraalii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Rickettsiaceae|g__Rickettsia|s__Rickettsia canadensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter genomosp. 15BJ,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter proteolyticus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Clavibacter|s__Clavibacter michiganensis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Acetobacter|s__Acetobacter syzygii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Cobetia|s__Cobetia marina,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus sp. RL,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Bavariicoccus|s__Bavariicoccus seileri,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella seminalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Paucilactobacillus|s__Paucilactobacillus wasatchensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Secundilactobacillus|s__Secundilactobacillus malefermentans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Solilutibacter|s__Solilutibacter tolerans,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp. oral taxon 386,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium|s__Carnobacterium inhibens,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|g__Exiguobacterium|s__Exiguobacterium indicum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Fulvimonas|s__Fulvimonas soli,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Nocardia|s__Nocardia nova,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Trueperales|f__Trueperaceae|g__Truepera|s__Truepera radiovictrix,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus|s__Thermus arciformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] minutum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia|s__Candidatus Erwinia dacicola,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Paenirhizobium|s__Paenirhizobium selenitireducens,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter upsaliensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium|s__Microbacterium sp. AR7-10,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. URMO17WK12:I2,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Aliarcobacter|s__Aliarcobacter butzleri,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax|s__Acidovorax sp. MR-S7,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas grimontii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. 57B-090624,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Brevibacillus|s__Brevibacillus parabrevis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella|s__Brucella lupini,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella|s__Brucella haematophila,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas kuykendallii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum|s__Actinobaculum massiliense,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Metapseudomonas|s__Metapseudomonas otitidis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium RIFCSPHIGHO2_01_FULL_63_240,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae|g__Pseudoalteromonas|s__Pseudoalteromonas nigrifaciens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rouxiella|s__Rouxiella badensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinotignum|s__Actinotignum urinale,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter|s__Psychrobacter immobilis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella|s__Shewanella baltica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia|s__Erwinia persicina,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Aurantimonadaceae|g__Aureimonas|s__Aureimonas altamirensis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium|s__Agrobacterium deltaense,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus pasadenensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. FS01,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinotignum|s__Actinotignum timonense,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kosakonia|s__Kosakonia oryzae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles|s__Roseateles terrae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Atlantibacter|s__Atlantibacter hermannii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|g__Paenirhodobacter|s__Paenirhodobacter enshiensis,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Oscillatoriales|f__Sirenicapillariaceae|g__Limnospira|s__Limnospira maxima,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc suionicum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Pseudolactococcus|s__Pseudolactococcus chungangensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium lepraemurium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivicanis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter|s__Achromobacter denitrificans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp. ESNIH1,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter canis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycolicibacterium|s__Mycolicibacterium llatzerense,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus geothermalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter brisouii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia tropica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Latilactobacillus|s__Latilactobacillus fuchuensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lentilactobacillus|s__Lentilactobacillus farraginis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter 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up
bsdb:39528484/7/1,39528484,"cross-sectional observational, not case-control",39528484,https://doi.org/10.1038/s41467-024-53934-7,NA,"Manghi P., Filosi M., Zolfo M., Casten L.G., Garcia-Valiente A., Mattevi S., Heidrich V., Golzato D., Perini S., Thomas A.M., Montalbano S., Cancellieri S., Waldron L., Hall J.B., Xu S., Volfovsky N., Green Snyder L., Feliciano P., Asnicar F., Valles-Colomer M., Michaelson J.J., Segata N. , Domenici E.",Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders,Nature communications,2024,NA,Experiment 7,United States of America,Homo sapiens,Saliva,UBERON:0001836,Cognitive function measurement,EFO:0008354,Low Developmental Coordination Disorder Questionnaires (DCDQ) scale,High Developmental Coordination Disorder Questionnaires (DCDQ) scale,High Developmental Coordination Disorder Questionnaires (DCDQ) scale refers to an ASD screening measures used to explore phenotypic aspects capable of explaining the observed differences in cognitive abilities.,NA,NA,NA,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.005,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Data 12,15 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in oral samples between Autism Spectrum Disorders children with Lower DCDQ and Upper DCDQ scale,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] sulci,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella jejuni,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium diversum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium asaccharolyticum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella scopos,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. ICM47,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. S6-Spd3,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC067H01,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC034E03,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 215,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp. T11011-6,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. HMSC035G02,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella infantium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica",1783272|1239|186801|3082720|543314|143393;3379134|976|200643|171549|171552|838|60133;1783272|1239|186801|3085636|186803|265975|1501329;3379134|976|200643|171549|171552|838|1177574;1783272|1239|909932|1843489|31977|906|187326;1783272|1239|186801|3082720|543314|86331|114527;1783272|1239|186801|3085636|186803|265975|1501332;3379134|976|200643|171549|171552|838|589437;1783272|201174|1760|2037|2049|1654|55565;1783272|201174|1760|2037|2049|1654|936548;1783272|1239|909932|1843489|31977|29465|39777;1783272|201174|1760|2037|2049|1654|1284680;3379134|976|200643|171549|171552|2974251|228604;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|91061|186826|1300|1301|113107;1783272|1239|91061|186826|1300|1301|1739491;3384189|32066|203490|203491|203492|848|860;1783272|1239|91061|186826|1300|1301|1739309;3384189|32066|203490|203491|1129771|32067|712359;1783272|1239|186801|3085636|186803|265975|237576;3379134|976|200643|171549|171552|838|28132;1783272|1239|909932|1843489|31977|29465|2027459;1783272|201174|84998|84999|1643824|2767353|1382;1783272|201174|1760|2037|2049|1654|1739406;3379134|29547|3031852|213849|72294|194|199;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|909932|1843489|31977|29465|1911679;1783272|201174|1760|2037|2049|2529408|1660,Complete,Svetlana up
bsdb:39528484/7/2,39528484,"cross-sectional observational, not case-control",39528484,https://doi.org/10.1038/s41467-024-53934-7,NA,"Manghi P., Filosi M., Zolfo M., Casten L.G., Garcia-Valiente A., Mattevi S., Heidrich V., Golzato D., Perini S., Thomas A.M., Montalbano S., Cancellieri S., Waldron L., Hall J.B., Xu S., Volfovsky N., Green Snyder L., Feliciano P., Asnicar F., Valles-Colomer M., Michaelson J.J., Segata N. , Domenici E.",Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders,Nature communications,2024,NA,Experiment 7,United States of America,Homo sapiens,Saliva,UBERON:0001836,Cognitive function measurement,EFO:0008354,Low Developmental Coordination Disorder Questionnaires (DCDQ) scale,High Developmental Coordination Disorder Questionnaires (DCDQ) scale,High Developmental Coordination Disorder Questionnaires (DCDQ) scale refers to an ASD screening measures used to explore phenotypic aspects capable of explaining the observed differences in cognitive abilities.,NA,NA,NA,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.005,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Data 12,15 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in oral samples between Autism Spectrum Disorders children with Lower DCDQ and Upper DCDQ scale,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 225,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella halliae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia rubra,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 879",1783272|1239|91061|186826|1300|1301|28037;1783272|1239|91061|186826|1300|1301|1303;1783272|201174|1760|85007|1653|1716|61592;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|91061|186826|1300|1301|1305;1783272|201174|1760|2037|2049|1654|544580;3379134|1224|28216|206351|481|32257|505;1783272|1239|91061|186826|1300|1301|45634;3384189|32066|203490|203491|1129771|32067|671213;1783272|201174|1760|2037|2049|1654|1655;3379134|1224|28216|206351|481|538|1795832;1783272|1239|91061|1385|90964|1279|1282;3379134|976|117743|200644|49546|1016|45242;1783272|201174|1760|85004|31953|196081|230143;3384189|32066|203490|203491|1129771|32067|157688;1783272|1239|91061|186826|1300|1301|1309;1783272|201174|1760|85009|31957|2801844|1547448;1783272|201174|1760|85007|1653|1716|43768;1783272|1239|91061|186826|1300|1301|1302;1783272|201174|1760|85009|31957|1912216|1747;3384189|32066|203490|203491|1129771|32067|1227267,Complete,Svetlana up
bsdb:39528484/8/1,39528484,"cross-sectional observational, not case-control",39528484,https://doi.org/10.1038/s41467-024-53934-7,NA,"Manghi P., Filosi M., Zolfo M., Casten L.G., Garcia-Valiente A., Mattevi S., Heidrich V., Golzato D., Perini S., Thomas A.M., Montalbano S., Cancellieri S., Waldron L., Hall J.B., Xu S., Volfovsky N., Green Snyder L., Feliciano P., Asnicar F., Valles-Colomer M., Michaelson J.J., Segata N. , Domenici E.",Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders,Nature communications,2024,NA,Experiment 8,United States of America,Homo sapiens,Saliva,UBERON:0001836,Cognitive impairment,HP:0100543,Low Intelligence Quotients(Low IQ ≤70),High Intelligence Quotients(High IQ > 85),High Intelligence Quotients(High IQ) was estimated from parent-reported data by an algorithm developed to estimate with high accuracy cognitive levels in large cohorts of ASD children. High IQ refers to intelligent quotients greater than 85.,413,784,NA,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.005,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Data 13,1 January 2025,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in oral samples between Autism Spectrum Disorders children with Low IQ and High IQ,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. S6-Spd3,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella shahii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium diversum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium asaccharolyticum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella jejuni,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] sulci,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. ICM47,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella scopos,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC067H01,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella tobetsuensis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. HMSC035G02,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC034E03,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 215,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 181,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 299,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 306,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella infantium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas flueggei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sputorum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. A12,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp. T11011-6,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium oral taxon 096,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum longum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella rimae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. F0442,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp. oral taxon 473,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] infirmum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC071D03,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum umeaense,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia exigua,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis",1783272|201174|1760|2037|2049|1654|55565;1783272|201174|1760|2037|2049|1654|1284680;3379134|976|200643|171549|171552|2974257|228603;1783272|1239|909932|1843489|31977|906|187326;1783272|1239|186801|3082720|543314|86331|114527;1783272|1239|186801|3085636|186803|265975|1501332;1783272|1239|186801|3085636|186803|265975|1501329;3379134|976|200643|171549|171552|838|1177574;3379134|976|200643|171549|171552|838|60133;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|186801|3082720|543314|143393;1783272|201174|1760|2037|2049|1654|936548;3379134|976|200643|171549|171552|2974251|228604;1783272|1239|909932|1843489|31977|29465|423477;3379134|976|200643|171549|171552|838|589437;3379134|976|200643|171549|171552|838|470565;1783272|1239|91061|186826|1300|1301|1739491;1783272|1239|909932|1843489|31977|29465|1110546;3384189|32066|203490|203491|203492|848|860;1783272|201174|84998|84999|1643824|2767353|1382;1783272|201174|1760|2037|2049|1654|1739406;3379134|976|200643|171549|171552|838|28132;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|186801|3085636|186803|265975|237576;1783272|1239|91061|186826|1300|1301|113107;1783272|1239|91061|186826|1300|1301|1739309;3384189|32066|203490|203491|1129771|32067|712359;1783272|201174|1760|2037|2049|1654|712121;3379134|976|200643|171549|171552|838|652716;3379134|29547|3031852|213849|72294|194|199;3379134|976|200643|171549|171552|838|712461;1783272|1239|909932|1843489|31977|29465|1911679;1783272|1239|909932|1843489|31977|29465|39778;3379134|976|200643|171549|171551|836|322095;1783272|1239|909932|909929|1843491|970|135080;3379134|1224|1236|135625|712|724|1078480;1783272|1239|91061|186826|1300|1301|1759399;1783272|1239|909932|1843489|31977|29465|2027459;1783272|1239|186801|3085636|186803|712982;1783272|1239|186801|3085636|186803|1213720|796942;1783272|201174|84998|84999|1643824|2767353|1383;3379134|976|200643|171549|171552|1283313|671218;1783272|201174|1760|2037|2049|2529408|1660;1783272|1239|91061|186826|1300|1301|999425;3379134|976|200643|171549|171552|1283313|712469;3379134|1224|28216|206351|481|482|484;1783272|1239|186801|3082720|543314|56774;1783272|1239|91061|186826|1300|1301|1739341;1783272|1239|186801|3085636|186803|1164882|617123;1783272|1239|91061|186826|1300|1301|68892;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|909932|1843489|31977|39948|218538;1783272|201174|84998|1643822|1643826|84108|84109;1783272|1239|91061|1385|539738|1378|84135,Complete,Svetlana up
bsdb:39528484/8/2,39528484,"cross-sectional observational, not case-control",39528484,https://doi.org/10.1038/s41467-024-53934-7,NA,"Manghi P., Filosi M., Zolfo M., Casten L.G., Garcia-Valiente A., Mattevi S., Heidrich V., Golzato D., Perini S., Thomas A.M., Montalbano S., Cancellieri S., Waldron L., Hall J.B., Xu S., Volfovsky N., Green Snyder L., Feliciano P., Asnicar F., Valles-Colomer M., Michaelson J.J., Segata N. , Domenici E.",Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders,Nature communications,2024,NA,Experiment 8,United States of America,Homo sapiens,Saliva,UBERON:0001836,Cognitive impairment,HP:0100543,Low Intelligence Quotients(Low IQ ≤70),High Intelligence Quotients(High IQ > 85),High Intelligence Quotients(High IQ) was estimated from parent-reported data by an algorithm developed to estimate with high accuracy cognitive levels in large cohorts of ASD children. High IQ refers to intelligent quotients greater than 85.,413,784,NA,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.005,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Data 13,1 January 2025,KateRasheed,"KateRasheed,WikiWorks",Differentially abundant taxa in oral samples between Autism Spectrum Disorders children with Low IQ and High IQ,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces massiliensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 414,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella halliae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 879,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Pauljensenia|s__Pauljensenia hongkongensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia georgiae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 056,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces radicidentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria|s__Kocuria marina|s__Kocuria marina subsp. indica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium pseudogenitalium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus simulans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter ursingii,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus|s__Paracoccus salipaludis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium accolens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Janibacter|s__Janibacter indicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium pseudodiphtheriticum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium namnetense,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus|s__Paracoccus yeei,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium kroppenstedtii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus capitis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. F0473,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum pigrum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium granulosum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria|s__Kocuria palustris,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 847,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria|s__Kocuria rhizophila,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter|s__Enhydrobacter aerosaccus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter curvus,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Faucicola|s__Faucicola osloensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema lecithinolyticum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 448,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda|s__Centipeda periodontii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas infelix,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus luteus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium valvarum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. oral taxon 138,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 897,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas noxia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ottowia|s__Ottowia sp. oral taxon 894,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 180,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. FOBRC6,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 225,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 498,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas artemidis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. oral taxon 920,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces johnsonii",1783272|201174|1760|2037|2049|1654|461393;1783272|201174|1760|2037|2049|1654|712122;1783272|201174|1760|85009|31957|2801844|1750;3379134|976|117743|200644|49546|1016|45242;1783272|201174|1760|85007|1653|1716|43768;1783272|201174|1760|85009|31957|1912216|1747;3379134|1224|28216|206351|481|538|1795832;3384189|32066|203490|203491|1129771|32067|1227267;1783272|201174|1760|2037|2049|2740557|178339;1783272|201174|1760|2037|2049|2529408|52768;1783272|1239|91061|186826|1300|1301|1302;1783272|1239|91061|186826|1300|1301|1309;1783272|1239|91061|186826|1300|1301|712620;1783272|201174|1760|2037|2049|1654|111015;1783272|201174|1760|85006|1268|57493|223184|1049583;1783272|201174|1760|85007|1653|1716|38303;1783272|1239|91061|1385|90964|1279|1286;3379134|1224|1236|2887326|468|469|108980;3379134|1224|28211|204455|31989|265|2032623;1783272|201174|1760|85007|1653|1716|38284;1783272|201174|1760|85006|85021|53457|857417;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|186801|3085636|186803|1766253|39491;1783272|201174|1760|85007|1653|1716|37637;1783272|201174|1760|85009|31957|1912216|1574624;3379134|1224|28211|204455|31989|265|147645;1783272|201174|1760|85007|1653|1716|161879;1783272|1239|186801|186802|216572|216851|853;4751|4890|3239874|2916678|766764|5475|5476;1783272|1239|91061|1385|90964|1279|29388;1783272|1239|909932|909929|1843491|970|999423;3384194|508458|649775|649776|3029087|1434006|651822;1783272|1239|91061|1385|539738|1378|29391;1783272|1239|91061|186826|186828|29393|29394;1783272|201174|1760|85009|31957|1912216|33011;1783272|201174|1760|85006|1268|57493|71999;3384189|32066|203490|203491|1129771|32067|1785996;1783272|201174|1760|85006|1268|57493|72000;3379134|1224|28211|356|212791|225324;3379134|29547|3031852|213849|72294|194|200;4751|5204|1538075|162474|742845|55193|76775;3379134|976|117743|200644|49546|1016|1017;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|909932|909929|1843491|970|69823;3379134|1224|1236|2887326|468|1604696|34062;1783272|201174|1760|85006|1268|32207|172042;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|91061|186826|1300|1301|1303;3379134|976|117743|200644|49546|1016|327575;3379134|203691|203692|136|2845253|157|53418;3379134|1224|28216|206351|481|538|539;3379134|1224|1236|135615|868|2717|2718;1783272|1239|91061|1385|90964|1279|1290;1783272|201174|1760|2037|2049|1654|712124;3379134|976|117743|200644|49546|1016|1018;1783272|1239|909932|909929|1843491|82202|82203;1783272|1239|909932|909929|1843491|970|135082;1783272|201174|1760|85006|1268|1269|1270;3379134|1224|1236|135615|868|2717|194702;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|45634;1783272|1239|909932|909929|1843491|970|712532;1783272|201174|1760|85006|1268|32207|2047;1783272|201174|1760|85007|1653|1716|61592;1783272|201174|1760|2037|2049|1654|2081702;1783272|1239|909932|909929|1843491|970|135083;3379134|1224|28216|80840|80864|219181|1658672;1783272|201174|1760|2037|2049|1654|651609;1783272|1239|91061|1385|90964|1279|1282;1783272|201174|1760|2037|2049|1654|544580;1783272|1239|91061|186826|1300|1301|1305;1783272|1239|909932|909929|1843491|970|936572;3384189|32066|203490|203491|1129771|32067|671213;3384189|32066|203490|203491|1129771|32067|40542;3384189|32066|203490|203491|1129771|32067|712368;1783272|1239|91061|186826|1300|1301|1343;1783272|201174|1760|2037|2049|1654|1655;3379134|29547|3031852|213849|72294|194|824;1783272|1239|909932|909929|1843491|970|671224;3384189|32066|203490|203491|1129771|32067|157688;1783272|1239|909932|909929|1843491|970|1884263;3379134|1224|28216|206351|481|32257|505;1783272|201174|1760|2037|2049|1654|544581,Complete,Svetlana up
bsdb:39538341/1/1,39538341,laboratory experiment,39538341,10.1186/s42523-024-00355-y,NA,"Pearce C.S., Bukovsky D., Douchant K., Katoch A., Greenlaw J., Gale D.J., Nashed J.Y., Brien D., Kuhlmeier V.A., Sabbagh M.A., Blohm G., De Felice F.G., Pare M., Cook D.J., Scott S.H., Munoz D.P., Sjaarda C.P., Tusche A., Sheth P.M., Winterborn A., Boehnke S. , Gallivan J.P.",Changes in social environment impact primate gut microbiota composition,Animal microbiome,2024,"Gut microbiota, Metagenomics, Monkeys, Primates, Social environment, Social living",Experiment 1,Canada,Macaca fascicularis,Feces,UBERON:0001988,Diet,EFO:0002755,Uncontrolled diet (T1 single),Controlled diet (T2 single),"Following T1Single data collection, at the beginning of the  Single Living phase, the enrichment elements of NHP’s diet for the remainder of the study (referred to as “controlled” diet) was strictly controlled. This controlled diet approach directly help to investigate how diet alterations impact GM composition during a period of stable single living, i.e., comparing 
the transition from uncontrolled (T1Single) to controlled diet (T2Single) during the Single Living phase.",13,13,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 1,Figure 2C and Figure S7A,27 November 2024,MyleeeA,"MyleeeA,WikiWorks","Differential relative abundance of bacterial families and genus exhibiting the diet effect. LEfSe analysis identified significantly different taxa between diet-uncontrolled (red, T1Single) and diet-controlled (light blue, T2Single) conditions.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Lentisphaerales|f__Lentisphaeraceae|g__Lentisphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Paramuribaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Aestuariispiraceae|g__Aestuariispira",3379134|1224|28216;1783272|1239|186801|186802|31979;1783272|201174|84998|84999|84107;1783272|1239|186801|186802;3379134|29547|3031852|213849|72293|209;3379134|29547|3031852|213849|72293;1783272|1239|186801|3082720|186804|1505657;1783272|1239|186801|186802|1392389;3379134|256845|1313211|278081|566277|256846;3379134|976|200643|171549|2005473|2518497;1783272|1239|186801|3082720|186804;1783272|1239|186801|186802|31979|1266;1783272|201174|84998|84999|84107|1473205;3379134|1224|28211|204441|3466454|1647175,Complete,Svetlana up
bsdb:39538341/1/2,39538341,laboratory experiment,39538341,10.1186/s42523-024-00355-y,NA,"Pearce C.S., Bukovsky D., Douchant K., Katoch A., Greenlaw J., Gale D.J., Nashed J.Y., Brien D., Kuhlmeier V.A., Sabbagh M.A., Blohm G., De Felice F.G., Pare M., Cook D.J., Scott S.H., Munoz D.P., Sjaarda C.P., Tusche A., Sheth P.M., Winterborn A., Boehnke S. , Gallivan J.P.",Changes in social environment impact primate gut microbiota composition,Animal microbiome,2024,"Gut microbiota, Metagenomics, Monkeys, Primates, Social environment, Social living",Experiment 1,Canada,Macaca fascicularis,Feces,UBERON:0001988,Diet,EFO:0002755,Uncontrolled diet (T1 single),Controlled diet (T2 single),"Following T1Single data collection, at the beginning of the  Single Living phase, the enrichment elements of NHP’s diet for the remainder of the study (referred to as “controlled” diet) was strictly controlled. This controlled diet approach directly help to investigate how diet alterations impact GM composition during a period of stable single living, i.e., comparing 
the transition from uncontrolled (T1Single) to controlled diet (T2Single) during the Single Living phase.",13,13,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 2,Figure 2C and Figure S7A,27 November 2024,MyleeeA,"MyleeeA,WikiWorks","Differential relative abundance of bacterial families and genus exhibiting the diet effect. LEfSe analysis identified significantly different taxa between diet-uncontrolled (red, T1Single) and diet-controlled (light blue, T2Single) conditions.",decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium",1783272|1239|909932|1843489|31977;3379134|976|200643|171549|171552;1783272|1239|91061|186826|33958;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|33958|2742598;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|2569097;1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|186802|3085642|2048137;1783272|1239|186801|3085636|186803|265975,Complete,Svetlana up
bsdb:39538341/3/1,39538341,laboratory experiment,39538341,10.1186/s42523-024-00355-y,NA,"Pearce C.S., Bukovsky D., Douchant K., Katoch A., Greenlaw J., Gale D.J., Nashed J.Y., Brien D., Kuhlmeier V.A., Sabbagh M.A., Blohm G., De Felice F.G., Pare M., Cook D.J., Scott S.H., Munoz D.P., Sjaarda C.P., Tusche A., Sheth P.M., Winterborn A., Boehnke S. , Gallivan J.P.",Changes in social environment impact primate gut microbiota composition,Animal microbiome,2024,"Gut microbiota, Metagenomics, Monkeys, Primates, Social environment, Social living",Experiment 3,Canada,Macaca fascicularis,Feces,UBERON:0001988,Diet measurement,EFO:0008111,T1 Single (Effect of Diet),T2 Single (Effect of Diet),Group with controlled diet (T2Single) during the Single Living phase.,NA,NA,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4b,24 January 2025,MyleeeA,"MyleeeA,WikiWorks",Changes in relative abundance between T1Single to T2Single using Mann-Whitney.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,1783272|1239|186801|186802|31979,Complete,Svetlana up
bsdb:39538341/3/2,39538341,laboratory experiment,39538341,10.1186/s42523-024-00355-y,NA,"Pearce C.S., Bukovsky D., Douchant K., Katoch A., Greenlaw J., Gale D.J., Nashed J.Y., Brien D., Kuhlmeier V.A., Sabbagh M.A., Blohm G., De Felice F.G., Pare M., Cook D.J., Scott S.H., Munoz D.P., Sjaarda C.P., Tusche A., Sheth P.M., Winterborn A., Boehnke S. , Gallivan J.P.",Changes in social environment impact primate gut microbiota composition,Animal microbiome,2024,"Gut microbiota, Metagenomics, Monkeys, Primates, Social environment, Social living",Experiment 3,Canada,Macaca fascicularis,Feces,UBERON:0001988,Diet measurement,EFO:0008111,T1 Single (Effect of Diet),T2 Single (Effect of Diet),Group with controlled diet (T2Single) during the Single Living phase.,NA,NA,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4a,24 January 2025,MyleeeA,"MyleeeA,WikiWorks",Changes in relative abundance between T1Single to T2Single using Mann-Whitney.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,1783272|1239|91061|186826|33958,Complete,Svetlana up
bsdb:39538341/4/1,39538341,laboratory experiment,39538341,10.1186/s42523-024-00355-y,NA,"Pearce C.S., Bukovsky D., Douchant K., Katoch A., Greenlaw J., Gale D.J., Nashed J.Y., Brien D., Kuhlmeier V.A., Sabbagh M.A., Blohm G., De Felice F.G., Pare M., Cook D.J., Scott S.H., Munoz D.P., Sjaarda C.P., Tusche A., Sheth P.M., Winterborn A., Boehnke S. , Gallivan J.P.",Changes in social environment impact primate gut microbiota composition,Animal microbiome,2024,"Gut microbiota, Metagenomics, Monkeys, Primates, Social environment, Social living",Experiment 4,Canada,Macaca fascicularis,Feces,UBERON:0001988,Social environment measurement,EFO:0010552,T2Single (effect of moving from single to pairwise living),T3Social(effect of moving from single to pairwise living),"The Protected Pairwise Social Living phase was implemented and lasted for 6 months, during which T3Social and T4Social data were collected.",NA,NA,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4a,24 January 2025,MyleeeA,"MyleeeA,WikiWorks",Changes in relative abundance between T2Single to T3pairwise using Mann-Whitney.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,1783272|1239|91061|186826|33958,Complete,Svetlana up
bsdb:39538341/4/2,39538341,laboratory experiment,39538341,10.1186/s42523-024-00355-y,NA,"Pearce C.S., Bukovsky D., Douchant K., Katoch A., Greenlaw J., Gale D.J., Nashed J.Y., Brien D., Kuhlmeier V.A., Sabbagh M.A., Blohm G., De Felice F.G., Pare M., Cook D.J., Scott S.H., Munoz D.P., Sjaarda C.P., Tusche A., Sheth P.M., Winterborn A., Boehnke S. , Gallivan J.P.",Changes in social environment impact primate gut microbiota composition,Animal microbiome,2024,"Gut microbiota, Metagenomics, Monkeys, Primates, Social environment, Social living",Experiment 4,Canada,Macaca fascicularis,Feces,UBERON:0001988,Social environment measurement,EFO:0010552,T2Single (effect of moving from single to pairwise living),T3Social(effect of moving from single to pairwise living),"The Protected Pairwise Social Living phase was implemented and lasted for 6 months, during which T3Social and T4Social data were collected.",NA,NA,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4b,24 January 2025,MyleeeA,"MyleeeA,WikiWorks",Changes in relative abundance between T2Single to T3pairwise using Mann-Whitney.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,1783272|1239|186801|186802|31979,Complete,Svetlana up
bsdb:39538341/5/1,39538341,laboratory experiment,39538341,10.1186/s42523-024-00355-y,NA,"Pearce C.S., Bukovsky D., Douchant K., Katoch A., Greenlaw J., Gale D.J., Nashed J.Y., Brien D., Kuhlmeier V.A., Sabbagh M.A., Blohm G., De Felice F.G., Pare M., Cook D.J., Scott S.H., Munoz D.P., Sjaarda C.P., Tusche A., Sheth P.M., Winterborn A., Boehnke S. , Gallivan J.P.",Changes in social environment impact primate gut microbiota composition,Animal microbiome,2024,"Gut microbiota, Metagenomics, Monkeys, Primates, Social environment, Social living",Experiment 5,Canada,Macaca fascicularis,Feces,UBERON:0001988,Social interaction measurement,EFO:0009592,T2Single (effect of moving from single to pairwise living),T4Social(effect of moving from single to pairwise living),"The Protected Pairwise Social Living phase was implemented and lasted for 6 months, during which T3Social and T4Social data were collected.",NA,NA,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4a,24 January 2025,MyleeeA,"MyleeeA,WikiWorks",Changes in relative abundance between T2Single to T4pairwise using Mann-Whitney.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,1783272|1239|91061|186826|33958,Complete,Svetlana up
bsdb:39538341/6/1,39538341,laboratory experiment,39538341,10.1186/s42523-024-00355-y,NA,"Pearce C.S., Bukovsky D., Douchant K., Katoch A., Greenlaw J., Gale D.J., Nashed J.Y., Brien D., Kuhlmeier V.A., Sabbagh M.A., Blohm G., De Felice F.G., Pare M., Cook D.J., Scott S.H., Munoz D.P., Sjaarda C.P., Tusche A., Sheth P.M., Winterborn A., Boehnke S. , Gallivan J.P.",Changes in social environment impact primate gut microbiota composition,Animal microbiome,2024,"Gut microbiota, Metagenomics, Monkeys, Primates, Social environment, Social living",Experiment 6,Canada,Macaca fascicularis,Feces,UBERON:0001988,Diet,EFO:0002755,Diet Effect Timepoint 2 (Decreasing),Diet Effect Timepoint 2 (Increasing),Diet alterations impact (Controlled diet/Timepoint 2) during the Single Living phase,NA,NA,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 6 and 7,24 January 2025,MyleeeA,"MyleeeA,WikiWorks",Significant taxa associated with Diet Effect in Timepoint 2,increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",3379134|200940|3031449|213115|194924;3379134|29547|3031852|213849|72293;3379134|200940|3031449|213115|194924|872,Complete,Svetlana up
bsdb:39538341/6/2,39538341,laboratory experiment,39538341,10.1186/s42523-024-00355-y,NA,"Pearce C.S., Bukovsky D., Douchant K., Katoch A., Greenlaw J., Gale D.J., Nashed J.Y., Brien D., Kuhlmeier V.A., Sabbagh M.A., Blohm G., De Felice F.G., Pare M., Cook D.J., Scott S.H., Munoz D.P., Sjaarda C.P., Tusche A., Sheth P.M., Winterborn A., Boehnke S. , Gallivan J.P.",Changes in social environment impact primate gut microbiota composition,Animal microbiome,2024,"Gut microbiota, Metagenomics, Monkeys, Primates, Social environment, Social living",Experiment 6,Canada,Macaca fascicularis,Feces,UBERON:0001988,Diet,EFO:0002755,Diet Effect Timepoint 2 (Decreasing),Diet Effect Timepoint 2 (Increasing),Diet alterations impact (Controlled diet/Timepoint 2) during the Single Living phase,NA,NA,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 6 and 7,24 January 2025,MyleeeA,"MyleeeA,WikiWorks",Significant taxa associated with Diet Effect in Timepoint 2,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus",1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958;3379134|976|200643|171549|171552;1783272|1239|909932|1843489|31977;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|33042;1783272|1239|909932|1843489|31977|39948;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|2742598,Complete,Svetlana up
bsdb:39538341/7/1,39538341,laboratory experiment,39538341,10.1186/s42523-024-00355-y,NA,"Pearce C.S., Bukovsky D., Douchant K., Katoch A., Greenlaw J., Gale D.J., Nashed J.Y., Brien D., Kuhlmeier V.A., Sabbagh M.A., Blohm G., De Felice F.G., Pare M., Cook D.J., Scott S.H., Munoz D.P., Sjaarda C.P., Tusche A., Sheth P.M., Winterborn A., Boehnke S. , Gallivan J.P.",Changes in social environment impact primate gut microbiota composition,Animal microbiome,2024,"Gut microbiota, Metagenomics, Monkeys, Primates, Social environment, Social living",Experiment 7,Canada,Macaca fascicularis,Feces,UBERON:0001988,Social interaction measurement,EFO:0009592,Social Living Effect Timepoint 2 (Decreasing),Social Living Effect Timepoint 2 (Increasing),Social living effect of moving from single living (Timepoint 2) to pairwise living (Timepoint 3).,NA,NA,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 6 and 7,24 January 2025,MyleeeA,"MyleeeA,WikiWorks",Significant taxa associated with Social living Effect in Timepoint 2,increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter",3379134|29547|3031852|213849|72293;3379134|29547|3031852|213849|72293|209,Complete,Svetlana up
bsdb:39538341/7/2,39538341,laboratory experiment,39538341,10.1186/s42523-024-00355-y,NA,"Pearce C.S., Bukovsky D., Douchant K., Katoch A., Greenlaw J., Gale D.J., Nashed J.Y., Brien D., Kuhlmeier V.A., Sabbagh M.A., Blohm G., De Felice F.G., Pare M., Cook D.J., Scott S.H., Munoz D.P., Sjaarda C.P., Tusche A., Sheth P.M., Winterborn A., Boehnke S. , Gallivan J.P.",Changes in social environment impact primate gut microbiota composition,Animal microbiome,2024,"Gut microbiota, Metagenomics, Monkeys, Primates, Social environment, Social living",Experiment 7,Canada,Macaca fascicularis,Feces,UBERON:0001988,Social interaction measurement,EFO:0009592,Social Living Effect Timepoint 2 (Decreasing),Social Living Effect Timepoint 2 (Increasing),Social living effect of moving from single living (Timepoint 2) to pairwise living (Timepoint 3).,NA,NA,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 6 and 7,24 January 2025,MyleeeA,"MyleeeA,WikiWorks",Significant taxa associated with Social living Effect in Timepoint 2,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958,Complete,Svetlana up
bsdb:39538341/8/1,39538341,laboratory experiment,39538341,10.1186/s42523-024-00355-y,NA,"Pearce C.S., Bukovsky D., Douchant K., Katoch A., Greenlaw J., Gale D.J., Nashed J.Y., Brien D., Kuhlmeier V.A., Sabbagh M.A., Blohm G., De Felice F.G., Pare M., Cook D.J., Scott S.H., Munoz D.P., Sjaarda C.P., Tusche A., Sheth P.M., Winterborn A., Boehnke S. , Gallivan J.P.",Changes in social environment impact primate gut microbiota composition,Animal microbiome,2024,"Gut microbiota, Metagenomics, Monkeys, Primates, Social environment, Social living",Experiment 8,Canada,Macaca fascicularis,Feces,UBERON:0001988,Social interaction measurement,EFO:0009592,Social Living Effect Timepoint 3 (Decreasing),Social Living Effect Timepoint 3 (Increasing),Social living effect in the protected pairwise living phase (Timepoint 3),NA,NA,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 6 and 7,24 January 2025,MyleeeA,"MyleeeA,WikiWorks",Significant taxa associated with Social living Effect in Timepoint 3,increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter",3379134|29547|3031852|213849|72293;3379134|29547|3031852|213849|72293|209,Complete,Svetlana up
bsdb:39549509/1/1,39549509,"cross-sectional observational, not case-control",39549509,10.1016/j.tube.2024.102577,NA,"Zhang H., Xue M., He X., Sun L., He Q., Wang Y. , Jin J.",Altered intestinal microbiota and fecal metabolites in patients with latent and active pulmonary tuberculosis,"Tuberculosis (Edinburgh, Scotland)",2024,"16S rRNA gene sequencing, Fecal metabolites, Gut microbiota, Latent pulmonary tuberculosis, Pulmonary tuberculosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,Healthy controls,Pulmonary tuberculosis patients,confirmed pulmonary tuberculosis,13,13,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,decreased,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 3A and B,16 July 2025,Nuerteye,Nuerteye,"Identification of differential microbial biomarkers. (A, B and C) Evolutionary branching plots showing the most divergent taxa identified by LEfSe.",increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|s__Prevotellaceae bacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__uncultured Lactobacillus sp.",1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|2049047;1783272|1239|91061|186826|33958|1578|153152,Complete,NA
bsdb:39549509/1/2,39549509,"cross-sectional observational, not case-control",39549509,10.1016/j.tube.2024.102577,NA,"Zhang H., Xue M., He X., Sun L., He Q., Wang Y. , Jin J.",Altered intestinal microbiota and fecal metabolites in patients with latent and active pulmonary tuberculosis,"Tuberculosis (Edinburgh, Scotland)",2024,"16S rRNA gene sequencing, Fecal metabolites, Gut microbiota, Latent pulmonary tuberculosis, Pulmonary tuberculosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,Healthy controls,Pulmonary tuberculosis patients,confirmed pulmonary tuberculosis,13,13,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,decreased,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 3A and B,16 July 2025,Nuerteye,Nuerteye,"Identification of differential microbial biomarkers. (A, B and C) Evolutionary branching plots showing the most divergent taxa identified by LEfSe.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__uncultured Roseburia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__uncultured Megasphaera sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.",1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|28050;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|186801|3085636|186803|841|512314;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|909932|1843489|31977|906|165188;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|186802|31979|1485|59620,Complete,NA
bsdb:39549509/2/1,39549509,"cross-sectional observational, not case-control",39549509,10.1016/j.tube.2024.102577,NA,"Zhang H., Xue M., He X., Sun L., He Q., Wang Y. , Jin J.",Altered intestinal microbiota and fecal metabolites in patients with latent and active pulmonary tuberculosis,"Tuberculosis (Edinburgh, Scotland)",2024,"16S rRNA gene sequencing, Fecal metabolites, Gut microbiota, Latent pulmonary tuberculosis, Pulmonary tuberculosis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,latent tuberculosis patients (LTBI),pulmonary tuberculosis (PTB),confirmed pulmonary tuberculosis patients,13,13,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,decreased,decreased,decreased,decreased,NA,decreased,Signature 1,Fig. 3C and D,16 July 2025,Nuerteye,Nuerteye,"Identification of differential microbial biomarkers. (A, B and C) Evolutionary branching plots showing the most divergent taxa identified by LEfSe. (B, D and F) Bar graphs showing LDA values for LEfSe analysis of bacterial abundance.",increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio sp.",1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;3379134|976|200643|171549|171552|1283313;3379134|200940|3031449|213115|194924|872|885,Complete,NA
bsdb:39549509/2/2,39549509,"cross-sectional observational, not case-control",39549509,10.1016/j.tube.2024.102577,NA,"Zhang H., Xue M., He X., Sun L., He Q., Wang Y. , Jin J.",Altered intestinal microbiota and fecal metabolites in patients with latent and active pulmonary tuberculosis,"Tuberculosis (Edinburgh, Scotland)",2024,"16S rRNA gene sequencing, Fecal metabolites, Gut microbiota, Latent pulmonary tuberculosis, Pulmonary tuberculosis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,latent tuberculosis patients (LTBI),pulmonary tuberculosis (PTB),confirmed pulmonary tuberculosis patients,13,13,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,decreased,decreased,decreased,decreased,NA,decreased,Signature 2,Fig. 3C and D,16 July 2025,Nuerteye,Nuerteye,"Identification of differential microbial biomarkers. (A, B and C) Evolutionary branching plots showing the most divergent taxa identified by LEfSe. (B, D and F) Bar graphs showing LDA values for LEfSe analysis of bacterial abundance.",decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3384189|32066|203490|203491;3384189|32066|203490;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803,Complete,NA
bsdb:39569373/1/1,39569373,time series / longitudinal observational,39569373,10.1016/j.isci.2024.111238,https://pmc.ncbi.nlm.nih.gov/articles/PMC11576381/,"Talukdar D., Sarkar M., Ahrodia T., Kumar S., De D., Nath S., Jana P., Verma J., Mehta O., Kothidar A., Yodhaanjali J.R., Sharma K., Bakshi S., Singh U., Kshetrapal P., Wadhwa N., Thiruvengadam R., Nair G.B., Bhatnagar S., Mukherjee S. , Das B.",Previse preterm birth in early pregnancy through vaginal microbiome signatures using metagenomics and dipstick assays,iScience,2024,"Diagnostics, Medical science, Medicine, Microbiology, Microbiome, Reproductive medicine, Women’s health",Experiment 1,India,Homo sapiens,Vagina,UBERON:0000996,Spontaneous preterm birth,EFO:0006917,Term birth-Trimester one (TB-T1),Preterm birth-Trimester one (PTB-T1),Samples collected during the first trimester of pregnancy (T1) from women who subsequently delivered preterm (PTB).,140,60,1 week,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,increased,NA,NA,Signature 1,Figure 7,26 November 2024,Aleru Divine,"Aleru Divine,WikiWorks",Differential abundance of the vaginal microbiome during the first trimester of pregnancy (T1) in women from India who delivered preterm (PTB) or at term (TB).,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella corporis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens",1783272|1239|91061|186826|33958|1578|147802;3379134|1224|1236|72274|135621|286|306;1783272|201174|84998|84999|1643824|2767327|82135;3379134|976|200643|171549|171552|838|28128;3384189|32066|203490|203491|1129771|168808|40543,Complete,Svetlana up
bsdb:39569373/1/2,39569373,time series / longitudinal observational,39569373,10.1016/j.isci.2024.111238,https://pmc.ncbi.nlm.nih.gov/articles/PMC11576381/,"Talukdar D., Sarkar M., Ahrodia T., Kumar S., De D., Nath S., Jana P., Verma J., Mehta O., Kothidar A., Yodhaanjali J.R., Sharma K., Bakshi S., Singh U., Kshetrapal P., Wadhwa N., Thiruvengadam R., Nair G.B., Bhatnagar S., Mukherjee S. , Das B.",Previse preterm birth in early pregnancy through vaginal microbiome signatures using metagenomics and dipstick assays,iScience,2024,"Diagnostics, Medical science, Medicine, Microbiology, Microbiome, Reproductive medicine, Women’s health",Experiment 1,India,Homo sapiens,Vagina,UBERON:0000996,Spontaneous preterm birth,EFO:0006917,Term birth-Trimester one (TB-T1),Preterm birth-Trimester one (PTB-T1),Samples collected during the first trimester of pregnancy (T1) from women who subsequently delivered preterm (PTB).,140,60,1 week,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,increased,NA,NA,Signature 2,Figure 7,26 November 2024,Rahila,"Rahila,WikiWorks",Differential abundance of the vaginal microbiome during the first trimester of pregnancy (T1) in women from India who delivered preterm (PTB) or at term (TB).,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii",1783272|1239|91061|186826|33958|1578|47770;1783272|1239|91061|186826|33958|1578|33959,Complete,Svetlana up
bsdb:39569373/2/1,39569373,time series / longitudinal observational,39569373,10.1016/j.isci.2024.111238,https://pmc.ncbi.nlm.nih.gov/articles/PMC11576381/,"Talukdar D., Sarkar M., Ahrodia T., Kumar S., De D., Nath S., Jana P., Verma J., Mehta O., Kothidar A., Yodhaanjali J.R., Sharma K., Bakshi S., Singh U., Kshetrapal P., Wadhwa N., Thiruvengadam R., Nair G.B., Bhatnagar S., Mukherjee S. , Das B.",Previse preterm birth in early pregnancy through vaginal microbiome signatures using metagenomics and dipstick assays,iScience,2024,"Diagnostics, Medical science, Medicine, Microbiology, Microbiome, Reproductive medicine, Women’s health",Experiment 2,India,Homo sapiens,Vagina,UBERON:0000996,Spontaneous preterm birth,EFO:0006917,Term birth-Trimester one (TB-T1),Preterm birth-Trimester one (PTB-T1),Samples collected during the first trimester of pregnancy (T1) from women who subsequently delivered preterm (PTB).,140,60,1 week,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,increased,increased,NA,NA,Signature 1,Figure 6A,19 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Boxplots showing the relative abundance (%) of L. iners and L. crispatus in preterm (PTB) and term (TB) samples at 1st trimester.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,1783272|1239|91061|186826|33958|1578|147802,Complete,Svetlana up
bsdb:39569373/2/2,39569373,time series / longitudinal observational,39569373,10.1016/j.isci.2024.111238,https://pmc.ncbi.nlm.nih.gov/articles/PMC11576381/,"Talukdar D., Sarkar M., Ahrodia T., Kumar S., De D., Nath S., Jana P., Verma J., Mehta O., Kothidar A., Yodhaanjali J.R., Sharma K., Bakshi S., Singh U., Kshetrapal P., Wadhwa N., Thiruvengadam R., Nair G.B., Bhatnagar S., Mukherjee S. , Das B.",Previse preterm birth in early pregnancy through vaginal microbiome signatures using metagenomics and dipstick assays,iScience,2024,"Diagnostics, Medical science, Medicine, Microbiology, Microbiome, Reproductive medicine, Women’s health",Experiment 2,India,Homo sapiens,Vagina,UBERON:0000996,Spontaneous preterm birth,EFO:0006917,Term birth-Trimester one (TB-T1),Preterm birth-Trimester one (PTB-T1),Samples collected during the first trimester of pregnancy (T1) from women who subsequently delivered preterm (PTB).,140,60,1 week,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,increased,increased,NA,NA,Signature 2,Figure 6D,19 December 2024,Aleru Divine,"Aleru Divine,WikiWorks",Boxplots showing the relative abundance (%) of L. iners and L. crispatus in preterm (PTB) and term (TB) samples at 1st trimester.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,1783272|1239|91061|186826|33958|1578|47770,Complete,Svetlana up
bsdb:39572530/1/1,39572530,case-control,39572530,10.1038/s41398-024-03183-5,NA,"Liu X., Ling Z., Cheng Y., Wu L., Shao L., Gao J., Lei W., Zhu Z., Ding W., Song Q., Zhao L. , Jin G.",Oral fungal dysbiosis and systemic immune dysfunction in Chinese patients with schizophrenia,Translational psychiatry,2024,NA,Experiment 1,China,Homo sapiens,Tongue,UBERON:0001723,Schizophrenia,MONDO:0005090,Healthy controls (Con),Schizophrenia patients (SZ),Patients with schizophrenia (SZ),97,118,1 month,ITS / ITS2,NA,Illumina,relative abundances,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,unchanged,decreased,Signature 1,"Figure 3A, 3B",24 October 2025,Tosin,Tosin,Differential oral fungal taxa between the SZ (schizophrenia) patients and healthy controls using the linear discriminant analysis (LDA) effect size (LEfSe) method,increased,"k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus,k__Fungi|p__Basidiomycota,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Erysiphales|f__Erysiphaceae|g__Blumeria,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales|f__Sclerotiniaceae|g__Botrytis,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Bulleraceae|g__Bullera,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Bulleraceae,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Erysiphales|f__Erysiphaceae,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Erysiphales,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales,k__Fungi|p__Ascomycota|c__Eurotiomycetes,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycodales|f__Saccharomycodaceae|g__Hanseniaspora,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales,k__Fungi|p__Ascomycota|c__Leotiomycetes,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales,k__Fungi|p__Basidiomycota|c__Malasseziomycetes,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales|f__Peniophoraceae|g__Peniophora,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales|f__Peniophoraceae,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Periconiaceae|g__Periconia,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Periconiaceae,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycodales|f__Saccharomycodaceae,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales|f__Sclerotiniaceae,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae|g__Trichosporon,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales",4751|4890|147545|5042|1131492;4751|4890|147545|5042|1131492|5052;4751|5204;4751|4890|147548|5120|34371|34372;4751|4890|147548|5178|28983|33196;4751|5204|155616|5234|1905116|4970;4751|5204|155616|5234|1905116;4751|4890|147548|5120|34371;4751|4890|147548|5120;4751|4890|147545|5042;4751|4890|147545;4751|4890|4891|3243779|34365|29832;4751|4890|147548|5178;4751|4890|147548;4751|5204|1538075|162474|742845|55193;4751|5204|1538075|162474|742845;4751|5204|1538075|162474;4751|5204|1538075;4751|5204|155619|452342|103393|40463;4751|5204|155619|452342|103393;4751|4890|147541|92860|1898439|97971;4751|4890|147541|92860|1898439;4751|4890|147541|92860;4751|5204|155619|452342;4751|4890|4891|4892|4893|4930;4751|4890|4891|4892|4893;4751|4890|4891|3243779|34365;4751|4890|147548|5178|28983;4751|5204|155616|1851469|1759442|5552;4751|5204|155616|1851469|1759442;4751|5204|155616|1851469,Complete,KateRasheed
bsdb:39572530/1/2,39572530,case-control,39572530,10.1038/s41398-024-03183-5,NA,"Liu X., Ling Z., Cheng Y., Wu L., Shao L., Gao J., Lei W., Zhu Z., Ding W., Song Q., Zhao L. , Jin G.",Oral fungal dysbiosis and systemic immune dysfunction in Chinese patients with schizophrenia,Translational psychiatry,2024,NA,Experiment 1,China,Homo sapiens,Tongue,UBERON:0001723,Schizophrenia,MONDO:0005090,Healthy controls (Con),Schizophrenia patients (SZ),Patients with schizophrenia (SZ),97,118,1 month,ITS / ITS2,NA,Illumina,relative abundances,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,2,"age,sex",NA,NA,unchanged,unchanged,unchanged,unchanged,decreased,Signature 2,"Figure 3A, 3B",24 October 2025,Tosin,Tosin,Differential oral fungal taxa between the SZ (schizophrenia) patients and healthy controls using the linear discriminant analysis (LDA) effect size (LEfSe) method,decreased,"k__Fungi|p__Basidiomycota|c__Agaricomycetes,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Pleosporaceae|g__Alternaria,k__Fungi|p__Ascomycota,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae|g__Cercospora,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Psathyrellaceae|g__Coprinellus,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Cryptococcaceae,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Cryptococcaceae|g__Cryptococcus,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Debaryomyces,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Pleosporaceae,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Psathyrellaceae,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Rhodotorula,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales,k__Fungi|p__Ascomycota|c__Saccharomycetes,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Tausonia,k__Fungi|p__Basidiomycota|c__Wallemiomycetes|o__Wallemiales|f__Wallemiaceae|g__Wallemia,k__Fungi|p__Basidiomycota|c__Wallemiomycetes|o__Wallemiales|f__Wallemiaceae,k__Fungi|p__Basidiomycota|c__Wallemiomycetes|o__Wallemiales,k__Fungi|p__Basidiomycota|c__Wallemiomycetes",4751|5204|155619;4751|4890|147541|92860|28556|5598;4751|4890;4751|4890|3239874|2916678|766764|5475;4751|4890|147541|2726947|93133|29002;4751|5204|155619|5338|184208|184430;4751|5204|155616|5234|1884633;4751|5204|155616|5234|1884633|5206;4751|5204|155616|90883;4751|4890|3239874|2916678|766764|4958;4751|4890|3239874|2916678|766764;4751|5204|155616|90883|1851551;4751|4890|147541|2726947|93133;4751|4890|147541|2726947;4751|4890|147541|92860|28556;4751|5204|155619|5338|184208;4751|5204|162481|231213|1799696|5533;4751|4890|4891|4892;4751|4890|4891|4892;4751|4890|4891;4751|5204|155616|90883|1851551|415704;4751|5204|431957|431958|431959|148959;4751|5204|431957|431958|431959;4751|5204|431957|431958;4751|5204|431957,Complete,KateRasheed
bsdb:39572530/2/1,39572530,case-control,39572530,10.1038/s41398-024-03183-5,NA,"Liu X., Ling Z., Cheng Y., Wu L., Shao L., Gao J., Lei W., Zhu Z., Ding W., Song Q., Zhao L. , Jin G.",Oral fungal dysbiosis and systemic immune dysfunction in Chinese patients with schizophrenia,Translational psychiatry,2024,NA,Experiment 2,China,Homo sapiens,Tongue,UBERON:0001723,Schizophrenia,MONDO:0005090,Healthy controls (Con),Schizophrenia patients (SZ),Patients with schizophrenia (SZ),97,118,1 month,ITS / ITS2,NA,Illumina,relative abundances,"Metastats,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,"age,sex",NA,NA,unchanged,unchanged,unchanged,unchanged,decreased,Signature 1,"Figure 4A, 4B, 4C and 4D",24 October 2025,Tosin,Tosin,"Comparisons of the relative abundance of the abundant fungal taxa at the level of bacterial phylum (A), family (B), genus (C), and species (D) in the oral microbiota.",increased,"k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae,k__Fungi|p__Basidiomycota,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae|g__Cutaneotrichosporon,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Dipodascaceae,k__Fungi|p__Basidiomycota|c__Exobasidiomycetes|o__Entylomatales|f__Entylomataceae,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Polyporales|f__Irpicaceae|g__Irpex,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Polyporales|f__Irpicaceae|g__Irpex|s__Irpex hydnoides,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Polyporales|f__Irpicaceae,k__Fungi|p__Ascomycota|c__Dothideomycetes|g__Leptospora,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Phaeosphaeriaceae|g__Neosetophoma,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales|f__Peniophoraceae|g__Peniophora,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales|f__Peniophoraceae,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Phaeosphaeriaceae,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Botryosphaeriales|f__Phyllostictaceae,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Ophiocordycipitaceae|g__Purpureocillium,k__Fungi|p__Basidiomycota|c__Exobasidiomycetes|o__Entylomatales|g__Tilletiopsis,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Tricholomataceae,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae|g__Trichosporon,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales|f__Peniophoraceae|g__Peniophora|s__Peniophora incarnata,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Ophiocordycipitaceae|g__Purpureocillium|s__Purpureocillium lilacinum,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae|g__Trichosporon|s__Trichosporon asahii,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Periconiaceae|g__Periconia|s__Periconia epilithographicola,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Polyporales|f__Polyporaceae|g__Dentocorticium|s__Dentocorticium bicolor",4751|4890|147545|5042|1131492;4751|5204;4751|5204|155616|1851469|1759442|1838142;4751|4890|3239873|3243772|34353;4751|5204|452283|62914|62635;4751|5204|155619|5303|1931355|5318;4751|5204|155619|5303|1931355|5318|199540;4751|5204|155619|5303|1931355;4751|4890|147541|100010;4751|5204|1538075|162474|742845|55193;4751|5204|1538075|162474|742845|55193|76775;4751|5204|1538075|162474|742845;4751|4890|147541|92860|5020|798068;4751|5204|155619|452342|103393|40463;4751|5204|155619|452342|103393;4751|4890|147541|92860|5020;4751|4890|147541|451869|1424649;4751|4890|147550|5125|474942|1052105;4751|5204|452283|62914|1500560;4751|5204|155619|5338|5351;4751|5204|155616|1851469|1759442|5552;4751|5204|155616|1851469|1759442;4751|5204|155619|452342|103393|40463|55350;4751|4890|147550|5125|474942|1052105|33203;4751|5204|155616|1851469|1759442|5552|82508;4751|4890|147541|92860|1898439|97971|2201227;4751|5204|155619|5303|5317|68800|2109718,Complete,KateRasheed
bsdb:39572530/2/2,39572530,case-control,39572530,10.1038/s41398-024-03183-5,NA,"Liu X., Ling Z., Cheng Y., Wu L., Shao L., Gao J., Lei W., Zhu Z., Ding W., Song Q., Zhao L. , Jin G.",Oral fungal dysbiosis and systemic immune dysfunction in Chinese patients with schizophrenia,Translational psychiatry,2024,NA,Experiment 2,China,Homo sapiens,Tongue,UBERON:0001723,Schizophrenia,MONDO:0005090,Healthy controls (Con),Schizophrenia patients (SZ),Patients with schizophrenia (SZ),97,118,1 month,ITS / ITS2,NA,Illumina,relative abundances,"Metastats,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,"age,sex",NA,NA,unchanged,unchanged,unchanged,unchanged,decreased,Signature 2,"Figure 4A, 4B, 4C and 4D",24 October 2025,Tosin,Tosin,"Comparisons of the relative abundance of the abundant fungal taxa at the level of bacterial phylum (A), family (B), genus (C), and species (D) in the oral microbiota.",decreased,"k__Fungi|p__Ascomycota,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Bolbitiaceae,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Chaetomiaceae,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Dactylonectria,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Debaryomyces,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Thelebolales|f__Pseudeurotiaceae|g__Gymnostellatospora,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|g__Monodictys,k__Fungi|p__Mucoromycota|c__Mortierellomycetes|o__Mortierellales|f__Mortierellaceae|g__Mortierella,k__Fungi|p__Mucoromycota|c__Mortierellomycetes|o__Mortierellales|f__Mortierellaceae,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Phaeosphaeriaceae|g__Setophoma,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Trichomonascaceae|g__Starmerella,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Trichomonascaceae|g__Starmerella|s__Starmerella etchellsii,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Chaetothyriales|g__Strelitziana,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Tausonia,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Typhulaceae|g__Typhula,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Typhulaceae,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Debaryomyces|s__Debaryomyces udenii,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Tausonia|s__Tausonia pullulans,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Agaricales|f__Psathyrellaceae|g__Coprinellus|s__Coprinellus flocculosus,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium|s__Fusarium avenaceum,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Trichocomaceae|g__Thermomyces|s__Thermomyces lanuginosus,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Cylindrocladiella|s__Cylindrocladiella variabilis,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|g__Monodictys|s__Monodictys castaneae,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Phaeosphaeriaceae|g__Setophoma|s__Setophoma vernoniae,k__Fungi|p__Mucoromycota|c__Mortierellomycetes|o__Mortierellales|f__Mortierellaceae|g__Mortierella|s__Mortierella antarctica,k__Fungi|p__Basidiomycota|c__Ustilaginomycetes|o__Ustilaginales|f__Ustilaginaceae|g__Farysia|s__Farysia magdalenana,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Thelebolales|f__Pseudeurotiaceae|g__Gymnostellatospora|s__Gymnostellatospora japonica,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Kurtzmaniella|s__[Candida] boleticola",4751|4890;4751|5204|155619|5338|5398;4751|4890|3239874|2916678|766764|5475;4751|4890|3239874|2916678|766764|5475|5476;4751|4890|147550|5139|35718;4751|4890|147550|5125|110618|1620264;4751|4890|3239874|2916678|766764|4958;4751|4890|147550|5125|110618|5506;4751|4890|147548|292491|34379|78131;4751|4890|147541|92860|71662;4751|1913637|2212732|214503|4854|4855;4751|1913637|2212732|214503|4854;4751|4890|4891|4892;4751|4890|147541|92860|5020|798159;4751|4890|3239873|3243772|410830|75735;4751|4890|3239873|3243772|410830|75735|45547;4751|4890|147545|34395|401628;4751|5204|155616|90883|1851551|415704;4751|5204|155619|5338|68808|68809;4751|5204|155619|5338|68808;4751|4890|3239874|2916678|766764|4958|28551;4751|5204|155616|90883|1851551|415704|82525;4751|5204|155619|5338|184208|184430|71705;4751|4890|147550|5125|110618|5506|40199;4751|4890|147545|5042|28568|5540|5541;4751|4890|147550|5125|110618|137494|1078122;4751|4890|147541|92860|71662|71663;4751|4890|147541|92860|5020|798159|1508281;4751|1913637|2212732|214503|4854|4855|979670;4751|5204|5257|5267|5268|63256|3376730;4751|4890|147548|292491|34379|78131|78132;4751|4890|3239874|2916678|766764|549703|45525,Complete,KateRasheed
bsdb:39572788/1/1,39572788,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira F.C., Ge X., Kristensen J.M., Kirkegaard R.H., Maritsch K., Szamosvári D., Imminger S., Seki D., Shazzad J.B., Zhu Y., Decorte M., Hausmann B., Berry D., Wasmund K., Schintlmeister A., Böttcher T., Cheng J.X. , Wagner M.",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 1,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,"Loxapine Succinate High (LOX-High), Loxapine Succinate Low(LOX-Low) and Entacapone Low(ENT-Low)  after 24hours of incubation",Entacapone High Concentration(ENT-High) after 24 hrs of incubation,"Entacapone High Concentration(ENT-High) after 24hrs of incubation, refers to the drug concentration given to the six healthy adult individuals after twenty-four hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.",9,3,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 5,21 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between the drug-amendment experiments(ENT-High, ENT-Low, LOX-High and LOX-Low) after 24hrs of incubation.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|s__uncultured Coriobacteriaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|1980681;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|189330;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|438033;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|216572|39492;1783272|201174|84998|1643822|1643826;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826;1783272|201174|84998|84999|84107|331632;1783272|1239|186801|3085636|186803|297314;1783272|1239|186801|186802|216572|707003,Complete,Svetlana up
bsdb:39572788/1/2,39572788,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira F.C., Ge X., Kristensen J.M., Kirkegaard R.H., Maritsch K., Szamosvári D., Imminger S., Seki D., Shazzad J.B., Zhu Y., Decorte M., Hausmann B., Berry D., Wasmund K., Schintlmeister A., Böttcher T., Cheng J.X. , Wagner M.",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 1,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,"Loxapine Succinate High (LOX-High), Loxapine Succinate Low(LOX-Low) and Entacapone Low(ENT-Low)  after 24hours of incubation",Entacapone High Concentration(ENT-High) after 24 hrs of incubation,"Entacapone High Concentration(ENT-High) after 24hrs of incubation, refers to the drug concentration given to the six healthy adult individuals after twenty-four hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.",9,3,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 5,21 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between the drug-amendment experiments(ENT-High, ENT-Low, LOX-High and LOX-Low) after 24hrs of incubation.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Pseudomonadati|p__Lentisphaerota,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",1783272|1239|186801|3085636|186803|1766253;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|526524|526525|128827|1470349;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;3379134|976|200643|171549|2005519|1348911;1783272|1239|186801|3085636|186803|33042;1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;1783272|201174|84998|1643822|1643826|644652;3366610|28890|183925|2158|2159|2172;3379134|976|200643|171549|2005525|375288;1783272|201174|84998|84999|84107|1473205;3379134|1224|28216|80840|995019|40544;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|3085636|186803|2316020|33039;3379134|256845;1783272|1798710|1906119;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|2005473;1783272|1239|186801|3085636|186803|297314;1783272|1239|186801|3085636|186803|1506553,Complete,Svetlana up
bsdb:39572788/2/1,39572788,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira F.C., Ge X., Kristensen J.M., Kirkegaard R.H., Maritsch K., Szamosvári D., Imminger S., Seki D., Shazzad J.B., Zhu Y., Decorte M., Hausmann B., Berry D., Wasmund K., Schintlmeister A., Böttcher T., Cheng J.X. , Wagner M.",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 2,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,"Loxapine Succinate High (LOX-High), Entacapone Concentration(ENT-High) and Entacapone Low(ENT-Low)  after 24hours of incubation",Loxapine Succinate Low Concentration(LOX-Low) after 24 hrs of incubation,Loxapine Succinate Low Concentration(LOX-Low) after 24 hrs of incubation refers to the drug concentration given to the six healthy adult individuals after twenty-four hours of incubation.,9,3,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 5,21 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between the drug-amendment experiments(ENT-High, ENT-Low, LOX-High and LOX-Low) after 24hrs of incubation.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|s__uncultured Coriobacteriales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",1783272|1239|186801|186802|1980681;1783272|201174|84998|1643822|1643826;3379134|976|117743|200644;1783272|1239|91061|186826;1783272|201174|84998|84999|349920;1783272|1239|186801|186802|216572|707003,Complete,Svetlana up
bsdb:39572788/2/2,39572788,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira F.C., Ge X., Kristensen J.M., Kirkegaard R.H., Maritsch K., Szamosvári D., Imminger S., Seki D., Shazzad J.B., Zhu Y., Decorte M., Hausmann B., Berry D., Wasmund K., Schintlmeister A., Böttcher T., Cheng J.X. , Wagner M.",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 2,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,"Loxapine Succinate High (LOX-High), Entacapone Concentration(ENT-High) and Entacapone Low(ENT-Low)  after 24hours of incubation",Loxapine Succinate Low Concentration(LOX-Low) after 24 hrs of incubation,Loxapine Succinate Low Concentration(LOX-Low) after 24 hrs of incubation refers to the drug concentration given to the six healthy adult individuals after twenty-four hours of incubation.,9,3,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 5,21 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between the drug-amendment experiments(ENT-High, ENT-Low, LOX-High and LOX-Low) after 24hrs of incubation.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,s__rumen bacterium NK4A214",3379134|976|200643|171549|815|816;1783272|201174|1760|2037|2049|1654;1783272|1239|186801|3085636|186803;1783272|1239|526524|526525|128827;877428,Complete,Svetlana up
bsdb:39572788/3/1,39572788,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira F.C., Ge X., Kristensen J.M., Kirkegaard R.H., Maritsch K., Szamosvári D., Imminger S., Seki D., Shazzad J.B., Zhu Y., Decorte M., Hausmann B., Berry D., Wasmund K., Schintlmeister A., Böttcher T., Cheng J.X. , Wagner M.",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 3,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,"Loxapine Succinate High (LOX-High), Loxapine Succinate Low(LOX-Low) and Entacapone High(ENT-High)  after 24hours of incubation",Entacapone Low Concentration(ENT-Low) after 24 hrs of incubation,Entacapone Low Concentration(ENT-Low) after 24 hrs of incubation refers to the drug concentration given to the six healthy adult individuals after twenty-four hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. The low drug concentration was previously used in a screening aimed at determining drug effects on pure culture isolates.,9,3,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 5,21 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between the drug-amendment experiments(ENT-High, ENT-Low, LOX-High and LOX-Low) after 24hrs of incubation.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",1783272|1239|186801|186802|1980681;1783272|201174|84998|1643822|1643826;3379134|976|117743|200644;1783272|1239|186801|186802|216572|707003,Complete,Svetlana up
bsdb:39572788/3/2,39572788,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira F.C., Ge X., Kristensen J.M., Kirkegaard R.H., Maritsch K., Szamosvári D., Imminger S., Seki D., Shazzad J.B., Zhu Y., Decorte M., Hausmann B., Berry D., Wasmund K., Schintlmeister A., Böttcher T., Cheng J.X. , Wagner M.",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 3,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,"Loxapine Succinate High (LOX-High), Loxapine Succinate Low(LOX-Low) and Entacapone High(ENT-High)  after 24hours of incubation",Entacapone Low Concentration(ENT-Low) after 24 hrs of incubation,Entacapone Low Concentration(ENT-Low) after 24 hrs of incubation refers to the drug concentration given to the six healthy adult individuals after twenty-four hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. The low drug concentration was previously used in a screening aimed at determining drug effects on pure culture isolates.,9,3,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 5,21 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between the drug-amendment experiments(ENT-High, ENT-Low, LOX-High and LOX-Low) after 24hrs of incubation.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|216572|707003,Complete,Svetlana up
bsdb:39572788/4/1,39572788,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira F.C., Ge X., Kristensen J.M., Kirkegaard R.H., Maritsch K., Szamosvári D., Imminger S., Seki D., Shazzad J.B., Zhu Y., Decorte M., Hausmann B., Berry D., Wasmund K., Schintlmeister A., Böttcher T., Cheng J.X. , Wagner M.",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 4,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,"Loxapine Succinate Low(LOX-Low), Entacapone High(ENT-High) and Entacapone Low(ENT-Low)  after 24hours of incubation",Loxapine Succinate High Concentration(LOX-High) after 24 hrs of incubation,"Loxapine Succinate High Concentration(LOX-High) after 24 hrs of incubation, refers to the drug concentration given to the six healthy adult individuals after twenty-four hours of incubation. Loxapine succinate is a tricyclic antipsychotic medication primarily used in the treatment of schizophrenia. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.",9,3,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 5,21 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between the drug-amendment experiments(ENT-High, ENT-Low, LOX-High and LOX-Low) after 24hrs of incubation.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|s__uncultured Coriobacteriales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|1980681;1783272|1239|186801|3085636|186803|2316020|33039;1783272|201174|84998|1643822|1643826;1783272|1239|91061|186826;1783272|201174|84998|84999|349920;1783272|1239|186801|186802|216572|707003,Complete,Svetlana up
bsdb:39572788/4/2,39572788,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira F.C., Ge X., Kristensen J.M., Kirkegaard R.H., Maritsch K., Szamosvári D., Imminger S., Seki D., Shazzad J.B., Zhu Y., Decorte M., Hausmann B., Berry D., Wasmund K., Schintlmeister A., Böttcher T., Cheng J.X. , Wagner M.",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 4,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,"Loxapine Succinate Low(LOX-Low), Entacapone High(ENT-High) and Entacapone Low(ENT-Low)  after 24hours of incubation",Loxapine Succinate High Concentration(LOX-High) after 24 hrs of incubation,"Loxapine Succinate High Concentration(LOX-High) after 24 hrs of incubation, refers to the drug concentration given to the six healthy adult individuals after twenty-four hours of incubation. Loxapine succinate is a tricyclic antipsychotic medication primarily used in the treatment of schizophrenia. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.",9,3,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 5,22 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between the drug-amendment experiments(ENT-High, ENT-Low, LOX-High and LOX-Low) after 24hrs of incubation.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|216572|946234;3379134|976|200643|171549|171552|577309;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|707003;1783272|1798710|1906119;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:39572788/5/1,39572788,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira F.C., Ge X., Kristensen J.M., Kirkegaard R.H., Maritsch K., Szamosvári D., Imminger S., Seki D., Shazzad J.B., Zhu Y., Decorte M., Hausmann B., Berry D., Wasmund K., Schintlmeister A., Böttcher T., Cheng J.X. , Wagner M.",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 5,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,Loxapine Succinate High (LOX-High) and Entacapone Low(ENT-Low)  after 6hours of incubation,Loxapine Succinate Low Concentration(LOX-Low) after 6hrs of incubation,Loxapine Succinate Low Concentration(LOX-Low) after 6hrs of incubation refers to the drug concentration given to the six healthy adult individuals after six hours of incubation. Loxapine succinate is a tricyclic antipsychotic medication primarily used in the treatment of schizophrenia. The low drug concentration was previously used in a screening aimed at determining drug effects on pure culture isolates.,6,3,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 5,22 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between the drug-amendment experiments(ENT-Low, LOX-High and LOX-Low) after 6hrs of incubation.",increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:39572788/5/2,39572788,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira F.C., Ge X., Kristensen J.M., Kirkegaard R.H., Maritsch K., Szamosvári D., Imminger S., Seki D., Shazzad J.B., Zhu Y., Decorte M., Hausmann B., Berry D., Wasmund K., Schintlmeister A., Böttcher T., Cheng J.X. , Wagner M.",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 5,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,Loxapine Succinate High (LOX-High) and Entacapone Low(ENT-Low)  after 6hours of incubation,Loxapine Succinate Low Concentration(LOX-Low) after 6hrs of incubation,Loxapine Succinate Low Concentration(LOX-Low) after 6hrs of incubation refers to the drug concentration given to the six healthy adult individuals after six hours of incubation. Loxapine succinate is a tricyclic antipsychotic medication primarily used in the treatment of schizophrenia. The low drug concentration was previously used in a screening aimed at determining drug effects on pure culture isolates.,6,3,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 5,22 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between the drug-amendment experiments(ENT-Low, LOX-High and LOX-Low) after 6hrs of incubation.",decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:39572788/6/1,39572788,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira F.C., Ge X., Kristensen J.M., Kirkegaard R.H., Maritsch K., Szamosvári D., Imminger S., Seki D., Shazzad J.B., Zhu Y., Decorte M., Hausmann B., Berry D., Wasmund K., Schintlmeister A., Böttcher T., Cheng J.X. , Wagner M.",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 6,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,Loxapine Succinate High (LOX-High) and Loxapine Succinate Low(LOX-Low) after 6hours of incubation,Entacapone Low Concentration(ENT-Low) after 6hrs of incubation,Entacapone Low Concentration(ENT-Low) after 6hrs of incubation refers to the drug concentration given to the six healthy adult individuals after six hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. The low drug concentration was previously used in a screening aimed at determining drug effects on pure culture isolates.,6,3,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 5,22 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between the drug-amendment experiments(ENT-Low, LOX-High and LOX-Low) after 6hrs of incubation.",increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:39572788/7/1,39572788,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira F.C., Ge X., Kristensen J.M., Kirkegaard R.H., Maritsch K., Szamosvári D., Imminger S., Seki D., Shazzad J.B., Zhu Y., Decorte M., Hausmann B., Berry D., Wasmund K., Schintlmeister A., Böttcher T., Cheng J.X. , Wagner M.",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 7,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,Loxapine Succinate Low(LOX-Low) and Entacapone Low(ENT-Low) after 6hours of incubation,Loxapine Succinate High Concentration(LOX-High) after 6hrs of incubation,Loxapine Succinate High Concentration(LOX-High) after 6hrs of incubation refers to the drug concentration given to the six healthy adult individuals after six hours of incubation.  Loxapine succinate is a tricyclic antipsychotic medication primarily used in the treatment of schizophrenia. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.,6,3,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 5,22 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between the drug-amendment experiments(ENT-Low, LOX-High and LOX-Low) after 6hrs of incubation.",increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,1783272|1239|91061|186826|1300|1301|1306,Complete,Svetlana up
bsdb:39572788/7/2,39572788,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira F.C., Ge X., Kristensen J.M., Kirkegaard R.H., Maritsch K., Szamosvári D., Imminger S., Seki D., Shazzad J.B., Zhu Y., Decorte M., Hausmann B., Berry D., Wasmund K., Schintlmeister A., Böttcher T., Cheng J.X. , Wagner M.",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 7,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,Loxapine Succinate Low(LOX-Low) and Entacapone Low(ENT-Low) after 6hours of incubation,Loxapine Succinate High Concentration(LOX-High) after 6hrs of incubation,Loxapine Succinate High Concentration(LOX-High) after 6hrs of incubation refers to the drug concentration given to the six healthy adult individuals after six hours of incubation.  Loxapine succinate is a tricyclic antipsychotic medication primarily used in the treatment of schizophrenia. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.,6,3,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 5,22 November 2024,KateRasheed,"KateRasheed,WikiWorks","Differential abundance of taxa between the drug-amendment experiments(ENT-Low, LOX-High and LOX-Low) after 6hrs of incubation.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|186801|186802|31979|1485|1506;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:39572788/8/1,39572788,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira F.C., Ge X., Kristensen J.M., Kirkegaard R.H., Maritsch K., Szamosvári D., Imminger S., Seki D., Shazzad J.B., Zhu Y., Decorte M., Hausmann B., Berry D., Wasmund K., Schintlmeister A., Böttcher T., Cheng J.X. , Wagner M.",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 8,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,No drug - Dimethyl sulfoxide only (DMSO only),Entacapone High Concentration(ENT-High) after 24 hrs of incubation - Donor 1,Entacapone High Concentration(ENT-High) after 24 hrs of incubation refers to the drug concentration given to donor 1 after twenty-four hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.,3,3,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 1,Supplementary Table 6,22 November 2024,KateRasheed,"KateRasheed,WikiWorks,Tosin",Differential abundance of taxa between No drug and ENT-High in Donor 1 after 24hrs of incubation.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,s__rumen bacterium NK4A214,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|s__uncultured Christensenellaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136",1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|1980681;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|31979|1485|1522;877428;1783272|1239|186801|3082768|990719|1229255;1783272|1239|186801|3085636|186803|297314;1783272|1239|186801|3085636|186803|877420,Complete,Svetlana up
bsdb:39572788/8/2,39572788,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira F.C., Ge X., Kristensen J.M., Kirkegaard R.H., Maritsch K., Szamosvári D., Imminger S., Seki D., Shazzad J.B., Zhu Y., Decorte M., Hausmann B., Berry D., Wasmund K., Schintlmeister A., Böttcher T., Cheng J.X. , Wagner M.",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 8,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,No drug - Dimethyl sulfoxide only (DMSO only),Entacapone High Concentration(ENT-High) after 24 hrs of incubation - Donor 1,Entacapone High Concentration(ENT-High) after 24 hrs of incubation refers to the drug concentration given to donor 1 after twenty-four hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.,3,3,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 2,Supplementary Table 6,22 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between No drug and ENT-High in Donor 1 after 24hrs of incubation.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|s__Enterococcaceae bacterium RF39,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|1506553;1783272|1239|91061|186826|33958|2759736;1783272|1239|186801|3085636|186803|248744;1783272|1239|526524|526525|2810280|3025755;3379134|976|117743|200644;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803|297314;1783272|1239|186801|186802|216572|707003;1783272|1239|91061|186826|81852|423410;1783272|1239|526524|526525|128827|61170;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:39572788/9/1,39572788,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira F.C., Ge X., Kristensen J.M., Kirkegaard R.H., Maritsch K., Szamosvári D., Imminger S., Seki D., Shazzad J.B., Zhu Y., Decorte M., Hausmann B., Berry D., Wasmund K., Schintlmeister A., Böttcher T., Cheng J.X. , Wagner M.",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 9,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,No drug - Dimethyl sulfoxide only (DMSO only),Entacapone High Concentration(ENT-High) after 24 hrs of incubation - Donor 2,Entacapone High Concentration(ENT-High) after 24 hrs of incubation refers to the drug concentration given to donor 2 after twenty-four hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.,3,3,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 1,Supplementary Table 6,22 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between No drug and ENT-High in Donor 2 after 24hrs of incubation.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Raoultibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|909932|1843488|909930|904;1783272|201174|1760|2037|2049|1654;1783272|1239|186801|3085636|186803|1766253;3379134|976|200643|171549|2005519|397864;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;3379134|1224|1236|91347|543|544;1783272|1239|186801|186802|1980681;1783272|201174|84998|84999|84107|102106;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|216572|216851;1783272|1239|91061|186826|186828|117563;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|91061|186826|33958|2759736;1783272|1239|186801|3085636|186803|248744;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|186802|216572;1783272|201174|84998|1643822|1643826|1926677;1783272|1239|186801|3082720|186804|1505652;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|91347|543;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:39572788/9/2,39572788,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira F.C., Ge X., Kristensen J.M., Kirkegaard R.H., Maritsch K., Szamosvári D., Imminger S., Seki D., Shazzad J.B., Zhu Y., Decorte M., Hausmann B., Berry D., Wasmund K., Schintlmeister A., Böttcher T., Cheng J.X. , Wagner M.",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 9,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,No drug - Dimethyl sulfoxide only (DMSO only),Entacapone High Concentration(ENT-High) after 24 hrs of incubation - Donor 2,Entacapone High Concentration(ENT-High) after 24 hrs of incubation refers to the drug concentration given to donor 2 after twenty-four hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.,3,3,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 2,Supplementary Table 6,22 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between No drug and ENT-High in Donor 2 after 24hrs of incubation.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|s__Enterococcaceae bacterium RF39,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136",3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802|1980681;1783272|1239|186801|3085636|186803|33042;1783272|1239|91061|186826|81852|423410;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;1783272|201174|84998|1643822|1643826|84108;3379134|1224|28216|80840|995019|40544;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|297314;1783272|1239|186801|186802|216572|707003;1783272|1239|186801|3085636|186803|877420,Complete,Svetlana up
bsdb:39572788/10/1,39572788,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira F.C., Ge X., Kristensen J.M., Kirkegaard R.H., Maritsch K., Szamosvári D., Imminger S., Seki D., Shazzad J.B., Zhu Y., Decorte M., Hausmann B., Berry D., Wasmund K., Schintlmeister A., Böttcher T., Cheng J.X. , Wagner M.",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 10,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,No drug - Dimethyl sulfoxide only (DMSO only),Entacapone High Concentration(ENT-High) after 24 hrs of incubation - Donor 3,"Entacapone High Concentration(ENT-High) after 24 hrs of incubation, refers to the drug concentration given to donor 3 after twenty-four hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.",3,3,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 1,Supplementary Table 6,22 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between No drug and ENT-High in Donor 3 after 24hrs of incubation.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Raoultibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania",1783272|1239|909932|1843488|909930|904;1783272|201174|1760|2037|2049|1654;1783272|1239|186801|3085636|186803|1766253;3379134|976|200643|171549|2005519|397864;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;3379134|1224|1236|91347|543|544;1783272|201174|84998|84999|84107|102106;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|216572|216851;1783272|1239|91061|186826|186828|117563;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|91061|186826|33958|2759736;1783272|1239|186801|3085636|186803|248744;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|186802|216572;1783272|201174|84998|1643822|1643826|1926677;1783272|1239|186801|3082720|186804|1505652;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|91347|543;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;1783272|1239|526524|526525|128827|61170,Complete,Svetlana up
bsdb:39572788/10/2,39572788,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira F.C., Ge X., Kristensen J.M., Kirkegaard R.H., Maritsch K., Szamosvári D., Imminger S., Seki D., Shazzad J.B., Zhu Y., Decorte M., Hausmann B., Berry D., Wasmund K., Schintlmeister A., Böttcher T., Cheng J.X. , Wagner M.",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 10,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,No drug - Dimethyl sulfoxide only (DMSO only),Entacapone High Concentration(ENT-High) after 24 hrs of incubation - Donor 3,"Entacapone High Concentration(ENT-High) after 24 hrs of incubation, refers to the drug concentration given to donor 3 after twenty-four hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.",3,3,3 months,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 2,Supplementary Table 6,22 November 2024,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of taxa between No drug and ENT-High in Donor 3 after 24hrs of incubation.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|s__Enterococcaceae bacterium RF39",3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802|1980681;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|40544;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|297314;1783272|1239|186801|186802|216572|707003;1783272|1239|186801|3085636|186803|877420;1783272|201174|84998|1643822|1643826|84108;1783272|201174;1783272|1239|91061|186826|81852|423410,Complete,Svetlana up
bsdb:39588509/2/1,39588509,case-control,39588509,10.3389/fcimb.2024.1495364,https://pmc.ncbi.nlm.nih.gov/articles/PMC11586350/,"Zhang A., Chen S., Zhu Y., Wu M., Lu B., Zhou X., Zhu Y., Xu X., Liu H., Zhu F. , Lin R.",Intestinal microbiome changes and mechanisms of maintenance hemodialysis patients with constipation,Frontiers in cellular and infection microbiology,2024,"16S rRNA, Constipation, Intestinal biomarker, Maintenance haemodialysis (MHD), gut microbiome",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,Healthy Control Group (HCG),Maintenance Hemodialysis with Constipation (MHDCG),Patients undergoing hemodialysis also experiencing constipation.,15,15,1 month,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,decreased,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 5 and 6,20 April 2025,Shulamite,Shulamite,Comparison of species abundance at the genus level.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Altererythrobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae|g__Filomicrobium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herminiimonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Ruegeria,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:352",3379134|74201|203494|48461|1647988|239934;3379134|1224|28211|204457|335929|361177;1783272|1239|526524|526525|128827|1937008;1783272|201174|84998|1643822|1643826|84111;1783272|1239|91061|186826|81852|1350;3379134|1224|28211|356|45401|119044;3379134|1224|28216|80840|75682|303379;3379134|1224|28211|204455|2854170|97050;3379134|74201;1783272|1239|186801|186802|31979|1485|1262798,Complete,KateRasheed
bsdb:39588509/2/2,39588509,case-control,39588509,10.3389/fcimb.2024.1495364,https://pmc.ncbi.nlm.nih.gov/articles/PMC11586350/,"Zhang A., Chen S., Zhu Y., Wu M., Lu B., Zhou X., Zhu Y., Xu X., Liu H., Zhu F. , Lin R.",Intestinal microbiome changes and mechanisms of maintenance hemodialysis patients with constipation,Frontiers in cellular and infection microbiology,2024,"16S rRNA, Constipation, Intestinal biomarker, Maintenance haemodialysis (MHD), gut microbiome",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,Healthy Control Group (HCG),Maintenance Hemodialysis with Constipation (MHDCG),Patients undergoing hemodialysis also experiencing constipation.,15,15,1 month,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,decreased,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 5 and 6,20 April 2025,Shulamite,"Shulamite,Ese",Comparison of species abundance at the genus level.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Kineothrix,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Pseudomonadati|p__Thermodesulfobacteriota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium",1783272|1239|186801|3085636|186803|1766253;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|3085642|580596;3379134|976|200643|171549|2005519|1348911;1783272|1239|909932|1843489|31977|39948;3379134|1224|1236|91347|543|547;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|2163168;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|33958|1243;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|3082720|186804|1501226;3379134|200940;1783272|1239|526524|526525|128827|331630,Complete,KateRasheed
bsdb:39588509/3/1,39588509,case-control,39588509,10.3389/fcimb.2024.1495364,https://pmc.ncbi.nlm.nih.gov/articles/PMC11586350/,"Zhang A., Chen S., Zhu Y., Wu M., Lu B., Zhou X., Zhu Y., Xu X., Liu H., Zhu F. , Lin R.",Intestinal microbiome changes and mechanisms of maintenance hemodialysis patients with constipation,Frontiers in cellular and infection microbiology,2024,"16S rRNA, Constipation, Intestinal biomarker, Maintenance haemodialysis (MHD), gut microbiome",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Clinical treatment,EFO:0007056,Healthy Control Group (HCG),Maintenance Hemodialysis without Constipation (MHDNCG),Hemodialysis patients who do not experience constipation.,15,15,1 month,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,decreased,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 5 and 6,20 April 2025,Shulamite,Shulamite,Comparison of species abundance at the genus level.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:352,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Verrucomicrobiota",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|186802|31979|1485|1262798;3379134|1224|28216|206351|481|482;1783272|1239|186801|3085636|186803;3379134|74201,Complete,KateRasheed
bsdb:39588509/3/2,39588509,case-control,39588509,10.3389/fcimb.2024.1495364,https://pmc.ncbi.nlm.nih.gov/articles/PMC11586350/,"Zhang A., Chen S., Zhu Y., Wu M., Lu B., Zhou X., Zhu Y., Xu X., Liu H., Zhu F. , Lin R.",Intestinal microbiome changes and mechanisms of maintenance hemodialysis patients with constipation,Frontiers in cellular and infection microbiology,2024,"16S rRNA, Constipation, Intestinal biomarker, Maintenance haemodialysis (MHD), gut microbiome",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Clinical treatment,EFO:0007056,Healthy Control Group (HCG),Maintenance Hemodialysis without Constipation (MHDNCG),Hemodialysis patients who do not experience constipation.,15,15,1 month,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,decreased,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 5 and 6,20 April 2025,Shulamite,"Shulamite,Ese",Comparison of species abundance at the genus level.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Alysiella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Neobittarella (ex Bilen et al. 2018),k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Pseudomonadati|p__Thermodesulfobacteriota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium",3379134|1224|28216|206351|481|194195;3379134|200940|3031449|213115|194924|35832;3379134|1224|1236|91347|543|544;3379134|976|200643|171549|2005519|1348911;1783272|1239|186801|3085636|186803|33042;3379134|1224|1236|91347|543|547;3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|33958|2759736;1783272|1239|91061|186826|33958|2767842;1783272|1239|91061|186826|33958|1243;1783272|1239|186801|186802|216572|2126544;1783272|1239|909932|909929|1843491|970;3379134|200940;1783272|1239|526524|526525|128827|331630,Complete,KateRasheed
bsdb:39588509/4/1,39588509,case-control,39588509,10.3389/fcimb.2024.1495364,https://pmc.ncbi.nlm.nih.gov/articles/PMC11586350/,"Zhang A., Chen S., Zhu Y., Wu M., Lu B., Zhou X., Zhu Y., Xu X., Liu H., Zhu F. , Lin R.",Intestinal microbiome changes and mechanisms of maintenance hemodialysis patients with constipation,Frontiers in cellular and infection microbiology,2024,"16S rRNA, Constipation, Intestinal biomarker, Maintenance haemodialysis (MHD), gut microbiome",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,Maintenance Hemodialysis without Constipation (MHDNCG),Maintenance Hemodialysis with Constipation (MHDCG),Patients undergoing hemodialysis also experiencing constipation.,15,15,1 month,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,decreased,decreased,increased,decreased,NA,increased,Signature 1,Figure 6,20 April 2025,Shulamite,Shulamite,Comparison of species abundance at the genus level.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae|g__Filomicrobium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales",1783272|1239|526524|526525|128827|174708;1783272|201174|84998|1643822|1643826|84111;1783272|1239|91061|186826|81852|1350;3379134|1224|28211|356|45401|119044;1783272|201174|84998|1643822|1643826|644652;1783272|1239|186801|3085636|186803|1164882;3379134|1224|28211|356,Complete,KateRasheed
bsdb:39588509/4/2,39588509,case-control,39588509,10.3389/fcimb.2024.1495364,https://pmc.ncbi.nlm.nih.gov/articles/PMC11586350/,"Zhang A., Chen S., Zhu Y., Wu M., Lu B., Zhou X., Zhu Y., Xu X., Liu H., Zhu F. , Lin R.",Intestinal microbiome changes and mechanisms of maintenance hemodialysis patients with constipation,Frontiers in cellular and infection microbiology,2024,"16S rRNA, Constipation, Intestinal biomarker, Maintenance haemodialysis (MHD), gut microbiome",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,Maintenance Hemodialysis without Constipation (MHDNCG),Maintenance Hemodialysis with Constipation (MHDCG),Patients undergoing hemodialysis also experiencing constipation.,15,15,1 month,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,decreased,decreased,increased,decreased,NA,increased,Signature 2,Figure 6,20 April 2025,Shulamite,Shulamite,Comparison of species abundance at the genus level.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Kineothrix,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Pirellulales|f__Pirellulaceae|g__Rhodopirellula,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",1783272|1239|186801|3085636|186803|2163168;3379134|203682|203683|2691354|2691357|265488;1783272|1239|91061|186826|33958|46255,Complete,KateRasheed
bsdb:39588509/5/1,39588509,case-control,39588509,10.3389/fcimb.2024.1495364,https://pmc.ncbi.nlm.nih.gov/articles/PMC11586350/,"Zhang A., Chen S., Zhu Y., Wu M., Lu B., Zhou X., Zhu Y., Xu X., Liu H., Zhu F. , Lin R.",Intestinal microbiome changes and mechanisms of maintenance hemodialysis patients with constipation,Frontiers in cellular and infection microbiology,2024,"16S rRNA, Constipation, Intestinal biomarker, Maintenance haemodialysis (MHD), gut microbiome",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,Maintenance Hemodialysis without Constipation (MHDNCG),Maintenance Hemodialysis with Constipation (MHDCG),Patients undergoing hemodialysis also experiencing constipation.,15,15,1 month,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,decreased,decreased,increased,decreased,NA,increased,Signature 1,Figure 7,20 April 2025,Shulamite,Shulamite,LEfSe analysis. The abundance difference analysis plots for the MHDCG and MHDNCG groups at the genus level.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Pirellulales|f__Pirellulaceae|g__Rhodopirellula,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Pirellulales|f__Pirellulaceae|g__Rhodopirellula,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",3379134|976|200643|171549|815|909656|310298;3379134|203682|203683|2691354|2691357|265488;1783272|1239|909932|1843489|31977;1783272|1239|91061|186826|33958|46255;3379134|203682|203683|2691354|2691357|265488;1783272|1239|91061|186826|33958|46255,Complete,KateRasheed
bsdb:39588509/5/2,39588509,case-control,39588509,10.3389/fcimb.2024.1495364,https://pmc.ncbi.nlm.nih.gov/articles/PMC11586350/,"Zhang A., Chen S., Zhu Y., Wu M., Lu B., Zhou X., Zhu Y., Xu X., Liu H., Zhu F. , Lin R.",Intestinal microbiome changes and mechanisms of maintenance hemodialysis patients with constipation,Frontiers in cellular and infection microbiology,2024,"16S rRNA, Constipation, Intestinal biomarker, Maintenance haemodialysis (MHD), gut microbiome",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Constipation,HP:0002019,Maintenance Hemodialysis without Constipation (MHDNCG),Maintenance Hemodialysis with Constipation (MHDCG),Patients undergoing hemodialysis also experiencing constipation.,15,15,1 month,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,decreased,decreased,increased,decreased,NA,increased,Signature 2,Figure 7,20 April 2025,Shulamite,Shulamite,LEfSe analysis. The abundance difference analysis plots for the MHDCG and MHDNCG groups at the genus level.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae|g__Filomicrobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Acidobacteriota|c__Vicinamibacteria,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae|g__Filomicrobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum",1783272|1239|526524|526525|128827|174708;3379134|1224|28216|80840|80864;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|81852|1350|1352;3379134|1224|28211|356|45401|119044;1783272|1239|186801|3085636|186803|1164882;1783272|1239|91061|186826;3379134|57723|1813735;1783272|1239|526524|526525|128827|174708;3379134|1224|28211|356|45401|119044;3379134|1224|28211|356;1783272|1239|186801|3085636|186803|1164882,Complete,KateRasheed
bsdb:39599737/1/1,39599737,"randomized controlled trial,time series / longitudinal observational",39599737,https://doi.org/10.3390/nu16223952,https://www.mdpi.com/2072-6643/16/22/3952,"Naghibi M., Pont-Beltran A., Lamelas A., Llobregat L., Martinez-Blanch J.F., Rojas A., Álvarez B., López Plaza B., Arcos Castellanos L., Chenoll E., Vijayakumar V. , Day R.","Effect of Postbiotic <i>Bifidobacterium longum</i> CECT 7347 on Gastrointestinal Symptoms, Serum Biochemistry, and Intestinal Microbiota in Healthy Adults: A Randomised, Parallel, Double-Blind, Placebo-Controlled Pilot Study",Nutrients,2024,"Anaerobutyricum, Anaerostripes, Blautia, Faecalibacterium, Phocaeicola, SCFAs, abundance, butyrate, calprotectin, gut health, healthy population, inflammation, microbiome, postbiotics",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Placebo patients at Week 0,Placebo patients at Week 4,Mild to moderate patients with digestive symptoms fed with Placebo (Maltodextrin) at Week 4,30,NA,Recent use of antibiotics,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 5 A, B",28 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant taxa by Differential Expression Sequencing 2 (DESeq2). Heatmaps showing the ‘log fold change’ (Log2FC) resulting from between time comparisons per group on (A) genera and (B) ASV abundances.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium",1783272|1239|186801|186802|1980681;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|216572|1905344,Complete,KateRasheed
bsdb:39599737/1/2,39599737,"randomized controlled trial,time series / longitudinal observational",39599737,https://doi.org/10.3390/nu16223952,https://www.mdpi.com/2072-6643/16/22/3952,"Naghibi M., Pont-Beltran A., Lamelas A., Llobregat L., Martinez-Blanch J.F., Rojas A., Álvarez B., López Plaza B., Arcos Castellanos L., Chenoll E., Vijayakumar V. , Day R.","Effect of Postbiotic <i>Bifidobacterium longum</i> CECT 7347 on Gastrointestinal Symptoms, Serum Biochemistry, and Intestinal Microbiota in Healthy Adults: A Randomised, Parallel, Double-Blind, Placebo-Controlled Pilot Study",Nutrients,2024,"Anaerobutyricum, Anaerostripes, Blautia, Faecalibacterium, Phocaeicola, SCFAs, abundance, butyrate, calprotectin, gut health, healthy population, inflammation, microbiome, postbiotics",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Placebo patients at Week 0,Placebo patients at Week 4,Mild to moderate patients with digestive symptoms fed with Placebo (Maltodextrin) at Week 4,30,NA,Recent use of antibiotics,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 5A, B",28 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant taxa by Differential Expression Sequencing 2 (DESeq2). Heatmaps showing the ‘log fold change’ (Log2FC) resulting from between time comparisons per group on (A) genera and (B) ASV abundances,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis",3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3082720|186804|1501226|1776391,Complete,KateRasheed
bsdb:39599737/2/1,39599737,"randomized controlled trial,time series / longitudinal observational",39599737,https://doi.org/10.3390/nu16223952,https://www.mdpi.com/2072-6643/16/22/3952,"Naghibi M., Pont-Beltran A., Lamelas A., Llobregat L., Martinez-Blanch J.F., Rojas A., Álvarez B., López Plaza B., Arcos Castellanos L., Chenoll E., Vijayakumar V. , Day R.","Effect of Postbiotic <i>Bifidobacterium longum</i> CECT 7347 on Gastrointestinal Symptoms, Serum Biochemistry, and Intestinal Microbiota in Healthy Adults: A Randomised, Parallel, Double-Blind, Placebo-Controlled Pilot Study",Nutrients,2024,"Anaerobutyricum, Anaerostripes, Blautia, Faecalibacterium, Phocaeicola, SCFAs, abundance, butyrate, calprotectin, gut health, healthy population, inflammation, microbiome, postbiotics",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Placebo patients at Week 4,Placebo patients at Week 8,Mild to moderate patients with digestive symptoms fed with Placebo (Maltodextrin) at Week 8,NA,27,Recent use of antibiotics,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 5A, B",28 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant taxa by Differential Expression Sequencing 2 (DESeq2). Heatmaps showing the ‘log fold change’ (Log2FC) resulting from between time comparisons per group on (A) genera and (B) ASV abundances,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerotaenia",1783272|1239|186801|3085636|3118652|2039240;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3085636|186803|1843206,Complete,KateRasheed
bsdb:39599737/3/1,39599737,"randomized controlled trial,time series / longitudinal observational",39599737,https://doi.org/10.3390/nu16223952,https://www.mdpi.com/2072-6643/16/22/3952,"Naghibi M., Pont-Beltran A., Lamelas A., Llobregat L., Martinez-Blanch J.F., Rojas A., Álvarez B., López Plaza B., Arcos Castellanos L., Chenoll E., Vijayakumar V. , Day R.","Effect of Postbiotic <i>Bifidobacterium longum</i> CECT 7347 on Gastrointestinal Symptoms, Serum Biochemistry, and Intestinal Microbiota in Healthy Adults: A Randomised, Parallel, Double-Blind, Placebo-Controlled Pilot Study",Nutrients,2024,"Anaerobutyricum, Anaerostripes, Blautia, Faecalibacterium, Phocaeicola, SCFAs, abundance, butyrate, calprotectin, gut health, healthy population, inflammation, microbiome, postbiotics",Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Placebo patients at Week 0,Placebo patients at Week 8,Mild to moderate patients with digestive symptoms fed with Placebo (Maltodextrin) at Week 8,30,27,Recent use of antibiotics,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 5A, B",28 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant taxa by Differential Expression Sequencing 2 (DESeq2). Heatmaps showing the ‘log fold change’ (Log2FC) resulting from between time comparisons per group on (A) genera and (B) ASV abundances,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerotaenia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerotaenia|s__Anaerotaenia torta",1783272|1239|186801|3085636|186803|1843206;1783272|1239|186801|3085636|3118652|2039240;1783272|1239|186801|186802|1980681;1783272|1239|186801|3085636|186803|2569097;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|1843206|433293,Complete,KateRasheed
bsdb:39599737/3/2,39599737,"randomized controlled trial,time series / longitudinal observational",39599737,https://doi.org/10.3390/nu16223952,https://www.mdpi.com/2072-6643/16/22/3952,"Naghibi M., Pont-Beltran A., Lamelas A., Llobregat L., Martinez-Blanch J.F., Rojas A., Álvarez B., López Plaza B., Arcos Castellanos L., Chenoll E., Vijayakumar V. , Day R.","Effect of Postbiotic <i>Bifidobacterium longum</i> CECT 7347 on Gastrointestinal Symptoms, Serum Biochemistry, and Intestinal Microbiota in Healthy Adults: A Randomised, Parallel, Double-Blind, Placebo-Controlled Pilot Study",Nutrients,2024,"Anaerobutyricum, Anaerostripes, Blautia, Faecalibacterium, Phocaeicola, SCFAs, abundance, butyrate, calprotectin, gut health, healthy population, inflammation, microbiome, postbiotics",Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Placebo patients at Week 0,Placebo patients at Week 8,Mild to moderate patients with digestive symptoms fed with Placebo (Maltodextrin) at Week 8,30,27,Recent use of antibiotics,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5A,28 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant taxa by Differential Expression Sequencing 2 (DESeq2). Heatmaps showing the ‘log fold change’ (Log2FC) resulting from between time comparisons per group on (A) genera,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,3379134|1224|1236|135625|712|724,Complete,KateRasheed
bsdb:39599737/4/1,39599737,"randomized controlled trial,time series / longitudinal observational",39599737,https://doi.org/10.3390/nu16223952,https://www.mdpi.com/2072-6643/16/22/3952,"Naghibi M., Pont-Beltran A., Lamelas A., Llobregat L., Martinez-Blanch J.F., Rojas A., Álvarez B., López Plaza B., Arcos Castellanos L., Chenoll E., Vijayakumar V. , Day R.","Effect of Postbiotic <i>Bifidobacterium longum</i> CECT 7347 on Gastrointestinal Symptoms, Serum Biochemistry, and Intestinal Microbiota in Healthy Adults: A Randomised, Parallel, Double-Blind, Placebo-Controlled Pilot Study",Nutrients,2024,"Anaerobutyricum, Anaerostripes, Blautia, Faecalibacterium, Phocaeicola, SCFAs, abundance, butyrate, calprotectin, gut health, healthy population, inflammation, microbiome, postbiotics",Experiment 4,Spain,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) patients at Week 0,Heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) patients at Week 4,Mild to moderate patients with digestive symptoms fed with heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) at Week 4,30,NA,Recent use of antibiotics,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 5A, B",28 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant taxa by Differential Expression Sequencing 2 (DESeq2). Heatmaps showing the ‘log fold change’ (Log2FC) resulting from between time comparisons per group on (A) genera and (B) ASV abundances,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus",1783272|1239|186801|186802|1980681;1783272|1239|186801|3085636|186803|2569097;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|815|909656;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|3085636|186803|207244|649756,Complete,KateRasheed
bsdb:39599737/5/1,39599737,"randomized controlled trial,time series / longitudinal observational",39599737,https://doi.org/10.3390/nu16223952,https://www.mdpi.com/2072-6643/16/22/3952,"Naghibi M., Pont-Beltran A., Lamelas A., Llobregat L., Martinez-Blanch J.F., Rojas A., Álvarez B., López Plaza B., Arcos Castellanos L., Chenoll E., Vijayakumar V. , Day R.","Effect of Postbiotic <i>Bifidobacterium longum</i> CECT 7347 on Gastrointestinal Symptoms, Serum Biochemistry, and Intestinal Microbiota in Healthy Adults: A Randomised, Parallel, Double-Blind, Placebo-Controlled Pilot Study",Nutrients,2024,"Anaerobutyricum, Anaerostripes, Blautia, Faecalibacterium, Phocaeicola, SCFAs, abundance, butyrate, calprotectin, gut health, healthy population, inflammation, microbiome, postbiotics",Experiment 5,Spain,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) patients at Week 4,Heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) patients at Week 8,Mild to moderate patients with digestive symptoms fed with heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) at Week 8,NA,26,Recent use of antibiotics,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5B,28 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant taxa by Differential Expression Sequencing 2 (DESeq2). Heatmaps showing the ‘log fold change’ (Log2FC) resulting from between time comparisons per group on (A) genera and (B) ASV abundances,increased,NA,NA,Complete,KateRasheed
bsdb:39599737/6/1,39599737,"randomized controlled trial,time series / longitudinal observational",39599737,https://doi.org/10.3390/nu16223952,https://www.mdpi.com/2072-6643/16/22/3952,"Naghibi M., Pont-Beltran A., Lamelas A., Llobregat L., Martinez-Blanch J.F., Rojas A., Álvarez B., López Plaza B., Arcos Castellanos L., Chenoll E., Vijayakumar V. , Day R.","Effect of Postbiotic <i>Bifidobacterium longum</i> CECT 7347 on Gastrointestinal Symptoms, Serum Biochemistry, and Intestinal Microbiota in Healthy Adults: A Randomised, Parallel, Double-Blind, Placebo-Controlled Pilot Study",Nutrients,2024,"Anaerobutyricum, Anaerostripes, Blautia, Faecalibacterium, Phocaeicola, SCFAs, abundance, butyrate, calprotectin, gut health, healthy population, inflammation, microbiome, postbiotics",Experiment 6,Spain,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) patients at Week 0,Heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) patients at Week 8,Mild to moderate patients with digestive symptoms fed with heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) at Week 8,30,26,Recent use of antibiotics,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 5A, B",28 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant taxa by Differential Expression Sequencing 2 (DESeq2). Heatmaps showing the ‘log fold change’ (Log2FC) resulting from between time comparisons per group on (A) genera and (B) ASV abundances.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae",1783272|1239|186801|3085636|186803|2569097;1783272|1239|186801|186802|3085642|2048137;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|572511|418240,Complete,KateRasheed
bsdb:39599737/6/2,39599737,"randomized controlled trial,time series / longitudinal observational",39599737,https://doi.org/10.3390/nu16223952,https://www.mdpi.com/2072-6643/16/22/3952,"Naghibi M., Pont-Beltran A., Lamelas A., Llobregat L., Martinez-Blanch J.F., Rojas A., Álvarez B., López Plaza B., Arcos Castellanos L., Chenoll E., Vijayakumar V. , Day R.","Effect of Postbiotic <i>Bifidobacterium longum</i> CECT 7347 on Gastrointestinal Symptoms, Serum Biochemistry, and Intestinal Microbiota in Healthy Adults: A Randomised, Parallel, Double-Blind, Placebo-Controlled Pilot Study",Nutrients,2024,"Anaerobutyricum, Anaerostripes, Blautia, Faecalibacterium, Phocaeicola, SCFAs, abundance, butyrate, calprotectin, gut health, healthy population, inflammation, microbiome, postbiotics",Experiment 6,Spain,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) patients at Week 0,Heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) patients at Week 8,Mild to moderate patients with digestive symptoms fed with heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) at Week 8,30,26,Recent use of antibiotics,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5A,28 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant taxa by Differential Expression Sequencing 2 (DESeq2). Heatmaps showing the ‘log fold change’ (Log2FC) resulting from between time comparisons per group on (A) genera,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Kineothrix,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803|2163168;1783272|1239|186801|3085636|186803|841;1783272|1239|526524|526525|2810280|3025755,Complete,KateRasheed
bsdb:39599737/7/1,39599737,"randomized controlled trial,time series / longitudinal observational",39599737,https://doi.org/10.3390/nu16223952,https://www.mdpi.com/2072-6643/16/22/3952,"Naghibi M., Pont-Beltran A., Lamelas A., Llobregat L., Martinez-Blanch J.F., Rojas A., Álvarez B., López Plaza B., Arcos Castellanos L., Chenoll E., Vijayakumar V. , Day R.","Effect of Postbiotic <i>Bifidobacterium longum</i> CECT 7347 on Gastrointestinal Symptoms, Serum Biochemistry, and Intestinal Microbiota in Healthy Adults: A Randomised, Parallel, Double-Blind, Placebo-Controlled Pilot Study",Nutrients,2024,"Anaerobutyricum, Anaerostripes, Blautia, Faecalibacterium, Phocaeicola, SCFAs, abundance, butyrate, calprotectin, gut health, healthy population, inflammation, microbiome, postbiotics",Experiment 7,Spain,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Placebo patients (Week 0-4),Heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) patients (Week 0-4),Mild to moderate patients with digestive symptoms fed with heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) at Week 0-4,NA,NA,Recent use of antibiotics,16S,34,Illumina,log transformation,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,28 November 2025,Fiddyhamma,Fiddyhamma,Boxplots on intra-subject differences between weeks 0–4 and weeks 4–8 times on each group of (A) genera and (B) ASV abundances normalised by DESeq2. Wilcox test was applied between groups on each period.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola",1783272|1239|186801|3085636|186803|2569097;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|2569097|39488;3379134|976|200643|171549|815|909656,Complete,KateRasheed
bsdb:39599737/9/1,39599737,"randomized controlled trial,time series / longitudinal observational",39599737,https://doi.org/10.3390/nu16223952,https://www.mdpi.com/2072-6643/16/22/3952,"Naghibi M., Pont-Beltran A., Lamelas A., Llobregat L., Martinez-Blanch J.F., Rojas A., Álvarez B., López Plaza B., Arcos Castellanos L., Chenoll E., Vijayakumar V. , Day R.","Effect of Postbiotic <i>Bifidobacterium longum</i> CECT 7347 on Gastrointestinal Symptoms, Serum Biochemistry, and Intestinal Microbiota in Healthy Adults: A Randomised, Parallel, Double-Blind, Placebo-Controlled Pilot Study",Nutrients,2024,"Anaerobutyricum, Anaerostripes, Blautia, Faecalibacterium, Phocaeicola, SCFAs, abundance, butyrate, calprotectin, gut health, healthy population, inflammation, microbiome, postbiotics",Experiment 9,Spain,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Placebo patients at Week 0,Placebo patients at Week 4,Mild to moderate patients with digestive symptoms fed with Placebo (Maltodextrin) at Week 4,30,NA,Recent use of antibiotics,16S,34,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 7A, Supplementary Figure 3",28 November 2025,Fiddyhamma,Fiddyhamma,Correlations: heatmaps showing the Maaslin2 Coefficient (Coeff) of correlations in genera abundances,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium",1783272|1239|186801|186802|1980681;1783272|1239|186801|186802|216572|1905344,Complete,KateRasheed
bsdb:39599737/9/2,39599737,"randomized controlled trial,time series / longitudinal observational",39599737,https://doi.org/10.3390/nu16223952,https://www.mdpi.com/2072-6643/16/22/3952,"Naghibi M., Pont-Beltran A., Lamelas A., Llobregat L., Martinez-Blanch J.F., Rojas A., Álvarez B., López Plaza B., Arcos Castellanos L., Chenoll E., Vijayakumar V. , Day R.","Effect of Postbiotic <i>Bifidobacterium longum</i> CECT 7347 on Gastrointestinal Symptoms, Serum Biochemistry, and Intestinal Microbiota in Healthy Adults: A Randomised, Parallel, Double-Blind, Placebo-Controlled Pilot Study",Nutrients,2024,"Anaerobutyricum, Anaerostripes, Blautia, Faecalibacterium, Phocaeicola, SCFAs, abundance, butyrate, calprotectin, gut health, healthy population, inflammation, microbiome, postbiotics",Experiment 9,Spain,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Placebo patients at Week 0,Placebo patients at Week 4,Mild to moderate patients with digestive symptoms fed with Placebo (Maltodextrin) at Week 4,30,NA,Recent use of antibiotics,16S,34,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 7A,28 November 2025,Fiddyhamma,Fiddyhamma,Correlations: heatmaps showing the Maaslin2 Coefficient (Coeff) of correlations in genera abundances,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|841,Complete,KateRasheed
bsdb:39599737/10/1,39599737,"randomized controlled trial,time series / longitudinal observational",39599737,https://doi.org/10.3390/nu16223952,https://www.mdpi.com/2072-6643/16/22/3952,"Naghibi M., Pont-Beltran A., Lamelas A., Llobregat L., Martinez-Blanch J.F., Rojas A., Álvarez B., López Plaza B., Arcos Castellanos L., Chenoll E., Vijayakumar V. , Day R.","Effect of Postbiotic <i>Bifidobacterium longum</i> CECT 7347 on Gastrointestinal Symptoms, Serum Biochemistry, and Intestinal Microbiota in Healthy Adults: A Randomised, Parallel, Double-Blind, Placebo-Controlled Pilot Study",Nutrients,2024,"Anaerobutyricum, Anaerostripes, Blautia, Faecalibacterium, Phocaeicola, SCFAs, abundance, butyrate, calprotectin, gut health, healthy population, inflammation, microbiome, postbiotics",Experiment 10,Spain,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Placebo patients at Week 0,Placebo patients at Week 8,Mild to moderate patients with digestive symptoms fed with Placebo (Maltodextrin) at Week 8,30,27,Recent use of antibiotics,16S,34,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 7A, Supplementary Figure 3",28 November 2025,Fiddyhamma,Fiddyhamma,Correlations: heatmaps showing the Maaslin2 Coefficient (Coeff) of correlations in genera abundances,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii",1783272|1239|186801|186802|1980681;1783272|1239|186801|3085636|186803|2569097;1783272|1239|186801|3085636|186803|2569097|39488,Complete,KateRasheed
bsdb:39599737/10/2,39599737,"randomized controlled trial,time series / longitudinal observational",39599737,https://doi.org/10.3390/nu16223952,https://www.mdpi.com/2072-6643/16/22/3952,"Naghibi M., Pont-Beltran A., Lamelas A., Llobregat L., Martinez-Blanch J.F., Rojas A., Álvarez B., López Plaza B., Arcos Castellanos L., Chenoll E., Vijayakumar V. , Day R.","Effect of Postbiotic <i>Bifidobacterium longum</i> CECT 7347 on Gastrointestinal Symptoms, Serum Biochemistry, and Intestinal Microbiota in Healthy Adults: A Randomised, Parallel, Double-Blind, Placebo-Controlled Pilot Study",Nutrients,2024,"Anaerobutyricum, Anaerostripes, Blautia, Faecalibacterium, Phocaeicola, SCFAs, abundance, butyrate, calprotectin, gut health, healthy population, inflammation, microbiome, postbiotics",Experiment 10,Spain,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Placebo patients at Week 0,Placebo patients at Week 8,Mild to moderate patients with digestive symptoms fed with Placebo (Maltodextrin) at Week 8,30,27,Recent use of antibiotics,16S,34,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 7A,28 November 2025,Fiddyhamma,Fiddyhamma,Correlations: heatmaps showing the Maaslin2 Coefficient (Coeff) of correlations in genera abundances,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,3379134|1224|1236|135625|712|724,Complete,KateRasheed
bsdb:39599737/11/1,39599737,"randomized controlled trial,time series / longitudinal observational",39599737,https://doi.org/10.3390/nu16223952,https://www.mdpi.com/2072-6643/16/22/3952,"Naghibi M., Pont-Beltran A., Lamelas A., Llobregat L., Martinez-Blanch J.F., Rojas A., Álvarez B., López Plaza B., Arcos Castellanos L., Chenoll E., Vijayakumar V. , Day R.","Effect of Postbiotic <i>Bifidobacterium longum</i> CECT 7347 on Gastrointestinal Symptoms, Serum Biochemistry, and Intestinal Microbiota in Healthy Adults: A Randomised, Parallel, Double-Blind, Placebo-Controlled Pilot Study",Nutrients,2024,"Anaerobutyricum, Anaerostripes, Blautia, Faecalibacterium, Phocaeicola, SCFAs, abundance, butyrate, calprotectin, gut health, healthy population, inflammation, microbiome, postbiotics",Experiment 11,Spain,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) patients at Week 0,Heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) patients at Week 4,Mild to moderate patients with digestive symptoms fed with heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) at Week 4,30,NA,Recent use of antibiotics,16S,34,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 7A, B, Supplenentary Figure 3",28 November 2025,Fiddyhamma,Fiddyhamma,Correlations: heatmaps showing the Maaslin2 Coefficient (Coeff) of correlations in genera abundances,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum",1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|186802|1980681;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;3379134|976|200643|171549|815|909656;1783272|1239|186801|3085636|186803|2569097,Complete,KateRasheed
bsdb:39599737/12/1,39599737,"randomized controlled trial,time series / longitudinal observational",39599737,https://doi.org/10.3390/nu16223952,https://www.mdpi.com/2072-6643/16/22/3952,"Naghibi M., Pont-Beltran A., Lamelas A., Llobregat L., Martinez-Blanch J.F., Rojas A., Álvarez B., López Plaza B., Arcos Castellanos L., Chenoll E., Vijayakumar V. , Day R.","Effect of Postbiotic <i>Bifidobacterium longum</i> CECT 7347 on Gastrointestinal Symptoms, Serum Biochemistry, and Intestinal Microbiota in Healthy Adults: A Randomised, Parallel, Double-Blind, Placebo-Controlled Pilot Study",Nutrients,2024,"Anaerobutyricum, Anaerostripes, Blautia, Faecalibacterium, Phocaeicola, SCFAs, abundance, butyrate, calprotectin, gut health, healthy population, inflammation, microbiome, postbiotics",Experiment 12,Spain,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) patients at Week 4,Heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) patients at Week 8,Mild to moderate patients with digestive symptoms fed with heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) at Week 8,NA,26,Recent use of antibiotics,16S,34,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 3,28 November 2025,Fiddyhamma,Fiddyhamma,Correlations: heatmaps showing the Maaslin2 Coefficient (Coeff) of correlations in genera abundances,increased,NA,NA,Complete,KateRasheed
bsdb:39599737/13/1,39599737,"randomized controlled trial,time series / longitudinal observational",39599737,https://doi.org/10.3390/nu16223952,https://www.mdpi.com/2072-6643/16/22/3952,"Naghibi M., Pont-Beltran A., Lamelas A., Llobregat L., Martinez-Blanch J.F., Rojas A., Álvarez B., López Plaza B., Arcos Castellanos L., Chenoll E., Vijayakumar V. , Day R.","Effect of Postbiotic <i>Bifidobacterium longum</i> CECT 7347 on Gastrointestinal Symptoms, Serum Biochemistry, and Intestinal Microbiota in Healthy Adults: A Randomised, Parallel, Double-Blind, Placebo-Controlled Pilot Study",Nutrients,2024,"Anaerobutyricum, Anaerostripes, Blautia, Faecalibacterium, Phocaeicola, SCFAs, abundance, butyrate, calprotectin, gut health, healthy population, inflammation, microbiome, postbiotics",Experiment 13,Spain,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) patients at Week 0,Heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) patients at Week 8,Mild to moderate patients with digestive symptoms fed with heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) at Week 8,30,26,Recent use of antibiotics,16S,34,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 7A, B, Supplementary Figure 3",28 November 2025,Fiddyhamma,Fiddyhamma,Correlations: heatmaps showing the Maaslin2 Coefficient (Coeff) of correlations in genera abundances,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Agathobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|2569097;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|3085642|2048137;1783272|1239|186801|186802|216572|216851,Complete,KateRasheed
bsdb:39599737/13/2,39599737,"randomized controlled trial,time series / longitudinal observational",39599737,https://doi.org/10.3390/nu16223952,https://www.mdpi.com/2072-6643/16/22/3952,"Naghibi M., Pont-Beltran A., Lamelas A., Llobregat L., Martinez-Blanch J.F., Rojas A., Álvarez B., López Plaza B., Arcos Castellanos L., Chenoll E., Vijayakumar V. , Day R.","Effect of Postbiotic <i>Bifidobacterium longum</i> CECT 7347 on Gastrointestinal Symptoms, Serum Biochemistry, and Intestinal Microbiota in Healthy Adults: A Randomised, Parallel, Double-Blind, Placebo-Controlled Pilot Study",Nutrients,2024,"Anaerobutyricum, Anaerostripes, Blautia, Faecalibacterium, Phocaeicola, SCFAs, abundance, butyrate, calprotectin, gut health, healthy population, inflammation, microbiome, postbiotics",Experiment 13,Spain,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) patients at Week 0,Heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) patients at Week 8,Mild to moderate patients with digestive symptoms fed with heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) at Week 8,30,26,Recent use of antibiotics,16S,34,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 7A,28 November 2025,Fiddyhamma,Fiddyhamma,Correlations: heatmaps showing the Maaslin2 Coefficient (Coeff) of correlations in genera abundances,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium",1783272|1239|186801|3085636|186803|841;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|186806|1730,Complete,KateRasheed
bsdb:39599758/1/1,39599758,randomized controlled trial,39599758,10.3390/nu16223971,NA,"Baldi S., Pagliai G., Di Gloria L., Pallecchi M., Barca F., Pieri B., Bartolucci G., Ramazzotti M., Amedei A., Palendri G. , Sofi F.",Beneficial Effects of Micronutrient Supplementation in Restoring the Altered Microbiota and Gut-Retina Axis in Patients with Neovascular Age-Related Macular Degeneration-A Randomized Clinical Trial,Nutrients,2024,"gut microbiota, gut–retina axis, lutein, nAMD, saffron, short-chain fatty acids, zeaxanthin",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Age-related macular degeneration,EFO:0001365,Healthy controls,nAMD (neovascular Age-related macular degeneration) patients,Elderly patients with nAMD (neovascular Age-related macular degeneration),15,30,2 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 1,Figure 3 and Table S2,11 June 2025,Anne-mariesharp,Anne-mariesharp,Significant differentially abundant taxa in stool samples of nAMD patients compared to HC,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",1783272|1239|186801|3085636|186803|2569097|39488;3379134|1224|1236|91347|543|1940338;1783272|1239|91061|186826;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|526524|526525|2810281|191303,Complete,KateRasheed
bsdb:39599758/1/2,39599758,randomized controlled trial,39599758,10.3390/nu16223971,NA,"Baldi S., Pagliai G., Di Gloria L., Pallecchi M., Barca F., Pieri B., Bartolucci G., Ramazzotti M., Amedei A., Palendri G. , Sofi F.",Beneficial Effects of Micronutrient Supplementation in Restoring the Altered Microbiota and Gut-Retina Axis in Patients with Neovascular Age-Related Macular Degeneration-A Randomized Clinical Trial,Nutrients,2024,"gut microbiota, gut–retina axis, lutein, nAMD, saffron, short-chain fatty acids, zeaxanthin",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Age-related macular degeneration,EFO:0001365,Healthy controls,nAMD (neovascular Age-related macular degeneration) patients,Elderly patients with nAMD (neovascular Age-related macular degeneration),15,30,2 months,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 2,Figure 3 and Table S2,11 June 2025,Anne-mariesharp,Anne-mariesharp,Significant differentially abundant taxa in stool samples of nAMD patients compared to HC,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum",3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976;3379134|1224|28216|80840;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|877420;3366610|28890|183925|2158|2159|2172;3379134|976|200643|171549|2005525|375288;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171552;3379134|1224|28216|80840|995019|40544;3379134|1224|28216|80840|995019;1783272|1239|186801|186802|216572|39492,Complete,KateRasheed
bsdb:39624839/1/1,39624839,laboratory experiment,39624839,10.3389/fphar.2024.1453989,NA,"Freschi M.L., Künstner A., Huber G., Stölting I., Busch H., Hirose M. , Raasch W.",Increase in body weight is lowered when mice received fecal microbiota transfer from donor mice treated with the AT<sub>1</sub> receptor antagonist telmisartan,Frontiers in pharmacology,2024,"AT1 receptor antagonist, desulovibrio, microbiota transfer, obesity, renin-angiotensin aldosterone system (RAAS), telmisartan, weight reduction",Experiment 1,Germany,Mus musculus,Feces,UBERON:0001988,Body weight,EFO:0004338,d0 (day 0),d49 (day 49),Stool samples collected at day 49 for microbiota analysis after the mice had already been fed High Fat Diet (HFD) for 7 weeks,6,6,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Fig. S3B, S4B, S5B, Table S1",7 April 2025,Anne-mariesharp,Anne-mariesharp,"Differential abundance analysis of phylum, family and genera between d0 and d49. At time point d0, the mice were still receiving chow diet, while d49 represents the time point immediately before FMT, when the two groups of mice had been fed HFD for 7 weeks but had not yet received microbiome transfer",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales|f__Candidatus Gastranaerophilaceae,k__Pseudomonadati|p__Deferribacterota,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Kineothrix,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Lawsonibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Schaedlerella,k__Pseudomonadati|p__Thermodesulfobacteriota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239|186801|3085636|186803|1427378;1783272|201174;1783272|1239|186801|186802|3082771;3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|3118652|2039240;1783272|1239|186801|186802|216572|244127;1783272|1239;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976;1783272|1239|186801|186802|3085642;1783272|1798710|1906119|3022868;3379134|200930;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;3379134|200940|3031449;1783272|1239|526524|526525|128827;1783272|1239|526524|526525|128827|1729679;1783272|1239|186801|3085636|186803|2163168;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958;1783272|1239|186801|186802|216572|2172004;1783272|1239|91061|186826|33958|2767887;1783272|1239|91061|186826|33958|2742598;3379134|976|200643|1970189|1573805;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;3379134|1224|1236|135625|712;3379134|976|200643|171549|171550;1783272|1239|186801|3085636|186803|2676048;3379134|200940;1783272|1239|526524|526525|2810280|3025755;3379134|74201;1783272|1239|186801|186802|3082771;3379134|976|200643|171549;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|2005473;1783272|1239|186801|186802|216572;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:39624839/1/2,39624839,laboratory experiment,39624839,10.3389/fphar.2024.1453989,NA,"Freschi M.L., Künstner A., Huber G., Stölting I., Busch H., Hirose M. , Raasch W.",Increase in body weight is lowered when mice received fecal microbiota transfer from donor mice treated with the AT<sub>1</sub> receptor antagonist telmisartan,Frontiers in pharmacology,2024,"AT1 receptor antagonist, desulovibrio, microbiota transfer, obesity, renin-angiotensin aldosterone system (RAAS), telmisartan, weight reduction",Experiment 1,Germany,Mus musculus,Feces,UBERON:0001988,Body weight,EFO:0004338,d0 (day 0),d49 (day 49),Stool samples collected at day 49 for microbiota analysis after the mice had already been fed High Fat Diet (HFD) for 7 weeks,6,6,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Fig. S3B, S4B, S5B, Table S1",7 April 2025,Anne-mariesharp,"Anne-mariesharp,KateRasheed","Differential abundance analysis of phylum, family and genera between d0 and d49. At time point d0, the mice were still receiving chow diet, while d49 represents the time point immediately before FMT, when the two groups of mice had been fed HFD for 7 weeks but had not yet received microbiome transfer",decreased,"p__Candidatus Altimarinota,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Duncaniella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Paramuribaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotellamassilia,k__Pseudomonadati|p__Pseudomonadota|s__Proteobacteria bacterium CAG:495,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium UBA3282,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:508,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:485",363464;95818|2093818|2093825|2171986;3379134|976|200643|171549|2005473|2518495;3379134|976|200643|171549|2005473;3379134|976|200643|171549|2005473|1918540;3379134|976|200643|171549|2005473|2518497;3379134|976|200643|171549|171552|1926672;3379134|1224|1262987;3379134|1224;3379134|1224|28216|80840|995019|1918598;1783272|1239|186801|3085636|186803|1952023;1783272|1239|186801|186802|31979|1485|1262815;3379134|976|200643|171549|171552|838|1262927,Complete,Svetlana up
bsdb:39624839/2/1,39624839,laboratory experiment,39624839,10.3389/fphar.2024.1453989,NA,"Freschi M.L., Künstner A., Huber G., Stölting I., Busch H., Hirose M. , Raasch W.",Increase in body weight is lowered when mice received fecal microbiota transfer from donor mice treated with the AT<sub>1</sub> receptor antagonist telmisartan,Frontiers in pharmacology,2024,"AT1 receptor antagonist, desulovibrio, microbiota transfer, obesity, renin-angiotensin aldosterone system (RAAS), telmisartan, weight reduction",Experiment 2,Germany,Mus musculus,Feces,UBERON:0001988,Body weight,EFO:0004338,BL/6>fVEH,BL/6>fTEL,"Mice that received fecal microbiota transfer (FMT) from donor mice pre-treated with telmisartan  (TEL (8mg/kg/d by gavage, 12 weeks))",12,12,NA,16S,34,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),T-Test",0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 5B, 6B, 7B",7 April 2025,Anne-mariesharp,Anne-mariesharp,"Differential abundance analysis of phylum, family and genus levels between BL/6>fVEH and BL/6>fTEL",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Rodentibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Pseudomonadati|p__Pseudomonadota|s__Proteobacteria bacterium CAG:495",3379134|1224|1236|135625|712;3379134|1224|1236|135625|712|1960084;1783272|1239|526524|526525|2810280|3025755;3379134|1224|1262987,Complete,Svetlana up
bsdb:39624839/2/2,39624839,laboratory experiment,39624839,10.3389/fphar.2024.1453989,NA,"Freschi M.L., Künstner A., Huber G., Stölting I., Busch H., Hirose M. , Raasch W.",Increase in body weight is lowered when mice received fecal microbiota transfer from donor mice treated with the AT<sub>1</sub> receptor antagonist telmisartan,Frontiers in pharmacology,2024,"AT1 receptor antagonist, desulovibrio, microbiota transfer, obesity, renin-angiotensin aldosterone system (RAAS), telmisartan, weight reduction",Experiment 2,Germany,Mus musculus,Feces,UBERON:0001988,Body weight,EFO:0004338,BL/6>fVEH,BL/6>fTEL,"Mice that received fecal microbiota transfer (FMT) from donor mice pre-treated with telmisartan  (TEL (8mg/kg/d by gavage, 12 weeks))",12,12,NA,16S,34,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),T-Test",0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 5B, 6B, 7B",7 April 2025,Anne-mariesharp,Anne-mariesharp,"Differential abundance analysis of phylum, family and genus levels between BL/6>fVEH and BL/6>fTEL",decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Kineothrix,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Schaedlerella,k__Pseudomonadati|p__Thermodesulfobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|201174;1783272|1239;1783272|1239|186801|186802|3085642;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;1783272|1239|526524|526525|128827;1783272|1239|186801|3085636|186803|2163168;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|2767887;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803|2676048;3379134|200940;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:39640675/1/1,39640675,case-control,39640675,https://doi.org/10.1016/j.heliyon.2024.e38507,https://www.sciencedirect.com/science/article/pii/S2405844024145380,"Chiba N., Suzuki S., Enriquez-Vera D., Utsunomiya A., Kubuki Y., Hidaka T., Shimoda K., Nakahata S., Yamada T. , Morishita K.",Succinic semialdehyde derived from the gut microbiota can promote the proliferation of adult T-cell leukemia/lymphoma cells,Heliyon,2024,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Adult T-cell leukemia/lymphoma,NA,Healthy controls and Low-risk human T-cell leukemia virus type 1 (HTLV-1) carriers (H + C),Adult T-cell leukemia/lymphoma (ATLL) patients and High-risk human T-cell leukemia virus type 1 (HTLV-1) carriers (A + HiC),Patients diagnosed with Adult T-cell leukemia/lymphoma (ATLL) and asymptomatic High-risk human T-cell leukemia virus type 1 (HTLV-1) carriers with proviral loads (PVLs) above 40 (per 1000 peripheral blood mononuclear cells (PBMCs)),49,19,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3A (Left column), 3C",4 November 2025,Adiba Patel,"Adiba Patel,Fiddyhamma","The distribution of P values for 46 bacterial genera with significant differences in abundance according to the two-tailed Brunner–Munzel test (left column, “BM”)",increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|200940|3031449|213115|194924|872;3379134|1224|1236|91347|543|570;1783272|1239|909932|1843488|909930;1783272|1239|186801|186802|216572,Complete,NA
bsdb:39640675/1/2,39640675,case-control,39640675,https://doi.org/10.1016/j.heliyon.2024.e38507,https://www.sciencedirect.com/science/article/pii/S2405844024145380,"Chiba N., Suzuki S., Enriquez-Vera D., Utsunomiya A., Kubuki Y., Hidaka T., Shimoda K., Nakahata S., Yamada T. , Morishita K.",Succinic semialdehyde derived from the gut microbiota can promote the proliferation of adult T-cell leukemia/lymphoma cells,Heliyon,2024,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,Adult T-cell leukemia/lymphoma,NA,Healthy controls and Low-risk human T-cell leukemia virus type 1 (HTLV-1) carriers (H + C),Adult T-cell leukemia/lymphoma (ATLL) patients and High-risk human T-cell leukemia virus type 1 (HTLV-1) carriers (A + HiC),Patients diagnosed with Adult T-cell leukemia/lymphoma (ATLL) and asymptomatic High-risk human T-cell leukemia virus type 1 (HTLV-1) carriers with proviral loads (PVLs) above 40 (per 1000 peripheral blood mononuclear cells (PBMCs)),49,19,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3A (Left column), 3C",4 November 2025,Adiba Patel,"Adiba Patel,Fiddyhamma","The distribution of P values for 46 bacterial genera with significant differences in abundance according to the two-tailed Brunner–Munzel test (left column, “BM”)",decreased,NA,NA,Complete,NA
bsdb:39640675/3/1,39640675,case-control,39640675,https://doi.org/10.1016/j.heliyon.2024.e38507,https://www.sciencedirect.com/science/article/pii/S2405844024145380,"Chiba N., Suzuki S., Enriquez-Vera D., Utsunomiya A., Kubuki Y., Hidaka T., Shimoda K., Nakahata S., Yamada T. , Morishita K.",Succinic semialdehyde derived from the gut microbiota can promote the proliferation of adult T-cell leukemia/lymphoma cells,Heliyon,2024,NA,Experiment 3,Japan,Homo sapiens,Feces,UBERON:0001988,Adult T-cell leukemia/lymphoma,NA,Healthy controls,Adult T-cell leukemia/lymphoma (ATLL),Adult T-cell leukemia/lymphoma (ATLL) is a refractory blood cancer with severe immunodeficiency resulting from retroviral infection.,8,17,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Supplementary Fig. S4B,11 January 2026,Fiddyhamma,Fiddyhamma,The relative abundance of the seven genera in cohort 2. P values were calculated by the two-tailed Brunner–Munzel test.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",3379134|1224|1236|91347|543|570;3379134|200940|3031449|213115|194924|872,Complete,NA
bsdb:39642873/1/1,39642873,"cross-sectional observational, not case-control",39642873,10.1016/j.xcrm.2024.101836,NA,"Kristensen M., de Steenhuijsen Piters W.A.A., Wildenbeest J., van Houten M.A., Zuurbier R.P., Hasrat R., Arp K., Chu M.L.J.N., Billard M., Heikkinen T., Cunningham S., Snape M., Drysdale S.B., Thwaites R.S., Martinon-Torres F., Pollard A.J., Openshaw P.J.M., Aerssen J., Binkowska J., Bont L. , Bogaert D.",The respiratory microbiome is linked to the severity of RSV infections and the persistence of symptoms in children,Cell reports. Medicine,2024,"16S, RSV, airway, birth cohort, case-control, microbiota, nasopharynx, respiratory, severity",Experiment 1,"Belgium,Finland,Netherlands,Spain,United Kingdom",Homo sapiens,Nasopharynx,UBERON:0001728,Respiratory Syncytial Virus Infection,EFO:1001413,Healthy Controls,RSV (Respiratory Syncytial Virus) Infection,Infants with RSV (Respiratory Syncytial Virus) infection during the first year of life.,52,374,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,age,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig 2E-F,26 March 2025,AmyUchay,"AmyUchay,PreciousChijioke",Taxonomic differences of nasopharyngeal microbiota in infants with RSV infection versus healthy controls.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella",3379134|1224|1236|135625|712|724;3379134|1224|1236|2887326|468|475,Complete,Svetlana up
bsdb:39642873/1/2,39642873,"cross-sectional observational, not case-control",39642873,10.1016/j.xcrm.2024.101836,NA,"Kristensen M., de Steenhuijsen Piters W.A.A., Wildenbeest J., van Houten M.A., Zuurbier R.P., Hasrat R., Arp K., Chu M.L.J.N., Billard M., Heikkinen T., Cunningham S., Snape M., Drysdale S.B., Thwaites R.S., Martinon-Torres F., Pollard A.J., Openshaw P.J.M., Aerssen J., Binkowska J., Bont L. , Bogaert D.",The respiratory microbiome is linked to the severity of RSV infections and the persistence of symptoms in children,Cell reports. Medicine,2024,"16S, RSV, airway, birth cohort, case-control, microbiota, nasopharynx, respiratory, severity",Experiment 1,"Belgium,Finland,Netherlands,Spain,United Kingdom",Homo sapiens,Nasopharynx,UBERON:0001728,Respiratory Syncytial Virus Infection,EFO:1001413,Healthy Controls,RSV (Respiratory Syncytial Virus) Infection,Infants with RSV (Respiratory Syncytial Virus) infection during the first year of life.,52,374,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,age,NA,unchanged,NA,NA,NA,NA,Signature 2,Fig 2E-F,26 March 2025,AmyUchay,"AmyUchay,PreciousChijioke",Taxonomic differences of nasopharyngeal microbiota in infants with RSV infection versus healthy controls.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum pigrum",1783272|201174|1760|85007|1653|1716;1783272|1239|91061|186826|186828|29393;1783272|1239|91061|186826|186828|29393|29394,Complete,Svetlana up
bsdb:39642873/2/1,39642873,"cross-sectional observational, not case-control",39642873,10.1016/j.xcrm.2024.101836,NA,"Kristensen M., de Steenhuijsen Piters W.A.A., Wildenbeest J., van Houten M.A., Zuurbier R.P., Hasrat R., Arp K., Chu M.L.J.N., Billard M., Heikkinen T., Cunningham S., Snape M., Drysdale S.B., Thwaites R.S., Martinon-Torres F., Pollard A.J., Openshaw P.J.M., Aerssen J., Binkowska J., Bont L. , Bogaert D.",The respiratory microbiome is linked to the severity of RSV infections and the persistence of symptoms in children,Cell reports. Medicine,2024,"16S, RSV, airway, birth cohort, case-control, microbiota, nasopharynx, respiratory, severity",Experiment 2,"Belgium,Finland,Netherlands,Spain,United Kingdom",Homo sapiens,Nasopharynx,UBERON:0001728,Respiratory Syncytial Virus Infection,EFO:1001413,Healthy Controls,RSV (Respiratory Syncytial Virus) Convalescence,Infants with RSV (Respiratory Syncytial Virus) Convalescence during the first year of life.,52,338,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,age,NA,decreased,NA,NA,NA,NA,Signature 1,Fig 2E - 2F,8 April 2025,PreciousChijioke,PreciousChijioke,Taxonomic differences of nasopharyngeal microbiota in infants with RSV infection versus healthy controls.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,3379134|1224|1236|2887326|468|475,Complete,Svetlana up
bsdb:39642873/2/2,39642873,"cross-sectional observational, not case-control",39642873,10.1016/j.xcrm.2024.101836,NA,"Kristensen M., de Steenhuijsen Piters W.A.A., Wildenbeest J., van Houten M.A., Zuurbier R.P., Hasrat R., Arp K., Chu M.L.J.N., Billard M., Heikkinen T., Cunningham S., Snape M., Drysdale S.B., Thwaites R.S., Martinon-Torres F., Pollard A.J., Openshaw P.J.M., Aerssen J., Binkowska J., Bont L. , Bogaert D.",The respiratory microbiome is linked to the severity of RSV infections and the persistence of symptoms in children,Cell reports. Medicine,2024,"16S, RSV, airway, birth cohort, case-control, microbiota, nasopharynx, respiratory, severity",Experiment 2,"Belgium,Finland,Netherlands,Spain,United Kingdom",Homo sapiens,Nasopharynx,UBERON:0001728,Respiratory Syncytial Virus Infection,EFO:1001413,Healthy Controls,RSV (Respiratory Syncytial Virus) Convalescence,Infants with RSV (Respiratory Syncytial Virus) Convalescence during the first year of life.,52,338,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,age,NA,decreased,NA,NA,NA,NA,Signature 2,Fig 2E - 2F,8 April 2025,PreciousChijioke,PreciousChijioke,Taxonomic differences of nasopharyngeal microbiota in infants with RSV infection versus healthy controls.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,1783272|201174|1760|85007|1653|1716,Complete,Svetlana up
bsdb:39642873/3/1,39642873,"cross-sectional observational, not case-control",39642873,10.1016/j.xcrm.2024.101836,NA,"Kristensen M., de Steenhuijsen Piters W.A.A., Wildenbeest J., van Houten M.A., Zuurbier R.P., Hasrat R., Arp K., Chu M.L.J.N., Billard M., Heikkinen T., Cunningham S., Snape M., Drysdale S.B., Thwaites R.S., Martinon-Torres F., Pollard A.J., Openshaw P.J.M., Aerssen J., Binkowska J., Bont L. , Bogaert D.",The respiratory microbiome is linked to the severity of RSV infections and the persistence of symptoms in children,Cell reports. Medicine,2024,"16S, RSV, airway, birth cohort, case-control, microbiota, nasopharynx, respiratory, severity",Experiment 3,"Belgium,Finland,Netherlands,Spain,United Kingdom",Homo sapiens,Nasopharynx,UBERON:0001728,Respiratory Syncytial Virus Infection,EFO:1001413,Healthy Controls,Mild RSV (Respiratory Syncytial Virus) group,Infants with Mild RSV (Respiratory Syncytial Virus) during the first year of life.,52,218,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig 3E - 3F,9 April 2025,AmyUchay,"AmyUchay,PreciousChijioke","Associations between microbiota diversity, stability and composition, and RSV infection severity",increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,3379134|1224|1236|2887326|468|475,Complete,Svetlana up
bsdb:39642873/3/2,39642873,"cross-sectional observational, not case-control",39642873,10.1016/j.xcrm.2024.101836,NA,"Kristensen M., de Steenhuijsen Piters W.A.A., Wildenbeest J., van Houten M.A., Zuurbier R.P., Hasrat R., Arp K., Chu M.L.J.N., Billard M., Heikkinen T., Cunningham S., Snape M., Drysdale S.B., Thwaites R.S., Martinon-Torres F., Pollard A.J., Openshaw P.J.M., Aerssen J., Binkowska J., Bont L. , Bogaert D.",The respiratory microbiome is linked to the severity of RSV infections and the persistence of symptoms in children,Cell reports. Medicine,2024,"16S, RSV, airway, birth cohort, case-control, microbiota, nasopharynx, respiratory, severity",Experiment 3,"Belgium,Finland,Netherlands,Spain,United Kingdom",Homo sapiens,Nasopharynx,UBERON:0001728,Respiratory Syncytial Virus Infection,EFO:1001413,Healthy Controls,Mild RSV (Respiratory Syncytial Virus) group,Infants with Mild RSV (Respiratory Syncytial Virus) during the first year of life.,52,218,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Fig 3E - 3F,9 April 2025,AmyUchay,"AmyUchay,PreciousChijioke","Associations between microbiota diversity, stability and composition, and RSV infection severity.",decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,1783272|201174|1760|85007|1653|1716,Complete,Svetlana up
bsdb:39642873/4/1,39642873,"cross-sectional observational, not case-control",39642873,10.1016/j.xcrm.2024.101836,NA,"Kristensen M., de Steenhuijsen Piters W.A.A., Wildenbeest J., van Houten M.A., Zuurbier R.P., Hasrat R., Arp K., Chu M.L.J.N., Billard M., Heikkinen T., Cunningham S., Snape M., Drysdale S.B., Thwaites R.S., Martinon-Torres F., Pollard A.J., Openshaw P.J.M., Aerssen J., Binkowska J., Bont L. , Bogaert D.",The respiratory microbiome is linked to the severity of RSV infections and the persistence of symptoms in children,Cell reports. Medicine,2024,"16S, RSV, airway, birth cohort, case-control, microbiota, nasopharynx, respiratory, severity",Experiment 4,"Belgium,Finland,Netherlands,Spain,United Kingdom",Homo sapiens,Nasopharynx,UBERON:0001728,Respiratory Syncytial Virus Infection,EFO:1001413,Healthy Controls,Moderate RSV (Respiratory Syncytial Virus) group,Infants with Moderate RSV (Respiratory Syncytial Virus) during the first year of life.,52,106,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig 3E - 3F,11 April 2025,PreciousChijioke,PreciousChijioke,"Associations between microbiota diversity, stability and composition, and RSV infection severity",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella",3379134|1224|1236|135625|712|724;3379134|1224|1236|2887326|468|475,Complete,Svetlana up
bsdb:39642873/4/2,39642873,"cross-sectional observational, not case-control",39642873,10.1016/j.xcrm.2024.101836,NA,"Kristensen M., de Steenhuijsen Piters W.A.A., Wildenbeest J., van Houten M.A., Zuurbier R.P., Hasrat R., Arp K., Chu M.L.J.N., Billard M., Heikkinen T., Cunningham S., Snape M., Drysdale S.B., Thwaites R.S., Martinon-Torres F., Pollard A.J., Openshaw P.J.M., Aerssen J., Binkowska J., Bont L. , Bogaert D.",The respiratory microbiome is linked to the severity of RSV infections and the persistence of symptoms in children,Cell reports. Medicine,2024,"16S, RSV, airway, birth cohort, case-control, microbiota, nasopharynx, respiratory, severity",Experiment 4,"Belgium,Finland,Netherlands,Spain,United Kingdom",Homo sapiens,Nasopharynx,UBERON:0001728,Respiratory Syncytial Virus Infection,EFO:1001413,Healthy Controls,Moderate RSV (Respiratory Syncytial Virus) group,Infants with Moderate RSV (Respiratory Syncytial Virus) during the first year of life.,52,106,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Fig 3E - 3F,11 April 2025,PreciousChijioke,PreciousChijioke,"Associations between microbiota diversity, stability and composition, and RSV infection severity",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum pigrum",1783272|201174|1760|85007|1653|1716;1783272|1239|91061|186826|186828|29393;1783272|1239|91061|186826|186828|29393|29394,Complete,Svetlana up
bsdb:39642873/5/1,39642873,"cross-sectional observational, not case-control",39642873,10.1016/j.xcrm.2024.101836,NA,"Kristensen M., de Steenhuijsen Piters W.A.A., Wildenbeest J., van Houten M.A., Zuurbier R.P., Hasrat R., Arp K., Chu M.L.J.N., Billard M., Heikkinen T., Cunningham S., Snape M., Drysdale S.B., Thwaites R.S., Martinon-Torres F., Pollard A.J., Openshaw P.J.M., Aerssen J., Binkowska J., Bont L. , Bogaert D.",The respiratory microbiome is linked to the severity of RSV infections and the persistence of symptoms in children,Cell reports. Medicine,2024,"16S, RSV, airway, birth cohort, case-control, microbiota, nasopharynx, respiratory, severity",Experiment 5,"Belgium,Finland,Netherlands,Spain,United Kingdom",Homo sapiens,Nasopharynx,UBERON:0001728,Respiratory Syncytial Virus Infection,EFO:1001413,Healthy Controls,Severe RSV (Respiratory Syncytial Virus) group,Infants with Severe RSV (Respiratory Syncytial Virus) during the first year of life.,52,47,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig 3E - 3F,11 April 2025,PreciousChijioke,PreciousChijioke,"Associations between microbiota diversity, stability and composition, and RSV infection severity.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|1300|1301;3379134|976|200643|171549|171551|836,Complete,Svetlana up
bsdb:39642873/5/2,39642873,"cross-sectional observational, not case-control",39642873,10.1016/j.xcrm.2024.101836,NA,"Kristensen M., de Steenhuijsen Piters W.A.A., Wildenbeest J., van Houten M.A., Zuurbier R.P., Hasrat R., Arp K., Chu M.L.J.N., Billard M., Heikkinen T., Cunningham S., Snape M., Drysdale S.B., Thwaites R.S., Martinon-Torres F., Pollard A.J., Openshaw P.J.M., Aerssen J., Binkowska J., Bont L. , Bogaert D.",The respiratory microbiome is linked to the severity of RSV infections and the persistence of symptoms in children,Cell reports. Medicine,2024,"16S, RSV, airway, birth cohort, case-control, microbiota, nasopharynx, respiratory, severity",Experiment 5,"Belgium,Finland,Netherlands,Spain,United Kingdom",Homo sapiens,Nasopharynx,UBERON:0001728,Respiratory Syncytial Virus Infection,EFO:1001413,Healthy Controls,Severe RSV (Respiratory Syncytial Virus) group,Infants with Severe RSV (Respiratory Syncytial Virus) during the first year of life.,52,47,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Fig 3E - 3F,11 April 2025,PreciousChijioke,PreciousChijioke,"Associations between microbiota diversity, stability and composition, and RSV infection severity.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum pigrum",1783272|201174|1760|85007|1653|1716;1783272|1239|91061|186826|186828|29393;1783272|1239|91061|186826|186828|29393|29394,Complete,Svetlana up
bsdb:39642873/6/1,39642873,"cross-sectional observational, not case-control",39642873,10.1016/j.xcrm.2024.101836,NA,"Kristensen M., de Steenhuijsen Piters W.A.A., Wildenbeest J., van Houten M.A., Zuurbier R.P., Hasrat R., Arp K., Chu M.L.J.N., Billard M., Heikkinen T., Cunningham S., Snape M., Drysdale S.B., Thwaites R.S., Martinon-Torres F., Pollard A.J., Openshaw P.J.M., Aerssen J., Binkowska J., Bont L. , Bogaert D.",The respiratory microbiome is linked to the severity of RSV infections and the persistence of symptoms in children,Cell reports. Medicine,2024,"16S, RSV, airway, birth cohort, case-control, microbiota, nasopharynx, respiratory, severity",Experiment 6,"Belgium,Finland,Netherlands,Spain,United Kingdom",Homo sapiens,Nasopharynx,UBERON:0001728,Respiratory Syncytial Virus Infection,EFO:1001413,No (symptoms),Blocked/runny nose,Infants with (blocked nose/cough/wheeze) during convalescence.,NA,NA,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 4A - 4B,11 April 2025,PreciousChijioke,PreciousChijioke,Associations between microbiota profiles at RSV convalescence and remaining symptoms.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,3379134|1224|1236|135625|712|724,Complete,Svetlana up
bsdb:39642873/6/2,39642873,"cross-sectional observational, not case-control",39642873,10.1016/j.xcrm.2024.101836,NA,"Kristensen M., de Steenhuijsen Piters W.A.A., Wildenbeest J., van Houten M.A., Zuurbier R.P., Hasrat R., Arp K., Chu M.L.J.N., Billard M., Heikkinen T., Cunningham S., Snape M., Drysdale S.B., Thwaites R.S., Martinon-Torres F., Pollard A.J., Openshaw P.J.M., Aerssen J., Binkowska J., Bont L. , Bogaert D.",The respiratory microbiome is linked to the severity of RSV infections and the persistence of symptoms in children,Cell reports. Medicine,2024,"16S, RSV, airway, birth cohort, case-control, microbiota, nasopharynx, respiratory, severity",Experiment 6,"Belgium,Finland,Netherlands,Spain,United Kingdom",Homo sapiens,Nasopharynx,UBERON:0001728,Respiratory Syncytial Virus Infection,EFO:1001413,No (symptoms),Blocked/runny nose,Infants with (blocked nose/cough/wheeze) during convalescence.,NA,NA,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 4A - 4B,11 April 2025,PreciousChijioke,PreciousChijioke,Associations between microbiota profiles at RSV convalescence and remaining symptoms.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum pigrum",1783272|1239|91061|186826|186828|29393;1783272|1239|91061|186826|186828|29393|29394,Complete,Svetlana up
bsdb:39642873/7/1,39642873,"cross-sectional observational, not case-control",39642873,10.1016/j.xcrm.2024.101836,NA,"Kristensen M., de Steenhuijsen Piters W.A.A., Wildenbeest J., van Houten M.A., Zuurbier R.P., Hasrat R., Arp K., Chu M.L.J.N., Billard M., Heikkinen T., Cunningham S., Snape M., Drysdale S.B., Thwaites R.S., Martinon-Torres F., Pollard A.J., Openshaw P.J.M., Aerssen J., Binkowska J., Bont L. , Bogaert D.",The respiratory microbiome is linked to the severity of RSV infections and the persistence of symptoms in children,Cell reports. Medicine,2024,"16S, RSV, airway, birth cohort, case-control, microbiota, nasopharynx, respiratory, severity",Experiment 7,"Belgium,Finland,Netherlands,Spain,United Kingdom",Homo sapiens,Nasopharynx,UBERON:0001728,Respiratory Syncytial Virus Infection,EFO:1001413,No (symptoms),Any (symptoms),Infants with Any (symptoms) during the first year of life.,NA,NA,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 4A - 4B,11 April 2025,PreciousChijioke,PreciousChijioke,Associations between microbiota profiles at RSV convalescence and remaining symptoms.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,3379134|1224|1236|135625|712|724,Complete,Svetlana up
bsdb:39644491/1/1,39644491,case-control,39644491,https://doi.org/10.1080/01902148.2024.2437377,NA,"Göktürk K., Tülek B., Kanat F., Maçin S., Arslan U., Shahbazova M. , Göktürk Ö.",Gut microbiota profiles of patients with idiopathic pulmonary fibrosis,Experimental lung research,2024,"Idiopathic pulmonary fibrosis, antifibrotic drug, gut microbiota dysbiosis",Experiment 1,Turkey,Homo sapiens,Feces,UBERON:0001988,Idiopathic pulmonary fibrosis,EFO:0000768,Healthy controls,Idiopathic pulmonary fibrosis patients (IPF),"Patients diagnosed with Idiopathic pulmonary fibrosis  within the last year who have received at least three months of continuous antifibrotic therapy, and newly diagnosed patients who have not yet started antifibrotic medication.",8,24,3 months,16S,123456789,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table 2,26 January 2026,Shiber256,Shiber256,Gut microbiota abundance in patients with idiopathic pulmonary fibrosis and healthy controls.,increased,"k__Pseudomonadati|p__Campylobacterota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:56",3379134|29547;3379134|1224|1236|91347;3379134|976|200643|171549|815;1783272|1239|526524|526525|128827;1783272|1239|526524|526525|128827|1573535;3379134|976|200643|171549|171552|1283313;1783272|1239|1263031,Complete,NA
bsdb:39644491/1/2,39644491,case-control,39644491,https://doi.org/10.1080/01902148.2024.2437377,NA,"Göktürk K., Tülek B., Kanat F., Maçin S., Arslan U., Shahbazova M. , Göktürk Ö.",Gut microbiota profiles of patients with idiopathic pulmonary fibrosis,Experimental lung research,2024,"Idiopathic pulmonary fibrosis, antifibrotic drug, gut microbiota dysbiosis",Experiment 1,Turkey,Homo sapiens,Feces,UBERON:0001988,Idiopathic pulmonary fibrosis,EFO:0000768,Healthy controls,Idiopathic pulmonary fibrosis patients (IPF),"Patients diagnosed with Idiopathic pulmonary fibrosis  within the last year who have received at least three months of continuous antifibrotic therapy, and newly diagnosed patients who have not yet started antifibrotic medication.",8,24,3 months,16S,123456789,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Table 2,26 January 2026,Shiber256,Shiber256,Gut microbiota abundance in patients with idiopathic pulmonary fibrosis and healthy controls.,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Bacilli|o__Staphylococcales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter",1783272|201174;1783272|201174|1760|85004;3379134|1224|28216|80840;1783272|1239|91061|3120442;1783272|1239|91061|1385|539738;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|1407607,Complete,NA
bsdb:39644491/2/1,39644491,case-control,39644491,https://doi.org/10.1080/01902148.2024.2437377,NA,"Göktürk K., Tülek B., Kanat F., Maçin S., Arslan U., Shahbazova M. , Göktürk Ö.",Gut microbiota profiles of patients with idiopathic pulmonary fibrosis,Experimental lung research,2024,"Idiopathic pulmonary fibrosis, antifibrotic drug, gut microbiota dysbiosis",Experiment 2,Turkey,Homo sapiens,Feces,UBERON:0001988,Idiopathic pulmonary fibrosis,EFO:0000768,Patients with Idiopathic Pulmonary Fibrosis (IPF) not using antifibrotic drugs,Patients with Idiopathic Pulmonary Fibrosis (IPF) using antifibrotic drugs,Patients diagnosed with Idiopathic pulmonary fibrosis (IPF) within the last year who have received at least three months of continuous antifibrotic therapy,12,12,3 months,16S,123456789,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 5,26 January 2026,Firdaws,Firdaws,Gut microbiota abundance in patients with idiopathic pulmonary fibrosis not using antifibrotic drugs and those using antifibrotic drugs.,decreased,NA,NA,Complete,NA
bsdb:39656003/1/1,39656003,case-control,39656003,10.1128/spectrum.01382-24,NA,"Yunusbayev B., Bogdanova A., Nadyrchenko N., Danilov L., Bogdanov V., Sergeev G., Altinbaev R., Bilalov F. , Yunusbaeva M.",Gut dysbiosis narrative in psoriasis: matched-pair approach identifies only subtle shifts correlated with elevated fecal calprotectin,Microbiology spectrum,2025,"dysbiosis, gut microbiota, lactate, low-grade Inflammation, psoriasis",Experiment 1,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Psoriasis,EFO:0000676,Healthy adult donors,Psoriasis patients,Patients with Psoriasis,47,53,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,sex,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2,24 March 2025,Tosin,Tosin,Differentially abundant bacteria in case-control matched pairs,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium mitsuokai,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:180,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. AM42-24,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum",3379134|976|200643|171549|815|816|371601;1783272|1239|526524|526525|2810280|135858|100886;1783272|1239|186801|186802|186806|1730|1262882;1783272|1239|909932|1843489|31977|906|907;3379134|976|200643|171549|171552|838|2293125;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|186801|186802|216572|1535,Complete,Svetlana up
bsdb:39656003/1/2,39656003,case-control,39656003,10.1128/spectrum.01382-24,NA,"Yunusbayev B., Bogdanova A., Nadyrchenko N., Danilov L., Bogdanov V., Sergeev G., Altinbaev R., Bilalov F. , Yunusbaeva M.",Gut dysbiosis narrative in psoriasis: matched-pair approach identifies only subtle shifts correlated with elevated fecal calprotectin,Microbiology spectrum,2025,"dysbiosis, gut microbiota, lactate, low-grade Inflammation, psoriasis",Experiment 1,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Psoriasis,EFO:0000676,Healthy adult donors,Psoriasis patients,Patients with Psoriasis,47,53,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,sex,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2,24 March 2025,Tosin,Tosin,Differentially abundant bacteria in case-control matched pairs,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister sp. CAG:357,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp. HMSC71H05,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans",3379134|976|200643|171549|815|816|291644;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|909932|1843489|31977|39948|1262869;3379134|1224|1236|135625|712|724|1608898;1783272|1239|186801|3085636|186803|28050|39485;3379134|1224|28216|80840|995019|577310|487175;1783272|1239|186801|3085636|186803|841|360807,Complete,Svetlana up
bsdb:39656003/2/1,39656003,case-control,39656003,10.1128/spectrum.01382-24,NA,"Yunusbayev B., Bogdanova A., Nadyrchenko N., Danilov L., Bogdanov V., Sergeev G., Altinbaev R., Bilalov F. , Yunusbaeva M.",Gut dysbiosis narrative in psoriasis: matched-pair approach identifies only subtle shifts correlated with elevated fecal calprotectin,Microbiology spectrum,2025,"dysbiosis, gut microbiota, lactate, low-grade Inflammation, psoriasis",Experiment 2,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Psoriasis,EFO:0000676,Healthy adult donors,Psoriasis patients,Patients with Psoriasis,47,53,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,sex,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure S6,24 March 2025,Tosin,"Tosin,Svetlana up","Differentially abundant bacterial species inferred using the  linear discriminant analysis, LEfSe",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:180,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. AM42-24",1783272|1239|909932|1843488|909930|904;3379134|976|200643|171549|815|816|338188;3379134|976|200643|171549|815|816|371601;28221;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|186801|186802|186806|1730|1262882;1783272|1239|526524|526525|128827|1573535;1783272|1239|526524|526525|128827|1573535|1735;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843489|31977|906|907;3379134|976|200643|171549|171552|838|2293125,Complete,Svetlana up
bsdb:39656003/2/2,39656003,case-control,39656003,10.1128/spectrum.01382-24,NA,"Yunusbayev B., Bogdanova A., Nadyrchenko N., Danilov L., Bogdanov V., Sergeev G., Altinbaev R., Bilalov F. , Yunusbaeva M.",Gut dysbiosis narrative in psoriasis: matched-pair approach identifies only subtle shifts correlated with elevated fecal calprotectin,Microbiology spectrum,2025,"dysbiosis, gut microbiota, lactate, low-grade Inflammation, psoriasis",Experiment 2,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Psoriasis,EFO:0000676,Healthy adult donors,Psoriasis patients,Patients with Psoriasis,47,53,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,sex,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure S6,24 March 2025,Tosin,"Tosin,Svetlana up","Differentially abundant bacterial species inferred using the linear discriminant analysis, LEfSe",decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister sp. CAG:357,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Pseudomonadati|p__Pseudomonadota|s__Proteobacteria bacterium CAG:139,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Pseudomonadati|p__Pseudomonadota",1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|39948|1262869;1783272|1239|186801|186802|186806|1730|39496;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;1783272|1239|186801|3085636|186803|28050|39485;3379134|1224|1262986;1783272|1239|186801|3085636|186803|841|360807;3379134|1224|28216|80840|995019;3379134|1224,Complete,Svetlana up
bsdb:39694919/1/1,39694919,randomized controlled trial,39694919,10.1080/19490976.2024.2442051,NA,"Zhang Y., Ji X., Chang K., Yin H., Zhao M. , Zhao L.",The regulatory effect of chitooligosaccharides on islet inflammation in T2D individuals after islet cell transplantation: the mechanism behind <i>Candida albicans</i> abundance and macrophage polarization,Gut microbes,2025,"Candida albicans, Islet cell transplantation, chitooligosaccharides, islet inflammation, macrophages",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Con (Control) group,ICT (islet cell transplantation) group,Patients with T2D (type 2 diabetes) who underwent ICT (islet cell transplantation),16,33,Current use of antibiotics,18S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,increased,NA,decreased,Signature 1,Figure 2I,26 March 2025,Tosin,Tosin,Differential abundant taxa between CON (control) and ICT (islet cell transplantation) groups by LeFse.,increased,"p__Ciliophora|c__Spirotrichea|o__Stichotrichida|f__Amphisiellidae|g__Amphisiella,p__Ciliophora|c__Spirotrichea|o__Stichotrichida|f__Amphisiellidae|g__Uroleptoides|s__Uroleptoides magnigranulosus,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida dubliniensis,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Cystofilobasidiaceae,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Cystofilobasidiaceae|g__Cystofilobasidium,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia globosa,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Nakaseomyces|s__Nakaseomyces glabratus",5878|33829|33832|99916|396410;5878|33829|33832|99916|2293724|414913;4751|4890|3239874|2916678|766764|5475;4751|4890|3239874|2916678|766764|5475|5476;4751|4890|3239874|2916678|766764|5475|42374;4751|5204|155616|90883|165808;4751|5204|155616|90883|165808|5410;4751|4890|3239874|2916678|766764;4751|5204|1538075|162474|742845|55193|76773;4751|4890|4891|4892|4893|374468|5478,Complete,Svetlana up
bsdb:39694919/1/2,39694919,randomized controlled trial,39694919,10.1080/19490976.2024.2442051,NA,"Zhang Y., Ji X., Chang K., Yin H., Zhao M. , Zhao L.",The regulatory effect of chitooligosaccharides on islet inflammation in T2D individuals after islet cell transplantation: the mechanism behind <i>Candida albicans</i> abundance and macrophage polarization,Gut microbes,2025,"Candida albicans, Islet cell transplantation, chitooligosaccharides, islet inflammation, macrophages",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Con (Control) group,ICT (islet cell transplantation) group,Patients with T2D (type 2 diabetes) who underwent ICT (islet cell transplantation),16,33,Current use of antibiotics,18S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,increased,NA,decreased,Signature 2,Figure 2I,26 March 2025,Tosin,Tosin,Differential abundant taxa between CON (control) and ICT (islet cell transplantation) groups by LeFse.,decreased,"k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Bulleribasidiaceae|g__Hannaella|s__Hannaella luteola,p__Cercozoa|c__Imbricatea,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Leucosporidiales|f__Leucosporidiaceae,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Leucosporidiales,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Leucosporidiales|f__Leucosporidiaceae|g__Leucosporidium,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Leucosporidiales|f__Leucosporidiaceae|g__Leucosporidium|s__Leucosporidium yakuticum,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Caryophyllales|f__Polygonaceae,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Caryophyllales|f__Polygonaceae|s__Polygonoideae|g__Rheum,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Caryophyllales|f__Polygonaceae|s__Polygonoideae|g__Rheum|s__Rheum spiciforme",4751|5204|155616|5234|1884640|663591|1198485;136419|1736114;4751|5204|162481|231212|1163720;4751|5204|162481|231212;4751|5204|162481|231212|1163720|5277;4751|5204|162481|231212|1163720|5277|231218;33090|35493|3398|3524|3615;33090|35493|3398|3524|3615|1110380|3620;33090|35493|3398|3524|3615|1110380|3620|240184,Complete,Svetlana up
bsdb:39694919/2/1,39694919,randomized controlled trial,39694919,10.1080/19490976.2024.2442051,NA,"Zhang Y., Ji X., Chang K., Yin H., Zhao M. , Zhao L.",The regulatory effect of chitooligosaccharides on islet inflammation in T2D individuals after islet cell transplantation: the mechanism behind <i>Candida albicans</i> abundance and macrophage polarization,Gut microbes,2025,"Candida albicans, Islet cell transplantation, chitooligosaccharides, islet inflammation, macrophages",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Con (Control) group,ICT (islet cell transplantation) group,Patients with T2D (type 2 diabetes) who underwent ICT (islet cell transplantation),16,33,Current use of antibiotics,18S,NA,Illumina,relative abundances,T-Test,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,increased,NA,decreased,Signature 1,"Figure 2d, F and H",26 March 2025,Tosin,Tosin,"Comparison of microbial distribution histogram at genus, species level. (d), (f) and (h) the significant analysis of gut fungi.",increased,"k__Fungi|p__Ascomycota,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida",4751|4890;4751|4890|3239874|2916678|766764|5475|5476;4751|4890|3239874|2916678|766764|5475,Complete,Svetlana up
bsdb:39694919/2/2,39694919,randomized controlled trial,39694919,10.1080/19490976.2024.2442051,NA,"Zhang Y., Ji X., Chang K., Yin H., Zhao M. , Zhao L.",The regulatory effect of chitooligosaccharides on islet inflammation in T2D individuals after islet cell transplantation: the mechanism behind <i>Candida albicans</i> abundance and macrophage polarization,Gut microbes,2025,"Candida albicans, Islet cell transplantation, chitooligosaccharides, islet inflammation, macrophages",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Con (Control) group,ICT (islet cell transplantation) group,Patients with T2D (type 2 diabetes) who underwent ICT (islet cell transplantation),16,33,Current use of antibiotics,18S,NA,Illumina,relative abundances,T-Test,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,increased,NA,decreased,Signature 2,"Figure 2d, 2F and 2H",26 March 2025,Tosin,Tosin,"Comparison of microbial distribution histogram at genus, species level. (d), (f) and (h) the significant analysis of gut fungi.",decreased,"p__Ciliophora,k__Fungi|p__Basidiomycota,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fagales|f__Fagaceae|g__Quercus,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales|f__Russulaceae|g__Russula,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales|f__Russulaceae|g__Russula|s__Russula exalbicans,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fagales|f__Fagaceae|g__Quercus|s__Quercus lobata",5878;4751|5204;33090|35493|3398|3502|3503|3511;4751|5204|155619|452342|5401|5402;4751|5204|155619|452342|5401|5402|152959;33090|35493|3398|3502|3503|3511|97700,Complete,Svetlana up
bsdb:39694919/3/1,39694919,randomized controlled trial,39694919,10.1080/19490976.2024.2442051,NA,"Zhang Y., Ji X., Chang K., Yin H., Zhao M. , Zhao L.",The regulatory effect of chitooligosaccharides on islet inflammation in T2D individuals after islet cell transplantation: the mechanism behind <i>Candida albicans</i> abundance and macrophage polarization,Gut microbes,2025,"Candida albicans, Islet cell transplantation, chitooligosaccharides, islet inflammation, macrophages",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,RA (Rapamycin alone) treatment group of HMA-T2D (Human Microbiota associated type 2 diabetes) mice,RC (Rapamycin + Chitooligosaccharides ) treatment group of HMA-T2D (Human Microbiota associated type 2 diabetes) mice,The HMA-T2D (Human Microbiota associated type 2 diabetes) mice gavaged with Rapamycin (RAPA) 5 mg/kg every other day and Chitooligosaccharides (COS) 350 mg/kg/day.,8,8,NA,18S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 1,Figure 8B and 8C,26 March 2025,Tosin,Tosin,Analysis of the gut fungal community abundance differences between the RA (Rapamycin alone) and RC (Rapamycin + Chitooligosaccharides) groups of HMA-T2D (Human Microbiota associated type 2 diabetes) mice by LEfSe analysis,increased,"k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Debaryomyces,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Debaryomyces|s__Debaryomyces hansenii,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Hyphopichia,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Hyphopichia|s__Hyphopichia burtonii,k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Mucor,k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Mucor|s__Mucor racemosus,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Filobasidiales|f__Filobasidiaceae|g__Naganishia,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Filobasidiales|f__Filobasidiaceae|g__Naganishia|s__Naganishia albida,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Nakaseomyces|s__Nakaseomyces glabratus,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Rhodotorula,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Rhodotorula|s__Rhodotorula mucilaginosa,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae|g__Trichosporon,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae|g__Trichosporon|s__Trichosporon japonicum,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|g__Yarrowia,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|g__Yarrowia|s__Yarrowia lipolytica",4751|4890|3239874|2916678|766764|4958;4751|4890|3239874|2916678|766764|4958|4959;4751|4890|3239874|2916678|766764|507510;4751|4890|3239874|2916678|766764|507510|717740;4751|1913637|2212703|4827|34489|4830;4751|1913637|2212703|4827|34489|4830|4841;4751|5204|155616|90886|5408|1851509;4751|5204|155616|90886|5408|1851509|100951;4751|4890|4891|4892|4893|374468|5478;4751|5204|162481|231213|1799696|5533;4751|5204|162481|231213|1799696|5533|5537;4751|5204|155616|1851469|1759442|5552;4751|5204|155616|1851469|1759442|5552|85853;4751|4890|3239873|3243772|4951;4751|4890|3239873|3243772|4951|4952,Complete,Svetlana up
bsdb:39694919/3/2,39694919,randomized controlled trial,39694919,10.1080/19490976.2024.2442051,NA,"Zhang Y., Ji X., Chang K., Yin H., Zhao M. , Zhao L.",The regulatory effect of chitooligosaccharides on islet inflammation in T2D individuals after islet cell transplantation: the mechanism behind <i>Candida albicans</i> abundance and macrophage polarization,Gut microbes,2025,"Candida albicans, Islet cell transplantation, chitooligosaccharides, islet inflammation, macrophages",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,RA (Rapamycin alone) treatment group of HMA-T2D (Human Microbiota associated type 2 diabetes) mice,RC (Rapamycin + Chitooligosaccharides ) treatment group of HMA-T2D (Human Microbiota associated type 2 diabetes) mice,The HMA-T2D (Human Microbiota associated type 2 diabetes) mice gavaged with Rapamycin (RAPA) 5 mg/kg every other day and Chitooligosaccharides (COS) 350 mg/kg/day.,8,8,NA,18S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 2,Figure 8B and 8C,28 March 2025,Tosin,Tosin,Analysis of the gut fungal community abundance differences between the RA (Rapamycin alone) and RC (Rapamycin + Chitooligosaccharides) groups of HMA-T2D (Human Microbiota associated type 2 diabetes) mice by LEfSe analysis,decreased,"k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Arxiozyma|s__Arxiozyma telluris,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycodales|f__Saccharomycodaceae|g__Hanseniaspora,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycodales|f__Saccharomycodaceae|g__Hanseniaspora|s__Hanseniaspora uvarum,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Kazachstania,p__Apicomplexa|c__Conoidasida|o__Neogregarinorida|f__Lipotrophidae|g__Mattesia,p__Apicomplexa|c__Conoidasida|o__Neogregarinorida|f__Lipotrophidae|g__Mattesia",4751|4890|4891|4892|4893|36906|36907;4751|4890|3239874|2916678|766764|5475|5476;4751|4890|4891|3243779|34365|29832;4751|4890|4891|3243779|34365|29832|29833;4751|4890|4891|4892|4893|71245;5794|1280412|238088|238089|238095;5794|1280412|238088|238089|238095,Complete,Svetlana up
bsdb:39694919/4/1,39694919,randomized controlled trial,39694919,10.1080/19490976.2024.2442051,NA,"Zhang Y., Ji X., Chang K., Yin H., Zhao M. , Zhao L.",The regulatory effect of chitooligosaccharides on islet inflammation in T2D individuals after islet cell transplantation: the mechanism behind <i>Candida albicans</i> abundance and macrophage polarization,Gut microbes,2025,"Candida albicans, Islet cell transplantation, chitooligosaccharides, islet inflammation, macrophages",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Type II diabetes mellitus,MONDO:0005148,CA (Candida albicans Alone) treatment group of HMA-T2D (Human Microbiota associated type 2 diabetes) mice,CC (Candida albicans + Chitooligosaccharides) treatment group of HMA-T2D (Human Microbiota associated type 2 diabetes) mice,The HMA-T2D (Human Microbiota associated type 2 diabetes) mice Gavaged with Candida albicans (2 × 108 CFU/0.2 mL every other day) and COS (chitooligosaccharides) 350 mg/kg/day,8,8,NA,18S,NA,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 1,Figure 8e,28 March 2025,Tosin,Tosin,The significance analysis of the fungi in the CA (Candida albicans Alone) and CC ( (Candida albicans + Chitooligosaccharides) groups of HMA-T2D (Human Microbiota associated type 2 diabetes) mice,decreased,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,4751|4890|3239874|2916678|766764|5475|5476,Complete,Svetlana up
bsdb:39695082/1/1,39695082,prospective cohort,39695082,10.1038/s41398-024-03208-z,https://www.nature.com/articles/s41398-024-03208-z,"Jiang Y., Qu Y., Shi L., Ou M., Du Z., Zhou Z., Zhou H. , Zhu H.",The role of gut microbiota and metabolomic pathways in modulating the efficacy of SSRIs for major depressive disorder,Translational psychiatry,2024,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Non-Responders,Responders,"First-episode Major Depressive Disorder patients who have not taken any other antidepressant medications; able to understand and cooperate with scale assessments and whose Serotonin Reuptake Inhibitors (SSRIs) (citalopram (20–40 mg/day), paroxetine (20–40 mg/day), and fluoxetine (20–40 mg/day)) treatments were effective.",61,65,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 1 H/I,10 March 2025,MyleeeA,"MyleeeA,Fiddyhamma",Differential analysis of species at the genus level between responders and non-responders.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Nesterenkonia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes,k__Bacillati|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|s__uncultured Thermoanaerobacterales bacterium",1783272|1239|909932|1843488|909930|904;3379134|200940|3031449|213115|194924|35832;1783272|1239|526524|526525|2810280|100883;1783272|201174|1760|85007|85029|37914;1783272|201174|84998|1643822|1643826|580024;3379134|1224|1236|135614|32033|68;1783272|1239|909932|909929|1843491|52225;1783272|201174|1760|85006|1268|57494;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|909932|1843488|909930|33024;3379134|1224|1236|135624|83763|83770;3384194|508458|649775|649776|649777|2753;1783272|1239|186801|68295|157468,Complete,KateRasheed
bsdb:39695082/1/2,39695082,prospective cohort,39695082,10.1038/s41398-024-03208-z,https://www.nature.com/articles/s41398-024-03208-z,"Jiang Y., Qu Y., Shi L., Ou M., Du Z., Zhou Z., Zhou H. , Zhu H.",The role of gut microbiota and metabolomic pathways in modulating the efficacy of SSRIs for major depressive disorder,Translational psychiatry,2024,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Major depressive disorder,MONDO:0002009,Non-Responders,Responders,"First-episode Major Depressive Disorder patients who have not taken any other antidepressant medications; able to understand and cooperate with scale assessments and whose Serotonin Reuptake Inhibitors (SSRIs) (citalopram (20–40 mg/day), paroxetine (20–40 mg/day), and fluoxetine (20–40 mg/day)) treatments were effective.",61,65,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 1 H/I,10 March 2025,MyleeeA,"MyleeeA,Fiddyhamma",Differential analysis of species at the genus level between responders and non-responders.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas",1783272|1239|91061|1385|539738|1378;1783272|1239|186801|3085636|186803|46205;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|1769710,Complete,KateRasheed
bsdb:39701092/1/1,39701092,time series / longitudinal observational,39701092,10.4143/crt.2024.521,NA,"Lee H.I., Jang B.S., Chang J.H., Kim E., Lee T.H., Park J.H. , Chie E.K.",Relationships between the Microbiome and Response to Neoadjuvant Chemoradiotherapy in Locally Advanced Rectal Cancer,Cancer research and treatment,2024,"Butyrates, Chemoradiotherapy, Microbiota, Rectal neoplasms, Response prediction model",Experiment 1,South Korea,Homo sapiens,Rectum,UBERON:0001052,Response to platinum-based neoadjuvant chemotherapy,EFO:0007943,Pre-nCRT (Pre-neoadjuvant chemoradiotherapy) Responders,Post-nCRT (Post-neoadjuvant chemoradiotherapy) Responders,Post-nCRT (Post-neoadjuvant chemoradiotherapy) samples from patients with locally advanced rectal cancer who were classified as responders to neoadjuvant chemoradiotherapy (TRG 0–1).,9,9,1 month,NA,NA,Illumina,relative abundances,LEfSe,1,FALSE,2,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 1,Figure 3A,7 May 2025,Tosin,"Tosin,Anne-mariesharp",Cladogram of differentially abundant taxa before and after nCRT (Neo-adjuvant chemoradiotherapy) in responders,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium",3379134|1224|1236|135624|84642;3379134|1224|1236|135624;3379134|1224|1236|135624|84642|642;3379134|976|200643|171549|815|816;3379134|1224|1236|91347;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|201174|1760|85007|1762;1783272|201174|1760|85007;1783272|201174|1760|85007|1762|1763,Complete,KateRasheed
bsdb:39701092/1/2,39701092,time series / longitudinal observational,39701092,10.4143/crt.2024.521,NA,"Lee H.I., Jang B.S., Chang J.H., Kim E., Lee T.H., Park J.H. , Chie E.K.",Relationships between the Microbiome and Response to Neoadjuvant Chemoradiotherapy in Locally Advanced Rectal Cancer,Cancer research and treatment,2024,"Butyrates, Chemoradiotherapy, Microbiota, Rectal neoplasms, Response prediction model",Experiment 1,South Korea,Homo sapiens,Rectum,UBERON:0001052,Response to platinum-based neoadjuvant chemotherapy,EFO:0007943,Pre-nCRT (Pre-neoadjuvant chemoradiotherapy) Responders,Post-nCRT (Post-neoadjuvant chemoradiotherapy) Responders,Post-nCRT (Post-neoadjuvant chemoradiotherapy) samples from patients with locally advanced rectal cancer who were classified as responders to neoadjuvant chemoradiotherapy (TRG 0–1).,9,9,1 month,NA,NA,Illumina,relative abundances,LEfSe,1,FALSE,2,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 2,Figure 3A,7 May 2025,Tosin,"Tosin,Anne-mariesharp",Cladogram of differentially abundant taxa before and after nCRT (Neo-adjuvant chemoradiotherapy) in responders,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus",3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3384194|1297|188787|68933|188786;3384194|1297|188787|68933;3384194|1297|188787|68933|188786|270,Complete,KateRasheed
bsdb:39701092/3/1,39701092,time series / longitudinal observational,39701092,10.4143/crt.2024.521,NA,"Lee H.I., Jang B.S., Chang J.H., Kim E., Lee T.H., Park J.H. , Chie E.K.",Relationships between the Microbiome and Response to Neoadjuvant Chemoradiotherapy in Locally Advanced Rectal Cancer,Cancer research and treatment,2024,"Butyrates, Chemoradiotherapy, Microbiota, Rectal neoplasms, Response prediction model",Experiment 3,South Korea,Homo sapiens,Rectum,UBERON:0001052,Response to platinum-based neoadjuvant chemotherapy,EFO:0007943,Pre-nCRT (Pre-neoadjuvant chemoradiotherapy) Non-responders,Post-nCRT (Post-neoadjuvant chemoradiotherapy) Non-responders,Post-nCRT (Post-neoadjuvant chemoradiotherapy) samples from patients with locally advanced rectal cancer who were classified as  Non-responders to neoadjuvant chemoradiotherapy (TRG 2–3).,17,17,1 month,NA,NA,Illumina,relative abundances,LEfSe,1,FALSE,2,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 1,Figure 3A,7 May 2025,Tosin,"Tosin,Anne-mariesharp",Differentially abundant taxa before and after nCRT (Neo-adjuvant chemoradiotherapy) : red nodes indicate increased abundance post-nCRT; green nodes show decreased abundance,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus",3379134|1224|1236|91347;3379134|1224|1236;3379134|1224|1236|135619|28256;3379134|1224|1236|135619|28256|2745;1783272|201174|1760|85007|1762;1783272|201174|1760|85007;1783272|201174|1760|85007|1762|1763;3379134|1224|1236|135619;3379134|1224|1236|72274|135621;3379134|1224|1236|72274;3379134|1224|1236|72274|135621|286;3384194|1297|188787|68933|188786;3384194|1297|188787|68933;3384194|1297|188787|68933|188786|270,Complete,KateRasheed
bsdb:39701092/3/2,39701092,time series / longitudinal observational,39701092,10.4143/crt.2024.521,NA,"Lee H.I., Jang B.S., Chang J.H., Kim E., Lee T.H., Park J.H. , Chie E.K.",Relationships between the Microbiome and Response to Neoadjuvant Chemoradiotherapy in Locally Advanced Rectal Cancer,Cancer research and treatment,2024,"Butyrates, Chemoradiotherapy, Microbiota, Rectal neoplasms, Response prediction model",Experiment 3,South Korea,Homo sapiens,Rectum,UBERON:0001052,Response to platinum-based neoadjuvant chemotherapy,EFO:0007943,Pre-nCRT (Pre-neoadjuvant chemoradiotherapy) Non-responders,Post-nCRT (Post-neoadjuvant chemoradiotherapy) Non-responders,Post-nCRT (Post-neoadjuvant chemoradiotherapy) samples from patients with locally advanced rectal cancer who were classified as  Non-responders to neoadjuvant chemoradiotherapy (TRG 2–3).,17,17,1 month,NA,NA,Illumina,relative abundances,LEfSe,1,FALSE,2,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 2,Figure 3A,7 May 2025,Tosin,Tosin,Differentially abundant taxa before and after nCRT (Neo-adjuvant chemoradiotherapy) : red nodes indicate increased abundance post-nCRT (Neo-adjuvant chemoradiotherapy) : green nodes show decreased abundance,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|1224|1236|135624|84642;3379134|1224|1236|135624;3379134|1224|1236|135624|84642|642;3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552,Complete,KateRasheed
bsdb:39701092/4/1,39701092,time series / longitudinal observational,39701092,10.4143/crt.2024.521,NA,"Lee H.I., Jang B.S., Chang J.H., Kim E., Lee T.H., Park J.H. , Chie E.K.",Relationships between the Microbiome and Response to Neoadjuvant Chemoradiotherapy in Locally Advanced Rectal Cancer,Cancer research and treatment,2024,"Butyrates, Chemoradiotherapy, Microbiota, Rectal neoplasms, Response prediction model",Experiment 4,South Korea,Homo sapiens,Rectum,UBERON:0001052,Response to platinum-based neoadjuvant chemotherapy,EFO:0007943,Pre-nCRT (Pre-neoadjuvant chemoradiotherapy) Non-responders,Pre-nCRT (Pre-neoadjuvant chemoradiotherapy) Responders,Pre-nCRT (Pre-neoadjuvant chemoradiotherapy) samples from patients with locally advanced rectal cancer who were later classified as responders to neoadjuvant chemoradiotherapy (TRG 0–1).,17,9,1 month,NA,NA,Illumina,relative abundances,"T-Test,ANOVA",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3B and 3C,7 May 2025,Tosin,"Tosin,Anne-mariesharp","Heatmap of pre-nCRT microbiome composition at family level and Relative abundance of four major butyrate-producing genera. R, responder; NR, non-responder",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263,Complete,KateRasheed
bsdb:39701092/5/1,39701092,time series / longitudinal observational,39701092,10.4143/crt.2024.521,NA,"Lee H.I., Jang B.S., Chang J.H., Kim E., Lee T.H., Park J.H. , Chie E.K.",Relationships between the Microbiome and Response to Neoadjuvant Chemoradiotherapy in Locally Advanced Rectal Cancer,Cancer research and treatment,2024,"Butyrates, Chemoradiotherapy, Microbiota, Rectal neoplasms, Response prediction model",Experiment 5,South Korea,Homo sapiens,Rectum,UBERON:0001052,Response to platinum-based neoadjuvant chemotherapy,EFO:0007943,Post-nCRT (Post-neoadjuvant chemoradiotherapy) Non-responders,Post-nCRT (Post-neoadjuvant chemoradiotherapy) Responders,Post-nCRT (Post-neoadjuvant chemoradiotherapy) samples from patients with locally advanced rectal cancer who were classified as responders to neoadjuvant chemoradiotherapy (TRG 0–1).,17,9,1 month,NA,NA,Illumina,relative abundances,"ANOVA,T-Test",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3D and 3E,7 May 2025,Tosin,"Tosin,Anne-mariesharp","Heatmap of post-nCRT microbiome composition at family level and Relative abundance of
four opportunistic pathogens",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543;1783272|201174|1760|85007|1762;1783272|201174|1760|85007|1762|1763;3379134|1224|1236|72274|135621;3379134|1224|1236|72274|135621|286,Complete,KateRasheed
bsdb:39707461/1/1,39707461,laboratory experiment,39707461,10.1186/s40168-024-01966-y,NA,"Huang S.C., Liu K.L., Chen P., Xu B.W., Ding W.L., Yue T.J., Lu Y.N., Li S.Y., Li J.K. , Jian F.C.",New insights into the combined effects of aflatoxin B1 and Eimeria ovinoidalis on uterine function by disrupting the gut-blood-reproductive axis in sheep,Microbiome,2024,"E. ovinoidalis, Aflatoxin B1, Coccidia, Gut microbiota, Mycotoxin, Reproduction toxicity",Experiment 1,China,Ovis aries,Feces,UBERON:0001988,Coccidiosis,EFO:0007212,"Combination of Con(control), AFB1 (Aflatoxin B1), AFB1 + E0 (Aflatoxin B1 + Eimeria ovinoidalis) treatment groups",E.0 (Eimeria ovinoidalis) treatment group,A treatment group with E.0 (Eimeria ovinoidalis) which is a coccidian parasite that has been identified as the most pathogenic species among sheep worldwide and received a single oral administration of 2 × 104 sporulated oocysts on day 0 only.,12,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3f,24 March 2025,Tosin,Tosin,Linear discriminant analysis effect size (LEfSe) comparison analysis between the groups.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria",3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|1224;3379134|1224|1236,Complete,Svetlana up
bsdb:39707461/2/1,39707461,laboratory experiment,39707461,10.1186/s40168-024-01966-y,NA,"Huang S.C., Liu K.L., Chen P., Xu B.W., Ding W.L., Yue T.J., Lu Y.N., Li S.Y., Li J.K. , Jian F.C.",New insights into the combined effects of aflatoxin B1 and Eimeria ovinoidalis on uterine function by disrupting the gut-blood-reproductive axis in sheep,Microbiome,2024,"E. ovinoidalis, Aflatoxin B1, Coccidia, Gut microbiota, Mycotoxin, Reproduction toxicity",Experiment 2,China,Ovis aries,Feces,UBERON:0001988,Coccidiosis,EFO:0007212,"Combination of Con(control), E.0 (Eimeria ovinoidalis), AFB1 + E0 (Aflatoxin B1 + Eimeria ovinoidalis) treatment groups",AFB1 (Aflatoxin B1) treatment group,"Treatment group with Aflatoxin B1 which is a mycotoxin produced by Aspergillus flavus and Aspergillus parasiticus, is a member of the aflatoxin family and is commonly found in cereals and animal feed all over the world, together with other fungal toxins and received daily oral administration of AFB1 at a dosage of 60 μg/kg",12,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3f,24 March 2025,Tosin,Tosin,Linear discriminant analysis effect size (LEfSe) comparison analysis between the groups.,increased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae",1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|186802|216572;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201;3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|203557,Complete,Svetlana up
bsdb:39707461/3/1,39707461,laboratory experiment,39707461,10.1186/s40168-024-01966-y,NA,"Huang S.C., Liu K.L., Chen P., Xu B.W., Ding W.L., Yue T.J., Lu Y.N., Li S.Y., Li J.K. , Jian F.C.",New insights into the combined effects of aflatoxin B1 and Eimeria ovinoidalis on uterine function by disrupting the gut-blood-reproductive axis in sheep,Microbiome,2024,"E. ovinoidalis, Aflatoxin B1, Coccidia, Gut microbiota, Mycotoxin, Reproduction toxicity",Experiment 3,China,Ovis aries,Feces,UBERON:0001988,Coccidiosis,EFO:0007212,"Combination of Con(control), E.0 (Eimeria ovinoidalis) and AFB1 (Aflatoxin B1) treatment groups",AFB1 + E0 (Aflatoxin B1 + Eimeria ovinoidalis) treatment group,Treatement group that received a single oral administration of 2 × 104 sporulated oocysts on day 0 along with daily oral administration of AFB1 at a dosage of 60 μg/kg.,12,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3f,25 March 2025,Tosin,Tosin,Linear discriminant analysis effect size (LEfSe) comparison analysis between the groups,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae",1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|189330;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815,Complete,Svetlana up
bsdb:39707461/4/1,39707461,laboratory experiment,39707461,10.1186/s40168-024-01966-y,NA,"Huang S.C., Liu K.L., Chen P., Xu B.W., Ding W.L., Yue T.J., Lu Y.N., Li S.Y., Li J.K. , Jian F.C.",New insights into the combined effects of aflatoxin B1 and Eimeria ovinoidalis on uterine function by disrupting the gut-blood-reproductive axis in sheep,Microbiome,2024,"E. ovinoidalis, Aflatoxin B1, Coccidia, Gut microbiota, Mycotoxin, Reproduction toxicity",Experiment 4,China,Ovis aries,Feces,UBERON:0001988,Coccidiosis,EFO:0007212,"Combination of E.0 (Eimeria ovinoidalis), AFB1 (Aflatoxin B1) and AFB1 + E0 (Aflatoxin B1 + Eimeria ovinoidalis treatment groups",Control (Con) treatment group,Treatment group that received daily oral administration of PBS solution and DMSO.,12,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3f,25 March 2025,Tosin,Tosin,Linear discriminant analysis effect size (LEfSe) comparison analysis between the groups,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium",1783272|1239;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;3379134|976|200643|171549|2005473;1783272|1239|186801|186802|186806|1730,Complete,Svetlana up
bsdb:39707461/5/1,39707461,laboratory experiment,39707461,10.1186/s40168-024-01966-y,NA,"Huang S.C., Liu K.L., Chen P., Xu B.W., Ding W.L., Yue T.J., Lu Y.N., Li S.Y., Li J.K. , Jian F.C.",New insights into the combined effects of aflatoxin B1 and Eimeria ovinoidalis on uterine function by disrupting the gut-blood-reproductive axis in sheep,Microbiome,2024,"E. ovinoidalis, Aflatoxin B1, Coccidia, Gut microbiota, Mycotoxin, Reproduction toxicity",Experiment 5,China,Ovis aries,Feces,UBERON:0001988,Coccidiosis,EFO:0007212,AFB1 (Aflatoxin B1) treatment group,AFB1 + E0 (Aflatoxin B1 + Eimeria ovinoidalis) treatment group,Treatment group that received a single oral administration of 2 × 104 sporulated oocysts on day 0 along with daily oral administration of AFB1 at a dosage of 60 μg/kg,4,4,NA,16S,34,Illumina,relative abundances,Dunn's test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 3i,25 March 2025,Tosin,Tosin,Relative abundance analysis of common differential genera,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|2383,Complete,Svetlana up
bsdb:39707461/6/1,39707461,laboratory experiment,39707461,10.1186/s40168-024-01966-y,NA,"Huang S.C., Liu K.L., Chen P., Xu B.W., Ding W.L., Yue T.J., Lu Y.N., Li S.Y., Li J.K. , Jian F.C.",New insights into the combined effects of aflatoxin B1 and Eimeria ovinoidalis on uterine function by disrupting the gut-blood-reproductive axis in sheep,Microbiome,2024,"E. ovinoidalis, Aflatoxin B1, Coccidia, Gut microbiota, Mycotoxin, Reproduction toxicity",Experiment 6,China,Ovis aries,Feces,UBERON:0001988,Coccidiosis,EFO:0007212,E.0 (Eimeria ovinoidalis) treatment group,AFB1 + E0 (Aflatoxin B1 + Eimeria ovinoidalis) treatment group,Treatment group that received a single oral administration of 2 × 104 sporulated oocysts on day 0 along with daily oral administration of AFB1 at a dosage of 60 μg/kg,4,4,NA,16S,34,Illumina,relative abundances,Dunn's test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 3E and 3I,25 March 2025,Tosin,Tosin,Relative abundance analysis of common differential genera,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",3379134|976;3379134|200940|3031449|213115|194924|872,Complete,Svetlana up
bsdb:39707461/7/1,39707461,laboratory experiment,39707461,10.1186/s40168-024-01966-y,NA,"Huang S.C., Liu K.L., Chen P., Xu B.W., Ding W.L., Yue T.J., Lu Y.N., Li S.Y., Li J.K. , Jian F.C.",New insights into the combined effects of aflatoxin B1 and Eimeria ovinoidalis on uterine function by disrupting the gut-blood-reproductive axis in sheep,Microbiome,2024,"E. ovinoidalis, Aflatoxin B1, Coccidia, Gut microbiota, Mycotoxin, Reproduction toxicity",Experiment 7,China,Ovis aries,Feces,UBERON:0001988,Coccidiosis,EFO:0007212,Con (Control) treatment group,AFB1 (Aflatoxin B1) treatment group,"Treatment group with Aflatoxin B1 which is a mycotoxin produced by Aspergillus flavus and Aspergillus parasiticus, is a member of the aflatoxin family and is commonly found in cereals and animal feed all over the world, together with other fungal toxins and received daily oral administration of AFB1 at a dosage of 60 μg/kg",4,4,NA,16S,34,Illumina,relative abundances,Dunn's test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 3I,25 March 2025,Tosin,Tosin,Relative abundance analysis of common differential genera,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,1783272|1239|186801|186802|186806|1730,Complete,Svetlana up
bsdb:39707461/8/1,39707461,laboratory experiment,39707461,10.1186/s40168-024-01966-y,NA,"Huang S.C., Liu K.L., Chen P., Xu B.W., Ding W.L., Yue T.J., Lu Y.N., Li S.Y., Li J.K. , Jian F.C.",New insights into the combined effects of aflatoxin B1 and Eimeria ovinoidalis on uterine function by disrupting the gut-blood-reproductive axis in sheep,Microbiome,2024,"E. ovinoidalis, Aflatoxin B1, Coccidia, Gut microbiota, Mycotoxin, Reproduction toxicity",Experiment 8,China,Ovis aries,Feces,UBERON:0001988,Coccidiosis,EFO:0007212,Con (Control) treatment group,E.0 (Eimeria ovinoidalis) treatment group,A treatment group with E.0 (Eimeria ovinoidalis) which is a coccidian parasite that has been identified as the most pathogenic species among sheep worldwide and received a single oral administration of 2 × 104 sporulated oocysts on day 0 only.,4,4,NA,16S,34,Illumina,relative abundances,Dunn's test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,increased,NA,unchanged,Signature 1,Figure 3E and 3I,25 March 2025,Tosin,Tosin,Relative abundance analysis of common differential genera,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium",1783272|1239;1783272|1239|186801|186802|186806|1730,Complete,Svetlana up
bsdb:39707461/9/1,39707461,laboratory experiment,39707461,10.1186/s40168-024-01966-y,NA,"Huang S.C., Liu K.L., Chen P., Xu B.W., Ding W.L., Yue T.J., Lu Y.N., Li S.Y., Li J.K. , Jian F.C.",New insights into the combined effects of aflatoxin B1 and Eimeria ovinoidalis on uterine function by disrupting the gut-blood-reproductive axis in sheep,Microbiome,2024,"E. ovinoidalis, Aflatoxin B1, Coccidia, Gut microbiota, Mycotoxin, Reproduction toxicity",Experiment 9,China,Ovis aries,Feces,UBERON:0001988,Coccidiosis,EFO:0007212,Con(control) treatment group,AFB1 + E0 (Aflatoxin B1 + Eimeria ovinoidalis) treatment group,Treatement group that received a single oral administration of 2 × 104 sporulated oocysts on day 0 along with daily oral administration of AFB1 at a dosage of 60 μg/kg.,4,4,NA,16S,34,Illumina,relative abundances,Dunn's test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 3I,25 March 2025,Tosin,Tosin,Relative abundance analysis of common differential genera,decreased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium",3379134|29547|3031852|213849|72294|194;3379134|1224|1236|135624|83763|83770;1783272|1239|186801|3085636|186803|2383,Complete,Svetlana up
bsdb:39707483/1/1,39707483,"cross-sectional observational, not case-control",39707483,https://doi.org/10.1186/s40168-024-01973-z,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01973-z,"Byrne A., Diener C., Brown B.P., Maust B.S., Feng C., Alinde B.L., Gibbons S.M., Koch M., Gray C.M., Jaspan H.B. , Nyangahu D.D.",Neonates exposed to HIV but uninfected exhibit an altered gut microbiota and inflammation associated with impaired breast milk antibody function,Microbiome,2024,"Gut microbiota, Inflammation, Neonates exposed to HIV but uninfected",Experiment 1,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,neonates HIV unexposed (nHU),neonates exposed to HIV (nHEU),neonates exposed to HIV during pregnancy,34,34,NA,WMS,NA,Illumina,NA,"Beta Binomial Regression,DESeq2",0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 2C,29 January 2025,Fiddyhamma,"Fiddyhamma,WikiWorks",Differentially abundant taxa between nHEU and nHU determined by both DESeq2 and corncob.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerocolumna|s__Anaerocolumna cellulosilytica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia liquoris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia pseudococcoides,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. M62/1,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia alvei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella grimontii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium phocaeense,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. YL32,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora saccharolytica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora sphenoides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Novisyntrophococcus|s__Novisyntrophococcus fermenticellae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia rectibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella boydii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella flexneri,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia parvula",1783272|1239|186801|3085636|186803|1843210|433286;1783272|1239|186801|3085636|186803|207244|105841;1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|186801|186802|216572|244127|169435;1783272|1239|186801|3085636|186803|572511|2779518;1783272|1239|186801|3085636|186803|572511|33035;1783272|1239|186801|3085636|186803|572511|1796616;1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|186801|186802|31979|1485|411486;1783272|1239|186801|3085636|186803|33042|33043;1783272|1239|186801|3085636|186803|2719313|1531;3379134|1224|1236|91347|1903412|568|569;3379134|1224|1236|91347|543|570|2058152;3379134|1224|1236|91347|543|570|573;1783272|1239|186801|3085636|186803|1506553|1871021;1783272|1239|186801|3085636|186803|1506553|1834196;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|2719231|84030;1783272|1239|186801|3085636|186803|2719231|29370;1783272|1239|186801|3085636|186803|2888809|2068655;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|3085636|186803|841|2763062;3379134|1224|1236|91347|543|620|621;3379134|1224|1236|91347|543|620|623;1783272|1239|91061|1385|90964|1279|1280;1783272|1239|91061|1385|90964|1279|1290;1783272|1239|186801|3085636|186803|572511|2877527,Complete,Svetlana up
bsdb:39707483/1/2,39707483,"cross-sectional observational, not case-control",39707483,https://doi.org/10.1186/s40168-024-01973-z,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01973-z,"Byrne A., Diener C., Brown B.P., Maust B.S., Feng C., Alinde B.L., Gibbons S.M., Koch M., Gray C.M., Jaspan H.B. , Nyangahu D.D.",Neonates exposed to HIV but uninfected exhibit an altered gut microbiota and inflammation associated with impaired breast milk antibody function,Microbiome,2024,"Gut microbiota, Inflammation, Neonates exposed to HIV but uninfected",Experiment 1,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,neonates HIV unexposed (nHU),neonates exposed to HIV (nHEU),neonates exposed to HIV during pregnancy,34,34,NA,WMS,NA,Illumina,NA,"Beta Binomial Regression,DESeq2",0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 2C,29 January 2025,Fiddyhamma,"Fiddyhamma,WikiWorks",Differentially abundant taxa between nHEU and nHU determined by both DESeq2 and corncob.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Tessaracoccus|s__Tessaracoccus flavus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella megalosphaeroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Phenylobacterium|s__Phenylobacterium zucineum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium sp. Marseille-Q4147,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum|s__Herbaspirillum sp. meg3,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter asburiae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Dickeya|s__Dickeya chrysanthemi,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia ubonensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 414,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces faecalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. Chiba101,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces slackii",1783272|201174|1760|85009|31957|72763|1610493;3379134|1224|28216|80840|995019|40544|2494234;1783272|201174|1760|2037|2049|2529408|1660;3379134|1224|28211|204458|76892|20|284016;1783272|1239|909932|1843488|909930|33024|2823317;3379134|1224|28216|80840|75682|963|2025949;3379134|1224|1236|91347|543|547|61645;1783272|201174|84998|1643822|1643826|84111|84112;3379134|1224|1236|91347|1903410|204037|556;3379134|1224|28216|80840|119060|32008|101571;1783272|201174|1760|85004|31953|1678|1685;3379134|976|200643|171549|815|816|818;1783272|201174|1760|2037|2049|1654|712122;1783272|201174|1760|2037|2049|1654|2722820;1783272|201174|1760|2037|2049|1654|1851395;1783272|201174|1760|2037|2049|1654|52774,Complete,Svetlana up
bsdb:39707483/2/1,39707483,"cross-sectional observational, not case-control",39707483,https://doi.org/10.1186/s40168-024-01973-z,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01973-z,"Byrne A., Diener C., Brown B.P., Maust B.S., Feng C., Alinde B.L., Gibbons S.M., Koch M., Gray C.M., Jaspan H.B. , Nyangahu D.D.",Neonates exposed to HIV but uninfected exhibit an altered gut microbiota and inflammation associated with impaired breast milk antibody function,Microbiome,2024,"Gut microbiota, Inflammation, Neonates exposed to HIV but uninfected",Experiment 2,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,neonates HIV unexposed (nHU),neonates exposed to HIV (nHEU),neonates exposed to HIV during pregnancy,34,34,NA,WMS,NA,Illumina,NA,"Beta Binomial Regression,DESeq2",0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 3D,29 January 2025,Fiddyhamma,"Fiddyhamma,WikiWorks",Differentially abundant gut viruses between nHEU and nHU by DESeq2 and corncob.,increased,"k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|f__Peduoviridae|g__Peduovirus,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|g__Biseptimavirus,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|g__Alegriavirus",2731360|2731618|2731619|2946167|140410;2731360|2731618|2731619|1623274;2731360|2731618|2731619|2843345,Complete,Svetlana up
bsdb:39707483/2/2,39707483,"cross-sectional observational, not case-control",39707483,https://doi.org/10.1186/s40168-024-01973-z,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01973-z,"Byrne A., Diener C., Brown B.P., Maust B.S., Feng C., Alinde B.L., Gibbons S.M., Koch M., Gray C.M., Jaspan H.B. , Nyangahu D.D.",Neonates exposed to HIV but uninfected exhibit an altered gut microbiota and inflammation associated with impaired breast milk antibody function,Microbiome,2024,"Gut microbiota, Inflammation, Neonates exposed to HIV but uninfected",Experiment 2,South Africa,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,neonates HIV unexposed (nHU),neonates exposed to HIV (nHEU),neonates exposed to HIV during pregnancy,34,34,NA,WMS,NA,Illumina,NA,"Beta Binomial Regression,DESeq2",0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 3D,29 January 2025,Fiddyhamma,"Fiddyhamma,WikiWorks",Differentially abundant gut viruses between nHEU and nHU by DESeq2 and corncob.,decreased,k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|s__Bronfenbrennervirinae|g__Peeveelvirus,2731360|2731618|2731619|2842523|2842946,Complete,Svetlana up
bsdb:39707483/3/1,39707483,"cross-sectional observational, not case-control",39707483,https://doi.org/10.1186/s40168-024-01973-z,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01973-z,"Byrne A., Diener C., Brown B.P., Maust B.S., Feng C., Alinde B.L., Gibbons S.M., Koch M., Gray C.M., Jaspan H.B. , Nyangahu D.D.",Neonates exposed to HIV but uninfected exhibit an altered gut microbiota and inflammation associated with impaired breast milk antibody function,Microbiome,2024,"Gut microbiota, Inflammation, Neonates exposed to HIV but uninfected",Experiment 3,South Africa,Homo sapiens,Feces,UBERON:0001988,Increased inflammatory response,HP:0012649,Immunoglobulin A (IgA) bound fraction neonates HIV unexposed (nHU),Immunoglobulin A (IgA) bound fraction neonates exposed to HIV (nHEU),IgA bound fraction neonates exposed to HIV during pregnancy,34,34,NA,WMS,NA,Illumina,NA,"Beta Binomial Regression,DESeq2",0.05,TRUE,NA,NA,NA,NA,NA,increased,NA,NA,NA,Signature 1,Figure 4F,29 January 2025,Fiddyhamma,"Fiddyhamma,WikiWorks",Differentially abundant bacterial taxa in IgA bound fraction,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus fermentans,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacterium|s__Amedibacterium intestinale,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia liquoris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia pseudococcoides,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. M62/1,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp. ART55/1,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena sp. Marseille-Q4148,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea|s__Faecalitalea cylindroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium phocaeense,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. YL32,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Novisyntrophococcus|s__Novisyntrophococcus fermenticellae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia rectibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Liu et al. 2021),k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bovis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas intestinalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 431,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Hoskinsella|s__Hoskinsella hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia parvula",1783272|1239|909932|1843488|909930|904|905;1783272|1239|526524|526525|128827|2749267|2583452;1783272|1239|186801|3085636|186803|207244|649756;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|818;1783272|1239|186801|3085636|186803|572511|1322;1783272|1239|186801|3085636|186803|572511|2779518;1783272|1239|186801|3085636|186803|572511|33035;1783272|1239|186801|3085636|186803|572511|1796616;1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|186801|186802|31979|1485|1502;1783272|1239|186801|186802|31979|1485|411486;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|33042|751585;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|2719313|1531;1783272|1239|91061|186826|81852|1350|1352;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|2005359|2823316;1783272|1239|526524|526525|128827|1573534|39483;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|1506553|1871021;1783272|1239|186801|3085636|186803|1506553|1834196;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|2888809|2068655;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|171552|838|28132;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|841|2763062;1783272|1239|186801|186802|216572|1263|3062497;1783272|1239|186801|186802|216572|1263|2564099;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|186801|3085636|186803|1769710|1653434;1783272|1239|91061|1385|90964|1279|1280;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|91061|186826|1300|1301|1305;1783272|1239|91061|186826|1300|1301|712633;1783272|1239|186801|3085636|186803|1506553|29347;1783272|1239|526524|526525|128827|3681505|2764325;1783272|1239|186801|3085636|186803|572511|2877527,Complete,Svetlana up
bsdb:39707483/3/2,39707483,"cross-sectional observational, not case-control",39707483,https://doi.org/10.1186/s40168-024-01973-z,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01973-z,"Byrne A., Diener C., Brown B.P., Maust B.S., Feng C., Alinde B.L., Gibbons S.M., Koch M., Gray C.M., Jaspan H.B. , Nyangahu D.D.",Neonates exposed to HIV but uninfected exhibit an altered gut microbiota and inflammation associated with impaired breast milk antibody function,Microbiome,2024,"Gut microbiota, Inflammation, Neonates exposed to HIV but uninfected",Experiment 3,South Africa,Homo sapiens,Feces,UBERON:0001988,Increased inflammatory response,HP:0012649,Immunoglobulin A (IgA) bound fraction neonates HIV unexposed (nHU),Immunoglobulin A (IgA) bound fraction neonates exposed to HIV (nHEU),IgA bound fraction neonates exposed to HIV during pregnancy,34,34,NA,WMS,NA,Illumina,NA,"Beta Binomial Regression,DESeq2",0.05,TRUE,NA,NA,NA,NA,NA,increased,NA,NA,NA,Signature 2,Fig 4E,29 January 2025,Fiddyhamma,"Fiddyhamma,WikiWorks",Differentially abundant bacterial taxa in IgA bound fraction,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces faecalis,1783272|201174|1760|2037|2049|1654|2722820,Complete,Svetlana up
bsdb:39731099/1/1,39731099,case-control,39731099,10.1186/s12866-024-03705-7,NA,"Hu Y., Wu Z., Yang X., Ding J., Wang Q., Fang H., Zhu L. , Hu M.",Reduced gut microbiota diversity in ulcerative colitis patients with latent tuberculosis infection during vedolizumab therapy: insights on prophylactic anti-tuberculosis effects,BMC microbiology,2024,"Gut microbiota, Latent tuberculosis infection, Prophylactic treatment, Ulcerative colitis, Vedolizumab",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,ulcerative colitis patients with non-latent tuberculosis (C0),ulcerative colitis patients with latent tuberculosis infection (AB0),ulcerative colitis patients with latent tuberculosis infection,9,12,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,Figure 2G,11 August 2025,Nuerteye,Nuerteye,"Impact of LTBI on the intestinal microbiota of patients with UC. LEfSe analysis highlights the enriched microbial taxa in non-LTBI (Enterobacteriaceae) and LTBI (Streptococcaceae, Sutterellaceae, Burkholderiales) groups. LDA analysis shows the impact of specific taxa on group differences (Enterobacteriaceae in non-LTBI; Sutterellaceae in LTBI).",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae",1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300;3379134|1224|28216|80840|995019|577310;3379134|1224|28216|80840;3379134|1224|28216|80840|995019,Complete,NA
bsdb:39731099/1/2,39731099,case-control,39731099,10.1186/s12866-024-03705-7,NA,"Hu Y., Wu Z., Yang X., Ding J., Wang Q., Fang H., Zhu L. , Hu M.",Reduced gut microbiota diversity in ulcerative colitis patients with latent tuberculosis infection during vedolizumab therapy: insights on prophylactic anti-tuberculosis effects,BMC microbiology,2024,"Gut microbiota, Latent tuberculosis infection, Prophylactic treatment, Ulcerative colitis, Vedolizumab",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,ulcerative colitis patients with non-latent tuberculosis (C0),ulcerative colitis patients with latent tuberculosis infection (AB0),ulcerative colitis patients with latent tuberculosis infection,9,12,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,Figure 2G-H,11 August 2025,Nuerteye,Nuerteye,"Impact of LTBI on the intestinal microbiota of patients with UC. LEfSe analysis highlights the enriched microbial taxa in non-LTBI (Enterobacteriaceae) and LTBI (Streptococcaceae, Sutterellaceae, Burkholderiales) groups. LDA analysis shows the impact of specific taxa on group differences (Enterobacteriaceae in non-LTBI; Sutterellaceae in LTBI).",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli,k__Thermotogati|p__Synergistota,k__Thermotogati|p__Synergistota|c__Synergistia,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales",3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|1940338;1783272|1239|91061|1385;1783272|1239|91061|1385|186817;1783272|1239|91061|1385|186817|1386;1783272|1239|91061;3384194|508458;3384194|508458|649775;3384194|508458|649775|649776|649777;3384194|508458|649775|649776;1783272|1239|526524|526525,Complete,NA
bsdb:39738315/1/1,39738315,randomized controlled trial,39738315,10.1038/s41598-024-80281-w,NA,"Ecklu-Mensah G., Miller R., Maseng M.G., Hawes V., Hinz D., Kim C. , Gilbert J.A.",Modulating the human gut microbiome and health markers through kombucha consumption: a controlled clinical study,Scientific reports,2024,"Diet, Fermented foods, Gut microbiome, Serum cytokines",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Control T-3 (time point 3),Kombucha T-3 (time point 3),"Participants on a beige diet, drinking 16 oz of kombucha daily at the end of the treatment, 4 weeks (time point 3).",8,16,3 months,WMS,NA,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4a,12 February 2025,YokoC,"YokoC,WikiWorks,KateRasheed",Log-fold-change for differentially abundant features at the species level in gut microbiome samples from control subjects vs kombucha treatment subjects at the end of the experiment (t-3).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Cuneatibacter|s__Cuneatibacter caecimuris,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus amylovorus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum|s__Varibaculum cambriense,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium vincentii,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella|s__Ezakiella coagulans,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus grossensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus mulieris,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus prevotii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides pacaensis",1783272|1239|186801|3085636|186803|1918450|1796618;3384189|32066|203490|203491|203492|848|851;1783272|1239|91061|186826|33958|1578|1604;1783272|201174|1760|2037|2049|184869|184870;3384189|32066|203490|203491|203492|848|155615;1783272|1239|1737404|1582879|46507;1783272|1239|1737404|1737405|1570339|162289|1465756;1783272|201174|1760|2037|2049|2050|2052;1783272|1239|1737404|1737405|1570339|165779|33034;1783272|1239|91061|186826|33958|1578|1596;3379134|976|200643|171549|171551|836|837;3379134|976|200643|171549|2005525|375288|2086575,Complete,Svetlana up
bsdb:39738315/1/2,39738315,randomized controlled trial,39738315,10.1038/s41598-024-80281-w,NA,"Ecklu-Mensah G., Miller R., Maseng M.G., Hawes V., Hinz D., Kim C. , Gilbert J.A.",Modulating the human gut microbiome and health markers through kombucha consumption: a controlled clinical study,Scientific reports,2024,"Diet, Fermented foods, Gut microbiome, Serum cytokines",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Control T-3 (time point 3),Kombucha T-3 (time point 3),"Participants on a beige diet, drinking 16 oz of kombucha daily at the end of the treatment, 4 weeks (time point 3).",8,16,3 months,WMS,NA,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4a,26 February 2025,YokoC,"YokoC,KateRasheed",Description: Log-fold-change for differentially abundant features at the species level in gut microbiome samples from control subjects vs kombucha treatment subjects at the end of the experiment (t-3).,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter actinomycetemcomitans,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister histaminiformans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium choloepi,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Heyndrickxia|s__Heyndrickxia coagulans,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma hominis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria mucosa,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella|s__Pasteurella multocida,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:1092,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:386,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:732,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:177,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sp. H121,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|g__Candidatus Alcium|s__Candidatus Alcium sp. F082,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Ellagibacter|s__Ellagibacter isourolithinifaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella albensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium indicum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Heyndrickxia|s__Heyndrickxia coagulans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:299,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella hominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Rodentibacter|s__Rodentibacter pneumotropicus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium celatum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Gallibacterium|s__Gallibacterium anatis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Peptidiphaga|s__Peptidiphaga gingivicola,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella swidsinskii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus|s__Actinobacillus lignieresii",3379134|1224|1236|135625|712|416916|714;1783272|1239|909932|1843489|31977|39948|209880;1783272|201174|1760|85004|31953|1678|2614131;1783272|1239|91061|1385|186817|2837504|1398;1783272|544448|2790996|2895623|2895509|2098;3379134|1224|28216|206351|481|482|488;3379134|1224|1236|135625|712|745|747;3379134|976|200643|171549|171552|838|1262919;3379134|976|200643|171549|171552|838|1262925;3379134|976|200643|171549|171552|838|1262934;1783272|201174|1760|85006|1268|32207|172042;1783272|1239|186801|186802|216572|1263|1262952;1783272|1239|91061|186826|1300|1301|1304;3379134|1224|28216|80840|995019|40544|40545;1783272|1239|526524|526525|2810281|191303|1712675;95818|2093818|2093825|2171986|1331051;3379134|976|200643|171549|3443717|1768115;1783272|201174|84998|1643822|1643826|2137577|2137581;3379134|976|200643|171549|171552|2974251|77768;1783272|201174|1760|85004|31953|1678|1691;1783272|1239|91061|1385|186817|2837504|1398;1783272|1239|186801|186802|31979|1485|1262792;3379134|976|200643|171549|171552|2974251|2518605;1783272|201174|1760|85004|31953|2701|2702;3379134|1224|1236|135625|712|1960084|758;1783272|1239|186801|186802|31979|1485|36834;3379134|976|200643|171549|171552|2974265|363265;3379134|1224|1236|135625|712|155493|750;3379134|1224|28216|80840|119060|47670|47671;1783272|201174|1760|2037|2049|2739835|2741497;1783272|201174|1760|85004|31953|2701|2792979;3379134|1224|1236|135625|712|713|720,Complete,Svetlana up
bsdb:39738315/2/1,39738315,randomized controlled trial,39738315,10.1038/s41598-024-80281-w,NA,"Ecklu-Mensah G., Miller R., Maseng M.G., Hawes V., Hinz D., Kim C. , Gilbert J.A.",Modulating the human gut microbiome and health markers through kombucha consumption: a controlled clinical study,Scientific reports,2024,"Diet, Fermented foods, Gut microbiome, Serum cytokines",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Kombucha T-1 (time point 1),Kombucha T-3 (time point 3),"Participants on a beige diet, drinking 16 oz of kombucha daily at the end of the treatment, 4 weeks (time point 3).",16,16,3 months,WMS,NA,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,NA,NA,NA,unchanged,Signature 1,Figure 4b,26 February 2025,YokoC,"YokoC,KateRasheed",Log-fold-change for differentially abundant features at the species level in gut microbiome samples from kombucha treatment subjects at the end of the experiment (t-3) vs the starting point (t-1).,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella soli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc kimchii",1783272|1239|91061|186826|33958|46255|155866;1783272|1239|91061|186826|33958|1243|136609,Complete,Svetlana up
bsdb:39738315/2/2,39738315,randomized controlled trial,39738315,10.1038/s41598-024-80281-w,NA,"Ecklu-Mensah G., Miller R., Maseng M.G., Hawes V., Hinz D., Kim C. , Gilbert J.A.",Modulating the human gut microbiome and health markers through kombucha consumption: a controlled clinical study,Scientific reports,2024,"Diet, Fermented foods, Gut microbiome, Serum cytokines",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Kombucha T-1 (time point 1),Kombucha T-3 (time point 3),"Participants on a beige diet, drinking 16 oz of kombucha daily at the end of the treatment, 4 weeks (time point 3).",16,16,3 months,WMS,NA,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,NA,NA,NA,unchanged,Signature 2,Figure 4b,26 February 2025,YokoC,"YokoC,KateRasheed",Log-fold-change for differentially abundant features at the species level in gut microbiome samples from kombucha treatment subjects at the end of the experiment (t-3) vs the starting point (t-1).,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Heyndrickxia|s__Heyndrickxia coagulans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria mucosa,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 348,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Heyndrickxia|s__Heyndrickxia coagulans",1783272|1239|91061|1385|186817|2837504|1398;3379134|1224|28216|206351|481|482|488;95818|671231;1783272|1239|91061|1385|186817|2837504|1398,Complete,Svetlana up
bsdb:39738315/3/1,39738315,randomized controlled trial,39738315,10.1038/s41598-024-80281-w,NA,"Ecklu-Mensah G., Miller R., Maseng M.G., Hawes V., Hinz D., Kim C. , Gilbert J.A.",Modulating the human gut microbiome and health markers through kombucha consumption: a controlled clinical study,Scientific reports,2024,"Diet, Fermented foods, Gut microbiome, Serum cytokines",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Kombucha T-2 (time point 2),Kombucha T-3 (time point 3),"Participants on a beige diet, drinking 16 oz of kombucha daily at the end of the treatment, 4 weeks (time point 3).",16,16,3 months,WMS,NA,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4c,4 March 2025,YokoC,"YokoC,KateRasheed",Log-fold-change for differentially abundant features at the species level in gut microbiome samples from kombucha treatment subjects at time point 3 vs time point 2.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella soli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc kimchii",1783272|1239|91061|186826|33958|46255|155866;1783272|1239|91061|186826|33958|1243|136609,Complete,Svetlana up
bsdb:39738315/3/2,39738315,randomized controlled trial,39738315,10.1038/s41598-024-80281-w,NA,"Ecklu-Mensah G., Miller R., Maseng M.G., Hawes V., Hinz D., Kim C. , Gilbert J.A.",Modulating the human gut microbiome and health markers through kombucha consumption: a controlled clinical study,Scientific reports,2024,"Diet, Fermented foods, Gut microbiome, Serum cytokines",Experiment 3,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Kombucha T-2 (time point 2),Kombucha T-3 (time point 3),"Participants on a beige diet, drinking 16 oz of kombucha daily at the end of the treatment, 4 weeks (time point 3).",16,16,3 months,WMS,NA,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4c,4 March 2025,YokoC,"YokoC,KateRasheed",Log-fold-change for differentially abundant features at the species level in gut microbiome samples from kombucha treatment subjects at time point 3 vs time point 2.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Heyndrickxia|s__Heyndrickxia coagulans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium celatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Heyndrickxia|s__Heyndrickxia coagulans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Peptidiphaga|s__Peptidiphaga gingivicola,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus|s__Actinobacillus lignieresii",1783272|1239|91061|1385|186817|2837504|1398;1783272|1239|91061|186826|33958;1783272|1239|186801|186802|31979|1485|36834;1783272|1239|91061|1385|186817|2837504|1398;1783272|201174|1760|2037|2049|2739835|2741497;3379134|1224|1236|135625|712|713|720,Complete,Svetlana up
bsdb:39748236/1/1,39748236,time series / longitudinal observational,39748236,10.1186/s40168-024-01936-4,NA,"Bongiovanni T., Santiago M., Zielinska K., Scheiman J., Barsa C., Jäger R., Pinto D., Rinaldi F., Giuliani G., Senatore T. , Kostic A.D.",A Lactobacillus consortium provides insights into the sleep-exercise-microbiome nexus in proof of concept studies of elite athletes and in the general population,Microbiome,2025,"Lactobacillus, Energy, Fatigue, Microbiome, Oxidative stress, Probiotic, Recovery, Sleep, Testosterone",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Oxidative Stress,EFO:1001905,Baseline,Placebo,Healthy male soccer players taking placebo pills blindly for the first period of 12weeks.,11,11,3 months,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 4b, Table 2",21 April 2025,Asoler2004,Asoler2004,Soccer players' taxa that significantly change after the ingestion of placebo pills,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis",1783272|1239|186801|3085636|186803|1766253|39491;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|3085636|186803|841|166486,Complete,KateRasheed
bsdb:39748236/1/2,39748236,time series / longitudinal observational,39748236,10.1186/s40168-024-01936-4,NA,"Bongiovanni T., Santiago M., Zielinska K., Scheiman J., Barsa C., Jäger R., Pinto D., Rinaldi F., Giuliani G., Senatore T. , Kostic A.D.",A Lactobacillus consortium provides insights into the sleep-exercise-microbiome nexus in proof of concept studies of elite athletes and in the general population,Microbiome,2025,"Lactobacillus, Energy, Fatigue, Microbiome, Oxidative stress, Probiotic, Recovery, Sleep, Testosterone",Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Oxidative Stress,EFO:1001905,Baseline,Placebo,Healthy male soccer players taking placebo pills blindly for the first period of 12weeks.,11,11,3 months,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 4b, Table 2",21 April 2025,Anne-mariesharp,Anne-mariesharp,Soccer players' taxa that significantly change after the ingestion of placebo pills,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,1783272|1239|186801|3085636|186803|2316020|33039,Complete,KateRasheed
bsdb:39748236/2/1,39748236,time series / longitudinal observational,39748236,10.1186/s40168-024-01936-4,NA,"Bongiovanni T., Santiago M., Zielinska K., Scheiman J., Barsa C., Jäger R., Pinto D., Rinaldi F., Giuliani G., Senatore T. , Kostic A.D.",A Lactobacillus consortium provides insights into the sleep-exercise-microbiome nexus in proof of concept studies of elite athletes and in the general population,Microbiome,2025,"Lactobacillus, Energy, Fatigue, Microbiome, Oxidative stress, Probiotic, Recovery, Sleep, Testosterone",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Oxidative Stress,EFO:1001905,Baseline,Probiotic,Healthy male soccer players taking probiotic pills blindly for the second period of 12 weeks.,11,11,3 months,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 4b, Table 2",22 April 2025,Asoler2004,Asoler2004,Soccer players' taxa that significantly change after the ingestion of probiotic pills,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis",1783272|1239|186801|3085636|186803|1766253|39491;3379134|976|200643|171549|171550|239759|28117;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|186802|216572|216851|853;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|3085636|186803|841|166486,Complete,KateRasheed
bsdb:39748236/2/2,39748236,time series / longitudinal observational,39748236,10.1186/s40168-024-01936-4,NA,"Bongiovanni T., Santiago M., Zielinska K., Scheiman J., Barsa C., Jäger R., Pinto D., Rinaldi F., Giuliani G., Senatore T. , Kostic A.D.",A Lactobacillus consortium provides insights into the sleep-exercise-microbiome nexus in proof of concept studies of elite athletes and in the general population,Microbiome,2025,"Lactobacillus, Energy, Fatigue, Microbiome, Oxidative stress, Probiotic, Recovery, Sleep, Testosterone",Experiment 2,Italy,Homo sapiens,Feces,UBERON:0001988,Oxidative Stress,EFO:1001905,Baseline,Probiotic,Healthy male soccer players taking probiotic pills blindly for the second period of 12 weeks.,11,11,3 months,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 4b, Table 2",22 April 2025,Asoler2004,"Asoler2004,Anne-mariesharp",Soccer players' taxa that significantly change after the ingestion of probiotic pills.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|909932|1843488|909930|33024|626940;1783272|1239|186801|3085636|186803|2316020|33039,Complete,KateRasheed
bsdb:39748236/4/1,39748236,time series / longitudinal observational,39748236,10.1186/s40168-024-01936-4,NA,"Bongiovanni T., Santiago M., Zielinska K., Scheiman J., Barsa C., Jäger R., Pinto D., Rinaldi F., Giuliani G., Senatore T. , Kostic A.D.",A Lactobacillus consortium provides insights into the sleep-exercise-microbiome nexus in proof of concept studies of elite athletes and in the general population,Microbiome,2025,"Lactobacillus, Energy, Fatigue, Microbiome, Oxidative stress, Probiotic, Recovery, Sleep, Testosterone",Experiment 4,Italy,Homo sapiens,Feces,UBERON:0001988,Oxidative Stress,EFO:1001905,Baseline,Probiotic,Healthy male soccer players taking probiotic pills blindly for the second period of 12 weeks.,11,11,3 months,WMS,NA,Illumina,log transformation,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4d,24 April 2025,Anne-mariesharp,Anne-mariesharp,The abundance of the Lactobacillaceae family increases with probiotic use but not placebo.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,1783272|1239|91061|186826|33958,Complete,KateRasheed
bsdb:39748884/1/1,39748884,case-control,39748884,10.3389/fcimb.2024.1492881,NA,"Zhou H., Pei Y., Xie Q., Nie W., Liu X., Xia H. , Jiang J.",Diagnosis and insight into the unique lung microbiota of pediatric pulmonary tuberculosis patients by bronchoalveolar lavage using metagenomic next-generation sequencing,Frontiers in cellular and infection microbiology,2024,"bronchoalveolar lavage fluid, conventional microbial test, metagenomic next-generation sequencing, microecology, pediatric pulmonary tuberculosis",Experiment 1,China,Homo sapiens,Lung,UBERON:0002048,Pulmonary tuberculosis,EFO:1000049,pediatric pneumonia patients (NTB group),pediatric pulmonary tuberculosis (PTB group),"showing positive TB culturing, TB-PCR, or mNGS result",21,43,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figures 3F, G; Supplementary Table 2",18 July 2025,Nuerteye,Nuerteye,"LEfSe analysis was performed to identify differentially abundant taxa, which are highlighted on the phylogenetic tree in cladogram format (F) and for which the linear discriminant analysis scores are shown (G)",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia|s__Gordonia polyisoprenivorans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium tuberculosis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rahnella|s__Rahnella sikkimica",1783272|201174|1760|85007|85026|2053|84595;1783272|201174|1760|85007|1762|1763|1773;3379134|1224|1236|91347|1903411|34037|1805933,Complete,NA
bsdb:39748884/1/2,39748884,case-control,39748884,10.3389/fcimb.2024.1492881,NA,"Zhou H., Pei Y., Xie Q., Nie W., Liu X., Xia H. , Jiang J.",Diagnosis and insight into the unique lung microbiota of pediatric pulmonary tuberculosis patients by bronchoalveolar lavage using metagenomic next-generation sequencing,Frontiers in cellular and infection microbiology,2024,"bronchoalveolar lavage fluid, conventional microbial test, metagenomic next-generation sequencing, microecology, pediatric pulmonary tuberculosis",Experiment 1,China,Homo sapiens,Lung,UBERON:0002048,Pulmonary tuberculosis,EFO:1000049,pediatric pneumonia patients (NTB group),pediatric pulmonary tuberculosis (PTB group),"showing positive TB culturing, TB-PCR, or mNGS result",21,43,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figures 3F, G; Supplementary Table 2",18 July 2025,Nuerteye,Nuerteye,"LEfSe analysis was performed to identify differentially abundant taxa, which are highlighted on the phylogenetic tree in cladogram format (F) and for which the linear discriminant analysis scores are shown (G)",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas putida,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella catarrhalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus|s__Rhodococcus opacus",3379134|1224|1236|72274|135621|286|303;3379134|1224|1236|2887326|468|475|480;1783272|201174|1760|85007|85025|1827|37919,Complete,NA
bsdb:39762435/1/1,39762435,meta-analysis,39762435,10.1038/s41564-024-01870-z,NA,"Fackelmann G., Manghi P., Carlino N., Heidrich V., Piccinno G., Ricci L., Piperni E., Arrè A., Bakker E., Creedon A.C., Francis L., Capdevila Pujol J., Davies R., Wolf J., Bermingham K.M., Berry S.E., Spector T.D., Asnicar F. , Segata N.","Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals",Nature microbiology,2025,NA,Experiment 1,"Italy,United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Omnivore,Vegetarian,Participants whose diet pattern excludes meat,19817,1088,NA,WMS,NA,Illumina,relative abundances,Wald Test,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3b,11 March 2025,Tosin,Tosin,"Meta-analysed correlations between SGB relative abundance and diet pattern (omnivore n = 19,817 in pink vs vegetarian n = 1,088 in purple).",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia saccharogumia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium",1783272|1239|909932|1843489|31977|39948|2582419;1783272|1239|186801|3085636|186803|28050;1783272|1239|526524|526525|2810280|3025755|341225;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|3085636|186803|1898203,Complete,NA
bsdb:39762435/1/2,39762435,meta-analysis,39762435,10.1038/s41564-024-01870-z,NA,"Fackelmann G., Manghi P., Carlino N., Heidrich V., Piccinno G., Ricci L., Piperni E., Arrè A., Bakker E., Creedon A.C., Francis L., Capdevila Pujol J., Davies R., Wolf J., Bermingham K.M., Berry S.E., Spector T.D., Asnicar F. , Segata N.","Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals",Nature microbiology,2025,NA,Experiment 1,"Italy,United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Omnivore,Vegetarian,Participants whose diet pattern excludes meat,19817,1088,NA,WMS,NA,Illumina,relative abundances,Wald Test,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3b,12 March 2025,Tosin,Tosin,"Meta-analysed correlations between SGB relative abundance and diet pattern (omnivore n = 19,817 in pink vs vegetarian n = 1,088 in purple).",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. An250,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas paravirosa,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. An138,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis|s__Merdimmobilis hominis,k__Bacillati|p__Bacillota|g__Negativibacillus|s__Negativibacillus massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Avimicrobium|s__Candidatus Avimicrobium caecorum,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Pararuminococcus|s__Candidatus Pararuminococcus gallinarum",3379134|976|200643|171549|171550|239759|28117;1783272|1239|186801|186802|3082771|1924093|1965604;3379134|200940|3031449|213115|194924|35832|35833;3379134|976|200643|171549|1853231|574697|1472417;1783272|1239|186801;1783272|1239|186801|2044939;1783272|1239|186801|186802|31979|1898204;1783272|1239|186801|3085636|186803|3569723|410072;3379134|200940|3031449|213115|194924;1783272|1239|526524|526525|128827;1783272|1239|186801|3085636|186803|1506553|1965560;1783272|1239|186801|186802|216572|3028852|2897707;1783272|1239|1980693|1871035;3379134|976|200643|171549|1853231|283168|28118;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|2485925;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801;1783272|1239|186801|2720800|2720821;1783272|1239|186801|2721115|2721144,Complete,NA
bsdb:39762435/2/1,39762435,meta-analysis,39762435,10.1038/s41564-024-01870-z,NA,"Fackelmann G., Manghi P., Carlino N., Heidrich V., Piccinno G., Ricci L., Piperni E., Arrè A., Bakker E., Creedon A.C., Francis L., Capdevila Pujol J., Davies R., Wolf J., Bermingham K.M., Berry S.E., Spector T.D., Asnicar F. , Segata N.","Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals",Nature microbiology,2025,NA,Experiment 2,"Italy,United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Omnivores,Vegan,"Participants whose diet patterns excludes both meat, dairy and other animal products",19817,656,NA,WMS,NA,Illumina,relative abundances,Wald Test,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3h,12 March 2025,Tosin,Tosin,"Meta-analysed correlations between SGB relative abundance and diet pattern between omnivores (n = 19,817 in pink) and vegans (n = 656 in green)",increased,"k__Bacillati|p__Bacillota|c__Bacilli|s__Bacilli bacterium,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF20-17LB,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AM33-3,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus sp. AM29-23AC,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",1783272|1239|91061|1903720;1783272|1239;1783272|1239|186801|186802|31979|1485|2292205;1783272|1239|186801|186802|31979|1485|2292304;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|1898203;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|186802|3085642|580596|2292295;1783272|1239|186801|186802|31979,Complete,NA
bsdb:39762435/2/2,39762435,meta-analysis,39762435,10.1038/s41564-024-01870-z,NA,"Fackelmann G., Manghi P., Carlino N., Heidrich V., Piccinno G., Ricci L., Piperni E., Arrè A., Bakker E., Creedon A.C., Francis L., Capdevila Pujol J., Davies R., Wolf J., Bermingham K.M., Berry S.E., Spector T.D., Asnicar F. , Segata N.","Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals",Nature microbiology,2025,NA,Experiment 2,"Italy,United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Omnivores,Vegan,"Participants whose diet patterns excludes both meat, dairy and other animal products",19817,656,NA,WMS,NA,Illumina,relative abundances,Wald Test,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3h,12 March 2025,Tosin,Tosin,"Meta-analysed correlations between SGB relative abundance and diet pattern between omnivores (n = 19,817 in pink) and vegans (n = 656 in green)",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. An250,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Pararuminococcus|s__Candidatus Pararuminococcus gallinarum,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis|s__Merdimmobilis hominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Avimicrobium|s__Candidatus Avimicrobium caecorum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Lawsonibacter|s__Lawsonibacter asaccharolyticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium",3379134|976|200643|171549|171550|239759|28117;1783272|1239|186801|186802|3082771|1924093|1965604;1783272|1239|186801|2721115|2721144;1783272|1239|186801;1783272|1239|186801|2044939;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|526524|526525|128827|2049044;1783272|1239|186801|186802|216572|3028852|2897707;3379134|976|200643|171549|1853231|283168|28118;1783272|1239|186801|186802|216572|2485925;1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|186801;1783272|1239|186801|2720800|2720821;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|186802|216572|2172004|2108523;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|186801|186802|31979|1898204,Complete,NA
bsdb:39762435/3/1,39762435,meta-analysis,39762435,10.1038/s41564-024-01870-z,NA,"Fackelmann G., Manghi P., Carlino N., Heidrich V., Piccinno G., Ricci L., Piperni E., Arrè A., Bakker E., Creedon A.C., Francis L., Capdevila Pujol J., Davies R., Wolf J., Bermingham K.M., Berry S.E., Spector T.D., Asnicar F. , Segata N.","Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals",Nature microbiology,2025,NA,Experiment 3,"Italy,United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Vegetarian,Vegan,"Participants whose diet patterns exclude both meat, dairy and other animal products.",1088,656,NA,WMS,NA,Illumina,relative abundances,Wald Test,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4b,14 March 2025,Victoria,Victoria,"Meta-analysed correlations between SGB relative abundance and diet pattern (vegetarian, n= 1,088 in purple vs vegan, n= 656 in green).",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. AF41-9,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. MSK.21.1,k__Bacillati|p__Bacillota",1783272|1239|186801|3085636|186803|1898203;1783272|1239|186801;1783272|1239|186801|186802|216572|1263|2292069;1783272|1239|186801|3085636|186803|572511|2742763;1783272|1239,Complete,NA
bsdb:39762435/3/2,39762435,meta-analysis,39762435,10.1038/s41564-024-01870-z,NA,"Fackelmann G., Manghi P., Carlino N., Heidrich V., Piccinno G., Ricci L., Piperni E., Arrè A., Bakker E., Creedon A.C., Francis L., Capdevila Pujol J., Davies R., Wolf J., Bermingham K.M., Berry S.E., Spector T.D., Asnicar F. , Segata N.","Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals",Nature microbiology,2025,NA,Experiment 3,"Italy,United Kingdom,United States of America",Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Vegetarian,Vegan,"Participants whose diet patterns exclude both meat, dairy and other animal products.",1088,656,NA,WMS,NA,Illumina,relative abundances,Wald Test,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4b,14 March 2025,Victoria,Victoria,"Meta-analysed correlations between SGB relative abundance and diet pattern (vegetarian, n= 1,088 in purple vs vegan, n= 656 in green).",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Massiliimalia|s__Massiliimalia massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania sp. Marseille-P2844,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Candidatus Borkfalkia|s__Candidatus Borkfalkia ceftriaxoniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Evtepia|s__Evtepia gabavorous,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus paracasei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus delbrueckii,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Lawsonibacter|s__Lawsonibacter asaccharolyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus rhamnosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus",1783272|1239|186801|186802|216572|2895461|1852384;3379134|976|200643|171549|2005525|375288|328812;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|526524|526525|128827|2049044;1783272|1239|526524|526525|128827|61170|1852366;1783272|1239|186801|3082768|990719|2508948|2508949;1783272|1239|186801|3085636|186803|1898203;1783272|1239|186801|186802|31979|1898204;1783272|1239|186801;1783272|1239|91061|186826|33958|1578|1579;1783272|1239|91061|186826|1300|1357|1358;1783272|1239|186801|186802|2211178|2211183;1783272|1239|91061|186826|33958|2759736|1597;1783272|1239|91061|186826|33958|1578|1584;1783272|1239;1783272|1239|186801|186802|216572|2172004|2108523;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|186801|2044939;1783272|1239|91061|186826|33958|2759736|47715;1783272|1239|186801|186802|216572|2485925;1783272|1239|91061|186826|1300|1301|1308,Complete,NA
bsdb:39768329/1/1,39768329,case-control,39768329,https://doi.org/10.3390/life14121621,https://www.mdpi.com/2075-1729/14/12/1621#app1-life-14-01621,"Do K.H., Park J., Kim N., Ryu D., Kim M.G., Ahn H., Kim H., Hwang J.G., Park M.K., Seo K.W. , Lee W.K.",Comparative Analysis of Gut Microbiota in Humans Living with and Without Companion Animals,"Life (Basel, Switzerland)",2024,"companion animal, environmental health, intestinal bacteria, intestinal microbiology",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Without companion animals (CA),With companion animals (CA),These are individuals cohabiting with companion animals,60,60,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 5,11 October 2025,Fiddyhamma,Fiddyhamma,Volcano plot of differentially abundant genera in gut microbiota between groups cohabiting with and without companion animals.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Dickeya,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas",3379134|1224|1236|91347|1903410|204037;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|119852;95818|2093818|2093825|2171986|1331051,Complete,Svetlana up
bsdb:39768329/1/2,39768329,case-control,39768329,https://doi.org/10.3390/life14121621,https://www.mdpi.com/2075-1729/14/12/1621#app1-life-14-01621,"Do K.H., Park J., Kim N., Ryu D., Kim M.G., Ahn H., Kim H., Hwang J.G., Park M.K., Seo K.W. , Lee W.K.",Comparative Analysis of Gut Microbiota in Humans Living with and Without Companion Animals,"Life (Basel, Switzerland)",2024,"companion animal, environmental health, intestinal bacteria, intestinal microbiology",Experiment 1,South Korea,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Without companion animals (CA),With companion animals (CA),These are individuals cohabiting with companion animals,60,60,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 5,11 October 2025,Fiddyhamma,Fiddyhamma,Volcano plot of differentially abundant genera in gut microbiota between groups cohabiting with and without companion animals.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Globicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Oceanobacillus",1783272|1239|91061|186826|186827|13075;1783272|1239|91061|1385|186817|182709,Complete,Svetlana up
bsdb:39768329/2/1,39768329,case-control,39768329,https://doi.org/10.3390/life14121621,https://www.mdpi.com/2075-1729/14/12/1621#app1-life-14-01621,"Do K.H., Park J., Kim N., Ryu D., Kim M.G., Ahn H., Kim H., Hwang J.G., Park M.K., Seo K.W. , Lee W.K.",Comparative Analysis of Gut Microbiota in Humans Living with and Without Companion Animals,"Life (Basel, Switzerland)",2024,"companion animal, environmental health, intestinal bacteria, intestinal microbiology",Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Without companion animals (CA),With companion animals (CA),These are individuals cohabiting with companion animals,60,60,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 6,11 October 2025,Fiddyhamma,Fiddyhamma,LEfSe analysis of gut microbiota in individuals cohabiting with and without companion animals. With CA: group cohabiting with companion animals; without CAs: group without companion animals.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:39768329/2/2,39768329,case-control,39768329,https://doi.org/10.3390/life14121621,https://www.mdpi.com/2075-1729/14/12/1621#app1-life-14-01621,"Do K.H., Park J., Kim N., Ryu D., Kim M.G., Ahn H., Kim H., Hwang J.G., Park M.K., Seo K.W. , Lee W.K.",Comparative Analysis of Gut Microbiota in Humans Living with and Without Companion Animals,"Life (Basel, Switzerland)",2024,"companion animal, environmental health, intestinal bacteria, intestinal microbiology",Experiment 2,South Korea,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Without companion animals (CA),With companion animals (CA),These are individuals cohabiting with companion animals,60,60,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 6,11 October 2025,Fiddyhamma,Fiddyhamma,LEfSe analysis of gut microbiota in individuals cohabiting with and without companion animals. With CA: group cohabiting with companion animals; without CAs: group without companion animals.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",1783272|1239|909932|909929|1843491;1783272|1239|909932|909929|1843491|158846,Complete,Svetlana up
bsdb:39772703/1/1,39772703,randomized controlled trial,39772703,10.1128/spectrum.01913-24,NA,"Meiners F., Kreikemeyer B., Newels P., Zude I., Walter M., Hartmann A., Palmer D., Fuellen G. , Barrantes I.",Strawberry dietary intervention influences diversity and increases abundances of SCFA-producing bacteria in healthy elderly people,Microbiology spectrum,2025,"aging, dietary intervention, human gut microbiome",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Group1-Visit1 (g1_vA),Group1-Visit2 (g1_vB),This group consists of participants after the intervention period. They consumed 500g of fresh strawberries every week for 10 weeks.,12,12,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 3,24 February 2025,Victoria,Victoria,"Taxa with significant changes in abundance after the strawberry intervention, with false discovery rate (FDR) < 0.05.",decreased,NA,NA,Complete,Svetlana up
bsdb:39772703/2/1,39772703,randomized controlled trial,39772703,10.1128/spectrum.01913-24,NA,"Meiners F., Kreikemeyer B., Newels P., Zude I., Walter M., Hartmann A., Palmer D., Fuellen G. , Barrantes I.",Strawberry dietary intervention influences diversity and increases abundances of SCFA-producing bacteria in healthy elderly people,Microbiology spectrum,2025,"aging, dietary intervention, human gut microbiome",Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Group2-Visit1 (g2_vA),Group2-Visit2 (g2_vB),"This group consists of participants after the intervention period. They consumed 1500g of fresh strawberries in the first two weeks, 2500g from week 3 to week 9, and 3750g in week 10.",14,14,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 3,25 February 2025,Victoria,Victoria,"Taxa with significant changes in abundance after the strawberry intervention, with false discovery rate (FDR) < 0.05.",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,1783272|1239|186801|186802|186806|1730|290054,Complete,Svetlana up
bsdb:39772703/3/1,39772703,randomized controlled trial,39772703,10.1128/spectrum.01913-24,NA,"Meiners F., Kreikemeyer B., Newels P., Zude I., Walter M., Hartmann A., Palmer D., Fuellen G. , Barrantes I.",Strawberry dietary intervention influences diversity and increases abundances of SCFA-producing bacteria in healthy elderly people,Microbiology spectrum,2025,"aging, dietary intervention, human gut microbiome",Experiment 3,Germany,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Group3-Visit1 (g3_vA),Group3-Visit2 (g3_vB),"This group consists of participants after the intervention period. They consumed 1500g of fresh strawberries and 100g of Freeze-dried strawberries in the first two weeks, 2500g of fresh strawberries from week 3 to week 9, and 3750g of fresh strawberries plus 100g of freeze-dried strawberries in week 10.",15,15,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 3,26 February 2025,Victoria,Victoria,"Taxa with significant changes in abundance after the strawberry intervention, with false discovery rate (FDR) < 0.05.",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:39772703/4/1,39772703,randomized controlled trial,39772703,10.1128/spectrum.01913-24,NA,"Meiners F., Kreikemeyer B., Newels P., Zude I., Walter M., Hartmann A., Palmer D., Fuellen G. , Barrantes I.",Strawberry dietary intervention influences diversity and increases abundances of SCFA-producing bacteria in healthy elderly people,Microbiology spectrum,2025,"aging, dietary intervention, human gut microbiome",Experiment 4,Germany,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Group4-Visit1 (g4_vA),Group4-Visit2 (g4_vB),"This group consists of participants after the intervention period. They consumed 1500g of fresh strawberries in the first two weeks, 2500g from week 3 to week 9, and 3750g in week 10. Additionally, they had 100g of Freeze-dried strawberries in week 1 and 200g in week 2 and week 10.",11,11,NA,16S,34,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 3,26 February 2025,Victoria,Victoria,"Taxa with significant changes in abundance after the strawberry intervention, with false discovery rate (FDR) < 0.05.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:39773949/1/1,39773949,case-control,39773949,10.1038/s41467-024-55798-3,NA,"Portlock T., Shama T., Kakon S.H., Hartjen B., Pook C., Wilson B.C., Bhuttor A., Ho D., Shennon I., Engelstad A.M., Di Lorenzo R., Greaves G., Rahman N., Kelsey C., Gluckman P.D., O'Sullivan J.M., Haque R., Forrester T. , Nelson C.A.",Interconnected pathways link faecal microbiota plasma lipids and brain activity to childhood malnutrition related cognition,Nature communications,2025,NA,Experiment 1,Bangladesh,Homo sapiens,Feces,UBERON:0001988,Malnutrition,EFO:0008572,Well-nourished infants,MAM (Moderate Acute Malnutrition) infants,Infants aged 12 ± 1 months diagnosed with Moderate Acute Malnutrition (Weight-for-Length Z-score between -2 and -3 SD),75,159,1 month,WMS,NA,Illumina,relative abundances,MaAsLin2,0.25,TRUE,NA,age,NA,decreased,decreased,NA,NA,NA,NA,Signature 1,"Figure 1f, Supplementary Data 3",20 March 2025,D-coder111,"D-coder111,Aleru Divine","This signature includes microbial taxa that were found to be significantly increased in infants with Moderate Acute Malnutrition (MAM) compared to well-nourished controls. Shotgun metagenomic sequencing of fecal samples (stool) identified an increased abundance of multiple bacterial taxa across different taxonomic levels.

The following taxa were significantly enriched in Moderate Acute Malnutrition(MAM) infants (MaAsLin2, q < 0.25).",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",1783272|201174|1760|85006|1268;1783272|201174|1760|85006;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300|1301|1304;;1783272|201174|1760|85006|1268|32207,Complete,Svetlana up
bsdb:39773949/1/2,39773949,case-control,39773949,10.1038/s41467-024-55798-3,NA,"Portlock T., Shama T., Kakon S.H., Hartjen B., Pook C., Wilson B.C., Bhuttor A., Ho D., Shennon I., Engelstad A.M., Di Lorenzo R., Greaves G., Rahman N., Kelsey C., Gluckman P.D., O'Sullivan J.M., Haque R., Forrester T. , Nelson C.A.",Interconnected pathways link faecal microbiota plasma lipids and brain activity to childhood malnutrition related cognition,Nature communications,2025,NA,Experiment 1,Bangladesh,Homo sapiens,Feces,UBERON:0001988,Malnutrition,EFO:0008572,Well-nourished infants,MAM (Moderate Acute Malnutrition) infants,Infants aged 12 ± 1 months diagnosed with Moderate Acute Malnutrition (Weight-for-Length Z-score between -2 and -3 SD),75,159,1 month,WMS,NA,Illumina,relative abundances,MaAsLin2,0.25,TRUE,NA,age,NA,decreased,decreased,NA,NA,NA,NA,Signature 2,Supplementary Data 3,20 March 2025,D-coder111,D-coder111,This signature includes taxa that were found to be significantly decreased in infants with Moderate Acute Malnutrition (MAM) compared to well-nourished controls. Shotgun metagenomic sequencing of fecal samples (stool) identified a reduced abundance of Bacteroides fragilis. Statistical analysis was performed using MaAsLin2 with Benjamini-Hochberg FDR correction (q < 0.25).,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,3379134|976|200643|171549|815|816|817,Complete,Svetlana up
bsdb:39787116/1/1,39787116,case-control,39787116,10.1371/journal.pone.0312606,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0312606,"Zhu H., Wu C., Wu H., Liu J., Ye W., Zhao T. , Li Z.",The gut microbiota-SCFA-inflammation axis in patients with AECOPD,PloS one,2025,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic obstructive pulmonary disease,EFO:0000341,Healthy Control Group (HC),AECOPD Group (Acute Exacerbation of Chronic Obstructive Pulmonary Disease),"Patients diagnosed with Acute Exacerbation of Chronic Obstructive Pulmonary Disease (AECOPD). It is a sudden worsening of COPD symptoms, including increased breathlessness, cough, mucus production, and inflammation.",18,24,2 weeks,16S,34,Illumina,relative abundances,Metastats,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,increased,NA,decreased,Signature 1,Fig S2-S7,25 March 2025,Aiyshaaaa,Aiyshaaaa,"The metastat analysis of taxa was demonstrated between two groups in Phylum,Class,Order,Family,Genus and Species level",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;1783272|1239|91061;1783272|1239;3384189|32066|203490|203491|203492|180162;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826;1783272|201174|1760|85006|1268;1783272|1239|909932;1783272|201174|1760|85006|1268|32207,Complete,Svetlana up
bsdb:39787116/1/2,39787116,case-control,39787116,10.1371/journal.pone.0312606,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0312606,"Zhu H., Wu C., Wu H., Liu J., Ye W., Zhao T. , Li Z.",The gut microbiota-SCFA-inflammation axis in patients with AECOPD,PloS one,2025,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic obstructive pulmonary disease,EFO:0000341,Healthy Control Group (HC),AECOPD Group (Acute Exacerbation of Chronic Obstructive Pulmonary Disease),"Patients diagnosed with Acute Exacerbation of Chronic Obstructive Pulmonary Disease (AECOPD). It is a sudden worsening of COPD symptoms, including increased breathlessness, cough, mucus production, and inflammation.",18,24,2 weeks,16S,34,Illumina,relative abundances,Metastats,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,increased,NA,decreased,Signature 2,Fig S2-S7,25 March 2025,Aiyshaaaa,Aiyshaaaa,"The metastat analysis of taxa was demonstrated between two groups in Phylum,Class,Order,Family,Genus and Species level",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,s__uncultured bacterium adhufec108",3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976;3379134|976|200643|171549|2005519|397864;1783272|1239|186801;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|976|200643|171549|815|909656|821;1783272|1239|909932|1843489|31977|29465;98641,Complete,Svetlana up
bsdb:39787116/2/1,39787116,case-control,39787116,10.1371/journal.pone.0312606,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0312606,"Zhu H., Wu C., Wu H., Liu J., Ye W., Zhao T. , Li Z.",The gut microbiota-SCFA-inflammation axis in patients with AECOPD,PloS one,2025,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Chronic obstructive pulmonary disease,EFO:0000341,Healthy Control Group (HC),AECOPD Group (Acute Exacerbation of Chronic Obstructive Pulmonary Disease),"Patients diagnosed with Acute Exacerbation of Chronic Obstructive Pulmonary Disease (AECOPD). It is a sudden worsening of COPD symptoms, including increased breathlessness, cough, mucus production, and inflammation.",18,24,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,increased,NA,decreased,Signature 1,Fig 5,26 March 2025,Aiyshaaaa,Aiyshaaaa,"LEfSe was used to analyze the differential bacterial abundance between two groups in Phylum,Class,Order,Family and Genus level",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;1783272|1239;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|3082720|543314|86331;1783272|1239|909932|1843489|31977,Complete,Svetlana up
bsdb:39787116/2/2,39787116,case-control,39787116,10.1371/journal.pone.0312606,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0312606,"Zhu H., Wu C., Wu H., Liu J., Ye W., Zhao T. , Li Z.",The gut microbiota-SCFA-inflammation axis in patients with AECOPD,PloS one,2025,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Chronic obstructive pulmonary disease,EFO:0000341,Healthy Control Group (HC),AECOPD Group (Acute Exacerbation of Chronic Obstructive Pulmonary Disease),"Patients diagnosed with Acute Exacerbation of Chronic Obstructive Pulmonary Disease (AECOPD). It is a sudden worsening of COPD symptoms, including increased breathlessness, cough, mucus production, and inflammation.",18,24,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,increased,NA,decreased,Signature 2,Fig 5,26 March 2025,Aiyshaaaa,Aiyshaaaa,"LEfSe was used to analyze the differential bacterial abundance between two groups in Phylum,Class,Order,Family and Genus level",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|1224|28211|3120395|433;1783272|1239|909932|1843489|31977|209879;3379134|1224|28211;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976;3379134|976|200643|171549|2005519|397864;3379134|1224|28216;3379134|1224|28216|80840;1783272|1239|526524|526525|2810280|135858;28221;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|1407607;3379134|1224|1236|135625|712|724;1783272|1239|526524|526525|128827|1573535;3379134|1224|1236|91347|1903414|581;3379134|976|200643|171549|171552|577309;3379134|1224|28216|80840|995019|577310;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|976|200643|171549|171551;3379134|1224|28211|204441;1783272|1239|186801|3082720|186804|1501226;3379134|1224|28216|80840|995019|40544;3379134|1224|28216|80840|995019;1783272|1239|909932|1843489|31977|29465;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:39788958/1/1,39788958,time series / longitudinal observational,39788958,https://doi.org/10.1038/s41522-024-00622-5,NA,"Sanchez-Orozco N.Y., Rosier B.T., Ruiz-Gutierrez A., Marquez-Sandoval F., Artacho A., Carrera-Quintanar L. , Mira A.",The blood pressure lowering effect of beetroot juice is impaired in periodontitis and recovered after periodontal treatment,NPJ biofilms and microbiomes,2025,NA,Experiment 1,Mexico,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Periodontitis,EFO:0000649,Healthy controls,Periodontitis Baseline (BL),Periodontitis before any periodontal treatment,13,13,3 months,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 1,Supplementary Figure 2A and Figure 6A,28 January 2025,Miss Lulu,"Miss Lulu,WikiWorks","Bar graphs show comparisons between healthy individuals (H) and
periodontitis patients at baseline (BL) in subgingival plaque",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces massiliensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia rubra,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049|1654|461393;1783272|201174|1760|2037|2049|1654|1655;1783272|201174|1760|85009|31957|2801844;1783272|201174|1760|85009|31957|2801844|1547448;3379134|976|117743|200644|2762318|59735;3379134|1224|1236|135615|868|2717;3379134|1224|1236|135615|868|2717|2718;1783272|201174|1760|85007|1653|1716;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;3379134|1224|28216|206351|481|32257;3379134|1224|28216|206351|481|32257|505;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|85006|1268|32207|2047;1783272|201174|1760|2037|2049|1654;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135625|712|724,Complete,Svetlana up
bsdb:39788958/1/2,39788958,time series / longitudinal observational,39788958,https://doi.org/10.1038/s41522-024-00622-5,NA,"Sanchez-Orozco N.Y., Rosier B.T., Ruiz-Gutierrez A., Marquez-Sandoval F., Artacho A., Carrera-Quintanar L. , Mira A.",The blood pressure lowering effect of beetroot juice is impaired in periodontitis and recovered after periodontal treatment,NPJ biofilms and microbiomes,2025,NA,Experiment 1,Mexico,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Periodontitis,EFO:0000649,Healthy controls,Periodontitis Baseline (BL),Periodontitis before any periodontal treatment,13,13,3 months,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 2,Supplementary Figure 2A and Figure 6A,28 January 2025,Miss Lulu,"Miss Lulu,WikiWorks","Bar graphs show comparisons between healthy individuals (H) and
periodontitis patients at baseline (BL) in subgingival plaque",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Lentimicrobiaceae|g__Lentimicrobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|171552|1283313|76122;1783272|1239|186801|3082720|3118655|44259;3379134|976|200643|171549|1840213|1840214;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|815|909656;3379134|976|200643|171549|171552|838|28131;1783272|1239|909932|1843489|31977,Complete,Svetlana up
bsdb:39788958/2/1,39788958,time series / longitudinal observational,39788958,https://doi.org/10.1038/s41522-024-00622-5,NA,"Sanchez-Orozco N.Y., Rosier B.T., Ruiz-Gutierrez A., Marquez-Sandoval F., Artacho A., Carrera-Quintanar L. , Mira A.",The blood pressure lowering effect of beetroot juice is impaired in periodontitis and recovered after periodontal treatment,NPJ biofilms and microbiomes,2025,NA,Experiment 2,Mexico,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Periodontitis,EFO:0000649,Periodontitis BL,Periodontitis D70,Periodontitis after 70 days of periodontal treatment,13,13,3 months,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Supplementary Figure 2B and Figure 6B,29 January 2025,Miss Lulu,"Miss Lulu,WikiWorks",Bar graphs show comparisons between D70 and BL in subgingival plaque.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049|1654|1655;1783272|201174|1760|2037|2049|1654|544580;1783272|1239|91061|186826|186828|117563;3379134|1224|28216|80840|119060|47670|47671;1783272|201174|1760|85006|1268|32207|2047;1783272|201174|1760|2037|2049|2529408|1660;1783272|201174|1760|2037|2049|1654;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:39788958/2/2,39788958,time series / longitudinal observational,39788958,https://doi.org/10.1038/s41522-024-00622-5,NA,"Sanchez-Orozco N.Y., Rosier B.T., Ruiz-Gutierrez A., Marquez-Sandoval F., Artacho A., Carrera-Quintanar L. , Mira A.",The blood pressure lowering effect of beetroot juice is impaired in periodontitis and recovered after periodontal treatment,NPJ biofilms and microbiomes,2025,NA,Experiment 2,Mexico,Homo sapiens,Subgingival dental plaque,UBERON:0016484,Periodontitis,EFO:0000649,Periodontitis BL,Periodontitis D70,Periodontitis after 70 days of periodontal treatment,13,13,3 months,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Supplementary Figure 2B and Figure 6B,29 January 2025,Miss Lulu,"Miss Lulu,WikiWorks",Bar graphs show comparisons between D70 and BL in subgingival plaque,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium",1783272|1239|186801|3082720|3118655|44259;3384194|508458|649775|649776|3029087|1434006;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|2005525|195950|28112;3384194|508458|649775|649776|3029087|1434006,Complete,Svetlana up
bsdb:39788958/3/1,39788958,time series / longitudinal observational,39788958,https://doi.org/10.1038/s41522-024-00622-5,NA,"Sanchez-Orozco N.Y., Rosier B.T., Ruiz-Gutierrez A., Marquez-Sandoval F., Artacho A., Carrera-Quintanar L. , Mira A.",The blood pressure lowering effect of beetroot juice is impaired in periodontitis and recovered after periodontal treatment,NPJ biofilms and microbiomes,2025,NA,Experiment 3,Mexico,Homo sapiens,Tongue,UBERON:0001723,Periodontitis,EFO:0000649,Healthy controls,Periodontitis Baseline (BL),Periodontitis before any periodontal treatment,13,14,3 months,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 1,Supplementary Figure 2C and Figure 6C,31 January 2025,Miss Lulu,"Miss Lulu,WikiWorks",Bar graphs show comparisons between H and BL in tongue coating.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|1224|1236|135625|712|713;3379134|1224|1236|135615|868|2717;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|1385|539738|1378|84135;3379134|1224|1236|135625|712|724;1783272|201174|1760|85006|1268|32207|2047;1783272|1239|909932|1843489|31977|29465|423477;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:39788958/3/2,39788958,time series / longitudinal observational,39788958,https://doi.org/10.1038/s41522-024-00622-5,NA,"Sanchez-Orozco N.Y., Rosier B.T., Ruiz-Gutierrez A., Marquez-Sandoval F., Artacho A., Carrera-Quintanar L. , Mira A.",The blood pressure lowering effect of beetroot juice is impaired in periodontitis and recovered after periodontal treatment,NPJ biofilms and microbiomes,2025,NA,Experiment 3,Mexico,Homo sapiens,Tongue,UBERON:0001723,Periodontitis,EFO:0000649,Healthy controls,Periodontitis Baseline (BL),Periodontitis before any periodontal treatment,13,14,3 months,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 2,Supplementary Figure 2C and Figure 6C,31 January 2025,Miss Lulu,"Miss Lulu,WikiWorks",Bar graphs show comparisons between H and BL in tongue coating.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:39788958/4/1,39788958,time series / longitudinal observational,39788958,https://doi.org/10.1038/s41522-024-00622-5,NA,"Sanchez-Orozco N.Y., Rosier B.T., Ruiz-Gutierrez A., Marquez-Sandoval F., Artacho A., Carrera-Quintanar L. , Mira A.",The blood pressure lowering effect of beetroot juice is impaired in periodontitis and recovered after periodontal treatment,NPJ biofilms and microbiomes,2025,NA,Experiment 4,Mexico,Homo sapiens,Tongue,UBERON:0001723,Periodontitis,EFO:0000649,Healthy controls,Periodontitis Baseline (D70),Periodontitis after 70 days of periodontal treatment,13,14,3 months,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 1,Supplementary Figure 2E and Figure 6E,31 January 2025,Miss Lulu,"Miss Lulu,WikiWorks",Bar graphs show comparisons between H and D70 in tongue coating.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus|s__Actinobacillus pleuropneumoniae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",3379134|1224|1236|135625|712|713;3379134|1224|1236|135625|712|713|715;3384189|32066|203490|203491|1129771|32067,Complete,Svetlana up
bsdb:39788958/5/1,39788958,time series / longitudinal observational,39788958,https://doi.org/10.1038/s41522-024-00622-5,NA,"Sanchez-Orozco N.Y., Rosier B.T., Ruiz-Gutierrez A., Marquez-Sandoval F., Artacho A., Carrera-Quintanar L. , Mira A.",The blood pressure lowering effect of beetroot juice is impaired in periodontitis and recovered after periodontal treatment,NPJ biofilms and microbiomes,2025,NA,Experiment 5,Mexico,Homo sapiens,Tongue,UBERON:0001723,Periodontitis,EFO:0000649,Periodontitis BL,Periodontitis Baseline (D70),Periodontitis after 70 days of periodontal treatment,14,14,3 months,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Supplementary Figure 2D and Figure 6D,31 January 2025,Miss Lulu,"Miss Lulu,WikiWorks",Bar graphs show comparisons between D70 and BL in tongue coating.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor",3379134|976|200643|171549|171551|836|837;1783272|1239|186801|3082720|3118655|44259|143361;1783272|1239|186801|3082720|3118655|44259,Complete,Svetlana up
bsdb:39791884/1/2,39791884,laboratory experiment,39791884,10.1128/spectrum.01799-24,NA,"Sterrett J.D., Quinn K.D., Doenges K.A., Nusbacher N.M., Levens C.L., Armstrong M.L., Reisdorph R.M., Smith H., Saba L.M., Kuhn K.A., Lozupone C.A. , Reisdorph N.A.",Appearance of green tea compounds in plasma following acute green tea consumption is modulated by the gut microbiome in mice,Microbiology spectrum,2025,"16S RNA, food, gnotobiotic, metabolomics, microbiome, multi-omics, nutrition, polyphenols, symbiosis",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Low complexity microbiome (LCM) mice,Human colonized (HU) mice,Mice were orally administered 200 μL of human fecal slurry (100 mg stool homogenized in 1 mL reduced phosphate-buffered saline [PBS]) at 4 weeks of age.,9,20,NA,16S,4,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Within results text (Taxonomic composition of fecal microbiomes),Figure 2",11 April 2025,Ese,"Ese,Ameenatoloko",Taxonomic composition between Low Complexity Microbiome and Humanized Microbiome mice.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",1783272|1239|186801|3085636|186803|2383;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3082720|186804,Complete,Svetlana up
bsdb:39801363/1/1,39801363,randomized controlled trial,39801363,10.1111/gbb.70012,NA,"Chevalier C., Tournier B.B., Marizzoni M., Park R., Paquis A., Ceyzériat K., Badina A.M., Lathuiliere A., Saleri S., Cillis F., Cattaneo A., Millet P. , Frisoni G.B.",Fecal Microbiota Transplantation (FMT) From a Human at Low Risk for Alzheimer's Disease Improves Short-Term Recognition Memory and Increases Neuroinflammation in a 3xTg AD Mouse Model,"Genes, brain, and behavior",2025,"3xTgAD mice, APOE, Alzheimer, fecal microbiota transplantation (FMT), microbiota, neuroinflammation",Experiment 1,Switzerland,Mus musculus,Cecum mucosa,UBERON:0000314,Response to transplant,EFO:0007043,Untreated Mice- Fecal Microbiota Transplant (Mice-FMT),Alzheimer's disease(AD) patient (AD-FMT),"This refers to a female 3xTgAD mice who received weekly FMT for 2 months from an 80-year-old Alzheimer's disease(AD) patient (human); with no protection to AD, clinical diagnosis of dementia, brain amyloidosis, APOEε4 carrier genotype, female gender.",NA,NA,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.02,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 3C,13 February 2025,KateRasheed,"KateRasheed,WikiWorks,Tosin",Differential abundance of genera between the FMT recipient mice,decreased,"k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes",1783272|1798710|1906119;1783272|1239|91061|186826|33958|2767887;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|186802|186806|1730|290054,Complete,Svetlana up
bsdb:39801363/2/1,39801363,randomized controlled trial,39801363,10.1111/gbb.70012,NA,"Chevalier C., Tournier B.B., Marizzoni M., Park R., Paquis A., Ceyzériat K., Badina A.M., Lathuiliere A., Saleri S., Cillis F., Cattaneo A., Millet P. , Frisoni G.B.",Fecal Microbiota Transplantation (FMT) From a Human at Low Risk for Alzheimer's Disease Improves Short-Term Recognition Memory and Increases Neuroinflammation in a 3xTg AD Mouse Model,"Genes, brain, and behavior",2025,"3xTgAD mice, APOE, Alzheimer, fecal microbiota transplantation (FMT), microbiota, neuroinflammation",Experiment 2,Switzerland,Mus musculus,Cecum mucosa,UBERON:0000314,Response to transplant,EFO:0007043,Untreated Mice- Fecal Microbiota Transplant (Mice-FMT),Apolipoprotein E (APOEe2 allele) - APOEe2-FMT,"This refers to a female 3xTgAD mice who received weekly FMT for 2 months from a cognitively healthy 73-year-old with the protective APOEe2 allele with genetic-related protection to AD (APOEε2 carrier), associated with no cognitive decline diagnosed, no brain amyloidosis, a high level of education, male gender.",NA,NA,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.02,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Fig. 3C,13 February 2025,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of genera between the FMT recipient mice,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,3379134|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:39801363/2/2,39801363,randomized controlled trial,39801363,10.1111/gbb.70012,NA,"Chevalier C., Tournier B.B., Marizzoni M., Park R., Paquis A., Ceyzériat K., Badina A.M., Lathuiliere A., Saleri S., Cillis F., Cattaneo A., Millet P. , Frisoni G.B.",Fecal Microbiota Transplantation (FMT) From a Human at Low Risk for Alzheimer's Disease Improves Short-Term Recognition Memory and Increases Neuroinflammation in a 3xTg AD Mouse Model,"Genes, brain, and behavior",2025,"3xTgAD mice, APOE, Alzheimer, fecal microbiota transplantation (FMT), microbiota, neuroinflammation",Experiment 2,Switzerland,Mus musculus,Cecum mucosa,UBERON:0000314,Response to transplant,EFO:0007043,Untreated Mice- Fecal Microbiota Transplant (Mice-FMT),Apolipoprotein E (APOEe2 allele) - APOEe2-FMT,"This refers to a female 3xTgAD mice who received weekly FMT for 2 months from a cognitively healthy 73-year-old with the protective APOEe2 allele with genetic-related protection to AD (APOEε2 carrier), associated with no cognitive decline diagnosed, no brain amyloidosis, a high level of education, male gender.",NA,NA,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.02,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Fig. 3C,13 February 2025,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of genera between the FMT recipient mice,decreased,"k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales",3379134|200930|68337|191393|2945020|248038;3379134|200940|3031449|213115|194924|872;1783272|201174|84998|1643822|1643826;3379134|976|200643|171549|171550|28138;1783272|1798710|1906119,Complete,Svetlana up
bsdb:39801363/3/1,39801363,randomized controlled trial,39801363,10.1111/gbb.70012,NA,"Chevalier C., Tournier B.B., Marizzoni M., Park R., Paquis A., Ceyzériat K., Badina A.M., Lathuiliere A., Saleri S., Cillis F., Cattaneo A., Millet P. , Frisoni G.B.",Fecal Microbiota Transplantation (FMT) From a Human at Low Risk for Alzheimer's Disease Improves Short-Term Recognition Memory and Increases Neuroinflammation in a 3xTg AD Mouse Model,"Genes, brain, and behavior",2025,"3xTgAD mice, APOE, Alzheimer, fecal microbiota transplantation (FMT), microbiota, neuroinflammation",Experiment 3,Switzerland,Mus musculus,Cecum mucosa,UBERON:0000314,Response to transplant,EFO:0007043,Untreated Mice- Fecal Microbiota Transplant (Mice-FMT),Healthy donor (Young-FMT),"Healthy donor (Young-FMT) refers to a female 3xTgAD mice who received weekly FMT for 2 months from a 22-year-old age-related protection to AD, with no APOE gene-related risk (ε3/ε3), no cognitive complaints, male gender.",NA,NA,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.02,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 3C,13 February 2025,KateRasheed,"KateRasheed,WikiWorks,Tosin",Differential abundance of genera between the FMT recipient mice,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819",3379134|976|200643|171549|1853231|574697;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|186802|216572|216851|1946507,Complete,Svetlana up
bsdb:39801363/3/2,39801363,randomized controlled trial,39801363,10.1111/gbb.70012,NA,"Chevalier C., Tournier B.B., Marizzoni M., Park R., Paquis A., Ceyzériat K., Badina A.M., Lathuiliere A., Saleri S., Cillis F., Cattaneo A., Millet P. , Frisoni G.B.",Fecal Microbiota Transplantation (FMT) From a Human at Low Risk for Alzheimer's Disease Improves Short-Term Recognition Memory and Increases Neuroinflammation in a 3xTg AD Mouse Model,"Genes, brain, and behavior",2025,"3xTgAD mice, APOE, Alzheimer, fecal microbiota transplantation (FMT), microbiota, neuroinflammation",Experiment 3,Switzerland,Mus musculus,Cecum mucosa,UBERON:0000314,Response to transplant,EFO:0007043,Untreated Mice- Fecal Microbiota Transplant (Mice-FMT),Healthy donor (Young-FMT),"Healthy donor (Young-FMT) refers to a female 3xTgAD mice who received weekly FMT for 2 months from a 22-year-old age-related protection to AD, with no APOE gene-related risk (ε3/ε3), no cognitive complaints, male gender.",NA,NA,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.02,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Fig. 3C,13 February 2025,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of genera between the FMT recipient mice,decreased,"k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales",3379134|200930|68337|191393|2945020|248038;3379134|200940|3031449|213115|194924|872;1783272|201174|84998|1643822|1643826;3379134|976|200643|171549|171550|28138;1783272|1798710|1906119,Complete,Svetlana up
bsdb:39801363/4/1,39801363,randomized controlled trial,39801363,10.1111/gbb.70012,NA,"Chevalier C., Tournier B.B., Marizzoni M., Park R., Paquis A., Ceyzériat K., Badina A.M., Lathuiliere A., Saleri S., Cillis F., Cattaneo A., Millet P. , Frisoni G.B.",Fecal Microbiota Transplantation (FMT) From a Human at Low Risk for Alzheimer's Disease Improves Short-Term Recognition Memory and Increases Neuroinflammation in a 3xTg AD Mouse Model,"Genes, brain, and behavior",2025,"3xTgAD mice, APOE, Alzheimer, fecal microbiota transplantation (FMT), microbiota, neuroinflammation",Experiment 4,Switzerland,Mus musculus,Cecum mucosa,UBERON:0000314,Response to transplant,EFO:0007043,Alzheimer's disease(AD) patient (AD-FMT),Apolipoprotein E (APOEe2 allele) - APOEe2-FMT,"APOEe2 allele (APOEe2-FMT) refers to a female 3xTgAD mice who received weekly FMT for 2 months from a cognitively healthy 73-year-old with the protective APOEe2 allele with genetic-related protection to AD (APOEε2 carrier), associated with no cognitive decline diagnosed, no brain amyloidosis, a high level of education, male gender.",NA,NA,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 3D,13 February 2025,KateRasheed,"KateRasheed,WikiWorks,Tosin",Differential abundance of genera between the FMT recipient mice when compared with AD-FMT,increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes",3379134|200940|3031449|213115|194924|35832;1783272|1239|91061|186826|33958|2767887;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|186806|1730|290054,Complete,Svetlana up
bsdb:39801363/4/2,39801363,randomized controlled trial,39801363,10.1111/gbb.70012,NA,"Chevalier C., Tournier B.B., Marizzoni M., Park R., Paquis A., Ceyzériat K., Badina A.M., Lathuiliere A., Saleri S., Cillis F., Cattaneo A., Millet P. , Frisoni G.B.",Fecal Microbiota Transplantation (FMT) From a Human at Low Risk for Alzheimer's Disease Improves Short-Term Recognition Memory and Increases Neuroinflammation in a 3xTg AD Mouse Model,"Genes, brain, and behavior",2025,"3xTgAD mice, APOE, Alzheimer, fecal microbiota transplantation (FMT), microbiota, neuroinflammation",Experiment 4,Switzerland,Mus musculus,Cecum mucosa,UBERON:0000314,Response to transplant,EFO:0007043,Alzheimer's disease(AD) patient (AD-FMT),Apolipoprotein E (APOEe2 allele) - APOEe2-FMT,"APOEe2 allele (APOEe2-FMT) refers to a female 3xTgAD mice who received weekly FMT for 2 months from a cognitively healthy 73-year-old with the protective APOEe2 allele with genetic-related protection to AD (APOEε2 carrier), associated with no cognitive decline diagnosed, no brain amyloidosis, a high level of education, male gender.",NA,NA,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Fig. 3D,13 February 2025,KateRasheed,"KateRasheed,WikiWorks,Taofeecoh",Differential abundance of genera between the FMT recipient mice when compared with AD-FMT,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium A2,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",1783272|1239|186801|186802|216572|244127;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|216572|1892380;1783272|1239|186801|3085636|186803|397290;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|3068309;1783272|1239|186801|3085636|186803|297314;1783272|1239|186801|186802|216572|707003,Complete,Svetlana up
bsdb:39801363/5/1,39801363,randomized controlled trial,39801363,10.1111/gbb.70012,NA,"Chevalier C., Tournier B.B., Marizzoni M., Park R., Paquis A., Ceyzériat K., Badina A.M., Lathuiliere A., Saleri S., Cillis F., Cattaneo A., Millet P. , Frisoni G.B.",Fecal Microbiota Transplantation (FMT) From a Human at Low Risk for Alzheimer's Disease Improves Short-Term Recognition Memory and Increases Neuroinflammation in a 3xTg AD Mouse Model,"Genes, brain, and behavior",2025,"3xTgAD mice, APOE, Alzheimer, fecal microbiota transplantation (FMT), microbiota, neuroinflammation",Experiment 5,Switzerland,Mus musculus,Cecum mucosa,UBERON:0000314,Response to transplant,EFO:0007043,Alzheimer's disease(AD) patient (AD-FMT),Healthy donor (Young-FMT),"Healthy donor (Young-FMT) refers to a female 3xTgAD mice who received weekly FMT for 2 months from a 22-year-old age-related protection to AD, with no APOE gene-related risk (ε3/ε3), no cognitive complaints, male gender.",NA,NA,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 3D,13 February 2025,KateRasheed,"KateRasheed,WikiWorks,Tosin",Differential abundance of genera between the FMT recipient mice when compared with AD-FMT,increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819",3379134|200940|3031449|213115|194924|35832;1783272|1239|91061|186826|33958|2767887;3379134|976|200643|171549|2005473|1918540;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|216572|216851|1946507,Complete,Svetlana up
bsdb:39801363/5/2,39801363,randomized controlled trial,39801363,10.1111/gbb.70012,NA,"Chevalier C., Tournier B.B., Marizzoni M., Park R., Paquis A., Ceyzériat K., Badina A.M., Lathuiliere A., Saleri S., Cillis F., Cattaneo A., Millet P. , Frisoni G.B.",Fecal Microbiota Transplantation (FMT) From a Human at Low Risk for Alzheimer's Disease Improves Short-Term Recognition Memory and Increases Neuroinflammation in a 3xTg AD Mouse Model,"Genes, brain, and behavior",2025,"3xTgAD mice, APOE, Alzheimer, fecal microbiota transplantation (FMT), microbiota, neuroinflammation",Experiment 5,Switzerland,Mus musculus,Cecum mucosa,UBERON:0000314,Response to transplant,EFO:0007043,Alzheimer's disease(AD) patient (AD-FMT),Healthy donor (Young-FMT),"Healthy donor (Young-FMT) refers to a female 3xTgAD mice who received weekly FMT for 2 months from a 22-year-old age-related protection to AD, with no APOE gene-related risk (ε3/ε3), no cognitive complaints, male gender.",NA,NA,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Fig. 3D,13 February 2025,KateRasheed,"KateRasheed,WikiWorks",Differential abundance of genera between the FMT recipient mice when compared with AD-FMT,decreased,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,3379134|200940|3031449|213115|194924|872,Complete,Svetlana up
bsdb:39813205/1/1,39813205,laboratory experiment,39813205,https://doi.org/10.1371/journal.pone.0315374,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0315374,"Sacchettino L., Costanzo M., Veneruso I., D'Argenio V., Mayer M., Napolitano F. , d'Angelo D.",Altered microbiome and metabolome profiling in fearful companion dogs: An exploratory study,PloS one,2025,NA,Experiment 1,Italy,Canis lupus familiaris,Feces,UBERON:0001988,Mental or behavioural disorder,EFO:0000677,Healthy Control,Fearful Dogs,"Dogs exhibiting generalized fear, assessed through behavioral tests and owner-reported questionnaries.",8,8,1 month,16S,456,Illumina,raw counts,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3,22 February 2025,Akritishakya,"Akritishakya,Fiddyhamma",Significantly different taxa identified between case and control groups by EdgeR analysis,increased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,1783272|1239|526524|526525|2810280,Complete,Svetlana up
bsdb:39813205/1/2,39813205,laboratory experiment,39813205,https://doi.org/10.1371/journal.pone.0315374,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0315374,"Sacchettino L., Costanzo M., Veneruso I., D'Argenio V., Mayer M., Napolitano F. , d'Angelo D.",Altered microbiome and metabolome profiling in fearful companion dogs: An exploratory study,PloS one,2025,NA,Experiment 1,Italy,Canis lupus familiaris,Feces,UBERON:0001988,Mental or behavioural disorder,EFO:0000677,Healthy Control,Fearful Dogs,"Dogs exhibiting generalized fear, assessed through behavioral tests and owner-reported questionnaries.",8,8,1 month,16S,456,Illumina,raw counts,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3,7 March 2025,Fiddyhamma,Fiddyhamma,Significantly different taxa identified between case and control groups by EdgeR analysis,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea",3379134|1224|1236;1783272|1239|186801|3085636|186803|189330,Complete,Svetlana up
bsdb:39818212/1/1,39818212,time series / longitudinal observational,39818212,10.1016/j.cell.2024.12.011,NA,"Usyk M., Carlson L., Schlecht N.F., Sollecito C.C., Grassi E., Wiek F., Viswanathan S., Strickler H.D., Nucci-Sack A., Diaz A. , Burk R.D.",Cervicovaginal microbiome and natural history of Chlamydia trachomatis in adolescents and young women,Cell,2025,"Chlamydia trachomatis, adolescent and young women, bacterial vaginosis, cervicovaginal, longitudinal cohort analysis, microbial network and CT infection, microbial risk score, microbiome, miscarriage, molBV algorithm, molecular Nugent score, pelvic inflammatory disease, post-treatment CVM changes, prospective cohort study, reinfection and clinical sequelae, risk factors for CT acquisition",Experiment 1,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,Chlamydia trachomatis,NCBITAXON:813,Chlamydia trichomonas Controls (t0),Chlamydia trichomonas Cases (t0),Individuals diagnosed with Chlamydia trachomatis infection at the cross sectional visits (t0) identified by Gen-Probe APTIMA test.,373,187,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,"age,ethnic group",NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 4E,6 March 2025,MyleeeA,MyleeeA,Results of ANCOM analysis of differentially abundant genera associated with Chlamydia trichomonas Cases (t0) vs Chlamydia trichomonas Controls (t0).,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia",1783272|201174|1760|2037|2049|1654;1783272|1239|1737404|1737405|1570339|165779;1783272|201174|1760|2037|2049|28263;1783272|201174|84998|84999|1643824|1380;3379134|204428|204429|51291|809|810;1783272|201174|1760|85004|31953|2701;1783272|1239|91061|1385|539738|1378;1783272|201174|1760|2037|2049|2050;1783272|544448|31969|2085|2092|2093;1783272|1239|1737404|1737405|1570339|543311;3379134|976|200643|171549|171552|838;3384189|32066|203490|203491|1129771|168808,Complete,KateRasheed
bsdb:39818212/1/2,39818212,time series / longitudinal observational,39818212,10.1016/j.cell.2024.12.011,NA,"Usyk M., Carlson L., Schlecht N.F., Sollecito C.C., Grassi E., Wiek F., Viswanathan S., Strickler H.D., Nucci-Sack A., Diaz A. , Burk R.D.",Cervicovaginal microbiome and natural history of Chlamydia trachomatis in adolescents and young women,Cell,2025,"Chlamydia trachomatis, adolescent and young women, bacterial vaginosis, cervicovaginal, longitudinal cohort analysis, microbial network and CT infection, microbial risk score, microbiome, miscarriage, molBV algorithm, molecular Nugent score, pelvic inflammatory disease, post-treatment CVM changes, prospective cohort study, reinfection and clinical sequelae, risk factors for CT acquisition",Experiment 1,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,Chlamydia trachomatis,NCBITAXON:813,Chlamydia trichomonas Controls (t0),Chlamydia trichomonas Cases (t0),Individuals diagnosed with Chlamydia trachomatis infection at the cross sectional visits (t0) identified by Gen-Probe APTIMA test.,373,187,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,"age,ethnic group",NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 4E,6 March 2025,MyleeeA,MyleeeA,Results of ANCOM analysis of differentially abundant genera associated with Chlamydia trichomonas Cases (t0) vs Chlamydia trichomonas Controls (t0).,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|33958|1578,Complete,KateRasheed
bsdb:39818212/2/1,39818212,time series / longitudinal observational,39818212,10.1016/j.cell.2024.12.011,NA,"Usyk M., Carlson L., Schlecht N.F., Sollecito C.C., Grassi E., Wiek F., Viswanathan S., Strickler H.D., Nucci-Sack A., Diaz A. , Burk R.D.",Cervicovaginal microbiome and natural history of Chlamydia trachomatis in adolescents and young women,Cell,2025,"Chlamydia trachomatis, adolescent and young women, bacterial vaginosis, cervicovaginal, longitudinal cohort analysis, microbial network and CT infection, microbial risk score, microbiome, miscarriage, molBV algorithm, molecular Nugent score, pelvic inflammatory disease, post-treatment CVM changes, prospective cohort study, reinfection and clinical sequelae, risk factors for CT acquisition",Experiment 2,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,Chlamydia trachomatis,NCBITAXON:813,Chlamydia trichomonas Cases (t-1),Chlamydia trichomonas Cases (t0),Individuals diagnosed with Chlamydia trachomatis infection at the cross sectional visits (t0) identified by Gen-Probe APTIMA test,187,187,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,"age,ethnic group,time from diagnosis",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4G,6 March 2025,MyleeeA,MyleeeA,Results of ANCOM analysis of differentially abundant genera associated with Chlamydia trichomonas Cases (t0) vs Chlamydia trichomonas Cases (t-1).,increased,"k__Pseudomonadati|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",3379134|204428|204429|51291|809|810;1783272|201174|84998|84999|1643824|1380;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|186802|31979|1485,Complete,KateRasheed
bsdb:39818212/2/2,39818212,time series / longitudinal observational,39818212,10.1016/j.cell.2024.12.011,NA,"Usyk M., Carlson L., Schlecht N.F., Sollecito C.C., Grassi E., Wiek F., Viswanathan S., Strickler H.D., Nucci-Sack A., Diaz A. , Burk R.D.",Cervicovaginal microbiome and natural history of Chlamydia trachomatis in adolescents and young women,Cell,2025,"Chlamydia trachomatis, adolescent and young women, bacterial vaginosis, cervicovaginal, longitudinal cohort analysis, microbial network and CT infection, microbial risk score, microbiome, miscarriage, molBV algorithm, molecular Nugent score, pelvic inflammatory disease, post-treatment CVM changes, prospective cohort study, reinfection and clinical sequelae, risk factors for CT acquisition",Experiment 2,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,Chlamydia trachomatis,NCBITAXON:813,Chlamydia trichomonas Cases (t-1),Chlamydia trichomonas Cases (t0),Individuals diagnosed with Chlamydia trachomatis infection at the cross sectional visits (t0) identified by Gen-Probe APTIMA test,187,187,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,"age,ethnic group,time from diagnosis",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4G,6 March 2025,MyleeeA,MyleeeA,Results of ANCOM analysis of differentially abundant genera associated with Chlamydia trichomonas Cases (t0) vs Chlamydia trichomonas Cases (t-1).,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma",1783272|1239|91061|186826|33958|1578;1783272|544448|2790996|2790998|2129,Complete,KateRasheed
bsdb:39818212/3/1,39818212,time series / longitudinal observational,39818212,10.1016/j.cell.2024.12.011,NA,"Usyk M., Carlson L., Schlecht N.F., Sollecito C.C., Grassi E., Wiek F., Viswanathan S., Strickler H.D., Nucci-Sack A., Diaz A. , Burk R.D.",Cervicovaginal microbiome and natural history of Chlamydia trachomatis in adolescents and young women,Cell,2025,"Chlamydia trachomatis, adolescent and young women, bacterial vaginosis, cervicovaginal, longitudinal cohort analysis, microbial network and CT infection, microbial risk score, microbiome, miscarriage, molBV algorithm, molecular Nugent score, pelvic inflammatory disease, post-treatment CVM changes, prospective cohort study, reinfection and clinical sequelae, risk factors for CT acquisition",Experiment 3,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,Risk factor,EFO:0003919,Molecular Bacterial vaginosis (mBV B),Molecular Bacterial vaginosis (mBV A),"Cervicovaginal microbiome community state types (CSTs) were generated using VALENCIA.30 To incorporate CST definitions into our mBV analysis we dichotomized mBV-positive (i.e., molBV 7-10 increased risk for CT infection) participants into mBV-A subtype if they concurrently had CST-IVA and molBV 7-10.",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. S3A,6 March 2025,MyleeeA,"MyleeeA,Ese",Results of ANCOM analysis of differentially abundant genera associated with mBV-A and mBV-B groups.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",1783272|201174|1760|2037|2049|1654;1783272|201174|84998|1643822|1643826|447020;3379134|29547|3031852|213849|72294|194;3379134|976|117743|200644|49546|237;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|3085636|186803|437755;3379134|976|200643|171549|171551|836,Complete,KateRasheed
bsdb:39818212/3/2,39818212,time series / longitudinal observational,39818212,10.1016/j.cell.2024.12.011,NA,"Usyk M., Carlson L., Schlecht N.F., Sollecito C.C., Grassi E., Wiek F., Viswanathan S., Strickler H.D., Nucci-Sack A., Diaz A. , Burk R.D.",Cervicovaginal microbiome and natural history of Chlamydia trachomatis in adolescents and young women,Cell,2025,"Chlamydia trachomatis, adolescent and young women, bacterial vaginosis, cervicovaginal, longitudinal cohort analysis, microbial network and CT infection, microbial risk score, microbiome, miscarriage, molBV algorithm, molecular Nugent score, pelvic inflammatory disease, post-treatment CVM changes, prospective cohort study, reinfection and clinical sequelae, risk factors for CT acquisition",Experiment 3,United States of America,Homo sapiens,Uterine cervix,UBERON:0000002,Risk factor,EFO:0003919,Molecular Bacterial vaginosis (mBV B),Molecular Bacterial vaginosis (mBV A),"Cervicovaginal microbiome community state types (CSTs) were generated using VALENCIA.30 To incorporate CST definitions into our mBV analysis we dichotomized mBV-positive (i.e., molBV 7-10 increased risk for CT infection) participants into mBV-A subtype if they concurrently had CST-IVA and molBV 7-10.",NA,NA,NA,16S,4,Illumina,centered log-ratio,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. S3A,6 March 2025,MyleeeA,"MyleeeA,Ese",Results of ANCOM analysis of differentially abundant genera associated with mBV-A and mBV-B groups.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella",1783272|1239|91061|186826|186827|1375;1783272|1239|1737404|1737405|1570339|165779;1783272|201174|84998|84999|1643824|1380;1783272|201174|1760|85004|31953|2701;1783272|1239|91061|1385|539738|1378,Complete,KateRasheed
bsdb:39819634/1/1,39819634,"cross-sectional observational, not case-control",39819634,10.1186/s40168-024-01982-y,NA,"Berbers R.M., Paganelli F.L., van Montfrans J.M., Ellerbroek P.M., Viveen M.C., Rogers M.R.C., Salomons M., Schuurmans J., van Stigt Thans M., Vanmaris R.M.M., Brosens L.A.A., van der Wal M.M., Dalm V.A.S.H., van Hagen P.M., van de Ven A.A.J.M., Uh H.W., van Wijk F., Willems R.J.L. , Leavis H.L.","Gut microbial dysbiosis, IgA, and Enterococcus in common variable immunodeficiency with immune dysregulation",Microbiome,2025,"Common variable immunodeficiency (CVID), Gut microbiota, Immune dysregulation, Pathobionts",Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Common variable immunodeficiency,MONDO:0015517,Healthy Control (HC),Common Variable Immunodeficiency (CVID),Patients living with Common Variable Immunodeficiency.,48,93,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 5A and Supplementary Table 4,11 February 2025,Taofeecoh,"Taofeecoh,WikiWorks",Differentially abundant bacteria identified in CVID patients (n=93) vs Healthy Controls (n=48),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Caproiciproducens,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota",3379134|976|200643|171549|171552|1283313;1783272|1239|91061;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3082771|1738645;1783272|1239|186801;1783272|201174|84998|1643822|1643826|84111;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|186806;1783272|1239|186801|186802|216572|946234;3379134|1224|1236;1783272|1239|91061|186826|1300|1357;1783272|1239|186801|186802|216572|459786;3379134|1224|28216|80840|995019|577310;3379134|1224;1783272|1239|186801|3085636|186803|1769710;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|3085636|186803|1506577;1783272|1239|909932|1843489|31977|29465;1783272|1239,Complete,Svetlana up
bsdb:39819634/1/2,39819634,"cross-sectional observational, not case-control",39819634,10.1186/s40168-024-01982-y,NA,"Berbers R.M., Paganelli F.L., van Montfrans J.M., Ellerbroek P.M., Viveen M.C., Rogers M.R.C., Salomons M., Schuurmans J., van Stigt Thans M., Vanmaris R.M.M., Brosens L.A.A., van der Wal M.M., Dalm V.A.S.H., van Hagen P.M., van de Ven A.A.J.M., Uh H.W., van Wijk F., Willems R.J.L. , Leavis H.L.","Gut microbial dysbiosis, IgA, and Enterococcus in common variable immunodeficiency with immune dysregulation",Microbiome,2025,"Common variable immunodeficiency (CVID), Gut microbiota, Immune dysregulation, Pathobionts",Experiment 1,Netherlands,Homo sapiens,Feces,UBERON:0001988,Common variable immunodeficiency,MONDO:0015517,Healthy Control (HC),Common Variable Immunodeficiency (CVID),Patients living with Common Variable Immunodeficiency.,48,93,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 5A and Supplementary Table 4,11 February 2025,Taofeecoh,"Taofeecoh,WikiWorks",Differentially abundant bacteria identified in CVID patients (n=93) vs Healthy Controls (n=48),decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales",1783272|201174;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3082720|186804|1501226;1783272|1239|909932|909929,Complete,Svetlana up
bsdb:39819634/2/1,39819634,"cross-sectional observational, not case-control",39819634,10.1186/s40168-024-01982-y,NA,"Berbers R.M., Paganelli F.L., van Montfrans J.M., Ellerbroek P.M., Viveen M.C., Rogers M.R.C., Salomons M., Schuurmans J., van Stigt Thans M., Vanmaris R.M.M., Brosens L.A.A., van der Wal M.M., Dalm V.A.S.H., van Hagen P.M., van de Ven A.A.J.M., Uh H.W., van Wijk F., Willems R.J.L. , Leavis H.L.","Gut microbial dysbiosis, IgA, and Enterococcus in common variable immunodeficiency with immune dysregulation",Microbiome,2025,"Common variable immunodeficiency (CVID), Gut microbiota, Immune dysregulation, Pathobionts",Experiment 2,Netherlands,Homo sapiens,Feces,UBERON:0001988,Common variable immunodeficiency,MONDO:0015517,Healthy Control (HC),Common Variable Immunodeficiency (CVID-med),Patients living with Common Variable Immunodeficiency without use of antibiotics or immunosuppressive therapy 3 months prior to sampling.,48,50,3 months,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 5,11 February 2025,Taofeecoh,"Taofeecoh,WikiWorks",Differentially abundant bacteria identified in CVID-med patients (Common Variable Immunodeficiency without medications) (n=50) vs Healthy Controls (n=48),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Caproiciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|186801|186802|216572|244127;1783272|1239|186801|186802|3082771|1738645;1783272|1239|186801|186802|186806;1783272|1239|91061|186826|1300|1357;1783272|1239|186801|3085636|186803|1769710;1783272|1239|186801|3085636|186803|1506577;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:39819634/3/1,39819634,"cross-sectional observational, not case-control",39819634,10.1186/s40168-024-01982-y,NA,"Berbers R.M., Paganelli F.L., van Montfrans J.M., Ellerbroek P.M., Viveen M.C., Rogers M.R.C., Salomons M., Schuurmans J., van Stigt Thans M., Vanmaris R.M.M., Brosens L.A.A., van der Wal M.M., Dalm V.A.S.H., van Hagen P.M., van de Ven A.A.J.M., Uh H.W., van Wijk F., Willems R.J.L. , Leavis H.L.","Gut microbial dysbiosis, IgA, and Enterococcus in common variable immunodeficiency with immune dysregulation",Microbiome,2025,"Common variable immunodeficiency (CVID), Gut microbiota, Immune dysregulation, Pathobionts",Experiment 3,Netherlands,Homo sapiens,Feces,UBERON:0001988,Common variable immunodeficiency,MONDO:0015517,Common Variable Immunodeficiency with infections only (CVIDio),Common Variable Immunodeficiency with immune dysregulation (CVIDid),Patients living with Common Variable Immunodeficiency with Immune dysregulation.,51,42,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,Signature 1,Fig. 5B and Supplementary Table 6,12 February 2025,Taofeecoh,"Taofeecoh,WikiWorks",Differentially abundant bacteria identified in CVIDid patients (n=42) vs CVIDio (n=51),increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350,Complete,Svetlana up
bsdb:39819634/4/1,39819634,"cross-sectional observational, not case-control",39819634,10.1186/s40168-024-01982-y,NA,"Berbers R.M., Paganelli F.L., van Montfrans J.M., Ellerbroek P.M., Viveen M.C., Rogers M.R.C., Salomons M., Schuurmans J., van Stigt Thans M., Vanmaris R.M.M., Brosens L.A.A., van der Wal M.M., Dalm V.A.S.H., van Hagen P.M., van de Ven A.A.J.M., Uh H.W., van Wijk F., Willems R.J.L. , Leavis H.L.","Gut microbial dysbiosis, IgA, and Enterococcus in common variable immunodeficiency with immune dysregulation",Microbiome,2025,"Common variable immunodeficiency (CVID), Gut microbiota, Immune dysregulation, Pathobionts",Experiment 4,Netherlands,Homo sapiens,Feces,UBERON:0001988,Common variable immunodeficiency,MONDO:0015517,Common Variable Immunodeficiency with infections only without medication (CVIDio-med),Common Variable Immunodeficiency with immune dysregulation without medication (CVIDid-med),Patients living with Common Variable Immunodeficiency and Immune dysregulation without use of antibiotics or immunosuppressive therapy 3 months prior to sampling.,32,18,3 months,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,Signature 1,Supplementary Table 7,12 February 2025,Taofeecoh,"Taofeecoh,WikiWorks",Differentially abundant bacteria identified in CVID with immune dysregulation without medication use (CVIDid -med. n=18) versus CVID with infections only without medication use (CVIDio -med. n=32),increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,s__gut metagenome",1783272|1239|91061|186826|81852;1783272|1239|186801|186802|186807;3379134|1224|1236|135625|712;3379134|1224|28211|204441;3379134|1224|1236|135625;3379134|1224|28211;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|216572|244127;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|135625|712|724;749906,Complete,Svetlana up
bsdb:39819634/5/1,39819634,"cross-sectional observational, not case-control",39819634,10.1186/s40168-024-01982-y,NA,"Berbers R.M., Paganelli F.L., van Montfrans J.M., Ellerbroek P.M., Viveen M.C., Rogers M.R.C., Salomons M., Schuurmans J., van Stigt Thans M., Vanmaris R.M.M., Brosens L.A.A., van der Wal M.M., Dalm V.A.S.H., van Hagen P.M., van de Ven A.A.J.M., Uh H.W., van Wijk F., Willems R.J.L. , Leavis H.L.","Gut microbial dysbiosis, IgA, and Enterococcus in common variable immunodeficiency with immune dysregulation",Microbiome,2025,"Common variable immunodeficiency (CVID), Gut microbiota, Immune dysregulation, Pathobionts",Experiment 5,Netherlands,Homo sapiens,Feces,UBERON:0001988,Common variable immunodeficiency,MONDO:0015517,Common Variable Immunodeficiency with Immunoglobulin A > 0.1g/L (CVID+IgA),Common Variable Immunodeficiency with Immunoglobulin A < 0.1g/L (CVID-IgA),Patients living with CVID with IgA <0.1 g/L,53,40,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,Signature 1,Supplementary Table 8,12 February 2025,Taofeecoh,"Taofeecoh,WikiWorks",Differentially abundant bacteria identified in CVID with Immunoglobulin A < 0.1g/L  (CVID-IgA n=40) versus CVID with Immunoglobulin A > 0.1g/L  (CVID+IgA n=53),increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350,Complete,Svetlana up
bsdb:39819634/6/1,39819634,"cross-sectional observational, not case-control",39819634,10.1186/s40168-024-01982-y,NA,"Berbers R.M., Paganelli F.L., van Montfrans J.M., Ellerbroek P.M., Viveen M.C., Rogers M.R.C., Salomons M., Schuurmans J., van Stigt Thans M., Vanmaris R.M.M., Brosens L.A.A., van der Wal M.M., Dalm V.A.S.H., van Hagen P.M., van de Ven A.A.J.M., Uh H.W., van Wijk F., Willems R.J.L. , Leavis H.L.","Gut microbial dysbiosis, IgA, and Enterococcus in common variable immunodeficiency with immune dysregulation",Microbiome,2025,"Common variable immunodeficiency (CVID), Gut microbiota, Immune dysregulation, Pathobionts",Experiment 6,Netherlands,Homo sapiens,Feces,UBERON:0001988,Common variable immunodeficiency,MONDO:0015517,Common Variable Immunodeficiency with Immunoglobulin A > 0.1g/L without medication use (CVID+IgA-med),Common Variable Immunodeficiency with Immunoglobulin A < 0.1g/L without medication use (CVID-IgA-med),Patients living with Common Variable Immunodeficiency (CVID) with Immunoglobulin A (IgA) <0.1 g/L without use of antibiotics or immunosuppressive therapy 3 months prior to sampling.,29,21,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,unchanged,NA,Signature 1,Supplementary Table 9,12 February 2025,Taofeecoh,"Taofeecoh,WikiWorks",Differentially abundant bacteria identified in CVID with Immunoglobulin A < 0.1g/L without medication use (CVID-IgA-med n=21) versus CVID with Immunoglobulin A > 0.1g/L  without medication use (CVID+IgA-med n=29).,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales",1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|81852;3379134|1224|1236|135625|712;3379134|1224|1236|135625,Complete,Svetlana up
bsdb:39819634/7/1,39819634,"cross-sectional observational, not case-control",39819634,10.1186/s40168-024-01982-y,NA,"Berbers R.M., Paganelli F.L., van Montfrans J.M., Ellerbroek P.M., Viveen M.C., Rogers M.R.C., Salomons M., Schuurmans J., van Stigt Thans M., Vanmaris R.M.M., Brosens L.A.A., van der Wal M.M., Dalm V.A.S.H., van Hagen P.M., van de Ven A.A.J.M., Uh H.W., van Wijk F., Willems R.J.L. , Leavis H.L.","Gut microbial dysbiosis, IgA, and Enterococcus in common variable immunodeficiency with immune dysregulation",Microbiome,2025,"Common variable immunodeficiency (CVID), Gut microbiota, Immune dysregulation, Pathobionts",Experiment 7,Netherlands,Homo sapiens,Feces,UBERON:0001988,Common variable immunodeficiency,MONDO:0015517,Healthy Control (HC) - Age confounder,Common Variable Immunodeficiency (CVID) -Age confounder,Patients living with Common Variable Immunodeficiency after controlling for age.,48,93,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,"age,sex",age,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 4,10 April 2025,Taofeecoh,"Taofeecoh,KateRasheed",Differentially abundant bacteria between healthy controls and CVID after controlling for age,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,Svetlana up
bsdb:39819634/7/2,39819634,"cross-sectional observational, not case-control",39819634,10.1186/s40168-024-01982-y,NA,"Berbers R.M., Paganelli F.L., van Montfrans J.M., Ellerbroek P.M., Viveen M.C., Rogers M.R.C., Salomons M., Schuurmans J., van Stigt Thans M., Vanmaris R.M.M., Brosens L.A.A., van der Wal M.M., Dalm V.A.S.H., van Hagen P.M., van de Ven A.A.J.M., Uh H.W., van Wijk F., Willems R.J.L. , Leavis H.L.","Gut microbial dysbiosis, IgA, and Enterococcus in common variable immunodeficiency with immune dysregulation",Microbiome,2025,"Common variable immunodeficiency (CVID), Gut microbiota, Immune dysregulation, Pathobionts",Experiment 7,Netherlands,Homo sapiens,Feces,UBERON:0001988,Common variable immunodeficiency,MONDO:0015517,Healthy Control (HC) - Age confounder,Common Variable Immunodeficiency (CVID) -Age confounder,Patients living with Common Variable Immunodeficiency after controlling for age.,48,93,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,"age,sex",age,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 4,11 April 2025,KateRasheed,KateRasheed,Differentially abundant bacteria between healthy controls and CVID after controlling for age,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia",1783272|201174|1760|85004;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|201174;1783272|1239|186801|3082720|186804|1501226,Complete,NA
bsdb:39819634/8/1,39819634,"cross-sectional observational, not case-control",39819634,10.1186/s40168-024-01982-y,NA,"Berbers R.M., Paganelli F.L., van Montfrans J.M., Ellerbroek P.M., Viveen M.C., Rogers M.R.C., Salomons M., Schuurmans J., van Stigt Thans M., Vanmaris R.M.M., Brosens L.A.A., van der Wal M.M., Dalm V.A.S.H., van Hagen P.M., van de Ven A.A.J.M., Uh H.W., van Wijk F., Willems R.J.L. , Leavis H.L.","Gut microbial dysbiosis, IgA, and Enterococcus in common variable immunodeficiency with immune dysregulation",Microbiome,2025,"Common variable immunodeficiency (CVID), Gut microbiota, Immune dysregulation, Pathobionts",Experiment 8,Netherlands,Homo sapiens,Feces,UBERON:0001988,Common variable immunodeficiency,MONDO:0015517,Healthy Control (HC) - Age confounder,Common Variable Immunodeficiency (CVID) -Age confounder,Patients living with Common Variable Immunodeficiency without use of antibiotics or immunosuppressive therapy 3 months prior to sampling; after controlling for age.,48,50,3 months,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,"age,sex",age,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 5,10 April 2025,Taofeecoh,"Taofeecoh,KateRasheed",Differentially abundant bacteria between healthy controls and CVID (without use of antibiotics or immunosuppressive therapy 3 months prior to sampling) after controlling for age,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Caproiciproducens,1783272|1239|186801|186802|3082771|1738645,Complete,Svetlana up
bsdb:39824829/1/1,39824829,"cross-sectional observational, not case-control",39824829,10.1038/s41467-025-56014-6,NA,"Jeyaram K., Lahti L., Tims S., Heilig H.G.H.J., van Gelder A.H., de Vos W.M., Smidt H. , Zoetendal E.G.",Fermented foods affect the seasonal stability of gut bacteria in an Indian rural population,Nature communications,2025,NA,Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Phenotype,EFO:0000651,European Individuals,Indian Individuals,"This group of individuals represents a traditional Indian agrarian population, which exhibits a Prevotella-driven gut microbiota who are long-term consumers of fermented foods.",78,78,6 months,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,decreased,NA,NA,NA,NA,Signature 1,Fig. 3B,17 March 2025,Joiejoie,Joiejoie,The overall relative abundance distributions of Prevotella melaninogenica.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,3379134|976|200643|171549|171552|838|28132,Complete,NA
bsdb:39824829/1/2,39824829,"cross-sectional observational, not case-control",39824829,10.1038/s41467-025-56014-6,NA,"Jeyaram K., Lahti L., Tims S., Heilig H.G.H.J., van Gelder A.H., de Vos W.M., Smidt H. , Zoetendal E.G.",Fermented foods affect the seasonal stability of gut bacteria in an Indian rural population,Nature communications,2025,NA,Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Phenotype,EFO:0000651,European Individuals,Indian Individuals,"This group of individuals represents a traditional Indian agrarian population, which exhibits a Prevotella-driven gut microbiota who are long-term consumers of fermented foods.",78,78,6 months,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,decreased,NA,NA,NA,NA,Signature 2,Fig. 3B,17 March 2025,Joiejoie,Joiejoie,The overall relative abundance and distributions of Bifidobacterium,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,NA
bsdb:39824829/2/1,39824829,"cross-sectional observational, not case-control",39824829,10.1038/s41467-025-56014-6,NA,"Jeyaram K., Lahti L., Tims S., Heilig H.G.H.J., van Gelder A.H., de Vos W.M., Smidt H. , Zoetendal E.G.",Fermented foods affect the seasonal stability of gut bacteria in an Indian rural population,Nature communications,2025,NA,Experiment 2,India,Homo sapiens,Feces,UBERON:0001988,Phenotype,EFO:0000651,Group A ( never consumed Hawaijar and Dahi ),"Groups B (consumed both Hawaijar and Dahi), C (consumed Hawaijar, not Dahi), and D (consumed Dahi, not Hawaijar)","This group consists of Individuals with a long-term dietary habit of consuming fermented foods (Dahi and/or Hawaijar) for at least 10 years, with a minimum frequency of 3 times per week.",20,58,6 months,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,decreased,NA,NA,NA,NA,Signature 1,Fig. 7A,17 March 2025,Joiejoie,Joiejoie,Diet alters the taxa's relative abundance on average with respect to the control diet (Group-A).,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium mitsuokai,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus",1783272|1239|526524|526525|2810280|135858|100886;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|2005525|195950;3379134|976|200643|171549|1853231|283168|28118,Complete,NA
bsdb:39824829/2/2,39824829,"cross-sectional observational, not case-control",39824829,10.1038/s41467-025-56014-6,NA,"Jeyaram K., Lahti L., Tims S., Heilig H.G.H.J., van Gelder A.H., de Vos W.M., Smidt H. , Zoetendal E.G.",Fermented foods affect the seasonal stability of gut bacteria in an Indian rural population,Nature communications,2025,NA,Experiment 2,India,Homo sapiens,Feces,UBERON:0001988,Phenotype,EFO:0000651,Group A ( never consumed Hawaijar and Dahi ),"Groups B (consumed both Hawaijar and Dahi), C (consumed Hawaijar, not Dahi), and D (consumed Dahi, not Hawaijar)","This group consists of Individuals with a long-term dietary habit of consuming fermented foods (Dahi and/or Hawaijar) for at least 10 years, with a minimum frequency of 3 times per week.",20,58,6 months,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,decreased,NA,NA,NA,NA,Signature 2,Fig. 7A,17 March 2025,Joiejoie,Joiejoie,Diet alters the taxa's relative abundance on average with respect to the control diet (Group-A).,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,3379134|976|200643|171549|171552|1283313|76122,Complete,NA
bsdb:39824829/3/1,39824829,"cross-sectional observational, not case-control",39824829,10.1038/s41467-025-56014-6,NA,"Jeyaram K., Lahti L., Tims S., Heilig H.G.H.J., van Gelder A.H., de Vos W.M., Smidt H. , Zoetendal E.G.",Fermented foods affect the seasonal stability of gut bacteria in an Indian rural population,Nature communications,2025,NA,Experiment 3,India,Homo sapiens,Feces,UBERON:0001988,Phenotype,EFO:0000651,Group A (never consumed Hawaijar and Dahi),"Groups B (consumed both Hawaijar and Dahi), C (consumed Hawaijar, not Dahi), and D (consumed Dahi, not Hawaijar)","This group consists of Individuals with a long-term dietary habit of consuming fermented foods (Dahi and/or Hawaijar) for at least 10 years, with a minimum frequency of 3 times per week.",20,58,6 months,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Fig. 7B,10 February 2025,Joiejoie,"Joiejoie,WikiWorks","Gut bacteria with significant seasonal effects on their relative abundance, compared to autumn, after controlling for diet and subject effects.",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella oralis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus equinus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter ruminicola,k__Pseudomonadati|p__Bacteroidota|s__uncultured Bacteroidota bacterium",1783272|1239|91061|186826|186827|1375;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171552|1283313|76122;1783272|1239|186801|186802|186806|264995;3379134|976|200643|171549|815|816|329854;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|46506;3379134|976|200643|171549|815|816|820;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|91061|186826|186828|117563;3379134|976|200643|171549|171552|2974257|28134;1783272|1239|91061|186826|33958|1578|1596;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|909656|821;3379134|1224|1236|91347|1903411|613;1783272|1239|91061|186826|1300|1301|1335;3379134|1224|28216|80840|995019|40544|40545;3379134|976|200643|171549|2005525|195950;1783272|1239|91061|186826|33958|46255;3379134|976|200643|171549|171552|558436|839;3379134|976|152509,Complete,NA
bsdb:39824829/4/1,39824829,"cross-sectional observational, not case-control",39824829,10.1038/s41467-025-56014-6,NA,"Jeyaram K., Lahti L., Tims S., Heilig H.G.H.J., van Gelder A.H., de Vos W.M., Smidt H. , Zoetendal E.G.",Fermented foods affect the seasonal stability of gut bacteria in an Indian rural population,Nature communications,2025,NA,Experiment 4,India,Homo sapiens,Feces,UBERON:0001988,Phenotype,EFO:0000651,European Subjects,Indian Subjects,"This group consists of Indian agrarian individuals who differed in their intake of fermented milk and soybean products, with seasonal sampling during hot-humid summer, autumn, and dry winter.",76,76,6 months,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Fig. S3,10 February 2025,Joiejoie,"Joiejoie,WikiWorks",The abundance distribution of gut microbiota taxa significantly differing between Indian and European subjects,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|91061|186826|33958|2767887|1624;1783272|1239|909932|909929|1843491|158846|158847;1783272|1239|909932|1843489|31977|906|907;1783272|1239|909932|1843489|31977|29465,Complete,NA
bsdb:39824829/4/2,39824829,"cross-sectional observational, not case-control",39824829,10.1038/s41467-025-56014-6,NA,"Jeyaram K., Lahti L., Tims S., Heilig H.G.H.J., van Gelder A.H., de Vos W.M., Smidt H. , Zoetendal E.G.",Fermented foods affect the seasonal stability of gut bacteria in an Indian rural population,Nature communications,2025,NA,Experiment 4,India,Homo sapiens,Feces,UBERON:0001988,Phenotype,EFO:0000651,European Subjects,Indian Subjects,"This group consists of Indian agrarian individuals who differed in their intake of fermented milk and soybean products, with seasonal sampling during hot-humid summer, autumn, and dry winter.",76,76,6 months,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Fig. S3,19 March 2025,Joiejoie,Joiejoie,The abundance distribution of gut microbiota taxa significantly differing between Indian and European subjects,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Thermoclostridium|s__Thermoclostridium stercorarium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii",1783272|1239|186801|3085636|186803|207244|105841;1783272|1239|186801|186802|216572|2304691|1510;1783272|1239|186801|3085636|186803|2569097|39488,Complete,NA
bsdb:39824829/5/1,39824829,"cross-sectional observational, not case-control",39824829,10.1038/s41467-025-56014-6,NA,"Jeyaram K., Lahti L., Tims S., Heilig H.G.H.J., van Gelder A.H., de Vos W.M., Smidt H. , Zoetendal E.G.",Fermented foods affect the seasonal stability of gut bacteria in an Indian rural population,Nature communications,2025,NA,Experiment 5,India,Homo sapiens,Feces,UBERON:0001988,Phenotype,EFO:0000651,Group-A (not consumed Dahi and Hawaijar),"Group-B ( consumed Dahi and Hawaijar),  Group-C ( consumed Hawaijar not Dahi), and Group-D ( consumed Dahi not Hawaijar).","This group includes Individuals in Groups B, C, and D who consumed fermented foods, with Group-B consuming both Dahi and Hawaijar, Group-C consuming only Hawaijar, and Group-D consuming only Dahi.",58,156,6 months,16S,NA,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Fig. S7A,19 March 2025,Joiejoie,Joiejoie,Long-term fermented food consumption affects Bacillus load in fecal samples across different diet groups.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,1783272|1239|91061|1385|186817|1386,Complete,NA
bsdb:39824829/6/1,39824829,"cross-sectional observational, not case-control",39824829,10.1038/s41467-025-56014-6,NA,"Jeyaram K., Lahti L., Tims S., Heilig H.G.H.J., van Gelder A.H., de Vos W.M., Smidt H. , Zoetendal E.G.",Fermented foods affect the seasonal stability of gut bacteria in an Indian rural population,Nature communications,2025,NA,Experiment 6,India,Homo sapiens,Feces,UBERON:0001988,Phenotype,EFO:0000651,Cluster-B/R,Cluster-P,"This group includes a Prevotella-driven gut microbiota cluster characterized by a significantly higher abundance of Prevotella melaninogenica, Prevotella tannerae, Prevotella oralis and Prevotella ruminicola.",97,117,6 months,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table S2,19 March 2025,Joiejoie,Joiejoie,The absolute abundance of gut bacterial taxa distinguishing Cluster-P (Prevotella-driven) and Cluster-B/R (Bifidobacterium/Ruminococcus-driven).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella oralis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter ruminicola",3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552|1283313|76122;3379134|976|200643|171549|171552|2974257|28134;3379134|976|200643|171549|171552|558436|839,Complete,NA
bsdb:39824829/6/2,39824829,"cross-sectional observational, not case-control",39824829,10.1038/s41467-025-56014-6,NA,"Jeyaram K., Lahti L., Tims S., Heilig H.G.H.J., van Gelder A.H., de Vos W.M., Smidt H. , Zoetendal E.G.",Fermented foods affect the seasonal stability of gut bacteria in an Indian rural population,Nature communications,2025,NA,Experiment 6,India,Homo sapiens,Feces,UBERON:0001988,Phenotype,EFO:0000651,Cluster-B/R,Cluster-P,"This group includes a Prevotella-driven gut microbiota cluster characterized by a significantly higher abundance of Prevotella melaninogenica, Prevotella tannerae, Prevotella oralis and Prevotella ruminicola.",97,117,6 months,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex","age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table S2,19 March 2025,Joiejoie,Joiejoie,The absolute abundance of gut bacterial taxa distinguishing Cluster-P (Prevotella-driven) and Cluster-B/R (Bifidobacterium/Ruminococcus-driven).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia|s__Marvinbryantia formatexigens,k__Viridiplantae|p__Streptophyta|c__Ginkgoopsida|o__Ginkgoales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum",1783272|1239|186801|3085636|186803|207244|105841;1783272|1239|186801|3085636|186803|248744|168384;33090|35493|29811|3308;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|2941495|1512,Complete,NA
bsdb:39825285/1/1,39825285,case-control,39825285,10.1186/s12887-024-05383-w,https://bmcpediatr.biomedcentral.com/articles/10.1186/s12887-024-05383-w,"Gong S., Yu Z., Ding Y., Wang Y., Li X. , Gu S.",Characteristics of functional constipation and analysis of intestinal microbiota in children aged 0-4 in Zunyi region,BMC pediatrics,2025,"Children, Functional constipation, Gut microbiota, Rome IV criteria, Zunyi",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Control group (CG),Functional constipation group (FCG),Individuals who have been diagnosed with the functional constipation(FCG). Functional constipation (FC) is a common pediatric gastrointestinal disorder causing infrequent and dry stools.,26,29,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,region,sex",NA,NA,increased,increased,decreased,NA,increased,Signature 1,Fig 7&8,19 March 2025,Aiyshaaaa,Aiyshaaaa,Differences in relative abundance of species at the phylum and genus  level between two groups,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum",1783272|1239|186801|3085636|186803|1766253;3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|186803|207244;1783272|1239;3379134|976|200643|171549|815|816;3379134|976;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|216572|216851;3379134|1224|28216|80840|995019|577310;3379134|1224;1783272|1239|186801|186802|216572|292632;3379134|74201;1783272|1239|186801|186802|31979|1485|1522,Complete,Svetlana up
bsdb:39825285/1/3,39825285,case-control,39825285,10.1186/s12887-024-05383-w,https://bmcpediatr.biomedcentral.com/articles/10.1186/s12887-024-05383-w,"Gong S., Yu Z., Ding Y., Wang Y., Li X. , Gu S.",Characteristics of functional constipation and analysis of intestinal microbiota in children aged 0-4 in Zunyi region,BMC pediatrics,2025,"Children, Functional constipation, Gut microbiota, Rome IV criteria, Zunyi",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Control group (CG),Functional constipation group (FCG),Individuals who have been diagnosed with the functional constipation(FCG). Functional constipation (FC) is a common pediatric gastrointestinal disorder causing infrequent and dry stools.,26,29,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,region,sex",NA,NA,increased,increased,decreased,NA,increased,Signature 3,Fig 7&8,19 March 2025,Aiyshaaaa,Aiyshaaaa,Differences in relative abundance of species at the phylum and genus level between two groups,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Actinomycetota",1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|2569097|39488;1783272|201174,Complete,Svetlana up
bsdb:39825285/2/1,39825285,case-control,39825285,10.1186/s12887-024-05383-w,https://bmcpediatr.biomedcentral.com/articles/10.1186/s12887-024-05383-w,"Gong S., Yu Z., Ding Y., Wang Y., Li X. , Gu S.",Characteristics of functional constipation and analysis of intestinal microbiota in children aged 0-4 in Zunyi region,BMC pediatrics,2025,"Children, Functional constipation, Gut microbiota, Rome IV criteria, Zunyi",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Control group (CG),Functional constipation group (FCG),Individuals who have been diagnosed with the functional constipation(FCG). Functional constipation (FC) is a common pediatric gastrointestinal disorder causing infrequent and dry stools.,26,29,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"age,region,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 9,19 March 2025,Aiyshaaaa,Aiyshaaaa,"LEfSe multi-level species difference discriminant analysis between two groups in Phylum,Class,Order,Family and Genus level",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;1783272|1239|91061;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976;1783272|1239|186801;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;3379134|1224|1236;1783272|1239|91061|186826;1783272|1239|186801|186802|216572;3379134|1224;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201,Complete,Svetlana up
bsdb:39825285/2/2,39825285,case-control,39825285,10.1186/s12887-024-05383-w,https://bmcpediatr.biomedcentral.com/articles/10.1186/s12887-024-05383-w,"Gong S., Yu Z., Ding Y., Wang Y., Li X. , Gu S.",Characteristics of functional constipation and analysis of intestinal microbiota in children aged 0-4 in Zunyi region,BMC pediatrics,2025,"Children, Functional constipation, Gut microbiota, Rome IV criteria, Zunyi",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Control group (CG),Functional constipation group (FCG),Individuals who have been diagnosed with the functional constipation(FCG). Functional constipation (FC) is a common pediatric gastrointestinal disorder causing infrequent and dry stools.,26,29,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"age,region,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 9,19 March 2025,Aiyshaaaa,Aiyshaaaa,"LEfSe multi-level species difference discriminant analysis between two groups in Phylum,Class,Order,Family and Genus level",decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia",1783272|201174;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85007|1653;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826;3379134|1224|1236|135625|712;1783272|201174|84992,Complete,Svetlana up
bsdb:39826123/1/1,39826123,"cross-sectional observational, not case-control",39826123,10.1016/j.celrep.2025.115252,NA,"Huang K.D., Müller M., Sivapornnukul P., Bielecka A.A., Amend L., Tawk C., Bruns A., Lesker T.R., Hahn A. , Strowig T.",Dietary selective effects manifest in the human gut microbiota from species composition to strain genetic makeup,Cell reports,2025,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Vegan,Omnivore,Omnivore refers to individuals regularly consuming a mixed diet of meat and meat products of ≥170 g/day).,33,28,NA,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.25,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 3A,17 March 2025,KateRasheed,KateRasheed,A panel of species that were differentially abundant in one diet type compared to the other.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. MSK.21.1,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF20-17LB,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium OF09-6,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium OM04-12BH,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. AF41-9",1783272|1239|186801|3085636|186803|572511|2742763;1783272|1239|186801|2044939;1783272|1239|186801|186802|31979|1485|2292205;1783272|1239|186801|3085636|186803|33042|33043;1783272|1239|186801|186802|186806|1730|39490;1783272|1239|186801|3085636|186803|1898203;1783272|1239|186801|3085636|186803|2293831;1783272|1239|186801|3085636|186803|2292272;1783272|1239|186801|186802|216572|1263|40519;1783272|1239|186801|186802|216572|1263|2292069,Complete,KateRasheed
bsdb:39826123/1/2,39826123,"cross-sectional observational, not case-control",39826123,10.1016/j.celrep.2025.115252,NA,"Huang K.D., Müller M., Sivapornnukul P., Bielecka A.A., Amend L., Tawk C., Bruns A., Lesker T.R., Hahn A. , Strowig T.",Dietary selective effects manifest in the human gut microbiota from species composition to strain genetic makeup,Cell reports,2025,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Vegan,Omnivore,Omnivore refers to individuals regularly consuming a mixed diet of meat and meat products of ≥170 g/day).,33,28,NA,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.25,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 3A,17 March 2025,KateRasheed,KateRasheed,A panel of species that were differentially abundant in one diet type compared to the other.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes inops,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister histaminiformans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. An250,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Candidatus Borkfalkia|s__Candidatus Borkfalkia ceftriaxoniphila,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Pseudobutyricicoccus|s__Candidatus Pseudobutyricicoccus lothianensis,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium phoceensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter|s__Dysosmobacter welbionis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Evtepia|s__Evtepia gabavorous,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter glycyrrhizinilyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis|s__Merdimmobilis hominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris",3379134|976|200643|171549|171550|239759|1501391;1783272|1239|909932|1843489|31977|39948|209880;1783272|1239|186801|186802|3082771|1924093|1965604;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|3085636|186803|572511|871665;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|3082768|990719|2508948|2508949;1783272|1239|186801|2721117|2721145;1783272|1239|186801|2044939;1783272|1239|186801|186802|31979|1898204;1783272|1239|186801|186802|1898207;1783272|1239|186801|186802|31979|1485|1650661;1783272|1239|186801|186802|216572|2591381|2093857;1783272|1239|186801|186802|2211178|2211183;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|91061|186826|1300|1357|1358;1783272|1239|186801|3085636|186803|2316020|342942;1783272|1239|186801|186802|216572|3028852|2897707;3379134|976|200643|171549|1853231|283168|28118;1783272|1239|186801|186802|216572|2485925;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|186801|3085636|186803|2316020|46228,Complete,KateRasheed
bsdb:39826123/2/1,39826123,"cross-sectional observational, not case-control",39826123,10.1016/j.celrep.2025.115252,NA,"Huang K.D., Müller M., Sivapornnukul P., Bielecka A.A., Amend L., Tawk C., Bruns A., Lesker T.R., Hahn A. , Strowig T.",Dietary selective effects manifest in the human gut microbiota from species composition to strain genetic makeup,Cell reports,2025,NA,Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Vegan,Flexitarian,Flexitarian refers to individuals maintaining a plant-based diet with an occasional consumption of meat and meat products of ≤50 g/day,33,31,NA,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.25,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 3A,17 March 2025,KateRasheed,KateRasheed,A panel of species that were differentially abundant in one diet type compared to the other.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. An250,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Avimonas|s__Candidatus Avimonas narfae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Candidatus Borkfalkia|s__Candidatus Borkfalkia ceftriaxoniphila,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium phoceensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter|s__Dysosmobacter welbionis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Evtepia|s__Evtepia gabavorous,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania filiformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. An138,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter glycyrrhizinilyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis|s__Merdimmobilis hominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus",3379134|976|200643|171549|171550|239759|328813;1783272|1239|186801|186802|3082771|1924093|1965604;1783272|1239|186801|186802|216572|244127|169435;1783272|1239|186801|3085636|186803|572511|871665;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|2720801|2720820;1783272|1239|186801|3082768|990719|2508948|2508949;1783272|1239|186801|2044939;1783272|1239|186801|186802|1898207;1783272|1239|186801|186802|31979|1485|1650661;1783272|1239|186801|186802|216572|2591381|2093857;1783272|1239|186801|186802|2211178|2211183;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|526524|526525|128827|61170|61171;1783272|1239|186801|3085636|186803|1506553|1965560;1783272|1239|186801|3085636|186803|1898203;1783272|1239|91061|186826|1300|1357|1358;1783272|1239|186801|3085636|186803|2316020|342942;1783272|1239|186801|186802|216572|3028852|2897707;3379134|976|200643|171549|171552|577309|454154;1783272|1239|91061|186826|1300|1301|1308,Complete,KateRasheed
bsdb:39826123/2/2,39826123,"cross-sectional observational, not case-control",39826123,10.1016/j.celrep.2025.115252,NA,"Huang K.D., Müller M., Sivapornnukul P., Bielecka A.A., Amend L., Tawk C., Bruns A., Lesker T.R., Hahn A. , Strowig T.",Dietary selective effects manifest in the human gut microbiota from species composition to strain genetic makeup,Cell reports,2025,NA,Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Vegan,Flexitarian,Flexitarian refers to individuals maintaining a plant-based diet with an occasional consumption of meat and meat products of ≤50 g/day,33,31,NA,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.25,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 3A,17 March 2025,KateRasheed,KateRasheed,A panel of species that were differentially abundant in one diet type compared to the other.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AM33-3,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella sp. GAM18,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. AF41-9",1783272|1239|186801|2044939;1783272|1239|186801|186802|31979|1485|2292304;1783272|1239|186801|186802|186806|1730|39490;1783272|1239|186801|3085636|186803|1898203;1783272|201174|84998|84999|1643824|133925|2109685;1783272|1239|186801|186802|216572|2485925;1783272|1239|186801|186802|216572|1263|2292069,Complete,KateRasheed
bsdb:39826123/3/1,39826123,"cross-sectional observational, not case-control",39826123,10.1016/j.celrep.2025.115252,NA,"Huang K.D., Müller M., Sivapornnukul P., Bielecka A.A., Amend L., Tawk C., Bruns A., Lesker T.R., Hahn A. , Strowig T.",Dietary selective effects manifest in the human gut microbiota from species composition to strain genetic makeup,Cell reports,2025,NA,Experiment 3,Germany,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Flexitarian,Omnivore,Omnivore refers to individuals regularly consuming a mixed diet of meat and meat products of ≥170 g/day).,31,28,NA,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.25,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 3A,17 March 2025,KateRasheed,KateRasheed,A panel of species that were differentially abundant in one diet type compared to the other.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium",1783272|1239|186801|2044939;1783272|1239|526524|526525|128827|2049044,Complete,KateRasheed
bsdb:39826123/3/2,39826123,"cross-sectional observational, not case-control",39826123,10.1016/j.celrep.2025.115252,NA,"Huang K.D., Müller M., Sivapornnukul P., Bielecka A.A., Amend L., Tawk C., Bruns A., Lesker T.R., Hahn A. , Strowig T.",Dietary selective effects manifest in the human gut microbiota from species composition to strain genetic makeup,Cell reports,2025,NA,Experiment 3,Germany,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Flexitarian,Omnivore,Omnivore refers to individuals regularly consuming a mixed diet of meat and meat products of ≥170 g/day).,31,28,NA,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.25,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 3A,17 March 2025,KateRasheed,KateRasheed,A panel of species that were differentially abundant in one diet type compared to the other.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium",1783272|1239|186801|2044939;1783272|1239|186801|3085636|186803|1898203,Complete,KateRasheed
bsdb:39826123/4/1,39826123,"cross-sectional observational, not case-control",39826123,10.1016/j.celrep.2025.115252,NA,"Huang K.D., Müller M., Sivapornnukul P., Bielecka A.A., Amend L., Tawk C., Bruns A., Lesker T.R., Hahn A. , Strowig T.",Dietary selective effects manifest in the human gut microbiota from species composition to strain genetic makeup,Cell reports,2025,NA,Experiment 4,Germany,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Vegan merged dataset (FrancescaDF_2019 + ShettySA_2022 + this study),Omnivore merged dataset (FrancescaDF_2019 + ShettySA_2022 + this study),Omnivore refers to individuals regularly consuming a mixed diet of meat and meat products of ≥170 g/day). The samples was from this study and two public datasets (FrancescaDF_2019 and ShetttySA_2022),103,103,NA,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.25,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S2C,17 March 2025,KateRasheed,KateRasheed,Differential abundant microbiome species across samples from this study and two public datasets (FrancescaDF_2019 and ShetttySA_2022),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes inops,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister histaminiformans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium phoceensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter glycyrrhizinilyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium",3379134|976|200643|171549|171550|239759|1501391;1783272|1239|909932|1843489|31977|39948|209880;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|2044939;1783272|1239|186801|186802|31979|1898204;1783272|1239|186801|186802|31979|1485|1650661;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|2316020|342942;1783272|1239|186801|186802|216572|2485925,Complete,KateRasheed
bsdb:39826123/4/2,39826123,"cross-sectional observational, not case-control",39826123,10.1016/j.celrep.2025.115252,NA,"Huang K.D., Müller M., Sivapornnukul P., Bielecka A.A., Amend L., Tawk C., Bruns A., Lesker T.R., Hahn A. , Strowig T.",Dietary selective effects manifest in the human gut microbiota from species composition to strain genetic makeup,Cell reports,2025,NA,Experiment 4,Germany,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Vegan merged dataset (FrancescaDF_2019 + ShettySA_2022 + this study),Omnivore merged dataset (FrancescaDF_2019 + ShettySA_2022 + this study),Omnivore refers to individuals regularly consuming a mixed diet of meat and meat products of ≥170 g/day). The samples was from this study and two public datasets (FrancescaDF_2019 and ShetttySA_2022),103,103,NA,WMS,NA,Illumina,arcsine square-root,MaAsLin2,0.25,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. S2C,17 March 2025,KateRasheed,KateRasheed,Differential abundant microbiome species across samples from this study and two public datasets (FrancescaDF_2019 and ShetttySA_2022),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF20-17LB,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium OF09-6,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium OM04-12BH",1783272|1239|186801|186802|31979|1485|2292205;1783272|1239|186801|3085636|186803|1898203;1783272|1239|186801|3085636|186803|2293831;1783272|1239|186801|3085636|186803|2292272,Complete,KateRasheed
bsdb:39834317/1/1,39834317,prospective cohort,39834317,10.1080/19490976.2025.2455789,NA,"Li K., Jin J., Liu Z., Chen C., Huang L. , Sun Y.",Dysbiosis of infant gut microbiota is related to the altered fatty acid composition of human milk from mothers with gestational diabetes mellitus: a prospective cohort study,Gut microbes,2025,"Gut microbiota, gestational diabetes mellitus, human milk, infant, lactation",Experiment 1,China,Homo sapiens,Colostrum,UBERON:0001914,Gestational diabetes,EFO:0004593,Normal group 0 (1-3 days after delivery),Gestational diabetes mellitus group 0 (GDM0) (1-3 days after delivery),Pregnant women with GDM (gestational diabetes mellitus) 1-3 days postpartum,48,45,3 months,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 5A and 5B,19 March 2025,Tosin,Tosin,Differential bacteria between Gestational diabetes mellitus (GDM) and normal groups at levels of phylum (A) and genus (B) at 1–3 days postpartum [Gestational diabetes mellitus0 (GDM0) and Normal0],decreased,"k__Pseudomonadati|p__Acidobacteriota,p__Candidatus Methylomirabilota,p__Candidatus Sumerlaeota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Dongiaceae|g__Dongia,k__Pseudomonadati|p__Gemmatimonadota,k__Pseudomonadati|p__Myxococcota,k__Pseudomonadati|p__Nitrospirota,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,p__Candidatus Altimarinota",3379134|57723;640293;200295;3379134|1224|28211|204441|3031144|1146845;3379134|142182;3379134|2818505;3379134|40117;3379134|976|117747|200666|84566|28453;3379134|976|117747|200666|84566;363464,Complete,Svetlana up
bsdb:39834317/2/1,39834317,prospective cohort,39834317,10.1080/19490976.2025.2455789,NA,"Li K., Jin J., Liu Z., Chen C., Huang L. , Sun Y.",Dysbiosis of infant gut microbiota is related to the altered fatty acid composition of human milk from mothers with gestational diabetes mellitus: a prospective cohort study,Gut microbes,2025,"Gut microbiota, gestational diabetes mellitus, human milk, infant, lactation",Experiment 2,China,Homo sapiens,Milk,UBERON:0001913,Gestational diabetes,EFO:0004593,Normal group 1 (1 month postpartum),Gestational diabetes mellitus group 1 (GDM1) (1 month postpartum),Pregnant women with GDM (gestational diabetes mellitus) 1 month postpartum,40,40,3 months,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 1,Figure 5A and 5B,19 March 2025,Tosin,Tosin,Differential bacteria between Gestational diabetes mellitus (GDM) and normal groups at levels of phylum (A) and genus (B) at 1 month postpartum [Gestational diabetes mellitus1 (GDM1) and Normal1],increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,p__Candidatus Altimarinota,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,p__Candidatus Saccharimonadota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae",3379134|1224|28211|204458|76892|41275;363464;1783272|1117;3379134|1224|28211|204457|41297|13687;3379134|1224|28216|80840;95818;3379134|1224|28211|204455|31989;3379134|976|117747|200666|84566,Complete,Svetlana up
bsdb:39834317/3/1,39834317,prospective cohort,39834317,10.1080/19490976.2025.2455789,NA,"Li K., Jin J., Liu Z., Chen C., Huang L. , Sun Y.",Dysbiosis of infant gut microbiota is related to the altered fatty acid composition of human milk from mothers with gestational diabetes mellitus: a prospective cohort study,Gut microbes,2025,"Gut microbiota, gestational diabetes mellitus, human milk, infant, lactation",Experiment 3,China,Homo sapiens,Colostrum,UBERON:0001914,Gestational diabetes,EFO:0004593,Normal group 0 (1-3 days after delivery),Gestational diabetes mellitus group 0 (GDM) (1-3 days after delivery),Pregnant women with GDM (gestational diabetes mellitus) 1-3 days postpartum,48,45,3 months,16S,34,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,"birth weight,body mass index",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 3,19 March 2025,Tosin,Tosin,Differential bacteria between GDM and normal groups with a p-time×group interaction < 0.05.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,3379134|1224|28211|204455|31989,Complete,Svetlana up
bsdb:39834317/3/2,39834317,prospective cohort,39834317,10.1080/19490976.2025.2455789,NA,"Li K., Jin J., Liu Z., Chen C., Huang L. , Sun Y.",Dysbiosis of infant gut microbiota is related to the altered fatty acid composition of human milk from mothers with gestational diabetes mellitus: a prospective cohort study,Gut microbes,2025,"Gut microbiota, gestational diabetes mellitus, human milk, infant, lactation",Experiment 3,China,Homo sapiens,Colostrum,UBERON:0001914,Gestational diabetes,EFO:0004593,Normal group 0 (1-3 days after delivery),Gestational diabetes mellitus group 0 (GDM) (1-3 days after delivery),Pregnant women with GDM (gestational diabetes mellitus) 1-3 days postpartum,48,45,3 months,16S,34,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,"birth weight,body mass index",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table 3,26 March 2025,Tosin,Tosin,Differential bacteria between GDM and normal groups with a p-time×group interaction < 0.05.,decreased,"k__Pseudomonadati|p__Acidobacteriota,p__Candidatus Altimarinota,p__Candidatus Methylomirabilota,p__Candidatus Sumerlaeota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Dongiaceae|g__Dongia,k__Pseudomonadati|p__Gemmatimonadota,k__Pseudomonadati|p__Myxococcota,k__Pseudomonadati|p__Nitrospirota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,p__Candidatus Saccharimonadota,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium",3379134|57723;363464;640293;200295;3379134|1224|28211|204441|3031144|1146845;3379134|142182;3379134|2818505;3379134|40117;3379134|1224|28211|204457|41297|13687;95818;3379134|976|117747|200666|84566;3379134|976|117747|200666|84566|28453,Complete,Svetlana up
bsdb:39834317/4/1,39834317,prospective cohort,39834317,10.1080/19490976.2025.2455789,NA,"Li K., Jin J., Liu Z., Chen C., Huang L. , Sun Y.",Dysbiosis of infant gut microbiota is related to the altered fatty acid composition of human milk from mothers with gestational diabetes mellitus: a prospective cohort study,Gut microbes,2025,"Gut microbiota, gestational diabetes mellitus, human milk, infant, lactation",Experiment 4,China,Homo sapiens,Milk,UBERON:0001913,Gestational diabetes,EFO:0004593,Normal group 1 (1 month postpartum),Gestational diabetes mellitus group 1 (GDM) (1 month postpartum),Pregnant women with GDM (gestational diabetes mellitus) 1 month postpartum,40,40,3 months,16S,34,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,"birth weight,body mass index",NA,unchanged,increased,unchanged,NA,increased,Signature 1,Table 3,26 March 2025,Tosin,Tosin,Differential bacteria between GDM and normal groups with a p-time×group interaction < 0.05.,increased,"p__Candidatus Altimarinota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,p__Candidatus Saccharimonadota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae",363464;3379134|1224|28211|204457|41297|13687;3379134|976|117747|200666|84566;95818;3379134|1224|28211|204455|31989,Complete,Svetlana up
bsdb:39843443/1/1,39843443,randomized controlled trial,39843443,10.1038/s41467-025-56084-6,NA,"Wu X., Tjahyo A.S., Volchanskaya V.S.B., Wong L.H., Lai X., Yong Y.N., Osman F., Tay S.L., Govindharajulu P., Ponnalagu S., Tso R., Teo H.S., Khoo K., Fan H., Goh C.C., Yap C.P.L., Leow M.K., Henry C.J., Haldar S. , Lim K.J.",A legume-enriched diet improves metabolic health in prediabetes mediated through gut microbiome: a randomized controlled trial,Nature communications,2025,NA,Experiment 1,Singapore,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Control Group (CG),Intervention Group (IG),"This group consists of participants who received the legume-enriched, calorie-restricted intervention diet, high in fiber and low-GI carbs, with legumes as the main protein source.",57,54,NA,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 3F & S4a,20 April 2025,Joiejoie,Joiejoie,Taxa that are significantly changed over time in intervention.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella quasipneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella variicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus|s__Monoglobus pectinilyticus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Tractidigestivibacter|s__Tractidigestivibacter scatoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|3085636|186803|1766253|39491;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|291644;1783272|201174|1760|85004|31953|1678;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|1392389|1297617;3379134|1224|1236|91347|543|570|1463165;3379134|1224|1236|91347|543|570|244366;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|186801|3085656|3085657|2039302|1981510;1783272|201174|84998|84999|1643824|133925;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|186801|3085636|186803|841|301301;33090|35493|3398|72025|3803|3814|508215;1783272|201174|1760|85006|1268|32207|43675;1783272|201174|84998|84999|1643824|2847313|1299998;1783272|1239|186801|3085636|186803,Complete,KateRasheed
bsdb:39843443/1/2,39843443,randomized controlled trial,39843443,10.1038/s41467-025-56084-6,NA,"Wu X., Tjahyo A.S., Volchanskaya V.S.B., Wong L.H., Lai X., Yong Y.N., Osman F., Tay S.L., Govindharajulu P., Ponnalagu S., Tso R., Teo H.S., Khoo K., Fan H., Goh C.C., Yap C.P.L., Leow M.K., Henry C.J., Haldar S. , Lim K.J.",A legume-enriched diet improves metabolic health in prediabetes mediated through gut microbiome: a randomized controlled trial,Nature communications,2025,NA,Experiment 1,Singapore,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Control Group (CG),Intervention Group (IG),"This group consists of participants who received the legume-enriched, calorie-restricted intervention diet, high in fiber and low-GI carbs, with legumes as the main protein source.",57,54,NA,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 3F & S4b,20 April 2025,Joiejoie,Joiejoie,Taxa that are significantly changed over time in intervention group.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. OM08-11,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. CAG:257,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:299,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:58,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella intestinalis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:424,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora saccharolytica,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549|815|816|2292284;3379134|976|200643|171549|815|816|46506;3379134|976|200643|171549|815|816|820;3379134|200940|3031449|213115|194924|35832;3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|572511|1322;1783272|1239|186801|3085636|186803|572511|1262756;1783272|1239|186801|186802|31979|1485|1262792;1783272|1239|186801|186802|31979|1485|1262824;1783272|201174|84998|84999|84107|102106|147207;1783272|201174|84998|1643822|1643826|84111;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|1263022;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|216572|946234|292800;3384189|32066|203490|203491|203492|848;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803|2719231|84030;1783272|1239|186801|3085636|186803|2316020|33038;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|815|909656|204516;1783272|1239|526524|526525|2810280|3025755;3379134|1224|28216|80840|995019|1918598;1783272|1239|186801|3085636|186803|2316020|46228;1783272|1239|186801|3085636|186803|2316020|33039,Complete,KateRasheed
bsdb:39843443/2/1,39843443,randomized controlled trial,39843443,10.1038/s41467-025-56084-6,NA,"Wu X., Tjahyo A.S., Volchanskaya V.S.B., Wong L.H., Lai X., Yong Y.N., Osman F., Tay S.L., Govindharajulu P., Ponnalagu S., Tso R., Teo H.S., Khoo K., Fan H., Goh C.C., Yap C.P.L., Leow M.K., Henry C.J., Haldar S. , Lim K.J.",A legume-enriched diet improves metabolic health in prediabetes mediated through gut microbiome: a randomized controlled trial,Nature communications,2025,NA,Experiment 2,Singapore,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Day 0 - Control (ctr),Day 1 - Control (ctr),This is the Day 1 timepoint within the control (ctr) group,NA,NA,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. S6,2 May 2025,Joiejoie,Joiejoie,Species that changed significantly in in vitro fermentation experiments,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|186802|216572|1263|40518,Complete,KateRasheed
bsdb:39843443/3/1,39843443,randomized controlled trial,39843443,10.1038/s41467-025-56084-6,NA,"Wu X., Tjahyo A.S., Volchanskaya V.S.B., Wong L.H., Lai X., Yong Y.N., Osman F., Tay S.L., Govindharajulu P., Ponnalagu S., Tso R., Teo H.S., Khoo K., Fan H., Goh C.C., Yap C.P.L., Leow M.K., Henry C.J., Haldar S. , Lim K.J.",A legume-enriched diet improves metabolic health in prediabetes mediated through gut microbiome: a randomized controlled trial,Nature communications,2025,NA,Experiment 3,Singapore,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Day 0 - Control (ctr),Day 2 - Control (ctr),This is the Day 2 timepoint within the control (ctr) group,NA,NA,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. S6,2 May 2025,Joiejoie,Joiejoie,Species that changed significantly in in vitro fermentation experiments,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|186802|216572|1263|40518,Complete,KateRasheed
bsdb:39843443/5/1,39843443,randomized controlled trial,39843443,10.1038/s41467-025-56084-6,NA,"Wu X., Tjahyo A.S., Volchanskaya V.S.B., Wong L.H., Lai X., Yong Y.N., Osman F., Tay S.L., Govindharajulu P., Ponnalagu S., Tso R., Teo H.S., Khoo K., Fan H., Goh C.C., Yap C.P.L., Leow M.K., Henry C.J., Haldar S. , Lim K.J.",A legume-enriched diet improves metabolic health in prediabetes mediated through gut microbiome: a randomized controlled trial,Nature communications,2025,NA,Experiment 5,Singapore,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Day 0 - Red bean fibre digested (RBD),Day 2 - Red bean fibre digested (RBD),This is the Day 2 time point within the Red bean fibre digested (RBD) group.,NA,NA,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. S6,2 May 2025,Joiejoie,Joiejoie,Species that changed significantly in in vitro fermentation experiments,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,1783272|1239|186801|3085636|186803|1766253|39491,Complete,KateRasheed
bsdb:39843443/6/1,39843443,randomized controlled trial,39843443,10.1038/s41467-025-56084-6,NA,"Wu X., Tjahyo A.S., Volchanskaya V.S.B., Wong L.H., Lai X., Yong Y.N., Osman F., Tay S.L., Govindharajulu P., Ponnalagu S., Tso R., Teo H.S., Khoo K., Fan H., Goh C.C., Yap C.P.L., Leow M.K., Henry C.J., Haldar S. , Lim K.J.",A legume-enriched diet improves metabolic health in prediabetes mediated through gut microbiome: a randomized controlled trial,Nature communications,2025,NA,Experiment 6,Singapore,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Day 1 - Red bean fibre digested (RBD),Day 2 - Red bean fibre digested (RBD),This is the Day 2 time point within the Red bean fibre digested (RBD) group.,NA,NA,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. S6,2 May 2025,Joiejoie,Joiejoie,Species that changed significantly in in vitro fermentation experiments,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,1783272|1239|186801|186802|216572|1263|40518,Complete,KateRasheed
bsdb:39843443/7/1,39843443,randomized controlled trial,39843443,10.1038/s41467-025-56084-6,NA,"Wu X., Tjahyo A.S., Volchanskaya V.S.B., Wong L.H., Lai X., Yong Y.N., Osman F., Tay S.L., Govindharajulu P., Ponnalagu S., Tso R., Teo H.S., Khoo K., Fan H., Goh C.C., Yap C.P.L., Leow M.K., Henry C.J., Haldar S. , Lim K.J.",A legume-enriched diet improves metabolic health in prediabetes mediated through gut microbiome: a randomized controlled trial,Nature communications,2025,NA,Experiment 7,Singapore,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Day 0 - Red bean fibre undigested (RBU),Day 1 - Red bean fibre undigested (RBU),This is the Day 1 time point within the Red bean fibre undigested (RBU) group.,NA,NA,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. S6,2 May 2025,Joiejoie,Joiejoie,Species that changed significantly in in vitro fermentation experiments,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|186802|216572|1263|40518,Complete,KateRasheed
bsdb:39843443/8/1,39843443,randomized controlled trial,39843443,10.1038/s41467-025-56084-6,NA,"Wu X., Tjahyo A.S., Volchanskaya V.S.B., Wong L.H., Lai X., Yong Y.N., Osman F., Tay S.L., Govindharajulu P., Ponnalagu S., Tso R., Teo H.S., Khoo K., Fan H., Goh C.C., Yap C.P.L., Leow M.K., Henry C.J., Haldar S. , Lim K.J.",A legume-enriched diet improves metabolic health in prediabetes mediated through gut microbiome: a randomized controlled trial,Nature communications,2025,NA,Experiment 8,Singapore,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Day 0 - Red bean fibre undigested (RBU),Day 2 - Red bean fibre undigested (RBU),This is the Day 2 time point within the Red bean fibre undigested (RBU) group.,NA,NA,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. S6,2 May 2025,Joiejoie,Joiejoie,Species that changed significantly in in vitro fermentation experiments,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,1783272|1239|186801|3085636|186803|1766253|39491,Complete,KateRasheed
bsdb:39843443/9/1,39843443,randomized controlled trial,39843443,10.1038/s41467-025-56084-6,NA,"Wu X., Tjahyo A.S., Volchanskaya V.S.B., Wong L.H., Lai X., Yong Y.N., Osman F., Tay S.L., Govindharajulu P., Ponnalagu S., Tso R., Teo H.S., Khoo K., Fan H., Goh C.C., Yap C.P.L., Leow M.K., Henry C.J., Haldar S. , Lim K.J.",A legume-enriched diet improves metabolic health in prediabetes mediated through gut microbiome: a randomized controlled trial,Nature communications,2025,NA,Experiment 9,Singapore,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Day 1 - Red bean fibre undigested (RBU),Day 2 - Red bean fibre undigested (RBU),This is the Day 2 time point within the Red bean fibre undigested (RBU) group.,NA,NA,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. S6,2 May 2025,Joiejoie,Joiejoie,Species that changed significantly in in vitro fermentation experiments,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,1783272|1239|186801|186802|216572|1263|40518,Complete,KateRasheed
bsdb:39843443/10/1,39843443,randomized controlled trial,39843443,10.1038/s41467-025-56084-6,NA,"Wu X., Tjahyo A.S., Volchanskaya V.S.B., Wong L.H., Lai X., Yong Y.N., Osman F., Tay S.L., Govindharajulu P., Ponnalagu S., Tso R., Teo H.S., Khoo K., Fan H., Goh C.C., Yap C.P.L., Leow M.K., Henry C.J., Haldar S. , Lim K.J.",A legume-enriched diet improves metabolic health in prediabetes mediated through gut microbiome: a randomized controlled trial,Nature communications,2025,NA,Experiment 10,Singapore,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Day 0 - Brown rice fibre digested (BRD),Day 1 - Brown rice fibre digested (BRD),This is the Day 1 time point within the Brown rice fibre digested (BRD) group.,NA,NA,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. S6,2 May 2025,Joiejoie,Joiejoie,Species that changed significantly in in vitro fermentation experiments,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|186802|216572|1263|40518,Complete,KateRasheed
bsdb:39843443/11/1,39843443,randomized controlled trial,39843443,10.1038/s41467-025-56084-6,NA,"Wu X., Tjahyo A.S., Volchanskaya V.S.B., Wong L.H., Lai X., Yong Y.N., Osman F., Tay S.L., Govindharajulu P., Ponnalagu S., Tso R., Teo H.S., Khoo K., Fan H., Goh C.C., Yap C.P.L., Leow M.K., Henry C.J., Haldar S. , Lim K.J.",A legume-enriched diet improves metabolic health in prediabetes mediated through gut microbiome: a randomized controlled trial,Nature communications,2025,NA,Experiment 11,Singapore,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Day 0 - Brown rice fibre digested (BRD),Day 2 - Brown rice fibre digested (BRD),This is the Day 2 time point within the Brown rice fibre digested (BRD) group.,NA,NA,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. S6,2 May 2025,Joiejoie,Joiejoie,Species that changed significantly in in vitro fermentation experiments,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|186802|216572|1263|40518,Complete,KateRasheed
bsdb:39843443/12/1,39843443,randomized controlled trial,39843443,10.1038/s41467-025-56084-6,NA,"Wu X., Tjahyo A.S., Volchanskaya V.S.B., Wong L.H., Lai X., Yong Y.N., Osman F., Tay S.L., Govindharajulu P., Ponnalagu S., Tso R., Teo H.S., Khoo K., Fan H., Goh C.C., Yap C.P.L., Leow M.K., Henry C.J., Haldar S. , Lim K.J.",A legume-enriched diet improves metabolic health in prediabetes mediated through gut microbiome: a randomized controlled trial,Nature communications,2025,NA,Experiment 12,Singapore,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Day 0 - Brown rice fibre undigested (BRU),Day 1 - Brown rice fibre undigested (BRU),This is the Day 1 time point within the Brown rice fibre undigested (BRU) group.,NA,NA,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. S6,2 May 2025,Joiejoie,Joiejoie,Species that changed significantly in in vitro fermentation experiments,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|186802|216572|1263|40518,Complete,KateRasheed
bsdb:39843443/13/1,39843443,randomized controlled trial,39843443,10.1038/s41467-025-56084-6,NA,"Wu X., Tjahyo A.S., Volchanskaya V.S.B., Wong L.H., Lai X., Yong Y.N., Osman F., Tay S.L., Govindharajulu P., Ponnalagu S., Tso R., Teo H.S., Khoo K., Fan H., Goh C.C., Yap C.P.L., Leow M.K., Henry C.J., Haldar S. , Lim K.J.",A legume-enriched diet improves metabolic health in prediabetes mediated through gut microbiome: a randomized controlled trial,Nature communications,2025,NA,Experiment 13,Singapore,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Day 0 - Brown rice fibre undigested (BRU),Day 2 - Brown rice fibre undigested (BRU),This is the Day 2 time point within the Brown rice fibre undigested (BRU) group.,NA,NA,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. S6,2 May 2025,Joiejoie,Joiejoie,Species that changed significantly in in vitro fermentation experiments,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|186802|216572|1263|40518,Complete,KateRasheed
bsdb:39843625/1/1,39843625,"cross-sectional observational, not case-control",39843625,10.1038/s41598-025-87216-z,NA,"Jarquín-Díaz V.H., Dayaram A., Soilemetzidou E.S., Desvars-Larrive A., Bohner J., Buuveibaatar B., Kaczensky P., Walzer C., Greenwood A.D. , Löber U.",Unraveling the distinctive gut microbiome of khulans (Equus hemionus hemionus) in comparison to their drinking water and closely related equids,Scientific reports,2025,"Equus hemionus hemionus, 16S rRNA full length gene sequencing, Freshwater microbiota, Gobi Desert, Microbiome, PacBio",Experiment 1,Mongolia,Equus hemionus hemionus,Rectum,UBERON:0001052,Lifestyle measurement,EFO:0010724,Captive Khulans,Wild Khulans,Samples retrieved from wild Khulans residing in the Mongolian Gobi Desert,12,21,NA,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,raw counts,DESeq2,0.001,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 3A,6 November 2025,Firdaws,Firdaws,Differentially abundant bacteria between wild and captive khulans.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Afipia|s__Afipia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Kiritimatiellota|c__Kiritimatiellia",3379134|1224|28211|356|41294|1033|1871052;1783272|1239|186801|3082720|543314;3379134|1224|28216|80840;3379134|29547|3031852|213849|72294|194|205;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|265975|1969407;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550;3379134|134625|1921781,Complete,KateRasheed
bsdb:39843625/1/2,39843625,"cross-sectional observational, not case-control",39843625,10.1038/s41598-025-87216-z,NA,"Jarquín-Díaz V.H., Dayaram A., Soilemetzidou E.S., Desvars-Larrive A., Bohner J., Buuveibaatar B., Kaczensky P., Walzer C., Greenwood A.D. , Löber U.",Unraveling the distinctive gut microbiome of khulans (Equus hemionus hemionus) in comparison to their drinking water and closely related equids,Scientific reports,2025,"Equus hemionus hemionus, 16S rRNA full length gene sequencing, Freshwater microbiota, Gobi Desert, Microbiome, PacBio",Experiment 1,Mongolia,Equus hemionus hemionus,Rectum,UBERON:0001052,Lifestyle measurement,EFO:0010724,Captive Khulans,Wild Khulans,Samples retrieved from wild Khulans residing in the Mongolian Gobi Desert,12,21,NA,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,raw counts,DESeq2,0.001,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 3A,6 November 2025,Firdaws,Firdaws,Differentially abundant bacteria between wild and captive khulans.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas kerstersii,3379134|1224|28216|80840|80864|283|225992,Complete,KateRasheed
bsdb:39843625/2/1,39843625,"cross-sectional observational, not case-control",39843625,10.1038/s41598-025-87216-z,NA,"Jarquín-Díaz V.H., Dayaram A., Soilemetzidou E.S., Desvars-Larrive A., Bohner J., Buuveibaatar B., Kaczensky P., Walzer C., Greenwood A.D. , Löber U.",Unraveling the distinctive gut microbiome of khulans (Equus hemionus hemionus) in comparison to their drinking water and closely related equids,Scientific reports,2025,"Equus hemionus hemionus, 16S rRNA full length gene sequencing, Freshwater microbiota, Gobi Desert, Microbiome, PacBio",Experiment 2,Mongolia,Equus hemionus hemionus,NA,NA,Environmental samples,NCBITAXON:33858,Sediment samples from the Great Gobi B and South East Gobi,Water samples from the Great Gobi B and South East Gobi,Water Samples retrieved from Wild Khulans residing in the Mongolian Gobi Desert (The Great Gobi B and South East Gobi),24,24,NA,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,raw counts,DESeq2,0.001,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,Figure 3B,6 November 2025,Firdaws,Firdaws,Differentially abundant bacteria between Water samples and Sediment samples retrieved from Wild Khulans residing in the Mongolian Gobi Desert,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter|s__Achromobacter marplatensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cyclobacteriaceae|g__Algoriphagus|s__Algoriphagus sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Arenimonas|s__Arenimonas aestuarii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Arenimonas|s__Arenimonas sp.,k__Pseudomonadati|p__Bdellovibrionota|c__Bacteriovoracia|o__Bacteriovoracales|f__Bacteriovoracaceae|g__Bacteriovorax|s__Bacteriovorax sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Blastomonadaceae|g__Blastomonas|s__Blastomonas sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Boseaceae|g__Bosea|s__Bosea sp. (in: a-proteobacteria),k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas|s__Brevundimonas sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas|s__Brevundimonas variabilis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hydrogenophaga|s__Hydrogenophaga sp.,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Isosphaerales|f__Isosphaeraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Methylophilaceae|g__Methylophilus|s__Methylophilus sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium|s__Novosphingobium sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Pirellulales|f__Pirellulaceae,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Planctomycetales|f__Planctomycetaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Polaromonas|s__Polaromonas sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudohongiellaceae|g__Pseudohongiella|s__Pseudohongiella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Pseudorhodobacter|s__Pseudorhodobacter sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Segnochrobactraceae|g__Pseudoxanthobacter|s__Pseudoxanthobacter sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Reyranellaceae|g__Reyranella|s__Reyranella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|g__Rhodobacter|s__Rhodobacter sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Pseudomonadati|p__Bacteroidota|c__Saprospiria|o__Saprospirales|f__Saprospiraceae,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Planctomycetales|f__Planctomycetaceae|g__Schlesneria|s__Schlesneria sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Simplicispira|s__Simplicispira sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Rubellimicrobium|s__Rubellimicrobium sp.",3379134|1224|28216|80840|506|222|470868;3379134|1224|28216|80840|506;3379134|976|768503|768507|563798|246875|1872435;3379134|1224|1236|135614|32033|490567|1708347;3379134|1224|1236|135614|32033|490567|1872635;3379134|3018035|3031419|2024979|263369|146784|2608087;3379134|1224|28211|204457|3423720|150203|1909299;3379134|1224|28211|356|2831100|85413|1871050;3379134|1224|28211|204458|76892|41275|1871086;3379134|1224|28211|204458|76892|41275|74312;3379134|1224|28216|80840|80864|47420|1904254;3379134|203682|203683|2691356|1763524;3379134|1224|28216|32003|32011|16|29541;3379134|1224|28211|204457|41297|165696|1874826;3379134|1224|28211|204455|31989;3379134|203682|203683|2691354|2691357;3379134|203682|203683|112|126;3379134|1224|28216|80840|80864|52972|1869339;3379134|1224|1236|72274|3085095|1524249|1979412;3379134|1224|1236|72274|135621|286|306;3379134|1224|28211|204455|31989|238783|1934400;3379134|1224|28211|356|2822331|433838|1925742;3379134|1224|28211|356|2844375|445219|1929291;3379134|1224|28211|356|82115;3379134|1224|28211|204455|1060|1062;3379134|1224|28211|204441;3379134|976|1937959|1936988|89374;3379134|203682|203683|112|126|656899|2762018;3379134|1224|28216|80840|80864|352450|2015802;3379134|1224|28211|204457|41297;3379134|74201|203494|48461|203557;3379134|74201|203494|48461;3379134|1224|28211|204455|2854170|295418|2509153,Complete,KateRasheed
bsdb:39843625/2/2,39843625,"cross-sectional observational, not case-control",39843625,10.1038/s41598-025-87216-z,NA,"Jarquín-Díaz V.H., Dayaram A., Soilemetzidou E.S., Desvars-Larrive A., Bohner J., Buuveibaatar B., Kaczensky P., Walzer C., Greenwood A.D. , Löber U.",Unraveling the distinctive gut microbiome of khulans (Equus hemionus hemionus) in comparison to their drinking water and closely related equids,Scientific reports,2025,"Equus hemionus hemionus, 16S rRNA full length gene sequencing, Freshwater microbiota, Gobi Desert, Microbiome, PacBio",Experiment 2,Mongolia,Equus hemionus hemionus,NA,NA,Environmental samples,NCBITAXON:33858,Sediment samples from the Great Gobi B and South East Gobi,Water samples from the Great Gobi B and South East Gobi,Water Samples retrieved from Wild Khulans residing in the Mongolian Gobi Desert (The Great Gobi B and South East Gobi),24,24,NA,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,raw counts,DESeq2,0.001,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,Figure 3B,7 November 2025,Firdaws,Firdaws,Differentially abundant bacteria between Water samples and Sediment samples retrieved from Wild Khulans residing in the Mongolian Gobi Desert,decreased,"k__Pseudomonadati|p__Acidobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax|s__Anaerovorax sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,c__Desulfitobacteriia|o__Desulfitobacteriales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus|s__Desulfobulbus sp.,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfocapsaceae|g__Desulfocapsa|s__Desulfocapsa sp.,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfocapsaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfocastanea|s__Desulfocastanea catecholica,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales|f__Desulfococcaceae|g__Desulfococcus|s__Desulfococcus sp.,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfomicrobiaceae|g__Desulfomicrobium|s__Desulfomicrobium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Fusibacteraceae|g__Fusibacter|s__Fusibacter sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Legionellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Proteiniclasticum|s__Proteiniclasticum sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Rhodocyclaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans|s__Saccharofermentans sp.,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae|g__Soehngenia|s__Soehngenia sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Sulfurovaceae|g__Sulfurovum|s__Sulfurovum sp.,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Syntrophia|o__Syntrophales|f__Syntrophaceae|g__Syntrophus|s__Syntrophus sp. (in: bacteria),k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Thauera|s__Thauera sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Trichococcus|s__Trichococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Youngiibacter|s__Youngiibacter sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|57723;1783272|1239|186801|3082720|543314|109326|1872534;3379134|1224|28216|80840;1783272|1239|186801|3082768|990719;1783272|1239|186801|3082768;1783272|1239|186801|186802|31979;3118665|3120411;3379134|200940|3031451|3024411|213121|893|895;3379134|200940|3031451|3024411|2886822|53318|2066021;3379134|200940|3031451|3024411|2886822;3379134|200940|3031451|3024411|213121|2916674|90729;3379134|200940|3024418|213118|2931039|896|2025834;3379134|200940|3031449|213115|213116|898|52017;1783272|1239|186801|186802|3679999|76008|2004507;1783272|1239|186801|3085636|186803;3379134|1224|1236|118969|444;3379134|1224|28216|80840|75682;3379134|976|200643|1970189|1471398;1783272|1239|186801|186802|31979|1155385|2053595;3379134|1224|28216|206389|75787;1783272|1239|186801|186802|216572|1200657|2775029;1783272|1239|1737404|1737405|1737406|253255|2555675;1783272|1239|909932|909929|1843490;3379134|29547|3031852|213849|2771472|265570|1969726;3379134|200940|3031648|2914038|213468|43773|48412;3379134|1224|28216|206389|2008794|33057|1905334;1783272|1239|91061|186826|186828|82802|1985464;1783272|1239|186801|186802|31979|1408818|2814028;1783272|1239|186801|186802;1783272|1239|186801|186802|216572,Complete,KateRasheed
bsdb:39848958/1/1,39848958,case-control,39848958,10.1038/s41598-024-81607-4,NA,NA,Microbiome analysis in individuals with human papillomavirus oral infection,Sci. Rep.,NA,"Microbiome , HIV, Human Papillomavirus",Experiment 1,Italy,Homo sapiens,Mouth,UBERON:0000165,Human papilloma virus infection,EFO:0001668,HIV-/HPV- (Human immuno deficiency virus negative/Human papilloma virus negative),HIV-/hrHPV+ (Human immuno deficiency virus negative/ High risk human papilloma virus positive),HIV (Human Immunodeficiency Virus) negative Patients with High risk human papillomavirus (HPV)  oral infection.,20,21,NA,16S,34,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,"age,alcohol consumption measurement,oral hygiene,smoking status",NA,unchanged,unchanged,increased,NA,NA,NA,Signature 1,"Figure 4, supplementary Figure 2",30 March 2025,Uzy-tessy,"Uzy-tessy,Tosin",Differential abundance of oral bacterial taxa at the genus and species level.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter sp. oral taxon 513,p__Candidatus Altimarinota|s__Gracilibacteria bacterium oral taxon 873,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 376,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 443,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Pseudomonadati|p__Bacteroidota|s__Bacteroidetes bacterium oral taxon 507,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium oral taxon 500,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|s__Veillonellaceae bacterium oral taxon 150",3379134|1224|1236|135625|712|416916|712150;363464|1226340;3379134|1224|1236|2887326|468|475;1783272|1239|1737404|1737405|1570339|543311;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171551|836|837;3379134|976|200643|171549|171552|838|712466;3379134|976|200643|171549|171552|838|712468;3384189|32066|203490|203491|1129771|168808;3379134|976|712909;1783272|1239|186801|3085636|186803|712991;1783272|1239|909932|1843489|31977|671234,Complete,Svetlana up
bsdb:39848958/1/2,39848958,case-control,39848958,10.1038/s41598-024-81607-4,NA,NA,Microbiome analysis in individuals with human papillomavirus oral infection,Sci. Rep.,NA,"Microbiome , HIV, Human Papillomavirus",Experiment 1,Italy,Homo sapiens,Mouth,UBERON:0000165,Human papilloma virus infection,EFO:0001668,HIV-/HPV- (Human immuno deficiency virus negative/Human papilloma virus negative),HIV-/hrHPV+ (Human immuno deficiency virus negative/ High risk human papilloma virus positive),HIV (Human Immunodeficiency Virus) negative Patients with High risk human papillomavirus (HPV)  oral infection.,20,21,NA,16S,34,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,"age,alcohol consumption measurement,oral hygiene,smoking status",NA,unchanged,unchanged,increased,NA,NA,NA,Signature 2,"Figure 4, supplementary Figure 2",31 March 2025,Uzy-tessy,"Uzy-tessy,Tosin",Differential abundance of oral bacteria taxa at the genus and specie level.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia|s__Alloscardovia omnicolens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium gonidiaformans,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia wadei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp. oral taxon 020,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 292,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 313,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum longum,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 349,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] infirmum",1783272|201174|1760|85004|31953|419014;1783272|201174|1760|85004|31953|419014|419015;1783272|201174|1760|85009|31957|1912216;1783272|201174|1760|85009|31957|1912216|1747;3384189|32066|203490|203491|203492|848|849;3384189|32066|203490|203491|1129771|32067|157687;1783272|1239|91061|186826|33958|2742598|1613;3379134|1224|28216|206351|481|482|712401;3379134|976|200643|171549|171552|838|470565;3379134|976|200643|171549|171552|838|671217;3379134|976|200643|171549|171552|838|652722;1783272|1239|186801|3085636|186803|1213720|796942;95818|713051;1783272|1239|186801|3082720|543314|56774,Complete,Svetlana up
bsdb:39848958/2/1,39848958,case-control,39848958,10.1038/s41598-024-81607-4,NA,NA,Microbiome analysis in individuals with human papillomavirus oral infection,Sci. Rep.,NA,"Microbiome , HIV, Human Papillomavirus",Experiment 2,Italy,Homo sapiens,Mouth,UBERON:0000165,Human papilloma virus infection,EFO:0001668,HIV+/HPV- (Human immuno deficiency virus positive / Human papilloma virus negative),HIV+/hrHPV+ (Human immuno deficiency virus positive/ High risk Human papilloma virus positive),HIV (Human Immunodeficiency Virus) positive Patients with High risk human papillomavirus (HPV)  oral infection.,10,12,NA,16S,34,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,"age,alcohol consumption measurement,oral hygiene,smoking status",NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,"Figure 4, supplementary Figure 2",7 April 2025,Uzy-tessy,"Uzy-tessy,Tosin",Differential abundance of oral bacteria taxa at the genus and specie level.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces radicidentis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium|s__Atopobium sp. oral taxon 416,k__Pseudomonadati|p__Bacteroidota|s__Bacteroidetes bacterium oral taxon 280,k__Pseudomonadati|p__Bacteroidota|s__Bacteroidetes bacterium oral taxon 516,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sp. oral taxon 336,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella sp. oral taxon 451,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella oralis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp. oral taxon 078,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 300,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 315,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia|s__Bulleidia extructa,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter aphrophilus,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp. oral taxon 271,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum",1783272|201174|1760|2037|2049|1654|111015;1783272|201174|84998|84999|1643824|1380|712157;3379134|976|712900;3379134|976|712912;1783272|1239|526524|526525|128827|118747;3379134|976|117743|200644|49546|1016|712216;1783272|1239|186801|3085636|186803|43996|712234;3379134|976|200643|171549|171552|2974257|28134;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|33958|1578|147802;1783272|1239|186801|3085636|186803|265975|652706;1783272|1239|1737404|1737405|1570339|162289;3379134|976|200643|171549|171552|838|712456;3379134|976|200643|171549|171552|838|712465;3379134|1224|28216|206351|481|71;1783272|1239|186801|3085636|186803|265975|1501329;1783272|1239|1737404|1737405|1570339|162289|33031;1783272|1239|526524|526525|128827|118747|118748;3379134|1224|1236|135625|712|416916|732;3379134|203691|203692|136|2845253|157|712746;3384194|508458|649775|649776|3029087|1434006|651822,Complete,Svetlana up
bsdb:39848958/2/2,39848958,case-control,39848958,10.1038/s41598-024-81607-4,NA,NA,Microbiome analysis in individuals with human papillomavirus oral infection,Sci. Rep.,NA,"Microbiome , HIV, Human Papillomavirus",Experiment 2,Italy,Homo sapiens,Mouth,UBERON:0000165,Human papilloma virus infection,EFO:0001668,HIV+/HPV- (Human immuno deficiency virus positive / Human papilloma virus negative),HIV+/hrHPV+ (Human immuno deficiency virus positive/ High risk Human papilloma virus positive),HIV (Human Immunodeficiency Virus) positive Patients with High risk human papillomavirus (HPV)  oral infection.,10,12,NA,16S,34,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,"age,alcohol consumption measurement,oral hygiene,smoking status",NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 2,"Figure 4, supplementary Figure 2",7 April 2025,Uzy-tessy,"Uzy-tessy,Tosin",Differential abundance of oral bacteria taxa at the genus and specie level.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Pseudomonadati|p__Bacteroidota|s__Bacteroidetes bacterium oral taxon 436,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella|s__Bergeyella sp. oral taxon 422,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila|s__Fastidiosipila sanguinis,p__Candidatus Altimarinota|s__Gracilibacteria bacterium oral taxon 871,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sp. oral taxon 123,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella sp. oral taxon 521,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium|s__Novosphingobium panipatense,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp. oral taxon 275,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella aurantiaca,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 306,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral taxon 355,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella serpentiformis,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp. oral taxon 227,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp. oral taxon 265,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Diaphorobacter|s__[Acidovorax] ebreus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Syntrophomonadaceae|s__Syntrophomonadaceae bacterium oral taxon 435",3379134|1224|28216|80840|80864|12916;3379134|976|712906;3379134|976|117743|200644|2762318|59735|712188;1783272|1239|186801|186802|216572|236752|236753;363464|1226338;3384189|32066|203490|203491|1129771|32067|157688;1783272|1239|909932|1843489|31977|906|712374;1783272|1239|909932|909929|1843491|52225|712391;3379134|1224|28211|204457|41297|165696|428991;3379134|976|200643|171549|171551|836|712435;3379134|976|200643|171549|171552|838|596085;3379134|976|200643|171549|171552|838|712461;95818|713056;3379134|976|200643|171549|2005525|195950|712710;3379134|203691|203692|136|2845253|157|712716;3379134|203691|203692|136|2845253|157|712744;1783272|1239|909932|1843489|31977|29465|423477;3379134|1224|28216|80840|80864|238749|721785;1783272|1239|186801|186802|68298|713048,Complete,Svetlana up
bsdb:39854172/1/2,39854172,"cross-sectional observational, not case-control",39854172,10.1093/infdis/jiaf043,https://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiaf043/7978852#502884056,"MacCann R., Li J., Leon A.A.G., Negi R., Alalwan D., Tinago W., McGettrick P., Cotter A.G., Landay A., Sabin C., O'Toole P.W. , Mallon P.W.","Associations between the gut microbiome, inflammation and cardiovascular profiles in people with HIV",The Journal of infectious diseases,2025,"HIV, cardiovascular disease, inflammation, microbiome",Experiment 1,Ireland,Homo sapiens,Feces,UBERON:0001988,Human immunodeficiency virus,NCBITAXON:12721,People Without HIV,People With HIV,Individuals who have been diagnosed with HIV (Human Immunodeficiency Virus),37,44,NA,16S,34,Illumina,centered log-ratio,ANCOM-BC,0.1,TRUE,NA,NA,"age,antiretroviral therapy,sex",NA,unchanged,unchanged,NA,NA,NA,Signature 2,Fig 2 And Fig-S2,1 April 2025,Aiyshaaaa,Aiyshaaaa,Differential abundance (DA) analysis of species and genus in people with human immunodeficiency virus (HIV) compared to those without HIV.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor|s__Acetatifactor muris,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio|s__Acetivibrio clariflavus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus fermentans,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia mucosicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio|s__Anaerovibrio lipolyticus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister propionicifaciens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalicoccus|s__Faecalicoccus pleomorphus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella jalaludinii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella uli,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter piscolens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Robbsia|s__Robbsia andropogonis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia turicensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella albensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas bovis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas ruminantium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia exigua,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio|s__Succinivibrio dextrinosolvens",1783272|1239|186801|3085636|186803|1427378|879566;1783272|1239|186801|3120394|3120654|35829|288965;1783272|1239|909932|1843488|909930|904|905;1783272|201174|84998|1643822|1643826|447020|580026;3379134|976|200643|171549|171552|1283313|671218;1783272|1239|909932|909929|1843491|82373|82374;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|909932|1843489|31977|39948|308994;1783272|1239|909932|1843489|31977|39948|487173;1783272|1239|526524|526525|128827|1573536|1323;1783272|1239|186801|186802|216572|946234;1783272|1239|909932|909929|1843491|158846|158847;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843489|31977|906|907;1783272|1239|909932|1843489|31977|906|187326;1783272|1239|909932|909929|1843491|52225;1783272|1239|909932|909929|1843491|52225|187979;1783272|1239|909932|909929|1843491|52225|52226;1783272|201174|84998|84999|1643824|133925;1783272|201174|84998|84999|1643824|133925|133926;3384194|508458|649775|649776|3029088|638847|638849;3379134|1224|28216|80840|119060|2038280|28092;1783272|201174|1760|2037|2049|2529408|131111;3379134|976|200643|171549|171552|2974251|77768;3379134|976|200643|171549|171552|2974251|228604;1783272|1239|909932|909929|1843491|970|416586;1783272|1239|909932|909929|1843491|970|971;1783272|201174|84998|1643822|1643826|84108|84109;3379134|1224|1236|135624|83763|83770|83771,Complete,Svetlana up
bsdb:39854172/1/3,39854172,"cross-sectional observational, not case-control",39854172,10.1093/infdis/jiaf043,https://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiaf043/7978852#502884056,"MacCann R., Li J., Leon A.A.G., Negi R., Alalwan D., Tinago W., McGettrick P., Cotter A.G., Landay A., Sabin C., O'Toole P.W. , Mallon P.W.","Associations between the gut microbiome, inflammation and cardiovascular profiles in people with HIV",The Journal of infectious diseases,2025,"HIV, cardiovascular disease, inflammation, microbiome",Experiment 1,Ireland,Homo sapiens,Feces,UBERON:0001988,Human immunodeficiency virus,NCBITAXON:12721,People Without HIV,People With HIV,Individuals who have been diagnosed with HIV (Human Immunodeficiency Virus),37,44,NA,16S,34,Illumina,centered log-ratio,ANCOM-BC,0.1,TRUE,NA,NA,"age,antiretroviral therapy,sex",NA,unchanged,unchanged,NA,NA,NA,Signature 3,Fig 2 And S2,1 April 2025,Aiyshaaaa,Aiyshaaaa,Differential abundance (DA) analysis of species in people with human immunodeficiency virus (HIV) compared to those without HIV.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus pullicaecorum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus|s__Cloacibacillus evryensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola barnesiae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter",1783272|1239|909932|1843488|909930|904;1783272|201174|84998|1643822|1643826|447020|446660;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|28111;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|2005519|397864|487174;1783272|1239|186801|186802|3085642|580596|501571;3379134|976|200643|171549|2005519|1348911|1099853;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|216572|1263|40518;3379134|1224|1236|135624|83763|83770;3384194|508458|649775|649776|649777|508459|508460;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|909656|376804;1783272|1239|186801|3085636|186803|1407607,Complete,Svetlana up
bsdb:39854172/3/1,39854172,"cross-sectional observational, not case-control",39854172,10.1093/infdis/jiaf043,https://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiaf043/7978852#502884056,"MacCann R., Li J., Leon A.A.G., Negi R., Alalwan D., Tinago W., McGettrick P., Cotter A.G., Landay A., Sabin C., O'Toole P.W. , Mallon P.W.","Associations between the gut microbiome, inflammation and cardiovascular profiles in people with HIV",The Journal of infectious diseases,2025,"HIV, cardiovascular disease, inflammation, microbiome",Experiment 3,Ireland,Homo sapiens,Feces,UBERON:0001988,Alcohol consumption measurement,EFO:0007878,Low Alcohol Intake,High Alcohol Intake,Higher alcohol consumption recorded in individuals diagnosed with HIV (Human Immunodeficiency Virus),NA,NA,NA,16S,34,Illumina,centered log-ratio,"ANCOM-BC,Spearman Correlation",0.1,TRUE,NA,NA,"age,antiretroviral therapy,sex",NA,NA,NA,NA,NA,NA,Signature 1,Fig-3,3 April 2025,Aiyshaaaa,Aiyshaaaa,Heatmap showing the correlation of the differentially abundant (DA) species with mean nutrient intake and the Healthy Food Diversity (HFD) index.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,3379134|976|200643|171549|815|816|28111,Complete,Svetlana up
bsdb:39854172/3/2,39854172,"cross-sectional observational, not case-control",39854172,10.1093/infdis/jiaf043,https://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiaf043/7978852#502884056,"MacCann R., Li J., Leon A.A.G., Negi R., Alalwan D., Tinago W., McGettrick P., Cotter A.G., Landay A., Sabin C., O'Toole P.W. , Mallon P.W.","Associations between the gut microbiome, inflammation and cardiovascular profiles in people with HIV",The Journal of infectious diseases,2025,"HIV, cardiovascular disease, inflammation, microbiome",Experiment 3,Ireland,Homo sapiens,Feces,UBERON:0001988,Alcohol consumption measurement,EFO:0007878,Low Alcohol Intake,High Alcohol Intake,Higher alcohol consumption recorded in individuals diagnosed with HIV (Human Immunodeficiency Virus),NA,NA,NA,16S,34,Illumina,centered log-ratio,"ANCOM-BC,Spearman Correlation",0.1,TRUE,NA,NA,"age,antiretroviral therapy,sex",NA,NA,NA,NA,NA,NA,Signature 2,Fig-3 And S5,3 April 2025,Aiyshaaaa,Aiyshaaaa,Heatmap showing the correlation of the differentially abundant (DA) species and genues level with mean nutrient intake and the Healthy Food Diversity (HFD) index.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio",1783272|201174|1760|85004|31953|1678|28026;3379134|1224|1236|135624|83763|83770,Complete,Svetlana up
bsdb:39854172/4/1,39854172,"cross-sectional observational, not case-control",39854172,10.1093/infdis/jiaf043,https://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiaf043/7978852#502884056,"MacCann R., Li J., Leon A.A.G., Negi R., Alalwan D., Tinago W., McGettrick P., Cotter A.G., Landay A., Sabin C., O'Toole P.W. , Mallon P.W.","Associations between the gut microbiome, inflammation and cardiovascular profiles in people with HIV",The Journal of infectious diseases,2025,"HIV, cardiovascular disease, inflammation, microbiome",Experiment 4,Ireland,Homo sapiens,Feces,UBERON:0001988,Protein intake measurement,EFO:0010810,Low Protein Intake,High Protein Intake,High Protein Intake recorded in individuals diagnosed with HIV (Human Immunodeficiency Virus),NA,NA,NA,16S,34,Illumina,centered log-ratio,"Spearman Correlation,ANCOM-BC",0.1,TRUE,NA,NA,"age,antiretroviral therapy,sex",NA,NA,NA,NA,NA,NA,Signature 1,Fig-3,7 April 2025,Aiyshaaaa,Aiyshaaaa,Heatmap showing the correlation of the differentially abundant (DA) species with mean nutrient intake and the Healthy Food Diversity (HFD) index.,decreased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,1783272|1239|909932|1843489|31977|39948|487173,Complete,Svetlana up
bsdb:39854172/5/1,39854172,"cross-sectional observational, not case-control",39854172,10.1093/infdis/jiaf043,https://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiaf043/7978852#502884056,"MacCann R., Li J., Leon A.A.G., Negi R., Alalwan D., Tinago W., McGettrick P., Cotter A.G., Landay A., Sabin C., O'Toole P.W. , Mallon P.W.","Associations between the gut microbiome, inflammation and cardiovascular profiles in people with HIV",The Journal of infectious diseases,2025,"HIV, cardiovascular disease, inflammation, microbiome",Experiment 5,Ireland,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Low HFD Index,High HFD Index,High Healthy Food Diversity Index recorded in individuals diagnosed with HIV (Human Immunodeficiency Virus),NA,NA,NA,16S,34,Illumina,centered log-ratio,"Spearman Correlation,ANCOM-BC",0.1,TRUE,NA,NA,"age,antiretroviral therapy,sex",NA,NA,NA,NA,NA,NA,Signature 1,Fig-3,7 April 2025,Aiyshaaaa,Aiyshaaaa,Heatmap showing the correlation of the differentially abundant (DA) species with mean nutrient intake and the Healthy Food Diversity (HFD) index.,increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas ruminantium,1783272|1239|909932|909929|1843491|970|971,Complete,Svetlana up
bsdb:39854172/5/2,39854172,"cross-sectional observational, not case-control",39854172,10.1093/infdis/jiaf043,https://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiaf043/7978852#502884056,"MacCann R., Li J., Leon A.A.G., Negi R., Alalwan D., Tinago W., McGettrick P., Cotter A.G., Landay A., Sabin C., O'Toole P.W. , Mallon P.W.","Associations between the gut microbiome, inflammation and cardiovascular profiles in people with HIV",The Journal of infectious diseases,2025,"HIV, cardiovascular disease, inflammation, microbiome",Experiment 5,Ireland,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Low HFD Index,High HFD Index,High Healthy Food Diversity Index recorded in individuals diagnosed with HIV (Human Immunodeficiency Virus),NA,NA,NA,16S,34,Illumina,centered log-ratio,"Spearman Correlation,ANCOM-BC",0.1,TRUE,NA,NA,"age,antiretroviral therapy,sex",NA,NA,NA,NA,NA,NA,Signature 2,Fig-3,7 April 2025,Aiyshaaaa,Aiyshaaaa,Heatmap showing the correlation of the differentially abundant (DA) species with mean nutrient intake and the Healthy Food Diversity (HFD) index.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,1783272|1239|186801|186802|186806|1730|39496,Complete,Svetlana up
bsdb:39854172/6/1,39854172,"cross-sectional observational, not case-control",39854172,10.1093/infdis/jiaf043,https://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiaf043/7978852#502884056,"MacCann R., Li J., Leon A.A.G., Negi R., Alalwan D., Tinago W., McGettrick P., Cotter A.G., Landay A., Sabin C., O'Toole P.W. , Mallon P.W.","Associations between the gut microbiome, inflammation and cardiovascular profiles in people with HIV",The Journal of infectious diseases,2025,"HIV, cardiovascular disease, inflammation, microbiome",Experiment 6,Ireland,Homo sapiens,Feces,UBERON:0001988,Fat intake measurement,EFO:0010809,Low PUFA Intake (Polyunsaturated Fat Intake),High PUFA Intake (Polyunsaturated Fat Intake),High Polyunsaturated Fat Intake recorded in individuals diagnosed with HIV (Human Immunodeficiency Virus),NA,NA,NA,16S,34,Illumina,centered log-ratio,"Spearman Correlation,ANCOM-BC",0.1,TRUE,NA,NA,"age,antiretroviral therapy,sex",NA,NA,NA,NA,NA,NA,Signature 1,Fig-3,7 April 2025,Aiyshaaaa,Aiyshaaaa,Heatmap showing the correlation of the differentially abundant (DA) species with mean nutrient intake and the Healthy Food Diversity (HFD) index.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola barnesiae,3379134|976|200643|171549|815|909656|376804,Complete,Svetlana up
bsdb:39854172/7/1,39854172,"cross-sectional observational, not case-control",39854172,10.1093/infdis/jiaf043,https://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiaf043/7978852#502884056,"MacCann R., Li J., Leon A.A.G., Negi R., Alalwan D., Tinago W., McGettrick P., Cotter A.G., Landay A., Sabin C., O'Toole P.W. , Mallon P.W.","Associations between the gut microbiome, inflammation and cardiovascular profiles in people with HIV",The Journal of infectious diseases,2025,"HIV, cardiovascular disease, inflammation, microbiome",Experiment 7,Ireland,Homo sapiens,Feces,UBERON:0001988,Cholesterol,CHEBI:16113,Low Cholesterol Intake,High Cholesterol Intake,High Cholesterol Intake recorded in individuals diagnosed with HIV (Human Immunodeficiency Virus),NA,NA,NA,16S,34,Illumina,centered log-ratio,"Spearman Correlation,ANCOM-BC",0.1,TRUE,NA,NA,"age,antiretroviral therapy,sex",NA,NA,NA,NA,NA,NA,Signature 1,Fig-3,7 April 2025,Aiyshaaaa,Aiyshaaaa,Heatmap showing the correlation of the differentially abundant (DA) species with mean nutrient intake and the Healthy Food Diversity (HFD) index.,decreased,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter piscolens,3384194|508458|649775|649776|3029088|638847|638849,Complete,Svetlana up
bsdb:39854172/8/1,39854172,"cross-sectional observational, not case-control",39854172,10.1093/infdis/jiaf043,https://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiaf043/7978852#502884056,"MacCann R., Li J., Leon A.A.G., Negi R., Alalwan D., Tinago W., McGettrick P., Cotter A.G., Landay A., Sabin C., O'Toole P.W. , Mallon P.W.","Associations between the gut microbiome, inflammation and cardiovascular profiles in people with HIV",The Journal of infectious diseases,2025,"HIV, cardiovascular disease, inflammation, microbiome",Experiment 8,Ireland,Homo sapiens,Feces,UBERON:0001988,Fat intake measurement,EFO:0010809,Low Trans Fat Intake,High Trans Fat Intake,High Trans Fat Intake recorded in individuals diagnosed with HIV (Human Immunodeficiency Virus),NA,NA,NA,16S,34,Illumina,centered log-ratio,"Spearman Correlation,ANCOM-BC",0.1,TRUE,NA,NA,"age,antiretroviral therapy,sex",NA,NA,NA,NA,NA,NA,Signature 1,Fig-3,8 April 2025,Aiyshaaaa,Aiyshaaaa,Heatmap showing the correlation of the differentially abundant (DA) species with mean nutrient intake and the Healthy Food Diversity (HFD) index.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,1783272|1239|186801|186802|216572|1263|40518,Complete,Svetlana up
bsdb:39854172/8/2,39854172,"cross-sectional observational, not case-control",39854172,10.1093/infdis/jiaf043,https://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiaf043/7978852#502884056,"MacCann R., Li J., Leon A.A.G., Negi R., Alalwan D., Tinago W., McGettrick P., Cotter A.G., Landay A., Sabin C., O'Toole P.W. , Mallon P.W.","Associations between the gut microbiome, inflammation and cardiovascular profiles in people with HIV",The Journal of infectious diseases,2025,"HIV, cardiovascular disease, inflammation, microbiome",Experiment 8,Ireland,Homo sapiens,Feces,UBERON:0001988,Fat intake measurement,EFO:0010809,Low Trans Fat Intake,High Trans Fat Intake,High Trans Fat Intake recorded in individuals diagnosed with HIV (Human Immunodeficiency Virus),NA,NA,NA,16S,34,Illumina,centered log-ratio,"Spearman Correlation,ANCOM-BC",0.1,TRUE,NA,NA,"age,antiretroviral therapy,sex",NA,NA,NA,NA,NA,NA,Signature 2,Fig-3,8 April 2025,Aiyshaaaa,Aiyshaaaa,Heatmap showing the correlation of the differentially abundant (DA) species with mean nutrient intake and the Healthy Food Diversity (HFD) index.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola barnesiae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter piscolens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella albensis",3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|818;1783272|1239|909932|909929|1843491|158846|158847;3379134|976|200643|171549|815|909656|376804;3384194|508458|649775|649776|3029088|638847|638849;3379134|976|200643|171549|171552|2974251|77768,Complete,Svetlana up
bsdb:39854172/9/1,39854172,"cross-sectional observational, not case-control",39854172,10.1093/infdis/jiaf043,https://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiaf043/7978852#502884056,"MacCann R., Li J., Leon A.A.G., Negi R., Alalwan D., Tinago W., McGettrick P., Cotter A.G., Landay A., Sabin C., O'Toole P.W. , Mallon P.W.","Associations between the gut microbiome, inflammation and cardiovascular profiles in people with HIV",The Journal of infectious diseases,2025,"HIV, cardiovascular disease, inflammation, microbiome",Experiment 9,Ireland,Homo sapiens,Feces,UBERON:0001988,Energy intake,EFO:0003939,Low Energy Intake,High Energy Intake,High Energy Intake recorded in individuals diagnosed with HIV (Human Immunodeficiency Virus),NA,NA,NA,16S,34,Illumina,centered log-ratio,"Spearman Correlation,ANCOM-BC",0.1,TRUE,NA,NA,"age,antiretroviral therapy,sex",NA,NA,NA,NA,NA,NA,Signature 1,Fig-3 and S5,9 April 2025,Aiyshaaaa,Aiyshaaaa,Heatmap showing the correlation of the differentially abundant (DA) species and genus level with mean nutrient intake and the Healthy Food Diversity (HFD) index.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola barnesiae",3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|909656|310297;3379134|976|200643|171549|815|909656|376804,Complete,Svetlana up
bsdb:39854172/10/1,39854172,"cross-sectional observational, not case-control",39854172,10.1093/infdis/jiaf043,https://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiaf043/7978852#502884056,"MacCann R., Li J., Leon A.A.G., Negi R., Alalwan D., Tinago W., McGettrick P., Cotter A.G., Landay A., Sabin C., O'Toole P.W. , Mallon P.W.","Associations between the gut microbiome, inflammation and cardiovascular profiles in people with HIV",The Journal of infectious diseases,2025,"HIV, cardiovascular disease, inflammation, microbiome",Experiment 10,Ireland,Homo sapiens,Feces,UBERON:0001988,Carbohydrate intake measurement,EFO:0010811,Low Carbohydrate Intake,High Carbohydrate Intake,High Carbohydrate Intake recorded in individuals diagnosed with HIV (Human Immunodeficiency Virus),NA,NA,NA,16S,34,Illumina,centered log-ratio,"Spearman Correlation,ANCOM-BC",0.1,TRUE,NA,NA,"age,antiretroviral therapy,sex",NA,NA,NA,NA,NA,NA,Signature 1,Fig-3,9 April 2025,Aiyshaaaa,Aiyshaaaa,Heatmap showing the correlation of the differentially abundant (DA) species with mean nutrient intake and the Healthy Food Diversity (HFD) index.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola barnesiae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius",3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|815|816|28111;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|2005519|397864|487174;3379134|976|200643|171549|815|909656|376804;3379134|976|200643|171549|815|909656|310297,Complete,Svetlana up
bsdb:39854172/11/1,39854172,"cross-sectional observational, not case-control",39854172,10.1093/infdis/jiaf043,https://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiaf043/7978852#502884056,"MacCann R., Li J., Leon A.A.G., Negi R., Alalwan D., Tinago W., McGettrick P., Cotter A.G., Landay A., Sabin C., O'Toole P.W. , Mallon P.W.","Associations between the gut microbiome, inflammation and cardiovascular profiles in people with HIV",The Journal of infectious diseases,2025,"HIV, cardiovascular disease, inflammation, microbiome",Experiment 11,Ireland,Homo sapiens,Feces,UBERON:0001988,Fat intake measurement,EFO:0010809,Low Saturated Fat Intake,High Saturated Fat Intake,High Saturated Fat Intake recorded in individuals diagnosed with HIV (Human Immunodeficiency Virus),NA,NA,NA,16S,34,Illumina,centered log-ratio,"Spearman Correlation,ANCOM-BC",0.1,TRUE,NA,NA,"age,antiretroviral therapy,sex",NA,NA,NA,NA,NA,NA,Signature 1,Fig-3,9 April 2025,Aiyshaaaa,Aiyshaaaa,Heatmap showing the correlation of the differentially abundant (DA) species with mean nutrient intake and the Healthy Food Diversity (HFD) index.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,1783272|1239|186801|186802|216572|1263|40518,Complete,Svetlana up
bsdb:39854172/11/2,39854172,"cross-sectional observational, not case-control",39854172,10.1093/infdis/jiaf043,https://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiaf043/7978852#502884056,"MacCann R., Li J., Leon A.A.G., Negi R., Alalwan D., Tinago W., McGettrick P., Cotter A.G., Landay A., Sabin C., O'Toole P.W. , Mallon P.W.","Associations between the gut microbiome, inflammation and cardiovascular profiles in people with HIV",The Journal of infectious diseases,2025,"HIV, cardiovascular disease, inflammation, microbiome",Experiment 11,Ireland,Homo sapiens,Feces,UBERON:0001988,Fat intake measurement,EFO:0010809,Low Saturated Fat Intake,High Saturated Fat Intake,High Saturated Fat Intake recorded in individuals diagnosed with HIV (Human Immunodeficiency Virus),NA,NA,NA,16S,34,Illumina,centered log-ratio,"Spearman Correlation,ANCOM-BC",0.1,TRUE,NA,NA,"age,antiretroviral therapy,sex",NA,NA,NA,NA,NA,NA,Signature 2,Fig-3,9 April 2025,Aiyshaaaa,Aiyshaaaa,Heatmap showing the correlation of the differentially abundant (DA) species with mean nutrient intake and the Healthy Food Diversity (HFD) index.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola barnesiae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter piscolens",3379134|976|200643|171549|815|816|28116;1783272|1239|909932|909929|1843491|158846|158847;3379134|976|200643|171549|815|909656|376804;3379134|976|200643|171549|815|909656|310297;3384194|508458|649775|649776|3029088|638847|638849,Complete,Svetlana up
bsdb:39854172/13/1,39854172,"cross-sectional observational, not case-control",39854172,10.1093/infdis/jiaf043,https://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiaf043/7978852#502884056,"MacCann R., Li J., Leon A.A.G., Negi R., Alalwan D., Tinago W., McGettrick P., Cotter A.G., Landay A., Sabin C., O'Toole P.W. , Mallon P.W.","Associations between the gut microbiome, inflammation and cardiovascular profiles in people with HIV",The Journal of infectious diseases,2025,"HIV, cardiovascular disease, inflammation, microbiome",Experiment 13,Ireland,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Low Fiber Intake,High Fiber Intake,High Fiber Intake recorded in individuals diagnosed with HIV (Human Immunodeficiency Virus),NA,NA,NA,16S,34,Illumina,centered log-ratio,"Spearman Correlation,ANCOM-BC",0.1,TRUE,NA,NA,"age,antiretroviral therapy,sex",NA,NA,NA,NA,NA,NA,Signature 1,Fig-3,9 April 2025,Aiyshaaaa,Aiyshaaaa,Heatmap showing the correlation of the differentially abundant (DA) species with mean nutrient intake and the Healthy Food Diversity (HFD) index.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,3379134|976|200643|171549|171550|239759|28117,Complete,Svetlana up
bsdb:39856212/6/1,39856212,"cross-sectional observational, not case-control",39856212,10.1038/s41598-025-87546-y,NA,"Boonchooduang N., Louthrenoo O., Likhitweerawong N., Kunasol C., Thonusin C., Sriwichaiin S., Nawara W., Chattipakorn N. , Chattipakorn S.C.",Impact of psychostimulants on microbiota and short-chain fatty acids alterations in children with attention-deficit/hyperactivity disorder,Scientific reports,2025,"ADHD, Biomarkers, Children, Gut microbiota, Psychostimulants, SCFAs",Experiment 6,Thailand,Homo sapiens,Feces,UBERON:0001988,Attention deficit-hyperactivity disorder,MONDO:0007743,Healthy controls,Unmedicated Attention-deficit hyperactivity disorder (ADHD),This group consists of children aged 6–12 years diagnosed with ADHD who have not received psychostimulant medication for their condition.,10,10,2 weeks,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 2,23 March 2025,Joiejoie,Joiejoie,Differential abundance of gut microbiota among healthy controls and children with unmedicated ADHD.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Kytococcaceae|g__Kytococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,s__unidentified,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium",1783272|1239|91061|186826|186827;3379134|1224|28211;3379134|1224|28211|204458|76892|41275;3379134|1224|28211|204458|76892;3379134|1224|28211|204458;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85006|145357;3379134|1224|28211|356|212791;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|1385|539738;3379134|1224|1236|135625|712|724;3379134|1224|28211|356;1783272|201174|1760|85006|2805426|57499;3384189|32066|203490|203491|1129771;1783272|201174|1760|85006;1783272|201174|1760|85006|1268|1269;3379134|1224|1236|2887326|468;1783272|201174|1760|85007;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481;3379134|1224|28211|204455|31989;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836;1783272|201174|1760|85009|31957;1783272|201174|1760|85009;3379134|1224|1236|72274|135621;3379134|1224|1236|72274;3379134|1224|1236|72274|135621|286;3379134|1224|28211|356|82115;3379134|1224|28211|204455;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;1783272|1239|909932|1843489|31977|29465;32644;1783272|201174|1760|85009|31957|1912216,Complete,Svetlana up
bsdb:39856212/6/2,39856212,"cross-sectional observational, not case-control",39856212,10.1038/s41598-025-87546-y,NA,"Boonchooduang N., Louthrenoo O., Likhitweerawong N., Kunasol C., Thonusin C., Sriwichaiin S., Nawara W., Chattipakorn N. , Chattipakorn S.C.",Impact of psychostimulants on microbiota and short-chain fatty acids alterations in children with attention-deficit/hyperactivity disorder,Scientific reports,2025,"ADHD, Biomarkers, Children, Gut microbiota, Psychostimulants, SCFAs",Experiment 6,Thailand,Homo sapiens,Feces,UBERON:0001988,Attention deficit-hyperactivity disorder,MONDO:0007743,Healthy controls,Unmedicated Attention-deficit hyperactivity disorder (ADHD),This group consists of children aged 6–12 years diagnosed with ADHD who have not received psychostimulant medication for their condition.,10,10,2 weeks,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Fig. 2,23 March 2025,Joiejoie,"Joiejoie,KateRasheed",Differential abundance of gut microbiota among healthy controls and children with unmedicated ADHD.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium DTU089,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:352,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Umbribacter|s__Umbribacter vaginalis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Pseudomonadati|p__Thermodesulfobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",1783272|1239|186801|186802|216572|258514;1783272|201174;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|186802|186806|264995;1783272|1239|186801|3085636|186803|207244;1783272|1239;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|2005519;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|1470353;1783272|1239|186801;1783272|1239|186801|186802|1671661;1783272|1239|186801|186802|31979|1485|1262798;1783272|201174|84998|84999|84107|102106;1783272|1239|526524|526525|2810280;1783272|201174|84998|84999|84107;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998|1643822|1643826|3472368|1588753;1783272|201174|84998;3379134|200940|3031449;1783272|201174|84998|1643822|1643826;3379134|1224|1236|91347|543;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;1783272|1239|91061|186826|1300|1357;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3082720|186804;1783272|201174|84998|1643822|1643826|84108;3379134|1224|28216|80840|995019|40544;3379134|1224|28216|80840|995019;3379134|200940;1783272|1239|186801|3085636|186803|1506577;3379134|74201;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Svetlana up
bsdb:39856212/7/1,39856212,"cross-sectional observational, not case-control",39856212,10.1038/s41598-025-87546-y,NA,"Boonchooduang N., Louthrenoo O., Likhitweerawong N., Kunasol C., Thonusin C., Sriwichaiin S., Nawara W., Chattipakorn N. , Chattipakorn S.C.",Impact of psychostimulants on microbiota and short-chain fatty acids alterations in children with attention-deficit/hyperactivity disorder,Scientific reports,2025,"ADHD, Biomarkers, Children, Gut microbiota, Psychostimulants, SCFAs",Experiment 7,Thailand,Homo sapiens,Feces,UBERON:0001988,Attention deficit-hyperactivity disorder,MONDO:0007743,Unmedicated ADHD,Medicated ADHD (ADHD + MPH),This group consists of children aged 6–12 years diagnosed with ADHD who are undergoing treatment with medication,10,10,2 weeks,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,"age,sex",NA,decreased,decreased,NA,NA,NA,unchanged,Signature 1,Fig. 2,23 March 2025,Joiejoie,Joiejoie,Differential abundance of gut microbiota among medicated ADHD and children with unmedicated ADHD.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes",1783272|201174|1760|85011;1783272|201174|1760|85011|2062;1783272|1239|186801|3085636|186803|207244,Complete,Svetlana up
bsdb:39856212/7/2,39856212,"cross-sectional observational, not case-control",39856212,10.1038/s41598-025-87546-y,NA,"Boonchooduang N., Louthrenoo O., Likhitweerawong N., Kunasol C., Thonusin C., Sriwichaiin S., Nawara W., Chattipakorn N. , Chattipakorn S.C.",Impact of psychostimulants on microbiota and short-chain fatty acids alterations in children with attention-deficit/hyperactivity disorder,Scientific reports,2025,"ADHD, Biomarkers, Children, Gut microbiota, Psychostimulants, SCFAs",Experiment 7,Thailand,Homo sapiens,Feces,UBERON:0001988,Attention deficit-hyperactivity disorder,MONDO:0007743,Unmedicated ADHD,Medicated ADHD (ADHD + MPH),This group consists of children aged 6–12 years diagnosed with ADHD who are undergoing treatment with medication,10,10,2 weeks,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,"age,sex",NA,decreased,decreased,NA,NA,NA,unchanged,Signature 2,Fig. 2,23 March 2025,Joiejoie,Joiejoie,Differential abundance of gut microbiota among medicated ADHD and children with unmedicated ADHD.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Kytococcaceae|g__Kytococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter",3379134|1224|28211;3379134|1224|1236|72274;3379134|1224|1236|135625;1783272|201174|1760|85007;3379134|1224|28211|204458;3379134|1224|28211|204455;1783272|201174|1760|85006;3379134|1224|1236|135625|712;1783272|201174|1760|85006|145357;1783272|1239|91061|1385|90964;3379134|1224|28216|206351|481;1783272|201174|1760|85007|1653;3379134|1224|28216|80840|119060;3379134|1224|28211|204458|76892;3379134|1224|28211|204455|31989;3379134|1224|1236|135625|712|724;3379134|1224|28211|356|212791;1783272|201174|1760|85006|2805426|57499;1783272|201174|1760|85006|1268|1269;1783272|1239|91061|1385|90964|1279;1783272|201174|1760|85007|1653|1716;3379134|1224|28211|204458|76892|41275;1783272|1239|186801|186802|216572;3379134|976|200643|171549|1853231|283168,Complete,Svetlana up
bsdb:39856212/8/1,39856212,"cross-sectional observational, not case-control",39856212,10.1038/s41598-025-87546-y,NA,"Boonchooduang N., Louthrenoo O., Likhitweerawong N., Kunasol C., Thonusin C., Sriwichaiin S., Nawara W., Chattipakorn N. , Chattipakorn S.C.",Impact of psychostimulants on microbiota and short-chain fatty acids alterations in children with attention-deficit/hyperactivity disorder,Scientific reports,2025,"ADHD, Biomarkers, Children, Gut microbiota, Psychostimulants, SCFAs",Experiment 8,Thailand,Homo sapiens,Feces,UBERON:0001988,Attention deficit-hyperactivity disorder,MONDO:0007743,Healthy controls,Medicated ADHD (ADHD + MPH),This group consists of children aged 6–12 years diagnosed with ADHD who are undergoing treatment with medication,10,10,2 weeks,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 2,23 March 2025,Joiejoie,Joiejoie,Differential abundance of gut microbiota among healthy controls and children with medicated ADHD,increased,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,1783272|1239|1737404|1737405|1570339|543311,Complete,Svetlana up
bsdb:39856736/1/1,39856736,laboratory experiment,39856736,10.1186/s40168-024-02020-7,NA,"Wang J., E G., Zhang M., Zhang Y., Bai T., Pu X., Liu J., Guo X., Sarker S. , Cheng L.",No rumen fermentation profiles and associated microbial diversities difference were found between Hu sheep and Karakul sheep fed a cottonseed hull diet,Microbiome,2025,"Dynamic changes, Hu sheep, Karakul sheep, Rumen bacteria, Rumen metabolome",Experiment 1,China,Ovis aries,Rumen,UBERON:0007365,Diet,EFO:0002755,IH (Hu sheep in Stage 1),IK (Karakul sheep in Stage 1),"The sheep in this group were in the weaning period (15 to 30 days) and they were fed a basic diet composed of lamb pellets (60%) and green hay (40%). On the final day, they were fasted for 24 hours (withholding water for 2 hours).",18,18,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 6 A&B,19 March 2025,Victoria,Victoria,The cladogram and influence distribution histogram of differential bacterial cladogram and influence distribution histogram showing significant differences in rumen bacteria between Hu sheep and Karakul sheep at stage 1.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota",3379134|976|200643|171549;3379134|976|200643;3379134|976,Complete,Svetlana up
bsdb:39856736/1/2,39856736,laboratory experiment,39856736,10.1186/s40168-024-02020-7,NA,"Wang J., E G., Zhang M., Zhang Y., Bai T., Pu X., Liu J., Guo X., Sarker S. , Cheng L.",No rumen fermentation profiles and associated microbial diversities difference were found between Hu sheep and Karakul sheep fed a cottonseed hull diet,Microbiome,2025,"Dynamic changes, Hu sheep, Karakul sheep, Rumen bacteria, Rumen metabolome",Experiment 1,China,Ovis aries,Rumen,UBERON:0007365,Diet,EFO:0002755,IH (Hu sheep in Stage 1),IK (Karakul sheep in Stage 1),"The sheep in this group were in the weaning period (15 to 30 days) and they were fed a basic diet composed of lamb pellets (60%) and green hay (40%). On the final day, they were fasted for 24 hours (withholding water for 2 hours).",18,18,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 6 A&B,19 March 2025,Victoria,Victoria,The cladogram and influence distribution histogram of differential bacterial cladogram and influence distribution histogram showing significant differences in rumen bacteria between Hu sheep and Karakul sheep at stage 1.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales",1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636,Complete,Svetlana up
bsdb:39856736/2/1,39856736,laboratory experiment,39856736,10.1186/s40168-024-02020-7,NA,"Wang J., E G., Zhang M., Zhang Y., Bai T., Pu X., Liu J., Guo X., Sarker S. , Cheng L.",No rumen fermentation profiles and associated microbial diversities difference were found between Hu sheep and Karakul sheep fed a cottonseed hull diet,Microbiome,2025,"Dynamic changes, Hu sheep, Karakul sheep, Rumen bacteria, Rumen metabolome",Experiment 2,China,Ovis aries,Rumen,UBERON:0007365,Diet,EFO:0002755,IIH (Hu sheep in Stage 2),IIK (Karakul sheep in Stage 2),"The sheep in this group were in the supplementary feeding period (31 to 90 days) and they were fed the supplementary feeding period diet, during this feeding period, cottonseed hulls were the main roughage source. On the final day, they were fasted for 24 hours (withholding water for 2 hours).",18,18,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,decreased,NA,unchanged,Signature 1,Figure 6 A&B,19 March 2025,Victoria,Victoria,The cladogram and influence distribution histogram of differential bacterial cladogram and influence distribution histogram showing significant differences in rumen bacteria between Hu sheep and Karakul sheep at stage 2.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Quinella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|g__Candidatus Alcium|s__Candidatus Alcium sp. F082",1783272|1239|186801|186802;1783272|1239|909932|1843489|31977|1567;1783272|1239|909932|909929|1843491;3379134|976|200643|171549|3443717|1768115,Complete,Svetlana up
bsdb:39856736/2/2,39856736,laboratory experiment,39856736,10.1186/s40168-024-02020-7,NA,"Wang J., E G., Zhang M., Zhang Y., Bai T., Pu X., Liu J., Guo X., Sarker S. , Cheng L.",No rumen fermentation profiles and associated microbial diversities difference were found between Hu sheep and Karakul sheep fed a cottonseed hull diet,Microbiome,2025,"Dynamic changes, Hu sheep, Karakul sheep, Rumen bacteria, Rumen metabolome",Experiment 2,China,Ovis aries,Rumen,UBERON:0007365,Diet,EFO:0002755,IIH (Hu sheep in Stage 2),IIK (Karakul sheep in Stage 2),"The sheep in this group were in the supplementary feeding period (31 to 90 days) and they were fed the supplementary feeding period diet, during this feeding period, cottonseed hulls were the main roughage source. On the final day, they were fasted for 24 hours (withholding water for 2 hours).",18,18,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,decreased,NA,unchanged,Signature 2,Figure 6 A&B,19 March 2025,Victoria,Victoria,The cladogram and influence distribution histogram of differential bacterial cladogram and influence distribution histogram showing significant differences in rumen bacteria between Hu sheep and Karakul sheep at stage 2.,decreased,"s__uncultured rumen bacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Succiniclasticum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",136703;1783272|1239|909932|1843488|909930;1783272|1239|909932|1843488;1783272|1239|909932|1843488|909930|40840;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552,Complete,Svetlana up
bsdb:39856736/3/1,39856736,laboratory experiment,39856736,10.1186/s40168-024-02020-7,NA,"Wang J., E G., Zhang M., Zhang Y., Bai T., Pu X., Liu J., Guo X., Sarker S. , Cheng L.",No rumen fermentation profiles and associated microbial diversities difference were found between Hu sheep and Karakul sheep fed a cottonseed hull diet,Microbiome,2025,"Dynamic changes, Hu sheep, Karakul sheep, Rumen bacteria, Rumen metabolome",Experiment 3,China,Ovis aries,Rumen,UBERON:0007365,Diet,EFO:0002755,IIIH (Hu sheep in Stage 3),IIIK (Karakul sheep in Stage 3),"The sheep in this group were in the complete feeding period (91 to 150 days) and they were fed the supplementary feeding period diet, during this feeding period, cottonseed hulls were the main roughage source. On the final day, they were fasted for 24 hours (withholding water for 2 hours).",18,18,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 6 A&B,19 March 2025,Victoria,Victoria,The cladogram and influence distribution histogram of differential bacterial cladogram and influence distribution histogram showing significant differences in rumen bacteria between Hu sheep and Karakul sheep at stage 3.,increased,"k__Bacillati|p__Bacillota|c__Bacilli,s__uncultured rumen bacterium,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium",1783272|1239|91061;136703;3384194|508458|649775|649776|3029087|1434006,Complete,Svetlana up
bsdb:39856736/3/2,39856736,laboratory experiment,39856736,10.1186/s40168-024-02020-7,NA,"Wang J., E G., Zhang M., Zhang Y., Bai T., Pu X., Liu J., Guo X., Sarker S. , Cheng L.",No rumen fermentation profiles and associated microbial diversities difference were found between Hu sheep and Karakul sheep fed a cottonseed hull diet,Microbiome,2025,"Dynamic changes, Hu sheep, Karakul sheep, Rumen bacteria, Rumen metabolome",Experiment 3,China,Ovis aries,Rumen,UBERON:0007365,Diet,EFO:0002755,IIIH (Hu sheep in Stage 3),IIIK (Karakul sheep in Stage 3),"The sheep in this group were in the complete feeding period (91 to 150 days) and they were fed the supplementary feeding period diet, during this feeding period, cottonseed hulls were the main roughage source. On the final day, they were fasted for 24 hours (withholding water for 2 hours).",18,18,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 6 A&B,19 March 2025,Victoria,Victoria,The cladogram and influence distribution histogram of differential bacterial cladogram and influence distribution histogram showing significant differences in rumen bacteria between Hu sheep and Karakul sheep at stage 3.,decreased,s__uncultured rumen bacterium,136703,Complete,Svetlana up
bsdb:39865153/1/1,39865153,"cross-sectional observational, not case-control",39865153,10.1038/s42003-025-07559-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC11770077/,"Wu Z., Jiang M., Jia M., Sang J., Wang Q., Xu Y., Qi L., Yang W. , Feng L.",The difference of oropharyngeal microbiome during acute respiratory viral infections in infants and children,Communications biology,2025,NA,Experiment 1,China,Homo sapiens,Oropharynx,UBERON:0001729,Respiratory tract infectious disease,MONDO:0024355,Inpatients,Outpatients,Children with Acute respiratory infections (ARI) who visited the hospital but did not require hospitalization.,49,60,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 2F and G,4 May 2025,Shulamite,Shulamite,LDA score and relative abundance of 15 significantly different taxa calculated by LEfSe analysis.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella|s__Brucella anthropi,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter|s__Achromobacter aegrifaciens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter|s__Achromobacter marplatensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter|s__Achromobacter xylosoxidans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas putida,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter kobei,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter|s__Achromobacter pestifer",3379134|1224|28211|356|118882;3379134|1224|28211|356|118882|234;3379134|1224|28211|356|118882|234|529;3379134|1224|28216|80840|506;3379134|1224|28216|80840|506|222;3379134|1224|28216|80840;3379134|1224|28216|80840|506|222|1287736;3379134|1224|28216|80840|506|222|470868;3379134|1224|28216|80840|506|222|85698;3379134|1224|1236|72274|135621|286|303;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347;3379134|1224|1236|91347|543|547|208224;3379134|1224|28216|80840|506|222|1353889,Complete,KateRasheed
bsdb:39865153/2/1,39865153,"cross-sectional observational, not case-control",39865153,10.1038/s42003-025-07559-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC11770077/,"Wu Z., Jiang M., Jia M., Sang J., Wang Q., Xu Y., Qi L., Yang W. , Feng L.",The difference of oropharyngeal microbiome during acute respiratory viral infections in infants and children,Communications biology,2025,NA,Experiment 2,China,Homo sapiens,Oropharynx,UBERON:0001729,Respiratory tract infectious disease,MONDO:0024355,Inpatients,Outpatients,Children with ARI who visited the hospital but did not require hospitalization.,49,60,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table S3,4 May 2025,Shulamite,Shulamite,Two-fold changes of microbial abundances between inpatients and outpatients.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter kobei,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter|s__Achromobacter marplatensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas putida,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella|s__Brucella anthropi,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter|s__Achromobacter aegrifaciens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter|s__Achromobacter xylosoxidans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter|s__Achromobacter insolitus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter|s__Achromobacter pestifer,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum|s__Ochrobactrum sp. CGA5",3379134|1224|1236|91347|543|547|208224;3379134|1224|28216|80840|506|222|470868;3379134|1224|1236|72274|135621|286|303;3379134|1224|28211|356|118882|234|529;3379134|1224|28216|80840|506|222|1287736;3379134|1224|28216|80840|506|222|85698;3379134|1224|28216|80840|506|222|217204;3379134|1224|28216|80840|506|222|1353889;3379134|1224|28211|356|118882|528|2583453,Complete,KateRasheed
bsdb:39865153/3/1,39865153,"cross-sectional observational, not case-control",39865153,10.1038/s42003-025-07559-1,https://pmc.ncbi.nlm.nih.gov/articles/PMC11770077/,"Wu Z., Jiang M., Jia M., Sang J., Wang Q., Xu Y., Qi L., Yang W. , Feng L.",The difference of oropharyngeal microbiome during acute respiratory viral infections in infants and children,Communications biology,2025,NA,Experiment 3,China,Homo sapiens,Oropharynx,UBERON:0001729,Fatigue,HP:0012378,Non-fatigue,Fatigue,Children who exhibited fatigue as part of their clinical presentation of ARI.,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,decreased,NA,NA,NA,unchanged,Signature 1,Table S4,4 May 2025,Shulamite,"Shulamite,Anne-mariesharp",Differences of taxonomic relative abundance between disease-related symptom groups by LEfSe analysis.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella catarrhalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas catoniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis",3379134|1224|1236|2887326|468|475|480;3379134|976|200643|171549|171551|836|41976;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|1300|1357|1358,Complete,KateRasheed
bsdb:39868783/1/1,39868783,"cross-sectional observational, not case-control",39868783,10.1128/spectrum.01255-24,NA,"Zhao H., Wang C., Narsing Rao M.P., Rafiq M., Luo G., Li S. , Kang Y.-.Q.",Effects of vaginal microbiota on <i>in vitro</i> fertilization outcomes in women with different infertility causes,Microbiology spectrum,2025,"embryo transfer, in vitro fertilization, infertility, intracytoplasmic sperm injection, vaginal microbiota, vaginal swab",Experiment 1,China,Homo sapiens,Vaginal fluid,UBERON:0036243,Female infertility,EFO:0008560,"Tubal Factor Infertility, Polycystic Ovary Syndrome(TFI, PCOS) group",Control group (NL),This group consists of fertile women.,77,37,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3D,31 March 2025,Victoria,Victoria,"Histogram of taxa with differential abundance among the NL, PCOS, and TFI groups using the computed LDA score.",increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia vaginalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Ensifer,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Dyella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Duganella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Streptosporangiales|f__Thermomonosporaceae|g__Actinomadura,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Acetobacter",3384189|32066|203490|203491|1129771|168808|187101;1783272|1239|186801|186802|186806|1730|142586;3379134|1224|28216|80840|75682|963;3379134|1224|28211|356|82115|106591;3379134|1224|1236|135614|1775411|231454;3379134|1224|28216|80840|75682|75654;1783272|201174|1760|85012|2012|1988;3379134|1224|28211|3120395|433|434,Complete,Svetlana up
bsdb:39868783/2/1,39868783,"cross-sectional observational, not case-control",39868783,10.1128/spectrum.01255-24,NA,"Zhao H., Wang C., Narsing Rao M.P., Rafiq M., Luo G., Li S. , Kang Y.-.Q.",Effects of vaginal microbiota on <i>in vitro</i> fertilization outcomes in women with different infertility causes,Microbiology spectrum,2025,"embryo transfer, in vitro fertilization, infertility, intracytoplasmic sperm injection, vaginal microbiota, vaginal swab",Experiment 2,China,Homo sapiens,Vaginal fluid,UBERON:0036243,Female infertility,EFO:0008560,"Polycystic Ovary Syndrome, Control(PCOS, NL) group",Tubal Factor Infertility group (TFI),This group consists of women with tubal factor infertility.,69,45,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3D,31 March 2025,Victoria,Victoria,"Histogram of taxa with differential abundance among the NL, PCOS, and TFI groups using the computed LDA score.",increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804,Complete,Svetlana up
bsdb:39868783/4/1,39868783,"cross-sectional observational, not case-control",39868783,10.1128/spectrum.01255-24,NA,"Zhao H., Wang C., Narsing Rao M.P., Rafiq M., Luo G., Li S. , Kang Y.-.Q.",Effects of vaginal microbiota on <i>in vitro</i> fertilization outcomes in women with different infertility causes,Microbiology spectrum,2025,"embryo transfer, in vitro fertilization, infertility, intracytoplasmic sperm injection, vaginal microbiota, vaginal swab",Experiment 4,China,Homo sapiens,Vaginal fluid,UBERON:0036243,Female infertility,EFO:0008560,Polycystic Ovary Syndrome (PCOS) group,Tubal factor infertility (TFI)  group,This group consists of women with tubal factor infertility.,32,45,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 4B,31 March 2025,Victoria,Victoria,t-test analysis of different microbes at the species and genus levels.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners",1783272|1239|91061|186826|33958|2767887;1783272|1239|91061|186826|33958|1578|147802,Complete,Svetlana up
bsdb:39868783/4/2,39868783,"cross-sectional observational, not case-control",39868783,10.1128/spectrum.01255-24,NA,"Zhao H., Wang C., Narsing Rao M.P., Rafiq M., Luo G., Li S. , Kang Y.-.Q.",Effects of vaginal microbiota on <i>in vitro</i> fertilization outcomes in women with different infertility causes,Microbiology spectrum,2025,"embryo transfer, in vitro fertilization, infertility, intracytoplasmic sperm injection, vaginal microbiota, vaginal swab",Experiment 4,China,Homo sapiens,Vaginal fluid,UBERON:0036243,Female infertility,EFO:0008560,Polycystic Ovary Syndrome (PCOS) group,Tubal factor infertility (TFI)  group,This group consists of women with tubal factor infertility.,32,45,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 4B,31 March 2025,Victoria,Victoria,t-test analysis of different microbes at the species and genus levels.,decreased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,1783272|1239|909932|1843489|31977|39948,Complete,Svetlana up
bsdb:39868783/5/1,39868783,"cross-sectional observational, not case-control",39868783,10.1128/spectrum.01255-24,NA,"Zhao H., Wang C., Narsing Rao M.P., Rafiq M., Luo G., Li S. , Kang Y.-.Q.",Effects of vaginal microbiota on <i>in vitro</i> fertilization outcomes in women with different infertility causes,Microbiology spectrum,2025,"embryo transfer, in vitro fertilization, infertility, intracytoplasmic sperm injection, vaginal microbiota, vaginal swab",Experiment 5,China,Homo sapiens,Vaginal fluid,UBERON:0036243,Polycystic ovary syndrome,EFO:0000660,Polycystic Ovary Syndrome.Pregnant (PCOS.P) group,Polycystic Ovary Syndrome.Non-pregnant (PCOS.NP) group,This group consists of infertile women with Polycystic Ovary Syndrome (PCOS) who are not pregnant.,10,22,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 5E,31 March 2025,Victoria,Victoria,Histogram of taxa with differential abundance computed using LDA scores.,increased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|s__Veillonellaceae bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister propionicifaciens",1783272|544448|31969|2085|2092;1783272|1239|909932|1843489|31977|2049049;3379134|1224|1236|72274|135621|286;3379134|1224|1236|72274|135621;1783272|1239|909932|1843489|31977|39948|308994,Complete,Svetlana up
bsdb:39868783/5/2,39868783,"cross-sectional observational, not case-control",39868783,10.1128/spectrum.01255-24,NA,"Zhao H., Wang C., Narsing Rao M.P., Rafiq M., Luo G., Li S. , Kang Y.-.Q.",Effects of vaginal microbiota on <i>in vitro</i> fertilization outcomes in women with different infertility causes,Microbiology spectrum,2025,"embryo transfer, in vitro fertilization, infertility, intracytoplasmic sperm injection, vaginal microbiota, vaginal swab",Experiment 5,China,Homo sapiens,Vaginal fluid,UBERON:0036243,Polycystic ovary syndrome,EFO:0000660,Polycystic Ovary Syndrome.Pregnant (PCOS.P) group,Polycystic Ovary Syndrome.Non-pregnant (PCOS.NP) group,This group consists of infertile women with Polycystic Ovary Syndrome (PCOS) who are not pregnant.,10,22,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 5E,31 March 2025,Victoria,Victoria,Histogram of taxa with differential abundance computed using LDA scores.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.",1783272|1239|186801|186802|31979|1485|1506;3384189|32066|203490|203491|1129771|32067|104608,Complete,Svetlana up
bsdb:39868783/6/1,39868783,"cross-sectional observational, not case-control",39868783,10.1128/spectrum.01255-24,NA,"Zhao H., Wang C., Narsing Rao M.P., Rafiq M., Luo G., Li S. , Kang Y.-.Q.",Effects of vaginal microbiota on <i>in vitro</i> fertilization outcomes in women with different infertility causes,Microbiology spectrum,2025,"embryo transfer, in vitro fertilization, infertility, intracytoplasmic sperm injection, vaginal microbiota, vaginal swab",Experiment 6,China,Homo sapiens,Vaginal fluid,UBERON:0036243,Female infertility,EFO:0008560,Tubal Factor Infertility.Pregnant (TFI.P) group,Tubal Factor Infertility.Non-pregnant (TFI.NP) group,This group consists of infertile women with Tubal Factor Infertility who are not pregnant.,21,24,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 5E,31 March 2025,Victoria,Victoria,Histogram of taxa with differential abundance computed using LDA scores.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemelliphila|s__Gemelliphila asaccharolytica,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae",3379134|1224|1236|72274|135621;3379134|1224|1236|72274|135621|286;1783272|1239|91061|1385|539738|3076174|502393;3379134|1224|28216|80840|119060|48736;3379134|1224|1236|135614|32033,Complete,Svetlana up
bsdb:39868783/6/2,39868783,"cross-sectional observational, not case-control",39868783,10.1128/spectrum.01255-24,NA,"Zhao H., Wang C., Narsing Rao M.P., Rafiq M., Luo G., Li S. , Kang Y.-.Q.",Effects of vaginal microbiota on <i>in vitro</i> fertilization outcomes in women with different infertility causes,Microbiology spectrum,2025,"embryo transfer, in vitro fertilization, infertility, intracytoplasmic sperm injection, vaginal microbiota, vaginal swab",Experiment 6,China,Homo sapiens,Vaginal fluid,UBERON:0036243,Female infertility,EFO:0008560,Tubal Factor Infertility.Pregnant (TFI.P) group,Tubal Factor Infertility.Non-pregnant (TFI.NP) group,This group consists of infertile women with Tubal Factor Infertility who are not pregnant.,21,24,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 5E,31 March 2025,Victoria,Victoria,Histogram of taxa with differential abundance computed using LDA scores.,decreased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter typhlonius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma parvum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",3379134|29547|3031852|213849|72293|209|76936;3379134|976|200643|171549|171551|836|28124;1783272|201174|1760|2037|2049;1783272|544448|2790996|2790998|2129|134821;1783272|201174|1760|2037|2049|1654;1783272|1239|909932|1843489|31977|906;1783272|1239|526524|526525|128827|174708;1783272|201174|1760|85004|31953|196081;1783272|201174|1760|85004|31953|196081|230143;1783272|1239|186801|3085636|186803|572511,Complete,Svetlana up
bsdb:39868783/7/1,39868783,"cross-sectional observational, not case-control",39868783,10.1128/spectrum.01255-24,NA,"Zhao H., Wang C., Narsing Rao M.P., Rafiq M., Luo G., Li S. , Kang Y.-.Q.",Effects of vaginal microbiota on <i>in vitro</i> fertilization outcomes in women with different infertility causes,Microbiology spectrum,2025,"embryo transfer, in vitro fertilization, infertility, intracytoplasmic sperm injection, vaginal microbiota, vaginal swab",Experiment 7,China,Homo sapiens,Vaginal fluid,UBERON:0036243,Ectopic pregnancy,NA,Non-ectopic pregnancy group,Ectopic pregnancy group,This group consists of women with Polysystic ovary syndrome(PCOS) and a history of ectopic pregnancy.,31,2,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4H,2 April 2025,Victoria,Victoria,Boxplot distribution of Lactobacillus abundance classified based on the history of ectopic pregnancy.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:39868783/8/1,39868783,"cross-sectional observational, not case-control",39868783,10.1128/spectrum.01255-24,NA,"Zhao H., Wang C., Narsing Rao M.P., Rafiq M., Luo G., Li S. , Kang Y.-.Q.",Effects of vaginal microbiota on <i>in vitro</i> fertilization outcomes in women with different infertility causes,Microbiology spectrum,2025,"embryo transfer, in vitro fertilization, infertility, intracytoplasmic sperm injection, vaginal microbiota, vaginal swab",Experiment 8,China,Homo sapiens,Vaginal fluid,UBERON:0036243,Ectopic pregnancy,NA,Non-ectopic pregnancy group,Ectopic pregnancy group,This group consists of women with Tubal factor infertility(TFI) and a history of ectopic pregnancy.,38,12,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4H,2 April 2025,Victoria,Victoria,Boxplot distribution of Lactobacillus abundance classified based on the history of ectopic pregnancy.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:39868783/9/1,39868783,"cross-sectional observational, not case-control",39868783,10.1128/spectrum.01255-24,NA,"Zhao H., Wang C., Narsing Rao M.P., Rafiq M., Luo G., Li S. , Kang Y.-.Q.",Effects of vaginal microbiota on <i>in vitro</i> fertilization outcomes in women with different infertility causes,Microbiology spectrum,2025,"embryo transfer, in vitro fertilization, infertility, intracytoplasmic sperm injection, vaginal microbiota, vaginal swab",Experiment 9,China,Homo sapiens,Vaginal fluid,UBERON:0036243,Body weight,EFO:0004338,24≤BMI<28 (Overweight) group,BMI>28 (Obese) group,This group consists of women with Polysystic ovary syndrome (PCOS) and are obese.,NA,NA,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4E,2 April 2025,Victoria,Victoria,Boxplot of the distribution of three bacterial genera based on their BMI levels.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:39868783/10/1,39868783,"cross-sectional observational, not case-control",39868783,10.1128/spectrum.01255-24,NA,"Zhao H., Wang C., Narsing Rao M.P., Rafiq M., Luo G., Li S. , Kang Y.-.Q.",Effects of vaginal microbiota on <i>in vitro</i> fertilization outcomes in women with different infertility causes,Microbiology spectrum,2025,"embryo transfer, in vitro fertilization, infertility, intracytoplasmic sperm injection, vaginal microbiota, vaginal swab",Experiment 10,China,Homo sapiens,Vaginal fluid,UBERON:0036243,Body weight,EFO:0004338,18.5≤BMI<24 (Normal weight) group,24≤BMI<28 (Overweight) group,This group consists of women with Polysystic ovary syndrome (PCOS) and are overweight.,NA,NA,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4E,2 April 2025,Victoria,Victoria,Boxplot of the distribution of three bacterial genera based on their BMI levels.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:39868783/11/1,39868783,"cross-sectional observational, not case-control",39868783,10.1128/spectrum.01255-24,NA,"Zhao H., Wang C., Narsing Rao M.P., Rafiq M., Luo G., Li S. , Kang Y.-.Q.",Effects of vaginal microbiota on <i>in vitro</i> fertilization outcomes in women with different infertility causes,Microbiology spectrum,2025,"embryo transfer, in vitro fertilization, infertility, intracytoplasmic sperm injection, vaginal microbiota, vaginal swab",Experiment 11,China,Homo sapiens,Vaginal fluid,UBERON:0036243,Body weight,EFO:0004338,BMI<18.5 (Under weight) group,18.5≤BMI<24 (Normal weight) group,This group consists of women with Tubal factor infertility (TFI) and have normal weight.,NA,NA,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4E,2 April 2025,Victoria,Victoria,Boxplot of the distribution of three bacterial genera based on their BMI levels.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:39868783/12/1,39868783,"cross-sectional observational, not case-control",39868783,10.1128/spectrum.01255-24,NA,"Zhao H., Wang C., Narsing Rao M.P., Rafiq M., Luo G., Li S. , Kang Y.-.Q.",Effects of vaginal microbiota on <i>in vitro</i> fertilization outcomes in women with different infertility causes,Microbiology spectrum,2025,"embryo transfer, in vitro fertilization, infertility, intracytoplasmic sperm injection, vaginal microbiota, vaginal swab",Experiment 12,China,Homo sapiens,Vaginal fluid,UBERON:0036243,Body weight,EFO:0004338,BMI<18.5 (Under weight) group,24≤BMI<28 (Overweight) group,This group consists of women with Tubal factor infertility (TFI) and are overweight.,NA,NA,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4E,2 April 2025,Victoria,Victoria,Boxplot of the distribution of three bacterial genera based on their BMI levels.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:39873191/1/1,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Oxalate measurement,EFO:0010517,5%K₂Ox-0day,5%K₂Ox-45day,"Rats at day 45 after exposure to a 5% K₂Ox(Potassium Oxalate) diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) crystal deposition",8,8,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1e,1 April 2025,Dorcas-od,"Dorcas-od,Anne-mariesharp",The different genera between the day 0 and day 45 of HDOx groups,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005",3379134|1224|28216|80840|995019|577310;1783272|1239|186801|186802|216572|3068309,Complete,KateRasheed
bsdb:39873191/1/2,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Oxalate measurement,EFO:0010517,5%K₂Ox-0day,5%K₂Ox-45day,"Rats at day 45 after exposure to a 5% K₂Ox(Potassium Oxalate) diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) crystal deposition",8,8,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1e,1 April 2025,Dorcas-od,"Dorcas-od,Anne-mariesharp",The different genera between the day 0 and day 45 of HDOx groups,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",1783272|1239|186801|186802|186806|1730|290054;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|707003,Complete,KateRasheed
bsdb:39873191/2/1,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Hydroxyproline measurement,EFO:0010498,5%Hyp-0day,5%Hyp-45day,"Rats at day 45 after exposure to a 5%Hyp(Hydroxyproline) oxalate precursor-diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) crystal deposition",8,8,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1f,2 April 2025,Dorcas-od,"Dorcas-od,Anne-mariesharp",The different genera between the day 0 and day 45 of HDOx groups,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005",3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|216572|119852;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|186802|216572|3068309,Complete,KateRasheed
bsdb:39873191/2/2,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Hydroxyproline measurement,EFO:0010498,5%Hyp-0day,5%Hyp-45day,"Rats at day 45 after exposure to a 5%Hyp(Hydroxyproline) oxalate precursor-diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) crystal deposition",8,8,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1f,2 April 2025,Dorcas-od,"Dorcas-od,Anne-mariesharp",The different genera between the day 0 and day 45 of HDOx groups,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",1783272|1239|186801|186802|186806|1730|290054;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572|707003,Complete,KateRasheed
bsdb:39873191/3/1,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 3,China,Rattus norvegicus,Feces,UBERON:0001988,Oxalate measurement,EFO:0010517,5%K₂Ox-0day,5%K₂Ox-45day,"Rats at day 45 after exposure to a 5% K₂Ox(Potassium Oxalate) diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) crystal deposition",8,8,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure S1,5 July 2025,Anne-mariesharp,Anne-mariesharp,The differential phylum between indicated groups,increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota",1783272|201174;3379134|976,Complete,KateRasheed
bsdb:39873191/3/2,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 3,China,Rattus norvegicus,Feces,UBERON:0001988,Oxalate measurement,EFO:0010517,5%K₂Ox-0day,5%K₂Ox-45day,"Rats at day 45 after exposure to a 5% K₂Ox(Potassium Oxalate) diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) crystal deposition",8,8,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure S1,5 July 2025,Anne-mariesharp,Anne-mariesharp,The differential phylum between indicated groups,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,KateRasheed
bsdb:39873191/4/1,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 4,China,Rattus norvegicus,Feces,UBERON:0001988,Oxalate measurement,EFO:0010517,5%K₂Ox-30day,5%K₂Ox-45day,"Rats at day 45 after exposure to a 5% K₂Ox(Potassium Oxalate) diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) crystal deposition",8,8,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure S1,5 July 2025,Anne-mariesharp,Anne-mariesharp,The differential phylum between indicated groups,increased,k__Bacillati|p__Actinomycetota,1783272|201174,Complete,KateRasheed
bsdb:39873191/5/1,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 5,China,Rattus norvegicus,Feces,UBERON:0001988,Oxalate measurement,EFO:0010517,Normal Group (45 days),5%K₂Ox (45 days),"Rats at day 45 after exposure to a 5% K2Ox diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx crystal deposition",8,8,NA,16S,34,Illumina,relative abundances,"ANOVA,Post-Hoc Pairwise",0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 4a,5 April 2025,Dorcas-od,"Dorcas-od,Anne-mariesharp",The effects of FMT on gut microbiota and metabolism.,increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota",1783272|201174;3379134|976;3379134|1224,Complete,KateRasheed
bsdb:39873191/5/2,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 5,China,Rattus norvegicus,Feces,UBERON:0001988,Oxalate measurement,EFO:0010517,Normal Group (45 days),5%K₂Ox (45 days),"Rats at day 45 after exposure to a 5% K2Ox diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx crystal deposition",8,8,NA,16S,34,Illumina,relative abundances,"ANOVA,Post-Hoc Pairwise",0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 4a,5 April 2025,Dorcas-od,Dorcas-od,The effects of FMT on gut microbiota and metabolism.,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,KateRasheed
bsdb:39873191/6/1,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 6,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Normal Group (45 days),5%K₂OxFMT (45 days),Rats exposed to a 5%K₂Ox diet and treated with fecal microbiota transplantation (FMT) from healthy rat donors every two days for 45 days,8,8,NA,16S,34,Illumina,relative abundances,"ANOVA,Post-Hoc Pairwise",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4a,5 April 2025,Dorcas-od,"Dorcas-od,Anne-mariesharp",The effects of FMT on gut microbiota and metabolism.,increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota",3379134|976;3379134|1224,Complete,KateRasheed
bsdb:39873191/6/2,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 6,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Normal Group (45 days),5%K₂OxFMT (45 days),Rats exposed to a 5%K₂Ox diet and treated with fecal microbiota transplantation (FMT) from healthy rat donors every two days for 45 days,8,8,NA,16S,34,Illumina,relative abundances,"ANOVA,Post-Hoc Pairwise",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4a,5 April 2025,Dorcas-od,Dorcas-od,The effects of FMT on gut microbiota and metabolism.,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,KateRasheed
bsdb:39873191/7/1,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 7,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,5%K₂Ox (45 days),5%K₂OxFMT (45 days),Rats exposed to a 5%K₂Ox diet and treated with fecal microbiota transplantation (FMT) from healthy rat donors every two days for 45 days,8,8,NA,16S,34,Illumina,relative abundances,"ANOVA,Post-Hoc Pairwise",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4a,6 April 2025,Dorcas-od,Dorcas-od,The effects of FMT on gut microbiota and metabolism.,increased,k__Bacillati|p__Bacillota,1783272|1239,Complete,KateRasheed
bsdb:39873191/7/2,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 7,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,5%K₂Ox (45 days),5%K₂OxFMT (45 days),Rats exposed to a 5%K₂Ox diet and treated with fecal microbiota transplantation (FMT) from healthy rat donors every two days for 45 days,8,8,NA,16S,34,Illumina,relative abundances,"ANOVA,Post-Hoc Pairwise",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4a,6 April 2025,Dorcas-od,"Dorcas-od,Anne-mariesharp",The effects of FMT on gut microbiota and metabolism.,decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota",1783272|201174;3379134|976,Complete,KateRasheed
bsdb:39873191/8/1,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 8,China,Rattus norvegicus,Feces,UBERON:0001988,Hydroxyproline measurement,EFO:0010498,Normal Group (45 days),5%Hyp (45 days),"Rats at day 45 after exposure to a 5%Hyp(Hydroxyproline) oxalate precursor-diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) crystal deposition",8,8,NA,16S,34,Illumina,relative abundances,"ANOVA,Post-Hoc Pairwise",0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,Figure 4a,6 April 2025,Dorcas-od,Dorcas-od,The effects of FMT on gut microbiota and metabolism.,increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Verrucomicrobiota",3379134|976;3379134|74201,Complete,KateRasheed
bsdb:39873191/8/2,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 8,China,Rattus norvegicus,Feces,UBERON:0001988,Hydroxyproline measurement,EFO:0010498,Normal Group (45 days),5%Hyp (45 days),"Rats at day 45 after exposure to a 5%Hyp(Hydroxyproline) oxalate precursor-diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) crystal deposition",8,8,NA,16S,34,Illumina,relative abundances,"ANOVA,Post-Hoc Pairwise",0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,Figure 4a,6 April 2025,Dorcas-od,Dorcas-od,The effects of FMT on gut microbiota and metabolism.,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,KateRasheed
bsdb:39873191/9/1,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 9,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,5%Hyp (45 days),5%HypFMT (45 days),Rats exposed to a 5%Hyp(Hydroxyproline) oxalate precursor-diet and treated with fecal microbiota transplantation (FMT) from healthy rat donors every two days for 45 days,8,8,NA,16S,34,Illumina,relative abundances,"ANOVA,Post-Hoc Pairwise",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4a,6 April 2025,Dorcas-od,"Dorcas-od,Anne-mariesharp",The effects of FMT on gut microbiota and metabolism.,increased,k__Bacillati|p__Bacillota,1783272|1239,Complete,KateRasheed
bsdb:39873191/9/2,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 9,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,5%Hyp (45 days),5%HypFMT (45 days),Rats exposed to a 5%Hyp(Hydroxyproline) oxalate precursor-diet and treated with fecal microbiota transplantation (FMT) from healthy rat donors every two days for 45 days,8,8,NA,16S,34,Illumina,relative abundances,"ANOVA,Post-Hoc Pairwise",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4a,6 April 2025,Dorcas-od,"Dorcas-od,Anne-mariesharp",The effects of FMT on gut microbiota and metabolism.,decreased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Verrucomicrobiota",3379134|976;3379134|74201,Complete,KateRasheed
bsdb:39873191/10/1,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 10,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,5%K₂Ox,5%K₂OxFMT,Rats exposed to a 5%K₂Ox diet and treated with fecal microbiota transplantation (FMT) from healthy rat donors,8,8,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure S7a,6 April 2025,Dorcas-od,"Dorcas-od,Anne-mariesharp",The effects of FMT on HDOx-induced differential bacteria (genus level),increased,NA,NA,Complete,KateRasheed
bsdb:39873191/10/2,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 10,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,5%K₂Ox,5%K₂OxFMT,Rats exposed to a 5%K₂Ox diet and treated with fecal microbiota transplantation (FMT) from healthy rat donors,8,8,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Figure 4b, Figure S7a, c",25 June 2025,Anne-mariesharp,Anne-mariesharp,The effects of FMT on HDOx-induced differential bacteria (genus level),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter",3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802|216572|100175,Complete,KateRasheed
bsdb:39873191/11/1,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 11,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,5%Hyp,5%HypFMT,Rats exposed to a 5%Hyp(Hydroxyproline) oxalate precursor-diet and treated with fecal microbiota transplantation (FMT) from healthy rat donors,8,8,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,"Figure 4c, Figure S7b, d",7 April 2025,Dorcas-od,"Dorcas-od,Anne-mariesharp",The effects of FMT on HDOx-induced differential bacteria (genus level),increased,"p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",95818|2093818|2093825|2171986|1331051;1783272|1239|186801|3085636|186803|248744;1783272|1239|186801|3085636|186803|177971;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|707003,Complete,KateRasheed
bsdb:39873191/11/2,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 11,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,5%Hyp,5%HypFMT,Rats exposed to a 5%Hyp(Hydroxyproline) oxalate precursor-diet and treated with fecal microbiota transplantation (FMT) from healthy rat donors,8,8,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,"Figure 4c, Figure S7b, d",7 April 2025,Dorcas-od,"Dorcas-od,Anne-mariesharp",The effects of FMT on HDOx-induced differential bacteria (genus level),decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|815|816;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802|216572|119852;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|186802|31979|1485,Complete,KateRasheed
bsdb:39873191/12/1,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 12,China,Rattus norvegicus,Feces,UBERON:0001988,Timepoint,EFO:0000724,Normal-0day,Normal-15day,"Healthy rats fed with a standard pellet diet, and had their sample collected at day 15",8,8,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure S1,9 April 2025,Dorcas-od,"Dorcas-od,Anne-mariesharp",The differential phylum between indicated groups,increased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota",1783272|1239;3379134|1224,Complete,KateRasheed
bsdb:39873191/12/2,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 12,China,Rattus norvegicus,Feces,UBERON:0001988,Timepoint,EFO:0000724,Normal-0day,Normal-15day,"Healthy rats fed with a standard pellet diet, and had their sample collected at day 15",8,8,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure S1,9 April 2025,Dorcas-od,"Dorcas-od,Anne-mariesharp",The differential phylum between indicated groups,decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,KateRasheed
bsdb:39873191/13/1,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 13,China,Rattus norvegicus,Feces,UBERON:0001988,Timepoint,EFO:0000724,Normal-0day,Normal-30day,"Healthy rats fed with a standard pellet diet, and had their sample collected at day 30",8,8,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure S1,10 April 2025,Dorcas-od,"Dorcas-od,Anne-mariesharp",The differential phylum between indicated groups,increased,k__Bacillati|p__Bacillota,1783272|1239,Complete,KateRasheed
bsdb:39873191/13/2,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 13,China,Rattus norvegicus,Feces,UBERON:0001988,Timepoint,EFO:0000724,Normal-0day,Normal-30day,"Healthy rats fed with a standard pellet diet, and had their sample collected at day 30",8,8,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure S1,10 April 2025,Dorcas-od,"Dorcas-od,Anne-mariesharp",The differential phylum between indicated groups,decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,KateRasheed
bsdb:39873191/14/1,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 14,China,Rattus norvegicus,Feces,UBERON:0001988,Timepoint,EFO:0000724,Normal-0day,Normal-45day,"Healthy rats fed with a standard pellet diet, and had their sample collected at day 45",8,8,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure S1,10 April 2025,Dorcas-od,"Dorcas-od,Anne-mariesharp",The differential phylum between indicated groups,increased,k__Bacillati|p__Bacillota,1783272|1239,Complete,KateRasheed
bsdb:39873191/14/2,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 14,China,Rattus norvegicus,Feces,UBERON:0001988,Timepoint,EFO:0000724,Normal-0day,Normal-45day,"Healthy rats fed with a standard pellet diet, and had their sample collected at day 45",8,8,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure S1,10 April 2025,Dorcas-od,"Dorcas-od,Anne-mariesharp",The differential phylum between indicated groups,decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,KateRasheed
bsdb:39873191/15/2,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 15,China,Rattus norvegicus,Feces,UBERON:0001988,Timepoint,EFO:0000724,Normal-15day,Normal-30day,"Healthy rats fed with a standard pellet diet, and had their sample collected at day 30",8,8,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure S1,12 April 2025,Dorcas-od,"Dorcas-od,Anne-mariesharp",The differential phylum between indicated groups,decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota",1783272|201174;3379134|1224,Complete,KateRasheed
bsdb:39873191/16/2,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 16,China,Rattus norvegicus,Feces,UBERON:0001988,Timepoint,EFO:0000724,Normal-15day,Normal-45day,"Healthy rats fed with a standard pellet diet, and had their sample collected at day 45",8,8,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure S1,12 April 2025,Dorcas-od,"Dorcas-od,Anne-mariesharp",The differential phylum between indicated groups,decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota",1783272|201174;3379134|1224,Complete,KateRasheed
bsdb:39873191/17/1,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 17,China,Rattus norvegicus,Feces,UBERON:0001988,Oxalate measurement,EFO:0010517,3%K₂Ox-0day,3%K₂Ox-15day,"Rats at day 15 after exposure to a 3% K₂Ox(Potassium Oxalate) diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) crystal deposition",8,8,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure S1,12 April 2025,Dorcas-od,"Dorcas-od,Anne-mariesharp",The differential phylum between indicated groups,increased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,KateRasheed
bsdb:39873191/17/2,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 17,China,Rattus norvegicus,Feces,UBERON:0001988,Oxalate measurement,EFO:0010517,3%K₂Ox-0day,3%K₂Ox-15day,"Rats at day 15 after exposure to a 3% K₂Ox(Potassium Oxalate) diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) crystal deposition",8,8,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure S1,12 April 2025,Dorcas-od,"Dorcas-od,Anne-mariesharp",The differential phylum between indicated groups,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,KateRasheed
bsdb:39873191/18/1,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 18,China,Rattus norvegicus,Feces,UBERON:0001988,Oxalate measurement,EFO:0010517,3%K₂Ox-15day,3%K₂Ox-30day,"Rats at day 30 after exposure to a 3% K₂Ox(Potassium Oxalate) diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) crystal deposition",8,8,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure S1,12 April 2025,Dorcas-od,"Dorcas-od,Anne-mariesharp",The differential phylum between indicated groups,decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,KateRasheed
bsdb:39873191/19/1,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 19,China,Rattus norvegicus,Feces,UBERON:0001988,Oxalate measurement,EFO:0010517,5%K₂Ox-0day,5%K₂Ox-15day,"Rats at day 15 after exposure to a 5% K₂Ox(Potassium Oxalate) diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) crystal deposition",8,8,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure S1,14 April 2025,Dorcas-od,"Dorcas-od,Anne-mariesharp",The differential phylum between indicated groups,increased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,KateRasheed
bsdb:39873191/19/2,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 19,China,Rattus norvegicus,Feces,UBERON:0001988,Oxalate measurement,EFO:0010517,5%K₂Ox-0day,5%K₂Ox-15day,"Rats at day 15 after exposure to a 5% K₂Ox(Potassium Oxalate) diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) crystal deposition",8,8,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure S1,14 April 2025,Dorcas-od,"Dorcas-od,Anne-mariesharp",The differential phylum between indicated groups,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,KateRasheed
bsdb:39873191/20/1,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 20,China,Rattus norvegicus,Feces,UBERON:0001988,Oxalate measurement,EFO:0010517,5%K₂Ox-0day,5%K₂Ox-30day,"Rats at day 30 after exposure to a 5% K₂Ox(Potassium Oxalate) diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) crystal deposition",8,8,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure S1,14 April 2025,Dorcas-od,"Dorcas-od,Anne-mariesharp",The differential phylum between indicated groups,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,KateRasheed
bsdb:39873191/22/1,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 22,China,Rattus norvegicus,Feces,UBERON:0001988,Oxalate measurement,EFO:0010517,5%K₂Ox-15day,5%K₂Ox-45day,"Rats at day 45 after exposure to a 5% K₂Ox(Potassium Oxalate) diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) crystal deposition",8,8,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure S1,14 April 2025,Dorcas-od,"Dorcas-od,Anne-mariesharp",The differential phylum between indicated groups,increased,k__Bacillati|p__Actinomycetota,1783272|201174,Complete,KateRasheed
bsdb:39873191/23/1,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 23,China,Rattus norvegicus,Feces,UBERON:0001988,Hydroxyproline measurement,EFO:0010498,5%Hyp-0day,5%Hyp-30day,"Rats at day 30 after exposure to a 5%Hyp(Hydroxyproline) oxalate precursor-diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) crystal deposition",8,8,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure S1,14 April 2025,Dorcas-od,"Dorcas-od,Anne-mariesharp",The differential phylum between indicated groups,increased,k__Bacillati|p__Bacillota,1783272|1239,Complete,KateRasheed
bsdb:39873191/23/2,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 23,China,Rattus norvegicus,Feces,UBERON:0001988,Hydroxyproline measurement,EFO:0010498,5%Hyp-0day,5%Hyp-30day,"Rats at day 30 after exposure to a 5%Hyp(Hydroxyproline) oxalate precursor-diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) crystal deposition",8,8,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure S1,14 April 2025,Dorcas-od,"Dorcas-od,Anne-mariesharp",The differential phylum between indicated groups,decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,KateRasheed
bsdb:39873191/24/1,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 24,China,Rattus norvegicus,Feces,UBERON:0001988,Hydroxyproline measurement,EFO:0010498,5%Hyp-30days,5%Hyp-45days,"Rats at day 45 after exposure to a 5%Hyp(Hydroxyproline) oxalate precursor-diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) crystal deposition",8,8,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure S1,23 June 2025,Anne-mariesharp,Anne-mariesharp,The differential phylum between indicated groups,increased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,KateRasheed
bsdb:39873191/24/2,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 24,China,Rattus norvegicus,Feces,UBERON:0001988,Hydroxyproline measurement,EFO:0010498,5%Hyp-30days,5%Hyp-45days,"Rats at day 45 after exposure to a 5%Hyp(Hydroxyproline) oxalate precursor-diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) crystal deposition",8,8,NA,16S,34,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure S1,23 June 2025,Anne-mariesharp,Anne-mariesharp,The differential phylum between indicated groups,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,KateRasheed
bsdb:39873191/25/1,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 25,China,Rattus norvegicus,Feces,UBERON:0001988,Oxalate measurement,EFO:0010517,5%K₂Ox-45days,Normal-45days,"Healthy rats fed with a standard pellet diet, and had their sample collected at day 45",8,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure S2a,24 June 2025,Anne-mariesharp,Anne-mariesharp,LEfSe analysis identified the most differentially abundant genera between the Normal group and the HDOx groups on day 45.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Aquiluna,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Actinomycetota|c__Thermoleophilia|o__Gaiellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",1783272|201174|1760|85006|85023|529881;1783272|1239;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|186801|186802|216572|216851;1783272|201174|1497346|1154584;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|3068309;3379134|74201|203494|48461|203557;1783272|1239|186801|186802|216572|707003,Complete,KateRasheed
bsdb:39873191/25/2,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 25,China,Rattus norvegicus,Feces,UBERON:0001988,Oxalate measurement,EFO:0010517,5%K₂Ox-45days,Normal-45days,"Healthy rats fed with a standard pellet diet, and had their sample collected at day 45",8,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure S2a,24 June 2025,Anne-mariesharp,Anne-mariesharp,LEfSe analysis identified the most differentially abundant genera between the Normal group and the HDOx groups on day 45.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Oligella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Pseudomonadati|p__Verrucomicrobiota|c__Spartobacteria|o__Chthoniobacterales|f__Chthoniobacteraceae|g__Candidatus Udaeobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota",3379134|976|200643|171549|171550|239759;3379134|1224|1236;3379134|1224;3379134|1224|28216|80840|119060;3379134|1224|28216|80840|506|90243;3379134|1224|28216|80840|995019|577310;1783272|201174|84998|84999;3379134|74201|134549|1836787|1836792|1921511;1783272|201174|84998;1783272|201174;1783272|201174|84998|84999|1643824;3379134|976|200643|171549|171552;3379134|976|200643|171549|2005473;3379134|976|200643;3379134|976|200643|171549;3379134|976,Complete,KateRasheed
bsdb:39873191/26/1,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 26,China,Rattus norvegicus,Feces,UBERON:0001988,Hydroxyproline measurement,EFO:0010498,5%Hyp-45days,Normal-45days,"Healthy rats fed with a standard pellet diet, and had their sample collected at day 45",8,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 1,Figure S2a,25 June 2025,Anne-mariesharp,Anne-mariesharp,LEfSe analysis identified the most differentially abundant genera between the Normal group and the HDOx groups on day 45.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Aquiluna,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bdellovibrionota|c__Bdellovibrionia|o__Bdellovibrionales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Nitrospirota|c__Thermodesulfovibrionia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",1783272|201174|1760|85006|85023|529881;1783272|1239;3379134|3018035|3031418|213481;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;3379134|40117|2811502;1783272|1239|186801|186802|216572|707003,Complete,KateRasheed
bsdb:39873191/26/2,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 26,China,Rattus norvegicus,Feces,UBERON:0001988,Hydroxyproline measurement,EFO:0010498,5%Hyp-45days,Normal-45days,"Healthy rats fed with a standard pellet diet, and had their sample collected at day 45",8,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 2,Figure S2a,25 June 2025,Anne-mariesharp,Anne-mariesharp,LEfSe analysis identified the most differentially abundant genera between the Normal group and the HDOx groups on day 45.,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Acidobacteriota|c__Terriglobia|o__Bryobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976;3379134|57723|204432|332160;3379134|1224|28216|80840|119060;3379134|976|200643|171549|2005473;3379134|1224|28216|80840|995019|577310;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201,Complete,KateRasheed
bsdb:39873191/27/1,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 27,China,Rattus norvegicus,Feces,UBERON:0001988,Oxalate measurement,EFO:0010517,5%K₂Ox-0day,5%K₂Ox-45days,"Rats at day 45 after exposure to a 5% K₂Ox diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx crystal deposition",8,8,NA,16S,34,Illumina,log transformation,Linear Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure S2c,25 June 2025,Anne-mariesharp,Anne-mariesharp,Differentially abundant genera of HDOx groups between the day 0 and day 45,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",1783272|1239|186801|3085636|186803|572511;3379134|1224|28216|80840|119060;3379134|1224|28216|80840|995019|577310;3379134|1224;1783272|201174;1783272|1239|186801|186802|216572|3068309;1783272|201174|84998;1783272|201174|84998|84999;1783272|201174|84998|84999|1643824;3379134|976|200643|171549|171552;3379134|976|200643;3379134|976;3379134|976|200643|171549,Complete,KateRasheed
bsdb:39873191/27/2,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 27,China,Rattus norvegicus,Feces,UBERON:0001988,Oxalate measurement,EFO:0010517,5%K₂Ox-0day,5%K₂Ox-45days,"Rats at day 45 after exposure to a 5% K₂Ox diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx crystal deposition",8,8,NA,16S,34,Illumina,log transformation,Linear Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure S2c,25 June 2025,Anne-mariesharp,Anne-mariesharp,Differentially abundant genera of HDOx groups between the day 0 and day 45,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia",1783272|1239;1783272|1239|91061;1783272|1239|91061|186826;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|707003;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1501226,Complete,KateRasheed
bsdb:39873191/28/1,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 28,China,Rattus norvegicus,Feces,UBERON:0001988,Hydroxyproline measurement,EFO:0010498,5%Hyp-0day,5%Hyp-45days,"Rats at day 45 after exposure to a 5%Hyp(Hydroxyproline) oxalate precursor-diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx crystal deposition",8,8,NA,16S,34,Illumina,log transformation,Linear Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure S2c,25 June 2025,Anne-mariesharp,Anne-mariesharp,Differentially abundant genera of HDOx groups between the day 0 and day 45,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|1224|28216|80840|119060;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|3068309;3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816,Complete,KateRasheed
bsdb:39873191/28/2,39873191,laboratory experiment,39873191,https://doi.org/10.1080/19490976.2025.2457490,NA,"An L., Li S., Chang Z., Lei M., He Z., Xu P., Zhang S., Jiang Z., Iqbal M.S., Sun X., Liu H., Duan X. , Wu W.",Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet,Gut microbes,2025,"Hyperoxaluria, fecal microbiota transplantation, gut microbiota, high dietary oxalate, metabolome",Experiment 28,China,Rattus norvegicus,Feces,UBERON:0001988,Hydroxyproline measurement,EFO:0010498,5%Hyp-0day,5%Hyp-45days,"Rats at day 45 after exposure to a 5%Hyp(Hydroxyproline) oxalate precursor-diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx crystal deposition",8,8,NA,16S,34,Illumina,log transformation,Linear Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure S2c,25 June 2025,Anne-mariesharp,Anne-mariesharp,Differentially abundant genera of HDOx groups between the day 0 and day 45,decreased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales",1783272|1239|91061;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958;1783272|1239|186801|186802|216572|3068309;1783272|1239|91061|186826,Complete,KateRasheed
bsdb:39880843/1/1,39880843,case-control,39880843,10.1038/s41398-025-03239-0,NA,"Tao S., Wu Y., Xiao L., Huang Y., Wang H., Tang Y., Liu S., Liu Y., Ma Q., Yin Y., Dai M., Xie M., Cai J., Zhao Z., Lv Q., Zhang J., Zhang M., Wei M., Chen Y., Li M. , Wang Q.",Alterations in fecal bacteriome virome interplay and microbiota-derived dysfunction in patients with schizophrenia,Translational psychiatry,2025,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Healthy control group (HC),Schizophrenia group (SCZ),Patients with schizophrenia,47,48,1 month,WMS,NA,DNBSEQ-T7,log transformation,MaAsLin2,0.05,FALSE,NA,sex,"age,body mass index,sex",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 2, Supplementary Table 2",13 October 2025,Tosin,Tosin,Differentially abundant gut bacteria between patients with schizophrenia and healthy controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus pullicaecorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus sp. AF24-19AC,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora saccharolytica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:279,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa",3379134|1224|1236|2887326|468|469;3379134|1224|1236|2887326|468|469|470;1783272|1239|186801|3085636|186803|572511|871665;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|3085642|580596|501571;1783272|1239|186801|186802|3085642|580596|2292199;1783272|1239|186801|3082720|186804|1870884;1783272|1239|186801|3082720|186804|1870884|1496;1783272|1239|526524|526525|2810280;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|2719313|358742;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|81852|1350|1352;1783272|1239|526524|526525|128827;1783272|1239|186801|3085636|186803|2719231;1783272|1239|186801|3085636|186803|2719231|84030;1783272|1239|91061|186826|33958|2767887;1783272|1239|186801|3085636|186803|2316020;1783272|1239|186801|3085636|186803|2316020|592978;1783272|1239|186801|3085636|186803|2316020|33038;3379134|1224|1236|2887326|468;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171552|838|1262924;1783272|1239|186801|186802|216572|1263;1783272|1239|526524|526525|2810280|3025755;1783272|1239|526524|526525|2810280|3025755|1547,Complete,NA
bsdb:39880843/1/2,39880843,case-control,39880843,10.1038/s41398-025-03239-0,NA,"Tao S., Wu Y., Xiao L., Huang Y., Wang H., Tang Y., Liu S., Liu Y., Ma Q., Yin Y., Dai M., Xie M., Cai J., Zhao Z., Lv Q., Zhang J., Zhang M., Wei M., Chen Y., Li M. , Wang Q.",Alterations in fecal bacteriome virome interplay and microbiota-derived dysfunction in patients with schizophrenia,Translational psychiatry,2025,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Healthy control group (HC),Schizophrenia group (SCZ),Patients with schizophrenia,47,48,1 month,WMS,NA,DNBSEQ-T7,log transformation,MaAsLin2,0.05,FALSE,NA,sex,"age,body mass index,sex",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 2, Supplementary Table 2",13 October 2025,Tosin,Tosin,Differentially abundant gut bacteria between patients with schizophrenia and healthy controls,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. NSJ-39,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides zhangwenhongii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. AF32-4BH,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. AM29-29,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. OM05-6,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. OM06-15AC,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia stercoris,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium 1_1_47,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas faecihominis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Candidatus Parasutterella gallistercoris,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Chitinophaga,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:269,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella tanakaei,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister sp. CAG:357,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter|s__Dysosmobacter sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:252,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:227,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella sp.,k__Pseudomonadati|p__Pseudomonadota|s__Proteobacteria bacterium CAG:139,k__Pseudomonadati|p__Pseudomonadota|s__Pseudomonadota bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. AM43-6,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. OM07-17,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|s__Sutterellaceae bacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae",1783272|201174|84998|1643822|1643826|447020|446660;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550|239759|2585118;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|171550|239759|1872444;3379134|976|200643|171549|815|816|2763019;3379134|976|200643|171549|815|816|2650157;1783272|1239|186801|3085636|186803|572511|2292967;1783272|1239|186801|3085636|186803|572511|2292975;1783272|1239|186801|3085636|186803|572511|2292983;1783272|1239|186801|3085636|186803|572511|2292984;1783272|1239|186801|3085636|186803|572511|871664;3379134|1224|28216|80840|1891238;3379134|1224|28216|80840|469610;3379134|976|200643|171549|1853231|574697|1472416;3379134|1224|28216|80840|995019|577310|2838727;3379134|976|1853228|1853229|563835|79328;1783272|1239|186801|186802|31979|1485|1262788;1783272|201174|84998|84999|84107|102106|626935;1783272|1239|909932|1843489|31977|39948|1262869;1783272|1239|186801|186802|216572|2591381|2591382;1783272|1239|186801|186802|186806|1730|1262887;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|1263010;1783272|1239|186801|3085636|186803|1407607|2773922;3379134|1224|28216|80840|995019|577310;3379134|1224|28216|80840|995019|577310|487175;3379134|1224|28216|80840|995019|577310|487175;3379134|1224|28216|80840|995019|577310|2049037;3379134|1224|1262986;3379134|1224|1977087;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|1263|2293216;1783272|1239|186801|186802|216572|1263|2293233;3379134|1224|28216|80840|995019|2026794;1783272|1239|526524|526525|2810281|191303;1783272|1239|526524|526525|2810281,Complete,NA
bsdb:39880843/2/1,39880843,case-control,39880843,10.1038/s41398-025-03239-0,NA,"Tao S., Wu Y., Xiao L., Huang Y., Wang H., Tang Y., Liu S., Liu Y., Ma Q., Yin Y., Dai M., Xie M., Cai J., Zhao Z., Lv Q., Zhang J., Zhang M., Wei M., Chen Y., Li M. , Wang Q.",Alterations in fecal bacteriome virome interplay and microbiota-derived dysfunction in patients with schizophrenia,Translational psychiatry,2025,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Healthy control group (HC),Schizophrenia group (SCZ),Patients with schizophrenia,47,48,1 month,WMS,NA,DNBSEQ-T7,log transformation,ANCOM-BC,0.05,FALSE,NA,sex,"age,body mass index,sex",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 2, Supplementary Table 2",13 October 2025,Tosin,Tosin,Differentially abundant gut bacteria between patients with schizophrenia and healthy controls,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:279,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus pullicaecorum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa",3379134|1224|1236|2887326|468|469;3379134|1224|1236|2887326|468|469|470;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|2719313|358742;1783272|1239|91061|186826|33958|2767887;1783272|1239|186801|3085636|186803|2316020|33038;3379134|976|200643|171549|171552|838|1262924;1783272|1239|186801|186802|3085642|580596|501571;1783272|1239|526524|526525|2810280|3025755|1547,Complete,NA
bsdb:39880843/2/2,39880843,case-control,39880843,10.1038/s41398-025-03239-0,NA,"Tao S., Wu Y., Xiao L., Huang Y., Wang H., Tang Y., Liu S., Liu Y., Ma Q., Yin Y., Dai M., Xie M., Cai J., Zhao Z., Lv Q., Zhang J., Zhang M., Wei M., Chen Y., Li M. , Wang Q.",Alterations in fecal bacteriome virome interplay and microbiota-derived dysfunction in patients with schizophrenia,Translational psychiatry,2025,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Healthy control group (HC),Schizophrenia group (SCZ),Patients with schizophrenia,47,48,1 month,WMS,NA,DNBSEQ-T7,log transformation,ANCOM-BC,0.05,FALSE,NA,sex,"age,body mass index,sex",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 2, Supplementary Table 2",14 October 2025,Tosin,Tosin,Differentially abundant gut bacteria between patients with schizophrenia and healthy controls,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides zhangwenhongii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. AM29-29,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia stercoris,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium 1_1_47,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus faecihominis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Candidatus Parasutterella gallistercoris,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Chitinophaga,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella tanakaei,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister sp. CAG:357,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:252,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:227,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella sp.,k__Pseudomonadati|p__Pseudomonadota|s__Proteobacteria bacterium CAG:139,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. OM07-17,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|s__Sutterellaceae bacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Pseudomonadati|p__Pseudomonadota|s__Pseudomonadota bacterium",3379134|976|200643|171549|171550|239759|2585118;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|171550|239759|1872444;3379134|976|200643|171549|815|816|2650157;1783272|1239|186801|3085636|186803|572511|2292975;1783272|1239|186801|3085636|186803|572511|871664;3379134|1224|28216|80840|1891238;3379134|1224|28216|80840|469610;1783272|1239|186801|186802|3085642|580596|1712515;3379134|1224|28216|80840|995019|577310|2838727;3379134|976|1853228|1853229|563835|79328;1783272|201174|84998|84999|84107|102106|626935;1783272|1239|909932|1843489|31977|39948|1262869;1783272|1239|186801|186802|186806|1730|1262887;1783272|1239|1263010;3379134|1224|28216|80840|995019|577310;3379134|1224|28216|80840|995019|577310|487175;3379134|1224|28216|80840|995019|577310|487175;3379134|1224|28216|80840|995019|577310|2049037;3379134|1224|1262986;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|1263|2293233;3379134|1224|28216|80840|995019|2026794;1783272|1239|526524|526525|2810281;3379134|1224|1977087,Complete,NA
bsdb:39880958/1/1,39880958,"cross-sectional observational, not case-control",39880958,10.1038/s41586-024-08485-8,NA,"Maghini D.G., Oduaran O.H., Olubayo L.A.I., Cook J.A., Smyth N., Mathema T., Belger C.W., Agongo G., Boua P.R., Choma S.S.R., Gómez-Olivé F.X., Kisiangani I., Mashaba G.R., Micklesfield L., Mohamed S.F., Nonterah E.A., Norris S., Sorgho H., Tollman S., Wafawanaka F., Tluway F., Ramsay M., Wirbel J., Bhatt A.S. , Hazelhurst S.",Expanding the human gut microbiome atlas of Africa,Nature,2025,NA,Experiment 1,"Kenya,South Africa",Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV-,People Living With HIV on Antiretroviral therapy (ART+ PLWH),"Women living with HIV in Agincourt, South Africa (n = 60), Soweto, South Africa (n = 50) and Nairobi, Kenya (n = 19)",719,119,NA,WMS,NA,NA,NA,Mixed-Effects Regression,0.01,TRUE,NA,NA,"antibiotic therapy,geographic area",NA,NA,NA,NA,decreased,NA,Signature 1,"Figure 4d, Supplementary Data 10",5 February 2025,Taofeecoh,"Taofeecoh,WikiWorks","Species-level prokaryotic differential abundance between seronegative and HIV+ participants in Agincourt (South Africa), Soweto (South Africa) and Nairobi (Kenya).",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia massiliensis (ex Durand et al. 2017),k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus|s__Cloacibacillus porcorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:58,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma|s__Dielma fastidiosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter|s__Dysosmobacter welbionis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Mailhella|s__Mailhella massiliensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella xylaniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter piscolens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC067H01,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia saccharogumia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Candidatus Caccocola|s__Candidatus Caccocola faecigallinarum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Pandoraea|s__Pandoraea faecigallinarum,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:137,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Merdibacter|s__Merdibacter massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:7,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella sp. CAG:521",1783272|1239|909932|1843488|909930|904|1852375;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|29523;1783272|1239|186801|3085636|186803|572511|1737424;3384194|508458|649775|649776|649777|508459|1197717;1783272|1239|186801|186802|31979|1485|1262824;1783272|1239|526524|526525|128827|1472649|1034346;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|186802|216572|2591381|2093857;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|2719313|358743;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|946234|292800;3384189|32066|203490|203491|203492|848|850;1783272|1239|91061|1385|539738|1378|84135;3379134|200940|3031449|213115|194924|1981028|1903261;1783272|1239|909932|909929|1843491|158846|437897;1783272|1239|186801|186802|216572|459786|1945593;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|171552|577309|454154;3379134|976|200643|171549|171552|577309|454155;3379134|976|200643|171549|815|909656;3379134|976|200643|171549|815|909656|204516;3384194|508458|649775|649776|3029088|638847|638849;1783272|1239|186801|186802|216572|1263|41978;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|91061|186826|1300|1301|1305;1783272|1239|91061|186826|1300|1301|1306;1783272|1239|91061|186826|1300|1301|1739491;1783272|1239|526524|526525|2810280|3025755|341225;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803|2316020|33039;3384194|508458|649775|649776|649777|2840654|2840712;3379134|1224|28216|80840|119060|93217|656179;1783272|1239|1263004;1783272|1239|526524|526525|128827|1935200|1871030;1783272|1239|186801|186802|31979|1485|1262832;3379134|1224|28216|80840|995019|40544|1262977,Complete,Svetlana up
bsdb:39880958/1/2,39880958,"cross-sectional observational, not case-control",39880958,10.1038/s41586-024-08485-8,NA,"Maghini D.G., Oduaran O.H., Olubayo L.A.I., Cook J.A., Smyth N., Mathema T., Belger C.W., Agongo G., Boua P.R., Choma S.S.R., Gómez-Olivé F.X., Kisiangani I., Mashaba G.R., Micklesfield L., Mohamed S.F., Nonterah E.A., Norris S., Sorgho H., Tollman S., Wafawanaka F., Tluway F., Ramsay M., Wirbel J., Bhatt A.S. , Hazelhurst S.",Expanding the human gut microbiome atlas of Africa,Nature,2025,NA,Experiment 1,"Kenya,South Africa",Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV-,People Living With HIV on Antiretroviral therapy (ART+ PLWH),"Women living with HIV in Agincourt, South Africa (n = 60), Soweto, South Africa (n = 50) and Nairobi, Kenya (n = 19)",719,119,NA,WMS,NA,NA,NA,Mixed-Effects Regression,0.01,TRUE,NA,NA,"antibiotic therapy,geographic area",NA,NA,NA,NA,decreased,NA,Signature 2,Supplementary Data 10,7 February 2025,Taofeecoh,"Taofeecoh,WikiWorks","Species-level prokaryotic differential abundance between seronegative and HIV+ participants in Agincourt (South Africa), Soweto (South Africa) and Nairobi (Kenya).",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Geddesella|s__Candidatus Geddesella stercoravicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|s__Christensenellaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium AF97-07pH10A,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:1193,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:226,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:349,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:433,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:448,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. CAG:82,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:124,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:129,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:238,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma|s__Mycoplasma sp. CAG:611,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:382,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella hominis,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Chloroflexota|c__Dehalococcoidia|o__Dehalococcoidales",1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|78346;1783272|1239|186801|2720808|2720834;1783272|1239|186801|3082768|990719|2054177;1783272|1239|186801|2044939;1783272|1239|186801|186802|31979|2996910;1783272|1239|186801|186802|1898207;1783272|1239|186801|186802|31979|1485|1262771;1783272|1239|186801|186802|31979|1485|1262781;1783272|1239|186801|186802|31979|1485|1262797;1783272|1239|186801|186802|31979|1485|1262806;1783272|1239|186801|186802|31979|1485|1262808;3379134|976|200643|171549|2005519|1348911|1099853;1783272|1239|186801|3082720|543314;1783272|1239|186801|186802|216572|216851|1851428;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|216851|1262898;1783272|1239|1263002;1783272|1239|1263003;1783272|1239|1263011;1783272|1239|186801|3085636|186803|1898203;1783272|544448|31969|2085|2092|2093|1262905;1783272|1239|186801|186802|216572|459786|1945593;1783272|1239|186801|186802|216572|2485925;1783272|1239|186801|186802|216572|1263|1262957;3379134|976|200643|171549|171552|2974251|2518605;1783272|1239;1783272|1239|91061|1385|186817|1386;3379134|976|200643|171549;1783272|1239|186801;1783272|1239|186801|3082720|543314;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;1783272|200795|301297|1202465,Complete,Svetlana up
bsdb:39898646/1/1,39898646,"cross-sectional observational, not case-control",39898646,10.1128/spectrum.02559-24,NA,"Zhao Y., Ferri J.T., White J.R., Schollenberger M.D., Peloza K., Sears C.L., Lipson E.J. , Shaikh F.Y.",Gut microbiome features associate with immune checkpoint inhibitor response in individuals with non-melanoma skin cancers: an exploratory study,Microbiology spectrum,2025,"Merkel cell carcinoma, basal cell carcinoma, cutaneous squamous cell carcinoma, immune checkpoint inhibitors, microbiome",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to immune checkpoint inhibitor,EFO:0600023,Non-responders (NR),Responders (R),This group consists of individual responders (R) to Immune checkpoint inhibitor (ICI) therapy.,6,9,NA,16S,12,Illumina,relative abundances,LEfSe,0.1,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 1C,30 March 2025,Joiejoie,Joiejoie,Differential abundance analysis performed by linear discriminant analysis effect size using the first fecal sample of each individual collected within 180 days.,increased,"k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Acetomicrobiaceae|g__Acetomicrobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Mahellales|f__Mahellaceae|g__Mahella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium",3384194|508458|649775|649776|3029086|49894;1783272|201174|1760|2037|2049|1654;1783272|1239|186801|186802|186806|264995;3379134|976|200643|171549|2005519|397864;1783272|1239|186801|186802|31979|1485;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|3120428|3120709|252965;1783272|201174|84998|1643822|1643826|447020;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|596767,Complete,Svetlana up
bsdb:39898646/2/1,39898646,"cross-sectional observational, not case-control",39898646,10.1128/spectrum.02559-24,NA,"Zhao Y., Ferri J.T., White J.R., Schollenberger M.D., Peloza K., Sears C.L., Lipson E.J. , Shaikh F.Y.",Gut microbiome features associate with immune checkpoint inhibitor response in individuals with non-melanoma skin cancers: an exploratory study,Microbiology spectrum,2025,"Merkel cell carcinoma, basal cell carcinoma, cutaneous squamous cell carcinoma, immune checkpoint inhibitors, microbiome",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to immune checkpoint inhibitor,EFO:0600023,Cutaneous squamous cell carcinoma Non-responders (CSCC NR),Cutaneous squamous cell carcinoma Responders (CSCC R),This group comprises individuals with Cutaneous squamous cell carcinoma who are responders to Immune checkpoint inhibitor (ICI) therapy.,6,9,NA,16S,12,Illumina,relative abundances,LEfSe,0.1,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 2A,30 March 2025,Joiejoie,Joiejoie,Differential abundance analysis performed by linear discriminant analysis effect size (LEfSe) using the first fecal sample for each individual collected within 180 days in CSCC.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter|s__Anaerosporobacter mobilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Fusibacteraceae|g__Fusibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium|s__Hydrogenoanaerobacterium saccharovorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Mahellales|f__Mahellaceae|g__Mahella,k__Bacillati|p__Bacillota|c__Clostridia|o__Mahellales|f__Mahellaceae|g__Mahella|s__Mahella australiensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira|s__Oscillospira guilliermondii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter|s__Oxalobacter formigenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus albus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus flavefaciens,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia cocleata,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__Ruminiclostridium cellobioparum|s__Ruminiclostridium cellobioparum subsp. termitidis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] viride,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii",1783272|1239|186801|3085636|186803|653683;1783272|1239|186801|3085636|186803|653683|264463;1783272|1239|186801|186802|216572|244127;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|329854;3379134|976|200643|171549|815|816|291645;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|2005519|397864|487174;1783272|1239|186801|186802|3679999|76008;1783272|1239|186801|186802|216572|596767;1783272|1239|186801|186802|216572|596767|474960;1783272|1239|186801|3120428|3120709|252965;1783272|1239|186801|3120428|3120709|252965|252966;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|459786|351091;1783272|1239|186801|186802|216572|119852|119853;3379134|1224|28216|80840|75682|846;3379134|1224|28216|80840|75682|846|847;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|1264;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|1263|1265;1783272|1239|526524|526525|2810280|3025755|69824;1783272|1239|186801|186802|216572|1508657|29355|29371;1783272|1239|186801|186802|216572|47246;3379134|976|200643|171549|2005525|375288|328812,Complete,Svetlana up
bsdb:39898646/2/2,39898646,"cross-sectional observational, not case-control",39898646,10.1128/spectrum.02559-24,NA,"Zhao Y., Ferri J.T., White J.R., Schollenberger M.D., Peloza K., Sears C.L., Lipson E.J. , Shaikh F.Y.",Gut microbiome features associate with immune checkpoint inhibitor response in individuals with non-melanoma skin cancers: an exploratory study,Microbiology spectrum,2025,"Merkel cell carcinoma, basal cell carcinoma, cutaneous squamous cell carcinoma, immune checkpoint inhibitors, microbiome",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to immune checkpoint inhibitor,EFO:0600023,Cutaneous squamous cell carcinoma Non-responders (CSCC NR),Cutaneous squamous cell carcinoma Responders (CSCC R),This group comprises individuals with Cutaneous squamous cell carcinoma who are responders to Immune checkpoint inhibitor (ICI) therapy.,6,9,NA,16S,12,Illumina,relative abundances,LEfSe,0.1,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 2A,30 March 2025,Joiejoie,Joiejoie,Differential abundance analysis performed by linear discriminant analysis effect size (LEfSe) using the first fecal sample for each individual collected within 180 days in CSCC.,decreased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris",3379134|200940|3031449|213115|194924|35832;3379134|200940|3031449|213115|194924|35832|35833;3379134|976|200643|171549|815|816|46506,Complete,Svetlana up
bsdb:39898662/1/1,39898662,laboratory experiment,39898662,10.1128/msphere.00887-24,NA,"Dong Y., Yang S., Zhang S., Zhao Y., Li X., Han M., Gai Z. , Zou K.","Modulatory impact of <i>Bifidobacterium longum</i> subsp. <i>longum</i> BL21 on the gut-brain-ovary axis in polycystic ovary syndrome: insights into metabolic regulation, inflammation mitigation, and neuroprotection",mSphere,2025,"Bifidobacterium longum subsp. longum, gut–brain–ovary axis, inflammation mitigation, metabolic regulation, polycystic ovarian syndrome",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Polycystic ovary syndrome (PCOS) + Bifidobacterium longum subsp. longum (BL21) group,Control (CTL) group,This group consists of pregnant mice used as controls.,16,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A,7 July 2025,Victoria,Victoria,"Results of the linear discriminant analysis effect size (LEfSe) analysis, showing the impact of BL21 treatment on differences in the abundance of bacterial taxa at the genus level. LEfSe analysis evaluates each significantly enriched bacterial taxonomic unit by calculating linear discriminant analysis (LDA) scores.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter",3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|1853231|283168;;1783272|1239|186801|186802|1980681;3379134|29547|3031852|213849|72293|209,Complete,KateRasheed
bsdb:39898662/2/1,39898662,laboratory experiment,39898662,10.1128/msphere.00887-24,NA,"Dong Y., Yang S., Zhang S., Zhao Y., Li X., Han M., Gai Z. , Zou K.","Modulatory impact of <i>Bifidobacterium longum</i> subsp. <i>longum</i> BL21 on the gut-brain-ovary axis in polycystic ovary syndrome: insights into metabolic regulation, inflammation mitigation, and neuroprotection",mSphere,2025,"Bifidobacterium longum subsp. longum, gut–brain–ovary axis, inflammation mitigation, metabolic regulation, polycystic ovarian syndrome",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control (CTL) + Bifidobacterium longum subsp. longum (BL21) group,Polycystic ovary syndrome (PCOS) group,This group consists of mice that were given dihydrotestosterone (DHT) to induce Polycystic ovary syndrome (PCOS).,16,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A,7 July 2025,Victoria,Victoria,"Results of the linear discriminant analysis effect size (LEfSe) analysis, showing the impact of BL21 treatment on differences in the abundance of bacterial taxa at the genus level. LEfSe analysis evaluates each significantly enriched bacterial taxonomic unit by calculating linear discriminant analysis (LDA) scores.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171552|1283313;3379134|1224|1236|91347|543|570,Complete,KateRasheed
bsdb:39898662/3/1,39898662,laboratory experiment,39898662,10.1128/msphere.00887-24,NA,"Dong Y., Yang S., Zhang S., Zhao Y., Li X., Han M., Gai Z. , Zou K.","Modulatory impact of <i>Bifidobacterium longum</i> subsp. <i>longum</i> BL21 on the gut-brain-ovary axis in polycystic ovary syndrome: insights into metabolic regulation, inflammation mitigation, and neuroprotection",mSphere,2025,"Bifidobacterium longum subsp. longum, gut–brain–ovary axis, inflammation mitigation, metabolic regulation, polycystic ovarian syndrome",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control (CTL) + Polycystic ovary syndrome (PCOS) group,Bifidobacterium longum subsp. longum (BL21) group,This group consists of mice that were given dihydrotestosterone (DHT) to induce Polycystic ovary syndrome (PCOS) and then administered a daily oral dose of 1 × 109 CFU of BL21 continuously for a total of 8 weeks as treatment.,16,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A,7 July 2025,Victoria,Victoria,"Results of the linear discriminant analysis effect size (LEfSe) analysis, showing the impact of BL21 treatment on differences in the abundance of bacterial taxa at the genus level. LEfSe analysis evaluates each significantly enriched bacterial taxonomic unit by calculating linear discriminant analysis (LDA) scores.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|3085642|580596;3379134|976|200643|171549|2005473|1918540;3379134|976|200643|171549|2005473;1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549|171550|28138;1783272|1239|186801|3085636|186803|572511;1783272|201174|1760|2037|2049|1654,Complete,KateRasheed
bsdb:39898662/4/1,39898662,laboratory experiment,39898662,10.1128/msphere.00887-24,NA,"Dong Y., Yang S., Zhang S., Zhao Y., Li X., Han M., Gai Z. , Zou K.","Modulatory impact of <i>Bifidobacterium longum</i> subsp. <i>longum</i> BL21 on the gut-brain-ovary axis in polycystic ovary syndrome: insights into metabolic regulation, inflammation mitigation, and neuroprotection",mSphere,2025,"Bifidobacterium longum subsp. longum, gut–brain–ovary axis, inflammation mitigation, metabolic regulation, polycystic ovarian syndrome",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control (CTL) group,Polycystic Ovary Syndrome (PCOS) group,This group consists of mice that were given dihydrotestosterone (DHT) to induce Polycystic ovary syndrome (PCOS)—pre-BL21 intervention.,8,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 6B,7 July 2025,Victoria,"Victoria,Tosin",LEfSe analysis results at the genus level between the DHT-induced PCOS mouse model and the control (CTL) group.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella",3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979|49082;3379134|29547|3031852|213849|72293|209;3379134|976|200643|171549|2005473;3379134|976|200643|171549|171550|28138,Complete,KateRasheed
bsdb:39898662/4/2,39898662,laboratory experiment,39898662,10.1128/msphere.00887-24,NA,"Dong Y., Yang S., Zhang S., Zhao Y., Li X., Han M., Gai Z. , Zou K.","Modulatory impact of <i>Bifidobacterium longum</i> subsp. <i>longum</i> BL21 on the gut-brain-ovary axis in polycystic ovary syndrome: insights into metabolic regulation, inflammation mitigation, and neuroprotection",mSphere,2025,"Bifidobacterium longum subsp. longum, gut–brain–ovary axis, inflammation mitigation, metabolic regulation, polycystic ovarian syndrome",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control (CTL) group,Polycystic Ovary Syndrome (PCOS) group,This group consists of mice that were given dihydrotestosterone (DHT) to induce Polycystic ovary syndrome (PCOS)—pre-BL21 intervention.,8,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 6B,7 July 2025,Victoria,Victoria,LEfSe analysis results at the genus level between the DHT-induced PCOS mouse model and the control (CTL) group.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|1853231|283168;1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85004|31953|1678;3379134|200940|3031449|213115|194924|872;3379134|976|200643|171549|171550|239759,Complete,KateRasheed
bsdb:39898662/5/1,39898662,laboratory experiment,39898662,10.1128/msphere.00887-24,NA,"Dong Y., Yang S., Zhang S., Zhao Y., Li X., Han M., Gai Z. , Zou K.","Modulatory impact of <i>Bifidobacterium longum</i> subsp. <i>longum</i> BL21 on the gut-brain-ovary axis in polycystic ovary syndrome: insights into metabolic regulation, inflammation mitigation, and neuroprotection",mSphere,2025,"Bifidobacterium longum subsp. longum, gut–brain–ovary axis, inflammation mitigation, metabolic regulation, polycystic ovarian syndrome",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Polycystic Ovary Syndrome (PCOS) group,Bifidobacterium longum subsp. longum (BL21) group,This group consists of mice that were given dihydrotestosterone (DHT) to induce Polycystic ovary syndrome (PCOS) and then administered a daily oral dose of 1 × 109 CFU of BL21 continuously for a total of 8 weeks as treatment.—post-BL21 intervention.,8,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,increased,NA,increased,Signature 1,Figure 6C,7 July 2025,Victoria,Victoria,Post-intervention LEfSe analysis results at the genus level between the DHT-induced PCOS mouse model and the BL21 treatment group.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|171550|28138;1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549|815|816,Complete,KateRasheed
bsdb:39898662/5/2,39898662,laboratory experiment,39898662,10.1128/msphere.00887-24,NA,"Dong Y., Yang S., Zhang S., Zhao Y., Li X., Han M., Gai Z. , Zou K.","Modulatory impact of <i>Bifidobacterium longum</i> subsp. <i>longum</i> BL21 on the gut-brain-ovary axis in polycystic ovary syndrome: insights into metabolic regulation, inflammation mitigation, and neuroprotection",mSphere,2025,"Bifidobacterium longum subsp. longum, gut–brain–ovary axis, inflammation mitigation, metabolic regulation, polycystic ovarian syndrome",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Polycystic Ovary Syndrome (PCOS) group,Bifidobacterium longum subsp. longum (BL21) group,This group consists of mice that were given dihydrotestosterone (DHT) to induce Polycystic ovary syndrome (PCOS) and then administered a daily oral dose of 1 × 109 CFU of BL21 continuously for a total of 8 weeks as treatment.—post-BL21 intervention.,8,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,increased,NA,increased,Signature 2,Figure 6C,7 July 2025,Victoria,Victoria,Post-intervention LEfSe analysis results at the genus level between the DHT-induced PCOS mouse model and the BL21 treatment group.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",3379134|976|200643|171549|1853231|283168;1783272|1239|186801|3085636|186803|1506553;3379134|976|200643|171549|2005473;3379134|29547|3031852|213849|72293|209;3379134|976|200643|171549|171550|239759,Complete,KateRasheed
bsdb:39898662/6/1,39898662,laboratory experiment,39898662,10.1128/msphere.00887-24,NA,"Dong Y., Yang S., Zhang S., Zhao Y., Li X., Han M., Gai Z. , Zou K.","Modulatory impact of <i>Bifidobacterium longum</i> subsp. <i>longum</i> BL21 on the gut-brain-ovary axis in polycystic ovary syndrome: insights into metabolic regulation, inflammation mitigation, and neuroprotection",mSphere,2025,"Bifidobacterium longum subsp. longum, gut–brain–ovary axis, inflammation mitigation, metabolic regulation, polycystic ovarian syndrome",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control (CTL_End) group,Bifidobacterium longum subsp. longum (BL21_Baseline) group,This group consists of mice that were given dihydrotestosterone (DHT) to induce Polycystic ovary syndrome (PCOS) (before BL21 intervention),8,8,NA,16S,34,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),Kruskall-Wallis",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5B,8 July 2025,Victoria,"Victoria,Chyono2",Violin plots illustrating differences in gut microbiota abundance at the phylum level before and after BL21 intervention at different time points. Different letters indicate statistically significant differences between groups.,decreased,k__Pseudomonadati|p__Thermodesulfobacteriota,3379134|200940,Complete,KateRasheed
bsdb:39898662/6/2,39898662,laboratory experiment,39898662,10.1128/msphere.00887-24,NA,"Dong Y., Yang S., Zhang S., Zhao Y., Li X., Han M., Gai Z. , Zou K.","Modulatory impact of <i>Bifidobacterium longum</i> subsp. <i>longum</i> BL21 on the gut-brain-ovary axis in polycystic ovary syndrome: insights into metabolic regulation, inflammation mitigation, and neuroprotection",mSphere,2025,"Bifidobacterium longum subsp. longum, gut–brain–ovary axis, inflammation mitigation, metabolic regulation, polycystic ovarian syndrome",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control (CTL_End) group,Bifidobacterium longum subsp. longum (BL21_Baseline) group,This group consists of mice that were given dihydrotestosterone (DHT) to induce Polycystic ovary syndrome (PCOS) (before BL21 intervention),8,8,NA,16S,34,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),Kruskall-Wallis",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5B,19 January 2026,Ese,"Ese,Tosin",Violin plots illustrating differences in gut microbiota abundance at the phylum level before and after BL21 intervention at different time points. Different letters indicate statistically significant differences between groups.,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,KateRasheed
bsdb:39898662/7/1,39898662,laboratory experiment,39898662,10.1128/msphere.00887-24,NA,"Dong Y., Yang S., Zhang S., Zhao Y., Li X., Han M., Gai Z. , Zou K.","Modulatory impact of <i>Bifidobacterium longum</i> subsp. <i>longum</i> BL21 on the gut-brain-ovary axis in polycystic ovary syndrome: insights into metabolic regulation, inflammation mitigation, and neuroprotection",mSphere,2025,"Bifidobacterium longum subsp. longum, gut–brain–ovary axis, inflammation mitigation, metabolic regulation, polycystic ovarian syndrome",Experiment 7,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control (CTL_Baseline) group,Control (CTL_End) group,This group consists of pregnant mice used as controls (after BL21 intervention),8,8,NA,16S,34,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),Kruskall-Wallis",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5B,8 July 2025,Victoria,"Victoria,Tosin,Ese",Violin plots illustrating differences in gut microbiota abundance at the phylum level before and after BL21 intervention at different time points.,increased,k__Pseudomonadati|p__Thermodesulfobacteriota,3379134|200940,Complete,KateRasheed
bsdb:39898662/7/2,39898662,laboratory experiment,39898662,10.1128/msphere.00887-24,NA,"Dong Y., Yang S., Zhang S., Zhao Y., Li X., Han M., Gai Z. , Zou K.","Modulatory impact of <i>Bifidobacterium longum</i> subsp. <i>longum</i> BL21 on the gut-brain-ovary axis in polycystic ovary syndrome: insights into metabolic regulation, inflammation mitigation, and neuroprotection",mSphere,2025,"Bifidobacterium longum subsp. longum, gut–brain–ovary axis, inflammation mitigation, metabolic regulation, polycystic ovarian syndrome",Experiment 7,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control (CTL_Baseline) group,Control (CTL_End) group,This group consists of pregnant mice used as controls (after BL21 intervention),8,8,NA,16S,34,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),Kruskall-Wallis",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5B,8 July 2025,Victoria,Victoria,Violin plots illustrating differences in gut microbiota abundance at the phylum level before and after BL21 intervention at different time points.,decreased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,KateRasheed
bsdb:39898662/8/1,39898662,laboratory experiment,39898662,10.1128/msphere.00887-24,NA,"Dong Y., Yang S., Zhang S., Zhao Y., Li X., Han M., Gai Z. , Zou K.","Modulatory impact of <i>Bifidobacterium longum</i> subsp. <i>longum</i> BL21 on the gut-brain-ovary axis in polycystic ovary syndrome: insights into metabolic regulation, inflammation mitigation, and neuroprotection",mSphere,2025,"Bifidobacterium longum subsp. longum, gut–brain–ovary axis, inflammation mitigation, metabolic regulation, polycystic ovarian syndrome",Experiment 8,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Polycystic Ovary Syndrome (PCOS_Baseline) group,Polycystic Ovary Syndrome (PCOS_End) group,This group consists of mice that were given dihydrotestosterone (DHT) to induce Polycystic ovary syndrome (PCOS) (after BL21 intervention).,8,8,NA,16S,34,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),Kruskall-Wallis",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5B,8 July 2025,Victoria,Victoria,Violin plots illustrating differences in gut microbiota abundance at the phylum level before and after BL21 intervention at different time points. Different letters indicate statistically significant differences between groups.,increased,k__Pseudomonadati|p__Thermodesulfobacteriota,3379134|200940,Complete,KateRasheed
bsdb:39898662/8/2,39898662,laboratory experiment,39898662,10.1128/msphere.00887-24,NA,"Dong Y., Yang S., Zhang S., Zhao Y., Li X., Han M., Gai Z. , Zou K.","Modulatory impact of <i>Bifidobacterium longum</i> subsp. <i>longum</i> BL21 on the gut-brain-ovary axis in polycystic ovary syndrome: insights into metabolic regulation, inflammation mitigation, and neuroprotection",mSphere,2025,"Bifidobacterium longum subsp. longum, gut–brain–ovary axis, inflammation mitigation, metabolic regulation, polycystic ovarian syndrome",Experiment 8,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Polycystic Ovary Syndrome (PCOS_Baseline) group,Polycystic Ovary Syndrome (PCOS_End) group,This group consists of mice that were given dihydrotestosterone (DHT) to induce Polycystic ovary syndrome (PCOS) (after BL21 intervention).,8,8,NA,16S,34,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),Kruskall-Wallis",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5B,8 July 2025,Victoria,"Victoria,Ese",Violin plots illustrating differences in gut microbiota abundance at the phylum level before and after BL21 intervention at different time points. Different letters indicate statistically significant differences between groups.,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,KateRasheed
bsdb:39898662/9/1,39898662,laboratory experiment,39898662,10.1128/msphere.00887-24,NA,"Dong Y., Yang S., Zhang S., Zhao Y., Li X., Han M., Gai Z. , Zou K.","Modulatory impact of <i>Bifidobacterium longum</i> subsp. <i>longum</i> BL21 on the gut-brain-ovary axis in polycystic ovary syndrome: insights into metabolic regulation, inflammation mitigation, and neuroprotection",mSphere,2025,"Bifidobacterium longum subsp. longum, gut–brain–ovary axis, inflammation mitigation, metabolic regulation, polycystic ovarian syndrome",Experiment 9,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Polycystic ovary syndrome (PCOS_Baseline) group,Bifidobacterium longum subsp. longum (BL21_Baseline) group,This group consists of mice that were given dihydrotestosterone (DHT) to induce Polycystic ovary syndrome (PCOS) (before BL21 intervention).,8,8,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 5B,19 January 2026,Ese,"Ese,Chyono2",Violin plots illustrating differences in gut microbiota abundance at the phylum level before and after BL21 intervention at different time points. Different letters indicate statistically significant differences between groups.,decreased,"k__Pseudomonadati|p__Campylobacterota,k__Pseudomonadati|p__Pseudomonadota",3379134|29547;3379134|1224,Complete,KateRasheed
bsdb:39898662/10/1,39898662,laboratory experiment,39898662,10.1128/msphere.00887-24,NA,"Dong Y., Yang S., Zhang S., Zhao Y., Li X., Han M., Gai Z. , Zou K.","Modulatory impact of <i>Bifidobacterium longum</i> subsp. <i>longum</i> BL21 on the gut-brain-ovary axis in polycystic ovary syndrome: insights into metabolic regulation, inflammation mitigation, and neuroprotection",mSphere,2025,"Bifidobacterium longum subsp. longum, gut–brain–ovary axis, inflammation mitigation, metabolic regulation, polycystic ovarian syndrome",Experiment 10,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Polycystic ovary syndrome (PCOS_End) group,Bifidobacterium longum subsp. longum (BL21_Baseline) group,This group consists of mice that were given dihydrotestosterone (DHT) to induce Polycystic ovary syndrome (PCOS) (before BL21 intervention),8,8,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5B,19 January 2026,Ese,"Ese,Chyono2",Violin plots illustrating differences in gut microbiota abundance at the phylum level before and after BL21 intervention at different time points. Different letters indicate statistically significant differences between groups.,increased,k__Bacillati|p__Bacillota,1783272|1239,Complete,KateRasheed
bsdb:39898662/10/2,39898662,laboratory experiment,39898662,10.1128/msphere.00887-24,NA,"Dong Y., Yang S., Zhang S., Zhao Y., Li X., Han M., Gai Z. , Zou K.","Modulatory impact of <i>Bifidobacterium longum</i> subsp. <i>longum</i> BL21 on the gut-brain-ovary axis in polycystic ovary syndrome: insights into metabolic regulation, inflammation mitigation, and neuroprotection",mSphere,2025,"Bifidobacterium longum subsp. longum, gut–brain–ovary axis, inflammation mitigation, metabolic regulation, polycystic ovarian syndrome",Experiment 10,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Polycystic ovary syndrome (PCOS_End) group,Bifidobacterium longum subsp. longum (BL21_Baseline) group,This group consists of mice that were given dihydrotestosterone (DHT) to induce Polycystic ovary syndrome (PCOS) (before BL21 intervention),8,8,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5B,19 January 2026,Ese,"Ese,Chyono2",Violin plots illustrating differences in gut microbiota abundance at the phylum level before and after BL21 intervention at different time points. Different letters indicate statistically significant differences between groups.,decreased,"k__Pseudomonadati|p__Campylobacterota,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Thermodesulfobacteriota",3379134|29547;3379134|1224;3379134|200940,Complete,KateRasheed
bsdb:39898662/11/1,39898662,laboratory experiment,39898662,10.1128/msphere.00887-24,NA,"Dong Y., Yang S., Zhang S., Zhao Y., Li X., Han M., Gai Z. , Zou K.","Modulatory impact of <i>Bifidobacterium longum</i> subsp. <i>longum</i> BL21 on the gut-brain-ovary axis in polycystic ovary syndrome: insights into metabolic regulation, inflammation mitigation, and neuroprotection",mSphere,2025,"Bifidobacterium longum subsp. longum, gut–brain–ovary axis, inflammation mitigation, metabolic regulation, polycystic ovarian syndrome",Experiment 11,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Polycystic ovary syndrome (PCOS_Baseline) group,Bifidobacterium longum subsp. longum (BL21_End) group,"This group consists of mice that were given dihydrotestosterone(DHT) to induce Polycystic ovary syndrome (PCOS) and had completed a daily administration of 1x10^9 CFU of BL21 continuously for a total of 8 weeks, representing the end of the BL21 intervention period.",8,8,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5B,19 January 2026,Ese,"Ese,Chyono2",Violin plots illustrating differences in gut microbiota abundance at the phylum level before and after BL21 intervention at different time points. Different letters indicate statistically significant differences between groups.,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,KateRasheed
bsdb:39898662/11/2,39898662,laboratory experiment,39898662,10.1128/msphere.00887-24,NA,"Dong Y., Yang S., Zhang S., Zhao Y., Li X., Han M., Gai Z. , Zou K.","Modulatory impact of <i>Bifidobacterium longum</i> subsp. <i>longum</i> BL21 on the gut-brain-ovary axis in polycystic ovary syndrome: insights into metabolic regulation, inflammation mitigation, and neuroprotection",mSphere,2025,"Bifidobacterium longum subsp. longum, gut–brain–ovary axis, inflammation mitigation, metabolic regulation, polycystic ovarian syndrome",Experiment 11,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Polycystic ovary syndrome (PCOS_Baseline) group,Bifidobacterium longum subsp. longum (BL21_End) group,"This group consists of mice that were given dihydrotestosterone(DHT) to induce Polycystic ovary syndrome (PCOS) and had completed a daily administration of 1x10^9 CFU of BL21 continuously for a total of 8 weeks, representing the end of the BL21 intervention period.",8,8,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5B,19 January 2026,Ese,"Ese,Chyono2",Violin plots illustrating differences in gut microbiota abundance at the phylum level before and after BL21 intervention at different time points. Different letters indicate statistically significant differences between groups.,decreased,k__Pseudomonadati|p__Campylobacterota,3379134|29547,Complete,KateRasheed
bsdb:39898662/12/1,39898662,laboratory experiment,39898662,10.1128/msphere.00887-24,NA,"Dong Y., Yang S., Zhang S., Zhao Y., Li X., Han M., Gai Z. , Zou K.","Modulatory impact of <i>Bifidobacterium longum</i> subsp. <i>longum</i> BL21 on the gut-brain-ovary axis in polycystic ovary syndrome: insights into metabolic regulation, inflammation mitigation, and neuroprotection",mSphere,2025,"Bifidobacterium longum subsp. longum, gut–brain–ovary axis, inflammation mitigation, metabolic regulation, polycystic ovarian syndrome",Experiment 12,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Polycystic ovary syndrome (PCOS_End) group,Bifidobacterium longum subsp. longum (BL21_End) group,"This group consists of mice that were given dihydrotestosterone(DHT) to induce Polycystic ovary syndrome (PCOS) and had completed a daily administration of 1x10^9 CFU of BL21 continuously for a total of 8 weeks, representing the end of the BL21 intervention period",8,8,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,NA,NA,NA,increased,increased,increased,NA,increased,Signature 1,Figure 5B,19 January 2026,Ese,"Ese,Chyono2",Violin plots illustrating differences in gut microbiota abundance at the phylum level before and after BL21 intervention at different time points. Different letters indicate statistically significant differences between groups.,increased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Campylobacterota,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Thermodesulfobacteriota",1783272|1239;3379134|29547;3379134|1224;3379134|200940,Complete,KateRasheed
bsdb:39898662/13/1,39898662,laboratory experiment,39898662,10.1128/msphere.00887-24,NA,"Dong Y., Yang S., Zhang S., Zhao Y., Li X., Han M., Gai Z. , Zou K.","Modulatory impact of <i>Bifidobacterium longum</i> subsp. <i>longum</i> BL21 on the gut-brain-ovary axis in polycystic ovary syndrome: insights into metabolic regulation, inflammation mitigation, and neuroprotection",mSphere,2025,"Bifidobacterium longum subsp. longum, gut–brain–ovary axis, inflammation mitigation, metabolic regulation, polycystic ovarian syndrome",Experiment 13,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control (CTL_Baseline) group,Polycystic ovary syndrome (PCOS_Baseline) group,This group consists of mice that were given dihydrotestosterone (DHT) to induce Polycystic ovary syndrome (PCOS) (before BL21 intervention).,8,8,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 5B,19 January 2026,Ese,"Ese,Tosin",Violin plots illustrating differences in gut microbiota abundance at the phylum level before and after BL21 intervention at different time points. Different letters indicate statistically significant differences between groups.,increased,"k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Campylobacterota",3379134|1224;3379134|29547,Complete,KateRasheed
bsdb:39898662/14/1,39898662,laboratory experiment,39898662,10.1128/msphere.00887-24,NA,"Dong Y., Yang S., Zhang S., Zhao Y., Li X., Han M., Gai Z. , Zou K.","Modulatory impact of <i>Bifidobacterium longum</i> subsp. <i>longum</i> BL21 on the gut-brain-ovary axis in polycystic ovary syndrome: insights into metabolic regulation, inflammation mitigation, and neuroprotection",mSphere,2025,"Bifidobacterium longum subsp. longum, gut–brain–ovary axis, inflammation mitigation, metabolic regulation, polycystic ovarian syndrome",Experiment 14,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control (CTL_Baseline) group,Polycystic ovary syndrome (PCOS_End) group,This group consists of mice that were given dihydrotestosterone (DHT) to induce Polycystic ovary syndrome (PCOS) (after BL21 intervention).,8,8,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5B,20 January 2026,Ese,Ese,Violin plots illustrating differences in gut microbiota abundance at the phylum level before and after BL21 intervention at different time points. Different letters indicate statistically significant differences between groups.,increased,k__Pseudomonadati|p__Thermodesulfobacteriota,3379134|200940,Complete,KateRasheed
bsdb:39898662/14/2,39898662,laboratory experiment,39898662,10.1128/msphere.00887-24,NA,"Dong Y., Yang S., Zhang S., Zhao Y., Li X., Han M., Gai Z. , Zou K.","Modulatory impact of <i>Bifidobacterium longum</i> subsp. <i>longum</i> BL21 on the gut-brain-ovary axis in polycystic ovary syndrome: insights into metabolic regulation, inflammation mitigation, and neuroprotection",mSphere,2025,"Bifidobacterium longum subsp. longum, gut–brain–ovary axis, inflammation mitigation, metabolic regulation, polycystic ovarian syndrome",Experiment 14,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control (CTL_Baseline) group,Polycystic ovary syndrome (PCOS_End) group,This group consists of mice that were given dihydrotestosterone (DHT) to induce Polycystic ovary syndrome (PCOS) (after BL21 intervention).,8,8,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5B,20 January 2026,Ese,Ese,Violin plots illustrating differences in gut microbiota abundance at the phylum level before and after BL21 intervention at different time points. Different letters indicate statistically significant differences between groups.,decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota",1783272|1239;3379134|1224,Complete,KateRasheed
bsdb:39898662/15/1,39898662,laboratory experiment,39898662,10.1128/msphere.00887-24,NA,"Dong Y., Yang S., Zhang S., Zhao Y., Li X., Han M., Gai Z. , Zou K.","Modulatory impact of <i>Bifidobacterium longum</i> subsp. <i>longum</i> BL21 on the gut-brain-ovary axis in polycystic ovary syndrome: insights into metabolic regulation, inflammation mitigation, and neuroprotection",mSphere,2025,"Bifidobacterium longum subsp. longum, gut–brain–ovary axis, inflammation mitigation, metabolic regulation, polycystic ovarian syndrome",Experiment 15,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control (CTL_End) group,Polycystic ovary syndrome (PCOS_Baseline) group,This group consists of mice that were given dihydrotestosterone (DHT) to induce Polycystic ovary syndrome (PCOS) (before BL21 intervention).,8,8,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5B,20 January 2026,Chyono2,Chyono2,Violin plots illustrating differences in gut microbiota abundance at the phylum level before and after BL21 intervention at different time points. Different letters indicate statistically significant differences between groups.,decreased,k__Pseudomonadati|p__Thermodesulfobacteriota,3379134|200940,Complete,KateRasheed
bsdb:39898662/16/1,39898662,laboratory experiment,39898662,10.1128/msphere.00887-24,NA,"Dong Y., Yang S., Zhang S., Zhao Y., Li X., Han M., Gai Z. , Zou K.","Modulatory impact of <i>Bifidobacterium longum</i> subsp. <i>longum</i> BL21 on the gut-brain-ovary axis in polycystic ovary syndrome: insights into metabolic regulation, inflammation mitigation, and neuroprotection",mSphere,2025,"Bifidobacterium longum subsp. longum, gut–brain–ovary axis, inflammation mitigation, metabolic regulation, polycystic ovarian syndrome",Experiment 16,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control (CTL_End) group,Polycystic ovary syndrome (PCOS_End) group,This group consists of mice that were given dihydrotestosterone (DHT) to induce Polycystic ovary syndrome (PCOS) (after BL21 intervention).,8,8,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Figure 5B,20 January 2026,Chyono2,Chyono2,Violin plots illustrating differences in gut microbiota abundance at the phylum level before and after BL21 intervention at different time points. Different letters indicate statistically significant differences between groups.,increased,k__Pseudomonadati|p__Thermodesulfobacteriota,3379134|200940,Complete,KateRasheed
bsdb:39898662/16/2,39898662,laboratory experiment,39898662,10.1128/msphere.00887-24,NA,"Dong Y., Yang S., Zhang S., Zhao Y., Li X., Han M., Gai Z. , Zou K.","Modulatory impact of <i>Bifidobacterium longum</i> subsp. <i>longum</i> BL21 on the gut-brain-ovary axis in polycystic ovary syndrome: insights into metabolic regulation, inflammation mitigation, and neuroprotection",mSphere,2025,"Bifidobacterium longum subsp. longum, gut–brain–ovary axis, inflammation mitigation, metabolic regulation, polycystic ovarian syndrome",Experiment 16,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control (CTL_End) group,Polycystic ovary syndrome (PCOS_End) group,This group consists of mice that were given dihydrotestosterone (DHT) to induce Polycystic ovary syndrome (PCOS) (after BL21 intervention).,8,8,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,Figure 5B,20 January 2026,Chyono2,Chyono2,Violin plots illustrating differences in gut microbiota abundance at the phylum level before and after BL21 intervention at different time points. Different letters indicate statistically significant differences between groups.,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,KateRasheed
bsdb:39898662/17/1,39898662,laboratory experiment,39898662,10.1128/msphere.00887-24,NA,"Dong Y., Yang S., Zhang S., Zhao Y., Li X., Han M., Gai Z. , Zou K.","Modulatory impact of <i>Bifidobacterium longum</i> subsp. <i>longum</i> BL21 on the gut-brain-ovary axis in polycystic ovary syndrome: insights into metabolic regulation, inflammation mitigation, and neuroprotection",mSphere,2025,"Bifidobacterium longum subsp. longum, gut–brain–ovary axis, inflammation mitigation, metabolic regulation, polycystic ovarian syndrome",Experiment 17,China,Mus musculus,Feces,UBERON:0001988,Polycystic ovary syndrome,EFO:0000660,Control (CTL_End) group,Bifidobacterium longum subsp. longum (BL21_End) group,"This group consists of mice that were given dihydrotestosterone(DHT) to induce Polycystic ovary syndrome (PCOS) and had completed a daily administration of 1x10^9 CFU of BL21 continuously for a total of 8 weeks, representing the end of the BL21 intervention period.",8,8,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5B,20 January 2026,Chyono2,Chyono2,Violin plots illustrating differences in gut microbiota abundance at the phylum level before and after BL21 intervention at different time points. Different letters indicate statistically significant differences between groups.,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,KateRasheed
bsdb:39920128/1/1,39920128,case-control,39920128,10.1038/s41522-025-00650-9,NA,"Popova P.V., Isakov A.O., Rusanova A.N., Sitkin S.I., Anopova A.D., Vasukova E.A., Tkachuk A.S., Nemikina I.S., Stepanova E.A., Eriskovskaya A.I., Stepanova E.A., Pustozerov E.A., Kokina M.A., Vasilieva E.Y., Vasilyeva L.B., Zgairy S., Rubin E., Even C., Turjeman S., Pervunina T.M., Grineva E.N., Koren O. , Shlyakhto E.V.",Personalized prediction of glycemic responses to food in women with diet-treated gestational diabetes: the role of the gut microbiota,NPJ biofilms and microbiomes,2025,NA,Experiment 1,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Pregnant women with lower postprandial glycemic response (PPGR) incremental area under the glycemic curve(iAUC120),Pregnant women with higher postprandial glycemic response (PPGR) incremental area under the glycemic curve(iAUC120),Pregnant women with higher postprandial glycemic response (PPGR) incremental area under the glycemic curve (iAUC120) (equal to or above median indices) at 120 minutes after meal.,NA,NA,2 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,10 March 2025,Tosin,Tosin,Results of LefSe analysis comparing relative abundance (RA) of microbial features of participants with PPGR (iAUC120) below and above median.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium edouardi,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter",1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|3569723|410072;1783272|201174|1760|85007;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|1506553|1926283;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|248744;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|186802|1980681,Complete,Folakunmi
bsdb:39920128/1/2,39920128,case-control,39920128,10.1038/s41522-025-00650-9,NA,"Popova P.V., Isakov A.O., Rusanova A.N., Sitkin S.I., Anopova A.D., Vasukova E.A., Tkachuk A.S., Nemikina I.S., Stepanova E.A., Eriskovskaya A.I., Stepanova E.A., Pustozerov E.A., Kokina M.A., Vasilieva E.Y., Vasilyeva L.B., Zgairy S., Rubin E., Even C., Turjeman S., Pervunina T.M., Grineva E.N., Koren O. , Shlyakhto E.V.",Personalized prediction of glycemic responses to food in women with diet-treated gestational diabetes: the role of the gut microbiota,NPJ biofilms and microbiomes,2025,NA,Experiment 1,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Pregnant women with lower postprandial glycemic response (PPGR) incremental area under the glycemic curve(iAUC120),Pregnant women with higher postprandial glycemic response (PPGR) incremental area under the glycemic curve(iAUC120),Pregnant women with higher postprandial glycemic response (PPGR) incremental area under the glycemic curve (iAUC120) (equal to or above median indices) at 120 minutes after meal.,NA,NA,2 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2,11 March 2025,Tosin,Tosin,Results of LefSe analysis comparing relative abundance (RA) of microbial features of participants with PPGR (iAUC120) below and above median.,decreased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella tayi,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus champanellensis",3379134|200940|3031449|213115|194924|35832|35833;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3082768|990719;1783272|1239|186801;1783272|1239|186801|3085636|186803|1432051|1432052;1783272|1239|186801|186802|186806|1730|290054;3379134|976|200643|171549|2005473;3379134|976|200643|171549|2005525|375288|823;1783272|1239|186801|3085636|186803|1769710;1783272|1239|186801|186802|216572|1263|1161942,Complete,Folakunmi
bsdb:39920128/2/1,39920128,case-control,39920128,10.1038/s41522-025-00650-9,NA,"Popova P.V., Isakov A.O., Rusanova A.N., Sitkin S.I., Anopova A.D., Vasukova E.A., Tkachuk A.S., Nemikina I.S., Stepanova E.A., Eriskovskaya A.I., Stepanova E.A., Pustozerov E.A., Kokina M.A., Vasilieva E.Y., Vasilyeva L.B., Zgairy S., Rubin E., Even C., Turjeman S., Pervunina T.M., Grineva E.N., Koren O. , Shlyakhto E.V.",Personalized prediction of glycemic responses to food in women with diet-treated gestational diabetes: the role of the gut microbiota,NPJ biofilms and microbiomes,2025,NA,Experiment 2,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Pregnant women with lower peak glycemic levels (GLUmax),Pregnant women with higher peak glycemic levels (GLUmax),Pregnant women with higher peak glucose levels equal to or above median,NA,NA,2 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,11 March 2025,Tosin,Tosin,Results of LefSe analysis comparing relative abundance (RA) of microbial features of participants with GLUmax below and above median.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|s__Enterococcaceae bacterium RF39",1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171552;1783272|1239|91061|186826|81852|423410,Complete,Folakunmi
bsdb:39920128/2/2,39920128,case-control,39920128,10.1038/s41522-025-00650-9,NA,"Popova P.V., Isakov A.O., Rusanova A.N., Sitkin S.I., Anopova A.D., Vasukova E.A., Tkachuk A.S., Nemikina I.S., Stepanova E.A., Eriskovskaya A.I., Stepanova E.A., Pustozerov E.A., Kokina M.A., Vasilieva E.Y., Vasilyeva L.B., Zgairy S., Rubin E., Even C., Turjeman S., Pervunina T.M., Grineva E.N., Koren O. , Shlyakhto E.V.",Personalized prediction of glycemic responses to food in women with diet-treated gestational diabetes: the role of the gut microbiota,NPJ biofilms and microbiomes,2025,NA,Experiment 2,Russian Federation,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Pregnant women with lower peak glycemic levels (GLUmax),Pregnant women with higher peak glycemic levels (GLUmax),Pregnant women with higher peak glucose levels equal to or above median,NA,NA,2 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,11 March 2025,Tosin,Tosin,Results of LefSe analysis comparing relative abundance (RA) of microbial features of participants with GLUmax below and above median.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus faecihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanosphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella tayi",1783272|1239|186801|186802|3085642|580596|1712515;1783272|1239|186801|3082720|186804|1505657|261299;1783272|1239|186801|3085636|186803|28050|39485;3366610|28890|183925|2158|2159|2316;1783272|1239|186801|3085636|186803|1769710;1783272|1239|186801|3085636|186803|1432051|1432052,Complete,Folakunmi
bsdb:39920804/2/1,39920804,laboratory experiment,39920804,10.1186/s40168-025-02042-9,NA,"Mooyottu S., Muyyarikkandy M.S., Yousefi F., Li G., Sahin O., Burrough E., Scaria J., Sponseller B. , Ramirez A.",Fecal microbiota transplantation modulates jejunal host-microbiota interface in weanling piglets,Microbiome,2025,"Fecal microbiota transplantation, Postweaning diarrhea, Weanling piglets",Experiment 2,United States of America,Sus scrofa domesticus,Jejunum,UBERON:0002115,Clinical treatment,EFO:0007056,Enterotoxigenic Escherichia coli (ETEC) challenge control group (EC),FMT-EC challenge group (FMT + EC),Enterotoxigenic Escherichia coli challenge (ETEC) group that received fecal microbiota preparation from 3-month-old healthy pigs on the 1st and 3rd day after weaning.,6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.1,TRUE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Figure 9F, Supplementary Material 3",25 February 2025,Taofeecoh,"Taofeecoh,Aleru Divine",Bacterial genera differentially abundant in ETEC-infected control piglets (EC) and ETEC-infected piglets that received prior FMT treatment (FMT-EC).,increased,"k__Bacillati,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Pseudoscardovia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",1783272;1783272|1239|91061;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;3379134|1224|1236;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|2742598;3379134|1224;1783272|201174|1760|85004|31953|1302778;1783272|1239|526524|526525|128827|123375;1783272|1239|186801|3085636|186803|84036;3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:39920804/2/2,39920804,laboratory experiment,39920804,10.1186/s40168-025-02042-9,NA,"Mooyottu S., Muyyarikkandy M.S., Yousefi F., Li G., Sahin O., Burrough E., Scaria J., Sponseller B. , Ramirez A.",Fecal microbiota transplantation modulates jejunal host-microbiota interface in weanling piglets,Microbiome,2025,"Fecal microbiota transplantation, Postweaning diarrhea, Weanling piglets",Experiment 2,United States of America,Sus scrofa domesticus,Jejunum,UBERON:0002115,Clinical treatment,EFO:0007056,Enterotoxigenic Escherichia coli (ETEC) challenge control group (EC),FMT-EC challenge group (FMT + EC),Enterotoxigenic Escherichia coli challenge (ETEC) group that received fecal microbiota preparation from 3-month-old healthy pigs on the 1st and 3rd day after weaning.,6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.1,TRUE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"Figure 9F, Supplementary Material 3",25 February 2025,Taofeecoh,Taofeecoh,Bacterial genera differentially abundant in ETEC-infected control piglets (EC) and ETEC-infected piglets that received prior FMT treatment (FMT-EC).,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Sharpea,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|201174;1783272|1239|186801|3082720|3030910;1783272|201174|84998|84999|1643824;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|186801;1783272|1239|526524|526525|2810280;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|186801|186802|186806;1783272|1239|186801|186802;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|2767887;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|909929|1843491|52225;1783272|1239|186801|3082720|543314|86331;1783272|201174|84998|84999|1643824|133925;1783272|1239|186801|186802|186806|113286;1783272|1239|526524|526525|2810280|519427;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977,Complete,Svetlana up
bsdb:39920804/3/1,39920804,laboratory experiment,39920804,10.1186/s40168-025-02042-9,NA,"Mooyottu S., Muyyarikkandy M.S., Yousefi F., Li G., Sahin O., Burrough E., Scaria J., Sponseller B. , Ramirez A.",Fecal microbiota transplantation modulates jejunal host-microbiota interface in weanling piglets,Microbiome,2025,"Fecal microbiota transplantation, Postweaning diarrhea, Weanling piglets",Experiment 3,United States of America,Sus scrofa domesticus,Jejunum,UBERON:0002115,Clinical treatment,EFO:0007056,Control group,Fecal microbiota transplantation (FMT) group.,3-week-old piglets that received fecal microbiota preparation from 3-month-old healthy pigs on the 1st and 3rd day after weaning.,6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.1,TRUE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,"Figures 1B, 2C, Supplementary Material 3",26 February 2025,Taofeecoh,Taofeecoh,Differentially abundant taxa between control and Fecal microbiota transplantation (FMT) groups.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetitomaculum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Pseudoscardovia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Syntrophococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK3A20",1783272|1239|186801|3085636|186803|31980;1783272|1239|909932|1843488|909930;1783272|1239|909932|1843488;1783272|1239|909932|1843488|909930|904;1783272|201174;3379134|1224|28211;1783272|1239|91061;1783272|1239;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;3379134|1224|28216|80840|119060;3379134|1224|28216|80840;1783272|1239|186801;1783272|1239|526524|526525|2810280;1783272|1117;1783272|1117|3028117;1783272|1239|909932|1843489|31977|39948;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|186801|186802|186806;1783272|1239|186801|186802;3379134|1224|1236;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|2767887;1783272|201174|1760|85006|1268;1783272|201174|1760|85006;3379134|1224;1783272|1239|186801|186802|186806|113286;1783272|201174|1760|85004|31953|1302778;3379134|1224|28211|766;33090|35493|3398|72025|3803|3814|508215;1783272|1239|186801|3085636|186803|177971;1783272|1239|526524|526525|128827|123375;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|84036;1783272|1239|186801|3085636|186803|877406,Complete,Svetlana up
bsdb:39920804/3/2,39920804,laboratory experiment,39920804,10.1186/s40168-025-02042-9,NA,"Mooyottu S., Muyyarikkandy M.S., Yousefi F., Li G., Sahin O., Burrough E., Scaria J., Sponseller B. , Ramirez A.",Fecal microbiota transplantation modulates jejunal host-microbiota interface in weanling piglets,Microbiome,2025,"Fecal microbiota transplantation, Postweaning diarrhea, Weanling piglets",Experiment 3,United States of America,Sus scrofa domesticus,Jejunum,UBERON:0002115,Clinical treatment,EFO:0007056,Control group,Fecal microbiota transplantation (FMT) group.,3-week-old piglets that received fecal microbiota preparation from 3-month-old healthy pigs on the 1st and 3rd day after weaning.,6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.1,TRUE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,"Figures 1B, 2C, Supplementary Material 3",26 February 2025,Taofeecoh,Taofeecoh,Differentially abundant taxa between control and Fecal microbiota transplantation (FMT) groups.,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Coleofasciculales|f__Coleofasciculaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Sharpea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae|g__Tumebacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Oscillatoriales|f__Microcoleaceae|g__Microcoleus|s__Microcoleus paludosus",1783272|201174;1783272|1239|91061|1385|186823;1783272|1239|186801|3082720|543314;1783272|201174|84998|84999|1643824;1783272|201174|1760|85004|31953|1678;1783272|1117|3028117|3079753|1892251;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|2742598;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|909929|1843491|52225;1783272|1239|186801|3082720|543314|86331;1783272|1239|909932;1783272|201174|84998|84999|1643824|133925;1783272|1239|186801|186802|216572;1783272|1239|909932|909929|1843491;1783272|1239|526524|526525|2810280|519427;1783272|1239|186801|186802|216572|292632;1783272|1239|91061|1385|186823|432330;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977;1783272|1239|186801|3082720|543314|35518;1783272|1239|186801|186802|216572|1263|438033;1783272|1117|3028117|1150|1892252|44471|450471,Complete,Svetlana up
bsdb:39939548/1/1,39939548,case-control,39939548,https://doi.org/10.1038/s41551-024-01318-z,https://www.nature.com/articles/s41551-024-01318-z,"Ballerini M., Galiè S., Tyagi P., Catozzi C., Raji H., Nabinejad A., Macandog A.D.G., Cordiale A., Slivinschi B.I., Kugiejko K.K., Freisa M., Occhetta P., Wargo J.A., Ferrucci P.F., Cocorocchio E., Segata N., Vignati A., Morgun A., Deleidi M., Manzo T., Rasponi M. , Nezi L.",A gut-on-a-chip incorporating human faecal samples and peristalsis predicts responses to immune checkpoint inhibitors for melanoma,Nature biomedical engineering,2025,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Response to immune checkpoint inhibitor,EFO:0600023,Non-Responsive Patients,Responsive Patients,Melanoma patients who are responsive to immunotherapy,5,4,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,figure 6 a.,19 February 2025,An05hka,An05hka,Heat map of top (responsive)R- and (non-responsive) NR-associated taxa based on Wilcoxon test unadjusted P < 0.05.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces radicidentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 448,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Bacilliculturomica|s__Bacilliculturomica massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. Marseille-P3684,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. SN20,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus",1783272|201174|1760|2037|2049|1654|111015;1783272|201174|1760|2037|2049|1654|712124;1783272|1239|186801|3082720|543314|2005387|1917867;3379134|976|200643|171549|815|816|2086579;1783272|1239|186801|186802|31979|1485|1776383;1783272|1239|186801|3085636|186803|33042|33043,Complete,Svetlana up
bsdb:39939548/1/2,39939548,case-control,39939548,https://doi.org/10.1038/s41551-024-01318-z,https://www.nature.com/articles/s41551-024-01318-z,"Ballerini M., Galiè S., Tyagi P., Catozzi C., Raji H., Nabinejad A., Macandog A.D.G., Cordiale A., Slivinschi B.I., Kugiejko K.K., Freisa M., Occhetta P., Wargo J.A., Ferrucci P.F., Cocorocchio E., Segata N., Vignati A., Morgun A., Deleidi M., Manzo T., Rasponi M. , Nezi L.",A gut-on-a-chip incorporating human faecal samples and peristalsis predicts responses to immune checkpoint inhibitors for melanoma,Nature biomedical engineering,2025,NA,Experiment 1,Italy,Homo sapiens,Feces,UBERON:0001988,Response to immune checkpoint inhibitor,EFO:0600023,Non-Responsive Patients,Responsive Patients,Melanoma patients who are responsive to immunotherapy,5,4,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,figure 6 a.,19 February 2025,An05hka,An05hka,Heat map of top (responsive)R- and (non-responsive) NR-associated taxa based on Wilcoxon test unadjusted P < 0.05,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister histaminiformans,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|s__Alphaproteobacteria bacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus prevotii,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Gallimonas|s__Candidatus Gallimonas merdae,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Neochristensenella|s__Candidatus Neochristensenella gallicola,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium sp. AM22-15,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF34-10BH,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea phocaeensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus raffinosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium kristiansenii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia spiroformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] hylemonae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter|s__Dysosmobacter welbionis",1783272|1239|909932|1843489|31977|39948|209880;3379134|1224|28211|1913988;1783272|1239|1737404|1737405|1570339|165779|33034;1783272|1239|186801|2720806|2720814;1783272|1239|186801|2721110|2721137;1783272|1239|526524|526525|2810280|135858|2292991;1783272|1239|186801|186802|31979|1898204;1783272|1239|186801|186802|31979|1485|2293011;1783272|1239|186801|3085636|186803|189330|2040291;1783272|1239|91061|186826|81852|1350|71452;1783272|1239|186801|3082720|543314|86331|2606708;1783272|1239|526524|526525|2810280|3025755|29348;1783272|1239|186801|3085636|186803|1506553|89153;1783272|1239|186801|186802|216572|2591381|2093857,Complete,Svetlana up
bsdb:39940045/1/1,39940045,randomized controlled trial,39940045,10.1186/s40168-024-02016-3,NA,"Schropp N., Bauer A., Stanislas V., Huang K.D., Lesker T.R., Bielecka A.A., Strowig T. , Michels K.B.",The impact of regular sauerkraut consumption on the human gut microbiota: a crossover intervention trial,Microbiome,2025,"Diversity, Fermented food, Gut microbiome, Pasteurization, SCFA, Sauerkraut, Short-chain fatty acids, Shotgun metagenomics",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Group A: Before Fresh Sauerkraut Intervention,Group A: Post Fresh Sauerkraut Intervention,Similar Participants after intervention with fresh Sauerkraut,41,41,3 months,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,unchanged,Signature 1,Figure 4,28 February 2025,Taofeecoh,Taofeecoh,Species with significant effects after fresh sauerkraut intervention.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus paracasei,1783272|1239|91061|186826|33958|2759736|1597,Complete,Svetlana up
bsdb:39940045/2/1,39940045,randomized controlled trial,39940045,10.1186/s40168-024-02016-3,NA,"Schropp N., Bauer A., Stanislas V., Huang K.D., Lesker T.R., Bielecka A.A., Strowig T. , Michels K.B.",The impact of regular sauerkraut consumption on the human gut microbiota: a crossover intervention trial,Microbiome,2025,"Diversity, Fermented food, Gut microbiome, Pasteurization, SCFA, Sauerkraut, Short-chain fatty acids, Shotgun metagenomics",Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Group B: Before Pasteurized Sauerkraut Intervention,Group B: Post Pasteurized Sauerkraut Intervention,Similar Participants after intervention with pasteurized Sauerkraut.,46,46,3 months,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,unchanged,Signature 1,Figure 4A,28 February 2025,Taofeecoh,Taofeecoh,Species with significant effects after pasteurized intervention,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,1783272|1239|186801|3085636|186803|207244|649756,Complete,Svetlana up
bsdb:39940045/2/2,39940045,randomized controlled trial,39940045,10.1186/s40168-024-02016-3,NA,"Schropp N., Bauer A., Stanislas V., Huang K.D., Lesker T.R., Bielecka A.A., Strowig T. , Michels K.B.",The impact of regular sauerkraut consumption on the human gut microbiota: a crossover intervention trial,Microbiome,2025,"Diversity, Fermented food, Gut microbiome, Pasteurization, SCFA, Sauerkraut, Short-chain fatty acids, Shotgun metagenomics",Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Group B: Before Pasteurized Sauerkraut Intervention,Group B: Post Pasteurized Sauerkraut Intervention,Similar Participants after intervention with pasteurized Sauerkraut.,46,46,3 months,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,unchanged,Signature 2,Figure 4A,28 February 2025,Taofeecoh,Taofeecoh,Species with significant effects after pasteurized intervention,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,1783272|1239|186801|3085636|186803|572511|40520,Complete,Svetlana up
bsdb:39940045/3/1,39940045,randomized controlled trial,39940045,10.1186/s40168-024-02016-3,NA,"Schropp N., Bauer A., Stanislas V., Huang K.D., Lesker T.R., Bielecka A.A., Strowig T. , Michels K.B.",The impact of regular sauerkraut consumption on the human gut microbiota: a crossover intervention trial,Microbiome,2025,"Diversity, Fermented food, Gut microbiome, Pasteurization, SCFA, Sauerkraut, Short-chain fatty acids, Shotgun metagenomics",Experiment 3,Germany,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Age Strata before Fresh Sauerkraut Intervention: Age ≥  50 (50-69),Age Strata after Fresh Sauerkraut Intervention: Age ≥  50 (50-69),Participants with age ≥ 50 (50-69) that received Fresh Sauerkraut Intervention.,NA,NA,3 months,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,unchanged,Signature 1,Supplementary Figure S11,4 March 2025,Taofeecoh,Taofeecoh,Species’ relative abundance before fresh intervention vs after fresh intervention,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus paracasei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei",1783272|1239|91061|186826|33958|2759736|1597;3379134|976|200643|171549|815|909656|357276,Complete,Svetlana up
bsdb:39940045/4/1,39940045,randomized controlled trial,39940045,10.1186/s40168-024-02016-3,NA,"Schropp N., Bauer A., Stanislas V., Huang K.D., Lesker T.R., Bielecka A.A., Strowig T. , Michels K.B.",The impact of regular sauerkraut consumption on the human gut microbiota: a crossover intervention trial,Microbiome,2025,"Diversity, Fermented food, Gut microbiome, Pasteurization, SCFA, Sauerkraut, Short-chain fatty acids, Shotgun metagenomics",Experiment 4,Germany,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Age Strata before Fresh Sauerkraut Intervention: Age < 50 (21-49),Age Strata after Fresh Sauerkraut Intervention: Age < 50 (21-49),Participants with age < 50 (21-49) that received fresh Sauerkraut Intervention.,NA,NA,3 months,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.1,TRUE,NA,NA,age,unchanged,unchanged,NA,NA,unchanged,unchanged,Signature 1,Supplementary Figure S11,4 March 2025,Taofeecoh,"Taofeecoh,KateRasheed",Species’ relative abundance before fresh intervention vs after fresh intervention,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus paracasei,1783272|1239|91061|186826|33958|2759736|1597,Complete,Svetlana up
bsdb:39940045/5/1,39940045,randomized controlled trial,39940045,10.1186/s40168-024-02016-3,NA,"Schropp N., Bauer A., Stanislas V., Huang K.D., Lesker T.R., Bielecka A.A., Strowig T. , Michels K.B.",The impact of regular sauerkraut consumption on the human gut microbiota: a crossover intervention trial,Microbiome,2025,"Diversity, Fermented food, Gut microbiome, Pasteurization, SCFA, Sauerkraut, Short-chain fatty acids, Shotgun metagenomics",Experiment 5,Germany,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Body Mass Index (BMI) Strata before Fresh Sauerkraut Intervention: BMI ≥ 25 (25-31),Body Mass Index (BMI) Strata after Fresh Sauerkraut Intervention: BMI ≥ 25 (25-31),Participants with BMI ≥ 25 (25-31) that received Fresh Sauerkraut.,NA,NA,3 months,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.1,TRUE,NA,NA,body mass index,unchanged,unchanged,NA,NA,unchanged,unchanged,Signature 1,Supplementary Figure S11,4 March 2025,Taofeecoh,Taofeecoh,Species’ relative abundance before fresh intervention vs after fresh intervention,decreased,NA,NA,Complete,Svetlana up
bsdb:39940045/5/2,39940045,randomized controlled trial,39940045,10.1186/s40168-024-02016-3,NA,"Schropp N., Bauer A., Stanislas V., Huang K.D., Lesker T.R., Bielecka A.A., Strowig T. , Michels K.B.",The impact of regular sauerkraut consumption on the human gut microbiota: a crossover intervention trial,Microbiome,2025,"Diversity, Fermented food, Gut microbiome, Pasteurization, SCFA, Sauerkraut, Short-chain fatty acids, Shotgun metagenomics",Experiment 5,Germany,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Body Mass Index (BMI) Strata before Fresh Sauerkraut Intervention: BMI ≥ 25 (25-31),Body Mass Index (BMI) Strata after Fresh Sauerkraut Intervention: BMI ≥ 25 (25-31),Participants with BMI ≥ 25 (25-31) that received Fresh Sauerkraut.,NA,NA,3 months,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.1,TRUE,NA,NA,body mass index,unchanged,unchanged,NA,NA,unchanged,unchanged,Signature 2,Supplementary Figure 11,24 March 2025,KateRasheed,KateRasheed,Species’ relative abundance before fresh intervention vs after fresh intervention,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus paracasei,1783272|1239|91061|186826|33958|2759736|1597,Complete,Svetlana up
bsdb:39940045/6/1,39940045,randomized controlled trial,39940045,10.1186/s40168-024-02016-3,NA,"Schropp N., Bauer A., Stanislas V., Huang K.D., Lesker T.R., Bielecka A.A., Strowig T. , Michels K.B.",The impact of regular sauerkraut consumption on the human gut microbiota: a crossover intervention trial,Microbiome,2025,"Diversity, Fermented food, Gut microbiome, Pasteurization, SCFA, Sauerkraut, Short-chain fatty acids, Shotgun metagenomics",Experiment 6,Germany,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,BMI Strata before Fresh Sauerkraut Intervention: BMI ≤ 25 (18-25),BMI Strata after Fresh Sauerkraut Intervention: BMI ≤  25 (18-25),Participants with BMI ≤  25 (18-25) that received fresh Sauerkraut Intervention.,NA,NA,3 months,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.1,TRUE,NA,NA,body mass index,unchanged,unchanged,NA,NA,unchanged,unchanged,Signature 1,Supplementary Figure S11,4 March 2025,Taofeecoh,"Taofeecoh,KateRasheed",Species’ relative abundance before fresh intervention vs after fresh intervention,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus paracasei,1783272|1239|91061|186826|33958|2759736|1597,Complete,Svetlana up
bsdb:39940045/7/1,39940045,randomized controlled trial,39940045,10.1186/s40168-024-02016-3,NA,"Schropp N., Bauer A., Stanislas V., Huang K.D., Lesker T.R., Bielecka A.A., Strowig T. , Michels K.B.",The impact of regular sauerkraut consumption on the human gut microbiota: a crossover intervention trial,Microbiome,2025,"Diversity, Fermented food, Gut microbiome, Pasteurization, SCFA, Sauerkraut, Short-chain fatty acids, Shotgun metagenomics",Experiment 7,Germany,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Fiber intake Strata before Pasteurized Sauerkraut Intervention: Fiber ≤ 30g (8-30g),Fiber intake Strata after Pasteurized Sauerkraut Intervention: Fiber ≤ 30g (8-30g),Participants with ≤ 30g (8-30g) fiber diet that received Pasteurized Sauerkraut Intervention.,NA,NA,3 months,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,unchanged,Signature 1,Supplementary Figure S11,4 March 2025,Taofeecoh,Taofeecoh,Species’ relative abundance before pasteurized intervention vs after pasteurized intervention,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus",1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|207244|649756,Complete,Svetlana up
bsdb:39940045/8/1,39940045,randomized controlled trial,39940045,10.1186/s40168-024-02016-3,NA,"Schropp N., Bauer A., Stanislas V., Huang K.D., Lesker T.R., Bielecka A.A., Strowig T. , Michels K.B.",The impact of regular sauerkraut consumption on the human gut microbiota: a crossover intervention trial,Microbiome,2025,"Diversity, Fermented food, Gut microbiome, Pasteurization, SCFA, Sauerkraut, Short-chain fatty acids, Shotgun metagenomics",Experiment 8,Germany,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Fiber intake Strata before fresh Sauerkraut Intervention: Fiber ≤ 30g (8-30g),Fiber intake Strata after fresh Sauerkraut Intervention: Fiber ≤ 30g (8-30g),Participants with ≤ 30g (8-30g) fiber diet that received fresh Sauerkraut Intervention.,NA,NA,3 months,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,unchanged,Signature 1,Supplementary Figure 11,5 March 2025,Taofeecoh,"Taofeecoh,KateRasheed",Species’ relative abundance before fresh intervention vs after fresh intervention,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus paracasei,1783272|1239|91061|186826|33958|2759736|1597,Complete,Svetlana up
bsdb:39940045/9/1,39940045,randomized controlled trial,39940045,10.1186/s40168-024-02016-3,NA,"Schropp N., Bauer A., Stanislas V., Huang K.D., Lesker T.R., Bielecka A.A., Strowig T. , Michels K.B.",The impact of regular sauerkraut consumption on the human gut microbiota: a crossover intervention trial,Microbiome,2025,"Diversity, Fermented food, Gut microbiome, Pasteurization, SCFA, Sauerkraut, Short-chain fatty acids, Shotgun metagenomics",Experiment 9,Germany,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Fiber intake Strata before fresh Sauerkraut Intervention: Fiber ≥ 30g (30-58g),Fiber intake Strata after fresh Sauerkraut Intervention: Fiber ≥ 30g (30-58g),Participants with ≥ 30g (30-58g) fiber diet that received fresh Sauerkraut Intervention.,NA,NA,3 months,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,unchanged,Signature 1,Supplementary Figure 11,24 March 2025,KateRasheed,KateRasheed,Species’ relative abundance before fresh intervention vs after fresh intervention,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus paracasei,1783272|1239|91061|186826|33958|2759736|1597,Complete,Svetlana up
bsdb:39940045/10/1,39940045,randomized controlled trial,39940045,10.1186/s40168-024-02016-3,NA,"Schropp N., Bauer A., Stanislas V., Huang K.D., Lesker T.R., Bielecka A.A., Strowig T. , Michels K.B.",The impact of regular sauerkraut consumption on the human gut microbiota: a crossover intervention trial,Microbiome,2025,"Diversity, Fermented food, Gut microbiome, Pasteurization, SCFA, Sauerkraut, Short-chain fatty acids, Shotgun metagenomics",Experiment 10,Germany,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Male Strata before fresh Sauerkraut Intervention,Male Strata after fresh Sauerkraut Intervention,Male participants that received Fresh Sauerkraut Intervention.,18,18,3 months,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.1,TRUE,NA,NA,sex,unchanged,unchanged,NA,NA,unchanged,unchanged,Signature 1,Supplementary Figure 11,24 March 2025,KateRasheed,KateRasheed,Species’ relative abundance before fresh intervention vs after fresh intervention,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus paracasei,1783272|1239|91061|186826|33958|2759736|1597,Complete,Svetlana up
bsdb:39940045/11/1,39940045,randomized controlled trial,39940045,10.1186/s40168-024-02016-3,NA,"Schropp N., Bauer A., Stanislas V., Huang K.D., Lesker T.R., Bielecka A.A., Strowig T. , Michels K.B.",The impact of regular sauerkraut consumption on the human gut microbiota: a crossover intervention trial,Microbiome,2025,"Diversity, Fermented food, Gut microbiome, Pasteurization, SCFA, Sauerkraut, Short-chain fatty acids, Shotgun metagenomics",Experiment 11,Germany,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Female Strata before fresh Sauerkraut Intervention,Female Strata after fresh Sauerkraut Intervention,Female participants that received Fresh Sauerkraut Intervention.,23,23,3 months,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.1,TRUE,NA,NA,sex,unchanged,unchanged,NA,NA,unchanged,unchanged,Signature 1,Supplementary Figure 11,24 March 2025,KateRasheed,KateRasheed,Species’ relative abundance before fresh intervention vs after fresh intervention,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus paracasei,1783272|1239|91061|186826|33958|2759736|1597,Complete,Svetlana up
bsdb:39940045/12/1,39940045,randomized controlled trial,39940045,10.1186/s40168-024-02016-3,NA,"Schropp N., Bauer A., Stanislas V., Huang K.D., Lesker T.R., Bielecka A.A., Strowig T. , Michels K.B.",The impact of regular sauerkraut consumption on the human gut microbiota: a crossover intervention trial,Microbiome,2025,"Diversity, Fermented food, Gut microbiome, Pasteurization, SCFA, Sauerkraut, Short-chain fatty acids, Shotgun metagenomics",Experiment 12,Germany,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Age Strata before pasteurized Sauerkraut Intervention: Age ≥  50 (50-69),Age Strata after pasteurized Sauerkraut Intervention: Age ≥  50 (50-69),Participants with age ≥ 50 (50-69) that received pasteurized Sauerkraut Intervention.,NA,NA,3 months,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.1,TRUE,NA,NA,age,unchanged,unchanged,NA,NA,unchanged,unchanged,Signature 1,Supplementary Figure 11,25 March 2025,KateRasheed,KateRasheed,Species’ relative abundance before pasteurized intervention vs after pasteurized intervention,increased,NA,NA,Complete,Svetlana up
bsdb:39940045/13/1,39940045,randomized controlled trial,39940045,10.1186/s40168-024-02016-3,NA,"Schropp N., Bauer A., Stanislas V., Huang K.D., Lesker T.R., Bielecka A.A., Strowig T. , Michels K.B.",The impact of regular sauerkraut consumption on the human gut microbiota: a crossover intervention trial,Microbiome,2025,"Diversity, Fermented food, Gut microbiome, Pasteurization, SCFA, Sauerkraut, Short-chain fatty acids, Shotgun metagenomics",Experiment 13,Germany,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Age Strata before pasteurized Sauerkraut Intervention: Age < 50 (21-49),Age Strata after pasteurized Sauerkraut Intervention: Age < 50 (21-49),Participants with age < 50 (21-49) that received pasteurized Sauerkraut Intervention.,NA,NA,3 months,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.1,TRUE,NA,NA,age,unchanged,unchanged,NA,NA,unchanged,unchanged,Signature 1,Supplementary Figure 11,25 March 2025,KateRasheed,KateRasheed,Species’ relative abundance before pasteurized intervention vs after pasteurized intervention,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,1783272|1239|186801|3085636|186803|207244|649756,Complete,Svetlana up
bsdb:39940045/14/1,39940045,randomized controlled trial,39940045,10.1186/s40168-024-02016-3,NA,"Schropp N., Bauer A., Stanislas V., Huang K.D., Lesker T.R., Bielecka A.A., Strowig T. , Michels K.B.",The impact of regular sauerkraut consumption on the human gut microbiota: a crossover intervention trial,Microbiome,2025,"Diversity, Fermented food, Gut microbiome, Pasteurization, SCFA, Sauerkraut, Short-chain fatty acids, Shotgun metagenomics",Experiment 14,Germany,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,BMI Strata before pasteurized Sauerkraut Intervention: BMI ≥ 25 (25-31),BMI Strata after pasteurized Sauerkraut Intervention: BMI ≥ 25 (25-31),Participants with BMI ≥ 25 (25-31) that received pasteurized Sauerkraut.,NA,NA,3 months,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.1,TRUE,NA,NA,body mass index,unchanged,unchanged,NA,NA,unchanged,unchanged,Signature 1,Supplementary Figure 11,25 March 2025,KateRasheed,KateRasheed,Species’ relative abundance before pasteurized intervention vs after pasteurized intervention,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,1783272|1239|186801|3085636|186803|572511|871665,Complete,Svetlana up
bsdb:39940045/15/1,39940045,randomized controlled trial,39940045,10.1186/s40168-024-02016-3,NA,"Schropp N., Bauer A., Stanislas V., Huang K.D., Lesker T.R., Bielecka A.A., Strowig T. , Michels K.B.",The impact of regular sauerkraut consumption on the human gut microbiota: a crossover intervention trial,Microbiome,2025,"Diversity, Fermented food, Gut microbiome, Pasteurization, SCFA, Sauerkraut, Short-chain fatty acids, Shotgun metagenomics",Experiment 15,Germany,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,BMI Strata before pasteurized Sauerkraut Intervention: BMI ≤ 25 (18-25),BMI Strata after pasteurized Sauerkraut Intervention: BMI ≤  25 (18-25),Participants with BMI ≤  25 (18-25) that received pasteurized Sauerkraut Intervention.,NA,NA,3 months,WMS,NA,Illumina,relative abundances,Mixed-Effects Regression,0.1,TRUE,NA,NA,body mass index,unchanged,unchanged,NA,NA,unchanged,unchanged,Signature 1,Supplementary Figure 11,25 March 2025,KateRasheed,KateRasheed,Species’ relative abundance before pasteurized intervention vs after pasteurized intervention,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,1783272|1239|186801|3085636|186803|207244|649756,Complete,Svetlana up
bsdb:39940316/1/1,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 1,United States of America,Homo sapiens,Internal cheek pouch,UBERON:0013640,Health study participation,EFO:0010130,Pre-Intervention for exclusive juice diet,Immediately post-intervention for exclusive juice diet,Effects of exclusive juice diet immediately after intervention on internal cheek sample.,5,5,NA,16S,45,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Results' Text 3.2.1,3 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in cheek samples; pre-intervention vs post-intervention for exclusive juice diet.,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,NA
bsdb:39940316/1/2,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 1,United States of America,Homo sapiens,Internal cheek pouch,UBERON:0013640,Health study participation,EFO:0010130,Pre-Intervention for exclusive juice diet,Immediately post-intervention for exclusive juice diet,Effects of exclusive juice diet immediately after intervention on internal cheek sample.,5,5,NA,16S,45,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Results' Text 3.2.1,3 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in cheek samples; pre-intervention vs post-intervention fo exclusive juice diet.,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,NA
bsdb:39940316/2/1,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 2,United States of America,Homo sapiens,Internal cheek pouch,UBERON:0013640,Health study participation,EFO:0010130,Pre-Intervention for plant-based food diet,Immediately post-intervention for plant-based food diet,Effects of plant-based food diet immediately after intervention on internal cheek sample.,5,5,NA,16S,45,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Results' Text 3.2.1,3 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in cheek samples; pre-intervention vs post-intervention for plant-based diet.,increased,"k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Pseudomonadota",3384189|32066;3379134|1224,Complete,NA
bsdb:39940316/2/2,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 2,United States of America,Homo sapiens,Internal cheek pouch,UBERON:0013640,Health study participation,EFO:0010130,Pre-Intervention for plant-based food diet,Immediately post-intervention for plant-based food diet,Effects of plant-based food diet immediately after intervention on internal cheek sample.,5,5,NA,16S,45,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Result Text,3 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in cheek samples; pre-intervention vs post-intervention for plant-based diet.,decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota",1783272|1239;3379134|976,Complete,NA
bsdb:39940316/3/1,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 3,United States of America,Homo sapiens,Internal cheek pouch,UBERON:0013640,Health study participation,EFO:0010130,Pre-Intervention for Juice plus food diet,Immediately post-intervention for Juice plus food diet,Effects of exclusive juice diet immediately after intervention on internal cheek sample.,4,4,NA,16S,45,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Results' Text 3.2.1,3 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in cheek samples; pre-intervention vs post-intervention for juice plus food diet.,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,NA
bsdb:39940316/4/1,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 4,United States of America,Homo sapiens,Internal cheek pouch,UBERON:0013640,Health study participation,EFO:0010130,Pre-Intervention for exclusive Juice diet,Immediately post-intervention for exclusive juice diet,Effects of exclusive juice diet immediately after intervention on internal cheek sample.,5,5,NA,16S,45,Illumina,centered log-ratio,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Results' Text 3.2.1,3 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in cheek samples; pre-intervention vs post-intervention for exclusive juice diet.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae",1783272|1239|91061|186826|186827;3379134|1224|28216|80840|119060;3379134|1224|1236|135615|868;3379134|1224|28216|80840|80864;3379134|976|117743|200644|49546;3384189|32066|203490|203491|203492;3379134|1224|28216|206351|481;3379134|203691|203692|136|137,Complete,NA
bsdb:39940316/4/2,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 4,United States of America,Homo sapiens,Internal cheek pouch,UBERON:0013640,Health study participation,EFO:0010130,Pre-Intervention for exclusive Juice diet,Immediately post-intervention for exclusive juice diet,Effects of exclusive juice diet immediately after intervention on internal cheek sample.,5,5,NA,16S,45,Illumina,centered log-ratio,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Results' Text 3.2.1,3 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in cheek samples; pre-intervention vs post-intervention for exclusive juice diet.,decreased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,1783272|1239|909932|1843489|31977,Complete,NA
bsdb:39940316/5/1,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 5,United States of America,Homo sapiens,Internal cheek pouch,UBERON:0013640,Health study participation,EFO:0010130,Pre-Intervention for plant-based food diet,Immediately post-intervention for plant-based food diet,Effects of plant-based food diet immediately after intervention on internal cheek sample.,5,5,NA,16S,45,Illumina,centered log-ratio,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Results' Text 3.2.1,3 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in cheek samples; pre-intervention vs post-intervention for plant-based diet.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae",3379134|1224|28216|80840|119060;3379134|1224|1236|135615|868;3384189|32066|203490|203491|203492;3379134|1224|28216|206351|481,Complete,NA
bsdb:39940316/5/2,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 5,United States of America,Homo sapiens,Internal cheek pouch,UBERON:0013640,Health study participation,EFO:0010130,Pre-Intervention for plant-based food diet,Immediately post-intervention for plant-based food diet,Effects of plant-based food diet immediately after intervention on internal cheek sample.,5,5,NA,16S,45,Illumina,centered log-ratio,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Results' Text 3.2.1,3 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in cheek samples; pre-intervention vs post-intervention for plant-based diet.,decreased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,1783272|1239|909932|1843489|31977,Complete,NA
bsdb:39940316/6/1,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 6,United States of America,Homo sapiens,Internal cheek pouch,UBERON:0013640,Health study participation,EFO:0010130,Pre-Intervention for Juice plus food diet,Immediately post-intervention for Juice plus food diet,Effects of exclusive juice diet immediately after intervention on internal cheek sample.,4,4,NA,16S,45,Illumina,centered log-ratio,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Results' Text 3.2.1,4 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in cheek samples; pre-intervention vs post-intervention for juice plus food diet.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae",1783272|1239|91061|186826|186827;3379134|1224|28216|80840|119060;3379134|1224|1236|135615|868;3379134|1224|28216|80840|80864;3379134|976|117743|200644|49546;3384189|32066|203490|203491|203492;3379134|1224|28216|206351|481;3379134|203691|203692|136|137;1783272|1239|1737404|1737405|1737406,Complete,NA
bsdb:39940316/6/2,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 6,United States of America,Homo sapiens,Internal cheek pouch,UBERON:0013640,Health study participation,EFO:0010130,Pre-Intervention for Juice plus food diet,Immediately post-intervention for Juice plus food diet,Effects of exclusive juice diet immediately after intervention on internal cheek sample.,4,4,NA,16S,45,Illumina,centered log-ratio,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Results' Text 3.2.1,4 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in cheek samples; pre-intervention vs post-intervention for juice plus food diet.,decreased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,1783272|1239|909932|1843489|31977,Complete,NA
bsdb:39940316/7/1,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 7,United States of America,Homo sapiens,Saliva,UBERON:0001836,Health study participation,EFO:0010130,Pre-Intervention for Juice diet,Immediately post-intervention for exclusive juice diet,Effects of exclusive juice diet immediately after intervention on saliva sample.,5,5,NA,16S,45,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Results' Text 3.2.1,4 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in saliva samples; pre-intervention vs post-intervention for exclusive juice diet.,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,NA
bsdb:39940316/7/2,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 7,United States of America,Homo sapiens,Saliva,UBERON:0001836,Health study participation,EFO:0010130,Pre-Intervention for Juice diet,Immediately post-intervention for exclusive juice diet,Effects of exclusive juice diet immediately after intervention on saliva sample.,5,5,NA,16S,45,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Results' Text 3.2.1,4 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in saliva samples; pre-intervention vs post-intervention fo exclusive juice diet.,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,NA
bsdb:39940316/8/1,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 8,United States of America,Homo sapiens,Saliva,UBERON:0001836,Health study participation,EFO:0010130,Pre-Intervention for plant-based food diet,Immediately post-intervention for plant-based food diet,Effects of plant-based food diet immediately after intervention on saliva sample.,5,5,NA,16S,45,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Results' Text 3.2.1,4 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in saliva samples; pre-intervention vs post-intervention for plant-based diet.,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,NA
bsdb:39940316/8/2,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 8,United States of America,Homo sapiens,Saliva,UBERON:0001836,Health study participation,EFO:0010130,Pre-Intervention for plant-based food diet,Immediately post-intervention for plant-based food diet,Effects of plant-based food diet immediately after intervention on saliva sample.,5,5,NA,16S,45,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Results' Text 3.2.1,4 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in saliva samples; pre-intervention vs post-intervention for plant-based diet.,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,NA
bsdb:39940316/9/1,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 9,United States of America,Homo sapiens,Saliva,UBERON:0001836,Health study participation,EFO:0010130,Pre-Intervention for Juice plus food diet,Immediately post-intervention for Juice plus food diet,Effects of exclusive juice diet immediately after intervention on saliva sample.,4,4,NA,16S,45,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Results' Text 3.2.1,4 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in saliva samples; pre-intervention vs post-intervention for juice plus food diet.,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,NA
bsdb:39940316/9/2,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 9,United States of America,Homo sapiens,Saliva,UBERON:0001836,Health study participation,EFO:0010130,Pre-Intervention for Juice plus food diet,Immediately post-intervention for Juice plus food diet,Effects of exclusive juice diet immediately after intervention on saliva sample.,4,4,NA,16S,45,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Results' Text 3.2.1,4 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in saliva samples; pre-intervention vs post-intervention for juice plus food diet.,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota",1783272|201174;1783272|1239,Complete,NA
bsdb:39940316/10/1,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 10,United States of America,Homo sapiens,Saliva,UBERON:0001836,Health study participation,EFO:0010130,Pre-Intervention for exclusive juice diet,Immediately post-intervention for exclusive juice diet,Effects of exclusive juice diet immediately after intervention on saliva sample.,5,5,NA,16S,45,Illumina,centered log-ratio,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Results' Text 3.2.1,4 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in saliva samples; pre-intervention vs post-intervention for exclusive juice diet.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae",3379134|1224|28216|80840|119060;3379134|29547|3031852|213849|72294;3379134|976|117743|200644|49546;3384189|32066|203490|203491|203492;3379134|1224|28216|206351|481;3379134|203691|203692|136|137,Complete,NA
bsdb:39940316/10/2,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 10,United States of America,Homo sapiens,Saliva,UBERON:0001836,Health study participation,EFO:0010130,Pre-Intervention for exclusive juice diet,Immediately post-intervention for exclusive juice diet,Effects of exclusive juice diet immediately after intervention on saliva sample.,5,5,NA,16S,45,Illumina,centered log-ratio,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Results' Text 3.2.1,4 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in saliva samples; pre-intervention vs post-intervention for exclusive juice diet.,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|201174|84998|84999|84107;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171552;1783272|1239|91061|186826|1300;1783272|1239|909932|1843489|31977,Complete,NA
bsdb:39940316/11/1,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 11,United States of America,Homo sapiens,Saliva,UBERON:0001836,Health study participation,EFO:0010130,Pre-Intervention for plant-based food diet,Immediately post-intervention for plant-based food diet,Effects of plant-based food diet immediately after intervention on saliva sample.,5,5,NA,16S,45,Illumina,centered log-ratio,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Results' Text 3.2.1,4 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in saliva samples; pre-intervention vs post-intervention for plant-based diet.,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae",3384189|32066|203490|203491|203492;3379134|1224|28216|206351|481,Complete,NA
bsdb:39940316/11/2,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 11,United States of America,Homo sapiens,Saliva,UBERON:0001836,Health study participation,EFO:0010130,Pre-Intervention for plant-based food diet,Immediately post-intervention for plant-based food diet,Effects of plant-based food diet immediately after intervention on saliva sample.,5,5,NA,16S,45,Illumina,centered log-ratio,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Results' Text 3.2.1,4 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in saliva samples; pre-intervention vs post-intervention for plant-based diet.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,1783272|1239|91061|186826|1300,Complete,NA
bsdb:39940316/12/1,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 12,United States of America,Homo sapiens,Saliva,UBERON:0001836,Health study participation,EFO:0010130,Pre-Intervention for Juice plus food diet,Immediately post-intervention for Juice plus food diet,Effects of exclusive juice diet immediately after intervention on saliva sample.,4,4,NA,16S,45,Illumina,centered log-ratio,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Results' Text 3.2.1,4 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in saliva samples; pre-intervention vs post-intervention for juice plus food diet.,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae",3384189|32066|203490|203491|203492;3379134|1224|28216|206351|481;3379134|203691|203692|136|137;1783272|1239|1737404|1737405|1737406,Complete,NA
bsdb:39940316/12/2,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 12,United States of America,Homo sapiens,Saliva,UBERON:0001836,Health study participation,EFO:0010130,Pre-Intervention for Juice plus food diet,Immediately post-intervention for Juice plus food diet,Effects of exclusive juice diet immediately after intervention on saliva sample.,4,4,NA,16S,45,Illumina,centered log-ratio,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Results' Text 3.2.1,4 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in saliva samples; pre-intervention vs post-intervention for juice plus food diet.,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|201174|84998|84999|84107;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171552;1783272|1239|91061|186826|1300;1783272|1239|909932|1843489|31977,Complete,NA
bsdb:39940316/13/1,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 13,United States of America,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Pre-Intervention for exclusive juice diet,Immediately post-intervention for exclusive juice diet,Effects of exclusive juice diet immediately after intervention on fecal sample.,5,5,NA,16S,45,Illumina,centered log-ratio,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Results' Text 3.2.2,4 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in fecal samples; pre-intervention vs post-intervention for exclusive juice diet.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae",3379134|1224|28216|80840|506;1783272|201174|84998|84999|84107;1783272|201174|1760|85007|1653;1783272|1239|526524|526525|128827;3379134|976|200643|171549|1853231;3379134|976|200643|171549|171551;3379134|976|200643|171549|171550;1783272|1239|1737404|1737405|1737406,Complete,NA
bsdb:39940316/14/1,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 14,United States of America,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Pre-Intervention for Juice plus food diet,Immediately post-intervention for Juice plus food diet,Effects of exclusive juice diet immediately after intervention on fecal sample.,4,4,NA,16S,45,Illumina,centered log-ratio,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Results' Text 3.2.2,4 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in fecal samples; pre-intervention vs post-intervention for juice plus food diet.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",1783272|201174|84998|84999|84107;3379134|1224|1236|91347|543;1783272|1239|526524|526525|128827;3379134|976|200643|171549|171551,Complete,NA
bsdb:39940316/15/1,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 15,United States of America,Homo sapiens,Internal cheek pouch,UBERON:0013640,Health study participation,EFO:0010130,Baseline,Pre-intervention,Effects of elimination diet on internal cheek sample.,14,14,NA,16S,45,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Results' Text 3.1.1,4 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in internal cheek samples after elimination diet; baseline vs pre-intervention.,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,NA
bsdb:39940316/15/2,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 15,United States of America,Homo sapiens,Internal cheek pouch,UBERON:0013640,Health study participation,EFO:0010130,Baseline,Pre-intervention,Effects of elimination diet on internal cheek sample.,14,14,NA,16S,45,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Results' Text 3.1.1,4 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in internal cheek samples after elimination diet; baseline vs pre-intervention.,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,NA
bsdb:39940316/16/1,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 16,United States of America,Homo sapiens,Saliva,UBERON:0001836,Health study participation,EFO:0010130,Baseline,Pre-intervention,Effects of elimination diet on saliva sample.,14,14,NA,16S,45,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Results' Text 3.1.1,4 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in saliva samples after elimination diet; baseline vs pre-intervention.,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,NA
bsdb:39940316/16/2,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 16,United States of America,Homo sapiens,Saliva,UBERON:0001836,Health study participation,EFO:0010130,Baseline,Pre-intervention,Effects of elimination diet on saliva sample.,14,14,NA,16S,45,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Results' Text 3.1.1,4 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in saliva samples after elimination diet; baseline vs pre-intervention.,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,NA
bsdb:39940316/17/1,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 17,United States of America,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Baseline,Pre-intervention,Effects of elimination diet on fecal sample.,14,14,NA,16S,45,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Results' Text 3.1.2,4 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in fecal samples after elimination diet; baseline vs pre-intervention.,increased,k__Bacillati|p__Bacillota,1783272|1239,Complete,NA
bsdb:39940316/18/1,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 18,United States of America,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Baseline,Pre-intervention,Effects of elimination diet on fecal sample.,14,14,NA,16S,45,Illumina,centered log-ratio,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Results' Text 3.1.2,4 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in fecal samples after elimination diet; baseline vs pre-intervention.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis",1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|572511|33035;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|841|2049040;1783272|1239|186801|3085636|186803|33042|2049024;3379134|976|200643|171549|815|816|820,Complete,NA
bsdb:39940316/18/2,39940316,randomized controlled trial,39940316,10.3390/nu17030458,NA,"Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote",Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition,MDPI,2025,"diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome",Experiment 18,United States of America,Homo sapiens,Feces,UBERON:0001988,Health study participation,EFO:0010130,Baseline,Pre-intervention,Effects of elimination diet on fecal sample.,14,14,NA,16S,45,Illumina,centered log-ratio,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Results' Text 3.1.2,4 March 2025,Taofeecoh,Taofeecoh,Relative abundance of bacterial in fecal samples after elimination diet; baseline vs pre-intervention.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium aurimucosum",3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|47678;1783272|201174|1760|85007|1653|1716|169292,Complete,NA
bsdb:39941005/1/1,39941005,laboratory experiment,39941005,10.3390/ijms26031236,https://pubmed.ncbi.nlm.nih.gov/39941005/,"Zhang Z., Liu B., Liu W., Liu X., Zhang C., Hu W. , Wu W.",Different Efficacy of Five Soluble Dietary Fibers on Alleviating Loperamide-Induced Constipation in Mice: Influences of Different Structural Features,International journal of molecular sciences,2025,"constipation, defecation function, gut microbiota, short-chain fatty acid, soluble dietary fiber, structural difference",Experiment 1,China,Mus musculus,Caecum,UBERON:0001153,Response to diet,EFO:0010757,Model control group (MC),Steamed sweet potato group (SDF-S),Male ICR mice administered Steamed sweet potato (SDF-S) the corresponding soluble fibers at doses of 400 mg/kg bw/d,12,12,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Figures 4A,D,E,G,H,I,J-L",15 April 2025,Thelee98,"Thelee98,Miss Lulu",Relative Abundance of genera in the gut microbiota of mice,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|3085636|3118652|2039240;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|1392389;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|186802|216572|459786;1783272|1239;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572,Complete,KateRasheed
bsdb:39941005/2/1,39941005,laboratory experiment,39941005,10.3390/ijms26031236,https://pubmed.ncbi.nlm.nih.gov/39941005/,"Zhang Z., Liu B., Liu W., Liu X., Zhang C., Hu W. , Wu W.",Different Efficacy of Five Soluble Dietary Fibers on Alleviating Loperamide-Induced Constipation in Mice: Influences of Different Structural Features,International journal of molecular sciences,2025,"constipation, defecation function, gut microbiota, short-chain fatty acid, soluble dietary fiber, structural difference",Experiment 2,China,Mus musculus,Caecum,UBERON:0001153,Response to diet,EFO:0010757,Model control group (MC),Oat Beta-glucan group (OB),Male ICR mice administered Oat Beta-glucan group (OB) the corresponding soluble fibers at doses of 400 mg/kg bw/d,12,12,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Figures 4A,B,C,K",24 April 2025,Miss Lulu,Miss Lulu,Relative Abundance of genera in the gut microbiota of mice,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum",1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171550|239759;3379134|200940|3031449|213115|194924;3379134|200930|68337|191393|2945020|248038,Complete,KateRasheed
bsdb:39941005/3/1,39941005,laboratory experiment,39941005,10.3390/ijms26031236,https://pubmed.ncbi.nlm.nih.gov/39941005/,"Zhang Z., Liu B., Liu W., Liu X., Zhang C., Hu W. , Wu W.",Different Efficacy of Five Soluble Dietary Fibers on Alleviating Loperamide-Induced Constipation in Mice: Influences of Different Structural Features,International journal of molecular sciences,2025,"constipation, defecation function, gut microbiota, short-chain fatty acid, soluble dietary fiber, structural difference",Experiment 3,China,Mus musculus,Caecum,UBERON:0001153,Response to diet,EFO:0010757,Model control group (MC),Normal control group (NC),Normal control Male ICR mice administered saline.,12,12,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Figures 4B,D,F,G,J-L",24 April 2025,Miss Lulu,Miss Lulu,Relative Abundance of genera in the gut microbiota of mice,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas",3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|186802|1392389,Complete,KateRasheed
bsdb:39941005/4/1,39941005,laboratory experiment,39941005,10.3390/ijms26031236,https://pubmed.ncbi.nlm.nih.gov/39941005/,"Zhang Z., Liu B., Liu W., Liu X., Zhang C., Hu W. , Wu W.",Different Efficacy of Five Soluble Dietary Fibers on Alleviating Loperamide-Induced Constipation in Mice: Influences of Different Structural Features,International journal of molecular sciences,2025,"constipation, defecation function, gut microbiota, short-chain fatty acid, soluble dietary fiber, structural difference",Experiment 4,China,Mus musculus,Caecum,UBERON:0001153,Response to diet,EFO:0010757,Model control group (MC),Positive treatment group (PT),"Male ICR mice administered to positive treatments, the corresponding soluble fibers at doses of 400 mg/kg bw/d",12,12,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Figures 4C,D,F,G,J",24 April 2025,Miss Lulu,Miss Lulu,Relative Abundance of genera in the gut microbiota of mice,increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|200940|3031449|213115|194924;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572,Complete,KateRasheed
bsdb:39941005/5/1,39941005,laboratory experiment,39941005,10.3390/ijms26031236,https://pubmed.ncbi.nlm.nih.gov/39941005/,"Zhang Z., Liu B., Liu W., Liu X., Zhang C., Hu W. , Wu W.",Different Efficacy of Five Soluble Dietary Fibers on Alleviating Loperamide-Induced Constipation in Mice: Influences of Different Structural Features,International journal of molecular sciences,2025,"constipation, defecation function, gut microbiota, short-chain fatty acid, soluble dietary fiber, structural difference",Experiment 5,China,Mus musculus,Caecum,UBERON:0001153,Response to diet,EFO:0010757,Model control group (MC),Polydextrose group (PD),"Male ICR mice administered to Polydextrose group (PD), the corresponding soluble fibers at doses of 400 mg/kg bw/d",12,12,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Figures 4B,C,D,E,F,G,J-L",24 April 2025,Miss Lulu,Miss Lulu,Relative Abundance of genera in the gut microbiota of mice,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|976|200643|171549|171550|239759;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|1263;1783272|1239;3379134|200940|3031449|213115|194924;1783272|1239|186801|186802|216572,Complete,KateRasheed
bsdb:39941005/6/1,39941005,laboratory experiment,39941005,10.3390/ijms26031236,https://pubmed.ncbi.nlm.nih.gov/39941005/,"Zhang Z., Liu B., Liu W., Liu X., Zhang C., Hu W. , Wu W.",Different Efficacy of Five Soluble Dietary Fibers on Alleviating Loperamide-Induced Constipation in Mice: Influences of Different Structural Features,International journal of molecular sciences,2025,"constipation, defecation function, gut microbiota, short-chain fatty acid, soluble dietary fiber, structural difference",Experiment 6,China,Mus musculus,Caecum,UBERON:0001153,Response to diet,EFO:0010757,Model control group (MC),Arabinogalactan group (AG),"Male ICR mice administered to Arabinogalactan group (AG), the corresponding soluble fibers at doses of 400 mg/kg bw/d",12,12,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Figures 4C,D,E,G,J-L",24 April 2025,Miss Lulu,Miss Lulu,Relative Abundance of genera in the gut microbiota of mice,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|186802|1392389;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|186802|216572|459786;1783272|1239;3379134|200940|3031449|213115|194924;1783272|1239|186801|186802|216572,Complete,KateRasheed
bsdb:39941005/7/1,39941005,laboratory experiment,39941005,10.3390/ijms26031236,https://pubmed.ncbi.nlm.nih.gov/39941005/,"Zhang Z., Liu B., Liu W., Liu X., Zhang C., Hu W. , Wu W.",Different Efficacy of Five Soluble Dietary Fibers on Alleviating Loperamide-Induced Constipation in Mice: Influences of Different Structural Features,International journal of molecular sciences,2025,"constipation, defecation function, gut microbiota, short-chain fatty acid, soluble dietary fiber, structural difference",Experiment 7,China,Mus musculus,Caecum,UBERON:0001153,Response to diet,EFO:0010757,Model control group (MC),Inulin group (IN),"Male ICR mice administered to Inulin group (IN), the corresponding soluble fibers at doses of 400 mg/kg bw/d.",12,12,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"4D,F,G,K,L",24 April 2025,Miss Lulu,Miss Lulu,Relative Abundance of genera in the gut microbiota of mice,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas",1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|186802|1392389,Complete,KateRasheed
bsdb:39950489/1/1,39950489,laboratory experiment,39950489,https://doi.org/10.1080/19490976.2025.2464942,https://pubmed.ncbi.nlm.nih.gov/39950489/,"Singh S., Abu Y., Antoine D., Gomez D., Tao J., Truitt B. , Roy S.",Probiotic supplementation mitigates sex-dependent nociceptive changes and gut dysbiosis induced by prenatal opioid exposure,Gut microbes,2025,"Prenatal opioid exposure, dysbiosis, gut microbiome, nociception, sex-based differences",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Response to opioid,EFO:0008541,Female offspring prenatally exposed to saline group (CSAL_F),Female offspring prenatally exposed to opioids group (MSAL_F),"Offspring born to dams that were exposed to opioids (hydromorphone pre-gestationally followed by methadone during gestation), representing the prenatal opioid exposure condition",10,10,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 2C,9 April 2025,Miss Lulu,Miss Lulu,Microbiome analysis of female offspring (CSAL_F vs. MSAL_F) (n = 10 per group in all experiments).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239|186801|186802|186806|1730|39497;1783272|1239|186801|3085636|186803|877420;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|216572|1263,Complete,Folakunmi
bsdb:39950489/1/2,39950489,laboratory experiment,39950489,https://doi.org/10.1080/19490976.2025.2464942,https://pubmed.ncbi.nlm.nih.gov/39950489/,"Singh S., Abu Y., Antoine D., Gomez D., Tao J., Truitt B. , Roy S.",Probiotic supplementation mitigates sex-dependent nociceptive changes and gut dysbiosis induced by prenatal opioid exposure,Gut microbes,2025,"Prenatal opioid exposure, dysbiosis, gut microbiome, nociception, sex-based differences",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Response to opioid,EFO:0008541,Female offspring prenatally exposed to saline group (CSAL_F),Female offspring prenatally exposed to opioids group (MSAL_F),"Offspring born to dams that were exposed to opioids (hydromorphone pre-gestationally followed by methadone during gestation), representing the prenatal opioid exposure condition",10,10,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 2C,9 April 2025,Miss Lulu,Miss Lulu,Microbiome analysis of female offspring (CSAL_F vs. MSAL_F) (n = 10 per group in all experiments).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",3379134|976|200643|171549|815|816;1783272|201174|84998|1643822|1643826|580024;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|91061|186826|33958|2767887;1783272|1239|186801|186802|31979|1485,Complete,Folakunmi
bsdb:39950489/2/1,39950489,laboratory experiment,39950489,https://doi.org/10.1080/19490976.2025.2464942,https://pubmed.ncbi.nlm.nih.gov/39950489/,"Singh S., Abu Y., Antoine D., Gomez D., Tao J., Truitt B. , Roy S.",Probiotic supplementation mitigates sex-dependent nociceptive changes and gut dysbiosis induced by prenatal opioid exposure,Gut microbes,2025,"Prenatal opioid exposure, dysbiosis, gut microbiome, nociception, sex-based differences",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Response to opioid,EFO:0008541,Male offspring prenatally exposed to saline group (CSAL_M),Male offspring prenatally exposed to opioids group (MSAL_M),"Offspring born to dams that were exposed to opioids (hydromorphone pre-gestationally followed by methadone during gestation), representing the prenatal opioid exposure condition",10,10,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 3C,9 April 2025,Miss Lulu,Miss Lulu,Microbiome analysis of male offspring (CSAL_M vs. MSAL_M) (n = 10 per group in all experiments).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Parvibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136",3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|2005473|1918540;3379134|976|200643|171549|1853231|283168;1783272|201174|84998|84999|84107|1427376;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|3085636|186803|877420,Complete,Folakunmi
bsdb:39950489/2/2,39950489,laboratory experiment,39950489,https://doi.org/10.1080/19490976.2025.2464942,https://pubmed.ncbi.nlm.nih.gov/39950489/,"Singh S., Abu Y., Antoine D., Gomez D., Tao J., Truitt B. , Roy S.",Probiotic supplementation mitigates sex-dependent nociceptive changes and gut dysbiosis induced by prenatal opioid exposure,Gut microbes,2025,"Prenatal opioid exposure, dysbiosis, gut microbiome, nociception, sex-based differences",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Response to opioid,EFO:0008541,Male offspring prenatally exposed to saline group (CSAL_M),Male offspring prenatally exposed to opioids group (MSAL_M),"Offspring born to dams that were exposed to opioids (hydromorphone pre-gestationally followed by methadone during gestation), representing the prenatal opioid exposure condition",10,10,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 3C,9 April 2025,Miss Lulu,Miss Lulu,Microbiome analysis of male offspring (CSAL_M vs. MSAL_M) (n = 10 per group in all experiments).,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|91061|1385|90964|1279,Complete,Folakunmi
bsdb:39950489/3/1,39950489,laboratory experiment,39950489,https://doi.org/10.1080/19490976.2025.2464942,https://pubmed.ncbi.nlm.nih.gov/39950489/,"Singh S., Abu Y., Antoine D., Gomez D., Tao J., Truitt B. , Roy S.",Probiotic supplementation mitigates sex-dependent nociceptive changes and gut dysbiosis induced by prenatal opioid exposure,Gut microbes,2025,"Prenatal opioid exposure, dysbiosis, gut microbiome, nociception, sex-based differences",Experiment 3,United States of America,Mus musculus,Feces,UBERON:0001988,Response to opioid,EFO:0008541,Control female offspring without prenatal exposure to probiotics(CSAL_F),Control female offspring with prenatal exposure to probiotics(CPRO_F),Female offspring from control group exposed prenatally to probiotics,10,10,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 6C,9 April 2025,Miss Lulu,"Miss Lulu,Tosin",Microbiome analysis of control female offspring with or without prenatal exposure to probiotics (CPRO_F vs CSAL_F) (n = 10 per group in all experiments).,increased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Parvibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. MD294",1783272|544448|31969|186332|186333|2086;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|186801|3085636|186803|1506553;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|2767887;1783272|201174|84998|84999|84107|1427376;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|31979|1485|97138,Complete,Folakunmi
bsdb:39950489/3/2,39950489,laboratory experiment,39950489,https://doi.org/10.1080/19490976.2025.2464942,https://pubmed.ncbi.nlm.nih.gov/39950489/,"Singh S., Abu Y., Antoine D., Gomez D., Tao J., Truitt B. , Roy S.",Probiotic supplementation mitigates sex-dependent nociceptive changes and gut dysbiosis induced by prenatal opioid exposure,Gut microbes,2025,"Prenatal opioid exposure, dysbiosis, gut microbiome, nociception, sex-based differences",Experiment 3,United States of America,Mus musculus,Feces,UBERON:0001988,Response to opioid,EFO:0008541,Control female offspring without prenatal exposure to probiotics(CSAL_F),Control female offspring with prenatal exposure to probiotics(CPRO_F),Female offspring from control group exposed prenatally to probiotics,10,10,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 6C,9 April 2025,Miss Lulu,Miss Lulu,Microbiome analysis of control female offspring with or without prenatal exposure to probiotics (CPRO_F vs CSAL_F) (n = 10 per group in all experiments).,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|526524|526525|128827|1729679;3379134|976|200643|171549|1853231|283168;1783272|1239|526524|526525|2810281|191303,Complete,Folakunmi
bsdb:39950489/4/1,39950489,laboratory experiment,39950489,https://doi.org/10.1080/19490976.2025.2464942,https://pubmed.ncbi.nlm.nih.gov/39950489/,"Singh S., Abu Y., Antoine D., Gomez D., Tao J., Truitt B. , Roy S.",Probiotic supplementation mitigates sex-dependent nociceptive changes and gut dysbiosis induced by prenatal opioid exposure,Gut microbes,2025,"Prenatal opioid exposure, dysbiosis, gut microbiome, nociception, sex-based differences",Experiment 4,United States of America,Mus musculus,Feces,UBERON:0001988,Response to opioid,EFO:0008541,POE female offspring without prenatal exposure to probiotics(MSAL_F),POE female offspring with prenatal exposure to probiotics(MPRO_F),Prenatal Opioid exposure female offspring with prenatal exposure to probiotics,10,10,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 7C,9 April 2025,Miss Lulu,Miss Lulu,Microbiome analysis of POE female offspring with or without prenatal exposure to probiotics (MPRO_F vs. MSAL_F) (n = 10 per group in all experiments).,increased,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,3379134|200940|3031449|213115|194924|872,Complete,Folakunmi
bsdb:39950489/4/2,39950489,laboratory experiment,39950489,https://doi.org/10.1080/19490976.2025.2464942,https://pubmed.ncbi.nlm.nih.gov/39950489/,"Singh S., Abu Y., Antoine D., Gomez D., Tao J., Truitt B. , Roy S.",Probiotic supplementation mitigates sex-dependent nociceptive changes and gut dysbiosis induced by prenatal opioid exposure,Gut microbes,2025,"Prenatal opioid exposure, dysbiosis, gut microbiome, nociception, sex-based differences",Experiment 4,United States of America,Mus musculus,Feces,UBERON:0001988,Response to opioid,EFO:0008541,POE female offspring without prenatal exposure to probiotics(MSAL_F),POE female offspring with prenatal exposure to probiotics(MPRO_F),Prenatal Opioid exposure female offspring with prenatal exposure to probiotics,10,10,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 7C,9 April 2025,Miss Lulu,"Miss Lulu,Svetlana up",Microbiome analysis of POE female offspring with or without prenatal exposure to probiotics (MPRO_F vs. MSAL_F) (n = 10 per group in all experiments).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] brachy",1783272|1239|186801|3085656|3085657|2039302;1783272|1239|186801|3082720|543314|35517,Complete,Folakunmi
bsdb:39950489/5/1,39950489,laboratory experiment,39950489,https://doi.org/10.1080/19490976.2025.2464942,https://pubmed.ncbi.nlm.nih.gov/39950489/,"Singh S., Abu Y., Antoine D., Gomez D., Tao J., Truitt B. , Roy S.",Probiotic supplementation mitigates sex-dependent nociceptive changes and gut dysbiosis induced by prenatal opioid exposure,Gut microbes,2025,"Prenatal opioid exposure, dysbiosis, gut microbiome, nociception, sex-based differences",Experiment 5,United States of America,Mus musculus,Feces,UBERON:0001988,Response to opioid,EFO:0008541,Control Male offspring without prenatal exposure to probiotics(CSAL_M),Control Male offspring with prenatal exposure to probiotics(CPRO_M),Male offspring from control group exposed prenatally to probiotics,10,10,NA,16S,4,Illumina,relative abundances,LEfSe,0.005,FALSE,2,age,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 8C,9 April 2025,Miss Lulu,"Miss Lulu,Folakunmi,Svetlana up,Tosin",Microbiome analysis of control male offspring with or without prenatal exposure to probiotics (CPRO_M vs. CSAL_M) (n = 10 per group in all experiments).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. MD294",1783272|1239|186801|186802|216572|244127;1783272|1239|186801|186802|1980681;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803|877420;1783272|1239|91061|186826|33958|2767887;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|31979|1485|97138,Complete,Folakunmi
bsdb:39950489/5/2,39950489,laboratory experiment,39950489,https://doi.org/10.1080/19490976.2025.2464942,https://pubmed.ncbi.nlm.nih.gov/39950489/,"Singh S., Abu Y., Antoine D., Gomez D., Tao J., Truitt B. , Roy S.",Probiotic supplementation mitigates sex-dependent nociceptive changes and gut dysbiosis induced by prenatal opioid exposure,Gut microbes,2025,"Prenatal opioid exposure, dysbiosis, gut microbiome, nociception, sex-based differences",Experiment 5,United States of America,Mus musculus,Feces,UBERON:0001988,Response to opioid,EFO:0008541,Control Male offspring without prenatal exposure to probiotics(CSAL_M),Control Male offspring with prenatal exposure to probiotics(CPRO_M),Male offspring from control group exposed prenatally to probiotics,10,10,NA,16S,4,Illumina,relative abundances,LEfSe,0.005,FALSE,2,age,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 8C,9 April 2025,Miss Lulu,Miss Lulu,Microbiome analysis of control male offspring with or without prenatal exposure to probiotics (CPRO_M vs. CSAL_M) (n = 10 per group in all experiments).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239|186801|3085656|3085657|2039302;1783272|1239|186801|186802|186806|1730|39496;1783272|201174|1760|85004|31953|1678;1783272|1239|526524|526525|128827|1729679;1783272|1239|91061|186826|33958|1578,Complete,Folakunmi
bsdb:39950489/6/1,39950489,laboratory experiment,39950489,https://doi.org/10.1080/19490976.2025.2464942,https://pubmed.ncbi.nlm.nih.gov/39950489/,"Singh S., Abu Y., Antoine D., Gomez D., Tao J., Truitt B. , Roy S.",Probiotic supplementation mitigates sex-dependent nociceptive changes and gut dysbiosis induced by prenatal opioid exposure,Gut microbes,2025,"Prenatal opioid exposure, dysbiosis, gut microbiome, nociception, sex-based differences",Experiment 6,United States of America,Mus musculus,Feces,UBERON:0001988,Response to opioid,EFO:0008541,POE Male offspring without prenatal exposure to probiotics(MSAL_M),POE Male offspring with prenatal exposure to probiotics(MPRO_M),Prenatal Opioid exposure Male offspring with prenatal exposure to probiotics,10,10,NA,16S,4,Illumina,relative abundances,LEfSe,0.005,FALSE,2,age,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 9C,9 April 2025,Miss Lulu,"Miss Lulu,Tosin",Microbiome analysis of POE male offspring with or without prenatal exposure to probiotics (MPRO_M vs. MSAL_M) (n = 10 per group in all experiments).,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. MD294",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|1392389;1783272|1239|91061|186826|33958|2767887;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|31979|1485|97138,Complete,Folakunmi
bsdb:39950489/6/2,39950489,laboratory experiment,39950489,https://doi.org/10.1080/19490976.2025.2464942,https://pubmed.ncbi.nlm.nih.gov/39950489/,"Singh S., Abu Y., Antoine D., Gomez D., Tao J., Truitt B. , Roy S.",Probiotic supplementation mitigates sex-dependent nociceptive changes and gut dysbiosis induced by prenatal opioid exposure,Gut microbes,2025,"Prenatal opioid exposure, dysbiosis, gut microbiome, nociception, sex-based differences",Experiment 6,United States of America,Mus musculus,Feces,UBERON:0001988,Response to opioid,EFO:0008541,POE Male offspring without prenatal exposure to probiotics(MSAL_M),POE Male offspring with prenatal exposure to probiotics(MPRO_M),Prenatal Opioid exposure Male offspring with prenatal exposure to probiotics,10,10,NA,16S,4,Illumina,relative abundances,LEfSe,0.005,FALSE,2,age,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 9C,9 April 2025,Miss Lulu,Miss Lulu,Microbiome analysis of POE male offspring with or without prenatal exposure to probiotics (MPRO_M vs. MSAL_M) (n = 10 per group in all experiments).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",3379134|976|200643|171549|171552|1283313;1783272|1239|526524|526525|2810281|191303,Complete,Folakunmi
bsdb:39953051/1/1,39953051,"cross-sectional observational, not case-control",39953051,10.1038/s41522-025-00653-6,NA,"Lan L.Y., Liu T.C., Gao S.M., Li Q., Yang L., Fei H.L., Zhong X.K., Wang Y.X., Zhu C.Y., Abel C., Kappeler P.M., Huang L.N. , Fan P.F.",Comparative study of gut microbiota reveals the adaptive strategies of gibbons living in suboptimal habitats,NPJ biofilms and microbiomes,2025,NA,Experiment 1,China,Nomascus hainanus,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Low + Middle feeding group - Nomascus hainanus,High feeding group - Nomascus hainanus,These refers to gibbon species living in high-quality (Nomascus hainanus) habitats with stable fruit production; who consumed high proportion of leaf per month.,NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Fig. 5, Supplementary Table 6",3 March 2025,KateRasheed,KateRasheed,"Linear Discriminant Analysis Effect Size (LEfSe) analyses revealed significant contributions to the differences in abundance across various bacteria taxonomic levels, from phylum to genus, among different gibbon species with varying proportions of leaf consumption.",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales,k__Pseudomonadati|p__Fibrobacterota|c__Fibrobacteria|o__Fibrobacterales|f__Fibrobacteraceae|g__Fibrobacter,k__Pseudomonadati|p__Fibrobacterota|c__Fibrobacteria|o__Fibrobacterales|f__Fibrobacteraceae|g__Fibrobacter|s__Fibrobacter intestinalis,k__Pseudomonadati|p__Fibrobacterota|c__Fibrobacteria|o__Fibrobacterales|f__Fibrobacteraceae,k__Pseudomonadati|p__Fibrobacterota|c__Fibrobacteria|o__Fibrobacterales,k__Pseudomonadati|p__Fibrobacterota|c__Fibrobacteria,k__Pseudomonadati|p__Fibrobacterota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK3A20,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia,k__Pseudomonadati|p__Spirochaetota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema ruminis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,s__uncultured bacterium",1783272|1239|909932|1843488|909930;1783272|1239|909932|1843488;3379134|65842|204430|218872|204431|832;3379134|65842|204430|218872|204431|832|28122;3379134|65842|204430|218872|204431;3379134|65842|204430|218872;3379134|65842|204430;3379134|65842;1783272|1239|186801|3085636|186803|877406;3379134|976|200643|171549|2005473;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|186802|216572|1263;3379134|203691|203692|136|137;3379134|203691|203692|136;3379134|203691|203692;3379134|203691;3379134|1224|28216|80840|995019|40544;3379134|203691|203692|136|2845253|157;3379134|203691|203692|136|2845253|157|744515;3379134|976|200643|171549;3379134|976|200643;1783272|1239|909932|1843488|909930|33024;77133,Complete,KateRasheed
bsdb:39953051/2/1,39953051,"cross-sectional observational, not case-control",39953051,10.1038/s41522-025-00653-6,NA,"Lan L.Y., Liu T.C., Gao S.M., Li Q., Yang L., Fei H.L., Zhong X.K., Wang Y.X., Zhu C.Y., Abel C., Kappeler P.M., Huang L.N. , Fan P.F.",Comparative study of gut microbiota reveals the adaptive strategies of gibbons living in suboptimal habitats,NPJ biofilms and microbiomes,2025,NA,Experiment 2,China,Nomascus concolor,Feces,UBERON:0001988,Diet measurement,EFO:0008111,High + Middle feeding group - Nomascus concolor,Low feeding group - Nomascus concolor,"These refers to gibbon species living in suboptimal habitats with lower and more variable fruit availability, relying more on leaves. They consumed low proportion of leaf per month.",NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Fig. 5, Supplementary Table 6",3 March 2025,KateRasheed,KateRasheed,"Linear Discriminant Analysis Effect Size (LEfSe) analyses revealed significant contributions to the differences in abundance across various bacteria taxonomic levels, from phylum to genus, among different gibbon species with varying proportions of leaf consumption.",increased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Marseilla|s__Marseilla massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,s__uncultured bacterium",1783272|544448|31969|186329|2146;1783272|544448|31969|186329;1783272|544448|31969|186332|186333|2086;1783272|1239|91061;1783272|1239;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976|200643|171549|171552|1926655|1841864;3379134|976|200643|171549|815|816;77133,Complete,KateRasheed
bsdb:39953051/3/1,39953051,"cross-sectional observational, not case-control",39953051,10.1038/s41522-025-00653-6,NA,"Lan L.Y., Liu T.C., Gao S.M., Li Q., Yang L., Fei H.L., Zhong X.K., Wang Y.X., Zhu C.Y., Abel C., Kappeler P.M., Huang L.N. , Fan P.F.",Comparative study of gut microbiota reveals the adaptive strategies of gibbons living in suboptimal habitats,NPJ biofilms and microbiomes,2025,NA,Experiment 3,China,Hoolock tianxing,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Low + Middle feeding group - Hoolock tianxing,High feeding group - Hoolock tianxing,"These refers to gibbon species living in suboptimal habitats with lower and more variable fruit availability, relying more on leaves. They had the lowest monthly fruit intake. This group consumed high proportion of leaf per month.",NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Fig. 5, Supplementary Table 6",3 March 2025,KateRasheed,KateRasheed,"Linear Discriminant Analysis Effect Size (LEfSe) analyses revealed significant contributions to the differences in abundance across various bacteria taxonomic levels, from phylum to genus, among different gibbon species with varying proportions of leaf consumption.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|s__Bacillota bacterium,k__Pseudomonadati|p__Bacteroidota|s__Bacteroidota bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Candidatus Izemoplasmatales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Catenisphaera,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter|s__Colidextribacter massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK3A20,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Liu et al. 2021),k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,s__bacterium YE64,s__rumen bacterium NK4A214,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Catenisphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Clostridia|o__Acetivibrionales|f__Acetivibrionaceae|g__Acetivibrio|s__uncultured Acetivibrio sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__uncultured Faecalibacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__uncultured Roseburia sp.,s__uncultured bacterium,s__uncultured prokaryote,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136",1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239;1783272|1239|1879010;3379134|976|1898104;1783272|1239|186801|186802|3085642;1783272|1239|186801|3085636|186803|830;1783272|544448|31969|2975519;1783272|1239|526524|526525|128827|1774107;1783272|1239|186801;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|1980681;1783272|1239|186801|186802|1980681|1870986;1783272|1239|186801|3085636|186803|3342669|45851;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|877406;1783272|1239|186801|3085636;3379134|976|200643|171549|2005473;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;3379134|1224|28211|204441;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|3062497;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|216572|39492;254754;877428;1783272|544448|31969|186329|2146;3379134|976|200643|171549;1783272|1239|526524|526525|128827|1774107;1783272|1239|186801|186802|31979|1485;1783272|1239|526524|526525|128827;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|909932|909929;1783272|1239|186801|3120394|3120654|35829|293326;1783272|1239|186801|186802|31979|1485|59620;1783272|1239|186801|186802|216572|216851|259315;1783272|1239|186801|3085636|186803|297314;1783272|1239|186801|186802|216572|707003;1783272|1239|186801|3085636|186803|841|512314;77133;198431;1783272|1239|186801|3085636|186803|877420,Complete,KateRasheed
bsdb:39953051/4/1,39953051,"cross-sectional observational, not case-control",39953051,10.1038/s41522-025-00653-6,NA,"Lan L.Y., Liu T.C., Gao S.M., Li Q., Yang L., Fei H.L., Zhong X.K., Wang Y.X., Zhu C.Y., Abel C., Kappeler P.M., Huang L.N. , Fan P.F.",Comparative study of gut microbiota reveals the adaptive strategies of gibbons living in suboptimal habitats,NPJ biofilms and microbiomes,2025,NA,Experiment 4,China,Hoolock tianxing,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Low + High feeding group - Hoolock tianxing,Middle feeding group - Hoolock tianxing,"These refers to gibbon species living in suboptimal habitats with lower and more variable fruit availability, relying more on leaves. They had the lowest monthly fruit intake. This group consumed middle (not high or low) proportion of leaf per month.",NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Fig. 5, Supplementary Table 6",3 March 2025,KateRasheed,KateRasheed,"Linear Discriminant Analysis Effect Size (LEfSe) analyses revealed significant contributions to the differences in abundance across various bacteria taxonomic levels, from phylum to genus, among different gibbon species with varying proportions of leaf consumption.",increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|s__Prevotellaceae bacterium,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Raoultibacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Raoultibacter|s__Raoultibacter sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|s__Sutterellaceae bacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|s__uncultured Anaeroplasmataceae bacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,s__uncultured bacterium,s__uncultured rumen bacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|s__uncultured Eggerthellaceae bacterium",1783272|201174|84992;1783272|201174;3379134|1224|1236|135624;1783272|544448|31969|186332|186333|2152;3379134|976|200643|171549;3379134|976|200643;3379134|976;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294;3379134|29547|3031852|213849;3379134|29547;1783272|1239|526524|526525|2810280;1783272|201174|84998|84999;1783272|201174|84998;1783272|201174|84998|1643822|1643826;3379134|29547|3031852;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;3379134|1224|1236;1783272|1239|186801|3085636|186803|1898203;1783272|1239|909932;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|2049047;3379134|1224;1783272|201174|84998|1643822|1643826|1926677;1783272|201174|84998|1643822|1643826|1926677|1926678;3379134|976|200643|171549|171550;1783272|1239|909932|909929|1843491;1783272|1239|526524|526525|128827|123375;3379134|1224|1236|135624|83763|83770;3379134|1224|1236|135624|83763;3379134|1224|28216|80840|995019|2026794;1783272|1239|909932|1843489|31977;3379134|976|200643|171549|171552|1283313;1783272|201174|84998|84999|1643824;1783272|201174|1760|85004|31953|1678;3379134|29547|3031852|213849|72294|194;1783272|201174|84998|84999;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|909932|909929|1843491;3379134|1224|1236|135624|83763|83770;1783272|1239|909932|1843489|31977;1783272|544448|31969|186332|186333|658266;1783272|1239|526524|526525|128827|331630;77133;136703;1783272|201174|84998|1643822|1643826|2321402,Complete,KateRasheed
bsdb:39953051/5/1,39953051,"cross-sectional observational, not case-control",39953051,10.1038/s41522-025-00653-6,NA,"Lan L.Y., Liu T.C., Gao S.M., Li Q., Yang L., Fei H.L., Zhong X.K., Wang Y.X., Zhu C.Y., Abel C., Kappeler P.M., Huang L.N. , Fan P.F.",Comparative study of gut microbiota reveals the adaptive strategies of gibbons living in suboptimal habitats,NPJ biofilms and microbiomes,2025,NA,Experiment 5,China,Hoolock tianxing,Feces,UBERON:0001988,Diet measurement,EFO:0008111,High + Middle feeding group - Hoolock tianxing,Low feeding group - Hoolock tianxing,"These refers to gibbon species living in suboptimal habitats with lower and more variable fruit availability, relying more on leaves. They had the lowest monthly fruit intake. This group consumed low proportion of leaf per month.",NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Fig. 5, Supplementary Table 6",3 March 2025,KateRasheed,KateRasheed,"Linear Discriminant Analysis Effect Size (LEfSe) analyses revealed significant contributions to the differences in abundance across various bacteria taxonomic levels, from phylum to genus, among different gibbon species with varying proportions of leaf consumption.",increased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Acholeplasma,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales|s__Candidatus Gastranaerophilales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK3A20,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Bacillati|p__Candidatus Melainabacteria|c__Vampirovibriophyceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,s__uncultured bacterium,s__uncultured rumen bacterium",1783272|544448|31969|186329|2146|2147;1783272|544448|31969|186329|2146;1783272|544448|31969|186329;3379134|976|200643|171549|171552|1283313;1783272|544448|31969|186332|186333|2086;1783272|201174|84998|84999|1643824;1783272|201174|84998|84999|1643824|1380;1783272|1239|91061;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1798710|1906119;1783272|1798710|1906119|2137880;1783272|1239|186801|186802|31979;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|33042|33043;1783272|1117;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803|877406;1783272|1239|186801|186802|31979|1266;1783272|1798710|3118680;3379134|976|200643|171549|815|816;1783272|1239|186801;1783272|1239|186801|186802|31979|1266;3379134|1224|28216|80840|995019|40544;77133;136703,Complete,KateRasheed
bsdb:39953051/6/1,39953051,"cross-sectional observational, not case-control",39953051,10.1038/s41522-025-00653-6,NA,"Lan L.Y., Liu T.C., Gao S.M., Li Q., Yang L., Fei H.L., Zhong X.K., Wang Y.X., Zhu C.Y., Abel C., Kappeler P.M., Huang L.N. , Fan P.F.",Comparative study of gut microbiota reveals the adaptive strategies of gibbons living in suboptimal habitats,NPJ biofilms and microbiomes,2025,NA,Experiment 6,China,Nomascus hainanus,Feces,UBERON:0001988,Diet measurement,EFO:0008111,High + Middle feeding group - Nomascus hainanus,Low feeding group - Nomascus hainanus,These refers to gibbon species living in high-quality (Nomascus hainanus) habitats with stable fruit production; who consumed low proportion of leaf per month.,NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Fig. 5, Supplementary Table 6",4 March 2025,KateRasheed,KateRasheed,"Linear Discriminant Analysis Effect Size (LEfSe) analyses revealed significant contributions to the differences in abundance across various bacteria taxonomic levels, from phylum to genus, among different gibbon species with varying proportions of leaf consumption.",increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__uncultured Lachnospira sp.,s__uncultured bacterium,s__uncultured organism",1783272|201174;3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|186801|186802|216572|292632;3379134|976|200643|171549|815|816;1783272|201174|84998|84999|84107|102106;3379134|976|200643|171549|171552;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|3085636|186803|28050|446043;77133;155900,Complete,KateRasheed
bsdb:39953051/7/1,39953051,"cross-sectional observational, not case-control",39953051,10.1038/s41522-025-00653-6,NA,"Lan L.Y., Liu T.C., Gao S.M., Li Q., Yang L., Fei H.L., Zhong X.K., Wang Y.X., Zhu C.Y., Abel C., Kappeler P.M., Huang L.N. , Fan P.F.",Comparative study of gut microbiota reveals the adaptive strategies of gibbons living in suboptimal habitats,NPJ biofilms and microbiomes,2025,NA,Experiment 7,China,Nomascus concolor,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Low + Middle feeding group - Nomascus concolor,High feeding group - Nomascus concolor,"These refers to gibbon species living in suboptimal habitats with lower and more variable fruit availability, relying more on leaves. They consumed high proportion of leaf per month.",NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Fig. 5, Supplementary Table 6",5 March 2025,KateRasheed,KateRasheed,"Linear Discriminant Analysis Effect Size (LEfSe) analyses revealed significant contributions to the differences in abundance across various bacteria taxonomic levels, from phylum to genus, among different gibbon species with varying proportions of leaf consumption.",increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales|s__Candidatus Gastranaerophilales bacterium,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Candidatus Melainabacteria|c__Vampirovibriophyceae,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|s__uncultured Eggerthellaceae bacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__uncultured Lachnospira sp.,s__uncultured bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK3A20",1783272|201174;1783272|544448|31969|186332|186333|2152;;1783272|1239|186801|186802|3085642;1783272|1798710|1906119;1783272|1798710|1906119|2137880;1783272|1239|186801;1783272|1239|526524|526525|2810280;1783272|201174|84998|84999;1783272|201174|84998;1783272|1117;1783272|1117|3028117;1783272|201174|84998|1643822|1643826;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;1783272|1239|526524|526525|128827|123375;1783272|1239|186801|186802|216572|292632;1783272|1798710|3118680;1783272|1117;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|292632;1783272|201174|84998|1643822|1643826|2321402;1783272|1239|526524|526525|128827|331630;1783272|1239|186801|3085636|186803|28050|446043;77133;1783272|1239|186801|3085636|186803|877406,Complete,KateRasheed
bsdb:39953051/8/1,39953051,"cross-sectional observational, not case-control",39953051,10.1038/s41522-025-00653-6,NA,"Lan L.Y., Liu T.C., Gao S.M., Li Q., Yang L., Fei H.L., Zhong X.K., Wang Y.X., Zhu C.Y., Abel C., Kappeler P.M., Huang L.N. , Fan P.F.",Comparative study of gut microbiota reveals the adaptive strategies of gibbons living in suboptimal habitats,NPJ biofilms and microbiomes,2025,NA,Experiment 8,China,Nomascus concolor,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Low + High feeding group - Nomascus concolor,Middle feeding group - Nomascus concolor,"These refers to gibbon species living in suboptimal habitats with lower and more variable fruit availability, relying more on leaves. They consumed middle (not high or low) proportion of leaf per month.",NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Fig. 5, Supplementary Table 6",5 March 2025,KateRasheed,KateRasheed,"Linear Discriminant Analysis Effect Size (LEfSe) analyses revealed significant contributions to the differences in abundance across various bacteria taxonomic levels, from phylum to genus, among different gibbon species with varying proportions of leaf consumption.",increased,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|s__uncultured Anaeroplasmataceae bacterium,1783272|544448|31969|186332|186333|658266,Complete,KateRasheed
bsdb:39953051/9/1,39953051,"cross-sectional observational, not case-control",39953051,10.1038/s41522-025-00653-6,NA,"Lan L.Y., Liu T.C., Gao S.M., Li Q., Yang L., Fei H.L., Zhong X.K., Wang Y.X., Zhu C.Y., Abel C., Kappeler P.M., Huang L.N. , Fan P.F.",Comparative study of gut microbiota reveals the adaptive strategies of gibbons living in suboptimal habitats,NPJ biofilms and microbiomes,2025,NA,Experiment 9,China,Nomascus hainanus,Feces,UBERON:0001988,Diet measurement,EFO:0008111,High + Low feeding group - Nomascus hainanus,Middle feeding group - Nomascus hainanus,These refers to gibbon species living in high-quality (Nomascus hainanus) habitats with stable fruit production; who consumed middle (not high or low) proportion of leaf per month.,NA,NA,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Fig. 5, Supplementary Table 6",5 March 2025,KateRasheed,KateRasheed,"Linear Discriminant Analysis Effect Size (LEfSe) analyses revealed significant contributions to the differences in abundance across various bacteria taxonomic levels, from phylum to genus, among different gibbon species with varying proportions of leaf consumption.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,s__uncultured bacterium,s__uncultured rumen bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK3A20",1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|186802|3085642;1783272|1239|186801|3085636|186803|1506577;77133;136703;1783272|1239|186801|3085636|186803|877406,Complete,KateRasheed
bsdb:39963956/1/1,39963956,randomized controlled trial,39963956,10.1080/19490976.2025.2463570,NA,"Ast H.K., Hammer M., Zhang S., Bruton A., Hatsu I.E., Leung B., McClure R., Srikanth P., Farris Y., Norby-Adams L., Robinette L.M., Arnold L.E., Swann J.R., Zhu J., Karstens L. , Johnstone J.M.",Gut microbiome changes with micronutrient supplementation in children with attention-deficit/hyperactivity disorder: the MADDY study,Gut microbes,2025,"ADHD, children, microbiome, micronutrients",Experiment 1,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Attention deficit-hyperactivity disorder,MONDO:0007743,Placebo,Micronutrient,Children with ADHD who received micronutrient supplementation after the 8 week randomized controlled trial(RCT) period,11,33,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,increased,increased,NA,NA,increased,NA,Signature 1,Figure 3B,23 March 2025,Mautin,"Mautin,Ese",Changes in relative abundance in gut microbial composition following micronutrient supplementation compared to placebo,increased,k__Pseudomonadati|p__Verrucomicrobiota,3379134|74201,Complete,Svetlana up
bsdb:39963956/1/2,39963956,randomized controlled trial,39963956,10.1080/19490976.2025.2463570,NA,"Ast H.K., Hammer M., Zhang S., Bruton A., Hatsu I.E., Leung B., McClure R., Srikanth P., Farris Y., Norby-Adams L., Robinette L.M., Arnold L.E., Swann J.R., Zhu J., Karstens L. , Johnstone J.M.",Gut microbiome changes with micronutrient supplementation in children with attention-deficit/hyperactivity disorder: the MADDY study,Gut microbes,2025,"ADHD, children, microbiome, micronutrients",Experiment 1,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Attention deficit-hyperactivity disorder,MONDO:0007743,Placebo,Micronutrient,Children with ADHD who received micronutrient supplementation after the 8 week randomized controlled trial(RCT) period,11,33,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,increased,increased,NA,NA,increased,NA,Signature 2,Figure 3B,23 March 2025,Mautin,"Mautin,Ese",Changes in relative abundance in gut microbial composition following micronutrient supplementation compared to placebo,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|201174;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|216572|216851,Complete,Svetlana up
bsdb:39963956/2/1,39963956,randomized controlled trial,39963956,10.1080/19490976.2025.2463570,NA,"Ast H.K., Hammer M., Zhang S., Bruton A., Hatsu I.E., Leung B., McClure R., Srikanth P., Farris Y., Norby-Adams L., Robinette L.M., Arnold L.E., Swann J.R., Zhu J., Karstens L. , Johnstone J.M.",Gut microbiome changes with micronutrient supplementation in children with attention-deficit/hyperactivity disorder: the MADDY study,Gut microbes,2025,"ADHD, children, microbiome, micronutrients",Experiment 2,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Attention deficit-hyperactivity disorder,MONDO:0007743,Placebo before intervention,Placebo after intervention,These are children with ADHD who received the placebo during the first study phase (baseline to week 8) and micronutrients during the second phase (week 8 to week 16),11,11,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,25 March 2025,Mautin,"Mautin,Ese",Significant within-group changes in bacterial abundance with placebo from baseline to week 8,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816,Complete,Svetlana up
bsdb:39963956/3/1,39963956,randomized controlled trial,39963956,10.1080/19490976.2025.2463570,NA,"Ast H.K., Hammer M., Zhang S., Bruton A., Hatsu I.E., Leung B., McClure R., Srikanth P., Farris Y., Norby-Adams L., Robinette L.M., Arnold L.E., Swann J.R., Zhu J., Karstens L. , Johnstone J.M.",Gut microbiome changes with micronutrient supplementation in children with attention-deficit/hyperactivity disorder: the MADDY study,Gut microbes,2025,"ADHD, children, microbiome, micronutrients",Experiment 3,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Attention deficit-hyperactivity disorder,MONDO:0007743,Micronutrient before intervention,Micronutrient after Intervention,"Children with ADHD who received a placebo first, followed by micronutrients (week 8 to week 16).",33,11,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,increased,unchanged,NA,NA,increased,NA,Signature 1,Table 2,31 March 2025,Mautin,Mautin,Significant within-group changes in bacterial abundance with micronutrients  from baseline to week 8.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976;3379134|976|200643|171549|171550,Complete,Svetlana up
bsdb:39963956/3/2,39963956,randomized controlled trial,39963956,10.1080/19490976.2025.2463570,NA,"Ast H.K., Hammer M., Zhang S., Bruton A., Hatsu I.E., Leung B., McClure R., Srikanth P., Farris Y., Norby-Adams L., Robinette L.M., Arnold L.E., Swann J.R., Zhu J., Karstens L. , Johnstone J.M.",Gut microbiome changes with micronutrient supplementation in children with attention-deficit/hyperactivity disorder: the MADDY study,Gut microbes,2025,"ADHD, children, microbiome, micronutrients",Experiment 3,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Attention deficit-hyperactivity disorder,MONDO:0007743,Micronutrient before intervention,Micronutrient after Intervention,"Children with ADHD who received a placebo first, followed by micronutrients (week 8 to week 16).",33,11,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,increased,unchanged,NA,NA,increased,NA,Signature 2,Table 2,31 March 2025,Mautin,Mautin,Significant within-group changes in bacterial abundance with micronutrients from baseline to week 8.,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota",1783272|201174;1783272|1239|186801|3085636|186803|1766253;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|292632;1783272|1239,Complete,Svetlana up
bsdb:39963956/4/1,39963956,randomized controlled trial,39963956,10.1080/19490976.2025.2463570,NA,"Ast H.K., Hammer M., Zhang S., Bruton A., Hatsu I.E., Leung B., McClure R., Srikanth P., Farris Y., Norby-Adams L., Robinette L.M., Arnold L.E., Swann J.R., Zhu J., Karstens L. , Johnstone J.M.",Gut microbiome changes with micronutrient supplementation in children with attention-deficit/hyperactivity disorder: the MADDY study,Gut microbes,2025,"ADHD, children, microbiome, micronutrients",Experiment 4,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Attention deficit-hyperactivity disorder,MONDO:0007743,Non-responders,Responders,Children with ADHD who showed improvement after micronutrients.,20,24,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,NA,Signature 1,Figure 6,5 April 2025,Mautin,Mautin,Change in Relative Abundance During Micronutrient Intervention,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:39963956/5/1,39963956,randomized controlled trial,39963956,10.1080/19490976.2025.2463570,NA,"Ast H.K., Hammer M., Zhang S., Bruton A., Hatsu I.E., Leung B., McClure R., Srikanth P., Farris Y., Norby-Adams L., Robinette L.M., Arnold L.E., Swann J.R., Zhu J., Karstens L. , Johnstone J.M.",Gut microbiome changes with micronutrient supplementation in children with attention-deficit/hyperactivity disorder: the MADDY study,Gut microbes,2025,"ADHD, children, microbiome, micronutrients",Experiment 5,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Attention deficit-hyperactivity disorder,MONDO:0007743,Responders before treatment,Responders after treatment,Children with ADHD who exhibited a clinical response to micronutrients.,24,24,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,increased,increased,NA,NA,increased,NA,Signature 1,Table 4,6 April 2025,Mautin,Mautin,Significant bacterial abundance within-group change following micronutrient treatment by response group.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:39963956/5/2,39963956,randomized controlled trial,39963956,10.1080/19490976.2025.2463570,NA,"Ast H.K., Hammer M., Zhang S., Bruton A., Hatsu I.E., Leung B., McClure R., Srikanth P., Farris Y., Norby-Adams L., Robinette L.M., Arnold L.E., Swann J.R., Zhu J., Karstens L. , Johnstone J.M.",Gut microbiome changes with micronutrient supplementation in children with attention-deficit/hyperactivity disorder: the MADDY study,Gut microbes,2025,"ADHD, children, microbiome, micronutrients",Experiment 5,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Attention deficit-hyperactivity disorder,MONDO:0007743,Responders before treatment,Responders after treatment,Children with ADHD who exhibited a clinical response to micronutrients.,24,24,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,increased,increased,NA,NA,increased,NA,Signature 2,Table 4,6 April 2025,Mautin,Mautin,Significant bacterial abundance within-group change following micronutrient treatment by response group.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota",1783272|1239|186801|3085636|186803|1766253;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|201174,Complete,Svetlana up
bsdb:39963956/6/2,39963956,randomized controlled trial,39963956,10.1080/19490976.2025.2463570,NA,"Ast H.K., Hammer M., Zhang S., Bruton A., Hatsu I.E., Leung B., McClure R., Srikanth P., Farris Y., Norby-Adams L., Robinette L.M., Arnold L.E., Swann J.R., Zhu J., Karstens L. , Johnstone J.M.",Gut microbiome changes with micronutrient supplementation in children with attention-deficit/hyperactivity disorder: the MADDY study,Gut microbes,2025,"ADHD, children, microbiome, micronutrients",Experiment 6,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Attention deficit-hyperactivity disorder,MONDO:0007743,Non-Responders before treatment,Non-Responders after treatment,Children with ADHD who did not exhibited a clinical response to micronutrients.,20,20,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,increased,NA,Signature 2,Table 4,6 April 2025,Mautin,Mautin,Significant bacterial abundance within-group change following micronutrient treatment by response group.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota",1783272|1239|186801|3085636|186803|1766253;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803;1783272|201174,Complete,Svetlana up
bsdb:39963956/7/1,39963956,randomized controlled trial,39963956,10.1080/19490976.2025.2463570,NA,"Ast H.K., Hammer M., Zhang S., Bruton A., Hatsu I.E., Leung B., McClure R., Srikanth P., Farris Y., Norby-Adams L., Robinette L.M., Arnold L.E., Swann J.R., Zhu J., Karstens L. , Johnstone J.M.",Gut microbiome changes with micronutrient supplementation in children with attention-deficit/hyperactivity disorder: the MADDY study,Gut microbes,2025,"ADHD, children, microbiome, micronutrients",Experiment 7,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Attention deficit-hyperactivity disorder,MONDO:0007743,Placebo first before micronutrient,Placebo first after micronutrient,Children with ADHD who received the placebo before receiving micronutrients (Week 8 to week 16),11,11,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S6,9 April 2025,Mautin,Mautin,Significant Bacterial Taxa Abundance Within Group Change Following Micronutrients Only.,increased,k__Pseudomonadati|p__Pseudomonadota,3379134|1224,Complete,Svetlana up
bsdb:39963956/7/2,39963956,randomized controlled trial,39963956,10.1080/19490976.2025.2463570,NA,"Ast H.K., Hammer M., Zhang S., Bruton A., Hatsu I.E., Leung B., McClure R., Srikanth P., Farris Y., Norby-Adams L., Robinette L.M., Arnold L.E., Swann J.R., Zhu J., Karstens L. , Johnstone J.M.",Gut microbiome changes with micronutrient supplementation in children with attention-deficit/hyperactivity disorder: the MADDY study,Gut microbes,2025,"ADHD, children, microbiome, micronutrients",Experiment 7,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Attention deficit-hyperactivity disorder,MONDO:0007743,Placebo first before micronutrient,Placebo first after micronutrient,Children with ADHD who received the placebo before receiving micronutrients (Week 8 to week 16),11,11,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S6,9 April 2025,Mautin,Mautin,Significant Bacterial Taxa Abundance Within Group Change Following Micronutrients Only.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,1783272|1239|186801|3085636|186803|1766253,Complete,Svetlana up
bsdb:39963956/8/1,39963956,randomized controlled trial,39963956,10.1080/19490976.2025.2463570,NA,"Ast H.K., Hammer M., Zhang S., Bruton A., Hatsu I.E., Leung B., McClure R., Srikanth P., Farris Y., Norby-Adams L., Robinette L.M., Arnold L.E., Swann J.R., Zhu J., Karstens L. , Johnstone J.M.",Gut microbiome changes with micronutrient supplementation in children with attention-deficit/hyperactivity disorder: the MADDY study,Gut microbes,2025,"ADHD, children, microbiome, micronutrients",Experiment 8,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Attention deficit-hyperactivity disorder,MONDO:0007743,Micronutrients Only before micronutrients,Micronutrients Only after micronutrients,Children with ADHD who received only micronutrients from baseline to week 8 .,33,33,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S6,9 April 2025,Mautin,Mautin,Significant Bacterial Taxa Abundance Within Group Change Following Micronutrients Only.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota",3379134|976|200643|171549|815|816;3379134|976|200643|171549|815;3379134|976|200643|171549|171550;3379134|976,Complete,Svetlana up
bsdb:39963956/8/2,39963956,randomized controlled trial,39963956,10.1080/19490976.2025.2463570,NA,"Ast H.K., Hammer M., Zhang S., Bruton A., Hatsu I.E., Leung B., McClure R., Srikanth P., Farris Y., Norby-Adams L., Robinette L.M., Arnold L.E., Swann J.R., Zhu J., Karstens L. , Johnstone J.M.",Gut microbiome changes with micronutrient supplementation in children with attention-deficit/hyperactivity disorder: the MADDY study,Gut microbes,2025,"ADHD, children, microbiome, micronutrients",Experiment 8,"Canada,United States of America",Homo sapiens,Feces,UBERON:0001988,Attention deficit-hyperactivity disorder,MONDO:0007743,Micronutrients Only before micronutrients,Micronutrients Only after micronutrients,Children with ADHD who received only micronutrients from baseline to week 8 .,33,33,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S6,9 April 2025,Mautin,Mautin,Significant Bacterial Taxa Abundance Within Group Change Following Micronutrients Only.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Actinomycetota",1783272|1239|186801|3085636|186803|1766253;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572|292632;1783272|201174,Complete,Svetlana up
bsdb:39966419/1/1,39966419,"cross-sectional observational, not case-control",39966419,10.1038/s41522-025-00665-2,NA,"Heidrich V., Fackelmann G., Malesevic M., Armanini F., Dey H., Mengoni C., Stanisavljevic N., Vukotic G. , Segata N.",Newly identified species from the dog dental plaque microbiome highlight little overlap with humans,NPJ biofilms and microbiomes,2025,NA,Experiment 1,Serbia,Canis lupus familiaris,Oral cavity,UBERON:0000167,Species design,EFO:0001753,Supragingival dental plaque from humans,Supragingival dental plaque from dogs,"Clinically healthy dogs with no signs of oral disease (e.g., gingivitis, periodontitis) after oral health assessment was performed at the Faculty of Veterinary Medicine, University of Belgrade",154,64,1 month,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text, Paragraph 8",14 July 2025,Ese,Ese,Differentially abundant species found in Supragingival dental plaque of dogs and humans,increased,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter rectus,3379134|29547|3031852|213849|72294|194|203,Complete,KateRasheed
bsdb:39966419/1/2,39966419,"cross-sectional observational, not case-control",39966419,10.1038/s41522-025-00665-2,NA,"Heidrich V., Fackelmann G., Malesevic M., Armanini F., Dey H., Mengoni C., Stanisavljevic N., Vukotic G. , Segata N.",Newly identified species from the dog dental plaque microbiome highlight little overlap with humans,NPJ biofilms and microbiomes,2025,NA,Experiment 1,Serbia,Canis lupus familiaris,Oral cavity,UBERON:0000167,Species design,EFO:0001753,Supragingival dental plaque from humans,Supragingival dental plaque from dogs,"Clinically healthy dogs with no signs of oral disease (e.g., gingivitis, periodontitis) after oral health assessment was performed at the Faculty of Veterinary Medicine, University of Belgrade",154,64,1 month,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Text, Paragraph 8",14 July 2025,Ese,Ese,Differentially abundant species found in Supragingival dental plaque of dogs and humans,decreased,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,3384189|32066|203490|203491|203492|848|860,Complete,KateRasheed
bsdb:39968350/1/1,39968350,"cross-sectional observational, not case-control",39968350,https://doi.org/10.1093/ismeco/ycaf008,NA,"Burke T, Davies CS, Dugdale HL, Hildebrand F, Komdeur J, Lee CZ, Silan E, Worsley SF","Metagenomic analyses of gut microbiome composition and function with age in a wild bird; little change, except increased transposase gene abundance",ISME Communications,2025,NA,Experiment 1,Seychelles,Acrocephalus sechellensis,Feces,UBERON:0001988,Aging,GO:0007568,Younger Seychelles warblers,Older Seychelles warblers,"Older Seychelles warblers are individual birds aged ≥ 6 years, representing the senescent life stage when survival and reproductive performance begin to decline",NA,NA,NA,WMS,NA,Illumina,raw counts,Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,decreased,Signature 1,Figure S6B,1 November 2025,Nina Takang,"WikiWorks,Nina Takang,Busiwa Liuma","This represents the set of gut bacterial species found to be significantly differentially abundant between birds sampled in their terminal year of life (terminal-year birds) and birds not in their terminal year (non-terminal birds), assessed using a Generalized Linear Latent Variable Model (GLLVM).",increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,3379134|1224|1236|91347|543|561|562,Complete,Svetlana up
bsdb:39968350/1/2,39968350,"cross-sectional observational, not case-control",39968350,https://doi.org/10.1093/ismeco/ycaf008,NA,"Burke T, Davies CS, Dugdale HL, Hildebrand F, Komdeur J, Lee CZ, Silan E, Worsley SF","Metagenomic analyses of gut microbiome composition and function with age in a wild bird; little change, except increased transposase gene abundance",ISME Communications,2025,NA,Experiment 1,Seychelles,Acrocephalus sechellensis,Feces,UBERON:0001988,Aging,GO:0007568,Younger Seychelles warblers,Older Seychelles warblers,"Older Seychelles warblers are individual birds aged ≥ 6 years, representing the senescent life stage when survival and reproductive performance begin to decline",NA,NA,NA,WMS,NA,Illumina,raw counts,Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,decreased,Signature 2,Fig S6B,25 November 2025,Busiwa Liuma,Busiwa Liuma,"This represents the set of gut bacterial species found to be significantly differentially abundant between birds sampled in their terminal year of life (terminal-year birds) and birds not in their terminal year (non-terminal birds), assessed using a Generalized Linear Latent Variable Model (GLLVM).",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella|s__Brucella pseudogrignonensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus garvieae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium|s__Microbacterium enclense",3379134|1224|28211|356|118882|234|419475;1783272|1239|91061|186826|1300|1357|1363;1783272|1239|91061|186826|1300|1357|1358;1783272|201174|1760|85006|85023|33882|993073,Complete,Svetlana up
bsdb:39968350/2/1,39968350,"cross-sectional observational, not case-control",39968350,https://doi.org/10.1093/ismeco/ycaf008,NA,"Burke T, Davies CS, Dugdale HL, Hildebrand F, Komdeur J, Lee CZ, Silan E, Worsley SF","Metagenomic analyses of gut microbiome composition and function with age in a wild bird; little change, except increased transposase gene abundance",ISME Communications,2025,NA,Experiment 2,Seychelles,Acrocephalus sechellensis,Feces,UBERON:0001988,Aging,GO:0007568,Seychelles warblers in their non-terminal year,Seychelles warblers in their terminal year,Birds whose fecal samples were collected during the final year of their life (the year in which they died).,NA,NA,NA,WMS,NA,Illumina,raw counts,Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,decreased,Signature 1,Fig S6D,25 November 2025,Busiwa Liuma,Busiwa Liuma,This represents the set of gut bacterial species found to be significantly differentially abundant between birds sampled in their terminal year of life (terminal-year birds) and birds not in their terminal year (non-terminal birds) assessed using a Generalized Linear Latent Variable Model (GLLVM).,increased,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella|s__Brucella pseudogrignonensis,3379134|1224|28211|356|118882|234|419475,Complete,Svetlana up
bsdb:39968350/2/2,39968350,"cross-sectional observational, not case-control",39968350,https://doi.org/10.1093/ismeco/ycaf008,NA,"Burke T, Davies CS, Dugdale HL, Hildebrand F, Komdeur J, Lee CZ, Silan E, Worsley SF","Metagenomic analyses of gut microbiome composition and function with age in a wild bird; little change, except increased transposase gene abundance",ISME Communications,2025,NA,Experiment 2,Seychelles,Acrocephalus sechellensis,Feces,UBERON:0001988,Aging,GO:0007568,Seychelles warblers in their non-terminal year,Seychelles warblers in their terminal year,Birds whose fecal samples were collected during the final year of their life (the year in which they died).,NA,NA,NA,WMS,NA,Illumina,raw counts,Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,decreased,Signature 2,Fig S6D,25 November 2025,Busiwa Liuma,Busiwa Liuma,"This represents the set of gut bacterial species found to be significantly differentially abundant between birds sampled in their terminal year of life (terminal-year birds) and birds not in their terminal year (non-terminal birds), assessed using a Generalized Linear Latent Variable Model (GLLVM).",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus garvieae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium|s__Microbacterium enclense,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Pantoea anthophila,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia santali",3379134|1224|1236|91347|543|561|562;1783272|1239|91061|186826|1300|1357|1363;1783272|201174|1760|85006|85023|33882|993073;3379134|1224|1236|91347|1903409|53335|470931;1783272|201174|1760|85006|1268|32207|2949643,Complete,Svetlana up
bsdb:39972378/1/1,39972378,case-control,39972378,10.1186/s12967-025-06190-2,NA,"Gu W., Huang Z., Fan Y., Li T., Yu X., Chen Z., Hu Y., Li A., Zhang F. , Fu Y.",Peripheral blood microbiome signature and Mycobacterium tuberculosis-derived rsRNA as diagnostic biomarkers for tuberculosis in human,Journal of translational medicine,2025,"Biomarker, Blood, Diagnosis, Microbiome, Tuberculosis, rsRNA",Experiment 1,China,Homo sapiens,Blood,UBERON:0000178,Pulmonary tuberculosis,EFO:1000049,Healthy controls,Active pulmonary tuberculosis,Culture-confirmed pulmonary tuberculosis (PTB),62,73,1 month,PCR,NA,RT-qPCR,relative abundances,LEfSe,0.05,NA,2,"age,sex",NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 1A and B,2 July 2025,Nuerteye,Nuerteye,"(A) Significantly differential taxa in terms of relative abundance (LDA score of ≥ 2) between TB and healthy control groups. (B) Significantly different taxa in the cladogram according to a LDA score of ≥ 2 (each circle represents phylogenetic levels from phylum to genus [inside to outside], and each diameter is proportional to the taxon’s abundance).",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Nostocaceae|g__Anabaena,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Nostocaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Pandoraea,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Priestia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae",1783272|201174|1760;1783272|201174;3379134|1224|28211;1783272|1117|3028117|1161|1162|1163;1783272|1239|91061|1385|186817;1783272|1239|91061|1385;1783272|1239|91061;1783272|1239;3379134|976;3379134|1224|28211|356|41294|374;1783272|201174|1760|85007|1653;1783272|201174|1760|85009|31957|1912216;1783272|1117;1783272|1117|3028117;3379134|976|117743|200644|49546;3379134|976|117743|200644|49546|237;3379134|1224|28211|356;1783272|201174|1760|85011;1783272|201174|1760|85006|1268;1783272|201174|1760|85006;1783272|201174|1760|85008|28056;1783272|201174|1760|85008;1783272|201174|1760|85007|1762;1783272|201174|1760|85007;1783272|201174|1760|85007|1762|1763;3379134|1224|28211|356|41294;1783272|201174|1760|85009|85015;1783272|201174|1760|85009|85015|1839;1783272|1117|3028117|1161|1162;1783272|1239|91061|1385|186822|44249;3379134|1224|28216|80840|119060|93217;3379134|1224|28211|204455|31989;1783272|1239|91061|1385|186817|2800373;1783272|201174|1760|85009;3379134|1224|28211|356|82115;3379134|1224|28211|356|82115|379;3379134|1224|28211|204455;1783272|201174|1760|85011|2062|1883;1783272|201174|1760|85011|2062,Complete,NA
bsdb:39972378/1/2,39972378,case-control,39972378,10.1186/s12967-025-06190-2,NA,"Gu W., Huang Z., Fan Y., Li T., Yu X., Chen Z., Hu Y., Li A., Zhang F. , Fu Y.",Peripheral blood microbiome signature and Mycobacterium tuberculosis-derived rsRNA as diagnostic biomarkers for tuberculosis in human,Journal of translational medicine,2025,"Biomarker, Blood, Diagnosis, Microbiome, Tuberculosis, rsRNA",Experiment 1,China,Homo sapiens,Blood,UBERON:0000178,Pulmonary tuberculosis,EFO:1000049,Healthy controls,Active pulmonary tuberculosis,Culture-confirmed pulmonary tuberculosis (PTB),62,73,1 month,PCR,NA,RT-qPCR,relative abundances,LEfSe,0.05,NA,2,"age,sex",NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Figure 1A and B,2 July 2025,Nuerteye,Nuerteye,"(A) Significantly differential taxa in terms of relative abundance (LDA score of ≥ 2) between TB and healthy control groups. (B) Significantly different taxa in the cladogram according to a LDA score of ≥ 2 (each circle represents phylogenetic levels from phylum to genus [inside to outside], and each diameter is proportional to the taxon’s abundance).",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae",3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|561;3379134|1224|1236;3379134|1224|1236|91347|543|570;3379134|1224|1236|135619;3379134|1224|1236|72274|135621;3379134|1224|1236|72274;3379134|1224;3379134|1224|1236|72274|135621|286;3379134|1224|1236|91347|543|590;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|135623|641|662;3379134|1224|1236|91347|1903411,Complete,NA
bsdb:39976263/1/1,39976263,"case-control,laboratory experiment",39976263,10.1080/19490976.2025.2467193,NA,"Huang W., Zhu W., Lin Y., Chan F.K.L., Xu Z. , Ng S.C.",<i>Roseburia hominis</i> improves host metabolism in diet-induced obesity,Gut microbes,2025,"Intestinal microbiology, Obesity, probiotics",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,High fat diet,EFO:0002757,High Fat Diet-Phosphate-buffered saline (HFD-PBS),High Fat Diet- Roseburia hominis (HFD-RH),"Mice were fed high-fat diet (40% fat), and orally challenged with 10⁹ colony forming units of 
Roseburia hominis",5,5,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4c and Figure 4d,4 April 2025,Z.uk.a,"Z.uk.a,Ese",LDA effect size at the genus and species level between HFD-RH and HFD-PBS group by LEfSe,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio fibrisolvens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter|s__Dysosmobacter welbionis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Herbinix,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Herbinix|s__Herbinix luporum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. YL32,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Mammaliicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Mammaliicoccus|s__Mammaliicoccus lentus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. PEA192,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas|s__Turicimonas muris,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter hominis",1783272|1239|186801|3085636|186803|830;1783272|1239|186801|3085636|186803|830|831;1783272|1239|186801|186802|216572|2591381;1783272|1239|186801|186802|216572|2591381|2093857;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|1663717;1783272|1239|186801|3085636|186803|1663717|1679721;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|1506553|1834196;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|33959;1783272|1239|91061|1385|90964|2803850;1783272|1239|91061|1385|90964|2803850|42858;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|459786|2109687;1783272|1239|186801|186802|216572|459786|351091;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|328812;3379134|1224|1236|72274|135621|286;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|186802|216572|1905344;1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|526524|526525|2810280|3025755;3379134|1224|28216|80840|995019|1918598;3379134|1224|28216|80840|995019|1918598|1796652;1783272|1239|186801|186802|31979|1485|1522;1783272|1239|186801|186802|216572|459786|2763056,Complete,KateRasheed
bsdb:39976263/1/2,39976263,"case-control,laboratory experiment",39976263,10.1080/19490976.2025.2467193,NA,"Huang W., Zhu W., Lin Y., Chan F.K.L., Xu Z. , Ng S.C.",<i>Roseburia hominis</i> improves host metabolism in diet-induced obesity,Gut microbes,2025,"Intestinal microbiology, Obesity, probiotics",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,High fat diet,EFO:0002757,High Fat Diet-Phosphate-buffered saline (HFD-PBS),High Fat Diet- Roseburia hominis (HFD-RH),"Mice were fed high-fat diet (40% fat), and orally challenged with 10⁹ colony forming units of 
Roseburia hominis",5,5,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4c and Figure 4d,4 April 2025,Z.uk.a,"Z.uk.a,Ese",LDA effect size at the genus and species level between HFD-RH and HFD-PBS group by LEfSe,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Berryella|s__Berryella intestinalis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella guodeyinii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum|s__Faecalibaculum rodentium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella sp. GAM18,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella sp. oral taxon 807,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella uli,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parafannyhessea|s__Parafannyhessea umbonata,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella|s__Parolsenella catena,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella|s__Parolsenella massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus xylosus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Thermophilibacter|s__Thermophilibacter immobilis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Berryella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia ilealis",1783272|201174|84998|1643822|1643826|2815775|1531429;1783272|201174|84998|1643822|1643826|84111;1783272|201174|84998|1643822|1643826|84111|2690837;1783272|1239|526524|526525|128827|1729679;1783272|1239|526524|526525|128827|1729679|1702221;1783272|201174|84998|84999|1643824|133925;1783272|201174|84998|84999|1643824|133925|2109685;1783272|201174|84998|84999|1643824|133925|712411;1783272|201174|84998|84999|1643824|133925|133926;1783272|201174|84998|84999|1643824|2847312|604330;1783272|201174|84998|84999|1643824|2082587;1783272|201174|84998|84999|1643824|2082587|2003188;1783272|201174|84998|84999|1643824|2082587|1871022;1783272|1239|186801|3082720|186804|1501226;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|1385|90964|1279|1288;1783272|201174|84998|84999|1643824|2847307|2779519;1783272|201174|84998|1643822|1643826|2815775;1783272|201174|84998|84999|1643824|133925|1805478;1783272|1239|186801|3082720|186804|1501226|1115758,Complete,KateRasheed
bsdb:39976263/2/1,39976263,"case-control,laboratory experiment",39976263,10.1080/19490976.2025.2467193,NA,"Huang W., Zhu W., Lin Y., Chan F.K.L., Xu Z. , Ng S.C.",<i>Roseburia hominis</i> improves host metabolism in diet-induced obesity,Gut microbes,2025,"Intestinal microbiology, Obesity, probiotics",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Body weight gain,EFO:0004566,Low Body Weight gain,High Body Weight gain,The Mice were characterized based on body weight gain.,5,5,NA,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4E,10 April 2025,Z.uk.a,Z.uk.a,Body weight gain correlation differential species in mice between HFD-PBS and HFD-RH groups,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia ilealis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus xylosus",1783272|1239|186801|3082720|186804|1501226|1115758;1783272|1239|91061|1385|90964|1279|1288,Complete,KateRasheed
bsdb:39976263/2/2,39976263,"case-control,laboratory experiment",39976263,10.1080/19490976.2025.2467193,NA,"Huang W., Zhu W., Lin Y., Chan F.K.L., Xu Z. , Ng S.C.",<i>Roseburia hominis</i> improves host metabolism in diet-induced obesity,Gut microbes,2025,"Intestinal microbiology, Obesity, probiotics",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Body weight gain,EFO:0004566,Low Body Weight gain,High Body Weight gain,The Mice were characterized based on body weight gain.,5,5,NA,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4E,10 April 2025,Z.uk.a,Z.uk.a,Body weight gain correlation of differential species in mice between HFD-PBS and HFD-RH groups,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Herbinix|s__Herbinix luporum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas|s__Turicimonas muris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio fibrisolvens",1783272|1239|186801|3085636|186803|1663717|1679721;3379134|1224|28216|80840|995019|1918598|1796652;1783272|1239|186801|3085636|186803|830|831,Complete,KateRasheed
bsdb:39976263/3/1,39976263,"case-control,laboratory experiment",39976263,10.1080/19490976.2025.2467193,NA,"Huang W., Zhu W., Lin Y., Chan F.K.L., Xu Z. , Ng S.C.",<i>Roseburia hominis</i> improves host metabolism in diet-induced obesity,Gut microbes,2025,"Intestinal microbiology, Obesity, probiotics",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Body mass index,EFO:0004340,Low Body Mass Index,High Body Mass Index,The Mice were differentiated based on changes in Body Mass Index.,5,5,NA,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4E,11 April 2025,Z.uk.a,Z.uk.a,Body Mass Index correlation of differential species in mice between HFD-PBS and HFD-RH groups,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia ilealis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus xylosus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum|s__Faecalibaculum rodentium",1783272|1239|186801|3082720|186804|1501226|1115758;1783272|1239|91061|1385|90964|1279|1288;1783272|1239|526524|526525|128827|1729679|1702221,Complete,KateRasheed
bsdb:39976263/3/2,39976263,"case-control,laboratory experiment",39976263,10.1080/19490976.2025.2467193,NA,"Huang W., Zhu W., Lin Y., Chan F.K.L., Xu Z. , Ng S.C.",<i>Roseburia hominis</i> improves host metabolism in diet-induced obesity,Gut microbes,2025,"Intestinal microbiology, Obesity, probiotics",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Body mass index,EFO:0004340,Low Body Mass Index,High Body Mass Index,The Mice were differentiated based on changes in Body Mass Index.,5,5,NA,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4E,11 April 2025,Z.uk.a,"Z.uk.a,Ese",Body Mass Index correlation of differential species in mice between HFD-PBS and HFD-RH groups,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio fibrisolvens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter|s__Dysosmobacter welbionis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Herbinix|s__Herbinix luporum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. YL32,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. PEA192,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas|s__Turicimonas muris",1783272|1239|186801|3085636|186803|830|831;1783272|1239|186801|186802|216572|2591381|2093857;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|1663717|1679721;1783272|1239|186801|3085636|186803|1506553|1834196;1783272|1239|186801|186802|216572|459786|2763056;1783272|1239|186801|186802|216572|459786|2109687;1783272|1239|186801|186802|216572|459786|351091;3379134|976|200643|171549|2005525|375288|328812;3379134|1224|28216|80840|995019|1918598|1796652,Complete,KateRasheed
bsdb:39976263/4/1,39976263,"case-control,laboratory experiment",39976263,10.1080/19490976.2025.2467193,NA,"Huang W., Zhu W., Lin Y., Chan F.K.L., Xu Z. , Ng S.C.",<i>Roseburia hominis</i> improves host metabolism in diet-induced obesity,Gut microbes,2025,"Intestinal microbiology, Obesity, probiotics",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Body fat percentage,EFO:0007800,Low Body Fat Percentage [Lee Index},High Body Fat Percentage [Lee Index],Group 1 consists of mice who were characterized by their Body fat percentage (Lee Index),5,5,NA,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4E,11 April 2025,Z.uk.a,Z.uk.a,Body Fat Percentage correlation differential species in mice between HFD-PBS and HFD-RH groups,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia ilealis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus xylosus",1783272|1239|186801|3082720|186804|1501226|1115758;1783272|1239|91061|1385|90964|1279|1288,Complete,KateRasheed
bsdb:39976263/4/2,39976263,"case-control,laboratory experiment",39976263,10.1080/19490976.2025.2467193,NA,"Huang W., Zhu W., Lin Y., Chan F.K.L., Xu Z. , Ng S.C.",<i>Roseburia hominis</i> improves host metabolism in diet-induced obesity,Gut microbes,2025,"Intestinal microbiology, Obesity, probiotics",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Body fat percentage,EFO:0007800,Low Body Fat Percentage [Lee Index},High Body Fat Percentage [Lee Index],Group 1 consists of mice who were characterized by their Body fat percentage (Lee Index),5,5,NA,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4E,11 April 2025,Z.uk.a,Z.uk.a,Body Fat Percentage correlation differential species in mice between HFD-PBS and HFD-RH groups,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter|s__Dysosmobacter welbionis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. YL32,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas|s__Turicimonas muris",1783272|1239|186801|186802|216572|2591381|2093857;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|1506553|1834196;1783272|1239|91061|186826|33958|1578|33959;1783272|1239|186801|186802|216572|459786|351091;3379134|976|200643|171549|2005525|375288|328812;3379134|1224|28216|80840|995019|1918598|1796652,Complete,KateRasheed
bsdb:39976263/5/1,39976263,"case-control,laboratory experiment",39976263,10.1080/19490976.2025.2467193,NA,"Huang W., Zhu W., Lin Y., Chan F.K.L., Xu Z. , Ng S.C.",<i>Roseburia hominis</i> improves host metabolism in diet-induced obesity,Gut microbes,2025,"Intestinal microbiology, Obesity, probiotics",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Insulin resistance,EFO:0002614,Low insulin resistance,High insulin resistance,The mice in Group 1 were selected as those with high insulin resistance,5,5,NA,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4E,13 April 2025,Z.uk.a,Z.uk.a,Insulin Receptors correlation differential species in mice between HFD-PBS and HFD-RH groups,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia ilealis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus xylosus",1783272|1239|186801|3082720|186804|1501226|1115758;1783272|1239|91061|1385|90964|1279|1288,Complete,KateRasheed
bsdb:39976263/5/2,39976263,"case-control,laboratory experiment",39976263,10.1080/19490976.2025.2467193,NA,"Huang W., Zhu W., Lin Y., Chan F.K.L., Xu Z. , Ng S.C.",<i>Roseburia hominis</i> improves host metabolism in diet-induced obesity,Gut microbes,2025,"Intestinal microbiology, Obesity, probiotics",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Insulin resistance,EFO:0002614,Low insulin resistance,High insulin resistance,The mice in Group 1 were selected as those with high insulin resistance,5,5,NA,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4E,13 April 2025,Z.uk.a,Z.uk.a,Insulin receptors correlation differential species in mice between HFD-PBS and HFD-RH groups,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. YL32,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas|s__Turicimonas muris",1783272|1239|186801|3085636|186803|1506553|1834196;1783272|1239|91061|186826|33958|1578|33959;3379134|976|200643|171549|2005525|375288|328812;3379134|1224|28216|80840|995019|1918598|1796652,Complete,KateRasheed
bsdb:39976263/6/1,39976263,"case-control,laboratory experiment",39976263,10.1080/19490976.2025.2467193,NA,"Huang W., Zhu W., Lin Y., Chan F.K.L., Xu Z. , Ng S.C.",<i>Roseburia hominis</i> improves host metabolism in diet-induced obesity,Gut microbes,2025,"Intestinal microbiology, Obesity, probiotics",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Total cholesterol measurement,EFO:0004574,Low total cholesterol,High total cholesterol,Group 1 consists of mice with High Cholesterol levels.,5,5,NA,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4E,13 April 2025,Z.uk.a,"Z.uk.a,Ese",Total Cholesterol correlation of differential species in mice between HFD-PBS and HFD-RH groups,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Berryella|s__Berryella intestinalis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum|s__Faecalibaculum rodentium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia ilealis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus xylosus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella guodeyinii",1783272|201174|84998|1643822|1643826|2815775|1531429;1783272|1239|526524|526525|128827|1729679|1702221;1783272|1239|186801|3082720|186804|1501226|1115758;1783272|1239|91061|1385|90964|1279|1288;1783272|201174|84998|1643822|1643826|84111|2690837,Complete,KateRasheed
bsdb:39976263/6/2,39976263,"case-control,laboratory experiment",39976263,10.1080/19490976.2025.2467193,NA,"Huang W., Zhu W., Lin Y., Chan F.K.L., Xu Z. , Ng S.C.",<i>Roseburia hominis</i> improves host metabolism in diet-induced obesity,Gut microbes,2025,"Intestinal microbiology, Obesity, probiotics",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Total cholesterol measurement,EFO:0004574,Low total cholesterol,High total cholesterol,Group 1 consists of mice with High Cholesterol levels.,5,5,NA,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4E,13 April 2025,Z.uk.a,"Z.uk.a,Ese,Victoria",Total Cholesterol correlation differential species in mice between HFD-PBS and HFD-RH groups,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio fibrisolvens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter|s__Dysosmobacter welbionis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Herbinix|s__Herbinix luporum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. YL32,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. PEA192,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas|s__Turicimonas muris",1783272|1239|186801|3085636|186803|830|831;1783272|1239|186801|186802|216572|2591381|2093857;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3085636|186803|1663717|1679721;1783272|1239|186801|3085636|186803|1506553|1834196;1783272|1239|186801|186802|216572|459786|2763056;1783272|1239|186801|186802|216572|459786|2109687;1783272|1239|186801|186802|216572|459786|351091;3379134|976|200643|171549|2005525|375288|328812;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|186802|216572|1905344|1550024;3379134|1224|28216|80840|995019|1918598|1796652,Complete,KateRasheed
bsdb:39976263/7/1,39976263,"case-control,laboratory experiment",39976263,10.1080/19490976.2025.2467193,NA,"Huang W., Zhu W., Lin Y., Chan F.K.L., Xu Z. , Ng S.C.",<i>Roseburia hominis</i> improves host metabolism in diet-induced obesity,Gut microbes,2025,"Intestinal microbiology, Obesity, probiotics",Experiment 7,China,Mus musculus,Feces,UBERON:0001988,Triglyceride change measurement,EFO:0007681,Low triglycerides,High triglycerides,Group 1 Mice were distinguished by High Triglyceride levels,5,5,NA,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4E,13 April 2025,Z.uk.a,Z.uk.a,Triglyceride correlation differential species in mice between HFD-PBS and HFD-RH groups,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum|s__Faecalibaculum rodentium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus xylosus",1783272|1239|526524|526525|128827|1729679|1702221;1783272|1239|91061|1385|90964|1279|1288,Complete,KateRasheed
bsdb:39976263/7/2,39976263,"case-control,laboratory experiment",39976263,10.1080/19490976.2025.2467193,NA,"Huang W., Zhu W., Lin Y., Chan F.K.L., Xu Z. , Ng S.C.",<i>Roseburia hominis</i> improves host metabolism in diet-induced obesity,Gut microbes,2025,"Intestinal microbiology, Obesity, probiotics",Experiment 7,China,Mus musculus,Feces,UBERON:0001988,Triglyceride change measurement,EFO:0007681,Low triglycerides,High triglycerides,Group 1 Mice were distinguished by High Triglyceride levels,5,5,NA,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4E,14 April 2025,Z.uk.a,Z.uk.a,Triglyceride correlation of differential species in mice between HFD-PBS and HFD-RH groups,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter|s__Dysosmobacter welbionis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Herbinix|s__Herbinix luporum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. YL32,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas|s__Turicimonas muris,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio fibrisolvens",1783272|1239|186801|186802|216572|2591381|2093857;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|1663717|1679721;1783272|1239|186801|3085636|186803|1506553|1834196;1783272|1239|91061|186826|33958|1578|33959;1783272|1239|186801|186802|216572|459786|351091;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|3085636|186803|841|166486;3379134|1224|28216|80840|995019|1918598|1796652;1783272|1239|186801|186802|31979|1485|1522;1783272|1239|186801|3085636|186803|830|831,Complete,KateRasheed
bsdb:39976263/8/1,39976263,"case-control,laboratory experiment",39976263,10.1080/19490976.2025.2467193,NA,"Huang W., Zhu W., Lin Y., Chan F.K.L., Xu Z. , Ng S.C.",<i>Roseburia hominis</i> improves host metabolism in diet-induced obesity,Gut microbes,2025,"Intestinal microbiology, Obesity, probiotics",Experiment 8,China,Mus musculus,Feces,UBERON:0001988,Aspartate aminotransferase measurement,EFO:0004736,Low in aspartate aminotransferase,High in aspartate aminotransferase,Mice were characterized by having high levels of aspartate aminotransferase enzymes,5,5,NA,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4E,14 April 2025,Z.uk.a,Z.uk.a,Aspartate aminotransferase levels show differential correlation between species in mice from the HFD-PBS and HFD-RH groups,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum|s__Faecalibaculum rodentium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia ilealis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus xylosus",1783272|1239|526524|526525|128827|1729679|1702221;1783272|1239|186801|3082720|186804|1501226|1115758;1783272|1239|91061|1385|90964|1279|1288,Complete,KateRasheed
bsdb:39976263/8/2,39976263,"case-control,laboratory experiment",39976263,10.1080/19490976.2025.2467193,NA,"Huang W., Zhu W., Lin Y., Chan F.K.L., Xu Z. , Ng S.C.",<i>Roseburia hominis</i> improves host metabolism in diet-induced obesity,Gut microbes,2025,"Intestinal microbiology, Obesity, probiotics",Experiment 8,China,Mus musculus,Feces,UBERON:0001988,Aspartate aminotransferase measurement,EFO:0004736,Low in aspartate aminotransferase,High in aspartate aminotransferase,Mice were characterized by having high levels of aspartate aminotransferase enzymes,5,5,NA,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4E,14 April 2025,Z.uk.a,Z.uk.a,Aspartate aminotransferase levels show differential correlation between species in mice from the HFD-PBS and HFD-RH groups,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. YL32,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii",1783272|1239|186801|3085636|186803|1506553|1834196;1783272|1239|91061|186826|33958|1578|33959;3379134|976|200643|171549|2005525|375288|328812,Complete,KateRasheed
bsdb:39976263/9/1,39976263,"case-control,laboratory experiment",39976263,10.1080/19490976.2025.2467193,NA,"Huang W., Zhu W., Lin Y., Chan F.K.L., Xu Z. , Ng S.C.",<i>Roseburia hominis</i> improves host metabolism in diet-induced obesity,Gut microbes,2025,"Intestinal microbiology, Obesity, probiotics",Experiment 9,China,Mus musculus,Feces,UBERON:0001988,Alanine measurement,EFO:0009765,Low in alanine transaminase,High in alanine transaminase,Mice in this group are characterized by high levels of alanine transaminase enzymes,5,5,NA,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4E,14 April 2025,Z.uk.a,Z.uk.a,Alanine transaminase correlation of differential species in mice between the HFD-PBS and HFD-RH groups,increased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum|s__Faecalibaculum rodentium,1783272|1239|526524|526525|128827|1729679|1702221,Complete,KateRasheed
bsdb:39976263/9/2,39976263,"case-control,laboratory experiment",39976263,10.1080/19490976.2025.2467193,NA,"Huang W., Zhu W., Lin Y., Chan F.K.L., Xu Z. , Ng S.C.",<i>Roseburia hominis</i> improves host metabolism in diet-induced obesity,Gut microbes,2025,"Intestinal microbiology, Obesity, probiotics",Experiment 9,China,Mus musculus,Feces,UBERON:0001988,Alanine measurement,EFO:0009765,Low in alanine transaminase,High in alanine transaminase,Mice in this group are characterized by high levels of alanine transaminase enzymes,5,5,NA,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4E,14 April 2025,Z.uk.a,Z.uk.a,Alanine transaminase correlation of differential species in mice between the HFD-PBS and HFD-RH groups,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Herbinix|s__Herbinix luporum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. YL32,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio fibrisolvens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii",1783272|1239|186801|3085636|186803|1663717|1679721;1783272|1239|186801|3085636|186803|1506553|1834196;1783272|1239|186801|3085636|186803|830|831;1783272|1239|186801|186802|31979|1485|1522;1783272|1239|91061|186826|33958|1578|33959,Complete,KateRasheed
bsdb:39976263/10/1,39976263,"case-control,laboratory experiment",39976263,10.1080/19490976.2025.2467193,NA,"Huang W., Zhu W., Lin Y., Chan F.K.L., Xu Z. , Ng S.C.",<i>Roseburia hominis</i> improves host metabolism in diet-induced obesity,Gut microbes,2025,"Intestinal microbiology, Obesity, probiotics",Experiment 10,China,Homo sapiens,Feces,UBERON:0001988,Obesity,EFO:0001073,Lean control,Obese patients,Subjects with BMI greater than or equal to 28 Kg/m2,47,53,NA,WMS,NA,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),T-Test",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1A,B & D",11 July 2025,Ese,"Ese,Victoria",The prevalence and relative abundance of bacteria in obese and lean subjects detected by metagenomics sequencing .,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,1783272|1239|186801|3085636|186803|841|301301,Complete,KateRasheed
bsdb:39976263/11/1,39976263,"case-control,laboratory experiment",39976263,10.1080/19490976.2025.2467193,NA,"Huang W., Zhu W., Lin Y., Chan F.K.L., Xu Z. , Ng S.C.",<i>Roseburia hominis</i> improves host metabolism in diet-induced obesity,Gut microbes,2025,"Intestinal microbiology, Obesity, probiotics",Experiment 11,China,Mus musculus,Feces,UBERON:0001988,Triglyceride,CHEBI:17855,Low Hepatic triglycerides,High Hepatic triglycerides,The mice in group 1 consists of mice with High levels of hepatic triglycerides,5,5,NA,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4E,14 April 2025,Z.uk.a,"Z.uk.a,Ese",Hepatic triglyceride correlation of differential species in mice between the HFD-PBS and HFD-RH groups,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Berryella|s__Berryella intestinalis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum|s__Faecalibaculum rodentium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia ilealis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus xylosus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella guodeyinii",1783272|201174|84998|1643822|1643826|2815775|1531429;1783272|1239|526524|526525|128827|1729679|1702221;1783272|1239|186801|3082720|186804|1501226|1115758;1783272|1239|91061|1385|90964|1279|1288;1783272|201174|84998|1643822|1643826|84111|2690837,Complete,KateRasheed
bsdb:39976263/11/2,39976263,"case-control,laboratory experiment",39976263,10.1080/19490976.2025.2467193,NA,"Huang W., Zhu W., Lin Y., Chan F.K.L., Xu Z. , Ng S.C.",<i>Roseburia hominis</i> improves host metabolism in diet-induced obesity,Gut microbes,2025,"Intestinal microbiology, Obesity, probiotics",Experiment 11,China,Mus musculus,Feces,UBERON:0001988,Triglyceride,CHEBI:17855,Low Hepatic triglycerides,High Hepatic triglycerides,The mice in group 1 consists of mice with High levels of hepatic triglycerides,5,5,NA,WMS,NA,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4E,14 April 2025,Z.uk.a,Z.uk.a,Hepatic triglyceride levels exhibit differential correlations with species in mice between the HFD-PBS and HFD-RH groups,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter|s__Dysosmobacter welbionis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. PEA192,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas|s__Turicimonas muris",1783272|1239|186801|186802|216572|2591381|2093857;1783272|1239|186801|186802|216572|216851|853;1783272|1239|91061|186826|33958|1578|33959;1783272|1239|186801|186802|216572|459786|2109687;1783272|1239|186801|186802|216572|459786|351091;3379134|976|200643|171549|2005525|375288|328812;3379134|1224|28216|80840|995019|1918598|1796652,Complete,KateRasheed
bsdb:39976263/12/1,39976263,"case-control,laboratory experiment",39976263,10.1080/19490976.2025.2467193,NA,"Huang W., Zhu W., Lin Y., Chan F.K.L., Xu Z. , Ng S.C.",<i>Roseburia hominis</i> improves host metabolism in diet-induced obesity,Gut microbes,2025,"Intestinal microbiology, Obesity, probiotics",Experiment 12,China,Mus musculus,Feces,UBERON:0001988,Response to high fat food intake,EFO:0007684,High Fat Diet- Roseburia hominis (HFD-RH) mice at baseline,High Fat Diet- Roseburia hominis (HFD-RH) mice at endpoint,Mice were characterized after the intervention of Roseburia hominis for 11 weeks,5,5,NA,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S2B,11 July 2025,Ese,Ese,The change of relative abundance of Roseburia hominis in HFD-fed mice before and after the intervention for 11 weeks.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,1783272|1239|186801|3085636|186803|841|301301,Complete,KateRasheed
bsdb:39978595/1/1,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Non Rejection (Pre Rejection),Rejection (Pre Rejection),Participants in the Rejection group were those who underwent kidney transplantation prior to rejection.,60,32,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.1,TRUE,NA,"age,chronic kidney disease,sex,time","age,antibiotic,body height,body mass index,body weight,sex",NA,unchanged,NA,decreased,NA,unchanged,Signature 1,Figure 2F,7 April 2025,MyleeeA,MyleeeA,Differential abundance analysis of bacterial taxa between Rejection (Pre Rejection) and Non-Rejection (Pre Rejection).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|186801|3085636|186803|653683;3384189|32066|203490|203491|203492|848;3379134|29547|3031852|213849|72293|209;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3379134|1224|28216|80840|119060|48736;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:39978595/1/2,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Non Rejection (Pre Rejection),Rejection (Pre Rejection),Participants in the Rejection group were those who underwent kidney transplantation prior to rejection.,60,32,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.1,TRUE,NA,"age,chronic kidney disease,sex,time","age,antibiotic,body height,body mass index,body weight,sex",NA,unchanged,NA,decreased,NA,unchanged,Signature 2,Figure 2F,7 April 2025,MyleeeA,"MyleeeA,Tosin",Differential abundance analysis of bacterial taxa between Rejection (Pre Rejection) and Non-Rejection (Pre Rejection).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050,Complete,Svetlana up
bsdb:39978595/2/1,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Non Rejection (Post Rejection),Rejection (Post Rejection),Participants in the Rejection group were those who showed rejection after kidney transplantation within a timeframe of 90 to 1000 days.,54,21,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.1,TRUE,NA,"age,chronic kidney disease,sex,time","age,antibiotic,body height,body mass index,body weight,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 5C,7 April 2025,MyleeeA,"MyleeeA,Tosin",Differential abundance analysis of bacterial taxa between Rejection (Post Rejection) and Non-Rejection (Post Rejection).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|s__uncultured actinomycete",3379134|1224|1236|135625|712|713;1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549|171552|1283313;1783272|1239|186801|3085636|186803|653683;1783272|1239|186801|186802|3085642|580596;3379134|29547|3031852|213849|72294|194;95818|2093818|2093825|2171986|1331051;3379134|976|117743|200644|49546|1016;3384194|508458|649775|649776|3029087|1434006;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;3379134|29547|3031852|213849|72293|209;3379134|1224|28216|80840|119060|47670;3384189|32066|203490|203491|1129771|32067;3379134|1224|28216|206351|481|482;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3379134|1224|1236|72274|135621|286;3379134|1224|28216|80840|119060|48736;1783272|201174|1760|85006|1268|32207;3379134|976|1853228|1853229|563835|504481;1783272|1239|909932|909929|1843491|970;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843488|909930;1783272|201174|1760|2037|2049;95818|2093818|2093825;1783272|201174|1760|2037|100235,Complete,Svetlana up
bsdb:39978595/2/2,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Non Rejection (Post Rejection),Rejection (Post Rejection),Participants in the Rejection group were those who showed rejection after kidney transplantation within a timeframe of 90 to 1000 days.,54,21,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.1,TRUE,NA,"age,chronic kidney disease,sex,time","age,antibiotic,body height,body mass index,body weight,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 5C,7 April 2025,MyleeeA,"MyleeeA,Tosin",Differential abundance analysis of bacterial taxa between Rejection (Post Rejection) and Non-Rejection (Post Rejection).,decreased,",k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,s__bacterium,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Pseudomonadati|p__Pseudomonadota|s__unidentified proteobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.",;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|33042;1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|1946507;1783272|1239|186801|186802|216572|946234;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3082720|186804|1501226;1869227;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;3379134|1224|2722;1783272|1239|186801|186802|31979|1485|59620,Complete,Svetlana up
bsdb:39978595/3/1,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 3,Germany,Homo sapiens,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,Rejection (Sample 1-Pre rejection),Rejection (Sample 2-Post rejection),Participants in the Rejection group were those who showed rejection after kidney transplantation within a timeframe of 90 to 1000 days post rejection.,32,21,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.1,TRUE,NA,NA,"age,antibiotic,body height,body mass index,body weight,sex",NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 5C,7 April 2025,MyleeeA,"MyleeeA,Tosin",Differential abundance analysis of bacterial taxa between Rejection (Pre Rejection) and Rejection (Post Rejection).,increased,",k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|33042;1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|1946507;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;1783272|1239|909932|1843488|909930;1783272|1239|186801|3085636;1783272|1239|186801|3085636|186803,Complete,Svetlana up
bsdb:39978595/3/2,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 3,Germany,Homo sapiens,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,Rejection (Sample 1-Pre rejection),Rejection (Sample 2-Post rejection),Participants in the Rejection group were those who showed rejection after kidney transplantation within a timeframe of 90 to 1000 days post rejection.,32,21,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.1,TRUE,NA,NA,"age,antibiotic,body height,body mass index,body weight,sex",NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 5C,7 April 2025,MyleeeA,"MyleeeA,Tosin",Differential abundance analysis of bacterial taxa between Rejection (Pre Rejection) and Rejection (Post Rejection).,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|s__uncultured actinomycete",3379134|1224|1236|135625|712|713;1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549|171552|1283313;1783272|1239|186801|3085636|186803|653683;3379134|29547|3031852|213849|72294|194;95818|2093818|2093825|2171986|1331051;3379134|976|117743|200644|49546|1016;3384194|508458|649775|649776|3029087|1434006;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;3379134|1224|28216|80840|119060|47670;3384189|32066|203490|203491|1129771|32067;3379134|1224|28216|206351|481|482;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3379134|1224|1236|72274|135621|286;3379134|1224|28216|80840|119060|48736;1783272|201174|1760|85006|1268|32207;3379134|976|1853228|1853229|563835|504481;1783272|1239|909932|909929|1843491|970;1783272|1239|909932|1843489|31977|29465;1783272|201174|1760|2037|2049;95818|2093818|2093825;1783272|201174|1760|2037|100235,Complete,Svetlana up
bsdb:39978595/4/1,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 4,Germany,Homo sapiens,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,Rejection (Sample 1-Pre rejection),Rejection (Sample 2-Post rejection),Participants in the Rejection group were those who showed rejection after kidney transplantation within a timeframe of 90 to 1000 days post rejection.,32,21,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 5d,7 April 2025,MyleeeA,MyleeeA,Differential abundance analysis of bacterial taxa between Rejection (Pre Rejection) and Rejection (Post Rejection).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|216851,Complete,Svetlana up
bsdb:39978595/4/2,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 4,Germany,Homo sapiens,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,Rejection (Sample 1-Pre rejection),Rejection (Sample 2-Post rejection),Participants in the Rejection group were those who showed rejection after kidney transplantation within a timeframe of 90 to 1000 days post rejection.,32,21,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 5d,8 April 2025,MyleeeA,MyleeeA,Differential abundance analysis of bacterial taxa between Rejection (Pre Rejection) and Rejection (Post Rejection).,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3384189|32066|203490|203491|203492|848;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:39978595/5/1,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 5,Germany,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Healthy controls,Chronic Kidney Disease (CKD),Patients with Chronic Kidney Disease (CKD) from an already published datasets.,479,217,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6B,8 April 2025,MyleeeA,MyleeeA,Differential abundance analysis of bacterial taxa between Chronic Kidney Disease (CKD) and Healthy Controls.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:39978595/5/2,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 5,Germany,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Healthy controls,Chronic Kidney Disease (CKD),Patients with Chronic Kidney Disease (CKD) from an already published datasets.,479,217,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6B,8 April 2025,MyleeeA,MyleeeA,Differential abundance analysis of bacterial taxa between Chronic Kidney Disease (CKD) and Healthy Controls.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|216851,Complete,Svetlana up
bsdb:39978595/6/1,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 6,Germany,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Non Rejection,Rejection,Participants in the rejection group were Propensity score matched and samples were obtained after Kidney Transplantation prior to rejection.,60,32,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,"age,chronic kidney disease,sex,time",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 6B,8 April 2025,MyleeeA,MyleeeA,Differential abundance analysis of bacterial taxa between Rejection and Non-Rejection.,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3384189|32066|203490|203491|203492|848;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:39978595/6/2,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 6,Germany,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Non Rejection,Rejection,Participants in the rejection group were Propensity score matched and samples were obtained after Kidney Transplantation prior to rejection.,60,32,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,"age,chronic kidney disease,sex,time",NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 6B,8 April 2025,MyleeeA,MyleeeA,Differential abundance analysis of bacterial taxa between Rejection and Non-Rejection.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|216851,Complete,Svetlana up
bsdb:39978595/7/1,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 7,Germany,Homo sapiens,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,Rejection (Decreased),Rejection (Increased),Patients experiencing kidney transplantation rejection at any time,NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.1,TRUE,NA,NA,"age,antibiotic,body height,body mass index,body weight,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 4,8 April 2025,MyleeeA,"MyleeeA,Tosin",Heatmap showing associations of bacterial genera with kidney transplant rejection.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|g__Negativibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,s__uncultured organism,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|s__uncultured actinomycete",3379134|1224|1236|135625|712|713;3379134|976|200643|171549|171552|1283313;1783272|1239|186801|186802|3085642|580596;3379134|29547|3031852|213849|72294|194;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378;3379134|29547|3031852|213849|72293|209;3384189|32066|203490|203491|1129771|32067;1783272|1239|1980693;3379134|1224|28216|206351|481|482;1783272|1239|1737404|1737405|1570339|543311;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3379134|1224|28216|80840|119060|48736;1783272|201174|1760|85006|1268|32207;1783272|201174|1760|2037|2049;1783272|1239|186801|3085656|3085657;3379134|976|200643|171549|2005473;3379134|976|200643|171549|171550;155900;1783272|1239|909932|1843488|909930;1783272|201174|1760|2037|100235,Complete,Svetlana up
bsdb:39978595/7/2,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 7,Germany,Homo sapiens,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,Rejection (Decreased),Rejection (Increased),Patients experiencing kidney transplantation rejection at any time,NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.1,TRUE,NA,NA,"age,antibiotic,body height,body mass index,body weight,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 4,8 April 2025,MyleeeA,"MyleeeA,Tosin",Heatmap showing associations of bacterial genera with kidney transplant rejection.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.,k__Pseudomonadati|p__Pseudomonadota|s__unidentified proteobacterium",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485;1783272|1239|526524|526525|128827|1472649;1783272|201174|84998|1643822|1643826|84111;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851|1946507;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|2005525;1783272|1239|186801|186802|31979|1485|59620;3379134|1224|2722,Complete,Svetlana up
bsdb:39978595/8/1,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 8,Germany,Homo sapiens,Feces,UBERON:0001988,Reaction time measurement,NA,Distance to Rejection (Decreasing),Distance to Rejection (Increasing),Participants grouped based on Distance to rejection of kidney transplantation at any sampling time,NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.1,TRUE,NA,NA,"age,antibiotic,body height,body mass index,body weight,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 4,8 April 2025,MyleeeA,"MyleeeA,Tosin",Heatmap showing associations of bacterial genera with kidney transplant rejection.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Hymenochaetales|f__Rickenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.",1783272|1239|186801|186802|216572|52784;;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|186802|216572|216851|1946507;1783272|1239|526524|526525|128827|1573534;1783272|1239|186801|186802|216572|946234;1783272|1239|526524|526525|128827|61170;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|171552|577309;3379134|1224|28216|80840|995019|40544;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643;1783272|1239|186801;1783272|1239|186801|186802;4751|5204|155619|139380|1124673;3379134|976|200643|171549|2005525;1783272|1239|186801|186802|31979|1485|59620,Complete,Svetlana up
bsdb:39978595/8/2,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 8,Germany,Homo sapiens,Feces,UBERON:0001988,Reaction time measurement,NA,Distance to Rejection (Decreasing),Distance to Rejection (Increasing),Participants grouped based on Distance to rejection of kidney transplantation at any sampling time,NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.1,TRUE,NA,NA,"age,antibiotic,body height,body mass index,body weight,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 4,8 April 2025,MyleeeA,"MyleeeA,Tosin",Heatmap showing associations of bacterial genera with kidney transplant rejection.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Nanosynbacterales|f__Candidatus Nanosynbacteraceae|g__Candidatus Nanosynbacter|s__Candidatus Nanosynbacter lyticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales",3379134|1224|1236|135625|712|713;1783272|1239|186801|3085636|186803|653683;3379134|29547|3031852|213849|72294|194;95818|2093818|2093819|2093822|2093823|2093824;1783272|1239|91061|186826|81852|1350;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|1300|1357;3384189|32066|203490|203491|1129771|32067;1783272|1239|1737404|1737405|1570339|543311;3379134|976|200643|171549|171552|838;1783272|1239|909932|909929|1843491|970;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;1783272|201174|1760|2037|2049;95818|2093818|2093825,Complete,Svetlana up
bsdb:39978595/9/1,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 9,Germany,Homo sapiens,Feces,UBERON:0001988,Reaction time measurement,NA,Distance to Kidney Transplantation (Decreasing),Distance to Kidney Transplantation (Increasing),Participants grouped based on Distance to kidney transplantation at any sampling time,NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.1,TRUE,NA,NA,"age,antibiotic,body height,body mass index,body weight,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 4,9 April 2025,MyleeeA,"MyleeeA,Tosin",Heatmap showing associations of bacterial genera with kidney transplant rejection.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota,,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085656|3085657|2039302;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|3085636|186803|841;3379134|1224|28216|80840|995019|40544;1783272|1239|186801|3085636|186803|1506577;1783272|201174;1783272|1239;;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;1783272|1239|186801|3085656|3085657,Complete,Svetlana up
bsdb:39978595/9/2,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 9,Germany,Homo sapiens,Feces,UBERON:0001988,Reaction time measurement,NA,Distance to Kidney Transplantation (Decreasing),Distance to Kidney Transplantation (Increasing),Participants grouped based on Distance to kidney transplantation at any sampling time,NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.1,TRUE,NA,NA,"age,antibiotic,body height,body mass index,body weight,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 4,9 April 2025,MyleeeA,"MyleeeA,Tosin",Heatmap showing associations of bacterial genera with kidney transplant rejection.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales",1783272|201174|1760|2037|2049|1654;3379134|976|200643|171549|171552|1283313;3379134|29547|3031852|213849|72294|194;3384189|32066|203490|203491|203492|848;1783272|1239|91061|186826|186828|117563;3379134|1224|28216|206351|481|482;3379134|1224|28216|80840|119060|48736;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|186826|1300|1301;95818|2093818|2093825,Complete,Svetlana up
bsdb:39978595/10/1,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 10,Germany,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Age (Decreasing),Age (Increasing),Participants here were grouped by age.,NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.1,TRUE,NA,NA,"age,antibiotic,body height,body mass index,body weight,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S4,8 April 2025,Victoria,"Victoria,Tosin",Heatmap showing associations of bacterial genera with kidney transplant rejection.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Bacillati|p__Bacillota|g__Negativibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,p__Rhodophyta|c__Florideophyceae|o__Batrachospermales|f__Batrachospermaceae|g__Paludicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,s__uncultured organism,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella",3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|244127;1783272|1239|91061|1385|186817|1386;;1783272|1239|186801|186802|3085642|580596;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802|1980681;3379134|200940|3031449|213115|194924|872;1783272|1239|526524|526525|128827|1472649;1783272|1239|186801|186802|216572|1892380;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|2742598;1783272|1239|186801|186802|216572|3028852;1783272|1239|186801|3085656|3085657|2039302;1783272|1239|1980693;1783272|1239|186801|186802|216572|459786;2763|2806|31370|31371|2729669;1783272|1239|186801|186802|216572|1263;1783272|201174|84998|1643822|1643826|84108;1783272|1239|186801|186802|216572|292632;1783272|1239|526524|526525|2810280|3025755;1783272|1239|909932|1843488|909930;1783272|1239|91061;3379134|976;1783272|1239|91061|186826|33958;1783272|1239|186801|186802|216572;155900;3379134|1224|28216|80840|995019|577310,Complete,Svetlana up
bsdb:39978595/10/2,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 10,Germany,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Age (Decreasing),Age (Increasing),Participants here were grouped by age.,NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.1,TRUE,NA,NA,"age,antibiotic,body height,body mass index,body weight,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure S4,8 April 2025,Victoria,"Victoria,Tosin",Heatmap showing associations of bacterial genera with kidney transplant rejection.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",1783272|1239|186801|3085636|3118652|2039240;1783272|1239|186801|3085636|186803|830;1783272|1239|186801|3085636|186803|1506553,Complete,Svetlana up
bsdb:39978595/11/1,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 11,Germany,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Donor Age(10-15)/Decreasing,Donor Age(10-15)/ Increasing,Participants in this group are donors between the ages of 10 and 15 years.,NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.1,TRUE,NA,NA,"age,antibiotic,body height,body mass index,body weight,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S4,8 April 2025,Victoria,"Victoria,Tosin",Heatmap showing associations of bacterial genera with kidney transplant rejection.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,1783272|1239|91061|186826|81852|1350,Complete,Svetlana up
bsdb:39978595/11/2,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 11,Germany,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Donor Age(10-15)/Decreasing,Donor Age(10-15)/ Increasing,Participants in this group are donors between the ages of 10 and 15 years.,NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.1,TRUE,NA,NA,"age,antibiotic,body height,body mass index,body weight,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure S4,8 April 2025,Victoria,"Victoria,Tosin",Heatmap showing associations of bacterial genera with kidney transplant rejection.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,1783272|1239|186801|186802|216572|216851|1946507,Complete,Svetlana up
bsdb:39978595/12/1,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 12,Germany,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Donor Age(15-20)/Decreasing,Donor Age(15-20)/ Increasing,Participants in this group are donors between the ages of 15 and 20 years.,NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.1,TRUE,NA,NA,"age,antibiotic,body height,body mass index,body weight,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S4,8 April 2025,Victoria,"Victoria,Tosin",Heatmap showing associations of bacterial genera with kidney transplant rejection.,increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus",3379134|200940|3031449|213115|194924|872;1783272|201174|84998|1643822|1643826|580024,Complete,Svetlana up
bsdb:39978595/13/1,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 13,Germany,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Donor Age(20-25)/Decreasing,Donor Age(20-25)/ Increasing,Participants in this group are donors between the ages of 20 and 25 years.,NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.1,TRUE,NA,NA,"age,antibiotic,body height,body mass index,body weight,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S4,8 April 2025,Victoria,"Victoria,Tosin",Heatmap showing associations of bacterial genera with kidney transplant rejection.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor",1783272|1239|909932|1843488|909930|904;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572|946234,Complete,Svetlana up
bsdb:39978595/13/2,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 13,Germany,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Donor Age(20-25)/Decreasing,Donor Age(20-25)/ Increasing,Participants in this group are donors between the ages of 20 and 25 years.,NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.1,TRUE,NA,NA,"age,antibiotic,body height,body mass index,body weight,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure S4,8 April 2025,Victoria,"Victoria,Tosin",Heatmap showing associations of bacterial genera with kidney transplant rejection.,decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,Svetlana up
bsdb:39978595/15/1,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 15,Germany,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Donor Age(40-45)/Decreasing,Donor Age(40-45)/ Increasing,Participants in this group are donors between the ages of 40 and 45 years.,NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.1,TRUE,NA,NA,"age,antibiotic,body height,body mass index,body weight,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S4,8 April 2025,Victoria,"Victoria,Tosin",Heatmap showing associations of bacterial genera with kidney transplant rejection.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,1783272|1239|186801|3085636|186803|830,Complete,Svetlana up
bsdb:39978595/16/1,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 16,Germany,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Donor Age(45-50)/ Decreasing,Donor Age(45-50)/ Increasing,Participants in this group are donors between the ages of 45 and 50 years.,NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.1,TRUE,NA,NA,"age,antibiotic,body height,body mass index,body weight,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S4,8 April 2025,Victoria,"Victoria,Tosin",Heatmap showing associations of bacterial genera with kidney transplant rejection.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,3379134|1224|28216|80840|119060|48736,Complete,Svetlana up
bsdb:39978595/16/2,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 16,Germany,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Donor Age(45-50)/ Decreasing,Donor Age(45-50)/ Increasing,Participants in this group are donors between the ages of 45 and 50 years.,NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.1,TRUE,NA,NA,"age,antibiotic,body height,body mass index,body weight,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure S4,8 April 2025,Victoria,"Victoria,Tosin",Heatmap showing associations of bacterial genera with kidney transplant rejection.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:39978595/17/1,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 17,Germany,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Donor Age(70-75)/ Decreasing,Donor Age(70-75)/ Increasing,Participants in this group are donors between the ages of 70 and 75 years.,NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.1,TRUE,NA,NA,"age,antibiotic,body height,body mass index,body weight,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S4,8 April 2025,Victoria,"Victoria,Tosin",Heatmap showing associations of bacterial genera with kidney transplant rejection.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacillati|p__Bacillota|c__Bacilli",1783272|1239|526524|526525|128827|61170;1783272|1239|91061,Complete,Svetlana up
bsdb:39978595/18/1,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 18,Germany,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Donor Age(75-80)/ Decreasing,Donor Age(75-80)/ Increasing,Participants in this group are donors between the ages of 75 and 80 years.,NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.1,TRUE,NA,NA,"age,antibiotic,body height,body mass index,body weight,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S4,8 April 2025,Victoria,"Victoria,Tosin",Heatmap showing associations of bacterial genera with kidney transplant rejection.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543|547;1783272|1239|526524|526525|2810280|3025755,Complete,Svetlana up
bsdb:39978595/19/1,39978595,time series / longitudinal observational,39978595,10.1016/j.ajt.2025.02.010,NA,"Holle J., Reitmeir R., Behrens F., Singh D., Schindler D., Potapenko O., McParland V., Anandakumar H., Kanzelmeyer N., Sommerer C., Hartleif S., Andrassy J., Heemann U., Neuenhahn M., Forslund-Startceva S.K., Gerhard M., Oh J., Wilck N., Löber U. , Bartolomaeus H.",Gut microbiome alterations precede graft rejection in kidney transplantation patients,American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons,2025,"graft rejection, gut microbiome, kidney transplantation, short-chain fatty acids",Experiment 19,Germany,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Donor Age(>80)/ Decreasing,Donor Age(>80)/ Increasing,Participants in this group are donors above the age of 80.,NA,NA,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.1,TRUE,NA,NA,"age,antibiotic,body height,body mass index,body weight,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S4,8 April 2025,Victoria,"Victoria,Tosin",Heatmap showing associations of bacterial genera with kidney transplant rejection.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543|1940338;1783272|1239|91061|186826|33958,Complete,Svetlana up
bsdb:39980327/1/1,39980327,randomized controlled trial,39980327,https://doi.org/10.1080/19490976.2025.2465896,https://pubmed.ncbi.nlm.nih.gov/39980327/,"Tobón-Cornejo S., Sanchez-Tapia M., Guizar-Heredia R., Velázquez Villegas L., Noriega L.G., Furuzawa-Carballeda J., Hernández-Pando R., Vázquez-Manjarrez N., Granados-Portillo O., López-Barradas A., Rebollar-Vega R., Maya O., Miller A.W., Serralde A., Guevara-Cruz M., Torres N. , Tovar A.R.",Increased dietary protein stimulates amino acid catabolism via the gut microbiota and secondary bile acid production,Gut microbes,2025,"Gut microbiota, amino acid catabolism, glucagon, high-protein diet, secondary bile acids",Experiment 1,United States of America,Mus musculus,Colon,UBERON:0001155,Response to diet,EFO:0010757,Low protein group- LP,High protein group- HP,Dietary regimen constituting of 50% protein for 10 days.,20,20,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4E,28 March 2025,Miss Lulu,Miss Lulu,Linear discriminant analysis (LDA) shows significant differences in the relative abundance of bacterial species in mice fed different protein concentrations.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia cocleata,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum|s__Mucispirillum schaedleri",3379134|1224|1236|91347|543|561|562;1783272|1239|526524|526525|2810280|3025755|69824;3379134|976|200643|171549|2005525|375288|823;3379134|200930|68337|191393|2945020|248038|248039,Complete,Svetlana up
bsdb:39980327/1/2,39980327,randomized controlled trial,39980327,https://doi.org/10.1080/19490976.2025.2465896,https://pubmed.ncbi.nlm.nih.gov/39980327/,"Tobón-Cornejo S., Sanchez-Tapia M., Guizar-Heredia R., Velázquez Villegas L., Noriega L.G., Furuzawa-Carballeda J., Hernández-Pando R., Vázquez-Manjarrez N., Granados-Portillo O., López-Barradas A., Rebollar-Vega R., Maya O., Miller A.W., Serralde A., Guevara-Cruz M., Torres N. , Tovar A.R.",Increased dietary protein stimulates amino acid catabolism via the gut microbiota and secondary bile acid production,Gut microbes,2025,"Gut microbiota, amino acid catabolism, glucagon, high-protein diet, secondary bile acids",Experiment 1,United States of America,Mus musculus,Colon,UBERON:0001155,Response to diet,EFO:0010757,Low protein group- LP,High protein group- HP,Dietary regimen constituting of 50% protein for 10 days.,20,20,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4E,28 March 2025,Miss Lulu,Miss Lulu,Linear discriminant analysis (LDA) shows significant differences in the relative abundance of bacterial species in mice fed different protein concentrations.,decreased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,3379134|74201|203494|48461|1647988|239934|239935,Complete,Svetlana up
bsdb:39980327/2/1,39980327,randomized controlled trial,39980327,https://doi.org/10.1080/19490976.2025.2465896,https://pubmed.ncbi.nlm.nih.gov/39980327/,"Tobón-Cornejo S., Sanchez-Tapia M., Guizar-Heredia R., Velázquez Villegas L., Noriega L.G., Furuzawa-Carballeda J., Hernández-Pando R., Vázquez-Manjarrez N., Granados-Portillo O., López-Barradas A., Rebollar-Vega R., Maya O., Miller A.W., Serralde A., Guevara-Cruz M., Torres N. , Tovar A.R.",Increased dietary protein stimulates amino acid catabolism via the gut microbiota and secondary bile acid production,Gut microbes,2025,"Gut microbiota, amino acid catabolism, glucagon, high-protein diet, secondary bile acids",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Baseline Participants,End of study Participants,Effect of high protein diet on humans after clinical trial was conducted.,19,19,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 10D,29 March 2025,Miss Lulu,Miss Lulu,Linear discriminant analysis (LDA) of the gut microbiota at the species level. Concentration of fecal secondary bile acids,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Anaerorhabdus|s__Anaerorhabdus furcosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] fimetarium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Paraeggerthella|s__Paraeggerthella hongkongensis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei",1783272|1239|526524|526525|128827|118966|118967;1783272|1239|186801|186802|204475|745368;3379134|976|200643|171549|2005525|375288|823;1783272|1239|186801|3085636|186803|1506553|99656;1783272|201174|84998|1643822|1643826|651554|230658;1783272|1239|526524|526525|128827|123375|102148,Complete,Svetlana up
bsdb:39980327/2/2,39980327,randomized controlled trial,39980327,https://doi.org/10.1080/19490976.2025.2465896,https://pubmed.ncbi.nlm.nih.gov/39980327/,"Tobón-Cornejo S., Sanchez-Tapia M., Guizar-Heredia R., Velázquez Villegas L., Noriega L.G., Furuzawa-Carballeda J., Hernández-Pando R., Vázquez-Manjarrez N., Granados-Portillo O., López-Barradas A., Rebollar-Vega R., Maya O., Miller A.W., Serralde A., Guevara-Cruz M., Torres N. , Tovar A.R.",Increased dietary protein stimulates amino acid catabolism via the gut microbiota and secondary bile acid production,Gut microbes,2025,"Gut microbiota, amino acid catabolism, glucagon, high-protein diet, secondary bile acids",Experiment 2,United States of America,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Baseline Participants,End of study Participants,Effect of high protein diet on humans after clinical trial was conducted.,19,19,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 10D,29 March 2025,Miss Lulu,Miss Lulu,Linear discriminant analysis (LDA) of the gut microbiota at the species level. Concentration of fecal secondary bile acids,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus pullicaecorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter|s__Papillibacter cinnamivorans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella balaenopterae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Macellibacteroides|s__Macellibacteroides fermentans",1783272|1239|186801|186802|3085642|580596|501571;1783272|1239|186801|186802|216572|100175|100176;1783272|1239|91061|186826|186828|117563|137733;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|2316020|46228;3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|2005519|397864|487174;1783272|1239|186801|3085636|186803|841|360807;3379134|976|200643|171549|171551|1159323|879969,Complete,Svetlana up
bsdb:39980327/3/1,39980327,randomized controlled trial,39980327,https://doi.org/10.1080/19490976.2025.2465896,https://pubmed.ncbi.nlm.nih.gov/39980327/,"Tobón-Cornejo S., Sanchez-Tapia M., Guizar-Heredia R., Velázquez Villegas L., Noriega L.G., Furuzawa-Carballeda J., Hernández-Pando R., Vázquez-Manjarrez N., Granados-Portillo O., López-Barradas A., Rebollar-Vega R., Maya O., Miller A.W., Serralde A., Guevara-Cruz M., Torres N. , Tovar A.R.",Increased dietary protein stimulates amino acid catabolism via the gut microbiota and secondary bile acid production,Gut microbes,2025,"Gut microbiota, amino acid catabolism, glucagon, high-protein diet, secondary bile acids",Experiment 3,United States of America,Mus musculus,Colon,UBERON:0001155,Response to diet,EFO:0010757,Normal protein group- NP,High protein group- HP,Dietary regimen constituting of 50% protein for 10 days.,20,20,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4D,1 April 2025,Miss Lulu,Miss Lulu,Gut microbiota is modified by dietary protein concentration in mice (genus),increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239|526524|526525|128827|174708;3379134|1224|28216|80840|995019|40544;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:39980327/3/2,39980327,randomized controlled trial,39980327,https://doi.org/10.1080/19490976.2025.2465896,https://pubmed.ncbi.nlm.nih.gov/39980327/,"Tobón-Cornejo S., Sanchez-Tapia M., Guizar-Heredia R., Velázquez Villegas L., Noriega L.G., Furuzawa-Carballeda J., Hernández-Pando R., Vázquez-Manjarrez N., Granados-Portillo O., López-Barradas A., Rebollar-Vega R., Maya O., Miller A.W., Serralde A., Guevara-Cruz M., Torres N. , Tovar A.R.",Increased dietary protein stimulates amino acid catabolism via the gut microbiota and secondary bile acid production,Gut microbes,2025,"Gut microbiota, amino acid catabolism, glucagon, high-protein diet, secondary bile acids",Experiment 3,United States of America,Mus musculus,Colon,UBERON:0001155,Response to diet,EFO:0010757,Normal protein group- NP,High protein group- HP,Dietary regimen constituting of 50% protein for 10 days.,20,20,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4D,1 April 2025,Miss Lulu,Miss Lulu,Gut microbiota is modified by dietary protein concentration in mice (genus),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",3379134|976|200643|171549|171550|28138;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|119852,Complete,Svetlana up
bsdb:39980327/4/1,39980327,randomized controlled trial,39980327,https://doi.org/10.1080/19490976.2025.2465896,https://pubmed.ncbi.nlm.nih.gov/39980327/,"Tobón-Cornejo S., Sanchez-Tapia M., Guizar-Heredia R., Velázquez Villegas L., Noriega L.G., Furuzawa-Carballeda J., Hernández-Pando R., Vázquez-Manjarrez N., Granados-Portillo O., López-Barradas A., Rebollar-Vega R., Maya O., Miller A.W., Serralde A., Guevara-Cruz M., Torres N. , Tovar A.R.",Increased dietary protein stimulates amino acid catabolism via the gut microbiota and secondary bile acid production,Gut microbes,2025,"Gut microbiota, amino acid catabolism, glucagon, high-protein diet, secondary bile acids",Experiment 4,United States of America,Mus musculus,Colon,UBERON:0001155,Response to diet,EFO:0010757,Low protein group- LP,High protein group- HP,Dietary regimen constituting of 50% protein for 10 days.,20,20,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4D,1 April 2025,Miss Lulu,Miss Lulu,Gut microbiota is modified by dietary protein concentration in mice (genus),increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239|526524|526525|128827|174708;3379134|1224|28216|80840|995019|40544;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:39980327/4/2,39980327,randomized controlled trial,39980327,https://doi.org/10.1080/19490976.2025.2465896,https://pubmed.ncbi.nlm.nih.gov/39980327/,"Tobón-Cornejo S., Sanchez-Tapia M., Guizar-Heredia R., Velázquez Villegas L., Noriega L.G., Furuzawa-Carballeda J., Hernández-Pando R., Vázquez-Manjarrez N., Granados-Portillo O., López-Barradas A., Rebollar-Vega R., Maya O., Miller A.W., Serralde A., Guevara-Cruz M., Torres N. , Tovar A.R.",Increased dietary protein stimulates amino acid catabolism via the gut microbiota and secondary bile acid production,Gut microbes,2025,"Gut microbiota, amino acid catabolism, glucagon, high-protein diet, secondary bile acids",Experiment 4,United States of America,Mus musculus,Colon,UBERON:0001155,Response to diet,EFO:0010757,Low protein group- LP,High protein group- HP,Dietary regimen constituting of 50% protein for 10 days.,20,20,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4D,1 April 2025,Miss Lulu,Miss Lulu,Gut microbiota is modified by dietary protein concentration in mice (genus),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",3379134|976|200643|171549|171550|28138;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|119852,Complete,Svetlana up
bsdb:39980327/5/1,39980327,randomized controlled trial,39980327,https://doi.org/10.1080/19490976.2025.2465896,https://pubmed.ncbi.nlm.nih.gov/39980327/,"Tobón-Cornejo S., Sanchez-Tapia M., Guizar-Heredia R., Velázquez Villegas L., Noriega L.G., Furuzawa-Carballeda J., Hernández-Pando R., Vázquez-Manjarrez N., Granados-Portillo O., López-Barradas A., Rebollar-Vega R., Maya O., Miller A.W., Serralde A., Guevara-Cruz M., Torres N. , Tovar A.R.",Increased dietary protein stimulates amino acid catabolism via the gut microbiota and secondary bile acid production,Gut microbes,2025,"Gut microbiota, amino acid catabolism, glucagon, high-protein diet, secondary bile acids",Experiment 5,United States of America,Mus musculus,Colon,UBERON:0001155,Response to diet,EFO:0010757,Low protein group- LP,Normal protein group- NP,Dietary regimen constituting of 20% protein for 10 days.,20,20,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4D,1 April 2025,Miss Lulu,Miss Lulu,Gut microbiota is modified by dietary protein concentration in mice (genus),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|119852;3379134|1224|28216|80840|995019|40544;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:39980327/5/2,39980327,randomized controlled trial,39980327,https://doi.org/10.1080/19490976.2025.2465896,https://pubmed.ncbi.nlm.nih.gov/39980327/,"Tobón-Cornejo S., Sanchez-Tapia M., Guizar-Heredia R., Velázquez Villegas L., Noriega L.G., Furuzawa-Carballeda J., Hernández-Pando R., Vázquez-Manjarrez N., Granados-Portillo O., López-Barradas A., Rebollar-Vega R., Maya O., Miller A.W., Serralde A., Guevara-Cruz M., Torres N. , Tovar A.R.",Increased dietary protein stimulates amino acid catabolism via the gut microbiota and secondary bile acid production,Gut microbes,2025,"Gut microbiota, amino acid catabolism, glucagon, high-protein diet, secondary bile acids",Experiment 5,United States of America,Mus musculus,Colon,UBERON:0001155,Response to diet,EFO:0010757,Low protein group- LP,Normal protein group- NP,Dietary regimen constituting of 20% protein for 10 days.,20,20,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4D,1 April 2025,Miss Lulu,Miss Lulu,Gut microbiota is modified by dietary protein concentration in mice.(genus),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum",3379134|976|200643|171549|171550|28138;1783272|1239|526524|526525|128827|174708,Complete,Svetlana up
bsdb:39994329/1/1,39994329,case-control,39994329,10.1038/s41598-025-89801-8,NA,"Abdelqader E.M., Mahmoud W.S., Gebreel H.M., Kamel M.M. , Abu-Elghait M.","Correlation between gut microbiota dysbiosis, metabolic syndrome and breast cancer",Scientific reports,2025,NA,Experiment 1,Egypt,Homo sapiens,Feces,UBERON:0001988,Breast cancer,MONDO:0007254,healthy controls,BC patients,"Female breast cancer patients receiving treatment, with non-metastatic invasive ductal carcinoma.",50,50,3 months,16S,NA,RT-qPCR,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,13 July 2025,Ecsharp,Ecsharp,Analysis contrasting the bacterial abundances in several groups. The data were shown as the median; the Mann-Whitney U test was used to analyze the differences between the two groups.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85004|31953|1678,Complete,NA
bsdb:39994329/2/1,39994329,case-control,39994329,10.1038/s41598-025-89801-8,NA,"Abdelqader E.M., Mahmoud W.S., Gebreel H.M., Kamel M.M. , Abu-Elghait M.","Correlation between gut microbiota dysbiosis, metabolic syndrome and breast cancer",Scientific reports,2025,NA,Experiment 2,Egypt,Homo sapiens,Feces,UBERON:0001988,Metabolic syndrome,EFO:0000195,healthy controls,BC patients with MetS,Female BC patients with metabolic syndrome (MetS). A confirmed case of MetS required the presence of three or more criteria: waist circumference exceeding 80 cm in females; fasting glucose levels of 100 mg/dL or higher; HDL cholesterol below 50 mg/dL in females; triglyceride levels of 150 mg/dL or higher; and blood pressure of 130/85 mmHg or higher.,50,30,3 months,16S,NA,RT-qPCR,NA,Kruskall-Wallis,0.05,FALSE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3 & 4,13 July 2025,Ecsharp,Ecsharp,The load of Lactobacillus bacteria (Fig. 3) and Bifidobacterium bacteria (Fig. 4) in the stools of separated patients regarding metabolic syndrome and control by Kruskall–Wallis test. Bacterial group count expressed as log10 equivalent bacteria/g of feces.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85004|31953|1678,Complete,NA
bsdb:39994329/3/1,39994329,case-control,39994329,10.1038/s41598-025-89801-8,NA,"Abdelqader E.M., Mahmoud W.S., Gebreel H.M., Kamel M.M. , Abu-Elghait M.","Correlation between gut microbiota dysbiosis, metabolic syndrome and breast cancer",Scientific reports,2025,NA,Experiment 3,Egypt,Homo sapiens,Feces,UBERON:0001988,Metabolic syndrome,EFO:0000195,healthy controls,BC patients MetS-free,Female BC patients with no metabolic syndrome (MetS) diagnosis. A confirmed case of MetS required the presence of three or more criteria: waist circumference exceeding 80 cm in females; fasting glucose levels of 100 mg/dL or higher; HDL cholesterol below 50 mg/dL in females; triglyceride levels of 150 mg/dL or higher; and blood pressure of 130/85 mmHg or higher.,50,20,3 months,16S,NA,RT-qPCR,NA,Kruskall-Wallis,0.05,FALSE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3 & 4,13 July 2025,Ecsharp,Ecsharp,The load of Lactobacillus bacteria (Fig. 3) and Bifidobacterium bacteria (Fig. 4) in the stools of separated patients regarding metabolic syndrome and control by Kruskall–Wallis test. Bacterial group count expressed as log10 equivalent bacteria/g of feces.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85004|31953|1678,Complete,NA
bsdb:39998243/1/1,39998243,case-control,39998243,https://doi.org/10.1128/spectrum.02582-24,NA,"Brochu H.N., Zhang Q., Song K., Wang L., Deare E.A., Williams J.D., Icenhour C.R. , Iyer L.K.",Characterization of vaginal microbiomes in clinician-collected bacterial vaginosis diagnosed samples,Microbiology spectrum,2025,"16S rRNA, bacterial vaginosis, vaginal microbiome",Experiment 1,United States of America,Homo sapiens,Vaginal fluid,UBERON:0036243,Bacterial vaginosis,EFO:0003932,Bacterial vaginosis-Negative,Bacterial vaginosis-Positive,Patients diagnosed with Bacterial vaginosis.,45,27,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figures 4A and 4B,17 March 2025,Miss Lulu,"Miss Lulu,Victoria",Differential abundance (DA) analysis and modularized co-occurrence network analysis of BV-POS and BV-NEG samples.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Lachnocurva|s__Candidatus Lachnocurva vaginae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales genomosp. BVAB2,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Umbribacter|s__Umbribacter vaginalis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemelliphila|s__Gemelliphila asaccharolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Mageeibacillus|s__Mageeibacillus indolicus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera genomosp. type 1,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia vaginalis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus christensenii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera hutchinsoni",1783272|201174|84998|84999|1643824|1380;1783272|1239|186801|3085636|186803|3397567|699240;1783272|1239|186801|186802|699241;1783272|201174|84998|1643822|1643826|3472368|1588753;1783272|1239|909932|1843489|31977|39948;1783272|201174|84998|84999|1643824|2767327|82135;1783272|201174|1760|85004|31953|2701;1783272|201174|1760|85004|31953|2701|2702;1783272|1239|91061|1385|539738|3076174|502393;3379134|976|200643|171549|171552|2974257|386414;1783272|1239|186801|186802|216572|1637257|884684;1783272|1239|909932|1843489|31977|906|3397622;1783272|1239|1737404|1737405|1570339|543311;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|419005;3384189|32066|203490|203491|1129771|168808;3384189|32066|203490|203491|1129771|168808|40543;3384189|32066|203490|203491|1129771|168808|187101;1783272|1239|909932|1843489|31977;1783272|1239|91061|186826|186827|1375|87541;1783272|1239|909932|1843489|31977|906|1588748,Complete,KateRasheed
bsdb:39998243/1/2,39998243,case-control,39998243,https://doi.org/10.1128/spectrum.02582-24,NA,"Brochu H.N., Zhang Q., Song K., Wang L., Deare E.A., Williams J.D., Icenhour C.R. , Iyer L.K.",Characterization of vaginal microbiomes in clinician-collected bacterial vaginosis diagnosed samples,Microbiology spectrum,2025,"16S rRNA, bacterial vaginosis, vaginal microbiome",Experiment 1,United States of America,Homo sapiens,Vaginal fluid,UBERON:0036243,Bacterial vaginosis,EFO:0003932,Bacterial vaginosis-Negative,Bacterial vaginosis-Positive,Patients diagnosed with Bacterial vaginosis.,45,27,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4A and 4B,17 March 2025,Miss Lulu,"Miss Lulu,Victoria",Differential abundance (DA) analysis and modularized co-occurrence network analysis of BV-POS and BV-NEG samples.,decreased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister propionicifaciens,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus jensenii,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp. oral clone HT002",1783272|1239|1737404|1737405|1570339|165779|1287640;1783272|201174|1760|85007|1653|1716;1783272|1239|909932|1843489|31977|39948|308994;1783272|1239|1737404|1582879;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|47770;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|91061|186826|33958|1578|109790;3379134|1224;3379134|1224|1236|72274|135621|286;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;1783272|544448|2790996|2790998|2129;1783272|1239|91061|186826|33958|1578|242643,Complete,KateRasheed
bsdb:39999841/1/1,39999841,case-control,39999841,10.1016/j.xcrm.2025.101979,NA,"Liao Y., Tong X.T., Zhou T., Xue W.Q., Wang T.M., He Y.Q., Zheng M.Q., Jia Y.J., Yang D.W., Wu Y.X., Zheng X.H., Zuo Z.X., Chen M.Y., Liu N. , Jia W.H.",Unveiling familial aggregation of nasopharyngeal carcinoma: Insights from oral microbiome dysbiosis,Cell reports. Medicine,2025,"cancer familial aggregation, nasopharyngeal carcinoma, oral microbiome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Nasopharyngeal squamous cell carcinoma,NA,Control,Nasopharyngeal Carcinoma (NPC) Case,Treatment-naive patients who were diagnosed with nasopharyngeal carcinoma.,170,167,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,sex","age,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,"Table 1, TableS7, Figure 3A, Figure S2a",2 November 2025,YokoC,"YokoC,Tosin","Table and heatmaps depicting the significant differential abundant oral ASVs identified by DESeq (differential expression analysis for sequence count data) analysis with adjusting age, gender, and cigarette smoking status (p < 0.05) were shown.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella loescheii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hongkongensis,s__Mannheimia sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium asaccharolyticum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella salivae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum longum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema socranskii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella|s__Bergeyella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp.",3379134|976|200643|171549|171552|1283313|76122;3379134|976|117743|200644|49546|1016;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|1385|539738|1378|1966354;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;3379134|976|200643|171549|171552|2974257|840;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|80840|119060|47670|47671;3384189|32066|203490|203491|1129771|32067|554406;2081794;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843489|31977|906|187326;1783272|1239|186801|3082720|543314|86331|2049035;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|3085636|186803|265975|1501332;1783272|1239|186801|3085636|186803|265975|237576;3379134|976|200643|171549|171552|2974251|228604;1783272|1239|186801|3085636|186803|1213720|796942;1783272|1239|91061|186826|1300|1301;3379134|203691|203692|136|2845253|157|53419;1783272|1239|909932|1843489|31977|29465;3384189|32066|203490|203491|203492|848|851;3379134|976|117743|200644|2762318|59735|1962306;3379134|1224|28216|206351|481|482|192066,Complete,KateRasheed
bsdb:39999841/1/2,39999841,case-control,39999841,10.1016/j.xcrm.2025.101979,NA,"Liao Y., Tong X.T., Zhou T., Xue W.Q., Wang T.M., He Y.Q., Zheng M.Q., Jia Y.J., Yang D.W., Wu Y.X., Zheng X.H., Zuo Z.X., Chen M.Y., Liu N. , Jia W.H.",Unveiling familial aggregation of nasopharyngeal carcinoma: Insights from oral microbiome dysbiosis,Cell reports. Medicine,2025,"cancer familial aggregation, nasopharyngeal carcinoma, oral microbiome",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Nasopharyngeal squamous cell carcinoma,NA,Control,Nasopharyngeal Carcinoma (NPC) Case,Treatment-naive patients who were diagnosed with nasopharyngeal carcinoma.,170,167,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,"age,sex","age,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3A, Figure S2a",2 November 2025,YokoC,"YokoC,Tosin","Table and heatmaps depicting the significant differential abundant oral ASVs identified by DESeq (differential expression analysis for sequence count data) analysis with adjusting age, gender, and cigarette smoking status (p < 0.05).",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Aminipila,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Conchiformibius,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella|s__Johnsonella sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Conchiformibius|s__Conchiformibius sp.,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales",3379134|976|200643|171549|171552|1283313|671218;1783272|1239|186801|3082720|543314|2060094;1783272|1239|909932|909929|1843491|82202;3379134|1224|28216|206351|481|334107;3379134|1224|28216|206351|481|538;1783272|1239|186801|3082720|3118655|44259;1783272|1239|186801|3085636|186803|43994|3059423;1783272|201174|1760|85006|1268|32207;3379134|1224|28216|206351|481|334107|3043297;95818|2093818|2093825,Complete,KateRasheed
bsdb:39999841/2/1,39999841,case-control,39999841,10.1016/j.xcrm.2025.101979,NA,"Liao Y., Tong X.T., Zhou T., Xue W.Q., Wang T.M., He Y.Q., Zheng M.Q., Jia Y.J., Yang D.W., Wu Y.X., Zheng X.H., Zuo Z.X., Chen M.Y., Liu N. , Jia W.H.",Unveiling familial aggregation of nasopharyngeal carcinoma: Insights from oral microbiome dysbiosis,Cell reports. Medicine,2025,"cancer familial aggregation, nasopharyngeal carcinoma, oral microbiome",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Nasopharyngeal squamous cell carcinoma,NA,Healthy controls,Nasopharyngeal Carcinoma (NPC),Untreated patients with Nasopharyngeal Carcinoma primarily identified through a rapid ascertainment network at hospitals within the study area.,496,499,NA,16S,4,Illumina,relative abundances,T-Test,0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure S3a, S3b, Table 1",3 November 2025,YokoC,YokoC,Bar plots for the relative abundance of heritable ASVs (species) and Genera in an independent case-control cohort. T-test with significance p < 0.05.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis",1783272|1239|91061|1385|539738|1378;1783272|1239|91061|1385|539738|1378|1966354;3379134|1224|28216|80840|119060|47670|47671,Complete,KateRasheed
bsdb:39999841/2/2,39999841,case-control,39999841,10.1016/j.xcrm.2025.101979,NA,"Liao Y., Tong X.T., Zhou T., Xue W.Q., Wang T.M., He Y.Q., Zheng M.Q., Jia Y.J., Yang D.W., Wu Y.X., Zheng X.H., Zuo Z.X., Chen M.Y., Liu N. , Jia W.H.",Unveiling familial aggregation of nasopharyngeal carcinoma: Insights from oral microbiome dysbiosis,Cell reports. Medicine,2025,"cancer familial aggregation, nasopharyngeal carcinoma, oral microbiome",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Nasopharyngeal squamous cell carcinoma,NA,Healthy controls,Nasopharyngeal Carcinoma (NPC),Untreated patients with Nasopharyngeal Carcinoma primarily identified through a rapid ascertainment network at hospitals within the study area.,496,499,NA,16S,4,Illumina,relative abundances,T-Test,0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S3a,9 December 2025,YokoC,"YokoC,Tosin",Bar plots for the relative abundance of heritable ASVs (species) and Genera in an independent case-control cohort. T-test with significance p < 0.05.,decreased,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,3384189|32066|203490|203491|203492|848|851,Complete,KateRasheed
bsdb:39999841/3/1,39999841,case-control,39999841,10.1016/j.xcrm.2025.101979,NA,"Liao Y., Tong X.T., Zhou T., Xue W.Q., Wang T.M., He Y.Q., Zheng M.Q., Jia Y.J., Yang D.W., Wu Y.X., Zheng X.H., Zuo Z.X., Chen M.Y., Liu N. , Jia W.H.",Unveiling familial aggregation of nasopharyngeal carcinoma: Insights from oral microbiome dysbiosis,Cell reports. Medicine,2025,"cancer familial aggregation, nasopharyngeal carcinoma, oral microbiome",Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Nasopharyngeal squamous cell carcinoma,NA,Sporadic cases nasopharyngeal carcinoma (NPC),Multiple cases nasopharyngeal carcinoma (NPC),Patients with nasopharyngeal carcinoma (NPC) who come from families with multiple cases of NPC in the first degree or second degree relatives.,101,66,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,Table S9 and Figure S4a,4 November 2025,YokoC,"YokoC,Tosin","Volcano plot showing the significant differential abundant oral ASVs between sporadic
and multiple NPC patients (Familial NPC). Differential abundant taxa were identified by DESeq analysis.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfomicrobiaceae|g__Desulfomicrobium|s__Desulfomicrobium orale,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Lentimicrobiaceae|g__Lentimicrobium|s__Lentimicrobium sp.,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas sp.",3379134|976|117743|200644|49546|1016|45242;3379134|976|117743|200644|49546|1016|44737;3379134|1224|1236|135615|868|2717|2718;1783272|201174|1760|85007|1653|1716|61592;1783272|201174|1760|85007|1653|1716|43768;3379134|200940|3031449|213115|213116|898|132132;3384189|32066|203490|203491|203492|848|851;1783272|1239|91061|1385|539738|1378|1966354;3379134|976|200643|171549|1840213|1840214|2034841;3384189|32066|203490|203491|1129771|32067|157688;1783272|1239|909932|1843489|31977|906|187326;3379134|976|200643|171549|171552|838|28132;3379134|1224|28216|80840|80864|283|34028,Complete,KateRasheed
bsdb:39999841/3/2,39999841,case-control,39999841,10.1016/j.xcrm.2025.101979,NA,"Liao Y., Tong X.T., Zhou T., Xue W.Q., Wang T.M., He Y.Q., Zheng M.Q., Jia Y.J., Yang D.W., Wu Y.X., Zheng X.H., Zuo Z.X., Chen M.Y., Liu N. , Jia W.H.",Unveiling familial aggregation of nasopharyngeal carcinoma: Insights from oral microbiome dysbiosis,Cell reports. Medicine,2025,"cancer familial aggregation, nasopharyngeal carcinoma, oral microbiome",Experiment 3,China,Homo sapiens,Saliva,UBERON:0001836,Nasopharyngeal squamous cell carcinoma,NA,Sporadic cases nasopharyngeal carcinoma (NPC),Multiple cases nasopharyngeal carcinoma (NPC),Patients with nasopharyngeal carcinoma (NPC) who come from families with multiple cases of NPC in the first degree or second degree relatives.,101,66,NA,16S,4,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,"age,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 2,Table S9,9 December 2025,YokoC,"YokoC,Tosin",Volcano plot showing the significant differential abundant oral ASVs between sporadic and multiple NPC patients (Familial NPC). Differential abundant taxa were identified by DESeq analysis.,decreased,NA,NA,Complete,KateRasheed
bsdb:40004140/1/1,40004140,laboratory experiment,40004140,https://doi.org/10.3390/ijms26041676,NA,"Liu L., Zhao Y., Yang W., Han L., Mo X., Sheng J., Tian Y. , Gao X.",Correlations Between Amelioration of Rotenone-Induced Parkinson's Symptoms by <i>Amomum tsaoko</i> Flavonoids and Gut Microbiota in Mice,International journal of molecular sciences,2025,"Bifidobacterium, Desulfovibrio, Faecalibaculum, Lachnospiraceae, Provotellaceae, constipation, gastrointestinal dysfunction, gut barrier, inflammation, movement disorders",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,Combination of Normal chow diet (NCD) and Rotenone gavage (ROT) groups,Amomum tsaoko flavonoid (ATF) group,Mice given 30 mg/kg·BW of rotenone and 50 mg/kg·BW of ATFs.,24,12,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 7D, S1A and S1B",12 April 2025,Tosin,Tosin,"Linear discriminant analysis (LDA) of three groups NCD (normal chow diet), ROT (rotenone gavage), and ATF (Amomum tsaoko flavonoid) groups",increased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Candidatus Izemoplasmatales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Umbribacter|s__Umbribacter vaginalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,p__Rhodophyta|c__Florideophyceae|o__Batrachospermales|f__Batrachospermaceae|g__Paludicola",1783272|544448|31969|186329|2146;1783272|544448|31969|186329;1783272|544448|31969|186332|186333|2086;1783272|1239|186801|186802|3085642;1783272|544448|31969|2975519;1783272|201174|84998|1643822|1643826|3472368|1588753;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730|290054;2763|2806|31370|31371|2729669,Complete,KateRasheed
bsdb:40004140/2/1,40004140,laboratory experiment,40004140,https://doi.org/10.3390/ijms26041676,NA,"Liu L., Zhao Y., Yang W., Han L., Mo X., Sheng J., Tian Y. , Gao X.",Correlations Between Amelioration of Rotenone-Induced Parkinson's Symptoms by <i>Amomum tsaoko</i> Flavonoids and Gut Microbiota in Mice,International journal of molecular sciences,2025,"Bifidobacterium, Desulfovibrio, Faecalibaculum, Lachnospiraceae, Provotellaceae, constipation, gastrointestinal dysfunction, gut barrier, inflammation, movement disorders",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,Combination of Amomum tsaoko flavonoid (ATF) and Rotenone gavage (ROT) groups,Normal chow diet (NCD) group,Mice in this group were administered sterilized ultrapure water (UP water).,24,12,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 7D, S1A and S1B",12 April 2025,Tosin,Tosin,"Linear discriminant analysis (LDA) of three groups NCD (normal chow diet), ROT (rotenone gavage), and ATF (Amomum tsaoko flavonoid) groups",increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Parvibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae",1783272|201174|84992;3379134|976|200643|171549|171550|239759;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3082768|990719|990721;1783272|1239|186801|3082768;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802;1783272|1239|526524|526525|128827|1729679;1783272|201174|84998|84999|84107|1427376;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3082768|990719,Complete,KateRasheed
bsdb:40004140/3/1,40004140,laboratory experiment,40004140,https://doi.org/10.3390/ijms26041676,NA,"Liu L., Zhao Y., Yang W., Han L., Mo X., Sheng J., Tian Y. , Gao X.",Correlations Between Amelioration of Rotenone-Induced Parkinson's Symptoms by <i>Amomum tsaoko</i> Flavonoids and Gut Microbiota in Mice,International journal of molecular sciences,2025,"Bifidobacterium, Desulfovibrio, Faecalibaculum, Lachnospiraceae, Provotellaceae, constipation, gastrointestinal dysfunction, gut barrier, inflammation, movement disorders",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,Combination of Amomum tsaoko flavonoid (ATF) and Normal chow diet (NCD) groups,Rotenone gavage (ROT) group,Mice in this group was given 30 mg/kg·BW of rotenone.,24,12,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 7D, S1A and S1B",13 April 2025,Tosin,Tosin,"Linear discriminant analysis (LDA) of three groups NCD (normal chow diet), ROT (rotenone gavage), and ATF (Amomum tsaoko flavonoid) groups",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum,k__Pseudomonadati|p__Thermodesulfobacteriota",1783272|1239|186801|3085636|186803|1427378;1783272|1239|186801|3085636|186803|572511;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;3379134|200940|3031449;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|3085636;1783272|1239|186801|3085636|186803|248744;1783272|1239|186801|186802|216572;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3082720|543314|35518;3379134|200940,Complete,KateRasheed
bsdb:40004140/4/1,40004140,laboratory experiment,40004140,https://doi.org/10.3390/ijms26041676,NA,"Liu L., Zhao Y., Yang W., Han L., Mo X., Sheng J., Tian Y. , Gao X.",Correlations Between Amelioration of Rotenone-Induced Parkinson's Symptoms by <i>Amomum tsaoko</i> Flavonoids and Gut Microbiota in Mice,International journal of molecular sciences,2025,"Bifidobacterium, Desulfovibrio, Faecalibaculum, Lachnospiraceae, Provotellaceae, constipation, gastrointestinal dysfunction, gut barrier, inflammation, movement disorders",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,Normal chow diet (NCD) group,Rotenone gavage (ROT) group,Mice in this group was given 30 mg/kg·BW of rotenone.,12,12,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 7E-H, Supplementary Figure 1c and 1D",13 April 2025,MyleeeA,MyleeeA,Differential microbial taxa abundant between Rotenone gavage (ROT) group and Normal chow diet (NCD) group.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Pseudomonadati|p__Thermodesulfobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",1783272|1239|186801|3085636|186803|572511;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|877420;1783272|1239|91061|186826|1300;3379134|200940;1783272|1239|186801|3082720|543314|35518;1783272|1239|526524|526525|128827,Complete,KateRasheed
bsdb:40004140/4/2,40004140,laboratory experiment,40004140,https://doi.org/10.3390/ijms26041676,NA,"Liu L., Zhao Y., Yang W., Han L., Mo X., Sheng J., Tian Y. , Gao X.",Correlations Between Amelioration of Rotenone-Induced Parkinson's Symptoms by <i>Amomum tsaoko</i> Flavonoids and Gut Microbiota in Mice,International journal of molecular sciences,2025,"Bifidobacterium, Desulfovibrio, Faecalibaculum, Lachnospiraceae, Provotellaceae, constipation, gastrointestinal dysfunction, gut barrier, inflammation, movement disorders",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,Normal chow diet (NCD) group,Rotenone gavage (ROT) group,Mice in this group was given 30 mg/kg·BW of rotenone.,12,12,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 7E-H, Supplementary Figure 1c and 1D",14 April 2025,Tosin,Tosin,Differential microbial taxa abundant between Rotenone gavage (ROT) group and Normal chow diet (NCD) group.,decreased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Parvibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",1783272|544448|31969|186329|2146;3379134|976|200643|171549|171550|239759;1783272|544448|31969|186332|186333|2086;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|526524|526525|128827|1729679;1783272|201174|84998|84999|84107|1427376;3379134|976|200643|171549|171550,Complete,KateRasheed
bsdb:40004140/5/1,40004140,laboratory experiment,40004140,https://doi.org/10.3390/ijms26041676,NA,"Liu L., Zhao Y., Yang W., Han L., Mo X., Sheng J., Tian Y. , Gao X.",Correlations Between Amelioration of Rotenone-Induced Parkinson's Symptoms by <i>Amomum tsaoko</i> Flavonoids and Gut Microbiota in Mice,International journal of molecular sciences,2025,"Bifidobacterium, Desulfovibrio, Faecalibaculum, Lachnospiraceae, Provotellaceae, constipation, gastrointestinal dysfunction, gut barrier, inflammation, movement disorders",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,Rotenone gavage (ROT) group,Amomum tsaoko flavonoid (ATF) group,Mice given 30 mg/kg·BW of rotenone and 50 mg/kg·BW of ATFs.,12,12,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 7E-H, Supplementary Figure 1c and 1D",14 April 2025,MyleeeA,MyleeeA,Differential microbial taxa abundant between Rotenone gavage (ROT) group and Amonum tsaoko flavonoid (ATF) group.,increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Candidatus Izemoplasmatales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Parvibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,p__Rhodophyta|c__Florideophyceae|o__Batrachospermales|f__Batrachospermaceae|g__Paludicola",1783272|201174;3379134|976|200643|171549|171550|239759;1783272|544448|31969|186332|186333|2086;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|3085642;1783272|544448|31969|2975519;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|186802|216572|216851;1783272|201174|84998|84999|84107|1427376;3379134|976|200643|171549|171550;2763|2806|31370|31371|2729669,Complete,KateRasheed
bsdb:40004140/5/2,40004140,laboratory experiment,40004140,https://doi.org/10.3390/ijms26041676,NA,"Liu L., Zhao Y., Yang W., Han L., Mo X., Sheng J., Tian Y. , Gao X.",Correlations Between Amelioration of Rotenone-Induced Parkinson's Symptoms by <i>Amomum tsaoko</i> Flavonoids and Gut Microbiota in Mice,International journal of molecular sciences,2025,"Bifidobacterium, Desulfovibrio, Faecalibaculum, Lachnospiraceae, Provotellaceae, constipation, gastrointestinal dysfunction, gut barrier, inflammation, movement disorders",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Traditional Chinese medicine type,EFO:0007637,Rotenone gavage (ROT) group,Amomum tsaoko flavonoid (ATF) group,Mice given 30 mg/kg·BW of rotenone and 50 mg/kg·BW of ATFs.,12,12,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 7E-H, Supplementary Figure 1c and 1D",14 April 2025,MyleeeA,MyleeeA,Differential microbial taxa abundant between Rotenone gavage (ROT) group and Amonum tsaoko flavonoid (ATF) group.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Pseudomonadati|p__Thermodesulfobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",1783272|1239|186801|3085636|186803|572511;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|877420;1783272|1239|91061|186826|1300;3379134|200940;1783272|1239|186801|3082720|543314|35518;1783272|1239|526524|526525|128827,Complete,KateRasheed
bsdb:40004140/6/1,40004140,laboratory experiment,40004140,https://doi.org/10.3390/ijms26041676,NA,"Liu L., Zhao Y., Yang W., Han L., Mo X., Sheng J., Tian Y. , Gao X.",Correlations Between Amelioration of Rotenone-Induced Parkinson's Symptoms by <i>Amomum tsaoko</i> Flavonoids and Gut Microbiota in Mice,International journal of molecular sciences,2025,"Bifidobacterium, Desulfovibrio, Faecalibaculum, Lachnospiraceae, Provotellaceae, constipation, gastrointestinal dysfunction, gut barrier, inflammation, movement disorders",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Weight percent,EFO:0002904,Fecal Weight (FW) Decreased,Fecal Weight (FW) Increased,The Fecal weight (FW) of the mice were determined within 6 h,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 8b,14 April 2025,MyleeeA,MyleeeA,Correlations between differential genera and defecation parameters. The color at each point of intersection indicates the value of the r coefficient (n = 8).,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Parvibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes",1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549|171550|239759;1783272|201174|84998|84999|84107|1427376;1783272|1239|186801|186802|186806|1730|290054,Complete,KateRasheed
bsdb:40004140/6/2,40004140,laboratory experiment,40004140,https://doi.org/10.3390/ijms26041676,NA,"Liu L., Zhao Y., Yang W., Han L., Mo X., Sheng J., Tian Y. , Gao X.",Correlations Between Amelioration of Rotenone-Induced Parkinson's Symptoms by <i>Amomum tsaoko</i> Flavonoids and Gut Microbiota in Mice,International journal of molecular sciences,2025,"Bifidobacterium, Desulfovibrio, Faecalibaculum, Lachnospiraceae, Provotellaceae, constipation, gastrointestinal dysfunction, gut barrier, inflammation, movement disorders",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Weight percent,EFO:0002904,Fecal Weight (FW) Decreased,Fecal Weight (FW) Increased,The Fecal weight (FW) of the mice were determined within 6 h,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 8b,14 April 2025,MyleeeA,MyleeeA,Correlations between differential genera and defecation parameters. The color at each point of intersection indicates the value of the r coefficient (n = 8).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",1783272|1239|186801|3082720|543314|35518;1783272|1239|526524|526525|128827,Complete,KateRasheed
bsdb:40004140/7/1,40004140,laboratory experiment,40004140,https://doi.org/10.3390/ijms26041676,NA,"Liu L., Zhao Y., Yang W., Han L., Mo X., Sheng J., Tian Y. , Gao X.",Correlations Between Amelioration of Rotenone-Induced Parkinson's Symptoms by <i>Amomum tsaoko</i> Flavonoids and Gut Microbiota in Mice,International journal of molecular sciences,2025,"Bifidobacterium, Desulfovibrio, Faecalibaculum, Lachnospiraceae, Provotellaceae, constipation, gastrointestinal dysfunction, gut barrier, inflammation, movement disorders",Experiment 7,China,Mus musculus,Feces,UBERON:0001988,Regulation of defecation,GO:2000292,Fecal Number (FN) Decreased,Fecal Number (FN) Increased,The Fecal number (FN) of the mice were determined within 6 h,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 8b,14 April 2025,MyleeeA,MyleeeA,Correlations between differential genera and defecation parameters. The color at each point of intersection indicates the value of the r coefficient (n = 8).,increased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Parvibacter,1783272|201174|84998|84999|84107|1427376,Complete,KateRasheed
bsdb:40004140/7/2,40004140,laboratory experiment,40004140,https://doi.org/10.3390/ijms26041676,NA,"Liu L., Zhao Y., Yang W., Han L., Mo X., Sheng J., Tian Y. , Gao X.",Correlations Between Amelioration of Rotenone-Induced Parkinson's Symptoms by <i>Amomum tsaoko</i> Flavonoids and Gut Microbiota in Mice,International journal of molecular sciences,2025,"Bifidobacterium, Desulfovibrio, Faecalibaculum, Lachnospiraceae, Provotellaceae, constipation, gastrointestinal dysfunction, gut barrier, inflammation, movement disorders",Experiment 7,China,Mus musculus,Feces,UBERON:0001988,Regulation of defecation,GO:2000292,Fecal Number (FN) Decreased,Fecal Number (FN) Increased,The Fecal number (FN) of the mice were determined within 6 h,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 8b,14 April 2025,MyleeeA,MyleeeA,Correlations between differential genera and defecation parameters. The color at each point of intersection indicates the value of the r coefficient (n = 8).,decreased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,1783272|1239|526524|526525|128827,Complete,KateRasheed
bsdb:40004140/8/1,40004140,laboratory experiment,40004140,https://doi.org/10.3390/ijms26041676,NA,"Liu L., Zhao Y., Yang W., Han L., Mo X., Sheng J., Tian Y. , Gao X.",Correlations Between Amelioration of Rotenone-Induced Parkinson's Symptoms by <i>Amomum tsaoko</i> Flavonoids and Gut Microbiota in Mice,International journal of molecular sciences,2025,"Bifidobacterium, Desulfovibrio, Faecalibaculum, Lachnospiraceae, Provotellaceae, constipation, gastrointestinal dysfunction, gut barrier, inflammation, movement disorders",Experiment 8,China,Mus musculus,Feces,UBERON:0001988,Regulation of defecation,GO:2000292,Fecal black stool time (FBST) Decreased,Fecal black stool time (FBST) Increased,High levels of fecal black stool time,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 8B,14 April 2025,Tosin,Tosin,Correlations between differential genera and defecation parameters. The color at each point of intersection indicates the value of the r coefficient (n = 8).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136",1783272|1239|186801|3085636|186803|572511;3379134|200940|3031449|213115|194924|872;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803|877420,Complete,KateRasheed
bsdb:40004140/8/2,40004140,laboratory experiment,40004140,https://doi.org/10.3390/ijms26041676,NA,"Liu L., Zhao Y., Yang W., Han L., Mo X., Sheng J., Tian Y. , Gao X.",Correlations Between Amelioration of Rotenone-Induced Parkinson's Symptoms by <i>Amomum tsaoko</i> Flavonoids and Gut Microbiota in Mice,International journal of molecular sciences,2025,"Bifidobacterium, Desulfovibrio, Faecalibaculum, Lachnospiraceae, Provotellaceae, constipation, gastrointestinal dysfunction, gut barrier, inflammation, movement disorders",Experiment 8,China,Mus musculus,Feces,UBERON:0001988,Regulation of defecation,GO:2000292,Fecal black stool time (FBST) Decreased,Fecal black stool time (FBST) Increased,High levels of fecal black stool time,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 8B,14 April 2025,Tosin,Tosin,Correlations between differential genera and defecation parameters. The color at each point of intersection indicates the value of the r coefficient (n = 8).,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,p__Rhodophyta|c__Florideophyceae|o__Batrachospermales|f__Batrachospermaceae|g__Paludicola,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Parvibacter",1783272|201174|1760|85004|31953|1678;1783272|1239|526524|526525|128827|1729679;2763|2806|31370|31371|2729669;1783272|201174|84998|84999|84107|1427376,Complete,KateRasheed
bsdb:40004140/9/1,40004140,laboratory experiment,40004140,https://doi.org/10.3390/ijms26041676,NA,"Liu L., Zhao Y., Yang W., Han L., Mo X., Sheng J., Tian Y. , Gao X.",Correlations Between Amelioration of Rotenone-Induced Parkinson's Symptoms by <i>Amomum tsaoko</i> Flavonoids and Gut Microbiota in Mice,International journal of molecular sciences,2025,"Bifidobacterium, Desulfovibrio, Faecalibaculum, Lachnospiraceae, Provotellaceae, constipation, gastrointestinal dysfunction, gut barrier, inflammation, movement disorders",Experiment 9,China,Mus musculus,Feces,UBERON:0001988,Regulation of defecation,GO:2000292,Fecal water content (FWC) Decreased,Fecal water content (FWC) Increased,High levels of fecal water content,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 8B,14 April 2025,Tosin,Tosin,Correlations between differential genera and defecation parameters. The color at each point of intersection indicates the value of the r coefficient (n = 8).,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum",1783272|201174|1760|85004|31953|1678;1783272|1239|526524|526525|128827|1729679,Complete,KateRasheed
bsdb:40004140/9/2,40004140,laboratory experiment,40004140,https://doi.org/10.3390/ijms26041676,NA,"Liu L., Zhao Y., Yang W., Han L., Mo X., Sheng J., Tian Y. , Gao X.",Correlations Between Amelioration of Rotenone-Induced Parkinson's Symptoms by <i>Amomum tsaoko</i> Flavonoids and Gut Microbiota in Mice,International journal of molecular sciences,2025,"Bifidobacterium, Desulfovibrio, Faecalibaculum, Lachnospiraceae, Provotellaceae, constipation, gastrointestinal dysfunction, gut barrier, inflammation, movement disorders",Experiment 9,China,Mus musculus,Feces,UBERON:0001988,Regulation of defecation,GO:2000292,Fecal water content (FWC) Decreased,Fecal water content (FWC) Increased,High levels of fecal water content,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 8B,14 April 2025,Tosin,Tosin,Correlations between differential genera and defecation parameters. The color at each point of intersection indicates the value of the r coefficient (n = 8).,decreased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136",3379134|200940|3031449|213115|194924|872;1783272|1239|526524|526525|128827;1783272|1239|186801|3085636|186803|877420,Complete,KateRasheed
bsdb:40004140/10/1,40004140,laboratory experiment,40004140,https://doi.org/10.3390/ijms26041676,NA,"Liu L., Zhao Y., Yang W., Han L., Mo X., Sheng J., Tian Y. , Gao X.",Correlations Between Amelioration of Rotenone-Induced Parkinson's Symptoms by <i>Amomum tsaoko</i> Flavonoids and Gut Microbiota in Mice,International journal of molecular sciences,2025,"Bifidobacterium, Desulfovibrio, Faecalibaculum, Lachnospiraceae, Provotellaceae, constipation, gastrointestinal dysfunction, gut barrier, inflammation, movement disorders",Experiment 10,China,Mus musculus,Feces,UBERON:0001988,Increased intestinal transit time,HP:0410204,Gastrointestinal transit rate Decreased,Gastrointestinal transit rate Increased,High levels of gastrointestinal transit rate,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 8B,14 April 2025,Tosin,Tosin,Correlations between differential genera and defecation parameters. The color at each point of intersection indicates the value of the r coefficient (n = 8).,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,KateRasheed
bsdb:40004140/10/2,40004140,laboratory experiment,40004140,https://doi.org/10.3390/ijms26041676,NA,"Liu L., Zhao Y., Yang W., Han L., Mo X., Sheng J., Tian Y. , Gao X.",Correlations Between Amelioration of Rotenone-Induced Parkinson's Symptoms by <i>Amomum tsaoko</i> Flavonoids and Gut Microbiota in Mice,International journal of molecular sciences,2025,"Bifidobacterium, Desulfovibrio, Faecalibaculum, Lachnospiraceae, Provotellaceae, constipation, gastrointestinal dysfunction, gut barrier, inflammation, movement disorders",Experiment 10,China,Mus musculus,Feces,UBERON:0001988,Increased intestinal transit time,HP:0410204,Gastrointestinal transit rate Decreased,Gastrointestinal transit rate Increased,High levels of gastrointestinal transit rate,NA,NA,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 8B,14 April 2025,Tosin,Tosin,Correlations between differential genera and defecation parameters. The color at each point of intersection indicates the value of the r coefficient (n = 8).,decreased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas",3379134|200940|3031449|213115|194924|872;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|1392389,Complete,KateRasheed
bsdb:40004729/1/1,40004729,case-control,40004729,10.3390/jcm14041198,NA,"Sánchez-Pellicer P., Álamo-Marzo J.M., Martínez-Villaescusa M., Núñez-Delegido E., Such-Ronda J.F., Huertas-López F., Serrano-López E.M., Martínez-Moreno D. , Navarro-López V.",Comparative Analysis of Gut Microbiota in Patients with Irritable Bowel Syndrome and Healthy Controls,Journal of clinical medicine,2025,"functional colonic diseases, gastrointestinal microbiome, high-throughput nucleotide sequencing, irritable bowel syndrome, microbiota",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS patients,"25 adults diagnosed with IBS according to Rome IV, mostly IBS-D, compared with 103 healthy controls from the same community.",103,24,"Antibiotics excluded 2 weeks prior; probiotics excluded 2 months prior. Controls excluded if recent illness, chronic disease, or continuous medication.",16S,34,Illumina,relative abundances,"LEfSe,Random Forest Analysis",0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"LEfSe (Figure 10, genus-level biomarkers)",29 November 2025,Aqc576444,Aqc576444,Bacteroides significantly increased in IBS patients compared with healthy controls (LEfSe LDA > 3; adjusted p < 0.05).,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,NA
bsdb:40004729/1/2,40004729,case-control,40004729,10.3390/jcm14041198,NA,"Sánchez-Pellicer P., Álamo-Marzo J.M., Martínez-Villaescusa M., Núñez-Delegido E., Such-Ronda J.F., Huertas-López F., Serrano-López E.M., Martínez-Moreno D. , Navarro-López V.",Comparative Analysis of Gut Microbiota in Patients with Irritable Bowel Syndrome and Healthy Controls,Journal of clinical medicine,2025,"functional colonic diseases, gastrointestinal microbiome, high-throughput nucleotide sequencing, irritable bowel syndrome, microbiota",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS patients,"25 adults diagnosed with IBS according to Rome IV, mostly IBS-D, compared with 103 healthy controls from the same community.",103,24,"Antibiotics excluded 2 weeks prior; probiotics excluded 2 months prior. Controls excluded if recent illness, chronic disease, or continuous medication.",16S,34,Illumina,relative abundances,"LEfSe,Random Forest Analysis",0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,LEfSe (Figure 10,29 November 2025,Aqc576444,Aqc576444,Faecalibacterium significantly decreased in IBS patients compared with healthy controls (LEfSe LDA > 3; adjusted p < 0.05),decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,1783272|1239|186801|186802|216572|216851,Complete,NA
bsdb:40004729/1/3,40004729,case-control,40004729,10.3390/jcm14041198,NA,"Sánchez-Pellicer P., Álamo-Marzo J.M., Martínez-Villaescusa M., Núñez-Delegido E., Such-Ronda J.F., Huertas-López F., Serrano-López E.M., Martínez-Moreno D. , Navarro-López V.",Comparative Analysis of Gut Microbiota in Patients with Irritable Bowel Syndrome and Healthy Controls,Journal of clinical medicine,2025,"functional colonic diseases, gastrointestinal microbiome, high-throughput nucleotide sequencing, irritable bowel syndrome, microbiota",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS patients,"25 adults diagnosed with IBS according to Rome IV, mostly IBS-D, compared with 103 healthy controls from the same community.",103,24,"Antibiotics excluded 2 weeks prior; probiotics excluded 2 months prior. Controls excluded if recent illness, chronic disease, or continuous medication.",16S,34,Illumina,relative abundances,"LEfSe,Random Forest Analysis",0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 3,LEfSe (Figure 10 — genus-level biomarkers),29 November 2025,Aqc576444,Aqc576444,“Blautia was significantly increased in IBS patients compared with healthy controls (LEfSe LDA > 3; adjusted p < 0.05).”,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,NA
bsdb:40004729/1/4,40004729,case-control,40004729,10.3390/jcm14041198,NA,"Sánchez-Pellicer P., Álamo-Marzo J.M., Martínez-Villaescusa M., Núñez-Delegido E., Such-Ronda J.F., Huertas-López F., Serrano-López E.M., Martínez-Moreno D. , Navarro-López V.",Comparative Analysis of Gut Microbiota in Patients with Irritable Bowel Syndrome and Healthy Controls,Journal of clinical medicine,2025,"functional colonic diseases, gastrointestinal microbiome, high-throughput nucleotide sequencing, irritable bowel syndrome, microbiota",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS patients,"25 adults diagnosed with IBS according to Rome IV, mostly IBS-D, compared with 103 healthy controls from the same community.",103,24,"Antibiotics excluded 2 weeks prior; probiotics excluded 2 months prior. Controls excluded if recent illness, chronic disease, or continuous medication.",16S,34,Illumina,relative abundances,"LEfSe,Random Forest Analysis",0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 4,LEfSe (Figure 10),29 November 2025,Aqc576444,Aqc576444,"Blautia increased in IBS patients vs controls (LDA > 3, p < 0.05).",increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,1783272|1239|186801|3085636|186803|572511,Complete,NA
bsdb:40004729/1/5,40004729,case-control,40004729,10.3390/jcm14041198,NA,"Sánchez-Pellicer P., Álamo-Marzo J.M., Martínez-Villaescusa M., Núñez-Delegido E., Such-Ronda J.F., Huertas-López F., Serrano-López E.M., Martínez-Moreno D. , Navarro-López V.",Comparative Analysis of Gut Microbiota in Patients with Irritable Bowel Syndrome and Healthy Controls,Journal of clinical medicine,2025,"functional colonic diseases, gastrointestinal microbiome, high-throughput nucleotide sequencing, irritable bowel syndrome, microbiota",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS patients,"25 adults diagnosed with IBS according to Rome IV, mostly IBS-D, compared with 103 healthy controls from the same community.",103,24,"Antibiotics excluded 2 weeks prior; probiotics excluded 2 months prior. Controls excluded if recent illness, chronic disease, or continuous medication.",16S,34,Illumina,relative abundances,"LEfSe,Random Forest Analysis",0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 5,LEfSe (Figure 10),29 November 2025,Aqc576444,Aqc576444,"Faecalibacterium decreased in IBS patients vs controls (LDA > 3, p < 0.05).",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,1783272|1239|186801|186802|216572|216851,Complete,NA
bsdb:40008452/1/1,40008452,laboratory experiment,40008452,https://doi.org/10.1080/19490976.2025.2471015,NA,"Chen A., Teng C., Wei J., Wu X., Zhang H., Chen P., Cai D., Qian H., Zhu H., Zheng X. , Chen X.",Gut microbial dysbiosis exacerbates long-term cognitive impairments by promoting intestinal dysfunction and neuroinflammation following neonatal hypoxia-ischemia,Gut microbes,2025,"Neonatal hypoxic-ischemic brain damage, cognitive impairments, fecal microbiota transplantation, microbiota-gut-brain axis, neuroinflammation",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Brain hypoxia-Ischemia,EFO:1000846,Sham Group,HI (hypoxic-ischemic) Group,Neonatal rats that underwent hypoxia-ischema (HI) to induce brain injury,8,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 2I and 2J,26 March 2025,IsaacImitini,"IsaacImitini,Tosin",Taxonomic significant differences in gut microbiota between rats in sham group and HI (hypoxic-ischemic) group using Lefse analysis,increased,"k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae",3379134|200930|68337|191393|191394;3379134|200930|68337|191393;3379134|200930|68337;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3379134|1224|1236;1783272|1239|91061|186826|33958;3379134|976|200643|171549|171552;1783272|1239|91061|186826|1300;3379134|1224|1236|135623|641,Complete,Svetlana up
bsdb:40008452/1/2,40008452,laboratory experiment,40008452,https://doi.org/10.1080/19490976.2025.2471015,NA,"Chen A., Teng C., Wei J., Wu X., Zhang H., Chen P., Cai D., Qian H., Zhu H., Zheng X. , Chen X.",Gut microbial dysbiosis exacerbates long-term cognitive impairments by promoting intestinal dysfunction and neuroinflammation following neonatal hypoxia-ischemia,Gut microbes,2025,"Neonatal hypoxic-ischemic brain damage, cognitive impairments, fecal microbiota transplantation, microbiota-gut-brain axis, neuroinflammation",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Brain hypoxia-Ischemia,EFO:1000846,Sham Group,HI (hypoxic-ischemic) Group,Neonatal rats that underwent hypoxia-ischema (HI) to induce brain injury,8,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 2I and 2J,27 March 2025,IsaacImitini,"IsaacImitini,Tosin",Taxonomic significant differences in gut microbiota between rats in sham group and HI (hypoxic-ischemic) group using LeFse analysis,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Pseudomonadati|p__Acidobacteriota|c__Terriglobia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae",3379134|74201|203494|48461|1647988;3379134|976|200643|171549|815;1783272|1239|91061|186826|81852;3379134|57723|204432;3379134|74201|203494|48461;3379134|74201|203494;3379134|256845|1313211|278082|255528;3379134|29547|3031852|213849|72293;1783272|1239|91061|1385|186818,Complete,Svetlana up
bsdb:40008452/2/1,40008452,laboratory experiment,40008452,https://doi.org/10.1080/19490976.2025.2471015,NA,"Chen A., Teng C., Wei J., Wu X., Zhang H., Chen P., Cai D., Qian H., Zhu H., Zheng X. , Chen X.",Gut microbial dysbiosis exacerbates long-term cognitive impairments by promoting intestinal dysfunction and neuroinflammation following neonatal hypoxia-ischemia,Gut microbes,2025,"Neonatal hypoxic-ischemic brain damage, cognitive impairments, fecal microbiota transplantation, microbiota-gut-brain axis, neuroinflammation",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Brain hypoxia-Ischemia,EFO:1000846,Sham group,HI (hypoxic-ischemic) group,Neonatal rats that underwent hypoxia-ischema (HI) to induce brain injury,8,8,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 2G and Figure 2K-O,27 March 2025,IsaacImitini,"IsaacImitini,Tosin",Relative abundance of significant differential taxa between Sham and HI (hypoxic ischemia) groups,increased,"k__Pseudomonadati|p__Pseudomonadota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",3379134|1224;3384189|32066|203490|203491|203492;3379134|1224|1236|91347|543;3379134|976|200643|171549|171552,Complete,Svetlana up
bsdb:40008452/2/2,40008452,laboratory experiment,40008452,https://doi.org/10.1080/19490976.2025.2471015,NA,"Chen A., Teng C., Wei J., Wu X., Zhang H., Chen P., Cai D., Qian H., Zhu H., Zheng X. , Chen X.",Gut microbial dysbiosis exacerbates long-term cognitive impairments by promoting intestinal dysfunction and neuroinflammation following neonatal hypoxia-ischemia,Gut microbes,2025,"Neonatal hypoxic-ischemic brain damage, cognitive impairments, fecal microbiota transplantation, microbiota-gut-brain axis, neuroinflammation",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,Brain hypoxia-Ischemia,EFO:1000846,Sham group,HI (hypoxic-ischemic) group,Neonatal rats that underwent hypoxia-ischema (HI) to induce brain injury,8,8,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 2G and Figure 2K-O,27 March 2025,IsaacImitini,"IsaacImitini,Tosin",Relative abundance of significant differential taxa between Sham and HI (hypoxic ischemia) groups,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae",1783272|1239|91061|186826|81852;3379134|74201|203494|48461|1647988,Complete,Svetlana up
bsdb:40008452/3/1,40008452,laboratory experiment,40008452,https://doi.org/10.1080/19490976.2025.2471015,NA,"Chen A., Teng C., Wei J., Wu X., Zhang H., Chen P., Cai D., Qian H., Zhu H., Zheng X. , Chen X.",Gut microbial dysbiosis exacerbates long-term cognitive impairments by promoting intestinal dysfunction and neuroinflammation following neonatal hypoxia-ischemia,Gut microbes,2025,"Neonatal hypoxic-ischemic brain damage, cognitive impairments, fecal microbiota transplantation, microbiota-gut-brain axis, neuroinflammation",Experiment 3,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Sham + Sham FMT (fecal microbiota transplantation) group,Sham + HI (hypoxic-ischemic) FMT (fecal microbiota transplantation) group,Sham group and HI (hypoxic-ischemic) donor rats who transferred fecal microbiota to sham group.,NA,NA,NA,PCR,NA,Illumina,relative abundances,T-Test,0.05,FALSE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7B,17 April 2025,Tosin,Tosin,Quantification of f_Enterobacteriaceae and f_Akkermansiaceae in fecal samples between [Sham + Sham FMT (fecal microbiota transplantation) group and Sham + HI (hypoxic-ischemic) FMT (fecal microbiota transplantation) group],increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,Svetlana up
bsdb:40008452/3/2,40008452,laboratory experiment,40008452,https://doi.org/10.1080/19490976.2025.2471015,NA,"Chen A., Teng C., Wei J., Wu X., Zhang H., Chen P., Cai D., Qian H., Zhu H., Zheng X. , Chen X.",Gut microbial dysbiosis exacerbates long-term cognitive impairments by promoting intestinal dysfunction and neuroinflammation following neonatal hypoxia-ischemia,Gut microbes,2025,"Neonatal hypoxic-ischemic brain damage, cognitive impairments, fecal microbiota transplantation, microbiota-gut-brain axis, neuroinflammation",Experiment 3,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Sham + Sham FMT (fecal microbiota transplantation) group,Sham + HI (hypoxic-ischemic) FMT (fecal microbiota transplantation) group,Sham group and HI (hypoxic-ischemic) donor rats who transferred fecal microbiota to sham group.,NA,NA,NA,PCR,NA,Illumina,relative abundances,T-Test,0.05,FALSE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 7C,17 April 2025,Tosin,Tosin,Quantification of f_Enterobacteriaceae and f_Akkermansiaceae in fecal samples between [Sham + Sham FMT (fecal microbiota transplantation) group and Sham + HI (hypoxic-ischemic) FMT (fecal microbiota transplantation) group],decreased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,3379134|74201|203494|48461|1647988,Complete,Svetlana up
bsdb:40008452/4/1,40008452,laboratory experiment,40008452,https://doi.org/10.1080/19490976.2025.2471015,NA,"Chen A., Teng C., Wei J., Wu X., Zhang H., Chen P., Cai D., Qian H., Zhu H., Zheng X. , Chen X.",Gut microbial dysbiosis exacerbates long-term cognitive impairments by promoting intestinal dysfunction and neuroinflammation following neonatal hypoxia-ischemia,Gut microbes,2025,"Neonatal hypoxic-ischemic brain damage, cognitive impairments, fecal microbiota transplantation, microbiota-gut-brain axis, neuroinflammation",Experiment 4,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,HI (hypoxic-ischemic) + Sham FMT (fecal microbiota transplantation) group,HI (hypoxic-ischemic) + HI (hypoxic-ischemic) FMT (fecal microbiota transplantation) group,HI (hypoxic-ischemic) group recipient rats who received fecal microbiota from HI group and sham group donor rats.,NA,NA,NA,PCR,NA,Illumina,relative abundances,T-Test,0.05,FALSE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7B,17 April 2025,Tosin,Tosin,Quantification of f_Enterobacteriaceae and f_Akkermansiaceae in fecal samples between [HI (hypoxic-ischemic) + Sham FMT (fecal microbiota transplantation) and HI (hypoxic-ischemic) + HI (hypoxic-ischemic) FMT (fecal microbiota transplantation) groups].,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,Svetlana up
bsdb:40008452/4/2,40008452,laboratory experiment,40008452,https://doi.org/10.1080/19490976.2025.2471015,NA,"Chen A., Teng C., Wei J., Wu X., Zhang H., Chen P., Cai D., Qian H., Zhu H., Zheng X. , Chen X.",Gut microbial dysbiosis exacerbates long-term cognitive impairments by promoting intestinal dysfunction and neuroinflammation following neonatal hypoxia-ischemia,Gut microbes,2025,"Neonatal hypoxic-ischemic brain damage, cognitive impairments, fecal microbiota transplantation, microbiota-gut-brain axis, neuroinflammation",Experiment 4,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,HI (hypoxic-ischemic) + Sham FMT (fecal microbiota transplantation) group,HI (hypoxic-ischemic) + HI (hypoxic-ischemic) FMT (fecal microbiota transplantation) group,HI (hypoxic-ischemic) group recipient rats who received fecal microbiota from HI group and sham group donor rats.,NA,NA,NA,PCR,NA,Illumina,relative abundances,T-Test,0.05,FALSE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 7C,17 April 2025,Tosin,Tosin,Quantification of f_Enterobacteriaceae and f_Akkermansiaceae in fecal samples between [HI (hypoxic-ischemic) + Sham FMT (fecal microbiota transplantation) and HI (hypoxic-ischemic) + HI (hypoxic-ischemic) FMT (fecal microbiota transplantation) groups].,decreased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,3379134|74201|203494|48461|1647988,Complete,Svetlana up
bsdb:40008452/5/1,40008452,laboratory experiment,40008452,https://doi.org/10.1080/19490976.2025.2471015,NA,"Chen A., Teng C., Wei J., Wu X., Zhang H., Chen P., Cai D., Qian H., Zhu H., Zheng X. , Chen X.",Gut microbial dysbiosis exacerbates long-term cognitive impairments by promoting intestinal dysfunction and neuroinflammation following neonatal hypoxia-ischemia,Gut microbes,2025,"Neonatal hypoxic-ischemic brain damage, cognitive impairments, fecal microbiota transplantation, microbiota-gut-brain axis, neuroinflammation",Experiment 5,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,HI (hypoxic-ischemic) + HI (hypoxic-ischemic) FMT (fecal microbiota transplantation) group,HI (hypoxic-ischemic) + DEX (dexamethasone)  FMT (fecal microbiota transplantation) group,"The rats in the HI+DEX (hypoxic-ischemic + dexamethasone) group were administered (dexamethasone) DEX (ST1254, beyotime, China) orally at a dosage of 1 mg/kg daily from the 7th postnatal day to the 3rd day after HI insult.",NA,NA,NA,PCR,NA,Illumina,relative abundances,T-Test,0.05,FALSE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 10C,17 April 2025,Tosin,Tosin,Quantification of f_Enterobacteriaceae and f_Akkermansiaceae in fecal samples between [HI (hypoxic-ischemic) + HI (hypoxic-ischemic) FMT (fecal microbiota transplantation and HI (hypoxic-ischemic) + DEX (dexamethasone) FMT (fecal microbiota transplantation) groups].,increased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,3379134|74201|203494|48461|1647988,Complete,Svetlana up
bsdb:40008452/5/2,40008452,laboratory experiment,40008452,https://doi.org/10.1080/19490976.2025.2471015,NA,"Chen A., Teng C., Wei J., Wu X., Zhang H., Chen P., Cai D., Qian H., Zhu H., Zheng X. , Chen X.",Gut microbial dysbiosis exacerbates long-term cognitive impairments by promoting intestinal dysfunction and neuroinflammation following neonatal hypoxia-ischemia,Gut microbes,2025,"Neonatal hypoxic-ischemic brain damage, cognitive impairments, fecal microbiota transplantation, microbiota-gut-brain axis, neuroinflammation",Experiment 5,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,HI (hypoxic-ischemic) + HI (hypoxic-ischemic) FMT (fecal microbiota transplantation) group,HI (hypoxic-ischemic) + DEX (dexamethasone)  FMT (fecal microbiota transplantation) group,"The rats in the HI+DEX (hypoxic-ischemic + dexamethasone) group were administered (dexamethasone) DEX (ST1254, beyotime, China) orally at a dosage of 1 mg/kg daily from the 7th postnatal day to the 3rd day after HI insult.",NA,NA,NA,PCR,NA,Illumina,relative abundances,T-Test,0.05,FALSE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 10B,17 April 2025,Tosin,Tosin,Quantification of f_Enterobacteriaceae and f_Akkermansiaceae in fecal samples between [HI (hypoxic-ischemic) + HI (hypoxic-ischemic) FMT (fecal microbiota transplantation and HI (hypoxic-ischemic) + DEX (dexamethasone)  FMT (fecal microbiota transplantation) groups].,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,Svetlana up
bsdb:40008452/6/1,40008452,laboratory experiment,40008452,https://doi.org/10.1080/19490976.2025.2471015,NA,"Chen A., Teng C., Wei J., Wu X., Zhang H., Chen P., Cai D., Qian H., Zhu H., Zheng X. , Chen X.",Gut microbial dysbiosis exacerbates long-term cognitive impairments by promoting intestinal dysfunction and neuroinflammation following neonatal hypoxia-ischemia,Gut microbes,2025,"Neonatal hypoxic-ischemic brain damage, cognitive impairments, fecal microbiota transplantation, microbiota-gut-brain axis, neuroinflammation",Experiment 6,China,Rattus norvegicus,Feces,UBERON:0001988,Brain hypoxia-Ischemia,EFO:1000846,Sham Group,HI (hypoxic-ischemic) Group,Neonatal rats that underwent hypoxia-ischema (HI) to induce brain injury,8,8,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure S3a,17 April 2025,Tosin,Tosin,"The effects of oral DEX (dexamethasone) treatment on the gut microbiota in the neonatal HIBD rats.
Quantification of f_Enterobacteriaceae and f_Akkermansiaceae in the fecal samples between Sham and HI (hypoxic-ischemic) Groups.",increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,Svetlana up
bsdb:40008452/6/2,40008452,laboratory experiment,40008452,https://doi.org/10.1080/19490976.2025.2471015,NA,"Chen A., Teng C., Wei J., Wu X., Zhang H., Chen P., Cai D., Qian H., Zhu H., Zheng X. , Chen X.",Gut microbial dysbiosis exacerbates long-term cognitive impairments by promoting intestinal dysfunction and neuroinflammation following neonatal hypoxia-ischemia,Gut microbes,2025,"Neonatal hypoxic-ischemic brain damage, cognitive impairments, fecal microbiota transplantation, microbiota-gut-brain axis, neuroinflammation",Experiment 6,China,Rattus norvegicus,Feces,UBERON:0001988,Brain hypoxia-Ischemia,EFO:1000846,Sham Group,HI (hypoxic-ischemic) Group,Neonatal rats that underwent hypoxia-ischema (HI) to induce brain injury,8,8,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure S3b,17 April 2025,Tosin,Tosin,"The effects of oral DEX treatment on the gut microbiota in the neonatal HIBD rats.
Quantification of f_Enterobacteriaceae and f_Akkermansiaceae in the fecal samples between Sham and HI (hypoxic-ischemic) Groups.",decreased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,3379134|74201|203494|48461|1647988,Complete,Svetlana up
bsdb:40008452/7/1,40008452,laboratory experiment,40008452,https://doi.org/10.1080/19490976.2025.2471015,NA,"Chen A., Teng C., Wei J., Wu X., Zhang H., Chen P., Cai D., Qian H., Zhu H., Zheng X. , Chen X.",Gut microbial dysbiosis exacerbates long-term cognitive impairments by promoting intestinal dysfunction and neuroinflammation following neonatal hypoxia-ischemia,Gut microbes,2025,"Neonatal hypoxic-ischemic brain damage, cognitive impairments, fecal microbiota transplantation, microbiota-gut-brain axis, neuroinflammation",Experiment 7,China,Rattus norvegicus,Feces,UBERON:0001988,Brain hypoxia-Ischemia,EFO:1000846,HI (hypoxic-ischemic) group,HI (hypoxic-ischemic) + DEX (dexamethasone) groups,"The rats in the HI+DEX (hypoxic-ischemic + dexamethasone) group were administered (dexamethasone) DEX (ST1254, beyotime, China) orally at a dosage of 1 mg/kg daily from the 7th postnatal day to the 3rd day after HI insult.",8,8,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S3b,17 April 2025,Tosin,Tosin,The effects of oral DEX treatment on the gut microbiota in the neonatal HIBD rats. Quantification of f_Enterobacteriaceae and f_Akkermansiaceae in the fecal samples between HI (hypoxic-ischemic) and HI + DEX (hypoxic-ischemic + dexamethasone) groups.,increased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,3379134|74201|203494|48461|1647988,Complete,Svetlana up
bsdb:40008452/7/2,40008452,laboratory experiment,40008452,https://doi.org/10.1080/19490976.2025.2471015,NA,"Chen A., Teng C., Wei J., Wu X., Zhang H., Chen P., Cai D., Qian H., Zhu H., Zheng X. , Chen X.",Gut microbial dysbiosis exacerbates long-term cognitive impairments by promoting intestinal dysfunction and neuroinflammation following neonatal hypoxia-ischemia,Gut microbes,2025,"Neonatal hypoxic-ischemic brain damage, cognitive impairments, fecal microbiota transplantation, microbiota-gut-brain axis, neuroinflammation",Experiment 7,China,Rattus norvegicus,Feces,UBERON:0001988,Brain hypoxia-Ischemia,EFO:1000846,HI (hypoxic-ischemic) group,HI (hypoxic-ischemic) + DEX (dexamethasone) groups,"The rats in the HI+DEX (hypoxic-ischemic + dexamethasone) group were administered (dexamethasone) DEX (ST1254, beyotime, China) orally at a dosage of 1 mg/kg daily from the 7th postnatal day to the 3rd day after HI insult.",8,8,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S3a,17 April 2025,Tosin,Tosin,The effects of oral DEX treatment on the gut microbiota in the neonatal HIBD rats. Quantification of f_Enterobacteriaceae and f_Akkermansiaceae in the fecal samples between HI (hypoxic-ischemic) and HI + DEX (hypoxic-ischemic + HI (Groups.,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,Svetlana up
bsdb:40013780/1/1,40013780,meta-analysis,40013780,10.1128/spectrum.00852-24,NA,"Wang Z., Chen Y., Li H., Yue Y. , Yu H.",Exploring oral microbiome in oral squamous cell carcinoma across environment-associated sample types,Microbiology spectrum,2025,"16S rRNA, meta-analysis, oncogenesis, oral microbiome, oral squamous cell carcinoma",Experiment 1,"China,Saudi Arabia,Sri Lanka,Yemen,India",Homo sapiens,Oral cavity,UBERON:0000167,Oral squamous cell carcinoma,EFO:0000199,NAT (Normal Adjacent Tissue),Cancer group,This group consists of samples from individuals diagnosed with oral squamous cell carcinoma (OSCC),78,166,NA,16S,4,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,geographic area,decreased,decreased,NA,NA,NA,decreased,Signature 1,Fig. 4E,29 March 2025,Francisca,"Francisca,Joiejoie",Relative abundance of significantly different bacterial genera between pairwise comparisons of the phenotypes in Bios samples.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Anoxybacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|91061|1385|3120669|150247;1783272|1239|91061|1385|186817|1386;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485;1783272|201174|84998|84999|84107|102106;1783272|1239|91061|186826|186828|117563;1783272|1239|909932|1843489|31977|906;3379134|1224|28216|206351|481;3379134|1224|1236|91347|1903411|613;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:40013780/2/1,40013780,meta-analysis,40013780,10.1128/spectrum.00852-24,NA,"Wang Z., Chen Y., Li H., Yue Y. , Yu H.",Exploring oral microbiome in oral squamous cell carcinoma across environment-associated sample types,Microbiology spectrum,2025,"16S rRNA, meta-analysis, oncogenesis, oral microbiome, oral squamous cell carcinoma",Experiment 2,"China,India,Saudi Arabia,Sri Lanka,Yemen",Homo sapiens,Oral cavity,UBERON:0000167,Oral squamous cell carcinoma,EFO:0000199,NAT (Normal Adjacent Tissue),FEP (Fibroepithelial polyp),This group refers to a benign oral mucosal lesion characterized by fibrous connective tissue overgrowth.,78,26,NA,16S,4,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,geographic area,decreased,decreased,NA,NA,NA,decreased,Signature 1,Fig. 4E,29 March 2025,Francisca,"Francisca,Joiejoie",Relative abundance of significantly different bacterial genera between pairwise comparisons of the phenotypes in Bios samples.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:40013780/2/2,40013780,meta-analysis,40013780,10.1128/spectrum.00852-24,NA,"Wang Z., Chen Y., Li H., Yue Y. , Yu H.",Exploring oral microbiome in oral squamous cell carcinoma across environment-associated sample types,Microbiology spectrum,2025,"16S rRNA, meta-analysis, oncogenesis, oral microbiome, oral squamous cell carcinoma",Experiment 2,"China,India,Saudi Arabia,Sri Lanka,Yemen",Homo sapiens,Oral cavity,UBERON:0000167,Oral squamous cell carcinoma,EFO:0000199,NAT (Normal Adjacent Tissue),FEP (Fibroepithelial polyp),This group refers to a benign oral mucosal lesion characterized by fibrous connective tissue overgrowth.,78,26,NA,16S,4,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,geographic area,decreased,decreased,NA,NA,NA,decreased,Signature 2,Fig. 4E,29 March 2025,Francisca,"Francisca,Joiejoie",Relative abundance of significantly different bacterial genera between pairwise comparisons of the phenotypes in Bios samples.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|1239|909932|1843489|31977|39948;1783272|1239|91061|1385|539738|1378;1783272|201174|1760|1643682|85030;1783272|1239|186801|3085636|186803|43994;1783272|1239|186801|3085636|186803|265975;1783272|1239|909932|1843488|909930|33024;3379134|1224|1236|72274|135621;1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:40013780/3/1,40013780,meta-analysis,40013780,10.1128/spectrum.00852-24,NA,"Wang Z., Chen Y., Li H., Yue Y. , Yu H.",Exploring oral microbiome in oral squamous cell carcinoma across environment-associated sample types,Microbiology spectrum,2025,"16S rRNA, meta-analysis, oncogenesis, oral microbiome, oral squamous cell carcinoma",Experiment 3,"China,India,Saudi Arabia,Sri Lanka,Yemen",Homo sapiens,Oral cavity,UBERON:0000167,Oral squamous cell carcinoma,EFO:0000199,FEP,Cancer,This group consists of samples from individuals diagnosed with oral squamous cell carcinoma (OSCC),26,166,NA,16S,4,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,geographic area,unchanged,increased,NA,NA,NA,increased,Signature 1,Fig. 4E,29 March 2025,Joiejoie,Joiejoie,Relative abundance of significantly different bacterial genera between pairwise comparisons of the phenotypes in Bios samples.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|526524|526525|128827|118747;3379134|976|117743|200644|49546|1016;3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:40013780/3/2,40013780,meta-analysis,40013780,10.1128/spectrum.00852-24,NA,"Wang Z., Chen Y., Li H., Yue Y. , Yu H.",Exploring oral microbiome in oral squamous cell carcinoma across environment-associated sample types,Microbiology spectrum,2025,"16S rRNA, meta-analysis, oncogenesis, oral microbiome, oral squamous cell carcinoma",Experiment 3,"China,India,Saudi Arabia,Sri Lanka,Yemen",Homo sapiens,Oral cavity,UBERON:0000167,Oral squamous cell carcinoma,EFO:0000199,FEP,Cancer,This group consists of samples from individuals diagnosed with oral squamous cell carcinoma (OSCC),26,166,NA,16S,4,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,geographic area,unchanged,increased,NA,NA,NA,increased,Signature 2,Fig. 4E,29 March 2025,Joiejoie,Joiejoie,Relative abundance of significantly different bacterial genera between pairwise comparisons of the phenotypes in Bios samples.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia",1783272|1239|909932|909929|1843491|158846;33090|35493|3398|72025|3803|3814|508215,Complete,Svetlana up
bsdb:40013832/1/1,40013832,"cross-sectional observational, not case-control",40013832,10.1128/msystems.00043-25,https://pmc.ncbi.nlm.nih.gov/articles/PMC11915818/,"Cai P., Yang Q., Lu J., Dai X. , Xiong J.",Fecal bacterial biomarkers and blood biochemical indicators as potential key factors in the development of colorectal cancer,mSystems,2025,"blood biochemical indicators, colorectal cancer, fecal microbiome, polyps, random forest model",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Volunteers ( H group),Colorectal Cancer stage I patients (C1 group),Patients diagnosed with Colorectal Cancer stage I (C1),120,35,1 month,16S,NA,Illumina,NA,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 4 and 2C,4 April 2025,Nithya,"Nithya,Shulamite,KateRasheed",Boxplot analysis of key differential genera from diagnosis model and dominant Phyla,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Fusobacteriati|p__Fusobacteriota",1783272|201174|84998|1643822|1643826|84111;1783272|1239|91061|1385|539738|1378;1783272|1239|186801|186802|216572|459786;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;3384189|32066,Complete,KateRasheed
bsdb:40013832/1/2,40013832,"cross-sectional observational, not case-control",40013832,10.1128/msystems.00043-25,https://pmc.ncbi.nlm.nih.gov/articles/PMC11915818/,"Cai P., Yang Q., Lu J., Dai X. , Xiong J.",Fecal bacterial biomarkers and blood biochemical indicators as potential key factors in the development of colorectal cancer,mSystems,2025,"blood biochemical indicators, colorectal cancer, fecal microbiome, polyps, random forest model",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Volunteers ( H group),Colorectal Cancer stage I patients (C1 group),Patients diagnosed with Colorectal Cancer stage I (C1),120,35,1 month,16S,NA,Illumina,NA,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Figure 2C and Figure 4,4 April 2025,Nithya,"Nithya,Shulamite",Boxplot analysis of key differential genera from diagnosis model and dominant Phyla,decreased,"k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Pseudomonadati|p__Pseudomonadota",1783272|1239|1737404|1582879;1783272|1239|186801|186802|1686313;3379134|1224,Complete,KateRasheed
bsdb:40013832/2/1,40013832,"cross-sectional observational, not case-control",40013832,10.1128/msystems.00043-25,https://pmc.ncbi.nlm.nih.gov/articles/PMC11915818/,"Cai P., Yang Q., Lu J., Dai X. , Xiong J.",Fecal bacterial biomarkers and blood biochemical indicators as potential key factors in the development of colorectal cancer,mSystems,2025,"blood biochemical indicators, colorectal cancer, fecal microbiome, polyps, random forest model",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Volunteers (H group),Colorectal Cancer stage II patients (C2 group),Patients diagnosed with Colorectal Cancer stage II (C2 group),120,101,1 month,16S,NA,Illumina,NA,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Figure 2C and Figure 4,11 April 2025,Nithya,"Nithya,Shulamite,KateRasheed",Boxplot analysis of key differential genera from diagnosis model and dominant phyla,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Pseudomonadati|p__Bacteroidota,k__Fusobacteriati|p__Fusobacteriota",1783272|1239|91061|1385|539738|1378;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;3379134|1224|1236|135622|267890|22;3379134|976;3384189|32066,Complete,KateRasheed
bsdb:40013832/2/2,40013832,"cross-sectional observational, not case-control",40013832,10.1128/msystems.00043-25,https://pmc.ncbi.nlm.nih.gov/articles/PMC11915818/,"Cai P., Yang Q., Lu J., Dai X. , Xiong J.",Fecal bacterial biomarkers and blood biochemical indicators as potential key factors in the development of colorectal cancer,mSystems,2025,"blood biochemical indicators, colorectal cancer, fecal microbiome, polyps, random forest model",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Volunteers (H group),Colorectal Cancer stage II patients (C2 group),Patients diagnosed with Colorectal Cancer stage II (C2 group),120,101,1 month,16S,NA,Illumina,NA,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 2,Figure 2C and Figure 4,11 April 2025,Nithya,"Nithya,Shulamite",Boxplot analysis of key differential genera from diagnosis model and dominant phyla,decreased,"k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota",1783272|1239|1737404|1582879;1783272|1239|186801|186802|1686313;3379134|1224|28216|206351|481|482;3379134|1224,Complete,KateRasheed
bsdb:40013832/3/1,40013832,"cross-sectional observational, not case-control",40013832,10.1128/msystems.00043-25,https://pmc.ncbi.nlm.nih.gov/articles/PMC11915818/,"Cai P., Yang Q., Lu J., Dai X. , Xiong J.",Fecal bacterial biomarkers and blood biochemical indicators as potential key factors in the development of colorectal cancer,mSystems,2025,"blood biochemical indicators, colorectal cancer, fecal microbiome, polyps, random forest model",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Volunteers (H group),Colorectal Cancer patients (CRC),Patients diagnosed with Colorectal Cancer (CRC),120,261,1 month,16S,NA,Illumina,NA,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A and 3B,4 April 2025,Nithya,"Nithya,Shulamite",Relative abundance ratios of genera between the Cancer and Healthy groups,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella",1783272|1239|186801|3085636|186803|43996;1783272|201174|84998|1643822|1643826|84111;1783272|1239|91061|1385|539738|1378;1783272|1239|186801|186802|216572|459786;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;3379134|1224|1236|135622|267890|22,Complete,KateRasheed
bsdb:40013832/3/2,40013832,"cross-sectional observational, not case-control",40013832,10.1128/msystems.00043-25,https://pmc.ncbi.nlm.nih.gov/articles/PMC11915818/,"Cai P., Yang Q., Lu J., Dai X. , Xiong J.",Fecal bacterial biomarkers and blood biochemical indicators as potential key factors in the development of colorectal cancer,mSystems,2025,"blood biochemical indicators, colorectal cancer, fecal microbiome, polyps, random forest model",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Volunteers (H group),Colorectal Cancer patients (CRC),Patients diagnosed with Colorectal Cancer (CRC),120,261,1 month,16S,NA,Illumina,NA,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3A and 3B,7 April 2025,Nithya,"Nithya,Shulamite",Relative abundance ratios of genera between the Cancer and Healthy groups,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum",1783272|201174|1760|85007|1653|1716;1783272|1239|1737404|1582879;1783272|1239|186801|186802|1686313;1783272|1239|1737404|1737405|1570339|150022;3379134|1224|28216|206351|481|482;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|91061|1385|90964|1279;1783272|201174|1760|2037|2049|184869,Complete,KateRasheed
bsdb:40013832/4/1,40013832,"cross-sectional observational, not case-control",40013832,10.1128/msystems.00043-25,https://pmc.ncbi.nlm.nih.gov/articles/PMC11915818/,"Cai P., Yang Q., Lu J., Dai X. , Xiong J.",Fecal bacterial biomarkers and blood biochemical indicators as potential key factors in the development of colorectal cancer,mSystems,2025,"blood biochemical indicators, colorectal cancer, fecal microbiome, polyps, random forest model",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Volunteers (H group),Colorectal Cancer stage III patients (C3 group),Patients diagnosed with Colorectal Cancer stage III (C3 group),120,110,1 month,16S,NA,Illumina,NA,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Figure 2C and Figure 4,9 April 2025,Shulamite,"Shulamite,Nithya,KateRasheed",Boxplot analysis of key differential genera from diagnosis model and dominant phyla,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota,k__Fusobacteriati|p__Fusobacteriota",1783272|201174|84998|1643822|1643826|84111;1783272|1239|91061|1385|539738|1378;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;3379134|976;3384189|32066,Complete,KateRasheed
bsdb:40013832/4/2,40013832,"cross-sectional observational, not case-control",40013832,10.1128/msystems.00043-25,https://pmc.ncbi.nlm.nih.gov/articles/PMC11915818/,"Cai P., Yang Q., Lu J., Dai X. , Xiong J.",Fecal bacterial biomarkers and blood biochemical indicators as potential key factors in the development of colorectal cancer,mSystems,2025,"blood biochemical indicators, colorectal cancer, fecal microbiome, polyps, random forest model",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Volunteers (H group),Colorectal Cancer stage III patients (C3 group),Patients diagnosed with Colorectal Cancer stage III (C3 group),120,110,1 month,16S,NA,Illumina,NA,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 2,Figure 2C and Figure 4,11 April 2025,Nithya,"Nithya,Shulamite,KateRasheed",Boxplot analysis of key differential genera from diagnosis model and dominant phyla,decreased,"k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|1239|1737404|1582879;1783272|1239|186801|186802|1686313;3379134|1224|28216|206351|481|482;3379134|1224;1783272|1239|91061|1385|90964|1279,Complete,KateRasheed
bsdb:40013832/5/1,40013832,"cross-sectional observational, not case-control",40013832,10.1128/msystems.00043-25,https://pmc.ncbi.nlm.nih.gov/articles/PMC11915818/,"Cai P., Yang Q., Lu J., Dai X. , Xiong J.",Fecal bacterial biomarkers and blood biochemical indicators as potential key factors in the development of colorectal cancer,mSystems,2025,"blood biochemical indicators, colorectal cancer, fecal microbiome, polyps, random forest model",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Patients with Polyps (P group),Patients with Colorectal Cancer stage I (C1),Patients diagonosed with Colorectal Cancer stage I (C1),92,35,1 month,16S,NA,Illumina,NA,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Figure 4 and 2C,10 April 2025,Nithya,"Nithya,KateRasheed",Boxplot analysis of key differential genera from diagnosis model and dominant phyla,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Fusobacteriati|p__Fusobacteriota",1783272|201174|84998|1643822|1643826|84111;1783272|1239|91061|1385|539738|1378;1783272|1239|186801|186802|216572|459786;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;3384189|32066,Complete,KateRasheed
bsdb:40013832/5/2,40013832,"cross-sectional observational, not case-control",40013832,10.1128/msystems.00043-25,https://pmc.ncbi.nlm.nih.gov/articles/PMC11915818/,"Cai P., Yang Q., Lu J., Dai X. , Xiong J.",Fecal bacterial biomarkers and blood biochemical indicators as potential key factors in the development of colorectal cancer,mSystems,2025,"blood biochemical indicators, colorectal cancer, fecal microbiome, polyps, random forest model",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Patients with Polyps (P group),Patients with Colorectal Cancer stage I (C1),Patients diagonosed with Colorectal Cancer stage I (C1),92,35,1 month,16S,NA,Illumina,NA,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,Figure 2C and 4,10 April 2025,Nithya,Nithya,Boxplot analysis of key differential genera from diagnosis model,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota",1783272|201174|1760|85007|1653|1716;1783272|1239|1737404|1582879;1783272|1239|186801|186802|1686313;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|91061|1385|90964|1279;3379134|1224,Complete,KateRasheed
bsdb:40013832/6/1,40013832,"cross-sectional observational, not case-control",40013832,10.1128/msystems.00043-25,https://pmc.ncbi.nlm.nih.gov/articles/PMC11915818/,"Cai P., Yang Q., Lu J., Dai X. , Xiong J.",Fecal bacterial biomarkers and blood biochemical indicators as potential key factors in the development of colorectal cancer,mSystems,2025,"blood biochemical indicators, colorectal cancer, fecal microbiome, polyps, random forest model",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Patients with Polyps (P group),Colorectal Cancer Patients (CRC),Patients diagnosed with Colorectal Cancer (CRC),92,261,1 month,16S,NA,Illumina,NA,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A and 3B,10 April 2025,Nithya,Nithya,Relative abundance ratios of genera between the CRC and Polyps groups,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum",1783272|201174|1760|85007|1653|1716;1783272|1239|1737404|1582879;1783272|1239|186801|186802|1686313;1783272|1239|1737404|1737405|1570339|150022;3379134|1224|28216|206351|481|482;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|91061|1385|90964|1279;1783272|201174|1760|2037|2049|184869,Complete,KateRasheed
bsdb:40013832/7/1,40013832,"cross-sectional observational, not case-control",40013832,10.1128/msystems.00043-25,https://pmc.ncbi.nlm.nih.gov/articles/PMC11915818/,"Cai P., Yang Q., Lu J., Dai X. , Xiong J.",Fecal bacterial biomarkers and blood biochemical indicators as potential key factors in the development of colorectal cancer,mSystems,2025,"blood biochemical indicators, colorectal cancer, fecal microbiome, polyps, random forest model",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Volunteers (H group),Colorectal Cancer patients stage IV (C4 group),Patients diagnosed with Colorectal Cancer stage IV (C4 group),120,15,1 month,16S,NA,Illumina,NA,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Figure 4 and 2C,11 April 2025,Nithya,"Nithya,KateRasheed",Boxplot analysis of key differential genera from diagnosis model and dominant phyla,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Fusobacteriati|p__Fusobacteriota",1783272|201174|84998|1643822|1643826|84111;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;3384189|32066,Complete,KateRasheed
bsdb:40013832/7/2,40013832,"cross-sectional observational, not case-control",40013832,10.1128/msystems.00043-25,https://pmc.ncbi.nlm.nih.gov/articles/PMC11915818/,"Cai P., Yang Q., Lu J., Dai X. , Xiong J.",Fecal bacterial biomarkers and blood biochemical indicators as potential key factors in the development of colorectal cancer,mSystems,2025,"blood biochemical indicators, colorectal cancer, fecal microbiome, polyps, random forest model",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy Volunteers (H group),Colorectal Cancer patients stage IV (C4 group),Patients diagnosed with Colorectal Cancer stage IV (C4 group),120,15,1 month,16S,NA,Illumina,NA,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,Figure 4 and 2C,11 April 2025,Nithya,"Nithya,KateRasheed",Boxplot analysis of key differential genera from diagnosis model and dominant phyla,decreased,"k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|1239|1737404|1582879;1783272|1239|186801|186802|1686313;3379134|1224;1783272|1239|91061|1385|90964|1279,Complete,KateRasheed
bsdb:40013832/8/1,40013832,"cross-sectional observational, not case-control",40013832,10.1128/msystems.00043-25,https://pmc.ncbi.nlm.nih.gov/articles/PMC11915818/,"Cai P., Yang Q., Lu J., Dai X. , Xiong J.",Fecal bacterial biomarkers and blood biochemical indicators as potential key factors in the development of colorectal cancer,mSystems,2025,"blood biochemical indicators, colorectal cancer, fecal microbiome, polyps, random forest model",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Patients with Polyps (P group),Patients with Colorectal Cancer stage II (C2),Patients diagonosed with Colorectal Cancer stage II (C2),92,101,1 month,16S,NA,Illumina,NA,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Figure 4 and 2C,11 April 2025,Nithya,"Nithya,KateRasheed",Boxplot analysis of key differential genera from diagnosis model and dominant phyla,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Fusobacteriati|p__Fusobacteriota",1783272|1239|91061|1385|539738|1378;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;3384189|32066,Complete,KateRasheed
bsdb:40013832/8/2,40013832,"cross-sectional observational, not case-control",40013832,10.1128/msystems.00043-25,https://pmc.ncbi.nlm.nih.gov/articles/PMC11915818/,"Cai P., Yang Q., Lu J., Dai X. , Xiong J.",Fecal bacterial biomarkers and blood biochemical indicators as potential key factors in the development of colorectal cancer,mSystems,2025,"blood biochemical indicators, colorectal cancer, fecal microbiome, polyps, random forest model",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Patients with Polyps (P group),Patients with Colorectal Cancer stage II (C2),Patients diagonosed with Colorectal Cancer stage II (C2),92,101,1 month,16S,NA,Illumina,NA,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,Figure 4 and 2C,11 April 2025,Nithya,Nithya,Boxplot analysis of key differential genera from diagnosis model and dominant phyla,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Pseudomonadati|p__Pseudomonadota",1783272|201174|1760|85007|1653|1716;1783272|1239|1737404|1582879;1783272|1239|186801|186802|1686313;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|91061|1385|90964|1279;1783272|201174|1760|2037|2049|184869;3379134|1224,Complete,KateRasheed
bsdb:40013832/9/1,40013832,"cross-sectional observational, not case-control",40013832,10.1128/msystems.00043-25,https://pmc.ncbi.nlm.nih.gov/articles/PMC11915818/,"Cai P., Yang Q., Lu J., Dai X. , Xiong J.",Fecal bacterial biomarkers and blood biochemical indicators as potential key factors in the development of colorectal cancer,mSystems,2025,"blood biochemical indicators, colorectal cancer, fecal microbiome, polyps, random forest model",Experiment 9,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Patients with Polyps (P group),Patients with Colorectal Cancer stage III (C3),Patients diagonosed with Colorectal Cancer stage III (C3),92,110,1 month,16S,NA,Illumina,NA,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 2C and Figure 4,11 April 2025,Nithya,"Nithya,Shulamite,KateRasheed",Boxplot analysis of key differential genera from diagnosis model and dominant phyla,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Bacteroidota",1783272|201174|84998|1643822|1643826|84111;1783272|1239|91061|1385|539738|1378;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;3384189|32066;3379134|976,Complete,KateRasheed
bsdb:40013832/9/2,40013832,"cross-sectional observational, not case-control",40013832,10.1128/msystems.00043-25,https://pmc.ncbi.nlm.nih.gov/articles/PMC11915818/,"Cai P., Yang Q., Lu J., Dai X. , Xiong J.",Fecal bacterial biomarkers and blood biochemical indicators as potential key factors in the development of colorectal cancer,mSystems,2025,"blood biochemical indicators, colorectal cancer, fecal microbiome, polyps, random forest model",Experiment 9,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Patients with Polyps (P group),Patients with Colorectal Cancer stage III (C3),Patients diagonosed with Colorectal Cancer stage III (C3),92,110,1 month,16S,NA,Illumina,NA,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Figure 4 and 2C,11 April 2025,Nithya,"Nithya,Shulamite,KateRasheed",Boxplot analysis of key differential genera from diagnosis model and dominant Phyla,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum",1783272|201174|1760|85007|1653|1716;1783272|1239|1737404|1582879;1783272|1239|186801|186802|1686313;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|1737404|1737405|1570339|162289;3379134|1224;1783272|1239|91061|1385|90964|1279;1783272|201174|1760|2037|2049|184869,Complete,KateRasheed
bsdb:40013832/10/1,40013832,"cross-sectional observational, not case-control",40013832,10.1128/msystems.00043-25,https://pmc.ncbi.nlm.nih.gov/articles/PMC11915818/,"Cai P., Yang Q., Lu J., Dai X. , Xiong J.",Fecal bacterial biomarkers and blood biochemical indicators as potential key factors in the development of colorectal cancer,mSystems,2025,"blood biochemical indicators, colorectal cancer, fecal microbiome, polyps, random forest model",Experiment 10,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Patients with Polyps (P group),Patients with Colorectal Cancer stage IV (C4),Patients diagonosed with Colorectal Cancer stage IV (C4),92,15,1 month,16S,NA,Illumina,NA,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Figure 4 and 2C,11 April 2025,Nithya,"Nithya,KateRasheed",Boxplot analysis of key differential genera from diagnosis model and dominant phyla,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Fusobacteriati|p__Fusobacteriota",1783272|201174|84998|1643822|1643826|84111;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3082720|186804|1257;3384189|32066,Complete,KateRasheed
bsdb:40013832/10/2,40013832,"cross-sectional observational, not case-control",40013832,10.1128/msystems.00043-25,https://pmc.ncbi.nlm.nih.gov/articles/PMC11915818/,"Cai P., Yang Q., Lu J., Dai X. , Xiong J.",Fecal bacterial biomarkers and blood biochemical indicators as potential key factors in the development of colorectal cancer,mSystems,2025,"blood biochemical indicators, colorectal cancer, fecal microbiome, polyps, random forest model",Experiment 10,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Patients with Polyps (P group),Patients with Colorectal Cancer stage IV (C4),Patients diagonosed with Colorectal Cancer stage IV (C4),92,15,1 month,16S,NA,Illumina,NA,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,Figure 4,11 April 2025,Nithya,Nithya,Boxplot analysis of key differential genera from diagnosis model,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia",1783272|1239|186801|186802|1686313;1783272|1239|91061|1385|90964|1279;1783272|1239|1737404|1582879;1783272|1239|1737404|1737405|1570339|150022,Complete,KateRasheed
bsdb:40021742/1/1,40021742,case-control,40021742,10.1038/s41598-025-91626-4,NA,"Deng D., Zhao L., Song H., Wang H., Cao H., Cui H., Zhou Y. , Cui R.",Microbiome analysis of gut microbiota in patients with colorectal polyps and healthy individuals,Scientific reports,2025,"Colorectal polyps, Gut microbiota, Microbiome analysis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Control groups (ctrl),Colorectal polyp group (CP),Patients undergoing colonoscopy and diagnosed with Colorectal polyps which are protrusions on the surface of the colorectum and serve as the primary precursors to CRC1 (Colorectal cancer 1).,30,30,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure 3a, 3b, supplementary Table 1",4 March 2025,Tosin,Tosin,Linear discriminant analysis effect size analysis of the colorectal propyl (CP) and control groups,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota",3379134|1224|1236|135625|712|416916;3379134|74201|203494|48461|1647988|239934;1783272|1239|91061;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|2005519;1783272|201174|1760|85007|1653;1783272|201174|1760|85007|1653|1716;1783272|201174|84998|1643822|1643826|84111;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;3379134|1224|1236|91347|543|561;1783272|1239|186801|186802|186806|1730;3379134|1224|1236;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826;3379134|1224;1783272|1239|186801|186802|216572|1263;3379134|1224|1236|91347|543|620;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;3379134|74201|203494|48461|203557;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201,Complete,Svetlana up
bsdb:40021742/1/2,40021742,case-control,40021742,10.1038/s41598-025-91626-4,NA,"Deng D., Zhao L., Song H., Wang H., Cao H., Cui H., Zhou Y. , Cui R.",Microbiome analysis of gut microbiota in patients with colorectal polyps and healthy individuals,Scientific reports,2025,"Colorectal polyps, Gut microbiota, Microbiome analysis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Control groups (ctrl),Colorectal polyp group (CP),Patients undergoing colonoscopy and diagnosed with Colorectal polyps which are protrusions on the surface of the colorectum and serve as the primary precursors to CRC1 (Colorectal cancer 1).,30,30,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 3a, 3b, supplemetary Table 1",5 March 2025,Tosin,Tosin,Linear discriminant analysis effect size analysis of the colorectal propyl (CP) and control groups,decreased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|201174|84992;1783272|201174;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|204475;1783272|1239|909932|909929|1843491|52225;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977,Complete,Svetlana up
bsdb:40026814/1/1,40026814,"cross-sectional observational, not case-control",40026814,10.2147/IJGM.S509592,NA,"Zhang X., Yin H., Yang X., Kang J. , Sui N.","Therapeutic Mechanism of Zhuyang Tongbian Decoction in Treating Functional Constipation: Insights from a Pilot Study Utilizing 16S rRNA Sequencing, Metagenomics, and Metabolomics",International journal of general medicine,2025,"Zhuyang Tongbian Decoction, functional constipation, intestinal flora, intestinal inflammation, metabolite",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy Volunteers (NC),Functional Constipation in Pre-Zhuyang Tongbian Decoction (FC_PreZY) group,FC_PreZY group was treated with Zhuyang Tongbian Decoction (ZTD) (raw drug concentration: 3.0 g/mL),20,20,1 month,16S,34,Illumina,relative abundances,NA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 2c,21 March 2025,PreciousChijioke,"PreciousChijioke,Ese",Comparison of significantly different flora before and after treatment with ZTD at the genus level,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,s__rumen bacterium NK4A214",1783272|201174|84998|84999|84107|102106;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|216572|1263;877428,Complete,Svetlana up
bsdb:40026814/1/2,40026814,"cross-sectional observational, not case-control",40026814,10.2147/IJGM.S509592,NA,"Zhang X., Yin H., Yang X., Kang J. , Sui N.","Therapeutic Mechanism of Zhuyang Tongbian Decoction in Treating Functional Constipation: Insights from a Pilot Study Utilizing 16S rRNA Sequencing, Metagenomics, and Metabolomics",International journal of general medicine,2025,"Zhuyang Tongbian Decoction, functional constipation, intestinal flora, intestinal inflammation, metabolite",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy Volunteers (NC),Functional Constipation in Pre-Zhuyang Tongbian Decoction (FC_PreZY) group,FC_PreZY group was treated with Zhuyang Tongbian Decoction (ZTD) (raw drug concentration: 3.0 g/mL),20,20,1 month,16S,34,Illumina,relative abundances,NA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 2c,21 March 2025,PreciousChijioke,PreciousChijioke,Comparison of significantly different flora before and after treatment with ZTD at the genus level,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|216572|292632,Complete,Svetlana up
bsdb:40026814/2/1,40026814,"cross-sectional observational, not case-control",40026814,10.2147/IJGM.S509592,NA,"Zhang X., Yin H., Yang X., Kang J. , Sui N.","Therapeutic Mechanism of Zhuyang Tongbian Decoction in Treating Functional Constipation: Insights from a Pilot Study Utilizing 16S rRNA Sequencing, Metagenomics, and Metabolomics",International journal of general medicine,2025,"Zhuyang Tongbian Decoction, functional constipation, intestinal flora, intestinal inflammation, metabolite",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Functional Constipation in Pre-Zhuyang Tongbian Decoction (FC_PreZY)  group,Pro-Zhuyang Tongbian Decoction (ProZY) group,Group after treatment with ZTD (raw drug concentration: 3.0 g/mL),20,20,1 month,16S,34,Illumina,relative abundances,NA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 2c,21 March 2025,PreciousChijioke,PreciousChijioke,Comparison of significantly different flora before and after treatment with ZTD at the genus level,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|216572|292632,Complete,Svetlana up
bsdb:40026814/2/2,40026814,"cross-sectional observational, not case-control",40026814,10.2147/IJGM.S509592,NA,"Zhang X., Yin H., Yang X., Kang J. , Sui N.","Therapeutic Mechanism of Zhuyang Tongbian Decoction in Treating Functional Constipation: Insights from a Pilot Study Utilizing 16S rRNA Sequencing, Metagenomics, and Metabolomics",International journal of general medicine,2025,"Zhuyang Tongbian Decoction, functional constipation, intestinal flora, intestinal inflammation, metabolite",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Functional Constipation in Pre-Zhuyang Tongbian Decoction (FC_PreZY)  group,Pro-Zhuyang Tongbian Decoction (ProZY) group,Group after treatment with ZTD (raw drug concentration: 3.0 g/mL),20,20,1 month,16S,34,Illumina,relative abundances,NA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 2c,21 March 2025,PreciousChijioke,PreciousChijioke,Comparison of significantly different flora before and after treatment with ZTD at the genus level,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,s__rumen bacterium NK4A214",1783272|201174|84998|84999|84107|102106;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|216572|1263;877428,Complete,Svetlana up
bsdb:40026814/4/1,40026814,"cross-sectional observational, not case-control",40026814,10.2147/IJGM.S509592,NA,"Zhang X., Yin H., Yang X., Kang J. , Sui N.","Therapeutic Mechanism of Zhuyang Tongbian Decoction in Treating Functional Constipation: Insights from a Pilot Study Utilizing 16S rRNA Sequencing, Metagenomics, and Metabolomics",International journal of general medicine,2025,"Zhuyang Tongbian Decoction, functional constipation, intestinal flora, intestinal inflammation, metabolite",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy volunteers (NC) + Pro-Zhuyang Tongbian Decoction (ProZY) group,Functional Constipation in Pre-Zhuyang Tongbian Decoction (FC_PreZY) group,Functional Constipation in Pre-Zhuyang Tongbian Decoction (FC_PreZY) group was treated with ZTD (raw drug concentration: 3.0 g/mL),20,20,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 4,22 March 2025,PreciousChijioke,"PreciousChijioke,KateRasheed",Analysis of differential flora at different taxonomic levels,increased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus equinus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,s__rumen bacterium NK4A214,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Pseudomonadati|p__Thermodesulfobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|1980681;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;3379134|200940|3031449;1783272|201174|84998|1643822|1643826;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|3082720|186804|1505657;3379134|976|200643|171549|2005473;1783272|1239|186801|186802|216572;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|186802|216572|1263|40519;1783272|201174|84998|84999|84107|1473205;1783272|1239|91061|186826|1300|1301|1335;1783272|1239|186801|3082720|186804|1505652;877428;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730|290054;3379134|200940;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|2316020|33039,Complete,Svetlana up
bsdb:40026814/5/1,40026814,"cross-sectional observational, not case-control",40026814,10.2147/IJGM.S509592,NA,"Zhang X., Yin H., Yang X., Kang J. , Sui N.","Therapeutic Mechanism of Zhuyang Tongbian Decoction in Treating Functional Constipation: Insights from a Pilot Study Utilizing 16S rRNA Sequencing, Metagenomics, and Metabolomics",International journal of general medicine,2025,"Zhuyang Tongbian Decoction, functional constipation, intestinal flora, intestinal inflammation, metabolite",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy volunteers (NC) + Functional Constipation in Pre-Zhuyang Tongbian Decoction (FC_PreZY ) group,Pro-Zhuyang Tongbian Decoction (ProZY) group,Group after treatment with ZTD (raw drug concentration: 3.0 g/mL),20,20,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 4,23 March 2025,PreciousChijioke,"PreciousChijioke,KateRasheed",Analysis of differential flora at different taxonomic levels,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,s__gut metagenome,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|s__Enterococcaceae bacterium RF39,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum",3379134|976|200643|171549|815|816|626929;1783272|1239|186801|186802|3085642;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3082768|990719;1783272|1239|186801|3082768;1783272|1239|186801|3085636|186803|28050;1783272|1239|91061|186826;3379134|976|200643|1970189|1573805;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|171552|577309;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|29466;749906;1783272|1239|91061;1783272|1239|186801|3085636|186803|877420;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|91061|186826|81852|423410;1783272|1239|186801|186802|216572|39492,Complete,Svetlana up
bsdb:40026814/6/1,40026814,"cross-sectional observational, not case-control",40026814,10.2147/IJGM.S509592,NA,"Zhang X., Yin H., Yang X., Kang J. , Sui N.","Therapeutic Mechanism of Zhuyang Tongbian Decoction in Treating Functional Constipation: Insights from a Pilot Study Utilizing 16S rRNA Sequencing, Metagenomics, and Metabolomics",International journal of general medicine,2025,"Zhuyang Tongbian Decoction, functional constipation, intestinal flora, intestinal inflammation, metabolite",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy Volunteers (NC),Functional Constipation in Zhuyang Tongbian Decoction (FC_PreZY) group,FC_PreZY group was treated with Zhuyang Tongbian Decoction (ZTD) (raw drug concentration: 3.0 g/mL),20,20,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 3a,28 March 2025,PreciousChijioke,PreciousChijioke,Comparison of the abundance of Bifidobacterium spp. and Lactobacillus spp. in each group,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:40026814/7/1,40026814,"cross-sectional observational, not case-control",40026814,10.2147/IJGM.S509592,NA,"Zhang X., Yin H., Yang X., Kang J. , Sui N.","Therapeutic Mechanism of Zhuyang Tongbian Decoction in Treating Functional Constipation: Insights from a Pilot Study Utilizing 16S rRNA Sequencing, Metagenomics, and Metabolomics",International journal of general medicine,2025,"Zhuyang Tongbian Decoction, functional constipation, intestinal flora, intestinal inflammation, metabolite",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Functional Constipation in Pre-Zhuyang Tongbian Decoction (FC_PreZY) group,Fuctional Constipation in Pro-Zhuyang Tongbian Decoction (FC_ProZY) group,FC_ProZY group after treatment with ZTD (raw drug concentration: 3.0 g/mL),20,20,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 3a,28 March 2025,PreciousChijioke,PreciousChijioke,Comparison of the abundance of Bifidobacterium spp. and Lactobacillus spp. in each group,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:40026814/8/1,40026814,"cross-sectional observational, not case-control",40026814,10.2147/IJGM.S509592,NA,"Zhang X., Yin H., Yang X., Kang J. , Sui N.","Therapeutic Mechanism of Zhuyang Tongbian Decoction in Treating Functional Constipation: Insights from a Pilot Study Utilizing 16S rRNA Sequencing, Metagenomics, and Metabolomics",International journal of general medicine,2025,"Zhuyang Tongbian Decoction, functional constipation, intestinal flora, intestinal inflammation, metabolite",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy Volunteers (NC),Functional Constipation in Pre-Control (FC_PreCG) group,FC_PreCG group was treated with lactulose orally,20,20,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 3a,29 March 2025,PreciousChijioke,PreciousChijioke,Comparison of the abundance of Bifidobacterium spp. and Lactobacillus spp. in each group,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:40026814/9/1,40026814,"cross-sectional observational, not case-control",40026814,10.2147/IJGM.S509592,NA,"Zhang X., Yin H., Yang X., Kang J. , Sui N.","Therapeutic Mechanism of Zhuyang Tongbian Decoction in Treating Functional Constipation: Insights from a Pilot Study Utilizing 16S rRNA Sequencing, Metagenomics, and Metabolomics",International journal of general medicine,2025,"Zhuyang Tongbian Decoction, functional constipation, intestinal flora, intestinal inflammation, metabolite",Experiment 9,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Functional Constipation in Pre-Control (FC_PreCG) group,Post-Control Group (ProCG),ProCG group after treatment with lactulose orally,20,20,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 3a,29 March 2025,PreciousChijioke,PreciousChijioke,Comparison of the abundance of Bifidobacterium spp. and Lactobacillus spp. in each group,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Svetlana up
bsdb:40026814/9/2,40026814,"cross-sectional observational, not case-control",40026814,10.2147/IJGM.S509592,NA,"Zhang X., Yin H., Yang X., Kang J. , Sui N.","Therapeutic Mechanism of Zhuyang Tongbian Decoction in Treating Functional Constipation: Insights from a Pilot Study Utilizing 16S rRNA Sequencing, Metagenomics, and Metabolomics",International journal of general medicine,2025,"Zhuyang Tongbian Decoction, functional constipation, intestinal flora, intestinal inflammation, metabolite",Experiment 9,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Functional Constipation in Pre-Control (FC_PreCG) group,Post-Control Group (ProCG),ProCG group after treatment with lactulose orally,20,20,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 3a,4 April 2025,PreciousChijioke,PreciousChijioke,Comparison of the abundance of Bifidobacterium spp. and Lactobacillus spp. in each group,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:40026814/10/1,40026814,"cross-sectional observational, not case-control",40026814,10.2147/IJGM.S509592,NA,"Zhang X., Yin H., Yang X., Kang J. , Sui N.","Therapeutic Mechanism of Zhuyang Tongbian Decoction in Treating Functional Constipation: Insights from a Pilot Study Utilizing 16S rRNA Sequencing, Metagenomics, and Metabolomics",International journal of general medicine,2025,"Zhuyang Tongbian Decoction, functional constipation, intestinal flora, intestinal inflammation, metabolite",Experiment 10,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Pro-Zhuyang Tongbian Decoction (ProZY),Post-Control Group (ProCG),ProCG group after treatment with lactulose orally,20,20,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 3a,4 April 2025,PreciousChijioke,PreciousChijioke,Comparison of the abundance of Bifidobacterium spp. and Lactobacillus spp. in each group,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,Svetlana up
bsdb:40026814/11/1,40026814,"cross-sectional observational, not case-control",40026814,10.2147/IJGM.S509592,NA,"Zhang X., Yin H., Yang X., Kang J. , Sui N.","Therapeutic Mechanism of Zhuyang Tongbian Decoction in Treating Functional Constipation: Insights from a Pilot Study Utilizing 16S rRNA Sequencing, Metagenomics, and Metabolomics",International journal of general medicine,2025,"Zhuyang Tongbian Decoction, functional constipation, intestinal flora, intestinal inflammation, metabolite",Experiment 11,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy Volunteers (NC),Functional Constipation in Pre-Zhuyang Tongbian Decoction (FC_PreZY) group,FC_PreZY group was treated with ZTD (raw drug concentration: 3.0 g/mL),20,20,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 3c,4 April 2025,PreciousChijioke,PreciousChijioke,Comparison of significantly different flora before and after treatment with ZTD at the species level,increased,s__uncultured bacterium,77133,Complete,Svetlana up
bsdb:40026814/11/2,40026814,"cross-sectional observational, not case-control",40026814,10.2147/IJGM.S509592,NA,"Zhang X., Yin H., Yang X., Kang J. , Sui N.","Therapeutic Mechanism of Zhuyang Tongbian Decoction in Treating Functional Constipation: Insights from a Pilot Study Utilizing 16S rRNA Sequencing, Metagenomics, and Metabolomics",International journal of general medicine,2025,"Zhuyang Tongbian Decoction, functional constipation, intestinal flora, intestinal inflammation, metabolite",Experiment 11,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Healthy Volunteers (NC),Functional Constipation in Pre-Zhuyang Tongbian Decoction (FC_PreZY) group,FC_PreZY group was treated with ZTD (raw drug concentration: 3.0 g/mL),20,20,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 3c,5 April 2025,PreciousChijioke,PreciousChijioke,Comparison of significantly different flora before and after treatment with ZTD at the species level,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,s__gut metagenome",3379134|1224|1236|91347|543|561|562;1783272|201174|1760|85004|31953|1678|1680;1783272|1239|186801|186802|216572|216851|853;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|28026;749906,Complete,Svetlana up
bsdb:40026814/12/1,40026814,"cross-sectional observational, not case-control",40026814,10.2147/IJGM.S509592,NA,"Zhang X., Yin H., Yang X., Kang J. , Sui N.","Therapeutic Mechanism of Zhuyang Tongbian Decoction in Treating Functional Constipation: Insights from a Pilot Study Utilizing 16S rRNA Sequencing, Metagenomics, and Metabolomics",International journal of general medicine,2025,"Zhuyang Tongbian Decoction, functional constipation, intestinal flora, intestinal inflammation, metabolite",Experiment 12,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Functional Constipation in Pre-Zhuyang Tongbian Decoction (FC_PreZY) group,Pro-Zhuyang Tongbian Decoction (ProZY) group,ProZY group after treatment with ZTD (raw drug concentration: 3.0 g/mL),20,20,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 3c,4 April 2025,PreciousChijioke,"PreciousChijioke,KateRasheed",Comparison of significantly different flora before and after treatment with ZTD at the species level,decreased,s__uncultured bacterium,77133,Complete,Svetlana up
bsdb:40026814/12/2,40026814,"cross-sectional observational, not case-control",40026814,10.2147/IJGM.S509592,NA,"Zhang X., Yin H., Yang X., Kang J. , Sui N.","Therapeutic Mechanism of Zhuyang Tongbian Decoction in Treating Functional Constipation: Insights from a Pilot Study Utilizing 16S rRNA Sequencing, Metagenomics, and Metabolomics",International journal of general medicine,2025,"Zhuyang Tongbian Decoction, functional constipation, intestinal flora, intestinal inflammation, metabolite",Experiment 12,China,Homo sapiens,Feces,UBERON:0001988,Chronic constipation,HP:0012450,Functional Constipation in Pre-Zhuyang Tongbian Decoction (FC_PreZY) group,Pro-Zhuyang Tongbian Decoction (ProZY) group,ProZY group after treatment with ZTD (raw drug concentration: 3.0 g/mL),20,20,1 month,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 3c,5 April 2025,PreciousChijioke,"PreciousChijioke,KateRasheed",Comparison of significantly different flora before and after treatment with ZTD at the species level,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,s__gut metagenome",1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|28026;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|186802|216572|216851|853;749906,Complete,Svetlana up
bsdb:40032727/1/1,40032727,"cross-sectional observational, not case-control",40032727,10.1080/19490976.2025.2469716,https://pmc.ncbi.nlm.nih.gov/articles/PMC11881836/#sec26,"Santiso-Bellón C., Randazzo W., Carmona-Vicente N., Peña-Gil N., Cárcamo-Calvo R., Lopez-Navarro S., Navarro-Lleó N., Yebra M.J., Monedero V., Buesa J., Gozalbo-Rovira R. , Rodríguez-Díaz J.",<i>Rhodococcus</i> spp. interacts with human norovirus in clinical samples and impairs its replication on human intestinal enteroids,Gut microbes,2025,"Human norovirus, Rhodococcus, gut microbiota, histo-blood group antigens, human intestinal enteroids, stool samples",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Viral disease,EFO:0000763,Total bacteria isolated before treatments + IgG isotype control pAb or the specific pAb + IgG isotype control pAb (T+C+N)),anti-NoV GII.4 Sydney 2012 pAb (NoV),Bacteria captured by anti-NoV GII.4 Sydney 2012 pAb,3,1,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 1a,31 March 2025,Shulamite,"Shulamite,Eniola","LDA of bacterial genera  quantified from clinical samples with NoV. The LDA score of 15 taxa with significant differences (p<0.05 in Kruskal-Wallis test, adjusted by FDR) in a LEfse analysis is presented.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Pandoraea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia",3379134|1224|28211|356|82115|357;1783272|1239|526524|526525|128827|174708;1783272|201174|1760|85006|85019|1696;3379134|1224|28216|80840|119060|93217;3379134|1224|1236|135614|32033|40323;3379134|1224|1236|72274|135621|286;3379134|1224|28211|356|119045|407;1783272|1239|91061|1385|90964|1279;1783272|201174|1760|85007|85025|1827;1783272|1239|526524|526525|128827|118747;3379134|976|117743|200644|2762318|59732;3379134|1224|28211|204457|41297|13687;3379134|1224|28211|356|118882|528;33090|35493|3398|72025|3803|3814|508215,Complete,Svetlana up
bsdb:40032727/1/2,40032727,"cross-sectional observational, not case-control",40032727,10.1080/19490976.2025.2469716,https://pmc.ncbi.nlm.nih.gov/articles/PMC11881836/#sec26,"Santiso-Bellón C., Randazzo W., Carmona-Vicente N., Peña-Gil N., Cárcamo-Calvo R., Lopez-Navarro S., Navarro-Lleó N., Yebra M.J., Monedero V., Buesa J., Gozalbo-Rovira R. , Rodríguez-Díaz J.",<i>Rhodococcus</i> spp. interacts with human norovirus in clinical samples and impairs its replication on human intestinal enteroids,Gut microbes,2025,"Human norovirus, Rhodococcus, gut microbiota, histo-blood group antigens, human intestinal enteroids, stool samples",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Viral disease,EFO:0000763,Total bacteria isolated before treatments + IgG isotype control pAb or the specific pAb + IgG isotype control pAb (T+C+N)),anti-NoV GII.4 Sydney 2012 pAb (NoV),Bacteria captured by anti-NoV GII.4 Sydney 2012 pAb,3,1,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 1a,31 March 2025,Shulamite,"Shulamite,Eniola","LDA of bacterial genera  quantified from clinical samples with NoV. The LDA score of 15 taxa with significant differences (p<0.05 in Kruskal-Wallis test, adjusted by FDR) in a LEfse analysis is presented.",decreased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|g__Candidatus Tremblayella,3379134|1224|28216|189384,Complete,Svetlana up
bsdb:40032727/2/1,40032727,"cross-sectional observational, not case-control",40032727,10.1080/19490976.2025.2469716,https://pmc.ncbi.nlm.nih.gov/articles/PMC11881836/#sec26,"Santiso-Bellón C., Randazzo W., Carmona-Vicente N., Peña-Gil N., Cárcamo-Calvo R., Lopez-Navarro S., Navarro-Lleó N., Yebra M.J., Monedero V., Buesa J., Gozalbo-Rovira R. , Rodríguez-Díaz J.",<i>Rhodococcus</i> spp. interacts with human norovirus in clinical samples and impairs its replication on human intestinal enteroids,Gut microbes,2025,"Human norovirus, Rhodococcus, gut microbiota, histo-blood group antigens, human intestinal enteroids, stool samples",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Viral disease,EFO:0000763,Anti-NoV GII.4 Sydney 2012 antibody. (NoV),IgG isotype control pAb (C),"Bacteria captured by the IgG isotype control pAb (C),",1,1,NA,16S,34,Illumina,relative abundances,Dunn's test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 1b and S2b,2 April 2025,Shulamite,"Shulamite,Eniola",Normalized counts of reads corresponding to Lactobacillus taiwanensis/johnsonii and Ligilactobacillus murinus/animalis and Abundance of Rhodococcustaxons. p<0.05 for Sidak's test comparing NoV subgroup with the rest of subgroups.,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,1783272|201174|1760|85007|85025|1827,Complete,Svetlana up
bsdb:40032727/3/1,40032727,"cross-sectional observational, not case-control",40032727,10.1080/19490976.2025.2469716,https://pmc.ncbi.nlm.nih.gov/articles/PMC11881836/#sec26,"Santiso-Bellón C., Randazzo W., Carmona-Vicente N., Peña-Gil N., Cárcamo-Calvo R., Lopez-Navarro S., Navarro-Lleó N., Yebra M.J., Monedero V., Buesa J., Gozalbo-Rovira R. , Rodríguez-Díaz J.",<i>Rhodococcus</i> spp. interacts with human norovirus in clinical samples and impairs its replication on human intestinal enteroids,Gut microbes,2025,"Human norovirus, Rhodococcus, gut microbiota, histo-blood group antigens, human intestinal enteroids, stool samples",Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Viral disease,EFO:0000763,Anti-NoV GII.4 Sydney 2012 antibody. (NoV),Isotype control antibody (N),Bacteria not recognized by the isotype control antibody nor the specific antibody,1,1,NA,16S,34,Illumina,relative abundances,Dunn's test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 1b and S2b,3 April 2025,Shulamite,"Shulamite,Eniola",Normalized counts of reads corresponding to Lactobacillus taiwanensis/johnsonii and Ligilactobacillus murinus/animalis and Abundance of Rhodococcus taxons. p<0.05 for Sidak's test comparing NoV subgroup with the rest of subgroups.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,1783272|201174|1760|85007|85025|1827,Complete,Svetlana up
bsdb:40032727/4/1,40032727,"cross-sectional observational, not case-control",40032727,10.1080/19490976.2025.2469716,https://pmc.ncbi.nlm.nih.gov/articles/PMC11881836/#sec26,"Santiso-Bellón C., Randazzo W., Carmona-Vicente N., Peña-Gil N., Cárcamo-Calvo R., Lopez-Navarro S., Navarro-Lleó N., Yebra M.J., Monedero V., Buesa J., Gozalbo-Rovira R. , Rodríguez-Díaz J.",<i>Rhodococcus</i> spp. interacts with human norovirus in clinical samples and impairs its replication on human intestinal enteroids,Gut microbes,2025,"Human norovirus, Rhodococcus, gut microbiota, histo-blood group antigens, human intestinal enteroids, stool samples",Experiment 4,Spain,Homo sapiens,Feces,UBERON:0001988,Viral disease,EFO:0000763,Total bacteria present in stools before experiment (T),Anti-NoV GII.4 Sydney 2012 antibody. (NoV),Bacteria recognised by the Anti-NoV GII.4 Sydney 2012 antibody. (NoV),1,1,NA,16S,34,Illumina,relative abundances,Dunn's test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 1b and S2b,3 April 2025,Shulamite,Shulamite,Normalized counts of reads corresponding to Lactobacillus taiwanensis/johnsonii and Ligilactobacillus murinus/animalis taxons and Abundance of Rhodococcus. p<0.05 for Sidak's test comparing NoV subgroup with the rest of subgroups.,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,1783272|201174|1760|85007|85025|1827,Complete,Svetlana up
bsdb:40032727/5/1,40032727,"cross-sectional observational, not case-control",40032727,10.1080/19490976.2025.2469716,https://pmc.ncbi.nlm.nih.gov/articles/PMC11881836/#sec26,"Santiso-Bellón C., Randazzo W., Carmona-Vicente N., Peña-Gil N., Cárcamo-Calvo R., Lopez-Navarro S., Navarro-Lleó N., Yebra M.J., Monedero V., Buesa J., Gozalbo-Rovira R. , Rodríguez-Díaz J.",<i>Rhodococcus</i> spp. interacts with human norovirus in clinical samples and impairs its replication on human intestinal enteroids,Gut microbes,2025,"Human norovirus, Rhodococcus, gut microbiota, histo-blood group antigens, human intestinal enteroids, stool samples",Experiment 5,Spain,Homo sapiens,Feces,UBERON:0001988,Viral disease,EFO:0000763,Anti-NoV GII.4 Sydney 2012 pAb + Total bacteria isolated before treatments + IgG isotype control pAb (NoV+T+C),Isotype control nor the specific pAb (N),Isotype control nor the specific pAb (N),3,1,NA,16S,34,Illumina,relative abundances,Dunn's test,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 1a,11 April 2025,Shulamite,Shulamite,"LDA of bacterial genera quantified from clinical samples with NoV. The LDA score of 15 taxa with significant differences (p<0.05 in Kruskal-Wallis test, adjusted by FDR) in a LEfse analysis is presented.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Pandoraea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",3379134|1224|28211|356|82115|357;1783272|1239|526524|526525|128827|174708;1783272|201174|1760|85006|85019|1696;3379134|1224|28216|80840|119060|93217;3379134|1224|1236|135614|32033|40323,Complete,Svetlana up
bsdb:40032727/5/2,40032727,"cross-sectional observational, not case-control",40032727,10.1080/19490976.2025.2469716,https://pmc.ncbi.nlm.nih.gov/articles/PMC11881836/#sec26,"Santiso-Bellón C., Randazzo W., Carmona-Vicente N., Peña-Gil N., Cárcamo-Calvo R., Lopez-Navarro S., Navarro-Lleó N., Yebra M.J., Monedero V., Buesa J., Gozalbo-Rovira R. , Rodríguez-Díaz J.",<i>Rhodococcus</i> spp. interacts with human norovirus in clinical samples and impairs its replication on human intestinal enteroids,Gut microbes,2025,"Human norovirus, Rhodococcus, gut microbiota, histo-blood group antigens, human intestinal enteroids, stool samples",Experiment 5,Spain,Homo sapiens,Feces,UBERON:0001988,Viral disease,EFO:0000763,Anti-NoV GII.4 Sydney 2012 pAb + Total bacteria isolated before treatments + IgG isotype control pAb (NoV+T+C),Isotype control nor the specific pAb (N),Isotype control nor the specific pAb (N),3,1,NA,16S,34,Illumina,relative abundances,Dunn's test,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 1a,11 April 2025,Shulamite,Shulamite,"LDA of bacterial genera quantified from clinical samples with NoV. The LDA score of 15 taxa with significant differences (p<0.05 in Kruskal-Wallis test, adjusted by FDR) in a LEfse analysis is presented.",decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|g__Candidatus Tremblayella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum",1783272|1239|526524|526525|128827|118747;3379134|1224|28216|189384;3379134|976|117743|200644|2762318|59732;3379134|1224|28211|356|119045|407;3379134|1224|1236|72274|135621|286;1783272|201174|1760|85007|85025|1827;33090|35493|3398|72025|3803|3814|508215;3379134|1224|28211|204457|41297|13687;1783272|1239|91061|1385|90964|1279;3379134|1224|28211|356|118882|528,Complete,Svetlana up
bsdb:40032727/6/3,40032727,"cross-sectional observational, not case-control",40032727,10.1080/19490976.2025.2469716,https://pmc.ncbi.nlm.nih.gov/articles/PMC11881836/#sec26,"Santiso-Bellón C., Randazzo W., Carmona-Vicente N., Peña-Gil N., Cárcamo-Calvo R., Lopez-Navarro S., Navarro-Lleó N., Yebra M.J., Monedero V., Buesa J., Gozalbo-Rovira R. , Rodríguez-Díaz J.",<i>Rhodococcus</i> spp. interacts with human norovirus in clinical samples and impairs its replication on human intestinal enteroids,Gut microbes,2025,"Human norovirus, Rhodococcus, gut microbiota, histo-blood group antigens, human intestinal enteroids, stool samples",Experiment 6,Spain,Homo sapiens,Feces,UBERON:0001988,Viral disease,EFO:0000763,Anti-NoV GII.4 Sydney 2012 pAb + isotype control nor the specific pAb + IgG isotype control pAb (NoV+N+C),Total bacteria isolated before treatments (T),Total bacteria isolated before treatments,3,1,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 3,Fig 1a,11 April 2025,Shulamite,Shulamite,"LDA of bacterial genera quantified from clinical samples with NoV. The LDA score of 15 taxa with significant differences (p<0.05 in Kruskal-Wallis test, adjusted by FDR) in a LEfse analysis is presented.",increased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|g__Candidatus Tremblayella,3379134|1224|28216|189384,Complete,Svetlana up
bsdb:40032727/6/4,40032727,"cross-sectional observational, not case-control",40032727,10.1080/19490976.2025.2469716,https://pmc.ncbi.nlm.nih.gov/articles/PMC11881836/#sec26,"Santiso-Bellón C., Randazzo W., Carmona-Vicente N., Peña-Gil N., Cárcamo-Calvo R., Lopez-Navarro S., Navarro-Lleó N., Yebra M.J., Monedero V., Buesa J., Gozalbo-Rovira R. , Rodríguez-Díaz J.",<i>Rhodococcus</i> spp. interacts with human norovirus in clinical samples and impairs its replication on human intestinal enteroids,Gut microbes,2025,"Human norovirus, Rhodococcus, gut microbiota, histo-blood group antigens, human intestinal enteroids, stool samples",Experiment 6,Spain,Homo sapiens,Feces,UBERON:0001988,Viral disease,EFO:0000763,Anti-NoV GII.4 Sydney 2012 pAb + isotype control nor the specific pAb + IgG isotype control pAb (NoV+N+C),Total bacteria isolated before treatments (T),Total bacteria isolated before treatments,3,1,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 4,Fig 1a,11 April 2025,Shulamite,Shulamite,"LDA of bacterial genera quantified from clinical samples with NoV. The LDA score of 15 taxa with significant differences (p<0.05 in Kruskal-Wallis test, adjusted by FDR) in a LEfSe analysis is presented.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Pandoraea",3379134|1224|28211|356|119045|407;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|135614|32033|40323;1783272|201174|1760|85007|85025|1827;1783272|1239|526524|526525|128827|118747;1783272|1239|526524|526525|128827|174708;33090|35493|3398|72025|3803|3814|508215;3379134|1224|28211|356|118882|528;3379134|1224|28211|204457|41297|13687;3379134|1224|28211|356|82115|357;3379134|976|117743|200644|2762318|59732;1783272|201174|1760|85006|85019|1696;3379134|1224|1236|72274|135621|286;3379134|1224|28216|80840|119060|93217,Complete,Svetlana up
bsdb:40032727/7/1,40032727,"cross-sectional observational, not case-control",40032727,10.1080/19490976.2025.2469716,https://pmc.ncbi.nlm.nih.gov/articles/PMC11881836/#sec26,"Santiso-Bellón C., Randazzo W., Carmona-Vicente N., Peña-Gil N., Cárcamo-Calvo R., Lopez-Navarro S., Navarro-Lleó N., Yebra M.J., Monedero V., Buesa J., Gozalbo-Rovira R. , Rodríguez-Díaz J.",<i>Rhodococcus</i> spp. interacts with human norovirus in clinical samples and impairs its replication on human intestinal enteroids,Gut microbes,2025,"Human norovirus, Rhodococcus, gut microbiota, histo-blood group antigens, human intestinal enteroids, stool samples",Experiment 7,Spain,Homo sapiens,Feces,UBERON:0001988,Viral disease,EFO:0000763,Anti-NoV GII.4 Sydney 2012 pAb + Isotype control nor the specific pAb +Total bacteria isolated before treatments (NoV+N+T),IgG isotype control pAb (C),Bacteria recognized by the IgG isotype control antibody,3,1,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 1a,11 April 2025,Shulamite,Shulamite,"LDA of bacterial genera quantified from clinical samples with NoV. The LDA score of 15 taxa with significant differences (p<0.05 in Kruskal-Wallis test, adjusted by FDR) in a LEfse analysis is presented.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|g__Candidatus Tremblayella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",1783272|201174|1760|85007|85025|1827;33090|35493|3398|72025|3803|3814|508215;1783272|1239|526524|526525|128827|118747;3379134|1224|28211|356|118882|528;3379134|1224|28216|189384;3379134|1224|28211|204457|41297|13687;1783272|1239|91061|1385|90964|1279;3379134|1224|28211|356|119045|407;3379134|976|117743|200644|2762318|59732;3379134|1224|1236|72274|135621|286,Complete,Svetlana up
bsdb:40032727/7/2,40032727,"cross-sectional observational, not case-control",40032727,10.1080/19490976.2025.2469716,https://pmc.ncbi.nlm.nih.gov/articles/PMC11881836/#sec26,"Santiso-Bellón C., Randazzo W., Carmona-Vicente N., Peña-Gil N., Cárcamo-Calvo R., Lopez-Navarro S., Navarro-Lleó N., Yebra M.J., Monedero V., Buesa J., Gozalbo-Rovira R. , Rodríguez-Díaz J.",<i>Rhodococcus</i> spp. interacts with human norovirus in clinical samples and impairs its replication on human intestinal enteroids,Gut microbes,2025,"Human norovirus, Rhodococcus, gut microbiota, histo-blood group antigens, human intestinal enteroids, stool samples",Experiment 7,Spain,Homo sapiens,Feces,UBERON:0001988,Viral disease,EFO:0000763,Anti-NoV GII.4 Sydney 2012 pAb + Isotype control nor the specific pAb +Total bacteria isolated before treatments (NoV+N+T),IgG isotype control pAb (C),Bacteria recognized by the IgG isotype control antibody,3,1,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 1a,11 April 2025,Shulamite,Shulamite,"LDA of bacterial genera quantified from clinical samples with NoV. The LDA score of 15 taxa with significant differences (p<0.05 in Kruskal-Wallis test, adjusted by FDR) in a LEfse analysis is presented.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Pandoraea",1783272|201174|1760|85006|85019|1696;3379134|1224|28211|356|82115|357;3379134|1224|1236|135614|32033|40323;1783272|1239|526524|526525|128827|174708;3379134|1224|28216|80840|119060|93217,Complete,Svetlana up
bsdb:40032727/8/1,40032727,"cross-sectional observational, not case-control",40032727,10.1080/19490976.2025.2469716,https://pmc.ncbi.nlm.nih.gov/articles/PMC11881836/#sec26,"Santiso-Bellón C., Randazzo W., Carmona-Vicente N., Peña-Gil N., Cárcamo-Calvo R., Lopez-Navarro S., Navarro-Lleó N., Yebra M.J., Monedero V., Buesa J., Gozalbo-Rovira R. , Rodríguez-Díaz J.",<i>Rhodococcus</i> spp. interacts with human norovirus in clinical samples and impairs its replication on human intestinal enteroids,Gut microbes,2025,"Human norovirus, Rhodococcus, gut microbiota, histo-blood group antigens, human intestinal enteroids, stool samples",Experiment 8,Spain,Homo sapiens,Feces,UBERON:0001988,Viral disease,EFO:0000763,Anti-NoV GII.4 Sydney 2012 pAb + Total bacteria isolated before treatments + IgG isotype control pAb (NoV+T+C),Isotype control nor the specific pAb (N),Bacteria unreactive to any antibodies,3,1,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. S2A,11 April 2025,Shulamite,"Shulamite,KateRasheed","LEfSe analysis of different subsamples (N, NoV, T and C) at the species level.",increased,NA,NA,Complete,Svetlana up
bsdb:40032727/8/2,40032727,"cross-sectional observational, not case-control",40032727,10.1080/19490976.2025.2469716,https://pmc.ncbi.nlm.nih.gov/articles/PMC11881836/#sec26,"Santiso-Bellón C., Randazzo W., Carmona-Vicente N., Peña-Gil N., Cárcamo-Calvo R., Lopez-Navarro S., Navarro-Lleó N., Yebra M.J., Monedero V., Buesa J., Gozalbo-Rovira R. , Rodríguez-Díaz J.",<i>Rhodococcus</i> spp. interacts with human norovirus in clinical samples and impairs its replication on human intestinal enteroids,Gut microbes,2025,"Human norovirus, Rhodococcus, gut microbiota, histo-blood group antigens, human intestinal enteroids, stool samples",Experiment 8,Spain,Homo sapiens,Feces,UBERON:0001988,Viral disease,EFO:0000763,Anti-NoV GII.4 Sydney 2012 pAb + Total bacteria isolated before treatments + IgG isotype control pAb (NoV+T+C),Isotype control nor the specific pAb (N),Bacteria unreactive to any antibodies,3,1,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. S2A,11 April 2025,Shulamite,Shulamite,"LEfSe analysis of different subsamples (N, NoV, T and C) at the species level.",decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus|s__Rhodococcus erythropolis,1783272|201174|1760|85007|85025|1827|1833,Complete,Svetlana up
bsdb:40032727/9/1,40032727,"cross-sectional observational, not case-control",40032727,10.1080/19490976.2025.2469716,https://pmc.ncbi.nlm.nih.gov/articles/PMC11881836/#sec26,"Santiso-Bellón C., Randazzo W., Carmona-Vicente N., Peña-Gil N., Cárcamo-Calvo R., Lopez-Navarro S., Navarro-Lleó N., Yebra M.J., Monedero V., Buesa J., Gozalbo-Rovira R. , Rodríguez-Díaz J.",<i>Rhodococcus</i> spp. interacts with human norovirus in clinical samples and impairs its replication on human intestinal enteroids,Gut microbes,2025,"Human norovirus, Rhodococcus, gut microbiota, histo-blood group antigens, human intestinal enteroids, stool samples",Experiment 9,Spain,Homo sapiens,Feces,UBERON:0001988,Viral disease,EFO:0000763,Anti-NoV GII.4 Sydney 2012 pAb + Isotype control nor the specific pAb +Total bacteria isolated before treatments (NoV+N+T),IgG isotype control pAb (C),Bacteria recognized by the IgG isotype control antibody,3,1,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. S2A,11 April 2025,Shulamite,Shulamite,"LEfSe analysis of different subsamples (N, NoV, T and C) at the species level",increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus|s__Rhodococcus erythropolis,1783272|201174|1760|85007|85025|1827|1833,Complete,Svetlana up
bsdb:40032727/9/2,40032727,"cross-sectional observational, not case-control",40032727,10.1080/19490976.2025.2469716,https://pmc.ncbi.nlm.nih.gov/articles/PMC11881836/#sec26,"Santiso-Bellón C., Randazzo W., Carmona-Vicente N., Peña-Gil N., Cárcamo-Calvo R., Lopez-Navarro S., Navarro-Lleó N., Yebra M.J., Monedero V., Buesa J., Gozalbo-Rovira R. , Rodríguez-Díaz J.",<i>Rhodococcus</i> spp. interacts with human norovirus in clinical samples and impairs its replication on human intestinal enteroids,Gut microbes,2025,"Human norovirus, Rhodococcus, gut microbiota, histo-blood group antigens, human intestinal enteroids, stool samples",Experiment 9,Spain,Homo sapiens,Feces,UBERON:0001988,Viral disease,EFO:0000763,Anti-NoV GII.4 Sydney 2012 pAb + Isotype control nor the specific pAb +Total bacteria isolated before treatments (NoV+N+T),IgG isotype control pAb (C),Bacteria recognized by the IgG isotype control antibody,3,1,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. S2A,12 April 2025,Shulamite,Shulamite,"LEfSe analysis of different subsamples (N, NoV, T and C) at the species level.",decreased,NA,NA,Complete,Svetlana up
bsdb:40032727/10/1,40032727,"cross-sectional observational, not case-control",40032727,10.1080/19490976.2025.2469716,https://pmc.ncbi.nlm.nih.gov/articles/PMC11881836/#sec26,"Santiso-Bellón C., Randazzo W., Carmona-Vicente N., Peña-Gil N., Cárcamo-Calvo R., Lopez-Navarro S., Navarro-Lleó N., Yebra M.J., Monedero V., Buesa J., Gozalbo-Rovira R. , Rodríguez-Díaz J.",<i>Rhodococcus</i> spp. interacts with human norovirus in clinical samples and impairs its replication on human intestinal enteroids,Gut microbes,2025,"Human norovirus, Rhodococcus, gut microbiota, histo-blood group antigens, human intestinal enteroids, stool samples",Experiment 10,Spain,Homo sapiens,Feces,UBERON:0001988,Viral disease,EFO:0000763,Anti-NoV GII.4 Sydney 2012 antibody. (NoV) + IgG isotype control pAb (C) + isotype control antibody nor the specific antibody (N),Total bacteria (T),Total bacteria isolated before treatments,3,1,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. S2A,11 April 2025,Shulamite,Shulamite,"LEfSe analysis of different subsamples (N, NoV, T and C) at the species level",decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus|s__Rhodococcus erythropolis,1783272|201174|1760|85007|85025|1827|1833,Complete,Svetlana up
bsdb:40032727/11/1,40032727,"cross-sectional observational, not case-control",40032727,10.1080/19490976.2025.2469716,https://pmc.ncbi.nlm.nih.gov/articles/PMC11881836/#sec26,"Santiso-Bellón C., Randazzo W., Carmona-Vicente N., Peña-Gil N., Cárcamo-Calvo R., Lopez-Navarro S., Navarro-Lleó N., Yebra M.J., Monedero V., Buesa J., Gozalbo-Rovira R. , Rodríguez-Díaz J.",<i>Rhodococcus</i> spp. interacts with human norovirus in clinical samples and impairs its replication on human intestinal enteroids,Gut microbes,2025,"Human norovirus, Rhodococcus, gut microbiota, histo-blood group antigens, human intestinal enteroids, stool samples",Experiment 11,Spain,Homo sapiens,Feces,UBERON:0001988,Viral disease,EFO:0000763,Total bacteria isolated before treatments + IgG isotype control pAb or the specific pAb + IgG isotype control pAb (T+C+N),Anti-NoV GII.4 Sydney 2012 antibody. (NoV),Bacteria recognized by the anti-NoV GII.4 Sydney 2012 antibody.,3,1,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. S2A,11 April 2025,Shulamite,Shulamite,"LEfSe analysis of different subsamples (N, NoV, T and C) at the species level.",increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus|s__Rhodococcus erythropolis,1783272|201174|1760|85007|85025|1827|1833,Complete,Svetlana up
bsdb:40042645/1/1,40042645,case-control,40042645,10.1007/s10048-025-00816-9,NA,"Rust C., Asmal L., O'Hare M., Pretorius E., Emsley R., Seedat S. , Hemmings S.",Investigating the gut microbiome in schizophrenia cases versus controls: South Africa's version,Neurogenetics,2025,"Alpha-diversity, Beta-diversity, Gut microbiome, Gut-brain-axis, Schizophrenia",Experiment 1,South Africa,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Controls,Schizophrenia (SCZ) cases,Schizophrenia cases consisting of 24 first-episode schizophrenia (SCZ) and 17 chronic schizophrenia (SCZ) cases.,48,41,1 month,16S,4,Illumina,log transformation,ANCOM-BC,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 2,25 November 2025,Chumzine,Chumzine,"Statistically significant differences in the relative abundance of taxa between schizophrenia (SCZ) cases and controls, prior to correction for multiple testing.",increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,1783272|1239|909932|1843488|909930|33024,Complete,KateRasheed
bsdb:40042645/1/2,40042645,case-control,40042645,10.1007/s10048-025-00816-9,NA,"Rust C., Asmal L., O'Hare M., Pretorius E., Emsley R., Seedat S. , Hemmings S.",Investigating the gut microbiome in schizophrenia cases versus controls: South Africa's version,Neurogenetics,2025,"Alpha-diversity, Beta-diversity, Gut microbiome, Gut-brain-axis, Schizophrenia",Experiment 1,South Africa,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Controls,Schizophrenia (SCZ) cases,Schizophrenia cases consisting of 24 first-episode schizophrenia (SCZ) and 17 chronic schizophrenia (SCZ) cases.,48,41,1 month,16S,4,Illumina,log transformation,ANCOM-BC,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 2,25 November 2025,Chumzine,Chumzine,"Statistically significant differences in the relative abundance of taxa between schizophrenia (SCZ) cases and controls, prior to correction for multiple testing.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|171552|838;1783272|1239|909932|1843489|31977|39948,Complete,KateRasheed
bsdb:40050445/1/1,40050445,prospective cohort,40050445,10.1038/s43856-025-00773-2,NA,"Akhi R., Lavrinienko A., Hakula M., Tjäderhane L., Hindström R., Nissinen A., Wang C., Auvinen J., Kullaa A.M., Ylöstalo P., Salo T., Kaikkonen K., Koskimäki J.J. , Hörkkö S.",Oral microbiome diversity associates with carotid intima media thickness in middle-aged male subjects,Communications medicine,2025,NA,Experiment 1,Finland,Homo sapiens,Saliva,UBERON:0001836,Carotid artery intima media thickness,EFO:0007117,Inverse association with male cIMT (carotid Intima Media Thickness),Positive association with male cIMT (carotid Intima Media Thickness),Subjects with Positive association with male cIMT (carotid Intima Media Thickness),NA,NA,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,"blood pressure,body mass index",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2B,7 April 2025,Montana-D,Montana-D,The association of males with low cIMT and high cIMT with statistically significant oral bacteria taxa,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976|200643|171549|171552|838;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843489|31977|29465,Complete,Svetlana up
bsdb:40050445/1/2,40050445,prospective cohort,40050445,10.1038/s43856-025-00773-2,NA,"Akhi R., Lavrinienko A., Hakula M., Tjäderhane L., Hindström R., Nissinen A., Wang C., Auvinen J., Kullaa A.M., Ylöstalo P., Salo T., Kaikkonen K., Koskimäki J.J. , Hörkkö S.",Oral microbiome diversity associates with carotid intima media thickness in middle-aged male subjects,Communications medicine,2025,NA,Experiment 1,Finland,Homo sapiens,Saliva,UBERON:0001836,Carotid artery intima media thickness,EFO:0007117,Inverse association with male cIMT (carotid Intima Media Thickness),Positive association with male cIMT (carotid Intima Media Thickness),Subjects with Positive association with male cIMT (carotid Intima Media Thickness),NA,NA,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,"blood pressure,body mass index",NA,NA,NA,NA,NA,NA,Signature 2,Figure 2B,7 April 2025,Montana-D,Montana-D,The association of males with low cIMT and high CIMT with statistically significant oral bacteria taxa.,decreased,"p__Candidatus Absconditibacteriota,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",221235;3379134|976|117743|200644|49546|1016;1783272|1239|91061|1385|539738|1378;3384189|32066|203490|203491|203492|848;3379134|1224|28216|206351|481|482;3379134|1224|1236|135625|712|416916;3379134|976|200643|171549|2005525|195950;3379134|203691|203692|136|2845253|157;3379134|1224|1236|135615|868|2717;3379134|976|200643|171549,Complete,Svetlana up
bsdb:40050917/1/1,40050917,time series / longitudinal observational,40050917,https://doi.org/10.1186/s12967-024-05832-1,NA,"Zou B., Liu S., Dong C., Shen H., Lv Y., He J., Li X., Ruan M., Huang Z. , Shu S.",Fecal microbiota transplantation restores gut microbiota diversity in children with active Crohn's disease: a prospective trial,Journal of translational medicine,2025,"Children, Core functional genera, Crohn’s disease, Efficacy and safety, Oral fecal microbiota capsules",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Healthy donors,Crohn’s disease,Patients with Crohn's disease,16,42,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Within-text result of ""Improvement in microbial dysbiosis following oral FMT administration""",24 March 2025,EniolaAde,"EniolaAde,Tosin",Relative abundance in patients with Crohns disease vs healthy donors,decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,KateRasheed
bsdb:40050917/1/2,40050917,time series / longitudinal observational,40050917,https://doi.org/10.1186/s12967-024-05832-1,NA,"Zou B., Liu S., Dong C., Shen H., Lv Y., He J., Li X., Ruan M., Huang Z. , Shu S.",Fecal microbiota transplantation restores gut microbiota diversity in children with active Crohn's disease: a prospective trial,Journal of translational medicine,2025,"Children, Core functional genera, Crohn’s disease, Efficacy and safety, Oral fecal microbiota capsules",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Crohn's disease,EFO:0000384,Healthy donors,Crohn’s disease,Patients with Crohn's disease,16,42,NA,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Within-text result of ""Improvement in microbial dysbiosis following oral FMT administration""",24 March 2025,EniolaAde,"EniolaAde,Tosin",Relative abundance in patients with crohns disease and healthy donor control,decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,KateRasheed
bsdb:40050917/2/1,40050917,time series / longitudinal observational,40050917,https://doi.org/10.1186/s12967-024-05832-1,NA,"Zou B., Liu S., Dong C., Shen H., Lv Y., He J., Li X., Ruan M., Huang Z. , Shu S.",Fecal microbiota transplantation restores gut microbiota diversity in children with active Crohn's disease: a prospective trial,Journal of translational medicine,2025,"Children, Core functional genera, Crohn’s disease, Efficacy and safety, Oral fecal microbiota capsules",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Healthy donors,Crohn’s disease (FMT0W) (Fecal microbiota transplantation before treatment),Patients with Crohn's disease before fecal microbiota transplantation treatment (FMT0W),16,17,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3.5,NA,NA,NA,decreased,decreased,increased,NA,decreased,Signature 1,Supplementary Figure 3,29 March 2025,EniolaAde,"EniolaAde,Tosin",LEfSe of the different genera in healthy donor control and patients with crohn’s disease before (fecal microbiota transplantation) FMT,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549;3379134|976|200643;3379134|976;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|909932;1783272|1239|186801|186802|216572;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|292632;3379134|1224|28216|80840|995019,Complete,KateRasheed
bsdb:40050917/2/2,40050917,time series / longitudinal observational,40050917,https://doi.org/10.1186/s12967-024-05832-1,NA,"Zou B., Liu S., Dong C., Shen H., Lv Y., He J., Li X., Ruan M., Huang Z. , Shu S.",Fecal microbiota transplantation restores gut microbiota diversity in children with active Crohn's disease: a prospective trial,Journal of translational medicine,2025,"Children, Core functional genera, Crohn’s disease, Efficacy and safety, Oral fecal microbiota capsules",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Healthy donors,Crohn’s disease (FMT0W) (Fecal microbiota transplantation before treatment),Patients with Crohn's disease before fecal microbiota transplantation treatment (FMT0W),16,17,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3.5,NA,NA,NA,decreased,decreased,increased,NA,decreased,Signature 2,Supplementary Figure 3,29 March 2025,EniolaAde,"EniolaAde,Tosin",LEfSe of the different genera in healthy donor control and patients with crohns disease before (fecal microbiota transplantation) FMT,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae",1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|201174|84998|84999|84107;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|1903414,Complete,KateRasheed
bsdb:40050917/3/1,40050917,time series / longitudinal observational,40050917,https://doi.org/10.1186/s12967-024-05832-1,NA,"Zou B., Liu S., Dong C., Shen H., Lv Y., He J., Li X., Ruan M., Huang Z. , Shu S.",Fecal microbiota transplantation restores gut microbiota diversity in children with active Crohn's disease: a prospective trial,Journal of translational medicine,2025,"Children, Core functional genera, Crohn’s disease, Efficacy and safety, Oral fecal microbiota capsules",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Healthy donors,Crohn’s disease (FMT0W) (Fecal microbiota transplantation before treatment),Patients with Crohn's disease before (fecal microbiota transplantation) FMT treatment,16,17,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,increased,NA,decreased,Signature 1,Supplementary figure 4,9 April 2025,EniolaAde,"EniolaAde,Tosin",Relative abundance of bacteria between healthy donor group and pre-FMT (pre-fecal microbiota transplantation),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",1783272|1239|186801|3085636|186803|1766253;3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|841;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|292632,Complete,KateRasheed
bsdb:40050917/3/2,40050917,time series / longitudinal observational,40050917,https://doi.org/10.1186/s12967-024-05832-1,NA,"Zou B., Liu S., Dong C., Shen H., Lv Y., He J., Li X., Ruan M., Huang Z. , Shu S.",Fecal microbiota transplantation restores gut microbiota diversity in children with active Crohn's disease: a prospective trial,Journal of translational medicine,2025,"Children, Core functional genera, Crohn’s disease, Efficacy and safety, Oral fecal microbiota capsules",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Healthy donors,Crohn’s disease (FMT0W) (Fecal microbiota transplantation before treatment),Patients with Crohn's disease before (fecal microbiota transplantation) FMT treatment,16,17,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,increased,NA,decreased,Signature 2,Supplementary Figure 4,9 April 2025,EniolaAde,"EniolaAde,Tosin",Relative proportion of bacteria between healthy donor group and pre-FMT (pre-fecal microbiota transplantation),increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,1783272|1239|186801|3082720|186804|1870884,Complete,KateRasheed
bsdb:40050917/4/1,40050917,time series / longitudinal observational,40050917,https://doi.org/10.1186/s12967-024-05832-1,NA,"Zou B., Liu S., Dong C., Shen H., Lv Y., He J., Li X., Ruan M., Huang Z. , Shu S.",Fecal microbiota transplantation restores gut microbiota diversity in children with active Crohn's disease: a prospective trial,Journal of translational medicine,2025,"Children, Core functional genera, Crohn’s disease, Efficacy and safety, Oral fecal microbiota capsules",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,FMT0W (Fecal microbiota transplantation before treatment),FMT5W (Fecal microbiota transplantation at week 5 after oral capsule treatment),Patients given fecal microbiota transplantation treatment after five weeks,17,8,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 1,Figure 6A,9 April 2025,EniolaAde,"EniolaAde,Tosin",Relative abundance genera between FMT0W (Fecal microbiota transplantation before treatment) and FMT5W (Fecal microbiota transplantation at week 5 after oral capsule treatment),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|292632,Complete,KateRasheed
bsdb:40050917/5/1,40050917,time series / longitudinal observational,40050917,https://doi.org/10.1186/s12967-024-05832-1,NA,"Zou B., Liu S., Dong C., Shen H., Lv Y., He J., Li X., Ruan M., Huang Z. , Shu S.",Fecal microbiota transplantation restores gut microbiota diversity in children with active Crohn's disease: a prospective trial,Journal of translational medicine,2025,"Children, Core functional genera, Crohn’s disease, Efficacy and safety, Oral fecal microbiota capsules",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,FMT0W (Fecal Microbiota Transplantation before treatment),FMT10W (Fecal microbiota transplantation at week 10 after oral capsule treatment),Patients given fecal microbiota transplantation treatment after Ten weeks,17,17,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,increased,decreased,NA,increased,Signature 1,Figure 6A,9 April 2025,EniolaAde,"EniolaAde,MyleeeA",Relative abundance of the core functional genera between FMT0W (Fecal microbiota transplantation before treatment) and FMT10W (Fecal microbiota transplantation at week 10 after oral capsule treatment) determined using the Wilcoxon rank-sum test.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",1783272|1239|186801|3085636|186803|1766253;3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|292632,Complete,KateRasheed
bsdb:40050917/6/1,40050917,time series / longitudinal observational,40050917,https://doi.org/10.1186/s12967-024-05832-1,NA,"Zou B., Liu S., Dong C., Shen H., Lv Y., He J., Li X., Ruan M., Huang Z. , Shu S.",Fecal microbiota transplantation restores gut microbiota diversity in children with active Crohn's disease: a prospective trial,Journal of translational medicine,2025,"Children, Core functional genera, Crohn’s disease, Efficacy and safety, Oral fecal microbiota capsules",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Healthy donors,Crohns disease-FMT0W (Fecal Microbiota Transplantation before treatment),Patients with Crohns disease before Fecal Microbiota Transplantation treatment,16,17,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,increased,NA,decreased,Signature 1,Figure 6A,10 April 2025,EniolaAde,"EniolaAde,MyleeeA",Relative abundance of the core functional genera between Crohns disease-FMT0W (Fecal Microbiota Transplantation before treatment) and Healthy donor determined using the Wilcoxon rank-sum test.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",1783272|1239|186801|3085636|186803|1766253;3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|292632,Complete,KateRasheed
bsdb:40050917/7/1,40050917,time series / longitudinal observational,40050917,https://doi.org/10.1186/s12967-024-05832-1,NA,"Zou B., Liu S., Dong C., Shen H., Lv Y., He J., Li X., Ruan M., Huang Z. , Shu S.",Fecal microbiota transplantation restores gut microbiota diversity in children with active Crohn's disease: a prospective trial,Journal of translational medicine,2025,"Children, Core functional genera, Crohn’s disease, Efficacy and safety, Oral fecal microbiota capsules",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Response to transplant,EFO:0007043,FMT0W (Fecal Microbiota Transplantation before treatment),FMT10W (Fecal microbiota transplantation at week 10 after oral capsule treatment),Patients given fecal microbiota transplantation treatment after Ten weeks,17,17,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,increased,increased,decreased,NA,increased,Signature 1,Supplementary Table 6,10 April 2025,EniolaAde,"EniolaAde,MyleeeA",Relative abundance of the core functional genera between Fecal Microbiota Transplantation week 0 (FMT0W) and Fecal Microbiota Transplantation week 10 (FMT10W).,increased,k__Pseudomonadati|p__Verrucomicrobiota,3379134|74201,Complete,KateRasheed
bsdb:40059170/1/1,40059170,"cross-sectional observational, not case-control",40059170,https://doi.org/10.1186/s12916-025-03969-4,NA,"Duan Y., Xu C., Wang W., Wang X., Xu N., Zhong J., Gong W., Zheng W., Wu Y.H., Myers A., Chu L., Lu Y., Delzell E., Hsing A.W., Yu M., He W. , Zhu S.",Smoking-related gut microbiota alteration is associated with obesity and obesity-related diseases: results from two cohorts with sibling comparison analyses,BMC medicine,2025,"Gut microbiota, Obesity, Obesity-related disease, Smoking",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Body mass index,EFO:0004340,Low BMI (Body Mass Index) (WELL-China cohort),High BMI (Body Mass Index) (WELL-China cohort),Individuals with high body mass index in the WELL-China cohort (the discovery cohort),NA,NA,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 1B (C2),23 April 2025,PreciousChijioke,"PreciousChijioke,Anne-mariesharp",Smoking-related microbial genera and obesity in the WELL-China cohort,decreased,",k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136",;1783272|1239|186801|3085636|186803|877420,Complete,KateRasheed
bsdb:40059170/2/1,40059170,"cross-sectional observational, not case-control",40059170,https://doi.org/10.1186/s12916-025-03969-4,NA,"Duan Y., Xu C., Wang W., Wang X., Xu N., Zhong J., Gong W., Zheng W., Wu Y.H., Myers A., Chu L., Lu Y., Delzell E., Hsing A.W., Yu M., He W. , Zhu S.",Smoking-related gut microbiota alteration is associated with obesity and obesity-related diseases: results from two cohorts with sibling comparison analyses,BMC medicine,2025,"Gut microbiota, Obesity, Obesity-related disease, Smoking",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Body fat percentage,EFO:0007800,Low body fat (WELL-China cohort),High body fat (WELL-China cohort),Individuals with high body fat percentage in the WELL-China cohort (the discovery cohort),NA,NA,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 1B (C2),23 April 2025,PreciousChijioke,"PreciousChijioke,Anne-mariesharp",Smoking-related microbial genera and obesity in the WELL-China cohort,decreased,",k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136",;1783272|1239|186801|3085636|186803|877420,Complete,KateRasheed
bsdb:40059170/3/2,40059170,"cross-sectional observational, not case-control",40059170,https://doi.org/10.1186/s12916-025-03969-4,NA,"Duan Y., Xu C., Wang W., Wang X., Xu N., Zhong J., Gong W., Zheng W., Wu Y.H., Myers A., Chu L., Lu Y., Delzell E., Hsing A.W., Yu M., He W. , Zhu S.",Smoking-related gut microbiota alteration is associated with obesity and obesity-related diseases: results from two cohorts with sibling comparison analyses,BMC medicine,2025,"Gut microbiota, Obesity, Obesity-related disease, Smoking",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Waist circumference,EFO:0004342,Low WC (Waist circumference) (WELL-China cohort),High WC (Waist circumference) (WELL-China cohort),Individuals with high waist circumference in the WELL-China cohort (the discovery cohort),NA,NA,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 1B (C2),24 April 2025,PreciousChijioke,"PreciousChijioke,Anne-mariesharp",Smoking-related microbial genera and obesity in the WELL-China cohort,decreased,",k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136",;1783272|1239|186801|3085636|186803|877420,Complete,KateRasheed
bsdb:40059170/4/1,40059170,"cross-sectional observational, not case-control",40059170,https://doi.org/10.1186/s12916-025-03969-4,NA,"Duan Y., Xu C., Wang W., Wang X., Xu N., Zhong J., Gong W., Zheng W., Wu Y.H., Myers A., Chu L., Lu Y., Delzell E., Hsing A.W., Yu M., He W. , Zhu S.",Smoking-related gut microbiota alteration is associated with obesity and obesity-related diseases: results from two cohorts with sibling comparison analyses,BMC medicine,2025,"Gut microbiota, Obesity, Obesity-related disease, Smoking",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Waist-hip ratio,EFO:0004343,Low WHR(Waist-hip ratio) (WELL-China cohort),High WHR(Waist-hip ratio) (WELL-China cohort),Individuals with high waist-hip ratio in the WELL-China cohort (the discovery cohort),NA,NA,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 1B (C2),24 April 2025,PreciousChijioke,"PreciousChijioke,Anne-mariesharp",Smoking-related microbial genera and obesity in the WELL-China cohort,decreased,",k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136",;1783272|1239|186801|3085636|186803|877420,Complete,KateRasheed
bsdb:40059170/5/1,40059170,"cross-sectional observational, not case-control",40059170,https://doi.org/10.1186/s12916-025-03969-4,NA,"Duan Y., Xu C., Wang W., Wang X., Xu N., Zhong J., Gong W., Zheng W., Wu Y.H., Myers A., Chu L., Lu Y., Delzell E., Hsing A.W., Yu M., He W. , Zhu S.",Smoking-related gut microbiota alteration is associated with obesity and obesity-related diseases: results from two cohorts with sibling comparison analyses,BMC medicine,2025,"Gut microbiota, Obesity, Obesity-related disease, Smoking",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Smoking status measurement,EFO:0006527,Never smokers of the WELL-China cohort,Current smokers of the WELL-China cohort,Current smokers of the WELL-China cohort (the discovery cohort),1126,1143,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Fig. 1B (C1) & Table S2,24 April 2025,PreciousChijioke,"PreciousChijioke,Anne-mariesharp",Smoking-related microbial genera identified in male participants of the WELL-China cohort.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;1783272|201174;1783272|201174|84998|84999|1643824|1380;1783272;1783272|1239|91061;1783272|1239|186801;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|186801|186802;3379134|1224|1236;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|1224;1783272|1239|526524|526525|128827|123375;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|3085636|186803|877420;,Complete,KateRasheed
bsdb:40059170/5/2,40059170,"cross-sectional observational, not case-control",40059170,https://doi.org/10.1186/s12916-025-03969-4,NA,"Duan Y., Xu C., Wang W., Wang X., Xu N., Zhong J., Gong W., Zheng W., Wu Y.H., Myers A., Chu L., Lu Y., Delzell E., Hsing A.W., Yu M., He W. , Zhu S.",Smoking-related gut microbiota alteration is associated with obesity and obesity-related diseases: results from two cohorts with sibling comparison analyses,BMC medicine,2025,"Gut microbiota, Obesity, Obesity-related disease, Smoking",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Smoking status measurement,EFO:0006527,Never smokers of the WELL-China cohort,Current smokers of the WELL-China cohort,Current smokers of the WELL-China cohort (the discovery cohort),1126,1143,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Fig. 1B (C1) & Table S2,27 April 2025,PreciousChijioke,"PreciousChijioke,Anne-mariesharp",Smoking-related microbial genera identified in male participants of the WELL-China cohort.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacillati,k__Bacillati|p__Bacillota|c__Bacilli,,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,p__Candidatus Saccharimonadota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kluyvera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] nodatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus",3379134|1224|28216|80840|506|222;1783272|1239|909932|1843488|909930;1783272|1239|909932|1843488|909930|904;1783272|201174;3379134|1224|28216|80840|506;1783272|1239|909932|1843489|31977|209879;1783272|1239|186801|3085636|186803|653683;1783272;1783272|1239|91061;;3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|1224|28216;3379134|200940|3031449|213115|194924|35832;3379134|1224|28216|80840;95818;1783272|1239|186801;1783272|201174|84998|84999|84107|102106;1783272|1239|526524|526525|2810280|100883;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;28221;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;3379134|1224|1236|91347|543|561;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730;1783272|1239|526524|526525|128827|1573534;3384189|32066|203490|203491|203492;3384189|32066|203490;3384189|32066;3384189|32066|203490|203491|203492|848;3379134|1224|1236;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|1649459;3379134|1224|1236|91347|543|579;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|877420;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|909932|1843489|31977|906;1783272|544448|31969;1783272|544448;1783272|1239|909932;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|75682;3379134|976|200643|171549|2005525|375288;3379134|1224|28216|80840|995019|577310;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|976|200643|171549|171551;3379134|1224;1783272|1239|186801|186802|216572|1263|438033;1783272|1239|909932|909929;3379134|1224|1236|91347|543|620;1783272|201174|84998|1643822|1643826|84108;1783272|1239|186801|186802|216572|292632;3379134|1224|28216|80840|995019|40544;1783272|1239|909932|1843489|31977;1783272|1239|91061|186826|33958|46255;1783272|1239|186801|3082720|543314|35518;1783272|1239|91061|186826|33958;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|3082768|990719;1783272|1239|186801|3085636|186803|33042,Complete,KateRasheed
bsdb:40059170/6/1,40059170,"cross-sectional observational, not case-control",40059170,https://doi.org/10.1186/s12916-025-03969-4,NA,"Duan Y., Xu C., Wang W., Wang X., Xu N., Zhong J., Gong W., Zheng W., Wu Y.H., Myers A., Chu L., Lu Y., Delzell E., Hsing A.W., Yu M., He W. , Zhu S.",Smoking-related gut microbiota alteration is associated with obesity and obesity-related diseases: results from two cohorts with sibling comparison analyses,BMC medicine,2025,"Gut microbiota, Obesity, Obesity-related disease, Smoking",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Smoking status measurement,EFO:0006527,Never smokers of the Lanxi cohort,Current smokers of the Lanxi cohort,Current smokers of the Lanxi cohort (the replication cohort),646,471,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Fig 1B (D1) & Table S2,27 April 2025,PreciousChijioke,"PreciousChijioke,Anne-mariesharp",Smoking-related microbial genera identified in male participants of the Lanxi cohort.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049;1783272|201174|1760|2037;1783272|201174;1783272|201174|84998|84999|1643824|1380;1783272|1239|91061;1783272|1239|186801;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|186801|186802;3379134|1224|1236;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;3379134|1224|1236|135625|712;3379134|1224|1236|135625;3379134|1224;1783272|1239|526524|526525|128827|123375;1783272|1239|186801|3085636|186803|1506577;;1783272|1239|186801|3085636|186803|877420;1783272|1239|91061|1385|539738|1378,Complete,KateRasheed
bsdb:40059170/6/2,40059170,"cross-sectional observational, not case-control",40059170,https://doi.org/10.1186/s12916-025-03969-4,NA,"Duan Y., Xu C., Wang W., Wang X., Xu N., Zhong J., Gong W., Zheng W., Wu Y.H., Myers A., Chu L., Lu Y., Delzell E., Hsing A.W., Yu M., He W. , Zhu S.",Smoking-related gut microbiota alteration is associated with obesity and obesity-related diseases: results from two cohorts with sibling comparison analyses,BMC medicine,2025,"Gut microbiota, Obesity, Obesity-related disease, Smoking",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Smoking status measurement,EFO:0006527,Never smokers of the Lanxi cohort,Current smokers of the Lanxi cohort,Current smokers of the Lanxi cohort (the replication cohort),646,471,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Fig 1B (D1) & Table S2,27 April 2025,PreciousChijioke,"PreciousChijioke,Anne-mariesharp",Smoking-related microbial genera identified in male participants of the Lanxi cohort.,decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|201174;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|976|200643|171549|2005519|397864;3384189|32066|203490|203491|203492|180162;3379134|1224|1236|91347|543|544;1783272|1239|186801;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|946234;3384189|32066|203490|203491|203492;3384189|32066|203490|203491;3384189|32066|203490;3384189|32066;3379134|1224|1236;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171551;3379134|976|200643|171549|171552;3379134|1224;1783272|201174|84998|1643822|1643826|84108;1783272|1239|526524|526525|2810281|191303;3379134|74201|203494|48461|203557;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201;1783272|1239|91061|1385|539738|1378;3379134|1224|1236|135625|712|724;1783272|1239|186801|186802|216572|1508657;3379134|976|200643|171549|171552|838,Complete,KateRasheed
bsdb:40059170/7/1,40059170,"cross-sectional observational, not case-control",40059170,https://doi.org/10.1186/s12916-025-03969-4,NA,"Duan Y., Xu C., Wang W., Wang X., Xu N., Zhong J., Gong W., Zheng W., Wu Y.H., Myers A., Chu L., Lu Y., Delzell E., Hsing A.W., Yu M., He W. , Zhu S.",Smoking-related gut microbiota alteration is associated with obesity and obesity-related diseases: results from two cohorts with sibling comparison analyses,BMC medicine,2025,"Gut microbiota, Obesity, Obesity-related disease, Smoking",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Body fat distribution,EFO:0004341,Low Android (WELL-China cohort),High Android (WELL-China cohort),Individuals with high android fat mass in the WELL-China cohort (the discovery cohort),NA,NA,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 1B (C2),18 June 2025,Anne-mariesharp,Anne-mariesharp,Smoking-related microbial genera and obesity in the WELL-China cohort,decreased,",k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136",;1783272|1239|186801|3085636|186803|877420,Complete,KateRasheed
bsdb:40059170/8/1,40059170,"cross-sectional observational, not case-control",40059170,https://doi.org/10.1186/s12916-025-03969-4,NA,"Duan Y., Xu C., Wang W., Wang X., Xu N., Zhong J., Gong W., Zheng W., Wu Y.H., Myers A., Chu L., Lu Y., Delzell E., Hsing A.W., Yu M., He W. , Zhu S.",Smoking-related gut microbiota alteration is associated with obesity and obesity-related diseases: results from two cohorts with sibling comparison analyses,BMC medicine,2025,"Gut microbiota, Obesity, Obesity-related disease, Smoking",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Body fat distribution,EFO:0004341,Low Gynoid (WELL-China cohort),High Gynoid (WELL-China cohort),Individuals with high gynoid fat mass in the WELL-China cohort (the discovery cohort),NA,NA,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 1B (C2),18 June 2025,Anne-mariesharp,Anne-mariesharp,Smoking-related microbial genera and obesity in the WELL-China cohort,increased,",k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136",;1783272|1239|186801|3085636|186803|877420,Complete,KateRasheed
bsdb:40059170/9/1,40059170,"cross-sectional observational, not case-control",40059170,https://doi.org/10.1186/s12916-025-03969-4,NA,"Duan Y., Xu C., Wang W., Wang X., Xu N., Zhong J., Gong W., Zheng W., Wu Y.H., Myers A., Chu L., Lu Y., Delzell E., Hsing A.W., Yu M., He W. , Zhu S.",Smoking-related gut microbiota alteration is associated with obesity and obesity-related diseases: results from two cohorts with sibling comparison analyses,BMC medicine,2025,"Gut microbiota, Obesity, Obesity-related disease, Smoking",Experiment 9,China,Homo sapiens,Feces,UBERON:0001988,Body fat distribution,EFO:0004341,Low AOI(Android-gynoid fat ratio) (WELL-China cohort),High AOI(Android-gynoid fat ratio) (WELL-China cohort),Individuals with high Android-gynoid fat ratio in the WELL-China cohort (the discovery cohort),NA,NA,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 1B (C2),18 June 2025,Anne-mariesharp,Anne-mariesharp,Smoking-related microbial genera and obesity in the WELL-China cohort,decreased,",k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136",;1783272|1239|186801|3085636|186803|877420,Complete,KateRasheed
bsdb:40059170/10/1,40059170,"cross-sectional observational, not case-control",40059170,https://doi.org/10.1186/s12916-025-03969-4,NA,"Duan Y., Xu C., Wang W., Wang X., Xu N., Zhong J., Gong W., Zheng W., Wu Y.H., Myers A., Chu L., Lu Y., Delzell E., Hsing A.W., Yu M., He W. , Zhu S.",Smoking-related gut microbiota alteration is associated with obesity and obesity-related diseases: results from two cohorts with sibling comparison analyses,BMC medicine,2025,"Gut microbiota, Obesity, Obesity-related disease, Smoking",Experiment 10,China,Homo sapiens,Feces,UBERON:0001988,Body mass index,EFO:0004340,Low BMI (Body Mass Index) (Lanxi cohort),High BMI (Body Mass Index) (Lanxi cohort),Individuals with high body mass index in the Lanxi cohort (the replication cohort),NA,NA,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 1B (D2),18 June 2025,Anne-mariesharp,Anne-mariesharp,Smoking-related microbial genera and obesity in the Lanxi cohort,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,1783272|1239|186801|3085636|186803|877420,Complete,KateRasheed
bsdb:40059170/11/1,40059170,"cross-sectional observational, not case-control",40059170,https://doi.org/10.1186/s12916-025-03969-4,NA,"Duan Y., Xu C., Wang W., Wang X., Xu N., Zhong J., Gong W., Zheng W., Wu Y.H., Myers A., Chu L., Lu Y., Delzell E., Hsing A.W., Yu M., He W. , Zhu S.",Smoking-related gut microbiota alteration is associated with obesity and obesity-related diseases: results from two cohorts with sibling comparison analyses,BMC medicine,2025,"Gut microbiota, Obesity, Obesity-related disease, Smoking",Experiment 11,China,Homo sapiens,Feces,UBERON:0001988,Body fat percentage,EFO:0007800,Low body fat (Lanxi cohort),High body fat (Lanxi cohort),Individuals with high body fat percentage in the Lanxi cohort (the replication cohort),NA,NA,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 1B (D2),18 June 2025,Anne-mariesharp,Anne-mariesharp,Smoking-related microbial genera and obesity in the Lanxi cohort,decreased,",k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136",;1783272|1239|186801|3085636|186803|877420,Complete,KateRasheed
bsdb:40059170/12/1,40059170,"cross-sectional observational, not case-control",40059170,https://doi.org/10.1186/s12916-025-03969-4,NA,"Duan Y., Xu C., Wang W., Wang X., Xu N., Zhong J., Gong W., Zheng W., Wu Y.H., Myers A., Chu L., Lu Y., Delzell E., Hsing A.W., Yu M., He W. , Zhu S.",Smoking-related gut microbiota alteration is associated with obesity and obesity-related diseases: results from two cohorts with sibling comparison analyses,BMC medicine,2025,"Gut microbiota, Obesity, Obesity-related disease, Smoking",Experiment 12,China,Homo sapiens,Feces,UBERON:0001988,Waist circumference,EFO:0004342,Low WC (Waist circumference) (Lanxi cohort),High WC (Waist circumference) (Lanxi cohort),Individuals with high waist circumference in the Lanxi cohort (the replication cohort),NA,NA,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 1B (D2),18 June 2025,Anne-mariesharp,Anne-mariesharp,Smoking-related microbial genera and obesity in the Lanxi cohort,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,1783272|1239|186801|3085636|186803|877420,Complete,KateRasheed
bsdb:40059170/13/1,40059170,"cross-sectional observational, not case-control",40059170,https://doi.org/10.1186/s12916-025-03969-4,NA,"Duan Y., Xu C., Wang W., Wang X., Xu N., Zhong J., Gong W., Zheng W., Wu Y.H., Myers A., Chu L., Lu Y., Delzell E., Hsing A.W., Yu M., He W. , Zhu S.",Smoking-related gut microbiota alteration is associated with obesity and obesity-related diseases: results from two cohorts with sibling comparison analyses,BMC medicine,2025,"Gut microbiota, Obesity, Obesity-related disease, Smoking",Experiment 13,China,Homo sapiens,Feces,UBERON:0001988,Waist-hip ratio,EFO:0004343,Low WHR(Waist-hip ratio) (Lanxi cohort),High WHR(Waist-hip ratio) (Lanxi cohort),Individuals with high waist-hip ratio in the Lanxi cohort (the replication cohort),NA,NA,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 1B (D2),18 June 2025,Anne-mariesharp,Anne-mariesharp,Smoking-related microbial genera and obesity in the Lanxi cohort,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",1783272|201174|84998|84999|1643824|1380;1783272|201174|1760|2037|2049|1654,Complete,KateRasheed
bsdb:40059170/13/2,40059170,"cross-sectional observational, not case-control",40059170,https://doi.org/10.1186/s12916-025-03969-4,NA,"Duan Y., Xu C., Wang W., Wang X., Xu N., Zhong J., Gong W., Zheng W., Wu Y.H., Myers A., Chu L., Lu Y., Delzell E., Hsing A.W., Yu M., He W. , Zhu S.",Smoking-related gut microbiota alteration is associated with obesity and obesity-related diseases: results from two cohorts with sibling comparison analyses,BMC medicine,2025,"Gut microbiota, Obesity, Obesity-related disease, Smoking",Experiment 13,China,Homo sapiens,Feces,UBERON:0001988,Waist-hip ratio,EFO:0004343,Low WHR(Waist-hip ratio) (Lanxi cohort),High WHR(Waist-hip ratio) (Lanxi cohort),Individuals with high waist-hip ratio in the Lanxi cohort (the replication cohort),NA,NA,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 1B (D2),18 June 2025,Anne-mariesharp,Anne-mariesharp,Smoking-related microbial genera and obesity in the Lanxi cohort,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,1783272|1239|186801|3085636|186803|877420,Complete,KateRasheed
bsdb:40059170/14/1,40059170,"cross-sectional observational, not case-control",40059170,https://doi.org/10.1186/s12916-025-03969-4,NA,"Duan Y., Xu C., Wang W., Wang X., Xu N., Zhong J., Gong W., Zheng W., Wu Y.H., Myers A., Chu L., Lu Y., Delzell E., Hsing A.W., Yu M., He W. , Zhu S.",Smoking-related gut microbiota alteration is associated with obesity and obesity-related diseases: results from two cohorts with sibling comparison analyses,BMC medicine,2025,"Gut microbiota, Obesity, Obesity-related disease, Smoking",Experiment 14,China,Homo sapiens,Feces,UBERON:0001988,Body fat distribution,EFO:0004341,Low Android (Lanxi cohort),High Android (Lanxi cohort),Individuals with high android fat mass in the Lanxi cohort (the replication cohort),NA,NA,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 1B (D2),18 June 2025,Anne-mariesharp,Anne-mariesharp,Smoking-related microbial genera and obesity in the Lanxi cohort,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136",3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|877420,Complete,KateRasheed
bsdb:40059170/15/1,40059170,"cross-sectional observational, not case-control",40059170,https://doi.org/10.1186/s12916-025-03969-4,NA,"Duan Y., Xu C., Wang W., Wang X., Xu N., Zhong J., Gong W., Zheng W., Wu Y.H., Myers A., Chu L., Lu Y., Delzell E., Hsing A.W., Yu M., He W. , Zhu S.",Smoking-related gut microbiota alteration is associated with obesity and obesity-related diseases: results from two cohorts with sibling comparison analyses,BMC medicine,2025,"Gut microbiota, Obesity, Obesity-related disease, Smoking",Experiment 15,China,Homo sapiens,Feces,UBERON:0001988,Body fat distribution,EFO:0004341,Low Gynoid (Lanxi cohort),High Gynoid (Lanxi cohort),Individuals with high gynoid fat mass in the Lanxi cohort (the replication cohort),NA,NA,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 1B (D2),18 June 2025,Anne-mariesharp,Anne-mariesharp,Smoking-related microbial genera and obesity in the Lanxi cohort,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,",3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|877420;,Complete,KateRasheed
bsdb:40059170/16/1,40059170,"cross-sectional observational, not case-control",40059170,https://doi.org/10.1186/s12916-025-03969-4,NA,"Duan Y., Xu C., Wang W., Wang X., Xu N., Zhong J., Gong W., Zheng W., Wu Y.H., Myers A., Chu L., Lu Y., Delzell E., Hsing A.W., Yu M., He W. , Zhu S.",Smoking-related gut microbiota alteration is associated with obesity and obesity-related diseases: results from two cohorts with sibling comparison analyses,BMC medicine,2025,"Gut microbiota, Obesity, Obesity-related disease, Smoking",Experiment 16,China,Homo sapiens,Feces,UBERON:0001988,Body fat distribution,EFO:0004341,Low AOI(Android-gynoid fat ratio) (Lanxi cohort),High AOI(Android-gynoid fat ratio) (Lanxi cohort),Individuals with high Android-gynoid fat ratio in the Lanxi cohort (the replication cohort),NA,NA,NA,16S,34,Illumina,arcsine square-root,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 1B (D2),18 June 2025,Anne-mariesharp,Anne-mariesharp,Smoking-related microbial genera and obesity in the Lanxi cohort,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,",3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|877420;,Complete,KateRasheed
bsdb:40084872/1/1,40084872,case-control,40084872,10.1128/spectrum.01772-24,NA,"Wang Y., He X., Gao Y., Xue M., Zhang H., Sun L., He Q. , Jin J.",Disorders of gut microbiota and fecal-serum metabolic patterns are associated with pulmonary tuberculosis and pulmonary tuberculosis comorbid type 2 diabetes mellitus,Microbiology spectrum,2025,"diabetes mellitus, fecal metabolites, gut microbiota, metabolic pathways, pulmonary tuberculosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,"Pulmonary tuberculosis,Diabetes mellitus","EFO:1000049,EFO:0000400",Combination of healthy volunteers (Health) and pulmonary tuberculosis patients with diabetes mellitus (PTB-DM),pulmonary tuberculosis (PTB) patients,"Diagnosed via TB-PCR, AFB, Xpert, plus clinical TB",26,13,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,Figure 3A and 3B,22 July 2025,Nuerteye,Nuerteye,"Identification of differential microbial biomarkers. Cladogram visualized the most differentially abundant taxa identified by LEfSe among the three groups. Comparisons of microbiota bacteria among the three groups. The histogram showed the LDA score computed for genera differentially abundant between groups and identified using LEfSe. Health: healthy people, PTB: pulmonary tuberculosis, PTB-DM: pulmonary tuberculosis patients with diabetes mellitus.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__uncultured Ruminococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__uncultured Faecalibacterium sp.",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|207244;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|171552|577309;1783272|1239|186801|186802|216572|1263|165186;1783272|1239|186801|186802|216572|216851|259315,Complete,NA
bsdb:40084872/2/1,40084872,case-control,40084872,10.1128/spectrum.01772-24,NA,"Wang Y., He X., Gao Y., Xue M., Zhang H., Sun L., He Q. , Jin J.",Disorders of gut microbiota and fecal-serum metabolic patterns are associated with pulmonary tuberculosis and pulmonary tuberculosis comorbid type 2 diabetes mellitus,Microbiology spectrum,2025,"diabetes mellitus, fecal metabolites, gut microbiota, metabolic pathways, pulmonary tuberculosis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,"Pulmonary tuberculosis,Diabetes mellitus","EFO:1000049,EFO:0000400",Combination of pulmonary tuberculosis (PTB) and pulmonary tuberculosis patients with diabetes mellitus (PTB-DM) group,pulmonary tuberculosis (PTB) patients,"Healthy participants in our study had normal lifestyles. In terms of diet, they maintained a balanced diet with a variety of foods. Their sleep patterns were regular, ensuring an adequate amount of sleep every night. They also engaged in regular physical exercise and had effective stress control methods.",26,13,1 year,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,increased,increased,increased,NA,NA,Signature 1,Figure 3A and 3B,22 July 2025,Nuerteye,Nuerteye,"Identification of differential microbial biomarkers. Cladogram visualized the most differentially abundant taxa identified by LEfSe among the three groups. Comparisons of microbiota bacteria among the three groups. The histogram showed the LDA score computed for genera differentially abundant between groups and identified using LEfSe. Health: healthy people, PTB: pulmonary tuberculosis, PTB-DM: pulmonary tuberculosis patients with diabetes mellitus.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella tanakaei,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__uncultured Roseburia sp.",1783272|1239|186801|186802|3085642|580596;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|201174|84998|84999|84107|102106|626935;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|186801|3085636|186803|28050;3379134|1224|28211|204441;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|841|512314,Complete,NA
bsdb:40084872/3/1,40084872,case-control,40084872,10.1128/spectrum.01772-24,NA,"Wang Y., He X., Gao Y., Xue M., Zhang H., Sun L., He Q. , Jin J.",Disorders of gut microbiota and fecal-serum metabolic patterns are associated with pulmonary tuberculosis and pulmonary tuberculosis comorbid type 2 diabetes mellitus,Microbiology spectrum,2025,"diabetes mellitus, fecal metabolites, gut microbiota, metabolic pathways, pulmonary tuberculosis",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,"Pulmonary tuberculosis,Diabetes mellitus","EFO:1000049,EFO:0000400",Combination of healthy volunteers (Health) and pulmonary tuberculosis (PTB) group,pulmonary tuberculosis and diabetes mellitus (PTB–DM),"Individuals presenting typical diabetic symptoms (polyuria, polydipsia, unexplained weight loss), fasting blood glucose ≥11.1 mmol or random blood glucose levels ≥ 11.1 mmol/L, and age between 18 and 65 years",26,13,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,Figure 3A and 3B,22 July 2025,Nuerteye,Nuerteye,"Identification of differential microbial biomarkers. Cladogram visualized the most differentially abundant taxa identified by LEfSe among the three groups. Comparisons of microbiota bacteria among the three groups. The histogram showed the LDA score computed for genera differentially abundant between groups and identified using LEfSe. Health: healthy people, PTB: pulmonary tuberculosis, PTB-DM: pulmonary tuberculosis patients with diabetes mellitus.",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",1783272|1239|91061|186826;1783272|1239|91061;3384189|32066|203490|203491;3384189|32066|203490|203491|203492;3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492|848|850;1783272|1239|186801|186802|216572|216851,Complete,NA
bsdb:40087549/1/1,40087549,"cross-sectional observational, not case-control",40087549,10.1186/s12866-025-03863-2,NA,"Wang X., Shang Y., Xing Y., Chen Y., Wu X. , Zhang H.",Captive environments reshape the compositions of carbohydrate active enzymes and virulence factors in wolf gut microbiome,BMC microbiology,2025,"Captive environmental, Ecological niches, Family canidae, Gut microbiome",Experiment 1,China,Vulpes vulpes,Feces,UBERON:0001988,Species design,EFO:0001753,Corsac fox,Red fox,Wild red fox whose fecal samples were collected from three different individuals residing in Hulun Lake area using the snow-fresh tracking method to ensure the feces were freshly deposited in the wild,3,3,NA,WMS,NA,Illumina,centered log-ratio,Welch's T-Test,0.01,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Supplementary Material 1: Supplementary Table 1,13 November 2025,Tosin,Tosin,"Results of an ALDEx2 (Analysis of Differential Abundance Taking Sample and Scale Variation Into Account) analysis of differential bacterial species between corsac fox and red fox (effect ≥ 3, p < 0.01)",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter proteolyticus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Aequorivita|s__Aequorivita sublithincola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. dk3624,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Allomuricauda|s__Allomuricauda sp.,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Allomuricauda|s__Allomuricauda sp. SCSIO 65647,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Amniculibacterium|s__Amniculibacterium sp. G2-70,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Anseongella|s__Anseongella ginsenosidimutans,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Apibacter|s__Apibacter raozihei,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cyclobacteriaceae|g__Aquiflexum|s__Aquiflexum balticum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Aquipluma|s__Aquipluma nitroreducens,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Arachidicoccus|s__Arachidicoccus ginsenosidivorans,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Arachidicoccus|s__Arachidicoccus terrestris,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Arenibacter|s__Arenibacter algicola,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. RZ2MS9,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas faecihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas paravirosa,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|g__Candidatus Azobacteroides|s__Candidatus Azobacteroides pseudotrichonymphae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sp. oral taxon 878,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Chitinophaga|s__Chitinophaga alhagiae,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Chitinophaga|s__Chitinophaga horti,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Chitinophaga|s__Chitinophaga pinensis,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Chitinophaga|s__Chitinophaga sp. HK235,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Christiangramia|s__Christiangramia salexigens,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium camelliae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium sp. 3008163,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium sp. IHB B 17019,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium|s__Cloacibacterium caeni,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus|s__Cupriavidus sp. WKF15,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Draconibacterium|s__Draconibacterium orientale,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Epilithonimonas|s__Epilithonimonas vandammei,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flagellimonas|s__Flagellimonas lutaonensis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium album,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium ammonificans,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium limnophilum,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium sediminis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium sp. 140616W15,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium sp. I3-2,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium sp. N1736,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Formosa|s__Formosa sediminum,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Formosa|s__Formosa sp. L2A11,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Planctomycetales|f__Planctomycetaceae|g__Gimesia|s__Gimesia alba,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Haliovirgaceae|g__Haliovirga|s__Haliovirga abyssi,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter|s__Hymenobacter monticola,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter|s__Hymenobacter sediminicola,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Ilyobacter|s__Ilyobacter polytropus,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Flammeovirgaceae|g__Imperialibacter|s__Imperialibacter roseus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Kaistella|s__Kaistella antarctica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae|g__Labilibaculum|s__Labilibaculum antarcticum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia wadei,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Lutibacter|s__Lutibacter sp. A64,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Mangrovibacterium|s__Mangrovibacterium marinum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Maribellus|s__Maribellus comscasis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae|g__Marinifilum|s__Marinifilum fragile,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Leadbetterellaceae|g__Marinilongibacter|s__Marinilongibacter aquaticus,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Mucilaginibacter|s__Mucilaginibacter ginsenosidivorans,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Niabella|s__Niabella soli,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Ornithobacterium|s__Ornithobacterium rhinotracheale,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Paraflavitalea|s__Paraflavitalea soli,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Parvicellaceae|g__Parvicella|s__Parvicella tangerina,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium sp. Marseille-Q4147,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Phnomibacter|s__Phnomibacter ginsenosidimutans,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Pontibacter|s__Pontibacter akesuensis,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Pontibacter|s__Pontibacter korlensis,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Pontibacter|s__Pontibacter pudoricolor,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Pontibacter|s__Pontibacter russatus,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Pontibacter|s__Pontibacter sp. SGAir0037,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp. oral taxon 275,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 299,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia mannitolilytica,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Rhodocytophagaceae|g__Rhodocytophaga|s__Rhodocytophaga rosea,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Riemerella|s__Riemerella columbina,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Roseivirgaceae|g__Roseivirga|s__Roseivirga spongicola,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Rufibacter|s__Rufibacter tibetensis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Salegentibacter|s__Salegentibacter mishustinae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia vaginalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Sodaliphilus|s__Sodaliphilus pleomorphus,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Solitalea|s__Solitalea canadensis,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium|s__Sphingobacterium daejeonense,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium|s__Sphingobacterium sp. CZ-2,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium|s__Sphingobacterium sp. ML3W,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium|s__Sphingobacterium sp. WM,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae|g__Spirosoma|s__Spirosoma endbachense,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Spirosomataceae|g__Tellurirhabdus|s__Tellurirhabdus bombi,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Spirosomataceae|g__Tellurirhabdus|s__Tellurirhabdus rosea,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Undibacterium|s__Undibacterium parvum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas|s__Xanthomonas prunicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Draconibacterium|s__uncultured Draconibacterium sp.,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Ilyobacter|s__uncultured Ilyobacter sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae|g__Marinifilum|s__uncultured Marinifilum sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinilabiliaceae|g__Xiashengella|s__Xiashengella succiniciproducens,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Aequorivita|s__Aequorivita marisscotiae",3379134|1224|1236|2887326|468|469|1776741;3379134|976|117743|200644|49546|153265|101385;3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|171550|239759|2662363;3379134|976|117743|200644|49546|111500|192149;3379134|976|117743|200644|49546|111500|2908843;3379134|976|117743|200644|49546|2715289|2767188;3379134|976|117747|200666|84566|1773450|496056;3379134|976|117743|200644|2762318|1778601|2500547;3379134|976|768503|768507|563798|280472|280473;3379134|976|200643|1970189|1471398|2792393|2010828;3379134|976|1853228|1853229|563835|1769012|496057;3379134|976|1853228|1853229|563835|1769012|2875539;3379134|976|117743|200644|49546|178469|616991;1783272|1239|91061|1385|186817|1386|1806216;3379134|976|200643|171549|1853231|574697|1472416;3379134|976|200643|171549|1853231|574697|1472417;3379134|976|200643|171549|511434|511435;3379134|976|117743|200644|49546|1016|327575;3379134|976|117743|200644|49546|1016|1316596;3379134|976|1853228|1853229|563835|79328|2203219;3379134|976|1853228|1853229|563835|79328|2920382;3379134|976|1853228|1853229|563835|79328|79329;3379134|976|1853228|1853229|563835|79328|2952571;3379134|976|117743|200644|49546|292691|1913577;3379134|976|117743|200644|2762318|59732|1265445;3379134|976|117743|200644|2762318|59732|2478663;3379134|976|117743|200644|2762318|59732|1721091;3379134|976|117743|200644|2762318|501783|2004710;3379134|1224|28216|80840|119060|106589|3032282;3379134|976|200643|1970189|1471398|1471399|1168034;3379134|976|117743|200644|2762318|2782229|2487072;3379134|976|117743|200644|49546|444459|516051;3379134|976|117743|200644|49546|237|2175091;3379134|976|117743|200644|49546|237|1751056;3379134|976|117743|200644|49546|237|3003262;3379134|976|117743|200644|49546|237|2201181;3379134|976|117743|200644|49546|237|2478552;3379134|976|117743|200644|49546|237|2748319;3379134|976|117743|200644|49546|237|2986823;3379134|976|117743|200644|49546|225842|2594004;3379134|976|117743|200644|49546|225842|2686363;3379134|203682|203683|112|126|1649453|2527973;3384189|32066|203490|203491|3072461|3072462|2996794;3379134|976|768503|768507|1853232|89966|1705399;3379134|976|768503|768507|1853232|89966|2761579;3384189|32066|203490|203491|203492|167639|167642;3379134|976|768503|768507|200667|1649461|1324217;3379134|976|117743|200644|2762318|2782231|266748;3379134|976|200643|1970189|1573805|2060722|1717717;3384189|32066|203490|203491|1129771|32067|40542;3384189|32066|203490|203491|1129771|32067|157687;3379134|976|117743|200644|49546|358023|2918526;3379134|976|200643|1970189|1471398|1573808|1639118;3379134|976|200643|1970189|1471398|2678352|2681766;3379134|976|200643|1970189|1573805|866673|570161;3379134|976|768503|768507|3141702|2975149|2975157;3379134|976|117747|200666|84566|423349|398053;3379134|976|1853228|1853229|563835|379899|446683;3379134|976|117743|200644|2762318|28250|28251;3379134|976|1853228|1853229|563835|2698688|2315862;3379134|976|117743|200644|2975259|2975260|2829795;1783272|1239|909932|1843488|909930|33024|33025;1783272|1239|909932|1843488|909930|33024|2823317;1783272|1239|909932|1843488|909930|33024|626940;3379134|976|1853228|1853229|563835|2836216|2676868;3379134|976|768503|768507|1853232|323449|388950;3379134|976|768503|768507|1853232|323449|400092;3379134|976|768503|768507|1853232|323449|2694930;3379134|976|768503|768507|1853232|323449|2694929;3379134|976|768503|768507|1853232|323449|2571030;3379134|976|200643|171549|171551|836|712435;3379134|976|200643|171549|171552|838|652716;3379134|1224|28216|80840|119060|48736|105219;3379134|976|768503|768507|3078917|455076|2704465;3379134|976|117743|200644|2762318|34084|103810;3379134|976|768503|768507|2762306|290180|333140;3379134|976|768503|768507|1853232|1379908|512763;3379134|976|117743|200644|49546|143222|270918;3384189|32066|203490|203491|1129771|168808|187101;3379134|976|200643|171549|2005473|2815786|2606626;3379134|976|117747|200666|84566|929509|995;3379134|976|117747|200666|84566|28453|371142;3379134|976|117747|200666|84566|28453|2557994;3379134|976|117747|200666|84566|28453|1538644;3379134|976|117747|200666|84566|28453|3031802;3379134|976|768503|768507|89373|107|2666025;3379134|976|768503|768507|2896860|2674996|2907205;3379134|976|768503|768507|2896860|2674996|2674997;3379134|1224|28216|80840|75682|401469|401471;3379134|1224|1236|135614|32033|338|2053930;3379134|976|200643|1970189|1471398|1471399|1573823;3384189|32066|203490|203491|203492|167639|544433;3379134|976|200643|1970189|1573805|866673|1127472;3379134|976|200643|1970189|558415|3129724|2949635;3379134|976|117743|200644|49546|153265|3040348,Complete,NA
bsdb:40087549/1/2,40087549,"cross-sectional observational, not case-control",40087549,10.1186/s12866-025-03863-2,NA,"Wang X., Shang Y., Xing Y., Chen Y., Wu X. , Zhang H.",Captive environments reshape the compositions of carbohydrate active enzymes and virulence factors in wolf gut microbiome,BMC microbiology,2025,"Captive environmental, Ecological niches, Family canidae, Gut microbiome",Experiment 1,China,Vulpes vulpes,Feces,UBERON:0001988,Species design,EFO:0001753,Corsac fox,Red fox,Wild red fox whose fecal samples were collected from three different individuals residing in Hulun Lake area using the snow-fresh tracking method to ensure the feces were freshly deposited in the wild,3,3,NA,WMS,NA,Illumina,centered log-ratio,Welch's T-Test,0.01,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,Supplementary Material 1: Supplementary Table 1,13 November 2025,Tosin,Tosin,"Results of an ALDEx2 (Analysis of Differential Abundance Taking Sample and Scale Variation Into Account) analysis of differential bacterial species between corsac fox and red fox (effect ≥ 3, p < 0.01)",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerocolumna|s__Anaerocolumna sedimenticola,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter|s__Arthrobacter sp. UKPF54-2,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus subtilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia liquoris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia luti,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia pseudococcoides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. SC05B48,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Cellulomonadaceae|g__Cellulomonas|s__Cellulomonas sp. ATA003,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium sp. SMC-4,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Novisyntrophococcus|s__Novisyntrophococcus fermenticellae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus|s__Rhodococcus sp. X156,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Amycolatopsis|s__Amycolatopsis nalaikhensis",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|3085636|186803|1843210|2696063;1783272|201174|1760|85006|1268|1663|2600159;1783272|1239|91061|1385|186817|1386|1423;1783272|1239|186801|3085636|186803|572511|1322;1783272|1239|186801|3085636|186803|572511|2779518;1783272|1239|186801|3085636|186803|572511|89014;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|572511|1796616;1783272|1239|186801|3085636|186803|572511|2479767;1783272|201174|1760|85006|85016|1707|3073064;1783272|1239|186801|3085636|186803|3570277|116085;1783272|201174|1760|85007|1762|1763|2857059;1783272|1239|186801|3085636|186803|2888809|2068655;1783272|201174|1760|85007|85025|1827|2499145;1783272|201174|1760|85010|2070|1813|715472,Complete,NA
bsdb:40087549/2/1,40087549,"cross-sectional observational, not case-control",40087549,10.1186/s12866-025-03863-2,NA,"Wang X., Shang Y., Xing Y., Chen Y., Wu X. , Zhang H.",Captive environments reshape the compositions of carbohydrate active enzymes and virulence factors in wolf gut microbiome,BMC microbiology,2025,"Captive environmental, Ecological niches, Family canidae, Gut microbiome",Experiment 2,China,Canis lupus,Feces,UBERON:0001988,Species design,EFO:0001753,Corsac fox,Wild wolf,"Wild wolves which were tracked using Global Positioning System (GPS) collars, and fecal samples were collected immediately after discharge from three different individuals residing in Hulun Lake area.",3,3,NA,WMS,NA,Illumina,centered log-ratio,Welch's T-Test,0.01,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Supplementary Material 1: Supplementary Table 1,15 November 2025,Tosin,Tosin,"Results of an ALDEx2 (Analysis of Differential Abundance Taking Sample and Scale Variation Into Account) analysis of differential bacterial species between corsac fox and wild wolf (effect ≥ 3, p < 0.01)",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter johnsonii,p__Apicomplexa|c__Aconoidasida|o__Piroplasmida|f__Babesiidae|g__Babesia|s__Babesia bigemina,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Paraflavitalea|s__Paraflavitalea soli,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Ilyobacter|s__uncultured Ilyobacter sp.,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Allomuricauda|s__Allomuricauda sp.,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia vaginalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Draconibacterium|s__Draconibacterium orientale,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Spirosomataceae|g__Tellurirhabdus|s__Tellurirhabdus bombi,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia cepacia,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Chitinophaga|s__Chitinophaga alhagiae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Polynucleobacter|s__Polynucleobacter necessarius,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Ilyobacter|s__Ilyobacter polytropus,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Pontibacter|s__Pontibacter korlensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio mangrovi,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Ornithobacterium|s__Ornithobacterium rhinotracheale,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium sp. N502536,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Haliovirgaceae|g__Haliovirga|s__Haliovirga abyssi,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium|s__Cetobacterium somerae,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter|s__Hymenobacter sp. 5516J-16,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Myroides|s__Myroides fluvii,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Euzebyella|s__Euzebyella marina,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus|s__Streptobacillus moniliformis,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Mucilaginibacter|s__Mucilaginibacter ginsenosidivorans,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Chitinophaga|s__Chitinophaga pinensis",3379134|1224|1236|2887326|468|469|40214;5794|422676|5863|32594|5864|5866;3379134|976|1853228|1853229|563835|2698688|2315862;3384189|32066|203490|203491|203492|167639|544433;3379134|976|117743|200644|49546|111500|192149;3384189|32066|203490|203491|1129771|168808|187101;3379134|976|200643|1970189|1471398|1471399|1168034;3379134|976|768503|768507|2896860|2674996|2907205;3379134|1224|28216|80840|119060|32008|292;3379134|976|1853228|1853229|563835|79328|2203219;3379134|1224|28216|80840|119060|44013|576610;3384189|32066|203490|203491|203492|167639|167642;3379134|976|768503|768507|1853232|323449|400092;3379134|1224|1236|135623|641|662|474394;3379134|976|117743|200644|2762318|28250|28251;3379134|976|117743|200644|49546|1016|1018;3379134|976|117743|200644|49546|237|2986837;3384189|32066|203490|203491|3072461|3072462|2996794;3384189|32066|203490|203491|203492|180162|188913;3379134|976|768503|768507|1853232|89966|2932253;3379134|976|117743|200644|49546|76831|2572594;3379134|976|117743|200644|49546|1287916|1761453;3384189|32066|203490|203491|1129771|34104|34105;3379134|976|117747|200666|84566|423349|398053;3379134|976|1853228|1853229|563835|79328|79329,Complete,NA
bsdb:40087549/2/2,40087549,"cross-sectional observational, not case-control",40087549,10.1186/s12866-025-03863-2,NA,"Wang X., Shang Y., Xing Y., Chen Y., Wu X. , Zhang H.",Captive environments reshape the compositions of carbohydrate active enzymes and virulence factors in wolf gut microbiome,BMC microbiology,2025,"Captive environmental, Ecological niches, Family canidae, Gut microbiome",Experiment 2,China,Canis lupus,Feces,UBERON:0001988,Species design,EFO:0001753,Corsac fox,Wild wolf,"Wild wolves which were tracked using Global Positioning System (GPS) collars, and fecal samples were collected immediately after discharge from three different individuals residing in Hulun Lake area.",3,3,NA,WMS,NA,Illumina,centered log-ratio,Welch's T-Test,0.01,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Supplementary Material 1: Supplementary Table 1,15 November 2025,Tosin,Tosin,"Results of an ALDEx2 (Analysis of Differential Abundance Taking Sample and Scale Variation Into Account) analysis of differential bacterial species between corsac fox and wild wolf (effect ≥ 3, p < 0.01)",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia argi,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia luti,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena",1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|3085636|186803|572511|1912897;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|572511|89014;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|189330|88431,Complete,NA
bsdb:40087549/3/1,40087549,"cross-sectional observational, not case-control",40087549,10.1186/s12866-025-03863-2,NA,"Wang X., Shang Y., Xing Y., Chen Y., Wu X. , Zhang H.",Captive environments reshape the compositions of carbohydrate active enzymes and virulence factors in wolf gut microbiome,BMC microbiology,2025,"Captive environmental, Ecological niches, Family canidae, Gut microbiome",Experiment 3,China,Canis lupus,Feces,UBERON:0001988,Species design,EFO:0001753,Red fox,Wild wolf,"Wild wolves which were tracked using Global Positioning System (GPS) collars, and fecal samples were collected immediately after discharge from three different individuals residing in Hulun Lake area.",3,3,NA,WMS,NA,Illumina,centered log-ratio,Welch's T-Test,0.01,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Supplementary Material 1: Supplementary Table 1,13 November 2025,Firdaws,Firdaws,"Results of an ALDEx2 (Analysis of Differential Abundance Taking Sample and Scale Variation Into Account) analysis of differential bacterial species between wild wolf and red fox (effect ≥ 3, p < 0.01)",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Halanaerobiales|f__Halobacteroidaceae|g__Acetohalobium|s__Acetohalobium arabaticum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter indicus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter johnsonii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter sp. C32I,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter sp. TTH0-4,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter sp. WY4,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas|s__Aeromonas caviae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas|s__Aeromonas hydrophila,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Aggregatimonas|s__Aggregatimonas sangjinii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes megaguti,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Proteinivoracaceae|g__Alkalicella|s__Alkalicella caledoniensis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Allomuricauda|s__Allomuricauda sp.,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter|s__Arcobacter aquimarinus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter|s__Arcobacter cloacae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter|s__Arcobacter porcinus,p__Apicomplexa|c__Aconoidasida|o__Piroplasmida|f__Babesiidae|g__Babesia|s__Babesia bigemina,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus pacificus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides coprosuis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides helcogenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. D2,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. HF-162,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. M10,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides zhangwenhongii,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Blattabacteriaceae|g__Blattabacterium|s__Blattabacterium cuenoti,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia cepacia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter upsaliensis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga cynodegmi,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Cellulophaga|s__Cellulophaga omnivescoria,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Chitinophaga|s__Chitinophaga alhagiae,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Chitinophaga|s__Chitinophaga oryzae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Christiangramia|s__Christiangramia salexigens,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium camelliae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium gleum,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium sp. 3008163,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium suipulveris,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus|s__Cloacibacillus porcorum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Colwelliaceae|g__Colwellia|s__Colwellia sp. M166,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas testosteroni,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Draconibacterium|s__Draconibacterium halophilum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Draconibacterium|s__Draconibacterium orientale,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Dyella|s__Dyella telluris,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Elizabethkingia|s__Elizabethkingia anophelis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Enterobacteriaceae endosymbiont of Donacia semicuprea,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|g__Exiguobacterium|s__Exiguobacterium sp. Helios,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Ferrimonadaceae|g__Ferrimonas|s__Ferrimonas lipolytica,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Flavisolibacter|s__Flavisolibacter ginsenosidimutans,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium gelatinilyticum,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium gilvum,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium haoranii,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium sp. N1846,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Formosa|s__Formosa sp. Hel1_31_208,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Fulvivirgaceae|g__Fulvivirga|s__Fulvivirga lutea,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium animalis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium polymorphum,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Gilvibacter|s__Gilvibacter sp. SZ-19,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Glutamicibacter|s__Glutamicibacter sp. M10,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Halarcobacter|s__Halarcobacter bivalviorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Halanaerobiales|f__Halothermotrichaceae|g__Halothermothrix|s__Halothermothrix orenii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella enoeca,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter|s__Hymenobacter busanensis,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter|s__Hymenobacter qilianensis,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Ericales|f__Balsaminaceae|g__Impatiens|s__Impatiens glandulifera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella denitrificans,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 498,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Levilactobacillus|s__Levilactobacillus suantsaii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Loigolactobacillus|s__Loigolactobacillus backii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Loigolactobacillus|s__Loigolactobacillus coryniformis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Lutibacter|s__Lutibacter sp. A80,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Lysobacter|s__Lysobacter capsici,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Malaciobacter|s__Malaciobacter marinus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae|g__Marinomonas|s__Marinomonas algicola,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Marivirgaceae|g__Marivirga|s__Marivirga tractuosa,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Entomoplasmatales|f__Entomoplasmataceae|g__Mesoplasma|s__Mesoplasma florum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Methylococcales|f__Methylococcaceae|g__Methylomonas|s__Methylomonas rapida,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Piscirickettsiaceae|g__Methylophaga|s__Methylophaga frappieri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Microbulbiferaceae|g__Microbulbifer|s__Microbulbifer sp. THAF38,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Mucilaginibacter|s__Mucilaginibacter daejeonensis,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Mucilaginibacter|s__Mucilaginibacter ginsenosidivorans,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Mucilaginibacter|s__Mucilaginibacter rubeus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Muriicola|s__Muriicola soli,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Myroides|s__Myroides odoratus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Anaplasmataceae|g__Neorickettsia|s__Neorickettsia risticii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus sp. Y412MC10,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia terrae,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Paraflavitalea|s__Paraflavitalea soli,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter|s__Pedobacter roseus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium sp. Marseille-Q4147,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium|s__Photobacterium damselae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Plesiomonas|s__Plesiomonas shigelloides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Polynucleobacter|s__Polynucleobacter sp. UB-Siik-W21,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Pontibacillus|s__Pontibacillus sp. HMF3514,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas cangingivalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas crevioricanis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella communis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella corporis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella dentalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella fusca,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Prevotella heparinolytica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella herbatica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella jejuni,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella multiformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. E13-17,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. E15-22,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. E2-28,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. E9-3,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. Rep29,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 475,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella veroralis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Proteiniphilum|s__Proteiniphilum saccharofermentans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus|s__Proteus vulgaris,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia|s__Providencia huaxiensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia|s__Providencia sneebia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae|g__Pseudoalteromonas|s__Pseudoalteromonas piscicida,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas putida,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pseudopedobacter|s__Pseudopedobacter saltans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter|s__Psychrobacter sp. AntiMn-1,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter|s__Psychrobacter sp. LV10R520-6,k__Fungi|p__Basidiomycota|c__Pucciniomycetes|o__Pucciniales|f__Pucciniaceae|g__Puccinia|s__Puccinia striiformis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rahnella|s__Rahnella victoriana,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae|g__Rheinheimera|s__Rheinheimera sp. MMS21-TC3,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Riemerella|s__Riemerella columbina,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Rufibacter|s__Rufibacter radiotolerans,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Spirosomataceae|g__Runella|s__Runella rosea,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Salegentibacter|s__Salegentibacter sp. T436,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella baroniae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella bryantii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella hominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella|s__Shewanella aestuarii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella|s__Shewanella decolorationis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella|s__Shewanella inventionis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia vaginalis,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae|g__Spirosoma|s__Spirosoma pollinicola,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Spongiibacteraceae|g__Spongiibacter|s__Spongiibacter taiwanensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae|g__Sporomusa|s__Sporomusa termitida,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus cohnii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus haemolyticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus lutrae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus nepalensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus simulans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Sterolibacteriaceae|g__Sterolibacterium|s__Sterolibacterium denitrificans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus didelphis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio|s__Succinivibrio dextrinosolvens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Sulfuricellaceae|g__Sulfuriferula|s__Sulfuriferula nivalis,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Spirosomataceae|g__Tellurirhabdus|s__Tellurirhabdus bombi,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Tenacibaculum|s__Tenacibaculum jejuense,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Tenacibaculum|s__Tenacibaculum retecalamus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Tenacibaculum|s__Tenacibaculum sp. HL-MS23,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Malvales|f__Malvaceae|s__Byttnerioideae|g__Theobroma|s__Theobroma cacao,k__Bacillati|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae|g__Thermoanaerobacterium|s__Thermoanaerobacterium xylanolyticum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Thiotrichaceae|g__Thiothrix|s__Thiothrix litoralis,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Torulaspora|s__Torulaspora delbrueckii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus|s__Vagococcus fluvialis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus|s__Vagococcus lutrae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio campbellii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio mimicus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio penaeicida,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio sp. SCSIO 43136,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio tapetis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio tritonius,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio tubiashii,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Weeksella|s__Weeksella virosa,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Winogradskyella|s__Winogradskyella forsetii,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Winogradskyella|s__Winogradskyella sp. PG-2,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Xanthomonas|s__Xanthomonas citri,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Zunongwangia|s__Zunongwangia sp. HRR-M8,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__uncultured Bacteroides sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinilabiliaceae|g__Carboxylicivirga|s__uncultured Carboxylicivirga sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Draconibacterium|s__uncultured Draconibacterium sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Nitrosomonadaceae|g__Nitrosomonas|s__Nitrosomonas sp. H1_AOB3,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Maribacter|s__Maribacter halichondriae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinilabiliaceae|g__Xiashengella|s__Xiashengella succiniciproducens",1783272|1239|186801|53433|53434|28186|28187;3379134|1224|1236|2887326|468|469|756892;3379134|1224|1236|2887326|468|469|40214;3379134|1224|1236|2887326|468|469|2950074;3379134|1224|1236|2887326|468|469|1646498;3379134|1224|1236|2887326|468|469|2708348;3379134|1224|1236|135624|84642|642|648;3379134|1224|1236|135624|84642|642|644;3379134|976|117743|200644|49546|2913017|2583587;3379134|976|200643|171549|171550|239759|626932;3379134|976|200643|171549|171550|239759|2364787;1783272|1239|186801|186802|1491775|2838170|2731377;3379134|976|117743|200644|49546|111500|192149;3379134|29547|3031852|213849|2808963|28196|1315211;3379134|29547|3031852|213849|2808963|28196|1054034;3379134|29547|3031852|213849|2808963|28196|1935204;5794|422676|5863|32594|5864|5866;1783272|1239|91061|1385|186817|1386|2026187;3379134|976|200643|171549|815|816|151276;3379134|976|200643|171549|815|816|28111;3379134|976|200643|171549|815|816|338188;3379134|976|200643|171549|815|816|290053;3379134|976|200643|171549|815|816|291644;3379134|976|200643|171549|815|816|29523;3379134|976|200643|171549|815|816|556259;3379134|976|200643|171549|815|816|2785531;3379134|976|200643|171549|815|816|2763022;3379134|976|200643|171549|815|816|2650157;3379134|976|117743|200644|39782|34098|1653831;3379134|1224|28216|80840|119060|32008|292;3379134|29547|3031852|213849|72294|194|28080;3379134|976|117743|200644|49546|1016|28189;3379134|976|117743|200644|49546|104264|1888890;3379134|976|1853228|1853229|563835|79328|2203219;3379134|976|1853228|1853229|563835|79328|2725414;3379134|976|117743|200644|49546|292691|1913577;3379134|976|117743|200644|2762318|59732|1265445;3379134|976|117743|200644|2762318|59732|250;3379134|976|117743|200644|2762318|59732|2478663;3379134|976|117743|200644|2762318|59732|2929800;3384194|508458|649775|649776|649777|508459|1197717;3379134|1224|1236|135622|267889|28228|2583805;3379134|1224|28216|80840|80864|283|285;3379134|976|200643|1970189|1471398|1471399|2706887;3379134|976|200643|1970189|1471398|1471399|1168034;3379134|1224|1236|135614|1775411|231454|2763498;3379134|976|117743|200644|2762318|308865|1117645;3379134|1224|1236|91347|543|2675783;1783272|1239|91061|1385|33986|2735868;3379134|1224|1236|135622|267892|44011|2724191;3379134|976|1853228|1853229|563835|398041|661481;3379134|976|117743|200644|49546|237|3003260;3379134|976|117743|200644|49546|237|1492737;3379134|976|117743|200644|49546|237|683124;3379134|976|117743|200644|49546|237|2986824;3379134|976|117743|200644|49546|225842|1798225;3379134|976|768503|768507|2762286|396811|2810512;3384189|32066|203490|203491|203492|848|76859;3384189|32066|203490|203491|203492|848|851;3384189|32066|203490|203491|203492|848|76857;3379134|976|117743|200644|49546|379070|754429;1783272|201174|1760|85006|1268|1742989|3023076;3379134|1224|1236|135625|712|724|727;3379134|1224|1236|135625|712|724|729;3379134|29547|3031852|213849|2808963|2321115|663364;1783272|1239|186801|53433|3046412|32636|31909;3379134|976|200643|171549|171552|2974257|28127;3379134|976|200643|171549|171552|2974257|76123;3379134|976|768503|768507|1853232|89966|2607656;3379134|976|768503|768507|1853232|89966|1385715;33090|35493|3398|41945|25692|35939|253017;3379134|1224|28216|206351|481|32257|502;3384189|32066|203490|203491|1129771|32067|712368;1783272|1239|91061|186826|33958|2767886|2292255;1783272|1239|91061|186826|33958|2767889|375175;1783272|1239|91061|186826|33958|2767889|1610;3379134|976|117743|200644|49546|358023|2918453;3379134|1224|1236|135614|32033|68|435897;3379134|29547|3031852|213849|2808963|2321114|505249;3379134|1224|1236|135619|135620|28253|2773454;3379134|976|768503|768507|2762301|869806|1006;1783272|544448|31969|186328|33925|46239|2151;3379134|1224|1236|135618|403|416|2963939;3379134|1224|1236|72273|135616|40222|754477;3379134|1224|1236|1706369|1706373|48073|2587856;3379134|976|117747|200666|84566|423349|398049;3379134|976|117747|200666|84566|423349|398053;3379134|976|117747|200666|84566|423349|2027860;3379134|976|117743|200644|49546|762641|2507538;3379134|976|117743|200644|49546|76831|256;3379134|1224|28211|766|942|33993|950;1783272|1239|91061|1385|186822|44249|481743;3379134|1224|28216|80840|119060|1822464|311230;3379134|976|1853228|1853229|563835|2698688|2315862;3379134|976|117747|200666|84566|84567|336820;1783272|1239|909932|1843488|909930|33024|33025;1783272|1239|909932|1843488|909930|33024|2823317;1783272|1239|909932|1843488|909930|33024|626940;3379134|1224|1236|135623|641|657|38293;3379134|1224|1236|91347|543|702|703;3379134|1224|28216|80840|119060|44013|1855646;1783272|1239|91061|1385|186817|289201|2692425;3379134|976|200643|171549|171551|836|36874;3379134|976|200643|171549|171551|836|393921;3379134|976|200643|171549|171552|838|28125;3379134|976|200643|171549|171552|838|2913614;3379134|976|200643|171549|171552|838|28128;3379134|976|200643|171549|171552|838|52227;3379134|976|200643|171549|171552|838|28129;3379134|976|200643|171549|171552|838|589436;3379134|976|200643|171549|815|816|28113;3379134|976|200643|171549|171552|838|2801997;3379134|976|200643|171549|171552|838|470565;3379134|976|200643|171549|171552|838|28131;3379134|976|200643|171549|171552|838|1177574;3379134|976|200643|171549|171552|838|28132;3379134|976|200643|171549|171552|838|282402;3379134|976|200643|171549|171552|838|28133;3379134|976|200643|171549|171552|838|2913616;3379134|976|200643|171549|171552|838|2937774;3379134|976|200643|171549|171552|838|2913620;3379134|976|200643|171549|171552|838|2913621;3379134|976|200643|171549|171552|838|2691580;3379134|976|200643|171549|171552|838|712471;3379134|976|200643|171549|171552|838|28137;3379134|976|200643|171549|2005520|294702|1642647;3379134|1224|1236|91347|1903414|583|585;3379134|1224|1236|91347|1903414|586|2027290;3379134|1224|1236|91347|1903414|586|516075;3379134|1224|1236|135622|267888|53246|43662;3379134|1224|1236|72274|135621|286|303;3379134|976|117747|200666|84566|1649482|151895;3379134|1224|1236|2887326|468|497|1720344;3379134|1224|1236|2887326|468|497|1415574;4751|5204|162484|5258|5262|5296|27350;3379134|1224|1236|91347|1903411|34037|1510570;3379134|1224|1236|135613|1046|67575|3072790;3379134|976|117743|200644|2762318|34084|103810;3379134|976|768503|768507|1853232|1379908|1379910;3379134|976|768503|768507|2896860|105|2259595;3379134|976|117743|200644|49546|143222|1729720;3379134|1224|1236|91347|543|590|28901;3379134|976|200643|171549|171552|2974251|305719;3379134|976|200643|171549|171552|2974251|77095;3379134|976|200643|171549|171552|2974251|2518605;3379134|976|200643|171549|171552|2974251|28135;3379134|1224|1236|135622|267890|22|1028752;3379134|1224|1236|135622|267890|22|256839;3379134|1224|1236|135622|267890|22|1738770;3384189|32066|203490|203491|1129771|168808|187101;3379134|976|768503|768507|89373|107|2057025;3379134|1224|1236|1706369|1706375|630749|1748242;1783272|1239|909932|909929|1843490|2375|2377;1783272|1239|91061|1385|90964|1279|1280;1783272|1239|91061|1385|90964|1279|29382;1783272|1239|91061|1385|90964|1279|1282;1783272|1239|91061|1385|90964|1279|1283;1783272|1239|91061|1385|90964|1279|1290;1783272|1239|91061|1385|90964|1279|155085;1783272|1239|91061|1385|90964|1279|214473;1783272|1239|91061|1385|90964|1279|1286;3379134|1224|28216|32003|2008793|157591|157592;1783272|1239|91061|186826|1300|1301|102886;3379134|1224|1236|135624|83763|83770|83771;3379134|1224|28216|32003|2772226|1778653|2675298;3379134|976|768503|768507|2896860|2674996|2907205;3379134|976|117743|200644|49546|104267|584609;3379134|976|117743|200644|49546|104267|3018315;3379134|976|117743|200644|49546|104267|3077734;33090|35493|3398|41938|3629|214909|3640|3641;1783272|1239|186801|68295|186814|28895|29329;3379134|1224|1236|72273|135617|1030|2891210;4751|4890|4891|4892|4893|4948|4950;1783272|1239|91061|186826|81852|2737|2738;1783272|1239|91061|186826|81852|2737|81947;1783272|1239|909932|1843489|31977|29465|39777;3379134|1224|1236|135623|641|662|680;3379134|1224|1236|135623|641|662|674;3379134|1224|1236|135623|641|662|104609;3379134|1224|1236|135623|641|662|2819101;3379134|1224|1236|135623|641|662|52443;3379134|1224|1236|135623|641|662|1435069;3379134|1224|1236|135623|641|662|29498;3379134|976|117743|200644|2762318|1013|1014;3379134|976|117743|200644|49546|286104|2686077;3379134|976|117743|200644|49546|286104|754409;3379134|1224|1236|135614|32033|338|346;3379134|976|117743|200644|49546|417127|3015170;3379134|976|200643|171549|815|816|162156;3379134|976|200643|1970189|558415|1628153|1628156;3379134|976|200643|1970189|1471398|1471399|1573823;3379134|1224|28216|32003|206379|914|2741553;3379134|976|117743|200644|49546|252356|2980554;3379134|976|200643|1970189|558415|3129724|2949635,Complete,NA
bsdb:40087549/3/2,40087549,"cross-sectional observational, not case-control",40087549,10.1186/s12866-025-03863-2,NA,"Wang X., Shang Y., Xing Y., Chen Y., Wu X. , Zhang H.",Captive environments reshape the compositions of carbohydrate active enzymes and virulence factors in wolf gut microbiome,BMC microbiology,2025,"Captive environmental, Ecological niches, Family canidae, Gut microbiome",Experiment 3,China,Canis lupus,Feces,UBERON:0001988,Species design,EFO:0001753,Red fox,Wild wolf,"Wild wolves which were tracked using Global Positioning System (GPS) collars, and fecal samples were collected immediately after discharge from three different individuals residing in Hulun Lake area.",3,3,NA,WMS,NA,Illumina,centered log-ratio,Welch's T-Test,0.01,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Supplementary Material 1: Supplementary Table 1,14 November 2025,Firdaws,Firdaws,"Results of an ALDEx2 (Analysis of Differential Abundance Taking Sample and Scale Variation Into Account) analysis of differential bacterial species between wild wolf and red fox (effect ≥ 3, p < 0.01)",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Aristaeellaceae|g__Aristaeella|s__Aristaeella hokkaidonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia parvula,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus|s__Cupriavidus basilensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Heliobacteriaceae|g__Heliomicrobium|s__Heliomicrobium modesticaldum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Simiaoa|s__Simiaoa sunii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",3379134|976|200643|171549|171550|239759|328814;1783272|1239|186801|186802|3046368|3046369|3046382;1783272|1239|186801|3085636|186803|572511|1322;1783272|1239|186801|3085636|186803|572511|2877527;3379134|1224|28216|80840|119060|106589|68895;1783272|1239|186801|186802|31984|2831443|35701;1783272|1239|186801|3085636|186803|2944193|2763672;1783272|1239|186801|3085636|186803|1506553|29347;1783272|1239|186801|3085636|186803|2316020|33039,Complete,NA
bsdb:40087549/4/1,40087549,"cross-sectional observational, not case-control",40087549,10.1186/s12866-025-03863-2,NA,"Wang X., Shang Y., Xing Y., Chen Y., Wu X. , Zhang H.",Captive environments reshape the compositions of carbohydrate active enzymes and virulence factors in wolf gut microbiome,BMC microbiology,2025,"Captive environmental, Ecological niches, Family canidae, Gut microbiome",Experiment 4,China,Canis lupus,Feces,UBERON:0001988,Species design,EFO:0001753,Domestic dog,Wild wolf,"Wild wolves which were tracked using Global Positioning System (GPS) collars, and fecal samples were collected immediately after discharge from three different individuals residing in Hulun Lake area.",14,3,NA,WMS,NA,Illumina,centered log-ratio,"Mann-Whitney (Wilcoxon),Welch's T-Test",0.01,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Supplementary Material 3: Supplementary Table 3,15 November 2025,Firdaws,Firdaws,"Results of an ALDEx2 (Analysis of Differential Abundance Taking Sample and Scale Variation Into Account) analysis of differential bacterial species between wild wolf and domestic dog (effect ≥ 3, p < 0.01)",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus atrophaeus,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter|s__Hymenobacter qilianensis,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter|s__Hymenobacter sp. 5317J-9",1783272|1239|91061|1385|186817|1386|1452;3379134|976|768503|768507|1853232|89966|1385715;3379134|976|768503|768507|1853232|89966|2932250,Complete,NA
bsdb:40087549/4/2,40087549,"cross-sectional observational, not case-control",40087549,10.1186/s12866-025-03863-2,NA,"Wang X., Shang Y., Xing Y., Chen Y., Wu X. , Zhang H.",Captive environments reshape the compositions of carbohydrate active enzymes and virulence factors in wolf gut microbiome,BMC microbiology,2025,"Captive environmental, Ecological niches, Family canidae, Gut microbiome",Experiment 4,China,Canis lupus,Feces,UBERON:0001988,Species design,EFO:0001753,Domestic dog,Wild wolf,"Wild wolves which were tracked using Global Positioning System (GPS) collars, and fecal samples were collected immediately after discharge from three different individuals residing in Hulun Lake area.",14,3,NA,WMS,NA,Illumina,centered log-ratio,"Mann-Whitney (Wilcoxon),Welch's T-Test",0.01,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Supplementary Material 3: Supplementary Table 3,15 November 2025,Firdaws,Firdaws,"Results of an ALDEx2 (Analysis of Differential Abundance Taking Sample and Scale Variation Into Account) analysis of differential bacterial species between wild wolf and domestic dog (effect ≥ 3, p < 0.01)",decreased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sp. H121,1783272|1239|526524|526525|2810281|191303|1712675,Complete,NA
bsdb:40087549/5/1,40087549,"cross-sectional observational, not case-control",40087549,10.1186/s12866-025-03863-2,NA,"Wang X., Shang Y., Xing Y., Chen Y., Wu X. , Zhang H.",Captive environments reshape the compositions of carbohydrate active enzymes and virulence factors in wolf gut microbiome,BMC microbiology,2025,"Captive environmental, Ecological niches, Family canidae, Gut microbiome",Experiment 5,China,Canis lupus,Feces,UBERON:0001988,Species design,EFO:0001753,Captive Wolf,Wild Wolf,"Wild wolves which were tracked using Global Positioning System (GPS) collars, and fecal samples were collected immediately after discharge from three different individuals residing in Hulun Lake area.",13,3,NA,WMS,NA,Illumina,centered log-ratio,Welch's T-Test,0.01,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Supplementary Material 3: Supplementary Table 3,15 November 2025,Fadimatou Inna,Fadimatou Inna,"Results of an ALDEx2 (Analysis of Differential Abundance Taking Sample and Scale Variation Into Account) analysis of differential bacterial species between wild wolf and domestic dog (effect ≥ 3, p < 0.01).",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus atrophaeus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. PHL 2737,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium elkanii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chitinibacteraceae|g__Chitinibacter|s__Chitinibacter bivalviorum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Colwelliaceae|g__Colwellia|s__Colwellia psychrerythraea,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas kerstersii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Paludibacterium|s__Paludibacterium sp. B53371,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Polynucleobacter|s__Polynucleobacter asymbioticus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces sp. S584,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio rumoiensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae|g__Rheinheimera|s__Rheinheimera sp. D18,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Rufibacter|s__Rufibacter radiotolerans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter venetianus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfuromonadia|o__Geobacterales|f__Geobacteraceae|g__Geomonas|s__Geomonas paludis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Litorivicinaceae|g__Litorivicinus|s__Litorivicinus lipolyticus,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Nibribacter|s__Nibribacter ruber,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Hahellaceae|g__Hahella|s__Hahella aquimaris,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Paraurantiacibacter|s__Paraurantiacibacter namhicola,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Chitinophaga|s__Chitinophaga oryzae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii",1783272|1239|91061|1385|186817|1386|1452;3379134|976|200643|171549|815|816|2162637;3379134|1224|28211|356|41294|374|29448;3379134|1224|28216|206351|2897177|230666|2739434;3379134|1224|1236|135622|267889|28228|28229;3379134|1224|28216|80840|80864|283|225992;3379134|1224|28216|206351|1499392|400060|2806263;3379134|1224|28216|80840|119060|44013|576611;1783272|201174|1760|85011|2062|1883|3096010;3379134|1224|1236|135623|641|662|76258;3379134|1224|1236|135613|1046|67575|2545632;3379134|976|768503|768507|1853232|1379908|1379910;3379134|1224|1236|2887326|468|469|52133;3379134|200940|3031651|3031668|213422|2651583|2740185;3379134|1224|1236|135619|449732|418700|418701;3379134|976|768503|768507|1853232|1649474|2698458;3379134|1224|1236|135619|224379|158481|3015983;3379134|1224|28211|204457|335929|2800682|645517;3379134|976|1853228|1853229|563835|79328|2725414;3379134|976|200643|171549|171550|239759|214856,Complete,NA
bsdb:40102379/1/1,40102379,randomized controlled trial,40102379,10.1038/s41467-025-57838-y,NA,"Deng L., Taelman S., Olm M.R., Toe L.C., Balini E., Ouédraogo L.O., Bastos-Moreira Y., Argaw A., Tesfamariam K., Sonnenburg E.D., Hanley-Cook G.T., Ouédraogo M., Ganaba R., Van Criekinge W., Huybregts L., Stock M., Kolsteren P., Sonnenburg J.L., Lachat C. , Dailey-Chwalibóg T.",Maternal balanced energy-protein supplementation reshapes the maternal gut microbiome and enhances carbohydrate metabolism in infants: a randomized controlled trial,Nature communications,2025,NA,Experiment 1,Burkina Faso,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Mother in third trimester (Tri3) - Intervention group,Mother in 1-2 months Postnatal (Pn12) - Intervention group,This group refers to mothers whose stool samples were collected in the intervention group at 1 - 2months postpartum.,71,66,NA,WMS,NA,Illumina,log transformation,Mixed-Effects Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Fig. 3C, D",7 April 2025,Joiejoie,"Joiejoie,Anne-mariesharp",Relative abundance of taxa shared between mothers and infants across time points,increased,NA,NA,Complete,KateRasheed
bsdb:40102379/2/1,40102379,randomized controlled trial,40102379,10.1038/s41467-025-57838-y,NA,"Deng L., Taelman S., Olm M.R., Toe L.C., Balini E., Ouédraogo L.O., Bastos-Moreira Y., Argaw A., Tesfamariam K., Sonnenburg E.D., Hanley-Cook G.T., Ouédraogo M., Ganaba R., Van Criekinge W., Huybregts L., Stock M., Kolsteren P., Sonnenburg J.L., Lachat C. , Dailey-Chwalibóg T.",Maternal balanced energy-protein supplementation reshapes the maternal gut microbiome and enhances carbohydrate metabolism in infants: a randomized controlled trial,Nature communications,2025,NA,Experiment 2,Burkina Faso,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Mother in third trimester (Tri3) - Intervention group,Mother in 5 - 6months Postnatal (Pn56) - Intervention group,This group refers to mothers whose stool samples were collected in the intervention group at 5 - 6months postpartum.,71,67,NA,WMS,NA,Illumina,log transformation,Mixed-Effects Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 3D,7 April 2025,Joiejoie,"Joiejoie,Anne-mariesharp,KateRasheed",Relative abundance of the top ten most abundant species in both mother and infant samples.,increased,NA,NA,Complete,KateRasheed
bsdb:40102379/3/1,40102379,randomized controlled trial,40102379,10.1038/s41467-025-57838-y,NA,"Deng L., Taelman S., Olm M.R., Toe L.C., Balini E., Ouédraogo L.O., Bastos-Moreira Y., Argaw A., Tesfamariam K., Sonnenburg E.D., Hanley-Cook G.T., Ouédraogo M., Ganaba R., Van Criekinge W., Huybregts L., Stock M., Kolsteren P., Sonnenburg J.L., Lachat C. , Dailey-Chwalibóg T.",Maternal balanced energy-protein supplementation reshapes the maternal gut microbiome and enhances carbohydrate metabolism in infants: a randomized controlled trial,Nature communications,2025,NA,Experiment 3,Burkina Faso,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Mother-Tri2 Control,Mother-Tri2 Intervention,This group refers to mothers whose stool samples were collected in the intervention group during the second trimester of pregnancy.,20,22,NA,WMS,NA,Illumina,log transformation,ANCOM-BC2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 5A,10 April 2025,Joiejoie,"Joiejoie,Anne-mariesharp",Differentially abundant taxa associated with the intervention at the second trimester (Tri2),decreased,NA,NA,Complete,KateRasheed
bsdb:40102379/4/1,40102379,randomized controlled trial,40102379,10.1038/s41467-025-57838-y,NA,"Deng L., Taelman S., Olm M.R., Toe L.C., Balini E., Ouédraogo L.O., Bastos-Moreira Y., Argaw A., Tesfamariam K., Sonnenburg E.D., Hanley-Cook G.T., Ouédraogo M., Ganaba R., Van Criekinge W., Huybregts L., Stock M., Kolsteren P., Sonnenburg J.L., Lachat C. , Dailey-Chwalibóg T.",Maternal balanced energy-protein supplementation reshapes the maternal gut microbiome and enhances carbohydrate metabolism in infants: a randomized controlled trial,Nature communications,2025,NA,Experiment 4,Burkina Faso,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Mother-Tri3 Control,Mother-Tri3 Intervention,This group refers to mothers whose stool samples were collected in the intervention group during the third trimester of pregnancy.,78,71,NA,WMS,NA,Illumina,log transformation,ANCOM-BC2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 5A,10 April 2025,Joiejoie,Joiejoie,Differentially abundant taxa associated with the intervention at the third trimester (Tri3),increased,NA,NA,Complete,KateRasheed
bsdb:40102379/4/2,40102379,randomized controlled trial,40102379,10.1038/s41467-025-57838-y,NA,"Deng L., Taelman S., Olm M.R., Toe L.C., Balini E., Ouédraogo L.O., Bastos-Moreira Y., Argaw A., Tesfamariam K., Sonnenburg E.D., Hanley-Cook G.T., Ouédraogo M., Ganaba R., Van Criekinge W., Huybregts L., Stock M., Kolsteren P., Sonnenburg J.L., Lachat C. , Dailey-Chwalibóg T.",Maternal balanced energy-protein supplementation reshapes the maternal gut microbiome and enhances carbohydrate metabolism in infants: a randomized controlled trial,Nature communications,2025,NA,Experiment 4,Burkina Faso,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Mother-Tri3 Control,Mother-Tri3 Intervention,This group refers to mothers whose stool samples were collected in the intervention group during the third trimester of pregnancy.,78,71,NA,WMS,NA,Illumina,log transformation,ANCOM-BC2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig. 5A,10 April 2025,Joiejoie,Joiejoie,Differentially abundant taxa associated with the intervention at the third trimester (Tri3),decreased,NA,NA,Complete,KateRasheed
bsdb:40102379/5/1,40102379,randomized controlled trial,40102379,10.1038/s41467-025-57838-y,NA,"Deng L., Taelman S., Olm M.R., Toe L.C., Balini E., Ouédraogo L.O., Bastos-Moreira Y., Argaw A., Tesfamariam K., Sonnenburg E.D., Hanley-Cook G.T., Ouédraogo M., Ganaba R., Van Criekinge W., Huybregts L., Stock M., Kolsteren P., Sonnenburg J.L., Lachat C. , Dailey-Chwalibóg T.",Maternal balanced energy-protein supplementation reshapes the maternal gut microbiome and enhances carbohydrate metabolism in infants: a randomized controlled trial,Nature communications,2025,NA,Experiment 5,Burkina Faso,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Mother-Pn12 Control,Mother-Pn12  Intervention,This group refers to mothers whose stool samples were collected in the intervention group at 1 to 2 months postpartum.,76,66,NA,WMS,NA,Illumina,log transformation,ANCOM-BC2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 5A,10 April 2025,Joiejoie,"Joiejoie,Anne-mariesharp",Differentially abundant taxa associated with the intervention at the postnatal 1–2 months (Pn12),increased,NA,NA,Complete,KateRasheed
bsdb:40102379/5/2,40102379,randomized controlled trial,40102379,10.1038/s41467-025-57838-y,NA,"Deng L., Taelman S., Olm M.R., Toe L.C., Balini E., Ouédraogo L.O., Bastos-Moreira Y., Argaw A., Tesfamariam K., Sonnenburg E.D., Hanley-Cook G.T., Ouédraogo M., Ganaba R., Van Criekinge W., Huybregts L., Stock M., Kolsteren P., Sonnenburg J.L., Lachat C. , Dailey-Chwalibóg T.",Maternal balanced energy-protein supplementation reshapes the maternal gut microbiome and enhances carbohydrate metabolism in infants: a randomized controlled trial,Nature communications,2025,NA,Experiment 5,Burkina Faso,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Mother-Pn12 Control,Mother-Pn12  Intervention,This group refers to mothers whose stool samples were collected in the intervention group at 1 to 2 months postpartum.,76,66,NA,WMS,NA,Illumina,log transformation,ANCOM-BC2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig. 5A,10 April 2025,Joiejoie,"Joiejoie,Anne-mariesharp",Differentially abundant taxa associated with the intervention at the postnatal 1–2 months (Pn12),decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter sp.,1783272|1239|186801|3085636|186803|1766253|2021311,Complete,KateRasheed
bsdb:40102379/6/1,40102379,randomized controlled trial,40102379,10.1038/s41467-025-57838-y,NA,"Deng L., Taelman S., Olm M.R., Toe L.C., Balini E., Ouédraogo L.O., Bastos-Moreira Y., Argaw A., Tesfamariam K., Sonnenburg E.D., Hanley-Cook G.T., Ouédraogo M., Ganaba R., Van Criekinge W., Huybregts L., Stock M., Kolsteren P., Sonnenburg J.L., Lachat C. , Dailey-Chwalibóg T.",Maternal balanced energy-protein supplementation reshapes the maternal gut microbiome and enhances carbohydrate metabolism in infants: a randomized controlled trial,Nature communications,2025,NA,Experiment 6,Burkina Faso,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Mother-Pn56 Control,Mother-Pn56 Intervention,This group refers to mothers whose stool samples were collected in the intervention group at 5 to 6 months postpartum.,75,67,NA,WMS,NA,Illumina,log transformation,ANCOM-BC2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 5A,10 April 2025,Joiejoie,"Joiejoie,Anne-mariesharp",Differentially abundant taxa associated with the intervention at the postnatal 5–6 months (Pn56),increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp.,1783272|1239|909932|1843489|31977|29465|1926307,Complete,KateRasheed
bsdb:40102379/6/2,40102379,randomized controlled trial,40102379,10.1038/s41467-025-57838-y,NA,"Deng L., Taelman S., Olm M.R., Toe L.C., Balini E., Ouédraogo L.O., Bastos-Moreira Y., Argaw A., Tesfamariam K., Sonnenburg E.D., Hanley-Cook G.T., Ouédraogo M., Ganaba R., Van Criekinge W., Huybregts L., Stock M., Kolsteren P., Sonnenburg J.L., Lachat C. , Dailey-Chwalibóg T.",Maternal balanced energy-protein supplementation reshapes the maternal gut microbiome and enhances carbohydrate metabolism in infants: a randomized controlled trial,Nature communications,2025,NA,Experiment 6,Burkina Faso,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Mother-Pn56 Control,Mother-Pn56 Intervention,This group refers to mothers whose stool samples were collected in the intervention group at 5 to 6 months postpartum.,75,67,NA,WMS,NA,Illumina,log transformation,ANCOM-BC2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig. 5A,10 April 2025,Joiejoie,"Joiejoie,Anne-mariesharp",Differentially abundant taxa associated with the intervention at the postnatal 5–6 months (Pn56),decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,3379134|976|200643|171549|815|816|817,Complete,KateRasheed
bsdb:40102379/7/1,40102379,randomized controlled trial,40102379,10.1038/s41467-025-57838-y,NA,"Deng L., Taelman S., Olm M.R., Toe L.C., Balini E., Ouédraogo L.O., Bastos-Moreira Y., Argaw A., Tesfamariam K., Sonnenburg E.D., Hanley-Cook G.T., Ouédraogo M., Ganaba R., Van Criekinge W., Huybregts L., Stock M., Kolsteren P., Sonnenburg J.L., Lachat C. , Dailey-Chwalibóg T.",Maternal balanced energy-protein supplementation reshapes the maternal gut microbiome and enhances carbohydrate metabolism in infants: a randomized controlled trial,Nature communications,2025,NA,Experiment 7,Burkina Faso,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Mother + Infant Control,Mother + Infant  Intervention,This group received a specific treatment or dietary intervention during pregnancy.,381,350,NA,WMS,NA,Illumina,log transformation,ANCOM-BC2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. 5C,10 April 2025,Joiejoie,"Joiejoie,Anne-mariesharp",Relative abundance of the 16 taxa that were significantly different between the intervention and control groups across all time points combined.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis",1783272|1239|186801|3085636|186803|1898203;3379134|976|200643|171549|815|816|817,Complete,KateRasheed
bsdb:40102379/7/2,40102379,randomized controlled trial,40102379,10.1038/s41467-025-57838-y,NA,"Deng L., Taelman S., Olm M.R., Toe L.C., Balini E., Ouédraogo L.O., Bastos-Moreira Y., Argaw A., Tesfamariam K., Sonnenburg E.D., Hanley-Cook G.T., Ouédraogo M., Ganaba R., Van Criekinge W., Huybregts L., Stock M., Kolsteren P., Sonnenburg J.L., Lachat C. , Dailey-Chwalibóg T.",Maternal balanced energy-protein supplementation reshapes the maternal gut microbiome and enhances carbohydrate metabolism in infants: a randomized controlled trial,Nature communications,2025,NA,Experiment 7,Burkina Faso,Homo sapiens,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Mother + Infant Control,Mother + Infant  Intervention,This group received a specific treatment or dietary intervention during pregnancy.,381,350,NA,WMS,NA,Illumina,log transformation,ANCOM-BC2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig. 5C,10 April 2025,Joiejoie,"Joiejoie,Anne-mariesharp",Relative abundance of the 16 taxa that were significantly different between the intervention and control groups across all time points combined.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp.",1783272|1239|186801|3085636|186803|1766253|2021311;1783272|1239|909932|1843489|31977|29465|1926307,Complete,KateRasheed
bsdb:40108637/1/1,40108637,prospective cohort,40108637,10.1186/s40168-025-02066-1,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-025-02066-1,"Gangiah T.K., Alisoltani A., Potgieter M., Bell L., Ross E., Iranzadeh A., McDonald Z., Allali I., Dabee S., Barnabas S., Blackburn J.M., Tabb D.L., Bekker L.G., Jaspan H.B., Passmore J.S., Mulder N. , Masson L.",Exploring the female genital tract mycobiome in young South African women using metaproteomics,Microbiome,2025,"Bacterial vaginosis, Female genital tract, Fungi, Metaproteomics, Mycobiome",Experiment 1,South Africa,Homo sapiens,Wall of vagina,UBERON:0036523,Bacterial vaginosis,EFO:0003932,BV- Negative (BV: Bacterial Vaginosis) at Visit 1,BV- Positive (BV: Bacterial Vaginosis) at Visit 1,women who were classified as having bacterial vaginosis (BV) based on the nugent score,47,57,2 weeks,NA,NA,Mass spectrometry,log transformation,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,27 March 2025,Montana-D,Montana-D,Differentially abundant fungal taxa between BV-negative and BV-positive at Visit 1.,increased,"k__Fungi|p__Zoopagomycota|c__Entomophthoromycetes|o__Entomophthorales|f__Ancylistaceae|g__Conidiobolus|s__Conidiobolus coronatus,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia sympodialis",4751|1913638|1399770|4857|34486|34487|34488;4751|5204|1538075|162474|742845|55193|76777,Complete,Svetlana up
bsdb:40108637/1/2,40108637,prospective cohort,40108637,10.1186/s40168-025-02066-1,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-025-02066-1,"Gangiah T.K., Alisoltani A., Potgieter M., Bell L., Ross E., Iranzadeh A., McDonald Z., Allali I., Dabee S., Barnabas S., Blackburn J.M., Tabb D.L., Bekker L.G., Jaspan H.B., Passmore J.S., Mulder N. , Masson L.",Exploring the female genital tract mycobiome in young South African women using metaproteomics,Microbiome,2025,"Bacterial vaginosis, Female genital tract, Fungi, Metaproteomics, Mycobiome",Experiment 1,South Africa,Homo sapiens,Wall of vagina,UBERON:0036523,Bacterial vaginosis,EFO:0003932,BV- Negative (BV: Bacterial Vaginosis) at Visit 1,BV- Positive (BV: Bacterial Vaginosis) at Visit 1,women who were classified as having bacterial vaginosis (BV) based on the nugent score,47,57,2 weeks,NA,NA,Mass spectrometry,log transformation,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,27 March 2025,Montana-D,Montana-D,Differentially abundant fungal taxa between BV-negative and BV-positive at Visit 1.,decreased,"k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Pleosporaceae|g__Alternaria|s__Alternaria alternata,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus alliaceus,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida orthopsilosis,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Metschnikowiaceae|g__Clavispora|s__Clavispora lusitaniae,k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Lichtheimiaceae|g__Lichtheimia|s__Lichtheimia corymbifera,k__Fungi|p__Zoopagomycota|c__Kickxellomycetes|o__Kickxellales|f__Kickxellaceae|g__Linderina|s__Linderina pennispora,k__Fungi|p__Mucoromycota|c__Mortierellomycetes|o__Mortierellales|f__Mortierellaceae|g__Lobosporangium|s__Lobosporangium transversale,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Lodderomyces|s__Lodderomyces elongisporus,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Boletales|f__Pisolithaceae|g__Pisolithus|s__Pisolithus tinctorius,k__Fungi|p__Ascomycota|c__Schizosaccharomycetes|o__Schizosaccharomycetales|f__Schizosaccharomycetaceae|g__Schizosaccharomyces|s__Schizosaccharomyces cryophilus,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Trichocomaceae|g__Talaromyces|s__Talaromyces marneffei,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae|g__Trichosporon|s__Trichosporon asahii,k__Fungi|p__Basidiomycota|c__Wallemiomycetes|o__Wallemiales|f__Wallemiaceae|g__Wallemia|s__Wallemia ichthyophaga,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Scheffersomyces|s__[Candida] thasaenensis",4751|4890|147541|92860|28556|5598|5599;4751|4890|147545|5042|1131492|5052|209559;4751|4890|3239874|2916678|766764|5475|5476;4751|4890|3239874|2916678|766764|5475|273371;4751|4890|3239874|2916678|27319|36910|36911;4751|1913637|2212703|4827|499202|688353|42458;4751|1913638|2219690|4861|4862|4867|61395;4751|1913637|2212732|214503|4854|299330|64571;4751|4890|3239874|2916678|766764|36913|36914;4751|5204|155619|68889|227329|37467|37468;4751|4890|147554|34346|4894|4895|866546;4751|4890|147545|5042|28568|5094|37727;4751|5204|155616|1851469|1759442|5552|82508;4751|5204|431957|431958|431959|148959|245174;4751|4890|3239874|2916678|766764|766733|1241568,Complete,Svetlana up
bsdb:40108637/2/3,40108637,prospective cohort,40108637,10.1186/s40168-025-02066-1,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-025-02066-1,"Gangiah T.K., Alisoltani A., Potgieter M., Bell L., Ross E., Iranzadeh A., McDonald Z., Allali I., Dabee S., Barnabas S., Blackburn J.M., Tabb D.L., Bekker L.G., Jaspan H.B., Passmore J.S., Mulder N. , Masson L.",Exploring the female genital tract mycobiome in young South African women using metaproteomics,Microbiome,2025,"Bacterial vaginosis, Female genital tract, Fungi, Metaproteomics, Mycobiome",Experiment 2,South Africa,Homo sapiens,Wall of vagina,UBERON:0036523,Bacterial vaginosis,EFO:0003932,BV- Negative (BV: Bacterial Vaginosis) at Visit 1,BV- Intermediate (BV: Bacterial Vaginosis) at Visit 1,women who were classified as having an intermediate bacterial vaginosis state based on the Nugent score,47,7,2 weeks,NA,NA,Mass spectrometry,log transformation,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 3,Table 1,27 March 2025,Montana-D,Montana-D,Differentially abundant fungal taxa between BV-intermediate and BV-negative at Visit 1.,decreased,"k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Metschnikowiaceae|g__Clavispora|s__Clavispora lusitaniae,k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Lichtheimiaceae|g__Lichtheimia|s__Lichtheimia corymbifera,k__Fungi|p__Mucoromycota|c__Mortierellomycetes|o__Mortierellales|f__Mortierellaceae|g__Lobosporangium|s__Lobosporangium transversale,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Lodderomyces|s__Lodderomyces elongisporus,k__Fungi|p__Basidiomycota|c__Ustilaginomycetes|o__Ustilaginales|f__Ustilaginaceae|g__Moesziomyces|s__Moesziomyces aphidis,k__Fungi|p__Basidiomycota|c__Ustilaginomycetes|o__Ustilaginales|g__Mycosarcoma|s__Mycosarcoma maydis,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Penicillium|s__Penicillium vulpinum,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Boletales|f__Pisolithaceae|g__Pisolithus|s__Pisolithus tinctorius,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Cucurbitariaceae|g__Pyrenochaeta|s__Pyrenochaeta sp.,k__Fungi|p__Chytridiomycota|c__Chytridiomycetes|o__Chytridiales|f__Chytriomycetaceae|g__Rhizoclosmatium|s__Rhizoclosmatium globosum,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae|g__Teratoramularia|s__Teratoramularia persicariae,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Torulaspora|s__Torulaspora delbrueckii,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Scheffersomyces|s__[Candida] thasaenensis",4751|4890|3239874|2916678|27319|36910|36911;4751|1913637|2212703|4827|499202|688353|42458;4751|1913637|2212732|214503|4854|299330|64571;4751|4890|3239874|2916678|766764|36913|36914;4751|5204|5257|5267|5268|63261|84754;4751|5204|5257|5267|2689624|5270;4751|4890|147545|5042|1131492|5073|29845;4751|5204|155619|68889|227329|37467|37468;4751|4890|147541|92860|221670|285810|1755437;4751|4761|451435|4810|1352827|109967|329046;4751|4890|147541|2726947|93133|1873342|1873344;4751|4890|4891|4892|4893|4948|4950;4751|4890|3239874|2916678|766764|766733|1241568,Complete,Svetlana up
bsdb:40108637/3/1,40108637,prospective cohort,40108637,10.1186/s40168-025-02066-1,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-025-02066-1,"Gangiah T.K., Alisoltani A., Potgieter M., Bell L., Ross E., Iranzadeh A., McDonald Z., Allali I., Dabee S., Barnabas S., Blackburn J.M., Tabb D.L., Bekker L.G., Jaspan H.B., Passmore J.S., Mulder N. , Masson L.",Exploring the female genital tract mycobiome in young South African women using metaproteomics,Microbiome,2025,"Bacterial vaginosis, Female genital tract, Fungi, Metaproteomics, Mycobiome",Experiment 3,South Africa,Homo sapiens,Wall of vagina,UBERON:0036523,Bacterial vaginosis,EFO:0003932,BV- Intermediate (BV: Bacterial Vaginosis) at Visit 1,BV- Positive (BV: Bacterial Vaginosis) at visit 1,women who were classified as having bacterial vaginosis based on the Nugent score.,7,57,2 weeks,NA,NA,Mass spectrometry,log transformation,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,27 March 2025,Montana-D,Montana-D,Differentially abundant fungal taxa between BV-positive and BV-intermediate at Visit 1.,increased,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Metschnikowiaceae|g__Clavispora|s__Clavispora lusitaniae,4751|4890|3239874|2916678|27319|36910|36911,Complete,Svetlana up
bsdb:40108637/4/1,40108637,prospective cohort,40108637,10.1186/s40168-025-02066-1,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-025-02066-1,"Gangiah T.K., Alisoltani A., Potgieter M., Bell L., Ross E., Iranzadeh A., McDonald Z., Allali I., Dabee S., Barnabas S., Blackburn J.M., Tabb D.L., Bekker L.G., Jaspan H.B., Passmore J.S., Mulder N. , Masson L.",Exploring the female genital tract mycobiome in young South African women using metaproteomics,Microbiome,2025,"Bacterial vaginosis, Female genital tract, Fungi, Metaproteomics, Mycobiome",Experiment 4,South Africa,Homo sapiens,Wall of vagina,UBERON:0036523,Bacterial vaginosis,EFO:0003932,BV- Negative (BV: Bacterial Vaginosis) at Visit 2,BV- Positive (BV: Bacterial Vaginosis) at Visit 2,women who were classified as having bacterial vaginosis based on the Nugent score.,38,37,2 weeks,NA,NA,Mass spectrometry,log transformation,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S2 (Supplementary file 2),28 March 2025,Montana-D,Montana-D,Differentially abundant fungal taxa between BV-positive and BV-negative at Visit 2.,increased,"k__Fungi|p__Zoopagomycota|c__Entomophthoromycetes|o__Entomophthorales|f__Ancylistaceae|g__Conidiobolus|s__Conidiobolus coronatus,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia sympodialis",4751|1913638|1399770|4857|34486|34487|34488;4751|5204|1538075|162474|742845|55193|76777,Complete,Svetlana up
bsdb:40108637/4/2,40108637,prospective cohort,40108637,10.1186/s40168-025-02066-1,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-025-02066-1,"Gangiah T.K., Alisoltani A., Potgieter M., Bell L., Ross E., Iranzadeh A., McDonald Z., Allali I., Dabee S., Barnabas S., Blackburn J.M., Tabb D.L., Bekker L.G., Jaspan H.B., Passmore J.S., Mulder N. , Masson L.",Exploring the female genital tract mycobiome in young South African women using metaproteomics,Microbiome,2025,"Bacterial vaginosis, Female genital tract, Fungi, Metaproteomics, Mycobiome",Experiment 4,South Africa,Homo sapiens,Wall of vagina,UBERON:0036523,Bacterial vaginosis,EFO:0003932,BV- Negative (BV: Bacterial Vaginosis) at Visit 2,BV- Positive (BV: Bacterial Vaginosis) at Visit 2,women who were classified as having bacterial vaginosis based on the Nugent score.,38,37,2 weeks,NA,NA,Mass spectrometry,log transformation,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S2 (supplementary file 2),28 March 2025,Montana-D,Montana-D,Differentially abundant fungal taxa between BV-positive and BV-negative at Visit 2.,decreased,"k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Fungi|p__Basidiomycota|c__Wallemiomycetes|o__Wallemiales|f__Wallemiaceae|g__Wallemia|s__Wallemia ichthyophaga,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Scheffersomyces|s__[Candida] thasaenensis",4751|4890|3239874|2916678|766764|5475|5476;4751|5204|431957|431958|431959|148959|245174;4751|4890|3239874|2916678|766764|766733|1241568,Complete,Svetlana up
bsdb:40108637/5/1,40108637,prospective cohort,40108637,10.1186/s40168-025-02066-1,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-025-02066-1,"Gangiah T.K., Alisoltani A., Potgieter M., Bell L., Ross E., Iranzadeh A., McDonald Z., Allali I., Dabee S., Barnabas S., Blackburn J.M., Tabb D.L., Bekker L.G., Jaspan H.B., Passmore J.S., Mulder N. , Masson L.",Exploring the female genital tract mycobiome in young South African women using metaproteomics,Microbiome,2025,"Bacterial vaginosis, Female genital tract, Fungi, Metaproteomics, Mycobiome",Experiment 5,South Africa,Homo sapiens,Wall of vagina,UBERON:0036523,Bacterial vaginosis,EFO:0003932,BV- Negative (BV: Bacterial Vaginosis) at Visit 2,BV- Positive (BV: Bacterial Vaginosis) at Visit 2,women classified as having bacterial vaginosis based on the Nugent score,38,37,2 weeks,NA,NA,Mass spectrometry,log transformation,Linear Regression,0.05,TRUE,NA,NA,vaginal pH,NA,NA,NA,NA,NA,NA,Signature 1,Table S1 (supplementary file 3),28 March 2025,Montana-D,Montana-D,Differentially abundant fungal taxa between BV-intermediate and BV-positive at Visit 2.,increased,"k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia sympodialis,k__Fungi|p__Zoopagomycota|c__Entomophthoromycetes|o__Entomophthorales|f__Ancylistaceae|g__Conidiobolus|s__Conidiobolus coronatus",4751|5204|1538075|162474|742845|55193|76777;4751|1913638|1399770|4857|34486|34487|34488,Complete,Svetlana up
bsdb:40108637/5/2,40108637,prospective cohort,40108637,10.1186/s40168-025-02066-1,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-025-02066-1,"Gangiah T.K., Alisoltani A., Potgieter M., Bell L., Ross E., Iranzadeh A., McDonald Z., Allali I., Dabee S., Barnabas S., Blackburn J.M., Tabb D.L., Bekker L.G., Jaspan H.B., Passmore J.S., Mulder N. , Masson L.",Exploring the female genital tract mycobiome in young South African women using metaproteomics,Microbiome,2025,"Bacterial vaginosis, Female genital tract, Fungi, Metaproteomics, Mycobiome",Experiment 5,South Africa,Homo sapiens,Wall of vagina,UBERON:0036523,Bacterial vaginosis,EFO:0003932,BV- Negative (BV: Bacterial Vaginosis) at Visit 2,BV- Positive (BV: Bacterial Vaginosis) at Visit 2,women classified as having bacterial vaginosis based on the Nugent score,38,37,2 weeks,NA,NA,Mass spectrometry,log transformation,Linear Regression,0.05,TRUE,NA,NA,vaginal pH,NA,NA,NA,NA,NA,NA,Signature 2,Table S1 (supplementary file 3),2 April 2025,Montana-D,Montana-D,Differentially abundant fungal taxa between women with BV-negative and BV-Positive based on a Nugent score at Visit 2,decreased,"k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Scheffersomyces|s__[Candida] thasaenensis",4751|4890|3239874|2916678|766764|5475|5476;4751|4890|3239874|2916678|766764|766733|1241568,Complete,Svetlana up
bsdb:40108637/8/1,40108637,prospective cohort,40108637,10.1186/s40168-025-02066-1,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-025-02066-1,"Gangiah T.K., Alisoltani A., Potgieter M., Bell L., Ross E., Iranzadeh A., McDonald Z., Allali I., Dabee S., Barnabas S., Blackburn J.M., Tabb D.L., Bekker L.G., Jaspan H.B., Passmore J.S., Mulder N. , Masson L.",Exploring the female genital tract mycobiome in young South African women using metaproteomics,Microbiome,2025,"Bacterial vaginosis, Female genital tract, Fungi, Metaproteomics, Mycobiome",Experiment 8,South Africa,Homo sapiens,Wall of vagina,UBERON:0036523,Bacterial vaginosis,EFO:0003932,BV- Negative (BV: Baterial Vaginosis) at Visit 1,BV- Positive (BV: Baterial Vaginosis) at Visit 1,women classified as having bacterial vaginosis (BV) based on the nugent score,47,57,2 weeks,NA,NA,Mass spectrometry,log transformation,Linear Regression,0.05,TRUE,NA,NA,vaginal pH,NA,NA,NA,NA,NA,NA,Signature 1,Table S1 (supplementary file 3),30 March 2025,Montana-D,Montana-D,Differentially abundant fungal taxa between BV-negative and BV- positive at visit 1,increased,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia sympodialis,4751|5204|1538075|162474|742845|55193|76777,Complete,Svetlana up
bsdb:40108637/8/2,40108637,prospective cohort,40108637,10.1186/s40168-025-02066-1,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-025-02066-1,"Gangiah T.K., Alisoltani A., Potgieter M., Bell L., Ross E., Iranzadeh A., McDonald Z., Allali I., Dabee S., Barnabas S., Blackburn J.M., Tabb D.L., Bekker L.G., Jaspan H.B., Passmore J.S., Mulder N. , Masson L.",Exploring the female genital tract mycobiome in young South African women using metaproteomics,Microbiome,2025,"Bacterial vaginosis, Female genital tract, Fungi, Metaproteomics, Mycobiome",Experiment 8,South Africa,Homo sapiens,Wall of vagina,UBERON:0036523,Bacterial vaginosis,EFO:0003932,BV- Negative (BV: Baterial Vaginosis) at Visit 1,BV- Positive (BV: Baterial Vaginosis) at Visit 1,women classified as having bacterial vaginosis (BV) based on the nugent score,47,57,2 weeks,NA,NA,Mass spectrometry,log transformation,Linear Regression,0.05,TRUE,NA,NA,vaginal pH,NA,NA,NA,NA,NA,NA,Signature 2,Table S1 (supplementary file 3),1 April 2025,Montana-D,Montana-D,Differentially abundant fungal taxa between women with BV-negative and BV-Positive at visit 1,decreased,"k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Scheffersomyces|s__[Candida] thasaenensis,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Lodderomyces|s__Lodderomyces elongisporus,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Trichocomaceae|g__Talaromyces|s__Talaromyces marneffei,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Fungi|p__Basidiomycota|c__Wallemiomycetes|o__Wallemiales|f__Wallemiaceae|g__Wallemia|s__Wallemia ichthyophaga,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Boletales|f__Pisolithaceae|g__Pisolithus|s__Pisolithus tinctorius,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Pleosporaceae|g__Alternaria|s__Alternaria alternata,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida orthopsilosis,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Kluyveromyces|s__Kluyveromyces marxianus,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Boletales|f__Rhizopogonaceae|g__Rhizopogon|s__Rhizopogon vinicolor",4751|4890|3239874|2916678|766764|766733|1241568;4751|4890|3239874|2916678|766764|36913|36914;4751|4890|147545|5042|28568|5094|37727;4751|4890|3239874|2916678|766764|5475|5476;4751|5204|431957|431958|431959|148959|245174;4751|5204|155619|68889|227329|37467|37468;4751|4890|147541|92860|28556|5598|5599;4751|4890|3239874|2916678|766764|5475|273371;4751|4890|4891|4892|4893|4910|4911;4751|5204|155619|68889|48595|5375|80600,Complete,Svetlana up
bsdb:40108637/9/1,40108637,prospective cohort,40108637,10.1186/s40168-025-02066-1,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-025-02066-1,"Gangiah T.K., Alisoltani A., Potgieter M., Bell L., Ross E., Iranzadeh A., McDonald Z., Allali I., Dabee S., Barnabas S., Blackburn J.M., Tabb D.L., Bekker L.G., Jaspan H.B., Passmore J.S., Mulder N. , Masson L.",Exploring the female genital tract mycobiome in young South African women using metaproteomics,Microbiome,2025,"Bacterial vaginosis, Female genital tract, Fungi, Metaproteomics, Mycobiome",Experiment 9,South Africa,Homo sapiens,Wall of vagina,UBERON:0036523,Bacterial vaginosis,EFO:0003932,BV- Intermediate (BV: Bacterial Vaginosis) at Visit 1,BV- Negative (BV: Baterial Vaginosis) at Visit 1,women classified as having an intermediate bacterial vaginosis state based on the Nugent score,47,7,2 weeks,NA,NA,Mass spectrometry,log transformation,Linear Regression,0.05,TRUE,NA,NA,vaginal pH,NA,NA,NA,NA,NA,NA,Signature 1,Table S1 (supplementary file 3),30 March 2025,Montana-D,Montana-D,Differentially abundant fungal taxa between BV-negative and BV-Intermediate based on  the Nugent score at Visit 1,increased,"k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Penicillium|s__Penicillium vulpinum,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Torulaspora|s__Torulaspora delbrueckii",4751|4890|147545|5042|1131492|5073|29845;4751|4890|4891|4892|4893|4948|4950,Complete,Svetlana up
bsdb:40108637/10/1,40108637,prospective cohort,40108637,10.1186/s40168-025-02066-1,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-025-02066-1,"Gangiah T.K., Alisoltani A., Potgieter M., Bell L., Ross E., Iranzadeh A., McDonald Z., Allali I., Dabee S., Barnabas S., Blackburn J.M., Tabb D.L., Bekker L.G., Jaspan H.B., Passmore J.S., Mulder N. , Masson L.",Exploring the female genital tract mycobiome in young South African women using metaproteomics,Microbiome,2025,"Bacterial vaginosis, Female genital tract, Fungi, Metaproteomics, Mycobiome",Experiment 10,South Africa,Homo sapiens,Wall of vagina,UBERON:0036523,Bacterial vaginosis,EFO:0003932,BV- Intermediate (BV: Bacterial Vaginosis) at Visit 1,BV- Positive (BV: Bacterial Vaginosis) at visit 1,women classified as having bacterial vaginosis based on the Nugent score.,7,37,2 weeks,NA,NA,Mass spectrometry,log transformation,Linear Regression,0.05,TRUE,NA,NA,vaginal pH,NA,NA,NA,NA,NA,NA,Signature 1,Table S1 (supplementary file 3),30 March 2025,Montana-D,Montana-D,Differentially abundant fungal taxa between BV-positive and BV-intermediate at Visit 1.,increased,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Metschnikowiaceae|g__Clavispora|s__Clavispora lusitaniae,4751|4890|3239874|2916678|27319|36910|36911,Complete,Svetlana up
bsdb:40111342/1/1,40111342,time series / longitudinal observational,40111342,10.1080/19490976.2025.2476563,NA,"Castonguay-Paradis S., Demers-Potvin É., Rochefort G., Lacroix S., Perron J., Martin C., Flamand N., Raymond F., Di Marzo V. , Veilleux A.",Seasonal variations in circulating endocannabinoidome mediators and gut microbiota composition in humans,Gut microbes,2025,"2‑monoacylglycerol, Dietary intakes, Gut microbiota, N-acylethanolamines, Seasons, Vitamin D",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Seasonality measurement,EFO:0006876,Winter season,Summer season,Participants who paid a visit the Institute of Nutrition and Functional Foods (INAF) in summer season,204,50,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2a and 2b,5 May 2025,Tosin,Tosin,"Cladogram representation of the paired-wise Wilcoxon analysis showing the taxonomic ranks from the innermost phylum ring to the outermost genera ring and boxplots representation of significant taxonomic ranks including the median, lower/higher quartiles and 1.5× inter-quartile range whiskers.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1506553;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171550;3379134|976|200643|171549|2005525;1783272|1239|186801|186802|216572|3068309,Complete,KateRasheed
bsdb:40111342/1/2,40111342,time series / longitudinal observational,40111342,10.1080/19490976.2025.2476563,NA,"Castonguay-Paradis S., Demers-Potvin É., Rochefort G., Lacroix S., Perron J., Martin C., Flamand N., Raymond F., Di Marzo V. , Veilleux A.",Seasonal variations in circulating endocannabinoidome mediators and gut microbiota composition in humans,Gut microbes,2025,"2‑monoacylglycerol, Dietary intakes, Gut microbiota, N-acylethanolamines, Seasons, Vitamin D",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,Seasonality measurement,EFO:0006876,Winter season,Summer season,Participants who paid a visit the Institute of Nutrition and Functional Foods (INAF) in summer season,204,50,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2a and 2b,5 May 2025,Tosin,Tosin,"Cladogram representation of the paired-wise Wilcoxon analysis showing the taxonomic ranks from the innermost phylum ring to the outermost genera ring and boxplots representation of significant taxonomic ranks including the median, lower/higher quartiles and 1.5× inter-quartile range whiskers.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter",1783272|201174|1760|85004|31953;1783272|201174|84998|84999|84107;1783272|201174|84998|84999|84107|102106;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|1407607;3379134|976|200643|1970189|1573805;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|1766253,Complete,KateRasheed
bsdb:40111342/2/1,40111342,time series / longitudinal observational,40111342,10.1080/19490976.2025.2476563,NA,"Castonguay-Paradis S., Demers-Potvin É., Rochefort G., Lacroix S., Perron J., Martin C., Flamand N., Raymond F., Di Marzo V. , Veilleux A.",Seasonal variations in circulating endocannabinoidome mediators and gut microbiota composition in humans,Gut microbes,2025,"2‑monoacylglycerol, Dietary intakes, Gut microbiota, N-acylethanolamines, Seasons, Vitamin D",Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Seasonality measurement,EFO:0006876,Low Seasonal Changes,High Seasonal Changes,Participants who were categorized to have been observed with higher composition of gut microbiota associated with seasonal changes in the circulating levels of NAEs (N-acyl-ethanolamines),NA,NA,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,1.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7D,5 May 2025,Montana-D,"Montana-D,Tosin","Linear discriminant analysis effect size (LEfSe) analysis identifying microbial taxa associated with seasonal changes in the dim 3 family groups and, consequently, with the circulating NAEs seasonal changes observed (Kruskal-Wallis tests p < 0.05 and LDA score >1.5)",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",1783272|201174|84998|84999|84107|102106;1783272|1239|909932|909929|1843491|158846;3379134|976|200643|171549|171552|577309,Complete,KateRasheed
bsdb:40111342/2/2,40111342,time series / longitudinal observational,40111342,10.1080/19490976.2025.2476563,NA,"Castonguay-Paradis S., Demers-Potvin É., Rochefort G., Lacroix S., Perron J., Martin C., Flamand N., Raymond F., Di Marzo V. , Veilleux A.",Seasonal variations in circulating endocannabinoidome mediators and gut microbiota composition in humans,Gut microbes,2025,"2‑monoacylglycerol, Dietary intakes, Gut microbiota, N-acylethanolamines, Seasons, Vitamin D",Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,Seasonality measurement,EFO:0006876,Low Seasonal Changes,High Seasonal Changes,Participants who were categorized to have been observed with higher composition of gut microbiota associated with seasonal changes in the circulating levels of NAEs (N-acyl-ethanolamines),NA,NA,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,1.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 7D,6 May 2025,Montana-D,Montana-D,"linear discriminant analysis effect size (LEfSe) analysis identifying microbial taxa associated with seasonal changes in the dim 3 family groups and, consequently, with the circulating NAEs seasonal changes observed (Kruskal-Wallis tests p < 0.05 and LDA score >1.5)",decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239|909932|1843488|909930|904;1783272|1239|186801|3085636|186803|572511;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572|216851;1783272|1239|91061|186826|33958|1578,Complete,KateRasheed
bsdb:40129950/1/1,40129950,case-control,40129950,10.3389/fphar.2025.1512815,NA,"Pei S., Yang L., Gao H., Liu Y., Lu J., Dai E.H., Meng C., Feng F. , Wang Y.",The association between the gut microbiome and antituberculosis drug-induced liver injury,Frontiers in pharmacology,2025,"anti-TB therapy, drug-induced liver injury, microbiome dysbiosis, probiotics, pulmonary tuberculosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,Non- ADLI controls,Antituberculosis Drug-Induced Liver Injury (ADLI) group,newly diagnosed patients with tuberculosis according to the WS 288–2017 Diagnosis of Pulmonary Tuberculosis standard,100,100,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 3A,23 July 2025,Nuerteye,Nuerteye,Longitudinal comparison of bacterial genera with and without liver injury in patients with pulmonary tuberculosis. Characteristics of genus changes from T1 to T2 in Non_ADLI group,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Mahellales|f__Mahellaceae|g__Mahella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Sanguibacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|186802|216572|292632;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|171552|1283313;1783272|1239|186801|186802|216572|1508657;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|3120428|3120709|252965;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|841;3379134|976|200643|171549|171551|1635148;3379134|976|200643|171549|2005473,Complete,NA
bsdb:40129950/1/2,40129950,case-control,40129950,10.3389/fphar.2025.1512815,NA,"Pei S., Yang L., Gao H., Liu Y., Lu J., Dai E.H., Meng C., Feng F. , Wang Y.",The association between the gut microbiome and antituberculosis drug-induced liver injury,Frontiers in pharmacology,2025,"anti-TB therapy, drug-induced liver injury, microbiome dysbiosis, probiotics, pulmonary tuberculosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,Non- ADLI controls,Antituberculosis Drug-Induced Liver Injury (ADLI) group,newly diagnosed patients with tuberculosis according to the WS 288–2017 Diagnosis of Pulmonary Tuberculosis standard,100,100,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 3A,23 July 2025,Nuerteye,Nuerteye,Longitudinal comparison of bacterial genera with and without liver injury in patients with pulmonary tuberculosis. Characteristics of genus changes from T1 to T2 in Non_ADLI group,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",3379134|1224|1236|91347|543|570;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543,Complete,NA
bsdb:40129950/2/1,40129950,case-control,40129950,10.3389/fphar.2025.1512815,NA,"Pei S., Yang L., Gao H., Liu Y., Lu J., Dai E.H., Meng C., Feng F. , Wang Y.",The association between the gut microbiome and antituberculosis drug-induced liver injury,Frontiers in pharmacology,2025,"anti-TB therapy, drug-induced liver injury, microbiome dysbiosis, probiotics, pulmonary tuberculosis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,Antituberculosis Drug-Induced Liver Injury (ADLI_T1) group,Antituberculosis Drug-Induced Liver Injury (ADLI_T2) group,"ADLI_T2, specimens from patients who developed liver injury following anti-TB
treatment.",100,100,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 3B,23 July 2025,Nuerteye,Nuerteye,"Longitudinal comparison of bacterial genera with and without liver injury in patients with pulmonary tuberculosis.  ADLI_T1—liver-damaged group at T1; ADLI_T2—liver-damaged
group at T2. Characteristics of genus changes from T1 to T2 in ADLI group.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,",1783272|1239|186801|3085636|186803|1766253;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|186802|216572|216851;1783272|1239|526524|526525|128827|1573535;3379134|976|200643|171549|171552|1283313;1783272|1239|1737404|1737405|1570339|543311;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|216851|1946507;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|3085636|186803|877420;3379134|976|200643|171549|2005473;,Complete,NA
bsdb:40129950/2/2,40129950,case-control,40129950,10.3389/fphar.2025.1512815,NA,"Pei S., Yang L., Gao H., Liu Y., Lu J., Dai E.H., Meng C., Feng F. , Wang Y.",The association between the gut microbiome and antituberculosis drug-induced liver injury,Frontiers in pharmacology,2025,"anti-TB therapy, drug-induced liver injury, microbiome dysbiosis, probiotics, pulmonary tuberculosis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,Antituberculosis Drug-Induced Liver Injury (ADLI_T1) group,Antituberculosis Drug-Induced Liver Injury (ADLI_T2) group,"ADLI_T2, specimens from patients who developed liver injury following anti-TB
treatment.",100,100,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 3B,23 July 2025,Nuerteye,Nuerteye,Longitudinal comparison of bacterial genera with and without liver injury in patients with pulmonary tuberculosis. ADLI_T1—liver-damaged group at T1; ADLI_T2—liver-damaged group at T2. Characteristics of genus changes from T1 to T2 in ADLI group.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",1783272|1239|186801|3085636|186803|207244;3379134|1224|1236|91347|543|544;3379134|976|200643|171549|2005519|1348911;3379134|1224|1236|91347|543|1940338;3379134|1224|1236|91347|543|570;3379134|976|200643|171549|171552|577309;3379134|1224|1236|91347|543,Complete,NA
bsdb:40129950/3/1,40129950,case-control,40129950,10.3389/fphar.2025.1512815,NA,"Pei S., Yang L., Gao H., Liu Y., Lu J., Dai E.H., Meng C., Feng F. , Wang Y.",The association between the gut microbiome and antituberculosis drug-induced liver injury,Frontiers in pharmacology,2025,"anti-TB therapy, drug-induced liver injury, microbiome dysbiosis, probiotics, pulmonary tuberculosis",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,Non-Antituberculosis Drug-Induced Liver Injury (Non_ADLI_T1) group,Antituberculosis Drug-Induced Liver Injury (ADLI_T1) group,"ADLI_T1, specimens collected from patients prior to the initiation of anti-TB treatment upon admission.",100,100,Patients had not used antibiotics in the past month prior to the study,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 4A,23 July 2025,Nuerteye,Nuerteye,Comparative analysis of bacterial genera at the same time point between pulmonary tuberculosis patients with liver injury and those without liver injury. Non_ADLI_T1—nonsevere-damaged group at T1; ADLI_T1—liver-damaged group at T1. Characteristics of genus differences between Non_ADLI group and ADLI group at T1.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Clavibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia",3379134|976|200643|171549|815|816;1783272|1239|909932|1843489|31977|29465;1783272|201174|1760|85006|85023|1573;1783272|201174|1760|85007|1653|1716;1783272|1239|1737404|1737405|1570339|165779;1783272|201174|1760|85004|31953|2701;1783272|1239|186801|3082720|186804|1257;3379134|1224|28216|80840|119060|47670,Complete,NA
bsdb:40129950/3/2,40129950,case-control,40129950,10.3389/fphar.2025.1512815,NA,"Pei S., Yang L., Gao H., Liu Y., Lu J., Dai E.H., Meng C., Feng F. , Wang Y.",The association between the gut microbiome and antituberculosis drug-induced liver injury,Frontiers in pharmacology,2025,"anti-TB therapy, drug-induced liver injury, microbiome dysbiosis, probiotics, pulmonary tuberculosis",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,Non-Antituberculosis Drug-Induced Liver Injury (Non_ADLI_T1) group,Antituberculosis Drug-Induced Liver Injury (ADLI_T1) group,"ADLI_T1, specimens collected from patients prior to the initiation of anti-TB treatment upon admission.",100,100,Patients had not used antibiotics in the past month prior to the study,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 4A,23 July 2025,Nuerteye,Nuerteye,Comparative analysis of bacterial genera at the same time point between pulmonary tuberculosis patients with liver injury and those without liver injury. Non_ADLI_T1—nonsevere-damaged group at T1; ADLI_T1—liver-damaged group at T1. Characteristics of genus differences between Non_ADLI group and ADLI group at T1.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Mailhella",1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|186802|186806|264995;3379134|200940|3031449|213115|194924|1981028,Complete,NA
bsdb:40129950/4/1,40129950,case-control,40129950,10.3389/fphar.2025.1512815,NA,"Pei S., Yang L., Gao H., Liu Y., Lu J., Dai E.H., Meng C., Feng F. , Wang Y.",The association between the gut microbiome and antituberculosis drug-induced liver injury,Frontiers in pharmacology,2025,"anti-TB therapy, drug-induced liver injury, microbiome dysbiosis, probiotics, pulmonary tuberculosis",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,Non-Antituberculosis Drug-Induced Liver Injury (Non-ADLI_T2) group,Antituberculosis Drug-Induced Liver Injury (ADLI_T2) group,"ADLI_T2, specimens from patients who developed liver injury following anti-TB treatment.",100,100,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 4B,23 July 2025,Nuerteye,Nuerteye,Comparative analysis of bacterial genera at the same time point between pulmonary tuberculosis patients with liver injury and those without liver injury. Non_ADLI_T2—nonseiver-damaged group at T2; ADLI_T2—liver-damaged group at T2. Characteristics of genus differences between Non_ADLI group and ADLI group at T2.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__Tyzzerella sp.",3379134|1224|1236|135615|868|2717;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|216572|216851;3379134|1224|28216|80840|119060;1783272|1239|186801|3085636|186803|1506577|2053632,Complete,NA
bsdb:40129950/4/2,40129950,case-control,40129950,10.3389/fphar.2025.1512815,NA,"Pei S., Yang L., Gao H., Liu Y., Lu J., Dai E.H., Meng C., Feng F. , Wang Y.",The association between the gut microbiome and antituberculosis drug-induced liver injury,Frontiers in pharmacology,2025,"anti-TB therapy, drug-induced liver injury, microbiome dysbiosis, probiotics, pulmonary tuberculosis",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,Non-Antituberculosis Drug-Induced Liver Injury (Non-ADLI_T2) group,Antituberculosis Drug-Induced Liver Injury (ADLI_T2) group,"ADLI_T2, specimens from patients who developed liver injury following anti-TB treatment.",100,100,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 4B,23 July 2025,Nuerteye,Nuerteye,Comparative analysis of bacterial genera at the same time point between pulmonary tuberculosis patients with liver injury and those without liver injury. Non_ADLI_T2—nonseiver-damaged group at T2; ADLI_T2—liver-damaged group at T2. Characteristics of genus differences between Non_ADLI group and ADLI group at T2.,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Actinomycetota|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae",3379134|74201|203494|48461|1647988|239934;1783272|201174|84995|84996|84997|42255;3379134|200940|3031449|213115|194924,Complete,NA
bsdb:40155303/1/1,40155303,case-control,40155303,10.1016/j.jmii.2025.03.010,NA,"Ko M.J., Liao C.H., Chiu Y.L., Tsai W.C., Yang J.Y., Pai M.F., Tsai P.H., Hsu S.P., Peng Y.S. , Wu H.Y.",Gut microbial signatures associated with uremic pruritus in hemodialysis patients,"Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi",2025,"Dialysis, Gastrointestinal microbiome, Microbiota, Pruritus, Skin diseases, Uremia",Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,Pruritus,HP:0000989,Non-pruritus,Uremic pruritus,Hemodialysis patients with uremic pruritus,36,57,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 3A, 3B",17 November 2025,Tosin,Tosin,Differentially abundant bacterial taxa between hemodialysis patients with and without uremic pruritus by LeFse (linear discriminant analysis effect size),increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales",1783272|1239|909932|1843489|31977|39948;3379134|1224|1236|135625|712;3379134|1224|1236|135625,Complete,KateRasheed
bsdb:40155303/1/2,40155303,case-control,40155303,10.1016/j.jmii.2025.03.010,NA,"Ko M.J., Liao C.H., Chiu Y.L., Tsai W.C., Yang J.Y., Pai M.F., Tsai P.H., Hsu S.P., Peng Y.S. , Wu H.Y.",Gut microbial signatures associated with uremic pruritus in hemodialysis patients,"Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi",2025,"Dialysis, Gastrointestinal microbiome, Microbiota, Pruritus, Skin diseases, Uremia",Experiment 1,Taiwan,Homo sapiens,Feces,UBERON:0001988,Pruritus,HP:0000989,Non-pruritus,Uremic pruritus,Hemodialysis patients with uremic pruritus,36,57,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 3A, 3B",17 November 2025,Tosin,Tosin,Differentially abundant bacterial taxa between hemodialysis patients with and without uremic pruritus by LeFse (linear discriminant analysis effect size),decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,1783272|201174|1760|85007,Complete,KateRasheed
bsdb:40164980/1/1,40164980,"cross-sectional observational, not case-control",40164980,10.1080/19490976.2025.2484385,NA,"Otani S., Louise Jespersen M., Brinch C., Duus Møller F., Pilgaard B., Egholm Bruun Jensen E., Leekitcharoenphon P., Aaby Svendsen C., Aarestrup A.H., Sonda T., Sylvina T.J., Leach J., Piel A., Stewart F., Sapountzis P., Kazyoba P.E., Kumburu H. , Aarestrup F.M.",Genomic and functional co-diversification imprint African Hominidae microbiomes to signal dietary and lifestyle adaptations,Gut microbes,2025,"African hominidae, Microbiome, evolution, host adaptation",Experiment 1,United Republic of Tanzania,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Chimpanzees (combined Issa Valley + Mahale chimpanzees),Humans (combined Hadza + non-indigenous adults + non-indigenous children),This group is a combined cohort of indigenous Hadza hunter-gatherers and non-indigenous urban and rural Tanzanian adults and children.,90,456,NA,WMS,NA,Illumina,centered log-ratio,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 3D & Supplementary Figure S3,29 April 2025,Joiejoie,"Joiejoie,Victoria",Statistically significant MAGs between human and chimpanzee gut microbiomes,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:83,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. ER4,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|2005359;1783272|1239|1262992;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|186802|204475;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|459786|1519439;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|1508657,Complete,KateRasheed
bsdb:40164980/1/2,40164980,"cross-sectional observational, not case-control",40164980,10.1080/19490976.2025.2484385,NA,"Otani S., Louise Jespersen M., Brinch C., Duus Møller F., Pilgaard B., Egholm Bruun Jensen E., Leekitcharoenphon P., Aaby Svendsen C., Aarestrup A.H., Sonda T., Sylvina T.J., Leach J., Piel A., Stewart F., Sapountzis P., Kazyoba P.E., Kumburu H. , Aarestrup F.M.",Genomic and functional co-diversification imprint African Hominidae microbiomes to signal dietary and lifestyle adaptations,Gut microbes,2025,"African hominidae, Microbiome, evolution, host adaptation",Experiment 1,United Republic of Tanzania,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Chimpanzees (combined Issa Valley + Mahale chimpanzees),Humans (combined Hadza + non-indigenous adults + non-indigenous children),This group is a combined cohort of indigenous Hadza hunter-gatherers and non-indigenous urban and rural Tanzanian adults and children.,90,456,NA,WMS,NA,Illumina,centered log-ratio,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 3D & Supplementary Figure S3,29 April 2025,Joiejoie,"Joiejoie,Victoria",Statistically significant MAGs between human and chimpanzee gut microbiomes,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:791,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Parasporobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|s__Prevotellaceae bacterium UBA6398,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium",1783272|1239|186801|3085636|186803|572511;1783272|201174|84998|84999|84107|102106;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|186806|1730;1783272|1239|1262993;1783272|1239|186801|3082720|543314|86331;1783272|1239|186801|3085636|186803|115543;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|1952510;1783272|201174|84998|84999|84107|1473205;1783272|1239|526524|526525|128827|123375,Complete,KateRasheed
bsdb:40164980/2/1,40164980,"cross-sectional observational, not case-control",40164980,10.1080/19490976.2025.2484385,NA,"Otani S., Louise Jespersen M., Brinch C., Duus Møller F., Pilgaard B., Egholm Bruun Jensen E., Leekitcharoenphon P., Aaby Svendsen C., Aarestrup A.H., Sonda T., Sylvina T.J., Leach J., Piel A., Stewart F., Sapountzis P., Kazyoba P.E., Kumburu H. , Aarestrup F.M.",Genomic and functional co-diversification imprint African Hominidae microbiomes to signal dietary and lifestyle adaptations,Gut microbes,2025,"African hominidae, Microbiome, evolution, host adaptation",Experiment 2,United Republic of Tanzania,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Hadza humans (indigenous hunter-gatherers),Non-indigenous humans (urban/rural Tanzanian adults and children),This group comprises of Non-indigenous Tanzanian adults and children living in urban and rural settings.,48,408,NA,WMS,NA,Illumina,centered log-ratio,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 3E & Supplementary Figure S3,29 April 2025,Joiejoie,"Joiejoie,Victoria",Statistically significant genera,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:180,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|3085636|186803|1427378;1783272|1239|186801|3085636|186803|1766253;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|33042;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|186806|1730|1262882;1783272|1239|186801|186802|216572|216851;1783272|1239|526524|526525|128827|1573535;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|841,Complete,KateRasheed
bsdb:40164980/2/2,40164980,"cross-sectional observational, not case-control",40164980,10.1080/19490976.2025.2484385,NA,"Otani S., Louise Jespersen M., Brinch C., Duus Møller F., Pilgaard B., Egholm Bruun Jensen E., Leekitcharoenphon P., Aaby Svendsen C., Aarestrup A.H., Sonda T., Sylvina T.J., Leach J., Piel A., Stewart F., Sapountzis P., Kazyoba P.E., Kumburu H. , Aarestrup F.M.",Genomic and functional co-diversification imprint African Hominidae microbiomes to signal dietary and lifestyle adaptations,Gut microbes,2025,"African hominidae, Microbiome, evolution, host adaptation",Experiment 2,United Republic of Tanzania,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Hadza humans (indigenous hunter-gatherers),Non-indigenous humans (urban/rural Tanzanian adults and children),This group comprises of Non-indigenous Tanzanian adults and children living in urban and rural settings.,48,408,NA,WMS,NA,Illumina,centered log-ratio,Welch's T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 3E & Supplementary Figure S3,29 April 2025,Joiejoie,"Joiejoie,Victoria",Statistically significant genera.,decreased,"k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:110,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium sp. UBA636",3379134|203691|203692|1643686|143786|29521;3379134|29547|3031852|213849|72294|194;1783272|201174|84998|84999|84107|102106;1783272|1239|1263000;1783272|1239|186801|3082720|543314|86331;1783272|201174|84998|84999|1643824|133925;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|1508657;1783272|201174|84998|1643822|1643826|84108;1783272|1239|526524|526525|128827|123375;1783272|1239|526524|526525|128827|123375|1947467,Complete,KateRasheed
bsdb:40172215/1/1,40172215,laboratory experiment,40172215,10.1080/19490976.2025.2486511,NA,"Brito Rodrigues P., de Rezende Rodovalho V., Sencio V., Benech N., Creskey M., Silva Angulo F., Delval L., Robil C., Gosset P., Machelart A., Haas J., Descat A., Goosens J.F., Beury D., Maurier F., Hot D., Wolowczuk I., Sokol H., Zhang X., Ramirez Vinolo M.A. , Trottein F.",Integrative metagenomics and metabolomics reveal age-associated gut microbiota and metabolite alterations in a hamster model of COVID-19,Gut microbes,2025,"SARS-CoV-2, Viral pneumonia, aging, disease markers, gut microbiota, metabolomics, metagenomics",Experiment 1,France,Mesocricetus auratus,Caecum,UBERON:0001153,Age,EFO:0000246,Young Hamsters,Aged Hamsters,Hamsters in the aged group were 22 months old.,3,6,NA,WMS,NA,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 1C,4 May 2025,MyleeeA,"MyleeeA,Victoria",Differential abundance of taxa between Young and Aged hamsters analyzed with Maaslin2 (adjusted P-value < 0.05).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus murinus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:873",3379134|976|200643|171549|171550|239759|328813;1783272|201174|1760|85004|31953|1678|28025;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|2767887|1622;3379134|976|200643|171549|171552|838|1262936,Complete,KateRasheed
bsdb:40172215/1/2,40172215,laboratory experiment,40172215,10.1080/19490976.2025.2486511,NA,"Brito Rodrigues P., de Rezende Rodovalho V., Sencio V., Benech N., Creskey M., Silva Angulo F., Delval L., Robil C., Gosset P., Machelart A., Haas J., Descat A., Goosens J.F., Beury D., Maurier F., Hot D., Wolowczuk I., Sokol H., Zhang X., Ramirez Vinolo M.A. , Trottein F.",Integrative metagenomics and metabolomics reveal age-associated gut microbiota and metabolite alterations in a hamster model of COVID-19,Gut microbes,2025,"SARS-CoV-2, Viral pneumonia, aging, disease markers, gut microbiota, metabolomics, metagenomics",Experiment 1,France,Mesocricetus auratus,Caecum,UBERON:0001153,Age,EFO:0000246,Young Hamsters,Aged Hamsters,Hamsters in the aged group were 22 months old.,3,6,NA,WMS,NA,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 1C,4 May 2025,MyleeeA,"MyleeeA,Victoria",Differential abundance of taxa between Young and Aged hamsters analyzed with Maaslin2 (adjusted P-value < 0.05).,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium modestum,1783272|201174|1760|85009|31957|1912216|2559073,Complete,KateRasheed
bsdb:40172215/2/1,40172215,laboratory experiment,40172215,10.1080/19490976.2025.2486511,NA,"Brito Rodrigues P., de Rezende Rodovalho V., Sencio V., Benech N., Creskey M., Silva Angulo F., Delval L., Robil C., Gosset P., Machelart A., Haas J., Descat A., Goosens J.F., Beury D., Maurier F., Hot D., Wolowczuk I., Sokol H., Zhang X., Ramirez Vinolo M.A. , Trottein F.",Integrative metagenomics and metabolomics reveal age-associated gut microbiota and metabolite alterations in a hamster model of COVID-19,Gut microbes,2025,"SARS-CoV-2, Viral pneumonia, aging, disease markers, gut microbiota, metabolomics, metagenomics",Experiment 2,France,Mesocricetus auratus,Caecum,UBERON:0001153,SARS-CoV-2-related disease,MONDO:0100318,Young and Aged D0 non-infected controls (Age effect),Young and Aged D7 Infected (Age effect),Young (2 months old) and Aged (22 months old) SARS-CoV-2-infected hamsters at Day 7 with age effect.,NA,NA,NA,WMS,NA,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3C,4 May 2025,MyleeeA,MyleeeA,Differential abundance of taxa between Young and Aged D0 non-infected controls (Age effect) and Young and Aged D7 Infected (Age effect) hamsters analyzed with Maaslin2 (adjusted P-value < 0.05).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;1783272|201174|84998|1643822|1643826;1783272|1239|91061|186826|33958|2767887;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|171550|28138;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|216851,Complete,KateRasheed
bsdb:40172215/2/2,40172215,laboratory experiment,40172215,10.1080/19490976.2025.2486511,NA,"Brito Rodrigues P., de Rezende Rodovalho V., Sencio V., Benech N., Creskey M., Silva Angulo F., Delval L., Robil C., Gosset P., Machelart A., Haas J., Descat A., Goosens J.F., Beury D., Maurier F., Hot D., Wolowczuk I., Sokol H., Zhang X., Ramirez Vinolo M.A. , Trottein F.",Integrative metagenomics and metabolomics reveal age-associated gut microbiota and metabolite alterations in a hamster model of COVID-19,Gut microbes,2025,"SARS-CoV-2, Viral pneumonia, aging, disease markers, gut microbiota, metabolomics, metagenomics",Experiment 2,France,Mesocricetus auratus,Caecum,UBERON:0001153,SARS-CoV-2-related disease,MONDO:0100318,Young and Aged D0 non-infected controls (Age effect),Young and Aged D7 Infected (Age effect),Young (2 months old) and Aged (22 months old) SARS-CoV-2-infected hamsters at Day 7 with age effect.,NA,NA,NA,WMS,NA,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3C,4 May 2025,MyleeeA,MyleeeA,Differential abundance of taxa between Young and Aged D0 non-infected controls (Age effect) and Young and Aged D7 Infected (Age effect) hamsters analyzed with Maaslin2 (adjusted P-value < 0.05).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:115,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:180,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:475,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:582,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:822,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Frisingicoccus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Kineothrix,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:303,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|3085636|186803|1427378;1783272|1239|186801|3085636|186803|207244;1783272|1239|91061;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|186802|186806|1730|1262878;1783272|1239|186801|186802|186806|1730|1262882;1783272|1239|1263026;1783272|1239|1262997;1783272|1239|1263032;1783272|1239|186801|3085636|186803|1918511;1783272|1239|91061|186826|186828|117563;1783272|1239|186801|3085636|186803|2163168;1783272|1239|186801|3085636|186803|1898203;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|841|1262944;3379134|1224|28216|80840|995019|1918598;1783272|1239|186801|3085636|186803,Complete,KateRasheed
bsdb:40172215/3/1,40172215,laboratory experiment,40172215,10.1080/19490976.2025.2486511,NA,"Brito Rodrigues P., de Rezende Rodovalho V., Sencio V., Benech N., Creskey M., Silva Angulo F., Delval L., Robil C., Gosset P., Machelart A., Haas J., Descat A., Goosens J.F., Beury D., Maurier F., Hot D., Wolowczuk I., Sokol H., Zhang X., Ramirez Vinolo M.A. , Trottein F.",Integrative metagenomics and metabolomics reveal age-associated gut microbiota and metabolite alterations in a hamster model of COVID-19,Gut microbes,2025,"SARS-CoV-2, Viral pneumonia, aging, disease markers, gut microbiota, metabolomics, metagenomics",Experiment 3,France,Mesocricetus auratus,Caecum,UBERON:0001153,SARS-CoV-2-related disease,MONDO:0100318,Young and Aged D0 non-infected controls (Time effect),Young and Aged D7 Infected (Time effect),Young (2 months old) and Aged (22 months old) SARS-CoV-2-infected hamsters at Day 7 of infection with time of infection effect.,NA,NA,NA,WMS,NA,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3C,4 May 2025,MyleeeA,MyleeeA,Differential abundance of taxa between Young and Aged D0 non-infected controls (Time effect) and Young and Aged D7 Infected (Time effect) hamsters analyzed with Maaslin2 (adjusted P-value < 0.05).,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:273,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA7177,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:822,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",1783272|201174|84998|1643822|1643826|447020;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979|1485|1262789;1783272|1239|186801|186802|216572|216851|1946510;1783272|1239|1263032;1783272|1239|91061|186826|33958|2742598;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|815|909656;1783272|1239|186801|186802|216572|1905344;1783272|1239|526524|526525|2810280|3025755,Complete,KateRasheed
bsdb:40172215/3/2,40172215,laboratory experiment,40172215,10.1080/19490976.2025.2486511,NA,"Brito Rodrigues P., de Rezende Rodovalho V., Sencio V., Benech N., Creskey M., Silva Angulo F., Delval L., Robil C., Gosset P., Machelart A., Haas J., Descat A., Goosens J.F., Beury D., Maurier F., Hot D., Wolowczuk I., Sokol H., Zhang X., Ramirez Vinolo M.A. , Trottein F.",Integrative metagenomics and metabolomics reveal age-associated gut microbiota and metabolite alterations in a hamster model of COVID-19,Gut microbes,2025,"SARS-CoV-2, Viral pneumonia, aging, disease markers, gut microbiota, metabolomics, metagenomics",Experiment 3,France,Mesocricetus auratus,Caecum,UBERON:0001153,SARS-CoV-2-related disease,MONDO:0100318,Young and Aged D0 non-infected controls (Time effect),Young and Aged D7 Infected (Time effect),Young (2 months old) and Aged (22 months old) SARS-CoV-2-infected hamsters at Day 7 of infection with time of infection effect.,NA,NA,NA,WMS,NA,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3C,4 May 2025,MyleeeA,MyleeeA,Differential abundance of taxa between Young and Aged D0 non-infected controls (Time effect) and Young and Aged D7 Infected (Time effect) hamsters analyzed with Maaslin2 (adjusted P-value < 0.05).,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Acetobacter|s__Acetobacter sp. CAG:267,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Angelakisella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:180,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Frisingicoccus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Ileibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Longicatena,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotellamassilia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium UBA7182",3379134|1224|28211|3120395|433|434|1262684;1783272|1239|526524|526525|128827|174708;1783272|1239|186801|186802|216572|1935176;1783272|1239|186801|186802|186806|1730|1262882;1783272|1239|186801|3085636|186803|1918511;3379134|29547|3031852|213849|72293;1783272|1239|526524|526525|128827|1937007;1783272|1239|91061|186826|33958|2767887;1783272|1239|526524|526525|128827|1918536;3379134|200930|68337|191393|2945020|248038;3379134|976|200643|171549|2005473;3379134|976|200643|171549|171552|1926672;1783272|1239|186801|3085636|186803|1952150,Complete,KateRasheed
bsdb:40172215/4/1,40172215,laboratory experiment,40172215,10.1080/19490976.2025.2486511,NA,"Brito Rodrigues P., de Rezende Rodovalho V., Sencio V., Benech N., Creskey M., Silva Angulo F., Delval L., Robil C., Gosset P., Machelart A., Haas J., Descat A., Goosens J.F., Beury D., Maurier F., Hot D., Wolowczuk I., Sokol H., Zhang X., Ramirez Vinolo M.A. , Trottein F.",Integrative metagenomics and metabolomics reveal age-associated gut microbiota and metabolite alterations in a hamster model of COVID-19,Gut microbes,2025,"SARS-CoV-2, Viral pneumonia, aging, disease markers, gut microbiota, metabolomics, metagenomics",Experiment 4,France,Mesocricetus auratus,Caecum,UBERON:0001153,SARS-CoV-2-related disease,MONDO:0100318,Young and Aged D0 non-infected controls (Age effect),Young and Aged D22 Infected (Age effect),Young (2 months old) and Aged (22 months old) SARS-CoV-2-infected hamsters at Day 22 with age effect.,NA,NA,NA,WMS,NA,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3D,4 May 2025,MyleeeA,MyleeeA,Differential abundance of taxa between Young and Aged D0 non-infected controls (Age effect) and Young and Aged D22 Infected (Age effect) hamsters analyzed with Maaslin2 (adjusted P-value < 0.05).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Duncaniella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:180,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:873,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|976|200643|171549|2005473|2518495;1783272|1239|186801|186802|186806|1730|1262882;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171552|838|1262936;3379134|976|200643|171549|171550|28138;1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:40172215/4/2,40172215,laboratory experiment,40172215,10.1080/19490976.2025.2486511,NA,"Brito Rodrigues P., de Rezende Rodovalho V., Sencio V., Benech N., Creskey M., Silva Angulo F., Delval L., Robil C., Gosset P., Machelart A., Haas J., Descat A., Goosens J.F., Beury D., Maurier F., Hot D., Wolowczuk I., Sokol H., Zhang X., Ramirez Vinolo M.A. , Trottein F.",Integrative metagenomics and metabolomics reveal age-associated gut microbiota and metabolite alterations in a hamster model of COVID-19,Gut microbes,2025,"SARS-CoV-2, Viral pneumonia, aging, disease markers, gut microbiota, metabolomics, metagenomics",Experiment 4,France,Mesocricetus auratus,Caecum,UBERON:0001153,SARS-CoV-2-related disease,MONDO:0100318,Young and Aged D0 non-infected controls (Age effect),Young and Aged D22 Infected (Age effect),Young (2 months old) and Aged (22 months old) SARS-CoV-2-infected hamsters at Day 22 with age effect.,NA,NA,NA,WMS,NA,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3D,4 May 2025,MyleeeA,MyleeeA,Differential abundance of taxa between Young and Aged D0 non-infected controls (Age effect) and Young and Aged D22 Infected (Age effect) hamsters analyzed with MaAslin2 (adjusted P-value < 0.05).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:127,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:510,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium",1783272|1239|186801|186802|31979|1485|1262774;1783272|1239|186801|186802|31979|1485|1262816;1783272|1239|186801|3085636|186803|1898203,Complete,KateRasheed
bsdb:40172215/5/1,40172215,laboratory experiment,40172215,10.1080/19490976.2025.2486511,NA,"Brito Rodrigues P., de Rezende Rodovalho V., Sencio V., Benech N., Creskey M., Silva Angulo F., Delval L., Robil C., Gosset P., Machelart A., Haas J., Descat A., Goosens J.F., Beury D., Maurier F., Hot D., Wolowczuk I., Sokol H., Zhang X., Ramirez Vinolo M.A. , Trottein F.",Integrative metagenomics and metabolomics reveal age-associated gut microbiota and metabolite alterations in a hamster model of COVID-19,Gut microbes,2025,"SARS-CoV-2, Viral pneumonia, aging, disease markers, gut microbiota, metabolomics, metagenomics",Experiment 5,France,Mesocricetus auratus,Caecum,UBERON:0001153,SARS-CoV-2-related disease,MONDO:0100318,Young and Aged D0 non-infected controls (Time effect),Young and Aged D22 Infected (Time effect),Young (2 months old) and Aged (22 months old) SARS-CoV-2-infected hamsters at Day 22 of infection with time of infection effect.,NA,NA,NA,WMS,NA,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3D,4 May 2025,MyleeeA,MyleeeA,Differential abundance of taxa between Young and Aged D0 non-infected controls (Time effect) and Young and Aged D22 Infected (Time effect) hamsters analyzed with MaAslin2 (adjusted P-value < 0.05).,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae|g__Anaerotignum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Angelakisella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Longicatena,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Mailhella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Parvibacter,k__Pseudomonadati|p__Pseudomonadota|s__Proteobacteria bacterium CAG:495",1783272|1239|526524|526525|128827|174708;1783272|1239|186801|3085636|3118652|2039240;1783272|1239|186801|186802|216572|1935176;1783272|1239|526524|526525|128827|1937008;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|33958|1243;1783272|1239|526524|526525|128827|1918536;3379134|200940|3031449|213115|194924|1981028;3379134|976|200643|171549|2005473;3379134|976|200643|171549|1853231|283168;1783272|201174|84998|84999|84107|1427376;3379134|1224|1262987,Complete,KateRasheed
bsdb:40175554/1/1,40175554,prospective cohort,40175554,10.1038/s41586-025-08796-4,NA,"Ryan F.J., Clarke M., Lynn M.A., Benson S.C., McAlister S., Giles L.C., Choo J.M., Rossouw C., Ng Y.Y., Semchenko E.A., Richard A., Leong L.E.X., Taylor S.L., Blake S.J., Mugabushaka J.I., Walker M., Wesselingh S.L., Licciardi P.V., Seib K.L., Tumes D.J., Richmond P., Rogers G.B., Marshall H.S. , Lynn D.J.",Bifidobacteria support optimal infant vaccine responses,Nature,2025,NA,Experiment 1,Australia,Homo sapiens,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,No Antibiotic (No-ABX) group [Week-1],Intrapartum Antibiotic (IP-ABX) group [Week-1],Infants whose mothers received intrapartum antibiotics (within 28 days before or during delivery) and had no direct infant antibiotic exposure up to 6 weeks of age.,80,49,NA,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.05,FALSE,NA,NA,"formula feeding,sex",NA,decreased,unchanged,NA,NA,NA,Signature 1,"Extented figure 6(g, h, i) And Supplementary Table 11a&b",10 April 2025,ShadeAkinremi,"ShadeAkinremi,Victoria,KateRasheed",Differentially abundant microbial species in stool samples collected from IP-ABX infants at week 1 compared to No-ABX infants. Only taxa detected in >5% of samples are considered for differential abundance analysis.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Atlantibacter|s__Atlantibacter hermannii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter amalonaticus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter youngae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter chengduensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter ludwigii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus raffinosus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Pantoea septica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus peroris,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp. CCUG 60358,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp. HMSC068C11,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria mucosa,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp. T11011-6",3379134|1224|1236|91347|543|1903434|565;3379134|1224|1236|91347|543|544|35703;3379134|1224|1236|91347|543|544|546;3379134|1224|1236|91347|543|544|545;3379134|1224|1236|91347|543|544|133448;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|547|2494701;3379134|1224|1236|91347|543|547|550;3379134|1224|1236|91347|543|547|158836;3379134|1224|1236|91347|543|547|299767;1783272|1239|91061|186826|81852|1350|71452;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712|724|729;3379134|1224|1236|91347|543|570|548;3379134|1224|1236|91347|543|570|573;3379134|1224|28216|206351|481|482|28449;3379134|1224|1236|91347|1903409|53335|472695;1783272|201174|1760|2037|2049|2529408|1660;1783272|1239|91061|186826|1300|1301|68892;1783272|1239|91061|186826|1300|1301|68891;3379134|1224|1236|135625|712|724|1859695;3379134|1224|1236|135625|712|724|1739522;3379134|1224|28216|206351|481|482|488;1783272|1239|909932|1843489|31977|29465|2027459,Complete,KateRasheed
bsdb:40175554/1/2,40175554,prospective cohort,40175554,10.1038/s41586-025-08796-4,NA,"Ryan F.J., Clarke M., Lynn M.A., Benson S.C., McAlister S., Giles L.C., Choo J.M., Rossouw C., Ng Y.Y., Semchenko E.A., Richard A., Leong L.E.X., Taylor S.L., Blake S.J., Mugabushaka J.I., Walker M., Wesselingh S.L., Licciardi P.V., Seib K.L., Tumes D.J., Richmond P., Rogers G.B., Marshall H.S. , Lynn D.J.",Bifidobacteria support optimal infant vaccine responses,Nature,2025,NA,Experiment 1,Australia,Homo sapiens,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,No Antibiotic (No-ABX) group [Week-1],Intrapartum Antibiotic (IP-ABX) group [Week-1],Infants whose mothers received intrapartum antibiotics (within 28 days before or during delivery) and had no direct infant antibiotic exposure up to 6 weeks of age.,80,49,NA,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.05,FALSE,NA,NA,"formula feeding,sex",NA,decreased,unchanged,NA,NA,NA,Signature 2,"Extented figure 6(g, h, i) And Supplementary Table 11a&b",10 April 2025,ShadeAkinremi,"ShadeAkinremi,Victoria,KateRasheed",Differentially abundant microbial species in stool samples collected from IP-ABX infants at week 1 compared to No-ABX infants. Only taxa detected in >5% of samples are considered for differential abundance analysis.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. infantis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp. N4G05",3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|1678|1686;1783272|201174|1760|85004|31953|1678|216816|1682;1783272|201174|1760|85004|31953|1678|28026;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|815|909656;1783272|201174|1760|85004|31953|1678|2013020,Complete,KateRasheed
bsdb:40175554/2/1,40175554,prospective cohort,40175554,10.1038/s41586-025-08796-4,NA,"Ryan F.J., Clarke M., Lynn M.A., Benson S.C., McAlister S., Giles L.C., Choo J.M., Rossouw C., Ng Y.Y., Semchenko E.A., Richard A., Leong L.E.X., Taylor S.L., Blake S.J., Mugabushaka J.I., Walker M., Wesselingh S.L., Licciardi P.V., Seib K.L., Tumes D.J., Richmond P., Rogers G.B., Marshall H.S. , Lynn D.J.",Bifidobacteria support optimal infant vaccine responses,Nature,2025,NA,Experiment 2,Australia,Homo sapiens,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,No Antibiotic (No-ABX) group [Week-1],Neonatal Antibotic (Neo-ABX) group [Week-1],"Infants who received at least 48 h of antibiotic treatment in the neonatal period (the first 28 days after birth), with or without maternal antibiotic exposure.",80,32,NA,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.05,FALSE,NA,NA,"formula feeding,sex",NA,decreased,decreased,NA,NA,NA,Signature 1,Supplementary Table 11b,14 April 2025,ShadeAkinremi,"ShadeAkinremi,Victoria,KateRasheed",Differentially abundant microbial species in stool samples collected from Neo-ABX infants at week 1 compared to No-ABX infants. Only taxa detected in >5% of samples are considered for differential abundance analysis.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543|547;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|561;3379134|1224|1236|135625|712|724;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:40175554/2/2,40175554,prospective cohort,40175554,10.1038/s41586-025-08796-4,NA,"Ryan F.J., Clarke M., Lynn M.A., Benson S.C., McAlister S., Giles L.C., Choo J.M., Rossouw C., Ng Y.Y., Semchenko E.A., Richard A., Leong L.E.X., Taylor S.L., Blake S.J., Mugabushaka J.I., Walker M., Wesselingh S.L., Licciardi P.V., Seib K.L., Tumes D.J., Richmond P., Rogers G.B., Marshall H.S. , Lynn D.J.",Bifidobacteria support optimal infant vaccine responses,Nature,2025,NA,Experiment 2,Australia,Homo sapiens,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,No Antibiotic (No-ABX) group [Week-1],Neonatal Antibotic (Neo-ABX) group [Week-1],"Infants who received at least 48 h of antibiotic treatment in the neonatal period (the first 28 days after birth), with or without maternal antibiotic exposure.",80,32,NA,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.05,FALSE,NA,NA,"formula feeding,sex",NA,decreased,decreased,NA,NA,NA,Signature 2,Supplementary Table 11a,15 April 2025,ShadeAkinremi,"ShadeAkinremi,Victoria,KateRasheed",Differentially abundant microbial species in stool samples collected from Neo-ABX infants at week 1 compared to No-ABX infants. Only taxa detected in >5% of samples are considered for differential abundance analysis.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium angulatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. CCH5-D3,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella sp. TF06-26,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella sp. AF25-2LB",1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|1683;1783272|201174|1760|85004|31953|1678|28026;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|91061|186826|1300|1301|1768764;1783272|201174|84998|84999|84107|102106|2018038;1783272|201174|84998|84999|84107|102106|2292226,Complete,KateRasheed
bsdb:40175554/3/1,40175554,prospective cohort,40175554,10.1038/s41586-025-08796-4,NA,"Ryan F.J., Clarke M., Lynn M.A., Benson S.C., McAlister S., Giles L.C., Choo J.M., Rossouw C., Ng Y.Y., Semchenko E.A., Richard A., Leong L.E.X., Taylor S.L., Blake S.J., Mugabushaka J.I., Walker M., Wesselingh S.L., Licciardi P.V., Seib K.L., Tumes D.J., Richmond P., Rogers G.B., Marshall H.S. , Lynn D.J.",Bifidobacteria support optimal infant vaccine responses,Nature,2025,NA,Experiment 3,Australia,Homo sapiens,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,No Antibiotic (No-ABX) group [Week-6],Neonatal Antibotic (Neo-ABX) group [Week-6],"Infants who received at least 48 h of antibiotic treatment in the neonatal period (the first 28 days after birth), with or without maternal antibiotic exposure.",80,32,NA,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.05,FALSE,NA,NA,"formula feeding,sex",NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Extented figure 6(j, k, l) And Supplementary Table 11a&b",15 April 2025,ShadeAkinremi,"ShadeAkinremi,Victoria,KateRasheed",Differentially abundant microbial species in stool samples collected from Neo-ABX infants at week 6 compared to No-ABX infants. Only taxa detected in >5% of samples are considered for differential abundance analysis.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium angulatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella sp. TF06-26,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp. N4G05",1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|1683;1783272|201174|1760|85004|31953|1678|1681;1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|1678|28026;1783272|201174|84998|84999|84107|102106|74426;1783272|201174|84998|84999|84107|102106|2018038;1783272|201174|1760|85004|31953|1678|2013020,Complete,KateRasheed
bsdb:40180909/1/1,40180909,prospective cohort,40180909,10.1038/s41531-025-00885-5,https://pmc.ncbi.nlm.nih.gov/articles/PMC11968880/#Sec10,"Bedarf J.R., Romano S., Heinzmann S.S., Duncan A., Traka M.H., Ng D., Segovia-Lizano D., Simon M.C., Narbad A., Wüllner U. , Hildebrand F.",A prebiotic dietary pilot intervention restores faecal metabolites and may be neuroprotective in Parkinson's Disease,NPJ Parkinson's disease,2025,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Healthy spouses after prebiotics (CO group),Parkinson's Disease patients after prebiotics (PD group),Patient diagnosed with parkinson disease after prebiotics.,10,10,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,unchanged,unchanged,increased,NA,NA,increased,Signature 1,Fig 2E,10 April 2025,Shulamite,Shulamite,"Several genera were markedly reduced in the PD group after prebiotics, paralleled by several trends",increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales,1783272|1239|186801|3082768,Complete,Svetlana up
bsdb:40180909/1/2,40180909,prospective cohort,40180909,10.1038/s41531-025-00885-5,https://pmc.ncbi.nlm.nih.gov/articles/PMC11968880/#Sec10,"Bedarf J.R., Romano S., Heinzmann S.S., Duncan A., Traka M.H., Ng D., Segovia-Lizano D., Simon M.C., Narbad A., Wüllner U. , Hildebrand F.",A prebiotic dietary pilot intervention restores faecal metabolites and may be neuroprotective in Parkinson's Disease,NPJ Parkinson's disease,2025,NA,Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Healthy spouses after prebiotics (CO group),Parkinson's Disease patients after prebiotics (PD group),Patient diagnosed with parkinson disease after prebiotics.,10,10,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,unchanged,unchanged,increased,NA,NA,increased,Signature 2,Fig 2E,10 April 2025,Shulamite,"Shulamite,KateRasheed","Several genera were markedly reduced in the PD group after prebiotics, paralleled by several trends",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae",1783272|1239|186801|3085636|186803|189330;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|3082720|543314,Complete,Svetlana up
bsdb:40180909/2/1,40180909,prospective cohort,40180909,10.1038/s41531-025-00885-5,https://pmc.ncbi.nlm.nih.gov/articles/PMC11968880/#Sec10,"Bedarf J.R., Romano S., Heinzmann S.S., Duncan A., Traka M.H., Ng D., Segovia-Lizano D., Simon M.C., Narbad A., Wüllner U. , Hildebrand F.",A prebiotic dietary pilot intervention restores faecal metabolites and may be neuroprotective in Parkinson's Disease,NPJ Parkinson's disease,2025,NA,Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Health spouse (CO )before prebiotics,Healthy spouse (CO) after prebiotics,Healthy spouses who do not have Parkinson's disease,10,10,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,unchanged,unchanged,decreased,NA,NA,decreased,Signature 1,Supplementary Fig 3C,10 April 2025,Shulamite,"Shulamite,KateRasheed",Before vs after comparisons (Wilcoxon signed-rank test revealed that several Bifidobacteria spp. increased after prebiotics boxplots show a relative abundance of taxa. n=4 were also enriched in CO individuals.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum",1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|28026,Complete,Svetlana up
bsdb:40180909/3/1,40180909,prospective cohort,40180909,10.1038/s41531-025-00885-5,https://pmc.ncbi.nlm.nih.gov/articles/PMC11968880/#Sec10,"Bedarf J.R., Romano S., Heinzmann S.S., Duncan A., Traka M.H., Ng D., Segovia-Lizano D., Simon M.C., Narbad A., Wüllner U. , Hildebrand F.",A prebiotic dietary pilot intervention restores faecal metabolites and may be neuroprotective in Parkinson's Disease,NPJ Parkinson's disease,2025,NA,Experiment 3,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,PD before prebiotics,PD after prebiotics,Parkinson's disease patient after prebiotics.,10,10,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,unchanged,Signature 1,Supplementary Fig. 3c,10 April 2025,Shulamite,Shulamite,"Before-vs.-after comparisons (Wilcoxon signed-rank test) revealed that several Bifidobacteria spp. increased after prebiotics. Boxplots show a relative abundance of taxa. n=6 Bifidobacteria spp. were the only sign. different in PD (Strept. Thermophilus, UMGS1975).",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium angulatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales",1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|1683;1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|28026;1783272|201174|1760|85004|31953|1678|78346;1783272|1239|186801|3082768,Complete,Svetlana up
bsdb:40180909/3/2,40180909,prospective cohort,40180909,10.1038/s41531-025-00885-5,https://pmc.ncbi.nlm.nih.gov/articles/PMC11968880/#Sec10,"Bedarf J.R., Romano S., Heinzmann S.S., Duncan A., Traka M.H., Ng D., Segovia-Lizano D., Simon M.C., Narbad A., Wüllner U. , Hildebrand F.",A prebiotic dietary pilot intervention restores faecal metabolites and may be neuroprotective in Parkinson's Disease,NPJ Parkinson's disease,2025,NA,Experiment 3,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,PD before prebiotics,PD after prebiotics,Parkinson's disease patient after prebiotics.,10,10,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,unchanged,Signature 2,Supplementary Fig. 3c,10 April 2025,Shulamite,Shulamite,"Before-vs.-after comparisons (Wilcoxon signed-rank test) revealed that several Bifidobacteria spp. increased after prebiotics. Boxplots show a relative abundance of taxa. n=6 Bifidobacteria spp. were the only sign. different in PD (Strept. Thermophilus, UMGS1975).",decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,1783272|1239|91061|186826|1300|1301|1308,Complete,Svetlana up
bsdb:40180909/4/1,40180909,prospective cohort,40180909,10.1038/s41531-025-00885-5,https://pmc.ncbi.nlm.nih.gov/articles/PMC11968880/#Sec10,"Bedarf J.R., Romano S., Heinzmann S.S., Duncan A., Traka M.H., Ng D., Segovia-Lizano D., Simon M.C., Narbad A., Wüllner U. , Hildebrand F.",A prebiotic dietary pilot intervention restores faecal metabolites and may be neuroprotective in Parkinson's Disease,NPJ Parkinson's disease,2025,NA,Experiment 4,Germany,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Health spouse (CO )before prebiotics,Parkinson's Disease before prebiotics,Patients diagnosed with Parkinson's disease before prebiotics.,10,10,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,unchanged,unchanged,unchanged,NA,NA,unchanged,Signature 1,Fig 2E,22 April 2025,Shulamite,Shulamite,"Several genera were markedly reduced in the PD group before prebiotics, paralleled by several trends",decreased,NA,NA,Complete,Svetlana up
bsdb:40189515/2/1,40189515,"cross-sectional observational, not case-control",40189515,10.1186/s12905-025-03689-0,NA,"Cai Z., Zhou Z., Huang S., Ma S., Chen Y., Cao Y. , Ma Y.",Gut microbiome in patients with early-stage and late-stage endometriosis,BMC women's health,2025,"Dysmenorrhea, Endometriosis, Gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Early-stage Endometriosis (Stage I-II),Late-stage Endometriosis (Stage III-IV),"Patients diagnosed with late-stage endometriosis (Stage III and Stage IV) according to the revised American Society for Reproductive Medicine (r-ASRM) classification system, confirmed by surgical and pathological examination.",39,36,6 months,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 2D & Fig. S1A,14 April 2025,Joiejoie,"Joiejoie,KateRasheed",Differential microbes between the early- and late-stage endometriosis groups.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Bartonellaceae|g__Bartonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Bombella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Commensalibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus cecorum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Orbales|f__Orbaceae|g__Frischella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Orbales|f__Orbaceae|g__Gilliamella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus apis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter|s__Oxalobacter formigenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Snodgrassella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,s__metagenome,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|s__uncultured Gammaproteobacteria bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,s__uncultured bacterium,s__uncultured organism,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|s__uncultured Hyphomicrobiales bacterium",1783272|201174|1760|85006|1268|1663;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|246787;3379134|976|200643|171549|815|816|820;3379134|1224|28211|356|772|773;1783272|1239|186801|3085636|186803|572511;3379134|1224|28211|3120395|433|1654741;3379134|1224|28211|3120395|433|1079922;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|81852|1350|44008;3379134|1224|1236|1240482|1240483|1335631;3379134|1224|1236|1240482|1240483|1193503;1783272|1239|186801|186802|1392389;1783272|1239|186801|186802|1392389|1297617;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|303541;3379134|1224|28216|80840|75682|846;3379134|1224|28216|80840|75682|846|847;1783272|1239|186801|3085636|186803|177971;3379134|1224|28216|206351|481|1193515;3379134|976|200643|171549|2005525;256318;3379134|1224|1236|86473;1783272|1239|186801|186802|216572|707003;77133;155900;3379134|1224|28211|356|208549,Complete,KateRasheed
bsdb:40189515/2/2,40189515,"cross-sectional observational, not case-control",40189515,10.1186/s12905-025-03689-0,NA,"Cai Z., Zhou Z., Huang S., Ma S., Chen Y., Cao Y. , Ma Y.",Gut microbiome in patients with early-stage and late-stage endometriosis,BMC women's health,2025,"Dysmenorrhea, Endometriosis, Gut microbiota",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Endometriosis,EFO:0001065,Early-stage Endometriosis (Stage I-II),Late-stage Endometriosis (Stage III-IV),"Patients diagnosed with late-stage endometriosis (Stage III and Stage IV) according to the revised American Society for Reproductive Medicine (r-ASRM) classification system, confirmed by surgical and pathological examination.",39,36,6 months,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Fig. 2D & Fig. S1A,14 April 2025,Joiejoie,"Joiejoie,KateRasheed",Differential microbes between the early- and late-stage endometriosis groups.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caecimuris,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Ericales|f__Theaceae|g__Gordonia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae|g__Pseudolabrys,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus flavefaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,s__rumen bacterium NK4A214,s__uncultured bacterium,s__uncultured organism,s__uncultured rumen bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.",3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|1796613;1783272|1239|186801|186802|3085642|580596;95818|2093818|2093825|2171986|1331051;3379134|1224|1236|91347|543|544;33090|35493|3398|41945|27065|79255;3379134|1224|28216|80840|75682|963;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|33959;1783272|1239|91061|186826|1300|1357;1783272|1239|909932|909929|1843491|158846;1783272|201174|1760|85007|1762|1763;1783272|1239|909932|1843488|909930|33024;3379134|1224|28211|356|69277|28100;3379134|976|200643|171549|171552|838;3379134|1224|28211|356|335928|556257;3379134|1224|28216|80840|119060|48736;1783272|1239|186801|186802|216572|3068309;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|1265;1783272|1239|186801|186802|216572|1200657;1783272|1239|186801|186802|216572|39492;877428;77133;155900;136703;1783272|1239|186801|186802|216572|1263|41978,Complete,KateRasheed
bsdb:40189515/5/1,40189515,"cross-sectional observational, not case-control",40189515,10.1186/s12905-025-03689-0,NA,"Cai Z., Zhou Z., Huang S., Ma S., Chen Y., Cao Y. , Ma Y.",Gut microbiome in patients with early-stage and late-stage endometriosis,BMC women's health,2025,"Dysmenorrhea, Endometriosis, Gut microbiota",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Dysmenorrhea,HP:0100607,Early-Stage-F (patients without dysmenorrhea),Early-Stage-T (patients with dysmenorrhea),This group consists of patients diagnosed with early-stage endometriosis (Stage I–II) who reported experiencing preoperative dysmenorrhea.,23,16,6 months,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 4A,14 April 2025,Joiejoie,Joiejoie,Differential species between dysmenorrhea positive and negative subgroups within the early-stage endometriosis group,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus flavefaciens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Ruoffia|s__Ruoffia tabacinasalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus",1783272|1239|91061|186826|1300|1357|1358;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|186801|186802|216572|1263|1265;1783272|1239|91061|186826|186827|2862144|87458;1783272|1239|91061|186826|1300|1301|1328;1783272|1239|91061|186826|33958|46255;1783272|1239|186801|3085636|186803|33042,Complete,KateRasheed
bsdb:40189515/6/1,40189515,"cross-sectional observational, not case-control",40189515,10.1186/s12905-025-03689-0,NA,"Cai Z., Zhou Z., Huang S., Ma S., Chen Y., Cao Y. , Ma Y.",Gut microbiome in patients with early-stage and late-stage endometriosis,BMC women's health,2025,"Dysmenorrhea, Endometriosis, Gut microbiota",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Dysmenorrhea,HP:0100607,Late-Stage-F (patients without dysmenorrhea),Late-Stage-T (patients with dysmenorrhea),This group refers to patients diagnosed with late-stage endometriosis (Stage III–IV) who reported experiencing preoperative dysmenorrhea.,19,17,6 months,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 4A,14 April 2025,Joiejoie,Joiejoie,Differential species between dysmenorrhea-positive and negative subgroups within the late-stage endometriosis group.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus|s__Cloacibacillus evryensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides gordonii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__uncultured Odoribacter sp.,s__uncultured rumen bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",3379134|976|200643|171549|815|816|329854;3379134|976|200643|171549|815|816|820;3384194|508458|649775|649776|649777|508459|508460;1783272|1239|186801|186802|31979|1485|1502;3379134|1224|28216|80840|75682|963;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|2005525|375288|574930;3379134|976|200643|171549|1853231|283168|876416;136703;1783272|1239|186801|3085636|186803|297314,Complete,KateRasheed
bsdb:40189515/6/2,40189515,"cross-sectional observational, not case-control",40189515,10.1186/s12905-025-03689-0,NA,"Cai Z., Zhou Z., Huang S., Ma S., Chen Y., Cao Y. , Ma Y.",Gut microbiome in patients with early-stage and late-stage endometriosis,BMC women's health,2025,"Dysmenorrhea, Endometriosis, Gut microbiota",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Dysmenorrhea,HP:0100607,Late-Stage-F (patients without dysmenorrhea),Late-Stage-T (patients with dysmenorrhea),This group refers to patients diagnosed with late-stage endometriosis (Stage III–IV) who reported experiencing preoperative dysmenorrhea.,19,17,6 months,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Fig. 4A,14 April 2025,Joiejoie,Joiejoie,Differential species between dysmenorrhea-positive and negative subgroups within the late-stage endometriosis group.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,1783272|1239|91061|186826,Complete,KateRasheed
bsdb:40189515/7/1,40189515,"cross-sectional observational, not case-control",40189515,10.1186/s12905-025-03689-0,NA,"Cai Z., Zhou Z., Huang S., Ma S., Chen Y., Cao Y. , Ma Y.",Gut microbiome in patients with early-stage and late-stage endometriosis,BMC women's health,2025,"Dysmenorrhea, Endometriosis, Gut microbiota",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Dysmenorrhea,HP:0100607,Early-stage-T,Late-stage-T,"This group refers to patients with dysmenorrhea diagnosed with late-stage endometriosis, as analyzed for gut microbiota composition.",16,17,6 months,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 6D,15 April 2025,Joiejoie,"Joiejoie,KateRasheed",Relative abundance levels of 10 differential species consistently enriched between early-stage and late-stage groups.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Bombella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Commensalibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Snodgrassella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|s__uncultured Hyphomicrobiales bacterium",3379134|1224|28211|3120395|433|1654741;3379134|1224|28211|3120395|433|1079922;3379134|1224|28216|206351|481|1193515;3379134|1224|28211|356|208549,Complete,KateRasheed
bsdb:40189515/7/2,40189515,"cross-sectional observational, not case-control",40189515,10.1186/s12905-025-03689-0,NA,"Cai Z., Zhou Z., Huang S., Ma S., Chen Y., Cao Y. , Ma Y.",Gut microbiome in patients with early-stage and late-stage endometriosis,BMC women's health,2025,"Dysmenorrhea, Endometriosis, Gut microbiota",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Dysmenorrhea,HP:0100607,Early-stage-T,Late-stage-T,"This group refers to patients with dysmenorrhea diagnosed with late-stage endometriosis, as analyzed for gut microbiota composition.",16,17,6 months,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 6D,25 April 2025,Joiejoie,"Joiejoie,KateRasheed",Relative abundance levels of 10 differential species consistently enriched between early-stage and late-stage groups.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caecimuris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter ruminicola,s__uncultured rumen bacterium",3379134|976|200643|171549|815|816|1796613;3379134|976|200643|171549|171552|558436|839;136703,Complete,KateRasheed
bsdb:40189515/8/1,40189515,"cross-sectional observational, not case-control",40189515,10.1186/s12905-025-03689-0,NA,"Cai Z., Zhou Z., Huang S., Ma S., Chen Y., Cao Y. , Ma Y.",Gut microbiome in patients with early-stage and late-stage endometriosis,BMC women's health,2025,"Dysmenorrhea, Endometriosis, Gut microbiota",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Dysmenorrhea,HP:0100607,Early-stage-F,Late-stage-F,"This group refers to patients without dysmenorrhea who are diagnosed with late-stage endometriosis, as examined for gut microbiota differences.",23,19,6 months,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 6D,15 April 2025,Joiejoie,"Joiejoie,KateRasheed",Relative abundance levels of 10 differential species consistently enriched between early-stage and late-stage groups.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Bombella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Commensalibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Snodgrassella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|s__uncultured Hyphomicrobiales bacterium",3379134|1224|28211|3120395|433|1654741;3379134|1224|28211|3120395|433|1079922;3379134|1224|28216|206351|481|1193515;3379134|1224|28211|356|208549,Complete,KateRasheed
bsdb:40189515/8/2,40189515,"cross-sectional observational, not case-control",40189515,10.1186/s12905-025-03689-0,NA,"Cai Z., Zhou Z., Huang S., Ma S., Chen Y., Cao Y. , Ma Y.",Gut microbiome in patients with early-stage and late-stage endometriosis,BMC women's health,2025,"Dysmenorrhea, Endometriosis, Gut microbiota",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Dysmenorrhea,HP:0100607,Early-stage-F,Late-stage-F,"This group refers to patients without dysmenorrhea who are diagnosed with late-stage endometriosis, as examined for gut microbiota differences.",23,19,6 months,16S,34,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 6D,25 April 2025,Joiejoie,"Joiejoie,KateRasheed",Relative abundance levels of 10 differential species consistently enriched between early-stage and late-stage groups,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caecimuris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter ruminicola,s__uncultured rumen bacterium",3379134|976|200643|171549|815|816|1796613;3379134|976|200643|171549|171552|558436|839;136703,Complete,KateRasheed
bsdb:40204761/1/1,40204761,"prospective cohort,time series / longitudinal observational",40204761,10.1038/s41598-025-95198-1,NA,"Li F., Hooi S.L., Choo Y.M., Teh C.S.J., Toh K.Y., Lim L.W.Z., Lee Y.Q., Chong C.W. , Ahmad Kamar A.",Progression of gut microbiome in preterm infants during the first three months,Scientific reports,2025,"16S amplicon sequencing, Gut microbiome, Meconium, NICU, Patent ductus arteriosus (PDA), Preterm infants",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Patent ductus arteriosus,NA,Term infants,Preterm infants,Preterm infants (<37 weeks gestational age) monitored for gut microbiome development across six timepoints within the first three months of life.,46,23,3 months,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,2,NA,"antibiotic exposure,gestational age",NA,NA,NA,NA,NA,NA,Signature 1,Figure 1A & 1B,24 October 2025,SheikhAlMamun,SheikhAlMamun,"The three most prevalent phyla were Proteobacteria (mean = term vs. preterm, 503.4E−3 vs. 451.6E-3), Firmicutes (322.2E−3 vs. 292.8E−3), and Actinobacteria (99.5E−3 vs. 106.1E−3) in the meconium of both term and preterm infants. (Fig. 1a). The top 20 genera of preterm infants represented a lower proportion of the overall diversity than term infants (Fig. 1b).",increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,",1783272|201174;1783272|1239;3379134|976|200643|171549|815|816;3379134|976;1783272|201174|1760|85004|31953|1678;1783272|1117;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|561;1783272|1239|91061|186826|33958|1578;,Complete,NA
bsdb:40204761/1/2,40204761,"prospective cohort,time series / longitudinal observational",40204761,10.1038/s41598-025-95198-1,NA,"Li F., Hooi S.L., Choo Y.M., Teh C.S.J., Toh K.Y., Lim L.W.Z., Lee Y.Q., Chong C.W. , Ahmad Kamar A.",Progression of gut microbiome in preterm infants during the first three months,Scientific reports,2025,"16S amplicon sequencing, Gut microbiome, Meconium, NICU, Patent ductus arteriosus (PDA), Preterm infants",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Patent ductus arteriosus,NA,Term infants,Preterm infants,Preterm infants (<37 weeks gestational age) monitored for gut microbiome development across six timepoints within the first three months of life.,46,23,3 months,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,2,NA,"antibiotic exposure,gestational age",NA,NA,NA,NA,NA,NA,Signature 2,Figure 1A & 1B,24 October 2025,SheikhAlMamun,SheikhAlMamun,"The three most prevalent phyla were Proteobacteria (mean = term vs. preterm, 503.4E−3 vs. 451.6E-3), Firmicutes (322.2E−3 vs. 292.8E−3), and Actinobacteria (99.5E−3 vs. 106.1E−3) in the meconium of both term and preterm infants. (Fig. 1a). The top 20 genera of preterm infants represented a lower proportion of the overall diversity than term infants (Fig. 1b).",decreased,"k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter",3379134|1224;1783272|1239|91061|186826|1300|1301;3379134|1224|1236|91347|543|570;3379134|1224|1236|72274|135621|286;1783272|1239|186801|186802|31979|1485;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|2887326|468|469,Complete,NA
bsdb:40204761/2/1,40204761,"prospective cohort,time series / longitudinal observational",40204761,10.1038/s41598-025-95198-1,NA,"Li F., Hooi S.L., Choo Y.M., Teh C.S.J., Toh K.Y., Lim L.W.Z., Lee Y.Q., Chong C.W. , Ahmad Kamar A.",Progression of gut microbiome in preterm infants during the first three months,Scientific reports,2025,"16S amplicon sequencing, Gut microbiome, Meconium, NICU, Patent ductus arteriosus (PDA), Preterm infants",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Patent ductus arteriosus,NA,Term infants,Preterm infants,"At the meconium stage, 6 and 22 genera were enriched in term and preterm infants, respectively (LDA > 3.0; Wilcoxon p value < 0.05). Escherichia (116.1E−3, p = 3.0E−3) was highly enriched in the term infants, whereas Pseudomonas (148.9E−3, p = 2.0E−4) dominated the preterm infants (Fig. 1h). Meanwhile, 17 and 28 species were enriched in term and preterm infants, respectively (LDA > 3.0; Wilcoxon p value < 0.05). Escherichia coli (1.4E−3, p = 3.0E−3) was significantly more abundant in the term infants, while Pseudomonas aeruginosa (2.9E−3, p = 1.0E−4) was significantly more abundant in the preterm infants (Fig. 1i).",28,17,3 months,16S,NA,Illumina,relative abundances,"LEfSe,PERMANOVA",0.05,TRUE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1h & 1i,24 October 2025,SheikhAlMamun,SheikhAlMamun,"Increased in Term infants (Green):
At the meconium stage, 6 and 22 genera were enriched in term and preterm infants, respectively (LDA > 3.0; Wilcoxon p value < 0.05). Escherichia (116.1E−3, p = 3.0E−3) was highly enriched in the term infants, whereas Pseudomonas (148.9E−3, p = 2.0E−4) dominated the preterm infants (Fig. 1h). Meanwhile, 17 and 28 species were enriched in term and preterm infants, respectively (LDA > 3.0; Wilcoxon p value < 0.05). Escherichia coli (1.4E−3, p = 3.0E−3) was significantly more abundant in the term infants, while Pseudomonas aeruginosa (2.9E−3, p = 1.0E−4) was significantly more abundant in the preterm infants (Fig. 1i).",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis",3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|28116;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|815|816|371601;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|1681;1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|1678|216816;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|561|562;3379134|1224|1236|135625|712|724;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525|375288|823,Complete,NA
bsdb:40204761/2/2,40204761,"prospective cohort,time series / longitudinal observational",40204761,10.1038/s41598-025-95198-1,NA,"Li F., Hooi S.L., Choo Y.M., Teh C.S.J., Toh K.Y., Lim L.W.Z., Lee Y.Q., Chong C.W. , Ahmad Kamar A.",Progression of gut microbiome in preterm infants during the first three months,Scientific reports,2025,"16S amplicon sequencing, Gut microbiome, Meconium, NICU, Patent ductus arteriosus (PDA), Preterm infants",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Patent ductus arteriosus,NA,Term infants,Preterm infants,"At the meconium stage, 6 and 22 genera were enriched in term and preterm infants, respectively (LDA > 3.0; Wilcoxon p value < 0.05). Escherichia (116.1E−3, p = 3.0E−3) was highly enriched in the term infants, whereas Pseudomonas (148.9E−3, p = 2.0E−4) dominated the preterm infants (Fig. 1h). Meanwhile, 17 and 28 species were enriched in term and preterm infants, respectively (LDA > 3.0; Wilcoxon p value < 0.05). Escherichia coli (1.4E−3, p = 3.0E−3) was significantly more abundant in the term infants, while Pseudomonas aeruginosa (2.9E−3, p = 1.0E−4) was significantly more abundant in the preterm infants (Fig. 1i).",28,17,3 months,16S,NA,Illumina,relative abundances,"LEfSe,PERMANOVA",0.05,TRUE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1h & 1i,24 October 2025,SheikhAlMamun,SheikhAlMamun,"Increased in Preterm infants (Red):
At the meconium stage, 6 and 22 genera were enriched in term and preterm infants, respectively (LDA > 3.0; Wilcoxon p value < 0.05). Escherichia (116.1E−3, p = 3.0E−3) was highly enriched in the term infants, whereas Pseudomonas (148.9E−3, p = 2.0E−4) dominated the preterm infants (Fig. 1h). Meanwhile, 17 and 28 species were enriched in term and preterm infants, respectively (LDA > 3.0; Wilcoxon p value < 0.05). Escherichia coli (1.4E−3, p = 3.0E−3) was significantly more abundant in the term infants, while Pseudomonas aeruginosa (2.9E−3, p = 1.0E−4) was significantly more abundant in the preterm infants (Fig. 1i).",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus haemolyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium neonatale,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus lugdunensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas fluorescens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium paraputrificum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium beijerinckii,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus harei,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium tuberculostearicum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus",1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|570;1783272|1239|186801|186802|31979|1485;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|2887326|468|469;3379134|1224|1236|72274|135621|286;1783272|1239|909932|1843489|31977|29465;1783272|1239|91061|186826|1300|1301;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|91061|186826|33958|1578;1783272|1239|1737404|1737405|1570339|150022;1783272|201174|1760|85009|31957|1743;1783272|201174|1760|85007|1653|1716;3379134|1224|28211|356|41294|374;3379134|1224|1236|91347|543;1783272|1239|91061|1385|539738|1378;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|91061|1385|90964|1279|1282;1783272|1239|91061|186826|81852|1350|1351;3379134|1224|1236|91347|543|570|573;1783272|1239|91061|1385|90964|1279|1283;1783272|1239|186801|186802|31979|1485|1502;3379134|1224|1236|91347|543|570|571;1783272|1239|186801|186802|31979|1485|137838;3379134|1224|1236|72274|135621|286|287;1783272|1239|91061|1385|90964|1279|1290;1783272|1239|1737404|1737405|1570339|150022|1260;1783272|1239|91061|1385|90964|1279|28035;3379134|1224|1236|72274|135621|286|294;1783272|1239|186801|186802|31979|1485|29363;1783272|1239|186801|186802|31979|1485|1520;1783272|1239|1737404|1737405|1570339|162289|54005;1783272|201174|1760|85007|1653|1716|38304;1783272|1239|91061|1385|90964|1279|1280,Complete,NA
bsdb:40204761/3/1,40204761,"prospective cohort,time series / longitudinal observational",40204761,10.1038/s41598-025-95198-1,NA,"Li F., Hooi S.L., Choo Y.M., Teh C.S.J., Toh K.Y., Lim L.W.Z., Lee Y.Q., Chong C.W. , Ahmad Kamar A.",Progression of gut microbiome in preterm infants during the first three months,Scientific reports,2025,"16S amplicon sequencing, Gut microbiome, Meconium, NICU, Patent ductus arteriosus (PDA), Preterm infants",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Patent ductus arteriosus,NA,“moderate to late preterm” infants,“extremely to very preterm” infants,"From the differential abundance analysis, compared with term infants, 27 and 24 species were enriched in “extremely to very preterm” infants and “moderate to late preterm” infants, respectively (LDA > 3.0; Wilcoxon p value < 0.05). Pseudomonas aeruginosa (p < 0.05) was significantly more abundant in both “extremely to very preterm” infants and “moderate to late preterm” infants (Fig. 2d,e).",27,24,3 months,16S,NA,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,TRUE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2d & 2e,26 October 2025,SheikhAlMamun,SheikhAlMamun,"From the differential abundance analysis, compared with term infants, 27 and 24 species were enriched in “extremely to very preterm” infants and “moderate to late preterm” infants, respectively (LDA > 3.0; Wilcoxon p value < 0.05). Pseudomonas aeruginosa (p < 0.05) was significantly more abundant in both “extremely to very preterm” infants and “moderate to late preterm” infants",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida parapsilosis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus prevotii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Mycoplasmoidaceae|g__Ureaplasma|s__Ureaplasma parvum,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium accolens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium butyricum",3379134|1224|1236|91347|543|570|573;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|91061|186826|1300|1301|1311;4751|4890|3239874|2916678|766764|5475|5480;1783272|1239|91061|1385|90964|1279|1282;1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|909932|1843489|31977|29465|29466;1783272|1239|1737404|1737405|1570339|165779|33034;3379134|1224|1236|91347|543|547|550;1783272|544448|2790996|2790998|2129|134821;1783272|1239|1737404|1737405|1570339|150022|1260;3379134|1224|1236|91347|543|570|571;1783272|201174|1760|85007|1653|1716|38284;1783272|201174|1760|85009|31957|1912216|1747;1783272|1239|186801|186802|31979|1485|1492,Complete,NA
bsdb:40204761/3/2,40204761,"prospective cohort,time series / longitudinal observational",40204761,10.1038/s41598-025-95198-1,NA,"Li F., Hooi S.L., Choo Y.M., Teh C.S.J., Toh K.Y., Lim L.W.Z., Lee Y.Q., Chong C.W. , Ahmad Kamar A.",Progression of gut microbiome in preterm infants during the first three months,Scientific reports,2025,"16S amplicon sequencing, Gut microbiome, Meconium, NICU, Patent ductus arteriosus (PDA), Preterm infants",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Patent ductus arteriosus,NA,“moderate to late preterm” infants,“extremely to very preterm” infants,"From the differential abundance analysis, compared with term infants, 27 and 24 species were enriched in “extremely to very preterm” infants and “moderate to late preterm” infants, respectively (LDA > 3.0; Wilcoxon p value < 0.05). Pseudomonas aeruginosa (p < 0.05) was significantly more abundant in both “extremely to very preterm” infants and “moderate to late preterm” infants (Fig. 2d,e).",27,24,3 months,16S,NA,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,TRUE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2d & 2e,26 October 2025,SheikhAlMamun,SheikhAlMamun,"From the differential abundance analysis, compared with term infants, 27 and 24 species were enriched in “extremely to very preterm” infants and “moderate to late preterm” infants, respectively (LDA > 3.0; Wilcoxon p value < 0.05). Pseudomonas aeruginosa (p < 0.05) was significantly more abundant in both “extremely to very preterm” infants and “moderate to late preterm” infants",decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|28116;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|186802|216572|216851|853;1783272|1239|91061|186826|33958|1578|33959;1783272|1239|91061|186826|33958|1578|33959;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|2005525|375288|823;3379134|1224|1236|72274|135621|286|287;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|31979|1485|1522,Complete,NA
bsdb:40204761/4/1,40204761,"prospective cohort,time series / longitudinal observational",40204761,10.1038/s41598-025-95198-1,NA,"Li F., Hooi S.L., Choo Y.M., Teh C.S.J., Toh K.Y., Lim L.W.Z., Lee Y.Q., Chong C.W. , Ahmad Kamar A.",Progression of gut microbiome in preterm infants during the first three months,Scientific reports,2025,"16S amplicon sequencing, Gut microbiome, Meconium, NICU, Patent ductus arteriosus (PDA), Preterm infants",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Patent ductus arteriosus,NA,(w1 vs. m3 = 340.4E−3 vs. 349.1E−3),(w1 vs. m3 = 611.9E−3 vs. 110.1E−3),"Between the PNA of one week and the PNA of three months, the most prevalent phyla were Proteobacteria, Firmicutes (w1 vs. m3 = 340.4E−3 vs. 349.1E−3), Actinobacteria, and Bacteroidetes. As gut microbes developed, Proteobacteria (w1 vs. m3 = 611.9E−3 vs. 110.1E−3) was gradually replaced by Actinobacteria (w1 vs. m3 = 41.4E−3 vs. 491.6E−3) and Bacteroidetes (w1 vs. m3 = 0.4E−3 vs. 34.8E−3). (Fig. 3a). At the genus level, Blautia (m1 = 15.7E−3) occupied a relatively higher abundance from the PNA of one month, Bifidobacterium (m3 = 442.4E−3) gained higher prevalence, while a reduction of Klebsiella (m3 = 18.3E−3) was apparent at the PNA of three months (Fig. 3b).",NA,NA,3 months,16S,NA,Illumina,relative abundances,NA,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A & 3B,2 November 2025,SheikhAlMamun,SheikhAlMamun,"Between the PNA of one week and the PNA of three months, the most prevalent phyla were Proteobacteria, Firmicutes (w1 vs. m3 = 340.4E−3 vs. 349.1E−3), Actinobacteria, and Bacteroidetes. As gut microbes developed, Proteobacteria (w1 vs. m3 = 611.9E−3 vs. 110.1E−3) was gradually replaced by Actinobacteria (w1 vs. m3 = 41.4E−3 vs. 491.6E−3) and Bacteroidetes (w1 vs. m3 = 0.4E−3 vs. 34.8E−3). (Fig. 3a). At the genus level, Blautia (m1 = 15.7E−3) occupied a relatively higher abundance from the PNA of one month, Bifidobacterium (m3 = 442.4E−3) gained higher prevalence, while a reduction of Klebsiella (m3 = 18.3E−3) was apparent at the PNA of three months (Fig. 3b).",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia",1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|1485;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1301;3379134|1224|1236|2887326|468|469;95818|2093818,Complete,NA
bsdb:40204761/4/2,40204761,"prospective cohort,time series / longitudinal observational",40204761,10.1038/s41598-025-95198-1,NA,"Li F., Hooi S.L., Choo Y.M., Teh C.S.J., Toh K.Y., Lim L.W.Z., Lee Y.Q., Chong C.W. , Ahmad Kamar A.",Progression of gut microbiome in preterm infants during the first three months,Scientific reports,2025,"16S amplicon sequencing, Gut microbiome, Meconium, NICU, Patent ductus arteriosus (PDA), Preterm infants",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Patent ductus arteriosus,NA,(w1 vs. m3 = 340.4E−3 vs. 349.1E−3),(w1 vs. m3 = 611.9E−3 vs. 110.1E−3),"Between the PNA of one week and the PNA of three months, the most prevalent phyla were Proteobacteria, Firmicutes (w1 vs. m3 = 340.4E−3 vs. 349.1E−3), Actinobacteria, and Bacteroidetes. As gut microbes developed, Proteobacteria (w1 vs. m3 = 611.9E−3 vs. 110.1E−3) was gradually replaced by Actinobacteria (w1 vs. m3 = 41.4E−3 vs. 491.6E−3) and Bacteroidetes (w1 vs. m3 = 0.4E−3 vs. 34.8E−3). (Fig. 3a). At the genus level, Blautia (m1 = 15.7E−3) occupied a relatively higher abundance from the PNA of one month, Bifidobacterium (m3 = 442.4E−3) gained higher prevalence, while a reduction of Klebsiella (m3 = 18.3E−3) was apparent at the PNA of three months (Fig. 3b).",NA,NA,3 months,16S,NA,Illumina,relative abundances,NA,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3A & 3B,2 November 2025,SheikhAlMamun,SheikhAlMamun,"Between the PNA of one week and the PNA of three months, the most prevalent phyla were Proteobacteria, Firmicutes (w1 vs. m3 = 340.4E−3 vs. 349.1E−3), Actinobacteria, and Bacteroidetes. As gut microbes developed, Proteobacteria (w1 vs. m3 = 611.9E−3 vs. 110.1E−3) was gradually replaced by Actinobacteria (w1 vs. m3 = 41.4E−3 vs. 491.6E−3) and Bacteroidetes (w1 vs. m3 = 0.4E−3 vs. 34.8E−3). (Fig. 3a). At the genus level, Blautia (m1 = 15.7E−3) occupied a relatively higher abundance from the PNA of one month, Bifidobacterium (m3 = 442.4E−3) gained higher prevalence, while a reduction of Klebsiella (m3 = 18.3E−3) was apparent at the PNA of three months (Fig. 3b).",decreased,"k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres,k__Pseudomonadati|p__Nitrospirota,k__Pseudomonadati|p__Pseudomonadota,k__Thermotogati|p__Synergistota,k__Bacillati|p__Mycoplasmatota,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,p__Candidatus Saccharimonadota|g__Candidatus Minimicrobia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",1783272|1117;3379134|200930|68337;3379134|40117;3379134|1224;3384194|508458;1783272|544448;3379134|74201;3379134|976|200643|171549|815|816;3379134|1224|28216|80840|119060|32008;95818|2905967;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|570;3379134|1224|1236|72274|135621|286,Complete,NA
bsdb:40214782/1/1,40214782,prospective cohort,40214782,10.1007/s00394-025-03668-z,NA,"Koponen K., McDonald D., Jousilahti P., Meric G., Inouye M., Lahti L., Niiranen T., Männistö S., Havulinna A., Knight R. , Salomaa V.",Associations of alcohol with the human gut microbiome and prospective health outcomes in the FINRISK 2002 cohort,European journal of nutrition,2025,"Alcohol, Epidemiology, Gut microbiome, Prospective",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Alcohol consumption measurement,EFO:0007878,Low alcohol intake,High alcohol intake,Individuals categorized as high-risk consumers of alcohol in Model 2,NA,NA,6 months,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.05,TRUE,NA,NA,"age,body mass index,diet,sex,smoking status",NA,decreased,NA,NA,NA,NA,Signature 1,"Table 2, Supplementary Table 1.",13 April 2025,Montana-D,Montana-D,"Differentially abundant taxa of top 10 species in model 2.
For a comprehensive listing of all significant species-level results in the fully adjusted model please see Supplemental Table 1.",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,3379134|976|200643|171549|815|816|246787,Complete,Svetlana up
bsdb:40214782/1/2,40214782,prospective cohort,40214782,10.1007/s00394-025-03668-z,NA,"Koponen K., McDonald D., Jousilahti P., Meric G., Inouye M., Lahti L., Niiranen T., Männistö S., Havulinna A., Knight R. , Salomaa V.",Associations of alcohol with the human gut microbiome and prospective health outcomes in the FINRISK 2002 cohort,European journal of nutrition,2025,"Alcohol, Epidemiology, Gut microbiome, Prospective",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Alcohol consumption measurement,EFO:0007878,Low alcohol intake,High alcohol intake,Individuals categorized as high-risk consumers of alcohol in Model 2,NA,NA,6 months,WMS,NA,Illumina,centered log-ratio,Linear Regression,0.05,TRUE,NA,NA,"age,body mass index,diet,sex,smoking status",NA,decreased,NA,NA,NA,NA,Signature 2,"Table 2, Supplementary Table 1.",13 April 2025,Montana-D,Montana-D,"Differentially abundant taxa of top 10 species in model 2.
 For a comprehensive listing of all significant species-level results in the fully adjusted model please see Supplemental Table 1.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter johnsonii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum",3379134|1224|1236|2887326|468|469|40214;1783272|201174|1760|85004|31953|1678|1681,Complete,Svetlana up
bsdb:40247863/1/1,40247863,"case-control,prospective cohort",40247863,10.1080/20002297.2025.2489613,NA,"Yu M., Lu Y., Zhang W., Gong X., Hao Z., Xu L., Wen Y., Dong X., Han F. , Gao X.",Preliminary analysis of salivary microbiota in catathrenia (nocturnal groaning) using machine learning algorithms,Journal of oral microbiology,2025,"Nocturnal groaning, Sleep-disordered breathing, biomarker, microbiota, upper airway",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Sleep Disorder,EFO:0008568,Healthy control group,Catathrenia group,Catathrenia group were confirmed by overnight video/audio polysomnography (PSG) and not combined with other sleeping disorders.,22,22,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,"Figure 2e, Fig. S1a-c, Fig. S2",11 November 2025,Firdaws,Firdaws,Relative abundance of microbiota in catathrenia and control groups verified by Linear discriminant analysis Effect Size (LEfSe) analysis,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Oscillatoriales|f__Microcoleaceae|g__Arthrospira,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Boseaceae|g__Bosea,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Flavitalea,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Leptothrix,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Oscillatoriales|f__Oscillatoriaceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Oscillatoriales,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",3379134|1224|28216|80840|506|222;1783272|201174|84992;3379134|1224|1236|2887326|468|469;1783272|201174|1760|2037|2049|1654;1783272|201174;3379134|1224|28211;1783272|201174|1760|85009|31957|2801844;1783272|1117|3028117|1150|1892252|35823;3379134|1224|28211|356|2831100|85413;3379134|1224|28211|204458|76892|41275;3379134|1224|28216|80840|119060|32008;3379134|1224|28216|80840|119060;3379134|1224|28216|80840;3379134|1224|28211|204458|76892;3379134|1224|28211|204458;3379134|976|1853228|1853229|563835;3379134|976|1853228|1853229;3379134|976|1853228;3379134|1224|28216|80840|80864;1783272|1117;3379134|1224|28216|80840|80864|80865;1783272|1239|91061|186826|186828|29393;3379134|976|1853228|1853229|563835|1210116;3379134|1224|28211|356;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|80840|2975441|88;3379134|1224|1236|135614|32033;3379134|1224|1236|135614;1783272|201174|1760|85006|85023;1783272|201174|1760|85006|85023|33882;1783272|201174|1760|85006;3379134|1224|1236|2887326|468|475;3379134|1224|1236|2887326|468;3379134|1224|28211|356|41294;1783272|1117|3028117|1150|1892254;1783272|1117|3028117|1150;1783272|1117|3028117;3379134|976|117747|200666|84566|84567;1783272|201174|1760|85009|31957;1783272|201174|1760|85009;3379134|1224|28216|80840|119060|48736;1783272|1239|186801|3085636|186803|177971;3379134|976|117747|200666|84566;3379134|976|117747|200666;3379134|976|117747;3379134|1224|28211|204457|41297;3379134|1224|28211|204457;3379134|1224|28211|204457|41297|13687;3379134|1224|1236|135614|32033|40323,Complete,KateRasheed
bsdb:40247863/1/2,40247863,"case-control,prospective cohort",40247863,10.1080/20002297.2025.2489613,NA,"Yu M., Lu Y., Zhang W., Gong X., Hao Z., Xu L., Wen Y., Dong X., Han F. , Gao X.",Preliminary analysis of salivary microbiota in catathrenia (nocturnal groaning) using machine learning algorithms,Journal of oral microbiology,2025,"Nocturnal groaning, Sleep-disordered breathing, biomarker, microbiota, upper airway",Experiment 1,China,Homo sapiens,Saliva,UBERON:0001836,Sleep Disorder,EFO:0008568,Healthy control group,Catathrenia group,Catathrenia group were confirmed by overnight video/audio polysomnography (PSG) and not combined with other sleeping disorders.,22,22,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,age,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,"Figure 2e, Fig. S1d-f, Fig. S2",11 November 2025,Firdaws,Firdaws,Relative abundance of microbiota in catathrenia and control groups verified by Linear discriminant analysis Effect Size (LEfSe) analysis,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales",3379134|976|200643|171549|171552|1283313;3379134|976|200643|171549;3379134|976|200643;3379134|976;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;1783272|201174|1760|85004|31953|2701;1783272|1239|909932;1783272|1239|186801|3082720|186804|1257;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|186801|3085636|186803|1213720;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977;1783272|1239|909932|1843489,Complete,KateRasheed
bsdb:40247863/2/1,40247863,"case-control,prospective cohort",40247863,10.1080/20002297.2025.2489613,NA,"Yu M., Lu Y., Zhang W., Gong X., Hao Z., Xu L., Wen Y., Dong X., Han F. , Gao X.",Preliminary analysis of salivary microbiota in catathrenia (nocturnal groaning) using machine learning algorithms,Journal of oral microbiology,2025,"Nocturnal groaning, Sleep-disordered breathing, biomarker, microbiota, upper airway",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Sleep Disorder,EFO:0008568,Pre treatment of Mandibular Advancement Devices (MAD) group,Post treatment of Mandibular Advancement Devices (MAD) group,Catathrenia patients received treatment with mandibular advancement devices (MADs) and were evaluated post-treatment.,22,10,3 months,16S,34,Illumina,NA,NA,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,Figure 5a,13 November 2025,Firdaws,Firdaws,Significant microbiota identified in the pretreatment and post treatment of Mandibular advancement devices (MAD) using XGBoost algorithm,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,3379134|976|200643|171549|171552|1283313,Complete,KateRasheed
bsdb:40247863/2/2,40247863,"case-control,prospective cohort",40247863,10.1080/20002297.2025.2489613,NA,"Yu M., Lu Y., Zhang W., Gong X., Hao Z., Xu L., Wen Y., Dong X., Han F. , Gao X.",Preliminary analysis of salivary microbiota in catathrenia (nocturnal groaning) using machine learning algorithms,Journal of oral microbiology,2025,"Nocturnal groaning, Sleep-disordered breathing, biomarker, microbiota, upper airway",Experiment 2,China,Homo sapiens,Saliva,UBERON:0001836,Sleep Disorder,EFO:0008568,Pre treatment of Mandibular Advancement Devices (MAD) group,Post treatment of Mandibular Advancement Devices (MAD) group,Catathrenia patients received treatment with mandibular advancement devices (MADs) and were evaluated post-treatment.,22,10,3 months,16S,34,Illumina,NA,NA,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 2,Figure 5a,13 November 2025,Firdaws,Firdaws,Significant microbiota identified in the pretreatment and post treatment of Mandibular advancement devices (MAD) using Random forest algorithm,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85006|1268|32207,Complete,KateRasheed
bsdb:40257273/1/1,40257273,time series / longitudinal observational,40257273,10.1128/spectrum.02916-24,NA,"Ma X., Duan C., Wang X., Tao Y., Yang L., Teng Y., Pan Y., Zhang M., Xu J., Sheng J., Wang X. , Jin P.",Human gut microbiota adaptation to high-altitude exposure: longitudinal analysis over acute and prolonged periods,Microbiology spectrum,2025,"16S rDNA, dysbacteriosis, gut microbiota, high altitude, longitudinal effects",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,High altitude adaptation,EFO:0009105,G-II + G-III (Group 2 and 3),G-I (Group 1 at 800 m),Group of healthy adult males at the baseline at 800 m altitude.,592,406,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5C,5 May 2025,YokoC,YokoC,LEfSe differential analysis comparing the baseline group at 800 m. of altitude vs. acute high-altitude group and prolonged high-altitude group after a 2 week return from 3 months at 4500 m).,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",1783272|201174|1760;1783272|201174;3379134|976|200643|171549|171552|1283313;1783272|1239|186801|3085636|186803|207244;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642|580596;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|1239|186801|3085636|186803|189330;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|1407607;3379134|1224|1236;3379134|1224;3379134|1224|1236|91347|543|1940338,Complete,KateRasheed
bsdb:40257273/2/1,40257273,time series / longitudinal observational,40257273,10.1128/spectrum.02916-24,NA,"Ma X., Duan C., Wang X., Tao Y., Yang L., Teng Y., Pan Y., Zhang M., Xu J., Sheng J., Wang X. , Jin P.",Human gut microbiota adaptation to high-altitude exposure: longitudinal analysis over acute and prolonged periods,Microbiology spectrum,2025,"16S rDNA, dysbacteriosis, gut microbiota, high altitude, longitudinal effects",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,High altitude adaptation,EFO:0009105,G-I + G-III (Group  and 3),G-2 (Group 2 acute altitude at 4500 m),"Group of healthy adult males seven days after ascending to 4,500 m.",592,406,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5C,21 May 2025,YokoC,YokoC,LEfSe differential analysis comparing the acute high-altitude group at 4500 m vs. the baseline group at 800 m. of altitude and prolonged high-altitude group (after a two week return from 3 months at 4500 m).,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales,k__Methanobacteriati|p__Methanobacteriota,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota,",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|2005519|397864;3379134|1224|28216;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;3379134|1224|28216|80840;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|3085636|186803|33042;28221;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|204475;3366610|28890|183925;3366610|28890|183925|2158|2159;3366610|28890|183925|2158;3366610|28890;3366610|28890|183925|2158|2159|2172;1783272|1239|909932|909929|1843491|52225;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|1263;3379134|1224|28216|80840|995019;3379134|74201|203494|48461|203557;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201;,Complete,KateRasheed
bsdb:40257273/3/1,40257273,time series / longitudinal observational,40257273,10.1128/spectrum.02916-24,NA,"Ma X., Duan C., Wang X., Tao Y., Yang L., Teng Y., Pan Y., Zhang M., Xu J., Sheng J., Wang X. , Jin P.",Human gut microbiota adaptation to high-altitude exposure: longitudinal analysis over acute and prolonged periods,Microbiology spectrum,2025,"16S rDNA, dysbacteriosis, gut microbiota, high altitude, longitudinal effects",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,High altitude adaptation,EFO:0009105,G-I + G-II (Group 1  and 2),G-3 (Group 3 after prolonged altitude at 800 m),Group of healthy adult males two weeks post-return to 800 m following 3 months at high altitude,812,186,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5C,21 May 2025,YokoC,YokoC,LEfSe differential analysis comparing the prolonged high-altitude group (after a two week return from 3 months at 4500 m) vs. the baseline group at 800 m. of altitude and acute high-altitude group at 4500 m.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,",1783272|1239|186801|3085636|186803|830;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803;1783272|1239|909932|909929|1843491|158846;3379134|200930|68337|191393|2945020|248038;1783272|1239|186801|3085636|186803|841;,Complete,KateRasheed
bsdb:40257273/4/1,40257273,time series / longitudinal observational,40257273,10.1128/spectrum.02916-24,NA,"Ma X., Duan C., Wang X., Tao Y., Yang L., Teng Y., Pan Y., Zhang M., Xu J., Sheng J., Wang X. , Jin P.",Human gut microbiota adaptation to high-altitude exposure: longitudinal analysis over acute and prolonged periods,Microbiology spectrum,2025,"16S rDNA, dysbacteriosis, gut microbiota, high altitude, longitudinal effects",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,High altitude adaptation,EFO:0009105,G-I (Group 1 baseline),G-2 (Group 2 acute altitude exposure at 4500 m),"Group of healthy adult males seven days after ascending to 4,500 m.",406,406,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,increased,increased,NA,increased,Signature 1,"Figure 5A. Within text, Results under ""Unique microflora characteristics"" section.",21 May 2025,YokoC,YokoC,Box plots for differential analysis of gut microbiota at the genus level between the acute high-altitude exposure group at 4500 m. vs. the baseline group at 800 m.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|204475;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|216572|1263;3379134|1224|1236|91347|543|1940338,Complete,KateRasheed
bsdb:40257273/4/2,40257273,time series / longitudinal observational,40257273,10.1128/spectrum.02916-24,NA,"Ma X., Duan C., Wang X., Tao Y., Yang L., Teng Y., Pan Y., Zhang M., Xu J., Sheng J., Wang X. , Jin P.",Human gut microbiota adaptation to high-altitude exposure: longitudinal analysis over acute and prolonged periods,Microbiology spectrum,2025,"16S rDNA, dysbacteriosis, gut microbiota, high altitude, longitudinal effects",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,High altitude adaptation,EFO:0009105,G-I (Group 1 baseline),G-2 (Group 2 acute altitude exposure at 4500 m),"Group of healthy adult males seven days after ascending to 4,500 m.",406,406,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,increased,increased,NA,increased,Signature 2,"Figure 5A. Within text, Results under ""Unique microflora characteristics"" section.",21 May 2025,YokoC,YokoC,Box plots for differential analysis of gut microbiota at the genus level between the acute high-altitude exposure group at 4500 m. vs. the baseline group at 800 m.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",3379134|976|200643|171549|171552|1283313;1783272|1239|186801|186802|216572|216851;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|3085636|186803|841,Complete,KateRasheed
bsdb:40257273/5/1,40257273,time series / longitudinal observational,40257273,10.1128/spectrum.02916-24,NA,"Ma X., Duan C., Wang X., Tao Y., Yang L., Teng Y., Pan Y., Zhang M., Xu J., Sheng J., Wang X. , Jin P.",Human gut microbiota adaptation to high-altitude exposure: longitudinal analysis over acute and prolonged periods,Microbiology spectrum,2025,"16S rDNA, dysbacteriosis, gut microbiota, high altitude, longitudinal effects",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,High altitude adaptation,EFO:0009105,G-3(Group 3 prolonged altitude exposure at 4500 m.),G-2 (Group 2 acute altitude exposure at 4500 m),"Group of healthy adult males seven days after ascending to 4,500 m.",186,406,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,increased,increased,NA,increased,Signature 1,"Figure 5A, Within text, Results under ""Unique microflora characteristics"" section.",21 May 2025,YokoC,YokoC,"Box plots for differential analysis of gut microbiota at the genus level between the acute high-altitude exposure group at 4500 m. and the prolonged high-altitude exposure group, two weeks post-return to 800 m following 3 months at high altitude.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|204475;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|216572|1263;3379134|1224|1236|91347|543|1940338,Complete,KateRasheed
bsdb:40257273/5/2,40257273,time series / longitudinal observational,40257273,10.1128/spectrum.02916-24,NA,"Ma X., Duan C., Wang X., Tao Y., Yang L., Teng Y., Pan Y., Zhang M., Xu J., Sheng J., Wang X. , Jin P.",Human gut microbiota adaptation to high-altitude exposure: longitudinal analysis over acute and prolonged periods,Microbiology spectrum,2025,"16S rDNA, dysbacteriosis, gut microbiota, high altitude, longitudinal effects",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,High altitude adaptation,EFO:0009105,G-3(Group 3 prolonged altitude exposure at 4500 m.),G-2 (Group 2 acute altitude exposure at 4500 m),"Group of healthy adult males seven days after ascending to 4,500 m.",186,406,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,increased,increased,NA,increased,Signature 2,"Figure 5A, Within text, Results under ""Unique microflora characteristics"" section.",21 May 2025,YokoC,YokoC,"Box plots for differential analysis of gut microbiota at the genus level between the acute high-altitude exposure group at 4500 m. and the prolonged high-altitude exposure group, two weeks post-return to 800 m following 3 months at high altitude.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|841;1783272|1239|909932|909929|1843491|158846;3379134|976|200643|171549|171552|1283313,Complete,KateRasheed
bsdb:40257273/6/1,40257273,time series / longitudinal observational,40257273,10.1128/spectrum.02916-24,NA,"Ma X., Duan C., Wang X., Tao Y., Yang L., Teng Y., Pan Y., Zhang M., Xu J., Sheng J., Wang X. , Jin P.",Human gut microbiota adaptation to high-altitude exposure: longitudinal analysis over acute and prolonged periods,Microbiology spectrum,2025,"16S rDNA, dysbacteriosis, gut microbiota, high altitude, longitudinal effects",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Smoking behavior,EFO:0004318,Non-Smokers,Smokers,Group of healthy adult males who smoke.,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7,22 May 2025,YokoC,YokoC,Heatmap of a Spearman correlation analysis of genera with lifestyle factors (smoking).,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,1783272|1239|186801|3085636|186803|841,Complete,KateRasheed
bsdb:40257273/6/2,40257273,time series / longitudinal observational,40257273,10.1128/spectrum.02916-24,NA,"Ma X., Duan C., Wang X., Tao Y., Yang L., Teng Y., Pan Y., Zhang M., Xu J., Sheng J., Wang X. , Jin P.",Human gut microbiota adaptation to high-altitude exposure: longitudinal analysis over acute and prolonged periods,Microbiology spectrum,2025,"16S rDNA, dysbacteriosis, gut microbiota, high altitude, longitudinal effects",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Smoking behavior,EFO:0004318,Non-Smokers,Smokers,Group of healthy adult males who smoke.,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 7,22 May 2025,YokoC,YokoC,Heatmap of a Spearman correlation analysis of genera with lifestyle factors (smoking).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|1853231|574697;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|1283313;3379134|200940|3031449|213115|194924|35832;1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572|459786,Complete,KateRasheed
bsdb:40257273/7/1,40257273,time series / longitudinal observational,40257273,10.1128/spectrum.02916-24,NA,"Ma X., Duan C., Wang X., Tao Y., Yang L., Teng Y., Pan Y., Zhang M., Xu J., Sheng J., Wang X. , Jin P.",Human gut microbiota adaptation to high-altitude exposure: longitudinal analysis over acute and prolonged periods,Microbiology spectrum,2025,"16S rDNA, dysbacteriosis, gut microbiota, high altitude, longitudinal effects",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Alcohol drinking,EFO:0004329,No alcohol use,Alcohol use,Group of healthy adult males who use alcohol.,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7,22 May 2025,YokoC,YokoC,Heatmap of a Spearman correlation analysis of genera with lifestyle factors (alcohol use).,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,1783272|1239|186801|3085636|186803|841,Complete,KateRasheed
bsdb:40257273/7/2,40257273,time series / longitudinal observational,40257273,10.1128/spectrum.02916-24,NA,"Ma X., Duan C., Wang X., Tao Y., Yang L., Teng Y., Pan Y., Zhang M., Xu J., Sheng J., Wang X. , Jin P.",Human gut microbiota adaptation to high-altitude exposure: longitudinal analysis over acute and prolonged periods,Microbiology spectrum,2025,"16S rDNA, dysbacteriosis, gut microbiota, high altitude, longitudinal effects",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Alcohol drinking,EFO:0004329,No alcohol use,Alcohol use,Group of healthy adult males who use alcohol.,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 7,22 May 2025,YokoC,YokoC,Heatmap of a Spearman correlation analysis of genera with lifestyle factors (alcohol use).,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea",1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|189330,Complete,KateRasheed
bsdb:40257273/8/1,40257273,time series / longitudinal observational,40257273,10.1128/spectrum.02916-24,NA,"Ma X., Duan C., Wang X., Tao Y., Yang L., Teng Y., Pan Y., Zhang M., Xu J., Sheng J., Wang X. , Jin P.",Human gut microbiota adaptation to high-altitude exposure: longitudinal analysis over acute and prolonged periods,Microbiology spectrum,2025,"16S rDNA, dysbacteriosis, gut microbiota, high altitude, longitudinal effects",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Lower age,Higher age,Group of healthy adult males between the ages of 18 - 25.,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7,22 May 2025,YokoC,YokoC,Heatmap of a Spearman correlation analysis of genera with lifestyle factors (age).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|841,Complete,KateRasheed
bsdb:40257273/8/2,40257273,time series / longitudinal observational,40257273,10.1128/spectrum.02916-24,NA,"Ma X., Duan C., Wang X., Tao Y., Yang L., Teng Y., Pan Y., Zhang M., Xu J., Sheng J., Wang X. , Jin P.",Human gut microbiota adaptation to high-altitude exposure: longitudinal analysis over acute and prolonged periods,Microbiology spectrum,2025,"16S rDNA, dysbacteriosis, gut microbiota, high altitude, longitudinal effects",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Lower age,Higher age,Group of healthy adult males between the ages of 18 - 25.,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 7,22 May 2025,YokoC,YokoC,Heatmap of a Spearman correlation analysis of genera with lifestyle factors (age).,decreased,"k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",3366610|28890|183925|2158|2159|2172;1783272|201174|84998|84999|84107|102106;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|216572|459786,Complete,KateRasheed
bsdb:40257273/9/1,40257273,time series / longitudinal observational,40257273,10.1128/spectrum.02916-24,NA,"Ma X., Duan C., Wang X., Tao Y., Yang L., Teng Y., Pan Y., Zhang M., Xu J., Sheng J., Wang X. , Jin P.",Human gut microbiota adaptation to high-altitude exposure: longitudinal analysis over acute and prolonged periods,Microbiology spectrum,2025,"16S rDNA, dysbacteriosis, gut microbiota, high altitude, longitudinal effects",Experiment 9,China,Homo sapiens,Feces,UBERON:0001988,Body mass index,EFO:0004340,Lower BMI (Body Mass Index),Higher BMI (Body Mass Index),Group of healthy adult males with a higher Body Mass Index (BMI).,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7,22 May 2025,YokoC,YokoC,Heatmap of a Spearman correlation analysis of genera with lifestyle factors (BMI).,increased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,1783272|201174|84998|84999|84107|102106,Complete,KateRasheed
bsdb:40257273/9/2,40257273,time series / longitudinal observational,40257273,10.1128/spectrum.02916-24,NA,"Ma X., Duan C., Wang X., Tao Y., Yang L., Teng Y., Pan Y., Zhang M., Xu J., Sheng J., Wang X. , Jin P.",Human gut microbiota adaptation to high-altitude exposure: longitudinal analysis over acute and prolonged periods,Microbiology spectrum,2025,"16S rDNA, dysbacteriosis, gut microbiota, high altitude, longitudinal effects",Experiment 9,China,Homo sapiens,Feces,UBERON:0001988,Body mass index,EFO:0004340,Lower BMI (Body Mass Index),Higher BMI (Body Mass Index),Group of healthy adult males with a higher Body Mass Index (BMI).,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 7,22 May 2025,YokoC,YokoC,Heatmap of a Spearman correlation analysis of genera with lifestyle factors (BMI).,decreased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,1783272|1239|909932|1843489|31977|39948,Complete,KateRasheed
bsdb:40257273/10/1,40257273,time series / longitudinal observational,40257273,10.1128/spectrum.02916-24,NA,"Ma X., Duan C., Wang X., Tao Y., Yang L., Teng Y., Pan Y., Zhang M., Xu J., Sheng J., Wang X. , Jin P.",Human gut microbiota adaptation to high-altitude exposure: longitudinal analysis over acute and prolonged periods,Microbiology spectrum,2025,"16S rDNA, dysbacteriosis, gut microbiota, high altitude, longitudinal effects",Experiment 10,China,Homo sapiens,Feces,UBERON:0001988,Tea consumption measurement,EFO:0010091,Lower tea consumption,Higher tea consumption,Group of healthy adult males with a higher Body Mass Index (BMI).,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7,22 May 2025,YokoC,YokoC,Heatmap of a Spearman correlation analysis of genera with lifestyle factors (tea consumption).,increased,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,3366610|28890|183925|2158|2159|2172,Complete,KateRasheed
bsdb:40258140/1/1,40258140,"cross-sectional observational, not case-control,laboratory experiment",40258140,10.1073/pnas.2419689122,NA,"Yoon H., Gerdes L.A., Beigel F., Sun Y., Kövilein J., Wang J., Kuhlmann T., Flierl-Hecht A., Haller D., Hohlfeld R., Baranzini S.E., Wekerle H. , Peters A.",Multiple sclerosis and gut microbiota: Lachnospiraceae from the ileum of MS twins trigger MS-like disease in germfree transgenic mice-An unbiased functional study,Proceedings of the National Academy of Sciences of the United States of America,2025,"CNS autoimmunity, MS/EAE, gnotobiotic mice, gut–brain axis, microbiota",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Unaffected twins,Affected twins,"Individuals with Multiple Sclerosis, from monozygotic twin pairs clinically discordant for multiple sclerosis.",81,81,3 months,16S,34,Illumina,relative abundances,Chi-Square,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 1E,1 May 2025,Anne-mariesharp,Anne-mariesharp,A phylogenetic tree showing the taxa nominally significant in Chi-squared test. The “Trend” in the legend indicates changes in abundance in affected twins (compared to unaffected twins).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Acutalibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Limenecus|s__Candidatus Limenecus avicola,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae|g__Candidatus Scatocola|s__Candidatus Scatocola faecipullorum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella tanakaei,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella tayi,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma|s__Enorma massiliensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalicoccus|s__Faecalicoccus pleomorphus,k__Bacillati|p__Bacillota|g__Negativibacillus|s__Negativibacillus massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella xylaniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Pilosibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:632,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UBA5905",1783272|1239|186801|186802|3082771|1918385;1783272|1239|186801|186802|216572|244127|169435;3379134|976|200643|171549;3379134|976|200643|171549|2005519|397864|487174;1783272|1239|186801|186802|31979|2840608|2840847;3379134|1224|28211|204441|41295|2840645|2840917;1783272|201174|84998|84999|84107|102106|626935;1783272|1239|526524|526525|2810280|100883|100884;1783272|1239|186801|3085636|186803|1432051|1432052;1783272|201174|84998|84999|84107|1472762|1472761;1783272|1239|91061|186826|81852;1783272|1239|186801|186802;1783272|1239|526524|526525|128827|1573536|1323;1783272|1239|1980693|1871035;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171552|577309|454155;1783272|1239|186801|186802|31979|2840582;1783272|1239|186801|186802|216572|39492;1783272|1239|186801|186802|31979|1485|1262830;1783272|1239|186801|186802|216572|1952410,Complete,KateRasheed
bsdb:40258140/1/2,40258140,"cross-sectional observational, not case-control,laboratory experiment",40258140,10.1073/pnas.2419689122,NA,"Yoon H., Gerdes L.A., Beigel F., Sun Y., Kövilein J., Wang J., Kuhlmann T., Flierl-Hecht A., Haller D., Hohlfeld R., Baranzini S.E., Wekerle H. , Peters A.",Multiple sclerosis and gut microbiota: Lachnospiraceae from the ileum of MS twins trigger MS-like disease in germfree transgenic mice-An unbiased functional study,Proceedings of the National Academy of Sciences of the United States of America,2025,"CNS autoimmunity, MS/EAE, gnotobiotic mice, gut–brain axis, microbiota",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Unaffected twins,Affected twins,"Individuals with Multiple Sclerosis, from monozygotic twin pairs clinically discordant for multiple sclerosis.",81,81,3 months,16S,34,Illumina,relative abundances,Chi-Square,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 1E,1 May 2025,Anne-mariesharp,Anne-mariesharp,A phylogenetic tree showing the taxa nominally significant in Chi-squared test. The “Trend” in the legend indicates changes in abundance in affected twins (compared to unaffected twins).,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella jalaludinii,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia ilealis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella buccae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium neonatale",3379134|1224|28216|80840|506|222;1783272|201174|84998|84999|84107|102106;1783272|1239|909932|1843489|31977|39948|487173;1783272|1239|91061|1385|539738|1378;1783272|1239|526524|526525|128827|61170|1468449;3379134|976|200643|171549|171552|2974265|363265;1783272|1239|909932|909929|1843491|52225|187979;1783272|1239|186801|3082720|186804|1501226|1115758;3379134|976|200643|171549|171552|2974251|28126;1783272|1239|186801|186802|31979|1485|137838,Complete,KateRasheed
bsdb:40258140/2/1,40258140,"cross-sectional observational, not case-control,laboratory experiment",40258140,10.1073/pnas.2419689122,NA,"Yoon H., Gerdes L.A., Beigel F., Sun Y., Kövilein J., Wang J., Kuhlmann T., Flierl-Hecht A., Haller D., Hohlfeld R., Baranzini S.E., Wekerle H. , Peters A.",Multiple sclerosis and gut microbiota: Lachnospiraceae from the ileum of MS twins trigger MS-like disease in germfree transgenic mice-An unbiased functional study,Proceedings of the National Academy of Sciences of the United States of America,2025,"CNS autoimmunity, MS/EAE, gnotobiotic mice, gut–brain axis, microbiota",Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Unaffected twins,Affected twins,"Individuals with Multiple Sclerosis, from monozygotic twin pairs clinically discordant for multiple sclerosis.",81,81,3 months,16S,34,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 1E,1 May 2025,Anne-mariesharp,Anne-mariesharp,A phylogenetic tree showing the taxa nominally significant in Linear Mixed Model test. The “Trend” in the legend indicates changes in abundance in affected twins (compared to unaffected twins).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Acutalibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus massiliensis (ex Liu et al. 2021),k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Limenecus|s__Candidatus Limenecus avicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:1024,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Mailhella|s__Mailhella massiliensis,k__Bacillati|p__Bacillota|g__Negativibacillus|s__Negativibacillus massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UBA5905,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Pilosibacter",1783272|1239|186801|186802|3082771|1918385;1783272|1239|186801|186802|216572|244127|2321404;3379134|976|200643|171549;3379134|976|200643|171549|2005519|397864|487174;1783272|1239|186801|186802|31979|2840608|2840847;1783272|1239|186801|186802|31979|1485|1262770;1783272|1239|186801|186802;1783272|1239|526524|526525|128827|61170;3379134|200940|3031449|213115|194924|1981028|1903261;1783272|1239|1980693|1871035;1783272|1239|186801|186802|216572|1952410;1783272|1239|186801|186802|31979|2840582,Complete,KateRasheed
bsdb:40258140/2/2,40258140,"cross-sectional observational, not case-control,laboratory experiment",40258140,10.1073/pnas.2419689122,NA,"Yoon H., Gerdes L.A., Beigel F., Sun Y., Kövilein J., Wang J., Kuhlmann T., Flierl-Hecht A., Haller D., Hohlfeld R., Baranzini S.E., Wekerle H. , Peters A.",Multiple sclerosis and gut microbiota: Lachnospiraceae from the ileum of MS twins trigger MS-like disease in germfree transgenic mice-An unbiased functional study,Proceedings of the National Academy of Sciences of the United States of America,2025,"CNS autoimmunity, MS/EAE, gnotobiotic mice, gut–brain axis, microbiota",Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,Multiple sclerosis,MONDO:0005301,Unaffected twins,Affected twins,"Individuals with Multiple Sclerosis, from monozygotic twin pairs clinically discordant for multiple sclerosis.",81,81,3 months,16S,34,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 1E,1 May 2025,Anne-mariesharp,Anne-mariesharp,A phylogenetic tree showing the taxa nominally significant in Linear Mixed Model test. The “Trend” in the legend indicates changes in abundance in affected twins (compared to unaffected twins).,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella buccae",1783272|1239|909932|1843489|31977|39948|487173;1783272|1239|91061|1385|539738|1378;1783272|1239|186801|3085636|186803|28050;3379134|976|200643|171549|171552|2974251|28126,Complete,KateRasheed
bsdb:40258140/3/1,40258140,"cross-sectional observational, not case-control,laboratory experiment",40258140,10.1073/pnas.2419689122,NA,"Yoon H., Gerdes L.A., Beigel F., Sun Y., Kövilein J., Wang J., Kuhlmann T., Flierl-Hecht A., Haller D., Hohlfeld R., Baranzini S.E., Wekerle H. , Peters A.",Multiple sclerosis and gut microbiota: Lachnospiraceae from the ileum of MS twins trigger MS-like disease in germfree transgenic mice-An unbiased functional study,Proceedings of the National Academy of Sciences of the United States of America,2025,"CNS autoimmunity, MS/EAE, gnotobiotic mice, gut–brain axis, microbiota",Experiment 3,Germany,Mus musculus,Feces,UBERON:0001988,Experimental autoimmune encephalomyelitis,EFO:0001066,Healthy,EAE (Experimental Autoimmune Encephalomyelitis),Gnotobiotic mice that developed Experimental Autoimmune Encephalomyelitis after being colonized with ileal microbiota from an MS (Multiple Sclerosis)-affected human twin (MS-Q).,NA,NA,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 3F,1 May 2025,Anne-mariesharp,Anne-mariesharp,Relative abundance of fecal microbiota in recipients of MS patient-derived ileal microbiota that showed a significant difference (unpaired t-test) between healthy and diseased animals.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella",3379134|1224|28216|80840|506|507;1783272|1239|186801|3085636|186803|1432051,Complete,KateRasheed
bsdb:40258140/3/2,40258140,"cross-sectional observational, not case-control,laboratory experiment",40258140,10.1073/pnas.2419689122,NA,"Yoon H., Gerdes L.A., Beigel F., Sun Y., Kövilein J., Wang J., Kuhlmann T., Flierl-Hecht A., Haller D., Hohlfeld R., Baranzini S.E., Wekerle H. , Peters A.",Multiple sclerosis and gut microbiota: Lachnospiraceae from the ileum of MS twins trigger MS-like disease in germfree transgenic mice-An unbiased functional study,Proceedings of the National Academy of Sciences of the United States of America,2025,"CNS autoimmunity, MS/EAE, gnotobiotic mice, gut–brain axis, microbiota",Experiment 3,Germany,Mus musculus,Feces,UBERON:0001988,Experimental autoimmune encephalomyelitis,EFO:0001066,Healthy,EAE (Experimental Autoimmune Encephalomyelitis),Gnotobiotic mice that developed Experimental Autoimmune Encephalomyelitis after being colonized with ileal microbiota from an MS (Multiple Sclerosis)-affected human twin (MS-Q).,NA,NA,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Figure 3F,1 May 2025,Anne-mariesharp,Anne-mariesharp,Relative abundance of fecal microbiota in recipients of MS patient-derived ileal microbiota that showed a significant difference (unpaired t-test) between healthy and diseased animals.,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota",3379134|74201|203494|48461|1647988|239934;1783272|1239|526524|526525|2810280|3025755;1783272|1239,Complete,KateRasheed
bsdb:40258140/4/1,40258140,"cross-sectional observational, not case-control,laboratory experiment",40258140,10.1073/pnas.2419689122,NA,"Yoon H., Gerdes L.A., Beigel F., Sun Y., Kövilein J., Wang J., Kuhlmann T., Flierl-Hecht A., Haller D., Hohlfeld R., Baranzini S.E., Wekerle H. , Peters A.",Multiple sclerosis and gut microbiota: Lachnospiraceae from the ileum of MS twins trigger MS-like disease in germfree transgenic mice-An unbiased functional study,Proceedings of the National Academy of Sciences of the United States of America,2025,"CNS autoimmunity, MS/EAE, gnotobiotic mice, gut–brain axis, microbiota",Experiment 4,Germany,Mus musculus,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,GF_HT (Germ Free_Healthy Twin) (Early 2weeks),GF-MS (Germ Free_Multiple Sclerosis) (Early 2weeks),Germ-free Gnotobiotic RR (Relapsing Remitting) SJL/J mice colonized with ileal microbiota from the Multiple Sclerosis twin (MS-Q) (2 weeks after colonization),8,8,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 1,Figure 4E,1 May 2025,Anne-mariesharp,Anne-mariesharp,Relative abundance of fecal microbiota from colonized RR mice that showed significant changes (unpaired t-test) at the genus level.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|976|200643|171549|815|816;3379134|1224|1236|91347|543|1940338,Complete,KateRasheed
bsdb:40258140/4/2,40258140,"cross-sectional observational, not case-control,laboratory experiment",40258140,10.1073/pnas.2419689122,NA,"Yoon H., Gerdes L.A., Beigel F., Sun Y., Kövilein J., Wang J., Kuhlmann T., Flierl-Hecht A., Haller D., Hohlfeld R., Baranzini S.E., Wekerle H. , Peters A.",Multiple sclerosis and gut microbiota: Lachnospiraceae from the ileum of MS twins trigger MS-like disease in germfree transgenic mice-An unbiased functional study,Proceedings of the National Academy of Sciences of the United States of America,2025,"CNS autoimmunity, MS/EAE, gnotobiotic mice, gut–brain axis, microbiota",Experiment 4,Germany,Mus musculus,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,GF_HT (Germ Free_Healthy Twin) (Early 2weeks),GF-MS (Germ Free_Multiple Sclerosis) (Early 2weeks),Germ-free Gnotobiotic RR (Relapsing Remitting) SJL/J mice colonized with ileal microbiota from the Multiple Sclerosis twin (MS-Q) (2 weeks after colonization),8,8,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 2,Figure 4E,1 May 2025,Anne-mariesharp,Anne-mariesharp,Relative abundance of fecal microbiota from colonized RR mice that showed significant changes (unpaired t-test) at the genus level.,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:40258140/5/1,40258140,"cross-sectional observational, not case-control,laboratory experiment",40258140,10.1073/pnas.2419689122,NA,"Yoon H., Gerdes L.A., Beigel F., Sun Y., Kövilein J., Wang J., Kuhlmann T., Flierl-Hecht A., Haller D., Hohlfeld R., Baranzini S.E., Wekerle H. , Peters A.",Multiple sclerosis and gut microbiota: Lachnospiraceae from the ileum of MS twins trigger MS-like disease in germfree transgenic mice-An unbiased functional study,Proceedings of the National Academy of Sciences of the United States of America,2025,"CNS autoimmunity, MS/EAE, gnotobiotic mice, gut–brain axis, microbiota",Experiment 5,Germany,Mus musculus,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,GF_HT (Germ Free_Healthy Twin) (End),GF-MS (Germ Free_Multiple Sclerosis) (End),Germ-free Gnotobiotic RR (Relapsing Remitting) SJL/J mice colonized with ileal microbiota from the Multiple Sclerosis twin (MS-Q) (at endpoint after colonization),8,8,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 1,Figure 4E,1 May 2025,Anne-mariesharp,Anne-mariesharp,Relative abundance of fecal microbiota from colonized RR mice that showed significant changes (unpaired t-test) at the genus level.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|1506553;3379134|1224|1236|91347|543|1940338,Complete,KateRasheed
bsdb:40258140/5/2,40258140,"cross-sectional observational, not case-control,laboratory experiment",40258140,10.1073/pnas.2419689122,NA,"Yoon H., Gerdes L.A., Beigel F., Sun Y., Kövilein J., Wang J., Kuhlmann T., Flierl-Hecht A., Haller D., Hohlfeld R., Baranzini S.E., Wekerle H. , Peters A.",Multiple sclerosis and gut microbiota: Lachnospiraceae from the ileum of MS twins trigger MS-like disease in germfree transgenic mice-An unbiased functional study,Proceedings of the National Academy of Sciences of the United States of America,2025,"CNS autoimmunity, MS/EAE, gnotobiotic mice, gut–brain axis, microbiota",Experiment 5,Germany,Mus musculus,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,GF_HT (Germ Free_Healthy Twin) (End),GF-MS (Germ Free_Multiple Sclerosis) (End),Germ-free Gnotobiotic RR (Relapsing Remitting) SJL/J mice colonized with ileal microbiota from the Multiple Sclerosis twin (MS-Q) (at endpoint after colonization),8,8,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 2,Figure 4E,1 May 2025,Anne-mariesharp,Anne-mariesharp,Relative abundance of fecal microbiota from colonized RR mice that showed significant changes (unpaired t-test) at the genus level.,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:40258140/6/1,40258140,"cross-sectional observational, not case-control,laboratory experiment",40258140,10.1073/pnas.2419689122,NA,"Yoon H., Gerdes L.A., Beigel F., Sun Y., Kövilein J., Wang J., Kuhlmann T., Flierl-Hecht A., Haller D., Hohlfeld R., Baranzini S.E., Wekerle H. , Peters A.",Multiple sclerosis and gut microbiota: Lachnospiraceae from the ileum of MS twins trigger MS-like disease in germfree transgenic mice-An unbiased functional study,Proceedings of the National Academy of Sciences of the United States of America,2025,"CNS autoimmunity, MS/EAE, gnotobiotic mice, gut–brain axis, microbiota",Experiment 6,Germany,Mus musculus,Ileum,UBERON:0002116,Transplant outcome measurement,EFO:0005198,GF_HT-Q (Germ Free_Healthy Twin),GF_MS-Q (Germ Free_Multiple Sclerosis),Germ-free Gnotobiotic RR (Relapsing Remitting) SJL/J mice colonized with ileal microbiota from the Multiple Sclerosis twin (MS-Q),8,8,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. S4G,1 May 2025,Anne-mariesharp,Anne-mariesharp,Relative abundance of ileal microbiota in humanized gnotobiotic RR mice that showed significant differences (unpaired t-test) at the genus level.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",1783272|1239|186801|3085636|186803|1506553;3379134|1224|1236|91347|543|1940338,Complete,KateRasheed
bsdb:40258140/6/2,40258140,"cross-sectional observational, not case-control,laboratory experiment",40258140,10.1073/pnas.2419689122,NA,"Yoon H., Gerdes L.A., Beigel F., Sun Y., Kövilein J., Wang J., Kuhlmann T., Flierl-Hecht A., Haller D., Hohlfeld R., Baranzini S.E., Wekerle H. , Peters A.",Multiple sclerosis and gut microbiota: Lachnospiraceae from the ileum of MS twins trigger MS-like disease in germfree transgenic mice-An unbiased functional study,Proceedings of the National Academy of Sciences of the United States of America,2025,"CNS autoimmunity, MS/EAE, gnotobiotic mice, gut–brain axis, microbiota",Experiment 6,Germany,Mus musculus,Ileum,UBERON:0002116,Transplant outcome measurement,EFO:0005198,GF_HT-Q (Germ Free_Healthy Twin),GF_MS-Q (Germ Free_Multiple Sclerosis),Germ-free Gnotobiotic RR (Relapsing Remitting) SJL/J mice colonized with ileal microbiota from the Multiple Sclerosis twin (MS-Q),8,8,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Fig. S4G,1 May 2025,Anne-mariesharp,Anne-mariesharp,Relative abundance of ileal microbiota in humanized gnotobiotic RR mice that showed significant differences (unpaired t-test) at the genus level.,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|74201|203494|48461|1647988|239934;1783272|1239|526524|526525|2810280|3025755;1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:40258140/7/1,40258140,"cross-sectional observational, not case-control,laboratory experiment",40258140,10.1073/pnas.2419689122,NA,"Yoon H., Gerdes L.A., Beigel F., Sun Y., Kövilein J., Wang J., Kuhlmann T., Flierl-Hecht A., Haller D., Hohlfeld R., Baranzini S.E., Wekerle H. , Peters A.",Multiple sclerosis and gut microbiota: Lachnospiraceae from the ileum of MS twins trigger MS-like disease in germfree transgenic mice-An unbiased functional study,Proceedings of the National Academy of Sciences of the United States of America,2025,"CNS autoimmunity, MS/EAE, gnotobiotic mice, gut–brain axis, microbiota",Experiment 7,Germany,Mus musculus,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,GF_HT (Germ Free_Healthy Twin) (Early 2weeks),GF_MS (Germ Free_Multiple Sclerosis) (Early 2weeks),Germ-free Gnotobiotic RR (Relapsing Remitting) SJL/J mice colonized with ileal microbiota from the Multiple sclerosis twin (MS-A) (2weeks after colonization),NA,NA,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig S5,1 May 2025,Anne-mariesharp,Anne-mariesharp,"Relative abundance of fecal microbiota from humanized gnotobiotic RR mice that showed
significant changes (unpaired t-test) at the genus level 2 weeks after the colonization and at the endpoint.",increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,1783272|1239|186801|186802|31979|1485|1522,Complete,KateRasheed
bsdb:40258140/7/2,40258140,"cross-sectional observational, not case-control,laboratory experiment",40258140,10.1073/pnas.2419689122,NA,"Yoon H., Gerdes L.A., Beigel F., Sun Y., Kövilein J., Wang J., Kuhlmann T., Flierl-Hecht A., Haller D., Hohlfeld R., Baranzini S.E., Wekerle H. , Peters A.",Multiple sclerosis and gut microbiota: Lachnospiraceae from the ileum of MS twins trigger MS-like disease in germfree transgenic mice-An unbiased functional study,Proceedings of the National Academy of Sciences of the United States of America,2025,"CNS autoimmunity, MS/EAE, gnotobiotic mice, gut–brain axis, microbiota",Experiment 7,Germany,Mus musculus,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,GF_HT (Germ Free_Healthy Twin) (Early 2weeks),GF_MS (Germ Free_Multiple Sclerosis) (Early 2weeks),Germ-free Gnotobiotic RR (Relapsing Remitting) SJL/J mice colonized with ileal microbiota from the Multiple sclerosis twin (MS-A) (2weeks after colonization),NA,NA,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig S5,1 May 2025,Anne-mariesharp,Anne-mariesharp,"Relative abundance of fecal microbiota from humanized gnotobiotic RR mice that showed
significant changes (unpaired t-test) at the genus level 2 weeks after the colonization and at the endpoint.",decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,KateRasheed
bsdb:40258140/8/1,40258140,"cross-sectional observational, not case-control,laboratory experiment",40258140,10.1073/pnas.2419689122,NA,"Yoon H., Gerdes L.A., Beigel F., Sun Y., Kövilein J., Wang J., Kuhlmann T., Flierl-Hecht A., Haller D., Hohlfeld R., Baranzini S.E., Wekerle H. , Peters A.",Multiple sclerosis and gut microbiota: Lachnospiraceae from the ileum of MS twins trigger MS-like disease in germfree transgenic mice-An unbiased functional study,Proceedings of the National Academy of Sciences of the United States of America,2025,"CNS autoimmunity, MS/EAE, gnotobiotic mice, gut–brain axis, microbiota",Experiment 8,Germany,Mus musculus,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,GF_HT (Germ Free_Healthy Twin) (End),GF_MS (Germ Free_Multiple Sclerosis) (End),Germ-free Gnotobiotic RR (Relapsing Remitting) SJL/J mice colonized with ileal microbiota from the Multiple sclerosis twin (MS-A) (at endpoint after colonization),NA,NA,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig S5,1 May 2025,Anne-mariesharp,Anne-mariesharp,Relative abundance of fecal microbiota from humanized gnotobiotic RR mice that showed significant changes (unpaired t-test) at the genus level 2 weeks after the colonization and at the endpoint.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum",1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|186802|31979|1485|1522,Complete,KateRasheed
bsdb:40258140/8/2,40258140,"cross-sectional observational, not case-control,laboratory experiment",40258140,10.1073/pnas.2419689122,NA,"Yoon H., Gerdes L.A., Beigel F., Sun Y., Kövilein J., Wang J., Kuhlmann T., Flierl-Hecht A., Haller D., Hohlfeld R., Baranzini S.E., Wekerle H. , Peters A.",Multiple sclerosis and gut microbiota: Lachnospiraceae from the ileum of MS twins trigger MS-like disease in germfree transgenic mice-An unbiased functional study,Proceedings of the National Academy of Sciences of the United States of America,2025,"CNS autoimmunity, MS/EAE, gnotobiotic mice, gut–brain axis, microbiota",Experiment 8,Germany,Mus musculus,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,GF_HT (Germ Free_Healthy Twin) (End),GF_MS (Germ Free_Multiple Sclerosis) (End),Germ-free Gnotobiotic RR (Relapsing Remitting) SJL/J mice colonized with ileal microbiota from the Multiple sclerosis twin (MS-A) (at endpoint after colonization),NA,NA,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig S5,1 May 2025,Anne-mariesharp,Anne-mariesharp,Relative abundance of fecal microbiota from humanized gnotobiotic RR mice that showed significant changes (unpaired t-test) at the genus level 2 weeks after the colonization and at the endpoint.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,KateRasheed
bsdb:40258140/9/1,40258140,"cross-sectional observational, not case-control,laboratory experiment",40258140,10.1073/pnas.2419689122,NA,"Yoon H., Gerdes L.A., Beigel F., Sun Y., Kövilein J., Wang J., Kuhlmann T., Flierl-Hecht A., Haller D., Hohlfeld R., Baranzini S.E., Wekerle H. , Peters A.",Multiple sclerosis and gut microbiota: Lachnospiraceae from the ileum of MS twins trigger MS-like disease in germfree transgenic mice-An unbiased functional study,Proceedings of the National Academy of Sciences of the United States of America,2025,"CNS autoimmunity, MS/EAE, gnotobiotic mice, gut–brain axis, microbiota",Experiment 9,Germany,Mus musculus,Ileum,UBERON:0002116,Experimental autoimmune encephalomyelitis,EFO:0001066,Healthy,EAE (Experimental Autoimmune Encephalomyelitis),Gnotobiotic mice that developed Experimental Autoimmune Encephalomyelitis after being colonized with ileal microbiota from an MS (Multiple Sclerosis)-affected human twin (MS-Q).,NA,NA,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig. S3F,2 May 2025,Anne-mariesharp,Anne-mariesharp,"Relative abundance of Eisenbergiella as sole genus of the ileal microbiota that showed a
significant difference (unpaired t-test) between healthy and diseased animals colonized with MSQ derived ileal microbiota.",increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,1783272|1239|186801|3085636|186803|1432051,Complete,KateRasheed
bsdb:40258140/11/1,40258140,"cross-sectional observational, not case-control,laboratory experiment",40258140,10.1073/pnas.2419689122,NA,"Yoon H., Gerdes L.A., Beigel F., Sun Y., Kövilein J., Wang J., Kuhlmann T., Flierl-Hecht A., Haller D., Hohlfeld R., Baranzini S.E., Wekerle H. , Peters A.",Multiple sclerosis and gut microbiota: Lachnospiraceae from the ileum of MS twins trigger MS-like disease in germfree transgenic mice-An unbiased functional study,Proceedings of the National Academy of Sciences of the United States of America,2025,"CNS autoimmunity, MS/EAE, gnotobiotic mice, gut–brain axis, microbiota",Experiment 11,Germany,Mus musculus,Feces,UBERON:0001988,Timepoint,EFO:0000724,GF_MS (Germ Free_Multiple Sclerosis) (Early 2weeks),GF_MS (Germ Free_Multiple Sclerosis) (End),Germ-free Gnotobiotic RR  (Relapsing Remitting) SJL/J mice colonized with ileal microbiota from the Multiple sclerosis twin (MS-A) (at endpoint after colonization),NA,NA,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig S5,4 May 2025,Anne-mariesharp,Anne-mariesharp,Relative abundance of fecal microbiota from humanized gnotobiotic RR mice that showed significant changes (unpaired t-test) at the genus level 2 weeks after the colonization and at the endpoint.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|1506553,Complete,KateRasheed
bsdb:40258140/11/2,40258140,"cross-sectional observational, not case-control,laboratory experiment",40258140,10.1073/pnas.2419689122,NA,"Yoon H., Gerdes L.A., Beigel F., Sun Y., Kövilein J., Wang J., Kuhlmann T., Flierl-Hecht A., Haller D., Hohlfeld R., Baranzini S.E., Wekerle H. , Peters A.",Multiple sclerosis and gut microbiota: Lachnospiraceae from the ileum of MS twins trigger MS-like disease in germfree transgenic mice-An unbiased functional study,Proceedings of the National Academy of Sciences of the United States of America,2025,"CNS autoimmunity, MS/EAE, gnotobiotic mice, gut–brain axis, microbiota",Experiment 11,Germany,Mus musculus,Feces,UBERON:0001988,Timepoint,EFO:0000724,GF_MS (Germ Free_Multiple Sclerosis) (Early 2weeks),GF_MS (Germ Free_Multiple Sclerosis) (End),Germ-free Gnotobiotic RR  (Relapsing Remitting) SJL/J mice colonized with ileal microbiota from the Multiple sclerosis twin (MS-A) (at endpoint after colonization),NA,NA,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig S5,4 May 2025,Anne-mariesharp,Anne-mariesharp,Relative abundance of fecal microbiota from humanized gnotobiotic RR mice that showed significant changes (unpaired t-test) at the genus level 2 weeks after the colonization and at the endpoint.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum,1783272|1239|186801|186802|31979|1485|1522,Complete,KateRasheed
bsdb:40258140/12/1,40258140,"cross-sectional observational, not case-control,laboratory experiment",40258140,10.1073/pnas.2419689122,NA,"Yoon H., Gerdes L.A., Beigel F., Sun Y., Kövilein J., Wang J., Kuhlmann T., Flierl-Hecht A., Haller D., Hohlfeld R., Baranzini S.E., Wekerle H. , Peters A.",Multiple sclerosis and gut microbiota: Lachnospiraceae from the ileum of MS twins trigger MS-like disease in germfree transgenic mice-An unbiased functional study,Proceedings of the National Academy of Sciences of the United States of America,2025,"CNS autoimmunity, MS/EAE, gnotobiotic mice, gut–brain axis, microbiota",Experiment 12,Germany,Mus musculus,Feces,UBERON:0001988,Timepoint,EFO:0000724,GF_HT (Germ Free_Healthy Twin) (Early 2weeks),GF_HT (Germ Free_Healthy Twin) (End),Germ-free Gnotobiotic RR (Relapsing Remitting) SJL/J mice colonized with ileal microbiota from the healthy twin (HT-A) (at endpoint after colonization),NA,NA,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig S5,4 May 2025,Anne-mariesharp,Anne-mariesharp,Relative abundance of fecal microbiota from humanized gnotobiotic RR mice that showed significant changes (unpaired t-test) at the genus level 2 weeks after the colonization and at the endpoint.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,KateRasheed
bsdb:40258729/1/1,40258729,case-control,40258729,10.1097/MD.0000000000042100,https://doi.org/10.1097/MD.0000000000042100,"Lwere K., Muwonge H., Sendagire H., Sajatovic M., Williams S.M., Gumukiriza-Onoria J.L., Buwembo D., Buwembo W., Nassanga R., Nakimbugwe R., Nazziwa A., Munabi I.G., Nakasujja N. , Kaddumukasa M.",Characterization of the gut microbiome in Alzheimer disease and mild cognitive impairment among older adults in Uganda: A case-control study,Medicine,2025,"Alzheimer disease, gut microbiome, mild cognitive impairment",Experiment 1,Uganda,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Cognitively healthy controls,AD patients,Individuals diagnosed with Alzheimer's Disease (AD),13,77,"Yes, excluded participants with recent antibiotic use within 6 weeks",16S,NA,Nanopore,relative abundances,LEfSe,0.05,TRUE,2,NA,"age,body mass index",NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 9,11 July 2025,Kristin.abraham,Kristin.abraham,Taxa enriched in Alzheimer’s disease patients.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Dickeya,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Thermomonas",3379134|1224|1236|91347|543|413496;3379134|1224|1236|91347|1903410|204037;3379134|1224|1236|91347|1903412|568;3379134|1224|1236|91347|543|160674;3379134|1224|1236|135614|32033|141948,Complete,NA
bsdb:40258729/1/2,40258729,case-control,40258729,10.1097/MD.0000000000042100,https://doi.org/10.1097/MD.0000000000042100,"Lwere K., Muwonge H., Sendagire H., Sajatovic M., Williams S.M., Gumukiriza-Onoria J.L., Buwembo D., Buwembo W., Nassanga R., Nakimbugwe R., Nazziwa A., Munabi I.G., Nakasujja N. , Kaddumukasa M.",Characterization of the gut microbiome in Alzheimer disease and mild cognitive impairment among older adults in Uganda: A case-control study,Medicine,2025,"Alzheimer disease, gut microbiome, mild cognitive impairment",Experiment 1,Uganda,Homo sapiens,Feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Cognitively healthy controls,AD patients,Individuals diagnosed with Alzheimer's Disease (AD),13,77,"Yes, excluded participants with recent antibiotic use within 6 weeks",16S,NA,Nanopore,relative abundances,LEfSe,0.05,TRUE,2,NA,"age,body mass index",NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 9,11 July 2025,Kristin.abraham,Kristin.abraham,Taxa depleted in Alzheimer’s disease patients.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Allorhizobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Anaerobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Boseaceae|g__Bosea,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Companilactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Coxiella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Pectobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Pseudophaeobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Rickettsiaceae|g__Rickettsia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax",3379134|1224|28211|356|82115|78526;1783272|1239|91061|1385|186817|704093;1783272|1239|91061|1385|186817|1386;3379134|1224|28211|356|2831100|85413;3379134|1224|28216|80840|119060|32008;1783272|1239|91061|186826|186828|2747;1783272|1239|91061|186826|33958|2767879;3379134|1224|1236|118969|118968|776;3379134|1224|28216|80840|119060|106589;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|33958|1243;3379134|1224|28216|80840|75682|149698;3379134|1224|28211|356|69277|68287;3379134|1224|28211|204457|41297|165696;1783272|1239|91061|1385|186822|44249;3379134|1224|28211|204455|31989|265;3379134|1224|1236|91347|1903410|122277;3379134|1224|1236|72274|135621|286;3379134|1224|28211|204455|31989|1541822;3379134|1224|28211|766|775|780;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;3379134|1224|28216|80840|80864|34072,Complete,NA
bsdb:40258729/2/1,40258729,case-control,40258729,10.1097/MD.0000000000042100,https://doi.org/10.1097/MD.0000000000042100,"Lwere K., Muwonge H., Sendagire H., Sajatovic M., Williams S.M., Gumukiriza-Onoria J.L., Buwembo D., Buwembo W., Nassanga R., Nakimbugwe R., Nazziwa A., Munabi I.G., Nakasujja N. , Kaddumukasa M.",Characterization of the gut microbiome in Alzheimer disease and mild cognitive impairment among older adults in Uganda: A case-control study,Medicine,2025,"Alzheimer disease, gut microbiome, mild cognitive impairment",Experiment 2,Uganda,Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Cognitively healthy controls,MCI cases,Individuals with Mild Cognitive Impairment (MCI),13,14,"Yes, excluded participants with recent antibiotic use within 6 weeks.",16S,NA,Nanopore,relative abundances,LEfSe,0.05,TRUE,2,NA,"age,body mass index",NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 8,26 July 2025,Kristin.abraham,Kristin.abraham,Taxa enriched in MCI cases.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,3379134|1224|1236|91347|1903412|568,Complete,NA
bsdb:40258729/2/2,40258729,case-control,40258729,10.1097/MD.0000000000042100,https://doi.org/10.1097/MD.0000000000042100,"Lwere K., Muwonge H., Sendagire H., Sajatovic M., Williams S.M., Gumukiriza-Onoria J.L., Buwembo D., Buwembo W., Nassanga R., Nakimbugwe R., Nazziwa A., Munabi I.G., Nakasujja N. , Kaddumukasa M.",Characterization of the gut microbiome in Alzheimer disease and mild cognitive impairment among older adults in Uganda: A case-control study,Medicine,2025,"Alzheimer disease, gut microbiome, mild cognitive impairment",Experiment 2,Uganda,Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Cognitively healthy controls,MCI cases,Individuals with Mild Cognitive Impairment (MCI),13,14,"Yes, excluded participants with recent antibiotic use within 6 weeks.",16S,NA,Nanopore,relative abundances,LEfSe,0.05,TRUE,2,NA,"age,body mass index",NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 8,26 July 2025,Kristin.abraham,Kristin.abraham,Taxa depleted in MCI cases.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Allorhizobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Anaerobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Coxiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Marinococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Pectobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|1224|28211|356|82115|78526;1783272|1239|91061|1385|186817|704093;1783272|1239|91061|1385|186817|1386;3379134|1224|1236|118969|118968|776;3379134|1224|1236|91347|543|547;1783272|1239|91061|186826|33958|1243;1783272|1239|91061|1385|186817|1370;3379134|1224|28211|356|69277|68287;3379134|1224|28211|204457|41297|165696;3379134|1224|28211|356|118882|528;1783272|1239|91061|1385|186822|44249;3379134|1224|1236|91347|1903410|122277;3379134|1224|1236|72274|135621|286;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301,Complete,NA
bsdb:40259408/1/1,40259408,laboratory experiment,40259408,10.1186/s40168-025-02101-1,NA,"Cuisiniere T., Hajjar R., Oliero M., Calvé A., Fragoso G., Rendos H.V., Gerkins C., Taleb N., Gagnon-Konamna M., Dagbert F., Loungnarath R., Sebajang H., Schwenter F., Wassef R., Ratelle R., De Broux É., Richard C. , Santos M.M.",Initial gut microbiota composition is a determining factor in the promotion of colorectal cancer by oral iron supplementation: evidence from a murine model,Microbiome,2025,"Colorectal cancer, Gut microbiota, Iron supplementation",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,FMT-HC (Fecal microbiota transplantation from healthy controls) mice fed 50 ppm iron,FMT-HC (Fecal microbiota transplantation from healthy controls) mice fed 500 ppm iron,This group refers to mice that received fecal microbiota transplantation from healthy human controls and were fed an iron excess (500 ppm) diet.,24,26,NA,16S,56,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,unchanged,NA,Signature 1,"Fig. 2B, 2E and S7",25 April 2025,Joiejoie,"Joiejoie,PreciousChijioke",Relative abundances of microbial taxa at phylum level.,increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes inops,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia ilealis",3379134|976;3379134|1224;3379134|74201;3379134|976|200643|171549|171550|239759|1501391;1783272|1239|186801|3082720|186804|1501226|1115758,Complete,KateRasheed
bsdb:40259408/1/2,40259408,laboratory experiment,40259408,10.1186/s40168-025-02101-1,NA,"Cuisiniere T., Hajjar R., Oliero M., Calvé A., Fragoso G., Rendos H.V., Gerkins C., Taleb N., Gagnon-Konamna M., Dagbert F., Loungnarath R., Sebajang H., Schwenter F., Wassef R., Ratelle R., De Broux É., Richard C. , Santos M.M.",Initial gut microbiota composition is a determining factor in the promotion of colorectal cancer by oral iron supplementation: evidence from a murine model,Microbiome,2025,"Colorectal cancer, Gut microbiota, Iron supplementation",Experiment 1,United States of America,Mus musculus,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,FMT-HC (Fecal microbiota transplantation from healthy controls) mice fed 50 ppm iron,FMT-HC (Fecal microbiota transplantation from healthy controls) mice fed 500 ppm iron,This group refers to mice that received fecal microbiota transplantation from healthy human controls and were fed an iron excess (500 ppm) diet.,24,26,NA,16S,56,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,unchanged,NA,Signature 2,"Fig. 2B, 2E and S7",25 April 2025,PreciousChijioke,"PreciousChijioke,Victoria",Relative abundances of microbial taxa at phylum level.,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum",1783272|201174;1783272|1239;1783272|201174|1760|85004|31953|1678|1694,Complete,KateRasheed
bsdb:40259408/2/1,40259408,laboratory experiment,40259408,10.1186/s40168-025-02101-1,NA,"Cuisiniere T., Hajjar R., Oliero M., Calvé A., Fragoso G., Rendos H.V., Gerkins C., Taleb N., Gagnon-Konamna M., Dagbert F., Loungnarath R., Sebajang H., Schwenter F., Wassef R., Ratelle R., De Broux É., Richard C. , Santos M.M.",Initial gut microbiota composition is a determining factor in the promotion of colorectal cancer by oral iron supplementation: evidence from a murine model,Microbiome,2025,"Colorectal cancer, Gut microbiota, Iron supplementation",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,FMT-HC (Fecal microbiota transplantation from healthy controls) mice fed 50 ppm iron,FMT-HC (Fecal microbiota transplantation from healthy controls) mice fed 500 ppm iron,This group refers to mice that received fecal microbiota transplantation from healthy human controls and were fed an iron excess (500 ppm) diet.,24,26,NA,16S,56,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,unchanged,NA,Signature 1,Fig. 2D,25 April 2025,PreciousChijioke,"PreciousChijioke,Victoria",Differential bacterial species.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia ilealis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes inops",1783272|1239|186801|3082720|186804|1501226|1115758;3379134|976|200643|171549|171550|239759|1501391,Complete,KateRasheed
bsdb:40259408/2/2,40259408,laboratory experiment,40259408,10.1186/s40168-025-02101-1,NA,"Cuisiniere T., Hajjar R., Oliero M., Calvé A., Fragoso G., Rendos H.V., Gerkins C., Taleb N., Gagnon-Konamna M., Dagbert F., Loungnarath R., Sebajang H., Schwenter F., Wassef R., Ratelle R., De Broux É., Richard C. , Santos M.M.",Initial gut microbiota composition is a determining factor in the promotion of colorectal cancer by oral iron supplementation: evidence from a murine model,Microbiome,2025,"Colorectal cancer, Gut microbiota, Iron supplementation",Experiment 2,United States of America,Mus musculus,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,FMT-HC (Fecal microbiota transplantation from healthy controls) mice fed 50 ppm iron,FMT-HC (Fecal microbiota transplantation from healthy controls) mice fed 500 ppm iron,This group refers to mice that received fecal microbiota transplantation from healthy human controls and were fed an iron excess (500 ppm) diet.,24,26,NA,16S,56,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,unchanged,NA,Signature 2,Fig. 2D,26 April 2025,Joiejoie,"Joiejoie,Victoria",Differential bacterial species.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,1783272|201174|1760|85004|31953|1678|1694,Complete,KateRasheed
bsdb:40259408/3/1,40259408,laboratory experiment,40259408,10.1186/s40168-025-02101-1,NA,"Cuisiniere T., Hajjar R., Oliero M., Calvé A., Fragoso G., Rendos H.V., Gerkins C., Taleb N., Gagnon-Konamna M., Dagbert F., Loungnarath R., Sebajang H., Schwenter F., Wassef R., Ratelle R., De Broux É., Richard C. , Santos M.M.",Initial gut microbiota composition is a determining factor in the promotion of colorectal cancer by oral iron supplementation: evidence from a murine model,Microbiome,2025,"Colorectal cancer, Gut microbiota, Iron supplementation",Experiment 3,United States of America,Mus musculus,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,FMT-CRC (Fecal microbiota transplantation from Colorectal cancer patients) mice fed 50 ppm iron,FMT-CRC (Fecal microbiota transplantation from Colorectal cancer patients) mice fed 500 ppm iron,This group refers to mice that received fecal microbiota transplantation from Colorectal cancer patients and were fed an iron excess (500 ppm) diet.,25,27,NA,16S,56,Illumina,raw counts,DESeq2,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,unchanged,NA,Signature 1,Fig. 2C,26 April 2025,Joiejoie,"Joiejoie,PreciousChijioke",Relative abundances of microbial taxa at family level.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,KateRasheed
bsdb:40259408/3/2,40259408,laboratory experiment,40259408,10.1186/s40168-025-02101-1,NA,"Cuisiniere T., Hajjar R., Oliero M., Calvé A., Fragoso G., Rendos H.V., Gerkins C., Taleb N., Gagnon-Konamna M., Dagbert F., Loungnarath R., Sebajang H., Schwenter F., Wassef R., Ratelle R., De Broux É., Richard C. , Santos M.M.",Initial gut microbiota composition is a determining factor in the promotion of colorectal cancer by oral iron supplementation: evidence from a murine model,Microbiome,2025,"Colorectal cancer, Gut microbiota, Iron supplementation",Experiment 3,United States of America,Mus musculus,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,FMT-CRC (Fecal microbiota transplantation from Colorectal cancer patients) mice fed 50 ppm iron,FMT-CRC (Fecal microbiota transplantation from Colorectal cancer patients) mice fed 500 ppm iron,This group refers to mice that received fecal microbiota transplantation from Colorectal cancer patients and were fed an iron excess (500 ppm) diet.,25,27,NA,16S,56,Illumina,raw counts,DESeq2,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,unchanged,NA,Signature 2,Fig. 2C,26 April 2025,PreciousChijioke,"PreciousChijioke,Victoria",Relative abundances of microbial taxa at family level.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",1783272|1239|186801|186802|31979;3379134|976|200643|171549|2005473,Complete,KateRasheed
bsdb:40259408/4/1,40259408,laboratory experiment,40259408,10.1186/s40168-025-02101-1,NA,"Cuisiniere T., Hajjar R., Oliero M., Calvé A., Fragoso G., Rendos H.V., Gerkins C., Taleb N., Gagnon-Konamna M., Dagbert F., Loungnarath R., Sebajang H., Schwenter F., Wassef R., Ratelle R., De Broux É., Richard C. , Santos M.M.",Initial gut microbiota composition is a determining factor in the promotion of colorectal cancer by oral iron supplementation: evidence from a murine model,Microbiome,2025,"Colorectal cancer, Gut microbiota, Iron supplementation",Experiment 4,United States of America,Mus musculus,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,FMT-CRC (Fecal microbiota transplantation from Colorectal cancer patients) mice fed 50 ppm iron,FMT-CRC  (Fecal microbiota transplantation from Colorectal cancer patients) mice fed 500 ppm iron,This group refers to mice that received fecal microbiota transplantation from Colorectal cancer patients and were fed an iron excess (500 ppm) diet.,25,27,NA,16S,56,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,unchanged,NA,Signature 1,"Fig. 2B, 2E and S7",26 April 2025,PreciousChijioke,"PreciousChijioke,Victoria",Relative abundances of microbial taxa at phylum level.,increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia ilealis,k__Pseudomonadati|p__Verrucomicrobiota",3379134|976;3379134|1224;1783272|1239|186801|3082720|186804|1501226|1115758;3379134|74201,Complete,KateRasheed
bsdb:40259408/4/2,40259408,laboratory experiment,40259408,10.1186/s40168-025-02101-1,NA,"Cuisiniere T., Hajjar R., Oliero M., Calvé A., Fragoso G., Rendos H.V., Gerkins C., Taleb N., Gagnon-Konamna M., Dagbert F., Loungnarath R., Sebajang H., Schwenter F., Wassef R., Ratelle R., De Broux É., Richard C. , Santos M.M.",Initial gut microbiota composition is a determining factor in the promotion of colorectal cancer by oral iron supplementation: evidence from a murine model,Microbiome,2025,"Colorectal cancer, Gut microbiota, Iron supplementation",Experiment 4,United States of America,Mus musculus,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,FMT-CRC (Fecal microbiota transplantation from Colorectal cancer patients) mice fed 50 ppm iron,FMT-CRC  (Fecal microbiota transplantation from Colorectal cancer patients) mice fed 500 ppm iron,This group refers to mice that received fecal microbiota transplantation from Colorectal cancer patients and were fed an iron excess (500 ppm) diet.,25,27,NA,16S,56,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,unchanged,NA,Signature 2,"Fig. 2B, 2E and S7",28 April 2025,PreciousChijioke,PreciousChijioke,Relative abundances of microbial taxa at phylum level.,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum|s__Faecalibaculum rodentium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum",1783272|201174;1783272|1239;1783272|1239|526524|526525|128827|1729679|1702221;1783272|201174|1760|85004|31953|1678|1694,Complete,KateRasheed
bsdb:40259408/5/1,40259408,laboratory experiment,40259408,10.1186/s40168-025-02101-1,NA,"Cuisiniere T., Hajjar R., Oliero M., Calvé A., Fragoso G., Rendos H.V., Gerkins C., Taleb N., Gagnon-Konamna M., Dagbert F., Loungnarath R., Sebajang H., Schwenter F., Wassef R., Ratelle R., De Broux É., Richard C. , Santos M.M.",Initial gut microbiota composition is a determining factor in the promotion of colorectal cancer by oral iron supplementation: evidence from a murine model,Microbiome,2025,"Colorectal cancer, Gut microbiota, Iron supplementation",Experiment 5,United States of America,Mus musculus,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,FMT-CRC (Fecal microbiota transplantation from Colorectal cancer patients) mice fed 50 ppm iron,FMT-CRC (Fecal microbiota transplantation from Colorectal cancer patients) mice fed 500 ppm iron,This group refers to mice that received fecal microbiota transplantation from Colorectal cancer patients and were fed an iron excess (500 ppm) diet.,25,27,NA,16S,56,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,unchanged,NA,Signature 1,Fig. 2D,9 May 2025,PreciousChijioke,PreciousChijioke,Differential bacterial species.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia ilealis,1783272|1239|186801|3082720|186804|1501226|1115758,Complete,KateRasheed
bsdb:40259408/5/2,40259408,laboratory experiment,40259408,10.1186/s40168-025-02101-1,NA,"Cuisiniere T., Hajjar R., Oliero M., Calvé A., Fragoso G., Rendos H.V., Gerkins C., Taleb N., Gagnon-Konamna M., Dagbert F., Loungnarath R., Sebajang H., Schwenter F., Wassef R., Ratelle R., De Broux É., Richard C. , Santos M.M.",Initial gut microbiota composition is a determining factor in the promotion of colorectal cancer by oral iron supplementation: evidence from a murine model,Microbiome,2025,"Colorectal cancer, Gut microbiota, Iron supplementation",Experiment 5,United States of America,Mus musculus,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,FMT-CRC (Fecal microbiota transplantation from Colorectal cancer patients) mice fed 50 ppm iron,FMT-CRC (Fecal microbiota transplantation from Colorectal cancer patients) mice fed 500 ppm iron,This group refers to mice that received fecal microbiota transplantation from Colorectal cancer patients and were fed an iron excess (500 ppm) diet.,25,27,NA,16S,56,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,unchanged,NA,Signature 2,Fig. 2D,9 May 2025,PreciousChijioke,PreciousChijioke,Differential bacterial species.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum|s__Faecalibaculum rodentium",1783272|201174|1760|85004|31953|1678|1694;1783272|1239|526524|526525|128827|1729679|1702221,Complete,KateRasheed
bsdb:40259408/6/1,40259408,laboratory experiment,40259408,10.1186/s40168-025-02101-1,NA,"Cuisiniere T., Hajjar R., Oliero M., Calvé A., Fragoso G., Rendos H.V., Gerkins C., Taleb N., Gagnon-Konamna M., Dagbert F., Loungnarath R., Sebajang H., Schwenter F., Wassef R., Ratelle R., De Broux É., Richard C. , Santos M.M.",Initial gut microbiota composition is a determining factor in the promotion of colorectal cancer by oral iron supplementation: evidence from a murine model,Microbiome,2025,"Colorectal cancer, Gut microbiota, Iron supplementation",Experiment 6,United States of America,Mus musculus,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,FMT-HC (Fecal microbiota transplantation from healthy controls) mice fed 50 ppm iron,FMT-HC (Fecal microbiota transplantation from healthy controls) mice fed 500 ppm iron,This group refers to mice that received fecal microbiota transplantation from healthy human controls and were fed an iron excess (500 ppm) diet.,24,26,NA,16S,56,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,unchanged,NA,Signature 1,Fig. 2C,9 May 2025,PreciousChijioke,PreciousChijioke,Relative abundances of microbial taxa at family level.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,3379134|1224|1236|91347|543,Complete,KateRasheed
bsdb:40259408/6/2,40259408,laboratory experiment,40259408,10.1186/s40168-025-02101-1,NA,"Cuisiniere T., Hajjar R., Oliero M., Calvé A., Fragoso G., Rendos H.V., Gerkins C., Taleb N., Gagnon-Konamna M., Dagbert F., Loungnarath R., Sebajang H., Schwenter F., Wassef R., Ratelle R., De Broux É., Richard C. , Santos M.M.",Initial gut microbiota composition is a determining factor in the promotion of colorectal cancer by oral iron supplementation: evidence from a murine model,Microbiome,2025,"Colorectal cancer, Gut microbiota, Iron supplementation",Experiment 6,United States of America,Mus musculus,Feces,UBERON:0001988,Transplant outcome measurement,EFO:0005198,FMT-HC (Fecal microbiota transplantation from healthy controls) mice fed 50 ppm iron,FMT-HC (Fecal microbiota transplantation from healthy controls) mice fed 500 ppm iron,This group refers to mice that received fecal microbiota transplantation from healthy human controls and were fed an iron excess (500 ppm) diet.,24,26,NA,16S,56,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,unchanged,NA,Signature 2,Fig. 2C,9 May 2025,PreciousChijioke,"PreciousChijioke,Victoria",Relative abundances of microbial taxa at family level.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",1783272|1239|186801|3082720|186804;1783272|1239|91061|186826|1300,Complete,KateRasheed
bsdb:40259408/7/1,40259408,laboratory experiment,40259408,10.1186/s40168-025-02101-1,NA,"Cuisiniere T., Hajjar R., Oliero M., Calvé A., Fragoso G., Rendos H.V., Gerkins C., Taleb N., Gagnon-Konamna M., Dagbert F., Loungnarath R., Sebajang H., Schwenter F., Wassef R., Ratelle R., De Broux É., Richard C. , Santos M.M.",Initial gut microbiota composition is a determining factor in the promotion of colorectal cancer by oral iron supplementation: evidence from a murine model,Microbiome,2025,"Colorectal cancer, Gut microbiota, Iron supplementation",Experiment 7,United States of America,Mus musculus,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Mice fed with Saline 50ppm,Mice fed with Saline 500ppm,This group refers to mice that received fecal microbiota transplantation from Colorectal cancer patients and were fed a saline (500 ppm) diet.,NA,NA,NA,16S,56,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 4B,13 May 2025,PreciousChijioke,"PreciousChijioke,Victoria",Fecal levels of F. rodentium (Fr) and H. biformis (Hb) quantified by real-time PCR in mice at endpoint.,decreased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum|s__Faecalibaculum rodentium,1783272|1239|526524|526525|128827|1729679|1702221,Complete,KateRasheed
bsdb:40259408/8/1,40259408,laboratory experiment,40259408,10.1186/s40168-025-02101-1,NA,"Cuisiniere T., Hajjar R., Oliero M., Calvé A., Fragoso G., Rendos H.V., Gerkins C., Taleb N., Gagnon-Konamna M., Dagbert F., Loungnarath R., Sebajang H., Schwenter F., Wassef R., Ratelle R., De Broux É., Richard C. , Santos M.M.",Initial gut microbiota composition is a determining factor in the promotion of colorectal cancer by oral iron supplementation: evidence from a murine model,Microbiome,2025,"Colorectal cancer, Gut microbiota, Iron supplementation",Experiment 8,United States of America,Mus musculus,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Mice fed with Saline 50ppm,Mice fed with Saline 500ppm,This group refers to mice that received fecal microbiota transplantation from Colorectal cancer patients and were fed with a Saline (500 ppm) diet.,NA,NA,NA,16S,56,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 5B,13 May 2025,PreciousChijioke,"PreciousChijioke,Victoria",Fecal levels of A. inops (Ai) and B. pseudolongum (Bp) quantified by real-time PCR in mice at endpoint.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes inops,3379134|976|200643|171549|171550|239759|1501391,Complete,KateRasheed
bsdb:40259408/8/2,40259408,laboratory experiment,40259408,10.1186/s40168-025-02101-1,NA,"Cuisiniere T., Hajjar R., Oliero M., Calvé A., Fragoso G., Rendos H.V., Gerkins C., Taleb N., Gagnon-Konamna M., Dagbert F., Loungnarath R., Sebajang H., Schwenter F., Wassef R., Ratelle R., De Broux É., Richard C. , Santos M.M.",Initial gut microbiota composition is a determining factor in the promotion of colorectal cancer by oral iron supplementation: evidence from a murine model,Microbiome,2025,"Colorectal cancer, Gut microbiota, Iron supplementation",Experiment 8,United States of America,Mus musculus,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Mice fed with Saline 50ppm,Mice fed with Saline 500ppm,This group refers to mice that received fecal microbiota transplantation from Colorectal cancer patients and were fed with a Saline (500 ppm) diet.,NA,NA,NA,16S,56,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5B,5 June 2025,Victoria,Victoria,Fecal levels of A. inops (Ai) and B. pseudolongum (Bp) quantified by real-time PCR in mice at endpoint.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,1783272|201174|1760|85004|31953|1678|1694,Complete,KateRasheed
bsdb:40259408/9/1,40259408,laboratory experiment,40259408,10.1186/s40168-025-02101-1,NA,"Cuisiniere T., Hajjar R., Oliero M., Calvé A., Fragoso G., Rendos H.V., Gerkins C., Taleb N., Gagnon-Konamna M., Dagbert F., Loungnarath R., Sebajang H., Schwenter F., Wassef R., Ratelle R., De Broux É., Richard C. , Santos M.M.",Initial gut microbiota composition is a determining factor in the promotion of colorectal cancer by oral iron supplementation: evidence from a murine model,Microbiome,2025,"Colorectal cancer, Gut microbiota, Iron supplementation",Experiment 9,United States of America,Mus musculus,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Mice fed with Saline 500ppm,Mice fed with F. rodentium strain ALO17 (Fr) 500ppm by weekly gavage,This group refers to mice that received fecal microbiota transplantation from Colorectal cancer patients and were fed with F. rodentium strain ALO17 (Fr) 500ppm by weekly gavage.,NA,NA,NA,16S,56,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,5 June 2025,Victoria,Victoria,Fecal levels of F. rodentium (Fr) quantified by real-time PCR in mice at endpoint.,increased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum|s__Faecalibaculum rodentium,1783272|1239|526524|526525|128827|1729679|1702221,Complete,KateRasheed
bsdb:40259408/10/1,40259408,laboratory experiment,40259408,10.1186/s40168-025-02101-1,NA,"Cuisiniere T., Hajjar R., Oliero M., Calvé A., Fragoso G., Rendos H.V., Gerkins C., Taleb N., Gagnon-Konamna M., Dagbert F., Loungnarath R., Sebajang H., Schwenter F., Wassef R., Ratelle R., De Broux É., Richard C. , Santos M.M.",Initial gut microbiota composition is a determining factor in the promotion of colorectal cancer by oral iron supplementation: evidence from a murine model,Microbiome,2025,"Colorectal cancer, Gut microbiota, Iron supplementation",Experiment 10,United States of America,Mus musculus,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Mice fed with Saline 500ppm,Mice fed with H. biformis strain VPI C17 - 5 (Hb) 500ppm by weekly gavage,This group refers to mice that received fecal microbiota transplantation from Colorectal cancer patients and were fed with H. biformis strain VPI C17 - 5 (Hb) 500ppm by weekly gavage.,NA,NA,NA,16S,56,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,5 June 2025,Victoria,Victoria,Fecal levels of H. biformis (Hb) quantified by real-time PCR in mice at endpoint.,increased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,1783272|1239|526524|526525|128827|1573535|1735,Complete,KateRasheed
bsdb:40259408/11/1,40259408,laboratory experiment,40259408,10.1186/s40168-025-02101-1,NA,"Cuisiniere T., Hajjar R., Oliero M., Calvé A., Fragoso G., Rendos H.V., Gerkins C., Taleb N., Gagnon-Konamna M., Dagbert F., Loungnarath R., Sebajang H., Schwenter F., Wassef R., Ratelle R., De Broux É., Richard C. , Santos M.M.",Initial gut microbiota composition is a determining factor in the promotion of colorectal cancer by oral iron supplementation: evidence from a murine model,Microbiome,2025,"Colorectal cancer, Gut microbiota, Iron supplementation",Experiment 11,United States of America,Mus musculus,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Mice fed with Saline 500ppm,Mice fed with Alistipes inops strain 627 (Ai) 500ppm by weekly gavage,This group refers to mice that received fecal microbiota transplantation from Colorectal cancer patients and were fed with Alistipes inops strain 627 (Ai) 500ppm by weekly gavage.,NA,NA,NA,16S,56,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5B,5 June 2025,Victoria,Victoria,Fecal levels of A. inops (Ai) quantified by real-time PCR in mice at endpoint.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes inops,3379134|976|200643|171549|171550|239759|1501391,Complete,KateRasheed
bsdb:40259408/12/1,40259408,laboratory experiment,40259408,10.1186/s40168-025-02101-1,NA,"Cuisiniere T., Hajjar R., Oliero M., Calvé A., Fragoso G., Rendos H.V., Gerkins C., Taleb N., Gagnon-Konamna M., Dagbert F., Loungnarath R., Sebajang H., Schwenter F., Wassef R., Ratelle R., De Broux É., Richard C. , Santos M.M.",Initial gut microbiota composition is a determining factor in the promotion of colorectal cancer by oral iron supplementation: evidence from a murine model,Microbiome,2025,"Colorectal cancer, Gut microbiota, Iron supplementation",Experiment 12,United States of America,Mus musculus,Feces,UBERON:0001988,Diet measurement,EFO:0008111,Mice fed with Saline 500ppm,Mice fed with Bifidobacterium pseudolongum strain 28 T (Bp) 500ppm by weekly gavage,This group refers to mice that received fecal microbiota transplantation from Colorectal cancer patients and were fed with Bifidobacterium pseudolongum strain 28 T (Bp) 500ppm by weekly gavage.,NA,NA,NA,16S,56,Illumina,relative abundances,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5B,5 June 2025,Victoria,Victoria,Fecal levels of B. pseudolongum (Bp) quantified by real-time PCR in mice at endpoint.,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,1783272|201174|1760|85004|31953|1678|1694,Complete,KateRasheed
bsdb:40274860/1/1,40274860,laboratory experiment,40274860,https://doi.org/10.1038/s41598-025-95357-4,https://www.nature.com/articles/s41598-025-95357-4,"Chengfu Zhang, Dongyang Lu, Hongzhuang Wang, Kun Li, Munwar Ali, Yong Zhu, Xiaoying Chen, Yang Liu",Comparative analysis of gut microbiota in free range and house fed yaks from Linzhou County,Scientific reports,NA,"House-fed, Grazing, Bos grunniens, Microbiota, 16S rRNA sequencing, Metabolomics",Experiment 1,China,Bos grunniens,Feces,UBERON:0001988,Diet,EFO:0002755,House-fed yaks (LS),Grazing yaks (LF),"Yaks that grazed freely on a pasture consisting of native grass species like Agropyron cristatum, Elymus nutans, Kobresia humilis, etc.",6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Result Text, Figure 7A, 7B",25 October 2025,Emma Nelly,Emma Nelly,"Bacterial taxa with significantly higher abundance in grazing yaks compared to house-fed yaks, as identified by LEfSe analysis (LDA > 2).",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales",1783272|201174|1760;1783272|201174;1783272|201174|1760|85006|1268|1663;1783272|201174|1760|85006|1268;1783272|201174|1760|85006,Complete,Svetlana up
bsdb:40274860/1/2,40274860,laboratory experiment,40274860,https://doi.org/10.1038/s41598-025-95357-4,https://www.nature.com/articles/s41598-025-95357-4,"Chengfu Zhang, Dongyang Lu, Hongzhuang Wang, Kun Li, Munwar Ali, Yong Zhu, Xiaoying Chen, Yang Liu",Comparative analysis of gut microbiota in free range and house fed yaks from Linzhou County,Scientific reports,NA,"House-fed, Grazing, Bos grunniens, Microbiota, 16S rRNA sequencing, Metabolomics",Experiment 1,China,Bos grunniens,Feces,UBERON:0001988,Diet,EFO:0002755,House-fed yaks (LS),Grazing yaks (LF),"Yaks that grazed freely on a pasture consisting of native grass species like Agropyron cristatum, Elymus nutans, Kobresia humilis, etc.",6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Result Text, Figure 7A, 7B",25 October 2025,Emma Nelly,"Emma Nelly,Anne-mariesharp","Bacterial taxa with significantly higher abundance in house-fed yaks compared to grazing yaks, as identified by LEfSe analysis (LDA > 2).",decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239;3379134|976|200643|171549;3379134|976|200643;3379134|976;1783272|1239|186801;1783272|1239|186801|186802;1783272|1239|186801|186802|216572,Complete,Svetlana up
bsdb:40274860/2/1,40274860,laboratory experiment,40274860,https://doi.org/10.1038/s41598-025-95357-4,https://www.nature.com/articles/s41598-025-95357-4,"Chengfu Zhang, Dongyang Lu, Hongzhuang Wang, Kun Li, Munwar Ali, Yong Zhu, Xiaoying Chen, Yang Liu",Comparative analysis of gut microbiota in free range and house fed yaks from Linzhou County,Scientific reports,NA,"House-fed, Grazing, Bos grunniens, Microbiota, 16S rRNA sequencing, Metabolomics",Experiment 2,China,Bos grunniens,Feces,UBERON:0001988,Diet,EFO:0002755,House-fed yaks (LS),Grazing yaks (LF),"Yaks that grazed freely on a pasture consisting of native grass species like Agropyron cristatum, Elymus nutans, Kobresia humilis, etc.",6,6,NA,ITS / ITS2,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Result Text, Figure 7C, 7D",25 October 2025,Emma Nelly,Emma Nelly,"Fungal taxa with significantly higher abundance in grazing yaks compared to house-fed yaks, as identified by LEfSe analysis (LDA > 2).",increased,"k__Fungi|p__Ascomycota,k__Fungi|p__Ascomycota|c__Dothideomycetes,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales,k__Fungi|p__Ascomycota|c__Leotiomycetes,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales|f__Sclerotiniaceae|g__Scleromitrula,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales|f__Sclerotiniaceae",4751|4890;4751|4890|147541;4751|4890|147548|5178;4751|4890|147548;4751|4890|147541|92860;4751|4890|147548|5178|28983|58904;4751|4890|147548|5178|28983,Complete,Svetlana up
bsdb:40274860/2/2,40274860,laboratory experiment,40274860,https://doi.org/10.1038/s41598-025-95357-4,https://www.nature.com/articles/s41598-025-95357-4,"Chengfu Zhang, Dongyang Lu, Hongzhuang Wang, Kun Li, Munwar Ali, Yong Zhu, Xiaoying Chen, Yang Liu",Comparative analysis of gut microbiota in free range and house fed yaks from Linzhou County,Scientific reports,NA,"House-fed, Grazing, Bos grunniens, Microbiota, 16S rRNA sequencing, Metabolomics",Experiment 2,China,Bos grunniens,Feces,UBERON:0001988,Diet,EFO:0002755,House-fed yaks (LS),Grazing yaks (LF),"Yaks that grazed freely on a pasture consisting of native grass species like Agropyron cristatum, Elymus nutans, Kobresia humilis, etc.",6,6,NA,ITS / ITS2,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Result Text,  Figure 7C, 7D",25 October 2025,Emma Nelly,Emma Nelly,"Fungal taxa with significantly higher abundance in house-fed yaks compared to grazing yaks, as identified by LEfSe analysis (LDA > 2).",decreased,"k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales,k__Fungi|p__Ascomycota|c__Sordariomycetes,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Stachybotryaceae|g__Myrothecium,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Stachybotryaceae",4751|4890|147550|5125;4751|4890|147550;4751|4890|147550|5125|1667166|5531;4751|4890|147550|5125|1667166,Complete,Svetlana up
bsdb:40274860/3/1,40274860,laboratory experiment,40274860,https://doi.org/10.1038/s41598-025-95357-4,https://www.nature.com/articles/s41598-025-95357-4,"Chengfu Zhang, Dongyang Lu, Hongzhuang Wang, Kun Li, Munwar Ali, Yong Zhu, Xiaoying Chen, Yang Liu",Comparative analysis of gut microbiota in free range and house fed yaks from Linzhou County,Scientific reports,NA,"House-fed, Grazing, Bos grunniens, Microbiota, 16S rRNA sequencing, Metabolomics",Experiment 3,China,Bos grunniens,Feces,UBERON:0001988,Diet,EFO:0002755,House-fed yaks (LS),Grazing yaks (LF),"Yaks that grazed freely on a pasture consisting of native grass species like Agropyron cristatum, Elymus nutans, Kobresia humilis, etc.",6,6,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Result Text, Figure 5A, 5B",1 November 2025,Emma Nelly,"Emma Nelly,Anne-mariesharp",Bacterial phyla and genera with significantly higher relative abundance in grazing yaks compared to house-fed yaks.,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter",1783272|201174;1783272|201174|1760|85006|1268|1663;1783272|1239|186801|3082720|186804|1505652,Complete,Svetlana up
bsdb:40274860/3/2,40274860,laboratory experiment,40274860,https://doi.org/10.1038/s41598-025-95357-4,https://www.nature.com/articles/s41598-025-95357-4,"Chengfu Zhang, Dongyang Lu, Hongzhuang Wang, Kun Li, Munwar Ali, Yong Zhu, Xiaoying Chen, Yang Liu",Comparative analysis of gut microbiota in free range and house fed yaks from Linzhou County,Scientific reports,NA,"House-fed, Grazing, Bos grunniens, Microbiota, 16S rRNA sequencing, Metabolomics",Experiment 3,China,Bos grunniens,Feces,UBERON:0001988,Diet,EFO:0002755,House-fed yaks (LS),Grazing yaks (LF),"Yaks that grazed freely on a pasture consisting of native grass species like Agropyron cristatum, Elymus nutans, Kobresia humilis, etc.",6,6,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Result Text, Figure 5A, 5B",1 November 2025,Emma Nelly,"Emma Nelly,Anne-mariesharp",Bacterial phyla and genera with significantly higher relative abundance in house-fed yaks compared to grazing yaks.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes",3379134|976|200643|171549|171550|239759;1783272|1239;3379134|976;1783272|1239|186801|3085636|186803|572511;95818|2093818|2093825|2171986|1331051;1783272|1239|186801|186802|31979|1485;3379134|976|200643|171549|2005473;;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|186806|1730|290054,Complete,Svetlana up
bsdb:40274860/4/1,40274860,laboratory experiment,40274860,https://doi.org/10.1038/s41598-025-95357-4,https://www.nature.com/articles/s41598-025-95357-4,"Chengfu Zhang, Dongyang Lu, Hongzhuang Wang, Kun Li, Munwar Ali, Yong Zhu, Xiaoying Chen, Yang Liu",Comparative analysis of gut microbiota in free range and house fed yaks from Linzhou County,Scientific reports,NA,"House-fed, Grazing, Bos grunniens, Microbiota, 16S rRNA sequencing, Metabolomics",Experiment 4,China,Bos grunniens,Feces,UBERON:0001988,Diet,EFO:0002755,House-fed yaks (LS),Grazing yaks (LF),"Yaks that grazed freely on a pasture consisting of native grass species like Agropyron cristatum, Elymus nutans, Kobresia humilis, etc.",6,6,NA,ITS / ITS2,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Result Text, Figure 6A, 6B",1 November 2025,Emma Nelly,"Emma Nelly,Anne-mariesharp",Fungal phyla and genera with significantly higher relative abundance in grazing yaks compared to house-fed yaks.,increased,"k__Fungi|p__Ascomycota,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Didymellaceae|g__Neoascochyta,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Didymosphaeriaceae|g__Paraphaeosphaeria",4751|4890;4751|4890|147550|5125;4751|4890|147541|92860|683158|1770170;4751|4890|147541|92860|221678|125369,Complete,Svetlana up
bsdb:40274860/4/2,40274860,laboratory experiment,40274860,https://doi.org/10.1038/s41598-025-95357-4,https://www.nature.com/articles/s41598-025-95357-4,"Chengfu Zhang, Dongyang Lu, Hongzhuang Wang, Kun Li, Munwar Ali, Yong Zhu, Xiaoying Chen, Yang Liu",Comparative analysis of gut microbiota in free range and house fed yaks from Linzhou County,Scientific reports,NA,"House-fed, Grazing, Bos grunniens, Microbiota, 16S rRNA sequencing, Metabolomics",Experiment 4,China,Bos grunniens,Feces,UBERON:0001988,Diet,EFO:0002755,House-fed yaks (LS),Grazing yaks (LF),"Yaks that grazed freely on a pasture consisting of native grass species like Agropyron cristatum, Elymus nutans, Kobresia humilis, etc.",6,6,NA,ITS / ITS2,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Result Text, Figure 6A, 6B",1 November 2025,Emma Nelly,"Emma Nelly,Anne-mariesharp",Fungal phyla and genera with significantly higher relative abundance in house-fed yaks compared to grazing yaks.,decreased,"k__Fungi|p__Basidiomycota,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Stachybotryaceae|g__Myrothecium,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Plectosphaerellaceae|g__Plectosphaerella",4751|5204;4751|4890|147550|5125|1667166|5531;4751|4890|147550|1028384|1033978|40657,Complete,Svetlana up
bsdb:40318838/1/1,40318838,case-control,40318838,10.1016/j.neuroscience.2025.04.050,https://www.ibroneuroscience.org/article/S0306-4522(25)00349-5/fulltext,"Rust C., van den Heuvel L.L., Bardien S., Carr J., Pretorius E., Seedat S. , Hemmings S.M.J.",Association between the relative abundance of butyrate-producing and mucin-degrading taxa and Parkinson's disease,Neuroscience,2025,"Alpha-diversity, Beta-diversity, Butyrate-producing bacteria, Gut microbiome, Gut-brain-axis, Parkinson’s disease",Experiment 1,South Africa,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Controls,Parkinson’s Disease (PD),"Individuals diagnosed with Parkinson’s Disease (PD), referred to as the case group",42,16,1 month,16S,4,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 1,17 November 2025,Tosin,Tosin,The relative abundance of taxa that were statistically different in PD (Parkinson’s disease) cases compared to controls which were assessed using ANCOM-BC (Analysis of Compositions of Microbiomes with Bias Correction),increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis",3379134|74201|203494|48461|1647988|239934;3379134|256845|1313211|278082|255528|172900,Complete,KateRasheed
bsdb:40318838/1/2,40318838,case-control,40318838,10.1016/j.neuroscience.2025.04.050,https://www.ibroneuroscience.org/article/S0306-4522(25)00349-5/fulltext,"Rust C., van den Heuvel L.L., Bardien S., Carr J., Pretorius E., Seedat S. , Hemmings S.M.J.",Association between the relative abundance of butyrate-producing and mucin-degrading taxa and Parkinson's disease,Neuroscience,2025,"Alpha-diversity, Beta-diversity, Butyrate-producing bacteria, Gut microbiome, Gut-brain-axis, Parkinson’s disease",Experiment 1,South Africa,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Controls,Parkinson’s Disease (PD),"Individuals diagnosed with Parkinson’s Disease (PD), referred to as the case group",42,16,1 month,16S,4,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 1,17 November 2025,Chyono2,"Chyono2,Tosin",The relative abundance of taxa that were statistically different in PD (Parkinson’s disease) cases compared to controls which were assessed using ANCOM-BC (Analysis of Compositions of Microbiomes with Bias Correction),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803;3379134|1224|1236|135625|712;1783272|1239|186801|3082720|186804;1783272|1239|186801|3085636|186803|841;1783272|1239|909932|1843489|31977|29465,Complete,KateRasheed
bsdb:40330727/1/1,40330727,case-control,40330727,10.3389/fmicb.2025.1538224,NA,"Marciniak A., Skrzypczak-Zielińska M., Zakerska-Banaszak O., Nowakowska E., Kozaczka A., Zemła B., Szpak A., Godlewski D., Charzewska J. , Pathak D.R.",Urinary and oral microbiota in Polish women: a pilot case-control study of breast cancer,Frontiers in microbiology,2025,"breast cancer, functional analysis, next-generation sequencing, oral microbiota, urinary microbiota",Experiment 1,Poland,Homo sapiens,Urine,UBERON:0001088,Breast cancer,MONDO:0007254,healthy controls,Breast cancer (BC) cases,"BC cases, regardless of subtype, with biological samples collected between 2004 and 2006 from 5 Regional Cancer Registries located in Poland",24,24,NA,16S,123456789,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,region of residence","age,alcohol drinking,body mass index,menopause,smoking status",NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 4,13 June 2025,Ecsharp,Ecsharp,Log 2 Fold changes of urine bacterial abundance between cases and healthy controls at different taxonomic levels,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,s__uncultured Pseudomonas sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|s__uncultured Gammaproteobacteria bacterium",3379134|1224|1236|72274;3379134|1224|1236|72274|135621;3379134|1224|1236;3379134|1224|1236|72274|135621|286;114707;3379134|1224|1236|86473,Complete,NA
bsdb:40330727/2/1,40330727,case-control,40330727,10.3389/fmicb.2025.1538224,NA,"Marciniak A., Skrzypczak-Zielińska M., Zakerska-Banaszak O., Nowakowska E., Kozaczka A., Zemła B., Szpak A., Godlewski D., Charzewska J. , Pathak D.R.",Urinary and oral microbiota in Polish women: a pilot case-control study of breast cancer,Frontiers in microbiology,2025,"breast cancer, functional analysis, next-generation sequencing, oral microbiota, urinary microbiota",Experiment 2,Poland,Homo sapiens,Oral cavity,UBERON:0000167,Breast cancer,MONDO:0007254,healthy controls,Breast cancer (BC) cases,"BC cases, regardless of subtype, with biological samples collected between 2004 and 2006 from 5 Regional Cancer Registries located in Poland",24,24,NA,16S,123456789,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,region of residence","age,alcohol drinking,body mass index,menopause,smoking status",NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 6,13 June 2025,Ecsharp,Ecsharp,Log 2 fold changes of oral wash bacterial abundance between cases and healthy controls at different taxonomic levels,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia para-adiacens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae|g__Cellulosimicrobium|s__Cellulosimicrobium cellulans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Pantoea agglomerans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Promicromonosporaceae|g__Cellulosimicrobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales",1783272|1239|91061|186826|186827|46123|191553;1783272|201174|1760|85006|85017|157920|1710;3379134|1224|1236|72274|135621|286|306;3379134|1224|1236|91347|1903409|53335|549;1783272|201174|1760|85006|85017|157920;3379134|1224|1236|72274|135621|286;3379134|1224|1236|91347|1903409|53335;3379134|976|200643|171549|171551;3379134|1224|1236|72274|135621;3379134|1224|1236|91347|1903409;3379134|1224|1236|72274,Complete,NA
bsdb:40335161/1/1,40335161,"laboratory experiment,randomized controlled trial",40335161,10.1136/gutjnl-2025-335353,https://gut.bmj.com/content/74/11/1828,"Mela V., Heras V., Iesmantaite M., García-Martín M.L., Bernal M., Posligua-García J.D., Subiri-Verdugo A., Martínez-Montoro J.I., Gómez-Pérez A.M., Bandera B., Moreno-Indias I. , Tinahones F.J.",Microbiota fasting-related changes ameliorate cognitive decline in obesity and boost ex vivo microglial function through the gut-brain axis,Gut,2025,"diet, metabolomics, microbiome, neurobiology, obesity",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Mediterranean (Med) diet (Basal),Mediterranean (Med) diet (Final),The individuals took the Mediterranean diet (low ketone bodies increase from the diet) for a time span of 3 months. They were followed up every month to undertake Neuropsychological and psychometric tests.,32,26,NA,16S,NA,Ion Torrent,log transformation,ANCOM-BC,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2H,13 October 2025,Saima-Younis,Saima-Younis,Significantly enriched bacterial genera in individuals with Mediterranean diet,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium",3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|186802|216572|1017280;1783272|1239|186801|186802|186806|1730|42322,Complete,Svetlana up
bsdb:40335161/2/1,40335161,"laboratory experiment,randomized controlled trial",40335161,10.1136/gutjnl-2025-335353,https://gut.bmj.com/content/74/11/1828,"Mela V., Heras V., Iesmantaite M., García-Martín M.L., Bernal M., Posligua-García J.D., Subiri-Verdugo A., Martínez-Montoro J.I., Gómez-Pérez A.M., Bandera B., Moreno-Indias I. , Tinahones F.J.",Microbiota fasting-related changes ameliorate cognitive decline in obesity and boost ex vivo microglial function through the gut-brain axis,Gut,2025,"diet, metabolomics, microbiome, neurobiology, obesity",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Ketogenic (Keto) diet (Basal),Ketogenic (Keto) diet (Final),The individuals took the Ketogenic diet (high ketone bodies increase from the diet) for a time span of 3 months. They were followed up every month to undertake Neuropsychological and psychometric tests.,32,28,NA,16S,NA,Ion Torrent,log transformation,ANCOM-BC,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2H,12 October 2025,Saima-Younis,Saima-Younis,Microbial genera which are enriched in obese individuals with Ketogenic diet,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas",1783272|201174|1760|2037|2049|1654;3379134|1224|1236|135624|84642|642,Complete,Svetlana up
bsdb:40335161/2/2,40335161,"laboratory experiment,randomized controlled trial",40335161,10.1136/gutjnl-2025-335353,https://gut.bmj.com/content/74/11/1828,"Mela V., Heras V., Iesmantaite M., García-Martín M.L., Bernal M., Posligua-García J.D., Subiri-Verdugo A., Martínez-Montoro J.I., Gómez-Pérez A.M., Bandera B., Moreno-Indias I. , Tinahones F.J.",Microbiota fasting-related changes ameliorate cognitive decline in obesity and boost ex vivo microglial function through the gut-brain axis,Gut,2025,"diet, metabolomics, microbiome, neurobiology, obesity",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Ketogenic (Keto) diet (Basal),Ketogenic (Keto) diet (Final),The individuals took the Ketogenic diet (high ketone bodies increase from the diet) for a time span of 3 months. They were followed up every month to undertake Neuropsychological and psychometric tests.,32,28,NA,16S,NA,Ion Torrent,log transformation,ANCOM-BC,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2H,12 October 2025,Saima-Younis,Saima-Younis,Microbial generas and species which are depleted in obese individuals with Ketogenic diet,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Paraclostridium,",3379134|1224|1236|91347|543|570;3379134|976|200643|171549|2005473;1783272|1239|186801|3082720|186804|1849822;,Complete,Svetlana up
bsdb:40335161/3/1,40335161,"laboratory experiment,randomized controlled trial",40335161,10.1136/gutjnl-2025-335353,https://gut.bmj.com/content/74/11/1828,"Mela V., Heras V., Iesmantaite M., García-Martín M.L., Bernal M., Posligua-García J.D., Subiri-Verdugo A., Martínez-Montoro J.I., Gómez-Pérez A.M., Bandera B., Moreno-Indias I. , Tinahones F.J.",Microbiota fasting-related changes ameliorate cognitive decline in obesity and boost ex vivo microglial function through the gut-brain axis,Gut,2025,"diet, metabolomics, microbiome, neurobiology, obesity",Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Alternate-day fasting (ADF) diet (Basal),Alternate-day fasting (ADF) diet (Final),The individuals took the ADF diet (low ketone bodies increase from the diet) for a time span of 3 months. They were followed up every month to undertake Neuropsychological and psychometric tests.,32,30,NA,16S,NA,Ion Torrent,log transformation,ANCOM-BC,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2H,12 October 2025,Saima-Younis,Saima-Younis,Microbial genera enriched in obese individuals with ADT diet,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis",1783272|1239|91061|186826|33958|1243;3379134|256845|1313211|278082|255528|172900,Complete,Svetlana up
bsdb:40335161/3/2,40335161,"laboratory experiment,randomized controlled trial",40335161,10.1136/gutjnl-2025-335353,https://gut.bmj.com/content/74/11/1828,"Mela V., Heras V., Iesmantaite M., García-Martín M.L., Bernal M., Posligua-García J.D., Subiri-Verdugo A., Martínez-Montoro J.I., Gómez-Pérez A.M., Bandera B., Moreno-Indias I. , Tinahones F.J.",Microbiota fasting-related changes ameliorate cognitive decline in obesity and boost ex vivo microglial function through the gut-brain axis,Gut,2025,"diet, metabolomics, microbiome, neurobiology, obesity",Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Response to diet,EFO:0010757,Alternate-day fasting (ADF) diet (Basal),Alternate-day fasting (ADF) diet (Final),The individuals took the ADF diet (low ketone bodies increase from the diet) for a time span of 3 months. They were followed up every month to undertake Neuropsychological and psychometric tests.,32,30,NA,16S,NA,Ion Torrent,log transformation,ANCOM-BC,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2H,12 October 2025,Saima-Younis,Saima-Younis,Microbial genera depleted in obese individuals with ADT diet,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia",1783272|1239|186801|3085636|186803|189330;1783272|1239|91061|186826|186828|117563;1783272|1239|186801|3082720|186804|1501226,Complete,Svetlana up
bsdb:40335161/4/1,40335161,"laboratory experiment,randomized controlled trial",40335161,10.1136/gutjnl-2025-335353,https://gut.bmj.com/content/74/11/1828,"Mela V., Heras V., Iesmantaite M., García-Martín M.L., Bernal M., Posligua-García J.D., Subiri-Verdugo A., Martínez-Montoro J.I., Gómez-Pérez A.M., Bandera B., Moreno-Indias I. , Tinahones F.J.",Microbiota fasting-related changes ameliorate cognitive decline in obesity and boost ex vivo microglial function through the gut-brain axis,Gut,2025,"diet, metabolomics, microbiome, neurobiology, obesity",Experiment 4,Spain,Homo sapiens,Feces,UBERON:0001988,Cognitive function measurement,EFO:0008354,Low Stroop interference score,High Stroop interference score,The reading of Stroop interference test taken on last follow-up session after 90 days of diet intervention.,96,84,NA,16S,NA,Ion Torrent,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2I,12 October 2025,Saima-Younis,Saima-Younis,Microbial genera which were found positively correlated with Stroop interference scores.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",3379134|74201|203494|48461|1647988|239934;3379134|200940|3031449|213115|194924|35832,Complete,Svetlana up
bsdb:40335161/5/1,40335161,"laboratory experiment,randomized controlled trial",40335161,10.1136/gutjnl-2025-335353,https://gut.bmj.com/content/74/11/1828,"Mela V., Heras V., Iesmantaite M., García-Martín M.L., Bernal M., Posligua-García J.D., Subiri-Verdugo A., Martínez-Montoro J.I., Gómez-Pérez A.M., Bandera B., Moreno-Indias I. , Tinahones F.J.",Microbiota fasting-related changes ameliorate cognitive decline in obesity and boost ex vivo microglial function through the gut-brain axis,Gut,2025,"diet, metabolomics, microbiome, neurobiology, obesity",Experiment 5,Spain,Homo sapiens,Feces,UBERON:0001988,Cognitive function measurement,EFO:0008354,Low Trail Making Test (TMT) A score,High Trail Making Test (TMT) A score,"The reading of TMT A for rote memory, taken on last follow-up session after 90 days of diet intervention.",96,84,NA,16S,NA,Ion Torrent,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2I,12 October 2025,Saima-Younis,Saima-Younis,The microbial genus whose abundance was positively correlated with TMT A,increased,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,3379134|200940|3031449|213115|194924|35832,Complete,Svetlana up
bsdb:40335161/6/1,40335161,"laboratory experiment,randomized controlled trial",40335161,10.1136/gutjnl-2025-335353,https://gut.bmj.com/content/74/11/1828,"Mela V., Heras V., Iesmantaite M., García-Martín M.L., Bernal M., Posligua-García J.D., Subiri-Verdugo A., Martínez-Montoro J.I., Gómez-Pérez A.M., Bandera B., Moreno-Indias I. , Tinahones F.J.",Microbiota fasting-related changes ameliorate cognitive decline in obesity and boost ex vivo microglial function through the gut-brain axis,Gut,2025,"diet, metabolomics, microbiome, neurobiology, obesity",Experiment 6,Spain,Homo sapiens,Feces,UBERON:0001988,Cognitive function measurement,EFO:0008354,Low Trial Making Test (TMT) B Scores,High Trial Making Test (TMT) B scores,The reading of TMT B (for executive functioning) taken on last follow-up session after 90 days of diet intervention.,96,84,NA,16S,NA,Ion Torrent,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2I,12 October 2025,Saima-Younis,Saima-Younis,Microbial genus which was found positively correlated with TMT B,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,1783272|1239|186801|3085636|186803|1766253,Complete,Svetlana up
bsdb:40335161/6/2,40335161,"laboratory experiment,randomized controlled trial",40335161,10.1136/gutjnl-2025-335353,https://gut.bmj.com/content/74/11/1828,"Mela V., Heras V., Iesmantaite M., García-Martín M.L., Bernal M., Posligua-García J.D., Subiri-Verdugo A., Martínez-Montoro J.I., Gómez-Pérez A.M., Bandera B., Moreno-Indias I. , Tinahones F.J.",Microbiota fasting-related changes ameliorate cognitive decline in obesity and boost ex vivo microglial function through the gut-brain axis,Gut,2025,"diet, metabolomics, microbiome, neurobiology, obesity",Experiment 6,Spain,Homo sapiens,Feces,UBERON:0001988,Cognitive function measurement,EFO:0008354,Low Trial Making Test (TMT) B Scores,High Trial Making Test (TMT) B scores,The reading of TMT B (for executive functioning) taken on last follow-up session after 90 days of diet intervention.,96,84,NA,16S,NA,Ion Torrent,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2I,12 October 2025,Saima-Younis,Saima-Younis,Microbial genus which was negatively correlated with TMT B,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,1783272|1239|186801|3085636|186803|189330,Complete,Svetlana up
bsdb:40335161/7/1,40335161,"laboratory experiment,randomized controlled trial",40335161,10.1136/gutjnl-2025-335353,https://gut.bmj.com/content/74/11/1828,"Mela V., Heras V., Iesmantaite M., García-Martín M.L., Bernal M., Posligua-García J.D., Subiri-Verdugo A., Martínez-Montoro J.I., Gómez-Pérez A.M., Bandera B., Moreno-Indias I. , Tinahones F.J.",Microbiota fasting-related changes ameliorate cognitive decline in obesity and boost ex vivo microglial function through the gut-brain axis,Gut,2025,"diet, metabolomics, microbiome, neurobiology, obesity",Experiment 7,Spain,Homo sapiens,Feces,UBERON:0001988,Cognitive function measurement,EFO:0008354,Low L&N scores,High L&N scores,"The reading of ""Letters and Numbers (L & D) from the Wechsler Adult Intelligence Scale (WAIS)"" taken on last follow-up session after 90 days of diet intervention.",96,84,NA,16S,NA,Ion Torrent,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2I,12 October 2025,Saima-Younis,Saima-Younis,A microbial genus which was positively correlated with L&N score,increased,NA,NA,Complete,Svetlana up
bsdb:40335161/8/1,40335161,"laboratory experiment,randomized controlled trial",40335161,10.1136/gutjnl-2025-335353,https://gut.bmj.com/content/74/11/1828,"Mela V., Heras V., Iesmantaite M., García-Martín M.L., Bernal M., Posligua-García J.D., Subiri-Verdugo A., Martínez-Montoro J.I., Gómez-Pérez A.M., Bandera B., Moreno-Indias I. , Tinahones F.J.",Microbiota fasting-related changes ameliorate cognitive decline in obesity and boost ex vivo microglial function through the gut-brain axis,Gut,2025,"diet, metabolomics, microbiome, neurobiology, obesity",Experiment 8,Spain,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Control (Con) group,Ketone bodies supplementation (KB) group,The mice received BHB supplement (KetoForce food supplement) in the drinking water to study the isolated effect of ketone bodies supplementation.,10,10,NA,16S,NA,Ion Torrent,log transformation,ANCOM-BC,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S2J,13 October 2025,Saima-Younis,Saima-Younis,Bacterial genus which were significantly enriched or depleted to ketone bodies supplementation in obese mice.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|186807;1783272|201174|84998|1643822|1643826,Complete,Svetlana up
bsdb:40335161/8/2,40335161,"laboratory experiment,randomized controlled trial",40335161,10.1136/gutjnl-2025-335353,https://gut.bmj.com/content/74/11/1828,"Mela V., Heras V., Iesmantaite M., García-Martín M.L., Bernal M., Posligua-García J.D., Subiri-Verdugo A., Martínez-Montoro J.I., Gómez-Pérez A.M., Bandera B., Moreno-Indias I. , Tinahones F.J.",Microbiota fasting-related changes ameliorate cognitive decline in obesity and boost ex vivo microglial function through the gut-brain axis,Gut,2025,"diet, metabolomics, microbiome, neurobiology, obesity",Experiment 8,Spain,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Control (Con) group,Ketone bodies supplementation (KB) group,The mice received BHB supplement (KetoForce food supplement) in the drinking water to study the isolated effect of ketone bodies supplementation.,10,10,NA,16S,NA,Ion Torrent,log transformation,ANCOM-BC,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S2J,13 October 2025,Saima-Younis,Saima-Younis,Bacterial genera which were significantly depleted due to ketone bodies supplementation in obese mice,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|186806|1730|290054;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958|1578;3379134|200930|68337|191393|2945020|248038;3379134|976|200643|171549|2005473;1783272|1239|186801|3085636|186803|841,Complete,Svetlana up
bsdb:40335465/1/1,40335465,"case-control,meta-analysis",40335465,10.1038/s41467-025-56829-3,https://doi.org/10.1038/s41467-025-56829-3,"Romano S., Wirbel J., Ansorge R., Schudoma C., Ducarmon Q.R., Narbad A. , Zeller G.",Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson's disease,Nature communications,2025,NA,Experiment 1,"Australia,Canada,China,Finland,Germany,Italy,Japan,Malaysia,Russian Federation,South Korea,United States of America",Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Controls,Parkinson's disease patients,Parkinson's disease cases across case-control studies,17,17,NA,16S,NA,NA,relative abundances,NA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6; Supplementary Data 4,1 July 2025,Kristin.abraham,Kristin.abraham,Taxa enriched in Parkinson's disease patients in 16S meta-analysis. Relative abundances determined using Agresti Generalized Odds Ratios.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Candidatus Fimivivens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Limiplasma,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Scatomorpha,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Metazoa|p__Arthropoda|c__Insecta|o__Lepidoptera|f__Copromorphidae|g__Copromorpha,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella sp. CAG:1427,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:83,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|244127;1783272|201174|1760|85004|31953|1678;3379134|200940|3031449|213115|194924|35832;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802|216572|2840632;1783272|1239|186801|186802|2840594;1783272|1239|186801|186802|2840598;3384194|508458|649775|649776|649777|508459;1783272|1239|186801|186802|31979|1485;33208|6656|50557|7088|753635|1181387;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|216572|2591381;1783272|201174|84998|1643822|1643826|84111|1262874;1783272|1239|186801|186802|186806|1730;1783272|1239|1262992;1783272|1239|186801|3085636|186803|1649459;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|2767887;1783272|1239|91061|186826|33958|2742598;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171551|836;1783272|1239|186801|186802|216572|1905344,Complete,NA
bsdb:40335465/1/2,40335465,"case-control,meta-analysis",40335465,10.1038/s41467-025-56829-3,https://doi.org/10.1038/s41467-025-56829-3,"Romano S., Wirbel J., Ansorge R., Schudoma C., Ducarmon Q.R., Narbad A. , Zeller G.",Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson's disease,Nature communications,2025,NA,Experiment 1,"Australia,Canada,China,Finland,Germany,Italy,Japan,Malaysia,Russian Federation,South Korea,United States of America",Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Controls,Parkinson's disease patients,Parkinson's disease cases across case-control studies,17,17,NA,16S,NA,NA,relative abundances,NA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6; Supplementary Data 4,1 July 2025,Kristin.abraham,Kristin.abraham,Taxa depleted in Parkinson's disease patients in 16S meta-analysis. Relative abundances determined using Agresti Generalized Odds Ratios.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Acetatifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Bariatricus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Choladocola,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Faecalibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:41,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Ventrimonas",1783272|1239|186801|3085636|186803|1427378;1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|1924081;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|2840621;1783272|1239|186801|3085636|186803|2719313;1783272|1239|526524|526525|2810280|2678885;1783272|1239|186801|186802|216572|216851;1783272|1239|1263021;1783272|1239|186801|3085636|186803|1407607;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|2840573,Complete,NA
bsdb:40335465/2/1,40335465,"case-control,meta-analysis",40335465,10.1038/s41467-025-56829-3,https://doi.org/10.1038/s41467-025-56829-3,"Romano S., Wirbel J., Ansorge R., Schudoma C., Ducarmon Q.R., Narbad A. , Zeller G.",Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson's disease,Nature communications,2025,NA,Experiment 2,"Germany,China,United States of America",Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,controls,Parkinson's disease patients,Parkinson's disease cases across case-control studies,7,7,NA,WMS,NA,NA,relative abundances,NA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6; Supplementary Data 5,2 July 2025,Kristin.abraham,Kristin.abraham,Taxa enriched in Parkinson's disease patients in SMG meta-analysis. Relative abundances determined using Agresti Generalized Odds Ratios.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus rubiinfantis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__Clostridiales bacterium S5-A14a,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. Marseille-P3244,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella tayi,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas massiliensis (ex Afouda et al. 2020),k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D5,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae sp. B_A14,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum",3379134|976|200643|171549|171550|239759|214856;1783272|1239|186801|186802|216572|244127|1720200;1783272|1239|186801|186802|1898207;1783272|1239|186801|3082720|543314|1230734;1783272|1239|186801|186802|31979|1485|1871020;1783272|1239|186801|3085636|186803|1432051|1432052;1783272|1239|186801|186802|1392389|1673721;1783272|1239|91061|186826|33958|1578|1596;1783272|1239|186801|186802|216572|459786|1945593;1783272|1239|186801|186802|216572|1520815;1783272|1239|186801|186802|216572|3023528;1783272|1239|186801|186802|216572|1905344|1550024;1783272|1239|91061|186826|1300|1301|1309;1783272|1239|186801|186802|216572|1535,Complete,NA
bsdb:40335465/2/2,40335465,"case-control,meta-analysis",40335465,10.1038/s41467-025-56829-3,https://doi.org/10.1038/s41467-025-56829-3,"Romano S., Wirbel J., Ansorge R., Schudoma C., Ducarmon Q.R., Narbad A. , Zeller G.",Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson's disease,Nature communications,2025,NA,Experiment 2,"Germany,China,United States of America",Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,controls,Parkinson's disease patients,Parkinson's disease cases across case-control studies,7,7,NA,WMS,NA,NA,relative abundances,NA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6; Supplementary Data 5,2 July 2025,Kristin.abraham,Kristin.abraham,Taxa depleted in Parkinson's disease patients in SMG meta-analysis. Relative abundances determined using Agresti Generalized Odds Ratios.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia massiliensis (ex Durand et al. 2017),k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Liu et al. 2021)",1783272|1239|186801|3085636|186803|572511|1737424;1783272|1239|186801|186802|3085642|580596|2049021;1783272|1239|186801|186802|31979|1485|1506;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|216851|1971605;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|186802|216572|1263|3062497,Complete,NA
bsdb:40337776/1/1,40337776,case-control,40337776,10.2147/IDR.S504587,NA,"Li Y., Li C., Fang Y., Zhang L., Ying X., Ren R., Zang Y., Ying D., Zhu S., Liu J. , Cao X.",Comprehensive Analysis of Pathogen Diversity and Diagnostic Biomarkers in Patients with Suspected Pulmonary Tuberculosis Through Metagenomic Next-Generation Sequencing,Infection and drug resistance,2025,"biomarkers, bronchoalveolar lavage fluid, lung microbiome, metagenomic next-generation sequencing, tuberculosis",Experiment 1,China,Homo sapiens,Lung,UBERON:0002048,Pulmonary tuberculosis,EFO:1000049,Non‑Tuberculosis,Tuberculosis (TB),Clinical (microbiological) confirmation of pulmonary tuberculosis.,111,87,NA,PCR,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A,1 July 2025,Nuerteye,Nuerteye,Microbial species with differential abundance between TB and Non-TB groups identified through LEfSe analysis with the thresholds of log10 LDA score≥2 and P value<0.05.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter curvus",1783272|1239|91061|186826|1300|1301|68892;3379134|29547|3031852|213849|72294|194|200,Complete,NA
bsdb:40337776/1/2,40337776,case-control,40337776,10.2147/IDR.S504587,NA,"Li Y., Li C., Fang Y., Zhang L., Ying X., Ren R., Zang Y., Ying D., Zhu S., Liu J. , Cao X.",Comprehensive Analysis of Pathogen Diversity and Diagnostic Biomarkers in Patients with Suspected Pulmonary Tuberculosis Through Metagenomic Next-Generation Sequencing,Infection and drug resistance,2025,"biomarkers, bronchoalveolar lavage fluid, lung microbiome, metagenomic next-generation sequencing, tuberculosis",Experiment 1,China,Homo sapiens,Lung,UBERON:0002048,Pulmonary tuberculosis,EFO:1000049,Non‑Tuberculosis,Tuberculosis (TB),Clinical (microbiological) confirmation of pulmonary tuberculosis.,111,87,NA,PCR,NA,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3A,1 July 2025,Nuerteye,Nuerteye,Microbial species with differential abundance between TB and Non-TB groups identified through LEfSe analysis with the thresholds of log10 LDA score≥2 and P value<0.05.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium striatum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia mannitolilytica",1783272|201174|1760|85007|1653|1716|43770;1783272|1239|91061|1385|90964|1279|1282;3379134|1224|28216|80840|119060|48736|105219,Complete,NA
bsdb:40359128/1/1,40359128,"cross-sectional observational, not case-control",40359128,10.1099/jmm.0.002013,NA,"Kamdougha H., Taminiau B., Fall P.A., Ben Amor S., Trigui A., Daube G. , Mnif B.",Alterations of ocular surface microbiome in glaucoma and its association with dry eye,Journal of medical microbiology,2025,"conjunctiva, dry eye disease, dysbiosis, glaucoma, microbiome, preservatives",Experiment 1,Tunisia,Homo sapiens,Conjunctiva,UBERON:0001811,Glaucoma,MONDO:0005041,HC (Healthy Controls),G-only (Glaucomatous patients without dry eye syndrome),Glaucomatous patients without dry eye syndrome,60,24,1 month,16S,123,Illumina,raw counts,DESeq2,0.05,TRUE,NA,age,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure 2A, Supplementary table 2",25 August 2025,Anne-mariesharp,Anne-mariesharp,"Most differentially abundant genera and phyla between groups, identified by
DESeq2.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium",1783272|201174|1760|2037|2049|1654;3379134|1224|28211|356|41294|374;1783272|201174|1760|85009|31957|1912216;3379134|1224|1236|91347|543|547;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|91347|1903414|583;3379134|1224;3379134|1224|1236|72274|135621|286;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|91347|543|1940338;3379134|1224|28216|206351|481|482;1783272|201174|1760|85007|1653|1716,Complete,KateRasheed
bsdb:40359128/2/1,40359128,"cross-sectional observational, not case-control",40359128,10.1099/jmm.0.002013,NA,"Kamdougha H., Taminiau B., Fall P.A., Ben Amor S., Trigui A., Daube G. , Mnif B.",Alterations of ocular surface microbiome in glaucoma and its association with dry eye,Journal of medical microbiology,2025,"conjunctiva, dry eye disease, dysbiosis, glaucoma, microbiome, preservatives",Experiment 2,Tunisia,Homo sapiens,Conjunctiva,UBERON:0001811,Glaucoma,MONDO:0005041,HC (Healthy Controls),G-DED (Glaucomatous patients with dry eye syndrome),Glaucomatous patients with dry eye syndrome,60,30,1 month,16S,123,Illumina,raw counts,DESeq2,0.05,TRUE,NA,age,NA,NA,unchanged,unchanged,increased,NA,NA,Signature 1,"Figure 2A, Supplementary table 2",25 August 2025,Anne-mariesharp,Anne-mariesharp,"Most differentially abundant genera and phyla between groups, identified by DESeq2.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|g__Exiguobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|g__Rhodobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|1224|1236|2887326|468|469;1783272|1239;3379134|976;3379134|1224|28216|80840|119060|32008;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85009|31957|1912216;3379134|1224|1236|91347|543|1940338;1783272|1239|91061|1385|33986;1783272|1239|91061|186826|186828|117563;3379134|1224|1236|135625|712|724;1783272|201174|1760|85006|1268|57493;3384189|32066|203490|203491|1129771|32067;3379134|1224|28216|80840|75682|149698;3379134|1224|28216|206351|481|482;3379134|1224|28211|204455|31989|265;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3379134|1224;3379134|1224|1236|72274|135621|286;3379134|1224|28211|204455|1060;3379134|1224|1236|91347|1903411|613;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465,Complete,KateRasheed
bsdb:40359128/2/2,40359128,"cross-sectional observational, not case-control",40359128,10.1099/jmm.0.002013,NA,"Kamdougha H., Taminiau B., Fall P.A., Ben Amor S., Trigui A., Daube G. , Mnif B.",Alterations of ocular surface microbiome in glaucoma and its association with dry eye,Journal of medical microbiology,2025,"conjunctiva, dry eye disease, dysbiosis, glaucoma, microbiome, preservatives",Experiment 2,Tunisia,Homo sapiens,Conjunctiva,UBERON:0001811,Glaucoma,MONDO:0005041,HC (Healthy Controls),G-DED (Glaucomatous patients with dry eye syndrome),Glaucomatous patients with dry eye syndrome,60,30,1 month,16S,123,Illumina,raw counts,DESeq2,0.05,TRUE,NA,age,NA,NA,unchanged,unchanged,increased,NA,NA,Signature 2,Supplementary table 2,25 August 2025,Anne-mariesharp,Anne-mariesharp,"Most differentially abundant genera between groups, identified by DESeq2.",decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,3379134|1224|1236|91347|543|547,Complete,KateRasheed
bsdb:40359128/3/1,40359128,"cross-sectional observational, not case-control",40359128,10.1099/jmm.0.002013,NA,"Kamdougha H., Taminiau B., Fall P.A., Ben Amor S., Trigui A., Daube G. , Mnif B.",Alterations of ocular surface microbiome in glaucoma and its association with dry eye,Journal of medical microbiology,2025,"conjunctiva, dry eye disease, dysbiosis, glaucoma, microbiome, preservatives",Experiment 3,Tunisia,Homo sapiens,Conjunctiva,UBERON:0001811,Dry eye syndrome,EFO:1000906,HC (Healthy Controls),DED-only (Dry eye syndrome patients without glaucoma),Dry eye syndrome (DED) patients without glaucoma,60,25,1 month,16S,123,Illumina,raw counts,DESeq2,0.05,TRUE,NA,age,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Supplementary table 2,25 August 2025,Anne-mariesharp,Anne-mariesharp,"Most differentially abundant genera between groups, identified by
DESeq2.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|1224|1236|2887326|468|469;3379134|1224|28211|356|41294|374;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85009|31957|1912216;3379134|1224|1236|91347|543|547;3379134|1224|1236|135625|712|724;3379134|1224|1236|72274|135621|286;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|91347|543|1940338,Complete,KateRasheed
bsdb:40359128/4/1,40359128,"cross-sectional observational, not case-control",40359128,10.1099/jmm.0.002013,NA,"Kamdougha H., Taminiau B., Fall P.A., Ben Amor S., Trigui A., Daube G. , Mnif B.",Alterations of ocular surface microbiome in glaucoma and its association with dry eye,Journal of medical microbiology,2025,"conjunctiva, dry eye disease, dysbiosis, glaucoma, microbiome, preservatives",Experiment 4,Tunisia,Homo sapiens,Conjunctiva,UBERON:0001811,Dry eye syndrome,EFO:1000906,G-only (Glaucomatous patients without dry eye syndrome),G-DED (Glaucomatous patients with dry eye syndrome),Glaucomatous patients with dry eye syndrome,24,30,1 month,16S,123,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure 2A, Supplementary table 2",26 August 2025,Anne-mariesharp,Anne-mariesharp,"Most differentially abundant genera and phyla between groups, identified by DESeq2.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|g__Rhodobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",3379134|1224|1236|2887326|468|469;1783272|1239;3379134|1224|1236|135625|712|724;1783272|201174|1760|85006|1268|57493;1783272|201174|1760|85006|1268|1269;3379134|1224|28211|204455|31989|265;3379134|1224;3379134|1224|28211|204455|1060;1783272|1239|91061|1385|90964|1279,Complete,KateRasheed
bsdb:40359128/4/2,40359128,"cross-sectional observational, not case-control",40359128,10.1099/jmm.0.002013,NA,"Kamdougha H., Taminiau B., Fall P.A., Ben Amor S., Trigui A., Daube G. , Mnif B.",Alterations of ocular surface microbiome in glaucoma and its association with dry eye,Journal of medical microbiology,2025,"conjunctiva, dry eye disease, dysbiosis, glaucoma, microbiome, preservatives",Experiment 4,Tunisia,Homo sapiens,Conjunctiva,UBERON:0001811,Dry eye syndrome,EFO:1000906,G-only (Glaucomatous patients without dry eye syndrome),G-DED (Glaucomatous patients with dry eye syndrome),Glaucomatous patients with dry eye syndrome,24,30,1 month,16S,123,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Supplementary table 2,26 August 2025,Anne-mariesharp,Anne-mariesharp,"Most differentially abundant genera between groups, identified by DESeq2.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus",3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|1903414|583,Complete,KateRasheed
bsdb:40359128/5/1,40359128,"cross-sectional observational, not case-control",40359128,10.1099/jmm.0.002013,NA,"Kamdougha H., Taminiau B., Fall P.A., Ben Amor S., Trigui A., Daube G. , Mnif B.",Alterations of ocular surface microbiome in glaucoma and its association with dry eye,Journal of medical microbiology,2025,"conjunctiva, dry eye disease, dysbiosis, glaucoma, microbiome, preservatives",Experiment 5,Tunisia,Homo sapiens,Conjunctiva,UBERON:0001811,Glaucoma,MONDO:0005041,DED-only (Dry eye syndrome patients without glaucoma),G-only (Glaucomatous patients without dry eye syndrome),Glaucomatous patients without dry eye syndrome,25,24,1 month,16S,123,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure 2A, Supplementary table 2",26 August 2025,Anne-mariesharp,Anne-mariesharp,"Most differentially abundant genera and phyla between groups, identified by DESeq2.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|1236|91347|543|547;3379134|1224,Complete,KateRasheed
bsdb:40359128/6/1,40359128,"cross-sectional observational, not case-control",40359128,10.1099/jmm.0.002013,NA,"Kamdougha H., Taminiau B., Fall P.A., Ben Amor S., Trigui A., Daube G. , Mnif B.",Alterations of ocular surface microbiome in glaucoma and its association with dry eye,Journal of medical microbiology,2025,"conjunctiva, dry eye disease, dysbiosis, glaucoma, microbiome, preservatives",Experiment 6,Tunisia,Homo sapiens,Conjunctiva,UBERON:0001811,Glaucoma,MONDO:0005041,DED-only (Dry eye syndrome patients without glaucoma),G-DED (Glaucomatous patients with dry eye syndrome),Glaucomatous patients with dry eye syndrome,25,30,1 month,16S,123,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 2A,27 August 2025,Anne-mariesharp,Anne-mariesharp,"Most differentially abundant phyla between groups, identified by DESeq2.",increased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Bacteroidota",1783272|1239;3379134|1224;3379134|976,Complete,KateRasheed
bsdb:40400039/1/1,40400039,laboratory experiment,40400039,10.1186/s40104-025-01191-z,NA,"Chen Y., Wang Y., Shaoyong W., He Y., Liu Y., Wei S., Gan Y., Sun L., Wang Y., Zong X., Xiang Y., Wang Y. , Jin M.",High-fertility sows reshape gut microbiota: the rise of serotonin-related bacteria and its impact on sustaining reproductive performance,Journal of animal science and biotechnology,2025,"Gut microbiome, Multi-omics analysis, Reproductive performance, Serotonin",Experiment 1,China,Sus scrofa domesticus,Feces,UBERON:0001988,Reproductive behaviour measurement,EFO:0007862,Low reproductive performance Jinhua sows (LRP),High reproductive performance Jinhua sows (HRP),"Jinhua sows with high reproductive performance, selected based on litter size, number of healthy piglets per litter, and parity.",31,31,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 2C,21 October 2025,Pamela,"Pamela,Fiddyhamma",Taxonomic differences in fecal microbiota between Sows with high and low reproductive performance.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|186801|186802|31979|1485;3366610|28890|183925|2158|2159|2172;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:40400039/1/2,40400039,laboratory experiment,40400039,10.1186/s40104-025-01191-z,NA,"Chen Y., Wang Y., Shaoyong W., He Y., Liu Y., Wei S., Gan Y., Sun L., Wang Y., Zong X., Xiang Y., Wang Y. , Jin M.",High-fertility sows reshape gut microbiota: the rise of serotonin-related bacteria and its impact on sustaining reproductive performance,Journal of animal science and biotechnology,2025,"Gut microbiome, Multi-omics analysis, Reproductive performance, Serotonin",Experiment 1,China,Sus scrofa domesticus,Feces,UBERON:0001988,Reproductive behaviour measurement,EFO:0007862,Low reproductive performance Jinhua sows (LRP),High reproductive performance Jinhua sows (HRP),"Jinhua sows with high reproductive performance, selected based on litter size, number of healthy piglets per litter, and parity.",31,31,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 2C,30 January 2026,Fiddyhamma,"Fiddyhamma,Anne-mariesharp",Taxonomic differences in fecal microbiota between Sows with high and low reproductive performance.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552,Complete,NA
bsdb:40400039/2/1,40400039,laboratory experiment,40400039,10.1186/s40104-025-01191-z,NA,"Chen Y., Wang Y., Shaoyong W., He Y., Liu Y., Wei S., Gan Y., Sun L., Wang Y., Zong X., Xiang Y., Wang Y. , Jin M.",High-fertility sows reshape gut microbiota: the rise of serotonin-related bacteria and its impact on sustaining reproductive performance,Journal of animal science and biotechnology,2025,"Gut microbiome, Multi-omics analysis, Reproductive performance, Serotonin",Experiment 2,China,Sus scrofa domesticus,Feces,UBERON:0001988,Reproductive behaviour measurement,EFO:0007862,Low reproductive performance Jinhua sows (LRP),High reproductive performance Jinhua sows (HRP),"Jinhua sows with high reproductive performance, selected based on litter size, number of healthy piglets per litter, and parity.",8,10,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 3E & S2C,19 October 2025,Pamela,Pamela,Taxonomic differences in fecal microbiota between sows with high and low reproductive performance.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp. G3(2012),k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax|s__Anaerovorax odorimutans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacillati|p__Bacillota|c__Clostridia|o__Caldicoprobacterales|f__Caldicoprobacteraceae|g__Caldicoprobacter|s__Caldicoprobacter oshimai,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Apopatosoma|s__Candidatus Apopatosoma intestinale,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea|s__Candidatus Soleaferrea massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium UC5.1-2F7,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium botulinum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:242,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. AB3007,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:145,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:238,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter arboriphilus,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter olleyae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter|s__Oxalobacter formigenes,k__Pseudomonadati|p__Pseudomonadota|s__Proteobacteria bacterium CAG:139,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus champanellensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus flavefaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:382,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus suis,k__Thermoproteati|p__Thermoproteota|c__Thermoprotei|o__Thermoproteales|f__Thermoproteaceae|g__Thermoproteus|s__Thermoproteus tenax,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,s__archaeon GW2011_AR9",1783272|1239|186801|186802|216572|244127|169435;1783272|1239|186801|186802|216572|244127|1235835;1783272|1239|186801|3082720|543314|109326|109327;1783272|201174|1760|85004|31953|1678|28025;1783272|201174|1760|85004|31953|1678|1694;1783272|1239|186801|3120405|715221|715222|551788;1783272|1239|186801|186802|3082828|1262966;1783272|1239|186801|186802|1470353|1470354;1783272|1239|186801|1697792;1783272|1239|186801|186802|31979|1485|1491;1783272|1239|186801|186802|31979|1485|1262783;1783272|1239|186801|186802|186806|1730|1392487;1783272|1239|1263005;1783272|1239|1263011;3366610|28890|183925|2158|2159|2172|39441;3366610|28890|183925|2158|2159|2172|294671;3379134|1224|28216|80840|75682|846|847;3379134|1224|1262986;1783272|1239|186801|186802|216572|1263|1161942;1783272|1239|186801|186802|216572|1263|1265;1783272|1239|186801|186802|216572|1263|1262957;1783272|1239|91061|186826|1300|1301|1307;1783275|28889|183924|2266|2267|2270|2271;1783272|1239|186801|186802|216572|1535;1783272|1239|186801|186802|216572|39492;1579369,Complete,Svetlana up
bsdb:40400039/2/2,40400039,laboratory experiment,40400039,10.1186/s40104-025-01191-z,NA,"Chen Y., Wang Y., Shaoyong W., He Y., Liu Y., Wei S., Gan Y., Sun L., Wang Y., Zong X., Xiang Y., Wang Y. , Jin M.",High-fertility sows reshape gut microbiota: the rise of serotonin-related bacteria and its impact on sustaining reproductive performance,Journal of animal science and biotechnology,2025,"Gut microbiome, Multi-omics analysis, Reproductive performance, Serotonin",Experiment 2,China,Sus scrofa domesticus,Feces,UBERON:0001988,Reproductive behaviour measurement,EFO:0007862,Low reproductive performance Jinhua sows (LRP),High reproductive performance Jinhua sows (HRP),"Jinhua sows with high reproductive performance, selected based on litter size, number of healthy piglets per litter, and parity.",8,10,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 3E & S2C,19 October 2025,Pamela,Pamela,Taxonomic differences in fecal microbiota between sows with high and low reproductive performance.,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp. CAG:344,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp. KLE1797,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. CAG:435,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:545,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:709,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:770,k__Thermoproteati|p__Nitrososphaerota|o__Candidatus Caldarchaeales|f__Candidatus Caldarchaeaceae|g__Candidatus Caldarchaeum|s__Candidatus Caldarchaeum subterraneum,k__Thermoproteati|p__Nitrososphaerota|c__Nitrososphaeria|o__Nitrosopumilales|f__Nitrosopumilaceae|g__Nitrosarchaeum|s__Candidatus Nitrosarchaeum limnium,k__Promethearchaeati|p__Candidatus Thorarchaeota|s__Candidatus Thorarchaeota archaeon SMTZ-45,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,k__Methanobacteriati|p__Methanobacteriota|c__Halobacteria|o__Halobacteriales|f__Haloarculaceae|g__Haloarcula|s__Haloarcula argentinensis,k__Methanobacteriati|p__Methanobacteriota|c__Halobacteria|o__Halobacteriales|f__Natrialbaceae|g__Halostagnicola|s__Halostagnicola larsenii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobacterium|s__Methanobacterium sp. MB1,k__Methanobacteriati|p__Methanobacteriota|c__Methanococci|o__Methanococcales|f__Methanocaldococcaceae|g__Methanocaldococcus|s__Methanocaldococcus infernus,k__Methanobacteriati|p__Methanobacteriota|c__Methanomicrobia|o__Methanomicrobiales|f__Methanomicrobiaceae|g__Methanoculleus|s__Methanoculleus sp. MAB1,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. FD3004,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. MA2016,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. P6B1,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. RM4,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:624,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Sharpea|s__Sharpea azabuensis,k__Methanobacteriati|p__Thermoplasmatota|c__Thermoplasmata|o__Thermoplasmatales|s__Thermoplasmatales archaeon SG8-52-4,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter brevis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Xylanibacter|s__Xylanibacter oryzae,s__archaeon GW2011_AR18",3379134|74201|203494|48461|1647988|239934|239935;3379134|74201|203494|48461|1647988|239934|239935;3379134|74201|203494|48461|1647988|239934|1262691;3379134|74201|203494|48461|1647988|239934|1574264;3379134|976|200643|171549|171550|239759|1262695;3379134|976|200643|171549|815|816|1262742;3379134|976|200643|171549|815|816|1262748;3379134|976|200643|171549|815|816|1262751;1783275|651137|3071582|3071583|1048752|311458;1783275|651137|1643678|31932|338190|1007082|1007084;1935183|1706441|1706443;1783272|1239|909932|1843489|31977|39948|487173;3366610|28890|183963|2235|1963268|2237|43776;3366610|28890|183963|2235|1644061|353799|353800;3379134|976|200643|171549|171552|2974257|28127;1783272|1239|909932|1843489|31977|906|907;3366610|28890|183925|2158|2159|2160|1379702;3366610|28890|183939|2182|196117|196118|67760;3366610|28890|224756|2191|2194|45989|86622;3379134|976|200643|171549|171552|838|1408309;3379134|976|200643|171549|171552|838|1408310;3379134|976|200643|171549|171552|838|1410613;3379134|976|200643|171549|171552|838|1200547;1783272|1239|186801|186802|216572|1263|1262965;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|526524|526525|2810280|519427|322505;3366610|2283796|183967|2301|1803819;3379134|976|200643|171549|171552|558436|83231;3379134|976|200643|171549|171552|558436|185293;1579376,Complete,Svetlana up
bsdb:40404683/1/1,40404683,"cross-sectional observational, not case-control",40404683,10.1038/s41598-025-01905-3,NA,"Terbtothakun P., Visedthorn S., Klomkliew P., Chanchaem P., Sawaswong V., Sivapornnukul P., Sunantawanit S., Khamwut A., Rotcheewaphan S., Kaewsapsak P. , Payungporn S.",Clinical metagenomics analysis of bacterial and fungal microbiota from sputum of patients suspected with tuberculosis infection based on nanopore sequencing,Scientific reports,2025,"Mycobacterium tuberculosis, 16S rDNA, Internal transcribed spacer (ITS), Metagenomics, Oxford nanopore technologies (ONT)",Experiment 1,Thailand,Homo sapiens,Sputum,UBERON:0007311,Pulmonary tuberculosis,EFO:1000049,Mycobacterium tuberculosis-negative (non-TB),Mycobacterium tuberculosis-positive,"Mycobacterium tuberculosis confirmed by standard tests (culture, Xpert, etc.)",41,56,NA,16S,123456789,Nanopore,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 2B;  4B; S2,10 July 2025,Nuerteye,Nuerteye,Differential abundance analysis was performed using Linear Discriminant Analysis Effect Size (LEfSe) on MTB and negative sputum samples. 2(B) Bar plots display differentially abundant bacterial taxa across various taxonomic ranks. 4(B) Bar plots display differentially abundant fungal taxa across various taxonomic ranks.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium tuberculosis,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida orthopsilosis",3379134|1224|1236|135614|32033|40323|40324;1783272|201174|1760|85007|1762|1763|1773;4751|4890|3239874|2916678|766764|5475|273371,Complete,NA
bsdb:40404683/1/2,40404683,"cross-sectional observational, not case-control",40404683,10.1038/s41598-025-01905-3,NA,"Terbtothakun P., Visedthorn S., Klomkliew P., Chanchaem P., Sawaswong V., Sivapornnukul P., Sunantawanit S., Khamwut A., Rotcheewaphan S., Kaewsapsak P. , Payungporn S.",Clinical metagenomics analysis of bacterial and fungal microbiota from sputum of patients suspected with tuberculosis infection based on nanopore sequencing,Scientific reports,2025,"Mycobacterium tuberculosis, 16S rDNA, Internal transcribed spacer (ITS), Metagenomics, Oxford nanopore technologies (ONT)",Experiment 1,Thailand,Homo sapiens,Sputum,UBERON:0007311,Pulmonary tuberculosis,EFO:1000049,Mycobacterium tuberculosis-negative (non-TB),Mycobacterium tuberculosis-positive,"Mycobacterium tuberculosis confirmed by standard tests (culture, Xpert, etc.)",41,56,NA,16S,123456789,Nanopore,relative abundances,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 2B; 4B; S2,10 July 2025,Nuerteye,Nuerteye,Differential abundance analysis was performed using Linear Discriminant Analysis Effect Size (LEfSe) on MTB and negative sputum samples. 2(B) Bar plots display differentially abundant bacterial taxa across various taxonomic ranks. 4(B) Bar plots display differentially abundant fungal taxa across various taxonomic ranks.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium striatum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa",3379134|976|200643|171549|171552|838|28132;1783272|1239|909932|1843489|31977|29465|29466;1783272|201174|1760|85007|1653|1716|43770;3379134|1224|1236|72274|135621|286|287,Complete,NA
bsdb:40406520/1/1,40406520,case-control,40406520,10.3389/fcimb.2025.1556153,https://doi.org/10.3389/fcimb.2025.1556153,"Zhai Q., Zhao L., Wang M., Li L., Li L.A., Ye M., Li M., Xu C. , Meng Y.",Integrated analysis of microbiome and metabolome reveals insights into cervical neoplasia aggravation in a Chinese cohort,Frontiers in cellular and infection microbiology,2025,"biomarkers, cervical cancer, cervical squamous intraepithelial lesion, integrated analysis, metabolome, microbiome",Experiment 1,China,Homo sapiens,Cervix epithelium,UBERON:0004801,Cervical carcinoma,EFO:0001061,Normal (Healthy Controls),Cervical carcinoma (CC),"Patients aged 30-73,with a confirmed pathological diagnosis of cervical carcinoma (CC). In the cohort of predominately squamous cell carcinoma (39 cases), with a smaller portion of adenocarcinomas (13 cases) and most cases were in early Stage I (30 cases), followed by Stage II (11 cases), and Stage III (8 cases), with only 3 cases in Stage IV. The majority of patients were infected with one or more high-risk HPV types.",53,52,1 week,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Results text,10 October 2025,Kyaw,"Kyaw,Folakunmi",Genus significantly increased in cervical cancer (CC) patients compared to normal (Healthy Controls).,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,3379134|1224|1236|72274|135621|286,Complete,Folakunmi
bsdb:40406520/1/2,40406520,case-control,40406520,10.3389/fcimb.2025.1556153,https://doi.org/10.3389/fcimb.2025.1556153,"Zhai Q., Zhao L., Wang M., Li L., Li L.A., Ye M., Li M., Xu C. , Meng Y.",Integrated analysis of microbiome and metabolome reveals insights into cervical neoplasia aggravation in a Chinese cohort,Frontiers in cellular and infection microbiology,2025,"biomarkers, cervical cancer, cervical squamous intraepithelial lesion, integrated analysis, metabolome, microbiome",Experiment 1,China,Homo sapiens,Cervix epithelium,UBERON:0004801,Cervical carcinoma,EFO:0001061,Normal (Healthy Controls),Cervical carcinoma (CC),"Patients aged 30-73,with a confirmed pathological diagnosis of cervical carcinoma (CC). In the cohort of predominately squamous cell carcinoma (39 cases), with a smaller portion of adenocarcinomas (13 cases) and most cases were in early Stage I (30 cases), followed by Stage II (11 cases), and Stage III (8 cases), with only 3 cases in Stage IV. The majority of patients were infected with one or more high-risk HPV types.",53,52,1 week,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Results text,10 October 2025,Kyaw,"Kyaw,Folakunmi",Genus significantly decreased in cervical cancer (CC) patients compared to normal (Healthy Controls).,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Folakunmi
bsdb:40441865/1/1,40441865,"laboratory experiment,prospective cohort",40441865,10.1136/gutjnl-2024-334565,https://gut.bmj.com/content/74/11/1847,"Li P., Lei Q., Yu X., Shen Y., Chen Y., Hou C., Hu B., Cui Y., Liu Z., Qin Y., Liu H., Lin D., Xu Y. , Wu D.",Commensal <i>Bacteroides</i> T6SS alleviate GI-aGVHD via mediating gut microbiota composition and bile acids metabolism,Gut,2025,"BACTERIAL INTERACTIONS, BILE ACID METABOLISM, GASTROINTESTINAL TRACT, INTESTINAL MICROBIOLOGY",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Acute graft vs. host disease,EFO:0004599,Non-acute graft-versus-host disease patients (non-aGVHD group),Gastrointestinal acute graft-versus-host disease patients (GI-aGVHD group),Patients with Gastrointestinal acute graft-versus-host disease at 4-6 weeks post-hematopoietic stem cell transplantation (HSCT),47,24,NA,16S,34,NA,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Figure 1H,8 November 2025,Deborah-Fabusuyi,"Deborah-Fabusuyi,Tosin",Fecal microbial taxa significantly depleted in GI-aGVHD patients compared to non-aGVHD controls at 4-6 weeks post-hematopoietic stem cell transplantation (HSCT) identified by (Linear discriminant analysis effect size) LEfSe analysis.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976;1783272|1239|186801;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171550;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802,Complete,KateRasheed
bsdb:40441865/1/2,40441865,"laboratory experiment,prospective cohort",40441865,10.1136/gutjnl-2024-334565,https://gut.bmj.com/content/74/11/1847,"Li P., Lei Q., Yu X., Shen Y., Chen Y., Hou C., Hu B., Cui Y., Liu Z., Qin Y., Liu H., Lin D., Xu Y. , Wu D.",Commensal <i>Bacteroides</i> T6SS alleviate GI-aGVHD via mediating gut microbiota composition and bile acids metabolism,Gut,2025,"BACTERIAL INTERACTIONS, BILE ACID METABOLISM, GASTROINTESTINAL TRACT, INTESTINAL MICROBIOLOGY",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Acute graft vs. host disease,EFO:0004599,Non-acute graft-versus-host disease patients (non-aGVHD group),Gastrointestinal acute graft-versus-host disease patients (GI-aGVHD group),Patients with Gastrointestinal acute graft-versus-host disease at 4-6 weeks post-hematopoietic stem cell transplantation (HSCT),47,24,NA,16S,34,NA,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Figure 1H,8 November 2025,Deborah-Fabusuyi,"Deborah-Fabusuyi,Tosin",Fecal microbial taxa significantly increased in GI-aGVHD patients compared to non-aGVHD controls at 4-6 weeks post-hematopoietic stem cell transplantation (HSCT) identified by (Linear discriminant analysis effect size) LEfSe analysis.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Atopostipes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus",1783272|1239|91061|186826|186828|292480;3379134|1224|28216|80840|119060;3379134|1224|28216|80840|119060|106589,Complete,KateRasheed
bsdb:40441865/2/1,40441865,"laboratory experiment,prospective cohort",40441865,10.1136/gutjnl-2024-334565,https://gut.bmj.com/content/74/11/1847,"Li P., Lei Q., Yu X., Shen Y., Chen Y., Hou C., Hu B., Cui Y., Liu Z., Qin Y., Liu H., Lin D., Xu Y. , Wu D.",Commensal <i>Bacteroides</i> T6SS alleviate GI-aGVHD via mediating gut microbiota composition and bile acids metabolism,Gut,2025,"BACTERIAL INTERACTIONS, BILE ACID METABOLISM, GASTROINTESTINAL TRACT, INTESTINAL MICROBIOLOGY",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Acute graft vs. host disease,EFO:0004599,Bacteroides fragilis Wild Type (WT),Bacteroides fragilis T6SS-deficient mutant (ΔT6SS),Bacteroides fragilis T6SS-deficient mutant (ΔT6SS) treated mice in aGVHD model,3,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4c,9 November 2025,Deborah-Fabusuyi,"Deborah-Fabusuyi,Tosin","Fecal microbial taxa with decreased abundance in mice treated with B. fragilis T6SS-deficient mutant compared to wild-type strain, 14 days post-allogeneic bone marrow transplantation",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|1224|28211;3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236;3379134|1224|1236|91347|543|570;3379134|976|200643|171549|2005473;3379134|1224;3379134|1224|1236|91347|543|1940338,Complete,KateRasheed
bsdb:40441865/2/2,40441865,"laboratory experiment,prospective cohort",40441865,10.1136/gutjnl-2024-334565,https://gut.bmj.com/content/74/11/1847,"Li P., Lei Q., Yu X., Shen Y., Chen Y., Hou C., Hu B., Cui Y., Liu Z., Qin Y., Liu H., Lin D., Xu Y. , Wu D.",Commensal <i>Bacteroides</i> T6SS alleviate GI-aGVHD via mediating gut microbiota composition and bile acids metabolism,Gut,2025,"BACTERIAL INTERACTIONS, BILE ACID METABOLISM, GASTROINTESTINAL TRACT, INTESTINAL MICROBIOLOGY",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Acute graft vs. host disease,EFO:0004599,Bacteroides fragilis Wild Type (WT),Bacteroides fragilis T6SS-deficient mutant (ΔT6SS),Bacteroides fragilis T6SS-deficient mutant (ΔT6SS) treated mice in aGVHD model,3,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4c,9 November 2025,Deborah-Fabusuyi,Deborah-Fabusuyi,"Fecal microbial taxa with increased abundance in mice treated with B. fragilis T6SS-deficient mutant compared to wild-type strain, 14 days post-allogeneic bone marrow transplantation",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;1783272|1239;3379134|976|200643|171549|815|816;1783272|1239|186801;1783272|1239|186801|3085636;3379134|74201|203494|48461;3379134|74201;1783272|1239|186801|3085636|186803;3379134|74201|203494;3379134|976|200643|171549|815,Complete,KateRasheed
bsdb:40441865/3/1,40441865,"laboratory experiment,prospective cohort",40441865,10.1136/gutjnl-2024-334565,https://gut.bmj.com/content/74/11/1847,"Li P., Lei Q., Yu X., Shen Y., Chen Y., Hou C., Hu B., Cui Y., Liu Z., Qin Y., Liu H., Lin D., Xu Y. , Wu D.",Commensal <i>Bacteroides</i> T6SS alleviate GI-aGVHD via mediating gut microbiota composition and bile acids metabolism,Gut,2025,"BACTERIAL INTERACTIONS, BILE ACID METABOLISM, GASTROINTESTINAL TRACT, INTESTINAL MICROBIOLOGY",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Acute graft vs. host disease,EFO:0004599,Phosphate-Buffered Saline (PBS) control group,Bacteroides fragilis Wild Type (WT),Bacteroides fragilis Wild Type-treated aGVHD(acute graft vs. host diesese) mice,3,3,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Online Supplemental Figure 4B,11 November 2025,Deborah-Fabusuyi,"Deborah-Fabusuyi,Tosin","Relative abundance of inflammatory bacteria in mice treated with Phosphate-Buffered Saline (PBS control) compared to wild-type strain, 14 days post-allogeneic bone marrow transplantation.",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,1783272|1239|186801|186802|216572|1263,Complete,KateRasheed
bsdb:40441865/3/2,40441865,"laboratory experiment,prospective cohort",40441865,10.1136/gutjnl-2024-334565,https://gut.bmj.com/content/74/11/1847,"Li P., Lei Q., Yu X., Shen Y., Chen Y., Hou C., Hu B., Cui Y., Liu Z., Qin Y., Liu H., Lin D., Xu Y. , Wu D.",Commensal <i>Bacteroides</i> T6SS alleviate GI-aGVHD via mediating gut microbiota composition and bile acids metabolism,Gut,2025,"BACTERIAL INTERACTIONS, BILE ACID METABOLISM, GASTROINTESTINAL TRACT, INTESTINAL MICROBIOLOGY",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Acute graft vs. host disease,EFO:0004599,Phosphate-Buffered Saline (PBS) control group,Bacteroides fragilis Wild Type (WT),Bacteroides fragilis Wild Type-treated aGVHD(acute graft vs. host diesese) mice,3,3,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Online Supplemental Figure 4A,11 November 2025,Deborah-Fabusuyi,"Deborah-Fabusuyi,Tosin","Relative abundance of inflammatory bacteria in mice treated with Phosphate-Buffered Saline (PBS control) compared to wild-type strain, 14 days post-allogeneic bone marrow transplantation.",increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,1783272|1239|186801|3085636|186803|1506553,Complete,KateRasheed
bsdb:40441865/4/1,40441865,"laboratory experiment,prospective cohort",40441865,10.1136/gutjnl-2024-334565,https://gut.bmj.com/content/74/11/1847,"Li P., Lei Q., Yu X., Shen Y., Chen Y., Hou C., Hu B., Cui Y., Liu Z., Qin Y., Liu H., Lin D., Xu Y. , Wu D.",Commensal <i>Bacteroides</i> T6SS alleviate GI-aGVHD via mediating gut microbiota composition and bile acids metabolism,Gut,2025,"BACTERIAL INTERACTIONS, BILE ACID METABOLISM, GASTROINTESTINAL TRACT, INTESTINAL MICROBIOLOGY",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Acute graft vs. host disease,EFO:0004599,Non-acute graft-versus-host disease patients (non-aGVHD group),Gastrointestinal acute graft-versus-host disease patients (GI-aGVHD group),Patients with Gastrointestinal acute graft-versus-host disease at 4-6 weeks post-hematopoietic stem cell transplantation (HSCT),47,24,NA,16S,34,NA,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,"Fig 1I, Online supplemental Figure 1C",15 November 2025,Deborah-Fabusuyi,"Deborah-Fabusuyi,Tosin",Dot plot that shows the fecal microbial taxa significantly depleted in GI-aGVHD patients compared to non-aGVHD controls at 4-6 weeks post-hematopoietic stem cell transplantation (HSCT),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|841,Complete,KateRasheed
bsdb:40441865/4/2,40441865,"laboratory experiment,prospective cohort",40441865,10.1136/gutjnl-2024-334565,https://gut.bmj.com/content/74/11/1847,"Li P., Lei Q., Yu X., Shen Y., Chen Y., Hou C., Hu B., Cui Y., Liu Z., Qin Y., Liu H., Lin D., Xu Y. , Wu D.",Commensal <i>Bacteroides</i> T6SS alleviate GI-aGVHD via mediating gut microbiota composition and bile acids metabolism,Gut,2025,"BACTERIAL INTERACTIONS, BILE ACID METABOLISM, GASTROINTESTINAL TRACT, INTESTINAL MICROBIOLOGY",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Acute graft vs. host disease,EFO:0004599,Non-acute graft-versus-host disease patients (non-aGVHD group),Gastrointestinal acute graft-versus-host disease patients (GI-aGVHD group),Patients with Gastrointestinal acute graft-versus-host disease at 4-6 weeks post-hematopoietic stem cell transplantation (HSCT),47,24,NA,16S,34,NA,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Online supplemental Figure 1C,14 January 2026,Tosin,Tosin,Dot plot that shows the fecal microbial taxa significantly depleted in GI-aGVHD patients compared to non-aGVHD controls at 4-6 weeks post-hematopoietic stem cell transplantation (HSCT),increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,1783272|1239|91061|186826|81852|1350,Complete,KateRasheed
bsdb:40441865/5/1,40441865,"laboratory experiment,prospective cohort",40441865,10.1136/gutjnl-2024-334565,https://gut.bmj.com/content/74/11/1847,"Li P., Lei Q., Yu X., Shen Y., Chen Y., Hou C., Hu B., Cui Y., Liu Z., Qin Y., Liu H., Lin D., Xu Y. , Wu D.",Commensal <i>Bacteroides</i> T6SS alleviate GI-aGVHD via mediating gut microbiota composition and bile acids metabolism,Gut,2025,"BACTERIAL INTERACTIONS, BILE ACID METABOLISM, GASTROINTESTINAL TRACT, INTESTINAL MICROBIOLOGY",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Acute graft vs. host disease,EFO:0004599,Bacteroides fragilis Wild Type (WT),Bacteroides fragilis T6SS-deficient mutant (ΔT6SS),Bacteroides fragilis T6SS-deficient mutant (ΔT6SS) treated mice in aGVHD model,3,3,NA,16S,34,Illumina,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Online Supplemental Figure 4A,14 January 2026,Tosin,Tosin,"Relative abundance of inflammatory bacteria in mice treated with Bacteroides fragilis T6SS-deficient mutant (ΔT6SS) compared to wild-type strain (WT), 14 days post-allogeneic bone marrow transplantation.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Robinsoniella",1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803|588605,Complete,KateRasheed
bsdb:40460079/2/1,40460079,"cross-sectional observational, not case-control",40460079,10.1371/journal.pone.0320698,NA,"Mutoni J.D., Van Hul M., Uwimana A., Petitfils C., Wong G.C., Puel A., Everard A., Alexiou H., Mutesa L., Coutelier J.P., Rujeni N. , Cani P.D.",Gut microbiota composition differences are associated with geographic location and age in malaria-endemic regions of Rwanda,PloS one,2025,NA,Experiment 2,Rwanda,Homo sapiens,Feces,UBERON:0001988,Environmental factor,EFO:0000469,Western Province,Eastern Province,Participants from the Eastern province of Rwanda,50,73,2 weeks,16S,4,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 2B,5 September 2025,Martha KJ,"Martha KJ,Tosin","Differentially abundant taxa between the Western and the Eastern provinces at phylum, family and genus levels",increased,",k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Pseudomonadati|p__Verrucomicrobiota",;3379134|1224|28216|80840|995019;1783272|1239|186801|3085636|186803|1506577;3379134|74201,Complete,NA
bsdb:40460079/2/2,40460079,"cross-sectional observational, not case-control",40460079,10.1371/journal.pone.0320698,NA,"Mutoni J.D., Van Hul M., Uwimana A., Petitfils C., Wong G.C., Puel A., Everard A., Alexiou H., Mutesa L., Coutelier J.P., Rujeni N. , Cani P.D.",Gut microbiota composition differences are associated with geographic location and age in malaria-endemic regions of Rwanda,PloS one,2025,NA,Experiment 2,Rwanda,Homo sapiens,Feces,UBERON:0001988,Environmental factor,EFO:0000469,Western Province,Eastern Province,Participants from the Eastern province of Rwanda,50,73,2 weeks,16S,4,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 2B,5 September 2025,Martha KJ,"Martha KJ,Tosin",Differentially abundant taxa between the Western and the Eastern provinces at phylum and family levels,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",1783272|1239;1783272|201174|84998|84999|84107;1783272|1239|526524|526525|128827,Complete,NA
bsdb:40460079/3/1,40460079,"cross-sectional observational, not case-control",40460079,10.1371/journal.pone.0320698,NA,"Mutoni J.D., Van Hul M., Uwimana A., Petitfils C., Wong G.C., Puel A., Everard A., Alexiou H., Mutesa L., Coutelier J.P., Rujeni N. , Cani P.D.",Gut microbiota composition differences are associated with geographic location and age in malaria-endemic regions of Rwanda,PloS one,2025,NA,Experiment 3,Rwanda,Homo sapiens,Feces,UBERON:0001988,Environmental factor,EFO:0000469,Western Province,Southern Province,Participants from the Southern province of Rwanda,50,46,2 weeks,16S,4,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 2B,5 September 2025,Martha KJ,"Martha KJ,Tosin",Differentially abundant taxa between the Western and the southern provinces at family level,increased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,3379134|1224|28216|80840|995019,Complete,NA
bsdb:40460079/4/1,40460079,"cross-sectional observational, not case-control",40460079,10.1371/journal.pone.0320698,NA,"Mutoni J.D., Van Hul M., Uwimana A., Petitfils C., Wong G.C., Puel A., Everard A., Alexiou H., Mutesa L., Coutelier J.P., Rujeni N. , Cani P.D.",Gut microbiota composition differences are associated with geographic location and age in malaria-endemic regions of Rwanda,PloS one,2025,NA,Experiment 4,Rwanda,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Preschool children,Adults,Participants aged 15 years and above,NA,NA,2 weeks,16S,4,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,unchanged,unchanged,increased,NA,NA,increased,Signature 1,Figure 4,5 September 2025,Martha KJ,"Martha KJ,Tosin","Differentially abundant taxa between adults and preschool children at phylum, family and genus levels",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae,k__Methanobacteriati|p__Methanobacteriota,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Spirochaetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Pseudomonadati|p__Thermodesulfobacteriota,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",1783272|1239|186801|3082720|543314;1783272|1239|186801|3082768|990719;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;1783272|1239|186801|3085636;3366610|28890|183925|2158|2159;3366610|28890;3366610|28890|183925|2158|2159|2172;1783272|1239|186801|186802|216572;3379134|1224|28216|80840|75682;1783272|1239|186801|186802|186807;3379134|976|200643|171549|171550;3379134|203691;3379134|976|200643|171549|2005525;3379134|200940;3379134|74201;3379134|256845|1313211|278082|255528;1783272|1239|526524|526525|128827|331630;1783272|1239|186801|3085636|186803|297314,Complete,NA
bsdb:40460079/4/2,40460079,"cross-sectional observational, not case-control",40460079,10.1371/journal.pone.0320698,NA,"Mutoni J.D., Van Hul M., Uwimana A., Petitfils C., Wong G.C., Puel A., Everard A., Alexiou H., Mutesa L., Coutelier J.P., Rujeni N. , Cani P.D.",Gut microbiota composition differences are associated with geographic location and age in malaria-endemic regions of Rwanda,PloS one,2025,NA,Experiment 4,Rwanda,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Preschool children,Adults,Participants aged 15 years and above,NA,NA,2 weeks,16S,4,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,unchanged,unchanged,increased,NA,NA,increased,Signature 2,Figure 4,5 September 2025,Martha KJ,"Martha KJ,Tosin","Differentially abundant taxa between adults and preschool children at phylum, family and genus levels",decreased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Campylobacterota",3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294;3379134|29547,Complete,NA
bsdb:40460079/5/1,40460079,"cross-sectional observational, not case-control",40460079,10.1371/journal.pone.0320698,NA,"Mutoni J.D., Van Hul M., Uwimana A., Petitfils C., Wong G.C., Puel A., Everard A., Alexiou H., Mutesa L., Coutelier J.P., Rujeni N. , Cani P.D.",Gut microbiota composition differences are associated with geographic location and age in malaria-endemic regions of Rwanda,PloS one,2025,NA,Experiment 5,Rwanda,Homo sapiens,Feces,UBERON:0001988,Age,EFO:0000246,Preschool children,School children,Children aged 5-14 years,NA,NA,2 weeks,16S,4,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,unchanged,unchanged,increased,NA,NA,increased,Signature 1,Figure 4,5 September 2025,Martha KJ,"Martha KJ,Tosin","Differentially abundant taxa between adults and school children at phylum, family and genus levels",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Moryella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",1783272|1239|186801|3085636|186803|437755;1783272|1239|186801|3085636|186803|297314,Complete,NA
bsdb:40461059/1/1,40461059,"laboratory experiment,prospective cohort",40461059,https://doi.org/10.1136/gutjnl-2024-334634,NA,"Laiola M., Koppe L., Larabi A., Thirion F., Lange C., Quinquis B., David A., Le Chatelier E., Benoit B., Sequino G., Chanon S., Vieille-Marchiset A., Herpe Y.E., Alvarez J.C., Glorieux G., Krukowski H., Huys G.R., Raes J., Fouque D., Massy Z.A., Ehrlich S.D., Stengel B. , Wagner S.",Toxic microbiome and progression of chronic kidney disease: insights from a longitudinal CKD-Microbiome Study,Gut,2025,"EPIDEMIOLOGY, MICROBIOME",Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Healthy controls,Chronic Kidney disease (CKD) patients,Individuals diagnosed with non‑dialysis chronic kidney disease,78,78,3 months,WMS,NA,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,diabetes mellitus,proton-pump inhibitor,sex",NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 2D and Supplemental Table 2,31 October 2025,Shaukat,"Shaukat,Firdaws",Significant different bacterial species between Healthy controls (HCs) and patients with Chronic kidney disease (CKD),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. CAG:144,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas faecihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:307,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:349,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:7,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:38,k__Bacillati|p__Bacillota|g__Negativibacillus|s__Negativibacillus massiliensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|s__Victivallales bacterium CCUG 44730,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis|s__Victivallis vadensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] sulci,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum|s__Azospirillum sp. 51_20,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Lawsonibacter",3379134|976|200643|171549|815|816|291644;3379134|976|200643|171549|815|816|1262736;3379134|976|200643|171549|1853231|574697|1472416;1783272|1239|186801|186802|31979|1485|1262795;1783272|1239|186801|186802|31979|1485|1262797;1783272|1239|186801|186802|31979|1485|1262832;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|186801|3085636|186803|2719313|358743;1783272|1239|186801|186802|186806|1730|1262889;1783272|1239|1980693|1871035;3379134|1224|28216|80840|995019|40544|40545;3379134|256845|1313211|278082|2094242;3379134|256845|1313211|278082|255528|172900|172901;1783272|1239|186801|3082720|543314|143393;1783272|1239|186801|3085636|186803|2719313;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|186802|216572;3379134|1224|28211|204441|2829815|191|1896972;1783272|1239|186801|186802|216572|2172004,Complete,KateRasheed
bsdb:40461059/1/2,40461059,"laboratory experiment,prospective cohort",40461059,https://doi.org/10.1136/gutjnl-2024-334634,NA,"Laiola M., Koppe L., Larabi A., Thirion F., Lange C., Quinquis B., David A., Le Chatelier E., Benoit B., Sequino G., Chanon S., Vieille-Marchiset A., Herpe Y.E., Alvarez J.C., Glorieux G., Krukowski H., Huys G.R., Raes J., Fouque D., Massy Z.A., Ehrlich S.D., Stengel B. , Wagner S.",Toxic microbiome and progression of chronic kidney disease: insights from a longitudinal CKD-Microbiome Study,Gut,2025,"EPIDEMIOLOGY, MICROBIOME",Experiment 1,France,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Healthy controls,Chronic Kidney disease (CKD) patients,Individuals diagnosed with non‑dialysis chronic kidney disease,78,78,3 months,WMS,NA,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,diabetes mellitus,proton-pump inhibitor,sex",NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Figure 2D and Supplemental Table 2,31 October 2025,Shaukat,"Shaukat,Firdaws",Significant different bacterial species between Healthy controls (HCs) and patients with Chronic kidney disease (CKD),decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio sp. CAG:318,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium celatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:221,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:451,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:192,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:176_63_11,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:321,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanosphaera|s__Methanosphaera stadtmanae,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus|s__Monoglobus pectinilyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter",1783272|201174|1760|2037|2049|1654|544580;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|830|1262761;1783272|1239|186801|186802|31979|1485|36834;1783272|1239|186801|186802|31979|1485|1262780;1783272|1239|186801|186802|31979|1485|1262809;1783272|201174|1760|85007|1653|1716|61592;1783272|1239|186801|186802|186806|1730|1262883;1783272|1239|1897031;1783272|1239|1263018;1783272|1239|186801|3082720|186804|1505657|261299;3366610|28890|183925|2158|2159|2316|2317;1783272|1239|186801|3085656|3085657|2039302|1981510;1783272|1239|186801|3082720|186804|1501226|1776391;1783272|1239|186801|3082720|186804|1870884;1783272|1239|186801|3082720|186804|1505657,Complete,KateRasheed
bsdb:40461059/3/1,40461059,"laboratory experiment,prospective cohort",40461059,https://doi.org/10.1136/gutjnl-2024-334634,NA,"Laiola M., Koppe L., Larabi A., Thirion F., Lange C., Quinquis B., David A., Le Chatelier E., Benoit B., Sequino G., Chanon S., Vieille-Marchiset A., Herpe Y.E., Alvarez J.C., Glorieux G., Krukowski H., Huys G.R., Raes J., Fouque D., Massy Z.A., Ehrlich S.D., Stengel B. , Wagner S.",Toxic microbiome and progression of chronic kidney disease: insights from a longitudinal CKD-Microbiome Study,Gut,2025,"EPIDEMIOLOGY, MICROBIOME",Experiment 3,France,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Moderate Chronic Kidney Disease (CKD) patients,Severe Chronic Kidney disease (CKD) patients,"Patients with severe chronic kidney disease, categorized by an estimated glomerular filtration rate (eGFR) ≥ 30 mL/min/1.73 m².",130,110,3 months,WMS,NA,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 7 and Figure 3A,12 January 2026,Firdaws,Firdaws,Significantly enriched species in severe chronic kidney disease versus moderate chronic kidney disease (Severe CKD vs Moderate CKD).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. CAG:268,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella minuta,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium pacaense,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio fairfieldensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:115,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:341,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas massiliensis (ex Liu et al. 2021),k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Evtepia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Massilioclostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Merdibacter,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Mailhella",3379134|976|200643|171549|171550|239759|1262693;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|338188;1783272|1239|186801|3082768|990719|990721|626937;1783272|1239|186801|186802|31979|1485|1917870;3379134|200940|3031449|213115|194924|872|44742;1783272|1239|186801|186802|186806|1730|1262878;1783272|1239|1263019;1783272|1239|526524|526525|128827|61170|1468449;1783272|1239|186801|186802|1392389|1297617;1783272|1239|186801|186802|1392389|3062493;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|186802|2211178;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|3085636;1783272|1239|186801|186802|31979|1935927;1783272|1239|526524|526525|128827|1935200;3379134|200940|3031449|213115|194924|1981028,Complete,KateRasheed
bsdb:40461059/3/2,40461059,"laboratory experiment,prospective cohort",40461059,https://doi.org/10.1136/gutjnl-2024-334634,NA,"Laiola M., Koppe L., Larabi A., Thirion F., Lange C., Quinquis B., David A., Le Chatelier E., Benoit B., Sequino G., Chanon S., Vieille-Marchiset A., Herpe Y.E., Alvarez J.C., Glorieux G., Krukowski H., Huys G.R., Raes J., Fouque D., Massy Z.A., Ehrlich S.D., Stengel B. , Wagner S.",Toxic microbiome and progression of chronic kidney disease: insights from a longitudinal CKD-Microbiome Study,Gut,2025,"EPIDEMIOLOGY, MICROBIOME",Experiment 3,France,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Moderate Chronic Kidney Disease (CKD) patients,Severe Chronic Kidney disease (CKD) patients,"Patients with severe chronic kidney disease, categorized by an estimated glomerular filtration rate (eGFR) ≥ 30 mL/min/1.73 m².",130,110,3 months,WMS,NA,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table 7 and Figure 3A,12 January 2026,Firdaws,Firdaws,Significantly enriched species in severe chronic kidney disease versus moderate chronic kidney disease (Severe CKD vs Moderate CKD).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. CAG:237,k__Bacillati|p__Bacillota|s__Firmicutes bacterium CAG:238,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UBA5891,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Frisingicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|3085636|186803|572511|1262755;1783272|1239|1263011;1783272|1239|186801|186802|216572|1952408;3379134|1224|28216|80840|995019|40544|40545;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843489|31977|29465|29466;95818|2093818|2093825|2171986;1783272|1239|186801|3085636|186803|2719313;1783272|1239|186801|3085636|186803|1918511;1783272|1239|186801|186802|204475;1783272|1239|186801|186802|216572,Complete,KateRasheed
bsdb:40461059/4/1,40461059,"laboratory experiment,prospective cohort",40461059,https://doi.org/10.1136/gutjnl-2024-334634,NA,"Laiola M., Koppe L., Larabi A., Thirion F., Lange C., Quinquis B., David A., Le Chatelier E., Benoit B., Sequino G., Chanon S., Vieille-Marchiset A., Herpe Y.E., Alvarez J.C., Glorieux G., Krukowski H., Huys G.R., Raes J., Fouque D., Massy Z.A., Ehrlich S.D., Stengel B. , Wagner S.",Toxic microbiome and progression of chronic kidney disease: insights from a longitudinal CKD-Microbiome Study,Gut,2025,"EPIDEMIOLOGY, MICROBIOME",Experiment 4,France,Mus musculus,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Healthy Volunteers stool-recipient mice: FMT-HV group,Chronic Kidney Disease stool-recipient mice: FMT-CKD group,Faecal microbiota transplantation (FMT) using stool samples from patients with Chronic Kidney Disease (CKD) into antibiotic-treated CKD mouse models.,6,8,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 11,12 January 2026,Firdaws,Firdaws,Significantly enriched species in chronic kidney disease (CKD) mice after fecal microbiota transplantation (FMT) from CKD patients or healthy volunteers (HV) .,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,3379134|976|200643|171549|171552|2974251|165179,Complete,KateRasheed
bsdb:40461059/4/2,40461059,"laboratory experiment,prospective cohort",40461059,https://doi.org/10.1136/gutjnl-2024-334634,NA,"Laiola M., Koppe L., Larabi A., Thirion F., Lange C., Quinquis B., David A., Le Chatelier E., Benoit B., Sequino G., Chanon S., Vieille-Marchiset A., Herpe Y.E., Alvarez J.C., Glorieux G., Krukowski H., Huys G.R., Raes J., Fouque D., Massy Z.A., Ehrlich S.D., Stengel B. , Wagner S.",Toxic microbiome and progression of chronic kidney disease: insights from a longitudinal CKD-Microbiome Study,Gut,2025,"EPIDEMIOLOGY, MICROBIOME",Experiment 4,France,Mus musculus,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Healthy Volunteers stool-recipient mice: FMT-HV group,Chronic Kidney Disease stool-recipient mice: FMT-CKD group,Faecal microbiota transplantation (FMT) using stool samples from patients with Chronic Kidney Disease (CKD) into antibiotic-treated CKD mouse models.,6,8,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table 11,12 January 2026,Firdaws,Firdaws,Significantly enriched species in chronic kidney disease (CKD) mice after fecal microbiota transplantation (FMT) from CKD patients or healthy volunteers (HV).,decreased,NA,NA,Complete,KateRasheed
bsdb:40461059/5/1,40461059,"laboratory experiment,prospective cohort",40461059,https://doi.org/10.1136/gutjnl-2024-334634,NA,"Laiola M., Koppe L., Larabi A., Thirion F., Lange C., Quinquis B., David A., Le Chatelier E., Benoit B., Sequino G., Chanon S., Vieille-Marchiset A., Herpe Y.E., Alvarez J.C., Glorieux G., Krukowski H., Huys G.R., Raes J., Fouque D., Massy Z.A., Ehrlich S.D., Stengel B. , Wagner S.",Toxic microbiome and progression of chronic kidney disease: insights from a longitudinal CKD-Microbiome Study,Gut,2025,"EPIDEMIOLOGY, MICROBIOME",Experiment 5,France,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Slow Chronic Kidney Disease (CKD) Progressors,Fast Chronic Kidney Disease (CKD) Progressors,Fast Chronic Kidney Disease (CKD) progressors were defined as a sustained 30% decline in estimated glomerular filtration rate (eGFR) over the 2.8-year follow-up or progression to Kidney Failure Renal Transplantation (KFRT) or death.,172,68,3 months,WMS,NA,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5B and Supplemental Table 12,12 January 2026,Firdaws,Firdaws,Absolute values of Cliff’s delta (CD) values of microbiome linked to CKD progression identified as significantly different between fast and slow progressors,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Cibiobacter|s__Candidatus Cibiobacter qucibialis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 57_20,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides johnsonii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Mailhella|s__Candidatus Mailhella excrementigallinarum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger qucibialis,k__Pseudomonadati|p__Verrucomicrobiota|c__Opitutia|o__Opitutales|f__Intestinicryptomonadaceae|g__Candidatus Merdousia|s__Candidatus Merdousia gallistercoris,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Bianqueaceae|g__Bianquea|s__Bianquea renquensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Duodenibacillus|s__Candidatus Duodenibacillus intestinigallinarum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Scatomorpha|s__Candidatus Scatomorpha intestinavium",3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|815|816|338188;1783272|1239|186801|186802|2527773|2500537;1783272|1239|186801|186802|216572|459786|1897011;3379134|976|200643|171549|2005525|375288|387661;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|3085636;3379134|200940|3031449|213115|194924|1981028|2838656;1783272|1239|186801|186802|204475|2997294;3379134|74201|414999|415000|3242731|2840660|2840874;1783272|1239|186801|186802|2944142|2944146|2763661;3379134|1224|28216|80840|995019|1980697|2838548;3379134|1224|1236|91347|543|544|545;1783272|1239|186801|186802|2840598|2840922,Complete,KateRasheed
bsdb:40461059/5/2,40461059,"laboratory experiment,prospective cohort",40461059,https://doi.org/10.1136/gutjnl-2024-334634,NA,"Laiola M., Koppe L., Larabi A., Thirion F., Lange C., Quinquis B., David A., Le Chatelier E., Benoit B., Sequino G., Chanon S., Vieille-Marchiset A., Herpe Y.E., Alvarez J.C., Glorieux G., Krukowski H., Huys G.R., Raes J., Fouque D., Massy Z.A., Ehrlich S.D., Stengel B. , Wagner S.",Toxic microbiome and progression of chronic kidney disease: insights from a longitudinal CKD-Microbiome Study,Gut,2025,"EPIDEMIOLOGY, MICROBIOME",Experiment 5,France,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Slow Chronic Kidney Disease (CKD) Progressors,Fast Chronic Kidney Disease (CKD) Progressors,Fast Chronic Kidney Disease (CKD) progressors were defined as a sustained 30% decline in estimated glomerular filtration rate (eGFR) over the 2.8-year follow-up or progression to Kidney Failure Renal Transplantation (KFRT) or death.,172,68,3 months,WMS,NA,Ion Torrent,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5B and Supplemental Table 12,12 January 2026,Firdaws,Firdaws,Absolute values of Cliff’s delta (CD) values of microbiome linked to CKD progression identified as significantly different between fast and slow progressors,decreased,NA,NA,Complete,KateRasheed
bsdb:40461059/6/1,40461059,"laboratory experiment,prospective cohort",40461059,https://doi.org/10.1136/gutjnl-2024-334634,NA,"Laiola M., Koppe L., Larabi A., Thirion F., Lange C., Quinquis B., David A., Le Chatelier E., Benoit B., Sequino G., Chanon S., Vieille-Marchiset A., Herpe Y.E., Alvarez J.C., Glorieux G., Krukowski H., Huys G.R., Raes J., Fouque D., Massy Z.A., Ehrlich S.D., Stengel B. , Wagner S.",Toxic microbiome and progression of chronic kidney disease: insights from a longitudinal CKD-Microbiome Study,Gut,2025,"EPIDEMIOLOGY, MICROBIOME",Experiment 6,France,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Slow Chronic Kidney Disease (CKD)  Progressors,Fast Chronic Kidney Disease (CKD) Progressors,Fast Chronic Kidney Disease (CKD)  progressors were defined as a sustained 30% decline in estimated glomerular filtration rate (eGFR) over the 2.8-year follow-up or progression to Kidney Failure Renal Transplantation (KFRT) or death.,172,68,3 months,WMS,NA,Ion Torrent,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 13,12 January 2026,Firdaws,Firdaws,"Microbiome Multivariable Association with Linear Models (MaAsLin) determining significant associations between gut microbiome features and Fast Chronic Kidney Disease (CKD) Progression, adjusting for estimated glomerular filtration rate (eGFR) and albuminuria.",increased,NA,NA,Complete,KateRasheed
bsdb:40461820/2/1,40461820,meta-analysis,40461820,10.1038/s41591-025-03693-9,NA,"Piccinno G., Thompson K.N., Manghi P., Ghazi A.R., Thomas A.M., Blanco-Míguez A., Asnicar F., Mladenovic K., Pinto F., Armanini F., Punčochář M., Piperni E., Heidrich V., Fackelmann G., Ferrero G., Tarallo S., Nguyen L.H., Yan Y., Keles N.A., Tuna B.G., Vymetalkova V., Trompetto M., Liska V., Hucl T., Vodicka P., Bencsiková B., Čarnogurská M., Popovici V., Marmorino F., Cremolini C., Pardini B., Cordero F., Song M., Chan A.T., Derosa L., Zitvogel L., Huttenhower C., Naccarati A., Budinska E. , Segata N.","Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer",Nature medicine,2025,NA,Experiment 2,"Austria,China,Czechia,France,Germany,India,Italy,Japan,Spain,Turkey,United States of America",Homo sapiens,Feces,UBERON:0001988,Colorectal Adenosquamous Carcinoma,EFO:1000190,Colorectal cancer (CRC) Stage 0-II,Colorectal cancer (CRC) Stage III-IV,Patients with colorectal cancer (CRC) at stage III-IV,NA,NA,NA,WMS,NA,Illumina,arcsine square-root,Meta-Analysis,0.01,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3B, Supplementary Table 6",22 November 2025,Tosin,Tosin,"Significant species (Hedges’ model effect size P < 0.01, none presented q < 0.1) found in association with Stages 0–II versus stages III–IV in meta-analysis considering the following comparisons (all presented I2 < 50%)",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Luoshenia|s__Luoshenia tenuis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia exigua,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|186801|3082768|990719|2944144|2763654;1783272|201174|84998|1643822|1643826|84108|84109;1783272|1239|186801|186802;1783272|1239|909932|1843489|31977|39948|39950;1783272|1239|91061|186826|1300|1301|1309;1783272|1239|91061|186826|1300|1301,Complete,NA
bsdb:40461820/2/2,40461820,meta-analysis,40461820,10.1038/s41591-025-03693-9,NA,"Piccinno G., Thompson K.N., Manghi P., Ghazi A.R., Thomas A.M., Blanco-Míguez A., Asnicar F., Mladenovic K., Pinto F., Armanini F., Punčochář M., Piperni E., Heidrich V., Fackelmann G., Ferrero G., Tarallo S., Nguyen L.H., Yan Y., Keles N.A., Tuna B.G., Vymetalkova V., Trompetto M., Liska V., Hucl T., Vodicka P., Bencsiková B., Čarnogurská M., Popovici V., Marmorino F., Cremolini C., Pardini B., Cordero F., Song M., Chan A.T., Derosa L., Zitvogel L., Huttenhower C., Naccarati A., Budinska E. , Segata N.","Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer",Nature medicine,2025,NA,Experiment 2,"Austria,China,Czechia,France,Germany,India,Italy,Japan,Spain,Turkey,United States of America",Homo sapiens,Feces,UBERON:0001988,Colorectal Adenosquamous Carcinoma,EFO:1000190,Colorectal cancer (CRC) Stage 0-II,Colorectal cancer (CRC) Stage III-IV,Patients with colorectal cancer (CRC) at stage III-IV,NA,NA,NA,WMS,NA,Illumina,arcsine square-root,Meta-Analysis,0.01,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3B, Supplementary Table 6",22 November 2025,Tosin,Tosin,"Significant species (Hedges’ model effect size P < 0.01, none presented q < 0.1) found in association with Stages 0–II versus stages III–IV in meta-analysis considering the following comparisons (all presented I2 < 50%)",decreased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,1783272|201174|84998|1643822|1643826,Complete,NA
bsdb:40461820/3/1,40461820,meta-analysis,40461820,10.1038/s41591-025-03693-9,NA,"Piccinno G., Thompson K.N., Manghi P., Ghazi A.R., Thomas A.M., Blanco-Míguez A., Asnicar F., Mladenovic K., Pinto F., Armanini F., Punčochář M., Piperni E., Heidrich V., Fackelmann G., Ferrero G., Tarallo S., Nguyen L.H., Yan Y., Keles N.A., Tuna B.G., Vymetalkova V., Trompetto M., Liska V., Hucl T., Vodicka P., Bencsiková B., Čarnogurská M., Popovici V., Marmorino F., Cremolini C., Pardini B., Cordero F., Song M., Chan A.T., Derosa L., Zitvogel L., Huttenhower C., Naccarati A., Budinska E. , Segata N.","Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer",Nature medicine,2025,NA,Experiment 3,"Austria,China,Czechia,France,Germany,India,Italy,Japan,Spain,Turkey,United States of America",Homo sapiens,Feces,UBERON:0001988,Colorectal Adenosquamous Carcinoma,NA,Colorectal cancer (CRC) Stage 0-III,Colorectal cancer (CRC) Stage IV,Patients with colorectal cancer (CRC) at stage IV,NA,NA,NA,WMS,NA,Illumina,arcsine square-root,Meta-Analysis,0.01,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3C, Supplementary Table 6",22 November 2025,Tosin,Tosin,"Significant species (Hedges’ model effect size P < 0.01, none presented q < 0.1) found in association with Stages 0–III versus stages IV in meta-analysis considering the following comparisons (all presented I2 < 50%)",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus",1783272|1239|186801|3085636|186803|1649459|154046;1783272|1239|186801|3085636|186803|2719313|333367;1783272|1239|186801|2044939;3379134|976|200643|171549|171550|239759|626932,Complete,NA
bsdb:40461820/3/2,40461820,meta-analysis,40461820,10.1038/s41591-025-03693-9,NA,"Piccinno G., Thompson K.N., Manghi P., Ghazi A.R., Thomas A.M., Blanco-Míguez A., Asnicar F., Mladenovic K., Pinto F., Armanini F., Punčochář M., Piperni E., Heidrich V., Fackelmann G., Ferrero G., Tarallo S., Nguyen L.H., Yan Y., Keles N.A., Tuna B.G., Vymetalkova V., Trompetto M., Liska V., Hucl T., Vodicka P., Bencsiková B., Čarnogurská M., Popovici V., Marmorino F., Cremolini C., Pardini B., Cordero F., Song M., Chan A.T., Derosa L., Zitvogel L., Huttenhower C., Naccarati A., Budinska E. , Segata N.","Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer",Nature medicine,2025,NA,Experiment 3,"Austria,China,Czechia,France,Germany,India,Italy,Japan,Spain,Turkey,United States of America",Homo sapiens,Feces,UBERON:0001988,Colorectal Adenosquamous Carcinoma,NA,Colorectal cancer (CRC) Stage 0-III,Colorectal cancer (CRC) Stage IV,Patients with colorectal cancer (CRC) at stage IV,NA,NA,NA,WMS,NA,Illumina,arcsine square-root,Meta-Analysis,0.01,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3C, Supplementary Table 6",22 November 2025,Tosin,Tosin,"Significant species (Hedges’ model effect size P < 0.01, none presented q < 0.1) found in association with Stages 0–III versus stages IV in meta-analysis considering the following comparisons (all presented I2 < 50%)",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Faecalibacillus|s__Faecalibacillus intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens",1783272|1239|186801|3085636|186803|1898203;1783272|1239|526524|526525|2810280|2678885|1982626;1783272|1239|186801|186802|216572|216851|853;1783272|201174|84998|1643822|1643826|447020|446660,Complete,NA
bsdb:40461820/4/1,40461820,meta-analysis,40461820,10.1038/s41591-025-03693-9,NA,"Piccinno G., Thompson K.N., Manghi P., Ghazi A.R., Thomas A.M., Blanco-Míguez A., Asnicar F., Mladenovic K., Pinto F., Armanini F., Punčochář M., Piperni E., Heidrich V., Fackelmann G., Ferrero G., Tarallo S., Nguyen L.H., Yan Y., Keles N.A., Tuna B.G., Vymetalkova V., Trompetto M., Liska V., Hucl T., Vodicka P., Bencsiková B., Čarnogurská M., Popovici V., Marmorino F., Cremolini C., Pardini B., Cordero F., Song M., Chan A.T., Derosa L., Zitvogel L., Huttenhower C., Naccarati A., Budinska E. , Segata N.","Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer",Nature medicine,2025,NA,Experiment 4,"Austria,China,Czechia,France,Germany,India,Italy,Japan,Spain,Turkey,United States of America",Homo sapiens,Feces,UBERON:0001988,Colorectal Adenosquamous Carcinoma,EFO:1000190,Right sided Colorectal cancer (Right CRC),Left sided Colorectal cancer (Left CRC),Colorectal cancer (CRC) in patients at the left side,NA,NA,NA,WMS,NA,Illumina,arcsine square-root,Meta-Analysis,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4E, Supplementary Table 6",22 November 2025,Tosin,Tosin,"SGBs (species-level genome bins) significantly associated (q < 0.1) either with right- or left-sided CRC (colorectal cancer). Meta-analysis Hedges’ g is indicated by a diamond, while the SMD (standardized mean difference) values corrected for age, sex and BMI (body mass index) are indicated by a star (blue if q < 0.1).",increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacillati|p__Bacillota|s__Bacillota bacterium,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Parachristensenella|s__Candidatus Parachristensenella avicola,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. Marseille-P3244,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Gehongia|s__Gehongia tenuis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia|s__Harryflintia acetispora,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Luoshenia|s__Luoshenia tenuis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D5,k__Bacillati|p__Bacillota|c__Clostridia",1783272|1239|1737404|1737405|1570339|165779|1287640;1783272|1239|1879010;1783272|1239|186801|2721113|2721140;1783272|1239|186801|2044939;1783272|1239|186801|186802|31979|1485|1871020;1783272|1239|526524|526525|128827|2049044;1783272|1239|186801|3082768|990719|2944147|2763655;1783272|1239|186801|186802|216572|1892380|1849041;1783272|1239|186801|186802|1392389|1297617;1783272|1239|186801|3082768|990719|2944144|2763654;1783272|1239|186801|186802|216572|2485925;1783272|1239|1737404|1737405|1570339|543311|33033;3379134|976|200643|171549|171551|836|28123;1783272|1239|186801|186802|216572|1520815;1783272|1239|186801,Complete,NA
bsdb:40461820/4/2,40461820,meta-analysis,40461820,10.1038/s41591-025-03693-9,NA,"Piccinno G., Thompson K.N., Manghi P., Ghazi A.R., Thomas A.M., Blanco-Míguez A., Asnicar F., Mladenovic K., Pinto F., Armanini F., Punčochář M., Piperni E., Heidrich V., Fackelmann G., Ferrero G., Tarallo S., Nguyen L.H., Yan Y., Keles N.A., Tuna B.G., Vymetalkova V., Trompetto M., Liska V., Hucl T., Vodicka P., Bencsiková B., Čarnogurská M., Popovici V., Marmorino F., Cremolini C., Pardini B., Cordero F., Song M., Chan A.T., Derosa L., Zitvogel L., Huttenhower C., Naccarati A., Budinska E. , Segata N.","Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer",Nature medicine,2025,NA,Experiment 4,"Austria,China,Czechia,France,Germany,India,Italy,Japan,Spain,Turkey,United States of America",Homo sapiens,Feces,UBERON:0001988,Colorectal Adenosquamous Carcinoma,EFO:1000190,Right sided Colorectal cancer (Right CRC),Left sided Colorectal cancer (Left CRC),Colorectal cancer (CRC) in patients at the left side,NA,NA,NA,WMS,NA,Illumina,arcsine square-root,Meta-Analysis,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 4E, Supplementary Table 6",22 November 2025,Tosin,Tosin,"SGBs (species-level genome bins) significantly associated (q < 0.1) either with right- or left-sided CRC (colorectal
cancer). Meta-analysis Hedges’ g is indicated by a diamond, while the SMD (standardized mean difference) values corrected for age, sex and BMI (body mass index) are indicated by a star (blue if q < 0.1).",decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister histaminiformans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AM22-11AC,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora amygdalina,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora celerecrescens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Trueperella|s__Trueperella pyogenes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula",1783272|1239|909932|1843489|31977|39948|209880;1783272|1239|186801|186802|31979|1485|2293024;1783272|1239|186801|3085636|186803|2719231|253257;1783272|1239|186801|3085636|186803|2719231|29354;1783272|1239|91061|186826|1300|1301|1318;1783272|201174|1760|2037|2049|1069494|1661;1783272|1239|909932|1843489|31977|29465|39777;1783272|1239|909932|1843489|31977|29465|29466,Complete,NA
bsdb:40491436/1/1,40491436,"cross-sectional observational, not case-control",40491436,10.3389/fcimb.2025.1565887,NA,"Li D., Zhang D.Y., Chen S.J., Lv Y.T., Huang S.M., Chen C., Zeng F., Chen R.X., Zhang X.D., Xiong J.X., Chen F.D., Jiang Y.H., Chen Z., Mo C.Y., Chen J.J., Zhu X.L., Zhang L.J. , Bai F.H.",Long-term alterations in gut microbiota following mild COVID-19 recovery: bacterial and fungal community shifts,Frontiers in cellular and infection microbiology,2025,"ROC curve analysis, bacterial-fungal co-occurrence network, fungal microbiota, gut microbiome, metagenomic sequencing, mild COVID-19, probiotics, random forest model",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,NC group (healthy individuals before COVID-19),C3M group (post-COVID-19 recovery group),participants who were three months post-COVID-19 recovery,51,27,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2G,11 January 2026,Ese,Ese,"Result of Linear Discriminant Analysis (LDA) effect size plot of bacterial species abundance differences between NC and C3M, analyzed using LEfSe and FDR correction (FDR-P < 0.05).",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia massiliensis (ex Liu et al. 2021),k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. AF19-10LB,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium KLE1615,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium fessum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp. AF36-15AT,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 2_1_46FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora amygdalina,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. AM23-20",1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|526524|526525|128827|2749846|31971;1783272|1239|186801|3085636|186803|572511|3062492;1783272|1239|186801|3085636|186803|572511|2292961;1783272|1239|186801|186802|1715004;1783272|1239|186801|186802|31979|1485|2126740;1783272|1239|186801|3085636|186803|189330|2292041;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|3085636|186803|742723;1783272|1239|186801|3085636|186803|2719231|253257;1783272|1239|186801|3085636|186803|841|2292066,Complete,NA
bsdb:40491436/1/2,40491436,"cross-sectional observational, not case-control",40491436,10.3389/fcimb.2025.1565887,NA,"Li D., Zhang D.Y., Chen S.J., Lv Y.T., Huang S.M., Chen C., Zeng F., Chen R.X., Zhang X.D., Xiong J.X., Chen F.D., Jiang Y.H., Chen Z., Mo C.Y., Chen J.J., Zhu X.L., Zhang L.J. , Bai F.H.",Long-term alterations in gut microbiota following mild COVID-19 recovery: bacterial and fungal community shifts,Frontiers in cellular and infection microbiology,2025,"ROC curve analysis, bacterial-fungal co-occurrence network, fungal microbiota, gut microbiome, metagenomic sequencing, mild COVID-19, probiotics, random forest model",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,NC group (healthy individuals before COVID-19),C3M group (post-COVID-19 recovery group),participants who were three months post-COVID-19 recovery,51,27,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2G,12 January 2026,Ese,Ese,"Result of Linear Discriminant Analysis (LDA) effect size plot of bacterial species abundance differences between NC and C3M, analyzed using LEfSe and FDR correction (FDR-P < 0.05).",decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora saccharolytica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sp. BL7",1783272|1239|909932|1843488|909930|904|187327;1783272|1239|909932|1843488|909930|904|1852375;1783272|1239|186801|3085636|186803|2569097|39488;3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|543|570|573;1783272|1239|186801|3085636|186803|2719231|84030;1783272|1239|909932|1843489|31977|906|1285585,Complete,NA
bsdb:40491436/2/1,40491436,"cross-sectional observational, not case-control",40491436,10.3389/fcimb.2025.1565887,NA,"Li D., Zhang D.Y., Chen S.J., Lv Y.T., Huang S.M., Chen C., Zeng F., Chen R.X., Zhang X.D., Xiong J.X., Chen F.D., Jiang Y.H., Chen Z., Mo C.Y., Chen J.J., Zhu X.L., Zhang L.J. , Bai F.H.",Long-term alterations in gut microbiota following mild COVID-19 recovery: bacterial and fungal community shifts,Frontiers in cellular and infection microbiology,2025,"ROC curve analysis, bacterial-fungal co-occurrence network, fungal microbiota, gut microbiome, metagenomic sequencing, mild COVID-19, probiotics, random forest model",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,NC group (healthy individuals before COVID-19),C6M group (post-COVID-19 recovery group),participants who were six months post-COVID-19 recovery,51,41,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2F,13 January 2026,Ese,Ese,"Result of Linear Discriminant Analysis (LDA) effect size plot of bacterial species abundance differences between NC and C6M, analyzed using LEfSe and FDR correction (FDR-P < 0.05).",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas umbilicata,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 2_1_46FAA,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia piriformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus equinus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella confusa",1783272|1239|909932|1843488|909930|904|1852375;3379134|976|200643|171549|815|816|371601;1783272|1239|186801|3085636|186803|2005355|1912855;1783272|1239|526524|526525|128827|61170|1468449;1783272|1239|186801|3085636|186803|742723;3379134|976|200643|171549|815|909656|821;1783272|201174|84998|1643822|1643826|84108|626934;1783272|1239|91061|186826|1300|1301|1335;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|91061|186826|33958|46255|1583,Complete,NA
bsdb:40491436/2/2,40491436,"cross-sectional observational, not case-control",40491436,10.3389/fcimb.2025.1565887,NA,"Li D., Zhang D.Y., Chen S.J., Lv Y.T., Huang S.M., Chen C., Zeng F., Chen R.X., Zhang X.D., Xiong J.X., Chen F.D., Jiang Y.H., Chen Z., Mo C.Y., Chen J.J., Zhu X.L., Zhang L.J. , Bai F.H.",Long-term alterations in gut microbiota following mild COVID-19 recovery: bacterial and fungal community shifts,Frontiers in cellular and infection microbiology,2025,"ROC curve analysis, bacterial-fungal co-occurrence network, fungal microbiota, gut microbiome, metagenomic sequencing, mild COVID-19, probiotics, random forest model",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,NC group (healthy individuals before COVID-19),C6M group (post-COVID-19 recovery group),participants who were six months post-COVID-19 recovery,51,41,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2F,14 January 2026,Ese,Ese,"Result of Linear Discriminant Analysis (LDA) effect size plot of bacterial species abundance differences between NC and C6M, analyzed using LEfSe and FDR correction (FDR-P < 0.05).",decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei",1783272|1239|909932|1843488|909930|904|187327;1783272|1239|186801|3085636|186803|2569097|39488;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|186802|31979|1898204;1783272|201174|84998|84999|84107|102106|74426;3379134|1224|1236|91347|543|547|158836,Complete,NA
bsdb:40491436/3/1,40491436,"cross-sectional observational, not case-control",40491436,10.3389/fcimb.2025.1565887,NA,"Li D., Zhang D.Y., Chen S.J., Lv Y.T., Huang S.M., Chen C., Zeng F., Chen R.X., Zhang X.D., Xiong J.X., Chen F.D., Jiang Y.H., Chen Z., Mo C.Y., Chen J.J., Zhu X.L., Zhang L.J. , Bai F.H.",Long-term alterations in gut microbiota following mild COVID-19 recovery: bacterial and fungal community shifts,Frontiers in cellular and infection microbiology,2025,"ROC curve analysis, bacterial-fungal co-occurrence network, fungal microbiota, gut microbiome, metagenomic sequencing, mild COVID-19, probiotics, random forest model",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,C3M group (post-COVID-19 recovery group),C6M group (post-COVID-19 recovery group),participants who were six months post-COVID-19 recovery,27,41,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2H,14 January 2026,Ese,Ese,"Result of Linear Discriminant Analysis (LDA) effect size plot of bacterial species differences between C3M and C6M, analyzed using LEfSe and FDR correction (FDR-P < 0.05)",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sp. BL7,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella confusa",3379134|976|200643|171549|815|816|626929;3379134|976|200643|171549|815|816|371601;3379134|1224|1236|91347|543|547|158836;3379134|1224|1236|91347|543|570|573;1783272|1239|909932|1843489|31977|906|1285585;1783272|1239|91061|186826|33958|46255|1583,Complete,NA
bsdb:40491436/3/2,40491436,"cross-sectional observational, not case-control",40491436,10.3389/fcimb.2025.1565887,NA,"Li D., Zhang D.Y., Chen S.J., Lv Y.T., Huang S.M., Chen C., Zeng F., Chen R.X., Zhang X.D., Xiong J.X., Chen F.D., Jiang Y.H., Chen Z., Mo C.Y., Chen J.J., Zhu X.L., Zhang L.J. , Bai F.H.",Long-term alterations in gut microbiota following mild COVID-19 recovery: bacterial and fungal community shifts,Frontiers in cellular and infection microbiology,2025,"ROC curve analysis, bacterial-fungal co-occurrence network, fungal microbiota, gut microbiome, metagenomic sequencing, mild COVID-19, probiotics, random forest model",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,C3M group (post-COVID-19 recovery group),C6M group (post-COVID-19 recovery group),participants who were six months post-COVID-19 recovery,27,41,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2H,15 January 2026,Ese,Ese,"Result of Linear Discriminant Analysis (LDA) effect size plot of bacterial species differences between C3M and C6M, analyzed using LEfSe and FDR correction (FDR-P < 0.05)",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia massiliensis (ex Liu et al. 2021),k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium fessum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|s__Eubacteriaceae bacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|s__Rikenellaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. AM23-20,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia|s__Senegalimassilia anaerobia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|526524|526525|128827|2749846|31971;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|3085636|186803|572511|3062492;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|186802|31979|1485|2126740;1783272|1239|186801|186802|186806|2049045;1783272|201174|84998|1643822|1643826|644652|471189;1783272|1239|186801|3085636|186803|28050|28052;3379134|976|200643|171549|171550|2049048;1783272|1239|186801|3085636|186803|841|2292066;1783272|201174|84998|84999|84107|1473205|1473216;1783272|1239|91061|186826|1300|1301|1318,Complete,NA
bsdb:40491436/4/1,40491436,"cross-sectional observational, not case-control",40491436,10.3389/fcimb.2025.1565887,NA,"Li D., Zhang D.Y., Chen S.J., Lv Y.T., Huang S.M., Chen C., Zeng F., Chen R.X., Zhang X.D., Xiong J.X., Chen F.D., Jiang Y.H., Chen Z., Mo C.Y., Chen J.J., Zhu X.L., Zhang L.J. , Bai F.H.",Long-term alterations in gut microbiota following mild COVID-19 recovery: bacterial and fungal community shifts,Frontiers in cellular and infection microbiology,2025,"ROC curve analysis, bacterial-fungal co-occurrence network, fungal microbiota, gut microbiome, metagenomic sequencing, mild COVID-19, probiotics, random forest model",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,NC group (healthy individuals before COVID-19),C3M group (post-COVID-19 recovery group),participants who were three months post-COVID-19 recovery,51,27,3 months,ITS / ITS2,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3F,14 January 2026,Ese,Ese,"Result of Linear Discriminant Analysis (LDA) effect size plot of fungal genera abundance differences between C3M and NC, analyzed using LEfSe and FDR correction (FDR-P < 0.05)",increased,"k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Polyporales|f__Phanerochaetaceae|g__Bjerkandera,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Kazachstania,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Kluyveromyces,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Monascus,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Didymosphaeriaceae|g__Pseudopithomyces,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Tausonia",4751|5204|155619|5303|396331|5330;4751|4890|4891|4892|4893|71245;4751|4890|4891|4892|4893|4910;4751|4890|147545|5042|1131492|5097;4751|4890|147541|92860|221678|1892769;4751|4890|4891|4892|4893|4930;4751|5204|155616|90883|1851551|415704,Complete,NA
bsdb:40491436/4/2,40491436,"cross-sectional observational, not case-control",40491436,10.3389/fcimb.2025.1565887,NA,"Li D., Zhang D.Y., Chen S.J., Lv Y.T., Huang S.M., Chen C., Zeng F., Chen R.X., Zhang X.D., Xiong J.X., Chen F.D., Jiang Y.H., Chen Z., Mo C.Y., Chen J.J., Zhu X.L., Zhang L.J. , Bai F.H.",Long-term alterations in gut microbiota following mild COVID-19 recovery: bacterial and fungal community shifts,Frontiers in cellular and infection microbiology,2025,"ROC curve analysis, bacterial-fungal co-occurrence network, fungal microbiota, gut microbiome, metagenomic sequencing, mild COVID-19, probiotics, random forest model",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,NC group (healthy individuals before COVID-19),C3M group (post-COVID-19 recovery group),participants who were three months post-COVID-19 recovery,51,27,3 months,ITS / ITS2,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3F,14 January 2026,Ese,Ese,"Result of Linear Discriminant Analysis (LDA) effect size plot of fungal genera abundance differences between C3M and NC, analyzed using LEfSe and FDR correction (FDR-P < 0.05)",decreased,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Cucurbitariaceae|g__Pyrenochaeta,4751|4890|147541|92860|221670|285810,Complete,NA
bsdb:40491436/5/1,40491436,"cross-sectional observational, not case-control",40491436,10.3389/fcimb.2025.1565887,NA,"Li D., Zhang D.Y., Chen S.J., Lv Y.T., Huang S.M., Chen C., Zeng F., Chen R.X., Zhang X.D., Xiong J.X., Chen F.D., Jiang Y.H., Chen Z., Mo C.Y., Chen J.J., Zhu X.L., Zhang L.J. , Bai F.H.",Long-term alterations in gut microbiota following mild COVID-19 recovery: bacterial and fungal community shifts,Frontiers in cellular and infection microbiology,2025,"ROC curve analysis, bacterial-fungal co-occurrence network, fungal microbiota, gut microbiome, metagenomic sequencing, mild COVID-19, probiotics, random forest model",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,NC group (healthy individuals before COVID-19),C6M group (post-COVID-19 recovery group),participants who were six months post-COVID-19 recovery,51,41,3 months,ITS / ITS2,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3G,14 January 2026,Ese,Ese,"Result of Linear Discriminant Analysis (LDA) effect size plot of fungal genera abundance differences between C6M and NC, analyzed using LEfSe and FDR correction (FDR-P < 0.05)",increased,"k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae|g__Vanrija,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Xeromyces",4751|4890|147550|5125|110618|5506;4751|5204|155616|1851469|1759442|1851468;4751|4890|147545|5042|1131492|89490,Complete,NA
bsdb:40491436/5/2,40491436,"cross-sectional observational, not case-control",40491436,10.3389/fcimb.2025.1565887,NA,"Li D., Zhang D.Y., Chen S.J., Lv Y.T., Huang S.M., Chen C., Zeng F., Chen R.X., Zhang X.D., Xiong J.X., Chen F.D., Jiang Y.H., Chen Z., Mo C.Y., Chen J.J., Zhu X.L., Zhang L.J. , Bai F.H.",Long-term alterations in gut microbiota following mild COVID-19 recovery: bacterial and fungal community shifts,Frontiers in cellular and infection microbiology,2025,"ROC curve analysis, bacterial-fungal co-occurrence network, fungal microbiota, gut microbiome, metagenomic sequencing, mild COVID-19, probiotics, random forest model",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,NC group (healthy individuals before COVID-19),C6M group (post-COVID-19 recovery group),participants who were six months post-COVID-19 recovery,51,41,3 months,ITS / ITS2,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3G,14 January 2026,Ese,Ese,"Results of Linear Discriminant Analysis (LDA) effect size plot of fungal genera abundance differences between C6M and NC, analyzed using LEfSe and FDR correction (FDR-P < 0.05)",decreased,"k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Glomerellaceae|g__Colletotrichum,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Cucurbitariaceae|g__Pyrenochaeta,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Plectosphaerellaceae|g__Verticillium,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales",4751|4890|147550|1028384|681950|5455;4751|4890|147541|92860|221670|285810;4751|4890|147550|1028384|1033978|1036719;4751|4890|147541|92860,Complete,NA
bsdb:40491436/6/1,40491436,"cross-sectional observational, not case-control",40491436,10.3389/fcimb.2025.1565887,NA,"Li D., Zhang D.Y., Chen S.J., Lv Y.T., Huang S.M., Chen C., Zeng F., Chen R.X., Zhang X.D., Xiong J.X., Chen F.D., Jiang Y.H., Chen Z., Mo C.Y., Chen J.J., Zhu X.L., Zhang L.J. , Bai F.H.",Long-term alterations in gut microbiota following mild COVID-19 recovery: bacterial and fungal community shifts,Frontiers in cellular and infection microbiology,2025,"ROC curve analysis, bacterial-fungal co-occurrence network, fungal microbiota, gut microbiome, metagenomic sequencing, mild COVID-19, probiotics, random forest model",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,C3M group (post-COVID-19 recovery group),C6M group (post-COVID-19 recovery group),participants who were six months post-COVID-19 recovery,27,41,3 months,ITS / ITS2,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3H,14 January 2026,Ese,Ese,"Results of Linear Discriminant Analysis (LDA) effect size plot of fungal genera abundance differences between C6M and C3M, analyzed using LEfSe and FDR correction (FDR-P < 0.05)",increased,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Pleosporaceae|g__Alternaria,4751|4890|147541|92860|28556|5598,Complete,NA
bsdb:40491436/6/2,40491436,"cross-sectional observational, not case-control",40491436,10.3389/fcimb.2025.1565887,NA,"Li D., Zhang D.Y., Chen S.J., Lv Y.T., Huang S.M., Chen C., Zeng F., Chen R.X., Zhang X.D., Xiong J.X., Chen F.D., Jiang Y.H., Chen Z., Mo C.Y., Chen J.J., Zhu X.L., Zhang L.J. , Bai F.H.",Long-term alterations in gut microbiota following mild COVID-19 recovery: bacterial and fungal community shifts,Frontiers in cellular and infection microbiology,2025,"ROC curve analysis, bacterial-fungal co-occurrence network, fungal microbiota, gut microbiome, metagenomic sequencing, mild COVID-19, probiotics, random forest model",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,COVID-19,MONDO:0100096,C3M group (post-COVID-19 recovery group),C6M group (post-COVID-19 recovery group),participants who were six months post-COVID-19 recovery,27,41,3 months,ITS / ITS2,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3H,14 January 2026,Ese,Ese,"Results of Linear Discriminant Analysis (LDA) effect size plot of fungal genera abundance differences between C6M and C3M, analyzed using LEfSe and FDR correction (FDR-P < 0.05)",decreased,"k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Kazachstania,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Kluyveromyces,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Monascus",4751|4890|4891|4892|4893|71245;4751|4890|4891|4892|4893|4910;4751|4890|147545|5042|1131492|5097,Complete,NA
bsdb:40550033/1/1,40550033,case-control,40550033,http://doi.org/10.1097/MD.0000000000043000,NA,"Chao H., Shan J., Che L.Q., Cheng Y., Li H.J. , Qian X.Y.",Correlations between serum cytokines and gut microbiota in patients with Graves' disease: A case-control study,Medicine,2025,"16S rRNA, Graves’ disease, correlation analysis, cytokines, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Healthy Control (HCs),Graves’ disease (GD),The participants in this group were untreated Graves’ disease (GD) patients.,30,30,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"age,sex",NA,increased,increased,increased,increased,NA,increased,Signature 1,Figure 2,24 July 2025,Aleru Divine,Aleru Divine,Statistical analysis of the difference in the gut microbiota between the Graves’ disease patients and the healthy controls.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius",3379134|976|200643|171549;3379134|976;3379134|976|200643;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|976|200643|171549|815|909656|310297,Complete,NA
bsdb:40550033/1/2,40550033,case-control,40550033,http://doi.org/10.1097/MD.0000000000043000,NA,"Chao H., Shan J., Che L.Q., Cheng Y., Li H.J. , Qian X.Y.",Correlations between serum cytokines and gut microbiota in patients with Graves' disease: A case-control study,Medicine,2025,"16S rRNA, Graves’ disease, correlation analysis, cytokines, gut microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Graves disease,EFO:0004237,Healthy Control (HCs),Graves’ disease (GD),The participants in this group were untreated Graves’ disease (GD) patients.,30,30,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"age,sex",NA,increased,increased,increased,increased,NA,increased,Signature 2,Figure 2,24 July 2025,Aleru Divine,Aleru Divine,Statistical analysis of the difference in the gut microbiota between the Graves’ disease patients and the healthy controls.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota",1783272|1239|909932|909929|1843491;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|186802|216572|292632;3379134|1224|1236|91347|543|570;1783272|1239|909932|1843489|31977|29465;3379134|976|200643|171549|815|816|817;3379134|1224|1236|91347|543|620;1783272|1239|909932|1843489|31977;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236;3379134|1224;1783272|1239,Complete,NA
bsdb:40568683/1/1,40568683,"case-control,laboratory experiment",40568683,10.1093/noajnl/vdaf085,NA,"Wang C., Fan Y., Zhang L., Zhao Z., Luo F., Sun K., Zeng M., Tian H., Peng M., Luo Y., Zhao H., He S. , Sun H.",Deciphering the contributions of fecal microbiota from patients with high-grade glioma to tumor development in a humanized microbiome mouse model of glioma,Neuro-oncology advances,2025,"Merdimonas, glioma, gut microbiota, metabolite, sphingosine 1-phosphate",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Glioma,EFO:0005543,Healthy control group (HC),Glioma disease group (G),"Patients with Glioma; a primary malignant tumor of the central nervous system, characterized by high invasiveness, aggressiveness, frequent recurrence, and poor prognosis.",22,30,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"age,body mass index,sex",NA,NA,unchanged,NA,unchanged,NA,increased,Signature 1,Figure 1H,29 December 2025,Shiber256,Shiber256,Linear discriminant analysis Effect Size (LEfSe) analysis identified the microbes at the family and genus level whose abundances significantly differed between the glioma (G) and Healthy Control (HC) groups.,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pseudescherichia,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;3379134|1224|1236;1783272|1239|91061|186826;1783272|1239|186801|3082720|186804;3379134|1224|1236|91347|543|2055880;3379134|1224;1783272|1239|186801|3082720|186804|1501226;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:40568683/1/2,40568683,"case-control,laboratory experiment",40568683,10.1093/noajnl/vdaf085,NA,"Wang C., Fan Y., Zhang L., Zhao Z., Luo F., Sun K., Zeng M., Tian H., Peng M., Luo Y., Zhao H., He S. , Sun H.",Deciphering the contributions of fecal microbiota from patients with high-grade glioma to tumor development in a humanized microbiome mouse model of glioma,Neuro-oncology advances,2025,"Merdimonas, glioma, gut microbiota, metabolite, sphingosine 1-phosphate",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Glioma,EFO:0005543,Healthy control group (HC),Glioma disease group (G),"Patients with Glioma; a primary malignant tumor of the central nervous system, characterized by high invasiveness, aggressiveness, frequent recurrence, and poor prognosis.",22,30,2 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"age,body mass index,sex",NA,NA,unchanged,NA,unchanged,NA,increased,Signature 2,Figure 1H,29 December 2025,Shiber256,Shiber256,Linear discriminant analysis Effect Size (LEfSe) analysis identified the microbes at the  family and genus level whose abundances significantly differed between the glioma (G) and Healthy Control (HC) groups.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae",1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|186802|216572|1940255;1783272|1239|186801|3085636|186803;1783272|1239|909932;1783272|1239|909932|909929;1783272|1239|909932|909929|1843490,Complete,KateRasheed
bsdb:40568683/2/1,40568683,"case-control,laboratory experiment",40568683,10.1093/noajnl/vdaf085,NA,"Wang C., Fan Y., Zhang L., Zhao Z., Luo F., Sun K., Zeng M., Tian H., Peng M., Luo Y., Zhao H., He S. , Sun H.",Deciphering the contributions of fecal microbiota from patients with high-grade glioma to tumor development in a humanized microbiome mouse model of glioma,Neuro-oncology advances,2025,"Merdimonas, glioma, gut microbiota, metabolite, sphingosine 1-phosphate",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Healthy Control Fecal Microbiota Transplantation Group (HC-FMT),High-Grade Glioma Fecal Microbiota Transplantation Group (HGG-FMT),"Six-week-old female BABL/C-nude mice that received a high-grade glioma patient's fecal suspension after a fast of 30 minutes,with each mouse receiving 80-120 μL daily for seven days.",6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Figure 2F,29 December 2025,Shiber256,"Shiber256,Tosin",Linear Discriminant Analysis Effect Size (LEfSe) analysis identified specific microbial taxa that significantly differentiate mice receiving fecal transplants from high-grade glioma patients (HGG-FMT) compared to healthy controls (HC-FMT).,increased,"k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales,k__Pseudomonadati|p__Deferribacterota,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Mailhella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Merdimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|g__Petrothermobacter,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres",3379134|200930|68337|191393|191394;3379134|200930|68337|191393;3379134|200930;28221;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;1783272|1239|186801|3085636|186803|1432051;3379134|200940|3031449|213115|194924|1981028;1783272|1239|186801|3085636|186803|2023266;3379134|976|200643|171549|2005473;3379134|976|200643|171549|2005473|1918540;3379134|200930|68337|191393|2036786;3379134|200930|68337,Complete,KateRasheed
bsdb:40568683/2/2,40568683,"case-control,laboratory experiment",40568683,10.1093/noajnl/vdaf085,NA,"Wang C., Fan Y., Zhang L., Zhao Z., Luo F., Sun K., Zeng M., Tian H., Peng M., Luo Y., Zhao H., He S. , Sun H.",Deciphering the contributions of fecal microbiota from patients with high-grade glioma to tumor development in a humanized microbiome mouse model of glioma,Neuro-oncology advances,2025,"Merdimonas, glioma, gut microbiota, metabolite, sphingosine 1-phosphate",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Healthy Control Fecal Microbiota Transplantation Group (HC-FMT),High-Grade Glioma Fecal Microbiota Transplantation Group (HGG-FMT),"Six-week-old female BABL/C-nude mice that received a high-grade glioma patient's fecal suspension after a fast of 30 minutes,with each mouse receiving 80-120 μL daily for seven days.",6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,Figure 2F,29 December 2025,Shiber256,Shiber256,Linear Discriminant Analysis Effect Size (LEfSe) analysis identified the specific microbial taxa that significantly differentiate mice receiving fecal transplants from high-grade glioma patients (HGG-FMT) compared to healthy controls (HC-FMT).,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae|g__Anaerospora,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae",1783272|1239|909932|909929|1843490|244825;1783272|1239|91061;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|2742598;1783272|1239|909932;1783272|1239|909932|909929;1783272|1239|909932|909929|1843490,Complete,KateRasheed
bsdb:40568683/3/1,40568683,"case-control,laboratory experiment",40568683,10.1093/noajnl/vdaf085,NA,"Wang C., Fan Y., Zhang L., Zhao Z., Luo F., Sun K., Zeng M., Tian H., Peng M., Luo Y., Zhao H., He S. , Sun H.",Deciphering the contributions of fecal microbiota from patients with high-grade glioma to tumor development in a humanized microbiome mouse model of glioma,Neuro-oncology advances,2025,"Merdimonas, glioma, gut microbiota, metabolite, sphingosine 1-phosphate",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Low-Grade Glioma Fecal Microbiota Transplantation Group (LGG-FMT),High-Grade Glioma Fecal Microbiota Transplantation Group (HGG-FMT),"Six-week-old female BABL/C-nude mice that received a high-grade glioma patient's fecal suspension after a fast of 30 minutes,with each mouse receiving 80-120 μL daily for seven days.",6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2G,30 December 2025,Shiber256,Shiber256,Linear discriminant analysis Effect Size (LEfSe) analysis Of gut microbiota composition in mice differences between High-Grade Glioma Fecal Microbiota Transplantation and Low Grade Glioma Fecal Microbiota Transplantation groups (HGG-FMT vs LGG-FMT).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Schaedlerella,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Mailhella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae",1783272|1239|186801|3085636|186803|2676048;28221;3379134|200940|3031449|213115|194924|1981028;3379134|200940|3031449|213115;3379134|200940|3031449|213115|194924,Complete,KateRasheed
bsdb:40568683/3/2,40568683,"case-control,laboratory experiment",40568683,10.1093/noajnl/vdaf085,NA,"Wang C., Fan Y., Zhang L., Zhao Z., Luo F., Sun K., Zeng M., Tian H., Peng M., Luo Y., Zhao H., He S. , Sun H.",Deciphering the contributions of fecal microbiota from patients with high-grade glioma to tumor development in a humanized microbiome mouse model of glioma,Neuro-oncology advances,2025,"Merdimonas, glioma, gut microbiota, metabolite, sphingosine 1-phosphate",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Low-Grade Glioma Fecal Microbiota Transplantation Group (LGG-FMT),High-Grade Glioma Fecal Microbiota Transplantation Group (HGG-FMT),"Six-week-old female BABL/C-nude mice that received a high-grade glioma patient's fecal suspension after a fast of 30 minutes,with each mouse receiving 80-120 μL daily for seven days.",6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2G,30 December 2025,Shiber256,Shiber256,Linear discriminant analysis Effect Size (LEfSe) analysis Of gut microbiota composition in mice differences between High-Grade Glioma Fecal Microbiota Transplantation and Low Grade Glioma Fecal Microbiota Transplantation groups (HGG-FMT vs LGG-FMT).,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",1783272|1239|91061|186826|33958|2742598;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171550,Complete,KateRasheed
bsdb:40595471/1/1,40595471,"cross-sectional observational, not case-control",40595471,10.1038/s41467-025-60131-7,NA,"Durack J., Piceno Y., Vuong H., Fanelli B., Good D.A., Hasan N.A., Dadlani M., Weiss L., Oh J., Kostic A.D., Dawson T.L., Caballero-Arias H. , Colwell R.R.",Yanomami skin microbiome complexity challenges prevailing concepts of healthy skin,Nature communications,2025,NA,Experiment 1,Venezuela,Homo sapiens,Retroarticular,UBERON:2000422,Body composition measurement,EFO:0005106,western HMP,adult Yanomami,"Individuals from a remote Yanomami community in Venezuela, living a seminomadic hunter-gatherer lifestyle in the Amazon rainforest",16,5,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 2D,12 August 2025,Ese,Ese,LEfSe analysis showing most differential bacterial species on retroauricular crease (RAC) of adult Yanomami and western HMP,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Allosaccharopolyspora|s__Allosaccharopolyspora coralli,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Arsenicicoccus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Blastococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Bordetella|s__Bordetella pertussis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium|s__Brachybacterium muris,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium|s__Brachybacterium paraconglomeratum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium|s__Brevibacterium ihuae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium appendicis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium jeddahense,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium mucifaciens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium pseudogenitalium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium tuberculostearicum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium ureicelerivorans,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus wulumuqiensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia|s__Dietzia cinnamea,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia|s__Dietzia lutea,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia|s__Dietzia maris,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Dietziaceae|g__Dietzia|s__Dietzia timorensis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter|s__Enhydrobacter aerosaccus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Faucicola|s__Faucicola osloensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Janibacter|s__Janibacter indicus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria|s__Kocuria marina,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria|s__Kocuria marina|s__Kocuria marina subsp. indica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Kocuria|s__Kocuria palustris,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Kytococcaceae|g__Kytococcus|s__Kytococcus sedentarius,k__Metazoa|p__Chordata|c__Actinopteri|o__Myctophiformes|f__Myctophidae|g__Lampadena|s__Lampadena luminosa,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus aloeverae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus luteus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus terreus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus yunnanensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermatophilaceae|g__Mobilicoccus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Nigerium|s__Nigerium massiliense,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus sophorae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus|s__Paracoccus aeridis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus arlettae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus haemolyticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus saprophyticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermacoccaceae|g__Yimella",1783272|1239|91061|186826|186827|46123;1783272|1239|91061|186826|186827|46123|46125;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049|1654|1655;1783272|201174|1760|85010|2070|2893576|2665642;1783272|201174|1760|85009|31957|2801844|1750;1783272|201174|1760|85006|85021|267408;1783272|201174|1760|1643682|85030|38501;3379134|1224|28216|80840|506|517|520;1783272|201174|1760|85006|85020|43668;1783272|201174|1760|85006|85020|43668|219301;1783272|201174|1760|85006|85020|43668|173362;1783272|201174|1760|85006|85019|1696|1631743;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85007|1653|1716|163202;1783272|201174|1760|85007|1653|1716|61592;1783272|201174|1760|85007|1653|1716|1414719;1783272|201174|1760|85007|1653|1716|57171;1783272|201174|1760|85007|1653|1716|38303;1783272|201174|1760|85007|1653|1716|38304;1783272|201174|1760|85007|1653|1716|401472;3384194|1297|188787|118964|183710|1298|980427;1783272|201174|1760|85006|145357|57495;1783272|201174|1760|85007|85029|37914;1783272|201174|1760|85007|85029|37914|321318;1783272|201174|1760|85007|85029|37914|546160;1783272|201174|1760|85007|85029|37914|37915;1783272|201174|1760|85007|85029|37914|499555;3379134|1224|28211|356|212791;3379134|1224|28211|356|212791|225324;3379134|1224|1236|2887326|468|1604696|34062;1783272|201174|1760|85006|85021|53457|857417;1783272|201174|1760|85006|1268|57493;1783272|201174|1760|85006|1268|57493|223184;1783272|201174|1760|85006|1268|57493|223184|1049583;1783272|201174|1760|85006|1268|57493|71999;1783272|201174|1760|85006|2805426|57499|1276;33208|7711|186623|68514|68515|123246|123247;3379134|1224|28211|356|69277|68287;1783272|201174|1760|85006|85023|33882;1783272|201174|1760|85006|1268;1783272|201174|1760|85006|1268|1269;1783272|201174|1760|85006|1268|1269|1391911;1783272|201174|1760|85006|1268|1269|1270;1783272|201174|1760|85006|1268|1269|574650;1783272|201174|1760|85006|1268|1269|566027;1783272|201174|1760|85006|85018|984996;1783272|201174|1760|85009|31957|2042653|1522317;1783272|1239|91061|1385|186822|44249|1333845;3379134|1224|28211|204455|31989|265|1966466;1783272|1239|91061|1385|90964|1279|29378;1783272|1239|91061|1385|90964|1279|1280;1783272|1239|91061|1385|90964|1279|1283;1783272|1239|91061|1385|90964|1279|1290;1783272|1239|91061|1385|90964|1279|29385;1783272|1239|91061|186826|1300|1301;1783272|201174|1760|85006|145357|908935,Complete,NA
bsdb:40595471/1/2,40595471,"cross-sectional observational, not case-control",40595471,10.1038/s41467-025-60131-7,NA,"Durack J., Piceno Y., Vuong H., Fanelli B., Good D.A., Hasan N.A., Dadlani M., Weiss L., Oh J., Kostic A.D., Dawson T.L., Caballero-Arias H. , Colwell R.R.",Yanomami skin microbiome complexity challenges prevailing concepts of healthy skin,Nature communications,2025,NA,Experiment 1,Venezuela,Homo sapiens,Retroarticular,UBERON:2000422,Body composition measurement,EFO:0005106,western HMP,adult Yanomami,"Individuals from a remote Yanomami community in Venezuela, living a seminomadic hunter-gatherer lifestyle in the Amazon rainforest",16,5,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 2D,13 August 2025,Ese,Ese,LEfSe analysis showing most differential bacteria on  retroauricular crease (RAC) of adult Yanomami and western HMP,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium granulosum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium namnetense,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium",1783272|201174|1760|85009|31957|1912216|1747;1783272|201174|1760|85009|31957|1912216|33011;1783272|201174|1760|85009|31957|1912216|1574624;1783272|201174|1760|85009|31957|1743,Complete,NA
bsdb:40595471/2/1,40595471,"cross-sectional observational, not case-control",40595471,10.1038/s41467-025-60131-7,NA,"Durack J., Piceno Y., Vuong H., Fanelli B., Good D.A., Hasan N.A., Dadlani M., Weiss L., Oh J., Kostic A.D., Dawson T.L., Caballero-Arias H. , Colwell R.R.",Yanomami skin microbiome complexity challenges prevailing concepts of healthy skin,Nature communications,2025,NA,Experiment 2,Venezuela,Homo sapiens,Retroarticular,UBERON:2000422,Body composition measurement,EFO:0005106,western HMP,adult Yanomami,"Individuals from a remote Yanomami community in Venezuela, living a seminomadic hunter-gatherer lifestyle in the Amazon rainforest",16,5,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 3B,13 August 2025,Ese,Ese,Most differential fungal taxa on retroauricular crease (RAC) of adult Yanomami and western HMP,increased,"k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Pichiales|f__Pichiaceae|g__Brettanomyces|s__Brettanomyces bruxellensis,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Botryosphaeriales|f__Botryosphaeriaceae|g__Lasiodiplodia|s__Lasiodiplodia theobromae,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia furfur,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia globosa,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia japonica,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Capnodiales|g__Microcyclospora|s__Microcyclospora tardicrescens",4751|4890|3239874|3243775|1156497|13366|5007;4751|4890|147541|451869|45131|66739|45133;4751|5204|1538075|162474|742845|55193|55194;4751|5204|1538075|162474|742845|55193|76773;4751|5204|1538075|162474|742845|55193|223818;4751|4890|147541|134362|766053|766056,Complete,NA
bsdb:40595471/2/2,40595471,"cross-sectional observational, not case-control",40595471,10.1038/s41467-025-60131-7,NA,"Durack J., Piceno Y., Vuong H., Fanelli B., Good D.A., Hasan N.A., Dadlani M., Weiss L., Oh J., Kostic A.D., Dawson T.L., Caballero-Arias H. , Colwell R.R.",Yanomami skin microbiome complexity challenges prevailing concepts of healthy skin,Nature communications,2025,NA,Experiment 2,Venezuela,Homo sapiens,Retroarticular,UBERON:2000422,Body composition measurement,EFO:0005106,western HMP,adult Yanomami,"Individuals from a remote Yanomami community in Venezuela, living a seminomadic hunter-gatherer lifestyle in the Amazon rainforest",16,5,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 3B,13 August 2025,Ese,Ese,Most differential fungal taxa on retroauricular crease (RAC) of adult Yanomami and western HMP,decreased,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia sp.,4751|5204|1538075|162474|742845|55193|2011732,Complete,NA
bsdb:40596506/1/1,40596506,prospective cohort,40596506,10.1038/s41598-025-06815-y,NA,"Tian X., Xie Y., Zhao Y., Lu X. , Wu N.",Multiomics analyses of gut microbiota and metabolites in people living with HIV before and during SARS-COV-2 infection,Scientific reports,2025,"Coronavirus disease 2019, Cytokine, Fecal metabolites, Gut microbiota, Human immunodeficiency virus",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,SARS-CoV-2-related disease,MONDO:0100318,Baseline,COVID-19,The coronavirus disease 2019 (COVID-19) group comprised adults living with human immunodeficiency virus (HIV) who developed laboratory-confirmed mild severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron infection and provided stool samples during the infection period.,36,36,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2E,6 November 2025,Tosin,Tosin,LDA (Linear discriminant analysis) score diagram and the significantly differentially abundant genera,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Geobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Nanosynbacterales|f__Candidatus Nanosynbacteraceae|g__Candidatus Nanosynbacter|s__Candidatus Nanosynbacter lyticus",1783272|1239|526524|526525|2810280|135858;3379134|1224|1236|91347|543|544;1783272|201174|1760|85007|1653|1716;1783272|1239|526524|526525|128827|1729679;1783272|1239|91061|1385|3120669|129337;1783272|1239|186801|3082720|186804|1505657;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|1385|90964|1279;1783272|1239|526524|526525|2810281|191303;95818|2093818|2093819|2093822|2093823|2093824,Complete,KateRasheed
bsdb:40596506/1/2,40596506,prospective cohort,40596506,10.1038/s41598-025-06815-y,NA,"Tian X., Xie Y., Zhao Y., Lu X. , Wu N.",Multiomics analyses of gut microbiota and metabolites in people living with HIV before and during SARS-COV-2 infection,Scientific reports,2025,"Coronavirus disease 2019, Cytokine, Fecal metabolites, Gut microbiota, Human immunodeficiency virus",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,SARS-CoV-2-related disease,MONDO:0100318,Baseline,COVID-19,The coronavirus disease 2019 (COVID-19) group comprised adults living with human immunodeficiency virus (HIV) who developed laboratory-confirmed mild severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron infection and provided stool samples during the infection period.,36,36,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2E,6 November 2025,Tosin,Tosin,LDA (Linear discriminant analysis) score diagram and the significantly differentially abundant genera,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Ruegeria,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter",1783272|1239|91061|186826|33958|2767842;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|2767887;1783272|1239|91061|186826|33958|2742598;1783272|1239|909932|909929|1843491|158846;3379134|1224|1236|135623|641|657;3379134|1224|28211|204455|2854170|97050;1783272|1239|186801|3082720|186804|1505652,Complete,KateRasheed
bsdb:40597612/1/1,40597612,case-control,40597612,10.1186/s12866-025-04091-4,NA,"Cai X., Lin Y., Wu B., Luo Y. , Li K.",Sputum microbiota profiles of patients with rifampicin-resistant tuberculosis during the intensive-phase treatment,BMC microbiology,2025,"16S rRNA gene sequencing, Rifampicin-resistant tuberculosis, Sputum microbiota",Experiment 1,China,Homo sapiens,Sputum,UBERON:0007311,Tuberculosis,NA,Healthy controls,rifampicin-resistant tuberculosis (RR-TB) patients,Smear/Xpert-confirmed rifampicin‑resistant pulmonary tuberculosis.,14,14,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,4,"age,sex",NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,Figure 4A–B,8 July 2025,Nuerteye,Nuerteye,(A) Significantly different taxa in terms of relative abundance (LDA score ≥ 4); (B) Cladogram highlighting significantly different taxa (LDA score ≥ 4),increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae",1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|186828|117563;3379134|1224|28216|80840|119060|47670;3379134|1224|1236|135625|712|724;3379134|976|200643|171549;3379134|976|200643;3379134|1224|1236|135625|712;3379134|1224|1236|135625;1783272|1239|91061;1783272|1239|91061|186826;1783272|1239|91061|186826|186828;3379134|1224|28216|80840|119060,Complete,NA
bsdb:40597612/1/2,40597612,case-control,40597612,10.1186/s12866-025-04091-4,NA,"Cai X., Lin Y., Wu B., Luo Y. , Li K.",Sputum microbiota profiles of patients with rifampicin-resistant tuberculosis during the intensive-phase treatment,BMC microbiology,2025,"16S rRNA gene sequencing, Rifampicin-resistant tuberculosis, Sputum microbiota",Experiment 1,China,Homo sapiens,Sputum,UBERON:0007311,Tuberculosis,NA,Healthy controls,rifampicin-resistant tuberculosis (RR-TB) patients,Smear/Xpert-confirmed rifampicin‑resistant pulmonary tuberculosis.,14,14,NA,16S,123,Illumina,relative abundances,LEfSe,0.05,TRUE,4,"age,sex",NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Figure 4A–B,8 July 2025,Nuerteye,Nuerteye,(A) Significantly different taxa in terms of relative abundance (LDA score ≥ 4); (B) Cladogram highlighting significantly different taxa (LDA score ≥ 4),decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3384189|32066|203490|203491|203492|848;3384189|32066|203490|203491|203492;3384189|32066|203490;3379134|976|200643|171549|171552|838,Complete,NA
bsdb:40618036/1/1,40618036,laboratory experiment,40618036,10.1186/s12866-025-04140-y,NA,"Sato K., Nakashima A., Fukuda S., Inoue J. , Kim Y.G.",Fasting builds a favorable environment for effective gut microbiota modulation by microbiota-accessible carbohydrates,BMC microbiology,2025,"6ʹ-sialyl lactose, Fasting, Fructo-oligosaccharides, Gut microbiota, Human milk oligosaccharides, IgA, Microbiota-accessible carbohydrates, Paramylon",Experiment 1,Japan,Mus musculus,Alimentary part of gastrointestinal system,UBERON:0005409,Fasting,EFO:0002756,Ad libitum,Fasting,C57BL/6J mice subjected to a 36-hour fasting period.,5,5,The study does not mention an antibiotic exclusion period.,16S,34,Illumina,relative abundances,"ANOVA,Dunn's test,Welch's T-Test,PERMANOVA",0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 1,26 October 2025,Wendeeeee,Wendeeeee,Increased abundance in exposed (fasting) group,increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|976;3379134|1224;1783272|1239|186801|186802|186806|1730|290054;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171552|1283313;3379134|1224|1236|91347|543|1940338,Complete,NA
bsdb:40618036/1/2,40618036,laboratory experiment,40618036,10.1186/s12866-025-04140-y,NA,"Sato K., Nakashima A., Fukuda S., Inoue J. , Kim Y.G.",Fasting builds a favorable environment for effective gut microbiota modulation by microbiota-accessible carbohydrates,BMC microbiology,2025,"6ʹ-sialyl lactose, Fasting, Fructo-oligosaccharides, Gut microbiota, Human milk oligosaccharides, IgA, Microbiota-accessible carbohydrates, Paramylon",Experiment 1,Japan,Mus musculus,Alimentary part of gastrointestinal system,UBERON:0005409,Fasting,EFO:0002756,Ad libitum,Fasting,C57BL/6J mice subjected to a 36-hour fasting period.,5,5,The study does not mention an antibiotic exclusion period.,16S,34,Illumina,relative abundances,"ANOVA,Dunn's test,Welch's T-Test,PERMANOVA",0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 1,26 October 2025,Wendeeeee,Wendeeeee,Decreased abundance in exposed (fasting) group,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239;1783272|1239|186801|3085636|186803|572511;1783272|1239|91061|186826|33958|1578,Complete,NA
bsdb:40618036/2/1,40618036,laboratory experiment,40618036,10.1186/s12866-025-04140-y,NA,"Sato K., Nakashima A., Fukuda S., Inoue J. , Kim Y.G.",Fasting builds a favorable environment for effective gut microbiota modulation by microbiota-accessible carbohydrates,BMC microbiology,2025,"6ʹ-sialyl lactose, Fasting, Fructo-oligosaccharides, Gut microbiota, Human milk oligosaccharides, IgA, Microbiota-accessible carbohydrates, Paramylon",Experiment 2,Japan,Mus musculus,Alimentary part of gastrointestinal system,UBERON:0005409,Fasting,EFO:0002756,Ad libitum + FOS (fructo-oligosaccharide),Fasting + FOS (fructo-oligosaccharide),BALB/cAJcl mice subjected to a 36-hour fasting period with 10% FOS administration.,5,5,The study does not mention an antibiotics exclusion period.,16S,34,Illumina,relative abundances,"ANOVA,Welch's T-Test,Dunn's test,PERMANOVA",0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 2,26 October 2025,Wendeeeee,Wendeeeee,Increased abundance in Fasting + FOS group,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota",1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|171552|1283313;3379134|976;3379134|1224|1236|91347|543|1940338;3379134|1224,Complete,NA
bsdb:40618036/2/2,40618036,laboratory experiment,40618036,10.1186/s12866-025-04140-y,NA,"Sato K., Nakashima A., Fukuda S., Inoue J. , Kim Y.G.",Fasting builds a favorable environment for effective gut microbiota modulation by microbiota-accessible carbohydrates,BMC microbiology,2025,"6ʹ-sialyl lactose, Fasting, Fructo-oligosaccharides, Gut microbiota, Human milk oligosaccharides, IgA, Microbiota-accessible carbohydrates, Paramylon",Experiment 2,Japan,Mus musculus,Alimentary part of gastrointestinal system,UBERON:0005409,Fasting,EFO:0002756,Ad libitum + FOS (fructo-oligosaccharide),Fasting + FOS (fructo-oligosaccharide),BALB/cAJcl mice subjected to a 36-hour fasting period with 10% FOS administration.,5,5,The study does not mention an antibiotics exclusion period.,16S,34,Illumina,relative abundances,"ANOVA,Welch's T-Test,Dunn's test,PERMANOVA",0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 2,26 October 2025,Wendeeeee,Wendeeeee,Decreased abundance in fasting + FOS group,decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia",1783272|1239;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572|1508657;95818|2093818,Complete,NA
bsdb:40618036/3/1,40618036,laboratory experiment,40618036,10.1186/s12866-025-04140-y,NA,"Sato K., Nakashima A., Fukuda S., Inoue J. , Kim Y.G.",Fasting builds a favorable environment for effective gut microbiota modulation by microbiota-accessible carbohydrates,BMC microbiology,2025,"6ʹ-sialyl lactose, Fasting, Fructo-oligosaccharides, Gut microbiota, Human milk oligosaccharides, IgA, Microbiota-accessible carbohydrates, Paramylon",Experiment 3,Japan,Mus musculus,Alimentary part of gastrointestinal system,UBERON:0005409,Fasting,EFO:0002756,Ad libitum + MACs (microbiota-accessible carbohydrates),Fasting + MACs,Mice subjected to 36-h fasting and administered MACs (FOS / 6SL / GOS / α-Cyd / HMOs),5,5,The study does not mention an antibiotics exclusion period.,16S,34,Illumina,relative abundances,"ANOVA,PERMANOVA,Welch's T-Test,Dunn's test",0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Fig 3b,c,d and Fig 4d, e, f",3 November 2025,Wendeeeee,Wendeeeee,Increased abundance in exposed group (Fasting + MACs),increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Actinomycetota",1783272|201174|84998|84999|1643824;3379134|976;1783272|201174|1760|85004|31953|1678;3379134|1224|28216|80840|119060;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|2005525|375288;3379134|1224;1783272|201174,Complete,NA
bsdb:40618036/3/2,40618036,laboratory experiment,40618036,10.1186/s12866-025-04140-y,NA,"Sato K., Nakashima A., Fukuda S., Inoue J. , Kim Y.G.",Fasting builds a favorable environment for effective gut microbiota modulation by microbiota-accessible carbohydrates,BMC microbiology,2025,"6ʹ-sialyl lactose, Fasting, Fructo-oligosaccharides, Gut microbiota, Human milk oligosaccharides, IgA, Microbiota-accessible carbohydrates, Paramylon",Experiment 3,Japan,Mus musculus,Alimentary part of gastrointestinal system,UBERON:0005409,Fasting,EFO:0002756,Ad libitum + MACs (microbiota-accessible carbohydrates),Fasting + MACs,Mice subjected to 36-h fasting and administered MACs (FOS / 6SL / GOS / α-Cyd / HMOs),5,5,The study does not mention an antibiotics exclusion period.,16S,34,Illumina,relative abundances,"ANOVA,PERMANOVA,Welch's T-Test,Dunn's test",0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Fig 4f,3 November 2025,Wendeeeee,Wendeeeee,Decreased abundance in exposed groups (Fasting + MACs),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,p__Candidatus Saccharimonadota|s__uncultured Candidatus Saccharibacteria bacterium",1783272|1239|186801|3085636|186803;3379134|976|200643|171549|171550|239759;1783272|1239|91061|186826|1300|1301;95818|179883,Complete,NA
bsdb:40618036/4/1,40618036,laboratory experiment,40618036,10.1186/s12866-025-04140-y,NA,"Sato K., Nakashima A., Fukuda S., Inoue J. , Kim Y.G.",Fasting builds a favorable environment for effective gut microbiota modulation by microbiota-accessible carbohydrates,BMC microbiology,2025,"6ʹ-sialyl lactose, Fasting, Fructo-oligosaccharides, Gut microbiota, Human milk oligosaccharides, IgA, Microbiota-accessible carbohydrates, Paramylon",Experiment 4,Japan,Mus musculus,Alimentary part of gastrointestinal system,UBERON:0005409,Fasting,EFO:0002756,Ad libitum + Paramylon,Fasting + Paramylon,Mice subjected to 36-hour fasting with Paramylon administration (10 mg/kg),5,5,The study does not mention an antibiotic exclusion time period,16S,34,Illumina,relative abundances,"ANOVA,PERMANOVA,Welch's T-Test,Dunn's test",0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 5,3 November 2025,Wendeeeee,Wendeeeee,Increased abundance in exposed group(Fasting + Paramylon),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella",3379134|976|200643|171549|815|816;3379134|976|200643|171549|171552|1283313;1783272|1239|186801|186802|186806|1730|290054;3379134|1224|28216|80840|119060;1783272|1239;1783272|1239|91061|1385|539738|1378,Complete,NA
bsdb:40618036/4/2,40618036,laboratory experiment,40618036,10.1186/s12866-025-04140-y,NA,"Sato K., Nakashima A., Fukuda S., Inoue J. , Kim Y.G.",Fasting builds a favorable environment for effective gut microbiota modulation by microbiota-accessible carbohydrates,BMC microbiology,2025,"6ʹ-sialyl lactose, Fasting, Fructo-oligosaccharides, Gut microbiota, Human milk oligosaccharides, IgA, Microbiota-accessible carbohydrates, Paramylon",Experiment 4,Japan,Mus musculus,Alimentary part of gastrointestinal system,UBERON:0005409,Fasting,EFO:0002756,Ad libitum + Paramylon,Fasting + Paramylon,Mice subjected to 36-hour fasting with Paramylon administration (10 mg/kg),5,5,The study does not mention an antibiotic exclusion time period,16S,34,Illumina,relative abundances,"ANOVA,PERMANOVA,Welch's T-Test,Dunn's test",0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 5,3 November 2025,Wendeeeee,Wendeeeee,Decreased abundance in exposed group(Fasting + Paramylon),decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3085636|186803,Complete,NA
bsdb:40629270/1/1,40629270,case-control,40629270,10.1186/s12866-025-04141-x,NA,"Sun B., Yu X., Qi H., Xu F., Jiao W., Fang M., Duan L., Zeng X., Yang X., Wang X., Zhu Y., Mi K., Shen A. , Sun L.",The gut dysbiosis and plasma lipid metabolisms signatures in children with active tuberculosis,BMC microbiology,2025,"Child, Gut microbiota, Lipids, Tuberculosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,Healthy controls,Active pulmonary tuberculosis,"positive Mycobacterium tuberculosis culture results or molecular testing results using
Xpert MTB/RIF Ultra.",80,98,NA,16S,34,Illumina,relative abundances,"LEfSe,Linear Discriminant Analysis",0.05,TRUE,2,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,Figure 1I,19 July 2025,Nuerteye,Nuerteye,Comparisons of the gut microbiota in in children with active TB and non-TB groups. LDA score histogram in tuberculosis children compared with healthy controls.,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella",1783272|1239|91061;1783272|1239|91061|186826;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|81852;1783272|1239|526524|526525;1783272|1239|186801|186802|216572|292632;1783272|1239|526524|526525|2810280|135858;1783272|1239|526524|526525|128827;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|526524|526525|128827|1573535,Complete,NA
bsdb:40629270/1/2,40629270,case-control,40629270,10.1186/s12866-025-04141-x,NA,"Sun B., Yu X., Qi H., Xu F., Jiao W., Fang M., Duan L., Zeng X., Yang X., Wang X., Zhu Y., Mi K., Shen A. , Sun L.",The gut dysbiosis and plasma lipid metabolisms signatures in children with active tuberculosis,BMC microbiology,2025,"Child, Gut microbiota, Lipids, Tuberculosis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,Healthy controls,Active pulmonary tuberculosis,"positive Mycobacterium tuberculosis culture results or molecular testing results using
Xpert MTB/RIF Ultra.",80,98,NA,16S,34,Illumina,relative abundances,"LEfSe,Linear Discriminant Analysis",0.05,TRUE,2,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 2,Figure 1I,19 July 2025,Nuerteye,Nuerteye,Comparisons of the gut microbiota in in children with active TB and non-TB groups. LDA score histogram in tuberculosis children compared with healthy controls.,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales",1783272|1239|909932|909929|1843491;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932;3379134|1224|1236;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976;3379134|976|200643;3379134|976|200643|171549,Complete,NA
bsdb:40629270/2/1,40629270,case-control,40629270,10.1186/s12866-025-04141-x,NA,"Sun B., Yu X., Qi H., Xu F., Jiao W., Fang M., Duan L., Zeng X., Yang X., Wang X., Zhu Y., Mi K., Shen A. , Sun L.",The gut dysbiosis and plasma lipid metabolisms signatures in children with active tuberculosis,BMC microbiology,2025,"Child, Gut microbiota, Lipids, Tuberculosis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,mild tuberculosis (mild TB),severe tuberculosis (severe TB),Cases with severe TB,65,33,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 2F,19 July 2025,Nuerteye,Nuerteye,Association of the gut microbiota with severity of TB. LDA score histogram,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria",3379134|1224|1236|91347|543|570;3379134|1224|1236,Complete,NA
bsdb:40629270/2/2,40629270,case-control,40629270,10.1186/s12866-025-04141-x,NA,"Sun B., Yu X., Qi H., Xu F., Jiao W., Fang M., Duan L., Zeng X., Yang X., Wang X., Zhu Y., Mi K., Shen A. , Sun L.",The gut dysbiosis and plasma lipid metabolisms signatures in children with active tuberculosis,BMC microbiology,2025,"Child, Gut microbiota, Lipids, Tuberculosis",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Pulmonary tuberculosis,EFO:1000049,mild tuberculosis (mild TB),severe tuberculosis (severe TB),Cases with severe TB,65,33,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 2F,19 July 2025,Nuerteye,Nuerteye,Association of the gut microbiota with severity of TB. LDA score histogram,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae",1783272|1239|186801|3085636|186803|572511;1783272|1239|91061|186826|33958|1243;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|186802|1392389|1297617;3379134|976|200643|171549|815|816;3379134|976|200643|171549|171550|239759|328814;3379134|1224|28216|80840|75682,Complete,NA
bsdb:40629292/1/2,40629292,"cross-sectional observational, not case-control",40629292,https://doi.org/10.1186/s12866-025-04094-1,NA,"Ying L., Yuhao W., Yafang H., Jiao L., Lina D., Qinze S., Chenghai Y., Shaoxiong Z., Yuexi G., Mingwang S., Zelin C., Chuangchuang W., Zihan G., Xin L., Lu M. , Lei Z.",Chronic stress is associated with altered gut microbiota profile and relevant metabolites in adolescents,BMC microbiology,2025,"16S rRNA, Adolescents, Chronic stress, Gut microbiota, Metabolism, Metagenomics",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Stress-related disorder,EFO:0010098,low stress + medium stress,high stress,Participants with high chronic stress levels,83,41,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2a,8 October 2025,Appleeyes,Appleeyes,Linear discriminant analysis (LDA) scores for the bacterial taxa differentially abundant in adolescents with different chronic stress levels (LDA > 2).,increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas plecoglossicida,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia",1783272|201174;3379134|1224|28211;;3379134|1224|1236|72274|135621|286|70775;3379134|1224|28211|204457|41297;3379134|1224|28211|204457;3379134|1224|28211|204457|41297|13687;3379134|1224|28211|204457|41297|13687;1783272|201174|84992,Complete,KateRasheed
bsdb:40629292/2/1,40629292,"cross-sectional observational, not case-control",40629292,https://doi.org/10.1186/s12866-025-04094-1,NA,"Ying L., Yuhao W., Yafang H., Jiao L., Lina D., Qinze S., Chenghai Y., Shaoxiong Z., Yuexi G., Mingwang S., Zelin C., Chuangchuang W., Zihan G., Xin L., Lu M. , Lei Z.",Chronic stress is associated with altered gut microbiota profile and relevant metabolites in adolescents,BMC microbiology,2025,"16S rRNA, Adolescents, Chronic stress, Gut microbiota, Metabolism, Metagenomics",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Stress-related disorder,EFO:0010098,low stress,high stress,Participants with high chronic stress levels for the metagenomic subset,29,30,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,figure 3c,8 October 2025,Appleeyes,Appleeyes,The specific bacteria taxa of two stress groups based on Linear Discriminant Analysis Effect Size (LEfSe) analysis.,increased,"k__Fungi|p__Ascomycota,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales,k__Fungi|p__Ascomycota|c__Saccharomycetes",4751|4890;4751|4890|4891|4892|4893|4930;4751|4890|4891|4892|4893;4751|4890|4891|4892;4751|4890|4891,Complete,KateRasheed
bsdb:40629292/2/2,40629292,"cross-sectional observational, not case-control",40629292,https://doi.org/10.1186/s12866-025-04094-1,NA,"Ying L., Yuhao W., Yafang H., Jiao L., Lina D., Qinze S., Chenghai Y., Shaoxiong Z., Yuexi G., Mingwang S., Zelin C., Chuangchuang W., Zihan G., Xin L., Lu M. , Lei Z.",Chronic stress is associated with altered gut microbiota profile and relevant metabolites in adolescents,BMC microbiology,2025,"16S rRNA, Adolescents, Chronic stress, Gut microbiota, Metabolism, Metagenomics",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Stress-related disorder,EFO:0010098,low stress,high stress,Participants with high chronic stress levels for the metagenomic subset,29,30,3 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,figure 3c,24 October 2025,Appleeyes,Appleeyes,The specific bacteria taxa of two stress groups based on Linear Discriminant Analysis Effect Size (LEfSe) analysis.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Chitinophaga|s__Chitinophaga silvisoli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Chitinophaga,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota,k__Methanobacteriati|p__Methanobacteriota,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Gelidibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__uncultured Ruminococcus sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus",1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826;1783272|1239|91061|186826|33958;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|909932|1843489|31977|39948;1783272|1239|909932|1843489|31977|39948|218538;3379134|976|1853228|1853229|563835|79328|2291814;1783272|1239|186801|3085636|186803|841|301302;3379134|74201|203494|48461|1647988|239934|239935;3379134|74201|203494|48461|1647988|239934;3379134|976|1853228|1853229|563835|79328;3379134|74201|203494|48461|1647988;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201;3366610|28890;3379134|976|117743|200644|49546|49279;1783272|1239|186801|186802|216572|1263|165186;1783272|1239|91061|186826|33958|46255;3379134|1224|28211;3379134|1224|28211|204455|31989;1783272|1239|909932|1843488|909930;1783272|1239|909932|1843488;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|186802|3082771|1924093,Complete,KateRasheed
bsdb:40629292/3/1,40629292,"cross-sectional observational, not case-control",40629292,https://doi.org/10.1186/s12866-025-04094-1,NA,"Ying L., Yuhao W., Yafang H., Jiao L., Lina D., Qinze S., Chenghai Y., Shaoxiong Z., Yuexi G., Mingwang S., Zelin C., Chuangchuang W., Zihan G., Xin L., Lu M. , Lei Z.",Chronic stress is associated with altered gut microbiota profile and relevant metabolites in adolescents,BMC microbiology,2025,"16S rRNA, Adolescents, Chronic stress, Gut microbiota, Metabolism, Metagenomics",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Stress-related disorder,EFO:0010098,low stress,high stress,Participants with high chronic stress levels for the metagenomic subset,29,30,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,figure 3e,8 October 2025,Appleeyes,Appleeyes,"The Wilcoxon rank-sum test was used to analyze the difference in the relative abundances in adolescents with low- and high-chronic stress. These analyses were based on gut microbial species that were significantly correlated with chronic stress, as identified by Spearman’s rank correlation.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Arenibacter|s__Arenibacter certesii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp. ART55_1,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Denitrificimonas|s__Denitrificimonas caeni,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio sp. An276,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas|s__Halomonas halocynthiae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. PEA192,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. AF17-11,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. AM36-18,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:108,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus suis",3379134|976|117743|200644|49546|178469|228955;1783272|1239|186801|3085636|186803|33042|2710826;3379134|1224|1236|72274|135621|2901261|521720;3379134|200940|3031449|213115|194924|872|1965618;3379134|1224|1236|135619|28256|2745|176290;1783272|1239|186801|186802|216572|459786|2109687;1783272|1239|909932|1843488|909930|33024|33025;1783272|1239|186801|3085636|186803|841|301302;1783272|1239|186801|186802|216572|1263|2293150;1783272|1239|186801|186802|216572|1263|2293209;1783272|1239|186801|186802|216572|1263|1262950;1783272|1239|91061|186826|1300|1301|1307,Complete,KateRasheed
bsdb:40629292/3/2,40629292,"cross-sectional observational, not case-control",40629292,https://doi.org/10.1186/s12866-025-04094-1,NA,"Ying L., Yuhao W., Yafang H., Jiao L., Lina D., Qinze S., Chenghai Y., Shaoxiong Z., Yuexi G., Mingwang S., Zelin C., Chuangchuang W., Zihan G., Xin L., Lu M. , Lei Z.",Chronic stress is associated with altered gut microbiota profile and relevant metabolites in adolescents,BMC microbiology,2025,"16S rRNA, Adolescents, Chronic stress, Gut microbiota, Metabolism, Metagenomics",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Stress-related disorder,EFO:0010098,low stress,high stress,Participants with high chronic stress levels for the metagenomic subset,29,30,3 months,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,figure 3e,8 October 2025,Appleeyes,Appleeyes,"The Wilcoxon rank-sum test was used to analyze the difference in the relative abundances in adolescents with low- and high-chronic stress. These analyses were based on gut microbial species that were significantly correlated with chronic stress, as identified by Spearman’s rank correlation.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter|s__Achromobacter insuavis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio sp. 3_1_syn3,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AM25-23AC",3379134|1224|28216|80840|506|222|1287735;1783272|201174|1760|85004|31953|1678|1686;1783272|201174|1760|85004|31953|1678|28026;3379134|200940|3031449|213115|194924|872|457398;1783272|1239|186801|186802|31979|1485|2305240,Complete,KateRasheed
bsdb:40629292/4/1,40629292,"cross-sectional observational, not case-control",40629292,https://doi.org/10.1186/s12866-025-04094-1,NA,"Ying L., Yuhao W., Yafang H., Jiao L., Lina D., Qinze S., Chenghai Y., Shaoxiong Z., Yuexi G., Mingwang S., Zelin C., Chuangchuang W., Zihan G., Xin L., Lu M. , Lei Z.",Chronic stress is associated with altered gut microbiota profile and relevant metabolites in adolescents,BMC microbiology,2025,"16S rRNA, Adolescents, Chronic stress, Gut microbiota, Metabolism, Metagenomics",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Stress-related disorder,EFO:0010098,low stress,high stress,Participants with high chronic stress levels,42,41,3 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 1,figure 2c and 2e,10 October 2025,Appleeyes,Appleeyes,The Kruskal-Wallis test was used to analyze differences in the relative abundances of bacteria taxa at the phylum and genus levels among adolescents with varying stress levels.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Thermodesulfobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|1263;3379134|200940;1783272|1239|186801|3085636|186803;3379134|976;3379134|74201;3379134|976|200643|171549|815|816;3379134|74201|203494|48461|1647988|239934,Complete,KateRasheed
bsdb:40629292/4/2,40629292,"cross-sectional observational, not case-control",40629292,https://doi.org/10.1186/s12866-025-04094-1,NA,"Ying L., Yuhao W., Yafang H., Jiao L., Lina D., Qinze S., Chenghai Y., Shaoxiong Z., Yuexi G., Mingwang S., Zelin C., Chuangchuang W., Zihan G., Xin L., Lu M. , Lei Z.",Chronic stress is associated with altered gut microbiota profile and relevant metabolites in adolescents,BMC microbiology,2025,"16S rRNA, Adolescents, Chronic stress, Gut microbiota, Metabolism, Metagenomics",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Stress-related disorder,EFO:0010098,low stress,high stress,Participants with high chronic stress levels,42,41,3 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,decreased,NA,decreased,Signature 2,figure 2c and 2e,10 October 2025,Appleeyes,Appleeyes,The Kruskal-Wallis test was used to analyze differences in the relative abundances of bacteria taxa at the phylum and genus levels among adolescents with varying stress levels.,increased,k__Bacillati|p__Chloroflexota,1783272|200795,Complete,KateRasheed
bsdb:40629292/5/1,40629292,"cross-sectional observational, not case-control",40629292,https://doi.org/10.1186/s12866-025-04094-1,NA,"Ying L., Yuhao W., Yafang H., Jiao L., Lina D., Qinze S., Chenghai Y., Shaoxiong Z., Yuexi G., Mingwang S., Zelin C., Chuangchuang W., Zihan G., Xin L., Lu M. , Lei Z.",Chronic stress is associated with altered gut microbiota profile and relevant metabolites in adolescents,BMC microbiology,2025,"16S rRNA, Adolescents, Chronic stress, Gut microbiota, Metabolism, Metagenomics",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Stress-related disorder,EFO:0010098,low stress,high stress,Participants with high chronic stress levels,29,30,3 months,WMS,NA,Illumina,relative abundances,Logistic Regression,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,figure 3f,10 October 2025,Appleeyes,Appleeyes,"Logistic regression analysis was used to analyze the adjusted associations between chronic stress and gut microbial species, identified in Fig. 3 (e). The logistic regression analysis adjusted for sex, age, food consumption, and body mass index as covariates.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:108,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus suis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium",1783272|1239|186801|186802|216572|1263|1262950;1783272|1239|91061|186826|1300|1301|1307;1783272|1239|909932|1843488|909930|33024|33025,Complete,KateRasheed
bsdb:40629292/5/2,40629292,"cross-sectional observational, not case-control",40629292,https://doi.org/10.1186/s12866-025-04094-1,NA,"Ying L., Yuhao W., Yafang H., Jiao L., Lina D., Qinze S., Chenghai Y., Shaoxiong Z., Yuexi G., Mingwang S., Zelin C., Chuangchuang W., Zihan G., Xin L., Lu M. , Lei Z.",Chronic stress is associated with altered gut microbiota profile and relevant metabolites in adolescents,BMC microbiology,2025,"16S rRNA, Adolescents, Chronic stress, Gut microbiota, Metabolism, Metagenomics",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Stress-related disorder,EFO:0010098,low stress,high stress,Participants with high chronic stress levels,29,30,3 months,WMS,NA,Illumina,relative abundances,Logistic Regression,0.05,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,figure 3f,10 October 2025,Appleeyes,Appleeyes,"Logistic regression analysis was used to analyze the adjusted associations between chronic stress and gut microbial species, identified in Fig. 3 (e). The logistic regression analysis adjusted for sex, age, food consumption, and body mass index as covariates.",increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,1783272|201174|1760|85004|31953|1678|1686,Complete,KateRasheed
bsdb:40629292/6/1,40629292,"cross-sectional observational, not case-control",40629292,https://doi.org/10.1186/s12866-025-04094-1,NA,"Ying L., Yuhao W., Yafang H., Jiao L., Lina D., Qinze S., Chenghai Y., Shaoxiong Z., Yuexi G., Mingwang S., Zelin C., Chuangchuang W., Zihan G., Xin L., Lu M. , Lei Z.",Chronic stress is associated with altered gut microbiota profile and relevant metabolites in adolescents,BMC microbiology,2025,"16S rRNA, Adolescents, Chronic stress, Gut microbiota, Metabolism, Metagenomics",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Stress-related disorder,EFO:0010098,medium stress + high stress,low stress,Participants with low chronic stress levels,82,42,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,figure 2a,16 October 2025,Appleeyes,Appleeyes,Linear discriminant analysis (LDA) scores for the bacterial taxa differentially abundant in adolescents with different chronic stress levels (LDA > 2).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Pseudomonadati|p__Thermodesulfobacteriota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__uncultured Phascolarctobacterium sp.",3379134|976|200643|171549|171552|1283313;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;3379134|200940|3031449;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|877420;3379134|200940;3379134|976|200643|171549|171552|1283313;3379134|200940|3031449|213115|194924|872;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803;1783272|1239|909932|1843488|909930|33024|512296,Complete,KateRasheed
bsdb:40629292/7/1,40629292,"cross-sectional observational, not case-control",40629292,https://doi.org/10.1186/s12866-025-04094-1,NA,"Ying L., Yuhao W., Yafang H., Jiao L., Lina D., Qinze S., Chenghai Y., Shaoxiong Z., Yuexi G., Mingwang S., Zelin C., Chuangchuang W., Zihan G., Xin L., Lu M. , Lei Z.",Chronic stress is associated with altered gut microbiota profile and relevant metabolites in adolescents,BMC microbiology,2025,"16S rRNA, Adolescents, Chronic stress, Gut microbiota, Metabolism, Metagenomics",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Stress-related disorder,EFO:0010098,low stress + high stress,medium stress,Participants with medium chronic stress levels,83,41,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,figure 2a,16 October 2025,Appleeyes,Appleeyes,Linear discriminant analysis (LDA) scores for the bacterial taxa differentially abundant in adolescents with different chronic stress levels (LDA > 2).,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. Nj-68,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp. BAB-5819,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella phocaeensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__uncultured Ruminococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|909932|1843488|909930|904;3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;3379134|976|200643|171549|171550|239759|328814;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|28116;3379134|976|200643;3379134|976;3379134|976|200643|171549|2005519|1348911|1099853;3379134|1224|1236|91347|543|547|424712;1783272|1239|186801|186802|1686313;1783272|1239|186801|3082720|186804|1505657;3379134|1224|1236|91347|543|570|1864757;3379134|976|200643|171549|2005473;1783272|201174|84998|84999|1643824|133925|1852385;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836;1783272|1239|186801|186802|216572|1263;3379134|1224|28216|80840|995019;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|815|816;3379134|976;1783272|1239|186801|186802|1686313;3379134|976|200643|171549|2005473;1783272|1239|186801|186802|216572|1263|165186;1783272|1239|186801|186802|216572,Complete,KateRasheed
bsdb:40629292/8/1,40629292,"cross-sectional observational, not case-control",40629292,https://doi.org/10.1186/s12866-025-04094-1,NA,"Ying L., Yuhao W., Yafang H., Jiao L., Lina D., Qinze S., Chenghai Y., Shaoxiong Z., Yuexi G., Mingwang S., Zelin C., Chuangchuang W., Zihan G., Xin L., Lu M. , Lei Z.",Chronic stress is associated with altered gut microbiota profile and relevant metabolites in adolescents,BMC microbiology,2025,"16S rRNA, Adolescents, Chronic stress, Gut microbiota, Metabolism, Metagenomics",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Stress-related disorder,EFO:0010098,low stress,medium stress,Participants with medium chronic stress levels,42,41,3 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,figure 2c and 2e,17 October 2025,Appleeyes,Appleeyes,The Kruskal-Wallis test was used to analyze differences in the relative abundances of bacteria taxa at the phylum and genus levels among adolescents with varying stress levels.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Thermodesulfobacteriota,k__Bacillati|p__Chloroflexota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|1263;3379134|200940;1783272|200795;1783272|1239|186801|3085636|186803,Complete,KateRasheed
bsdb:40629292/8/2,40629292,"cross-sectional observational, not case-control",40629292,https://doi.org/10.1186/s12866-025-04094-1,NA,"Ying L., Yuhao W., Yafang H., Jiao L., Lina D., Qinze S., Chenghai Y., Shaoxiong Z., Yuexi G., Mingwang S., Zelin C., Chuangchuang W., Zihan G., Xin L., Lu M. , Lei Z.",Chronic stress is associated with altered gut microbiota profile and relevant metabolites in adolescents,BMC microbiology,2025,"16S rRNA, Adolescents, Chronic stress, Gut microbiota, Metabolism, Metagenomics",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Stress-related disorder,EFO:0010098,low stress,medium stress,Participants with medium chronic stress levels,42,41,3 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,figure 2c and 2e,17 October 2025,Appleeyes,Appleeyes,The Kruskal-Wallis test was used to analyze differences in the relative abundances of bacteria taxa at the phylum and genus levels among adolescents with varying stress levels.,increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",3379134|976;3379134|74201;3379134|976|200643|171549|815|816;3379134|74201|203494|48461|1647988|239934,Complete,KateRasheed
bsdb:40629292/9/1,40629292,"cross-sectional observational, not case-control",40629292,https://doi.org/10.1186/s12866-025-04094-1,NA,"Ying L., Yuhao W., Yafang H., Jiao L., Lina D., Qinze S., Chenghai Y., Shaoxiong Z., Yuexi G., Mingwang S., Zelin C., Chuangchuang W., Zihan G., Xin L., Lu M. , Lei Z.",Chronic stress is associated with altered gut microbiota profile and relevant metabolites in adolescents,BMC microbiology,2025,"16S rRNA, Adolescents, Chronic stress, Gut microbiota, Metabolism, Metagenomics",Experiment 9,China,Homo sapiens,Feces,UBERON:0001988,Stress-related disorder,EFO:0010098,medium stress,high stress,Participants with high chronic stress levels,41,41,3 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,figure 2c and 2e,17 October 2025,Appleeyes,Appleeyes,The Kruskal-Wallis test was used to analyze differences in the relative abundances of bacteria taxa at the phylum and genus levels among adolescents with varying stress levels.,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Verrucomicrobiota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Thermodesulfobacteriota",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|815|816;3379134|976;1783272|1239|186801|186802|216572|1263;3379134|74201;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803;3379134|200940,Complete,KateRasheed
bsdb:40629292/9/2,40629292,"cross-sectional observational, not case-control",40629292,https://doi.org/10.1186/s12866-025-04094-1,NA,"Ying L., Yuhao W., Yafang H., Jiao L., Lina D., Qinze S., Chenghai Y., Shaoxiong Z., Yuexi G., Mingwang S., Zelin C., Chuangchuang W., Zihan G., Xin L., Lu M. , Lei Z.",Chronic stress is associated with altered gut microbiota profile and relevant metabolites in adolescents,BMC microbiology,2025,"16S rRNA, Adolescents, Chronic stress, Gut microbiota, Metabolism, Metagenomics",Experiment 9,China,Homo sapiens,Feces,UBERON:0001988,Stress-related disorder,EFO:0010098,medium stress,high stress,Participants with high chronic stress levels,41,41,3 months,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,figure 2c and 2e,17 October 2025,Appleeyes,Appleeyes,The Kruskal-Wallis test was used to analyze differences in the relative abundances of bacteria taxa at the phylum and genus levels among adolescents with varying stress levels.,increased,k__Bacillati|p__Chloroflexota,1783272|200795,Complete,KateRasheed
bsdb:40665409/1/1,40665409,prospective cohort,40665409,https://doi.org/10.1186/s13073-025-01508-7,NA,"Lyu L., Fan Y., Vogt J.K., Clos-Garcia M., Bonnefond A., Pedersen H.K., Dutta A., Koivula R., Sharma S., Allin K.H., Brorsson C., Cederberg H., Chabanova E., De Masi F., Dermitzakis E., Elders P.J., Blom M.T., Hollander M., Eriksen R., Forgie I., Frost G., Giordano G.N., Grallert H., Haid M., Hansen T.H., Jablonka B., Kokkola T., Mahajan A., Mari A., McDonald T.J., Musholt P.B., Pavo I., Prehn C., Ridderstråle M., Ruetten H., Hart L.M.'., Schwenk J.M., Stankevic E., Thomsen H.S., Vangipurapu J., Vestergaard H., Viñuela A., Walker M., Hansen T., Linneberg A., Nielsen H.B., Brunak S., McCarthy M.I., Froguel P., Adamski J., Franks P.W., Laakso M., Beulens J.W.J., Pearson E. , Pedersen O.",The dynamics of the gut microbiota in prediabetes during a four-year follow-up among European patients-an IMI-DIRECT prospective study,Genome medicine,2025,"Gut bacterial genetics, Gut bacterial microbiota, Gut viral microbiota, Insulin sensitivity, Long-term dynamics, Metabolism, Microbial functional pathways, Prediabetes",Experiment 1,"Sweden,Netherlands,Denmark,Finland",Homo sapiens,Feces,UBERON:0001988,"Prediabetes syndrome,Insulin resistance","EFO:1001121,EFO:0002614",Non progressors,Progressors,"Individuals with prediabetes at baseline who progressed to type 2 diabetes during the four-year follow-up, as defined by HbA1c, fasting glucose, and OGTT criteria from the IMI-DIRECT protocol.",400,100,NA,16S,123456789,Illumina,relative abundances,"Fisher's Exact Test,Linear Regression,Spearman Correlation",0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4A,30 November 2025,SheikhAlMamun,SheikhAlMamun,"Gut bacterial genetics stability within the individual and between individuals. To evaluate the dynamics of bacterial genetics within bacterial
species over time and between individuals, we calculated intra-individual and inter-individual distance for each species from their structural
variant (SV) profiles. A Profiles of Jaccard distance of deletion structural variants (dSVs)",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. L2-50,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella sp. 4_8_47FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 3_1_46FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. SR1/5,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Wegman et al. 2014)",1783272|1239|186801|3085636|186803|207244|649756;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|186802|31979|1485|411489;1783272|201174|84998|84999|84107|102106|742722;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|665950;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|1263|657323;1783272|1239|186801|186802|216572|1263|1160721,Complete,NA
bsdb:40665409/1/2,40665409,prospective cohort,40665409,https://doi.org/10.1186/s13073-025-01508-7,NA,"Lyu L., Fan Y., Vogt J.K., Clos-Garcia M., Bonnefond A., Pedersen H.K., Dutta A., Koivula R., Sharma S., Allin K.H., Brorsson C., Cederberg H., Chabanova E., De Masi F., Dermitzakis E., Elders P.J., Blom M.T., Hollander M., Eriksen R., Forgie I., Frost G., Giordano G.N., Grallert H., Haid M., Hansen T.H., Jablonka B., Kokkola T., Mahajan A., Mari A., McDonald T.J., Musholt P.B., Pavo I., Prehn C., Ridderstråle M., Ruetten H., Hart L.M.'., Schwenk J.M., Stankevic E., Thomsen H.S., Vangipurapu J., Vestergaard H., Viñuela A., Walker M., Hansen T., Linneberg A., Nielsen H.B., Brunak S., McCarthy M.I., Froguel P., Adamski J., Franks P.W., Laakso M., Beulens J.W.J., Pearson E. , Pedersen O.",The dynamics of the gut microbiota in prediabetes during a four-year follow-up among European patients-an IMI-DIRECT prospective study,Genome medicine,2025,"Gut bacterial genetics, Gut bacterial microbiota, Gut viral microbiota, Insulin sensitivity, Long-term dynamics, Metabolism, Microbial functional pathways, Prediabetes",Experiment 1,"Sweden,Netherlands,Denmark,Finland",Homo sapiens,Feces,UBERON:0001988,"Prediabetes syndrome,Insulin resistance","EFO:1001121,EFO:0002614",Non progressors,Progressors,"Individuals with prediabetes at baseline who progressed to type 2 diabetes during the four-year follow-up, as defined by HbA1c, fasting glucose, and OGTT criteria from the IMI-DIRECT protocol.",400,100,NA,16S,123456789,Illumina,relative abundances,"Fisher's Exact Test,Linear Regression,Spearman Correlation",0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 4A,30 November 2025,SheikhAlMamun,SheikhAlMamun,"Gut bacterial genetics stability within the individual and between individuals. To evaluate the dynamics of bacterial genetics within bacterial
species over time and between individuals, we calculated intra-individual and inter-individual distance for each species from their structural
variant (SV) profiles. A Profiles of Jaccard distance of deletion structural variants (dSVs)",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,s__bacterium LF-3,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. ER4",3379134|976|200643|171549|171552|2974251|165179;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|2005525|375288|823;3379134|976|200643|171549|171550|239759|2585118;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|2005519|397864|487174;3379134|976|200643|171549|2005525|375288|46503;3366610|28890|183925|2158|2159|2172|2173;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|171552|577309|454154;1504823;3379134|976|200643|171549|171550|239759|328814;1783272|1239|186801|186802|216572|459786|1519439,Complete,NA
bsdb:40665409/2/1,40665409,prospective cohort,40665409,https://doi.org/10.1186/s13073-025-01508-7,NA,"Lyu L., Fan Y., Vogt J.K., Clos-Garcia M., Bonnefond A., Pedersen H.K., Dutta A., Koivula R., Sharma S., Allin K.H., Brorsson C., Cederberg H., Chabanova E., De Masi F., Dermitzakis E., Elders P.J., Blom M.T., Hollander M., Eriksen R., Forgie I., Frost G., Giordano G.N., Grallert H., Haid M., Hansen T.H., Jablonka B., Kokkola T., Mahajan A., Mari A., McDonald T.J., Musholt P.B., Pavo I., Prehn C., Ridderstråle M., Ruetten H., Hart L.M.'., Schwenk J.M., Stankevic E., Thomsen H.S., Vangipurapu J., Vestergaard H., Viñuela A., Walker M., Hansen T., Linneberg A., Nielsen H.B., Brunak S., McCarthy M.I., Froguel P., Adamski J., Franks P.W., Laakso M., Beulens J.W.J., Pearson E. , Pedersen O.",The dynamics of the gut microbiota in prediabetes during a four-year follow-up among European patients-an IMI-DIRECT prospective study,Genome medicine,2025,"Gut bacterial genetics, Gut bacterial microbiota, Gut viral microbiota, Insulin sensitivity, Long-term dynamics, Metabolism, Microbial functional pathways, Prediabetes",Experiment 2,"Sweden,Netherlands,Denmark,Finland",Homo sapiens,Feces,UBERON:0001988,"Insulin resistance,Prediabetes syndrome","EFO:0002614,EFO:1001121",Non progressors,Progressors,"To evaluate the genetic stability of the gut bacterial
species using the DMI metric, inter-individual and
intra-individual dissimilarities were calculated separately
for both deletion SVs and variable SVs. For both
types of bacterial SVs, we found a wide range of DMI values
across bacterial species",350,269,NA,16S,123456789,Illumina,relative abundances,Spearman Correlation,0.05,NA,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,30 November 2025,SheikhAlMamun,SheikhAlMamun,"profiles of Canberra distance of variable structural
variants (vSVs) of 39 bacterial species. Degree of microbial individuality (DMI) was labeled. Each box plot represents the distance calculated
from the genetic structural variant profiles within one bacterial species (see Methods), with light-colored boxes indicating intra-individual distances,
while dark-colored boxes are showing inter-individual distances. Bacterial species are listed along the y-axis in descending order based on their DMI
values. Distances are displayed on the x-axis",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. L2-50,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella sp. 4_8_47FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Allocoprococcus|s__Allocoprococcus comes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 3_1_46FAA,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Wegman et al. 2014),k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. SR1/5",1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|3085636|186803|207244|649756;1783272|201174|1760|85004|31953|1678|1680;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|186802|31979|1485|411489;1783272|201174|84998|84999|84107|102106|742722;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|3569723|410072;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|665950;1783272|1239|186801|3085636|186803|841|301301;1783272|1239|186801|3085636|186803|841|166486;1783272|1239|186801|186802|216572|1263|1160721;1783272|1239|186801|186802|216572|1263|40518;1783272|1239|186801|186802|216572|1263|41978;1783272|1239|186801|186802|216572|1263|657323,Complete,NA
bsdb:40665409/2/2,40665409,prospective cohort,40665409,https://doi.org/10.1186/s13073-025-01508-7,NA,"Lyu L., Fan Y., Vogt J.K., Clos-Garcia M., Bonnefond A., Pedersen H.K., Dutta A., Koivula R., Sharma S., Allin K.H., Brorsson C., Cederberg H., Chabanova E., De Masi F., Dermitzakis E., Elders P.J., Blom M.T., Hollander M., Eriksen R., Forgie I., Frost G., Giordano G.N., Grallert H., Haid M., Hansen T.H., Jablonka B., Kokkola T., Mahajan A., Mari A., McDonald T.J., Musholt P.B., Pavo I., Prehn C., Ridderstråle M., Ruetten H., Hart L.M.'., Schwenk J.M., Stankevic E., Thomsen H.S., Vangipurapu J., Vestergaard H., Viñuela A., Walker M., Hansen T., Linneberg A., Nielsen H.B., Brunak S., McCarthy M.I., Froguel P., Adamski J., Franks P.W., Laakso M., Beulens J.W.J., Pearson E. , Pedersen O.",The dynamics of the gut microbiota in prediabetes during a four-year follow-up among European patients-an IMI-DIRECT prospective study,Genome medicine,2025,"Gut bacterial genetics, Gut bacterial microbiota, Gut viral microbiota, Insulin sensitivity, Long-term dynamics, Metabolism, Microbial functional pathways, Prediabetes",Experiment 2,"Sweden,Netherlands,Denmark,Finland",Homo sapiens,Feces,UBERON:0001988,"Insulin resistance,Prediabetes syndrome","EFO:0002614,EFO:1001121",Non progressors,Progressors,"To evaluate the genetic stability of the gut bacterial
species using the DMI metric, inter-individual and
intra-individual dissimilarities were calculated separately
for both deletion SVs and variable SVs. For both
types of bacterial SVs, we found a wide range of DMI values
across bacterial species",350,269,NA,16S,123456789,Illumina,relative abundances,Spearman Correlation,0.05,NA,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 4B,30 November 2025,SheikhAlMamun,SheikhAlMamun,"profiles of Canberra distance of variable structural
variants (vSVs) of 39 bacterial species. Degree of microbial individuality (DMI) was labeled. Each box plot represents the distance calculated
from the genetic structural variant profiles within one bacterial species (see Methods), with light-colored boxes indicating intra-individual distances,
while dark-colored boxes are showing inter-individual distances. Bacterial species are listed along the y-axis in descending order based on their DMI
values. Distances are displayed on the x-axis",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella corporis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,s__bacterium LF-3,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. ER4",3379134|976|200643|171549|171552|838|28128;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|2005525|375288|823;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759|2585118;3379134|976|200643|171549|171550|239759|328814;3366610|28890|183925|2158|2159|2172|2173;3379134|976|200643|171549|815|816|820;3379134|976|200643|171549|2005519|397864|487174;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|171552|577309|454154;1504823;1783272|1239|186801|186802|216572|459786|1519439,Complete,NA
bsdb:40665409/3/1,40665409,prospective cohort,40665409,https://doi.org/10.1186/s13073-025-01508-7,NA,"Lyu L., Fan Y., Vogt J.K., Clos-Garcia M., Bonnefond A., Pedersen H.K., Dutta A., Koivula R., Sharma S., Allin K.H., Brorsson C., Cederberg H., Chabanova E., De Masi F., Dermitzakis E., Elders P.J., Blom M.T., Hollander M., Eriksen R., Forgie I., Frost G., Giordano G.N., Grallert H., Haid M., Hansen T.H., Jablonka B., Kokkola T., Mahajan A., Mari A., McDonald T.J., Musholt P.B., Pavo I., Prehn C., Ridderstråle M., Ruetten H., Hart L.M.'., Schwenk J.M., Stankevic E., Thomsen H.S., Vangipurapu J., Vestergaard H., Viñuela A., Walker M., Hansen T., Linneberg A., Nielsen H.B., Brunak S., McCarthy M.I., Froguel P., Adamski J., Franks P.W., Laakso M., Beulens J.W.J., Pearson E. , Pedersen O.",The dynamics of the gut microbiota in prediabetes during a four-year follow-up among European patients-an IMI-DIRECT prospective study,Genome medicine,2025,"Gut bacterial genetics, Gut bacterial microbiota, Gut viral microbiota, Insulin sensitivity, Long-term dynamics, Metabolism, Microbial functional pathways, Prediabetes",Experiment 3,"Denmark,Finland,Netherlands,Sweden",Homo sapiens,Feces,UBERON:0001988,"Insulin resistance,Prediabetes syndrome","EFO:0002614,EFO:1001121",Non progressors,Progressors,"Participants classified as “progressors” showed measurable longitudinal progression in metabolic or microbiome-associated traits. In this study, progressors were examined for gut bacterial genetic stability by comparing inter-individual and intra-individual dissimilarities using the DMI metric across deletion and variable structural variants.",350,269,48 months,16S,123456789,Illumina,relative abundances,Spearman Correlation,0.05,NA,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A & 6B,30 November 2025,SheikhAlMamun,SheikhAlMamun,"The study explores correlations between the relative abundance of bacterial species and gut bacterial community indices or host metabolic variables. Key species driving community changes are identified through linear regression models. In Figure A, bacterial species are plotted against beta coefficients and standard error, with the top 10 ranked by adjusted p values, indicated by yellow (positive) and blue (negative) dots, where larger dots represent stronger correlations. Figure B shows correlations between bacterial abundance and metabolic changes, also color-coded for strength. Analyses adjust for covariates like age, sex, centers, and bacterial cell load, with significant correlations observed (adjusted p < 0.1).",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. An250,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium UC5.1-1E11,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:253,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:433,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. CAG:451,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|s__Coriobacteriia bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea sp. AF36-15AT,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Evtepia|s__Evtepia gabavorous,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D5,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. AM43-6,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. CAG:382,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__uncultured Blautia sp.,k__Bacillati|p__Bacillota|c__Clostridia|s__uncultured Clostridia bacterium",1783272|1239|186801|186802|3082771|1924093|1965604;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|1697793;1783272|1239|186801|186802|31979|1485|1262785;1783272|1239|186801|186802|31979|1485|1262806;1783272|1239|186801|186802|31979|1485|1262809;1783272|201174|84998|2052159;1783272|1239|186801|3085636|186803|189330|2292041;1783272|1239|186801|186802|2211178|2211183;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|186802|1392389|1297617;1783272|1239|186801|3085636|186803|1898203;1783272|1239|186801|186802|216572|1520815;1783272|1239|186801|186802|216572|1263|2293216;1783272|1239|186801|186802|216572|1263|1262957;1783272|1239|186801|3085636|186803|572511|765821;1783272|1239|186801|244328,Complete,NA
bsdb:40665409/3/2,40665409,prospective cohort,40665409,https://doi.org/10.1186/s13073-025-01508-7,NA,"Lyu L., Fan Y., Vogt J.K., Clos-Garcia M., Bonnefond A., Pedersen H.K., Dutta A., Koivula R., Sharma S., Allin K.H., Brorsson C., Cederberg H., Chabanova E., De Masi F., Dermitzakis E., Elders P.J., Blom M.T., Hollander M., Eriksen R., Forgie I., Frost G., Giordano G.N., Grallert H., Haid M., Hansen T.H., Jablonka B., Kokkola T., Mahajan A., Mari A., McDonald T.J., Musholt P.B., Pavo I., Prehn C., Ridderstråle M., Ruetten H., Hart L.M.'., Schwenk J.M., Stankevic E., Thomsen H.S., Vangipurapu J., Vestergaard H., Viñuela A., Walker M., Hansen T., Linneberg A., Nielsen H.B., Brunak S., McCarthy M.I., Froguel P., Adamski J., Franks P.W., Laakso M., Beulens J.W.J., Pearson E. , Pedersen O.",The dynamics of the gut microbiota in prediabetes during a four-year follow-up among European patients-an IMI-DIRECT prospective study,Genome medicine,2025,"Gut bacterial genetics, Gut bacterial microbiota, Gut viral microbiota, Insulin sensitivity, Long-term dynamics, Metabolism, Microbial functional pathways, Prediabetes",Experiment 3,"Denmark,Finland,Netherlands,Sweden",Homo sapiens,Feces,UBERON:0001988,"Insulin resistance,Prediabetes syndrome","EFO:0002614,EFO:1001121",Non progressors,Progressors,"Participants classified as “progressors” showed measurable longitudinal progression in metabolic or microbiome-associated traits. In this study, progressors were examined for gut bacterial genetic stability by comparing inter-individual and intra-individual dissimilarities using the DMI metric across deletion and variable structural variants.",350,269,48 months,16S,123456789,Illumina,relative abundances,Spearman Correlation,0.05,NA,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 6A & 6B,30 November 2025,SheikhAlMamun,SheikhAlMamun,"Correlations between temporal changes in relative abundance of bacterial
species and temporal changes of host metabolic variables, highlighting changes in relative abundance of bacterial species with parallel changes
in host metabolism. Y-axis lists bacterial species, while x-axis lists host metabolic variable. The dots are colored yellow for positive coefficient
values and blue for negative coefficient values with color intensity indicating the effect size. Dots size indicates the − log10 (adjusted p value)
of the correlation, with larger dots showing smaller adjusted p value. In A and B, beta coefficients and adjusted p values were calculated from linear
regression models after adjusting for co-variates of individual’s age at baseline, sex, study centers, and delta value of bacterial cell load. All
correlations shown are statistically significant after adjustment for multiple comparisons using the Benjamin-Hochberg procedure, with adjusted p
value < 0.1. OGTT means oral glucose tolerance test",decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella corporis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. CAG:155,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Pseudomonadota|s__Proteobacteria bacterium CAG:495,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter|s__Oxalobacter formigenes",1783272|1239|909932|1843488|909930|33024|626940;3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|171552|838|28128;3379134|976|200643|171549|815|816|329854;1783272|1239|186801|186802|216572|459786|1262910;3379134|976|200643|171549|171550|239759|28117;3379134|1224|1262987;3379134|976|200643|171549|2005525|375288|328812;3379134|1224|28216|80840|75682|846|847,Complete,NA
bsdb:40685148/1/1,40685148,time series / longitudinal observational,40685148,https://doi.org/10.1111/jcpe.14201,https://onlinelibrary.wiley.com/doi/10.1111/jcpe.14201,"Stephen A.S., Worrall S., Somani C., Allaker R.P., Davies J., Nibali L. , Donos N.",Non-Surgical Periodontal Therapy Modulates Oral Microbiome in Primary Immunodeficient Children,Journal of clinical periodontology,2025,"16S ribosomal RNA sequencing, microbiota, neutropenia, oral microbiome, periodontal therapy, primary immunodeficiency diseases, subgingival plaque",Experiment 1,United Kingdom,Homo sapiens,Gingival groove,UBERON:0008805,Primary immunodeficiency,MONDO:0003778,Healthy non-Primary Immunodeficiency(PID) children at baseline.,Primary Immunodeficiency (PID) children at baseline,"Primary immunodeficiencies (PIDs) encompass a diverse group of conditions characterised by a compromised immune response, making individuals more susceptible to infections, autoimmunity and malignancies. Subgingival plaque was collected from 3 first molars and 1 first incissor of children without Primary Immunodeficiency(PID) at baseline.",24,24,NA,16S,12,Illumina,log transformation,ANCOM-BC,0.005,NA,NA,age,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,"fig 3b, & S3",22 October 2025,Chyono2,Chyono2,Differential abundance of microbial taxa in Primary Immunodeficiency(PID) and non-Primary Immunodeficiency(PID) children at baseline using ANCOM BC analysis on non-rarefied aggregated taxa up to genus and species levels.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces dentalis,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sp. oral taxon 863,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Proteales|f__Proteaceae|g__Helicia|s__Helicia australasica,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia shahii,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma salivarium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp. oral taxon 078,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella micans,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas artemidis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas infelix,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella sp. oral taxon 808,p__Candidatus Absconditibacteriota|s__candidate division SR1 bacterium taxon 345,p__Candidatus Absconditibacteriota|s__candidate division SR1 bacterium taxon 345",1783272|201174|1760|2037|2049|1654|272548;3379134|29547|3031852|213849|72294|194|199;3379134|29547|3031852|213849|72294|194|204;3379134|976|117743|200644|49546|1016|1227265;33090|35493|3398|232378|4328|83718|83719;1783272|201174|84998|84999|1643824|2767353|1382;3384189|32066|203490|203491|1129771|32067|157691;1783272|544448|2790996|2895623|2895509|2124;1783272|1239|186801|3085636|186803|265975|652706;1783272|1239|186801|3082720|186804|1257|341694;3379134|976|200643|171549|171552|838|189723;1783272|1239|909932|909929|1843491|970|671224;1783272|1239|909932|909929|1843491|970|135082;3379134|976|200643|171549|2005525|195950|712711;221235|713029;221235|713029,Complete,NA
bsdb:40685148/1/2,40685148,time series / longitudinal observational,40685148,https://doi.org/10.1111/jcpe.14201,https://onlinelibrary.wiley.com/doi/10.1111/jcpe.14201,"Stephen A.S., Worrall S., Somani C., Allaker R.P., Davies J., Nibali L. , Donos N.",Non-Surgical Periodontal Therapy Modulates Oral Microbiome in Primary Immunodeficient Children,Journal of clinical periodontology,2025,"16S ribosomal RNA sequencing, microbiota, neutropenia, oral microbiome, periodontal therapy, primary immunodeficiency diseases, subgingival plaque",Experiment 1,United Kingdom,Homo sapiens,Gingival groove,UBERON:0008805,Primary immunodeficiency,MONDO:0003778,Healthy non-Primary Immunodeficiency(PID) children at baseline.,Primary Immunodeficiency (PID) children at baseline,"Primary immunodeficiencies (PIDs) encompass a diverse group of conditions characterised by a compromised immune response, making individuals more susceptible to infections, autoimmunity and malignancies. Subgingival plaque was collected from 3 first molars and 1 first incissor of children without Primary Immunodeficiency(PID) at baseline.",24,24,NA,16S,12,Illumina,log transformation,ANCOM-BC,0.005,NA,NA,age,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,fig 3b & S3,22 October 2025,Chyono2,Chyono2,Differential abundance of microbial taxa in Primary Immunodeficiency (PID) children non-Primary Immunodeficiency (PID) children at baseline using ANCOM BC analysis on non-rarefied aggregated taxa up to genus and species levels. .,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus intermedius,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius",1783272|201174|1760|2037|2049|1654;3379134|1224|28216|206351|481|482;1783272|201174|1760|85006|1268|32207|172042;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300|1301|1338;1783272|1239|91061|186826|1300|1301|1304,Complete,NA
bsdb:40685148/2/1,40685148,time series / longitudinal observational,40685148,https://doi.org/10.1111/jcpe.14201,https://onlinelibrary.wiley.com/doi/10.1111/jcpe.14201,"Stephen A.S., Worrall S., Somani C., Allaker R.P., Davies J., Nibali L. , Donos N.",Non-Surgical Periodontal Therapy Modulates Oral Microbiome in Primary Immunodeficient Children,Journal of clinical periodontology,2025,"16S ribosomal RNA sequencing, microbiota, neutropenia, oral microbiome, periodontal therapy, primary immunodeficiency diseases, subgingival plaque",Experiment 2,United Kingdom,Homo sapiens,Gingival groove,UBERON:0008805,Primary immunodeficiency,MONDO:0003778,Primary Immunodeficiency (PID)children pre-therapy,Primary Immunodeficiency(PID)children at 6 months post-therapy,Subgingival plaque was collected from three first molar and one first incisor sites of  Primary Immunodeficiency(PID) children after therapy,24,24,NA,16S,12,Illumina,log transformation,ANCOM-BC,0.05,NA,NA,age,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,fig 3A & S2,22 October 2025,Chyono2,Chyono2,Differential abundance of microbial taxa in PID and non-PID children pre & post-therapy using ANCOM BC analysis on non-rarefied aggregated taxa up to genus and species levels.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella sp. oral taxon 011,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales|f__Russulaceae|g__Gymnomyces|s__Gymnomyces sp. Trappe 13006,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella kingae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria mucosa,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sicca,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ottowia|s__Ottowia sp. oral taxon 894,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces espinosus",3379134|1224|28216|206351|481|538|712272;4751|5204|155619|452342|5401|129530|234081;3379134|1224|28216|206351|481|32257|504;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481|482|495;3379134|1224|28216|206351|481|482|488;3379134|1224|28216|206351|481|482|490;3379134|1224|28216|206351|481|482|28449;3379134|1224|28216|80840|80864|219181|1658672;1783272|201174|1760|85006|1268|32207|2047;1783272|201174|1760|85011|2062|1883|1965,Complete,NA
bsdb:40685148/2/2,40685148,time series / longitudinal observational,40685148,https://doi.org/10.1111/jcpe.14201,https://onlinelibrary.wiley.com/doi/10.1111/jcpe.14201,"Stephen A.S., Worrall S., Somani C., Allaker R.P., Davies J., Nibali L. , Donos N.",Non-Surgical Periodontal Therapy Modulates Oral Microbiome in Primary Immunodeficient Children,Journal of clinical periodontology,2025,"16S ribosomal RNA sequencing, microbiota, neutropenia, oral microbiome, periodontal therapy, primary immunodeficiency diseases, subgingival plaque",Experiment 2,United Kingdom,Homo sapiens,Gingival groove,UBERON:0008805,Primary immunodeficiency,MONDO:0003778,Primary Immunodeficiency (PID)children pre-therapy,Primary Immunodeficiency(PID)children at 6 months post-therapy,Subgingival plaque was collected from three first molar and one first incisor sites of  Primary Immunodeficiency(PID) children after therapy,24,24,NA,16S,12,Illumina,log transformation,ANCOM-BC,0.05,NA,NA,age,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,fig 3A & S2,22 October 2025,Chyono2,Chyono2,Differential abundance of microbial taxa in PID and non-PID children pre & post-therapy using ANCOMBC  analysis on non-rarefied aggregated taxa up to genus and species levels.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema socranskii",1783272|1239|91061|1385|539738|1378|1379;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301;3379134|203691|203692|136|2845253|157|53419,Complete,NA
bsdb:40685148/3/1,40685148,time series / longitudinal observational,40685148,https://doi.org/10.1111/jcpe.14201,https://onlinelibrary.wiley.com/doi/10.1111/jcpe.14201,"Stephen A.S., Worrall S., Somani C., Allaker R.P., Davies J., Nibali L. , Donos N.",Non-Surgical Periodontal Therapy Modulates Oral Microbiome in Primary Immunodeficient Children,Journal of clinical periodontology,2025,"16S ribosomal RNA sequencing, microbiota, neutropenia, oral microbiome, periodontal therapy, primary immunodeficiency diseases, subgingival plaque",Experiment 3,United Kingdom,Homo sapiens,Gingival groove,UBERON:0008805,Primary immunodeficiency,MONDO:0003778,Primary Immunodeficiency(PID) Children Pre-therapy,Primary Immunodeficiency(PID)children at 6months post therapy,Subgingival plaque was collected from 3 first molars and 1 first incissor at 6 months post therapy from children with Primary Immunodeficiency(PID).,24,24,NA,16S,12,Illumina,relative abundances,Beta Binomial Regression,0.05,NA,NA,age,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,Fig4A,22 October 2025,Chyono2,Chyono2,Differential abundance analysis of microbial taxa post therapy in PID children using the corncob method.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flava",3379134|1224|28216|206351|481|482|1107316;3379134|1224|28216|206351|481|482|34026,Complete,NA
bsdb:40685148/3/2,40685148,time series / longitudinal observational,40685148,https://doi.org/10.1111/jcpe.14201,https://onlinelibrary.wiley.com/doi/10.1111/jcpe.14201,"Stephen A.S., Worrall S., Somani C., Allaker R.P., Davies J., Nibali L. , Donos N.",Non-Surgical Periodontal Therapy Modulates Oral Microbiome in Primary Immunodeficient Children,Journal of clinical periodontology,2025,"16S ribosomal RNA sequencing, microbiota, neutropenia, oral microbiome, periodontal therapy, primary immunodeficiency diseases, subgingival plaque",Experiment 3,United Kingdom,Homo sapiens,Gingival groove,UBERON:0008805,Primary immunodeficiency,MONDO:0003778,Primary Immunodeficiency(PID) Children Pre-therapy,Primary Immunodeficiency(PID)children at 6months post therapy,Subgingival plaque was collected from 3 first molars and 1 first incissor at 6 months post therapy from children with Primary Immunodeficiency(PID).,24,24,NA,16S,12,Illumina,relative abundances,Beta Binomial Regression,0.05,NA,NA,age,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Fig4A,22 October 2025,Chyono2,Chyono2,Differential abundance analysis of microbial taxa post therapy in PID children using the corncob method.,decreased,NA,NA,Complete,NA
bsdb:40685148/4/1,40685148,time series / longitudinal observational,40685148,https://doi.org/10.1111/jcpe.14201,https://onlinelibrary.wiley.com/doi/10.1111/jcpe.14201,"Stephen A.S., Worrall S., Somani C., Allaker R.P., Davies J., Nibali L. , Donos N.",Non-Surgical Periodontal Therapy Modulates Oral Microbiome in Primary Immunodeficient Children,Journal of clinical periodontology,2025,"16S ribosomal RNA sequencing, microbiota, neutropenia, oral microbiome, periodontal therapy, primary immunodeficiency diseases, subgingival plaque",Experiment 4,United Kingdom,Homo sapiens,Gingival groove,UBERON:0008805,Primary immunodeficiency,MONDO:0003778,Non-Primary Immunodeficiency(PID) Children at baseline,Primary Immunodeficiency(PID)children at baseline,"Primary immunodeficiencies (PIDs) encompass a diverse group of conditions characterised by a compromised immune response, making individuals more susceptible to infections, autoimmunity and malignancies. Subgingival microbiome samples were collected from Primary Immunodeficiency (PID) Children at baseline",24,24,NA,16S,12,Illumina,relative abundances,Beta Binomial Regression,0.05,NA,NA,age,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,Fig4B,22 October 2025,Chyono2,Chyono2,Differential abundance analysis of microbial taxa at baseline between Primary Immunodeficiency(PID) and non-Primary Immunodeficiency(PID) children using the corncob method.,increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sp. oral taxon 332,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Paraburkholderia|s__Paraburkholderia kururiensis|s__Paraburkholderia kururiensis subsp. kururiensis",3379134|29547|3031852|213849|72294|194|199;3379134|976|117743|200644|49546|1016|712213;3379134|1224|28216|80840|119060|1822464|984307|89498,Complete,NA
bsdb:40685148/4/2,40685148,time series / longitudinal observational,40685148,https://doi.org/10.1111/jcpe.14201,https://onlinelibrary.wiley.com/doi/10.1111/jcpe.14201,"Stephen A.S., Worrall S., Somani C., Allaker R.P., Davies J., Nibali L. , Donos N.",Non-Surgical Periodontal Therapy Modulates Oral Microbiome in Primary Immunodeficient Children,Journal of clinical periodontology,2025,"16S ribosomal RNA sequencing, microbiota, neutropenia, oral microbiome, periodontal therapy, primary immunodeficiency diseases, subgingival plaque",Experiment 4,United Kingdom,Homo sapiens,Gingival groove,UBERON:0008805,Primary immunodeficiency,MONDO:0003778,Non-Primary Immunodeficiency(PID) Children at baseline,Primary Immunodeficiency(PID)children at baseline,"Primary immunodeficiencies (PIDs) encompass a diverse group of conditions characterised by a compromised immune response, making individuals more susceptible to infections, autoimmunity and malignancies. Subgingival microbiome samples were collected from Primary Immunodeficiency (PID) Children at baseline",24,24,NA,16S,12,Illumina,relative abundances,Beta Binomial Regression,0.05,NA,NA,age,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,fig 4B,24 October 2025,Chyono2,Chyono2,Differential abundance of microbial taxa at baseline between Primary Immunodeficiency(PID) children and non-Primary Immunodeficiency(PID)children using the Corncob method.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 171,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius",1783272|201174|1760|2037|2049|1654|706438;1783272|201174|1760|85009|85015|1839;1783272|201174|1760|85006|1268|32207|172042;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300|1301|1304,Complete,NA
bsdb:40685148/5/1,40685148,time series / longitudinal observational,40685148,https://doi.org/10.1111/jcpe.14201,https://onlinelibrary.wiley.com/doi/10.1111/jcpe.14201,"Stephen A.S., Worrall S., Somani C., Allaker R.P., Davies J., Nibali L. , Donos N.",Non-Surgical Periodontal Therapy Modulates Oral Microbiome in Primary Immunodeficient Children,Journal of clinical periodontology,2025,"16S ribosomal RNA sequencing, microbiota, neutropenia, oral microbiome, periodontal therapy, primary immunodeficiency diseases, subgingival plaque",Experiment 5,United Kingdom,Homo sapiens,Gingival groove,UBERON:0008805,Primary immunodeficiency,MONDO:0003778,Non-Primary Immunodeficiency(PID) Children at baseline,Primary Immunodeficiency(PID)children at baseline with neutrophil count,Subgingival microbiome plaques were collected at baseline from PID children with measurable neutrophil counts.,24,24,NA,16S,12,Illumina,relative abundances,Beta Binomial Regression,0.05,NA,NA,age,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,fig 4c,23 October 2025,Chyono2,Chyono2,Correlation of CLR-transformed abundance with absolute neutrophil counts for the PID children at baseline. Associations with coefficients > 0.4 and < −0.4,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|201174|1760|2037|2049|1654;3379134|976|117743|200644|49546|1016;1783272|1239|91061|1385|539738|1378|1379;3379134|976|200643|171549|171552|838,Complete,NA
bsdb:40688000/1/1,40688000,case-control,40688000,https://doi.org/10.1016/j.csbj.2025.06.006,https://www.csbj.org/article/S2001-0370(25)00224-7/fulltext,"Belkessa S., Pasolli E., Medrouh B., Berg R.P.K.D., Andersen L.O.'., Nielsen H.V. , Stensvold C.R.",Structure analysis of human gut microbiota associated with single-celled gut protists using Next-Generation Sequencing of 16S and 18S rRNA genes,Computational and structural biotechnology journal,2025,"Amplicon, Commensal, Host-pathogen interactions, Microbiome, Protozoa, Single-celled protists",Experiment 1,Algeria,Homo sapiens,Feces,UBERON:0001988,Protozoa infectious disease,MONDO:0002428,Giardia-negative individuals,Giardia-positive individuals,"Individuals with Giardia duodenalis; one of the most common pathogenic protozoa of the human intestine with the ability to cause diarrhea, malabsorption, malnutrition, delayed cognitive function in children, and protracted post-infectious bowel syndromes",31,60,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4A,28 October 2025,Chyono2,"Chyono2,Fiddyhamma",Linear discriminant analysis Effect Size (LEfSe) result of prokaryotic species composition across unicellular eukaryote carrier status at the species level between Giardia-negative (strong blue) compared with Giardia-positive (pure yellow),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae",1783272|201174|1760|85004|31953|1678|28026;3379134|1224|1236|91347|543|570|573,Complete,KateRasheed
bsdb:40688000/1/2,40688000,case-control,40688000,https://doi.org/10.1016/j.csbj.2025.06.006,https://www.csbj.org/article/S2001-0370(25)00224-7/fulltext,"Belkessa S., Pasolli E., Medrouh B., Berg R.P.K.D., Andersen L.O.'., Nielsen H.V. , Stensvold C.R.",Structure analysis of human gut microbiota associated with single-celled gut protists using Next-Generation Sequencing of 16S and 18S rRNA genes,Computational and structural biotechnology journal,2025,"Amplicon, Commensal, Host-pathogen interactions, Microbiome, Protozoa, Single-celled protists",Experiment 1,Algeria,Homo sapiens,Feces,UBERON:0001988,Protozoa infectious disease,MONDO:0002428,Giardia-negative individuals,Giardia-positive individuals,"Individuals with Giardia duodenalis; one of the most common pathogenic protozoa of the human intestine with the ability to cause diarrhea, malabsorption, malnutrition, delayed cognitive function in children, and protracted post-infectious bowel syndromes",31,60,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4A,29 October 2025,Chyono2,"Chyono2,Fiddyhamma",Linear discriminant analysis Effect Size (LEfSe) result of prokaryotic species composition across unicellular eukaryote carrier status at the species level between Giardia-negative (strong blue) compared with Giardia-positive (pure yellow),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium cellulovorans,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas rupellensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans (ex Liu et al. 2021)",3379134|976|200643|171549|815|816|28111;1783272|1239|186801|186802|31979|1485|1493;1783272|1239|909932|909929|1843491|158846|491921;3379134|1224|28216|80840|995019|577310|487175;3379134|976|200643|171549|815|909656|204516;1783272|1239|186801|186802|216572|1263|3062497,Complete,KateRasheed
bsdb:40688000/2/1,40688000,case-control,40688000,https://doi.org/10.1016/j.csbj.2025.06.006,https://www.csbj.org/article/S2001-0370(25)00224-7/fulltext,"Belkessa S., Pasolli E., Medrouh B., Berg R.P.K.D., Andersen L.O.'., Nielsen H.V. , Stensvold C.R.",Structure analysis of human gut microbiota associated with single-celled gut protists using Next-Generation Sequencing of 16S and 18S rRNA genes,Computational and structural biotechnology journal,2025,"Amplicon, Commensal, Host-pathogen interactions, Microbiome, Protozoa, Single-celled protists",Experiment 2,Algeria,Homo sapiens,Feces,UBERON:0001988,Protozoa infectious disease,MONDO:0002428,Blastocystis-negative individuals,Blastocystis-positive individuals,Individuals with Blastocystis; a single-celled eucaryotic organism that lives in the intestines. Samples were considered positive for Blastocystis if at least > 1.5 % of the total reads in the sample were assigned to Blastocystis at the genus level.,47,44,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure 4B,29 October 2025,Chyono2,"Chyono2,Fiddyhamma",Linear discriminant analysis Effect Size (LEfSe) result of prokaryotic species composition across unicellular eukaryote carrier status at the species level between Blastocystis-negative (strong blue) compared with Blastocystis-positive (pure yellow).,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium mitsuokai,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eshraghiella|s__Eshraghiella crossota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella jalaludinii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio|s__Succinivibrio dextrinosolvens,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema succinifaciens,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",1783272|1239|526524|526525|2810280|135858|100886;3379134|200940|3031449|213115|194924|872|901;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|3342669|45851;1783272|1239|526524|526525|128827|1573535|1735;1783272|1239|909932|909929|1843491|52225|187979;3379134|1224|1236|135624|83763|83770|83771;3379134|203691|203692|136|2845253|157|167;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|459786,Complete,KateRasheed
bsdb:40688000/2/2,40688000,case-control,40688000,https://doi.org/10.1016/j.csbj.2025.06.006,https://www.csbj.org/article/S2001-0370(25)00224-7/fulltext,"Belkessa S., Pasolli E., Medrouh B., Berg R.P.K.D., Andersen L.O.'., Nielsen H.V. , Stensvold C.R.",Structure analysis of human gut microbiota associated with single-celled gut protists using Next-Generation Sequencing of 16S and 18S rRNA genes,Computational and structural biotechnology journal,2025,"Amplicon, Commensal, Host-pathogen interactions, Microbiome, Protozoa, Single-celled protists",Experiment 2,Algeria,Homo sapiens,Feces,UBERON:0001988,Protozoa infectious disease,MONDO:0002428,Blastocystis-negative individuals,Blastocystis-positive individuals,Individuals with Blastocystis; a single-celled eucaryotic organism that lives in the intestines. Samples were considered positive for Blastocystis if at least > 1.5 % of the total reads in the sample were assigned to Blastocystis at the genus level.,47,44,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Figure 4B,29 October 2025,Chyono2,"Chyono2,Fiddyhamma",Linear discriminant analysis Effect Size (LEfSe) result of procaryotic species composition across unicellular eucaryote carrier status at the species level between Blastocystis-negative (strong blue) compared to Blastocystis-positive (pure yellow).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae|g__Elusimicrobium|s__Elusimicrobium minutum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter faecis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",3379134|976|200643|171549|815|816|818;3379134|74152|641853|641854|641876|423604|423605;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|3085636|186803|2316020|592978;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|526524|526525|2810281|191303|154288;1783272|1239|186801|3085636|186803|2316020|33039,Complete,KateRasheed
bsdb:40688000/3/1,40688000,case-control,40688000,https://doi.org/10.1016/j.csbj.2025.06.006,https://www.csbj.org/article/S2001-0370(25)00224-7/fulltext,"Belkessa S., Pasolli E., Medrouh B., Berg R.P.K.D., Andersen L.O.'., Nielsen H.V. , Stensvold C.R.",Structure analysis of human gut microbiota associated with single-celled gut protists using Next-Generation Sequencing of 16S and 18S rRNA genes,Computational and structural biotechnology journal,2025,"Amplicon, Commensal, Host-pathogen interactions, Microbiome, Protozoa, Single-celled protists",Experiment 3,Algeria,Homo sapiens,Feces,UBERON:0001988,Protozoa infectious disease,MONDO:0002428,Entamoeba-negative individuals,Entamoeba-positive individuals,Individuals with Entamoeba; a single-celled eucaryotic organism that lives in the intestines.,76,15,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4C,29 October 2025,Chyono2,"Chyono2,Fiddyhamma",Linear discriminant analysis Effect Size (LEfSe) result of prokaryotic species composition across unicellular eukaryote carrier status at the species level between Entamoeba-negative (strong blue) compared with Entamoeba-positive (pure yellow),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium mitsuokai,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium cellulovorans,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia sedimentorum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles|s__Roseateles terrae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",1783272|201174|1760|85004|31953|1678|1680;1783272|1239|526524|526525|2810280|135858|100886;1783272|1239|186801|186802|31979|1485|1493;1783272|1239|526524|526525|128827|1573535|1735;1783272|1239|186801|3082720|186804|1501226|1368474;3379134|1224|28216|80840|2975441|93681|431060;3379134|976|200643|171549|171550|239759,Complete,KateRasheed
bsdb:40688000/3/2,40688000,case-control,40688000,https://doi.org/10.1016/j.csbj.2025.06.006,https://www.csbj.org/article/S2001-0370(25)00224-7/fulltext,"Belkessa S., Pasolli E., Medrouh B., Berg R.P.K.D., Andersen L.O.'., Nielsen H.V. , Stensvold C.R.",Structure analysis of human gut microbiota associated with single-celled gut protists using Next-Generation Sequencing of 16S and 18S rRNA genes,Computational and structural biotechnology journal,2025,"Amplicon, Commensal, Host-pathogen interactions, Microbiome, Protozoa, Single-celled protists",Experiment 3,Algeria,Homo sapiens,Feces,UBERON:0001988,Protozoa infectious disease,MONDO:0002428,Entamoeba-negative individuals,Entamoeba-positive individuals,Individuals with Entamoeba; a single-celled eucaryotic organism that lives in the intestines.,76,15,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4C,29 October 2025,Chyono2,"Chyono2,Fiddyhamma",Linear discriminant analysis Effect Size (LEfSe) result of procaryotic species composition across unicellular eucaryote carrier status at the species level between Entamoeba-negative (strong blue) compared with Entamoeba-positive (pure yellow),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium angulatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",3379134|976|200643|171549|815|816|291644;1783272|201174|1760|85004|31953|1678|1683;1783272|201174|1760|85004|31953|1678|28026;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|3085636|186803|841|301302;3379134|1224|28216|80840|995019|40544|40545;1783272|1239|186801|3085636|186803|2316020|33039,Complete,KateRasheed
bsdb:40688000/4/1,40688000,case-control,40688000,https://doi.org/10.1016/j.csbj.2025.06.006,https://www.csbj.org/article/S2001-0370(25)00224-7/fulltext,"Belkessa S., Pasolli E., Medrouh B., Berg R.P.K.D., Andersen L.O.'., Nielsen H.V. , Stensvold C.R.",Structure analysis of human gut microbiota associated with single-celled gut protists using Next-Generation Sequencing of 16S and 18S rRNA genes,Computational and structural biotechnology journal,2025,"Amplicon, Commensal, Host-pathogen interactions, Microbiome, Protozoa, Single-celled protists",Experiment 4,Algeria,Homo sapiens,Feces,UBERON:0001988,Protozoa infectious disease,MONDO:0002428,Archamoebae-negative individuals,Archamoebae-positive individuals,"Individuals with Archamoebae; a group of anaerobic, free-living or parasitic organisms single-celled eucaryotic organism that lives in the intestines.",73,18,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4D,29 October 2025,Chyono2,"Chyono2,Fiddyhamma",Linear discriminant analysis Effect Size (LEfSe) result of prokaryotic species composition across unicellular eukaryote carrier status at the species level between Archamoebae-negative (strong blue) compared with Archamoebae-positive (pure yellow),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium mitsuokai,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium cellulovorans,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae|g__Elusimicrobium|s__Elusimicrobium minutum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio|s__Succinivibrio dextrinosolvens,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema berlinense,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",1783272|201174|1760|85004|31953|1678|1680;1783272|1239|526524|526525|2810280|135858|100886;1783272|1239|186801|186802|31979|1485|1493;3379134|74152|641853|641854|641876|423604|423605;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|526524|526525|128827|1573535|1735;3379134|976|200643|171549|171552|2974265|363265;3379134|1224|1236|135624|83763|83770|83771;3379134|203691|203692|136|2845253|157|225004;3379134|976|200643|171549|171550|239759,Complete,KateRasheed
bsdb:40688000/4/2,40688000,case-control,40688000,https://doi.org/10.1016/j.csbj.2025.06.006,https://www.csbj.org/article/S2001-0370(25)00224-7/fulltext,"Belkessa S., Pasolli E., Medrouh B., Berg R.P.K.D., Andersen L.O.'., Nielsen H.V. , Stensvold C.R.",Structure analysis of human gut microbiota associated with single-celled gut protists using Next-Generation Sequencing of 16S and 18S rRNA genes,Computational and structural biotechnology journal,2025,"Amplicon, Commensal, Host-pathogen interactions, Microbiome, Protozoa, Single-celled protists",Experiment 4,Algeria,Homo sapiens,Feces,UBERON:0001988,Protozoa infectious disease,MONDO:0002428,Archamoebae-negative individuals,Archamoebae-positive individuals,"Individuals with Archamoebae; a group of anaerobic, free-living or parasitic organisms single-celled eucaryotic organism that lives in the intestines.",73,18,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4D,29 October 2025,Chyono2,"Chyono2,Fiddyhamma",Linear discriminant analysis Effect Size (LEfSe) result of prokaryotic species composition across unicellular eukaryote carrier status at the species level between Archamoebae-negative (strong blue) compared with Archamoebae-positive (pure yellow),decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium angulatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",1783272|1239|186801|3085636|186803|207244|649756;3379134|976|200643|171549|815|816|28116;1783272|201174|1760|85004|31953|1678|1683;1783272|201174|1760|85004|31953|1678|28026;3379134|1224|1236|91347|543|561|562;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|3085636|186803|841|301302;3379134|1224|28216|80840|995019|40544|40545;3379134|1224|28216|80840|995019|40544,Complete,KateRasheed
bsdb:40708214/1/1,40708214,randomized controlled trial,40708214,https://doi.org/10.1002/nau.70119,NA,"van Veen F.E.E., Serkani Z.E., Berendsen S., Kraaij R., Bode L., Hays J.P., Scheepe J.R. , Blok B.F.M.",The Urinary Microbiome in Women Using Single-Use Versus Reusable Catheters for Intermittent Catheterization: An Exploratory Substudy of the COMPaRE Trial,Neurourology and urodynamics,2025,"microbiota, sustainable development, urinary bladder, urinary catheters, urinary tract infections",Experiment 1,Netherlands,Homo sapiens,Urine,UBERON:0001088,Urinary retention,HP:0000016,Week 0 (single-use catheter - reusable group),Week 6 (reusable catheter - reusable group),"Patients using reusable catheters (Cliny or PureCath brands) cleaned and stored in 1:80 dilution of 2% sodium hypochlorite, with each catheter used for 2 weeks",12,12,3 months,16S,123,Illumina,raw counts,DESeq2,0.01,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,unchanged,NA,Signature 1,"Figure 5, Within Text: 3.4 “ Differential Abundance Analysis”",12 August 2025,Martha KJ,"Martha KJ,Tosin",Differential abundance of ASVs. Volcano plot of estimated Log2 fold Change in ASV abundance between single‐use and reusable catheters (reusable group: Week 0 vs. 6) and corresponding Benjamini‐Hochberg corrected p‐values from negative binomial Wald tests as implemented in the DESeq,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia",1783272|1239|909932|1843489|31977|29465;1783272|1239|1737404|1737405|1570339|150022,Complete,Svetlana up
bsdb:40708214/1/2,40708214,randomized controlled trial,40708214,https://doi.org/10.1002/nau.70119,NA,"van Veen F.E.E., Serkani Z.E., Berendsen S., Kraaij R., Bode L., Hays J.P., Scheepe J.R. , Blok B.F.M.",The Urinary Microbiome in Women Using Single-Use Versus Reusable Catheters for Intermittent Catheterization: An Exploratory Substudy of the COMPaRE Trial,Neurourology and urodynamics,2025,"microbiota, sustainable development, urinary bladder, urinary catheters, urinary tract infections",Experiment 1,Netherlands,Homo sapiens,Urine,UBERON:0001088,Urinary retention,HP:0000016,Week 0 (single-use catheter - reusable group),Week 6 (reusable catheter - reusable group),"Patients using reusable catheters (Cliny or PureCath brands) cleaned and stored in 1:80 dilution of 2% sodium hypochlorite, with each catheter used for 2 weeks",12,12,3 months,16S,123,Illumina,raw counts,DESeq2,0.01,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,unchanged,NA,Signature 2,"Figure 5, Within Text: 3.4 “ Differential Abundance Analysis”",12 August 2025,Martha KJ,"Martha KJ,Tosin",Differential abundance of ASVs. Volcano plot of estimated Log2 fold Change in ASV abundance between single‐use and reusable catheters (reusable group: Week 0 vs. 6) and corresponding Benjamini‐Hochberg corrected p‐values from negative binomial Wald tests as implemented in the DESeq.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",1783272|1239|91061|186826|186827|1375;3379134|1224|1236|91347|543|1940338,Complete,Svetlana up
bsdb:40713506/1/1,40713506,case-control,40713506,10.1186/s12866-025-04184-0,NA,"Zhang T., Tong C., Wang J., Gao S., Li K. , Wang X.",An analysis of the vaginal microbiota in women positive for group B Streptococcus during the third trimester of pregnancy,BMC microbiology,2025,"Group B Streptococcus, Pregnant, Vagina, Vaginal microbiota",Experiment 1,China,Homo sapiens,Vagina,UBERON:0000996,Streptococcal infection,EFO:1001476,GBSneg (group B Streptococcus culture-negative) pregnant women,GBSpos (group B Streptococcus culture-positive) pregnant women,Pregnant women who tested positive for GBS (group B Streptococcus) by culture during the third trimester,31,22,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"gestational age,parity",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 6,7 October 2025,Tosin,Tosin,Linear discriminant analysis (LDA) effect size (LEfSe) biomarker analysis showing taxa with significant differential abundance in GBS (group B streptococcus) culture-negative versus GBS (group B streptococcus) culture-positive pregnant women,increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae",1783272|201174|84992;1783272|201174;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1311,Complete,KateRasheed
bsdb:40713506/1/2,40713506,case-control,40713506,10.1186/s12866-025-04184-0,NA,"Zhang T., Tong C., Wang J., Gao S., Li K. , Wang X.",An analysis of the vaginal microbiota in women positive for group B Streptococcus during the third trimester of pregnancy,BMC microbiology,2025,"Group B Streptococcus, Pregnant, Vagina, Vaginal microbiota",Experiment 1,China,Homo sapiens,Vagina,UBERON:0000996,Streptococcal infection,EFO:1001476,GBSneg (group B Streptococcus culture-negative) pregnant women,GBSpos (group B Streptococcus culture-positive) pregnant women,Pregnant women who tested positive for GBS (group B Streptococcus) by culture during the third trimester,31,22,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,"gestational age,parity",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 6,7 October 2025,Tosin,Tosin,Linear discriminant analysis (LDA) effect size (LEfSe) biomarker analysis showing taxa with significant differential abundance in GBS (group B streptococcus) culture-negative versus GBS (group B streptococcus) culture-positive pregnant women,decreased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners",1783272|1239|91061;1783272|1239;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|1578|47770;1783272|1239|91061|186826|33958|1578|147802,Complete,KateRasheed
bsdb:40739184/1/1,40739184,laboratory experiment,40739184,https://doi.org/10.1186/s12866-025-04198-8,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04198-8#ref-CR29,"Tang H.B., Si Y.X., Li H.D., Dang W. , Lu H.L.","Intestinal microbial dysbiosis under nitrite stress in juvenile three-keeled pond turtles, Mauremys reevesii",BMC microbiology,2025,"Cultured freshwater turtle, Functional metagenomics, Intestinal microbial dysbiosis, Nitrite stress, Pathogenic prevalence",Experiment 1,China,Mauremys reevesii,Intestine,UBERON:0000160,Nitrite measurement,EFO:0010138,1mg/L + 10mg/L + 100mg/L exposed group,0mg/L exposed group,Healthy juvenile turtles not exposed to nitrite which served as controls,15,5,NA,16S,34,Illumina,relative abundances,"LEfSe,Kruskall-Wallis",0.05,TRUE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,17 October 2025,Chumzine,"Chumzine,Fiddyhamma",Differentially abundant bacterial taxa among groups were identified by LefSe analysis with LDA scores > 3.0 and Kruskal-Wallis test P < 0.05,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Beijerinckiaceae,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Gemmatales|f__Gemmataceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Intrasporangiaceae|g__Nostocoides,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Pirellulales|f__Pirellulaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|g__Rhodobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Rhodopseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Roseomonadaceae|g__Roseomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae,k__Pseudomonadati|p__Lentisphaerota,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Gemmatales|f__Gemmataceae",3379134|1224|28211|356|45404;3379134|976|1853228|1853229|563835;1783272|1239|526524|526525|128827;3379134|203682|203683|2691355|1914233;3379134|1224|28211|356;1783272|201174|1760|85006|85021;3379134|1224|28211|356|69277|68287;1783272|201174|1760|85006|85021|99479;3379134|203682|203683|2691354|2691357;1783272|1239|186801|3085636|186803|46205;3379134|1224|28211|204455|1060;3379134|1224|28211|356|41294|1073;3379134|1224|28211|3120395|3385906|125216;3379134|1224|1236|135624|83763;3379134|1224|28211|356|335928;3379134|256845;3379134|203682|203683|2691355|1914233,Complete,KateRasheed
bsdb:40739184/2/1,40739184,laboratory experiment,40739184,https://doi.org/10.1186/s12866-025-04198-8,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04198-8#ref-CR29,"Tang H.B., Si Y.X., Li H.D., Dang W. , Lu H.L.","Intestinal microbial dysbiosis under nitrite stress in juvenile three-keeled pond turtles, Mauremys reevesii",BMC microbiology,2025,"Cultured freshwater turtle, Functional metagenomics, Intestinal microbial dysbiosis, Nitrite stress, Pathogenic prevalence",Experiment 2,China,Mauremys reevesii,Intestine,UBERON:0000160,Nitrite measurement,EFO:0010138,0mg/L + 10mg/L + 100mg/L exposed group,1mg/L exposed group,Healthy juvenile turtles exposed to 1mg/L nitrite which served as a low-concentration group,15,5,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,LEfSe",0.05,TRUE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,23 October 2025,Chumzine,"Chumzine,Fiddyhamma",Differentially abundant bacterial taxa among groups were identified by LefSe analysis with LDA scores > 3.0 and Kruskal-Wallis test P < 0.05,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Alsobacteraceae|g__Alsobacter,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio,p__Candidatus Altimarinota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermatophilaceae,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Isosphaerales|f__Isosphaeraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Kaistiaceae|g__Kaistia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Kaistiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium FD2005,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Paenarthrobacter,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Isosphaerales|f__Isosphaeraceae|g__Paludisphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Polynucleobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Schwartzia,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Isosphaerales|f__Isosphaeraceae|g__Singulisphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Thauera,p__Candidatus Altimarinota|g__Candidatus Altimarinus",3379134|1224|28211|356|2792775|1502180;1783272|1239|909932|909929|1843491|82373;363464;1783272|201174|1760|85006|85018;3379134|203682|203683|2691356|1763524;3379134|1224|28211|356|2831111|166953;3379134|1224|28211|356|2831111;1783272|1239|186801|3085636|186803|1410623;1783272|201174|1760|85006|1268|1742992;3379134|203682|203683|2691356|1763524|1763521;1783272|1239|186801|3082720|186804;3379134|1224|28216|80840|119060|44013;3379134|976|200643|171549|171550;1783272|1239|186801|3082720|186804|1501226;1783272|1239|909932|909929|1843491|55506;3379134|203682|203683|2691356|1763524|466152;1783272|1239|186801|3082720|186804|1505652;3379134|1224|28216|206389|2008794|33057;363464|1432330,Complete,KateRasheed
bsdb:40739184/3/1,40739184,laboratory experiment,40739184,https://doi.org/10.1186/s12866-025-04198-8,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04198-8#ref-CR29,"Tang H.B., Si Y.X., Li H.D., Dang W. , Lu H.L.","Intestinal microbial dysbiosis under nitrite stress in juvenile three-keeled pond turtles, Mauremys reevesii",BMC microbiology,2025,"Cultured freshwater turtle, Functional metagenomics, Intestinal microbial dysbiosis, Nitrite stress, Pathogenic prevalence",Experiment 3,China,Mauremys reevesii,Intestine,UBERON:0000160,Nitrite measurement,EFO:0010138,0mg/L + 1mg/L + 100mg/L exposed group,10mg/L exposed group,Healthy juvenile turtles exposed to 10mg/L nitrite which served as elevated nitrite concentration group,15,5,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,LEfSe",0.05,TRUE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,23 October 2025,Chumzine,Chumzine,Differentially abundant bacterial taxa among groups were identified by LefSe analysis with LDA scores > 3.0 and Kruskal-Wallis test P < 0.05,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Flectobacillaceae|g__Flectobacillus,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976|768503|768507|3141701|101;3379134|976|1853228|1853229|563835|504481;1783272|1239|909932|1843489|31977|29465,Complete,KateRasheed
bsdb:40739184/4/1,40739184,laboratory experiment,40739184,https://doi.org/10.1186/s12866-025-04198-8,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04198-8#ref-CR29,"Tang H.B., Si Y.X., Li H.D., Dang W. , Lu H.L.","Intestinal microbial dysbiosis under nitrite stress in juvenile three-keeled pond turtles, Mauremys reevesii",BMC microbiology,2025,"Cultured freshwater turtle, Functional metagenomics, Intestinal microbial dysbiosis, Nitrite stress, Pathogenic prevalence",Experiment 4,China,Mauremys reevesii,Intestine,UBERON:0000160,Nitrite measurement,EFO:0010138,0mg/L + 1mg/L + 10mg/L exposed group,100mg/L exposed group,Healthy juvenile turtles exposed to 100mg/L nitrite which served as elevated nitrite concentration group,15,5,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,LEfSe",0.05,TRUE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,23 October 2025,Chumzine,"Chumzine,Fiddyhamma",Differentially abundant bacterial taxa among groups were identified by LefSe analysis with LDA scores > 3.0 and Kruskal-Wallis test P < 0.05,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Crocinitomicaceae|g__Fluviicola,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Nevskiales|f__Nevskiaceae|g__Nevskia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Nevskiales|f__Nevskiaceae,k__Pseudomonadati|p__Chlamydiota|c__Chlamydiia|o__Parachlamydiales|f__Parachlamydiaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Crocinitomicaceae",3379134|1224|28216|80840|119060;3379134|976|117743|200644|1853230|332102;3379134|1224|1236|1775403|568386|64001;3379134|1224|1236|1775403|568386;3379134|204428|204429|1963360|92713;3379134|976|117743|200644|1853230,Complete,KateRasheed
bsdb:40739603/1/1,40739603,case-control,40739603,https://doi.org/10.1186/s12866-025-04193-z,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04193-z,"Tao R., Wang X., Zhen X., Xia R., Chen K., Zhang H., Deng Y. , Zhang S.",Skin Microbiome alterations in heroin users revealed by full-length 16S rRNA sequencing,BMC microbiology,2025,"Full-length 16S rRNA, Heroin, Human Microbiome, Machine learning, Skin microbiota",Experiment 1,China,Homo sapiens,Nose skin,UBERON:0015476,Opioid use measurement,EFO:0009937,Non Users / Healthy control (Nasal skin),Heroin Users (Nasal skin),"People who make use of, inhale or ingest heroin",30,30,3 months,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,unchanged,unchanged,NA,unchanged,Signature 1,Figure 5A,8 October 2025,Fiddyhamma,Fiddyhamma,"Differential bacterial species analysis of the (a) nasal skin (NaS), samples between heroin users and healthy controls.",decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Idiomarinaceae|g__Aliidiomarina,3379134|1224|1236|135622|267893|1249554,Complete,KateRasheed
bsdb:40739603/2/1,40739603,case-control,40739603,https://doi.org/10.1186/s12866-025-04193-z,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04193-z,"Tao R., Wang X., Zhen X., Xia R., Chen K., Zhang H., Deng Y. , Zhang S.",Skin Microbiome alterations in heroin users revealed by full-length 16S rRNA sequencing,BMC microbiology,2025,"Full-length 16S rRNA, Heroin, Human Microbiome, Machine learning, Skin microbiota",Experiment 2,China,Homo sapiens,Oral epithelium,UBERON:0002424,Opioid use measurement,EFO:0009937,Non Users / Healthy control (Oral epithelial skin),Heroin Users (Oral epithelial skin),"People who make use of, inhale or ingest heroin",30,30,3 months,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,decreased,unchanged,NA,decreased,Signature 1,Figure 5B,8 October 2025,Fiddyhamma,Fiddyhamma,"Differential bacterial species analysis of the (b) oral epithelial skin (OrE), samples between heroin users and healthy controls.",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Lentimicrobiaceae|g__Lentimicrobium,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Wolinella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85009|31957|2801844;3379134|976|117743|200644|2762318|59735;1783272|1239|186801|186802|31979|1485;3379134|1224|28216|80840|119060|47670;3379134|976|200643|171549|1840213|1840214;3379134|976|117747|200666|84566|84567;3379134|29547|3031852|213849|72293|843;1783272|1239|186801|3082720|186804,Complete,KateRasheed
bsdb:40739603/3/1,40739603,case-control,40739603,https://doi.org/10.1186/s12866-025-04193-z,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04193-z,"Tao R., Wang X., Zhen X., Xia R., Chen K., Zhang H., Deng Y. , Zhang S.",Skin Microbiome alterations in heroin users revealed by full-length 16S rRNA sequencing,BMC microbiology,2025,"Full-length 16S rRNA, Heroin, Human Microbiome, Machine learning, Skin microbiota",Experiment 3,China,Homo sapiens,Skin of palm of manus,UBERON:0013777,Opioid use measurement,EFO:0009937,Non Users / Healthy control (Palm skin),Heroin Users (Palm skin),"People who make use of, inhale or ingest heroin",30,30,3 months,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,decreased,unchanged,NA,decreased,Signature 1,Figure 5C,9 October 2025,Fiddyhamma,Fiddyhamma,"Differential bacterial species analysis of the (c) palm skin (PaS), samples between heroin users and healthy controls.",increased,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,3379134|1224|28211|356|212791,Complete,KateRasheed
bsdb:40751224/1/1,40751224,laboratory experiment,40751224,10.1186/s40168-025-02165-z,https://link.springer.com/article/10.1186/s40168-025-02165-z,"Reinoso-Peláez E.L., Saura M., González C., Ramón M., Calvo J.H. , Serrano M.",The influence of vaginal microbiota on ewe fertility: a metagenomic and functional genomic approach,Microbiome,2025,"Artificial insemination, Fertility, Metagenomics, Microbiome, Microbiome-wide prediction, Ovine, Random forest, Reproductive success, Vaginal microbiota",Experiment 1,Spain,Ovis aries,Vagina,UBERON:0000996,Pregnancy,EFO:0002950,Non-pregnant Ewe Global model (All)  herds,Pregnant Ewe Global model (All) herds,Pregnant Ewe among all herds in the Global model,153,144,NA,WMS,NA,Nanopore,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 1,"Figure 5, Supplemental Figures 7, 9-13",27 November 2025,Fiddyhamma,Fiddyhamma,Heat maps and box plots of significant differential abundance results between pregnant and non-pregnant in ewes in Global model (All) herds,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Tissierellaceae|g__Tissierella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Helcococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Histophilus,k__Heunggongvirae|p__Uroviricota,k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Campylobacterota",3379134|976|200643|171549|815|909656;1783272|1239|1737404|1737405|1737406|41273;3379134|203691|203692|136|2845253|157;3384189|32066|203490|203491|203492|848;1783272|1239|1737404|1737405|1570339|31983;1783272|1239|91061|1385|539738|1378;1783272|1239|1737404|1737405|1570339|162289;3379134|29547|3031852|213849|72294|194;3384189|32066|203490|203491|1129771|34104;3379134|976|200643|171549|815|816;3379134|1224|1236|135625|712|214906;2731360|2731618;3384189|32066;3379134|29547,Complete,KateRasheed
bsdb:40751224/2/1,40751224,laboratory experiment,40751224,10.1186/s40168-025-02165-z,https://link.springer.com/article/10.1186/s40168-025-02165-z,"Reinoso-Peláez E.L., Saura M., González C., Ramón M., Calvo J.H. , Serrano M.",The influence of vaginal microbiota on ewe fertility: a metagenomic and functional genomic approach,Microbiome,2025,"Artificial insemination, Fertility, Metagenomics, Microbiome, Microbiome-wide prediction, Ovine, Random forest, Reproductive success, Vaginal microbiota",Experiment 2,Spain,Ovis aries,Vagina,UBERON:0000996,Pregnancy,EFO:0002950,Non-pregnant Ewe Manchega RN (MRN) herds,Pregnant Ewe Manchega RN (MRN) herds,Pregnant Ewe in the Manchega RN (MRN) breed which are primarily used for both milk and meat production.,37,18,NA,WMS,NA,Nanopore,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 1,"Figure 5, Supplementary Figures 7, 10",27 November 2025,Fiddyhamma,Fiddyhamma,Heat maps and box plots of significant differential abundance results between pregnant and non-pregnant in ewes in Manchega RN (MRN) herds,decreased,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,3384189|32066|203490|203491|203492|848,Complete,KateRasheed
bsdb:40751224/3/1,40751224,laboratory experiment,40751224,10.1186/s40168-025-02165-z,https://link.springer.com/article/10.1186/s40168-025-02165-z,"Reinoso-Peláez E.L., Saura M., González C., Ramón M., Calvo J.H. , Serrano M.",The influence of vaginal microbiota on ewe fertility: a metagenomic and functional genomic approach,Microbiome,2025,"Artificial insemination, Fertility, Metagenomics, Microbiome, Microbiome-wide prediction, Ovine, Random forest, Reproductive success, Vaginal microbiota",Experiment 3,Spain,Ovis aries,Vagina,UBERON:0000996,Pregnancy,EFO:0002950,Non-pregnant Ewe Manchega VL (MVL) herds,Pregnant Ewe Manchega VL (MVL) herds,Pregnant Ewe in the Manchega VL (MVL) breed which are primarily used for both milk and meat production.,16,25,NA,WMS,NA,Nanopore,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 1,"Figure 5, Supplementary Figures 7, 9, 11, 13",27 November 2025,Fiddyhamma,Fiddyhamma,Heat maps and box plots of significant differential abundance results between pregnant and non-pregnant in ewes in Manchega VL (MVL) herds,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Mycoplasmatota|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Mycoplasmopsis,k__Bacillati|p__Mycoplasmatota",1783272|201174|1760|2037|2049|1654;1783272|544448|2790996|2895623|2767358;1783272|544448,Complete,KateRasheed
bsdb:40751224/4/1,40751224,laboratory experiment,40751224,10.1186/s40168-025-02165-z,https://link.springer.com/article/10.1186/s40168-025-02165-z,"Reinoso-Peláez E.L., Saura M., González C., Ramón M., Calvo J.H. , Serrano M.",The influence of vaginal microbiota on ewe fertility: a metagenomic and functional genomic approach,Microbiome,2025,"Artificial insemination, Fertility, Metagenomics, Microbiome, Microbiome-wide prediction, Ovine, Random forest, Reproductive success, Vaginal microbiota",Experiment 4,Spain,Ovis aries,Vagina,UBERON:0000996,Pregnancy,EFO:0002950,Non-pregnant Ewe Rasa Aragonesa (R) herds,Pregnant Ewe Rasa Aragonesa (R) herds,Pregnant Ewe in the Rasa Aragonesa (R) breed which are primarily used for meat production.,53,70,NA,WMS,NA,Nanopore,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 1,"Figure 5, Supplementary Figures 7, 9-11, 13",27 November 2025,Fiddyhamma,Fiddyhamma,Heat maps and box plots of significant differential abundance results between pregnant and non-pregnant in ewes in Rasa Aragonesa (R) herds,decreased,"k__Fusobacteriati|p__Fusobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Histophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Trueperella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Caviibacter",3384189|32066;3379134|1224|1236|135625|712|214906;3379134|976|200643|171549|815|816;3384189|32066|203490|203491|1129771|34104;1783272|201174|1760|2037|2049|1069494;3384189|32066|203490|203491|1129771|1792239,Complete,KateRasheed
bsdb:40753175/1/1,40753175,"cross-sectional observational, not case-control",40753175,10.1038/s41522-025-00778-8,https://www.nature.com/articles/s41522-025-00778-8#citeas,"D'Aloisio L.D., Ballal M., Ghosh S., Haskey N., Abulizi N., Karimianghadim R., Liu C., Sruthi P., Nagarajan L., Vasudevan S., Shetty V., Purandare M., Bhaumik U., Howlader D.R., Pakpour S., Barnett J. , Gibson D.L.",The adoption of a westernized gut microbiome in Indian Immigrants and Indo-Canadians is associated with dietary acculturation,NPJ biofilms and microbiomes,2025,NA,Experiment 1,"Canada,India",Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Euro-Canadians + Euro-Immigrants + Indo-Canadians + Indo-Immigrants,Indian cohort,These are Indians residing in India,113,61,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig.1E and Table 4,13 October 2025,Oluwabunmi,"Oluwabunmi,Fiddyhamma",Significantly differential bacterial genera identified by linear discriminant analysis (LDA) effect size (LEfSe) in fecal samples across Indian cohort and Differentially Abundant Bacteria From Shotgun Sequence Data,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister hominis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sp. BL7,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius",1783272|1239|909932|1843488|909930|904;3379134|976|200643|171549;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|561;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|909929|1843491|52225;3379134|976|200643|171549|815|909656;1783272|1239|909932|909929|1843491;1783272|1239|909932|909929;1783272|1239|909932|1843489|31977;1783272|1239|909932|1843489;3379134|976|200643|171549;1783272|1239|909932|1843489|31977|39948|2582419;3379134|1224|1236|91347|543|561|562;1783272|1239|909932|1843488|909930|904|187327;1783272|1239|909932|1843489|31977|906|1285585;3379134|976|200643|171549|815|909656|310297,Complete,KateRasheed
bsdb:40753175/3/1,40753175,"cross-sectional observational, not case-control",40753175,10.1038/s41522-025-00778-8,https://www.nature.com/articles/s41522-025-00778-8#citeas,"D'Aloisio L.D., Ballal M., Ghosh S., Haskey N., Abulizi N., Karimianghadim R., Liu C., Sruthi P., Nagarajan L., Vasudevan S., Shetty V., Purandare M., Bhaumik U., Howlader D.R., Pakpour S., Barnett J. , Gibson D.L.",The adoption of a westernized gut microbiome in Indian Immigrants and Indo-Canadians is associated with dietary acculturation,NPJ biofilms and microbiomes,2025,NA,Experiment 3,"Canada,India",Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Indian + Indo-Immigrant + Euro-Canadian + Euro-Immigrant,Indo-Canadian,Canadians born in Canada from Indian ancestry,157,17,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig.1E and Table 4,20 October 2025,Oluwabunmi,"Oluwabunmi,Fiddyhamma",Significantly differential bacterial genera identified by linear discriminant analysis (LDA) effect size (LEfSe) in fecal samples of Indo-Canadians and Differentially Abundant Bacteria From Shotgun Sequence Data,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia massiliensis (ex Liu et al. 2021),k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium",1783272|1239|186801|3085636|186803|2569097;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|572511;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998|1643822|1643826;1783272|201174|84998|1643822;1783272|1239|186801|186802|204475;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|2316020;1783272|1239|186801|3085636|186803|2569097|39488;1783272|1239|186801|186802|216572|216851|853;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|186802|204475|745368;1783272|1239|186801|3085636|186803|572511|3062492;1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|2044939,Complete,KateRasheed
bsdb:40753175/4/1,40753175,"cross-sectional observational, not case-control",40753175,10.1038/s41522-025-00778-8,https://www.nature.com/articles/s41522-025-00778-8#citeas,"D'Aloisio L.D., Ballal M., Ghosh S., Haskey N., Abulizi N., Karimianghadim R., Liu C., Sruthi P., Nagarajan L., Vasudevan S., Shetty V., Purandare M., Bhaumik U., Howlader D.R., Pakpour S., Barnett J. , Gibson D.L.",The adoption of a westernized gut microbiome in Indian Immigrants and Indo-Canadians is associated with dietary acculturation,NPJ biofilms and microbiomes,2025,NA,Experiment 4,"Canada,India",Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Indian + Indo-Immigrants + Indo-Canadians + Euro-Immigrants,Euro-Canadians,Caucasian individuals born in Canada with European ancestry,133,41,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig.1E and Table 4,24 October 2025,Oluwabunmi,"Oluwabunmi,Fiddyhamma",Significantly differential bacterial genera identified by linear discriminant analysis (LDA) effect size (LEfSe) in fecal samples of Euro-Canadians and Differentially Abundant Bacteria From Shotgun Sequence Data,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF34-10BH",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803|1898203;1783272|1239|186801|3085636|186803|572511|871665;3379134|976|200643|171549|815|909656|821;1783272|1239|186801|186802|31979|1485|2293011,Complete,KateRasheed
bsdb:40753175/5/1,40753175,"cross-sectional observational, not case-control",40753175,10.1038/s41522-025-00778-8,https://www.nature.com/articles/s41522-025-00778-8#citeas,"D'Aloisio L.D., Ballal M., Ghosh S., Haskey N., Abulizi N., Karimianghadim R., Liu C., Sruthi P., Nagarajan L., Vasudevan S., Shetty V., Purandare M., Bhaumik U., Howlader D.R., Pakpour S., Barnett J. , Gibson D.L.",The adoption of a westernized gut microbiome in Indian Immigrants and Indo-Canadians is associated with dietary acculturation,NPJ biofilms and microbiomes,2025,NA,Experiment 5,"Canada,India",Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Indian + Indo-Immigrants + Indo-Canadians + Euro-Canadians,Euro-Immigrants,Immigrants with European ancestry from westernized countries,151,23,2 months,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig.1E and Table 4,24 October 2025,Oluwabunmi,"Oluwabunmi,Fiddyhamma",Significantly differential bacterial genera identified by linear discriminant analysis (LDA) effect size (LEfSe) in fecal samples of Euro-Immigrants and and Differentially Abundant Bacteria From Shotgun Sequence Data,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora celerecrescens",1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|2719231;1783272|1239|186801;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|2044939;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|3085636|186803|2719231|29354,Complete,KateRasheed
bsdb:40753175/11/1,40753175,"cross-sectional observational, not case-control",40753175,10.1038/s41522-025-00778-8,https://www.nature.com/articles/s41522-025-00778-8#citeas,"D'Aloisio L.D., Ballal M., Ghosh S., Haskey N., Abulizi N., Karimianghadim R., Liu C., Sruthi P., Nagarajan L., Vasudevan S., Shetty V., Purandare M., Bhaumik U., Howlader D.R., Pakpour S., Barnett J. , Gibson D.L.",The adoption of a westernized gut microbiome in Indian Immigrants and Indo-Canadians is associated with dietary acculturation,NPJ biofilms and microbiomes,2025,NA,Experiment 11,"Canada,India",Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Euro-Canadians + Euro-Immigrants + Indo-Canadians + Indo-Immigrants,Indian cohort,These are Indians residing in India with traditional diets rich in complex carbohydrates and fibre.,113,61,2 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Suppl Fig.S3, Table S2",27 October 2025,Oluwabunmi,"Oluwabunmi,Fiddyhamma","LEfSe (Linear discriminate analysis Effect Size) cladogram results, depicting differentially abundant bacteria across
cohorts, with genus set as lowest taxonomic rank in fecal samples of Indian cohorts",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister hominis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella hominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Leyella|s__Leyella stercorea",1783272|1239|909932|1843488|909930|904;3379134|976|200643|171549|815;3379134|976|200643|171549;1783272|1239|909932|1843489|31977|39948|2582419;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|2767887;1783272|1239|91061|186826|33958|2767887|1623;1783272|1239|909932|909929|1843491|52225;1783272|1239|909932|909929|1843491|52225|52226;3379134|976|200643|171549|171552|838;1783272|1239|909932|909929;3379134|1224|1236|135624|83763|83770;3379134|1224|1236|135624|83763;1783272|1239|909932|1843489;3379134|976|200643|171549|171552|2974251|2518605;3379134|976|200643|171549|171552|2974251|165179;3379134|976|200643|171549|171552|2974265|363265,Complete,KateRasheed
bsdb:40753175/12/1,40753175,"cross-sectional observational, not case-control",40753175,10.1038/s41522-025-00778-8,https://www.nature.com/articles/s41522-025-00778-8#citeas,"D'Aloisio L.D., Ballal M., Ghosh S., Haskey N., Abulizi N., Karimianghadim R., Liu C., Sruthi P., Nagarajan L., Vasudevan S., Shetty V., Purandare M., Bhaumik U., Howlader D.R., Pakpour S., Barnett J. , Gibson D.L.",The adoption of a westernized gut microbiome in Indian Immigrants and Indo-Canadians is associated with dietary acculturation,NPJ biofilms and microbiomes,2025,NA,Experiment 12,"Canada,India",Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Indian + Indo-Canadian + Euro-Canadian + Euro-Immigrant,Indo-immigrant,Indians who migrated to Canada,142,32,2 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Suppl Fig. S3, Table S2",27 October 2025,Oluwabunmi,"Oluwabunmi,Fiddyhamma","LEfSe (Linear discriminate analysis Effect Size) cladogram results, depicting differentially abundant bacteria across cohorts, with genus set as lowest taxonomic rank in fecal samples of Indo-immigrants cohorts",increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium sp. sp000437715,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales",1783272|1239|526524|526525|2810280|135858;1783272|1239|526524|526525|2810280|135858|3435886;1783272|1239|909932|1843489|31977|39948|487173;1783272|1239|526524|526525,Complete,KateRasheed
bsdb:40753175/13/1,40753175,"cross-sectional observational, not case-control",40753175,10.1038/s41522-025-00778-8,https://www.nature.com/articles/s41522-025-00778-8#citeas,"D'Aloisio L.D., Ballal M., Ghosh S., Haskey N., Abulizi N., Karimianghadim R., Liu C., Sruthi P., Nagarajan L., Vasudevan S., Shetty V., Purandare M., Bhaumik U., Howlader D.R., Pakpour S., Barnett J. , Gibson D.L.",The adoption of a westernized gut microbiome in Indian Immigrants and Indo-Canadians is associated with dietary acculturation,NPJ biofilms and microbiomes,2025,NA,Experiment 13,"Canada,India",Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Indian + Indo-Immigrant + Euro-Canadian + Euro-Immigrant,Indo-Canadian,Canadians born in Canada from Indian ancestry,157,17,2 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Suppl Fig. S3, Table S2",27 October 2025,Oluwabunmi,"Oluwabunmi,Fiddyhamma","LEfSe (Linear discriminate analysis Effect Size) cladogram results, depicting differentially abundant bacteria across cohorts, with genus set as lowest taxonomic rank in fecal samples of Indo-canadians cohorts",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|186801|3085636|186803|1766253|39491;1783272|1239|186801|3085636|186803|2569097;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|207244|649756;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;1783272|1239|186801|3082720;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:40753175/14/1,40753175,"cross-sectional observational, not case-control",40753175,10.1038/s41522-025-00778-8,https://www.nature.com/articles/s41522-025-00778-8#citeas,"D'Aloisio L.D., Ballal M., Ghosh S., Haskey N., Abulizi N., Karimianghadim R., Liu C., Sruthi P., Nagarajan L., Vasudevan S., Shetty V., Purandare M., Bhaumik U., Howlader D.R., Pakpour S., Barnett J. , Gibson D.L.",The adoption of a westernized gut microbiome in Indian Immigrants and Indo-Canadians is associated with dietary acculturation,NPJ biofilms and microbiomes,2025,NA,Experiment 14,"Canada,India",Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Indian + Indo-Immigrant + Indo-Canadian + Euro-Immigrant,Euro-Canadian,Caucasian individuals born in Canada with European ancestry,133,41,2 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Suppl Fig. S3, Table S2",27 October 2025,Oluwabunmi,"Oluwabunmi,Fiddyhamma","LEfSe (Linear discriminate analysis Effect Size) cladogram results, depicting differentially abundant bacteria across cohorts, with genus set as lowest taxonomic rank in fecal samples of Euro-canadians cohorts",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Paramuribaculum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|2005473;3379134|976|200643|171549|2005473|2518497;1783272|1239|186801|186802;1783272|1239|186801|186802|216572,Complete,KateRasheed
bsdb:40753175/15/1,40753175,"cross-sectional observational, not case-control",40753175,10.1038/s41522-025-00778-8,https://www.nature.com/articles/s41522-025-00778-8#citeas,"D'Aloisio L.D., Ballal M., Ghosh S., Haskey N., Abulizi N., Karimianghadim R., Liu C., Sruthi P., Nagarajan L., Vasudevan S., Shetty V., Purandare M., Bhaumik U., Howlader D.R., Pakpour S., Barnett J. , Gibson D.L.",The adoption of a westernized gut microbiome in Indian Immigrants and Indo-Canadians is associated with dietary acculturation,NPJ biofilms and microbiomes,2025,NA,Experiment 15,"Canada,India",Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Indians + Indo-Immigrants + Indo-Canadians +Euro-Canadians,Euro-Immigrants,immigrants with European ancestry from a westernized country,151,23,2 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,3.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Suppl Fig. S3, Table S2",27 October 2025,Oluwabunmi,"Oluwabunmi,Fiddyhamma","LEfSe (Linear discriminate analysis Effect Size) cladogram results, depicting differentially abundant bacteria across cohorts, with genus set as lowest taxonomic rank in fecal samples of Euro-immigrants cohorts",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",1783272|1239|186801|186802|3082771;1783272|201174|84998|1643822|1643826;3379134|976|200643|171549|171550,Complete,KateRasheed
bsdb:40766067/1/1,40766067,case-control,40766067,10.3389/fmed.2025.1615717,NA,"Han L.L., Mei C.F. , Xue H.",Exploring the relationship between co-abundance of gut microbiota and novel metabolic pathways in different subtypes of irritable bowel syndrome: insights from the American Gut Project,Frontiers in medicine,2025,"American Gut Project, co-abundance group, gut microbiota, irritable bowel syndrome subtypes, metabolic pathways",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,non-IBS controls,IBS-D,"Participants meeting Rome IV criteria for diarrhea-predominant irritable bowel syndrome (IBS-D), based on self-reported symptoms and matched to non-IBS controls from the American Gut Project.",365,365,"Yes,  antibiotic use within 6 months prior to enrollment was excluded.",16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2B; Results Section 3.2 (IBS-C vs non-IBS),8 January 2026,Aqc576444,Aqc576444,Faecalibacterium is part of a co-abundance group that shows a significant decrease in average relative abundance in IBS-C compared with matched non-IBS controls.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,1783272|1239|186801|186802|216572|216851,Complete,NA
bsdb:40766067/1/2,40766067,case-control,40766067,10.3389/fmed.2025.1615717,NA,"Han L.L., Mei C.F. , Xue H.",Exploring the relationship between co-abundance of gut microbiota and novel metabolic pathways in different subtypes of irritable bowel syndrome: insights from the American Gut Project,Frontiers in medicine,2025,"American Gut Project, co-abundance group, gut microbiota, irritable bowel syndrome subtypes, metabolic pathways",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,non-IBS controls,IBS-D,"Participants meeting Rome IV criteria for diarrhea-predominant irritable bowel syndrome (IBS-D), based on self-reported symptoms and matched to non-IBS controls from the American Gut Project.",365,365,"Yes,  antibiotic use within 6 months prior to enrollment was excluded.",16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3B; Results Section 3.3 (IBS-D vs non-IBS),8 January 2026,Aqc576444,Aqc576444,Coprococcus is part of a co-abundance group  that shows a significant increase in average relative abundance in IBS-D compared with matched non-IBS controls.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,1783272|1239|186801|3085636|186803|33042,Complete,NA
bsdb:40766067/1/3,40766067,case-control,40766067,10.3389/fmed.2025.1615717,NA,"Han L.L., Mei C.F. , Xue H.",Exploring the relationship between co-abundance of gut microbiota and novel metabolic pathways in different subtypes of irritable bowel syndrome: insights from the American Gut Project,Frontiers in medicine,2025,"American Gut Project, co-abundance group, gut microbiota, irritable bowel syndrome subtypes, metabolic pathways",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,non-IBS controls,IBS-D,"Participants meeting Rome IV criteria for diarrhea-predominant irritable bowel syndrome (IBS-D), based on self-reported symptoms and matched to non-IBS controls from the American Gut Project.",365,365,"Yes,  antibiotic use within 6 months prior to enrollment was excluded.",16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 3,Figure 3B; Results Section 3.3 (IBS-D vs non-IBS),8 January 2026,Aqc576444,Aqc576444,Lactobacillus and Ruminococcus are members of a co-abundance group  that shows a significant decrease in average relative abundance in IBS-D compared with matched non-IBS controls.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572|1263,Complete,NA
bsdb:40768832/1/1,40768832,randomized controlled trial,40768832,https://doi.org/10.1016/j.ebiom.2025.105876,NA,"Cintado E., Muela P., Martín-Rodríguez L., Alcaide I., Tezanos P., Vlckova K., Valderrama B., Bastiaanssen T.F.S., Rodríguez-Muñoz M., de Ceballos M.L., Aburto M.R., Cryan J.F. , Trejo J.L.",Gut microbiota regulates exercise-induced hormetic modulation of cognitive function,EBioMedicine,2025,"Adult hippocampal neurogenesis, Cognition, Fecal microbiota transplant, Mice, Microbiota, Moderate exercise",Experiment 1,Spain,Mus musculus,Feces,UBERON:0001988,Hippocampal fissure volume,EFO:0009404,RUN (Moderate Runners),SED (Sedentary Controls),Animals that remained sedentary in their home cages for the 32-day protocol (6 weeks + 2 days) as a baseline comparison for the exercise groups.,5,10,Used for FMT protocol: Ampicillin 1g/L; Gentamicin 1g/L; Vancomycin 0.5g/L; Imipenem 0.25g/L for 4 days.,16S,123456789,Illumina,relative abundances,"ANOVA,Kruskall-Wallis,PERMANOVA",0.05,TRUE,NA,NA,NA,NA,increased,increased,increased,NA,NA,Signature 1,Figure 4E,24 November 2025,SheikhAlMamun,SheikhAlMamun,"Taxonomy proportion by groups. Rare taxa include all families or genera representing <1% of the total for each sample or animal. (e) The proportion of Families is shown as stacked bar plots for the top 16 families, including relevant taxa such as Bacteroidaceae, Prevotellaceae, Lachnospiraceae, and Rikenellaceae.",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|201174|1760|85004|31953;1783272|1239|186801|186802|31979;1783272|1239|526524|526525|128827;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958;1783272|1239|186801|186802|216572,Complete,NA
bsdb:40768832/1/2,40768832,randomized controlled trial,40768832,https://doi.org/10.1016/j.ebiom.2025.105876,NA,"Cintado E., Muela P., Martín-Rodríguez L., Alcaide I., Tezanos P., Vlckova K., Valderrama B., Bastiaanssen T.F.S., Rodríguez-Muñoz M., de Ceballos M.L., Aburto M.R., Cryan J.F. , Trejo J.L.",Gut microbiota regulates exercise-induced hormetic modulation of cognitive function,EBioMedicine,2025,"Adult hippocampal neurogenesis, Cognition, Fecal microbiota transplant, Mice, Microbiota, Moderate exercise",Experiment 1,Spain,Mus musculus,Feces,UBERON:0001988,Hippocampal fissure volume,EFO:0009404,RUN (Moderate Runners),SED (Sedentary Controls),Animals that remained sedentary in their home cages for the 32-day protocol (6 weeks + 2 days) as a baseline comparison for the exercise groups.,5,10,Used for FMT protocol: Ampicillin 1g/L; Gentamicin 1g/L; Vancomycin 0.5g/L; Imipenem 0.25g/L for 4 days.,16S,123456789,Illumina,relative abundances,"ANOVA,Kruskall-Wallis,PERMANOVA",0.05,TRUE,NA,NA,NA,NA,increased,increased,increased,NA,NA,Signature 2,Figure 4E,24 November 2025,SheikhAlMamun,SheikhAlMamun,"Taxonomy proportion by groups. Rare taxa include all families or genera representing <1% of the total for each sample or animal. (e) The proportion of Families is shown as stacked bar plots for the top 16 families, including relevant taxa such as Bacteroidaceae, Prevotellaceae, Lachnospiraceae,  and Rikenellaceae.",decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales|f__Desulfobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae",3379134|74201|203494|48461|1647988;3379134|976|200643|171549|815;3379134|200930|68337|191393|191394;3379134|200940|3024418|213118|3023783;3379134|976|200643|1970189|1573805;3379134|976|200643|171549|2005473;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171552;3379134|976|200643|171549|171550;3379134|1224|28216|80840|995019,Complete,NA
bsdb:40768832/2/1,40768832,randomized controlled trial,40768832,https://doi.org/10.1016/j.ebiom.2025.105876,NA,"Cintado E., Muela P., Martín-Rodríguez L., Alcaide I., Tezanos P., Vlckova K., Valderrama B., Bastiaanssen T.F.S., Rodríguez-Muñoz M., de Ceballos M.L., Aburto M.R., Cryan J.F. , Trejo J.L.",Gut microbiota regulates exercise-induced hormetic modulation of cognitive function,EBioMedicine,2025,"Adult hippocampal neurogenesis, Cognition, Fecal microbiota transplant, Mice, Microbiota, Moderate exercise",Experiment 2,Spain,Mus musculus,Feces,UBERON:0001988,Hippocampal fissure volume,EFO:0009404,RUN (Moderate Runners),SED (Sedentary Controls),Animals that remained sedentary in their home cages for the 32-day protocol (6 weeks + 2 days) as a baseline comparison for the exercise groups.,5,10,Used for FMT protocol: Ampicillin 1g/L; Gentamicin 1g/L; Vancomycin 0.5g/L; Imipenem 0.25g/L for 4 days.,16S,123456789,Illumina,NA,"ANOVA,Kruskall-Wallis,PERMANOVA",0.05,TRUE,NA,NA,NA,NA,increased,increased,increased,NA,NA,Signature 1,Figure 4F,24 November 2025,SheikhAlMamun,SheikhAlMamun,"Taxonomy proportion by groups. (f) Proportion of genera Taxonomic composition is shown as stacked bar plots for the top 20 families and the 33 most abundant genera, including relevant taxa such as Bacteroidaceae, Prevotellaceae, Lachnospiraceae, and Rikenellaceae.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",1783272|1239|186801|186802|31979|1485;1783272|1239|526524|526525|128827|1937008;1783272|1239|186801|186802|186806|1730|42322;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|1898203;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|33958|2767887;3379134|976|200643|171549|171552;1783272|1239|186801|186802|216572|1263;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3085636|186803|297314;1783272|1239|186801|3085636|186803|1506553,Complete,NA
bsdb:40768832/2/2,40768832,randomized controlled trial,40768832,https://doi.org/10.1016/j.ebiom.2025.105876,NA,"Cintado E., Muela P., Martín-Rodríguez L., Alcaide I., Tezanos P., Vlckova K., Valderrama B., Bastiaanssen T.F.S., Rodríguez-Muñoz M., de Ceballos M.L., Aburto M.R., Cryan J.F. , Trejo J.L.",Gut microbiota regulates exercise-induced hormetic modulation of cognitive function,EBioMedicine,2025,"Adult hippocampal neurogenesis, Cognition, Fecal microbiota transplant, Mice, Microbiota, Moderate exercise",Experiment 2,Spain,Mus musculus,Feces,UBERON:0001988,Hippocampal fissure volume,EFO:0009404,RUN (Moderate Runners),SED (Sedentary Controls),Animals that remained sedentary in their home cages for the 32-day protocol (6 weeks + 2 days) as a baseline comparison for the exercise groups.,5,10,Used for FMT protocol: Ampicillin 1g/L; Gentamicin 1g/L; Vancomycin 0.5g/L; Imipenem 0.25g/L for 4 days.,16S,123456789,Illumina,NA,"ANOVA,Kruskall-Wallis,PERMANOVA",0.05,TRUE,NA,NA,NA,NA,increased,increased,increased,NA,NA,Signature 2,Figure 4F,24 November 2025,SheikhAlMamun,SheikhAlMamun,"Taxonomy proportion by groups. (f) Proportion of genera Taxonomic composition is shown as stacked bar plots for the top 20 families and the 33 most abundant genera, including relevant taxa such as Bacteroidaceae, Prevotellaceae, Lachnospiraceae,  and Rikenellaceae.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp. oral clone HT002,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;95818|2093818|2093825|2171986|1331051;1783272|1239|186801|186802|1980681;3379134|29547|3031852|213849|72293|209;1783272|1239|91061|186826|33958|1578|242643;3379134|200930|68337|191393|2945020;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171550|28138;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572|459786,Complete,NA
bsdb:40778780/1/1,40778780,"cross-sectional observational, not case-control",40778780,10.1128/msystems.00467-25,https://doi.org/10.1128/msystems.00467-25,"Castro-Severyn J., Pacheco N., Valdivia G., Krüger G.I., Pardo-Esté C., Remonsellez F., Gaggero A., Arriagada G., Valiente-Echeverria F., Olivares-Pacheco J., Valdes J.H. , Saavedra C.P.",Impact of seasonal variation on the oral and nasopharyngeal microbiome in school-aged children: the school MicroBE initiative,mSystems,2025,"nasopharyngeal microbiome, oral microbiome, public health, schoolers, transition",Experiment 1,Chile,Homo sapiens,Nasopharynx,UBERON:0001728,Time,EFO:0000721,Nasopharyngeal Sample Clusters (N-II + N-III + N-IV + N-V + N-VI + N-VIII + N-X + N-XI + N-XII + N-XIII),Nasopharyngeal Sample Cluster (N-I),"Nasopharyngeal Sample Cluster (N-I) from 3 sampling time points (Autumn, Spring, Winter)",NA,NA,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S1,15 October 2025,Addanma,"Addanma,Fiddyhamma",Boxplot of relative abundances of most abundant genus In nasopharyngeal samples from 3 sampling times per group.Significance was assessed using a Student’s t-test,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|1224|1236|135625|712|724;3379134|1224|28216|80840|75682|963;3379134|1224|1236|2887326|468|475;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171551|836;3379134|1224|1236|91347|1903414|583;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:40778780/2/1,40778780,"cross-sectional observational, not case-control",40778780,10.1128/msystems.00467-25,https://doi.org/10.1128/msystems.00467-25,"Castro-Severyn J., Pacheco N., Valdivia G., Krüger G.I., Pardo-Esté C., Remonsellez F., Gaggero A., Arriagada G., Valiente-Echeverria F., Olivares-Pacheco J., Valdes J.H. , Saavedra C.P.",Impact of seasonal variation on the oral and nasopharyngeal microbiome in school-aged children: the school MicroBE initiative,mSystems,2025,"nasopharyngeal microbiome, oral microbiome, public health, schoolers, transition",Experiment 2,Chile,Homo sapiens,Nasopharynx,UBERON:0001728,Time,EFO:0000721,Nasopharyngeal Sample Clusters (N-I + N-III + N-IV + N-V + N-VI + N-VIII + N-X + N-XI + N-XII + N-XIII),Nasopharyngeal Sample Cluster (N-II),"Nasopharyngeal Sample Cluster (N-II) from 3 sampling time points (Autumn, Spring, Winter)",NA,NA,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S1,15 October 2025,Addanma,"Addanma,Fiddyhamma",Boxplot of relative abundances of most abundant genus In nasopharyngeal samples from 3 sampling times per group.Significance was assessed using a Student’s t-test,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",1783272|1239|91061|186826|1300|1301;3379134|1224|28216|80840|75682|963;3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|186828|29393;3379134|1224|1236|2887326|468|475;3379134|1224|1236|91347|1903414|583;1783272|1239|91061|1385|90964|1279;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171551|836,Complete,Svetlana up
bsdb:40778780/3/1,40778780,"cross-sectional observational, not case-control",40778780,10.1128/msystems.00467-25,https://doi.org/10.1128/msystems.00467-25,"Castro-Severyn J., Pacheco N., Valdivia G., Krüger G.I., Pardo-Esté C., Remonsellez F., Gaggero A., Arriagada G., Valiente-Echeverria F., Olivares-Pacheco J., Valdes J.H. , Saavedra C.P.",Impact of seasonal variation on the oral and nasopharyngeal microbiome in school-aged children: the school MicroBE initiative,mSystems,2025,"nasopharyngeal microbiome, oral microbiome, public health, schoolers, transition",Experiment 3,Chile,Homo sapiens,Nasopharynx,UBERON:0001728,Time,EFO:0000721,Nasopharyngeal Sample Clusters (N-I + N-II + N-IV + N-V + N-VI + N-VIII + N-X + N-XI + N-XII + N-XIII),Nasopharyngeal Sample Cluster (N-III),"Nasopharyngeal Sample Cluster (N-III) from 3 sampling time points (Autumn, Spring, Winter)",NA,NA,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S1,3 December 2025,Fiddyhamma,Fiddyhamma,Boxplot of relative abundances of most abundant genus In nasopharyngeal samples from 3 sampling times per group.Significance was assessed using a Student’s t-test,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",3379134|1224|28216|80840|75682|963;3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|186828|29393;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171551|836,Complete,Svetlana up
bsdb:40778780/4/1,40778780,"cross-sectional observational, not case-control",40778780,10.1128/msystems.00467-25,https://doi.org/10.1128/msystems.00467-25,"Castro-Severyn J., Pacheco N., Valdivia G., Krüger G.I., Pardo-Esté C., Remonsellez F., Gaggero A., Arriagada G., Valiente-Echeverria F., Olivares-Pacheco J., Valdes J.H. , Saavedra C.P.",Impact of seasonal variation on the oral and nasopharyngeal microbiome in school-aged children: the school MicroBE initiative,mSystems,2025,"nasopharyngeal microbiome, oral microbiome, public health, schoolers, transition",Experiment 4,Chile,Homo sapiens,Nasopharynx,UBERON:0001728,Time,EFO:0000721,Nasopharyngeal Sample Clusters (N-I + N-II + N-III + N-V + N-VI + N-VIII + N-X + N-XI + N-XII + N-XIII),Nasopharyngeal Sample Cluster (N-IV),"Nasopharyngeal Sample Cluster (N-IV) from 3 sampling time points (Autumn, Spring, Winter)",NA,NA,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S1,3 December 2025,Fiddyhamma,Fiddyhamma,Boxplot of relative abundances of most abundant genus In nasopharyngeal samples from 3 sampling times per group. Significance was assessed using a Student’s t-test,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",3379134|1224|28216|80840|75682|963;3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|186828|29393;3379134|1224|1236|2887326|468|475;3379134|1224|1236|91347|1903414|583;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171551|836,Complete,Svetlana up
bsdb:40778780/5/1,40778780,"cross-sectional observational, not case-control",40778780,10.1128/msystems.00467-25,https://doi.org/10.1128/msystems.00467-25,"Castro-Severyn J., Pacheco N., Valdivia G., Krüger G.I., Pardo-Esté C., Remonsellez F., Gaggero A., Arriagada G., Valiente-Echeverria F., Olivares-Pacheco J., Valdes J.H. , Saavedra C.P.",Impact of seasonal variation on the oral and nasopharyngeal microbiome in school-aged children: the school MicroBE initiative,mSystems,2025,"nasopharyngeal microbiome, oral microbiome, public health, schoolers, transition",Experiment 5,Chile,Homo sapiens,Nasopharynx,UBERON:0001728,Time,EFO:0000721,Nasopharyngeal Sample Clusters (N-I + N-II + N-III + N-IV + N-VI + N-VIII + N-X + N-XI + N-XII + N-XIII),Nasopharyngeal Sample Cluster (N-V),"Nasopharyngeal Sample Cluster (N-V) from 3 sampling time points (Autumn, Spring, Winter)",NA,NA,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S1,3 December 2025,Fiddyhamma,Fiddyhamma,Boxplot of relative abundances of most abundant genus In nasopharyngeal samples from 3 sampling times per group.Significance was assessed using a Student’s t-test,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum",1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;3379134|1224|28216|80840|75682|963;3379134|1224|1236|135625|712|724;3379134|976|200643|171549|171551|836;3379134|1224|28216|206351|481|482;3379134|1224|1236|91347|1903414|583;3379134|1224|1236|2887326|468|475;1783272|1239|91061|186826|186828|29393,Complete,Svetlana up
bsdb:40778780/7/1,40778780,"cross-sectional observational, not case-control",40778780,10.1128/msystems.00467-25,https://doi.org/10.1128/msystems.00467-25,"Castro-Severyn J., Pacheco N., Valdivia G., Krüger G.I., Pardo-Esté C., Remonsellez F., Gaggero A., Arriagada G., Valiente-Echeverria F., Olivares-Pacheco J., Valdes J.H. , Saavedra C.P.",Impact of seasonal variation on the oral and nasopharyngeal microbiome in school-aged children: the school MicroBE initiative,mSystems,2025,"nasopharyngeal microbiome, oral microbiome, public health, schoolers, transition",Experiment 7,Chile,Homo sapiens,Nasopharynx,UBERON:0001728,Time,EFO:0000721,Nasopharyngeal Sample Clusters (N-I + N-II + N-III + N-IV + N-V + N-VI + N-X + N-XI + N-XII + N-XIII),Nasopharyngeal Sample Cluster (N-VIII),"Nasopharyngeal Sample Cluster (N-VIIII) from 3 sampling time points (Autumn, Spring, Winter)",NA,NA,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S1,4 December 2025,Fiddyhamma,Fiddyhamma,Boxplot of relative abundances of most abundant genus In nasopharyngeal samples from 3 sampling times per group.Significance was assessed using a Student’s t-test,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",3379134|1224|28216|80840|75682|963;3379134|1224|1236|135625|712|724;3379134|1224|1236|2887326|468|475;3379134|1224|1236|91347|1903414|583;1783272|1239|91061|1385|90964|1279;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171551|836,Complete,Svetlana up
bsdb:40778780/8/1,40778780,"cross-sectional observational, not case-control",40778780,10.1128/msystems.00467-25,https://doi.org/10.1128/msystems.00467-25,"Castro-Severyn J., Pacheco N., Valdivia G., Krüger G.I., Pardo-Esté C., Remonsellez F., Gaggero A., Arriagada G., Valiente-Echeverria F., Olivares-Pacheco J., Valdes J.H. , Saavedra C.P.",Impact of seasonal variation on the oral and nasopharyngeal microbiome in school-aged children: the school MicroBE initiative,mSystems,2025,"nasopharyngeal microbiome, oral microbiome, public health, schoolers, transition",Experiment 8,Chile,Homo sapiens,Nasopharynx,UBERON:0001728,Time,EFO:0000721,Nasopharyngeal Sample Clusters (N-I + N-II + N-III + N-IV + N-V + N-VI + N-VIII + N-XI + N-XII + N-XIII),Nasopharyngeal Sample Cluster (N-X),"Nasopharyngeal Sample Cluster (N-X) from 3 sampling time points (Autumn, Spring, Winter)",NA,NA,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S1,4 December 2025,Fiddyhamma,Fiddyhamma,Boxplot of relative abundances of most abundant genus In nasopharyngeal samples from 3 sampling times per group.Significance was assessed using a Student’s t-test,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|1224|28216|80840|75682|963;3379134|1224|1236|135625|712|724;3379134|1224|1236|2887326|468|475;3379134|1224|1236|91347|1903414|583;1783272|1239|91061|1385|90964|1279;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171551|836;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:40778780/9/1,40778780,"cross-sectional observational, not case-control",40778780,10.1128/msystems.00467-25,https://doi.org/10.1128/msystems.00467-25,"Castro-Severyn J., Pacheco N., Valdivia G., Krüger G.I., Pardo-Esté C., Remonsellez F., Gaggero A., Arriagada G., Valiente-Echeverria F., Olivares-Pacheco J., Valdes J.H. , Saavedra C.P.",Impact of seasonal variation on the oral and nasopharyngeal microbiome in school-aged children: the school MicroBE initiative,mSystems,2025,"nasopharyngeal microbiome, oral microbiome, public health, schoolers, transition",Experiment 9,Chile,Homo sapiens,Nasopharynx,UBERON:0001728,Time,EFO:0000721,Nasopharyngeal Sample Clusters (N-I + N-II + N-III + N-IV + N-V + N-VI + N-VIII + N-X + N-XII + N-XIII),Nasopharyngeal Sample Cluster (N-XI),"Nasopharyngeal Sample Cluster (N-XI) from 3 sampling time points (Autumn, Spring, Winter)",NA,NA,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S1,4 December 2025,Fiddyhamma,Fiddyhamma,Boxplot of relative abundances of most abundant genus In nasopharyngeal samples from 3 sampling times per group.Significance was assessed using a Student’s t-test,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|1224|28216|80840|75682|963;3379134|1224|1236|135625|712|724;3379134|1224|1236|2887326|468|475;3379134|1224|1236|91347|1903414|583;1783272|1239|91061|1385|90964|1279;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171551|836;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:40778780/10/1,40778780,"cross-sectional observational, not case-control",40778780,10.1128/msystems.00467-25,https://doi.org/10.1128/msystems.00467-25,"Castro-Severyn J., Pacheco N., Valdivia G., Krüger G.I., Pardo-Esté C., Remonsellez F., Gaggero A., Arriagada G., Valiente-Echeverria F., Olivares-Pacheco J., Valdes J.H. , Saavedra C.P.",Impact of seasonal variation on the oral and nasopharyngeal microbiome in school-aged children: the school MicroBE initiative,mSystems,2025,"nasopharyngeal microbiome, oral microbiome, public health, schoolers, transition",Experiment 10,Chile,Homo sapiens,Nasopharynx,UBERON:0001728,Time,EFO:0000721,Nasopharyngeal Sample Clusters (N-I + N-II + N-III + N-IV + N-V + N-VI + N-VIII + N-X + N-XI + N-XIII),Nasopharyngeal Sample Cluster (N-XII),"Nasopharyngeal Sample Cluster (N-XII) from 3 sampling time points (Autumn, Spring, Winter)",NA,NA,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S1,4 December 2025,Fiddyhamma,Fiddyhamma,Boxplot of relative abundances of most abundant genus In nasopharyngeal samples from 3 sampling times per group.Significance was assessed using a Student’s t-test,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|1224|28216|80840|75682|963;3379134|1224|1236|135625|712|724;3379134|1224|1236|2887326|468|475;3379134|1224|1236|91347|1903414|583;1783272|1239|91061|1385|90964|1279;3379134|976|200643|171549|171551|836;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:40778780/11/1,40778780,"cross-sectional observational, not case-control",40778780,10.1128/msystems.00467-25,https://doi.org/10.1128/msystems.00467-25,"Castro-Severyn J., Pacheco N., Valdivia G., Krüger G.I., Pardo-Esté C., Remonsellez F., Gaggero A., Arriagada G., Valiente-Echeverria F., Olivares-Pacheco J., Valdes J.H. , Saavedra C.P.",Impact of seasonal variation on the oral and nasopharyngeal microbiome in school-aged children: the school MicroBE initiative,mSystems,2025,"nasopharyngeal microbiome, oral microbiome, public health, schoolers, transition",Experiment 11,Chile,Homo sapiens,Nasopharynx,UBERON:0001728,Time,EFO:0000721,Nasopharyngeal Sample Clusters (N-I + N-II + N-III + N-IV + N-V + N-VI + N-VIII + N-X + N-XI + N-XII),Nasopharyngeal Sample Cluster (N-XIII),"Nasopharyngeal Sample Cluster (N-XIII) from 3 sampling time points (Autumn, Spring, Winter)",NA,NA,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S1,4 December 2025,Fiddyhamma,Fiddyhamma,Boxplot of relative abundances of most abundant genus In nasopharyngeal samples from 3 sampling times per group.Significance was assessed using a Student’s t-test,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|1224|28216|80840|75682|963;3379134|1224|1236|135625|712|724;3379134|1224|1236|2887326|468|475;3379134|1224|1236|91347|1903414|583;1783272|1239|91061|1385|90964|1279;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171551|836;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:40778780/12/1,40778780,"cross-sectional observational, not case-control",40778780,10.1128/msystems.00467-25,https://doi.org/10.1128/msystems.00467-25,"Castro-Severyn J., Pacheco N., Valdivia G., Krüger G.I., Pardo-Esté C., Remonsellez F., Gaggero A., Arriagada G., Valiente-Echeverria F., Olivares-Pacheco J., Valdes J.H. , Saavedra C.P.",Impact of seasonal variation on the oral and nasopharyngeal microbiome in school-aged children: the school MicroBE initiative,mSystems,2025,"nasopharyngeal microbiome, oral microbiome, public health, schoolers, transition",Experiment 12,Chile,Homo sapiens,Oral cavity,UBERON:0000167,Time,EFO:0000721,Oral Sample Clusters (O-II + O-III + O-IV + O-V + O-VI + O-VII + O-VIII + O-IX),Oral Sample Cluster (O-I),"Oral Sample Cluster (O-I) from 3 sampling time points (Autumn, Spring, Winter)",NA,NA,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S1,4 December 2025,Fiddyhamma,Fiddyhamma,Boxplot of relative abundances of most abundant genus in oral samples from 3 sampling times per group.Significance was assessed using a Student’s t-test,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella",1783272|1239|91061|1385|90964|1279;1783272|201174|1760|85007|1653|1716;3379134|1224|28211|356|69277|28100;3379134|1224|1236|91347|1903414|583;1783272|1239|91061|186826|1300|1301;3379134|1224|28216|80840|75682|963;3379134|1224|1236|135625|712|724;3379134|1224|1236|2887326|468|475,Complete,Svetlana up
bsdb:40778780/13/1,40778780,"cross-sectional observational, not case-control",40778780,10.1128/msystems.00467-25,https://doi.org/10.1128/msystems.00467-25,"Castro-Severyn J., Pacheco N., Valdivia G., Krüger G.I., Pardo-Esté C., Remonsellez F., Gaggero A., Arriagada G., Valiente-Echeverria F., Olivares-Pacheco J., Valdes J.H. , Saavedra C.P.",Impact of seasonal variation on the oral and nasopharyngeal microbiome in school-aged children: the school MicroBE initiative,mSystems,2025,"nasopharyngeal microbiome, oral microbiome, public health, schoolers, transition",Experiment 13,Chile,Homo sapiens,Oral cavity,UBERON:0000167,Time,EFO:0000721,Oral Sample Clusters (O-I + O-III + O-IV + O-V + O-VI + O-VII + O-VIII + O-IX),Oral Sample Cluster (O-II),"Oral Sample Cluster (O-II) from 3 sampling time points (Autumn, Spring, Winter)",NA,NA,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S1,4 December 2025,Fiddyhamma,Fiddyhamma,Boxplot of relative abundances of most abundant genus in oral samples from 3 sampling times per group.Significance was assessed using a Student’s t-test,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|1760|85007|1653|1716;3379134|1224|1236|135625|712|724;3379134|1224|28216|80840|75682|963;3379134|1224|1236|2887326|468|475;3379134|1224|28211|356|69277|28100;3379134|1224|1236|91347|1903414|583;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:40778780/14/1,40778780,"cross-sectional observational, not case-control",40778780,10.1128/msystems.00467-25,https://doi.org/10.1128/msystems.00467-25,"Castro-Severyn J., Pacheco N., Valdivia G., Krüger G.I., Pardo-Esté C., Remonsellez F., Gaggero A., Arriagada G., Valiente-Echeverria F., Olivares-Pacheco J., Valdes J.H. , Saavedra C.P.",Impact of seasonal variation on the oral and nasopharyngeal microbiome in school-aged children: the school MicroBE initiative,mSystems,2025,"nasopharyngeal microbiome, oral microbiome, public health, schoolers, transition",Experiment 14,Chile,Homo sapiens,Oral cavity,UBERON:0000167,Time,EFO:0000721,Oral Sample Clusters (O-I + O-II + O-IV + O-V + O-VI + O-VII + O-VIII + O-IX),Oral Sample Cluster (O-III),"Oral Sample Cluster (O-III) from 3 sampling time points (Autumn, Spring, Winter)",NA,NA,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S1,4 December 2025,Fiddyhamma,Fiddyhamma,Boxplot of relative abundances of most abundant genus in oral samples from 3 sampling times per group.Significance was assessed using a Student’s t-test,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|201174|1760|85007|1653|1716;3379134|1224|1236|135625|712|724;3379134|1224|28216|80840|75682|963;3379134|1224|1236|2887326|468|475;3379134|1224|28211|356|69277|28100;3379134|1224|1236|91347|1903414|583;1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:40778780/15/1,40778780,"cross-sectional observational, not case-control",40778780,10.1128/msystems.00467-25,https://doi.org/10.1128/msystems.00467-25,"Castro-Severyn J., Pacheco N., Valdivia G., Krüger G.I., Pardo-Esté C., Remonsellez F., Gaggero A., Arriagada G., Valiente-Echeverria F., Olivares-Pacheco J., Valdes J.H. , Saavedra C.P.",Impact of seasonal variation on the oral and nasopharyngeal microbiome in school-aged children: the school MicroBE initiative,mSystems,2025,"nasopharyngeal microbiome, oral microbiome, public health, schoolers, transition",Experiment 15,Chile,Homo sapiens,Oral cavity,UBERON:0000167,Time,EFO:0000721,Oral Sample Clusters (O-I + O-II + O-III + O-V + O-VI + O-VII + O-VIII + O-IX),Oral Sample Cluster (O-IV),"Oral Sample Cluster (O-IV) from 3 sampling time points (Autumn, Spring, Winter)",NA,NA,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S1,4 December 2025,Fiddyhamma,Fiddyhamma,Boxplot of relative abundances of most abundant genus in oral samples from 3 sampling times per group.Significance was assessed using a Student’s t-test,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|1760|85007|1653|1716;3379134|1224|1236|135625|712|724;3379134|1224|28216|80840|75682|963;3379134|1224|1236|2887326|468|475;3379134|1224|28211|356|69277|28100;3379134|1224|1236|91347|1903414|583;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:40778780/16/1,40778780,"cross-sectional observational, not case-control",40778780,10.1128/msystems.00467-25,https://doi.org/10.1128/msystems.00467-25,"Castro-Severyn J., Pacheco N., Valdivia G., Krüger G.I., Pardo-Esté C., Remonsellez F., Gaggero A., Arriagada G., Valiente-Echeverria F., Olivares-Pacheco J., Valdes J.H. , Saavedra C.P.",Impact of seasonal variation on the oral and nasopharyngeal microbiome in school-aged children: the school MicroBE initiative,mSystems,2025,"nasopharyngeal microbiome, oral microbiome, public health, schoolers, transition",Experiment 16,Chile,Homo sapiens,Oral cavity,UBERON:0000167,Time,EFO:0000721,Oral Sample Clusters (O-I + O-II + O-III + O-IV + O-VI + O-VII + O-VIII + O-IX),Oral Sample Cluster (O-V),"Oral Sample Cluster (O-V) from 3 sampling time points (Autumn, Spring, Winter)",NA,NA,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S1,4 December 2025,Fiddyhamma,Fiddyhamma,Boxplot of relative abundances of most abundant genus in oral samples from 3 sampling times per group.Significance was assessed using a Student’s t-test,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum",1783272|1239|91061|1385|90964|1279;3379134|1224|1236|91347|1903414|583;1783272|201174|1760|85007|1653|1716;3379134|1224|28211|356|69277|28100;1783272|1239|91061|186826|1300|1301;3379134|1224|1236|2887326|468|475;3379134|1224|1236|135625|712|724;3379134|1224|28216|80840|75682|963,Complete,Svetlana up
bsdb:40778780/17/1,40778780,"cross-sectional observational, not case-control",40778780,10.1128/msystems.00467-25,https://doi.org/10.1128/msystems.00467-25,"Castro-Severyn J., Pacheco N., Valdivia G., Krüger G.I., Pardo-Esté C., Remonsellez F., Gaggero A., Arriagada G., Valiente-Echeverria F., Olivares-Pacheco J., Valdes J.H. , Saavedra C.P.",Impact of seasonal variation on the oral and nasopharyngeal microbiome in school-aged children: the school MicroBE initiative,mSystems,2025,"nasopharyngeal microbiome, oral microbiome, public health, schoolers, transition",Experiment 17,Chile,Homo sapiens,Oral cavity,UBERON:0000167,Time,EFO:0000721,Oral Sample Clusters (O-I + O-II + O-III + O-IV + O-V + O-VII + O-VIII + O-IX),Oral Sample Cluster (O-VI),"Oral Sample Cluster (O-VI) from 3 sampling time points (Autumn, Spring, Winter)",NA,NA,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S1,4 December 2025,Fiddyhamma,Fiddyhamma,Boxplot of relative abundances of most abundant genus in oral samples from 3 sampling times per group.Significance was assessed using a Student’s t-test,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium",1783272|1239|91061|1385|90964|1279;3379134|1224|1236|91347|1903414|583;3379134|1224|1236|2887326|468|475;3379134|1224|1236|135625|712|724;3379134|1224|28216|80840|75682|963;1783272|1239|91061|186826|1300|1301;3379134|1224|28211|356|69277|28100;3379134|1224|28216|206351|481|482;1783272|201174|1760|85007|1653|1716,Complete,Svetlana up
bsdb:40778780/18/1,40778780,"cross-sectional observational, not case-control",40778780,10.1128/msystems.00467-25,https://doi.org/10.1128/msystems.00467-25,"Castro-Severyn J., Pacheco N., Valdivia G., Krüger G.I., Pardo-Esté C., Remonsellez F., Gaggero A., Arriagada G., Valiente-Echeverria F., Olivares-Pacheco J., Valdes J.H. , Saavedra C.P.",Impact of seasonal variation on the oral and nasopharyngeal microbiome in school-aged children: the school MicroBE initiative,mSystems,2025,"nasopharyngeal microbiome, oral microbiome, public health, schoolers, transition",Experiment 18,Chile,Homo sapiens,Oral cavity,UBERON:0000167,Time,EFO:0000721,Oral Sample Clusters (O-I + O-II + O-III + O-IV + O-V + O-VI + O-VIII + O-IX),Oral Sample Cluster (O-VII),"Oral Sample Cluster (O-VII) from 3 sampling time points (Autumn, Spring, Winter)",NA,NA,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S1,4 December 2025,Fiddyhamma,Fiddyhamma,Boxplot of relative abundances of most abundant genus in oral samples from 3 sampling times per group.Significance was assessed using a Student’s t-test,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061|1385|90964|1279;3379134|1224|1236|91347|1903414|583;1783272|201174|1760|85007|1653|1716;3379134|1224|28211|356|69277|28100;3379134|1224|28216|80840|75682|963;3379134|1224|1236|135625|712|724;3379134|1224|1236|2887326|468|475;1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:40778780/19/1,40778780,"cross-sectional observational, not case-control",40778780,10.1128/msystems.00467-25,https://doi.org/10.1128/msystems.00467-25,"Castro-Severyn J., Pacheco N., Valdivia G., Krüger G.I., Pardo-Esté C., Remonsellez F., Gaggero A., Arriagada G., Valiente-Echeverria F., Olivares-Pacheco J., Valdes J.H. , Saavedra C.P.",Impact of seasonal variation on the oral and nasopharyngeal microbiome in school-aged children: the school MicroBE initiative,mSystems,2025,"nasopharyngeal microbiome, oral microbiome, public health, schoolers, transition",Experiment 19,Chile,Homo sapiens,Oral cavity,UBERON:0000167,Time,EFO:0000721,Oral Sample Clusters (O-I + O-II + O-III + O-IV + O-V + O-VI + O-VII + O-IX),Oral Sample Cluster (O-VIII),"Oral Sample Cluster (O-VIII) from 3 sampling time points (Autumn, Spring, Winter)",NA,NA,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S1,4 December 2025,Fiddyhamma,Fiddyhamma,Boxplot of relative abundances of most abundant genus in oral samples from 3 sampling times per group.Significance was assessed using a Student’s t-test,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;1783272|201174|1760|85007|1653|1716;3379134|1224|28211|356|69277|28100;3379134|1224|1236|2887326|468|475;3379134|1224|1236|91347|1903414|583;3379134|1224|28216|80840|75682|963;3379134|1224|1236|135625|712|724,Complete,Svetlana up
bsdb:40778780/20/1,40778780,"cross-sectional observational, not case-control",40778780,10.1128/msystems.00467-25,https://doi.org/10.1128/msystems.00467-25,"Castro-Severyn J., Pacheco N., Valdivia G., Krüger G.I., Pardo-Esté C., Remonsellez F., Gaggero A., Arriagada G., Valiente-Echeverria F., Olivares-Pacheco J., Valdes J.H. , Saavedra C.P.",Impact of seasonal variation on the oral and nasopharyngeal microbiome in school-aged children: the school MicroBE initiative,mSystems,2025,"nasopharyngeal microbiome, oral microbiome, public health, schoolers, transition",Experiment 20,Chile,Homo sapiens,Oral cavity,UBERON:0000167,Time,EFO:0000721,Oral Sample Clusters (O-I + O-II + O-III + O-IV + O-V + O-VI + O-VII + O-VIII),Oral Sample Cluster (O-IX),"Oral Sample Cluster (O-IX) from 3 sampling time points (Autumn, Spring, Winter)",NA,NA,3 months,16S,34,Illumina,relative abundances,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S1,4 December 2025,Fiddyhamma,Fiddyhamma,Boxplot of relative abundances of most abundant genus in oral samples from 3 sampling times per group.Significance was assessed using a Student’s t-test,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus",3379134|1224|28216|80840|75682|963;3379134|1224|1236|135625|712|724;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|1385|90964|1279;3379134|1224|1236|2887326|468|475;1783272|201174|1760|85007|1653|1716;3379134|1224|28211|356|69277|28100;3379134|1224|1236|91347|1903414|583,Complete,Svetlana up
bsdb:40783398/1/1,40783398,laboratory experiment,40783398,10.1038/s41522-025-00799-3,https://www.nature.com/articles/s41522-025-00799-3,"Shen Y., Sun D., Chen K., Jiang J., Shao D., Yang L., Sun C., Liu D., Ke Y., Wu C., Walsh T.R., Shen J., Lv Z. , Wang Y.",High-fat and low-fiber diet elevates the gut resistome: a comparative metagenomic study,NPJ biofilms and microbiomes,2025,NA,Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Mice before high-fat diet (pre-diet),Mice after high-fat diet (post-diet),High-fat (Western-style) diet administered to C57BL/6 J mice for 21 days under SPF conditions.,NA,NA,NA,WMS,NA,Illumina,relative abundances,"Kruskall-Wallis,LEfSe",0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 2B,30 October 2025,Conwauzor,Conwauzor,Genus-level relative abundances showing significant changes after high-fat feeding.,increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",3379134|200940|3031449|213115|194924|872;1783272|1239|91061|186826|81852|1350;1783272|201174|84998|1643822|1643826|580024;1783272|1239|91061|186826|1300|1357;1783272|201174|84998|84999|1643824|133925;1783272|1239|91061|1385|90964|1279,Complete,NA
bsdb:40783398/1/2,40783398,laboratory experiment,40783398,10.1038/s41522-025-00799-3,https://www.nature.com/articles/s41522-025-00799-3,"Shen Y., Sun D., Chen K., Jiang J., Shao D., Yang L., Sun C., Liu D., Ke Y., Wu C., Walsh T.R., Shen J., Lv Z. , Wang Y.",High-fat and low-fiber diet elevates the gut resistome: a comparative metagenomic study,NPJ biofilms and microbiomes,2025,NA,Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Mice before high-fat diet (pre-diet),Mice after high-fat diet (post-diet),High-fat (Western-style) diet administered to C57BL/6 J mice for 21 days under SPF conditions.,NA,NA,NA,WMS,NA,Illumina,relative abundances,"Kruskall-Wallis,LEfSe",0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 2B,30 October 2025,Conwauzor,Conwauzor,Relative abundances showing significant changes after high-fat feeding.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Mucispirillaceae|g__Mucispirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|189330;3379134|200930|68337|191393|2945020|248038;3379134|976|200643|171549|1853231|283168;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|186802|31979|49082;3379134|1224|28216|80840;1783272|1239|186801|3085636|186803,Complete,NA
bsdb:40783398/2/1,40783398,laboratory experiment,40783398,10.1038/s41522-025-00799-3,https://www.nature.com/articles/s41522-025-00799-3,"Shen Y., Sun D., Chen K., Jiang J., Shao D., Yang L., Sun C., Liu D., Ke Y., Wu C., Walsh T.R., Shen J., Lv Z. , Wang Y.",High-fat and low-fiber diet elevates the gut resistome: a comparative metagenomic study,NPJ biofilms and microbiomes,2025,NA,Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Mice before high-fiber diet (pre-diet),Mice after high-fiber diet (post-diet),"Mice fed with diet enriched in complex carbohydrates and plant fibres, low in fat (~10 % kcal fat); fed for 21 days under SPF conditions.",NA,NA,NA,WMS,NA,Illumina,relative abundances,"LEfSe,Kruskall-Wallis",0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 2B,31 October 2025,Conwauzor,Conwauzor,Relative abundance bar plot showing enrichment of some genera after high-fiber diet.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella",3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;3379134|200940|3031449|213115|194924|35832;3379134|976|200643|171549|2005525|375288;1783272|201174|84998|84999|1643824|133925,Complete,NA
bsdb:40783398/2/2,40783398,laboratory experiment,40783398,10.1038/s41522-025-00799-3,https://www.nature.com/articles/s41522-025-00799-3,"Shen Y., Sun D., Chen K., Jiang J., Shao D., Yang L., Sun C., Liu D., Ke Y., Wu C., Walsh T.R., Shen J., Lv Z. , Wang Y.",High-fat and low-fiber diet elevates the gut resistome: a comparative metagenomic study,NPJ biofilms and microbiomes,2025,NA,Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Mice before high-fiber diet (pre-diet),Mice after high-fiber diet (post-diet),"Mice fed with diet enriched in complex carbohydrates and plant fibres, low in fat (~10 % kcal fat); fed for 21 days under SPF conditions.",NA,NA,NA,WMS,NA,Illumina,relative abundances,"LEfSe,Kruskall-Wallis",0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 2B,31 October 2025,Conwauzor,Conwauzor,Relative abundance bar plot showing depletion of some genera after high-fiber diet.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|244127;1783272|1239|186801|3085636|186803|572511;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802|186806|1730;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;1783272|1239|186801|186802|216572|292632;1783272|1239|186801|3085636|186803,Complete,NA
bsdb:40783398/3/1,40783398,laboratory experiment,40783398,10.1038/s41522-025-00799-3,https://www.nature.com/articles/s41522-025-00799-3,"Shen Y., Sun D., Chen K., Jiang J., Shao D., Yang L., Sun C., Liu D., Ke Y., Wu C., Walsh T.R., Shen J., Lv Z. , Wang Y.",High-fat and low-fiber diet elevates the gut resistome: a comparative metagenomic study,NPJ biofilms and microbiomes,2025,NA,Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,High-fat + High-fiber diets (post-diet),Normal diet (post-diet),Mice fed with normal diet for 21 days,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Fig 2,14 November 2025,Conwauzor,Conwauzor,Differential taxa among three diets in mice.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|1853231|283168;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|186802|31979|49082;3379134|1224|28216|80840;1783272|1239|186801|3085636|186803,Complete,NA
bsdb:40783398/4/1,40783398,laboratory experiment,40783398,10.1038/s41522-025-00799-3,https://www.nature.com/articles/s41522-025-00799-3,"Shen Y., Sun D., Chen K., Jiang J., Shao D., Yang L., Sun C., Liu D., Ke Y., Wu C., Walsh T.R., Shen J., Lv Z. , Wang Y.",High-fat and low-fiber diet elevates the gut resistome: a comparative metagenomic study,NPJ biofilms and microbiomes,2025,NA,Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,High-fat + Normal diets (post-diet),High fiber diet (post-diet),Mice fed with high fiber diet for 21 days,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 2,14 November 2025,Conwauzor,Conwauzor,Differential taxa among three diets in mice,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|31979|1485;1783272|201174|1760|85004|31953|1678;3379134|200940|3031449|213115|194924|35832,Complete,NA
bsdb:40783398/5/1,40783398,laboratory experiment,40783398,10.1038/s41522-025-00799-3,https://www.nature.com/articles/s41522-025-00799-3,"Shen Y., Sun D., Chen K., Jiang J., Shao D., Yang L., Sun C., Liu D., Ke Y., Wu C., Walsh T.R., Shen J., Lv Z. , Wang Y.",High-fat and low-fiber diet elevates the gut resistome: a comparative metagenomic study,NPJ biofilms and microbiomes,2025,NA,Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Response to diet,EFO:0010757,High-fiber + Normal diets (post-diet),High-fat diet (post-diet),Mice fed with high fat diet for 21 days,NA,NA,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 2,14 November 2025,Conwauzor,Conwauzor,Differential taxa among three diets in mice,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium",1783272|201174|84998|84999|1643824|133925;3379134|1224|1236|91347|543|561;1783272|1239|91061|186826|81852|1350;3379134|200940|3031449|213115|194924|872;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|186802|216572|244127;3379134|976|200643|171549|1853231|574697;1783272|201174|84998|1643822|1643826|580024;1783272|1239|186801|186802|216572|292632;1783272|1239|91061|1385|90964|1279;1783272|1239|186801|186802|186806|1730,Complete,NA
bsdb:40790469/1/1,40790469,case-control,40790469,https://doi.org/10.1186/s12866-025-04206-x,https://pubmed.ncbi.nlm.nih.gov/40790469/,"Qin M., Ding W., Qin L., Liang R., Guo Y., Zhao Y., Xu H., Wen Y., Pang Y. , Li L.",Dysbiosis associated with enhanced microbial mobility across the respiratory tract in pulmonary tuberculosis patients,BMC microbiology,2025,"Interaction, Microbiota, Pulmonary tuberculosis, Respiratory tract",Experiment 1,China,Homo sapiens,Oral cavity,UBERON:0000167,Pulmonary tuberculosis,EFO:1000049,Healthy control (HC) group,Pulmonary tuberculosis (PTB) group,"All PTB participants were diagnosed with pulmonary tuberculosis (PTB), had no prior history of tuberculosis (TB), tested positive for Mycobacterium tuberculosis (MTB) through pathogen detection, and showed radiological signs consistent with PTB without any other concurrent pulmonary diseases.",14,22,2 weeks,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,increased,unchanged,NA,increased,Signature 1,Figure 4d and S3a,12 October 2025,Firdaws,Firdaws,Differential abundance of the most dominant taxa in the oral specimen of PTB and HC groups at the genus and species levels.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces israelii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus ilei,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus koreensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus rubneri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. A12",1783272|201174|1760|2037|2049|1654|1659;1783272|201174|1760|85006|1268|32207|2047;1783272|201174|1760|85006|1268|32207|43675;1783272|1239|91061|186826|1300|1301|1156431;1783272|1239|91061|186826|1300|1301|2382163;1783272|1239|91061|186826|1300|1301|1234680;1783272|1239|91061|186826|1300|1301|1759399,Complete,KateRasheed
bsdb:40790469/1/2,40790469,case-control,40790469,https://doi.org/10.1186/s12866-025-04206-x,https://pubmed.ncbi.nlm.nih.gov/40790469/,"Qin M., Ding W., Qin L., Liang R., Guo Y., Zhao Y., Xu H., Wen Y., Pang Y. , Li L.",Dysbiosis associated with enhanced microbial mobility across the respiratory tract in pulmonary tuberculosis patients,BMC microbiology,2025,"Interaction, Microbiota, Pulmonary tuberculosis, Respiratory tract",Experiment 1,China,Homo sapiens,Oral cavity,UBERON:0000167,Pulmonary tuberculosis,EFO:1000049,Healthy control (HC) group,Pulmonary tuberculosis (PTB) group,"All PTB participants were diagnosed with pulmonary tuberculosis (PTB), had no prior history of tuberculosis (TB), tested positive for Mycobacterium tuberculosis (MTB) through pathogen detection, and showed radiological signs consistent with PTB without any other concurrent pulmonary diseases.",14,22,2 weeks,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,increased,unchanged,NA,increased,Signature 2,Figure 4d and S3a,13 October 2025,Firdaws,Firdaws,Differential abundance of the most dominant taxa in the oral specimen of PTB and HC groups at the genus and species levels.,decreased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella denitrificans,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella dentalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella veroralis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema medium,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema putidum,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema socranskii,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema vincentii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter sp. 2125159857,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp. OMZ 906,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp. OMZ 857,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter sp. Marseille-P9115,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sp. FDAARGOS_737,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp. OMZ 305,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp. OMZ 803,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga endodontalis",3379134|29547|3031852|213849|72294|194|199;3379134|976|117743|200644|49546|1016|327575;3379134|976|117743|200644|49546|1016|1019;1783272|1239|909932|1843489|31977|39948|39950;3379134|1224|28216|206351|481|32257|502;1783272|1239|1737404|1737405|1570339|543311|33033;3379134|976|200643|171549|171552|838|52227;3379134|976|200643|171549|171552|838|28137;3379134|976|200643|171549|171552|2974251|28135;1783272|1239|909932|909929|1843491|970|69823;3379134|203691|203692|136|2845253|157|158;3379134|203691|203692|136|2845253|157|58231;3379134|203691|203692|136|2845253|157|221027;3379134|203691|203692|136|2845253|157|53419;3379134|203691|203692|136|2845253|157|69710;3379134|1224|1236|135625|712|416916|2820817;3379134|203691|203692|136|2845253|157|2563662;3379134|203691|203692|136|2845253|157|1643513;3379134|1224|1236|135625|712|416916|2866570;3379134|976|117743|200644|49546|1016|2545799;3379134|203691|203692|136|2845253|157|1659192;3379134|203691|203692|136|2845253|157|120682;3379134|976|117743|200644|49546|1016|2708117,Complete,KateRasheed
bsdb:40790469/2/1,40790469,case-control,40790469,https://doi.org/10.1186/s12866-025-04206-x,https://pubmed.ncbi.nlm.nih.gov/40790469/,"Qin M., Ding W., Qin L., Liang R., Guo Y., Zhao Y., Xu H., Wen Y., Pang Y. , Li L.",Dysbiosis associated with enhanced microbial mobility across the respiratory tract in pulmonary tuberculosis patients,BMC microbiology,2025,"Interaction, Microbiota, Pulmonary tuberculosis, Respiratory tract",Experiment 2,China,Homo sapiens,"Oral cavity,Carina of trachea","UBERON:0006679,UBERON:0000167",Pulmonary tuberculosis,EFO:1000049,Tracheal Carina (TC) samples in PTB group,Oral samples (OS) in PTB group,Oral samples (OS) collected from PTB participants,22,22,2 weeks,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,increased,unchanged,NA,increased,Signature 1,Figure 3d,13 October 2025,Firdaws,Firdaws,Relative abundance of Oral samples (OS) compared to Tracheal Carina (TC) samples in PTB patients.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 171,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis",1783272|201174|1760|2037|2049|1654|1655;1783272|201174|1760|2037|2049|1654|544580;1783272|201174|1760|2037|2049|1654|706438;3379134|1224|28216|80840|119060|47670|47671;1783272|201174|1760|85006|1268|32207|172042;1783272|1239|91061|186826|1300|1301|1305,Complete,KateRasheed
bsdb:40790469/3/1,40790469,case-control,40790469,https://doi.org/10.1186/s12866-025-04206-x,https://pubmed.ncbi.nlm.nih.gov/40790469/,"Qin M., Ding W., Qin L., Liang R., Guo Y., Zhao Y., Xu H., Wen Y., Pang Y. , Li L.",Dysbiosis associated with enhanced microbial mobility across the respiratory tract in pulmonary tuberculosis patients,BMC microbiology,2025,"Interaction, Microbiota, Pulmonary tuberculosis, Respiratory tract",Experiment 3,China,Homo sapiens,Carina of trachea,UBERON:0006679,Pulmonary tuberculosis,EFO:1000049,Healthy control (HC) group,Pulmonary tuberculosis (PTB) group,"All PTB participants were diagnosed with pulmonary tuberculosis (PTB), had no prior history of tuberculosis (TB), tested positive for Mycobacterium tuberculosis (MTB) through pathogen detection, and showed radiological signs consistent with PTB without any other concurrent pulmonary diseases.",14,22,2 weeks,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 4e and S3b,14 October 2025,Firdaws,Firdaws,Differentially abundant microbial species in the Tracheal Carina (TC) of PTB patients compared to healthy controls (HC).,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas sp. SUN019,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",1783272|201174|1760|85006|1268|32207|172042;3379134|1224|28211|204457|41297|13687|2937788;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|909932|1843489|31977|29465|39778,Complete,KateRasheed
bsdb:40790469/3/2,40790469,case-control,40790469,https://doi.org/10.1186/s12866-025-04206-x,https://pubmed.ncbi.nlm.nih.gov/40790469/,"Qin M., Ding W., Qin L., Liang R., Guo Y., Zhao Y., Xu H., Wen Y., Pang Y. , Li L.",Dysbiosis associated with enhanced microbial mobility across the respiratory tract in pulmonary tuberculosis patients,BMC microbiology,2025,"Interaction, Microbiota, Pulmonary tuberculosis, Respiratory tract",Experiment 3,China,Homo sapiens,Carina of trachea,UBERON:0006679,Pulmonary tuberculosis,EFO:1000049,Healthy control (HC) group,Pulmonary tuberculosis (PTB) group,"All PTB participants were diagnosed with pulmonary tuberculosis (PTB), had no prior history of tuberculosis (TB), tested positive for Mycobacterium tuberculosis (MTB) through pathogen detection, and showed radiological signs consistent with PTB without any other concurrent pulmonary diseases.",14,22,2 weeks,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 4e and S3b,14 October 2025,Firdaws,Firdaws,Differentially abundant microbial species in the Tracheal Carina (TC) of PTB patients compared to healthy controls (HC).,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum pigrum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus|s__Lactiplantibacillus plantarum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus haemolyticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. LPB0220,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Chitinophaga|s__Chitinophaga pinensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Ectopseudomonas|s__Ectopseudomonas guguanensis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Marixanthomonas|s__Marixanthomonas sp. SCSIO 43207,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium|s__Photobacterium sp. DA100,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycolicibacterium|s__Mycolicibacterium nivoides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter|s__Arthrobacter sp. NicSoilC5",1783272|1239|91061|186826|186828|29393|29394;1783272|1239|91061|186826|33958|2767842|1590;1783272|1239|91061|1385|90964|1279|1283;1783272|1239|91061|186826|1300|1301|2610896;3379134|976|1853228|1853229|563835|79328|79329;3379134|1224|1236|72274|135621|3236654|1198456;3379134|976|117743|200644|49546|387658|2779360;3379134|1224|1236|135623|641|657|3027472;1783272|201174|1760|85007|1762|1866885|2487344;1783272|201174|1760|85006|1268|1663|2831000,Complete,KateRasheed
bsdb:40790469/4/1,40790469,case-control,40790469,https://doi.org/10.1186/s12866-025-04206-x,https://pubmed.ncbi.nlm.nih.gov/40790469/,"Qin M., Ding W., Qin L., Liang R., Guo Y., Zhao Y., Xu H., Wen Y., Pang Y. , Li L.",Dysbiosis associated with enhanced microbial mobility across the respiratory tract in pulmonary tuberculosis patients,BMC microbiology,2025,"Interaction, Microbiota, Pulmonary tuberculosis, Respiratory tract",Experiment 4,China,Homo sapiens,Lung,UBERON:0002048,Pulmonary tuberculosis,EFO:1000049,Healthy side (HS) of the lung in Healthy control (HC) group (HS_HC),Affected side (AS) of the lung in Pulmonary tuberculosis (PTB) group (AS_PTB),Samples collected from Affected side of the lung in PTB patients,14,22,2 weeks,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 4f,15 October 2025,Firdaws,Firdaws,Differentially abundant microbial species in the Affected side (AS) of the lung of PTB patients compared to HS of the lung of healthy controls (HC).,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,1783272|201174|1760|85006|1268|32207|43675,Complete,KateRasheed
bsdb:40790469/4/2,40790469,case-control,40790469,https://doi.org/10.1186/s12866-025-04206-x,https://pubmed.ncbi.nlm.nih.gov/40790469/,"Qin M., Ding W., Qin L., Liang R., Guo Y., Zhao Y., Xu H., Wen Y., Pang Y. , Li L.",Dysbiosis associated with enhanced microbial mobility across the respiratory tract in pulmonary tuberculosis patients,BMC microbiology,2025,"Interaction, Microbiota, Pulmonary tuberculosis, Respiratory tract",Experiment 4,China,Homo sapiens,Lung,UBERON:0002048,Pulmonary tuberculosis,EFO:1000049,Healthy side (HS) of the lung in Healthy control (HC) group (HS_HC),Affected side (AS) of the lung in Pulmonary tuberculosis (PTB) group (AS_PTB),Samples collected from Affected side of the lung in PTB patients,14,22,2 weeks,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 4f,15 October 2025,Firdaws,Firdaws,Differentially abundant microbial species in the Affected side (AS) of the lung of PTB patients compared to HS of the lung of healthy controls (HC).,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Caldibacillus|s__Caldibacillus thermoamylovorans,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. Pc102",1783272|1239|91061|1385|186817|1276290|35841;3379134|1224|1236|72274|135621|286|2678261,Complete,KateRasheed
bsdb:40790469/5/1,40790469,case-control,40790469,https://doi.org/10.1186/s12866-025-04206-x,https://pubmed.ncbi.nlm.nih.gov/40790469/,"Qin M., Ding W., Qin L., Liang R., Guo Y., Zhao Y., Xu H., Wen Y., Pang Y. , Li L.",Dysbiosis associated with enhanced microbial mobility across the respiratory tract in pulmonary tuberculosis patients,BMC microbiology,2025,"Interaction, Microbiota, Pulmonary tuberculosis, Respiratory tract",Experiment 5,China,Homo sapiens,"Oral cavity,Lung","UBERON:0000167,UBERON:0002048",Pulmonary tuberculosis,EFO:1000049,Healthy side (HS) of the lung samples in PTB group,Oral samples (OS) in PTB group,Oral samples (OS) collected from PTB participants,22,22,2 weeks,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,increased,unchanged,NA,increased,Signature 1,Figure 3d,16 October 2025,Firdaws,Firdaws,Relative abundance of oral samples compared to Healthy side (HS) of the lung samples in PTB patients.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 171,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis",3379134|1224|28216|80840|119060|47670|47671;1783272|201174|1760|2037|2049|1654|1655;1783272|201174|1760|85006|1268|32207|172042;1783272|201174|1760|2037|2049|1654|706438;1783272|201174|1760|2037|2049|1654|544580;1783272|1239|91061|186826|1300|1301|1305,Complete,KateRasheed
bsdb:40790469/6/1,40790469,case-control,40790469,https://doi.org/10.1186/s12866-025-04206-x,https://pubmed.ncbi.nlm.nih.gov/40790469/,"Qin M., Ding W., Qin L., Liang R., Guo Y., Zhao Y., Xu H., Wen Y., Pang Y. , Li L.",Dysbiosis associated with enhanced microbial mobility across the respiratory tract in pulmonary tuberculosis patients,BMC microbiology,2025,"Interaction, Microbiota, Pulmonary tuberculosis, Respiratory tract",Experiment 6,China,Homo sapiens,"Oral cavity,Lung","UBERON:0000167,UBERON:0002048",Pulmonary tuberculosis,EFO:1000049,Affected side (AS) of the lung samples in PTB group,Oral samples in PTB group,Oral samples collected from PTB participants,22,22,2 weeks,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,increased,unchanged,NA,increased,Signature 1,Figure 3d,16 October 2025,Firdaws,Firdaws,Relative abundance of oral samples compared to Affected side (AS) of the lung samples in PTB patients.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 171,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis",1783272|201174|1760|2037|2049|1654|1655;1783272|201174|1760|2037|2049|1654|544580;1783272|201174|1760|2037|2049|1654|706438;3379134|1224|28216|80840|119060|47670|47671;1783272|201174|1760|85006|1268|32207|172042;1783272|1239|91061|186826|1300|1301|1305,Complete,KateRasheed
bsdb:40790469/7/1,40790469,case-control,40790469,https://doi.org/10.1186/s12866-025-04206-x,https://pubmed.ncbi.nlm.nih.gov/40790469/,"Qin M., Ding W., Qin L., Liang R., Guo Y., Zhao Y., Xu H., Wen Y., Pang Y. , Li L.",Dysbiosis associated with enhanced microbial mobility across the respiratory tract in pulmonary tuberculosis patients,BMC microbiology,2025,"Interaction, Microbiota, Pulmonary tuberculosis, Respiratory tract",Experiment 7,China,Homo sapiens,"Left lung,Right lung","UBERON:0002168,UBERON:0002167",Pulmonary tuberculosis,EFO:1000049,Affected side (AS) of the lung samples in PTB group,Healthy side (HS) of the lung samples in PTB group,Healthy side (HS) of the lung samples collected from PTB participants,22,22,2 weeks,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,increased,unchanged,NA,increased,Signature 1,Figure 3d,16 October 2025,Firdaws,Firdaws,Relative abundance of Healthy side (HS) of the lung samples compared to Affected side (AS) of the lung samples in PTB patients.,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,1783272|201174|1760|2037|2049|1654|1655,Complete,KateRasheed
bsdb:40790469/8/1,40790469,case-control,40790469,https://doi.org/10.1186/s12866-025-04206-x,https://pubmed.ncbi.nlm.nih.gov/40790469/,"Qin M., Ding W., Qin L., Liang R., Guo Y., Zhao Y., Xu H., Wen Y., Pang Y. , Li L.",Dysbiosis associated with enhanced microbial mobility across the respiratory tract in pulmonary tuberculosis patients,BMC microbiology,2025,"Interaction, Microbiota, Pulmonary tuberculosis, Respiratory tract",Experiment 8,China,Homo sapiens,Lung,UBERON:0002048,Pulmonary tuberculosis,EFO:1000049,Healthy side (HS) of the lung in Healthy control (HC) group (HS_HC),Healthy side (HS) of the lung in Pulmonary tuberculosis (PTB) group (HS_PTB),Samples collected from Healthy side of the lung in PTB patients,14,22,2 weeks,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 4f,16 October 2025,Firdaws,Firdaws,Differentially abundant microbial species in the Healthy side (HS) of the lung of PTB patients compared to HS of the lung of healthy controls (HC).,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,1783272|201174|1760|85006|1268|32207|43675,Complete,KateRasheed
bsdb:40790469/8/2,40790469,case-control,40790469,https://doi.org/10.1186/s12866-025-04206-x,https://pubmed.ncbi.nlm.nih.gov/40790469/,"Qin M., Ding W., Qin L., Liang R., Guo Y., Zhao Y., Xu H., Wen Y., Pang Y. , Li L.",Dysbiosis associated with enhanced microbial mobility across the respiratory tract in pulmonary tuberculosis patients,BMC microbiology,2025,"Interaction, Microbiota, Pulmonary tuberculosis, Respiratory tract",Experiment 8,China,Homo sapiens,Lung,UBERON:0002048,Pulmonary tuberculosis,EFO:1000049,Healthy side (HS) of the lung in Healthy control (HC) group (HS_HC),Healthy side (HS) of the lung in Pulmonary tuberculosis (PTB) group (HS_PTB),Samples collected from Healthy side of the lung in PTB patients,14,22,2 weeks,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 4f,16 October 2025,Firdaws,Firdaws,Differentially abundant microbial species in the Healthy side (HS) of the lung of PTB patients compared to HS of the lung of healthy controls (HC).,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. Pc102,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter johnsonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Caldibacillus|s__Caldibacillus thermoamylovorans",3379134|1224|1236|72274|135621|286|2678261;3379134|1224|1236|2887326|468|469|40214;1783272|1239|91061|1385|186817|1276290|35841,Complete,KateRasheed
bsdb:40790470/1/1,40790470,time series / longitudinal observational,40790470,10.1186/s12866-025-04260-5,NA,"Xu C., Li W., Lin L., Zhang D., Lei J., Pan D., Liang S., Chen Y., Wan Y. , He J.",High-throughput sequencing to analyze changes in the human scalp microbiome during the use of a shampoo,BMC microbiology,2025,"High-throughput sequencing, Human scalp, Microbial community, Scalp health care, Shampoo",Experiment 1,China,Homo sapiens,Skin of scalp,UBERON:8300000,Environmental exposure measurement,EFO:0008360,Participants before Shampoo use (Day 0),Participants after Shampoo use (Day 28),Participants who applied the test shampoo for 28 days after refraining from other hair products for at least three days prior to treatment.,20,20,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2E,10 October 2025,Pamela,Pamela,Taxonomic differences in the scalp bacterial microbiota before and after shampoo use.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Sterolibacteriaceae|g__Methyloversatilis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Rhodocyclales|f__Rhodocyclaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas",3379134|1224|28211|356|212791;3379134|1224|28216|32003|2008793|378210;3379134|1224|28216|206389|75787;3379134|1224|28211|204457|41297|13687;3379134|1224|1236|135614|32033|40323,Complete,Svetlana up
bsdb:40790470/1/2,40790470,time series / longitudinal observational,40790470,10.1186/s12866-025-04260-5,NA,"Xu C., Li W., Lin L., Zhang D., Lei J., Pan D., Liang S., Chen Y., Wan Y. , He J.",High-throughput sequencing to analyze changes in the human scalp microbiome during the use of a shampoo,BMC microbiology,2025,"High-throughput sequencing, Human scalp, Microbial community, Scalp health care, Shampoo",Experiment 1,China,Homo sapiens,Skin of scalp,UBERON:8300000,Environmental exposure measurement,EFO:0008360,Participants before Shampoo use (Day 0),Participants after Shampoo use (Day 28),Participants who applied the test shampoo for 28 days after refraining from other hair products for at least three days prior to treatment.,20,20,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2E,11 October 2025,Pamela,Pamela,Taxonomic differences in the scalp bacterial microbiota before and after shampoo use.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Chloroflexota|c__Ktedonobacteria|o__Ktedonobacterales|f__Ktedonobacteraceae,k__Bacillati|p__Chloroflexota|c__Ktedonobacteria|o__Ktedonobacterales",3379134|1224|1236|2887326|468|469;1783272|200795|388447|388448|388449;1783272|200795|388447|388448,Complete,Svetlana up
bsdb:40790470/2/1,40790470,time series / longitudinal observational,40790470,10.1186/s12866-025-04260-5,NA,"Xu C., Li W., Lin L., Zhang D., Lei J., Pan D., Liang S., Chen Y., Wan Y. , He J.",High-throughput sequencing to analyze changes in the human scalp microbiome during the use of a shampoo,BMC microbiology,2025,"High-throughput sequencing, Human scalp, Microbial community, Scalp health care, Shampoo",Experiment 2,China,Homo sapiens,Skin of scalp,UBERON:8300000,Environmental exposure measurement,EFO:0008360,Participants before Shampoo use (Day 0),Participants after Shampoo use (Day 28),Participants who applied the test shampoo for 28 days after refraining from other hair products for at least three days prior to treatment.,20,20,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Figure 3E,11 October 2025,Pamela,Pamela,Taxonomic differences in the scalp fungal microbiota before and after shampoo use.,increased,"k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Didymellaceae|g__Ascochyta,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Didymellaceae|g__Ascochyta|s__Ascochyta medicaginicola,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus gracilis,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus penicillioides,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus reticulatus,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Didymellaceae|g__Epicoccum,k__Fungi|p__Basidiomycota|c__Ustilaginomycetes|o__Ustilaginales|f__Ustilaginaceae|g__Moesziomyces,k__Fungi|p__Basidiomycota|c__Ustilaginomycetes|o__Ustilaginales|f__Ustilaginaceae|g__Moesziomyces|s__Moesziomyces aphidis,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Didymellaceae|g__Neoascochyta,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Didymellaceae|g__Neoascochyta|s__Neoascochyta tardicrescens,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Penicillium|s__Penicillium jiangxiense,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Trichomonascaceae|g__Starmerella|s__Starmerella etchellsii",4751|4890|147541|92860|683158|5453;4751|4890|147541|92860|683158|5453|107450;4751|4890|147545|5042|1131492|5052|41958;4751|4890|147545|5042|1131492|5052|41959;4751|4890|147545|5042|1131492|5052|1915376;4751|4890|147541|92860|683158|104397;4751|5204|5257|5267|5268|63261;4751|5204|5257|5267|5268|63261|84754;4751|4890|147541|92860|683158|1770170;4751|4890|147541|92860|683158|1770170|2301472;4751|4890|147545|5042|1131492|5073|1506166;4751|4890|3239873|3243772|410830|75735|45547,Complete,Svetlana up
bsdb:40790470/2/2,40790470,time series / longitudinal observational,40790470,10.1186/s12866-025-04260-5,NA,"Xu C., Li W., Lin L., Zhang D., Lei J., Pan D., Liang S., Chen Y., Wan Y. , He J.",High-throughput sequencing to analyze changes in the human scalp microbiome during the use of a shampoo,BMC microbiology,2025,"High-throughput sequencing, Human scalp, Microbial community, Scalp health care, Shampoo",Experiment 2,China,Homo sapiens,Skin of scalp,UBERON:8300000,Environmental exposure measurement,EFO:0008360,Participants before Shampoo use (Day 0),Participants after Shampoo use (Day 28),Participants who applied the test shampoo for 28 days after refraining from other hair products for at least three days prior to treatment.,20,20,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Figure 3E,12 October 2025,Pamela,Pamela,Taxonomic differences in the scalp fungal microbiota before and after shampoo use.,decreased,"k__Fungi|p__Ascomycota|c__Archaeorhizomycetes|o__Archaeorhizomycetales|f__Archaeorhizomycetaceae|g__Archaeorhizomyces,k__Fungi|p__Ascomycota|c__Archaeorhizomycetes|o__Archaeorhizomycetales|f__Archaeorhizomycetaceae,k__Fungi|p__Ascomycota|c__Archaeorhizomycetes|o__Archaeorhizomycetales,k__Fungi|p__Ascomycota|c__Archaeorhizomycetes,k__Fungi|p__Mucoromycota,k__Fungi|p__Mucoromycota|c__Mortierellomycetes|o__Mortierellales|f__Mortierellaceae,k__Fungi|p__Mucoromycota|c__Mortierellomycetes|o__Mortierellales,k__Fungi|p__Mucoromycota|c__Mortierellomycetes,k__Fungi|p__Mucoromycota,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Naviculisporaceae,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Sporormiaceae|g__Preussia,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Naviculisporaceae|g__Pseudorhypophila,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Naviculisporaceae|g__Pseudorhypophila|s__Pseudorhypophila marina,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Sporormiaceae",4751|4890|1075807|1075813|1075814|1075815;4751|4890|1075807|1075813|1075814;4751|4890|1075807|1075813;4751|4890|1075807;4751|1913637;4751|1913637|2212732|214503|4854;4751|1913637|2212732|214503;4751|1913637|2212732;4751|1913637;4751|4890|147550|5139|2905925;4751|4890|147541|92860|55176|265084;4751|4890|147550|5139|2905925|3385929;4751|4890|147550|5139|2905925|3385929|573856;4751|4890|147550|5139;4751|4890|147541|92860|55176,Complete,Svetlana up
bsdb:40790561/1/1,40790561,prospective cohort,40790561,https://doi.org/10.1186/s12866-025-04242-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04242-7,"Chen X., Chen F., Wu S., Lv P. , Li P.",Vaginal microbiota alterations under supraphysiological estradiol state during in vitro fertilization-embryo transfer (IVF-ET) and the association with reproductive outcomes,BMC microbiology,2025,"In vitro fertilization-embryo transfer (IVF-ET), Pregnancy outcomes, Supraphysiological estradiol (E2) level, Vaginal microbiome",Experiment 1,China,Homo sapiens,Vagina,UBERON:0000996,Estradiol measurement,EFO:0004697,Hormone replacement cycle group (HRT) + Low-estradiol group (LE) + Median-estradiol group (ME) + High-estradiol group (HE),Natural Cycle Group (NC),Patients undergoing frozen-thawed embryo transfer were designated as the natural cycle (NC) group,77,15,Recent use of antibiotics,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,20 October 2025,Kimbrene Kakande,"Kimbrene Kakande,Fiddyhamma",Differentially abundant species across the groups with different peak estradiol levels. Histogram of Linear discriminant analysis Effect Size (LEfSe) analysis for vaginal microbiome across above groups. Linear discriminant analysis (LDA) scores greater than 3 are presented (NC: natural cycle group; HRT: hormone replacement cycle group; LE: low-estradiol group; ME: median-estradiol group; HE: high-estradiol group),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hydrogenophaga,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Phenylobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hydrogenophaga,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Phenylobacterium|s__uncultured Phenylobacterium sp.",3379134|1224|28216|80840|80864|47420;3379134|1224|28211|204458|76892|20;3379134|1224|28216|80840|80864|47420;3379134|1224|28211|204458|76892|20|349273,Complete,KateRasheed
bsdb:40790561/2/1,40790561,prospective cohort,40790561,https://doi.org/10.1186/s12866-025-04242-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04242-7,"Chen X., Chen F., Wu S., Lv P. , Li P.",Vaginal microbiota alterations under supraphysiological estradiol state during in vitro fertilization-embryo transfer (IVF-ET) and the association with reproductive outcomes,BMC microbiology,2025,"In vitro fertilization-embryo transfer (IVF-ET), Pregnancy outcomes, Supraphysiological estradiol (E2) level, Vaginal microbiome",Experiment 2,China,Homo sapiens,Vagina,UBERON:0000996,Estradiol measurement,EFO:0004697,Natural Cycle Group (NC) + Low-estradiol group (LE) + Median-estradiol group (ME) + High-estradiol group (HE),Hormone replacement cycle group (HRT),Patients undergoing frozen-thawed embryo transfer were designated as the hormone replacement cycle (HRT) group.,82,10,Recent use of antibiotics,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,1 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant species across the groups with different peak estradiol levels. Histogram of Linear discriminant analysis Effect Size (LEfSe) analysis for vaginal microbiome across above groups. Linear discriminant analysis (LDA) scores greater than 3 are presented (NC: natural cycle group; HRT: hormone replacement cycle group; LE: low-estradiol group; ME: median-estradiol group; HE: high-estradiol group),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia",3379134|1224|28216|80840;3379134|1224|1236|91347|543|1940338;3379134|1224|28211|356;1783272|1239|91061|186826|33958|1578|147802;3379134|1224|28216|80840|119060|48736;3379134|1224|28216|80840|119060|48736,Complete,KateRasheed
bsdb:40790561/3/1,40790561,prospective cohort,40790561,https://doi.org/10.1186/s12866-025-04242-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04242-7,"Chen X., Chen F., Wu S., Lv P. , Li P.",Vaginal microbiota alterations under supraphysiological estradiol state during in vitro fertilization-embryo transfer (IVF-ET) and the association with reproductive outcomes,BMC microbiology,2025,"In vitro fertilization-embryo transfer (IVF-ET), Pregnancy outcomes, Supraphysiological estradiol (E2) level, Vaginal microbiome",Experiment 3,China,Homo sapiens,Vagina,UBERON:0000996,Estradiol measurement,EFO:0004697,Natural Cycle Group (NC) + Hormone replacement cycle group (HRT) + Median-estradiol group (ME) + High-estradiol group (HE),Low-estradiol group (LE),"Participants undergoing fresh embryo transfer were divided into three groups based on the estradiol level on the trigger day, designated as low-estradiol (LE) group with the estradiol levels < 5,000pmol/L.",76,16,Recent use of antibiotics,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,1 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant species across the groups with different peak estradiol levels. Histogram of Linear discriminant analysis Effect Size (LEfSe) analysis for vaginal microbiome across above groups. Linear discriminant analysis (LDA) scores greater than 3 are presented (NC: natural cycle group; HRT: hormone replacement cycle group; LE: low-estradiol group; ME: median-estradiol group; HE: high-estradiol group),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__uncultured Prevotella sp.",3379134|976|200643|171549;3379134|976|200643;3379134|976;1783272|1239|186801;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|976|200643|171549|171552|838|159272,Complete,KateRasheed
bsdb:40790561/4/1,40790561,prospective cohort,40790561,https://doi.org/10.1186/s12866-025-04242-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04242-7,"Chen X., Chen F., Wu S., Lv P. , Li P.",Vaginal microbiota alterations under supraphysiological estradiol state during in vitro fertilization-embryo transfer (IVF-ET) and the association with reproductive outcomes,BMC microbiology,2025,"In vitro fertilization-embryo transfer (IVF-ET), Pregnancy outcomes, Supraphysiological estradiol (E2) level, Vaginal microbiome",Experiment 4,China,Homo sapiens,Vagina,UBERON:0000996,Estradiol measurement,EFO:0004697,Natural Cycle Group (NC) + Hormone replacement cycle group (HRT) + Low-estradiol group (LE) + High-estradiol group (HE),Median-estradiol group (ME),"Participants undergoing fresh embryo transfer were divided into three groups based on the estradiol level on the trigger day, designated as median-estradiol (ME) group with the estradiol levels ranged from 5,000 to 11,000pmol/L.",66,26,Recent use of antibiotics,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,1 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant species across the groups with different peak estradiol levels. Histogram of Linear discriminant analysis Effect Size (LEfSe) analysis for vaginal microbiome across above groups. Linear discriminant analysis (LDA) scores greater than 3 are presented (NC: natural cycle group; HRT: hormone replacement cycle group; LE: low-estradiol group; ME: median-estradiol group; HE: high-estradiol group),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus",3379134|1224|1236|91347|543|570|573;1783272|1239|91061|186826|1300|1301|1328,Complete,KateRasheed
bsdb:40790561/5/1,40790561,prospective cohort,40790561,https://doi.org/10.1186/s12866-025-04242-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04242-7,"Chen X., Chen F., Wu S., Lv P. , Li P.",Vaginal microbiota alterations under supraphysiological estradiol state during in vitro fertilization-embryo transfer (IVF-ET) and the association with reproductive outcomes,BMC microbiology,2025,"In vitro fertilization-embryo transfer (IVF-ET), Pregnancy outcomes, Supraphysiological estradiol (E2) level, Vaginal microbiome",Experiment 5,China,Homo sapiens,Vagina,UBERON:0000996,Estradiol measurement,EFO:0004697,Natural Cycle Group (NC) + Hormone replacement cycle group (HRT) + Low-estradiol group (LE) + Median-estradiol group (ME),High-estradiol group (HE),"Participants undergoing fresh embryo transfer were divided into three groups based on the estradiol level on the trigger day, designated as high-estradiol (HE) group with the estradiol levels > 11,000pmol/L.",67,25,Recent use of antibiotics,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,1 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant species across the groups with different peak estradiol levels. Histogram of Linear discriminant analysis Effect Size (LEfSe) analysis for vaginal microbiome across above groups.  Linear discriminant analysis (LDA) scores greater than 3 are presented (NC: natural cycle group; HRT: hormone replacement cycle group; LE: low-estradiol group; ME: median-estradiol group; HE: high-estradiol group),increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Shuttleworthella",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;1783272|1239|186801|3085636|186803|177971;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201;3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|186803|177971,Complete,KateRasheed
bsdb:40790561/6/1,40790561,prospective cohort,40790561,https://doi.org/10.1186/s12866-025-04242-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04242-7,"Chen X., Chen F., Wu S., Lv P. , Li P.",Vaginal microbiota alterations under supraphysiological estradiol state during in vitro fertilization-embryo transfer (IVF-ET) and the association with reproductive outcomes,BMC microbiology,2025,"In vitro fertilization-embryo transfer (IVF-ET), Pregnancy outcomes, Supraphysiological estradiol (E2) level, Vaginal microbiome",Experiment 6,China,Homo sapiens,Vagina,UBERON:0000996,Estradiol measurement,EFO:0004697,Low Estradiol level,High Estradiol level,"Participants with estradiol levels > 11,000pmol/L.",NA,NA,Recent use of antibiotics,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,1 November 2025,Fiddyhamma,Fiddyhamma,Correlation of vaginal microbiota with the peak of estradiol,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus",3379134|74201|203494|48461|1647988|239934;1783272|1239|91061|186826|1300|1301|1328,Complete,KateRasheed
bsdb:40790561/6/2,40790561,prospective cohort,40790561,https://doi.org/10.1186/s12866-025-04242-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04242-7,"Chen X., Chen F., Wu S., Lv P. , Li P.",Vaginal microbiota alterations under supraphysiological estradiol state during in vitro fertilization-embryo transfer (IVF-ET) and the association with reproductive outcomes,BMC microbiology,2025,"In vitro fertilization-embryo transfer (IVF-ET), Pregnancy outcomes, Supraphysiological estradiol (E2) level, Vaginal microbiome",Experiment 6,China,Homo sapiens,Vagina,UBERON:0000996,Estradiol measurement,EFO:0004697,Low Estradiol level,High Estradiol level,"Participants with estradiol levels > 11,000pmol/L.",NA,NA,Recent use of antibiotics,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,1 November 2025,Fiddyhamma,Fiddyhamma,Correlation of vaginal microbiota with the peak of estradiol,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,3379134|1224|1236|91347|543|1940338,Complete,KateRasheed
bsdb:40790561/7/1,40790561,prospective cohort,40790561,https://doi.org/10.1186/s12866-025-04242-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04242-7,"Chen X., Chen F., Wu S., Lv P. , Li P.",Vaginal microbiota alterations under supraphysiological estradiol state during in vitro fertilization-embryo transfer (IVF-ET) and the association with reproductive outcomes,BMC microbiology,2025,"In vitro fertilization-embryo transfer (IVF-ET), Pregnancy outcomes, Supraphysiological estradiol (E2) level, Vaginal microbiome",Experiment 7,China,Homo sapiens,Vagina,UBERON:0000996,Pregnancy,EFO:0002950,Biochemical pregnancy (BP) group + Abortion (AB) group + Ongoing pregnancy (OP) group,Un-Pregnancy (UP),These are patients no longer pregnant,78,14,Recent use of antibiotics,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,1 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant species across the groups with different pregnancy outcomes. Histogram of Linear discriminant analysis Effect Size (LEfSe) analysis for vaginal microbiome across above groups. Linear discriminant analysis (LDA) scores greater than 2 are presented (UP: un-pregnancy group; BP: biochemical pregnancy group; AB: abortion group),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Beijerinckiaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|1224|28211|356|45404;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:40790561/8/1,40790561,prospective cohort,40790561,https://doi.org/10.1186/s12866-025-04242-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04242-7,"Chen X., Chen F., Wu S., Lv P. , Li P.",Vaginal microbiota alterations under supraphysiological estradiol state during in vitro fertilization-embryo transfer (IVF-ET) and the association with reproductive outcomes,BMC microbiology,2025,"In vitro fertilization-embryo transfer (IVF-ET), Pregnancy outcomes, Supraphysiological estradiol (E2) level, Vaginal microbiome",Experiment 8,China,Homo sapiens,Vagina,UBERON:0000996,Pregnancy,EFO:0002950,Un-pregnancy (UP) group + Abortion (AB) group + Ongoing pregnancy (OP) group,Biochemical pregnancy (BP) group,An early miscarriage that occurs after a positive pregnancy test but before the pregnancy is visible on an ultrasound.,87,5,Recent use of antibiotics,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,1 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant species across the groups with different pregnancy outcomes. Histogram of Linear discriminant analysis Effect Size (LEfSe) analysis for vaginal microbiome across above groups. Linear discriminant analysis (LDA) scores greater than 2 are presented (UP: un-pregnancy group; BP: biochemical pregnancy group; AB: abortion group),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",1783272|201174|1760|85004|31953|1678;1783272|201174|84998|1643822|1643826;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|1300|1357|1358;1783272|201174|1760|85004|31953|1678;3379134|976|200643|171549|171551|836,Complete,KateRasheed
bsdb:40790561/9/1,40790561,prospective cohort,40790561,https://doi.org/10.1186/s12866-025-04242-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04242-7,"Chen X., Chen F., Wu S., Lv P. , Li P.",Vaginal microbiota alterations under supraphysiological estradiol state during in vitro fertilization-embryo transfer (IVF-ET) and the association with reproductive outcomes,BMC microbiology,2025,"In vitro fertilization-embryo transfer (IVF-ET), Pregnancy outcomes, Supraphysiological estradiol (E2) level, Vaginal microbiome",Experiment 9,China,Homo sapiens,Vagina,UBERON:0000996,Abortion,EFO:1001491,Un-pregnancy (UP) group + Biochemical pregnancy (BP) group + Ongoing pregnancy (OP) group,Abortion (AB) group,Patients who had early abortion of pregnancy,89,3,Recent use of antibiotics,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,1 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant species across the groups with different pregnancy outcomes. Histogram of Linear discriminant analysis Effect Size (LEfSe) analysis for vaginal microbiome across above groups. Linear discriminant analysis (LDA) scores greater than 2 are presented (UP: un-pregnancy group; BP: biochemical pregnancy group; AB: abortion group),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium|s__Atopobium sp. S3PFAA1-4,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__uncultured Aerococcus sp.,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales",3379134|1224|28211|3120395|433;3379134|1224|28211|3120395;1783272|1239|91061|186826|186827;1783272|1239|91061|186826|186827|1375;1783272|201174|84998|84999|1643824;1783272|201174|84998|84999|1643824|1380;1783272|201174|84998|84999|1643824|1380|1219589;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|909932|1843489|31977;1783272|201174|84998|84999|1643824|1380;95818|2093818|2093825|2171986;95818|2093818|2093825|2171986|1331051;1783272|1239|91061|186826|186827|1375|189667;95818|2093818|2093825,Complete,KateRasheed
bsdb:40790561/10/1,40790561,prospective cohort,40790561,https://doi.org/10.1186/s12866-025-04242-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04242-7,"Chen X., Chen F., Wu S., Lv P. , Li P.",Vaginal microbiota alterations under supraphysiological estradiol state during in vitro fertilization-embryo transfer (IVF-ET) and the association with reproductive outcomes,BMC microbiology,2025,"In vitro fertilization-embryo transfer (IVF-ET), Pregnancy outcomes, Supraphysiological estradiol (E2) level, Vaginal microbiome",Experiment 10,China,Homo sapiens,Vagina,UBERON:0000996,Pregnancy,EFO:0002950,Ongoing pregnancy (OP) group,Un-pregnancy (UP) group,These are patients no longer pregnant,70,14,Recent use of antibiotics,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4 and text,2 November 2025,Fiddyhamma,Fiddyhamma,"Comparison of vaginal microbiota in the groups of different pregnancy outcomes. Variables are presented as median (P25-P75) (Kruskal-Wallis test). Statistical significance is considered at p < 0.05. Superscript letters a, b are used to represent the significance of differences between groups.",increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:40790561/11/1,40790561,prospective cohort,40790561,https://doi.org/10.1186/s12866-025-04242-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04242-7,"Chen X., Chen F., Wu S., Lv P. , Li P.",Vaginal microbiota alterations under supraphysiological estradiol state during in vitro fertilization-embryo transfer (IVF-ET) and the association with reproductive outcomes,BMC microbiology,2025,"In vitro fertilization-embryo transfer (IVF-ET), Pregnancy outcomes, Supraphysiological estradiol (E2) level, Vaginal microbiome",Experiment 11,China,Homo sapiens,Vagina,UBERON:0000996,Abortion,EFO:1001491,Ongoing pregnancy (OP) group,Abortion (AB) group,Patients who had early abortion of pregnancy,70,3,Recent use of antibiotics,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4 and text,2 November 2025,Fiddyhamma,Fiddyhamma,"Comparison of vaginal microbiota in the groups of different pregnancy outcomes. Variables are presented as median (P25-P75) (Kruskal-Wallis test). Statistical significance is considered at p < 0.05. Superscript letters a, b are used to represent the significance of differences between groups.",increased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,1783272|201174|84998|84999|1643824|1380,Complete,KateRasheed
bsdb:40790561/12/1,40790561,prospective cohort,40790561,https://doi.org/10.1186/s12866-025-04242-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04242-7,"Chen X., Chen F., Wu S., Lv P. , Li P.",Vaginal microbiota alterations under supraphysiological estradiol state during in vitro fertilization-embryo transfer (IVF-ET) and the association with reproductive outcomes,BMC microbiology,2025,"In vitro fertilization-embryo transfer (IVF-ET), Pregnancy outcomes, Supraphysiological estradiol (E2) level, Vaginal microbiome",Experiment 12,China,Homo sapiens,Vagina,UBERON:0000996,Pregnancy,EFO:0002950,Ongoing pregnancy (OP),Biochemical pregnancy (BP) group,An early miscarriage that occurs after a positive pregnancy test but before the pregnancy is visible on an ultrasound.,70,5,Recent use of antibiotics,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4 and text,2 November 2025,Fiddyhamma,Fiddyhamma,"Comparison of vaginal microbiota in the groups of different pregnancy outcomes. Variables are presented as median (P25-P75) (Kruskal-Wallis test). Statistical significance is considered at p < 0.05. Superscript letters a, b are used to represent the significance of differences between groups.",increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,KateRasheed
bsdb:40790561/13/1,40790561,prospective cohort,40790561,https://doi.org/10.1186/s12866-025-04242-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04242-7,"Chen X., Chen F., Wu S., Lv P. , Li P.",Vaginal microbiota alterations under supraphysiological estradiol state during in vitro fertilization-embryo transfer (IVF-ET) and the association with reproductive outcomes,BMC microbiology,2025,"In vitro fertilization-embryo transfer (IVF-ET), Pregnancy outcomes, Supraphysiological estradiol (E2) level, Vaginal microbiome",Experiment 13,China,Homo sapiens,Vagina,UBERON:0000996,Estradiol measurement,EFO:0004697,Hormone replacement cycle group (HRT),Median-estradiol group (ME),"Participants undergoing fresh embryo transfer were divided into three groups based on the estradiol level on the trigger day, designated as median-estradiol (ME) group with the estradiol levels ranged from 5,000 to 11,000pmol/L.",10,26,Recent use of antibiotics,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,3 November 2025,Fiddyhamma,Fiddyhamma,"Comparison of vaginal microbiota in the groups with different estradiol levels. Variables are presented as median (P25-P75) (Kruskal-Wallis test). Statistical significance is considered at p < 0.05. Superscript letters a, b, c are used to represent the significance of differences between groups.",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus",3379134|74201|203494|48461|1647988|239934;1783272|1239|91061|186826|1300|1301|1328,Complete,KateRasheed
bsdb:40790561/13/2,40790561,prospective cohort,40790561,https://doi.org/10.1186/s12866-025-04242-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04242-7,"Chen X., Chen F., Wu S., Lv P. , Li P.",Vaginal microbiota alterations under supraphysiological estradiol state during in vitro fertilization-embryo transfer (IVF-ET) and the association with reproductive outcomes,BMC microbiology,2025,"In vitro fertilization-embryo transfer (IVF-ET), Pregnancy outcomes, Supraphysiological estradiol (E2) level, Vaginal microbiome",Experiment 13,China,Homo sapiens,Vagina,UBERON:0000996,Estradiol measurement,EFO:0004697,Hormone replacement cycle group (HRT),Median-estradiol group (ME),"Participants undergoing fresh embryo transfer were divided into three groups based on the estradiol level on the trigger day, designated as median-estradiol (ME) group with the estradiol levels ranged from 5,000 to 11,000pmol/L.",10,26,Recent use of antibiotics,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,15 January 2026,Fiddyhamma,Fiddyhamma,"Comparison of vaginal microbiota in the groups with different estradiol levels. Variables are presented as median (P25-P75) (Kruskal-Wallis test). Statistical significance is considered at p < 0.05. Superscript letters a, b, c are used to represent the significance of differences between groups.",decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,3379134|1224|1236|91347|543|1940338,Complete,KateRasheed
bsdb:40790561/14/1,40790561,prospective cohort,40790561,https://doi.org/10.1186/s12866-025-04242-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04242-7,"Chen X., Chen F., Wu S., Lv P. , Li P.",Vaginal microbiota alterations under supraphysiological estradiol state during in vitro fertilization-embryo transfer (IVF-ET) and the association with reproductive outcomes,BMC microbiology,2025,"In vitro fertilization-embryo transfer (IVF-ET), Pregnancy outcomes, Supraphysiological estradiol (E2) level, Vaginal microbiome",Experiment 14,China,Homo sapiens,Vagina,UBERON:0000996,Estradiol measurement,EFO:0004697,Natural Cycle Group (NC),Low-estradiol group (LE),"Participants undergoing fresh embryo transfer were divided into three groups based on the estradiol level on the trigger day, designated as low-estradiol (LE) group with the estradiol levels < 5,000pmol/L.",15,16,Recent use of antibiotics,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,3 November 2025,Fiddyhamma,Fiddyhamma,"Comparison of vaginal microbiota in the groups with different estradiol levels. Variables are presented as median (P25-P75) (Kruskal-Wallis test). Statistical significance is considered at p < 0.05. Superscript letters a, b, c are used to represent the significance of differences between groups.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus",3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301|1328,Complete,KateRasheed
bsdb:40790561/15/1,40790561,prospective cohort,40790561,https://doi.org/10.1186/s12866-025-04242-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04242-7,"Chen X., Chen F., Wu S., Lv P. , Li P.",Vaginal microbiota alterations under supraphysiological estradiol state during in vitro fertilization-embryo transfer (IVF-ET) and the association with reproductive outcomes,BMC microbiology,2025,"In vitro fertilization-embryo transfer (IVF-ET), Pregnancy outcomes, Supraphysiological estradiol (E2) level, Vaginal microbiome",Experiment 15,China,Homo sapiens,Vagina,UBERON:0000996,Estradiol measurement,EFO:0004697,Hormone replacement cycle group (HRT),High-estradiol group (HE),"Participants undergoing fresh embryo transfer were divided into three groups based on the estradiol level on the trigger day, designated as high-estradiol (HE) group with the estradiol levels > 11,000pmol/L.",10,25,Recent use of antibiotics,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,3 November 2025,Fiddyhamma,Fiddyhamma,"Comparison of vaginal microbiota in the groups with different estradiol levels. Variables are presented as median (P25-P75) (Kruskal-Wallis test). Statistical significance is considered at p < 0.05. Superscript letters a, b, c are used to represent the significance of differences between groups.",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|1300|1301|1328,Complete,KateRasheed
bsdb:40790561/15/2,40790561,prospective cohort,40790561,https://doi.org/10.1186/s12866-025-04242-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04242-7,"Chen X., Chen F., Wu S., Lv P. , Li P.",Vaginal microbiota alterations under supraphysiological estradiol state during in vitro fertilization-embryo transfer (IVF-ET) and the association with reproductive outcomes,BMC microbiology,2025,"In vitro fertilization-embryo transfer (IVF-ET), Pregnancy outcomes, Supraphysiological estradiol (E2) level, Vaginal microbiome",Experiment 15,China,Homo sapiens,Vagina,UBERON:0000996,Estradiol measurement,EFO:0004697,Hormone replacement cycle group (HRT),High-estradiol group (HE),"Participants undergoing fresh embryo transfer were divided into three groups based on the estradiol level on the trigger day, designated as high-estradiol (HE) group with the estradiol levels > 11,000pmol/L.",10,25,Recent use of antibiotics,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,15 January 2026,Fiddyhamma,Fiddyhamma,"Comparison of vaginal microbiota in the groups with different estradiol levels. Variables are presented as median (P25-P75) (Kruskal-Wallis test). Statistical significance is considered at p < 0.05. Superscript letters a, b, c are used to represent the significance of differences between groups.",decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,3379134|1224|1236|91347|543|1940338,Complete,KateRasheed
bsdb:40790561/16/1,40790561,prospective cohort,40790561,https://doi.org/10.1186/s12866-025-04242-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04242-7,"Chen X., Chen F., Wu S., Lv P. , Li P.",Vaginal microbiota alterations under supraphysiological estradiol state during in vitro fertilization-embryo transfer (IVF-ET) and the association with reproductive outcomes,BMC microbiology,2025,"In vitro fertilization-embryo transfer (IVF-ET), Pregnancy outcomes, Supraphysiological estradiol (E2) level, Vaginal microbiome",Experiment 16,China,Homo sapiens,Vagina,UBERON:0000996,Estradiol measurement,EFO:0004697,Natural Cycle Group (NC),Median-estradiol group (ME),"Participants undergoing fresh embryo transfer were divided into three groups based on the estradiol level on the trigger day, designated as median-estradiol (ME) group with the estradiol levels ranged from 5,000 to 11,000pmol/L.",15,26,Recent use of antibiotics,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,3 November 2025,Fiddyhamma,Fiddyhamma,"Comparison of vaginal microbiota in the groups with different estradiol levels. Variables are presented as median (P25-P75) (Kruskal-Wallis test). Statistical significance is considered at p < 0.05. Superscript letters a, b, c are used to represent the significance of differences between groups.",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners",1783272|1239|91061|186826|1300|1301|1328;1783272|1239|91061|186826|33958|1578|147802,Complete,KateRasheed
bsdb:40790561/17/1,40790561,prospective cohort,40790561,https://doi.org/10.1186/s12866-025-04242-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04242-7,"Chen X., Chen F., Wu S., Lv P. , Li P.",Vaginal microbiota alterations under supraphysiological estradiol state during in vitro fertilization-embryo transfer (IVF-ET) and the association with reproductive outcomes,BMC microbiology,2025,"In vitro fertilization-embryo transfer (IVF-ET), Pregnancy outcomes, Supraphysiological estradiol (E2) level, Vaginal microbiome",Experiment 17,China,Homo sapiens,Vagina,UBERON:0000996,Estradiol measurement,EFO:0004697,Natural Cycle Group (NC),Hormone replacement cycle group (HRT),Patients undergoing frozen-thawed embryo transfer were designated as the hormone replacement cycle (HRT) group.,15,10,Recent use of antibiotics,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,3 November 2025,Fiddyhamma,Fiddyhamma,"Comparison of vaginal microbiota in the groups with different estradiol levels. Variables are presented as median (P25-P75) (Kruskal-Wallis test). Statistical significance is considered at p < 0.05. Superscript letters a, b, c are used to represent the significance of differences between groups.",increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,1783272|1239|91061|186826|33958|1578|147802,Complete,KateRasheed
bsdb:40790561/17/2,40790561,prospective cohort,40790561,https://doi.org/10.1186/s12866-025-04242-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04242-7,"Chen X., Chen F., Wu S., Lv P. , Li P.",Vaginal microbiota alterations under supraphysiological estradiol state during in vitro fertilization-embryo transfer (IVF-ET) and the association with reproductive outcomes,BMC microbiology,2025,"In vitro fertilization-embryo transfer (IVF-ET), Pregnancy outcomes, Supraphysiological estradiol (E2) level, Vaginal microbiome",Experiment 17,China,Homo sapiens,Vagina,UBERON:0000996,Estradiol measurement,EFO:0004697,Natural Cycle Group (NC),Hormone replacement cycle group (HRT),Patients undergoing frozen-thawed embryo transfer were designated as the hormone replacement cycle (HRT) group.,15,10,Recent use of antibiotics,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,15 January 2026,Fiddyhamma,Fiddyhamma,"Comparison of vaginal microbiota in the groups with different estradiol levels. Variables are presented as median (P25-P75) (Kruskal-Wallis test). Statistical significance is considered at p < 0.05. Superscript letters a, b, c are used to represent the significance of differences between groups.",decreased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,3379134|74201|203494|48461|1647988|239934,Complete,KateRasheed
bsdb:40790561/18/1,40790561,prospective cohort,40790561,https://doi.org/10.1186/s12866-025-04242-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04242-7,"Chen X., Chen F., Wu S., Lv P. , Li P.",Vaginal microbiota alterations under supraphysiological estradiol state during in vitro fertilization-embryo transfer (IVF-ET) and the association with reproductive outcomes,BMC microbiology,2025,"In vitro fertilization-embryo transfer (IVF-ET), Pregnancy outcomes, Supraphysiological estradiol (E2) level, Vaginal microbiome",Experiment 18,China,Homo sapiens,Vagina,UBERON:0000996,Pregnancy,EFO:0002950,Un-pregnancy (UP) group,Biochemical pregnancy (BP) group,An early miscarriage that occurs after a positive pregnancy test but before the pregnancy is visible on an ultrasound.,14,5,Recent use of antibiotics,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4 and text,15 January 2026,Fiddyhamma,Fiddyhamma,"Comparison of vaginal microbiota in the groups of different pregnancy outcomes. Variables are presented as median (P25-P75) (Kruskal-Wallis test). Statistical significance is considered at p < 0.05. Superscript letters a, b are used to represent the significance of differences between groups.",increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,KateRasheed
bsdb:40790561/19/1,40790561,prospective cohort,40790561,https://doi.org/10.1186/s12866-025-04242-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04242-7,"Chen X., Chen F., Wu S., Lv P. , Li P.",Vaginal microbiota alterations under supraphysiological estradiol state during in vitro fertilization-embryo transfer (IVF-ET) and the association with reproductive outcomes,BMC microbiology,2025,"In vitro fertilization-embryo transfer (IVF-ET), Pregnancy outcomes, Supraphysiological estradiol (E2) level, Vaginal microbiome",Experiment 19,China,Homo sapiens,Vagina,UBERON:0000996,Estradiol measurement,EFO:0004697,Low-estradiol group (LE),Median-estradiol group (ME),"Participants undergoing fresh embryo transfer were divided into three groups based on the estradiol level on the trigger day, designated as median-estradiol (ME) group with the estradiol levels ranged from 5,000 to 11,000pmol/L.",16,26,Recent use of antibiotics,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Table 2,15 January 2026,Fiddyhamma,Fiddyhamma,"Comparison of vaginal microbiota in the groups with different estradiol levels. Variables are presented as median (P25-P75) (Kruskal-Wallis test). Statistical significance is considered at p < 0.05. Superscript letters a, b, c are used to represent the significance of differences between groups.",increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,1783272|1239|91061|186826|33958|1578|147802,Complete,KateRasheed
bsdb:40790561/19/2,40790561,prospective cohort,40790561,https://doi.org/10.1186/s12866-025-04242-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04242-7,"Chen X., Chen F., Wu S., Lv P. , Li P.",Vaginal microbiota alterations under supraphysiological estradiol state during in vitro fertilization-embryo transfer (IVF-ET) and the association with reproductive outcomes,BMC microbiology,2025,"In vitro fertilization-embryo transfer (IVF-ET), Pregnancy outcomes, Supraphysiological estradiol (E2) level, Vaginal microbiome",Experiment 19,China,Homo sapiens,Vagina,UBERON:0000996,Estradiol measurement,EFO:0004697,Low-estradiol group (LE),Median-estradiol group (ME),"Participants undergoing fresh embryo transfer were divided into three groups based on the estradiol level on the trigger day, designated as median-estradiol (ME) group with the estradiol levels ranged from 5,000 to 11,000pmol/L.",16,26,Recent use of antibiotics,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Table 2,15 January 2026,Fiddyhamma,Fiddyhamma,"Comparison of vaginal microbiota in the groups with different estradiol levels. Variables are presented as median (P25-P75) (Kruskal-Wallis test). Statistical significance is considered at p < 0.05. Superscript letters a, b, c are used to represent the significance of differences between groups.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",3379134|1224|1236|91347|543|1940338;3379134|976|200643|171549|171552|838,Complete,KateRasheed
bsdb:40790561/20/1,40790561,prospective cohort,40790561,https://doi.org/10.1186/s12866-025-04242-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04242-7,"Chen X., Chen F., Wu S., Lv P. , Li P.",Vaginal microbiota alterations under supraphysiological estradiol state during in vitro fertilization-embryo transfer (IVF-ET) and the association with reproductive outcomes,BMC microbiology,2025,"In vitro fertilization-embryo transfer (IVF-ET), Pregnancy outcomes, Supraphysiological estradiol (E2) level, Vaginal microbiome",Experiment 20,China,Homo sapiens,Vagina,UBERON:0000996,Estradiol measurement,EFO:0004697,Hormone replacement cycle (HRT),Low-estradiol group (LE),"Participants undergoing fresh embryo transfer were divided into three groups based on the estradiol level on the trigger day, designated as low-estradiol (LE) group with the estradiol levels < 5,000pmol/L.",10,16,Recent use of antibiotics,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Table 2,15 January 2026,Fiddyhamma,Fiddyhamma,"Comparison of vaginal microbiota in the groups with different estradiol levels. Variables are presented as median (P25-P75) (Kruskal-Wallis test). Statistical significance is considered at p < 0.05. Superscript letters a, b, c are used to represent the significance of differences between groups.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus",3379134|976|200643|171549|171552|838;3379134|74201|203494|48461|1647988|239934;1783272|1239|91061|186826|1300|1301|1328,Complete,KateRasheed
bsdb:40790561/20/2,40790561,prospective cohort,40790561,https://doi.org/10.1186/s12866-025-04242-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04242-7,"Chen X., Chen F., Wu S., Lv P. , Li P.",Vaginal microbiota alterations under supraphysiological estradiol state during in vitro fertilization-embryo transfer (IVF-ET) and the association with reproductive outcomes,BMC microbiology,2025,"In vitro fertilization-embryo transfer (IVF-ET), Pregnancy outcomes, Supraphysiological estradiol (E2) level, Vaginal microbiome",Experiment 20,China,Homo sapiens,Vagina,UBERON:0000996,Estradiol measurement,EFO:0004697,Hormone replacement cycle (HRT),Low-estradiol group (LE),"Participants undergoing fresh embryo transfer were divided into three groups based on the estradiol level on the trigger day, designated as low-estradiol (LE) group with the estradiol levels < 5,000pmol/L.",10,16,Recent use of antibiotics,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Table 2,15 January 2026,Fiddyhamma,Fiddyhamma,"Comparison of vaginal microbiota in the groups with different estradiol levels. Variables are presented as median (P25-P75) (Kruskal-Wallis test). Statistical significance is considered at p < 0.05. Superscript letters a, b, c are used to represent the significance of differences between groups.",decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,1783272|1239|91061|186826|33958|1578|147802,Complete,KateRasheed
bsdb:40790561/21/1,40790561,prospective cohort,40790561,https://doi.org/10.1186/s12866-025-04242-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04242-7,"Chen X., Chen F., Wu S., Lv P. , Li P.",Vaginal microbiota alterations under supraphysiological estradiol state during in vitro fertilization-embryo transfer (IVF-ET) and the association with reproductive outcomes,BMC microbiology,2025,"In vitro fertilization-embryo transfer (IVF-ET), Pregnancy outcomes, Supraphysiological estradiol (E2) level, Vaginal microbiome",Experiment 21,China,Homo sapiens,Vagina,UBERON:0000996,Estradiol measurement,EFO:0004697,Low-estradiol group (LE),High-estradiol group (HE),"Participants undergoing fresh embryo transfer were divided into three groups based on the estradiol level on the trigger day, designated as high-estradiol (HE) group with the estradiol levels > 11,000pmol/L.",16,25,Recent use of antibiotics,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Table 2,15 January 2026,Fiddyhamma,Fiddyhamma,"Comparison of vaginal microbiota in the groups with different estradiol levels. Variables are presented as median (P25-P75) (Kruskal-Wallis test). Statistical significance is considered at p < 0.05. Superscript letters a, b, c are used to represent the significance of differences between groups.",increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,1783272|1239|91061|186826|33958|1578|147802,Complete,KateRasheed
bsdb:40790561/21/2,40790561,prospective cohort,40790561,https://doi.org/10.1186/s12866-025-04242-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04242-7,"Chen X., Chen F., Wu S., Lv P. , Li P.",Vaginal microbiota alterations under supraphysiological estradiol state during in vitro fertilization-embryo transfer (IVF-ET) and the association with reproductive outcomes,BMC microbiology,2025,"In vitro fertilization-embryo transfer (IVF-ET), Pregnancy outcomes, Supraphysiological estradiol (E2) level, Vaginal microbiome",Experiment 21,China,Homo sapiens,Vagina,UBERON:0000996,Estradiol measurement,EFO:0004697,Low-estradiol group (LE),High-estradiol group (HE),"Participants undergoing fresh embryo transfer were divided into three groups based on the estradiol level on the trigger day, designated as high-estradiol (HE) group with the estradiol levels > 11,000pmol/L.",16,25,Recent use of antibiotics,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Table 2,19 January 2026,Fiddyhamma,Fiddyhamma,"Comparison of vaginal microbiota in the groups with different estradiol levels. Variables are presented as median (P25-P75) (Kruskal-Wallis test). Statistical significance is considered at p < 0.05. Superscript letters a, b, c are used to represent the significance of differences between groups.",decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,3379134|1224|1236|91347|543|1940338,Complete,KateRasheed
bsdb:40790561/22/1,40790561,prospective cohort,40790561,https://doi.org/10.1186/s12866-025-04242-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04242-7,"Chen X., Chen F., Wu S., Lv P. , Li P.",Vaginal microbiota alterations under supraphysiological estradiol state during in vitro fertilization-embryo transfer (IVF-ET) and the association with reproductive outcomes,BMC microbiology,2025,"In vitro fertilization-embryo transfer (IVF-ET), Pregnancy outcomes, Supraphysiological estradiol (E2) level, Vaginal microbiome",Experiment 22,China,Homo sapiens,Vagina,UBERON:0000996,Estradiol measurement,EFO:0004697,Median-estradiol group (ME),High-estradiol group (HE),"Participants undergoing fresh embryo transfer were divided into three groups based on the estradiol level on the trigger day, designated as high-estradiol (HE) group with the estradiol levels > 11,000pmol/L.",26,25,Recent use of antibiotics,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,15 January 2026,Fiddyhamma,Fiddyhamma,"Comparison of vaginal microbiota in the groups with different estradiol levels. Variables are presented as median (P25-P75) (Kruskal-Wallis test). Statistical significance is considered at p < 0.05. Superscript letters a, b, c are used to represent the significance of differences between groups.",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,KateRasheed
bsdb:40790561/23/1,40790561,prospective cohort,40790561,https://doi.org/10.1186/s12866-025-04242-7,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04242-7,"Chen X., Chen F., Wu S., Lv P. , Li P.",Vaginal microbiota alterations under supraphysiological estradiol state during in vitro fertilization-embryo transfer (IVF-ET) and the association with reproductive outcomes,BMC microbiology,2025,"In vitro fertilization-embryo transfer (IVF-ET), Pregnancy outcomes, Supraphysiological estradiol (E2) level, Vaginal microbiome",Experiment 23,China,Homo sapiens,Vagina,UBERON:0000996,Estradiol measurement,EFO:0004697,Natural cycle group (NC),High-estradiol group (HE),"Participants undergoing fresh embryo transfer were divided into three groups based on the estradiol level on the trigger day, designated as high-estradiol (HE) group with the estradiol levels > 11,000pmol/L.",15,25,Recent use of antibiotics,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,15 January 2026,Fiddyhamma,Fiddyhamma,"Comparison of vaginal microbiota in the groups with different estradiol levels. Variables are presented as median (P25-P75) (Kruskal-Wallis test). Statistical significance is considered at p < 0.05. Superscript letters a, b, c are used to represent the significance of differences between groups.",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus",1783272|1239|91061|186826|33958|1578|147802;1783272|1239|91061|186826|1300|1301|1328,Complete,KateRasheed
bsdb:40792492/1/1,40792492,prospective cohort,40792492,10.1128/spectrum.01775-25,NA,"Xie H., Meng L., Duan X., Liang X., Huang T., Ma G., Luo H., Tang X. , Xiao X.",Establishment of the early gut microbiota in vaginally delivered infants: the influence of maternal gut microbiota outweighs vaginal microbiota,Microbiology spectrum,2025,"16S rDNA, correlation network, gut microbiota, infant, microbial transmission",Experiment 1,China,Homo sapiens,Meconium,UBERON:0007109,Delivery method,EFO:0000395,Meconium microbiota of cesarean-section infants (CIF1).,Meconium microbiota of vaginally delivered infants (VIF1).,These are the meconium microbiota of vaginally delivered infants  (VIF1).,7,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 4A,13 October 2025,Mautin,"Mautin,Ese",Distinct differences in composition between cesarean-section infants (CIF1) and meconium microbiota of vaginally delivered infants (VIF1).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas azotoformans",1783272|1239|186801;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;3379134|1224|1236|2887326|468;3379134|1224|1236|72274|135621;3379134|1224|1236|72274;3379134|1224|1236|72274|135621|286;3379134|1224|1236|72274|135621|286|47878,Complete,KateRasheed
bsdb:40792492/2/1,40792492,prospective cohort,40792492,10.1128/spectrum.01775-25,NA,"Xie H., Meng L., Duan X., Liang X., Huang T., Ma G., Luo H., Tang X. , Xiao X.",Establishment of the early gut microbiota in vaginally delivered infants: the influence of maternal gut microbiota outweighs vaginal microbiota,Microbiology spectrum,2025,"16S rDNA, correlation network, gut microbiota, infant, microbial transmission",Experiment 2,China,Homo sapiens,"Meconium,Feces","UBERON:0007109,UBERON:0001988",Delivery method,EFO:0000395,Meconium microbiota of vaginally delivered infants (VIF1).,Gut microbiota of 14-day-old vaginally delivered infants (VIF2).,These are the gut microbiota of 14-day-old vaginally delivered infants (VIF2).,8,16,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,increased,NA,unchanged,NA,NA,Signature 1,Figure 4B,13 October 2025,Mautin,"Mautin,Ese",Significant variations observed in composition between the VIF1 and the gut microbiota of 14-day-old vaginally delivered infants (VIF2).,increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Pectobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis",1783272|201174;3379134|976|200643|171549;3379134|976|200643|171549|815|816;3379134|976|200643;3379134|976;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|216816;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|186801|186802;3379134|1224|1236|91347|1903410;3379134|1224|1236|91347|1903410|122277;3379134|976|200643|171549|815;3379134|976|200643|171549|815|909656|821;1783272|201174;1783272|1239|186801|186802|31979|1485;3379134|976|200643|171549|815|816|817,Complete,KateRasheed
bsdb:40792492/2/2,40792492,prospective cohort,40792492,10.1128/spectrum.01775-25,NA,"Xie H., Meng L., Duan X., Liang X., Huang T., Ma G., Luo H., Tang X. , Xiao X.",Establishment of the early gut microbiota in vaginally delivered infants: the influence of maternal gut microbiota outweighs vaginal microbiota,Microbiology spectrum,2025,"16S rDNA, correlation network, gut microbiota, infant, microbial transmission",Experiment 2,China,Homo sapiens,"Meconium,Feces","UBERON:0007109,UBERON:0001988",Delivery method,EFO:0000395,Meconium microbiota of vaginally delivered infants (VIF1).,Gut microbiota of 14-day-old vaginally delivered infants (VIF2).,These are the gut microbiota of 14-day-old vaginally delivered infants (VIF2).,8,16,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,increased,NA,unchanged,NA,NA,Signature 2,Figure 4B,13 October 2025,Mautin,"Mautin,Ese",Significant variations were observed in composition between the VIF1 and the gut microbiota of 14-day-old vaginally delivered infants (VIF2).,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia pickettii",3379134|1224|28216|80840|119060;3379134|1224|1236;3379134|1224;3379134|1224|28216|80840|119060|48736;3379134|1224|28216|80840;3379134|1224|28216|80840|119060|48736|329,Complete,KateRasheed
bsdb:40792492/3/1,40792492,prospective cohort,40792492,10.1128/spectrum.01775-25,NA,"Xie H., Meng L., Duan X., Liang X., Huang T., Ma G., Luo H., Tang X. , Xiao X.",Establishment of the early gut microbiota in vaginally delivered infants: the influence of maternal gut microbiota outweighs vaginal microbiota,Microbiology spectrum,2025,"16S rDNA, correlation network, gut microbiota, infant, microbial transmission",Experiment 3,China,Homo sapiens,"Meconium,Feces","UBERON:0007109,UBERON:0001988",Delivery method,EFO:0000395,Meconium microbiota of cesarean-section infants (C1F1).,Gut microbiota of 14-day-old infants delivered by cesarean section (C1F2).,These are the gut microbiota of 14-day-old infants delivered by cesarean section  (C1F2).,7,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 4C,13 October 2025,Mautin,"Mautin,Ese",Notable disparities in composition were indicated between the CIF1 and the gut microbiota of 14-day-old infants delivered by cesarean section (CIF2).,increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium",1783272|201174;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|216816;1783272|201174;1783272|1239|909932|1843489|31977|29465|39777;1783272|201174|1760|85004|31953|1678|1689,Complete,KateRasheed
bsdb:40792492/3/2,40792492,prospective cohort,40792492,10.1128/spectrum.01775-25,NA,"Xie H., Meng L., Duan X., Liang X., Huang T., Ma G., Luo H., Tang X. , Xiao X.",Establishment of the early gut microbiota in vaginally delivered infants: the influence of maternal gut microbiota outweighs vaginal microbiota,Microbiology spectrum,2025,"16S rDNA, correlation network, gut microbiota, infant, microbial transmission",Experiment 3,China,Homo sapiens,"Meconium,Feces","UBERON:0007109,UBERON:0001988",Delivery method,EFO:0000395,Meconium microbiota of cesarean-section infants (C1F1).,Gut microbiota of 14-day-old infants delivered by cesarean section (C1F2).,These are the gut microbiota of 14-day-old infants delivered by cesarean section  (C1F2).,7,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 4C,13 October 2025,Mautin,"Mautin,Ese",Notable disparities in composition were indicated between the CIF1 and the gut microbiota of 14-day-old infants delivered by cesarean section (CIF2).,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia pickettii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas azotoformans",3379134|1224|28211;3379134|1224|28216|80840|119060;3379134|1224|28216|80840;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;3379134|1224|1236|72274|135621;3379134|1224|1236|72274|135621|286;3379134|1224|28216|80840|119060|48736;3379134|1224|28216|80840|119060|48736|329;3379134|1224|1236|72274|135621|286|47878,Complete,KateRasheed
bsdb:40803752/1/1,40803752,prospective cohort,40803752,10.1136/gutjnl-2025-335986,NA,"Lucas-Ruiz F., Vidal-Correoso D., Mateo S.V., de la Torre-Álamo M.M., Jover-Aguilar M., Alconchel F., Martínez-Alarcón L., Lopez-Lopez V., Ríos-Zambudio A., Cascales P., Pelegrín P., Pons J.A., Ramírez P. , Baroja-Mazo A.",Intrahepatic donor microbiota-based metataxonomic signature detected in organ preservation solution enables prediction of short-term liver transplant outcomes,Gut,2025,"LIVER TRANSPLANTATION, MACHINE LEARNING, MICROBIOME",Experiment 1,Spain,Homo sapiens,Bile duct,NA,Response to liver transplant,NA,Hypoabundant in Non-survivor recipients,Hyperabundant in Non-survivor recipients,"Recipients were monitored for early allograft dysfunction following liver transplantation, and patients died due to clinical outcomes related to the procedure.",NA,NA,NA,16S,23456789,Ion Torrent,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 1B, Supplementary Table 1 and Supplementary Figure 5",17 November 2025,Firdaws,Firdaws,"MaAsLin2 (Multivariate Association with Linear Models 2) analysis of differentially abundant taxa at the genus, family, order, class, and phylum levels in relation to survival.",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Gemmobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Porphyrobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Rubrivivax,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingobiaceae|g__Sphingobium,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia,k__Pseudomonadati|p__Spirochaetota,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|g__Tepidimonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",3379134|1224|1236|135625|712|713;1783272|1239|91061|1385|186817;1783272|1239|91061|1385|186817|1386;3379134|1224|28216;3379134|1224|28216|80840;3379134|976|117743|200644|2762318|501783;1783272|1239|91061|186826|81852;3379134|1224|28211|204457|335929;3379134|1224|28211|204455|31989|204456;3379134|1224|28216|80840|75682|149698;1783272|1239|909932|1843489|31977|906;3379134|1224|28216|80840|75682;3379134|1224|28211|204457|335929|1111;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;3379134|1224|28211|356|82115;3379134|1224|28216|80840|2975441|28067;3379134|1224|28211|204457|3423717|165695;3379134|203691|203692|136|137;3379134|203691|203692|136;3379134|203691|203692;3379134|203691;3379134|1224|28216|80840|114248;1783272|1239|909932|1843489|31977;1783272|1239|91061|186826|33958|46255,Complete,NA
bsdb:40803752/1/2,40803752,prospective cohort,40803752,10.1136/gutjnl-2025-335986,NA,"Lucas-Ruiz F., Vidal-Correoso D., Mateo S.V., de la Torre-Álamo M.M., Jover-Aguilar M., Alconchel F., Martínez-Alarcón L., Lopez-Lopez V., Ríos-Zambudio A., Cascales P., Pelegrín P., Pons J.A., Ramírez P. , Baroja-Mazo A.",Intrahepatic donor microbiota-based metataxonomic signature detected in organ preservation solution enables prediction of short-term liver transplant outcomes,Gut,2025,"LIVER TRANSPLANTATION, MACHINE LEARNING, MICROBIOME",Experiment 1,Spain,Homo sapiens,Bile duct,NA,Response to liver transplant,NA,Hypoabundant in Non-survivor recipients,Hyperabundant in Non-survivor recipients,"Recipients were monitored for early allograft dysfunction following liver transplantation, and patients died due to clinical outcomes related to the procedure.",NA,NA,NA,16S,23456789,Ion Torrent,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 1B, Supplementary Table 1 and Supplementary Figure 5",17 November 2025,Firdaws,Firdaws,"MaAsLin2 (Multivariate Association with Linear Models 2) analysis of differentially abundant taxa at the genus, family, order, class, and phylum levels in relation to survival.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae|g__Hyphomicrobium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Modestobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Uruburuella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium",3379134|1224|28211|356|45401|81;3384189|32066|203490|203491|1129771|32067;3384189|32066|203490|203491|1129771;1783272|201174|1760|1643682|85030|88138;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481;3379134|1224|28216|206351;3379134|976|117747|200666|84566|28453;3379134|1224|28216|206351|481|299568;1783272|1239|91061|186826|186828|2747,Complete,NA
bsdb:40803752/2/1,40803752,prospective cohort,40803752,10.1136/gutjnl-2025-335986,NA,"Lucas-Ruiz F., Vidal-Correoso D., Mateo S.V., de la Torre-Álamo M.M., Jover-Aguilar M., Alconchel F., Martínez-Alarcón L., Lopez-Lopez V., Ríos-Zambudio A., Cascales P., Pelegrín P., Pons J.A., Ramírez P. , Baroja-Mazo A.",Intrahepatic donor microbiota-based metataxonomic signature detected in organ preservation solution enables prediction of short-term liver transplant outcomes,Gut,2025,"LIVER TRANSPLANTATION, MACHINE LEARNING, MICROBIOME",Experiment 2,Spain,Homo sapiens,Bile duct,NA,Response to liver transplant,NA,Hypoabundant in Acute Rejection (AR) recipients,Hyperabundant in Acute Rejection (AR) recipients,"Recipients were monitored for early allograft dysfunction following liver transplantation, and patients developed Acute Rejection (AR) related to the procedure.",NA,NA,NA,16S,23456789,Ion Torrent,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 1C, Supplementary Table 1 and Supplementary Figure 5",17 November 2025,Firdaws,Firdaws,"MaAsLin2 (Multivariate Association with Linear Models 2) analysis of differentially abundant taxa at the genus, family, order, class, and phylum levels in relation to Acute Rejection (AR).",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alishewanella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae,k__Pseudomonadati|p__Bdellovibrionota|c__Bdellovibrionia|o__Bdellovibrionales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Beijerinckiaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Cellulomonadaceae|g__Cellulomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Curvibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae,k__Pseudomonadati|p__Planctomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae|g__Rheinheimera,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Rickettsiella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Uruburuella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",3379134|1224|1236|135622|72275|111142;3379134|1224|1236|135622|72275;3379134|3018035|3031418|213481;3379134|1224|28211|356|45404;1783272|1239|91061|186826|186828|2747;3379134|1224|28211|204458|76892;3379134|1224|28211|204458;1783272|201174|1760|85006|85016|1707;3379134|1224|1236|91347|543|544;3379134|1224|28216|80840|80864|281915;1783272|1239|91061|1385|539738|1378;3379134|1224|28211|356|45401;3379134|203682;3379134|1224|1236|135613|1046|67575;3379134|1224|1236|118969|118968|59195;3379134|1224|28216|206351|481|299568;1783272|1239|91061|186826|33958|46255,Complete,NA
bsdb:40803752/2/2,40803752,prospective cohort,40803752,10.1136/gutjnl-2025-335986,NA,"Lucas-Ruiz F., Vidal-Correoso D., Mateo S.V., de la Torre-Álamo M.M., Jover-Aguilar M., Alconchel F., Martínez-Alarcón L., Lopez-Lopez V., Ríos-Zambudio A., Cascales P., Pelegrín P., Pons J.A., Ramírez P. , Baroja-Mazo A.",Intrahepatic donor microbiota-based metataxonomic signature detected in organ preservation solution enables prediction of short-term liver transplant outcomes,Gut,2025,"LIVER TRANSPLANTATION, MACHINE LEARNING, MICROBIOME",Experiment 2,Spain,Homo sapiens,Bile duct,NA,Response to liver transplant,NA,Hypoabundant in Acute Rejection (AR) recipients,Hyperabundant in Acute Rejection (AR) recipients,"Recipients were monitored for early allograft dysfunction following liver transplantation, and patients developed Acute Rejection (AR) related to the procedure.",NA,NA,NA,16S,23456789,Ion Torrent,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 1C, Supplementary Table 1 and Supplementary Figure 5",17 November 2025,Firdaws,Firdaws,"MaAsLin2 (Multivariate Association with Linear Models 2) analysis of differentially abundant taxa at the genus, family, order, class, and phylum levels in relation to Acute Rejection (AR).",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|g__Alkalimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",3379134|1224|1236|135625|712|713;3379134|1224|1236|265980;3379134|1224|1236|118969|118968;3379134|200940|3031449|213115;3379134|1224|28216|80840|75682|963;3384189|32066|203490|203491|1129771|32067;3379134|1224|1236|135614|32033|40323;3379134|1224|1236;1783272|1239|91061|186826|33958,Complete,NA
bsdb:40803752/3/1,40803752,prospective cohort,40803752,10.1136/gutjnl-2025-335986,NA,"Lucas-Ruiz F., Vidal-Correoso D., Mateo S.V., de la Torre-Álamo M.M., Jover-Aguilar M., Alconchel F., Martínez-Alarcón L., Lopez-Lopez V., Ríos-Zambudio A., Cascales P., Pelegrín P., Pons J.A., Ramírez P. , Baroja-Mazo A.",Intrahepatic donor microbiota-based metataxonomic signature detected in organ preservation solution enables prediction of short-term liver transplant outcomes,Gut,2025,"LIVER TRANSPLANTATION, MACHINE LEARNING, MICROBIOME",Experiment 3,Spain,Homo sapiens,Bile duct,NA,Response to liver transplant,NA,Hypoabudant in hepatic arterial thrombosis (HAT) recipients,Hyperabundant in hepatic arterial thrombosis (HAT) recipients,"Recipients were monitored for early allograft dysfunction following liver transplantation, and patients developed hepatic arterial thrombosis related to the procedure",NA,NA,NA,16S,23456789,Ion Torrent,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 1D, Supplementary Table 1 and Supplementary Figure 5",19 November 2025,Tosin,Tosin,"MaAsLin2 (Multivariate Association with Linear Models 2) analysis of differentially abundant taxa at genus, family, order and class levels in relation to hepatic arterial thrombosis (HAT)",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Blastococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Entomoplasmatales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Pseudomonadati|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales,k__Pseudomonadati|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Hydrogenophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae",1783272|201174|1760|2037|2049|1654;1783272|1239|91061|1385|186817;1783272|1239|91061|1385;1783272|1239|91061|1385|186817|1386;3379134|976|200643|171549;3379134|976|200643;1783272|201174|1760|1643682|85030|38501;1783272|1239|91061|1385|186818;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|91061|186826|81852|1350;1783272|544448|31969|186328;1783272|1239|526524;1783272|1239|186801|186802|186806;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|204475;3379134|1224|2008785|119069;3379134|1224|2008785|119069|206349|70774;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|1300|1357;3379134|1224|28216|80840|75682|149698;1783272|1239|909932|1843489|31977|906;1783272|1239|186801|186802|216572;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|186801|186802|216572|1263;3379134|1224|28211|204457;1783272|1239|91061|186826|33958|46255;1783272|1239|91061|186826|81852,Complete,NA
bsdb:40803752/3/2,40803752,prospective cohort,40803752,10.1136/gutjnl-2025-335986,NA,"Lucas-Ruiz F., Vidal-Correoso D., Mateo S.V., de la Torre-Álamo M.M., Jover-Aguilar M., Alconchel F., Martínez-Alarcón L., Lopez-Lopez V., Ríos-Zambudio A., Cascales P., Pelegrín P., Pons J.A., Ramírez P. , Baroja-Mazo A.",Intrahepatic donor microbiota-based metataxonomic signature detected in organ preservation solution enables prediction of short-term liver transplant outcomes,Gut,2025,"LIVER TRANSPLANTATION, MACHINE LEARNING, MICROBIOME",Experiment 3,Spain,Homo sapiens,Bile duct,NA,Response to liver transplant,NA,Hypoabudant in hepatic arterial thrombosis (HAT) recipients,Hyperabundant in hepatic arterial thrombosis (HAT) recipients,"Recipients were monitored for early allograft dysfunction following liver transplantation, and patients developed hepatic arterial thrombosis related to the procedure",NA,NA,NA,16S,23456789,Ion Torrent,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 1D, Supplementary Table 1 and Supplementary Figure 5",19 November 2025,Tosin,Tosin,MaAsLin2 (Multivariate Association with Linear Models 2) analysis of differentially abundant taxa in the genus level in relation to hepatic arterial thrombosis,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Modestobacter,1783272|201174|1760|1643682|85030|88138,Complete,NA
bsdb:40803752/4/1,40803752,prospective cohort,40803752,10.1136/gutjnl-2025-335986,NA,"Lucas-Ruiz F., Vidal-Correoso D., Mateo S.V., de la Torre-Álamo M.M., Jover-Aguilar M., Alconchel F., Martínez-Alarcón L., Lopez-Lopez V., Ríos-Zambudio A., Cascales P., Pelegrín P., Pons J.A., Ramírez P. , Baroja-Mazo A.",Intrahepatic donor microbiota-based metataxonomic signature detected in organ preservation solution enables prediction of short-term liver transplant outcomes,Gut,2025,"LIVER TRANSPLANTATION, MACHINE LEARNING, MICROBIOME",Experiment 4,Spain,Homo sapiens,Bile duct,NA,Response to liver transplant,NA,Hypoabundant in biliary tract complications (BC) recipients,Hyperabundant in biliary tract complications (BC) recipients,"Recipients were monitored for early allograft dysfunction following liver transplantation, and patients developed hepatic arterial thrombosis related to the procedure",NA,NA,NA,16S,23456789,Ion Torrent,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 1E, Supplementary Table 1 and Supplementary Figure 5",19 November 2025,Tosin,Tosin,"MaAsLin2 (Multivariate Association with Linear Models 2) analysis of differentially abundant taxa at genus, family, and phylum levels in relation to biliary tract complications (BC)",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Alpinimonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Cellvibrio,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Ornithinimicrobiaceae|g__Ornithinimicrobium,k__Pseudomonadati|p__Planctomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Pseudorhodobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae",3379134|1224|1236|135625|712|713;1783272|201174|1760|85006|85023|1132766;1783272|201174|1760|85006|85020|43668;3379134|1224|1236|1706369|1706371|10;1783272|201174|1760|85006|85020;1783272|201174|1760|85006|85023|33882;1783272|201174|1760|85008|28056;1783272|201174|1760|85006|2805590|125287;3379134|203682;3379134|1224|28211|204455|31989|238783;3379134|1224|28211|356|82115,Complete,NA
bsdb:40803752/4/2,40803752,prospective cohort,40803752,10.1136/gutjnl-2025-335986,NA,"Lucas-Ruiz F., Vidal-Correoso D., Mateo S.V., de la Torre-Álamo M.M., Jover-Aguilar M., Alconchel F., Martínez-Alarcón L., Lopez-Lopez V., Ríos-Zambudio A., Cascales P., Pelegrín P., Pons J.A., Ramírez P. , Baroja-Mazo A.",Intrahepatic donor microbiota-based metataxonomic signature detected in organ preservation solution enables prediction of short-term liver transplant outcomes,Gut,2025,"LIVER TRANSPLANTATION, MACHINE LEARNING, MICROBIOME",Experiment 4,Spain,Homo sapiens,Bile duct,NA,Response to liver transplant,NA,Hypoabundant in biliary tract complications (BC) recipients,Hyperabundant in biliary tract complications (BC) recipients,"Recipients were monitored for early allograft dysfunction following liver transplantation, and patients developed hepatic arterial thrombosis related to the procedure",NA,NA,NA,16S,23456789,Ion Torrent,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 1E, Supplementary Table 1 and Supplementary Figure 5",19 November 2025,Tosin,Tosin,"MaAsLin2 (Multivariate Association with Linear Models 2) analysis of differentially abundant taxa at genus, family, order and class levels in relation to biliary tract complications (BC)",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum,k__Pseudomonadati|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Hydrogenophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Modestobacter,k__Bacillati|p__Bacillota|c__Negativicutes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Uruburuella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",1783272|1239|91061|186826|186828|2747;1783272|1239|186801;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|91061|186826|186828|29393;3379134|1224|2008785|119069|206349|70774;1783272|1239|91061|186826|1300|1357;1783272|201174|1760|1643682|85030|88138;1783272|1239|909932;3379134|1224|1236|91347|1903409|53335;1783272|1239|909932|909929;3379134|1224|28216|206351|481|299568;1783272|1239|909932|1843489|31977,Complete,NA
bsdb:40803752/5/1,40803752,prospective cohort,40803752,10.1136/gutjnl-2025-335986,NA,"Lucas-Ruiz F., Vidal-Correoso D., Mateo S.V., de la Torre-Álamo M.M., Jover-Aguilar M., Alconchel F., Martínez-Alarcón L., Lopez-Lopez V., Ríos-Zambudio A., Cascales P., Pelegrín P., Pons J.A., Ramírez P. , Baroja-Mazo A.",Intrahepatic donor microbiota-based metataxonomic signature detected in organ preservation solution enables prediction of short-term liver transplant outcomes,Gut,2025,"LIVER TRANSPLANTATION, MACHINE LEARNING, MICROBIOME",Experiment 5,Spain,Homo sapiens,Bile duct,NA,Response to liver transplant,NA,Decreased Acute Rejection (AR) correlation levels,Increased Acute Rejection (AR) correlation levels,Increased correlation levels in Acute Rejection (AR).,NA,NA,NA,16S,23456789,Ion Torrent,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1F,18 November 2025,Firdaws,Firdaws,Heatmap of significant amplicon sequence variant (ASV) correlations (Spearman) with Acute Rejection (AR).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alishewanella|s__Alishewanella tabrizica,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae|g__Arsukibacterium|s__Arsukibacterium perlucidum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus licheniformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium|s__Carnobacterium maltaromaticum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium mucifaciens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Idiomarinaceae|g__Idiomarina,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lentilactobacillus|s__Lentilactobacillus parafarraginis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus|s__Paracoccus marinus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Pseudolactococcus|s__Pseudolactococcus raffinolactis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia insidiosa,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Uruburuella|s__Uruburuella suis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio cyclitrophicus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales",3379134|1224|1236|135622|72275|111142|671278;3379134|1224|1236|135613|1046|336830|368811;1783272|1239|91061|1385|186817|1386|1402;1783272|1239|91061|186826|186828|2747|2751;1783272|201174|1760|85007|1653|1716|57171;3379134|1224|1236|135622|267893|135575;1783272|1239|91061|186826|33958|2767893|390842;3379134|1224|28211|204455|31989|265|288426;1783272|1239|91061|186826|1300|3436058|1366;3379134|1224|28216|80840|119060|48736|190721;3379134|1224|28216|206351|481|299568|252130;3379134|1224|1236|135623|641|662|47951;1783272|1239|91061|186826|33958|46255;3379134|1224|28211|766,Complete,NA
bsdb:40803752/5/2,40803752,prospective cohort,40803752,10.1136/gutjnl-2025-335986,NA,"Lucas-Ruiz F., Vidal-Correoso D., Mateo S.V., de la Torre-Álamo M.M., Jover-Aguilar M., Alconchel F., Martínez-Alarcón L., Lopez-Lopez V., Ríos-Zambudio A., Cascales P., Pelegrín P., Pons J.A., Ramírez P. , Baroja-Mazo A.",Intrahepatic donor microbiota-based metataxonomic signature detected in organ preservation solution enables prediction of short-term liver transplant outcomes,Gut,2025,"LIVER TRANSPLANTATION, MACHINE LEARNING, MICROBIOME",Experiment 5,Spain,Homo sapiens,Bile duct,NA,Response to liver transplant,NA,Decreased Acute Rejection (AR) correlation levels,Increased Acute Rejection (AR) correlation levels,Increased correlation levels in Acute Rejection (AR).,NA,NA,NA,16S,23456789,Ion Torrent,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1F,18 November 2025,Firdaws,Firdaws,Heatmap of significant amplicon sequence variant (ASV) correlations (Spearman) with Acute Rejection (AR).,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium propinquum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium pseudodiphtheriticum,k__Pseudomonadati|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Hydrogenophilus|s__Hydrogenophilus thermoluteolus",1783272|201174|1760|85007|1653|1716|43769;1783272|201174|1760|85007|1653|1716|37637;3379134|1224|2008785|119069|206349|70774|297,Complete,NA
bsdb:40803752/6/1,40803752,prospective cohort,40803752,10.1136/gutjnl-2025-335986,NA,"Lucas-Ruiz F., Vidal-Correoso D., Mateo S.V., de la Torre-Álamo M.M., Jover-Aguilar M., Alconchel F., Martínez-Alarcón L., Lopez-Lopez V., Ríos-Zambudio A., Cascales P., Pelegrín P., Pons J.A., Ramírez P. , Baroja-Mazo A.",Intrahepatic donor microbiota-based metataxonomic signature detected in organ preservation solution enables prediction of short-term liver transplant outcomes,Gut,2025,"LIVER TRANSPLANTATION, MACHINE LEARNING, MICROBIOME",Experiment 6,Spain,Homo sapiens,Bile duct,NA,Response to liver transplant,NA,Decreased non-survival correlation levels,Increased non-survival correlation levels,Increased correlation levels in non-survivors.,NA,NA,NA,16S,23456789,Ion Torrent,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1F,18 November 2025,Firdaws,Firdaws,Heatmap of significant amplicon sequence variant (ASV) correlations (Spearman) with non-survival.,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus murdochii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus licheniformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium mycetoides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Curvibacter|s__Curvibacter sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter|s__Oxalobacter formigenes,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella corporis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus petrasii",1783272|1239|1737404|1737405|1570339|165779|411577;1783272|1239|91061|1385|186817|1386|1402;1783272|1239|91061|1385|186818;3379134|976|117743|200644|2762318|501783;1783272|201174|1760|85007|1653|1716|38302;3379134|1224|28216|80840|80864|281915|1888168;3379134|1224|28211|204457|335929;3379134|1224|1236|135619|135620;3379134|1224|28216|80840|75682|846|847;1783272|1239|1737404|1737405|1570339|162289;3379134|976|200643|171549|171552|838|28128;1783272|1239|186801|186802|216572|1263;1783272|201174|1760|2037|2049|2529408|1660;1783272|1239|91061|186826|33958|46255;1783272|1239|91061|1385|90964|1279|1276936,Complete,NA
bsdb:40803752/6/2,40803752,prospective cohort,40803752,10.1136/gutjnl-2025-335986,NA,"Lucas-Ruiz F., Vidal-Correoso D., Mateo S.V., de la Torre-Álamo M.M., Jover-Aguilar M., Alconchel F., Martínez-Alarcón L., Lopez-Lopez V., Ríos-Zambudio A., Cascales P., Pelegrín P., Pons J.A., Ramírez P. , Baroja-Mazo A.",Intrahepatic donor microbiota-based metataxonomic signature detected in organ preservation solution enables prediction of short-term liver transplant outcomes,Gut,2025,"LIVER TRANSPLANTATION, MACHINE LEARNING, MICROBIOME",Experiment 6,Spain,Homo sapiens,Bile duct,NA,Response to liver transplant,NA,Decreased non-survival correlation levels,Increased non-survival correlation levels,Increased correlation levels in non-survivors.,NA,NA,NA,16S,23456789,Ion Torrent,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1F,18 November 2025,Firdaws,Firdaws,Heatmap of significant amplicon sequence variant (ASV) correlations (Spearman) with non-survival.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae|g__Arsukibacterium|s__Arsukibacterium perlucidum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium|s__Carnobacterium maltaromaticum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium propinquum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lentilactobacillus|s__Lentilactobacillus parafarraginis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella|s__Shewanella oneidensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus equinus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Uruburuella|s__Uruburuella suis",3379134|1224|1236|135613|1046|336830|368811;1783272|1239|91061|186826|186828|2747|2751;1783272|201174|1760|85007|1653|1716|43769;1783272|1239|91061|186826|33958|2767893|390842;3379134|1224|1236|135622|267890|22|70863;1783272|1239|91061|186826|1300|1301|1335;3379134|1224|28216|206351|481|299568|252130,Complete,NA
bsdb:40803752/7/1,40803752,prospective cohort,40803752,10.1136/gutjnl-2025-335986,NA,"Lucas-Ruiz F., Vidal-Correoso D., Mateo S.V., de la Torre-Álamo M.M., Jover-Aguilar M., Alconchel F., Martínez-Alarcón L., Lopez-Lopez V., Ríos-Zambudio A., Cascales P., Pelegrín P., Pons J.A., Ramírez P. , Baroja-Mazo A.",Intrahepatic donor microbiota-based metataxonomic signature detected in organ preservation solution enables prediction of short-term liver transplant outcomes,Gut,2025,"LIVER TRANSPLANTATION, MACHINE LEARNING, MICROBIOME",Experiment 7,Spain,Homo sapiens,Bile duct,NA,Response to liver transplant,NA,Decreased hepatic arterial thrombosis (HAT) correlation levels,Increased hepatic arterial thrombosis (HAT) correlation levels,Increased correlation levels in hepatic arterial thrombosis (HAT),NA,NA,NA,16S,23456789,Ion Torrent,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1F,19 November 2025,Tosin,Tosin,Heatmap of significant amplicon sequence variant (ASV) correlations (Spearman) with hepatic arterial thrombosis (HAT),increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus murdochii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus licheniformis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Roseomonadaceae|g__Belnapia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium glucuronolyticum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium mycetoides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Cryptosporangiales|f__Cryptosporangiaceae|g__Cryptosporangium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Curvibacter|s__Curvibacter sp.,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Idiomarinaceae|g__Idiomarina,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella|s__Morganella morganii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Ornithinimicrobiaceae|g__Ornithinimicrobium|s__Ornithinimicrobium kibberense,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter|s__Oxalobacter formigenes,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Pseudolactococcus|s__Pseudolactococcus raffinolactis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus petrasii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica",1783272|1239|1737404|1737405|1570339|165779|411577;1783272|1239|91061|1385|186817|1386|1402;3379134|1224|28211|3120395|3385906|365532;1783272|1239|91061|1385|186818;1783272|201174|1760|85007|1653|1716|39791;1783272|201174|1760|85007|1653|1716|38302;1783272|201174|1760|2495577|622454|65502;3379134|1224|28216|80840|80864|281915|1888168;3379134|1224|28211|204457|335929;1783272|1239|186801|186802|216572|216851|853;3379134|1224|1236|135622|267893|135575;3379134|1224|1236|91347|1903414|581|582;1783272|201174|1760|85006|2805590|125287|282060;3379134|1224|28216|80840|75682|846|847;1783272|1239|1737404|1737405|1570339|162289;3379134|976|200643|171549|171551;1783272|1239|91061|186826|1300|3436058|1366;3379134|1224|28211|766;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|1385|90964|1279|1276936;1783272|1239|91061|186826|33958|46255;1783272|201174|1760|2037|2049|2529408|1660,Complete,NA
bsdb:40803752/7/2,40803752,prospective cohort,40803752,10.1136/gutjnl-2025-335986,NA,"Lucas-Ruiz F., Vidal-Correoso D., Mateo S.V., de la Torre-Álamo M.M., Jover-Aguilar M., Alconchel F., Martínez-Alarcón L., Lopez-Lopez V., Ríos-Zambudio A., Cascales P., Pelegrín P., Pons J.A., Ramírez P. , Baroja-Mazo A.",Intrahepatic donor microbiota-based metataxonomic signature detected in organ preservation solution enables prediction of short-term liver transplant outcomes,Gut,2025,"LIVER TRANSPLANTATION, MACHINE LEARNING, MICROBIOME",Experiment 7,Spain,Homo sapiens,Bile duct,NA,Response to liver transplant,NA,Decreased hepatic arterial thrombosis (HAT) correlation levels,Increased hepatic arterial thrombosis (HAT) correlation levels,Increased correlation levels in hepatic arterial thrombosis (HAT),NA,NA,NA,16S,23456789,Ion Torrent,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1F,19 November 2025,Tosin,Tosin,Heatmap of significant amplicon sequence variant (ASV) correlations (Spearman) with hepatic arterial thrombosis (HAT),decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lentilactobacillus|s__Lentilactobacillus parafarraginis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Modestobacter",1783272|1239|91061|186826|33958|2767893|390842;1783272|201174|1760|1643682|85030|88138,Complete,NA
bsdb:40803752/8/1,40803752,prospective cohort,40803752,10.1136/gutjnl-2025-335986,NA,"Lucas-Ruiz F., Vidal-Correoso D., Mateo S.V., de la Torre-Álamo M.M., Jover-Aguilar M., Alconchel F., Martínez-Alarcón L., Lopez-Lopez V., Ríos-Zambudio A., Cascales P., Pelegrín P., Pons J.A., Ramírez P. , Baroja-Mazo A.",Intrahepatic donor microbiota-based metataxonomic signature detected in organ preservation solution enables prediction of short-term liver transplant outcomes,Gut,2025,"LIVER TRANSPLANTATION, MACHINE LEARNING, MICROBIOME",Experiment 8,Spain,Homo sapiens,Bile duct,NA,Response to liver transplant,NA,Decreased biliary tract complications (BC) correlation levels,Increased biliary tract complications (BC) correlation levels,Increased correlation levels in biliary tract complications (BC),NA,NA,NA,16S,23456789,Ion Torrent,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1F,19 November 2025,Tosin,Tosin,Heatmap of significant amplicon sequence variant (ASV) correlations (Spearman) with biliary tract complications (BC),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XII. Incertae Sedis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia mannitolilytica",1783272|1239|186801|186802|543313;3379134|1224|28216|80840|119060|48736|105219,Complete,NA
bsdb:40803752/8/2,40803752,prospective cohort,40803752,10.1136/gutjnl-2025-335986,NA,"Lucas-Ruiz F., Vidal-Correoso D., Mateo S.V., de la Torre-Álamo M.M., Jover-Aguilar M., Alconchel F., Martínez-Alarcón L., Lopez-Lopez V., Ríos-Zambudio A., Cascales P., Pelegrín P., Pons J.A., Ramírez P. , Baroja-Mazo A.",Intrahepatic donor microbiota-based metataxonomic signature detected in organ preservation solution enables prediction of short-term liver transplant outcomes,Gut,2025,"LIVER TRANSPLANTATION, MACHINE LEARNING, MICROBIOME",Experiment 8,Spain,Homo sapiens,Bile duct,NA,Response to liver transplant,NA,Decreased biliary tract complications (BC) correlation levels,Increased biliary tract complications (BC) correlation levels,Increased correlation levels in biliary tract complications (BC),NA,NA,NA,16S,23456789,Ion Torrent,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1F,19 November 2025,Tosin,Tosin,Heatmap of significant amplicon sequence variant (ASV) correlations (Spearman) with biliary tract complications (BC),decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus licheniformis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium|s__Carnobacterium maltaromaticum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lentilactobacillus|s__Lentilactobacillus parafarraginis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus equinus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Uruburuella|s__Uruburuella suis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio cyclitrophicus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Pseudolactococcus|s__Pseudolactococcus raffinolactis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Idiomarinaceae|g__Idiomarina,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae|g__Marinomonas|s__Marinomonas sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces massiliensis,k__Pseudomonadati|p__Pseudomonadota|c__Hydrogenophilia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Hydrogenophilus|s__Hydrogenophilus thermoluteolus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Geodermatophilales|f__Geodermatophilaceae|g__Modestobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium propinquum",1783272|1239|91061|1385|186817|1386|1402;1783272|1239|91061|186826|186828|2747|2751;1783272|1239|91061|186826|33958|2767893|390842;1783272|1239|91061|186826|1300|1301|1335;3379134|1224|28216|206351|481|299568|252130;3379134|1224|1236|135623|641|662|47951;1783272|1239|91061|186826|1300|3436058|1366;3379134|1224|1236|135622|267893|135575;3379134|1224|1236|135619|135620|28253|1904862;1783272|201174|1760|2037|2049|1654|461393;3379134|1224|2008785|119069|206349|70774|297;1783272|201174|1760|1643682|85030|88138;1783272|201174|1760|85007|1653|1716|43769,Complete,NA
bsdb:40813371/1/1,40813371,prospective cohort,40813371,https://doi.org/10.1038/s41467-025-62584-2,https://rdcu.be/eLMoF,"Kiu R., Darby E.M., Alcon-Giner C., Acuna-Gonzalez A., Camargo A., Lamberte L.E., Phillips S., Sim K., Shaw A.G., Clarke P., van Schaik W., Kroll J.S. , Hall L.J.",Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants,Nature communications,2025,NA,Experiment 1,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Non-Probiotic Supplemented(Overall),Probiotic Supplemented(Overall),Very Low Birth Weight Infants who received probiotics containing Bifidobacterium bifidum and Lactobacillus acidophilus,19,15,NA,WMS,NA,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Fig 1g and Supplementary 2a,24 October 2025,Sally Kinyua,Sally Kinyua,"Over the 3 weeks Bifidobacterium bifidum showed a significant presence and increase in Probiotic Supplemented cohort as compared to Non-probiotic supplemented cohort, Bifidobacterium breve and Bifidobacterium longum also increased over the weeks in the PS cohort",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|201174|1760|85004|31953|1678|1681;1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|1578,Complete,KateRasheed
bsdb:40813371/1/2,40813371,prospective cohort,40813371,https://doi.org/10.1038/s41467-025-62584-2,https://rdcu.be/eLMoF,"Kiu R., Darby E.M., Alcon-Giner C., Acuna-Gonzalez A., Camargo A., Lamberte L.E., Phillips S., Sim K., Shaw A.G., Clarke P., van Schaik W., Kroll J.S. , Hall L.J.",Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants,Nature communications,2025,NA,Experiment 1,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Non-Probiotic Supplemented(Overall),Probiotic Supplemented(Overall),Very Low Birth Weight Infants who received probiotics containing Bifidobacterium bifidum and Lactobacillus acidophilus,19,15,NA,WMS,NA,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Supplementary Fig 2a,24 October 2025,Sally Kinyua,Sally Kinyua,According to the Mean Relative Abudance represented in fig 1h some bacterias presence decreased in the Probiotic Supplemented cohort gradually over the 3 weeks as compared to the Non Probiotic Supplemeted cohort.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|570;1783272|1239|909932|1843489|31977|29465,Complete,KateRasheed
bsdb:40813371/2/1,40813371,prospective cohort,40813371,https://doi.org/10.1038/s41467-025-62584-2,https://rdcu.be/eLMoF,"Kiu R., Darby E.M., Alcon-Giner C., Acuna-Gonzalez A., Camargo A., Lamberte L.E., Phillips S., Sim K., Shaw A.G., Clarke P., van Schaik W., Kroll J.S. , Hall L.J.",Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants,Nature communications,2025,NA,Experiment 2,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Non-Probiotic Supplemented(Week 1),Probiotic Supplemented(Week 1),Very Low Birth Weight Infants who received probiotics containing Bifidobacterium bifidum and Lactobacillus acidophilus,19,15,NA,WMS,NA,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,NA,NA,increased,Signature 1,Fig 1g,24 October 2025,Sally Kinyua,Sally Kinyua,During week 1 Bifidobacterium and Lactobacillus had a significant increase in the Probiotic Supplemeted cohort as compared to the Non Probiotic Supplemeted cohort,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|1578,Complete,KateRasheed
bsdb:40813371/2/2,40813371,prospective cohort,40813371,https://doi.org/10.1038/s41467-025-62584-2,https://rdcu.be/eLMoF,"Kiu R., Darby E.M., Alcon-Giner C., Acuna-Gonzalez A., Camargo A., Lamberte L.E., Phillips S., Sim K., Shaw A.G., Clarke P., van Schaik W., Kroll J.S. , Hall L.J.",Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants,Nature communications,2025,NA,Experiment 2,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Non-Probiotic Supplemented(Week 1),Probiotic Supplemented(Week 1),Very Low Birth Weight Infants who received probiotics containing Bifidobacterium bifidum and Lactobacillus acidophilus,19,15,NA,WMS,NA,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,NA,NA,increased,Signature 2,Fig 1h,24 October 2025,Sally Kinyua,Sally Kinyua,During week 1 some bacterias showed a decrease in the Probiotic Supplemented Cohort as compared to Non Probiotic Supplemented cohort.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum",3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|570;1783272|1239|909932|1843489|31977|29465;1783272|201174|1760|85004|31953|1678|216816,Complete,KateRasheed
bsdb:40813371/3/1,40813371,prospective cohort,40813371,https://doi.org/10.1038/s41467-025-62584-2,https://rdcu.be/eLMoF,"Kiu R., Darby E.M., Alcon-Giner C., Acuna-Gonzalez A., Camargo A., Lamberte L.E., Phillips S., Sim K., Shaw A.G., Clarke P., van Schaik W., Kroll J.S. , Hall L.J.",Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants,Nature communications,2025,NA,Experiment 3,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Non-Probiotic Supplemented(Week 2),Probiotic Supplemented(Week 2),Very Low Birth Weight Infants who received probiotics containing Bifidobacterium bifidum and Lactobacillus acidophilus,19,15,NA,WMS,NA,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 1,Fig 1g,28 October 2025,Sally Kinyua,Sally Kinyua,There was a significant statistical increase of the bacteria in week 2 in the Probiotic Supplemeted cohort as compared to the Non Probiotic cohort.Bifidobacterium bifidum shows a significant increase during week 2.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|201174|1760|85004|31953|1678;1783272|201174|1760|85004|31953|1678|1681;1783272|1239|91061|186826|33958|1578,Complete,KateRasheed
bsdb:40813371/3/2,40813371,prospective cohort,40813371,https://doi.org/10.1038/s41467-025-62584-2,https://rdcu.be/eLMoF,"Kiu R., Darby E.M., Alcon-Giner C., Acuna-Gonzalez A., Camargo A., Lamberte L.E., Phillips S., Sim K., Shaw A.G., Clarke P., van Schaik W., Kroll J.S. , Hall L.J.",Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants,Nature communications,2025,NA,Experiment 3,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Non-Probiotic Supplemented(Week 2),Probiotic Supplemented(Week 2),Very Low Birth Weight Infants who received probiotics containing Bifidobacterium bifidum and Lactobacillus acidophilus,19,15,NA,WMS,NA,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 2,Fig 1h,28 October 2025,Sally Kinyua,Sally Kinyua,During week 2 some bacterias showed a significant decrease in the Probiotic Supplemented cohort as compared to the Non Probiotic Supplemeted cohort.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|570;1783272|1239|909932|1843489|31977|29465,Complete,KateRasheed
bsdb:40813371/4/1,40813371,prospective cohort,40813371,https://doi.org/10.1038/s41467-025-62584-2,https://rdcu.be/eLMoF,"Kiu R., Darby E.M., Alcon-Giner C., Acuna-Gonzalez A., Camargo A., Lamberte L.E., Phillips S., Sim K., Shaw A.G., Clarke P., van Schaik W., Kroll J.S. , Hall L.J.",Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants,Nature communications,2025,NA,Experiment 4,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Non-Probiotic Supplemented(Week 3),Probiotic Supplemented(Week 3),Very Low Birth Weight Infants who received probiotics containing Bifidobacterium bifidum and Lactobacillus acidophilus.,18,12,NA,WMS,NA,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 1,Fig 1g,28 October 2025,Sally Kinyua,Sally Kinyua,During week 3 some of the bacteria had a significant increase in the Probiotic Supplemented cohort as compared to the Non Probiotic Supplemented cohort.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|1578,Complete,KateRasheed
bsdb:40813371/4/2,40813371,prospective cohort,40813371,https://doi.org/10.1038/s41467-025-62584-2,https://rdcu.be/eLMoF,"Kiu R., Darby E.M., Alcon-Giner C., Acuna-Gonzalez A., Camargo A., Lamberte L.E., Phillips S., Sim K., Shaw A.G., Clarke P., van Schaik W., Kroll J.S. , Hall L.J.",Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants,Nature communications,2025,NA,Experiment 4,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Non-Probiotic Supplemented(Week 3),Probiotic Supplemented(Week 3),Very Low Birth Weight Infants who received probiotics containing Bifidobacterium bifidum and Lactobacillus acidophilus.,18,12,NA,WMS,NA,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 2,Fig 1h,29 October 2025,Sally Kinyua,Sally Kinyua,During week 3 some of the bacterias in the Probiotic Supplemented cohort decreased significantly as compared to the Non Supplemented cohort,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|1224|1236|91347|543|561;3379134|1224|1236|91347|543|570;1783272|1239|909932|1843489|31977|29465,Complete,KateRasheed
bsdb:40813371/5/1,40813371,prospective cohort,40813371,https://doi.org/10.1038/s41467-025-62584-2,https://rdcu.be/eLMoF,"Kiu R., Darby E.M., Alcon-Giner C., Acuna-Gonzalez A., Camargo A., Lamberte L.E., Phillips S., Sim K., Shaw A.G., Clarke P., van Schaik W., Kroll J.S. , Hall L.J.",Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants,Nature communications,2025,NA,Experiment 5,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Non Probiotic Control(overall),Non Probiotic Antibiotic Treated(overall),Very Low Birth Weight preterm infants in the NPS cohort who received benzylpenicillin and gentamicin within 48hours of birth.,10,9,NA,WMS,NA,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 2i,29 October 2025,Sally Kinyua,Sally Kinyua,Some bacterias increased significantly in the NPS Antibiotic treated cohort compared to the NPS Antibiotic control.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85004|31953|1678,Complete,KateRasheed
bsdb:40813371/8/1,40813371,prospective cohort,40813371,https://doi.org/10.1038/s41467-025-62584-2,https://rdcu.be/eLMoF,"Kiu R., Darby E.M., Alcon-Giner C., Acuna-Gonzalez A., Camargo A., Lamberte L.E., Phillips S., Sim K., Shaw A.G., Clarke P., van Schaik W., Kroll J.S. , Hall L.J.",Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants,Nature communications,2025,NA,Experiment 8,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Non Probiotic Control(Week 3),Non Probiotic Antibiotic Treated(Week 3),Very Low Birth Weight preterm infants in the NPS cohort who received benzylpenicillin and gentamicin within 48hours of birth.,10,3,NA,WMS,NA,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 2i,30 October 2025,Sally Kinyua,Sally Kinyua,During week 3 there was a significant statistical increase Bifidobacterium in NPS Antibiotic treated cohort as compared to the NPS Control cohort.,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,KateRasheed
bsdb:40813371/8/2,40813371,prospective cohort,40813371,https://doi.org/10.1038/s41467-025-62584-2,https://rdcu.be/eLMoF,"Kiu R., Darby E.M., Alcon-Giner C., Acuna-Gonzalez A., Camargo A., Lamberte L.E., Phillips S., Sim K., Shaw A.G., Clarke P., van Schaik W., Kroll J.S. , Hall L.J.",Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants,Nature communications,2025,NA,Experiment 8,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Non Probiotic Control(Week 3),Non Probiotic Antibiotic Treated(Week 3),Very Low Birth Weight preterm infants in the NPS cohort who received benzylpenicillin and gentamicin within 48hours of birth.,10,3,NA,WMS,NA,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 2i,30 October 2025,Sally Kinyua,Sally Kinyua,During week 3  the NPS Antibiotic cohort had a significant decrease in NPS Antibiotic treated cohort as compared to the NPS Control cohort.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,1783272|201174|1760|85009|31957|1912216,Complete,KateRasheed
bsdb:40813371/9/1,40813371,prospective cohort,40813371,https://doi.org/10.1038/s41467-025-62584-2,https://rdcu.be/eLMoF,"Kiu R., Darby E.M., Alcon-Giner C., Acuna-Gonzalez A., Camargo A., Lamberte L.E., Phillips S., Sim K., Shaw A.G., Clarke P., van Schaik W., Kroll J.S. , Hall L.J.",Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants,Nature communications,2025,NA,Experiment 9,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Probiotic Supplemented-Control(Overall),Probiotic Supplemented(-Antibiotic Treated(Overall),Very Low Birth Weight preterm infants in the PS cohort who received benzylpenicillin and gentamicin within 48hours of birth.,3,12,NA,WMS,NA,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 2i,31 October 2025,Sally Kinyua,Sally Kinyua,In the PS Antibiotic treated cohort some of bacteria taxa had a significant increase as compared to the PS Control cohort.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85009|31957|1912216;3379134|1224|1236|91347|543|561,Complete,KateRasheed
bsdb:40813371/9/2,40813371,prospective cohort,40813371,https://doi.org/10.1038/s41467-025-62584-2,https://rdcu.be/eLMoF,"Kiu R., Darby E.M., Alcon-Giner C., Acuna-Gonzalez A., Camargo A., Lamberte L.E., Phillips S., Sim K., Shaw A.G., Clarke P., van Schaik W., Kroll J.S. , Hall L.J.",Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants,Nature communications,2025,NA,Experiment 9,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Probiotic Supplemented-Control(Overall),Probiotic Supplemented(-Antibiotic Treated(Overall),Very Low Birth Weight preterm infants in the PS cohort who received benzylpenicillin and gentamicin within 48hours of birth.,3,12,NA,WMS,NA,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 2i,31 October 2025,Sally Kinyua,Sally Kinyua,Overally there was a significant decrease of some of the bacteria in PS Antibiotic treated cohort as compared to the PS Control cohort.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061|186826|81852|1350;1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:40813371/10/1,40813371,prospective cohort,40813371,https://doi.org/10.1038/s41467-025-62584-2,https://rdcu.be/eLMoF,"Kiu R., Darby E.M., Alcon-Giner C., Acuna-Gonzalez A., Camargo A., Lamberte L.E., Phillips S., Sim K., Shaw A.G., Clarke P., van Schaik W., Kroll J.S. , Hall L.J.",Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants,Nature communications,2025,NA,Experiment 10,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Probiotic Supplemented-Control(Week 1),Probiotic Supplemented(-Antibiotic Treated(Week 1),Very Low Birth Weight preterm infants in the PS cohort who received benzylpenicillin and gentamicin within 48hours of birth.,3,4,NA,WMS,NA,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 2i,31 October 2025,Sally Kinyua,Sally Kinyua,During week 1 some of the bacteria increased in the PS Antibiotic treated cohort as compared to the PS Control.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:40813371/10/2,40813371,prospective cohort,40813371,https://doi.org/10.1038/s41467-025-62584-2,https://rdcu.be/eLMoF,"Kiu R., Darby E.M., Alcon-Giner C., Acuna-Gonzalez A., Camargo A., Lamberte L.E., Phillips S., Sim K., Shaw A.G., Clarke P., van Schaik W., Kroll J.S. , Hall L.J.",Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants,Nature communications,2025,NA,Experiment 10,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Probiotic Supplemented-Control(Week 1),Probiotic Supplemented(-Antibiotic Treated(Week 1),Very Low Birth Weight preterm infants in the PS cohort who received benzylpenicillin and gentamicin within 48hours of birth.,3,4,NA,WMS,NA,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig 2i,31 October 2025,Sally Kinyua,Sally Kinyua,During week 1 Enterococcus  showed a significant decrease in the PS Antibiotic treated cohort as compared to the PS Control cohort.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,1783272|1239|91061|186826|81852|1350,Complete,KateRasheed
bsdb:40813371/11/1,40813371,prospective cohort,40813371,https://doi.org/10.1038/s41467-025-62584-2,https://rdcu.be/eLMoF,"Kiu R., Darby E.M., Alcon-Giner C., Acuna-Gonzalez A., Camargo A., Lamberte L.E., Phillips S., Sim K., Shaw A.G., Clarke P., van Schaik W., Kroll J.S. , Hall L.J.",Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants,Nature communications,2025,NA,Experiment 11,United Kingdom,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Probiotic Supplemented-Control(Week 2),Probiotic Supplemented(-Antibiotic Treated(Week 2),Very Low Birth Weight preterm infants in the PS cohort who received benzylpenicillin and gentamicin within 48hours of birth.,3,4,NA,WMS,NA,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 2i,31 October 2025,Sally Kinyua,Sally Kinyua,During week 2 there was no significant increase in the PS Antibiotic treated cohort as compared to the PS Control cohort but there was a significant decrease.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|1760|85009|31957|1912216;1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:40819064/1/1,40819064,"cross-sectional observational, not case-control",40819064,10.1186/s12866-025-04278-9,NA,"Renzi S., Meriggi N., Paola M.D., Bacci G., Cerasuolo B., Gori A., Casari S., Banci E., de Blasi A., Diallo S., Kabore B., Derra K., Tinto H., De Filippo C., De Mast Q., Lionetti P. , Cavalieri D.",Exploring the influence of urbanization on gut mycobiota through dietary habits in Burkina Faso,BMC microbiology,2025,"Burkina Faso, Dietary habits, Fungal diversity, Fungi, Gut mycobiota, Microbiota, Rural-to-Urban, Sub-Saharan Africa, Urbanization",Experiment 1,Burkina Faso,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Burkina Faso Rural (BF-R),Burkina Faso Semi-urban (BF-SU),"This cohort included ten polygamous or 
monogamous families, each comprising one father, 
one or two mothers, and up to four children. 
Participants resided in Nanoro, a semi-urbanized 
area with a population estimated between 33,000 
and 34,000. People live in groups of small brick 
houses with limited access to electricity. Water is 
collected from public wells.
 Sewage systems and water treatment plants were 
absent. Their diet is still traditional Burkinabè and 
plant-based, but also occasionally including meat and 
dried fish, and limited processed and Western-like 
foods.",51,50,NA,ITS / ITS2,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,unchanged,decreased,Signature 1,Fig. 4 & Fig. S8,28 October 2025,Peter03,Peter03,These taxa were found to increase in abundance in the Burkina Faso Semi-Urban individuals compared to their Rural counterparts,increased,k__Fungi|p__Ascomycota,4751|4890,Complete,KateRasheed
bsdb:40819064/1/2,40819064,"cross-sectional observational, not case-control",40819064,10.1186/s12866-025-04278-9,NA,"Renzi S., Meriggi N., Paola M.D., Bacci G., Cerasuolo B., Gori A., Casari S., Banci E., de Blasi A., Diallo S., Kabore B., Derra K., Tinto H., De Filippo C., De Mast Q., Lionetti P. , Cavalieri D.",Exploring the influence of urbanization on gut mycobiota through dietary habits in Burkina Faso,BMC microbiology,2025,"Burkina Faso, Dietary habits, Fungal diversity, Fungi, Gut mycobiota, Microbiota, Rural-to-Urban, Sub-Saharan Africa, Urbanization",Experiment 1,Burkina Faso,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Burkina Faso Rural (BF-R),Burkina Faso Semi-urban (BF-SU),"This cohort included ten polygamous or 
monogamous families, each comprising one father, 
one or two mothers, and up to four children. 
Participants resided in Nanoro, a semi-urbanized 
area with a population estimated between 33,000 
and 34,000. People live in groups of small brick 
houses with limited access to electricity. Water is 
collected from public wells.
 Sewage systems and water treatment plants were 
absent. Their diet is still traditional Burkinabè and 
plant-based, but also occasionally including meat and 
dried fish, and limited processed and Western-like 
foods.",51,50,NA,ITS / ITS2,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,unchanged,decreased,Signature 2,Fig. 4 & Fig. S8,20 October 2025,Peter03,Peter03,"The abundance of these microbial signatures seemed to decrease with urbanization,  evidenced by their low presence in Burkina Faso Semi-Urban Cohort.",decreased,"k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Kluyveromyces|s__Kluyveromyces marxianus,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Trimorphomycetaceae|g__Saitozyma|s__Saitozyma flava,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Davidiella,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Pichiales|f__Pichiaceae|g__Pichia,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales",4751|4890|4891|4892|4893|4910|4911;4751|5204|155616|5234|1890237|1890244|5416;4751|4890|147541|2726946|452563|237557;4751|4890|3239874|3243775|1156497|4919;4751|4890|147541|92860,Complete,KateRasheed
bsdb:40819064/2/2,40819064,"cross-sectional observational, not case-control",40819064,10.1186/s12866-025-04278-9,NA,"Renzi S., Meriggi N., Paola M.D., Bacci G., Cerasuolo B., Gori A., Casari S., Banci E., de Blasi A., Diallo S., Kabore B., Derra K., Tinto H., De Filippo C., De Mast Q., Lionetti P. , Cavalieri D.",Exploring the influence of urbanization on gut mycobiota through dietary habits in Burkina Faso,BMC microbiology,2025,"Burkina Faso, Dietary habits, Fungal diversity, Fungi, Gut mycobiota, Microbiota, Rural-to-Urban, Sub-Saharan Africa, Urbanization",Experiment 2,Burkina Faso,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Burkina Faso Rural (BF-R),Burkina Faso Urban (BF-U),"Ten monogamous families, each with one mother 
and father and up to four children were selected 
among wealthy urban families from the capital city 
of Ouagadougou These families resided in concrete 
or brick buildings with access to electricity, sewage 
infrastructure and private sources of drinkable water. 
While the diet remained predominantly Burkinabè, 
it included a broader range of foods typical of an 
industrialized dietary pattern, including sugar rich 
beverages, canned goods, and highly processed 
foods rich in preservatives. These families have 
access to healthcare and sanitation infrastructure, 
thereby markedly reducing the risk of infection and 
malnutrition",51,45,NA,ITS / ITS2,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,decreased,Signature 2,Fig. 4 & Fig. S8,20 October 2025,Peter03,Peter03,"The abundance of these microbial signatures were found to decrease with urbanization,  evidenced by their low presence in Burkina Faso Urban Cohort.",decreased,"k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Phaffomycetales|f__Phaffomycetaceae|g__Cyberlindnera|s__Cyberlindnera fabianii,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Davidiella,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Diutina|s__Diutina mesorugosa,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Didymellaceae|g__Epicoccum|s__Epicoccum sorghinum,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Kluyveromyces|s__Kluyveromyces marxianus,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales,k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Rhizopodaceae|g__Rhizopus,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Trimorphomycetaceae|g__Saitozyma|s__Saitozyma flava,k__Fungi|p__Basidiomycota|c__Ustilaginomycetes|o__Ustilaginales|f__Ustilaginaceae",4751|4890|4891|3243778|115784|604195|36022;4751|4890|147541|2726946|452563|237557;4751|4890|3239874|2916678|766764|1910789|1229076;4751|4890|147541|92860|683158|104397|749593;4751|4890|147550|5125|110618|5506;4751|4890|4891|4892|4893|4910|4911;4751|4890|147541|92860;4751|1913637|2212703|4827|1344955|4842;4751|5204|155616|5234|1890237|1890244|5416;4751|5204|5257|5267|5268,Complete,KateRasheed
bsdb:40819064/3/1,40819064,"cross-sectional observational, not case-control",40819064,10.1186/s12866-025-04278-9,NA,"Renzi S., Meriggi N., Paola M.D., Bacci G., Cerasuolo B., Gori A., Casari S., Banci E., de Blasi A., Diallo S., Kabore B., Derra K., Tinto H., De Filippo C., De Mast Q., Lionetti P. , Cavalieri D.",Exploring the influence of urbanization on gut mycobiota through dietary habits in Burkina Faso,BMC microbiology,2025,"Burkina Faso, Dietary habits, Fungal diversity, Fungi, Gut mycobiota, Microbiota, Rural-to-Urban, Sub-Saharan Africa, Urbanization",Experiment 3,Burkina Faso,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Burkina Faso Semi-Urban (BF-SU),Burkina Faso Urban (BF-U),"Ten monogamous families, each with one mother 
and father and up to four children were selected 
among wealthy urban families from the capital city 
of Ouagadougou These families resided in concrete 
or brick buildings with access to electricity, sewage 
infrastructure and private sources of drinkable water. 
While the diet remained predominantly Burkinabè, 
it included a broader range of foods typical of an 
industrialized dietary pattern, including sugar rich 
beverages, canned goods, and highly processed 
foods rich in preservatives. These families have 
access to healthcare and sanitation infrastructure, 
thereby markedly reducing the risk of infection and 
malnutrition.",50,45,NA,ITS / ITS2,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Fig. S8,28 October 2025,Peter03,Peter03,These taxa were found to be more abundant in Burkina Faso Urban than in Burkina Faso Semi-Urban individuals.,increased,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Pichiales|f__Pichiaceae|g__Pichia,4751|4890|3239874|3243775|1156497|4919,Complete,KateRasheed
bsdb:40819064/3/2,40819064,"cross-sectional observational, not case-control",40819064,10.1186/s12866-025-04278-9,NA,"Renzi S., Meriggi N., Paola M.D., Bacci G., Cerasuolo B., Gori A., Casari S., Banci E., de Blasi A., Diallo S., Kabore B., Derra K., Tinto H., De Filippo C., De Mast Q., Lionetti P. , Cavalieri D.",Exploring the influence of urbanization on gut mycobiota through dietary habits in Burkina Faso,BMC microbiology,2025,"Burkina Faso, Dietary habits, Fungal diversity, Fungi, Gut mycobiota, Microbiota, Rural-to-Urban, Sub-Saharan Africa, Urbanization",Experiment 3,Burkina Faso,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Burkina Faso Semi-Urban (BF-SU),Burkina Faso Urban (BF-U),"Ten monogamous families, each with one mother 
and father and up to four children were selected 
among wealthy urban families from the capital city 
of Ouagadougou These families resided in concrete 
or brick buildings with access to electricity, sewage 
infrastructure and private sources of drinkable water. 
While the diet remained predominantly Burkinabè, 
it included a broader range of foods typical of an 
industrialized dietary pattern, including sugar rich 
beverages, canned goods, and highly processed 
foods rich in preservatives. These families have 
access to healthcare and sanitation infrastructure, 
thereby markedly reducing the risk of infection and 
malnutrition.",50,45,NA,ITS / ITS2,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,Fig. S8,28 October 2025,Peter03,Peter03,These taxa were found to be less abundant in Burkina Faso Urban than in Burkina Faso Semi-Urban individuals.,decreased,"k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium,k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Rhizopodaceae|g__Rhizopus,k__Fungi|p__Basidiomycota|c__Ustilaginomycetes|o__Ustilaginales|f__Ustilaginaceae",4751|4890|147550|5125|110618|5506;4751|1913637|2212703|4827|1344955|4842;4751|5204|5257|5267|5268,Complete,KateRasheed
bsdb:40819064/4/1,40819064,"cross-sectional observational, not case-control",40819064,10.1186/s12866-025-04278-9,NA,"Renzi S., Meriggi N., Paola M.D., Bacci G., Cerasuolo B., Gori A., Casari S., Banci E., de Blasi A., Diallo S., Kabore B., Derra K., Tinto H., De Filippo C., De Mast Q., Lionetti P. , Cavalieri D.",Exploring the influence of urbanization on gut mycobiota through dietary habits in Burkina Faso,BMC microbiology,2025,"Burkina Faso, Dietary habits, Fungal diversity, Fungi, Gut mycobiota, Microbiota, Rural-to-Urban, Sub-Saharan Africa, Urbanization",Experiment 4,"Burkina Faso,Italy",Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Italian Urban (IT-U),Burkina Faso Rural (BF-R),"Ten polygamous households, composed by one 
father, at least two mothers and up to four children, 
were randomly selected from the rural villages of 
Boulpon, Poessi and Godo, located in Boulkimede 
province, with respective populations of 4400, 
2200 and 894. Residents rely on subsistence farming 
and small livestock rearing (e.g., chickens and 
goats) in close contact with humans. Housing 
consists of clusters of huts built using soil, wood, 
and straw. These villages lack electricity, sewage 
systems and water treatment infrastructures; water 
is collected from public reservoirs, streams or 
wells. These households are isolated and in poor 
contact with urban areas. Their diet is traditional 
Burkinabè and predominantly plant-based. Access to healthcare, antibiotics 
and sanitation is limited resulting in high risk of 
infectious diseases and malnutrition.",122,51,NA,ITS / ITS2,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,increased,increased,Signature 1,Fig. 4 & Fig. S8,20 October 2025,Peter03,Peter03,These microbial signatures were found to be more dominant in the Burkina Faso Rural Cohort than in Italian Urban Cohort,increased,"k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus flavus,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus penicillioides,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida tropicalis,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Phaffomycetales|f__Phaffomycetaceae|g__Cyberlindnera|s__Cyberlindnera fabianii,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Diutina|s__Diutina mesorugosa,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Didymellaceae|g__Epicoccum|s__Epicoccum sorghinum,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Kluyveromyces|s__Kluyveromyces marxianus,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Trimorphomycetaceae|g__Saitozyma|s__Saitozyma flava,k__Fungi|p__Ascomycota,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Davidiella,k__Fungi,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Plectosphaerellaceae|g__Plectosphaerella,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales,k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Rhizopodaceae|g__Rhizopus,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae|g__Trichosporon,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Pichiales|f__Pichiaceae|g__Pichia,k__Fungi|p__Basidiomycota|c__Ustilaginomycetes|o__Ustilaginales|f__Ustilaginaceae",4751|4890|147545|5042|1131492|5052|5059;4751|4890|147545|5042|1131492|5052|41959;4751|4890|3239874|2916678|766764|5475|5482;4751|4890|4891|3243778|115784|604195|36022;4751|4890|3239874|2916678|766764|1910789|1229076;4751|4890|147541|92860|683158|104397|749593;4751|4890|4891|4892|4893|4910|4911;4751|5204|1538075|162474|742845|55193|76775;4751|5204|155616|5234|1890237|1890244|5416;4751|4890;4751|4890|147545|5042|1131492|5052;4751|4890|3239874|2916678|766764|5475;4751|4890|147541|2726946|452563|237557;4751;4751|4890|147550|5125|110618|5506;4751|4890|147550|1028384|1033978|40657;4751|4890|147541|92860;4751|1913637|2212703|4827|1344955|4842;4751|5204|155616|1851469|1759442|5552;4751|4890|3239874|3243775|1156497|4919;4751|5204|5257|5267|5268,Complete,KateRasheed
bsdb:40819064/4/2,40819064,"cross-sectional observational, not case-control",40819064,10.1186/s12866-025-04278-9,NA,"Renzi S., Meriggi N., Paola M.D., Bacci G., Cerasuolo B., Gori A., Casari S., Banci E., de Blasi A., Diallo S., Kabore B., Derra K., Tinto H., De Filippo C., De Mast Q., Lionetti P. , Cavalieri D.",Exploring the influence of urbanization on gut mycobiota through dietary habits in Burkina Faso,BMC microbiology,2025,"Burkina Faso, Dietary habits, Fungal diversity, Fungi, Gut mycobiota, Microbiota, Rural-to-Urban, Sub-Saharan Africa, Urbanization",Experiment 4,"Burkina Faso,Italy",Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Italian Urban (IT-U),Burkina Faso Rural (BF-R),"Ten polygamous households, composed by one 
father, at least two mothers and up to four children, 
were randomly selected from the rural villages of 
Boulpon, Poessi and Godo, located in Boulkimede 
province, with respective populations of 4400, 
2200 and 894. Residents rely on subsistence farming 
and small livestock rearing (e.g., chickens and 
goats) in close contact with humans. Housing 
consists of clusters of huts built using soil, wood, 
and straw. These villages lack electricity, sewage 
systems and water treatment infrastructures; water 
is collected from public reservoirs, streams or 
wells. These households are isolated and in poor 
contact with urban areas. Their diet is traditional 
Burkinabè and predominantly plant-based. Access to healthcare, antibiotics 
and sanitation is limited resulting in high risk of 
infectious diseases and malnutrition.",122,51,NA,ITS / ITS2,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,increased,increased,Signature 2,Fig. 4 & Fig. S8,20 October 2025,Peter03,Peter03,"The abundance of these microbial signatures were found to decrease with decreasing  urbanization,  evidenced by their high presence in Italian Urban Cohort over Burkina Faso Rural Cohort.",decreased,"k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Cordycipitaceae|g__Leptobacillium|s__Leptobacillium leptobactrum,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Rhodotorula|s__Rhodotorula mucilaginosa,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Spathaspora|s__[Candida] sake,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Debaryomyces,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Penicillium,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Eurotium",4751|4890|147550|5125|474943|1924249|93594;4751|5204|162481|231213|1799696|5533|5537;4751|4890|3239874|2916678|766764|412764|39397;4751|4890|3239874|2916678|766764|4958;4751|4890|147545|5042|1131492|5073;4751|4890|147545|5042|1131492|28569,Complete,KateRasheed
bsdb:40819064/5/1,40819064,"cross-sectional observational, not case-control",40819064,10.1186/s12866-025-04278-9,NA,"Renzi S., Meriggi N., Paola M.D., Bacci G., Cerasuolo B., Gori A., Casari S., Banci E., de Blasi A., Diallo S., Kabore B., Derra K., Tinto H., De Filippo C., De Mast Q., Lionetti P. , Cavalieri D.",Exploring the influence of urbanization on gut mycobiota through dietary habits in Burkina Faso,BMC microbiology,2025,"Burkina Faso, Dietary habits, Fungal diversity, Fungi, Gut mycobiota, Microbiota, Rural-to-Urban, Sub-Saharan Africa, Urbanization",Experiment 5,"Burkina Faso,Italy",Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Italian Urban (IT-U),Burkina Faso Semi-Urban (BF-SU),"This cohort included ten polygamous or 
monogamous families, each comprising one father, 
one or two mothers, and up to four children. 
Participants resided in Nanoro, a semi-urbanized 
area with a population estimated between 33,000 
and 34,000. People live in groups of small brick 
houses with limited access to electricity. Water is 
collected from public wells. Similar to rural areas, 
sewage systems and water treatment plants were 
absent. Their diet is still traditional Burkinabè and 
plant-based, but also occasionally including meat and 
dried fish, and limited processed and Western-like 
foods. Despite improved food access, this cohort 
remained at risk of malnutrition and infectious 
diseases",122,50,NA,ITS / ITS2,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,unchanged,increased,Signature 1,Fig. 4 & Fig. S8,20 October 2025,Peter03,Peter03,"The abundance of these microbial signatures were found to increase with decreased urbanization,  evidenced by their high presence in Burkina Faso Semi-Urban Cohorts.",increased,"k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus flavus,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus penicillioides,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida tropicalis,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Phaffomycetales|f__Phaffomycetaceae|g__Cyberlindnera|s__Cyberlindnera fabianii,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Diutina|s__Diutina mesorugosa,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Didymellaceae|g__Epicoccum|s__Epicoccum sorghinum,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Trimorphomycetaceae|g__Saitozyma|s__Saitozyma flava,k__Fungi|p__Ascomycota,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida,k__Fungi,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Pichiales|f__Pichiaceae|g__Pichia,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Plectosphaerellaceae|g__Plectosphaerella,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales,k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Rhizopodaceae|g__Rhizopus,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae|g__Trichosporon",4751|4890|147545|5042|1131492|5052|5059;4751|4890|147545|5042|1131492|5052|41959;4751|4890|3239874|2916678|766764|5475|5482;4751|4890|4891|3243778|115784|604195|36022;4751|4890|3239874|2916678|766764|1910789|1229076;4751|4890|147541|92860|683158|104397|749593;4751|5204|1538075|162474|742845|55193|76775;4751|5204|155616|5234|1890237|1890244|5416;4751|4890;4751|4890|147545|5042|1131492|5052;4751|4890|3239874|2916678|766764|5475;4751;4751|4890|147550|5125|110618|5506;4751|4890|3239874|3243775|1156497|4919;4751|4890|147550|1028384|1033978|40657;4751|4890|147541|92860;4751|1913637|2212703|4827|1344955|4842;4751|5204|155616|1851469|1759442|5552,Complete,KateRasheed
bsdb:40819064/5/2,40819064,"cross-sectional observational, not case-control",40819064,10.1186/s12866-025-04278-9,NA,"Renzi S., Meriggi N., Paola M.D., Bacci G., Cerasuolo B., Gori A., Casari S., Banci E., de Blasi A., Diallo S., Kabore B., Derra K., Tinto H., De Filippo C., De Mast Q., Lionetti P. , Cavalieri D.",Exploring the influence of urbanization on gut mycobiota through dietary habits in Burkina Faso,BMC microbiology,2025,"Burkina Faso, Dietary habits, Fungal diversity, Fungi, Gut mycobiota, Microbiota, Rural-to-Urban, Sub-Saharan Africa, Urbanization",Experiment 5,"Burkina Faso,Italy",Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Italian Urban (IT-U),Burkina Faso Semi-Urban (BF-SU),"This cohort included ten polygamous or 
monogamous families, each comprising one father, 
one or two mothers, and up to four children. 
Participants resided in Nanoro, a semi-urbanized 
area with a population estimated between 33,000 
and 34,000. People live in groups of small brick 
houses with limited access to electricity. Water is 
collected from public wells. Similar to rural areas, 
sewage systems and water treatment plants were 
absent. Their diet is still traditional Burkinabè and 
plant-based, but also occasionally including meat and 
dried fish, and limited processed and Western-like 
foods. Despite improved food access, this cohort 
remained at risk of malnutrition and infectious 
diseases",122,50,NA,ITS / ITS2,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,unchanged,increased,Signature 2,Fig. 4 & Fig. S8,20 October 2025,Peter03,Peter03,"The abundance of these microbial signatures were found to decrease with decrease in urbanization,  evidenced by their low presence in Burkina Faso Semi-Urban Cohort.",decreased,"k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Rhodotorula|s__Rhodotorula mucilaginosa,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Spathaspora|s__[Candida] sake,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Debaryomyces,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Eurotium,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Penicillium",4751|5204|162481|231213|1799696|5533|5537;4751|4890|3239874|2916678|766764|412764|39397;4751|4890|3239874|2916678|766764|4958;4751|4890|147545|5042|1131492|28569;4751|4890|147545|5042|1131492|5073,Complete,KateRasheed
bsdb:40819064/6/1,40819064,"cross-sectional observational, not case-control",40819064,10.1186/s12866-025-04278-9,NA,"Renzi S., Meriggi N., Paola M.D., Bacci G., Cerasuolo B., Gori A., Casari S., Banci E., de Blasi A., Diallo S., Kabore B., Derra K., Tinto H., De Filippo C., De Mast Q., Lionetti P. , Cavalieri D.",Exploring the influence of urbanization on gut mycobiota through dietary habits in Burkina Faso,BMC microbiology,2025,"Burkina Faso, Dietary habits, Fungal diversity, Fungi, Gut mycobiota, Microbiota, Rural-to-Urban, Sub-Saharan Africa, Urbanization",Experiment 6,"Burkina Faso,Italy",Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Italian Urban (IT-U),Burkina Faso Urban (BF-U),"Ten monogamous families, each with one mother 
and father and up to four children were, selected 
among wealthy urban families from the capital city 
of Ouagadougou These families resided in concrete 
or brick buildings with access to electricity, sewage 
infrastructure and private sources of drinkable water. 
While the diet remained predominantly Burkinabè, 
it included a broader range of foods typical of an 
industrialized dietary pattern, including sugar rich 
beverages, canned goods, and highly processed 
foods rich in preservatives. These families have 
access to healthcare and sanitation infrastructure, 
thereby markedly reducing the risk of infection and 
malnutrition.",122,45,NA,ITS / ITS2,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,increased,increased,Signature 1,Fig. 4 & Fig. S8,20 October 2025,Peter03,Peter03,These species increased in abundance in the Burkina Faso Urban Cohort over Italian Urban Cohort.,increased,"k__Fungi|p__Ascomycota,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus flavus,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus penicillioides,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida tropicalis,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Diutina|s__Diutina mesorugosa,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Didymellaceae|g__Epicoccum|s__Epicoccum sorghinum,k__Fungi,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Kluyveromyces|s__Kluyveromyces marxianus,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Pichiales|f__Pichiaceae|g__Pichia,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Plectosphaerellaceae|g__Plectosphaerella,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Trimorphomycetaceae|g__Saitozyma|s__Saitozyma flava,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae|g__Trichosporon,k__Fungi|p__Basidiomycota|c__Ustilaginomycetes|o__Ustilaginales|f__Ustilaginaceae",4751|4890;4751|4890|147545|5042|1131492|5052;4751|4890|147545|5042|1131492|5052|5059;4751|4890|147545|5042|1131492|5052|41959;4751|4890|3239874|2916678|766764|5475;4751|4890|3239874|2916678|766764|5475|5482;4751|4890|3239874|2916678|766764|1910789|1229076;4751|4890|147541|92860|683158|104397|749593;4751;4751|4890|4891|4892|4893|4910|4911;4751|5204|1538075|162474|742845|55193|76775;4751|4890|3239874|3243775|1156497|4919;4751|4890|147550|1028384|1033978|40657;4751|4890|147541|92860;4751|5204|155616|5234|1890237|1890244|5416;4751|5204|155616|1851469|1759442|5552;4751|5204|5257|5267|5268,Complete,KateRasheed
bsdb:40819064/6/2,40819064,"cross-sectional observational, not case-control",40819064,10.1186/s12866-025-04278-9,NA,"Renzi S., Meriggi N., Paola M.D., Bacci G., Cerasuolo B., Gori A., Casari S., Banci E., de Blasi A., Diallo S., Kabore B., Derra K., Tinto H., De Filippo C., De Mast Q., Lionetti P. , Cavalieri D.",Exploring the influence of urbanization on gut mycobiota through dietary habits in Burkina Faso,BMC microbiology,2025,"Burkina Faso, Dietary habits, Fungal diversity, Fungi, Gut mycobiota, Microbiota, Rural-to-Urban, Sub-Saharan Africa, Urbanization",Experiment 6,"Burkina Faso,Italy",Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Italian Urban (IT-U),Burkina Faso Urban (BF-U),"Ten monogamous families, each with one mother 
and father and up to four children were, selected 
among wealthy urban families from the capital city 
of Ouagadougou These families resided in concrete 
or brick buildings with access to electricity, sewage 
infrastructure and private sources of drinkable water. 
While the diet remained predominantly Burkinabè, 
it included a broader range of foods typical of an 
industrialized dietary pattern, including sugar rich 
beverages, canned goods, and highly processed 
foods rich in preservatives. These families have 
access to healthcare and sanitation infrastructure, 
thereby markedly reducing the risk of infection and 
malnutrition.",122,45,NA,ITS / ITS2,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,increased,increased,Signature 2,Fig. 4 & Fig. S8,20 October 2025,Peter03,Peter03,These species were found to decrease in the Burkina Faso Urban Cohort.,decreased,"k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Debaryomyces,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Eurotium,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Cordycipitaceae|g__Leptobacillium|s__Leptobacillium leptobactrum,k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Penicillium,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Rhodotorula|s__Rhodotorula mucilaginosa,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Spathaspora|s__[Candida] sake,k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Rhizopodaceae|g__Rhizopus",4751|4890|3239874|2916678|766764|4958;4751|4890|147545|5042|1131492|28569;4751|4890|147550|5125|474943|1924249|93594;4751|4890|147545|5042|1131492|5073;4751|5204|162481|231213|1799696|5533|5537;4751|4890|3239874|2916678|766764|412764|39397;4751|1913637|2212703|4827|1344955|4842,Complete,KateRasheed
bsdb:40825855/1/1,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 1,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,24 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 24 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 1b,30 September 2025,YokoC,YokoC,Heatmap showing bacterial enrichment profiles at 24 hours fermentation time point compared to the start of fermentation (0 hours) for the Genus taxonomic level.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|g__Candidatus Kinetoplastidibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Cohaesibacteraceae|g__Cohaesibacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Anaplasmataceae|g__Ehrlichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Frateuria,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Jeotgalibaca,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Listeria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Oenococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Polynucleobacter,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Entomoplasmatales|f__Spiroplasmataceae|g__Spiroplasma,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Tatumella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",1783272|1239|91061|186826|186827|1375;3379134|1224|28216|33055;3379134|1224|28211|356|655351|655352;3379134|1224|28211|766|942|943;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|135614|1775411|70411;3384189|32066|203490|203491|203492|848;1783272|1239|91061|186826|186828|1470540;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|33958|1243;1783272|1239|91061|1385|186820|1637;1783272|1239|91061|1385|186817|400634;1783272|1239|91061|186826|33958|46254;1783272|1239|91061|186826|33958|1253;3379134|1224|28216|80840|119060|44013;1783272|544448|31969|186328|2131|2132;3379134|1224|1236|91347|1903409|82986;1783272|1239|91061|186826|81852|2737;1783272|1239|91061|186826|33958|46255,Complete,NA
bsdb:40825855/1/2,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 1,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,24 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 24 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 1b,30 September 2025,YokoC,YokoC,Heatmap showing bacterial enrichment profiles at 24 hours fermentation time point compared to the start of fermentation (0 hours) for the Genus taxonomic level.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Oscillatoriales|f__Microcoleaceae|g__Arthrospira,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Candidatus Midichloriaceae|g__Candidatus Midichloria,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Gomontiellales|f__Gomontiellaceae|g__Crinalium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfohalobiaceae|g__Desulfohalobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Dickeya,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Chroococcales|f__Geminocystaceae|g__Geminocystis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Leptolyngbyales|f__Leptolyngbyaceae|g__Leptolyngbya,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Budviciaceae|g__Limnobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Lonsdalea,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Chroococcales|f__Microcystaceae|g__Microcystis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Mixta,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Nissabacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Ornithobacterium,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Oscillatoriales|f__Oscillatoriaceae|g__Oscillatoria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Pectobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Photorhabdus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Bruguierivoracaceae|g__Sodalis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingopyxidaceae|g__Sphingopyxis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Synechococcales|f__Synechococcaceae|g__Synechococcus",3379134|1224|28216|80840|506|222;3379134|1224|28216|80840|80864|12916;3379134|1224|28211|356|82115|357;1783272|1117|3028117|1150|1892252|35823;3379134|1224|1236|91347|1903410|71655;3379134|1224|28211|204458|76892|41275;3379134|1224|28211|766|1328881|411566;1783272|1117|3028117|3079757|1892255|241421;3379134|1224|28216|80840|119060|106589;3379134|200940|3031449|213115|213117|45662;3379134|1224|1236|91347|1903410|204037;3379134|1224|1236|91347|1903409|551;1783272|1117|3028117|1118|2815910|669357;3379134|1224|28216|80840|75682|963;3379134|976|768503|768507|1853232|89966;1783272|1117|3028117|3079749|1890438|47251;3379134|1224|1236|91347|1903416|2172100;3379134|1224|1236|91347|1903410|1082702;1783272|1117|3028117|1118|1890449|1125;3379134|1224|1236|91347|1903409|2100764;3379134|1224|1236|91347|1903411|1964366;3379134|976|117743|200644|2762318|28250;1783272|1117|3028117|1150|1892254|1158;3379134|1224|1236|91347|1903409|53335;3379134|1224|1236|135625|712|745;3379134|1224|1236|91347|1903410|122277;3379134|1224|1236|91347|1903414|29487;1783272|201174|1760|85007|85025|1827;3379134|1224|1236|91347|2812006|84565;3379134|1224|28211|204457|41297|13687;3379134|1224|28211|204457|3423718|165697;3379134|1224|1236|135614|32033|40323;1783272|1117|3028117|1890424|1890426|1129,Complete,NA
bsdb:40825855/2/1,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 2,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,48 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 48 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 1b,2 October 2025,YokoC,YokoC,Heatmap showing bacterial enrichment profiles at 48 hours fermentation time point compared to the start of fermentation (0 hours) for the Genus taxonomic level.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Acetobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Asaia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Anaplasmataceae|g__Ehrlichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Frateuria,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Gluconacetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Gluconobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Granulibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Jeotgalibaca,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Komagataeibacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Kozakia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Listeria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Melissococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Neoasaia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Neokomagataea,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Oceanobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Oenococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Parasaccharibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Polynucleobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|g__Rhodobacter,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Entomoplasmatales|f__Spiroplasmataceae|g__Spiroplasma,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Sporosarcina,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Swingsia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Tetragenococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Zymomonadaceae|g__Zymomonas",3379134|1224|28211|3120395|433|434;1783272|1239|91061|186826|186827|1375;3379134|1224|28211|3120395|433|91914;1783272|1239|91061|1385|186817|1386;1783272|1239|91061|186826|186828|2747;3379134|1224|28211|766|942|943;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|135614|1775411|70411;3384189|32066|203490|203491|203492|848;3379134|1224|28211|3120395|433|89583;3379134|1224|28211|3120395|433|441;3379134|1224|28211|3120395|433|364409;1783272|1239|91061|186826|186828|1470540;3379134|1224|28211|3120395|433|1434011;3379134|1224|28211|3120395|433|153497;1783272|1239|186801|3085636|186803|1506553;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1357;1783272|1239|91061|186826|33958|1243;1783272|1239|91061|1385|186820|1637;1783272|1239|91061|1385|186817|400634;1783272|1239|91061|186826|81852|33969;3379134|1224|28211|3120395|433|320496;3379134|1224|28211|3120395|433|1223423;1783272|1239|91061|1385|186817|182709;1783272|1239|91061|186826|33958|46254;3379134|1224|28211|3120395|433|1602345;1783272|1239|91061|186826|33958|1253;3379134|1224|28216|80840|119060|44013;3379134|1224|28211|204455|1060;1783272|544448|31969|186328|2131|2132;1783272|1239|91061|1385|186818|1569;3379134|1224|28211|3120395|433|1649499;1783272|1239|91061|186826|81852|51668;1783272|1239|91061|186826|81852|2737;1783272|1239|91061|186826|33958|46255;3379134|1224|28211|204457|2844881|541,Complete,NA
bsdb:40825855/2/2,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 2,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,48 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 48 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,NA,2 October 2025,YokoC,YokoC,Heatmap showing bacterial enrichment profiles at 48 hours fermentation time point compared to the start of fermentation (0 hours) for the Genus taxonomic level.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Atlantibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Buttiauxella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Cellvibrio,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Chania,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Gomontiellales|f__Gomontiellaceae|g__Crinalium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Dickeya,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Edwardsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Chroococcales|f__Geminocystaceae|g__Geminocystis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Gibbsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hydrogenophaga,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Izhakiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kluyvera,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kosakonia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Leclercia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Lelliottia,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Leptolyngbyales|f__Leptolyngbyaceae|g__Leptolyngbya,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Budviciaceae|g__Limnobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Lonsdalea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Mixta,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Coleofasciculales|f__Coleofasciculaceae|g__Moorena,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Neorhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Nissabacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Obesumbacterium,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Oscillatoriales|f__Oscillatoriaceae|g__Oscillatoria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Pectobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Photorhabdus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pluralibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Budviciaceae|g__Pragia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pseudescherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rahnella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae|g__Rhodococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shimwellia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Bruguierivoracaceae|g__Sodalis,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Cytophagaceae|g__Spirosoma,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Synechococcales|f__Synechococcaceae|g__Synechococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Xenorhabdus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia",3379134|1224|1236|91347|543|1903434;3379134|1224|1236|91347|1903410|71655;3379134|1224|1236|91347|543|82976;3379134|1224|1236|91347|543|158483;3379134|1224|1236|1706369|1706371|10;3379134|1224|1236|91347|1903411|1745211;3379134|1224|1236|91347|543|544;1783272|1117|3028117|3079757|1892255|241421;3379134|1224|1236|91347|543|413496;3379134|1224|1236|91347|1903410|204037;3379134|1224|1236|91347|1903412|635;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|1903409|551;3379134|1224|1236|91347|543|561;1783272|1117|3028117|1118|2815910|669357;3379134|1224|1236|91347|1903411|929812;3379134|1224|1236|91347|1903412|568;3379134|1224|28216|80840|80864|47420;3379134|976|768503|768507|1853232|89966;3379134|1224|1236|91347|1903409|1780190;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|543|579;3379134|1224|1236|91347|543|1330547;3379134|1224|1236|91347|543|83654;3379134|1224|1236|91347|543|1330545;1783272|1117|3028117|3079749|1890438|47251;3379134|1224|1236|91347|1903416|2172100;3379134|1224|1236|91347|1903410|1082702;3379134|1224|1236|91347|1903409|2100764;1783272|1117|3028117|3079753|1892251|1155738;3379134|1224|1236|91347|1903414|581;3379134|1224|28211|356|82115|1525371;3379134|1224|1236|91347|1903411|1964366;3379134|1224|1236|91347|1903412|82982;1783272|1117|3028117|1150|1892254|1158;3379134|1224|1236|91347|1903409|53335;3379134|1224|1236|135625|712|745;3379134|1224|1236|91347|1903410|122277;3379134|1224|1236|91347|1903414|29487;3379134|1224|1236|91347|543|1330546;3379134|1224|1236|91347|1903416|82984;3379134|1224|1236|91347|1903414|583;3379134|1224|1236|91347|1903414|586;3379134|1224|1236|91347|543|2055880;3379134|1224|1236|91347|1903411|34037;3379134|1224|1236|91347|543|160674;1783272|201174|1760|85007|85025|1827;3379134|1224|1236|91347|543|590;3379134|1224|1236|91347|1903411|613;3379134|1224|1236|91347|543|620;3379134|1224|1236|91347|543|1335483;3379134|1224|1236|91347|2812006|84565;3379134|976|768503|768507|89373|107;1783272|1117|3028117|1890424|1890426|1129;3379134|1224|1236|91347|1903414|626;3379134|1224|1236|91347|1903411|629,Complete,NA
bsdb:40825855/3/1,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 3,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,72 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 72 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 1b,7 October 2025,YokoC,YokoC,Heatmap showing bacterial enrichment profiles at 72 hours fermentation time point compared to the start of fermentation (0 hours) for the Genus taxonomic level.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Acetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acidocellaceae|g__Acidiphilium,k__Pseudomonadati|p__Pseudomonadota|c__Acidithiobacillia|o__Acidithiobacillales|f__Acidithiobacillaceae|g__Acidithiobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Alloyangia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Altererythrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Asaia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae|g__Azorhizobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Brochothrix,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Candidatus Izemoplasmatales|f__Candidatus Izemoplasmataceae|g__Candidatus Izemoplasma,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Castellaniella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Crassaminicella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae|g__Filomicrobium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Gluconacetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Gluconobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Gracilibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Granulibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Intestinibaculum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Jeotgalibaca,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Komagataeibacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Kozakia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Listeria,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Lutibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae|g__Magnetospirillum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Marinilactibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Melissococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae|g__Methyloceanibacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Myroides,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Neoasaia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Oceanobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Oenococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Parasaccharibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Psychrobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Salicibibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Salinisphaerales|f__Salinisphaeraceae|g__Salinisphaera,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Solibacillus,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Entomoplasmatales|f__Spiroplasmataceae|g__Spiroplasma,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Sporosarcina,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Swingsia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Tetragenococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae|g__Thermoanaerobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Virgibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Zymomonadaceae|g__Zymomonas",3379134|1224|28211|3120395|433|434;3379134|1224|28211|3120395|3385905|522;3379134|1224|1807140|225057|225058|119977;1783272|1239|91061|186826|186827|1375;3379134|1224|28211|204455|2854170|2919626;3379134|1224|28211|204457|335929|361177;3379134|1224|28211|3120395|433|91914;3379134|1224|28211|356|335928|6;1783272|1239|91061|1385|186817|1386;1783272|1239|186801|3085636|186803|572511;1783272|1239|91061|1385|186820|2755;1783272|544448|31969|2975519|2975520|2975549;1783272|1239|91061|186826|186828|2747;3379134|1224|28216|80840|506|359336;1783272|1239|186801|3082720|186804|1870884;1783272|1239|186801|186802|31979|1848399;1783272|1239|91061|186826|81852|1350;1783272|1239|526524|526525|128827|1647;3379134|1224|28211|356|45401|119044;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378;3379134|1224|28211|3120395|433|89583;3379134|1224|28211|3120395|433|441;1783272|1239|91061|1385|186817|74385;3379134|1224|28211|3120395|433|364409;1783272|1239|526524|526525|128827|2679910;1783272|1239|91061|186826|186828|1470540;3379134|1224|28211|3120395|433|1434011;3379134|1224|28211|3120395|433|153497;1783272|1239|186801|3085636|186803|1506553;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1357;3384189|32066|203490|203491|1129771|32067;1783272|1239|91061|186826|33958|1243;1783272|1239|91061|1385|186820|1637;3379134|976|117743|200644|49546|358023;1783272|1239|91061|1385|186817|400634;3379134|1224|28211|204441|41295|13134;1783272|1239|91061|186826|186828|191769;1783272|1239|91061|186826|81852|33969;3379134|1224|28211|356|45401|1484898;3379134|976|117743|200644|49546|76831;3379134|1224|28211|3120395|433|320496;1783272|1239|91061|1385|186817|182709;1783272|1239|91061|186826|33958|46254;3379134|1224|28211|3120395|433|1602345;1783272|1239|91061|186826|33958|1253;1783272|1239|91061|1385|186817|1221880;1783272|1239|91061|1385|186817|2685905;3379134|1224|1236|742030|742031|180541;1783272|1239|91061|1385|186818|648800;1783272|544448|31969|186328|2131|2132;1783272|1239|91061|1385|186818|1569;3379134|1224|28211|3120395|433|1649499;1783272|1239|91061|186826|81852|51668;1783272|1239|186801|68295|186814|28895;1783272|1239|91061|186826|81852|2737;1783272|1239|91061|1385|186817|84406;3379134|1224|28211|204457|2844881|541,Complete,NA
bsdb:40825855/3/2,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 3,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,72 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 72 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 1b,7 October 2025,YokoC,YokoC,Heatmap showing bacterial enrichment profiles at 72 hours fermentation time point compared to the start of fermentation (0 hours) for the Genus taxonomic level.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Arsenophonus,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Oscillatoriales|f__Microcoleaceae|g__Arthrospira,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Atlantibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Buttiauxella,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Calotrichaceae|g__Calothrix,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|g__Candidatus Azobacteroides,p__Candidatus Bipolaricaulota|c__Candidatus Bipolaricaulia|o__Candidatus Bipolaricaulales|f__Candidatus Bipolaricaulaceae|g__Candidatus Bipolaricaulis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Candidatus Hodgkinia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Candidatus Midichloriaceae|g__Candidatus Midichloria,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Candidatus Phytoplasma,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Chania,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Gomontiellales|f__Gomontiellaceae|g__Crinalium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Nostocaceae|g__Cylindrospermum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfohalobiaceae|g__Desulfohalobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Dickeya,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Edwardsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Hapalosiphonaceae|g__Fischerella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Frankiales|f__Frankiaceae|g__Frankia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae|g__Frateuria,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Chroococcales|f__Geminocystaceae|g__Geminocystis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Gibbsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hydrogenophaga,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Izhakiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kluyvera,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kosakonia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Leclercia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Lelliottia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Budviciaceae|g__Leminorella,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Leptolyngbyales|f__Leptolyngbyaceae|g__Leptolyngbya,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Budviciaceae|g__Limnobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Lonsdalea,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Oscillatoriales|f__Microcoleaceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Chroococcales|f__Microcystaceae|g__Microcystis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Mixta,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Coleofasciculales|f__Coleofasciculaceae|g__Moorena,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Neorhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Nissabacter,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Nodulariaceae|g__Nodularia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Spongiibacteraceae|g__Oceanicoccus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Ornithobacterium,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Oscillatoriales|f__Oscillatoriaceae|g__Oscillatoria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Pectobacterium,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Photorhabdus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Phytobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Plesiomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pluralibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Budviciaceae|g__Pragia,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Synechococcales|f__Prochlorococcaceae|g__Prochlorococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pseudescherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rahnella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shimwellia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Bruguierivoracaceae|g__Sodalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Synechococcales|f__Synechococcaceae|g__Synechococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Tatumella,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Nostocaceae|g__Trichormus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Woeseiales|f__Woeseiaceae|g__Woeseia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Xenorhabdus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia",3379134|1224|1236|135624|84642|642;3379134|1224|1236|91347|1903414|637;1783272|1117|3028117|1150|1892252|35823;3379134|1224|1236|91347|543|1903434;3379134|1224|1236|91347|1903410|71655;3379134|1224|28211|204458|76892|41275;3379134|1224|1236|91347|543|82976;1783272|1117|3028117|1161|2661849|1186;3379134|29547|3031852|213849|72294|194;3379134|976|200643|171549|511434;67810|3121607|3121608|3121609|2250122;3379134|1224|28211|356|573657;3379134|1224|28211|766|1328881|411566;1783272|544448|31969|186329|2146|33926;3379134|1224|1236|91347|543|158483;3379134|1224|1236|91347|1903411|1745211;3379134|1224|1236|91347|543|544;1783272|1117|3028117|3079757|1892255|241421;3379134|1224|1236|91347|543|413496;1783272|1117|3028117|1161|1162|56106;3379134|200940|3031449|213115|213117|45662;3379134|1224|1236|91347|1903410|204037;3379134|1224|1236|91347|1903412|635;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|1903409|551;3379134|1224|1236|91347|543|561;1783272|1117|3028117|1161|1892263|1190;1783272|201174|1760|85013|74712|1854;3379134|1224|1236|135614|1775411|70411;1783272|1117|3028117|1118|2815910|669357;3379134|1224|1236|91347|1903411|929812;3379134|1224|1236|91347|1903412|568;3379134|1224|1236|135619|28256|2745;3379134|1224|28216|80840|80864|47420;3379134|976|768503|768507|1853232|89966;3379134|1224|1236|91347|1903409|1780190;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|543|579;3379134|1224|1236|91347|543|1330547;3379134|1224|1236|91347|543|83654;3379134|1224|1236|91347|543|1330545;3379134|1224|1236|91347|1903416|82980;1783272|1117|3028117|3079749|1890438|47251;3379134|1224|1236|91347|1903416|2172100;3379134|1224|1236|91347|1903410|1082702;1783272|1117|3028117|1150|1892252;1783272|1117|3028117|1118|1890449|1125;3379134|1224|1236|91347|1903409|2100764;1783272|1117|3028117|3079753|1892251|1155738;3379134|1224|1236|91347|1903414|581;3379134|1224|28211|356|82115|1525371;3379134|1224|1236|91347|1903411|1964366;1783272|1117|3028117|1161|3079761|159191;3379134|1224|1236|1706369|1706375|1084558;3379134|976|117743|200644|2762318|28250;1783272|1117|3028117|1150|1892254|1158;3379134|1224|1236|91347|1903409|53335;3379134|1224|1236|135625|712|745;3379134|1224|1236|91347|1903410|122277;3379134|976|117747|200666|84566|84567;3379134|1224|1236|91347|1903414|29487;3379134|1224|1236|91347|543|447792;3379134|1224|1236|91347|543|702;3379134|1224|1236|91347|543|1330546;3379134|1224|1236|91347|1903416|82984;1783272|1117|3028117|1890424|2881426|1218;3379134|1224|1236|91347|1903414|583;3379134|1224|1236|91347|1903414|586;3379134|1224|1236|91347|543|2055880;3379134|1224|1236|91347|1903411|34037;3379134|1224|1236|91347|543|160674;3379134|1224|1236|91347|543|590;3379134|1224|1236|91347|1903411|613;3379134|1224|1236|135622|267890|22;3379134|1224|1236|91347|543|620;3379134|1224|1236|91347|543|1335483;3379134|1224|1236|91347|2812006|84565;3379134|1224|1236|135614|32033|40323;1783272|1117|3028117|1890424|1890426|1129;3379134|1224|1236|91347|1903409|82986;1783272|1117|3028117|1161|1162|264688;3379134|1224|1236|3104269|1738654|1738655;3379134|1224|1236|91347|1903414|626;3379134|1224|1236|91347|1903411|629,Complete,NA
bsdb:40825855/4/1,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 4,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,96 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 96 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 1b,7 October 2025,YokoC,YokoC,Heatmap showing bacterial enrichment profiles at 96 hours fermentation time point compared to the start of fermentation (0 hours) for the Genus taxonomic level.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Acetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acidocellaceae|g__Acidiphilium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Acidipropionibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Acidithiobacillia|o__Acidithiobacillales|f__Acidithiobacillaceae|g__Acidithiobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae|g__Azorhizobium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Candidatus Pelagibacterales|f__Candidatus Pelagibacteraceae|g__Candidatus Pelagibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Castellaniella,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Anaplasmataceae|g__Ehrlichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|g__Exiguobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae|g__Filomicrobium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Anoxybacillaceae|g__Geobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Gluconacetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Granulibacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Intestinibaculum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Komagataeibacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Kozakia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Leptospirales|f__Leptospiraceae|g__Leptospira,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Listeria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae|g__Magnetospirillum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Melissococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae|g__Methyloceanibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micromonosporales|f__Micromonosporaceae|g__Micromonospora,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Neoasaia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Neokomagataea,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Nitrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Niveispirillum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Oenococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Parasaccharibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Polaromonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Rhodopseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Roseomonadaceae|g__Roseomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Salinisphaerales|f__Salinisphaeraceae|g__Salinisphaera,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Sporosarcina,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Swingsia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Syntrophia|o__Syntrophales|f__Syntrophaceae|g__Syntrophus,k__Bacillati|p__Bacillota|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae|g__Thermoanaerobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Virgibacillus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Zymomonadaceae|g__Zymomonas,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Maribacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Olleya,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Kutzneria,k__Pseudomonadati|p__Myxococcota|c__Myxococcia|o__Myxococcales|f__Archangiaceae|g__Cystobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Phaeobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Alloyangia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylocystaceae|g__Methylocystis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Shinella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Ketobacteraceae|g__Ketobacter",3379134|1224|28211|3120395|433|434;3379134|1224|28211|3120395|3385905|522;1783272|201174|1760|85009|31957|1912215;3379134|1224|1807140|225057|225058|119977;1783272|1239|91061|186826|186827|1375;1783272|201174|1760|85006|1268|1663;3379134|1224|28211|356|335928|6;1783272|1239|91061|1385|186817|1386;1783272|1239|186801|3085636|186803|572511;1783272|201174|1760|85006|85020|43668;1783272|201174|1760|85006|85019|1696;3379134|1224|28211|54526|1655514|198251;1783272|1239|91061|186826|186828|2747;3379134|1224|28216|80840|506|359336;3379134|1224|28211|766|942|943;1783272|1239|91061|186826|81852|1350;1783272|1239|526524|526525|128827|1647;1783272|1239|91061|1385|33986;1783272|1239|526524|526525|128827|1573534;3379134|1224|28211|356|45401|119044;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|3120669|129337;3379134|1224|28211|3120395|433|89583;3379134|1224|28211|3120395|433|364409;3379134|29547|3031852|213849|72293|209;1783272|1239|526524|526525|128827|2679910;3379134|1224|28211|3120395|433|1434011;3379134|1224|28211|3120395|433|153497;1783272|1239|186801|3085636|186803|1506553;1783272|1239|91061|186826|33958|1578;3379134|203691|203692|1643688|170|171;1783272|1239|91061|186826|33958|1243;1783272|1239|91061|1385|186820|1637;1783272|1239|91061|1385|186817|400634;3379134|1224|28211|204441|41295|13134;1783272|1239|91061|186826|81852|33969;3379134|1224|28211|356|45401|1484898;1783272|201174|1760|85008|28056|84593;3379134|1224|28211|3120395|433|320496;3379134|1224|28211|3120395|433|1223423;3379134|1224|28211|356|41294|911;3379134|1224|28211|204441|2829815|1543704;1783272|1239|91061|186826|33958|46254;3379134|1224|28211|3120395|433|1602345;1783272|1239|91061|186826|33958|1253;3379134|1224|28216|80840|80864|52972;3379134|1224|28211|356|41294|1073;3379134|1224|28211|3120395|3385906|125216;3379134|1224|1236|742030|742031|180541;1783272|1239|91061|1385|186818|1569;3379134|1224|28211|3120395|433|1649499;3379134|200940|3031648|2914038|213468|43773;1783272|1239|186801|68295|186814|28895;1783272|1239|91061|186826|81852|2737;1783272|1239|91061|1385|186817|84406;3379134|1224|28211|204457|2844881|541;3379134|976|117743|200644|49546|252356;3379134|976|117743|200644|49546|336276;1783272|201174|1760|85010|2070|43356;3379134|2818505|32015|29|39|42;3379134|1224|28211|204455|2854170|302485;3379134|1224|28211|204455|2854170|2919626;3379134|1224|28211|356|31993|133;3379134|1224|28211|356|82115|323620;3379134|1224|1236|72274|3085096|2025617,Complete,NA
bsdb:40825855/4/2,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 4,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,96 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 96 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 1b,7 October 2025,YokoC,YokoC,Heatmap showing bacterial enrichment profiles at 96 hours fermentation time point compared to the start of fermentation (0 hours) for the Genus taxonomic level.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Arsenophonus,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Oscillatoriales|f__Microcoleaceae|g__Arthrospira,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Atlantibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Buttiauxella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|g__Candidatus Azobacteroides,p__Candidatus Bipolaricaulota|c__Candidatus Bipolaricaulia|o__Candidatus Bipolaricaulales|f__Candidatus Bipolaricaulaceae|g__Candidatus Bipolaricaulis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Candidatus Hodgkinia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Candidatus Midichloriaceae|g__Candidatus Midichloria,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Candidatus Phytoplasma,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Chania,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Gomontiellales|f__Gomontiellaceae|g__Crinalium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Nostocaceae|g__Cylindrospermum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfohalobiaceae|g__Desulfohalobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Dickeya,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Edwardsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Hapalosiphonaceae|g__Fischerella,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Chroococcales|f__Geminocystaceae|g__Geminocystis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Gibbsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hydrogenophaga,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae|g__Hymenobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Izhakiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kluyvera,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kosakonia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Leclercia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Lelliottia,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Leptolyngbyales|f__Leptolyngbyaceae|g__Leptolyngbya,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Budviciaceae|g__Limnobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Lonsdalea,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Oscillatoriales|f__Microcoleaceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Chroococcales|f__Microcystaceae|g__Microcystis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Mixta,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Nissabacter,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Nodulariaceae|g__Nodularia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Ornithobacterium,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Oscillatoriales|f__Oscillatoriaceae|g__Oscillatoria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Pectobacterium,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Photorhabdus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pluralibacter,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Polaribacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Budviciaceae|g__Pragia,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Synechococcales|f__Prochlorococcaceae|g__Prochlorococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pseudescherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rahnella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shimwellia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Bruguierivoracaceae|g__Sodalis,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Synechococcales|f__Synechococcaceae|g__Synechococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Tatumella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Xenorhabdus,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Oscillatoriales|f__Microcoleaceae|g__Trichodesmium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Phytobacter",3379134|1224|1236|91347|1903414|637;1783272|1117|3028117|1150|1892252|35823;3379134|1224|1236|91347|543|1903434;3379134|1224|1236|91347|1903410|71655;3379134|1224|28211|204458|76892|41275;3379134|1224|1236|91347|543|82976;3379134|29547|3031852|213849|72294|194;3379134|976|200643|171549|511434;67810|3121607|3121608|3121609|2250122;3379134|1224|28211|356|573657;3379134|1224|28211|766|1328881|411566;1783272|544448|31969|186329|2146|33926;3379134|1224|1236|91347|543|158483;3379134|1224|1236|91347|1903411|1745211;3379134|1224|1236|91347|543|544;1783272|1239|186801|186802|31979|1485;1783272|1117|3028117|3079757|1892255|241421;3379134|1224|1236|91347|543|413496;1783272|1117|3028117|1161|1162|56106;3379134|200940|3031449|213115|213117|45662;3379134|1224|1236|91347|1903410|204037;3379134|1224|1236|91347|1903412|635;3379134|1224|1236|91347|543|547;3379134|1224|1236|91347|1903409|551;3379134|1224|1236|91347|543|561;1783272|1117|3028117|1161|1892263|1190;1783272|1117|3028117|1118|2815910|669357;3379134|1224|1236|91347|1903411|929812;3379134|1224|1236|91347|1903412|568;3379134|1224|28216|80840|80864|47420;3379134|976|768503|768507|1853232|89966;3379134|1224|1236|91347|1903409|1780190;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|543|579;3379134|1224|1236|91347|543|1330547;3379134|1224|1236|91347|543|83654;3379134|1224|1236|91347|543|1330545;1783272|1117|3028117|3079749|1890438|47251;3379134|1224|1236|91347|1903416|2172100;3379134|1224|1236|91347|1903410|1082702;1783272|1117|3028117|1150|1892252;1783272|1117|3028117|1118|1890449|1125;3379134|1224|1236|91347|1903409|2100764;3379134|1224|1236|91347|1903411|1964366;1783272|1117|3028117|1161|3079761|159191;3379134|976|117743|200644|2762318|28250;1783272|1117|3028117|1150|1892254|1158;3379134|1224|1236|91347|1903409|53335;3379134|1224|1236|135625|712|745;3379134|1224|1236|91347|1903410|122277;3379134|976|117747|200666|84566|84567;3379134|1224|1236|91347|1903414|29487;3379134|1224|1236|91347|543|1330546;3379134|976|117743|200644|49546|52959;3379134|1224|1236|91347|1903416|82984;1783272|1117|3028117|1890424|2881426|1218;3379134|1224|1236|91347|1903414|586;3379134|1224|1236|91347|543|2055880;3379134|1224|1236|91347|1903411|34037;3379134|1224|1236|91347|543|160674;3379134|1224|1236|91347|543|590;3379134|1224|1236|91347|543|1335483;3379134|1224|1236|91347|2812006|84565;1783272|1117|3028117|1890424|1890426|1129;3379134|1224|1236|91347|1903409|82986;3379134|1224|1236|91347|1903414|626;1783272|1117|3028117|1150|1892252|1205;3379134|1224|1236|91347|1903411|613;3379134|1224|1236|91347|1903411|629;3379134|1224|1236|91347|1903414|581;3379134|1224|1236|91347|1903414|583;3379134|1224|1236|91347|543|447792,Complete,NA
bsdb:40825855/5/1,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 5,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,24 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 24 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 1c,7 October 2025,YokoC,YokoC,Heatmap showing bacterial enrichment profiles at 24 hours fermentation time point compared to the start of fermentation (0 hours) for the Family taxonomic level.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Cohaesibacteraceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Entomoplasmatales|f__Spiroplasmataceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",1783272|1239|91061|186826|186827;1783272|1239|91061|186826|186828;1783272|1239|91061|186826|81852;3384189|32066|203490|203491|203492;1783272|1239|91061|1385|186820;3379134|1224|1236|135614|1775411;1783272|1239|91061|186826|1300;3379134|1224|28211|356|655351;1783272|544448|31969|186328|2131;1783272|1239|91061|186826|33958,Complete,NA
bsdb:40825855/5/2,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 5,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,24 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 24 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 1c,7 October 2025,YokoC,YokoC,Heatmap showing bacterial enrichment profiles at 24 hours fermentation time point compared to the start of fermentation (0 hours) for the Family taxonomic level.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Nocardiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Gomontiellales|f__Gomontiellaceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Chroococcales|f__Microcystaceae",3379134|1224|28211|204458|76892;3379134|1224|1236|135613|1046;3379134|976|768503|768507|1853232;1783272|201174|1760|85007|85025;3379134|1224|1236|91347|1903410;1783272|201174|1760|85009|31957;1783272|1117|3028117|3079757|1892255;1783272|1117|3028117|1118|1890449,Complete,NA
bsdb:40825855/6/1,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 6,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,48 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 48 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 1c,7 October 2025,YokoC,YokoC,Heatmap showing bacterial enrichment profiles at 48 hours fermentation time point compared to the start of fermentation (0 hours) for the Family taxonomic level.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Rhodanobacteraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Entomoplasmatales|f__Spiroplasmataceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",3379134|1224|28211|3120395|433;1783272|1239|91061|186826|186827;1783272|1239|91061|1385|186817;1783272|1239|91061|186826|186828;1783272|1239|91061|186826|81852;3384189|32066|203490|203491|203492;1783272|1239|91061|1385|186820;3379134|1224|1236|135614|1775411;1783272|1239|91061|186826|1300;1783272|544448|31969|186328|2131;1783272|1239|91061|186826|33958,Complete,NA
bsdb:40825855/6/2,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 6,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,48 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 48 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 1c,8 October 2025,YokoC,YokoC,Heatmap showing bacterial enrichment profiles at 48 hours fermentation time point compared to the start of fermentation (0 hours) for the Family taxonomic level.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae",3379134|1224|1236|91347|543;3379134|1224|1236|91347|1903414;3379134|1224|1236|91347|1903410;1783272|201174|1760|85009|31957;1783272|1239|909932|909929|1843491;3379134|1224|1236|91347|1903411;3379134|1224|1236|91347|1903412,Complete,NA
bsdb:40825855/7/1,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 7,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,72 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 72 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 1c,8 October 2025,YokoC,YokoC,Heatmap showing bacterial enrichment profiles at 72 hours fermentation time point compared to the start of fermentation (0 hours) for the Family taxonomic level.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Acidithiobacillia|o__Acidithiobacillales|f__Acidithiobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Entomoplasmatales|f__Entomoplasmataceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Halanaerobiales|f__Halanaerobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Entomoplasmatales|f__Spiroplasmataceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Candidatus Nanopelagicales|f__Candidatus Nanopelagicaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Salinisphaerales|f__Salinisphaeraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Candidatus Pelagibacterales|f__Candidatus Pelagibacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Thiotrichales|f__Francisellaceae",3379134|1224|28211|3120395|433;3379134|1224|1807140|225057|225058;1783272|1239|91061|186826|186827;1783272|1239|91061|1385|186817;1783272|1239|91061|186826|186828;1783272|1239|91061|186826|81852;1783272|544448|31969|186328|33925;1783272|1239|526524|526525|128827;3379134|1224|28211|204457|335929;3384189|32066|203490|203491|203492;1783272|1239|186801|53433|972;3379134|1224|28211|356|45401;1783272|1239|186801|3085636|186803;3384189|32066|203490|203491|1129771;1783272|1239|91061|1385|186820;1783272|1239|1737404|1737405|1570339;1783272|1239|186801|3082720|186804;1783272|544448|31969|186328|2131;1783272|1239|91061|1385|90964;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|33958;1783272|1239|91061|1385|186818;1783272|201174|1760|2039638|2162846;3379134|1224|1236|742030|742031;3379134|1224|28211|54526|1655514;3379134|1224|1236|72273|34064,Complete,NA
bsdb:40825855/7/2,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 7,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,72 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 72 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 1c,8 October 2025,YokoC,YokoC,Heatmap showing bacterial enrichment profiles at 72 hours fermentation time point compared to the start of fermentation (0 hours) for the Family taxonomic level.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfohalobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Hymenobacteraceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Oscillatoriales|f__Microcoleaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhodobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Spongiibacteraceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Synechococcales|f__Synechococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Oscillatoriales|f__Oscillatoriaceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Chroococcales|f__Chroococcaceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Chroococcales|f__Prochloraceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Gomontiellales|f__Gomontiellaceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Chroococcales|f__Microcystaceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Leptolyngbyales|f__Leptolyngbyaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Frankiales|f__Frankiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Budviciaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Candidatus Midichloriaceae",3379134|1224|1236|135624|84642;3379134|1224|28216|80840|80864;3379134|200940|3031449|213115|213117;3379134|1224|1236|91347|543;3379134|1224|1236|91347|1903409;3379134|976|768503|768507|1853232;1783272|1117|3028117|1150|1892252;3379134|1224|1236|91347|1903414;3379134|1224|1236|135625|712;3379134|1224|1236|91347|1903410;1783272|201174|1760|85009|31957;3379134|1224|28211|356|119043;3379134|1224|1236|135622|267890;3379134|1224|1236|1706369|1706375;1783272|1117|3028117|1890424|1890426;3379134|1224|1236|91347|1903411;1783272|1117|3028117|1150|1892254;1783272|1117|3028117|1118|1890464;1783272|1117|3028117|1118|1213;1783272|1117|3028117|3079757|1892255;1783272|1117|3028117|1118|1890449;1783272|1117|3028117|3079749|1890438;1783272|201174|1760|85013|74712;3379134|1224|1236|91347|1903412;3379134|1224|1236|91347|1903416;3379134|1224|28211|766|1328881,Complete,NA
bsdb:40825855/8/1,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 8,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,96 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 96 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 1c,8 October 2025,YokoC,YokoC,Heatmap showing bacterial enrichment profiles at 96 hours fermentation time point compared to the start of fermentation (0 hours) for the Family taxonomic level.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Acidithiobacillia|o__Acidithiobacillales|f__Acidithiobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Listeriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylocystaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Salinisphaerales|f__Salinisphaeraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Candidatus Pelagibacterales|f__Candidatus Pelagibacteraceae,k__Pseudomonadati|p__Myxococcota|c__Myxococcia|o__Myxococcales|f__Archangiaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Syntrophia|o__Syntrophales|f__Syntrophaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Leptospirales|f__Leptospiraceae",3379134|1224|28211|3120395|433;3379134|1224|1807140|225057|225058;1783272|1239|91061|186826|186827;1783272|1239|91061|1385|186817;1783272|201174|1760|85006|85019;1783272|1239|91061|186826|186828;3384194|1297|188787|118964|183710;1783272|201174|1760|85006|85020;1783272|201174|84998|1643822|1643826;1783272|1239|91061|186826|81852;1783272|1239|526524|526525|128827;3384189|32066|203490|203491|203492;3379134|29547|3031852|213849|72293;3379134|1224|28211|356|45401;1783272|1239|186801|3085636|186803;1783272|1239|91061|1385|186820;3379134|1224|28211|356|31993;1783272|201174|1760|85007|1762;1783272|1239|1737404|1737405|1570339;1783272|201174|1760|85010|2070;3379134|1224|28211|204441|41295;3379134|1224|28211|204457|41297;3379134|203691|203692|136|137;1783272|1239|91061|186826|1300;1783272|201174|1760|85011|2062;3379134|1224|28211|356|335928;1783272|1239|91061|186826|33958;3379134|1224|1236|742030|742031;3379134|1224|28211|54526|1655514;3379134|2818505|32015|29|39;3379134|200940|3031648|2914038|213468;3379134|203691|203692|1643688|170,Complete,NA
bsdb:40825855/8/2,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 8,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,96 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 96 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 1c,8 October 2025,YokoC,YokoC,Heatmap showing bacterial enrichment profiles at 96 hours fermentation time point compared to the start of fermentation (0 hours) for the Family taxonomic level.,decreased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfohalobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Oscillatoriales|f__Microcoleaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Nostocaceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Oscillatoriales|f__Oscillatoriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhodobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Spongiibacteraceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Synechococcales|f__Synechococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Candidatus Midichloriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Budviciaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Leptolyngbyales|f__Leptolyngbyaceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Hapalosiphonaceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Chroococcales|f__Chroococcaceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Chroococcales|f__Prochloraceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Chroococcales|f__Microcystaceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Gomontiellales|f__Gomontiellaceae",3379134|200940|3031449|213115|213117;3379134|1224|1236|91347|543;3379134|1224|1236|91347|1903409;1783272|1117|3028117|1150|1892252;3379134|1224|1236|91347|1903414;1783272|1117|3028117|1161|1162;1783272|1117|3028117|1150|1892254;3379134|1224|1236|135625|712;3379134|1224|1236|91347|1903410;3379134|1224|28211|356|119043;3379134|1224|1236|1706369|1706375;1783272|1117|3028117|1890424|1890426;3379134|1224|1236|91347|1903411;3379134|1224|28211|766|1328881;3379134|1224|1236|91347|1903416;3379134|1224|1236|91347|1903412;1783272|1117|3028117|3079749|1890438;1783272|1117|3028117|1161|1892263;1783272|1117|3028117|1118|1890464;1783272|1117|3028117|1118|1213;1783272|1117|3028117|1118|1890449;1783272|1117|3028117|3079757|1892255,Complete,NA
bsdb:40825855/9/1,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 9,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,24 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 24 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 1d,8 October 2025,YokoC,YokoC,Heatmap showing fungal enrichment profiles at 24 hours fermentation time point compared to the start of fermentation (0 hours) for the species taxonomic level.,increased,"k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida orthopsilosis,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Debaryomyces|s__Debaryomyces hansenii,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Kluyveromyces|s__Kluyveromyces marxianus,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Pichiales|f__Pichiaceae|g__Komagataella|s__Komagataella phaffii,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Scheffersomyces|s__Scheffersomyces stipitis,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Trichomonascaceae|g__Sugiyamaella|s__Sugiyamaella lignohabitans,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Eremothecium|s__Eremothecium cymbalariae,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Huiozyma|s__Huiozyma naganishii,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Henningerozyma|s__Henningerozyma blattae,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Zygosaccharomyces|s__Zygosaccharomyces rouxii,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Nakaseomyces|s__Nakaseomyces glabratus,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Lachancea|s__Lachancea thermotolerans,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Naumovozyma|s__Naumovozyma castellii,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Tetrapisispora|s__Tetrapisispora phaffii,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Naumovozyma|s__Naumovozyma dairenensis,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces eubayanus,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Eremothecium|s__Eremothecium gossypii,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Kazachstania|s__Kazachstania africana,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Eremothecium|s__Eremothecium sinecaudum,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Kluyveromyces|s__Kluyveromyces lactis",4751|4890|3239874|2916678|766764|5475|5476;4751|4890|3239874|2916678|766764|5475|273371;4751|4890|3239874|2916678|766764|4958|4959;4751|4890|4891|4892|4893|4910|4911;4751|4890|3239874|3243775|1156497|460517|460519;4751|4890|3239874|2916678|766764|766733|4924;4751|4890|3239873|3243772|410830|410829|796027;4751|4890|4891|4892|4893|33170|45285;4751|4890|4891|4892|4893|3163251|588726;4751|4890|4891|4892|4893|4930|4932;4751|4890|4891|4892|4893|3163253|1071379;4751|4890|4891|4892|4893|4953|4956;4751|4890|4891|4892|4893|374468|5478;4751|4890|4891|4892|4893|300275|381046;4751|4890|4891|4892|4893|278028|27288;4751|4890|4891|4892|4893|113604|113608;4751|4890|4891|4892|4893|278028|27289;4751|4890|4891|4892|4893|4930|1080349;4751|4890|4891|4892|4893|33170|33169;4751|4890|4891|4892|4893|71245|432096;4751|4890|4891|4892|4893|33170|45286;4751|4890|4891|4892|4893|4910|28985,Complete,NA
bsdb:40825855/9/2,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 9,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,24 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 24 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 1d,8 October 2025,YokoC,YokoC,Heatmap showing fungal enrichment profiles at 24 hours fermentation time point compared to the start of fermentation (0 hours) for the species taxonomic level.,decreased,"k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus fumigatus,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Glomerellaceae|g__Colletotrichum|s__Colletotrichum higginsianum,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae|g__Zymoseptoria|s__Zymoseptoria tritici,k__Fungi|p__Basidiomycota|c__Ustilaginomycetes|o__Ustilaginales|g__Mycosarcoma|s__Mycosarcoma maydis,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae|g__Cercospora|s__Cercospora beticola,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales|f__Sclerotiniaceae|g__Botrytis|s__Botrytis cinerea,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Chaetomiaceae|g__Thermothielavioides|s__Thermothielavioides terrestris",4751|4890|147545|5042|1131492|5052|746128;4751|4890|147550|1028384|681950|5455|80884;4751|5204|1538075|162474|742845|55193|76775;4751|4890|147541|2726947|93133|1047167|1047171;4751|5204|5257|5267|2689624|5270;4751|4890|147541|2726947|93133|29002|122368;4751|4890|147548|5178|28983|33196|40559;4751|4890|147550|5139|35718|2609811|2587410,Complete,NA
bsdb:40825855/10/1,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 10,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,48 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 48 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 1d,8 October 2025,YokoC,YokoC,Heatmap showing fungal enrichment profiles at 48 hours fermentation time point compared to the start of fermentation (0 hours) for the species taxonomic level.,increased,"k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida orthopsilosis,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Eremothecium|s__Eremothecium gossypii,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Eremothecium|s__Eremothecium sinecaudum,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Henningerozyma|s__Henningerozyma blattae,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Kazachstania|s__Kazachstania africana,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Kluyveromyces|s__Kluyveromyces lactis,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Pichiales|f__Pichiaceae|g__Komagataella|s__Komagataella phaffii,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Lachancea|s__Lachancea thermotolerans,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Nakaseomyces|s__Nakaseomyces glabratus,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Naumovozyma|s__Naumovozyma castellii,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Naumovozyma|s__Naumovozyma dairenensis,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Pichiales|f__Pichiaceae|g__Pichia|s__Pichia kudriavzevii,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces eubayanus,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Scheffersomyces|s__Scheffersomyces stipitis,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Trichomonascaceae|g__Sugiyamaella|s__Sugiyamaella lignohabitans,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Tetrapisispora|s__Tetrapisispora phaffii,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Zygosaccharomyces|s__Zygosaccharomyces rouxii",4751|4890|3239874|2916678|766764|5475|5476;4751|4890|3239874|2916678|766764|5475|273371;4751|4890|4891|4892|4893|33170|33169;4751|4890|4891|4892|4893|33170|45286;4751|4890|4891|4892|4893|3163253|1071379;4751|4890|4891|4892|4893|71245|432096;4751|4890|4891|4892|4893|4910|28985;4751|4890|3239874|3243775|1156497|460517|460519;4751|4890|4891|4892|4893|300275|381046;4751|4890|4891|4892|4893|374468|5478;4751|4890|4891|4892|4893|278028|27288;4751|4890|4891|4892|4893|278028|27289;4751|4890|3239874|3243775|1156497|4919|4909;4751|4890|4891|4892|4893|4930|4932;4751|4890|4891|4892|4893|4930|1080349;4751|4890|3239874|2916678|766764|766733|4924;4751|4890|3239873|3243772|410830|410829|796027;4751|4890|4891|4892|4893|113604|113608;4751|4890|4891|4892|4893|4953|4956,Complete,NA
bsdb:40825855/10/2,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 10,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,48 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 48 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 1d,8 October 2025,YokoC,YokoC,Heatmap showing fungal enrichment profiles at 48 hours fermentation time point compared to the start of fermentation (0 hours) for the species taxonomic level.,decreased,"k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus fumigatus,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Glomerellaceae|g__Colletotrichum|s__Colletotrichum higginsianum,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium|s__Fusarium fujikuroi,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Sordariaceae|g__Neurospora|s__Neurospora crassa,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae|g__Zymoseptoria|s__Zymoseptoria tritici,k__Fungi|p__Basidiomycota|c__Ustilaginomycetes|o__Ustilaginales|g__Mycosarcoma|s__Mycosarcoma maydis,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae|g__Cercospora|s__Cercospora beticola,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales|f__Sclerotiniaceae|g__Botrytis|s__Botrytis cinerea,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Chaetomiaceae|g__Thermothielavioides|s__Thermothielavioides terrestris,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium|s__Fusarium oxysporum,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium|s__Fusarium verticillioides,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium|s__Fusarium graminearum,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium|s__Fusarium pseudograminearum,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium|s__Fusarium venenatum",4751|4890|147545|5042|1131492|5052|746128;4751|4890|147550|1028384|681950|5455|80884;4751|4890|147550|5125|110618|5506|5127;4751|5204|1538075|162474|742845|55193|76775;4751|4890|147550|5139|5148|5140|5141;4751|4890|147541|2726947|93133|1047167|1047171;4751|5204|5257|5267|2689624|5270;4751|4890|147541|2726947|93133|29002|122368;4751|4890|147548|5178|28983|33196|40559;4751|4890|147550|5139|35718|2609811|2587410;4751|4890|147550|5125|110618|5506|5507;4751|4890|147550|5125|110618|5506|117187;4751|4890|147550|5125|110618|5506|5518;4751|4890|147550|5125|110618|5506|101028;4751|4890|147550|5125|110618|5506|56646,Complete,NA
bsdb:40825855/11/1,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 11,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,72 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 72 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 1d,8 October 2025,YokoC,YokoC,Heatmap showing fungal enrichment profiles at 72 hours fermentation time point compared to the start of fermentation (0 hours) for the species taxonomic level.,increased,"k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus fumigatus,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Cryptococcaceae|g__Cryptococcus|s__Cryptococcus neoformans,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Trichomonascaceae|g__Sugiyamaella|s__Sugiyamaella lignohabitans,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|g__Yarrowia|s__Yarrowia lipolytica,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Pichiales|f__Pichiaceae|g__Pichia|s__Pichia kudriavzevii,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Eremothecium|s__Eremothecium gossypii",4751|4890|147545|5042|1131492|5052|746128;4751|5204|155616|5234|1884633|5206|5207;4751|4890|3239873|3243772|410830|410829|796027;4751|4890|3239873|3243772|4951|4952;4751|4890|3239874|3243775|1156497|4919|4909;4751|4890|4891|4892|4893|4930|4932;4751|4890|4891|4892|4893|33170|33169,Complete,NA
bsdb:40825855/11/2,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 11,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,72 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 72 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 1d,8 October 2025,YokoC,YokoC,Heatmap showing fungal enrichment profiles at 72 hours fermentation time point compared to the start of fermentation (0 hours) for the species taxonomic level.,decreased,"k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Debaryomyces|s__Debaryomyces hansenii,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae|g__Cercospora|s__Cercospora beticola,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium|s__Fusarium fujikuroi,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium|s__Fusarium verticillioides,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium|s__Fusarium pseudograminearum",4751|4890|3239874|2916678|766764|4958|4959;4751|4890|147541|2726947|93133|29002|122368;4751|4890|147550|5125|110618|5506|5127;4751|4890|147550|5125|110618|5506|117187;4751|4890|147550|5125|110618|5506|101028,Complete,NA
bsdb:40825855/12/1,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 12,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,96 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 96 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 1d,8 October 2025,YokoC,YokoC,Heatmap showing fungal enrichment profiles at 96 hours fermentation time point compared to the start of fermentation (0 hours) for the species taxonomic level.,increased,"k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus fumigatus,k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Cryptococcaceae|g__Cryptococcus|s__Cryptococcus neoformans,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Trichomonascaceae|g__Sugiyamaella|s__Sugiyamaella lignohabitans,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|g__Yarrowia|s__Yarrowia lipolytica,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae",4751|4890|147545|5042|1131492|5052|746128;4751|5204|155616|5234|1884633|5206|5207;4751|4890|3239873|3243772|410830|410829|796027;4751|4890|3239873|3243772|4951|4952;4751|4890|4891|4892|4893|4930|4932,Complete,NA
bsdb:40825855/12/2,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 12,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,96 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 96 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 1d,8 October 2025,YokoC,YokoC,Heatmap showing fungal enrichment profiles at 96 hours fermentation time point compared to the start of fermentation (0 hours) for the species taxonomic level.,decreased,"k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Scheffersomyces|s__Scheffersomyces stipitis,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium|s__Fusarium pseudograminearum,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium|s__Fusarium verticillioides,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium|s__Fusarium venenatum",4751|4890|3239874|2916678|766764|766733|4924;4751|4890|147550|5125|110618|5506|101028;4751|4890|147550|5125|110618|5506|117187;4751|4890|147550|5125|110618|5506|56646,Complete,NA
bsdb:40825855/13/1,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 13,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,24 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 24 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 1e,8 October 2025,YokoC,YokoC,Heatmap showing fungal enrichment profiles at 24 hours fermentation time point compared to the start of fermentation (0 hours) for the genus taxonomic level.,increased,"k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Kluyveromyces,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Scheffersomyces,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Trichomonascaceae|g__Sugiyamaella,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Tetrapisispora,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Naumovozyma,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Zygosaccharomyces,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Eremothecium,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Lachancea",4751|4890|4891|4892|4893|4910;4751|4890|4891|4892|4893|4930;4751|4890|3239874|2916678|766764|766733;4751|4890|3239873|3243772|410830|410829;4751|4890|4891|4892|4893|113604;4751|4890|4891|4892|4893|278028;4751|4890|4891|4892|4893|4953;4751|4890|4891|4892|4893|33170;4751|4890|4891|4892|4893|300275,Complete,NA
bsdb:40825855/13/2,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 13,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,24 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 24 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 1e,8 October 2025,YokoC,YokoC,Heatmap showing fungal enrichment profiles at 24 hours fermentation time point compared to the start of fermentation (0 hours) for the genus taxonomic level.,decreased,"k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Glomerellaceae|g__Colletotrichum,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Sordariaceae|g__Neurospora,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae|g__Zymoseptoria,k__Fungi|p__Basidiomycota|c__Ustilaginomycetes|o__Ustilaginales|f__Ustilaginaceae|g__Ustilago,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae|g__Cercospora,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales|f__Sclerotiniaceae|g__Botrytis,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Chaetomiaceae|g__Thermothielavioides",4751|4890|147550|1028384|681950|5455;4751|5204|1538075|162474|742845|55193;4751|4890|147550|5139|5148|5140;4751|4890|147541|2726947|93133|1047167;4751|5204|5257|5267|5268|5269;4751|4890|147541|2726947|93133|29002;4751|4890|147548|5178|28983|33196;4751|4890|147550|5139|35718|2609811,Complete,NA
bsdb:40825855/14/1,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 14,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,48 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 48 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 1e,8 October 2025,YokoC,YokoC,Heatmap showing fungal enrichment profiles at 48 hours fermentation time point compared to the start of fermentation (0 hours) for the genus taxonomic level.,increased,"k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Trichomonascaceae|g__Sugiyamaella,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Pichiales|f__Pichiaceae|g__Pichia",4751|4890|4891|4892|4893|4930;4751|4890|3239873|3243772|410830|410829;4751|4890|3239874|3243775|1156497|4919,Complete,NA
bsdb:40825855/14/2,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 14,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,48 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 48 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 1e,8 October 2025,YokoC,YokoC,Heatmap showing fungal enrichment profiles at 48 hours fermentation time point compared to the start of fermentation (0 hours) for the genus taxonomic level.,decreased,"k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales|f__Sclerotiniaceae|g__Botrytis,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae|g__Cercospora,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Glomerellales|f__Glomerellaceae|g__Colletotrichum,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Sordariaceae|g__Neurospora,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Clavicipitaceae|g__Pochonia,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Magnaporthales|f__Pyriculariaceae|g__Pyricularia,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Chaetomiaceae|g__Thermothielavioides,k__Fungi|p__Basidiomycota|c__Ustilaginomycetes|o__Ustilaginales|f__Ustilaginaceae|g__Ustilago,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae|g__Zymoseptoria",4751|4890|147545|5042|1131492|5052;4751|4890|147548|5178|28983|33196;4751|4890|147541|2726947|93133|29002;4751|4890|147550|1028384|681950|5455;4751|4890|147550|5125|110618|5506;4751|5204|1538075|162474|742845|55193;4751|4890|147550|5139|5148|5140;4751|4890|147550|5125|34397|243023;4751|4890|147550|639021|2528436|48558;4751|4890|147550|5139|35718|2609811;4751|5204|5257|5267|5268|5269;4751|4890|147541|2726947|93133|1047167,Complete,NA
bsdb:40825855/15/1,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 15,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,72 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 72 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 1e,8 October 2025,YokoC,YokoC,Heatmap showing fungal enrichment profiles at 72 hours fermentation time point compared to the start of fermentation (0 hours) for the genus taxonomic level.,increased,"k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Trichomonascaceae|g__Sugiyamaella,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|g__Yarrowia,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Pichiales|f__Pichiaceae|g__Pichia",4751|4890|4891|4892|4893|4930;4751|4890|3239873|3243772|410830|410829;4751|4890|3239873|3243772|4951;4751|4890|3239874|3243775|1156497|4919,Complete,NA
bsdb:40825855/15/2,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 15,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,72 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 72 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 1e,8 October 2025,YokoC,YokoC,Heatmap showing fungal enrichment profiles at 72 hours fermentation time point compared to the start of fermentation (0 hours) for the genus taxonomic level.,increased,"k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae|g__Zymoseptoria,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae|g__Cercospora,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales|f__Sclerotiniaceae|g__Botrytis,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Debaryomyces",4751|4890|147541|2726947|93133|1047167;4751|4890|147541|2726947|93133|29002;4751|4890|147548|5178|28983|33196;4751|4890|147550|5125|110618|5506;4751|4890|3239874|2916678|766764|4958,Complete,NA
bsdb:40825855/16/1,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 16,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,96 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 96 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 1e,8 October 2025,YokoC,YokoC,Heatmap showing fungal enrichment profiles at 96 hours fermentation time point compared to the start of fermentation (0 hours) for the genus taxonomic level.,increased,"k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Trichomonascaceae|g__Sugiyamaella,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|g__Yarrowia",4751|4890|147545|5042|1131492|5052;4751|4890|4891|4892|4893|4930;4751|4890|3239873|3243772|410830|410829;4751|4890|3239873|3243772|4951,Complete,NA
bsdb:40825855/16/2,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 16,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,96 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 96 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 1e,8 October 2025,YokoC,YokoC,Heatmap showing fungal enrichment profiles at 96 hours fermentation time point compared to the start of fermentation (0 hours) for the genus taxonomic level.,decreased,"k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Debaryomyces,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae|g__Fusarium,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Scheffersomyces,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae|g__Zymoseptoria,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae|g__Cercospora,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales|f__Sclerotiniaceae|g__Botrytis",4751|4890|3239874|2916678|766764|4958;4751|4890|147550|5125|110618|5506;4751|4890|3239874|2916678|766764|766733;4751|4890|147541|2726947|93133|1047167;4751|4890|147541|2726947|93133|29002;4751|4890|147548|5178|28983|33196,Complete,NA
bsdb:40825855/17/1,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 17,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,24 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 24 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 1f,8 October 2025,YokoC,YokoC,Heatmap showing fungal enrichment profiles at 24 hours fermentation time point compared to the start of fermentation (0 hours) for the family taxonomic level.,increased,"k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Trichomonascaceae,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Pichiales|f__Pichiaceae,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Phaffomycetales|f__Phaffomycetaceae",4751|4890|3239874|2916678|766764;4751|4890|4891|4892|4893;4751|4890|3239873|3243772|410830;4751|4890|3239874|3243775|1156497;4751|4890|4891|3243778|115784,Complete,NA
bsdb:40825855/17/2,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 17,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,24 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 24 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 1f,8 October 2025,YokoC,YokoC,Heatmap showing fungal enrichment profiles at 24 hours fermentation time point compared to the start of fermentation (0 hours) for the family taxonomic level.,decreased,"k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae",4751|5204|1538075|162474|742845;4751|4890|147541|2726947|93133,Complete,NA
bsdb:40825855/18/1,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 18,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,48 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 48 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 1f,8 October 2025,YokoC,YokoC,Heatmap showing fungal enrichment profiles at 48 hours fermentation time point compared to the start of fermentation (0 hours) for the family taxonomic level.,increased,"k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Trichomonascaceae,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Pichiales|f__Pichiaceae,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Phaffomycetales|f__Phaffomycetaceae",4751|4890|3239874|2916678|766764;4751|4890|4891|4892|4893;4751|4890|3239873|3243772|410830;4751|4890|3239874|3243775|1156497;4751|4890|4891|3243778|115784,Complete,NA
bsdb:40825855/18/2,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 18,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,48 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 48 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 1f,8 October 2025,YokoC,YokoC,Heatmap showing fungal enrichment profiles at 48 hours fermentation time point compared to the start of fermentation (0 hours) for the family taxonomic level.,decreased,"k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae",4751|5204|1538075|162474|742845;4751|4890|147541|2726947|93133;4751|4890|147550|5125|110618,Complete,NA
bsdb:40825855/19/1,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 19,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,72 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 72 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 1f,8 October 2025,YokoC,YokoC,Heatmap showing fungal enrichment profiles at 72 hours fermentation time point compared to the start of fermentation (0 hours) for the genus taxonomic level.,increased,"k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Trichomonascaceae,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Dipodascaceae",4751|4890|4891|4892|4893;4751|4890|3239873|3243772|410830;4751|4890|3239873|3243772|34353,Complete,NA
bsdb:40825855/19/2,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 19,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,72 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 72 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 1f,8 October 2025,YokoC,YokoC,Heatmap showing fungal enrichment profiles at 72 hours fermentation time point compared to the start of fermentation (0 hours) for the family taxonomic level.,decreased,"k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Chaetomiaceae,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales|f__Sclerotiniaceae",4751|4890|147550|5139|35718;4751|4890|147541|2726947|93133;4751|4890|147550|5125|110618;4751|4890|147548|5178|28983,Complete,NA
bsdb:40825855/20/1,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 20,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,96 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 96 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 1f,8 October 2025,YokoC,YokoC,Heatmap showing fungal enrichment profiles at 96 hours fermentation time point compared to the start of fermentation (0 hours) for the family taxonomic level.,increased,"k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae,k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Trichomonascaceae,k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Dipodascaceae",4751|4890|147545|5042|1131492;4751|4890|4891|4892|4893;4751|4890|3239873|3243772|410830;4751|4890|3239873|3243772|34353,Complete,NA
bsdb:40825855/20/2,40825855,prospective cohort,40825855,10.1038/s41564-025-02077-6,NA,"Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E. , Castrillo G.",A defined microbial community reproduces attributes of fine flavour chocolate fermentation,Nature microbiology,2025,NA,Experiment 20,Colombia,Theobroma cacao,NA,NA,Diet,EFO:0002755,0 hrs fermentation,96 hrs fermentation,200-400 kg of cocoa beans undergoing fermentation for 96 hours in wooden boxes at ambient temperature.,NA,NA,NA,WMS,NA,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 1f,8 October 2025,YokoC,YokoC,Heatmap showing fungal enrichment profiles at 96 hours fermentation time point compared to the start of fermentation (0 hours) for the family taxonomic level.,decreased,"k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Mycosphaerellales|f__Mycosphaerellaceae,k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Nectriaceae,k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Helotiales|f__Sclerotiniaceae",4751|4890|147541|2726947|93133;4751|4890|147550|5125|110618;4751|4890|147548|5178|28983,Complete,NA
bsdb:40827923/1/1,40827923,case-control,40827923,https://doi.org/10.1128/spectrum.03376-24,NA,"Zhu C., Li L.-.Y., Li C., Wu L., Zhang Y.-.Y., Yao Y., Yang J., Wang S.-.Y., Xing L.-.M., Zeng X.-.T. , Fang C.",Profiles of oral microbiota and metabolites in periodontitis and benign prostatic hyperplasia patients: a pilot study,Microbiology spectrum,2025,"benign prostatic hyperplasia, metabolites, microbiome, periodontitis",Experiment 1,China,Homo sapiens,Gingival groove,UBERON:0008805,Benign prostatic hyperplasia,EFO:0000284,Healthy group,Benign prostatic hyperplasia (BPH) group,Participants diagnosed with Benign prostatic hyperplasia (BPH),12,12,NA,16S,34,DNBSEQ-G400,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 2,28 October 2025,Firdaws,Firdaws,Significantly differential microorganisms (species level) among Benign prostatic hyperplasia (BPH) group and Healthy group,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas infelix,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena",3379134|976|117743|200644|49546|1016|45242;3379134|976|117743|200644|49546|1016|327575;3379134|976|117743|200644|49546|1016|1018;3379134|1224|28216|206351|481|482|495;1783272|1239|909932|909929|1843491|970|135082;1783272|1239|909932|909929|1843491|970|69823,Complete,KateRasheed
bsdb:40827923/1/2,40827923,case-control,40827923,https://doi.org/10.1128/spectrum.03376-24,NA,"Zhu C., Li L.-.Y., Li C., Wu L., Zhang Y.-.Y., Yao Y., Yang J., Wang S.-.Y., Xing L.-.M., Zeng X.-.T. , Fang C.",Profiles of oral microbiota and metabolites in periodontitis and benign prostatic hyperplasia patients: a pilot study,Microbiology spectrum,2025,"benign prostatic hyperplasia, metabolites, microbiome, periodontitis",Experiment 1,China,Homo sapiens,Gingival groove,UBERON:0008805,Benign prostatic hyperplasia,EFO:0000284,Healthy group,Benign prostatic hyperplasia (BPH) group,Participants diagnosed with Benign prostatic hyperplasia (BPH),12,12,NA,16S,34,DNBSEQ-G400,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 2,28 October 2025,Firdaws,Firdaws,Significantly differential microorganisms (species level) among Benign prostatic hyperplasia (BPH) group and Healthy group,decreased,"k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema maltophilum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella halliae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Faucicola|s__Faucicola osloensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Limnobacter|s__Limnobacter alexandrii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles|s__Roseateles saccharophilus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chitinibacteraceae|g__Chitinimonas|s__Chitinimonas taiwanensis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas|s__Brevundimonas subvibrioides,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas koreensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Kytococcaceae|g__Kytococcus|s__Kytococcus sedentarius,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus|s__Paracoccus aminophilus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium|s__Brevibacterium pityocampae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium|s__Brachybacterium faecium",3379134|203691|203692|136|2845253|157|51160;3379134|1224|28216|206351|481|538|1795832;3379134|1224|1236|2887326|468|1604696|34062;3379134|1224|28216|80840|119060|131079|2570352;3379134|1224|28216|80840|2975441|93681|304;3379134|1224|28216|206351|2897177|240411|240412;3379134|1224|28211|204458|76892|41275|74313;3379134|1224|28211|204457|41297|13687|93064;1783272|201174|1760|85006|2805426|57499|1276;3379134|1224|28211|204455|31989|265|34003;1783272|201174|1760|85006|85019|1696|506594;1783272|201174|1760|85006|85020|43668|43669,Complete,KateRasheed
bsdb:40827923/2/1,40827923,case-control,40827923,https://doi.org/10.1128/spectrum.03376-24,NA,"Zhu C., Li L.-.Y., Li C., Wu L., Zhang Y.-.Y., Yao Y., Yang J., Wang S.-.Y., Xing L.-.M., Zeng X.-.T. , Fang C.",Profiles of oral microbiota and metabolites in periodontitis and benign prostatic hyperplasia patients: a pilot study,Microbiology spectrum,2025,"benign prostatic hyperplasia, metabolites, microbiome, periodontitis",Experiment 2,China,Homo sapiens,Gingival groove,UBERON:0008805,Periodontitis,EFO:0000649,Healthy group,Periodontitis group,Participants diagnosed with Periodontitis,12,12,NA,16S,34,DNBSEQ-G400,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,decreased,NA,NA,Signature 1,Figure 2,28 October 2025,Firdaws,Firdaws,Significantly differential microorganisms (species level) among Periodontitis group and Healthy group,increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella halliae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella|s__Johnsonella ignava,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Metaprevotella|s__Metaprevotella massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter|s__Peptoanaerobacter stomatis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas catoniae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Prevotella heparinolytica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Schwartzia|s__Schwartzia succinivorans,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas dianae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum longum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema socranskii",3379134|29547|3031852|213849|72294|194|199;3379134|29547|3031852|213849|72294|194|824;3379134|29547|3031852|213849|72294|194|2762557;3379134|976|117743|200644|49546|1016|45242;3379134|1224|28216|206351|481|538|1795832;3384194|508458|649775|649776|3029087|1434006|651822;3384189|32066|203490|203491|203492|848|851;1783272|1239|186801|3085636|186803|43994|43995;3384189|32066|203490|203491|1129771|32067|40542;3384189|32066|203490|203491|1129771|32067|157688;3379134|976|200643|171549|171552|1980689|1870999;1783272|1239|186801|3082720|3118655|1913599|796937;1783272|1239|186801|3082720|186804|1257|341694;3379134|976|200643|171549|171551|836|41976;3379134|976|200643|171549|171551|836|837;3379134|976|200643|171549|815|816|28113;1783272|1239|909932|909929|1843491|55506|55507;1783272|1239|909932|909929|1843491|970|135079;1783272|1239|186801|3085636|186803|1213720|796942;1783272|1239|91061|186826|1300|1301|76860;3379134|203691|203692|136|2845253|157|59892;3379134|203691|203692|136|2845253|157|53419,Complete,KateRasheed
bsdb:40827923/2/2,40827923,case-control,40827923,https://doi.org/10.1128/spectrum.03376-24,NA,"Zhu C., Li L.-.Y., Li C., Wu L., Zhang Y.-.Y., Yao Y., Yang J., Wang S.-.Y., Xing L.-.M., Zeng X.-.T. , Fang C.",Profiles of oral microbiota and metabolites in periodontitis and benign prostatic hyperplasia patients: a pilot study,Microbiology spectrum,2025,"benign prostatic hyperplasia, metabolites, microbiome, periodontitis",Experiment 2,China,Homo sapiens,Gingival groove,UBERON:0008805,Periodontitis,EFO:0000649,Healthy group,Periodontitis group,Participants diagnosed with Periodontitis,12,12,NA,16S,34,DNBSEQ-G400,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,decreased,NA,NA,Signature 2,Figure 2,28 October 2025,Firdaws,Firdaws,Significantly differential microorganisms (species level) among Periodontitis group and Healthy group,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas infelix,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema medium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas koreensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Kytococcaceae|g__Kytococcus|s__Kytococcus sedentarius,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus|s__Paracoccus aminophilus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas panni,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium|s__Brachybacterium faecium",1783272|1239|909932|909929|1843491|970|135082;1783272|1239|909932|909929|1843491|970|69823;1783272|1239|186801|3082720|3118655|44259|143361;3379134|203691|203692|136|2845253|157|158;3379134|203691|203692|136|2845253|157|58231;3379134|1224|28211|204457|41297|13687|93064;1783272|201174|1760|85006|2805426|57499|1276;3379134|1224|28211|204455|31989|265|34003;3379134|1224|28211|204457|41297|13687|237612;1783272|201174|1760|85006|85020|43668|43669,Complete,KateRasheed
bsdb:40827923/3/1,40827923,case-control,40827923,https://doi.org/10.1128/spectrum.03376-24,NA,"Zhu C., Li L.-.Y., Li C., Wu L., Zhang Y.-.Y., Yao Y., Yang J., Wang S.-.Y., Xing L.-.M., Zeng X.-.T. , Fang C.",Profiles of oral microbiota and metabolites in periodontitis and benign prostatic hyperplasia patients: a pilot study,Microbiology spectrum,2025,"benign prostatic hyperplasia, metabolites, microbiome, periodontitis",Experiment 3,China,Homo sapiens,Gingival groove,UBERON:0008805,"Benign prostatic hyperplasia,Periodontitis","EFO:0000284,EFO:0000649",Healthy group,Periodontitis combined with Benign prostatic hyperplasia (P-BPH) group,Participants diagnosed with Periodontitis and Benign prostatic hyperplasia (P-BPH),12,12,NA,16S,34,DNBSEQ-G400,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 2,28 October 2025,Firdaws,Firdaws,Significantly differential microorganisms (species level) among Periodontitis combined with Benign prostatic hyperplasia group (P-BPH) and Healthy group,increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter massiliensis,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Catonella|s__Catonella morbi,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus|s__Desulfobulbus oligotrophicus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella|s__Johnsonella ignava,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Metaprevotella|s__Metaprevotella massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus|s__Peptococcus simiae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema maltophilum,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema medium,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema socranskii",3379134|29547|3031852|213849|72294|194|824;3379134|29547|3031852|213849|72294|194|2762557;3379134|976|117743|200644|49546|1016|45242;1783272|1239|186801|3085636|186803|43996|43997;3379134|200940|3031451|3024411|213121|893|1909699;1783272|1239|186801|3082720|3118655|44259|143361;3384194|508458|649775|649776|3029087|1434006|651822;3384189|32066|203490|203491|203492|848|851;1783272|1239|186801|3085636|186803|43994|43995;3379134|976|200643|171549|171552|1980689|1870999;1783272|1239|186801|186802|186807|2740|1643805;1783272|1239|186801|3082720|186804|1257|341694;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|171551|836|837;3379134|976|200643|171549|171552|838|28131;3379134|976|200643|171549|2005525|195950|28112;3379134|203691|203692|136|2845253|157|59892;3379134|203691|203692|136|2845253|157|158;3379134|203691|203692|136|2845253|157|51160;3379134|203691|203692|136|2845253|157|58231;3379134|203691|203692|136|2845253|157|53419,Complete,KateRasheed
bsdb:40827923/3/2,40827923,case-control,40827923,https://doi.org/10.1128/spectrum.03376-24,NA,"Zhu C., Li L.-.Y., Li C., Wu L., Zhang Y.-.Y., Yao Y., Yang J., Wang S.-.Y., Xing L.-.M., Zeng X.-.T. , Fang C.",Profiles of oral microbiota and metabolites in periodontitis and benign prostatic hyperplasia patients: a pilot study,Microbiology spectrum,2025,"benign prostatic hyperplasia, metabolites, microbiome, periodontitis",Experiment 3,China,Homo sapiens,Gingival groove,UBERON:0008805,"Benign prostatic hyperplasia,Periodontitis","EFO:0000284,EFO:0000649",Healthy group,Periodontitis combined with Benign prostatic hyperplasia (P-BPH) group,Participants diagnosed with Periodontitis and Benign prostatic hyperplasia (P-BPH),12,12,NA,16S,34,DNBSEQ-G400,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 2,29 October 2025,Firdaws,Firdaws,Significantly differential microorganisms (species level) among Periodontitis combined with Benign prostatic hyperplasia group (P-BPH) and Healthy group,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter variabilis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter venetianus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chitinibacteraceae|g__Chitinimonas|s__Chitinimonas taiwanensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas aquatica,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus geothermalis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium longum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Faucicola|s__Faucicola osloensis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Kytococcaceae|g__Kytococcus|s__Kytococcus sedentarius,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus|s__Paracoccus aminophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas oryzihabitans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles|s__Roseateles saccharophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas koreensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Vogesella|s__Vogesella urethralis",3379134|1224|1236|2887326|468|469|70346;3379134|1224|1236|2887326|468|469|52133;3379134|976|200643|171549|815|816|46506;3379134|976|200643|171549|815|816|820;3379134|1224|28216|206351|2897177|240411|240412;3379134|1224|28216|80840|80864|283|225991;3384194|1297|188787|118964|183710|1298|68909;1783272|1239|909932|1843489|31977|39948|39950;1783272|1239|186801|186802|216572|216851|1851428;3379134|1224|1236|2887326|468|1604696|34062;1783272|201174|1760|85006|2805426|57499|1276;3379134|1224|28211|204455|31989|265|34003;3379134|1224|1236|72274|135621|286|287;3379134|1224|1236|72274|135621|286|47885;3379134|1224|28216|80840|2975441|93681|304;1783272|1239|909932|909929|1843491|970|69823;3379134|1224|28211|204457|41297|13687|93064;3379134|1224|28216|206351|1499392|57739|2592656,Complete,KateRasheed
bsdb:40827923/4/1,40827923,case-control,40827923,https://doi.org/10.1128/spectrum.03376-24,NA,"Zhu C., Li L.-.Y., Li C., Wu L., Zhang Y.-.Y., Yao Y., Yang J., Wang S.-.Y., Xing L.-.M., Zeng X.-.T. , Fang C.",Profiles of oral microbiota and metabolites in periodontitis and benign prostatic hyperplasia patients: a pilot study,Microbiology spectrum,2025,"benign prostatic hyperplasia, metabolites, microbiome, periodontitis",Experiment 4,China,Homo sapiens,Gingival groove,UBERON:0008805,"Benign prostatic hyperplasia,Periodontitis","EFO:0000284,EFO:0000649",Benign prostatic hyperplasia (BPH) group,Periodontitis combined with Benign prostatic hyperplasia (P-BPH) group,Participants diagnosed with Periodontitis and Benign prostatic hyperplasia (P-BPH),12,12,NA,16S,34,DNBSEQ-G400,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 2,28 October 2025,Firdaws,Firdaws,Significantly differential microorganisms (species level) among Periodontitis combined with Benign prostatic hyperplasia group (P-BPH) and BPH group,increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter massiliensis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus|s__Desulfobulbus oligotrophicus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema medium",3379134|29547|3031852|213849|72294|194|2762557;3379134|200940|3031451|3024411|213121|893|1909699;1783272|1239|186801|3082720|3118655|44259|143361;3384194|508458|649775|649776|3029087|1434006|651822;3379134|976|200643|171549|171551|836|837;3379134|976|200643|171549|2005525|195950|28112;3379134|203691|203692|136|2845253|157|58231,Complete,KateRasheed
bsdb:40827923/4/2,40827923,case-control,40827923,https://doi.org/10.1128/spectrum.03376-24,NA,"Zhu C., Li L.-.Y., Li C., Wu L., Zhang Y.-.Y., Yao Y., Yang J., Wang S.-.Y., Xing L.-.M., Zeng X.-.T. , Fang C.",Profiles of oral microbiota and metabolites in periodontitis and benign prostatic hyperplasia patients: a pilot study,Microbiology spectrum,2025,"benign prostatic hyperplasia, metabolites, microbiome, periodontitis",Experiment 4,China,Homo sapiens,Gingival groove,UBERON:0008805,"Benign prostatic hyperplasia,Periodontitis","EFO:0000284,EFO:0000649",Benign prostatic hyperplasia (BPH) group,Periodontitis combined with Benign prostatic hyperplasia (P-BPH) group,Participants diagnosed with Periodontitis and Benign prostatic hyperplasia (P-BPH),12,12,NA,16S,34,DNBSEQ-G400,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 2,29 October 2025,Firdaws,Firdaws,Significantly differential microorganisms (species level) among Periodontitis combined with Benign prostatic hyperplasia group (P-BPH) and BPH group,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hongkongensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas oryzihabitans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Vogesella|s__Vogesella urethralis",3379134|976|200643|171549|815|816|46506;3379134|976|117743|200644|49546|1016|1018;3384189|32066|203490|203491|1129771|32067|554406;3379134|1224|1236|72274|135621|286|287;3379134|1224|1236|72274|135621|286|47885;3379134|1224|28216|206351|1499392|57739|2592656,Complete,KateRasheed
bsdb:40827923/5/1,40827923,case-control,40827923,https://doi.org/10.1128/spectrum.03376-24,NA,"Zhu C., Li L.-.Y., Li C., Wu L., Zhang Y.-.Y., Yao Y., Yang J., Wang S.-.Y., Xing L.-.M., Zeng X.-.T. , Fang C.",Profiles of oral microbiota and metabolites in periodontitis and benign prostatic hyperplasia patients: a pilot study,Microbiology spectrum,2025,"benign prostatic hyperplasia, metabolites, microbiome, periodontitis",Experiment 5,China,Homo sapiens,Gingival groove,UBERON:0008805,"Periodontitis,Benign prostatic hyperplasia","EFO:0000649,EFO:0000284",Periodontitis group,Periodontitis combined with Benign prostatic hyperplasia (P-BPH) group,Participants diagnosed with Periodontitis and Benign prostatic hyperplasia (P-BPH),12,12,NA,16S,34,DNBSEQ-G400,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,increased,NA,NA,Signature 1,Figure 2,28 October 2025,Firdaws,Firdaws,Significantly differential microorganisms (species level) among Periodontitis combined with Benign prostatic hyperplasia group (P-BPH) and Periodontitis group,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia",1783272|1239|186801|3082720|3118655|44259|143361;3379134|976|200643|171549|2005525|195950|28112,Complete,KateRasheed
bsdb:40827923/5/2,40827923,case-control,40827923,https://doi.org/10.1128/spectrum.03376-24,NA,"Zhu C., Li L.-.Y., Li C., Wu L., Zhang Y.-.Y., Yao Y., Yang J., Wang S.-.Y., Xing L.-.M., Zeng X.-.T. , Fang C.",Profiles of oral microbiota and metabolites in periodontitis and benign prostatic hyperplasia patients: a pilot study,Microbiology spectrum,2025,"benign prostatic hyperplasia, metabolites, microbiome, periodontitis",Experiment 5,China,Homo sapiens,Gingival groove,UBERON:0008805,"Periodontitis,Benign prostatic hyperplasia","EFO:0000649,EFO:0000284",Periodontitis group,Periodontitis combined with Benign prostatic hyperplasia (P-BPH) group,Participants diagnosed with Periodontitis and Benign prostatic hyperplasia (P-BPH),12,12,NA,16S,34,DNBSEQ-G400,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,increased,NA,NA,Signature 2,Figure 2,29 October 2025,Firdaws,Firdaws,Significantly differential microorganisms (species level) among Periodontitis combined with Benign prostatic hyperplasia group (P-BPH) and Periodontitis group,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia rubra,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium longum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella loescheii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum umeaense,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella rimae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hongkongensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium asaccharolyticum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas catoniae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella aurantiaca,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas oryzihabitans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas noxia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella serpentiformis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Vogesella|s__Vogesella urethralis",1783272|201174|1760|85009|31957|2801844|1547448;3379134|976|200643|171549|815|816|46506;3379134|976|200643|171549|815|816|820;3379134|29547|3031852|213849|72294|194|199;3379134|976|117743|200644|49546|1016|1019;1783272|201174|1760|85007|1653|1716|43768;3379134|1224|1236|91347|543|547|158836;1783272|1239|186801|186802|216572|216851|1851428;3379134|976|200643|171549|171552|2974257|840;3379134|976|200643|171549|171552|2974257|425941;1783272|1239|186801|3085636|186803|1164882|617123;1783272|201174|84998|84999|1643824|2767353|1383;3384189|32066|203490|203491|1129771|32067|157688;3384189|32066|203490|203491|1129771|32067|554406;1783272|1239|186801|3085636|186803|265975|1501332;3379134|976|200643|171549|815|909656|357276;3379134|976|200643|171549|171551|836|41976;3379134|976|200643|171549|171552|838|596085;3379134|1224|1236|72274|135621|286|47885;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|909932|909929|1843491|970|135083;3379134|976|200643|171549|2005525|195950|712710;3379134|1224|28216|206351|1499392|57739|2592656,Complete,NA
bsdb:40827923/6/1,40827923,case-control,40827923,https://doi.org/10.1128/spectrum.03376-24,NA,"Zhu C., Li L.-.Y., Li C., Wu L., Zhang Y.-.Y., Yao Y., Yang J., Wang S.-.Y., Xing L.-.M., Zeng X.-.T. , Fang C.",Profiles of oral microbiota and metabolites in periodontitis and benign prostatic hyperplasia patients: a pilot study,Microbiology spectrum,2025,"benign prostatic hyperplasia, metabolites, microbiome, periodontitis",Experiment 6,China,Homo sapiens,Gingival groove,UBERON:0008805,Benign prostatic hyperplasia,EFO:0000284,Healthy group,Benign prostatic hyperplasia (BPH) group,Participants diagnosed with Benign prostatic hyperplasia (BPH),12,12,NA,16S,34,DNBSEQ-G400,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure S2B,29 October 2025,Firdaws,Firdaws,"Significantly differential microorganism (family, genus and species) in the Benign prostatic hyperplasia (BPH) group compared with the healthy group (BPH vs Healthy).",increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas infelix,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga",3379134|976|117743|200644|49546|1016|45242;1783272|1239|909932|909929|1843491|970|135082;3379134|976|117743|200644|49546;3379134|976|117743|200644|49546|1016,Complete,KateRasheed
bsdb:40827923/6/2,40827923,case-control,40827923,https://doi.org/10.1128/spectrum.03376-24,NA,"Zhu C., Li L.-.Y., Li C., Wu L., Zhang Y.-.Y., Yao Y., Yang J., Wang S.-.Y., Xing L.-.M., Zeng X.-.T. , Fang C.",Profiles of oral microbiota and metabolites in periodontitis and benign prostatic hyperplasia patients: a pilot study,Microbiology spectrum,2025,"benign prostatic hyperplasia, metabolites, microbiome, periodontitis",Experiment 6,China,Homo sapiens,Gingival groove,UBERON:0008805,Benign prostatic hyperplasia,EFO:0000284,Healthy group,Benign prostatic hyperplasia (BPH) group,Participants diagnosed with Benign prostatic hyperplasia (BPH),12,12,NA,16S,34,DNBSEQ-G400,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure S2B,29 October 2025,Firdaws,Firdaws,"Significantly differential microorganism (order, family, genus and species) in the Benign prostatic hyperplasia (BPH) group compared with the healthy group (BPH vs Healthy).",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Limnobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Limnobacter|s__Limnobacter alexandrii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus|s__Paracoccus aminophilus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales",3379134|1224|28211|204457|335929;3379134|1224|28216|80840|119060|131079;3379134|1224|28216|80840|119060|131079|2570352;1783272|201174|1760|85006|85023;3379134|1224|28211|204455|31989|265|34003;3379134|1224|28211|204457,Complete,KateRasheed
bsdb:40827923/7/1,40827923,case-control,40827923,https://doi.org/10.1128/spectrum.03376-24,NA,"Zhu C., Li L.-.Y., Li C., Wu L., Zhang Y.-.Y., Yao Y., Yang J., Wang S.-.Y., Xing L.-.M., Zeng X.-.T. , Fang C.",Profiles of oral microbiota and metabolites in periodontitis and benign prostatic hyperplasia patients: a pilot study,Microbiology spectrum,2025,"benign prostatic hyperplasia, metabolites, microbiome, periodontitis",Experiment 7,China,Homo sapiens,Gingival groove,UBERON:0008805,Periodontitis,EFO:0000649,Healthy group,Periodontitis group,Participants diagnosed with Periodontitis,12,12,NA,16S,34,DNBSEQ-G400,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,decreased,NA,NA,Signature 1,Figure S2C,29 October 2025,Firdaws,Firdaws,"Significantly differential microorganism (phylum, class, order, family, genus and species) in the Periodontitis group compared with the healthy group (Periodontitis vs Healthy).",increased,"k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter massiliensis,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Metaprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Metaprevotella|s__Metaprevotella massiliensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas dianae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia,k__Pseudomonadati|p__Spirochaetota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales,k__Thermotogati|p__Synergistota|c__Synergistia,k__Thermotogati|p__Synergistota,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema medium,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria",3379134|976;3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294|194|2762557;3379134|29547|3031852|213849|72294;3379134|29547|3031852|213849;3379134|29547;3379134|976|117743|200644|49546|1016|45242;1783272|1239|186801;1783272|1239|186801|186802;3379134|976|200643|171549|171552|2974257;3379134|976|200643|171549|171552|1980689;3379134|976|200643|171549|171552|1980689|1870999;1783272|1239|186801|3082720|186804;1783272|1239|186801|3082720|186804|1257;1783272|1239|186801|3082720|186804|1257|341694;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836;1783272|1239|909932|909929|1843491|970|135079;1783272|1239|909932|909929|1843491|970|69823;3379134|203691|203692|136;3379134|203691|203692;3379134|203691;1783272|1239|91061|186826|1300|1301|76860;3384194|508458|649775|649776|649777;3384194|508458|649775|649776;3384194|508458|649775;3384194|508458;3379134|203691|203692|136|2845253|157;3379134|203691|203692|136|2845253|157|59892;3379134|203691|203692|136|2845253|157|158;3379134|203691|203692|136|2845253|157|58231;3379134|203691|203692|136|2845253;3379134|29547|3031852,Complete,KateRasheed
bsdb:40827923/7/2,40827923,case-control,40827923,https://doi.org/10.1128/spectrum.03376-24,NA,"Zhu C., Li L.-.Y., Li C., Wu L., Zhang Y.-.Y., Yao Y., Yang J., Wang S.-.Y., Xing L.-.M., Zeng X.-.T. , Fang C.",Profiles of oral microbiota and metabolites in periodontitis and benign prostatic hyperplasia patients: a pilot study,Microbiology spectrum,2025,"benign prostatic hyperplasia, metabolites, microbiome, periodontitis",Experiment 7,China,Homo sapiens,Gingival groove,UBERON:0008805,Periodontitis,EFO:0000649,Healthy group,Periodontitis group,Participants diagnosed with Periodontitis,12,12,NA,16S,34,DNBSEQ-G400,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,decreased,NA,NA,Signature 2,Figure S2C,29 October 2025,Firdaws,Firdaws,"Significantly differential microorganism (order, family, genus and species) in the Periodontitis group compared with the healthy group (Periodontitis vs Healthy).",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium amycolatum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Pseudarthrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas panni,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingosinicellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Ureibacillus|s__Ureibacillus terrenus",1783272|201174|1760|85007|1653|1716|43765;3379134|1224|28211|204457|335929;1783272|201174|1760|85006|85023;1783272|201174|1760|85006|85023|33882;1783272|201174|1760|85006|1268|1742993;3379134|1224|28211|204457|41297;3379134|1224|28211|204457;3379134|1224|28211|204457|41297|13687;3379134|1224|28211|204457|41297|13687|237612;3379134|1224|28211|204457|2820280;1783272|1239|91061|1385|186818|160795|118246,Complete,KateRasheed
bsdb:40827923/8/1,40827923,case-control,40827923,https://doi.org/10.1128/spectrum.03376-24,NA,"Zhu C., Li L.-.Y., Li C., Wu L., Zhang Y.-.Y., Yao Y., Yang J., Wang S.-.Y., Xing L.-.M., Zeng X.-.T. , Fang C.",Profiles of oral microbiota and metabolites in periodontitis and benign prostatic hyperplasia patients: a pilot study,Microbiology spectrum,2025,"benign prostatic hyperplasia, metabolites, microbiome, periodontitis",Experiment 8,China,Homo sapiens,Gingival groove,UBERON:0008805,"Benign prostatic hyperplasia,Periodontitis","EFO:0000284,EFO:0000649",Benign prostatic hyperplasia (BPH) group,Periodontitis combined with Benign prostatic hyperplasia (P-BPH) group,Participants diagnosed with Periodontitis and Benign prostatic hyperplasia (P-BPH),12,12,NA,16S,34,DNBSEQ-G400,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure S2D,29 October 2025,Firdaws,Firdaws,"Significantly differential microorganisms ( class, order, family, genus and species level) among Periodontitis combined with Benign prostatic hyperplasia group (P-BPH) and Benign prostatic hyperplasia group (P-BPH vs BPH).",increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter massiliensis,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria",3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294|194|2762557;3379134|29547|3031852|213849|72294;3379134|29547|3031852|213849;3379134|29547;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836|837;3379134|976|200643|171549|2005525|195950|28112;3379134|29547|3031852,Complete,KateRasheed
bsdb:40827923/8/2,40827923,case-control,40827923,https://doi.org/10.1128/spectrum.03376-24,NA,"Zhu C., Li L.-.Y., Li C., Wu L., Zhang Y.-.Y., Yao Y., Yang J., Wang S.-.Y., Xing L.-.M., Zeng X.-.T. , Fang C.",Profiles of oral microbiota and metabolites in periodontitis and benign prostatic hyperplasia patients: a pilot study,Microbiology spectrum,2025,"benign prostatic hyperplasia, metabolites, microbiome, periodontitis",Experiment 8,China,Homo sapiens,Gingival groove,UBERON:0008805,"Benign prostatic hyperplasia,Periodontitis","EFO:0000284,EFO:0000649",Benign prostatic hyperplasia (BPH) group,Periodontitis combined with Benign prostatic hyperplasia (P-BPH) group,Participants diagnosed with Periodontitis and Benign prostatic hyperplasia (P-BPH),12,12,NA,16S,34,DNBSEQ-G400,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure S2D,29 October 2025,Firdaws,Firdaws,Significantly differential microorganisms (species level) among Periodontitis combined with Benign prostatic hyperplasia group (P-BPH) and Benign prostatic hyperplasia group (P-BPH vs BPH).,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas oryzihabitans,3379134|1224|1236|72274|135621|286|47885,Complete,KateRasheed
bsdb:40827923/9/1,40827923,case-control,40827923,https://doi.org/10.1128/spectrum.03376-24,NA,"Zhu C., Li L.-.Y., Li C., Wu L., Zhang Y.-.Y., Yao Y., Yang J., Wang S.-.Y., Xing L.-.M., Zeng X.-.T. , Fang C.",Profiles of oral microbiota and metabolites in periodontitis and benign prostatic hyperplasia patients: a pilot study,Microbiology spectrum,2025,"benign prostatic hyperplasia, metabolites, microbiome, periodontitis",Experiment 9,China,Homo sapiens,Gingival groove,UBERON:0008805,"Benign prostatic hyperplasia,Periodontitis","EFO:0000284,EFO:0000649",Benign prostatic hyperplasia (BPH) and Healthy group,Periodontitis combined with Benign prostatic hyperplasia (P-BPH) group,Participants diagnosed with Periodontitis and Benign prostatic hyperplasia (P-BPH),24,12,NA,16S,34,DNBSEQ-G400,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S2A,29 October 2025,Firdaws,Firdaws,"Significantly differential microorganisms (phylum, class, order, family, genus and species level) among Periodontitis combined with Benign prostatic hyperplasia group (P-BPH) and  Benign prostatic hyperplasia (BPH) and Healthy group (P-BPH vs BPH & Healthy).",increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter massiliensis,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobacteria|o__Desulfobacterales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfobulbia|o__Desulfobulbales|f__Desulfobulbaceae|g__Desulfobulbus|s__Desulfobulbus oligotrophicus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor alocis,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Bacillati|p__Mycoplasmatota|c__Mollicutes,k__Bacillati|p__Mycoplasmatota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia,k__Pseudomonadati|p__Spirochaetota,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales,k__Thermotogati|p__Synergistota|c__Synergistia,k__Thermotogati|p__Synergistota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema medium,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria",3379134|29547|3031852|213849|72294|194;3379134|29547|3031852|213849|72294|194|2762557;3379134|29547|3031852|213849|72294;3379134|29547|3031852|213849;3379134|29547;28221;3379134|200940|3024418|213118;3379134|200940|3031451|3024411|213121;3379134|200940|3031451|3024411|213121|893;3379134|200940|3031451|3024411|213121|893|1909699;1783272|1239|186801|3082720|3118655|44259;1783272|1239|186801|3082720|3118655|44259|143361;3384194|508458|649775|649776|3029087|1434006;3384194|508458|649775|649776|3029087|1434006|651822;1783272|544448|31969;1783272|544448;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171551;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171551|836|837;3379134|203691|203692|136;3379134|203691|203692;3379134|203691;3384194|508458|649775|649776|649777;3384194|508458|649775|649776;3384194|508458|649775;3384194|508458;3379134|976|200643|171549|2005525|195950|28112;3379134|203691|203692|136|2845253|157;3379134|203691|203692|136|2845253|157|158;3379134|203691|203692|136|2845253|157|58231;3379134|203691|203692|136|2845253;3379134|29547|3031852,Complete,KateRasheed
bsdb:40827923/10/1,40827923,case-control,40827923,https://doi.org/10.1128/spectrum.03376-24,NA,"Zhu C., Li L.-.Y., Li C., Wu L., Zhang Y.-.Y., Yao Y., Yang J., Wang S.-.Y., Xing L.-.M., Zeng X.-.T. , Fang C.",Profiles of oral microbiota and metabolites in periodontitis and benign prostatic hyperplasia patients: a pilot study,Microbiology spectrum,2025,"benign prostatic hyperplasia, metabolites, microbiome, periodontitis",Experiment 10,China,Homo sapiens,Gingival groove,UBERON:0008805,Benign prostatic hyperplasia,EFO:0000284,Periodontitis combined with Benign prostatic hyperplasia (P-BPH) and Healthy group,Benign prostatic hyperplasia (BPH) group,Participants diagnosed with Benign prostatic hyperplasia (BPH),24,12,NA,16S,34,DNBSEQ-G400,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S2A,15 December 2025,Firdaws,Firdaws,"Significantly differential microorganisms (family, genus and species level) among Benign prostatic hyperplasia (BPH) and Periodontitis combined with Benign prostatic hyperplasia group (P-BPH) and Healthy group (BPH vs P-BPH & Healthy).",increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae",3379134|976|117743|200644|49546|1016;3379134|976|117743|200644|49546|1016|45242;3379134|976|117743|200644|49546,Complete,KateRasheed
bsdb:40827923/11/1,40827923,case-control,40827923,https://doi.org/10.1128/spectrum.03376-24,NA,"Zhu C., Li L.-.Y., Li C., Wu L., Zhang Y.-.Y., Yao Y., Yang J., Wang S.-.Y., Xing L.-.M., Zeng X.-.T. , Fang C.",Profiles of oral microbiota and metabolites in periodontitis and benign prostatic hyperplasia patients: a pilot study,Microbiology spectrum,2025,"benign prostatic hyperplasia, metabolites, microbiome, periodontitis",Experiment 11,China,Homo sapiens,Gingival groove,UBERON:0008805,"Periodontitis,Benign prostatic hyperplasia","EFO:0000649,EFO:0000284",Periodontitis combined with Benign prostatic hyperplasia (P-BPH) and Benign prostatic hyperplasia (BPH) group,Healthy group,Healthy participants not diagnosed with Benign prostatic hyperplasia (BPH) or Periodontitis combined with BPH group (P-BPH),24,12,NA,16S,34,DNBSEQ-G400,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S2A,15 December 2025,Firdaws,Firdaws,"Significantly differential microorganisms (order, family, genus and species level) among Periodontitis combined with  Benign prostatic hyperplasia group (P-BPH) and Benign prostatic hyperplasia (BPH) and Healthy group (Healthy vs P-BPH & BPH).",increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chitinibacteraceae|g__Chitinimonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chitinibacteraceae|g__Chitinimonas|s__Chitinimonas taiwanensis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas koreensis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingosinicellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Ureibacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Ureibacillus|s__Ureibacillus terrenus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Vogesella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Vogesella|s__Vogesella urethralis",1783272|1239|91061|1385|186818;3379134|1224|28216|206351|2897177|240411;3379134|1224|28216|206351|2897177|240411|240412;3379134|1224|28216|206351|1499392;3379134|1224|28211|204457|335929;3379134|1224|28211|204457;3379134|1224|28211|204457|41297|13687;3379134|1224|28211|204457|41297|13687|93064;3379134|1224|28211|204457|2820280;1783272|1239|91061|1385|186818|160795;1783272|1239|91061|1385|186818|160795|118246;3379134|1224|28216|206351|1499392|57739;3379134|1224|28216|206351|1499392|57739|2592656,Complete,KateRasheed
bsdb:40849619/1/1,40849619,"cross-sectional observational, not case-control",40849619,https://doi.org/10.1186/s12866-025-04325-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04325-5#citeas,"Yang Y., Shen J., Wei S., Ye M., Zhao X., Zhou J., Tong L., Hu J., Song Y., Wu S. , Xu N.",Characteristics of gut and lung microbiota in patients with lung masses and their relationship with clinical features,BMC microbiology,2025,"Clinical features, Gut microbiota, Lung masses, Lung microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Lung carcinoma,EFO:0001071,Benign mass,Malignant mass,Patients with malignant lung masses in the feces group,190,48,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,Supplementary Figure 2B,14 October 2025,EniolaAde,EniolaAde,Microbiota composition analysis of feces group in patients with benign and malignant masses at species level,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium ulcerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__uncultured Adlercreutzia sp.,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__uncultured Bilophila sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__uncultured Blautia sp.,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__uncultured Holdemanella sp.",1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|3085636|186803|189330|39486;3384189|32066|203490|203491|203492|848|861;1783272|1239|186801|3085636|186803|248744;1783272|201174|84998|1643822|1643826|447020|875803;3379134|200940|3031449|213115|194924|35832|529385;1783272|1239|186801|3085636|186803|572511|765821;1783272|1239|526524|526525|128827|1573535|1763549,Complete,Folakunmi
bsdb:40849619/1/2,40849619,"cross-sectional observational, not case-control",40849619,https://doi.org/10.1186/s12866-025-04325-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04325-5#citeas,"Yang Y., Shen J., Wei S., Ye M., Zhao X., Zhou J., Tong L., Hu J., Song Y., Wu S. , Xu N.",Characteristics of gut and lung microbiota in patients with lung masses and their relationship with clinical features,BMC microbiology,2025,"Clinical features, Gut microbiota, Lung masses, Lung microbiota",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Lung carcinoma,EFO:0001071,Benign mass,Malignant mass,Patients with malignant lung masses in the feces group,190,48,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 2,Supplementary Figure 2B,14 October 2025,EniolaAde,EniolaAde,Microbiota composition analysis of feces group in patients with benign and malignant masses at species level,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__uncultured Dorea sp.,1783272|1239|186801|3085636|186803|189330|286138,Complete,Folakunmi
bsdb:40849619/2/1,40849619,"cross-sectional observational, not case-control",40849619,https://doi.org/10.1186/s12866-025-04325-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04325-5#citeas,"Yang Y., Shen J., Wei S., Ye M., Zhao X., Zhou J., Tong L., Hu J., Song Y., Wu S. , Xu N.",Characteristics of gut and lung microbiota in patients with lung masses and their relationship with clinical features,BMC microbiology,2025,"Clinical features, Gut microbiota, Lung masses, Lung microbiota",Experiment 2,China,Homo sapiens,Alveolus of lung,UBERON:0002299,Lung carcinoma,EFO:0001071,Benign mass,Malignant mass,Patients with malignant lung masses in the bronchoalveolar lavage fluid (BALF) group,26,8,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,Supplementary Figure 2D,14 October 2025,EniolaAde,EniolaAde,Microbiota composition analysis of bronchoalveolar lavage fluid (BALF) group in patients with benign and malignant masses at species level,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__uncultured Muribaculaceae bacterium,3379134|976|200643|171549|2005473|2301481,Complete,Folakunmi
bsdb:40849619/2/2,40849619,"cross-sectional observational, not case-control",40849619,https://doi.org/10.1186/s12866-025-04325-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04325-5#citeas,"Yang Y., Shen J., Wei S., Ye M., Zhao X., Zhou J., Tong L., Hu J., Song Y., Wu S. , Xu N.",Characteristics of gut and lung microbiota in patients with lung masses and their relationship with clinical features,BMC microbiology,2025,"Clinical features, Gut microbiota, Lung masses, Lung microbiota",Experiment 2,China,Homo sapiens,Alveolus of lung,UBERON:0002299,Lung carcinoma,EFO:0001071,Benign mass,Malignant mass,Patients with malignant lung masses in the bronchoalveolar lavage fluid (BALF) group,26,8,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 2,Supplementary Figure 2D,15 October 2025,EniolaAde,EniolaAde,Microbiota composition analysis of bronchoalveolar lavage fluid (BALF) group in patients with benign and malignant masses at species level,decreased,"p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral clone DR034,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella loescheii,p__Candidatus Saccharimonadota",95818|163602;3384189|32066|203490|203491|1129771|32067;1783272|201174|1760|2037|2049|2529408|1660;1783272|201174|84998|84999|1643824|1380;3379134|976|200643|171549|171552|2974257|840;95818,Complete,Folakunmi
bsdb:40849619/3/1,40849619,"cross-sectional observational, not case-control",40849619,https://doi.org/10.1186/s12866-025-04325-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04325-5#citeas,"Yang Y., Shen J., Wei S., Ye M., Zhao X., Zhou J., Tong L., Hu J., Song Y., Wu S. , Xu N.",Characteristics of gut and lung microbiota in patients with lung masses and their relationship with clinical features,BMC microbiology,2025,"Clinical features, Gut microbiota, Lung masses, Lung microbiota",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Lung carcinoma,EFO:0001071,Benign mass,Malignant mass,Patients with malignant lung masses in the feces group,190,48,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,Figure 3C,14 October 2025,EniolaAde,EniolaAde,Differential taxa using Linear discriminant analysis effect size (LEfSe) between benign and malignant masses in feces group,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium ulcerans,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__uncultured Adlercreutzia sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__uncultured Blautia sp.,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__uncultured Holdemanella sp.",1783272|201174|84998|1643822|1643826|447020;1783272|1239;1783272|201174|84998|1643822|1643826;3384189|32066|203490|203491|203492|848|861;1783272|1239|526524|526525|128827|1573535;1783272|1239|909932|909929|1843491;1783272|201174|84998|1643822|1643826|447020|875803;1783272|1239|186801|3085636|186803|572511|765821;1783272|1239|526524|526525|128827|1573535|1763549,Complete,Folakunmi
bsdb:40849619/3/2,40849619,"cross-sectional observational, not case-control",40849619,https://doi.org/10.1186/s12866-025-04325-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04325-5#citeas,"Yang Y., Shen J., Wei S., Ye M., Zhao X., Zhou J., Tong L., Hu J., Song Y., Wu S. , Xu N.",Characteristics of gut and lung microbiota in patients with lung masses and their relationship with clinical features,BMC microbiology,2025,"Clinical features, Gut microbiota, Lung masses, Lung microbiota",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Lung carcinoma,EFO:0001071,Benign mass,Malignant mass,Patients with malignant lung masses in the feces group,190,48,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 2,Figure 3C,14 October 2025,EniolaAde,EniolaAde,Differential taxa using Linear discriminant analysis effect size (LEfSe) between benign and malignant masses in feces group,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__uncultured Dorea sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. FJAT-27916",1783272|1239|186801|3085636|186803|189330|286138;1783272|1239|186801|3085636|186803|189330;1783272|1239|91061|1385|186817|1386|1679169,Complete,Folakunmi
bsdb:40849619/4/1,40849619,"cross-sectional observational, not case-control",40849619,https://doi.org/10.1186/s12866-025-04325-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04325-5#citeas,"Yang Y., Shen J., Wei S., Ye M., Zhao X., Zhou J., Tong L., Hu J., Song Y., Wu S. , Xu N.",Characteristics of gut and lung microbiota in patients with lung masses and their relationship with clinical features,BMC microbiology,2025,"Clinical features, Gut microbiota, Lung masses, Lung microbiota",Experiment 4,China,Homo sapiens,Alveolus of lung,UBERON:0002299,Lung carcinoma,EFO:0001071,Benign mass,Malignant mass,Patients with malignant lung masses in the bronchoalveolar lavage fluid (BALF) group,26,8,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,Figure 3D,14 October 2025,EniolaAde,EniolaAde,Differential taxa using Linear discriminant analysis effect size (LEfSe) between benign and malignant masses in bronchoalveolar lavage fluid (BALF) group,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] brachy,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|s__uncultured Muribaculaceae bacterium",1783272|1239|186801|3085636|186803;3379134|1224;1783272|1239|186801|3082720|543314|35517;3379134|976|200643|171549|2005473|2301481,Complete,Folakunmi
bsdb:40849619/4/2,40849619,"cross-sectional observational, not case-control",40849619,https://doi.org/10.1186/s12866-025-04325-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04325-5#citeas,"Yang Y., Shen J., Wei S., Ye M., Zhao X., Zhou J., Tong L., Hu J., Song Y., Wu S. , Xu N.",Characteristics of gut and lung microbiota in patients with lung masses and their relationship with clinical features,BMC microbiology,2025,"Clinical features, Gut microbiota, Lung masses, Lung microbiota",Experiment 4,China,Homo sapiens,Alveolus of lung,UBERON:0002299,Lung carcinoma,EFO:0001071,Benign mass,Malignant mass,Patients with malignant lung masses in the bronchoalveolar lavage fluid (BALF) group,26,8,2 weeks,16S,34,Illumina,relative abundances,LEfSe,0.05,NA,3,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 2,Figure 3D,14 October 2025,EniolaAde,EniolaAde,Differential taxa using Linear discriminant analysis effect size (LEfSe) between benign and malignant masses in bronchoalveolar lavage fluid (BALF) group,decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,p__Candidatus Saccharimonadota,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,p__Candidatus Saccharimonadota|s__TM7 phylum sp. oral clone DR034,p__Candidatus Saccharimonadota",1783272|1239;3379134|29547|3031852|213849|72294;95818;1783272|1239|909932|1843489|31977|906;1783272|1239|909932|1843489|31977|906|187326;95818|163602;95818,Complete,Folakunmi
bsdb:40849619/5/1,40849619,"cross-sectional observational, not case-control",40849619,https://doi.org/10.1186/s12866-025-04325-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04325-5#citeas,"Yang Y., Shen J., Wei S., Ye M., Zhao X., Zhou J., Tong L., Hu J., Song Y., Wu S. , Xu N.",Characteristics of gut and lung microbiota in patients with lung masses and their relationship with clinical features,BMC microbiology,2025,"Clinical features, Gut microbiota, Lung masses, Lung microbiota",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Lung carcinoma,EFO:0001071,Small cell lung cancer (SCLC),Non-small cell lung cancer (NSCLC),Patients with non-small cell lung cancer (NSCLC) in the feces group,29,155,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4A,15 October 2025,EniolaAde,EniolaAde,Differential abundance between small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC) in feces group,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus",3379134|976|200643|171549|815|816;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|3085642|580596,Complete,Folakunmi
bsdb:40849619/5/2,40849619,"cross-sectional observational, not case-control",40849619,https://doi.org/10.1186/s12866-025-04325-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04325-5#citeas,"Yang Y., Shen J., Wei S., Ye M., Zhao X., Zhou J., Tong L., Hu J., Song Y., Wu S. , Xu N.",Characteristics of gut and lung microbiota in patients with lung masses and their relationship with clinical features,BMC microbiology,2025,"Clinical features, Gut microbiota, Lung masses, Lung microbiota",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Lung carcinoma,EFO:0001071,Small cell lung cancer (SCLC),Non-small cell lung cancer (NSCLC),Patients with non-small cell lung cancer (NSCLC) in the feces group,29,155,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4A,15 October 2025,EniolaAde,EniolaAde,Differential abundance between small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC) in feces group,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Anaerobiospirillum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Succiniclasticum",3379134|1224|1236|72274|135621|286;3379134|1224|1236|135624|83763|13334;1783272|1239|186801|186802|216572|1892380;1783272|201174|84998|84999|1643824;1783272|1239|909932|1843488|909930|40840,Complete,Folakunmi
bsdb:40849619/6/1,40849619,"cross-sectional observational, not case-control",40849619,https://doi.org/10.1186/s12866-025-04325-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04325-5#citeas,"Yang Y., Shen J., Wei S., Ye M., Zhao X., Zhou J., Tong L., Hu J., Song Y., Wu S. , Xu N.",Characteristics of gut and lung microbiota in patients with lung masses and their relationship with clinical features,BMC microbiology,2025,"Clinical features, Gut microbiota, Lung masses, Lung microbiota",Experiment 6,China,Homo sapiens,Alveolus of lung,UBERON:0002299,Lung carcinoma,EFO:0001071,Small cell lung cancer (NSCLC),Non-small cell lung cancer (NSCLC),Patients with non-small cell lung cancer (NSCLC) in the bronchoalveolar lavage fluid (BALF) group,6,20,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,15 October 2025,EniolaAde,EniolaAde,Differential abundance at the genus level between small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC) in  bronchoalveolar lavage fluid (BALF) group,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Pseudomonadati|p__Pseudomonadota",3379134|1224|28211|204458|76892|41275;1783272|1117;3379134|1224|28211|204455|31989|265;3379134|1224,Complete,Folakunmi
bsdb:40849619/6/2,40849619,"cross-sectional observational, not case-control",40849619,https://doi.org/10.1186/s12866-025-04325-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04325-5#citeas,"Yang Y., Shen J., Wei S., Ye M., Zhao X., Zhou J., Tong L., Hu J., Song Y., Wu S. , Xu N.",Characteristics of gut and lung microbiota in patients with lung masses and their relationship with clinical features,BMC microbiology,2025,"Clinical features, Gut microbiota, Lung masses, Lung microbiota",Experiment 6,China,Homo sapiens,Alveolus of lung,UBERON:0002299,Lung carcinoma,EFO:0001071,Small cell lung cancer (NSCLC),Non-small cell lung cancer (NSCLC),Patients with non-small cell lung cancer (NSCLC) in the bronchoalveolar lavage fluid (BALF) group,6,20,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4B,15 October 2025,EniolaAde,EniolaAde,Differential abundance at the genus level between small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC) in  bronchoalveolar lavage fluid (BALF) group,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|s__uncultured Leptotrichiaceae bacterium",1783272|1239|186801|3085636|186803|43994;1783272|1239|186801|3085636|186803|33042;3379134|203691|203692|136|2845253|157;3384189|32066|203490|203491|1129771|1334014,Complete,Folakunmi
bsdb:40849619/7/1,40849619,"cross-sectional observational, not case-control",40849619,https://doi.org/10.1186/s12866-025-04325-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04325-5#citeas,"Yang Y., Shen J., Wei S., Ye M., Zhao X., Zhou J., Tong L., Hu J., Song Y., Wu S. , Xu N.",Characteristics of gut and lung microbiota in patients with lung masses and their relationship with clinical features,BMC microbiology,2025,"Clinical features, Gut microbiota, Lung masses, Lung microbiota",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Smoking status measurement,EFO:0006527,Non smoking,Smoking,Lung cancer patients with a history of smoking in the feces group,146,44,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4C,15 October 2025,EniolaAde,EniolaAde,Differential abundance at genus level between non smoking and smoking lung cancer patients in the feces group,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|244127;1783272|201174|84998|84999|1643824|1380;3379134|976|200643|171549|2005525|375288,Complete,Folakunmi
bsdb:40849619/7/2,40849619,"cross-sectional observational, not case-control",40849619,https://doi.org/10.1186/s12866-025-04325-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04325-5#citeas,"Yang Y., Shen J., Wei S., Ye M., Zhao X., Zhou J., Tong L., Hu J., Song Y., Wu S. , Xu N.",Characteristics of gut and lung microbiota in patients with lung masses and their relationship with clinical features,BMC microbiology,2025,"Clinical features, Gut microbiota, Lung masses, Lung microbiota",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Smoking status measurement,EFO:0006527,Non smoking,Smoking,Lung cancer patients with a history of smoking in the feces group,146,44,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4C,15 October 2025,EniolaAde,EniolaAde,Differential abundance at genus between non smoking and smoking lung cancer patients in the feces group,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,1783272|1239|186801|3085636|186803|207244,Complete,Folakunmi
bsdb:40849619/9/1,40849619,"cross-sectional observational, not case-control",40849619,https://doi.org/10.1186/s12866-025-04325-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04325-5#citeas,"Yang Y., Shen J., Wei S., Ye M., Zhao X., Zhou J., Tong L., Hu J., Song Y., Wu S. , Xu N.",Characteristics of gut and lung microbiota in patients with lung masses and their relationship with clinical features,BMC microbiology,2025,"Clinical features, Gut microbiota, Lung masses, Lung microbiota",Experiment 9,China,Homo sapiens,Alveolus of lung,UBERON:0002299,Smoking status measurement,EFO:0006527,Non smoking,Smoking,Lung cancer patients with a history of smoking in the the bronchoalveolar lavage fluid (BALF) group,13,13,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4D,16 October 2025,EniolaAde,EniolaAde,Differential abundance between non smoking and smoking lung cancer patients in bronchoalveolar lavage fluid (BALF) group,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Nevskiales|f__Nevskiaceae|g__Nevskia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Sphaerochaetaceae|g__Sphaerochaeta,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Sphaerotilus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|201174|84998|84999|84107|102106;3379134|1224|28216|80840|119060|106589;3379134|1224|1236|1775403|568386|64001;3379134|976|200643|171549|815|909656;3379134|203691|203692|136|2791015|399320;3379134|1224|28216|80840|2975441|34102;1783272|1239|526524|526525|2810281|191303;3379134|976|200643|171549|171552|838,Complete,Folakunmi
bsdb:40849619/9/2,40849619,"cross-sectional observational, not case-control",40849619,https://doi.org/10.1186/s12866-025-04325-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04325-5#citeas,"Yang Y., Shen J., Wei S., Ye M., Zhao X., Zhou J., Tong L., Hu J., Song Y., Wu S. , Xu N.",Characteristics of gut and lung microbiota in patients with lung masses and their relationship with clinical features,BMC microbiology,2025,"Clinical features, Gut microbiota, Lung masses, Lung microbiota",Experiment 9,China,Homo sapiens,Alveolus of lung,UBERON:0002299,Smoking status measurement,EFO:0006527,Non smoking,Smoking,Lung cancer patients with a history of smoking in the the bronchoalveolar lavage fluid (BALF) group,13,13,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4D,16 October 2025,EniolaAde,EniolaAde,Differential abundance between non smoking and smoking lung cancer patients in bronchoalveolar lavage fluid (BALF) group,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia",3379134|1224|28216|80840|80864|283;1783272|201174|1760|85004|31953|196081,Complete,Folakunmi
bsdb:40849619/10/1,40849619,"cross-sectional observational, not case-control",40849619,https://doi.org/10.1186/s12866-025-04325-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04325-5#citeas,"Yang Y., Shen J., Wei S., Ye M., Zhao X., Zhou J., Tong L., Hu J., Song Y., Wu S. , Xu N.",Characteristics of gut and lung microbiota in patients with lung masses and their relationship with clinical features,BMC microbiology,2025,"Clinical features, Gut microbiota, Lung masses, Lung microbiota",Experiment 10,China,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Partial response (PR)_Complete response (CR),Stable disease (SD),Lung cancer patients with stable disease who responded to chemotherapy combined with immunotherapy in feces group,46,32,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4E,16 October 2025,EniolaAde,EniolaAde,Differential abundance between lung cancer patients who had partial response_complete response and stable disease in response to chemotherapy combined with immunotherapy in feces group,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus",3379134|1224|28216|80840|80864|80865;3379134|1224|28211|204455|31989|265,Complete,Folakunmi
bsdb:40849619/10/2,40849619,"cross-sectional observational, not case-control",40849619,https://doi.org/10.1186/s12866-025-04325-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04325-5#citeas,"Yang Y., Shen J., Wei S., Ye M., Zhao X., Zhou J., Tong L., Hu J., Song Y., Wu S. , Xu N.",Characteristics of gut and lung microbiota in patients with lung masses and their relationship with clinical features,BMC microbiology,2025,"Clinical features, Gut microbiota, Lung masses, Lung microbiota",Experiment 10,China,Homo sapiens,Feces,UBERON:0001988,Treatment outcome measurement,EFO:0008383,Partial response (PR)_Complete response (CR),Stable disease (SD),Lung cancer patients with stable disease who responded to chemotherapy combined with immunotherapy in feces group,46,32,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4E,16 October 2025,EniolaAde,EniolaAde,Differential abundance between lung cancer patients who had partial response_complete response and stable disease in response to chemotherapy combined with immunotherapy in feces group,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila",1783272|1239|186801|3085636|186803|1769710;1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|186802|216572|236752,Complete,Folakunmi
bsdb:40849619/11/1,40849619,"cross-sectional observational, not case-control",40849619,https://doi.org/10.1186/s12866-025-04325-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04325-5#citeas,"Yang Y., Shen J., Wei S., Ye M., Zhao X., Zhou J., Tong L., Hu J., Song Y., Wu S. , Xu N.",Characteristics of gut and lung microbiota in patients with lung masses and their relationship with clinical features,BMC microbiology,2025,"Clinical features, Gut microbiota, Lung masses, Lung microbiota",Experiment 11,China,Homo sapiens,Alveolus of lung,UBERON:0002299,Treatment outcome measurement,EFO:0008383,Partial response (PR)_Complete response (CR),Stable disease (SD),Lung cancer patients with stable disease who responded to chemotherapy combined with immunotherapy in bronchoalveolar lavage fluid (BALF) group,4,6,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4F,16 October 2025,EniolaAde,EniolaAde,Differential abundance between lung cancer patients who had partial response_complete response and stable disease in response to chemotherapy combined with immunotherapy in the bronchoalveolar lavage fluid (BALF) group,increased,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,3379134|1224|28211|204457|41297|13687,Complete,Folakunmi
bsdb:40849619/11/2,40849619,"cross-sectional observational, not case-control",40849619,https://doi.org/10.1186/s12866-025-04325-5,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04325-5#citeas,"Yang Y., Shen J., Wei S., Ye M., Zhao X., Zhou J., Tong L., Hu J., Song Y., Wu S. , Xu N.",Characteristics of gut and lung microbiota in patients with lung masses and their relationship with clinical features,BMC microbiology,2025,"Clinical features, Gut microbiota, Lung masses, Lung microbiota",Experiment 11,China,Homo sapiens,Alveolus of lung,UBERON:0002299,Treatment outcome measurement,EFO:0008383,Partial response (PR)_Complete response (CR),Stable disease (SD),Lung cancer patients with stable disease who responded to chemotherapy combined with immunotherapy in bronchoalveolar lavage fluid (BALF) group,4,6,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4F,16 October 2025,EniolaAde,EniolaAde,Differential abundance between lung cancer patients who had partial response_complete response and stable disease in response to chemotherapy combined with immunotherapy in the bronchoalveolar lavage fluid (BALF) group,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",3379134|976|200643|171549|171552|1283313;3379134|976|117743|200644|2762318|59735;3379134|976|117743|200644|49546|1016;3379134|1224|28216|80840|80864|283;3379134|1224|28216|80840|119060|47670;1783272|1239|909932|909929|1843491|970;1783272|1239|909932|909929|1843491|970,Complete,Folakunmi
bsdb:40851038/1/1,40851038,laboratory experiment,40851038,https://doi.org/10.1038/s41522-025-00811-w,NA,"Binyamin D., Turjeman S., Asulin N., Schweitzer R. , Koren O.",The microbiome is associated with obesity-related metabolome signature in the process of aging,NPJ biofilms and microbiomes,2025,NA,Experiment 1,Israel,Mus musculus,Feces,UBERON:0001988,Aging,GO:0007568,Young mice (8 weeks old),Aged mice (18 months old),Aged mice refers to 18-month-old conventionally raised female Swiss-Webster mice,30,30,NA,16S,4,Illumina,log transformation,ANCOM-BC,0.001,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2D/ Supplementary Table 2,17 October 2025,Jesulolufemi,"Jesulolufemi,Anne-mariesharp",Log fold change of significantly differentially abundant taxa identified by analysis of microbiome composition with bias correction (ANCOM-BC),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|841;1783272|1239|526524|526525|2810281|191303;3379134|1224|1236|91347|543,Complete,Svetlana up
bsdb:40851038/1/2,40851038,laboratory experiment,40851038,https://doi.org/10.1038/s41522-025-00811-w,NA,"Binyamin D., Turjeman S., Asulin N., Schweitzer R. , Koren O.",The microbiome is associated with obesity-related metabolome signature in the process of aging,NPJ biofilms and microbiomes,2025,NA,Experiment 1,Israel,Mus musculus,Feces,UBERON:0001988,Aging,GO:0007568,Young mice (8 weeks old),Aged mice (18 months old),Aged mice refers to 18-month-old conventionally raised female Swiss-Webster mice,30,30,NA,16S,4,Illumina,log transformation,ANCOM-BC,0.001,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2D/ Supplementary Table 2,17 October 2025,Jesulolufemi,Jesulolufemi,Log fold change of significantly differentially abundant taxa identified by analysis of microbiome composition with bias correction (ANCOM-BC),decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",1783272|201174|84998|1643822|1643826|447020;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|189330;3379134|976|200643|171549|171552|838;3379134|976|200643|171549;3379134|976|200643|171549|171550,Complete,Svetlana up
bsdb:40851038/2/1,40851038,laboratory experiment,40851038,https://doi.org/10.1038/s41522-025-00811-w,NA,"Binyamin D., Turjeman S., Asulin N., Schweitzer R. , Koren O.",The microbiome is associated with obesity-related metabolome signature in the process of aging,NPJ biofilms and microbiomes,2025,NA,Experiment 2,Israel,Mus musculus,Feces,UBERON:0001988,Aging,GO:0007568,Young mice (8 weeks old),Aged mice (18 months old),Aged mice refers to 18-month-old conventionally raised female Swiss-Webster mice,30,30,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S5B,16 November 2025,Jesulolufemi,"Jesulolufemi,Anne-mariesharp",Relative abundance of linoleic correlated bacteria in young and aged mice,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,1783272|1239|186801|186802|216572|119852,Complete,Svetlana up
bsdb:40879391/1/1,40879391,prospective cohort,40879391,10.1111/all.70033,NA,"Devotta H., Lavelle A., Korpela K., Hurley S., Shannon E., Lunjani N., Ambikan A., Neogi U., Venter C., Walter J., Hourihane J. , O'Mahony L.",Microbial Sharing Between Siblings Supports Metabolic Functions Protective Against Allergy,Allergy,2025,"environment, food allergy, hygiene hypothesis, microbiome",Experiment 1,Ireland,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Infants without siblings at 6 months of age,Infants with siblings at 6 months of age,"Infants with older siblings where 130 had one sibling, 41 had two siblings, and 16 had three siblings",164,187,1 month,WMS,NA,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"breast feeding,mode of birth",NA,unchanged,NA,unchanged,unchanged,unchanged,Signature 1,"Figure 1C, Supplementary Table 2",17 November 2025,Tosin,Tosin,Individual FDR (false discovery rate) adjusted significant taxa differences for 6 months of age,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta",3379134|976|200643|171549|815|816|817;1783272|201174|1760|85004|31953|1678|1681;1783272|201174|1760|85004|31953|1678|1685;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|28026;1783272|201174|84998|1643822|1643826|84111|84112,Complete,KateRasheed
bsdb:40879391/1/2,40879391,prospective cohort,40879391,10.1111/all.70033,NA,"Devotta H., Lavelle A., Korpela K., Hurley S., Shannon E., Lunjani N., Ambikan A., Neogi U., Venter C., Walter J., Hourihane J. , O'Mahony L.",Microbial Sharing Between Siblings Supports Metabolic Functions Protective Against Allergy,Allergy,2025,"environment, food allergy, hygiene hypothesis, microbiome",Experiment 1,Ireland,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Infants without siblings at 6 months of age,Infants with siblings at 6 months of age,"Infants with older siblings where 130 had one sibling, 41 had two siblings, and 16 had three siblings",164,187,1 month,WMS,NA,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"breast feeding,mode of birth",NA,unchanged,NA,unchanged,unchanged,unchanged,Signature 2,"Figure 1C, Supplementary Table 2",17 November 2025,Tosin,Tosin,Individual FDR (false discovery rate) adjusted significant taxa differences for 6 months of age,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium paraputrificum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium",1783272|1239|186801|186802|31979|1485|29363;1783272|201174|1760|85004|31953|1678|1689,Complete,KateRasheed
bsdb:40879391/2/1,40879391,prospective cohort,40879391,10.1111/all.70033,NA,"Devotta H., Lavelle A., Korpela K., Hurley S., Shannon E., Lunjani N., Ambikan A., Neogi U., Venter C., Walter J., Hourihane J. , O'Mahony L.",Microbial Sharing Between Siblings Supports Metabolic Functions Protective Against Allergy,Allergy,2025,"environment, food allergy, hygiene hypothesis, microbiome",Experiment 2,Ireland,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Infants without siblings at 12 months of age,Infants with siblings at 12 months of age,"Infants with older siblings where 130 had one sibling, 41 had two siblings, and 16 had three siblings",156,187,1 month,WMS,NA,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"breast feeding,mode of birth",NA,unchanged,NA,unchanged,unchanged,unchanged,Signature 1,"Figure 1D, Supplementary Table 2",18 November 2025,Tosin,Tosin,Individual FDR (false discovery rate) adjusted significant taxa differences for 12 months of age,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia luti,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium UC5.1-1D1,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter|s__Dysosmobacter welbionis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Evtepia|s__Evtepia gabavorous,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Acutalibacteraceae|g__Hydrogeniiclostridium|s__Hydrogeniiclostridium mannosilyticum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora amygdalina,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|171550|239759|328813;1783272|1239|186801|3085636|186803|207244|649756;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|28116;1783272|201174|1760|85004|31953|1678|1681;1783272|201174|1760|85004|31953|1678|1686;1783272|201174|1760|85004|31953|1678|216816;1783272|201174|1760|85004|31953|1678|28026;1783272|1239|186801|3085636|186803|572511|89014;1783272|1239|186801|1697794;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|186802|216572|2591381|2093857;1783272|1239|186801|186802|2211178|2211183;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|204475|745368;1783272|1239|186801|186802|3082771|2764317|2764322;1783272|1239|186801|3085636|186803|2719231|253257;3379134|1224|28216|80840|995019|577310|487175;1783272|1239|186801|3085636|186803|2316020|33039;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802|216572|216851,Complete,KateRasheed
bsdb:40879391/2/2,40879391,prospective cohort,40879391,10.1111/all.70033,NA,"Devotta H., Lavelle A., Korpela K., Hurley S., Shannon E., Lunjani N., Ambikan A., Neogi U., Venter C., Walter J., Hourihane J. , O'Mahony L.",Microbial Sharing Between Siblings Supports Metabolic Functions Protective Against Allergy,Allergy,2025,"environment, food allergy, hygiene hypothesis, microbiome",Experiment 2,Ireland,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Infants without siblings at 12 months of age,Infants with siblings at 12 months of age,"Infants with older siblings where 130 had one sibling, 41 had two siblings, and 16 had three siblings",156,187,1 month,WMS,NA,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"breast feeding,mode of birth",NA,unchanged,NA,unchanged,unchanged,unchanged,Signature 2,"Figure 1D, Supplementary Table 2",18 November 2025,Tosin,Tosin,Individual FDR (false discovery rate) adjusted significant taxa differences for 12 months of age,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas umbilicata,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus rhamnosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella buccae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalimonas|s__Faecalimonas nexilis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium butyricum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula",1783272|201174|1760|85004|31953|1678|28025;1783272|201174|1760|85004|31953|1678|1689;1783272|1239|186801|3085636|186803|572511|1322;1783272|1239|186801|3085636|186803|2719313|1531;3379134|1224|1236|91347|543|561|562;1783272|1239|186801|3085636|186803|2005355|1912855;1783272|1239|91061|186826|33958|2759736|47715;1783272|1239|186801|3085636|186803|2316020|33038;1783272|1239|909932|1843489|31977|906|187326;3379134|976|200643|171549|171552|2974251|28126;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|909932|1843489|31977|29465|423477;1783272|1239|186801|3085636|186803|2005355|29361;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|186801|186802|31979|1485|1492;1783272|1239|909932|1843489|31977|29465|29466,Complete,KateRasheed
bsdb:40885910/1/1,40885910,case-control,40885910,10.1186/s12866-025-04259-y,NA,"Huang W., Chai Y., Li X., Zhang Q., Yan Z., Wang Y., Tao X., Zhang J. , Qiu F.",Metagenomics and metabolomics to evaluate the potential role of gut microbiota and blood metabolites in patients with cerebral infarction,BMC microbiology,2025,"Biomarker, Cerebral infarction, Metabolite, Microbiome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Cerebral infarction,MONDO:0002679,Healthy controls (H),Cerebral infarction (N),Patients with cerebral infarction (N),30,30,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 3A and 3B,9 October 2025,Tosin,Tosin,Cladogram and lefse results showing significant differential abundance between Healthy controls (H) and Patients with cerebral infarction (N),increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Candidatus Epulonipiscium,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena fissicatena,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Parascardovia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,c__Peptococcia|o__Peptococcales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|s__[Eubacterium] brachy",1783272|201174;1783272|201174|1760|85004|31953|419014;1783272|1239|186801|3082720|543314;1783272|201174|1760|85009|31957|2801844;1783272|201174|84998|84999|1643824;1783272|1239|186801|3085636|186803|2383;1783272|1239|186801;1783272|201174|84998|84999;1783272|201174|84998;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85009|31957|1912216;1783272|1239|186801|3085636|186803|1432051;3379134|1224|1236|91347|543;1783272|1239|526524|526525|128827;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|216572|216851|1946507;1783272|1239|186801|3085636|186803|2005359|290055;1783272|201174|1760|85006|85023|33882;1783272|201174|1760|2037|2049|2050;1783272|201174|84998|84999|1643824|133925;1783272|1239|186801|186802|216572;1783272|201174|1760|85004|31953|196082;1783272|1239|186801|186802|186807;3118672|3120435;1783272|201174|1760|85009|31957;1783272|201174|1760|85009;1783272|1239|186801|186802|216572|1508657;1783272|1239|186801|3082720|543314|35517,Complete,KateRasheed
bsdb:40885910/1/2,40885910,case-control,40885910,10.1186/s12866-025-04259-y,NA,"Huang W., Chai Y., Li X., Zhang Q., Yan Z., Wang Y., Tao X., Zhang J. , Qiu F.",Metagenomics and metabolomics to evaluate the potential role of gut microbiota and blood metabolites in patients with cerebral infarction,BMC microbiology,2025,"Biomarker, Cerebral infarction, Metabolite, Microbiome",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Cerebral infarction,MONDO:0002679,Healthy controls (H),Cerebral infarction (N),Patients with cerebral infarction (N),30,30,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 3A and 3B,9 October 2025,Tosin,Tosin,Cladogram and lefse results showing significant differential abundance between Healthy controls (H) and Patients with cerebral infarction (N),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Beijerinckiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Synechococcales|f__Prochlorococcaceae|g__Cyanobium|s__Cyanobium gracile,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Synechococcales|f__Prochlorococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Sulfurimonadaceae|g__Sulfuricurvum,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Sulfurimonadaceae,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae|o__Synechococcales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",3379134|1224|28216|80840|506|222;3379134|1224|28216|80840|506;1783272|201174|1760|85006|1268|1663;1783272|1239;3379134|1224|28211|356|45404;1783272|1239|186801|186802|3085642;1783272|1239|186801|186802|3085642|580596;3379134|29547|3031852|213849;3379134|29547;1783272|1117;1783272|1117|3028117|1890424|2881426|167375|59930;1783272|1117|3028117;3379134|29547|3031852;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803|1407607;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|3085636|186803|28050|39485;1783272|1239|186801|3085636|186803|877420;3379134|1224|1236|135625|712;3379134|1224|1236|135625;1783272|1239|91061|186826|33958|1253;1783272|1117|3028117|1890424|2881426;1783272|1239|526524|526525|128827|123375;1783272|1239|186801|186802|216572|292632;3379134|29547|3031852|213849|2771471|286130;3379134|29547|3031852|213849|2771471;1783272|1117|3028117|1890424;1783272|1239|186801|3085636|186803|1506577;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977,Complete,KateRasheed
bsdb:40886797/1/1,40886797,prospective cohort,40886797,https://doi.org/10.1016/j.ijid.2025.108031,NA,"Woltsche J., Pacher-Deutsch C., Fürst S., Gulden L., Schwarzl J., Feldbacher N., Nepel M., Rebol L., Hasl N., Rieper V., Stadlbauer V. , Horvath A.",Distinct urinary microbiome signatures are associated with urinary tract infection risk in patients with liver cirrhosis: A pilot study,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2025,"Cirrhosis, Urinary microbiome, Urinary tract infection",Experiment 1,Austria,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,No Urinary Tract Infection group,Diagnosed Urinary Tract Infection group,"These were patients with liver cirrhosis who developed at least one urinary tract infection (dUTI) within a 3-year follow-up period after urine sample collection. The group included 17 participants, mostly male (71%), who had more advanced liver disease compared to the non-urinary tract infection group. (No_UTI)",22,17,1 month,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Fig. 3B & 3C,16 October 2025,Busiwa Liuma,Busiwa Liuma,Microbial species and genera enriched in the diagnosed urinary tract infection group (dUTI) vs  the No urinary tract infection group (No_UTI),increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,Svetlana up
bsdb:40886797/1/2,40886797,prospective cohort,40886797,https://doi.org/10.1016/j.ijid.2025.108031,NA,"Woltsche J., Pacher-Deutsch C., Fürst S., Gulden L., Schwarzl J., Feldbacher N., Nepel M., Rebol L., Hasl N., Rieper V., Stadlbauer V. , Horvath A.",Distinct urinary microbiome signatures are associated with urinary tract infection risk in patients with liver cirrhosis: A pilot study,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2025,"Cirrhosis, Urinary microbiome, Urinary tract infection",Experiment 1,Austria,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,No Urinary Tract Infection group,Diagnosed Urinary Tract Infection group,"These were patients with liver cirrhosis who developed at least one urinary tract infection (dUTI) within a 3-year follow-up period after urine sample collection. The group included 17 participants, mostly male (71%), who had more advanced liver disease compared to the non-urinary tract infection group. (No_UTI)",22,17,1 month,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,Fig. 3B & 3C,16 October 2025,Busiwa Liuma,"Busiwa Liuma,Anne-mariesharp",Microbial species and genera depleted in the diagnosed urinary tract infection group(dUTI) vs. the No urinary tract infection group( No_UTI),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Chlamydiota|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia|s__Chlamydia trachomatis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__uncultured Dialister sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|204428|204429|51291|809|810|813;1783272|201174|1760|85007|1653;1783272|1239|909932|1843489|31977|39948;1783272|201174|1760|85007;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|1239|909932|1843489|31977|39948|278064;1783272|1239|909932|1843489|31977|39948,Complete,Svetlana up
bsdb:40886797/2/1,40886797,prospective cohort,40886797,https://doi.org/10.1016/j.ijid.2025.108031,NA,"Woltsche J., Pacher-Deutsch C., Fürst S., Gulden L., Schwarzl J., Feldbacher N., Nepel M., Rebol L., Hasl N., Rieper V., Stadlbauer V. , Horvath A.",Distinct urinary microbiome signatures are associated with urinary tract infection risk in patients with liver cirrhosis: A pilot study,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2025,"Cirrhosis, Urinary microbiome, Urinary tract infection",Experiment 2,Austria,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,No Urinary Tract Infection group,Diagnosed Urinary Tract Infection group,"These were patients with liver cirrhosis who developed at least one urinary tract infection (dUTI) within a 3-year follow-up period after urine sample collection. The group included 17 participants, mostly male (71%), who had more advanced liver disease compared to the non-urinary tract infection group. (No_UTI)",22,17,1 month,16S,12,Illumina,centered log-ratio,ANCOM,0.05,FALSE,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,unchanged,Signature 1,Fig. 3A,26 October 2025,Busiwa Liuma,"Busiwa Liuma,Anne-mariesharp",These were patients with liver cirrhosis who developed at least one urinary tract infection (dUTI) within a 3-year follow-up period after urine sample collection. The figure depicts the results of the Analysis of Composition of Microbiomes (ANCOM) comparing the urinary microbiome composition between patients with liver cirrhosis who had decreased abundance in the diagnosed Urinary Tract Infection group (ANCOM).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__uncultured Corynebacterium sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__uncultured Dialister sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",3379134|976|200643|171549;3379134|976|200643;3379134|976;1783272|201174|1760|85007|1653;1783272|1239|909932|1843489|31977|39948;1783272|201174|1760|85007;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552;1783272|201174|1760|85007|1653|1716|159447;1783272|1239|909932|1843489|31977|39948|278064;1783272|1239|909932|1843489|31977|39948,Complete,Svetlana up
bsdb:40886797/3/1,40886797,prospective cohort,40886797,https://doi.org/10.1016/j.ijid.2025.108031,NA,"Woltsche J., Pacher-Deutsch C., Fürst S., Gulden L., Schwarzl J., Feldbacher N., Nepel M., Rebol L., Hasl N., Rieper V., Stadlbauer V. , Horvath A.",Distinct urinary microbiome signatures are associated with urinary tract infection risk in patients with liver cirrhosis: A pilot study,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2025,"Cirrhosis, Urinary microbiome, Urinary tract infection",Experiment 3,Austria,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,Male dUTI (diagnosed Urinary Tract Infection) group,Female dUTI (diagnosed Urinary Tract Infection) group,Female patients with diagnosed Urinary Tract Infection (dUTI),9,5,1 month,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. S5D,26 October 2025,Busiwa Liuma,Busiwa Liuma,The figure compares the relative abundance of Lactobacillus between male diagnosed urinary tract infection(dUTI)and female diagnosed urinary tract infection (dUTI)groups with liver cirrhosis who developed a diagnosed urinary tract infection (dUTI). The analysis highlights microbial differences attributable to biological sex. The female diagnosed urinary tract infection (dUTI)group showed a significantly higher abundance of Lactobacillus than male diagnosed urinary tract infection (dUTI)patients.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:40899693/1/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 1,China,Ursus maritimus,Feces,UBERON:0001988,Interspecies interaction between organisms,GO:0044419,Brown bear (Ursus arctos),Polar bear (Ursus maritimus),"Adult polar bears (Ursus maritimus) housed in the Beijing Zoo, where they were managed under consistent conditions, including diet and housing.",4,4,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 1c,13 October 2025,YokoC,YokoC,Boxplots for the significant differences in relative abundance of the Fimicutes and Fusobacteriota phyla (Kruskal–Wallis test).,increased,k__Fusobacteriati|p__Fusobacteriota,3384189|32066,Complete,KateRasheed
bsdb:40899693/2/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 2,China,Ailuropoda melanoleuca,Feces,UBERON:0001988,Interspecies interaction between organisms,GO:0044419,Polar bears (Ursus maritimus),Panda bear (Ailuropoda melanoleuca),"Juvenile and adult panda bears (Ailuropoda melanoleuca) housed in the Beijing Zoo, where they were managed under consistent conditions, including diet and housing.",4,10,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 1b,13 October 2025,YokoC,YokoC,Boxplots for the significant differences in relative abundance of the Fimicutes and Fusobacteriota phyla (Kruskal–Wallis test).,increased,k__Bacillati|p__Bacillota,1783272|1239,Complete,KateRasheed
bsdb:40899693/2/2,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 2,China,Ailuropoda melanoleuca,Feces,UBERON:0001988,Interspecies interaction between organisms,GO:0044419,Polar bears (Ursus maritimus),Panda bear (Ailuropoda melanoleuca),"Juvenile and adult panda bears (Ailuropoda melanoleuca) housed in the Beijing Zoo, where they were managed under consistent conditions, including diet and housing.",4,10,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 1c,13 October 2025,YokoC,YokoC,Boxplots for the significant differences in relative abundance of the Fimicutes and Fusobacteriota phyla (Kruskal–Wallis test).,decreased,k__Fusobacteriati|p__Fusobacteriota,3384189|32066,Complete,KateRasheed
bsdb:40899693/3/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 3,China,Ailuropoda melanoleuca,Feces,UBERON:0001988,Interspecies interaction between organisms,GO:0044419,Asian black bear (Ursus thibetanus),Panda bear (Ailuropoda melanoleuca),"Juvenile and adult panda bears (Ailuropoda melanoleuca) housed in the Beijing Zoo, where they were managed under consistent conditions, including diet and housing.",3,10,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 1c,14 October 2025,YokoC,YokoC,Boxplots for the significant differences in relative abundance of the Fimicutes and Fusobacteriota phyla (Kruskal–Wallis test).,decreased,k__Fusobacteriati|p__Fusobacteriota,3384189|32066,Complete,KateRasheed
bsdb:40899693/4/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 4,China,Ailuropoda melanoleuca,Feces,UBERON:0001988,Interspecies interaction between organisms,GO:0044419,Brown bear (Ursus arctos),Panda bear (Ailuropoda melanoleuca),"Juvenile and adult panda bears (Ailuropoda melanoleuca) housed in the Beijing Zoo, where they were managed under consistent conditions, including diet and housing.",4,10,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 1b,14 October 2025,YokoC,YokoC,Boxplots for the significant differences in relative abundance of the Fimicutes and Fusobacteriota phyla (Kruskal–Wallis test).,increased,k__Bacillati|p__Bacillota,1783272|1239,Complete,KateRasheed
bsdb:40899693/5/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 5,China,Ailuropoda melanoleuca,Feces,UBERON:0001988,Interspecies interaction between organisms,GO:0044419,Brown bear (Ursus arctos) + Asian Black bear (Ursus thibetanus) + Polar bear (Ursus maritimus),Panda bear (Ailuropoda melanoleuca),"Juvenile and adult panda bears (Ailuropoda melanoleuca) housed in the Beijing Zoo, where they were managed under consistent conditions, including diet and housing.",11,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1f,14 October 2025,YokoC,YokoC,Barplots for a LEfSe analysis of relative abundance of the genus with significant differences in the four bear groups (LDA score > 3 and a significance of a < 0.05).,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:40899693/6/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 6,China,Ursus arctos,Feces,UBERON:0001988,Interspecies interaction between organisms,GO:0044419,Panda bear (Ailuropoda melanoleuca) + Asian Black bear (Ursus thibetanus) + Polar bear (Ursus maritimus),Brown bear (Ursus arctos),"Juvenile and adult brown bears (Ursus arctos) housed in the Beijing Zoo, where they were managed under consistent conditions, including diet and housing.",17,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1f,14 October 2025,YokoC,YokoC,Barplots for a LEfSe analysis of relative abundance of the genus with significant differences in the four bear groups (LDA score > 3 and a significance of a < 0.05).,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1357;1783272|1239|186801|186802|31979|1266;1783272|1239|186801|3085636|186803|1506553,Complete,KateRasheed
bsdb:40899693/7/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 7,China,Ursus thibetanus,Feces,UBERON:0001988,Interspecies interaction between organisms,GO:0044419,Panda bear (Ailuropoda melanoleuca) + Brown bear (Ursus arctos) + Polar bear (Ursus maritimus),Asian Black bear (Ursus thibetanus),"Juvenile and adult asian black bears (Ursus thibetanus) housed in the Beijing Zoo, where they were managed under consistent conditions, including diet and housing.",18,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1f,14 October 2025,YokoC,YokoC,Barplots for a LEfSe analysis of relative abundance of the genus with significant differences in the four bear groups (LDA score > 3 and a significance of a < 0.05).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter",3379134|976|200643|171549|171552|1283313;1783272|1239|186801|3082720|186804|1501226;1783272|1239|186801|3082720|186804|1505652,Complete,KateRasheed
bsdb:40899693/8/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 8,China,Ursus maritimus,Feces,UBERON:0001988,Interspecies interaction between organisms,GO:0044419,Panda bear (Ailuropoda melanoleuca) + Brown bear (Ursus arctos) + Asian black bears (Ursus thibetanus),Polar bear (Ursus maritimus),"Juvenile and adult asian black bears (Ursus thibetanus) housed in the Beijing Zoo, where they were managed under consistent conditions, including diet and housing.",17,4,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1f,14 October 2025,YokoC,YokoC,Barplots for a LEfSe analysis of relative abundance of the genus with significant differences in the four bear groups (LDA score > 3 and a significance of a < 0.05).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Plesiomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",3379134|976|200643|171549|171550|239759;3384189|32066|203490|203491|203492|180162;3379134|1224|1236|91347|543|570;3379134|1224|1236|91347|543|702;1783272|1239|186801|186802|31979|1485,Complete,KateRasheed
bsdb:40899693/9/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 9,China,Ursus maritimus,Feces,UBERON:0001988,"Seasonal gut microbiome measurement,Interspecies interaction between organisms","EFO:0007753,GO:0044419",Brown bear (Ursus arctos) spring,Polar bear (Ursus maritimus) spring,"Adult polar bears (Ursus maritimus) housed in the Beijing Zoo, where they were managed under consistent conditions, including diet and housing. Sampled during the spring season.",4,4,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2b and Figure 2c,14 October 2025,YokoC,YokoC,"Significant differences among the three phyla and the three genera with the highest relative abundance. Two-way Anova for bear species (polar bear vs, brown bear) and seasons (spring).",increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,1783272|1239|186801|186802|31979|1485,Complete,KateRasheed
bsdb:40899693/10/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 10,China,Ailuropoda melanoleuca,Feces,UBERON:0001988,"Seasonal gut microbiome measurement,Interspecies interaction between organisms","EFO:0007753,GO:0044419",Polar bear (Ursus maritimus) spring,Panda bear (Ailuropoda melanoleuca) spring,"Adult and juvenile Panda bears (Ailuropoda melanoleuca) housed in the Beijing Zoo, where they were managed under consistent conditions, including diet and housing. Samples in spring.",4,10,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2D,14 October 2025,YokoC,YokoC,Significant differences among the three phyla and the three genera with the highest relative abundance. Two-way Anova for bear species (panda bear vs polar bear) and seasons (spring).,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:40899693/10/2,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 10,China,Ailuropoda melanoleuca,Feces,UBERON:0001988,"Seasonal gut microbiome measurement,Interspecies interaction between organisms","EFO:0007753,GO:0044419",Polar bear (Ursus maritimus) spring,Panda bear (Ailuropoda melanoleuca) spring,"Adult and juvenile Panda bears (Ailuropoda melanoleuca) housed in the Beijing Zoo, where they were managed under consistent conditions, including diet and housing. Samples in spring.",4,10,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2d,14 October 2025,YokoC,YokoC,Significant differences among the three phyla and the three genera with the highest relative abundance. Two-way Anova for bear species (panda bear and polar bear) and seasons (spring).,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,1783272|1239|186801|186802|31979|1485,Complete,KateRasheed
bsdb:40899693/11/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 11,China,Ailuropoda melanoleuca,Feces,UBERON:0001988,"Seasonal gut microbiome measurement,Interspecies interaction between organisms","EFO:0007753,GO:0044419",Asian Black Bear (Ursus thibetanus) spring,Panda bear (Ailuropoda melanoleuca) spring,"Adult and juvenile Panda bears (Ailuropoda melanoleuca) housed in the Beijing Zoo, where they were managed under consistent conditions, including diet and housing. Samples were collected during spring.",3,10,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2d,14 October 2025,YokoC,YokoC,Significant differences among the three phyla and the three genera with the highest relative abundance. Two-way Anova for bear species (panda bear vs Asian black bear) and seasons (spring).,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:40899693/12/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 12,China,Ailuropoda melanoleuca,Feces,UBERON:0001988,"Seasonal gut microbiome measurement,Interspecies interaction between organisms","EFO:0007753,GO:0044419",Brown bear (Ursus arctos) spring,Panda bear (Ailuropoda melanoleuca) spring,"Adult and juvenile Panda bears (Ailuropoda melanoleuca) housed in the Beijing Zoo, where they were managed under consistent conditions, including diet and housing. Samples were collected in spring.",4,10,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2d,14 October 2025,YokoC,YokoC,Significant differences among the three phyla and the three genera with the highest relative abundance. Two-way Anova for bear species (panda bear vs. brown bear) and seasons (spring).,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:40899693/12/2,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 12,China,Ailuropoda melanoleuca,Feces,UBERON:0001988,"Seasonal gut microbiome measurement,Interspecies interaction between organisms","EFO:0007753,GO:0044419",Brown bear (Ursus arctos) spring,Panda bear (Ailuropoda melanoleuca) spring,"Adult and juvenile Panda bears (Ailuropoda melanoleuca) housed in the Beijing Zoo, where they were managed under consistent conditions, including diet and housing. Samples were collected in spring.",4,10,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2d,14 October 2025,YokoC,YokoC,Significant differences among the three phyla and the three genera with the highest relative abundance. Two-way Anova for bear species (panda bear and brown bear) and seasons (spring).,decreased,NA,NA,Complete,KateRasheed
bsdb:40899693/13/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 13,China,Ailuropoda melanoleuca,Feces,UBERON:0001988,"Seasonal gut microbiome measurement,Interspecies interaction between organisms","EFO:0007753,GO:0044419",Brown bear (Ursus arctos) winter,Panda bear (Ailuropoda melanoleuca) winter,"Adult and juvenile Panda bears (Ailuropoda melanoleuca) housed in the Beijing Zoo, where they were managed under consistent conditions, including diet and housing. Samples were collected during the winter.",4,10,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2c and 2d,14 October 2025,YokoC,YokoC,Significant differences among the three phyla and the three genera with the highest relative abundance. Two-way Anova for bear species (panda bear vs. brown bear) and seasons (winter).,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239;1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:40899693/14/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 14,China,Ailuropoda melanoleuca,Feces,UBERON:0001988,"Seasonal gut microbiome measurement,Interspecies interaction between organisms","EFO:0007753,GO:0044419",Polar bear (Ursus maritimus) winter,Panda bear (Ailuropoda melanoleuca) winter,"Adult and juvenile Panda bears (Ailuropoda melanoleuca) housed in the Beijing Zoo, where they were managed under consistent conditions, including diet and housing. Samples were collected during the winter.",4,10,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2d,14 October 2025,YokoC,YokoC,Significant differences among the three phyla and the three genera with the highest relative abundance. Two-way Anova for bear species (panda bear vs. polar bear) and seasons (winter).,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:40899693/15/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 15,China,Ailuropoda melanoleuca,Feces,UBERON:0001988,"Seasonal gut microbiome measurement,Interspecies interaction between organisms","EFO:0007753,GO:0044419",Asian black bear (Ursus thibetanus) winter,Panda bear (Ailuropoda melanoleuca) winter,"Adult and juvenile Panda bears (Ailuropoda melanoleuca) housed in the Beijing Zoo, where they were managed under consistent conditions, including diet and housing. Samples were collected during the winter.",3,10,NA,16S,34,Illumina,relative abundances,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2d,14 October 2025,YokoC,YokoC,Significant differences among the three phyla and the three genera with the highest relative abundance. Two-way Anova for bear species (panda bear vs Asian black bear) and seasons (winter).,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:40899693/16/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 16,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Brown-FMT(W) + Black-FMT(W) + Polar-FMT(W)  + Control,Panda-FMT(W) (Fecal Microbiota Transplant Winter),"Mice that received a fecal microbiota transplant from zoo pandas, which was collected in winter.",20,5,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4g,14 October 2025,YokoC,YokoC,Barplots for a LEfSe analysis of relative abundance of the genus with significant differences (LDA score > 3 and a significance of p < 0.05).,increased,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Phenylobacterium,3379134|1224|28211|204458|76892|20,Complete,KateRasheed
bsdb:40899693/17/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 17,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Brown-FMT(W) + Black-FMT(W) + Panda-FMT(W) + Control,Polar-FMT (Fecal Microbiota Transplant Winter),"Mice that received a fecal microbiota transplant from zoo polar bears, which was collected in winter.",20,5,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4g,14 October 2025,YokoC,YokoC,Barplots for a LEfSe analysis of relative abundance of the genus with significant differences (LDA score > 3 and a significance of p < 0.05).,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,1783272|1239|186801|3085636|186803|1407607,Complete,KateRasheed
bsdb:40899693/18/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 18,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Polar-FMT + Black-FMT(W) + Panda-FMT(W) + Control,Brown-FMT (Fecal Microbiota Transplant Winter),"Mice that received a fecal microbiota transplant from zoo brown bears, which was collected in winter.",20,5,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4g,14 October 2025,YokoC,YokoC,Barplots for a LEfSe analysis of relative abundance of the genus with significant differences(LDA score > 3 and a significance of p < 0.05).,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,KateRasheed
bsdb:40899693/19/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 19,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Polar-FMT + Brown-FMT(W) + Panda-FMT(W) + Control,Black-FMT (Fecal Microbiota Transplant Winter),"Mice that received a fecal microbiota transplant from zoo Asian black bears, which was collected in winter.",20,5,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4g,14 October 2025,YokoC,YokoC,Barplots for a LEfSe analysis of relative abundance of the genus with significant differences (LDA score > 3 and a significance of p < 0.05).,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Cytophagia|o__Cytophagales|f__Fulvivirgaceae|g__Ohtaekwangia",1783272|201174|84998|1643822|1643826|580024;3379134|976|200643|171549|2005473;3379134|976|768503|768507|2762286|1210119,Complete,KateRasheed
bsdb:40899693/20/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 20,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Polar-FMT (W) + Brown-FMT(W) + Panda-FMT(W) + Black-FMT(W),Control (W) winter,Mice that that did not receive a fecal microbiota transplant (FMT) for the winter season.,20,5,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4g,14 October 2025,YokoC,YokoC,Barplots for a LEfSe analysis of the relative abundance of the genus with significant differences (LDA score > 3 and a significance of p < 0.05).,increased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas",3379134|200940|3031449|213115|194924|872;3379134|29547|3031852|213849|72293|209;3379134|1224|1236;1783272|1239|186801|3085636|186803|1769710,Complete,KateRasheed
bsdb:40899693/21/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 21,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Control,Panda-FMT(W) (Fecal Microbiota Transplant Winter),"Mice that received a fecal microbiota transplant from pandas, which was collected in winter.",5,5,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4d,15 October 2025,YokoC,YokoC,Boxplots for the significant differences in relative abundance of phyla (Kruskal–Wallis test).,decreased,k__Pseudomonadati|p__Spirochaetota,3379134|203691,Complete,KateRasheed
bsdb:40899693/23/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 23,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Panda-FMT (W) (Fecal Microbiota Transplant Winter),Polar-FMT(W) (Fecal Microbiota Transplant Winter),"Mice that received a fecal microbiota transplant from zoo Polar bears, which was collected in winter.",5,5,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4f,15 October 2025,YokoC,YokoC,Boxplots for the significant differences in relative abundance of phyla (Kruskal–Wallis test).,increased,k__Pseudomonadati|p__Acidobacteriota,3379134|57723,Complete,KateRasheed
bsdb:40899693/25/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 25,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Polar-FMT (S) (Fecal Microbiota Transplant Summer),Brown-FMT(S) (Fecal Microbiota Transplant Summer),"Mice that received a fecal microbiota transplant from zoo brown bears, which was collected in summer.",7,7,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 6f,15 October 2025,YokoC,YokoC,Boxplots for the significant differences in relative abundance of phyla (Kruskal–Wallis test).,increased,k__Fusobacteriati|p__Fusobacteriota,3384189|32066,Complete,KateRasheed
bsdb:40899693/27/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 27,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Polar-FMT (S) (Fecal Microbiota Transplant Summer),Black-FMT(S) (Fecal Microbiota Transplant Summer),"Mice that received a fecal microbiota transplant from zoo Asian black bears, which was collected in summer.",7,7,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 6f and Figure 6g,15 October 2025,YokoC,YokoC,Boxplots for the significant differences in relative abundance of phyla (Kruskal–Wallis test).,increased,k__Fusobacteriati|p__Fusobacteriota,3384189|32066,Complete,KateRasheed
bsdb:40899693/27/2,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 27,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Polar-FMT (S) (Fecal Microbiota Transplant Summer),Black-FMT(S) (Fecal Microbiota Transplant Summer),"Mice that received a fecal microbiota transplant from zoo Asian black bears, which was collected in summer.",7,7,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 6f and Figure 6g,15 October 2025,YokoC,YokoC,Boxplots for the significant differences in relative abundance of phyla (Kruskal–Wallis test).,decreased,k__Pseudomonadati|p__Thermodesulfobacteriota,3379134|200940,Complete,KateRasheed
bsdb:40899693/28/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 28,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Control,Black-FMT(S) (Fecal Microbiota Transplant Summer),"Mice that received a fecal microbiota transplant from zoo Asian black bears, which was collected in summer.",7,7,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 6f,15 October 2025,YokoC,YokoC,Boxplots for the significant differences in relative abundance of phyla (Kruskal–Wallis test).,increased,k__Fusobacteriati|p__Fusobacteriota,3384189|32066,Complete,KateRasheed
bsdb:40899693/29/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 29,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Control,Brown-FMT(S) (Fecal Microbiota Transplant Summer),"Mice that received a fecal microbiota transplant from zoo brown bears, which was collected in summer.",7,7,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 6f,15 October 2025,YokoC,YokoC,Boxplots for the significant differences in relative abundance of phyla (Kruskal–Wallis test).,increased,k__Fusobacteriati|p__Fusobacteriota,3384189|32066,Complete,KateRasheed
bsdb:40899693/30/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 30,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Control,Panda-FMT(S) (Fecal Microbiota Transplant Summer),"Mice that received a fecal microbiota transplant from zoo panda bears, which was collected in summer.",7,7,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 6f,22 October 2025,YokoC,YokoC,Boxplots for the significant differences in relative abundance of phyla (Kruskal–Wallis test).,increased,k__Fusobacteriati|p__Fusobacteriota,3384189|32066,Complete,KateRasheed
bsdb:40899693/31/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 31,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Control,Polar-FMT(S) (Fecal Microbiota Transplant Summer),"Mice that received a fecal microbiota transplant from zoo polar bears, which was collected in summer.",7,7,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 6d,15 October 2025,YokoC,YokoC,Boxplots for the significant differences in relative abundance of phyla (Kruskal–Wallis test).,increased,k__Bacillati|p__Bacillota,1783272|1239,Complete,KateRasheed
bsdb:40899693/31/2,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 31,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Control,Polar-FMT(S) (Fecal Microbiota Transplant Summer),"Mice that received a fecal microbiota transplant from zoo polar bears, which was collected in summer.",7,7,NA,16S,34,Illumina,relative abundances,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 6e,15 October 2025,YokoC,YokoC,Boxplots for the significant differences in relative abundance of phyla (Kruskal–Wallis test).,decreased,k__Pseudomonadati|p__Bacteroidota,3379134|976,Complete,KateRasheed
bsdb:40899693/32/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 32,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Control-FMT(S) + Black-FMT(S) + Panda-FMT(S) + Polar-FMT(S),Brown-FMT(S) (Fecal Microbiota Transplant Summer),"Mice that received a fecal microbiota transplant from zoo brown bears, which was collected in summer.",28,7,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6h,15 October 2025,YokoC,YokoC,Barplots for a LEfSe analysis of relative abundance of the genus with significant differences (LDA score > 3 and a significance of a < 0.05).,increased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum",1783272|544448|31969|186332|186333|2086;3379134|1224|28211|356|41294|374;3379134|29547|3031852|213849|72293|209;1783272|1239|186801|3085656|3085657|2039302;3379134|1224|28216|206351|481|482;3379134|1224|28211|204457|41297|13687;1783272|1239|186801|186802|216572|39492,Complete,KateRasheed
bsdb:40899693/33/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 33,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Control-FMT(S) + Brown-FMT(S) + Panda-FMT(S) + Polar-FMT(S),Black-FMT(S) (Fecal Microbiota Transplant Summer),"Mice that received a fecal microbiota transplant from zoo Asian black bears, which was collected in summer.",28,7,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6h,15 October 2025,YokoC,YokoC,Barplots for a LEfSe analysis of relative abundance of the genus with significant differences (LDA score > 3 and a significance of a < 0.05).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cellvibrionales|f__Halieaceae|g__Halioglobus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",3379134|976|200643|171549|2005473|1918540;3379134|200940|3031449|213115|194924|35832;3379134|1224|1236|1706369|1706372|1217416;1783272|1239|186801|186802|216572|1263,Complete,KateRasheed
bsdb:40899693/35/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 35,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Control-FMT(S) + Brown-FMT(S) + Black-FMT(S) + Polar-FMT(S),Panda-FMT(S) (Fecal Microbiota Transplant Summer),"Mice that received a fecal microbiota transplant from zoo panda bears, which was collected in summer.",28,7,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6h,15 October 2025,YokoC,YokoC,Barplots for a LEfSe analysis of relative abundance of the genus with significant differences (LDA score > 3 and a significance of a < 0.05).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Roseobacteraceae|g__Marivita",3379134|976|200643|171549|815|816;1783272|1239|91061|1385|539738|1378;1783272|1239|186801|3085636|186803|248744;3379134|1224|28211|204455|2854170|659428,Complete,KateRasheed
bsdb:40899693/36/1,40899693,"laboratory experiment,time series / longitudinal observational",40899693,10.1093/ismejo/wraf201,NA,"Bo T., Xu X., Liu H., Tang L., Xu H., Zhao S., Lv J. , Wang D.",Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda,The ISME journal,2025,"FMT, Ursidae, energy metabolism, gut microbiota, season",Experiment 36,China,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Panda-FMT(S) + Brown-FMT(S) + Black-FMT(S) + Polar-FMT(S),Control,Mice that did not receive a fecal microbiota transplant or any other treatment.,28,7,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6h,15 October 2025,YokoC,YokoC,Barplots for a LEfSe analysis of relative abundance of the genus with significant differences (LDA score > 3 and a significance of a < 0.05).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,c__Deltaproteobacteria|o__Bradymonadales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Nitrosomonadaceae|g__Nitrosomonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Quinella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas",3379134|976|200643|171549|171552|1283313;28221|1779134;3379134|1224|1236|91347|543|547;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|2005473;3379134|1224|28216|32003|206379|914;1783272|1239|909932|1843489|31977|1567;3379134|203691|203692|136|2845253|157;3379134|1224|28216|32003;95818|2093818|2093825|2171986|1331051,Complete,KateRasheed
bsdb:40913049/1/1,40913049,laboratory experiment,40913049,https://doi.org/10.1038/s41467-025-63473-4,https://www.nature.com/articles/s41467-025-63473-4,"Park H., Cheon J., Kim H., Kim J., Kim J., Shin J.Y., Kim H., Ryu G., Chung I.Y., Kim J.H., Kim D., Zhang Z., Wu H., Beck K.R., Bäckhed F., Kim H.J., Lee Y. , Koh A.",Gut microbial production of imidazole propionate drives Parkinson's pathologies,Nature communications,2025,NA,Experiment 1,Republic of Korea,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control mice colonized with Streptococcus mutans,Parkinson’s disease mice colonized with Streptococcus mutans,Germ-free (GF) mice experimentally colonized with live Streptococcus mutans thereby inducing Parkinson’s-like pathology,NA,NA,NA,16S,34,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 1A (Source data),9 October 2025,Yuvashree 1708,"Yuvashree 1708,Fiddyhamma",Colonization of Streptococcus mutans in germ-free (GF) mice.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium UC5.1-1E11,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter|s__Dysosmobacter welbionis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|s__Rikenellaceae bacterium",3379134|976|200643|171549|171550|239759|328814;1783272|1239|186801|1697793;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|186802|216572|2591381|2093857;3379134|1224|28216|80840|995019|577310|487175;3379134|976|200643|171549|171550|2049048,Complete,KateRasheed
bsdb:40913049/1/2,40913049,laboratory experiment,40913049,https://doi.org/10.1038/s41467-025-63473-4,https://www.nature.com/articles/s41467-025-63473-4,"Park H., Cheon J., Kim H., Kim J., Kim J., Shin J.Y., Kim H., Ryu G., Chung I.Y., Kim J.H., Kim D., Zhang Z., Wu H., Beck K.R., Bäckhed F., Kim H.J., Lee Y. , Koh A.",Gut microbial production of imidazole propionate drives Parkinson's pathologies,Nature communications,2025,NA,Experiment 1,Republic of Korea,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control mice colonized with Streptococcus mutans,Parkinson’s disease mice colonized with Streptococcus mutans,Germ-free (GF) mice experimentally colonized with live Streptococcus mutans thereby inducing Parkinson’s-like pathology,NA,NA,NA,16S,34,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 1A(Source data),31 October 2025,Fiddyhamma,"Fiddyhamma,Yuvashree 1708",Colonization of Streptococcus mutans in germ-free(GF)mice,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia argi,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia luti,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Cibiobacter|s__Candidatus Cibiobacter qucibialis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio fairfieldensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|s__Eubacteriaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Longicatena|s__Longicatena caecimuris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter glycyrrhizinilyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. ER4,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia|s__Thomasclavelia ramosa,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Vescimonas|s__Vescimonas coprocola,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum",3379134|976|200643|171549|815|816|820;1783272|1239|186801|3085636|186803|572511|1912897;1783272|1239|186801|3085636|186803|572511|89014;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|186802|2527773|2500537;3379134|200940|3031449|213115|194924|872|44742;1783272|1239|186801|186802|186806|2049045;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|186802|204475|745368;1783272|1239|526524|526525|128827|1918536|1796635;1783272|1239|186801|3085636|186803|2316020|342942;1783272|1239|186801|186802|216572|459786|1519439;1783272|1239|526524|526525|2810280|3025755|1547;1783272|1239|186801|186802|216572|2892396|2714355;1783272|1239|186801|186802|216572|39492,Complete,KateRasheed
bsdb:40913049/3/1,40913049,laboratory experiment,40913049,https://doi.org/10.1038/s41467-025-63473-4,https://www.nature.com/articles/s41467-025-63473-4,"Park H., Cheon J., Kim H., Kim J., Kim J., Shin J.Y., Kim H., Ryu G., Chung I.Y., Kim J.H., Kim D., Zhang Z., Wu H., Beck K.R., Bäckhed F., Kim H.J., Lee Y. , Koh A.",Gut microbial production of imidazole propionate drives Parkinson's pathologies,Nature communications,2025,NA,Experiment 3,Republic of Korea,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control mice colonized with Streptococcus mutans,Parkinson’s disease mice colonized with Streptococcus mutans,Germ-free (GF) mice experimentally colonized with live Streptococcus mutans thereby inducing Parkinson’s-like pathology,NA,NA,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 1A (source data),11 October 2025,Yuvashree 1708,"Yuvashree 1708,Fiddyhamma",Colonization of Streptococcus mutans in germ-free (GF) mice.,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium UC5.1-1E11,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Dysosmobacter|s__Dysosmobacter welbionis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|s__Rikenellaceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas intestinalis",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|171550|239759|328814;1783272|1239|186801|3085636|186803|207244|105841;1783272|1239|186801|1697793;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|3085636|186803|189330|39486;1783272|1239|186801|186802|216572|2591381|2093857;1783272|1239|186801|3085636|186803|2719313|1531;3379134|1224|28216|80840|995019|577310|487175;3379134|976|200643|171549|171550|2049048;1783272|1239|186801|3085636|186803|1769710|1653434,Complete,KateRasheed
bsdb:40913049/3/2,40913049,laboratory experiment,40913049,https://doi.org/10.1038/s41467-025-63473-4,https://www.nature.com/articles/s41467-025-63473-4,"Park H., Cheon J., Kim H., Kim J., Kim J., Shin J.Y., Kim H., Ryu G., Chung I.Y., Kim J.H., Kim D., Zhang Z., Wu H., Beck K.R., Bäckhed F., Kim H.J., Lee Y. , Koh A.",Gut microbial production of imidazole propionate drives Parkinson's pathologies,Nature communications,2025,NA,Experiment 3,Republic of Korea,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control mice colonized with Streptococcus mutans,Parkinson’s disease mice colonized with Streptococcus mutans,Germ-free (GF) mice experimentally colonized with live Streptococcus mutans thereby inducing Parkinson’s-like pathology,NA,NA,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 1A (source data),31 October 2025,Fiddyhamma,"Fiddyhamma,Yuvashree 1708",Colonization of Streptococcus mutans in germ-free (GF) mice.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia argi,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia luti,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Cibiobacter|s__Candidatus Cibiobacter qucibialis,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio fairfieldensis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Longicatena|s__Longicatena caecimuris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter glycyrrhizinilyticus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. ER4,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Vescimonas|s__Vescimonas coprocola",3379134|976|200643|171549|815|816|820;1783272|1239|186801|3085636|186803|572511|1912897;1783272|1239|186801|3085636|186803|572511|89014;1783272|1239|186801|3085636|186803|572511|40520;1783272|1239|186801|186802|2527773|2500537;3379134|200940|3031449|213115|194924|872|44742;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|186802|204475|745368;1783272|1239|526524|526525|128827|1918536|1796635;1783272|1239|186801|3085636|186803|2316020|342942;1783272|1239|186801|186802|216572|459786|1519439;1783272|1239|186801|186802|216572|2892396|2714355,Complete,KateRasheed
bsdb:40913049/4/1,40913049,laboratory experiment,40913049,https://doi.org/10.1038/s41467-025-63473-4,https://www.nature.com/articles/s41467-025-63473-4,"Park H., Cheon J., Kim H., Kim J., Kim J., Shin J.Y., Kim H., Ryu G., Chung I.Y., Kim J.H., Kim D., Zhang Z., Wu H., Beck K.R., Bäckhed F., Kim H.J., Lee Y. , Koh A.",Gut microbial production of imidazole propionate drives Parkinson's pathologies,Nature communications,2025,NA,Experiment 4,Republic of Korea,Mus musculus,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control mice colonized with Streptococcus mutans,Parkinson’s disease mice colonized with Streptococcus mutans,Germ-free (GF) mice experimentally colonized with live Streptococcus mutans thereby inducing Parkinson’s-like pathology,NA,NA,NA,16S,34,Illumina,log transformation,"ANCOM-BC,MaAsLin2",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 1A (Figure),15 October 2025,Yuvashree 1708,"Yuvashree 1708,Fiddyhamma",Colonization of Streptococcus mutans in germ-free (GF) mice.,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,1783272|1239|91061|186826|1300|1301|1309,Complete,KateRasheed
bsdb:40914795/1/1,40914795,"cross-sectional observational, not case-control",40914795,10.1186/s12866-025-04170-6,NA,"Shah S., Mu C., Shen-Tu G., Rohmann N., Schlicht K., Laudes M. , Shearer J.",Influence of dietary components on the gut microbiota of middle-aged adults: the gut-Mediterranean connection,BMC microbiology,2025,"Diet composition, Gut microbiota, Mediterranean diet, Metabolite, Nutrition",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,NA,NA,Q1 (Quartile 1) - Low level of diet,Q4 (Quartile 4) - High level of diet,Participants with a modified Mediterranean diet score (mMDS) based quartile: Q4 (mMDS 7 and 8),64,36,3 months,16S,34,Illumina,relative abundances,LEfSe,0.25,TRUE,3,NA,"age,body mass index,sex",NA,increased,NA,NA,NA,NA,Signature 1,Figure 3A,14 September 2025,SheikhAlMamun,SheikhAlMamun,Cladogram diagram showing the microbial taxa with significant differences between the study groups.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella corporis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae",1783272|1239|186801|3085636|186803|572511|40520;3379134|1224|28216|80840;3379134|976|200643|171549|171552|838|28128;3379134|976|200643|171549|171552;3379134|1224|28216|80840|995019,Complete,NA
bsdb:40914795/1/2,40914795,"cross-sectional observational, not case-control",40914795,10.1186/s12866-025-04170-6,NA,"Shah S., Mu C., Shen-Tu G., Rohmann N., Schlicht K., Laudes M. , Shearer J.",Influence of dietary components on the gut microbiota of middle-aged adults: the gut-Mediterranean connection,BMC microbiology,2025,"Diet composition, Gut microbiota, Mediterranean diet, Metabolite, Nutrition",Experiment 1,Canada,Homo sapiens,Feces,UBERON:0001988,NA,NA,Q1 (Quartile 1) - Low level of diet,Q4 (Quartile 4) - High level of diet,Participants with a modified Mediterranean diet score (mMDS) based quartile: Q4 (mMDS 7 and 8),64,36,3 months,16S,34,Illumina,relative abundances,LEfSe,0.25,TRUE,3,NA,"age,body mass index,sex",NA,increased,NA,NA,NA,NA,Signature 2,Figure 3A,14 September 2025,SheikhAlMamun,SheikhAlMamun,Cladogram diagram showing the microbial taxa with significant differences between the study groups,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales",1783272|1239|91061|1385;1783272|1239|91061|1385;1783272|1239|186801|3085636|186803|572511|1322;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|1239|91061|1385|539738|1378;1783272|1239|91061|1385|539738|1378|84135;1783272|1239|91061|186826,Complete,NA
bsdb:40914795/2/1,40914795,"cross-sectional observational, not case-control",40914795,10.1186/s12866-025-04170-6,NA,"Shah S., Mu C., Shen-Tu G., Rohmann N., Schlicht K., Laudes M. , Shearer J.",Influence of dietary components on the gut microbiota of middle-aged adults: the gut-Mediterranean connection,BMC microbiology,2025,"Diet composition, Gut microbiota, Mediterranean diet, Metabolite, Nutrition",Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,NA,NA,Q1 (Quartile 1) - Low level of diet,Q4 (Quartile 4) - High level of diet,Participants with a modified Mediterranean diet score (mMDS) based quartile: Q4 (mMDS 7 and 8),64,36,3 months,16S,34,Illumina,relative abundances,MaAsLin2,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,increased,NA,NA,NA,NA,Signature 1,Figure 3B,18 September 2025,SheikhAlMamun,SheikhAlMamun,"Microbiome Multivariable Association with Linear Models (MaAsLin2) analysis showing relationship between diet and gut microbial features (diet as fixed effects and age, sex, and body mass index as random effects)",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|976|200643|171549|2005519|1348911;3384189|32066|203490|203491|203492|848;3379134|976|200643|171549|171552|838;1783272|1239|526524|526525|2810281|191303;3379134|976|200643|171549|2005525|375288,Complete,NA
bsdb:40914795/2/2,40914795,"cross-sectional observational, not case-control",40914795,10.1186/s12866-025-04170-6,NA,"Shah S., Mu C., Shen-Tu G., Rohmann N., Schlicht K., Laudes M. , Shearer J.",Influence of dietary components on the gut microbiota of middle-aged adults: the gut-Mediterranean connection,BMC microbiology,2025,"Diet composition, Gut microbiota, Mediterranean diet, Metabolite, Nutrition",Experiment 2,Canada,Homo sapiens,Feces,UBERON:0001988,NA,NA,Q1 (Quartile 1) - Low level of diet,Q4 (Quartile 4) - High level of diet,Participants with a modified Mediterranean diet score (mMDS) based quartile: Q4 (mMDS 7 and 8),64,36,3 months,16S,34,Illumina,relative abundances,MaAsLin2,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,increased,NA,NA,NA,NA,Signature 2,Figure  3B,18 September 2025,SheikhAlMamun,SheikhAlMamun,"Microbiome Multivariable Association with Linear Models (MaAsLin2) analysis showing relationship between diet and gut microbial features (diet as fixed effects and age, sex, and body mass index as random effects)",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella",1783272|1239|186801|3082720|543314|109326;1783272|1239|526524|526525|128827|1573535,Complete,NA
bsdb:40914795/3/1,40914795,"cross-sectional observational, not case-control",40914795,10.1186/s12866-025-04170-6,NA,"Shah S., Mu C., Shen-Tu G., Rohmann N., Schlicht K., Laudes M. , Shearer J.",Influence of dietary components on the gut microbiota of middle-aged adults: the gut-Mediterranean connection,BMC microbiology,2025,"Diet composition, Gut microbiota, Mediterranean diet, Metabolite, Nutrition",Experiment 3,Canada,Homo sapiens,Feces,UBERON:0001988,NA,NA,Q1 (Quartile 1) - Low level of diet,Q4 (Quartile 4) - High level of diet,"Association between Mediterranean food components and gut microbiome. A Spearman correlation analysis between modified Mediterranean diet score (mMDS) and its dietary components. B Redundancy analysis to estimate explained variation (%) in gut microbial data by dietary groups, and its covariates (age, BMI, sex, PA, and BP); C Spearman correlation analysis of food components and differentially abundant taxa.",NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5C- Experiment 1,14 October 2025,SheikhAlMamun,SheikhAlMamun,"Experiment 1 – Whole Grains

Consumption of whole grains was associated with an increase in Clostridium XIVb, Parabacteroides, and Holdemanella. These bacteria are efficient degraders of resistant starches and contribute to metabolic resilience, reinforcing the role of grain-derived fiber in shaping gut ecology.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella",3379134|976|200643|171549|2005525|375288;1783272|1239|526524|526525|128827|1573535,Complete,NA
bsdb:40914795/4/1,40914795,"cross-sectional observational, not case-control",40914795,10.1186/s12866-025-04170-6,NA,"Shah S., Mu C., Shen-Tu G., Rohmann N., Schlicht K., Laudes M. , Shearer J.",Influence of dietary components on the gut microbiota of middle-aged adults: the gut-Mediterranean connection,BMC microbiology,2025,"Diet composition, Gut microbiota, Mediterranean diet, Metabolite, Nutrition",Experiment 4,Canada,Homo sapiens,Feces,UBERON:0001988,NA,NA,Q1 (Quartile 1) - Low level of diet,Q4 (Quartile 4) - High level of diet,"Association between Mediterranean food components and gut microbiome. A Spearman correlation analysis between modified Mediterranean diet score (mMDS) and its dietary components. B Redundancy analysis to estimate explained variation (%) in gut microbial data by dietary groups, and its covariates (age, BMI, sex, PA, and BP); C Spearman correlation analysis of food components and differentially abundant taxa.",NA,NA,3 months,16S,34,Illumina,NA,Spearman Correlation,0.05,FALSE,NA,NA,"age,body mass index,diet,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 5C,14 October 2025,SheikhAlMamun,SheikhAlMamun,"Experiment 2 – Legumes

Higher legume intake was associated with an increase in Prevotella, Holdemanella, and Anaerovorax. These taxa are recognized fiber degraders that produce short-chain fatty acids (SCFAs), suggesting legumes promote beneficial microbial activity related to carbohydrate metabolism.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax",3379134|976|200643|171549|171552|838;1783272|1239|526524|526525|128827|1573535;1783272|1239|186801|3082720|543314|109326,Complete,NA
bsdb:40914795/5/1,40914795,"cross-sectional observational, not case-control",40914795,10.1186/s12866-025-04170-6,NA,"Shah S., Mu C., Shen-Tu G., Rohmann N., Schlicht K., Laudes M. , Shearer J.",Influence of dietary components on the gut microbiota of middle-aged adults: the gut-Mediterranean connection,BMC microbiology,2025,"Diet composition, Gut microbiota, Mediterranean diet, Metabolite, Nutrition",Experiment 5,Canada,Homo sapiens,Feces,UBERON:0001988,NA,NA,Q1 (Quartile 1) - Low level of diet,Q4 (Quartile 4) - High level of diet,"Association between Mediterranean food components and gut microbiome. A Spearman correlation analysis between modified Mediterranean diet score (mMDS) and its dietary components. B Redundancy analysis to estimate explained variation (%) in gut microbial data by dietary groups, and its covariates (age, BMI, sex, PA, and BP); C Spearman correlation analysis of food components and differentially abundant taxa.",NA,NA,3 months,16S,34,Illumina,NA,Spearman Correlation,0.05,FALSE,NA,NA,"age,blood pressure,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 5C,14 October 2025,SheikhAlMamun,SheikhAlMamun,"Experiment 3 – Fruits

Increased fruit consumption was linked to a significant increase in Anaerovorax. This taxon participates in the fermentation of plant-derived polysaccharides and contributes to SCFA production, indicating a positive role of fruits in supporting gut microbial health.",increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,1783272|1239|186801|3082720|543314|109326,Complete,NA
bsdb:40914795/6/1,40914795,"cross-sectional observational, not case-control",40914795,10.1186/s12866-025-04170-6,NA,"Shah S., Mu C., Shen-Tu G., Rohmann N., Schlicht K., Laudes M. , Shearer J.",Influence of dietary components on the gut microbiota of middle-aged adults: the gut-Mediterranean connection,BMC microbiology,2025,"Diet composition, Gut microbiota, Mediterranean diet, Metabolite, Nutrition",Experiment 6,Canada,Homo sapiens,Feces,UBERON:0001988,NA,NA,Q1 (Quartile 1) - Low level of diet,Q4 (Quartile 4) - High level of diet,"Association between Mediterranean food components and gut microbiome. A Spearman correlation analysis between modified Mediterranean diet score (mMDS) and its dietary components. B Redundancy analysis to estimate explained variation (%) in gut microbial data by dietary groups, and its covariates (age, BMI, sex, PA, and BP); C Spearman correlation analysis of food components and differentially abundant taxa.",NA,NA,3 months,16S,34,Illumina,NA,Spearman Correlation,0.05,FALSE,NA,NA,"age,blood pressure,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 5C,14 October 2025,SheikhAlMamun,SheikhAlMamun,"Experiment 4 – Saturated Fats (SFA)

Higher intake of saturated fats was associated with an increase in Turicibacter and a decrease in Prevotella. This reflects the shift from fiber-degrading to fat-tolerant taxa with higher SFA intake.",increased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,1783272|1239|526524|526525|2810281|191303,Complete,NA
bsdb:40914795/6/2,40914795,"cross-sectional observational, not case-control",40914795,10.1186/s12866-025-04170-6,NA,"Shah S., Mu C., Shen-Tu G., Rohmann N., Schlicht K., Laudes M. , Shearer J.",Influence of dietary components on the gut microbiota of middle-aged adults: the gut-Mediterranean connection,BMC microbiology,2025,"Diet composition, Gut microbiota, Mediterranean diet, Metabolite, Nutrition",Experiment 6,Canada,Homo sapiens,Feces,UBERON:0001988,NA,NA,Q1 (Quartile 1) - Low level of diet,Q4 (Quartile 4) - High level of diet,"Association between Mediterranean food components and gut microbiome. A Spearman correlation analysis between modified Mediterranean diet score (mMDS) and its dietary components. B Redundancy analysis to estimate explained variation (%) in gut microbial data by dietary groups, and its covariates (age, BMI, sex, PA, and BP); C Spearman correlation analysis of food components and differentially abundant taxa.",NA,NA,3 months,16S,34,Illumina,NA,Spearman Correlation,0.05,FALSE,NA,NA,"age,blood pressure,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 5C,23 October 2025,SheikhAlMamun,SheikhAlMamun,"Experiment 4 – Saturated Fats (SFA)

Higher intake of saturated fats was associated with an increase in Turicibacter and a decrease in Prevotella. This reflects the shift from fiber-degrading to fat-tolerant taxa with higher SFA intake.",decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,NA
bsdb:40914795/7/1,40914795,"cross-sectional observational, not case-control",40914795,10.1186/s12866-025-04170-6,NA,"Shah S., Mu C., Shen-Tu G., Rohmann N., Schlicht K., Laudes M. , Shearer J.",Influence of dietary components on the gut microbiota of middle-aged adults: the gut-Mediterranean connection,BMC microbiology,2025,"Diet composition, Gut microbiota, Mediterranean diet, Metabolite, Nutrition",Experiment 7,Canada,Homo sapiens,Feces,UBERON:0001988,NA,NA,Q1 (Quartile 1) - Low level of diet,Q4 (Quartile 4) - High level of diet,"Association between Mediterranean food components and gut microbiome. A Spearman correlation analysis between modified Mediterranean diet score (mMDS) and its dietary components. B Redundancy analysis to estimate explained variation (%) in gut microbial data by dietary groups, and its covariates (age, BMI, sex, PA, and BP); C Spearman correlation analysis of food components and differentially abundant taxa.",NA,NA,3 months,16S,34,Illumina,NA,Spearman Correlation,0.05,FALSE,NA,NA,"age,blood pressure,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 5C,14 October 2025,SheikhAlMamun,SheikhAlMamun,"Experiment 5 – Fish (Protein Source)

Fish consumption was positively correlated with increased Turicibacter, indicating a diet-induced enrichment of taxa potentially involved in lipid metabolism and bile acid transformation.",increased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,1783272|1239|526524|526525|2810281|191303,Complete,NA
bsdb:40914795/8/1,40914795,"cross-sectional observational, not case-control",40914795,10.1186/s12866-025-04170-6,NA,"Shah S., Mu C., Shen-Tu G., Rohmann N., Schlicht K., Laudes M. , Shearer J.",Influence of dietary components on the gut microbiota of middle-aged adults: the gut-Mediterranean connection,BMC microbiology,2025,"Diet composition, Gut microbiota, Mediterranean diet, Metabolite, Nutrition",Experiment 8,Canada,Homo sapiens,Feces,UBERON:0001988,NA,NA,Q1 (Quartile 1) - Low level of diet,Q4 (Quartile 4) - High level of diet,"Association between Mediterranean food components and gut microbiome. A Spearman correlation analysis between modified Mediterranean diet score (mMDS) and its dietary components. B Redundancy analysis to estimate explained variation (%) in gut microbial data by dietary groups, and its covariates (age, BMI, sex, PA, and BP); C Spearman correlation analysis of food components and differentially abundant taxa.",NA,NA,3 months,16S,34,Illumina,NA,Spearman Correlation,0.05,FALSE,NA,NA,"age,blood pressure,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 5C,14 October 2025,SheikhAlMamun,SheikhAlMamun,"Experiment 6 – Fatty Acid Ratio (FA ratio)

A higher dietary fatty acid ratio (unsaturated/saturated fats) was positively associated with Prevotella, reflecting improved fiber metabolism and a microbial profile aligned with the Mediterranean dietary pattern.",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,NA
bsdb:40914795/9/1,40914795,"cross-sectional observational, not case-control",40914795,10.1186/s12866-025-04170-6,NA,"Shah S., Mu C., Shen-Tu G., Rohmann N., Schlicht K., Laudes M. , Shearer J.",Influence of dietary components on the gut microbiota of middle-aged adults: the gut-Mediterranean connection,BMC microbiology,2025,"Diet composition, Gut microbiota, Mediterranean diet, Metabolite, Nutrition",Experiment 9,Canada,Homo sapiens,Feces,UBERON:0001988,NA,NA,Q1 (Quartile 1) - Low level of diet,Q4 (Quartile 4) - High level of diet,"Association between Mediterranean food components and gut microbiome. A Spearman correlation analysis between modified Mediterranean diet score (mMDS) and its dietary components. B Redundancy analysis to estimate explained variation (%) in gut microbial data by dietary groups, and its covariates (age, BMI, sex, PA, and BP); C Spearman correlation analysis of food components and differentially abundant taxa.",NA,NA,3 months,16S,34,Illumina,NA,Spearman Correlation,0.05,FALSE,NA,NA,"age,blood pressure,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 5C,14 October 2025,SheikhAlMamun,SheikhAlMamun,"Experiment 7 – Alcohol

Alcohol consumption (likely from moderate red wine intake) was positively associated with Prevotella. This aligns with evidence linking polyphenol-rich alcoholic beverages with higher microbial diversity and beneficial taxa.",increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,NA
bsdb:40919785/1/1,40919785,"laboratory experiment,randomized controlled trial",40919785,10.1128/spectrum.01299-25,NA,"Zou Y.-.y., Yu B.-.j., He C., Ding L., Xu X., Wan J.-.h., Lei Y.-.p., Huang X., Xiong H.-.f., He W.-.h., Luo L.-.y., Xia L., Lv N.-.h. , Zhu Y.",Rifaximin reduces gut-derived inflammation in severe acute pancreatitis: an experimental animal model and randomized controlled trial,Microbiology spectrum,2025,"acute pancreatitis, gut microbiota, rifaximin, systemic inflammatory response syndrome",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Control (Con),Rifaximin (Rif),Wilcoxon rank-sum test identified the most differentially abundant phyla and genera between Con group and Rif group.,NA,NA,NA,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2E,28 September 2025,SheikhAlMamun,SheikhAlMamun,Wilcoxon rank-sum test identified the most differentially abundant phyla and genera between Con group and Rif group.,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Caryophanaceae|g__Sporosarcina",1783272|201174|1760|85007|1653|1716;3379134|1224|1236|91347|543|570;1783272|1239|91061|186826|33958|1578;3379134|1224;1783272|1239|91061|1385|186818|1569,Complete,NA
bsdb:40919785/1/2,40919785,"laboratory experiment,randomized controlled trial",40919785,10.1128/spectrum.01299-25,NA,"Zou Y.-.y., Yu B.-.j., He C., Ding L., Xu X., Wan J.-.h., Lei Y.-.p., Huang X., Xiong H.-.f., He W.-.h., Luo L.-.y., Xia L., Lv N.-.h. , Zhu Y.",Rifaximin reduces gut-derived inflammation in severe acute pancreatitis: an experimental animal model and randomized controlled trial,Microbiology spectrum,2025,"acute pancreatitis, gut microbiota, rifaximin, systemic inflammatory response syndrome",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Control (Con),Rifaximin (Rif),Wilcoxon rank-sum test identified the most differentially abundant phyla and genera between Con group and Rif group.,NA,NA,NA,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2E,28 September 2025,SheikhAlMamun,SheikhAlMamun,Wilcoxon rank-sum test identified the most differentially abundant phyla and genera between Con group and Rif group.,decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Atopostipes,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,,k__Pseudomonadati|p__Thermodesulfobacteriota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|201174;3379134|976|200643|171549|171550|239759;1783272|1239|91061|186826|186828|292480;3379134|1224|1236|91347|543|544;3379134|200940|3031449|213115|194924|872;1783272|1239|91061|186826|186827|66831;1783272|1239|186801|3085636|186803|1506553;;3379134|200940;1783272|1239|186801|186802|1980681;1783272|1239|91061|1385|90964|1279,Complete,NA
bsdb:40919785/2/1,40919785,"laboratory experiment,randomized controlled trial",40919785,10.1128/spectrum.01299-25,NA,"Zou Y.-.y., Yu B.-.j., He C., Ding L., Xu X., Wan J.-.h., Lei Y.-.p., Huang X., Xiong H.-.f., He W.-.h., Luo L.-.y., Xia L., Lv N.-.h. , Zhu Y.",Rifaximin reduces gut-derived inflammation in severe acute pancreatitis: an experimental animal model and randomized controlled trial,Microbiology spectrum,2025,"acute pancreatitis, gut microbiota, rifaximin, systemic inflammatory response syndrome",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Acute pancreatitis,EFO:1000652,CerBom,CerBomRif,"Wilcoxon rank-sum test identified the most differentially abundant phyla and genera between Cer + Bom group and Cer + Bom + Rif group. *P < 0.05, **P < 0.01, and ***P < 0.001. Rif, rifaximin; Cer, caerulein; Bom, bombesin; Con, control; PCoA, principal coordinate analysis.",NA,NA,NA,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2F,28 September 2025,SheikhAlMamun,SheikhAlMamun,"Wilcoxon rank-sum test identified the most differentially abundant phyla and genera between Cer + Bom group and Cer + Bom + Rif group. *P < 0.05, **P < 0.01, and ***P < 0.001. Rif, rifaximin; Cer, caerulein; Bom, bombesin; Con, control; PCoA, principal coordinate analysis. Increased in CerBomRif (blue)",increased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,,k__Pseudomonadati|p__Verrucomicrobiota,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas",1783272|201174;3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;1783272|201174|1760|85004|31953|1678;1783272|1239|526524|526525|128827|1729679;3379134|29547|3031852|213849|72293|209;3379134|1224|28216|80840|995019|577310;;3379134|74201;95818|2093818|2093825|2171986|1331051,Complete,NA
bsdb:40919785/2/2,40919785,"laboratory experiment,randomized controlled trial",40919785,10.1128/spectrum.01299-25,NA,"Zou Y.-.y., Yu B.-.j., He C., Ding L., Xu X., Wan J.-.h., Lei Y.-.p., Huang X., Xiong H.-.f., He W.-.h., Luo L.-.y., Xia L., Lv N.-.h. , Zhu Y.",Rifaximin reduces gut-derived inflammation in severe acute pancreatitis: an experimental animal model and randomized controlled trial,Microbiology spectrum,2025,"acute pancreatitis, gut microbiota, rifaximin, systemic inflammatory response syndrome",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Acute pancreatitis,EFO:1000652,CerBom,CerBomRif,"Wilcoxon rank-sum test identified the most differentially abundant phyla and genera between Cer + Bom group and Cer + Bom + Rif group. *P < 0.05, **P < 0.01, and ***P < 0.001. Rif, rifaximin; Cer, caerulein; Bom, bombesin; Con, control; PCoA, principal coordinate analysis.",NA,NA,NA,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2F,28 September 2025,SheikhAlMamun,SheikhAlMamun,"Wilcoxon rank-sum test identified the most differentially abundant phyla and genera between Cer + Bom group and Cer + Bom + Rif group. *P < 0.05, **P < 0.01, and ***P < 0.001. Rif, rifaximin; Cer, caerulein; Bom, bombesin; Con, control; PCoA, principal coordinate analysis.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Thermodesulfobacteriota",3379134|976|200643|171549|171552|1283313;3379134|200940|3031449|213115|194924|872;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|1506553;3379134|1224;3379134|200940,Complete,NA
bsdb:40919785/3/1,40919785,"laboratory experiment,randomized controlled trial",40919785,10.1128/spectrum.01299-25,NA,"Zou Y.-.y., Yu B.-.j., He C., Ding L., Xu X., Wan J.-.h., Lei Y.-.p., Huang X., Xiong H.-.f., He W.-.h., Luo L.-.y., Xia L., Lv N.-.h. , Zhu Y.",Rifaximin reduces gut-derived inflammation in severe acute pancreatitis: an experimental animal model and randomized controlled trial,Microbiology spectrum,2025,"acute pancreatitis, gut microbiota, rifaximin, systemic inflammatory response syndrome",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Acute pancreatitis,EFO:1000652,Con_T0,Con_T1,Rifaximin induces specific alterations in the abundance and function of the gut microbiota in patients predicted to SAP.  The top 30 differentially abundant bacterial species before and after treatment in the control group.,0,30,3 months,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7A,28 September 2025,SheikhAlMamun,SheikhAlMamun,Rifaximin induces specific alterations in the abundance and function of the gut microbiota in patients predicted to SAP. (A) The top 30 differentially abundant bacterial species before and after treatment in the control group.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus hirae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp.",1783272|1239|186801|3085636|186803|207244|649756;1783272|1239|186801|186802|1898207;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|91061|186826|81852|1350|1352;1783272|1239|91061|186826|81852|1350|1354;1783272|1239|91061|186826|81852|1350|35783;1783272|1239|186801|3085636|186803|841|2049040,Complete,NA
bsdb:40919785/3/2,40919785,"laboratory experiment,randomized controlled trial",40919785,10.1128/spectrum.01299-25,NA,"Zou Y.-.y., Yu B.-.j., He C., Ding L., Xu X., Wan J.-.h., Lei Y.-.p., Huang X., Xiong H.-.f., He W.-.h., Luo L.-.y., Xia L., Lv N.-.h. , Zhu Y.",Rifaximin reduces gut-derived inflammation in severe acute pancreatitis: an experimental animal model and randomized controlled trial,Microbiology spectrum,2025,"acute pancreatitis, gut microbiota, rifaximin, systemic inflammatory response syndrome",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Acute pancreatitis,EFO:1000652,Con_T0,Con_T1,Rifaximin induces specific alterations in the abundance and function of the gut microbiota in patients predicted to SAP.  The top 30 differentially abundant bacterial species before and after treatment in the control group.,0,30,3 months,16S,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 7A,28 September 2025,SheikhAlMamun,SheikhAlMamun,Rifaximin induces specific alterations in the abundance and function of the gut microbiota in patients predicted to SAP. (A) The top 30 differentially abundant bacterial species before and after treatment in the control group.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter asburiae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella sonnei,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella flexneri,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella megalosphaeroides",3379134|1224|1236|91347|543|561|562;1783272|1239|909932|909929|1843491|158846|437897;3379134|976|200643|171549|171550|239759|28117;3384189|32066|203490|203491|203492|848|850;1783272|1239|186801|186802|1898207;3379134|976|200643|171549|1853231|574697|544645;3379134|1224|1236|91347|543|547|61645;3379134|1224|1236|91347|543|620|624;3379134|976|200643|171549|171550|239759|328814;3379134|1224|1236|91347|543|620|623;3379134|1224|28216|80840|995019|40544|2494234,Complete,NA
bsdb:40919785/4/1,40919785,"laboratory experiment,randomized controlled trial",40919785,10.1128/spectrum.01299-25,NA,"Zou Y.-.y., Yu B.-.j., He C., Ding L., Xu X., Wan J.-.h., Lei Y.-.p., Huang X., Xiong H.-.f., He W.-.h., Luo L.-.y., Xia L., Lv N.-.h. , Zhu Y.",Rifaximin reduces gut-derived inflammation in severe acute pancreatitis: an experimental animal model and randomized controlled trial,Microbiology spectrum,2025,"acute pancreatitis, gut microbiota, rifaximin, systemic inflammatory response syndrome",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Acute pancreatitis,EFO:1000652,(Lower in RL_T1),(Higher in RL_T1),The top 30 differentially abundant bacterial species before and after treatment in the rifaximin group.,0,30,3 months,16S,NA,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7B,6 October 2025,SheikhAlMamun,SheikhAlMamun,Rifaximin induces specific alterations in the abundance and function of the gut microbiota in patients predicted to SAP.  (B) The top 30 differentially abundant bacterial species before and after treatment in the rifaximin group.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. AF28-13AC",1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|91061|186826|1300|1301|1318;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803|1649459|154046;1783272|1239|186801|3085636|186803|1898203;1783272|1239|186801|186802|216572|216851|1971605;1783272|1239|186801|3085636|186803|841|360807;1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|572511|418240;1783272|1239|186801|186802|216572|216851|2292234,Complete,NA
bsdb:40919785/4/2,40919785,"laboratory experiment,randomized controlled trial",40919785,10.1128/spectrum.01299-25,NA,"Zou Y.-.y., Yu B.-.j., He C., Ding L., Xu X., Wan J.-.h., Lei Y.-.p., Huang X., Xiong H.-.f., He W.-.h., Luo L.-.y., Xia L., Lv N.-.h. , Zhu Y.",Rifaximin reduces gut-derived inflammation in severe acute pancreatitis: an experimental animal model and randomized controlled trial,Microbiology spectrum,2025,"acute pancreatitis, gut microbiota, rifaximin, systemic inflammatory response syndrome",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Acute pancreatitis,EFO:1000652,(Lower in RL_T1),(Higher in RL_T1),The top 30 differentially abundant bacterial species before and after treatment in the rifaximin group.,0,30,3 months,16S,NA,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 7B,9 October 2025,SheikhAlMamun,SheikhAlMamun,Fig 7 Rifaximin induces specific alterations in the abundance and function of the gut microbiota in patients predicted to SAP. (B) The top 30 differentially abundant bacterial species before and after treatment in the rifaximin group.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella corporis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella|s__Tyzzerella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:520,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella veroralis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp. AF19-14,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.,s__uncultured bacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus",3379134|976|200643|171549|171552|838|28128;3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|47678;3379134|1224|1236|91347|543|547|158836;1783272|1239|186801|3085636|186803|1506577|2053632;3379134|976|200643|171549|171552|838|1262929;1783272|1239|909932|1843488|909930|33024|33025;3379134|976|200643|171549|171552|838|59823;3379134|976|200643|171549|171552|838|28137;3379134|976|200643|171549|815|816|338188;3379134|976|200643|171549|2005525|375288|2293114;3379134|1224|1236|91347|543|570|548;3379134|976|200643|171549|171550|239759|28117;3379134|976|200643|171549|815|816|28111;1783272|1239|186801|186802|31979|1485|59620;77133;3379134|976|200643|171549|815|816|246787,Complete,NA
bsdb:40919785/4/3,40919785,"laboratory experiment,randomized controlled trial",40919785,10.1128/spectrum.01299-25,NA,"Zou Y.-.y., Yu B.-.j., He C., Ding L., Xu X., Wan J.-.h., Lei Y.-.p., Huang X., Xiong H.-.f., He W.-.h., Luo L.-.y., Xia L., Lv N.-.h. , Zhu Y.",Rifaximin reduces gut-derived inflammation in severe acute pancreatitis: an experimental animal model and randomized controlled trial,Microbiology spectrum,2025,"acute pancreatitis, gut microbiota, rifaximin, systemic inflammatory response syndrome",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Acute pancreatitis,EFO:1000652,(Lower in RL_T1),(Higher in RL_T1),The top 30 differentially abundant bacterial species before and after treatment in the rifaximin group.,0,30,3 months,16S,NA,Illumina,NA,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 3,Figure 7B,9 October 2025,SheikhAlMamun,SheikhAlMamun,Fig 7 Rifaximin induces specific alterations in the abundance and function of the gut microbiota in patients predicted to SAP. (B) The top 30 differentially abundant bacterial species before and after treatment in the rifaximin group.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei",3379134|976|200643|171549|815|816|817;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|47678;1783272|1239|186801|3085636|186803|2719313|208479;1783272|1239|91061|186826|1300|1301|1318;3379134|1224|1236|91347|543|547|158836,Complete,NA
bsdb:40925897/1/1,40925897,time series / longitudinal observational,40925897,10.1038/s41467-025-63466-3,NA,"Oguri N., Kobayashi C., Ozawa Y., Kimura T., Nishinarita Y., Wada H., Nemoto N., Narita M., Tanigaki S., Hanawa T., Miyoshi J. , Hisamatsu T.",Vaginal Lactobacillus crispatus in early pregnancy associates with favorable gestational outcomes in a Japanese maternal-neonatal microbiome cohort,Nature communications,2025,NA,Experiment 1,Japan,Homo sapiens,Vagina,UBERON:0000996,Pregnancy,EFO:0002950,Postpartum,Pregnancy,"Patients whose pregnancies are at weeks 12, 20, 30 and 36",36,162,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2A,24 October 2025,Temmie,Temmie,Comparison of the relative abundance of bacterial genera in the vaginal microbiome between pregnancy and the postpartum period,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:40925897/1/2,40925897,time series / longitudinal observational,40925897,10.1038/s41467-025-63466-3,NA,"Oguri N., Kobayashi C., Ozawa Y., Kimura T., Nishinarita Y., Wada H., Nemoto N., Narita M., Tanigaki S., Hanawa T., Miyoshi J. , Hisamatsu T.",Vaginal Lactobacillus crispatus in early pregnancy associates with favorable gestational outcomes in a Japanese maternal-neonatal microbiome cohort,Nature communications,2025,NA,Experiment 1,Japan,Homo sapiens,Vagina,UBERON:0000996,Pregnancy,EFO:0002950,Postpartum,Pregnancy,"Patients whose pregnancies are at weeks 12, 20, 30 and 36",36,162,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2A,24 October 2025,Temmie,Temmie,Comparison of the relative abundance of bacterial genera in the vaginal microbiome between pregnancy and the postpartum period,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|g__Acidibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Myxococcota|o__Haliangiales|f__Kofleriaceae|g__Haliangium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,",3379134|1224|1236|1549619;1783272|201174|1760|2037|2049|1654;1783272|1239|1737404|1737405|1570339|165779;1783272|201174|84998|84999|1643824|1380;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;3379134|1224|28211|356|41294|374;3379134|29547|3031852|213849|72294|194;3379134|1224|28211|204458|76892;1783272|201174|1760|85007|1653|1716;1783272|1239|909932|1843489|31977|39948;3379134|1224|1236|91347|543|561;1783272|1239|186801|186802|1686313;1783272|1239|1737404|1737405|1570339|150022;3384189|32066|203490|203491|203492|848;3379134|2818505|3031714|224464|162027;1783272|1239|186801|186802|404402;1783272|1239|186801|3085636|186803;1783272|201174|1760|85007|2805586|1847725;1783272|201174|1760|85007|1762|1763;1783272|1239|1737404|1737405|1570339|162289;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171552|838;3379134|1224|1236|72274|135621|286;3379134|1224|28211|204457|41297|13687;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;1783272|201174|1760|2037|2049|184869;,Complete,Svetlana up
bsdb:40925897/2/1,40925897,time series / longitudinal observational,40925897,10.1038/s41467-025-63466-3,NA,"Oguri N., Kobayashi C., Ozawa Y., Kimura T., Nishinarita Y., Wada H., Nemoto N., Narita M., Tanigaki S., Hanawa T., Miyoshi J. , Hisamatsu T.",Vaginal Lactobacillus crispatus in early pregnancy associates with favorable gestational outcomes in a Japanese maternal-neonatal microbiome cohort,Nature communications,2025,NA,Experiment 2,Japan,Homo sapiens,Rectum,UBERON:0001052,Pregnancy,EFO:0002950,Postpartum,Pregnancy,"Patients whose pregnancies are at weeks 12, 20, 30 and 36",36,162,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4C,24 October 2025,Temmie,Temmie,Comparison of bacterial genera in the maternal gut microbiome between pregnancy and the postpartum period,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:40925897/2/2,40925897,time series / longitudinal observational,40925897,10.1038/s41467-025-63466-3,NA,"Oguri N., Kobayashi C., Ozawa Y., Kimura T., Nishinarita Y., Wada H., Nemoto N., Narita M., Tanigaki S., Hanawa T., Miyoshi J. , Hisamatsu T.",Vaginal Lactobacillus crispatus in early pregnancy associates with favorable gestational outcomes in a Japanese maternal-neonatal microbiome cohort,Nature communications,2025,NA,Experiment 2,Japan,Homo sapiens,Rectum,UBERON:0001052,Pregnancy,EFO:0002950,Postpartum,Pregnancy,"Patients whose pregnancies are at weeks 12, 20, 30 and 36",36,162,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4C,24 October 2025,Temmie,Temmie,Comparison of bacterial genera in the maternal gut microbiome between pregnancy and the postpartum period,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Howardella,1783272|1239|186801|186802|404402,Complete,Svetlana up
bsdb:40925897/3/1,40925897,time series / longitudinal observational,40925897,10.1038/s41467-025-63466-3,NA,"Oguri N., Kobayashi C., Ozawa Y., Kimura T., Nishinarita Y., Wada H., Nemoto N., Narita M., Tanigaki S., Hanawa T., Miyoshi J. , Hisamatsu T.",Vaginal Lactobacillus crispatus in early pregnancy associates with favorable gestational outcomes in a Japanese maternal-neonatal microbiome cohort,Nature communications,2025,NA,Experiment 3,Japan,Homo sapiens,Rectum,UBERON:0001052,Pregnancy,EFO:0002950,Early pregnancy (Week 12),Late pregnancy (Week 36),Patients whose pregnancies are at week 36,40,39,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,Signature 1,Figure 4D,24 October 2025,Temmie,Temmie,Comparison of bacterial genera in the maternal gut microbiome between early pregnancy (Week 12) and late pregnancy (Week 36),increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,Svetlana up
bsdb:40925897/3/2,40925897,time series / longitudinal observational,40925897,10.1038/s41467-025-63466-3,NA,"Oguri N., Kobayashi C., Ozawa Y., Kimura T., Nishinarita Y., Wada H., Nemoto N., Narita M., Tanigaki S., Hanawa T., Miyoshi J. , Hisamatsu T.",Vaginal Lactobacillus crispatus in early pregnancy associates with favorable gestational outcomes in a Japanese maternal-neonatal microbiome cohort,Nature communications,2025,NA,Experiment 3,Japan,Homo sapiens,Rectum,UBERON:0001052,Pregnancy,EFO:0002950,Early pregnancy (Week 12),Late pregnancy (Week 36),Patients whose pregnancies are at week 36,40,39,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,NA,Signature 2,Figure 4D,24 October 2025,Temmie,Temmie,Comparison of bacterial genera in the maternal gut microbiome between early pregnancy (Week 12) and late pregnancy (Week 36),decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|201174|1760|85007|2805586|1847725;3379134|976|200643|171549|171552|838,Complete,Svetlana up
bsdb:40925897/5/1,40925897,time series / longitudinal observational,40925897,10.1038/s41467-025-63466-3,NA,"Oguri N., Kobayashi C., Ozawa Y., Kimura T., Nishinarita Y., Wada H., Nemoto N., Narita M., Tanigaki S., Hanawa T., Miyoshi J. , Hisamatsu T.",Vaginal Lactobacillus crispatus in early pregnancy associates with favorable gestational outcomes in a Japanese maternal-neonatal microbiome cohort,Nature communications,2025,NA,Experiment 5,Japan,Homo sapiens,Rectum,UBERON:0001052,Gut microbiome measurement,EFO:0007874,Day 1,Day 4,Gut microbiome of neonates four (4) days after birth,28,43,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 5d,25 October 2025,EniolaAde,EniolaAde,Comparison of the relative abundant taxa in the neonatal gut microbiome between Day 1 and Day 4 after birth,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia",3379134|1224|1236|135625|712|724;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;33090|35493|3398|72025|3803|3814|508215,Complete,Svetlana up
bsdb:40925897/5/2,40925897,time series / longitudinal observational,40925897,10.1038/s41467-025-63466-3,NA,"Oguri N., Kobayashi C., Ozawa Y., Kimura T., Nishinarita Y., Wada H., Nemoto N., Narita M., Tanigaki S., Hanawa T., Miyoshi J. , Hisamatsu T.",Vaginal Lactobacillus crispatus in early pregnancy associates with favorable gestational outcomes in a Japanese maternal-neonatal microbiome cohort,Nature communications,2025,NA,Experiment 5,Japan,Homo sapiens,Rectum,UBERON:0001052,Gut microbiome measurement,EFO:0007874,Day 1,Day 4,Gut microbiome of neonates four (4) days after birth,28,43,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 5d,25 October 2025,EniolaAde,EniolaAde,Comparison of the relative abundant taxa in the neonatal gut microbiome between Day 1 and Day 4 after birth,decreased,"c__Candidatus Babeliae|o__Candidatus Babeliales,p__Candidatus Altimarinota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylorubrum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Qipengyuania,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae|g__Rheinheimera,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Myxococcota|o__Polyangiales|f__Polyangiaceae|g__Pajaroellobacter,k__Pseudomonadati|p__Bdellovibrionota|c__Oligoflexia,p__Candidatus Parcubacteria,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfurisporaceae|g__Desulfurispora,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Armatimonadota|c__Fimbriimonadia|o__Fimbriimonadales|f__Fimbriimonadaceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Myxococcota|o__Haliangiales|f__Kofleriaceae|g__Haliangium,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Obscuribacterales|f__Candidatus Obscuribacteraceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|g__Acidibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,",2497643|2497644;363464;3379134|1224|28211|356|119045|2282523;3379134|1224|28211|204457|335929|1855416;1783272|1239|526524|526525|2810280|3025755;1783272|1239|1737404|1737405|1570339|150022;3379134|976|117743|200644|2762318|59732;3379134|1224|1236|135613|1046|67575;3379134|1224|1236|135619|28256|2745;3379134|976|200643|171549|171552|838;3379134|2818505|3031712|49|1882917;3379134|3018035|1553900;221216;3384189|32066|203490|203491|203492|848;1783272|1239|186801|186802|3064153|510701;1783272|1239|186801|3085636|186803;1783272|67819|1663419|1663425|1663426;1783272|1239|186801;3379134|1224|1236|2887326|468|469;3379134|1224|1236|91347|543|620;3379134|976|117743|200644|49546|237;3379134|976|1853228|1853229|563835|504481;3379134|1224|28216|80840|80864;3379134|1224|28211|356|41294|374;3379134|2818505|3031714|224464|162027;1783272|1798710|1906152|3121626;1783272|201174|1760|85007|1762|1763;1783272|1239|91061|186826|33958|1578;3379134|1224|1236|1549619;3379134|1224|1236|72274|135621|286;3379134|1224|28211|204458|76892;3379134|1224|28211|204457|41297|13687;,Complete,Svetlana up
bsdb:40925897/6/1,40925897,time series / longitudinal observational,40925897,10.1038/s41467-025-63466-3,NA,"Oguri N., Kobayashi C., Ozawa Y., Kimura T., Nishinarita Y., Wada H., Nemoto N., Narita M., Tanigaki S., Hanawa T., Miyoshi J. , Hisamatsu T.",Vaginal Lactobacillus crispatus in early pregnancy associates with favorable gestational outcomes in a Japanese maternal-neonatal microbiome cohort,Nature communications,2025,NA,Experiment 6,Japan,Homo sapiens,Rectum,UBERON:0001052,Gut microbiome measurement,EFO:0007874,Day 4,Month 1,Gut microbiome of neonates one (1) month after birth,43,39,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 1,Figure 5e,25 October 2025,EniolaAde,EniolaAde,Comparison of the relative abundant taxa in the neonatal gut microbiome between Day 4 and month 1 after birth,increased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella",1783272|1239|1737404|1737405|1570339|150022;1783272|1239|1737404|1737405|1570339|165779;1783272|1239|1737404|1737405|1570339|162289;3379134|1224|1236|91347|543|547;1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|81852|1350;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|2037|2049|184869;1783272|1239|909932|1843489|31977|29465;3379134|976|200643|171549|171552|838;1783272|201174|1760|85009|31957|1912216;3379134|1224|1236|91347|543|620;1783272|1239|91061|186826|1300|1301;1783272|201174|1760|85007|2805586|1847725;1783272|1239|186801|186802|31979|1485;1783272|1239|909932|1843489|31977|39948;1783272|201174|84998|1643822|1643826|84111,Complete,Svetlana up
bsdb:40925897/6/2,40925897,time series / longitudinal observational,40925897,10.1038/s41467-025-63466-3,NA,"Oguri N., Kobayashi C., Ozawa Y., Kimura T., Nishinarita Y., Wada H., Nemoto N., Narita M., Tanigaki S., Hanawa T., Miyoshi J. , Hisamatsu T.",Vaginal Lactobacillus crispatus in early pregnancy associates with favorable gestational outcomes in a Japanese maternal-neonatal microbiome cohort,Nature communications,2025,NA,Experiment 6,Japan,Homo sapiens,Rectum,UBERON:0001052,Gut microbiome measurement,EFO:0007874,Day 4,Month 1,Gut microbiome of neonates one (1) month after birth,43,39,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 2,Figure 5e,25 October 2025,EniolaAde,EniolaAde,Comparison of the relative abundant taxa in the neonatal gut microbiome between Day 4 and month 1 after birth,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|1239|91061|1385|539738|1378;33090|35493|3398|72025|3803|3814|508215;1783272|1239|91061|1385|186817|1386;1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:40928220/1/1,40928220,"cross-sectional observational, not case-control",40928220,https://doi.org/10.1128/msystems.00044-25,NA,"Dong L., Yang J., Wu H., Sun Y., Liu J., Yuan H., Wang M., Dai Y., Teng F., Jing G. , Yang F.",Metagenomic research on the structural difference of plaque microbiome from different caries stages and the construction of a caries diagnostic model,mSystems,2025,"2bRAD sequencing for microbiome, dentin caries, diagnostic model, different caries stages, microbiome",Experiment 1,China,Homo sapiens,Dental plaque,UBERON:0016482,Dental caries,EFO:0003819,Relative health(RH)+Enamel caries(EC)+Dentin caries(DC),Confident health,"Plaque samples were collected from the buccal surface of caries-free subjects, defined as confident health(CH).",45,15,3 months,WMS,NA,2b-RAD,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 3B & S1b,10 October 2025,Chyono2,Chyono2,"Dominant species and genus with significant differences in different groups were detected by LDA effect size (LEfSe) analysis(LDA>4.0,P<0.05).",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia",1783272|201174|1760|85009|31957|2801844;1783272|201174|1760|85009|31957|2801844|1750;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85007|1653|1716|61592;1783272|201174|1760|85007|1653|1716|43768;3379134|1224|28216|80840|119060|47670;3379134|1224|28216|206351|481|482;3379134|1224|28216|206351|481|482|1107316;1783272|201174|1760|85006|1268|32207|172042;1783272|201174|1760|85006|1268|32207,Complete,KateRasheed
bsdb:40928220/2/1,40928220,"cross-sectional observational, not case-control",40928220,https://doi.org/10.1128/msystems.00044-25,NA,"Dong L., Yang J., Wu H., Sun Y., Liu J., Yuan H., Wang M., Dai Y., Teng F., Jing G. , Yang F.",Metagenomic research on the structural difference of plaque microbiome from different caries stages and the construction of a caries diagnostic model,mSystems,2025,"2bRAD sequencing for microbiome, dentin caries, diagnostic model, different caries stages, microbiome",Experiment 2,China,Homo sapiens,Dental plaque,UBERON:0016482,Dental caries,EFO:0003819,Enamel caries(EC) +Dentin caries(DC)+Confident Health(CH),Relative health(RH) group,"The RH group samples were collected from spatially paired “healthy” sites specifically, the non-cavitated buccal surfaces of caries-active deciduous molars.",45,15,3 months,WMS,NA,2b-RAD,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig 3B & S1b,11 October 2025,Chyono2,Chyono2,"Dominant species and genus with significant differences in different groups were detected by LDA effect size (LEfSe) analysis (LDA > 4.0, P < 0.05).",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga",1783272|201174|1760|2037|2049|1654|1655;1783272|201174|1760|2037|2049|1654|544580;3379134|976|117743|200644|49546|1016,Complete,KateRasheed
bsdb:40928220/3/1,40928220,"cross-sectional observational, not case-control",40928220,https://doi.org/10.1128/msystems.00044-25,NA,"Dong L., Yang J., Wu H., Sun Y., Liu J., Yuan H., Wang M., Dai Y., Teng F., Jing G. , Yang F.",Metagenomic research on the structural difference of plaque microbiome from different caries stages and the construction of a caries diagnostic model,mSystems,2025,"2bRAD sequencing for microbiome, dentin caries, diagnostic model, different caries stages, microbiome",Experiment 3,China,Homo sapiens,Dental plaque,UBERON:0016482,Dental caries,EFO:0003819,Relative Health(RH) +Dentin Caries(DC) +Confident Health(CH),Enamel Caries group,15 enamel caries (EC) samples were collected from the enamel layers of caries-active teeth.,45,15,3 months,WMS,NA,2b-RAD,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,fig3b & figS1b,11 October 2025,Chyono2,Chyono2,"Dominant species and genus with significant differences in different groups were detected by LDA effect size (LEfSe) analysis (LDA > 4.0, P < 0.05)",increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula",3384189|32066|203490|203491|203492|848;3379134|1224|1236|135625|712|724|727;3379134|1224|28216|80840|119060|47670|47671;3379134|976|200643|171549|171551|836|1583331;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1303;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|29466,Complete,KateRasheed
bsdb:40928220/4/1,40928220,"cross-sectional observational, not case-control",40928220,https://doi.org/10.1128/msystems.00044-25,NA,"Dong L., Yang J., Wu H., Sun Y., Liu J., Yuan H., Wang M., Dai Y., Teng F., Jing G. , Yang F.",Metagenomic research on the structural difference of plaque microbiome from different caries stages and the construction of a caries diagnostic model,mSystems,2025,"2bRAD sequencing for microbiome, dentin caries, diagnostic model, different caries stages, microbiome",Experiment 4,China,Homo sapiens,Dental plaque,UBERON:0016482,Dental caries,EFO:0003819,Enamel caries(EC) +Relative health(RH) + Confident Health(CH),Dentin Caries(DC group),15 dentin caries (DC) samples were collected from the dentin layers of caries-active teeth.,45,15,3 months,WMS,NA,2b-RAD,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,fig3b & figS1b,11 October 2025,Chyono2,Chyono2,"Dominant species and genus with significant differences in different groups were detected by LDA effect size(LEfSe)analysis (LDA>4.0,P<0.05)",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium acidifaciens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia|s__Massilia sp. GV045",3379134|976|200643|171549|171552|1283313;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|171552|838;1783272|201174|1760|85009|31957|1743;1783272|201174|1760|85009|31957|1743|556499;1783272|201174|1760|85004|31953|196081|230143;1783272|1239|91061|186826|1300|1301|1309;3379134|1224|28216|80840|75682|149698|2135672,Complete,KateRasheed
bsdb:40938872/1/1,40938872,prospective cohort,40938872,https://doi.org/10.1371/journal.pone.0320712,NA,"Ghouri Y.A., Ericsson A.C., Anderson J.M., George J.G., Parks E.J. , Anguah K.O.B.",Repopulation of the gut microbiota after a screening colonoscopy,PloS one,2025,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal health,EFO:0008460,Day 0 (Pre-colonoscopy),Day 3 (Post-colonoscopy),Day 3 post-colonoscopy refers to the third day of follow-up after a colorectal cancer screening colonoscopy,15,15,30 days,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,9 October 2025,Jesulolufemi,Jesulolufemi,Taxa at Day 3 post-colonoscopy compared to Day 0 baseline,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",3379134|976|200643|171549|815|816;1783272|1239|909932|1843489|31977|29465,Complete,KateRasheed
bsdb:40938872/1/2,40938872,prospective cohort,40938872,https://doi.org/10.1371/journal.pone.0320712,NA,"Ghouri Y.A., Ericsson A.C., Anderson J.M., George J.G., Parks E.J. , Anguah K.O.B.",Repopulation of the gut microbiota after a screening colonoscopy,PloS one,2025,NA,Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal health,EFO:0008460,Day 0 (Pre-colonoscopy),Day 3 (Post-colonoscopy),Day 3 post-colonoscopy refers to the third day of follow-up after a colorectal cancer screening colonoscopy,15,15,30 days,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6,9 October 2025,Jesulolufemi,Jesulolufemi,Taxa at Day 3 post-colonoscopy compared to Day 0 baseline,decreased,k__Bacillati|p__Bacillota,1783272|1239,Complete,KateRasheed
bsdb:40954286/1/1,40954286,laboratory experiment,40954286,https://doi.org/10.1038/s42255-025-01356-0,NA,"Alexis Anica, Amandine Verlande, Cholsoon Jang, Daniel Onofre, Gina Lee, Hosung Bae, Johnny Le, Jongwon Baek, Joohwan Kim, Ki-Hong Jang, Miranda E. Kelly, Miranda L. Lopez, Sang Hee Park, Selma Masri, Sung Kook Chun, Sunhee Jung, Won-Suk Song, Yujin Chun, Yasmine Alam, Varvara I. Rubtsova",Dietary fibre-adapted gut microbiome clears dietary fructose and reverses hepatic steatosis,Nature metabolism,2025,NA,Experiment 1,United States of America,Mus musculus,Jejunum,UBERON:0002115,Response to diet,EFO:0010757,Mice fed High fructose corn syrup (HFCS) alone  + Mice fed High fructose corn syrup (HFCS) with inulin,Mice fed Control water,Mice fed standard drinking water,16,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A,21 October 2025,Jamesonyebuchi,"Jamesonyebuchi,Fiddyhamma",Linear discriminant analysis effect size analysis (LEFSE) of jejunal microbial taxa.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae",1783272|1239|186801|186802|31979;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|81852;1783272|1239|186801|3082720|186804,Complete,NA
bsdb:40954286/2/1,40954286,laboratory experiment,40954286,https://doi.org/10.1038/s42255-025-01356-0,NA,"Alexis Anica, Amandine Verlande, Cholsoon Jang, Daniel Onofre, Gina Lee, Hosung Bae, Johnny Le, Jongwon Baek, Joohwan Kim, Ki-Hong Jang, Miranda E. Kelly, Miranda L. Lopez, Sang Hee Park, Selma Masri, Sung Kook Chun, Sunhee Jung, Won-Suk Song, Yujin Chun, Yasmine Alam, Varvara I. Rubtsova",Dietary fibre-adapted gut microbiome clears dietary fructose and reverses hepatic steatosis,Nature metabolism,2025,NA,Experiment 2,United States of America,Mus musculus,Jejunum,UBERON:0002115,Response to diet,EFO:0010757,Mice fed Control water  + Mice fed High fructose corn syrup (HFCS) with inulin,Mice fed High fructose corn syrup (HFCS) alone,Mice fed Mice fed High fructose corn syrup alone in their drinking water,16,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A,6 January 2026,Fiddyhamma,Fiddyhamma,Linear discriminant analysis effect size analysis (LEFSE) of jejunal microbial taxa.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia",1783272|1239|91061|186826|33958;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998,Complete,NA
bsdb:40954286/3/1,40954286,laboratory experiment,40954286,https://doi.org/10.1038/s42255-025-01356-0,NA,"Alexis Anica, Amandine Verlande, Cholsoon Jang, Daniel Onofre, Gina Lee, Hosung Bae, Johnny Le, Jongwon Baek, Joohwan Kim, Ki-Hong Jang, Miranda E. Kelly, Miranda L. Lopez, Sang Hee Park, Selma Masri, Sung Kook Chun, Sunhee Jung, Won-Suk Song, Yujin Chun, Yasmine Alam, Varvara I. Rubtsova",Dietary fibre-adapted gut microbiome clears dietary fructose and reverses hepatic steatosis,Nature metabolism,2025,NA,Experiment 3,United States of America,Mus musculus,Jejunum,UBERON:0002115,Response to diet,EFO:0010757,Mice fed Control water  + Mice fed High fructose corn syrup (HFCS) alone,Mice fed High fructose corn syrup (HFCS) with inulin,Mice fed High fructose corn syrup (HFCS) with inulin-enriched diet by replacing a small portion of corn starch (10% w/w) with inulin,16,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A,6 January 2026,Fiddyhamma,Fiddyhamma,Linear discriminant analysis effect size analysis (LEFSE) of jejunal microbial taxa.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia",1783272|1239|186801|3085636|186803;3379134|74201|203494|48461|203557;3379134|74201|203494|48461;3379134|74201|203494;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524,Complete,NA
bsdb:40954286/4/1,40954286,laboratory experiment,40954286,https://doi.org/10.1038/s42255-025-01356-0,NA,"Alexis Anica, Amandine Verlande, Cholsoon Jang, Daniel Onofre, Gina Lee, Hosung Bae, Johnny Le, Jongwon Baek, Joohwan Kim, Ki-Hong Jang, Miranda E. Kelly, Miranda L. Lopez, Sang Hee Park, Selma Masri, Sung Kook Chun, Sunhee Jung, Won-Suk Song, Yujin Chun, Yasmine Alam, Varvara I. Rubtsova",Dietary fibre-adapted gut microbiome clears dietary fructose and reverses hepatic steatosis,Nature metabolism,2025,NA,Experiment 4,United States of America,Mus musculus,Caecum,UBERON:0001153,Response to diet,EFO:0010757,Mice fed High fructose corn syrup (HFCS) alone  + Mice fed High fructose corn syrup (HFCS) with inulin,Mice fed Control water,Mice fed standard drinking water,16,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6B,6 January 2026,Fiddyhamma,Fiddyhamma,Linear discriminant analysis effect size analysis (LEFSE) of caecal microbial taxa.,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",1783272|1239|91061;1783272|1239|526524|526525|128827;1783272|1239|526524|526525;1783272|1239|526524;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|1300,Complete,NA
bsdb:40954286/5/1,40954286,laboratory experiment,40954286,https://doi.org/10.1038/s42255-025-01356-0,NA,"Alexis Anica, Amandine Verlande, Cholsoon Jang, Daniel Onofre, Gina Lee, Hosung Bae, Johnny Le, Jongwon Baek, Joohwan Kim, Ki-Hong Jang, Miranda E. Kelly, Miranda L. Lopez, Sang Hee Park, Selma Masri, Sung Kook Chun, Sunhee Jung, Won-Suk Song, Yujin Chun, Yasmine Alam, Varvara I. Rubtsova",Dietary fibre-adapted gut microbiome clears dietary fructose and reverses hepatic steatosis,Nature metabolism,2025,NA,Experiment 5,United States of America,Mus musculus,Caecum,UBERON:0001153,Response to diet,EFO:0010757,Mice fed Control water  + Mice fed High fructose corn syrup (HFCS) with inulin,Mice fed High fructose corn syrup (HFCS) alone,Mice fed High fructose corn syrup alone in their drinking water,16,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6B,6 January 2026,Fiddyhamma,Fiddyhamma,Linear discriminant analysis effect size analysis (LEFSE) of caecal microbial taxa.,increased,"k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres|o__Deferribacterales,k__Pseudomonadati|p__Deferribacterota|c__Deferribacteres,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia",3379134|200930|68337|191393|191394;3379134|200930|68337|191393;3379134|200930|68337;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998,Complete,NA
bsdb:40954286/6/1,40954286,laboratory experiment,40954286,https://doi.org/10.1038/s42255-025-01356-0,NA,"Alexis Anica, Amandine Verlande, Cholsoon Jang, Daniel Onofre, Gina Lee, Hosung Bae, Johnny Le, Jongwon Baek, Joohwan Kim, Ki-Hong Jang, Miranda E. Kelly, Miranda L. Lopez, Sang Hee Park, Selma Masri, Sung Kook Chun, Sunhee Jung, Won-Suk Song, Yujin Chun, Yasmine Alam, Varvara I. Rubtsova",Dietary fibre-adapted gut microbiome clears dietary fructose and reverses hepatic steatosis,Nature metabolism,2025,NA,Experiment 6,United States of America,Mus musculus,Caecum,UBERON:0001153,Response to diet,EFO:0010757,Mice fed Control water  + Mice fed High fructose corn syrup (HFCS) alone,Mice fed High fructose corn syrup (HFCS) with inulin,Mice fed High fructose corn syrup (HFCS) with inulin-enriched diet by replacing a small portion of corn starch (10% w/w) with inulin,16,8,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6B,6 January 2026,Fiddyhamma,Fiddyhamma,Linear discriminant analysis effect size analysis (LEFSE) of caecal microbial taxa.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria",3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643;3379134|1224|28211|204441|41295;3379134|1224|28211|204441;3379134|1224|28211,Complete,NA
bsdb:40954286/7/1,40954286,laboratory experiment,40954286,https://doi.org/10.1038/s42255-025-01356-0,NA,"Alexis Anica, Amandine Verlande, Cholsoon Jang, Daniel Onofre, Gina Lee, Hosung Bae, Johnny Le, Jongwon Baek, Joohwan Kim, Ki-Hong Jang, Miranda E. Kelly, Miranda L. Lopez, Sang Hee Park, Selma Masri, Sung Kook Chun, Sunhee Jung, Won-Suk Song, Yujin Chun, Yasmine Alam, Varvara I. Rubtsova",Dietary fibre-adapted gut microbiome clears dietary fructose and reverses hepatic steatosis,Nature metabolism,2025,NA,Experiment 7,United States of America,Mus musculus,Caecum,UBERON:0001153,Response to diet,EFO:0010757,Mice fed High fructose corn syrup (HFCS) alone,Mice fed High fructose corn syrup (HFCS) with inulin,Mice fed High fructose corn syrup (HFCS) with inulin-enriched diet by replacing a small portion of corn starch (10% w/w) with inulin,8,8,NA,16S,34,Illumina,relative abundances,"ANOVA,Post-Hoc Pairwise",1e-4,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 6G (right panel),6 January 2026,Fiddyhamma,Fiddyhamma,Relative abundance of Bacteroides acidifaciens in caecal contents,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,3379134|976|200643|171549|815|816|85831,Complete,NA
bsdb:40954286/8/1,40954286,laboratory experiment,40954286,https://doi.org/10.1038/s42255-025-01356-0,NA,"Alexis Anica, Amandine Verlande, Cholsoon Jang, Daniel Onofre, Gina Lee, Hosung Bae, Johnny Le, Jongwon Baek, Joohwan Kim, Ki-Hong Jang, Miranda E. Kelly, Miranda L. Lopez, Sang Hee Park, Selma Masri, Sung Kook Chun, Sunhee Jung, Won-Suk Song, Yujin Chun, Yasmine Alam, Varvara I. Rubtsova",Dietary fibre-adapted gut microbiome clears dietary fructose and reverses hepatic steatosis,Nature metabolism,2025,NA,Experiment 8,United States of America,Mus musculus,Caecum,UBERON:0001153,Response to diet,EFO:0010757,Mice fed Control water,Mice fed High fructose corn syrup (HFCS) with inulin,Mice fed High fructose corn syrup (HFCS) with inulin-enriched diet by replacing a small portion of corn starch (10% w/w) with inulin,8,8,NA,16S,34,Illumina,relative abundances,"ANOVA,Post-Hoc Pairwise",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6G (right panel),6 January 2026,Fiddyhamma,Fiddyhamma,Relative abundance of Bacteroides acidifaciens in caecal contents,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,3379134|976|200643|171549|815|816|85831,Complete,NA
bsdb:40981487/1/1,40981487,prospective cohort,40981487,https://doi.org/10.1128/msystems.00933-25,NA,"Song K., Luo J., Zhang Y., Wu D., Chen H. , Dai M.",Gut microbiome mediates the associations between lifestyle factors and risk of colorectal high-risk adenoma: results from a population-based cohort study,mSystems,2025,"colorectum, gut microbiota, lifestyle, mediation, precancerous lesions",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Control group,High-risk adenomas,Patients who have colorectal cancer with high-risk adenomas,1253,272,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,alcohol consumption measurement,family history of cancer,polyp,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A,8 October 2025,Temmie,Temmie,Analysis of the differential microbiota between high-risk adenomas (HRA) and control group,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella",3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378,Complete,Svetlana up
bsdb:40981487/1/2,40981487,prospective cohort,40981487,https://doi.org/10.1128/msystems.00933-25,NA,"Song K., Luo J., Zhang Y., Wu D., Chen H. , Dai M.",Gut microbiome mediates the associations between lifestyle factors and risk of colorectal high-risk adenoma: results from a population-based cohort study,mSystems,2025,"colorectum, gut microbiota, lifestyle, mediation, precancerous lesions",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Control group,High-risk adenomas,Patients who have colorectal cancer with high-risk adenomas,1253,272,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,alcohol consumption measurement,family history of cancer,polyp,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 2,Figure 3A,8 October 2025,Temmie,Temmie,Analysis of the differential microbiota between high-risk adenomas (HRA) and control group,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|1239|91061|186826|33958|1253;3379134|1224|1236|91347|1903414|583;3379134|1224|1236|72274|135621|286;1783272|1239|91061|1385|90964|1279,Complete,Svetlana up
bsdb:40981487/2/1,40981487,prospective cohort,40981487,https://doi.org/10.1128/msystems.00933-25,NA,"Song K., Luo J., Zhang Y., Wu D., Chen H. , Dai M.",Gut microbiome mediates the associations between lifestyle factors and risk of colorectal high-risk adenoma: results from a population-based cohort study,mSystems,2025,"colorectum, gut microbiota, lifestyle, mediation, precancerous lesions",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Alcohol consumption measurement,EFO:0007878,Low Alcohol Consumption,High Alcohol Consumption,Participants with high levels of alcohol consumption,NA,NA,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,body mass index,family history of cancer,polyp,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2A,12 October 2025,Temmie,Temmie,Association between the gut genera and the lifestyle factor (alcohol consumption) in the Chinese Cohort,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|g__Negativibacillus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",3384189|32066|203490|203491|203492|848;1783272|1239|526524|526525|128827|1573535;1783272|1239|909932|909929|1843491|158846;1783272|1239|1980693;1783272|201174|84998|1643822|1643826|84108;1783272|1239|186801|186802|31979|1485,Complete,Svetlana up
bsdb:40981487/2/2,40981487,prospective cohort,40981487,https://doi.org/10.1128/msystems.00933-25,NA,"Song K., Luo J., Zhang Y., Wu D., Chen H. , Dai M.",Gut microbiome mediates the associations between lifestyle factors and risk of colorectal high-risk adenoma: results from a population-based cohort study,mSystems,2025,"colorectum, gut microbiota, lifestyle, mediation, precancerous lesions",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Alcohol consumption measurement,EFO:0007878,Low Alcohol Consumption,High Alcohol Consumption,Participants with high levels of alcohol consumption,NA,NA,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,body mass index,family history of cancer,polyp,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 2A,12 October 2025,Temmie,Temmie,Association between the gut genera and the lifestyle factor (alcohol consumption) in the Chinese Cohort,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|186806|1730|39496;1783272|1239|186801|186802|186806|1730|39497;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|216572|292632,Complete,Svetlana up
bsdb:40981487/3/1,40981487,prospective cohort,40981487,https://doi.org/10.1128/msystems.00933-25,NA,"Song K., Luo J., Zhang Y., Wu D., Chen H. , Dai M.",Gut microbiome mediates the associations between lifestyle factors and risk of colorectal high-risk adenoma: results from a population-based cohort study,mSystems,2025,"colorectum, gut microbiota, lifestyle, mediation, precancerous lesions",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Body mass index,EFO:0004340,Low Body mass index,High Body mass index,Participants with high body mass index,NA,NA,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,body mass index,family history of cancer,polyp,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2A,12 October 2025,Temmie,Temmie,Association between gut genera and lifestyle risk factor (body mass index) in the Chinese cohort,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",1783272|1239|909932|1843489|31977|209879;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|3085636|186803|1766253;1783272|201174|84998|84999|84107|102106;1783272|1239|91061|186826|33958|46255,Complete,Svetlana up
bsdb:40981487/3/2,40981487,prospective cohort,40981487,https://doi.org/10.1128/msystems.00933-25,NA,"Song K., Luo J., Zhang Y., Wu D., Chen H. , Dai M.",Gut microbiome mediates the associations between lifestyle factors and risk of colorectal high-risk adenoma: results from a population-based cohort study,mSystems,2025,"colorectum, gut microbiota, lifestyle, mediation, precancerous lesions",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Body mass index,EFO:0004340,Low Body mass index,High Body mass index,Participants with high body mass index,NA,NA,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,body mass index,family history of cancer,polyp,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 2A,13 October 2025,Temmie,Temmie,Association between gut genera and lifestyle risk factor (body mass index) in the Chinese cohort,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;3379134|976|200643|171549|1853231|574697;1783272|1239|186801|186802|216572|946234;3379134|1224|1236|135625|712|724;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|3085636|186803|2316020|33038;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|171552|838;1783272|1239|526524|526525|2810280|3025755;1783272|1239|526524|526525|2810281|191303,Complete,Svetlana up
bsdb:40981487/4/1,40981487,prospective cohort,40981487,https://doi.org/10.1128/msystems.00933-25,NA,"Song K., Luo J., Zhang Y., Wu D., Chen H. , Dai M.",Gut microbiome mediates the associations between lifestyle factors and risk of colorectal high-risk adenoma: results from a population-based cohort study,mSystems,2025,"colorectum, gut microbiota, lifestyle, mediation, precancerous lesions",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Smoking status measurement,EFO:0006527,Low Cigarette consumption,High Cigarette consumption,Participants with a high level of cigarette consumption,NA,NA,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,alcohol consumption measurement,family history of cancer,polyp,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2A,13 October 2025,Temmie,Temmie,Association between gut genera and lifestyle risk factor (CIGARETTE CONSUMPTION) in the Chinese cohort,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter gnavus",1783272|201174|1760|2037|2049|1654;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|3085636|186803|2316020|33038,Complete,Svetlana up
bsdb:40981487/4/2,40981487,prospective cohort,40981487,https://doi.org/10.1128/msystems.00933-25,NA,"Song K., Luo J., Zhang Y., Wu D., Chen H. , Dai M.",Gut microbiome mediates the associations between lifestyle factors and risk of colorectal high-risk adenoma: results from a population-based cohort study,mSystems,2025,"colorectum, gut microbiota, lifestyle, mediation, precancerous lesions",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Smoking status measurement,EFO:0006527,Low Cigarette consumption,High Cigarette consumption,Participants with a high level of cigarette consumption,NA,NA,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,"age,alcohol consumption measurement,family history of cancer,polyp,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 2,Figure 2A,13 October 2025,Temmie,Temmie,Association between gut genera and lifestyle risk factor (CIGARETTE CONSUMPTION) in the Chinese cohort,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,3379134|1224|1236|135625|712|724,Complete,Svetlana up
bsdb:40981487/5/1,40981487,prospective cohort,40981487,https://doi.org/10.1128/msystems.00933-25,NA,"Song K., Luo J., Zhang Y., Wu D., Chen H. , Dai M.",Gut microbiome mediates the associations between lifestyle factors and risk of colorectal high-risk adenoma: results from a population-based cohort study,mSystems,2025,"colorectum, gut microbiota, lifestyle, mediation, precancerous lesions",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Alcohol consumption measurement,EFO:0007878,Low Alcohol Consumption (Japanese cohort),High Alcohol Consumption (Japanese cohort),Participants with high levels of alcohol consumption in the Japanese cohort,NA,NA,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,"age,body mass index,sex","age,alcohol consumption measurement,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2B,13 October 2025,Temmie,Temmie,Association between gut genera and lifestyle risk factor (ALCOHOL CONSUMPTION) in the EXTERNAL Japanese cohort,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Paratractidigestivibacter,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Intestinibacillus",1783272|1239|909932|1843489|31977|209879;1783272|1239|909932|909929|1843491|158846;1783272|1239|909932|1843489|31977|906;1783272|201174|84998|84999|1643824|2847314;3384189|32066|203490|203491|203492|848;1783272|1239|186801|186802|3085642|1928820,Complete,Svetlana up
bsdb:40981487/5/2,40981487,prospective cohort,40981487,https://doi.org/10.1128/msystems.00933-25,NA,"Song K., Luo J., Zhang Y., Wu D., Chen H. , Dai M.",Gut microbiome mediates the associations between lifestyle factors and risk of colorectal high-risk adenoma: results from a population-based cohort study,mSystems,2025,"colorectum, gut microbiota, lifestyle, mediation, precancerous lesions",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Alcohol consumption measurement,EFO:0007878,Low Alcohol Consumption (Japanese cohort),High Alcohol Consumption (Japanese cohort),Participants with high levels of alcohol consumption in the Japanese cohort,NA,NA,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,"age,body mass index,sex","age,alcohol consumption measurement,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 2B,13 October 2025,Temmie,Temmie,Association between gut genera and lifestyle risk factor (ALCOHOL CONSUMPTION) in the external Japanese cohort,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572|216851;1783272|201174|1760|85004|31953|1678,Complete,Svetlana up
bsdb:40981487/6/1,40981487,prospective cohort,40981487,https://doi.org/10.1128/msystems.00933-25,NA,"Song K., Luo J., Zhang Y., Wu D., Chen H. , Dai M.",Gut microbiome mediates the associations between lifestyle factors and risk of colorectal high-risk adenoma: results from a population-based cohort study,mSystems,2025,"colorectum, gut microbiota, lifestyle, mediation, precancerous lesions",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Body mass index,EFO:0004340,Low Body mass index (Japanese cohort),High Body mass index (Japanese cohort),Participants with high body mass index in the Japanese cohort,NA,NA,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,"age,body mass index,sex","age,alcohol consumption measurement,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2B,13 October 2025,Temmie,Temmie,Association between gut genera and lifestyle risk factor (BODY MASS INDEX) in the EXTERNAL Japanese cohort.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella",1783272|1239|909932|1843488|909930|904;1783272|1239|909932|1843489|31977|209879;3384189|32066|203490|203491|203492|848;1783272|1239|186801|186802|31979|1485;1783272|1239|91061|186826|186828|117563,Complete,Svetlana up
bsdb:40981487/6/2,40981487,prospective cohort,40981487,https://doi.org/10.1128/msystems.00933-25,NA,"Song K., Luo J., Zhang Y., Wu D., Chen H. , Dai M.",Gut microbiome mediates the associations between lifestyle factors and risk of colorectal high-risk adenoma: results from a population-based cohort study,mSystems,2025,"colorectum, gut microbiota, lifestyle, mediation, precancerous lesions",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Body mass index,EFO:0004340,Low Body mass index (Japanese cohort),High Body mass index (Japanese cohort),Participants with high body mass index in the Japanese cohort,NA,NA,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,"age,body mass index,sex","age,alcohol consumption measurement,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 2B,13 October 2025,Temmie,Temmie,Association between gut genera and lifestyle risk factor (BODY MASS INDEX) based on an EXTERNAL Japanese cohort,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",3379134|1224|1236|135624|84642;1783272|201174|1760|85004|31953|1678;3384194|508458|649775|649776|649777|508459;1783272|1239|186801|3085636|186803|1432051;1783272|1239|91061|186826|81852;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|186802|1392389;1783272|1239|186801|3085636|186803;3379134|1224|28211|356|119045|407;1783272|1239|186801|186802|216572;1783272|1239|186801;3379134|200940|3031449|213115|194924|872,Complete,Svetlana up
bsdb:40981487/7/1,40981487,prospective cohort,40981487,https://doi.org/10.1128/msystems.00933-25,NA,"Song K., Luo J., Zhang Y., Wu D., Chen H. , Dai M.",Gut microbiome mediates the associations between lifestyle factors and risk of colorectal high-risk adenoma: results from a population-based cohort study,mSystems,2025,"colorectum, gut microbiota, lifestyle, mediation, precancerous lesions",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Smoking status measurement,EFO:0006527,High Cigarette consumption (Japanese cohort),Low Cigarette consumption (Japanese cohort),Participants with high levels of cigarette consumption in the Japanese Cohort,NA,NA,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,"age,body mass index,sex","age,alcohol consumption measurement,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2B,13 October 2025,Temmie,Temmie,Association between gut genera and lifestyle risk factor (CIGARETTE CONSUMPTION) in the EXTERNAL Japanese c\ohort,increased,"k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Solibaculum,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",3379134|203691|203692|1643686|143786|29521;1783272|1239|186801|186802|216572|2842531;1783272|1239|526524|526525|128827,Complete,Svetlana up
bsdb:40981487/7/2,40981487,prospective cohort,40981487,https://doi.org/10.1128/msystems.00933-25,NA,"Song K., Luo J., Zhang Y., Wu D., Chen H. , Dai M.",Gut microbiome mediates the associations between lifestyle factors and risk of colorectal high-risk adenoma: results from a population-based cohort study,mSystems,2025,"colorectum, gut microbiota, lifestyle, mediation, precancerous lesions",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Smoking status measurement,EFO:0006527,High Cigarette consumption (Japanese cohort),Low Cigarette consumption (Japanese cohort),Participants with high levels of cigarette consumption in the Japanese Cohort,NA,NA,NA,16S,4,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,"age,body mass index,sex","age,alcohol consumption measurement,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 2B,13 October 2025,Temmie,Temmie,Association between gut genera and lifestyle risk factor (CIGARETTE CONSUMPTION) in the EXTERNAL Japanese cohort,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Merdimmobilis",3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|2719231;1783272|1239|186801|186802|216572|3028852,Complete,Svetlana up
bsdb:40981487/8/1,40981487,prospective cohort,40981487,https://doi.org/10.1128/msystems.00933-25,NA,"Song K., Luo J., Zhang Y., Wu D., Chen H. , Dai M.",Gut microbiome mediates the associations between lifestyle factors and risk of colorectal high-risk adenoma: results from a population-based cohort study,mSystems,2025,"colorectum, gut microbiota, lifestyle, mediation, precancerous lesions",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Control group,High-risk adenomas,Patients who have high-risk adenomas,1253,272,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3B,14 October 2025,Temmie,Temmie,LefSe analysis of the differences in genera in the high-risk adenoma group and control group,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter",1783272|201174|1760|2037|2049|1654;3384189|32066|203490|203491|203492|848;1783272|1239|91061|1385|539738|1378;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3082720|186804|1505652,Complete,Svetlana up
bsdb:40981487/8/2,40981487,prospective cohort,40981487,https://doi.org/10.1128/msystems.00933-25,NA,"Song K., Luo J., Zhang Y., Wu D., Chen H. , Dai M.",Gut microbiome mediates the associations between lifestyle factors and risk of colorectal high-risk adenoma: results from a population-based cohort study,mSystems,2025,"colorectum, gut microbiota, lifestyle, mediation, precancerous lesions",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Control group,High-risk adenomas,Patients who have high-risk adenomas,1253,272,NA,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3B,14 October 2025,Temmie,Temmie,LefSe analysis of the differences in genera between the high-risk adenoma group and the control group,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",1783272|1239|909932|1843489|31977|39948;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|28050;1783272|1239|186801|186802|216572|459786;3379134|1224|28216|80840|995019|577310;3379134|976|200643|171549|171552,Complete,Svetlana up
bsdb:40982577/1/1,40982577,laboratory experiment,40982577,10.1099/jmm.0.002069,https://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.002069#html_fulltext,"Lu M.L., Wu J.L., Zhu J.W., Liu L., Li M.Z., Yu Y. , Pan L.",Changes in the gut microbiota in mice exposed to chronic intermittent hypoxia,Journal of medical microbiology,2025,"gut microbiota, intermittent hypoxia, normoxia, obstructive sleep apnoea",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Hypoxia,EFO:0009444,Post Intervention Normoxia (NM6),Post Intervention Chronic Intermittent Hypoxia (CIH6),"Mice placed into a hypoxic simulation chamber daily from 8 : 00 am to 4 : 00 pm, exposing them to a Chronic Intermittent Hypoxia environment for 8 h daily for 6 weeks.",10,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Figure 4A, B",29 October 2025,Conwauzor,"Conwauzor,Fiddyhamma",LEfSe analysis (LDA score > 2.5) and relative abundance comparisons identifying taxa with significant differential abundance between the NM6 (normoxia) and CIH6 (chronic intermittent hypoxia) groups.,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",1783272|1239|91061;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005519|397864;3379134|976|200643|171549|2005519;1783272|1239|91061|186826|33958;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|171550,Complete,KateRasheed
bsdb:40982577/1/2,40982577,laboratory experiment,40982577,10.1099/jmm.0.002069,https://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.002069#html_fulltext,"Lu M.L., Wu J.L., Zhu J.W., Liu L., Li M.Z., Yu Y. , Pan L.",Changes in the gut microbiota in mice exposed to chronic intermittent hypoxia,Journal of medical microbiology,2025,"gut microbiota, intermittent hypoxia, normoxia, obstructive sleep apnoea",Experiment 1,China,Mus musculus,Feces,UBERON:0001988,Hypoxia,EFO:0009444,Post Intervention Normoxia (NM6),Post Intervention Chronic Intermittent Hypoxia (CIH6),"Mice placed into a hypoxic simulation chamber daily from 8 : 00 am to 4 : 00 pm, exposing them to a Chronic Intermittent Hypoxia environment for 8 h daily for 6 weeks.",10,10,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,"Fig 4A, B",29 October 2025,Conwauzor,"Conwauzor,Fiddyhamma",LEfSe analysis (LDA score > 2.5) and relative abundance comparisons identifying taxa with significant differential abundance between the NM6 (normoxia) and CIH6 (chronic intermittent hypoxia) groups.,decreased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Paraeggerthella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",1783272|201174|84992;1783272|201174|1760|2037;1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678;1783272|1239|909932|1843489|31977|39948;3379134|29547|3031852|213849|72293|209;3379134|976|200643|171549|2005473;1783272|201174|84998|1643822|1643826|651554;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552,Complete,KateRasheed
bsdb:40982577/2/1,40982577,laboratory experiment,40982577,10.1099/jmm.0.002069,https://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.002069#html_fulltext,"Lu M.L., Wu J.L., Zhu J.W., Liu L., Li M.Z., Yu Y. , Pan L.",Changes in the gut microbiota in mice exposed to chronic intermittent hypoxia,Journal of medical microbiology,2025,"gut microbiota, intermittent hypoxia, normoxia, obstructive sleep apnoea",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Oxygen,CHEBI:15379,Pre Intervention Normoxia (NM0),Post Intervention Normoxia (NM6),Post Intervention Normoxia (NM6) mice with oxygen content levels of 21% (normoxic state),10,10,NA,16S,34,Illumina,relative abundances,T-Test,0.01,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Figure 3C, D",30 December 2025,Fiddyhamma,Fiddyhamma,"Comparison of composition and distribution of mouse gut microbiota at the phylum, genus levels.",increased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,p__Candidatus Saccharimonadota",1783272|1239;3379134|976|200643|171549|171552|838;95818,Complete,KateRasheed
bsdb:40982577/2/2,40982577,laboratory experiment,40982577,10.1099/jmm.0.002069,https://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.002069#html_fulltext,"Lu M.L., Wu J.L., Zhu J.W., Liu L., Li M.Z., Yu Y. , Pan L.",Changes in the gut microbiota in mice exposed to chronic intermittent hypoxia,Journal of medical microbiology,2025,"gut microbiota, intermittent hypoxia, normoxia, obstructive sleep apnoea",Experiment 2,China,Mus musculus,Feces,UBERON:0001988,Oxygen,CHEBI:15379,Pre Intervention Normoxia (NM0),Post Intervention Normoxia (NM6),Post Intervention Normoxia (NM6) mice with oxygen content levels of 21% (normoxic state),10,10,NA,16S,34,Illumina,relative abundances,T-Test,0.01,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 3E,30 December 2025,Fiddyhamma,Fiddyhamma,Comparison of composition and distribution of mouse gut microbiota at the genus levels.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,3379134|976|200643|171549|171550|28138,Complete,KateRasheed
bsdb:40982577/3/2,40982577,laboratory experiment,40982577,10.1099/jmm.0.002069,https://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.002069#html_fulltext,"Lu M.L., Wu J.L., Zhu J.W., Liu L., Li M.Z., Yu Y. , Pan L.",Changes in the gut microbiota in mice exposed to chronic intermittent hypoxia,Journal of medical microbiology,2025,"gut microbiota, intermittent hypoxia, normoxia, obstructive sleep apnoea",Experiment 3,China,Mus musculus,Feces,UBERON:0001988,Hypoxia,EFO:0009444,Pre Intervention Chronic Intermittent Hypoxia (CIH0),Post Intervention Chronic Intermittent Hypoxia (CIH6),"Mice placed into a hypoxic simulation chamber daily from 8 : 00 am to 4 : 00 pm, exposing them to a Chronic Intermittent Hypoxia environment for 8 h daily for 6 weeks.",10,10,NA,16S,34,Illumina,relative abundances,T-Test,0.01,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Figure 3C, E",30 December 2025,Fiddyhamma,Fiddyhamma,"Comparison of composition and distribution of mouse gut microbiota at the phylum, genus levels.",increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",1783272|1239;1783272|1239|186801|186802|216572|119852,Complete,KateRasheed
bsdb:40982577/4/1,40982577,laboratory experiment,40982577,10.1099/jmm.0.002069,https://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.002069#html_fulltext,"Lu M.L., Wu J.L., Zhu J.W., Liu L., Li M.Z., Yu Y. , Pan L.",Changes in the gut microbiota in mice exposed to chronic intermittent hypoxia,Journal of medical microbiology,2025,"gut microbiota, intermittent hypoxia, normoxia, obstructive sleep apnoea",Experiment 4,China,Mus musculus,Feces,UBERON:0001988,Hypoxia,EFO:0009444,Post Intervention Normoxia (NM6),Post Intervention Chronic Intermittent Hypoxia (CIH6),"Mice placed into a hypoxic simulation chamber daily from 8 : 00 am to 4 : 00 pm, exposing them to a Chronic Intermittent Hypoxia environment for 8 h daily for 6 weeks.",10,10,NA,16S,34,Illumina,relative abundances,T-Test,0.01,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3D,30 December 2025,Fiddyhamma,Fiddyhamma,Comparison of composition and distribution of mouse gut microbiota at the genus levels.,decreased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,KateRasheed
bsdb:40982577/5/1,40982577,laboratory experiment,40982577,10.1099/jmm.0.002069,https://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.002069#html_fulltext,"Lu M.L., Wu J.L., Zhu J.W., Liu L., Li M.Z., Yu Y. , Pan L.",Changes in the gut microbiota in mice exposed to chronic intermittent hypoxia,Journal of medical microbiology,2025,"gut microbiota, intermittent hypoxia, normoxia, obstructive sleep apnoea",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Hypoxia,EFO:0009444,Pre Intervention Chronic Intermittent Hypoxia (CIH0),Post Intervention Chronic Intermittent Hypoxia (CIH6),"Mice placed into a hypoxic simulation chamber daily from 8 : 00 am to 4 : 00 pm, exposing them to a Chronic Intermittent Hypoxia environment for 8 h daily for 6 weeks.",10,10,NA,16S,34,Illumina,relative abundances,T-Test,0.001,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 3D,30 December 2025,Fiddyhamma,Fiddyhamma,Comparison of composition and distribution of mouse gut microbiota at the genus levels.,increased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,1783272|1239|526524|526525|128827|174708,Complete,NA
bsdb:40982577/5/2,40982577,laboratory experiment,40982577,10.1099/jmm.0.002069,https://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.002069#html_fulltext,"Lu M.L., Wu J.L., Zhu J.W., Liu L., Li M.Z., Yu Y. , Pan L.",Changes in the gut microbiota in mice exposed to chronic intermittent hypoxia,Journal of medical microbiology,2025,"gut microbiota, intermittent hypoxia, normoxia, obstructive sleep apnoea",Experiment 5,China,Mus musculus,Feces,UBERON:0001988,Hypoxia,EFO:0009444,Pre Intervention Chronic Intermittent Hypoxia (CIH0),Post Intervention Chronic Intermittent Hypoxia (CIH6),"Mice placed into a hypoxic simulation chamber daily from 8 : 00 am to 4 : 00 pm, exposing them to a Chronic Intermittent Hypoxia environment for 8 h daily for 6 weeks.",10,10,NA,16S,34,Illumina,relative abundances,T-Test,0.001,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Figure 3D, E",30 December 2025,Fiddyhamma,Fiddyhamma,Comparison of composition and distribution of mouse gut microbiota at the genus levels.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|201174|1760|85004|31953|1678;1783272|1239|91061|186826|33958|1578,Complete,NA
bsdb:40982577/6/1,40982577,laboratory experiment,40982577,10.1099/jmm.0.002069,https://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.002069#html_fulltext,"Lu M.L., Wu J.L., Zhu J.W., Liu L., Li M.Z., Yu Y. , Pan L.",Changes in the gut microbiota in mice exposed to chronic intermittent hypoxia,Journal of medical microbiology,2025,"gut microbiota, intermittent hypoxia, normoxia, obstructive sleep apnoea",Experiment 6,China,Mus musculus,Feces,UBERON:0001988,Oxygen,CHEBI:15379,Pre Intervention Normoxia (NM0),Post Intervention Normoxia (NM6),Post Intervention Normoxia (NM6) mice with oxygen content levels of 21% (normoxic state),10,10,NA,16S,34,Illumina,relative abundances,T-Test,0.001,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 3E,30 December 2025,Fiddyhamma,Fiddyhamma,Comparison of composition and distribution of mouse gut microbiota at the genus levels.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,KateRasheed
bsdb:40982577/8/1,40982577,laboratory experiment,40982577,10.1099/jmm.0.002069,https://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.002069#html_fulltext,"Lu M.L., Wu J.L., Zhu J.W., Liu L., Li M.Z., Yu Y. , Pan L.",Changes in the gut microbiota in mice exposed to chronic intermittent hypoxia,Journal of medical microbiology,2025,"gut microbiota, intermittent hypoxia, normoxia, obstructive sleep apnoea",Experiment 8,China,Mus musculus,Feces,UBERON:0001988,Hypoxia,EFO:0009444,Pre Intervention Normoxia (NM0),Pre Intervention Chronic Intermittent Hypoxia (CIH0),"Mice placed into a hypoxic simulation chamber daily from 8 : 00 am to 4 : 00 pm, exposing them to a Chronic Intermittent Hypoxia environment for 8 h daily for 6 weeks.",10,10,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3C,30 December 2025,Fiddyhamma,Fiddyhamma,Comparison of composition and distribution of mouse gut microbiota at the phylum levels.,increased,k__Bacillati|p__Cyanobacteriota,1783272|1117,Complete,KateRasheed
bsdb:40982577/9/1,40982577,laboratory experiment,40982577,10.1099/jmm.0.002069,https://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.002069#html_fulltext,"Lu M.L., Wu J.L., Zhu J.W., Liu L., Li M.Z., Yu Y. , Pan L.",Changes in the gut microbiota in mice exposed to chronic intermittent hypoxia,Journal of medical microbiology,2025,"gut microbiota, intermittent hypoxia, normoxia, obstructive sleep apnoea",Experiment 9,China,Mus musculus,Feces,UBERON:0001988,Oxygen,CHEBI:15379,Pre Intervention Normoxia (NM0),Post Intervention Normoxia (NM6),Post Intervention Normoxia (NM6) mice with oxygen content levels of 21% (normoxic state),10,10,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Figure 3C, D and E",30 December 2025,Fiddyhamma,Fiddyhamma,"Comparison of composition and distribution of mouse gut microbiota at the phylum, genus levels.",increased,"k__Pseudomonadati|p__Pseudomonadota,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",3379134|1224;1783272|1239|526524|526525|128827|174708;3379134|1224|28216|80840|995019|40544;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|171552|838;3379134|29547|3031852|213849|72293|209;3379134|976|200643|171549|815|816,Complete,NA
bsdb:40982577/9/2,40982577,laboratory experiment,40982577,10.1099/jmm.0.002069,https://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.002069#html_fulltext,"Lu M.L., Wu J.L., Zhu J.W., Liu L., Li M.Z., Yu Y. , Pan L.",Changes in the gut microbiota in mice exposed to chronic intermittent hypoxia,Journal of medical microbiology,2025,"gut microbiota, intermittent hypoxia, normoxia, obstructive sleep apnoea",Experiment 9,China,Mus musculus,Feces,UBERON:0001988,Oxygen,CHEBI:15379,Pre Intervention Normoxia (NM0),Post Intervention Normoxia (NM6),Post Intervention Normoxia (NM6) mice with oxygen content levels of 21% (normoxic state),10,10,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Figure 3C, D and E",30 December 2025,Fiddyhamma,Fiddyhamma,"Comparison of composition and distribution of mouse gut microbiota at the phylum, genus levels.",decreased,"k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter",3379134|74201;3379134|74201|203494|48461|1647988|239934;3379134|200940|3031449|213115|194924|872;3379134|976|200643|171549|1853231|283168,Complete,NA
bsdb:40982577/10/1,40982577,laboratory experiment,40982577,10.1099/jmm.0.002069,https://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.002069#html_fulltext,"Lu M.L., Wu J.L., Zhu J.W., Liu L., Li M.Z., Yu Y. , Pan L.",Changes in the gut microbiota in mice exposed to chronic intermittent hypoxia,Journal of medical microbiology,2025,"gut microbiota, intermittent hypoxia, normoxia, obstructive sleep apnoea",Experiment 10,China,Mus musculus,Feces,UBERON:0001988,Hypoxia,EFO:0009444,Post Intervention Normoxia (NM6),Post Intervention Chronic Intermittent Hypoxia (CIH6),"Mice placed into a hypoxic simulation chamber daily from 8 : 00 am to 4 : 00 pm, exposing them to a Chronic Intermittent Hypoxia environment for 8 h daily for 6 weeks.",10,10,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3E,30 December 2025,Fiddyhamma,Fiddyhamma,Comparison of composition and distribution of mouse gut microbiota at the genus levels.,decreased,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,3379134|29547|3031852|213849|72293|209,Complete,KateRasheed
bsdb:40982577/11/1,40982577,laboratory experiment,40982577,10.1099/jmm.0.002069,https://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.002069#html_fulltext,"Lu M.L., Wu J.L., Zhu J.W., Liu L., Li M.Z., Yu Y. , Pan L.",Changes in the gut microbiota in mice exposed to chronic intermittent hypoxia,Journal of medical microbiology,2025,"gut microbiota, intermittent hypoxia, normoxia, obstructive sleep apnoea",Experiment 11,China,Mus musculus,Feces,UBERON:0001988,Hypoxia,EFO:0009444,Pre Intervention Chronic Intermittent Hypoxia (CIH0),Post Intervention Chronic Intermittent Hypoxia (CIH6),"Mice placed into a hypoxic simulation chamber daily from 8 : 00 am to 4 : 00 pm, exposing them to a Chronic Intermittent Hypoxia environment for 8 h daily for 6 weeks.",10,10,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Figure 3C, D",30 December 2025,Fiddyhamma,Fiddyhamma,"Comparison of composition and distribution of mouse gut microbiota at the phylum, genus levels.",decreased,"k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",3379134|74201;3379134|74201|203494|48461|1647988|239934;1783272|1239|526524|526525|2810281|191303,Complete,KateRasheed
bsdb:40982577/11/2,40982577,laboratory experiment,40982577,10.1099/jmm.0.002069,https://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.002069#html_fulltext,"Lu M.L., Wu J.L., Zhu J.W., Liu L., Li M.Z., Yu Y. , Pan L.",Changes in the gut microbiota in mice exposed to chronic intermittent hypoxia,Journal of medical microbiology,2025,"gut microbiota, intermittent hypoxia, normoxia, obstructive sleep apnoea",Experiment 11,China,Mus musculus,Feces,UBERON:0001988,Hypoxia,EFO:0009444,Pre Intervention Chronic Intermittent Hypoxia (CIH0),Post Intervention Chronic Intermittent Hypoxia (CIH6),"Mice placed into a hypoxic simulation chamber daily from 8 : 00 am to 4 : 00 pm, exposing them to a Chronic Intermittent Hypoxia environment for 8 h daily for 6 weeks.",10,10,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Figure 3C, D and E",30 December 2025,Fiddyhamma,Fiddyhamma,"Comparison of composition and distribution of mouse gut microbiota at the phylum, genus levels.",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,p__Candidatus Saccharimonadota",3379134|976|200643|171549|815|816;3379134|976|200643|171549|171552|577309;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|1263;3379134|1224|28216|80840|995019|40544;95818,Complete,KateRasheed
bsdb:40982577/12/1,40982577,laboratory experiment,40982577,10.1099/jmm.0.002069,https://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.002069#html_fulltext,"Lu M.L., Wu J.L., Zhu J.W., Liu L., Li M.Z., Yu Y. , Pan L.",Changes in the gut microbiota in mice exposed to chronic intermittent hypoxia,Journal of medical microbiology,2025,"gut microbiota, intermittent hypoxia, normoxia, obstructive sleep apnoea",Experiment 12,China,Mus musculus,Feces,UBERON:0001988,Oxygen,CHEBI:15379,Pre Intervention Normoxia (NM0),Post Intervention Normoxia (NM6),Post Intervention Normoxia (NM6) mice with oxygen content levels of 21% (normoxic state),10,10,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 3D,30 December 2025,Fiddyhamma,Fiddyhamma,Comparison of composition and distribution of mouse gut microbiota at the genus levels.,decreased,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,1783272|1239|526524|526525|2810281|191303,Complete,KateRasheed
bsdb:40982577/13/1,40982577,laboratory experiment,40982577,10.1099/jmm.0.002069,https://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.002069#html_fulltext,"Lu M.L., Wu J.L., Zhu J.W., Liu L., Li M.Z., Yu Y. , Pan L.",Changes in the gut microbiota in mice exposed to chronic intermittent hypoxia,Journal of medical microbiology,2025,"gut microbiota, intermittent hypoxia, normoxia, obstructive sleep apnoea",Experiment 13,China,Mus musculus,Feces,UBERON:0001988,Hypoxia,EFO:0009444,Post Intervention Normoxia (NM6),Post Intervention Chronic Intermittent Hypoxia (CIH6),"Mice placed into a hypoxic simulation chamber daily from 8 : 00 am to 4 : 00 pm, exposing them to a Chronic Intermittent Hypoxia environment for 8 h daily for 6 weeks.",10,10,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3E,30 December 2025,Fiddyhamma,Fiddyhamma,Comparison of composition and distribution of mouse gut microbiota at the genus levels.,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,KateRasheed
bsdb:40982577/13/2,40982577,laboratory experiment,40982577,10.1099/jmm.0.002069,https://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.002069#html_fulltext,"Lu M.L., Wu J.L., Zhu J.W., Liu L., Li M.Z., Yu Y. , Pan L.",Changes in the gut microbiota in mice exposed to chronic intermittent hypoxia,Journal of medical microbiology,2025,"gut microbiota, intermittent hypoxia, normoxia, obstructive sleep apnoea",Experiment 13,China,Mus musculus,Feces,UBERON:0001988,Hypoxia,EFO:0009444,Post Intervention Normoxia (NM6),Post Intervention Chronic Intermittent Hypoxia (CIH6),"Mice placed into a hypoxic simulation chamber daily from 8 : 00 am to 4 : 00 pm, exposing them to a Chronic Intermittent Hypoxia environment for 8 h daily for 6 weeks.",10,10,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 3E,30 December 2025,Fiddyhamma,Fiddyhamma,Comparison of composition and distribution of mouse gut microbiota at the genus levels.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,KateRasheed
bsdb:40982577/14/1,40982577,laboratory experiment,40982577,10.1099/jmm.0.002069,https://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.002069#html_fulltext,"Lu M.L., Wu J.L., Zhu J.W., Liu L., Li M.Z., Yu Y. , Pan L.",Changes in the gut microbiota in mice exposed to chronic intermittent hypoxia,Journal of medical microbiology,2025,"gut microbiota, intermittent hypoxia, normoxia, obstructive sleep apnoea",Experiment 14,China,Mus musculus,Feces,UBERON:0001988,Hypoxia,EFO:0009444,Pre Intervention Chronic Intermittent Hypoxia (CIH0),Post Intervention Chronic Intermittent Hypoxia (CIH6),"Mice placed into a hypoxic simulation chamber daily from 8 : 00 am to 4 : 00 pm, exposing them to a Chronic Intermittent Hypoxia environment for 8 h daily for 6 weeks.",10,10,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 3E,30 December 2025,Fiddyhamma,Fiddyhamma,Comparison of composition and distribution of mouse gut microbiota at the genus levels.,increased,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,3379134|29547|3031852|213849|72293|209,Complete,KateRasheed
bsdb:40982577/14/2,40982577,laboratory experiment,40982577,10.1099/jmm.0.002069,https://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.002069#html_fulltext,"Lu M.L., Wu J.L., Zhu J.W., Liu L., Li M.Z., Yu Y. , Pan L.",Changes in the gut microbiota in mice exposed to chronic intermittent hypoxia,Journal of medical microbiology,2025,"gut microbiota, intermittent hypoxia, normoxia, obstructive sleep apnoea",Experiment 14,China,Mus musculus,Feces,UBERON:0001988,Hypoxia,EFO:0009444,Pre Intervention Chronic Intermittent Hypoxia (CIH0),Post Intervention Chronic Intermittent Hypoxia (CIH6),"Mice placed into a hypoxic simulation chamber daily from 8 : 00 am to 4 : 00 pm, exposing them to a Chronic Intermittent Hypoxia environment for 8 h daily for 6 weeks.",10,10,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Figure 3D, E",30 December 2025,Fiddyhamma,Fiddyhamma,Comparison of composition and distribution of mouse gut microbiota at the genus levels.,decreased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella",3379134|200940|3031449|213115|194924|872;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|171550|28138,Complete,KateRasheed
bsdb:40993517/1/1,40993517,laboratory experiment,40993517,https://doi.org/10.1186/s12866-025-04333-5,NA,"Abbondio M., Palomba A., Serra M., Fraumene C., Di Meo C., Marongiu F., Sau R., Pagnozzi D., Laconi E., Tanca A. , Uzzau S.",Consumption of traditional Sardinian fermented milk promotes changes in the rat gut microbiota composition and functions,BMC microbiology,2025,NA,Experiment 1,Italy,Rattus norvegicus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Ctrl (Control group) after 8 weeks.,FM (Fermented milk group) after 8 weeks.,Rats fed standard chow-diet supplemented with casu axedu (Traditional Sardinian fermented sheep milk) for 8 weeks.,6,6,NA,16S,4,Illumina,centered log-ratio,MaAsLin2,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3 & Supplementary dataset 13,11 October 2025,Fadimatou Inna,Fadimatou Inna,"Comparison of gut microbiota composition between rats fed a standard chow diet (control group) and those fed chow supplemented with fermented milk casu axedu (20% w/w) over eight weeks (W8), analysed using 16S rRNA gene sequencing and metaproteomics.",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia glucerasea,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales",1783272|1239|909932|1843488|909930;1783272|1239|909932|1843488;1783272|1239|186801|3085636|186803|572511|536633;3379134|1224|1236|91347;1783272|1239|91061|186826;1783272|1239|91061|186826|1300|1357|1358;1783272|1239|186801|3085656;1783272|1239|909932|1843488|909930|33024;3379134|976|200643|171549|171552|838;3379134|1224|1236|72274,Complete,KateRasheed
bsdb:40993517/1/2,40993517,laboratory experiment,40993517,https://doi.org/10.1186/s12866-025-04333-5,NA,"Abbondio M., Palomba A., Serra M., Fraumene C., Di Meo C., Marongiu F., Sau R., Pagnozzi D., Laconi E., Tanca A. , Uzzau S.",Consumption of traditional Sardinian fermented milk promotes changes in the rat gut microbiota composition and functions,BMC microbiology,2025,NA,Experiment 1,Italy,Rattus norvegicus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Ctrl (Control group) after 8 weeks.,FM (Fermented milk group) after 8 weeks.,Rats fed standard chow-diet supplemented with casu axedu (Traditional Sardinian fermented sheep milk) for 8 weeks.,6,6,NA,16S,4,Illumina,centered log-ratio,MaAsLin2,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3,13 October 2025,Fadimatou Inna,Fadimatou Inna,"Comparison of gut microbiota composition between rats fed a standard chow diet (control group) and those fed chow supplemented with fermented milk casu axedu (20% w/w) over eight weeks, analysed using 16S rRNA gene sequencing and metaproteomics.",decreased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter rodentium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei",3379134|29547|3031852|213849|72293|209|59617;3379134|976|200643|171549|815|909656|357276,Complete,KateRasheed
bsdb:40993517/2/1,40993517,laboratory experiment,40993517,https://doi.org/10.1186/s12866-025-04333-5,NA,"Abbondio M., Palomba A., Serra M., Fraumene C., Di Meo C., Marongiu F., Sau R., Pagnozzi D., Laconi E., Tanca A. , Uzzau S.",Consumption of traditional Sardinian fermented milk promotes changes in the rat gut microbiota composition and functions,BMC microbiology,2025,NA,Experiment 2,Italy,Rattus norvegicus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Ctrl (control) diet after 8 weeks,FM (fermented milk) diet after 8 weeks,Gut microbiota of rats after 8 weeks of dietary treatment comparing fermented milk-fed (FM) rats to control (Ctrl) rats.,6,6,NA,16S,4,Illumina,relative abundances,T-Test,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4,12 October 2025,Fadimatou Inna,Fadimatou Inna,Comparison of gut microbiota composition between rats fed a standard chow diet (control group) and those fed chow supplemented with fermented milk casu axedu (20% w/w) over eight weeks.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus albus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens",1783272|1239|186801|186802|216572|1263|1264;3379134|976|200643|171549|815|909656|204516;1783272|1239|909932|1843488|909930|33024|626940,Complete,KateRasheed
bsdb:40993517/3/1,40993517,laboratory experiment,40993517,https://doi.org/10.1186/s12866-025-04333-5,NA,"Abbondio M., Palomba A., Serra M., Fraumene C., Di Meo C., Marongiu F., Sau R., Pagnozzi D., Laconi E., Tanca A. , Uzzau S.",Consumption of traditional Sardinian fermented milk promotes changes in the rat gut microbiota composition and functions,BMC microbiology,2025,NA,Experiment 3,Italy,Rattus norvegicus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Ctrl (control) diet T0,FM (fermented milk) diet at T0,Gut microbiota of rats at T0 week of dietary treatment comparing fermented milk-fed (FM) rats to control (Ctrl) rats.,6,6,NA,16S,4,Illumina,centered log-ratio,MaAsLin2,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary dataset 13,30 October 2025,Fadimatou Inna,Fadimatou Inna,"Comparison of gut microbiota composition at baseline (T0 week) between rats fed a standard chow diet and those receiving chow supplemented with fermented milk (Casu axedu, 20% w/w), prior to the 8-week intervention, analyzed using 16S rRNA gene sequencing and metaproteomics.",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",1783272|1239|186801|3085636;1783272|1239|186801|3085636|186803,Complete,KateRasheed
bsdb:40993517/4/1,40993517,laboratory experiment,40993517,https://doi.org/10.1186/s12866-025-04333-5,NA,"Abbondio M., Palomba A., Serra M., Fraumene C., Di Meo C., Marongiu F., Sau R., Pagnozzi D., Laconi E., Tanca A. , Uzzau S.",Consumption of traditional Sardinian fermented milk promotes changes in the rat gut microbiota composition and functions,BMC microbiology,2025,NA,Experiment 4,Italy,Rattus norvegicus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Ctrl (control) diet after 2 weeks,FM (fermented milk) diet after 2 weeks,Gut microbiota of rats after 2 weeks of dietary treatment comparing fermented milk-fed (FM) rats to control (Ctrl) rats.,6,6,NA,16S,4,Illumina,centered log-ratio,MaAsLin2,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary dataset 13,30 October 2025,Fadimatou Inna,Fadimatou Inna,"Comparison of gut microbiota composition at W2 between rats fed a standard chow diet and those receiving chow supplemented with fermented milk (Casu axedu, 20% w/w) analyzed using 16S rRNA gene sequencing and metaproteomics.",increased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc mesenteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",1783272|544448|31969|186329|2146;1783272|544448|31969|186329;1783272|544448|31969|186332|186333|2086;1783272|1239|91061|186826|1300|1357|1358;1783272|1239|91061|186826|33958|1243;1783272|1239|91061|186826|33958|1243|1245;1783272|1239|91061|186826|33958,Complete,KateRasheed
bsdb:40993517/4/2,40993517,laboratory experiment,40993517,https://doi.org/10.1186/s12866-025-04333-5,NA,"Abbondio M., Palomba A., Serra M., Fraumene C., Di Meo C., Marongiu F., Sau R., Pagnozzi D., Laconi E., Tanca A. , Uzzau S.",Consumption of traditional Sardinian fermented milk promotes changes in the rat gut microbiota composition and functions,BMC microbiology,2025,NA,Experiment 4,Italy,Rattus norvegicus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Ctrl (control) diet after 2 weeks,FM (fermented milk) diet after 2 weeks,Gut microbiota of rats after 2 weeks of dietary treatment comparing fermented milk-fed (FM) rats to control (Ctrl) rats.,6,6,NA,16S,4,Illumina,centered log-ratio,MaAsLin2,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplementary dataset 13,5 November 2025,Fadimatou Inna,Fadimatou Inna,"Comparison of gut microbiota composition at W2 between rats fed a standard chow diet and those receiving chow supplemented with fermented milk (Casu axedu, 20% w/w) analyzed using 16S rRNA gene sequencing and metaproteomics.",decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae|g__Candidatus Saccharimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus murinus",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|820;95818|2093818|2093825|2171986|1331051;3379134|1224|1236|91347|543;1783272|1239|91061|186826|33958|2767887|1622,Complete,KateRasheed
bsdb:40993517/5/1,40993517,laboratory experiment,40993517,https://doi.org/10.1186/s12866-025-04333-5,NA,"Abbondio M., Palomba A., Serra M., Fraumene C., Di Meo C., Marongiu F., Sau R., Pagnozzi D., Laconi E., Tanca A. , Uzzau S.",Consumption of traditional Sardinian fermented milk promotes changes in the rat gut microbiota composition and functions,BMC microbiology,2025,NA,Experiment 5,Italy,Rattus norvegicus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Ctrl (control) diet after 6 weeks,FM (fermented milk) diet after 6 weeks,Gut microbiota of rats after 6 weeks of dietary treatment comparing fermented milk-fed (FM) rats to control (Ctrl) rats.,6,6,NA,16S,4,Illumina,centered log-ratio,MaAsLin2,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary dataset 13,30 October 2025,Fadimatou Inna,Fadimatou Inna,"Comparison of gut microbiota composition at W6 between rats fed a standard chow diet and those receiving chow supplemented with fermented milk (Casu axedu, 20% w/w) analyzed using 16S rRNA gene sequencing and metaproteomics.",increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",1783272|1239|909932|1843488|909930;1783272|1239|909932|1843488;1783272|1239|91061|186826|1300|1357|1358;1783272|1239|186801|186802|216572;1783272|1239|909932|1843488|909930|33024,Complete,KateRasheed
bsdb:40993517/5/2,40993517,laboratory experiment,40993517,https://doi.org/10.1186/s12866-025-04333-5,NA,"Abbondio M., Palomba A., Serra M., Fraumene C., Di Meo C., Marongiu F., Sau R., Pagnozzi D., Laconi E., Tanca A. , Uzzau S.",Consumption of traditional Sardinian fermented milk promotes changes in the rat gut microbiota composition and functions,BMC microbiology,2025,NA,Experiment 5,Italy,Rattus norvegicus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Ctrl (control) diet after 6 weeks,FM (fermented milk) diet after 6 weeks,Gut microbiota of rats after 6 weeks of dietary treatment comparing fermented milk-fed (FM) rats to control (Ctrl) rats.,6,6,NA,16S,4,Illumina,centered log-ratio,MaAsLin2,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplementary dataset 13,6 November 2025,Fadimatou Inna,Fadimatou Inna,"Comparison of gut microbiota composition at W6 between rats fed a standard chow diet and those receiving chow supplemented with fermented milk (Casu axedu, 20% w/w) analyzed using 16S rRNA gene sequencing and metaproteomics.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales",3379134|1224|1236|91347|543;3379134|1224|1236|91347;1783272|1239|91061|186826;1783272|1239|186801|3085656;3379134|1224|1236|72274,Complete,KateRasheed
bsdb:40993517/7/1,40993517,laboratory experiment,40993517,https://doi.org/10.1186/s12866-025-04333-5,NA,"Abbondio M., Palomba A., Serra M., Fraumene C., Di Meo C., Marongiu F., Sau R., Pagnozzi D., Laconi E., Tanca A. , Uzzau S.",Consumption of traditional Sardinian fermented milk promotes changes in the rat gut microbiota composition and functions,BMC microbiology,2025,NA,Experiment 7,Italy,Rattus norvegicus,Feces,UBERON:0001988,Response to diet,EFO:0010757,Ctrl (control) diet after 4 weeks,FM (fermented milk) diet after 4 weeks,Rats fed standard chow-diet supplemented with casu axedu (Traditional Sardinian fermented sheep milk) for 4 weeks.,6,6,NA,16S,4,Illumina,centered log-ratio,MaAsLin2,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary dataset 13,31 October 2025,Fadimatou Inna,Fadimatou Inna,"Comparison of gut microbiota composition at W4 between rats fed a standard chow diet and those receiving chow supplemented with fermented milk (Casu axedu, 20% w/w) analyzed using 16S rRNA gene sequencing and metaproteomics.",decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus murinus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis",1783272|1239|91061|186826|33958|2767887|1622;3379134|976|200643|171549|2005525|375288|823,Complete,KateRasheed
bsdb:40995227/1/1,40995227,"cross-sectional observational, not case-control",40995227,10.3389/fcimb.2025.1651316,NA,"Lee S.H., Kim E.B., Park S.C., Nam S.J., Cho H., Jeon H.J. , Lee S.P.",Evaluation of the gastric microbiota based on body mass index using 16S rRNA gene sequencing,Frontiers in cellular and infection microbiology,2025,"16S rRNA sequencing, body mass index, gastric microbiota, metabolic dysregulation, obesity",Experiment 1,South Korea,Homo sapiens,Mucosa of stomach,UBERON:0001199,Obesity,EFO:0001073,Normal weight,Overweight/obese,Participants with a body mass index of 23.0–24.9 kg/m² for overweight and ≥25.0 kg/m² for obese,10,20,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,decreased,NA,unchanged,Signature 1,Figure 2C and 2D,10 October 2025,EniolaAde,EniolaAde,Linear discriminant analysis effect size (LEfSe) analysis for abundance between overweight/obese and normal weight groups,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Planctomycetota|c__Planctomycetia|o__Pirellulales|f__Lacipirellulaceae|g__Bythopirellula|s__Bythopirellula polymerisocia,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Desulfitobacteriaceae|g__Desulfosporosinus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Duncaniella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Duncaniella|s__Duncaniella dubosii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum|s__Muribaculum gordoncarteri,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Nitrosomonadaceae|g__Nitrosomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Rhodopseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Rhodopseudomonas|s__Rhodopseudomonas palustris,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter bilis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei",1783272|201174|84998|1643822|1643826|447020;3379134|976|200643|171549|815|816|47678;3379134|203682|203683|2691354|2691359|1400386|2528003;3384194|1297|188787|118964|183710|1298;1783272|1239|186801|186802|2937909|79206;3379134|976|200643|171549|2005473|2518495;3379134|976|200643|171549|2005473|2518495|2518971;3379134|976|200643|171549|2005473|1918540;3379134|976|200643|171549|2005473|1918540|2530390;3379134|1224|28216|32003|206379|914;3379134|1224|28211|356|41294|1073;3379134|1224|28211|356|41294|1073|1076;1783272|1239|526524|526525|2810281|191303|2735723;3379134|1224|1236|91347|543|158876;3379134|1224|1236|91347|543|158876|158877,Complete,ChiomaBlessing
bsdb:40995227/1/2,40995227,"cross-sectional observational, not case-control",40995227,10.3389/fcimb.2025.1651316,NA,"Lee S.H., Kim E.B., Park S.C., Nam S.J., Cho H., Jeon H.J. , Lee S.P.",Evaluation of the gastric microbiota based on body mass index using 16S rRNA gene sequencing,Frontiers in cellular and infection microbiology,2025,"16S rRNA sequencing, body mass index, gastric microbiota, metabolic dysregulation, obesity",Experiment 1,South Korea,Homo sapiens,Mucosa of stomach,UBERON:0001199,Obesity,EFO:0001073,Normal weight,Overweight/obese,Participants with a body mass index of 23.0–24.9 kg/m² for overweight and ≥25.0 kg/m² for obese,10,20,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,decreased,NA,unchanged,Signature 2,Figure 2C and 2D,11 October 2025,EniolaAde,EniolaAde,Linear discriminant analysis effect size (LEfSe) analysis for abundance between overweight/obese and normal weight groups,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium australiense,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus rubneri,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria perflava,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius",3379134|1224|28211|356|41294|374;3379134|1224|28211|356|41294|374|2721161;3379134|29547|3031852|213849|72294|194|199;3379134|976|117743|200644|49546|1016;1783272|201174|84998|84999|84107|102106;3379134|1224|1236|135625|712|724;3379134|1224|1236|135625|712|724|729;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|28132;33090|35493|3398|72025|3803|3814|508215;1783272|201174|1760|85006|1268|32207|43675;3379134|976|200643|171549|171552|2974251;1783272|1239|91061|186826|1300|1301|1234680;1783272|1239|909932|1843489|31977|29465;1783272|1239|909932|1843489|31977|29465|39777;3379134|1224|28216|206351|481|482|33053;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|91061|186826|1300|1301|1304,Complete,ChiomaBlessing
bsdb:40995227/2/1,40995227,"cross-sectional observational, not case-control",40995227,10.3389/fcimb.2025.1651316,NA,"Lee S.H., Kim E.B., Park S.C., Nam S.J., Cho H., Jeon H.J. , Lee S.P.",Evaluation of the gastric microbiota based on body mass index using 16S rRNA gene sequencing,Frontiers in cellular and infection microbiology,2025,"16S rRNA sequencing, body mass index, gastric microbiota, metabolic dysregulation, obesity",Experiment 2,South Korea,Homo sapiens,Mucosa of stomach,UBERON:0001199,Obesity,EFO:0001073,Overweight/obese,Normal weight,Participants with a body mass index of 18.5–22.9 kg/m²,20,10,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,"Supplementary Figure 3 and text page 4, subheading ""Composition of gastric microbiota"", paragraph 3",11 October 2025,EniolaAde,EniolaAde,Differential abundance between normal weight and overweight/obese group,increased,"k__Bacillati|p__Actinomycetota|c__Acidimicrobiia|o__Acidimicrobiales,k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Lamiales|f__Lamiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum|s__Muribaculum gordoncarteri,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Rhodopseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae|g__Rhodospirillum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales",1783272|201174|84992|84993;1783272|201174|84992;3379134|976|200643|171549|815|816|47678;1783272|1239|526524;33090|35493|3398|4143|4136;3379134|976|200643|171549|2005473;3379134|976|200643|171549|2005473|1918540;3379134|976|200643|171549|2005473|1918540|2530390;3379134|1224|28211|356|41294|1073;3379134|1224|28211|204441|41295|1081;3379134|1224|1236|91347|543|158876;3379134|1224|1236|91347|543|158876|158877;1783272|1239|526524|526525,Complete,ChiomaBlessing
bsdb:40995227/3/1,40995227,"cross-sectional observational, not case-control",40995227,10.3389/fcimb.2025.1651316,NA,"Lee S.H., Kim E.B., Park S.C., Nam S.J., Cho H., Jeon H.J. , Lee S.P.",Evaluation of the gastric microbiota based on body mass index using 16S rRNA gene sequencing,Frontiers in cellular and infection microbiology,2025,"16S rRNA sequencing, body mass index, gastric microbiota, metabolic dysregulation, obesity",Experiment 3,South Korea,Homo sapiens,Mucosa of stomach,UBERON:0001199,Obesity,EFO:0001073,Normal/Overweight,Obese,Participants with a body mass mass ≥25.0 kg/m²),20,10,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Supplementary Figure 3,11 October 2025,EniolaAde,EniolaAde,Differential abundance between obese weight and normal/overweight group,increased,"k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinilabiliaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__[Clostridium] innocuum",1783272|1239|909932;1783272|201174|84998|84999;3379134|976|200643|171549|171552|2974251;1783272|1239|186801|186802|216572|1263|438033;3379134|976|200643|1970189|558415;3379134|976|200643|1970189;1783272|1239|186801|186802|31979|1485|1522,Complete,ChiomaBlessing
bsdb:40995227/4/1,40995227,"cross-sectional observational, not case-control",40995227,10.3389/fcimb.2025.1651316,NA,"Lee S.H., Kim E.B., Park S.C., Nam S.J., Cho H., Jeon H.J. , Lee S.P.",Evaluation of the gastric microbiota based on body mass index using 16S rRNA gene sequencing,Frontiers in cellular and infection microbiology,2025,"16S rRNA sequencing, body mass index, gastric microbiota, metabolic dysregulation, obesity",Experiment 4,South Korea,Homo sapiens,Mucosa of stomach,UBERON:0001199,Obesity,EFO:0001073,Normal/Obese,Overweight,Participants with a body mass index of 23.0–24.9 kg/m²,20,10,1 month,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Supplementary Figure 3,11 October 2025,EniolaAde,EniolaAde,Differential abundance between overweight and normal/obese group,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria perflava,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus pittmaniae",3379134|1224|1236|135625|712|724;3379134|1224|1236|135625;3379134|1224|1236|135625|712;3379134|976|200643|171549|171552;3379134|1224|1236|135625|712|724|729;3379134|976|200643|171549|171552|838;3379134|1224|28216|206351;3379134|1224|28216|206351|481;3379134|1224|28216|206351|481|482;1783272|1239|909932|1843489;1783272|1239|909932|1843489|31977;3379134|1224|28216|206351|481|482|33053;3379134|1224|1236|135625|712|724|249188,Complete,ChiomaBlessing
bsdb:40999363/1/1,40999363,laboratory experiment,40999363,10.1186/s12866-025-04302-y,NA,"Pan Y., Luo Y., Wu G., Lu Y., Yang P., Kong P., Zheng C., Wang C., Yang L. , Li X.",Gut microbiota dysbiosis promotes coronary heart disease comorbid with depression through lipopolysaccharides and Toll-like receptor 4,BMC microbiology,2025,"Coronary heart disease, Depression, Gut microbiota, Lipopolysaccharides, TLR4 receptors",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Fecal Microbiota Transplant (FMT)-Normal,Fecal Microbiota Transplant (FMT)-Disease,Healthy rats receiving fecal microbiota transplantation from model rats for coronary heart disease comorbid with depression (CHDWD).,7,7,NA,16S,34,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),T-Test",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,21 October 2025,Nina Takang,"Nina Takang,Tosin",Differences in microbiota between the Fecal microbiota transplant (FMT)-Normal and Fecal microbiota transplant (FMT)-Disease groups,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Oligella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pygmaiobacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",3379134|1224|1236|2887326|468|469;1783272|1239|526524|526525|128827|174708;1783272|201174|1760|85004|31953|1678;3379134|200940|3031449|213115|194924|35832;1783272|201174|84998|1643822|1643826|580024;3379134|1224|28216|80840|506|90243;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|186802|216572|1929305;1783272|1239|526524|526525|2810281|191303,Complete,NA
bsdb:40999363/1/2,40999363,laboratory experiment,40999363,10.1186/s12866-025-04302-y,NA,"Pan Y., Luo Y., Wu G., Lu Y., Yang P., Kong P., Zheng C., Wang C., Yang L. , Li X.",Gut microbiota dysbiosis promotes coronary heart disease comorbid with depression through lipopolysaccharides and Toll-like receptor 4,BMC microbiology,2025,"Coronary heart disease, Depression, Gut microbiota, Lipopolysaccharides, TLR4 receptors",Experiment 1,China,Rattus norvegicus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Fecal Microbiota Transplant (FMT)-Normal,Fecal Microbiota Transplant (FMT)-Disease,Healthy rats receiving fecal microbiota transplantation from model rats for coronary heart disease comorbid with depression (CHDWD).,7,7,NA,16S,34,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),T-Test",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,21 October 2025,Nina Takang,"Nina Takang,YokoC,Tosin",Differences in microbiota between the Fecal microbiota transplant (FMT)-Normal and Fecal microbiota transplant (FMT)-Disease groups,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,p__Rhodophyta|c__Florideophyceae|o__Batrachospermales|f__Batrachospermaceae|g__Paludicola,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",1783272|1239|909932|909929|1843491|82373;3379134|976|200643|171549|1853231|283168;2763|2806|31370|31371|2729669;1783272|1239|186801|3085636|186803|1506577,Complete,NA
bsdb:40999363/2/1,40999363,laboratory experiment,40999363,10.1186/s12866-025-04302-y,NA,"Pan Y., Luo Y., Wu G., Lu Y., Yang P., Kong P., Zheng C., Wang C., Yang L. , Li X.",Gut microbiota dysbiosis promotes coronary heart disease comorbid with depression through lipopolysaccharides and Toll-like receptor 4,BMC microbiology,2025,"Coronary heart disease, Depression, Gut microbiota, Lipopolysaccharides, TLR4 receptors",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,"Coronary artery disease,Depressive disorder","EFO:0001645,MONDO:0002050",Control,Diseased model,"Male Sprague–Dawley rats that were used to establish a model of coronary heart disease comorbid with depression (CHDWD). The model was induced through a high-fat diet, chronic unpredictable mild stress (CUMS), and a coronary artery ligation surgery. Rats that met the predefined diagnostic criteria were considered successfully modeled.",8,8,NA,16S,34,Illumina,relative abundances,"T-Test,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 1,21 October 2025,YokoC,"YokoC,Tosin",Table showing the significant differences of the taxa between the Control and Coronary heart disease comorbid with depression (CHDWD) model.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__uncultured Clostridium sp.",1783272|1239|186801|186802|1470353;1783272|1239|526524|526525|128827|1470349;1783272|1239|186801|3085636|186803|189330;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|2005525|375288;1783272|1239|91061|1385|90964|1279;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|186802|31979|1485|59620,Complete,NA
bsdb:40999363/2/2,40999363,laboratory experiment,40999363,10.1186/s12866-025-04302-y,NA,"Pan Y., Luo Y., Wu G., Lu Y., Yang P., Kong P., Zheng C., Wang C., Yang L. , Li X.",Gut microbiota dysbiosis promotes coronary heart disease comorbid with depression through lipopolysaccharides and Toll-like receptor 4,BMC microbiology,2025,"Coronary heart disease, Depression, Gut microbiota, Lipopolysaccharides, TLR4 receptors",Experiment 2,China,Rattus norvegicus,Feces,UBERON:0001988,"Coronary artery disease,Depressive disorder","EFO:0001645,MONDO:0002050",Control,Diseased model,"Male Sprague–Dawley rats that were used to establish a model of coronary heart disease comorbid with depression (CHDWD). The model was induced through a high-fat diet, chronic unpredictable mild stress (CUMS), and a coronary artery ligation surgery. Rats that met the predefined diagnostic criteria were considered successfully modeled.",8,8,NA,16S,34,Illumina,relative abundances,"T-Test,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 1,21 October 2025,YokoC,"YokoC,Tosin",Table showing the significant differences of the taxa between the Control and the Coronary heart disease comorbid with depression (CHDWD) model.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Thermodesulfobacteriota",1783272|1239|186801|186802|216572|1940255;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|3085636|186803|265975;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300|1301;3379134|200940,Complete,NA
bsdb:41000236/1/1,41000236,"cross-sectional observational, not case-control",41000236,10.1080/20002297.2025.2560016,NA,"Zhan J., Huang Y., Meng X., Wang Y., Liang J., Zhu F., She R., Huang S. , Huo L.",Microbiome differences between trauma- and caries-derived periapical lesions using next-generation sequencing,Journal of oral microbiology,2025,"Trauma teeth, campylobacter, microbiome, next-generation sequencing, periapical lesions",Experiment 1,China,Homo sapiens,Dental pulp,UBERON:0001754,Periapical Periodontitis,EFO:1001391,Caries,Trauma,Patients suffering from chronic apical periodontitis due to trauma,10,10,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,Figure 5A,12 October 2025,EniolaAde,EniolaAde,Differential abundance of taxa between caries and trauma group,increased,k__Pseudomonadati|p__Campylobacterota,3379134|29547,Complete,Svetlana up
bsdb:41000236/1/2,41000236,"cross-sectional observational, not case-control",41000236,10.1080/20002297.2025.2560016,NA,"Zhan J., Huang Y., Meng X., Wang Y., Liang J., Zhu F., She R., Huang S. , Huo L.",Microbiome differences between trauma- and caries-derived periapical lesions using next-generation sequencing,Journal of oral microbiology,2025,"Trauma teeth, campylobacter, microbiome, next-generation sequencing, periapical lesions",Experiment 1,China,Homo sapiens,Dental pulp,UBERON:0001754,Periapical Periodontitis,EFO:1001391,Caries,Trauma,Patients suffering from chronic apical periodontitis due to trauma,10,10,3 months,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,Figure 5B and 5C,12 October 2025,EniolaAde,EniolaAde,Differential abundance of taxa between caries group and trauma group,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor villosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris",1783272|1239|186801|3082720|3118655|44259;1783272|1239|186801|3082720|3118655|44259|29374;1783272|1239|186801|3085636|186803|265975;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|2974251|28135,Complete,Svetlana up
bsdb:41000236/2/1,41000236,"cross-sectional observational, not case-control",41000236,10.1080/20002297.2025.2560016,NA,"Zhan J., Huang Y., Meng X., Wang Y., Liang J., Zhu F., She R., Huang S. , Huo L.",Microbiome differences between trauma- and caries-derived periapical lesions using next-generation sequencing,Journal of oral microbiology,2025,"Trauma teeth, campylobacter, microbiome, next-generation sequencing, periapical lesions",Experiment 2,China,Homo sapiens,Dental pulp,UBERON:0001754,Periapical Periodontitis,EFO:1001391,Caries,Trauma,Patients suffering from chronic apical periodontitis due to trauma,10,10,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,Figure 6A and 6B,13 October 2025,EniolaAde,EniolaAde,Taxa differing in abundance between caries group and trauma as determined by Linear discriminant analysis Effect Size (LEFSe),increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales,k__Pseudomonadati|p__Campylobacterota,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria",3379134|29547|3031852|213849|72294;3379134|29547|3031852|213849;3379134|29547;3379134|29547|3031852,Complete,Svetlana up
bsdb:41000236/2/2,41000236,"cross-sectional observational, not case-control",41000236,10.1080/20002297.2025.2560016,NA,"Zhan J., Huang Y., Meng X., Wang Y., Liang J., Zhu F., She R., Huang S. , Huo L.",Microbiome differences between trauma- and caries-derived periapical lesions using next-generation sequencing,Journal of oral microbiology,2025,"Trauma teeth, campylobacter, microbiome, next-generation sequencing, periapical lesions",Experiment 2,China,Homo sapiens,Dental pulp,UBERON:0001754,Periapical Periodontitis,EFO:1001391,Caries,Trauma,Patients suffering from chronic apical periodontitis due to trauma,10,10,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,Figure 6A and 6B,13 October 2025,EniolaAde,EniolaAde,Taxa differing in abundance between caries group and trauma as determined by Linear discriminant analysis Effect Size (LEFSe),decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera geminata,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor|s__Filifactor villosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella baroniae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella oris,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Kitasatosporales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces abikoensis",1783272|1239|909932|1843489|31977|156454;1783272|1239|909932|1843489|31977|906|156456;1783272|1239|186801|3082720|3118655|44259;1783272|1239|186801|3082720|3118655|44259|29374;1783272|1239|186801|3085636;1783272|1239|186801|3085636|186803|265975;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|2974251|305719;3379134|976|200643|171549|171552|2974251|28135;1783272|1239|909932|909929|1843491|970|69823;1783272|201174|1760|85011|2062|1883|1977,Complete,Svetlana up
bsdb:41011244/1/1,41011244,"cross-sectional observational, not case-control,randomized controlled trial",41011244,10.3390/ph18091376,https://doi.org/10.3390/ph18091376,"Valencia-Buitrago M., Oliveira-Carvalho R.D., Cardoso V., Triviño-Valencia J., Salamanca-Duque L.M., Martínez-Díaz V., Zabaleta J., Galeano-Vanegas N.F. , Naranjo-Galvis C.A.",Metagenomic Characterization of Gut Microbiota in Children with Autism Spectrum Disorder: Microbial Signatures and Modulation by Anti-Inflammatory Diet and Probiotics,"Pharmaceuticals (Basel, Switzerland)",2025,"Colombian children, anti-inflammatory diet, autism spectrum disorder, gastrointestinal disorders, gut microbiota, metagenomics, probiotics",Experiment 1,Colombia,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Typically Developing (TD),Autism Spectrum Disorder (ASD),"Participants had a confirmed clinical diagnosis of high-functioning Autism Spectrum Disorder (Level I, DSM-5), based on criteria established by pediatric neurology or child psychiatry professionals in accordance with the national clinical protocol for ASD diagnosis and care (MinSalud, 2015). The condition is a neurodevelopmental disorder characterized by difficulties in social communication and the presence of restricted, repetitive, and inflexible patterns of behavior, typically manifesting in early childhood.",7,23,3 months,WMS,NA,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 4,10 October 2025,Amara-Chikaodili,Amara-Chikaodili,"Genera found to be significantly more abundant in fecal samples of children with ASD compared to typically developing (TD) controls (Welch's t-test, Benjamini-Hochberg FDR p<0.05).",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae|g__Monoglobus",1783272|1239|186801|3082720|186804|1870884;1783272|1239|526524|526525|2810280|3025755;3379134|976|200643|171549|171550|239759;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|31979|1266;1783272|1239|186801|3085656|3085657|2039302,Complete,Svetlana up
bsdb:41011244/2/1,41011244,"cross-sectional observational, not case-control,randomized controlled trial",41011244,10.3390/ph18091376,https://doi.org/10.3390/ph18091376,"Valencia-Buitrago M., Oliveira-Carvalho R.D., Cardoso V., Triviño-Valencia J., Salamanca-Duque L.M., Martínez-Díaz V., Zabaleta J., Galeano-Vanegas N.F. , Naranjo-Galvis C.A.",Metagenomic Characterization of Gut Microbiota in Children with Autism Spectrum Disorder: Microbial Signatures and Modulation by Anti-Inflammatory Diet and Probiotics,"Pharmaceuticals (Basel, Switzerland)",2025,"Colombian children, anti-inflammatory diet, autism spectrum disorder, gastrointestinal disorders, gut microbiota, metagenomics, probiotics",Experiment 2,Colombia,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,Typically Developing (No FGIDs),Autism Spectrum Disorder (No FGIDs),"Participants had a confirmed clinical diagnosis of high-functioning Autism Spectrum Disorder (Level I, DSM-5) and no Functional Gastrointestinal Disorders (FGIDs).",3,8,3 months,WMS,NA,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 6,10 October 2025,Amara-Chikaodili,Amara-Chikaodili,"Genera found to be significantly more abundant in fecal samples of children with Autism Spectrum Disorder (ASD without FGIDs) compared to typically developing (TD) controls without FGIDs (Welch's t-test, Benjamini-Hochberg FDR p<0.05).",increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|2005525|375288,Complete,Svetlana up
bsdb:41011244/3/1,41011244,"cross-sectional observational, not case-control,randomized controlled trial",41011244,10.3390/ph18091376,https://doi.org/10.3390/ph18091376,"Valencia-Buitrago M., Oliveira-Carvalho R.D., Cardoso V., Triviño-Valencia J., Salamanca-Duque L.M., Martínez-Díaz V., Zabaleta J., Galeano-Vanegas N.F. , Naranjo-Galvis C.A.",Metagenomic Characterization of Gut Microbiota in Children with Autism Spectrum Disorder: Microbial Signatures and Modulation by Anti-Inflammatory Diet and Probiotics,"Pharmaceuticals (Basel, Switzerland)",2025,"Colombian children, anti-inflammatory diet, autism spectrum disorder, gastrointestinal disorders, gut microbiota, metagenomics, probiotics",Experiment 3,Colombia,Homo sapiens,Feces,UBERON:0001988,Therapeutic Procedure,EFO:0010063,Autism Spectrum Disorder Diet PRE-intervention,Autism Spectrum Disorder Diet POST-intervention,"A specific anti-inflammatory dietary protocol, designated as ""NeuroGutPlus,"" which was formulated using regionally accessible, polyphenol-rich, and fiber-dense foods, administered over a 12-week intervention period to children with Autism Spectrum Disorder (Level I, DSM-5)",5,5,3 months,WMS,NA,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 12,10 October 2025,Amara-Chikaodili,Amara-Chikaodili,Genera with significantly increased relative abundance (Welch's t-test) in Autism Spectrum Disorder children (ASD) POST-intervention compared to PRE-intervention after 12 weeks of an anti-inflammatory diet (Benjamini-Hochberg FDR p<0.05).,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Altererythrobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Novisyntrophococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas",1783272|201174|84998|1643822|1643826|447020;3379134|1224|28211|204457|335929|361177;1783272|1239|186801|186802|186806|1730;3379134|1224|1236|2887326|468|475;1783272|1239|186801|3085636|186803|2888809;1783272|1239|186801|3085636|186803|1769710,Complete,Svetlana up
bsdb:41011244/4/1,41011244,"cross-sectional observational, not case-control,randomized controlled trial",41011244,10.3390/ph18091376,https://doi.org/10.3390/ph18091376,"Valencia-Buitrago M., Oliveira-Carvalho R.D., Cardoso V., Triviño-Valencia J., Salamanca-Duque L.M., Martínez-Díaz V., Zabaleta J., Galeano-Vanegas N.F. , Naranjo-Galvis C.A.",Metagenomic Characterization of Gut Microbiota in Children with Autism Spectrum Disorder: Microbial Signatures and Modulation by Anti-Inflammatory Diet and Probiotics,"Pharmaceuticals (Basel, Switzerland)",2025,"Colombian children, anti-inflammatory diet, autism spectrum disorder, gastrointestinal disorders, gut microbiota, metagenomics, probiotics",Experiment 4,Colombia,Homo sapiens,Feces,UBERON:0001988,Therapeutic Procedure,EFO:0010063,ASD Probiotics PRE-intervention,ASD Probiotics POST-intervention,"Administration of a multi-strain probiotic formulation over a 12-week intervention period to children with high-functioning Autism Spectrum Disorder (Level I, DSM-5). This action is intended to alter the pathologic process of ASD-associated dysbiosis.",6,6,3 months,WMS,NA,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 13,10 October 2025,Amara-Chikaodili,Amara-Chikaodili,Genera with significantly altered relative abundance (Welch's t-test) in ASD children POST-intervention compared to PRE-intervention after 12 weeks of probiotic supplementation (Benjamini-Hochberg FDR p<0.05).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Altererythrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia",3379134|1224|28211|204457|335929|361177;3379134|1224|1236|2887326|468|475;1783272|1239|186801|3082720|186804|1501226,Complete,ChiomaBlessing
bsdb:41011244/4/2,41011244,"cross-sectional observational, not case-control,randomized controlled trial",41011244,10.3390/ph18091376,https://doi.org/10.3390/ph18091376,"Valencia-Buitrago M., Oliveira-Carvalho R.D., Cardoso V., Triviño-Valencia J., Salamanca-Duque L.M., Martínez-Díaz V., Zabaleta J., Galeano-Vanegas N.F. , Naranjo-Galvis C.A.",Metagenomic Characterization of Gut Microbiota in Children with Autism Spectrum Disorder: Microbial Signatures and Modulation by Anti-Inflammatory Diet and Probiotics,"Pharmaceuticals (Basel, Switzerland)",2025,"Colombian children, anti-inflammatory diet, autism spectrum disorder, gastrointestinal disorders, gut microbiota, metagenomics, probiotics",Experiment 4,Colombia,Homo sapiens,Feces,UBERON:0001988,Therapeutic Procedure,EFO:0010063,ASD Probiotics PRE-intervention,ASD Probiotics POST-intervention,"Administration of a multi-strain probiotic formulation over a 12-week intervention period to children with high-functioning Autism Spectrum Disorder (Level I, DSM-5). This action is intended to alter the pathologic process of ASD-associated dysbiosis.",6,6,3 months,WMS,NA,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 13,10 October 2025,Amara-Chikaodili,Amara-Chikaodili,Genera with significantly altered relative abundance (Welch's t-test) in ASD children POST-intervention compared to PRE-intervention after 12 weeks of probiotic supplementation (Benjamini-Hochberg FDR p<0.05).,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,1783272|1239|186801|3085636|186803|28050,Complete,ChiomaBlessing
bsdb:41011244/6/1,41011244,"cross-sectional observational, not case-control,randomized controlled trial",41011244,10.3390/ph18091376,https://doi.org/10.3390/ph18091376,"Valencia-Buitrago M., Oliveira-Carvalho R.D., Cardoso V., Triviño-Valencia J., Salamanca-Duque L.M., Martínez-Díaz V., Zabaleta J., Galeano-Vanegas N.F. , Naranjo-Galvis C.A.",Metagenomic Characterization of Gut Microbiota in Children with Autism Spectrum Disorder: Microbial Signatures and Modulation by Anti-Inflammatory Diet and Probiotics,"Pharmaceuticals (Basel, Switzerland)",2025,"Colombian children, anti-inflammatory diet, autism spectrum disorder, gastrointestinal disorders, gut microbiota, metagenomics, probiotics",Experiment 6,Colombia,Homo sapiens,Feces,UBERON:0001988,Digestive system disease,EFO:0000405,(TD_No FGIDs),(TD_FGIDs),"The presence of Functional Gastrointestinal Disorders (FGIDs), which are disorders of gut-brain interaction. This comparison contrasts Typically Developing children with FGIDs (Group 1) against Typically Developing children without FGIDs (Group 0).",3,4,3 months,WMS,NA,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 7,17 October 2025,Amara-Chikaodili,Amara-Chikaodili,"Genera showing significantly altered relative abundance (Welch's t-test) in Typically Developing children with FGIDs compared to those without FGIDs. Both genera were more abundant in the TD group without FGIDs (Group 0), reflecting depletion of beneficial taxa associated with GI symptomatology (Benjamini-Hochberg FDR p<0.05).",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus",1783272|1239|186801|3085636|186803|2569097;1783272|1239|186801|3085636|186803|33042,Complete,ChiomaBlessing
bsdb:41011244/7/1,41011244,"cross-sectional observational, not case-control,randomized controlled trial",41011244,10.3390/ph18091376,https://doi.org/10.3390/ph18091376,"Valencia-Buitrago M., Oliveira-Carvalho R.D., Cardoso V., Triviño-Valencia J., Salamanca-Duque L.M., Martínez-Díaz V., Zabaleta J., Galeano-Vanegas N.F. , Naranjo-Galvis C.A.",Metagenomic Characterization of Gut Microbiota in Children with Autism Spectrum Disorder: Microbial Signatures and Modulation by Anti-Inflammatory Diet and Probiotics,"Pharmaceuticals (Basel, Switzerland)",2025,"Colombian children, anti-inflammatory diet, autism spectrum disorder, gastrointestinal disorders, gut microbiota, metagenomics, probiotics",Experiment 7,Colombia,Homo sapiens,Feces,UBERON:0001988,"Autism spectrum disorder,Digestive system disease","EFO:0003756,EFO:0000405",TD (Overall),(ASD_FGIDs),"The coexistence of Autism Spectrum Disorder (ASD), defined by clinical diagnosis (Level I, DSM-5), and the presence of Functional Gastrointestinal Disorders (FGIDs).",7,15,3 months,WMS,NA,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,unchanged,unchanged,decreased,NA,NA,NA,Signature 1,Figure 8,17 October 2025,Amara-Chikaodili,Amara-Chikaodili,Genera with significantly altered relative abundance (Welch's t-test) in ASD children with FGIDs (ASD_FGIDs) compared to the overall TD control group (Benjamini-Hochberg FDR p<0.05).,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005525|375288;1783272|1239|909932|1843488|909930|33024,Complete,ChiomaBlessing
bsdb:41011244/7/2,41011244,"cross-sectional observational, not case-control,randomized controlled trial",41011244,10.3390/ph18091376,https://doi.org/10.3390/ph18091376,"Valencia-Buitrago M., Oliveira-Carvalho R.D., Cardoso V., Triviño-Valencia J., Salamanca-Duque L.M., Martínez-Díaz V., Zabaleta J., Galeano-Vanegas N.F. , Naranjo-Galvis C.A.",Metagenomic Characterization of Gut Microbiota in Children with Autism Spectrum Disorder: Microbial Signatures and Modulation by Anti-Inflammatory Diet and Probiotics,"Pharmaceuticals (Basel, Switzerland)",2025,"Colombian children, anti-inflammatory diet, autism spectrum disorder, gastrointestinal disorders, gut microbiota, metagenomics, probiotics",Experiment 7,Colombia,Homo sapiens,Feces,UBERON:0001988,"Autism spectrum disorder,Digestive system disease","EFO:0003756,EFO:0000405",TD (Overall),(ASD_FGIDs),"The coexistence of Autism Spectrum Disorder (ASD), defined by clinical diagnosis (Level I, DSM-5), and the presence of Functional Gastrointestinal Disorders (FGIDs).",7,15,3 months,WMS,NA,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,unchanged,unchanged,decreased,NA,NA,NA,Signature 2,Figure 8,17 October 2025,Amara-Chikaodili,Amara-Chikaodili,Genera with significantly altered relative abundance (Welch's t-test) in ASD children with FGIDs (ASD_FGIDs) compared to the overall TD control group (Benjamini-Hochberg FDR p<0.05).,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,ChiomaBlessing
bsdb:41011244/8/1,41011244,"cross-sectional observational, not case-control,randomized controlled trial",41011244,10.3390/ph18091376,https://doi.org/10.3390/ph18091376,"Valencia-Buitrago M., Oliveira-Carvalho R.D., Cardoso V., Triviño-Valencia J., Salamanca-Duque L.M., Martínez-Díaz V., Zabaleta J., Galeano-Vanegas N.F. , Naranjo-Galvis C.A.",Metagenomic Characterization of Gut Microbiota in Children with Autism Spectrum Disorder: Microbial Signatures and Modulation by Anti-Inflammatory Diet and Probiotics,"Pharmaceuticals (Basel, Switzerland)",2025,"Colombian children, anti-inflammatory diet, autism spectrum disorder, gastrointestinal disorders, gut microbiota, metagenomics, probiotics",Experiment 8,Colombia,Homo sapiens,Feces,UBERON:0001988,Autism spectrum disorder,EFO:0003756,(TD_FGIDs),(ASD_FGIDs),"The coexistence of Autism Spectrum Disorder (ASD), defined by a confirmed clinical diagnosis of high-functioning Autism Spectrum Disorder (Level I, DSM-5), and Functional Gastrointestinal Disorders (FGIDs). This experiment specifically compares this group (Group 1) against Typically Developing children who also have FGIDs (Group 0).",4,15,3 months,WMS,NA,Illumina,relative abundances,Welch's T-Test,0.05,TRUE,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 9,18 October 2025,Amara-Chikaodili,"Amara-Chikaodili,ChiomaBlessing",Genera with significantly altered relative abundance (Welch's t-test) in ASD children with FGIDs (ASD_FGIDs) compared to Typically developing children with FGIDs (TD_FGIDs). All listed genera were increased in the (ASD_FGIDs) group (Benjamini-Hochberg FDR p<0.05).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Enterocloster,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",1783272|1239|186801|3085636|186803|2569097;1783272|1239|186801|3082720|186804|1870884;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|3085636|186803|2719313;1783272|1239|186801|3085636|186803|1649459;3379134|1224|1236|91347|543|570;1783272|1239|186801|3085636|186803|1506553;1783272|1239|526524|526525|2810280|3025755;1783272|1239|186801|186802|31979|1485,Complete,ChiomaBlessing
bsdb:41011443/1/1,41011443,case-control,41011443,https://doi.org/10.3390/microorganisms13092112,https://www.mdpi.com/2076-2607/13/9/2112#app1-microorganisms-13-02112,"Rouskas K., Mamalaki E., Ntanasi E., Pantoura M., Anezaki M., Emmanouil C., Novau-Ferré N., Bulló M., Dimas A.S., Papandreou C., Yannakoulia M., Argiriou A. , Scarmeas N.",Gut Microbiome Alterations in Mild Cognitive Impairment: Findings from the ALBION Greek Cohort,Microorganisms,2025,"Alzheimer’s disease, discrimination model, gut microbiota, microbiome, microbiota-gut–brain axis, mild cognitive impairment",Experiment 1,Greece,Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Cognitively Normal (CN),Mild Cognitive Impairment (MCI),Milld cognitive impairment (MCI) Is an early prodromal stage of Alzheimer disease (AD),49,50,3 months,16S,34,Illumina,centered log-ratio,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",unchanged,unchanged,NA,NA,unchanged,unchanged,Signature 1,Figure 3A and Table S2,17 October 2025,Fiddyhamma,Fiddyhamma,Differentially abundant genera between the cognitively normal and individuals with MCI. Volcano plots display −log10 adjusted p-values and log2 fold changes for (A) genera between the two groups. Significant changes are highlighted in blue (increased at MCI) or yellow (decreased at MCI) color,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium",1783272|1239|186801|186802|1470353;1783272|1239|186801|186802|216572|596767,Complete,Svetlana up
bsdb:41011443/1/2,41011443,case-control,41011443,https://doi.org/10.3390/microorganisms13092112,https://www.mdpi.com/2076-2607/13/9/2112#app1-microorganisms-13-02112,"Rouskas K., Mamalaki E., Ntanasi E., Pantoura M., Anezaki M., Emmanouil C., Novau-Ferré N., Bulló M., Dimas A.S., Papandreou C., Yannakoulia M., Argiriou A. , Scarmeas N.",Gut Microbiome Alterations in Mild Cognitive Impairment: Findings from the ALBION Greek Cohort,Microorganisms,2025,"Alzheimer’s disease, discrimination model, gut microbiota, microbiome, microbiota-gut–brain axis, mild cognitive impairment",Experiment 1,Greece,Homo sapiens,Feces,UBERON:0001988,Cognitive impairment,HP:0100543,Cognitively Normal (CN),Mild Cognitive Impairment (MCI),Milld cognitive impairment (MCI) Is an early prodromal stage of Alzheimer disease (AD),49,50,3 months,16S,34,Illumina,centered log-ratio,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",unchanged,unchanged,NA,NA,unchanged,unchanged,Signature 2,Figure 3A and Table S2,17 October 2025,Fiddyhamma,Fiddyhamma,Differentially abundant genera between the cognitively normal and individuals with MCI. Volcano plots display −log10 adjusted p-values and log2 fold changes for (A) genera between the two groups. Significant changes are highlighted in blue (increased at MCI) or yellow (decreased at MCI) color,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Sellimonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",3379134|976|200643|171549|2005519|397864;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|3085636|186803|1769710;1783272|1239|186801|186802|216572|292632,Complete,Svetlana up
bsdb:41011452/1/1,41011452,case-control,41011452,10.3390/microorganisms13092121,NA,"Ramírez-Hernández M.D.C., Gaytán-Cervantes J., González-Torres C., Loyola-Cruz M.Á., García-Mendiola R.E., Cruz-Cruz C., Cortés-Ortíz I.A., García-Moncada E., López-Flores T., Durán-Manuel E.M., Gómez-Mancilla N., Oviedo-López M.F., Jiménez-Zamarripa C.A., Rojas-Bernabé A., García-Hernández O.A., Puente-Rivera J., López-Ornelas A., Nieto-Velázquez N.G., Blanco-Hernández D.M.R., Castañeda-Ortega J.C., Hernández-Castellanos B., Anaya-Saavedra G., Calzada-Mendoza C.C. , Bello-López J.M.",Oral Microbiota Dysbiosis in Male HIV Patients: Comparative Analysis of Candidiasis and HPV-Associated Lesions,Microorganisms,2025,"HIV, massive sequencing, oral lesions, oral microbiota",Experiment 1,Mexico,Homo sapiens,Saliva,UBERON:0001836,HIV infection,EFO:0000764,HP (HIV Negative Patients),C_HIV (Confirmed HIV viral suppression),HIV-positive patients with confirmed viral suppression (undetectable viral load) and on ART (antiretroviral therapy) BETA (Bictegravir/Emtricitabine/Tenofovir Alafenamide) regimen.,23,22,NA,16S,123,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5a,23 November 2025,YokoC,"YokoC,Tosin",Volcano plot of differential abundance between groups by biplots analysis of the oral microbiota.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter piscolens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella enoeca",1783272|1239|186801|3085636|186803|43994;3384189|32066|203490|203491|1129771|32067;1783272|1239|91061|186826|33958|2742598;3379134|976|200643|171549|171551|836|837;3379134|1224|1236|72274|135621|286|287;3384194|508458|649775|649776|3029088|638847|638849;1783272|201174|1760|85006|1268|32207|2047;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|2974257|76123,Complete,KateRasheed
bsdb:41011452/1/2,41011452,case-control,41011452,10.3390/microorganisms13092121,NA,"Ramírez-Hernández M.D.C., Gaytán-Cervantes J., González-Torres C., Loyola-Cruz M.Á., García-Mendiola R.E., Cruz-Cruz C., Cortés-Ortíz I.A., García-Moncada E., López-Flores T., Durán-Manuel E.M., Gómez-Mancilla N., Oviedo-López M.F., Jiménez-Zamarripa C.A., Rojas-Bernabé A., García-Hernández O.A., Puente-Rivera J., López-Ornelas A., Nieto-Velázquez N.G., Blanco-Hernández D.M.R., Castañeda-Ortega J.C., Hernández-Castellanos B., Anaya-Saavedra G., Calzada-Mendoza C.C. , Bello-López J.M.",Oral Microbiota Dysbiosis in Male HIV Patients: Comparative Analysis of Candidiasis and HPV-Associated Lesions,Microorganisms,2025,"HIV, massive sequencing, oral lesions, oral microbiota",Experiment 1,Mexico,Homo sapiens,Saliva,UBERON:0001836,HIV infection,EFO:0000764,HP (HIV Negative Patients),C_HIV (Confirmed HIV viral suppression),HIV-positive patients with confirmed viral suppression (undetectable viral load) and on ART (antiretroviral therapy) BETA (Bictegravir/Emtricitabine/Tenofovir Alafenamide) regimen.,23,22,NA,16S,123,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5a,23 November 2025,YokoC,"YokoC,Tosin",Volcano plot of differential abundance between groups by biplots analysis of the oral microbiota.,decreased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Acholeplasma,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas japonica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum",1783272|544448|31969|186329|2146|2147;3379134|976|200643|171549|815|816;3379134|976|200643|171549|171552|2974257|386414;3379134|976|200643|171549|171552|838|28130;3379134|1224|1236|72274|135621|286|256466;1783272|1239|91061|186826|1300|1301|1343;3379134|203691|203692|136|2845253|157;3379134|203691|203692|136|2845253|157|59892,Complete,KateRasheed
bsdb:41011452/2/1,41011452,case-control,41011452,10.3390/microorganisms13092121,NA,"Ramírez-Hernández M.D.C., Gaytán-Cervantes J., González-Torres C., Loyola-Cruz M.Á., García-Mendiola R.E., Cruz-Cruz C., Cortés-Ortíz I.A., García-Moncada E., López-Flores T., Durán-Manuel E.M., Gómez-Mancilla N., Oviedo-López M.F., Jiménez-Zamarripa C.A., Rojas-Bernabé A., García-Hernández O.A., Puente-Rivera J., López-Ornelas A., Nieto-Velázquez N.G., Blanco-Hernández D.M.R., Castañeda-Ortega J.C., Hernández-Castellanos B., Anaya-Saavedra G., Calzada-Mendoza C.C. , Bello-López J.M.",Oral Microbiota Dysbiosis in Male HIV Patients: Comparative Analysis of Candidiasis and HPV-Associated Lesions,Microorganisms,2025,"HIV, massive sequencing, oral lesions, oral microbiota",Experiment 2,Mexico,Homo sapiens,Saliva,UBERON:0001836,HIV infection,EFO:0000764,HP (HIV Negative Patients),ND_HIV (HIV-positive newly diagnosed without antiretroviral treatment),HIV-positive newly diagnosed patients without antiretroviral treatment at the time of inclusion in the study. This group showed a mean of 265 CD4+ cells/mL (range: 30–749) and detectable viral loads between 2.1 × 103 to 2.5 × 105 copies/mL.,23,23,NA,16S,123,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5b,23 November 2025,YokoC,"YokoC,Tosin",Volcano plot of differential abundance between groups by biplots analysis of the oral microbiota.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus urinaeequi,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium pumilum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|1239|91061|186826|186827|1375|51665;1783272|1239|186801|3085636|186803|43994;3384189|32066|203490|203491|1129771|32067;1783272|1239|91061|186826|33958|2742598;1783272|1239|186801|3082720|543314|86331|86332;3379134|976|200643|171549|171552|838|28130;1783272|201174|1760|85006|1268|32207|2047;3379134|976|200643|171549|171552|838,Complete,KateRasheed
bsdb:41011452/2/2,41011452,case-control,41011452,10.3390/microorganisms13092121,NA,"Ramírez-Hernández M.D.C., Gaytán-Cervantes J., González-Torres C., Loyola-Cruz M.Á., García-Mendiola R.E., Cruz-Cruz C., Cortés-Ortíz I.A., García-Moncada E., López-Flores T., Durán-Manuel E.M., Gómez-Mancilla N., Oviedo-López M.F., Jiménez-Zamarripa C.A., Rojas-Bernabé A., García-Hernández O.A., Puente-Rivera J., López-Ornelas A., Nieto-Velázquez N.G., Blanco-Hernández D.M.R., Castañeda-Ortega J.C., Hernández-Castellanos B., Anaya-Saavedra G., Calzada-Mendoza C.C. , Bello-López J.M.",Oral Microbiota Dysbiosis in Male HIV Patients: Comparative Analysis of Candidiasis and HPV-Associated Lesions,Microorganisms,2025,"HIV, massive sequencing, oral lesions, oral microbiota",Experiment 2,Mexico,Homo sapiens,Saliva,UBERON:0001836,HIV infection,EFO:0000764,HP (HIV Negative Patients),ND_HIV (HIV-positive newly diagnosed without antiretroviral treatment),HIV-positive newly diagnosed patients without antiretroviral treatment at the time of inclusion in the study. This group showed a mean of 265 CD4+ cells/mL (range: 30–749) and detectable viral loads between 2.1 × 103 to 2.5 × 105 copies/mL.,23,23,NA,16S,123,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5b,23 November 2025,YokoC,"YokoC,Tosin",Volcano plot of differential abundance between groups by biplots analysis of the oral microbiota.,decreased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Acholeplasma,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio fairfieldensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas japonica,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter piscolens,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga",1783272|544448|31969|186329|2146|2147;1783272|201174|1760|2037|2049|1654|55565;3379134|976|200643|171549|815|816;3379134|200940|3031449|213115|194924|872|44742;3379134|976|200643|171549|171552|2974257|386414;3379134|976|200643|171549|171551|836;3379134|1224|1236|72274|135621|286|256466;3384194|508458|649775|649776|3029088|638847|638849;1783272|1239|91061|186826|1300|1301|1343;3379134|203691|203692|136|2845253|157;3379134|203691|203692|136|2845253|157|59892;3379134|976|117743|200644|49546|1016,Complete,KateRasheed
bsdb:41011452/3/1,41011452,case-control,41011452,10.3390/microorganisms13092121,NA,"Ramírez-Hernández M.D.C., Gaytán-Cervantes J., González-Torres C., Loyola-Cruz M.Á., García-Mendiola R.E., Cruz-Cruz C., Cortés-Ortíz I.A., García-Moncada E., López-Flores T., Durán-Manuel E.M., Gómez-Mancilla N., Oviedo-López M.F., Jiménez-Zamarripa C.A., Rojas-Bernabé A., García-Hernández O.A., Puente-Rivera J., López-Ornelas A., Nieto-Velázquez N.G., Blanco-Hernández D.M.R., Castañeda-Ortega J.C., Hernández-Castellanos B., Anaya-Saavedra G., Calzada-Mendoza C.C. , Bello-López J.M.",Oral Microbiota Dysbiosis in Male HIV Patients: Comparative Analysis of Candidiasis and HPV-Associated Lesions,Microorganisms,2025,"HIV, massive sequencing, oral lesions, oral microbiota",Experiment 3,Mexico,Homo sapiens,Saliva,UBERON:0001836,"HIV infection,Oral candidiasis","EFO:0007406,EFO:0000764",HP (HIV Negative Patients),Candida_HIV (HIV Positive patients with oral candidiasis),"HIV-positive patients with oral candidiasis, diagnosed clinically and by direct observation of pseudohyphae. These patients were on ART, with an undetectable viral load and an average of 433 CD4+ cells/mL (range: 74–893).",23,23,NA,16S,123,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5c,23 November 2025,YokoC,"YokoC,Tosin",Volcano plot of differential abundance between groups by biplots analysis of the oral microbiota.,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus delbrueckii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium|s__Mogibacterium pumilum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella enoeca",3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|43994;1783272|1239|91061|186826|33958|1578|1584;3384189|32066|203490|203491|1129771|32067;1783272|1239|91061|186826|33958|2742598;1783272|1239|186801|3082720|543314|86331|86332;1783272|201174|1760|85006|1268|32207|2047;1783272|1239|91061|186826|1300|1301|1303;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|2974257|76123,Complete,KateRasheed
bsdb:41011452/3/2,41011452,case-control,41011452,10.3390/microorganisms13092121,NA,"Ramírez-Hernández M.D.C., Gaytán-Cervantes J., González-Torres C., Loyola-Cruz M.Á., García-Mendiola R.E., Cruz-Cruz C., Cortés-Ortíz I.A., García-Moncada E., López-Flores T., Durán-Manuel E.M., Gómez-Mancilla N., Oviedo-López M.F., Jiménez-Zamarripa C.A., Rojas-Bernabé A., García-Hernández O.A., Puente-Rivera J., López-Ornelas A., Nieto-Velázquez N.G., Blanco-Hernández D.M.R., Castañeda-Ortega J.C., Hernández-Castellanos B., Anaya-Saavedra G., Calzada-Mendoza C.C. , Bello-López J.M.",Oral Microbiota Dysbiosis in Male HIV Patients: Comparative Analysis of Candidiasis and HPV-Associated Lesions,Microorganisms,2025,"HIV, massive sequencing, oral lesions, oral microbiota",Experiment 3,Mexico,Homo sapiens,Saliva,UBERON:0001836,"HIV infection,Oral candidiasis","EFO:0007406,EFO:0000764",HP (HIV Negative Patients),Candida_HIV (HIV Positive patients with oral candidiasis),"HIV-positive patients with oral candidiasis, diagnosed clinically and by direct observation of pseudohyphae. These patients were on ART, with an undetectable viral load and an average of 433 CD4+ cells/mL (range: 74–893).",23,23,NA,16S,123,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5c,23 November 2025,YokoC,"YokoC,Tosin",Volcano plot of differential abundance between groups by biplots analysis of the oral microbiota.,decreased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Acholeplasma,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas japonica,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter piscolens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sinensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",1783272|544448|31969|186329|2146|2147;1783272|201174|1760|2037|2049|1654|1655;3379134|976|200643|171549|815|816;3379134|976|200643|171549|171552|2974257|386414;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|171552|838|28130;3379134|976|200643|171549|171552|838|28131;3379134|1224|1236|72274|135621|286|256466;3384194|508458|649775|649776|3029088|638847|638849;1783272|1239|909932|909929|1843491|970;1783272|1239|91061|186826|1300|1301|176090;1783272|1239|91061|186826|1300|1301|1343;3379134|203691|203692|136|2845253|157;3379134|203691|203692|136|2845253|157|59892;3379134|976|200643|171549|171552|838,Complete,KateRasheed
bsdb:41011452/4/1,41011452,case-control,41011452,10.3390/microorganisms13092121,NA,"Ramírez-Hernández M.D.C., Gaytán-Cervantes J., González-Torres C., Loyola-Cruz M.Á., García-Mendiola R.E., Cruz-Cruz C., Cortés-Ortíz I.A., García-Moncada E., López-Flores T., Durán-Manuel E.M., Gómez-Mancilla N., Oviedo-López M.F., Jiménez-Zamarripa C.A., Rojas-Bernabé A., García-Hernández O.A., Puente-Rivera J., López-Ornelas A., Nieto-Velázquez N.G., Blanco-Hernández D.M.R., Castañeda-Ortega J.C., Hernández-Castellanos B., Anaya-Saavedra G., Calzada-Mendoza C.C. , Bello-López J.M.",Oral Microbiota Dysbiosis in Male HIV Patients: Comparative Analysis of Candidiasis and HPV-Associated Lesions,Microorganisms,2025,"HIV, massive sequencing, oral lesions, oral microbiota",Experiment 4,Mexico,Homo sapiens,Saliva,UBERON:0001836,"HIV infection,Human papilloma virus infection","EFO:0001668,EFO:0000764",HP (HIV Negative Patients),HPV_HIV (HIV Positive patients with human papillomavirus oral lesions),"HIV-positive patients on ART (antiretroviral therapy) with confirmed HPV (human papillomavirus) oral lesions (multifocal epithelial hyperplasia), with undetectable viral load, with an average CD4+ levels of 339 cells/mL (range: 197–639).",23,8,NA,16S,123,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5d,24 November 2025,YokoC,"YokoC,Tosin",Volcano plot of differential abundance between groups by biplots analysis of the oral microbiota.,increased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Acholeplasma,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus urinaeequi,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Johnsonella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus delbrueckii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella micans,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Pseudoleptotrichia|s__Pseudoleptotrichia goodfellowii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter|s__Pseudoramibacter alactolyticus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella|s__Simonsiella muelleri,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema pedis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",1783272|544448|31969|186329|2146|2147;1783272|201174|1760|2037|2049|1654|55565;1783272|201174|1760|2037|2049|1654|1655;1783272|1239|91061|186826|186827|1375|51665;1783272|1239|186801|3085636|186803|43994;1783272|1239|91061|186826|33958|1578|1584;1783272|1239|91061|186826|33958|2742598;3379134|976|200643|171549|171552|838;3379134|976|200643|171549|171552|838|189723;3384189|32066|203490|203491|1129771|2755140|157692;1783272|1239|186801|186802|186806|113286|113287;1783272|201174|1760|85006|1268|32207|2047;3379134|1224|28216|206351|481|71|72;3379134|203691|203692|136|2845253|157|409322;3384189|32066|203490|203491|1129771|32067,Complete,KateRasheed
bsdb:41011452/4/2,41011452,case-control,41011452,10.3390/microorganisms13092121,NA,"Ramírez-Hernández M.D.C., Gaytán-Cervantes J., González-Torres C., Loyola-Cruz M.Á., García-Mendiola R.E., Cruz-Cruz C., Cortés-Ortíz I.A., García-Moncada E., López-Flores T., Durán-Manuel E.M., Gómez-Mancilla N., Oviedo-López M.F., Jiménez-Zamarripa C.A., Rojas-Bernabé A., García-Hernández O.A., Puente-Rivera J., López-Ornelas A., Nieto-Velázquez N.G., Blanco-Hernández D.M.R., Castañeda-Ortega J.C., Hernández-Castellanos B., Anaya-Saavedra G., Calzada-Mendoza C.C. , Bello-López J.M.",Oral Microbiota Dysbiosis in Male HIV Patients: Comparative Analysis of Candidiasis and HPV-Associated Lesions,Microorganisms,2025,"HIV, massive sequencing, oral lesions, oral microbiota",Experiment 4,Mexico,Homo sapiens,Saliva,UBERON:0001836,"HIV infection,Human papilloma virus infection","EFO:0001668,EFO:0000764",HP (HIV Negative Patients),HPV_HIV (HIV Positive patients with human papillomavirus oral lesions),"HIV-positive patients on ART (antiretroviral therapy) with confirmed HPV (human papillomavirus) oral lesions (multifocal epithelial hyperplasia), with undetectable viral load, with an average CD4+ levels of 339 cells/mL (range: 197–639).",23,8,NA,16S,123,Illumina,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5d,24 November 2025,YokoC,YokoC,Volcano plot of differential abundance between groups by biplots analysis of the oral microbiota.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella timonensis,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas japonica,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium",3379134|976|200643|171549|171552|2974257|386414;3379134|203691|203692|136|2845253|157;3379134|203691|203692|136|2845253|157|59892;3379134|1224|1236|72274|135621|286|256466;1783272|1239|91061|186826|1300|1301|1343;3379134|976|200643|171549|171552|838;1783272|201174|1760|85009|31957|1743,Complete,KateRasheed
bsdb:41029180/1/1,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 1,"United States of America,Thailand",Mus musculus,Feces,UBERON:0001988,Environmental factor,EFO:0000469,Baseline Donor pair-1 (dp1) Thailand (Thai) colonized mice,Baseline Donor pair-1 (dp1) United States (US) colonized mice,These are mice colonized with donor pair-1 (dp1) late middle-aged United States (US) donor stool,8,6,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Supplemental Tables 2, 3",8 November 2025,Fiddyhamma,Fiddyhamma,"Differentially abundant taxa at family, genus level between United States (U.S) and Thailand (Thai) donor baseline mouse samples in Donor pair-1 (dp1)",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,",1783272|201174|84998|1643822|1643826|447020;3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|946234;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|248744;3379134|976|200643|171549|2005525|375288;3379134|976|200643|171549|2005525;,Complete,NA
bsdb:41029180/1/2,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 1,"United States of America,Thailand",Mus musculus,Feces,UBERON:0001988,Environmental factor,EFO:0000469,Baseline Donor pair-1 (dp1) Thailand (Thai) colonized mice,Baseline Donor pair-1 (dp1) United States (US) colonized mice,These are mice colonized with donor pair-1 (dp1) late middle-aged United States (US) donor stool,8,6,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Supplemental Tables 2, 3",8 November 2025,Fiddyhamma,Fiddyhamma,"Differentially abundant taxa at family, genus level between United States (U.S) and Thailand (Thai) donor baseline mouse samples in Donor pair-1 (dp1)",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",1783272|1239|186801|3085636|186803|1766253;1783272|1239|1737404|1737405|1570339|165779;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953;1783272|201174|1760|85004|31953|1678;3379134|1224|28216|80840|119060;1783272|201174|84998|1643822|1643826|84111;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|1940338;1783272|1239|186801|186802|216572|216851;1783272|1239|1737404|1737405|1570339|150022;1783272|1239|186801|3085636|186803|1407607;3379134|1224|1236|91347|543|570;3379134|1224|28216|80840|995019|577310;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;3379134|1224|28216|80840|995019|40544,Complete,NA
bsdb:41029180/2/1,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 2,"Thailand,United States of America",Mus musculus,Feces,UBERON:0001988,Environmental factor,EFO:0000469,Baseline Donor pair-2 (dp2) Thailand (Thai) colonized mice,Baseline Donor pair-2 (dp2) United States (US) colonized mice,These are mice colonized with donor pair-2 (dp2) late middle-aged United States (US) donor stool,5,7,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Supplemental Tables 2, 3",8 November 2025,Fiddyhamma,Fiddyhamma,"Differentially abundant taxa at family, genus level between United States (U.S) and Thailand (Thai) donor baseline mouse samples in Donor pair-2 (dp2)",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,",1783272|1239|186801|3085636|186803|1766253;3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;3379134|976|200643|171549|171550|239759;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171550;,Complete,NA
bsdb:41029180/2/2,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 2,"Thailand,United States of America",Mus musculus,Feces,UBERON:0001988,Environmental factor,EFO:0000469,Baseline Donor pair-2 (dp2) Thailand (Thai) colonized mice,Baseline Donor pair-2 (dp2) United States (US) colonized mice,These are mice colonized with donor pair-2 (dp2) late middle-aged United States (US) donor stool,5,7,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Supplemental Tables 2, 3",9 November 2025,Fiddyhamma,Fiddyhamma,"Differentially abundant taxa at family, genus level between United States (U.S) and Thailand (Thai) donor baseline mouse samples in Donor pair-2 (dp2)",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pluralibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter",3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;3379134|1224|28216|80840|119060;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;1783272|1239|526524|526525|128827|1472649;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;3384189|32066|203490|203491|203492;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|1649459;1783272|1239|186801|3085636|186803|1506553;1783272|1239|91061|186826|33958;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|3082720|186804;3379134|1224|1236|91347|543|1330546;3379134|976|200643|171549|2005525;1783272|1239|186801|3082720|186804|1505652,Complete,NA
bsdb:41029180/3/1,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 3,"Thailand,United States of America",Mus musculus,Feces,UBERON:0001988,Environmental factor,EFO:0000469,2-weeks of SAS (single vinyl isolator with a shared air supply) Donor pair-1 (dp1) Thailand (Thai) colonized mice,2-weeks of SAS (single vinyl isolator with a shared air supply) Donor pair-1 (dp1) United States (US) colonized mice,"Colonized germ-free mice with stool from United States (US) donor pair-1 (dp1) placed in a single vinyl isolator with a shared air supply (SAS), separated by a barrier to prevent direct contact, for 2 weeks",8,6,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplemental Table 4,9 November 2025,Fiddyhamma,Fiddyhamma,Family-level differentially abundant taxa in Thailand (Thai) and United States (U.S) donor cohorts after 2 weeks of shared air supply (SAS).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",3379134|976|200643|171549|815;3379134|976|200643|171549|2005519;1783272|201174|1760|85004|31953;3379134|1224|28216|80840|119060;1783272|201174|84998|84999|84107;3379134|200940|3031449|213115|194924;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|1300,Complete,NA
bsdb:41029180/3/2,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 3,"Thailand,United States of America",Mus musculus,Feces,UBERON:0001988,Environmental factor,EFO:0000469,2-weeks of SAS (single vinyl isolator with a shared air supply) Donor pair-1 (dp1) Thailand (Thai) colonized mice,2-weeks of SAS (single vinyl isolator with a shared air supply) Donor pair-1 (dp1) United States (US) colonized mice,"Colonized germ-free mice with stool from United States (US) donor pair-1 (dp1) placed in a single vinyl isolator with a shared air supply (SAS), separated by a barrier to prevent direct contact, for 2 weeks",8,6,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,increased,NA,NA,NA,NA,Signature 2,Supplemental Table 4,9 November 2025,Fiddyhamma,Fiddyhamma,Family-level differentially abundant taxa in Thailand (Thai) and United States (U.S) donor cohorts after 2 weeks of shared air supply (SAS).,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae",3379134|74201|203494|48461|1647988;1783272|1239|186801|3082768|990719;1783272|1239|526524|526525|128827;1783272|1239|186801|186802|186806;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171550;3379134|976|200643|171549|2005525,Complete,NA
bsdb:41029180/4/1,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 4,"Thailand,United States of America",Mus musculus,Feces,UBERON:0001988,Environmental factor,EFO:0000469,2-weeks of SAS (single vinyl isolator with a shared air supply) Donor pair-2 (dp2) Thailand (Thai) colonized mice,2-weeks of SAS (single vinyl isolator with a shared air supply) Donor pair-2 (dp2) United States (US) colonized mice,"Colonized germ-free mice with stool from United States (US) donor pair-2 (dp2) placed in a single vinyl isolator with a shared air supply (SAS), separated by a barrier to prevent direct contact, for 2 weeks",5,7,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplemental Table 4,9 November 2025,Fiddyhamma,Fiddyhamma,Family-level differentially abundant taxa in Thailand (Thai) and United States (U.S) donor cohorts after 2 weeks of shared air supply (SAS).,increased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,1783272|201174|84998|84999|84107,Complete,NA
bsdb:41029180/4/2,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 4,"Thailand,United States of America",Mus musculus,Feces,UBERON:0001988,Environmental factor,EFO:0000469,2-weeks of SAS (single vinyl isolator with a shared air supply) Donor pair-2 (dp2) Thailand (Thai) colonized mice,2-weeks of SAS (single vinyl isolator with a shared air supply) Donor pair-2 (dp2) United States (US) colonized mice,"Colonized germ-free mice with stool from United States (US) donor pair-2 (dp2) placed in a single vinyl isolator with a shared air supply (SAS), separated by a barrier to prevent direct contact, for 2 weeks",5,7,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,increased,NA,NA,NA,NA,Signature 2,Supplemental Table 4,9 November 2025,Fiddyhamma,Fiddyhamma,Family-level differentially abundant taxa in Thailand (Thai) and United States (U.S) donor cohorts after 2 weeks of shared air supply (SAS).,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",3379134|74201|203494|48461|1647988;1783272|201174|84998|84999|84107;1783272|1239|91061|186826|33958,Complete,NA
bsdb:41029180/5/1,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 5,"Thailand,United States of America",Mus musculus,Feces,UBERON:0001988,Environmental factor,EFO:0000469,4-weeks of SAS (single vinyl isolator with a shared air supply) Donor pair-1 (dp1) Thailand (Thai) colonized mice,4-weeks of SAS (single vinyl isolator with a shared air supply) Donor pair-1 (dp1) United States (US) colonized mice,"Colonized germ-free mice with stool from United States (US) donor pair-1 (dp1) placed in a single vinyl isolator with a shared air supply (SAS), separated by a barrier to prevent direct contact, for 4 weeks",6,4,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplemental Table 4,9 November 2025,Fiddyhamma,Fiddyhamma,Family-level differentially abundant taxa in Thailand (Thai) and United States (U.S) donor cohorts after 2 weeks of shared air supply (SAS).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",3379134|976|200643|171549|815;1783272|201174|1760|85004|31953;3379134|1224|28216|80840|119060;1783272|201174|84998|1643822|1643826;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|1300,Complete,NA
bsdb:41029180/5/2,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 5,"Thailand,United States of America",Mus musculus,Feces,UBERON:0001988,Environmental factor,EFO:0000469,4-weeks of SAS (single vinyl isolator with a shared air supply) Donor pair-1 (dp1) Thailand (Thai) colonized mice,4-weeks of SAS (single vinyl isolator with a shared air supply) Donor pair-1 (dp1) United States (US) colonized mice,"Colonized germ-free mice with stool from United States (US) donor pair-1 (dp1) placed in a single vinyl isolator with a shared air supply (SAS), separated by a barrier to prevent direct contact, for 4 weeks",6,4,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,increased,NA,NA,NA,NA,Signature 2,Supplemental Table 4,9 November 2025,Fiddyhamma,Fiddyhamma,Family-level differentially abundant taxa in Thailand (Thai) and United States (U.S) donor cohorts after 2 weeks of shared air supply (SAS).,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,",3379134|74201|203494|48461|1647988;3379134|976|200643|171549|2005519;3379134|200940|3031449|213115|194924;1783272|1239|526524|526525|128827;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;3379134|976|200643|171549|171550;3379134|976|200643|171549|2005525;,Complete,NA
bsdb:41029180/6/1,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 6,"Thailand,United States of America",Mus musculus,Feces,UBERON:0001988,Environmental factor,EFO:0000469,4-weeks of SAS (single vinyl isolator with a shared air supply) Donor pair-2 (dp2) Thailand (Thai) colonized mice,4-weeks of SAS (single vinyl isolator with a shared air supply) Donor pair-2 (dp2) United States (US) colonized mice,"Colonized germ-free mice with stool from United States (US) donor pair-2 (dp2) placed in a single vinyl isolator with a shared air supply (SAS), separated by a barrier to prevent direct contact, for 4 weeks",5,7,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplemental Table 4,9 November 2025,Fiddyhamma,Fiddyhamma,Family-level differentially abundant taxa in Thailand (Thai) and United States (U.S) donor cohorts after 2 weeks of shared air supply (SAS).,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",3379134|1224|28216|80840|119060;1783272|201174|84998|84999|84107,Complete,NA
bsdb:41029180/6/2,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 6,"Thailand,United States of America",Mus musculus,Feces,UBERON:0001988,Environmental factor,EFO:0000469,4-weeks of SAS (single vinyl isolator with a shared air supply) Donor pair-2 (dp2) Thailand (Thai) colonized mice,4-weeks of SAS (single vinyl isolator with a shared air supply) Donor pair-2 (dp2) United States (US) colonized mice,"Colonized germ-free mice with stool from United States (US) donor pair-2 (dp2) placed in a single vinyl isolator with a shared air supply (SAS), separated by a barrier to prevent direct contact, for 4 weeks",5,7,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,increased,NA,NA,NA,NA,Signature 2,Supplemental Table 4,9 November 2025,Fiddyhamma,Fiddyhamma,Family-level differentially abundant taxa in Thailand (Thai) and United States (U.S) donor cohorts after 2 weeks of shared air supply (SAS).,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",3379134|74201|203494|48461|1647988;1783272|1239|91061|186826|33958,Complete,NA
bsdb:41029180/7/1,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 7,"Thailand,United States of America",Mus musculus,Feces,UBERON:0001988,Diet,EFO:0002755,Order A; Baseline Thailand (Thai) pre intervention mice,Order A; Thailand (Thai) colonized intervention mice fed with NNS & HFCS (non-nutritive sweeteners (NNS) and high-fructose corn syrup (HFCS)),Thailand (Thai) colonized intervention mice fed with NNS & HFCS (non-nutritive sweeteners (NNS) and high-fructose corn syrup (HFCS) according to the Order (A) in which dietary components were added,8,5,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 7,10 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant genera in the Thailand donor group compared with baseline samples in Order A experiments.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Paraclostridium,1783272|1239|186801|3082720|186804|1849822,Complete,NA
bsdb:41029180/8/1,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 8,"Thailand,United States of America",Mus musculus,Feces,UBERON:0001988,Diet,EFO:0002755,Order A; Baseline Thailand (Thai) pre intervention mice,Order A;Thailand (Thai) colonized intervention mice fed with ADDITIVES,Thailand (Thai) colonized intervention mice fed with ADDITIVES according to the Order (A) in which dietary components were added,8,5,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 7,10 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant genera in the Thailand donor group compared with baseline samples in Order A experiments.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Paraclostridium,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",3379134|1224|1236|91347|1903414|581;1783272|1239|186801|3082720|186804|1849822;1783272|1239|1737404|1737405|1570339|162289;1783272|1239|91061|186826|1300|1301,Complete,NA
bsdb:41029180/9/1,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 9,"Thailand,United States of America",Mus musculus,Feces,UBERON:0001988,Diet,EFO:0002755,Order A; Baseline United States (US) pre intervention mice,Order A; United States (US) colonized intervention mice fed with MEAT,United States (US) colonized intervention mice fed with MEAT according to the Order (A) in which dietary components were added,6,6,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 8,10 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant genera in the United States donor group compared with baseline samples in Order A experiments.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea",1783272|201174|84998|84999|84107|102106;1783272|1239|186801|186802|216572|1892380;1783272|1239|526524|526525|128827|1573534,Complete,NA
bsdb:41029180/9/2,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 9,"Thailand,United States of America",Mus musculus,Feces,UBERON:0001988,Diet,EFO:0002755,Order A; Baseline United States (US) pre intervention mice,Order A; United States (US) colonized intervention mice fed with MEAT,United States (US) colonized intervention mice fed with MEAT according to the Order (A) in which dietary components were added,6,6,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table 8,10 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant genera in the United States donor group compared with baseline samples in Order A experiments.,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,3379134|976|200643|171549|171550|239759,Complete,NA
bsdb:41029180/10/1,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 10,"Thailand,United States of America",Mus musculus,Feces,UBERON:0001988,Diet,EFO:0002755,Order A; Baseline United States (US) pre intervention mice,Order A; United States (US) colonized intervention mice fed with FLUORIDE (F),United States (US) colonized intervention mice fed with FLUORIDE according to the Order (A) in which dietary components were added,6,6,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 8,10 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant genera in the United States donor group compared with baseline samples in Order A experiments.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",1783272|201174|84998|84999|84107|102106;1783272|1239|186801|186802|216572|1892380;3379134|1224|28216|80840|995019|577310;3379134|1224|28216|80840|995019|40544,Complete,NA
bsdb:41029180/10/2,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 10,"Thailand,United States of America",Mus musculus,Feces,UBERON:0001988,Diet,EFO:0002755,Order A; Baseline United States (US) pre intervention mice,Order A; United States (US) colonized intervention mice fed with FLUORIDE (F),United States (US) colonized intervention mice fed with FLUORIDE according to the Order (A) in which dietary components were added,6,6,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table 8,10 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant genera in the United States donor group compared with baseline samples in Order A experiments.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,1783272|1239|186801|3085636|186803|1506553,Complete,NA
bsdb:41029180/11/1,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 11,"Thailand,United States of America",Mus musculus,Feces,UBERON:0001988,Diet,EFO:0002755,Order A; Baseline United States (US) pre intervention mice,Order A; United States (US) colonized intervention mice fed with NNS & HFCS (non-nutritive sweeteners (NNS) and high-fructose corn syrup (HFCS)),United States (US) colonized intervention mice fed with NNS & HFCS (non-nutritive sweeteners (NNS) and high-fructose corn syrup (HFCS) according to the Order (A) in which dietary components were added,6,6,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 8,10 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant genera in the United States donor group compared with baseline samples in Order A experiments.,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea",1783272|1239|526524|526525|128827|1470349;3379134|1224|1236|91347|543|544;1783272|201174|84998|84999|84107|102106;3379134|1224|28216|80840|995019|577310;1783272|1239|186801|3085636|186803|248744;1783272|1239|186801|186802|216572|1892380;1783272|1239|526524|526525|128827|1573534,Complete,NA
bsdb:41029180/11/2,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 11,"Thailand,United States of America",Mus musculus,Feces,UBERON:0001988,Diet,EFO:0002755,Order A; Baseline United States (US) pre intervention mice,Order A; United States (US) colonized intervention mice fed with NNS & HFCS (non-nutritive sweeteners (NNS) and high-fructose corn syrup (HFCS)),United States (US) colonized intervention mice fed with NNS & HFCS (non-nutritive sweeteners (NNS) and high-fructose corn syrup (HFCS) according to the Order (A) in which dietary components were added,6,6,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table 8,10 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant genera in the United States donor group compared with baseline samples in Order A experiments.,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,1783272|1239|186801|3085636|186803|572511,Complete,NA
bsdb:41029180/12/1,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 12,"Thailand,United States of America",Mus musculus,Feces,UBERON:0001988,Diet,EFO:0002755,Order A; Baseline United States (US) pre intervention mice,Order A; United States (US) colonized intervention mice fed with ADDITIVES,United States (US) colonized intervention mice fed with ADDITIVES according to the Order (A) in which dietary components were added,6,6,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 8,10 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant genera in the United States donor group compared with baseline samples in Order A experiments.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella",1783272|1239|186801|3085636|186803|207244;1783272|1239|526524|526525|128827|1470349;3379134|1224|1236|91347|543|544;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|186802|216572|1892380;1783272|1239|186801|3085636|186803|248744;3379134|1224|28216|80840|995019|577310,Complete,NA
bsdb:41029180/12/2,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 12,"Thailand,United States of America",Mus musculus,Feces,UBERON:0001988,Diet,EFO:0002755,Order A; Baseline United States (US) pre intervention mice,Order A; United States (US) colonized intervention mice fed with ADDITIVES,United States (US) colonized intervention mice fed with ADDITIVES according to the Order (A) in which dietary components were added,6,6,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table 8,10 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant genera in the United States donor group compared with baseline samples in Order A experiments.,decreased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,3379134|74201|203494|48461|1647988|239934,Complete,NA
bsdb:41029180/13/1,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 13,"Thailand,United States of America",Mus musculus,Feces,UBERON:0001988,Diet,EFO:0002755,Order B; Baseline Thailand (Thai) pre intervention mice,Order B; Thailand (Thai) colonized intervention mice fed with FLUORIDE,Thailand (Thai) colonized intervention mice fed with FLUORIDE according to the Order (B) in which dietary components were added,8,4,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 7,10 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant genera in the Thailand donor group compared with baseline samples in Order B experiments.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,1783272|1239|186801|3085636|186803|248744,Complete,NA
bsdb:41029180/13/2,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 13,"Thailand,United States of America",Mus musculus,Feces,UBERON:0001988,Diet,EFO:0002755,Order B; Baseline Thailand (Thai) pre intervention mice,Order B; Thailand (Thai) colonized intervention mice fed with FLUORIDE,Thailand (Thai) colonized intervention mice fed with FLUORIDE according to the Order (B) in which dietary components were added,8,4,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table 7,10 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant genera in the Thailand donor group compared with baseline samples in Order B experiments.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,NA
bsdb:41029180/14/1,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 14,"Thailand,United States of America",Mus musculus,Feces,UBERON:0001988,Diet,EFO:0002755,Order B; Baseline Thailand (Thai) pre intervention mice,Order B; Thailand (Thai) colonized intervention mice fed with ADDITIVES,Thailand (Thai) colonized intervention mice fed with ADDITIVES according to the Order (B) in which dietary components were added,8,4,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 7,10 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant genera in the Thailand donor group compared with baseline samples in Order B experiments.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,1783272|1239|186801|3085636|186803|248744,Complete,NA
bsdb:41029180/14/2,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 14,"Thailand,United States of America",Mus musculus,Feces,UBERON:0001988,Diet,EFO:0002755,Order B; Baseline Thailand (Thai) pre intervention mice,Order B; Thailand (Thai) colonized intervention mice fed with ADDITIVES,Thailand (Thai) colonized intervention mice fed with ADDITIVES according to the Order (B) in which dietary components were added,8,4,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table 7,10 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant genera in the Thailand donor group compared with baseline samples in Order B experiments.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,NA
bsdb:41029180/15/1,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 15,"Thailand,United States of America",Mus musculus,Feces,UBERON:0001988,Diet,EFO:0002755,Order B; Baseline Thailand (Thai) pre intervention mice,Order B; Thailand (Thai) colonized intervention mice fed with MEAT,Thailand (Thai) colonized intervention mice fed with MEAT according to the Order (B) in which dietary components were added,8,4,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 7,10 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant genera in the Thailand donor group compared with baseline samples in Order B experiments.,decreased,"k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|1737404|1737405|1570339|162289;1783272|1239|91061|186826|1300|1301,Complete,NA
bsdb:41029180/16/1,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 16,"Thailand,United States of America",Mus musculus,Feces,UBERON:0001988,Diet,EFO:0002755,Order B; Baseline United States (US) pre intervention mice,Order B; United States (US) colonized intervention mice fed with FLUORIDE,United States (US) colonized intervention mice fed with FLUORIDE according to the Order (B) in which dietary components were added,7,5,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 8,10 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant genera in the United States donor group compared with baseline samples in Order B experiments.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,",1783272|1239|186801|3085636|186803|207244;1783272|1239|91061|186826|81852|1350;,Complete,NA
bsdb:41029180/17/1,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 17,"Thailand,United States of America",Mus musculus,Feces,UBERON:0001988,Diet,EFO:0002755,Order B; Baseline United States (US) pre intervention mice,Order B; United States (US) colonized intervention mice fed with ADDITIVES,United States (US) colonized intervention mice fed with ADDITIVES according to the Order (B) in which dietary components were added,7,5,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 8,10 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant genera in the United States donor group compared with baseline samples in Order B experiments.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,1783272|1239|186801|3085636|186803|207244,Complete,NA
bsdb:41029180/18/1,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 18,"Thailand,United States of America",Mus musculus,Feces,UBERON:0001988,Diet,EFO:0002755,Order B; Baseline United States (US) pre intervention mice,Order B; United States (US) colonized intervention mice fed with MEAT,United States (US) colonized intervention mice fed with MEAT according to the Order (B) in which dietary components were added,7,5,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 8,10 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant genera in the United States donor group compared with baseline samples in Order B experiments.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",1783272|1239|186801|3085636|186803|207244;1783272|201174|84998|84999|84107|102106,Complete,NA
bsdb:41029180/18/2,41029180,laboratory experiment,41029180,doi.org/10.1080/19490976.2025.2562345,https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2562345#d1e471,"Comba I.Y., Hoops S., Till L., Vangay P.J., Johnson S., Xiao Y., Louwies T., Culhane Pera K., Pergament S., Knights D. , Kashyap P.C.",Shared environments can facilitate microbial transmission and alter metabolic outcomes,Gut microbes,2025,"Akkermansia, Immigration, Lactobacillus, food additives, gut microbiome, industrialization, microbiome transmission, non-nutritive sweeteners",Experiment 18,"Thailand,United States of America",Mus musculus,Feces,UBERON:0001988,Diet,EFO:0002755,Order B; Baseline United States (US) pre intervention mice,Order B; United States (US) colonized intervention mice fed with MEAT,United States (US) colonized intervention mice fed with MEAT according to the Order (B) in which dietary components were added,7,5,NA,16S,4,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table 8,10 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant genera in the United States donor group compared with baseline samples in Order B experiments.,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella",1783272|201174|84998|1643822|1643826|447020;3379134|74201|203494|48461|1647988|239934;1783272|1239|186801|3085636|186803|1766253;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3085636|186803|1649459,Complete,NA
bsdb:41039241/1/1,41039241,"cross-sectional observational, not case-control",41039241,https://doi.org/10.1186/s12866-025-04367-9,NA,"Kang C., Lee J., Baek M.G., Kim N.E., Son H., Yoo S. , Yi H.",Urinary microbiome in non-muscle invasive bladder cancer: impact of sample types and sex differences,BMC microbiology,2025,"Bladder cancer, Bladder microbiome, Catheterized urine, Curvibacter, Microbiome, Midstream urine, Mucosal tissue, Urinary microbiota",Experiment 1,South Korea,Homo sapiens,Urine,UBERON:0001088,Urothelial carcinoma,EFO:0008528,Non cancer controls with cancer-like symptoms (ETC),Urothelial carcinoma (UC),Patients diagnosed with urothelial carcinoma of the bladder,13,29,NA,16S,34,Illumina,log transformation,"Linear Regression,ANCOM-BC",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3A, Within text: “Bacteria associated with urothelial carcinoma”",18 October 2025,Susan githaiga,"Susan githaiga,Tosin",Volcano plot highlighting Curvibacter as the only genus significantly associated with urothelial carcinoma (UC) compared to non-cancer controls with cancer-like symptoms (ETC) (p < 0.05 and effect size >0.1).,increased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Curvibacter,3379134|1224|28216|80840|80864|281915,Complete,KateRasheed
bsdb:41039266/1/1,41039266,case-control,41039266,10.1186/s12866-025-04344-2,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04344-2,"Tavanaeian S., Feizabadi M.M., Falsafi S., Aghdaei H.A. , Houri H.",Oral and fecal microbiome alterations in pancreatic cancer: insights into potential diagnostic biomarkers,BMC microbiology,2025,"Fusobacterium nucleatum, Neisseria elongata, Fecal microbiome, Oral microbiome, Pancreatic cancer",Experiment 1,Iran,Homo sapiens,Feces,UBERON:0001988,Pancreatic carcinoma,EFO:0002618,Healthy control group,Pancreatic cancer patients,Newly diagnosed Pancreatic cancer patients between the ages of 20 -70 who have not begun treatments,20,20,NA,16S,NA,RT-qPCR,log transformation,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,13 October 2025,Deborah-Fabusuyi,"Deborah-Fabusuyi,Tosin",Differential abundance of gut microbiota between Pancreatic cancer patients and Healthy controls,increased,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,3384189|32066|203490|203491|203492|848|851,Complete,KateRasheed
bsdb:41039266/1/2,41039266,case-control,41039266,10.1186/s12866-025-04344-2,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04344-2,"Tavanaeian S., Feizabadi M.M., Falsafi S., Aghdaei H.A. , Houri H.",Oral and fecal microbiome alterations in pancreatic cancer: insights into potential diagnostic biomarkers,BMC microbiology,2025,"Fusobacterium nucleatum, Neisseria elongata, Fecal microbiome, Oral microbiome, Pancreatic cancer",Experiment 1,Iran,Homo sapiens,Feces,UBERON:0001988,Pancreatic carcinoma,EFO:0002618,Healthy control group,Pancreatic cancer patients,Newly diagnosed Pancreatic cancer patients between the ages of 20 -70 who have not begun treatments,20,20,NA,16S,NA,RT-qPCR,log transformation,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1,13 October 2025,Deborah-Fabusuyi,"Deborah-Fabusuyi,Tosin",Differential abundance of gut microbiota between Pancreatic cancer patients and Healthy controls,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis",1783272|201174|1760|85004|31953|1678|1681;1783272|1239|186801|3085636|186803|841|166486,Complete,KateRasheed
bsdb:41039266/2/1,41039266,case-control,41039266,10.1186/s12866-025-04344-2,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04344-2,"Tavanaeian S., Feizabadi M.M., Falsafi S., Aghdaei H.A. , Houri H.",Oral and fecal microbiome alterations in pancreatic cancer: insights into potential diagnostic biomarkers,BMC microbiology,2025,"Fusobacterium nucleatum, Neisseria elongata, Fecal microbiome, Oral microbiome, Pancreatic cancer",Experiment 2,Iran,Homo sapiens,Saliva,UBERON:0001836,Pancreatic carcinoma,EFO:0002618,Healthy control group,Pancreatic cancer patients,Newly diagnosed Pancreatic cancer patients between the ages of 20 -70 who have not begun treatments,20,20,NA,16S,NA,RT-qPCR,log transformation,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,13 October 2025,Deborah-Fabusuyi,"Deborah-Fabusuyi,Tosin",Differential abundance of oral microbiota between Pancreatic cancer patients and Healthy controls,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,1783272|1239|91061|186826|186828|117563|46124,Complete,KateRasheed
bsdb:41039266/2/2,41039266,case-control,41039266,10.1186/s12866-025-04344-2,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04344-2,"Tavanaeian S., Feizabadi M.M., Falsafi S., Aghdaei H.A. , Houri H.",Oral and fecal microbiome alterations in pancreatic cancer: insights into potential diagnostic biomarkers,BMC microbiology,2025,"Fusobacterium nucleatum, Neisseria elongata, Fecal microbiome, Oral microbiome, Pancreatic cancer",Experiment 2,Iran,Homo sapiens,Saliva,UBERON:0001836,Pancreatic carcinoma,EFO:0002618,Healthy control group,Pancreatic cancer patients,Newly diagnosed Pancreatic cancer patients between the ages of 20 -70 who have not begun treatments,20,20,NA,16S,NA,RT-qPCR,log transformation,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1,13 October 2025,Deborah-Fabusuyi,"Deborah-Fabusuyi,Tosin",Differential abundance of oral microbiota between Pancreatic cancer patients and Healthy controls,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,3379134|1224|28216|206351|481|482|495,Complete,KateRasheed
bsdb:41039272/1/1,41039272,laboratory experiment,41039272,https://doi.org/10.1186/s12866-025-04368-8,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04368-8,"Cao Z., Wang D., Cui Y., Huang F., Liu Y., Dai J., Wu W., Dai Z., Xie J., Zhu X., Hu X. , Xu Y.","Diet, nutrient characteristics and gut microbiome between summer and winter drive adaptive strategies of East China sika deer (Cervus nippon kopschi) in the Yangtze River basin",BMC microbiology,2025,"Cervus nippon kopschi, Adaptation, Diet, Gut microbiota, Nutrition",Experiment 1,China,Cervus nippon kopschi,Feces,UBERON:0001988,Seasonal gut microbiome measurement,EFO:0007753,Summer group (SLu),Winter group (WLu),"Samples collected from Sika deer during the winter period from December 8th to 10th, 2020 (winter)",30,30,NA,16S,567,NA,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,increased,increased,increased,increased,NA,increased,Signature 1,"Figure 5A,B",28 October 2025,Fiddyhamma,Fiddyhamma,LEfSe analysis to identify significant differences in gut microbiota composition between summer and winter groups,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",1783272|1239|91061|1385;1783272|1239;3379134|976|200643|171549|815;3379134|976|200643|171549;3379134|976|200643;3379134|976;1783272|1239|186801;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|216572|1263;3379134|976|200643|171549|171552|577309,Complete,KateRasheed
bsdb:41039272/1/2,41039272,laboratory experiment,41039272,https://doi.org/10.1186/s12866-025-04368-8,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04368-8,"Cao Z., Wang D., Cui Y., Huang F., Liu Y., Dai J., Wu W., Dai Z., Xie J., Zhu X., Hu X. , Xu Y.","Diet, nutrient characteristics and gut microbiome between summer and winter drive adaptive strategies of East China sika deer (Cervus nippon kopschi) in the Yangtze River basin",BMC microbiology,2025,"Cervus nippon kopschi, Adaptation, Diet, Gut microbiota, Nutrition",Experiment 1,China,Cervus nippon kopschi,Feces,UBERON:0001988,Seasonal gut microbiome measurement,EFO:0007753,Summer group (SLu),Winter group (WLu),"Samples collected from Sika deer during the winter period from December 8th to 10th, 2020 (winter)",30,30,NA,16S,567,NA,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,increased,increased,increased,increased,NA,increased,Signature 2,"Figure 5A,B",28 October 2025,Fiddyhamma,Fiddyhamma,LEfSe analysis to identify significant differences in gut microbiota composition between summer and winter groups,decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas",1783272|201174;3379134|1224|28211|356|82115|357;3379134|1224|28211;1783272|1239|91061;3379134|1224|28216;3379134|1224|28211|204458|76892|41275;3379134|1224|28216|80840;3379134|1224|28211|204458|76892;3379134|1224|28211|204458;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;3379134|1224|1236;3379134|1224|28211|356;1783272|1239|91061|186826;3379134|1224|28211|204457|41297|165696;3379134|1224|28216|80840|75682;3379134|1224;3379134|1224|28211|356|82115;3379134|1224|28211|204457|41297;3379134|1224|28211|204457;3379134|1224|28211|204457|41297|13687,Complete,KateRasheed
bsdb:41048034/1/1,41048034,"cross-sectional observational, not case-control",41048034,https://doi.org/10.1111/1755-0998.70054,https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.70054,"Wright S.L., Abdul-Aziz M., Blaha G.N., Ta C.K., Gancz A., Ademola-Popoola I.J., Szécsényi-Nagy A., Sereno P.C. , Weyrich L.S.",Wet Lab Protocols Matter: Choice of DNA Extraction and Library Preparation Protocols Bias Ancient Oral Microbiome Recovery,Molecular ecology resources,2025,"ancient DNA, dental calculus, laboratory methods, metagenomics, oral microbiome",Experiment 1,Niger,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Library preparation,OBI:0000711,Double Stranded Library method (DSL),Single Stranded Library method (SSL),This is a library preparation method following a modified protocol originally described by Till Gansauge & Matthias Meyer (2013).”,NA,NA,NA,WMS,NA,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 5 and Supplementary Table 8,25 November 2025,Fiddyhamma,Fiddyhamma,"MaAsLin2 (Multivariate Association with Linear Models 2)  results for the Nigerien unfiltered (i.e., pre-decontamination filtered) datasets",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces dentalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 414,k__Bacillati|p__Chloroflexota|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae|s__Anaerolineaceae bacterium oral taxon 439,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfomicrobiaceae|g__Desulfomicrobium|s__Desulfomicrobium orale,k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter millerae,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter oralis,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter sp. YE315,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella sp. oral taxon 807,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|s__Peptostreptococcaceae bacterium oral taxon 113,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Priestia|s__Priestia aryabhattai,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia cardiffensis",1783272|201174|1760|2037|2049|1654|272548;1783272|201174|1760|2037|2049|1654|712122;1783272|200795|292625|292629|292628|1889813;3379134|200940|3031449|213115|213116|898|132132;3384194|508458|649775|649776|3029087|1434006|651822;3366610|28890|183925|2158|2159|2172|230361;3366610|28890|183925|2158|2159|2172|66851;3366610|28890|183925|2158|2159|2172|2173;3366610|28890|183925|2158|2159|2172|1609968;1783272|201174|84998|84999|1643824|133925|712411;1783272|1239|1737404|1737405|1570339|543311|33033;1783272|1239|186801|3082720|186804|1321783;1783272|1239|91061|1385|186817|2800373|412384;1783272|201174|1760|2037|2049|2529408|181487,Complete,KateRasheed
bsdb:41048034/1/2,41048034,"cross-sectional observational, not case-control",41048034,https://doi.org/10.1111/1755-0998.70054,https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.70054,"Wright S.L., Abdul-Aziz M., Blaha G.N., Ta C.K., Gancz A., Ademola-Popoola I.J., Szécsényi-Nagy A., Sereno P.C. , Weyrich L.S.",Wet Lab Protocols Matter: Choice of DNA Extraction and Library Preparation Protocols Bias Ancient Oral Microbiome Recovery,Molecular ecology resources,2025,"ancient DNA, dental calculus, laboratory methods, metagenomics, oral microbiome",Experiment 1,Niger,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Library preparation,OBI:0000711,Double Stranded Library method (DSL),Single Stranded Library method (SSL),This is a library preparation method following a modified protocol originally described by Till Gansauge & Matthias Meyer (2013).”,NA,NA,NA,WMS,NA,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Supplementary Table 8,25 November 2025,Fiddyhamma,Fiddyhamma,"MaAsLin2 (Multivariate Association with Linear Models 2) results for the Nigerien unfiltered (i.e., pre-decontamination filtered) datasets",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter venetianus,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas aquatica,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas testosteroni,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas putida,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia",3379134|1224|1236|2887326|468|469|52133;3379134|1224|28216|80840|80864|283|225991;3379134|1224|28216|80840|80864|283|285;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|91061|186826|81852|1350|1352;3379134|1224|1236|72274|135621|286|287;3379134|1224|1236|72274|135621|286|303;3379134|1224|1236|135614|32033|40323|40324,Complete,KateRasheed
bsdb:41048034/2/1,41048034,"cross-sectional observational, not case-control",41048034,https://doi.org/10.1111/1755-0998.70054,https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.70054,"Wright S.L., Abdul-Aziz M., Blaha G.N., Ta C.K., Gancz A., Ademola-Popoola I.J., Szécsényi-Nagy A., Sereno P.C. , Weyrich L.S.",Wet Lab Protocols Matter: Choice of DNA Extraction and Library Preparation Protocols Bias Ancient Oral Microbiome Recovery,Molecular ecology resources,2025,"ancient DNA, dental calculus, laboratory methods, metagenomics, oral microbiome",Experiment 2,Niger,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Extraction protocol,EFO:0000490,Dabney et al. (2013) method (via the PB buffer) DNA extraction type,Rohland & Hofreiter (2007) silica-based method (via the Qiagen QG buffer) DNA extraction type,This is a silica-based DNA extraction protocol adapted from Rohland & Hofreiter (2007) (via the Qiagen QG buffer),NA,NA,NA,WMS,NA,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Supplementary Table 14,25 November 2025,Fiddyhamma,Fiddyhamma,"MaAsLin2 (Multivariate Association with Linear Models 2)  results for the Nigerien filtered (i.e., post-decontamination filtered) datasets",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Anaplasmataceae|g__Anaplasma|s__Anaplasma phagocytophilum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Rugositalea|s__Rugositalea oryzae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Xenophilus|s__Xenophilus azovorans",3379134|1224|28211|766|942|768|948;3379134|1224|28211|356|41294|3466653|674703;3379134|1224|28216|80840|80864|151754|151755,Complete,KateRasheed
bsdb:41048034/3/1,41048034,"cross-sectional observational, not case-control",41048034,https://doi.org/10.1111/1755-0998.70054,https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.70054,"Wright S.L., Abdul-Aziz M., Blaha G.N., Ta C.K., Gancz A., Ademola-Popoola I.J., Szécsényi-Nagy A., Sereno P.C. , Weyrich L.S.",Wet Lab Protocols Matter: Choice of DNA Extraction and Library Preparation Protocols Bias Ancient Oral Microbiome Recovery,Molecular ecology resources,2025,"ancient DNA, dental calculus, laboratory methods, metagenomics, oral microbiome",Experiment 3,Niger,Homo sapiens,Supragingival dental plaque,UBERON:0016485,Library preparation,OBI:0000711,Double Stranded Library method (DSL),Single Stranded Library method (SSL),This is a library preparation method following a modified protocol originally described by Till Gansauge & Matthias Meyer (2013).,NA,NA,NA,WMS,NA,Illumina,log transformation,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Supplementary Table 14,25 November 2025,Tosin,Tosin,"MaAsLin2 (Multivariate Association with Linear Models 2) results for the Nigerien filtered (i.e., post-decontamination filtered) datasets",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax|s__Acidovorax sp. KKS102,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales|f__Anaplasmataceae|g__Anaplasma|s__Anaplasma phagocytophilum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|s__Comamonadaceae bacterium URHA0028,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Curvibacter|s__Curvibacter sp. PAE-UM,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Methylibium|s__Methylibium petroleiphilum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides|s__Nocardioides sp. CF8,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides|s__Nocardioides sp. Leaf307,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Polaromonas|s__Polaromonas glacialis,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Rhodopseudomonas|s__Rhodopseudomonas palustris,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Rugositalea|s__Rugositalea oryzae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Xenophilus|s__Xenophilus azovorans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ramlibacter|s__Ramlibacter tataouinensis,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|s__Chitinophagaceae bacterium IBVUCB2,k__Pseudomonadati|p__Nitrospirota|c__Nitrospiria|o__Nitrospirales|f__Nitrospiraceae|g__Nitrospira|s__Nitrospira cf. moscoviensis SBR1015,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Polaromonas|s__Polaromonas naphthalenivorans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax|s__Variovorax paradoxus,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium xinjiangense,k__Bacillati|p__Actinomycetota|c__Thermoleophilia|o__Solirubrobacterales|f__Conexibacteraceae|g__Conexibacter|s__Conexibacter woesei,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium|s__Bradyrhizobium erythrophlei,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas syringae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Reyranellaceae|g__Reyranella|s__Reyranella massiliensis",3379134|1224|28216|80840|80864|12916|358220;3379134|1224|28211|766|942|768|948;3379134|1224|28216|80840|80864|1298913;3379134|1224|28216|80840|80864|281915|1714344;3379134|1224|28216|80840|2975441|316612|105560;1783272|201174|1760|85009|85015|1839|110319;1783272|201174|1760|85009|85015|1839|1736331;3379134|1224|28216|80840|80864|52972|866564;3379134|1224|28211|356|41294|1073|1076;3379134|1224|28211|356|41294|3466653|674703;3379134|1224|28216|80840|80864|151754|151755;1783272|1239|91061|186826|1300|1301|1313;3379134|1224|28216|80840|80864|174951|94132;3379134|976|1853228|1853229|563835|1985174;3379134|40117|203693|189778|189779|1234|96242;3379134|1224|28216|80840|80864|52972|216465;3379134|1224|28216|80840|80864|34072|34073;3379134|976|117743|200644|49546|237|178356;1783272|201174|1497346|588673|320583|191494|191495;3379134|1224|28211|356|41294|374|1437360;3379134|1224|1236|72274|135621|286|317;3379134|1224|28211|356|2844375|445219|445220,Complete,KateRasheed
bsdb:41052039/1/1,41052039,"cross-sectional observational, not case-control",41052039,https://doi.org/10.1371/journal.pone.0332108,NA,"Seetaraso T., Gruneck L., Jinatham V., Kantakat S., Albert M.L., Therdtatha P., Inta A., Srikummool M., Kampuansai J. , Popluechai S.",Effects of ethnicity and geography on the fecal microbiota and dietary habits of Tibeto-Burman hill tribes in Northern Thailand,PloS one,2025,NA,Experiment 1,Thailand,Homo sapiens,Feces,UBERON:0001988,"Population,Ethnic group","IDOMAL:0001254,EFO:0001799", Lahu ethnic group residing in Chiang Mai province (LahuCM),Akha ethnic group residing in Chiang Mai Province (AkhaCM),Participants from Akha ethnic group residing in Chiang Mai Province (AkhaCM),19,22,3 months,16S,NA,RT-qPCR,log transformation,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,S2 Table and Figure 1,20 October 2025,Firdaws,Firdaws,The relative abundance of gut microbiota between Akha ethnic group residing in Chiang Mai Province (AkhaCM) and Lahu ethnic group residing in Chiang Mai Province (LahuCM),increased,k__Bacillati|p__Actinomycetota,1783272|201174,Complete,NA
bsdb:41052039/2/1,41052039,"cross-sectional observational, not case-control",41052039,https://doi.org/10.1371/journal.pone.0332108,NA,"Seetaraso T., Gruneck L., Jinatham V., Kantakat S., Albert M.L., Therdtatha P., Inta A., Srikummool M., Kampuansai J. , Popluechai S.",Effects of ethnicity and geography on the fecal microbiota and dietary habits of Tibeto-Burman hill tribes in Northern Thailand,PloS one,2025,NA,Experiment 2,Thailand,Homo sapiens,Feces,UBERON:0001988,"Population,Ethnic group","IDOMAL:0001254,EFO:0001799", Akha ethnic group residing in Chiang Mai Province (AkhaCM),Akha ethnic group residing in Chiang Rai Province (AkhaCR),Participants from Akha ethnic group residing in Chiang Rai Province (AkhaCR),22,23,3 months,16S,NA,RT-qPCR,log transformation,"T-Test,Mann-Whitney (Wilcoxon),Welch's T-Test",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,S8 Table and Figure 1,20 October 2025,Firdaws,Firdaws,The relative abundance of gut microbiota between Akha ethnic group residing in Chiang Rai Province (AkhaCR) and Akha ethnic group residing in Chiang Mai Province (AkhaCM),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella minuta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta",1783272|201174|1760|2037|2049|1654;1783272|1239;3379134|976|200643|171549|815|816;3379134|976;1783272|1239|186801|3082768|990719|990721|626937;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|216851|853;3366610|28890|183925;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|572511|33035,Complete,NA
bsdb:41052039/4/1,41052039,"cross-sectional observational, not case-control",41052039,https://doi.org/10.1371/journal.pone.0332108,NA,"Seetaraso T., Gruneck L., Jinatham V., Kantakat S., Albert M.L., Therdtatha P., Inta A., Srikummool M., Kampuansai J. , Popluechai S.",Effects of ethnicity and geography on the fecal microbiota and dietary habits of Tibeto-Burman hill tribes in Northern Thailand,PloS one,2025,NA,Experiment 4,Thailand,Homo sapiens,Feces,UBERON:0001988,"Population,Ethnic group","IDOMAL:0001254,EFO:0001799", Lahu ethnic group residing in Chiang Mai province (LahuCM),Akha ethnic group residing in Chiang Mai Province (AkhaCM),Participants from Akha ethnic group residing in Chiang Mai Province (AkhaCM),19,22,3 months,16S,NA,RT-qPCR,log transformation,PLS-DA (Partial least square discriminant analysis),0.001,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,S1 Figure A,20 October 2025,Firdaws,Firdaws,The relative abundance of gut microbiota between Akha ethnic group residing in Chiang Mai Province (AkhaCM) and Lahu ethnic group residing in Chiang Mai Province (LahuCM),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella minuta,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta",1783272|201174|1760|2037|2049|1654;1783272|201174;3379134|74201|203494|48461|1647988|239934|239935;1783272|1239;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|817;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3082768|990719|990721|626937;1783272|1239|186801|186802|216572|216851|853;3379134|1224|1236;1783272|1239|91061|186826|33958|1578;3366610|28890|183925;1783272|1239|91061|1385|90964|1279;3366610|28890|183925|2158|2159|2172|2173;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|572511|33035,Complete,NA
bsdb:41052039/4/2,41052039,"cross-sectional observational, not case-control",41052039,https://doi.org/10.1371/journal.pone.0332108,NA,"Seetaraso T., Gruneck L., Jinatham V., Kantakat S., Albert M.L., Therdtatha P., Inta A., Srikummool M., Kampuansai J. , Popluechai S.",Effects of ethnicity and geography on the fecal microbiota and dietary habits of Tibeto-Burman hill tribes in Northern Thailand,PloS one,2025,NA,Experiment 4,Thailand,Homo sapiens,Feces,UBERON:0001988,"Population,Ethnic group","IDOMAL:0001254,EFO:0001799", Lahu ethnic group residing in Chiang Mai province (LahuCM),Akha ethnic group residing in Chiang Mai Province (AkhaCM),Participants from Akha ethnic group residing in Chiang Mai Province (AkhaCM),19,22,3 months,16S,NA,RT-qPCR,log transformation,PLS-DA (Partial least square discriminant analysis),0.001,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,S1 Figure A,20 October 2025,Firdaws,Firdaws,The relative abundance of gut microbiota between Akha ethnic group residing in Chiang Mai Province (AkhaCM) and Lahu ethnic group residing in Chiang Mai Province (LahuCM),decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Bacteroidota",3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|841;1783272|1239|91061|186826|81852|1350;1783272|1239|91061|1385|90964|1279;1783272|1239|186801|3085636|186803|33042;3379134|976|200643|171549|171552|838;3379134|976,Complete,NA
bsdb:41052039/5/1,41052039,"cross-sectional observational, not case-control",41052039,https://doi.org/10.1371/journal.pone.0332108,NA,"Seetaraso T., Gruneck L., Jinatham V., Kantakat S., Albert M.L., Therdtatha P., Inta A., Srikummool M., Kampuansai J. , Popluechai S.",Effects of ethnicity and geography on the fecal microbiota and dietary habits of Tibeto-Burman hill tribes in Northern Thailand,PloS one,2025,NA,Experiment 5,Thailand,Homo sapiens,Feces,UBERON:0001988,"Population,Diet","IDOMAL:0001254,EFO:0002755",Lahu and Lisu ethnic group residing in Chiang Rai Province (LahuCR and LisuCR) (Processed foods),Akha ethnic group residing in Chiang Rai province (AkhaCR) (Processed foods),Participants from Akha ethnic group residing in Chiang Rai Province (AkhaCR) that consumed processed foods.,38,23,3 months,16S,NA,RT-qPCR,log transformation,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,S7 Table,20 October 2025,Firdaws,Firdaws,"Relationship between the relative abundance of gut microbiota (phylum, genus and species) and dietary habits (processed food) in Chiang Rai Province. Akha ethnic group residing in Chiang Rai Province (AkhaCR) and the Lahu and Lisu ethnic group residing in Chiang Rai Province (LahuCR and LisuCR)",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii",1783272|1239|186801|3085636|186803|841;3366610|28890|183925|2158|2159|2172|2173,Complete,NA
bsdb:41052039/5/2,41052039,"cross-sectional observational, not case-control",41052039,https://doi.org/10.1371/journal.pone.0332108,NA,"Seetaraso T., Gruneck L., Jinatham V., Kantakat S., Albert M.L., Therdtatha P., Inta A., Srikummool M., Kampuansai J. , Popluechai S.",Effects of ethnicity and geography on the fecal microbiota and dietary habits of Tibeto-Burman hill tribes in Northern Thailand,PloS one,2025,NA,Experiment 5,Thailand,Homo sapiens,Feces,UBERON:0001988,"Population,Diet","IDOMAL:0001254,EFO:0002755",Lahu and Lisu ethnic group residing in Chiang Rai Province (LahuCR and LisuCR) (Processed foods),Akha ethnic group residing in Chiang Rai province (AkhaCR) (Processed foods),Participants from Akha ethnic group residing in Chiang Rai Province (AkhaCR) that consumed processed foods.,38,23,3 months,16S,NA,RT-qPCR,log transformation,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,S7 Table,20 October 2025,Firdaws,Firdaws,"Relationship between the relative abundance of gut microbiota (phylum, genus and species) and dietary habits (processed food) in Chiang Rai Province. Akha ethnic group residing in Chiang Rai Province (AkhaCR) and the Lahu and Lisu ethnic group residing in Chiang Rai Province (LahuCR and LisuCR)",decreased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila",1783272|1239;1783272|201174;3379134|1224|1236;3379134|976|200643|171549|171552|838;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|815|816|817;3379134|976;3379134|976|200643|171549|815|816;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|81852|1350;1783272|201174|1760|2037|2049|1654;3379134|74201|203494|48461|1647988|239934|239935,Complete,NA
bsdb:41052039/6/1,41052039,"cross-sectional observational, not case-control",41052039,https://doi.org/10.1371/journal.pone.0332108,NA,"Seetaraso T., Gruneck L., Jinatham V., Kantakat S., Albert M.L., Therdtatha P., Inta A., Srikummool M., Kampuansai J. , Popluechai S.",Effects of ethnicity and geography on the fecal microbiota and dietary habits of Tibeto-Burman hill tribes in Northern Thailand,PloS one,2025,NA,Experiment 6,Thailand,Homo sapiens,Feces,UBERON:0001988,"Population,Diet","IDOMAL:0001254,EFO:0002755",Lahu and Lisu ethnic group residing in Chiang Rai Province (LahuCR and LisuCR) (Non-processed foods),Akha ethnic group residing in Chiang Rai province (AkhaCR) (Non-processed foods),Participants from Akha ethnic group residing in Chiang Rai Province (AkhaCR) that consumed non-processed foods.,38,23,3 months,16S,NA,RT-qPCR,log transformation,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,S7 Table,20 October 2025,Firdaws,Firdaws,"Relationship between the relative abundance of gut microbiota (phylum, genus and species) and dietary habits (non-processed foods) in Chiang Rai Province. Akha ethnic group residing in Chiang Rai Province (AkhaCR) and the Lahu and Lisu ethnic group residing in Chiang Rai Province (LahuCR and LisuCR)",increased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",1783272|201174;1783272|1239|186801|3085636|186803|572511|33035;3366610|28890|183925;3366610|28890|183925|2158|2159|2172|2173;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|841;1783272|1239|91061|1385|90964|1279;1783272|1239;3379134|976;3379134|1224|1236;3379134|976|200643|171549|815|816;1783272|201174|1760|2037|2049|1654;1783272|1239|186801|186802|216572|216851|853,Complete,NA
bsdb:41052039/6/2,41052039,"cross-sectional observational, not case-control",41052039,https://doi.org/10.1371/journal.pone.0332108,NA,"Seetaraso T., Gruneck L., Jinatham V., Kantakat S., Albert M.L., Therdtatha P., Inta A., Srikummool M., Kampuansai J. , Popluechai S.",Effects of ethnicity and geography on the fecal microbiota and dietary habits of Tibeto-Burman hill tribes in Northern Thailand,PloS one,2025,NA,Experiment 6,Thailand,Homo sapiens,Feces,UBERON:0001988,"Population,Diet","IDOMAL:0001254,EFO:0002755",Lahu and Lisu ethnic group residing in Chiang Rai Province (LahuCR and LisuCR) (Non-processed foods),Akha ethnic group residing in Chiang Rai province (AkhaCR) (Non-processed foods),Participants from Akha ethnic group residing in Chiang Rai Province (AkhaCR) that consumed non-processed foods.,38,23,3 months,16S,NA,RT-qPCR,log transformation,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,S7 Table,20 October 2025,Firdaws,Firdaws,"Relationship between the relative abundance of gut microbiota (phylum, genus and species) and dietary habits (non-processed foods) in Chiang Rai Province. Akha ethnic group residing in Chiang Rai Province (AkhaCR) and the Lahu and Lisu ethnic group residing in Chiang Rai Province (LahuCR and LisuCR)",decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella minuta,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|815|816|817;1783272|1239|186801|3082768|990719|990721|626937;1783272|1239|91061|186826|81852|1350;3384189|32066|203490|203491|203492|848;1783272|201174|1760|2037|2049|1654;1783272|1239;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|216572|216851|853;3379134|1224|1236;3379134|976;1783272|1239|91061|1385|90964|1279,Complete,NA
bsdb:41052039/7/1,41052039,"cross-sectional observational, not case-control",41052039,https://doi.org/10.1371/journal.pone.0332108,NA,"Seetaraso T., Gruneck L., Jinatham V., Kantakat S., Albert M.L., Therdtatha P., Inta A., Srikummool M., Kampuansai J. , Popluechai S.",Effects of ethnicity and geography on the fecal microbiota and dietary habits of Tibeto-Burman hill tribes in Northern Thailand,PloS one,2025,NA,Experiment 7,Thailand,Homo sapiens,Feces,UBERON:0001988,"Population,Ethnic group","IDOMAL:0001254,EFO:0001799",Akha ethnic group residing in Chiang Mai Province (AkhaCM) ,Lahu ethnic group residing in Chiang Mai province (LahuCM),Participants from Lahua ethnic group residing in Chiang Mai Province (LahuCM),22,19,3 months,16S,NA,RT-qPCR,log transformation,PLS-DA (Partial least square discriminant analysis),0.001,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,S1 Figure B,20 October 2025,Firdaws,Firdaws,The relative abundance of gut microbiota between Lahu ethnic group residing in Chiang Mai Province (LahuCM) and Akha ethnic group residing in Chiang Mai Province (AkhaCM),increased,"k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella minuta,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila",3379134|976;1783272|1239|186801|3085636|186803|572511|33035;1783272|1239|186801|3085636|186803|33042;1783272|1239|91061|186826|81852|1350;3366610|28890|183925|2158|2159|2172|2173;3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|216851|853;3379134|976|200643|171549|815|816;1783272|1239|186801|3082768|990719|990721|626937;1783272|201174|1760|2037|2049|1654;3379134|1224|1236;3366610|28890|183925;1783272|1239|91061|186826|33958|1578;1783272|201174|1760|85004|31953|1678;1783272|1239;3384189|32066|203490|203491|203492|848;3379134|74201|203494|48461|1647988|239934|239935,Complete,NA
bsdb:41052039/7/2,41052039,"cross-sectional observational, not case-control",41052039,https://doi.org/10.1371/journal.pone.0332108,NA,"Seetaraso T., Gruneck L., Jinatham V., Kantakat S., Albert M.L., Therdtatha P., Inta A., Srikummool M., Kampuansai J. , Popluechai S.",Effects of ethnicity and geography on the fecal microbiota and dietary habits of Tibeto-Burman hill tribes in Northern Thailand,PloS one,2025,NA,Experiment 7,Thailand,Homo sapiens,Feces,UBERON:0001988,"Population,Ethnic group","IDOMAL:0001254,EFO:0001799",Akha ethnic group residing in Chiang Mai Province (AkhaCM) ,Lahu ethnic group residing in Chiang Mai province (LahuCM),Participants from Lahua ethnic group residing in Chiang Mai Province (LahuCM),22,19,3 months,16S,NA,RT-qPCR,log transformation,PLS-DA (Partial least square discriminant analysis),0.001,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,S1 Figure B,23 October 2025,Firdaws,Firdaws,The relative abundance of gut microbiota between Lahu ethnic group residing in Chiang Mai Province (LahuCM) and Akha ethnic group residing in Chiang Mai Province (AkhaCM),decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",1783272|201174;3379134|976|200643|171549|815|816|817;1783272|1239|91061|1385|90964|1279,Complete,NA
bsdb:41052039/8/1,41052039,"cross-sectional observational, not case-control",41052039,https://doi.org/10.1371/journal.pone.0332108,NA,"Seetaraso T., Gruneck L., Jinatham V., Kantakat S., Albert M.L., Therdtatha P., Inta A., Srikummool M., Kampuansai J. , Popluechai S.",Effects of ethnicity and geography on the fecal microbiota and dietary habits of Tibeto-Burman hill tribes in Northern Thailand,PloS one,2025,NA,Experiment 8,Thailand,Homo sapiens,Feces,UBERON:0001988,"Population,Ethnic group","IDOMAL:0001254,EFO:0001799",Lisu ethnic group residing in Chiang Rai Province (LisuCR),Akha ethnic group residing in Chiang Rai Province (AkhaCR) ,Participants from Akha ethnic group residing in Chiang Rai Province (AkhaCR),22,23,3 months,16S,NA,RT-qPCR,log transformation,"ANOVA,Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,S3 Table,20 October 2025,Firdaws,Firdaws,The relative abundance of gut microbiota between Akha ethnic group residing in Chiang Rai Province (AkhaCR) and Lisu ethnic group residing in Chiang Rai Province (LisuCR),increased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella minuta",1783272|1239;3379134|1224|1236;1783272|1239|186801|186802|216572|1263;1783272|201174|1760|2037|2049|1654;1783272|1239|186801|3082768|990719|990721|626937,Complete,NA
bsdb:41052039/9/1,41052039,"cross-sectional observational, not case-control",41052039,https://doi.org/10.1371/journal.pone.0332108,NA,"Seetaraso T., Gruneck L., Jinatham V., Kantakat S., Albert M.L., Therdtatha P., Inta A., Srikummool M., Kampuansai J. , Popluechai S.",Effects of ethnicity and geography on the fecal microbiota and dietary habits of Tibeto-Burman hill tribes in Northern Thailand,PloS one,2025,NA,Experiment 9,Thailand,Homo sapiens,Feces,UBERON:0001988,"Population,Ethnic group","IDOMAL:0001254,EFO:0001799",Lisu ethnic group residing in Chiang Rai Province (LisuCR),Lahu ethnic group residing in Chiang Rai Province (LahuCR) ,Participants from Lahu ethnic group residing in Chiang Rai Province (LahuCR),22,16,3 months,16S,NA,RT-qPCR,log transformation,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,S3 Table,20 October 2025,Firdaws,Firdaws,The relative abundance of gut microbiota between Lahu ethnic group residing in Chiang Rai Province (LahuCR) and Lisu ethnic group residing in Chiang Rai Province (LisuCR),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|201174|1760|2037|2049|1654;1783272|1239|91061|186826|33958|1578,Complete,NA
bsdb:41052039/10/1,41052039,"cross-sectional observational, not case-control",41052039,https://doi.org/10.1371/journal.pone.0332108,NA,"Seetaraso T., Gruneck L., Jinatham V., Kantakat S., Albert M.L., Therdtatha P., Inta A., Srikummool M., Kampuansai J. , Popluechai S.",Effects of ethnicity and geography on the fecal microbiota and dietary habits of Tibeto-Burman hill tribes in Northern Thailand,PloS one,2025,NA,Experiment 10,Thailand,Homo sapiens,Feces,UBERON:0001988,"Population,Ethnic group","IDOMAL:0001254,EFO:0001799", Akha ethnic group residing in Chiang Mai Province (AkhaCM),Akha ethnic group residing in Chiang Rai Province (AkhaCR),Participants from Akha ethnic group residing in Chiang Rai Province (AkhaCR),22,23,3 months,16S,NA,RT-qPCR,log transformation,PLS-DA (Partial least square discriminant analysis),0.001,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A,21 October 2025,Firdaws,Firdaws,The relative abundance of gut microbiota between Akha ethnic group residing in Chiang Rai Province (AkhaCR) and Akha ethnic group residing in Chiang Mai Province (AkhaCM),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella minuta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota",1783272|201174|1760|2037|2049|1654;3379134|74201|203494|48461|1647988|239934|239935;1783272|1239;3379134|976|200643|171549|815|816;3379134|976;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511|33035;1783272|1239|186801|3082768|990719|990721|626937;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|216851|853;3384189|32066|203490|203491|203492|848;3379134|1224|1236;1783272|1239|91061|186826|33958|1578;3366610|28890|183925;3366610|28890|183925|2158|2159|2172|2173;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300|1301;1783272|201174,Complete,NA
bsdb:41052039/10/2,41052039,"cross-sectional observational, not case-control",41052039,https://doi.org/10.1371/journal.pone.0332108,NA,"Seetaraso T., Gruneck L., Jinatham V., Kantakat S., Albert M.L., Therdtatha P., Inta A., Srikummool M., Kampuansai J. , Popluechai S.",Effects of ethnicity and geography on the fecal microbiota and dietary habits of Tibeto-Burman hill tribes in Northern Thailand,PloS one,2025,NA,Experiment 10,Thailand,Homo sapiens,Feces,UBERON:0001988,"Population,Ethnic group","IDOMAL:0001254,EFO:0001799", Akha ethnic group residing in Chiang Mai Province (AkhaCM),Akha ethnic group residing in Chiang Rai Province (AkhaCR),Participants from Akha ethnic group residing in Chiang Rai Province (AkhaCR),22,23,3 months,16S,NA,RT-qPCR,log transformation,PLS-DA (Partial least square discriminant analysis),0.001,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3A,24 October 2025,Firdaws,Firdaws,The relative abundance of gut microbiota between Akha ethnic group residing in Chiang Rai Province (AkhaCR) and Akha ethnic group residing in Chiang Mai Province (AkhaCM),decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis",1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|81852|1350;3379134|976|200643|171549|815|816|817,Complete,NA
bsdb:41052039/11/1,41052039,"cross-sectional observational, not case-control",41052039,https://doi.org/10.1371/journal.pone.0332108,NA,"Seetaraso T., Gruneck L., Jinatham V., Kantakat S., Albert M.L., Therdtatha P., Inta A., Srikummool M., Kampuansai J. , Popluechai S.",Effects of ethnicity and geography on the fecal microbiota and dietary habits of Tibeto-Burman hill tribes in Northern Thailand,PloS one,2025,NA,Experiment 11,Thailand,Homo sapiens,Feces,UBERON:0001988,"Population,Ethnic group","IDOMAL:0001254,EFO:0001799", Lahu ethnic group residing in Chiang Mai Province (LahuCM),Lahu ethnic group residing in Chiang Rai Province (LahuCR),Participants from Lahu ethnic group residing in Chiang Rai Province (LahuCR),19,16,3 months,16S,NA,RT-qPCR,log transformation,PLS-DA (Partial least square discriminant analysis),0.001,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3B,21 October 2025,Firdaws,Firdaws,The relative abundance of gut microbiota between Lahu ethnic group residing in Chiang Rai Province (LahuCR) and Lahu ethnic group residing in Chiang Mai Province (LahuCM),increased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella minuta,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria",1783272|1239;3379134|976;3379134|976|200643|171549|815|816;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549|815|816|817;1783272|201174;3379134|976|200643|171549|171552|838;1783272|201174|1760|2037|2049|1654;1783272|201174|1760|85004|31953|1678;3366610|28890|183925;1783272|1239|186801|3085636|186803|572511|33035;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3082768|990719|990721|626937;3379134|74201|203494|48461|1647988|239934|239935;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803|33042;3366610|28890|183925|2158|2159|2172|2173;3379134|1224|1236,Complete,NA
bsdb:41052039/11/2,41052039,"cross-sectional observational, not case-control",41052039,https://doi.org/10.1371/journal.pone.0332108,NA,"Seetaraso T., Gruneck L., Jinatham V., Kantakat S., Albert M.L., Therdtatha P., Inta A., Srikummool M., Kampuansai J. , Popluechai S.",Effects of ethnicity and geography on the fecal microbiota and dietary habits of Tibeto-Burman hill tribes in Northern Thailand,PloS one,2025,NA,Experiment 11,Thailand,Homo sapiens,Feces,UBERON:0001988,"Population,Ethnic group","IDOMAL:0001254,EFO:0001799", Lahu ethnic group residing in Chiang Mai Province (LahuCM),Lahu ethnic group residing in Chiang Rai Province (LahuCR),Participants from Lahu ethnic group residing in Chiang Rai Province (LahuCR),19,16,3 months,16S,NA,RT-qPCR,log transformation,PLS-DA (Partial least square discriminant analysis),0.001,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3B,24 October 2025,Firdaws,Firdaws,The relative abundance of gut microbiota between Lahu ethnic group residing in Chiang Rai Province (LahuCR) and Lahu ethnic group residing in Chiang Mai Province (LahuCM),decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|81852|1350;3384189|32066|203490|203491|203492|848;1783272|1239|91061|186826|1300|1301,Complete,NA
bsdb:41052039/12/1,41052039,"cross-sectional observational, not case-control",41052039,https://doi.org/10.1371/journal.pone.0332108,NA,"Seetaraso T., Gruneck L., Jinatham V., Kantakat S., Albert M.L., Therdtatha P., Inta A., Srikummool M., Kampuansai J. , Popluechai S.",Effects of ethnicity and geography on the fecal microbiota and dietary habits of Tibeto-Burman hill tribes in Northern Thailand,PloS one,2025,NA,Experiment 12,Thailand,Homo sapiens,Feces,UBERON:0001988,"Population,Ethnic group","IDOMAL:0001254,EFO:0001799", Akha ethnic group and Lisu ethnic group residing in Chiang Rai Province (AkhaCR & LisuCR),Lahu ethnic group residing in Chiang Rai Province (LahuCR),Participants from Lahu ethnic group residing in Chiang Rai Province (LahuCR),45,16,3 months,16S,NA,RT-qPCR,log transformation,PLS-DA (Partial least square discriminant analysis),0.001,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,S1 Figure C,21 October 2025,Firdaws,Firdaws,The relative abundance of gut microbiota between (Akha and Lisu ethnic group residing in Chiang Rai Province (AkhaCR and LisuCR)) and Lahu ethnic group residing in Chiang Rai Province (LahuCR),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella minuta,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|1760|2037|2049|1654;1783272|201174;3379134|74201|203494|48461|1647988|239934|239935;1783272|1239;3379134|976|200643|171549|815|816;3379134|976|200643|171549|815|816|817;3379134|976;1783272|1239|186801|3085636|186803|572511|33035;1783272|1239|186801|3082768|990719|990721|626937;1783272|1239|186801|3085636|186803|33042;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|216572|216851|853;3384189|32066|203490|203491|203492|848;3379134|1224|1236;1783272|1239|91061|186826|33958|1578;3366610|28890|183925;3379134|976|200643|171549|171552|838;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|186826|1300|1301,Complete,NA
bsdb:41052039/12/2,41052039,"cross-sectional observational, not case-control",41052039,https://doi.org/10.1371/journal.pone.0332108,NA,"Seetaraso T., Gruneck L., Jinatham V., Kantakat S., Albert M.L., Therdtatha P., Inta A., Srikummool M., Kampuansai J. , Popluechai S.",Effects of ethnicity and geography on the fecal microbiota and dietary habits of Tibeto-Burman hill tribes in Northern Thailand,PloS one,2025,NA,Experiment 12,Thailand,Homo sapiens,Feces,UBERON:0001988,"Population,Ethnic group","IDOMAL:0001254,EFO:0001799", Akha ethnic group and Lisu ethnic group residing in Chiang Rai Province (AkhaCR & LisuCR),Lahu ethnic group residing in Chiang Rai Province (LahuCR),Participants from Lahu ethnic group residing in Chiang Rai Province (LahuCR),45,16,3 months,16S,NA,RT-qPCR,log transformation,PLS-DA (Partial least square discriminant analysis),0.001,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,S1 Figure C,24 October 2025,Firdaws,Firdaws,The relative abundance of gut microbiota between (Akha and Lisu ethnic group residing in Chiang Rai Province (AkhaCR and LisuCR)) and Lahu ethnic group residing in Chiang Rai Province (LahuCR),decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|1239|91061|1385|90964|1279;3366610|28890|183925|2158|2159|2172|2173;1783272|201174|1760|85004|31953|1678,Complete,NA
bsdb:41052039/13/1,41052039,"cross-sectional observational, not case-control",41052039,https://doi.org/10.1371/journal.pone.0332108,NA,"Seetaraso T., Gruneck L., Jinatham V., Kantakat S., Albert M.L., Therdtatha P., Inta A., Srikummool M., Kampuansai J. , Popluechai S.",Effects of ethnicity and geography on the fecal microbiota and dietary habits of Tibeto-Burman hill tribes in Northern Thailand,PloS one,2025,NA,Experiment 13,Thailand,Homo sapiens,Feces,UBERON:0001988,"Population,Ethnic group","IDOMAL:0001254,EFO:0001799",Lisu and Lahu ethnic group residing in Chiang Rai Province (LisuCR & LahuCR),Akha ethnic group residing in Chiang Rai Province (AkhaCR),Participants from Akha ethnic group residing in Chiang Rai Province (AkhaCR),38,23,3 months,16S,NA,RT-qPCR,log transformation,PLS-DA (Partial least square discriminant analysis),0.001,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,S1 Figure C,21 October 2025,Firdaws,Firdaws,The relative abundance of gut microbiota between Akha ethnic group residing in Chiang Rai Province (AkhaCR) and the Lisu and Lahu ethnic group residing in Chiang Rai Province (LisuCR & LahuCR).,increased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella minuta,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila",1783272|1239;3379134|976|200643|171549|815|816;3379134|976;1783272|1239|186801|3085636|186803|572511|33035;1783272|1239|186801|3082768|990719|990721|626937;1783272|1239|186801|186802|216572|216851|853;3384189|32066|203490|203491|203492|848;3379134|1224|1236;3366610|28890|183925;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|201174|1760|2037|2049|1654;1783272|1239|91061|186826|33958|1578;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|33042;1783272|1239|91061|186826|81852|1350;3379134|976|200643|171549|171552|838;1783272|201174;3379134|976|200643|171549|815|816|817;3379134|74201|203494|48461|1647988|239934|239935,Complete,NA
bsdb:41052039/15/1,41052039,"cross-sectional observational, not case-control",41052039,https://doi.org/10.1371/journal.pone.0332108,NA,"Seetaraso T., Gruneck L., Jinatham V., Kantakat S., Albert M.L., Therdtatha P., Inta A., Srikummool M., Kampuansai J. , Popluechai S.",Effects of ethnicity and geography on the fecal microbiota and dietary habits of Tibeto-Burman hill tribes in Northern Thailand,PloS one,2025,NA,Experiment 15,Thailand,Homo sapiens,Feces,UBERON:0001988,"Population,Diet","IDOMAL:0001254,EFO:0002755", Lahu ethnic group residing in Chiang Mai province (LahuCM) (Processed food),Akha ethnic group residing in Chiang Mai Province (AkhaCM) (Processed food),Participants from Akha ethnic group residing in Chiang Mai Province (AkhaCM) that consumed processed foods.,19,22,3 months,16S,NA,RT-qPCR,log transformation,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,S6 Table,22 October 2025,Firdaws,Firdaws,"Relationship between the relative abundance of gut microbiota (phylum, genus and species) and dietary habits (processed food) in Chiang Mai Province (Akha ethnic group residing in Chiang Mai Province (AkhaCM) and Lahu ethnic group residing in Chiang Mai Province (LahuCM))",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Actinomycetota",1783272|201174|1760|2037|2049|1654;3379134|74201|203494|48461|1647988|239934|239935;1783272|1239;3379134|976;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511|33035;1783272|1239|91061|186826|81852|1350;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|3085636|186803|841;1783272|1239|91061|186826|1300|1301;1783272|201174,Complete,NA
bsdb:41052039/15/2,41052039,"cross-sectional observational, not case-control",41052039,https://doi.org/10.1371/journal.pone.0332108,NA,"Seetaraso T., Gruneck L., Jinatham V., Kantakat S., Albert M.L., Therdtatha P., Inta A., Srikummool M., Kampuansai J. , Popluechai S.",Effects of ethnicity and geography on the fecal microbiota and dietary habits of Tibeto-Burman hill tribes in Northern Thailand,PloS one,2025,NA,Experiment 15,Thailand,Homo sapiens,Feces,UBERON:0001988,"Population,Diet","IDOMAL:0001254,EFO:0002755", Lahu ethnic group residing in Chiang Mai province (LahuCM) (Processed food),Akha ethnic group residing in Chiang Mai Province (AkhaCM) (Processed food),Participants from Akha ethnic group residing in Chiang Mai Province (AkhaCM) that consumed processed foods.,19,22,3 months,16S,NA,RT-qPCR,log transformation,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,S6 Table,22 October 2025,Firdaws,Firdaws,Relationship between the relative abundance of gut microbiota (genus and species) and dietary habits (processed food) in Chiang Mai Province (Akha ethnic group residing in Chiang Mai Province (AkhaCM) and Lahu ethnic group residing in Chiang Mai Province (LahuCM)),decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Actinomycetota",3379134|976|200643|171549|815|816;3384189|32066|203490|203491|203492|848;3366610|28890|183925|2158|2159|2172|2173;1783272|1239|91061|1385|90964|1279;1783272|201174,Complete,NA
bsdb:41052039/16/1,41052039,"cross-sectional observational, not case-control",41052039,https://doi.org/10.1371/journal.pone.0332108,NA,"Seetaraso T., Gruneck L., Jinatham V., Kantakat S., Albert M.L., Therdtatha P., Inta A., Srikummool M., Kampuansai J. , Popluechai S.",Effects of ethnicity and geography on the fecal microbiota and dietary habits of Tibeto-Burman hill tribes in Northern Thailand,PloS one,2025,NA,Experiment 16,Thailand,Homo sapiens,Feces,UBERON:0001988,"Population,Diet","IDOMAL:0001254,EFO:0002755",Lahu ethnic group residing in Chiang Mai province (LahuCM) (Non-processed food),Akha ethnic group residing in Chiang Mai Province (AkhaCM) (Non-processed food) ,Participants from Akha ethnic group residing in Chiang Mai Province (AkhaCM) that consumed non-processed foods.,19,22,3 months,16S,NA,RT-qPCR,log transformation,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,S6 Table,22 October 2025,Firdaws,Firdaws,Relationship between the relative abundance of gut microbiota (genus and species) and dietary habits (non-processed food) in Chiang Mai Province (Akha ethnic group residing in Chiang Mai Province (AkhaCM) and Lahu ethnic group residing in Chiang Mai Province (LahuCM)),increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella minuta",1783272|1239|186801|186802|216572|216851|853;3379134|976|200643|171549|171552|838;1783272|1239|91061|186826|33958|1578;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|3082768|990719|990721|626937,Complete,NA
bsdb:41052039/16/2,41052039,"cross-sectional observational, not case-control",41052039,https://doi.org/10.1371/journal.pone.0332108,NA,"Seetaraso T., Gruneck L., Jinatham V., Kantakat S., Albert M.L., Therdtatha P., Inta A., Srikummool M., Kampuansai J. , Popluechai S.",Effects of ethnicity and geography on the fecal microbiota and dietary habits of Tibeto-Burman hill tribes in Northern Thailand,PloS one,2025,NA,Experiment 16,Thailand,Homo sapiens,Feces,UBERON:0001988,"Population,Diet","IDOMAL:0001254,EFO:0002755",Lahu ethnic group residing in Chiang Mai province (LahuCM) (Non-processed food),Akha ethnic group residing in Chiang Mai Province (AkhaCM) (Non-processed food) ,Participants from Akha ethnic group residing in Chiang Mai Province (AkhaCM) that consumed non-processed foods.,19,22,3 months,16S,NA,RT-qPCR,log transformation,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,S6 Table,22 October 2025,Firdaws,Firdaws,"Relationship between the relative abundance of gut microbiota (phylum, genus and species) and dietary habits (non-processed food) in Chiang Mai Province (Akha ethnic group residing in Chiang Mai Province (AkhaCM) and Lahu ethnic group residing in Chiang Mai Province (LahuCM))",decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Pseudomonadati|p__Bacteroidota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|g__Christensenella|s__Christensenella minuta,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia",1783272|201174|1760|2037|2049|1654;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|815|816|817;3379134|976;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|33042;3366610|28890|183925;1783272|1239|186801|186802|216572|1263;1783272|1239|91061|1385|90964|1279;1783272|1239|91061|186826|1300|1301;3384189|32066|203490|203491|203492|848;1783272|1239|186801|3082768|990719|990721|626937;1783272|1239|91061|186826|33958|1578;1783272|1239|186801|3085636|186803|841,Complete,NA
bsdb:41052658/1/1,41052658,"cross-sectional observational, not case-control",41052658,https://doi.org/10.1016/j.jnutbio.2025.110139,https://www.sciencedirect.com/science/article/abs/pii/S0955286325003018?via=ihub,"Lima L.S., Ribeiro M., Cardozo L.F.M.F., Bittner R., Ribeiro-Alves M., Schultz J., Rosado A.S., Leite P.E.C., Nakao L.S., Schurgers L.J. , Mafra D.",Association of Poor Vitamin K Status with Inflammation and Gut Microbiota in Hemodialysis Patients: A Cross-Sectional Study,The Journal of nutritional biochemistry,2025,"Chronic Kidney Disease, Gut Microbiota, Inflammation, Menaquinone, Renal Dialysis, Vitamin K",Experiment 1,Brazil,Homo sapiens,Feces,UBERON:0001988,Vitamin K measurement,EFO:0004618,"Adequate vitamin K status Dephosphorylated, Uncarboxylated Matrix Gla Protein (dp-ucMGP ≤ 500 pmol/L)","Inadequate vitamin K status Dephosphorylated, Uncarboxylated Matrix Gla Protein (dp-ucMGP > 500 pmol/L)","Hemodialysis patients with inadequate vitamin k status, defined as a Dephosphorylated, Uncarboxylated Matrix Gla Protein (dp-ucMGP) concentration greater than 500 pmol/L.",18,5,3 months,16S,4,Illumina,raw counts,Zero-Inflated Beta Regression,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,5 November 2025,Fiddyhamma,Fiddyhamma,Bacterial genera with higher abundance in hemodialysis patients with inadequate vitamin K status,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotellamassilia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Massiliprevotella",1783272|201174|84998|1643822|1643826|84108;1783272|201174|84998|84999|84107|102106;3379134|976|200643|171549|171552|838;1783272|1239|526524|526525|128827|1573535;3379134|200940|3031449|213115|194924|872;3379134|976|200643|171549|2005519|397864;1783272|1239|186801|186802|1980681;3379134|976|200643|171549|171552|1926672;1783272|201174|84998|84999|84107|1473205;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|204475;1783272|1239|186801|3085636|186803|189330;1783272|1239|526524|526525|2810281|191303;3379134|976|200643|171549|171552|1981037,Complete,KateRasheed
bsdb:41052658/1/2,41052658,"cross-sectional observational, not case-control",41052658,https://doi.org/10.1016/j.jnutbio.2025.110139,https://www.sciencedirect.com/science/article/abs/pii/S0955286325003018?via=ihub,"Lima L.S., Ribeiro M., Cardozo L.F.M.F., Bittner R., Ribeiro-Alves M., Schultz J., Rosado A.S., Leite P.E.C., Nakao L.S., Schurgers L.J. , Mafra D.",Association of Poor Vitamin K Status with Inflammation and Gut Microbiota in Hemodialysis Patients: A Cross-Sectional Study,The Journal of nutritional biochemistry,2025,"Chronic Kidney Disease, Gut Microbiota, Inflammation, Menaquinone, Renal Dialysis, Vitamin K",Experiment 1,Brazil,Homo sapiens,Feces,UBERON:0001988,Vitamin K measurement,EFO:0004618,"Adequate vitamin K status Dephosphorylated, Uncarboxylated Matrix Gla Protein (dp-ucMGP ≤ 500 pmol/L)","Inadequate vitamin K status Dephosphorylated, Uncarboxylated Matrix Gla Protein (dp-ucMGP > 500 pmol/L)","Hemodialysis patients with inadequate vitamin k status, defined as a Dephosphorylated, Uncarboxylated Matrix Gla Protein (dp-ucMGP) concentration greater than 500 pmol/L.",18,5,3 months,16S,4,Illumina,raw counts,Zero-Inflated Beta Regression,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,5 November 2025,Fiddyhamma,Fiddyhamma,Bacterial genera with lower abundance in hemodialysis patients with inadequate vitamin K status.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Flintibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Lactonifactor,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Neglectibacter",1783272|1239|186801|186802|216572|1940255;3379134|976|200643|171549|815|816;1783272|1239|186801|186802|1918454;1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|186802|216572|244127;3379134|200940|3031449|213115|194924|35832;1783272|1239|186801|186802|31979|420345;1783272|1239|186801|186802|216572|1924105,Complete,KateRasheed
bsdb:41053825/1/1,41053825,case-control,41053825,https://doi.org/10.1186/s40168-025-02227-2,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-025-02227-2,"Villette R., Ortís Sunyer J., Novikova P.V., Aho V.T.E., Petrov V.A., Hickl O., Busi S.B., De Rudder C., Kunath B.J., Heintz-Buschart A., Trezzi J.P., Halder R., Jäger C., Lebrun L.A., Daujeumont A., Schade S., Janzen A., Jehmlich N., von Bergen M., Laczny C.C., May P., Trenkwalder C., Oertel W., Mollenhauer B. , Wilmes P.",Integrated multi-omics highlights alterations of gut microbiome functions in prodromal and idiopathic Parkinson's disease,Microbiome,2025,"Bile acids, Flagella, Gene expression, Gut microbiome, Multi-omics, Parkinson’s disease",Experiment 1,Germany,Homo sapiens,Feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Metagenomic taxonomic composition (taxMG) In Healthy Controls,Metagenomic taxonomic composition (taxMG) in Parkinson disease patients,"Parkinson's disease is a progressive brain disorder that affects movement, caused by the death of brain cells that produce dopamine.",49,46,1 month,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2G,29 October 2025,Tihabwangye Joshua,"Tihabwangye Joshua,Fiddyhamma",Differential abundance analysis using SIAMCAT (Statistical Inference of Associations between Microbial Communities And host phenoTypes) for Metagenomic taxonomic composition (taxMG).,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,3379134|976|200643|171549|171550|239759|2585118,Complete,Svetlana up
bsdb:41053825/2/1,41053825,case-control,41053825,https://doi.org/10.1186/s40168-025-02227-2,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-025-02227-2,"Villette R., Ortís Sunyer J., Novikova P.V., Aho V.T.E., Petrov V.A., Hickl O., Busi S.B., De Rudder C., Kunath B.J., Heintz-Buschart A., Trezzi J.P., Halder R., Jäger C., Lebrun L.A., Daujeumont A., Schade S., Janzen A., Jehmlich N., von Bergen M., Laczny C.C., May P., Trenkwalder C., Oertel W., Mollenhauer B. , Wilmes P.",Integrated multi-omics highlights alterations of gut microbiome functions in prodromal and idiopathic Parkinson's disease,Microbiome,2025,"Bile acids, Flagella, Gene expression, Gut microbiome, Multi-omics, Parkinson’s disease",Experiment 2,Germany,Homo sapiens,Feces,UBERON:0001988,REM sleep behavior disorder,EFO:0007462,Metagenomic taxonomic composition (taxMG) In Healthy Controls,Metagenomic taxonomic composition (taxMG) in idiopathic REM sleep behavior disorder (iRBD) patients,Idiopathic REM sleep behavior disorder is a prodromal stage of Parkinson disease and a sleep disorder where people physically act out their dreams because the normal muscle paralysis of REM sleep is absent.,49,27,2 years,WMS,NA,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2G,30 October 2025,Fiddyhamma,Fiddyhamma,Differential abundance analysis using SIAMCAT (Statistical Inference of Associations between Microbial Communities And host phenoTypes) for Metagenomic taxonomic composition (taxMG).,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,3379134|976|200643|171549|171550|239759|2585118,Complete,Svetlana up
bsdb:41055348/1/1,41055348,"cross-sectional observational, not case-control",41055348,https://doi.org/10.1128/spectrum.01247-25,https://journals.asm.org/doi/10.1128/spectrum.01247-25,"Cecilia Morales, Erlen Cruz, Florencia Neffa, Gerdhard L. Jessen, Javier Zeballos, Luciana Robino, María José González, Nicole Canales-Huerta, Nicolás Navarro, Pablo Zunino, Paola Scavone, Rafael Sauto","Urogenital microbiome, intracellular bacterial communities, and their contribution to urinary tract infections",Microbiology spectrum,2025,"EQUC, intracellular bacterial communities, urinary microbiome, urinary tract infection",Experiment 1,Uruguay,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,Female asymptomatic with IBC,Male asymptomatic with IBC,Male participants without UTI symptoms but with detected Intracellular Bacterial Communities,9,5,1 month,16S,NA,Nanopore,NA,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,13 October 2025,Emma Nelly,Emma Nelly,Gammaproteobacteria was significantly more abundant in asymptomatic males with IBC compared to asymptomatic females with IBC.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,3379134|1224|1236,Complete,KateRasheed
bsdb:41055348/1/2,41055348,"cross-sectional observational, not case-control",41055348,https://doi.org/10.1128/spectrum.01247-25,https://journals.asm.org/doi/10.1128/spectrum.01247-25,"Cecilia Morales, Erlen Cruz, Florencia Neffa, Gerdhard L. Jessen, Javier Zeballos, Luciana Robino, María José González, Nicole Canales-Huerta, Nicolás Navarro, Pablo Zunino, Paola Scavone, Rafael Sauto","Urogenital microbiome, intracellular bacterial communities, and their contribution to urinary tract infections",Microbiology spectrum,2025,"EQUC, intracellular bacterial communities, urinary microbiome, urinary tract infection",Experiment 1,Uruguay,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,Female asymptomatic with IBC,Male asymptomatic with IBC,Male participants without UTI symptoms but with detected Intracellular Bacterial Communities,9,5,1 month,16S,NA,Nanopore,NA,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,14 October 2025,Emma Nelly,Emma Nelly,The class Bacilli was significantly decreased in asymptomatic males with Intracellular Bacterial Communities (IBC) compared to asymptomatic females with IBC.,decreased,k__Bacillati|p__Bacillota|c__Bacilli,1783272|1239|91061,Complete,KateRasheed
bsdb:41055348/2/1,41055348,"cross-sectional observational, not case-control",41055348,https://doi.org/10.1128/spectrum.01247-25,https://journals.asm.org/doi/10.1128/spectrum.01247-25,"Cecilia Morales, Erlen Cruz, Florencia Neffa, Gerdhard L. Jessen, Javier Zeballos, Luciana Robino, María José González, Nicole Canales-Huerta, Nicolás Navarro, Pablo Zunino, Paola Scavone, Rafael Sauto","Urogenital microbiome, intracellular bacterial communities, and their contribution to urinary tract infections",Microbiology spectrum,2025,"EQUC, intracellular bacterial communities, urinary microbiome, urinary tract infection",Experiment 2,Uruguay,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,Asymptomatic Females,Symptomatic Females,Females with signs and symptoms of urinary tract infection,18,22,1 month,16S,NA,Nanopore,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,increased,unchanged,Signature 1,Table 2,9 October 2025,Emma Nelly,Emma Nelly,"The class Bacilli was significantly decreased in abundance in symptomatic females compared to asymptomatic females, as identified by differential abundance analysis (DESeq2) at the class level.",decreased,k__Bacillati|p__Bacillota|c__Bacilli,1783272|1239|91061,Complete,KateRasheed
bsdb:41055348/3/1,41055348,"cross-sectional observational, not case-control",41055348,https://doi.org/10.1128/spectrum.01247-25,https://journals.asm.org/doi/10.1128/spectrum.01247-25,"Cecilia Morales, Erlen Cruz, Florencia Neffa, Gerdhard L. Jessen, Javier Zeballos, Luciana Robino, María José González, Nicole Canales-Huerta, Nicolás Navarro, Pablo Zunino, Paola Scavone, Rafael Sauto","Urogenital microbiome, intracellular bacterial communities, and their contribution to urinary tract infections",Microbiology spectrum,2025,"EQUC, intracellular bacterial communities, urinary microbiome, urinary tract infection",Experiment 3,Uruguay,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,Asymptomatic Males,Symptomatic Male,Males with signs and symptoms of urinary tract infection,20,37,1 month,16S,NA,Nanopore,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,9 October 2025,Emma Nelly,Emma Nelly,"The class Gammaproteobacteria was significantly increased in abundance in symptomatic males compared to asymptomatic males, as identified by differential abundance analysis (DESeq2) at the class level.",increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,3379134|1224|1236,Complete,KateRasheed
bsdb:41055348/4/1,41055348,"cross-sectional observational, not case-control",41055348,https://doi.org/10.1128/spectrum.01247-25,https://journals.asm.org/doi/10.1128/spectrum.01247-25,"Cecilia Morales, Erlen Cruz, Florencia Neffa, Gerdhard L. Jessen, Javier Zeballos, Luciana Robino, María José González, Nicole Canales-Huerta, Nicolás Navarro, Pablo Zunino, Paola Scavone, Rafael Sauto","Urogenital microbiome, intracellular bacterial communities, and their contribution to urinary tract infections",Microbiology spectrum,2025,"EQUC, intracellular bacterial communities, urinary microbiome, urinary tract infection",Experiment 4,Uruguay,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,Asymptomatic Male,Asymptomatic Female,Female participants without any urinary tract infection symptoms,20,18,1 month,16S,NA,Nanopore,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,increased,Signature 1,Table 2,9 October 2025,Emma Nelly,Emma Nelly,"The class Bacilli was significantly increased in abundance in asymptomatic females compared to asymptomatic males, as identified by differential abundance analysis (DESeq2) at the class level.",increased,k__Bacillati|p__Bacillota|c__Bacilli,1783272|1239|91061,Complete,KateRasheed
bsdb:41055348/5/1,41055348,"cross-sectional observational, not case-control",41055348,https://doi.org/10.1128/spectrum.01247-25,https://journals.asm.org/doi/10.1128/spectrum.01247-25,"Cecilia Morales, Erlen Cruz, Florencia Neffa, Gerdhard L. Jessen, Javier Zeballos, Luciana Robino, María José González, Nicole Canales-Huerta, Nicolás Navarro, Pablo Zunino, Paola Scavone, Rafael Sauto","Urogenital microbiome, intracellular bacterial communities, and their contribution to urinary tract infections",Microbiology spectrum,2025,"EQUC, intracellular bacterial communities, urinary microbiome, urinary tract infection",Experiment 5,Uruguay,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,Female asymptomatic without IBC,Female asymptomatic with IBC,Female participants without Urinart tract infection symptoms but with detected Intracellular Bacterial Communities,9,9,1 month,16S,NA,Nanopore,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 October 2025,Emma Nelly,Emma Nelly,The class Gammaproteobacteria was significantly increased in abundance in asymptomatic females with IBC compared to those without IBC.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,3379134|1224|1236,Complete,KateRasheed
bsdb:41055348/5/2,41055348,"cross-sectional observational, not case-control",41055348,https://doi.org/10.1128/spectrum.01247-25,https://journals.asm.org/doi/10.1128/spectrum.01247-25,"Cecilia Morales, Erlen Cruz, Florencia Neffa, Gerdhard L. Jessen, Javier Zeballos, Luciana Robino, María José González, Nicole Canales-Huerta, Nicolás Navarro, Pablo Zunino, Paola Scavone, Rafael Sauto","Urogenital microbiome, intracellular bacterial communities, and their contribution to urinary tract infections",Microbiology spectrum,2025,"EQUC, intracellular bacterial communities, urinary microbiome, urinary tract infection",Experiment 5,Uruguay,Homo sapiens,Urine,UBERON:0001088,Urinary tract infection,EFO:0003103,Female asymptomatic without IBC,Female asymptomatic with IBC,Female participants without Urinart tract infection symptoms but with detected Intracellular Bacterial Communities,9,9,1 month,16S,NA,Nanopore,raw counts,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,10 October 2025,Emma Nelly,Emma Nelly,The class Gammaproteobacteria was significantly increased in abundance in asymptomatic females with IBC compared to those without IBC.,decreased,k__Bacillati|p__Bacillota|c__Bacilli,1783272|1239|91061,Complete,KateRasheed
bsdb:41056245/1/1,41056245,case-control,41056245,10.1371/journal.pone.0333676,NA,"Roongpiboonsopit D., Wairit S., Nithisathienchai C., Pakdee A., Cheibchalard T., Sayasathid J., Wilantho A., Tongsima S. , Somboonna N.",Oral microbiome dysbiosis in acute ischemic stroke and transient ischemic attack patients,PloS one,2025,NA,Experiment 1,Thailand,Homo sapiens,Saliva,UBERON:0001836,Ischemic stroke,HP:0002140,Healthy control,Stroke patient groups,The stroke patient groups comprised acute ischemic stroke (AIS) patients with brain infarction confirmed by computed tomography (CT) or magnetic resonance imaging (MRI) and transient ischemic attack (TIA) patients with neurological deficits lasting less than 24 hours without infarction on magnetic resonance imaging (MRI) scans,20,41,Recent use of antibiotics,16S,34,Illumina,centered log-ratio,T-Test,0.05,FALSE,NA,"age,sex",NA,NA,unchanged,increased,NA,NA,increased,Signature 1,Figure 2,21 October 2025,Tosin,Tosin,Taxa with statistical different relative abundances between control vs. stroke groups (p < 0.05),increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,1783272|1239|91061|186826|1300|1301|68892,Complete,KateRasheed
bsdb:41056245/2/1,41056245,case-control,41056245,10.1371/journal.pone.0333676,NA,"Roongpiboonsopit D., Wairit S., Nithisathienchai C., Pakdee A., Cheibchalard T., Sayasathid J., Wilantho A., Tongsima S. , Somboonna N.",Oral microbiome dysbiosis in acute ischemic stroke and transient ischemic attack patients,PloS one,2025,NA,Experiment 2,Thailand,Homo sapiens,Saliva,UBERON:0001836,Ischemic stroke,HP:0002140,Healthy control,Stroke patient groups,The stroke patient groups comprised acute ischemic stroke (AIS) patients with brain infarction confirmed by computed tomography (CT) or magnetic resonance imaging (MRI) and transient ischemic attack (TIA) patients with neurological deficits lasting less than 24 hours without infarction on magnetic resonance imaging (MRI) scans,20,41,Recent use of antibiotics,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,increased,NA,NA,increased,Signature 1,Figure 4B,21 October 2025,Tosin,"Tosin,Poornima",LEfSe (Linear discriminant analysis effect size) for bacterial species biomarkers representing healthy control vs. stroke patient groups,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella rimae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",1783272|1239|91061|1385;1783272|1239|91061;1783272|1239;1783272|1239|186801|186802;1783272|1239|186801|3082720|3118655|44259;3384189|32066|203490|203491;1783272|1239|91061|186826|186828|117563;1783272|1239|91061|186826;1783272|1239|91061|186826|33958|1578;1783272|201174|84998|84999|1643824|2767353|1383;3384189|32066|203490|203491|1129771;3379134|976|200643|171549|2005523|346096;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|171552|838|28133;1783272|201174|1760|85006|1268|32207|2047;1783272|1239|91061|186826|1300|1301|1328;3379134|203691|203692|136|2845253|157,Complete,KateRasheed
bsdb:41056245/2/2,41056245,case-control,41056245,10.1371/journal.pone.0333676,NA,"Roongpiboonsopit D., Wairit S., Nithisathienchai C., Pakdee A., Cheibchalard T., Sayasathid J., Wilantho A., Tongsima S. , Somboonna N.",Oral microbiome dysbiosis in acute ischemic stroke and transient ischemic attack patients,PloS one,2025,NA,Experiment 2,Thailand,Homo sapiens,Saliva,UBERON:0001836,Ischemic stroke,HP:0002140,Healthy control,Stroke patient groups,The stroke patient groups comprised acute ischemic stroke (AIS) patients with brain infarction confirmed by computed tomography (CT) or magnetic resonance imaging (MRI) and transient ischemic attack (TIA) patients with neurological deficits lasting less than 24 hours without infarction on magnetic resonance imaging (MRI) scans,20,41,Recent use of antibiotics,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,increased,NA,NA,increased,Signature 2,Figure 4B,21 October 2025,Tosin,Tosin,LEfSe (Linear discriminant analysis effect size) for bacterial species biomarkers representing healthy control vs. stroke patient groups,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula",3379134|1224|1236|135625|712|724|729;3379134|1224|28216|206351|481|482|28449;3379134|976|200643|171549|171552|838|28132;1783272|1239|909932|1843489|31977|29465|29466,Complete,KateRasheed
bsdb:41056270/1/1,41056270,"cross-sectional observational, not case-control",41056270,10.1371/journal.pone.0333612,NA,"Ahmed S., Hexun Z., Yano Y., Okami Y., Azahar N.M., Kondo K., Arima H., Torii S., Moniruzzaman M., Ganbaatar G., Kadota A., Andoh A., Shiino A., Ueshima H. , Miura K.",Relationship between Gut microbiome and brain volumes among Japanese Men,PloS one,2025,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,White matter volume measurement,EFO:0008320,Lower white matter volume (WMV),Higher white matter volume (WMV),Participants with higher white matter volume (WMV),NA,NA,NA,16S,34,Illumina,raw counts,Linear Discriminant Analysis,0.05,TRUE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,30 October 2025,Reddicx,Reddicx,Linear discriminant analysis to identify taxa that were present in at least 50% of participants’ WMV in the SESSA Study (2010-2014).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,s__uncultured organism,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|1239|186801|3085636|186803|207244;3379134|976|200643|171549|815|816|46506;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636;1783272|1239|186801|3085636|186803|1407607;155900;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|815|816,Complete,KateRasheed
bsdb:41056270/1/2,41056270,"cross-sectional observational, not case-control",41056270,10.1371/journal.pone.0333612,NA,"Ahmed S., Hexun Z., Yano Y., Okami Y., Azahar N.M., Kondo K., Arima H., Torii S., Moniruzzaman M., Ganbaatar G., Kadota A., Andoh A., Shiino A., Ueshima H. , Miura K.",Relationship between Gut microbiome and brain volumes among Japanese Men,PloS one,2025,NA,Experiment 1,Japan,Homo sapiens,Feces,UBERON:0001988,White matter volume measurement,EFO:0008320,Lower white matter volume (WMV),Higher white matter volume (WMV),Participants with higher white matter volume (WMV),NA,NA,NA,16S,34,Illumina,raw counts,Linear Discriminant Analysis,0.05,TRUE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,30 October 2025,Reddicx,"Reddicx,Fiddyhamma",Linear discriminant analysis to identify taxa that were present in at least 50% of participants’ WMV in the SESSA Study (2010-2014).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|976|200643|171549|171550|239759;1783272|1239|91061;3379134|976|200643|171549|815|816|820;1783272|1239|186801|3082720|186804|1505657;1783272|1239|91061|186826;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171550;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1304;3379134|976|200643|171549|815|816|818;1783272|1239|186801|186802|216572,Complete,KateRasheed
bsdb:41056270/2/1,41056270,"cross-sectional observational, not case-control",41056270,10.1371/journal.pone.0333612,NA,"Ahmed S., Hexun Z., Yano Y., Okami Y., Azahar N.M., Kondo K., Arima H., Torii S., Moniruzzaman M., Ganbaatar G., Kadota A., Andoh A., Shiino A., Ueshima H. , Miura K.",Relationship between Gut microbiome and brain volumes among Japanese Men,PloS one,2025,NA,Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Grey matter volume measurement,EFO:0005420,Lower grey matter volume (GMV),Higher grey matter volume (GMV),Participants with higher grey matter volume (GMV),NA,NA,NA,16S,34,Illumina,raw counts,Linear Discriminant Analysis,0.05,TRUE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,30 October 2025,Reddicx,"Reddicx,Fiddyhamma",Linear discriminant analysis to identify taxa that were present in at least 50% of participants’ GMV in the SESSA Study (2010-2014).,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,s__uncultured organism,k__Bacillati|p__Actinomycetota",1783272|1239|186801|3085636|186803|1766253;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801;1783272|201174|84998|84999|84107|102106;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;155900;1783272|201174,Complete,KateRasheed
bsdb:41056270/2/2,41056270,"cross-sectional observational, not case-control",41056270,10.1371/journal.pone.0333612,NA,"Ahmed S., Hexun Z., Yano Y., Okami Y., Azahar N.M., Kondo K., Arima H., Torii S., Moniruzzaman M., Ganbaatar G., Kadota A., Andoh A., Shiino A., Ueshima H. , Miura K.",Relationship between Gut microbiome and brain volumes among Japanese Men,PloS one,2025,NA,Experiment 2,Japan,Homo sapiens,Feces,UBERON:0001988,Grey matter volume measurement,EFO:0005420,Lower grey matter volume (GMV),Higher grey matter volume (GMV),Participants with higher grey matter volume (GMV),NA,NA,NA,16S,34,Illumina,raw counts,Linear Discriminant Analysis,0.05,TRUE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,30 October 2025,Reddicx,"Reddicx,Fiddyhamma",Linear discriminant analysis to identify taxa that were present in at least 50% of participants’ GMV in the SESSA Study (2010-2014).,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron",3379134|976|200643|171549|171550|239759;1783272|1239|91061;3379134|976|200643|171549|815|816|820;1783272|1239|186801|3082720|186804|1505657;1783272|1239|91061|186826;3379134|976|200643|1970189|1573805;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|1853231|283168|28118;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171550;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1304;1783272|1239|186801|186802|216572;3379134|976|200643|171549|815|816|818,Complete,KateRasheed
bsdb:41056270/3/1,41056270,"cross-sectional observational, not case-control",41056270,10.1371/journal.pone.0333612,NA,"Ahmed S., Hexun Z., Yano Y., Okami Y., Azahar N.M., Kondo K., Arima H., Torii S., Moniruzzaman M., Ganbaatar G., Kadota A., Andoh A., Shiino A., Ueshima H. , Miura K.",Relationship between Gut microbiome and brain volumes among Japanese Men,PloS one,2025,NA,Experiment 3,Japan,Homo sapiens,Feces,UBERON:0001988,White matter volume measurement,EFO:0008320,Lower white matter volume (WMV),Higher white matter volume (WMV),Participants with higher white matter volume (WMV) in Model 1,NA,NA,NA,16S,34,Illumina,raw counts,Linear Regression,0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 5,29 October 2025,Reddicx,"Reddicx,Fiddyhamma",Multivariable adjusted linear regression analysis to identify taxa that were present in at least 50% of participants in the SESSA Study (2010-2014) in terms of WMV for participants in model 1,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae",1783272|1239|186801|186802|186807;3379134|976|200643|171549|171550;1783272|1239|186801|3082768|990719;1783272|1239|91061|186826|33958;1783272|1239|186801|186802|216572;1783272|1239|186801|3082720|543314,Complete,KateRasheed
bsdb:41056270/3/2,41056270,"cross-sectional observational, not case-control",41056270,10.1371/journal.pone.0333612,NA,"Ahmed S., Hexun Z., Yano Y., Okami Y., Azahar N.M., Kondo K., Arima H., Torii S., Moniruzzaman M., Ganbaatar G., Kadota A., Andoh A., Shiino A., Ueshima H. , Miura K.",Relationship between Gut microbiome and brain volumes among Japanese Men,PloS one,2025,NA,Experiment 3,Japan,Homo sapiens,Feces,UBERON:0001988,White matter volume measurement,EFO:0008320,Lower white matter volume (WMV),Higher white matter volume (WMV),Participants with higher white matter volume (WMV) in Model 1,NA,NA,NA,16S,34,Illumina,raw counts,Linear Regression,0.01,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 5,29 October 2025,Reddicx,"Reddicx,Fiddyhamma",Multivariable adjusted linear regression analysis to identify taxa that were present in at least 50% of participants in the SESSA Study (2010-2014) in terms of WMV for participants in model 1,increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3384189|32066|203490|203491|203492;1783272|1239|186801|3085636|186803,Complete,KateRasheed
bsdb:41056270/4/1,41056270,"cross-sectional observational, not case-control",41056270,10.1371/journal.pone.0333612,NA,"Ahmed S., Hexun Z., Yano Y., Okami Y., Azahar N.M., Kondo K., Arima H., Torii S., Moniruzzaman M., Ganbaatar G., Kadota A., Andoh A., Shiino A., Ueshima H. , Miura K.",Relationship between Gut microbiome and brain volumes among Japanese Men,PloS one,2025,NA,Experiment 4,Japan,Homo sapiens,Feces,UBERON:0001988,Grey matter volume measurement,EFO:0005420,Lower grey matter volume (GMV),Higher grey matter volume (GMV),Participants with higher grey matter volume (GMV) in Model 1,NA,NA,NA,16S,34,Illumina,raw counts,Linear Regression,0.01,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 1,Figure 5,29 October 2025,Reddicx,"Reddicx,Fiddyhamma",Multivariable adjusted linear regression analysis to identify taxa that were present in at least 50% of participants in the SESSA Study (2010-2014) in terms of GMV for participants in model 1,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae",1783272|201174|1760|85004|31953;1783272|201174|84998|1643822|1643826;1783272|1239|909932|909929|1843491,Complete,KateRasheed
bsdb:41056270/4/2,41056270,"cross-sectional observational, not case-control",41056270,10.1371/journal.pone.0333612,NA,"Ahmed S., Hexun Z., Yano Y., Okami Y., Azahar N.M., Kondo K., Arima H., Torii S., Moniruzzaman M., Ganbaatar G., Kadota A., Andoh A., Shiino A., Ueshima H. , Miura K.",Relationship between Gut microbiome and brain volumes among Japanese Men,PloS one,2025,NA,Experiment 4,Japan,Homo sapiens,Feces,UBERON:0001988,Grey matter volume measurement,EFO:0005420,Lower grey matter volume (GMV),Higher grey matter volume (GMV),Participants with higher grey matter volume (GMV) in Model 1,NA,NA,NA,16S,34,Illumina,raw counts,Linear Regression,0.01,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 2,Figure 5,29 October 2025,Reddicx,"Reddicx,Fiddyhamma",Multivariable adjusted linear regression analysis to identify taxa that were present in at least 50% of participants in the SESSA Study (2010-2014) in terms of GMV for participants in model 1,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",3379134|74201|203494|48461|1647988;3379134|200940|3031449|213115|194924;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;3379134|976|117743|200644|49546;3379134|976|200643|1970189|1573805;3379134|976|200643|171549|171550;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|33958,Complete,KateRasheed
bsdb:41056270/5/1,41056270,"cross-sectional observational, not case-control",41056270,10.1371/journal.pone.0333612,NA,"Ahmed S., Hexun Z., Yano Y., Okami Y., Azahar N.M., Kondo K., Arima H., Torii S., Moniruzzaman M., Ganbaatar G., Kadota A., Andoh A., Shiino A., Ueshima H. , Miura K.",Relationship between Gut microbiome and brain volumes among Japanese Men,PloS one,2025,NA,Experiment 5,Japan,Homo sapiens,Feces,UBERON:0001988,White matter volume measurement,EFO:0008320,Lower white matter volume (WMV),Higher white matter volume (WMV),Participants with higher white matter volume (WMV) in model 2,NA,NA,NA,16S,34,Illumina,raw counts,Linear Regression,0.01,TRUE,NA,NA,age,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 5,29 October 2025,Reddicx,"Reddicx,Fiddyhamma",Multivariable adjusted linear regression analysis to identify taxa that were present in at least 50% of participants in the SESSA Study (2010-2014) in terms of WMV for participants in model 2,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,1783272|1239|186801|3085636|186803,Complete,KateRasheed
bsdb:41056270/5/2,41056270,"cross-sectional observational, not case-control",41056270,10.1371/journal.pone.0333612,NA,"Ahmed S., Hexun Z., Yano Y., Okami Y., Azahar N.M., Kondo K., Arima H., Torii S., Moniruzzaman M., Ganbaatar G., Kadota A., Andoh A., Shiino A., Ueshima H. , Miura K.",Relationship between Gut microbiome and brain volumes among Japanese Men,PloS one,2025,NA,Experiment 5,Japan,Homo sapiens,Feces,UBERON:0001988,White matter volume measurement,EFO:0008320,Lower white matter volume (WMV),Higher white matter volume (WMV),Participants with higher white matter volume (WMV) in model 2,NA,NA,NA,16S,34,Illumina,raw counts,Linear Regression,0.01,TRUE,NA,NA,age,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 5,29 October 2025,Reddicx,"Reddicx,Fiddyhamma",Multivariable adjusted linear regression analysis to identify taxa that were present in at least 50% of participants in the SESSA Study (2010-2014) in terms of WMV for participants in model 2,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|186802|186807;1783272|1239|91061|186826|33958;1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|216572,Complete,KateRasheed
bsdb:41056270/6/1,41056270,"cross-sectional observational, not case-control",41056270,10.1371/journal.pone.0333612,NA,"Ahmed S., Hexun Z., Yano Y., Okami Y., Azahar N.M., Kondo K., Arima H., Torii S., Moniruzzaman M., Ganbaatar G., Kadota A., Andoh A., Shiino A., Ueshima H. , Miura K.",Relationship between Gut microbiome and brain volumes among Japanese Men,PloS one,2025,NA,Experiment 6,Japan,Homo sapiens,Feces,UBERON:0001988,Grey matter volume measurement,EFO:0005420,Lower grey matter volume (GMV),Higher grey matter volume (GMV),Participants with higher grey matter volume (GMV) in Model 2,NA,NA,NA,16S,34,Illumina,raw counts,Linear Regression,0.01,TRUE,NA,NA,age,NA,increased,NA,NA,NA,increased,Signature 1,Figure 5,29 October 2025,Reddicx,"Reddicx,Fiddyhamma",Multivariable adjusted linear regression analysis to identify taxa that were present in at least 50% of participants in the SESSA Study (2010-2014) in terms of GMV for participants in model 2,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae",1783272|201174|1760|85004|31953;1783272|201174|84998|1643822|1643826;1783272|1239|909932|909929|1843491,Complete,KateRasheed
bsdb:41056270/6/2,41056270,"cross-sectional observational, not case-control",41056270,10.1371/journal.pone.0333612,NA,"Ahmed S., Hexun Z., Yano Y., Okami Y., Azahar N.M., Kondo K., Arima H., Torii S., Moniruzzaman M., Ganbaatar G., Kadota A., Andoh A., Shiino A., Ueshima H. , Miura K.",Relationship between Gut microbiome and brain volumes among Japanese Men,PloS one,2025,NA,Experiment 6,Japan,Homo sapiens,Feces,UBERON:0001988,Grey matter volume measurement,EFO:0005420,Lower grey matter volume (GMV),Higher grey matter volume (GMV),Participants with higher grey matter volume (GMV) in Model 2,NA,NA,NA,16S,34,Illumina,raw counts,Linear Regression,0.01,TRUE,NA,NA,age,NA,increased,NA,NA,NA,increased,Signature 2,Figure 5,29 October 2025,Reddicx,"Reddicx,Fiddyhamma",Multivariable adjusted linear regression analysis to identify taxa that were present in at least 50% of participants in the SESSA Study (2010-2014) in terms of GMV for participants in model 2,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",3379134|74201|203494|48461|1647988;3379134|200940|3031449|213115|194924;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;3379134|976|200643|1970189|1573805;3379134|976|200643|171549|171550;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|33958,Complete,KateRasheed
bsdb:41056270/7/1,41056270,"cross-sectional observational, not case-control",41056270,10.1371/journal.pone.0333612,NA,"Ahmed S., Hexun Z., Yano Y., Okami Y., Azahar N.M., Kondo K., Arima H., Torii S., Moniruzzaman M., Ganbaatar G., Kadota A., Andoh A., Shiino A., Ueshima H. , Miura K.",Relationship between Gut microbiome and brain volumes among Japanese Men,PloS one,2025,NA,Experiment 7,Japan,Homo sapiens,Feces,UBERON:0001988,White matter volume measurement,EFO:0008320,Lower white matter volume (WMV),Higher white matter volume (WMV),Participants with higher white matter volume (WMV) in model 3,NA,NA,NA,16S,34,Illumina,raw counts,Linear Regression,0.01,TRUE,NA,NA,"age,alcohol drinking,body mass index,hypertension,physical activity,smoking status",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 5,29 October 2025,Reddicx,"Reddicx,Fiddyhamma",Multivariable adjusted linear regression analysis to identify taxa that were present in at least 50% of participants in the SESSA Study (2010-2014) in terms of WMV for participants in model 3,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,1783272|1239|186801|3085636|186803,Complete,KateRasheed
bsdb:41056270/7/2,41056270,"cross-sectional observational, not case-control",41056270,10.1371/journal.pone.0333612,NA,"Ahmed S., Hexun Z., Yano Y., Okami Y., Azahar N.M., Kondo K., Arima H., Torii S., Moniruzzaman M., Ganbaatar G., Kadota A., Andoh A., Shiino A., Ueshima H. , Miura K.",Relationship between Gut microbiome and brain volumes among Japanese Men,PloS one,2025,NA,Experiment 7,Japan,Homo sapiens,Feces,UBERON:0001988,White matter volume measurement,EFO:0008320,Lower white matter volume (WMV),Higher white matter volume (WMV),Participants with higher white matter volume (WMV) in model 3,NA,NA,NA,16S,34,Illumina,raw counts,Linear Regression,0.01,TRUE,NA,NA,"age,alcohol drinking,body mass index,hypertension,physical activity,smoking status",NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 5,29 October 2025,Reddicx,"Reddicx,Fiddyhamma",Multivariable adjusted linear regression analysis to identify taxa that were present in at least 50% of participants in the SESSA Study (2010-2014) in terms of WMV for participants in model 3,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",1783272|1239|186801|186802|186807;1783272|1239|186801|3082768|990719;1783272|1239|91061|186826|33958,Complete,KateRasheed
bsdb:41056270/8/1,41056270,"cross-sectional observational, not case-control",41056270,10.1371/journal.pone.0333612,NA,"Ahmed S., Hexun Z., Yano Y., Okami Y., Azahar N.M., Kondo K., Arima H., Torii S., Moniruzzaman M., Ganbaatar G., Kadota A., Andoh A., Shiino A., Ueshima H. , Miura K.",Relationship between Gut microbiome and brain volumes among Japanese Men,PloS one,2025,NA,Experiment 8,Japan,Homo sapiens,Feces,UBERON:0001988,Grey matter volume measurement,EFO:0005420,Lower grey matter volume (GMV),Higher grey matter volume (GMV),Participants with higher grey matter volume (GMV) in model 3,NA,NA,NA,16S,34,Illumina,raw counts,Linear Regression,0.01,TRUE,NA,NA,"age,alcohol drinking,body mass index,hypertension,physical activity,smoking status",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 5,29 October 2025,Reddicx,"Reddicx,Fiddyhamma",Multivariable adjusted linear regression analysis to identify taxa that were present in at least 50% of participants in the SESSA Study (2010-2014) in terms of GMV for participants in model 3,increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae",1783272|201174|1760|85004|31953;1783272|201174|84998|1643822|1643826;1783272|1239|909932|909929|1843491,Complete,KateRasheed
bsdb:41056270/8/2,41056270,"cross-sectional observational, not case-control",41056270,10.1371/journal.pone.0333612,NA,"Ahmed S., Hexun Z., Yano Y., Okami Y., Azahar N.M., Kondo K., Arima H., Torii S., Moniruzzaman M., Ganbaatar G., Kadota A., Andoh A., Shiino A., Ueshima H. , Miura K.",Relationship between Gut microbiome and brain volumes among Japanese Men,PloS one,2025,NA,Experiment 8,Japan,Homo sapiens,Feces,UBERON:0001988,Grey matter volume measurement,EFO:0005420,Lower grey matter volume (GMV),Higher grey matter volume (GMV),Participants with higher grey matter volume (GMV) in model 3,NA,NA,NA,16S,34,Illumina,raw counts,Linear Regression,0.01,TRUE,NA,NA,"age,alcohol drinking,body mass index,hypertension,physical activity,smoking status",NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 5,29 October 2025,Reddicx,"Reddicx,Fiddyhamma",Multivariable adjusted linear regression analysis to identify taxa that were present in at least 50% of participants in the SESSA Study (2010-2014) in terms of GMV for participants in model 3,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",3379134|74201|203494|48461|1647988;3379134|200940|3031449|213115|194924;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;3379134|976|200643|1970189|1573805;3379134|976|200643|171549|171550,Complete,KateRasheed
bsdb:41056270/9/1,41056270,"cross-sectional observational, not case-control",41056270,10.1371/journal.pone.0333612,NA,"Ahmed S., Hexun Z., Yano Y., Okami Y., Azahar N.M., Kondo K., Arima H., Torii S., Moniruzzaman M., Ganbaatar G., Kadota A., Andoh A., Shiino A., Ueshima H. , Miura K.",Relationship between Gut microbiome and brain volumes among Japanese Men,PloS one,2025,NA,Experiment 9,Japan,Homo sapiens,Feces,UBERON:0001988,Hippocampal volume,EFO:0005035,Lower hippocampal brain volume (HBV),Higher hippocampal brain volume (HBV),Participants with high Hippocampal brain volume (HBV).,NA,NA,NA,16S,34,Illumina,raw counts,Linear Discriminant Analysis,0.05,TRUE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary figure S3,2 November 2025,Reddicx,"Reddicx,Fiddyhamma",Linear discriminant analysis (LDA) shows microbiomes related to higher and lower brain volumes in the hippocampus.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,s__uncultured organism",1783272|1239|186801|3085636|186803|207244;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|3085642;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|3085636|186803|1407607;1783272|1239|186801|3085636|186803|1506553;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;155900,Complete,KateRasheed
bsdb:41056270/9/2,41056270,"cross-sectional observational, not case-control",41056270,10.1371/journal.pone.0333612,NA,"Ahmed S., Hexun Z., Yano Y., Okami Y., Azahar N.M., Kondo K., Arima H., Torii S., Moniruzzaman M., Ganbaatar G., Kadota A., Andoh A., Shiino A., Ueshima H. , Miura K.",Relationship between Gut microbiome and brain volumes among Japanese Men,PloS one,2025,NA,Experiment 9,Japan,Homo sapiens,Feces,UBERON:0001988,Hippocampal volume,EFO:0005035,Lower hippocampal brain volume (HBV),Higher hippocampal brain volume (HBV),Participants with high Hippocampal brain volume (HBV).,NA,NA,NA,16S,34,Illumina,raw counts,Linear Discriminant Analysis,0.05,TRUE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary figure S3,2 November 2025,Reddicx,"Reddicx,Fiddyhamma","Linear discriminant analysis (LDA) shows microbiomes related to 
higher and lower brain volumes in the hippocampus.",decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,s__metagenome,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius",3379134|976|200643|171549|171550|239759;1783272|1239|91061;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|818;3379134|976|200643|171549|815|816|820;1783272|1239|186801|3082720|186804|1505657;1783272|1239|91061|186826;3379134|976|200643|1970189|1573805;3379134|976|200643|171549|1853231|283168;3379134|976|200643|171549|1853231|283168|28118;3379134|976|200643|171549|2005525|375288|46503;1783272|1239|186801|3082720|186804;3379134|976|200643|171549|171550;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;256318;1783272|1239|186801|186802|216572;1783272|1239|91061|186826|1300|1301|1304,Complete,KateRasheed
bsdb:41056270/10/1,41056270,"cross-sectional observational, not case-control",41056270,10.1371/journal.pone.0333612,NA,"Ahmed S., Hexun Z., Yano Y., Okami Y., Azahar N.M., Kondo K., Arima H., Torii S., Moniruzzaman M., Ganbaatar G., Kadota A., Andoh A., Shiino A., Ueshima H. , Miura K.",Relationship between Gut microbiome and brain volumes among Japanese Men,PloS one,2025,NA,Experiment 10,Japan,Homo sapiens,Feces,UBERON:0001988,Hippocampal volume,EFO:0005035,Lower hippocampal brain volume (HBV),Higher hippocampal brain volume (HBV),Participants with high Hippocampal brain volume (HBV) for Model 1 (unadjusted).,NA,NA,NA,16S,34,Illumina,raw counts,Linear Regression,0.01,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 1,Supplementary figure S4,1 November 2025,Reddicx,"Reddicx,Fiddyhamma","Multivariable adjusted linear regression analysis to identify taxa that 
were present in the hippocampus in at least 50% of participants in SESSA Study (2010-2014) for participants in model 1",increased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3384189|32066|203490|203491|203492;1783272|1239|186801|3085636|186803,Complete,KateRasheed
bsdb:41056270/10/2,41056270,"cross-sectional observational, not case-control",41056270,10.1371/journal.pone.0333612,NA,"Ahmed S., Hexun Z., Yano Y., Okami Y., Azahar N.M., Kondo K., Arima H., Torii S., Moniruzzaman M., Ganbaatar G., Kadota A., Andoh A., Shiino A., Ueshima H. , Miura K.",Relationship between Gut microbiome and brain volumes among Japanese Men,PloS one,2025,NA,Experiment 10,Japan,Homo sapiens,Feces,UBERON:0001988,Hippocampal volume,EFO:0005035,Lower hippocampal brain volume (HBV),Higher hippocampal brain volume (HBV),Participants with high Hippocampal brain volume (HBV) for Model 1 (unadjusted).,NA,NA,NA,16S,34,Illumina,raw counts,Linear Regression,0.01,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 2,Supplementary figure S4,1 November 2025,Reddicx,"Reddicx,Fiddyhamma","Multivariable adjusted linear regression analysis to identify taxa that 
were present in the hippocampus in at least 50% of participants in SESSA Study (2010-2014) for participants in model 1",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae",1783272|1239|186801|186802|186807;3379134|976|200643|171549|171550;1783272|1239|186801|186802|216572;1783272|1239|186801|3082768|990719;1783272|1239|91061|186826|33958;1783272|1239|186801|3082720|543314,Complete,KateRasheed
bsdb:41056270/11/1,41056270,"cross-sectional observational, not case-control",41056270,10.1371/journal.pone.0333612,NA,"Ahmed S., Hexun Z., Yano Y., Okami Y., Azahar N.M., Kondo K., Arima H., Torii S., Moniruzzaman M., Ganbaatar G., Kadota A., Andoh A., Shiino A., Ueshima H. , Miura K.",Relationship between Gut microbiome and brain volumes among Japanese Men,PloS one,2025,NA,Experiment 11,Japan,Homo sapiens,Feces,UBERON:0001988,Hippocampal volume,EFO:0005035,Lower hippocampal brain volume (HBV),Higher hippocampal brain volume (HBV),Participants with high Hippocampal brain volume (HBV) for Model 2 (adjusted).,NA,NA,NA,16S,34,Illumina,raw counts,Linear Regression,0.01,TRUE,NA,NA,age,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary figure S4,1 November 2025,Reddicx,"Reddicx,Fiddyhamma","Multivariable adjusted linear regression analysis to identify taxa that 
were present in the hippocampus in at least 50% of participants in SESSA Study (2010-2014) for participants in model 2",increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,1783272|1239|186801|3085636|186803,Complete,KateRasheed
bsdb:41056270/11/2,41056270,"cross-sectional observational, not case-control",41056270,10.1371/journal.pone.0333612,NA,"Ahmed S., Hexun Z., Yano Y., Okami Y., Azahar N.M., Kondo K., Arima H., Torii S., Moniruzzaman M., Ganbaatar G., Kadota A., Andoh A., Shiino A., Ueshima H. , Miura K.",Relationship between Gut microbiome and brain volumes among Japanese Men,PloS one,2025,NA,Experiment 11,Japan,Homo sapiens,Feces,UBERON:0001988,Hippocampal volume,EFO:0005035,Lower hippocampal brain volume (HBV),Higher hippocampal brain volume (HBV),Participants with high Hippocampal brain volume (HBV) for Model 2 (adjusted).,NA,NA,NA,16S,34,Illumina,raw counts,Linear Regression,0.01,TRUE,NA,NA,age,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplementary figure S4,1 November 2025,Reddicx,"Reddicx,Fiddyhamma","Multivariable adjusted linear regression analysis to identify taxa that 
were present in the hippocampus in at least 50% of participants in SESSA Study (2010-2014) for participants in model 2",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|1239|186801|186802|186807;1783272|1239|91061|186826|33958;1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|216572,Complete,KateRasheed
bsdb:41056270/12/1,41056270,"cross-sectional observational, not case-control",41056270,10.1371/journal.pone.0333612,NA,"Ahmed S., Hexun Z., Yano Y., Okami Y., Azahar N.M., Kondo K., Arima H., Torii S., Moniruzzaman M., Ganbaatar G., Kadota A., Andoh A., Shiino A., Ueshima H. , Miura K.",Relationship between Gut microbiome and brain volumes among Japanese Men,PloS one,2025,NA,Experiment 12,Japan,Homo sapiens,Feces,UBERON:0001988,Hippocampal volume,EFO:0005035,Lower hippocampal brain volume (HBV),Higher hippocampal brain volume (HBV),Participants with high Hippocampal brain volume (HBV) for Model 3 (over-adjusted).,NA,NA,NA,16S,34,Illumina,raw counts,Linear Regression,0.01,TRUE,NA,NA,"age,alcohol drinking,body mass index,hypertension,physical activity,smoking status",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary Figure S4,1 November 2025,Reddicx,"Reddicx,Fiddyhamma","Multivariable adjusted linear regression analysis to identify taxa that 
were present in the hippocampus in at least 50% of participants in SESSA Study (2010-2014) for participants in model 3",increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,1783272|1239|186801|3085636|186803,Complete,KateRasheed
bsdb:41056270/12/2,41056270,"cross-sectional observational, not case-control",41056270,10.1371/journal.pone.0333612,NA,"Ahmed S., Hexun Z., Yano Y., Okami Y., Azahar N.M., Kondo K., Arima H., Torii S., Moniruzzaman M., Ganbaatar G., Kadota A., Andoh A., Shiino A., Ueshima H. , Miura K.",Relationship between Gut microbiome and brain volumes among Japanese Men,PloS one,2025,NA,Experiment 12,Japan,Homo sapiens,Feces,UBERON:0001988,Hippocampal volume,EFO:0005035,Lower hippocampal brain volume (HBV),Higher hippocampal brain volume (HBV),Participants with high Hippocampal brain volume (HBV) for Model 3 (over-adjusted).,NA,NA,NA,16S,34,Illumina,raw counts,Linear Regression,0.01,TRUE,NA,NA,"age,alcohol drinking,body mass index,hypertension,physical activity,smoking status",NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplementary figure S4,1 November 2025,Reddicx,"Reddicx,Fiddyhamma","Multivariable adjusted linear regression analysis to identify taxa that 
were present in the hippocampus in at least 50% of participants in SESSA Study (2010-2014) for participants in model 3",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",1783272|1239|186801|186802|186807;1783272|1239|186801|3082768|990719;1783272|1239|91061|186826|33958,Complete,KateRasheed
bsdb:41068590/1/1,41068590,"cross-sectional observational, not case-control",41068590,10.1186/s12866-025-04420-7,https://doi.org/10.1186/s12866-025-04420-7,"Chen Y., Miao Q., Bao R., Qu H., Shen J., Li N., Luan S., Yin X., Pan J. , Hu B.",Distinct lung microbiota community states are associated with pulmonary nontuberculous mycobacterial disease prognosis,BMC microbiology,2025,"Lung microbiota, Metagenomic sequencing, Nontuberculous mycobacterial pulmonary disease, Pneumotype",Experiment 1,China,Homo sapiens,Lung,UBERON:0002048,Pulmonary non-tuberculous mycobacterial infection,MONDO:0018469,Pulmonary tuberculosis (PTB),Pulmonary nontuberculous mycobacterial disease (PNTM),"Patients with nontuberculous mycobacterial pulmonary disease diagnosed based on American Thoracic Association/American Infectious Diseases Association criteria (39 with Mycobacterium avium complex, 12 with M. abscessus, 11 with M. kansasii, 7 with other NTM species)",46,69,NA,WMS,NA,BGISEQ-500 Sequencing,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S1A,16 October 2025,Nina Takang,Nina Takang,Bacterial depleted in the lung microbiota of patients with pulmonary nontuberculous mycobacterial disease relative to patients with pulmonary tuberculosis,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Pleosporaceae|g__Alternaria",3379134|1224|1236|2887326|468|469;3379134|1224|28216|80840|119060|32008;3379134|1224|28216|80840|80864|80865;3379134|1224|1236|91347|543|561;3379134|1224|1236|135614|32033|40323;4751|4890|147541|92860|28556|5598,Complete,KateRasheed
bsdb:41068590/2/1,41068590,"cross-sectional observational, not case-control",41068590,10.1186/s12866-025-04420-7,https://doi.org/10.1186/s12866-025-04420-7,"Chen Y., Miao Q., Bao R., Qu H., Shen J., Li N., Luan S., Yin X., Pan J. , Hu B.",Distinct lung microbiota community states are associated with pulmonary nontuberculous mycobacterial disease prognosis,BMC microbiology,2025,"Lung microbiota, Metagenomic sequencing, Nontuberculous mycobacterial pulmonary disease, Pneumotype",Experiment 2,China,Homo sapiens,Lung,UBERON:0002048,Pulmonary non-tuberculous mycobacterial infection,MONDO:0018469,PTB (Pulmonary Tuberculosis),PNTM (Pulmonary Non-tuberculous Mycobacterial Disease),"Patients with nontuberculous mycobacterial pulmonary disease diagnosed based on ATS/IDSA criteria (39 with M. avium complex, 12 with M. abscessus, 11 with M. kansasii, 7 with other NTM species)",46,69,NA,WMS,NA,BGISEQ-500 Sequencing,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S1B,16 October 2025,Nina Takang,Nina Takang,"Bacterial species with increased abundance in pulmonary nontuberculous mycobacterial disease compared to pulmonary tuberculosis, including nontuberculous mycobacterial species and opportunistic pathogens",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium paraintracellulare,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacteroides|s__Mycobacteroides abscessus",1783272|201174|1760|85007|1762|1763|1138383;1783272|201174|1760|85007|1762|670516|36809,Complete,KateRasheed
bsdb:41068590/2/2,41068590,"cross-sectional observational, not case-control",41068590,10.1186/s12866-025-04420-7,https://doi.org/10.1186/s12866-025-04420-7,"Chen Y., Miao Q., Bao R., Qu H., Shen J., Li N., Luan S., Yin X., Pan J. , Hu B.",Distinct lung microbiota community states are associated with pulmonary nontuberculous mycobacterial disease prognosis,BMC microbiology,2025,"Lung microbiota, Metagenomic sequencing, Nontuberculous mycobacterial pulmonary disease, Pneumotype",Experiment 2,China,Homo sapiens,Lung,UBERON:0002048,Pulmonary non-tuberculous mycobacterial infection,MONDO:0018469,PTB (Pulmonary Tuberculosis),PNTM (Pulmonary Non-tuberculous Mycobacterial Disease),"Patients with nontuberculous mycobacterial pulmonary disease diagnosed based on ATS/IDSA criteria (39 with M. avium complex, 12 with M. abscessus, 11 with M. kansasii, 7 with other NTM species)",46,69,NA,WMS,NA,BGISEQ-500 Sequencing,raw counts,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S1B,29 October 2025,Nina Takang,Nina Takang,"Bacterial species with significantly decreased abundance in pulmonary nontuberculous mycobacterial disease compared to pulmonary tuberculosis (enriched in TB). These species show positive log2FoldChange (enriched in TB) in DESeq2 analysis. Text states ""224 species"" total with lower relative abundance in PNTM; only clearly readable species from figure are listed.",decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Alicycliphilus|s__Alicycliphilus denitrificans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia ambifaria,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia cepacia,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia dolosa,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia multivorans,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia|s__Delftia tsuruhatensis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Faucicola|s__Faucicola osloensis,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium orygis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium tuberculosis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium tuberculosis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium tuberculosis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria perflava,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sicca,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas parapaucimobilis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium canetti",3379134|1224|28216|80840|80864|201096|179636;3379134|1224|28216|80840|119060|32008|152480;3379134|1224|28216|80840|119060|32008|292;3379134|1224|28216|80840|119060|32008|152500;3379134|1224|28216|80840|119060|32008|87883;3379134|976|117743|200644|49546|1016|1019;3379134|1224|28216|80840|80864|80865|180282;3379134|1224|1236|91347|543|561|562;3379134|1224|1236|2887326|468|1604696|34062;3384189|32066|203490|203491|203492|848|860;1783272|1239|91061|1385|539738|1378|1379;3379134|1224|28216|80840|119060|47670|47671;4751|5204|1538075|162474|742845|55193|76775;1783272|201174|1760|85007|1762|1763|1305738;1783272|201174|1760|85007|1762|1763|1773;1783272|201174|1760|85007|1762|1763|1773;1783272|201174|1760|85007|1762|1763|1773;3379134|1224|28216|206351|481|482|495;3379134|1224|28216|206351|481|482|484;3379134|1224|28216|206351|481|482|33053;3379134|1224|28216|206351|481|482|490;3379134|976|200643|171549|171551|836|28124;3379134|976|200643|171549|171552|838|28131;1783272|201174|1760|85006|1268|32207|2047;3379134|1224|28211|204457|41297|13687|28213;3379134|1224|1236|135614|32033|40323|40324;1783272|201174|1760|85007|1762|1763|78331,Complete,KateRasheed
bsdb:41068590/3/1,41068590,"cross-sectional observational, not case-control",41068590,10.1186/s12866-025-04420-7,https://doi.org/10.1186/s12866-025-04420-7,"Chen Y., Miao Q., Bao R., Qu H., Shen J., Li N., Luan S., Yin X., Pan J. , Hu B.",Distinct lung microbiota community states are associated with pulmonary nontuberculous mycobacterial disease prognosis,BMC microbiology,2025,"Lung microbiota, Metagenomic sequencing, Nontuberculous mycobacterial pulmonary disease, Pneumotype",Experiment 3,China,Homo sapiens,Lung,UBERON:0002048,Pulmonary non-tuberculous mycobacterial infection,MONDO:0018469,Dirichlet Multinomial Mixtures Pneumotype 1 (DMM1),Dirichlet Multinomial Mixtures Pneumotype 2 (DMM2),"PNTM patients classified into pneumotype 2 based on Dirichlet Multinomial Mixture modeling of lung microbiota composition; characterized by enrichment in Ralstonia, Aspergillus, Bradyrhizobium, Rhizobium, Prevotella, and Neisseria",31,29,NA,WMS,NA,BGISEQ-500 Sequencing,relative abundances,Logistic Regression,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S3,28 October 2025,Nina Takang,Nina Takang,Bacterial with decreased abundance in pneumotype 2 (better prognosis) compared to pneumotype 1 (worse prognosis) among patients with pulmonary nontuberculous mycobacterial disease,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium",3379134|976|200643|171549|171552|838;3379134|1224|28216|206351|481|482;3379134|1224|1236|72274|135621|286;1783272|201174|1760|85007|1762|1763,Complete,KateRasheed
bsdb:41068590/3/2,41068590,"cross-sectional observational, not case-control",41068590,10.1186/s12866-025-04420-7,https://doi.org/10.1186/s12866-025-04420-7,"Chen Y., Miao Q., Bao R., Qu H., Shen J., Li N., Luan S., Yin X., Pan J. , Hu B.",Distinct lung microbiota community states are associated with pulmonary nontuberculous mycobacterial disease prognosis,BMC microbiology,2025,"Lung microbiota, Metagenomic sequencing, Nontuberculous mycobacterial pulmonary disease, Pneumotype",Experiment 3,China,Homo sapiens,Lung,UBERON:0002048,Pulmonary non-tuberculous mycobacterial infection,MONDO:0018469,Dirichlet Multinomial Mixtures Pneumotype 1 (DMM1),Dirichlet Multinomial Mixtures Pneumotype 2 (DMM2),"PNTM patients classified into pneumotype 2 based on Dirichlet Multinomial Mixture modeling of lung microbiota composition; characterized by enrichment in Ralstonia, Aspergillus, Bradyrhizobium, Rhizobium, Prevotella, and Neisseria",31,29,NA,WMS,NA,BGISEQ-500 Sequencing,relative abundances,Logistic Regression,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S3,28 October 2025,Nina Takang,Nina Takang,"Bacterial with increased abundance in pneumotype 2 (better prognosis) compared to pneumotype 1 (worse prognosis) among patients with pulmonary nontuberculous mycobacterial disease, associated with favorable clinical outcomes",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Bradyrhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium",3379134|1224|28211|356|41294|374;3379134|1224|28216|80840|119060|48736;3379134|1224|28211|356|82115|379,Complete,KateRasheed
bsdb:41077329/1/1,41077329,prospective cohort,41077329,10.1016/j.ijid.2025.108117,NA,"González-Rico C., Hernández M., Rodríguez-Grande J., Fernández-Luis S., Rodríguez A.B., González-Huerta A.J., Velasco E.L., López L.V., García I.G., de Las Revillas F.A., Fariñas-Álvarez C., Montes J.C., Ocampo-Sosa A., Fernández-Martínez M. , Fariñas M.C.",Changes in the bacterial profile and diversity of the gut microbiota in allogeneic hematopoietic stem cell transplant recipients,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2025,"16S rRNA gene sequencing, Allogeneic hematopoietic stem cell transplantation, differential abundance, diversity, gut microbiota",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,Surviving patients,Deceased patients,Patients who died during the study follow-up,74,21,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 1,figure 4,23 October 2025,Blegodwin,Blegodwin,Taxa identified by LEfSe analysis as being significantly enriched (higher abundance) in patients who died during follow-up (Group 1) compared to survivors (Group 0).,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacillati|p__Bacillota|c__Bacilli,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Pseudomonadati|p__Verrucomicrobiota",3379134|74201|203494|48461|1647988|239934;3379134|74201|203494|48461|1647988;1783272|1239|91061;1783272|1239|91061|186826|81852;1783272|1239|91061|1385|90964;1783272|1239|91061|1385|90964|1279;3379134|74201|203494|48461;3379134|74201|203494;3379134|74201,Complete,KateRasheed
bsdb:41077329/1/2,41077329,prospective cohort,41077329,10.1016/j.ijid.2025.108117,NA,"González-Rico C., Hernández M., Rodríguez-Grande J., Fernández-Luis S., Rodríguez A.B., González-Huerta A.J., Velasco E.L., López L.V., García I.G., de Las Revillas F.A., Fariñas-Álvarez C., Montes J.C., Ocampo-Sosa A., Fernández-Martínez M. , Fariñas M.C.",Changes in the bacterial profile and diversity of the gut microbiota in allogeneic hematopoietic stem cell transplant recipients,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2025,"16S rRNA gene sequencing, Allogeneic hematopoietic stem cell transplantation, differential abundance, diversity, gut microbiota",Experiment 1,Spain,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,Surviving patients,Deceased patients,Patients who died during the study follow-up,74,21,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 2,Figure 4,23 October 2025,Blegodwin,"Blegodwin,KateRasheed",Taxa identified by LEfSe analysis as being significantly lower abundance in patients who died during follow-up (Group 1) compared to survivors (Group 0).,decreased,"k__Bacillati|p__Actinomycetota,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales",1783272|201174;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636;1783272|1239|186801|186802|216572;1783272|1239|186801|186802,Complete,KateRasheed
bsdb:41077329/2/1,41077329,prospective cohort,41077329,10.1016/j.ijid.2025.108117,NA,"González-Rico C., Hernández M., Rodríguez-Grande J., Fernández-Luis S., Rodríguez A.B., González-Huerta A.J., Velasco E.L., López L.V., García I.G., de Las Revillas F.A., Fariñas-Álvarez C., Montes J.C., Ocampo-Sosa A., Fernández-Martínez M. , Fariñas M.C.",Changes in the bacterial profile and diversity of the gut microbiota in allogeneic hematopoietic stem cell transplant recipients,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2025,"16S rRNA gene sequencing, Allogeneic hematopoietic stem cell transplantation, differential abundance, diversity, gut microbiota",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Acute graft vs. host disease,EFO:0004599,Patients without acute GI-GVHD,Patients with acute GI-GVHD grade >2,Patients who developed acute gastrointestinal graft-versus-host disease (GI-GVHD) grade >2,NA,NA,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 1,Supplementary Figure S5A,23 October 2025,Blegodwin,Blegodwin,Taxa with significantly higher relative abundance in patients with GI-GVHD grade >2 (Group 1) compared to those with no GI-GVHD (Group 0).,increased,NA,NA,Complete,KateRasheed
bsdb:41077329/2/2,41077329,prospective cohort,41077329,10.1016/j.ijid.2025.108117,NA,"González-Rico C., Hernández M., Rodríguez-Grande J., Fernández-Luis S., Rodríguez A.B., González-Huerta A.J., Velasco E.L., López L.V., García I.G., de Las Revillas F.A., Fariñas-Álvarez C., Montes J.C., Ocampo-Sosa A., Fernández-Martínez M. , Fariñas M.C.",Changes in the bacterial profile and diversity of the gut microbiota in allogeneic hematopoietic stem cell transplant recipients,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2025,"16S rRNA gene sequencing, Allogeneic hematopoietic stem cell transplantation, differential abundance, diversity, gut microbiota",Experiment 2,Spain,Homo sapiens,Feces,UBERON:0001988,Acute graft vs. host disease,EFO:0004599,Patients without acute GI-GVHD,Patients with acute GI-GVHD grade >2,Patients who developed acute gastrointestinal graft-versus-host disease (GI-GVHD) grade >2,NA,NA,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 2,Figure 2,23 October 2025,Blegodwin,Blegodwin,Taxa with significantly lower relative abundance in patients with GI-GVHD grade >2 (Group 1) compared to those with no GI-GVHD (Group 0).,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,1783272|1239|186801|3085636|186803|572511,Complete,KateRasheed
bsdb:41077329/3/1,41077329,prospective cohort,41077329,10.1016/j.ijid.2025.108117,NA,"González-Rico C., Hernández M., Rodríguez-Grande J., Fernández-Luis S., Rodríguez A.B., González-Huerta A.J., Velasco E.L., López L.V., García I.G., de Las Revillas F.A., Fariñas-Álvarez C., Montes J.C., Ocampo-Sosa A., Fernández-Martínez M. , Fariñas M.C.",Changes in the bacterial profile and diversity of the gut microbiota in allogeneic hematopoietic stem cell transplant recipients,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2025,"16S rRNA gene sequencing, Allogeneic hematopoietic stem cell transplantation, differential abundance, diversity, gut microbiota",Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Bacteriemia,EFO:0003033,Patients without bacteriemia.,Patients who experienced an episode of bacteriemia during follow-up,Patients who experienced an episode of bacteraemia during follow-up.,NA,NA,NA,16S,34,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 1,Supplementary Figure S5B,26 October 2025,Blegodwin,Blegodwin,Taxa with significantly higher relative abundances in patients with bacteremia (Group 1) compared to those without (Group 0).,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,KateRasheed
bsdb:41077329/3/2,41077329,prospective cohort,41077329,10.1016/j.ijid.2025.108117,NA,"González-Rico C., Hernández M., Rodríguez-Grande J., Fernández-Luis S., Rodríguez A.B., González-Huerta A.J., Velasco E.L., López L.V., García I.G., de Las Revillas F.A., Fariñas-Álvarez C., Montes J.C., Ocampo-Sosa A., Fernández-Martínez M. , Fariñas M.C.",Changes in the bacterial profile and diversity of the gut microbiota in allogeneic hematopoietic stem cell transplant recipients,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2025,"16S rRNA gene sequencing, Allogeneic hematopoietic stem cell transplantation, differential abundance, diversity, gut microbiota",Experiment 3,Spain,Homo sapiens,Feces,UBERON:0001988,Bacteriemia,EFO:0003033,Patients without bacteriemia.,Patients who experienced an episode of bacteriemia during follow-up,Patients who experienced an episode of bacteraemia during follow-up.,NA,NA,NA,16S,34,Illumina,relative abundances,"Mann-Whitney (Wilcoxon),Kruskall-Wallis",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 2,"Figure 2, Supplementary Figure S5B",26 October 2025,Blegodwin,Blegodwin,Taxa with significantly lower relative abundance in patients with bacteremia (Group 1) compared to those without (Group 0).,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,1783272|1239|186801|3085636|186803|572511,Complete,KateRasheed
bsdb:41077329/4/1,41077329,prospective cohort,41077329,10.1016/j.ijid.2025.108117,NA,"González-Rico C., Hernández M., Rodríguez-Grande J., Fernández-Luis S., Rodríguez A.B., González-Huerta A.J., Velasco E.L., López L.V., García I.G., de Las Revillas F.A., Fariñas-Álvarez C., Montes J.C., Ocampo-Sosa A., Fernández-Martínez M. , Fariñas M.C.",Changes in the bacterial profile and diversity of the gut microbiota in allogeneic hematopoietic stem cell transplant recipients,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2025,"16S rRNA gene sequencing, Allogeneic hematopoietic stem cell transplantation, differential abundance, diversity, gut microbiota",Experiment 4,Spain,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,Baseline samples,Day 14 post-HSCT samples,Samples collected 14 days (± 3 days) after allogeneic hematopoietic stem cell transplantation,4,58,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 1,"Figure 1A, Figure 1B",27 October 2025,Blegodwin,Blegodwin,Taxa with significantly higher relative abundance at Day 14 post-HSCT (Group 1) compared to Baseline (Group 0).,increased,NA,NA,Complete,KateRasheed
bsdb:41077329/4/2,41077329,prospective cohort,41077329,10.1016/j.ijid.2025.108117,NA,"González-Rico C., Hernández M., Rodríguez-Grande J., Fernández-Luis S., Rodríguez A.B., González-Huerta A.J., Velasco E.L., López L.V., García I.G., de Las Revillas F.A., Fariñas-Álvarez C., Montes J.C., Ocampo-Sosa A., Fernández-Martínez M. , Fariñas M.C.",Changes in the bacterial profile and diversity of the gut microbiota in allogeneic hematopoietic stem cell transplant recipients,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2025,"16S rRNA gene sequencing, Allogeneic hematopoietic stem cell transplantation, differential abundance, diversity, gut microbiota",Experiment 4,Spain,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,Baseline samples,Day 14 post-HSCT samples,Samples collected 14 days (± 3 days) after allogeneic hematopoietic stem cell transplantation,4,58,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 2,"Figure 1A, Figure 1B",27 October 2025,Blegodwin,Blegodwin,Taxa with significantly lower relative abundance at Day 14 post-HSCT (Group 1) compared to Baseline (Group 0).,decreased,k__Bacillati|p__Actinomycetota,1783272|201174,Complete,KateRasheed
bsdb:41077329/5/1,41077329,prospective cohort,41077329,10.1016/j.ijid.2025.108117,NA,"González-Rico C., Hernández M., Rodríguez-Grande J., Fernández-Luis S., Rodríguez A.B., González-Huerta A.J., Velasco E.L., López L.V., García I.G., de Las Revillas F.A., Fariñas-Álvarez C., Montes J.C., Ocampo-Sosa A., Fernández-Martínez M. , Fariñas M.C.",Changes in the bacterial profile and diversity of the gut microbiota in allogeneic hematopoietic stem cell transplant recipients,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2025,"16S rRNA gene sequencing, Allogeneic hematopoietic stem cell transplantation, differential abundance, diversity, gut microbiota",Experiment 5,Spain,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,Baseline samples,Day 30 post-HSCT samples,Samples collected 30 days (± 3 days) after allogeneic hematopoietic stem cell transplantation.,4,11,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 1,"Figure 1A, Figure 1B",27 October 2025,Blegodwin,Blegodwin,Taxa with significantly higher relative abundance at Day 30 post-HSCT (Group 1) compared to Baseline (Group 0).,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:41077329/5/2,41077329,prospective cohort,41077329,10.1016/j.ijid.2025.108117,NA,"González-Rico C., Hernández M., Rodríguez-Grande J., Fernández-Luis S., Rodríguez A.B., González-Huerta A.J., Velasco E.L., López L.V., García I.G., de Las Revillas F.A., Fariñas-Álvarez C., Montes J.C., Ocampo-Sosa A., Fernández-Martínez M. , Fariñas M.C.",Changes in the bacterial profile and diversity of the gut microbiota in allogeneic hematopoietic stem cell transplant recipients,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2025,"16S rRNA gene sequencing, Allogeneic hematopoietic stem cell transplantation, differential abundance, diversity, gut microbiota",Experiment 5,Spain,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,Baseline samples,Day 30 post-HSCT samples,Samples collected 30 days (± 3 days) after allogeneic hematopoietic stem cell transplantation.,4,11,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 2,"Figure 1A, Figure 1B",27 October 2025,Blegodwin,Blegodwin,Taxa with significantly lower relative abundance at Day 30 post-HSCT (Group 1) compared to Baseline (Group 0).,decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota",1783272|201174;3379134|976,Complete,KateRasheed
bsdb:41077329/6/1,41077329,prospective cohort,41077329,10.1016/j.ijid.2025.108117,NA,"González-Rico C., Hernández M., Rodríguez-Grande J., Fernández-Luis S., Rodríguez A.B., González-Huerta A.J., Velasco E.L., López L.V., García I.G., de Las Revillas F.A., Fariñas-Álvarez C., Montes J.C., Ocampo-Sosa A., Fernández-Martínez M. , Fariñas M.C.",Changes in the bacterial profile and diversity of the gut microbiota in allogeneic hematopoietic stem cell transplant recipients,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2025,"16S rRNA gene sequencing, Allogeneic hematopoietic stem cell transplantation, differential abundance, diversity, gut microbiota",Experiment 6,Spain,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,Baseline samples,Day 60 post-HSCT samples,Samples collected 60 days (± 3 days) after allogeneic hematopoietic stem cell transplantation.,4,7,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 1,"Figure 1A, Figure 1B",27 October 2025,Blegodwin,Blegodwin,Taxa with significantly higher relative abundance at Day 60 post-HSCT (Group 1) compared to Baseline (Group 0).,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:41077329/6/2,41077329,prospective cohort,41077329,10.1016/j.ijid.2025.108117,NA,"González-Rico C., Hernández M., Rodríguez-Grande J., Fernández-Luis S., Rodríguez A.B., González-Huerta A.J., Velasco E.L., López L.V., García I.G., de Las Revillas F.A., Fariñas-Álvarez C., Montes J.C., Ocampo-Sosa A., Fernández-Martínez M. , Fariñas M.C.",Changes in the bacterial profile and diversity of the gut microbiota in allogeneic hematopoietic stem cell transplant recipients,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2025,"16S rRNA gene sequencing, Allogeneic hematopoietic stem cell transplantation, differential abundance, diversity, gut microbiota",Experiment 6,Spain,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,Baseline samples,Day 60 post-HSCT samples,Samples collected 60 days (± 3 days) after allogeneic hematopoietic stem cell transplantation.,4,7,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 2,"Figure 1A, Figure 1B",27 October 2025,Blegodwin,Blegodwin,Taxa with significantly lower relative abundance at Day 60 post-HSCT (Group 1) compared to Baseline (Group 0).,decreased,"k__Bacillati|p__Actinomycetota,k__Pseudomonadati|p__Bacteroidota",1783272|201174;3379134|976,Complete,KateRasheed
bsdb:41077329/7/1,41077329,prospective cohort,41077329,10.1016/j.ijid.2025.108117,NA,"González-Rico C., Hernández M., Rodríguez-Grande J., Fernández-Luis S., Rodríguez A.B., González-Huerta A.J., Velasco E.L., López L.V., García I.G., de Las Revillas F.A., Fariñas-Álvarez C., Montes J.C., Ocampo-Sosa A., Fernández-Martínez M. , Fariñas M.C.",Changes in the bacterial profile and diversity of the gut microbiota in allogeneic hematopoietic stem cell transplant recipients,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2025,"16S rRNA gene sequencing, Allogeneic hematopoietic stem cell transplantation, differential abundance, diversity, gut microbiota",Experiment 7,Spain,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,Baseline samples,Day 100 post-HSCT samples,Samples collected 100 days (± 3 days) after allogeneic hematopoietic stem cell transplantation.,4,4,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 1,"Figure 1A, Figure 1B",27 October 2025,Blegodwin,Blegodwin,Taxa with significantly higher relative abundance at Day 100 post-HSCT (Group 1) compared to Baseline (Group 0).,increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:41077329/7/2,41077329,prospective cohort,41077329,10.1016/j.ijid.2025.108117,NA,"González-Rico C., Hernández M., Rodríguez-Grande J., Fernández-Luis S., Rodríguez A.B., González-Huerta A.J., Velasco E.L., López L.V., García I.G., de Las Revillas F.A., Fariñas-Álvarez C., Montes J.C., Ocampo-Sosa A., Fernández-Martínez M. , Fariñas M.C.",Changes in the bacterial profile and diversity of the gut microbiota in allogeneic hematopoietic stem cell transplant recipients,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2025,"16S rRNA gene sequencing, Allogeneic hematopoietic stem cell transplantation, differential abundance, diversity, gut microbiota",Experiment 7,Spain,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,Baseline samples,Day 100 post-HSCT samples,Samples collected 100 days (± 3 days) after allogeneic hematopoietic stem cell transplantation.,4,4,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 2,Figure 1B,27 October 2025,Blegodwin,Blegodwin,Taxa with significantly lower relative abundance at Day 100 post-HSCT (Group 1) compared to Baseline (Group 0).,decreased,NA,NA,Complete,KateRasheed
bsdb:41077329/8/1,41077329,prospective cohort,41077329,10.1016/j.ijid.2025.108117,NA,"González-Rico C., Hernández M., Rodríguez-Grande J., Fernández-Luis S., Rodríguez A.B., González-Huerta A.J., Velasco E.L., López L.V., García I.G., de Las Revillas F.A., Fariñas-Álvarez C., Montes J.C., Ocampo-Sosa A., Fernández-Martínez M. , Fariñas M.C.",Changes in the bacterial profile and diversity of the gut microbiota in allogeneic hematopoietic stem cell transplant recipients,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2025,"16S rRNA gene sequencing, Allogeneic hematopoietic stem cell transplantation, differential abundance, diversity, gut microbiota",Experiment 8,Spain,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,Surviving patients,Deceased patients,Patients who died during the study follow-up,74,21,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 1,Figure 5,1 November 2025,Blegodwin,Blegodwin,Taxa selected from the LEfSe analysis that were confirmed by the Wilcoxon rank-sum test (Mann-Whitney U test) to have a significantly higher relative abundance in patients who died (Group 1) compared to survivors (Group 0).,increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",3379134|74201|203494|48461|1647988|239934;1783272|1239|91061|1385|90964|1279,Complete,KateRasheed
bsdb:41077329/8/2,41077329,prospective cohort,41077329,10.1016/j.ijid.2025.108117,NA,"González-Rico C., Hernández M., Rodríguez-Grande J., Fernández-Luis S., Rodríguez A.B., González-Huerta A.J., Velasco E.L., López L.V., García I.G., de Las Revillas F.A., Fariñas-Álvarez C., Montes J.C., Ocampo-Sosa A., Fernández-Martínez M. , Fariñas M.C.",Changes in the bacterial profile and diversity of the gut microbiota in allogeneic hematopoietic stem cell transplant recipients,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2025,"16S rRNA gene sequencing, Allogeneic hematopoietic stem cell transplantation, differential abundance, diversity, gut microbiota",Experiment 8,Spain,Homo sapiens,Feces,UBERON:0001988,Response to allogeneic hematopoietic stem cell transplant,EFO:0007044,Surviving patients,Deceased patients,Patients who died during the study follow-up,74,21,NA,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 2,Figure 5,1 November 2025,Blegodwin,Blegodwin,Taxa selected from the LEfSe analysis that were confirmed by the Wilcoxon rank-sum test to have a significantly lower relative abundance in patients who died (Group 1) compared to survivors (Group 0).,decreased,NA,NA,Complete,KateRasheed
bsdb:41077329/9/1,41077329,prospective cohort,41077329,10.1016/j.ijid.2025.108117,NA,"González-Rico C., Hernández M., Rodríguez-Grande J., Fernández-Luis S., Rodríguez A.B., González-Huerta A.J., Velasco E.L., López L.V., García I.G., de Las Revillas F.A., Fariñas-Álvarez C., Montes J.C., Ocampo-Sosa A., Fernández-Martínez M. , Fariñas M.C.",Changes in the bacterial profile and diversity of the gut microbiota in allogeneic hematopoietic stem cell transplant recipients,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2025,"16S rRNA gene sequencing, Allogeneic hematopoietic stem cell transplantation, differential abundance, diversity, gut microbiota",Experiment 9,Spain,Homo sapiens,Feces,UBERON:0001988,Acute graft vs. host disease,EFO:0004599,Patients with acute GI-GVHD grade =< 2,Patients with acute GI-GVHD grade > 2,Patients who developed acute gastrointestinal graft-versus-host disease (GI-GVHD) grade > 2,NA,NA,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 1,Supplementary Figure S5A,2 November 2025,Blegodwin,Blegodwin,Relative abundance increased in patients with severe (Grade > 2) acute GI-GVHD compared to patients with (Grade =< 2) acute GI-GVHD.,increased,NA,NA,Complete,KateRasheed
bsdb:41077329/9/2,41077329,prospective cohort,41077329,10.1016/j.ijid.2025.108117,NA,"González-Rico C., Hernández M., Rodríguez-Grande J., Fernández-Luis S., Rodríguez A.B., González-Huerta A.J., Velasco E.L., López L.V., García I.G., de Las Revillas F.A., Fariñas-Álvarez C., Montes J.C., Ocampo-Sosa A., Fernández-Martínez M. , Fariñas M.C.",Changes in the bacterial profile and diversity of the gut microbiota in allogeneic hematopoietic stem cell transplant recipients,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2025,"16S rRNA gene sequencing, Allogeneic hematopoietic stem cell transplantation, differential abundance, diversity, gut microbiota",Experiment 9,Spain,Homo sapiens,Feces,UBERON:0001988,Acute graft vs. host disease,EFO:0004599,Patients with acute GI-GVHD grade =< 2,Patients with acute GI-GVHD grade > 2,Patients who developed acute gastrointestinal graft-versus-host disease (GI-GVHD) grade > 2,NA,NA,NA,16S,34,Illumina,relative abundances,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 2,Figure 2,2 November 2025,Blegodwin,Blegodwin,Taxa with significantly lower relative abundance in patients with GI-GVHD grade >2 (Group 1) compared to those with GI-GVHD grade <2 (Group 0).,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,1783272|1239|186801|3085636|186803|572511,Complete,KateRasheed
bsdb:41077329/10/1,41077329,prospective cohort,41077329,10.1016/j.ijid.2025.108117,NA,"González-Rico C., Hernández M., Rodríguez-Grande J., Fernández-Luis S., Rodríguez A.B., González-Huerta A.J., Velasco E.L., López L.V., García I.G., de Las Revillas F.A., Fariñas-Álvarez C., Montes J.C., Ocampo-Sosa A., Fernández-Martínez M. , Fariñas M.C.",Changes in the bacterial profile and diversity of the gut microbiota in allogeneic hematopoietic stem cell transplant recipients,International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases,2025,"16S rRNA gene sequencing, Allogeneic hematopoietic stem cell transplantation, differential abundance, diversity, gut microbiota",Experiment 10,Spain,Homo sapiens,Feces,UBERON:0001988,Graft versus host disease,MONDO:0013730,Patients without GI-GVHD,Patients with GI-GVHD,Patients who developed gastrointestinal graft-versus-host disease (GI-GVHD) post-HSCT.,NA,NA,NA,16S,34,Illumina,relative abundances,Logistic Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,sex",NA,NA,NA,NA,decreased,NA,Signature 1,"Supplementary Figure S2A, Main text page 13",2 November 2025,Blegodwin,Blegodwin,"Association of Blautia abundance with GI-GVHD post-HSCT, adjusted for multiple confounders.",decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,1783272|1239|186801|3085636|186803|572511,Complete,KateRasheed
bsdb:41089933/1/1,41089933,"cross-sectional observational, not case-control",41089933,10.1016/j.crmicr.2025.100480,NA,"Song Y., Xu X., Xie M., Tao J., Jin H., Liu Y., Liu L., Song X., Meng S., Cheong I.H., Wang Y. , Wei Q.",The lung microbiome in patients with HIV complicated with community-acquired pneumonia: a cross-sectional pilot study,Current research in microbial sciences,2025,"16S rRNA, Community-acquired pneumonia (CAP), HIV, Lung microbiome",Experiment 1,China,Homo sapiens,Alveolus of lung,UBERON:0002299,Pneumonia,EFO:0003106,HIV group (CD4+ <200cells/μl),AIDS group (CD4+≥200cells/μl),AIDS group with community-acquired pneumonia  (CD4+≥200cells/μl),54,36,2 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 4B,15 October 2025,Temmie,"WikiWorks,Temmie",Differential analysis between the HIV group and the AIDS group based on LDA score (LEfSe analysis),increased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella dentalis,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rickettsiales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Thermotogati|p__Deinococcota|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus",3379134|1224|28211;1783272|544448|31969|186332|186333|2152;3379134|976|200643|171549|815;3379134|976|200643|171549|815|816;3379134|1224|28216|80840|80864;1783272|1239|526524|526525|2810280;3384194|1297|188787|118964|183710;3379134|1224|28216|80840|80864|80865;1783272|1239|186801|186802;3379134|976|200643|171549|171552|838|52227;1783272|201174|1760|85009;3379134|1224|28211|766;1783272|1239|186801|186802|216572|1263;3384189|32066|203490|203491|1129771;3384194|1297|188787|118964|183710|1298,Complete,Svetlana up
bsdb:41089933/1/2,41089933,"cross-sectional observational, not case-control",41089933,10.1016/j.crmicr.2025.100480,NA,"Song Y., Xu X., Xie M., Tao J., Jin H., Liu Y., Liu L., Song X., Meng S., Cheong I.H., Wang Y. , Wei Q.",The lung microbiome in patients with HIV complicated with community-acquired pneumonia: a cross-sectional pilot study,Current research in microbial sciences,2025,"16S rRNA, Community-acquired pneumonia (CAP), HIV, Lung microbiome",Experiment 1,China,Homo sapiens,Alveolus of lung,UBERON:0002299,Pneumonia,EFO:0003106,HIV group (CD4+ <200cells/μl),AIDS group (CD4+≥200cells/μl),AIDS group with community-acquired pneumonia  (CD4+≥200cells/μl),54,36,2 months,16S,4,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,unchanged,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 4B,15 October 2025,Temmie,"WikiWorks,Temmie",Differential analysis between the HIV group and AIDS group based on the LDA score (LEfSe),decreased,"k__Bacillati|p__Chloroflexota,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Marinilabiliales|f__Marinilabiliaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Verrucomicrobiota|c__Spartobacteria|o__Chthoniobacterales|f__Chthoniobacteraceae|g__Chthoniobacter",1783272|200795;1783272|201174|1760|85009|31957|1912216;3379134|976|200643|1970189|558415;1783272|201174|1760|85009|31957;3379134|1224|28216|80840|119060|48736;3379134|74201|134549|1836787|1836792|295577,Complete,Svetlana up
bsdb:41102296/1/1,41102296,case-control,41102296,https://doi.org/10.1038/s41598-025-20266-5,https://www.nature.com/articles/s41598-025-20266-5,"Udomkarnjananun S., Chuaypen N., Metta K., Dissayabutra T., Sodsai P., Kittiskulnam P. , Tangkijvanich P.",Dietary composition modulate gut microbiota and related biomarkers in patients with chronic kidney disease,Scientific reports,2025,"Chronic kidney disease, Cytokines, Diet, Gut barrier integrity, Gut microbiota, TMAO",Experiment 1,Thailand,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Healthy Controls,Chronic Kidney Disease patients (CKD),Patients in stages G3 and G4 of Chronic Kidney Disease (CKD),19,135,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 2A,22 October 2025,Fiddyhamma,Fiddyhamma,The median relative abundance of key bacterial taxa (A) healthy controls vs. all patients with chronic kidney disease,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,1783272|1239|186801|3085636|186803|1506553,Complete,KateRasheed
bsdb:41102296/1/2,41102296,case-control,41102296,https://doi.org/10.1038/s41598-025-20266-5,https://www.nature.com/articles/s41598-025-20266-5,"Udomkarnjananun S., Chuaypen N., Metta K., Dissayabutra T., Sodsai P., Kittiskulnam P. , Tangkijvanich P.",Dietary composition modulate gut microbiota and related biomarkers in patients with chronic kidney disease,Scientific reports,2025,"Chronic kidney disease, Cytokines, Diet, Gut barrier integrity, Gut microbiota, TMAO",Experiment 1,Thailand,Homo sapiens,Feces,UBERON:0001988,Chronic kidney disease,EFO:0003884,Healthy Controls,Chronic Kidney Disease patients (CKD),Patients in stages G3 and G4 of Chronic Kidney Disease (CKD),19,135,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table 2A,22 October 2025,Fiddyhamma,Fiddyhamma,The median relative abundance of key bacterial taxa (A) healthy controls vs. all patients with chronic kidney disease,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",1783272|201174|1760|85004|31953|1678;1783272|1239|186801|3085636|186803|33042;1783272|1239|186801|186802|216572|216851;3379134|976|200643|171549|171552|577309;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|292632;3379134|1224|28216|80840|995019|40544,Complete,KateRasheed
bsdb:41102296/2/1,41102296,case-control,41102296,https://doi.org/10.1038/s41598-025-20266-5,https://www.nature.com/articles/s41598-025-20266-5,"Udomkarnjananun S., Chuaypen N., Metta K., Dissayabutra T., Sodsai P., Kittiskulnam P. , Tangkijvanich P.",Dietary composition modulate gut microbiota and related biomarkers in patients with chronic kidney disease,Scientific reports,2025,"Chronic kidney disease, Cytokines, Diet, Gut barrier integrity, Gut microbiota, TMAO",Experiment 2,Thailand,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Low-protein and High-fiber diet Chronic Kidney Disease (CKD) patients,High-protein and Low-fiber diet Chronic Kidney Disease (CKD) patients,"Non-dialysis Chronic Kidney Disease (CKD) patients adhering to a high-protein, low-fiber diet. Individuals consuming ≥ 0.8 g/kg/day were classified as having high protein intake, fiiber intake was categorized based on the median intake of the study population, which was 8 g/day.",17,32,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 2B,22 October 2025,Fiddyhamma,Fiddyhamma,The median relative abundance of key bacterial taxa (B) the low protein-high fiber diet vs. the high protein-low fiber diet.,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia",1783272|1239|186801|186802|31979|1485;3379134|1224|1236|91347|543|570;1783272|1239|186801|3082720|186804|1501226,Complete,KateRasheed
bsdb:41102296/2/2,41102296,case-control,41102296,https://doi.org/10.1038/s41598-025-20266-5,https://www.nature.com/articles/s41598-025-20266-5,"Udomkarnjananun S., Chuaypen N., Metta K., Dissayabutra T., Sodsai P., Kittiskulnam P. , Tangkijvanich P.",Dietary composition modulate gut microbiota and related biomarkers in patients with chronic kidney disease,Scientific reports,2025,"Chronic kidney disease, Cytokines, Diet, Gut barrier integrity, Gut microbiota, TMAO",Experiment 2,Thailand,Homo sapiens,Feces,UBERON:0001988,Diet,EFO:0002755,Low-protein and High-fiber diet Chronic Kidney Disease (CKD) patients,High-protein and Low-fiber diet Chronic Kidney Disease (CKD) patients,"Non-dialysis Chronic Kidney Disease (CKD) patients adhering to a high-protein, low-fiber diet. Individuals consuming ≥ 0.8 g/kg/day were classified as having high protein intake, fiiber intake was categorized based on the median intake of the study population, which was 8 g/day.",17,32,NA,16S,4,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table 2B,22 October 2025,Fiddyhamma,Fiddyhamma,The median relative abundance of key bacterial taxa (B) the low protein-high fiber diet vs. the high protein-low fiber diet.,decreased,NA,NA,Complete,KateRasheed
bsdb:41105770/1/1,41105770,case-control,41105770,https://doi.org/10.1126/sciadv.adw1410,https://www.science.org/doi/10.1126/sciadv.adw1410,"Pattaroni C., Macowan M., Chatzis R., Iacono G., Cardwell B., Gore M., Custovic A., Shields M.D., Power U.F., Grigg J., Roberts G., Ghazal P., Schwarze J., Turner S., Bush A., Saglani S., Lloyd C.M. , Marsland B.J.","Bacterial communities co-develop with respiratory immunity early in life, linking dysbiosis to systemic monocyte signature and wheezing",Science advances,2025,NA,Experiment 1,United Kingdom,Homo sapiens,Nose epithelium,UBERON:0019306,Age,EFO:0000246,Decreased with age (Week 1) in the Longitudinal (long) study group,Increased with age (Year 1) in the Longitudinal (long) study group,Increasing age of participants in the Longitudinal (long) study group,29,28,NA,16S,12,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Figure 2R,25 November 2025,Fiddyhamma,Fiddyhamma,Differential abundance (DA) of nasal bacterial microbiota using LINDA: Linear (Lin) Model for Differential Abundance (DA) Analysis of High-dimensional Compositional Data between week 1 and year 1; top 20 taxa shown.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis",3379134|976|200643|171549|171552|1283313;3379134|976|117743|200644|2762318|59735;1783272|1239|91061|1385|539738|1378|84135;3379134|1224|1236|135625|712|724;3379134|976|200643|171549|171552|2974257|425941;1783272|1239|91061|186826;3384189|32066|203490|203491|1129771|32067;3379134|1224|1236|2887326|468|475;3379134|1224|28216|206351|481|482;3379134|976|200643|171549|171551|836;3379134|976|200643|171549|171551|836|1583331;3384189|32066|203490|203491|1129771|34104;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|1305,Complete,KateRasheed
bsdb:41105770/1/2,41105770,case-control,41105770,https://doi.org/10.1126/sciadv.adw1410,https://www.science.org/doi/10.1126/sciadv.adw1410,"Pattaroni C., Macowan M., Chatzis R., Iacono G., Cardwell B., Gore M., Custovic A., Shields M.D., Power U.F., Grigg J., Roberts G., Ghazal P., Schwarze J., Turner S., Bush A., Saglani S., Lloyd C.M. , Marsland B.J.","Bacterial communities co-develop with respiratory immunity early in life, linking dysbiosis to systemic monocyte signature and wheezing",Science advances,2025,NA,Experiment 1,United Kingdom,Homo sapiens,Nose epithelium,UBERON:0019306,Age,EFO:0000246,Decreased with age (Week 1) in the Longitudinal (long) study group,Increased with age (Year 1) in the Longitudinal (long) study group,Increasing age of participants in the Longitudinal (long) study group,29,28,NA,16S,12,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 2,Figure 2R,25 November 2025,Fiddyhamma,Fiddyhamma,Differential abundance (DA) of nasal bacterial microbiota using LINDA: Linear (Lin) Model for Differential Abundance (DA) Analysis of High-dimensional Compositional Data between week 1 and year 1; top 20 taxa shown.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,1783272|1239|91061|1385|90964|1279,Complete,KateRasheed
bsdb:41105770/2/1,41105770,case-control,41105770,https://doi.org/10.1126/sciadv.adw1410,https://www.science.org/doi/10.1126/sciadv.adw1410,"Pattaroni C., Macowan M., Chatzis R., Iacono G., Cardwell B., Gore M., Custovic A., Shields M.D., Power U.F., Grigg J., Roberts G., Ghazal P., Schwarze J., Turner S., Bush A., Saglani S., Lloyd C.M. , Marsland B.J.","Bacterial communities co-develop with respiratory immunity early in life, linking dysbiosis to systemic monocyte signature and wheezing",Science advances,2025,NA,Experiment 2,United Kingdom,Homo sapiens,Nose epithelium,UBERON:0019306,Wheezing,EFO:0009715,Controls without Daycare correction (Cross sectional (CS) group),Parent-reported Wheezers without Daycare correction (Cross sectional (CS) group),Children in the Cross sectional (CS) group who had any wheezing events occurring within the first year,114,119,NA,16S,12,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Figure 4C,20 November 2025,Fiddyhamma,Fiddyhamma,Result of nasal bacteria LINDA: Linear (Lin) Model for Differential Abundance (DA) Analysis of High-dimensional Compositional Data testing between parent-reported wheezers and controls unadjusted for daycare attendance.,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella catarrhalis",3379134|1224|1236|135625|712|724|727;3379134|1224|1236|2887326|468|475|480,Complete,KateRasheed
bsdb:41105770/2/2,41105770,case-control,41105770,https://doi.org/10.1126/sciadv.adw1410,https://www.science.org/doi/10.1126/sciadv.adw1410,"Pattaroni C., Macowan M., Chatzis R., Iacono G., Cardwell B., Gore M., Custovic A., Shields M.D., Power U.F., Grigg J., Roberts G., Ghazal P., Schwarze J., Turner S., Bush A., Saglani S., Lloyd C.M. , Marsland B.J.","Bacterial communities co-develop with respiratory immunity early in life, linking dysbiosis to systemic monocyte signature and wheezing",Science advances,2025,NA,Experiment 2,United Kingdom,Homo sapiens,Nose epithelium,UBERON:0019306,Wheezing,EFO:0009715,Controls without Daycare correction (Cross sectional (CS) group),Parent-reported Wheezers without Daycare correction (Cross sectional (CS) group),Children in the Cross sectional (CS) group who had any wheezing events occurring within the first year,114,119,NA,16S,12,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,Figure 4C,20 November 2025,Fiddyhamma,Fiddyhamma,Result of nasal bacteria LINDA: Linear (Lin) Model for Differential Abundance (DA) Analysis of High-dimensional Compositional Data testing between parent-reported wheezers and controls unadjusted for daycare attendance.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella nanceiensis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis",1783272|201174|1760|2037|2049|1654;3384189|32066|203490|203491|203492|848|860;1783272|1239|91061|1385|539738|1378|1379;1783272|1239|91061|1385|539738|1378|84135;3379134|976|200643|171549|171552|2974257|425941;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|28037,Complete,KateRasheed
bsdb:41105770/3/1,41105770,case-control,41105770,https://doi.org/10.1126/sciadv.adw1410,https://www.science.org/doi/10.1126/sciadv.adw1410,"Pattaroni C., Macowan M., Chatzis R., Iacono G., Cardwell B., Gore M., Custovic A., Shields M.D., Power U.F., Grigg J., Roberts G., Ghazal P., Schwarze J., Turner S., Bush A., Saglani S., Lloyd C.M. , Marsland B.J.","Bacterial communities co-develop with respiratory immunity early in life, linking dysbiosis to systemic monocyte signature and wheezing",Science advances,2025,NA,Experiment 3,United Kingdom,Homo sapiens,Nose epithelium,UBERON:0019306,Wheezing,EFO:0009715,Controls with Daycare correction (Cross sectional (CS) group),Parent-reported Wheezers with Daycare correction (Cross sectional (CS) group,Children in the Cross sectional (CS) group adjusted for Daycare attendance who had any wheezing events occurring within the first year,114,119,NA,16S,12,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Figure 4D,20 November 2025,Fiddyhamma,Fiddyhamma,Result of nasal bacteria LINDA: Linear (Lin) Model for Differential Abundance (DA) Analysis of High-dimensional Compositional Data testing between parent-reported wheezers and controls adjusted for daycare attendance.,increased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,3379134|1224|1236|135625|712|724|727,Complete,KateRasheed
bsdb:41105770/3/2,41105770,case-control,41105770,https://doi.org/10.1126/sciadv.adw1410,https://www.science.org/doi/10.1126/sciadv.adw1410,"Pattaroni C., Macowan M., Chatzis R., Iacono G., Cardwell B., Gore M., Custovic A., Shields M.D., Power U.F., Grigg J., Roberts G., Ghazal P., Schwarze J., Turner S., Bush A., Saglani S., Lloyd C.M. , Marsland B.J.","Bacterial communities co-develop with respiratory immunity early in life, linking dysbiosis to systemic monocyte signature and wheezing",Science advances,2025,NA,Experiment 3,United Kingdom,Homo sapiens,Nose epithelium,UBERON:0019306,Wheezing,EFO:0009715,Controls with Daycare correction (Cross sectional (CS) group),Parent-reported Wheezers with Daycare correction (Cross sectional (CS) group,Children in the Cross sectional (CS) group adjusted for Daycare attendance who had any wheezing events occurring within the first year,114,119,NA,16S,12,Illumina,relative abundances,Linear Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,Figure 4D,20 November 2025,Fiddyhamma,Fiddyhamma,Result of nasal bacteria LINDA: Linear (Lin) Model for Differential Abundance (DA) Analysis of High-dimensional Compositional Data testing between parent-reported wheezers and controls adjusted for daycare attendance.,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|201174|1760|2037|2049|1654;1783272|1239|91061|1385|539738|1378|1379;1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:41105770/4/1,41105770,case-control,41105770,https://doi.org/10.1126/sciadv.adw1410,https://www.science.org/doi/10.1126/sciadv.adw1410,"Pattaroni C., Macowan M., Chatzis R., Iacono G., Cardwell B., Gore M., Custovic A., Shields M.D., Power U.F., Grigg J., Roberts G., Ghazal P., Schwarze J., Turner S., Bush A., Saglani S., Lloyd C.M. , Marsland B.J.","Bacterial communities co-develop with respiratory immunity early in life, linking dysbiosis to systemic monocyte signature and wheezing",Science advances,2025,NA,Experiment 4,United Kingdom,Homo sapiens,Nose epithelium,UBERON:0019306,Environmental factor,EFO:0000469,No Daycare attendance Cross sectional (CS) group,With Daycare attendance Cross sectional (CS) group,Children in the Cross sectional group who received daycare attendance,NA,NA,NA,16S,12,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Figure 3I,20 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant bacterial taxa associated with daycare,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella catarrhalis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae",3379134|1224|1236|2887326|468|475|480;3379134|1224|1236|135625|712|724|727;3379134|1224|1236|2887326|468,Complete,KateRasheed
bsdb:41105770/4/2,41105770,case-control,41105770,https://doi.org/10.1126/sciadv.adw1410,https://www.science.org/doi/10.1126/sciadv.adw1410,"Pattaroni C., Macowan M., Chatzis R., Iacono G., Cardwell B., Gore M., Custovic A., Shields M.D., Power U.F., Grigg J., Roberts G., Ghazal P., Schwarze J., Turner S., Bush A., Saglani S., Lloyd C.M. , Marsland B.J.","Bacterial communities co-develop with respiratory immunity early in life, linking dysbiosis to systemic monocyte signature and wheezing",Science advances,2025,NA,Experiment 4,United Kingdom,Homo sapiens,Nose epithelium,UBERON:0019306,Environmental factor,EFO:0000469,No Daycare attendance Cross sectional (CS) group,With Daycare attendance Cross sectional (CS) group,Children in the Cross sectional group who received daycare attendance,NA,NA,NA,16S,12,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,Figure 3I,20 November 2025,Fiddyhamma,Fiddyhamma,Differentially abundant bacterial taxa associated with daycare,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica",3379134|976|200643|171549|171551|836;1783272|1239|91061|186826|1300|1301|1305;3379134|1224|28216|206351|481|482;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|1385|539738|1378|1379;1783272|201174|1760|85007|1653|1716;1783272|201174|1760|85006|1268|32207;1783272|1239|91061|186826;3384189|32066|203490|203491|203492|848|860;1783272|201174|1760|2037|2049|1654;1783272|1239|91061|186826|1300|1301|28037;1783272|1239|909932|1843489|31977|29465|39777,Complete,KateRasheed
bsdb:41105770/5/1,41105770,case-control,41105770,https://doi.org/10.1126/sciadv.adw1410,https://www.science.org/doi/10.1126/sciadv.adw1410,"Pattaroni C., Macowan M., Chatzis R., Iacono G., Cardwell B., Gore M., Custovic A., Shields M.D., Power U.F., Grigg J., Roberts G., Ghazal P., Schwarze J., Turner S., Bush A., Saglani S., Lloyd C.M. , Marsland B.J.","Bacterial communities co-develop with respiratory immunity early in life, linking dysbiosis to systemic monocyte signature and wheezing",Science advances,2025,NA,Experiment 5,United Kingdom,Homo sapiens,Nose epithelium,UBERON:0019306,Time,EFO:0000721,"Sampling season: Summer, Autumn Cross sectional (CS) group",Sampling season: Winter Cross sectional (CS) group,Children in the Cross sectional group during Sampling season (Winter),NA,NA,NA,ITS / ITS2,NA,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3K,25 November 2025,Fiddyhamma,Fiddyhamma,Fungal taxa associated with season (summer versus winter),increased,"k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Cladosporium,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Polyporales|f__Phanerochaetaceae|g__Bjerkandera,k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Polyporales|f__Polyporaceae|g__Trametes|s__Trametes versicolor,k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Polyporales|f__Fomitopsidaceae|g__Daedalea|s__Daedalea confragosa",4751|4890|147541|2726946|452563|5498;4751|5204|155619|5303|396331|5330;4751|4890|147541|2726946|452563;4751|5204|155619|5303|5317|5324|5325;4751|5204|155619|5303|1769247|40436|2028083,Complete,KateRasheed
bsdb:41105770/5/2,41105770,case-control,41105770,https://doi.org/10.1126/sciadv.adw1410,https://www.science.org/doi/10.1126/sciadv.adw1410,"Pattaroni C., Macowan M., Chatzis R., Iacono G., Cardwell B., Gore M., Custovic A., Shields M.D., Power U.F., Grigg J., Roberts G., Ghazal P., Schwarze J., Turner S., Bush A., Saglani S., Lloyd C.M. , Marsland B.J.","Bacterial communities co-develop with respiratory immunity early in life, linking dysbiosis to systemic monocyte signature and wheezing",Science advances,2025,NA,Experiment 5,United Kingdom,Homo sapiens,Nose epithelium,UBERON:0019306,Time,EFO:0000721,"Sampling season: Summer, Autumn Cross sectional (CS) group",Sampling season: Winter Cross sectional (CS) group,Children in the Cross sectional group during Sampling season (Winter),NA,NA,NA,ITS / ITS2,NA,Illumina,relative abundances,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3K,25 November 2025,Fiddyhamma,Fiddyhamma,Fungal taxa associated with season (summer versus winter),decreased,"k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Cladosporium|s__Cladosporium herbarum,k__Fungi|p__Ascomycota|c__Dothideomycetes,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Sporobolomyces,k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Sporobolomyces|s__Sporobolomyces ruberrimus",4751|4890|147541|2726946|452563|5498|29918;4751|4890|147541;4751|5204|162481|231213|1799696|5429;4751|5204|162481|231213|1799696|5429|86828,Complete,KateRasheed
bsdb:41108012/1/1,41108012,"cross-sectional observational, not case-control",41108012,https://doi.org/10.1186/s42523-025-00464-2,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00464-2,"Woolley C.S.C., Muwonge A., de C Bronsvoort B.M., Schoenebeck J.J., Handel I.G., Chamberlain K., Rose E. , Clements D.N.",The gut microbiota of Labrador retriever puppies: a longitudinal cohort study,Animal microbiome,2025,"16S rRNA, Epidemiology, Labrador retrievers, Longitudinal studies",Experiment 1,United Kingdom,Canis lupus familiaris,Feces,UBERON:0001988,Timepoint,EFO:0000724,Decreased in wave 2,Increased in wave 2,Puppies whose owners provided faecal samples and Digestive health questionnaire (DHQs) at second timepoint when they were seven months of age,NA,NA,NA,16S,3,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 8; Suppl. figure 47,31 October 2025,Adiba Patel,"Adiba Patel,Fiddyhamma",Heatmap showing significantly differentially abundant amplicon sequence variants in Labrador Retriever puppy faecal samples,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|216572,Complete,KateRasheed
bsdb:41108012/1/2,41108012,"cross-sectional observational, not case-control",41108012,https://doi.org/10.1186/s42523-025-00464-2,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00464-2,"Woolley C.S.C., Muwonge A., de C Bronsvoort B.M., Schoenebeck J.J., Handel I.G., Chamberlain K., Rose E. , Clements D.N.",The gut microbiota of Labrador retriever puppies: a longitudinal cohort study,Animal microbiome,2025,"16S rRNA, Epidemiology, Labrador retrievers, Longitudinal studies",Experiment 1,United Kingdom,Canis lupus familiaris,Feces,UBERON:0001988,Timepoint,EFO:0000724,Decreased in wave 2,Increased in wave 2,Puppies whose owners provided faecal samples and Digestive health questionnaire (DHQs) at second timepoint when they were seven months of age,NA,NA,NA,16S,3,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 8; Suppl. figure 47,31 October 2025,Adiba Patel,"Adiba Patel,Fiddyhamma",Heatmap showing significantly differentially abundant amplicon sequence variants in Labrador Retriever puppy faecal samples,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira",3379134|976|200643|171549|815|816;1783272|201174|1760|85004|31953|1678;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|186802|31979|49082;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803;1783272|1239|186801|3082720|186804;3379134|29547|3031852|213849|72293|209;3379134|203691|203692|1643686|143786|29521,Complete,KateRasheed
bsdb:41108012/2/1,41108012,"cross-sectional observational, not case-control",41108012,https://doi.org/10.1186/s42523-025-00464-2,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00464-2,"Woolley C.S.C., Muwonge A., de C Bronsvoort B.M., Schoenebeck J.J., Handel I.G., Chamberlain K., Rose E. , Clements D.N.",The gut microbiota of Labrador retriever puppies: a longitudinal cohort study,Animal microbiome,2025,"16S rRNA, Epidemiology, Labrador retrievers, Longitudinal studies",Experiment 2,United Kingdom,Canis lupus familiaris,Feces,UBERON:0001988,Abnormal eating behavior,HP:0100738,Low Coprophagia score,High Coprophagia score,Puppies whose owners reported coprophagia behavior (eating feces),NA,NA,NA,16S,3,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 8; Suppl. figure 47,31 October 2025,Adiba Patel,"Adiba Patel,Fiddyhamma",Heatmap showing significantly differentially abundant amplicon sequence variants in Labrador Retriever puppy faecal samples,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",3379134|976|200643|171549|815|816;3379134|976|200643|171549|2005525|375288;1783272|1239|186801|186802|31979;3379134|976|200643|171549|171552|1283313;1783272|201174|1760|85004|31953|1678;1783272|1239|186801|186802|186807|2740;1783272|1239|186801|3085636|186803;1783272|1239|526524|526525|2810281|191303;1783272|1239|526524|526525|128827,Complete,KateRasheed
bsdb:41108012/3/3,41108012,"cross-sectional observational, not case-control",41108012,https://doi.org/10.1186/s42523-025-00464-2,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00464-2,"Woolley C.S.C., Muwonge A., de C Bronsvoort B.M., Schoenebeck J.J., Handel I.G., Chamberlain K., Rose E. , Clements D.N.",The gut microbiota of Labrador retriever puppies: a longitudinal cohort study,Animal microbiome,2025,"16S rRNA, Epidemiology, Labrador retrievers, Longitudinal studies",Experiment 3,United Kingdom,Canis lupus familiaris,Feces,UBERON:0001988,Diarrhea,HP:0002014,Decreased in diarrhea within 4 weeks,Increased in diarrhea within 4 weeks,Puppies whose owners reported diarrhea in the last 4 weeks,NA,NA,NA,16S,3,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 3,Fig. 8; Suppl. figure 47,13 January 2026,Fiddyhamma,Fiddyhamma,Heatmap showing significantly differentially abundant amplicon sequence variants in Labrador Retriever puppy faecal samples,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter",1783272|1239|186801|186802|31979|49082;1783272|1239|186801|3085636|186803;3379134|29547|3031852|213849|72293|209,Complete,KateRasheed
bsdb:41108012/3/4,41108012,"cross-sectional observational, not case-control",41108012,https://doi.org/10.1186/s42523-025-00464-2,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00464-2,"Woolley C.S.C., Muwonge A., de C Bronsvoort B.M., Schoenebeck J.J., Handel I.G., Chamberlain K., Rose E. , Clements D.N.",The gut microbiota of Labrador retriever puppies: a longitudinal cohort study,Animal microbiome,2025,"16S rRNA, Epidemiology, Labrador retrievers, Longitudinal studies",Experiment 3,United Kingdom,Canis lupus familiaris,Feces,UBERON:0001988,Diarrhea,HP:0002014,Decreased in diarrhea within 4 weeks,Increased in diarrhea within 4 weeks,Puppies whose owners reported diarrhea in the last 4 weeks,NA,NA,NA,16S,3,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 4,Fig. 8; Suppl. figure 47,13 January 2026,Fiddyhamma,Fiddyhamma,Heatmap showing significantly differentially abundant amplicon sequence variants in Labrador Retriever puppy faecal samples,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,3379134|976|200643|171549|171552|1283313,Complete,KateRasheed
bsdb:41108012/4/1,41108012,"cross-sectional observational, not case-control",41108012,https://doi.org/10.1186/s42523-025-00464-2,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00464-2,"Woolley C.S.C., Muwonge A., de C Bronsvoort B.M., Schoenebeck J.J., Handel I.G., Chamberlain K., Rose E. , Clements D.N.",The gut microbiota of Labrador retriever puppies: a longitudinal cohort study,Animal microbiome,2025,"16S rRNA, Epidemiology, Labrador retrievers, Longitudinal studies",Experiment 4,United Kingdom,Canis lupus familiaris,Feces,UBERON:0001988,Diarrhea,HP:0002014,Decreased in diarrhea within 4-8 weeks,Increased in diarrhea within 4-8 weeks,Puppies whose owners reported diarrhea between 4-8 weeks,NA,NA,NA,16S,3,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 8; Suppl. figure 47,13 January 2026,Fiddyhamma,Fiddyhamma,Heatmap showing significantly differentially abundant amplicon sequence variants in Labrador Retriever puppy faecal samples,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Cellulosilyticaceae|g__Cellulosilyticum",3379134|976|200643|171549;1783272|1239|186801|3085636|3018741|698776,Complete,NA
bsdb:41108012/5/1,41108012,"cross-sectional observational, not case-control",41108012,https://doi.org/10.1186/s42523-025-00464-2,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00464-2,"Woolley C.S.C., Muwonge A., de C Bronsvoort B.M., Schoenebeck J.J., Handel I.G., Chamberlain K., Rose E. , Clements D.N.",The gut microbiota of Labrador retriever puppies: a longitudinal cohort study,Animal microbiome,2025,"16S rRNA, Epidemiology, Labrador retrievers, Longitudinal studies",Experiment 5,United Kingdom,Canis lupus familiaris,Feces,UBERON:0001988,Diarrhea,HP:0002014,Decreased in diarrhea over 16 weeks,Increased in diarrhea over 16 weeks,Puppies whose owners reported diarrhea over 16 weeks,NA,NA,NA,16S,3,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 8; Suppl. figure 47,13 January 2026,Fiddyhamma,Fiddyhamma,Heatmap showing significantly differentially abundant amplicon sequence variants in Labrador Retriever puppy faecal samples,increased,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,1783272|201174|1760|85004|31953|1678,Complete,NA
bsdb:41108012/6/1,41108012,"cross-sectional observational, not case-control",41108012,https://doi.org/10.1186/s42523-025-00464-2,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00464-2,"Woolley C.S.C., Muwonge A., de C Bronsvoort B.M., Schoenebeck J.J., Handel I.G., Chamberlain K., Rose E. , Clements D.N.",The gut microbiota of Labrador retriever puppies: a longitudinal cohort study,Animal microbiome,2025,"16S rRNA, Epidemiology, Labrador retrievers, Longitudinal studies",Experiment 6,United Kingdom,Canis lupus familiaris,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Decreased in antibiotics use under 1 week,Increased in antibiotics use under 1 week,Puppies whose owners reported antibiotics use under 1 week,NA,NA,NA,16S,3,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 8; Suppl. figure 47,13 January 2026,Fiddyhamma,Fiddyhamma,Heatmap showing significantly differentially abundant amplicon sequence variants in Labrador Retriever puppy faecal samples,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma",1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803;3379134|1224|28216|80840|995019|577310;3379134|1224|1236|91347|543|1940338;1783272|544448|31969|186332|186333|2086,Complete,NA
bsdb:41108012/6/2,41108012,"cross-sectional observational, not case-control",41108012,https://doi.org/10.1186/s42523-025-00464-2,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00464-2,"Woolley C.S.C., Muwonge A., de C Bronsvoort B.M., Schoenebeck J.J., Handel I.G., Chamberlain K., Rose E. , Clements D.N.",The gut microbiota of Labrador retriever puppies: a longitudinal cohort study,Animal microbiome,2025,"16S rRNA, Epidemiology, Labrador retrievers, Longitudinal studies",Experiment 6,United Kingdom,Canis lupus familiaris,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Decreased in antibiotics use under 1 week,Increased in antibiotics use under 1 week,Puppies whose owners reported antibiotics use under 1 week,NA,NA,NA,16S,3,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 8; Suppl. figure 47,13 January 2026,Fiddyhamma,Fiddyhamma,Heatmap showing significantly differentially abundant amplicon sequence variants in Labrador Retriever puppy faecal samples,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",3379134|1224|28216|80840|995019|40544;1783272|1239|526524|526525|128827|1573535;1783272|1239|526524|526525|2810280|135858;1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803,Complete,NA
bsdb:41108012/7/1,41108012,"cross-sectional observational, not case-control",41108012,https://doi.org/10.1186/s42523-025-00464-2,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00464-2,"Woolley C.S.C., Muwonge A., de C Bronsvoort B.M., Schoenebeck J.J., Handel I.G., Chamberlain K., Rose E. , Clements D.N.",The gut microbiota of Labrador retriever puppies: a longitudinal cohort study,Animal microbiome,2025,"16S rRNA, Epidemiology, Labrador retrievers, Longitudinal studies",Experiment 7,United Kingdom,Canis lupus familiaris,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Decreased in antibiotics use 4-8 weeks ago,Increased in antibiotics use 4-8 weeks ago,Puppies whose owners reported antibiotics use 4-8 weeks ago,NA,NA,NA,16S,3,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 8; Suppl. figure 47,13 January 2026,Fiddyhamma,Fiddyhamma,Heatmap showing significantly differentially abundant amplicon sequence variants in Labrador Retriever puppy faecal samples,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,NA
bsdb:41108012/7/2,41108012,"cross-sectional observational, not case-control",41108012,https://doi.org/10.1186/s42523-025-00464-2,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00464-2,"Woolley C.S.C., Muwonge A., de C Bronsvoort B.M., Schoenebeck J.J., Handel I.G., Chamberlain K., Rose E. , Clements D.N.",The gut microbiota of Labrador retriever puppies: a longitudinal cohort study,Animal microbiome,2025,"16S rRNA, Epidemiology, Labrador retrievers, Longitudinal studies",Experiment 7,United Kingdom,Canis lupus familiaris,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Decreased in antibiotics use 4-8 weeks ago,Increased in antibiotics use 4-8 weeks ago,Puppies whose owners reported antibiotics use 4-8 weeks ago,NA,NA,NA,16S,3,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 8; Suppl. figure 47,13 January 2026,Fiddyhamma,Fiddyhamma,Heatmap showing significantly differentially abundant amplicon sequence variants in Labrador Retriever puppy faecal samples,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,3379134|976|200643|171549|171552|838,Complete,NA
bsdb:41108012/8/1,41108012,"cross-sectional observational, not case-control",41108012,https://doi.org/10.1186/s42523-025-00464-2,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00464-2,"Woolley C.S.C., Muwonge A., de C Bronsvoort B.M., Schoenebeck J.J., Handel I.G., Chamberlain K., Rose E. , Clements D.N.",The gut microbiota of Labrador retriever puppies: a longitudinal cohort study,Animal microbiome,2025,"16S rRNA, Epidemiology, Labrador retrievers, Longitudinal studies",Experiment 8,United Kingdom,Canis lupus familiaris,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Decreased in antibiotics use 8-16 weeks ago,Increased in antibiotics use 8-16 weeks ago,Puppies whose owners reported antibiotics use 8-16 weeks ago,NA,NA,NA,16S,3,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 8; Suppl. figure 47,13 January 2026,Fiddyhamma,Fiddyhamma,Heatmap showing significantly differentially abundant amplicon sequence variants in Labrador Retriever puppy faecal samples,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Allofournierella",1783272|1239|526524|526525|128827;1783272|1239|186801|186802|216572|1940255,Complete,NA
bsdb:41108012/9/1,41108012,"cross-sectional observational, not case-control",41108012,https://doi.org/10.1186/s42523-025-00464-2,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00464-2,"Woolley C.S.C., Muwonge A., de C Bronsvoort B.M., Schoenebeck J.J., Handel I.G., Chamberlain K., Rose E. , Clements D.N.",The gut microbiota of Labrador retriever puppies: a longitudinal cohort study,Animal microbiome,2025,"16S rRNA, Epidemiology, Labrador retrievers, Longitudinal studies",Experiment 9,United Kingdom,Canis lupus familiaris,Feces,UBERON:0001988,Environmental exposure measurement,EFO:0008360,Low dog contact score,High dog contact score,Puppies whose owners reported contact with other dogs,NA,NA,NA,16S,3,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 8; Suppl. figure 47,13 January 2026,Fiddyhamma,Fiddyhamma,Heatmap showing significantly differentially abundant amplicon sequence variants in Labrador Retriever puppy faecal samples,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",3379134|976|200643|171549|171552|1283313;1783272|1239|526524|526525|128827;3379134|1224|28216|80840|995019|40544,Complete,NA
bsdb:41108012/9/2,41108012,"cross-sectional observational, not case-control",41108012,https://doi.org/10.1186/s42523-025-00464-2,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00464-2,"Woolley C.S.C., Muwonge A., de C Bronsvoort B.M., Schoenebeck J.J., Handel I.G., Chamberlain K., Rose E. , Clements D.N.",The gut microbiota of Labrador retriever puppies: a longitudinal cohort study,Animal microbiome,2025,"16S rRNA, Epidemiology, Labrador retrievers, Longitudinal studies",Experiment 9,United Kingdom,Canis lupus familiaris,Feces,UBERON:0001988,Environmental exposure measurement,EFO:0008360,Low dog contact score,High dog contact score,Puppies whose owners reported contact with other dogs,NA,NA,NA,16S,3,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 8; Suppl. figure 47,13 January 2026,Fiddyhamma,Fiddyhamma,Heatmap showing significantly differentially abundant amplicon sequence variants in Labrador Retriever puppy faecal samples,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",1783272|201174|1760|85004|31953|1678;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|186802|3085642|580596;3379134|976|200643|171549|815|816,Complete,NA
bsdb:41108012/10/1,41108012,"cross-sectional observational, not case-control",41108012,https://doi.org/10.1186/s42523-025-00464-2,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00464-2,"Woolley C.S.C., Muwonge A., de C Bronsvoort B.M., Schoenebeck J.J., Handel I.G., Chamberlain K., Rose E. , Clements D.N.",The gut microbiota of Labrador retriever puppies: a longitudinal cohort study,Animal microbiome,2025,"16S rRNA, Epidemiology, Labrador retrievers, Longitudinal studies",Experiment 10,United Kingdom,Canis lupus familiaris,Feces,UBERON:0001988,Environmental exposure measurement,EFO:0008360,Low household waste score,High household waste score,Puppies whose owners reported consumption of household waste,NA,NA,NA,16S,3,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 8; Suppl. figure 47,13 January 2026,Fiddyhamma,Fiddyhamma,Heatmap showing significantly differentially abundant amplicon sequence variants in Labrador Retriever puppy faecal samples,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella",1783272|1239|186801|186802|31979|1485;1783272|1239|186801|3085636|186803|1506577,Complete,NA
bsdb:41108012/10/2,41108012,"cross-sectional observational, not case-control",41108012,https://doi.org/10.1186/s42523-025-00464-2,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00464-2,"Woolley C.S.C., Muwonge A., de C Bronsvoort B.M., Schoenebeck J.J., Handel I.G., Chamberlain K., Rose E. , Clements D.N.",The gut microbiota of Labrador retriever puppies: a longitudinal cohort study,Animal microbiome,2025,"16S rRNA, Epidemiology, Labrador retrievers, Longitudinal studies",Experiment 10,United Kingdom,Canis lupus familiaris,Feces,UBERON:0001988,Environmental exposure measurement,EFO:0008360,Low household waste score,High household waste score,Puppies whose owners reported consumption of household waste,NA,NA,NA,16S,3,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 8; Suppl. figure 47,13 January 2026,Fiddyhamma,Fiddyhamma,Heatmap showing significantly differentially abundant amplicon sequence variants in Labrador Retriever puppy faecal samples,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",3379134|976|200643|171549|2005525|375288;1783272|1239|909932|1843489|31977|906;1783272|201174|1760|85004|31953|1678,Complete,NA
bsdb:41108012/11/1,41108012,"cross-sectional observational, not case-control",41108012,https://doi.org/10.1186/s42523-025-00464-2,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00464-2,"Woolley C.S.C., Muwonge A., de C Bronsvoort B.M., Schoenebeck J.J., Handel I.G., Chamberlain K., Rose E. , Clements D.N.",The gut microbiota of Labrador retriever puppies: a longitudinal cohort study,Animal microbiome,2025,"16S rRNA, Epidemiology, Labrador retrievers, Longitudinal studies",Experiment 11,United Kingdom,Canis lupus familiaris,Feces,UBERON:0001988,Smoking status measurement,EFO:0006527,Decreased in smoking status (yes),Increased in smoking status (yes),Puppies whose owners reported smoking status as yes,NA,NA,NA,16S,3,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 8; Suppl. figure 47,13 January 2026,Fiddyhamma,Fiddyhamma,Heatmap showing significantly differentially abundant amplicon sequence variants in Labrador Retriever puppy faecal samples,increased,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,3379134|1224|28216|80840|995019|577310,Complete,NA
bsdb:41108012/12/1,41108012,"cross-sectional observational, not case-control",41108012,https://doi.org/10.1186/s42523-025-00464-2,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00464-2,"Woolley C.S.C., Muwonge A., de C Bronsvoort B.M., Schoenebeck J.J., Handel I.G., Chamberlain K., Rose E. , Clements D.N.",The gut microbiota of Labrador retriever puppies: a longitudinal cohort study,Animal microbiome,2025,"16S rRNA, Epidemiology, Labrador retrievers, Longitudinal studies",Experiment 12,United Kingdom,Canis lupus familiaris,Feces,UBERON:0001988,Hair color,EFO:0003924,Decreased in color-chocolate,Increased in color-chocolate,Puppies whose owners reported their fur color as chocolate,NA,NA,NA,16S,3,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 8; Suppl. figure 47,13 January 2026,Fiddyhamma,Fiddyhamma,Heatmap showing significantly differentially abundant amplicon sequence variants in Labrador Retriever puppy faecal samples,increased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,3379134|976|200643|171549|815|816,Complete,NA
bsdb:41108012/13/1,41108012,"cross-sectional observational, not case-control",41108012,https://doi.org/10.1186/s42523-025-00464-2,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00464-2,"Woolley C.S.C., Muwonge A., de C Bronsvoort B.M., Schoenebeck J.J., Handel I.G., Chamberlain K., Rose E. , Clements D.N.",The gut microbiota of Labrador retriever puppies: a longitudinal cohort study,Animal microbiome,2025,"16S rRNA, Epidemiology, Labrador retrievers, Longitudinal studies",Experiment 13,United Kingdom,Canis lupus familiaris,Feces,UBERON:0001988,Hair color,EFO:0003924,Decreased in color-fox red,Increased in color-fox red,Puppies whose owners reported their fur color as fox red,NA,NA,NA,16S,3,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 8; Suppl. figure 47,13 January 2026,Fiddyhamma,Fiddyhamma,Heatmap showing significantly differentially abundant amplicon sequence variants in Labrador Retriever puppy faecal samples,decreased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,1783272|1239|186801|186802|216572,Complete,NA
bsdb:41108012/14/1,41108012,"cross-sectional observational, not case-control",41108012,https://doi.org/10.1186/s42523-025-00464-2,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00464-2,"Woolley C.S.C., Muwonge A., de C Bronsvoort B.M., Schoenebeck J.J., Handel I.G., Chamberlain K., Rose E. , Clements D.N.",The gut microbiota of Labrador retriever puppies: a longitudinal cohort study,Animal microbiome,2025,"16S rRNA, Epidemiology, Labrador retrievers, Longitudinal studies",Experiment 14,United Kingdom,Canis lupus familiaris,Feces,UBERON:0001988,Timepoint,EFO:0000724,Decreased in wave 3,Increased in wave 3,Puppies whose owners provided faecal samples and Digestive health questionnaire (DHQs) at second timepoint when they were twelve months of age,NA,NA,NA,16S,3,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 8; Suppl. figure 47,13 January 2026,Fiddyhamma,Fiddyhamma,Heatmap showing significantly differentially abundant amplicon sequence variants in Labrador Retriever puppy faecal samples,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia",3379134|976|200643|171549|815|816;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|3085636|186803;3379134|1224|28216|80840|995019|577310;1783272|544448|31969|186332|186333|2086;1783272|1239|526524|526525|2810280|3025755,Complete,NA
bsdb:41108012/14/2,41108012,"cross-sectional observational, not case-control",41108012,https://doi.org/10.1186/s42523-025-00464-2,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00464-2,"Woolley C.S.C., Muwonge A., de C Bronsvoort B.M., Schoenebeck J.J., Handel I.G., Chamberlain K., Rose E. , Clements D.N.",The gut microbiota of Labrador retriever puppies: a longitudinal cohort study,Animal microbiome,2025,"16S rRNA, Epidemiology, Labrador retrievers, Longitudinal studies",Experiment 14,United Kingdom,Canis lupus familiaris,Feces,UBERON:0001988,Timepoint,EFO:0000724,Decreased in wave 3,Increased in wave 3,Puppies whose owners provided faecal samples and Digestive health questionnaire (DHQs) at second timepoint when they were twelve months of age,NA,NA,NA,16S,3,Illumina,relative abundances,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 8; Suppl. figure 47,13 January 2026,Fiddyhamma,Fiddyhamma,Heatmap showing significantly differentially abundant amplicon sequence variants in Labrador Retriever puppy faecal samples,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Neoarthromitus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Tyzzerella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Anaerobiospirillum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",3379134|976|200643|171549|815|816;3379134|203691|203692|1643686|143786|29521;3379134|29547|3031852|213849|72293|209;1783272|1239|186801|186802|186806|1730;1783272|1239|186801|3085636|186803|572511;1783272|1239|186801|186802|31979|49082;1783272|1239|186801|3085636|186803|189330;1783272|1239|186801|3085636|186803|1506577;1783272|1239|186801|3085636|186803;1783272|1239|186801|186802|3085642|580596;1783272|1239|186801|186802|216572;3379134|1224|1236|135624|83763|13334;3379134|1224|1236|135624;3379134|1224|28216|80840|995019|40544;1783272|201174|1760|85004|31953|1678;1783272|201174|84998|84999|84107|102106,Complete,NA
bsdb:41118383/1/1,41118383,case-control,41118383,10.1371/journal.pone.0334311,NA,"Huang A., Su M., Zhang S., Zhao C., Luo Y., Long Y., Lin D., Li S., Shen C., Li Q., Cai Y., Wang L., Liu J. , Chen C.",Alterations in the gut microbiota of alcoholic cirrhosis patients infected with Clonorchis sinensis in the Pearl River Delta region of China,PloS one,2025,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Clonorchiasis,EFO:0007210,Non-infected alcoholic cirrhosis patients (Non),Clonorchis sinensis-infected alcoholic cirrhosis patients (Cs),Patients diagnosed with alcoholic liver cirrhosis who are infected with the liver fluke Clonorchis sinensis,32,32,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Figure 4C, 4D",31 October 2025,Nina Takang,"Nina Takang,Tosin",Cladogram and Histogram from linear discriminant analysis effect size (LEfSe) analysis between alcoholic cirrhosis patients with Clonorchis sinensis infection (Cs) compared to alcoholic cirrhosis patients without Clonorchis sinensis infection (Non).,increased,"k__Bacillati|p__Bacillota,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacillati|p__Actinomycetota|c__Coriobacteriia,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae",1783272|1239;1783272|201174|84998|84999|84107|102106;1783272|1239|526524|526525|2810280;1783272|1239|186801|3085636|186803|33042;1783272|201174|84998|84999|84107;1783272|201174|84998|84999;1783272|201174|84998;1783272|1239|186801|3085636|186803|189330;1783272|1239|909932|909929|1843491|158846;3379134|976|200643|171549|171552;1783272|1239|186801|3085636|186803|841;1783272|1239|909932|909929|1843491,Complete,KateRasheed
bsdb:41118383/1/2,41118383,case-control,41118383,10.1371/journal.pone.0334311,NA,"Huang A., Su M., Zhang S., Zhao C., Luo Y., Long Y., Lin D., Li S., Shen C., Li Q., Cai Y., Wang L., Liu J. , Chen C.",Alterations in the gut microbiota of alcoholic cirrhosis patients infected with Clonorchis sinensis in the Pearl River Delta region of China,PloS one,2025,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Clonorchiasis,EFO:0007210,Non-infected alcoholic cirrhosis patients (Non),Clonorchis sinensis-infected alcoholic cirrhosis patients (Cs),Patients diagnosed with alcoholic liver cirrhosis who are infected with the liver fluke Clonorchis sinensis,32,32,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Figure 4C, 4D",31 October 2025,Nina Takang,"Nina Takang,Tosin",Cladogram and Histogram from linear discriminant analysis effect size (LEfSe) analysis between alcoholic cirrhosis patients with Clonorchis sinensis infection (Cs) compared to alcoholic cirrhosis patients without Clonorchis sinensis infection (Non).,decreased,"k__Pseudomonadati|p__Acidobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Pseudomonadati|p__Pseudomonadota,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|57723;3379134|1224|1236|91347;3379134|1224|1236|91347|543;3379134|1224|1236;3379134|1224|1236|135625|712|724;3379134|1224;3379134|1224|1236|91347|543|1940338,Complete,KateRasheed
bsdb:41121269/1/1,41121269,case-control,41121269,https://doi.org/10.1186/s13099-025-00712-5,https://pubmed.ncbi.nlm.nih.gov/41121269/,"Haque S., Bantun F., Jalal N.A., Faidah H., Babalghith A.O., Alobaidy M.A., Aldairi A.F. , Ahmad F.",Gut microbiota alterations and their association with tumorigenic pathways in colorectal cancer: insights from a pooled analysis of 109 microbiome datasets,Gut pathogens,2025,"Colorectal cancer, Gut microbiota, Immune checkpoint inhibitors, Inflammation",Experiment 1,Austria,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls,Colorectal cancer (CRC) patients,"Colorectal cancer (CRC) patients included in this study consisted of 46 individuals with a confirmed diagnosis of colorectal cancer; a type of cancer that starts in the colon (large intestine) or rectum, often developing from small, benign growths called polyps that become cancerous over time.",63,46,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure 3A and Figure 4A,10 December 2025,Arnold Pakis,"Arnold Pakis,Tosin",Differential abundance and predictive microbial taxa in colorectal cancer (CRC) using Linear Discriminant Analysis Effect Size (LEfSe).,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri",3379134|976|200643|171549|171550|239759|328813;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|28111;1783272|1239|909932|1843489|31977|39948|218538;3366610|28890|183925|2158|2159|2172|2173;3379134|976|200643|171549|2005525|375288|46503;3379134|976|200643|171549|171552|2974251|165179,Complete,KateRasheed
bsdb:41121269/1/2,41121269,case-control,41121269,https://doi.org/10.1186/s13099-025-00712-5,https://pubmed.ncbi.nlm.nih.gov/41121269/,"Haque S., Bantun F., Jalal N.A., Faidah H., Babalghith A.O., Alobaidy M.A., Aldairi A.F. , Ahmad F.",Gut microbiota alterations and their association with tumorigenic pathways in colorectal cancer: insights from a pooled analysis of 109 microbiome datasets,Gut pathogens,2025,"Colorectal cancer, Gut microbiota, Immune checkpoint inhibitors, Inflammation",Experiment 1,Austria,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls,Colorectal cancer (CRC) patients,"Colorectal cancer (CRC) patients included in this study consisted of 46 individuals with a confirmed diagnosis of colorectal cancer; a type of cancer that starts in the colon (large intestine) or rectum, often developing from small, benign growths called polyps that become cancerous over time.",63,46,NA,16S,NA,Illumina,relative abundances,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Figure 3A and Figure 4A,10 December 2025,Arnold Pakis,"Arnold Pakis,Tosin",Differential abundance and predictive microbial taxa in colorectal cancer (CRC) using Linear Discriminant Analysis Effect Size (LEfSe),decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Otoolea|s__[Clostridium] symbiosum,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi",1783272|201174|1760|85004|31953|1678|28025;1783272|1239|186801|186802|216572|1263|457412;1783272|1239|91061|186826|1300|1301|1308;1783272|1239|186801|3085636|186803|2941495|1512;3379134|1224|1236|72274|135621|286;1783272|1239|186801|3085636|186803|1649459|154046,Complete,KateRasheed
bsdb:41121269/2/1,41121269,case-control,41121269,https://doi.org/10.1186/s13099-025-00712-5,https://pubmed.ncbi.nlm.nih.gov/41121269/,"Haque S., Bantun F., Jalal N.A., Faidah H., Babalghith A.O., Alobaidy M.A., Aldairi A.F. , Ahmad F.",Gut microbiota alterations and their association with tumorigenic pathways in colorectal cancer: insights from a pooled analysis of 109 microbiome datasets,Gut pathogens,2025,"Colorectal cancer, Gut microbiota, Immune checkpoint inhibitors, Inflammation",Experiment 2,Austria,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls,Colorectal cancer (CRC) patients,"Colorectal cancer (CRC) patients included in this study consisted of 46 individuals with a confirmed diagnosis of colorectal cancer; a type of cancer that starts in the colon (large intestine) or rectum, often developing from small, benign growths called polyps that become cancerous over time.",63,46,NA,16S,NA,Illumina,centered log-ratio,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure 3C,19 January 2026,Tosin,Tosin,Differentially abundant and predictive microbial taxa in colorectal cancer (CRC) using random forest (RF) analyses.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium D16,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella hathewayi",3379134|976|200643|171549|171550|239759|328813;1783272|1239|909932|1843489|31977|39948|218538;1783272|1239|91061|1385|539738|1378|29391;3366610|28890|183925|2158|2159|2172|2173;1783272|1239|186801|186802|216572|1017280|106588;1783272|1239|186801|186802|216572|552398;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|526524|526525|128827|123375|102148;1783272|1239|186801|186802|216572|459786;1783272|1239|1737404|1737405|1570339|543311;3379134|976|200643|171549|171550|239759|214856;1783272|1239|526524|526525|128827|1573535|1735;3379134|976|200643|171549|171550|239759|28117;1783272|1239|186801|3085636|186803|1649459|154046,Complete,KateRasheed
bsdb:41121269/2/2,41121269,case-control,41121269,https://doi.org/10.1186/s13099-025-00712-5,https://pubmed.ncbi.nlm.nih.gov/41121269/,"Haque S., Bantun F., Jalal N.A., Faidah H., Babalghith A.O., Alobaidy M.A., Aldairi A.F. , Ahmad F.",Gut microbiota alterations and their association with tumorigenic pathways in colorectal cancer: insights from a pooled analysis of 109 microbiome datasets,Gut pathogens,2025,"Colorectal cancer, Gut microbiota, Immune checkpoint inhibitors, Inflammation",Experiment 2,Austria,Homo sapiens,Feces,UBERON:0001988,Colorectal cancer,EFO:0005842,Healthy controls,Colorectal cancer (CRC) patients,"Colorectal cancer (CRC) patients included in this study consisted of 46 individuals with a confirmed diagnosis of colorectal cancer; a type of cancer that starts in the colon (large intestine) or rectum, often developing from small, benign growths called polyps that become cancerous over time.",63,46,NA,16S,NA,Illumina,centered log-ratio,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Figure 3C,19 January 2026,Tosin,Tosin,Differentially abundant and predictive microbial taxa in colorectal cancer (CRC) using random forest (RF) analyses.,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,1783272|1239|91061|186826|1300|1301|1308,Complete,KateRasheed
bsdb:41126356/1/1,41126356,"case-control,laboratory experiment",41126356,https://doi.org/10.1186/s40168-025-02204-9,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-025-02204-9,"Ba F., Wang W., Huang Y., Zhang S., Qiu B., Xie S., Xu L., Gao W., Zhang X., Wen Z., Wang Q., Gao H., Sheng G., Berglund B., Li P., Li L. , Yao M.",Improving fecal transplantation precision for enhanced maturation of intestinal function in germ-free mice through microencapsulation and probiotic intervention,Microbiome,2025,"Pediococcus pentosaceus Li05, Bile acids, Fecal microbiota transplantation, Gut microbiota, Intestinal function, Microencapsulation, Sporobiota",Experiment 1,China,Mus musculus,"Colon,Feces","UBERON:0001155,UBERON:0001988","Abnormality of the gastrointestinal tract,Abnormal intestine morphology","HP:0002242,HP:0011024","C(NF, LF)","Li05-modulated(eNF, eLF)",germ-free mice receiving fecal microbiota derived from donors treated with probiotic Pediococcus pentosaceus Li05 and/or microencapsulated formulations.,12,12,NA,16S,34,Illumina,relative abundances,"ANOVA,Kruskall-Wallis,LEfSe,Pearson Correlation",0.05,FALSE,2,NA,NA,unchanged,decreased,unchanged,unchanged,unchanged,unchanged,Signature 1,Supplementary Table (S4); Figure 6 (b&c),30 October 2025,Adiba Patel,Adiba Patel,"Probiotic Li05 treatment enhanced colonization of beneficial gut commensals, especially mucin-degraders (Akkermansia) and short-chain fatty acid producers (Lachnospiraceae, Ruminococcus) correlating with improved gut barrier and epithelial maturation.",increased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum|s__Faecalibaculum rodentium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum|s__Muribaculum intestinale,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava",3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|815|816|85831;3379134|976|200643|171549|815|816|820;1783272|1239|526524|526525|128827|1729679|1702221;1783272|1239|186801|3085636|186803|877420;1783272|1239|91061|186826|33958|1578|33959;3379134|976|200643|171549|2005525|375288|823;1783272|1239|91061|186826|33958|1578|33959;3379134|976|200643|171549|171550|239759|214856;3379134|976|200643|171549|2005473|1918540|1796646;3379134|976|200643|171549|171552|1283313|671218,Complete,NA
bsdb:41126356/1/2,41126356,"case-control,laboratory experiment",41126356,https://doi.org/10.1186/s40168-025-02204-9,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-025-02204-9,"Ba F., Wang W., Huang Y., Zhang S., Qiu B., Xie S., Xu L., Gao W., Zhang X., Wen Z., Wang Q., Gao H., Sheng G., Berglund B., Li P., Li L. , Yao M.",Improving fecal transplantation precision for enhanced maturation of intestinal function in germ-free mice through microencapsulation and probiotic intervention,Microbiome,2025,"Pediococcus pentosaceus Li05, Bile acids, Fecal microbiota transplantation, Gut microbiota, Intestinal function, Microencapsulation, Sporobiota",Experiment 1,China,Mus musculus,"Colon,Feces","UBERON:0001155,UBERON:0001988","Abnormality of the gastrointestinal tract,Abnormal intestine morphology","HP:0002242,HP:0011024","C(NF, LF)","Li05-modulated(eNF, eLF)",germ-free mice receiving fecal microbiota derived from donors treated with probiotic Pediococcus pentosaceus Li05 and/or microencapsulated formulations.,12,12,NA,16S,34,Illumina,relative abundances,"ANOVA,Kruskall-Wallis,LEfSe,Pearson Correlation",0.05,FALSE,2,NA,NA,unchanged,decreased,unchanged,unchanged,unchanged,unchanged,Signature 2,Figure 6,30 October 2025,Adiba Patel,Adiba Patel,"Li05 modulation suppressed opportunistic/pathogenic taxa, reducing inflammatory potential and intestinal permeability.",decreased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio desulfuricans,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter hepaticus,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",3379134|200940|3031449|213115|194924|872|876;1783272|1239|91061|186826|81852|1350|1351;3379134|29547|3031852|213849|72293|209|32025;1783272|1239|526524|526525|2810281|191303|154288;3379134|1224|1236|91347|543|1940338,Complete,NA
bsdb:41126356/1/3,41126356,"case-control,laboratory experiment",41126356,https://doi.org/10.1186/s40168-025-02204-9,https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-025-02204-9,"Ba F., Wang W., Huang Y., Zhang S., Qiu B., Xie S., Xu L., Gao W., Zhang X., Wen Z., Wang Q., Gao H., Sheng G., Berglund B., Li P., Li L. , Yao M.",Improving fecal transplantation precision for enhanced maturation of intestinal function in germ-free mice through microencapsulation and probiotic intervention,Microbiome,2025,"Pediococcus pentosaceus Li05, Bile acids, Fecal microbiota transplantation, Gut microbiota, Intestinal function, Microencapsulation, Sporobiota",Experiment 1,China,Mus musculus,"Colon,Feces","UBERON:0001155,UBERON:0001988","Abnormality of the gastrointestinal tract,Abnormal intestine morphology","HP:0002242,HP:0011024","C(NF, LF)","Li05-modulated(eNF, eLF)",germ-free mice receiving fecal microbiota derived from donors treated with probiotic Pediococcus pentosaceus Li05 and/or microencapsulated formulations.,12,12,NA,16S,34,Illumina,relative abundances,"ANOVA,Kruskall-Wallis,LEfSe,Pearson Correlation",0.05,FALSE,2,NA,NA,unchanged,decreased,unchanged,unchanged,unchanged,unchanged,Signature 3,Figure 8; Supplementary Table 66,31 October 2025,Adiba Patel,Adiba Patel,"Early-life–associated and opportunistic genera decreased in abundance as puppies aged, consistent with the transition from a milk-adapted to an adult-like gut microbiota.",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens",1783272|1239|186801|186802|31979;1783272|201174|1760|85004|31953|1678;1783272|201174|84998|84999|84107|102106;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|1940338;1783272|1239|91061|186826|1300|1301;1783272|1239|186801|186802|31979|1485|1502,Complete,NA
bsdb:41137177/1/1,41137177,time series / longitudinal observational,41137177,https://doi.org/10.1186/s42523-025-00477-x,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00477-x#citeas,"Correa F., Luise D., Palladino G., Estellé J., Turroni S., Scicchitano D., Babbi G., Rampelli S., Candela M., Martelli P.L., Stefanelli C., Perez-Calvo E. , Trevisi P.",Early antimicrobial regimen shapes gut microbiota and health trajectories in pigs: a longitudinal study from weaning to finishing,Animal microbiome,2025,"AMR, Metagenomics, Microbial diversity, Oxidative stress, Polyamines",Experiment 1,Italy,Sus scrofa domesticus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Swine Production Chain 1(SPC2) T1- 21 days of life,Swine Production Chain 2(SPC1) T1- 21 days of life,SPC1 pigs that received a seven-day group treatment with lincomycin–spectinomycin,48,48,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,NA,unchanged,NA,Signature 1,Figure 2J,12 November 2025,Sally Kinyua,"Sally Kinyua,Temmie",LEfSe analysis discriminating between SPC1 and SPC2 at T1,increased,NA,NA,Complete,NA
bsdb:41137177/2/1,41137177,time series / longitudinal observational,41137177,https://doi.org/10.1186/s42523-025-00477-x,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00477-x#citeas,"Correa F., Luise D., Palladino G., Estellé J., Turroni S., Scicchitano D., Babbi G., Rampelli S., Candela M., Martelli P.L., Stefanelli C., Perez-Calvo E. , Trevisi P.",Early antimicrobial regimen shapes gut microbiota and health trajectories in pigs: a longitudinal study from weaning to finishing,Animal microbiome,2025,"AMR, Metagenomics, Microbial diversity, Oxidative stress, Polyamines",Experiment 2,Italy,Sus scrofa domesticus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Swine Production Chain 1(SPC2) T2- 42 days of life,Swine Production Chain 2(SPC1) T2- 42 days of life,SPC1 pigs that received a seven-day group treatment with lincomycin–spectinomycin,48,48,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,NA,decreased,NA,Signature 1,Figure 2K & Figure 3F,12 November 2025,Sally Kinyua,"Sally Kinyua,Temmie",LEfSe plots of genera discriminating between SPC1 and SPC2 at T2,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera",1783272|1239|186801|3085636|186803|189330|88431;1783272|1239|186801|3085636|186803|1407607|1150298;1783272|1239|909932|1843489|31977|906,Complete,NA
bsdb:41137177/2/2,41137177,time series / longitudinal observational,41137177,https://doi.org/10.1186/s42523-025-00477-x,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00477-x#citeas,"Correa F., Luise D., Palladino G., Estellé J., Turroni S., Scicchitano D., Babbi G., Rampelli S., Candela M., Martelli P.L., Stefanelli C., Perez-Calvo E. , Trevisi P.",Early antimicrobial regimen shapes gut microbiota and health trajectories in pigs: a longitudinal study from weaning to finishing,Animal microbiome,2025,"AMR, Metagenomics, Microbial diversity, Oxidative stress, Polyamines",Experiment 2,Italy,Sus scrofa domesticus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Swine Production Chain 1(SPC2) T2- 42 days of life,Swine Production Chain 2(SPC1) T2- 42 days of life,SPC1 pigs that received a seven-day group treatment with lincomycin–spectinomycin,48,48,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,decreased,decreased,NA,decreased,NA,Signature 2,Figure 2K & Figure 3F,12 November 2025,Sally Kinyua,"Sally Kinyua,Temmie",LEfSe plots of genera discriminating between SPC1 and SPC2 at T2,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp. oral clone HT002,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",1783272|1239|91061|186826|33958|1578|33959;1783272|1239|91061|186826|33958|1578|242643;1783272|1239|91061|186826|33958|2742598;3379134|976|200643|171549|2005473;1783272|1239|909932|1843488|909930|33024;1783272|1239|186801|3085636|186803|3570277|116085;1783272|1239|186801|186802|216572|3068309;3379134|203691|203692|136|2845253|157,Complete,NA
bsdb:41137177/3/1,41137177,time series / longitudinal observational,41137177,https://doi.org/10.1186/s42523-025-00477-x,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00477-x#citeas,"Correa F., Luise D., Palladino G., Estellé J., Turroni S., Scicchitano D., Babbi G., Rampelli S., Candela M., Martelli P.L., Stefanelli C., Perez-Calvo E. , Trevisi P.",Early antimicrobial regimen shapes gut microbiota and health trajectories in pigs: a longitudinal study from weaning to finishing,Animal microbiome,2025,"AMR, Metagenomics, Microbial diversity, Oxidative stress, Polyamines",Experiment 3,Italy,Sus scrofa domesticus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Swine Production Chain 1(SPC2) T3- 80 days of life,Swine Production Chain 2(SPC1) T3- 80 days of life,SPC1 pigs that received a seven-day group treatment with lincomycin–spectinomycin,47,46,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,increased,NA,unchanged,NA,Signature 1,Figure 2L & Figure 3G,12 November 2025,Sally Kinyua,"Sally Kinyua,Temmie",LEfSe plots of genera discriminating between SPC1 and SPC2 at T3,increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus porcorum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus amylovorus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",1783272|1239|186801|186802|3085642|580596|1945634;1783272|1239|91061|186826|33958|1578|1604;3379134|976|200643|171549|171552|838;3379134|203691|203692|136|2845253|157,Complete,NA
bsdb:41137177/3/2,41137177,time series / longitudinal observational,41137177,https://doi.org/10.1186/s42523-025-00477-x,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00477-x#citeas,"Correa F., Luise D., Palladino G., Estellé J., Turroni S., Scicchitano D., Babbi G., Rampelli S., Candela M., Martelli P.L., Stefanelli C., Perez-Calvo E. , Trevisi P.",Early antimicrobial regimen shapes gut microbiota and health trajectories in pigs: a longitudinal study from weaning to finishing,Animal microbiome,2025,"AMR, Metagenomics, Microbial diversity, Oxidative stress, Polyamines",Experiment 3,Italy,Sus scrofa domesticus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Swine Production Chain 1(SPC2) T3- 80 days of life,Swine Production Chain 2(SPC1) T3- 80 days of life,SPC1 pigs that received a seven-day group treatment with lincomycin–spectinomycin,47,46,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,increased,NA,unchanged,NA,Signature 2,Figure 2L & Figure 2G,12 November 2025,Sally Kinyua,"Sally Kinyua,Temmie",LEfSe plots of genera discriminating between SPC1 and SPC2 at T3,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp. oral clone HT002,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii",1783272|1239|186801|186802|3085642;1783272|1239|186801|186802|216572|216851;1783272|1239|91061|186826|33958|1578|242643;1783272|1239|909932|1843489|31977|906;1783272|1239|91061|186826|33958|1578|33959;1783272|1239|91061|186826|33958|2742598|1598;1783272|1239|909932|1843489|31977|906|907,Complete,NA
bsdb:41137177/4/1,41137177,time series / longitudinal observational,41137177,https://doi.org/10.1186/s42523-025-00477-x,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00477-x#citeas,"Correa F., Luise D., Palladino G., Estellé J., Turroni S., Scicchitano D., Babbi G., Rampelli S., Candela M., Martelli P.L., Stefanelli C., Perez-Calvo E. , Trevisi P.",Early antimicrobial regimen shapes gut microbiota and health trajectories in pigs: a longitudinal study from weaning to finishing,Animal microbiome,2025,"AMR, Metagenomics, Microbial diversity, Oxidative stress, Polyamines",Experiment 4,Italy,Sus scrofa domesticus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Swine Production Chain 1(SPC2) T4- 98 days of life,Swine Production Chain 2(SPC1) T4- 98 days of life,SPC1 pigs that received a seven-day group treatment with lincomycin–spectinomycin,47,46,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,increased,NA,increased,NA,Signature 1,Figure 2M & Figure 3H,12 November 2025,Sally Kinyua,Sally Kinyua,LEfSe plots of bacterial species significantly associated with SPC1 or SPC at T4,increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus|s__Butyricicoccus porcorum,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Pseudocoprococcus|s__Pseudocoprococcus catus",3379134|976|200643|171549|171552|838;1783272|1239|186801|186802|3085642|580596|1945634;1783272|1239|91061|186826|33958|1578|33959;1783272|1239|91061|186826|33958|2742598|1598;1783272|1239|186801|3085636|186803|3570277|116085,Complete,NA
bsdb:41137177/4/2,41137177,time series / longitudinal observational,41137177,https://doi.org/10.1186/s42523-025-00477-x,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00477-x#citeas,"Correa F., Luise D., Palladino G., Estellé J., Turroni S., Scicchitano D., Babbi G., Rampelli S., Candela M., Martelli P.L., Stefanelli C., Perez-Calvo E. , Trevisi P.",Early antimicrobial regimen shapes gut microbiota and health trajectories in pigs: a longitudinal study from weaning to finishing,Animal microbiome,2025,"AMR, Metagenomics, Microbial diversity, Oxidative stress, Polyamines",Experiment 4,Italy,Sus scrofa domesticus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Swine Production Chain 1(SPC2) T4- 98 days of life,Swine Production Chain 2(SPC1) T4- 98 days of life,SPC1 pigs that received a seven-day group treatment with lincomycin–spectinomycin,47,46,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,increased,NA,increased,NA,Signature 2,Figure 2M & Figure 3H,14 November 2025,Sally Kinyua,Sally Kinyua,LEfSe plots of bacterial species significantly associated with SPC1 or SPC at T4,decreased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium mitsuokai,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus fermentans",1783272|1239|526524|526525|2810280|135858;1783272|1239|909932|1843489|31977|906;3379134|976|200643|171549|2005473;1783272|1239|909932|1843489|31977|906|907;1783272|1239|526524|526525|2810280|135858|100886;1783272|1239|909932|1843488|909930|33024|626940;1783272|201174|84998|84999|84107|102106|74426;1783272|1239|909932|1843488|909930|904|905,Complete,NA
bsdb:41137177/5/1,41137177,time series / longitudinal observational,41137177,https://doi.org/10.1186/s42523-025-00477-x,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00477-x#citeas,"Correa F., Luise D., Palladino G., Estellé J., Turroni S., Scicchitano D., Babbi G., Rampelli S., Candela M., Martelli P.L., Stefanelli C., Perez-Calvo E. , Trevisi P.",Early antimicrobial regimen shapes gut microbiota and health trajectories in pigs: a longitudinal study from weaning to finishing,Animal microbiome,2025,"AMR, Metagenomics, Microbial diversity, Oxidative stress, Polyamines",Experiment 5,Italy,Sus scrofa domesticus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Swine Production Chain 1(SCP2) T5- 278 days of life,Swine Production Chain 2(SCP1) T5- 278days of life,SPC1 pigs that received a seven-day group treatment with lincomycin–spectinomycin,42,41,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,increased,NA,unchanged,NA,Signature 1,Figure 2N & Figure 3J,12 November 2025,Sally Kinyua,"Sally Kinyua,Temmie",LEfSe plots of genera discriminating between SPC1 and SPC2 at T5,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis",1783272|1239|91061|186826|33958|1578|33959;1783272|1239|91061|186826|33958|2742598|1598;3379134|203691|203692|136|2845253|157;1783272|1239|526524|526525|2810281|191303|154288,Complete,NA
bsdb:41137177/5/2,41137177,time series / longitudinal observational,41137177,https://doi.org/10.1186/s42523-025-00477-x,https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-025-00477-x#citeas,"Correa F., Luise D., Palladino G., Estellé J., Turroni S., Scicchitano D., Babbi G., Rampelli S., Candela M., Martelli P.L., Stefanelli C., Perez-Calvo E. , Trevisi P.",Early antimicrobial regimen shapes gut microbiota and health trajectories in pigs: a longitudinal study from weaning to finishing,Animal microbiome,2025,"AMR, Metagenomics, Microbial diversity, Oxidative stress, Polyamines",Experiment 5,Italy,Sus scrofa domesticus,Feces,UBERON:0001988,Response to antibiotic,GO:0046677,Swine Production Chain 1(SCP2) T5- 278 days of life,Swine Production Chain 2(SCP1) T5- 278days of life,SPC1 pigs that received a seven-day group treatment with lincomycin–spectinomycin,42,41,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,increased,NA,unchanged,NA,Signature 2,Figure 2N & Figure 3J,14 November 2025,Sally Kinyua,Sally Kinyua,LEfSe plots of genera discriminating between SPC1 and SPC2 at T5,decreased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella copri,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium mitsuokai,k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens",1783272|1239|909932|1843489|31977|906;1783272|1239|909932|909929|1843491|52225;3379134|976|200643|171549|171552|2974251|165179;1783272|1239|909932|1843489|31977|906|907;1783272|1239|526524|526525|2810280|135858|100886;1783272|1239|909932|1843488|909930|33024|626940;1783272|201174|84998|84999|84107|102106|74426,Complete,NA
bsdb:41194195/1/1,41194195,laboratory experiment,41194195,10.1186/s42523-025-00482-0,NA,"Cansado-Utrilla C., Saldaña M.A., Golovko G., Khanipov K., Watson R.K., Wild A.L., Brettell L.E., Weaver S.C., Heinz E. , Hughes G.L.",Mosquito host background impacts microbiome-Zika virus interactions in field- and laboratory-reared Aedes aegypti,Animal microbiome,2025,NA,Experiment 1,United States of America,Aedes aegypti,"Body proper,Insect leg","UBERON:0013702,UBERON:0005895",Environmental history,EFO:0004444,Unexposed Galveston Aedes aegypti lab-line mosquitoes,Unexposed Rio Grande Valley (RGV) Aedes aegypti lab-line mosquitoes,Unexposed female Aedes aegypti lab-line mosquitoes from Rio Grande Valley (RGV) which consisted of blood meal without the Zika virus,40,40,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3E,8 November 2025,Tosin,Tosin,The heatmap showing the ANCOM-BC (Analysis of compositions of microbiomes with bias correction) results (adjusted p-value < 0.05) of enriched taxa (red) or depleted taxa (blue) in RGV (Rio Grande Valley) mosquitoes in comparison with Galveston mosquitoes within the unexposed group,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Alkanindiges,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Asaia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Duganella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leucobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Methylophilaceae|g__Methylophilus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Nevskiales|f__Nevskiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Perlucidibacaceae|g__Perlucidibaca,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Phenylobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Roseomonadaceae|g__Rhodovarius,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Taibaiella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Verrucomicrobium",3379134|1224|1236|2887326|468|469;3379134|1224|1236|2887326|468|222991;3379134|1224|28211|3120395|433|91914;3379134|1224|28211|204441|2829815|191;3379134|976|200643|171549;3379134|1224|28216|80840|75682|75654;1783272|201174|1760|85006|85023|55968;3379134|1224|28211|356|69277|68287;3379134|1224|28216|32003|32011|16;3379134|1224|1236|1775403|568386;1783272|201174|1760|85009|85015|1839;3379134|1224|28211|356|118882|528;3379134|976|117747|200666|84566|84567;3379134|1224|1236|72274|2887331|661182;3379134|1224|28211|204458|76892|20;3379134|1224|28216|80840|119060|48736;3379134|1224|28211|3120395|3385906|268408;3379134|976|1853228|1853229|563835|1434702;3379134|1224|28216|80840|80864|34072;3379134|74201|203494|48461|203557|2735,Complete,KateRasheed
bsdb:41194195/1/2,41194195,laboratory experiment,41194195,10.1186/s42523-025-00482-0,NA,"Cansado-Utrilla C., Saldaña M.A., Golovko G., Khanipov K., Watson R.K., Wild A.L., Brettell L.E., Weaver S.C., Heinz E. , Hughes G.L.",Mosquito host background impacts microbiome-Zika virus interactions in field- and laboratory-reared Aedes aegypti,Animal microbiome,2025,NA,Experiment 1,United States of America,Aedes aegypti,"Body proper,Insect leg","UBERON:0013702,UBERON:0005895",Environmental history,EFO:0004444,Unexposed Galveston Aedes aegypti lab-line mosquitoes,Unexposed Rio Grande Valley (RGV) Aedes aegypti lab-line mosquitoes,Unexposed female Aedes aegypti lab-line mosquitoes from Rio Grande Valley (RGV) which consisted of blood meal without the Zika virus,40,40,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3E,8 November 2025,Tosin,Tosin,The heatmap showing the ANCOM-BC (Analysis of compositions of microbiomes with bias correction) results (adjusted p-value < 0.05) of enriched taxa (red) or depleted taxa (blue) in RGV (Rio Grande Valley) mosquitoes in comparison with Galveston mosquitoes within the unexposed group,decreased,"k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Buttiauxella,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kluyvera,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Mucilaginibacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Rosenbergiella,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",3379134|74201|203494|48461|1647988|239934;3379134|976|200643|171549|171550|239759;3379134|1224|28211|204458|76892|41275;3379134|1224|1236|91347|543|82976;3379134|976|1853228|1853229|563835;3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543;3379134|976|117743|200644|49546|237;3379134|1224|1236|91347|543|579;1783272|1239|186801|3085636|186803;1783272|1239|91061|186826|33958|1578;3379134|976|117747|200666|84566|423349;1783272|201174|1760|85007|1762|1763;3379134|1224|28211|204457|41297|165696;3379134|1224|28211|204455|31989|265;3379134|1224|1236|91347|543|160674;3379134|1224|1236|91347|1903409|1356488;1783272|1239|526524|526525|2810281|191303,Complete,KateRasheed
bsdb:41194195/2/1,41194195,laboratory experiment,41194195,10.1186/s42523-025-00482-0,NA,"Cansado-Utrilla C., Saldaña M.A., Golovko G., Khanipov K., Watson R.K., Wild A.L., Brettell L.E., Weaver S.C., Heinz E. , Hughes G.L.",Mosquito host background impacts microbiome-Zika virus interactions in field- and laboratory-reared Aedes aegypti,Animal microbiome,2025,NA,Experiment 2,United States of America,Aedes aegypti,"Body proper,Insect leg","UBERON:0005895,UBERON:0013702",Exposure,EFO:0000487,Exposed Galveston Aedes aegypti lab-line mosquitoes,Exposed Rio Grande Valley (RGV) Aedes aegypti lab-line mosquitoes,Female Aedes aegypti lab-line mosquitoes from Rio Grande Valley (RGV) exposed but not infected with ZIKV (Zika virus infection),NA,NA,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3E,10 November 2025,Tosin,Tosin,The heatmap showing the ANCOM-BC (Analysis of compositions of microbiomes with bias correction) results (adjusted p-value < 0.05) of enriched taxa (red) or depleted taxa (blue) in RGV (Rio Grande Valley) mosquitoes in comparison with Galveston mosquitoes within the exposed group,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Perlucidibacaceae|g__Perlucidibaca,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Taibaiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Alkanindiges,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Asaia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Verrucomicrobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Buttiauxella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Rosenbergiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kluyvera,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Mucilaginibacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Duganella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leucobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Methylophilaceae|g__Methylophilus",3379134|1224|1236|72274|2887331|661182;3379134|976|1853228|1853229|563835|1434702;3379134|1224|1236|2887326|468|222991;3379134|1224|28211|204441|2829815|191;3379134|1224|28211|356|69277|68287;3379134|74201|203494|48461|1647988|239934;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549;1783272|1239|526524|526525|2810281|191303;3379134|1224|1236|91347|543|160674;3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543;1783272|1239|186801|3085636|186803;3379134|1224|28211|3120395|433|91914;3379134|74201|203494|48461|203557|2735;3379134|1224|1236|91347|543|82976;3379134|976|117743|200644|49546|237;3379134|976|200643|171549|171550|239759;3379134|1224|28211|204458|76892|41275;3379134|1224|28211|204455|31989|265;3379134|1224|1236|91347|1903409|1356488;3379134|1224|1236|91347|543|579;3379134|976|117747|200666|84566|423349;3379134|1224|28216|80840|75682|75654;3379134|1224|28216|80840|80864|34072;1783272|201174|1760|85006|85023|55968;3379134|1224|28216|32003|32011|16,Complete,KateRasheed
bsdb:41194195/2/2,41194195,laboratory experiment,41194195,10.1186/s42523-025-00482-0,NA,"Cansado-Utrilla C., Saldaña M.A., Golovko G., Khanipov K., Watson R.K., Wild A.L., Brettell L.E., Weaver S.C., Heinz E. , Hughes G.L.",Mosquito host background impacts microbiome-Zika virus interactions in field- and laboratory-reared Aedes aegypti,Animal microbiome,2025,NA,Experiment 2,United States of America,Aedes aegypti,"Body proper,Insect leg","UBERON:0005895,UBERON:0013702",Exposure,EFO:0000487,Exposed Galveston Aedes aegypti lab-line mosquitoes,Exposed Rio Grande Valley (RGV) Aedes aegypti lab-line mosquitoes,Female Aedes aegypti lab-line mosquitoes from Rio Grande Valley (RGV) exposed but not infected with ZIKV (Zika virus infection),NA,NA,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3E,10 November 2025,Tosin,Tosin,The heatmap showing the ANCOM-BC (Analysis of compositions of microbiomes with bias correction) results (adjusted p-value < 0.05) of enriched taxa (red) or depleted taxa (blue) in RGV (Rio Grande Valley) mosquitoes in comparison with Galveston mosquitoes within the exposed group,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Phenylobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Roseomonadaceae|g__Rhodovarius,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Nevskiales|f__Nevskiaceae,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium",1783272|201174|1760|85007|1762|1763;3379134|976|117747|200666|84566|84567;3379134|1224|28211|204458|76892|20;3379134|1224|28211|356|118882|528;3379134|1224|28216|80840|119060|48736;1783272|201174|1760|85009|85015|1839;3379134|1224|28211|3120395|3385906|268408;3379134|1224|1236|2887326|468|469;3379134|1224|1236|1775403|568386;3379134|976|1853228|1853229|563835;3379134|1224|28211|204457|41297|165696,Complete,KateRasheed
bsdb:41194195/3/1,41194195,laboratory experiment,41194195,10.1186/s42523-025-00482-0,NA,"Cansado-Utrilla C., Saldaña M.A., Golovko G., Khanipov K., Watson R.K., Wild A.L., Brettell L.E., Weaver S.C., Heinz E. , Hughes G.L.",Mosquito host background impacts microbiome-Zika virus interactions in field- and laboratory-reared Aedes aegypti,Animal microbiome,2025,NA,Experiment 3,United States of America,Aedes aegypti,"Body proper,Insect leg","UBERON:0005895,UBERON:0013702",Zika virus infectious disease,MONDO:0018661,Infected Galveston Aedes aegypti lab-line mosquitoes,Infected Rio Grande Valley (RGV) Aedes aegypti lab-line mosquitoes,Female Aedes aegypti lab-line mosquitoes from Rio Grande Valley (RGV) infected with ZIKV (Zika virus infection),NA,NA,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3E,10 November 2025,Tosin,Tosin,The heatmap showing the ANCOM-BC (Analysis of compositions of microbiomes with bias correction) results (adjusted p-value < 0.05) of enriched taxa (red) or depleted taxa (blue) in RGV (Rio Grande Valley) mosquitoes in comparison with Galveston mosquitoes within the infected group,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Perlucidibacaceae|g__Perlucidibaca,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Taibaiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Alkanindiges,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Azospirillum,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Asaia,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Verrucomicrobium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Buttiauxella,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodobacterales|f__Paracoccaceae|g__Paracoccus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Rosenbergiella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kluyvera,k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Mucilaginibacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Roseomonadaceae|g__Rhodovarius",3379134|1224|1236|72274|2887331|661182;3379134|976|1853228|1853229|563835|1434702;3379134|1224|1236|2887326|468|222991;3379134|1224|28211|204441|2829815|191;3379134|1224|28211|356|69277|68287;3379134|74201|203494|48461|1647988|239934;1783272|1239|91061|186826|33958|1578;3379134|976|200643|171549;1783272|1239|526524|526525|2810281|191303;1783272|1239|186801|3085636|186803;3379134|1224|28211|3120395|433|91914;3379134|74201|203494|48461|203557|2735;1783272|201174|1760|85007|1762|1763;3379134|1224|1236|91347|543|82976;3379134|976|117743|200644|49546|237;3379134|976|200643|171549|171550|239759;3379134|1224|28211|204458|76892|41275;3379134|1224|28211|204455|31989|265;3379134|1224|1236|91347|1903409|1356488;3379134|1224|1236|91347|543|579;3379134|976|117747|200666|84566|423349;3379134|1224|28211|356|118882|528;3379134|1224|28216|80840|119060|48736;1783272|201174|1760|85009|85015|1839;3379134|1224|28211|3120395|3385906|268408,Complete,KateRasheed
bsdb:41194195/3/2,41194195,laboratory experiment,41194195,10.1186/s42523-025-00482-0,NA,"Cansado-Utrilla C., Saldaña M.A., Golovko G., Khanipov K., Watson R.K., Wild A.L., Brettell L.E., Weaver S.C., Heinz E. , Hughes G.L.",Mosquito host background impacts microbiome-Zika virus interactions in field- and laboratory-reared Aedes aegypti,Animal microbiome,2025,NA,Experiment 3,United States of America,Aedes aegypti,"Body proper,Insect leg","UBERON:0005895,UBERON:0013702",Zika virus infectious disease,MONDO:0018661,Infected Galveston Aedes aegypti lab-line mosquitoes,Infected Rio Grande Valley (RGV) Aedes aegypti lab-line mosquitoes,Female Aedes aegypti lab-line mosquitoes from Rio Grande Valley (RGV) infected with ZIKV (Zika virus infection),NA,NA,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3E,10 November 2025,Tosin,Tosin,The heatmap showing the ANCOM-BC (Analysis of compositions of microbiomes with bias correction) results (adjusted p-value < 0.05) of enriched taxa (red) or depleted taxa (blue) in RGV (Rio Grande Valley) mosquitoes in comparison with Galveston mosquitoes within the infected group,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Duganella,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leucobacter,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Nitrosomonadales|f__Methylophilaceae|g__Methylophilus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Phenylobacterium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Pseudomonadati|p__Bacteroidota|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Nevskiales|f__Nevskiaceae",3379134|976|117747|200666|84566|84567;3379134|1224|1236|91347|543|160674;3379134|1224|1236|91347|543|544;3379134|1224|1236|91347|543;3379134|1224|28216|80840|75682|75654;3379134|1224|28216|80840|80864|34072;1783272|201174|1760|85006|85023|55968;3379134|1224|28216|32003|32011|16;3379134|1224|28211|204458|76892|20;3379134|1224|1236|2887326|468|469;3379134|976|1853228|1853229|563835;3379134|1224|28211|204457|41297|165696;3379134|1224|1236|1775403|568386,Complete,KateRasheed
bsdb:41194195/4/1,41194195,laboratory experiment,41194195,10.1186/s42523-025-00482-0,NA,"Cansado-Utrilla C., Saldaña M.A., Golovko G., Khanipov K., Watson R.K., Wild A.L., Brettell L.E., Weaver S.C., Heinz E. , Hughes G.L.",Mosquito host background impacts microbiome-Zika virus interactions in field- and laboratory-reared Aedes aegypti,Animal microbiome,2025,NA,Experiment 4,United States of America,Aedes aegypti,"Body proper,Insect leg","UBERON:0013702,UBERON:0005895",Exposure,EFO:0000487,Unexposed Galveston Aedes aegypti lab-line mosquitoes,Exposed Galveston Aedes aegypti lab-line mosquitoes,Female Aedes aegypti lab-line mosquitoes from Galveston exposed but not infected with ZIKV (Zika virus infection),40,NA,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4A,10 November 2025,Tosin,Tosin,Significant differential abundance of microbes between unexposed vs exposed Galveston lab mosquitoes,increased,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Asaia,3379134|1224|28211|3120395|433|91914,Complete,KateRasheed
bsdb:41194195/4/2,41194195,laboratory experiment,41194195,10.1186/s42523-025-00482-0,NA,"Cansado-Utrilla C., Saldaña M.A., Golovko G., Khanipov K., Watson R.K., Wild A.L., Brettell L.E., Weaver S.C., Heinz E. , Hughes G.L.",Mosquito host background impacts microbiome-Zika virus interactions in field- and laboratory-reared Aedes aegypti,Animal microbiome,2025,NA,Experiment 4,United States of America,Aedes aegypti,"Body proper,Insect leg","UBERON:0013702,UBERON:0005895",Exposure,EFO:0000487,Unexposed Galveston Aedes aegypti lab-line mosquitoes,Exposed Galveston Aedes aegypti lab-line mosquitoes,Female Aedes aegypti lab-line mosquitoes from Galveston exposed but not infected with ZIKV (Zika virus infection),40,NA,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4A,10 November 2025,Tosin,Tosin,Significant differential abundance of microbes between unexposed vs exposed Galveston lab mosquitoes,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter",3379134|1224|1236|91347|543|160674;3379134|1224|1236|91347|543;3379134|1224|1236|91347|543|544,Complete,KateRasheed
bsdb:41194195/5/1,41194195,laboratory experiment,41194195,10.1186/s42523-025-00482-0,NA,"Cansado-Utrilla C., Saldaña M.A., Golovko G., Khanipov K., Watson R.K., Wild A.L., Brettell L.E., Weaver S.C., Heinz E. , Hughes G.L.",Mosquito host background impacts microbiome-Zika virus interactions in field- and laboratory-reared Aedes aegypti,Animal microbiome,2025,NA,Experiment 5,United States of America,Aedes aegypti,"Body proper,Insect leg","UBERON:0005895,UBERON:0013702",Zika virus infectious disease,MONDO:0018661,Unexposed Galveston Aedes aegypti lab-line mosquitoes,Infected Galveston Aedes aegypti lab-line mosquitoes,Female Aedes aegypti lab-line mosquitoes from Galveston infected with ZIKV (Zika virus infection),40,NA,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4B,10 November 2025,Tosin,Tosin,Significant differential abundance of microbes between unexposed vs infected Galveston lab mosquitoes,increased,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Acetobacteraceae|g__Asaia,3379134|1224|28211|3120395|433|91914,Complete,KateRasheed
bsdb:41194195/5/2,41194195,laboratory experiment,41194195,10.1186/s42523-025-00482-0,NA,"Cansado-Utrilla C., Saldaña M.A., Golovko G., Khanipov K., Watson R.K., Wild A.L., Brettell L.E., Weaver S.C., Heinz E. , Hughes G.L.",Mosquito host background impacts microbiome-Zika virus interactions in field- and laboratory-reared Aedes aegypti,Animal microbiome,2025,NA,Experiment 5,United States of America,Aedes aegypti,"Body proper,Insect leg","UBERON:0005895,UBERON:0013702",Zika virus infectious disease,MONDO:0018661,Unexposed Galveston Aedes aegypti lab-line mosquitoes,Infected Galveston Aedes aegypti lab-line mosquitoes,Female Aedes aegypti lab-line mosquitoes from Galveston infected with ZIKV (Zika virus infection),40,NA,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4B,10 November 2025,Tosin,Tosin,Significant differential abundance of microbes between unexposed vs infected Galveston lab mosquitoes,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,3379134|1224|1236|91347|543|160674,Complete,KateRasheed
bsdb:41194195/6/1,41194195,laboratory experiment,41194195,10.1186/s42523-025-00482-0,NA,"Cansado-Utrilla C., Saldaña M.A., Golovko G., Khanipov K., Watson R.K., Wild A.L., Brettell L.E., Weaver S.C., Heinz E. , Hughes G.L.",Mosquito host background impacts microbiome-Zika virus interactions in field- and laboratory-reared Aedes aegypti,Animal microbiome,2025,NA,Experiment 6,United States of America,Aedes aegypti,"Body proper,Insect leg","UBERON:0005895,UBERON:0013702",Zika virus infectious disease,MONDO:0018661,Exposed Rio Grande Valley (RGV) Aedes aegypti lab-line mosquitoes,Infected Rio Grande Valley (RGV) Aedes aegypti lab-line mosquitoes,Female Aedes aegypti lab-line mosquitoes from Rio Grande Valley (RGV) infected with ZIKV (Zika virus infection),NA,NA,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4C,10 November 2025,Tosin,Tosin,Significant differential abundance of microbes between exposed vs infected Rio Grande Valley (RGV) lab mosquitoes,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",3379134|1224|1236|91347|543|160674;3379134|1224|1236|91347|543,Complete,KateRasheed
bsdb:41194195/7/1,41194195,laboratory experiment,41194195,10.1186/s42523-025-00482-0,NA,"Cansado-Utrilla C., Saldaña M.A., Golovko G., Khanipov K., Watson R.K., Wild A.L., Brettell L.E., Weaver S.C., Heinz E. , Hughes G.L.",Mosquito host background impacts microbiome-Zika virus interactions in field- and laboratory-reared Aedes aegypti,Animal microbiome,2025,NA,Experiment 7,United States of America,Aedes aegypti,"Body proper,Insect leg","UBERON:0005895,UBERON:0013702",Exposure,EFO:0000487,Unexposed Rio Grande Valley (RGV) Aedes aegypti lab-line mosquitoes,Exposed Rio Grande Valley (RGV) Aedes aegypti lab-line mosquitoes,Female Aedes aegypti lab-line mosquitoes from Rio Grande Valley (RGV) exposed but not infected with ZIKV (Zika virus infection),40,NA,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4D,10 November 2025,Tosin,Tosin,Significant differential abundance of microbes between unexposed vs exposed Rio Grande Valley (RGV) lab mosquitoes,increased,"k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",1783272|1239|526524|526525|2810281|191303;1783272|1239|91061|186826|33958|1578,Complete,KateRasheed
bsdb:41194195/8/1,41194195,laboratory experiment,41194195,10.1186/s42523-025-00482-0,NA,"Cansado-Utrilla C., Saldaña M.A., Golovko G., Khanipov K., Watson R.K., Wild A.L., Brettell L.E., Weaver S.C., Heinz E. , Hughes G.L.",Mosquito host background impacts microbiome-Zika virus interactions in field- and laboratory-reared Aedes aegypti,Animal microbiome,2025,NA,Experiment 8,United States of America,Aedes aegypti,"Body proper,Insect leg","UBERON:0013702,UBERON:0005895",Zika virus infectious disease,MONDO:0018661,Unexposed Rio Grande Valley (RGV) Aedes aegypti lab-line mosquitoes,Infected Rio Grande Valley (RGV) Aedes aegypti lab-line mosquitoes,Female Aedes aegypti lab-line mosquitoes from Rio Grande Valley (RGV) infected with ZIKV (Zika virus infection),40,NA,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 4E,10 November 2025,Tosin,Tosin,Significant differential abundance of microbes between unexposed vs infected Rio Grande Valley (RGV) lab mosquitoes,increased,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,3379134|74201|203494|48461|1647988|239934,Complete,KateRasheed
bsdb:41194195/8/2,41194195,laboratory experiment,41194195,10.1186/s42523-025-00482-0,NA,"Cansado-Utrilla C., Saldaña M.A., Golovko G., Khanipov K., Watson R.K., Wild A.L., Brettell L.E., Weaver S.C., Heinz E. , Hughes G.L.",Mosquito host background impacts microbiome-Zika virus interactions in field- and laboratory-reared Aedes aegypti,Animal microbiome,2025,NA,Experiment 8,United States of America,Aedes aegypti,"Body proper,Insect leg","UBERON:0013702,UBERON:0005895",Zika virus infectious disease,MONDO:0018661,Unexposed Rio Grande Valley (RGV) Aedes aegypti lab-line mosquitoes,Infected Rio Grande Valley (RGV) Aedes aegypti lab-line mosquitoes,Female Aedes aegypti lab-line mosquitoes from Rio Grande Valley (RGV) infected with ZIKV (Zika virus infection),40,NA,NA,16S,34,Illumina,log transformation,ANCOM-BC,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 4E,10 November 2025,Tosin,Tosin,Significant differential abundance of microbes between unexposed vs infected Rio Grande Valley (RGV) lab mosquitoes,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,3379134|1224|1236|91347|543|544,Complete,KateRasheed
bsdb:41205569/1/1,41205569,laboratory experiment,41205569,10.1016/j.ecoenv.2025.119311,NA,"Mayr A.V., Weinhold A., Nolzen A., Keller A. , Ayasse M.",The neonicotinoid Acetamiprid alters the chemical profile of the primitive eusocial bee Lasioglossum malachurum,Ecotoxicology and environmental safety,2025,"Bee health, Chemical communication, Chemical ecology, Cuticular lipids, Functional traits, Halictidae, Insecticides, Microbiome, Wild bees",Experiment 1,Germany,Lasioglossum malachurum,Intestine,UBERON:0000160,Pesticide exposure measurement,EFO:0007840,Field,Acetamiprid,Colony of bees that was fed a sugar solution containing the neonicotinoid Acetamiprid at a 50 ng/g concentration.,19,18,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Figure 3a, Text in 3.3 section Results",11 November 2025,YokoC,YokoC,Boxplots for the relative abundance of Apilactobacillus from the microbiome analysis of field bees compared to the 7 day treatment groups from the laboratory experiment (Acetamiprid and control).,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Apilactobacillus,1783272|1239|91061|186826|33958|2767877,Complete,NA
bsdb:41205569/2/1,41205569,laboratory experiment,41205569,10.1016/j.ecoenv.2025.119311,NA,"Mayr A.V., Weinhold A., Nolzen A., Keller A. , Ayasse M.",The neonicotinoid Acetamiprid alters the chemical profile of the primitive eusocial bee Lasioglossum malachurum,Ecotoxicology and environmental safety,2025,"Bee health, Chemical communication, Chemical ecology, Cuticular lipids, Functional traits, Halictidae, Insecticides, Microbiome, Wild bees",Experiment 2,Germany,Lasioglossum malachurum,Intestine,UBERON:0000160,Pesticide exposure measurement,EFO:0007840,Field,Laboratory Control,Laboratory colony of bees that was fed a sugar solution for 7 days.,19,21,NA,16S,4,Illumina,raw counts,Linear Regression,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Figure 3a, Text in 3.3 section Results",11 November 2025,YokoC,YokoC,Boxplots for the relative abundance of Apilactobacillus from the microbiome analysis of field bees compared to the 7 day treatment groups from the laboratory experiment (Acetamiprid and control).,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Apilactobacillus,1783272|1239|91061|186826|33958|2767877,Complete,NA
bsdb:41209719/1/1,41209719,"cross-sectional observational, not case-control",41209719,https://doi.org/10.1016/j.crmicr.2025.100492,https://www.sciencedirect.com/science/article/pii/S2666517425001531?via=ihub,"Amina Tufail, Bushra Nisar Khan, Fumin Lei, Gang Song, Jianshi Jin, Jundong Duan, Na Zhao, Sandi Willows-Munro, Tingbei Bo, Yanhua Qu","Exploring microbiome shifts across taxonomic and ecological groups of birds at a key stopover site in Punjab, Pakistan",Current Research in Microbial Sciences,NA,"Avian ecological types, Punjab, River Ravi, Zoonotic pathogens, functional prediction, gut microbiome, habitat",Experiment 1,Pakistan,Aves,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Wader,Kingfisher,"Kingfishers are a family, the Alcedinidae, of small to medium-sized, brightly coloured birds in the order Coraciiformes.",10,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6A,28 October 2025,Adiba Patel,"Lwaldron,Fiddyhamma,Adiba Patel",Linear discriminant analysis effect size (LEfSe) identifying bacterial genera with significant differences among avian ecological types,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pygmaiobacter",1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|3085636|186803|1432051;3379134|74152|641853;1783272|1239|186801|186802|216572|1929305,Complete,KateRasheed
bsdb:41209719/1/2,41209719,"cross-sectional observational, not case-control",41209719,https://doi.org/10.1016/j.crmicr.2025.100492,https://www.sciencedirect.com/science/article/pii/S2666517425001531?via=ihub,"Amina Tufail, Bushra Nisar Khan, Fumin Lei, Gang Song, Jianshi Jin, Jundong Duan, Na Zhao, Sandi Willows-Munro, Tingbei Bo, Yanhua Qu","Exploring microbiome shifts across taxonomic and ecological groups of birds at a key stopover site in Punjab, Pakistan",Current Research in Microbial Sciences,NA,"Avian ecological types, Punjab, River Ravi, Zoonotic pathogens, functional prediction, gut microbiome, habitat",Experiment 1,Pakistan,Aves,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Wader,Kingfisher,"Kingfishers are a family, the Alcedinidae, of small to medium-sized, brightly coloured birds in the order Coraciiformes.",10,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6A,12 November 2025,Adiba Patel,"Lwaldron,Fiddyhamma,Adiba Patel",Linear discriminant analysis effect size (LEfSe) identifying bacterial genera with significant differences among avian ecological types,decreased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,1783272|1239|91061|186826|33958|1578,Complete,KateRasheed
bsdb:41209719/2/1,41209719,"cross-sectional observational, not case-control",41209719,https://doi.org/10.1016/j.crmicr.2025.100492,https://www.sciencedirect.com/science/article/pii/S2666517425001531?via=ihub,"Amina Tufail, Bushra Nisar Khan, Fumin Lei, Gang Song, Jianshi Jin, Jundong Duan, Na Zhao, Sandi Willows-Munro, Tingbei Bo, Yanhua Qu","Exploring microbiome shifts across taxonomic and ecological groups of birds at a key stopover site in Punjab, Pakistan",Current Research in Microbial Sciences,NA,"Avian ecological types, Punjab, River Ravi, Zoonotic pathogens, functional prediction, gut microbiome, habitat",Experiment 2,Pakistan,Aves,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Gruiformes,Coraciiformes,"Kingfishers are a family, the Alcedinidae, of small to medium-sized, brightly coloured birds in the order Coraciiformes.",2,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6C,15 November 2025,Adiba Patel,"Lwaldron,Fiddyhamma,Adiba Patel",Linear discriminant analysis effect size (LEfSe) identifying bacterial genera with significant differences among avian taxonomic orders.,increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pygmaiobacter",1783272|201174|84998|1643822|1643826|84111;1783272|1239|186801|3085636|186803|1432051;1783272|1239|186801|186802|216572|1929305,Complete,KateRasheed
bsdb:41209719/2/2,41209719,"cross-sectional observational, not case-control",41209719,https://doi.org/10.1016/j.crmicr.2025.100492,https://www.sciencedirect.com/science/article/pii/S2666517425001531?via=ihub,"Amina Tufail, Bushra Nisar Khan, Fumin Lei, Gang Song, Jianshi Jin, Jundong Duan, Na Zhao, Sandi Willows-Munro, Tingbei Bo, Yanhua Qu","Exploring microbiome shifts across taxonomic and ecological groups of birds at a key stopover site in Punjab, Pakistan",Current Research in Microbial Sciences,NA,"Avian ecological types, Punjab, River Ravi, Zoonotic pathogens, functional prediction, gut microbiome, habitat",Experiment 2,Pakistan,Aves,Feces,UBERON:0001988,Gut microbiome measurement,EFO:0007874,Gruiformes,Coraciiformes,"Kingfishers are a family, the Alcedinidae, of small to medium-sized, brightly coloured birds in the order Coraciiformes.",2,3,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6C,15 November 2025,Adiba Patel,"Lwaldron,Fiddyhamma,Adiba Patel",Linear discriminant analysis effect size (LEfSe) identifying bacterial genera with significant differences among avian taxonomic orders.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Marinilactibacillus,k__Bacillati|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",1783272|1239|91061|186826|186828|191769;1783272|1239|1737404|1737405|1570339|1161127;1783272|201174|1760|2037|2049|1654,Complete,KateRasheed
bsdb:41210299/1/1,41210299,case-control,41210299,10.1016/j.bbih.2025.101123,NA,"Zeng J., Zhu X., Ba H., Li S., Yang C., Huang P., Chen A., Bian Y., Li C. , Zhang S.",Integrative evidence for causal links between gut microbiota and Schizophrenia: A Mendelian randomization and 16S rRNA study,"Brain, behavior, & immunity - health",2025,"16S rRNA sequencing, Bifidobacterium, Gut-brain axis, Mendelian randomization, Schizophrenia",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,Healthy controls (HC),Schizophrenia group (SCZ),Male patients with schizophrenia (SCZ),21,21,2 weeks,16S,34,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 4I,23 November 2025,Allan,"Allan,Tosin","Bar plots showing the mean relative abundance of taxa in patients with schizophrenia (SCZ, red) and healthy controls (HC, blue).",increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",1783272|201174|1760|85004|31953;1783272|201174|1760|85004;1783272|201174|1760|85004|31953|1678,Complete,KateRasheed
bsdb:41220770/1/1,41220770,case-control,41220770,10.21037/jgo-2025-432,https://jgo.amegroups.org/article/view/107323/html,"Jung K., Joo M., Nam K., Cho J.H., Cho Y.S., Nam S. , Nam S.Y.",Oral microbial alterations by smoking and metabolic factors in esophageal squamous cell carcinoma,Journal of gastrointestinal oncology,2025,"Esophageal cancer, metabolic factors, oral microbiome, smoking",Experiment 1,South Korea,Homo sapiens,Mouth mucosa,UBERON:0003729,Esophageal squamous cell carcinoma,EFO:0005922,Age <65 control group,Age <65 in esophageal squamous cell carcinoma patients (ESCC),Patients with esophageal squamous cell carcinoma under 65 years of age,10,9,1 month,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2E & Table 3,23 November 2025,Chyono2,Chyono2,Age-stratified analysis of oral microbiome diversity and taxonomy profiles (genus-species)  in patients with esophageal squamous cell carcinoma under age 65(<65)and controls under age 65(<65).,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis",3379134|1224|1236|135625|712|724|729;1783272|1239|91061|186826|1300|1301|68892,Complete,KateRasheed
bsdb:41220770/2/1,41220770,case-control,41220770,10.21037/jgo-2025-432,https://jgo.amegroups.org/article/view/107323/html,"Jung K., Joo M., Nam K., Cho J.H., Cho Y.S., Nam S. , Nam S.Y.",Oral microbial alterations by smoking and metabolic factors in esophageal squamous cell carcinoma,Journal of gastrointestinal oncology,2025,"Esophageal cancer, metabolic factors, oral microbiome, smoking",Experiment 2,South Korea,Homo sapiens,Mouth mucosa,UBERON:0003729,Esophageal squamous cell carcinoma,EFO:0005922,Age <65 in Esophageal squamous cell carcinoma(ESCC) patients,Age≥65 in Esophageal squamous cell carcinoma(ESCC) patients,Patients with esophageal squamous cell carcinoma who were 65 years or older,9,12,1 month,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2E & Table 3,23 November 2025,Chyono2,Chyono2,Age stratified analysis of oral microbiome diversity and taxonomy profiles between esophageal squamous cell carcinoma patients who were 65 years or older(≥65) and esophageal squamous cell carcinoma patients under 65 (<65),increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,1783272|1239|909932|1843489|31977|29465|39778,Complete,KateRasheed
bsdb:41220770/3/1,41220770,case-control,41220770,10.21037/jgo-2025-432,https://jgo.amegroups.org/article/view/107323/html,"Jung K., Joo M., Nam K., Cho J.H., Cho Y.S., Nam S. , Nam S.Y.",Oral microbial alterations by smoking and metabolic factors in esophageal squamous cell carcinoma,Journal of gastrointestinal oncology,2025,"Esophageal cancer, metabolic factors, oral microbiome, smoking",Experiment 3,South Korea,Homo sapiens,Mouth mucosa,UBERON:0003729,Esophageal squamous cell carcinoma,EFO:0005922,Never smoking patients (NSP),Current or past smoking esophageal squamous cell carcinoma patients(CSP),Esophageal squamous cell carcinoma patients who are currently smokers or have a history of smoking,11,10,1 month,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3D & Table 4,23 November 2025,Chyono2,Chyono2,Taxonomic analysis of oral microbiome diversity between never smoking (NSP) esophageal squamous cell carcinoma patients and current or past smoking (CSP) esophageal squamous cell carcinoma patients.,decreased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Filifactor",3379134|976|200643|171549|171551|836|28124;1783272|1239|91061|186826|1300|1301|68892;1783272|1239|186801|3082720|3118655|44259,Complete,KateRasheed
bsdb:41220770/4/1,41220770,case-control,41220770,10.21037/jgo-2025-432,https://jgo.amegroups.org/article/view/107323/html,"Jung K., Joo M., Nam K., Cho J.H., Cho Y.S., Nam S. , Nam S.Y.",Oral microbial alterations by smoking and metabolic factors in esophageal squamous cell carcinoma,Journal of gastrointestinal oncology,2025,"Esophageal cancer, metabolic factors, oral microbiome, smoking",Experiment 4,South Korea,Homo sapiens,Mouth mucosa,UBERON:0003729,Esophageal squamous cell carcinoma,EFO:0005922,Never-smoking control (NSC),Never smoking patients (NSP),Esophageal squamous cell carcinoma patients who have never smoked,17,11,1 month,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3D & Table 4,23 November 2025,Chyono2,Chyono2,Taxonomic analysis of oral microbiome diversity between never-smoking esophageal squamous cell carcinoma patients (NSP) and never- smoking control (NSC),increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,1783272|1239|186801|186802,Complete,KateRasheed
bsdb:41220770/6/1,41220770,case-control,41220770,10.21037/jgo-2025-432,https://jgo.amegroups.org/article/view/107323/html,"Jung K., Joo M., Nam K., Cho J.H., Cho Y.S., Nam S. , Nam S.Y.",Oral microbial alterations by smoking and metabolic factors in esophageal squamous cell carcinoma,Journal of gastrointestinal oncology,2025,"Esophageal cancer, metabolic factors, oral microbiome, smoking",Experiment 6,South Korea,Homo sapiens,Mouth mucosa,UBERON:0003729,Esophageal squamous cell carcinoma,EFO:0005922,Triglyceride(TG) levels ≥150 mg/dL in control,Triglyceride (TG) levels <150 mg/dL in esophageal squamous cell carcinoma patients (ESCC),Esophageal squamous cell carcinoma patients with triglyceride (TG) levels less than 150mg/dL,5,11,1 month,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,increased,NA,NA,NA,NA,NA,Signature 1,Figure 5D & Table 6,24 November 2025,Chyono2,Chyono2,Taxonomic analysis of oral microbiome diversity between the triglyceride (TG) levels of esophageal squamous cell carcinoma patients less than 150 mg/dL (<150 mg/dL) and the triglyceride (TG)levels of control group of 150 mg/dL or more (≥150 mg/dL),increased,"k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",3379134|29547|3031852|213849|72294|194;1783272|201174|1760|85007|1653|1716;3384189|32066|203490|203491|1129771|32067,Complete,KateRasheed
bsdb:41220770/7/1,41220770,case-control,41220770,10.21037/jgo-2025-432,https://jgo.amegroups.org/article/view/107323/html,"Jung K., Joo M., Nam K., Cho J.H., Cho Y.S., Nam S. , Nam S.Y.",Oral microbial alterations by smoking and metabolic factors in esophageal squamous cell carcinoma,Journal of gastrointestinal oncology,2025,"Esophageal cancer, metabolic factors, oral microbiome, smoking",Experiment 7,South Korea,Homo sapiens,Mouth mucosa,UBERON:0003729,Esophageal squamous cell carcinoma,EFO:0005922,Triglyceride(TG) levels <150 mg/dL in esophageal squamous cell carcinoma patients,Triglyceride (TG) levels ≥150 mg/dL in esophageal squamous cell carcinoma patients,Esophageal squamous cell carcinoma patients with triglyceride (TG) levels of 150mg/dL or more (≥150 mg/dL),11,4,1 month,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,increased,NA,NA,NA,NA,NA,Signature 1,Figure 5D & Table 6,24 November 2025,Chyono2,Chyono2,Taxonomic analysis of  the oral microbiome diversity between esophageal squamous cell carcinoma patients with triglyceride (TG) levels less than 150mg/dL (<150mg/dL) and triglyceride (TG) levels of 150mg/dL or more (≥150 mg/dL),increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:41220770/8/1,41220770,case-control,41220770,10.21037/jgo-2025-432,https://jgo.amegroups.org/article/view/107323/html,"Jung K., Joo M., Nam K., Cho J.H., Cho Y.S., Nam S. , Nam S.Y.",Oral microbial alterations by smoking and metabolic factors in esophageal squamous cell carcinoma,Journal of gastrointestinal oncology,2025,"Esophageal cancer, metabolic factors, oral microbiome, smoking",Experiment 8,South Korea,Homo sapiens,Mouth mucosa,UBERON:0003729,Esophageal squamous cell carcinoma,EFO:0005922,Low density lipoprotein (LDL) levels ≤100 mg/dL in control,Low density lipoprotein (LDL) levels ≤100 mg/dL in esophageal squamous cell carcinoma patients,Esophageal squamous cell carcinoma patients with low density lipoprotein (LDL) levels less or equal to100mg/dL  (≤100 mg/dL),9,5,1 month,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6D & Table 7,24 November 2025,Chyono2,Chyono2,Taxonomic analysis of the oral microbiome diversity between low density lipoprotein (LDL) of esophageal squamous cell carcinoma patients less or equal to 100mg/dL (≤100 mg/dL)  and the low density lipoprotein( LDL) control group less or equal to 100mg/dL (≤100 mg/dL),decreased,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,3379134|1224|1236|135625|712|724|729,Complete,KateRasheed
bsdb:41220770/9/1,41220770,case-control,41220770,10.21037/jgo-2025-432,https://jgo.amegroups.org/article/view/107323/html,"Jung K., Joo M., Nam K., Cho J.H., Cho Y.S., Nam S. , Nam S.Y.",Oral microbial alterations by smoking and metabolic factors in esophageal squamous cell carcinoma,Journal of gastrointestinal oncology,2025,"Esophageal cancer, metabolic factors, oral microbiome, smoking",Experiment 9,South Korea,Homo sapiens,Mouth mucosa,UBERON:0003729,Esophageal squamous cell carcinoma,EFO:0005922,Low density lipoprotein (LDL) levels ≤100 mg/dL in esophageal squamous cell carcinoma patients,Low density lipoprotein (LDL) levels >100mg/dL in esophageal squamous cell carcinoma patients,Esophageal squamous cell carcinoma patients with low density lipoprotein (LDL) levels greater than 100mg/dL  (>100 mg/dL),5,5,1 month,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6D & Table 7,24 November 2025,Chyono2,Chyono2,Taxonomic analysis of the oral microbiome diversity between esophageal squamous cell carcinoma patients low density lipoprotein (LDL) levels less or equal to 100mg/dL (≤100 mg/dL) and greater than 100mg/dL (>100mg/dL),increased,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,1783272|1239|909932|1843489|31977|29465|39778,Complete,KateRasheed
bsdb:41220770/10/1,41220770,case-control,41220770,10.21037/jgo-2025-432,https://jgo.amegroups.org/article/view/107323/html,"Jung K., Joo M., Nam K., Cho J.H., Cho Y.S., Nam S. , Nam S.Y.",Oral microbial alterations by smoking and metabolic factors in esophageal squamous cell carcinoma,Journal of gastrointestinal oncology,2025,"Esophageal cancer, metabolic factors, oral microbiome, smoking",Experiment 10,South Korea,Homo sapiens,Mouth mucosa,UBERON:0003729,Esophageal squamous cell carcinoma,EFO:0005922,Patients without previous malignant disease (NMP) in esophageal squamous cell carcinoma (ESCC) group,Patients with previous malignant disease(WMP) in esophageal squamous cell carcinoma (ESCC) group,Esophageal squamous cell carcinoma patients who previously had a malignant disease,10,11,1 month,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplementary Figure1C & Supplementary Table1,25 November 2025,Chyono2,Chyono2,Oral microbiome diversity in patients with esophageal squamous cell carcinoma based on malignant disease history.,increased,"k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium",1783272|1239|909932|1843489|31977|29465|39778;1783272|1239|186801|3085636|186803|265975,Complete,KateRasheed
bsdb:41220770/12/1,41220770,case-control,41220770,10.21037/jgo-2025-432,https://jgo.amegroups.org/article/view/107323/html,"Jung K., Joo M., Nam K., Cho J.H., Cho Y.S., Nam S. , Nam S.Y.",Oral microbial alterations by smoking and metabolic factors in esophageal squamous cell carcinoma,Journal of gastrointestinal oncology,2025,"Esophageal cancer, metabolic factors, oral microbiome, smoking",Experiment 12,South Korea,Homo sapiens,Mouth mucosa,UBERON:0003729,Esophageal squamous cell carcinoma,EFO:0005922,Esophageal squamous cell carcinoma patients with lower-segment tumors,Esophageal squamous cell carcinoma patients with upper-segment tumors,Esophageal squamous cell carcinoma patients with upper-segment tumors,8,7,1 month,16S,123456789,PacBio Vega (VS)/Revio (RS)/Sequel II,relative abundances,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 2G & Supplementary Table 2,25 November 2025,Chyono2,Chyono2,Oral microbiome diversity in patients with esophageal squamous cell carcinoma based on tumor locations between upper-segment tumors and lower-segment tumors,decreased,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,3379134|976|200643|171549|171552|838|60133,Complete,KateRasheed
bsdb:41221531/1/1,41221531,case-control,41221531,https://doi.org/10.3389/fmed.2025.1682925,https://www.frontiersin.org/journals/medicine/articles/10.3389/fmed.2025.1682925/full,"Xiong J., Li L., Ao M., Tu Y., Tu K. , Li L.",Effects of menopausal hormone therapy on gut microbiota in postmenopausal women and the relationship with bone metabolism,Frontiers in medicine,2025,"MHT, bone metabolism, gut microbiota, osteoporosis, postmenopausal",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Hormone replacement therapy,EFO:0003961,Menopausal Hormone Replacement Therapy negative patients (MHT - group),Menopausal Hormone Replacement Therapy positive patients (MHT + group),Postmenopausal women who had taken hormone-replacement therapy for a duration exceeding 6 months (Menopausal Hormone Replacement Therapy + group),14,17,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,increased,NA,NA,increased,Signature 1,"Figure 3D, E and Text",16 November 2025,Fiddyhamma,"Fiddyhamma,Tosin","Bar chart of LDA value distribution in linear discriminant analysis effect size (LEfSe) and  
Evolutionary branch diagram of differential intestinal microbiota. CG, control group (Menopausal Hormone Replacement Therapy negative patients ); HT, hormone treatment (Menopausal Hormone Replacement Therapy positive patients).",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,c__Peptococcia|o__Peptococcales,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Pseudomonadati|p__Thermodesulfobacteriota,k__Pseudomonadati|p__Verrucomicrobiota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Raoultibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae",3379134|1224|28216|80840;1783272|1239|186801;1783272|1239|186801|186802|1980681;1783272|1239|186801|3085636|186803|33042;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;3379134|200940|3031449;1783272|1239|186801|186802|216572;1783272|1239|186801|186802|186807;3118672|3120435;3379134|1224|28216|80840|995019;3379134|200940;3379134|74201;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572|459786;1783272|201174|84998|1643822|1643826|1926677;1783272|1239|186801|186802|216572|216851|1946507;1783272|1239|186801|3082768|990719,Complete,KateRasheed
bsdb:41221531/1/2,41221531,case-control,41221531,https://doi.org/10.3389/fmed.2025.1682925,https://www.frontiersin.org/journals/medicine/articles/10.3389/fmed.2025.1682925/full,"Xiong J., Li L., Ao M., Tu Y., Tu K. , Li L.",Effects of menopausal hormone therapy on gut microbiota in postmenopausal women and the relationship with bone metabolism,Frontiers in medicine,2025,"MHT, bone metabolism, gut microbiota, osteoporosis, postmenopausal",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Hormone replacement therapy,EFO:0003961,Menopausal Hormone Replacement Therapy negative patients (MHT - group),Menopausal Hormone Replacement Therapy positive patients (MHT + group),Postmenopausal women who had taken hormone-replacement therapy for a duration exceeding 6 months (Menopausal Hormone Replacement Therapy + group),14,17,3 months,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,increased,NA,NA,increased,Signature 2,"Figure 3D, E and Text",16 November 2025,Fiddyhamma,Fiddyhamma,"Bar chart of LDA value distribution in linear discriminant analysis effect size (LEfSe) and  
Evolutionary branch diagram of differential intestinal microbiota. CG, control group (Menopausal Hormone Replacement Therapy negative patients ); HT, hormone treatment (Menopausal Hormone Replacement Therapy positive patients).",decreased,"p__Candidatus Saccharimonadota|c__Candidatus Saccharimonadia|o__Candidatus Saccharimonadales|f__Candidatus Saccharimonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium",95818|2093818|2093825|2171986;3379134|1224|1236|91347|543|1940338;1783272|1239|909932|909929|1843491|158846;1783272|1239|186801|3085636|186803|265975,Complete,KateRasheed
bsdb:41221531/3/1,41221531,case-control,41221531,https://doi.org/10.3389/fmed.2025.1682925,https://www.frontiersin.org/journals/medicine/articles/10.3389/fmed.2025.1682925/full,"Xiong J., Li L., Ao M., Tu Y., Tu K. , Li L.",Effects of menopausal hormone therapy on gut microbiota in postmenopausal women and the relationship with bone metabolism,Frontiers in medicine,2025,"MHT, bone metabolism, gut microbiota, osteoporosis, postmenopausal",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Osteoporosis,EFO:0003882,High serum procollagen type I N propeptide (P1NP),Low serum procollagen type I N propeptide (P1NP),Patients with low serum procollagen type I N propeptide (P1NP),NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4A, Supplementary materials 1, 2",17 November 2025,Fiddyhamma,Fiddyhamma,Correlations between intestinal flora and clinical indexes.,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter",1783272|1239|186801|3082768|990719;1783272|1239|186801|3085636|186803|33042;3379134|976|200643|171549|1853231|283168,Complete,KateRasheed
bsdb:41221531/4/1,41221531,case-control,41221531,https://doi.org/10.3389/fmed.2025.1682925,https://www.frontiersin.org/journals/medicine/articles/10.3389/fmed.2025.1682925/full,"Xiong J., Li L., Ao M., Tu Y., Tu K. , Li L.",Effects of menopausal hormone therapy on gut microbiota in postmenopausal women and the relationship with bone metabolism,Frontiers in medicine,2025,"MHT, bone metabolism, gut microbiota, osteoporosis, postmenopausal",Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Hormone measurement,EFO:0004730,Low Calcitonin level (CT),High Calcitonin level (CT),Patients with High Calcitonin level (CT),NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4A, Supplementary materials 1, 2",17 November 2025,Fiddyhamma,Fiddyhamma,Correlations between intestinal flora and clinical indexes.,increased,NA,NA,Complete,KateRasheed
bsdb:41221531/5/1,41221531,case-control,41221531,https://doi.org/10.3389/fmed.2025.1682925,https://www.frontiersin.org/journals/medicine/articles/10.3389/fmed.2025.1682925/full,"Xiong J., Li L., Ao M., Tu Y., Tu K. , Li L.",Effects of menopausal hormone therapy on gut microbiota in postmenopausal women and the relationship with bone metabolism,Frontiers in medicine,2025,"MHT, bone metabolism, gut microbiota, osteoporosis, postmenopausal",Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Osteocalcin measurement,NA,High Osteocalcin level (OC),Low Osteocalcin level (OC),Patients with Low Osteocalcin level (OC),NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4A, Supplementary materials 1, 2",17 November 2025,Fiddyhamma,Fiddyhamma,Correlations between intestinal flora and clinical indexes.,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|201174|84998|1643822|1643826|447020;1783272|1239|186801|3082768|990719;1783272|1239|186801|3085636|186803|33042;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572,Complete,KateRasheed
bsdb:41221531/6/1,41221531,case-control,41221531,https://doi.org/10.3389/fmed.2025.1682925,https://www.frontiersin.org/journals/medicine/articles/10.3389/fmed.2025.1682925/full,"Xiong J., Li L., Ao M., Tu Y., Tu K. , Li L.",Effects of menopausal hormone therapy on gut microbiota in postmenopausal women and the relationship with bone metabolism,Frontiers in medicine,2025,"MHT, bone metabolism, gut microbiota, osteoporosis, postmenopausal",Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Bone mineral content measurement,EFO:0007621,High Bone Mineral Content for the Lumbar Spine BMC(LS),Low Bone Mineral Content for the Lumbar Spine BMC(LS),Patients with Low Bone Mineral Content for the Lumbar Spine BMC(LS),NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4A, Supplementary materials 1, 2",17 November 2025,Fiddyhamma,Fiddyhamma,Correlations between intestinal flora and clinical indexes.,increased,NA,NA,Complete,KateRasheed
bsdb:41221531/7/1,41221531,case-control,41221531,https://doi.org/10.3389/fmed.2025.1682925,https://www.frontiersin.org/journals/medicine/articles/10.3389/fmed.2025.1682925/full,"Xiong J., Li L., Ao M., Tu Y., Tu K. , Li L.",Effects of menopausal hormone therapy on gut microbiota in postmenopausal women and the relationship with bone metabolism,Frontiers in medicine,2025,"MHT, bone metabolism, gut microbiota, osteoporosis, postmenopausal",Experiment 7,China,Homo sapiens,Feces,UBERON:0001988,Bone mineral content measurement,EFO:0007621,High Bone Mineral Content for the femoral neck BMC(FN),Low Bone Mineral Content for the femoral neck BMC(FN),Patients with Low Bone Mineral Content for the femoral neck BMC(FN),NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4A, Supplementary materials 1, 2",17 November 2025,Fiddyhamma,Fiddyhamma,Correlations between intestinal flora and clinical indexes.,increased,NA,NA,Complete,KateRasheed
bsdb:41221531/8/1,41221531,case-control,41221531,https://doi.org/10.3389/fmed.2025.1682925,https://www.frontiersin.org/journals/medicine/articles/10.3389/fmed.2025.1682925/full,"Xiong J., Li L., Ao M., Tu Y., Tu K. , Li L.",Effects of menopausal hormone therapy on gut microbiota in postmenopausal women and the relationship with bone metabolism,Frontiers in medicine,2025,"MHT, bone metabolism, gut microbiota, osteoporosis, postmenopausal",Experiment 8,China,Homo sapiens,Feces,UBERON:0001988,Femoral neck bone mineral density,EFO:0007785,High Bone Mineral Density for the femoral neck BMD(FN),Low Bone Mineral Density for the femoral neck BMD(FN),Patients with Low Bone Mineral Density for the femoral neck BMD(FN),NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4A, Supplementary materials 1, 2",17 November 2025,Fiddyhamma,Fiddyhamma,Correlations between intestinal flora and clinical indexes.,increased,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,1783272|1239|186801|3085636|186803|33042,Complete,KateRasheed
bsdb:41221531/9/1,41221531,case-control,41221531,https://doi.org/10.3389/fmed.2025.1682925,https://www.frontiersin.org/journals/medicine/articles/10.3389/fmed.2025.1682925/full,"Xiong J., Li L., Ao M., Tu Y., Tu K. , Li L.",Effects of menopausal hormone therapy on gut microbiota in postmenopausal women and the relationship with bone metabolism,Frontiers in medicine,2025,"MHT, bone metabolism, gut microbiota, osteoporosis, postmenopausal",Experiment 9,China,Homo sapiens,Feces,UBERON:0001988,Fasting blood glucose measurement,EFO:0004465,Low Fasting Glucose level,High Fasting Glucose level,Patients with High Fasting Glucose level,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4A, Supplementary materials 1, 2",25 November 2025,Fiddyhamma,Fiddyhamma,Correlations between intestinal flora and clinical indexes.,decreased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Raoultibacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",1783272|201174|84998|1643822|1643826|1926677;1783272|1239|186801|186802|1980681;3379134|976|200643|171549|1853231|283168;1783272|1239|186801|186802|216572,Complete,KateRasheed
bsdb:41221531/11/1,41221531,case-control,41221531,https://doi.org/10.3389/fmed.2025.1682925,https://www.frontiersin.org/journals/medicine/articles/10.3389/fmed.2025.1682925/full,"Xiong J., Li L., Ao M., Tu Y., Tu K. , Li L.",Effects of menopausal hormone therapy on gut microbiota in postmenopausal women and the relationship with bone metabolism,Frontiers in medicine,2025,"MHT, bone metabolism, gut microbiota, osteoporosis, postmenopausal",Experiment 11,China,Homo sapiens,Feces,UBERON:0001988,High density lipoprotein cholesterol measurement,EFO:0004612,Increased High Density Lipoprotein (HDL) level,Decreased High Density Lipoprotein (HDL) level,Patients with Decreased High Density Lipoprotein (HDL) level,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4A, Supplementary materials 1, 2",25 November 2025,Fiddyhamma,Fiddyhamma,Correlations between intestinal flora and clinical indexes.,decreased,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,1783272|201174|84998|1643822|1643826|447020,Complete,KateRasheed
bsdb:41221531/12/1,41221531,case-control,41221531,https://doi.org/10.3389/fmed.2025.1682925,https://www.frontiersin.org/journals/medicine/articles/10.3389/fmed.2025.1682925/full,"Xiong J., Li L., Ao M., Tu Y., Tu K. , Li L.",Effects of menopausal hormone therapy on gut microbiota in postmenopausal women and the relationship with bone metabolism,Frontiers in medicine,2025,"MHT, bone metabolism, gut microbiota, osteoporosis, postmenopausal",Experiment 12,China,Homo sapiens,Feces,UBERON:0001988,Low density lipoprotein cholesterol measurement,EFO:0004611,Decreased Low Density Lipoprotein (LDL) level,Increased Low Density Lipoprotein (LDL) level,Patients with Increased Low Density Lipoprotein (LDL) level,NA,NA,3 months,16S,34,Illumina,relative abundances,Spearman Correlation,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4A, Supplementary materials 1, 2",25 November 2025,Fiddyhamma,Fiddyhamma,Correlations between intestinal flora and clinical indexes.,decreased,NA,NA,Complete,KateRasheed
bsdb:41225454/1/1,41225454,"case-control,time series / longitudinal observational",41225454,10.1186/s12884-025-08421-2,https://bmcpregnancychildbirth.biomedcentral.com/articles/10.1186/s12884-025-08421-2,"Ohmichi-Tomiwa M., Kato-Kogoe N., Kudo A., Fujita D., Sakaguchi S., Tsuda K., Omori M., Hayashi E., Nakamura S., Nakano T., Ohmichi M., Tamaki J. , Ueno T.",Exploratory study of the oral microbiota in pregnant women with hypothyroidism and their infants,BMC pregnancy and childbirth,2025,"Hypothyroidism, Nested case–control study, Offspring, Oral microbiota, Pregnancy",Experiment 1,Japan,Homo sapiens,Saliva,UBERON:0001836,Hypothyroidism,EFO:0004705,Control group,Hypothyroid (HypoT) group,Pregnant women with hypothyroidism (M0),30,31,NA,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Fig 4a,16 November 2025,Deborah-Fabusuyi,"Deborah-Fabusuyi,Tosin",Differentially abundant bacterial taxa between Pregnant women with hypothyroidism and Control groups identified by linear discriminant analysis effect size (LEfSe),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacillati|p__Cyanobacteriota,k__Bacillati|p__Cyanobacteriota|c__Cyanophyceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Defluviitaleaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|s__Enterococcaceae bacterium RF39",3379134|1224|28211;3379134|976|200643|171549|815;3379134|1224|1236|135615|868;3379134|1224|1236|135615;1783272|1239|186801;1783272|201174|84998|84999|84107;1783272|1117;1783272|1117|3028117;1783272|1239|186801|3085636|1185407;1783272|1239|186801|186802;3379134|1224|28211|356;1783272|1239|91061|186826|33958;3384189|32066|203490|203491|1129771;1783272|1239|186801|186802|216572;3379134|1224|1236|72274|135621;3379134|1224|28211|356|82115;1783272|1239|91061|186826|81852|423410,Complete,KateRasheed
bsdb:41225454/1/2,41225454,"case-control,time series / longitudinal observational",41225454,10.1186/s12884-025-08421-2,https://bmcpregnancychildbirth.biomedcentral.com/articles/10.1186/s12884-025-08421-2,"Ohmichi-Tomiwa M., Kato-Kogoe N., Kudo A., Fujita D., Sakaguchi S., Tsuda K., Omori M., Hayashi E., Nakamura S., Nakano T., Ohmichi M., Tamaki J. , Ueno T.",Exploratory study of the oral microbiota in pregnant women with hypothyroidism and their infants,BMC pregnancy and childbirth,2025,"Hypothyroidism, Nested case–control study, Offspring, Oral microbiota, Pregnancy",Experiment 1,Japan,Homo sapiens,Saliva,UBERON:0001836,Hypothyroidism,EFO:0004705,Control group,Hypothyroid (HypoT) group,Pregnant women with hypothyroidism (M0),30,31,NA,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Figure 4a,16 November 2025,Deborah-Fabusuyi,"Deborah-Fabusuyi,Tosin",Differentially abundant bacterial taxa between Pregnant women with hypothyroidism and Control groups identified by linear discriminant analysis effect size (LEfSe),increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,1783272|1239|91061|186826|33958,Complete,KateRasheed
bsdb:41225454/2/1,41225454,"case-control,time series / longitudinal observational",41225454,10.1186/s12884-025-08421-2,https://bmcpregnancychildbirth.biomedcentral.com/articles/10.1186/s12884-025-08421-2,"Ohmichi-Tomiwa M., Kato-Kogoe N., Kudo A., Fujita D., Sakaguchi S., Tsuda K., Omori M., Hayashi E., Nakamura S., Nakano T., Ohmichi M., Tamaki J. , Ueno T.",Exploratory study of the oral microbiota in pregnant women with hypothyroidism and their infants,BMC pregnancy and childbirth,2025,"Hypothyroidism, Nested case–control study, Offspring, Oral microbiota, Pregnancy",Experiment 2,Japan,Homo sapiens,Saliva,UBERON:0001836,Hypothyroidism,EFO:0004705,Control group,Hypothyroid (HypoT) group,One month post-partum women with hypothyroidism (M1),30,31,NA,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Fig 4b,16 November 2025,Deborah-Fabusuyi,"Deborah-Fabusuyi,Tosin",Differentially abundant bacterial taxa between One month post-partum women with Hypothyroidism and Control groups identified by linear discriminant analysis effect size (LEfSe),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|s__Enterococcaceae bacterium RF39",3379134|1224|28211;3384189|32066|203490|203491|203492;3379134|1224|28211|356;3379134|1224|28211|356|82115;1783272|1239|91061|186826|81852|423410,Complete,KateRasheed
bsdb:41225454/2/2,41225454,"case-control,time series / longitudinal observational",41225454,10.1186/s12884-025-08421-2,https://bmcpregnancychildbirth.biomedcentral.com/articles/10.1186/s12884-025-08421-2,"Ohmichi-Tomiwa M., Kato-Kogoe N., Kudo A., Fujita D., Sakaguchi S., Tsuda K., Omori M., Hayashi E., Nakamura S., Nakano T., Ohmichi M., Tamaki J. , Ueno T.",Exploratory study of the oral microbiota in pregnant women with hypothyroidism and their infants,BMC pregnancy and childbirth,2025,"Hypothyroidism, Nested case–control study, Offspring, Oral microbiota, Pregnancy",Experiment 2,Japan,Homo sapiens,Saliva,UBERON:0001836,Hypothyroidism,EFO:0004705,Control group,Hypothyroid (HypoT) group,One month post-partum women with hypothyroidism (M1),30,31,NA,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4b,17 November 2025,Deborah-Fabusuyi,Deborah-Fabusuyi,Differentially abundant bacterial taxa between One month post-partum women with Hypothyroidism and Control groups identified by linear discriminant analysis effect size (LEfSe),increased,NA,NA,Complete,KateRasheed
bsdb:41225454/3/1,41225454,"case-control,time series / longitudinal observational",41225454,10.1186/s12884-025-08421-2,https://bmcpregnancychildbirth.biomedcentral.com/articles/10.1186/s12884-025-08421-2,"Ohmichi-Tomiwa M., Kato-Kogoe N., Kudo A., Fujita D., Sakaguchi S., Tsuda K., Omori M., Hayashi E., Nakamura S., Nakano T., Ohmichi M., Tamaki J. , Ueno T.",Exploratory study of the oral microbiota in pregnant women with hypothyroidism and their infants,BMC pregnancy and childbirth,2025,"Hypothyroidism, Nested case–control study, Offspring, Oral microbiota, Pregnancy",Experiment 3,Japan,Homo sapiens,Saliva,UBERON:0001836,Hypothyroidism,EFO:0004705,Control group,Hypothyroid (HypoT) group,One month old infants of women with hypothyroidism (C),30,31,NA,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4c,16 November 2025,Deborah-Fabusuyi,"Deborah-Fabusuyi,Tosin",Differentially abundant bacterial taxa between One month old infants of women with Hypothyroidism and Control groups identified by linear discriminant analysis effect size (LEfSe),decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae",3379134|1224|28211;3379134|1224|28211|356;1783272|1239|91061|186826|33958;3379134|1224|1236|135614|32033;3379134|1224|1236|135614;1783272|201174|1760|85006|85023;3379134|1224|28211|356|82115,Complete,KateRasheed
bsdb:41225454/3/2,41225454,"case-control,time series / longitudinal observational",41225454,10.1186/s12884-025-08421-2,https://bmcpregnancychildbirth.biomedcentral.com/articles/10.1186/s12884-025-08421-2,"Ohmichi-Tomiwa M., Kato-Kogoe N., Kudo A., Fujita D., Sakaguchi S., Tsuda K., Omori M., Hayashi E., Nakamura S., Nakano T., Ohmichi M., Tamaki J. , Ueno T.",Exploratory study of the oral microbiota in pregnant women with hypothyroidism and their infants,BMC pregnancy and childbirth,2025,"Hypothyroidism, Nested case–control study, Offspring, Oral microbiota, Pregnancy",Experiment 3,Japan,Homo sapiens,Saliva,UBERON:0001836,Hypothyroidism,EFO:0004705,Control group,Hypothyroid (HypoT) group,One month old infants of women with hypothyroidism (C),30,31,NA,16S,12,Illumina,relative abundances,LEfSe,0.05,FALSE,2.5,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4c,16 November 2025,Deborah-Fabusuyi,"Deborah-Fabusuyi,Tosin",Differentially abundant bacterial taxa between One month old infants of women with Hypothyroidism and Control groups identified by linear discriminant analysis effect size (LEfSe),increased,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,1783272|1239|91061|186826|81852,Complete,KateRasheed
bsdb:41225454/4/1,41225454,"case-control,time series / longitudinal observational",41225454,10.1186/s12884-025-08421-2,https://bmcpregnancychildbirth.biomedcentral.com/articles/10.1186/s12884-025-08421-2,"Ohmichi-Tomiwa M., Kato-Kogoe N., Kudo A., Fujita D., Sakaguchi S., Tsuda K., Omori M., Hayashi E., Nakamura S., Nakano T., Ohmichi M., Tamaki J. , Ueno T.",Exploratory study of the oral microbiota in pregnant women with hypothyroidism and their infants,BMC pregnancy and childbirth,2025,"Hypothyroidism, Nested case–control study, Offspring, Oral microbiota, Pregnancy",Experiment 4,Japan,Homo sapiens,Saliva,UBERON:0001836,Hypothyroidism,EFO:0004705,Control group,Hypothyroid (HypoT) group,Pregnant women with hypothyroidism (M0),30,31,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 5a,16 November 2025,Deborah-Fabusuyi,Deborah-Fabusuyi,Relative abundance of the family Rhizobiaceae in the Pregnant women with Hypothyroidism compared to the Control groups,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,3379134|1224|28211|356|82115,Complete,KateRasheed
bsdb:41225454/5/1,41225454,"case-control,time series / longitudinal observational",41225454,10.1186/s12884-025-08421-2,https://bmcpregnancychildbirth.biomedcentral.com/articles/10.1186/s12884-025-08421-2,"Ohmichi-Tomiwa M., Kato-Kogoe N., Kudo A., Fujita D., Sakaguchi S., Tsuda K., Omori M., Hayashi E., Nakamura S., Nakano T., Ohmichi M., Tamaki J. , Ueno T.",Exploratory study of the oral microbiota in pregnant women with hypothyroidism and their infants,BMC pregnancy and childbirth,2025,"Hypothyroidism, Nested case–control study, Offspring, Oral microbiota, Pregnancy",Experiment 5,Japan,Homo sapiens,Saliva,UBERON:0001836,Hypothyroidism,EFO:0004705,Control group,Hypothyroid (HypoT) group,One month post-partum women with hypothyroidism (M1),30,31,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 5a,16 November 2025,Deborah-Fabusuyi,Deborah-Fabusuyi,Relative abundance of the family Rhizobiaceae in the one month post-partum women with Hypothyroidism compared to the Control groups,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,3379134|1224|28211|356|82115,Complete,KateRasheed
bsdb:41225454/6/1,41225454,"case-control,time series / longitudinal observational",41225454,10.1186/s12884-025-08421-2,https://bmcpregnancychildbirth.biomedcentral.com/articles/10.1186/s12884-025-08421-2,"Ohmichi-Tomiwa M., Kato-Kogoe N., Kudo A., Fujita D., Sakaguchi S., Tsuda K., Omori M., Hayashi E., Nakamura S., Nakano T., Ohmichi M., Tamaki J. , Ueno T.",Exploratory study of the oral microbiota in pregnant women with hypothyroidism and their infants,BMC pregnancy and childbirth,2025,"Hypothyroidism, Nested case–control study, Offspring, Oral microbiota, Pregnancy",Experiment 6,Japan,Homo sapiens,Saliva,UBERON:0001836,Hypothyroidism,EFO:0004705,Control group,Hypothyroid (HypoT) group,One month old infants of women with hypothyroidism (C),30,31,NA,16S,12,Illumina,relative abundances,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 5a,16 November 2025,Deborah-Fabusuyi,Deborah-Fabusuyi,Relative abundance of the family Rhizobiaceae in the one month old infants of women with Hypothyroidism compared to the Control groups,decreased,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,3379134|1224|28211|356|82115,Complete,KateRasheed
bsdb:41252249/1/1,41252249,"cross-sectional observational, not case-control",41252249,https://doi.org/10.1016/j.celrep.2025.116573,https://www.cell.com/cell-reports/fulltext/S2211-1247(25)01345-2,"Febinia C.A., Luqman H., Kusuma P., Priliani L., Lewis J., Wihandani D.M., Pinatih G.N., Sudoyo H., Almeida A., Malik S.G. , Jacobs G.S.",From sporulation to village differentiation: The shaping of the social microbiome over rural-to-urban lifestyle transition in Indonesia,Cell reports,2025,"CP: microbiology, Indonesia, Southeast Asia, gut microbiome, hunter-gatherer, lifestyle, social microbiome, sporulation, transition",Experiment 1,"Indonesia,Singapore",Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Cluster 1 + 2 (Others),Cluster 3,Cluster 3 (urban region) in the Indonesian-Singaporean dataset comprised of Denspasar and Singaporean samples,102,123,NA,WMS,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table S4.1,8 December 2025,Fiddyhamma,Fiddyhamma,Results for differential abundance analysis of family-level relative abundance between the urban category (cluster 3) and others (clusters 1 & 2),increased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",1783272|201174|1760|85004|31953;1783272|1239|186801|3085636|186803;1783272|201174|84998|1643822|1643826;1783272|201174|84998|84999|84107;3379134|976|200643|171549|171550;1783272|1239|186801|186802|186807;3379134|976|200643|171549|2005519;3366610|28890|183925|2158|2159;1783272|1239|186801|186802|3085642;1783272|1239|186801|186802|216572;1783272|1239|91061|186826|1300;1783272|1239|526524|526525|128827,Complete,Svetlana up
bsdb:41252249/1/2,41252249,"cross-sectional observational, not case-control",41252249,https://doi.org/10.1016/j.celrep.2025.116573,https://www.cell.com/cell-reports/fulltext/S2211-1247(25)01345-2,"Febinia C.A., Luqman H., Kusuma P., Priliani L., Lewis J., Wihandani D.M., Pinatih G.N., Sudoyo H., Almeida A., Malik S.G. , Jacobs G.S.",From sporulation to village differentiation: The shaping of the social microbiome over rural-to-urban lifestyle transition in Indonesia,Cell reports,2025,"CP: microbiology, Indonesia, Southeast Asia, gut microbiome, hunter-gatherer, lifestyle, social microbiome, sporulation, transition",Experiment 1,"Indonesia,Singapore",Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Cluster 1 + 2 (Others),Cluster 3,Cluster 3 (urban region) in the Indonesian-Singaporean dataset comprised of Denspasar and Singaporean samples,102,123,NA,WMS,NA,Illumina,relative abundances,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table S4.1,8 December 2025,Fiddyhamma,Fiddyhamma,Results for differential abundance analysis of family-level relative abundance between the urban category (cluster 3) and others (clusters 1 & 2),decreased,"k__Bacillati|p__Mycoplasmatota|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Anaerotignaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacillati|p__Vulcanimicrobiota|c__Candidatus Xenobia|o__Candidatus Xenobiales|f__Candidatus Xenobiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Elusimicrobiota|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Marinicellaceae,k__Methanobacteriati|p__Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomethylophilaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Monoglobales|f__Monoglobaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Pumilibacteraceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Sphaerochaetaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales|f__Candidatus Gastranaerophilaceae",1783272|544448|31969|186332|186333;1783272|1239|186801|3085636|3118652;1783272|1239|186801|3082720|543314;3379134|976|200643|171549|815;3379134|203691|203692|1643686|143786;3379134|1224|28216|80840|119060;3379134|29547|3031852|213849|72294;1783272|1154676|2829292|2829294|2829295;1783272|1239|186801|3082768|990719;1783272|1239|186801|186802|31979;3379134|200940|3031449|213115|194924;3379134|74152|641853|641854|641876;3379134|1224|1236|135614|3120710;3366610|2283796|183967|1235850|2517203;1783272|1239|186801|3085656|3085657;3379134|976|200643|171549|2005473;1783272|1239|186801|186802|216572;3379134|976|200643|171549|2005523;3379134|1224|1236|135625|712;1783272|1239|186801|186802|2941492;3379134|203691|203692|136|2791015;3379134|1224|1236|135624|83763;3379134|203691|203692|136|2845253;3379134|256845|1313211|278082|255528;1783272|1798710|1906119|3022868,Complete,Svetlana up
bsdb:41252249/2/1,41252249,"cross-sectional observational, not case-control",41252249,https://doi.org/10.1016/j.celrep.2025.116573,https://www.cell.com/cell-reports/fulltext/S2211-1247(25)01345-2,"Febinia C.A., Luqman H., Kusuma P., Priliani L., Lewis J., Wihandani D.M., Pinatih G.N., Sudoyo H., Almeida A., Malik S.G. , Jacobs G.S.",From sporulation to village differentiation: The shaping of the social microbiome over rural-to-urban lifestyle transition in Indonesia,Cell reports,2025,"CP: microbiology, Indonesia, Southeast Asia, gut microbiome, hunter-gatherer, lifestyle, social microbiome, sporulation, transition",Experiment 2,"Indonesia,Singapore",Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Decreasing Lifestyle in Indonesian-Singaporean dataset,Increasing Lifestyle in Indonesian-Singaporean dataset,"Increasing association with lifestyle (ordinal continuous variable; remote=0, rural=0.5, urban=1) in Indonesian-Singaporean sample dataset",NA,NA,NA,WMS,NA,Illumina,raw counts,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2E, Supplementary Table S4.2",21 December 2025,Fiddyhamma,Fiddyhamma,"Microbiome Multivariate Association with Linear Models (MaAsLin2) results for the association of Metagenome Assembled Genome (MAG) relative abundance with the lifestyle cline, adjusted for age and sex in the Indonesian-Singaporean dataset",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Avimicrobium|s__Candidatus Avimicrobium caecorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium saudiense,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Faecalibacillus|s__Faecalibacillus intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium longum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Jutongia|s__Jutongia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Lawsonibacter|s__Lawsonibacter asaccharolyticus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pusillibacter|s__Pusillibacter faecalis",1783272|201174|84998|1643822|1643826|447020|446660;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|28111;3379134|976|200643|171549|815|816|329854;1783272|1239|186801|2720800|2720821;1783272|1239|186801|186802|31979|1485|1414720;1783272|201174|84998|84999|84107|102106;1783272|1239|186801|3085636|186803|189330|39486;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|526524|526525|2810280|2678885|1982626;1783272|1239|186801|186802|216572|216851|1851428;1783272|1239|186801|186802|216572|946234|292800;1783272|1239|186801|3082720|186804|1505657|261299;1783272|1239|186801|3085636|186803|2944194|2763664;1783272|1239|186801|186802|216572|2172004|2108523;1783272|1239|91061|186826|33958|2767887|1623;3379134|976|200643|171549|2005525|375288|823;1783272|1239|186801|186802|216572|2892397|2714358,Complete,Svetlana up
bsdb:41252249/2/2,41252249,"cross-sectional observational, not case-control",41252249,https://doi.org/10.1016/j.celrep.2025.116573,https://www.cell.com/cell-reports/fulltext/S2211-1247(25)01345-2,"Febinia C.A., Luqman H., Kusuma P., Priliani L., Lewis J., Wihandani D.M., Pinatih G.N., Sudoyo H., Almeida A., Malik S.G. , Jacobs G.S.",From sporulation to village differentiation: The shaping of the social microbiome over rural-to-urban lifestyle transition in Indonesia,Cell reports,2025,"CP: microbiology, Indonesia, Southeast Asia, gut microbiome, hunter-gatherer, lifestyle, social microbiome, sporulation, transition",Experiment 2,"Indonesia,Singapore",Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Decreasing Lifestyle in Indonesian-Singaporean dataset,Increasing Lifestyle in Indonesian-Singaporean dataset,"Increasing association with lifestyle (ordinal continuous variable; remote=0, rural=0.5, urban=1) in Indonesian-Singaporean sample dataset",NA,NA,NA,WMS,NA,Illumina,raw counts,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2E, Supplementary Table S4.2",21 December 2025,Fiddyhamma,Fiddyhamma,"Microbiome Multivariate Association with Linear Models (MaAsLin2) results for the association of Metagenome Assembled Genome (MAG) relative abundance with the lifestyle cline, adjusted for age and sex in the Indonesian-Singaporean dataset",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecousia,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium mitsuokai,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Mailhella|s__Candidatus Mailhella excrementigallinarum",1783272|1239|186801|186802|216572|2840588;1783272|1239|526524|526525|2810280|135858|100886;3379134|200940|3031449|213115|194924|1981028|2838656,Complete,Svetlana up
bsdb:41252249/3/1,41252249,"cross-sectional observational, not case-control",41252249,https://doi.org/10.1016/j.celrep.2025.116573,https://www.cell.com/cell-reports/fulltext/S2211-1247(25)01345-2,"Febinia C.A., Luqman H., Kusuma P., Priliani L., Lewis J., Wihandani D.M., Pinatih G.N., Sudoyo H., Almeida A., Malik S.G. , Jacobs G.S.",From sporulation to village differentiation: The shaping of the social microbiome over rural-to-urban lifestyle transition in Indonesia,Cell reports,2025,"CP: microbiology, Indonesia, Southeast Asia, gut microbiome, hunter-gatherer, lifestyle, social microbiome, sporulation, transition",Experiment 3,Indonesia,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Decreasing Lifestyle in Indonesian dataset,Increasing Lifestyle in Indonesian dataset,"Increasing association with lifestyle (ordinal continuous variable; remote=0, rural=0.5, urban=1) in Indonesian only sample dataset",NA,NA,NA,WMS,NA,Illumina,raw counts,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2E, Supplementary Table S4.3",8 December 2025,Fiddyhamma,Fiddyhamma,"Microbiome Multivariate Association with Linear Models (MaAsLin2) results for the association of Metagenome Assembled Genome (MAG) relative abundance with the lifestyle cline, adjusted for age and sex in the Indonesian only dataset",increased,"k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacillati|p__Bacillota|c__Clostridia|g__Candidatus Avimicrobium|s__Candidatus Avimicrobium caecorum,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium saudiense,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Faecalibacillus|s__Faecalibacillus intestinalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pusillibacter|s__Pusillibacter faecalis",1783272|201174|84998|1643822|1643826|447020|446660;3379134|74201|203494|48461|1647988|239934|239935;3379134|976|200643|171549|815|816|47678;3379134|976|200643|171549|815|816|28111;3379134|976|200643|171549|815|816|329854;1783272|1239|186801|2720800|2720821;1783272|1239|186801|186802|31979|1485|1414720;1783272|1239|186801|3085636|186803|189330|39486;1783272|201174|84998|1643822|1643826|84111|84112;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|526524|526525|2810280|2678885|1982626;1783272|1239|91061|186826|33958|2767887|1623;1783272|1239|186801|186802|216572|2892397|2714358,Complete,Svetlana up
bsdb:41252249/3/2,41252249,"cross-sectional observational, not case-control",41252249,https://doi.org/10.1016/j.celrep.2025.116573,https://www.cell.com/cell-reports/fulltext/S2211-1247(25)01345-2,"Febinia C.A., Luqman H., Kusuma P., Priliani L., Lewis J., Wihandani D.M., Pinatih G.N., Sudoyo H., Almeida A., Malik S.G. , Jacobs G.S.",From sporulation to village differentiation: The shaping of the social microbiome over rural-to-urban lifestyle transition in Indonesia,Cell reports,2025,"CP: microbiology, Indonesia, Southeast Asia, gut microbiome, hunter-gatherer, lifestyle, social microbiome, sporulation, transition",Experiment 3,Indonesia,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Decreasing Lifestyle in Indonesian dataset,Increasing Lifestyle in Indonesian dataset,"Increasing association with lifestyle (ordinal continuous variable; remote=0, rural=0.5, urban=1) in Indonesian only sample dataset",NA,NA,NA,WMS,NA,Illumina,raw counts,MaAsLin2,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2E, Supplementary Table S4.3",8 December 2025,Fiddyhamma,Fiddyhamma,"Microbiome Multivariate Association with Linear Models (MaAsLin2) results for the association of Metagenome Assembled Genome (MAG) relative abundance with the lifestyle cline, adjusted for age and sex in the Indonesian only dataset",decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Jutongia|s__Jutongia hominis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecousia",1783272|1239|186801|3085636|186803|2944194|2763664;1783272|1239|186801|186802|216572|2840588,Complete,Svetlana up
bsdb:41280921/1/1,41280921,NA,41280921,10.3389/fimmu.2025.1695321,NA,"Li X., Yuan Q., Huang H. , Wang L.",Gut microbiota in irritable bowel syndrome: a narrative review of mechanisms and microbiome-based therapies,Frontiers in immunology,2025,"fecal microbiota transplantation, gut microbiota, immune response, irritable bowel syndrome, pathogenesis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS patients,"Adults meeting Rome IV criteria for IBS; included IBS-D, IBS-C, and IBS-M subtypes.",30,60,"No antibiotics, probiotics, prebiotics, or synbiotics within 4 weeks prior to sampling.",16S,34,Illumina,relative abundances,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,2,"age,sex","age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2A – LEfSe taxa decreased in IBS,29 November 2025,Aqc576444,Aqc576444,"IBS patients showed significantly decreased levels of Faecalibacterium, Roseburia, Ruminococcus, and other short-chain fatty acid–producing taxa compared with healthy controls, identified by LEfSe (LDA > 2, FDR < 0.05).",increased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus",1783272|1239|186801|186802|216572|216851;1783272|1239|186801|3085636|186803|841;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|3085636|186803;1783272|1239|186801|3085636|186803|33042,Complete,NA
bsdb:41280921/1/2,41280921,NA,41280921,10.3389/fimmu.2025.1695321,NA,"Li X., Yuan Q., Huang H. , Wang L.",Gut microbiota in irritable bowel syndrome: a narrative review of mechanisms and microbiome-based therapies,Frontiers in immunology,2025,"fecal microbiota transplantation, gut microbiota, immune response, irritable bowel syndrome, pathogenesis",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Healthy controls,IBS patients,"Adults meeting Rome IV criteria for IBS; included IBS-D, IBS-C, and IBS-M subtypes.",30,60,"No antibiotics, probiotics, prebiotics, or synbiotics within 4 weeks prior to sampling.",16S,34,Illumina,relative abundances,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,TRUE,2,"age,sex","age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 2B – LEfSe taxa increased in IBS,29 November 2025,Aqc576444,Aqc576444,"IBS patients showed significantly increased abundances of Enterobacteriaceae, Escherichia-Shigella, Streptococcus, and other opportunistic taxa compared with controls, based on LEfSe analysis (LDA > 2, FDR < 0.05).",increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella",3379134|1224|1236|91347|543;1783272|1239|91061|186826|1300|1301;1783272|1239|909932|1843489|31977|29465;3379134|1224|1236|91347|543|570,Complete,NA
bsdb:41375452/1/1,41375452,"cross-sectional observational, not case-control",41375452,https://doi.org/10.3390/ani15233393,NA,"Wang Z., Yang C., Li Y., Dong B., Song Q., Bai H., Jiang Y., Chang G. , Chen G.",Multi-Omics Insights into the Relationship Between Intestinal Microbiota and Abdominal Fat Deposition in Meat Ducks,Animals : an open access journal from MDPI,2025,"16S rRNA gene, abdominal fat deposition, intestinal microbiota, meat duck, metagenome",Experiment 1,China,Anas platyrhynchos,Jejunum,UBERON:0002115,Body fat distribution,EFO:0004341,Jejunum of Low Abdominal Fat Rate Group :KC-L,Jejunum of High Abdominal Fat Rate Group :KC-H,"Jejunum (KC-H) of  F2 generation of Cherry Valley Duck and Runzhou Crested White Duck that exhibit a significantly high accumulation of abdominal fat, quantified by an abdominal fat rate between 1.5% and 2.25% of their eviscerated weight.",6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A,16 December 2025,Shiber256,Shiber256,Linear discriminant analysis Effect Size (LEfSe) analysis of Intestinal flora in the Jejunum between high and low abdominal fat rate groups (KC-H vs KC-L).,increased,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales,3379134|1224|28211|204441,Complete,KateRasheed
bsdb:41375452/1/2,41375452,"cross-sectional observational, not case-control",41375452,https://doi.org/10.3390/ani15233393,NA,"Wang Z., Yang C., Li Y., Dong B., Song Q., Bai H., Jiang Y., Chang G. , Chen G.",Multi-Omics Insights into the Relationship Between Intestinal Microbiota and Abdominal Fat Deposition in Meat Ducks,Animals : an open access journal from MDPI,2025,"16S rRNA gene, abdominal fat deposition, intestinal microbiota, meat duck, metagenome",Experiment 1,China,Anas platyrhynchos,Jejunum,UBERON:0002115,Body fat distribution,EFO:0004341,Jejunum of Low Abdominal Fat Rate Group :KC-L,Jejunum of High Abdominal Fat Rate Group :KC-H,"Jejunum (KC-H) of  F2 generation of Cherry Valley Duck and Runzhou Crested White Duck that exhibit a significantly high accumulation of abdominal fat, quantified by an abdominal fat rate between 1.5% and 2.25% of their eviscerated weight.",6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3A,16 December 2025,Shiber256,Shiber256,Linear discriminant analysis Effect Size (LEfSe) analysis of Intestinal flora in the Jejunum between high and low abdominal fat rate groups (KC-H vs KC-L).,decreased,"k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Dermabacteraceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Ignatzschineriaceae|g__Ignatzschineria,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae",1783272|201174|1760|85006|85020|43668;1783272|201174|1760|85006|85020;3379134|1224|1236|135615|3018589|112008;3379134|1224|28211|356|69277;1783272|201174|1760|85006|85019|1696;3379134|1224|28211|356|69277,Complete,KateRasheed
bsdb:41375452/2/1,41375452,"cross-sectional observational, not case-control",41375452,https://doi.org/10.3390/ani15233393,NA,"Wang Z., Yang C., Li Y., Dong B., Song Q., Bai H., Jiang Y., Chang G. , Chen G.",Multi-Omics Insights into the Relationship Between Intestinal Microbiota and Abdominal Fat Deposition in Meat Ducks,Animals : an open access journal from MDPI,2025,"16S rRNA gene, abdominal fat deposition, intestinal microbiota, meat duck, metagenome",Experiment 2,China,Anas platyrhynchos,Caecum,UBERON:0001153,Body fat distribution,EFO:0004341,Cecum  of the Low Abdominal Fat Rate Group:MC-L,Cecum of the High Abdominal Fat Rate Group:MC-H,"Cecum (MC-H) of  F2 generation of Cherry Valley Duck and Runzhou Crested White Duck that exhibit a significantly high accumulation of abdominal fat, quantified by an abdominal fat rate between 1.5% and 2.25% of their eviscerated weight.",6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3B,16 December 2025,Shiber256,Shiber256,Linear discriminant analysis Effect Size (LEfSe) analysis of Intestinal flora in the Cecum between high and low abdominal fat rate groups (MC-H vs MC-L).,increased,k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,1783272|1798710|1906119,Complete,KateRasheed
bsdb:41375452/2/2,41375452,"cross-sectional observational, not case-control",41375452,https://doi.org/10.3390/ani15233393,NA,"Wang Z., Yang C., Li Y., Dong B., Song Q., Bai H., Jiang Y., Chang G. , Chen G.",Multi-Omics Insights into the Relationship Between Intestinal Microbiota and Abdominal Fat Deposition in Meat Ducks,Animals : an open access journal from MDPI,2025,"16S rRNA gene, abdominal fat deposition, intestinal microbiota, meat duck, metagenome",Experiment 2,China,Anas platyrhynchos,Caecum,UBERON:0001153,Body fat distribution,EFO:0004341,Cecum  of the Low Abdominal Fat Rate Group:MC-L,Cecum of the High Abdominal Fat Rate Group:MC-H,"Cecum (MC-H) of  F2 generation of Cherry Valley Duck and Runzhou Crested White Duck that exhibit a significantly high accumulation of abdominal fat, quantified by an abdominal fat rate between 1.5% and 2.25% of their eviscerated weight.",6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3B,16 December 2025,Shiber256,Shiber256,Linear discriminant analysis Effect Size (LEfSe) analysis of Intestinal flora in the Cecum between high and low abdominal fat rate groups (MC-H vs MC-L).,decreased,"k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria,k__Pseudomonadati|p__Lentisphaerota,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales,k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",3379134|256845|1313211;3379134|256845;1783272|1239|186801|186802|216572|292632;3379134|256845|1313211|278082|255528;3379134|256845|1313211|278082;3379134|256845|1313211|278082|255528|172900;1783272|1239|186801|186802|216572|216851,Complete,KateRasheed
bsdb:41375452/3/1,41375452,"cross-sectional observational, not case-control",41375452,https://doi.org/10.3390/ani15233393,NA,"Wang Z., Yang C., Li Y., Dong B., Song Q., Bai H., Jiang Y., Chang G. , Chen G.",Multi-Omics Insights into the Relationship Between Intestinal Microbiota and Abdominal Fat Deposition in Meat Ducks,Animals : an open access journal from MDPI,2025,"16S rRNA gene, abdominal fat deposition, intestinal microbiota, meat duck, metagenome",Experiment 3,China,Anas platyrhynchos,Ileum,UBERON:0002116,Body fat distribution,EFO:0004341,Ileum of the Low Abdominal Fat Rate Group:HC-L,Ileum of the High Abdominal Fat Rate Group:HC-H,"Ileum (HC-H) of F2 generation of Cherry Valley Duck and Runzhou Crested White Duck that exhibit a significantly high accumulation of abdominal fat, quantified by an abdominal fat rate between 1.5% and 2.25% of their eviscerated weight.",6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3C,18 December 2025,Shiber256,Shiber256,Linear discriminant analysis Effect Size (LEfSe) analysis of Intestinal flora in the Ileum between high and low abdominal fat rate groups (HC-H vs HC-L).,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Microvirga,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Metazoa|p__Nematoda|c__Enoplea|o__Trichinellida|f__Trichinellidae|g__Trichinella|s__Trichinella pseudospiralis,k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,s__bacterium SM9-19",1783272|1239|91061;3379134|1224|28216|80840|80864;3379134|1224|1236|91347;3379134|1224|1236|91347|543;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|1940338;3379134|1224|1236;1783272|1239|91061|186826;3379134|1224|28211|356|119045|186650;3379134|1224|1236|72274|135621;33208|6231|119088|6329|6332|6333|6337;3379134|1224|28216|80840|80864|283;1783272|1239|91061|186826|81852|1350;3379134|1224|28211|204457|41297|13687;298633,Complete,KateRasheed
bsdb:41375452/3/2,41375452,"cross-sectional observational, not case-control",41375452,https://doi.org/10.3390/ani15233393,NA,"Wang Z., Yang C., Li Y., Dong B., Song Q., Bai H., Jiang Y., Chang G. , Chen G.",Multi-Omics Insights into the Relationship Between Intestinal Microbiota and Abdominal Fat Deposition in Meat Ducks,Animals : an open access journal from MDPI,2025,"16S rRNA gene, abdominal fat deposition, intestinal microbiota, meat duck, metagenome",Experiment 3,China,Anas platyrhynchos,Ileum,UBERON:0002116,Body fat distribution,EFO:0004341,Ileum of the Low Abdominal Fat Rate Group:HC-L,Ileum of the High Abdominal Fat Rate Group:HC-H,"Ileum (HC-H) of F2 generation of Cherry Valley Duck and Runzhou Crested White Duck that exhibit a significantly high accumulation of abdominal fat, quantified by an abdominal fat rate between 1.5% and 2.25% of their eviscerated weight.",6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3C,18 December 2025,Shiber256,Shiber256,Linear discriminant analysis Effect Size (LEfSe) analysis of Intestinal flora in the Ileum between high and low abdominal fat rate groups (HC-H vs HC-L).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacillati|p__Cyanobacteriota,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Phenylobacterium,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Pseudomonadati|p__Lentisphaerota",1783272|1239|186801|186802|216572|52784;1783272|1117;3379134|1224|28211|204458|76892|20;3379134|976|200643|171549|171552|1283313;1783272|201174|1760|85006|1268|32207;3379134|256845,Complete,KateRasheed
bsdb:41375452/4/1,41375452,"cross-sectional observational, not case-control",41375452,https://doi.org/10.3390/ani15233393,NA,"Wang Z., Yang C., Li Y., Dong B., Song Q., Bai H., Jiang Y., Chang G. , Chen G.",Multi-Omics Insights into the Relationship Between Intestinal Microbiota and Abdominal Fat Deposition in Meat Ducks,Animals : an open access journal from MDPI,2025,"16S rRNA gene, abdominal fat deposition, intestinal microbiota, meat duck, metagenome",Experiment 4,China,Anas platyrhynchos,Rectum,UBERON:0001052,Body fat distribution,EFO:0004341,Rectum of the Low Abdominal Fat Rate Group:ZC-L,Rectum of the High Abdominal Fat Rate Group:ZC-H,"Rectum (ZC-H) of F2 generation of Cherry Valley Duck and Runzhou Crested White Duck that exhibit a significantly high accumulation of abdominal fat, quantified by an abdominal fat rate between 1.5% and 2.25% of their eviscerated weight.",6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3D,18 December 2025,Shiber256,Shiber256,Linear discriminant analysis Effect Size (LEfSe) analysis of Intestinal flora in the Rectum between high and low abdominal fat rate groups (ZC-H vs ZC-L).,increased,"k__Bacillati|p__Bacillota|c__Bacilli,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Macrococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus henryi,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",1783272|1239|91061;3379134|200940|3031449|213115|194924|35832;1783272|1239|91061|186826|81852;1783272|1239|91061|186826|81852|1350;3379134|1224|1236|91347|543|1940338;1783272|1239|91061|186826;1783272|1239|91061|1385|90964|69965;1783272|1239|186801|186802|216572|459786;1783272|1239|91061|186826|1300;1783272|1239|91061|186826|1300|1301;1783272|1239|91061|186826|1300|1301|439219;3379134|1224|1236|135625|712;1783272|1239|91061|186826|1300|1301,Complete,KateRasheed
bsdb:41375452/4/2,41375452,"cross-sectional observational, not case-control",41375452,https://doi.org/10.3390/ani15233393,NA,"Wang Z., Yang C., Li Y., Dong B., Song Q., Bai H., Jiang Y., Chang G. , Chen G.",Multi-Omics Insights into the Relationship Between Intestinal Microbiota and Abdominal Fat Deposition in Meat Ducks,Animals : an open access journal from MDPI,2025,"16S rRNA gene, abdominal fat deposition, intestinal microbiota, meat duck, metagenome",Experiment 4,China,Anas platyrhynchos,Rectum,UBERON:0001052,Body fat distribution,EFO:0004341,Rectum of the Low Abdominal Fat Rate Group:ZC-L,Rectum of the High Abdominal Fat Rate Group:ZC-H,"Rectum (ZC-H) of F2 generation of Cherry Valley Duck and Runzhou Crested White Duck that exhibit a significantly high accumulation of abdominal fat, quantified by an abdominal fat rate between 1.5% and 2.25% of their eviscerated weight.",6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3D,18 December 2025,Shiber256,Shiber256,Linear discriminant analysis Effect Size (LEfSe) analysis of Intestinal flora in the Rectum between high and low abdominal fat rate groups (ZC-H vs ZC-L).,decreased,"k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Latilactobacillus|s__Latilactobacillus sakei,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas paucimobilis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella cibaria,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea",1783272|1239|186801;1783272|1239|186801|186802;3379134|976|117743|200644|49546|237;1783272|201174|84998|1643822|1643826|644652;1783272|1239|91061|186826|33958|2767885|1599;1783272|201174|1760|85010|2070;1783272|201174|1760|85010;3379134|1224|28211|204457|41297|13687;3379134|1224|28211|204457|41297|13687|13689;1783272|1239|91061|186826|33958|46255|137591;1783272|1239|186801|186802|1470353,Complete,KateRasheed
bsdb:41375452/5/1,41375452,"cross-sectional observational, not case-control",41375452,https://doi.org/10.3390/ani15233393,NA,"Wang Z., Yang C., Li Y., Dong B., Song Q., Bai H., Jiang Y., Chang G. , Chen G.",Multi-Omics Insights into the Relationship Between Intestinal Microbiota and Abdominal Fat Deposition in Meat Ducks,Animals : an open access journal from MDPI,2025,"16S rRNA gene, abdominal fat deposition, intestinal microbiota, meat duck, metagenome",Experiment 5,China,Anas platyrhynchos,Duodenum,UBERON:0002114,Body fat distribution,EFO:0004341,Duodenum of the Low Abdominal Fat Rate Group:SC-L,Duodenum of the High Abdominal Fat Rate Group:SC-H,"Duodenum (SC-H) of  F2 generation of Cherry Valley Duck and Runzhou Crested White Duck that exhibit a significantly high accumulation of abdominal fat, quantified by an abdominal fat rate between 1.5% and 2.25% of their eviscerated weight.",6,6,NA,16S,34,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3E,18 December 2025,Shiber256,Shiber256,Linear discriminant analysis Effect Size (LEfSe) analysis of Intestinal flora in the Duodenum between high and low abdominal fat rate groups (SC-H vs SC-L).,decreased,"k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",3384189|32066|203490|203491|1129771|32067;3384189|32066|203490|203491|1129771;1783272|1239|186801|186802|216572;1783272|1239|91061|186826|33958|1578,Complete,KateRasheed
bsdb:41375452/6/1,41375452,"cross-sectional observational, not case-control",41375452,https://doi.org/10.3390/ani15233393,NA,"Wang Z., Yang C., Li Y., Dong B., Song Q., Bai H., Jiang Y., Chang G. , Chen G.",Multi-Omics Insights into the Relationship Between Intestinal Microbiota and Abdominal Fat Deposition in Meat Ducks,Animals : an open access journal from MDPI,2025,"16S rRNA gene, abdominal fat deposition, intestinal microbiota, meat duck, metagenome",Experiment 6,China,Anas platyrhynchos,Caecum,UBERON:0001153,Body fat distribution,EFO:0004341,Cecum of Low Abdominal Fat Rate Group : L-MC,Cecum of High Abdominal Fat Rate Group : H-MC,"Cecal samples of F2 generation of Cherry Valley Duck and Runzhou Crested White Duck that exhibit a significantly high accumulation of abdominal fat, quantified by an abdominal fat rate between 1.5% and 2.25% of their eviscerated weight. (H-MC)",3,3,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 6B and Figure 6C,19 December 2025,Firdaws,Firdaws,Linear discriminant analysis Effect Size (LEfSe) analysis of cecal microbiota differences between high and low abdominal fat percentage groups (H-MC vs L-MC),increased,"k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Pseudomonadati|p__Bacteroidota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes communis,k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales",3379134|976|200643|171549;3379134|976|200643;3379134|976;3379134|976|200643|171549|1853231;1783272|201174|84998|1643822|1643826;3379134|976|200643|171549|171550|239759|2585118;1783272|201174|84998|1643822,Complete,KateRasheed
bsdb:41375452/6/2,41375452,"cross-sectional observational, not case-control",41375452,https://doi.org/10.3390/ani15233393,NA,"Wang Z., Yang C., Li Y., Dong B., Song Q., Bai H., Jiang Y., Chang G. , Chen G.",Multi-Omics Insights into the Relationship Between Intestinal Microbiota and Abdominal Fat Deposition in Meat Ducks,Animals : an open access journal from MDPI,2025,"16S rRNA gene, abdominal fat deposition, intestinal microbiota, meat duck, metagenome",Experiment 6,China,Anas platyrhynchos,Caecum,UBERON:0001153,Body fat distribution,EFO:0004341,Cecum of Low Abdominal Fat Rate Group : L-MC,Cecum of High Abdominal Fat Rate Group : H-MC,"Cecal samples of F2 generation of Cherry Valley Duck and Runzhou Crested White Duck that exhibit a significantly high accumulation of abdominal fat, quantified by an abdominal fat rate between 1.5% and 2.25% of their eviscerated weight. (H-MC)",3,3,NA,WMS,NA,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 6B and Figure 6C,19 December 2025,Firdaws,Firdaws,Linear discriminant analysis Effect Size (LEfSe) analysis of cecal microbiota differences between high and low abdominal fat percentage groups (H-MC vs L-MC),decreased,"k__Bacillati|p__Bacillota,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. An19,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacillati|p__Bacillota|c__Clostridia,k__Bacillati|p__Bacillota|c__Clostridia|s__Clostridia bacterium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium CHKCI001,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,c__Deltaproteobacteria,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:180,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor sp. An306,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium sp. An181,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Mordavella,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__uncultured Bacteroides sp.",1783272|1239;3379134|976|200643|171549|815|816|1965580;1783272|1239|186801|3085636|186803|830;1783272|1239|186801;1783272|1239|186801|2044939;1783272|1239|186801|186802|1780378;1783272|1239|186801|3085636|186803|33042;28221;3379134|200940|3031449|213115|194924|872;3379134|200940|3031449|213115|194924;3379134|200940|3031449|213115;1783272|1239|186801|186802;1783272|1239|186801|186802|186806|1730|1262882;1783272|1239|186801|186802|216572|216851|853;1783272|1239|186801|186802|216572|946234|1965629;1783272|1239|186801|3085636|186803|1506553|1965575;1783272|1239|186801|186802|31979|1981033;1783272|1239|186801|186802|216572;1783272|1239|91061|1385|186822;1783272|1239|91061|1385|186822|44249;1783272|1239|186801|186802|216572|1263;1783272|1239|186801|186802|216572|1263|438033;1783272|1239|909932|1843489|31977;1783272|1239|909932|1843489;1783272|1239|186801|186802|31979;1783272|1239|186801|186802|31979|1485;1783272|1239|186801|186802;1783272|1239|186801|3085636|186803;3379134|976|200643|171549|815|816|162156,Complete,KateRasheed
bsdb:41375452/7/1,41375452,"cross-sectional observational, not case-control",41375452,https://doi.org/10.3390/ani15233393,NA,"Wang Z., Yang C., Li Y., Dong B., Song Q., Bai H., Jiang Y., Chang G. , Chen G.",Multi-Omics Insights into the Relationship Between Intestinal Microbiota and Abdominal Fat Deposition in Meat Ducks,Animals : an open access journal from MDPI,2025,"16S rRNA gene, abdominal fat deposition, intestinal microbiota, meat duck, metagenome",Experiment 7,China,Anas platyrhynchos,Caecum,UBERON:0001153,Body fat distribution,EFO:0004341,Cecum of Low Abdominal Fat Rate Group : L-MC,Cecum of High Abdominal Fat Rate Group : H-MC,"Cecal samples of F2 generation of Cherry Valley Duck and Runzhou Crested White Duck that exhibit a significantly high accumulation of abdominal fat, quantified by an abdominal fat rate between 1.5% and 2.25% of their eviscerated weight. (H-MC)",3,3,NA,WMS,NA,Illumina,relative abundances,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 6D,19 December 2025,Firdaws,Firdaws,Welch’s t-test analysis of cecal microorganisms that differ significantly between high and low abdominal fat rates.,decreased,"k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. An19,k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",3379134|200940|3031449|213115;3379134|976|200643|171549|815|816|1965580;1783272|1239|186801|186802|216572|216851|853,Complete,KateRasheed
bsdb:41404876/1/1,41404876,"cross-sectional observational, not case-control",41404876,https://doi.org/10.1128/spectrum.00368-25,NA,"Van Beeck W., Eilers T., Smets W., Delanghe L., Vandenheuvel D., Tuyaerts I., Van Malderen J., Ahannach S., Michiels K., Dricot C., Van de Vliet N., Huys A.J., De Boever P. , Lebeer S.","Sonmat, a citizen-science enabled Kimjang kimchi case study on associations between hand and kimchi microbiota",Microbiology spectrum,2025,"Kimchi, Kimjang, citizen science, fermentation microbiota, fermented food, skin microbiota",Experiment 1,Belgium,Homo sapiens,NA,NA,Lactobacillus kimchii,NCBITAXON:103818,Individually made kimchi,Kimjang group-made kimchi,"A collaborative preparation where participants worked together on a single, large batch of kimchi ingredients following traditional Kimjang practices, which was then evenly divided into separate jars for fermentation and analysis.",25,9,NA,16S,4,Illumina,log transformation,ANCOM-BC2,0.05,TRUE,NA,NA,NA,decreased,NA,unchanged,NA,decreased,unchanged,Signature 1,Figure 3B,6 January 2026,Shiber256,Shiber256,Differential abundance of microbiota between individually made and group-made kimchi microbiome as calculated with ANCOM-BC2,increased,"k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",3379134|1224|1236|91347|543|547;1783272|1239|91061|186826|33958|46255,Complete,NA
bsdb:41404876/1/2,41404876,"cross-sectional observational, not case-control",41404876,https://doi.org/10.1128/spectrum.00368-25,NA,"Van Beeck W., Eilers T., Smets W., Delanghe L., Vandenheuvel D., Tuyaerts I., Van Malderen J., Ahannach S., Michiels K., Dricot C., Van de Vliet N., Huys A.J., De Boever P. , Lebeer S.","Sonmat, a citizen-science enabled Kimjang kimchi case study on associations between hand and kimchi microbiota",Microbiology spectrum,2025,"Kimchi, Kimjang, citizen science, fermentation microbiota, fermented food, skin microbiota",Experiment 1,Belgium,Homo sapiens,NA,NA,Lactobacillus kimchii,NCBITAXON:103818,Individually made kimchi,Kimjang group-made kimchi,"A collaborative preparation where participants worked together on a single, large batch of kimchi ingredients following traditional Kimjang practices, which was then evenly divided into separate jars for fermentation and analysis.",25,9,NA,16S,4,Illumina,log transformation,ANCOM-BC2,0.05,TRUE,NA,NA,NA,decreased,NA,unchanged,NA,decreased,unchanged,Signature 2,Figure 3B,6 January 2026,Shiber256,Shiber256,Differential abundance of microbiota between individually made and group-made kimchi microbiome as calculated with ANCOM-BC2.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Latilactobacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc",1783272|1239|91061|186826|33958|2767885;1783272|1239|91061|186826|33958|1243,Complete,NA
bsdb:41404876/2/1,41404876,"cross-sectional observational, not case-control",41404876,https://doi.org/10.1128/spectrum.00368-25,NA,"Van Beeck W., Eilers T., Smets W., Delanghe L., Vandenheuvel D., Tuyaerts I., Van Malderen J., Ahannach S., Michiels K., Dricot C., Van de Vliet N., Huys A.J., De Boever P. , Lebeer S.","Sonmat, a citizen-science enabled Kimjang kimchi case study on associations between hand and kimchi microbiota",Microbiology spectrum,2025,"Kimchi, Kimjang, citizen science, fermentation microbiota, fermented food, skin microbiota",Experiment 2,Belgium,Homo sapiens,Skin of palm of manus,UBERON:0013777,Lactobacillus kimchii,NCBITAXON:103818,Individually made kimchi,Hand skin,"Consists of  individual participants whose hands (palm, back of the hand, and between the fingers) were swabbed to match their respective individual kimchi samples.",19,19,NA,16S,4,Illumina,log transformation,ANCOM-BC2,0.05,TRUE,NA,NA,NA,increased,increased,increased,NA,increased,increased,Signature 1,Figure 4B,18 January 2026,Shiber256,Shiber256,ANCOM-BC2 analysis identified bacterial genera whose abundances significantly differed between the hand skin and the kimchi microbiome.,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter",1783272|1239|91061|1385|90964|1279;3379134|1224|1236|72274|135621|286;3379134|1224|28211|356|212791,Complete,NA
bsdb:41404876/2/2,41404876,"cross-sectional observational, not case-control",41404876,https://doi.org/10.1128/spectrum.00368-25,NA,"Van Beeck W., Eilers T., Smets W., Delanghe L., Vandenheuvel D., Tuyaerts I., Van Malderen J., Ahannach S., Michiels K., Dricot C., Van de Vliet N., Huys A.J., De Boever P. , Lebeer S.","Sonmat, a citizen-science enabled Kimjang kimchi case study on associations between hand and kimchi microbiota",Microbiology spectrum,2025,"Kimchi, Kimjang, citizen science, fermentation microbiota, fermented food, skin microbiota",Experiment 2,Belgium,Homo sapiens,Skin of palm of manus,UBERON:0013777,Lactobacillus kimchii,NCBITAXON:103818,Individually made kimchi,Hand skin,"Consists of  individual participants whose hands (palm, back of the hand, and between the fingers) were swabbed to match their respective individual kimchi samples.",19,19,NA,16S,4,Illumina,log transformation,ANCOM-BC2,0.05,TRUE,NA,NA,NA,increased,increased,increased,NA,increased,increased,Signature 2,Figure 4B,18 January 2026,Shiber256,Shiber256,ANCOM-BC2 analysis identified bacterial genera whose abundances significantly differed between the hand skin and the kimchi microbiome.,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Latilactobacillus,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter",1783272|1239|91061|186826|33958|1243;1783272|1239|91061|186826|33958|2767885;3379134|1224|1236|91347|543|547,Complete,NA
bsdb:10.5603.mrj.99890/1/1,10.5603.mrj.99890,case-control,10.5603.mrj.99890,https://doi.org/10.5603/mrj.99890,NA,"Anastasia Timofeeva, Inna Ponomarova, Svitlana Kryshchuk, Tamara Lisyana",Features of vaginal microbiota in women with vulvovaginal candidiasis,Medical Research Journal,2024,"candida, conditionally pathogenic microorganisms, vaginal microbiota, vulvovaginal candidiasis",Experiment 1,Ukraine,Homo sapiens,Vagina,UBERON:0000996,Vulvovaginal candidiasis,EFO:0007543,Healthy Controls,Vulvovaginal candidiasis group,Participants in this group were women with Vulvovaginal candidiasis (VVC),30,60,NA,NA,NA,NA,relative abundances,T-Test,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,3 June 2025,"Lwaldron, Aleru Divine","Lwaldron,Aleru Divine",Candida fungi in patients with vulvovaginal candidiasis,increased,"k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida tropicalis,k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida parapsilosis",4751|4890|3239874|2916678|766764|5475|5476;4751|4890|3239874|2916678|766764|5475|5482;4751|4890|3239874|2916678|766764|5475|5480,Complete,NA
bsdb:10.53388.2025825001/1/1,10.53388.2025825001,case-control,10.53388.2025825001,10.53388/2025825001,https://doi.org/10.53388/2025825001,"Ai-Qin Zhang, Jia-Ying Yang, Jing-Er Zhang, Meng-Ying Sun, Xiang Qian, Zhuo Chen",Study on the diversity and difference of intratumoral flora in patients with triple negative breast cancer,Cancer Advances,2025,"5R 16S, difference, diversity, intratumoral flora, triple negative breast cancer",Experiment 1,China,Homo sapiens,Breast,UBERON:0000310,Triple-negative breast cancer,NA,adjacent non-cancerous tissues,TNBC tumor tissues,"Patients diagnosed with TNBC through surgical pathology and/or biopsy, who met the study’s inclusion criteria and were admitted to the Department of Breast Surgery at Zhejiang Cancer Hospital between January 1, 2022, and November 30, 2022.",14,14,3 months,16S,2345678,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,unchanged,NA,NA,Signature 1,Figure 5 (A),21 June 2025,"Lwaldron, Ecsharp","Lwaldron,Ecsharp",LDA value distribution of TNBC tumor tissues and adjacent tissues. (A) LEfSe analysis LDA score.,increased,"k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Renibacterium",3379134|976|117743|200644|49546|237;3379134|976|117743|200644|49546;1783272|201174|1760|85006|1268|1645,Complete,NA
bsdb:10.5603.mrj.99890/1/2,10.5603.mrj.99890,case-control,10.5603.mrj.99890,https://doi.org/10.5603/mrj.99890,NA,"Anastasia Timofeeva, Inna Ponomarova, Svitlana Kryshchuk, Tamara Lisyana",Features of vaginal microbiota in women with vulvovaginal candidiasis,Medical Research Journal,2024,"candida, conditionally pathogenic microorganisms, vaginal microbiota, vulvovaginal candidiasis",Experiment 1,Ukraine,Homo sapiens,Vagina,UBERON:0000996,Vulvovaginal candidiasis,EFO:0007543,Healthy Controls,Vulvovaginal candidiasis group,Participants in this group were women with Vulvovaginal candidiasis (VVC),30,60,NA,NA,NA,NA,relative abundances,T-Test,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,NA,3 June 2025,"Lwaldron, Aleru Divine","Lwaldron,Aleru Divine",NA,NA,NA,NA,Complete,NA
bsdb:10.53388.2025825001/1/2,10.53388.2025825001,case-control,10.53388.2025825001,10.53388/2025825001,https://doi.org/10.53388/2025825001,"Ai-Qin Zhang, Jia-Ying Yang, Jing-Er Zhang, Meng-Ying Sun, Xiang Qian, Zhuo Chen",Study on the diversity and difference of intratumoral flora in patients with triple negative breast cancer,Cancer Advances,2025,"5R 16S, difference, diversity, intratumoral flora, triple negative breast cancer",Experiment 1,China,Homo sapiens,Breast,UBERON:0000310,Triple-negative breast cancer,NA,adjacent non-cancerous tissues,TNBC tumor tissues,"Patients diagnosed with TNBC through surgical pathology and/or biopsy, who met the study’s inclusion criteria and were admitted to the Department of Breast Surgery at Zhejiang Cancer Hospital between January 1, 2022, and November 30, 2022.",14,14,3 months,16S,2345678,Illumina,relative abundances,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,unchanged,NA,NA,Signature 2,Figure 5 (A),21 June 2025,"Lwaldron, Ecsharp","Lwaldron,Ecsharp",LDA value distribution of TNBC tumor tissues and adjacent tissues. (A) LEfSe analysis LDA score.,decreased,"k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Caldibacillus|s__Caldibacillus thermoamylovorans,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Nitrobacteraceae|g__Afipia,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Roseomonadaceae|g__Roseomonas,k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Acetobacterales|f__Roseomonadaceae|g__Roseomonas|s__Roseomonas mucosa,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae",3379134|1224|28216|80840|80864|283;1783272|1239|91061|1385|186817;1783272|1239|91061|1385|186817|1386;1783272|1239|91061|1385|186817|1276290|35841;3379134|1224|28211|204458|76892|75;3379134|1224|28211|356|41294|1033;1783272|1239|91061|186826|186827|1375;1783272|1239|91061|186826|186827;3379134|1224|28211|3120395|3385906|125216;3379134|1224|28211|3120395|3385906|125216|207340;1783272|201174|1760|85009|31957,Complete,NA
bsdb:10.5603.mrj.99890/2/1,10.5603.mrj.99890,case-control,10.5603.mrj.99890,https://doi.org/10.5603/mrj.99890,NA,"Anastasia Timofeeva, Inna Ponomarova, Svitlana Kryshchuk, Tamara Lisyana",Features of vaginal microbiota in women with vulvovaginal candidiasis,Medical Research Journal,2024,"candida, conditionally pathogenic microorganisms, vaginal microbiota, vulvovaginal candidiasis",Experiment 2,Ukraine,Homo sapiens,Vagina,UBERON:0000996,Vulvovaginal candidiasis,EFO:0007543,Healthy Controls,Vulvovaginal candidiasis group,Participants in this group were women with Vulvovaginal candidiasis (VVC),30,60,NA,NA,NA,NA,relative abundances,T-Test,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,3 June 2025,"Lwaldron, Aleru Divine","Lwaldron,Aleru Divine",Microflora of the vagina in patients with candidiasis vulvovaginitis,increased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.,k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp.",1783272|1239|91061|1385|90964|1279|1282;1783272|1239|91061|1385|90964|1279|1280;1783272|1239|91061|186826|81852|1350|1351;1783272|1239|91061|186826|1300|1301|1311;3379134|1224|1236|91347|543|561|562;3379134|1224|1236|91347|543|570|576;3379134|1224|1236|91347|543|547|42895;1783272|1239|909932|1843489|31977|29465|1926307,Complete,NA
bsdb:10.5603.mrj.99890/2/2,10.5603.mrj.99890,case-control,10.5603.mrj.99890,https://doi.org/10.5603/mrj.99890,NA,"Anastasia Timofeeva, Inna Ponomarova, Svitlana Kryshchuk, Tamara Lisyana",Features of vaginal microbiota in women with vulvovaginal candidiasis,Medical Research Journal,2024,"candida, conditionally pathogenic microorganisms, vaginal microbiota, vulvovaginal candidiasis",Experiment 2,Ukraine,Homo sapiens,Vagina,UBERON:0000996,Vulvovaginal candidiasis,EFO:0007543,Healthy Controls,Vulvovaginal candidiasis group,Participants in this group were women with Vulvovaginal candidiasis (VVC),30,60,NA,NA,NA,NA,relative abundances,T-Test,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,3 June 2025,"Lwaldron, Aleru Divine","Lwaldron,Aleru Divine",Microflora of the vagina in patients with candidiasis vulvovaginitis,decreased,"k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.",1783272|1239|91061|186826|33958|1578|1591;1783272|201174|1760|85004|31953|1678|41200;3379134|976|200643|171549|815|816|29523;3379134|976|200643|171549|171552|838|59823,Complete,NA